Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold932
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: 32800
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Found at i:7398 original size:40 final size:40
Alignment explanation
Indices: 7361--7543 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
7351 GCTACTCGTT
*
7361 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
7401 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
7441 CCAATGCCTTCGGG-CTTAGCCCAGAATTAGTAACTC-CA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
7479 CAAATGCCTTC--GATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
7519 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
7544 CATCATTCGA
Statistics
Matches: 121, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
36 1 0.01
38 26 0.21
39 26 0.21
40 64 0.53
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:7537 original size:78 final size:79
Alignment explanation
Indices: 7361--7541 Score: 192
Period size: 77 Copynumber: 2.3 Consensus size: 79
7351 GCTACTCGTT
* **
7361 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTC-GGACTTAACCCGG
* *
7426 ATTTAGTAACTCGCAC
64 ATATAGTAACTAGCAC
* **
7442 CAATGCCTTCGGG-CTTAGCCCAGAAT-TAGTAACTC-CACAAATGCCTTC-GATCTTAGTCCGG
1 CAAAGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCGG
* *
7503 ATATGGTCACTTAGCA-
64 ATATAGTAAC-TAGCAC
7519 CAAAGCCTTCGGGACTTAGCCCG
1 CAAAGCCTTCGGGACTTAGCCCG
7542 GACATCATTC
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
76 2 0.02
77 28 0.33
78 25 0.29
79 16 0.19
80 11 0.13
81 3 0.04
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (79 bp):
CAAAGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGAT
ATAGTAACTAGCAC
Found at i:26355 original size:27 final size:27
Alignment explanation
Indices: 26324--26501 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
26314 TATATGAGTC
* * * *
26324 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
26351 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
26378 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
26406 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
26433 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
26460 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
26487 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
26502 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:26463 original size:82 final size:81
Alignment explanation
Indices: 26345--26500 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
26335 TGCTATATAA
* *
26345 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
26410 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
26427 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
26491 CACTTAGTGC
65 CACTTAGTGC
26501 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.