Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3656
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: 27790
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:6304 original size:40 final size:40
Alignment explanation
Indices: 6260--6524 Score: 297
Period size: 40 Copynumber: 6.7 Consensus size: 40
6250 GCTCCTCGTT
* *
6260 CAAATGCCTTCGGGACATAGCCTGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
6300 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
6340 CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
6380 CAAATGCCTTCGGG-CTTAGCCCGGAATTAATATCTCGAA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
6419 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTATCTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
6459 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
6500 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6525 CATCATTCAA
Statistics
Matches: 197, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
38 2 0.01
39 31 0.16
40 152 0.77
41 12 0.06
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:6444 original size:119 final size:122
Alignment explanation
Indices: 6260--6524 Score: 312
Period size: 119 Copynumber: 2.2 Consensus size: 122
6250 GCTCCTCGTT
* * *
6260 CAAATGCCTTCGGGACATAGCCTGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGAACAAATGCCTTCGGGACTTAACCCG
* *
6324 GATTTAGTAACTCGCACAAATGCCTTCGAGA-CTTAACCCGGATTTAGTAAC-TCGCA
66 GATTTAGTAACTCGCACAAATGCCTTCG-GATCTTAACCCGGATATAGTAACTTAGCA
* **
6380 CAAATGCCTTCGGG-CTTAGCCCGGAATTA-A-TATCTCGAACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTATAGTAACTCGAACAAATGCCTTCGGGA-CTTAACC
* * ** * * *
6441 CGGATTTAGTATCTCGTACAAATGCCTTCGGATCTTAGTCTGGATATGGTCACTTAGCA
64 CGGATTTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCA
6500 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6525 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
118 5 0.04
119 83 0.67
120 33 0.27
121 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (122 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGAACAAATGCCTTCGGGACTTAACCCG
GATTTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCA
Found at i:6446 original size:79 final size:80
Alignment explanation
Indices: 6260--6471 Score: 268
Period size: 79 Copynumber: 2.7 Consensus size: 80
6250 GCTCCTCGTT
* * * *
6260 CAAATGCCTTCGGGACATAGCCTGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGAGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* * *
6324 GATTTAGTAACTCGCA
65 GAATTAATAACTCGAA
*
6340 CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
6404 AATTAATATCTCGAA
66 AATTAATAACTCGAA
** * *
6419 CAAATGCCTTCG-GATCTTAGTCCGGATTTAGTATCTCGTACAAATGCCTTCGG
1 CAAATGCCTTCGAGA-CTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGG
6472 ATCTTAGTCT
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
78 2 0.02
79 66 0.56
80 47 0.40
81 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (80 bp):
CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAATAACTCGAA
Found at i:12260 original size:40 final size:40
Alignment explanation
Indices: 12075--12268 Score: 247
Period size: 38 Copynumber: 5.0 Consensus size: 40
12065 TTGAATGATG
* * * *
12075 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
12115 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
12154 TCCGGACTAAGT-CCGAAGGCATTTGTGCGAG-TACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
12192 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
12231 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
12269 TCCGAACCGA
Statistics
Matches: 138, Mismatches: 10, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
37 4 0.03
38 50 0.36
39 28 0.20
40 48 0.35
41 8 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:21713 original size:43 final size:42
Alignment explanation
Indices: 21640--21768 Score: 143
Period size: 42 Copynumber: 3.0 Consensus size: 42
21630 CACACGATAC
* *
21640 CATACTAATGCCATATCCCAGATATAGTCTTACATGTAATCT
1 CATACCAATGCCATATCCCAGATATGGTCTTACATGTAATCT
* * * * *
21682 CGTATCAATGCCAATAGCCCAGCTATGGTCTTACACG-AAGTCT
1 CATACCAATGCC-ATATCCCAGATATGGTCTTACATGTAA-TCT
* * *
21725 CATACCGATGCTATATCCCAGATATGGTCCTACATGTAATCT
1 CATACCAATGCCATATCCCAGATATGGTCTTACATGTAATCT
21767 CA
1 CA
21769 GTAACCCTAA
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
42 36 0.52
43 33 0.48
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (42 bp):
CATACCAATGCCATATCCCAGATATGGTCTTACATGTAATCT
Found at i:24030 original size:40 final size:39
Alignment explanation
Indices: 23947--24211 Score: 286
Period size: 40 Copynumber: 6.6 Consensus size: 39
23937 TTGAATGATG
* * *
23947 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAAA
**
23987 TCCGAACTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
24027 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
24067 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
* *
24106 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGATACTAAA
* *
24146 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-AAATTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-TACTA-AA
*
24187 -CCGGGCTATGTCTCGAAGGCATTTG
1 TCCGGGCTAAGTC-CGAAGGCATTTG
24212 AACGAGGAGC
Statistics
Matches: 201, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
39 37 0.18
40 151 0.75
41 12 0.06
42 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:24183 original size:119 final size:121
Alignment explanation
Indices: 23947--24211 Score: 319
Period size: 119 Copynumber: 2.2 Consensus size: 121
23937 TTGAATGATG
*
23947 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGAACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGAACTAAGATCCGAAGGCATT
*
24011 TGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTA-A
66 TGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAAATACTATA
* * * ***
24066 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGAACTAAGAT-CCGAAGGCA
* **
24128 TTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGC-AAATTACTATA
64 TTTGTGCGAGATACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAAA-TACTATA
* * *
24186 ACCGGGCTATGTCTCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
24212 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
118 4 0.03
119 89 0.71
120 32 0.26
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (121 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGAACTAAGATCCGAAGGCATT
TGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAAATACTATA
Found at i:24233 original size:119 final size:119
Alignment explanation
Indices: 24000--24244 Score: 302
Period size: 119 Copynumber: 2.1 Consensus size: 119
23990 GAACTAAGAT
*
24000 CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAAATACTA
* ** * *
24065 ATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
66 ATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATC
* **
24119 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGC-AAATTAC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAAA-TAC
* * *
24182 T-ATAACCGGGCTATGTCTCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATC
64 TAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATC
24238 CCGAAGG
1 CCGAAGG
24245 TACGTGATTT
Statistics
Matches: 109, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
118 5 0.05
119 80 0.73
120 24 0.22
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.25
Consensus pattern (119 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAAATACTA
ATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATC
Done.