Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1015
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: 50473
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Found at i:2736 original size:39 final size:40
Alignment explanation
Indices: 2691--2861 Score: 222
Period size: 39 Copynumber: 4.3 Consensus size: 40
2681 GCTCCTCGTT
* * *
2691 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
2731 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
2770 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
2810 CAAAGGCCTTCGGG-CTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
2849 CAAATGCCTTCGG
1 CAAATGCCTTCGG
2862 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 67 0.56
40 52 0.44
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:2791 original size:40 final size:39
Alignment explanation
Indices: 2693--2914 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
2683 TCCTCGTTCA
* * * *
2693 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
2732 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
2771 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
2811 AAAGGCCTTCGGG-CTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
2850 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
2891 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
2915 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 68 0.43
40 79 0.50
41 8 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:2874 original size:79 final size:79
Alignment explanation
Indices: 2691--2914 Score: 240
Period size: 79 Copynumber: 2.8 Consensus size: 79
2681 GCTCCTCGTT
* * * * *
2691 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
2755 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* *
2770 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
2834 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
2849 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
2913 GA
63 GA
2915 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
78 4 0.03
79 86 0.70
80 32 0.26
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:2923 original size:41 final size:41
Alignment explanation
Indices: 2846--2923 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2836 TTTGTATCTC
* * *
2846 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2887 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2924 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:15960 original size:36 final size:36
Alignment explanation
Indices: 15920--15992 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
15910 GGGAGTGGGG
*
15920 AGGTGTTTAGGGTGTTGAAGGCTGAACGAATTTTTA
1 AGGTGTTTAGGGTGTTGAAGGCTGAACAAATTTTTA
15956 AGGTGTTTAGGGTGTTGAAGGCTGAACAAATTTTTA
1 AGGTGTTTAGGGTGTTGAAGGCTGAACAAATTTTTA
15992 A
1 A
15993 AGTGATTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.36
Consensus pattern (36 bp):
AGGTGTTTAGGGTGTTGAAGGCTGAACAAATTTTTA
Found at i:17744 original size:20 final size:20
Alignment explanation
Indices: 17721--17794 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
17711 TGTGATATTT
* *
17721 ATGGCTTTGTGCCACTATTG
1 ATGGCTTCGTGCCACTACTG
*
17741 ATGGCTTCGTGCCGCTACTG
1 ATGGCTTCGTGCCACTACTG
* * *
17761 ATGGCTTCGAGCCGCTACTC
1 ATGGCTTCGTGCCACTACTG
*
17781 ATGGCTTTGTGCCA
1 ATGGCTTCGTGCCA
17795 TAAACTGATA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.14, C:0.27, G:0.27, T:0.32
Consensus pattern (20 bp):
ATGGCTTCGTGCCACTACTG
Found at i:24794 original size:20 final size:20
Alignment explanation
Indices: 24766--24860 Score: 102
Period size: 20 Copynumber: 4.8 Consensus size: 20
24756 ATTGCTGCGA
*
24766 TATTTATGGCTTTGTGCCAC
1 TATTGATGGCTTTGTGCCAC
*
24786 TATTGATGGCTCTGTGCCAC
1 TATTGATGGCTTTGTGCCAC
* *
24806 TATTCATGGCTTTTTGCCAC
1 TATTGATGGCTTTGTGCCAC
* * * *
24826 TACTGATGGCTTCGAGCCGC
1 TATTGATGGCTTTGTGCCAC
24846 TACTT-ATGGCTTTGT
1 TA-TTGATGGCTTTGT
24861 CCCATATACT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 59 0.98
21 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.40
Consensus pattern (20 bp):
TATTGATGGCTTTGTGCCAC
Found at i:24855 original size:40 final size:39
Alignment explanation
Indices: 24769--24860 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 39
24759 GCTGCGATAT
* *
24769 TTATGGCTTTGTGCCACTATTGATGGCTCTGTGCCACTA
1 TTATGGCTTTGTGCCACTACTGATGGCTCTGAGCCACTA
* *
24808 TTCATGGCTTTTTGCCACTACTGATGGCT-TCGAGCCGCTA
1 TT-ATGGCTTTGTGCCACTACTGATGGCTCT-GAGCCACTA
24848 CTTATGGCTTTGT
1 -TTATGGCTTTGT
24861 CCCATATACT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
39 3 0.07
40 40 0.89
41 2 0.04
ACGTcount: A:0.14, C:0.24, G:0.23, T:0.39
Consensus pattern (39 bp):
TTATGGCTTTGTGCCACTACTGATGGCTCTGAGCCACTA
Found at i:24901 original size:25 final size:26
Alignment explanation
Indices: 24867--24916 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
24857 TTGTCCCATA
24867 TACTGATACTGGCAGC-TTGCTGCGT
1 TACTGATACTGGCAGCTTTGCTGCGT
*
24892 TACTGTTACTGGCAGCTTTGCTGCG
1 TACTGATACTGGCAGCTTTGCTGCG
24917 ATATTGGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.14, C:0.24, G:0.28, T:0.34
Consensus pattern (26 bp):
TACTGATACTGGCAGCTTTGCTGCGT
Found at i:27015 original size:12 final size:12
Alignment explanation
Indices: 26995--27026 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
26985 TAGGAGGGAG
26995 TTGAGGAGAGAT
1 TTGAGGAGAGAT
27007 TTGAGGAGAGAT
1 TTGAGGAGAGAT
*
27019 TTTAGGAG
1 TTGAGGAG
27027 GAAATTGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (12 bp):
TTGAGGAGAGAT
Found at i:28919 original size:20 final size:20
Alignment explanation
Indices: 28891--28962 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
28881 ATTGCTGCGA
*
28891 TATTTATGGCTTTGTGCCAC
1 TATTGATGGCTTTGTGCCAC
* *
28911 TATTGATGGTTTTGGGCCAC
1 TATTGATGGCTTTGTGCCAC
**
28931 TATTGATGGCTTTGTGCCGG
1 TATTGATGGCTTTGTGCCAC
*
28951 TACTGATGGCTT
1 TATTGATGGCTT
28963 CAAGCCGCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.14, C:0.17, G:0.28, T:0.42
Consensus pattern (20 bp):
TATTGATGGCTTTGTGCCAC
Found at i:32414 original size:15 final size:15
Alignment explanation
Indices: 32394--32422 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32384 GAAAAAGAGT
32394 TAATCTTCACTTGCG
1 TAATCTTCACTTGCG
32409 TAATCTTCACTTGC
1 TAATCTTCACTTGC
32423 ATACAGTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (15 bp):
TAATCTTCACTTGCG
Found at i:47491 original size:27 final size:27
Alignment explanation
Indices: 47460--47636 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
47450 TAAATTGTAC
47460 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
47487 TGCACTAAG-GTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
** * *
47512 ATGCACTAAGTGTGCGAAATGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
47540 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
47568 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
47595 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
47622 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
47637 GACTCAATAT
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
26 21 0.17
27 84 0.66
28 22 0.17
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:47581 original size:55 final size:54
Alignment explanation
Indices: 47460--47636 Score: 196
Period size: 55 Copynumber: 3.3 Consensus size: 54
47450 TAAATTGTAC
* **
47460 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAG-GTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
** * ** *
47512 ATGCACTAAGTGTGCGAAATGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAG-TTGAATATGT
* * * *
47568 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
*
47622 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
47637 GACTCAATAT
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
52 1 0.01
53 30 0.29
54 28 0.27
55 43 0.42
56 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
Found at i:47636 original size:82 final size:80
Alignment explanation
Indices: 47457--47610 Score: 211
Period size: 82 Copynumber: 1.9 Consensus size: 80
47447 GATTAAATTG
* *
47457 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGGTGCGAAATGAATATGATGCACTAAG
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGGTGCGAAATGAATACGATGCACTAAG
47522 TGTGCGAAATGACCA
66 TGTGCGAAATGACCA
* * ** *
47537 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAG-GTGCGAAATGAATACGAT-GCACT
47601 AAGTGTGCGA
63 AAGTGTGCGA
47611 GTTGATTATA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
80 17 0.27
81 20 0.31
82 27 0.42
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (80 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGGTGCGAAATGAATACGATGCACTAAG
TGTGCGAAATGACCA
Done.