Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold716
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: 23692
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:1255 original size:13 final size:13
Alignment explanation
Indices: 1237--1263 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1227 ACATTATGCT
1237 TTGTATCGATACA
1 TTGTATCGATACA
1250 TTGTATCGATACA
1 TTGTATCGATACA
1263 T
1 T
1264 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1293 original size:20 final size:19
Alignment explanation
Indices: 1247--1299 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
1237 TTGTATCGAT
*
1247 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
1266 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
1285 ACAATTGTATCGATA
1 AC-ATTGTATCGATA
1300 TATGAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:4154 original size:29 final size:29
Alignment explanation
Indices: 4088--4154 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
4078 CCACTATTTG
*
4088 ACACCTGAG-TTGAAGCCCATGCTAGCTA
1 ACACCTGAGTTTAAAGCCCATGCTAGCTA
*
4116 ACA-CTCGAGTTTAAAGCCTATAG-TAGCTA
1 ACACCT-GAGTTTAAAGCCCAT-GCTAGCTA
*
4145 GCACCTGAGT
1 ACACCTGAGT
4155 CAAAGCACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 2 0.06
28 6 0.19
29 21 0.66
30 3 0.09
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (29 bp):
ACACCTGAGTTTAAAGCCCATGCTAGCTA
Found at i:5483 original size:17 final size:17
Alignment explanation
Indices: 5474--5510 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
5464 AAAAGAAAGC
5474 AAGAAAAAAAAGGAAAA
1 AAGAAAAAAAAGGAAAA
5491 AAGAAAAAAAAAGGAAAA
1 AAG-AAAAAAAAGGAAAA
5509 AA
1 AA
5511 AAGAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAGGAAAA
Found at i:5489 original size:18 final size:17
Alignment explanation
Indices: 5450--5507 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
5440 TTTGGTTTTG
*
5450 GGAAAGAAGGAATAAAAA
1 GGAAAGAA-GAAAAAAAA
5468 -GAAAGCAAGAAAAAAAA
1 GGAAAG-AAGAAAAAAAA
*
5485 GGAAAAAAGAAAAAAAAA
1 GGAAAGAAG-AAAAAAAA
5503 GGAAA
1 GGAAA
5508 AAAAAGAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 16 0.46
18 19 0.54
ACGTcount: A:0.74, C:0.02, G:0.22, T:0.02
Consensus pattern (17 bp):
GGAAAGAAGAAAAAAAA
Found at i:5491 original size:10 final size:10
Alignment explanation
Indices: 5476--5513 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5466 AAGAAAGCAA
5476 GAAAAAAAAG
1 GAAAAAAAAG
5486 G--AAAAAAG
1 GAAAAAAAAG
*
5494 AAAAAAAAAG
1 GAAAAAAAAG
5504 GAAAAAAAAG
1 GAAAAAAAAG
5514 AAAGCAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 7 0.29
10 17 0.71
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAG
Found at i:8709 original size:13 final size:12
Alignment explanation
Indices: 8693--8755 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 12
8683 TATAATTAGA
8693 ATATATAATATTT
1 ATATA-AATATTT
8706 ATATAAATATTT
1 ATATAAATATTT
8718 -TATTACAATATTAT
1 ATA-TA-AATATT-T
8732 ATATAAATAATTT
1 ATATAAAT-ATTT
*
8745 ATTTAAATATT
1 ATATAAATATT
8756 AAATATTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
11 2 0.05
12 12 0.27
13 22 0.50
14 6 0.14
15 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATAAATATTT
Found at i:8737 original size:26 final size:26
Alignment explanation
Indices: 8699--8761 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
8689 TAGAATATAT
*
8699 AATATT-TATATAAATATTTTA-TTA
1 AATATTATATATAAATAATTTATTTA
8723 CAATATTATATATAAATAATTTATTTA
1 -AATATTATATATAAATAATTTATTTA
*
8750 AATATTAAATAT
1 AATATTATATAT
8762 TATATAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 6 0.18
26 25 0.74
27 3 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
AATATTATATATAAATAATTTATTTA
Found at i:10211 original size:2 final size:2
Alignment explanation
Indices: 10198--10229 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10188 TAATACGTAC
*
10198 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10230 TAAGAATCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12176 original size:2 final size:2
Alignment explanation
Indices: 12165--12206 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
12155 TTGGGTGAAG
12165 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12206 A
1 A
12207 ACGACCTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15999 original size:2 final size:2
Alignment explanation
Indices: 15992--16029 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15982 TATTATCCAT
15992 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
16030 ATGTGTGCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:16407 original size:14 final size:14
Alignment explanation
Indices: 16388--16420 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16378 ATCAATCTGA
16388 TATAATACTATGTT
1 TATAATACTATGTT
*
16402 TATAATATTATGTT
1 TATAATACTATGTT
16416 TATAA
1 TATAA
16421 ATAATGCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (14 bp):
TATAATACTATGTT
Found at i:21357 original size:33 final size:32
Alignment explanation
Indices: 21315--21416 Score: 101
Period size: 33 Copynumber: 3.3 Consensus size: 32
21305 ATGACAAAAT
21315 AATGGCATAAATAAAGTATTTAGATATTGAAAC
1 AATGGCATAAATAAAGTATTTAGATA-TGAAAC
21348 AATGGCATAAA-AAA--A-TT-GATA--AAAC
1 AATGGCATAAATAAAGTATTTAGATATGAAAC
** *
21373 AATGGCATACGTAAAGTATTTAGATATCGAAAT
1 AATGGCATAAATAAAGTATTTAGATAT-GAAAC
*
21406 AATGACATAAA
1 AATGGCATAAA
21417 AAATTGACAA
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
25 13 0.24
26 3 0.05
28 5 0.09
29 4 0.07
30 5 0.09
32 3 0.05
33 22 0.40
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (32 bp):
AATGGCATAAATAAAGTATTTAGATATGAAAC
Found at i:21388 original size:58 final size:57
Alignment explanation
Indices: 21301--21427 Score: 173
Period size: 58 Copynumber: 2.2 Consensus size: 57
21291 TGAGTACGAT
* * *
21301 AAATATGACAAAATAATGGCATAAATAAAGTATTTAGATATTGAAACAATGGCATAAAA
1 AAAT-TGACAAAACAATGGCATAAATAAAGTATTTAGATATCGAAACAATGACAT-AAA
* ** *
21360 AAATTGATAAAACAATGGCATACGTAAAGTATTTAGATATCGAAATAATGACATAAA
1 AAATTGACAAAACAATGGCATAAATAAAGTATTTAGATATCGAAACAATGACATAAA
21417 AAATTGACAAA
1 AAATTGACAAA
21428 CATTGTTGTC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 13 0.22
58 43 0.72
59 4 0.07
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.25
Consensus pattern (57 bp):
AAATTGACAAAACAATGGCATAAATAAAGTATTTAGATATCGAAACAATGACATAAA
Done.