Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Tc07v2_t010030.1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3054
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:945 original size:144 final size:144
Alignment explanation
Indices: 674--938 Score: 417
Period size: 144 Copynumber: 1.8 Consensus size: 144
664 AATCAACTTT
* *
674 CAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTAGAAGTTTTATTCTTATATGATACT
1 CAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTACAAGTTTTATTCTTATATGATAAT
* *
739 GCCTTGAAGGGAAGTGTGCCTGAGGAAATTGAGAATTTGACAAGATTAAGCGACTTAGCCCTCAA
66 GCCTTGAAGGGAAGTGTGCCTGAAGAAATCGAGAATTTGACAAGATTAAGCGACTTAGCCCTCAA
804 TGGGAATGATCTAA
131 TGGGAATGATCTAA
*
818 CAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTACAAGTTTTAATT-TTATCT-AGTA
1 CAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTACAAGTTTT-ATTCTTATATGA-TA
* * * *
881 ATGCCTTGGAGGGAAGTGTGCCTGAAGAAATCGGGAATTTGACGAGATTAAGCTACTT
64 ATGCCTTGAAGGGAAGTGTGCCTGAAGAAATCGAGAATTTGACAAGATTAAGCGACTT
939 GTCCCTCTAT
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
143 1 0.01
144 106 0.96
145 3 0.03
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (144 bp):
CAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTACAAGTTTTATTCTTATATGATAAT
GCCTTGAAGGGAAGTGTGCCTGAAGAAATCGAGAATTTGACAAGATTAAGCGACTTAGCCCTCAA
TGGGAATGATCTAA
Found at i:962 original size:144 final size:144
Alignment explanation
Indices: 674--975 Score: 414
Period size: 144 Copynumber: 2.1 Consensus size: 144
664 AATCAACTTT
* *
674 CAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTAGAAGTTTTATTCTTATATGATACT
1 CAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTACAAGTTTTATTCTTATATGATAAT
* *
739 GCCTTGAAGGGAAGTGTGCCTGAGGAAATTGAGAATTTGACAAGATTAAGCGACTTAGCCCTCAA
66 GCCTTGAAGGGAAGTGTGCCTGAAGAAATCGAGAATTTGACAAGATTAAGCGACTTAGCCCTCAA
* ** *
804 TGGGAATGATCTAA
131 TAGGAACAACCTAA
*
818 CAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTACAAGTTTTAATT-TTATCT-AGTA
1 CAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTACAAGTTTT-ATTCTTATATGA-TA
* * * *
881 ATGCCTTGGAGGGAAGTGTGCCTGAAGAAATCGGGAATTTGACGAGATTAAGCTACTT-GTCCCT
64 ATGCCTTGAAGGGAAGTGTGCCTGAAGAAATCGAGAATTTGACAAGATTAAGCGACTTAG-CCCT
*
945 CTATAGGAACAACCTAA
128 CAATAGGAACAACCTAA
962 CAGGT-GAAATTCCA
1 CAGGTAG-AATTCCA
976 TCAGCTATTG
Statistics
Matches: 140, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
143 3 0.02
144 134 0.96
145 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (144 bp):
CAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTACAAGTTTTATTCTTATATGATAAT
GCCTTGAAGGGAAGTGTGCCTGAAGAAATCGAGAATTTGACAAGATTAAGCGACTTAGCCCTCAA
TAGGAACAACCTAA
Found at i:1086 original size:72 final size:72
Alignment explanation
Indices: 952--1119 Score: 182
Period size: 72 Copynumber: 2.3 Consensus size: 72
942 CCTCTATAGG
* * * * *
952 AACAACCTAACAGGTGAAATTCCATCAGCTATTGGAAGCCTGACTTCTATTATACGCCTTGATCT
1 AACAACTTGACAGGTGAAATTCCATCAGCTATTGGAAACCTGACTTCTATTACACGCATTGAT-T
1017 TTC-GAAT
65 TTCGGAAT
* * *
1024 AACAGCTTGACAGGTGAAATTCCATCAGCTGTTGGAAACCTGTCTTCTATT-CA-GCATATTGAT
1 AACAACTTGACAGGTGAAATTCCATCAGCTATTGGAAACCTGACTTCTATTACACGC--ATTGAT
*
1087 TTTCGGATT
64 TTTCGGAAT
*
1096 AACAACTTGGCAGGT-AGAATTCCA
1 AACAACTTGACAGGTGA-AATTCCA
1120 ACCAGTTTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
70 2 0.02
71 6 0.07
72 73 0.90
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (72 bp):
AACAACTTGACAGGTGAAATTCCATCAGCTATTGGAAACCTGACTTCTATTACACGCATTGATTT
TCGGAAT
Found at i:1257 original size:288 final size:288
Alignment explanation
Indices: 817--1407 Score: 793
Period size: 288 Copynumber: 2.1 Consensus size: 288
807 GAATGATCTA
* * * *
817 ACAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGAGTTACAAGTTTTAATTTTATCTAGTAA
1 ACAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGACTTACAAGTTTTAAGTTTATATAGAAA
* * ** *
882 TGCCTTGGAGGGAAGTGTGCCTGAAGAAATCGGGAATTTGACGAGATTAAGCTACTTGTCCCTCT
66 TACCTTGGAGGGAAGTGTGCCTCAAGAAATCGGGAATTTGACGAGATTAAAATACTTGTCCCTCG
* *
947 ATAGGAACAACCTAACAGGTGAAATTCCATCAGCTATTGGAAGCCTGACTTCTATTATACG-CCT
131 AGAGGAACAACCTAACAGGTGAAATTCCATCAGCTATTGGAAGCCTAACTTCTATTA-ACGACCT
* * *
1011 TGA-TCTTTCGAATAACAGCTTGACAGGTGAAATTCCATCAGCTGTTGGAAACCTGTCTTCTATT
195 TGAGT-TTTCGAATAACAACTTGACAGGTGAAATTCCATCAGCTGTTGGAAACATGACTTCTATT
* *
1075 CAGCATATTGA-TTTTCGGATTAACAACTTG
259 CAGAATATTGATTTTTCGCA-TAACAACTTG
* * **
1105 GCAGGTAGAATTCCAACCAGTTTATTCAAGTGCCAAGACTTAGTA-TTTCTAAGTTTATATAGAA
1 ACAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGACTTACAAGTTT-TAAGTTTATATAGAA
* * *
1169 ATACCTTGGAGGGAAGTGTGCCTCAAGAAATTGGGAATTTGACTG-GATTAAAATACTTTTCTCT
65 ATACCTTGGAGGGAAGTGTGCCTCAAGAAATCGGGAATTTGAC-GAGATTAAAATACTTGTCCCT
*
1233 CG-GAGAGAACAACCT-ACAAGGTGAAATTCCATCAGCTATTGGAAGCCTAACTTCTATTAAGGA
129 CGAGAG-GAACAACCTAAC-AGGTGAAATTCCATCAGCTATTGGAAGCCTAACTTCTATTAACGA
* *
1296 GCTTGAGTTTTCGCATAACAACTTGACAGGTGAAATTCCATCAGCTGTTGGAAACATGACTTCTA
192 CCTTGAGTTTTCGAATAACAACTTGACAGGTGAAATTCCATCAGCTGTTGGAAACATGACTTCTA
** *
1361 TTGTGAATCTTGATTTTTCGCATAACAACTTG
257 TTCAGAATATTGATTTTTCGCATAACAACTTG
1393 ACAGGT-GAAATTCCA
1 ACAGGTAG-AATTCCA
1408 TCAGCTATTG
Statistics
Matches: 265, Mismatches: 30, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
287 10 0.04
288 246 0.93
289 9 0.03
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (288 bp):
ACAGGTAGAATTCCAACCAGTTTATTCAAGTGCAAAGACTTACAAGTTTTAAGTTTATATAGAAA
TACCTTGGAGGGAAGTGTGCCTCAAGAAATCGGGAATTTGACGAGATTAAAATACTTGTCCCTCG
AGAGGAACAACCTAACAGGTGAAATTCCATCAGCTATTGGAAGCCTAACTTCTATTAACGACCTT
GAGTTTTCGAATAACAACTTGACAGGTGAAATTCCATCAGCTGTTGGAAACATGACTTCTATTCA
GAATATTGATTTTTCGCATAACAACTTG
Found at i:1479 original size:72 final size:71
Alignment explanation
Indices: 1251--1466 Score: 281
Period size: 72 Copynumber: 3.0 Consensus size: 71
1241 ACAACCTACA
* * * *
1251 AGGTGAAATTCCATCAGCTATTGGAAGCCTAACTTCTATTAAGGAGCTTGAGTTTTCGCATAACA
1 AGGTGAAATTCCATCAGCTATTGGAAGCCTGACTTCTATTATGG-TCTTGATTTTTCGCATAACA
1316 ACTTGAC
65 ACTTGAC
* * * * *
1323 AGGTGAAATTCCATCAGCTGTTGGAAACATGACTTCTATTGTGAATCTTGATTTTTCGCATAACA
1 AGGTGAAATTCCATCAGCTATTGGAAGCCTGACTTCTATTATG-GTCTTGATTTTTCGCATAACA
1388 ACTTGAC
65 ACTTGAC
* * *
1395 AGGTGAAATTCCATCAGCTATTGGAAGCCTGACTTCTCTT-TGGTTCCTTGATTTTTGGCACAAC
1 AGGTGAAATTCCATCAGCTATTGGAAGCCTGACTTCTATTATGG-T-CTTGATTTTTCGCATAAC
1459 AACTTGAC
64 AACTTGAC
1467 CGGACGGCTT
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
71 3 0.02
72 122 0.98
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (71 bp):
AGGTGAAATTCCATCAGCTATTGGAAGCCTGACTTCTATTATGGTCTTGATTTTTCGCATAACAA
CTTGAC
Done.