Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 123 of 325
Found at i:39466803 original size:20 final size:20
Alignment explanation
Indices: 39466743--39466803 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
39466733 CCAATAAAAT
*
39466743 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
39466763 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
39466784 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
39466804 GTCAGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:39469262 original size:22 final size:22
Alignment explanation
Indices: 39469234--39469277 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
39469224 TTTTGAACCA
*
39469234 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCATACCAAATCCC
*
39469256 TTACCATTTCATACCAATTCCC
1 TTACCATTTCATACCAAATCCC
39469278 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.36, G:0.02, T:0.34
Consensus pattern (22 bp):
TTACCATTTCATACCAAATCCC
Found at i:39471091 original size:16 final size:16
Alignment explanation
Indices: 39471070--39471101 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39471060 CATTCTGCAT
39471070 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
39471086 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
39471102 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:39471514 original size:45 final size:45
Alignment explanation
Indices: 39471450--39471673 Score: 421
Period size: 45 Copynumber: 5.0 Consensus size: 45
39471440 TTCAGCCATG
*
39471450 ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTAGTCAA
1 ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAA
*
39471495 ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAA
1 ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAA
39471540 ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAA
1 ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAA
39471585 ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAA
1 ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAA
*
39471630 ATGCTTCCTCAAATTCTTCTATGAATTATGCATGATGTTGGTCA
1 ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCA
39471674 CCTCTTCTTT
Statistics
Matches: 175, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 175 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (45 bp):
ATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAA
Found at i:39472886 original size:30 final size:29
Alignment explanation
Indices: 39472852--39472924 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
39472842 TTCTTGTTCA
*
39472852 TCTTTTTCTTTTCTTACTTTCTTTTCTCTC
1 TCTTTTTCTTTTCTTACTTTATTTT-TCTC
* **
39472882 TCTTTTTCTATTCTTGTTTTATTTTTCTC
1 TCTTTTTCTTTTCTTACTTTATTTTTCTC
*
39472911 AC-TTTTCTTTTCTT
1 TCTTTTTCTTTTCTT
39472925 TTTTACATTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 11 0.30
29 5 0.14
30 21 0.57
ACGTcount: A:0.05, C:0.22, G:0.01, T:0.71
Consensus pattern (29 bp):
TCTTTTTCTTTTCTTACTTTATTTTTCTC
Found at i:39481767 original size:23 final size:22
Alignment explanation
Indices: 39481716--39481767 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
39481706 CCTCGTCTTT
*
39481716 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
39481738 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
39481761 TTCTTTT
1 TTCTTTT
39481768 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:39485138 original size:20 final size:20
Alignment explanation
Indices: 39485115--39485161 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39485105 GGGTTAAGAT
*
39485115 TGAGCTGAAC-TGAGCTTGAG
1 TGAGCTG-ACTTGAGCTCGAG
*
39485135 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGACTTGAGCTCGAG
39485155 TGAGCTG
1 TGAGCTG
39485162 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.21, C:0.15, G:0.36, T:0.28
Consensus pattern (20 bp):
TGAGCTGACTTGAGCTCGAG
Found at i:39486579 original size:16 final size:16
Alignment explanation
Indices: 39486560--39486636 Score: 76
Period size: 15 Copynumber: 5.1 Consensus size: 16
39486550 TCTGACCATT
39486560 AATAATTCAAAAAAAA
1 AATAATTCAAAAAAAA
39486576 AAT-ATAT-AAAAAAAA
1 AATAAT-TCAAAAAAAA
*
39486591 AAT--TTGAAAAAAAA
1 AATAATTCAAAAAAAA
**
39486605 AA-AATTTGAAAAAAA
1 AATAATTCAAAAAAAA
39486620 AA-AATTCAAAAAAAA
1 AATAATTCAAAAAAAA
39486635 AA
1 AA
39486637 GTTTGTATTC
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
13 1 0.02
14 11 0.21
15 37 0.70
16 4 0.08
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
AATAATTCAAAAAAAA
Found at i:39486588 original size:15 final size:15
Alignment explanation
Indices: 39486568--39486636 Score: 81
Period size: 14 Copynumber: 4.7 Consensus size: 15
39486558 TTAATAATTC
39486568 AAAAAAAAAATATAT-
1 AAAAAAAAAATAT-TG
39486583 AAAAAAAAAAT-TTG
1 AAAAAAAAAATATTG
*
39486597 AAAAAAAAAAAATTTG
1 AAAAAAAAAATA-TTG
*
39486613 AAAAAAAAAA-ATTC
1 AAAAAAAAAATATTG
39486627 AAAAAAAAAA
1 AAAAAAAAAA
39486637 GTTTGTATTC
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
13 1 0.02
14 23 0.47
15 12 0.24
16 13 0.27
ACGTcount: A:0.80, C:0.01, G:0.03, T:0.16
Consensus pattern (15 bp):
AAAAAAAAAATATTG
Found at i:39486695 original size:12 final size:12
Alignment explanation
Indices: 39486678--39486702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39486668 TTTAGTATTG
39486678 AAGAAAAAAAAA
1 AAGAAAAAAAAA
39486690 AAGAAAAAAAAA
1 AAGAAAAAAAAA
39486702 A
1 A
39486703 TTCGGAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:39486753 original size:32 final size:32
Alignment explanation
Indices: 39486680--39486759 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 32
39486670 TAGTATTGAA
**
39486680 GAAAAAAAAAAAGAAAAAAAAAATTCGGAATT
1 GAAAAAAAAAAAGAAAAAAAAAATTCAAAATT
39486712 -AAAACAAAAAAAGAAGAAAAAAAA-TCAAAATT
1 GAAAA-AAAAAAAGAA-AAAAAAAATTCAAAATT
39486744 GAAAAAAAAAAA-AAAA
1 GAAAAAAAAAAAGAAAA
39486760 GTGATTGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 2 0.05
31 6 0.14
32 23 0.53
33 12 0.28
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.09
Consensus pattern (32 bp):
GAAAAAAAAAAAGAAAAAAAAAATTCAAAATT
Found at i:39487676 original size:21 final size:20
Alignment explanation
Indices: 39487647--39487692 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
39487637 AATCTTGAAT
*
39487647 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
39487668 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
39487688 GAAAA
1 GAAAA
39487693 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:39494180 original size:24 final size:25
Alignment explanation
Indices: 39494153--39494206 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
39494143 ATGAGTGATA
*
39494153 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
39494177 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
39494201 AAAAAA
1 AAAAAA
39494207 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:39499791 original size:22 final size:22
Alignment explanation
Indices: 39499763--39499806 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39499753 TTTTGAACCA
39499763 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
39499785 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
39499807 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:39500136 original size:13 final size:13
Alignment explanation
Indices: 39500120--39500144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39500110 AAAGAGTTCA
39500120 AAAAAAAAATTTT
1 AAAAAAAAATTTT
39500133 AAAAAAAAATTT
1 AAAAAAAAATTT
39500145 CGTTATAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAAAAATTTT
Found at i:39500800 original size:15 final size:15
Alignment explanation
Indices: 39500768--39500801 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39500758 GTTCAACGAA
*
39500768 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
39500783 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
39500798 GAGG
1 GAGG
39500802 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:39504477 original size:30 final size:30
Alignment explanation
Indices: 39504382--39504478 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
39504372 AGCTCAATCC
*
39504382 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
* * * **
39504412 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
39504442 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
39504472 TAGCTCA
1 TAGCTCA
39504479 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:39505167 original size:22 final size:22
Alignment explanation
Indices: 39505139--39505182 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39505129 TTTTGAACCA
39505139 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
39505161 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
39505183 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:39507007 original size:48 final size:48
Alignment explanation
Indices: 39506952--39507057 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
39506942 TTGTCTTTTC
*
39506952 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
** *
39507000 TTTCTTTTTTGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
39507048 TTTCTTTTTC
1 TTTCTTTTTC
39507058 CATGACACTC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
48 38 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:39507054 original size:18 final size:17
Alignment explanation
Indices: 39507033--39507158 Score: 78
Period size: 18 Copynumber: 7.1 Consensus size: 17
39507023 TTTTCACATC
39507033 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTC-ATTT
* *
39507051 CTTTTTCCATGACACTCGTTT
1 CTTTTT-CA--A-TCTCATTT
* *
39507072 CTTTTACACTCTCATTT
1 CTTTTTCAATCTCATTT
*
39507089 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCA-TTT
* *
39507108 CTTTTTCAATTTCTTGTT
1 CTTTTTCAATCTCAT-TT
* *
39507126 CCTTTTC--TTTCATTT
1 CTTTTTCAATCTCATTT
39507141 CTTTTTCAATCTC-TTT
1 CTTTTTCAATCTCATTT
39507157 CT
1 CT
39507159 CCTTTTCTCG
Statistics
Matches: 83, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
15 8 0.10
16 10 0.12
17 14 0.17
18 29 0.35
19 8 0.10
20 2 0.02
21 9 0.11
22 3 0.04
ACGTcount: A:0.14, C:0.27, G:0.02, T:0.56
Consensus pattern (17 bp):
CTTTTTCAATCTCATTT
Found at i:39509732 original size:20 final size:20
Alignment explanation
Indices: 39509709--39509754 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
39509699 GGGTTAAGAT
*
39509709 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39509729 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
39509749 TGAGCT
1 TGAGCT
39509755 AGAAACGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.13, G:0.35, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:39510839 original size:20 final size:20
Alignment explanation
Indices: 39510793--39510839 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
39510783 AGCTCGTTTC
*
39510793 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
39510813 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
39510833 CAGCTCA
1 CAGCTCA
39510840 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:39512388 original size:9 final size:9
Alignment explanation
Indices: 39512374--39512408 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
39512364 AGAAGTGAGC
39512374 AAAAAAAGA
1 AAAAAAAGA
*
39512383 AAAAAAAGT
1 AAAAAAAGA
39512392 AAAAAAAGA
1 AAAAAAAGA
39512401 ACAAAAAA
1 A-AAAAAA
39512409 AAGTGAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.86, C:0.03, G:0.09, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:39512417 original size:22 final size:21
Alignment explanation
Indices: 39512359--39512417 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
39512349 GAAATTCAAA
* *
39512359 AAAAAAGAAGTGAGCAAAAAAAG
1 AAAAAA-AAGTGA-AAAAAAAAC
39512382 AAAAAAAAGT-AAAAAAAGAAC
1 AAAAAAAAGTGAAAAAAA-AAC
39512403 AAAAAAAAGTGAAAA
1 AAAAAAAAGTGAAAA
39512418 GTCTTGTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 5 0.16
21 13 0.41
22 8 0.25
23 6 0.19
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.05
Consensus pattern (21 bp):
AAAAAAAAGTGAAAAAAAAAC
Found at i:39515278 original size:20 final size:20
Alignment explanation
Indices: 39515232--39515278 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
39515222 AGCTCGTTTC
*
39515232 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
39515252 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
39515272 CAGCTCA
1 CAGCTCA
39515279 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:39521657 original size:24 final size:23
Alignment explanation
Indices: 39521614--39521658 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
39521604 TTTCTTTTGT
*
39521614 TTCTTTTTCTAATTCATTTTCTC
1 TTCTTTTTCAAATTCATTTTCTC
*
39521637 TTCTTTCTTCAAATTCTTTTTC
1 TTCTTT-TTCAAATTCATTTTC
39521659 ACTCTCAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.64
Consensus pattern (23 bp):
TTCTTTTTCAAATTCATTTTCTC
Found at i:39524830 original size:20 final size:21
Alignment explanation
Indices: 39524784--39524830 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
39524774 GTAAGCTCGG
39524784 TTGAGCTCAAACGAGCTGTAA
1 TTGAGCTCAAACGAGCTGTAA
** *
39524805 -CAAGCTCAAATGAGCTG-AA
1 TTGAGCTCAAACGAGCTGTAA
39524824 TTGAGCT
1 TTGAGCT
39524831 GGACAGAGCT
Statistics
Matches: 20, Mismatches: 5, Indels: 3
0.71 0.18 0.11
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (21 bp):
TTGAGCTCAAACGAGCTGTAA
Found at i:39525663 original size:14 final size:14
Alignment explanation
Indices: 39525619--39525650 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39525609 GAGATTGAAC
39525619 TTTTTTTTCGATTT
1 TTTTTTTTCGATTT
39525633 TTTTTTTTCGATTT
1 TTTTTTTTCGATTT
39525647 TTTT
1 TTTT
39525651 CAATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (14 bp):
TTTTTTTTCGATTT
Found at i:39525673 original size:24 final size:25
Alignment explanation
Indices: 39525619--39525673 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
39525609 GAGATTGAAC
*
39525619 TTTTTTTTCGATTTTTTTTTTTCGA
1 TTTTTTTTCGAATTTTTTTTTTCGA
39525644 -TTTTTTTC-AATTTTTTTTTT-GA
1 TTTTTTTTCGAATTTTTTTTTTCGA
39525666 TTTTTTTT
1 TTTTTTTT
39525674 AACTTGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 18 0.64
24 8 0.29
ACGTcount: A:0.09, C:0.05, G:0.05, T:0.80
Consensus pattern (25 bp):
TTTTTTTTCGAATTTTTTTTTTCGA
Found at i:39526072 original size:14 final size:14
Alignment explanation
Indices: 39526025--39526072 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
39526015 GTACGAATGG
*
39526025 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
39526039 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
39526053 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
39526067 ATTGGT
1 AATGGT
39526073 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:39532535 original size:11 final size:11
Alignment explanation
Indices: 39532519--39532569 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
39532509 CATAAATTAC
39532519 TTTTTTTCGAT
1 TTTTTTTCGAT
*
39532530 TTTTTTT-TAT
1 TTTTTTTCGAT
39532540 TTTTTTTCGATT
1 TTTTTTTCGA-T
*
39532552 TTTTTTTCAAT
1 TTTTTTTCGAT
39532563 TTTTTTT
1 TTTTTTT
39532570 AACTTGTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.26
11 16 0.46
12 10 0.29
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.80
Consensus pattern (11 bp):
TTTTTTTCGAT
Found at i:39532536 original size:12 final size:12
Alignment explanation
Indices: 39532519--39532569 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
39532509 CATAAATTAC
39532519 TTTTTTTCGATT
1 TTTTTTTCGATT
39532531 TTTTTTT--A-T
1 TTTTTTTCGATT
39532540 TTTTTTTCGATT
1 TTTTTTTCGATT
*
39532552 TTTTTTTCAATT
1 TTTTTTTCGATT
39532564 TTTTTT
1 TTTTTT
39532570 AACTTGTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
9 8 0.23
10 1 0.03
11 1 0.03
12 25 0.71
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.80
Consensus pattern (12 bp):
TTTTTTTCGATT
Found at i:39532545 original size:21 final size:22
Alignment explanation
Indices: 39532519--39532569 Score: 86
Period size: 21 Copynumber: 2.3 Consensus size: 22
39532509 CATAAATTAC
39532519 TTTTTTTCGATTTTTTTTT-AT
1 TTTTTTTCGATTTTTTTTTAAT
39532540 TTTTTTTCGATTTTTTTTTCAAT
1 TTTTTTTCGATTTTTTTTT-AAT
39532563 TTTTTTT
1 TTTTTTT
39532570 AACTTGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 19 0.68
23 9 0.32
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.80
Consensus pattern (22 bp):
TTTTTTTCGATTTTTTTTTAAT
Found at i:39532953 original size:14 final size:14
Alignment explanation
Indices: 39532921--39532966 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
39532911 ACGAATGGAA
39532921 TGGTAGGAACGAAA-
1 TGGTAGGAAC-AAAT
*
39532935 GGGTAGGAACAAAT
1 TGGTAGGAACAAAT
*
39532949 TGGTATGAACAAAT
1 TGGTAGGAACAAAT
39532963 TGGT
1 TGGT
39532967 CAGTTTAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 3 0.11
14 25 0.89
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (14 bp):
TGGTAGGAACAAAT
Found at i:39539607 original size:21 final size:20
Alignment explanation
Indices: 39539556--39539608 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
39539546 GGCCCAAGTG
*
39539556 TAAAGTTTTATTTTATTTATT
1 TAAA-TTTTATTTTACTTATT
**
39539577 TATTTATTTATTTTACTTAGTT
1 TAAAT-TTTATTTTACTTA-TT
39539599 TAAATTTTAT
1 TAAATTTTAT
39539609 ATTCGTCCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (20 bp):
TAAATTTTATTTTACTTATT
Found at i:39543469 original size:23 final size:22
Alignment explanation
Indices: 39543417--39543469 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39543407 TCCACGTCTT
*
39543417 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39543439 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39543462 TTTCTTTT
1 TTTCTTTT
39543470 TCCCTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39565886 original size:47 final size:47
Alignment explanation
Indices: 39565823--39566066 Score: 371
Period size: 47 Copynumber: 5.2 Consensus size: 47
39565813 CCCTTCGGGA
* *
39565823 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
39565870 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
39565917 CTTATCTCATATATACACCTTCAGATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39565964 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39566011 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39566058 CTTATCACA
1 CTTATCACA
39566067 CACCTTGTAC
Statistics
Matches: 179, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 179 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:39565995 original size:25 final size:25
Alignment explanation
Indices: 39565967--39566045 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
39565957 ACTCGGCCTT
39565967 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
39565992 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
39566014 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
39566039 ATCACAT
1 ATCACAT
39566046 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:39569498 original size:39 final size:39
Alignment explanation
Indices: 39569444--39569639 Score: 184
Period size: 39 Copynumber: 5.0 Consensus size: 39
39569434 TTCAGTGATG
39569444 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
39569483 TATATCCGGACTTAAGGTCTGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * * * *
39569522 TATAACTGGACTTAAGGTACGCAGGCTACGTGCTAGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * * *
39569561 TATGTCCGGGC-TAAAGTCCCGCAGGCT-TCGAGCTGGTAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTAT-GTGCTGGAAT
** **
39569600 TATA-CCGGGTTTAAATTCCTGCAGGCT-TGTGCTGGTAAT
1 TATATCCGGACTTAAGGTCC-GCAGGCTATGTGCTGG-AAT
39569639 T
1 T
39569640 GGTTTCAAGT
Statistics
Matches: 128, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
38 18 0.14
39 110 0.86
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:39576343 original size:39 final size:39
Alignment explanation
Indices: 39576289--39576484 Score: 220
Period size: 39 Copynumber: 5.0 Consensus size: 39
39576279 TTCAGTGATG
39576289 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
39576328 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * *
39576367 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * * *
39576406 TATGTCCGGGC-TAAAGTCTCGCAGGCT-TCGAGCTGGTAT
1 TATATCCGGACTTAAGGTC-CGCAGGCTAT-GTGCTGGAAT
** **
39576445 TATA-CCGGGTTTAAATTCTCGCAGGCT-TGTGCTGGTAAT
1 TATATCCGGACTTAAGGTC-CGCAGGCTATGTGCTGG-AAT
39576484 T
1 T
39576485 GGTTTCAAGT
Statistics
Matches: 137, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
38 17 0.12
39 120 0.88
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:39582999 original size:39 final size:39
Alignment explanation
Indices: 39582945--39583060 Score: 214
Period size: 39 Copynumber: 3.0 Consensus size: 39
39582935 TTCAGTGATG
39582945 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
39582984 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* *
39583023 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAA
39583061 ATATGTCCAG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:39583097 original size:78 final size:78
Alignment explanation
Indices: 39582945--39583108 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 78
39582935 TTCAGTGATG
* * * *
39582945 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGTCCGCAGGC
1 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGGC
*
39583010 TATGTGCTGGAAT
66 TATGAGCTGGAAT
* *
39583023 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCAGG-C-TAAAGTCTCGCCG
1 TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCC-GGACTTAAAGTC-CGCAG
*
39583086 GCT-TCGAGCTGGTAT
64 GCTAT-GAGCTGGAAT
39583101 TAT-ACCGG
1 TATAACCGG
39583109 GTTTAAATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 12 0.16
78 61 0.81
79 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (78 bp):
TATAACCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATATCCGGACTTAAAGTCCGCAGGC
TATGAGCTGGAAT
Found at i:39585035 original size:15 final size:15
Alignment explanation
Indices: 39585015--39585045 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39585005 CGACATGGTA
39585015 TCTATCTTAGATTTC
1 TCTATCTTAGATTTC
*
39585030 TCTATCTTGGATTTC
1 TCTATCTTAGATTTC
39585045 T
1 T
39585046 TTACTTGCTT
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:0.16, C:0.19, G:0.10, T:0.55
Consensus pattern (15 bp):
TCTATCTTAGATTTC
Found at i:39587446 original size:11 final size:10
Alignment explanation
Indices: 39587421--39587481 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
39587411 ACCAATAAAA
39587421 TAAA-TGAGC
1 TAAATTGAGC
*
39587430 TGAATTGTAGC
1 TAAATTG-AGC
39587441 TAAATTGAGC
1 TAAATTGAGC
**
39587451 TTGATTGAGC
1 TAAATTGAGC
39587461 TGAAA-TGAGC
1 T-AAATTGAGC
*
39587471 TTAATTGAGC
1 TAAATTGAGC
39587481 T
1 T
39587482 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:39587482 original size:20 final size:20
Alignment explanation
Indices: 39587422--39587482 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
39587412 CCAATAAAAT
*
39587422 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTTAATTG-AGCTG
*
39587442 AAATTGAGCTTGATTGAGCTG
1 AAA-TGAGCTTAATTGAGCTG
39587463 AAATGAGCTTAATTGAGCTG
1 AAATGAGCTTAATTGAGCTG
39587483 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAATGAGCTTAATTGAGCTG
Found at i:39589914 original size:20 final size:20
Alignment explanation
Indices: 39589891--39589941 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
39589881 ACCATGGCAT
*
39589891 GCATTAAATGACTTAAATGG
1 GCATTAGATGACTTAAATGG
39589911 GCATTAGATGACTTAAATGG
1 GCATTAGATGACTTAAATGG
39589931 GCATTAGATGA
1 GCATTAGATGA
39589942 TGGTTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (20 bp):
GCATTAGATGACTTAAATGG
Found at i:39594004 original size:15 final size:15
Alignment explanation
Indices: 39593984--39594052 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
39593974 GTATCTTGGG
39593984 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
39593999 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
39594014 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
39594029 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
39594044 TTTCTTTAT
1 TTTCTTTAT
39594053 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:39594053 original size:30 final size:30
Alignment explanation
Indices: 39593975--39594062 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
39593965 CATAGTATCG
* * * *
39593975 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
39594005 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
39594035 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
39594063 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:39595112 original size:27 final size:27
Alignment explanation
Indices: 39595082--39595136 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
39595072 TCTTCGGCAC
39595082 CGAATATGAGATTAAAAGTGAAGACCA
1 CGAATATGAGATTAAAAGTGAAGACCA
39595109 CGAATATGAGATTAAAAGTGAAGACCA
1 CGAATATGAGATTAAAAGTGAAGACCA
39595136 C
1 C
39595137 TTTCTGGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.13, G:0.22, T:0.18
Consensus pattern (27 bp):
CGAATATGAGATTAAAAGTGAAGACCA
Found at i:39596063 original size:46 final size:45
Alignment explanation
Indices: 39596013--39596188 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
39596003 TGGTTGAGCA
39596013 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
39596059 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
39596106 TCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
39596152 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39596189 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.62
47 31 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:39596169 original size:93 final size:93
Alignment explanation
Indices: 39596010--39596180 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
39596000 GGATGGTTGA
* * *
39596010 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39596075 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
39596103 GCATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39596168 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
39596181 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:39598341 original size:43 final size:41
Alignment explanation
Indices: 39598186--39598342 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 41
39598176 TGTGTTATCG
*
39598186 TGTAAGACCACGTCTGAGACGTTGGCATCA-ACTTATGATTTAC
1 TGTAAGACCACGTCTGGGACGTTGGCATCATA-TT-TGA-TTAC
* * * * *
39598229 GTGTAAGACCATGTTTGGGACATCGGCATCATATTTGATTTC
1 -TGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTAC
* *
39598271 GGTCAAGACC-CTGTCTGGGATAG-TGGCATCGATATTTGATTAC
1 TGT-AAGACCAC-GTCTGGGA-CGTTGGCATC-ATATTTGATTAC
39598314 ATGTAAGACCACGTCTGGGACGTTGGCAT
1 -TGTAAGACCACGTCTGGGACGTTGGCAT
39598343 TGTACGAGTT
Statistics
Matches: 90, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
41 2 0.02
42 23 0.26
43 34 0.38
44 30 0.33
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTAC
Found at i:39600300 original size:19 final size:19
Alignment explanation
Indices: 39600276--39600315 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39600266 TTCTGATTTT
*
39600276 GTTCCAATTCAAGGATAGA
1 GTTCCAATTCAAGGACAGA
* *
39600295 GTTCCACTTCGAGGACAGA
1 GTTCCAATTCAAGGACAGA
39600314 GT
1 GT
39600316 ATTCTTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (19 bp):
GTTCCAATTCAAGGACAGA
Found at i:39620332 original size:24 final size:23
Alignment explanation
Indices: 39620268--39620371 Score: 111
Period size: 24 Copynumber: 4.3 Consensus size: 23
39620258 AAGCTCCTCC
*
39620268 TGAGCTGATGAACAGTAAGCTCTA
1 TGAGCTGA-AAACAGTAAGCTCTA
*
39620292 TTGAGCTG-AAACGGTAAGCTCTGA
1 -TGAGCTGAAAACAGTAAGCTCT-A
39620316 TGAGCTGAAAACAGTAAGCTCATA
1 TGAGCTGAAAACAGTAAGCTC-TA
* * *
39620340 CGAGCTTAGAACAGTAAGCTCTTA
1 TGAGCTGAAAACAGTAAGCTC-TA
39620364 TGAGCTGA
1 TGAGCTGA
39620372 TATATTGGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
23 19 0.28
24 40 0.60
25 8 0.12
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (23 bp):
TGAGCTGAAAACAGTAAGCTCTA
Found at i:39620358 original size:48 final size:48
Alignment explanation
Indices: 39620268--39620373 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 48
39620258 AAGCTCCTCC
* * *
39620268 TGAGCTGATGAACAGTAAGCTCTATTGAGCTGAAACGGTAAGCTCTGA
1 TGAGCTGATAAACAGTAAGCTCTATCGAGCTGAAACAGTAAGCTCTGA
* *
39620316 TGAGCTGA-AAACAGTAAGCTC-ATACGAGCTTAGAACAGTAAGCTCTTA
1 TGAGCTGATAAACAGTAAGCTCTAT-CGAGCTGA-AACAGTAAGCTCTGA
39620364 TGAGCTGATA
1 TGAGCTGATA
39620374 TATTGGTAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
46 2 0.04
47 18 0.36
48 29 0.58
49 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (48 bp):
TGAGCTGATAAACAGTAAGCTCTATCGAGCTGAAACAGTAAGCTCTGA
Found at i:39621921 original size:302 final size:300
Alignment explanation
Indices: 39621376--39621940 Score: 733
Period size: 302 Copynumber: 1.9 Consensus size: 300
39621366 TCCACTAACC
* * * * *
39621376 ATAAATGGTCTATTTACCACTTAAGGACCTTTACTTTAATGTTCTACAGTTATTTGACACTTTTA
1 ATAAATGGTCTAATTACCACTTAAGGACCTCTACTTTAAAGTTATACAGCTATTTGACACTTTTA
* * * * *
39621441 GCTAATAGAACACAAGTTTTACGCTTTACGTGATTCATTCCTTTTTACCAAATTAAGCATTCAAA
66 ACTAATAGAACACAACTTTTACACTTTACGCGATTCAGTCCTTTTTACCAAATTAAGCATTCAAA
* * * ** * * * * *
39621506 TAGTAACATTTCTTTACAAAAAATTCACATAATAATTCTATCATGCTGTAAACCTTATTAAAATA
131 GAGTAAAATTTATAAACAAAAAATTCACACAATAACTCAATCATGCTGTAAACATTATAAAAATA
* * **
39621571 ATAAAATAAATATTTTAACCTCATATTTGTGGTCTCAAAACCACTATTCTGATTTGACTAAAAAA
196 ATAAAATAAATATTTTAACCTCAGATTTGTGGTCCCAAAACCACTATTCCAATTTGACT-AAAAA
39621636 CGGGTTGTTACAAATAATGTCCATCTTTGTCCTATAAGTTT
260 CGGGTTGTTACAAATAATGTCCATCTTTGTCCTATAAGTTT
* *
39621677 ATAAATGGTCTAATTACCACTT-AGATACCTCTACTTTAAAGTTATATAGCTATTTGACACTTTT
1 ATAAATGGTCTAATTACCACTTAAG-GACCTCTACTTTAAAGTTATACAGCTATTTGACACTTTT
* * *
39621741 AACTAATAGAACA-ATACTTTTGCACTTTACGCGATTTAGTCCTTTTTTACCGAATTAAGCATTC
65 AACTAATAGAACACA-ACTTTTACACTTTACGCGATTCAGTCC-TTTTTACCAAATTAAGCATTC
* ** * *
39621805 AAACGA-TAAAATTTATAAACGAAACTTTCACACAATCACTCAATCATGTTGTAAACATTA-AAA
128 AAA-GAGTAAAATTTATAAACAAAAAATTCACACAATAACTCAATCATGCTGTAAACATTATAAA
*
39621868 TAATAATAAAATAAATATTTTAACCTTAGATTTGTGGTCCCAAAACCACTATTCCAATTTGACTA
192 -AATAATAAAATAAATATTTTAACCTCAGATTTGTGGTCCCAAAACCACTATTCCAATTTGACTA
39621933 AAAACGGG
256 AAAACGGG
39621941 CTACTACATA
Statistics
Matches: 224, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
300 3 0.01
301 98 0.44
302 122 0.54
303 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (300 bp):
ATAAATGGTCTAATTACCACTTAAGGACCTCTACTTTAAAGTTATACAGCTATTTGACACTTTTA
ACTAATAGAACACAACTTTTACACTTTACGCGATTCAGTCCTTTTTACCAAATTAAGCATTCAAA
GAGTAAAATTTATAAACAAAAAATTCACACAATAACTCAATCATGCTGTAAACATTATAAAAATA
ATAAAATAAATATTTTAACCTCAGATTTGTGGTCCCAAAACCACTATTCCAATTTGACTAAAAAC
GGGTTGTTACAAATAATGTCCATCTTTGTCCTATAAGTTT
Found at i:39623388 original size:16 final size:16
Alignment explanation
Indices: 39623367--39623402 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39623357 CTAGATCGAC
*
39623367 AAAAGCCGAAATGCCA
1 AAAAGCCAAAATGCCA
*
39623383 AAAAGCCAAAATGTCA
1 AAAAGCCAAAATGCCA
39623399 AAAA
1 AAAA
39623403 ACTGAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.19, G:0.14, T:0.08
Consensus pattern (16 bp):
AAAAGCCAAAATGCCA
Found at i:39623663 original size:29 final size:29
Alignment explanation
Indices: 39623625--39623738 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 29
39623615 GCATGAGTAT
*
39623625 AAGGTGATTTGGGCCTAACGGGCCATATA
1 AAGGTGATTTGGGCCTAATGGGCCATATA
* * *
39623654 AAGGTGATTTGGACCTGATGGGCCATATG
1 AAGGTGATTTGGGCCTAATGGGCCATATA
* * *
39623683 AATGTGAATTGGGCCTGATGGGCCATATA
1 AAGGTGATTTGGGCCTAATGGGCCATATA
* *
39623712 AATGAGA-TTGGGCC-AAGTGGGCCATAT
1 AAGGTGATTTGGGCCTAA-TGGGCCATAT
39623739 GCATGTATGT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
27 1 0.01
28 17 0.23
29 56 0.76
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.25
Consensus pattern (29 bp):
AAGGTGATTTGGGCCTAATGGGCCATATA
Found at i:39630422 original size:47 final size:47
Alignment explanation
Indices: 39630371--39630530 Score: 239
Period size: 47 Copynumber: 3.4 Consensus size: 47
39630361 TTGTGATGTG
* * *
39630371 AGTGTATATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
39630418 AGTGTATATATGTGATAGGGTCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* * *
39630465 AGTGTATATATGTGATAGGGCCGAGTGGCCAATGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
*
39630512 AGTGTATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
39630531 TCCCGAAGGG
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 103 1.00
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.30
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
Found at i:39630706 original size:37 final size:37
Alignment explanation
Indices: 39630649--39630727 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
39630639 CCGAGCTCTA
* * * *
39630649 AAGACCCGATGACTACGTGTGGGGATTTTGTCTGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
**
39630686 AAGACCCGATAACTTTGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
39630723 AAGAC
1 AAGAC
39630728 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:39632225 original size:40 final size:40
Alignment explanation
Indices: 39631942--39632213 Score: 418
Period size: 40 Copynumber: 6.8 Consensus size: 40
39631932 GAGAATTGAG
39631942 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
39631982 AGTGATATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
39632022 AGTGATGTATCCGGGCTAAGTTCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
39632062 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
39632102 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* ** *
39632142 AGTGATATATCCGTGCTAAACCCCGAAGAACATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
39632182 GGTGTTATATCCGGGCTAGGTCTCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
39632214 ATCATGCTGG
Statistics
Matches: 210, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 210 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:39636040 original size:47 final size:47
Alignment explanation
Indices: 39635989--39636244 Score: 377
Period size: 47 Copynumber: 5.4 Consensus size: 47
39635979 TTGTGATGTG
*
39635989 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA
* *
39636036 AGTGTATATATGTGATAAGGTCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA
*
39636083 AGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA
* **
39636132 AATGTATATATGTGATAAGGCCTAATGGCTGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA
* * * * *
39636179 AGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA
*
39636226 AGTGTATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
39636245 TCCCGAAGGG
Statistics
Matches: 187, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
47 144 0.77
49 43 0.23
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA
Found at i:39636110 original size:96 final size:94
Alignment explanation
Indices: 39635989--39636244 Score: 377
Period size: 96 Copynumber: 2.7 Consensus size: 94
39635979 TTGTGATGTG
*
39635989 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
39636054 GGTCGAATGGCCAATGTGATGAATGTGAA
66 GGCCGAATGGCCAATGTGATGAATGTGAA
* *
39636083 AGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAATGTATATATGTGAT
1 AGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGAT
* **
39636148 AAGGCCTAATGGCTGATGTGATGAATGTGAA
64 AAGGCCGAATGGCCAATGTGATGAATGTGAA
* * * * * *
39636179 AGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
39636244 G
66 G
39636245 TCCCGAAGGG
Statistics
Matches: 145, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
94 58 0.40
96 87 0.60
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (94 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAA
GGCCGAATGGCCAATGTGATGAATGTGAA
Found at i:39636418 original size:37 final size:37
Alignment explanation
Indices: 39636362--39636440 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
39636352 CCGAGCTCTA
* * *
39636362 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
39636399 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
39636436 AAGAC
1 AAGAC
39636441 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:39641559 original size:30 final size:30
Alignment explanation
Indices: 39641523--39641588 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
39641513 TCTGTGGCAG
*
39641523 AGTATGAACGTGAATTTGTAAGACTCAGCA
1 AGTATGAACGCGAATTTGTAAGACTCAGCA
39641553 AGTATGAACGCGAATTTGTAAGACTCAGCA
1 AGTATGAACGCGAATTTGTAAGACTCAGCA
39641583 AGTATG
1 AGTATG
39641589 CCCAGAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (30 bp):
AGTATGAACGCGAATTTGTAAGACTCAGCA
Found at i:39646842 original size:68 final size:67
Alignment explanation
Indices: 39646770--39646946 Score: 200
Period size: 67 Copynumber: 2.6 Consensus size: 67
39646760 CATCATGTGT
* * * *
39646770 ACAAGAGAGCTACGAGATACTATGTGATAGCTAGGTCACATGTGT-GATAC-GG-GATGTATACC
1 ACAAGAGAGCTACGAGATA--A-ATG-TAGCTAGGTCACATGTGTGGATACAGGTGAAGGACACC
39646832 ATGTAG
62 ATGTAG
* * * *
39646838 ACAAGAGAGCTACGGGATAAATGTAGCTAGGTCGCATGTGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCACATGTGTGGATACAGGTGAAGGACACCATGT
39646903 AG
66 AG
* *
39646905 ACAAGAGAGCTACGAGATAAA-GTGGCTAGGTCACATGGGTGG
1 ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCACATGTGTGG
39646947 TACTAAGTGG
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 17 0.18
65 5 0.05
66 21 0.22
67 33 0.35
68 18 0.19
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCACATGTGTGGATACAGGTGAAGGACACCATGT
AG
Found at i:39649251 original size:16 final size:16
Alignment explanation
Indices: 39649230--39649263 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39649220 GTTGTAATGC
*
39649230 CCCAAAAATCTCGAAA
1 CCCAAAAATCCCGAAA
39649246 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
39649262 CC
1 CC
39649264 TTGAATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.38, G:0.06, T:0.09
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:39650842 original size:28 final size:28
Alignment explanation
Indices: 39650738--39650848 Score: 116
Period size: 29 Copynumber: 3.9 Consensus size: 28
39650728 TGAATATAAG
* * *
39650738 GTGACTTGGGCCTAACGGGCCATATAAAG
1 GTGA-TTGGGCCTGATGGGCCATATAAAT
* *
39650767 GTGATTTGGGCCTGATGGGCCATGTGAAT
1 GTGA-TTGGGCCTGATGGGCCATATAAAT
39650796 GTGAATTGGGCCTGATGGGCCATATAAAT
1 GTG-ATTGGGCCTGATGGGCCATATAAAT
* *
39650825 GAGATTGGGCC-AAGTGGGCCATAT
1 GTGATTGGGCCTGA-TGGGCCATAT
39650849 GCATGTATAT
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.01
28 18 0.26
29 50 0.71
30 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.25
Consensus pattern (28 bp):
GTGATTGGGCCTGATGGGCCATATAAAT
Found at i:39655975 original size:21 final size:21
Alignment explanation
Indices: 39655951--39655992 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
39655941 CTAAAGCTTA
39655951 AAATAATCTAACTCAGTTATC
1 AAATAATCTAACTCAGTTATC
39655972 AAATAATCTAACTCAGTTATC
1 AAATAATCTAACTCAGTTATC
39655993 CATAGCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
AAATAATCTAACTCAGTTATC
Found at i:39656368 original size:18 final size:18
Alignment explanation
Indices: 39656347--39656394 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
39656337 TCAGCAAGTT
39656347 CTTCTTCTTCAGCAGGAA
1 CTTCTTCTTCAGCAGGAA
*
39656365 CTTCCTCTTCTTTAGCAGGAA
1 C-T--TCTTCTTCAGCAGGAA
39656386 CTTCCTTCT
1 CTT-CTTCT
39656395 CAACAACTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 1 0.04
21 16 0.64
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40
Consensus pattern (18 bp):
CTTCTTCTTCAGCAGGAA
Found at i:39656375 original size:21 final size:21
Alignment explanation
Indices: 39656349--39656391 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
39656339 AGCAAGTTCT
39656349 TCTTCTTCAGCAGGAACTTCC
1 TCTTCTTCAGCAGGAACTTCC
*
39656370 TCTTCTTTAGCAGGAACTTCC
1 TCTTCTTCAGCAGGAACTTCC
39656391 T
1 T
39656392 TCTCAACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (21 bp):
TCTTCTTCAGCAGGAACTTCC
Found at i:39659397 original size:93 final size:93
Alignment explanation
Indices: 39659289--39659460 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
39659279 GTCCATAAGT
* *
39659289 GAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCAGACTCAACTCAACGAGCTCGGA-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
39659353 ACGAGCTCGGATGCCTAGTTACATATCTC
65 ACGAGCTCGGATGCCTAGTTACATATCTC
* *
39659382 GAACTCAGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
39659447 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
39659461 CAAACATCCT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 71 0.97
94 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATATCTC
Found at i:39659452 original size:46 final size:46
Alignment explanation
Indices: 39659280--39659456 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
39659270 ATGTAACCTG
*
39659280 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCA
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA-CATTCGCA
*
39659326 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTA
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A
* ** * * *
39659370 GTTACATATCTCGAACTCAGACTCAACTCAATGAGTTCGGACATTCGCA
1 --TCCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCA
*
39659419 TCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
39659457 TGCCCAAACA
Statistics
Matches: 109, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.62
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCA
Found at i:39662618 original size:26 final size:25
Alignment explanation
Indices: 39662555--39662622 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
39662545 AGAGCATACG
* * *
39662555 TGGGCCAAAGCCCATTACAAATCACT
1 TGGGCC-AAGCCCATAACAAACCAAT
39662581 TGGGTCTC-AGCCCATAACAGAACCAAT
1 TGGG-C-CAAGCCCATAACA-AACCAAT
39662608 TGGGCCAAGCCCATA
1 TGGGCCAAGCCCATA
39662623 TCAGTAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.03
26 23 0.66
27 10 0.29
28 1 0.03
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (25 bp):
TGGGCCAAGCCCATAACAAACCAAT
Found at i:39663067 original size:22 final size:22
Alignment explanation
Indices: 39663036--39663097 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
39663026 AATACGTTTG
*
39663036 GCACACAGCCATAATCAGGTTA
1 GCACAAAGCCATAATCAGGTTA
* ** *
39663058 GCACAGAGCCAT-ATGTTGGTTG
1 GCACAAAGCCATAAT-CAGGTTA
39663080 GCACAAAGCCATAATCAG
1 GCACAAAGCCATAATCAG
39663098 AATAATTGGC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (22 bp):
GCACAAAGCCATAATCAGGTTA
Found at i:39663297 original size:41 final size:42
Alignment explanation
Indices: 39663239--39663361 Score: 178
Period size: 41 Copynumber: 3.0 Consensus size: 42
39663229 AAAAGCCACC
* * *
39663239 GGTGGATCCACGTTCGTCAAGCAACCATATGATCCTTAATTA
1 GGTGGATCCACGGTCGTCAAGCAACCATGTGATCCTCAATTA
* *
39663281 -GTGGATCCACGGTCGTCAAGCAACCATGCGATTCTCAA-TA
1 GGTGGATCCACGGTCGTCAAGCAACCATGTGATCCTCAATTA
*
39663321 GGTGGATCCACAGTCGTCAAGCAACCATGTGATCCTCAATT
1 GGTGGATCCACGGTCGTCAAGCAACCATGTGATCCTCAATT
39663362 TCTTCCTCTA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
40 2 0.03
41 68 0.96
42 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (42 bp):
GGTGGATCCACGGTCGTCAAGCAACCATGTGATCCTCAATTA
Found at i:39663651 original size:27 final size:27
Alignment explanation
Indices: 39663621--39664041 Score: 114
Period size: 27 Copynumber: 15.6 Consensus size: 27
39663611 GTAAATCTAC
**
39663621 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTTTGTAATTTTGT
* *
39663648 AAACCAATGGTCTTTTTGTAATTTT-T
1 AAACCAAGGGTATTTTTGTAATTTTGT
*
39663674 GAAAGTCAAGGGTATTTTTGTAATTTTGT
1 -AAA-CCAAGGGTATTTTTGTAATTTTGT
* * * * **
39663703 AAATCAGGGGTACTTTTGTCATTTTCC
1 AAACCAAGGGTATTTTTGTAATTTTGT
* * * **
39663730 AAATCAAGGGTTTTTTTATTAATTTTCC
1 AAACCAAGGGTATTTTT-GTAATTTTGT
* * * **
39663758 AAATC-AGAGGCATTTTTATAATTTTAC
1 AAACCAAG-GGTATTTTTGTAATTTTGT
* ** **
39663785 AAATCAAGGGTATTTCGGTAATTTTAC
1 AAACCAAGGGTATTTTTGTAATTTTGT
*** * * **
39663812 AAGTTAAGAGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTTTGTAATTTTGT
** * * **
39663839 AAGTCGAGGGTATTTTAGTAATTTTAC
1 AAACCAAGGGTATTTTTGTAATTTTGT
*** ** *
39663866 AGGTCAAGGGTATTTCGGTAATTTTAT
1 AAACCAAGGGTATTTTTGTAATTTTGT
***** **
39663893 AGGTTGAGGGTA-TTTTGATAATTTTCC
1 AAACCAAGGGTATTTTTG-TAATTTTGT
* * * * **
39663920 AAATCAGGGGTATATTTGTTATTTTAC
1 AAACCAAGGGTATTTTTGTAATTTTGT
* * * ** **
39663947 AAA-TAGAAGATATTTCGGTAATTTTCC
1 AAACCA-AGGGTATTTTTGTAATTTTGT
* * **
39663974 AAATCAGGGGTATTTTCCTAATTTTGT
1 AAACCAAGGGTATTTTTGTAATTTTGT
* *
39664001 AAGCCAAGGGTA-TTTAGTAATTTTGT
1 AAACCAAGGGTATTTTTGTAATTTTGT
39664027 AAACCAAGGGTATTT
1 AAACCAAGGGTATTT
39664042 CAGTAATCCT
Statistics
Matches: 307, Mismatches: 76, Indels: 22
0.76 0.19 0.05
Matches are distributed among these distances:
26 28 0.09
27 229 0.75
28 49 0.16
29 1 0.00
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.42
Consensus pattern (27 bp):
AAACCAAGGGTATTTTTGTAATTTTGT
Found at i:39663720 original size:55 final size:54
Alignment explanation
Indices: 39663618--39663863 Score: 178
Period size: 55 Copynumber: 4.5 Consensus size: 54
39663608 TTGGTAAATC
* * *
39663618 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCA-ATGGT-CTTTTTGTAATTT
1 TACAAATCAAGGGTATTTCTGTAATTTTGTAAATCAGA-GGTAC-TTTTGTAATTT
** * * *
39663672 TTGAAAGTCAAGGGTATTTTTGTAATTTTGTAAATCAGGGGTACTTTTGTCATTT
1 TACAAA-TCAAGGGTATTTCTGTAATTTTGTAAATCAGAGGTACTTTTGTAATTT
* * * * ** * * *
39663727 TCCAAATCAAGGGTTTTTTTATTAATTTTCCAAATCAGAGGCATTTTTATAATTT
1 TACAAATCAAGGGTATTTCT-GTAATTTTGTAAATCAGAGGTACTTTTGTAATTT
* ** * *
39663782 TACAAATCAAGGGTATTTCGGTAATTTTACAAGTTA-AGAGTA-TTTTGGTAATTT
1 TACAAATCAAGGGTATTTCTGTAATTTTGTAAATCAGAG-GTACTTTT-GTAATTT
* *
39663836 TACAAGTCGAGGGTATTT-TAGTAATTTT
1 TACAAATCAAGGGTATTTCT-GTAATTTT
39663864 ACAGGTCAAG
Statistics
Matches: 153, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
53 6 0.04
54 61 0.40
55 85 0.56
56 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (54 bp):
TACAAATCAAGGGTATTTCTGTAATTTTGTAAATCAGAGGTACTTTTGTAATTT
Found at i:39663864 original size:81 final size:80
Alignment explanation
Indices: 39663676--39664048 Score: 270
Period size: 81 Copynumber: 4.6 Consensus size: 80
39663666 TAATTTTTGA
* ** * * * * * *
39663676 AAGTCAAGGGTATTTTTGTAATTTTGTAAATCAGGGGTACTTT-TGTCATTTTCCAAATCAAGGG
1 AAGTC-AGGGTATTTTAGTAATTTTACAAATCAAGGGTA-TTTCGGTAATTTTACAAGTTAAGGG
* * *
39663740 TTTTTTTATTAATTTTCC
64 TATTTTGA-TAATTTTAC
* * *
39663758 AAATCAGAGGCATTTTTA-TAATTTTACAAATCAAGGGTATTTCGGTAATTTTACAAGTTAAGAG
1 AAGTCAG-GGTA-TTTTAGTAATTTTACAAATCAAGGGTATTTCGGTAATTTTACAAGTTAAGGG
*
39663822 TATTTTGGTAATTTTAC
64 TATTTTGATAATTTTAC
** * * *
39663839 AAGTCGAGGGTATTTTAGTAATTTTACAGGTCAAGGGTATTTCGGTAATTTTATAGGTTGAGGGT
1 AAGTC-AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTCGGTAATTTTACAAGTTAAGGGT
*
39663904 ATTTTGATAATTTTCC
65 ATTTTGATAATTTTAC
* * * * * * * *
39663920 AAATCAGGGGTATATTT-GTTATTTTACAAAT-AGAAGATATTTCGGTAATTTTCCAAATCAGGG
1 AAGTCA-GGGTAT-TTTAGTAATTTTACAAATCA-AGGGTATTTCGGTAATTTTACAAGTTAAGG
** **
39663983 GTATTTTCCTAATTTTGT
63 GTATTTTGATAATTTTAC
* ** * *
39664001 AAGCCAAGGGTA-TTTAGTAATTTTGTAAACCAAGGGTATTTCAGTAAT
1 AAGTC-AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTCGGTAAT
39664049 CCTAACCTAC
Statistics
Matches: 228, Mismatches: 52, Indels: 24
0.75 0.17 0.08
Matches are distributed among these distances:
79 3 0.01
80 30 0.13
81 140 0.61
82 51 0.22
83 4 0.02
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (80 bp):
AAGTCAGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTCGGTAATTTTACAAGTTAAGGGTA
TTTTGATAATTTTAC
Found at i:39663998 original size:54 final size:54
Alignment explanation
Indices: 39663682--39663998 Score: 203
Period size: 54 Copynumber: 5.9 Consensus size: 54
39663672 TTGAAAGTCA
** ** * *
39663682 AGGGTATTTTTGTAATTTTGTAAATCAGGGGTACTTTT-GTCATTTTCCAAATCA-
1 AGGGTATTTCGGTAATTTTCCAAATCAGGGGTA-TTTTCGTAATTTTACAAAT-AG
* *** * * **
39663736 AGGGTTTTTTTATTAATTTTCCAAATCAGAGGCATTTTTATAATTTTACAAATCA-
1 AGGG-TATTTCGGTAATTTTCCAAATCAGGGGTATTTTCGTAATTTTACAAAT-AG
* * * * * * * *
39663791 AGGGTATTTCGGTAATTTTACAAGTTAAGAGTATTTTGGTAATTTTACAAGTCG
1 AGGGTATTTCGGTAATTTTCCAAATCAGGGGTATTTTCGTAATTTTACAAATAG
** * ** * * ** *
39663845 AGGGTATTTTAGTAATTTTACAGGTCAAGGGTA-TTTCGGTAATTTTATAGGTTG
1 AGGGTATTTCGGTAATTTTCCAAATCAGGGGTATTTTC-GTAATTTTACAAATAG
* * *
39663899 AGGGTATTTTGATAATTTTCCAAATCAGGGGTATATTT-GTTATTTTACAAATAG
1 AGGGTATTTCGGTAATTTTCCAAATCAGGGGTAT-TTTCGTAATTTTACAAATAG
* * *
39663953 AAGATATTTCGGTAATTTTCCAAATCAGGGGTATTTTCCTAATTTT
1 AGGGTATTTCGGTAATTTTCCAAATCAGGGGTATTTTCGTAATTTT
39663999 GTAAGCCAAG
Statistics
Matches: 205, Mismatches: 51, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
53 6 0.03
54 157 0.77
55 39 0.19
56 3 0.01
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (54 bp):
AGGGTATTTCGGTAATTTTCCAAATCAGGGGTATTTTCGTAATTTTACAAATAG
Found at i:39664025 original size:26 final size:27
Alignment explanation
Indices: 39663957--39664048 Score: 98
Period size: 26 Copynumber: 3.4 Consensus size: 27
39663947 AAATAGAAGA
* ** * *
39663957 TATTTCGGTAATTTTCCAAATCAGGGG
1 TATTTCAGTAATTTTGTAAACCAAGGG
* *
39663984 TATTTTC-CTAATTTTGTAAGCCAAGGG
1 TA-TTTCAGTAATTTTGTAAACCAAGGG
39664011 TATTT-AGTAATTTTGTAAACCAAGGG
1 TATTTCAGTAATTTTGTAAACCAAGGG
39664037 TATTTCAGTAAT
1 TATTTCAGTAAT
39664049 CCTAACCTAC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
26 26 0.48
27 24 0.44
28 4 0.07
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (27 bp):
TATTTCAGTAATTTTGTAAACCAAGGG
Found at i:39664068 original size:27 final size:26
Alignment explanation
Indices: 39664038--39664141 Score: 109
Period size: 27 Copynumber: 3.8 Consensus size: 26
39664028 AACCAAGGGT
39664038 ATTTCAGTAATCCTAACCTACAGGGGC
1 ATTTCAGTAAT-CTAACCTACAGGGGC
* * *
39664065 ATTTTAGTAAGTCTATCCTATAGGGGC
1 ATTTCAGTAA-TCTAACCTACAGGGGC
* *
39664092 ATTTCAGTAATTCTACCCTACAGGGGT
1 ATTTCAGTAA-TCTAACCTACAGGGGC
* *
39664119 ATTTCAGTATTACTAGCCTACAG
1 ATTTCAGTAAT-CTAACCTACAG
39664142 ATATGAGATT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.02
27 63 0.97
28 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (26 bp):
ATTTCAGTAATCTAACCTACAGGGGC
Found at i:39666804 original size:22 final size:22
Alignment explanation
Indices: 39666771--39666832 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
39666761 AATACGTTTG
39666771 GCACACAA-CCATAATCAGGTTA
1 GCACA-AAGCCATAATCAGGTTA
* * *
39666793 GCACAGAGCCAT-ATGTAGGTTG
1 GCACAAAGCCATAAT-CAGGTTA
*
39666815 GCGCAAAGCCATAATCAG
1 GCACAAAGCCATAATCAG
39666833 AATAATTGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
21 3 0.10
22 26 0.84
23 2 0.06
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (22 bp):
GCACAAAGCCATAATCAGGTTA
Found at i:39667035 original size:41 final size:41
Alignment explanation
Indices: 39666975--39667095 Score: 161
Period size: 41 Copynumber: 3.0 Consensus size: 41
39666965 AAAAGGACCG
** * * * *
39666975 GTGGATCCACGGTCATCAAGCAACCATACGATCCTTAATCG
1 GTGGATCCACAATCGTCAAGCAACCATGCGATCCTCAATCA
*
39667016 GTGGATCCACAATTGTCAAGCAACCATGCGATCCTCAATCA
1 GTGGATCCACAATCGTCAAGCAACCATGCGATCCTCAATCA
**
39667057 GTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
1 GTGGATCCACAATCGTCAAGCAACCATGCGATCCTCAAT
39667096 TTCTTCCTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (41 bp):
GTGGATCCACAATCGTCAAGCAACCATGCGATCCTCAATCA
Found at i:39667361 original size:27 final size:27
Alignment explanation
Indices: 39667331--39667401 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
39667321 TTTCACCTTA
*
39667331 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAAATCTACAAAC
* * * *
39667358 CAAGGGTATTTCGGTAATTTTGCAAAC
1 CAAGGGTATTTTGGTAAATCTACAAAC
* *
39667385 CAATGGTATTTTTGTAA
1 CAAGGGTATTTTGGTAA
39667402 TTTTTAAAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAAATCTACAAAC
Found at i:39667402 original size:27 final size:27
Alignment explanation
Indices: 39667353--39667720 Score: 258
Period size: 27 Copynumber: 13.6 Consensus size: 27
39667343 GGTAAATCTA
* * *
39667353 CAAACCAAGGGTATTTCGGTAATTTTG
1 CAAATCAAGGGTATTTCTGTAATTTTC
* * * *
39667380 CAAACCAATGGTATTTTTGTAATTTTT
1 CAAATCAAGGGTATTTCTGTAATTTTC
* * *
39667407 AAAAGTCAAGGGTATTTCTGTAATTCTG
1 CAAA-TCAAGGGTATTTCTGTAATTTTC
* * *
39667435 TAAATCAGGGGTATTTATGTAATTTTC
1 CAAATCAAGGGTATTTCTGTAATTTTC
39667462 CAAATCAAGGGTATTTC-GATAATTTTC
1 CAAATCAAGGGTATTTCTG-TAATTTTC
* * * *
39667489 CAAATTAGGGGTATTTTTGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTC
* *
39667516 CAAATCAAGGGTATTTCGGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTC
** * * ** *
39667543 CAGGTCGAGAGTATTTCAATAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTC
* * * *
39667570 CAAGTCGAGGGTATTTCAGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTC
** ** * *
39667597 CAGGTTGAGGGTATTTCGGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTC
** * *
39667624 CAGGTCGATGGTATTTC-GATAATTTTC
1 CAAATCAAGGGTATTTCTG-TAATTTTC
* * *
39667651 GAAATCATGGGTATATT-TGTAATTTTA
1 CAAATCAAGGGTAT-TTCTGTAATTTTC
*
39667678 TAAATCAAGGGTATTTC-GATAATTTTC
1 CAAATCAAGGGTATTTCTG-TAATTTTC
*
39667705 CAAATCAGGGGTATTT
1 CAAATCAAGGGTATTT
39667721 TGCTACTTTT
Statistics
Matches: 280, Mismatches: 53, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
26 5 0.02
27 250 0.89
28 25 0.09
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (27 bp):
CAAATCAAGGGTATTTCTGTAATTTTC
Found at i:39667499 original size:54 final size:54
Alignment explanation
Indices: 39667351--39667720 Score: 313
Period size: 54 Copynumber: 6.8 Consensus size: 54
39667341 TTGGTAAATC
* * * * ** *
39667351 TACAAACCAAGGGTATTTCGGTAATTTTGCAAACCAATGGTATTTTTGTAATTTT
1 TACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGGGGTATTTATGTAA-TTT
* **
39667406 TA-AAAGTCAAGGGTATTTCTG-TAATTCTGTAAATCAGGGGTATTTATGTAATTT
1 TACAAA-TCAAGGGTATTTC-GATAATTTTCCAAATCAGGGGTATTTATGTAATTT
* * *
39667460 TCCAAATCAAGGGTATTTCGATAATTTTCCAAATTAGGGGTATTTTTGTAATTT
1 TACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGGGGTATTTATGTAATTT
* * ** * *
39667514 TACAAATCAAGGGTATTTCGGTAATTTTACAGGTC-GAGAGTATTTCA-ATAATTT
1 TACAAATCAAGGGTATTTCGATAATTTTCCAAATCAG-GGGTATTT-ATGTAATTT
* * * ** * **
39667568 TACAAGTCGAGGGTATTTC-AGTAATTTTACAGGT-TGAGGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTCGA-TAATTTTCCAAATCAG-GGGTATTTATGTAATTT
** * * * *
39667622 TACAGGTCGATGGTATTTCGATAATTTTCGAAATCATGGGTATATT-TGTAATTT
1 TACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGGGGTAT-TTATGTAATTT
*
39667676 TATAAATCAAGGGTATTTCGATAATTTTCCAAATCAGGGGTATTT
1 TACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGGGGTATTT
39667721 TGCTACTTTT
Statistics
Matches: 259, Mismatches: 44, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
53 4 0.02
54 210 0.81
55 44 0.17
56 1 0.00
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.40
Consensus pattern (54 bp):
TACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGGGGTATTTATGTAATTT
Found at i:39667538 original size:81 final size:81
Alignment explanation
Indices: 39667351--39667720 Score: 332
Period size: 81 Copynumber: 4.6 Consensus size: 81
39667341 TTGGTAAATC
* * * * * **
39667351 TACAAACCAAGGGTATTTCGGTAATTTTGCAAACCAATGGTATTTTTG-TAATTTTTAAAAGTCA
1 TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTA-TTTCGATAATTTTCCAAA-TCA
* *
39667415 AGGGTATTTCTGTAATTC
64 GGGGTATTTCTGTAATTT
** * ** * *
39667433 TGTAAATCAGGGGTATTTATGTAATTTTCCAAATCAAGGGTATTTCGATAATTTTCCAAATTAGG
1 TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGG
*
39667498 GGTATTTTTGTAATTT
66 GGTATTTCTGTAATTT
** * * * * *
39667514 TACAAATCAAGGGTATTTCGGTAATTTTACAGGTCGAGAGTATTTCAATAATTTTACAAGTC-GA
1 TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTCCAAATCAG-
*
39667578 GGGTATTTCAGTAATTT
65 GGGTATTTCTGTAATTT
** ** ** * * * *
39667595 TACAGGTTGAGGGTATTTCGGTAATTTTACAGGTCGATGGTATTTCGATAATTTTCGAAATCATG
1 TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGG
39667660 GGTATATT-TGTAATTT
66 GGTAT-TTCTGTAATTT
* * * *
39667676 TATAAATCAAGGGTATTTCGATAATTTTCCAAATCAGGGGTATTT
1 TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTT
39667721 TGCTACTTTT
Statistics
Matches: 228, Mismatches: 56, Indels: 9
0.78 0.19 0.03
Matches are distributed among these distances:
80 1 0.00
81 182 0.80
82 45 0.20
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.40
Consensus pattern (81 bp):
TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGG
GGTATTTCTGTAATTT
Found at i:39667758 original size:26 final size:27
Alignment explanation
Indices: 39667670--39667781 Score: 91
Period size: 27 Copynumber: 4.2 Consensus size: 27
39667660 GGTATATTTG
* * *
39667670 TAATTTTATAAATCAAGGGTATTTCGA
1 TAATTTTGTAAACCAAGGGTATTTCAA
** * * ***
39667697 TAATTTTCCAAATCAGGGGTATTTTGC
1 TAATTTTGTAAACCAAGGGTATTTCAA
* * *
39667724 TACTTTTGTAAGCCAATGGTA-TTCAA
1 TAATTTTGTAAACCAAGGGTATTTCAA
*
39667750 TAATTTTGTAAACCAAGGGTATTTCAG
1 TAATTTTGTAAACCAAGGGTATTTCAA
39667777 TAATT
1 TAATT
39667782 CTACCCTACA
Statistics
Matches: 65, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
26 20 0.31
27 45 0.69
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (27 bp):
TAATTTTGTAAACCAAGGGTATTTCAA
Found at i:39667800 original size:27 final size:27
Alignment explanation
Indices: 39667770--39667873 Score: 163
Period size: 27 Copynumber: 3.9 Consensus size: 27
39667760 AACCAAGGGT
39667770 ATTTCAGTAATTCTACCCTACAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
* *
39667797 ATTTCAGTAATTCTATCTTACAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
*
39667824 ATTTCAGTAATTCTACCCTACAGGGGT
1 ATTTCAGTAATTCTACCCTACAGGGGC
* *
39667851 ATTTCAGTAATACTAGCCTACAG
1 ATTTCAGTAATTCTACCCTACAG
39667874 ATATTAGATT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (27 bp):
ATTTCAGTAATTCTACCCTACAGGGGC
Found at i:39670546 original size:22 final size:22
Alignment explanation
Indices: 39670513--39670574 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
39670503 AATACGTTTG
39670513 GCACACAA-CCATAATCAGGTTA
1 GCACA-AAGCCATAATCAGGTTA
* * *
39670535 GCACAGAGCCAT-ATGTAGGTTG
1 GCACAAAGCCATAAT-CAGGTTA
*
39670557 GCGCAAAGCCATAATCAG
1 GCACAAAGCCATAATCAG
39670575 AATAATTGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
21 3 0.10
22 26 0.84
23 2 0.06
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (22 bp):
GCACAAAGCCATAATCAGGTTA
Found at i:39670776 original size:41 final size:41
Alignment explanation
Indices: 39670716--39670836 Score: 161
Period size: 41 Copynumber: 3.0 Consensus size: 41
39670706 AAAAGGACCG
** * * * *
39670716 GTGGATCCACGGTCATCAAGCAACCATACGATCCTTAATCG
1 GTGGATCCACAATCGTCAAGCAACCATGCGATCCTCAATCA
*
39670757 GTGGATCCACAATTGTCAAGCAACCATGCGATCCTCAATCA
1 GTGGATCCACAATCGTCAAGCAACCATGCGATCCTCAATCA
**
39670798 GTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
1 GTGGATCCACAATCGTCAAGCAACCATGCGATCCTCAAT
39670837 TTCTTCCTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (41 bp):
GTGGATCCACAATCGTCAAGCAACCATGCGATCCTCAATCA
Found at i:39671103 original size:27 final size:27
Alignment explanation
Indices: 39671073--39671143 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
39671063 TTTCACCTTA
*
39671073 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAAATCTACAAAC
* * * *
39671100 CAAGGGTATTTCGGTAATTTTGCAAAC
1 CAAGGGTATTTTGGTAAATCTACAAAC
* *
39671127 CAATGGTATTTTTGTAA
1 CAAGGGTATTTTGGTAA
39671144 TTTTTGAAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAAATCTACAAAC
Found at i:39671144 original size:27 final size:27
Alignment explanation
Indices: 39671095--39671522 Score: 244
Period size: 27 Copynumber: 15.9 Consensus size: 27
39671085 GGTAAATCTA
* *
39671095 CAAACCAAGGGTATTTCGGTAATTTTG
1 CAAATCAAGGGTATTTCTGTAATTTTG
* * *
39671122 CAAACCAATGGTATTTTTGTAATTTTTG
1 CAAATCAAGGGTATTTCTGTAA-TTTTG
*
39671150 -AAAGTCAAGGGTATTTCTGTAATTCTG
1 CAAA-TCAAGGGTATTTCTGTAATTTTG
* * * *
39671177 TAAATCAGGGGTATTTATGTAATTTTC
1 CAAATCAAGGGTATTTCTGTAATTTTG
*
39671204 CAAATCAAGGGTATTTC-GATAATTTTC
1 CAAATCAAGGGTATTTCTG-TAATTTTG
* * * *
39671231 CAAATTAGGGGTATTTTTGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTG
* *
39671258 CAAATCAAGGGTATTTCGGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTG
** * * ** *
39671285 CAGGTCGAGAGTATTTCAATAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTG
* * * *
39671312 CAAGTCGAGGGTATTTCAGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTG
** ** * *
39671339 CAGGTTGAGGGTATTTCGGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTG
** * *
39671366 CAGGTCGATGGTATTTC-GATAATTTT-
1 CAAATCAAGGGTATTTCTG-TAATTTTG
* *
39671392 CGAAATCATGGGTATATT-TGTAATTTTA
1 C-AAATCAAGGGTAT-TTCTGTAATTTTG
* *
39671420 TAAATCAAGGGTATTTC-GATAATTTTC
1 CAAATCAAGGGTATTTCTG-TAATTTTG
* *
39671447 CAAATCAGGGGTATTT-TGCTACTTTTG
1 CAAATCAAGGGTATTTCTG-TAATTTTG
* ** * **
39671474 TAAGCCAATGGTA-TTCAATAA-TTTG
1 CAAATCAAGGGTATTTCTGTAATTTTG
* * *
39671499 TAAACCAAGGGTATTTCAGTAATT
1 CAAATCAAGGGTATTTCTGTAATT
39671523 CTACCCTACA
Statistics
Matches: 325, Mismatches: 60, Indels: 32
0.78 0.14 0.08
Matches are distributed among these distances:
25 15 0.05
26 17 0.05
27 266 0.82
28 27 0.08
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (27 bp):
CAAATCAAGGGTATTTCTGTAATTTTG
Found at i:39671159 original size:55 final size:54
Alignment explanation
Indices: 39671093--39671463 Score: 325
Period size: 54 Copynumber: 6.9 Consensus size: 54
39671083 TTGGTAAATC
* * **
39671093 TACAAACCAAGGGTATTTCGGTAATTTTGCAAACCAATGGTATTTTTGTAATTT
1 TACAAATCAAGGGTATTTCGGTAATTTTGCAAATCAGGGGTATTTTTGTAATTT
** * * * *
39671147 TTGAAAGTCAAGGGTATTTCTGTAATTCTGTAAATCAGGGGTATTTATGTAATTT
1 TACAAA-TCAAGGGTATTTCGGTAATTTTGCAAATCAGGGGTATTTTTGTAATTT
* * * *
39671202 TCCAAATCAAGGGTATTTCGATAATTTTCCAAATTAGGGGTATTTTTGTAATTT
1 TACAAATCAAGGGTATTTCGGTAATTTTGCAAATCAGGGGTATTTTTGTAATTT
* ** * ***
39671256 TACAAATCAAGGGTATTTCGGTAATTTTACAGGTC-GAGAGTATTTCAATAATTT
1 TACAAATCAAGGGTATTTCGGTAATTTTGCAAATCAG-GGGTATTTTTGTAATTT
* * * * ** * **
39671310 TACAAGTCGAGGGTATTTCAGTAATTTTACAGGT-TGAGGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTCGGTAATTTTGCAAATCAG-GGGTATTTTTGTAATTT
** * * * * *
39671364 TACAGGTCGATGGTATTTCGATAATTTT-CGAAATCATGGGTATATTTGTAATTT
1 TACAAATCAAGGGTATTTCGGTAATTTTGC-AAATCAGGGGTATTTTTGTAATTT
* * *
39671418 TATAAATCAAGGGTATTTCGATAATTTTCCAAATCAGGGGTATTTT
1 TACAAATCAAGGGTATTTCGGTAATTTTGCAAATCAGGGGTATTTT
39671464 GCTACTTTTG
Statistics
Matches: 258, Mismatches: 53, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
53 2 0.01
54 211 0.82
55 45 0.17
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
TACAAATCAAGGGTATTTCGGTAATTTTGCAAATCAGGGGTATTTTTGTAATTT
Found at i:39671280 original size:81 final size:81
Alignment explanation
Indices: 39671093--39671462 Score: 332
Period size: 81 Copynumber: 4.6 Consensus size: 81
39671083 TTGGTAAATC
* * * * * **
39671093 TACAAACCAAGGGTATTTCGGTAATTTTGCAAACCAATGGTATTTTTG-TAATTTTTGAAAGTCA
1 TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTA-TTTCGATAATTTTCCAAA-TCA
* *
39671157 AGGGTATTTCTGTAATTC
64 GGGGTATTTCTGTAATTT
** * ** * *
39671175 TGTAAATCAGGGGTATTTATGTAATTTTCCAAATCAAGGGTATTTCGATAATTTTCCAAATTAGG
1 TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGG
*
39671240 GGTATTTTTGTAATTT
66 GGTATTTCTGTAATTT
** * * * * *
39671256 TACAAATCAAGGGTATTTCGGTAATTTTACAGGTCGAGAGTATTTCAATAATTTTACAAGTC-GA
1 TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTCCAAATCAG-
*
39671320 GGGTATTTCAGTAATTT
65 GGGTATTTCTGTAATTT
** ** ** * * * *
39671337 TACAGGTTGAGGGTATTTCGGTAATTTTACAGGTCGATGGTATTTCGATAATTTTCGAAATCATG
1 TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGG
39671402 GGTATATT-TGTAATTT
66 GGTAT-TTCTGTAATTT
* * * *
39671418 TATAAATCAAGGGTATTTCGATAATTTTCCAAATCAGGGGTATTT
1 TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTT
39671463 TGCTACTTTT
Statistics
Matches: 228, Mismatches: 56, Indels: 9
0.78 0.19 0.03
Matches are distributed among these distances:
80 1 0.00
81 182 0.80
82 45 0.20
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (81 bp):
TACAAATCAAGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTCCAAATCAGG
GGTATTTCTGTAATTT
Found at i:39671506 original size:25 final size:26
Alignment explanation
Indices: 39671470--39671522 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
39671460 TTTTGCTACT
* *
39671470 TTTGTAAGCCAATGGTA-TTCAATAA
1 TTTGTAAACCAAGGGTATTTCAATAA
*
39671495 TTTGTAAACCAAGGGTATTTCAGTAA
1 TTTGTAAACCAAGGGTATTTCAATAA
39671521 TT
1 TT
39671523 CTACCCTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (26 bp):
TTTGTAAACCAAGGGTATTTCAATAA
Found at i:39671546 original size:27 final size:27
Alignment explanation
Indices: 39671511--39671614 Score: 163
Period size: 27 Copynumber: 3.9 Consensus size: 27
39671501 AACCAAGGGT
39671511 ATTTCAGTAATTCTACCCTACAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
* *
39671538 ATTTCAGTAATTCTATCTTACAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
*
39671565 ATTTCAGTAATTCTACCCTACAGGGGT
1 ATTTCAGTAATTCTACCCTACAGGGGC
* *
39671592 ATTTCAGTAATACTAGCCTACAG
1 ATTTCAGTAATTCTACCCTACAG
39671615 ATATTAGATT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (27 bp):
ATTTCAGTAATTCTACCCTACAGGGGC
Found at i:39674505 original size:40 final size:40
Alignment explanation
Indices: 39674457--39674641 Score: 255
Period size: 40 Copynumber: 4.6 Consensus size: 40
39674447 CTTGCACAAG
*
39674457 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
39674497 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
39674537 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
39674577 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
39674618 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
39674642 CATTCGAATA
Statistics
Matches: 125, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 95 0.76
41 29 0.23
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:39682551 original size:40 final size:40
Alignment explanation
Indices: 39682497--39682680 Score: 219
Period size: 40 Copynumber: 4.6 Consensus size: 40
39682487 CTTGCACAAG
*
39682497 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
** * *
39682537 GCCTTCGGAACTTAGCCCGGATATAGTCGCTAGCCCAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
39682577 GCCTTCGGGTCTTAGCCCAGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
39682617 GACTTCGGATCTTAGTCCGG-TATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
39682657 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
39682681 CATTCGAATA
Statistics
Matches: 117, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
39 7 0.06
40 107 0.91
41 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:39685586 original size:22 final size:22
Alignment explanation
Indices: 39685552--39685616 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
39685542 GCAAATACGT
* *
39685552 TTGGCACACAGCCATAATCAGG
1 TTGGCATAAAGCCATAATCAGG
*
39685574 TTGGCATAGAGCCATATAT-AGG
1 TTGGCATAAAGCCATA-ATCAGG
*
39685596 TTGGCGTAAAGCCATAATCAG
1 TTGGCATAAAGCCATAATCAG
39685617 AATAATTGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.05
22 33 0.89
23 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (22 bp):
TTGGCATAAAGCCATAATCAGG
Found at i:39685822 original size:41 final size:42
Alignment explanation
Indices: 39685759--39685879 Score: 140
Period size: 41 Copynumber: 3.0 Consensus size: 42
39685749 AAGGCCACTG
* * *
39685759 GTGGATCCAC-AGTCGTCAAGCAACCATACGATCGTTAATTA
1 GTGGATCCACGAGTCGTCAAGCAACCATACGATCCTCAATCA
** * *
39685800 GTGGATCCACGA-TCGTTTAGCAACCATGCGATCCTCAATCG
1 GTGGATCCACGAGTCGTCAAGCAACCATACGATCCTCAATCA
* *
39685841 GTGGATCCACG-GTCATCAAGCAACCATGCGATCCTCAAT
1 GTGGATCCACGAGTCGTCAAGCAACCATACGATCCTCAAT
39685880 TTCTTCCTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 67 0.99
42 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (42 bp):
GTGGATCCACGAGTCGTCAAGCAACCATACGATCCTCAATCA
Found at i:39686170 original size:27 final size:28
Alignment explanation
Indices: 39686144--39686299 Score: 153
Period size: 27 Copynumber: 5.8 Consensus size: 28
39686134 ATCTATAAAC
*
39686144 CAAGGGTATTT-TAGTAATTTTGGAAAC
1 CAAGGGTATTTCTAGTAATTTTGGAAAT
* *
39686171 CAATGGTATTTCTA-TAATTTTTGAAAGT
1 CAAGGGTATTTCTAGTAATTTTGGAAA-T
*
39686199 CAAGGGTATTTCT-GTAATTTTGTAAAT
1 CAAGGGTATTTCTAGTAATTTTGGAAAT
* * **
39686226 TAGGGGTATTTCT-GTAATTTTCCAAAT
1 CAAGGGTATTTCTAGTAATTTTGGAAAT
**
39686253 CAAGGGTATTT-TAGTAATTTTTCAAAT
1 CAAGGGTATTTCTAGTAATTTTGGAAAT
* *
39686280 TAGGGGTATTTCTA-TAATTT
1 CAAGGGTATTTCTAGTAATTT
39686300 ACAAATTGAT
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
26 1 0.01
27 82 0.75
28 26 0.24
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (28 bp):
CAAGGGTATTTCTAGTAATTTTGGAAAT
Found at i:39686280 original size:54 final size:54
Alignment explanation
Indices: 39686144--39686299 Score: 190
Period size: 54 Copynumber: 2.9 Consensus size: 54
39686134 ATCTATAAAC
* ** ** **
39686144 CAAGGGTATTTTAGTAATTTTGGAAACCAATGGTATTTCTATAATTTTTGAAAGT
1 CAAGGGTATTTTAGTAATTTT-TAAATTAGGGGTATTTCTATAATTTTCCAAAGT
*
39686199 CAAGGGTATTTCT-GTAATTTTGTAAATTAGGGGTATTTCTGTAATTTTCCAAA-T
1 CAAGGGTATTT-TAGTAATTTT-TAAATTAGGGGTATTTCTATAATTTTCCAAAGT
39686253 CAAGGGTATTTTAGTAATTTTTCAAATTAGGGGTATTTCTATAATTT
1 CAAGGGTATTTTAGTAATTTTT-AAATTAGGGGTATTTCTATAATTT
39686300 ACAAATTGAT
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
53 2 0.02
54 43 0.48
55 43 0.48
56 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (54 bp):
CAAGGGTATTTTAGTAATTTTTAAATTAGGGGTATTTCTATAATTTTCCAAAGT
Found at i:39686340 original size:27 final size:27
Alignment explanation
Indices: 39686175--39686502 Score: 226
Period size: 27 Copynumber: 12.1 Consensus size: 27
39686165 GGAAACCAAT
* *
39686175 GGTATTTCTATAATTTTTGA-AAGTCAAG
1 GGTATTTCTGTAA-TTTT-ACAAGTCGAG
* *
39686203 GGTATTTCTGTAATTTTGTA-AATTAG-G
1 GGTATTTCTGTAA-TTT-TACAAGTCGAG
* * *
39686230 GGTATTTCTGTAATTTTCCAAATCAAG
1 GGTATTTCTGTAATTTTACAAGTCGAG
* * *
39686257 GGTATTT-TAGTAATTTTTCAAAT-TAGG
1 GGTATTTCT-GTAATTTTACAAGTCGA-G
* * * *
39686284 GGTATTTCTATAA-TTTACAAATTGAT
1 GGTATTTCTGTAATTTTACAAGTCGAG
*
39686310 GGTATTTCTGTAATTTTATAAGTCGAG
1 GGTATTTCTGTAATTTTACAAGTCGAG
** *
39686337 GGTATTTCAATAATTTTACAAGTTGAG
1 GGTATTTCTGTAATTTTACAAGTCGAG
* *
39686364 GGTATTTC-GATAATTTTACAGGTTGAG
1 GGTATTTCTG-TAATTTTACAAGTCGAG
* *
39686391 GGTATTTCGGTAATTTTACAGGTCGAG
1 GGTATTTCTGTAATTTTACAAGTCGAG
*
39686418 GGTATTT-TGGTAATTTTACAAGTCGAT
1 GGTATTTCT-GTAATTTTACAAGTCGAG
* * *
39686445 GATATTTC-GATAATTTTCCAAATC-AGG
1 GGTATTTCTG-TAATTTTACAAGTCGA-G
* * * *
39686472 GGTATATCTGTAGTTTTACAAATAGAG
1 GGTATTTCTGTAATTTTACAAGTCGAG
39686499 GGTA
1 GGTA
39686503 CTTTGGTAAT
Statistics
Matches: 246, Mismatches: 38, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
25 1 0.00
26 30 0.12
27 190 0.77
28 24 0.10
29 1 0.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
GGTATTTCTGTAATTTTACAAGTCGAG
Found at i:39686420 original size:81 final size:81
Alignment explanation
Indices: 39686201--39686514 Score: 305
Period size: 81 Copynumber: 3.9 Consensus size: 81
39686191 TTGAAAGTCA
** * * *
39686201 AGGGTATTTCTG-TAATTTTGTAAATT-AGGGGTATTTCTGTAATTTTCCAAATCAAGGGTATTT
1 AGGGTATTTC-GATAATTTTACAAATTGA-GGGTATTTCTGTAATTTTACAAGTCGAGGGTATTT
* *
39686264 TAGTAATTTTTCAAATT-
64 TAGTAATTTTACAAGTTG
* * * *
39686281 AGGGGTATTTCTATAA-TTTACAAATTGATGGTATTTCTGTAATTTTATAAGTCGAGGGTATTTC
1 A-GGGTATTTCGATAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAGTCGAGGGTATTTT
*
39686345 AATAATTTTACAAGTTG
65 AGTAATTTTACAAGTTG
** * * *
39686362 AGGGTATTTCGATAATTTTACAGGTTGAGGGTATTTCGGTAATTTTACAGGTCGAGGGTATTTTG
1 AGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAGTCGAGGGTATTTTA
*
39686427 GTAATTTTACAAGTCG
66 GTAATTTTACAAGTTG
* * * * * * * * *
39686443 ATGATATTTCGATAATTTTCCAAA-TCAGGGGTATATCTGTAGTTTTACAAATAGAGGGTACTTT
1 AGGGTATTTCGATAATTTTACAAATTGA-GGGTATTTCTGTAATTTTACAAGTCGAGGGTATTTT
*
39686507 GGTAATTT
65 AGTAATTT
39686515 CCCAAATAAG
Statistics
Matches: 192, Mismatches: 36, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
80 67 0.35
81 125 0.65
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (81 bp):
AGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAGTCGAGGGTATTTTA
GTAATTTTACAAGTTG
Found at i:39686475 original size:54 final size:55
Alignment explanation
Indices: 39686229--39686542 Score: 220
Period size: 54 Copynumber: 5.8 Consensus size: 55
39686219 TGTAAATTAG
* * * * *
39686229 GGGTATTTCTG-TAATTTTCCAAATCA-AGGGTATTTTAGTAATTTTTCAAAT-TA
1 GGGTATTTC-GATAATTTTACAAATCAGAGGGTATTTTGGTAATTTTACAAGTCGA
* * * *
39686282 GGGGTATTTCTATAA-TTTACAAAT-TGATGGTATTTCT-GTAATTTTATAAGTCGA
1 -GGGTATTTCGATAATTTTACAAATCAGAGGGTATTT-TGGTAATTTTACAAGTCGA
* * * * * * *
39686336 GGGTATTTCAATAATTTTACAAGT-TGAGGGTATTTCGATAATTTTACAGGTTGA
1 GGGTATTTCGATAATTTTACAAATCAGAGGGTATTTTGGTAATTTTACAAGTCGA
* **
39686390 GGGTATTTCGGTAATTTTACAGGTC-GAGGGTATTTTGGTAATTTTACAAGTCGA
1 GGGTATTTCGATAATTTTACAAATCAGAGGGTATTTTGGTAATTTTACAAGTCGA
* * * * * * *
39686444 TGATATTTCGATAATTTTCCAAATCAG-GGGTATATCT-GTAGTTTTACAAATAGA
1 GGGTATTTCGATAATTTTACAAATCAGAGGGTAT-TTTGGTAATTTTACAAGTCGA
* ** * *
39686498 GGGTACTTT-GGTAATTTCCCAAATAAG-GGGTATTTCGGTAATTTT
1 GGGTA-TTTCGATAATTTTACAAATCAGAGGGTATTTTGGTAATTTT
39686543 GTAAACCAAG
Statistics
Matches: 208, Mismatches: 41, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
53 41 0.20
54 161 0.77
55 6 0.03
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (55 bp):
GGGTATTTCGATAATTTTACAAATCAGAGGGTATTTTGGTAATTTTACAAGTCGA
Found at i:39686520 original size:27 final size:27
Alignment explanation
Indices: 39686447--39686541 Score: 86
Period size: 27 Copynumber: 3.5 Consensus size: 27
39686437 AAGTCGATGA
* * *
39686447 TATTTCGATAATTTTCCAAATCAGGGG
1 TATTTCGGTAATTTCCCAAATAAGGGG
* * * **
39686474 TATATCTGTAGTTTTACAAAT-AGAGGG
1 TATTTCGGTAATTTCCCAAATAAG-GGG
39686501 TACTTT-GGTAATTTCCCAAATAAGGGG
1 TA-TTTCGGTAATTTCCCAAATAAGGGG
39686528 TATTTCGGTAATTT
1 TATTTCGGTAATTT
39686542 TGTAAACCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
26 5 0.09
27 45 0.83
28 4 0.07
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (27 bp):
TATTTCGGTAATTTCCCAAATAAGGGG
Found at i:39686568 original size:26 final size:27
Alignment explanation
Indices: 39686525--39686619 Score: 149
Period size: 26 Copynumber: 3.6 Consensus size: 27
39686515 CCCAAATAAG
*
39686525 GGGTATTTCGGTAATTTTGTAAACCAA
1 GGGTATTTCAGTAATTTTGTAAACCAA
39686552 GGGTA-TTCAGTAATTTTGTAAACCAA
1 GGGTATTTCAGTAATTTTGTAAACCAA
*
39686578 GGGCA-TTCAGTAATTTTGTAAACCAA
1 GGGTATTTCAGTAATTTTGTAAACCAA
*
39686604 GAGTATTTCAGTAATT
1 GGGTATTTCAGTAATT
39686620 CTACCCTACA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
26 48 0.76
27 15 0.24
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.36
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTGTAAACCAA
Found at i:39688952 original size:50 final size:49
Alignment explanation
Indices: 39688888--39688986 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
39688878 TGCCAAAAAT
*
39688888 TACATTTTTTCCCCTAAAACATTTGACATTTTTACAATTTAGTCCCTAGG
1 TACATTTTTGCCCCT-AAACATTTGACATTTTTACAATTTAGTCCCTAGG
*
39688938 TACATTTTTGCCCCTAAACTTTTGACATTTTTACAATTTAGTCCCTAGG
1 TACATTTTTGCCCCTAAACATTTGACATTTTTACAATTTAGTCCCTAGG
39688987 CTCGTAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 33 0.70
50 14 0.30
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.42
Consensus pattern (49 bp):
TACATTTTTGCCCCTAAACATTTGACATTTTTACAATTTAGTCCCTAGG
Found at i:39697347 original size:19 final size:18
Alignment explanation
Indices: 39697310--39697353 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
39697300 ATACATACAG
39697310 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
39697327 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
39697346 TACTAATT
1 TAATAATT
39697354 CAAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:39707457 original size:48 final size:48
Alignment explanation
Indices: 39707386--39707481 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
39707376 TGACAGAGTA
39707386 TGTGCAAAAATTCGTGAGACTAAGTTGGTATGCCCGAGAGTGTGTTTC
1 TGTGCAAAAATTCGTGAGACTAAGTTGGTATGCCCGAGAGTGTGTTTC
39707434 TGTGCAAAAATTCGTGAGACTAAGTTGGTATGCCCGAGAGTGTGTTTC
1 TGTGCAAAAATTCGTGAGACTAAGTTGGTATGCCCGAGAGTGTGTTTC
39707482 GATCAAAGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (48 bp):
TGTGCAAAAATTCGTGAGACTAAGTTGGTATGCCCGAGAGTGTGTTTC
Found at i:39715534 original size:27 final size:27
Alignment explanation
Indices: 39715504--39715557 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39715494 TCATACAACC
* *
39715504 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
39715531 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
39715558 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:39722740 original size:21 final size:22
Alignment explanation
Indices: 39722702--39722749 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
39722692 ATAATTTTCA
* *
39722702 TTTTT-TTTCATGTTCAAGTTT
1 TTTTTATTTCATGTACAAGATT
39722723 TTTTTATTTCAT-TACAAGATT
1 TTTTTATTTCATGTACAAGATT
*
39722744 TCTTTA
1 TTTTTA
39722750 CTCCATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTTTATTTCATGTACAAGATT
Found at i:39724752 original size:40 final size:40
Alignment explanation
Indices: 39724673--39724890 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
39724663 AAGCCAAGTA
* * * * *
39724673 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCACTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
39724712 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
39724752 CCTTCGGGACTTAGGCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
39724792 CCTTCGTGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * *
39724832 CCTTCGGGACTTAACCC-GAAACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
39724872 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39724891 TTATCATCCA
Statistics
Matches: 158, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
39 15 0.09
40 142 0.90
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39733814 original size:49 final size:49
Alignment explanation
Indices: 39733640--39734241 Score: 962
Period size: 49 Copynumber: 12.6 Consensus size: 49
39733630 CCCTTCGGGA
* ** * * *
39733640 CTTATCACAT-T-TATACACTTTCACATCCATCATGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39733687 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39733734 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39733781 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39733830 CTTATCAC--ATATATACACTTTCACATTCGTCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39733877 CTTATCAC--ATATATACACTTTCACATTCGTCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39733924 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39733973 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39734022 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39734071 CTTACCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39734120 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39734169 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39734216 CTTATAACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
39734242 CACAATTATC
Statistics
Matches: 526, Mismatches: 21, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
46 1 0.00
47 231 0.44
49 294 0.56
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39734277 original size:96 final size:95
Alignment explanation
Indices: 39733640--39734241 Score: 903
Period size: 96 Copynumber: 6.3 Consensus size: 95
39733630 CCCTTCGGGA
* ** * * * * *
39733640 CTTATCACAT-T-TATACACTTTCACATCCATCATGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
39733703 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
*
39733734 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
39733797 ACACTTTCACATTCATCACATCGGCCATTAGGC
63 ACACTTTCACATTCATCACATCGGCCATTAGGC
*
39733830 CTTATCAC--ATATATACACTTTCACATTCGTCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
39733893 ACTTTCACATTCGTCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
39733924 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
39733989 ACACTTTCACATTCATCACATCGGCCATTAGGC
63 ACACTTTCACATTCATCACATCGGCCATTAGGC
*
39734022 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTACCACATATATAT
1 CTTATCACATATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
*
39734087 ACACTTTCACATTCATCACATTGGCCATTAGGC
63 ACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39734120 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
39734185 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
*
39734216 CTTATAACATATATATACA-TTCACAT
1 CTTATCACATATATATACACTTCACAT
39734242 CACAATTATC
Statistics
Matches: 479, Mismatches: 21, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
93 1 0.00
94 96 0.20
96 194 0.41
98 188 0.39
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (95 bp):
CTTATCACATATATATACACTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
CTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39738575 original size:48 final size:48
Alignment explanation
Indices: 39738500--39738682 Score: 180
Period size: 48 Copynumber: 3.9 Consensus size: 48
39738490 CACATAGTAG
* *
39738500 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* * *
39738548 GATGCCAATGCCGTGTCTCAGACATGGTCTTACATGAGATCATGCATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCA--CATATC
* * ** * * *
39738598 GAAGCCAAT---A-G-CCTAGTTATGGTCTTACATGATG-TCTCATATT
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATG-GGATCACATATC
*
39738641 GATGCCAATGCCATGTCCCAGACATGGTCTTGCATGGGATCA
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCA
39738683 TGCATATCTC
Statistics
Matches: 105, Mismatches: 21, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
43 13 0.12
45 18 0.17
46 3 0.03
47 2 0.02
48 55 0.52
50 14 0.13
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (48 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:39738682 original size:93 final size:93
Alignment explanation
Indices: 39738522--39738690 Score: 259
Period size: 93 Copynumber: 1.8 Consensus size: 93
39738512 ATATCCCAGA
* *
39738522 TATGGTCTTACATGGGATCACATATCGATGCCAATGCCGTGTCTCAGACATGGTCTTACATGAGA
1 TATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGA
39738587 TCATGCATATCGAAGCCAATAGCCTAGT
66 TCATGCATATCGAAGCCAATAGCCTAGT
* * * * *
39738615 TATGGTCTTACATGATG-TCTCATATTGATGCCAATGCCATGTCCCAGACATGGTCTTGCATGGG
1 TATGGTCTTACATG-GGATCACATATCGATGCCAATGCCATGTCCCAGACATGGTCTTACATGAG
39738679 ATCATGCATATC
65 ATCATGCATATC
39738691 TCTAACGTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
93 67 0.99
94 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (93 bp):
TATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGA
TCATGCATATCGAAGCCAATAGCCTAGT
Found at i:39740132 original size:9 final size:9
Alignment explanation
Indices: 39740118--39740142 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39740108 ATCATGTGTG
39740118 AATGGTAAA
1 AATGGTAAA
39740127 AATGGTAAA
1 AATGGTAAA
39740136 AATGGTA
1 AATGGTA
39740143 GAAACATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (9 bp):
AATGGTAAA
Done.