Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2528
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: 28420
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Found at i:1310 original size:19 final size:19
Alignment explanation
Indices: 1288--1331 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
1278 ACTTTCGACA
1288 TAAAAGTATTTCGGTAACC
1 TAAAAGTATTTCGGTAACC
1307 TAAAAGTATTTCGGTAACC
1 TAAAAGTATTTCGGTAACC
1326 TAAAAG
1 TAAAAG
1332 ACTCGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
TAAAAGTATTTCGGTAACC
Found at i:3169 original size:13 final size:13
Alignment explanation
Indices: 3151--3178 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3141 CAACATATTT
3151 TATGACAAAATCA
1 TATGACAAAATCA
3164 TATGACAAAATCA
1 TATGACAAAATCA
3177 TA
1 TA
3179 ATCATACCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (13 bp):
TATGACAAAATCA
Found at i:5205 original size:65 final size:65
Alignment explanation
Indices: 5108--5550 Score: 398
Period size: 65 Copynumber: 6.8 Consensus size: 65
5098 AAAGAATGAT
**
5108 AGTTGAAATGGGTTGACCAAGGTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATGAAACCTA
1 AGTTGAAAAAGGTTGACCAAGGTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATGAAACCTA
* * * * * * *
5173 A-TTAAAAAAAAGTTGGCCAAGGTGAAACTAGAATAGTCAACTAAGGGTGACCAAGATAAAACCT
1 AGTT-GAAAAAGGTTGACCAAGGTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATGAAACCT
5237 A
65 A
* * * * * * * **
5238 AGTTGAAAAGGGTTAACTAGGGCGAAACCA-ACATAGTCAACTAAAGGTAACTAAAATGAAACCT
1 AGTTGAAAAAGGTTGACCAAGGTGAAACTAGA-ATAGTCAACTAAAGGTGACTAGGATGAAACCT
5302 A
65 A
* ** ** * * ** *
5303 AGTTGAAAAGGGTTG-GTAAGGCCAAACTAGAATAGTCAATTAAAGGTCACTAGGACAAAACTTA
1 AGTTGAAAAAGGTTGACCAAGGTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATGAAACCTA
* * *
5367 AGTCG-AAAAGGTTTGACCAAGG-AAAAGCTAGAATTGAT-AACTAAAAGG-GACTAGGATGAAA
1 AGTTGAAAAAGG-TTGACCAAGGTGAAA-CTAGAATAG-TCAACT-AAAGGTGACTAGGATGAAA
5428 CCTA
62 CCTA
* * *
5432 AGTTGAAAAGGGTTGACCAAGGTGAAACCAGAATAGTCAACTAAAGGTGACTAGGATGAAACTTA
1 AGTTGAAAAAGGTTGACCAAGGTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATGAAACCTA
* ** * * * * *
5497 AG-TAAAAAAAATTGACTAGGGTGAAACAAAAATAGTCAACTAAGGGTGACTAGG
1 AGTTGAAAAAGGTTGACCAAGGTGAAACTAGAATAGTCAACTAAAGGTGACTAGG
5551 TCAAAACTTA
Statistics
Matches: 304, Mismatches: 61, Indels: 27
0.78 0.16 0.07
Matches are distributed among these distances:
63 5 0.02
64 98 0.32
65 185 0.61
66 16 0.05
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (65 bp):
AGTTGAAAAAGGTTGACCAAGGTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATGAAACCTA
Found at i:5538 original size:129 final size:128
Alignment explanation
Indices: 5128--5550 Score: 422
Period size: 129 Copynumber: 3.3 Consensus size: 128
5118 GGTTGACCAA
* * **
5128 GGTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATGAAACCTAA-TTAAAAAAAAGTTGGCCA
1 GGTGAAACTAAAATAGTCAACTAAAGGTGACTAGGATGAAACCTAAGTT-GAAAAGGGTT-GCCA
* * * * * *
5192 AGGTGAAACTAGAATAGTCAACTAAGGGTGACCAAGATAAAACCTAAGTTGAAAAGGGTTAACTA
64 AGGTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATAAAACTTAAG-TGAAAAGGATTGACTA
5257 G
128 G
* * * * ** **
5258 GGCGAAACCAACATAGTCAACTAAAGGTAACTAAAATGAAACCTAAGTTGAAAAGGGTTGGTAAG
1 GGTGAAACTAAAATAGTCAACTAAAGGTGACTAGGATGAAACCTAAGTTGAAAAGGGTTGCCAAG
** * * * * * *
5323 GCCAAACTAGAATAGTCAATTAAAGGTCACTAGGACAAAACTTAAGTCGAAAAGGTTTGACCAA
66 GTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATAAAACTTAAGT-GAAAAGGATTGACTAG
* * *
5387 GG-AAAAGCTAGAATTGAT-AACTAAAAGG-GACTAGGATGAAACCTAAGTTGAAAAGGGTTGAC
1 GGTGAAA-CTAAAATAG-TCAACT-AAAGGTGACTAGGATGAAACCTAAGTTGAAAAGGGTTG-C
* * * **
5449 CAAGGTGAAACCAGAATAGTCAACTAAAGGTGACTAGGATGAAACTTAAGTAAAAAAAATTGACT
62 CAAGGTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATAAAACTTAAGTGAAAAGGATTGACT
5514 AG
127 AG
* *
5516 GGTGAAACAAAAATAGTCAACTAAGGGTGACTAGG
1 GGTGAAACTAAAATAGTCAACTAAAGGTGACTAGG
5551 TCAAAACTTA
Statistics
Matches: 231, Mismatches: 53, Indels: 19
0.76 0.17 0.06
Matches are distributed among these distances:
128 9 0.04
129 122 0.53
130 98 0.42
131 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (128 bp):
GGTGAAACTAAAATAGTCAACTAAAGGTGACTAGGATGAAACCTAAGTTGAAAAGGGTTGCCAAG
GTGAAACTAGAATAGTCAACTAAAGGTGACTAGGATAAAACTTAAGTGAAAAGGATTGACTAG
Found at i:7417 original size:13 final size:13
Alignment explanation
Indices: 7399--7423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7389 CAATTCATCA
7399 TGTATCGATACAT
1 TGTATCGATACAT
7412 TGTATCGATACA
1 TGTATCGATACA
7424 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7422 original size:33 final size:33
Alignment explanation
Indices: 7380--7443 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
7370 TTGAAGCAAG
7380 GTATCGATACAAT-T-CATCATGTATCGATACATT
1 GTATCGATACAATGTGC--CATGTATCGATACATT
7413 GTATCGATACAATGTGCCATGTATCGATACA
1 GTATCGATACAATGTGCCATGTATCGATACA
7444 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (33 bp):
GTATCGATACAATGTGCCATGTATCGATACATT
Found at i:7531 original size:13 final size:13
Alignment explanation
Indices: 7513--7539 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7503 TACAATGAAC
7513 ATGTATCGATACA
1 ATGTATCGATACA
7526 ATGTATCGATACA
1 ATGTATCGATACA
7539 A
1 A
7540 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:7555 original size:33 final size:32
Alignment explanation
Indices: 7496--7558 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
7486 AATTGTCTAA
*
7496 GTATCGATACAATGAACATGTATCGATACAAT
1 GTATCGATACAAAGAACATGTATCGATACAAT
7528 GTATCGATACAAAGCATA-ATGTATCGATACA
1 GTATCGATACAAAG-A-ACATGTATCGATACA
7559 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.46
33 14 0.50
34 1 0.04
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (32 bp):
GTATCGATACAAAGAACATGTATCGATACAAT
Found at i:8956 original size:20 final size:20
Alignment explanation
Indices: 8923--8961 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8913 TGATAAGAAT
* *
8923 ATTTATTCATTTTTTATTTA
1 ATTTATTCAATTTTAATTTA
*
8943 ATTTATTTAATTTTAATTT
1 ATTTATTCAATTTTAATTT
8962 GGTTTATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTATTCAATTTTAATTTA
Found at i:9856 original size:21 final size:20
Alignment explanation
Indices: 9823--9861 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9813 TATTTTCCTA
*
9823 TTTTTTCTGTTTTTCTCTTT
1 TTTTTTCTCTTTTTCTCTTT
9843 TTTTTCTCTCTTTTTCTCT
1 TTTTT-TCTCTTTTTCTCT
9862 ATCTTTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTTTCTCTTTTTCTCTTT
Found at i:9868 original size:21 final size:19
Alignment explanation
Indices: 9815--9868 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
9805 ATCCTAACTA
*
9815 TTTTC-CTATTTTTTCTGT
1 TTTTCTCTATTTTTTCTCT
*
9833 TTTTCTCTTTTTTTTCTCTCT
1 TTTTCTC-TATTTTT-TCTCT
*
9854 TTTTCTCTATCTTTT
1 TTTTCTCTATTTTTT
9869 GTCTGCTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 5 0.17
19 2 0.07
20 11 0.38
21 11 0.38
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTCTCTATTTTTTCTCT
Found at i:13419 original size:19 final size:19
Alignment explanation
Indices: 13376--13448 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
13366 CACACCTAGA
*
13376 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
13396 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
13415 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
13435 TGTATCGATACATG
1 TGTATCGATACATG
13449 AAACTGACAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 17 0.35
20 30 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:13602 original size:19 final size:20
Alignment explanation
Indices: 13578--13615 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13568 ATAATTTCAA
*
13578 ATCAA-TGTTTCGATACATT
1 ATCAATTGTATCGATACATT
13597 ATCAATTGTATCGATACAT
1 ATCAATTGTATCGATACAT
13616 GGCTACGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (20 bp):
ATCAATTGTATCGATACATT
Found at i:14387 original size:4 final size:4
Alignment explanation
Indices: 14373--14404 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
14363 CCAATTAAAT
14373 ATAA GATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATA
14405 TAAAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:14749 original size:165 final size:165
Alignment explanation
Indices: 14540--15000 Score: 499
Period size: 163 Copynumber: 2.8 Consensus size: 165
14530 ATATATGCAA
* * * * * * * * *
14540 AAAAATTCAAAATTCATG-AAATAATTTGAAATTTTCAAAACTGATTTAATGTGGATTTAATAAC
1 AAAAATTGAAAACTCATGAAAATAA-ATGAATTTTTGAAAACTGATTTAATATGAATTAAATAAT
* * *
14604 AATATTAGATGAATTTTAAAAATTTTAAACTAAGAAAAATCTTTCTAAAAACATTTACGGAGTAG
65 AATATTTGATGAATTTTAAAAATTTTAAACTAAAAAAAATCTTTCCAAAAACATTTACGGAGTAG
* * * *
14669 AAAATTCAGTTTTTTGGTAATA-AAGAAATT-TGAAAG
130 AAAACTCAGTATTTCGGAAATAGAA-AAATTCT-AAAG
* * *
14705 AAAAATTGAAAACTCACGAAAATAAGTGAATTTTTGAAAACTGATTTAATATGAATGAAATAATA
1 AAAAATTGAAAACTCATGAAAATAAATGAATTTTTGAAAACTGATTTAATATGAATTAAATAATA
* * * * * *
14770 ATATTTGATGAATTTTAAAAA-TTAAAACCAAAAAAAATC-TCCCCAAAACATTTACCGAATAGA
66 ATATTTGATGAATTTTAAAAATTTTAAACTAAAAAAAATCTTTCCAAAAACATTTACGGAGTAGA
* *
14833 AAACTCCGTATTTCGGAAATAGAAAAATTCTAAGG
131 AAACTCAGTATTTCGGAAATAGAAAAATTCTAAAG
* *
14868 AAAAA-TGAAAAACTCATGAAAATAAATGAATTTTTGAAAATTGA-TTAGTATGAATTAAATAAT
1 AAAAATTG-AAAACTCATGAAAATAAATGAATTTTTGAAAACTGATTTAATATGAATTAAATAAT
* * * * *
14931 AATATTTGATGAATTTTAAAAATTTTAAA-TCAATAAAAATCCTCTCGAAAAA-ATTTACGAAGA
65 AATATTTGATGAATTTTAAAAATTTTAAACT-AAAAAAAAT-CTTTCCAAAAACATTTACGGAGT
14994 AGAAAAC
128 AGAAAAC
15001 CTCGTAATTT
Statistics
Matches: 246, Mismatches: 42, Indels: 17
0.81 0.14 0.06
Matches are distributed among these distances:
162 41 0.17
163 94 0.38
164 33 0.13
165 72 0.29
166 6 0.02
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.31
Consensus pattern (165 bp):
AAAAATTGAAAACTCATGAAAATAAATGAATTTTTGAAAACTGATTTAATATGAATTAAATAATA
ATATTTGATGAATTTTAAAAATTTTAAACTAAAAAAAATCTTTCCAAAAACATTTACGGAGTAGA
AAACTCAGTATTTCGGAAATAGAAAAATTCTAAAG
Found at i:26082 original size:20 final size:20
Alignment explanation
Indices: 26057--26150 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
26047 ATTTGCCTGC
26057 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
26077 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
* *
26097 ATGTATTGATACATTGAATG
1 ATGTATCGATACATTGAATA
26117 ATGTATCGATACAATT-AATA
1 ATGTATCGATAC-ATTGAATA
*
26137 ATGTATCGCTACAT
1 ATGTATCGATACAT
26151 CTGGGTAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 2 0.03
20 63 0.93
21 3 0.04
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:26587 original size:20 final size:20
Alignment explanation
Indices: 26561--26615 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
26551 CTGCCAGTTT
26561 CATGTATCGATACAATTGAA-
1 CATGTATCGATACAATT-AAG
* *
26581 TATGTATCTATACAA-TAAG
1 CATGTATCGATACAATTAAG
26600 CATGTATCGATACAAT
1 CATGTATCGATACAAT
26616 GTATTCATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.07
19 14 0.48
20 13 0.45
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTAAG
Done.