cd-hit-2d excluding from clusters good aligments

[laugior]

Running this command:
cd-hit-2d -i main_set -i2 transcriptos_alternativos -o comparacion_70 -c 0.70 -M 8000 -T 15 -g 1 -G 0 -aS 0.3 -aL 0.3 -A 0.3

Both -i and -i2 are nucleotide

The following cluster is created:

Cluster 6508
0 1305aa, >NonamEVm004010t1... *
1 1303aa, >NonamEVm004010t2... at 1:1177:129:1305/100.00%

in -i2 exists >NonamEVm004010t4 which has 100% identity with >NonamEVm004010t1 (when aligned with external tool). (Identity 100% cover 92%)
NonamEVm004010t4 is found on non-redundant sequences from db2 output

Alignment

NonamEVm004010t1 CGCAAGCAAGGCACGCCGCTTTCACGCCCCAAGCCCGCCGTCGAGCCGGAATGCGGTGCC

NonamEVm004010t4 --------------------------------------------------------------------------------------------

NonamEVm004010t1 CAATTGGTTCCGCATTTCGGCTGCGCAAATGCAACGCCAGTCGCCAGACCACACAGCCTA
NonamEVm004010t4 -------------------------------------------------------------------------------------------

NonamEVm004010t1 TTCCCCGCCGCTCGATCTGCAACCACTCTGCTCCGACGTGACCCTCGAGCCACGACCCGT
NonamEVm004010t4 ------------CGCTCGATCTGCAACCACTCTGCTCCGACGTGACCCTCGAGCCACGACCCGT

NonamEVm004010t1 AACACCTGCTTTACTTCCATATTCCGTTTGCATCGCCTTTCGCTCTCTTTTTCCCATCCT
NonamEVm004010t4 AACACCTGCTTTACTTCCATATTCCGTTTGCATCGCCTTTCGCTCTCTTTTTCCCATCCT

NonamEVm004010t1 CACGAACTGGCGATCCACCACCTCCCCAATATGATTCCCTCTTCTTCGTCCAAGCTCTTC
NonamEVm004010t4 CACGAACTGGCGATCCACCACCTCCCCAATATGATTCCCTCTTCTTCGTCCAAGCTCTTC

NonamEVm004010t1 TTGCGATCCAGCGTCGCCGCCTCTCGTGCCACCATGACCGCGCGGCCGGCCATTCGCGCC
NonamEVm004010t4 TTGCGATCCAGCGTCGCCGCCTCTCGTGCCACCATGACCGCGCGGCCGGCCATTCGCGCC

NonamEVm004010t1 TTTTCAACGTCTCTCGCTAGCCAAAAGGAGGTCAAGAACGTCACAGTCTTCGGTGCCGGC
NonamEVm004010t4 TTTTCAACGTCTCTCGCTAGCCAAAAGGAGGTCAAGAACGTCACAGTCTTCGGTGCCGGC

NonamEVm004010t1 CTCATGGGCGCCGGCATCGCTCAGGTCCTGGCGCACAAGGGAAAGTACAACGTCACTCTC
NonamEVm004010t4 CTCATGGGCGCCGGCATCGCTCAGGTCCTGGCGCACAAGGGAAAGTACAACGTCACTCTC

NonamEVm004010t1 TCGGACGTCACCGACAAGGCGCTCGCCAACGGACAGTCGATTATCTCCAAGTCACTCACA
NonamEVm004010t4 TCGGACGTCACCGACAAGGCGCTCGCCAACGGACAGTCGATTATCTCCAAGTCACTCACA

NonamEVm004010t1 AGGATCGCAAAGAAGGCCTTGGCCGAATCGTCGGCCGACGAGCAGTCCCACTTTGTCAAA
NonamEVm004010t4 AGGATCGCAAAGAAGGCCTTGGCCGAATCGTCGGCCGACGAGCAGTCCCACTTTGTCAAA

NonamEVm004010t1 GGCATCGTTGATTCGATCAAGGTCACCACCGATCCCGAGGCCGCCGTGGAAGACACCGAC
NonamEVm004010t4 GGCATCGTTGATTCGATCAAGGTCACCACCGATCCCGAGGCCGCCGTGGAAGACACCGAC

NonamEVm004010t1 CTCGTTATCGAGGCCATCATCGAGAACGTCGGCATCAAGAAGGACCTCTTTGGCTTCCTC
NonamEVm004010t4 CTCGTTATCGAGGCCATCATCGAGAACGTCGGCATCAAGAAGGACCTCTTTGGCTTCCTC

NonamEVm004010t1 GACGGCAAGGCGCCCAAGGACGCTATCTTTGCGACCAACACGAGCTCGCTCAGCATCACC
NonamEVm004010t4 GACGGCAAGGCGCCCAAGGACGCTATCTTTGCGACCAACACGAGCTCGCTCAGCATCACC

NonamEVm004010t1 GACGTCGCCGAGGCTGTCGAGAGAAAGGAGCGGTTCGCCGGCTTCCACGCCTTCAACCCG
NonamEVm004010t4 GACGTCGCCGAGGCTGTCGAGAGAAAGGAGCGGTTCGCCGGCTTCCACGCCTTCAACCCG

NonamEVm004010t1 GTGCCCCAGATGAAGCTGGTCGAGATCGTGCGCACCAGCCAGACCAGCGACGAGACCTAC
NonamEVm004010t4 GTGCCCCAGATGAAGCTGGTCGAGATCGTGCGCACCAGCCAGACCAGCGACGAGACCTAC

NonamEVm004010t1 GACAGCCTGATGGAGGTGGCCAAGAGGATGGGCAAGGTCCCCGTCACTTGCGTCGACTCG
NonamEVm004010t4 GACAGCCTGATGGAGGTGGCCAAGAGGATGGGCAAGGTCCCCGTCACTTGCGTCGACTCG

NonamEVm004010t1 CCGG--------------------------------------------------------
NonamEVm004010t4 CCGGGGTGAGTCGACAGCTCCGACTAGGAGGCATCCCGATGTGTCCGGAAACGCTTTCCC

NonamEVm004010t1 --------------------------------------------------GATTCATCGT
NonamEVm004010t4 CTCTGAAGAAACTCCTGGCGACTCTGCCTTTCGTCTCCTGCTGCGGCACAGATTCATCGT

NonamEVm004010t1 CAACCGACTGCTGGTACCCTACATGTTTGAGGCCATCCGACTCGTTGAGCGAGGCGAGGC
NonamEVm004010t4 CAACCGACTGCTGGTACCCTACATGTTTGAGGCCATCCGACTCGTTGAGCGAGGCGAGGC

NonamEVm004010t1 GTCGATCAAGGATGTGGACACCGCTATGAAGCTCGGCGCTGGATACCCCATGGGTCCGTT
NonamEVm004010t4 GTCGATCAAGGATGTGGACACCGCTATGAAGCTCGGCGCTGGATACCCCATGGGTCCGTT

NonamEVm004010t1 TGAGCTCGCCGATCTGGTCGGCCTCGATACGCTGTCCCACATTGCCAAGGGCTGGAGGGA
NonamEVm004010t4 TGAGCTCGCCGATCTGGTCGGCCTCGATACGCTGTCCCACATTGCCAAGGGCTGGAGGGA

NonamEVm004010t1 GACTCGGGTCAAGACGGGAGAGATCAGCGCCGAGGCGGTCAAGGAATCGAAGCTGCTCGA
NonamEVm004010t4 GACTCGGGTCAAGACGGGAGAGATCAGCGCCGAGGCGGTCAAGGAATCGAAGCTGCTCGA

NonamEVm004010t1 GGATCTGGTGGCCCAGGGCAAGCTTGGCAAAAAGAGCGGAGAGAAGGGCGGTTTCTACAA
NonamEVm004010t4 GGATCTGGTGGCCCAGGGCAAGCTTGGCAAAAAGAGCGGAGAGAAGGGCGGTTTCTACAA

NonamEVm004010t1 ATACCCGGCGTCCAATAAGTGAGGCGAGGCA-----------------------------
NonamEVm004010t4 ATACCCGGCGTCCAATAAGTGAGGCGAGGCAGCTTTCCGGATGGTCTCTGCTAGCCGATC

NonamEVm004010t1 ------------------------------------------------------------
NonamEVm004010t4 GAGGACAGATCGGTTGAGGCACCAGTGTAGGGCTGCATCATTGGATCAGCAATGAGGAAG

NonamEVm004010t1 -------------------------------------
NonamEVm004010t4 GCGGTTGCGTACAAATACAAAGAGTGATAGAAGGTGC

Can someone explain this behavior? is something wrong with my command?