Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3129
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: 51720
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2163 original size:24 final size:24
Alignment explanation
Indices: 2131--2182 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2121 GGCAACATGG
*
2131 CAGCCGCAGCCGCAGCCT-TTGCAA
1 CAGCAGCAGCCGCAG-CTATTGCAA
* *
2155 CAGCAGCAGCTGCTGCTATTGCAA
1 CAGCAGCAGCCGCAGCTATTGCAA
2179 CAGC
1 CAGC
2183 TGCGGAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.15
Consensus pattern (24 bp):
CAGCAGCAGCCGCAGCTATTGCAA
Found at i:15549 original size:25 final size:25
Alignment explanation
Indices: 15519--15575 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
15509 CTTCCCAATT
** *
15519 ATGGCTCTTATAAGCTTCCCGTTAC
1 ATGGCTCACATAAGCTTCCCATTAC
* *
15544 ATGGCTCACATGAGCTTCCCATTAT
1 ATGGCTCACATAAGCTTCCCATTAC
15569 ATGGCTC
1 ATGGCTC
15576 GAAAGAGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (25 bp):
ATGGCTCACATAAGCTTCCCATTAC
Found at i:15583 original size:25 final size:25
Alignment explanation
Indices: 15531--15586 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
15521 GGCTCTTATA
* *
15531 AGCTTCCCGTTACATGGCTCACATG
1 AGCTTCCCATTACATGGCTCACAAG
*
15556 AGCTTCCCATTATATGGCTCGA-AAG
1 AGCTTCCCATTACATGGCTC-ACAAG
15581 AGCTTC
1 AGCTTC
15587 TCGTTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (25 bp):
AGCTTCCCATTACATGGCTCACAAG
Found at i:15600 original size:25 final size:27
Alignment explanation
Indices: 15565--15615 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
15555 GAGCTTCCCA
15565 TTATATGGCTCGAAAGAGC-TTCTCGT
1 TTATATGGCTCGAAAGAGCATTCTCGT
* *
15591 TTATAT-GCTCGTATGAGCATTCTCG
1 TTATATGGCTCGAAAGAGCATTCTCG
15616 GATACGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (27 bp):
TTATATGGCTCGAAAGAGCATTCTCGT
Found at i:17260 original size:99 final size:99
Alignment explanation
Indices: 17135--17332 Score: 351
Period size: 99 Copynumber: 2.0 Consensus size: 99
17125 GATTTCACCA
*
17135 CTAAGACAAAGAGTGATCCATCGAGTAGGAGACACAAGACAAGATATATAGCCTACACTATTCTA
1 CTAAGACAAAGAGTGATCCATCGAGTAGGAGACACAAGACAAGATATATAGCATACACTATTCTA
17200 AAGTATCATCTCAACTTAGAGAAGTCACCATATT
66 AAGTATCATCTCAACTTAGAGAAGTCACCATATT
* * *
17234 CTAAGACAAATAGTGATCGATTGAGTAGGAGACACAAGACAAGATATATAGCATACACTATTCTA
1 CTAAGACAAAGAGTGATCCATCGAGTAGGAGACACAAGACAAGATATATAGCATACACTATTCTA
*
17299 AAGTATCATCTCAACTTTGAGAAGTCACCATATT
66 AAGTATCATCTCAACTTAGAGAAGTCACCATATT
17333 GAGCATCTTT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (99 bp):
CTAAGACAAAGAGTGATCCATCGAGTAGGAGACACAAGACAAGATATATAGCATACACTATTCTA
AAGTATCATCTCAACTTAGAGAAGTCACCATATT
Found at i:18782 original size:25 final size:25
Alignment explanation
Indices: 18730--18783 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
18720 CACAAACGCA
18730 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTATGAGCGTCCTGATATAG
* *
18755 GCTCTTTTGTGAGCTTCCTGATAT-G
1 GCTC-TTTATGAGCGTCCTGATATAG
18780 GCTC
1 GCTC
18784 GCTTGAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (25 bp):
GCTCTTTATGAGCGTCCTGATATAG
Found at i:19912 original size:42 final size:42
Alignment explanation
Indices: 19853--19932 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
19843 TCCATACGGA
19853 CGTGTGTCTCAACCATGTGTAACACACGGCCACACGCACGAG
1 CGTGTGTCTCAACCATGTGTAACACACGGCCACACGCACGAG
* * * * *
19895 CGTGTGTCTCAGCCATGTTTGACACACGGTCACGCGCA
1 CGTGTGTCTCAACCATGTGTAACACACGGCCACACGCA
19933 TGGGCTGGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (42 bp):
CGTGTGTCTCAACCATGTGTAACACACGGCCACACGCACGAG
Found at i:21624 original size:21 final size:21
Alignment explanation
Indices: 21583--21624 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21573 ATATAAATAT
*
21583 TAATATAAAAATTTTAACTAA
1 TAATATAAAAATTTGAACTAA
21604 TAATAT-AAAATTTGAATCTAA
1 TAATATAAAAATTTGAA-CTAA
21625 CCCGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATATAAAAATTTGAACTAA
Found at i:26122 original size:41 final size:40
Alignment explanation
Indices: 26000--26131 Score: 128
Period size: 41 Copynumber: 3.4 Consensus size: 40
25990 GTTTGGCACC
* * *
26000 CAGTGCCTCATC-AGATAATTCGAAGTAATAATTTGACACT
1 CAGTGCCTCATCGA-ATAATCCGAAGTAGTAAATTGACACT
* ** * * *
26040 CAGTGTCTCATCGGCTAAACCG-A--AGTAAATTGGCACC
1 CAGTGCCTCATCGAATAATCCGAAGTAGTAAATTGACACT
26077 CAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGACACT
1 CAGTGCCTCATCGAA-TAATCCGAAGTAGTAAATTGACACT
*
26118 CAGTGTCTCATCGA
1 CAGTGCCTCATCGA
26132 CTCGAAGTCG
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
37 22 0.31
38 6 0.08
39 2 0.03
40 16 0.23
41 25 0.35
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (40 bp):
CAGTGCCTCATCGAATAATCCGAAGTAGTAAATTGACACT
Found at i:26571 original size:21 final size:20
Alignment explanation
Indices: 26546--26589 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
26536 TCTTGGTTCG
26546 TTTCTATTCTGTTTCTTTCTA
1 TTTCTATTCTGTTTCTTT-TA
* *
26567 TTTCTTTTTTGTTTCTTTTA
1 TTTCTATTCTGTTTCTTTTA
26587 TTT
1 TTT
26590 ATTATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTCTATTCTGTTTCTTTTA
Found at i:27727 original size:29 final size:29
Alignment explanation
Indices: 27643--27731 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
27633 AATTGAATTA
* *
27643 AAATCAAAGTTTCATGTA-CACATATGAACC
1 AAATCAAAG-TTCATGTATCAAAT-TGCACC
* *
27673 ACAATTCAAATTTCATGTGT-ATAATTGCACC
1 A-AA-TCAAAGTTCATGTATCA-AATTGCACC
27704 AAATCAAAGTTCATGTATCAAATTGCAC
1 AAATCAAAGTTCATGTATCAAATTGCAC
27732 ATTAGACCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
29 21 0.44
30 4 0.08
31 16 0.33
32 7 0.15
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.30
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATCAAATTGCACC
Found at i:30904 original size:20 final size:20
Alignment explanation
Indices: 30879--30918 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
30869 GGCCAGTTTT
30879 GTATTTGTTTCTAAGAAGTA
1 GTATTTGTTTCTAAGAAGTA
30899 GTATTTGTTTCTAAGAAGTA
1 GTATTTGTTTCTAAGAAGTA
30919 TTTTTGAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (20 bp):
GTATTTGTTTCTAAGAAGTA
Found at i:31709 original size:19 final size:17
Alignment explanation
Indices: 31685--31742 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 17
31675 ATAATAGATT
31685 AAAATAATTTAAAAATATA
1 AAAATAA-TTAAAAA-ATA
31704 AAAAT-ATTAAAAAAATA
1 AAAATAATT-AAAAAATA
*
31721 AAATTAAATTAAAAAATA
1 AAAAT-AATTAAAAAATA
31739 AAAA
1 AAAA
31743 GTTCATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 9 0.26
18 17 0.50
19 8 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATAATTAAAAAATA
Found at i:31716 original size:18 final size:18
Alignment explanation
Indices: 31685--31742 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
31675 ATAATAGATT
*
31685 AAAATAATTTAAAAATATA
1 AAAAT-ATTAAAAAATATA
31704 AAAATATTAAAAAA-ATA
1 AAAATATTAAAAAATATA
*
31721 AAATTAAATTAAAAAATA-A
1 AAA--ATATTAAAAAATATA
31740 AAA
1 AAA
31743 GTTCATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.18
18 8 0.24
19 19 0.56
20 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATATTAAAAAATATA
Found at i:42878 original size:12 final size:12
Alignment explanation
Indices: 42861--42903 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
42851 GTAACCGTTT
42861 TTTCTTAATCCA
1 TTTCTTAATCCA
*
42873 TTTCTTAATCCGTTT
1 TTTCTTAATCC---A
42888 TTTCTTAATCCA
1 TTTCTTAATCCA
42900 TTTC
1 TTTC
42904 CTTAGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 15 0.58
15 11 0.42
ACGTcount: A:0.19, C:0.23, G:0.02, T:0.56
Consensus pattern (12 bp):
TTTCTTAATCCA
Found at i:42893 original size:15 final size:15
Alignment explanation
Indices: 42855--42898 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
42845 CAACGCGTAA
42855 CCGTTTTTTCTTAAT
1 CCGTTTTTTCTTAAT
*
42870 CC---ATTTCTTAAT
1 CCGTTTTTTCTTAAT
42882 CCGTTTTTTCTTAAT
1 CCGTTTTTTCTTAAT
42897 CC
1 CC
42899 ATTTCCTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 11 0.46
15 13 0.54
ACGTcount: A:0.16, C:0.25, G:0.05, T:0.55
Consensus pattern (15 bp):
CCGTTTTTTCTTAAT
Done.