Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold748
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: 61450
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:217 original size:16 final size:14
Alignment explanation
Indices: 187--213 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
177 TTGTTTTTTG
187 TTTTTTTTTAAAAT
1 TTTTTTTTTAAAAT
201 TTTTTTTTTAAAA
1 TTTTTTTTTAAAA
214 AATTGGATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTTTTAAAAT
Found at i:2313 original size:13 final size:13
Alignment explanation
Indices: 2295--2319 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2285 ATTAATTTTT
2295 CTATTATATAATG
1 CTATTATATAATG
2308 CTATTATATAAT
1 CTATTATATAAT
2320 ATTGAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
CTATTATATAATG
Found at i:3603 original size:21 final size:24
Alignment explanation
Indices: 3559--3610 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
3549 TTAAATATAA
3559 TATAAATAAAATAAATTATCAATTT
1 TATAAATAAAAT-AATTATCAATTT
*
3584 TTTAAATAAAAT-ATT-T-AATTT
1 TATAAATAAAATAATTATCAATTT
3605 TATAAA
1 TATAAA
3611 AAGTGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 10 0.40
22 1 0.04
23 3 0.12
25 11 0.44
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAAATAAAATAATTATCAATTT
Found at i:7256 original size:30 final size:30
Alignment explanation
Indices: 7208--7274 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
7198 TTATAATTAC
** *
7208 AAATATATTAAAATTTATAATTATTTTAATTT
1 AAATA-ATTAAAATTTATAAAAAATTTAA-TT
*
7240 AAATAATTAATA-TTATAAAAAATTTAATT
1 AAATAATTAAAATTTATAAAAAATTTAATT
7269 AAATAA
1 AAATAA
7275 AATTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 8 0.26
30 12 0.39
31 6 0.19
32 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AAATAATTAAAATTTATAAAAAATTTAATT
Found at i:7551 original size:23 final size:23
Alignment explanation
Indices: 7488--7551 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
7478 TTAAAAAAAT
* *
7488 ATTTAAATATTATTTTTATATTA
1 ATTTAAATATAATTTTTAAATTA
*
7511 ATATT-AATATATTTTTTAAATTAA
1 AT-TTAAATATAATTTTTAAATT-A
7535 ATTTAAATA-AATTTTTA
1 ATTTAAATATAATTTTTA
7552 TTATTTAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 25 0.74
24 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAAATATAATTTTTAAATTA
Found at i:15570 original size:13 final size:13
Alignment explanation
Indices: 15552--15577 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15542 ATACATTGTT
15552 CATTGTATCGATA
1 CATTGTATCGATA
15565 CATTGTATCGATA
1 CATTGTATCGATA
15578 TATTTAGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:32618 original size:9 final size:9
Alignment explanation
Indices: 32604--32675 Score: 87
Period size: 9 Copynumber: 7.9 Consensus size: 9
32594 GTCCTTTACG
32604 AAAAAAAAC
1 AAAAAAAAC
32613 --AAAAAAC
1 AAAAAAAAC
32620 AAAAAAAAC
1 AAAAAAAAC
32629 AAAAAACAA-
1 AAAAAA-AAC
32638 AAAAAAAAC
1 AAAAAAAAC
32647 AAAAAAAAAC
1 -AAAAAAAAC
32657 AAAAAAAACC
1 AAAAAAAA-C
32667 AAGAAAAAA
1 AA-AAAAAA
32676 ATAGCAAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.12
8 2 0.04
9 27 0.48
10 14 0.25
11 6 0.11
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:32625 original size:16 final size:15
Alignment explanation
Indices: 32604--32687 Score: 89
Period size: 16 Copynumber: 5.5 Consensus size: 15
32594 GTCCTTTACG
32604 AAAAAAAACAAAAAAC
1 AAAAAAAA-AAAAAAC
32620 AAAAAAAACAAAAAAC
1 AAAAAAAA-AAAAAAC
32636 AAAAAAAAAACAAAA-
1 AAAAAAAAAA-AAAAC
*
32651 AAAAACAAAAAAAAC
1 AAAAAAAAAAAAAAC
* * * *
32666 CAAGAAAAAAATAGC
1 AAAAAAAAAAAAAAC
32681 AAAAAAA
1 AAAAAAA
32688 GCAGAAAGGG
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
14 4 0.07
15 26 0.45
16 28 0.48
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:32626 original size:10 final size:10
Alignment explanation
Indices: 32604--32676 Score: 83
Period size: 11 Copynumber: 6.8 Consensus size: 10
32594 GTCCTTTACG
32604 AAAAAAAACAA
1 AAAAAAAAC-A
*
32615 AAAACAAAAAA
1 AAAA-AAAACA
32626 AACAAAAAACAA
1 AA-AAAAAAC-A
32638 AAAAAAAACA
1 AAAAAAAACA
32648 AAAAAAAACA
1 AAAAAAAACA
*
32658 AAAAAAACCA
1 AAAAAAAACA
32668 AGAAAAAAA
1 A-AAAAAAA
32677 TAGCAAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
10 21 0.39
11 24 0.44
12 9 0.17
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:32647 original size:34 final size:33
Alignment explanation
Indices: 32603--32687 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 33
32593 CGTCCTTTAC
32603 GAAAAAAAACAAAAAACAAAAAAAACAAAAAACAA
1 GAAAAAAAACAAAAAA-AAAAAAAA-AAAAAACAA
* *
32638 -AAAAAAAAC-AAAAAAAAACAAAAAAAACCAA
1 GAAAAAAAACAAAAAAAAAAAAAAAAAAAACAA
32669 GAAAAAAATAGCAAAAAAA
1 GAAAAAAA-A-CAAAAAAA
32688 GCAGAAAGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
31 8 0.18
32 14 0.32
33 6 0.14
34 10 0.23
35 6 0.14
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.01
Consensus pattern (33 bp):
GAAAAAAAACAAAAAAAAAAAAAAAAAAAACAA
Found at i:32676 original size:1 final size:1
Alignment explanation
Indices: 32604--32664 Score: 68
Period size: 1 Copynumber: 61.0 Consensus size: 1
32594 GTCCTTTACG
* * * * * *
32604 AAAAAAAACAAAAAACAAAAAAAACAAAAAACAAAAAAAAAACAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
32665 CCAAGAAAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:33985 original size:29 final size:29
Alignment explanation
Indices: 33916--35627 Score: 2054
Period size: 28 Copynumber: 59.6 Consensus size: 29
33906 TCTTCAAAAT
*
33916 CCACAAGTCAGCGGCACTCTTTT-AAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
33944 CCATAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
33973 CCATAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
34001 CCACAAGTCAGTAGCAC-CCTTTAAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
34029 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
** *
34058 CCACAAGTTGGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
34086 CCACAAGTTAGTGGCACCCTTTT-AAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
34114 CCACAAGTTAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
34143 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
34172 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
34201 CCACAAATCAGTGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
34229 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
34258 CCATAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
34286 CCATAAGTCAGGGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
34314 CCACGTAAGTCAGTGGCAC-CCTTTCAAAGC
1 CCAC--AAGTCAGTGGCACTCTTTTCAAAGC
*
34344 CCACAAGTCAGTGGCACTTTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
34373 CCACAAATCAATGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
34402 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
34431 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
34460 CCACAAATCAGTGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
34488 CCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
34517 CCATAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
34545 CCATAAGTCAGGGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
34573 CCACGTAAGTCAGTGGCAC-CCTTTCAAAGC
1 CCAC--AAGTCAGTGGCACTCTTTTCAAAGC
*
34603 CCACAAGTCAGTGGCACTTTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
34632 CCACAAATCAATGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
34661 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
34689 CTACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
34718 CCATAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
34746 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* **
34774 CCACGCAAGTCAGTAGCAC-CCATTCAAAGC
1 CCA--CAAGTCAGTGGCACTCTTTTCAAAGC
* * *
34804 CCACAAGTTAGTGGCATTATTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
34833 CCATAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
34862 CCACAAGTCAGTGGCACTC-TTTCAATGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * * *
34890 TCATAAGTCAGGGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
34918 CCACAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
34946 CCACAAGTCAGTGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
34974 CCACGCAAGTCAGTGGCACCCATTT-AAAGC
1 CCA--CAAGTCAGTGGCACTCTTTTCAAAGC
* *
35004 CCACAAGTTAGTGGCACTATTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
35033 CCATAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
35062 CCACAAGTTAGTGGCACTC-TTTCAATGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * * *
35090 TCATAAGTCAGGGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
35118 CCACAAGTCAGTGGGAC-C-TTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
35145 CCATGCAAGTCAGTGGCAC-CCTTTCAAAGC
1 CCA--CAAGTCAGTGGCACTCTTTTCAAAGC
*
35175 CCACAAATCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
35204 CCACAAGTCAGTGGTACAC-TTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * * *
35232 CCATAAGTTAGTGGCATTTTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
35261 CCATAAGTTAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
35290 CCACAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * * *
35318 CCATAAGTTAGTAGCAC-CCTTTCAAAGCC
1 CCACAAGTCAGTGGCACTCTTTTCAAAG-C
* * *
35347 CACACAAGTCAGTGGTAC-CCTTTCAAATCC
1 C-CACAAGTCAGTGGCACTCTTTTCAAA-GC
* * *
35377 CTCGCAAGTTAGTGGCAC-CCTTTCAAAGC
1 C-CACAAGTCAGTGGCACTCTTTTCAAAGC
* *
35406 CCACAAGTCAATGGCACCCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
35435 CCACAAGTCAATGGCAC-CCTTTAAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
35463 CTACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
35492 CCACAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
35520 CCACAAGTTAGTGGCAC-CATTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
35548 CCACAAGTTAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTTCAAAGC
*
35577 CCACATGAGTCGGTGGCAACTCTTTTCAAAGC
1 CCACA--AGTCAGTGGC-ACTCTTTTCAAAGC
*
35609 CCACATAAGTTAGTGGCAC
1 CCAC--AAGTCAGTGGCAC
35628 CATTTTTTTA
Statistics
Matches: 1484, Mismatches: 154, Indels: 89
0.86 0.09 0.05
Matches are distributed among these distances:
27 16 0.01
28 656 0.44
29 612 0.41
30 159 0.11
31 14 0.01
32 26 0.02
34 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (29 bp):
CCACAAGTCAGTGGCACTCTTTTCAAAGC
Found at i:34002 original size:57 final size:57
Alignment explanation
Indices: 33916--35627 Score: 1965
Period size: 57 Copynumber: 29.8 Consensus size: 57
33906 TCTTCAAAAT
* * * *
33916 CCACAAGTCAGCGGCA-CTCTTTTAAAGCCCATAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * * *
33973 CCATAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTAGCAC-CCTTTAAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* **
34029 CCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTGGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * * * *
34086 CCACAAGTTAGTGGCACCCTTTTAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* *
34143 CCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * *
34201 CCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * * *
34258 CCATAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTCAGGGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* **
34314 CCACGTAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTTTTTTCAAAGC
1 CCAC--AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * * *
34373 CCACAAATCAATGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* *
34431 CCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * *
34488 CCACAAGTCAGTGGCACTCTTTTCAAAGCCCATAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * *
34545 CCATAAGTCAGGGGCACCCTTTCAAAGCCCACGTAAGTCAGTGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCAC--AAGTCAGTGGCACTCCTTTCAAAGC
** * * *
34603 CCACAAGTCAGTGGCACTTTTTTCAAAGCCCACAAATCAATGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * *
34661 CCACAAGTCAGTGGCACCCTTTCAAAGCCTACAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* *
34718 CCATAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * * * * **
34774 CCACGCAAGTCAGTAGCACCCATTCAAAGCCCACAAGTTAGTGGCATTATTTTCAAAGC
1 CCA--CAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * *
34833 CCATAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAATGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * * *
34890 TCATAAGTCAGGGGCATCCTTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
*
34946 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACGCAAGTCAGTGGCAC-CCATTT-AAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCC-TTTCAAAGC
* ** * *
35004 CCACAAGTTAGTGGCACTATTTTCAAAGCCCATAAGTCAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * * * *
35062 CCACAAGTTAGTGGCA-CTCTTTCAATGCTCATAAGTCAGGGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
*
35118 CCACAAGTCAGTGGGA-CCTTTCAAAGCCCATGCAAGTCAGTGGCAC-CCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCCTTTCAAAGC
* * * *
35175 CCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGTAC-ACTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * ** * * *
35232 CCATAAGTTAGTGGCATTTTTTTCAAAGCCCATAAGTTAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * * *
35290 CCACAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTTAGTAGCAC-CCTTTCAAAGCC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG-C
* * * * *
35347 CACACAAGTCAGTGGTACCCTTTCAAATCCCTCGCAAGTTAGTGGCAC-CCTTTCAAAGC
1 C-CACAAGTCAGTGGCATCCTTTCAAA-GCC-CACAAGTCAGTGGCACTCCTTTCAAAGC
* * * *
35406 CCACAAGTCAATGGCACCCTTTTCAAAGCCCACAAGTCAATGGCAC-CCTTTAAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * *
35463 CTACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * *
35520 CCACAAGTTAGTGGCA-CCATTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * *
35577 CCACATGAGTCGGTGGCAACTCTTTTCAAAGCCCACATAAGTTAGTGGCAC
1 CCACA--AGTCAGTGGC-A-TCCTTTCAAAGCCCAC--AAGTCAGTGGCAC
35628 CATTTTTTTA
Statistics
Matches: 1431, Mismatches: 174, Indels: 94
0.84 0.10 0.06
Matches are distributed among these distances:
55 13 0.01
56 208 0.15
57 660 0.46
58 414 0.29
59 85 0.06
60 24 0.02
61 13 0.01
62 1 0.00
63 13 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (57 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
Found at i:36218 original size:20 final size:20
Alignment explanation
Indices: 36190--36306 Score: 173
Period size: 20 Copynumber: 5.8 Consensus size: 20
36180 TTTCACCGAG
* *
36190 ATGTATCGATATATTTTTCA
1 ATGTATCGATACATTCTTCA
* * *
36210 ATATATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
36230 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
36250 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
36270 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
36290 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
36307 GTCTTTTTAC
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.01
20 86 0.98
21 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:47302 original size:22 final size:23
Alignment explanation
Indices: 47254--47302 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
47244 GTAGCCTTTG
*
47254 ACCATGCATTTATTTACTATGTT
1 ACCATGCATTTATTAACTATGTT
47277 -CCATGCATTT-TTAAC-ATGTCT
1 ACCATGCATTTATTAACTATGT-T
47298 ACCAT
1 ACCAT
47303 CTCATTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 5 0.22
22 14 0.61
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (23 bp):
ACCATGCATTTATTAACTATGTT
Found at i:52273 original size:27 final size:27
Alignment explanation
Indices: 52243--52310 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
52233 ATTTATCGGA
*
52243 GATACTCCAACCCTATTCCTCCGAGGG
1 GATACTCCAACCCCATTCCTCCGAGGG
52270 GATACTCCAACCCCATTCCTCCGAGGG
1 GATACTCCAACCCCATTCCTCCGAGGG
52297 GATACTCCAACCCC
1 GATACTCCAACCCC
52311 GCTTTTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (27 bp):
GATACTCCAACCCCATTCCTCCGAGGG
Found at i:54433 original size:21 final size:21
Alignment explanation
Indices: 54407--54451 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
54397 GGGTTCATTT
54407 TTTACCCTTATTCTTTTATTC
1 TTTACCCTTATTCTTTTATTC
54428 TTTACCCTTATTCTTTTATTC
1 TTTACCCTTATTCTTTTATTC
54449 TTT
1 TTT
54452 GCAATTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTACCCTTATTCTTTTATTC
Found at i:57261 original size:22 final size:22
Alignment explanation
Indices: 57222--57283 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
57212 CAAAATTATG
57222 AAAAAGT-CAAAAGTAAAAGCACA
1 AAAAAGTGCAAAAGTAAAA-CA-A
*
57245 AAAAA-TG-AAAAGAAAAACAA
1 AAAAAGTGCAAAAGTAAAACAA
57265 AAAAAGTGCAAAAGTAAAA
1 AAAAAGTGCAAAAGTAAAA
57284 TAAGGAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 6 0.18
21 4 0.12
22 19 0.56
23 5 0.15
ACGTcount: A:0.71, C:0.08, G:0.13, T:0.08
Consensus pattern (22 bp):
AAAAAGTGCAAAAGTAAAACAA
Done.