Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 56
Found at i:357861 original size:25 final size:25
Alignment explanation
Indices: 357813--357864 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
357803 TCGACTACTC
357813 TAAATTTTGTAAGTCTCAACTAATT
1 TAAATTTTGTAAGTCTCAACTAATT
* * *
357838 TAAATTTTGTAGGTCTCGATTAATT
1 TAAATTTTGTAAGTCTCAACTAATT
357863 TA
1 TA
357865 GTAAGAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.46
Consensus pattern (25 bp):
TAAATTTTGTAAGTCTCAACTAATT
Found at i:360532 original size:22 final size:22
Alignment explanation
Indices: 360497--360538 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
360487 GATATTAGAT
* *
360497 ATATTAATTTTAATAATTTTAA
1 ATATTAAATATAATAATTTTAA
*
360519 ATATTAAATATAATTATTTT
1 ATATTAAATATAATAATTTT
360539 TTTACTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTAAATATAATAATTTTAA
Found at i:360773 original size:12 final size:12
Alignment explanation
Indices: 360758--360827 Score: 65
Period size: 12 Copynumber: 5.6 Consensus size: 12
360748 AGTTAGTTAG
360758 TTGTATAGTAGC
1 TTGTATAGTAGC
360770 TTGTAGTTAGTTAG-
1 TTGTA--TAG-TAGC
360784 TTGTATAGTAGC
1 TTGTATAGTAGC
360796 TTGTAGTTAGTTAG-
1 TTGTA--TAG-TAGC
360810 TTGTATAGTAGC
1 TTGTATAGTAGC
360822 TT-TATA
1 TTGTATA
360828 CTTGTAAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
11 10 0.20
12 18 0.36
14 16 0.32
15 6 0.12
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.47
Consensus pattern (12 bp):
TTGTATAGTAGC
Found at i:360782 original size:30 final size:26
Alignment explanation
Indices: 360741--360823 Score: 157
Period size: 26 Copynumber: 3.2 Consensus size: 26
360731 GTTTCTTTAC
*
360741 AGCTGGTAGTTAGTTAGTTGTATAGT
1 AGCTTGTAGTTAGTTAGTTGTATAGT
360767 AGCTTGTAGTTAGTTAGTTGTATAGT
1 AGCTTGTAGTTAGTTAGTTGTATAGT
360793 AGCTTGTAGTTAGTTAGTTGTATAGT
1 AGCTTGTAGTTAGTTAGTTGTATAGT
360819 AGCTT
1 AGCTT
360824 TATACTTGTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.45
Consensus pattern (26 bp):
AGCTTGTAGTTAGTTAGTTGTATAGT
Found at i:368556 original size:2 final size:2
Alignment explanation
Indices: 368551--368601 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
368541 TGATGGGGGG
*
368551 GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
368593 -A AA GA GA GA
1 GA GA GA GA GA
368602 CTCCATGGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
GA
Found at i:371407 original size:31 final size:33
Alignment explanation
Indices: 371369--371434 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 33
371359 ATGACGGTAG
* *
371369 AGTGATCATTTTGTTATAAAT-GAATAAA-ATT
1 AGTGATCATTTTGTTACAAATCGAAAAAACATT
371400 AGTGATCATTTTGTTACAAATCGAAAAAACATT
1 AGTGATCATTTTGTTACAAATCGAAAAAACATT
371433 AG
1 AG
371435 CTCTCATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 20 0.65
32 6 0.19
33 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (33 bp):
AGTGATCATTTTGTTACAAATCGAAAAAACATT
Found at i:372381 original size:27 final size:27
Alignment explanation
Indices: 372351--372405 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
372341 CATCCCTCCC
372351 TCCCATCTTTTAAAACTTATAATTTAA
1 TCCCATCTTTTAAAACTTATAATTTAA
*
372378 TCCCATCTTTTAAAATTTATAATTTAA
1 TCCCATCTTTTAAAACTTATAATTTAA
372405 T
1 T
372406 TTTTAGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.47
Consensus pattern (27 bp):
TCCCATCTTTTAAAACTTATAATTTAA
Found at i:377639 original size:22 final size:22
Alignment explanation
Indices: 377611--377671 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
377601 AGCTTAAACT
*
377611 AAAGTGCCTCAGCACTGATACA
1 AAAGTGCCTCAGCACTAATACA
*
377633 AAAGTGCATTCA-CACTAATACA
1 AAAGTGC-CTCAGCACTAATACA
377655 AAAGTGCCAT-AGCACTA
1 AAAGTGCC-TCAGCACTA
377672 GGAAAGACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.03
22 29 0.88
23 3 0.09
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.20
Consensus pattern (22 bp):
AAAGTGCCTCAGCACTAATACA
Found at i:378857 original size:5 final size:5
Alignment explanation
Indices: 378847--378989 Score: 184
Period size: 5 Copynumber: 27.8 Consensus size: 5
378837 TTGACAACGT
*
378847 TATTA TATTA TATTA TATTA TATTA TATTA -ATTA TATATA GATATA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA TAT-TA TATTA
*
378898 TATTA TATTATA TATTA TATTA T-TTA TATTA TATTA TTTATA TATTA
1 TATTA TA-T-TA TATTA TATTA TATTA TATTA TATTA TAT-TA TATTA
378945 TATTA T-TTA TATATA TATTA TATTA TATATA TATTA TATTA TATT
1 TATTA TATTA TAT-TA TATTA TATTA TAT-TA TATTA TATTA TATT
378990 TAAACTCGAC
Statistics
Matches: 125, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
4 12 0.10
5 84 0.67
6 25 0.20
7 4 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:378895 original size:41 final size:40
Alignment explanation
Indices: 378850--378989 Score: 185
Period size: 41 Copynumber: 3.4 Consensus size: 40
378840 ACAACGTTAT
*
378850 TATATTATATTATATTATATTATATTAATTATATATAGATA
1 TATATTATATTATATTATATTATATTAATTATAT-TATATA
*
378891 TATATTATATTATATTATATATTATATTATTTATATTATAT-
1 TATATTATATTATA-T-TATATTATATTAATTATATTATATA
*
378932 TATTTATATATTATATTAT-TTATATATATATTATATTATATA
1 TATAT-TATATTATATTATATTATAT-TA-ATTATATTATATA
378974 TATATTATATTATATT
1 TATATTATATTATATT
378990 TAAACTCGAC
Statistics
Matches: 88, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
39 6 0.07
40 5 0.06
41 41 0.47
42 18 0.20
43 18 0.20
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (40 bp):
TATATTATATTATATTATATTATATTAATTATATTATATA
Found at i:378986 original size:36 final size:35
Alignment explanation
Indices: 378850--378986 Score: 186
Period size: 36 Copynumber: 3.8 Consensus size: 35
378840 ACAACGTTAT
*
378850 TATATTATATTATATTATATTATATTAATTATATA
1 TATATTATATTATATTATATTATATTATTTATATA
* *
378885 TAGATATATATTATATTATATTATA-TATTATATTATT
1 TATAT-TATATTATATTATATTATATTATT-TA-TATA
*
378922 TATATTATATTATTTATATATTATATTATTTATATA
1 TATATTATATTATAT-TATATTATATTATTTATATA
378958 TATATTATATTATATATATATTATATTAT
1 TATATTATATTATAT-TATATTATATTAT
378987 ATTTAAACTC
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
35 7 0.08
36 61 0.68
37 18 0.20
38 4 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
TATATTATATTATATTATATTATATTATTTATATA
Found at i:385881 original size:24 final size:26
Alignment explanation
Indices: 385835--385882 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
385825 ACACATACTA
385835 AATCTTACTTGAACAGAGTTATAGGT
1 AATCTTACTTGAACAGAGTTATAGGT
385861 AATC-TAC-TGAA-AGAGTCTATAG
1 AATCTTACTTGAACAGAGT-TATAG
385883 TTACTCACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 9 0.43
25 3 0.14
26 4 0.19
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (26 bp):
AATCTTACTTGAACAGAGTTATAGGT
Found at i:395310 original size:21 final size:21
Alignment explanation
Indices: 395281--395324 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
395271 AATCGGTAAA
*
395281 TTACGTAAAATATTATTATTT
1 TTACGTAAAATATTAATATTT
*
395302 TTACTTAAAATATTAATATTT
1 TTACGTAAAATATTAATATTT
395323 TT
1 TT
395325 TAATATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
TTACGTAAAATATTAATATTT
Found at i:395642 original size:15 final size:16
Alignment explanation
Indices: 395624--395666 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
395614 TACTTATTAG
395624 ATTTATA-TAAAAAAT
1 ATTTATATTAAAAAAT
*
395639 ATTTTTATTAAAAAAT
1 ATTTATATTAAAAAAT
395655 ATTT-T-TTAAAAA
1 ATTTATATTAAAAA
395667 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 7 0.27
15 7 0.27
16 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTATATTAAAAAAT
Found at i:395662 original size:17 final size:17
Alignment explanation
Indices: 395625--395660 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
395615 ACTTATTAGA
395625 TTTATATAAAAAATATT
1 TTTATATAAAAAATATT
395642 TTTAT-TAAAAAATATT
1 TTTATATAAAAAATATT
395658 TTT
1 TTT
395661 TAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATATAAAAAATATT
Found at i:406381 original size:22 final size:21
Alignment explanation
Indices: 406331--406383 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
406321 AGAACTAGGT
406331 AGTATCGATACTCTTAACTTG
1 AGTATCGATACTCTTAACTTG
*
406352 AGTATCGATACTCCTTTA-TTG
1 AGTATCGATACT-CTTAACTTG
406373 AGGTATCGATA
1 A-GTATCGATA
406384 TTGCCCCGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
AGTATCGATACTCTTAACTTG
Found at i:413377 original size:20 final size:21
Alignment explanation
Indices: 413329--413387 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
413319 CGATAGCTTA
* *
413329 TCATTACAAATTTAGATACCTC
1 TCATTAC-AATGTAGATAACTC
413351 GTCATTACAATGTAGATAACT-
1 -TCATTACAATGTAGATAACTC
*
413372 TCATTACCATGT-GATA
1 TCATTACAATGTAGATA
413388 TGATACACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 4 0.12
20 11 0.33
22 11 0.33
23 7 0.21
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (21 bp):
TCATTACAATGTAGATAACTC
Found at i:416347 original size:10 final size:10
Alignment explanation
Indices: 416332--416362 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
416322 TTTTATAACA
416332 AATCAGATTG
1 AATCAGATTG
416342 AATCAGATTG
1 AATCAGATTG
416352 AATCAGATTG
1 AATCAGATTG
416362 A
1 A
416363 TACTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (10 bp):
AATCAGATTG
Found at i:419249 original size:24 final size:24
Alignment explanation
Indices: 419215--419273 Score: 109
Period size: 24 Copynumber: 2.4 Consensus size: 24
419205 ATCTCTAGGC
419215 GATGATGTGGAGACTGGGGTTTTCT
1 GATGA-GTGGAGACTGGGGTTTTCT
419240 GATGAGTGGAGACTGGGGTTTTCT
1 GATGAGTGGAGACTGGGGTTTTCT
419264 GATGAGTGGA
1 GATGAGTGGA
419274 TTGCAATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 29 0.85
25 5 0.15
ACGTcount: A:0.19, C:0.07, G:0.42, T:0.32
Consensus pattern (24 bp):
GATGAGTGGAGACTGGGGTTTTCT
Found at i:422724 original size:27 final size:29
Alignment explanation
Indices: 422686--422750 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
422676 AATTTCATAT
* *
422686 ATAAAGTTT-AAAATTA-CGATTAATTAC
1 ATAATGTTTAAAAATTATCGATTAACTAC
422713 ATAATGTTTAAAAATTATCGATTAACTAC
1 ATAATGTTTAAAAATTATCGATTAACTAC
422742 ATAATGTTT
1 ATAATGTTT
422751 TCTGCCGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 8 0.24
28 7 0.21
29 19 0.56
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (29 bp):
ATAATGTTTAAAAATTATCGATTAACTAC
Found at i:424726 original size:41 final size:41
Alignment explanation
Indices: 424681--424795 Score: 126
Period size: 41 Copynumber: 2.8 Consensus size: 41
424671 CACCCTTAGA
* *
424681 ACCCTCACCCTCA-TTGTTGACTTTTCAACCTCACCATCAGC
1 ACCCTCACCCTCAGTT-TAGACTTCTCAACCTCACCATCAGC
* *
424722 ACCCTCACCCTCAGTTTAGACTTCTCAACCTCACCCTGAGC
1 ACCCTCACCCTCAGTTTAGACTTCTCAACCTCACCATCAGC
** *
424763 ACCCTCAGTCTCAATTTTCA-ACTTCTCAACCTC
1 ACCCTCACCCTC-AGTTT-AGACTTCTCAACCTC
424796 TGTCTCATGC
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 44 0.69
42 19 0.30
43 1 0.02
ACGTcount: A:0.23, C:0.42, G:0.07, T:0.29
Consensus pattern (41 bp):
ACCCTCACCCTCAGTTTAGACTTCTCAACCTCACCATCAGC
Found at i:434113 original size:65 final size:64
Alignment explanation
Indices: 434038--434197 Score: 236
Period size: 65 Copynumber: 2.5 Consensus size: 64
434028 GAATAAATTG
*
434038 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTC-GGGT-TTTTAT
1 AACATCGAATGCATTTTATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTATTTT-T
434100 GA
64 -A
*
434102 AATTATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTTA
1 AA-CATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTTA
*
434167 AACATCAAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
434198 CCTTAGTGCA
Statistics
Matches: 88, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
64 30 0.34
65 50 0.57
66 4 0.05
67 4 0.05
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTTA
Found at i:438667 original size:24 final size:24
Alignment explanation
Indices: 438640--438691 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
438630 CGTTCATTTA
*
438640 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
438664 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
438688 CGTT
1 CGTT
438692 TATGTTCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.15, G:0.27, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:438678 original size:14 final size:14
Alignment explanation
Indices: 438661--438711 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
438651 GTTCGGTTAT
438661 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
438675 GTTCGGTTA---T-
1 GTTCGTTTATGTTC
438685 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
438699 GTTCATTTATGTT
1 GTTCGTTTATGTT
438712 TAACCTAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
10 8 0.27
11 1 0.03
13 1 0.03
14 20 0.67
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:438678 original size:34 final size:34
Alignment explanation
Indices: 438627--438707 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
438617 CATAGGTCTC
438627 GTTCGTTCATTTACGTTC-GTGAACGTTCGGTTAT
1 GTTCGTTCATTTACGTTCGGT-AACGTTCGGTTAT
* * * *
438661 GTTCGTTTATGTT-CGTTCGGTTATGTTCGTTTAT
1 GTTCGTTCAT-TTACGTTCGGTAACGTTCGGTTAT
438695 GTTCGTTCATTTA
1 GTTCGTTCATTTA
438708 TGTTTAACCT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 2 0.05
34 33 0.85
35 4 0.10
ACGTcount: A:0.12, C:0.15, G:0.22, T:0.51
Consensus pattern (34 bp):
GTTCGTTCATTTACGTTCGGTAACGTTCGGTTAT
Found at i:438692 original size:24 final size:24
Alignment explanation
Indices: 438650--438711 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
438640 CGTTCGTGAA
438650 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
438674 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
**
438698 CGTTCATTTATGTT
1 CGTTCGGTTATGTT
438712 TAACCTAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:438700 original size:10 final size:10
Alignment explanation
Indices: 438651--438701 Score: 57
Period size: 10 Copynumber: 4.7 Consensus size: 10
438641 GTTCGTGAAC
*
438651 GTTCGGTTAT
1 GTTCGTTTAT
438661 GTTCGTTTAT
1 GTTCGTTTAT
438671 GTTCGTTCGGTTAT
1 GTTCG-T---TTAT
438685 GTTCGTTTAT
1 GTTCGTTTAT
438695 GTTCGTT
1 GTTCGTT
438702 CATTTATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 25 0.69
11 1 0.03
13 1 0.03
14 9 0.25
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.55
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:439394 original size:15 final size:15
Alignment explanation
Indices: 439374--439402 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
439364 AGATATGTAG
439374 CATCGGAGGGATTTA
1 CATCGGAGGGATTTA
439389 CATCGGAGGGATTT
1 CATCGGAGGGATTT
439403 CGGATCTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (15 bp):
CATCGGAGGGATTTA
Found at i:439761 original size:36 final size:36
Alignment explanation
Indices: 439714--439817 Score: 208
Period size: 36 Copynumber: 2.9 Consensus size: 36
439704 TAATCAGCTC
439714 TTACGCTATTTATCACTGTAGATTTGGTTGATGCTT
1 TTACGCTATTTATCACTGTAGATTTGGTTGATGCTT
439750 TTACGCTATTTATCACTGTAGATTTGGTTGATGCTT
1 TTACGCTATTTATCACTGTAGATTTGGTTGATGCTT
439786 TTACGCTATTTATCACTGTAGATTTGGTTGAT
1 TTACGCTATTTATCACTGTAGATTTGGTTGAT
439818 TTGCATTGTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.47
Consensus pattern (36 bp):
TTACGCTATTTATCACTGTAGATTTGGTTGATGCTT
Found at i:439886 original size:10 final size:10
Alignment explanation
Indices: 439871--439944 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
439861 GGTCTCCAAT
439871 GTTTATGTTC
1 GTTTATGTTC
439881 GTTTATGTTC
1 GTTTATGTTC
*
439891 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
**
439903 GTCCATGTTC
1 GTTTATGTTC
439913 GTTTATGTTC
1 GTTTATGTTC
439923 G----TGTTC
1 GTTTATGTTC
439929 GTTTATGTTC
1 GTTTATGTTC
439939 GTTTAT
1 GTTTAT
439945 TTATTAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.68
11 6 0.12
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:439895 original size:16 final size:16
Alignment explanation
Indices: 439876--439940 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
439866 CCAATGTTTA
439876 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* * *
439892 TGTTCATTTATGTCCA
1 TGTTCGTTTATGTTCG
439908 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
439924 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
439940 T
1 T
439941 TTATTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.09, C:0.14, G:0.22, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:439916 original size:32 final size:32
Alignment explanation
Indices: 439875--439936 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
439865 TCCAATGTTT
439875 ATGTTCGTTTATGTTCGTGTTCATTTATGTCC
1 ATGTTCGTTTATGTTCGTGTTCATTTATGTCC
*
439907 ATGTTCGTTTATGTTCGTGTTCGTTTATGT
1 ATGTTCGTTTATGTTCGTGTTCATTTATGT
439937 TCGTTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.11, C:0.13, G:0.21, T:0.55
Consensus pattern (32 bp):
ATGTTCGTTTATGTTCGTGTTCATTTATGTCC
Found at i:440029 original size:16 final size:16
Alignment explanation
Indices: 440010--440050 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
440000 AAATTGTTTT
440010 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
440026 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
440042 T-TT-ATTTAT
1 TGTTCATTTAT
440051 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:440202 original size:20 final size:19
Alignment explanation
Indices: 440155--440205 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
440145 TGGGCTTGAT
* *
440155 AGTATCGATACTACTATTC
1 AGTATCGATACTAATATGC
440174 ATGGTATCGATACTAATATAGC
1 A--GTATCGATACTAATAT-GC
440196 AGTATCGATA
1 AGTATCGATA
440206 TTATTTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 9 0.33
21 15 0.56
22 2 0.07
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (19 bp):
AGTATCGATACTAATATGC
Found at i:440297 original size:20 final size:20
Alignment explanation
Indices: 440274--440325 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
440264 GTTCACACAG
*
440274 TATCATTACTATTCATACAA
1 TATCAATACTATTCATACAA
**
440294 TATCGGTACTATTCATACAA
1 TATCAATACTATTCATACAA
440314 TA-CAATACTATT
1 TATCAATACTATT
440326 TATAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (20 bp):
TATCAATACTATTCATACAA
Found at i:441681 original size:19 final size:20
Alignment explanation
Indices: 441645--441692 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
441635 TCTAAATCCT
* *
441645 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTAG
441665 TTTTCAAAA-TCCATTTTAG
1 TTTTCAAAATTCCATTTTAG
*
441684 CTTTCAAAA
1 TTTTCAAAA
441693 GAAAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAG
Found at i:443102 original size:18 final size:18
Alignment explanation
Indices: 443076--443123 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
443066 ATTTTTTAGC
*
443076 ATCGGTACTGTTCATGGT
1 ATCGATACTGTTCATGGT
443094 ATCGATACTATTGTTCATGGT
1 ATCGATAC---TGTTCATGGT
*
443115 ATAGATACT
1 ATCGATACT
443124 ATTGTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 8 0.32
21 17 0.68
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (18 bp):
ATCGATACTGTTCATGGT
Found at i:443110 original size:21 final size:21
Alignment explanation
Indices: 443084--443131 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
443074 GCATCGGTAC
*
443084 TGTTCATGGTATCGATACTAT
1 TGTTCATGGTATAGATACTAT
443105 TGTTCATGGTATAGATACTAT
1 TGTTCATGGTATAGATACTAT
443126 TGTTCA
1 TGTTCA
443132 CACAGTGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (21 bp):
TGTTCATGGTATAGATACTAT
Found at i:443185 original size:19 final size:20
Alignment explanation
Indices: 443128--443192 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
443118 GATACTATTG
* * *
443128 TTCACACAGTGTCTGTACTA
1 TTCATACAGTATCGGTACTA
*
443148 TTCATACATTATCGGTACTA
1 TTCATACAGTATCGGTACTA
*
443168 TTCATATAGTAT-GGTACTA
1 TTCATACAGTATCGGTACTA
443187 TTCATA
1 TTCATA
443193 ATTTTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.40
Consensus pattern (20 bp):
TTCATACAGTATCGGTACTA
Found at i:445436 original size:15 final size:15
Alignment explanation
Indices: 445413--445449 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
445403 CGTAGGACGC
445413 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
445428 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
445443 CTACATC
1 CTACATC
445450 GAGGACGACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.16
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:445603 original size:28 final size:28
Alignment explanation
Indices: 445562--445633 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
445552 TTTCATATGT
445562 TCATGTA-CTCATGTCATTCTCTTGTGA
1 TCATGTAGCTCATGTCATTCTCTTGTGA
445589 TCATGTAGCTCATGTCATTCTCTTGTGA
1 TCATGTAGCTCATGTCATTCTCTTGTGA
445617 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
445634 CTTCATCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 7 0.16
28 37 0.84
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (28 bp):
TCATGTAGCTCATGTCATTCTCTTGTGA
Found at i:445673 original size:12 final size:12
Alignment explanation
Indices: 445658--445692 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
445648 CATTCACAGG
445658 TCATATCACATA
1 TCATATCACATA
445670 TCATATCACATA
1 TCATATCACATA
*
445682 GCATATCACAT
1 TCATATCACAT
445693 GAACATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.40, C:0.26, G:0.03, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:446100 original size:64 final size:64
Alignment explanation
Indices: 445992--446168 Score: 221
Period size: 64 Copynumber: 2.8 Consensus size: 64
445982 TAATGACAGT
* * * * ** * * **
445992 ATGCATCGATGTACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-GTCACTATTAATGGG
* *
446056 ATGCATCGATGCACTACTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTGTCACTATTAATGGG
*
446120 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT
446169 CTTTAATTTA
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 1 0.01
64 97 0.99
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:452374 original size:15 final size:15
Alignment explanation
Indices: 452351--452456 Score: 176
Period size: 15 Copynumber: 7.1 Consensus size: 15
452341 CGTAGGACTC
452351 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
452366 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
452381 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
* *
452396 CTACGTCCCGAAGAA
1 CTACATCCCGAAGGA
452411 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
452426 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
452441 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
452456 C
1 C
452457 CATTATACCC
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 83 1.00
ACGTcount: A:0.31, C:0.34, G:0.22, T:0.13
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:452387 original size:30 final size:30
Alignment explanation
Indices: 452351--452456 Score: 203
Period size: 30 Copynumber: 3.5 Consensus size: 30
452341 CGTAGGACTC
452351 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
*
452381 CTACATCCCGAAGGACTACGTCCCGAAGAA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
452411 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
452441 CTACATCCCGAAGGAC
1 CTACATCCCGAAGGAC
452457 CATTATACCC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 74 1.00
ACGTcount: A:0.31, C:0.34, G:0.22, T:0.13
Consensus pattern (30 bp):
CTACATCCCGAAGGACTACGTCCCGAAGGA
Found at i:452561 original size:26 final size:27
Alignment explanation
Indices: 452532--452621 Score: 87
Period size: 26 Copynumber: 3.3 Consensus size: 27
452522 TTATTCTTAT
452532 ATTTCATATGTTCATGTA-CTCATGTC
1 ATTTCATATGTTCATGTAGCTCATGTC
*
452558 ATTTC-TCTTGTGATCATGTAGCTCATGTC
1 ATTTCAT-ATGT--TCATGTAGCTCATGTC
* * *
452587 ATTT-TTCTGATCATGTAGCTCATGTC
1 ATTTCATATGTTCATGTAGCTCATGTC
*
452613 ACTTCATAT
1 ATTTCATAT
452622 CATATTCTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
25 1 0.02
26 27 0.52
27 2 0.04
28 9 0.17
29 13 0.25
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (27 bp):
ATTTCATATGTTCATGTAGCTCATGTC
Found at i:452585 original size:29 final size:26
Alignment explanation
Indices: 452543--452613 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 26
452533 TTTCATATGT
*
452543 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCA-TT-T-TTCTGA
452571 TCATGTAGCTCATGTCATTTTTCTGA
1 TCATGTAGCTCATGTCATTTTTCTGA
452597 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
452614 CTTCATATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 22 0.54
27 1 0.02
28 9 0.22
29 9 0.22
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (26 bp):
TCATGTAGCTCATGTCATTTTTCTGA
Found at i:452646 original size:12 final size:12
Alignment explanation
Indices: 452629--452674 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
452619 TATCATATTC
*
452629 TCATATCACAGG
1 TCATATCACAGA
*
452641 TCATATCACATA
1 TCATATCACAGA
*
452653 TCATATCACATA
1 TCATATCACAGA
*
452665 GCATATCACA
1 TCATATCACA
452675 TGAACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:452660 original size:24 final size:24
Alignment explanation
Indices: 452629--452675 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
452619 TATCATATTC
*
452629 TCATATCACA-GGTCATATCACATA
1 TCATATCACATAG-CATATCACATA
452653 TCATATCACATAGCATATCACAT
1 TCATATCACATAGCATATCACAT
452676 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (24 bp):
TCATATCACATAGCATATCACATA
Found at i:452675 original size:12 final size:12
Alignment explanation
Indices: 452642--452675 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
452632 TATCACAGGT
*
452642 CATATCACATAT
1 CATATCACATAG
452654 CATATCACATAG
1 CATATCACATAG
452666 CATATCACAT
1 CATATCACAT
452676 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (12 bp):
CATATCACATAG
Found at i:456425 original size:20 final size:19
Alignment explanation
Indices: 456384--456436 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
456374 GCTTAGACGT
456384 AGTTTCGAAACATTCATAAA
1 AGTTTCGAAAC-TTCATAAA
* *
456404 AGTTTCGAAACTTCCCTTAA
1 AGTTTCGAAACTT-CATAAA
*
456424 AGTTTCAAAACTT
1 AGTTTCGAAACTT
456437 TGGGTTCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (19 bp):
AGTTTCGAAACTTCATAAA
Found at i:457116 original size:40 final size:40
Alignment explanation
Indices: 457071--457147 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
457061 TCGCGAAATA
*
457071 ATTTAAGAAAACATG-AATTTATAATGTTAGAATGAAAAAG
1 ATTTAAGAAAACA-GAAATTTAGAATGTTAGAATGAAAAAG
* * *
457111 ATTTAAGAGATCAGAAATTTAGAATGTTAGAGTGAAA
1 ATTTAAGAAAACAGAAATTTAGAATGTTAGAATGAAA
457148 TAATTTGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.30
Consensus pattern (40 bp):
ATTTAAGAAAACAGAAATTTAGAATGTTAGAATGAAAAAG
Found at i:460026 original size:29 final size:29
Alignment explanation
Indices: 459983--460038 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
459973 AGTGTGATAG
459983 AGTGAGAGTGCATGTTTAGGGTTGGTTTT
1 AGTGAGAGTGCATGTTTAGGGTTGGTTTT
*
460012 AGTGAGAGTGTATGTTTAGGGTTGGTT
1 AGTGAGAGTGCATGTTTAGGGTTGGTT
460039 CTAGGAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.02, G:0.39, T:0.41
Consensus pattern (29 bp):
AGTGAGAGTGCATGTTTAGGGTTGGTTTT
Found at i:480301 original size:21 final size:21
Alignment explanation
Indices: 480272--480314 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
480262 CTTCAAGAGC
*
480272 AGATACAGAGCCATCATGAGT
1 AGATACAGAGCCATCACGAGT
*
480293 AGATGCAGAGCCATCACGAGT
1 AGATACAGAGCCATCACGAGT
480314 A
1 A
480315 CAACCAAGAA
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:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (21 bp):
AGATACAGAGCCATCACGAGT
Found at i:484840 original size:28 final size:28
Alignment explanation
Indices: 484807--484860 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
484797 GAAATATTAA
484807 AAAAATAATATATTTTAAATACTTAAAT
1 AAAAATAATATATTTTAAATACTTAAAT
* * *
484835 AAAAATAGTTTATTTTAAATAGTTAA
1 AAAAATAATATATTTTAAATACTTAA
484861 TTTGATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (28 bp):
AAAAATAATATATTTTAAATACTTAAAT
Found at i:486731 original size:2 final size:2
Alignment explanation
Indices: 486724--486748 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
486714 TTAGTTTGTT
486724 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
486749 TACGATTTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:487655 original size:2 final size:2
Alignment explanation
Indices: 487648--487674 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
487638 GCTCACCTAT
487648 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
487675 TCAGTGACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:488578 original size:3 final size:3
Alignment explanation
Indices: 488570--488610 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
488560 TAGTTTACTC
* *
488570 TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
488611 ATGTGTCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:488596 original size:21 final size:21
Alignment explanation
Indices: 488570--488612 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
488560 TAGTTTACTC
488570 TTATTATTATTATTATAATAA
1 TTATTATTATTATTATAATAA
*
488591 TTATTATTATTATTATATTAA
1 TTATTATTATTATTATAATAA
488612 T
1 T
488613 GTGTCTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTATTATTATTATAATAA
Found at i:490169 original size:9 final size:10
Alignment explanation
Indices: 490147--490181 Score: 54
Period size: 9 Copynumber: 3.5 Consensus size: 10
490137 TTTATTTTTC
490147 ATATATCTATA
1 ATATAT-TATA
490158 ATATATTA-A
1 ATATATTATA
490167 ATATATTATA
1 ATATATTATA
490177 ATATA
1 ATATA
490182 AATATTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 8 0.35
11 6 0.26
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (10 bp):
ATATATTATA
Found at i:496319 original size:29 final size:29
Alignment explanation
Indices: 496277--496359 Score: 148
Period size: 29 Copynumber: 2.9 Consensus size: 29
496267 GCTTGTGTTA
496277 ATCTCTCCATATATGACACAAAGATGTAG
1 ATCTCTCCATATATGACACAAAGATGTAG
496306 ATCTCTCCATATATGACACAAAGATGTAG
1 ATCTCTCCATATATGACACAAAGATGTAG
* *
496335 ATCTCTCCATATATAACACGAAGAT
1 ATCTCTCCATATATGACACAAAGAT
496360 ATATGGGGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.28
Consensus pattern (29 bp):
ATCTCTCCATATATGACACAAAGATGTAG
Found at i:499614 original size:27 final size:27
Alignment explanation
Indices: 499579--499645 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
499569 TGGTTGTATT
* *
499579 AAAAGAGTATTTTTAATATTAAATAAA
1 AAAATAGTATTTTAAATATTAAATAAA
* ** *
499606 TAAATAGTATAATAAATGTTAAATAAA
1 AAAATAGTATTTTAAATATTAAATAAA
499633 AAAATATGTATTT
1 AAAATA-GTATTT
499646 GACCAAATGG
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.37
Consensus pattern (27 bp):
AAAATAGTATTTTAAATATTAAATAAA
Found at i:509585 original size:9 final size:9
Alignment explanation
Indices: 509571--509596 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
509561 TTAATTAGAA
509571 TCTTAATGT
1 TCTTAATGT
509580 TCTTAATGT
1 TCTTAATGT
509589 TCTTAATG
1 TCTTAATG
509597 AACTGTACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (9 bp):
TCTTAATGT
Found at i:522690 original size:20 final size:19
Alignment explanation
Indices: 522667--522704 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
522657 GTTACAACCA
*
522667 GTCAAATCGGTTCAAAATCG
1 GTCAAACCGG-TCAAAATCG
522687 GTCAAACCGGTCAAAATC
1 GTCAAACCGGTCAAAATC
522705 TGTGTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (19 bp):
GTCAAACCGGTCAAAATCG
Found at i:529587 original size:27 final size:27
Alignment explanation
Indices: 529444--529598 Score: 116
Period size: 28 Copynumber: 5.6 Consensus size: 27
529434 TAACACCTTT
* *
529444 TTTTAAAAAATTTATGAAAATATCATCA
1 TTTTAAAAAAATTA-CAAAATATCATCA
* *
529472 TTTTCAAAATAATTACTAAAATAAC-TCTA
1 TTTT-AAAAAAATTAC-AAAATATCATC-A
* **
529501 TTTTCAAAAAATTACTAAAATATCATTT
1 TTTTAAAAAAATTAC-AAAATATCATCA
* *
529529 TTTTTAAAAAATTATAAAATTATCATTC-
1 TTTTAAAAAAATTACAAAA-TATCA-TCA
* *
529557 TTTTAAAAAAATTACAAAATAGCACCA
1 TTTTAAAAAAATTACAAAATATCATCA
* *
529584 TTTTCAAATAATTAC
1 TTTTAAAAAAATTAC
529599 CACCACTAAT
Statistics
Matches: 102, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.01
27 21 0.21
28 58 0.57
29 22 0.22
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.39
Consensus pattern (27 bp):
TTTTAAAAAAATTACAAAATATCATCA
Found at i:532144 original size:85 final size:79
Alignment explanation
Indices: 532005--532156 Score: 214
Period size: 85 Copynumber: 1.8 Consensus size: 79
531995 TGCATGCAAT
*
532005 TTGAATTCGGTTATGTATATTTTAATTTTTTATTTTAAATTGTCATTTTTATGAACTTATTTGGT
1 TTGAATTCGGTTATGTAGATTTTAATTTTTTATTTTAAATTGTCATTTTTATGAACTTATTTGGT
532070 GACGGTGAACGAAA
66 GACGGTGAACGAAA
* * *
532084 TTGAATTCGGTTAATGTAGATTTTTAATTGCTAATTTGTTTTAGATTTTCATTTTTATGAACTTA
1 TTGAATTCGGTT-ATGTAGA-TTTTAATT--T--TTTATTTTAAATTGTCATTTTTATGAACTTA
532149 TTTGGTGA
60 TTTGGTGA
532157 ACACTCTCCT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
79 12 0.19
80 6 0.10
81 8 0.13
83 1 0.02
85 36 0.57
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.51
Consensus pattern (79 bp):
TTGAATTCGGTTATGTAGATTTTAATTTTTTATTTTAAATTGTCATTTTTATGAACTTATTTGGT
GACGGTGAACGAAA
Found at i:537844 original size:199 final size:204
Alignment explanation
Indices: 537468--537875 Score: 571
Period size: 199 Copynumber: 2.0 Consensus size: 204
537458 AAGATTCAGC
* *
537468 TGATACAGAAGAGAAAATGCGAAGGTGTCACCACCTCGTAGAAAAGCAACAAGAGAAGAAACACC
1 TGATACAGAAGAGAAAATACGAAGGTGTCACCACCTCGTAGAAAA-CAACAAGAGAAGAAAAACC
* *
537533 AGAGAAGATGAGGAATATGGCCAAGAAAGATGGTGGAACTTCTGATTTGTCCACTTCAAACTCTA
65 AGAGAAGATGAGAAATATGGCCAAGAAAGATGGAGGAAC-TCTGATTTGTCCACTTCAAACTCTA
* * *
537598 GGCGAGCGAATGCTGTTAATAATTATGAAGCAAATAACTTTGGATATAGACAATATGATCCTGAG
129 GGCGAGCGAATGCTGTTAATAATTACGAAACAAATAACGTTGGATATAGACAATATGATCCTGAG
*
537663 CCTTCCACTGA
194 CCTCCCACTGA
* * * *
537674 TGATACAGAAGAGAAAGTAACGAAGGTGTCGCCA-CTCGTAG-AAA-AA-TAGAGAAGAAAAACT
1 TGATACAGAAGAGAAAAT-ACGAAGGTGTCACCACCTCGTAGAAAACAACAAGAGAAGAAAAACC
* *
537735 GGAGAAGATGAGAAATATGGCCAAGAAAGATGGAGGAGA-TCTGA-TTGTCC-TTTCAAACTCTA
65 AGAGAAGATGAGAAATATGGCCAAGAAAGATGGAGGA-ACTCTGATTTGTCCACTTCAAACTCTA
* *
537797 GGC-AGGTGAATGCTGTTAATAATTACGAAACAAGTAACGTTGGATATAGACAATATGATCCTGA
129 GGCGA-GCGAATGCTGTTAATAATTACGAAACAAATAACGTTGGATATAGACAATATGATCCTGA
537861 GCCTCCCACTGA
193 GCCTCCCACTGA
537873 TGA
1 TGA
537876 GAAATCAATG
Statistics
Matches: 183, Mismatches: 16, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
198 1 0.01
199 82 0.45
200 6 0.03
201 5 0.03
202 46 0.25
203 3 0.02
205 3 0.02
206 24 0.13
207 13 0.07
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (204 bp):
TGATACAGAAGAGAAAATACGAAGGTGTCACCACCTCGTAGAAAACAACAAGAGAAGAAAAACCA
GAGAAGATGAGAAATATGGCCAAGAAAGATGGAGGAACTCTGATTTGTCCACTTCAAACTCTAGG
CGAGCGAATGCTGTTAATAATTACGAAACAAATAACGTTGGATATAGACAATATGATCCTGAGCC
TCCCACTGA
Found at i:540380 original size:14 final size:13
Alignment explanation
Indices: 540357--540387 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
540347 GTATGTGTGG
540357 TATAACACATATA
1 TATAACACATATA
540370 TATACACACATATA
1 TATA-ACACATATA
540384 TATA
1 TATA
540388 TTACATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAACACATATA
Found at i:543714 original size:23 final size:23
Alignment explanation
Indices: 543684--543756 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
543674 AAAAAATGAA
543684 AAACGTGCCACAAATACAGAGAT
1 AAACGTGCCACAAATACAGAGAT
* *
543707 AAACGTGCCACAAAGATAGAGAT
1 AAACGTGCCACAAATACAGAGAT
* * *
543730 AAATGTGCAACACATACAGAGAT
1 AAACGTGCCACAAATACAGAGAT
543753 AAAC
1 AAAC
543757 ATGCAACACT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.49, C:0.19, G:0.18, T:0.14
Consensus pattern (23 bp):
AAACGTGCCACAAATACAGAGAT
Found at i:543761 original size:23 final size:23
Alignment explanation
Indices: 543684--543765 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
543674 AAAAAATGAA
* *
543684 AAACGTGCCACAAATACAGAGAT
1 AAACGTGCAACACATACAGAGAT
* * * *
543707 AAACGTGCCACAAAGATAGAGAT
1 AAACGTGCAACACATACAGAGAT
*
543730 AAATGTGCAACACATACAGAGAT
1 AAACGTGCAACACATACAGAGAT
*
543753 AAACATGCAACAC
1 AAACGTGCAACAC
543766 TGACAGAATT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (23 bp):
AAACGTGCAACACATACAGAGAT
Found at i:553695 original size:73 final size:74
Alignment explanation
Indices: 553576--553724 Score: 291
Period size: 73 Copynumber: 2.0 Consensus size: 74
553566 CTTATTTCTG
553576 AATTTTCTTTTAAATAGTACCTCTTCCGATTGTAACAACAGTGAAGTATCCCTAATTTCTGCAA-
1 AATTTTCTTTTAAATAGTACCTCTTCCGATTGTAACAACAGTGAAGTATCCCTAATTTCTGCAAT
553640 TAAATGTTA
66 TAAATGTTA
553649 AATTTTCTTTTAAATAGTACCTCTTCCGATTGTAACAACAGTGAAGTATCCCTAATTTCTGCAAT
1 AATTTTCTTTTAAATAGTACCTCTTCCGATTGTAACAACAGTGAAGTATCCCTAATTTCTGCAAT
553714 TAAATGTTA
66 TAAATGTTA
553723 AA
1 AA
553725 ACCGGCAATA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 64 0.85
74 11 0.15
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (74 bp):
AATTTTCTTTTAAATAGTACCTCTTCCGATTGTAACAACAGTGAAGTATCCCTAATTTCTGCAAT
TAAATGTTA
Found at i:554376 original size:64 final size:64
Alignment explanation
Indices: 554165--554460 Score: 296
Period size: 64 Copynumber: 4.6 Consensus size: 64
554155 CCAATAAAAC
* * * * *
554165 AGTCCTAAGATCGATGTAAATGGTTCCATCTC-TTTTTTCTGGAATTCTGATAAAATGAGATTGA
1 AGTCCTAAGATCG-TGTAAATGATTCCATCTCGTTTGTTATGGAATTCTAATAAAATGAGATAGA
* * * * *
554229 AGTCCTGAA-ATTGGTGTAAATGATCCCATCTCATTTGTTATGGAATTCTGATAAAATGAGATTG
1 AGTCCT-AAGA-TCGTGTAAATGATTCCATCTCGTTTGTTATGGAATTCTAATAAAATGAGATAG
554293 A
64 A
554294 AGTCCTAAGATCGATGTAAATGATTCCATCTCGTTTGTTATGG-ATTCTAATAAAATGAGATAGA
1 AGTCCTAAGATCG-TGTAAATGATTCCATCTCGTTTGTTATGGAATTCTAATAAAATGAGATAGA
* * * * * * * *
554358 AGTCCTAAAATCAGTGTAAACGA-TCCTATCTCG-TTGTTCTAGAACTCCAATAGAATGACATAG
1 AGTCCTAAGATC-GTGTAAATGATTCC-ATCTCGTTTGTTATGGAATTCTAATAAAATGAGATAG
554421 A
64 A
* * * *
554422 AGTCCTAAGTTCGGTGTAAATGCTCCCATCTTGTTTGTT
1 AGTCCTAAGATC-GTGTAAATGATTCCATCTCGTTTGTT
554461 CTAATAGACT
Statistics
Matches: 197, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
63 10 0.05
64 111 0.56
65 76 0.39
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (64 bp):
AGTCCTAAGATCGTGTAAATGATTCCATCTCGTTTGTTATGGAATTCTAATAAAATGAGATAGA
Found at i:563037 original size:12 final size:13
Alignment explanation
Indices: 563011--563036 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
563001 GACAATGTCA
563011 TGTCATGTTTTTT
1 TGTCATGTTTTTT
563024 TGTCATGTTTTTT
1 TGTCATGTTTTTT
563037 GATAGAAAGT
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:0.08, G:0.15, T:0.69
Consensus pattern (13 bp):
TGTCATGTTTTTT
Found at i:574900 original size:19 final size:20
Alignment explanation
Indices: 574876--574923 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
574866 TGACTATTCA
*
574876 GTATCG-TACTCGACTGTTG
1 GTATCGATACCCGACTGTTG
**
574895 GTATCGATACCCTCCTGTTG
1 GTATCGATACCCGACTGTTG
574915 GTATCGATA
1 GTATCGATA
574924 TCCCCTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (20 bp):
GTATCGATACCCGACTGTTG
Found at i:583761 original size:30 final size:30
Alignment explanation
Indices: 583648--583761 Score: 90
Period size: 30 Copynumber: 3.8 Consensus size: 30
583638 GACCACGCGG
583648 TGCTGCAGCTGAT-CT-TACTGGACCACT-CCC
1 TGCTGCAGCTGATCCTGT-C-GGACCA-TGCCC
* * * * * *
583678 TGTTGTAGCTGATCCTGCCGAACCACGCCT
1 TGCTGCAGCTGATCCTGTCGGACCATGCCC
* *
583708 TGCTGCAACTGATCCTATCGGACCATGCCC
1 TGCTGCAGCTGATCCTGTCGGACCATGCCC
* *
583738 TGCTGCAGCTGATTCTGTTGGACC
1 TGCTGCAGCTGATCCTGTCGGACC
583762 TCAACCTACT
Statistics
Matches: 63, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
30 60 0.95
31 3 0.05
ACGTcount: A:0.17, C:0.33, G:0.23, T:0.27
Consensus pattern (30 bp):
TGCTGCAGCTGATCCTGTCGGACCATGCCC
Found at i:584955 original size:23 final size:23
Alignment explanation
Indices: 584902--584955 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
584892 ACTACACTCA
*
584902 ATTTACTTTTGCCAAGACATTTCC
1 ATTTA-TTTTGCCAAGACATCTCC
* *
584926 ATCTATTTTGCCACA-ACATCTCT
1 ATTTATTTTGCCA-AGACATCTCC
584949 ATTTATT
1 ATTTATT
584956 GCCACATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (23 bp):
ATTTATTTTGCCAAGACATCTCC
Found at i:594085 original size:14 final size:14
Alignment explanation
Indices: 594066--594094 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
594056 ATGTAAAAAC
594066 TTAGAAACTTTTGA
1 TTAGAAACTTTTGA
594080 TTAGAAACTTTTGA
1 TTAGAAACTTTTGA
594094 T
1 T
594095 CATAACTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (14 bp):
TTAGAAACTTTTGA
Found at i:599542 original size:22 final size:22
Alignment explanation
Indices: 599514--599557 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
599504 GTCATAACTC
*
599514 TATTTTGATTTATACTTTATGG
1 TATTTTGATTTATACTCTATGG
599536 TATTTTGATTTATACTCTATGG
1 TATTTTGATTTATACTCTATGG
599558 ATGCATTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.07, G:0.14, T:0.57
Consensus pattern (22 bp):
TATTTTGATTTATACTCTATGG
Found at i:601497 original size:3 final size:3
Alignment explanation
Indices: 601474--601543 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
601464 TATCTATATA
* * *
601474 TAT TAA TAT TATT TAT T-T TAT TAT TAT CAT TAA TAT TAT TAT TA-
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
601518 TGT TAA TAT TAA TAT TAAT TAT TAT T
1 TAT TAT TAT TAT TAT T-AT TAT TAT T
601544 TTTTTGCAGG
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
2 3 0.06
3 42 0.82
4 6 0.12
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:601508 original size:27 final size:26
Alignment explanation
Indices: 601460--601548 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 26
601450 TTTCATCCGA
601460 ATTTTATCTATATATATTAATATTATTT
1 ATTTTAT-TAT-TATATTAATATTATTT
601488 ATTTTATTATTATCATTAATATTATTATT
1 ATTTTATTATTAT-ATTAATATTA-T-TT
* *
601517 ATGTTAATATTAATATTAATTATTATTT
1 ATTTTATTATT-ATATTAA-TATTATTT
601545 -TTTT
1 ATTTT
601549 GCAGGCCAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
26 3 0.06
27 16 0.30
28 10 0.19
29 17 0.32
30 7 0.13
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (26 bp):
ATTTTATTATTATATTAATATTATTT
Found at i:601510 original size:15 final size:14
Alignment explanation
Indices: 601472--601543 Score: 62
Period size: 12 Copynumber: 5.1 Consensus size: 14
601462 TTTATCTATA
601472 TATATTAATATTAT
1 TATATTAATATTAT
*
601486 T-TATT-TTATTAT
1 TATATTAATATTAT
601498 TATCATTAATATTAT
1 TAT-ATTAATATTAT
601513 TATTATGTTAATATTA-
1 TA-TA--TTAATATTAT
601529 -ATATTAATTATTAT
1 TATATTAA-TATTAT
601543 T
1 T
601544 TTTTTGCAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
12 11 0.23
13 10 0.21
14 6 0.13
15 10 0.21
16 1 0.02
17 9 0.19
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (14 bp):
TATATTAATATTAT
Found at i:602576 original size:7 final size:7
Alignment explanation
Indices: 602566--602598 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
602556 ATATACCGTA
602566 TATATAT
1 TATATAT
602573 TATATAT
1 TATATAT
602580 TATATAT
1 TATATAT
602587 TATATAT
1 TATATAT
602594 TATAT
1 TATAT
602599 TTGTGATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATAT
Found at i:602671 original size:16 final size:16
Alignment explanation
Indices: 602631--602672 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
602621 TATTTATATA
*
602631 TATATTT-TATGTATG
1 TATATTTATGTGTATG
* *
602646 TATGTCTATGTGTATG
1 TATATTTATGTGTATG
602662 TATATTTATGT
1 TATATTTATGT
602673 ACATATATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.57
Consensus pattern (16 bp):
TATATTTATGTGTATG
Found at i:607997 original size:21 final size:20
Alignment explanation
Indices: 607973--608018 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
607963 CATATTACTA
* *
607973 TTTATGTATGGTATGTACATT
1 TTTATGCATGGTATGCA-ATT
*
607994 TTTATGCATGTTATGCAATT
1 TTTATGCATGGTATGCAATT
608014 TTTAT
1 TTTAT
608019 TTTATTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (20 bp):
TTTATGCATGGTATGCAATT
Found at i:619298 original size:9 final size:9
Alignment explanation
Indices: 619258--619302 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
619248 AAAATGAGTG
619258 AAAATGAAA
1 AAAATGAAA
619267 AAAAT-AAA
1 AAAATGAAA
619275 AAAA--AAA
1 AAAATGAAA
*
619282 AATGATGAAA
1 AA-AATGAAA
619292 AAAATGAAA
1 AAAATGAAA
619301 AA
1 AA
619303 TGAGGGTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 5 0.16
8 8 0.26
9 13 0.42
10 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (9 bp):
AAAATGAAA
Found at i:620448 original size:53 final size:55
Alignment explanation
Indices: 620294--620507 Score: 330
Period size: 54 Copynumber: 3.9 Consensus size: 55
620284 AGATTTCCCA
*
620294 ACGATTATTGAAGATTGTTCGAGTC-CTATACTCTCTGAAGAAATA-GGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTC-ATACTCTCTGAAGAAATAGGGAGCAGAC
620348 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
620403 ATGATTGTTGAAGA-TGTTCGA-TCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
620456 ACGATTGTTGAAGATTGTTCGAGTTTCATACTCCCT-AGAGAAAGAGGGAGCA
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGA-AGAAATAGGGAGCA
620508 AACCCGTTTG
Statistics
Matches: 149, Mismatches: 6, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
53 45 0.30
54 57 0.38
55 47 0.32
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:620524 original size:108 final size:108
Alignment explanation
Indices: 620303--620552 Score: 317
Period size: 108 Copynumber: 2.3 Consensus size: 108
620293 AACGATTATT
620303 GAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGAGCAGACACGATTGTTGAAGATTGTTC
1 GAAGA-TGTTCGAGTCCTATACTCTCTGAAGAAATAGGAGCAGACACGATTGTTGAAGATTGTTC
* * * * **
620368 GAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTT
65 GAGTCTCATACTCCCTGAAGAAAGAGGGAGCAAACACGATTGAA
620412 GAAGATGTTCGA-T-CTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
1 GAAGATGTTCGAGTCCT-ATACTCTCTGAAGAAATA-GGAGCAGACACGATTGTTGAAGATTGTT
* * *
620475 CGAGTTTCATACTCCCT-AGAGAAAGAGGGAGCAAACCCGTTTGAA
64 CGAGTCTCATACTCCCTGA-AGAAAGAGGGAGCAAACACGATTGAA
* * * * *
620520 GAAGATATTCGAGTTCTATTCTCCCTGAGGAAA
1 GAAGATGTTCGAGTCCTATACTCTCTGAAGAAA
620553 GAGGGAGTGA
Statistics
Matches: 123, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
106 2 0.02
107 20 0.16
108 80 0.65
109 19 0.15
110 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (108 bp):
GAAGATGTTCGAGTCCTATACTCTCTGAAGAAATAGGAGCAGACACGATTGTTGAAGATTGTTCG
AGTCTCATACTCCCTGAAGAAAGAGGGAGCAAACACGATTGAA
Found at i:620597 original size:105 final size:106
Alignment explanation
Indices: 620472--620675 Score: 259
Period size: 105 Copynumber: 1.9 Consensus size: 106
620462 GTTGAAGATT
* * * *
620472 GTTCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAGAAGA-TATTCGAGTTC
1 GTTCGAGTTCCACACTCCCTAGAGAAAGAGGGAACAAACCCGCTTGAAGAAGATTATTCGAGTTC
* * * *
620536 TATTCTCCCTGAGGA-AAGAGGGAGTGAACCCGTTTAAAGAC
66 CATACTCCCTGA-AACAAGAGGGAGCGAACCCGTTTAAAGAC
* ** * *
620577 GTTCGAGTTCCACACTCCCTAGATAAAGAGGGAATGAACCCGCTTGCAGAAGATTGTTCGAGTTC
1 GTTCGAGTTCCACACTCCCTAGAGAAAGAGGGAACAAACCCGCTTGAAGAAGATTATTCGAGTTC
*
620642 CATACTCCCTGAAACAATAGGGAGCGAACCCGTT
66 CATACTCCCTGAAACAAGAGGGAGCGAACCCGTT
620676 AGCAGAAGAT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
105 46 0.55
106 37 0.45
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (106 bp):
GTTCGAGTTCCACACTCCCTAGAGAAAGAGGGAACAAACCCGCTTGAAGAAGATTATTCGAGTTC
CATACTCCCTGAAACAAGAGGGAGCGAACCCGTTTAAAGAC
Found at i:620709 original size:55 final size:53
Alignment explanation
Indices: 620303--620781 Score: 259
Period size: 55 Copynumber: 8.9 Consensus size: 53
620293 AACGATTATT
* * * * **
620303 GAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATA-GGAGC-AGACACGATTGTT
1 GAAGATTGTTCGAGTTCTATACTCCCTGAA-AAAGAGGGAGCGA-ACCCG-TTGCA
* * ** **
620357 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGC-AGACATGATTGTT
1 GAAGATTGTTCGAGTTCT-ATACTCCCTGAA-AAAGAGGGAGCGA-ACCCG-TTGCA
* * * **
620412 GAAGA-TGTTCGA--TCTCATACTCTCTGAAGAAATAGGGAGC-AGACACGATTGTT
1 GAAGATTGTTCGAGTTCT-ATACTCCCTGAA-AAAGAGGGAGCGA-ACCCG-TTGCA
* * *
620465 GAAGATTGTTCGAGTT-TCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAA
1 GAAGATTGTTCGAGTTCT-ATACTCCCT-GAAAAAGAGGGAGCGAACCCG-TTGCA
* * * * *
620520 GAAGA-TATTCGAGTTCTATTCTCCCTGAGGAAAGAGGGAGTGAACCCGTT-TA
1 GAAGATTGTTCGAGTTCTATACTCCCTGA-AAAAGAGGGAGCGAACCCGTTGCA
* * * * **
620572 -AAGA-CGTTCGAGTTCCACACTCCCTAGATAAAGAGGGAATGAACCCGCTTGCA
1 GAAGATTGTTCGAGTTCTATACTCCCT-GAAAAAGAGGGAGCGAACCCG-TTGCA
* *
620625 GAAGATTGTTCGAGTTCCATACTCCCTGAAACAATAGGGAGCGAACCCGTTAGCA
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAA-AAGAGGGAGCGAACCCGTT-GCA
* * * **
620680 GAAGATTATTCGAGTTCTATACTCCCTGAAACAATAGGGAGTGAACCCGTCCCCA
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAA-AAGAGGGAGCGAACCCGT-TGCA
* * * ** *
620735 GAATATTCTTCAAGTTCTATGTTCCCTG--AACGTAGGGAGCGAACCCG
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAAAG-AGGGAGCGAACCCG
620782 ATTTTGAAGA
Statistics
Matches: 365, Mismatches: 42, Indels: 37
0.82 0.09 0.08
Matches are distributed among these distances:
51 37 0.10
52 6 0.02
53 66 0.18
54 89 0.24
55 163 0.45
56 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (53 bp):
GAAGATTGTTCGAGTTCTATACTCCCTGAAAAAGAGGGAGCGAACCCGTTGCA
Found at i:622747 original size:25 final size:24
Alignment explanation
Indices: 622710--622757 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
622700 ATTACTATTT
* *
622710 TATGTATGGTATGTACATTTTTATG
1 TATGCATGGTATGCA-ATTTTTATG
*
622735 TATGCATGTTATGCAATTTTTAT
1 TATGCATGGTATGCAATTTTTAT
622758 TTTTTTCAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.52
Consensus pattern (24 bp):
TATGCATGGTATGCAATTTTTATG
Found at i:625258 original size:16 final size:17
Alignment explanation
Indices: 625237--625279 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
625227 ATTATTTGTT
625237 TATTATCATAATATT-A
1 TATTATCATAATATTAA
**
625253 TATTATGTTAATATTAA
1 TATTATCATAATATTAA
625270 TATTAATCAT
1 TATT-ATCAT
625280 TATTTTTTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 13 0.62
17 5 0.24
18 3 0.14
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (17 bp):
TATTATCATAATATTAA
Found at i:626292 original size:7 final size:7
Alignment explanation
Indices: 626271--626309 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
626261 ATATATCCCG
626271 TATATA-
1 TATATAT
*
626277 TAGATAT
1 TATATAT
626284 TATATAT
1 TATATAT
626291 TATATAT
1 TATATAT
626298 TATATAT
1 TATATAT
626305 TATAT
1 TATAT
626310 TTGTGATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (7 bp):
TATATAT
Found at i:626901 original size:19 final size:18
Alignment explanation
Indices: 626875--626916 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
626865 AATTCAAATT
626875 AAAA-ATCAAATTTCATAA
1 AAAATATCAAATTTC-TAA
* *
626893 AAAATATCAATTTTCTCA
1 AAAATATCAAATTTCTAA
626911 AAAATA
1 AAAATA
626917 AAATCATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATCAAATTTCTAA
Found at i:628529 original size:20 final size:19
Alignment explanation
Indices: 628504--628550 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
628494 ATCGTTAGAC
628504 AAAATATTAATCCAAA-AAAT
1 AAAATATTAAT--AAATAAAT
*
628524 AAAATAATAATAAATAAAT
1 AAAATATTAATAAATAAAT
628543 -AAATATTA
1 AAAATATTA
628551 TTATTGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 10 0.42
19 4 0.17
20 10 0.42
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATATTAATAAATAAAT
Found at i:634164 original size:5 final size:5
Alignment explanation
Indices: 634154--634183 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
634144 GATTCACTGT
634154 CCCAC CCCAC CCCAC CCCAC CCCAC CCCAC
1 CCCAC CCCAC CCCAC CCCAC CCCAC CCCAC
634184 AGCACCCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.80, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCAC
Found at i:634189 original size:15 final size:15
Alignment explanation
Indices: 634155--634190 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
634145 ATTCACTGTC
*
634155 CCACCCCACCCCACC
1 CCACCCCACCCCACA
634170 CCACCCCACCCCACA
1 CCACCCCACCCCACA
*
634185 GCACCC
1 CCACCC
634191 AAGGAGCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.75, G:0.03, T:0.00
Consensus pattern (15 bp):
CCACCCCACCCCACA
Found at i:635252 original size:30 final size:30
Alignment explanation
Indices: 635218--635286 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
635208 ATGTGGTAGA
* *
635218 TCCATGTGGACTAAATGCTAACATGGTATG
1 TCCATGTGGACTAAATACTAACATGGCATG
** *
635248 TCCATGCAGACTAAATACTGACATGGCATG
1 TCCATGTGGACTAAATACTAACATGGCATG
*
635278 TCCACGTGG
1 TCCATGTGG
635287 TATGTCCATT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (30 bp):
TCCATGTGGACTAAATACTAACATGGCATG
Found at i:639238 original size:31 final size:31
Alignment explanation
Indices: 639202--639261 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
639192 AACTTATAAG
* *
639202 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
639233 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
639262 CATACAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:639780 original size:20 final size:20
Alignment explanation
Indices: 639757--639894 Score: 161
Period size: 20 Copynumber: 6.8 Consensus size: 20
639747 ATTCGCGTTG
639757 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
639777 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* **
639798 AAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
639818 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
639838 CATTTCGCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGAT--TTTC
*
639860 CA-GTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
*
639879 CGTTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
639895 AGTCTACAGT
Statistics
Matches: 97, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
19 3 0.03
20 63 0.65
21 27 0.28
22 4 0.04
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.39
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:639824 original size:61 final size:61
Alignment explanation
Indices: 639757--639894 Score: 233
Period size: 61 Copynumber: 2.3 Consensus size: 61
639747 ATTCGCGTTG
639757 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-AAAATCGCGTTGCGATTTTC
* *
639818 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTTTC
*
639879 CGTTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
639895 AGTCTACAGT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
61 72 0.99
62 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.24, T:0.39
Consensus pattern (61 bp):
CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTTTC
Found at i:639867 original size:41 final size:42
Alignment explanation
Indices: 639825--639963 Score: 203
Period size: 41 Copynumber: 3.4 Consensus size: 42
639815 TTCCATTTCG
639825 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCG-
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGT
* *
639866 CGTTGCGATTTTCCGTTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGT
* *
639908 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTCGT
*
639949 CGTTGTGATTTTCCA
1 CGTTGCGATTTTCCA
639964 AATTCGTTGT
Statistics
Matches: 91, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.01
41 74 0.81
42 14 0.15
43 2 0.02
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (42 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGT
Found at i:639868 original size:21 final size:21
Alignment explanation
Indices: 639842--639916 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
639832 ATTTTCCATT
639842 TCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATAGTCTACAG
* *
639863 TCGCGTTGCGAT--T-TTCCG
1 TCGCGTTGCGATAGTCTACAG
639881 TTTCGCGTTGCGATAGTCTACAG
1 --TCGCGTTGCGATAGTCTACAG
*
639904 TTGTCGTTGCGAT
1 TCG-CGTTGCGAT
639917 TTTCCAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
18 3 0.07
19 1 0.02
20 12 0.28
21 14 0.33
22 10 0.23
23 3 0.07
ACGTcount: A:0.13, C:0.23, G:0.28, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCTACAG
Found at i:639964 original size:41 final size:41
Alignment explanation
Indices: 639825--639979 Score: 199
Period size: 41 Copynumber: 3.8 Consensus size: 41
639815 TTCCATTTCG
* *
639825 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTCG-
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
**
639866 CGTTGCGATTTTCC-GTTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
639908 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
* *
639949 CGTTGTGATTTTCCAAATTCGTTGTGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
639980 TAAAAAAAGA
Statistics
Matches: 106, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
41 90 0.85
42 14 0.13
43 2 0.02
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:639976 original size:19 final size:19
Alignment explanation
Indices: 639907--639972 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
639897 TCTACAGTTG
639907 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
639926 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
*
639947 GTCGTTGTGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
639967 TCGTTG
1 TCGTTG
639973 TGATAGTTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 16 0.46
20 5 0.14
21 5 0.14
22 9 0.26
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:640066 original size:6 final size:6
Alignment explanation
Indices: 640055--640130 Score: 99
Period size: 6 Copynumber: 13.5 Consensus size: 6
640045 GACACGTATT
* *
640055 ACCACG ACCACG ACCAGG ACCACG ACCACG AACACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
640103 ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
640131 CGAGACGAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
5 25 0.38
6 41 0.62
ACGTcount: A:0.30, C:0.51, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:640111 original size:5 final size:5
Alignment explanation
Indices: 640089--640133 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
640079 ACCACGAACA
640089 CGACC ACGACC ACGACC CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC CGA
640134 GACGAGACGA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 28 0.72
6 11 0.28
ACGTcount: A:0.24, C:0.56, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:640656 original size:6 final size:6
Alignment explanation
Indices: 640645--640679 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
640635 GTCTCGGGTG
* *
640645 GTGGTC GTGGTC GTAGCC GTGGTC GTGGTC GTGGT
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGT
640680 AATACGTGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.17, G:0.49, T:0.31
Consensus pattern (6 bp):
GTGGTC
Found at i:640825 original size:41 final size:41
Alignment explanation
Indices: 640775--641076 Score: 502
Period size: 41 Copynumber: 7.4 Consensus size: 41
640765 ACAACTGTAG
640775 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
640816 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
640856 GACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
640898 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
640938 GACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
640980 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
641020 GACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
641062 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
641077 TTTTCAACTA
Statistics
Matches: 243, Mismatches: 12, Indels: 12
0.91 0.04 0.04
Matches are distributed among these distances:
40 3 0.01
41 237 0.98
42 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:640893 original size:82 final size:82
Alignment explanation
Indices: 640755--641076 Score: 626
Period size: 82 Copynumber: 3.9 Consensus size: 82
640745 TCTTTTTTTT
*
640755 AATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTA
1 AATCGCAACG-CGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTA
640820 TCGCAACGCGAAATGGAA
65 TCGCAACGCGAAATGGAA
640838 AATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
1 AATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
640903 CGCAACGCGAAATGGAA
66 CGCAACGCGAAATGGAA
640920 AATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
1 AATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
640985 CGCAACGCGAAATGGAA
66 CGCAACGCGAAATGGAA
641002 AATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
1 AATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
641067 CGCAACGCGA
66 CGCAACGCGA
641077 TTTTCAACTA
Statistics
Matches: 238, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
82 228 0.96
83 10 0.04
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (82 bp):
AATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
CGCAACGCGAAATGGAA
Found at i:641110 original size:41 final size:41
Alignment explanation
Indices: 641065--641183 Score: 202
Period size: 41 Copynumber: 2.9 Consensus size: 41
641055 ATTTTCAACT
641065 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
* *
641106 ATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
* *
641147 AACGCAACGCGATTTTCAACTATCGCAATGCGAAATG
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
641184 CAACGTGAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:641110 original size:123 final size:122
Alignment explanation
Indices: 640755--641117 Score: 489
Period size: 123 Copynumber: 2.9 Consensus size: 122
640745 TCTTTTTTTT
*
640755 AATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTA
1 AATCGCAACG-CGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTA
* *
640820 TCGCAACGCGAAATGGAAAATCGCAACGCG-ACTGTAGACTATCGCAACGCGAAATGGAA
65 TCGCAACGCGAAATGGAAAATCGCAACGCGAAATG--GAATATCGCAACGCGAAATGGAA
* * * *
640879 AATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-AGACT
1 AATCGCAACGCGACTGT-AGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA-ACT
** **
640942 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAA
64 ATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGGAA-TATCGCAACGCGAAATGGAA
641002 AATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
1 AATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
** ** * *
641067 CGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
66 CGCAACGCGAAATGGAA-AATCGCAACGCGAAATGGAATATCGCAACGCGA
641118 TCTCCAACTA
Statistics
Matches: 208, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
122 3 0.01
123 177 0.85
124 28 0.13
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (122 bp):
AATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
CGCAACGCGAAATGGAAAATCGCAACGCGAAATGGAATATCGCAACGCGAAATGGAA
Found at i:641153 original size:123 final size:121
Alignment explanation
Indices: 640777--641158 Score: 419
Period size: 123 Copynumber: 3.1 Consensus size: 121
640767 AACTGTAGAC
640777 TATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
1 TATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
* * ** **
640842 GCAACGCG-ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAA
66 GCAACGCGAAATG--GAATATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGGAA
* *
640899 CTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAATGGAAAA
1 -TATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAATGGAAAA
** ** * *
640963 TCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCG-ACTGTAGAC
64 TCGCAACGCGAAATGGAA-TATCGCAACGCGAAATGGAAAATCGCAACGCGAAATG--GAA
** ** *
641023 TATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTAT
1 TATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAA-AAT
* ** ** *
641088 CGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAA
65 CGCAACGCGAAATGGAATATCGCAACGCGAAATGGAA-AATCGCAACGCGAAATGGAA
* *
641146 AAACGCAACGCGA
1 TATCGCAACGCGA
641159 TTTTCAACTA
Statistics
Matches: 217, Mismatches: 33, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
122 3 0.01
123 182 0.84
124 29 0.13
125 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (121 bp):
TATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
GCAACGCGAAATGGAATATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGGAA
Found at i:641474 original size:20 final size:19
Alignment explanation
Indices: 641427--641474 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
641417 AACTTAAATC
*
641427 AAATAATTAAAATAAATATA
1 AAATAATT-TAATAAATATA
641447 AAAT--TTTAATAATATATA
1 AAATAATTTAATAA-ATATA
641465 AAATAATTTA
1 AAATAATTTA
641475 TATATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 5 0.21
18 11 0.46
20 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAATTTAATAAATATA
Found at i:641507 original size:18 final size:19
Alignment explanation
Indices: 641458--641507 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
641448 AATTTTAATA
*
641458 ATATAT-AAAATAATTTAT
1 ATATATAAAAATAATCTAT
*
641476 ATATAAAATTAAAT-ATCTAT
1 ATATATAA--AAATAATCTAT
641496 ATATATAAAAAT
1 ATATATAAAAAT
641508 TAATATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 9 0.35
19 1 0.04
20 12 0.46
21 4 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATATAAAAATAATCTAT
Found at i:641512 original size:22 final size:23
Alignment explanation
Indices: 641473--641537 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
641463 TAAAATAATT
641473 TATATAT-AAAATTAAATATCT-A
1 TATATATAAAAATT-AATATCTAA
*
641495 TATATATAAAAATTAATATTTAA
1 TATATATAAAAATTAATATCTAA
* *
641518 TTTATTTAAAAAATTAATAT
1 TATATAT-AAAAATTAATAT
641538 AAAAATATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 13 0.35
23 12 0.32
24 12 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TATATATAAAAATTAATATCTAA
Found at i:641534 original size:24 final size:24
Alignment explanation
Indices: 641468--641537 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
641458 ATATATAAAA
*
641468 TAATTTATATATAAAATTAAATATC
1 TAATTTATATAAAAAATT-AATATC
* *
641493 T-ATATATAT-AAAAATTAATATT
1 TAATTTATATAAAAAATTAATATC
*
641515 TAATTTATTTAAAAAATTAATAT
1 TAATTTATATAAAAAATTAATAT
641538 AAAAATATCT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 6 0.16
23 12 0.32
24 19 0.50
25 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATTTATATAAAAAATTAATATC
Found at i:641543 original size:36 final size:36
Alignment explanation
Indices: 641498--641573 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
641488 ATATCTATAT
* *
641498 ATATAAAAATTAATATTTAAT-TTAT-TTAAAAAATTA
1 ATATAAAAA-T-ATATATAATATAATATTAAAAAATTA
*
641534 ATATAAAAATATCTATAATATAATATTAAAAAATTA
1 ATATAAAAATATATATAATATAATATTAAAAAATTA
641570 ATAT
1 ATAT
641574 TTAATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 7 0.20
35 4 0.11
36 24 0.69
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (36 bp):
ATATAAAAATATATATAATATAATATTAAAAAATTA
Found at i:641571 original size:14 final size:14
Alignment explanation
Indices: 641554--641601 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
641544 ATCTATAATA
641554 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
641568 TAATATT---TAAT
1 TAATATTAAAAAAT
641579 T--TATTAAAAAAT
1 TAATATTAAAAAAT
641591 TAATATTAAAA
1 TAATATTAAAA
641602 TCAAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
9 4 0.15
11 4 0.15
12 4 0.15
14 15 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:641573 original size:19 final size:20
Alignment explanation
Indices: 641549--641596 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
641539 AAAATATCTA
641549 TAATATAA-TATTAAAAAAT
1 TAATATAATTATTAAAAAAT
641568 TAATATTTAATTTATTAAAAAAT
1 TAATA--TAA-TTATTAAAAAAT
641591 TAATAT
1 TAATAT
641597 TAAAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 5 0.20
21 4 0.16
23 16 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATAATTATTAAAAAAT
Found at i:641610 original size:16 final size:16
Alignment explanation
Indices: 641591--641624 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
641581 ATTAAAAAAT
*
641591 TAATATTAAAATCAAA
1 TAATATAAAAATCAAA
*
641607 TAATATAAAAATTAAA
1 TAATATAAAAATCAAA
641623 TA
1 TA
641625 TAAAACTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATATAAAAATCAAA
Done.