Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1819
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: 35229
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3808 original size:97 final size:97
Alignment explanation
Indices: 3651--3885 Score: 344
Period size: 97 Copynumber: 2.4 Consensus size: 97
3641 TTTATTTATC
* ** * * * * *
3651 GGGATACTCCAACCTTATTCTTCCGAAGGGATACTCCAACCCCGCTTTTAAATACGTCAAAGTTT
1 GGGACACTCCAACCCCATTCCTCCGAGGGGATACTTCAACCCCGCTTTTAAACACATCAAAGTTT
3716 AAATCTTATTCTCACTTAAATTGTCATCATCG
66 AAATCTTATTCTCACTTAAATTGTCATCATCG
* * *
3748 GGGACATTTCAACCCCATTCCTCCGAGGGGATACTTCAACCCCGCTTTTAAACGCATCAAAGTTT
1 GGGACACTCCAACCCCATTCCTCCGAGGGGATACTTCAACCCCGCTTTTAAACACATCAAAGTTT
*
3813 AAATTTTATTCTCACTTAAATTGTCATCATCG
66 AAATCTTATTCTCACTTAAATTGTCATCATCG
* *
3845 GGGACACTCCAGCCCCATTCCTCCGAGGGAATACTTCAACC
1 GGGACACTCCAACCCCATTCCTCCGAGGGGATACTTCAACC
3886 TTGTTTTTCA
Statistics
Matches: 122, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 122 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.30
Consensus pattern (97 bp):
GGGACACTCCAACCCCATTCCTCCGAGGGGATACTTCAACCCCGCTTTTAAACACATCAAAGTTT
AAATCTTATTCTCACTTAAATTGTCATCATCG
Found at i:5618 original size:86 final size:86
Alignment explanation
Indices: 5462--5625 Score: 294
Period size: 86 Copynumber: 1.9 Consensus size: 86
5452 TTACGTAAGT
5462 AATAATGTGCGAACATTTCACCTACATTTGCATTTTCATATTACGCTTCATTTTTCTTTACTGGG
1 AATAATGTGCGAACATTTCACCTACATTTGCATTTTCATATTACGCTTCATTTTTCTTTACTGGG
5527 GCATGCTGTTATGTGCGAAGA
66 GCATGCTGTTATGTGCGAAGA
* *
5548 AATAATGTGCGAACATTGTCACCTACGTTTGTATTTTCATATTACGCTTCATTTTT-TTTACTGG
1 AATAATGTGCGAACATT-TCACCTACATTTGCATTTTCATATTACGCTTCATTTTTCTTTACTGG
5612 GGCATGCTGTTATG
65 GGCATGCTGTTATG
5626 CTGTCCGGTC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
86 39 0.52
87 36 0.48
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (86 bp):
AATAATGTGCGAACATTTCACCTACATTTGCATTTTCATATTACGCTTCATTTTTCTTTACTGGG
GCATGCTGTTATGTGCGAAGA
Found at i:8634 original size:22 final size:23
Alignment explanation
Indices: 8564--8635 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 23
8554 CAAAATGACC
*
8564 AAAAAAAG-GTCAAAAGCAAAAGT
1 AAAAAAAGTG-CAAAAGCAAAACT
* * *
8587 ACAAAATA-TG-AAAAGAAAAACA
1 A-AAAAAAGTGCAAAAGCAAAACT
8609 AAAAAAAGTGCAAAAGCAAAA-T
1 AAAAAAAGTGCAAAAGCAAAACT
8631 AAAAA
1 AAAAA
8636 GGGAATAACA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
21 5 0.13
22 17 0.45
23 10 0.26
24 6 0.16
ACGTcount: A:0.71, C:0.08, G:0.12, T:0.08
Consensus pattern (23 bp):
AAAAAAAGTGCAAAAGCAAAACT
Found at i:10603 original size:87 final size:84
Alignment explanation
Indices: 10459--10621 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 84
10449 GACCGGACAG
10459 CATAACAGCATGCCCCAGTAAAAAAATGAAGCGTAATATGAAAATACAAACGTAGGTGACAATGT
1 CATAACAGCATGCCCCAGTAAAAAAATGAAGCGTAATATGAAAATACAAACGTAGGTGA-AATGT
10524 TCGCACATTATTTCTTCGCA
65 TCGCACATTATTTCTTCGCA
* *
10544 CATAACAGCATGCCCCAGTAAAGAAAAATGAAGCGTAATATGAAAATGCAAATGTAGGTGAAATG
1 CATAACAGCATGCCCCAGT-AA-AAAAATGAAGCGTAATATGAAAATACAAACGTAGGTGAAATG
10609 TTCGCACATTATT
64 TTCGCACATTATT
10622 ACTTACGTAA
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
85 19 0.26
86 19 0.26
87 36 0.49
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (84 bp):
CATAACAGCATGCCCCAGTAAAAAAATGAAGCGTAATATGAAAATACAAACGTAGGTGAAATGTT
CGCACATTATTTCTTCGCA
Found at i:12319 original size:97 final size:97
Alignment explanation
Indices: 12199--12417 Score: 339
Period size: 97 Copynumber: 2.3 Consensus size: 97
12189 TGAAAAACAA
* * *
12199 GGTTGAAGTATTCCCTCGGAGGAATGGGGCTGGAGTGTCCCCGATGATGACAATTTAAGTGAGAA
1 GGTTGAAGTATCCCCTCGGAGGAATGGGGCTGAAATGTCCCCGATGATGACAATTTAAGTGAGAA
* *
12264 TAAAATTTAAACTTTGATGCGTTTAAAAGCGG
66 TAAAATTTAAACTTTGACGCATTTAAAAGCGG
*
12296 GGTTGAAGTATCCCCTCGGAGGAATGGGGTTGAAATGTCCCCGATGATGACAATTTAAGTGAGAA
1 GGTTGAAGTATCCCCTCGGAGGAATGGGGCTGAAATGTCCCCGATGATGACAATTTAAGTGAGAA
* *
12361 TAAGATTTAAACTTTGACGTATTTAAAAGCGG
66 TAAAATTTAAACTTTGACGCATTTAAAAGCGG
* * *
12393 GGTTGGAGTATCCCTTCGGAAGAAT
1 GGTTGAAGTATCCCCTCGGAGGAAT
12418 AAGGTTGGAG
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 111 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (97 bp):
GGTTGAAGTATCCCCTCGGAGGAATGGGGCTGAAATGTCCCCGATGATGACAATTTAAGTGAGAA
TAAAATTTAAACTTTGACGCATTTAAAAGCGG
Found at i:12450 original size:97 final size:97
Alignment explanation
Indices: 12199--12447 Score: 259
Period size: 97 Copynumber: 2.6 Consensus size: 97
12189 TGAAAAACAA
* * ** * * * * * *
12199 GGTTGAAGTATTCCCTCGGAGGAATGGGGCTGGAGTGTCCCCGATGATGACAATTTAAGTGAGAA
1 GGTTGAAGTATCCCCTCGGAAGAATAAGGTTGAAATATCCCCGATAATGAAAATTTAAGTGAGAA
* *
12264 TAAAATTTAAACTTTGATGCGTTTAAAAGCGG
66 TAAAATTTAAACTTTGACGCATTTAAAAGCGG
* ** * * *
12296 GGTTGAAGTATCCCCTCGGAGGAATGGGGTTGAAATGTCCCCGATGATGACAATTTAAGTGAGAA
1 GGTTGAAGTATCCCCTCGGAAGAATAAGGTTGAAATATCCCCGATAATGAAAATTTAAGTGAGAA
* *
12361 TAAGATTTAAACTTTGACGTATTTAAAAGCGG
66 TAAAATTTAAACTTTGACGCATTTAAAAGCGG
* * * *
12393 GGTTGGAGTATCCCTTCGGAAGAATAAGGTTGGAGTAT-CCCGATAAAT-AAAATTT
1 GGTTGAAGTATCCCCTCGGAAGAATAAGGTTGAAATATCCCCGAT-AATGAAAATTT
12448 TAATGTTTTT
Statistics
Matches: 133, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
96 12 0.09
97 121 0.91
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (97 bp):
GGTTGAAGTATCCCCTCGGAAGAATAAGGTTGAAATATCCCCGATAATGAAAATTTAAGTGAGAA
TAAAATTTAAACTTTGACGCATTTAAAAGCGG
Found at i:18057 original size:15 final size:17
Alignment explanation
Indices: 18025--18059 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
18015 CTTTTATTAT
18025 TAAAATTTTATCTTAAA
1 TAAAATTTTATCTTAAA
18042 TAAAA-TTTAT-TTAAA
1 TAAAATTTTATCTTAAA
18057 TAA
1 TAA
18060 TATCACTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 5 0.28
17 5 0.28
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATTTTATCTTAAA
Found at i:18318 original size:29 final size:29
Alignment explanation
Indices: 18286--18348 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
18276 TAAGGATACA
*
18286 TTTAATATTCAAACAAATTTGA-TCAAATT
1 TTTAATATTCAAACAAATTT-ATTCAAAAT
*
18315 TTTAATATTCAATCAAATTTATTCAAAAT
1 TTTAATATTCAAACAAATTTATTCAAAAT
18344 TTTAA
1 TTTAA
18349 GACCCTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (29 bp):
TTTAATATTCAAACAAATTTATTCAAAAT
Found at i:19262 original size:16 final size:16
Alignment explanation
Indices: 19235--19274 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
19225 TGTTAACATA
*
19235 AAATTTTT-ATTTTTT
1 AAATTTTTAATTTTTG
*
19250 TAATTTTTAATTTTTG
1 AAATTTTTAATTTTTG
19266 AAATTTTTA
1 AAATTTTTA
19275 CTATGATGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
AAATTTTTAATTTTTG
Found at i:19563 original size:2 final size:2
Alignment explanation
Indices: 19538--19578 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
19528 GAGTCTAAGA
* * *
19538 AT AT AT AA AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19579 AATGGTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:19575 original size:12 final size:12
Alignment explanation
Indices: 19538--19581 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
19528 GAGTCTAAGA
19538 ATATATAAATAT
1 ATATATAAATAT
*
19550 AAATATAAATAT
1 ATATATAAATAT
19562 ATATAT--ATAT
1 ATATATAAATAT
19572 ATATATAAAT
1 ATATATAAAT
19582 GGTATAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 10 0.36
12 18 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:20380 original size:11 final size:11
Alignment explanation
Indices: 20364--20388 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20354 CATCAAACCT
20364 TTGGGAATAGG
1 TTGGGAATAGG
20375 TTGGGAATAGG
1 TTGGGAATAGG
20386 TTG
1 TTG
20389 AACAGCCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (11 bp):
TTGGGAATAGG
Found at i:27007 original size:20 final size:20
Alignment explanation
Indices: 26982--27023 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
26972 AAGAATTGAA
26982 GAGGGATACTTGAGAGGGAT
1 GAGGGATACTTGAGAGGGAT
*
27002 GAGGGATGCTTGAGAGGGAT
1 GAGGGATACTTGAGAGGGAT
27022 GA
1 GA
27024 CGGAGCCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.48, T:0.19
Consensus pattern (20 bp):
GAGGGATACTTGAGAGGGAT
Found at i:27165 original size:27 final size:27
Alignment explanation
Indices: 27104--27174 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
27094 AAACAAGCCT
* *
27104 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
27132 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
27159 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
27175 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:31579 original size:20 final size:20
Alignment explanation
Indices: 31551--31599 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
31541 AGAAAGAATT
31551 GAAGAGGGATACAAGAGAGG
1 GAAGAGGGATACAAGAGAGG
* * **
31571 GATGAGGGATGCTTGAGAGG
1 GAAGAGGGATACAAGAGAGG
31591 GAAGAGGGA
1 GAAGAGGGA
31600 GCCTCTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.49, T:0.10
Consensus pattern (20 bp):
GAAGAGGGATACAAGAGAGG
Found at i:31749 original size:24 final size:27
Alignment explanation
Indices: 31676--31746 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
31666 AAACAAGCCT
* *
31676 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
31704 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
31731 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
31747 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:33355 original size:16 final size:18
Alignment explanation
Indices: 33324--33360 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
33314 AATTTCCGAA
33324 TATCAAAACTAAATTT-T
1 TATCAAAACTAAATTTAT
33341 TATCAAAAC-AAATTTAT
1 TATCAAAACTAAATTTAT
33358 TAT
1 TAT
33361 TCCGTGTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
TATCAAAACTAAATTTAT
Found at i:33649 original size:2 final size:2
Alignment explanation
Indices: 33642--33689 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
33632 AAACTCCTCT
33642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33684 TA TA TA
1 TA TA TA
33690 GATGAAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35163 original size:22 final size:23
Alignment explanation
Indices: 35133--35176 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
35123 AAGGGTTTAA
*
35133 AATATATTATTATTTTTAAATAT
1 AATATATTATTATTTTAAAATAT
35156 AATA-ATTATTATTTTAAAATA
1 AATATATTATTATTTTAAAATA
35177 AAAATACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATATTATTATTTTAAAATAT
Found at i:35187 original size:20 final size:21
Alignment explanation
Indices: 35140--35194 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
35130 TAAAATATAT
*
35140 TATTATTTTTAAATATAATAAT
1 TATTA-TTTTAAATATAATAAA
35162 TATTATTTTAAA-ATAA-AAA
1 TATTATTTTAAATATAATAAA
35181 TACTTA-TTTAAATA
1 TA-TTATTTTAAATA
35195 AGACATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.33
20 8 0.27
21 7 0.23
22 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTATTTTAAATATAATAAA
Done.