Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1650
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: 15657
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Found at i:2446 original size:40 final size:40
Alignment explanation
Indices: 2241--2457 Score: 224
Period size: 40 Copynumber: 5.6 Consensus size: 40
2231 TGAATGATGT
* * * *
2241 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
2281 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAT--
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
*
2319 CCGGGCTAAG--CCGAAGGCATTTGTGCGAG--ACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-A
2355 CCGGGCTAAG-CCCGAAGGCATTTGTGCGA-TTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
2392 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
2433 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
2458 AACGAGTAGC
Statistics
Matches: 153, Mismatches: 12, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
34 4 0.03
36 29 0.19
37 18 0.12
38 23 0.15
39 18 0.12
40 51 0.33
41 10 0.07
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:2479 original size:79 final size:76
Alignment explanation
Indices: 2329--2490 Score: 184
Period size: 79 Copynumber: 2.1 Consensus size: 76
2319 CCGGGCTAAG
* * ** *
2329 CCGAAGGCATTTGTGCGAGACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGATTACTAAATC
1 CCGAAGGCAATTGTGCGAGACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTACTAAATC
*
2394 CGGGTTAAGTC
66 CGGGTTAAATC
*
2405 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCAATTGTGCGAG--ACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTA-CT
* *
2469 ATATCC-GGTTAAATT
61 AAATCCGGGTTAAATC
2484 CCGAAGG
1 CCGAAGG
2491 TACGTGATTT
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
76 18 0.25
77 2 0.03
78 12 0.17
79 33 0.46
80 7 0.10
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (76 bp):
CCGAAGGCAATTGTGCGAGACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTACTAAATC
CGGGTTAAATC
Found at i:9734 original size:79 final size:81
Alignment explanation
Indices: 9598--9782 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
9588 TTGAATGATG
* *
9598 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
9662 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
9677 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
9739 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
9757 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
9783 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:9796 original size:40 final size:40
Alignment explanation
Indices: 9599--9782 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
9589 TGAATGATGT
* * * *
9599 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
9639 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
9679 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
9717 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
9758 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
9783 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:9804 original size:79 final size:79
Alignment explanation
Indices: 9651--9815 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
9641 GGACTAAGAT
* * **
9651 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
9716 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
9730 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
9793 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
9809 CCGAAGG
1 CCGAAGG
9816 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:14529 original size:40 final size:40
Alignment explanation
Indices: 14401--14585 Score: 248
Period size: 40 Copynumber: 4.6 Consensus size: 40
14391 AACCCAAGTA
* * *
14401 CCTTCGGGATTTAG-CCGGATATAGCAATTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
* *
14440 CCTTCGGGACTTAGCCCGGGTATAACAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATG
*
14483 CCTTCGGGACTTCGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATG
* *
14523 CCTTCGGGACTTAGCCCGGATATAGGAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
14563 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
14586 CATCCGAATA
Statistics
Matches: 129, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
39 13 0.10
40 80 0.62
43 35 0.27
44 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
Done.