Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004048.1 Hibiscus syriacus cultivar Beakdansim tig00008843_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: 625444
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:487483 original size:57 final size:56
Alignment explanation
Indices: 487383--487542 Score: 239
Period size: 57 Copynumber: 2.8 Consensus size: 56
487373 TGCAACACAG
* * * *
487383 TTTCTAAATTCGCAACGCTGATTACTGATATAGATAAAAAGTACTATCGCAATGTGAT
1 TTTC-AAATTCGCAACGCTAATTACCGATATAG-TAAACAGTACTATCGCAATGCGAT
487441 TTTCAAATTCGCAACGCTAATTACCGATATATGTAAACAGTACTATCGCAATGCGAT
1 TTTCAAATTCGCAACGCTAATTACCGATATA-GTAAACAGTACTATCGCAATGCGAT
*
487498 TTTCAAATTCGCAACGTTAATTACCGATATAGGTAAACAGTACTA
1 TTTCAAATTCGCAACGCTAATTACCGATATA-GTAAACAGTACTA
487543 AAATTCGCGT
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
57 90 0.95
58 5 0.05
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (56 bp):
TTTCAAATTCGCAACGCTAATTACCGATATAGTAAACAGTACTATCGCAATGCGAT
Found at i:487568 original size:20 final size:20
Alignment explanation
Indices: 487543--487621 Score: 140
Period size: 20 Copynumber: 3.9 Consensus size: 20
487533 AACAGTACTA
*
487543 AAATTCGCGTTACGATTTAC
1 AAATTCGCGTTGCGATTTAC
487563 AAATTCGCGTTGCGATTTAC
1 AAATTCGCGTTGCGATTTAC
487583 AAATTCGCGTTGCGATTTAC
1 AAATTCGCGTTGCGATTTAC
487603 AAATTCGCGTTGCGTATTT
1 AAATTCGCGTTGCG-ATTT
487622 GGAAACTGTG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
20 53 0.93
21 4 0.07
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (20 bp):
AAATTCGCGTTGCGATTTAC
Found at i:495706 original size:18 final size:20
Alignment explanation
Indices: 495680--495721 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 20
495670 ATATGAGAAT
*
495680 AATTGCATG-TTTT-TATTA
1 AATTACATGATTTTCTATTA
495698 AATTACATGCATTTTCTATTA
1 AATTACATG-ATTTTCTATTA
495719 AAT
1 AAT
495722 GAGATTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
AATTACATGATTTTCTATTA
Found at i:496646 original size:36 final size:36
Alignment explanation
Indices: 496606--496674 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
496596 TTGTTTTATT
496606 CGACTCATTACTCGTTAAACTCATTAAAATTTTGTC
1 CGACTCATTACTCGTTAAACTCATTAAAATTTTGTC
* ** *
496642 CGACTCGTTGTTTGTTAAACTCATTAAAATTTT
1 CGACTCATTACTCGTTAAACTCATTAAAATTTT
496675 ACTCGATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (36 bp):
CGACTCATTACTCGTTAAACTCATTAAAATTTTGTC
Found at i:499611 original size:23 final size:23
Alignment explanation
Indices: 499584--499630 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
499574 CAGTTATTAC
499584 ACTAAAAGTGGAGTT-GAGTAATT
1 ACTAAAAGTGGAGTTAG-GTAATT
499607 ACTAAAAGTGGAGTTAGGTAATT
1 ACTAAAAGTGGAGTTAGGTAATT
499630 A
1 A
499631 GAAATTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (23 bp):
ACTAAAAGTGGAGTTAGGTAATT
Found at i:500677 original size:2 final size:2
Alignment explanation
Indices: 500670--500724 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
500660 TACCATTAAT
500670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
500712 TA TA TA CA TA TA T
1 TA TA TA TA TA TA T
500725 TTAGCAGTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:503550 original size:32 final size:32
Alignment explanation
Indices: 503468--503550 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 32
503458 TAAAAATTTA
*
503468 CTCGATTCG-TGCTCATTAAGAAATTTTGTTG
1 CTCGACTCGTTGCTCATTAAGAAATTTTGTTG
** **
503499 CTTTACTC-TTGCTTGTTAAGAAATTTTGTTG
1 CTCGACTCGTTGCTCATTAAGAAATTTTGTTG
503530 CTCGACTCGTTGCTCATTAAG
1 CTCGACTCGTTGCTCATTAAG
503551 GTCATTAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
31 31 0.76
32 10 0.24
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (32 bp):
CTCGACTCGTTGCTCATTAAGAAATTTTGTTG
Found at i:503821 original size:21 final size:21
Alignment explanation
Indices: 503783--503832 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
503773 TTGGGTGTAG
*
503783 TAAAATAATAATTATTAATTAT
1 TAAATTAATAATTATTAATT-T
*
503805 TAAATTAAT-ATTTTTAATTT
1 TAAATTAATAATTATTAATTT
*
503825 TTAATTAA
1 TAAATTAA
503833 AAAAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 9 0.36
22 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATTAATAATTATTAATTT
Found at i:506017 original size:21 final size:21
Alignment explanation
Indices: 505993--506043 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
505983 TTGAGATAAA
* *
505993 ATCTGAACTCGACTAGATCTG
1 ATCTGAAATCAACTAGATCTG
506014 ATCTGAAATCAACTAGATCTG
1 ATCTGAAATCAACTAGATCTG
506035 ATCTGAAAT
1 ATCTGAAAT
506044 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (21 bp):
ATCTGAAATCAACTAGATCTG
Found at i:507337 original size:23 final size:23
Alignment explanation
Indices: 507310--507361 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
507300 ATTCTCCTTT
507310 CATCTGACTAATTATCATTCTAC
1 CATCTGACTAATTATCATTCTAC
**
507333 CATCTGTTTAATTATCATTCTAC
1 CATCTGACTAATTATCATTCTAC
507356 CATCTG
1 CATCTG
507362 TTTGATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (23 bp):
CATCTGACTAATTATCATTCTAC
Found at i:507362 original size:23 final size:23
Alignment explanation
Indices: 507318--507364 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
507308 TTCATCTGAC
507318 TAATTATCATTCTACCATCTGTT
1 TAATTATCATTCTACCATCTGTT
507341 TAATTATCATTCTACCATCTGTT
1 TAATTATCATTCTACCATCTGTT
507364 T
1 T
507365 GATGATATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.04, T:0.49
Consensus pattern (23 bp):
TAATTATCATTCTACCATCTGTT
Found at i:518921 original size:22 final size:21
Alignment explanation
Indices: 518853--518926 Score: 51
Period size: 22 Copynumber: 3.3 Consensus size: 21
518843 TAGTGGTAAG
* * *
518853 AAATTTCTTATAATTAATGTT
1 AAATTTATTATAATTTATATT
*
518874 AATATTTATTATTATGTT-TAATTT
1 AA-ATTTATTATAAT-TTAT-A-TT
518898 AAATTTATTATGAATTTATATT
1 AAATTTATTAT-AATTTATATT
*
518920 AATTTTA
1 AAATTTA
518927 ATTTTTTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 2 0.05
22 19 0.46
23 13 0.32
24 7 0.17
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (21 bp):
AAATTTATTATAATTTATATT
Found at i:520547 original size:42 final size:42
Alignment explanation
Indices: 520457--520547 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
520447 ATGATGATGC
* * *
520457 CCAA-CCCTCCAGTTCATATGCCATCTCCTCAGGGGTATATG
1 CCAAGCCCACCAGTTCATATGCCATCTCCGCAGGGGTACATG
* * *
520498 CCAAGCCCACCAGTTTATATGCCATCTCCGCAGGGTTACATT
1 CCAAGCCCACCAGTTCATATGCCATCTCCGCAGGGGTACATG
*
520540 CCTAGCCC
1 CCAAGCCC
520548 TCAGGGTTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.25
Consensus pattern (42 bp):
CCAAGCCCACCAGTTCATATGCCATCTCCGCAGGGGTACATG
Found at i:520554 original size:21 final size:21
Alignment explanation
Indices: 520528--520639 Score: 149
Period size: 21 Copynumber: 5.3 Consensus size: 21
520518 GCCATCTCCG
520528 CAGGGTTACATTCCTAGCCCT
1 CAGGGTTACATTCCTAGCCCT
520549 CAGGGTTACATTCCTAGCTCGC-
1 CAGGGTTACATTCCTAGC-C-CT
520571 CA-GGTTACATTCCTAGCCCT
1 CAGGGTTACATTCCTAGCCCT
*
520591 CAGGGTTACATTCCTAGCCCGC
1 CAGGGTTACATTCCTAGCCC-T
* *
520613 CA-GGTTACATACCTAGCCCG
1 CAGGGTTACATTCCTAGCCCT
520633 CAGGGTT
1 CAGGGTT
520640 TTATGACACC
Statistics
Matches: 82, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.01
20 5 0.06
21 70 0.85
22 5 0.06
23 1 0.01
ACGTcount: A:0.20, C:0.33, G:0.21, T:0.26
Consensus pattern (21 bp):
CAGGGTTACATTCCTAGCCCT
Found at i:520578 original size:42 final size:42
Alignment explanation
Indices: 520531--520639 Score: 191
Period size: 42 Copynumber: 2.6 Consensus size: 42
520521 ATCTCCGCAG
*
520531 GGTTACATTCCTAGCCCTCAGGGTTACATTCCTAGCTCGCCA
1 GGTTACATTCCTAGCCCTCAGGGTTACATTCCTAGCCCGCCA
520573 GGTTACATTCCTAGCCCTCAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCTAGCCCTCAGGGTTACATTCCTAGCCCGCCA
* *
520615 GGTTACATACCTAGCCCGCAGGGTT
1 GGTTACATTCCTAGCCCTCAGGGTT
520640 TTATGACACC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.19, C:0.33, G:0.21, T:0.27
Consensus pattern (42 bp):
GGTTACATTCCTAGCCCTCAGGGTTACATTCCTAGCCCGCCA
Found at i:521229 original size:21 final size:21
Alignment explanation
Indices: 521205--521257 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
521195 ACACTTAGGG
521205 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
521226 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
521247 TACCGATTCCC
1 AACCGATTCCC
521258 CACGCTCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:521473 original size:13 final size:13
Alignment explanation
Indices: 521452--521506 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
521442 AAGTTCGATA
*
521452 AATTCAAATACTT
1 AATTGAAATACTT
521465 AATTGAAATACTT
1 AATTGAAATACTT
* *
521478 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
521492 AATTGAAATACTT
1 AATTGAAATACTT
521505 AA
1 AA
521507 ATACTTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:521588 original size:32 final size:32
Alignment explanation
Indices: 521492--521590 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
521482 AACTCAACAT
* * *
521492 AATTGAAATACTTAAATACTTCAAAGTTTGATA
1 AATTCAAATACTTAAAAACTTC-AAGTTCGATA
521525 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
521558 AATTCAAATACTTAAAAACTTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCAAGTTCGATA
521590 A
1 A
521591 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 49 0.79
34 1 0.02
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (32 bp):
AATTCAAATACTTAAAAACTTCAAGTTCGATA
Found at i:521623 original size:20 final size:21
Alignment explanation
Indices: 521585--521623 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
521575 ACTTCAAGTT
521585 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
521606 CGATAATTGAAA-AAAGTT
1 CGATAATTGAAACAAAGTT
521624 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:521632 original size:21 final size:21
Alignment explanation
Indices: 521587--521632 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
521577 TTCAAGTTCG
**
521587 ATAATTGAAACAAAGTTTACG
1 ATAATTGAAACAAAGTTTAAA
521608 ATAATTGAAA-AAAGTTATAAA
1 ATAATTGAAACAAAGTT-TAAA
521629 ATAA
1 ATAA
521633 ACTACATTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (21 bp):
ATAATTGAAACAAAGTTTAAA
Found at i:523929 original size:22 final size:24
Alignment explanation
Indices: 523904--523955 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
523894 TTAAACACAG
*
523904 ACCGGTTTTTT-TCCGG-ATAAAA
1 ACCGGTTTTTTATCCGGTAAAAAA
523926 ACCGGTTTTTTATCCGGTAAAAAA
1 ACCGGTTTTTTATCCGGTAAAAAA
523950 ACCGGT
1 ACCGGT
523956 CTAGGTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 11 0.41
23 5 0.19
24 11 0.41
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (24 bp):
ACCGGTTTTTTATCCGGTAAAAAA
Found at i:524632 original size:14 final size:14
Alignment explanation
Indices: 524613--524647 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
524603 AATTTATCCA
524613 ATTAAAACATATAC
1 ATTAAAACATATAC
524627 ATTAAAACATATAC
1 ATTAAAACATATAC
524641 ATTAAAA
1 ATTAAAA
524648 TCAACTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (14 bp):
ATTAAAACATATAC
Found at i:530104 original size:29 final size:29
Alignment explanation
Indices: 530070--530128 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
530060 CCTAAATTAA
530070 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
530099 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
530128 T
1 T
530129 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:534786 original size:29 final size:29
Alignment explanation
Indices: 534752--534810 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
534742 CCTAAATTAA
534752 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
534781 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
534810 T
1 T
534811 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:537954 original size:21 final size:21
Alignment explanation
Indices: 537903--537954 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
537893 ATTTAAAATT
*
537903 ATAAAATTTTAAGAGATAAAA
1 ATAAATTTTTAAGAGATAAAA
* *
537924 ATAAATTTTTAATAGA-AAAT
1 ATAAATTTTTAAGAGATAAAA
537944 ATATAATTTTT
1 ATA-AATTTTT
537955 TTAAAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (21 bp):
ATAAATTTTTAAGAGATAAAA
Found at i:537974 original size:18 final size:18
Alignment explanation
Indices: 537939--537977 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
537929 TTTTTAATAG
**
537939 AAAATATATAATTTTTTT
1 AAAATATATAATAATTTT
*
537957 AAAATATATGATAATTTT
1 AAAATATATAATAATTTT
537975 AAA
1 AAA
537978 TTTTTAGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AAAATATATAATAATTTT
Found at i:538783 original size:17 final size:17
Alignment explanation
Indices: 538761--538794 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
538751 TCGGGACTTT
538761 GAAGGAACAGATTCTCA
1 GAAGGAACAGATTCTCA
538778 GAAGGAACAGATTCTCA
1 GAAGGAACAGATTCTCA
538795 TAAGCTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.18
Consensus pattern (17 bp):
GAAGGAACAGATTCTCA
Found at i:539840 original size:19 final size:21
Alignment explanation
Indices: 539800--539840 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
539790 CAATTACATA
539800 TATAATATTTTCGGGTTCGGG
1 TATAATATTTTCGGGTTCGGG
539821 TATAATA-TTTCGGG-TCGGG
1 TATAATATTTTCGGGTTCGGG
539840 T
1 T
539841 TCGGGGACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 7 0.35
21 7 0.35
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41
Consensus pattern (21 bp):
TATAATATTTTCGGGTTCGGG
Found at i:549746 original size:21 final size:21
Alignment explanation
Indices: 549722--549780 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
549712 CTTTCTTTCT
*
549722 AGGGATCAATCCTTTTCTCC-A
1 AGGGATCGATCCTTTTC-CCGA
*
549743 AGGGATCGATCATTTGTCCCGA
1 AGGGATCGATCCTTT-TCCCGA
*
549765 GGGGATCGATCCTTTT
1 AGGGATCGATCCTTTT
549781 GAAAAGGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (21 bp):
AGGGATCGATCCTTTTCCCGA
Found at i:551360 original size:24 final size:25
Alignment explanation
Indices: 551332--551387 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
551322 TATATATACA
*
551332 AACTTAAAAAATATTTTTTA-TATT
1 AACTTAAAAAATATATTTTATTATT
* **
551356 CACTTATTAAATATATTTTATTATT
1 AACTTAAAAAATATATTTTATTATT
551381 AACTTAA
1 AACTTAA
551388 TTTAATAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (25 bp):
AACTTAAAAAATATATTTTATTATT
Found at i:551398 original size:27 final size:27
Alignment explanation
Indices: 551335--551398 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
551325 ATATACAAAC
* * *
551335 TTAAAAAATATTTTTTATATTCACTTA
1 TTAAATAATATTTTATATATTAACTTA
551362 TTAAAT-ATATTTTAT-TATTAACTTAA
1 TTAAATAATATTTTATATATTAACTT-A
*
551388 TTTAATAATAT
1 TTAAATAATAT
551399 GATATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 8 0.26
26 14 0.45
27 9 0.29
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAAATAATATTTTATATATTAACTTA
Found at i:551427 original size:24 final size:24
Alignment explanation
Indices: 551338--551434 Score: 61
Period size: 30 Copynumber: 3.7 Consensus size: 24
551328 TACAAACTTA
* *
551338 AAAAATAT-TTTTTATATTCACTT
1 AAAAATATATTTTTATTTTCATTT
* *
551361 ATTAAATATATTTTATTATTAACTTAATTT
1 A-AAAATATA-TTT-TTATT---TTCATTT
551391 AATAATATGATATTTTTATTTTCATTT
1 AA-AA-AT-ATATTTTTATTTTCATTT
551418 AAAAATATATGTTTTAT
1 AAAAATATAT-TTTTAT
551435 GTTAAAATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
23 1 0.02
24 10 0.18
25 8 0.14
26 5 0.09
27 12 0.21
30 13 0.23
31 5 0.09
32 3 0.05
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (24 bp):
AAAAATATATTTTTATTTTCATTT
Found at i:554283 original size:30 final size:31
Alignment explanation
Indices: 554247--554309 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
554237 ACTTTACCTC
*
554247 TTTTTTTAATTAATTTATT-ATACTTTT-AAT
1 TTTTTTTAATTAATTCATTGA-ACTTTTGAAT
*
554277 TTTTTTTAATTTATTCATTGAACTTTTGAAT
1 TTTTTTTAATTAATTCATTGAACTTTTGAAT
554308 TT
1 TT
554310 CTCATGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (31 bp):
TTTTTTTAATTAATTCATTGAACTTTTGAAT
Found at i:554589 original size:21 final size:21
Alignment explanation
Indices: 554541--554594 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
554531 CAGTTTCCAG
* *
554541 ATTCGCAACGCGATTATGACA
1 ATTCGCAATGCGATTATCACA
* *
554562 A-TCGCAATGCGATTTTCCCA
1 ATTCGCAATGCGATTATCACA
554582 ATTCGCAATGCGA
1 ATTCGCAATGCGA
554595 ATAAGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
ATTCGCAATGCGATTATCACA
Found at i:554669 original size:14 final size:14
Alignment explanation
Indices: 554650--554676 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
554640 CTAATTCGCA
554650 TTGCGATTTACATG
1 TTGCGATTTACATG
554664 TTGCGATTTACAT
1 TTGCGATTTACAT
554677 AGCGCCATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTTACATG
Found at i:555299 original size:14 final size:14
Alignment explanation
Indices: 555265--555367 Score: 80
Period size: 14 Copynumber: 6.6 Consensus size: 14
555255 TTTCATTTTG
*
555265 CGTTGCAATTCTCT
1 CGTTGCGATTCTCT
555279 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
555293 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
555312 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
555326 CGTTGCGATAATCATTTCG
1 CGTTGCGAT--TC---TCT
555345 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
555359 TGTTGCGAT
1 CGTTGCGAT
555368 AGTCATTTCC
Statistics
Matches: 73, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
14 42 0.58
16 5 0.07
17 5 0.07
19 21 0.29
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:555299 original size:33 final size:31
Alignment explanation
Indices: 555279--555388 Score: 148
Period size: 33 Copynumber: 3.3 Consensus size: 31
555269 GCAATTCTCT
555279 CGTTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 CGTTGCGATTCTCTCGTTGCGA--TTCATTTCG
555312 CGTTGCGATTCTCTCGTTGCGATAATCATTTCG
1 CGTTGCGATTCTCTCGTTGCGAT--TCATTTCG
*
555345 CGTTGCGATTCTCTTGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCTCGTTGCGAT--TCATTT-CG
555379 CGTTGCGATT
1 CGTTGCGATT
555389 TTCATTATCT
Statistics
Matches: 72, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
31 1 0.01
33 59 0.82
34 12 0.17
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.42
Consensus pattern (31 bp):
CGTTGCGATTCTCTCGTTGCGATTCATTTCG
Found at i:555393 original size:20 final size:20
Alignment explanation
Indices: 555360--555416 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
555350 CGATTCTCTT
**
555360 GTTGCGATAGTCATTTCCGC
1 GTTGCGATTTTCATTTCCGC
*
555380 GTTGCGATTTTCATTAT-CTC
1 GTTGCGATTTTCATT-TCCGC
555400 GTTGCGATTTTCATTTC
1 GTTGCGATTTTCATTTC
555417 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (20 bp):
GTTGCGATTTTCATTTCCGC
Found at i:557213 original size:95 final size:89
Alignment explanation
Indices: 557048--557232 Score: 271
Period size: 91 Copynumber: 2.0 Consensus size: 89
557038 TAGATTGCTT
*
557048 AGTAAATTTATTTGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
557113 GTCTTTTTGTTTTGTCTTTTGGTTGA
66 GTC--TTTGTTTTGTCTTTTGGTTGA
* * * *
557139 AGTAAATTTATTCGGTTGTTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
557204 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
62 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
557232 A
1 A
557233 AGTTTGAAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 32 0.38
93 25 0.29
94 2 0.02
95 26 0.31
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.49
Consensus pattern (89 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTGTTTTGTCTTTTGGTTGA
Found at i:557530 original size:21 final size:21
Alignment explanation
Indices: 557506--557572 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
557496 TCATTCCTCG
557506 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
557527 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
557548 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
557569 AGAG
1 AGAG
557573 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:557530 original size:42 final size:42
Alignment explanation
Indices: 557479--557572 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
557469 CTACTCCTAT
* *
557479 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * *
557521 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
557563 CATTCAAGAG
1 CGTTCAAGAG
557573 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:558942 original size:14 final size:14
Alignment explanation
Indices: 558923--558958 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
558913 ATTGTTTAAT
558923 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
558937 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
558951 TGATTTGT
1 TGATTTGT
558959 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:559087 original size:19 final size:19
Alignment explanation
Indices: 559065--559142 Score: 112
Period size: 19 Copynumber: 4.4 Consensus size: 19
559055 AAAAATTACT
559065 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
559084 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
559103 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
559117 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
559136 ATCGCAA
1 ATCGCAA
559143 CGACAAAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 36 0.69
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:559125 original size:33 final size:33
Alignment explanation
Indices: 559081--559176 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
559071 ATGCGAAATG
*
559081 AAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAC
*
559114 AGAATCGCAATGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAC
*
559147 AAAATCGCAACGCGAAACT-AAAATCGCAAC
1 AAAATCGCAATGCGAAA-TGAAAATCGCAAC
559177 ACGAAACTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 57 0.98
34 1 0.02
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
AAAATCGCAATGCGAAATGAAAATCGCAACGAC
Found at i:559171 original size:19 final size:19
Alignment explanation
Indices: 559116--559192 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
559106 GCAACGAGAG
*
559116 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
559135 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
559149 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
559168 AATCGCAACACGAAACTAA
1 AATCGCAACGCGAAACTAA
*
559187 ATTCGC
1 AATCGC
559193 GTTGCGATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 33 0.66
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:559234 original size:33 final size:33
Alignment explanation
Indices: 559192--559318 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
559182 ACTAAATTCG
* * *
559192 CGTTGCGATTTTCATTCCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
559225 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
559258 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
559291 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
559319 AGTAATTTTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:559251 original size:19 final size:19
Alignment explanation
Indices: 559227--559318 Score: 96
Period size: 19 Copynumber: 5.4 Consensus size: 19
559217 GATTCCCTCG
559227 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
559246 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
559260 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
559279 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
559293 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
559312 TTGCGAT
1 TTGCGAT
559319 AGTAATTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 12 0.20
16 14 0.24
17 14 0.24
19 19 0.32
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:559265 original size:14 final size:14
Alignment explanation
Indices: 559213--559300 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
559203 TCATTCCGCT
*
559213 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
559227 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
559244 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
559260 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
559277 CATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
559293 TTGCGATT
1 TTGCGATT
559301 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:559384 original size:20 final size:20
Alignment explanation
Indices: 559312--559384 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
559302 TCATTTCGCA
* *
559312 TTGCGATAGTAATTTTCGCG
1 TTGCGATAGTCATTTTCGTG
* ****
559332 TTGCGATAGACATTAAAATG
1 TTGCGATAGTCATTTTCGTG
559352 ATTGCGA-ATGTCATTTTCGTG
1 -TTGCGATA-GTCATTTTCGTG
559373 TTGCGATAGTCA
1 TTGCGATAGTCA
559385 AATGATTGCC
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:561664 original size:12 final size:12
Alignment explanation
Indices: 561647--561683 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
561637 TCTTCGGGGA
561647 CTTTTTCTTCTT
1 CTTTTTCTTCTT
*
561659 CTTTTTCTTCCT
1 CTTTTTCTTCTT
561671 CTTTTTCTTCTT
1 CTTTTTCTTCTT
561683 C
1 C
561684 AGGGTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:561892 original size:24 final size:24
Alignment explanation
Indices: 561858--561911 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
561848 CTGAAACATC
*
561858 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
561882 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
561906 ATCAAA
1 ATCAAA
561912 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:562709 original size:20 final size:21
Alignment explanation
Indices: 562684--562735 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
562674 TTTTCCTAAT
*
562684 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
562704 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
562725 TCGCAATGCGA
1 TCGCAATGCGA
562736 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:562809 original size:20 final size:20
Alignment explanation
Indices: 562720--562811 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
562710 TGCGAATTTG
* *
562720 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
562740 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* * *
562760 ACAAAATCGCAATGAGATTCT
1 -GAAAATCGCAACGAGATACT
** *
562781 GAATTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
562801 GAAAATCGCAA
1 GAAAATCGCAA
562812 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 40 0.74
21 14 0.26
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:564757 original size:41 final size:42
Alignment explanation
Indices: 564712--564803 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
564702 CCTCTTCAAC
564712 GATGACAGTG-GCCTCTTGAACG-GTGGAGGGGACTCTTGAGG
1 GATGACAG-GAGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* * *
564753 GATGATAGGAGCCTCTTGAATGATTGGAGGGGACTCTTGAGG
1 GATGACAGGAGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
564795 GATGACAGG
1 GATGACAGG
564804 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
40 1 0.02
41 18 0.40
42 26 0.58
ACGTcount: A:0.23, C:0.14, G:0.40, T:0.23
Consensus pattern (42 bp):
GATGACAGGAGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:565178 original size:20 final size:19
Alignment explanation
Indices: 565147--565233 Score: 75
Period size: 20 Copynumber: 4.4 Consensus size: 19
565137 TAGTTTACTT
* * *
565147 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAA-TGACTA
*
565167 TCGCAATGCGAAAATGACTA
1 TCGCAACGCG-AAATGACTA
*
565187 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
* **
565207 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
565226 TCGCAACG
1 TCGCAACG
565234 ACAAAATCGC
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
19 14 0.26
20 36 0.67
21 4 0.07
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:565191 original size:40 final size:39
Alignment explanation
Indices: 565147--565265 Score: 101
Period size: 33 Copynumber: 3.2 Consensus size: 39
565137 TAGTTTACTT
* * **
565147 TCGCAACAC-GAAACTTACTTTCGCAATGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAATGCG-AAATGAAAA
* *
565187 TCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACACGGAAATGACTATCGCAATGCGAAATGAAAA
565226 TCGC-A-AC-GACAA--A--ATCGCAATGCGAAATGAAAA
1 TCGCAACACGGA-AATGACTATCGCAATGCGAAATGAAAA
565259 TCGCAAC
1 TCGCAAC
565266 GACAAAATCG
Statistics
Matches: 67, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
33 24 0.36
34 1 0.01
36 2 0.03
37 3 0.04
38 1 0.01
39 11 0.16
40 21 0.31
41 4 0.06
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (39 bp):
TCGCAACACGGAAATGACTATCGCAATGCGAAATGAAAA
Found at i:565241 original size:14 final size:14
Alignment explanation
Indices: 565222--565278 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
565212 ATGCGAAATG
565222 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
565236 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
565255 AAAATCGCAACGAC
1 AAAATCGCAACGAC
565269 AAAATCGCAA
1 AAAATCGCAA
565279 TGCGAAACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:565293 original size:33 final size:33
Alignment explanation
Indices: 565206--565285 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
565196 GGAAATGGCT
565206 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
565239 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
565272 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
565286 CACAAATCAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:565334 original size:14 final size:14
Alignment explanation
Indices: 565315--565372 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
565305 TTCATTTCAT
565315 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
*
565329 GTTGCGATTTTCATTTC
1 GTTGCGA-TTT--TGTC
565346 GCATTGCGATTTTGTC
1 G--TTGCGATTTTGTC
565362 GTTGCGATTTT
1 GTTGCGATTTT
565373 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:565339 original size:33 final size:33
Alignment explanation
Indices: 565297--565388 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
565287 ACAAATCACA
**
565297 TTGCGATTTTCATTTCATGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCACATTGCGATTTTGTCG
*
565330 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCACATTGCGATTTTGTCG
*
565363 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCACATTGCGAT
565389 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACATTGCGATTTTGTCG
Found at i:565354 original size:19 final size:19
Alignment explanation
Indices: 565330--565388 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
565320 GATTTTGTCG
565330 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
565349 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
565363 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
565382 TTGCGAT
1 TTGCGAT
565389 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 13 0.39
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:565407 original size:20 final size:19
Alignment explanation
Indices: 565373--565427 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
565363 TTGCGATTTT
*
565373 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
565392 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
565412 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
565428 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:565989 original size:18 final size:18
Alignment explanation
Indices: 565966--566013 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
565956 CGGGTCGATC
565966 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
565984 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
566002 AGGTGATGGCTC
1 AGGTGATGGCTC
566014 CCAAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:567381 original size:20 final size:20
Alignment explanation
Indices: 567333--567391 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
567323 AATAGTTTCT
* *
567333 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
567353 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
567373 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
567392 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:567682 original size:22 final size:22
Alignment explanation
Indices: 567654--567697 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
567644 GATGGAGATA
*
567654 GACGGATTTCGCCGGATATGGG
1 GACGGATTTCGCCGGAGATGGG
*
567676 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
567698 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.43, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:567983 original size:41 final size:41
Alignment explanation
Indices: 567924--568001 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
567914 CGAAATTAAG
567924 TATCGAGTTGCGAAAGTCAGTATCGCGTTGCAATTTTGTAT
1 TATCGAGTTGCGAAAGTCAGTATCGCGTTGCAATTTTGTAT
* * *
567965 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT
1 TATCGAGTTGCGAAAGTCAGTATCGCGTTGCAATTTT
568002 CCAAATTCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.37
Consensus pattern (41 bp):
TATCGAGTTGCGAAAGTCAGTATCGCGTTGCAATTTTGTAT
Found at i:567998 original size:20 final size:20
Alignment explanation
Indices: 567884--567997 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
567874 GATTATGTAT
* *
567884 TATCTCGTTGCGAAAGTTAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
567904 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
567924 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
567944 TATCGCGTTGC-AATTTTGT-AT
1 TATCGCGTTGCGAA---AGTCAG
*
567965 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
567985 TATCGCGTTGCGA
1 TATCGCGTTGCGA
567998 TTTTCCAAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.05
20 56 0.75
21 12 0.16
22 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:568016 original size:21 final size:20
Alignment explanation
Indices: 567987--568038 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
567977 ATAGTCAGTA
* *
567987 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
**
568008 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
568028 TCGCATTGCGA
1 TCGCATTGCGA
568039 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:568017 original size:41 final size:41
Alignment explanation
Indices: 567931--568019 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
567921 AAGTATCGAG
* ** * *
567931 TTGCGAAAGTCAGTATCGCGTTGCAATTTTGTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCAATTTTCAAATATCGCA
*
567972 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTATCGCGTTGCAATTTT-CAAATATCGCA
568013 TTGCGAT
1 TTGCGAT
568020 TTACTTATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 39 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCAATTTTCAAATATCGCA
Found at i:569749 original size:28 final size:28
Alignment explanation
Indices: 569717--569774 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
569707 GACGGTGGCT
569717 AGTAATGGGATTAGAATGATGAATTTTA
1 AGTAATGGGATTAGAATGATGAATTTTA
*
569745 AGTAATGGGTTTAGAATGATGAATTTTA
1 AGTAATGGGATTAGAATGATGAATTTTA
569773 AG
1 AG
569775 GGTTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (28 bp):
AGTAATGGGATTAGAATGATGAATTTTA
Found at i:572994 original size:19 final size:19
Alignment explanation
Indices: 572972--573014 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
572962 TTTGAGTTTC
*
572972 TGTTTGGTTCATGTTCGTT
1 TGTTTGGTTCATGTTCATT
*
572991 TGTTTGGTTCGTGTTCATT
1 TGTTTGGTTCATGTTCATT
573010 TGTTT
1 TGTTT
573015 TTTTTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.05, C:0.09, G:0.26, T:0.60
Consensus pattern (19 bp):
TGTTTGGTTCATGTTCATT
Found at i:574074 original size:25 final size:25
Alignment explanation
Indices: 574041--574088 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
574031 GGTCCTCCTA
574041 AAACTAAATTAAATTAAAAAAATTT
1 AAACTAAATTAAATTAAAAAAATTT
*
574066 AAACTAAATTAAATTAGAAAAAT
1 AAACTAAATTAAATTAAAAAAAT
574089 AAAACTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (25 bp):
AAACTAAATTAAATTAAAAAAATTT
Found at i:574806 original size:62 final size:63
Alignment explanation
Indices: 574704--574830 Score: 204
Period size: 62 Copynumber: 2.0 Consensus size: 63
574694 CATAGGAAGC
* * *
574704 AATTGCACACTCATTAGTTTGAGAAAATTACTAAATTTAATTTATTGTATTAAAAGGAAA-AA
1 AATTGCACACCCATTAGTTTGAGAAAATTACTAAAATTAATTTAATGTATTAAAAGGAAAGAA
574766 AATTGCACACCCATT-GTTTTGAGAAAATTACTAAAATTAATTTAATGTATTAAAAGGAAAGAA
1 AATTGCACACCCATTAG-TTTGAGAAAATTACTAAAATTAATTTAATGTATTAAAAGGAAAGAA
574829 AA
1 AA
574831 AACAAGGAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
61 1 0.02
62 55 0.92
63 4 0.07
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (63 bp):
AATTGCACACCCATTAGTTTGAGAAAATTACTAAAATTAATTTAATGTATTAAAAGGAAAGAA
Found at i:579508 original size:28 final size:28
Alignment explanation
Indices: 579459--579512 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
579449 AGAGGTGTAC
579459 AAAAAAATCCGAATATCCGATTTTGGGT
1 AAAAAAATCCGAATATCCGATTTTGGGT
579487 AAAAAATATCCGAA-A-CCGGATTTTGG
1 AAAAAA-ATCCGAATATCC-GATTTTGG
579513 AAAAACCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 2 0.08
28 15 0.62
29 7 0.29
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (28 bp):
AAAAAAATCCGAATATCCGATTTTGGGT
Found at i:579517 original size:27 final size:28
Alignment explanation
Indices: 579459--579517 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
579449 AGAGGTGTAC
579459 AAAAAAATCCGAATATCCGATTTTGGGTA
1 AAAAAAATCCGAATATCCGATTTTGGG-A
*
579488 AAAAATATCCGAA-A-CCGGATTTT-GGA
1 AAAAAAATCCGAATATCC-GATTTTGGGA
579514 AAAA
1 AAAA
579518 CCGGTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.18
27 4 0.14
28 7 0.25
29 12 0.43
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAAAAATCCGAATATCCGATTTTGGGA
Found at i:579618 original size:24 final size:24
Alignment explanation
Indices: 579589--579721 Score: 121
Period size: 24 Copynumber: 5.5 Consensus size: 24
579579 AAATTGAACG
579589 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGATTAAAA
* * *
579613 ATCGGTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTT--TACCGGATTAAAA
*
579639 ACCAG-TTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGATTAAAA
* *
579662 ACCGGTTTTTTCAAACCGGA-AAAAA
1 ACCGGTTTTTT--TACCGGATTAAAA
*
579687 ATCGG-TTTTTTATCCGGA-TAAACA
1 ACCGGTTTTTTTA-CCGGATTAAA-A
579711 ACCGGTTTTTT
1 ACCGGTTTTTT
579722 AAAAAAACTG
Statistics
Matches: 87, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
22 1 0.01
23 23 0.26
24 25 0.29
25 18 0.21
26 20 0.23
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (24 bp):
ACCGGTTTTTTTACCGGATTAAAA
Found at i:579630 original size:26 final size:24
Alignment explanation
Indices: 579589--579723 Score: 141
Period size: 23 Copynumber: 5.5 Consensus size: 24
579579 AAATTGAACG
*
579589 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTAACCGGATTAAAA
* *
579613 ATCGGTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTT--AACCGGATTAAAA
*
579639 ACCAGTTTTTT-ACCGGATTAAAA
1 ACCGGTTTTTTAACCGGATTAAAA
*
579662 ACCGGTTTTTTCAAACCGGA-AAAAA
1 ACCGGTTTTTT--AACCGGATTAAAA
* *
579687 ATCGGTTTTTTATCCGGA-TAAACA
1 ACCGGTTTTTTAACCGGATTAAA-A
579711 ACCGGTTTTTTAA
1 ACCGGTTTTTTAA
579724 AAAAACTGAT
Statistics
Matches: 92, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
23 30 0.33
24 22 0.24
25 14 0.15
26 26 0.28
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (24 bp):
ACCGGTTTTTTAACCGGATTAAAA
Found at i:579648 original size:49 final size:48
Alignment explanation
Indices: 579595--579721 Score: 193
Period size: 49 Copynumber: 2.6 Consensus size: 48
579585 AACGACCGGT
*
579595 TTTTTTACCGGATTAAAAATCGGTTTTTTCAAACCGGATAAAAAACCAG
1 TTTTTTACCGGATTAAAAACCGGTTTTTTCAAACCGGA-AAAAAACCAG
* *
579644 TTTTTTACCGGATTAAAAACCGGTTTTTTCAAACCGGAAAAAAATCGG
1 TTTTTTACCGGATTAAAAACCGGTTTTTTCAAACCGGAAAAAAACCAG
579692 TTTTTTATCCGGA-TAAACAACCGGTTTTTT
1 TTTTTTA-CCGGATTAAA-AACCGGTTTTTT
579722 AAAAAAACTG
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
48 19 0.26
49 54 0.74
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (48 bp):
TTTTTTACCGGATTAAAAACCGGTTTTTTCAAACCGGAAAAAAACCAG
Found at i:581565 original size:2 final size:2
Alignment explanation
Indices: 581553--581589 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
581543 TAAAATTAAT
*
581553 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
581590 GACTTCCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:584778 original size:21 final size:21
Alignment explanation
Indices: 584758--584899 Score: 130
Period size: 20 Copynumber: 6.9 Consensus size: 21
584748 ATTCGCGTTG
*
584758 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* ** *
584779 AAAATCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
*
584799 CATTTCGCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGT-TC
* *
584821 CA-GTCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
* *
584840 CATTTCACGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* * *
584861 AAATTCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
584881 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
584900 CTACAGTTGT
Statistics
Matches: 91, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.03
20 43 0.47
21 42 0.46
22 3 0.03
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (21 bp):
CATTTCGCGTTGCGATAGTTC
Found at i:584803 original size:41 final size:41
Alignment explanation
Indices: 584758--584899 Score: 232
Period size: 41 Copynumber: 3.5 Consensus size: 41
584748 ATTCGCGTTG
584758 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
584799 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
* *
584840 CATTTCACGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
584881 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
584900 CTACAGTTGT
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
40 1 0.01
41 91 0.98
42 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:584854 original size:82 final size:83
Alignment explanation
Indices: 584758--584924 Score: 300
Period size: 82 Copynumber: 2.0 Consensus size: 83
584748 ATTCGCGTTG
*
584758 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
584823 GTCG-CGTTGCGATTTTC
66 GTCGTCGTTGCGATTTTC
*
584840 CATTTCACGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
*
584905 GTTGTCGTTGCGATTTTC
66 GTCGTCGTTGCGATTTTC
584923 CA
1 CA
584925 AATTCGTTGT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 66 0.81
83 15 0.19
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (83 bp):
CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
GTCGTCGTTGCGATTTTC
Found at i:584933 original size:82 final size:81
Alignment explanation
Indices: 584765--584946 Score: 285
Period size: 82 Copynumber: 2.2 Consensus size: 81
584755 TTGCATTTCG
584765 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGT
1 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGT
*
584830 TGCGATTTTCCATTTCA
66 TGCGATTTTCCAATT-A
* *
584847 CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCG
1 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCG-CG
584912 TTGCGATTTTCCAAATT-
65 TTGCGATTTTCC-AATTA
* *
584929 CGTTGTGATAGTTAAAAA
1 CGTTGCGATAGTTGAAAA
584947 AAAAGATTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
82 75 0.82
83 14 0.15
84 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (81 bp):
CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGT
TGCGATTTTCCAATTA
Found at i:584939 original size:41 final size:40
Alignment explanation
Indices: 584758--584924 Score: 196
Period size: 41 Copynumber: 4.0 Consensus size: 40
584748 ATTCGCGTTG
* * *
584758 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCT-ACAGTTGCGTTGCGATTTTC
*
584799 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCTACAGTTGCGTTGCGATTTTC
*
584840 CATTTCACGTTGCGATAGT-TGA-AATTCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCT-ACAGTT-GCGTTGCGATTTTC
584881 CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTC
584923 CA
1 CA
584925 AATTCGTTGT
Statistics
Matches: 113, Mismatches: 7, Indels: 11
0.86 0.05 0.08
Matches are distributed among these distances:
40 3 0.03
41 90 0.80
42 20 0.18
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (40 bp):
CATTTCCGTTGCGATAGTCTACAGTTGCGTTGCGATTTTC
Found at i:585014 original size:6 final size:6
Alignment explanation
Indices: 585003--585074 Score: 92
Period size: 6 Copynumber: 12.2 Consensus size: 6
584993 GAAGACACGT
*
585003 ATTACC ATTACC ATTACC ATTACC ATTACC AATACC ATTACC A-TACC
1 ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC
* * * *
585050 AATACC AATACC AATACC AATACC A
1 ATTACC ATTACC ATTACC ATTACC A
585075 CGACCACGAC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.08
6 58 0.92
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (6 bp):
ATTACC
Found at i:585026 original size:18 final size:18
Alignment explanation
Indices: 585003--585074 Score: 110
Period size: 18 Copynumber: 4.1 Consensus size: 18
584993 GAAGACACGT
*
585003 ATTACCATTACCATTACC
1 ATTACCATTACCAATACC
585021 ATTACCATTACCAATACC
1 ATTACCATTACCAATACC
585039 ATTACCA-TACCAATACC
1 ATTACCATTACCAATACC
* *
585056 AATACCAATACCAATACC
1 ATTACCATTACCAATACC
585074 A
1 A
585075 CGACCACGAC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
17 16 0.31
18 35 0.69
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (18 bp):
ATTACCATTACCAATACC
Found at i:585080 original size:6 final size:6
Alignment explanation
Indices: 585071--585101 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
585061 CAATACCAAT
585071 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
585102 GACGAGACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:585086 original size:18 final size:18
Alignment explanation
Indices: 585065--585101 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
585055 CAATACCAAT
*
585065 ACCAATACCACGACCACG
1 ACCAAGACCACGACCACG
*
585083 ACCACGACCACGACCACG
1 ACCAAGACCACGACCACG
585101 A
1 A
585102 GACGAGACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.46, G:0.14, T:0.03
Consensus pattern (18 bp):
ACCAAGACCACGACCACG
Found at i:585617 original size:6 final size:6
Alignment explanation
Indices: 585601--585674 Score: 141
Period size: 6 Copynumber: 12.5 Consensus size: 6
585591 GTCCGTCTCG
585601 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
585648 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
585675 AATACGTGTC
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 63 0.93
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:585798 original size:21 final size:21
Alignment explanation
Indices: 585773--585846 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
585763 AATTTGGAAA
585773 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** * **
585794 ATCGCAACGCGA-AATGAAAA
1 ATCGCAACGCGATTTTCAACT
*
585814 AACGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
585835 ATCGCAACGCGA
1 ATCGCAACGCGA
585847 AATGCAACGC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:585832 original size:41 final size:41
Alignment explanation
Indices: 585770--585850 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
585760 ACGAATTTGG
*
585770 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGA
1 AAAAACGCAACGCGATTTTCAACTATCGCAACGCGAAATGA
585811 AAAAACGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1 AAAAACGCAACGCGATTTTCAACTATCGCAACGCGAAATG
585851 CAACGCGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
AAAAACGCAACGCGATTTTCAACTATCGCAACGCGAAATGA
Found at i:589081 original size:9 final size:8
Alignment explanation
Indices: 589069--589178 Score: 53
Period size: 10 Copynumber: 12.2 Consensus size: 8
589059 AATATTTTAT
589069 ATATAATTA
1 ATATAA-TA
*
589078 ATATAAAAA
1 ATAT-AATA
589087 ATATAA-A
1 ATATAATA
*
589094 ATATTATA
1 ATATAATA
589102 TATATAATTA
1 -ATATAA-TA
*
589112 ATATAAAAA
1 ATAT-AATA
589121 ATATAA-A
1 ATATAATA
589128 ATATATATA
1 ATATA-ATA
589137 TATATATATA
1 -ATATA-ATA
589147 TATATATATA
1 -ATATA-ATA
589157 TATATATATA
1 -ATATA-ATA
589167 TATATATATA
1 -ATATA-ATA
589177 AT
1 AT
589179 CGGGGCGGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 16
0.82 0.04 0.15
Matches are distributed among these distances:
7 12 0.13
8 6 0.07
9 26 0.29
10 45 0.51
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAATA
Found at i:589097 original size:25 final size:25
Alignment explanation
Indices: 589069--589162 Score: 64
Period size: 27 Copynumber: 3.6 Consensus size: 25
589059 AATATTTTAT
589069 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* * *
589094 ATATTATATATATAATTAATATAAAAA
1 ATATAATATATATAA--AAAATATAAA
* * * *
589121 ATATAAAATATATATATATATATATAT
1 ATATAATATATATA-AAAAATATA-AA
589148 ATATATATATATATA
1 ATATA-ATATATATA
589163 TATATATATA
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
25 12 0.22
26 7 0.13
27 26 0.48
28 9 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:589104 original size:34 final size:34
Alignment explanation
Indices: 589057--589142 Score: 154
Period size: 34 Copynumber: 2.5 Consensus size: 34
589047 CCCGAACCCG
*
589057 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
589091 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
589125 AAAATATATATATATATA
1 AAAATAT-TATATATATA
589143 TATATATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 40 0.80
35 10 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:589133 original size:2 final size:2
Alignment explanation
Indices: 589128--589176 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
589118 AAAATATAAA
589128 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
589170 AT AT AT A
1 AT AT AT A
589177 ATCGGGGCGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:589150 original size:34 final size:34
Alignment explanation
Indices: 589066--589176 Score: 128
Period size: 34 Copynumber: 3.4 Consensus size: 34
589056 GAAAATATTT
589066 TATATATA-AT-TA-ATATAAAAAATATAAAATA
1 TATATATATATATATATATAAAAAATATAAAATA
589097 T-TATATATATA-ATTAATATAAAAAATATAAAATA
1 TATATATATATATA-T-ATATAAAAAATATAAAATA
* * *
589131 TATATATATATATATATAT-ATATATAT-ATATA
1 TATATATATATATATATATAAAAAATATAAAATA
589163 TATATATATATATA
1 TATATATATATATA
589177 ATCGGGGCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
30 6 0.09
31 4 0.06
32 18 0.26
33 6 0.09
34 24 0.34
35 11 0.16
36 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
TATATATATATATATATATAAAAAATATAAAATA
Found at i:589444 original size:16 final size:16
Alignment explanation
Indices: 589423--589453 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
589413 ATAAATTCTT
589423 TAAAAATATTTTTATG
1 TAAAAATATTTTTATG
589439 TAAAAATATTTTTAT
1 TAAAAATATTTTTAT
589454 TCGATTTACG
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TAAAAATATTTTTATG
Found at i:590305 original size:60 final size:59
Alignment explanation
Indices: 590236--590387 Score: 205
Period size: 60 Copynumber: 2.5 Consensus size: 59
590226 TTATTAAGTA
* * *
590236 CATCGACTATTAAAAGTTATAAAATGATCATTAAACTATACAGGGTTTCTTTGTTGAGTC
1 CATCAACTATTAAAAGTTACAAAATGATCATT-AACTATAAAGGGTTTCTTTGTTGAGTC
* * *
590296 CATCAACTATTAAAAGTTACAAAATGAGCACCTAATTATAAAGGGTTTCTTTGTTGAGTC
1 CATCAACTATTAAAAGTTACAAAATGATCA-TTAACTATAAAGGGTTTCTTTGTTGAGTC
* * *
590356 CCTCAACCATTAAAAGTTACAAAATGGTCATT
1 CATCAACTATTAAAAGTTACAAAATGATCATT
590388 CGACTATTCA
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
59 1 0.01
60 78 0.98
61 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (59 bp):
CATCAACTATTAAAAGTTACAAAATGATCATTAACTATAAAGGGTTTCTTTGTTGAGTC
Found at i:590807 original size:42 final size:42
Alignment explanation
Indices: 590748--590854 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
590738 CATCAAGACC
590748 CAAGCTTTCTCTATCATTTAACCACTGTCTGAAACCAGAGCT
1 CAAGCTTTCTCTATCATTTAACCACTGTCTGAAACCAGAGCT
*
590790 CAAGCTTTCTCTATCATTTAACCTCTGTCTGAAACCAGAGCT
1 CAAGCTTTCTCTATCATTTAACCACTGTCTGAAACCAGAGCT
*
590832 CAAACTTTCTCTATCATTTAACC
1 CAAGCTTTCTCTATCATTTAACC
590855 GCAGGGCTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (42 bp):
CAAGCTTTCTCTATCATTTAACCACTGTCTGAAACCAGAGCT
Found at i:594933 original size:58 final size:58
Alignment explanation
Indices: 594794--594942 Score: 135
Period size: 58 Copynumber: 2.6 Consensus size: 58
594784 CTCAAAGTAT
* * * *
594794 GACCCTCATTCTATATTGGTCGC-TAAACTTTTAAATATTCTGATTTTATCCTAAACTAT
1 GACCTTCATTCTAAATTGGTC-CTTAAACTTTTAAATATTC-GATTTTATCCCAAACTAC
* *
594853 GA-CTATCATTCTAAATTAGTCCTTAAACTTTTACAT-TTC-ATTTTCATCCCCAAACTAC
1 GACCT-TCATTCTAAATTGGTCCTTAAACTTTTAAATATTCGATTTT-AT-CCCAAACTAC
* * **
594911 GACCTTCATTCTAGACTGGTCCTCGAACTTTT
1 GACCTTCATTCTAAATTGGTCCTTAAACTTTT
594943 CGAACATCCT
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
56 5 0.07
57 2 0.03
58 37 0.50
59 30 0.41
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (58 bp):
GACCTTCATTCTAAATTGGTCCTTAAACTTTTAAATATTCGATTTTATCCCAAACTAC
Found at i:596359 original size:28 final size:28
Alignment explanation
Indices: 596290--596351 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
596280 TAGCCTTACC
* * *
596290 ATAACTTGTCAAATAGCTGGAGCTTTAT
1 ATAACTCGTAAAATAACTGGAGCTTTAT
*
596318 ATAACTCGTAAAATAACTGGAGTTTTAT
1 ATAACTCGTAAAATAACTGGAGCTTTAT
596346 ATAACT
1 ATAACT
596352 GCTTAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (28 bp):
ATAACTCGTAAAATAACTGGAGCTTTAT
Found at i:598307 original size:21 final size:20
Alignment explanation
Indices: 598275--598313 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
598265 TAAAAACATT
*
598275 TTTTAAGATATTTATACTCA
1 TTTTAAGATATTGATACTCA
*
598295 TTTTATGAGTATTGATACT
1 TTTTAAGA-TATTGATACT
598314 GATCCTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTTAAGATATTGATACTCA
Found at i:598758 original size:34 final size:34
Alignment explanation
Indices: 598716--598791 Score: 152
Period size: 34 Copynumber: 2.2 Consensus size: 34
598706 TATATTCTGG
598716 TCGGGTCGGGTCTCGTGTGGAAACTCCTTTGTTC
1 TCGGGTCGGGTCTCGTGTGGAAACTCCTTTGTTC
598750 TCGGGTCGGGTCTCGTGTGGAAACTCCTTTGTTC
1 TCGGGTCGGGTCTCGTGTGGAAACTCCTTTGTTC
598784 TCGGGTCG
1 TCGGGTCG
598792 ATCGGTGGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.08, C:0.24, G:0.34, T:0.34
Consensus pattern (34 bp):
TCGGGTCGGGTCTCGTGTGGAAACTCCTTTGTTC
Found at i:599754 original size:16 final size:16
Alignment explanation
Indices: 599733--599763 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
599723 ACATGTGGCA
599733 TGACACATGACATCAG
1 TGACACATGACATCAG
599749 TGACACATGACATCA
1 TGACACATGACATCA
599764 TTAATTTGGA
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:0.26, G:0.16, T:0.19
Consensus pattern (16 bp):
TGACACATGACATCAG
Found at i:600372 original size:29 final size:29
Alignment explanation
Indices: 600334--600390 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
600324 GATTTTTTAG
* *
600334 TTTAACCAAAATAACTAAATTTTAAAAAA
1 TTTAAACAAAAAAACTAAATTTTAAAAAA
*
600363 TTTAAACAAAAAAATTAAATTTTAAAAA
1 TTTAAACAAAAAAACTAAATTTTAAAAA
600391 TAAGAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (29 bp):
TTTAAACAAAAAAACTAAATTTTAAAAAA
Found at i:601126 original size:14 final size:14
Alignment explanation
Indices: 601107--601136 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
601097 TAGATCTGAA
601107 TTTTTTTCTTTTCT
1 TTTTTTTCTTTTCT
601121 TTTTTTTCTTTTCT
1 TTTTTTTCTTTTCT
601135 TT
1 TT
601137 AATTTACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTTCTTTTCT
Found at i:601304 original size:23 final size:23
Alignment explanation
Indices: 601267--601310 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
601257 ACACGTTTTT
601267 TTGTTTTCTTTATTGATCATTTGG
1 TTGTTTTCTTTATTGAT-ATTTGG
601291 TTGTTTT-TTTATTGATATTT
1 TTGTTTTCTTTATTGATATTT
601311 TTTCAGGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.68
Consensus pattern (23 bp):
TTGTTTTCTTTATTGATATTTGG
Found at i:604533 original size:2 final size:2
Alignment explanation
Indices: 604526--604553 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
604516 AAAGGTCTAA
604526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
604554 CTTATATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:604735 original size:24 final size:24
Alignment explanation
Indices: 604707--604773 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 24
604697 TCAGTATCGA
604707 GTTTATTTCTATAATAATCATAGT
1 GTTTATTTCTATAATAATCATAGT
*
604731 GTTTATTATATTTATATAATAATCATAGT
1 G----TT-TATTTCTATAATAATCATAGT
604760 GTTTATTTCTATAA
1 GTTTATTTCTATAA
604774 ATGATCAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
24 11 0.31
25 2 0.06
28 2 0.06
29 21 0.58
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.52
Consensus pattern (24 bp):
GTTTATTTCTATAATAATCATAGT
Found at i:604742 original size:29 final size:29
Alignment explanation
Indices: 604710--604766 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
604700 GTATCGAGTT
*
604710 TATTTCTATAATAATCATAGTGTTTATTA
1 TATTTATATAATAATCATAGTGTTTATTA
604739 TATTTATATAATAATCATAGTGTTTATT
1 TATTTATATAATAATCATAGTGTTTATT
604767 TCTATAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (29 bp):
TATTTATATAATAATCATAGTGTTTATTA
Found at i:608362 original size:10 final size:10
Alignment explanation
Indices: 608325--608366 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
608315 GTTCTGTTTT
608325 TTTTTATTTAA
1 TTTTT-TTTAA
*
608336 TTTTTTAATAA
1 TTTTTT-TTAA
608347 TTTTTTTTAA
1 TTTTTTTTAA
608357 TTTTTTTTAA
1 TTTTTTTTAA
608367 AAATTCTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 14 0.50
11 14 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:615492 original size:2 final size:2
Alignment explanation
Indices: 615485--615519 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
615475 CTACGCTCTC
615485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
615520 ATAGAAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:616111 original size:3 final size:3
Alignment explanation
Indices: 616105--616132 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
616095 CTAAAAAAAT
616105 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
616133 TAATAAGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:619721 original size:15 final size:15
Alignment explanation
Indices: 619701--619740 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
619691 CTTGGTCATT
*
619701 TCTTCTTCATCATCC
1 TCTTCTTCACCATCC
*
619716 TCTTCTTCACCATCG
1 TCTTCTTCACCATCC
619731 TCTTCTTCAC
1 TCTTCTTCAC
619741 TTGAGATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.12, C:0.40, G:0.03, T:0.45
Consensus pattern (15 bp):
TCTTCTTCACCATCC
Found at i:619814 original size:15 final size:16
Alignment explanation
Indices: 619786--619828 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
619776 GCAACACATT
*
619786 TTTCTTTCTTTTCTTG
1 TTTCTTTCTCTTCTTG
619802 TTTCTTCTCTTCTTCTTG
1 TTTCTT-TC-TCTTCTTG
619820 -TTCTTTCTC
1 TTTCTTTCTC
619829 ATTTTCCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 2 0.08
16 8 0.33
17 7 0.29
18 7 0.29
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTCTTTCTCTTCTTG
Found at i:619827 original size:18 final size:17
Alignment explanation
Indices: 619786--619834 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
619776 GCAACACATT
619786 TTTCTT-TCTTTTCTTG
1 TTTCTTCTCTTTTCTTG
619802 TTTCTTCTCTTCTTCTTG
1 TTTCTTCTCTT-TTCTTG
619820 -TTCTTTCTCATTTTC
1 TTTC-TTCTC-TTTTC
619835 CATCATCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.21
17 7 0.24
18 14 0.48
19 2 0.07
ACGTcount: A:0.02, C:0.24, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTCTTCTCTTTTCTTG
Found at i:621288 original size:21 final size:21
Alignment explanation
Indices: 621262--621319 Score: 84
Period size: 19 Copynumber: 2.9 Consensus size: 21
621252 AAAATGATCG
621262 ATCATTTGGTCAAAGGGACCA
1 ATCATTTGGTCAAAGGGACCA
* *
621283 ATCATTT-TTC-AAGGGATCA
1 ATCATTTGGTCAAAGGGACCA
621302 ATCATTTGGTCAAAGGGA
1 ATCATTTGGTCAAAGGGA
621320 TCATTCCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 15 0.47
20 4 0.12
21 13 0.41
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (21 bp):
ATCATTTGGTCAAAGGGACCA
Found at i:621320 original size:21 final size:21
Alignment explanation
Indices: 621257--621322 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
621247 ATTGTAAAAT
*
621257 GATCGATCATTTGGTCAAAGG
1 GATCAATCATTTGGTCAAAGG
* *
621278 GACCAATCATTT-TTC-AAGG
1 GATCAATCATTTGGTCAAAGG
621297 GATCAATCATTTGGTCAAAGG
1 GATCAATCATTTGGTCAAAGG
621318 GATCA
1 GATCA
621323 TTCCTTTTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 15 0.39
20 4 0.11
21 19 0.50
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (21 bp):
GATCAATCATTTGGTCAAAGG
Done.