Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5197.1
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: 30087
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:13625 original size:22 final size:22
Alignment explanation
Indices: 13598--13652 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
13588 TTGTTGGTGA
13598 TGCTATGTTTTGTGCTGTTTAG
1 TGCTATGTTTTGTGCTGTTTAG
* * *
13620 TGCTATTTTTTGTGTTGTTTGG
1 TGCTATGTTTTGTGCTGTTTAG
13642 TG-T-TGTTTTGT
1 TGCTATGTTTTGT
13653 TGTTGTGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 7 0.24
21 1 0.03
22 21 0.72
ACGTcount: A:0.05, C:0.05, G:0.27, T:0.62
Consensus pattern (22 bp):
TGCTATGTTTTGTGCTGTTTAG
Found at i:13656 original size:11 final size:11
Alignment explanation
Indices: 13626--13739 Score: 131
Period size: 11 Copynumber: 10.5 Consensus size: 11
13616 TTAGTGCTAT
*
13626 TTTTTGTGTTG
1 TTTTGGTGTTG
13637 -TTTGGTGTTG
1 TTTTGGTGTTG
*
13647 TTTTGTTGTTG
1 TTTTGGTGTTG
*
13658 TGTTGGTGTTG
1 TTTTGGTGTTG
*
13669 TTTTAGTGTTG
1 TTTTGGTGTTG
*
13680 TTTTGTTGTTG
1 TTTTGGTGTTG
*
13691 TGTTGGTGTTG
1 TTTTGGTGTTG
*
13702 TTTTGGTGCTG
1 TTTTGGTGTTG
* *
13713 TTTTGTTGCTG
1 TTTTGGTGTTG
*
13724 TTTTGGTGCTG
1 TTTTGGTGTTG
13735 TTTTG
1 TTTTG
13740 TTACTATTTT
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
10 9 0.10
11 79 0.90
ACGTcount: A:0.01, C:0.03, G:0.33, T:0.63
Consensus pattern (11 bp):
TTTTGGTGTTG
Found at i:13682 original size:33 final size:33
Alignment explanation
Indices: 13631--13739 Score: 166
Period size: 33 Copynumber: 3.3 Consensus size: 33
13621 GCTATTTTTT
13631 GTGTTG-TTTGGTGTTGTTTTGTTGTTGTGTTG
1 GTGTTGTTTTGGTGTTGTTTTGTTGTTGTGTTG
*
13663 GTGTTGTTTTAGTGTTGTTTTGTTGTTGTGTTG
1 GTGTTGTTTTGGTGTTGTTTTGTTGTTGTGTTG
* * *
13696 GTGTTGTTTTGGTGCTGTTTTGTTGCTGTTTTG
1 GTGTTGTTTTGGTGTTGTTTTGTTGTTGTGTTG
*
13729 GTGCTGTTTTG
1 GTGTTGTTTTG
13740 TTACTATTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 6 0.09
33 64 0.91
ACGTcount: A:0.01, C:0.03, G:0.35, T:0.61
Consensus pattern (33 bp):
GTGTTGTTTTGGTGTTGTTTTGTTGTTGTGTTG
Found at i:13749 original size:22 final size:22
Alignment explanation
Indices: 13702--13749 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
13692 GTTGGTGTTG
* *
13702 TTTTGGTGCTGTTTTGTTGCTG
1 TTTTGGTGCTGTTTTGTTACTA
13724 TTTTGGTGCTGTTTTGTTACTA
1 TTTTGGTGCTGTTTTGTTACTA
13746 TTTT
1 TTTT
13750 TATACTTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.04, C:0.08, G:0.25, T:0.62
Consensus pattern (22 bp):
TTTTGGTGCTGTTTTGTTACTA
Found at i:14479 original size:11 final size:11
Alignment explanation
Indices: 14457--14498 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
14447 TAAACCTTAA
*
14457 TGCTGCTTTGG
1 TGCTGTTTTGG
*
14468 TGTTGTTTTGG
1 TGCTGTTTTGG
14479 TGCTGTTTTGG
1 TGCTGTTTTGG
*
14490 TGGTGTTTT
1 TGCTGTTTT
14499 ATTGTTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.00, C:0.07, G:0.36, T:0.57
Consensus pattern (11 bp):
TGCTGTTTTGG
Found at i:14488 original size:22 final size:22
Alignment explanation
Indices: 14457--14498 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
14447 TAAACCTTAA
*
14457 TGCTGCTTTGGTGTTGTTTTGG
1 TGCTGCTTTGGTGGTGTTTTGG
*
14479 TGCTGTTTTGGTGGTGTTTT
1 TGCTGCTTTGGTGGTGTTTT
14499 ATTGTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.36, T:0.57
Consensus pattern (22 bp):
TGCTGCTTTGGTGGTGTTTTGG
Found at i:16584 original size:3 final size:3
Alignment explanation
Indices: 16576--16609 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
16566 AGGTTGAGAA
16576 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16610 TCGTAGGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22311 original size:16 final size:16
Alignment explanation
Indices: 22290--22350 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
22280 CAGTAAATGA
22290 TTAACTCCATTCCAAT
1 TTAACTCCATTCCAAT
* ** *
22306 TTAACTTCATTTGATTCT
1 TTAACTCCATTCCA--AT
22324 TTAACTCCATTCCAAT
1 TTAACTCCATTCCAAT
*
22340 TTAACTTCATT
1 TTAACTCCATT
22351 TGATTCTTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 22 0.65
18 12 0.35
ACGTcount: A:0.28, C:0.25, G:0.02, T:0.46
Consensus pattern (16 bp):
TTAACTCCATTCCAAT
Found at i:22328 original size:18 final size:18
Alignment explanation
Indices: 22305--22359 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
22295 TCCATTCCAA
22305 TTTAACTTCATTTGATTC
1 TTTAACTTCATTTGATTC
* ** *
22323 TTTAACTCCATTCCA--A
1 TTTAACTTCATTTGATTC
22339 TTTAACTTCATTTGATTC
1 TTTAACTTCATTTGATTC
22357 TTT
1 TTT
22360 TTAATAGTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
16 12 0.44
18 15 0.56
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.53
Consensus pattern (18 bp):
TTTAACTTCATTTGATTC
Found at i:22328 original size:34 final size:34
Alignment explanation
Indices: 22290--22359 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
22280 CAGTAAATGA
22290 TTAACTCCATTCCAATTTAACTTCATTTGATTCT
1 TTAACTCCATTCCAATTTAACTTCATTTGATTCT
22324 TTAACTCCATTCCAATTTAACTTCATTTGATTCT
1 TTAACTCCATTCCAATTTAACTTCATTTGATTCT
22358 TT
1 TT
22360 TTAATAGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (34 bp):
TTAACTCCATTCCAATTTAACTTCATTTGATTCT
Found at i:23466 original size:17 final size:16
Alignment explanation
Indices: 23431--23479 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
23421 TATTATTTTT
23431 TTTAATTTTTTTAAAAATA
1 TTTAATTTTTTT---AATA
*
23450 TTTATTTTATTTTAATA
1 TTTAATTT-TTTTAATA
23467 TTTAATTTTTTTA
1 TTTAATTTTTTTA
23480 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 11 0.41
19 7 0.26
20 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTAATTTTTTTAATA
Found at i:26475 original size:49 final size:50
Alignment explanation
Indices: 26417--26561 Score: 175
Period size: 49 Copynumber: 2.9 Consensus size: 50
26407 GTAGCCAAAC
* *
26417 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA-T
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACAAAGT
* * ***
26466 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACATGATCAAAGT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-CAAAGT
** * *
26517 TATTGGGTACGCATAGTAGCCTGTACTTAGTACTGCACATGCGAC
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGAC
26562 TAGCTACATA
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
49 38 0.49
50 4 0.05
51 36 0.46
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (50 bp):
TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACAAAGT
Found at i:27403 original size:30 final size:30
Alignment explanation
Indices: 27369--27429 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
27359 TCCTTAACTC
27369 AAACTTTGGAAAATTTACAATTTTACCCCT
1 AAACTTTGGAAAATTTACAATTTTACCCCT
* * * * *
27399 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAATTTACAATTTTACCCCT
27429 A
1 A
27430 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTGGAAAATTTACAATTTTACCCCT
Done.