Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold925
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: 34221
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:651 original size:38 final size:39
Alignment explanation
Indices: 465--644 Score: 192
Period size: 39 Copynumber: 4.6 Consensus size: 39
455 TTGAATGATG
* * * *
465 TCCGGCTAAGT-CCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
503 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGG-CTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
543 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCC-GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
582 TCCGGTTAAGTCCCGAAGGCAATTGTGCGAGTTAC-ATAA
1 TCCGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
621 -CCGGCTATGTCCCGAAGGCATTTG
1 TCCGGCTAAGTCCCGAAGGCATTTG
645 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
38 33 0.27
39 58 0.48
40 22 0.18
41 9 0.07
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:651 original size:77 final size:77
Alignment explanation
Indices: 516--677 Score: 195
Period size: 77 Copynumber: 2.1 Consensus size: 77
506 GGACTAAGAT
* **
516 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTA-CTA
1 CCGAAGGCAATTGTGCGAGATACTAA-TCCGGGCTAAGCCCGAAGGCATTTGAACGAG-TAGCTA
*
580 AATCCGGTTAAGTC
64 AATCCGGTTAAATC
* *
594 CCGAAGGCAATTGTGCGAGTTACATAA-CC-GGCTATGTCCCGAAGGCATTTGAACGAGTAGCTA
1 CCGAAGGCAATTGTGCGAGATAC-TAATCCGGGCTAAG-CCCGAAGGCATTTGAACGAGTAGCTA
* *
657 TATCCGGTTAAATT
64 AATCCGGTTAAATC
671 CCGAAGG
1 CCGAAGG
678 TACGTGATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
76 8 0.11
77 41 0.56
78 21 0.29
79 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (77 bp):
CCGAAGGCAATTGTGCGAGATACTAATCCGGGCTAAGCCCGAAGGCATTTGAACGAGTAGCTAAA
TCCGGTTAAATC
Found at i:8465 original size:79 final size:81
Alignment explanation
Indices: 8329--8513 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
8319 TTGAATGATG
* *
8329 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
8393 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
8408 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
8470 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
8488 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
8514 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:8527 original size:40 final size:40
Alignment explanation
Indices: 8330--8513 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
8320 TGAATGATGT
* * * *
8330 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
8370 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
8410 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
8448 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
8489 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
8514 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:8535 original size:79 final size:79
Alignment explanation
Indices: 8382--8546 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
8372 GGACTAAGAT
* * **
8382 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
8447 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
8461 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
8524 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
8540 CCGAAGG
1 CCGAAGG
8547 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:14333 original size:31 final size:31
Alignment explanation
Indices: 14298--14360 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
14288 AGGCAATCTA
**
14298 ACCATGCCACACCATCTTGCTAAATGATCCC
1 ACCATGCCACACCATCTCACTAAATGATCCC
** *
14329 ACCATGCCTTACCATCTCACTAAGTGATCCC
1 ACCATGCCACACCATCTCACTAAATGATCCC
14360 A
1 A
14361 TCACACCTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.38, G:0.10, T:0.24
Consensus pattern (31 bp):
ACCATGCCACACCATCTCACTAAATGATCCC
Found at i:14404 original size:61 final size:62
Alignment explanation
Indices: 14322--14461 Score: 176
Period size: 61 Copynumber: 2.3 Consensus size: 62
14312 TCTTGCTAAA
* * * * *
14322 TGATCCCACCATGCCTTACCATCTCACT-AAGTGATCCCATCACACCTCACCAGCTTGTGAGG
1 TGATCCCACCATGCCTCACCATCTC-CTGAAGTAATCCCATCACACATCACCACCTTGCGAGG
* * *
14384 TGA-CCCACCGTGCCTCACCATCTCGTGAGGTAATCCCATCACACATCACCACCTTGCGAGG
1 TGATCCCACCATGCCTCACCATCTCCTGAAGTAATCCCATCACACATCACCACCTTGCGAGG
*
14445 TGATCCCATCATGCCTC
1 TGATCCCACCATGCCTC
14462 TATCATACCT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
60 1 0.02
61 51 0.77
62 14 0.21
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.23
Consensus pattern (62 bp):
TGATCCCACCATGCCTCACCATCTCCTGAAGTAATCCCATCACACATCACCACCTTGCGAGG
Found at i:27224 original size:39 final size:40
Alignment explanation
Indices: 27138--27241 Score: 174
Period size: 39 Copynumber: 2.6 Consensus size: 40
27128 AGCTCGGTTA
*
27138 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
* *
27178 TAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
27217 TAGTAACTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
27242 ATCTTAGTCC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.58
40 25 0.42
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
Found at i:27281 original size:79 final size:80
Alignment explanation
Indices: 27138--27294 Score: 203
Period size: 79 Copynumber: 2.0 Consensus size: 80
27128 AGCTCGGTTA
* * *
27138 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGG
27203 G-CTTAGCCCGGAAT
66 GACTTAGCCCGGAAT
** * * *
27217 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCTTTC
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACCAAAGCCTTC
27280 GGGACTTAGCCCGGA
64 GGGACTTAGCCCGGA
27295 CATCATTCGA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 3 0.04
79 49 0.73
80 15 0.22
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGG
GACTTAGCCCGGAAT
Found at i:27294 original size:40 final size:40
Alignment explanation
Indices: 27091--27294 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
27081 CGGAATTTAA
** * *
27091 CCGGATATAGCT-ACTCGTTCAAATGCCTTTGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
27131 TCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
27171 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
27210 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
27250 CCGGATATGGTCACTTAGCACAAA-GCTTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
27290 CCGGA
1 CCGGA
27295 CATCATTCGA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 90 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:31855 original size:27 final size:27
Alignment explanation
Indices: 31824--32000 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
31814 TAAATTGTAC
31824 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* **
31851 TGCACTAAGTGTGCGAAATGA--ATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
31876 GATGCACTAAGTGTGCGA-TTGACCATGC
1 -A-GCACTAAGTGTGCGATTTGACTATGT
*
31904 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
31932 AGCACTAAGTGTGAGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31959 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31986 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
32001 GACTCAATAT
Statistics
Matches: 126, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
25 4 0.03
26 18 0.14
27 79 0.63
28 25 0.20
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:31964 original size:81 final size:81
Alignment explanation
Indices: 31825--31979 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 81
31815 AAATTGTACA
* * *
31825 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATGTGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGAGAAATGAACGTGATGCACTAAGTGT
31890 GCGA-TTGACCATGCG
66 GCGAGTTGACCATGCG
**
31905 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGAGATTTGATTACGT-A-GCACTAAG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGAGAAATGA--ACGTGATGCACTAAG
31968 TGTGCGAGTTGA
63 TGTGCGAGTTGA
31980 TTATATAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
80 15 0.23
81 43 0.65
82 5 0.08
83 3 0.05
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGAGAAATGAACGTGATGCACTAAGTGT
GCGAGTTGACCATGCG
Done.