Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1853
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: 19743
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:5977 original size:19 final size:19
Alignment explanation
Indices: 5950--5995 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
5940 TACCAAAGTG
*
5950 GGCCTATTGGCCCATTTTC
1 GGCCCATTGGCCCATTTTC
5969 GGCCCATTGGCCCATTTTC
1 GGCCCATTGGCCCATTTTC
*
5988 AGCCCATT
1 GGCCCATT
5996 AAGCCCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.35, G:0.20, T:0.33
Consensus pattern (19 bp):
GGCCCATTGGCCCATTTTC
Found at i:6333 original size:26 final size:27
Alignment explanation
Indices: 6304--6357 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
6294 TCACACAAGT
*
6304 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
6330 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
6357 T
1 T
6358 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:6390 original size:27 final size:27
Alignment explanation
Indices: 6360--6557 Score: 225
Period size: 27 Copynumber: 7.3 Consensus size: 27
6350 GGCAAAATGG
* * * *
6360 TAATTTTACCCCACAAGGGTATCTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
6387 TAATTCTACCCTACAGGGGTATTTTGG
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
6414 TATTTCTACCCTACAAGGGTATTTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
* * *
6441 TAATTTTATCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
6468 TAATTCTACCTTACAGGGGTATTTCAA
1 TAATTCTACCCTACAGGGGTATTTCGA
*
6495 TAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
* * * * *
6522 TAATTCTACCTTCCAGGAGTATTTTGG
1 TAATTCTACCCTACAGGGGTATTTCGA
6549 TAATTCTAC
1 TAATTCTAC
6558 AACTTATCCA
Statistics
Matches: 144, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 144 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTCGA
Found at i:9898 original size:79 final size:81
Alignment explanation
Indices: 9796--9980 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
9786 GCTCCTCGTT
* *
9796 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
9859 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
9876 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
9940 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
9956 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9981 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:9980 original size:40 final size:40
Alignment explanation
Indices: 9796--9980 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
9786 GCTCCTCGTT
* *
9796 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
9836 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
9876 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
9915 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
9956 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9981 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:17596 original size:40 final size:40
Alignment explanation
Indices: 17508--17689 Score: 207
Period size: 39 Copynumber: 4.7 Consensus size: 40
17498 GCTCCTCGTT
*
17508 CAAATGCCTTCGGGACATAG-CCGG-TTATAGTAA-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
17546 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
17586 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
17625 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
17666 CAAA-GCCTTC-GGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
17690 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
38 20 0.16
39 53 0.42
40 44 0.35
41 8 0.06
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:17650 original size:79 final size:80
Alignment explanation
Indices: 17508--17689 Score: 205
Period size: 79 Copynumber: 2.3 Consensus size: 80
17498 GCTCCTCGTT
* *
17508 CAAATGCCTTCGGGACATAG-CCGG-TTATAGTAATCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGAATATAGTAATCGCACAAATGCCTTCGGGACTTAACCCGG
* *
17571 ATTTAGTAAC-TCGCA
65 ATATAGTAACTTAGCA
* **
17586 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTA-ATCGCACAAATGCCTTCGGGA-CTTAACCCG
* *
17649 GATATGGTCACTTAGCA
64 GATATAGTAACTTAGCA
*
17666 CAAA-GCCTTCGGACTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGA
17690 CATCATTCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
77 4 0.04
78 26 0.29
79 51 0.57
80 8 0.09
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAATCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCA
Done.