Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold136
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: 1039917
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.32
Warning! 114553 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:449462 original size:24 final size:24
Alignment explanation
Indices: 449428--449481 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
449418 TTGTTTAGGG
449428 AGTTTTATTTGTTTATAATATAGC
1 AGTTTTATTTGTTTATAATATAGC
* *
449452 AGTTTTGTTTGTTTATGATATAGC
1 AGTTTTATTTGTTTATAATATAGC
449476 AGTTTT
1 AGTTTT
449482 CTTTTCGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.04, G:0.17, T:0.56
Consensus pattern (24 bp):
AGTTTTATTTGTTTATAATATAGC
Found at i:459826 original size:103 final size:103
Alignment explanation
Indices: 459647--459841 Score: 309
Period size: 103 Copynumber: 1.9 Consensus size: 103
459637 AGTCAGTATA
* * * ** *
459647 TTTTGGTTAAAATAGTCTATTGGTATCCTAGCTTATTCTTTTTCCTGTAAGATAATGATTAGTGT
1 TTTTGGTTAAAATAATCTATTGGTATCCTAGCTGATTCTGTTTCCTACAAGATAATGACTAGTGT
459712 CTCAAATATGTTTGGTTGCAGGATATTTCTTCAGATTT
66 CTCAAATATGTTTGGTTGCAGGATATTTCTTCAGATTT
* * *
459750 TTTTGGTTAAAATAATCTATTGGTATCTTAGCTGATTCTGTTTCCTACAAGATAGTGGCTAGTGT
1 TTTTGGTTAAAATAATCTATTGGTATCCTAGCTGATTCTGTTTCCTACAAGATAATGACTAGTGT
459815 CTCAAATATGTTTGGTTGCAGGATATT
66 CTCAAATATGTTTGGTTGCAGGATATT
459842 CATACTTCCT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 83 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (103 bp):
TTTTGGTTAAAATAATCTATTGGTATCCTAGCTGATTCTGTTTCCTACAAGATAATGACTAGTGT
CTCAAATATGTTTGGTTGCAGGATATTTCTTCAGATTT
Found at i:461256 original size:2 final size:2
Alignment explanation
Indices: 461249--461275 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
461239 TTGTTTTGCG
461249 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
461276 ATCTATTTTC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:463232 original size:2 final size:2
Alignment explanation
Indices: 463227--463253 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
463217 ACTAATCTTA
463227 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
463254 GCTATCTAAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:464895 original size:19 final size:20
Alignment explanation
Indices: 464854--464898 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
464844 TTTCTTTCAG
* *
464854 TTTTTTTTGTTCAGTTTTGT
1 TTTTTTTTGTTCAGATTTCT
*
464874 TTTTTTTTTTTCA-ATTTCT
1 TTTTTTTTGTTCAGATTTCT
464893 TTTTTT
1 TTTTTT
464899 ATGCTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTTTTGTTCAGATTTCT
Found at i:470212 original size:22 final size:24
Alignment explanation
Indices: 470162--470227 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 24
470152 TGATTATGCA
*
470162 ATTTTTAGTTTGTTTATTTCCTTC
1 ATTTTTAGTTTGTTTATTTCATTC
*
470186 A--TTTAGTTT-TTTTTTTCATT-
1 ATTTTTAGTTTGTTTATTTCATTC
*
470206 ATTTTTA-TTTATTTATTT-ATTC
1 ATTTTTAGTTTGTTTATTTCATTC
470228 TAATTAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
20 1 0.03
21 15 0.43
22 18 0.51
24 1 0.03
ACGTcount: A:0.17, C:0.08, G:0.05, T:0.71
Consensus pattern (24 bp):
ATTTTTAGTTTGTTTATTTCATTC
Found at i:480805 original size:2 final size:2
Alignment explanation
Indices: 480798--480850 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
480788 TATGTCAGAA
480798 CT CT CT CT 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 CT CT CT CT
480840 CT CT CT CT CT C
1 CT CT CT CT CT C
480851 ATGAGACAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:486698 original size:147 final size:147
Alignment explanation
Indices: 486431--486724 Score: 588
Period size: 147 Copynumber: 2.0 Consensus size: 147
486421 GTGTGTTATT
486431 TTCCTCCATTTTGGTGGTTGTTAAGCTCCTTAGTCCTTAGCCCAATAGTGTTCAACCATGCATGC
1 TTCCTCCATTTTGGTGGTTGTTAAGCTCCTTAGTCCTTAGCCCAATAGTGTTCAACCATGCATGC
486496 TTGAGAACTGAGGGACATTATTTTCTGTAATATTCTTTAAATTTAACATTTTCCTTACCAGAATT
66 TTGAGAACTGAGGGACATTATTTTCTGTAATATTCTTTAAATTTAACATTTTCCTTACCAGAATT
486561 AGATTAAAATGGAATTC
131 AGATTAAAATGGAATTC
486578 TTCCTCCATTTTGGTGGTTGTTAAGCTCCTTAGTCCTTAGCCCAATAGTGTTCAACCATGCATGC
1 TTCCTCCATTTTGGTGGTTGTTAAGCTCCTTAGTCCTTAGCCCAATAGTGTTCAACCATGCATGC
486643 TTGAGAACTGAGGGACATTATTTTCTGTAATATTCTTTAAATTTAACATTTTCCTTACCAGAATT
66 TTGAGAACTGAGGGACATTATTTTCTGTAATATTCTTTAAATTTAACATTTTCCTTACCAGAATT
486708 AGATTAAAATGGAATTC
131 AGATTAAAATGGAATTC
486725 GTAACTGAAC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (147 bp):
TTCCTCCATTTTGGTGGTTGTTAAGCTCCTTAGTCCTTAGCCCAATAGTGTTCAACCATGCATGC
TTGAGAACTGAGGGACATTATTTTCTGTAATATTCTTTAAATTTAACATTTTCCTTACCAGAATT
AGATTAAAATGGAATTC
Found at i:487040 original size:2 final size:2
Alignment explanation
Indices: 487035--487081 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
487025 CACACTAATC
* *
487035 CT CT CT CT CT CT CT CT CT CT AT CT C- CC 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 CT CT CT CT
487076 CT CT CT
1 CT CT CT
487082 ATAAATCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.02, C:0.51, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:488305 original size:13 final size:13
Alignment explanation
Indices: 488287--488312 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
488277 TTATCGTTTC
488287 TGTTTCTCTTTTA
1 TGTTTCTCTTTTA
488300 TGTTTCTCTTTTA
1 TGTTTCTCTTTTA
488313 CAGTCATGAA
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (13 bp):
TGTTTCTCTTTTA
Found at i:493741 original size:20 final size:20
Alignment explanation
Indices: 493713--493753 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
493703 AGTTAGATTC
493713 AAAAGTTTAAATTTATTTTTT
1 AAAAGTTTAAATTT-TTTTTT
493734 AAAA-TTTAAATTTTTTTTT
1 AAAAGTTTAAATTTTTTTTT
493753 A
1 A
493754 CTTTTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 9 0.45
21 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
AAAAGTTTAAATTTTTTTTT
Found at i:493949 original size:29 final size:29
Alignment explanation
Indices: 493876--493954 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
493866 TAAATAAGTT
493876 AATAATTTTA-AT-TTTTAATTTTTATTAA
1 AATAATTTTATATATTTTAA-TTTTATTAA
493904 AAT--TTTTAT-TAATTTTTAATTTTATTAA
1 AATAATTTTATAT-A-TTTTAATTTTATTAA
* *
493932 AATAAATTTATATATTTTTATTT
1 AATAATTTTATATATTTTAATTT
493955 ATATACAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
26 6 0.14
28 15 0.36
29 14 0.33
30 6 0.14
31 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
AATAATTTTATATATTTTAATTTTATTAA
Found at i:496212 original size:28 final size:28
Alignment explanation
Indices: 496193--496262 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 28
496183 TTATTTGTTA
496193 TTATATTTATATTATTTTTTATATTATAT
1 TTAT-TTTATATTATTTTTTATATTATAT
* *
496222 TTATTTTATATTATATTTTA-ATTATTT
1 TTATTTTATATTATTTTTTATATTATAT
496249 TGTAATTTTATATT
1 T-T-ATTTTATATT
496263 TGTATGGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 7 0.19
28 16 0.43
29 14 0.38
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (28 bp):
TTATTTTATATTATTTTTTATATTATAT
Found at i:496230 original size:16 final size:16
Alignment explanation
Indices: 496193--496239 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
496183 TTATTTGTTA
*
496193 TTATATTTATATTATTTT
1 TTATA-TTATATT-TATT
496211 TTATATTATATTTATT
1 TTATATTATATTTATT
496227 TTATATTATATTT
1 TTATATTATATTT
496240 TAATTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 16 0.57
17 7 0.25
18 5 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATATTATATTTATT
Found at i:496249 original size:21 final size:19
Alignment explanation
Indices: 496134--496249 Score: 71
Period size: 21 Copynumber: 5.8 Consensus size: 19
496124 TTAAATGTTA
* *
496134 TATATTTATATAAATTTTAT
1 TATATTTA-ATTATTTTTAT
496154 TATATTAATAATTTATGTTTTA-
1 TATATT--TAA-TTAT-TTTTAT
*
496176 TAAATTT--TTATTTGTTAT
1 TATATTTAATTATTT-TTAT
496194 TATATTTATATTA-TTTT-T
1 TATATTTA-ATTATTTTTAT
*
496212 TATATTATATTTATTTTATAT
1 TATATT-TAATTATTTT-TAT
496233 TATATTTTAATTATTTT
1 TATA-TTTAATTATTTT
496250 GTAATTTTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 27
0.70 0.06 0.25
Matches are distributed among these distances:
16 2 0.03
17 7 0.09
18 16 0.21
19 7 0.09
20 10 0.13
21 18 0.24
22 11 0.14
23 5 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TATATTTAATTATTTTTAT
Found at i:496456 original size:2 final size:2
Alignment explanation
Indices: 496449--496474 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
496439 CTCTTTTCTC
496449 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
496475 CACATTTAGT
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:503302 original size:26 final size:25
Alignment explanation
Indices: 503272--503334 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
503262 TTTCTATATT
503272 AATATTAATTTATGTTTTTATAATTA
1 AATATTAATTTAT-TTTTTATAATTA
* * *
503298 AATATAAATAATATTTTTTATCATTA
1 AATATTAAT-TTATTTTTTATAATTA
503324 AATCA-TAATTT
1 AAT-ATTAATTT
503335 GGGTTGGATC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 1 0.03
26 25 0.83
27 4 0.13
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (25 bp):
AATATTAATTTATTTTTTATAATTA
Found at i:506832 original size:2 final size:2
Alignment explanation
Indices: 506827--506852 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
506817 CTGGACGAGC
506827 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
506853 TTTTGTGTTC
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:507097 original size:2 final size:2
Alignment explanation
Indices: 507090--507117 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
507080 TGTATGTATG
507090 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
507118 ATTTCTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:507702 original size:22 final size:23
Alignment explanation
Indices: 507675--507731 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
507665 TAAAACTATG
*
507675 TAATATAAATATTATTCATAAAA
1 TAATATAAATATTATTAATAAAA
* *
507698 T-ATATAAAAATTATTAATAATA
1 TAATATAAATATTATTAATAAAA
*
507720 TAAAATAAATAT
1 TAATATAAATAT
507732 CATAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATATAAATATTATTAATAAAA
Found at i:508054 original size:23 final size:22
Alignment explanation
Indices: 508011--508059 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
508001 TTGTGATTGT
* *
508011 ATTTAAATAAGTCAATAACTTTA
1 ATTTAAATAAATAAATAAC-TTA
508034 ATTTAAATTAAATAAAT-ACTTA
1 ATTTAAA-TAAATAAATAACTTA
508056 ATTT
1 ATTT
508060 TGAGTTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 9 0.39
24 7 0.30
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTAAATAAATAAATAACTTA
Found at i:508304 original size:2 final size:2
Alignment explanation
Indices: 508297--508321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
508287 TAGCTCAGAT
508297 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
508322 TTACGTACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:508781 original size:3 final size:3
Alignment explanation
Indices: 508773--508800 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
508763 TTAGCATTTG
508773 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
508801 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:523471 original size:4 final size:4
Alignment explanation
Indices: 523462--523487 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
523452 CTCCCTCTCT
523462 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
523488 CTGTAATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:526021 original size:102 final size:102
Alignment explanation
Indices: 525845--526038 Score: 325
Period size: 102 Copynumber: 1.9 Consensus size: 102
525835 GGTCAGTATA
* * ** *
525845 TTTTGGTTAAAATAGTCTATTGGTATCTTAGCTTATTCTTTTTCCTGTAAGATAATGATTAGTGT
1 TTTTGGTTAAAATAGTCTATTGGTATCTTAGCTTATTCTGTTGCCTACAAGATAATGACTAGTGT
525910 CTCAAATATGTTTGGTTGCAGGATATTTCTTCGGATT
66 CTCAAATATGTTTGGTTGCAGGATATTTCTTCGGATT
* *
525947 TTTTGGTTAAAATAGTCTTTTGGTATCTTAGCTTATTCTGTTGCCTACAAGATAATGGCTAGTGT
1 TTTTGGTTAAAATAGTCTATTGGTATCTTAGCTTATTCTGTTGCCTACAAGATAATGACTAGTGT
526012 CTCAAATATGTTTGGTTGCAGGATATT
66 CTCAAATATGTTTGGTTGCAGGATATT
526039 CATACTTCCT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 85 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (102 bp):
TTTTGGTTAAAATAGTCTATTGGTATCTTAGCTTATTCTGTTGCCTACAAGATAATGACTAGTGT
CTCAAATATGTTTGGTTGCAGGATATTTCTTCGGATT
Found at i:527445 original size:2 final size:2
Alignment explanation
Indices: 527438--527469 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
527428 TTTGTTGTGG
527438 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
527470 GAATCTATTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:529440 original size:2 final size:2
Alignment explanation
Indices: 529435--529477 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
529425 ACTAATCTTA
529435 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
529477 T
1 T
529478 GCTATCTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:531133 original size:22 final size:22
Alignment explanation
Indices: 531089--531135 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
531079 TTTCTTTCAG
*
531089 TTTTTTTTGTTCAGTTTTGTTT
1 TTTTTTTTGTTCAATTTTGTTT
* *
531111 TTTTTTTTTTTCAA-TTTATTT
1 TTTTTTTTGTTCAATTTTGTTT
531132 TTTT
1 TTTT
531136 ATGCTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.09, C:0.04, G:0.06, T:0.81
Consensus pattern (22 bp):
TTTTTTTTGTTCAATTTTGTTT
Found at i:535725 original size:3 final size:3
Alignment explanation
Indices: 535717--535769 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
535707 ATATATACAC
535717 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
535765 TAA TA
1 TAA TA
535770 TATTGGTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:539432 original size:2 final size:2
Alignment explanation
Indices: 539425--539473 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
539415 TGTCTTCTTT
539425 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
539467 TA TA TA T
1 TA TA TA T
539474 TTCTGAGTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:542037 original size:2 final size:2
Alignment explanation
Indices: 542030--542058 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
542020 TTTTTAATGC
542030 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
542059 CCTACATAAT
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:543173 original size:109 final size:111
Alignment explanation
Indices: 543014--543228 Score: 335
Period size: 110 Copynumber: 2.0 Consensus size: 111
543004 TTTTAAGGGT
* *
543014 ATTTTTATTGGTTTTTAATTTTTAAAATTTATCAAATATTATTATTTAATTCATATTAAATTA-T
1 ATTTTTATTGGTTTTTAATTTTTAAAATTAATCAAATATTATTATTTAATTCATATTAAATCAGT
*
543078 TTTTTAAAATTCATTTATTTTCATGAATTTTTAAATTTTTTCTTGC
66 TTTTTAAAATTCATTCATTTTCATGAATTTTTAAATTTTTTCTTGC
* * * *
543124 ATTTTTCTTGGTTTTTAATTTTT-AAATTAATCAAATATTGTTATTTAATTTATATTATATCAGT
1 ATTTTTATTGGTTTTTAATTTTTAAAATTAATCAAATATTATTATTTAATTCATATTAAATCAGT
* *
543188 TTTTTAAAATTCATTCATTTTTATGAATTTTTGAATTTTTT
66 TTTTTAAAATTCATTCATTTTCATGAATTTTTAAATTTTTT
543229 ATTTGAAATT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
109 34 0.36
110 61 0.64
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (111 bp):
ATTTTTATTGGTTTTTAATTTTTAAAATTAATCAAATATTATTATTTAATTCATATTAAATCAGT
TTTTTAAAATTCATTCATTTTCATGAATTTTTAAATTTTTTCTTGC
Found at i:543479 original size:12 final size:12
Alignment explanation
Indices: 543462--543486 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
543452 AATCAGATCT
543462 TTTCTCTCTCTC
1 TTTCTCTCTCTC
543474 TTTCTCTCTCTC
1 TTTCTCTCTCTC
543486 T
1 T
543487 CTCTTAGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTCTCTCTCTC
Found at i:543854 original size:37 final size:37
Alignment explanation
Indices: 543813--543887 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
543803 TCCCTCCAGG
543813 AGGATTTGTTGTAAAAAAAAGCATAATGGTCAGCTGA
1 AGGATTTGTTGTAAAAAAAAGCATAATGGTCAGCTGA
* *
543850 AGGATTTGTTGTCAAAAAGAGCATAATGGTCAGCTGA
1 AGGATTTGTTGTAAAAAAAAGCATAATGGTCAGCTGA
543887 A
1 A
543888 AAAAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (37 bp):
AGGATTTGTTGTAAAAAAAAGCATAATGGTCAGCTGA
Found at i:543935 original size:32 final size:32
Alignment explanation
Indices: 543899--543959 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
543889 AAAAAAAAAG
* *
543899 AGAAAAGAGAGAGAAAAGCAAGAAAAAATATA
1 AGAAAAGAGAGAAAAAAACAAGAAAAAATATA
* *
543931 AGAAAATAGGGAAAAAAACAAGAAAAAAT
1 AGAAAAGAGAGAAAAAAACAAGAAAAAAT
543960 TAGGTTAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (32 bp):
AGAAAAGAGAGAAAAAAACAAGAAAAAATATA
Found at i:544012 original size:21 final size:22
Alignment explanation
Indices: 543965--544006 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
543955 AAAATTAGGT
*
543965 TAGTTTTTATCTCTACCTAAGC
1 TAGTTTTTATCTCTACCAAAGC
543987 TAGTTTTTATCTCTACCAAA
1 TAGTTTTTATCTCTACCAAA
544007 TCAGTTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (22 bp):
TAGTTTTTATCTCTACCAAAGC
Found at i:548198 original size:3 final size:3
Alignment explanation
Indices: 548190--548226 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
548180 CATGAAATGA
548190 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
548227 TAAAAAATAT
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):
AAT
Found at i:548717 original size:16 final size:17
Alignment explanation
Indices: 548696--548734 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
548686 TGTTATTTGT
* *
548696 AATTTTTATTACAA-TA
1 AATTTTTAATAAAAGTA
548712 AATTTTTAATAAAAGTA
1 AATTTTTAATAAAAGTA
548729 AATTTT
1 AATTTT
548735 ACTTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTTTTAATAAAAGTA
Found at i:548768 original size:16 final size:17
Alignment explanation
Indices: 548744--548777 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
548734 TACTTTAAAT
548744 ATAACAAATTAT-ATAA
1 ATAACAAATTATAATAA
*
548760 ATAAGAAATTATAATAA
1 ATAACAAATTATAATAA
548777 A
1 A
548778 CATATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
ATAACAAATTATAATAA
Found at i:557542 original size:26 final size:25
Alignment explanation
Indices: 557512--557574 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
557502 TTTCTATATT
557512 AATATTAATTTATGTTTTTATAATTA
1 AATATTAATTTAT-TTTTTATAATTA
* * *
557538 AATATAAATAATATTTTTTATCATTA
1 AATATTAAT-TTATTTTTTATAATTA
557564 AATCA-TAATTT
1 AAT-ATTAATTT
557575 GGGTTGGATC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 1 0.03
26 25 0.83
27 4 0.13
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (25 bp):
AATATTAATTTATTTTTTATAATTA
Found at i:558078 original size:24 final size:24
Alignment explanation
Indices: 558034--558092 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
558024 TGAGTGAGAT
558034 ATTTTCTTATTAAATTATTTT-CGA
1 ATTTTCTT-TTAAATTATTTTGCGA
* *
558058 ATTTTCTTTTAATTCTTTTTTGCGA
1 ATTTTCTTTTAAAT-TATTTTGCGA
* *
558083 CTTTTTTTTT
1 ATTTTCTTTT
558093 TAGTTTTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 5 0.17
24 13 0.45
25 11 0.38
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.66
Consensus pattern (24 bp):
ATTTTCTTTTAAATTATTTTGCGA
Found at i:565524 original size:10 final size:10
Alignment explanation
Indices: 565511--565537 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
565501 GTTGTGGGAG
565511 AGAAGCAAAA
1 AGAAGCAAAA
565521 AGAAGCAAAA
1 AGAAGCAAAA
565531 AGAAGCA
1 AGAAGCA
565538 GTTTTAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.67, C:0.11, G:0.22, T:0.00
Consensus pattern (10 bp):
AGAAGCAAAA
Found at i:567559 original size:2 final size:2
Alignment explanation
Indices: 567552--567587 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
567542 TGCTTTTTCT
567552 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
567588 AGCATGAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:568671 original size:6 final size:6
Alignment explanation
Indices: 568662--568700 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
568652 TGGATTTCCC
568662 TTTCTT TTTCTT TTTC-T TTTCTT TTTCTT TTTCCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT-CTT TTT
568701 TTTATTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
7 6 0.19
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:568683 original size:11 final size:11
Alignment explanation
Indices: 568662--568692 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
568652 TGGATTTCCC
568662 TTTCTTTTTCTT
1 TTTC-TTTTCTT
568674 TTTCTTTTCTT
1 TTTCTTTTCTT
568685 TTTCTTTT
1 TTTCTTTT
568693 TCCTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:568684 original size:17 final size:17
Alignment explanation
Indices: 568660--568708 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
568650 TCTGGATTTC
568660 CCTTTCTTTTTCTTTTT
1 CCTTTCTTTTTCTTTTT
*
568677 CTTTTCTTTTTCTTTTT
1 CCTTTCTTTTTCTTTTT
*
568694 CCTTT-TTTTTATTTT
1 CCTTTCTTTTTCTTTT
568709 CACAGGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (17 bp):
CCTTTCTTTTTCTTTTT
Found at i:570524 original size:102 final size:102
Alignment explanation
Indices: 570348--570541 Score: 325
Period size: 102 Copynumber: 1.9 Consensus size: 102
570338 GGTCAGTTTA
* ** *
570348 TTTTGGTTAAAATAGTCTATTGGTATCTTAGCTTATTCTTTTTCCTGTAAGATAATGATTAGTGT
1 TTTTGGTTAAAATAGTCTATTGGTATCTTAGCTTATTCTGTTTCCTACAAGATAATGACTAGTGT
570413 CTCAAATATGTTTGGTTGCAGGATATTTCTTCTGATT
66 CTCAAATATGTTTGGTTGCAGGATATTTCTTCTGATT
* *
570450 TTTTGGTTAAAATAGTCTTTTGGTATCTTAGCTTATTCTGTTTCCTACAAGATAATGGCTAGTGT
1 TTTTGGTTAAAATAGTCTATTGGTATCTTAGCTTATTCTGTTTCCTACAAGATAATGACTAGTGT
*
570515 CTCAAATATGTTTGTTTGCAGGATATT
66 CTCAAATATGTTTGGTTGCAGGATATT
570542 CATACTTCCT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 85 1.00
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (102 bp):
TTTTGGTTAAAATAGTCTATTGGTATCTTAGCTTATTCTGTTTCCTACAAGATAATGACTAGTGT
CTCAAATATGTTTGGTTGCAGGATATTTCTTCTGATT
Found at i:572006 original size:18 final size:17
Alignment explanation
Indices: 571983--572024 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
571973 TTCTTTCAGT
571983 TTTTTTTGTTCAGTTTC
1 TTTTTTTGTTCAGTTTC
* *
572000 GTTTTTTTTTTCGGTTTC
1 -TTTTTTTGTTCAGTTTC
572018 TTTTTTT
1 TTTTTTT
572025 AATGCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.02, C:0.10, G:0.12, T:0.76
Consensus pattern (17 bp):
TTTTTTTGTTCAGTTTC
Found at i:572021 original size:17 final size:19
Alignment explanation
Indices: 571976--572024 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
571966 AAGCATTTTC
571976 TTTCAGTTTTTTTTGTTCAG
1 TTTC-GTTTTTTTTGTTCAG
*
571996 TTTCGTTTTTTTT-TTCGG
1 TTTCGTTTTTTTTGTTCAG
572014 TTTC-TTTTTTT
1 TTTCGTTTTTTT
572025 AATGCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.25
18 8 0.29
19 9 0.32
20 4 0.14
ACGTcount: A:0.04, C:0.10, G:0.12, T:0.73
Consensus pattern (19 bp):
TTTCGTTTTTTTTGTTCAG
Found at i:574299 original size:2 final size:2
Alignment explanation
Indices: 574292--574325 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
574282 AGTTTGCTAA
574292 AT 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 AT
574326 CTGAGTAGAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:575406 original size:2 final size:2
Alignment explanation
Indices: 575399--575428 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
575389 ATCAATAATC
575399 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
575429 CGATCAAAGA
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):
AT
Found at i:576436 original size:22 final size:24
Alignment explanation
Indices: 576411--576455 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
576401 TTTTAATTTA
*
576411 TATTAA-A-ATAATTATATTTTTT
1 TATTAATATATAATTAAATTTTTT
576433 TATTAATATATAATTAAATTTTT
1 TATTAATATATAATTAAATTTTT
576456 ACTATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TATTAATATATAATTAAATTTTTT
Found at i:576456 original size:22 final size:21
Alignment explanation
Indices: 576385--576469 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 21
576375 TTGAGTAAAT
576385 TTAAATTTTTATT-AAT-T--
1 TTAAATTTTTATTAAATATAA
* *
576402 TTTAATTTATATTAAA-ATAA
1 TTAAATTTTTATTAAATATAA
*
576422 TTATATTTTTTTATTAATATATAA
1 TTA-A-ATTTTTATTAA-ATATAA
576446 TTAAATTTTTACTATAAATATAA
1 TTAAATTTTTA-T-TAAATATAA
576469 T
1 T
576470 AATCTATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
17 11 0.21
18 3 0.06
20 2 0.04
21 1 0.02
22 15 0.29
23 10 0.19
24 10 0.19
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATTTTTATTAAATATAA
Found at i:577787 original size:22 final size:22
Alignment explanation
Indices: 577762--577806 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
577752 TTTTTTTTTG
577762 CTTCATATGACTGTTTTTATAT
1 CTTCATATGACTGTTTTTATAT
* *
577784 CTTCATGTGGCTGTTTTTATAT
1 CTTCATATGACTGTTTTTATAT
577806 C
1 C
577807 CTTTGATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (22 bp):
CTTCATATGACTGTTTTTATAT
Found at i:580056 original size:208 final size:208
Alignment explanation
Indices: 579698--580119 Score: 844
Period size: 208 Copynumber: 2.0 Consensus size: 208
579688 TTTTGTAAAT
579698 CTGATTCAAGTAAATGTGCTATTTTTTGCGTCGTCGAATCCTACCACGAATGGTTTTTTTCCTTA
1 CTGATTCAAGTAAATGTGCTATTTTTTGCGTCGTCGAATCCTACCACGAATGGTTTTTTTCCTTA
579763 TGAAACTAGATATTTTTTCTTGACATTTTGTTTGCATTCCCATTCAACCGAAAATGCACTGCTGC
66 TGAAACTAGATATTTTTTCTTGACATTTTGTTTGCATTCCCATTCAACCGAAAATGCACTGCTGC
579828 CCTTTTAACTTGCTAGAGAAATCATAGTCTTTGCTGATGGAAGTCCATTTGAAAAAATCATTCTG
131 CCTTTTAACTTGCTAGAGAAATCATAGTCTTTGCTGATGGAAGTCCATTTGAAAAAATCATTCTG
579893 GGTATGTTCCCTC
196 GGTATGTTCCCTC
579906 CTGATTCAAGTAAATGTGCTATTTTTTGCGTCGTCGAATCCTACCACGAATGGTTTTTTTCCTTA
1 CTGATTCAAGTAAATGTGCTATTTTTTGCGTCGTCGAATCCTACCACGAATGGTTTTTTTCCTTA
579971 TGAAACTAGATATTTTTTCTTGACATTTTGTTTGCATTCCCATTCAACCGAAAATGCACTGCTGC
66 TGAAACTAGATATTTTTTCTTGACATTTTGTTTGCATTCCCATTCAACCGAAAATGCACTGCTGC
580036 CCTTTTAACTTGCTAGAGAAATCATAGTCTTTGCTGATGGAAGTCCATTTGAAAAAATCATTCTG
131 CCTTTTAACTTGCTAGAGAAATCATAGTCTTTGCTGATGGAAGTCCATTTGAAAAAATCATTCTG
580101 GGTATGTTCCCTC
196 GGTATGTTCCCTC
580114 CTGATT
1 CTGATT
580120 GGAGTCATCT
Statistics
Matches: 214, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
208 214 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (208 bp):
CTGATTCAAGTAAATGTGCTATTTTTTGCGTCGTCGAATCCTACCACGAATGGTTTTTTTCCTTA
TGAAACTAGATATTTTTTCTTGACATTTTGTTTGCATTCCCATTCAACCGAAAATGCACTGCTGC
CCTTTTAACTTGCTAGAGAAATCATAGTCTTTGCTGATGGAAGTCCATTTGAAAAAATCATTCTG
GGTATGTTCCCTC
Found at i:584481 original size:2 final size:2
Alignment explanation
Indices: 584476--584518 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
584466 TCATGCAATG
*
584476 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
584518 C
1 C
584519 ATTAATATTT
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:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:586432 original size:16 final size:16
Alignment explanation
Indices: 586383--586437 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
586373 TAATCGATAA
*
586383 TTATATTTAAATTTTT
1 TTATTTTTAAATTTTT
586399 TTATTATTT--ATTTATT
1 TTATT-TTTAAATTT-TT
*
586415 TTATTTTTAAAATTTT
1 TTATTTTTAAATTTTT
586431 TTATTTT
1 TTATTTT
586438 ATAATGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 7 0.21
16 20 0.61
17 6 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTTAAATTTTT
Found at i:586522 original size:30 final size:30
Alignment explanation
Indices: 586486--586544 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
586476 TTTTTATTCA
586486 TTTTTATATTATTTA-TATTTAATATTATAT
1 TTTTTATATTATTTAGTATTTAA-ATTATAT
*
586516 TTTTTATTTTATTTATGTATTTAAATTAT
1 TTTTTATATTATTTA-GTATTTAAATTAT
586545 TAAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 14 0.54
31 5 0.19
32 7 0.27
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (30 bp):
TTTTTATATTATTTAGTATTTAAATTATAT
Found at i:586943 original size:19 final size:18
Alignment explanation
Indices: 586885--586963 Score: 50
Period size: 19 Copynumber: 4.0 Consensus size: 18
586875 AAGTGTTTTT
*
586885 TTTTAATTAAGATTAAAA
1 TTTTAATTAAAATTAAAA
* * *
586903 TATTAAATTATAAAAATCAAA
1 T-TTTAA-T-TAAAATTAAAA
586924 TTTTATATTAAAATTAAAA
1 TTTTA-ATTAAAATTAAAA
*
586943 TATTGAATTATAAATTTAAAA
1 T-TTTAATTA-AAA-TTAAAA
586964 AAAAATTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.02
19 18 0.39
20 11 0.24
21 16 0.35
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (18 bp):
TTTTAATTAAAATTAAAA
Found at i:586961 original size:21 final size:20
Alignment explanation
Indices: 586896--586963 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
586886 TTTAATTAAG
586896 ATTAAAATATTAAATTATAAA
1 ATTAAAATATTAAATTAT-AA
* * * *
586917 AATCAAATTTTATATTA-AA
1 ATTAAAATATTAAATTATAA
*
586936 ATTAAAATATTGAATTATAA
1 ATTAAAATATTAAATTATAA
586956 ATTTAAAA
1 A-TTAAAA
586964 AAAAATTAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 14 0.39
20 3 0.08
21 19 0.53
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
ATTAAAATATTAAATTATAA
Found at i:587470 original size:16 final size:17
Alignment explanation
Indices: 587427--587472 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
587417 TGAGATATAT
*
587427 TTTAATTGGAATTCTTG
1 TTTAATTGTAATTCTTG
*
587444 TTTTATATGTAATT-TTG
1 TTTAAT-TGTAATTCTTG
587461 TTTAATTGTAAT
1 TTTAATTGTAAT
587473 ATATATCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 6 0.24
17 13 0.52
18 6 0.24
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.59
Consensus pattern (17 bp):
TTTAATTGTAATTCTTG
Found at i:589875 original size:20 final size:20
Alignment explanation
Indices: 589850--589894 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
589840 AAATAAAATT
* *
589850 TTTTTAAGTATTCAATTTAA
1 TTTTTAAGTATTAAAATTAA
**
589870 TTTTTATTTATTAAAATTAA
1 TTTTTAAGTATTAAAATTAA
589890 TTTTT
1 TTTTT
589895 TATTTTATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTAAGTATTAAAATTAA
Found at i:591003 original size:31 final size:31
Alignment explanation
Indices: 590968--591035 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
590958 TTACGATATT
* ** *
590968 TTTTAAATATTTACAAATATTAAAATT-TTAA
1 TTTTAAATA-TTAAAAATAAAAAAATTGATAA
*
590999 TTTTAATTATTAAAAATAAAAAAATTGATAA
1 TTTTAAATATTAAAAATAAAAAAATTGATAA
591030 TTTTAA
1 TTTTAA
591036 TTAATTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
TTTTAAATATTAAAAATAAAAAAATTGATAA
Found at i:591106 original size:2 final size:2
Alignment explanation
Indices: 591099--591130 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
591089 AACGACTTAC
591099 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
591131 GAAATGTCTG
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:593872 original size:26 final size:25
Alignment explanation
Indices: 593843--593913 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
593833 TATTTTTTAC
*
593843 AATTAAATATAAATAAATATTTTATT
1 AATTAAATATAAATAAA-ATTTAATT
* *
593869 AATTAAATAATAATTTAAATTTAATT
1 AATTAAAT-ATAAATAAAATTTAATT
* *
593895 AAATCAATATAAATTAAAA
1 AATTAAATATAAA-TAAAA
593914 ATAATATATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
25 4 0.11
26 25 0.69
27 7 0.19
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
AATTAAATATAAATAAAATTTAATT
Found at i:595547 original size:16 final size:16
Alignment explanation
Indices: 595526--595559 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
595516 TTTAATTTTA
595526 AATAAATATTAAATAT
1 AATAAATATTAAATAT
*
595542 AATAAATATTTAATAT
1 AATAAATATTAAATAT
595558 AA
1 AA
595560 GTATATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAATATTAAATAT
Found at i:596430 original size:5 final size:5
Alignment explanation
Indices: 596413--596442 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
596403 CAAAATTTAT
*
596413 ATAAA ATATA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
596443 TAATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:597763 original size:21 final size:23
Alignment explanation
Indices: 597719--597765 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
597709 ATTAATATTT
597719 ATTTATATATATTTAATAATTAA
1 ATTTATATATATTTAATAATTAA
* * *
597742 ATTTATA-ATTTTTATTAATAAA
1 ATTTATATATATTTAATAATTAA
597764 AT
1 AT
597766 AATAAATAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTATATATATTTAATAATTAA
Found at i:599052 original size:28 final size:28
Alignment explanation
Indices: 598989--599074 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 28
598979 ATATTAGTTT
* * *
598989 TTTTAAATATTTATATTAATAAAATAATA
1 TTTTAAATATTAATATAAAT-ATATAATA
599018 TTTTAAATATTAATATAAATATATAATA
1 TTTTAAATATTAATATAAATATATAATA
* *
599046 TTTTAAA-AATAA-A-AAATATTTAATA
1 TTTTAAATATTAATATAAATATATAATA
599071 TTTT
1 TTTT
599075 TATATTTGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
25 15 0.29
26 1 0.02
27 4 0.08
28 14 0.27
29 18 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTTAAATATTAATATAAATATATAATA
Found at i:605859 original size:2 final size:2
Alignment explanation
Indices: 605852--605901 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
605842 TAAAAATAAA
* *
605852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AGG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
605895 CT AT AT A
1 AT AT AT A
605902 ATGAGCTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:608351 original size:10 final size:11
Alignment explanation
Indices: 608331--608364 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
608321 TTAGGGTTGA
608331 TTTTTCTTTTT
1 TTTTTCTTTTT
608342 TTTTTCTTTTT
1 TTTTTCTTTTT
*
608353 TTTTTCTCTTT
1 TTTTTCTTTTT
608364 T
1 T
608365 GGGTATGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:616283 original size:19 final size:19
Alignment explanation
Indices: 616255--616291 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
616245 GATTGAGTGA
616255 TAAAAAAA-TTTAATTTTT
1 TAAAAAAATTTTAATTTTT
616273 TAAATAAAATTTTAATTTT
1 TAAA-AAAATTTTAATTTT
616292 AAATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAAAAATTTTAATTTTT
Found at i:617615 original size:15 final size:16
Alignment explanation
Indices: 617595--617628 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
617585 TTGTTAAAAT
617595 TTAAATAT-ATTTATA
1 TTAAATATAATTTATA
617610 TTAAATATAAATTTATA
1 TTAAATAT-AATTTATA
617627 TT
1 TT
617629 TGATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATATAATTTATA
Found at i:622457 original size:2 final size:2
Alignment explanation
Indices: 622450--622479 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
622440 TAGCTAAGGA
622450 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
622480 GTGTTAACAA
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):
AT
Found at i:623939 original size:20 final size:20
Alignment explanation
Indices: 623916--623961 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
623906 ATATTTTATC
623916 ATATTATAATTT-TATTTAAA
1 ATATT-TAATTTATATTTAAA
*
623936 ATATTTATTTTATATTTAAA
1 ATATTTAATTTATATTTAAA
*
623956 TTATTT
1 ATATTT
623962 TTATATCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTTAATTTATATTTAAA
Found at i:629348 original size:21 final size:20
Alignment explanation
Indices: 629320--629363 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
629310 TAAAGTTTAT
* * *
629320 AAAAAAATTATTAAACATAA
1 AAAAAAATAAATAAAAATAA
629340 AAAATAAATAAATAAAAATAA
1 AAAA-AAATAAATAAAAATAA
629361 AAA
1 AAA
629364 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAAAATAAATAAAAATAA
Found at i:629502 original size:25 final size:26
Alignment explanation
Indices: 629440--629505 Score: 91
Period size: 25 Copynumber: 2.6 Consensus size: 26
629430 TCATTGCATA
629440 CATTTCATGCATTTCACATAACATTT
1 CATTTCATGCATTTCACATAACATTT
* *
629466 CA-TGCATGCATTTCACATAA-TTTT
1 CATTTCATGCATTTCACATAACATTT
*
629490 CATTTCATTCATTTCA
1 CATTTCATGCATTTCA
629506 TTTCATGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.14
25 28 0.80
26 2 0.06
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.44
Consensus pattern (26 bp):
CATTTCATGCATTTCACATAACATTT
Found at i:629506 original size:14 final size:14
Alignment explanation
Indices: 629487--629544 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
629477 TTCACATAAT
*
629487 TTTCATTTCATTCA
1 TTTCATTTCATGCA
629501 TTTCATTTCATGCA
1 TTTCATTTCATGCA
* *
629515 TTTCACTT-A-ACA
1 TTTCATTTCATGCA
*
629527 TTTCA-TGCATGCA
1 TTTCATTTCATGCA
629540 TTTCA
1 TTTCA
629545 CATAATTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 1 0.03
12 8 0.22
13 8 0.22
14 20 0.54
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.48
Consensus pattern (14 bp):
TTTCATTTCATGCA
Found at i:629511 original size:64 final size:64
Alignment explanation
Indices: 629440--629561 Score: 226
Period size: 64 Copynumber: 1.9 Consensus size: 64
629430 TCATTGCATA
*
629440 CATTTCATGCATTTCACATAACATTTCATGCATGCATTTCACATAATTTTCATTTCATTCATTT
1 CATTTCATGCATTTCACATAACATTTCATGCATGCATTTCACATAATTTTCACTTCATTCATTT
*
629504 CATTTCATGCATTTCACTTAACATTTCATGCATGCATTTCACATAATTTTCACTTCAT
1 CATTTCATGCATTTCACATAACATTTCATGCATGCATTTCACATAATTTTCACTTCAT
629562 ACATGCATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (64 bp):
CATTTCATGCATTTCACATAACATTTCATGCATGCATTTCACATAATTTTCACTTCATTCATTT
Found at i:629541 original size:25 final size:25
Alignment explanation
Indices: 629499--629599 Score: 80
Period size: 25 Copynumber: 3.8 Consensus size: 25
629489 TCATTTCATT
* *
629499 CATTTCATTTCATGCATTTCACTTAA
1 CATTTCATTGCATGCATTTCA-ATAA
629525 CATTTCA-TGCATGCATTTCACATAA
1 CATTTCATTGCATGCATTTCA-ATAA
* * *
629550 -TTTTCACTTCATACATGCATTTCAAAAA
1 CATTTCA--T--TGCATGCATTTCAATAA
629578 CATTTCATTGCATTGCATTTCA
1 CATTTCATTGCA-TGCATTTCA
629600 TTACATTGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
24 5 0.08
25 19 0.31
26 16 0.26
27 1 0.02
28 3 0.05
29 17 0.28
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.42
Consensus pattern (25 bp):
CATTTCATTGCATGCATTTCAATAA
Found at i:629542 original size:39 final size:38
Alignment explanation
Indices: 629461--629544 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 38
629451 TTTCACATAA
* * *
629461 CATTTCATGCATGCATTTCACATAATTTTCATTTCATT
1 CATTTCATGCATGCATTTCACATAAATTTCATTGCATG
* *
629499 CATTTCATTTCATGCATTTCACTTAACATTTCA-TGCATG
1 CATTTCA-TGCATGCATTTCACATAA-ATTTCATTGCATG
629538 CATTTCA
1 CATTTCA
629545 CATAATTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 7 0.18
39 27 0.69
40 5 0.13
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (38 bp):
CATTTCATGCATGCATTTCACATAAATTTCATTGCATG
Found at i:629583 original size:29 final size:29
Alignment explanation
Indices: 629528--629584 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
629518 CACTTAACAT
* * *
629528 TTCATGCATGCATTTCACATAATTTTCAC
1 TTCATACATGCATTTCACAAAAATTTCAC
629557 TTCATACATGCATTTCA-AAAACATTTCA
1 TTCATACATGCATTTCACAAAA-ATTTCA
629585 TTGCATTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (29 bp):
TTCATACATGCATTTCACAAAAATTTCAC
Found at i:629596 original size:15 final size:15
Alignment explanation
Indices: 629578--629618 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
629568 ATTTCAAAAA
629578 CATTTCATTGCATTG
1 CATTTCATTGCATTG
*
629593 CATTTCATTACATTG
1 CATTTCATTGCATTG
629608 C-TTTCA-TGCAT
1 CATTTCATTGCAT
629619 GAAAGTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 4 0.17
14 5 0.21
15 15 0.62
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (15 bp):
CATTTCATTGCATTG
Found at i:629606 original size:25 final size:24
Alignment explanation
Indices: 629490--629606 Score: 78
Period size: 25 Copynumber: 4.6 Consensus size: 24
629480 ACATAATTTT
*
629490 CATTTCATT-CATTTCATTTCATG
1 CATTTCATTACATTTCATTGCATG
629513 CATTTCACTTAACATTTCA-TGCATG
1 CATTTCA-TT-ACATTTCATTGCATG
* *
629538 CATTTCACATA-ATTTTCACTTCATACATG
1 CATTTCA-TTACA-TTTCA--T--TGCATG
**
629567 CATTTCAAAAACATTTCATTGCATTG
1 CATTTC-ATTACATTTCATTGCA-TG
629593 CATTTCATTACATT
1 CATTTCATTACATT
629607 GCTTTCATGC
Statistics
Matches: 75, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
23 8 0.11
24 8 0.11
25 23 0.31
26 15 0.20
27 1 0.01
29 18 0.24
30 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (24 bp):
CATTTCATTACATTTCATTGCATG
Found at i:630149 original size:30 final size:31
Alignment explanation
Indices: 630115--630180 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 31
630105 GCAACGTGAA
*
630115 AGCAGCATCTACGAT-AAAAAATCAGCTTCC
1 AGCAGCATCCACGATCAAAAAATCAGCTTCC
*
630145 AGCAGCATCCACGTTCGAAAAAATCAGCTTCC
1 AGCAGCATCCACGATC-AAAAAATCAGCTTCC
630177 AGCA
1 AGCA
630181 AGCAACCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 13 0.41
32 19 0.59
ACGTcount: A:0.38, C:0.29, G:0.15, T:0.18
Consensus pattern (31 bp):
AGCAGCATCCACGATCAAAAAATCAGCTTCC
Found at i:630195 original size:104 final size:104
Alignment explanation
Indices: 630082--630301 Score: 334
Period size: 104 Copynumber: 2.1 Consensus size: 104
630072 CTTCGAGCAG
* * *
630082 CTTCTAATCCACGGAGAAAAAAAGCAACGTGAAAGCAGCATCTACGATAAAAAATCAGCTTCCAG
1 CTTC-AATCCACGGAGAAAAAAAGCAACGTGAAAGCAGCATCCACGATAAAAAACCAGCTTCCAA
*
630147 CAGCATCCACGTTCGAAAAAA-TCAGCTTCCAGCAAGCAAC
65 CAGCATCCACGTTCAAAAAAACT-AGCTTCCAGCAAGCAAC
** *
630187 CTTCAATCCACGGAGAAGGAAAGCAACGTGAAAGCAGCATCCACGATCAAAAACCAGCTTCCAAC
1 CTTCAATCCACGGAGAAAAAAAGCAACGTGAAAGCAGCATCCACGATAAAAAACCAGCTTCCAAC
*
630252 AGCATCCACGTTCAAAAAAACTAGCTTCCAGCAAGCAGC
66 AGCATCCACGTTCAAAAAAACTAGCTTCCAGCAAGCAAC
*
630291 CTCCAATCCAC
1 CTTCAATCCAC
630302 CATCAAACAG
Statistics
Matches: 105, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
104 100 0.95
105 5 0.05
ACGTcount: A:0.40, C:0.30, G:0.16, T:0.15
Consensus pattern (104 bp):
CTTCAATCCACGGAGAAAAAAAGCAACGTGAAAGCAGCATCCACGATAAAAAACCAGCTTCCAAC
AGCATCCACGTTCAAAAAAACTAGCTTCCAGCAAGCAAC
Found at i:630424 original size:240 final size:239
Alignment explanation
Indices: 629963--630404 Score: 598
Period size: 240 Copynumber: 1.8 Consensus size: 239
629953 GCAGAGGGGG
* ** * * *
629963 AGGAAAGCAACGTGAAAGCAGCATCCACTATCAAAAATTAGCTTCCAGCAGTATCCACATTCGAA
1 AGGAAAGCAACGTGAAAGCAGCATCCACGATCAAAAACCAGCTTCCAACAGCATCCACATTCAAA
* * * * * *
630028 AAAACCAGCTTCCAGCAAGCAGCTTTCAATTCACGATCAAACAACTTCGAGCAGCTTCTAATCCA
66 AAAACCAGCTTCCAGCAAGCAGCCTCCAATCCACCATCAAACAACTTCGAGCAGCCTCCAATCCA
* * * * *
630093 CGGAGAAAAAAAGCAACGTGAAAGCAGCATCTACGATAAAAAATCAGCTTCCAGCAGCATCCACG
131 CGAACAAAAAAAGCAACGTAAAAGCAGCATCCACGATAAAAAACCAGCTTCCAGCAGCATCCACG
*
630158 TTCGAAAAAATCAGCTTCCAGCAAGCAACCTTCAATCCACGGAGA
196 ATC-AAAAAATCAGCTTCCAGCAAGCAACCTTCAATCCACGGAGA
*
630203 AGGAAAGCAACGTGAAAGCAGCATCCACGATCAAAAACCAGCTTCCAACAGCATCCACGTTCAAA
1 AGGAAAGCAACGTGAAAGCAGCATCCACGATCAAAAACCAGCTTCCAACAGCATCCACATTCAAA
* *
630268 AAAACTAGCTTCCAGCAAGCAGCCTCCAATCCACCATCAAACAGCTTCGAGCAGCCTCCAATCCA
66 AAAACCAGCTTCCAGCAAGCAGCCTCCAATCCACCATCAAACAACTTCGAGCAGCCTCCAATCCA
*** *
630333 CGAACAAGCACGGCAGCAACG-AAAAGGCAGCATCCACGATCAAAAACCAGCTTCCAGCAGCATC
131 CGAACAA--A-AAAAGCAACGTAAAA-GCAGCATCCACGATAAAAAACCAGCTTCCAGCAGCATC
*
630397 TACGATCA
192 CACGATCA
630405 CGGACAGCTT
Statistics
Matches: 172, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
240 120 0.70
242 5 0.03
243 47 0.27
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.15
Consensus pattern (239 bp):
AGGAAAGCAACGTGAAAGCAGCATCCACGATCAAAAACCAGCTTCCAACAGCATCCACATTCAAA
AAAACCAGCTTCCAGCAAGCAGCCTCCAATCCACCATCAAACAACTTCGAGCAGCCTCCAATCCA
CGAACAAAAAAAGCAACGTAAAAGCAGCATCCACGATAAAAAACCAGCTTCCAGCAGCATCCACG
ATCAAAAAATCAGCTTCCAGCAAGCAACCTTCAATCCACGGAGA
Found at i:630564 original size:124 final size:124
Alignment explanation
Indices: 630344--630591 Score: 397
Period size: 124 Copynumber: 2.0 Consensus size: 124
630334 GAACAAGCAC
* * *
630344 GGCAGCAACGAAAAGGCAGCATCCACGATCAAAAACCAGCTTCCAGCAGCATCTACGATCACGGA
1 GGCAGCAACGAAAAGGCAACATCCACGATAAAAAACCAGCTTCCAGCAGCATCCACGATCACGGA
* * * * *
630409 CAGCTTCCAGCAAGCAGCCCGCAAGGTCCAGCAACTTCCCGCATCCATCTCAGCTCACG
66 CAACTTCCAACAAGCAGCCCACAAGCTCCAGCAACTTCCCGCATCCACCTCAGCTCACG
*
630468 GGCAGCAACGAAAAGGCAACATCCACGATAAAAAATCAGCTTCCAGCAGCATCCACGATCACGGA
1 GGCAGCAACGAAAAGGCAACATCCACGATAAAAAACCAGCTTCCAGCAGCATCCACGATCACGGA
* *
630533 CAACTTCCAACAAGCAGCCCACAAGCTCCAGCAGCTTCCCGCATCTACCTCAGCTCACG
66 CAACTTCCAACAAGCAGCCCACAAGCTCCAGCAACTTCCCGCATCCACCTCAGCTCACG
630592 AACAGCTTCC
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 113 1.00
ACGTcount: A:0.32, C:0.36, G:0.19, T:0.13
Consensus pattern (124 bp):
GGCAGCAACGAAAAGGCAACATCCACGATAAAAAACCAGCTTCCAGCAGCATCCACGATCACGGA
CAACTTCCAACAAGCAGCCCACAAGCTCCAGCAACTTCCCGCATCCACCTCAGCTCACG
Found at i:633244 original size:29 final size:30
Alignment explanation
Indices: 633211--633269 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
633201 TGCGGGCTGC
*
633211 TTGCTGGAAGCT-GTTTGTGATCGTGGATG
1 TTGCTGAAAGCTGGTTTGTGATCGTGGATG
* *
633240 TTGCTGAAAGTTGGTTTTTGATCGTGGATG
1 TTGCTGAAAGCTGGTTTGTGATCGTGGATG
633270 CTGTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.15, C:0.08, G:0.36, T:0.41
Consensus pattern (30 bp):
TTGCTGAAAGCTGGTTTGTGATCGTGGATG
Found at i:633351 original size:32 final size:30
Alignment explanation
Indices: 633315--633381 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
633305 TGGAGGCTGC
*
633315 TTGCTCGAAGTTAGTTTTTTTGAACGTGGATG
1 TTGCTCGAAGTT-G-GTTTTTGAACGTGGATG
* *
633347 TTGCTGGAAGTTGGTTTTTGATCGTGGATG
1 TTGCTCGAAGTTGGTTTTTGAACGTGGATG
*
633377 CTGCT
1 TTGCT
633382 TTCACGTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 19 0.61
31 1 0.03
32 11 0.35
ACGTcount: A:0.15, C:0.10, G:0.31, T:0.43
Consensus pattern (30 bp):
TTGCTCGAAGTTGGTTTTTGAACGTGGATG
Found at i:633455 original size:136 final size:135
Alignment explanation
Indices: 633297--633667 Score: 544
Period size: 136 Copynumber: 2.7 Consensus size: 135
633287 TCGTGCTTGT
* * * * *
633297 TCGTGGATTGGAGGCTGCTTGCTCGAAGTTAGTTTTTTTGAACGTGGATGTTGCTGGAAGTTGGT
1 TCGTGGATTGGAGGCTGCTTGCTGGAAGTT-GTTTTTTCGAACGTGGATGCTGCTGGAAGCTGAT
*
633362 TTTTGATCGTGGATGCTGCTTTCACGTTGTTTTCCTTCTCCATAGATTTGAGGCTGCTCGAAGCT
65 TTTTGATCGTGGATGCTGCTTTCACGTTGTTTTCCTTCTCCATAGATTGGAGGCTGCTCGAAGCT
633427 GTTTAA
130 GTTTAA
633433 TCGTGGATTGGAGGCTGCTTGCTGGAAGTTGATTTTTTCGAACGTGGATGCTGCTGGAAGCTGAT
1 TCGTGGATTGGAGGCTGCTTGCTGGAAGTTG-TTTTTTCGAACGTGGATGCTGCTGGAAGCTGAT
* ** * * *
633498 TTTTTATCGTGGATGCTGCTTTCACGTTGTTTTTTTTCTTCGTGGATTGGAGGCTGCTCGAAGCT
65 TTTTGATCGTGGATGCTGCTTTCACGTTGTTTTCCTTCTCCATAGATTGGAGGCTGCTCGAAGCT
*
633563 GTTTGA
130 GTTTAA
* * *
633569 TCGTGGATTGGAGGCTGCTTGCTGGAAGCTGGTTTTTTCGAACATGGATGCTGCTGAAAGCTGAT
1 TCGTGGATTGGAGGCTGCTTGCTGGAAG-TTGTTTTTTCGAACGTGGATGCTGCTGGAAGCTGAT
* * *
633634 TTTTGATCGTGAATGTTGCTTTCACGTTGCTTTC
65 TTTTGATCGTGGATGCTGCTTTCACGTTGTTTTC
633668 TTCCCCTTCT
Statistics
Matches: 212, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
135 1 0.00
136 209 0.99
137 2 0.01
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.40
Consensus pattern (135 bp):
TCGTGGATTGGAGGCTGCTTGCTGGAAGTTGTTTTTTCGAACGTGGATGCTGCTGGAAGCTGATT
TTTGATCGTGGATGCTGCTTTCACGTTGTTTTCCTTCTCCATAGATTGGAGGCTGCTCGAAGCTG
TTTAA
Found at i:633493 original size:68 final size:68
Alignment explanation
Indices: 633414--633631 Score: 187
Period size: 68 Copynumber: 3.2 Consensus size: 68
633404 TAGATTTGAG
*
633414 GCTGCTCGAAGCTGTTTAATCGTGGATTGGAGGCTGCTTGCTGGAAGTTGATTTTTTCGAACGTG
1 GCTGCTCGAAGCTGTTTAATCGTGGATTGGAGGCTGCTTGCTGGAAGTTGATTTTTTCGAACATG
633479 GAT
66 GAT
* * * ** ** ** **
633482 GCTGCTGGAAGCTGATTTTTTATCGTGGA-T----GCTGCTTTCACGTTGTTTTTTTTCTTCGTG
1 GCTGCTCGAAGCTG---TTTAATCGTGGATTGGAGGCTGCTTGCTGGAAGTTGATTTT-TTCGAA
* *
633542 GATTGGAG
62 CA-TGGAT
* * *
633550 GCTGCTCGAAGCTGTTTGATCGTGGATTGGAGGCTGCTTGCTGGAAGCTGGTTTTTTCGAACATG
1 GCTGCTCGAAGCTGTTTAATCGTGGATTGGAGGCTGCTTGCTGGAAGTTGATTTTTTCGAACATG
633615 GAT
66 GAT
633618 GCTGCT-GAAAGCTG
1 GCTGCTCG-AAGCTG
633632 ATTTTTGATC
Statistics
Matches: 111, Mismatches: 28, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
65 11 0.10
66 17 0.15
67 5 0.05
68 46 0.41
69 5 0.05
70 16 0.14
71 11 0.10
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.37
Consensus pattern (68 bp):
GCTGCTCGAAGCTGTTTAATCGTGGATTGGAGGCTGCTTGCTGGAAGTTGATTTTTTCGAACATG
GAT
Found at i:633511 original size:30 final size:31
Alignment explanation
Indices: 633452--633517 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 31
633442 GGAGGCTGCT
*
633452 TGCTGGAAGTTGATTTTTTCGAACGTGGATGC
1 TGCTGGAAGCTGATTTTTTC-AACGTGGATGC
*
633484 TGCTGGAAGCTGATTTTTT-ATCGTGGATGC
1 TGCTGGAAGCTGATTTTTTCAACGTGGATGC
633514 TGCT
1 TGCT
633518 TTCACGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 14 0.44
32 18 0.56
ACGTcount: A:0.17, C:0.14, G:0.30, T:0.39
Consensus pattern (31 bp):
TGCTGGAAGCTGATTTTTTCAACGTGGATGC
Found at i:634043 original size:15 final size:15
Alignment explanation
Indices: 634013--634053 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
634003 ATCAACTTTC
634013 ATGC-ATGAAA-GCA
1 ATGCAATGAAATGCA
634026 ATGCAATGAAATGCA
1 ATGCAATGAAATGCA
634041 ATGCAATGAAATG
1 ATGCAATGAAATG
634054 TTTTTGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 4 0.15
14 6 0.23
15 16 0.62
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (15 bp):
ATGCAATGAAATGCA
Found at i:634147 original size:14 final size:14
Alignment explanation
Indices: 634128--634160 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
634118 AAATGTTACG
634128 TGAAATGCATAAAA
1 TGAAATGCATAAAA
*
634142 TGAAATGCATGAAA
1 TGAAATGCATAAAA
634156 TGAAA
1 TGAAA
634161 ATTATGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.21
Consensus pattern (14 bp):
TGAAATGCATAAAA
Found at i:634200 original size:26 final size:25
Alignment explanation
Indices: 634142--634208 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 25
634132 ATGCATAAAA
634142 TGAAATGCATGAAATGAAAATTATG
1 TGAAATGCATGAAATGAAAATTATG
* *
634167 TGAAATGCATG-CATGAAATGTTAATG
1 TGAAATGCATGAAATGAAA-ATT-ATG
634193 TGAAATGCATGAAATG
1 TGAAATGCATGAAATG
634209 TATGCAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 6 0.17
25 13 0.36
26 14 0.39
27 3 0.08
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.28
Consensus pattern (25 bp):
TGAAATGCATGAAATGAAAATTATG
Found at i:634299 original size:21 final size:21
Alignment explanation
Indices: 634262--634318 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
634252 CTTTTTTTTT
634262 ATTTTATTATTTT--TTTATAA
1 ATTTT-TTATTTTAATTTATAA
**
634282 ATTTTTTATTTTAATTTATTT
1 ATTTTTTATTTTAATTTATAA
*
634303 AGTTTTTATGTTTAAT
1 ATTTTTTAT-TTTAAT
634319 AATTTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 7 0.23
20 5 0.16
21 13 0.42
22 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
ATTTTTTATTTTAATTTATAA
Found at i:634323 original size:21 final size:21
Alignment explanation
Indices: 634284--634323 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
634274 TTTTATAAAT
*
634284 TTTTTATTTTAATTTATTTAG
1 TTTTTATTTTAATTAATTTAG
634305 TTTTTATGTTTAA-TAATTT
1 TTTTTAT-TTTAATTAATTT
634324 TTTTATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTTATTTTAATTAATTTAG
Found at i:634680 original size:15 final size:17
Alignment explanation
Indices: 634649--634680 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
634639 CAAGAAGAAT
634649 AAAACAAGAATGCAGGA
1 AAAACAAGAATGCAGGA
634666 AAAACAA-AA-GCAGGA
1 AAAACAAGAATGCAGGA
634681 CCACACAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.62, C:0.12, G:0.22, T:0.03
Consensus pattern (17 bp):
AAAACAAGAATGCAGGA
Found at i:634896 original size:43 final size:43
Alignment explanation
Indices: 634805--635550 Score: 681
Period size: 42 Copynumber: 17.7 Consensus size: 43
634795 AAGTCTCTAA
* * * * *
634805 GGTCAAAGCCAACGGGCAGACTTAGGGA-AAAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAG
*
634847 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAG
* * * * *
634890 GGTCAAAGCCAAAAAGCAGACTTAGGGAAAG-AAAGTCTTCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAG
*
634932 GGTCAAAGCCGACAGGCAGACTAAGGGATAAAAAAGTCTTCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAG
* * *
634975 GGTCAAAGCCGATAGGCAGACTAAGGGATAGGAAAGTCTTCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAG
* * * *
635018 GGTCAAAGCCGATAGGCAGACTGAGGGAAAGGAAAGT-TTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTT-CAG
* * * *
635061 AGTCAAAGCCGACAGACAGACTGAGGG-TTGAAAAGTC--CAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAG
* * *
635101 GATCAAAGTCGACAGGCAGACTAAGGGAT-GAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAG
* * *
635143 GGTCAAAGCCGATAGGCAGACTGAGGG-TTGAAAAGTC-TCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTC-AG
* * *
635185 GGTCAAAGCCGACAGACAGACTGAGGGA-AGGAAAGTC-TCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTC-AG
* * * * *
635227 GGTCAAAGTCGA-TGGACAAACTGAGGGA-AGGAAAGTC-TCTAG
1 GGTCAAAGCCGACAGG-CAGACTAAGGGATAGAAAAGTCTTC-AG
* * * *
635269 GGTTAAAGCCGACAGGCAGACTGAAGGG-TAGGAATGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACT-AAGGGATAGAAAAGTCTTCAG
* * * *
635312 GGTTAAA-CCGACAGGCAGACTAAGGG-TAAAAAAATCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAG
* * *
635353 GGTCAAAGCCGACAGGCAAACTAAGGAATAGGAAAGTC-TCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTC-AG
* ** * * *
635396 GATCAAAGTTGACAGGCATACTGAGGGAAAGAAAAGT-TTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTT-CAG
* * * *
635439 GGTCAAAGCCGACAGGCAGACTGAGGGAAAG-AAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAG
* * * * *
635481 GGACGAAGTCAACAGGCAGACTAAGAGAT-GAAAAGTC-TCAAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTC-AG
*
635523 GGTCAAAGCCGACAGACAGACTAAGGGA
1 GGTCAAAGCCGACAGGCAGACTAAGGGA
635551 AAACAGAAAA
Statistics
Matches: 585, Mismatches: 96, Indels: 46
0.80 0.13 0.06
Matches are distributed among these distances:
40 33 0.06
41 28 0.05
42 282 0.48
43 240 0.41
44 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.30, T:0.14
Consensus pattern (43 bp):
GGTCAAAGCCGACAGGCAGACTAAGGGATAGAAAAGTCTTCAG
Found at i:638760 original size:48 final size:48
Alignment explanation
Indices: 638704--638800 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
638694 AGTGAACACC
*
638704 TTGAGAACACTGTTTTTGAGGCTGCACTGACTGTTAACGTTACATAGT
1 TTGAGAACACTGTTTTTGAGGCTGCACTGACTGTTAACGGTACATAGT
638752 TTGAGAACACTGTTTTTGAGGCTGCACTGACTGTTAACGGTACATAGT
1 TTGAGAACACTGTTTTTGAGGCTGCACTGACTGTTAACGGTACATAGT
638800 T
1 T
638801 AATATTGGAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (48 bp):
TTGAGAACACTGTTTTTGAGGCTGCACTGACTGTTAACGGTACATAGT
Found at i:640453 original size:12 final size:13
Alignment explanation
Indices: 640436--640485 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
640426 CAATACGATT
640436 ATAATAT-AAAAA
1 ATAATATAAAAAA
640448 ATAATATAAAATAA
1 ATAATATAAAA-AA
*
640462 ATTATAATAAAAAA
1 ATAAT-ATAAAAAA
640476 ATAATATAAA
1 ATAATATAAA
640486 TATGATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 7 0.21
13 8 0.24
14 12 0.36
15 6 0.18
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAATATAAAAAA
Found at i:641517 original size:2 final size:2
Alignment explanation
Indices: 641510--641548 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
641500 TTTCAAACAA
641510 AT AT 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 A
641549 GGAATTCAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:645499 original size:10 final size:10
Alignment explanation
Indices: 645482--645531 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
645472 TATTATATAT
645482 TTAT-ATAAA
1 TTATAATAAA
645491 TTATAATAAA
1 TTATAATAAA
*
645501 TTAATAAATTATA
1 TT-AT-AA-TAAA
645514 TTATAATAAA
1 TTATAATAAA
645524 TTATAATA
1 TTATAATA
645532 TATTTATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
9 4 0.11
10 18 0.51
11 4 0.11
12 4 0.11
13 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTATAATAAA
Found at i:645522 original size:15 final size:15
Alignment explanation
Indices: 645486--645533 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 15
645476 ATATATTTAT
645486 ATAAATTATAATAAATTA
1 ATAAATTATAAT--A-TA
*
645504 ATAAATTATATTATA
1 ATAAATTATAATATA
645519 ATAAATTATAATATA
1 ATAAATTATAATATA
645534 TTTATATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
18 11 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATTATAATATA
Found at i:646143 original size:14 final size:14
Alignment explanation
Indices: 646105--646161 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
646095 AATCAAATTC
*
646105 AATAATTTATATAT
1 AATATTTTATATAT
*
646119 ACATA-TATATATAT
1 A-ATATTTTATATAT
646133 AATATTTTATAT-T
1 AATATTTTATATAT
* *
646146 AAAATTTTAAATAT
1 AATATTTTATATAT
646160 AA
1 AA
646162 ATATAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 14 0.39
14 19 0.53
15 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTTTATATAT
Found at i:648456 original size:3 final size:3
Alignment explanation
Indices: 648448--648473 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
648438 TTAAATGCTT
648448 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
648474 ATTATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:649273 original size:29 final size:29
Alignment explanation
Indices: 649241--649335 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 29
649231 TGATCTTAAC
649241 ATATTTATATTATATTTATATATTTTATT
1 ATATTTATATTATATTTATATATTTTATT
*
649270 ATATTT-TAATTATATTTA-AAATTTATATT
1 ATATTTAT-ATTATATTTATATATTT-TATT
* * *
649299 ATAATTA-ATTA-ATTAAT-TAATTTATT
1 ATATTTATATTATATTTATATATTTTATT
649325 ATATTTATATT
1 ATATTTATATT
649336 TAATATTATC
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
26 10 0.18
27 10 0.18
28 10 0.18
29 25 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
ATATTTATATTATATTTATATATTTTATT
Found at i:649344 original size:18 final size:17
Alignment explanation
Indices: 649241--649344 Score: 65
Period size: 18 Copynumber: 6.8 Consensus size: 17
649231 TGATCTTAAC
649241 ATATTTATATTATATTT
1 ATATTTATATTATATTT
649258 ATA--TAT-TT-TA-TT
1 ATATTTATATTATATTT
649270 ATATTT-TAATTATATTT
1 ATATTTAT-ATTATATTT
* *
649287 AAAATTTATATTATAATT
1 -ATATTTATATTATATTT
649305 A-A-TTA-ATTA-A-TT
1 ATATTTATATTATATTT
649317 A-A-TT-TATTATATTT
1 ATATTTATATTATATTT
649331 ATATTTAATATTAT
1 ATATTT-ATATTAT
649345 CAATAAATTT
Statistics
Matches: 70, Mismatches: 2, Indels: 29
0.69 0.02 0.29
Matches are distributed among these distances:
12 15 0.21
13 5 0.07
14 10 0.14
15 9 0.13
16 5 0.07
17 6 0.09
18 19 0.27
19 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTATATTATATTT
Found at i:650241 original size:29 final size:28
Alignment explanation
Indices: 650198--650252 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
650188 CTATTTTTAC
* *
650198 AATATTAAATTTAAATTAAATTAAAAAAT
1 AATAATAAATATAAA-TAAATTAAAAAAT
*
650227 AATAATAAATATAAATATATTAAAAA
1 AATAATAAATATAAATAAATTAAAAA
650253 TTATTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
AATAATAAATATAAATAAATTAAAAAAT
Found at i:650521 original size:22 final size:21
Alignment explanation
Indices: 650470--650526 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
650460 TCACTTTTGC
650470 ATTTAATATTTAATATTTATT
1 ATTTAATATTTAATATTTATT
*
650491 TTTTAAATATTT-ATATTTATGT
1 ATTT-AATATTTAATATTTAT-T
*
650513 GATTTAATAATTAA
1 -ATTTAATATTTAA
650527 ATAAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 11 0.38
22 14 0.48
23 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTTAATATTTAATATTTATT
Found at i:651869 original size:12 final size:12
Alignment explanation
Indices: 651839--651919 Score: 53
Period size: 11 Copynumber: 7.0 Consensus size: 12
651829 AGTTTTAACG
*
651839 TATAAAAAATAA
1 TATAAAATATAA
*
651851 T-TAAAATATAT
1 TATAAAATATAA
651862 TATAAAATATAA
1 TATAAAATATAA
*
651874 -ATAACATA-AA
1 TATAAAATATAA
* *
651884 TTTATAAATATTA
1 TATA-AAATATAA
* *
651897 TTTTAAATATAA
1 TATAAAATATAA
*
651909 T-TATAATATAA
1 TATAAAATATAA
651920 AAATAAAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
10 2 0.04
11 26 0.48
12 22 0.41
13 4 0.07
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:651873 original size:23 final size:23
Alignment explanation
Indices: 651839--651914 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
651829 AGTTTTAACG
*
651839 TATAAAAAATAATTAAAATATAT
1 TATAAAATATAATTAAAATATAT
* * *
651862 TATAAAATATAAATAACATAAAT
1 TATAAAATATAATTAAAATATAT
* *
651885 T-TATAAATATTATTTTAAATATAAT
1 TATA-AAATA-TAATTAAAATAT-AT
651910 TATAA
1 TATAA
651915 TATAAAAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
22 2 0.05
23 25 0.62
24 7 0.17
25 4 0.10
26 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (23 bp):
TATAAAATATAATTAAAATATAT
Found at i:653362 original size:18 final size:18
Alignment explanation
Indices: 653335--653373 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
653325 CAGGAATTCA
653335 GGCTTGGGCTTTCGCTTC
1 GGCTTGGGCTTTCGCTTC
*
653353 GGCTTTGGCTTTCGCTTC
1 GGCTTGGGCTTTCGCTTC
653371 GGC
1 GGC
653374 ATTAGCTCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.28, G:0.33, T:0.38
Consensus pattern (18 bp):
GGCTTGGGCTTTCGCTTC
Found at i:653444 original size:16 final size:16
Alignment explanation
Indices: 653420--653470 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
653410 ATTTATATAT
653420 TTATATATTTTTATAAA
1 TTAT-TATTTTTATAAA
653437 TTATTATTATTT-TAAA
1 TTATTATT-TTTATAAA
* *
653453 ATATTATTTATATAAA
1 TTATTATTTTTATAAA
653469 TT
1 TT
653471 TTAATATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 2 0.07
16 20 0.69
17 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTATTTTTATAAA
Found at i:653467 original size:32 final size:31
Alignment explanation
Indices: 653425--653497 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
653415 TATATTTATA
* * *
653425 TATTTTTATAAATTATTATTATTTTAA-AATAT
1 TATTTATATAAATT-TTAATATATTAATAAT-T
653457 TATTTATATAAATTTTAATATATTAATAATT
1 TATTTATATAAATTTTAATATATTAATAATT
*
653488 TAATTATATA
1 TATTTATATA
653498 TTTTATATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 20 0.56
32 16 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TATTTATATAAATTTTAATATATTAATAATT
Found at i:654008 original size:31 final size:30
Alignment explanation
Indices: 653940--654009 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
653930 ATTTTTACTT
*
653940 TTAAAAA-A-TATTAAAATATTTAATTTCA
1 TTAAAAATATTATTAAAATATTTAATTTAA
*
653968 TTAAAAATATTATTAAAATTTTTTAA-TTAA
1 TTAAAAATATTATTAAAA-TATTTAATTTAA
653998 TTAAATAATATT
1 TTAAA-AATATT
654010 TATAAACACT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 7 0.19
29 1 0.03
30 16 0.44
31 12 0.33
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
TTAAAAATATTATTAAAATATTTAATTTAA
Found at i:654995 original size:23 final size:24
Alignment explanation
Indices: 654969--655032 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 24
654959 TTTTAAATAT
654969 AATATAATTATAATA-AATAAAAA
1 AATATAATTATAATATAATAAAAA
*
654992 AATAT--TTAAAATATAAT-AAAA
1 AATATAATTATAATATAATAAAAA
* *
655013 AATTTAAATATAATATAATA
1 AATATAATTATAATATAATA
655033 TTAAATATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 15 0.45
22 3 0.09
23 15 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AATATAATTATAATATAATAAAAA
Found at i:655023 original size:18 final size:18
Alignment explanation
Indices: 654985--655040 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
654975 ATTATAATAA
654985 ATAA-AAAAATATTTAAAAT
1 ATAATAAAAA-ATTT-AAAT
655004 ATAATAAAAAATTTAAAT
1 ATAATAAAAAATTTAAAT
* *
655022 ATAATATAATA-TTAAAT
1 ATAATAAAAAATTTAAAT
655039 AT
1 AT
655041 CAAAATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.24
18 13 0.38
19 8 0.24
20 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAAAAAATTTAAAT
Found at i:655050 original size:17 final size:17
Alignment explanation
Indices: 654954--655047 Score: 59
Period size: 18 Copynumber: 5.2 Consensus size: 17
654944 AAGTAAATTT
*
654954 AATAATTTTAAATATAA
1 AATAATATTAAATATAA
*
654971 TATAATTATAATAAATA-AA
1 AATAA-TAT--TAAATATAA
654990 AA-AATATTTAAAATATAA
1 AATAATA-TT-AAATATAA
*
655008 TAA-AAAATTTAAATATAA
1 -AATAATA-TTAAATATAA
*
655026 TATAATATTAAATATCAA
1 AATAATATTAAATAT-AA
655044 AATA
1 AATA
655048 TATAACAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
16 1 0.02
17 20 0.33
18 23 0.38
19 11 0.18
20 6 0.10
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATATTAAATATAA
Done.