Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 31
Found at i:1685180 original size:80 final size:80
Alignment explanation
Indices: 1685037--1685304 Score: 419
Period size: 80 Copynumber: 3.3 Consensus size: 80
1685027 GCAATCCATA
* * *
1685037 ATTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCCTATTTTAAAATAA
1 ATTTAAAATAAATCAATCCATACAACTACA--A--T--AATAAATCAATCCATATTTTAAAATAA
1685102 ATCAATCCATACTAATAAATT
60 ATCAATCCATACTAATAAATT
1685123 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
1 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
**
1685188 TGATACTAATAAATT
66 CCATACTAATAAATT
*
1685203 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCATATTTTAAAATAAATCAAT
1 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
*
1685268 CCATACAAATAAATT
66 CCATACTAATAAATT
1685283 ATTTAAAATAAATCAATCCATA
1 ATTTAAAATAAATCAATCCATA
1685305 TTTTAAAATA
Statistics
Matches: 173, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
80 143 0.83
82 1 0.01
84 1 0.01
86 28 0.16
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.32
Consensus pattern (80 bp):
ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
CCATACTAATAAATT
Found at i:1685358 original size:15 final size:15
Alignment explanation
Indices: 1685329--1685445 Score: 128
Period size: 15 Copynumber: 7.4 Consensus size: 15
1685319 AATCCATACT
1685329 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1685343 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1685358 AATAAATTAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
1685380 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
1685395 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
1685410 AATACATTATTTTAA
1 AATAAATTATTTTAA
1685425 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1685440 AATAAA
1 AATAAA
1685446 CAACCTTATT
Statistics
Matches: 87, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.10
15 61 0.70
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1685371 original size:69 final size:67
Alignment explanation
Indices: 1685274--1685433 Score: 207
Period size: 67 Copynumber: 2.4 Consensus size: 67
1685264 CAATCCATAC
* *
1685274 AAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATTAATCCATACTAATAAATTA
1 AAATAAATTATTTTAAAATAAATTAATCCATATTTTAAAAT-AATTAAT-CATA-AAATAAATTA
1685338 -TTTA
63 TTTTA
* * **
1685342 AAATAAATTATTTTAAAATAAATTAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTT
1 AAATAAATTATTTTAAAATAAATTAATCCATATTTTAAAATAATTAATCATAAAATAAATTATTT
1685407 TA
66 TA
* *
1685409 TAATACATTATTTTAAAATAAATTA
1 AAATAAATTATTTTAAAATAAATTA
1685434 TTTTAAAATA
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
66 9 0.11
67 29 0.35
68 16 0.20
69 28 0.34
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (67 bp):
AAATAAATTATTTTAAAATAAATTAATCCATATTTTAAAATAATTAATCATAAAATAAATTATTT
TA
Found at i:1685378 original size:22 final size:22
Alignment explanation
Indices: 1685284--1685384 Score: 87
Period size: 22 Copynumber: 4.5 Consensus size: 22
1685274 AAATAAATTA
*
1685284 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATTAATCCATAT
1685306 TTTAAAATAAATTAATCCATA-
1 TTTAAAATAAATTAATCCATAT
* * * * **
1685327 CTAATAAATTATTTAAAATAAATTAT
1 TTTA-AAATAAATT--AATCCA-TAT
1685353 TTTAAAATAAATTAATCCATAT
1 TTTAAAATAAATTAATCCATAT
*
1685375 TTTATAATAA
1 TTTAAAATAA
1685385 TTTATTTTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
21 2 0.03
22 39 0.65
23 4 0.07
24 4 0.07
25 9 0.15
26 2 0.03
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAAATAAATTAATCCATAT
Found at i:1686248 original size:20 final size:20
Alignment explanation
Indices: 1686223--1686260 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1686213 ATTAGCGTTG
*
1686223 CGAAATTCGAGTTGCGAAAA
1 CGAAATCCGAGTTGCGAAAA
*
1686243 CGAAATCCGCGTTGCGAA
1 CGAAATCCGAGTTGCGAA
1686261 TTTGAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (20 bp):
CGAAATCCGAGTTGCGAAAA
Found at i:1686267 original size:20 final size:20
Alignment explanation
Indices: 1686253--1686301 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1686243 CGAAATCCGC
*
1686253 GTTGCGAATTTGAAAAATGA
1 GTTGCGAATTTGAAAAACGA
*
1686273 GTTGCGAATTTGAAAAATGA
1 GTTGCGAATTTGAAAAACGA
1686293 GTTGCGAAT
1 GTTGCGAAT
1686302 AGTTGTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.31
Consensus pattern (20 bp):
GTTGCGAATTTGAAAAACGA
Found at i:1686404 original size:99 final size:98
Alignment explanation
Indices: 1686233--1686465 Score: 333
Period size: 99 Copynumber: 2.4 Consensus size: 98
1686223 CGAAATTCGA
* * * *
1686233 GTTGCGAAAACGAAATCCGCGTTGCGAATTTGAAAAATGAGTTGCGAATTTGAAAAATGAGTTGC
1 GTTGCGAAAACGAAATTCGCGTTGCGATTTTGAAAAATCAATTGCGAATTTGAAAAATGAGTTGC
*
1686298 GAATAGTTGTGTTTACCTATATCGGTAATTAGC
66 AAATAGTTGTGTTTACCTATATCGGTAATTAGC
* * * *
1686331 GTTGCGAAAACGAAATTCGCGTTGCGATTTTGGAGAATCACATTGTGAATTTGAAAACTGAGTTG
1 GTTGCGAAAACGAAATTCGCGTTGCGATTTTGAAAAATCA-ATTGCGAATTTGAAAAATGAGTTG
1686396 CAAATAGTTGTGTTTACCTATATCGGTAATTAGC
65 CAAATAGTTGTGTTTACCTATATCGGTAATTAGC
***
1686430 GTTGCGAATTTGAGAA-TCGCGTTGCGATTTTGAAAA
1 GTTGCGAAAACGA-AATTCGCGTTGCGATTTTGAAAA
1686466 CTGTGTTGCA
Statistics
Matches: 119, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
98 35 0.29
99 82 0.69
100 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.32
Consensus pattern (98 bp):
GTTGCGAAAACGAAATTCGCGTTGCGATTTTGAAAAATCAATTGCGAATTTGAAAAATGAGTTGC
AAATAGTTGTGTTTACCTATATCGGTAATTAGC
Found at i:1687644 original size:18 final size:18
Alignment explanation
Indices: 1687621--1687661 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1687611 AATTATTAGA
1687621 AAATATAT-TAATTTTTAT
1 AAATATATAT-ATTTTTAT
1687639 AAATATATATATTTTTAT
1 AAATATATATATTTTTAT
1687657 AAATA
1 AAATA
1687662 AGATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATATATATTTTTAT
Found at i:1687667 original size:17 final size:18
Alignment explanation
Indices: 1687631--1687669 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1687621 AAATATATTA
*
1687631 ATTTTTATAAATATATAT
1 ATTTTTATAAATATAGAT
1687649 ATTTTTATAAATA-AGAT
1 ATTTTTATAAATATAGAT
1687666 ATTT
1 ATTT
1687670 ATTTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTTTATAAATATAGAT
Found at i:1688128 original size:14 final size:13
Alignment explanation
Indices: 1688093--1688137 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1688083 TAAAATAATA
1688093 ATAATAATTAAAAT
1 ATAA-AATTAAAAT
**
1688107 ATTGAATTAAACAT
1 ATAAAATTAAA-AT
1688121 ATAAAATTAAAAT
1 ATAAAATTAAAAT
1688134 ATAA
1 ATAA
1688138 CTAAACAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (13 bp):
ATAAAATTAAAAT
Found at i:1688142 original size:25 final size:28
Alignment explanation
Indices: 1688093--1688144 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
1688083 TAAAATAATA
*
1688093 ATAATAATTAAAATATTGAATTAAACAT
1 ATAATAATTAAAATATTGAACTAAACAT
1688121 ATAA-AATTAAAATA-T-AACTAAACA
1 ATAATAATTAAAATATTGAACTAAACA
1688145 ATGACTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 1 0.04
27 10 0.43
28 4 0.17
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (28 bp):
ATAATAATTAAAATATTGAACTAAACAT
Found at i:1689565 original size:11 final size:11
Alignment explanation
Indices: 1689549--1689615 Score: 91
Period size: 11 Copynumber: 6.0 Consensus size: 11
1689539 ACAGGGCCTG
1689549 TAATAATAATA
1 TAATAATAATA
1689560 TAATAATAATA
1 TAATAATAATA
1689571 TAATAATAATA
1 TAATAATAATA
1689582 T-ATAATAATAA
1 TAATAATAAT-A
* *
1689593 TAATATTTATAA
1 TAATAATAAT-A
1689605 TAATAATAATA
1 TAATAATAATA
1689616 ATTTTTAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
10 8 0.16
11 26 0.52
12 16 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAATAATAATA
Found at i:1689622 original size:21 final size:21
Alignment explanation
Indices: 1689549--1689632 Score: 99
Period size: 19 Copynumber: 4.3 Consensus size: 21
1689539 ACAGGGCCTG
*
1689549 TAATAATAATA-TAATAATAA
1 TAATAATAATATTTATAATAA
*
1689569 T-ATAATAATA-ATAT-ATAA
1 TAATAATAATATTTATAATAA
1689587 TAATAATAATATTTATAATAA
1 TAATAATAATATTTATAATAA
*
1689608 TAATAATAAT-TTT-TAAAAA
1 TAATAATAATATTTATAATAA
1689627 TAATAA
1 TAATAA
1689633 AAGAAAAAGG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
18 5 0.09
19 31 0.54
20 7 0.12
21 14 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATAATAATATTTATAATAA
Found at i:1689632 original size:3 final size:3
Alignment explanation
Indices: 1689549--1689617 Score: 97
Period size: 3 Copynumber: 23.3 Consensus size: 3
1689539 ACAGGGCCTG
1689549 TAA TAA TAA T-A TAA TAA TAA T-A TAA TAA TAA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
* *
1689593 TAA TAT TTA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1689618 TTTTAAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 52 0.88
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1691996 original size:60 final size:60
Alignment explanation
Indices: 1691901--1692027 Score: 204
Period size: 60 Copynumber: 2.1 Consensus size: 60
1691891 AACACACTAT
*
1691901 TCTATCTTGTTTCCATGAAGTACGAACATGCAAACTTATATCTT-ACCAAATTTTCATCTA
1 TCTATCTTGTTTCCATGAAGCACGAACATGCAAACTTATAT-TTGACCAAATTTTCATCTA
*
1691961 T-TATCTTGTTTCCATGGAAGCACGAACATGCAAACTTATATTTGACCAACTTTTCATCTA
1 TCTATCTTGTTTCCAT-GAAGCACGAACATGCAAACTTATATTTGACCAAATTTTCATCTA
1692021 TCTATCT
1 TCTATCT
1692028 ATCTATCTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
59 16 0.26
60 41 0.66
61 5 0.08
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (60 bp):
TCTATCTTGTTTCCATGAAGCACGAACATGCAAACTTATATTTGACCAAATTTTCATCTA
Found at i:1693702 original size:16 final size:17
Alignment explanation
Indices: 1693668--1693707 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1693658 TTATATGAAA
*
1693668 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
1693685 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
1693701 TGATATG
1 TGATATG
1693708 CCATATGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:1694309 original size:23 final size:23
Alignment explanation
Indices: 1694275--1694361 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
1694265 ACATATTATA
1694275 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1694298 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1694321 CGGTC-CTTCGG-GACAAAATTCTACG
1 TGG-CACTACGGTG-C--AATTCTACG
1694346 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
1694362 ATTTATATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 2 0.04
25 16 0.31
26 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1698698 original size:16 final size:17
Alignment explanation
Indices: 1698664--1698703 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1698654 TTATATGAAA
*
1698664 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
1698681 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
1698697 TGATATG
1 TGATATG
1698704 CCATATGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:1699303 original size:23 final size:23
Alignment explanation
Indices: 1699269--1699355 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
1699259 ACATATTATA
1699269 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1699292 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
1699315 CGGTCA-TTCGAG-ACAAAATTCTACG
1 TGG-CACTACG-GTGC--AATTCTACG
1699340 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
1699356 ATTTATATGA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
23 30 0.60
24 6 0.12
25 14 0.28
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1699976 original size:22 final size:23
Alignment explanation
Indices: 1699933--1699982 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1699923 CATAGATGGG
*
1699933 AATTTTTATAATGATGAAAGGTT
1 AATTTTTATAATGATGAAAGGTA
*
1699956 AATTTTTATAA-G-TTAATAGGTA
1 AATTTTTATAATGATGAA-AGGTA
1699978 AATTT
1 AATTT
1699983 CGAAAAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.12
22 10 0.42
23 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (23 bp):
AATTTTTATAATGATGAAAGGTA
Found at i:1702053 original size:32 final size:31
Alignment explanation
Indices: 1702015--1702136 Score: 156
Period size: 32 Copynumber: 3.8 Consensus size: 31
1702005 ACCTTTCTAA
*
1702015 CATACTAACATTCTAACTTTTATTCGATTGTT
1 CATACTAACATTCTAACTTTTATT-TATTGTT
*
1702047 CGTACTAACATTCTAACTTTTATTTTATTGTT
1 CATACTAACATTCTAACTTTTA-TTTATTGTT
*
1702079 CATACTAACATTCTAACTTTTACTTTATTATT
1 CATACTAACATTCTAACTTTTA-TTTATTGTT
*
1702111 CTTACTAAC-TTACTAACATTTTATTT
1 CATACTAACATT-CTAAC-TTTTATTT
1702137 TATTTCACAA
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
31 2 0.02
32 72 0.89
33 7 0.09
ACGTcount: A:0.29, C:0.18, G:0.03, T:0.50
Consensus pattern (31 bp):
CATACTAACATTCTAACTTTTATTTATTGTT
Found at i:1702084 original size:64 final size:65
Alignment explanation
Indices: 1702015--1702140 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 65
1702005 ACCTTTCTAA
*
1702015 CATACTAACATTCTAACTTTTA-TTCGATTGTTCGTACTAACATT-CTAAC-TTTTATTTTATTG
1 CATACTAACATTCTAACTTTTACTT-GATTATTCGTACTAAC-TTACTAACATTTTATTTTATTG
1702077 TT
64 TT
* *
1702079 CATACTAACATTCTAACTTTTACTTTATTATTCTTACTAACTTACTAACATTTTATTTTATT
1 CATACTAACATTCTAACTTTTACTTGATTATTCGTACTAACTTACTAACATTTTATTTTATT
1702141 TCACAAACTA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
63 2 0.04
64 40 0.71
65 14 0.25
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (65 bp):
CATACTAACATTCTAACTTTTACTTGATTATTCGTACTAACTTACTAACATTTTATTTTATTGTT
Found at i:1709997 original size:123 final size:122
Alignment explanation
Indices: 1709681--1710013 Score: 321
Period size: 123 Copynumber: 2.7 Consensus size: 122
1709671 ACAATGTCAT
* ** *
1709681 ATGAAAGCGGCCATAACTCTTCAATATGGATGAAAAGTGTCATCTTTAACACCAAA--TTATCGT
1 ATGAAAGCGGCCAGAACTCTTCAATATGGATGAGCAGTGTCATCTTCAACACCAAATTTTATC-T
** * ** *
1709744 CAGATTGACCCTATTTCCTTAACAAGAAGGAACAGTGTCATCTTTAGCAAACAAATTAC
65 -AGATTGACCAGATTTCCTCAACAAGAAGGAACAACGTCATCTTTAACAAACAAATTAC
** * * * * ** * * *
1709803 ATGAAAGCGGGTAGAACTCTTCAACACGAATGAGCAGAGTCATCTTCAACACCGTATTATCTCCA
1 ATGAAAGCGGCCAGAACTCTTCAATATGGATGAGCAGTGTCATCTTCAACACCAAATTTTATCTA
* * * * * *
1709868 TATTGACTAGATTTTTCTCAACGAGAAGGAACAACGTCATCTTTAACAAATAATTTATC
66 GATTGACCAGA-TTTCCTCAACAAGAAGGAACAACGTCATCTTTAACAAACAAATTA-C
*
1709927 -TGAAAGCGGCCAGATCTCTTCAATATGGATGAGCAGTGTCATCTTCAACACCAAATTTTATCTA
1 ATGAAAGCGGCCAGAACTCTTCAATATGGATGAGCAGTGTCATCTTCAACACCAAATTTTATCTA
* * **
1709991 GGTTGACCTGAAGTCCTCAACAA
66 GATTGACCAGATTTCCTCAACAA
1710014 AGTTACAGTG
Statistics
Matches: 160, Mismatches: 47, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
122 60 0.38
123 96 0.60
124 4 0.03
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (122 bp):
ATGAAAGCGGCCAGAACTCTTCAATATGGATGAGCAGTGTCATCTTCAACACCAAATTTTATCTA
GATTGACCAGATTTCCTCAACAAGAAGGAACAACGTCATCTTTAACAAACAAATTAC
Found at i:1711295 original size:32 final size:31
Alignment explanation
Indices: 1711259--1711356 Score: 121
Period size: 32 Copynumber: 3.2 Consensus size: 31
1711249 TTTTCTAACT
* *
1711259 TACTAATATTCTAAATTTTATTCTATTGTTCG
1 TACTAATATTCTAACTTTTATT-TATTGTTCA
1711291 TACTAATATTCTAACTTTTA-TT-TT-TTCA
1 TACTAATATTCTAACTTTTATTTATTGTTCA
* *
1711319 TACTAACATTCTAACTTTTACTTTATTGTTCT
1 TACTAATATTCTAACTTTTA-TTTATTGTTCA
1711351 TACTAA
1 TACTAA
1711357 CTTAACATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
28 22 0.38
29 2 0.03
30 3 0.05
31 3 0.05
32 28 0.48
ACGTcount: A:0.29, C:0.15, G:0.03, T:0.53
Consensus pattern (31 bp):
TACTAATATTCTAACTTTTATTTATTGTTCA
Found at i:1711547 original size:16 final size:16
Alignment explanation
Indices: 1711527--1711568 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1711517 TTTTTATTGT
1711527 ATTTATTTTTCCAGGA
1 ATTTATTTTTCCAGGA
* * *
1711543 CTTTAATTTT-CAGTA
1 ATTTATTTTTCCAGGA
1711558 ATTTATTTTTC
1 ATTTATTTTTC
1711569 TGCACCCTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 2
0.74 0.19 0.07
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.57
Consensus pattern (16 bp):
ATTTATTTTTCCAGGA
Found at i:1712165 original size:6 final size:5
Alignment explanation
Indices: 1712105--1712152 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
1712095 TTCTATCTTA
* * *
1712105 TTATT TTATT TTATT TTATT TTATC TCATT CTATTT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTA-TT TTATT TTATT TT
1712153 TATCTTTATC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
5 32 0.89
6 4 0.11
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:1714213 original size:20 final size:20
Alignment explanation
Indices: 1714175--1714227 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
1714165 AAATTTACGT
* *
1714175 ATCAAAATTACTATTAAATC
1 ATCAAAATTAATATCAAATC
* *
1714195 ATCACAATTAATATCAAATT
1 ATCAAAATTAATATCAAATC
**
1714215 AAAAAAATTAATA
1 ATCAAAATTAATA
1714228 CTAATAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (20 bp):
ATCAAAATTAATATCAAATC
Found at i:1715098 original size:28 final size:28
Alignment explanation
Indices: 1715066--1715143 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
1715056 ATTACTTAAA
*
1715066 TTAATTATTATTTTAATAAAAATGTAAT
1 TTAATTATTATTTTAATAAAAATATAAT
* * * *
1715094 TTAATTATAATTCTATTAAAATTATAAT
1 TTAATTATTATTTTAATAAAAATATAAT
* *
1715122 TAAATGATTAATTTTAAATAAA
1 TTAATTATT-ATTTT-AATAAA
1715144 TACTTATATT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
28 29 0.76
29 4 0.11
30 5 0.13
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (28 bp):
TTAATTATTATTTTAATAAAAATATAAT
Found at i:1716989 original size:22 final size:22
Alignment explanation
Indices: 1716934--1716990 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
1716924 GCGATTCTGG
1716934 CTATCGCATTGCGATTTTCCAA
1 CTATCGCATTGCGATTTTCCAA
* * *
1716956 AT-TCGCGTTGCGATTTTCCGA
1 CTATCGCATTGCGATTTTCCAA
*
1716977 CTATCGCAATGCGA
1 CTATCGCATTGCGA
1716991 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (22 bp):
CTATCGCATTGCGATTTTCCAA
Found at i:1717022 original size:20 final size:20
Alignment explanation
Indices: 1716975--1717045 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1716965 GCGATTTTCC
1716975 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
1716995 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGAATAT
* * * *
1717015 GACTATCGCAACGAGATTTT
1 GACTATCGCAATGCGAATAT
1717035 GACTATCGCAA
1 GACTATCGCAA
1717046 CGAGATTCTG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:1717043 original size:40 final size:39
Alignment explanation
Indices: 1716999--1717114 Score: 117
Period size: 40 Copynumber: 2.9 Consensus size: 39
1716989 GAATATGTAA
* *
1716999 ATCGCAATGCGAGTATGACTATCGCAACGAGATTTTGACT
1 ATCGCAACGCGA-TCTGACTATCGCAACGAGATTTTGACT
* * * *
1717039 ATCGCAACGAGATTCTGACTGTCGCAACGCGATTCTGACT
1 ATCGCAACGCGA-TCTGACTATCGCAACGAGATTTTGACT
* *
1717079 GTCACAACGCGATGCTGACTATCGCAAC-ATGATTTT
1 ATCGCAACGCGAT-CTGACTATCGCAACGA-GATTTT
1717115 CAAAGCGCCA
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
39 1 0.02
40 60 0.98
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (39 bp):
ATCGCAACGCGATCTGACTATCGCAACGAGATTTTGACT
Found at i:1717046 original size:20 final size:20
Alignment explanation
Indices: 1717014--1717106 Score: 123
Period size: 20 Copynumber: 4.7 Consensus size: 20
1717004 AATGCGAGTA
*
1717014 TGACTATCGCAACGAGATTT
1 TGACTATCGCAACGAGATTC
1717034 TGACTATCGCAACGAGATTC
1 TGACTATCGCAACGAGATTC
* *
1717054 TGACTGTCGCAACGCGATTC
1 TGACTATCGCAACGAGATTC
* * * *
1717074 TGACTGTCACAACGCGATGC
1 TGACTATCGCAACGAGATTC
1717094 TGACTATCGCAAC
1 TGACTATCGCAAC
1717107 ATGATTTTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (20 bp):
TGACTATCGCAACGAGATTC
Found at i:1717311 original size:22 final size:22
Alignment explanation
Indices: 1717286--1717328 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1717276 GGCGACATCC
1717286 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1717308 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
1717329 CGCCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1717802 original size:20 final size:20
Alignment explanation
Indices: 1717713--1717819 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
1717703 AGAATCACAA
*
1717713 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
1717732 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** ** *
1717751 TGCGATAGTCAAATTCGAGT
1 TGCGATTTTCATTTTCGCGT
** *
1717771 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
1717791 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
1717811 TGCGATTTT
1 TGCGATTTT
1717820 AAGTTTCAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
19 26 0.34
20 51 0.66
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1719752 original size:20 final size:20
Alignment explanation
Indices: 1719727--1719814 Score: 140
Period size: 20 Copynumber: 4.4 Consensus size: 20
1719717 TAGTTTACTT
1719727 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
1719747 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
1719767 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
1719787 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
1719807 TCACAACG
1 TCGCAACG
1719815 AAAGAATCGC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1719882 original size:20 final size:20
Alignment explanation
Indices: 1719857--1719971 Score: 169
Period size: 20 Copynumber: 5.8 Consensus size: 20
1719847 GCGATTCTCT
* **
1719857 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
1719877 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1719897 CGTTGC-ATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1719916 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
1719936 CGTTGCGATAGTTATTTTCA
1 CGTTGCGATAGTCATTTTCG
1719956 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
1719972 CGTGTTGCGA
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
19 19 0.22
20 69 0.78
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1719916 original size:39 final size:40
Alignment explanation
Indices: 1719857--1719971 Score: 169
Period size: 39 Copynumber: 2.9 Consensus size: 40
1719847 GCGATTCTCT
* ** *
1719857 CGTTGTGATAGTCAAATTCGCGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCG
1719897 CGTTGC-ATAGTCATTTTCGCGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCG
* *
1719936 CGTTGCGATAGTTATTTTCACGTTGCGATAGTCATT
1 CGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATT
1719972 CGTGTTGCGA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 36 0.53
40 32 0.47
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.41
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCG
Found at i:1719936 original size:59 final size:60
Alignment explanation
Indices: 1719857--1719971 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 60
1719847 GCGATTCTCT
* * *
1719857 CGTTGTGATAGTCAAATTCGCGTTGTGATAGTCATTTTCGCGTTGC-ATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCACGTTGCGATAGTCATTTTCG
** *
1719916 CGTTGCGATAGTCATTTTCGCGTTGCGATAGTTATTTTCACGTTGCGATAGTCATT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCACGTTGCGATAGTCATT
1719972 CGTGTTGCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
59 40 0.82
60 9 0.18
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.41
Consensus pattern (60 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCACGTTGCGATAGTCATTTTCG
Found at i:1719993 original size:38 final size:39
Alignment explanation
Indices: 1719877--1719982 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 39
1719867 GTCAAATTCG
* * * *
1719877 CGTTGTGATAGTCATTTTCGCGTTGC-ATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCGCGTTGCGATAGTTAGTTTCA
*
1719916 CGTTGCGATAGTCATTTTCGCGTTGCGATAGTTATTTTCA
1 CGTTGCGATAGTCA-TTTCGCGTTGCGATAGTTAGTTTCA
*
1719956 CGTTGCGATAGTCA-TTCGTGTTGCGAT
1 CGTTGCGATAGTCATTTCGCGTTGCGAT
1719983 TTTAAGTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
38 12 0.19
39 25 0.40
40 25 0.40
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.42
Consensus pattern (39 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATAGTTAGTTTCA
Found at i:1720558 original size:21 final size:21
Alignment explanation
Indices: 1720471--1720561 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
1720461 GACTCACCTG
*
1720471 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
1720493 T-ATCGTTCAAGCGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
* *
1720513 TCATC-CTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
1720533 CCATCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
1720554 TCATCGTT
1 TCATCGTT
1720562 GAAGGGTCCC
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
20 18 0.33
21 35 0.65
22 1 0.02
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1720573 original size:41 final size:41
Alignment explanation
Indices: 1720468--1720576 Score: 107
Period size: 41 Copynumber: 2.6 Consensus size: 41
1720458 CCCGACTCAC
* *
1720468 CTGTCATCGTTCAAGAGG--CCTCCCCTATCGTTCAAGCGGCCC
1 CTGTCATCGTTCAAG-GGTCCCT-CCC-ATCGTTCAAGAGGCCA
* * *
1720510 CTATCATC-CTCAAGAGTCCCCTCCCATCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGGGT-CCCTCCCATCGTTCAAGAGGCCA
*
1720551 CTGTCATCGTTGAAGGGTCCCTCCCA
1 CTGTCATCGTTCAAGGGTCCCTCCCA
1720577 ACATTCTAGA
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
40 1 0.02
41 34 0.63
42 16 0.30
43 3 0.06
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.24
Consensus pattern (41 bp):
CTGTCATCGTTCAAGGGTCCCTCCCATCGTTCAAGAGGCCA
Found at i:1722180 original size:20 final size:20
Alignment explanation
Indices: 1722157--1722194 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1722147 CACTAAACTC
*
1722157 AAAATCGCAATGCGAAAGAA
1 AAAATCGCAACGCGAAAGAA
*
1722177 AAAATTGCAACGCGAAAG
1 AAAATCGCAACGCGAAAG
1722195 TCAATTAGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.21, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAGAA
Found at i:1722264 original size:20 final size:20
Alignment explanation
Indices: 1722237--1722475 Score: 174
Period size: 20 Copynumber: 12.8 Consensus size: 20
1722227 GCGATTTTCT
* *
1722237 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
1722257 CCTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1722277 CGTTGTGATACTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1722297 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1722317 CGTTGTGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
1722331 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
1722350 CCGTTGCGATAGTCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
*
1722371 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
1722385 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1722405 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* * *
1722419 AGTTACGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1722439 CGTTGCGATAGTTGAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1722459 CATTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1722476 GAATGTGTAA
Statistics
Matches: 169, Mismatches: 30, Indels: 40
0.71 0.13 0.17
Matches are distributed among these distances:
14 33 0.20
16 3 0.02
18 3 0.02
19 1 0.01
20 127 0.75
21 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1722394 original size:34 final size:34
Alignment explanation
Indices: 1722351--1722447 Score: 167
Period size: 34 Copynumber: 2.9 Consensus size: 34
1722341 GTCAAATAGC
1722351 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1722385 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* * *
1722419 AGTTACGATAATCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT
1722448 AGTTGAATTC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:1722409 original size:54 final size:55
Alignment explanation
Indices: 1722276--1722413 Score: 210
Period size: 54 Copynumber: 2.5 Consensus size: 55
1722266 AATCAAATTC
* * *
1722276 GCGTTGTGATACTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTCT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
*
1722331 -CGTTGCGATAGTCAAA-TAGCCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-T
1 GCGTTGCGATAGTCAAATTCG-CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
1722384 GCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGAT
1722414 TTTTGAGTTA
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
53 3 0.04
54 70 0.93
55 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (55 bp):
GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:1722669 original size:118 final size:118
Alignment explanation
Indices: 1722461--1722693 Score: 448
Period size: 118 Copynumber: 2.0 Consensus size: 118
1722451 TGAATTCGCA
* *
1722461 TTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGCAATGTTCAAAC
1 TTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAAATCATAGCAATGTTCAAAC
1722526 TCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAGCG
66 TCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAGCG
1722579 TTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAAATCATAGCAATGTTCAAAC
1 TTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAAATCATAGCAATGTTCAAAC
1722644 TCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1722694 TACAACGTTT
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (118 bp):
TTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAAATCATAGCAATGTTCAAAC
TCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAGCG
Found at i:1724839 original size:12 final size:13
Alignment explanation
Indices: 1724809--1724841 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1724799 CCCGTGGCAT
1724809 TTTCTTCAGGGAC
1 TTTCTTCAGGGAC
*
1724822 TTTCTTCGGGGA-
1 TTTCTTCAGGGAC
1724834 TTTCTTCA
1 TTTCTTCA
1724842 TCTTCTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (13 bp):
TTTCTTCAGGGAC
Found at i:1725067 original size:24 final size:24
Alignment explanation
Indices: 1725033--1725086 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1725023 CTGAAACATC
1725033 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1725057 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1725081 ATCAAA
1 ATCAAA
1725087 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1725933 original size:20 final size:20
Alignment explanation
Indices: 1725909--1726049 Score: 124
Period size: 20 Copynumber: 7.0 Consensus size: 20
1725899 AAATTCAGTG
* *
1725909 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
1725929 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
*
1725949 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
* * *
1725969 TTGCGAT-TTCCATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
1725989 TTGCGATAGTCAGAAATCGCA
1 TTGCGATAGTCAG-AATCGCA
** * * *
1726010 ACGCGA-ATTTGGAAAATCGCA
1 TTGCGATA-GT-CAGAATCGCA
*
1726031 ATGCGATAGTCAGAATCGC
1 TTGCGATAGTCAGAATCGC
1726050 GTTACGAATC
Statistics
Matches: 98, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
19 1 0.01
20 70 0.71
21 25 0.26
22 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:1726015 original size:21 final size:21
Alignment explanation
Indices: 1725991--1726049 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1725981 TATTCGCATT
1725991 GCGATAGTCAGAAATCGCAAC
1 GCGATAGTCAGAAATCGCAAC
* ** *
1726012 GCGA-ATTTGGAAAATCGCAAT
1 GCGATAGTCAG-AAATCGCAAC
1726033 GCGATAGTCAG-AATCGC
1 GCGATAGTCAGAAATCGC
1726050 GTTACGAATC
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
20 9 0.31
21 17 0.59
22 3 0.10
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (21 bp):
GCGATAGTCAGAAATCGCAAC
Found at i:1726064 original size:41 final size:42
Alignment explanation
Indices: 1725984--1726065 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 42
1725974 ATTTCCATAT
* * *
1725984 TCGCATTGCGATAGTCAGAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATAGTCAGAAATCGCAACACGAATCTGGAAAA
***
1726026 TCGCAATGCGATAGTCAG-AATCGCGTTACGAATCTGGAAA
1 TCGCAATGCGATAGTCAGAAATCGCAACACGAATCTGGAAA
1726066 CTGATTTGCG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 17 0.50
42 17 0.50
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (42 bp):
TCGCAATGCGATAGTCAGAAATCGCAACACGAATCTGGAAAA
Found at i:1727120 original size:20 final size:20
Alignment explanation
Indices: 1727091--1727150 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
1727081 CAAGCATGTT
*
1727091 TAAAAGTCTATATTTAAATA
1 TAAAAATCTATATTTAAATA
1727111 TAAAAATCTATATTTAAATA
1 TAAAAATCTATATTTAAATA
1727131 TAAAAATCTATATTTAAATA
1 TAAAAATCTATATTTAAATA
1727151 CTTGAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAAATCTATATTTAAATA
Found at i:1733877 original size:146 final size:146
Alignment explanation
Indices: 1733605--1733898 Score: 466
Period size: 146 Copynumber: 2.0 Consensus size: 146
1733595 CTAAATACTC
** *
1733605 AATTCAGTTTATAAAATAGTTGACTCAATTTTTTCGATTTGAGTTTATAAAATTTAAATAAAGTC
1 AATTCAGTTTATAAAATAGTTGACTCAAAATTTTCGATATGAGTTTATAAAATTTAAATAAAGTC
* * * *
1733670 AAATTGAATTGAATTTTCGAGTTTTTGTTTAAATTTAATTATAAATATTTATCATATTATAATAT
66 AAATTGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
*
1733735 TATTTTATTCTAATTT
131 TATTTGATTCTAATTT
*
1733751 AATTCA-TCTTATAAAATAGTTGACTCAAAATTTTCGATATGAGTTTATAAAATTTAAATCAAGT
1 AATTCAGT-TTATAAAATAGTTGACTCAAAATTTTCGATATGAGTTTATAAAATTTAAATAAAGT
*
1733815 CGAAA-TGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTGTAAATATTTATAATACTATAAT
65 C-AAATTGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAAT
1733879 ATTATTTGATTCTAATTT
129 ATTATTTGATTCTAATTT
1733897 AA
1 AA
1733899 ATAGTTTTTT
Statistics
Matches: 136, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
145 1 0.01
146 132 0.97
147 3 0.02
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (146 bp):
AATTCAGTTTATAAAATAGTTGACTCAAAATTTTCGATATGAGTTTATAAAATTTAAATAAAGTC
AAATTGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
TATTTGATTCTAATTT
Found at i:1734873 original size:65 final size:64
Alignment explanation
Indices: 1734801--1734945 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 64
1734791 TGGCTGTCCA
* *
1734801 AGTGCATCGATGCACTAG-GGTATACATCGGTGCAT-AAATCAGCTTCGATGTTTCAAAATAACT
1 AGTGCATCGATGCA-T-GTCGTATACATCGGTGCATAAAATCA-CTTCGATGTTTCAAAATAACC
1734864 AG
63 AG
* * * * * * *
1734866 GGTGCATCGATGCATGTCTTGTGCATCGGTGCATAAAATCATTTCGATGTTTTAAAATAGCCAG
1 AGTGCATCGATGCATGTCGTATACATCGGTGCATAAAATCACTTCGATGTTTCAAAATAACCAG
1734930 AGTGCATCGATGCATG
1 AGTGCATCGATGCATG
1734946 GTTTGTGCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
63 1 0.01
64 48 0.71
65 19 0.28
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (64 bp):
AGTGCATCGATGCATGTCGTATACATCGGTGCATAAAATCACTTCGATGTTTCAAAATAACCAG
Found at i:1734901 original size:64 final size:63
Alignment explanation
Indices: 1734825--1734967 Score: 189
Period size: 64 Copynumber: 2.2 Consensus size: 63
1734815 CTAGGGTATA
* *
1734825 CATCGGTGCATAAATCAGCTTCGATGTTTCAAAATAACTAGGGTGCATCGATGCAT-GTCTTGTG
1 CATCGGTGCATAAATCA-CTTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGT-TTGTG
* * *
1734889 CATCGGTGCATAAAATCATTTCGATGTTTTAAAATAGCCAGAGTGCATCGATGCATGGTTTGTG
1 CATCGGTGCAT-AAATCACTTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGTTTGTG
* *
1734953 CATCAGTGAATAAAT
1 CATCGGTGCATAAAT
1734968 TGTATTCGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
63 4 0.06
64 58 0.83
65 8 0.11
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (63 bp):
CATCGGTGCATAAATCACTTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGTTTGTG
Found at i:1737550 original size:18 final size:18
Alignment explanation
Indices: 1737527--1737562 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1737517 GCAGTTTTGA
1737527 GAGTGGTG-TGAGAGAGAG
1 GAGTGGTGAT-AGAGAGAG
1737545 GAGTGGTGATAGAGAGAG
1 GAGTGGTGATAGAGAGAG
1737563 TTTTAGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.31, C:0.00, G:0.53, T:0.17
Consensus pattern (18 bp):
GAGTGGTGATAGAGAGAG
Found at i:1737674 original size:23 final size:22
Alignment explanation
Indices: 1737648--1737731 Score: 80
Period size: 24 Copynumber: 3.7 Consensus size: 22
1737638 CTGTTGAGTA
*
1737648 CATCGATGCATATTCAAGGAGTG
1 CATCGATGCACATTCAAGG-GTG
* * *
1737671 CATCGGTGCACCTTC-ATGGTG
1 CATCGATGCACATTCAAGGGTG
*
1737692 TATCGATGCACATTCATAGGGATG
1 CATCGATGCACATTCA-AGGG-TG
*
1737716 CATCGATGCACCTTCA
1 CATCGATGCACATTCA
1737732 TAGTGTATCG
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 15 0.31
24 16 0.33
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGGTG
Found at i:1737723 original size:24 final size:23
Alignment explanation
Indices: 1737648--1737746 Score: 91
Period size: 21 Copynumber: 4.4 Consensus size: 23
1737638 CTGTTGAGTA
*
1737648 CATCGATGCATATTCA-AGGAGTG
1 CATCGATGCACATTCATAGGA-TG
* *
1737671 CATCGGTGCACCTTCAT-GG-TG
1 CATCGATGCACATTCATAGGATG
*
1737692 TATCGATGCACATTCATAGGGATG
1 CATCGATGCACATTCATA-GGATG
*
1737716 CATCGATGCACCTTCATA-G-TG
1 CATCGATGCACATTCATAGGATG
*
1737737 TATCGATGCA
1 CATCGATGCA
1737747 TTATGCACAA
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
21 27 0.43
22 1 0.02
23 17 0.27
24 18 0.29
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.28
Consensus pattern (23 bp):
CATCGATGCACATTCATAGGATG
Found at i:1737728 original size:45 final size:44
Alignment explanation
Indices: 1737649--1737746 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 44
1737639 TGTTGAGTAC
* * *
1737649 ATCGATGCATATTCAAGGAGTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGAGTGCATCGATGCACCTTCATAGTGT
1737693 ATCGATGCACATTCATAGG-GATGCATCGATGCACCTTCATAGTGT
1 ATCGATGCACATTCA-AGGAG-TGCATCGATGCACCTTCATAGTGT
1737738 ATCGATGCA
1 ATCGATGCA
1737747 TTATGCACAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
44 15 0.31
45 34 0.69
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGATGCACCTTCATAGTGT
Found at i:1738690 original size:25 final size:25
Alignment explanation
Indices: 1738658--1738708 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1738648 TTGACCTATA
1738658 CAATTTAACATCCACACATTTACCT
1 CAATTTAACATCCACACATTTACCT
1738683 CAATTTAACATCCACACATTTACCT
1 CAATTTAACATCCACACATTTACCT
1738708 C
1 C
1738709 CTTCATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.31
Consensus pattern (25 bp):
CAATTTAACATCCACACATTTACCT
Found at i:1745108 original size:3 final size:3
Alignment explanation
Indices: 1745102--1745152 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
1745092 GTATTATTTG
* *
1745102 TAA TAA TAA TAA T-A TAA TAA TAG TAA TAG TAA TAA TAA TAA -AA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
1745149 TAA T
1 TAA T
1745153 TACTATCGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1746527 original size:64 final size:63
Alignment explanation
Indices: 1746438--1746602 Score: 190
Period size: 64 Copynumber: 2.6 Consensus size: 63
1746428 TGGTTGCCCA
* * * *
1746438 AGTGCATCGGTACATAGG-GTGTGCATCGGTGCATAAACCAGCTTCGATGTTTCAAAATAACCAG
1 AGTGCATCGATACAT-GGTTTGTGCATCGGTGCATAAACCA-ATTCGATATTTCAAAATAACCAG
* * * * *
1746502 GGTGCATCGATATAT-GTCTTGTGCATCGGTGCATAAAATCAATTCGATATTTTAAAATAGCCAG
1 AGTGCATCGATACATGGT-TTGTGCATCGGTGCAT-AAACCAATTCGATATTTCAAAATAACCAG
*
1746566 AGTGCATCGATGCATGGTTTGTGCATCGGTGCATAAA
1 AGTGCATCGATACATGGTTTGTGCATCGGTGCATAAA
1746603 TTGCATTCGA
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
62 1 0.01
63 3 0.04
64 74 0.87
65 7 0.08
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATACATGGTTTGTGCATCGGTGCATAAACCAATTCGATATTTCAAAATAACCAG
Found at i:1747216 original size:34 final size:35
Alignment explanation
Indices: 1747169--1747247 Score: 126
Period size: 34 Copynumber: 2.3 Consensus size: 35
1747159 GGGGTTGACC
*
1747169 ATGTAATTAAAGTATTTTGGAA-TTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTGGAATTTTG-GGTTTAGA
1747204 AT-TAATTGAAGTATTTTGGAATTTTGGGTTTAGA
1 ATGTAATTGAAGTATTTTGGAATTTTGGGTTTAGA
1747238 ATGTAATTGA
1 ATGTAATTGA
1747248 TGATTGTGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
34 28 0.68
35 13 0.32
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGGAATTTTGGGTTTAGA
Found at i:1751168 original size:14 final size:14
Alignment explanation
Indices: 1751149--1751176 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1751139 ACTAGCATCA
1751149 TCGTTGCTTTCAAG
1 TCGTTGCTTTCAAG
1751163 TCGTTGCTTTCAAG
1 TCGTTGCTTTCAAG
1751177 CACTGACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
TCGTTGCTTTCAAG
Found at i:1752962 original size:20 final size:20
Alignment explanation
Indices: 1752937--1752977 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1752927 GTATTATACT
*
1752937 AACGTAAATACATTTCCACA
1 AACGTAAATAAATTTCCACA
1752957 AACGTAAATAAATTTCCACA
1 AACGTAAATAAATTTCCACA
1752977 A
1 A
1752978 CAAACTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.24
Consensus pattern (20 bp):
AACGTAAATAAATTTCCACA
Found at i:1758635 original size:19 final size:20
Alignment explanation
Indices: 1758608--1758649 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
1758598 ATTTTTTAAT
1758608 TTTTAATTT-TCTTTTATTCA
1 TTTTAATTTAT-TTTTATTCA
*
1758628 TTTT-ATTTATTTTTATTTA
1 TTTTAATTTATTTTTATTCA
1758647 TTT
1 TTT
1758650 CGATCTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTAATTTATTTTTATTCA
Found at i:1761743 original size:23 final size:23
Alignment explanation
Indices: 1761709--1761764 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1761699 AACAAAAAGT
*
1761709 AAAAAGAAAAAATAAAAATAAAC
1 AAAAAGAAAAAAGAAAAATAAAC
* *
1761732 AAAAA-AAGAAAAGGAAAAT-AAG
1 AAAAAGAA-AAAAGAAAAATAAAC
1761754 AAAAAGAAAAA
1 AAAAAGAAAAA
1761765 CAAACAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (23 bp):
AAAAAGAAAAAAGAAAAATAAAC
Found at i:1761754 original size:14 final size:14
Alignment explanation
Indices: 1761702--1761764 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 14
1761692 AAAGAGCAAC
1761702 AAAAAGTAAAAAGAAA
1 AAAAAG-AAAAAG-AA
* *
1761718 AAATAAAAATAAACAA
1 AAA-AAGAA-AAAGAA
*
1761734 AAAAAGAAAAGGAA
1 AAAAAGAAAAAGAA
*
1761748 AATAAGAAAAAGAA
1 AAAAAGAAAAAGAA
1761762 AAA
1 AAA
1761765 CAAACAAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
14 18 0.49
15 4 0.11
16 10 0.27
17 5 0.14
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:1762857 original size:31 final size:32
Alignment explanation
Indices: 1762797--1762902 Score: 153
Period size: 31 Copynumber: 3.4 Consensus size: 32
1762787 AGGAACAATG
*
1762797 GGGGCATCTTTGAAGATTCAACATTAAATGTT
1 GGGGCATCTTTGAAGATTCAACATCAAATGTT
*
1762829 GGGGCACCTTTGAAGA-TCAACATCAAATGTT
1 GGGGCATCTTTGAAGATTCAACATCAAATGTT
* * *
1762860 GGGGCATTTTTG-AGATTCAACATCGAATATT
1 GGGGCATCTTTGAAGATTCAACATCAAATGTT
1762891 GGGGCATCTTTG
1 GGGGCATCTTTG
1762903 GGAATTCAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
30 3 0.05
31 48 0.73
32 15 0.23
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (32 bp):
GGGGCATCTTTGAAGATTCAACATCAAATGTT
Found at i:1763254 original size:64 final size:64
Alignment explanation
Indices: 1763096--1763401 Score: 411
Period size: 64 Copynumber: 4.8 Consensus size: 64
1763086 CAGCTTTTAG
* *
1763096 AGTCAATTTCAACTTCACAACGAATGATATTGAACTCAAAAAACAACTTTTCAATTTCATTC-A
1 AGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAACAACTTTTCAATTTCATTCAA
* * *
1763159 AGTCAATTTTAACTTCACACCGAAGGATATTGGACTCAACAAACAA-TATTTCAATTTCATTCAA
1 AGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAACAACT-TTTCAATTTCATTCAA
* * * *
1763223 AATCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAATAACTTTTCAGTTTCATT-AA
1 AGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAACAACTTTTCAATTTCATTCAA
* * * * *
1763286 GAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTGAACAAACAACTTTCCAGTTTCATTCAG
1 -AGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAACAACTTTTCAATTTCATTCAA
*
1763351 AGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCCAATCAATACAACT
1 AGTCAATTTCAACTTCACAACGAAGGATATTGAACT-CAA-CAA-ACAACT
1763402 CTGGATTGGA
Statistics
Matches: 217, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
62 1 0.00
63 57 0.26
64 146 0.67
65 4 0.02
66 3 0.01
67 6 0.03
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (64 bp):
AGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAACAACTTTTCAATTTCATTCAA
Found at i:1764461 original size:81 final size:81
Alignment explanation
Indices: 1764262--1764742 Score: 601
Period size: 81 Copynumber: 5.9 Consensus size: 81
1764252 TATCTATCAA
** * * * *
1764262 CAAAGACC-TCTGAGTTTAATTACATTCAGTTCAAAGGCA-CATCATTTGCAGCATAACTTAAGT
1 CAAAGACCTTC-GAGTTCGATTACACTCAGCTCAAAGGCACCATCATTTGCAGCATAACTCAAGG
*
1764325 CAAGAAGGGTTATCTGCCAAC
65 CGAGAAGGGTTATCTG----C
* * *
1764346 CAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACCATCATTTGCAGCATATA-TTAAGT
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACCATCATTTGCAGCATA-ACTCAAGG
* *
1764410 CGAGAAGGGATATCCGC
65 CGAGAAGGGTTATCTGC
* *
1764427 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGTACCATCATTTGCAACATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACCATCATTTGCAGCATAACTCAAGGC
1764492 GAGAAGGGTTATCTGC
66 GAGAAGGGTTATCTGC
* *
1764508 CAAAGACCTTCGAGTTCGATTATACTCAGCTCAAAGGCACCATCATTTTCAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACCATCATTTGCAGCATAACTCAAGGC
* *
1764573 GATAAGGGTTATCTTC
66 GAGAAGGGTTATCTGC
* * * * *
1764589 CAAAGACCTTCAAGTTTGATTACACTCAGCTCAAAGGCACCATCATTTGTAACAGAACTCAAGGC
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACCATCATTTGCAGCATAACTCAAGGC
1764654 GAGAAGGGTTATCTGC
66 GAGAAGGGTTATCTGC
* * * * * * *
1764670 CAAACACCTTCGAGCTCGGTT-CTACTAAACTCAAAGGCACCATCATTTACAGCATAGCTCAAGG
1 CAAAGACCTTCGAGTTCGATTAC-ACTCAGCTCAAAGGCACCATCATTTGCAGCATAACTCAAGG
1764734 CGAGAAGGG
65 CGAGAAGGG
1764743 CTATATGTTA
Statistics
Matches: 352, Mismatches: 40, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
80 2 0.01
81 279 0.79
84 33 0.09
85 37 0.11
86 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (81 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACCATCATTTGCAGCATAACTCAAGGC
GAGAAGGGTTATCTGC
Found at i:1766172 original size:30 final size:30
Alignment explanation
Indices: 1766137--1766204 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
1766127 GTCCTTTTAG
1766137 TTTCTGTTAATACTATTTTTAT-CTTTTAAA
1 TTTCTGTTAATACTATTTTTATAC-TTTAAA
** * *
1766167 TTTCTGTTTGTATTATTTTTGTACTTTAAA
1 TTTCTGTTAATACTATTTTTATACTTTAAA
1766197 TTTCTGTT
1 TTTCTGTT
1766205 TTTTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.21, C:0.09, G:0.07, T:0.63
Consensus pattern (30 bp):
TTTCTGTTAATACTATTTTTATACTTTAAA
Found at i:1771112 original size:24 final size:24
Alignment explanation
Indices: 1771076--1771148 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
1771066 GAGTCGAGGG
*
1771076 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGCAGTCCTTCGGGACAAA
*
1771100 TTCTACGTAGTCCTTCGGGACAAA
1 TTCTACGCAGTCCTTCGGGACAAA
* * * *
1771124 TTCTATGCGGTCTTTCAGGACAAA
1 TTCTACGCAGTCCTTCGGGACAAA
1771148 T
1 T
1771149 CTATGTGGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (24 bp):
TTCTACGCAGTCCTTCGGGACAAA
Found at i:1771162 original size:24 final size:24
Alignment explanation
Indices: 1771117--1771162 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1771107 TAGTCCTTCG
*
1771117 GGACAAATTCTATGCGGTCTTTCA
1 GGACAAATTCTATGCGGACTTTCA
*
1771141 GGACAAA-TCTATGTGGCACTTT
1 GGACAAATTCTATGCGG-ACTTT
1771163 GGTGCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (24 bp):
GGACAAATTCTATGCGGACTTTCA
Found at i:1778005 original size:26 final size:26
Alignment explanation
Indices: 1777968--1778027 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
1777958 CCCCTCTGGT
*
1777968 TTTGGACTTGAAACTTAGACTCCTTA
1 TTTGGACCTGAAACTTAGACTCCTTA
*
1777994 TTTGGACCTGAACCTTAGACTCCTTA
1 TTTGGACCTGAAACTTAGACTCCTTA
1778020 TTTGGACC
1 TTTGGACC
1778028 AAATAACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (26 bp):
TTTGGACCTGAAACTTAGACTCCTTA
Found at i:1778097 original size:22 final size:23
Alignment explanation
Indices: 1778072--1778128 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
1778062 TGAAATGAAA
*
1778072 ATAATAAATAATTTACAATA-AT
1 ATAATAAATAATATACAATACAT
*
1778094 ATAATAAATAATATACTATACTAT
1 ATAATAAATAATATACAATAC-AT
*
1778118 ATAATATATAA
1 ATAATAAATAA
1778129 ATATTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 18 0.60
24 12 0.40
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAATAAATAATATACAATACAT
Found at i:1778181 original size:37 final size:38
Alignment explanation
Indices: 1778133--1778434 Score: 185
Period size: 39 Copynumber: 8.0 Consensus size: 38
1778123 ATATAAATAT
*
1778133 TTTTTAAAAACTATATA-ATATATATATTTTCAAAATG
1 TTTTCAAAAACTATATATATATATATATTTTCAAAATG
* *
1778170 TTTTCAAAAACTATATATTATATATATATATTCAAAATA
1 TTTTCAAAAACTATATA-TATATATATATTTTCAAAATG
1778209 TTTTCAAAAACTATATTATATATATATATATATATATATTTTCAAAATG
1 TTTTCAAAAAC-----------TATATATATATATATATTTTCAAAATG
* *
1778258 TTTTCAAATATA-TATATATATATATATATATATATTATAAATA
1 TTTTCAAA-A-ACTATATATATATATATAT-T-T-TCA-AAATG
*
1778301 TTTTCAAAAAC--TAGATAT-TATATA---T----ATG
1 TTTTCAAAAACTATATATATATATATATTTTCAAAATG
*
1778329 TTTTCAAAAACTATATATATTATATATATTTTCAAAATA
1 TTTTCAAAAACTATATATA-TATATATATTTTCAAAATG
* * *
1778368 TTTTC-AAAAC------TATATATATGTTTTAAAAACG
1 TTTTCAAAAACTATATATATATATATATTTTCAAAATG
* *
1778399 TTTTTAAAAACTATATAT-TATATATGTTTTCAAAAT
1 TTTTCAAAAACTATATATATATATATATTTTCAAAAT
1778435 TTTATATAGT
Statistics
Matches: 209, Mismatches: 18, Indels: 76
0.69 0.06 0.25
Matches are distributed among these distances:
28 13 0.06
30 5 0.02
31 20 0.10
32 13 0.06
33 1 0.00
35 1 0.00
37 32 0.15
38 6 0.03
39 59 0.28
40 7 0.03
41 2 0.01
42 3 0.01
43 12 0.06
49 27 0.13
50 7 0.03
51 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (38 bp):
TTTTCAAAAACTATATATATATATATATTTTCAAAATG
Found at i:1778198 original size:39 final size:39
Alignment explanation
Indices: 1778127--1778384 Score: 188
Period size: 39 Copynumber: 6.6 Consensus size: 39
1778117 TATAATATAT
*
1778127 AAATATTTTTTAAAAACTATATA--ATATATATATTTTCA
1 AAATA-TTTTCAAAAACTATATATTATATATATATTTTCA
* *
1778165 AAATGTTTTCAAAAACTATATATTATATATATATATTCA
1 AAATATTTTCAAAAACTATATATTATATATATATTTTCA
1778204 AAATATTTTCAAAAACTATATTATATATATATATATATATATATTTTCA
1 AAATATTTTCAAAAAC---------TATATAT-TATATATATATTTTCA
*
1778253 AAATGTTTTCAAATATA-TATATATATATATATATATATATT-A
1 AAATATTTTCAAA-A-ACTATATAT-TATATATATAT-T-TTCA
* *
1778295 TAAATATTTTCAAAAACTAGATATTATATATATGTTTTCA
1 -AAATATTTTCAAAAACTATATATTATATATATATTTTCA
*
1778335 AAA-A----C---TA-TATATA-T-TATATATATTTTCA
1 AAATATTTTCAAAAACTATATATTATATATATATTTTCA
1778363 AAATATTTTC-AAAACTATATAT
1 AAATATTTTCAAAAACTATATAT
1778385 ATGTTTTAAA
Statistics
Matches: 179, Mismatches: 13, Indels: 57
0.72 0.05 0.23
Matches are distributed among these distances:
28 16 0.09
29 2 0.01
30 5 0.03
31 1 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 6 0.03
37 16 0.09
38 5 0.03
39 34 0.19
40 2 0.01
41 30 0.17
42 9 0.05
43 14 0.08
48 7 0.04
49 27 0.15
50 1 0.01
51 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.46
Consensus pattern (39 bp):
AAATATTTTCAAAAACTATATATTATATATATATTTTCA
Found at i:1778256 original size:49 final size:49
Alignment explanation
Indices: 1778181--1778327 Score: 200
Period size: 49 Copynumber: 3.1 Consensus size: 49
1778171 TTTCAAAAAC
*
1778181 TATATAT-TATATATATATATTCAAAATATTTTCAAAAACTATATTATA
1 TATATATATATATATATATTTTCAAAATATTTTCAAAAACTATATTATA
*
1778229 TATATATATATATATATATTTTCAAAATGTTTTC--AAA-TATA-TATA
1 TATATATATATATATATATTTTCAAAATATTTTCAAAAACTATATTATA
*
1778274 TATATATATATATATATATTAT--AAATATTTTCAAAAACTAGATATTATA
1 TATATATATATATATATATTTTCAAAATATTTTCAAAAACT--ATATTATA
1778323 TATAT
1 TATAT
1778328 GTTTTCAAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
43 9 0.10
45 28 0.32
46 5 0.06
47 3 0.03
48 10 0.11
49 33 0.38
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (49 bp):
TATATATATATATATATATTTTCAAAATATTTTCAAAAACTATATTATA
Found at i:1778272 original size:2 final size:2
Alignment explanation
Indices: 1778265--1778301 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1778255 ATGTTTTCAA
*
1778265 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1778302 TTTCAAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1778322 original size:26 final size:27
Alignment explanation
Indices: 1778289--1778365 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 27
1778279 ATATATATAT
1778289 ATATTATAAATATTTTCAAAAAC-TAG
1 ATATTATAAATATTTTCAAAAACATAG
* *
1778315 ATATTATATATATGTTTTCAAAAACTATAT
1 ATATTATA-A-ATATTTTCAAAAAC-ATAG
*
1778345 ATATTATATATATTTTCAAAA
1 ATATTATAAATATTTTCAAAA
1778366 TATTTTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
26 8 0.19
27 1 0.02
28 24 0.56
30 10 0.23
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (27 bp):
ATATTATAAATATTTTCAAAAACATAG
Found at i:1779819 original size:19 final size:19
Alignment explanation
Indices: 1779792--1779867 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 19
1779782 TTATTTTTAT
*
1779792 GTTAGTATTTTTTTAAATA
1 GTTATTATTTTTTTAAATA
1779811 GTTATTATTTTTATATTAATATA
1 GTTATTA-TTTT-T-TTAA-ATA
* *
1779834 TTATATTATTTTTTT-ATTA
1 GT-TATTATTTTTTTAAATA
*
1779853 ATTATTAATTTTTTT
1 GTTATT-ATTTTTTT
1779868 TTGCTAATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
18 4 0.09
19 17 0.36
20 5 0.11
21 3 0.06
22 5 0.11
23 8 0.17
24 5 0.11
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (19 bp):
GTTATTATTTTTTTAAATA
Found at i:1779868 original size:21 final size:23
Alignment explanation
Indices: 1779813--1779878 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
1779803 TTTAAATAGT
*
1779813 TATTATTTTTATATTAATATATTA
1 TATTATTTTTTTATTAAT-TATTA
1779837 TATTATTTTTTTATTAATTATTA
1 TATTATTTTTTTATTAATTATTA
**
1779860 -ATT-TTTTTTTGCTAATTAT
1 TATTATTTTTTTATTAATTAT
1779879 ATTGTTTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 14 0.36
22 3 0.08
23 5 0.13
24 17 0.44
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTATTTTTTTATTAATTATTA
Found at i:1779886 original size:21 final size:19
Alignment explanation
Indices: 1779833--1779886 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
1779823 ATATTAATAT
1779833 ATTATATTATTTTTTTATTA
1 ATTATATT-TTTTTTTATTA
**
1779853 ATTATTAATTTTTTTTTGCTA
1 ATTA-T-ATTTTTTTTTATTA
*
1779874 ATTATATTGTTTT
1 ATTATATTTTTTT
1779887 GTCTACAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 7 0.24
20 5 0.17
21 14 0.48
22 3 0.10
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.69
Consensus pattern (19 bp):
ATTATATTTTTTTTTATTA
Found at i:1780013 original size:17 final size:17
Alignment explanation
Indices: 1779991--1780044 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1779981 AATGTTAATA
1779991 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1780008 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1780025 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1780042 TTT
1 TTT
1780045 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1781556 original size:21 final size:21
Alignment explanation
Indices: 1781526--1781573 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1781516 GCAGGGGTAC
* *
1781526 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1781547 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1781568 ATGCCA
1 ATGCCA
1781574 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1781607 original size:21 final size:21
Alignment explanation
Indices: 1781581--1781621 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1781571 CCATCTCCGC
1781581 AGGGTTACATTCCGAGCCCGT
1 AGGGTTACATTCCGAGCCCGT
*
1781602 AGGGTTACATTCCTAGCCCG
1 AGGGTTACATTCCGAGCCCG
1781622 CCAGGTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (21 bp):
AGGGTTACATTCCGAGCCCGT
Found at i:1781628 original size:21 final size:21
Alignment explanation
Indices: 1781604--1781664 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
1781594 GAGCCCGTAG
*
1781604 GGTTACATTCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
1781625 GGTTACATGCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
*
1781646 AGTTACATGCCTAGCCCGC
1 GGTTACATGCCTAGCCCGC
1781665 AGGGTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.38, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTTACATGCCTAGCCCGCCA
Found at i:1781630 original size:42 final size:42
Alignment explanation
Indices: 1781583--1781664 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1781573 ATCTCCGCAG
* * * *
1781583 GGTTACATTCCGAGCCCG-TAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATGCCGAGCCCGCCA-AGTTACATGCCTAGCCCGCCA
*
1781625 GGTTACATGCCTAGCCCGCCAAGTTACATGCCTAGCCCGC
1 GGTTACATGCCGAGCCCGCCAAGTTACATGCCTAGCCCGC
1781665 AGGGTTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.20, C:0.35, G:0.23, T:0.22
Consensus pattern (42 bp):
GGTTACATGCCGAGCCCGCCAAGTTACATGCCTAGCCCGCCA
Found at i:1782229 original size:6 final size:6
Alignment explanation
Indices: 1782218--1782242 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1782208 TTCGAAATTT
1782218 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
1782243 TATTATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1782266 original size:40 final size:41
Alignment explanation
Indices: 1782190--1782272 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 41
1782180 AAATGTTTTT
* *
1782190 AAAATACAAATTATATTATTCGAAATTTAAAATAAAA-ATA
1 AAAATAAAAATAATATTATTCGAAATTTAAAATAAAATATA
**
1782230 AAAATAAAAATAATATTATTC-AAATTTAGATTTAAAATATA
1 AAAATAAAAATAATATTATTCGAAATTTA-AAATAAAATATA
1782271 AA
1 AA
1782273 TTATAGTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 7 0.19
40 25 0.68
41 5 0.14
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (41 bp):
AAAATAAAAATAATATTATTCGAAATTTAAAATAAAATATA
Found at i:1783495 original size:16 final size:17
Alignment explanation
Indices: 1783459--1783498 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1783449 AATATATTAC
*
1783459 AAATATATGTATTATCT
1 AAATATATGTATTATCA
*
1783476 AAATATATTTA-TATCA
1 AAATATATGTATTATCA
1783492 AAATATA
1 AAATATA
1783499 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (17 bp):
AAATATATGTATTATCA
Found at i:1784147 original size:18 final size:18
Alignment explanation
Indices: 1784112--1784171 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
1784102 TGAGTCCATT
* *
1784112 AAAAAAA-TAAATTTTAA
1 AAAAAAATTAAAATATAA
1784129 AAAAAAATTAAAATATAA
1 AAAAAAATTAAAATATAA
* * *
1784147 ATAAAATTTATAAATGTAGA
1 AAAAAAATTA-AAATATA-A
1784167 AAAAA
1 AAAAA
1784172 TTAGCTGGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 7 0.21
18 16 0.47
19 6 0.18
20 5 0.15
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAAAAATTAAAATATAA
Found at i:1786953 original size:16 final size:16
Alignment explanation
Indices: 1786932--1786963 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1786922 ACACTGCAGG
1786932 GTGTATCGGTACACTA
1 GTGTATCGGTACACTA
*
1786948 GTGTATCTGTACACTA
1 GTGTATCGGTACACTA
1786964 ATTGTATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (16 bp):
GTGTATCGGTACACTA
Found at i:1787314 original size:21 final size:19
Alignment explanation
Indices: 1787286--1787346 Score: 79
Period size: 18 Copynumber: 3.2 Consensus size: 19
1787276 TGTTAAATGA
*
1787286 AAAAGATAGCAATTGTTAAC
1 AAAAGATACCAATTGTT-AC
*
1787306 AAAAGGATATCAATTGTTA-
1 AAAA-GATACCAATTGTTAC
1787325 AAAAGATACCAATTGTTAC
1 AAAAGATACCAATTGTTAC
1787344 AAA
1 AAA
1787347 TTGTTGGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
18 13 0.35
19 7 0.19
20 5 0.14
21 12 0.32
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (19 bp):
AAAAGATACCAATTGTTAC
Found at i:1793636 original size:28 final size:28
Alignment explanation
Indices: 1793603--1793669 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
1793593 GTTTACAATT
* *
1793603 TTTTTTTTTTGAAATTTTGGCTTTTTTTG
1 TTTTTTTTGTG-AATTTTGGCCTTTTTTG
** *
1793632 TTTTTTTTGTGTTTTTTTGCCTTTTTTG
1 TTTTTTTTGTGAATTTTGGCCTTTTTTG
1793660 TTTTTTTTGT
1 TTTTTTTTGT
1793670 AAAAAAATAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 23 0.70
29 10 0.30
ACGTcount: A:0.04, C:0.04, G:0.13, T:0.78
Consensus pattern (28 bp):
TTTTTTTTGTGAATTTTGGCCTTTTTTG
Found at i:1793639 original size:19 final size:18
Alignment explanation
Indices: 1793617--1793669 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
1793607 TTTTTTGAAA
*
1793617 TTTTGGCTTTTTTTGTTTT
1 TTTTGG-TTTTTTTGTCTT
*
1793636 TTTTGTGTTTTTTTGCCTT
1 TTTTG-GTTTTTTTGTCTT
*
1793655 TTTTGTTTTTTTTGT
1 TTTTGGTTTTTTTGT
1793670 AAAAAAATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 8 0.28
19 20 0.69
20 1 0.03
ACGTcount: A:0.00, C:0.06, G:0.15, T:0.79
Consensus pattern (18 bp):
TTTTGGTTTTTTTGTCTT
Found at i:1793665 original size:9 final size:9
Alignment explanation
Indices: 1793624--1793669 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
1793614 AAATTTTGGC
1793624 TTTTTTTGT
1 TTTTTTTGT
1793633 TTTTTTTGT
1 TTTTTTTGT
*
1793642 GTTTTTTTGC
1 -TTTTTTTGT
*
1793652 CTTTTTTGT
1 TTTTTTTGT
1793661 TTTTTTTGT
1 TTTTTTTGT
1793670 AAAAAAATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.83
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:1805002 original size:125 final size:124
Alignment explanation
Indices: 1804780--1805016 Score: 420
Period size: 125 Copynumber: 1.9 Consensus size: 124
1804770 ACATTCAAGT
* *
1804780 TAAGATAATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCATACCAAGGAG
1 TAAGAAAATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAG
* *
1804845 GCATGAAGAGTGAGCCTTACAATTTGAGGTGATGGGGTATTTTGAAGGCTCGTACCGGTA
66 GCATGAAGAATGAGCCTTACAATTTGAGGTGAT-GGGCATTTTGAAGGCTCGTACCGGTA
*
1804905 TAAGAAAATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGATAAGATTCAGACCAAGGAG
1 TAAGAAAATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAG
1804970 GCATGAAGAATGAGCCTTACAATTTGAGGTGATGGGCATTTTGAAGG
66 GCATGAAGAATGAGCCTTACAATTTGAGGTGATGGGCATTTTGAAGG
1805017 TGTGTACCAA
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
124 13 0.12
125 94 0.88
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (124 bp):
TAAGAAAATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAG
GCATGAAGAATGAGCCTTACAATTTGAGGTGATGGGCATTTTGAAGGCTCGTACCGGTA
Found at i:1806587 original size:40 final size:41
Alignment explanation
Indices: 1806539--1806648 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 41
1806529 TCACACTTAG
* * *
1806539 TAAGTCCTTCGGGCCATCAATAAGTCTTTTGAGCATGATGC
1 TAAGTCCTTCGGGCCATCAATAAGCCTTTTGAGCAAGATGA
* * * **
1806580 TTA-TCCTTCGAGTCATCTGTAAGCCTTTTGAGCAAGATGA
1 TAAGTCCTTCGGGCCATCAATAAGCCTTTTGAGCAAGATGA
* *
1806620 TAAGACCTTCGGGCCATCCATAAGACCTT
1 TAAGTCCTTCGGGCCATCAATAAG-CCTT
1806649 CGGGCAAGGT
Statistics
Matches: 53, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
40 32 0.60
41 17 0.32
42 4 0.08
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (41 bp):
TAAGTCCTTCGGGCCATCAATAAGCCTTTTGAGCAAGATGA
Found at i:1807012 original size:214 final size:214
Alignment explanation
Indices: 1806324--1807045 Score: 849
Period size: 214 Copynumber: 3.3 Consensus size: 214
1806314 CTGAAATTTT
* * * *
1806324 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATATATAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATTTGTAA
* * *
1806389 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGATCTTCGGGTAGGATGTTTTCAA
66 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAA
* * * * **
1806454 AGGAATTTGAAAATGAGAAAATGATGTTTAAAGAAGATGAAATTTTTGAAAACTAAGAATTCAAT
131 ATGAATTTGAAAATGAGAAAATGATGTTTTAAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAAT
* *
1806519 TTCTAAAATTTCACACTTA
196 TTCCAATATTTCACACTTA
* * *
1806538 GTAAGTCCTTCGGGCCATCAATAAGTCTTTTGAGCATGATGCTT--ATCCTTCGAGTCATCTGTA
1 -TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATTTGTA
* *
1806601 AGCCTTTTGAGCAAGATGATAAGACCTTCGGGCCATCCATAAGACCTTCGGGCAAGGTGTCTTT-
65 AGCCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGT-TTTC
* * * *
1806665 ACATGAATTTGAAGAATGAGAAAGTGATGTTTTGAGAAAATGAAATTTTTGAAAAGTAAGAAAGT
129 AAATGAATTTGAA-AATGAGAAAATGATGTTTTAAGAAAATGAAATTTTTGAAAAGTAAGAAAGC
** * * *
1806730 TTTCTTACCTAGTAAATTATTTTTAAAATTTA
193 AAT-TT-CC-----AA-TA--TTTCACACTTA
* *
1806762 TAAGTCCTTCGGGCCATCAGTAAGTCCTTCGAGCATGATGTTTAAATCCTTCGAGTCATTTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATTTGTAA
* * * * * ** *
1806827 GTCTTTAGAGCAAGATCATTAGTCATTCGGGCCATCCATAAGACCTTCGAACAAGATGTTTTCAT
66 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAA
* * *
1806892 ATGAATTTGAAAATGAGAAAATGATGTTTTAAGAAAATGAAA-TTTTGAGAAGTAAGAAGGCGAT
131 ATGAATTTGAAAATGAGAAAATGATGTTTTAAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAAT
* *
1806956 TTCCAATACTTCGCACTATA
196 TTCCAATATTTCACACT-TA
* * * * *
1806976 TAAGTCCTTCGGGCCATCAGTACGTCTGTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATTTGTAA
1807041 GCCTT
66 GCCTT
1807046 CACAGAAGAG
Statistics
Matches: 429, Mismatches: 62, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
213 85 0.20
214 112 0.26
215 45 0.10
216 3 0.01
221 4 0.01
222 3 0.01
223 56 0.13
224 40 0.09
225 81 0.19
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (214 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGAGTCATTTGTAA
GCCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAA
ATGAATTTGAAAATGAGAAAATGATGTTTTAAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAAT
TTCCAATATTTCACACTTA
Found at i:1807122 original size:80 final size:80
Alignment explanation
Indices: 1806989--1807228 Score: 279
Period size: 80 Copynumber: 3.0 Consensus size: 80
1806979 GTCCTTCGGG
* * * **
1806989 CCATCAGTACGTCTGTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTCATAAGCCTTCACAGAAG
1807054 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAT
* *
1807069 CCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCAGGTAATTCATAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTCATAAGCCTTCACAGAAG
1807134 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAT
* * * * * * * ** *
1807149 CCATTAGCAAGCCTTCCAAGCATGATGATTAACTCC-TCCGAGCCA-TCTTAAGCCTTCACCA-A
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAG-GTAATTCATAAGCCTTCA-CAGA
*
1807211 AAAGTAGTGAAGCAAAT
64 AGAGTAGTGAAGCAAAT
1807228 C
1 C
1807229 AATCTTAAGC
Statistics
Matches: 138, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
79 33 0.24
80 105 0.76
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTCATAAGCCTTCACAGAAG
AGTAGTGAAGCAAAT
Found at i:1807237 original size:37 final size:37
Alignment explanation
Indices: 1807193--1807344 Score: 250
Period size: 37 Copynumber: 4.1 Consensus size: 37
1807183 CCTCCGAGCC
* *
1807193 ATCTTAAGCCTTCACCAAAAAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
1807230 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
*
1807267 ATCTTAAGCCTTCACCGAAGAGTATTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
* * *
1807304 ATCTTAAGCCTTCATCGAAGAGTAGTGGAGCAAATCG
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
1807341 ATCT
1 ATCT
1807345 CGAGTCCTAT
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 108 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
Found at i:1807543 original size:3 final size:3
Alignment explanation
Indices: 1807530--1807567 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
1807520 ATATTATAAA
*
1807530 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1807568 TTTTTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1809743 original size:2 final size:2
Alignment explanation
Indices: 1809736--1809765 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1809726 CATGTTAATA
*
1809736 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1809766 TACTTTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1811911 original size:18 final size:18
Alignment explanation
Indices: 1811888--1811944 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
1811878 TTTTTATATC
1811888 AAAGAAAAAAATAAAATA
1 AAAGAAAAAAATAAAATA
** *
1811906 AAAGAACGAGATAAAATA
1 AAAGAAAAAAATAAAATA
* * *
1811924 AAATAAAATAATAAGATA
1 AAAGAAAAAAATAAAATA
1811942 AAA
1 AAA
1811945 ATAAAGCAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAGAAAAAAATAAAATA
Found at i:1811921 original size:23 final size:24
Alignment explanation
Indices: 1811889--1811949 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
1811879 TTTTATATCA
*
1811889 AAGAAAAAAATAAAATAAAAGAAC
1 AAGATAAAAATAAAATAAAAGAAC
* * *
1811913 GAGAT-AAAATAAAATAAAATAAT
1 AAGATAAAAATAAAATAAAAGAAC
1811936 AAGATAAAAATAAA
1 AAGATAAAAATAAA
1811950 GCAAAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (24 bp):
AAGATAAAAATAAAATAAAAGAAC
Found at i:1811962 original size:23 final size:23
Alignment explanation
Indices: 1811895--1811962 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
1811885 ATCAAAGAAA
* * **
1811895 AAAATAAAATAAAAGAACGAGAT
1 AAAATAAAACAAAATAAAAAGAT
* *
1811918 AAAATAAAATAAAATAATAAGAT
1 AAAATAAAACAAAATAAAAAGAT
*
1811941 AAAAATAAAGCAAAA-AAAAAGA
1 -AAAATAAAACAAAATAAAAAGA
1811963 GAAGATCATC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 26 0.68
24 12 0.32
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.13
Consensus pattern (23 bp):
AAAATAAAACAAAATAAAAAGAT
Found at i:1812542 original size:4 final size:4
Alignment explanation
Indices: 1812533--1812559 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1812523 AGTGCTGGAA
1812533 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1812560 CATAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1813579 original size:13 final size:14
Alignment explanation
Indices: 1813561--1813590 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1813551 AAAGTATATC
1813561 ATTTTCTA-TTTTT
1 ATTTTCTACTTTTT
1813574 ATTTTCTACTTTTT
1 ATTTTCTACTTTTT
1813588 ATT
1 ATT
1813591 ACGAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTCTACTTTTT
Found at i:1816351 original size:131 final size:131
Alignment explanation
Indices: 1816147--1816477 Score: 459
Period size: 131 Copynumber: 2.5 Consensus size: 131
1816137 CCGATCAAAC
* * * * *
1816147 ATAAATGATCTCTCGTGCCTTAAATCAGTCATTTATTACTCTAATTGAAATGAAGAGATATCCCT
1 ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATTGAAATGAAGAGATATCACT
* * * * *
1816212 ATTTCATCTT-AAAATTCAATATCGATTCGAGTGAAAACA-ATAATATCTAATGATTTTCAATTG
66 ATTCCATCTTAAAAATT-AATATCGATTCAAGAGAAAA-AGATAATATCAAATGATTTTCAATCG
1816275 AGA
129 AGA
*
1816278 ATACATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATTGAAATGAAGAGATATCACT
1 ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATTGAAATGAAGAGATATCACT
* * *
1816343 ATTCCATCTTAAAAATTAATATTGATTCAAGAGAAAAAGGTAATATCAAATTATTTTCAATCGAG
66 ATTCCATCTTAAAAATTAATATCGATTCAAGAGAAAAAGATAATATCAAATGATTTTCAATCGAG
1816408 A
131 A
** * * *
1816409 ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAACCGAAATAAAAAGATATTACT
1 ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATTGAAATGAAGAGATATCACT
1816474 ATTC
66 ATTC
1816478 TCAACATCGA
Statistics
Matches: 178, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
130 1 0.01
131 171 0.96
132 6 0.03
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (131 bp):
ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATTGAAATGAAGAGATATCACT
ATTCCATCTTAAAAATTAATATCGATTCAAGAGAAAAAGATAATATCAAATGATTTTCAATCGAG
A
Found at i:1820424 original size:16 final size:16
Alignment explanation
Indices: 1820403--1820433 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1820393 TAAATAAATA
1820403 AAAAGTTAGCTGTTAG
1 AAAAGTTAGCTGTTAG
*
1820419 AAAAGTTAGTTGTTA
1 AAAAGTTAGCTGTTA
1820434 ACAGTCCGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (16 bp):
AAAAGTTAGCTGTTAG
Found at i:1820514 original size:17 final size:17
Alignment explanation
Indices: 1820492--1820541 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
1820482 CAAGGTCATA
1820492 TAATAATTCAAACAAAT
1 TAATAATTCAAACAAAT
1820509 TAATAA---AAA-AAA-
1 TAATAATTCAAACAAAT
1820521 T--TAATTCAAACAAAT
1 TAATAATTCAAACAAAT
1820536 TAATAA
1 TAATAA
1820542 AAATATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 14
0.65 0.00 0.35
Matches are distributed among these distances:
10 3 0.12
12 1 0.04
13 6 0.23
14 6 0.23
15 1 0.04
17 9 0.35
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (17 bp):
TAATAATTCAAACAAAT
Found at i:1820537 original size:14 final size:14
Alignment explanation
Indices: 1820495--1820539 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
1820485 GGTCATATAA
1820495 TAATTCAAACAAAT
1 TAATTCAAACAAAT
* *
1820509 TAA-TAAAAAAAAT
1 TAATTCAAACAAAT
1820522 TAATTCAAACAAAT
1 TAATTCAAACAAAT
1820536 TAAT
1 TAAT
1820540 AAAAATATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATTCAAACAAAT
Found at i:1833965 original size:198 final size:197
Alignment explanation
Indices: 1833613--1834230 Score: 979
Period size: 198 Copynumber: 3.1 Consensus size: 197
1833603 TTATAATTCC
* *
1833613 ATACCTTAAATTTATATTATAAATTATTAAATATAAAATTTATTCCTAACATAAAATCTACATCT
1 ATACCTT-CATTT-TATTATAAATTATTAAATATAAAATTTA-TCCTAACATAAAATCTAAATCT
* * *
1833678 GTTATTGATTAGGTCCGATCATAACTTTGCGGACTGTTTTTGGGATGCTCATACGTTAGCTCAAT
63 GTTATTGATTAGGTCCGATCATAACTTTGCGGAGTGTTTTTGGGATGCTCATACGTTAGCTCGAG
*
1833743 AAGGTTTGACATAGGTTGATATAAAATAATAAAAGCAATATATATTATATGATAAGGTTTGTCGT
128 AAGGTTTGACATAGGTTGATATAAAATAATAAAAGCAGTATATATTATATGATAAGGTTTGTCGT
1833808 CATCT
193 CATCT
*
1833813 ATACCTTCATTTTATTATAAATTATTAAATATAAAATTTATCACTAACATAAAATCTATATCTGT
1 ATACCTTCATTTTATTATAAATTATTAAATATAAAATTTATC-CTAACATAAAATCTAAATCTGT
* * *
1833878 TATTGATTAGGTCTGATTATAACTTTGCGGAGTGTTTTTGGGATGTTCATACGTTAGCTCGAGAA
65 TATTGATTAGGTCCGATCATAACTTTGCGGAGTGTTTTTGGGATGCTCATACGTTAGCTCGAGAA
*
1833943 GGTTTGACATAGGTTGATATAAAACAATAAAAGCAGTATATATTATATGATAAGGTTTGTCGTCA
130 GGTTTGACATAGGTTGATATAAAATAATAAAAGCAGTATATATTATATGATAAGGTTTGTCGTCA
1834008 TCT
195 TCT
* * *
1834011 ATACCTTCATTTTATTATAACTTATTAAATATAAAATTTACCCCTAACATAAAATCTAAATCTAT
1 ATACCTTCATTTTATTATAAATTATTAAATATAAAATTTA-TCCTAACATAAAATCTAAATCTGT
* ** *
1834076 TATTGATTAGGTCCGATCATTA-TATTATGGAGTATTTTT-GGATGCTCATACGTTAGCTCGAGA
65 TATTGATTAGGTCCGATCATAACT-TTGCGGAGTGTTTTTGGGATGCTCATACGTTAGCTCGAGA
* * *
1834139 AGGTTTGATATAGGTTGATATAAAATAATAAAATCAGTATATATTATATGATAAAGTTTGTCGTC
129 AGGTTTGACATAGGTTGATATAAAATAATAAAAGCAGTATATATTATATGATAAGGTTTGTCGTC
1834204 ATCT
194 ATCT
1834208 ATACCTTCATTTTATTATAAATT
1 ATACCTTCATTTTATTATAAATT
1834231 TGTAACAGCA
Statistics
Matches: 389, Mismatches: 26, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
197 113 0.29
198 264 0.68
199 5 0.01
200 7 0.02
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.40
Consensus pattern (197 bp):
ATACCTTCATTTTATTATAAATTATTAAATATAAAATTTATCCTAACATAAAATCTAAATCTGTT
ATTGATTAGGTCCGATCATAACTTTGCGGAGTGTTTTTGGGATGCTCATACGTTAGCTCGAGAAG
GTTTGACATAGGTTGATATAAAATAATAAAAGCAGTATATATTATATGATAAGGTTTGTCGTCAT
CT
Found at i:1835617 original size:23 final size:23
Alignment explanation
Indices: 1835589--1835647 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
1835579 CTTGAGACTC
*
1835589 AAACTCGACTGAAGCCCAATTTT
1 AAACTCGACTCAAGCCCAATTTT
* * * *
1835612 AAACTCAATTCAAGCTCGATTTT
1 AAACTCGACTCAAGCCCAATTTT
*
1835635 AAACTCGATTCAA
1 AAACTCGACTCAA
1835648 ACTAGATTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (23 bp):
AAACTCGACTCAAGCCCAATTTT
Found at i:1835655 original size:23 final size:23
Alignment explanation
Indices: 1835607--1835655 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1835597 CTGAAGCCCA
* *
1835607 ATTTTAAACTCAATTCAAGCTCG
1 ATTTTAAACTCAATTCAAACTAG
*
1835630 ATTTTAAACTCGATTCAAACTAG
1 ATTTTAAACTCAATTCAAACTAG
1835653 ATT
1 ATT
1835656 CAAGCTCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (23 bp):
ATTTTAAACTCAATTCAAACTAG
Found at i:1835666 original size:11 final size:11
Alignment explanation
Indices: 1835619--1835688 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
1835609 TTTAAACTCA
1835619 ATTCAAGCTCG
1 ATTCAAGCTCG
* *
1835630 ATTTTAAACTCG
1 A-TTCAAGCTCG
* *
1835642 ATTCAAACTAG
1 ATTCAAGCTCG
1835653 ATTCAAGCTCG
1 ATTCAAGCTCG
** *
1835664 ATTTTGAGCTTG
1 A-TTCAAGCTCG
1835676 ATTCAAGCTCG
1 ATTCAAGCTCG
1835687 AT
1 AT
1835689 GGGTTTTAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
11 28 0.62
12 17 0.38
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (11 bp):
ATTCAAGCTCG
Found at i:1837839 original size:7 final size:7
Alignment explanation
Indices: 1837827--1837881 Score: 83
Period size: 7 Copynumber: 7.9 Consensus size: 7
1837817 CATAATCGGA
1837827 TTTAGGG
1 TTTAGGG
1837834 TTTAGGG
1 TTTAGGG
*
1837841 TTTAGGA
1 TTTAGGG
*
1837848 TTTAGGA
1 TTTAGGG
*
1837855 TTTAGGA
1 TTTAGGG
1837862 TTTAGGG
1 TTTAGGG
1837869 TTTAGGG
1 TTTAGGG
1837876 TTTAGG
1 TTTAGG
1837882 ATTCATTACA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:1837850 original size:21 final size:21
Alignment explanation
Indices: 1837825--1837884 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
1837815 CACATAATCG
*
1837825 GATTTAGGGTTTAGGGTTTAG
1 GATTTAGGGTTTAGGATTTAG
*
1837846 GATTTAGGATTTAGGATTTAG
1 GATTTAGGGTTTAGGATTTAG
*
1837867 GGTTTAGGGTTTAGGATT
1 GATTTAGGGTTTAGGATT
1837885 CATTACAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (21 bp):
GATTTAGGGTTTAGGATTTAG
Done.