Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7432.1
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: 6943
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Found at i:289 original size:44 final size:43
Alignment explanation
Indices: 227--732 Score: 320
Period size: 44 Copynumber: 11.7 Consensus size: 43
217 ACTAGATGCG
* * *
227 ATCTGCT-CTCTGTAACTTCAGAGAGATAAGATATAAGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TAAGGTTTTA
* * * *
270 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTA-AGGTTTTA
**** *
314 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAAGGT-TTTA
* * *
359 GTCTGCCCCACTGCAACTTCA-GGAGGATAAGACTT--GCTTACTTA
1 ATCTGCTCCACTGCAACTTCAGGGA-GATAAGA-TTAAGGTT--TTA
* * * ***
403 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATT--TGATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAAGGTTTTA
* *
444 ATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TAAGGTTTTA
* * *
487 AT-TCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
1 ATCT-GCTCCACTGCAACTTCAGGGAGATAAGATTA-AGGTTTTA
**** *
531 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAAGGT-TTTA
* * * * * *
576 GTTTGCCCCACTACAACTTTA-GGAGGATAAGACTT--GCTTACTTA
1 ATCTGCTCCACTGCAACTTCAGGGA-GATAAGA-TTAAGGTT--TTA
* * * * ***
620 GTCTGCTCCACTGCAACTTCAGAGAGATAAGACT-A-GATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAAGGTTTTA
* *
661 ATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TAAGGTTTTA
**
704 ATCCACTCCACTGCAACTTCAGGGAGATA
1 ATCTGCTCCACTGCAACTTCAGGGAGATA
733 GGATCTACAA
Statistics
Matches: 362, Mismatches: 75, Indels: 51
0.74 0.15 0.10
Matches are distributed among these distances:
40 46 0.13
41 14 0.04
42 4 0.01
43 31 0.09
44 196 0.54
45 71 0.20
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAAGGTTTTA
Found at i:408 original size:89 final size:88
Alignment explanation
Indices: 315--653 Score: 290
Period size: 89 Copynumber: 3.9 Consensus size: 88
305 TCGGCTTTAA
315 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATCTTCAGTCTGCCCCACTGCAACTTCA
380 G-GAGGATAAGACTTGCTTACTTAG
65 GAGA-GATAAGACTTGCTTACTTAG
* * * *
404 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-A--TGC-GATCTG-CTCTCTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCTTCAG-TCTGCCCCACTGCAACTTCA
* * *
464 GAGAGATAAGATCTAAGGTT--TTAA
65 GAGAGATAAGA-CT-TGCTTACTTAG
* * ** * * *
488 T-TCGCTCCACTGCAACTTCAGGGAGATAGGA-TTATCGGCTTTAATCTGCTCCACTGCAACTTC
1 TCT-GCTCCACTGCAACTTCAGGGAGATAAGACTT-GCATCTTCAGTCTGCCCCACTGCAACTTC
* *
551 AGGGAGATAAGACTTGC-CATCTTCAG
64 AGAGAGATAAGACTTGCTTA-CTT-AG
* * * * * *
577 TTTGCCCCACTACAACTTTA-GGAGGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAACTTC
1 TCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCAT-CTTCAGTCTGCCCCACTGCAACTTC
640 AGAGAGATAAGACT
64 AGAGAGATAAGACT
654 AGATGCGATC
Statistics
Matches: 201, Mismatches: 30, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
83 3 0.01
84 53 0.26
85 10 0.05
86 4 0.02
87 8 0.04
88 27 0.13
89 90 0.45
90 6 0.03
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (88 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCTTCAGTCTGCCCCACTGCAACTTCAG
AGAGATAAGACTTGCTTACTTAG
Found at i:511 original size:217 final size:217
Alignment explanation
Indices: 131--736 Score: 1032
Period size: 217 Copynumber: 2.8 Consensus size: 217
121 TAGGAATTAG
* * * * * * * *
131 TGCCTTCTTCAGTCTACCTCGCTGTAACTTCAGGAGGATAAGACTTGCTTATTTAGTATGCTTCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
* * * *
196 CTGCAACTTCAAGGAAATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATAT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
261 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
131 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
326 GCAACTTCAGGGAGATAAGACT
196 GCAACTTCAGGGAGATAAGACT
348 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
* *
413 CTGCAACTTCAGGGAGATAAGATTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
*
478 AAGGTTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
131 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
543 GCAACTTCAGGGAGATAAGACT
196 GCAACTTCAGGGAGATAAGACT
* * *
565 TGCCATCTTCAGTTTGCCCCACTACAACTTTAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
*
630 CTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
66 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
*
695 AAGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGAT
131 AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
737 CTACAATCTT
Statistics
Matches: 366, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 366 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (217 bp):
TGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCA
CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
AAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACT
GCAACTTCAGGGAGATAAGACT
Found at i:607 original size:173 final size:175
Alignment explanation
Indices: 274--732 Score: 458
Period size: 173 Copynumber: 2.6 Consensus size: 175
264 GTTTTAATCC
* * * *
274 GCTCCACTGCAACTTCAGGGAGATAGGAT-TATCGGCTTTAATCTGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGAGAGATAAGATCTA-AGGATTTAATCTGCTCCACTGCAACTTCAGGG
* ** * * * *
338 AGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTT
65 AGATAAGA-TT-ACGGCTTTAATCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCATACTT
* * * *
402 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-ATGC-GA-TCT
127 AGTCTGCCCCACTACAACTTCAGGGAGATAAGACTTGCATACTGAGTCT
* *
448 GCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAAT-TCGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGAGAGATAAGATCTAAGGATTTAATCT-GCTCCACTGCAACTTCAGGG
*
511 AGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCAT-CTTC
65 AGATAAGATTA-CGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATACTT-
* * * *
575 AGTTTGCCCCACTACAACTTTA-GGAGGATAAGACTTGCTTACTTAGTCT
127 AGTCTGCCCCACTACAACTTCAGGGA-GATAAGACTTGCATACTGAGTCT
*** * *
624 GCTCCACTGCAACTTCAGAGAGATAAGA-CT-A-GATGCGATCTGCT-CTCTGCAACTTCAGAGA
1 GCTCCACTGCAACTTCAGAGAGATAAGATCTAAGGATTTAATCTGCTCCACTGCAACTTCAGGGA
* * **
685 GATAAGATCTAAGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATA
66 GATAAGAT-TACGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
733 GGATCTACAA
Statistics
Matches: 239, Mismatches: 33, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
172 44 0.18
173 145 0.61
174 16 0.07
175 3 0.01
176 8 0.03
177 23 0.10
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (175 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATCTAAGGATTTAATCTGCTCCACTGCAACTTCAGGGA
GATAAGATTACGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGTC
TGCCCCACTACAACTTCAGGGAGATAAGACTTGCATACTGAGTCT
Found at i:860 original size:132 final size:132
Alignment explanation
Indices: 724--1112 Score: 670
Period size: 132 Copynumber: 2.9 Consensus size: 132
714 CTGCAACTTC
*
724 AGGGAGATAGGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGGGAGACAAGGCTTGGTGGC
*
789 TTAAATCTGCTTCCCACTATCTTGGAAAAATAAGATCCGCCGTCTTCGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAAATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
854 TT
131 TT
* * *
856 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGTTGCTGAGGGAGACAAAGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGGGAGACAAGGCTTGGTGGC
* *
921 TTAAATCTGCTTCCCACTATCTTGGAAATATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGC
66 TTAAATCTGCTTCCCACTATCTTGGAAAAATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
986 TT
131 TT
* *
988 AGGGAGATAAGATCTACAATCTTCAACCTTCTTCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
1 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGGGAGACAAGGCTTGGTGGC
* * *
1053 TTAAATCTGCTTCCCACTATCTTAGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACT
66 TTAAATCTGCTTCCCACTATCTTGGAAAAATAAGATTCGCCGTCTTCGATCTGCTCCACT
1113 GTCAATACAG
Statistics
Matches: 242, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 242 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (132 bp):
AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGGGAGACAAGGCTTGGTGGC
TTAAATCTGCTTCCCACTATCTTGGAAAAATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGC
TT
Found at i:2401 original size:14 final size:14
Alignment explanation
Indices: 2378--2424 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
2368 TTTCTTTCAC
2378 TTTTATTTTTTGTTT
1 TTTTA-TTTTTGTTT
2393 TTTTATTTTTGTTT
1 TTTTATTTTTGTTT
*
2407 TTGTT-TTTTCGTTT
1 TT-TTATTTTTGTTT
2421 TTTT
1 TTTT
2425 TAATCTGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 2 0.07
14 21 0.70
15 7 0.23
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.85
Consensus pattern (14 bp):
TTTTATTTTTGTTT
Found at i:2421 original size:20 final size:20
Alignment explanation
Indices: 2384--2422 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2374 TCACTTTTAT
*
2384 TTTTTGTTTTTTTATTTTTG
1 TTTTTGTTTTTTCATTTTTG
*
2404 TTTTTGTTTTTTCGTTTTT
1 TTTTTGTTTTTTCATTTTT
2423 TTTAATCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.85
Consensus pattern (20 bp):
TTTTTGTTTTTTCATTTTTG
Done.