Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold389
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: 14584
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Found at i:1293 original size:3 final size:3
Alignment explanation
Indices: 1232--1284 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
1222 TTTGTTAACT
* *
1232 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
*
1277 TTA GTA TT
1 TTA TTA TT
1285 GGTATTATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1365 original size:22 final size:23
Alignment explanation
Indices: 1318--1366 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
1308 ATCTCTATTC
*
1318 ATATATACTTATGTATTTTCAAAT
1 ATATATACTTATGTATTATC-AAT
1342 ATATATATCTTAT-TATTATC-AT
1 ATATATA-CTTATGTATTATCAAT
1364 ATA
1 ATA
1367 AGTGCTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.22
24 13 0.57
25 5 0.22
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATATACTTATGTATTATCAAT
Found at i:1449 original size:32 final size:32
Alignment explanation
Indices: 1396--1487 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
1386 GTACATATTT
* * *
1396 TACATATAATT-TGTTTA-ATATATATACGTA
1 TACATATATTTATTTTTATATATATATACATA
*
1426 TAC-TCATATTTCTTTTTATATATATATACATA
1 TACAT-ATATTTATTTTTATATATATATACATA
*
1458 TACATATTTTTATTTTTATAAGTATATATA
1 TACATATATTTATTTTTAT-A-TATATATA
1488 TTTATATGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
29 1 0.02
30 8 0.16
31 5 0.10
32 27 0.53
33 2 0.04
34 8 0.16
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (32 bp):
TACATATATTTATTTTTATATATATATACATA
Found at i:14166 original size:86 final size:85
Alignment explanation
Indices: 13971--14234 Score: 288
Period size: 86 Copynumber: 3.1 Consensus size: 85
13961 GACAGATCAA
* * *
13971 TGAAGACAAAGGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCC
1 TGAAGA-AAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-ACACAAAGCCTTG-C
** * *
14035 TCTTTCGGTTGTG-ATAGAGCTGGT
63 TCCATC-GTT-TGCATGGAGCTAGT
*
14059 TGAAGAAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATC
1 TGAAGAAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGC-TC
14123 CATCGATTTGCAGTGGAGCTAGT
65 CATCG-TTTGCA-TGGAGCTAGT
** *
14146 T-AAGAAGTAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCTCC
1 TGAAGAAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCTCC
*
14209 ATCGGTTGCATTGGAGC-AGAT
66 ATCGTTTGCA-TGGAGCTAG-T
14230 TGAAG
1 TGAAG
14235 CCAGAGATCT
Statistics
Matches: 155, Mismatches: 13, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
83 2 0.01
84 13 0.08
85 22 0.14
86 65 0.42
87 47 0.30
88 6 0.04
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (85 bp):
TGAAGAAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCTCC
ATCGTTTGCATGGAGCTAGT
Found at i:14265 original size:86 final size:86
Alignment explanation
Indices: 13994--14280 Score: 246
Period size: 86 Copynumber: 3.3 Consensus size: 86
13984 TCTTGCCTTT
* * * * ** * * *
13994 CTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCG-GTTG-TGATAGAGCTG
1 CTGCATTAACAGCGAAGCAGATCAAAGACA-AAGCCTTGCATCCATCGAGTTGCAG-TGGAGCTA
** * *
14057 GTTGAAGAAAAAGATCTTGCCTTC
64 GTT-AAGAAGTAGATCTTACCTCC
* *
14081 CTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCCATCGATTTGCAGTGGAGCTAG
1 CTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCATCCATCGAGTTGCAGTGGAGCTAG
* *
14145 TTAAGAAGTAGATCTTGCCTTC
65 TTAAGAAGTAGATCTTACCTCC
*
14167 CTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGC-TCCATCG-GTTGCATTGGAGC-AGA
1 CTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCATCCATCGAGTTGCAGTGGAGCTAG-
* *
14229 TTGAAGCCAG-AGATCTTATCTCC
65 TT-AAG-AAGTAGATCTTACCTCC
* * *
14252 CTGAGATTTACAGCGGAGCAGATCAAAGA
1 CTG-CATTAACAGCGAAGCAGATCAAAGA
14281 TAGTAATCCT
Statistics
Matches: 169, Mismatches: 23, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
83 2 0.01
84 13 0.08
85 26 0.15
86 89 0.53
87 36 0.21
88 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (86 bp):
CTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCATCCATCGAGTTGCAGTGGAGCTAGT
TAAGAAGTAGATCTTACCTCC
Found at i:14470 original size:127 final size:123
Alignment explanation
Indices: 14242--14505 Score: 302
Period size: 127 Copynumber: 2.1 Consensus size: 123
14232 AAGCCAGAGA
* * *
14242 TCTTATCTCCCTGAGATTTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTAC
1 TCTTATCTCCCTGAGATTTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATTAC
* * *
14307 ATGGAGCGGATTAAGGATCTTATCTCTCTGAAGTTACAGTAGAGGAAGATCACATCAGG
66 ATGGAGCGGATAAAGGATCTTATCTCTCTGAAGTTACAGCAGA-GAAGATCACATCAAG
* *
14366 TCTTATCTCCCTGAGA-TTACAGTGGA-CAGATCGAAGACACT-ATCCTATCTCCCTGA-ATTAC
1 TCTTATCTCCCTGAGATTTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATTAC
* * * * *
14427 AGTGGAGTGGGTTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGGTCGCATCAAG
66 A-TGGAG-CGG-----ATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAG
*
14492 TCTTATTTCCCTGA
1 TCTTATCTCCCTGA
14506 AGATGCAGTG
Statistics
Matches: 119, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
120 6 0.05
121 19 0.16
122 14 0.12
123 9 0.08
124 16 0.13
126 24 0.20
127 31 0.26
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (123 bp):
TCTTATCTCCCTGAGATTTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATTAC
ATGGAGCGGATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAG
Done.