Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2569
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: 22706
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:557 original size:19 final size:19
Alignment explanation
Indices: 533--569 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
523 CTATGTATGG
*
533 AAAATTACTGTTATACCCC
1 AAAATTACCGTTATACCCC
552 AAAATTACCGTTATACCC
1 AAAATTACCGTTATACCC
570 TAGGGTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAATTACCGTTATACCCC
Found at i:717 original size:27 final size:25
Alignment explanation
Indices: 676--830 Score: 154
Period size: 27 Copynumber: 6.0 Consensus size: 25
666 GAGGAAGCGT
*
676 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCAC--ATATCTGA
*
703 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCAC--ATATCTGA
*
730 TCTGGTGGCTATGCCACATTATCTGA
1 TCTGGTGGCTCTGCCACA-TATCTGA
*
756 TCTGGTGGCTCTGCCAC--ATCTGT
1 TCTGGTGGCTCTGCCACATATCTGA
779 TCTGTGGTGGCTCTGCCACATATCTGTA
1 TC--TGGTGGCTCTGCCACATATCTG-A
* *
807 TCTGGTGACT-TCGTCACATATCTG
1 TCTGGTGGCTCT-GCCACATATCTG
831 GCAGCCTGCT
Statistics
Matches: 111, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.06
25 17 0.15
26 40 0.36
27 45 0.41
28 2 0.02
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (25 bp):
TCTGGTGGCTCTGCCACATATCTGA
Found at i:783 original size:54 final size:52
Alignment explanation
Indices: 674--813 Score: 189
Period size: 53 Copynumber: 2.7 Consensus size: 52
664 TGGAGGAAGC
674 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCAC--ATATCTGATCTGGTGGCTCTGCCACATATATCT
728 GTTCTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCAC----ATCT
1 GTTCTGGTGGCTATGCCACA-TATCTGATCTGGTGGCTCTGCCACATATATCT
*
777 GTTCTGTGGTGGCTCTGCCACATATCTGTATCTGGTG
1 GTTC--TGGTGGCTATGCCACATATCTG-ATCTGGTG
814 ACTTCGTCAC
Statistics
Matches: 81, Mismatches: 1, Indels: 11
0.87 0.01 0.12
Matches are distributed among these distances:
49 8 0.10
50 6 0.07
51 23 0.28
52 1 0.01
53 24 0.30
54 19 0.23
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (52 bp):
GTTCTGGTGGCTATGCCACATATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:825 original size:51 final size:49
Alignment explanation
Indices: 674--816 Score: 171
Period size: 51 Copynumber: 2.8 Consensus size: 49
664 TGGAGGAAGC
* *
674 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCAC-ATTATCTGATCTGGTGACTCTGCCAC----ATCT
*
728 GTTCTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATCT
1 GTTCTGGTGGCTATGCCACATTATCTGATCTGGTGACTCTGCCACATCT
*
777 GTTCTGTGGTGGCTCTGCCACA-TATCTGTATCTGGTGACT
1 GTTC--TGGTGGCTATGCCACATTATCTG-ATCTGGTGACT
817 TCGTCACATA
Statistics
Matches: 83, Mismatches: 3, Indels: 9
0.87 0.03 0.09
Matches are distributed among these distances:
49 8 0.10
50 6 0.07
51 25 0.30
53 25 0.30
54 19 0.23
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.35
Consensus pattern (49 bp):
GTTCTGGTGGCTATGCCACATTATCTGATCTGGTGACTCTGCCACATCT
Found at i:3816 original size:18 final size:19
Alignment explanation
Indices: 3775--3813 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3765 GTGTTACAAT
*
3775 AATTGGACCCGAGATTGAA
1 AATTGGACCCAAGATTGAA
*
3794 AATTGGACCTAAGATTGAA
1 AATTGGACCCAAGATTGAA
3813 A
1 A
3814 TTGAGCTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (19 bp):
AATTGGACCCAAGATTGAA
Found at i:4201 original size:61 final size:57
Alignment explanation
Indices: 4129--4262 Score: 160
Period size: 61 Copynumber: 2.3 Consensus size: 57
4119 TTCAAAAATA
* * *
4129 ATATTATTTTAATATTTTTAATATTTAATTTAATTTAATACTTATCTTGTAGATAAGTATT
1 ATATTAATTTAATATTTTTAATATTAAATTTAATCTAATACTTATC-T-T-GATAAGT-TT
* * ** *
4190 CTATTACTTTAATAAATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTTT
1 ATATTAATTTAATATTTTTAATATTAAATTTAATCTAATACTTATCTTGATAAGTTT
4247 ATATTAATTTAATATT
1 ATATTAATTTAATATT
4263 AAAGTAATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 14 0.23
58 7 0.11
59 1 0.02
60 1 0.02
61 39 0.63
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (57 bp):
ATATTAATTTAATATTTTTAATATTAAATTTAATCTAATACTTATCTTGATAAGTTT
Found at i:4893 original size:10 final size:10
Alignment explanation
Indices: 4860--4894 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
4850 TTCTATTGTA
4860 TTTTCTTTTT
1 TTTTCTTTTT
4870 TTTTAC-TTTT
1 TTTT-CTTTTT
4880 TTTTCTTTTT
1 TTTTCTTTTT
4890 TTTTC
1 TTTTC
4895 CCGATTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.04
10 21 0.91
11 1 0.04
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:6499 original size:49 final size:49
Alignment explanation
Indices: 6427--6524 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
6417 ATGTCGCGGG
6427 AGCTCGATAAAACATTTATCTTTCCTTTTAAGCATTACTATTAAAGACT
1 AGCTCGATAAAACATTTATCTTTCCTTTTAAGCATTACTATTAAAGACT
6476 AGCTCGATAAAACATTTATCTTTCCTTTTAAGCATTACTATTAAAGACT
1 AGCTCGATAAAACATTTATCTTTCCTTTTAAGCATTACTATTAAAGACT
6525 TATGTTTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (49 bp):
AGCTCGATAAAACATTTATCTTTCCTTTTAAGCATTACTATTAAAGACT
Found at i:16417 original size:13 final size:13
Alignment explanation
Indices: 16401--16425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16391 AAAAAAATGT
16401 TTGAATTTGTTGG
1 TTGAATTTGTTGG
16414 TTGAATTTGTTG
1 TTGAATTTGTTG
16426 ATATGCAGGG
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:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (13 bp):
TTGAATTTGTTGG
Found at i:16637 original size:7 final size:7
Alignment explanation
Indices: 16625--16649 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16615 TGAACGTGAC
16625 AATAATT
1 AATAATT
16632 AATAATT
1 AATAATT
16639 AATAATT
1 AATAATT
16646 AATA
1 AATA
16650 TACAAGACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AATAATT
Found at i:19537 original size:87 final size:87
Alignment explanation
Indices: 19286--19547 Score: 364
Period size: 89 Copynumber: 3.0 Consensus size: 87
19276 GTAAAAAAGG
* * * *
19286 CCTCAAACTTTTTCAAAACAAGCAATTAAGTCCCTACTCTTTTATGCACTCAATTGGATACTTGA
1 CCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACT-TTTT-TTCACTCAATTGGGTACTTGA
*
19351 ACTTTCAAAATGTATCAAAAAGGC
64 ACTTTCAAAATGTATCAAAAAGAC
* * * *
19375 TCTCAAACTTTTTAAAAAAAAAAGCAATTAAGCCCC-CCTTTTTTTGCACTCAATTTGGTACTTG
1 CCTCAAACTTTTT--CAAAAAAAGCAATTAAGCCCCTACTTTTTTT-CACTCAATTGGGTACTTG
19439 AACTTTCAAAATGTATCAAAAAGAC
63 AACTTTCAAAATGTATCAAAAAGAC
*
19464 CCTCAAACTTTTTCAAAAAAAGCTATTAAGCCCCTACTTTTTTTCACTCAATTGGGTACTTGAAC
1 CCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTCACTCAATTGGGTACTTGAAC
* *
19529 TATCAAAATGCATCAAAAA
66 TTTCAAAATGTATCAAAAA
19548 AATCCTTTGA
Statistics
Matches: 153, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
87 56 0.37
88 9 0.06
89 68 0.44
90 2 0.01
91 18 0.12
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (87 bp):
CCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTCACTCAATTGGGTACTTGAAC
TTTCAAAATGTATCAAAAAGAC
Found at i:20035 original size:29 final size:30
Alignment explanation
Indices: 19964--20035 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
19954 TAAAATTTCA
*
19964 TTTTTCT-ATTTTTCTATATTTTTATAATT
1 TTTTTCTAATTTTTCTATAGTTTTATAATT
* *
19993 TTTTT-TACAATTTT-TATGGTTTTATAATT
1 TTTTTCTA-ATTTTTCTATAGTTTTATAATT
20022 TTTTTCTAATTTTT
1 TTTTTCTAATTTTT
20036 AATAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 1 0.03
29 28 0.78
30 7 0.19
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (30 bp):
TTTTTCTAATTTTTCTATAGTTTTATAATT
Found at i:20066 original size:25 final size:26
Alignment explanation
Indices: 20032--20082 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
20022 TTTTTCTAAT
*
20032 TTTTAATAAAATTTAA-ATATTTTAA
1 TTTTAATAAAATTTAATAAATTTTAA
*
20057 TTTTATTAAAATTTAATAAATTTTAA
1 TTTTAATAAAATTTAATAAATTTTAA
20083 CGAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTTAATAAAATTTAATAAATTTTAA
Found at i:21170 original size:15 final size:15
Alignment explanation
Indices: 21150--21179 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21140 AATTTATATT
21150 TTTTATTTTATTTTC
1 TTTTATTTTATTTTC
21165 TTTTATTTTATTTTC
1 TTTTATTTTATTTTC
21180 ACAAATTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTTATTTTC
Found at i:21686 original size:14 final size:15
Alignment explanation
Indices: 21667--21696 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21657 GTTTATTATA
21667 TGTG-AAGTATCATG
1 TGTGAAAGTATCATG
21681 TGTGAAAGTATCATG
1 TGTGAAAGTATCATG
21696 T
1 T
21697 CTAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (15 bp):
TGTGAAAGTATCATG
Done.