Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 4 of 19
Found at i:583567 original size:15 final size:15
Alignment explanation
Indices: 583547--583598 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
583537 ATAAATATTT
*
583547 AAAATTTATATAATA
1 AAAATTTATAAAATA
583562 AAAA-TTATTAAAATA
1 AAAATTTA-TAAAATA
583577 TTAAAATTTATAAAATA
1 --AAAATTTATAAAATA
583594 AAAAT
1 AAAAT
583599 ATATTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 3 0.09
15 15 0.47
17 11 0.34
18 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATTTATAAAATA
Found at i:583583 original size:32 final size:34
Alignment explanation
Indices: 583539--583603 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
583529 ATGAGTATAT
*
583539 AAATATTTAAAATTTATATAATAAAAAT-TATTA
1 AAATATTTAAAATTTATAAAATAAAAATATATTA
583572 AAATA-TTAAAATTTATAAAATAAAAATATATT
1 AAATATTTAAAATTTATAAAATAAAAATATATT
583604 TTAAACATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAATATTTAAAATTTATAAAATAAAAATATATTA
Found at i:584989 original size:32 final size:33
Alignment explanation
Indices: 584948--585011 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
584938 ACGTAAATAT
* *
584948 ATGTTTTAAAATTTATATAA-TATAAATTATTA
1 ATGTATTAAAATTTATATAAGTATAAAATATTA
584980 ATGTATTAAAATTTATATAAGTATAAAATATT
1 ATGTATTAAAATTTATATAAGTATAAAATATT
585012 TTAAATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (33 bp):
ATGTATTAAAATTTATATAAGTATAAAATATTA
Found at i:585006 original size:17 final size:17
Alignment explanation
Indices: 584954--585008 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
584944 ATATATGTTT
584954 TAAAATTTATATAA-TA
1 TAAAATTTATATAAGTA
584970 T-AAA-TTAT-TAATGTA
1 TAAAATTTATATAA-GTA
584985 TTAAAATTTATATAAGTA
1 -TAAAATTTATATAAGTA
585003 TAAAAT
1 TAAAAT
585009 ATTTTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.09
14 4 0.12
15 5 0.15
16 2 0.06
17 9 0.27
18 7 0.21
19 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAGTA
Found at i:585038 original size:15 final size:14
Alignment explanation
Indices: 585001--585057 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
584991 TTTATATAAG
*
585001 TATAAAATATTTTA
1 TATAAAATATTATA
*
585015 AATATAAATATTATA
1 TATA-AAATATTATA
*
585030 TCATAAAATATATAAA
1 T-ATAAAATAT-TATA
585046 TATAAAA-ATTAT
1 TATAAAATATTAT
585058 CAAATTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 2 0.06
14 5 0.14
15 21 0.60
16 7 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TATAAAATATTATA
Found at i:585245 original size:23 final size:23
Alignment explanation
Indices: 585219--585262 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
585209 TATAATTATT
585219 TTTAAAAAAT-AATATTTAATAAA
1 TTTAAAAAATAAAT-TTTAATAAA
*
585242 TTTAAAAATTAAATTTTAATA
1 TTTAAAAAATAAATTTTAATA
585263 TTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAAAAATAAATTTTAATAAA
Found at i:585280 original size:17 final size:16
Alignment explanation
Indices: 585255--585292 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
585245 AAAAATTAAA
585255 TTTTAATATTTATAATT
1 TTTTAATA-TTATAATT
*
585272 TTTTTATATTATAATT
1 TTTTAATATTATAATT
585288 TTTTA
1 TTTTA
585293 TCAGTAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATATTATAATT
Found at i:586391 original size:18 final size:17
Alignment explanation
Indices: 586357--586398 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
586347 TAATTTTAAA
586357 ATAAAATTAAAAAAATT
1 ATAAAATTAAAAAAATT
**
586374 ATAAATATTAAATTAATT
1 ATAAA-ATTAAAAAAATT
586392 -TAAAATT
1 ATAAAATT
586399 TAAATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
18 10 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAATTAAAAAAATT
Found at i:586416 original size:28 final size:28
Alignment explanation
Indices: 586361--586440 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
586351 TTTAAAATAA
*
586361 AATTAAAAAAATTATAA-ATATT-AA-ATT
1 AATTTAAAAAA-TA-AATATATTAAATATT
**
586388 AATTTAAAATTTAAATATATTAAATATT
1 AATTTAAAAAATAAATATATTAAATATT
*
586416 ATTTTAAAAAATAAATATA-TAAATA
1 AATTTAAAAAATAAATATATTAAATA
586441 ATTTTATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
25 2 0.05
26 7 0.16
27 16 0.36
28 19 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AATTTAAAAAATAAATATATTAAATATT
Found at i:586746 original size:21 final size:21
Alignment explanation
Indices: 586722--586824 Score: 59
Period size: 19 Copynumber: 5.2 Consensus size: 21
586712 AATGGAAAGA
586722 AAATAAATAATATAAATATAT
1 AAATAAATAATATAAATATAT
586743 AAAT-AAT-AT-TAAATATGAT
1 AAATAAATAATATAAATAT-AT
**
586762 --ATAAA-AAT-TTTAT-TAT
1 AAATAAATAATATAAATATAT
586778 AATATAATATAATATAAA-A-AT
1 AA-ATAA-ATAATATAAATATAT
586799 -AATATAATAATATATAA-ATAT
1 AAATA-AATAATATA-AATATAT
586820 AAATA
1 AAATA
586825 TATTAAAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 27
0.67 0.04 0.28
Matches are distributed among these distances:
16 2 0.03
17 3 0.05
18 14 0.22
19 19 0.30
20 9 0.14
21 11 0.17
22 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (21 bp):
AAATAAATAATATAAATATAT
Found at i:586765 original size:29 final size:30
Alignment explanation
Indices: 586728--586826 Score: 105
Period size: 29 Copynumber: 3.3 Consensus size: 30
586718 AAGAAAATAA
*
586728 ATAATATAAATATATA-AATAATATTAAAT
1 ATAATATAAAAATATATAATAATATTAAAT
* * *
586757 ATGATATAAAAATTTTATTATAATA-T-AAT
1 ATAATATAAAAA-TATATAATAATATTAAAT
586786 ATAATATAAAAATAATATAATAATATATAAAT
1 ATAATATAAAAAT-ATATAATAATAT-TAAAT
586818 ATAAATATA
1 AT-AATATA
586827 TTAAAATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
28 1 0.02
29 33 0.59
30 4 0.07
31 7 0.12
32 5 0.09
33 6 0.11
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (30 bp):
ATAATATAAAAATATATAATAATATTAAAT
Found at i:586769 original size:23 final size:24
Alignment explanation
Indices: 586728--586852 Score: 87
Period size: 24 Copynumber: 5.1 Consensus size: 24
586718 AAGAAAATAA
*
586728 ATAATATAAATATATAAATAATATT
1 ATAATAT-AATATAAAAATAATATT
* *
586753 A-AATATGATATAAAAATTTTATTATAAT
1 ATAATATAATATAAAAA---TA--ATATT
*
586781 ATAATATAATATAAAAATAATATA
1 ATAATATAATATAAAAATAATATT
* *
586805 ATAATATATAAATATAAAT-ATATT
1 ATAATATA-ATATAAAAATAATATT
* *
586829 AAAAT-TTATATAAAAATAA-ATT
1 ATAATATAATATAAAAATAATATT
586851 AT
1 AT
586853 TAATGTCTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
22 12 0.15
23 10 0.13
24 24 0.31
25 9 0.12
26 4 0.05
28 5 0.06
29 14 0.18
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (24 bp):
ATAATATAATATAAAAATAATATT
Found at i:586845 original size:22 final size:24
Alignment explanation
Indices: 586781--586856 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 24
586771 TTATTATAAT
586781 ATAATATA-ATATAAAAATAATATA
1 ATAATATATATATAAAAATAAT-TA
* *
586805 ATAATATATAAATATAAATATATTA
1 ATAATATATATATAAAAATA-ATTA
586830 A-AAT-T-TATATAAAAATAAATTA
1 ATAATATATATATAAAAAT-AATTA
*
586852 TTAAT
1 ATAAT
586857 GTCTTAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 13 0.30
23 5 0.12
24 11 0.26
25 12 0.28
26 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAATATATATATAAAAATAATTA
Found at i:587246 original size:22 final size:21
Alignment explanation
Indices: 587211--587266 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
587201 TGTCTATTTA
* *
587211 ATTTTTTATATTTAATATATT
1 ATTTTTTATATTTAAAAAATT
*
587232 ATTTTCTTATTTTTAAAAAATT
1 ATTTT-TTATATTTAAAAAATT
**
587254 ATTAATTATATTT
1 ATTTTTTATATTT
587267 TATTAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTTATATTTAAAAAATT
Found at i:587496 original size:26 final size:27
Alignment explanation
Indices: 587447--587497 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
587437 TCTTTTCTTT
*
587447 TTTTTTTCATTATTCATCTGATTAAGA
1 TTTTTTTCATTATTAATCTGATTAAGA
587474 TTTTTTT-ATTTATTAATCT-ATTAA
1 TTTTTTTCA-TTATTAATCTGATTAA
587498 TTTATTCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTTTTTCATTATTAATCTGATTAAGA
Found at i:591513 original size:23 final size:23
Alignment explanation
Indices: 591449--591520 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
591439 TATTTTAAAA
* * *
591449 TTTATATTATTATTTAAAATAAT
1 TTTATATTAATATTTATAATTAT
* * *
591472 ATTAAAATAATA--TATAATTAT
1 TTTATATTAATATTTATAATTAT
591493 TTTATATTAATATTTATAATTAT
1 TTTATATTAATATTTATAATTAT
591516 ATTTA
1 -TTTA
591521 AATAATTTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
21 16 0.43
23 17 0.46
24 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTATATTAATATTTATAATTAT
Found at i:591526 original size:23 final size:23
Alignment explanation
Indices: 591459--591526 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
591449 TTTATATTAT
* * *
591459 TATTTAAAATAATATTAAAATAA
1 TATTTATAATTATATTTAAATAA
*
591482 TA--TATAATTAT-TTTATATTAA
1 TATTTATAATTATATTTA-AATAA
591503 TATTTATAATTATATTTAAATAA
1 TATTTATAATTATATTTAAATAA
591526 T
1 T
591527 TTTTTATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
23 16 0.44
24 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTTATAATTATATTTAAATAA
Found at i:593674 original size:2 final size:2
Alignment explanation
Indices: 593667--593709 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
593657 CTTTCTCTTT
*
593667 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
593709 T
1 T
593710 TGAAAAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:602790 original size:17 final size:17
Alignment explanation
Indices: 602768--602800 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
602758 TTTTTATTTA
602768 AATTATATT-ATATAATT
1 AATTAT-TTAATATAATT
602785 AATTATTTAATATAAT
1 AATTATTTAATATAAT
602801 ATATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATTTAATATAATT
Found at i:606252 original size:13 final size:12
Alignment explanation
Indices: 606210--606249 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
606200 ATTTAATTTT
606210 TTAAAAATTTAAA
1 TTAAAAA-TTAAA
606223 TTAAAATATTAAA
1 TTAAAA-ATTAAA
*
606236 TTAAAAAATAAA
1 TTAAAAATTAAA
606248 TT
1 TT
606250 TAATTAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 7 0.28
13 17 0.68
14 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAAATTAAA
Found at i:606267 original size:19 final size:18
Alignment explanation
Indices: 606218--606270 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
606208 TTTTAAAAAT
* * *
606218 TTAAATTAAAATATTAAA
1 TTAAAATAAAAAATTTAA
*
606236 TTAAAA-AATAAATTTAA
1 TTAAAATAAAAAATTTAA
606253 TTAAAAGTAAAAAATTTA
1 TTAAAA-TAAAAAATTTA
606271 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 14 0.50
18 5 0.18
19 9 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TTAAAATAAAAAATTTAA
Found at i:606496 original size:19 final size:21
Alignment explanation
Indices: 606459--606501 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
606449 TTCAAAAAAG
*
606459 TATAATTTTATATTTTTATTA
1 TATAATTTTATATTATTATTA
606480 TATAATTTT-T-TTATTATTA
1 TATAATTTTATATTATTATTA
606499 TAT
1 TAT
606502 CTTAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 1 0.05
21 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATAATTTTATATTATTATTA
Found at i:608044 original size:13 final size:13
Alignment explanation
Indices: 608018--608061 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
608008 CATCAAAATT
608018 TTTTAAAAATATAA
1 TTTTAAAAA-ATAA
608032 TTTTAAAAAATAA
1 TTTTAAAAAATAA
*
608045 TTCTT-AAAGATAA
1 TT-TTAAAAAATAA
608058 TTTT
1 TTTT
608062 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 2 0.07
13 15 0.54
14 11 0.39
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (13 bp):
TTTTAAAAAATAA
Found at i:608077 original size:20 final size:21
Alignment explanation
Indices: 608048--608086 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
608038 AAAATAATTC
*
608048 TTAAAGATAATT-TTTATTTT
1 TTAAAAATAATTATTTATTTT
608068 TTAAAAATAATTATTTATT
1 TTAAAAATAATTATTTATT
608087 ACTCTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TTAAAAATAATTATTTATTTT
Found at i:608447 original size:5 final size:5
Alignment explanation
Indices: 608434--608488 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
608424 TAATAAATAT
* *
608434 TTATC TTATA TTATA TTATA TTATA TATATA TT-TA TT-TA TTTATG TTA-A
1 TTATA TTATA TTATA TTATA TTATA T-TATA TTATA TTATA -TTATA TTATA
608483 TTATA T
1 TTATA T
608489 AAATGTTCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
4 9 0.21
5 28 0.65
6 6 0.14
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:608503 original size:29 final size:30
Alignment explanation
Indices: 608440--608510 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 30
608430 ATATTTATCT
* *
608440 TATA-TTATATTATATTATATATATATTTA
1 TATATTTATATTATATTATATAAATATTCA
* * *
608469 TTTATTTATGTTA-ATTATATAAATGTTCA
1 TATATTTATATTATATTATATAAATATTCA
608498 TATATTTAT-TTAT
1 TATATTTATATTAT
608511 TTTTATTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 3 0.09
29 24 0.71
30 7 0.21
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (30 bp):
TATATTTATATTATATTATATAAATATTCA
Found at i:608522 original size:21 final size:21
Alignment explanation
Indices: 608497--608552 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
608487 ATAAATGTTC
608497 ATATATTTATTTATTTTTATT
1 ATATATTTATTTATTTTTATT
* * *
608518 ATATA-ATATTTTAATTTTGTT
1 ATATATTTA-TTTATTTTTATT
608539 A-ATATTATATTTAT
1 ATATATT-TATTTAT
608553 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
20 5 0.19
21 20 0.74
22 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATATATTTATTTATTTTTATT
Found at i:609195 original size:32 final size:33
Alignment explanation
Indices: 609127--609197 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
609117 AAGATGATTA
* * * *
609127 TTAAAATTAATTTTTTATTTATTTTTAAAATTT
1 TTAAAAATAATTTATTAATTATTTTTAAAATCT
**
609160 TTAAAAATAA-TTATTAATTATTTTTAATCTCT
1 TTAAAAATAATTTATTAATTATTTTTAAAATCT
609192 TTAAAA
1 TTAAAA
609198 TTTATAATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 23 0.72
33 9 0.28
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (33 bp):
TTAAAAATAATTTATTAATTATTTTTAAAATCT
Found at i:609448 original size:2 final size:2
Alignment explanation
Indices: 609441--609470 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
609431 TTAATCGAAT
609441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
609471 CACGTCTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:612055 original size:28 final size:28
Alignment explanation
Indices: 611990--612080 Score: 66
Period size: 26 Copynumber: 3.4 Consensus size: 28
611980 TATTTTTAAT
* * * *
611990 TATATT-TTATATATAA-TAAAATAAAA
1 TATATTATAATATATAATTTAAATTATA
* *
612016 TATATTTTTATA-ATAATTTAAAATTATA
1 TATATTATAATATATAATTT-AAATTATA
* *
612044 TA-A-TATAATATATCATTTATATTATA
1 TATATTATAATATATAATTTAAATTATA
612070 TATATTATAAT
1 TATATTATAAT
612081 TTTTATATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
26 24 0.46
27 14 0.27
28 14 0.27
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
TATATTATAATATATAATTTAAATTATA
Found at i:612065 original size:21 final size:20
Alignment explanation
Indices: 612010--612096 Score: 56
Period size: 21 Copynumber: 4.3 Consensus size: 20
612000 ATATAATAAA
* *
612010 ATAAAATAT-ATTTTTATA-
1 ATAATATATAATTTATATAT
* *
612028 ATAATTTA-AAATTATATAAT
1 ATAATATATAATTTATAT-AT
*
612048 ATAATATATCATTTATAT-T
1 ATAATATATAATTTATATAT
*
612067 ATATATATTATAATTTTTATAT
1 ATA-ATA-TATAATTTATATAT
612089 AATAATAT
1 -ATAATAT
612097 CAATAATTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
18 12 0.23
19 5 0.10
20 10 0.19
21 18 0.35
22 4 0.08
23 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATATATAATTTATATAT
Found at i:612085 original size:23 final size:23
Alignment explanation
Indices: 612059--612107 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
612049 TAATATATCA
* *
612059 TTTATATTATATATAT-TATAATT
1 TTTATATAATA-ATATCAATAATT
612082 TTTATATAATAATATCAATAATT
1 TTTATATAATAATATCAATAATT
612105 TTT
1 TTT
612108 GCTACAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTATATAATAATATCAATAATT
Found at i:612302 original size:17 final size:19
Alignment explanation
Indices: 612270--612307 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
612260 TTATCAATTT
612270 AATTTAATTT-ATTTTTAA
1 AATTTAATTTAATTTTTAA
612288 AATTT-ATTTAATTTTTAA
1 AATTTAATTTAATTTTTAA
612306 AA
1 AA
612308 CTAAACTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTTAATTTAATTTTTAA
Found at i:613768 original size:17 final size:17
Alignment explanation
Indices: 613746--613781 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
613736 ATTTTATTAT
*
613746 TTAAAAATATTAAAATA
1 TTAAAAAAATTAAAATA
*
613763 TTAAAAAAATTAAATTA
1 TTAAAAAAATTAAAATA
613780 TT
1 TT
613782 TATTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAAAATTAAAATA
Found at i:614968 original size:19 final size:19
Alignment explanation
Indices: 614946--614985 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
614936 TATTTTAAAA
*
614946 TTTTAAAT-TATTATTTATT
1 TTTTAAATAT-TTATATATT
614965 TTTTAAATATTTATATATT
1 TTTTAAATATTTATATATT
614984 TT
1 TT
614986 ATAATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTAAATATTTATATATT
Found at i:614985 original size:17 final size:19
Alignment explanation
Indices: 614945--614992 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
614935 TTATTTTAAA
*
614945 ATTTTAAATTATTATTTAT
1 ATTTTAAATTATTATATAT
*
614964 TTTTTAAA-TATT-TATAT
1 ATTTTAAATTATTATATAT
614981 ATTTTATAATTA
1 ATTTTA-AATTA
614993 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 9 0.38
18 6 0.25
19 9 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTAAATTATTATATAT
Found at i:615017 original size:19 final size:20
Alignment explanation
Indices: 614993--615044 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
614983 TTTATAATTA
614993 ATTTTAAATAAAATA-TATT
1 ATTTTAAATAAAATATTATT
*
615012 ATTTTAATTAAAA-ATTATT
1 ATTTTAAATAAAATATTATT
*
615031 ATTTTAAATTAAAT
1 ATTTTAAATAAAAT
615045 CAAACCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTAAATAAAATATTATT
Found at i:618224 original size:24 final size:25
Alignment explanation
Indices: 618195--618257 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
618185 AGGGTGATAT
618195 TCATTATAATTAATCATAAT-AATA
1 TCATTATAATTAATCATAATAAATA
* *
618219 TCATTATATTTATAATTATAATAAATA
1 TCATTATA-AT-TAATCATAATAAATA
*
618246 T-AATATAATTAA
1 TCATTATAATTAA
618258 AAATTATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 11 0.34
25 2 0.06
26 14 0.44
27 5 0.16
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (25 bp):
TCATTATAATTAATCATAATAAATA
Found at i:618552 original size:2 final size:2
Alignment explanation
Indices: 618540--618580 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
618530 TGAAAAATGC
*
618540 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
618581 GTATGTGCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:618791 original size:23 final size:22
Alignment explanation
Indices: 618757--618800 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
618747 CGTGATTATA
618757 AATTTAATAAATTATT-ATAATT
1 AATTTAATAAA-TATTGATAATT
618779 AATTATAATAAATATTGATAAT
1 AATT-TAATAAATATTGATAAT
618801 AAAAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATTTAATAAATATTGATAATT
Found at i:621826 original size:15 final size:16
Alignment explanation
Indices: 621785--621831 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
621775 ATAAATATTT
621785 TAAAATTTATATAATA
1 TAAAATTTATATAATA
*
621801 T-AAA-TTATTATTATA
1 TAAAATTTA-TATAATA
621816 TCAAAATTTATATAAT
1 T-AAAATTTATATAAT
621832 GTTAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
14 3 0.12
15 10 0.40
16 1 0.04
17 8 0.32
18 3 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:622320 original size:31 final size:29
Alignment explanation
Indices: 622276--622333 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
622266 ATATTATAAA
*
622276 TAAATTATAAAATTTATC-ATTATATTTTT
1 TAAATTATAAAATTAATCGA-TATATTTTT
622305 TAAATTATAATAAATTAATCGATATATTT
1 TAAATTAT-A-AAATTAATCGATATATTT
622334 AATTTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 8 0.32
30 1 0.04
31 15 0.60
32 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (29 bp):
TAAATTATAAAATTAATCGATATATTTTT
Found at i:622720 original size:3 final size:3
Alignment explanation
Indices: 622712--622746 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
622702 GCCTAATTTC
622712 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
622747 AAAATTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:623840 original size:8 final size:8
Alignment explanation
Indices: 623827--623852 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
623817 GGATAATCTT
623827 AAAAAATA
1 AAAAAATA
623835 AAAAAATA
1 AAAAAATA
623843 AAAAAATA
1 AAAAAATA
623851 AA
1 AA
623853 GTAGCTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:632004 original size:13 final size:13
Alignment explanation
Indices: 631986--632011 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
631976 ACAAAGATCG
631986 ATGTATCGATACA
1 ATGTATCGATACA
631999 ATGTATCGATACA
1 ATGTATCGATACA
632012 TTGAGTAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:632494 original size:25 final size:25
Alignment explanation
Indices: 632466--632570 Score: 85
Period size: 25 Copynumber: 4.3 Consensus size: 25
632456 ATTTAGATTC
632466 AAATTAAATAAATTAATTTATAATTA
1 AAATTAAATAAATTAATTTATAA-TA
* *
632492 AATTTAAATAAA--AATTT-TAATT
1 AAATTAAATAAATTAATTTATAATA
* **
632514 AAATTAAATCAATTTAAAATATAA-A
1 AAATTAAAT-AAATTAATTTATAATA
* *
632539 AAATTAATTAATTTTAATTTAT-ATA
1 AAATTAAATAA-ATTAATTTATAATA
632564 AAATTAA
1 AAATTAA
632571 TTTTATTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
22 9 0.14
23 5 0.08
24 8 0.13
25 27 0.43
26 14 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATTAAATAAATTAATTTATAATA
Found at i:632569 original size:21 final size:20
Alignment explanation
Indices: 632544--632594 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
632534 ATAAAAAATT
632544 AATTAATTTTAATTT-ATATAA
1 AATTAATTTT-ATTTAATAT-A
632565 AATTAATTTTATTTAATATA
1 AATTAATTTTATTTAATATA
632585 AATTATATTT
1 AATTA-ATTT
632595 ATCATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTAATTTTATTTAATATA
Found at i:632725 original size:3 final size:3
Alignment explanation
Indices: 632717--632765 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
632707 TGAGATTGAT
* *
632717 TTA TTA TTA TTA TTA TTA CTA TTG TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
632763 TTA
1 TTA
632766 GCTTTATCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:633034 original size:19 final size:20
Alignment explanation
Indices: 632996--633042 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
632986 ATATATTATA
*
632996 AAATTAAATATTAAAAATTT
1 AAATTTAATATTAAAAATTT
* *
633016 ATATTTAATA-TAAATATTT
1 AAATTTAATATTAAAAATTT
633035 AAATTTAA
1 AAATTTAA
633043 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTTAATATTAAAAATTT
Found at i:633132 original size:11 final size:11
Alignment explanation
Indices: 633113--633152 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
633103 ATTAAATTGT
633113 TATTATATTTAA
1 TATT-TATTTAA
633125 TATTTATTTAA
1 TATTTATTTAA
633136 TA-TT-TTTAA
1 TATTTATTTAA
633145 -ATTTATTT
1 TATTTATTT
633153 TAAATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.04
9 7 0.27
10 5 0.19
11 9 0.35
12 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:637369 original size:18 final size:17
Alignment explanation
Indices: 637321--637369 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
637311 TTGAAAGTTT
*
637321 AAATTATTATTAAATAAT
1 AAATTA-TATTAAATAAA
* *
637339 AATTTAAATTAAATTAAA
1 AAATTATATTAAA-TAAA
637357 AAATTATATTAAA
1 AAATTATATTAAA
637370 AATTTAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTATATTAAATAAA
Found at i:637393 original size:16 final size:16
Alignment explanation
Indices: 637369--637404 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
637359 ATTATATTAA
*
637369 AAATTTAATTATAAAT
1 AAATCTAATTATAAAT
*
637385 AAATCTAATTATAATT
1 AAATCTAATTATAAAT
637401 AAAT
1 AAAT
637405 TATTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATCTAATTATAAAT
Found at i:637416 original size:13 final size:14
Alignment explanation
Indices: 637376--637418 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 14
637366 TAAAAATTTA
*
637376 ATTATAAATAAATCT
1 ATTATAATTAAAT-T
637391 AATTATAATTAAATT
1 -ATTATAATTAAATT
637406 ATTAT-ATTAAATT
1 ATTATAATTAAATT
637419 CAAATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
15 1 0.04
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATAATTAAATT
Found at i:639866 original size:27 final size:26
Alignment explanation
Indices: 639820--639876 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
639810 CATGATTTAA
* *
639820 AAATTTTTATAATAATATTTATAATT
1 AAATTTTAATAAAAATATTTATAATT
* *
639846 AAATTTTAACTAAAAATATTTTTATTT
1 AAATTTTAA-TAAAAATATTTATAATT
639873 AAAT
1 AAAT
639877 AATAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATTTTAATAAAAATATTTATAATT
Found at i:639901 original size:47 final size:44
Alignment explanation
Indices: 639825--639933 Score: 107
Period size: 47 Copynumber: 2.4 Consensus size: 44
639815 TTTAAAAATT
*
639825 TTTATAATAAT-ATTTATAATTAAATTTT-AACTAAAAATATTTTTA
1 TTTA-AATAATAATTTA-AATTAAATTTTAAACTAAAAA-ATTTGTA
* *
639870 TTTAAATAATAATTTAAATTAAATTTATTTAAATTATAAAATTTGTA
1 TTTAAATAATAATTTAAATTAAA--T-TTTAAACTAAAAAATTTGTA
*
639917 TTTAAA-ATTAATTTAAA
1 TTTAAATAATAATTTAAA
639934 AAATATTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
44 13 0.24
45 9 0.16
46 11 0.20
47 15 0.27
48 7 0.13
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (44 bp):
TTTAAATAATAATTTAAATTAAATTTTAAACTAAAAAATTTGTA
Found at i:640914 original size:31 final size:32
Alignment explanation
Indices: 640876--640937 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
640866 TATCAATATT
640876 TATTTAATAAAA-T-TAATATAAAATATTTATA
1 TATTTAATAAAATTATAATAT-AAATATTTATA
640907 TATTTAATAAAATTATAATATAAATATTTAT
1 TATTTAATAAAATTATAATATAAATATTTAT
640938 TTAGATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 12 0.41
32 11 0.38
33 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TATTTAATAAAATTATAATATAAATATTTATA
Found at i:640938 original size:28 final size:26
Alignment explanation
Indices: 640859--640940 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 26
640849 TTAAATATTA
*
640859 AAAATT-ATATCAATATTTATTTAAT
1 AAAATTAATATAAATATTTATTTAAT
640884 AAAATTAATATAAAATATTTATATATTTAAT
1 AAAATTAATAT-AAATA--T-T-TATTTAAT
640915 AAAATTATAATATAAATATTTATTTA
1 AAAA-T-TAATATAAATATTTATTTA
640941 GATTAATTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
25 6 0.12
26 4 0.08
27 4 0.08
28 6 0.12
29 2 0.04
30 2 0.04
31 12 0.25
32 6 0.12
33 6 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
AAAATTAATATAAATATTTATTTAAT
Found at i:640947 original size:33 final size:31
Alignment explanation
Indices: 640879--640947 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
640869 CAATATTTAT
*
640879 TTAATAAAATTAATATAAAATATTTATATAT
1 TTAATAAAATTAATATAAAATATTTATATAA
*
640910 TTAATAAAATT-ATAATATAAATATTTATTTAGA
1 TTAATAAAATTAAT-ATA-AAATATTTATATA-A
640943 TTAAT
1 TTAAT
640948 TTTTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 2 0.06
31 14 0.42
32 12 0.36
33 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
TTAATAAAATTAATATAAAATATTTATATAA
Found at i:641081 original size:2 final size:2
Alignment explanation
Indices: 641074--641133 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
641064 CACTTGGGGT
641074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
641116 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
641134 CAACTTATTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:643016 original size:15 final size:15
Alignment explanation
Indices: 642963--643022 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
642953 ATAAGTCAAA
642963 TTATTT-ATTT-AAT
1 TTATTTAATTTAAAT
* * *
642976 TTATATAAATAAAAT
1 TTATTTAATTTAAAT
642991 TT-TTATAAATTTAAAT
1 TTATT-T-AATTTAAAT
643007 TTATTTAATTTAAAT
1 TTATTTAATTTAAAT
643022 T
1 T
643023 ATTATTTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
13 5 0.14
14 3 0.08
15 16 0.44
16 10 0.28
17 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTTAATTTAAAT
Found at i:643022 original size:31 final size:30
Alignment explanation
Indices: 642969--643027 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
642959 CAAATTATTT
*
642969 ATTTAATTTATATAAATAAAATTTTTATAA
1 ATTTAATTTATATAAATAAAATTATTATAA
* * *
642999 ATTTAAATTTATTTAATTTAAATTATTAT
1 ATTT-AATTTATATAAATAAAATTATTAT
643028 TTATATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTTAATTTATATAAATAAAATTATTATAA
Found at i:643045 original size:17 final size:17
Alignment explanation
Indices: 642999--643057 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
642989 ATTTTTATAA
*
642999 ATTT-AAATTTATTTA-
1 ATTTAAAATATATTTAT
*
643014 ATTTAAATTATTATTTAT
1 ATTTAAAATA-TATTTAT
* *
643032 ATATAAAATATATTTTT
1 ATTTAAAATATATTTAT
643049 ATTTAAAAT
1 ATTTAAAAT
643058 TAATTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 4 0.11
16 3 0.09
17 20 0.57
18 8 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAAAATATATTTAT
Found at i:643069 original size:11 final size:12
Alignment explanation
Indices: 643053--643092 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
643043 ATTTTTATTT
643053 AAAATTAAT-TA
1 AAAATTAATATA
*
643064 AAAATTTATATA
1 AAAATTAATATA
*
643076 AATATTAATATA
1 AAAATTAATATA
643088 AAAAT
1 AAAAT
643093 AATCAAACAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:643090 original size:23 final size:22
Alignment explanation
Indices: 643046--643092 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
643036 AAAATATATT
*
643046 TTTATTTAAAATTAATTAAAAA
1 TTTATATAAAATTAATTAAAAA
643068 TTTATATAAATATTAATATAAAAA
1 TTTATATAAA-ATTAAT-TAAAAA
643092 T
1 T
643093 AATCAAACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 6 0.27
24 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTATATAAAATTAATTAAAAA
Found at i:643752 original size:3 final size:3
Alignment explanation
Indices: 643746--643777 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
643736 TTTTGGCAAA
*
643746 AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
643778 AAATGTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:646154 original size:25 final size:23
Alignment explanation
Indices: 646117--646178 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 23
646107 TGATTATAAA
* *
646117 AATATATATATAAAATTTTAATTTAT
1 AATA-ATAAATAAAA-TTT-ATTAAT
646143 AATAATAAAT-AAA-TTATTAAT
1 AATAATAAATAAAATTTATTAAT
*
646164 AATATTAAATAAAAT
1 AATAATAAATAAAAT
646179 CTGTTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 14 0.45
22 5 0.16
24 3 0.10
25 5 0.16
26 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAATAAATAAAATTTATTAAT
Found at i:646157 original size:87 final size:88
Alignment explanation
Indices: 646039--646228 Score: 312
Period size: 87 Copynumber: 2.2 Consensus size: 88
646029 TTTTTATTTT
* * * *
646039 TATACATTTAAAATTAAAATAAATAGA-AAATTATTAATAATATTAAATAAAATCTGTTTAAATT
1 TATAAATTTAAATTTATAAT-AATAAATAAATTATTAATAATATTAAATAAAATCTGTTTAAATT
646103 GTGATGATTATAAAAATATATATA
65 GTGATGATTATAAAAATATATATA
*
646127 TA-AAATTTTAATTTATAATAATAAATAAATTATTAATAATATTAAATAAAATCTGTTTAAATTG
1 TATAAATTTAAATTTATAATAATAAATAAATTATTAATAATATTAAATAAAATCTGTTTAAATTG
646191 TGATGATTATAAAAATATATATA
66 TGATGATTATAAAAATATATATA
646214 TATAAATTTAAATTT
1 TATAAATTTAAATTT
646229 TCAAGTAAAT
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
86 5 0.05
87 76 0.81
88 13 0.14
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (88 bp):
TATAAATTTAAATTTATAATAATAAATAAATTATTAATAATATTAAATAAAATCTGTTTAAATTG
TGATGATTATAAAAATATATATA
Found at i:646500 original size:12 final size:12
Alignment explanation
Indices: 646483--646527 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
646473 AAATATAAAA
646483 ATTATTTATATT
1 ATTATTTATATT
646495 ATTATTTATATT
1 ATTATTTATATT
646507 A-TATTTATAATT
1 ATTATTTAT-ATT
*
646519 ATTTTTTAT
1 ATTATTTAT
646528 TTTTTATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 7 0.23
12 17 0.57
13 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTATTTATATT
Found at i:646536 original size:17 final size:21
Alignment explanation
Indices: 646483--646537 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
646473 AAATATAAAA
646483 ATTAT-TTATATTATTATTTAT
1 ATTATATT-TATTATTATTTAT
*
646504 ATTATATTTATAATTATTT-T
1 ATTATATTTATTATTATTTAT
646524 -TTAT-TTT-TTATTAT
1 ATTATATTTATTATTAT
646538 AAATATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 6 0.19
18 3 0.10
19 4 0.13
20 1 0.03
21 15 0.48
22 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTATATTTATTATTATTTAT
Found at i:646544 original size:29 final size:33
Alignment explanation
Indices: 646482--646546 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 33
646472 AAAATATAAA
**
646482 AATTATTTATATTATTATTTATATTATATTTAT
1 AATTATTTATATTATTATTTATATTATAAATAT
646515 AATTATTT-T-TTATT-TTT-TATTATAAATAT
1 AATTATTTATATTATTATTTATATTATAAATAT
646544 AAT
1 AAT
646547 AAATAATATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 13 0.43
30 3 0.10
31 5 0.17
32 1 0.03
33 8 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (33 bp):
AATTATTTATATTATTATTTATATTATAAATAT
Found at i:647574 original size:12 final size:11
Alignment explanation
Indices: 647548--647620 Score: 85
Period size: 11 Copynumber: 6.5 Consensus size: 11
647538 ATAATTATAA
647548 AATATAAAAAT
1 AATATAAAAAT
*
647559 ATTATAAAAAT
1 AATATAAAAAT
647570 AAT-TAAAATAT
1 AATATAAAA-AT
*
647581 TATATAAAATAT
1 AATATAAAA-AT
647593 AATATAAAAAAT
1 AATAT-AAAAAT
*
647605 AATATAAATAT
1 AATATAAAAAT
647616 AATAT
1 AATAT
647621 GAATATAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
10 5 0.09
11 26 0.48
12 19 0.35
13 4 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:647586 original size:46 final size:46
Alignment explanation
Indices: 647530--647618 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
647520 AATAATTTTG
* *
647530 AATATGATATAATTATAAAATAT-AAAAATATTATAAAAATAATTAA
1 AATATGATATAA-AATAAAATATAAAAAATAATATAAAAATAATTAA
* * *
647576 AATATTATATAAAATATAATATAAAAAATAATATAAATATAAT
1 AATATGATATAAAATAAAATATAAAAAATAATATAAAAATAAT
647619 ATGAATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
45 8 0.22
46 29 0.78
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (46 bp):
AATATGATATAAAATAAAATATAAAAAATAATATAAAAATAATTAA
Found at i:647588 original size:40 final size:39
Alignment explanation
Indices: 647536--647639 Score: 121
Period size: 35 Copynumber: 2.7 Consensus size: 39
647526 TTTGAATATG
647536 ATATAATTATAAAATATAAAAATATTATAAAAATAAT-TAAA
1 ATATAA-TATAAAATATAAAAATATTA-AAAAATAATAT-AA
*
647577 ATATTATATAAAATAT---AATA-TAAAAAATAATATAA
1 ATATAATATAAAATATAAAAATATTAAAAAATAATATAA
*
647612 ATATAATAT-GAATATAAAAATATTAAAA
1 ATATAATATAAAATATAAAAATATTAAAA
647640 TTTATAAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
34 5 0.09
35 19 0.35
36 3 0.05
37 8 0.15
38 5 0.09
40 10 0.18
41 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (39 bp):
ATATAATATAAAATATAAAAATATTAAAAAATAATATAA
Found at i:647626 original size:46 final size:45
Alignment explanation
Indices: 647527--647650 Score: 112
Period size: 46 Copynumber: 2.7 Consensus size: 45
647517 TTAAATAATT
* *
647527 TTGAATATGATATAATTATAAAATATAAAAATATTATAAAAATAA
1 TTGAATATGATATAAATATAAAATATAAAAATAATATAAAAATAA
* * * *
647572 TTAAAATATTATATAAA-ATATAATATAAAAAATAATATAAATATAA
1 TT-GAATATGATATAAATATAAAATAT-AAAAATAATATAAAAATAA
*
647618 TATGAATAT-A-A-AAATATTAAAATTTATAAAATA
1 T-TGAATATGATATAAATA-TAAAATATA-AAAATA
647651 TAAATTATTA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
43 3 0.05
44 3 0.05
45 23 0.36
46 34 0.53
47 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (45 bp):
TTGAATATGATATAAATATAAAATATAAAAATAATATAAAAATAA
Found at i:647737 original size:17 final size:17
Alignment explanation
Indices: 647694--647737 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
647684 CATAATATAT
* *
647694 TAAGTATAATTATAATA
1 TAAGTATAAATAAAATA
647711 TAAGAATATAAATAAAATA
1 TAAG--TATAAATAAAATA
647730 TAAGTATA
1 TAAGTATA
647738 TGAATTAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.35
19 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (17 bp):
TAAGTATAAATAAAATA
Found at i:648163 original size:25 final size:24
Alignment explanation
Indices: 648135--648181 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
648125 CTCATTTTAT
648135 ATTTTAAAATTAATT-AAAATAAAAA
1 ATTTTAAAA-T-ATTAAAAATAAAAA
648160 ATTTTAAAATATTAAAAATAAA
1 ATTTTAAAATATTAAAAATAAA
648182 TATAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 9 0.43
25 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
ATTTTAAAATATTAAAAATAAAAA
Found at i:648455 original size:30 final size:30
Alignment explanation
Indices: 648410--648486 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
648400 AAATTTTAAT
* *
648410 ATTTATACTCAAATAAATTTTTAA-TCTTTA
1 ATTTATACTTAAATAAATCTTTAACT-TTTA
* * *
648440 ATTTCTATTTAAATAAGTCTTTAACTTTTA
1 ATTTATACTTAAATAAATCTTTAACTTTTA
648470 ATTTATACTTAAATAAA
1 ATTTATACTTAAATAAA
648487 CTATTATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 37 0.97
31 1 0.03
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.49
Consensus pattern (30 bp):
ATTTATACTTAAATAAATCTTTAACTTTTA
Found at i:649953 original size:2 final size:2
Alignment explanation
Indices: 649946--649977 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
649936 CGGTCCATTA
649946 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
649978 TATTCTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:650272 original size:83 final size:83
Alignment explanation
Indices: 650169--650321 Score: 234
Period size: 83 Copynumber: 1.8 Consensus size: 83
650159 TCTAATCCGA
* * *
650169 AAAAAAAAAATTTTGACTTGACTTAAAACTGGATACTTTATATTATTAAATTTTGTAAGATAAAC
1 AAAAAAAAAATTTTAACTTGACTTAAAACTGGATACTTTATATTATTAAATTTTATAAGACAAAC
650234 AAAAATGATTTTAATCCC
66 AAAAATGATTTTAATCCC
* * * * *
650252 AAAAAAAAACTTTTAACTTGATTTAAAACTTGATGCTTTATATTATTAAATTTTATAAGGCAAAC
1 AAAAAAAAAATTTTAACTTGACTTAAAACTGGATACTTTATATTATTAAATTTTATAAGACAAAC
650317 AAAAA
66 AAAAA
650322 AATTTAAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 62 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (83 bp):
AAAAAAAAAATTTTAACTTGACTTAAAACTGGATACTTTATATTATTAAATTTTATAAGACAAAC
AAAAATGATTTTAATCCC
Found at i:661369 original size:11 final size:11
Alignment explanation
Indices: 661353--661378 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
661343 TGGCGGAGGA
661353 AGAGGAGAGAG
1 AGAGGAGAGAG
661364 AGAGGAGAGAG
1 AGAGGAGAGAG
661375 AGAG
1 AGAG
661379 TAACGCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (11 bp):
AGAGGAGAGAG
Found at i:661640 original size:24 final size:22
Alignment explanation
Indices: 661599--661646 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
661589 TAATTTAAAT
661599 AATATAAAATATAATAAAATATA
1 AATATAAAATATAATAAAAT-TA
**
661622 AATATATAAATATTTTAAAATTA
1 AATATA-AAATATAATAAAATTA
661645 AA
1 AA
661647 ACAACATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AATATAAAATATAATAAAATTA
Found at i:661641 original size:34 final size:33
Alignment explanation
Indices: 661594--661694 Score: 100
Period size: 34 Copynumber: 3.0 Consensus size: 33
661584 AAAAATAATT
* *
661594 TAAATAATATAAAATATAATAAAATATAAATATA
1 TAAATATTTTAAAAT-TAATAAAATATAAATATA
*
661628 TAAATATTTTAAAATTAA-AACAACATAAAT-TA
1 TAAATATTTTAAAATTAATAA-AATATAAATATA
* *
661660 TTAATATATTTAAATTTATATAAAATATAAA-ATA
1 TAAATAT-TTTAAAATTA-ATAAAATATAAATATA
661694 T
1 T
661695 TTTAAATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
32 10 0.18
33 20 0.36
34 24 0.43
35 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAATATTTTAAAATTAATAAAATATAAATATA
Found at i:661866 original size:29 final size:26
Alignment explanation
Indices: 661820--661886 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 26
661810 ATTCGTATAT
* *
661820 TATAATATTTATATATTTTATTATATTA
1 TATAATATTTAAAAATTTTA-TAT-TTA
661848 TAATAATATTTAAAAATTTTATATTTA
1 T-ATAATATTTAAAAATTTTATATTTA
*
661875 TATAAAATTTAA
1 TATAATATTTAA
661887 TATATTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.29
27 4 0.11
28 4 0.11
29 17 0.49
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TATAATATTTAAAAATTTTATATTTA
Found at i:667546 original size:21 final size:22
Alignment explanation
Indices: 667491--667559 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 22
667481 AGCTACAGTA
667491 AATTATTATGATT-ATTATTTTAT
1 AATTATTAT-ATTAATT-TTTTAT
*
667514 AATT-TAAT-TTAATTTTTT-T
1 AATTATTATATTAATTTTTTAT
* *
667533 AATTATTATATTAATTTATAAT
1 AATTATTATATTAATTTTTTAT
667555 AATTA
1 AATTA
667560 ATTAAGATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
19 5 0.13
20 9 0.24
21 11 0.29
22 9 0.24
23 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (22 bp):
AATTATTATATTAATTTTTTAT
Found at i:672026 original size:17 final size:17
Alignment explanation
Indices: 672004--672038 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
671994 AAAAAATTAA
*
672004 ATATATTCGTATTAAAT
1 ATATATTCATATTAAAT
*
672021 ATATATTCATATTTAAT
1 ATATATTCATATTAAAT
672038 A
1 A
672039 CTCACCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (17 bp):
ATATATTCATATTAAAT
Found at i:672856 original size:13 final size:13
Alignment explanation
Indices: 672833--672873 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
672823 TTGAAATTCA
*
672833 ACAGAAACAGAGT
1 ACAGAAGCAGAGT
*
672846 ACAGCAGCAGAGT
1 ACAGAAGCAGAGT
*
672859 ACAGAATCAGAGT
1 ACAGAAGCAGAGT
672872 AC
1 AC
672874 CTACAACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (13 bp):
ACAGAAGCAGAGT
Found at i:676731 original size:6 final size:6
Alignment explanation
Indices: 676720--676806 Score: 78
Period size: 6 Copynumber: 15.3 Consensus size: 6
676710 TGACAAAATG
* *
676720 AATTTA AATTTA AAATTA TATTTA AA---A AATTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
676765 AATATA AA-TTA AATTT- TATTT- AATTAAA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AA
676807 AATATTTTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
3 3 0.05
5 11 0.17
6 47 0.72
7 4 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:676751 original size:21 final size:21
Alignment explanation
Indices: 676725--676766 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
676715 AAATGAATTT
*
676725 AAATTTAAAATTATATTTAAA
1 AAATTTAAAATTAAATTTAAA
*
676746 AAATTTAAATTTAAATTTAAA
1 AAATTTAAAATTAAATTTAAA
676767 TATAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTTAAAATTAAATTTAAA
Found at i:677664 original size:33 final size:32
Alignment explanation
Indices: 677587--677681 Score: 84
Period size: 33 Copynumber: 2.9 Consensus size: 32
677577 TGATTTAAAT
* * *
677587 TATTATTT-AATATTAATTTTAAAAAATTAATTA
1 TATTATTTAAATATTAA-TATAAAATATT-TTTA
* *
677620 TAATATATAAATATTAATATAAAATATTTTTAA
1 TATTATTTAAATATTAATATAAAATATTTTT-A
* * *
677653 TATTATTTAAATAATAAAATAATATATTT
1 TATTATTTAAATATTAATATAAAATATTT
677682 AATTAATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
32 2 0.04
33 40 0.80
34 8 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TATTATTTAAATATTAATATAAAATATTTTTA
Found at i:677668 original size:30 final size:30
Alignment explanation
Indices: 677634--677694 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
677624 ATATAAATAT
* * *
677634 TAATATAA-AATATTTTTAATATTATTTAAA
1 TAATAAAATAATATATTTAAT-TAATTTAAA
677664 TAATAAAATAATATATTTAATTAATTTAAA
1 TAATAAAATAATATATTTAATTAATTTAAA
677694 T
1 T
677695 TTAATTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TAATAAAATAATATATTTAATTAATTTAAA
Found at i:678565 original size:18 final size:20
Alignment explanation
Indices: 678532--678572 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
678522 CTCTCTTCGA
*
678532 TTTAATTCATAATAATAT-T
1 TTTAATTCAAAATAATATAT
678551 TTTAATT-AAAATAATATAT
1 TTTAATTCAAAATAATATAT
678570 TTT
1 TTT
678573 TATTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAATTCAAAATAATATAT
Found at i:678586 original size:21 final size:21
Alignment explanation
Indices: 678540--678580 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
678530 GATTTAATTC
678540 ATAATAATATTTTTAATTAAA
1 ATAATAATATTTTTAATTAAA
*
678561 ATAAT-ATATTTTTATTTAAA
1 ATAATAATATTTTTAATTAAA
678581 TTTAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAATAATATTTTTAATTAAA
Found at i:678609 original size:29 final size:29
Alignment explanation
Indices: 678551--678652 Score: 75
Period size: 29 Copynumber: 3.4 Consensus size: 29
678541 TAATAATATT
* * * *
678551 TTTAATTAAAATAATATATTTTTATTTAAA
1 TTTAATTATAA-AATATATATTAATATAAA
678581 TTTAATTATAAAATATATATTAATATAAAA
1 TTTAATTATAAAATATATATTAATAT-AAA
* *
678611 ATT-ATTTTAAAA-AT-TATTAAATAATAAA
1 TTTAATTATAAAATATATATT-AAT-ATAAA
678639 TTTAAATTTATAAA
1 TTT-AA-TTATAAA
678653 TTAAATAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
27 4 0.07
28 10 0.17
29 22 0.38
30 16 0.28
31 6 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAATTATAAAATATATATTAATATAAA
Found at i:678613 original size:31 final size:29
Alignment explanation
Indices: 678577--678669 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
678567 TATTTTTATT
678577 TAAATTTAATTATAAAATATATATTAATATAA
1 TAAATTTAATTATAAAA-AT-TATTAA-ATAA
*
678609 -AAA-TT-ATTTTAAAAATTATTAAATAA
1 TAAATTTAATTATAAAAATTATTAAATAA
* *
678635 TAAATTTAAATT-TATAAATTAAATAAA-AA
1 TAAATTT-AATTATAAAAATT-ATTAAATAA
678664 TAAATT
1 TAAATT
678670 AAAAATTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
26 4 0.08
27 9 0.17
28 4 0.08
29 23 0.43
30 10 0.19
31 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAATTTAATTATAAAAATTATTAAATAA
Found at i:678678 original size:22 final size:25
Alignment explanation
Indices: 678626--678683 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 25
678616 TTTAAAAATT
*
678626 ATTAAATAATAAATTTAAATTTATAA
1 ATTAAATAATAAA-TTAAATTTAAAA
678652 ATTAAATAA-AAA-TAAA-TTAAAA
1 ATTAAATAATAAATTAAATTTAAAA
678674 ATTAAA-AATA
1 ATTAAATAATA
678684 TTTTTGAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.07
22 12 0.40
23 4 0.13
25 3 0.10
26 9 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
ATTAAATAATAAATTAAATTTAAAA
Found at i:678682 original size:29 final size:29
Alignment explanation
Indices: 678617--678682 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
678607 AAAAATTATT
* * *
678617 TTAAAAATTATTAAATAATAAATTTAAAT
1 TTAAAAATTAATAAATAATAAATTAAAAA
*
678646 TTATAAATTAAATAAA-AATAAATTAAAAA
1 TTAAAAATT-AATAAATAATAAATTAAAAA
678675 TTAAAAAT
1 TTAAAAAT
678683 ATTTTTGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
TTAAAAATTAATAAATAATAAATTAAAAA
Found at i:679719 original size:2 final size:2
Alignment explanation
Indices: 679712--679755 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
679702 TCTTTTCTTT
*
679712 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
679754 TA
1 TA
679756 AAAGACATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:684360 original size:3 final size:3
Alignment explanation
Indices: 684352--684406 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
684342 TTCTTCAATG
684352 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
684399 ATA ATA AT
1 ATA ATA AT
684407 TGCTTGAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:685320 original size:17 final size:18
Alignment explanation
Indices: 685289--685324 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
685279 TTAGGCTCAA
*
685289 ATTTATTATTTAAATATT
1 ATTTATTATTAAAATATT
685307 ATTTA-TATTAAAATATT
1 ATTTATTATTAAAATATT
685324 A
1 A
685325 AAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTATTATTAAAATATT
Found at i:685721 original size:13 final size:12
Alignment explanation
Indices: 685703--685747 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
685693 CTTAAATTTT
685703 TTTATTATTAATA
1 TTTATTA-TAATA
685716 TTTATTATAATTA
1 TTTATTATAA-TA
* *
685729 ATTATAATAATA
1 TTTATTATAATA
685741 TTTATTA
1 TTTATTA
685748 CATTCACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTATTATAATA
Found at i:687184 original size:40 final size:38
Alignment explanation
Indices: 687140--687228 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
687130 TTTTTTAAAT
* *
687140 TAATATGTTAAGTTTAACTAATAAT-TTAAAGATAAATATA
1 TAATATATTAA-TTTAA-TAA-AATATTAAAAATAAATATA
* * *
687180 TAATATATTTATTTGATAAATTATTAAAAATAAATATA
1 TAATATATTAATTTAATAAAATATTAAAAATAAATATA
687218 TAATATATTAA
1 TAATATATTAA
687229 AAAACTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
37 2 0.05
38 27 0.64
39 4 0.10
40 9 0.21
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (38 bp):
TAATATATTAATTTAATAAAATATTAAAAATAAATATA
Found at i:688029 original size:2 final size:2
Alignment explanation
Indices: 688017--688055 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
688007 TTACACTTAC
*
688017 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
688056 AAGCTACATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:689087 original size:34 final size:33
Alignment explanation
Indices: 689007--689087 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 33
688997 AGTTTGATTT
*
689007 AATTTTAAATTGATTAATAAAAAAATTATTTTAA
1 AATTTTAAAAT-ATTAATAAAAAAATTATTTTAA
* *
689041 AAATATATAAATATTAATATAAAAATATT-TTTTAA
1 AATTTTA-AAATATTAATA-AAAAA-ATTATTTTAA
689076 AATTTTAAAATA
1 AATTTTAAAATA
689088 ATTCAAAACT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
34 17 0.44
35 19 0.49
36 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
AATTTTAAAATATTAATAAAAAAATTATTTTAA
Found at i:689796 original size:22 final size:23
Alignment explanation
Indices: 689745--689800 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
689735 AAATATTAAA
*
689745 AAATTATTTT-TATATTAATATT
1 AAATTATTTTATATATTAAAATT
*
689767 -TATATATTTTATA-ATTAAAATT
1 AAAT-TATTTTATATATTAAAATT
689789 AAATTATTTTAT
1 AAATTATTTTAT
689801 TTTATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 2 0.07
22 22 0.79
23 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATTATTTTATATATTAAAATT
Found at i:692681 original size:2 final size:2
Alignment explanation
Indices: 692669--692719 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
692659 TTACACTTAC
* *
692669 AT AT GT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
692711 AT AT AT AT A
1 AT AT AT AT A
692720 AAGCTACATC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:695468 original size:28 final size:28
Alignment explanation
Indices: 695409--695488 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
695399 CCACCCATTT
695409 ATTTGTCAAAAATGGTGGTTATTTTGTG
1 ATTTGTCAAAAATGGTGGTTATTTTGTG
*
695437 -TTTGTAAAAAATGGTGGTT-TCCTTTG-G
1 ATTTGTCAAAAATGGTGGTTAT--TTTGTG
* *
695464 ATTTGTCAAATATGGAGGCTTATTT
1 ATTTGTCAAAAATGGTGG-TTATTT
695489 ATTTGTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 1 0.02
27 19 0.44
28 20 0.47
29 2 0.05
30 1 0.02
ACGTcount: A:0.25, C:0.06, G:0.24, T:0.45
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGGTTATTTTGTG
Found at i:698079 original size:21 final size:22
Alignment explanation
Indices: 698050--698095 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
698040 TGTTCAGACA
** *
698050 AGTAGTACTCCGTAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
698072 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
698093 AGT
1 AGT
698096 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:701629 original size:34 final size:33
Alignment explanation
Indices: 701581--701801 Score: 259
Period size: 34 Copynumber: 6.5 Consensus size: 33
701571 TGGTAAAAAC
*
701581 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
701614 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
701648 CACCCATTTAATCAATAATGGTAAGCTACCAAAATT
1 CA-CCATTTAATCAACAATGGTAACCTACC-AAA-T
* *
701684 C-TCATTTAATCAACAATGGTAAGCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* * *
701716 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
701750 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
701784 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
701802 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 15, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
32 2 0.01
33 25 0.15
34 125 0.77
35 8 0.05
36 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:701725 original size:102 final size:101
Alignment explanation
Indices: 701581--701801 Score: 345
Period size: 102 Copynumber: 2.2 Consensus size: 101
701571 TGGTAAAAAC
* *
701581 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
701646 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAATT
66 ATCACCCATTTAATCAACAATGGTAAACTACC-AAA-T
* * * *
701684 C-TCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
701748 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
701784 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
701802 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
100 2 0.02
101 18 0.17
102 87 0.81
103 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:706267 original size:34 final size:33
Alignment explanation
Indices: 706214--706432 Score: 253
Period size: 34 Copynumber: 6.5 Consensus size: 33
706204 TGGTAAAAAC
*
706214 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
706247 CTACCATTTAGTCAATAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
706281 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
706315 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
706349 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
706383 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
706417 CACCATTTAATCAACA
1 CACCATTTAATCAACA
706433 CCACATACAT
Statistics
Matches: 160, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 21 0.13
34 133 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:706335 original size:68 final size:67
Alignment explanation
Indices: 706216--706432 Score: 283
Period size: 68 Copynumber: 3.2 Consensus size: 67
706206 GTAAAAACCA
* * * *
706216 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAATAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
706281 CAC
65 CAC
* * * *
706284 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
706349 CTC
65 CAC
* * * *
706352 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
706417 CA-
65 CAC
706419 CCATTTAATCAACA
1 CCATTTAATCAACA
706433 CCACATACAT
Statistics
Matches: 129, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 15 0.12
68 113 0.88
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:706358 original size:102 final size:101
Alignment explanation
Indices: 706214--706432 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
706204 TGGTAAAAAC
* * *
706214 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAATAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
706279 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
706315 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
706380 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
706417 CACCATTTAATCAACA
1 CACCATTTAATCAACA
706433 CCACATACAT
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 14 0.13
102 91 0.87
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:707364 original size:2 final size:2
Alignment explanation
Indices: 707357--707403 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
707347 GCAAAATAAA
707357 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
707399 AG AG A
1 AG AG A
707404 TGATCAAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:709096 original size:2 final size:2
Alignment explanation
Indices: 709089--709135 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
709079 AAACTGGATG
709089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
709131 TA TA T
1 TA TA T
709136 CTAACTGATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:718473 original size:2 final size:2
Alignment explanation
Indices: 718462--718501 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
718452 TCAGTACCAA
718462 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
718502 CATAGACGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:719172 original size:27 final size:28
Alignment explanation
Indices: 719137--719203 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
719127 TATTATTAAT
719137 ATTAT-ATAAATATTTTATCATAAT-TA
1 ATTATAATAAATATTTTATCATAATATA
* *
719163 ATTATAAT-AATA-TTTATTATATTCATA
1 ATTATAATAAATATTTTATCATAAT-ATA
719190 ATTATAATAAATAT
1 ATTATAATAAATAT
719204 GATATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
25 9 0.26
26 9 0.26
27 12 0.35
28 4 0.12
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTATAATAAATATTTTATCATAATATA
Found at i:719185 original size:35 final size:33
Alignment explanation
Indices: 719092--719185 Score: 77
Period size: 37 Copynumber: 2.8 Consensus size: 33
719082 CGTTCCAAAA
*
719092 TAATTAT-ATAATTATTTAATA-ATTTTAATAAT
1 TAATTATAATAA-TATTTATTATATTTTAATAAT
* * *
719124 T-TTTATTATTAATATTATATAAATATTTTATCATAAT
1 TAATTA-TAATAATATT-TAT-TATATTTTA--ATAAT
719161 TAATTATAATAATATTTATTATATT
1 TAATTATAATAATATTTATTATATT
719186 CATAATTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
31 3 0.06
32 6 0.13
33 5 0.11
34 1 0.02
35 11 0.23
36 3 0.06
37 15 0.32
38 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (33 bp):
TAATTATAATAATATTTATTATATTTTAATAAT
Found at i:719369 original size:18 final size:20
Alignment explanation
Indices: 719323--719370 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
719313 ATGTGTAAAA
719323 TATATTATATTTATATAAATT
1 TATATTATA-TTATATAAATT
*
719344 T-TAATATATTA-AT-AATT
1 TATATTATATTATATAAATT
719361 TATATTATAT
1 TATATTATAT
719371 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 3 0.12
20 6 0.25
21 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATTATATTATATAAATT
Found at i:719370 original size:20 final size:22
Alignment explanation
Indices: 719289--719409 Score: 66
Period size: 20 Copynumber: 5.8 Consensus size: 22
719279 TTTTACGTAT
*
719289 TTATATATATTTTATATTATA-A
1 TTATATA-AATTTATATTATATA
* *
719311 TTATGTGTAAA-ATATATTATAT-
1 TTA--TATAAATTTATATTATATA
719333 TTATATAAATTT-TA--ATATA
1 TTATATAAATTTATATTATATA
719352 TTA-AT-AATTTATATTATATAAA
1 TTATATAAATTTATATTATAT--A
* *
719374 TTTTA-AAATATATATTAT-TA
1 TTATATAAATTTATATTATATA
*
719394 TTATAT-ATTTTATATT
1 TTATATAAATTTATATT
719410 TTACCTATGT
Statistics
Matches: 76, Mismatches: 10, Indels: 28
0.67 0.09 0.25
Matches are distributed among these distances:
17 5 0.07
18 8 0.11
19 3 0.04
20 24 0.32
21 1 0.01
22 19 0.25
23 13 0.17
24 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATATAAATTTATATTATATA
Found at i:719384 original size:14 final size:14
Alignment explanation
Indices: 719334--719400 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 14
719324 ATATTATATT
719334 TATATAAATTTTAA
1 TATATAAATTTTAA
*
719348 TATATTAATAATTTATAT
1 TATA-T-A-AATTT-TAA
719366 TATATAAATTTTAA
1 TATATAAATTTTAA
* * *
719380 AATATATATTATTAT
1 TATATAAATT-TTAA
719395 TATATA
1 TATATA
719401 TTTTATATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
14 14 0.33
15 14 0.33
16 2 0.05
17 6 0.14
18 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATAAATTTTAA
Done.