Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5956.1
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: 15623
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:1941 original size:79 final size:79
Alignment explanation
Indices: 1832--2725 Score: 1641
Period size: 79 Copynumber: 11.3 Consensus size: 79
1822 TACTCGTTCA
* *
1832 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1896 TTTAGTAACTCGCACC
64 TTTAGTAACTCGCACC
1912 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1977 TAGTAACTCGCACC
66 TAGTAACTCGCACC
1991 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
2056 TAGTAACTCGCACC
66 TAGTAACTCGCACC
2070 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
2135 TAGTAACTCGCACC
66 TAGTAACTCGCACC
2149 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
2214 TAGTAACTCGCACC
66 TAGTAACTCGCACC
2228 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
2293 TAGTAACTCGCACC
66 TAGTAACTCGCACC
2307 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
2372 TAGTAACTCGCACC
66 TAGTAACTCGCACC
2386 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
2451 TAGTAACTCGCACC
66 TAGTAACTCGCACC
2465 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
2530 TAGTAACTCGCACC
66 TAGTAACTCGCACC
2544 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
2609 TAGTAACTCGCACC
66 TAGTAACTCGCACC
** *
2623 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGAAT
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGAT
* * *
2687 ATAGTCACTTAGCA-C
65 TTAGTAAC-TCGCACC
*
2702 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGG-CTTAGCCCGGA
2726 CATCATTCGA
Statistics
Matches: 801, Mismatches: 9, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
78 3 0.00
79 770 0.96
80 28 0.03
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
TAGTAACTCGCACC
Found at i:5469 original size:79 final size:81
Alignment explanation
Indices: 5333--5515 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
5323 TTGAATGATG
* *
5333 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
5397 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
5412 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
5474 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
5492 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
5516 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:5531 original size:40 final size:40
Alignment explanation
Indices: 5334--5517 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
5324 TGAATGATGT
* * * *
5334 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
5374 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
5414 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
5452 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
5493 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
5518 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:5539 original size:79 final size:79
Alignment explanation
Indices: 5386--5550 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
5376 GGACTAAGAT
* **
5386 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
5451 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
5465 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
5528 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
5544 CCGAAGG
1 CCGAAGG
5551 TATGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:13429 original size:80 final size:79
Alignment explanation
Indices: 13284--13455 Score: 188
Period size: 80 Copynumber: 2.2 Consensus size: 79
13274 ATGTCCAGGC
* **
13284 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAACGAG
13349 TTA-CTAAATCCGGGT
66 -TAGCTAAATCC-GGT
* * * * *
13364 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCATTTGAACG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCATTTGAACG
*
13427 AGTAGCTATATCCGGT
64 AGTAGCTAAATCCGGT
* *
13443 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
13456 TATGTGATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
79 17 0.22
80 54 0.69
81 7 0.09
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAACGAG
TAGCTAAATCCGGT
Found at i:13436 original size:40 final size:40
Alignment explanation
Indices: 13281--13422 Score: 173
Period size: 40 Copynumber: 3.5 Consensus size: 40
13271 ATGATGTCCA
* * * *
13281 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCG
*
13321 GACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AATCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
*
13361 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
*
13401 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
13423 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
39 2 0.02
40 76 0.86
41 10 0.11
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
Done.