Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008982.1 Hibiscus syriacus cultivar Beakdansim tig00112344_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: 2253222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2151434 original size:80 final size:80
Alignment explanation
Indices: 2151343--2151492 Score: 300
Period size: 80 Copynumber: 1.9 Consensus size: 80
2151333 TATTTTAAAA
2151343 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2151408 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
2151423 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2151488 TTATT
66 TTATT
2151493 TTAAATAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:2151440 original size:134 final size:134
Alignment explanation
Indices: 2151298--2151663 Score: 705
Period size: 134 Copynumber: 2.7 Consensus size: 134
2151288 TTTTAAAATA
2151298 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
2151363 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
2151428 ATTG
131 ATTG
*
2151432 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
2151497 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
2151562 ATTG
131 ATTG
*
2151566 ATTTATTTTAAATAATCTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
*
2151631 ATAATTTATTAGTATGAATTGATTTATTTTAAA
66 ATAATTTATTAGTATGGATTGATTTATTTTAAA
2151664 TAATTTATTT
Statistics
Matches: 228, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 228 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (134 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
ATTG
Found at i:2151463 original size:32 final size:32
Alignment explanation
Indices: 2151422--2151529 Score: 146
Period size: 32 Copynumber: 3.7 Consensus size: 32
2151412 TATTGTAGTT
2151422 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2151454 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2151477 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2151508 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
2151530 ATATGGATTG
Statistics
Matches: 66, Mismatches: 0, Indels: 20
0.77 0.00 0.23
Matches are distributed among these distances:
22 14 0.21
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 36 0.55
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:2151480 original size:22 final size:22
Alignment explanation
Indices: 2151455--2151497 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2151445 AATTTATTAG
2151455 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2151477 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2151498 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2151561 original size:80 final size:80
Alignment explanation
Indices: 2151477--2151955 Score: 698
Period size: 80 Copynumber: 5.9 Consensus size: 80
2151467 TATTTTAAAA
2151477 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2151542 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
* *
2151557 TATGGATTGATTTATTTTAAATAATCTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
2151622 TTATTTTAAATAATTTA-TTAG
66 TTA--TT--AT--TGTAGTT-G
* * *
2151643 TATGAATTGATTTATTTTAAATAATTTATTTGTATGGATTAATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2151708 TTATTATT-TAGTTG
66 TTATTATTGTAGTTG
2151722 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA-ATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
2151785 TTATTTTAAATAATTTA-TTAG
66 TTA--TT--AT--TGTAGTT-G
* * *
2151806 TATGGACTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2151871 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
2151886 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2151951 TTATT
66 TTATT
2151956 TTAAATAATT
Statistics
Matches: 361, Mismatches: 19, Indels: 38
0.86 0.05 0.09
Matches are distributed among these distances:
77 13 0.04
78 3 0.01
79 52 0.14
80 139 0.39
81 4 0.01
82 6 0.02
83 3 0.01
84 56 0.16
85 5 0.01
86 80 0.22
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:2151602 original size:32 final size:31
Alignment explanation
Indices: 2151556--2151695 Score: 154
Period size: 32 Copynumber: 4.7 Consensus size: 31
2151546 TATTGTAGTT
*
2151556 GTATGGATTGATTTATTTTAAATAATCTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
2151588 GTATAGATTGATTTATTTT-AA-AA--TA-T-
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
2151614 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
*
2151642 GTATGAATTGATTTATTTTAAATAATTTATTT
1 GTATG-ATTGATTTATTTTAAATAATTTATTA
*
2151674 GTATGGATTAATTTATTTTAAA
1 GTAT-GATTGATTTATTTTAAA
2151696 ATATGGATTG
Statistics
Matches: 94, Mismatches: 3, Indels: 22
0.79 0.03 0.18
Matches are distributed among these distances:
22 14 0.15
23 2 0.02
24 2 0.02
26 3 0.03
27 2 0.02
28 3 0.03
30 2 0.02
31 3 0.03
32 62 0.66
33 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (31 bp):
GTATGATTGATTTATTTTAAATAATTTATTA
Found at i:2151639 original size:14 final size:14
Alignment explanation
Indices: 2151620--2151673 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
2151610 ATATGGATTG
2151620 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
2151634 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
2151652 ATTTATTTTAAATA
1 ATTTATTTTAAATA
2151666 ATTTATTT
1 ATTTATTT
2151674 GTATGGATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:2151757 original size:32 final size:32
Alignment explanation
Indices: 2151713--2151774 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
2151703 TTGATTTATT
2151713 ATTTAGTTGTATGGATTGATTTATTTTAAATA
1 ATTTAGTTGTATGGATTGATTTATTTTAAATA
2151745 ATTTA-TTAGTATGGATTGATTTATTTTAAA
1 ATTTAGTT-GTATGGATTGATTTATTTTAAA
2151775 ATGGATTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.07
32 27 0.93
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (32 bp):
ATTTAGTTGTATGGATTGATTTATTTTAAATA
Found at i:2151780 original size:20 final size:20
Alignment explanation
Indices: 2151755--2151794 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2151745 ATTTATTAGT
2151755 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
2151775 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
2151795 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (20 bp):
ATGGATTGATTTATTTTAAA
Found at i:2151817 original size:32 final size:32
Alignment explanation
Indices: 2151775--2151858 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
2151765 TTATTTTAAA
2151775 ATGGATTGATTTATTTTAAATAATTTATTAGT
1 ATGGATTGATTTATTTTAAATAATTTATTAGT
* *
2151807 ATGGACTGATTTATTTTAAATAATTTATTTGT
1 ATGGATTGATTTATTTTAAATAATTTATTAGT
*
2151839 ATAGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
2151859 ATATGGATTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (32 bp):
ATGGATTGATTTATTTTAAATAATTTATTAGT
Found at i:2151943 original size:22 final size:22
Alignment explanation
Indices: 2151918--2151960 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2151908 AATTTATTAG
2151918 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2151940 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2151961 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2152020 original size:31 final size:31
Alignment explanation
Indices: 2151985--2152043 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2151975 AGTTATATGG
* *
2151985 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
2152016 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
2152044 CTTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:2161046 original size:3 final size:3
Alignment explanation
Indices: 2161038--2161143 Score: 203
Period size: 3 Copynumber: 35.0 Consensus size: 3
2161028 TTACACTCTT
2161038 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
2161087 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2161135 ATA ATA ATA
1 ATA ATA ATA
2161144 GCTAAAAGTT
Statistics
Matches: 102, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 99 0.97
4 3 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2161425 original size:24 final size:24
Alignment explanation
Indices: 2161396--2161493 Score: 128
Period size: 24 Copynumber: 4.2 Consensus size: 24
2161386 ATAAGAATAA
*
2161396 TTTTATCTTTGTGACACGTTTATT
1 TTTTATCTTTATGACACGTTTATT
* *
2161420 TTTTATCTTTGTGGCACGTTTATT
1 TTTTATCTTTATGACACGTTTATT
*
2161444 TTTTATCTTTATGACAAGTTTA-T
1 TTTTATCTTTATGACACGTTTATT
* *
2161467 TTATGTCTTTATGACACGTTT-TT
1 TTTTATCTTTATGACACGTTTATT
2161490 TTTT
1 TTTT
2161494 GTTTTTTTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
23 23 0.35
24 42 0.65
ACGTcount: A:0.17, C:0.11, G:0.12, T:0.59
Consensus pattern (24 bp):
TTTTATCTTTATGACACGTTTATT
Found at i:2163354 original size:29 final size:30
Alignment explanation
Indices: 2163284--2163374 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 30
2163274 AATTGGTTTT
* * *
2163284 ATGGAAAATAATTT-ACGGAAAATGGATTAC
1 ATGGAAAAT-GTTTAACGTAAAATGAATTAC
* *
2163314 CTGGAAACTGTTTAACGTAAAATGAATTAC
1 ATGGAAAATGTTTAACGTAAAATGAATTAC
*
2163344 AT-GAAAATGTTTTACGTAAAATGAATTAC
1 ATGGAAAATGTTTAACGTAAAATGAATTAC
2163373 AT
1 AT
2163375 TTTCTGAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
29 30 0.58
30 22 0.42
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (30 bp):
ATGGAAAATGTTTAACGTAAAATGAATTAC
Found at i:2163372 original size:14 final size:14
Alignment explanation
Indices: 2163328--2163372 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2163318 AAACTGTTTA
2163328 ACGTAAAATGAATT
1 ACGTAAAATGAATT
* **
2163342 ACATGAAAATGTTTT
1 ACGT-AAAATGAATT
2163357 ACGTAAAATGAATT
1 ACGTAAAATGAATT
2163371 AC
1 AC
2163373 ATTTTCTGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (14 bp):
ACGTAAAATGAATT
Found at i:2163807 original size:19 final size:19
Alignment explanation
Indices: 2163771--2163821 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
2163761 TTGATATTTT
*
2163771 TATTAAAATGATACTAAAA
1 TATTAAAATAATACTAAAA
* *
2163790 TATTAAATTAATA-TTAAA
1 TATTAAAATAATACTAAAA
*
2163808 TAAATAAAATAATA
1 T-ATTAAAATAATA
2163822 TATTTCTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TATTAAAATAATACTAAAA
Found at i:2165484 original size:21 final size:21
Alignment explanation
Indices: 2165450--2165523 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
2165440 ATTATTACTA
*
2165450 TCGCAATGCGATTTT-CCAATT
1 TCGCATTGCGATTTTCCCAA-T
*
2165471 TCGCATTGCAATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
2165492 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
2165513 TCGCAATGCGA
1 TCGCATTGCGA
2165524 ATAAGTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 44 0.92
22 4 0.08
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:2165558 original size:41 final size:41
Alignment explanation
Indices: 2165513--2165727 Score: 156
Period size: 41 Copynumber: 5.3 Consensus size: 41
2165503 TTTTCCCAAT
* *
2165513 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTTGCAAAA
* * * * *
2165554 TCGCAATACG-ATAC-TGACTATCGCAACGCG-ATAATACAAAA
1 TCGCAATGCGAATACGT-A-AATCGCAATGCGAAT-TTGCAAAA
* * * *
2165595 TCGCAATGCGATTTACGT-ATTCGC-ATCGCG-ATTTTCATAAT
1 TCGCAATGCGA-ATACGTAAATCGCAAT-GCGAATTTGCA-AAA
* * *
2165636 TTGCAATGCGAATACGTAAATCGCAATGCGAATTAGAAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTTGCAAAA
* * * **
2165677 TCGCAATACAAATACGTAAATCGCAATGCGAATCTG-ACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTTGCAAAA
2165717 TCGCAATGCGA
1 TCGCAATGCGA
2165728 TTTACATAGT
Statistics
Matches: 132, Mismatches: 31, Indels: 23
0.71 0.17 0.12
Matches are distributed among these distances:
39 1 0.01
40 26 0.20
41 95 0.72
42 6 0.05
43 3 0.02
44 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (41 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATTTGCAAAA
Found at i:2165663 original size:20 final size:20
Alignment explanation
Indices: 2165513--2165709 Score: 100
Period size: 20 Copynumber: 9.7 Consensus size: 20
2165503 TTTTCCCAAT
*
2165513 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
** *
2165533 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
2165554 TCGCAATACG-ATAC-TGACTA
1 TCGCAATGCGAATACGT-A-AA
* *
2165574 TCGCAACGCGATAATAC-AAAA
1 TCGCAATGCG--AATACGTAAA
* *
2165595 TCGCAATGCGATTTACGT-AT
1 TCGCAATGCGA-ATACGTAAA
* * * *
2165615 TCGC-ATCGCGATTTTCATAAT
1 TCGCAAT-GCGA-ATACGTAAA
*
2165636 TTGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2165656 TCGCAATGCGAATTA-GAAAAA
1 TCGCAATGCGAA-TACG-TAAA
* *
2165677 TCGCAATACAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2165697 TCGCAATGCGAAT
1 TCGCAATGCGAAT
2165710 CTGACTATCG
Statistics
Matches: 133, Mismatches: 30, Indels: 28
0.70 0.16 0.15
Matches are distributed among these distances:
19 5 0.04
20 72 0.54
21 49 0.37
22 3 0.02
23 4 0.03
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2165758 original size:12 final size:12
Alignment explanation
Indices: 2165737--2165766 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2165727 ATTTACATAG
*
2165737 TTTCATAAATTA
1 TTTCACAAATTA
2165749 TTTCACAAATTA
1 TTTCACAAATTA
2165761 TTTCAC
1 TTTCAC
2165767 TCTAACATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTCACAAATTA
Found at i:2165823 original size:27 final size:27
Alignment explanation
Indices: 2165793--2165861 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
2165783 CATAATTTCT
2165793 TAAATTCATAATTTCACTCTAACATTC
1 TAAATTCATAATTTCACTCTAACATTC
2165820 TAAATTCATAATTTCACTCTAACATTC
1 TAAATTCATAATTTCACTCTAACATTC
2165847 TAAATTCATAATTTC
1 TAAATTCATAATTTC
2165862 TTAAATTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATTCATAATTTCACTCTAACATTC
Found at i:2165973 original size:39 final size:39
Alignment explanation
Indices: 2165916--2166021 Score: 128
Period size: 39 Copynumber: 2.7 Consensus size: 39
2165906 TATAATTTTC
*
2165916 AAATTATTTCAC-TCTAACATTCTAAATTCATAATTTCTT
1 AAATTATTTCACAT-TAACATTCTAAATTCATAATTTCAT
* **
2165955 AAATT-TTGTTACCA-TAACATTCTAAATTTTTAATTTCAT
1 AAATTATT-TCA-CATTAACATTCTAAATTCATAATTTCAT
2165994 AAATTATTTCACATTAACATTCTAAATT
1 AAATTATTTCACATTAACATTCTAAATT
2166022 ATTGTTTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
38 4 0.07
39 50 0.88
40 3 0.05
ACGTcount: A:0.38, C:0.15, G:0.01, T:0.46
Consensus pattern (39 bp):
AAATTATTTCACATTAACATTCTAAATTCATAATTTCAT
Found at i:2166108 original size:22 final size:22
Alignment explanation
Indices: 2166067--2166109 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2166057 TGAAATTTAA
* * *
2166067 TTATATTTTTTATTTTATTATT
1 TTATAATTTTTATCTAATTATT
2166089 TTATAATTTTTATCTAATTAT
1 TTATAATTTTTATCTAATTAT
2166110 GTAATTTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATAATTTTTATCTAATTATT
Found at i:2168839 original size:14 final size:14
Alignment explanation
Indices: 2168822--2168868 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
2168812 GAATGAACAT
*
2168822 AAACGAACATAATC
1 AAACGAACATAACC
2168836 AAACGAACATAACC
1 AAACGAACATAACC
* *
2168850 GAATGAACATAACC
1 AAACGAACATAACC
*
2168864 GAACG
1 AAACG
2168869 TTCACGAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.53, C:0.23, G:0.13, T:0.11
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:2176364 original size:43 final size:43
Alignment explanation
Indices: 2176315--2176664 Score: 255
Period size: 43 Copynumber: 8.1 Consensus size: 43
2176305 GAACAAAAAC
* *
2176315 CGCCGCAATAGGTCAATATCTATTA-CGACGTTTTTTGAACAAA
1 CGCCGCAAAAGGTCAATATCTA-TAGCGACGTTTTTGGAACAAA
* * *
2176358 CGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAATAAA
1 CGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGAACAAA
* * * * * * * *
2176401 CGCCGCAAAAAGT-TATGCTATATAGCGGCGTTTCTAGAAAAAA
1 CGCCGCAAAAGGTCAAT-ATCTATAGCGACGTTTTTGGAACAAA
* * *
2176444 AGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATACAAA
1 CGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGA-ACAAA
* * * * * * *
2176487 TGCCGTAAAAGGTC-AGACCTATAGTGGCGGTTTTGGACACAAA
1 CGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGA-ACAAA
* * * *
2176530 CGCCGTAAAAGGTC-AGACCTATAGTGACGTTTTTGGACACAAA
1 CGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGA-ACAAA
* * * * **
2176573 CGCCGCAAAATGTC-ATACCTATAACGGCGTTTTTTAACACAAA
1 CGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGA-ACAAA
* * * *
2176616 CGCCGCAAAAAGTC-AGACCTATAGCGGCGTTTTTGGATACAAA
1 CGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGA-ACAAA
2176659 CGCCGC
1 CGCCGC
2176665 TAATTACCTT
Statistics
Matches: 260, Mismatches: 43, Indels: 8
0.84 0.14 0.03
Matches are distributed among these distances:
42 21 0.08
43 239 0.92
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (43 bp):
CGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTGGAACAAA
Found at i:2176457 original size:129 final size:127
Alignment explanation
Indices: 2176292--2176664 Score: 367
Period size: 129 Copynumber: 2.9 Consensus size: 127
2176282 CCGCCAAAGT
* * *
2176292 TAGCGGCGTTTGAGAACAAAAACCGCCGCAATAGGTCAATATCTATTACGACGTTTTTTGA-ACA
1 TAGCGGCGTTTTAGAA-AAAAA--GCCGCAAAAGGTC-ATATCTATTACGGCGTTTTTTGACACA
* * * *
2176356 AACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-ATAAACGCCGCAAAAAGTTATG-C
62 AACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAAAAGTCA-GAC
2176419 TATA
125 -ATA
* * *
2176423 TAGCGGCGTTTCTAGAAAAAAAGCCGCAAAAGGTCAGATCTA-TAGCGGCGTTTTTGGATACAAA
1 TAGCGGCGTTT-TAGAAAAAAAGCCGCAAAAGGTCATATCTATTA-CGGCGTTTTTTGACACAAA
* * * * * * *
2176487 TGCCGTAAAAGGTCAGACCTATAGTGGCGGTTTTGGACACAAACGCCGTAAAAGGTCAGACCTA
64 CGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAAAAGTCAGACATA
* * * * * * * * *
2176551 TAGTGACGTTTTTGGACACAAACGCCGCAAAATGTCATACCTATAACGGCGTTTTTTAACACAAA
1 TAGCGGCG-TTTTAGA-AAAAAAGCCGCAAAAGGTCATATCTATTACGGCGTTTTTTGACACAAA
* *
2176616 CGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGC
64 CGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGC
2176665 TAATTACCTT
Statistics
Matches: 199, Mismatches: 35, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
127 2 0.01
128 48 0.24
129 128 0.64
130 1 0.01
131 16 0.08
132 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (127 bp):
TAGCGGCGTTTTAGAAAAAAAGCCGCAAAAGGTCATATCTATTACGGCGTTTTTTGACACAAACG
CCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAAAAGTCAGACATA
Found at i:2176565 original size:86 final size:86
Alignment explanation
Indices: 2176353--2176664 Score: 339
Period size: 86 Copynumber: 3.6 Consensus size: 86
2176343 CGTTTTTTGA
* * * * *
2176353 ACAAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-ATAAACGCCGCAAAAAGTTAT
1 ACAAACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCA-
2176417 G--CTATATAGCGGC-GTTTCTAGAA-
64 GACCTATA-A-CGGCGGTTT-T-GAAC
* * * *
2176440 A-AAAAGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAATGCCGTAAAAGGTCAGA
1 ACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGA
** *
2176504 CCTATAGTGGCGGTTTTGGAC
66 CCTATAACGGCGGTTTTGAAC
* * * * * *
2176525 ACAAACGCCGTAAAAGGTCAGACCTATAGTGACGTTTTTGGACACAAACGCCGCAAAATGTCATA
1 ACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGA
* *
2176590 CCTATAACGGCGTTTTTTAAC
66 CCTATAACGGCGGTTTTGAAC
*
2176611 ACAAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGC
1 ACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGC
2176665 TAATTACCTT
Statistics
Matches: 189, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
84 2 0.01
85 28 0.15
86 153 0.81
87 6 0.03
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (86 bp):
ACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGA
CCTATAACGGCGGTTTTGAAC
Found at i:2183016 original size:22 final size:22
Alignment explanation
Indices: 2182971--2183019 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2182961 AAATTTAGCA
* *
2182971 TTCAATACTGTTCACGGTATTG
1 TTCATTACTGTTCACGGTACTG
**
2182993 TTCATTACTGTTCATTGTACTG
1 TTCATTACTGTTCACGGTACTG
2183015 TTCAT
1 TTCAT
2183020 ACCGTATAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.47
Consensus pattern (22 bp):
TTCATTACTGTTCACGGTACTG
Found at i:2188752 original size:36 final size:36
Alignment explanation
Indices: 2188700--2188770 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
2188690 CTCTATCAAC
* *
2188700 CGAAAATGTTATATTCTTTATAACATTTTTGATTGT
1 CGAAAATGTTACATTCTTCATAACATTTTTGATTGT
*
2188736 CGAAAATGTTACATTCTTCATAGCATTTTTGATTG
1 CGAAAATGTTACATTCTTCATAACATTTTTGATTG
2188771 CGTCCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (36 bp):
CGAAAATGTTACATTCTTCATAACATTTTTGATTGT
Found at i:2188907 original size:19 final size:19
Alignment explanation
Indices: 2188885--2188922 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2188875 TTCAATATTT
*
2188885 TTATATTTT-ATCAATTTAA
1 TTAT-TTTTAATCAAATTAA
2188904 TTATTTTTAATCAAATTAA
1 TTATTTTTAATCAAATTAA
2188923 GATTCCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTTTTAATCAAATTAA
Found at i:2189089 original size:15 final size:15
Alignment explanation
Indices: 2189069--2189099 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2189059 ATTGACATGA
*
2189069 TATAATATATTATTT
1 TATAATATACTATTT
2189084 TATAATATACTATTT
1 TATAATATACTATTT
2189099 T
1 T
2189100 TTAAAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TATAATATACTATTT
Found at i:2195373 original size:25 final size:25
Alignment explanation
Indices: 2195345--2195407 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 25
2195335 TACTTGACAG
2195345 AGAATGAAGAAAAAGATGA-AGAAGA
1 AGAATGAAGAAAAAGAT-ACAGAAGA
2195370 AGAAATTAGAAGAAAAAGATACAGAAGA
1 AG-AA-T-GAAGAAAAAGATACAGAAGA
*
2195398 AGAAAGAAGA
1 AGAATGAAGA
2195408 CGAAGAAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
25 7 0.21
26 2 0.06
27 4 0.12
28 20 0.61
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (25 bp):
AGAATGAAGAAAAAGATACAGAAGA
Found at i:2199547 original size:22 final size:21
Alignment explanation
Indices: 2199522--2199562 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2199512 AGGAGAATAT
2199522 AAATCAAAACAAGAAAAAATGC
1 AAATCAAAACAA-AAAAAATGC
* *
2199544 AAATTAAAACGAAAAAAAT
1 AAATCAAAACAAAAAAAAT
2199563 ATTGTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.71, C:0.10, G:0.07, T:0.12
Consensus pattern (21 bp):
AAATCAAAACAAAAAAAATGC
Found at i:2201830 original size:16 final size:17
Alignment explanation
Indices: 2201799--2201833 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2201789 ACACCTAACG
*
2201799 TTTAGTTTTTGTTTCAT
1 TTTAGTTTTTGGTTCAT
2201816 TTTAG-TTTTGGTTCAT
1 TTTAGTTTTTGGTTCAT
2201832 TT
1 TT
2201834 AGTACCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.06, G:0.14, T:0.69
Consensus pattern (17 bp):
TTTAGTTTTTGGTTCAT
Found at i:2202628 original size:19 final size:19
Alignment explanation
Indices: 2202604--2202643 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2202594 GTTTAATTTG
2202604 TCTCGAGATTCCCTTGAAA
1 TCTCGAGATTCCCTTGAAA
2202623 TCTCGAGATTCCCTTGAAA
1 TCTCGAGATTCCCTTGAAA
2202642 TC
1 TC
2202644 GATAAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.33
Consensus pattern (19 bp):
TCTCGAGATTCCCTTGAAA
Found at i:2203113 original size:31 final size:31
Alignment explanation
Indices: 2203069--2203133 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
2203059 TGTTTCTCAA
* * *
2203069 ATTAGTTTATAGTTCATGTTTCAGGTTTGTG
1 ATTAATTTATAGTTCATGTTTAAGGTCTGTG
*
2203100 ATTAATTTCTAGTTCATGTTTAAGGTCTGTG
1 ATTAATTTATAGTTCATGTTTAAGGTCTGTG
2203131 ATT
1 ATT
2203134 GTCTCTTAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.51
Consensus pattern (31 bp):
ATTAATTTATAGTTCATGTTTAAGGTCTGTG
Found at i:2212931 original size:2 final size:2
Alignment explanation
Indices: 2212924--2212951 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2212914 TTTAATTCAA
2212924 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
2212952 GATGGTCCAA
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:2221035 original size:18 final size:19
Alignment explanation
Indices: 2220998--2221035 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2220988 TACGGAATGT
*
2220998 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GAGAATAA
2221018 AAGATTATCA-GAGAATAA
1 AAGATTATCAGGAGAATAA
2221036 GATTACTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGAGAATAA
Found at i:2221215 original size:37 final size:37
Alignment explanation
Indices: 2221181--2221250 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
2221171 TACAAATTGT
2221181 AAAATATTTATAT-ATTTTCTTTA-ATAAATTAAATTC
1 AAAATATTTATATAATTTTCTTTACA-AAATTAAATTC
* *
2221217 ATAATATTTATATAATTTTGTTTACAAAATTAAA
1 AAAATATTTATATAATTTTCTTTACAAAATTAAA
2221251 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 12 0.40
37 17 0.57
38 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (37 bp):
AAAATATTTATATAATTTTCTTTACAAAATTAAATTC
Found at i:2230216 original size:13 final size:13
Alignment explanation
Indices: 2230195--2230224 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2230185 CTTAGTTATG
*
2230195 AAAATTTAAATTT
1 AAAACTTAAATTT
2230208 AAAACTTAAATTT
1 AAAACTTAAATTT
2230221 AAAA
1 AAAA
2230225 ATCCGATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAACTTAAATTT
Found at i:2230380 original size:13 final size:13
Alignment explanation
Indices: 2230362--2230390 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2230352 GAATCAAAGA
2230362 AAAAAAATTAAAT
1 AAAAAAATTAAAT
2230375 AAAAAAATTAAAT
1 AAAAAAATTAAAT
2230388 AAA
1 AAA
2230391 TTAAGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAAATTAAAT
Found at i:2231699 original size:39 final size:36
Alignment explanation
Indices: 2231632--2231797 Score: 133
Period size: 39 Copynumber: 4.4 Consensus size: 36
2231622 ATATAAAAAG
* *
2231632 TTTTCAAAAACATATA-ATATATAAATTTTCAAAATGC
1 TTTTTAAAAAC-TATATAT-TATATATTTTCAAAATGC
* *
2231669 TTTTGTGAAAACTATATATTATACGTATTTTCAAAA-AC
1 TTTT-TAAAAACTATATATTATA--TATTTTCAAAATGC
* * * *
2231707 GTTTTAAAAAAT-TATA-TATATAATTTCAAAAATGT
1 TTTTTAAAAACTATATATTATATATTTTC-AAAATGC
2231742 TTTTTAAAAACTATATATTATATATATTTTCAAAATGTC
1 TTTTTAAAAACTATATA-T-TATATATTTTCAAAATG-C
*
2231781 TTTTAAAAAAACTATAT
1 TTTT-TAAAAACTATAT
2231798 TGTTGAGTTA
Statistics
Matches: 102, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
33 6 0.06
34 4 0.04
35 14 0.14
36 8 0.08
37 18 0.18
38 17 0.17
39 24 0.24
40 11 0.11
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (36 bp):
TTTTTAAAAACTATATATTATATATTTTCAAAATGC
Found at i:2231752 original size:72 final size:75
Alignment explanation
Indices: 2231626--2231776 Score: 197
Period size: 72 Copynumber: 2.1 Consensus size: 75
2231616 AATAATATAT
*
2231626 AAAAAGTTTTCAAAAACATATAATATATAAATTTTCAAAATGCTTTTGTGAAAACTATATATTAT
1 AAAAAGTTTTCAAAAACATATAATATATAAATTTTCAAAATGCTTTTGTAAAAACTATATATTAT
*
2231691 ACGTATTTTC
66 ACATATTTTC
*
2231701 AAAAACGTTTT-AAAAA-AT-T-ATATATATAA-TTTCAAAAATG-TTTTTTAAAAACTATATAT
1 AAAAA-GTTTTCAAAAACATATAATATATA-AATTTTC-AAAATGCTTTTGTAAAAACTATATAT
*
2231760 TATATATATTTTC
63 TATACATATTTTC
2231773 AAAA
1 AAAA
2231777 TGTCTTTTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
72 43 0.62
73 9 0.13
74 2 0.03
75 10 0.14
76 5 0.07
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (75 bp):
AAAAAGTTTTCAAAAACATATAATATATAAATTTTCAAAATGCTTTTGTAAAAACTATATATTAT
ACATATTTTC
Found at i:2232944 original size:28 final size:28
Alignment explanation
Indices: 2232904--2232961 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2232894 AAGATTTTTG
2232904 AAATCAAGTTTTGAAATTAGAAAATTAA
1 AAATCAAGTTTTGAAATTAGAAAATTAA
2232932 AAATCAAGTTTTGAAATTAGAAAATTAA
1 AAATCAAGTTTTGAAATTAGAAAATTAA
2232960 AA
1 AA
2232962 TTAGAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.31
Consensus pattern (28 bp):
AAATCAAGTTTTGAAATTAGAAAATTAA
Found at i:2232968 original size:21 final size:20
Alignment explanation
Indices: 2232917--2232971 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
2232907 TCAAGTTTTG
2232917 AAATTAGAAAATTAAAAATCA
1 AAATTAG-AAATTAAAAATCA
** * *
2232938 AGTTTTGAAATTAGAAAATTA
1 AAATTAGAAATTA-AAAATCA
2232959 AAATTAGAAATTA
1 AAATTAGAAATTA
2232972 CTCCCCCTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (20 bp):
AAATTAGAAATTAAAAATCA
Found at i:2233001 original size:21 final size:22
Alignment explanation
Indices: 2232969--2233014 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
2232959 AAATTAGAAA
2232969 TTACTCCCCCTTACTTTAACAC
1 TTACTCCCCCTTACTTTAACAC
2232991 TTACT-CCCCTTACTTTAACAC
1 TTACTCCCCCTTACTTTAACAC
2233012 TTA
1 TTA
2233015 TTCTTCTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.24, C:0.37, G:0.00, T:0.39
Consensus pattern (22 bp):
TTACTCCCCCTTACTTTAACAC
Found at i:2235285 original size:20 final size:20
Alignment explanation
Indices: 2235245--2235306 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
2235235 AGCAGAACCC
*
2235245 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATT-CCCT
** *
2235266 GTGGGGGGAATCGGTTCCCT
1 CAGGGGGGAATCGATTCCCT
2235286 CAGGGGGGAATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
2235306 C
1 C
2235307 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.23
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:2239133 original size:22 final size:21
Alignment explanation
Indices: 2239091--2239130 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2239081 GAGTTTGTTT
*
2239091 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2239112 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2239131 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2242025 original size:21 final size:21
Alignment explanation
Indices: 2242001--2242100 Score: 78
Period size: 21 Copynumber: 4.8 Consensus size: 21
2241991 GGAGGGACCA
2242001 CTTGAATGATGACAGGGGCTT
1 CTTGAATGATGACAGGGGCTT
* * **
2242022 CTTGAAAGGTGGGAGGGGCCTT
1 CTTGAATGATGACAGGGG-CTT
* *
2242044 -TTGAAGGATGATAGGGGCTT
1 CTTGAATGATGACAGGGGCTT
* * * *
2242064 CTTGAACGAT-AGGAGAGGCCT
1 CTTGAATGATGA-CAGGGGCTT
2242085 CTTGAATGATGACAGG
1 CTTGAATGATGACAGG
2242101 TGAATCGGGC
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
20 4 0.07
21 52 0.87
22 4 0.07
ACGTcount: A:0.25, C:0.13, G:0.37, T:0.25
Consensus pattern (21 bp):
CTTGAATGATGACAGGGGCTT
Found at i:2242033 original size:42 final size:41
Alignment explanation
Indices: 2241975--2242100 Score: 155
Period size: 42 Copynumber: 3.0 Consensus size: 41
2241965 CATGTGAATC
*
2241975 GGGC-TCTTGAACGGTGGGAGGGACCACTTGAATGATGACAG
1 GGGCTTCTTGAACGGTGGGAGGG-CCTCTTGAATGATGACAG
* * * *
2242016 GGGCTTCTTGAAAGGTGGGAGGGGCCTTTTGAAGGATGATAG
1 GGGCTTCTTGAACGGTGGGA-GGGCCTCTTGAATGATGACAG
* *
2242058 GGGCTTCTTGAACGATAGGAGAGGCCTCTTGAATGATGACAG
1 GGGCTTCTTGAACGGTGGGAG-GGCCTCTTGAATGATGACAG
2242100 G
1 G
2242101 TGAATCGGGC
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
41 5 0.07
42 63 0.89
43 3 0.04
ACGTcount: A:0.24, C:0.14, G:0.39, T:0.23
Consensus pattern (41 bp):
GGGCTTCTTGAACGGTGGGAGGGCCTCTTGAATGATGACAG
Found at i:2242457 original size:63 final size:62
Alignment explanation
Indices: 2242390--2242511 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 62
2242380 CGTAGAGCGA
* *
2242390 CTACCTCATCACGTAAAGTA-GATACCTCACCACGTAAAGCACCATTGTCATCGCGTAAAACCT
1 CTACCTCACCACGTAAAG-ACG-TACCTCACCACGTAAAGCACCATTGTCATCACGTAAAACCT
* * * * *
2242453 CTACCTCACCACTTAAAGACCGTACCTCATCACGTCATGCACCATTGTCGTCACGTAAA
1 CTACCTCACCACGTAAAGA-CGTACCTCACCACGTAAAGCACCATTGTCATCACGTAAA
2242512 GTACCGACCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 48 0.96
64 1 0.02
ACGTcount: A:0.31, C:0.34, G:0.12, T:0.23
Consensus pattern (62 bp):
CTACCTCACCACGTAAAGACGTACCTCACCACGTAAAGCACCATTGTCATCACGTAAAACCT
Found at i:2244257 original size:19 final size:19
Alignment explanation
Indices: 2244218--2244273 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
2244208 TCTGAAACTT
2244218 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCG-AAATG
2244238 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
2244257 AAAATCACAACGC-AAAT
1 AAAATCGCAACGCGAAAT
2244274 TCATTTTCGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 4 0.11
19 17 0.49
20 14 0.40
ACGTcount: A:0.52, C:0.21, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:2244315 original size:20 final size:20
Alignment explanation
Indices: 2244286--2244325 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2244276 ATTTTCGTAA
2244286 CGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
2244306 CGTTGTGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
2244326 TGATACGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.17, G:0.20, T:0.53
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:2244708 original size:22 final size:22
Alignment explanation
Indices: 2244665--2244711 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2244655 ATAGAGGGGG
* * **
2244665 TCGCCGGATATGTGGATGGATT
1 TCGCCGGAGATGGGGACAGATT
2244687 TCGCCGGAGATGGGGACAGATT
1 TCGCCGGAGATGGGGACAGATT
2244709 TCG
1 TCG
2244712 TCGTAGAGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.38, T:0.26
Consensus pattern (22 bp):
TCGCCGGAGATGGGGACAGATT
Found at i:2244864 original size:20 final size:20
Alignment explanation
Indices: 2244841--2244933 Score: 93
Period size: 20 Copynumber: 4.7 Consensus size: 20
2244831 ATAATATTCG
2244841 CGTTGCGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* *
2244861 CGTTACGATTTACCTATT-T
1 CGTTGCGATTTACATATTAT
* **
2244880 GAGTTGCGAATTTGAC-T-TTCG
1 -CGTTGCG-ATTT-ACATATTAT
2244901 CGTTGCGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
2244921 CGTTGCGATTTAC
1 CGTTGCGATTTAC
2244934 CTTTTCGCGT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
18 2 0.03
19 6 0.10
20 44 0.75
21 5 0.08
22 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:2244907 original size:60 final size:60
Alignment explanation
Indices: 2244837--2244953 Score: 191
Period size: 60 Copynumber: 1.9 Consensus size: 60
2244827 GAAAATAATA
2244837 TTCGCGTTGCGATTTACATATTATCGTTACGATTTACCTATTT-GAGTTGCGAATTTGACT
1 TTCGCGTTGCGATTTACATATTATCGTTACGATTTACCT-TTTCGAGTTGCGAATTTGACT
* * *
2244897 TTCGCGTTGCGATTTACATATTATCGTTGCGATTTACCTTTTCGCGTTGTGAATTTG
1 TTCGCGTTGCGATTTACATATTATCGTTACGATTTACCTTTTCGAGTTGCGAATTTG
2244954 GAAAATCGCG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
59 3 0.06
60 50 0.94
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (60 bp):
TTCGCGTTGCGATTTACATATTATCGTTACGATTTACCTTTTCGAGTTGCGAATTTGACT
Found at i:2244944 original size:20 final size:20
Alignment explanation
Indices: 2244837--2244945 Score: 80
Period size: 20 Copynumber: 5.5 Consensus size: 20
2244827 GAAAATAATA
* *
2244837 TTCGCGTTGCGATTTACATA
1 TTCGCGTTGCGATTTACCTT
** *
2244857 TTATCGTTACGATTTACCTAT
1 TTCGCGTTGCGATTTACCT-T
*
2244878 TT-GAGTTGCGAATTTGA-C-T
1 TTCGCGTTGCG-ATTT-ACCTT
* *
2244897 TTCGCGTTGCGATTTACATA
1 TTCGCGTTGCGATTTACCTT
**
2244917 TTATCGTTGCGATTTACCTT
1 TTCGCGTTGCGATTTACCTT
2244937 TTCGCGTTG
1 TTCGCGTTG
2244946 TGAATTTGGA
Statistics
Matches: 66, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
18 1 0.02
19 7 0.11
20 50 0.76
21 7 0.11
22 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.44
Consensus pattern (20 bp):
TTCGCGTTGCGATTTACCTT
Found at i:2244962 original size:21 final size:21
Alignment explanation
Indices: 2244938--2244977 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2244928 ATTTACCTTT
*
2244938 TCGCGTTGTGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
2244959 TCGCGTTGCGAATTTGGAA
1 TCGCGTTGCGAATTTGGAA
2244978 CCTGTGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAAAA
Found at i:2245026 original size:19 final size:19
Alignment explanation
Indices: 2244938--2245028 Score: 58
Period size: 20 Copynumber: 4.6 Consensus size: 19
2244928 ATTTACCTTT
* *
2244938 TCGCGTTGTGAATTTGGAAAA
1 TCGCGTTGCGAATTT-G-AGA
2244959 TCGCGTTGCGAATTTG-GAA
1 TCGCGTTGCGAATTTGAG-A
* * * *
2244978 CCTGTGTTGCGAAATTGAAGT
1 TC-GCGTTGCGAATTTG-AGA
*
2244999 TCGCATTGCGAATTTGAGA
1 TCGCGTTGCGAATTTGAGA
*
2245018 TCGTGTTGCGA
1 TCGCGTTGCGA
2245029 TTTTATTGGT
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
19 13 0.25
20 24 0.45
21 15 0.28
22 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (19 bp):
TCGCGTTGCGAATTTGAGA
Found at i:2250246 original size:2 final size:2
Alignment explanation
Indices: 2250239--2250277 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2250229 TGTATCACGC
2250239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2250278 CATGTCCGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2250784 original size:32 final size:33
Alignment explanation
Indices: 2250739--2250855 Score: 109
Period size: 30 Copynumber: 3.5 Consensus size: 33
2250729 TGTTAGATAA
*
2250739 GAAATAAT-AAATAAATATTAAATAAATCAAAG
1 GAAAAAATAAAATAAATATTAAATAAATCAAAG
*
2250771 G-AAAAATAAAATAAA-A-TAAATGAATCAAAG
1 GAAAAAATAAAATAAATATTAAATAAATCAAAG
*
2250801 GAAAAAGATAAAAAAAAAAAAATATT-AATAAATCAAAAG
1 GAAAAA-AT-----AAAATAAATATTAAATAAATC-AAAG
2250840 GAAAAAATAAAATAAA
1 GAAAAAATAAAATAAA
2250856 ATAAAAAATT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
30 14 0.20
31 10 0.14
32 10 0.14
33 7 0.10
37 7 0.10
38 10 0.14
39 11 0.16
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (33 bp):
GAAAAAATAAAATAAATATTAAATAAATCAAAG
Found at i:2250857 original size:24 final size:24
Alignment explanation
Indices: 2250808--2250862 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
2250798 AAGGAAAAAG
** *
2250808 ATAAAAAAAAAAAAATATTAATAA
1 ATAAAAAGGAAAAAATATAAATAA
*
2250832 ATCAAAAGGAAAAAATA-AAATAAA
1 ATAAAAAGGAAAAAATATAAAT-AA
2250856 ATAAAAA
1 ATAAAAA
2250863 ATTTTAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (24 bp):
ATAAAAAGGAAAAAATATAAATAA
Found at i:2250871 original size:38 final size:38
Alignment explanation
Indices: 2250772--2250862 Score: 107
Period size: 38 Copynumber: 2.3 Consensus size: 38
2250762 AAATCAAAGG
*
2250772 AAAAATAAAATAAAATA--AATGAATCAAAGGAAAAAGAT
1 AAAAA-AAAA-AAAATATTAATAAATCAAAGGAAAAAGAT
2250810 AAAAAAAAAAAAATATTAATAAATCAAAAGGAAAAA-AT
1 AAAAAAAAAAAAATATTAATAAATC-AAAGGAAAAAGAT
2250848 AAAATAAAATAAAAA
1 AAAA-AAAA-AAAAA
2250863 ATTTTAAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
36 6 0.13
37 4 0.09
38 18 0.38
39 14 0.30
40 5 0.11
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (38 bp):
AAAAAAAAAAAAATATTAATAAATCAAAGGAAAAAGAT
Found at i:2250897 original size:14 final size:14
Alignment explanation
Indices: 2250874--2250933 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 14
2250864 TTTTAAATTT
*
2250874 TAAAAGTAATAAAA
1 TAAAAATAATAAAA
2250888 TAAAAATAATAAGAA
1 TAAAAATAATAA-AA
2250903 GTAAAAAATAAATAAAA
1 -T-AAAAAT-AATAAAA
2250920 TAAATAA-AATAAAA
1 TAAA-AATAATAAAA
2250934 AACATACTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 18 0.45
15 5 0.12
16 4 0.10
17 8 0.20
18 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (14 bp):
TAAAAATAATAAAA
Found at i:2250910 original size:23 final size:24
Alignment explanation
Indices: 2250877--2250922 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
2250867 TAAATTTTAA
2250877 AAGTAATAAAATAAA-AATAATAAG
1 AAGTAATAAAATAAATAA-AATAAG
2250901 AAGTAA-AAAATAAATAAAATAA
1 AAGTAATAAAATAAATAAAATAA
2250923 ATAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (24 bp):
AAGTAATAAAATAAATAAAATAAG
Found at i:2250925 original size:27 final size:25
Alignment explanation
Indices: 2250885--2250935 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
2250875 AAAAGTAATA
2250885 AAATAAAAATAATAAGAAGTAAAAAAT
1 AAATAAAAATAATAA-AA-TAAAAAAT
2250912 AAAT-AAAATAAATAAAATAAAAAA
1 AAATAAAAAT-AATAAAATAAAAAA
2250936 CATACTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.30
26 7 0.30
27 9 0.39
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (25 bp):
AAATAAAAATAATAAAATAAAAAAT
Found at i:2250944 original size:26 final size:26
Alignment explanation
Indices: 2250885--2250946 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
2250875 AAAAGTAATA
*
2250885 AAATAAAAATAATAAGAAGTAAAAAAT
1 AAAT-AAAATAATAAGAAGTAAAAAAC
2250912 AAATAAAATAAATAA-AA-TAAAAAAC
1 AAATAAAAT-AATAAGAAGTAAAAAAC
*
2250937 ATACTAAAAT
1 A-AATAAAAT
2250947 TAAAAGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 8 0.26
26 14 0.45
27 9 0.29
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.19
Consensus pattern (26 bp):
AAATAAAATAATAAGAAGTAAAAAAC
Found at i:2250970 original size:21 final size:22
Alignment explanation
Indices: 2250944--2251000 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
2250934 AACATACTAA
*
2250944 AATTAAAAGGAAAAAATG-AAT
1 AATTAAAAGGAAAAAATGCAAG
* *
2250965 AATTAAAA-TAAAAAATGCTAG
1 AATTAAAAGGAAAAAATGCAAG
2250986 AATTAAAAAGGAAAA
1 AATT-AAAAGGAAAA
2251001 GGAAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.28
21 13 0.45
22 4 0.14
23 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.12, T:0.19
Consensus pattern (22 bp):
AATTAAAAGGAAAAAATGCAAG
Found at i:2250996 original size:43 final size:44
Alignment explanation
Indices: 2250918--2251000 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
2250908 AAATAAATAA
2250918 AATAAATAAAATAAAAAACATACTAAAATTAAAAGGAAAAAATG
1 AATAAATAAAATAAAAAACATACTAAAATTAAAAGGAAAAAATG
* * *
2250962 AATAATTAAAAT-AAAAA-ATGCTAGAATTAAAAAGGAAAA
1 AATAAATAAAATAAAAAACATACTAAAATT-AAAAGGAAAA
2251001 GGAAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 9 0.26
43 15 0.43
44 11 0.31
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.19
Consensus pattern (44 bp):
AATAAATAAAATAAAAAACATACTAAAATTAAAAGGAAAAAATG
Found at i:2252084 original size:1 final size:1
Alignment explanation
Indices: 2252078--2252126 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
2252068 TTGGACCTTT
* * * * *
2252078 AAAAAAAAACAAAGAAAAAATAAAAAAAAATAAAAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2252127 TATTAATAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.02, G:0.02, T:0.06
Consensus pattern (1 bp):
A
Found at i:2252104 original size:19 final size:19
Alignment explanation
Indices: 2252077--2252128 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 19
2252067 ATTGGACCTT
*
2252077 TAAAAAAAAACAAAGAAAAAA
1 TAAAAAAAAA-TAA-AAAAAA
2252098 TAAAAAAAAATAAAAAAAA
1 TAAAAAAAAATAAAAAAAA
2252117 TAAAAAAAAATA
1 TAAAAAAAAATA
2252129 TTAATAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 2 0.07
21 10 0.33
ACGTcount: A:0.87, C:0.02, G:0.02, T:0.10
Consensus pattern (19 bp):
TAAAAAAAAATAAAAAAAA
Found at i:2252105 original size:8 final size:9
Alignment explanation
Indices: 2252092--2252125 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
2252082 AAAAACAAAG
2252092 AAAAAATAAA
1 AAAAAAT-AA
2252102 AAAAAATAA
1 AAAAAATAA
2252111 AAAAAATAA
1 AAAAAATAA
2252120 AAAAAA
1 AAAAAA
2252126 ATATTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAATAA
Found at i:2252105 original size:10 final size:10
Alignment explanation
Indices: 2252077--2252128 Score: 79
Period size: 10 Copynumber: 5.2 Consensus size: 10
2252067 ATTGGACCTT
2252077 TAAAAAAAAA
1 TAAAAAAAAA
*
2252087 CAAAGAAAAAA
1 TAAA-AAAAAA
2252098 TAAAAAAAAA
1 TAAAAAAAAA
2252108 T-AAAAAAAA
1 TAAAAAAAAA
2252117 TAAAAAAAAA
1 TAAAAAAAAA
2252127 TA
1 TA
2252129 TTAATAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
9 9 0.24
10 20 0.53
11 9 0.24
ACGTcount: A:0.87, C:0.02, G:0.02, T:0.10
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:2252205 original size:35 final size:36
Alignment explanation
Indices: 2252165--2252559 Score: 232
Period size: 35 Copynumber: 11.2 Consensus size: 36
2252155 TTAATAATAA
*
2252165 TAAAAATATTTT-AAAACTATATTATATATATATAT
1 TAAAAATGTTTTCAAAACTATATTATATATATATAT
*
2252200 TAAAAATGTTTTCAAAACTATA-TATATATGTAT-T
1 TAAAAATGTTTTCAAAACTATATTATATATATATAT
*
2252234 TCAAAATGTTTTCAAAAACTATATTATATATATATATT
1 TAAAAATGTTTTC-AAAACTATATTATATATATATA-T
*
2252272 ATATTGAAAATATTTTCAAAA--ATA-TATAT-TATATAT
1 -TA---AAAATGTTTTCAAAACTATATTATATATATATAT
*** *
2252308 T-TTCATGTTTTC-AAA--A-A--CTATATATATAT
1 TAAAAATGTTTTCAAAACTATATTATATATATATAT
* *
2252337 TCAAAA-GTTTTCAAAAAAAATATATTATATATAT-T-T
1 TAAAAATGTTTTC---AAAACTATATTATATATATATAT
* *
2252373 TCAAAATGTTTTCAAAAACTATA-TAT-TATATATTTT
1 TAAAAATGTTTTC-AAAACTATATTATATATATA-TAT
* *
2252409 TCAAAATGTTTTCAAAAACTA-ATATATTATATATATTTT
1 TAAAAATGTTTTC-AAAACTATAT-TA-TATATATA-TAT
* * *
2252448 TCAAAATGTTTTTTTAAAAACTATA-TATATATAT-TTT
1 TAAAAATG---TTTTCAAAACTATATTATATATATATAT
**
2252485 TCCAAATGTTTTCAAAACTATA-TA-ATATATAT-T
1 TAAAAATGTTTTCAAAACTATATTATATATATATAT
* *
2252518 TCGAAAATG-TTTCAAAAACTATATTATA-ATATATAC
1 T-AAAAATGTTTTC-AAAACTATATTATATATATATAT
2252554 TAAAAA
1 TAAAAA
2252560 GCCCCAGACG
Statistics
Matches: 299, Mismatches: 23, Indels: 76
0.75 0.06 0.19
Matches are distributed among these distances:
28 3 0.01
29 15 0.05
30 5 0.02
31 7 0.02
33 20 0.07
34 46 0.15
35 55 0.18
36 52 0.17
37 25 0.08
38 14 0.05
39 29 0.10
40 2 0.01
41 11 0.04
42 15 0.05
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
TAAAAATGTTTTCAAAACTATATTATATATATATAT
Found at i:2252245 original size:34 final size:34
Alignment explanation
Indices: 2252167--2252552 Score: 319
Period size: 34 Copynumber: 10.9 Consensus size: 34
2252157 AATAATAATA
* *
2252167 AAAATATTTT-AAAACTATATTATATATATATATTA
1 AAAATGTTTTCAAAACTATA-TATATATATAT-TTC
*
2252202 AAAATGTTTTCAAAACTATATATATATGTATTTC
1 AAAATGTTTTCAAAACTATATATATATATATTTC
*
2252236 AAAATGTTTTCAAAAACTATATTATATATATATATTATATTG
1 AAAATGTTTTC-AAAAC-----TATATATATATA-TAT-TTC
* *
2252278 AAAATATTTTCAAAAATATATAT-TATATATTTTC
1 AAAATGTTTTCAAAACTATATATATATATA-TTTC
*
2252312 ---ATGTTTTCAAAA--A-CTATATATATA-TTC
1 AAAATGTTTTCAAAACTATATATATATATATTTC
**
2252339 AAAA-GTTTTCAAAAAAAATATATTATATATATTTTC
1 AAAATGTTTTC-AAAACTATATA-TATATATA-TTTC
*
2252375 AAAATGTTTTCAAAAACTATATATTATATATTTTTC
1 AAAATGTTTTC-AAAACTATATA-TATATATATTTC
2252411 AAAATGTTTTCAAAAACTAATATATTATATATATTTTTC
1 AAAATGTTTTC-AAAACT-ATATA-TATATATA--TTTC
* *
2252450 AAAATGTTTTTTTAAAAACTATATATATATATTTTTC
1 AAAATG---TTTTCAAAACTATATATATATATATTTC
*
2252487 CAAATGTTTTCAAAACTATATA-ATATATATTTC
1 AAAATGTTTTCAAAACTATATATATATATATTTC
2252520 GAAAATG-TTTCAAAAACTATATTATAATATATA
1 -AAAATGTTTTC-AAAACTATA-TAT-ATATATA
2252553 CTAAAAAGCC
Statistics
Matches: 297, Mismatches: 21, Indels: 64
0.78 0.05 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 13 0.04
30 5 0.02
31 11 0.04
32 1 0.00
33 16 0.05
34 54 0.18
35 31 0.10
36 45 0.15
37 53 0.18
39 17 0.06
40 16 0.05
41 13 0.04
42 16 0.05
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (34 bp):
AAAATGTTTTCAAAACTATATATATATATATTTC
Found at i:2252297 original size:30 final size:30
Alignment explanation
Indices: 2252263--2252366 Score: 104
Period size: 30 Copynumber: 3.4 Consensus size: 30
2252253 TATATTATAT
* *
2252263 ATATATATTATATTGAAAATATTTTCAAAA
1 ATATATATTATATTCAAAATGTTTTCAAAA
****
2252293 ATATATATTATATATTTTCATGTTTTCAAAA
1 ATATATATTATAT-TCAAAATGTTTTCAAAA
2252324 ACTATATA-TATATTCAAAA-GTTTTCAAAAA
1 A-TATATATTATATTCAAAATGTTTTC-AAAA
*
2252354 AAATATATTATAT
1 ATATATATTATAT
2252367 ATATTTTCAA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
29 11 0.18
30 25 0.42
31 18 0.30
32 6 0.10
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (30 bp):
ATATATATTATATTCAAAATGTTTTCAAAA
Found at i:2252298 original size:76 final size:74
Alignment explanation
Indices: 2252177--2252552 Score: 326
Period size: 76 Copynumber: 5.3 Consensus size: 74
2252167 AAAATATTTT
* * *
2252177 AAAACTATAT-TATATATATA-TA-TTAAAAATGTTTTCAAAACTATATATATATGTATTTCAAA
1 AAAACTATATATATATATATATTATTTCAAAATGTTTTCAAAAATATATATATATATATTTCAAA
2252239 ATGTTTTCA
66 ATGTTTTCA
* *
2252248 AAAACTATATTATATATATATATTATATTGAAAATATTTTCAAAAATATATAT-TATATATTTTC
1 AAAACTATA-TATATATATATATTAT-TTCAAAATGTTTTCAAAAATATATATATATATA-TTTC
2252312 ---ATGTTTTCA
63 AAAATGTTTTCA
*
2252321 AAAAC--------TATATATA-TA-TTCAAAA-GTTTTCAAAAAAAATATATTATATATATTTTC
1 AAAACTATATATATATATATATTATTTCAAAATGTTTTC-AAAAATATATA-TATATATA-TTTC
2252375 AAAATGTTTTCA
63 AAAATGTTTTCA
2252387 AAAAC--TATATAT-TATATATT-TTTCAAAATGTTTTCAAAAACTAATATATTATATATATTTT
1 AAAACTATATATATATATATATTATTTCAAAATGTTTTCAAAAA-T-ATATA-TATATATA--TT
*
2252448 TCAAAATGTTTTTTTA
61 TCAAAATG--TTTTCA
* *
2252464 AAAAC----TATATATATATATT-TTTCCAAATGTTTTCAAAACTATATA-ATATATATTTCGAA
1 AAAACTATATATATATATATATTATTTCAAAATGTTTTCAAAAATATATATATATATATTTC-AA
2252523 AATG-TTTCA
65 AATGTTTTCA
2252532 AAAACTATAT-TATAATATATA
1 AAAACTATATATAT-ATATATA
2252553 CTAAAAAGCC
Statistics
Matches: 260, Mismatches: 12, Indels: 65
0.77 0.04 0.19
Matches are distributed among these distances:
60 5 0.02
61 16 0.06
62 1 0.00
63 13 0.05
64 8 0.03
66 14 0.05
68 9 0.03
70 4 0.02
71 24 0.09
72 30 0.12
73 30 0.12
74 21 0.08
75 22 0.08
76 53 0.20
77 10 0.04
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (74 bp):
AAAACTATATATATATATATATTATTTCAAAATGTTTTCAAAAATATATATATATATATTTCAAA
ATGTTTTCA
Found at i:2252339 original size:27 final size:27
Alignment explanation
Indices: 2252301--2252378 Score: 70
Period size: 29 Copynumber: 2.9 Consensus size: 27
2252291 AAATATATAT
* **
2252301 TATATATTTTCATGTTTTCAAAAACTA
1 TATATATATTCATGTTTTCAAAAAAAA
*
2252328 TATATATATTCAAAAGTTTTCAAAAAAAA
1 TATATATATTC--ATGTTTTCAAAAAAAA
*
2252357 TATAT-TATAT-ATATTTTCAAAA
1 TATATATAT-TCATGTTTTCAAAA
2252379 TGTTTTCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
26 10 0.24
27 10 0.24
28 3 0.07
29 19 0.45
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (27 bp):
TATATATATTCATGTTTTCAAAAAAAA
Found at i:2252366 original size:102 final size:102
Alignment explanation
Indices: 2252167--2252545 Score: 305
Period size: 111 Copynumber: 3.6 Consensus size: 102
2252157 AATAATAATA
***
2252167 AAAATATTTT--AAAACTATATTATATATATATATTAAAAATGTTTTC-AAAACTATATATATAT
1 AAAATATTTTCAAAAACTATA-TAT-TATATAT-TTTTCAATGTTTTCAAAAAC--TATATATA-
* * *
2252229 GTATTTCAAAATGTTTTCAAAAACTATATTATATATATATATTATATTG
60 -TATTTCAAAATGTTTTCAAAAA--A-AATATAT-TATATA-TATTTTC
2252278 AAAATATTTTCAAAAA-TATATATTATATA-TTTTC-ATGTTTTCAAAAACTATATATATA-TTC
1 AAAATATTTTCAAAAACTATATATTATATATTTTTCAATGTTTTCAAAAACTATATATATATTTC
2252339 AAAA-GTTTTCAAAAAAAATATATTATATATATTTTC
66 AAAATGTTTTCAAAAAAAATATATTATATATATTTTC
*
2252375 AAAATGTTTTCAAAAACTATATATTATATATTTTTCAAAATGTTTTCAAAAACTAATATATTATA
1 AAAATATTTTCAAAAACTATATATTATATATTTTTC--AATGTTTTCAAAAAC-----TA-TATA
*** *
2252440 TATATTTTTCAAAATGTTTTTTTAAAAACTATA-TATATATATTTTTC
58 TATA--TTTCAAAATGTTTTCAAAAAAAATATATTATATATA-TTTTC
* * * ***
2252487 CAAATGTTTTC-AAAACTATATAATATATATTTCGAAAATG-TTTCAAAAACTATAT-TATA
1 AAAATATTTTCAAAAACTATATATTATATATTT-TTCAATGTTTTCAAAAACTATATATATA
2252546 ATATATACTA
Statistics
Matches: 232, Mismatches: 16, Indels: 49
0.78 0.05 0.16
Matches are distributed among these distances:
97 20 0.09
98 19 0.08
99 11 0.05
100 1 0.00
102 29 0.12
103 10 0.04
104 4 0.02
106 8 0.03
107 10 0.04
108 15 0.06
109 10 0.04
110 10 0.04
111 48 0.21
112 33 0.14
113 4 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (102 bp):
AAAATATTTTCAAAAACTATATATTATATATTTTTCAATGTTTTCAAAAACTATATATATATTTC
AAAATGTTTTCAAAAAAAATATATTATATATATTTTC
Found at i:2252552 original size:37 final size:35
Alignment explanation
Indices: 2252258--2252552 Score: 285
Period size: 37 Copynumber: 8.4 Consensus size: 35
2252248 AAAACTATAT
* *
2252258 TATATATATATATTATATTGAAAATATTTTCAAAAA-
1 TATATATATATA-TAT-TTCAAAATGTTTTCAAAAAC
2252294 TATATAT-TATATATTTTC---ATGTTTTCAAAAAC
1 TATATATATATATA-TTTCAAAATGTTTTCAAAAAC
*
2252326 ----TATATATATA-TTCAAAA-GTTTTCAAAAAA
1 TATATATATATATATTTCAAAATGTTTTCAAAAAC
*
2252355 AATATATTATATATATTTTCAAAATGTTTTCAAAAAC
1 TATATA-TATATATA-TTTCAAAATGTTTTCAAAAAC
*
2252392 TATATATTATATATTTTTCAAAATGTTTTCAAAAAC
1 TATATA-TATATATATTTCAAAATGTTTTCAAAAAC
*
2252428 TAATATATTATATATATTTTTCAAAATGTTTTTTTAAAAAC
1 T-ATATA-TATATATA--TTTCAAAATG--TTTTCAAAAAC
* *
2252469 TATATATATATATTTTTCCAAATGTTTTC-AAAAC
1 TATATATATATATATTTCAAAATGTTTTCAAAAAC
2252503 TATATA-ATATATATTTCGAAAATG-TTTCAAAAAC
1 TATATATATATATATTTC-AAAATGTTTTCAAAAAC
2252537 TATATTATAATATATA
1 TATA-TAT-ATATATA
2252553 CTAAAAAGCC
Statistics
Matches: 222, Mismatches: 13, Indels: 47
0.79 0.05 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 17 0.08
30 1 0.00
31 12 0.05
33 16 0.07
34 37 0.17
35 11 0.05
36 36 0.16
37 53 0.24
39 17 0.08
40 5 0.02
41 11 0.05
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (35 bp):
TATATATATATATATTTCAAAATGTTTTCAAAAAC
Done.