Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1263
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: 52437
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Found at i:7442 original size:39 final size:40
Alignment explanation
Indices: 7341--7564 Score: 255
Period size: 39 Copynumber: 5.7 Consensus size: 40
7331 TTGAATGATG
* *
7341 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
7380 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
7421 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
7460 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
7499 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
7538 AACCGGGCTATGTCCCGAAGGCGTTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
7565 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
39 75 0.46
40 75 0.46
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:7578 original size:40 final size:40
Alignment explanation
Indices: 7342--7564 Score: 235
Period size: 40 Copynumber: 5.6 Consensus size: 40
7332 TGAATGATGT
* * * *
7342 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
7382 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
* *
7422 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-A
7461 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
7499 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
7540 CCGGGCTATGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
7565 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
39 74 0.46
40 78 0.48
41 10 0.06
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:7586 original size:79 final size:79
Alignment explanation
Indices: 7394--7597 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 79
7384 GGACTAAGAT
** * * * *
7394 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
*
7458 ATTCCGGGCTAAGC
66 ATACCGGGCTAAGC
** *
7472 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
*
7536 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
* * * *
7552 CCGAAGGCGTTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGG
7598 TACGTGATTT
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
78 37 0.34
79 48 0.44
80 24 0.22
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:12957 original size:27 final size:27
Alignment explanation
Indices: 12920--13124 Score: 250
Period size: 27 Copynumber: 7.6 Consensus size: 27
12910 TAAATTGTAC
12920 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
12947 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
12974 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13000 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
13028 GGCACTAAGTGTGCAAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
13056 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13083 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
13110 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
13125 GACTCAATAT
Statistics
Matches: 154, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
27 132 0.86
28 22 0.14
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:13057 original size:109 final size:108
Alignment explanation
Indices: 12921--13124 Score: 311
Period size: 109 Copynumber: 1.9 Consensus size: 108
12911 AAATTGTACA
* * *
12921 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGT
1 GCACTAAGTGTGCAATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
12986 GCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
66 GCGAAATGAATAT-ATAGCACTAAGTGTGCGAATTGACCATGCG
*
13029 GCACTAAGTGTGCAAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCAA-TTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTG
** * *
13094 TGCGAGTTGATTATATAGCACTGAGTGTGCG
65 TGCGAAATGAATATATAGCACTAAGTGTGCG
13125 GACTCAATAT
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
108 16 0.19
109 70 0.81
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (108 bp):
GCACTAAGTGTGCAATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
GCGAAATGAATATATAGCACTAAGTGTGCGAATTGACCATGCG
Found at i:19497 original size:40 final size:40
Alignment explanation
Indices: 19452--19676 Score: 247
Period size: 40 Copynumber: 5.6 Consensus size: 40
19442 CTTGCGCAAG
* * * *
19452 GCCTTCGCGTCTTAGCCCGGATGTGGTCACTAGCATC-AAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCA-CAAAT
*
19492 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
* *
19532 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
19572 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-GCTAGCACAAAT
* * * * *
19612 GCCTTCGGATCTTAGTCCGGGTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-GCTAGCACAAAT
* * *
19653 GCCTTCAGGACTTAGCTCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
19677 CATTCGAATA
Statistics
Matches: 156, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 2 0.01
40 126 0.81
41 28 0.18
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:27316 original size:42 final size:43
Alignment explanation
Indices: 27220--27379 Score: 130
Period size: 43 Copynumber: 3.7 Consensus size: 43
27210 AGCTCATACA
* * * * *
27220 ATGCCAACGTCCCAGA-TGTGGTCTTACATGTAATCA-AATATCA
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGAAATCACAA-ATCG
* * * * *
27263 ATGCCACTGTCCTAGACAGGGTCTTACACGAGATCATATAT-G
1 ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCACAAATCG
* *
27305 ATGCCAATGTCCCAGACATGATCTTACACGTAAATCACAAATCG
1 ATGCCAATGTCCCAGACAGGGTCTTACACG-AAATCACAAATCG
* *
27349 ATGCCAACGTCCCAGAC-GTGGCCTTACACGA
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGA
27380 TAACACATAT
Statistics
Matches: 92, Mismatches: 20, Indels: 10
0.75 0.16 0.08
Matches are distributed among these distances:
42 26 0.28
43 38 0.41
44 28 0.30
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCACAAATCG
Found at i:33796 original size:42 final size:44
Alignment explanation
Indices: 33706--33843 Score: 140
Period size: 43 Copynumber: 3.2 Consensus size: 44
33696 CAATGTCAAC
* * * * * *
33706 GTCCTAGACATGGTCTTACATG-TAATCA-AATATTGATGCCACT
1 GTCCCAGACAGGGTCTTACACGAAAATCACAA-ATCGATGCCAAT
* * *
33749 GTCCCAGATAGGGTCTTACAC-AAAATCATATA-CGATGCCAAT
1 GTCCCAGACAGGGTCTTACACGAAAATCACAAATCGATGCCAAT
* *
33791 GTCCCAGACATGGTCTTACACGTAAATCACAAATCGATGCCAAT
1 GTCCCAGACAGGGTCTTACACGAAAATCACAAATCGATGCCAAT
33835 GTCCCAGAC
1 GTCCCAGAC
33844 GTTGTCTTAC
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
42 27 0.35
43 31 0.40
44 20 0.26
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (44 bp):
GTCCCAGACAGGGTCTTACACGAAAATCACAAATCGATGCCAAT
Found at i:33840 original size:44 final size:43
Alignment explanation
Indices: 33706--33854 Score: 160
Period size: 42 Copynumber: 3.5 Consensus size: 43
33696 CAATGTCAAC
* * * *
33706 GTCCTAGACATGGTCTTACATGT-AATCAAATATTGATGCCACT
1 GTCCCAGACATGGTCTTACACGTAAATCAAA-ATCGATGCCAAT
* * * *
33749 GTCCCAGATAGGGTCTTACAC-AAAATC-ATATACGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAAATCAAAAT-CGATGCCAAT
33791 GTCCCAGACATGGTCTTACACGTAAATCACAAATCGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAAATCA-AAATCGATGCCAAT
* *
33835 GTCCCAGACGTTGTCTTACA
1 GTCCCAGACATGGTCTTACA
33855 TGATAACACA
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
41 2 0.02
42 28 0.32
43 26 0.30
44 28 0.32
45 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAAATCAAAATCGATGCCAAT
Found at i:34556 original size:23 final size:24
Alignment explanation
Indices: 34525--34569 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
34515 CATATTTCAT
*
34525 AAATTAACAAT-TCAAAACTCACA
1 AAATCAACAATGTCAAAACTCACA
*
34548 AAATCAACAATGTCATAACTCA
1 AAATCAACAATGTCAAAACTCA
34570 AAATCATCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.53, C:0.22, G:0.02, T:0.22
Consensus pattern (24 bp):
AAATCAACAATGTCAAAACTCACA
Found at i:36690 original size:25 final size:25
Alignment explanation
Indices: 36662--36740 Score: 108
Period size: 25 Copynumber: 3.2 Consensus size: 25
36652 GAATTAATAT
*
36662 GCTCTCACGAGCTGTAAATCAGTAA
1 GCTCTCATGAGCTGTAAATCAGTAA
36687 GCTCAT-ATGAGCTG-AGAATCAGTAA
1 GCTC-TCATGAGCTGTA-AATCAGTAA
*
36712 GCTCTCATAAGCTGTAAATCAGTAA
1 GCTCTCATGAGCTGTAAATCAGTAA
36737 GCTC
1 GCTC
36741 ATATAAGCTG
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.04
25 44 0.92
26 2 0.04
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (25 bp):
GCTCTCATGAGCTGTAAATCAGTAA
Found at i:36746 original size:25 final size:25
Alignment explanation
Indices: 36671--36751 Score: 121
Period size: 25 Copynumber: 3.2 Consensus size: 25
36661 TGCTCTCACG
*
36671 AGCTGTAAATCAGTAAGCTCATATG
1 AGCTGTAAATCAGTAAGCTCATATA
36696 AGCTG-AGAATCAGTAAGCTC-TCATA
1 AGCTGTA-AATCAGTAAGCTCAT-ATA
36721 AGCTGTAAATCAGTAAGCTCATATA
1 AGCTGTAAATCAGTAAGCTCATATA
36746 AGCTGT
1 AGCTGT
36752 GGTGTGTTCG
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
24 2 0.04
25 47 0.92
26 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (25 bp):
AGCTGTAAATCAGTAAGCTCATATA
Found at i:38676 original size:79 final size:79
Alignment explanation
Indices: 38573--38793 Score: 281
Period size: 79 Copynumber: 2.8 Consensus size: 79
38563 GCTCCTCGTT
* *
38573 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
*
38638 TTTAGTAACTCGCA
66 ATTAGTAACTCGCA
*
38652 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCAC-AATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC-
*
38714 GAATTAGTATCTCGCA
64 GAATTAGTAACTCGCA
* * * * *
38730 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
38793 G
64 G
38794 GACATCATTC
Statistics
Matches: 124, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
77 11 0.09
78 50 0.40
79 51 0.41
80 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
ATTAGTAACTCGCA
Found at i:38795 original size:40 final size:40
Alignment explanation
Indices: 38573--38795 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
38563 GCTCCTCGTT
* *
38573 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
38613 CAAATGCCTTCGGGACTTAACCC-GATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
38652 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
38692 C-AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
38730 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
38771 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38796 CATCATTCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
38 24 0.15
39 58 0.36
40 68 0.42
41 12 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:50709 original size:39 final size:39
Alignment explanation
Indices: 50538--50758 Score: 234
Period size: 39 Copynumber: 5.6 Consensus size: 39
50528 TTGAATGATG
* * * *
50538 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
50577 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
50617 TCCGGGCTAAGCCCG-AGGCATTTGTGCGAGATA-TAAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
50654 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
50693 TCCGGGTTAAGTCCGAAGGCAATTGTGCGAGTTTACTATAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAG-TTACTA-AA
* *
50734 -CCGGGCTATGTCCCGAAGGCGTTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
50759 AACGAGAGCT
Statistics
Matches: 157, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
37 19 0.12
38 35 0.22
39 44 0.28
40 39 0.25
41 20 0.13
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Done.