Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold876
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: 58528
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:2975 original size:82 final size:82
Alignment explanation
Indices: 2875--3042 Score: 309
Period size: 82 Copynumber: 2.0 Consensus size: 82
2865 AAATTGGTGC
*
2875 CTCAGTCAATAATGCCTTCAATTTCTCAAAACTTTGCTGAAATTTTTTAGATCATTCGAACTTAA
1 CTCAGTCAATAATGCCTTCAATTTCTCAAAACATTGCTGAAATTTTTTAGATCATTCGAACTTAA
2940 CATCCTTTTGCAACAAT
66 CATCCTTTTGCAACAAT
*
2957 CTCAGTCAATAATGCCTTCGATTTCTCAAAACATTGCTGAAATTTTTTAGATCATTCGAACTTAA
1 CTCAGTCAATAATGCCTTCAATTTCTCAAAACATTGCTGAAATTTTTTAGATCATTCGAACTTAA
*
3022 CATCCTTTTGCAATAAT
66 CATCCTTTTGCAACAAT
3039 CTCA
1 CTCA
3043 TCATAGGAGT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.38
Consensus pattern (82 bp):
CTCAGTCAATAATGCCTTCAATTTCTCAAAACATTGCTGAAATTTTTTAGATCATTCGAACTTAA
CATCCTTTTGCAACAAT
Found at i:7850 original size:28 final size:28
Alignment explanation
Indices: 7784--7911 Score: 175
Period size: 28 Copynumber: 4.5 Consensus size: 28
7774 CATGAGATTG
* * **
7784 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
7813 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
7841 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
7870 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
7898 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
7912 GACTTACTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 45 0.51
29 44 0.49
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:7873 original size:57 final size:57
Alignment explanation
Indices: 7784--7911 Score: 186
Period size: 57 Copynumber: 2.2 Consensus size: 57
7774 CATGAGATTG
*
7784 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* * * *
7841 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
*
7898 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
7912 GACTTACTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:15919 original size:28 final size:28
Alignment explanation
Indices: 15853--16008 Score: 213
Period size: 28 Copynumber: 5.5 Consensus size: 28
15843 CATGAGATTG
* * **
15853 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
15882 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
15910 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
15939 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
15967 ACACTAAGTGTGCGAGTTCGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
15995 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
16009 GACTTACTAT
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
28 72 0.62
29 44 0.38
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:15942 original size:57 final size:57
Alignment explanation
Indices: 15853--16007 Score: 215
Period size: 57 Copynumber: 2.7 Consensus size: 57
15843 CATGAGATTG
* * * *
15853 GCACTAAGTGTGCGGGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCAAGTTTGATTATATA
*
15910 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCAAGTTTGATTATATA
* * *
15967 ACACTAAGTGTGCGAGTTCGATTATATAA-CACTAAGTGTGC
1 GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGC
16008 GGACTTACTA
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
56 12 0.13
57 74 0.83
58 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTGATTATGTAAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:20532 original size:40 final size:40
Alignment explanation
Indices: 20495--20626 Score: 160
Period size: 40 Copynumber: 3.3 Consensus size: 40
20485 GCTACTCGTT
*
20495 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
20535 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* ** * * * *
20575 CCAATGCCTTCAAG-CTTAGCCTGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
20614 CAAATGCCTTCGG
1 CAAATGCCTTCGG
20627 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 32 0.40
40 46 0.57
41 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:20620 original size:39 final size:40
Alignment explanation
Indices: 20523--20624 Score: 143
Period size: 39 Copynumber: 2.6 Consensus size: 40
20513 AGCCCGGTTA
** *
20523 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCAAGACTTAACCCGGAAT
* * *
20563 TAGTAACTCGCACCAATGCCTTCAAG-CTTAGCCTGGAAT
1 TAGTAACTCGCACAAATGCCTTCAAGACTTAACCCGGAAT
20602 TAGTAACTCGCACAAATGCCTTC
1 TAGTAACTCGCACAAATGCCTTC
20625 GGATCTTAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 32 0.58
40 23 0.42
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCAAGACTTAACCCGGAAT
Found at i:26248 original size:39 final size:39
Alignment explanation
Indices: 26194--26459 Score: 388
Period size: 39 Copynumber: 6.8 Consensus size: 39
26184 CAAGACACTA
* * *
26194 GAAATGCAGCCGGGCTAAAGTCCCGCAGGCTTCGTGTTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
26233 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* * * *
26272 GAAATGTATCCGAGCTAAACTCCTGCAAGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* * * *
26311 GAAATGTATCCGGGCTAAAGTCTCACAGGCTTCCTGTTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* * *
26350 GAAATGTATCTGGGCTAAAGTCCCGTAGGCTTCGTACTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
26389 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* *
26428 GAAATTTATCCGAGCTAAAGTCCCGCAGGCTT
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTT
26460 TGTGTTGGTA
Statistics
Matches: 200, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 200 1.00
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (39 bp):
GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
Found at i:29719 original size:23 final size:24
Alignment explanation
Indices: 29666--29720 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
29656 CTTATCATAA
* * * *
29666 GAAGCTCACACAGAGCCATTTCGG
1 GAAGCTTACAAAGAGCCATATCAG
29690 GAAGCTTACAAAGAGCC-TATCAG
1 GAAGCTTACAAAGAGCCATATCAG
29713 GAAGCTTA
1 GAAGCTTA
29721 TCTGGGCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (24 bp):
GAAGCTTACAAAGAGCCATATCAG
Found at i:29780 original size:25 final size:23
Alignment explanation
Indices: 29731--29781 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
29721 TCTGGGCTAT
* *
29731 ATAACGGGAAGCTCATAAGAGCC
1 ATAACGGGAAGCTCAAAAGAACC
*
29754 ATAATCGGGAAGGTCACAAAGAACC
1 ATAA-CGGGAAGCTCA-AAAGAACC
29779 ATA
1 ATA
29782 TTGAGAAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.17
24 10 0.43
25 9 0.39
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (23 bp):
ATAACGGGAAGCTCAAAAGAACC
Found at i:37552 original size:15 final size:16
Alignment explanation
Indices: 37534--37563 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
37524 TTATCCTCAC
37534 TTTTATTA-TTATTTT
1 TTTTATTATTTATTTT
37549 TTTTATTATTTATTT
1 TTTTATTATTTATTT
37564 AGTTATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATTATTTATTTT
Found at i:39803 original size:40 final size:40
Alignment explanation
Indices: 39748--39931 Score: 248
Period size: 40 Copynumber: 4.6 Consensus size: 40
39738 TATTCGGATG
*
39748 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTCCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTGCT
*
39788 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTG-CT
* *
39828 ATATCCGGGCGAAGTCCCGAAGGCATTTGTGCGAGTAGTTGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTGCT
* *
39871 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-TTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTGCT
*
39910 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
39932 TACTTGGGTT
Statistics
Matches: 128, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
38 15 0.12
39 10 0.08
40 68 0.53
43 33 0.26
44 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTGCT
Found at i:44650 original size:79 final size:82
Alignment explanation
Indices: 44539--44723 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
44529 GCTACTCGTT
* * *
44539 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
44602 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
44619 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
44682 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
44699 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
44724 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:44723 original size:40 final size:40
Alignment explanation
Indices: 44520--44723 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
44510 CGGAATTTAA
** *
44520 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
44560 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
44600 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
44639 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
44679 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
44719 CCGGA
1 CCGGA
44724 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:51935 original size:79 final size:81
Alignment explanation
Indices: 51811--51994 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
51801 GCTACTCGTT
* *
51811 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTC-GGATCTTAACCCG
* *
51874 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
51890 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCAC-AATGCCTTCGGATCTTAACCCG
* *
51953 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
51970 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
51995 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 48 0.53
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:51994 original size:40 final size:40
Alignment explanation
Indices: 51792--51994 Score: 229
Period size: 39 Copynumber: 5.1 Consensus size: 40
51782 CGGAATTTAA
** *
51792 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
51832 CCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
51871 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
51910 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
51950 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
51990 CCGGA
1 CCGGA
51995 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.01
39 68 0.49
40 57 0.41
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.