Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1766
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: 17631
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:576 original size:1 final size:1
Alignment explanation
Indices: 570--697 Score: 130
Period size: 1 Copynumber: 128.0 Consensus size: 1
560 CTAAAACAAT
* * * * *
570 AAAAAAAAAAGAAAAAAAAAACAAAAAAAAAAAAAAATAAAAAAAGAAAAAAAATAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * * * * * *
635 AAAATTAAAAAAAAACAAAAAAAATATAAACAAAAAAAAAAACAAAAACAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
698 TTTCATAATT
Statistics
Matches: 101, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 101 1.00
ACGTcount: A:0.89, C:0.05, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:593 original size:25 final size:23
Alignment explanation
Indices: 562--697 Score: 164
Period size: 25 Copynumber: 5.5 Consensus size: 23
552 ATTAATTTCT
562 AAAACAATAAAAAAAAAAGAAAAAA
1 AAAACAA-AAAAAAAAAA-AAAAAA
587 AAAACAAAAAAAAAAAAAAATAAA
1 AAAACAAAAAAAAAAAAAAA-AAA
*
611 AAAAGAAAAAAAATAAAAAAAAAA
1 AAAACAAAAAAAA-AAAAAAAAAA
*
635 AAAATTAAAAAAAAACAAAAAAAATA
1 AAAA-CAAAAAAAAA-AAAAAAAA-A
*
661 TAAACAAAAAAAAAAACAAAAACAA
1 AAAACAAAAAAAAAAA-AAAAA-AA
686 AAAACAAAAAAA
1 AAAACAAAAAAA
698 TTTCATAATT
Statistics
Matches: 99, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.03
24 35 0.35
25 56 0.57
26 5 0.05
ACGTcount: A:0.88, C:0.05, G:0.01, T:0.05
Consensus pattern (23 bp):
AAAACAAAAAAAAAAAAAAAAAA
Found at i:652 original size:59 final size:59
Alignment explanation
Indices: 562--699 Score: 176
Period size: 59 Copynumber: 2.4 Consensus size: 59
552 ATTAATTTCT
*
562 AAAACAATAAAAAAAAAAGA--AAAAAAAAACAAAAAAAA-A-AAAAAATAAAAAAAGAAAA
1 AAAACAA-AAAAAAAAAAAATTAAAAAAAAACAAAAAAAATATAAAAAA-AAAAAAA-AAAA
* * *
620 AAAATAAAAAAAAAAAAAATTAAAAAAAAACAAAAAAAATATAAACAAAAAAAAAAACA
1 AAAACAAAAAAAAAAAAAATTAAAAAAAAACAAAAAAAATATAAAAAAAAAAAAAAAAA
*
679 AAAACAAAAAACAAAAAAATT
1 AAAACAAAAAAAAAAAAAATT
700 TCATAATTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
57 11 0.16
58 6 0.09
59 40 0.57
60 8 0.11
61 5 0.07
ACGTcount: A:0.87, C:0.05, G:0.01, T:0.07
Consensus pattern (59 bp):
AAAACAAAAAAAAAAAAAATTAAAAAAAAACAAAAAAAATATAAAAAAAAAAAAAAAAA
Found at i:4551 original size:30 final size:30
Alignment explanation
Indices: 4517--4613 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
4507 AGCTCACTCC
4517 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
4547 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
4577 CAGCTCAACTTTAGCTCACGGGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
4607 TAGCTCA
1 TAGCTCA
4614 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:10838 original size:25 final size:25
Alignment explanation
Indices: 10793--10840 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
10783 ACAACTTCTA
* *
10793 AAGAAAACTCAAGAGAGAATTCTTG
1 AAGAAAACCCAAGAGAAAATTCTTG
10818 AAGAAAACCCCAA-AGAAAATTCT
1 AAGAAAA-CCCAAGAGAAAATTCT
10841 GCACTCAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17
Consensus pattern (25 bp):
AAGAAAACCCAAGAGAAAATTCTTG
Found at i:12480 original size:30 final size:30
Alignment explanation
Indices: 12446--12542 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
12436 TAAACTAAAA
12446 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
12476 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
12506 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
12536 TGAGCTA
1 TGAGCTA
12543 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:14704 original size:30 final size:30
Alignment explanation
Indices: 14633--14714 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
14623 CTTTTGTTTC
* *
14633 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
14664 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
*
14693 ATTTTCTTTTTCATT-TCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
14715 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 12 0.27
30 25 0.56
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.63
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:14729 original size:11 final size:11
Alignment explanation
Indices: 14715--14746 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
14705 ATTTCTTTTT
14715 GCTTTTCAAAG
1 GCTTTTCAAAG
14726 GCTTTTTCAAAG
1 GC-TTTTCAAAG
14738 GCTTTTCAA
1 GCTTTTCAA
14747 GTTCTCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.41
Consensus pattern (11 bp):
GCTTTTCAAAG
Found at i:14834 original size:14 final size:13
Alignment explanation
Indices: 14794--14851 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 13
14784 CTCTTGCCTC
*
14794 TCTTTTCTTTTATT
1 TCTTTTCTTTT-CT
14808 TCATTTTCTTTTTCT
1 TC-TTTTC-TTTTCT
14823 TCTTTTGCTTTTCTT
1 TCTTTT-CTTTTC-T
14838 TCTTTTCTTTTCT
1 TCTTTTCTTTTCT
14851 T
1 T
14852 TGTTTTCTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
13 2 0.05
14 17 0.44
15 16 0.41
16 4 0.10
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (13 bp):
TCTTTTCTTTTCT
Found at i:14841 original size:4 final size:5
Alignment explanation
Indices: 14794--14852 Score: 61
Period size: 5 Copynumber: 12.0 Consensus size: 5
14784 CTCTTGCCTC
* *
14794 TCTTT TCTTT T-ATT TCATTT TCTTT T-TCT TCTTT TGCTTT TC-TT TCTTT
1 TCTTT TCTTT TCTTT TC-TTT TCTTT TCTTT TCTTT T-CTTT TCTTT TCTTT
14843 TCTTT TCTTT
1 TCTTT TCTTT
14853 GTTTTCTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
4 10 0.22
5 26 0.58
6 9 0.20
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:14852 original size:14 final size:14
Alignment explanation
Indices: 14794--14859 Score: 80
Period size: 15 Copynumber: 4.6 Consensus size: 14
14784 CTCTTGCCTC
*
14794 TCTTTTCTTTTATT
1 TCTTTTCTTTTCTT
14808 TCATTTTCTTTT-TCT
1 TC-TTTTCTTTTCT-T
14823 TCTTTTGCTTTTCTT
1 TCTTTT-CTTTTCTT
14838 TCTTTTCTTTTCTT
1 TCTTTTCTTTTCTT
*
14852 TGTTTTCT
1 TCTTTTCT
14860 CTTTACAAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
14 22 0.47
15 24 0.51
16 1 0.02
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTTCTT
Done.