Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2817
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: 31152
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:1634 original size:40 final size:39
Alignment explanation
Indices: 1550--1733 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
1540 TTGAATGATG
* * * *
1550 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
1590 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
1630 TCCGGGCTAAG-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
1668 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
1709 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
1734 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
38 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:1685 original size:78 final size:80
Alignment explanation
Indices: 1550--1733 Score: 216
Period size: 78 Copynumber: 2.3 Consensus size: 80
1540 TTGAATGATG
*
1550 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
1614 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
1629 TTCCGGGCTAAG-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
1691 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
1708 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
1734 AACGAGGAGC
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
77 1 0.01
78 57 0.63
79 8 0.09
80 24 0.27
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATA
Found at i:9554 original size:40 final size:39
Alignment explanation
Indices: 9470--9654 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
9460 TTGAATGATG
* * * *
9470 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
9510 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
9550 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
9589 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
9630 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
9655 AACGAGAGCT
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
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 (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:9606 original size:79 final size:81
Alignment explanation
Indices: 9470--9654 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
9460 TTGAATGATG
*
9470 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
9534 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
9549 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
9611 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
9629 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
9655 AACGAGAGCT
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:9671 original size:79 final size:77
Alignment explanation
Indices: 9523--9686 Score: 197
Period size: 79 Copynumber: 2.1 Consensus size: 77
9513 GGACTAAGAT
* **
9523 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAG-TACTAA
*
9588 ATCCGGGTTAAGTC
65 ATCC-GGTTAAATC
* *
9602 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-AGCT
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTA-CT
* *
9665 ATATCCGGTTAAATT
63 AAATCCGGTTAAATC
9680 CCGAAGG
1 CCGAAGG
9687 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
78 17 0.23
79 39 0.53
80 18 0.24
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTACTAAA
TCCGGTTAAATC
Found at i:15621 original size:46 final size:46
Alignment explanation
Indices: 15571--15746 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
15561 TGTTTGGGCA
15571 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
15617 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
** * *
15662 CATTTGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
15710 CCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
15747 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 59 0.56
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:17714 original size:40 final size:40
Alignment explanation
Indices: 17587--17717 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 40
17577 TATCTCACAT
* * * * * * *
17587 ACTAAGTACCGTACATAGTCGAAGCTATCTCAAATAGCAC
1 ACTAAGTGCCATATATAGACGAAGCTATGTCGAATCGCAC
*
17627 ACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCGCAC
1 ACTAAGTGCCATATATAGACGAAGCTATGTCGAATCGCAC
* * *
17667 ACTAAGTGTCATATATAGACGAAGCTATGTCGTATTGCAC
1 ACTAAGTGCCATATATAGACGAAGCTATGTCGAATCGCAC
17707 ACTAAGTGCCA
1 ACTAAGTGCCA
17718 CAAATAACCG
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (40 bp):
ACTAAGTGCCATATATAGACGAAGCTATGTCGAATCGCAC
Found at i:18680 original size:30 final size:30
Alignment explanation
Indices: 18644--18707 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
18634 CCTTGAGCTA
18644 TTAGAACTTAAGTTTTACGCTTTACGTGAT
1 TTAGAACTTAAGTTTTACGCTTTACGTGAT
18674 TTAGAACTTAAGTTTTACGCTTTACGTGAT
1 TTAGAACTTAAGTTTTACGCTTTACGTGAT
18704 TTAG
1 TTAG
18708 TCCTTTCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (30 bp):
TTAGAACTTAAGTTTTACGCTTTACGTGAT
Found at i:21313 original size:40 final size:40
Alignment explanation
Indices: 21276--21460 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
21266 GCTACTCGTT
*
21276 CAAATGCCTTCGGGACATAGCCC-GATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
21316 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
21356 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
21395 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
21436 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
21461 CATCATTCGA
Statistics
Matches: 128, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 78 0.61
41 15 0.12
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:21387 original size:79 final size:81
Alignment explanation
Indices: 21278--21460 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
21268 TACTCGTTCA
* *
21278 AATGCCTTCGGGACATAGCCC-GATTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
21341 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
21358 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
21421 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
21437 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
21461 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.64
80 30 0.33
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:29415 original size:79 final size:81
Alignment explanation
Indices: 29302--29484 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
29292 TACTCGTTCA
* *
29302 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
29365 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
29382 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
29445 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
29461 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
29485 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:29484 original size:40 final size:40
Alignment explanation
Indices: 29281--29484 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
29271 TCGAATTTAA
** *
29281 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29321 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29361 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
29400 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
29440 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
29480 CCGGA
1 CCGGA
29485 CATCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 95 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.