Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 136 of 185
Found at i:41680272 original size:98 final size:98
Alignment explanation
Indices: 41680107--41680375 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
41680097 TAAGTGTAGC
* * *
41680107 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
41680172 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
41680206 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
41680271 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
41680304 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
41680369 GATCAGA
66 GATCAGA
41680376 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:41684472 original size:27 final size:26
Alignment explanation
Indices: 41684434--41684488 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
41684424 TCGGGTATTT
*
41684434 TTCGGTAATTCGGTTAATTC-GGTTAA
1 TTCGGTAATTCGGGTAATTCAGG-TAA
41684460 TTCGGTTAATTCGGGTAATTCAGGTAA
1 TTCGG-TAATTCGGGTAATTCAGGTAA
41684487 TT
1 TT
41684489 TTTAACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.19
27 19 0.73
28 2 0.08
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.42
Consensus pattern (26 bp):
TTCGGTAATTCGGGTAATTCAGGTAA
Found at i:41684488 original size:9 final size:9
Alignment explanation
Indices: 41684434--41684480 Score: 78
Period size: 9 Copynumber: 5.3 Consensus size: 9
41684424 TCGGGTATTT
41684434 TTCGG-TAA
1 TTCGGTTAA
41684442 TTCGGTTAA
1 TTCGGTTAA
41684451 TTCGGTTAA
1 TTCGGTTAA
41684460 TTCGGTTAA
1 TTCGGTTAA
*
41684469 TTCGGGTAA
1 TTCGGTTAA
41684478 TTC
1 TTC
41684481 AGGTAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
8 5 0.14
9 32 0.86
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:41684665 original size:12 final size:12
Alignment explanation
Indices: 41684648--41684672 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41684638 AGTAATTTCG
41684648 GGTCGGTTAACC
1 GGTCGGTTAACC
41684660 GGTCGGTTAACC
1 GGTCGGTTAACC
41684672 G
1 G
41684673 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:41699035 original size:12 final size:12
Alignment explanation
Indices: 41698993--41699038 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
41698983 TATTTTTTAT
*
41698993 AAAAATAT-TTA
1 AAAAATATATAA
41699004 AAAAAT-TA-AA
1 AAAAATATATAA
41699014 AGAAAATATATAA
1 A-AAAATATATAA
41699027 AAAAATATATAA
1 AAAAATATATAA
41699039 TTTTTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 3 0.10
11 11 0.37
12 13 0.43
13 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
AAAAATATATAA
Found at i:41699067 original size:27 final size:26
Alignment explanation
Indices: 41699016--41699078 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
41699006 AAATTAAAAG
*
41699016 AAAATATATAAAAAAATATATAATTTT
1 AAAA-ATATAAAAAAATATATAATTAT
*
41699043 TAAAATATAAAAGAAAT-TATAAATTAT
1 AAAAATATAAAA-AAATATAT-AATTAT
41699070 AAAAATATA
1 AAAAATATA
41699079 TGTGTCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAAATATAAAAAAATATATAATTAT
Found at i:41702488 original size:25 final size:26
Alignment explanation
Indices: 41702439--41702488 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
41702429 ATTTTTATTT
*
41702439 TTATTAAAATATATTTAATAATAACC
1 TTATTAAAATATATATAATAATAACC
*
41702465 TTATTAAAATTTA-ATAATAATAAC
1 TTATTAAAATATATATAATAATAAC
41702489 AATAATCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
TTATTAAAATATATATAATAATAACC
Found at i:41704410 original size:16 final size:17
Alignment explanation
Indices: 41704389--41704435 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
41704379 ACCCTAACAA
41704389 CTCTATTCCATTACA-C
1 CTCTATTCCATTACAGC
** *
41704405 CTCTATTTAATTATAGC
1 CTCTATTCCATTACAGC
41704422 C-CTATTCCATTACA
1 CTCTATTCCATTACA
41704436 ATCAACCAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.28, C:0.30, G:0.02, T:0.40
Consensus pattern (17 bp):
CTCTATTCCATTACAGC
Found at i:41705268 original size:26 final size:25
Alignment explanation
Indices: 41705228--41705276 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
41705218 ATGAACGCCC
41705228 TTCTTTGCTCTCTGCTCTCTGCTGG
1 TTCTTTGCTCTCTGCTCTCTGCTGG
*
41705253 TTCTTTGTTTCTCTGCTCTCTGCT
1 TTCTTTG-CTCTCTGCTCTCTGCT
41705277 ACGCTGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.00, C:0.31, G:0.16, T:0.53
Consensus pattern (25 bp):
TTCTTTGCTCTCTGCTCTCTGCTGG
Found at i:41705286 original size:31 final size:33
Alignment explanation
Indices: 41705228--41705290 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
41705218 ATGAACGCCC
* *
41705228 TTCTTTGCTCTCTGCTCTCTGCTGGTTCTTTGT
1 TTCTCTGCTCTCTGCTCACTGCTGGTTCTTTGT
41705261 TTCTCTGCTCTCTGCT-AC-GCTGGTTCTTTG
1 TTCTCTGCTCTCTGCTCACTGCTGGTTCTTTG
41705291 CCCTCATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 12 0.43
32 1 0.04
33 15 0.54
ACGTcount: A:0.02, C:0.29, G:0.19, T:0.51
Consensus pattern (33 bp):
TTCTCTGCTCTCTGCTCACTGCTGGTTCTTTGT
Found at i:41708285 original size:3 final size:3
Alignment explanation
Indices: 41708277--41708311 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
41708267 CTTAAAATGA
41708277 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41708312 AGTTTAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41709513 original size:27 final size:26
Alignment explanation
Indices: 41709482--41709559 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 26
41709472 CTAGACTACA
41709482 TTTTAATTCTTTTATAAATCTATAAAT
1 TTTTAATTCTTTTATAAAT-TATAAAT
* * *
41709509 TTTTAGTTCTTTTATATAAATTTTTAAT
1 TTTTAATTC-TTT-TATAAATTATAAAT
*
41709537 TTTTAATT-TTTGATAAATGTATA
1 TTTTAATTCTTTTATAAAT-TATA
41709560 TAATATATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
25 6 0.15
26 5 0.12
27 8 0.20
28 15 0.37
29 7 0.17
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTTAATTCTTTTATAAATTATAAAT
Found at i:41709540 original size:19 final size:21
Alignment explanation
Indices: 41709502--41709541 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41709492 TTTATAAATC
*
41709502 TATAAATTTTTAGTTCTTTTA
1 TATAAATTTTTAGATCTTTTA
41709523 TATAAATTTTTA-AT-TTTTA
1 TATAAATTTTTAGATCTTTTA
41709542 ATTTTTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 1 0.06
21 12 0.67
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TATAAATTTTTAGATCTTTTA
Found at i:41712966 original size:2 final size:2
Alignment explanation
Indices: 41712953--41713008 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
41712943 TTAGAACAAA
*
41712953 AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41712995 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
41713009 TAGTGTATCC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41715827 original size:42 final size:42
Alignment explanation
Indices: 41715756--41715841 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 42
41715746 ACAAAAACGC
* *
41715756 CGCCGCTAAAGAACATGGTTTTTAGCGGCGTTTTTGTT-TAAG
1 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT-TTCTAAG
*
41715798 CGCCTCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAG
41715840 CG
1 CG
41715842 TCGGCACTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 2 0.05
42 38 0.95
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAG
Found at i:41716234 original size:21 final size:21
Alignment explanation
Indices: 41716169--41716236 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
41716159 TGCTCTGCTT
* * *
41716169 TGCTTCTCTCGCTGCAGCTTT
1 TGCTTCCCTCGCTGCAGCCTC
* *
41716190 TGCTTCCCTCGCTGCAGTCAC
1 TGCTTCCCTCGCTGCAGCCTC
*
41716211 TGCTTCCCTCGCTGCCGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
41716232 TGCTT
1 TGCTT
41716237 TAAGTTGTAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.04, C:0.41, G:0.19, T:0.35
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCAGCCTC
Found at i:41721522 original size:9 final size:9
Alignment explanation
Indices: 41721505--41721777 Score: 216
Period size: 9 Copynumber: 31.4 Consensus size: 9
41721495 TATGTATTAA
*
41721505 GTAAATTAT
1 GTAAGTTAT
41721514 GTAAGTTAT
1 GTAAGTTAT
*
41721523 GTACGTGTA-
1 GTAAGT-TAT
41721532 -TAAGTTAT
1 GTAAGTTAT
41721540 GTAAGTTAT
1 GTAAGTTAT
*
41721549 GT-A-TTAA
1 GTAAGTTAT
*
41721556 GTAAGCTAT
1 GTAAGTTAT
*
41721565 GTAAGTTGT
1 GTAAGTTAT
41721574 GT-A-TTAT
1 GTAAGTTAT
41721581 GTAAGTTAT
1 GTAAGTTAT
41721590 GTAAGTTAT
1 GTAAGTTAT
** *
41721599 CAAAGTAAT
1 GTAAGTTAT
*
41721608 GTATGTTAT
1 GTAAGTTAT
41721617 GTAAG-T-T
1 GTAAGTTAT
41721624 GTAAGTTATT
1 GTAAGTTA-T
*
41721634 GTGTA-TTAT
1 GT-AAGTTAT
41721643 GTAAGTTAT
1 GTAAGTTAT
41721652 GTAAGTTAAAT
1 GTAAGTT--AT
41721663 GT-A-TTAT
1 GTAAGTTAT
*
41721670 GTAGGTTAT
1 GTAAGTTAT
* *
41721679 ATAAGTTGT
1 GTAAGTTAT
*
41721688 GTAAGATAT
1 GTAAGTTAT
*
41721697 TTAAGTTAT
1 GTAAGTTAT
* *
41721706 GTGAGTTTT
1 GTAAGTTAT
41721715 GT-A-TTAT
1 GTAAGTTAT
41721722 GTAAGTTAT
1 GTAAGTTAT
*
41721731 GTAAGTTTT
1 GTAAGTTAT
41721740 GT-A-TTAT
1 GTAAGTTAT
41721747 GTAAGTTAT
1 GTAAGTTAT
*
41721756 GTAGGTTAT
1 GTAAGTTAT
*
41721765 GTAAGTTTT
1 GTAAGTTAT
41721774 GTAA
1 GTAA
41721778 TGTACAAGTG
Statistics
Matches: 207, Mismatches: 37, Indels: 40
0.73 0.13 0.14
Matches are distributed among these distances:
7 32 0.15
8 15 0.07
9 146 0.71
10 9 0.04
11 5 0.02
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:41721524 original size:25 final size:25
Alignment explanation
Indices: 41721494--41721598 Score: 133
Period size: 25 Copynumber: 4.2 Consensus size: 25
41721484 TGATATATAT
*
41721494 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
41721519 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
*
41721545 TTATGTATTAAGTAAGCTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* *
41721570 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
41721595 TTAT
1 TTAT
41721599 CAAAGTAATG
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.03
25 44 0.64
26 19 0.28
27 2 0.03
28 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:41721594 original size:34 final size:34
Alignment explanation
Indices: 41721509--41721776 Score: 190
Period size: 34 Copynumber: 8.0 Consensus size: 34
41721499 TATTAAGTAA
*
41721509 ATTATGTAAGTTATGTACGTGTA--TAAGTTATGT
1 ATTATGTAAGTTATGTAAGT-TATGTAAGTTATGT
* * *
41721542 AAGTTATGT-A-TTAAGTAAGCTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGT
** *
41721576 ATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
41721610 ATGTTATGTAAG-T-TGTAAGTTAT-T--G---TGT
1 A--TTATGTAAGTTATGTAAGTTATGTAAGTTATGT
41721638 ATTATGTAAGTTATGTAAGTTAAATGT-A-TTATGT
1 ATTATGTAAGTTATGTAAGTT--ATGTAAGTTATGT
* * * *
41721672 AGGTTATATAAGTTGTGTAAGATATTTAAGTTATGT
1 A--TTATGTAAGTTATGTAAGTTATGTAAGTTATGT
* *
41721708 GAGTTTTGT-A-TTATGTAAGTTATGTAAGTTTTGT
1 -A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGT
* *
41721742 ATTATGTAAGTTATGTAGGTTATGTAAGTTTTGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
41721776 A
1 A
41721777 ATGTACAAGT
Statistics
Matches: 188, Mismatches: 23, Indels: 46
0.73 0.09 0.18
Matches are distributed among these distances:
26 9 0.05
27 1 0.01
28 12 0.06
30 2 0.01
31 2 0.01
32 13 0.07
33 11 0.06
34 91 0.48
35 9 0.05
36 37 0.20
37 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (34 bp):
ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
Found at i:41721672 original size:62 final size:61
Alignment explanation
Indices: 41721570--41721687 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 61
41721560 GCTATGTAAG
* *
41721570 TTGTGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTATGTTATGTAAGTTGTAAGTTA
1 TTGTGTATTATGTAAGTTATGTAAGTTA-CAAAGTAATGTAGGTTATATAAGTTGTAAGTTA
*
41721632 TTGTGTATTATGTAAGTTATGTAAGTTA-AATGTATTATGTAGGTTATATAAGTTGT
1 TTGTGTATTATGTAAGTTATGTAAGTTACAAAGTA--ATGTAGGTTATATAAGTTGT
41721688 GTAAGATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 5 0.10
62 46 0.90
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (61 bp):
TTGTGTATTATGTAAGTTATGTAAGTTACAAAGTAATGTAGGTTATATAAGTTGTAAGTTA
Found at i:41721732 original size:25 final size:25
Alignment explanation
Indices: 41721698--41721767 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
41721688 GTAAGATATT
*
41721698 TAAGTTATGTGAGTTTTGTATTATG
1 TAAGTTATGTAAGTTTTGTATTATG
41721723 TAAGTTATGTAAGTTTTGTATTATG
1 TAAGTTATGTAAGTTTTGTATTATG
* *
41721748 TAAGTTATGTAGGTTATGTA
1 TAAGTTATGTAAGTTTTGTA
41721768 AGTTTTGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (25 bp):
TAAGTTATGTAAGTTTTGTATTATG
Found at i:41721821 original size:25 final size:26
Alignment explanation
Indices: 41721793--41721841 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
41721783 AAGTGTCAGG
*
41721793 TTATTGTT-ATTAAATTTTAATAAGA
1 TTATTGTTAACTAAATTTTAATAAGA
*
41721818 TTATTGTTAACTATATTTTAATAA
1 TTATTGTTAACTAAATTTTAATAA
41721842 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (26 bp):
TTATTGTTAACTAAATTTTAATAAGA
Found at i:41721848 original size:6 final size:6
Alignment explanation
Indices: 41721837--41721866 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
41721827 ACTATATTTT
41721837 AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA
41721867 TAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:41722824 original size:31 final size:31
Alignment explanation
Indices: 41722782--41722865 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
41722772 GAGCTCTTAG
* *
41722782 CCAT-TTAGCAGCAGAAATCAATAGAAGGTA
1 CCATCTTAGCAGCAAAAACCAATAGAAGGTA
41722812 CCATCTTAGCAGCAAAAACCAATAGAAGGTA
1 CCATCTTAGCAGCAAAAACCAATAGAAGGTA
*
41722843 CCATCTTAGCTGCAAAAACCAAT
1 CCATCTTAGCAGCAAAAACCAAT
41722866 TAAAATCCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 4 0.08
31 46 0.92
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (31 bp):
CCATCTTAGCAGCAAAAACCAATAGAAGGTA
Found at i:41725629 original size:696 final size:696
Alignment explanation
Indices: 41724298--41725689 Score: 2775
Period size: 696 Copynumber: 2.0 Consensus size: 696
41724288 ATGCCACAAC
41724298 GAGTTAATAAACTAAGCATTTGTGTCACTTAGAACCCTAATAACATAATAAGAAGTAAAAAACAA
1 GAGTTAATAAACTAAGCATTTGTGTCACTTAGAACCCTAATAACATAATAAGAAGTAAAAAACAA
41724363 AAAAGTATTTGTAATTTTTTTGAATTTGGTGTCACAAAAGCAAGTGTCAGGTCAACCACTGAATA
66 AAAAGTATTTGTAATTTTTTTGAATTTGGTGTCACAAAAGCAAGTGTCAGGTCAACCACTGAATA
41724428 TTTATATTAATGTACAAGTATGTAATATTTATAATGTACTCTAAAAAATTATACGTAAAAAATAA
131 TTTATATTAATGTACAAGTATGTAATATTTATAATGTACTCTAAAAAATTATACGTAAAAAATAA
41724493 TAATTTAGTGTATATTAATGTTTAAATAACATATACCCTTCAGCAGAAATCATTGAAGCCTTTAC
196 TAATTTAGTGTATATTAATGTTTAAATAACATATACCCTTCAGCAGAAATCATTGAAGCCTTTAC
41724558 GCAGTTCAGCGTACAATTCATTTCATTAAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAAAT
261 GCAGTTCAGCGTACAATTCATTTCATTAAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAAAT
41724623 TTTGAGGGCCAACTAAACTCGTCAATGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTT
326 TTTGAGGGCCAACTAAACTCGTCAATGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTT
41724688 GCGGCGTTTTTCATAGAAACGCCACTAAATATTCACTTTATTTATAAGTATTTGCGACTATTGTA
391 GCGGCGTTTTTCATAGAAACGCCACTAAATATTCACTTTATTTATAAGTATTTGCGACTATTGTA
41724753 TCCATATTTGCGGCGTTTTAGTAAAAAACGCCACTAAAATTTCAAGTACAGAAAGAGACGGTGCC
456 TCCATATTTGCGGCGTTTTAGTAAAAAACGCCACTAAAATTTCAAGTACAGAAAGAGACGGTGCC
41724818 GTTTTATTAAAATATAAGTAAATTTTCTGGCGTTTTCATAAAAAATGCCACAAATGATTAACTGA
521 GTTTTATTAAAATATAAGTAAATTTTCTGGCGTTTTCATAAAAAATGCCACAAATGATTAACTGA
41724883 AACGACGCCGTTTTCCAGTTTAAAGATAATTTACGACGTTTTTCGAAAAACGCCACAAATAAAAA
586 AACGACGCCGTTTTCCAGTTTAAAGATAATTTACGACGTTTTTCGAAAAACGCCACAAATAAAAA
41724948 TGCAATAAATATTTGCTAAAATTTGAATAAATTTTATTATTTATTT
651 TGCAATAAATATTTGCTAAAATTTGAATAAATTTTATTATTTATTT
41724994 GAGTTAATAAACTAAGCATTTGTGTCACTTAGAACCCTAATAACATAATAAGAAGTAAAAAACAA
1 GAGTTAATAAACTAAGCATTTGTGTCACTTAGAACCCTAATAACATAATAAGAAGTAAAAAACAA
41725059 AAAAGTATTTGTAATTTTTTTGAATTTGGTGTCACAAAAGCAAGTGTCAGGTCAACCACTGAATA
66 AAAAGTATTTGTAATTTTTTTGAATTTGGTGTCACAAAAGCAAGTGTCAGGTCAACCACTGAATA
41725124 TTTATATTAATGTACAAGTATGTAATATTTATAATGTACTCTAAAAAATTATACGTAAAAAATAA
131 TTTATATTAATGTACAAGTATGTAATATTTATAATGTACTCTAAAAAATTATACGTAAAAAATAA
*
41725189 TAATTTAGTGTATATTAATGTTTAAATAACATATACCCTTCAGCAGAAATCATTGAAGCCTTTAG
196 TAATTTAGTGTATATTAATGTTTAAATAACATATACCCTTCAGCAGAAATCATTGAAGCCTTTAC
41725254 GCAGTTCAGCGTACAATTCATTTCATTAAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAAAT
261 GCAGTTCAGCGTACAATTCATTTCATTAAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAAAT
41725319 TTTGAGGGCCAACTAAACTCGTCAATGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTT
326 TTTGAGGGCCAACTAAACTCGTCAATGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTT
41725384 GCGGCGTTTTTCATAGAAACGCCACTAAATATTCACTTTATTTATAAGTATTTGCGACTATTGTA
391 GCGGCGTTTTTCATAGAAACGCCACTAAATATTCACTTTATTTATAAGTATTTGCGACTATTGTA
41725449 TCCATATTTGCGGCGTTTTAGTAAAAAACGCCACTAAAATTTCAAGTACAGAAAGAGACGGTGCC
456 TCCATATTTGCGGCGTTTTAGTAAAAAACGCCACTAAAATTTCAAGTACAGAAAGAGACGGTGCC
41725514 GTTTTATTAAAATATAAGTAAATTTTCTGGCGTTTTCATAAAAAATGCCACAAATGATTAACTGA
521 GTTTTATTAAAATATAAGTAAATTTTCTGGCGTTTTCATAAAAAATGCCACAAATGATTAACTGA
41725579 AACGACGCCGTTTTCCAGTTTAAAGATAATTTACGACGTTTTTCGAAAAACGCCACAAATAAAAA
586 AACGACGCCGTTTTCCAGTTTAAAGATAATTTACGACGTTTTTCGAAAAACGCCACAAATAAAAA
41725644 TGCAATAAATATTTGCTAAAATTTGAATAAATTTTATTATTTATTT
651 TGCAATAAATATTTGCTAAAATTTGAATAAATTTTATTATTTATTT
41725690 ATTTATCTCT
Statistics
Matches: 695, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
696 695 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (696 bp):
GAGTTAATAAACTAAGCATTTGTGTCACTTAGAACCCTAATAACATAATAAGAAGTAAAAAACAA
AAAAGTATTTGTAATTTTTTTGAATTTGGTGTCACAAAAGCAAGTGTCAGGTCAACCACTGAATA
TTTATATTAATGTACAAGTATGTAATATTTATAATGTACTCTAAAAAATTATACGTAAAAAATAA
TAATTTAGTGTATATTAATGTTTAAATAACATATACCCTTCAGCAGAAATCATTGAAGCCTTTAC
GCAGTTCAGCGTACAATTCATTTCATTAAGCGGCGCTTAAAGAAAACGCCACAAATCTTACAAAT
TTTGAGGGCCAACTAAACTCGTCAATGAAACGGCTCCGTTTTATTCAATTTTTCAAATATTATTT
GCGGCGTTTTTCATAGAAACGCCACTAAATATTCACTTTATTTATAAGTATTTGCGACTATTGTA
TCCATATTTGCGGCGTTTTAGTAAAAAACGCCACTAAAATTTCAAGTACAGAAAGAGACGGTGCC
GTTTTATTAAAATATAAGTAAATTTTCTGGCGTTTTCATAAAAAATGCCACAAATGATTAACTGA
AACGACGCCGTTTTCCAGTTTAAAGATAATTTACGACGTTTTTCGAAAAACGCCACAAATAAAAA
TGCAATAAATATTTGCTAAAATTTGAATAAATTTTATTATTTATTT
Found at i:41725876 original size:38 final size:39
Alignment explanation
Indices: 41725802--41725887 Score: 113
Period size: 38 Copynumber: 2.2 Consensus size: 39
41725792 CCAAATCCCT
*
41725802 AACCCATAACCCCTAAATCCTCCTTAACCCTTAAAGCATA
1 AACCC-TAACCCCTAAATCCTCCTTAACCCCTAAAGCATA
*
41725842 AACCCTAACCTCTAAAT-CT-CTCTAACCCCTAAAGCATA
1 AACCCTAACCCCTAAATCCTCCT-TAACCCCTAAAGCATA
*
41725880 ACCCCTAA
1 AACCCTAA
41725888 AAATTTTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 2 0.05
38 24 0.57
39 11 0.26
40 5 0.12
ACGTcount: A:0.37, C:0.38, G:0.02, T:0.22
Consensus pattern (39 bp):
AACCCTAACCCCTAAATCCTCCTTAACCCCTAAAGCATA
Found at i:41726052 original size:21 final size:21
Alignment explanation
Indices: 41726027--41726071 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
41726017 AAATCCTCCT
*
41726027 TAACCCTTAAAGCATAAACCC
1 TAACCCCTAAAGCATAAACCC
*
41726048 TAACCCCTAAAGCATAACCCC
1 TAACCCCTAAAGCATAAACCC
41726069 TAA
1 TAA
41726072 AAATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.36, G:0.04, T:0.18
Consensus pattern (21 bp):
TAACCCCTAAAGCATAAACCC
Found at i:41726361 original size:14 final size:14
Alignment explanation
Indices: 41726344--41726373 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41726334 TTACCGTTGA
41726344 AACCCTAAACCCCT
1 AACCCTAAACCCCT
*
41726358 AACCCTTAACCCCT
1 AACCCTAAACCCCT
41726372 AA
1 AA
41726374 ATCCTCCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.47, G:0.00, T:0.17
Consensus pattern (14 bp):
AACCCTAAACCCCT
Found at i:41727037 original size:112 final size:114
Alignment explanation
Indices: 41726750--41727061 Score: 346
Period size: 112 Copynumber: 2.8 Consensus size: 114
41726740 CGCTACACCT
* * * * * *
41726750 AAAACGCCGCTAAATCCCCGAAAGGCTAAGAAACAGTGTCATTGGGCTTAGGTTTTCTTGTGGTG
1 AAAACGCCGCTAAATCCCCGAAAAGCTCAGAAACGGTGTCGTTGGGCTTAGGTTTTCTTGCGGCG
*
41726815 CTTTTTTAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTTTTAAA
66 CTTTTTCAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTTTTAAA
* * * * * *
41726864 AAAACGCCGCTAAAT-CCTG-AAAGCACAAAAAACGGTGCCGTTGGGCTTAGTTTTTTTTTGCGG
1 AAAACGCCGCTAAATCCCCGAAAAGCTC-AGAAACGGTGTCGTTGGGCTTAG-GTTTTCTTGCGG
* * * * *
41726927 CGCTATTCCAAAAACGCCGCTAAATC-CT-TGCATTAGCGGCGCTTCTT-TA
64 CGCTTTTTCAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTT-TTAAA
* * * * *
41726976 GAAACGCCGCTAAATCCCCGAAAAGCTCTGAAATGGTGTCGTTGTGCTTTGGTTTTCTTGCGGCG
1 AAAACGCCGCTAAATCCCCGAAAAGCTCAGAAACGGTGTCGTTGGGCTTAGGTTTTCTTGCGGCG
*
41727041 CTTTTTCAAAAACGCCACTAA
66 CTTTTTCAAAAACGCCGCTAA
41727062 TGACTCGAAA
Statistics
Matches: 161, Mismatches: 32, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
112 64 0.40
113 46 0.29
114 51 0.32
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (114 bp):
AAAACGCCGCTAAATCCCCGAAAAGCTCAGAAACGGTGTCGTTGGGCTTAGGTTTTCTTGCGGCG
CTTTTTCAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTTTTAAA
Found at i:41727094 original size:186 final size:183
Alignment explanation
Indices: 41726850--41727188 Score: 445
Period size: 186 Copynumber: 1.8 Consensus size: 183
41726840 CTGAGCATTA
* * * *
41726850 GCGGCGCTTTTAAAAAAACGCCGCTAAATCCTGAAAGCACAAAAAACGGTGCCGTTGGGCTTAGT
1 GCGGCGCTTTTAAAAAAACGCCACTAAATACTGAAAGCACAAAAAACGGCGCCGTTGGGATTAG-
* *
41726915 TTTTTTTTGCGGCGCTATTC-CAAAAACGCCGCTAAA-TCCTTG-CATTAGCGGCGCTTCT-TTA
65 -ATTTTTTGCGGCGCT-TTCTCAAAAACGCCGCTAAAGGCC-TGACATTAGCGGCGCTT-TATTA
*
41726976 GAAACGCCGCTAAATCCCCGAAAAGCTCTGAAATGGTGTCGTTGTGCTTTGGTTTTCTT
126 AAAACGCCGCTAAATCCCCG-AAAGCTCTGAAATGGTGTCGTTGTGCTTTGGTTTTCTT
** * * *
41727035 GCGGCGCTTTTTCAAAAACGCCACT-AATGACTCGAAAGCTCAGAAAACGGCGTCGTTGGGATTA
1 GCGGCGCTTTTAAAAAAACGCCACTAAAT-ACT-GAAAGCACAAAAAACGGCGCCGTTGGGATTA
*
41727099 GATTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGGCCTGAACATTAGCGGCGCTTTATTAAA
64 GATTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCTG-ACATTAGCGGCGCTTTATTAAA
41727164 AACGCCGCTAAATCCCCGAAAGCTC
128 AACGCCGCTAAATCCCCGAAAGCTC
41727189 GGTAAACGAC
Statistics
Matches: 134, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
183 3 0.02
184 34 0.25
185 34 0.25
186 63 0.47
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (183 bp):
GCGGCGCTTTTAAAAAAACGCCACTAAATACTGAAAGCACAAAAAACGGCGCCGTTGGGATTAGA
TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCTGACATTAGCGGCGCTTTATTAAAAAC
GCCGCTAAATCCCCGAAAGCTCTGAAATGGTGTCGTTGTGCTTTGGTTTTCTT
Found at i:41727246 original size:113 final size:113
Alignment explanation
Indices: 41727035--41727239 Score: 272
Period size: 113 Copynumber: 1.8 Consensus size: 113
41727025 TGGTTTTCTT
* * *
41727035 GCGGCGCTTTTTCAAAAACGCCACTAATGACTCGAAAGCTCAGAAAACGGCGTCGTTGGGATTAG
1 GCGGCGCTTTTTCAAAAACGCCACTAATGACCCGAAAGCTCAGAAAACGACGTCGTTCGGATTAG
41727100 ATTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGGCCTGAACATTA
66 ATTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGGCCTGAACATTA
* * * * *
41727148 GCGGCGCTTTATT-AAAAACGCCGCTAAAT-CCCCGAAAGCTCGGTAAACGACGTCGTTCGGCTT
1 GCGGCGCTTT-TTCAAAAACGCCACT-AATGACCCGAAAGCTCAGAAAACGACGTCGTTCGGATT
* *
41727211 AGGTTTTTTGCGGTGCTTTCT-ATAAAACG
64 AGATTTTTTGCGGCGCTTTCTCA-AAAACG
41727240 CTGCTAATTC
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
112 1 0.01
113 73 0.92
114 5 0.06
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (113 bp):
GCGGCGCTTTTTCAAAAACGCCACTAATGACCCGAAAGCTCAGAAAACGACGTCGTTCGGATTAG
ATTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGGCCTGAACATTA
Found at i:41740559 original size:18 final size:19
Alignment explanation
Indices: 41740538--41740577 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
41740528 AAAAAANAAA
* *
41740538 AAAAGGAA-AAATGAAATG
1 AAAAGGAATAAAAGAAAAG
41740556 AAAAGGAATAAAAGAAAAG
1 AAAAGGAATAAAAGAAAAG
41740575 AAA
1 AAA
41740578 CTACAAATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (19 bp):
AAAAGGAATAAAAGAAAAG
Found at i:41740559 original size:19 final size:20
Alignment explanation
Indices: 41740537--41740577 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
41740527 AAAAAAANAA
* *
41740537 AAAAAGGAA-AAATGAAATG
1 AAAAAGGAATAAAAGAAAAG
41740556 -AAAAGGAATAAAAGAAAAG
1 AAAAAGGAATAAAAGAAAAG
41740575 AAA
1 AAA
41740578 CTACAAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
18 8 0.44
19 8 0.44
20 2 0.11
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (20 bp):
AAAAAGGAATAAAAGAAAAG
Found at i:41741196 original size:25 final size:25
Alignment explanation
Indices: 41741162--41741214 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
41741152 TAGAGCACTT
*
41741162 AGTGCCTTTAGGTCAGTACATC-CA
1 AGTGCCTTTAAGTCAGTACATCTCA
41741186 AGTGCTCTTTAAGTCAGTACATCTCA
1 AGTGC-CTTTAAGTCAGTACATCTCA
41741212 AGT
1 AGT
41741215 TGCAAAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 5 0.19
25 16 0.62
26 5 0.19
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (25 bp):
AGTGCCTTTAAGTCAGTACATCTCA
Found at i:41748524 original size:199 final size:199
Alignment explanation
Indices: 41748182--41748544 Score: 519
Period size: 199 Copynumber: 1.8 Consensus size: 199
41748172 CCCTTGGCAC
* *
41748182 TGCTAAGTTTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTATTGATCTAGTCAATG
1 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATG
* * * * *
41748247 ATTAGTATAATGATGATGGGCCACTTCAAACTTTAGTAAGAGTTTGAAAGAATAACTCACCTACT
66 ATCAGTATAATAATGATGGACCACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
* *
41748312 GATATACTTGGTGATAATCATGATAGGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
131 GACATAATTGGTGATAATCATGATAGGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
41748377 ACAT
196 ACAT
* * *
41748381 TGCTAAGTCTAAAGAAAAGTTAGAAGTAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAGTG
1 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATG
* * * * * * * *
41748446 ATCAGTCTAATAATGATGGACCACTTTAACCTTTAGCAAGAGTTAGGAAGAATCACTTATCTATT
66 ATCAGTATAATAATGATGGACCACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
** *
41748511 GACATAATTGGTGATGTTCATGATGGGATCAAAA
131 GACATAATTGGTGATAATCATGATAGGATCAAAA
41748545 TAAGGGGTAG
Statistics
Matches: 141, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
199 141 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (199 bp):
TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATG
ATCAGTATAATAATGATGGACCACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
GACATAATTGGTGATAATCATGATAGGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
ACAT
Found at i:41750685 original size:30 final size:31
Alignment explanation
Indices: 41750646--41750705 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
41750636 AGAGGTGGGA
41750646 TGGGAAGGGAATAAAAGTTTTAAGGGAAAAG
1 TGGGAAGGGAATAAAAGTTTTAAGGGAAAAG
* **
41750677 TGGG-AGGGAGTAAAAGTTTTTGGGGAAAA
1 TGGGAAGGGAATAAAAGTTTTAAGGGAAAA
41750706 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAGTTTTAAGGGAAAAG
Found at i:41750937 original size:9 final size:9
Alignment explanation
Indices: 41750919--41750955 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
41750909 TATAGTTTGA
41750919 TATTCGAAT
1 TATTCGAAT
*
41750928 TATTCAAAT
1 TATTCGAAT
*
41750937 TATTCGAGT
1 TATTCGAAT
41750946 TATTCGAAT
1 TATTCGAAT
41750955 T
1 T
41750956 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41755137 original size:16 final size:16
Alignment explanation
Indices: 41755103--41755155 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
41755093 ATAGCATTAG
41755103 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
41755119 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
41755135 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
41755151 TCATG
1 TCATG
41755156 AGTATATAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:41757928 original size:3 final size:3
Alignment explanation
Indices: 41757922--41757948 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
41757912 GACCACGATG
41757922 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
41757949 GAAACTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41760872 original size:35 final size:35
Alignment explanation
Indices: 41760826--41760896 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
41760816 AGTAAAAGAT
41760826 AGAATCAAGATTTGAGATAAAGTATATTCCGTAAG
1 AGAATCAAGATTTGAGATAAAGTATATTCCGTAAG
41760861 AGAATCAAGATTTGAGATAAAGTATATTCCGTAAG
1 AGAATCAAGATTTGAGATAAAGTATATTCCGTAAG
41760896 A
1 A
41760897 CAAACCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (35 bp):
AGAATCAAGATTTGAGATAAAGTATATTCCGTAAG
Found at i:41772181 original size:73 final size:73
Alignment explanation
Indices: 41772100--41772245 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
41772090 ATTCTGACAA
*
41772100 ATAGAATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTG
1 ATAGAATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTA
41772165 TGTAAAAC
66 TGTAAAAC
41772173 ATAGAATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTA
1 ATAGAATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTA
41772238 TGTAAAAC
66 TGTAAAAC
41772246 TTATTATCTT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (73 bp):
ATAGAATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTA
TGTAAAAC
Found at i:41793638 original size:37 final size:37
Alignment explanation
Indices: 41793590--41793684 Score: 120
Period size: 37 Copynumber: 2.5 Consensus size: 37
41793580 TTAATGAATG
*
41793590 CATGATTAAGCATGCCATTGAGATTGTTAAACCAG-AAC
1 CATGA-TAAGCATGCCATTGAAATTGTTAAA-CAGAAAC
* * *
41793628 CATGATAAGCATGCCACTGAAATTGTTAAACTGAAAG
1 CATGATAAGCATGCCATTGAAATTGTTAAACAGAAAC
*
41793665 CATGATAAACATGCCATTGA
1 CATGATAAGCATGCCATTGA
41793685 TATTTTTACT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
36 2 0.04
37 43 0.86
38 5 0.10
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (37 bp):
CATGATAAGCATGCCATTGAAATTGTTAAACAGAAAC
Found at i:41794507 original size:72 final size:68
Alignment explanation
Indices: 41794431--41794568 Score: 188
Period size: 72 Copynumber: 2.0 Consensus size: 68
41794421 TGATTAAACT
* * *
41794431 TAATCACTTTAATATTAAATTAATAGAATATTTATCTACAAAATAATTATTAAAATT-AATTTAA
1 TAATCACTTTAATAGTAAATTAATAAAATA-TTAT-T--AAAATAAGTATT-AAATTAAATTTAA
41794495 TATTAAGC
61 TATTAAGC
*
41794503 TAATCACTTTAATAGTAAATTAATAAAATATTATTAAGATAAGTATTAAATTAAATTTAATATTA
1 TAATCACTTTAATAGTAAATTAATAAAATATTATTAAAATAAGTATTAAATTAAATTTAATATTA
41794568 A
66 A
41794569 ATCTATTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
67 5 0.08
68 23 0.38
70 1 0.02
71 4 0.07
72 28 0.46
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (68 bp):
TAATCACTTTAATAGTAAATTAATAAAATATTATTAAAATAAGTATTAAATTAAATTTAATATTA
AGC
Found at i:41799308 original size:21 final size:21
Alignment explanation
Indices: 41799282--41799372 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
41799272 GTGTTTTACT
* *
41799282 TTCTGTTTAGCTCTTTCGAGC
1 TTCTGTTAAGCTCTTACGAGC
41799303 TTCTGTTAAGCTCTTACGAGC
1 TTCTGTTAAGCTCTTACGAGC
* * * *
41799324 TTCTATTCAA-TTCTTATGAGT
1 TTCTGTT-AAGCTCTTACGAGC
* * *
41799345 TTTTGTTCAGCTCTCACGAGC
1 TTCTGTTAAGCTCTTACGAGC
41799366 TTCTGTT
1 TTCTGTT
41799373 GGCGTGTTCA
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.02
21 51 0.94
22 2 0.04
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTGTTAAGCTCTTACGAGC
Found at i:41802339 original size:51 final size:52
Alignment explanation
Indices: 41802249--41802367 Score: 165
Period size: 52 Copynumber: 2.3 Consensus size: 52
41802239 GTAGAAATTG
* *
41802249 TGAAAATGGAGAAATGAGAAACATTTGGAAATGATTGTGG-TTTTCTCCAAAA
1 TGAAAATGGAGAAATGAG-AACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
*
41802301 TGAAAATGGAGAAATGTAG-TCATTTGGAAATGAATGTGGTTTTTCTCAAAAA
1 TGAAAATGGAGAAATG-AGAACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
41802353 TGAAAAT-GA-AAATGA
1 TGAAAATGGAGAAATGA
41802368 CTTGGAAATG
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
49 1 0.02
50 5 0.08
51 20 0.32
52 34 0.55
53 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (52 bp):
TGAAAATGGAGAAATGAGAACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
Found at i:41803301 original size:22 final size:22
Alignment explanation
Indices: 41803273--41803318 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
41803263 TATGATTTTT
*
41803273 AAAAAAA-AAGTTACTCTCTTGA
1 AAAAAAATAAATTAC-CTCTTGA
*
41803295 AAAAAAATAAATTTCCTCTTGA
1 AAAAAAATAAATTACCTCTTGA
41803317 AA
1 AA
41803319 GTTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (22 bp):
AAAAAAATAAATTACCTCTTGA
Found at i:41805783 original size:18 final size:18
Alignment explanation
Indices: 41805737--41805785 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
41805727 TAGAGTTATG
41805737 GGCCCACATGCCCGTGTA
1 GGCCCACATGCCCGTGTA
* *
41805755 GGCCTATATGCCCGTGTA
1 GGCCCACATGCCCGTGTA
41805773 GGCCCACATGCCC
1 GGCCCACATGCCC
41805786 ATATTGGCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.16, C:0.39, G:0.27, T:0.18
Consensus pattern (18 bp):
GGCCCACATGCCCGTGTA
Found at i:41805784 original size:36 final size:32
Alignment explanation
Indices: 41805737--41805821 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 32
41805727 TAGAGTTATG
41805737 GGCCCACATGCCCGTGTAGGCCTATATGCCCGTGT
1 GGCCCACATGCCCGTGTAGGCC--T-TGCCCGTGT
* * * *
41805772 AGGCCCACATGCCCATATTGGCCTTGCTCGTGT
1 -GGCCCACATGCCCGTGTAGGCCTTGCCCGTGT
41805805 GGCCCACATGCCCGTGT
1 GGCCCACATGCCCGTGT
41805822 GGCATGATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
32 15 0.35
33 8 0.19
34 1 0.02
36 19 0.44
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (32 bp):
GGCCCACATGCCCGTGTAGGCCTTGCCCGTGT
Found at i:41809994 original size:20 final size:20
Alignment explanation
Indices: 41809969--41810007 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
41809959 TACTCGCTTC
41809969 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
41809989 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
41810008 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:41812461 original size:21 final size:21
Alignment explanation
Indices: 41812432--41812474 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41812422 ACACCGAAAC
* *
41812432 AGGCTTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCAGCGTTTTTT
41812453 AGGCCTTTAGCAGCGTTTTTT
1 AGGCCTTTAGCAGCGTTTTTT
41812474 A
1 A
41812475 ACGCCGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (21 bp):
AGGCCTTTAGCAGCGTTTTTT
Found at i:41812643 original size:62 final size:61
Alignment explanation
Indices: 41812565--41812684 Score: 159
Period size: 62 Copynumber: 2.0 Consensus size: 61
41812555 GTTTATGTGA
* * ** * * *
41812565 AAAAACGCTGCTAAAGATCATGGTCTTTAGCGGCGTTTTTTGCAAAAGCGCCGCTAAAGGTG
1 AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCG-CTTTTACAAAAACGCCGCTAAAGGTG
*
41812627 AAAAGCGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTAAAG
41812685 ATCACAAGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
61 20 0.40
62 30 0.60
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (61 bp):
AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTAAAGGTG
Found at i:41812697 original size:42 final size:43
Alignment explanation
Indices: 41812627--41812813 Score: 157
Period size: 42 Copynumber: 4.3 Consensus size: 43
41812617 GCTAAAGGTG
* * *
41812627 AAAAGCGCCGCTAAAGATCACGACCTTTAGCGGCGC-TTTTAC
1 AAAAACGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTAC
41812669 AAAAACGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTATC
1 AAAAACGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTA-C
* * * ** * * *
41812713 ACAAACACCGCTAAAGGTCATGATCTTTAGCGACGCTTTTTGCC
1 AAAAACGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTT-AC
* * * * **
41812757 ACAAACGCCGCTATAA-A--ACAAGCCTTTAGCGTCACTTCTCGC
1 AAAAACGCCGCTA-AAGATCACAAG-CTTTAGCGGCGCTTTTTAC
41812799 AAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
41812814 AACATAACAT
Statistics
Matches: 118, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.02
42 48 0.41
43 18 0.15
44 48 0.41
45 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTAC
Found at i:41812741 original size:44 final size:43
Alignment explanation
Indices: 41812632--41812769 Score: 170
Period size: 44 Copynumber: 3.2 Consensus size: 43
41812622 AGGTGAAAAG
*
41812632 CGCCGCTAAAGATCACGACCTTTAGCGGCGC-TTTTACAAAAA
1 CGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTACACAAA
* *
41812674 CGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTATCACAAA
1 CGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTA-CACAAA
* * * * * *
41812718 CACCGCTAAAGGTCATGATCTTTAGCGACGCTTTTTGCCACAAA
1 CGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTT-ACACAAA
41812762 CGCCGCTA
1 CGCCGCTA
41812770 TAAAACAAGC
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 29 0.35
43 5 0.06
44 48 0.59
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTACACAAA
Found at i:41812860 original size:18 final size:19
Alignment explanation
Indices: 41812833--41812869 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41812823 TTTAAAAAAA
*
41812833 TTTATTTAAATATT-TATT
1 TTTATATAAATATTATATT
41812851 TTTATATAAATATTATATT
1 TTTATATAAATATTATATT
41812870 ATGTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATAAATATTATATT
Found at i:41813866 original size:16 final size:16
Alignment explanation
Indices: 41813845--41813875 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41813835 AGTCCCAAAC
41813845 TATTGTAAACATCAGT
1 TATTGTAAACATCAGT
41813861 TATTGTAAACATCAG
1 TATTGTAAACATCAG
41813876 ATAGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
TATTGTAAACATCAGT
Found at i:41814884 original size:20 final size:21
Alignment explanation
Indices: 41814859--41814898 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41814849 AAAATTTTAT
*
41814859 TTATTTT-TATTTGTTAAAAA
1 TTATTTTATATATGTTAAAAA
41814879 TTATTTTATATATGTTAAAA
1 TTATTTTATATATGTTAAAA
41814899 TGAGATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATTTTATATATGTTAAAAA
Found at i:41817068 original size:41 final size:40
Alignment explanation
Indices: 41817022--41817216 Score: 216
Period size: 41 Copynumber: 4.8 Consensus size: 40
41817012 CCACAATTGC
41817022 CCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCT-AATA
1 CCTGAGCATTAGCGGCGCTTT-TAAAAAACGCCGCTAAATA
* * *
41817062 CTCTGAGCATTAGCGGCGTTTTTTCAAAAACGCCGCTAAAGA
1 C-CTGAGCATTAGCGGCG-CTTTTAAAAAACGCCGCTAAATA
** * * *
41817104 CCCAATCATTAGTGGCGCTTTTTAAAAA-GCCGCTAAA-A
1 CCTGAGCATTAGCGGCGCTTTTAAAAAACGCCGCTAAATA
* *
41817142 CCCTGAGCATTAGCTGCGCATTTTAAAAAACGCCGATAAATA
1 -CCTGAGCATTAGCGGCGC-TTTTAAAAAACGCCGCTAAATA
*
41817184 CCTGAGCATTAGCGGCGCTTTACAAAAAACGCC
1 CCTGAGCATTAGCGGCGCTTT-TAAAAAACGCC
41817217 ACAAATCCCC
Statistics
Matches: 129, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
39 22 0.17
40 22 0.17
41 76 0.59
42 8 0.06
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (40 bp):
CCTGAGCATTAGCGGCGCTTTTAAAAAACGCCGCTAAATA
Found at i:41817171 original size:80 final size:82
Alignment explanation
Indices: 41817026--41817216 Score: 235
Period size: 80 Copynumber: 2.4 Consensus size: 82
41817016 AATTGCCCTG
* * ** *
41817026 AGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAATACTCTGAGCATTAGCGGCGTTTTTTCAAAA
1 AGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCATTTTAAAAA
*
41817091 ACGCCGCTAAAGACCCA
66 ACGCCGATAAAGACCCA
* * * *
41817108 ATCATTAGTGGCGCTTT-TTAAAAA-GCCGCTAAAACCCTGAGCATTAGCTGCGCATTTTAAAAA
1 AGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCATTTTAAAAA
* **
41817171 ACGCCGATAAATACCTG
66 ACGCCGATAAAGACCCA
41817188 AGCATTAGCGGCGCTTTAC-AAAAAACGCC
1 AGCATTAGCGGCGCTTT-CTAAAAAACGCC
41817217 ACAAATCCCC
Statistics
Matches: 90, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
80 61 0.68
81 11 0.12
82 18 0.20
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (82 bp):
AGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCATTTTAAAAA
ACGCCGATAAAGACCCA
Found at i:41817325 original size:39 final size:38
Alignment explanation
Indices: 41817272--41817391 Score: 125
Period size: 39 Copynumber: 3.1 Consensus size: 38
41817262 TTGCGGCGCC
* *
41817272 TTTTGAAAAA-CGCCGCTAATGCTCATTTTTAGCAGTG
1 TTTTCAAAAAGCGCCGCTAATGCTCATTTTTAGCGGTG
* * *
41817309 TTTTCCAAAAAGCGCCGCTAATACTCAATCTTTAGCGGCG
1 TTTT-CAAAAAGCGCCGCTAATGCTC-ATTTTTAGCGGTG
*** *
41817349 TTTTTTTAAAGCGCCGCTAATGCTTGATTTTTAGCGGTG
1 TTTTCAAAAAGCGCCGCTAATGC-TCATTTTTAGCGGTG
41817388 TTTT
1 TTTT
41817392 TTATCCAAAC
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
37 4 0.06
38 5 0.07
39 43 0.64
40 15 0.22
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (38 bp):
TTTTCAAAAAGCGCCGCTAATGCTCATTTTTAGCGGTG
Found at i:41829249 original size:23 final size:23
Alignment explanation
Indices: 41829223--41829276 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
41829213 GTTACTAAGC
* * *
41829223 ATATATTAATAATTAATATAATA
1 ATATAATAATAATTAAAATAAAA
*
41829246 ATATAATAATATTTAAAATAAAA
1 ATATAATAATAATTAAAATAAAA
*
41829269 ATAAAATA
1 ATATAATA
41829277 TAAATAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATAATAATAATTAAAATAAAA
Found at i:41836802 original size:14 final size:15
Alignment explanation
Indices: 41836783--41836815 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41836773 GGTATAAAAT
*
41836783 AAAT-AAAGTAATAA
1 AAATAAAAGAAATAA
41836797 AAATAAAAGAAATAA
1 AAATAAAAGAAATAA
41836812 AAAT
1 AAAT
41836816 GCTAGATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATAAAAGAAATAA
Found at i:41839214 original size:33 final size:33
Alignment explanation
Indices: 41839154--41839223 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
41839144 CACAAAGATC
* *
41839154 CAAATGTTTATATGCTCATCAAATACATATAAA
1 CAAATGTTCATATACTCATCAAATACATATAAA
* * * *
41839187 CAAATGTTCATATACTTATCCATTACATATAAC
1 CAAATGTTCATATACTCATCAAATACATATAAA
41839220 CAAA
1 CAAA
41839224 ATCATATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (33 bp):
CAAATGTTCATATACTCATCAAATACATATAAA
Found at i:41839340 original size:41 final size:42
Alignment explanation
Indices: 41839265--41839345 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 42
41839255 CTTAATTTAA
* * *
41839265 CAGATTCACCGGCACTTAGCTTGCTAGGCTTATAGCCTGATT
1 CAGATTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATT
*
41839307 CAGA-TCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 CAGATTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGA
41839346 ATAATTTCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 31 0.89
42 4 0.11
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (42 bp):
CAGATTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATT
Found at i:41841110 original size:51 final size:49
Alignment explanation
Indices: 41841055--41841512 Score: 285
Period size: 51 Copynumber: 9.8 Consensus size: 49
41841045 GAATTGTAAT
*
41841055 TTTAATCTACTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGC--GTAGC
** * * * *
41841106 TTTAATCTATTCCACTGCAACTTTAGGGAGATAAAATTTGTAACTTGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGC--GTAGC
* * * * *
41841157 TTTAATCTGTTCCACTGCAAATT-TAGAGAAATAAGA-TT-T-GCG-ATC
1 TTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTGTAGCGTAGC
* * * * *
41841202 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTCGTAACTTGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGC--GTAGC
* * * *
41841253 TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TT-T-GC-TATC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
* * * **
41841298 TTCAATCTACTTCGTTGCAACTTC-AGGTAGATAAGATTTGTA---T--C
1 TTTAATCTGCTCCACTGCAACTTCAAGG-AGATAAGATTTGTAGCGTAGC
*
41841342 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TT-TA-C-TATC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
* * *
41841387 TTCAATCTGCTCCACTTCAACCTT-AGGGAGA-AGAGATTTGTA--GT---
1 TTTAATCTGCTCCACTGCAA-CTTCAAGGAGATA-AGATTTGTAGCGTAGC
* * * *
41841431 TTTAATCTGCTCTATTGCAACTTCAGGGGGATAAGATTTGT---G--GC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
* *
41841475 TTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATT
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT
41841513 CTCCACGATG
Statistics
Matches: 327, Mismatches: 55, Indels: 57
0.74 0.13 0.13
Matches are distributed among these distances:
42 2 0.01
43 7 0.02
44 95 0.29
45 89 0.27
46 11 0.03
47 5 0.02
48 3 0.01
49 2 0.01
50 5 0.02
51 108 0.33
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (49 bp):
TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
Found at i:41841236 original size:45 final size:45
Alignment explanation
Indices: 41841026--41841512 Score: 362
Period size: 44 Copynumber: 10.5 Consensus size: 45
41841016 TGCAACCCAT
* * *
41841026 TGCAACTTCAGGG-GTATAGGAATTG-TAAT-TTTAATCTACTCCAC
1 TGCAACTTCAGGGAG-ATAAGATTTGCT-ATCTTTAATCTGCTCCAC
* * **
41841070 TGCAACTTCAAGGAGATAAGATTTGTAGCTTGTAGCTTTAATCTATTCCAC
1 TGCAACTTCAGGGAGATAAGA-TT-T-GC---TATCTTTAATCTGCTCCAC
* * * *
41841121 TGCAACTTTAGGGAGATAAAATTTGTAACTTGTAGCTTTAATCTGTTCCAC
1 TGCAACTTCAGGGAGATAAGATTTG---C---TATCTTTAATCTGCTCCAC
* * * * * *
41841172 TGCAAATTTAGAGAAATAAGATTTGCGATCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
* * * *
41841217 TGTAACTTCAGGGAGATAAGATTCGTAACTTGTAGCTTTAATCTGTTCCAC
1 TGCAACTTCAGGGAGATAAGATT--T-GC---TATCTTTAATCTGCTCCAC
* * * * **
41841268 TGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTACTTCGT
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
*
41841313 TGCAACTTCAGGTAGATAAGATTTG-TATCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
* * *
41841357 TGCAACTTCAAGGAGATAAGATTTACTATCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
* * *
41841402 TTCAACCTT-AGGGAGA-AGAGATTTG-TAGT-TTTAATCTGCTCTAT
1 TGCAA-CTTCAGGGAGATA-AGATTTGCTA-TCTTTAATCTGCTCCAC
* **
41841446 TGCAACTTCAGGGGGATAAGATTTG-TGGCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
*
41841490 TACAACTTCAGGGAGATAAGATT
1 TGCAACTTCAGGGAGATAAGATT
41841513 CTCCACGATG
Statistics
Matches: 356, Mismatches: 62, Indels: 50
0.76 0.13 0.11
Matches are distributed among these distances:
43 3 0.01
44 120 0.34
45 106 0.30
46 4 0.01
47 2 0.01
48 4 0.01
49 2 0.01
50 3 0.01
51 112 0.31
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (45 bp):
TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
Found at i:41841246 original size:96 final size:95
Alignment explanation
Indices: 41841116--41841512 Score: 392
Period size: 96 Copynumber: 4.3 Consensus size: 95
41841106 TTTAATCTAT
* * * *
41841116 TCCACTGCAACTTTAGGGAGATAAAATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAATTT
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTC
*
41841181 AGAGAAATAAGATTTGCGATCTTCAATCTGC
65 AGAGAAATAAGATTTGCTATCTTCAATCTGC
*
41841212 TCCACTGTAACTTCAGGGAGATAAGATTCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTC
1 TCCACTGCAACTTCAGGGAGATAAGATT-GTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTC
* *
41841277 AGGGAAATAAGATTTGCTATCTTCAATCTAC
65 AGAGAAATAAGATTTGCTATCTTCAATCTGC
* ** * * *
41841308 TTCGTTGCAACTTCAGGTAGATAAGA---T---TTGTATCTTTAATCTGCTCCACTGCAACTTCA
1 TCCACTGCAACTTCAGGGAGATAAGATTGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTCA
* *
41841367 -AGGAGATAAGATTTACTATCTTCAATCTGC
66 GA-GAAATAAGATTTGCTATCTTCAATCTGC
* * * * * *
41841397 TCCACTTCAACCTT-AGGGAG--AAGA--G--ATTTGTAGTTTTAATCTGCTCTATTGCAACTTC
1 TCCACTGCAA-CTTCAGGGAGATAAGATTGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTC
* ** ** *
41841455 AGGGGGATAAGATTTG-TGGCTTTAATCTGC
65 AGAGAAATAAGATTTGCTATCTTCAATCTGC
*
41841485 TCCACTACAACTTCAGGGAGATAAGATT
1 TCCACTGCAACTTCAGGGAGATAAGATT
41841513 CTCCACGATG
Statistics
Matches: 254, Mismatches: 35, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
87 7 0.03
88 26 0.10
89 105 0.41
90 7 0.03
92 1 0.00
95 2 0.01
96 106 0.42
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (95 bp):
TCCACTGCAACTTCAGGGAGATAAGATTGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTCA
GAGAAATAAGATTTGCTATCTTCAATCTGC
Found at i:41841424 original size:89 final size:88
Alignment explanation
Indices: 41841150--41841512 Score: 349
Period size: 89 Copynumber: 4.0 Consensus size: 88
41841140 AATTTGTAAC
* * * * * * *
41841150 TTGTAGCTTTAATCTGTTCCACTGCAAATTTAGAGAAATAAGATTTGCGATCTTCAATCTGCTCC
1 TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-CTATCTTCAATCTGCTCC
41841215 ACTGT-AACTTCAGGGAGATAAGATTCGT
65 ACT-TCAACTTCAGGGAGATAAGA----T
* * * *
41841243 AACTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTAC
1 ---TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-CTATCTTCAATCTGC
* * *
41841308 TTC-GTTGCAACTTCAGGTAGATAAGAT
62 TCCACTT-CAACTTCAGGGAGATAAGAT
*
41841335 TTGTATCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTACTATCTTCAATCTGCTCC
1 TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-CTATCTTCAATCTGCTCC
41841400 ACTTCAACCTT-AGGGAGA-AGAGAT
65 ACTTCAA-CTTCAGGGAGATA-AGAT
* * * * ** *
41841424 TTGTAGT-TTTAATCTGCTCTATTGCAACTTCAGGGGGATAAGATTTGTGGCTTTAATCTGCTCC
1 TTGTA-TCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTCTATCTTCAATCTGCTCC
*
41841488 ACTACAACTTCAGGGAGATAAGAT
65 ACTTCAACTTCAGGGAGATAAGAT
41841512 T
1 T
41841513 CTCCACGATG
Statistics
Matches: 233, Mismatches: 26, Indels: 24
0.82 0.09 0.08
Matches are distributed among these distances:
87 3 0.01
88 33 0.14
89 112 0.48
90 6 0.03
92 1 0.00
94 1 0.00
95 1 0.00
96 76 0.33
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (88 bp):
TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTCTATCTTCAATCTGCTCCA
CTTCAACTTCAGGGAGATAAGAT
Found at i:41842099 original size:11 final size:11
Alignment explanation
Indices: 41842069--41842129 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
41842059 CCGGCCCATT
41842069 TTTTAATAAATA
1 TTTTAA-AAATA
**
41842081 TTAAAAAAATA
1 TTTTAAAAATA
41842092 TTTTAAAAATA
1 TTTTAAAAATA
*
41842103 ---AAAAAATA
1 TTTTAAAAATA
*
41842111 TTTTAAAAGTA
1 TTTTAAAAATA
41842122 TTTTAAAA
1 TTTTAAAA
41842130 TTAAAAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
8 7 0.18
11 28 0.72
12 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:41842106 original size:19 final size:19
Alignment explanation
Indices: 41842082--41842118 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
41842072 TAATAAATAT
41842082 TAAAAAAATATTTTAAAAA
1 TAAAAAAATATTTTAAAAA
41842101 TAAAAAAATATTTTAAAA
1 TAAAAAAATATTTTAAAA
41842119 GTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAAAATATTTTAAAAA
Found at i:41842112 original size:30 final size:30
Alignment explanation
Indices: 41842076--41842136 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
41842066 ATTTTTTAAT
41842076 AAATATTAAAAAAATATTTTAAAAATAAAA
1 AAATATTAAAAAAATATTTTAAAAATAAAA
** * *
41842106 AAATATTTTAAAAGTATTTTAAAATTAAAA
1 AAATATTAAAAAAATATTTTAAAAATAAAA
41842136 A
1 A
41842137 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (30 bp):
AAATATTAAAAAAATATTTTAAAAATAAAA
Found at i:41846390 original size:85 final size:85
Alignment explanation
Indices: 41846289--41846460 Score: 308
Period size: 85 Copynumber: 2.0 Consensus size: 85
41846279 AACCCACCCT
* * *
41846289 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTGTGCATAATTCGGGTAAAATCGAA
1 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGAGTAAAATCGAA
41846354 AAAATTTGGTTAACAGACCG
66 AAAATTTGGTTAACAGACCG
41846374 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGAGTAAAATCGAA
1 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGAGTAAAATCGAA
*
41846439 AAAATTTGGTTAACCGACCG
66 AAAATTTGGTTAACAGACCG
41846459 AA
1 AA
41846461 TTCGGTTAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.20
Consensus pattern (85 bp):
AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGAGTAAAATCGAA
AAAATTTGGTTAACAGACCG
Found at i:41846641 original size:13 final size:13
Alignment explanation
Indices: 41846623--41846652 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
41846613 AGCCCAAACT
41846623 CAATTACCCAACC
1 CAATTACCCAACC
41846636 CAATTACCCAACC
1 CAATTACCCAACC
41846649 CAAT
1 CAAT
41846653 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:41846804 original size:9 final size:9
Alignment explanation
Indices: 41846792--41846859 Score: 84
Period size: 9 Copynumber: 7.4 Consensus size: 9
41846782 AAGATAAAAA
*
41846792 AATTCAGGT
1 AATTCGGGT
41846801 AATTCGGGT
1 AATTCGGGT
*
41846810 ATTTTTC-GGT
1 A--ATTCGGGT
*
41846820 AATTCGGTT
1 AATTCGGGT
41846829 AATTCGGGT
1 AATTCGGGT
41846838 AATTCGGGT
1 AATTCGGGT
41846847 AATTCGGGT
1 AATTCGGGT
41846856 AATT
1 AATT
41846860 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
8 3 0.06
9 41 0.80
10 4 0.08
11 3 0.06
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:41847036 original size:12 final size:12
Alignment explanation
Indices: 41847019--41847043 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41847009 AGTAATTTCG
41847019 GGTCGGTTAACC
1 GGTCGGTTAACC
41847031 GGTCGGTTAACC
1 GGTCGGTTAACC
41847043 G
1 G
41847044 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:41849440 original size:16 final size:15
Alignment explanation
Indices: 41849421--41849454 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
41849411 AATAAGCAAG
41849421 TAAATAAATAAATGGA
1 TAAATAAATAAAT-GA
41849437 TAAATAAATAAATGA
1 TAAATAAATAAATGA
41849452 TAA
1 TAA
41849455 TAAGAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
TAAATAAATAAATGA
Found at i:41856006 original size:17 final size:19
Alignment explanation
Indices: 41855986--41856026 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
41855976 ATACTTCTTA
*
41855986 AAAAATAAAA-A-ATGTAT
1 AAAAATAAAATATATATAT
*
41856003 AAAAGTAAAATATATATAT
1 AAAAATAAAATATATATAT
41856022 AAAAA
1 AAAAA
41856027 ATTGATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAATAAAATATATATAT
Found at i:41857226 original size:30 final size:31
Alignment explanation
Indices: 41857191--41857252 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
41857181 AAACCTTTTT
* *
41857191 ACTTTCCCCCCAATACTTTTAC-TCCCTCCC
1 ACTTTCCCCCCAAAACTTTTACACCCCTCCC
**
41857221 ACTTTCCCCTTAAAACTTTTACACCCCTCCC
1 ACTTTCCCCCCAAAACTTTTACACCCCTCCC
41857252 A
1 A
41857253 TCCCACCCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.21, C:0.47, G:0.00, T:0.32
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACACCCCTCCC
Found at i:41860395 original size:20 final size:20
Alignment explanation
Indices: 41860368--41860420 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
41860358 TATTATATTC
41860368 CCAATATATTATAGATAAAT
1 CCAATATATTATAGATAAAT
* * *
41860388 CGAATATATTAGAGATAAGT
1 CCAATATATTATAGATAAAT
*
41860408 CCAATACATTATA
1 CCAATATATTATA
41860421 TAAGCTCAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.32
Consensus pattern (20 bp):
CCAATATATTATAGATAAAT
Found at i:41860507 original size:18 final size:18
Alignment explanation
Indices: 41860473--41860506 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41860463 AGAATGGGCT
41860473 TAAAAATATTATGAAAAC
1 TAAAAATATTATGAAAAC
41860491 TAAAAATATT-TGAAAA
1 TAAAAATATTATGAAAA
41860507 AAACTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
TAAAAATATTATGAAAAC
Found at i:41861874 original size:17 final size:18
Alignment explanation
Indices: 41861854--41861891 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41861844 TTTATATATT
*
41861854 ATATTAT-TTATTATAAA
1 ATATTATCTTACTATAAA
*
41861871 ATATTTTCTTACTATAAA
1 ATATTATCTTACTATAAA
41861889 ATA
1 ATA
41861892 AATTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTATCTTACTATAAA
Found at i:41866644 original size:21 final size:21
Alignment explanation
Indices: 41866618--41866657 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41866608 TAATGTCATA
41866618 TCAGTATTTTCATCTTGAATT
1 TCAGTATTTTCATCTTGAATT
*
41866639 TCAGTATTTTCATTTTGAA
1 TCAGTATTTTCATCTTGAA
41866658 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
TCAGTATTTTCATCTTGAATT
Found at i:41874967 original size:24 final size:24
Alignment explanation
Indices: 41874940--41874986 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41874930 AAACCTAATT
41874940 CTAATCAAA-GTAAAATATATTATG
1 CTAAT-AAATGTAAAATATATTATG
*
41874964 CTAATAAATGTTAAATATATTAT
1 CTAATAAATGTAAAATATATTAT
41874987 ATTCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAATAAATGTAAAATATATTATG
Found at i:41875002 original size:24 final size:24
Alignment explanation
Indices: 41874952--41875002 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
41874942 AATCAAAGTA
* **
41874952 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
* *
41874976 AAATATATTATATTCATAAATACT
1 AAATATATTATACTAATAAATACT
41875000 AAA
1 AAA
41875003 CCTTCTAGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:41877142 original size:22 final size:24
Alignment explanation
Indices: 41877117--41877182 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
41877107 TTGACATCCT
41877117 TTCTTGTTCTG-GTT-GAAATAGA
1 TTCTTGTTCTGTGTTAGAAATAGA
* *
41877139 TTCTTTTTGTGTGTTAGAAATAGA
1 TTCTTGTTCTGTGTTAGAAATAGA
* * *
41877163 TTCTTTTTGTGGGTTAGAAA
1 TTCTTGTTCTGTGTTAGAAA
41877183 AGTATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
22 9 0.23
23 3 0.08
24 27 0.69
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (24 bp):
TTCTTGTTCTGTGTTAGAAATAGA
Found at i:41877159 original size:24 final size:24
Alignment explanation
Indices: 41877127--41877182 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
41877117 TTCTTGTTCT
41877127 GGTT-GAAATAGATTCTTTTTGTG
1 GGTTAGAAATAGATTCTTTTTGTG
*
41877150 TGTTAGAAATAGATTCTTTTTGTG
1 GGTTAGAAATAGATTCTTTTTGTG
41877174 GGTTAGAAA
1 GGTTAGAAA
41877183 AGTATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.27, C:0.04, G:0.25, T:0.45
Consensus pattern (24 bp):
GGTTAGAAATAGATTCTTTTTGTG
Found at i:41877629 original size:23 final size:23
Alignment explanation
Indices: 41877584--41877630 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41877574 AACTTATATT
* *
41877584 TAAAATTCAAATATATATAAAAA
1 TAAAATTCAAATATAAACAAAAA
* *
41877607 TAAAATTCAAATTTAAACCAAAA
1 TAAAATTCAAATATAAACAAAAA
41877630 T
1 T
41877631 GATATTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAATTCAAATATAAACAAAAA
Found at i:41887564 original size:25 final size:25
Alignment explanation
Indices: 41887530--41887579 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
41887520 AAATGAACTG
*
41887530 TTGAACAATTTGTTCGATCTTTGCA
1 TTGAACAATTTGTTCGATCTCTGCA
41887555 TTGAACAATTTGTTCGATCTCTGCA
1 TTGAACAATTTGTTCGATCTCTGCA
41887580 CAAACTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (25 bp):
TTGAACAATTTGTTCGATCTCTGCA
Found at i:41892955 original size:19 final size:19
Alignment explanation
Indices: 41892920--41892957 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41892910 TCTAGTTTCA
**
41892920 GATAAAATTTATGGATCTT
1 GATAAAATTTACAGATCTT
41892939 GATAAAATTTACAGATCTT
1 GATAAAATTTACAGATCTT
41892958 AATTTGGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (19 bp):
GATAAAATTTACAGATCTT
Found at i:41906033 original size:15 final size:15
Alignment explanation
Indices: 41906013--41906044 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41906003 CTATGAACCT
41906013 TAGTAAAATTCGGCC
1 TAGTAAAATTCGGCC
41906028 TAGTAAAATTCGGCC
1 TAGTAAAATTCGGCC
41906043 TA
1 TA
41906045 ACTATAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (15 bp):
TAGTAAAATTCGGCC
Found at i:41911715 original size:3 final size:3
Alignment explanation
Indices: 41911707--41911732 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41911697 TTCAAATTTA
41911707 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
41911733 GAGAAAGGTG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41920085 original size:20 final size:20
Alignment explanation
Indices: 41920062--41920101 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41920052 TAACGGGACC
41920062 GCTGATGTGG-CAAGTTAACT
1 GCTGATGTGGCCAA-TTAACT
41920082 GCTGATGTGGCCAATTAACT
1 GCTGATGTGGCCAATTAACT
41920102 TGCCACGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
GCTGATGTGGCCAATTAACT
Found at i:41920333 original size:81 final size:81
Alignment explanation
Indices: 41920198--41920347 Score: 300
Period size: 81 Copynumber: 1.9 Consensus size: 81
41920188 AAGAAGAAGA
41920198 AGAACAGACCATATAAAAAAAGTCTTCTTTGCCTAATTTGGTGGGGTCTGATTCTTTGCCATTGA
1 AGAACAGACCATATAAAAAAAGTCTTCTTTGCCTAATTTGGTGGGGTCTGATTCTTTGCCATTGA
41920263 AACACCATTTTTTTGC
66 AACACCATTTTTTTGC
41920279 AGAACAGACCATATAAAAAAAGTCTTCTTTGCCTAATTTGGTGGGGTCTGATTCTTTGCCATTGA
1 AGAACAGACCATATAAAAAAAGTCTTCTTTGCCTAATTTGGTGGGGTCTGATTCTTTGCCATTGA
41920344 AACA
66 AACA
41920348 TCTTCTTCTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (81 bp):
AGAACAGACCATATAAAAAAAGTCTTCTTTGCCTAATTTGGTGGGGTCTGATTCTTTGCCATTGA
AACACCATTTTTTTGC
Found at i:41920356 original size:3 final size:3
Alignment explanation
Indices: 41920348--41920384 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
41920338 CATTGAAACA
41920348 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
41920385 GACTCTCTTC
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:41920935 original size:3 final size:3
Alignment explanation
Indices: 41920906--41920972 Score: 59
Period size: 3 Copynumber: 23.3 Consensus size: 3
41920896 CTATTTTTTC
* * * *
41920906 TCT TCT CCT TCT TAT TCT TCT TAT TCT TCT TCT TCT TC- TCC TCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
41920952 TTT TCT TCT TTT TC- TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT T
41920973 AAACCCTAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 6 0.12
3 45 0.88
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:41922340 original size:18 final size:16
Alignment explanation
Indices: 41922298--41922340 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
41922288 TGTCGTTCGT
41922298 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
41922315 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
41922334 TTTCAAA
1 TTTCAAA
41922341 ACTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:41923326 original size:17 final size:18
Alignment explanation
Indices: 41923295--41923328 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
41923285 CATAATGTTT
41923295 GCCCGTGTGAGCCCACAC
1 GCCCGTGTGAGCCCACAC
41923313 GCCCGTGT-AGCCCACA
1 GCCCGTGTGAGCCCACA
41923329 TGACCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.18, C:0.44, G:0.26, T:0.12
Consensus pattern (18 bp):
GCCCGTGTGAGCCCACAC
Found at i:41926065 original size:20 final size:21
Alignment explanation
Indices: 41926013--41926066 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
41926003 GAGGGGTCAA
41926013 CACAC-AT-GTGTGGAAGGAGG
1 CACACGATCGTGTGGAA-GAGG
*
41926033 CACAGGATCGTGTGGAA-AGG
1 CACACGATCGTGTGGAAGAGG
41926053 CACACG-TCAGTGTG
1 CACACGATC-GTGTG
41926067 CGCCAGGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 17 0.59
21 2 0.07
22 8 0.28
ACGTcount: A:0.28, C:0.19, G:0.37, T:0.17
Consensus pattern (21 bp):
CACACGATCGTGTGGAAGAGG
Found at i:41927834 original size:31 final size:31
Alignment explanation
Indices: 41927790--41927848 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
41927780 TTTTTCTCAA
*
41927790 TTAAATTAAAATTAAAATTTTATATATACAT
1 TTAAATCAAAATTAAAATTTTATATATACAT
* *
41927821 TTAAATCATAATTAAAGTTTTATATATA
1 TTAAATCAAAATTAAAATTTTATATATA
41927849 ATTATACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
TTAAATCAAAATTAAAATTTTATATATACAT
Found at i:41932216 original size:16 final size:17
Alignment explanation
Indices: 41932187--41932219 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41932177 ATCACAATAA
41932187 AATAAAATTCTAATATT
1 AATAAAATTCTAATATT
*
41932204 AATAAACTT-TAATATT
1 AATAAAATTCTAATATT
41932220 TTGATATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAAATTCTAATATT
Found at i:41933562 original size:9 final size:9
Alignment explanation
Indices: 41933550--41933577 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41933540 TTTTATTACA
41933550 ACAATTAAT
1 ACAATTAAT
41933559 ACAATTAAT
1 ACAATTAAT
41933568 ACAATTAAT
1 ACAATTAAT
41933577 A
1 A
41933578 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41933599 original size:68 final size:68
Alignment explanation
Indices: 41933520--41933729 Score: 397
Period size: 68 Copynumber: 3.1 Consensus size: 68
41933510 TCAAGTTTGT
41933520 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
41933585 AAA
66 AAA
41933588 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
41933653 AAA
66 AAA
41933656 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
41933719 AAT
66 AAA
41933722 TTTACTAA
1 TTTACTAA
41933730 CAATTAATTT
Statistics
Matches: 141, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 113 0.80
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:41933630 original size:9 final size:9
Alignment explanation
Indices: 41933618--41933645 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41933608 TTTTATTACA
41933618 ACAATTAAT
1 ACAATTAAT
41933627 ACAATTAAT
1 ACAATTAAT
41933636 ACAATTAAT
1 ACAATTAAT
41933645 A
1 A
41933646 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41933739 original size:16 final size:16
Alignment explanation
Indices: 41933718--41933759 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
41933708 AATAATTTGA
*
41933718 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
41933734 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
41933750 TAGTTTTAAT
1 TAATTTTAAT
41933760 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:41933743 original size:22 final size:22
Alignment explanation
Indices: 41933733--41933793 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
41933723 TTACTAACAA
* * *
41933733 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
41933755 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
41933777 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
41933794 CGGGCCAGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:41939695 original size:37 final size:37
Alignment explanation
Indices: 41939653--41939801 Score: 244
Period size: 37 Copynumber: 4.0 Consensus size: 37
41939643 GGTAGTTTTA
* *
41939653 GCTACACTTATCTAATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
41939690 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
41939727 GTTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
41939764 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
41939801 G
1 G
41939802 TAGCTTTAGC
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:41939745 original size:74 final size:78
Alignment explanation
Indices: 41939617--41939847 Score: 272
Period size: 74 Copynumber: 2.9 Consensus size: 78
41939607 TTTGAGTACT
** *
41939617 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTAATCAAGTGACAAAGT
1 TCTGATCAAGAAACAAAGTGATAAGTGG-AG--TTA--TACACTTATCTGATCAAGTGACAAAGT
41939682 GATAAGTGGCTACACTTA
61 GATAAGTGGCTACACTTA
*
41939700 TCTGATCAAGAAACAAAGTGATAAGT-G-G-T-TACACTTATCTGATCAAGAGACAAAGTGATAA
1 TCTGATCAAGAAACAAAGTGATAAGTGGAGTTATACACTTATCTGATCAAGTGACAAAGTGATAA
41939761 GTGGCTACACTTA
66 GTGGCTACACTTA
** * *
41939774 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGGCAAAGT
1 TCTGATCAAGAAACAAAGTGATAAGTGG-AG--TTA--TACACTTATCTGATCAAGTGACAAAGT
41939839 GATAAGTGG
61 GATAAGTGG
41939848 TAGCCTAGCT
Statistics
Matches: 130, Mismatches: 9, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
74 66 0.51
75 1 0.01
77 2 0.02
80 2 0.02
82 1 0.01
83 58 0.45
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (78 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGAGTTATACACTTATCTGATCAAGTGACAAAGTGATAA
GTGGCTACACTTA
Found at i:41939873 original size:45 final size:46
Alignment explanation
Indices: 41939764--41939887 Score: 191
Period size: 46 Copynumber: 2.8 Consensus size: 46
41939754 GTGATAAGTG
* *
41939764 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTA
*
41939810 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGC-CTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTA
*
41939855 GCTACACTTATCTAATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
41939888 AGGTCATATG
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.29
46 40 0.55
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTA
Found at i:41959840 original size:13 final size:13
Alignment explanation
Indices: 41959813--41959850 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
41959803 GGAATCATAT
*
41959813 AAAA-ATTTAAAA
1 AAAATATTTTAAA
*
41959825 AAAATGTTTTAAA
1 AAAATATTTTAAA
41959838 AAAATATTTTAAA
1 AAAATATTTTAAA
41959851 TTTTATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (13 bp):
AAAATATTTTAAA
Found at i:41960328 original size:25 final size:24
Alignment explanation
Indices: 41960292--41960339 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
41960282 AATAAAAATT
*
41960292 AATATTATTTTTATTTATTTTATAA
1 AATATTATTTTTAATT-TTTTATAA
41960317 AATATT-TCTTTTAATTTTTTATA
1 AATATTAT-TTTTAATTTTTTATA
41960340 CACCTAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
AATATTATTTTTAATTTTTTATAA
Found at i:41960561 original size:16 final size:16
Alignment explanation
Indices: 41960523--41960568 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
41960513 TTCTGGACAT
*
41960523 AACTTTTAATTTTTTT
1 AACTTTTAATTTTTTG
* *
41960539 TATTTTTAATTTTTTG
1 AACTTTTAATTTTTTG
41960555 AACTTTTGAATTTT
1 AACTTTT-AATTTT
41960569 ATTTAATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (16 bp):
AACTTTTAATTTTTTG
Found at i:41960636 original size:16 final size:16
Alignment explanation
Indices: 41960611--41960641 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41960601 TATAGATTTA
*
41960611 TAAATTTTTTAAAATT
1 TAAATCTTTTAAAATT
41960627 TAAATCTTTTAAAAT
1 TAAATCTTTTAAAAT
41960642 ATTTTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATCTTTTAAAATT
Found at i:41968138 original size:51 final size:51
Alignment explanation
Indices: 41968079--41968197 Score: 177
Period size: 51 Copynumber: 2.4 Consensus size: 51
41968069 TTTTCTCTAG
* *
41968079 TTAATTTAAATTAATTAAAAGATAGATAATAAAAAATTATATCATCACTAA
1 TTAATTTAAATTAATTAAAAAATAAATAATAAAAAATTATATCATCACTAA
* *
41968130 TTAATTTAAACTAATTAAAAAATAAATAATAAAAAATTATATTATCACTAA
1 TTAATTTAAATTAATTAAAAAATAAATAATAAAAAATTATATCATCACTAA
* *
41968181 -TAAATTAAATTATTTAA
1 TTAATTTAAATTAATTAA
41968198 GTGATAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 14 0.23
51 47 0.77
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (51 bp):
TTAATTTAAATTAATTAAAAAATAAATAATAAAAAATTATATCATCACTAA
Found at i:41974967 original size:58 final size:58
Alignment explanation
Indices: 41974893--41975008 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
41974883 ATTAACTTTT
*
41974893 AGAAAAAAAAATTAAAAATGATTAAAAATATATAAAAGGAAGAAAAGATGTTTATTTA
1 AGAAAAAAAAAGTAAAAATGATTAAAAATATATAAAAGGAAGAAAAGATGTTTATTTA
41974951 AGAAAAAAAAAGTAAAAATGATTAAAAATATATAAAAGGAAGAAAAGATGTTTATTTA
1 AGAAAAAAAAAGTAAAAATGATTAAAAATATATAAAAGGAAGAAAAGATGTTTATTTA
41975009 TTATTTTAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (58 bp):
AGAAAAAAAAAGTAAAAATGATTAAAAATATATAAAAGGAAGAAAAGATGTTTATTTA
Found at i:41975459 original size:21 final size:21
Alignment explanation
Indices: 41975433--41975472 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41975423 TATTTAACGC
*
41975433 TAAATCTCGAACCTTGAACAT
1 TAAATCTCGAACCTCGAACAT
*
41975454 TAAATCTTGAACCTCGAAC
1 TAAATCTCGAACCTCGAAC
41975473 CCTAAGGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (21 bp):
TAAATCTCGAACCTCGAACAT
Found at i:41975654 original size:22 final size:22
Alignment explanation
Indices: 41975629--41975684 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
41975619 TTTGGGTTTA
41975629 AGGTTTAAGGG-TTTGAGATTAT
1 AGGTTT-AGGGTTTTGAGATTAT
*
41975651 AGGTTTAGGGTTTTGAGATTCT
1 AGGTTTAGGGTTTTGAGATTAT
* *
41975673 AGATTTTGGGTT
1 AGGTTTAGGGTT
41975685 CAGGGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.21, C:0.02, G:0.32, T:0.45
Consensus pattern (22 bp):
AGGTTTAGGGTTTTGAGATTAT
Found at i:41977473 original size:17 final size:17
Alignment explanation
Indices: 41977451--41977503 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
41977441 AAATCTTAAA
*
41977451 TTTTGATACCCATATCT
1 TTTTGATACCTATATCT
**
41977468 TTTTGATATTTATATCT
1 TTTTGATACCTATATCT
* *
41977485 TTCTGGTACCTATATCT
1 TTTTGATACCTATATCT
41977502 TT
1 TT
41977504 GACTTTCTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.08, T:0.55
Consensus pattern (17 bp):
TTTTGATACCTATATCT
Found at i:41979585 original size:29 final size:30
Alignment explanation
Indices: 41979538--41979605 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
41979528 TGGCCCAAGA
* *
41979538 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
41979568 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
41979598 GCAAATAT
1 GTAAATAT
41979606 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:41982089 original size:46 final size:46
Alignment explanation
Indices: 41982037--41982172 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
41982027 GCTCTTTGAA
* * *
41982037 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
41982083 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
41982129 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
41982173 TCAAAGATAA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 80 0.99
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:41984598 original size:17 final size:17
Alignment explanation
Indices: 41984573--41984621 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
41984563 AAATCTCAGA
41984573 TTTTGATACCCATATAT
1 TTTTGATACCCATATAT
* *
41984590 TTTTTATACCTATATAT
1 TTTTGATACCCATATAT
*
41984607 TTCTGATACCCATAT
1 TTTTGATACCCATAT
41984622 CTTTGACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (17 bp):
TTTTGATACCCATATAT
Found at i:41991262 original size:29 final size:30
Alignment explanation
Indices: 41991203--41991260 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
41991193 TCCAAACTTT
*
41991203 GGGGCAAAAATGTAATTATGCAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
*
41991233 GGGGC-AAAATCGTAATTTTGAAAAAGTT
1 GGGGCAAAAAT-GTAATTATGAAAAAGTT
41991261 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Done.