Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold868
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: 20839
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:1723 original size:50 final size:48
Alignment explanation
Indices: 1645--1830 Score: 221
Period size: 50 Copynumber: 3.8 Consensus size: 48
1635 TTGTGAATAG
1645 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTATTAAGTC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA-A-TATTAAGTC
* * * *
1695 ACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACTT-CGTC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAAT-A-TTAAGTC
* * * * *
1745 ACGTGTGTAGTACTAAATGCAGGCTACTACGTGTATCAGATGTGAGGTC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA-ATATTAAGTC
*
1794 ACGTGTGTAGTACAAAGTGCAGGCTACTACGTGTACC
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACC
1831 GGATTGTTGG
Statistics
Matches: 116, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
48 1 0.01
49 40 0.34
50 71 0.61
51 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (48 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAATATTAAGTC
Found at i:1850 original size:49 final size:48
Alignment explanation
Indices: 1648--1854 Score: 202
Period size: 50 Copynumber: 4.2 Consensus size: 48
1638 TGAATAGACG
* * * *
1648 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTATTAAGTCACA
1 TGTGTAGTACAAAGTGCAGGCTACTACGTGTACCAGA-TGTT-GGTCACA
* * * * *
1698 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCA-ATGACTTCGTCACG
1 TGTGTAGTACAAAGTGCAGGCTACTACGTGTAC-CAGATG--TTGGTCACA
* * *
1748 TGTGTAGTACTAAA-TGCAGGCTACTACGTGTATCAGATGTGAGGTCACG
1 TGTGTAGTAC-AAAGTGCAGGCTACTACGTGTACCAGATGT-TGGTCACA
* *
1797 TGTGTAGTACAAAGTGCAGGCTACTACGTGTACCGGATTGTTGGTCGCA
1 TGTGTAGTACAAAGTGCAGGCTACTACGTGTACCAGA-TGTTGGTCACA
1846 TGTGTAGTA
1 TGTGTAGTA
1855 GTCAGTACAA
Statistics
Matches: 133, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
48 4 0.03
49 54 0.41
50 69 0.52
51 6 0.05
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (48 bp):
TGTGTAGTACAAAGTGCAGGCTACTACGTGTACCAGATGTTGGTCACA
Found at i:9153 original size:50 final size:49
Alignment explanation
Indices: 9078--9202 Score: 178
Period size: 50 Copynumber: 2.5 Consensus size: 49
9068 TGAATACACG
* *
9078 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTATT-AGTCGCA
* * * *
9128 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTATTAGTCGCA
*
9177 TGTGTAGTACTAAGTGTAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
9203 TGCGTATCAG
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
49 31 0.46
50 37 0.54
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTATTAGTCGCA
Found at i:9198 original size:49 final size:50
Alignment explanation
Indices: 9078--9213 Score: 184
Period size: 49 Copynumber: 2.7 Consensus size: 50
9068 TGAATACACG
* * *
9078 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGACTATTAAGTCGCA
* * *
9128 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATTATT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGACTATTAAGTCGCA
* * *
9177 TGTGTAGTACTAAGTGTAGGCTACTATGCGTATCAGA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
9214 TAGCTTCGGC
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
49 39 0.51
50 37 0.49
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGACTATTAAGTCGCA
Found at i:11602 original size:39 final size:40
Alignment explanation
Indices: 11557--11780 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
11547 GCTCCTCGTT
* * * *
11557 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
11597 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
11636 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
11676 CAAAGGCCTTCGGG-CTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
11715 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
11756 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
11781 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 66 0.42
40 78 0.50
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:11660 original size:79 final size:78
Alignment explanation
Indices: 11557--11781 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 78
11547 GCTCCTCGTT
* * *
11557 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
*
11622 TTTAATAACTCGCA
66 CTT-ATAACTCGCA
* * * *
11636 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAA-GCCTTCGGGACTTAACCCGG
* *
11700 AACTTGTATCTCGCA
65 -ACTTATAACTCGCA
* * * * * *
11715 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCA-CACAAAGCCTTCGGGACTTAACCCG
11779 GAC
64 GAC
11782 AGCATTCAAT
Statistics
Matches: 121, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
78 3 0.02
79 91 0.75
80 27 0.22
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
CTTATAACTCGCA
Found at i:11789 original size:41 final size:41
Alignment explanation
Indices: 11712--11789 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
11702 CTTGTATCTC
* * *
11712 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
11753 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
11790 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:19110 original size:39 final size:40
Alignment explanation
Indices: 19065--19288 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
19055 GCTCCTCGTT
* * * *
19065 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
19105 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
19144 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
19184 CAAAGGCCTTCGGG-CTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
19223 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
19264 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
19289 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 66 0.42
40 78 0.50
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:19168 original size:79 final size:78
Alignment explanation
Indices: 19065--19289 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 78
19055 GCTCCTCGTT
* * *
19065 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
*
19130 TTTAATAACTCGCA
66 CTT-ATAACTCGCA
* * * *
19144 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAA-GCCTTCGGGACTTAACCCGG
* *
19208 AACTTGTATCTCGCA
65 -ACTTATAACTCGCA
* * * * * *
19223 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCA-CACAAAGCCTTCGGGACTTAACCCG
19287 GAC
64 GAC
19290 AGCATTCAAT
Statistics
Matches: 121, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
78 3 0.02
79 91 0.75
80 27 0.22
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
CTTATAACTCGCA
Found at i:19297 original size:41 final size:41
Alignment explanation
Indices: 19220--19297 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
19210 CTTGTATCTC
* * *
19220 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
19261 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
19298 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
Done.