Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold952
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: 39176
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Found at i:10020 original size:55 final size:56
Alignment explanation
Indices: 9955--10069 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
9945 AGCATGGCTG
* *
9955 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
10011 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
10066 CCAG
1 CCAG
10070 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.56
56 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:10032 original size:27 final size:27
Alignment explanation
Indices: 9980--10069 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
9970 GTGACAGAGT
9980 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
10009 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
10036 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
10064 CACCAG
1 CACCAG
10070 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:10221 original size:28 final size:28
Alignment explanation
Indices: 10177--10238 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
10167 ATTAACCCTA
*
10177 GGGTATAAAGGTCATTTTGCATACATAG
1 GGGTATAAAGGTAATTTTGCATACATAG
*
10205 GGGTATAATGGTAATTTTGCATACATAG
1 GGGTATAAAGGTAATTTTGCATACATAG
10233 GGGTAT
1 GGGTAT
10239 TAGTACATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (28 bp):
GGGTATAAAGGTAATTTTGCATACATAG
Found at i:17887 original size:27 final size:27
Alignment explanation
Indices: 17835--17924 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 27
17825 GTGACAGAGT
*
17835 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGGGC
* *
17864 CACTAGAACAGATATGTGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGGGC
**
17891 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGAT-ATTTGTGGCAGGGC
17919 CACCAG
1 CACCAG
17925 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 23 0.43
28 24 0.45
29 6 0.11
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGGGC
Found at i:18086 original size:27 final size:28
Alignment explanation
Indices: 18030--18120 Score: 134
Period size: 27 Copynumber: 3.3 Consensus size: 28
18020 AAATTAACCC
*
18030 TAGGGGTATAGA-GGTCATTTTGCATACA
1 TAGGGGTATA-ATGGTAATTTTGCATACA
*
18058 TAGGGGTATAATTGTAA-TTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
18085 TA-GGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
18112 TAGGGGTAT
1 TAGGGGTAT
18121 TCTAGTACAT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
26 13 0.23
27 25 0.44
28 19 0.33
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:19994 original size:56 final size:56
Alignment explanation
Indices: 19931--20070 Score: 199
Period size: 56 Copynumber: 2.5 Consensus size: 56
19921 CATGGCATCG
* *
19931 ATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCA
1 ATATATGTGTGAGAGTAAGACCACGTTTAATACGTTGCCATCGATATGTGATTCCA
* **
19987 ATATATGTGTGATAGTAAGACCACGTTTAATACGTTGCCATCGATATGTGATTCTG
1 ATATATGTGTGAGAGTAAGACCACGTTTAATACGTTGCCATCGATATGTGATTCCA
* *
20043 ATATATGTGATTACATGTAAGACCACGT
1 ATATATGTG-TGAGA-GTAAGACCACGT
20071 CTGGGACGTT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
56 60 0.80
57 3 0.04
58 12 0.16
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (56 bp):
ATATATGTGTGAGAGTAAGACCACGTTTAATACGTTGCCATCGATATGTGATTCCA
Found at i:22263 original size:40 final size:40
Alignment explanation
Indices: 22173--22397 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
22163 TCGAATGATG
* * * *
22173 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
22213 TCCGGACTAAGAT-CCGAAGCCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
22253 TCTGGGCTAAG-CCCGAAGGCA-TTGATGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTAAA
* *
22292 TCGGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
22332 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
22373 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
22398 AACGAGTAGC
Statistics
Matches: 160, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
38 3 0.02
39 29 0.18
40 115 0.72
41 13 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:22404 original size:80 final size:80
Alignment explanation
Indices: 22173--22397 Score: 262
Period size: 79 Copynumber: 2.8 Consensus size: 80
22163 TCGAATGATG
* * * * * *
22173 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGCCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
* *
22236 TTGTGCGAGATACTAAT
64 TTGTGCGAGTTACTAAA
* * *
22253 TCTGGGCTAAG-CCCGAAGGCA-TTGATGCGAGTTACTA-AATCGGGGTTAAGTCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCAT
22315 TTGTGCGAGTTACTAAA
64 TTGTGCGAGTTACTAAA
* *
22332 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
22397 G
66 G
22398 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
78 2 0.02
79 58 0.48
80 57 0.47
81 5 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGTTACTAAA
Found at i:27694 original size:47 final size:47
Alignment explanation
Indices: 27631--27735 Score: 183
Period size: 47 Copynumber: 2.2 Consensus size: 47
27621 CCCTTCGGGA
* *
27631 CTTATCACATTTATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
*
27678 CTTATCACATATATACACTTTCACATCCATCACATTGGTCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
27725 CTTATCACATA
1 CTTATCACATA
27736 ATTAACACTA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:32551 original size:39 final size:40
Alignment explanation
Indices: 32457--32679 Score: 215
Period size: 40 Copynumber: 5.7 Consensus size: 40
32447 GCTCCTCGTT
* * * *
32457 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAA-TCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
32496 C-AATGCCTTCGGGACTTAA-CCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
32534 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
32574 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
32614 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
32655 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
32680 CAGCATTCAA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
37 11 0.07
38 21 0.14
39 23 0.15
40 85 0.55
41 14 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:32626 original size:80 final size:77
Alignment explanation
Indices: 32457--32626 Score: 198
Period size: 77 Copynumber: 2.2 Consensus size: 77
32447 GCTCCTCGTT
* * * *
32457 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAATCACACAATGCCTTCGGGACTTAACCGGATT
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAATCACACAAGGCCTTCGGGACTTAACCGGACT
32522 TAATAACTCGCA
66 TAATAACTCGCA
* * * * *
32534 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTA-ATCACAC-AAGGCCTTCGGGACTTAA-CCGG
* *
32599 AACTT-GTATCTCGCA
63 -ACTTAATAACTCGCA
32614 CAAATGCCTTCGG
1 CAAATGCCTTCGG
32627 ATCTTAGTCC
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
77 29 0.38
78 5 0.06
79 16 0.21
80 24 0.31
81 3 0.04
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAATCACACAAGGCCTTCGGGACTTAACCGGACT
TAATAACTCGCA
Found at i:32688 original size:41 final size:41
Alignment explanation
Indices: 32611--32688 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
32601 CTTGTATCTC
* * *
32611 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
32652 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
32689 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.