Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold897
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: 5843
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Found at i:2114 original size:58 final size:56
Alignment explanation
Indices: 1867--2229 Score: 233
Period size: 58 Copynumber: 6.4 Consensus size: 56
1857 TGTTAAGCAC
* * *
1867 ATTATGTCATTTCATGCA-ATTAGAGTTATTTTAGTCATTTTTCATG-TTTTAAGACT
1 ATTATGTAATTTCATGCATTTTA-AGTTATTTTAGTCATTTTT-ATGATTTAAAGACT
* * * * *
1923 ATCATGTAATTTCATACATTTTAAGATT-TTTTA-TCATATTCTAAGATTTAAAGACC
1 ATTATGTAATTTCATGCATTTTAAG-TTATTTTAGTCAT-TTTTATGATTTAAAGACT
* * * *** * *
1979 ATTAAGCAAATTCATGCATTTT-AGTGTCCATTAGTCA-TTTGATGATTT-AGGACT
1 ATTATGTAATTTCATGCATTTTAAGT-TATTTTAGTCATTTTTATGATTTAAAGACT
* * *
2033 ATTA-GTAATTTTATGTATTTTAAGTTCATTTTAGTTATTTTCTATGATTTAAAGACT
1 ATTATGTAATTTCATGCATTTTAAGTT-ATTTTAGTCATTTT-TATGATTTAAAGACT
* * * * *
2090 ATTATGTAACTTCATGCATTTTAAGATCATTTTAAT-ATTTTTTTATGATTTAAGGACA
1 ATTATGTAATTTCATGCATTTTAAG-TTATTTTAGTCA--TTTTTATGATTTAAAGACT
* * * * * * *
2148 ATTATGCAAATTCTTACATTTTAGAGTTATTTTAGTAATTTTTTCATGATTT-AGGACC
1 ATTATGTAATTTCATGCATTTTA-AGTTATTTTAGTCA-TTTTT-ATGATTTAAAGACT
* *
2206 ATTTATGCAATTTTATGCATTTTA
1 A-TTATGTAATTTCATGCATTTTA
2230 GAGTCACTCT
Statistics
Matches: 239, Mismatches: 48, Indels: 37
0.74 0.15 0.11
Matches are distributed among these distances:
53 14 0.06
54 18 0.08
55 20 0.08
56 60 0.25
57 18 0.08
58 76 0.32
59 33 0.14
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.48
Consensus pattern (56 bp):
ATTATGTAATTTCATGCATTTTAAGTTATTTTAGTCATTTTTATGATTTAAAGACT
Found at i:2227 original size:59 final size:57
Alignment explanation
Indices: 2020--2268 Score: 213
Period size: 58 Copynumber: 4.3 Consensus size: 57
2010 TAGTCATTTG
* * * *
2020 ATGATTTAGGACTATTA-GTAATTTTATGTATTTTAAGTTCATTTTAGTTATTTTCT-
1 ATGATTTAGGACTATTATGCAATTTTATGCATTTTAAG-TCATTTTAATAATTTTCTC
* * * * * *
2076 ATGATTTAAAGACTATTATGTAACTTCATGCATTTTAAGATCATTTTAAT-ATTTTTTT
1 ATGATTT-AGGACTATTATGCAATTTTATGCATTTTAAG-TCATTTTAATAATTTTCTC
* * * *
2134 ATGATTTAAGGACAATTATGCAAATTCTTA--CATTTTAGAGTTATTTTAGTAATTTTTTC
1 ATGATTT-AGGACTATTATGC-AATT-TTATGCATTTTA-AGTCATTTTAATAATTTTCTC
* *
2193 ATGATTTAGGACCATTTATGCAATTTTATGCATTTTAGAGTCACTCTTAAATAA-TTTCTC
1 ATGATTTAGGACTA-TTATGCAATTTTATGCATTTTA-AGTCA-T-TTTAATAATTTTCTC
2253 ATGATTTAGGACTATT
1 ATGATTTAGGACTATT
2269 TTTGTATTTC
Statistics
Matches: 160, Mismatches: 21, Indels: 21
0.79 0.10 0.10
Matches are distributed among these distances:
56 7 0.04
57 18 0.11
58 69 0.43
59 39 0.24
60 21 0.13
61 6 0.04
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.49
Consensus pattern (57 bp):
ATGATTTAGGACTATTATGCAATTTTATGCATTTTAAGTCATTTTAATAATTTTCTC
Found at i:2460 original size:76 final size:78
Alignment explanation
Indices: 2350--2518 Score: 198
Period size: 78 Copynumber: 2.2 Consensus size: 78
2340 GTTAACCTTT
* * * * *
2350 ATGTCAAAACTAAGTCCATTAAAGTCATTTAGATAA-GC-ACCTTAAAACCAAGTCCTTAGGGTC
1 ATGTCAAAA-TATGTCCATCAAAGTCATTTAGATAATACTACCATAAAACCAAGTCCTTAGGATC
**
2413 ATATGGGAATATCC
65 ATATGAAAATATCC
** *
2427 ATGTCAAAATATGTCCATCATTGTCATTTAGATAATACTACCATAAAACCAAGTCTTTAGGATCA
1 ATGTCAAAATATGTCCATCAAAGTCATTTAGATAATACTACCATAAAACCAAGTCCTTAGGATCA
* *
2492 TATGAAAATTTTC
66 TATGAAAATATCC
*
2505 ATGTCAAAACATGT
1 ATGTCAAAATATGT
2519 GCATTAGGGG
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
76 22 0.29
77 10 0.13
78 45 0.58
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (78 bp):
ATGTCAAAATATGTCCATCAAAGTCATTTAGATAATACTACCATAAAACCAAGTCCTTAGGATCA
TATGAAAATATCC
Found at i:2534 original size:78 final size:78
Alignment explanation
Indices: 2350--2544 Score: 182
Period size: 78 Copynumber: 2.5 Consensus size: 78
2340 GTTAACCTTT
* * ** * * *
2350 ATGTCAAAACTAAGTCCATTAAAGTCATTTAGATAA-GC-ACCTTAAAACCAAGTCCTTAGGGTC
1 ATGTCAAAAC-ATGTCCATCAGGGTCATTTAGATAATACTACCATAAAACCAAGTCCTTAGGATC
**
2413 ATATGGGAATATCC
65 ATATGAAAATATCC
* ** *
2427 ATGTCAAAATATGTCCATCATTGTCATTTAGATAATACTACCATAAAACCAAGTCTTTAGGATCA
1 ATGTCAAAACATGTCCATCAGGGTCATTTAGATAATACTACCATAAAACCAAGTCCTTAGGATCA
* *
2492 TATGAAAATTTTC
66 TATGAAAATATCC
* *
2505 ATGTCAAAACATGTGCATTAGGGGT-ATTTA-AGTAATACTA
1 ATGTCAAAACATGTCCATCA-GGGTCATTTAGA-TAATACTA
2545 ACTTGAAGTC
Statistics
Matches: 96, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
76 21 0.22
77 11 0.11
78 62 0.65
79 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.31
Consensus pattern (78 bp):
ATGTCAAAACATGTCCATCAGGGTCATTTAGATAATACTACCATAAAACCAAGTCCTTAGGATCA
TATGAAAATATCC
Done.