Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1255
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: 34135
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Found at i:3121 original size:29 final size:28
Alignment explanation
Indices: 3070--3140 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
3060 ATCAACCGCG
* * *
3070 CACACTTAGTGCCATGCACTTTAAACTCA
1 CACACTTAGTGCCATACAATTT-AACCCA
** *
3099 CACACTTAGTGCTGTACAATTTAACCCG
1 CACACTTAGTGCCATACAATTTAACCCA
3127 CACACTTAGTGCCA
1 CACACTTAGTGCCA
3141 ATCTCATGAC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 16 0.47
29 18 0.53
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.27
Consensus pattern (28 bp):
CACACTTAGTGCCATACAATTTAACCCA
Found at i:5447 original size:40 final size:40
Alignment explanation
Indices: 5336--5449 Score: 165
Period size: 40 Copynumber: 2.9 Consensus size: 40
5326 CGAATACACG
* * * * *
5336 TCACCAGCATGATTGCTCTTCGGGATTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
5376 TCACTAGCACGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
5416 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCG
5450 AATTTAGTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:5531 original size:40 final size:40
Alignment explanation
Indices: 5349--5531 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
5339 CCAGCATGAT
* * *
5349 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACCAA
* * **
5389 TGCTCTTTGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACCAA
* * * *
5429 TGCTCTTCGGGACTTAGCCCGAATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACCAA
* *
5470 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACCAA
*
5510 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
5532 CATCTTCGAA
Statistics
Matches: 117, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
39 3 0.03
40 95 0.81
41 19 0.16
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACCAA
Found at i:5878 original size:28 final size:29
Alignment explanation
Indices: 5834--5911 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
5824 CTTAATAATC
*
5834 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
5864 AACTCGCACAC-TAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
5892 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
5912 ATCTCACAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 3 0.07
28 21 0.50
29 15 0.36
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.23
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:5954 original size:43 final size:43
Alignment explanation
Indices: 5893--6112 Score: 431
Period size: 43 Copynumber: 5.1 Consensus size: 43
5883 TGCATTTCAA
5893 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
5936 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
5979 GCCCGCACACTTAGTGCCAATCTCACAATCCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAA-CCGTGAACACTTATT
6023 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
6066 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
6109 GCCC
1 GCCC
6113 ATGCTCTTTA
Statistics
Matches: 176, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
43 133 0.76
44 43 0.24
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:6038 original size:87 final size:86
Alignment explanation
Indices: 5893--6112 Score: 431
Period size: 87 Copynumber: 2.5 Consensus size: 86
5883 TGCATTTCAA
5893 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATC
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATC
5958 TCACAACCGTGAACACTTATT
66 TCACAACCGTGAACACTTATT
5979 GCCCGCACACTTAGTGCCAATCTCACAATCCGTGAACACTTATTGCCCGCACACTTAGTGCCAAT
1 GCCCGCACACTTAGTGCCAATCTCACAA-CCGTGAACACTTATTGCCCGCACACTTAGTGCCAAT
6044 CTCACAACCGTGAACACTTATT
65 CTCACAACCGTGAACACTTATT
6066 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCC
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCC
6113 ATGCTCTTTA
Statistics
Matches: 133, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
86 47 0.35
87 86 0.65
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.23
Consensus pattern (86 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATC
TCACAACCGTGAACACTTATT
Found at i:16589 original size:26 final size:26
Alignment explanation
Indices: 16548--16597 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
16538 AAGAAAATTT
* *
16548 CTTCTGAAATTCAATAGT-CACATATA
1 CTTCTGAAAATAAATA-TACACATATA
16574 CTTCTGAAAATAAATATACACATA
1 CTTCTGAAAATAAATATACACATA
16598 GAATGCCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (26 bp):
CTTCTGAAAATAAATATACACATATA
Found at i:25657 original size:17 final size:17
Alignment explanation
Indices: 25635--25670 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
25625 TCTCACCATC
*
25635 TAGGCACTTTAATTTAA
1 TAGGCACTTCAATTTAA
25652 TAGGCACTTCAATTTAA
1 TAGGCACTTCAATTTAA
25669 TA
1 TA
25671 TACTTCCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (17 bp):
TAGGCACTTCAATTTAA
Found at i:30990 original size:18 final size:17
Alignment explanation
Indices: 30963--30997 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30953 CCGAATATAC
30963 ATATATTCAATATCAAA
1 ATATATTCAATATCAAA
*
30980 ATATCATTCAATCTCAAA
1 ATAT-ATTCAATATCAAA
30998 GCCATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATATTCAATATCAAA
Found at i:31495 original size:43 final size:42
Alignment explanation
Indices: 31386--31498 Score: 104
Period size: 43 Copynumber: 2.6 Consensus size: 42
31376 ATATCATACA
* * * * *
31386 ATGCCAACGTCCCAGACGTAGTCTTACATGCAATCGCATATC
1 ATGCCAACGTCCCAAAAGTGGTCTTACACGCAATCACATATC
* * *
31428 AGTGCC-ACAGTCACAGACAG-GGTCTTACACGTAATCACATATC
1 A-TGCCAAC-GTCCCA-AAAGTGGTCTTACACGCAATCACATATC
31471 GATGCCAACGTCCCAAAAGTGGTCTTAC
1 -ATGCCAACGTCCCAAAAGTGGTCTTAC
31499 TCGAGAACAC
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
42 6 0.11
43 45 0.82
44 4 0.07
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAAAAGTGGTCTTACACGCAATCACATATC
Done.