Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold182
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: 1166161
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 6 of 10
Found at i:499076 original size:18 final size:18
Alignment explanation
Indices: 499050--499088 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
499040 AAAATAAAAA
*
499050 TTATTTTTAT-ATTAATAT
1 TTATATTTATAATTAA-AT
499068 TTATATTTATAATTAAAT
1 TTATATTTATAATTAAAT
499086 TTA
1 TTA
499089 AATAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTTATAATTAAAT
Found at i:499433 original size:30 final size:30
Alignment explanation
Indices: 499368--499471 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
499358 ACCACATTAT
* *
499368 TTAAGTAAATTTTTAGATT-TTTAA--TATAA
1 TTAAATAAATTTTT--ATTCTTTAATTTATAC
499397 TTAAATAAATTTTTATTCTTTAATTTATAC
1 TTAAATAAATTTTTATTCTTTAATTTATAC
* * * *
499427 TTAAATAAATTATTA-ACATTTACTTTGTAC
1 TTAAATAAATTTTTATTC-TTTAATTTATAC
*
499457 TAAAATAAATTTTTA
1 TTAAATAAATTTTTA
499472 GTATAAATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
27 3 0.05
28 5 0.08
29 14 0.22
30 41 0.65
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (30 bp):
TTAAATAAATTTTTATTCTTTAATTTATAC
Found at i:499484 original size:23 final size:22
Alignment explanation
Indices: 499458--499526 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
499448 ACTTTGTACT
499458 AAAATAAATTTTTAGTATAAATAA
1 AAAATAAATTTTTA-TATAAAT-A
** **
499482 AAAATTTATTTCAATATAAATAA
1 AAAATAAATTTTTATATAAAT-A
* *
499505 AAAATAAATATTTATTTAAATA
1 AAAATAAATTTTTATATAAATA
499527 TAATAAAATA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
22 1 0.03
23 24 0.69
24 10 0.29
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (22 bp):
AAAATAAATTTTTATATAAATA
Found at i:499526 original size:29 final size:28
Alignment explanation
Indices: 499474--499558 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 28
499464 AATTTTTAGT
* *
499474 ATAAATAA-AAAATTTATTTCAATATAA
1 ATAAAAAATAAAATTTATTTAAATATAA
499501 ATAAAAAATAAATATTTATTTAAATAT-A
1 ATAAAAAATAAA-ATTTATTTAAATATAA
* *
499529 ATAAAATATATAAATTTATTTAAAAATAA
1 ATAAAAAATA-AAATTTATTTAAATATAA
499558 A
1 A
499559 AACAATTCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.14
28 26 0.52
29 17 0.34
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (28 bp):
ATAAAAAATAAAATTTATTTAAATATAA
Found at i:499836 original size:2 final size:2
Alignment explanation
Indices: 499829--499857 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
499819 ACAGAACAAA
499829 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 A
499858 CATCGCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:499951 original size:11 final size:11
Alignment explanation
Indices: 499912--499959 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
499902 AATGTTAGGA
*
499912 ATATATATATAT
1 ATATTTATAT-T
499924 ATATATTAT-TT
1 ATAT-TTATATT
499935 AT-TTTATATT
1 ATATTTATATT
499945 ATATTTATATT
1 ATATTTATATT
499956 ATAT
1 ATAT
499960 AATTATCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 4 0.12
10 5 0.16
11 15 0.47
12 5 0.16
13 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTATATT
Found at i:502662 original size:22 final size:21
Alignment explanation
Indices: 502606--502673 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 21
502596 TATGATATAA
502606 AATTATAAATATTTTTAAATTTAT
1 AATTATAAATA-TTTTAAA--TAT
* *
502630 ATATAAAAAATATTTTAAATAT
1 A-ATTATAAATATTTTAAATAT
*
502652 AATTATGAAATA-TTAAAATAT
1 AATTAT-AAATATTTTAAATAT
502673 A
1 A
502674 TGAATAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 12 0.32
22 9 0.24
24 8 0.22
25 8 0.22
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (21 bp):
AATTATAAATATTTTAAATAT
Found at i:503521 original size:11 final size:11
Alignment explanation
Indices: 503507--503571 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
503497 TAATTTTTAT
*
503507 ATATAATATGA
1 ATATAATATAA
503518 ATATAATATAAA
1 ATATAATAT-AA
* *
503530 AAATAATAAAAA
1 ATATAAT-ATAA
*
503542 ATATATTATAA
1 ATATAATATAA
*
503553 ATAT-ATATAT
1 ATATAATATAA
503563 ATATAATAT
1 ATATAATAT
503572 GATATAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
10 8 0.19
11 20 0.47
12 14 0.33
13 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATATAATATAA
Found at i:503537 original size:12 final size:13
Alignment explanation
Indices: 503517--503579 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 13
503507 ATATAATATG
503517 AATATAATATAAA
1 AATATAATATAAA
503530 AA-ATAATA-AAA
1 AATATAATATAAA
*
503541 AATATATTATAAA
1 AATATAATATAAA
* *
503554 TATAT-ATATATAT
1 AATATAATATA-AA
*
503567 AATATGATATAAA
1 AATATAATATAAA
503580 TATACGGTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 5 0.12
12 15 0.38
13 15 0.38
14 5 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
AATATAATATAAA
Found at i:503576 original size:10 final size:9
Alignment explanation
Indices: 503504--503583 Score: 58
Period size: 9 Copynumber: 8.7 Consensus size: 9
503494 TCGTAATTTT
503504 TATATATAA
1 TATATATAA
503513 TATGAATATAA
1 TAT--ATATAA
* *
503524 TATAAAAAA
1 TATATATAA
* *
503533 TAATAAAAAA
1 T-ATATATAA
503543 TATATTATAA
1 TATA-TATAA
503553 -ATATAT-A
1 TATATATAA
503560 TATATATAA
1 TATATATAA
503569 TATGATATAA
1 TAT-ATATAA
503579 -ATATA
1 TATATA
503584 CGGTATTTGT
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
7 1 0.02
8 12 0.20
9 20 0.33
10 18 0.30
11 9 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (9 bp):
TATATATAA
Found at i:503576 original size:16 final size:15
Alignment explanation
Indices: 503504--503583 Score: 55
Period size: 16 Copynumber: 5.5 Consensus size: 15
503494 TCGTAATTTT
503504 TATATATAATATGA-A
1 TATATATAATAT-ATA
*
503519 TATAATATAA-A-AAA
1 TAT-ATATAATATATA
* *
503533 TA-ATAAAAAATATA
1 TATATATAATATATA
503547 T-TATA-AATATATA
1 TATATATAATATATA
503560 TATATATAATATGATA
1 TATATATAATAT-ATA
*
503576 TAAATATA
1 TATATATA
503584 CGGTATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
12 5 0.09
13 10 0.19
14 13 0.25
15 9 0.17
16 16 0.30
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TATATATAATATATA
Found at i:504832 original size:2 final size:2
Alignment explanation
Indices: 504825--504857 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
504815 CAAGTTTTAT
*
504825 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
504858 TTACATTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:505752 original size:23 final size:22
Alignment explanation
Indices: 505731--505774 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
505721 CCAACTTTTG
505731 ATTATATATTTTATTTATTTTTAA
1 ATTA-ATATTTTA-TTATTTTTAA
*
505755 ATTAATTTTTTATTATTTTT
1 ATTAATATTTTATTATTTTT
505775 TAATCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 7 0.37
24 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTAATATTTTATTATTTTTAA
Found at i:506175 original size:14 final size:14
Alignment explanation
Indices: 506156--506186 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
506146 TAAAATATAA
*
506156 TTTTTTATTTTTAT
1 TTTTTTAATTTTAT
506170 TTTTTTAATTTTAT
1 TTTTTTAATTTTAT
506184 TTT
1 TTT
506187 AAATATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTAATTTTAT
Found at i:506195 original size:20 final size:20
Alignment explanation
Indices: 506158--506197 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
506148 AAATATAATT
* * *
506158 TTTTATTTTTATTTTTTTAA
1 TTTTATTTTAAATATTTTAA
506178 TTTTATTTTAAATATTTTAA
1 TTTTATTTTAAATATTTTAA
506198 ATAATTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTTTAAATATTTTAA
Found at i:506840 original size:3 final size:3
Alignment explanation
Indices: 506832--506868 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
506822 ACGTGCAGGG
506832 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
506869 CACGTGCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:506922 original size:15 final size:15
Alignment explanation
Indices: 506880--506923 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
506870 ACGTGCAGAG
*
506880 ATAAATAATTTAAAT
1 ATAAATTATTTAAAT
506895 ATAAATT-TTTAAAT
1 ATAAATTATTTAAAT
**
506909 ATTTATTATTTAAAT
1 ATAAATTATTTAAAT
506924 TTATTTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAAATTATTTAAAT
Found at i:506948 original size:38 final size:36
Alignment explanation
Indices: 506902--506972 Score: 106
Period size: 38 Copynumber: 1.9 Consensus size: 36
506892 AATATAAATT
* *
506902 TTTAAATATTTATTATTTAAATTTATTTTGATTTTAA
1 TTTAAATATTTAATATTTAAATTAATTTT-ATTTTAA
506939 TTTATAATATTTAATATTTAAATTAATTTTATTT
1 TTTA-AATATTTAATATTTAAATTAATTTTATTT
506973 ATATGGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 8 0.26
38 23 0.74
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (36 bp):
TTTAAATATTTAATATTTAAATTAATTTTATTTTAA
Found at i:506952 original size:31 final size:31
Alignment explanation
Indices: 506908--506975 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
506898 AATTTTTAAA
** *
506908 TATTTAT--TATTTAA-ATTTATTTTGATTT
1 TATTTATAATATTTAATATTTAAATTAATTT
506936 TAATTTATAATATTTAATATTTAAATTAATTT
1 T-ATTTATAATATTTAATATTTAAATTAATTT
506968 TATTTATA
1 TATTTATA
506976 TGGATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 1 0.03
29 6 0.18
31 14 0.42
32 12 0.36
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (31 bp):
TATTTATAATATTTAATATTTAAATTAATTT
Found at i:507076 original size:17 final size:16
Alignment explanation
Indices: 507054--507093 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
507044 TTTAAAAATA
*
507054 ATTTAATAAATTTAGAT
1 ATTTAACAAATTTA-AT
*
507071 ATTTAACGAATTTAAT
1 ATTTAACAAATTTAAT
507087 ATTTAAC
1 ATTTAAC
507094 GAATATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (16 bp):
ATTTAACAAATTTAAT
Found at i:507090 original size:16 final size:17
Alignment explanation
Indices: 507062--507097 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
507052 TAATTTAATA
507062 AATTTAGATATTTAACG
1 AATTTAGATATTTAACG
507079 AATTTA-ATATTTAACG
1 AATTTAGATATTTAACG
507095 AAT
1 AAT
507098 ATTATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (17 bp):
AATTTAGATATTTAACG
Found at i:507804 original size:28 final size:28
Alignment explanation
Indices: 507751--507804 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
507741 TTTTTATTAA
* *
507751 AATTTTATTTTTATAATTAAATTTAAAT
1 AATTTTATTTTAATAATAAAATTTAAAT
*
507779 AATTTT-TTTTAATTATAAAATATTAA
1 AATTTTATTTTAATAATAAAAT-TTAA
507805 TTCGGATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTTTATTTTAATAATAAAATTTAAAT
Found at i:510131 original size:20 final size:21
Alignment explanation
Indices: 510081--510134 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
510071 ATTAAAAGAG
*
510081 TATAATTATTTT-TATTTATT
1 TATAATAATTTTATATTTATT
*
510101 TTTAATAATTTTATATTTATT
1 TATAATAATTTTATATTTATT
*
510122 TATAA-GATTTTAT
1 TATAATAATTTTAT
510135 TATAATTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TATAATAATTTTATATTTATT
Found at i:510661 original size:12 final size:12
Alignment explanation
Indices: 510644--510853 Score: 80
Period size: 12 Copynumber: 17.2 Consensus size: 12
510634 TGATAATTTT
*
510644 AAATATGATATA
1 AAATATAATATA
510656 AAATATAATAT-
1 AAATATAATATA
510667 AAA-ATAAT-TA
1 AAATATAATATA
510677 AAATATAATATA
1 AAATATAATATA
* *
510689 AAATATGACATA
1 AAATATAATATA
*
510701 ATAATA-AAAATA
1 A-AATATAATATA
**
510713 ATTTA-AATATA
1 AAATATAATATA
* *
510724 ATATA-AATTTA
1 AAATATAATATA
*
510735 TAAATATATTATA
1 -AAATATAATATA
*
510748 ATTTATATAATAT-
1 A--AATATAATATA
510761 AAATCATTAATATA
1 AAAT-A-TAATATA
* *
510775 TTAAATTTTATATA
1 --AAATATAATATA
*
510789 AATATATAATATTTT
1 AA-ATATAATA--TA
*
510804 AATTATAAT-TA
1 AAATATAATATA
*
510815 TAATATACATA-A
1 AAATATA-ATATA
*
510827 ACATATAA-ATA
1 AAATATAATATA
*
510838 TAATATGAATATA
1 AAATAT-AATATA
510851 AAA
1 AAA
510854 AATACATAAA
Statistics
Matches: 147, Mismatches: 30, Indels: 41
0.67 0.14 0.19
Matches are distributed among these distances:
9 1 0.01
10 9 0.06
11 38 0.26
12 46 0.31
13 26 0.18
14 20 0.14
15 3 0.02
16 4 0.03
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (12 bp):
AAATATAATATA
Found at i:510680 original size:21 final size:21
Alignment explanation
Indices: 510654--510730 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
510644 AAATATGATA
510654 TAAAATATAATATAAAATAAT
1 TAAAATATAATATAAAATAAT
510675 TAAAATATAATATAAAAT-A-
1 TAAAATATAATATAAAATAAT
* *
510694 TGACATAATAATA-AAAATAAT
1 TAAAAT-ATAATATAAAATAAT
*
510715 TTAAATATAATATAAA
1 TAAAATATAATATAAA
510731 TTTATAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 9 0.19
20 14 0.29
21 25 0.52
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (21 bp):
TAAAATATAATATAAAATAAT
Found at i:510683 original size:28 final size:28
Alignment explanation
Indices: 510651--510730 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 28
510641 TTTAAATATG
*
510651 ATATAAAATATAATATAAAATAATTAAA
1 ATATAAAATATAATATAAAATAATAAAA
* *
510679 ATATAATATAAAATATGACATAATAATAAAA
1 ATATAAAATATAATAT-A-A-AATAATAAAA
*
510710 ATAATTTAAATATAATATAAA
1 AT-A-TAAAATATAATATAAA
510731 TTTATAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
28 14 0.34
29 1 0.02
30 2 0.05
31 12 0.29
32 2 0.05
33 10 0.24
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (28 bp):
ATATAAAATATAATATAAAATAATAAAA
Found at i:510724 original size:11 final size:11
Alignment explanation
Indices: 510643--510851 Score: 92
Period size: 11 Copynumber: 19.8 Consensus size: 11
510633 TTGATAATTT
*
510643 TAAATATGATA
1 TAAATATAATA
510654 TAAAATATAATA
1 T-AAATATAATA
510666 TAAA-ATAAT-
1 TAAATATAATA
510675 TAAAATATAATA
1 T-AAATATAATA
510687 TAAA-AT-AT-
1 TAAATATAATA
* *
510695 GACATAATAATA
1 TAAAT-ATAATA
*
510707 -AAA-ATAATT
1 TAAATATAATA
510716 TAAATATAATA
1 TAAATATAATA
510727 TAAAT-T--TA
1 TAAATATAATA
*
510735 TAAATATATTA
1 TAAATATAATA
*
510746 T-AAT-TTATA
1 TAAATATAATA
510755 T-AATATAAATCA
1 TAAATAT-AAT-A
*
510767 TTAATAT-AT-
1 TAAATATAATA
* *
510776 TAAATTTTATA
1 TAAATATAATA
510787 TAAATAT-ATA
1 TAAATATAATA
* *
510797 -ATATTTTAATTA
1 TA-AATATAA-TA
*
510809 TAATTATAATA
1 TAAATATAATA
* *
510820 TACATAAACATA
1 TAAATATA-ATA
510832 TAAATATAATA
1 TAAATATAATA
*
510843 TGAATATAA
1 TAAATATAA
510852 AAAATACATA
Statistics
Matches: 153, Mismatches: 21, Indels: 48
0.69 0.09 0.22
Matches are distributed among these distances:
8 9 0.06
9 22 0.14
10 28 0.18
11 58 0.38
12 30 0.20
13 6 0.04
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (11 bp):
TAAATATAATA
Found at i:510756 original size:33 final size:33
Alignment explanation
Indices: 510710--510818 Score: 105
Period size: 32 Copynumber: 3.2 Consensus size: 33
510700 AATAATAAAA
510710 ATAATTTAAATATAATATAAATTTATAAATATATT
1 ATAATTT--ATATAATATAAATTTATAAATATATT
* *
510745 ATAATTTATATAATATAAA-TCATTAATATATT
1 ATAATTTATATAATATAAATTTATAAATATATT
* *
510777 A-AATTTTATATAAATATATAATATTTTAATTATAATT
1 ATAA-TTTATAT-AATATA-AAT-TTATAAATAT-ATT
510814 ATAAT
1 ATAAT
510819 ATACATAAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
31 2 0.03
32 19 0.31
33 18 0.30
34 2 0.03
35 7 0.11
36 6 0.10
37 5 0.08
38 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (33 bp):
ATAATTTATATAATATAAATTTATAAATATATT
Found at i:510810 original size:22 final size:19
Alignment explanation
Indices: 510731--510820 Score: 63
Period size: 20 Copynumber: 5.0 Consensus size: 19
510721 ATAATATAAA
* *
510731 TTTATA-AATATATTATAA
1 TTTATATAATATATAATAT
510749 TTTATATAATATA-AATCA-
1 TTTATATAATATATAAT-AT
510767 -TTA-AT-ATAT-TAA-AT
1 TTTATATAATATATAATAT
510781 TTTATATAAATATATAATAT
1 TTTATAT-AATATATAATAT
510801 TTTAATTATAAT-TATAATAT
1 TTT-A-TATAATATATAATAT
510821 ACATAAACAT
Statistics
Matches: 59, Mismatches: 1, Indels: 22
0.72 0.01 0.27
Matches are distributed among these distances:
13 1 0.02
15 9 0.15
16 4 0.07
17 3 0.05
18 12 0.20
19 10 0.17
20 13 0.22
21 4 0.07
22 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATATAATATATAATAT
Found at i:510838 original size:6 final size:6
Alignment explanation
Indices: 510651--510852 Score: 54
Period size: 6 Copynumber: 33.2 Consensus size: 6
510641 TTTAAATATG
* *
510651 ATATAA A-ATATA ATATAA A-ATAA TTA-AA ATAT-A ATATAAA ATATGAC
1 ATATAA ATATA-A ATATAA ATATAA ATATAA ATATAA ATAT-AA ATAT-AA
*
510698 ATA-ATA ATA-AA A-AT-A ATTTAA ATAT-A ATATAA ATTTATAA ATAT-A
1 ATATA-A ATATAA ATATAA ATATAA ATATAA ATATAA A--TATAA ATATAA
* * **
510743 TTATAA TTTATATA ATATAA ATCATTAA TATATTAA AT-TTT ATATAA
1 ATATAA -ATATA-A ATATAA AT-A-TAA -ATA-TAA ATATAA ATATAA
* * *
510790 ATATATA ATATTTTAA TTATAA TTAT-A ATATAC ATA-AA CATATAA ATAT-A
1 ATATA-A ATA---TAA ATATAA ATATAA ATATAA ATATAA -ATATAA ATATAA
*
510840 ATATGA ATATAA A
1 ATATAA ATATAA A
510853 AAATACATAA
Statistics
Matches: 150, Mismatches: 18, Indels: 56
0.67 0.08 0.25
Matches are distributed among these distances:
4 3 0.02
5 42 0.28
6 53 0.35
7 30 0.20
8 15 0.10
9 5 0.03
10 2 0.01
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (6 bp):
ATATAA
Found at i:512191 original size:17 final size:18
Alignment explanation
Indices: 512169--512203 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
512159 TATTAATATA
*
512169 AAAATT-TAATAGTATTT
1 AAAATTATAATAGAATTT
512186 AAAATTATAATAGAATTT
1 AAAATTATAATAGAATTT
512204 TTTAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
AAAATTATAATAGAATTT
Found at i:512354 original size:14 final size:14
Alignment explanation
Indices: 512331--512380 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
512321 ATTTTTAATA
*
512331 ATATTTTATTTATT
1 ATATTATATTTATT
512345 ATATTATATTTA-T
1 ATATTATATTTATT
512358 A-A-TATATTT-TT
1 ATATTATATTTATT
*
512369 ATATCATATTTA
1 ATATTATATTTA
512381 AAATAATCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
11 9 0.30
12 2 0.07
13 8 0.27
14 11 0.37
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTATATTTATT
Found at i:512371 original size:24 final size:25
Alignment explanation
Indices: 512337--512385 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
512327 AATAATATTT
* *
512337 TATTTATTATATTATATTTATAATA
1 TATTTATTATATCATATTTAAAATA
512362 TATTT-TTATATCATATTTAAAATA
1 TATTTATTATATCATATTTAAAATA
512386 ATCAGTAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTTATTATATCATATTTAAAATA
Found at i:512936 original size:3 final size:3
Alignment explanation
Indices: 512928--512969 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
512918 TGAAAAGCTA
512928 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
512970 CTGAAGCTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:516821 original size:26 final size:27
Alignment explanation
Indices: 516787--516852 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 27
516777 AATTTTATTT
*
516787 TATTATTTATTATATT-ATTAAAATAA
1 TATTTTTTATTATATTAATTAAAATAA
*
516813 TATTTTTTA-TA-ATTAAATTTAAATAA
1 TATTTTTTATTATATT-AATTAAAATAA
*
516839 AATATTTTTATTAT
1 TAT-TTTTTATTAT
516853 TAAATTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 3 0.09
25 2 0.06
26 19 0.59
27 6 0.19
28 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TATTTTTTATTATATTAATTAAAATAA
Found at i:516870 original size:27 final size:27
Alignment explanation
Indices: 516807--516858 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
516797 TATATTATTA
*
516807 AAATAATAT-TTTTTATAATTAAATTT
1 AAATAAAATATTTTTATAATTAAATTT
*
516833 AAATAAAATATTTTTATTATTAAATT
1 AAATAAAATATTTTTATAATTAAATT
516859 ATAATTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AAATAAAATATTTTTATAATTAAATTT
Found at i:525981 original size:108 final size:107
Alignment explanation
Indices: 525866--526082 Score: 355
Period size: 108 Copynumber: 2.0 Consensus size: 107
525856 AAAGCAGTAC
* *
525866 ATTTCTCTGGAAATTAAACCTGATCTCAGGCTCAATAAAGACATTTTCTAAAATAGTCTATTTAT
1 ATTTCTCTGGAAATTAAACCTGATCTCAGGCTCAATAAAGACATTTCCTAAAATAATCTATTTAT
525931 ATAACCAAAATTATGCCCAGAAAAGAGCCAAAA-AATTTGCTCA
66 ATAACCAAAATTATGCCCA-AAAAGAGCCAAAAGAA-TTGCTCA
* * *
525974 ATTTCTCTGGAAATTAAAGCTGATCTCAGGCTCAATAAAGACATTTCCTAAAATAATCTGTTTGT
1 ATTTCTCTGGAAATTAAACCTGATCTCAGGCTCAATAAAGACATTTCCTAAAATAATCTATTTAT
*
526039 ATAACCAAAATTATGCCCAAAACGAGCCAAAAGAATTGCTCA
66 ATAACCAAAATTATGCCCAAAAAGAGCCAAAAGAATTGCTCA
526081 AT
1 AT
526083 AAGTTAATTT
Statistics
Matches: 102, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
107 21 0.21
108 81 0.79
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (107 bp):
ATTTCTCTGGAAATTAAACCTGATCTCAGGCTCAATAAAGACATTTCCTAAAATAATCTATTTAT
ATAACCAAAATTATGCCCAAAAAGAGCCAAAAGAATTGCTCA
Found at i:528426 original size:19 final size:20
Alignment explanation
Indices: 528399--528444 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
528389 GGCGATCGGA
* *
528399 TTTTCTATTTTCT-ATTTTT
1 TTTTTTATTATCTAATTTTT
528418 TTTTTTATTATCTGAATTTTT
1 TTTTTTATTATCT-AATTTTT
528439 TTTTTT
1 TTTTTT
528445 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
21 12 0.52
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTTTATTATCTAATTTTT
Found at i:529249 original size:25 final size:26
Alignment explanation
Indices: 529206--529256 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
529196 AAAACCTGAT
529206 TTATTATTTATAATAATATTAAAATA
1 TTATTATTTATAATAATATTAAAATA
* *
529232 TTATT-TTTATAATTATATTTAAATA
1 TTATTATTTATAATAATATTAAAATA
529257 AAAGTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTATTATTTATAATAATATTAAAATA
Found at i:543742 original size:24 final size:23
Alignment explanation
Indices: 543678--543742 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
543668 ATATTTTTAA
543678 TTTATTTTTAATTTAATTATAAT
1 TTTATTTTTAATTTAATTATAAT
* * *
543701 TATTAATTTTGATATTAATATATTAT
1 T-TTATTTTTAAT-TTAAT-TATAAT
*
543727 TTTATTTTTTATTTAA
1 TTTATTTTTAATTTAA
543743 AATAAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 13 0.38
25 14 0.41
26 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTATTTTTAATTTAATTATAAT
Found at i:544011 original size:11 final size:11
Alignment explanation
Indices: 543959--543994 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
543949 TGTATACTTA
543959 AATTATAAT-AT
1 AATT-TAATAAT
543970 AATTTAATAAT
1 AATTTAATAAT
543981 AATTTAATAAT
1 AATTTAATAAT
543992 AAT
1 AAT
543995 AAAAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:544265 original size:26 final size:27
Alignment explanation
Indices: 544218--544270 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
544208 ATAATTTTTT
544218 AATTTATATTTAAATAATTAAAAAATA
1 AATTTATATTTAAATAATTAAAAAATA
*
544245 AATTTATA-TTAATATAATAAAAAAAT
1 AATTTATATTTAA-ATAATTAAAAAAT
544271 TTAAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AATTTATATTTAAATAATTAAAAAATA
Found at i:546324 original size:2 final size:2
Alignment explanation
Indices: 546317--546355 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
546307 GTAGCAATTC
546317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
546356 GTAAGCTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:549913 original size:32 final size:32
Alignment explanation
Indices: 549876--549949 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
549866 GAAGAAATTA
*
549876 AAATATAATGATTATATATCTTAAAATTTATAT
1 AAATATAATGATTA-ATATATTAAAATTTATAT
* *
549909 -AATATGAATTATTAATGTATTAAAATTTATAT
1 AAATAT-AATGATTAATATATTAAAATTTATAT
549941 AAATATAAT
1 AAATATAAT
549950 ATATTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 24 0.67
33 12 0.33
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (32 bp):
AAATATAATGATTAATATATTAAAATTTATAT
Found at i:550482 original size:28 final size:29
Alignment explanation
Indices: 550422--550482 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
550412 TTATCGAAAT
*
550422 TAAATTAAATTTTATTTTTTATAACATAA
1 TAAAATAAATTTTATTTTTTATAACATAA
550451 -AAAATAAATTTT-TTATTTT-TAA-ATTAA
1 TAAAATAAATTTTATT-TTTTATAACA-TAA
550478 TAAAA
1 TAAAA
550483 AATTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
26 1 0.04
27 8 0.29
28 19 0.68
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAAATAAATTTTATTTTTTATAACATAA
Found at i:551180 original size:20 final size:22
Alignment explanation
Indices: 551143--551184 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
551133 AATTTATTAA
551143 ATAAAAATTATATTTTTTATTT
1 ATAAAAATTATATTTTTTATTT
551165 ATAAAAA-TAT-TTTTTTATTT
1 ATAAAAATTATATTTTTTATTT
551185 TTTAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 3 0.15
22 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATAAAAATTATATTTTTTATTT
Found at i:551552 original size:8 final size:8
Alignment explanation
Indices: 551539--551629 Score: 57
Period size: 8 Copynumber: 11.2 Consensus size: 8
551529 AATAAATTTG
551539 ATATAAAT
1 ATATAAAT
551547 ATATAAAT
1 ATATAAAT
*
551555 -TATTAAT
1 ATATAAAT
551562 ATATTAAAATTT
1 ATA-T-AAA--T
551574 ATATAAAT
1 ATATAAAT
551582 ATA-AAAT
1 ATATAAAT
*
551589 ATTTAAA-
1 ATATAAAT
*
551596 ATATGAATT
1 ATAT-AAAT
551605 ATGATAAA-
1 AT-ATAAAT
551613 ATA-AAAT
1 ATATAAAT
*
551620 ATAAAAAT
1 ATATAAAT
551628 AT
1 AT
551630 TATACAAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
6 3 0.05
7 19 0.29
8 27 0.41
9 5 0.08
10 7 0.11
11 1 0.02
12 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (8 bp):
ATATAAAT
Found at i:551580 original size:27 final size:26
Alignment explanation
Indices: 551546--551597 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
551536 TTGATATAAA
*
551546 TATATAAAT-TATTAATATATTAAAATT
1 TATATAAATATA-AAATAT-TTAAAATT
551573 TATATAAATATAAAATATTTAAAAT
1 TATATAAATATAAAATATTTAAAAT
551598 ATGAATTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 14 0.61
28 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TATATAAATATAAAATATTTAAAATT
Found at i:551586 original size:17 final size:17
Alignment explanation
Indices: 551532--551588 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
551522 AAAATAAAAT
551532 AAATTTGATATAAATATA
1 AAATTT-ATATAAATATA
551550 TAAA-TTAT-TAATATATTA
1 -AAATTTATATAA-ATA-TA
551568 AAATTTATATAAATATA
1 AAATTTATATAAATATA
551585 AAAT
1 AAAT
551589 ATTTAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.09
17 14 0.41
18 11 0.32
19 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:551619 original size:31 final size:30
Alignment explanation
Indices: 551572--551629 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
551562 ATATTAAAAT
*
551572 TTATATAAATATAAAATATTTAAAATATGAA
1 TTATATAAATATAAAATA-TAAAAATATGAA
551603 TTATGATAAA-ATAAAATATAAAAATAT
1 TTAT-ATAAATATAAAATATAAAAATAT
551630 TATACAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 12 0.48
32 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (30 bp):
TTATATAAATATAAAATATAAAAATATGAA
Found at i:552484 original size:32 final size:32
Alignment explanation
Indices: 552443--552508 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
552433 TAAGTTTGCT
552443 TTGACATAAATGACAAAAACAAAGCATGACAG
1 TTGACATAAATGACAAAAACAAAGCATGACAG
*
552475 TTGACATAAATGACAAGAACAAAGCATGACAG
1 TTGACATAAATGACAAAAACAAAGCATGACAG
552507 TT
1 TT
552509 TCATGTCTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (32 bp):
TTGACATAAATGACAAAAACAAAGCATGACAG
Found at i:554274 original size:44 final size:44
Alignment explanation
Indices: 554226--554386 Score: 118
Period size: 46 Copynumber: 3.5 Consensus size: 44
554216 TTTAGTATTC
* *
554226 ATTTATTTATATTATAATTATATATTTTATCATGTT-ATAATTAT
1 ATTTATATATATTATAATTATATATTTTATCATATTAATAATT-T
*
554270 ATTTA-ATATATTTATATTTATATTAATTTTAAT-ATATTAATAATTT
1 ATTTATATATA-TTATAATTATA-T-ATTTT-ATCATATTAATAATTT
* * * *
554316 ATATTATATAAATTTTAAATTATATATTTATATCAAATT-AT-TTTT
1 AT-TTATATATATTAT-AATTATATATTT-TATCATATTAATAATTT
554361 AATTTTATATATATTAT-ATTCATATA
1 -A-TTTATATATATTATAATT-ATATA
554387 ATTATATCTA
Statistics
Matches: 94, Mismatches: 10, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
43 4 0.04
44 18 0.19
45 9 0.10
46 32 0.34
47 21 0.22
48 10 0.11
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (44 bp):
ATTTATATATATTATAATTATATATTTTATCATATTAATAATTT
Found at i:554284 original size:21 final size:20
Alignment explanation
Indices: 554226--554293 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 20
554216 TTTAGTATTC
*
554226 ATTTATTTATATTATAATTAT
1 ATTTATATAT-TTATAATTAT
*
554247 ATATTTTATCATGTTATAATTAT
1 AT-TTATAT-AT-TTATAATTAT
*
554270 ATTTAATATATTTATATTTAT
1 ATTT-ATATATTTATAATTAT
554291 ATT
1 ATT
554294 AATTTTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 14 0.36
22 8 0.21
23 17 0.44
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (20 bp):
ATTTATATATTTATAATTAT
Found at i:554285 original size:6 final size:6
Alignment explanation
Indices: 554229--554348 Score: 56
Period size: 6 Copynumber: 19.5 Consensus size: 6
554219 AGTATTCATT
*
554229 TATTTA TA-TTA TAATTATA TATTTTA TCATGTTA TAATTA TATTTA -A--TA
1 TATTTA TATTTA T-ATT-TA TA-TTTA T-AT-TTA TATTTA TATTTA TATTTA
* **
554278 TATTTA TATTTA TATTAA T-TTTAA TATATTAA TAATTTA TA-TTA TATAAA
1 TATTTA TATTTA TATTTA TATTT-A TAT-TT-A T-ATTTA TATTTA TATTTA
*
554328 T-TTTA AATTATA TATTTA TAT
1 TATTTA TATT-TA TATTTA TAT
554349 CAAATTATTT
Statistics
Matches: 88, Mismatches: 10, Indels: 32
0.68 0.08 0.25
Matches are distributed among these distances:
3 2 0.02
4 1 0.01
5 14 0.16
6 37 0.42
7 15 0.17
8 17 0.19
9 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (6 bp):
TATTTA
Found at i:554315 original size:27 final size:26
Alignment explanation
Indices: 554271--554321 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
554261 TATAATTATA
*
554271 TTTAATATATTTATATTTATATTAAT
1 TTTAATATATTAATATTTATATTAAT
554297 TTTAATATATTAATAATTTATATTA
1 TTTAATATATTAAT-ATTTATATTA
554322 TATAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTAATATATTAATATTTATATTAAT
Found at i:554332 original size:16 final size:16
Alignment explanation
Indices: 554280--554341 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
554270 ATTTAATATA
*
554280 TTTATATTTATATTAAT
1 TTTATA-TTATATAAAT
*
554297 TTTA-A-TATATTAATAA
1 TTTATATTATA-TAA-AT
554313 TTTATATTATATAAAT
1 TTTATATTATATAAAT
*
554329 TTTAAATTATATA
1 TTTATATTATATA
554342 TTTATATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 4 0.11
15 2 0.05
16 19 0.51
17 8 0.22
18 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATATTATATAAAT
Found at i:554689 original size:20 final size:19
Alignment explanation
Indices: 554649--554690 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
554639 TATATTATTT
* *
554649 TTTAATATTTATAATTGAA
1 TTTAATATTTATAAGTAAA
554668 TTTAATTATTTATAAGTAAA
1 TTTAA-TATTTATAAGTAAA
554688 TTT
1 TTT
554691 TTTATATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTAATATTTATAAGTAAA
Found at i:556853 original size:2 final size:2
Alignment explanation
Indices: 556846--556879 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
556836 AAACAATCAG
556846 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
556880 TTATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:560098 original size:43 final size:47
Alignment explanation
Indices: 560011--560108 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 47
560001 TTTCGTTAGA
*
560011 ATTAATAT-TTAATAATTAAAAAATATTTTTTATAAAACATATAAAT
1 ATTAATATATAAATAATTAAAAAATATTTTTTATAAAACATATAAAT
* *
560057 ATTAATATATAAATAATT-TAAAAT-TTTTTTAT-TAA-ATATAAAT
1 ATTAATATATAAATAATTAAAAAATATTTTTTATAAAACATATAAAT
*
560100 AATAA-ATAT
1 ATTAATATAT
560109 TGATAGTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
42 4 0.09
43 12 0.26
44 2 0.04
45 8 0.17
46 13 0.28
47 8 0.17
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (47 bp):
ATTAATATATAAATAATTAAAAAATATTTTTTATAAAACATATAAAT
Found at i:560661 original size:36 final size:34
Alignment explanation
Indices: 560617--560694 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 34
560607 TTAAAAATAA
560617 TTAA-ATTAA-TATAAAATAAAATATATGATAAATTT
1 TTAATATTAATTATAAAATAAAA-ATATG-T-AATTT
*
560652 TTAATATTAATTGTAAAATAAAAATATGTAATTT
1 TTAATATTAATTATAAAATAAAAATATGTAATTT
560686 TTAAATATT
1 TT-AATATT
560695 TATAAGATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
34 7 0.18
35 11 0.28
36 10 0.26
37 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (34 bp):
TTAATATTAATTATAAAATAAAAATATGTAATTT
Found at i:562030 original size:13 final size:15
Alignment explanation
Indices: 562003--562034 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
561993 TTTTAAATAT
562003 AAAAATATAATTTTA
1 AAAAATATAATTTTA
562018 AAAAATAT-A-TTTA
1 AAAAATATAATTTTA
562031 AAAA
1 AAAA
562035 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATATAATTTTA
Found at i:562617 original size:23 final size:22
Alignment explanation
Indices: 562569--562617 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
562559 ATATTTAAAA
*
562569 ATTAAATAGTAAATTTAAATAGT
1 ATTAAATA-TAAATTTAAATAAT
562592 ATTAAAT-TAAATTTAAGTATAAT
1 ATTAAATATAAATTTAA--ATAAT
562615 ATT
1 ATT
562618 TTTAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (22 bp):
ATTAAATATAAATTTAAATAAT
Found at i:562645 original size:21 final size:21
Alignment explanation
Indices: 562621--562678 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
562611 TAATATTTTT
*
562621 AAATT-TAATTTGAATTAATTA
1 AAATTATAATTT-AATTAATAA
*
562642 AAATTATTATTTAATTAATAA
1 AAATTATAATTTAATTAATAA
*
562663 AAA--ATATTTTAATTAA
1 AAATTATAATTTAATTAA
562679 ATTAAATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 11 0.34
21 16 0.50
22 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATTATAATTTAATTAATAA
Found at i:563926 original size:2 final size:2
Alignment explanation
Indices: 563915--563949 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
563905 TGTTAGTGTC
563915 AT AT -T 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 AT AT
563950 TCATTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:565194 original size:46 final size:46
Alignment explanation
Indices: 565107--565205 Score: 137
Period size: 46 Copynumber: 2.1 Consensus size: 46
565097 TATATATATT
*
565107 GATATTTAAAATTTTGAATCCAAACTTATTGATATAATCTTTTAAGA
1 GATATTTAAAATTTTGAAT-CAAACTTATCGATATAATCTTTTAAGA
* * *
565154 GATATTTAAAGTTTTGAAT-AGAACTTATCGATATCATCTTTTAATA
1 GATATTTAAAATTTTGAATCA-AACTTATCGATATAATCTTTTAAGA
565200 GATATT
1 GATATT
565206 AAATATACGA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
45 1 0.02
46 28 0.60
47 18 0.38
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.43
Consensus pattern (46 bp):
GATATTTAAAATTTTGAATCAAACTTATCGATATAATCTTTTAAGA
Found at i:566348 original size:20 final size:20
Alignment explanation
Indices: 566323--566424 Score: 63
Period size: 18 Copynumber: 5.2 Consensus size: 20
566313 CCATCATGAA
566323 TATATAATATATTTATAATT
1 TATATAATATATTTATAATT
* *
566343 TATATATTA-ATATTATATTT
1 TATATAATATAT-TTATAATT
*
566363 ATATTATAATTATATTTAAAATT
1 -TA-TATAA-TATATTTATAATT
*
566386 T-TAT-ATAT-TTATATAAGT
1 TATATAATATATT-TATAATT
* *
566404 T-T-TAATATATTAAAAATT
1 TATATAATATATTTATAATT
566422 TAT
1 TAT
566425 TTTATATAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
17 3 0.05
18 19 0.30
19 6 0.10
20 18 0.29
21 2 0.03
22 5 0.08
23 8 0.13
24 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (20 bp):
TATATAATATATTTATAATT
Found at i:566365 original size:17 final size:17
Alignment explanation
Indices: 566345--566380 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
566335 TTATAATTTA
566345 TATATTA-ATATTATATT
1 TATATTATA-ATTATATT
566362 TATATTATAATTATATT
1 TATATTATAATTATATT
566379 TA
1 TA
566381 AAATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTATAATTATATT
Found at i:566377 original size:11 final size:11
Alignment explanation
Indices: 566325--566378 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
566315 ATCATGAATA
566325 TATAA-TATATT
1 TATAATTATA-T
566336 TATAATT-TA-
1 TATAATTATAT
566345 TAT-ATTAATAT
1 TATAATT-ATAT
*
566356 TATATTTATAT
1 TATAATTATAT
566367 TATAATTATAT
1 TATAATTATAT
566378 T
1 T
566379 TAAAATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 2 0.06
11 25 0.69
12 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATAATTATAT
Found at i:566394 original size:16 final size:17
Alignment explanation
Indices: 566373--566422 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 17
566363 ATATTATAAT
566373 TATATTTAAAATTTT-A
1 TATATTTAAAATTTTAA
566389 TATATTTATATAAGTTTTAA
1 TATATTTA-A-AA-TTTTAA
*
566409 TATATTAAAAATTT
1 TATATTTAAAATTT
566423 ATTTTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 8 0.28
17 4 0.14
18 4 0.14
19 5 0.17
20 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TATATTTAAAATTTTAA
Found at i:567098 original size:23 final size:24
Alignment explanation
Indices: 567063--567120 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
567053 ATATCATATT
* * * *
567063 TAAATTATTAATTTTTTATTATTA
1 TAAATAATAAATTTTTAATAATTA
*
567087 TAAA-AATAAATTTTTAATAATTT
1 TAAATAATAAATTTTTAATAATTA
567110 TAAATAATAAA
1 TAAATAATAAA
567121 ATAAATTTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATAATAAATTTTTAATAATTA
Found at i:567187 original size:14 final size:15
Alignment explanation
Indices: 567151--567181 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
567141 ATTCGAACTT
567151 AAAAATTTTTAAATA
1 AAAAATTTTTAAATA
567166 AAAAATTTTTAAATA
1 AAAAATTTTTAAATA
567181 A
1 A
567182 TTATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAAATTTTTAAATA
Found at i:567733 original size:31 final size:30
Alignment explanation
Indices: 567668--567727 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
567658 TAACCATATT
*
567668 TAAATTATTATATTTTACATAAATTTTAATA
1 TAAATAATTATA-TTTACATAAATTTTAATA
*
567699 TAAATAATTATA-TTATATAAATTTTAATA
1 TAAATAATTATATTTACATAAATTTTAATA
567728 AATAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
31 11 0.41
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
TAAATAATTATATTTACATAAATTTTAATA
Found at i:568278 original size:19 final size:21
Alignment explanation
Indices: 568244--568282 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
568234 TTTTATTAAT
568244 ATAATATGATTAAATTTATTG
1 ATAATATGATTAAATTTATTG
568265 ATAATAT-A-TAAATTTATT
1 ATAATATGATTAAATTTATT
568283 TATTATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
ATAATATGATTAAATTTATTG
Found at i:568464 original size:3 final size:3
Alignment explanation
Indices: 568456--568492 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
568446 ACAAAAAATA
568456 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
568493 TTACTCATCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:569943 original size:23 final size:23
Alignment explanation
Indices: 569924--569978 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
569914 TCGAATTATT
569924 ATTTAATAATAAAAATAATTTAA
1 ATTTAATAATAAAAATAATTTAA
* *
569947 ATTTAATTATAAAAA-ATATATAA
1 ATTTAATAATAAAAATA-ATTTAA
569970 ATATTAATA
1 AT-TTAATA
569979 TAATATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 21 0.78
24 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTAATAATAAAAATAATTTAA
Found at i:571147 original size:14 final size:13
Alignment explanation
Indices: 571123--571155 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
571113 AAATATTTAA
571123 AAAATAAAAAATT
1 AAAATAAAAAATT
571136 AAAATAATAAAATT
1 AAAATAA-AAAATT
571150 AAAATA
1 AAAATA
571156 TTATACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAAAAATT
Found at i:571758 original size:36 final size:35
Alignment explanation
Indices: 571692--571764 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 35
571682 AATTTATCAT
*
571692 AAATAAAATAATATTATTTTAATTAAAAATTAATAA
1 AAATAAAATAAAATTATTTTAATTAAAAATTAA-AA
*
571728 AAATAAAATAAAATTATTTTAA-TATGAAATTAAAA
1 AAATAAAATAAAATTATTTTAATTA-AAAATTAAAA
571763 AA
1 AA
571765 TATTTATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (35 bp):
AAATAAAATAAAATTATTTTAATTAAAAATTAAAA
Found at i:573308 original size:27 final size:27
Alignment explanation
Indices: 573246--573298 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
573236 TCGTGTTATT
*
573246 ATTTTAAAATATTTAATTTAATTTGTTTA
1 ATTTT-AAATATTTAATTTAAGTTG-TTA
573275 ATTTTAAAT-TTTAATTTAAGTTGT
1 ATTTTAAATATTTAATTTAAGTTGT
573299 AATCATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 13 0.57
28 4 0.17
29 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (27 bp):
ATTTTAAATATTTAATTTAAGTTGTTA
Found at i:573335 original size:38 final size:37
Alignment explanation
Indices: 573276--573403 Score: 121
Period size: 38 Copynumber: 3.3 Consensus size: 37
573266 ATTTGTTTAA
* * *
573276 TTTTAAATTTTAATTTAAGTTGTAATCATTTAATTAT
1 TTTTAAATTTAAATTAAAGTTGTAATCATCTAATTAT
* **
573313 TTTTTAATTTAAATTAAGAGTTGTAATTGTCTAATTAT
1 TTTTAAATTTAAATTAA-AGTTGTAATCATCTAATTAT
* * *
573351 TTTAAAACTTTAATTTAATTAGTTTTTAATCATCTAATTAT
1 TTTTAAA-TTTAAATTAA--AG-TTGTAATCATCTAATTAT
*
573392 TTTTAAAATTAA
1 TTTTAAATTTAA
573404 TTATAATTAT
Statistics
Matches: 72, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
37 14 0.19
38 22 0.31
39 9 0.12
40 6 0.08
41 21 0.29
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (37 bp):
TTTTAAATTTAAATTAAAGTTGTAATCATCTAATTAT
Found at i:573370 original size:22 final size:21
Alignment explanation
Indices: 573344--573436 Score: 67
Period size: 22 Copynumber: 4.7 Consensus size: 21
573334 TGTAATTGTC
573344 TAATTA-TTTTAAAACTTTAATT
1 TAATTAGTTTTAAAA--TTAATT
* * *
573366 TAATTAGTTTT-TAA-TCATC
1 TAATTAGTTTTAAAATTAATT
*
573385 TAATTATTTTTAAAATTAATT
1 TAATTAGTTTTAAAATTAATT
573406 ATAATTA-TTTTAAAA-T--TT
1 -TAATTAGTTTTAAAATTAATT
573424 TAATTA-TTTTAAA
1 TAATTAGTTTTAAA
573437 TTCCTAAACT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
17 13 0.22
18 2 0.03
19 13 0.22
20 3 0.05
21 11 0.18
22 14 0.23
23 4 0.07
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (21 bp):
TAATTAGTTTTAAAATTAATT
Found at i:573406 original size:16 final size:17
Alignment explanation
Indices: 573365--573407 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
573355 AAACTTTAAT
*
573365 TTAATTAGTTTTTAATCA
1 TTAATTA-TTTTTAATAA
573383 TCTAATTATTTTTAA-AA
1 T-TAATTATTTTTAATAA
573400 TTAATTAT
1 TTAATTAT
573408 AATTATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 2 0.09
18 8 0.35
19 6 0.26
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAATTATTTTTAATAA
Found at i:573427 original size:17 final size:17
Alignment explanation
Indices: 573402--573436 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
573392 TTTTAAAATT
573402 AATTATAATTATTTTAA
1 AATTATAATTATTTTAA
*
573419 AATTTTAATTATTTTAA
1 AATTATAATTATTTTAA
573436 A
1 A
573437 TTCCTAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTATAATTATTTTAA
Found at i:573586 original size:39 final size:37
Alignment explanation
Indices: 573503--573596 Score: 100
Period size: 39 Copynumber: 2.5 Consensus size: 37
573493 AGATTACAAC
* * *
573503 TTAAATTTTAAAATAATTAAATTATTATAACCTTTAAT
1 TTAAATTTTAAAATAATTAAATGATTACAA-CTTCAAT
*
573541 TTAAATTTTAAAAATAATTAGATGATTACAA-TTCAAT
1 TTAAATTTT-AAAATAATTAAATGATTACAACTTCAAT
* *
573578 TTAAAAATTTAAATTAATT
1 TT-AAATTTTAAAATAATT
573597 TTTTATAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
37 15 0.31
38 15 0.31
39 18 0.38
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (37 bp):
TTAAATTTTAAAATAATTAAATGATTACAACTTCAAT
Found at i:580055 original size:12 final size:13
Alignment explanation
Indices: 580027--580064 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
580017 TATCAGTTCG
580027 ATTTAATAAATTT
1 ATTTAATAAATTT
580040 ATTTAATAAA-TT
1 ATTTAATAAATTT
*
580052 ATTTTAT-AATTT
1 ATTTAATAAATTT
580064 A
1 A
580065 AATTAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 2 0.09
12 11 0.48
13 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTAATAAATTT
Found at i:580068 original size:30 final size:31
Alignment explanation
Indices: 580033--580092 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
580023 TTCGATTTAA
*
580033 TAAATTTATTT-AATAAATTATTT-TATAATT
1 TAAATTAATTTAAAT-AATTATTTATATAATT
580063 TAAATTAATTTAAATAATTATTTATATAAT
1 TAAATTAATTTAAATAATTATTTATATAAT
580093 AAATAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TAAATTAATTTAAATAATTATTTATATAATT
Found at i:580111 original size:40 final size:36
Alignment explanation
Indices: 580067--580147 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 36
580057 ATAATTTAAA
* *
580067 TTAATTTAAATAATTATTTATATAATAAATAATATATTTT
1 TTAATTT-AATAA-TATATAT-TAATAAATAA-ATAATTT
*
580107 TTAATTTAATTATATATATTAATAAATAAATAATTT
1 TTAATTTAATAATATATATTAATAAATAAATAATTT
580143 TTAAT
1 TTAAT
580148 ATTATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 11 0.29
37 10 0.26
38 6 0.16
39 4 0.11
40 7 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TTAATTTAATAATATATATTAATAAATAAATAATTT
Found at i:580125 original size:36 final size:36
Alignment explanation
Indices: 580077--580147 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
580067 TTAATTTAAA
* *
580077 TAATTATTTATA-TAATAAATAATATATTTTTTAATT
1 TAATTATATATATTAATAAATAA-ATAATTTTTAATT
580113 TAATTATATATATTAATAAATAAATAATTTTTAAT
1 TAATTATATATATTAATAAATAAATAATTTTTAAT
580148 ATTATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 22 0.69
37 10 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TAATTATATATATTAATAAATAAATAATTTTTAATT
Found at i:586520 original size:2 final size:2
Alignment explanation
Indices: 586513--586542 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
586503 AAATTCAAAT
586513 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
586543 CACACACGGT
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:587114 original size:3 final size:3
Alignment explanation
Indices: 587106--587139 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
587096 CCAATCTCAG
587106 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
587140 CATCAATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:590371 original size:2 final size:2
Alignment explanation
Indices: 590364--590398 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
590354 CAAGTACAAC
590364 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
590399 TGTAGTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:593055 original size:227 final size:226
Alignment explanation
Indices: 592659--593109 Score: 726
Period size: 227 Copynumber: 2.0 Consensus size: 226
592649 CCCTGTCTAG
* *
592659 AGTACTAATCTAGCACCTACTATCAAAGATTTAAACAATGTGAAAGATTCTCAAGTTATTTACTA
1 AGTACTAATCTAACACCTACTACCAAAGATTTAAACAATGTGAAAGATTCTCAAGTTATTTACTA
* * *
592724 TTGCTAGTTTGTTATAGCATGCAAACATAGAACAAATAATGGATATCTGAGAGCAGGAGAGAAAA
66 TTGCTAGATTATTATAGCATGCAAACATAGAACAAATAATGGATATCTGAGAGCAGAAGAGAAAA
* * * *
592789 TAAAGAAAAGCCACCATAATTTCCATCATATTGCAATTCAATGAAAATATATGATTGGCTTGTTT
131 TAAAGAAAAGCCACCATAATTTCCATCATATTACAATTCAATGAAAATATATAATTAGCATGTTT
*
592854 CAGCCTTTTTTTTTTTTTTAATTTTCATACTAA
196 CAGCC-TTTTTTTTTTCTT-ATTTTCATACTAA
* * *
592887 AGTACTAATCTAATACAC-ACTACCAAAGATTTAAACTATGTGAAAGATTCTCCAGTTATTTACT
1 AGTACTAATCTAACAC-CTACTACCAAAGATTTAAACAATGTGAAAGATTCTCAAGTTATTTACT
*
592951 ATTGTTA-ATTATTATAGCATGCAAACATAGAACAAATAATGGATATCTGAGAGCAGAAGAGAAA
65 ATTGCTAGATTATTATAGCATGCAAACATAGAACAAATAATGGATATCTGAGAGCAGAAGAGAAA
*
593015 ATAAAGAAAATCCACCATAATTTCCATCATATTACAATTCAATGAAAATATATAATTAGCATGTT
130 ATAAAGAAAAGCCACCATAATTTCCATCATATTACAATTCAATGAAAATATATAATTAGCATGTT
593080 TCAGCCTTTTTTTTTTCTTATTTTCATACT
195 TCAGCCTTTTTTTTTTCTTATTTTCATACT
593110 CTACTCCAAC
Statistics
Matches: 207, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
225 11 0.05
226 12 0.06
227 120 0.58
228 63 0.30
229 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.35
Consensus pattern (226 bp):
AGTACTAATCTAACACCTACTACCAAAGATTTAAACAATGTGAAAGATTCTCAAGTTATTTACTA
TTGCTAGATTATTATAGCATGCAAACATAGAACAAATAATGGATATCTGAGAGCAGAAGAGAAAA
TAAAGAAAAGCCACCATAATTTCCATCATATTACAATTCAATGAAAATATATAATTAGCATGTTT
CAGCCTTTTTTTTTTCTTATTTTCATACTAA
Found at i:593699 original size:2 final size:2
Alignment explanation
Indices: 593694--593720 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
593684 ATTCACTGAC
593694 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
593721 CTTGAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:596006 original size:18 final size:20
Alignment explanation
Indices: 595973--596009 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
595963 ATATTTTGTG
595973 TAATTATATAAATTAAAAAA
1 TAATTATATAAATTAAAAAA
595993 TAATTA-AT-AATTAAAAA
1 TAATTATATAAATTAAAAA
596010 TATTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAATTATATAAATTAAAAAA
Found at i:596349 original size:30 final size:30
Alignment explanation
Indices: 596315--596374 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
596305 TATTTACCTA
596315 ATAAAAAATAAACTTATTCCAATGTTGAAT
1 ATAAAAAATAAACTTATTCCAATGTTGAAT
596345 ATAAAAAATAAACTTATTCCAATGTTGAAT
1 ATAAAAAATAAACTTATTCCAATGTTGAAT
596375 TTCAGACTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (30 bp):
ATAAAAAATAAACTTATTCCAATGTTGAAT
Found at i:602011 original size:6 final size:6
Alignment explanation
Indices: 602000--602034 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
601990 GATGTTTATT
*
602000 CATATA CATATA CATATA CATATA CATATA TATAT
1 CATATA CATATA CATATA CATATA CATATA CATAT
602035 TTTCCTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (6 bp):
CATATA
Found at i:602084 original size:14 final size:14
Alignment explanation
Indices: 602062--602095 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
602052 ATTTTATGTG
602062 TATACATATGTATA
1 TATACATATGTATA
*
602076 TATATATATGTATA
1 TATACATATGTATA
*
602090 CATACA
1 TATACA
602096 CACACAACTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (14 bp):
TATACATATGTATA
Found at i:602505 original size:12 final size:12
Alignment explanation
Indices: 602466--602512 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
602456 AATTATTATT
602466 ATATATATTTTA
1 ATATATATTTTA
*
602478 CTGATATA-TTTA
1 AT-ATATATTTTA
602490 ATAT-T-TTTTA
1 ATATATATTTTA
602500 ATATATATTTTA
1 ATATATATTTTA
602512 A
1 A
602513 AATTATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 9 0.31
11 3 0.10
12 12 0.41
13 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (12 bp):
ATATATATTTTA
Found at i:602641 original size:10 final size:10
Alignment explanation
Indices: 602626--602696 Score: 54
Period size: 11 Copynumber: 6.6 Consensus size: 10
602616 ATATTGACTC
602626 AAAAATAATA
1 AAAAATAATA
602636 AAAAATAATTA
1 AAAAATAA-TA
602647 AAATAA-AATA
1 AAA-AATAATA
*
602657 TAATATATAATA
1 -AA-AAATAATA
* *
602669 TAACATAATA
1 AAAAATAATA
602679 TAAAAATAATTA
1 -AAAAATAA-TA
602691 AAAAAT
1 AAAAAT
602697 TATTTTTACT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
10 17 0.35
11 23 0.47
12 9 0.18
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAAATAATA
Found at i:602670 original size:12 final size:12
Alignment explanation
Indices: 602626--602693 Score: 53
Period size: 10 Copynumber: 6.3 Consensus size: 12
602616 ATATTGACTC
602626 AAAA-ATAATA-
1 AAAATATAATAT
602636 AAAA-ATAAT-T
1 AAAATATAATAT
*
602646 AAAATAAAATAT
1 AAAATATAATAT
*
602658 AATATATAATAT
1 AAAATATAATAT
*
602670 --AACATAATAT
1 AAAATATAATAT
602680 AAAA-ATAAT-T
1 AAAATATAATAT
602690 AAAA
1 AAAA
602694 AATTATTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
10 26 0.54
11 9 0.19
12 13 0.27
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAATATAATAT
Found at i:602678 original size:60 final size:60
Alignment explanation
Indices: 602565--602679 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
602555 TTTGTCGACC
* * **
602565 CAAAAATAATAAAAAATAATTAAAATAAAATATAAAATATGACGTAATGTAATATTGACT
1 CAAAAATAATAAAAAATAATTAAAATAAAATATAAAATATAACATAACATAATATTGACT
* *
602625 CAAAAATAATAAAAAATAATTAAAATAAAATATAATATATAATATAACATAATAT
1 CAAAAATAATAAAAAATAATTAAAATAAAATATAAAATATAACATAACATAATAT
602680 AAAAATAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.29
Consensus pattern (60 bp):
CAAAAATAATAAAAAATAATTAAAATAAAATATAAAATATAACATAACATAATATTGACT
Found at i:602922 original size:17 final size:16
Alignment explanation
Indices: 602885--602946 Score: 65
Period size: 17 Copynumber: 3.9 Consensus size: 16
602875 TATATTTTAT
*
602885 TATAAAATAAATATGAA
1 TATAATATAAATAT-AA
602902 TATAATATAAATATAA
1 TATAATATAAATATAA
* *
602918 TTATATTA-AAATTTAA
1 -TATAATATAAATATAA
602934 -ATAATATAAATAT
1 TATAATATAAATAT
602947 TTTAAAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 5 0.13
15 5 0.13
16 9 0.24
17 19 0.50
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
TATAATATAAATATAA
Found at i:602939 original size:25 final size:26
Alignment explanation
Indices: 602902--602968 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
602892 TAAATATGAA
*
602902 TATAATATAAATATAATTATATTAAAAT
1 TATAA-AT-AATATAAATATATTAAAAT
*
602930 T-TAAATAATATAAATATTTTAAAAT
1 TATAAATAATATAAATATATTAAAAT
*
602955 TATAAA-AATCTAAA
1 TATAAATAATATAAA
602969 AAAAGCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 25 0.71
26 6 0.17
27 3 0.09
28 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (26 bp):
TATAAATAATATAAATATATTAAAAT
Found at i:603361 original size:20 final size:22
Alignment explanation
Indices: 603322--603374 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
603312 AAAATTTTTT
603322 ATTTTAATTTTGATTAATTTATAA
1 ATTTT-ATTTTGATTAATTTA-AA
603346 A-TTTATTTT-ATT-ATTTAAA
1 ATTTTATTTTGATTAATTTAAA
603365 ATTTTATTTT
1 ATTTTATTTT
603375 TATATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.11
20 13 0.46
21 3 0.11
22 5 0.18
23 3 0.11
24 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTATTTTGATTAATTTAAA
Found at i:603397 original size:22 final size:22
Alignment explanation
Indices: 603369--603410 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
603359 TTTAAAATTT
603369 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
603391 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
603411 AATAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:604181 original size:293 final size:291
Alignment explanation
Indices: 603473--604312 Score: 1247
Period size: 293 Copynumber: 2.9 Consensus size: 291
603463 GTACTTCATA
* * *
603473 TTCATGCAATGTTATTATAAAGAATTATAATATAACATGTAATCTTTAACATA-TTT-AATTAGA
1 TTCATGCAATGTTATTATAAAGAATAATAACATAACATGTAATCTTCAACATATTTTCAATTAGA
* * *
603536 TTTGATTAATTCGTGCATTTTATCGTATCATAATAACATTTAAAATATTTTATTCTTATGTAATT
66 TTTAATTAATTCGTGCATTTTATCGTATCATAATAATATTTAAAATATTATATTCTTATGTAATT
* * * * *
603601 TTTTATATGTTAATAATTTGTATTTTTTAAAATTTAAATATTTATGTATTTATGTTATATTTTAA
131 TTTTATATGTTAATAATTTATATTTTATAAATTTTGAATATTTATGTATTTATGTTATACTTTAA
* * * *
603666 TTA-TTTTT-T-TCATATTCAGATAATCATATTTAATATTATTTGATATATTTTTAATGTTAAAC
196 TTATTTTTTATATCTTATTTAGATAATCATATTTAATATTATCT-ATATATTTTTAATGTTGAAC
603728 ATTGCATGGATCATAAGTTCCATTTAATAGAT
260 ATTGCATGGATCATAAGTTCCATTTAATAGAT
*
603760 TTCATGCAAAGTTA-T-T-----ATAATAACATAACATGTAATCTTCAACATATTTTCAATTAGA
1 TTCATGCAATGTTATTATAAAGAATAATAACATAACATGTAATCTTCAACATATTTTCAATTAGA
* * * * * *
603818 TTTAATTAATTCATGTATTTTATCATATCAAAATAGTATTTAAAATATTATATTCTTATCTAATT
66 TTTAATTAATTCGTGCATTTTATCGTATCATAATAATATTTAAAATATTATATTCTTATGTAATT
603883 TTTTATATGTTAATAATTTATATTTTATAAATTTTGAATATTTATGTATTTATGTTATACTTTAA
131 TTTTATATGTTAATAATTTATATTTTATAAATTTTGAATATTTATGTATTTATGTTATACTTTAA
603948 TTATTTTTTCATATCTTATTTAGATAATCATATTTAATATTATCTAATATATTTTTAATGTTGAA
196 TTATTTTTT-ATATCTTATTTAGATAATCATATTTAATATTATCT-ATATATTTTTAATGTTGAA
604013 CATTGCATGGATCATAAG-TCCGATTTAATAGAT
259 CATTGCATGGATCATAAGTTCC-ATTTAATAGAT
*
604046 TTCATGCAATGTTATTATAAAGAATAATAACATAACATGTAATCTTCAACATATTTTCCATTAGA
1 TTCATGCAATGTTATTATAAAGAATAATAACATAACATGTAATCTTCAACATATTTTCAATTAGA
* * *
604111 TCTAATTAATTCGTACATTTTATCGTATCATAATAATATTTAAAATATTATATTTTTATGTAATT
66 TTTAATTAATTCGTGCATTTTATCGTATCATAATAATATTTAAAATATTATATTCTTATGTAATT
* * * *
604176 TTTTATATATTAATAATTTATATTTTATAAATTTTGAATATTTATATATTTGTATTATACTTTAA
131 TTTTATATGTTAATAATTTATATTTTATAAATTTTGAATATTTATGTATTTATGTTATACTTTAA
* * *
604241 TTATTTTTTTATATATTATTTAAATAATCATATTTAATATTATCTATATACTTTTAATGTTGAAC
196 TTA-TTTTTTATATCTTATTTAGATAATCATATTTAATATTATCTATATATTTTTAATGTTGAAC
604306 ATTGCAT
260 ATTGCAT
604313 TTAATAGATT
Statistics
Matches: 497, Mismatches: 41, Indels: 25
0.88 0.07 0.04
Matches are distributed among these distances:
280 27 0.05
281 3 0.01
282 126 0.25
283 5 0.01
285 5 0.01
286 90 0.18
287 14 0.03
288 1 0.00
292 26 0.05
293 194 0.39
294 6 0.01
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.50
Consensus pattern (291 bp):
TTCATGCAATGTTATTATAAAGAATAATAACATAACATGTAATCTTCAACATATTTTCAATTAGA
TTTAATTAATTCGTGCATTTTATCGTATCATAATAATATTTAAAATATTATATTCTTATGTAATT
TTTTATATGTTAATAATTTATATTTTATAAATTTTGAATATTTATGTATTTATGTTATACTTTAA
TTATTTTTTATATCTTATTTAGATAATCATATTTAATATTATCTATATATTTTTAATGTTGAACA
TTGCATGGATCATAAGTTCCATTTAATAGAT
Found at i:609096 original size:6 final size:6
Alignment explanation
Indices: 609087--609129 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
609077 ATTTTTATAA
*
609087 TTAATT TTAATT TTAATT TTAATT ATTCATATT TAAATT TTAA
1 TTAATT TTAATT TTAATT TTAATT -TT-A-ATT TTAATT TTAA
609130 GTTAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 24 0.75
7 3 0.09
8 2 0.06
9 3 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (6 bp):
TTAATT
Found at i:609167 original size:27 final size:30
Alignment explanation
Indices: 609106--609167 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
609096 ATTTTAATTT
609106 TAATTATTCATATTTAAATTTTAAGTTAAA
1 TAATTATTCATATTTAAATTTTAAGTTAAA
*
609136 T-ATTA-TGATATTTAAA-TTTAA-TTAAA
1 TAATTATTCATATTTAAATTTTAAGTTAAA
609162 TAATTA
1 TAATTA
609168 AATTTAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.20
27 9 0.30
28 10 0.33
29 4 0.13
30 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (30 bp):
TAATTATTCATATTTAAATTTTAAGTTAAA
Found at i:609249 original size:14 final size:14
Alignment explanation
Indices: 609230--609275 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
609220 AATTTTAAAT
609230 ATAAAATAAATATA
1 ATAAAATAAATATA
*
609244 ATAAAATTAATA-A
1 ATAAAATAAATATA
*
609257 ATTAAAA-AATTATA
1 A-TAAAATAAATATA
609271 ATAAA
1 ATAAA
609276 TAATACATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAATAAATATA
Found at i:609276 original size:18 final size:18
Alignment explanation
Indices: 609234--609268 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
609224 TTAAATATAA
609234 AATAAATATAATAAAATT
1 AATAAATATAATAAAATT
609252 AATAAAT-TAA-AAAATT
1 AATAAATATAATAAAATT
609268 A
1 A
609269 TAATAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 3 0.18
18 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAATATAATAAAATT
Found at i:609285 original size:29 final size:29
Alignment explanation
Indices: 609225--609290 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 29
609215 TTAATAATTT
*
609225 TAAATATAAAATAAATATAATAAAATTAA
1 TAAATATAAAATAAATATAATAAAAATAA
*
609254 TAAAT-TAAAA-AATTATAATAAATAATACA
1 TAAATATAAAATAAATATAATAAA-AATA-A
609283 TAATATAT
1 TAA-ATAT
609291 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 11 0.35
28 8 0.26
29 9 0.29
30 2 0.06
31 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (29 bp):
TAAATATAAAATAAATATAATAAAAATAA
Found at i:609299 original size:26 final size:24
Alignment explanation
Indices: 609270--609318 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
609260 AAAAAATTAT
609270 AATAAATAATACATAATATATTTAAA
1 AATAAATAAT--ATAATATATTTAAA
*
609296 AATAATTAATATAATATATTTAA
1 AATAAATAATATAATATATTTAA
609319 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.59
26 9 0.41
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAAATAATATAATATATTTAAA
Found at i:609343 original size:24 final size:24
Alignment explanation
Indices: 609274--609343 Score: 53
Period size: 22 Copynumber: 3.1 Consensus size: 24
609264 AATTATAATA
* * *
609274 AATAATACATA-ATATATTTA-AA
1 AATAATATATATATATATATATAT
*
609296 AATAAT-TA-ATATA-ATATATTT
1 AATAATATATATATATATATATAT
609317 AAT-ATATATATATATATATATAAT
1 AATAATATATATATATATATAT-AT
609341 AAT
1 AAT
609344 TTATATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
20 7 0.19
21 9 0.24
22 11 0.30
23 6 0.16
24 4 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
AATAATATATATATATATATATAT
Found at i:609349 original size:14 final size:14
Alignment explanation
Indices: 609282--609346 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
609272 TAAATAATAC
609282 ATAATATATTTAA-
1 ATAATATATTTAAT
609295 A-AATA-A-TTAAT
1 ATAATATATTTAAT
609306 ATAATATATTTAAT
1 ATAATATATTTAAT
*
609320 ATATATATATATATAT
1 ATA-ATATATTTA-AT
609336 ATAATA-ATTTA
1 ATAATATATTTA
609347 TATCCTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
10 4 0.09
11 2 0.05
12 8 0.18
13 2 0.05
14 12 0.27
15 11 0.25
16 5 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATAATATATTTAAT
Found at i:609724 original size:20 final size:20
Alignment explanation
Indices: 609688--609725 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
609678 ATATTAAAAT
*
609688 TATTTTTATTAATATTTATA
1 TATTTTTAATAATATTTATA
609708 TATTTTATAATAA-ATTTA
1 TATTTT-TAATAATATTTA
609726 AATAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTTTAATAATATTTATA
Found at i:610760 original size:2 final size:2
Alignment explanation
Indices: 610753--610778 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
610743 ATGAAACACA
610753 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
610779 TCACACTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:611240 original size:2 final size:2
Alignment explanation
Indices: 611228--611265 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
611218 TACATAAATC
*
611228 AT AT AT CT 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 AT AT AT
611266 CGTATGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:614101 original size:20 final size:20
Alignment explanation
Indices: 614063--614101 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
614053 ATTATATTTT
*
614063 ATATTATAATTATATTTAAA
1 ATATTATAATTATAGTTAAA
614083 ATATTATATATTA-AGTTAA
1 ATATTATA-ATTATAGTTAA
614102 TTACATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
ATATTATAATTATAGTTAAA
Found at i:615176 original size:20 final size:21
Alignment explanation
Indices: 615153--615191 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
615143 TATAAAATAC
615153 TTTTTAA-ATATTATTTTTTA
1 TTTTTAACATATTATTTTTTA
615173 TTTTTAACATATTATTTTT
1 TTTTTAACATATTATTTTT
615192 CTACTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTAACATATTATTTTTTA
Found at i:616520 original size:30 final size:32
Alignment explanation
Indices: 616465--616525 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
616455 AAACGTATTA
*
616465 TTAATATATAAAAAATACAATAATAT-AATAT
1 TTAATATATAAAAAAAACAATAATATGAATAT
616496 TTAA-ATATAAAAAAAACACA-AATATGAATA
1 TTAATATATAAAAAAAACA-ATAATATGAATA
616526 CATAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (32 bp):
TTAATATATAAAAAAAACAATAATATGAATAT
Found at i:616562 original size:15 final size:14
Alignment explanation
Indices: 616542--616583 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
616532 TTTTTTAATC
616542 TTTTTCTTTCTTTCT
1 TTTTTCTTT-TTTCT
616557 TTTTTCATTTTTTCT
1 TTTTTC-TTTTTTCT
*
616572 TATTTCTTTTTT
1 TTTTTCTTTTTT
616584 TTAGCCATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 16 0.64
16 3 0.12
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTTCT
Done.