Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3716
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: 42604
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:1421 original size:38 final size:40
Alignment explanation
Indices: 1337--1517 Score: 196
Period size: 39 Copynumber: 4.6 Consensus size: 40
1327 CTACTTCGTT
*
1337 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
1377 CAAATG-CTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
1415 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * ** *
1454 CAAATGCCTTC-GGATCTTAGTCCGGATAT-GGCACTTAGCAA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGC-A
1495 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
1518 ACATCATTCG
Statistics
Matches: 120, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
38 29 0.24
39 47 0.39
40 36 0.30
41 8 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:9539 original size:79 final size:81
Alignment explanation
Indices: 9430--9612 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
9420 TACTCGTTCA
* * *
9430 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTC-GGATCTTAACCCGG
* *
9493 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
9510 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCACACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCGGA
* *
9573 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
9589 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
9613 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:9612 original size:40 final size:40
Alignment explanation
Indices: 9428--9612 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
9418 GCTACTCGTT
* * *
9428 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
* * *
9468 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
*
9508 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCA-CA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACT-AGCA
* * *
9547 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TAGCA
9588 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9613 CATCATTCGA
Statistics
Matches: 124, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
38 2 0.02
39 30 0.24
40 81 0.65
41 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
Found at i:22367 original size:191 final size:191
Alignment explanation
Indices: 22021--22380 Score: 535
Period size: 191 Copynumber: 1.9 Consensus size: 191
22011 CAAGAACTCA
* * **
22021 CACACTTAGTGTCATTACATTTAAACTGAAGCTATCTCCGTATCGCACACTTAGTGCCTCATATA
1 CACACTTAGTGCCATCACATTTAAACCAAAGCTATCTCCGTATCGCACACTTAGTGCCTCATATA
* * * *
22086 GCCGAAGCTATTCCAATTCGCAGACTAAATGCTATTTATAGCCGAAGCTATCTCGAAACGCACAC
66 GACGAAGCTATTCCAATTCACACACTAAATGCTATTTATAGCCGAAGCTATCTCAAAACGCACAC
* * *
22151 TAAGTGCCAAACACAGTATACTTGTCGTTGTACACAGTCGTAATTGCAAATAACAATTTCG
131 TAAGTGACAAACACAGTAGACTTGTCGCTGTACACAGTCGTAATTGCAAATAACAATTTCG
*
22212 CACACTTCGTGCCATCACATTTAAACCAAAGCTATCT-CGATATCGCACACTTAGTGCCTCATAT
1 CACACTTAGTGCCATCACATTTAAACCAAAGCTATCTCCG-TATCGCACACTTAGTGCCTCATAT
* * *
22276 AGACGAAGCTATTCCAATTCACACACTAAGTGC-ATTTTATAGCTGAAGCTATCTCAAAATGCAC
65 AGACGAAGCTATTCCAATTCACACACTAAATGCTA-TTTATAGCCGAAGCTATCTCAAAACGCAC
* *
22340 ACTACGTGACAAACATAGTAGACTTGTCGCTGTACACAGTC
129 ACTAAGTGACAAACACAGTAGACTTGTCGCTGTACACAGTC
22381 ATAGTCGTAA
Statistics
Matches: 150, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
190 3 0.02
191 147 0.98
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.28
Consensus pattern (191 bp):
CACACTTAGTGCCATCACATTTAAACCAAAGCTATCTCCGTATCGCACACTTAGTGCCTCATATA
GACGAAGCTATTCCAATTCACACACTAAATGCTATTTATAGCCGAAGCTATCTCAAAACGCACAC
TAAGTGACAAACACAGTAGACTTGTCGCTGTACACAGTCGTAATTGCAAATAACAATTTCG
Found at i:34763 original size:46 final size:45
Alignment explanation
Indices: 34613--34778 Score: 169
Period size: 46 Copynumber: 3.6 Consensus size: 45
34603 AGCTCATATT
* *
34613 TCATGTTGATGCCATGTCCCAGACATGGTCTTACAGTGACTATCATC
1 TCATGTCGATGCCATGTCCCAGACAT-GTCTTACACTGACT-TCATC
* *
34660 TCATAGTCGATG-CATGTCCCAGACATGTCTTACACTGGCTTACGTC
1 TCAT-GTCGATGCCATGTCCCAGACATGTCTTACACTGACTT-CATC
* *
34706 TCAAGGCCGATG-CATGTCCCAGACATGTCTTACACTAGAAC-TCATC
1 TC-ATGTCGATGCCATGTCCCAGACATGTCTTACACT-G-ACTTCATC
*
34752 TCGATGTCGATGCCAT-TCCCAAACATG
1 TC-ATGTCGATGCCATGTCCCAGACATG
34779 GTCATACATT
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
45 1 0.01
46 69 0.68
47 24 0.24
48 7 0.07
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (45 bp):
TCATGTCGATGCCATGTCCCAGACATGTCTTACACTGACTTCATC
Found at i:40103 original size:11 final size:11
Alignment explanation
Indices: 40087--40119 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
40077 TTTGAACTTC
40087 AATTAATAATT
1 AATTAATAATT
*
40098 AATTAATTATT
1 AATTAATAATT
40109 AATTAATAATT
1 AATTAATAATT
40120 CAAAAAACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AATTAATAATT
Done.