Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold721
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: 37164
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:7409 original size:40 final size:40
Alignment explanation
Indices: 7325--7548 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
7315 TTGAATGATG
* * * *
7325 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
7365 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
7405 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
7444 TCCGGGTTAAGTCCCGATGGCATTTGTGCGAG-TACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
7483 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
7524 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
7549 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
39 72 0.45
40 79 0.49
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:7466 original size:79 final size:79
Alignment explanation
Indices: 7325--7548 Score: 285
Period size: 79 Copynumber: 2.8 Consensus size: 79
7315 TTGAATGATG
* * * * *
7325 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
*
7388 TTGTGCGAGATACTAAT
64 TTGTGCGAG-TACTAAA
* * *
7405 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGATGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
7469 GTGCGAGTACTAAA
66 GTGCGAGTACTAAA
* *
7483 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
7547 TG
65 TG
7549 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
78 17 0.13
79 90 0.71
80 19 0.15
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGTACTAAA
Found at i:7570 original size:79 final size:79
Alignment explanation
Indices: 7325--7581 Score: 236
Period size: 79 Copynumber: 3.3 Consensus size: 79
7315 TTGAATGATG
* * * * * * *
7325 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
** * *
7388 TTGTGCGAGATACTAAT
64 TTGAACGAG-GACTAAA
* * *
7405 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGATGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
** *
7469 GTGCGAGTACTAAA
66 GAACGAGGACTAAA
* *
7483 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
*
7547 TGAACGAGGAGCTATA
65 TGAACGAGGA-CTAAA
* *
7563 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
7582 TACGTGATTT
Statistics
Matches: 152, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
78 17 0.11
79 109 0.72
80 26 0.17
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GAACGAGGACTAAA
Found at i:11358 original size:64 final size:64
Alignment explanation
Indices: 11257--11389 Score: 248
Period size: 64 Copynumber: 2.1 Consensus size: 64
11247 AGCTCTTAAG
*
11257 TTTTCAAGGAGGCCTTTAGTTTGAATCCCCTTACTCCCATATTTTTATTAAATTTTTGCACACT
1 TTTTCAAGGAGGCCTTTAGTTTGAATCCCCTTACTCCCATATTTTTATTAAATTTCTGCACACT
*
11321 TTTTCAAGGAGGTCTTTAGTTTGAATCCCCTTACTCCCATATTTTTATTAAATTTCTGCACACT
1 TTTTCAAGGAGGCCTTTAGTTTGAATCCCCTTACTCCCATATTTTTATTAAATTTCTGCACACT
11385 TTTTC
1 TTTTC
11390 TACATTAACT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.45
Consensus pattern (64 bp):
TTTTCAAGGAGGCCTTTAGTTTGAATCCCCTTACTCCCATATTTTTATTAAATTTCTGCACACT
Found at i:13939 original size:19 final size:19
Alignment explanation
Indices: 13915--13953 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
13905 AACTTAGACC
*
13915 ATTAGAAAAATGTTTTCAA
1 ATTAGAAAAATGGTTTCAA
13934 ATTAGAAAAATGGTTTCAA
1 ATTAGAAAAATGGTTTCAA
13953 A
1 A
13954 AAACTTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (19 bp):
ATTAGAAAAATGGTTTCAA
Found at i:25680 original size:21 final size:23
Alignment explanation
Indices: 25632--25677 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
25622 ATGAAAAAGG
25632 AAACATATATATAAATGCGATGA
1 AAACATATATATAAATGCGATGA
25655 AAACA-AT-TATAAATGC-ATGA
1 AAACATATATATAAATGCGATGA
25675 AAA
1 AAA
25678 ACACATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 9 0.39
22 2 0.09
23 5 0.22
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.24
Consensus pattern (23 bp):
AAACATATATATAAATGCGATGA
Found at i:29764 original size:40 final size:40
Alignment explanation
Indices: 29588--29810 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
29578 TCCTCGTTCA
* * * * *
29588 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
29627 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
29667 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
29707 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
29747 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
29787 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29811 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Done.