Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3461
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: 33611
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Found at i:408 original size:47 final size:47
Alignment explanation
Indices: 353--500 Score: 135
Period size: 47 Copynumber: 3.1 Consensus size: 47
343 ATATTCACCC
*
353 CACATTGGCGCATTCGGCCTA-CACACATATGCATGCCTCACAATTCAT
1 CACATTGGC-CATTCGGCCTATCACACATATGCATGCATCAC-ATTCAT
* * *
401 C-CATTGGCCGATTCGGCCTTATCACATATATTCATGTATCACATTCAT
1 CACATTGGCC-ATTCGGCC-TATCACACATATGCATGCATCACATTCAT
* * *
449 CACATTGGCCACTCGGCCT-TCCTCATATATGCA--CATTCACATTTCAT
1 CACATTGGCCATTCGGCCTAT-CACACATATGCATGCA-TCACA-TTCAT
496 CACAT
1 CACAT
501 AAAATCCTAA
Statistics
Matches: 85, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
45 1 0.01
46 7 0.08
47 36 0.42
48 17 0.20
49 24 0.28
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (47 bp):
CACATTGGCCATTCGGCCTATCACACATATGCATGCATCACATTCAT
Found at i:4244 original size:15 final size:15
Alignment explanation
Indices: 4224--4253 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4214 AATTATAGGA
*
4224 TTGCCATCCAGGATT
1 TTGCCATCCAAGATT
4239 TTGCCATCCAAGATT
1 TTGCCATCCAAGATT
4254 GCTGGGACTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (15 bp):
TTGCCATCCAAGATT
Found at i:6378 original size:28 final size:28
Alignment explanation
Indices: 6315--6465 Score: 241
Period size: 28 Copynumber: 5.4 Consensus size: 28
6305 ATATTAAGTC
*
6315 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
6342 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
6370 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
6398 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
6426 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
6455 CGCACACTTAG
1 CGCACACTTAG
6466 CGCCAATCTC
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
27 22 0.19
28 79 0.68
29 16 0.14
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:14396 original size:28 final size:28
Alignment explanation
Indices: 14333--14483 Score: 241
Period size: 28 Copynumber: 5.4 Consensus size: 28
14323 ATATTAAGTC
*
14333 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
14360 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
14388 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
14416 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
14444 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
14473 CGCACACTTAG
1 CGCACACTTAG
14484 CGCCAATCTC
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
27 22 0.19
28 79 0.68
29 16 0.14
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:18985 original size:30 final size:29
Alignment explanation
Indices: 18942--19005 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 29
18932 CAAGTAGCTG
18942 AAGCTAGTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTAAATCGCACACTTAGTGCCA
*
18971 AAGCTAGTTTAAATCGTACACTTAGTGCCA
1 AAGCTAG-TTAAATCGCACACTTAGTGCCA
19001 AAGCT
1 AAGCT
19006 TCCGATTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.21
30 26 0.79
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTAGTGCCA
Found at i:24615 original size:39 final size:40
Alignment explanation
Indices: 24572--24833 Score: 282
Period size: 40 Copynumber: 6.6 Consensus size: 40
24562 TCCTCGTTCA
* * * *
24572 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
*
24611 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
24651 AATGCCTTCGGGACTTAACCCGGATTTA-TAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
* *
24690 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
* * * * *
24730 AAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCACG
** * * * *
24770 AATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACG
* *
24810 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
24834 CAGCATTCAA
Statistics
Matches: 194, Mismatches: 22, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
39 77 0.40
40 106 0.55
41 11 0.06
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
Found at i:24673 original size:79 final size:79
Alignment explanation
Indices: 24570--24833 Score: 282
Period size: 79 Copynumber: 3.3 Consensus size: 79
24560 GCTCCTCGTT
* * *
24570 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTA-TAACTCACACGAATGCCTTCGGGACTTAACCCGG
24634 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* *
24649 CGAATGCCTTCGGGACTTAACCCGGATTTATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTATAACTCACACGAATGCCTTCGGGACTTAACCCGGA
* *
24714 TTTAGTATCTCGCA
66 TTTAATAACTCGCA
* * * * * * * **
24728 CAAAGGCCTTCGGGGCTTAACCCGGAACTTGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTATAACTCACACGAATGCCTTCGGGA-CTTAACCCG
* * * *
24792 GATATATTCACTTAGCA
64 GATTTAATAAC-TCGCA
*
24809 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
24834 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
78 9 0.06
79 88 0.56
80 53 0.34
81 8 0.05
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTATAACTCACACGAATGCCTTCGGGACTTAACCCGGA
TTTAATAACTCGCA
Found at i:24842 original size:41 final size:41
Alignment explanation
Indices: 24765--24842 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
24755 CTTGTATCTC
* * *
24765 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
24806 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
24843 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:32545 original size:38 final size:37
Alignment explanation
Indices: 32499--32673 Score: 174
Period size: 38 Copynumber: 4.6 Consensus size: 37
32489 TCCTCGTTCA
* * * *
32499 AATGCCTTCGGGACATAGCCCGTTTTAGTAACTCACAC
1 AATG-CTTCGGGACTTAACCCGATTTAGTAACTCGCAC
* *
32537 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAG
1 AATG-CTTCGGGACTTAACCC-GATTTAGTAACTCGCAC
*
32576 AATGCTTCGGGACTT-ACCGGATTTAGTAACTCGCAC
1 AATGCTTCGGGACTTAACCCGATTTAGTAACTCGCAC
*
32612 GAAGTGCTTCGGGACTTAACCCGTGATTTAGTATCTCGCAC
1 -AA-TGCTTCGGGACTTAACCC--GATTTAGTAACTCGCAC
* *
32653 AAAGGCTT-GGGGCTTAACCCG
1 -AATGCTTCGGGACTTAACCCG
32674 GGAACTTGTA
Statistics
Matches: 117, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
36 15 0.13
37 6 0.05
38 43 0.37
39 31 0.26
40 4 0.03
41 18 0.15
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (37 bp):
AATGCTTCGGGACTTAACCCGATTTAGTAACTCGCAC
Found at i:32626 original size:76 final size:78
Alignment explanation
Indices: 32499--32651 Score: 206
Period size: 76 Copynumber: 2.0 Consensus size: 78
32489 TCCTCGTTCA
*
32499 AATGCCTTCGGGACATAGCCCGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCG-GATT
1 AATGCCTTCGGGACATAGCCCGATTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGTGATT
32563 TAATAACTCGCAG
66 TAATAACTCGCAG
* * *
32576 AATG-CTTCGGGACTTA-CCGGATTTAGTAACTCGCACGAAGTG-CTTCGGGACTTAACCCGTGA
1 AATGCCTTCGGGACATAGCCCGATTTAGTAACTCACAC-AA-TGCCTTCGGGACTTAACCCGTGA
* *
32638 TTTAGTATCTCGCA
64 TTTAATAACTCGCA
32652 CAAAGGCTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
75 17 0.25
76 30 0.45
77 20 0.30
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (78 bp):
AATGCCTTCGGGACATAGCCCGATTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGTGATT
TAATAACTCGCAG
Found at i:32685 original size:39 final size:41
Alignment explanation
Indices: 32542--32693 Score: 142
Period size: 39 Copynumber: 3.9 Consensus size: 41
32532 CACACAATGC
* * * *
32542 CTTCGGGACTTAACCC-GGATTTAATAACTCGCA-GAA-TG
1 CTTCGGGACTTAACCCGGGACTTAGTATCTCGCACAAAGTG
* * *
32580 CTTCGGGACTT-A-CC-GGATTTAGTAACTCGCACGAAGTG
1 CTTCGGGACTTAACCCGGGACTTAGTATCTCGCACAAAGTG
* *
32618 CTTCGGGACTTAACCCGTGATTTAGTATCTCGCACAAAG-G
1 CTTCGGGACTTAACCCGGGACTTAGTATCTCGCACAAAGTG
*
32658 CTT-GGGGCTTAACCCGGGAACTT-GTATCTCGCACAA
1 CTTCGGGACTTAACCCGGG-ACTTAGTATCTCGCACAA
32694 TGCCTTCGGA
Statistics
Matches: 101, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
36 18 0.18
37 4 0.04
38 24 0.24
39 27 0.27
40 9 0.09
41 19 0.19
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (41 bp):
CTTCGGGACTTAACCCGGGACTTAGTATCTCGCACAAAGTG
Done.