Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168095.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_341, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33083
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Found at i:662 original size:13 final size:13
Alignment explanation
Indices: 623--665 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
613 GAAAAATTAT
*
623 AAAATAGA-ACAA
1 AAAATAGACAAAA
*
635 AAAATAG-CAAGA
1 AAAATAGACAAAA
647 AAAATAGACAAAA
1 AAAATAGACAAAA
660 AAAATA
1 AAAATA
666 AAGAAATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAATAGACAAAA
Found at i:669 original size:23 final size:23
Alignment explanation
Indices: 623--671 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
613 GAAAAATTAT
*
623 AAAATAGAACAAAAAATAGCAAGA
1 AAAATAGAAAAAAAAATA-CAAGA
647 AAAATAGACAAAAAAAATA-AAGA
1 AAAATAGA-AAAAAAAATACAAGA
670 AA
1 AA
672 TGAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 8 0.35
25 9 0.39
ACGTcount: A:0.76, C:0.06, G:0.10, T:0.08
Consensus pattern (23 bp):
AAAATAGAAAAAAAAATACAAGA
Found at i:679 original size:16 final size:15
Alignment explanation
Indices: 658--687 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
648 AAATAGACAA
658 AAAAAATAAAGAAATG
1 AAAAAATAAA-AAATG
674 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
688 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:724 original size:12 final size:12
Alignment explanation
Indices: 709--783 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 12
699 TAAAAATTTT
709 TAAAAATATAAA
1 TAAAAATATAAA
721 TAAAAA-ATAAA
1 TAAAAATATAAA
732 TGAAAAA-ATAAA
1 T-AAAAATATAAA
* * *
744 TTAAGAGA-AAA
1 TAAAAATATAAA
**
755 TATTAATATAAAA
1 TAAAAATAT-AAA
*
768 GAAAAAT-TAAA
1 TAAAAATATAAA
779 TAAAA
1 TAAAA
784 TACGAAAAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
11 22 0.46
12 19 0.40
13 7 0.15
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (12 bp):
TAAAAATATAAA
Found at i:725 original size:11 final size:12
Alignment explanation
Indices: 710--744 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
700 AAAAATTTTT
710 AAAAATATAAAT-
1 AAAAA-ATAAATG
722 AAAAAATAAATG
1 AAAAAATAAATG
734 AAAAAATAAAT
1 AAAAAATAAAT
745 TAAGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (12 bp):
AAAAAATAAATG
Found at i:1153 original size:15 final size:17
Alignment explanation
Indices: 1133--1168 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1123 AATGAAATAC
1133 AAAATAT-AAA-TTGAG
1 AAAATATAAAATTTGAG
1148 AAAATATAAAATTTGAG
1 AAAATATAAAATTTGAG
1165 AAAA
1 AAAA
1169 AATGAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 3 0.16
17 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (17 bp):
AAAATATAAAATTTGAG
Found at i:1197 original size:19 final size:20
Alignment explanation
Indices: 1165--1203 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1155 AAAATTTGAG
*
1165 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
1185 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
1204 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:1536 original size:16 final size:17
Alignment explanation
Indices: 1498--1537 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1488 AAAATACAAC
*
1498 AAAAAATATAAAAAGTA
1 AAAAAATATAAAAAGGA
*
1515 AGAAAATA-AAAAAGGA
1 AAAAAATATAAAAAGGA
1531 AAAAAAT
1 AAAAAAT
1538 TGAAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAAATATAAAAAGGA
Found at i:2986 original size:26 final size:27
Alignment explanation
Indices: 2925--2986 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
2915 AAGGGATTAC
* * * *
2925 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
2952 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
2978 AAAATGAAA
1 AAAATGAAA
2987 GATAAAAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (27 bp):
AAAATGAAAAAAAGTAATTAAGAAAAA
Found at i:3327 original size:15 final size:14
Alignment explanation
Indices: 3291--3343 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 14
3281 AAAATACAAT
3291 AAAAATATAAAAAGTA
1 AAAAATA-AAAAAG-A
3307 AGAAAATAAAAAAGA
1 A-AAAATAAAAAAGA
3322 CAAAAATGAAAAAA-A
1 -AAAAAT-AAAAAAGA
3337 AAAAATA
1 AAAAATA
3344 GTTCAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.03
14 6 0.18
15 7 0.21
16 14 0.41
17 6 0.18
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.11
Consensus pattern (14 bp):
AAAAATAAAAAAGA
Found at i:3711 original size:12 final size:12
Alignment explanation
Indices: 3672--3713 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
3662 GAAAATTTAT
3672 AAAATAGA-ACAA
1 AAAATAGACA-AA
3684 AAAATAG-CAAGA
1 AAAATAGACAA-A
3696 AAAATAGACAAA
1 AAAATAGACAAA
3708 AAAATA
1 AAAATA
3714 AAAAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:3749 original size:12 final size:11
Alignment explanation
Indices: 3705--3756 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 11
3695 AAAAATAGAC
3705 AAAA-AAATAA
1 AAAATAAATAA
**
3715 AAAAT-TTTAA
1 AAAATAAATAA
*
3725 AATATAAATAA
1 AAAATAAATAA
3736 AAAATAAATGAA
1 AAAATAAAT-AA
3748 AAAATAAAT
1 AAAATAAAT
3757 TAAGAGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 11 0.33
11 11 0.33
12 11 0.33
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:4174 original size:22 final size:21
Alignment explanation
Indices: 4140--4180 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4130 AAAAGCAAGA
4140 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
4162 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
4181 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:4209 original size:20 final size:19
Alignment explanation
Indices: 4171--4225 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
4161 CAAAATATAT
**
4171 AAAATAAAATTTG-AGAAA
1 AAAATAAAAAATGAAGAAA
4189 AAAATGAGAAAAA-GAAGAAA
1 AAAAT-A-AAAAATGAAGAAA
4209 AAAATAAAAAATGAAGA
1 AAAATAAAAAATGAAGA
4226 GGCAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 10 0.32
19 8 0.26
20 13 0.42
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAATAAAAAATGAAGAAA
Found at i:4219 original size:19 final size:20
Alignment explanation
Indices: 4184--4225 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4174 ATAAAATTTG
*
4184 AGAAAAAAATGAGAAAAAGA
1 AGAAAAAAATGAAAAAAAGA
*
4204 AGAAAAAAAT-AAAAAATGA
1 AGAAAAAAATGAAAAAAAGA
4223 AGA
1 AGA
4226 GGCAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (20 bp):
AGAAAAAAATGAAAAAAAGA
Found at i:4257 original size:66 final size:68
Alignment explanation
Indices: 4127--4260 Score: 173
Period size: 67 Copynumber: 2.0 Consensus size: 68
4117 AAAAGATTTA
* ****
4127 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAATACAAAATATATAAAATAAAATTTGAGAAAAAA
1 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAA
4192 ATG
66 ATG
* * *
4195 AGAAAAAG-AAGAAAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAATAAAACAAAAAGAAAAA
1 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAA-AAAAAGAAAAA
4258 AAT
65 AAT
4261 TTATAGAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
66 12 0.21
67 37 0.65
68 8 0.14
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.13
Consensus pattern (68 bp):
AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAA
ATG
Found at i:4550 original size:27 final size:27
Alignment explanation
Indices: 4495--4550 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
4485 AAATTAAAGC
* *
4495 AAAAGAAAAAAGATAAATAAAGCACAA
1 AAAAGAAAAAACATAAATAAAGCAAAA
4522 AAAAGAAAAATACA-AAATACAA-CAAAA
1 AAAAGAAAAA-ACATAAATA-AAGCAAAA
4549 AA
1 AA
4551 TATAAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.77, C:0.09, G:0.07, T:0.07
Consensus pattern (27 bp):
AAAAGAAAAAACATAAATAAAGCAAAA
Found at i:4583 original size:16 final size:17
Alignment explanation
Indices: 4545--4584 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
4535 AAAATACAAC
*
4545 AAAAAATATAAAAAGTA
1 AAAAAATATAAAAAGGA
*
4562 AGAAAATA-AAAAAGGA
1 AAAAAATATAAAAAGGA
4578 AAAAAAT
1 AAAAAAT
4585 TGAAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAAATATAAAAAGGA
Found at i:5031 original size:9 final size:9
Alignment explanation
Indices: 4990--5038 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
4980 CAAAAATAGC
4990 AAAAAAAAT
1 AAAAAAAAT
*
4999 AAATAAAAT
1 AAAAAAAAT
*
5008 AAAAAAGAT
1 AAAAAAAAT
**
5017 TCAAAAAAT
1 AAAAAAAAT
5026 AAAAAAAA-
1 AAAAAAAAT
5034 AAAAA
1 AAAAA
5039 TTTTGAACTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
8 5 0.16
9 27 0.84
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:6372 original size:15 final size:15
Alignment explanation
Indices: 6322--6372 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
6312 AAAATACAAT
6322 AAAAATATAAAAAGTAA
1 AAAAATA-AAAAAG-AA
* *
6339 GAAAATAAAAAAGAC
1 AAAAATAAAAAAGAA
*
6354 AAAAATGAAAAA-AA
1 AAAAATAAAAAAGAA
6368 AAAAA
1 AAAAA
6373 GTTCAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 6 0.21
15 11 0.38
16 6 0.21
17 6 0.21
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (15 bp):
AAAAATAAAAAAGAA
Found at i:6740 original size:12 final size:12
Alignment explanation
Indices: 6701--6742 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
6691 GAAAATTTAT
6701 AAAATAGA-ACAA
1 AAAATAGACA-AA
6713 AAAATAG-CAAGA
1 AAAATAGACAA-A
6725 AAAATAGACAAA
1 AAAATAGACAAA
6737 AAAATA
1 AAAATA
6743 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:6756 original size:16 final size:15
Alignment explanation
Indices: 6735--6764 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6725 AAAATAGACA
6735 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
6751 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
6765 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:6806 original size:11 final size:11
Alignment explanation
Indices: 6786--6820 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
6776 TAAAAAATTT
*
6786 TAAAATATAAA
1 TAAAAAATAAA
6797 TAAAAAATAAA
1 TAAAAAATAAA
6808 TGAAAAAATAAA
1 T-AAAAAATAAA
6820 T
1 T
6821 TAAGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:7221 original size:22 final size:21
Alignment explanation
Indices: 7187--7227 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
7177 AAAAGCAAGA
7187 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
7209 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
7228 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:7267 original size:20 final size:21
Alignment explanation
Indices: 7233--7273 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
7223 AAAATTTGAG
*
7233 AAAAAAATGAGAAAAAGAAGA
1 AAAAAAATGAAAAAAAGAAGA
*
7254 AAAAAAAT-AAAAAATGAAGA
1 AAAAAAATGAAAAAAAGAAGA
7274 GGCAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (21 bp):
AAAAAAATGAAAAAAAGAAGA
Found at i:7305 original size:67 final size:68
Alignment explanation
Indices: 7174--7308 Score: 166
Period size: 68 Copynumber: 2.0 Consensus size: 68
7164 AAAAGATTTA
* ****
7174 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAATACAAAATATATAAAATAAAATTTGAGAAAAAA
1 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAA
7239 ATG
66 ATG
* * *
7242 AGAAAAAG-AAGAAAAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAATAAAAAAAAAAGAAAA
1 AGAAAAAGCAAG-AAAAAAATAAAAAATGAAAAGACAAAATATATAAAAT-AAAAAAAAAGAAAA
7305 AAAT
64 AAAT
7309 TTATAGAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
67 11 0.19
68 46 0.81
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (68 bp):
AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAA
ATG
Found at i:7547 original size:24 final size:24
Alignment explanation
Indices: 7520--7579 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
7510 AAACTATAAA
7520 AAAAGAAAGAAAGA-AAATTAAAGC
1 AAAAGAAAGAAAGATAAA-TAAAGC
7544 AAAAGAAA-AAAGATAAATAAAGC
1 AAAAGAAAGAAAGATAAATAAAGC
*
7567 ACAAAAAAAGAAA
1 A-AAAGAAAGAAA
7580 AAATACAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 12 0.38
24 17 0.53
25 3 0.09
ACGTcount: A:0.75, C:0.05, G:0.13, T:0.07
Consensus pattern (24 bp):
AAAAGAAAGAAAGATAAATAAAGC
Found at i:7555 original size:23 final size:22
Alignment explanation
Indices: 7520--7580 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
7510 AAACTATAAA
7520 AAAAGAAAGAAAGAAAATTAAAGC
1 AAAAGAAA-AAAGAAAA-TAAAGC
7544 AAAAGAAAAAAGATAAATAAAGC
1 AAAAGAAAAAAGA-AAATAAAGC
*
7567 -ACA-AAAAAAGAAAA
1 AAAAGAAAAAAGAAAA
7581 AATACAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 3 0.09
21 8 0.23
22 2 0.06
23 11 0.31
24 11 0.31
ACGTcount: A:0.75, C:0.05, G:0.13, T:0.07
Consensus pattern (22 bp):
AAAAGAAAAAAGAAAATAAAGC
Found at i:7591 original size:16 final size:15
Alignment explanation
Indices: 7569--7632 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 15
7559 AATAAAGCAC
7569 AAAAAAAGAAAAAAT
1 AAAAAAAGAAAAAAT
*
7584 ACAAAAAACAAAAAAT
1 A-AAAAAAGAAAAAAT
*
7600 ATAAAAAGTAAGAAAAT
1 AAAAAAAG-AA-AAAAT
*
7617 AAAAAAGGACAAAAAT
1 AAAAAAAGA-AAAAAT
7633 TGAAGAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
15 6 0.15
16 22 0.55
17 12 0.30
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.09
Consensus pattern (15 bp):
AAAAAAAGAAAAAAT
Found at i:8992 original size:20 final size:20
Alignment explanation
Indices: 8967--9005 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
8957 ATTAGTTTAT
8967 AAAATACGAACAAA-AATAAA
1 AAAATA-GAACAAATAATAAA
*
8987 AAAATATAACAAATAATAA
1 AAAATAGAACAAATAATAA
9006 GAAATAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (20 bp):
AAAATAGAACAAATAATAAA
Found at i:9099 original size:26 final size:27
Alignment explanation
Indices: 9038--9099 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
9028 AAGGGATTAC
* * * *
9038 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
9065 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
9091 AAAATGAAA
1 AAAATGAAA
9100 GATAAAAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (27 bp):
AAAATGAAAAAAAGTAATTAAGAAAAA
Found at i:9821 original size:12 final size:12
Alignment explanation
Indices: 9782--9823 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
9772 GAAAATTTAT
9782 AAAATAGA-ACAA
1 AAAATAGACA-AA
9794 AAAATAG-CAAGA
1 AAAATAGACAA-A
9806 AAAATAGACAAA
1 AAAATAGACAAA
9818 AAAATA
1 AAAATA
9824 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:9837 original size:16 final size:15
Alignment explanation
Indices: 9816--9845 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9806 AAAATAGACA
9816 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
9832 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
9846 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:10352 original size:19 final size:20
Alignment explanation
Indices: 10320--10358 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
10310 AAAGTTTGAG
*
10320 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
10340 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
10359 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:10717 original size:16 final size:17
Alignment explanation
Indices: 10680--10718 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
10670 AAAATACAAC
*
10680 AAAAATATAAAAAGTAA
1 AAAAATATAAAAAGGAA
*
10697 GAAAATA-AAAAAGGAA
1 AAAAATATAAAAAGGAA
10713 AAAAAT
1 AAAAAT
10719 TGAAGAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (17 bp):
AAAAATATAAAAAGGAA
Found at i:12058 original size:20 final size:20
Alignment explanation
Indices: 12033--12071 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12023 ATTAGTTTAT
12033 AAAATACGAACAAA-AATAAA
1 AAAATA-GAACAAATAATAAA
*
12053 AAAATATAACAAATAATAA
1 AAAATAGAACAAATAATAA
12072 GAAATAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (20 bp):
AAAATAGAACAAATAATAAA
Found at i:12505 original size:15 final size:14
Alignment explanation
Indices: 12469--12521 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 14
12459 AAAATACAAT
12469 AAAAATATAAAAAGTA
1 AAAAATA-AAAAAG-A
12485 AGAAAATAAAAAAGA
1 A-AAAATAAAAAAGA
12500 CAAAAATGAAAAAA-A
1 -AAAAAT-AAAAAAGA
12515 AAAAATA
1 AAAAATA
12522 GTTCAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.03
14 6 0.18
15 7 0.21
16 14 0.41
17 6 0.18
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.11
Consensus pattern (14 bp):
AAAAATAAAAAAGA
Found at i:12887 original size:12 final size:12
Alignment explanation
Indices: 12848--12889 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
12838 GAAAATTTAT
12848 AAAATAGA-ACAA
1 AAAATAGACA-AA
12860 AAAATAG-CAAGA
1 AAAATAGACAA-A
12872 AAAATAGACAAA
1 AAAATAGACAAA
12884 AAAATA
1 AAAATA
12890 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:12903 original size:16 final size:15
Alignment explanation
Indices: 12882--12911 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12872 AAAATAGACA
12882 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
12898 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
12912 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:12961 original size:12 final size:11
Alignment explanation
Indices: 12934--12968 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
12924 AAAAAATTTT
*
12934 TAAAATATAAA
1 TAAAAAATAAA
12945 TAAAAAATAAA
1 TAAAAAATAAA
12956 TGAAAAAATAAA
1 T-AAAAAATAAA
12968 T
1 T
12969 TAAGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:13371 original size:22 final size:21
Alignment explanation
Indices: 13337--13377 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
13327 AAAAGCAAGA
13337 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
13359 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
13378 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:13415 original size:19 final size:20
Alignment explanation
Indices: 13383--13421 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
13373 AAAATTTGAG
*
13383 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
13403 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
13422 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:13451 original size:66 final size:67
Alignment explanation
Indices: 13324--13454 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 67
13314 AAAAGATTTA
* ****
13324 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAATACAAAATATATAAAATAAAATTTGAGAAAAAA
1 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAA
13389 TG
66 TG
* * *
13391 AGAAAAAG-AAGAAAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAATAAAAAAAAAAGAAAAA
1 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAAT-AAAAAAAAAGAAAAA
13454 A
65 A
13455 AATTATAGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
65 8 0.15
66 39 0.71
67 8 0.15
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (67 bp):
AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAATATATAAAATAAAAAAAAAGAAAAAA
TG
Found at i:13759 original size:16 final size:17
Alignment explanation
Indices: 13721--13760 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
13711 AAAATACAAC
*
13721 AAAAAATATAAAAAGTA
1 AAAAAATATAAAAAGGA
*
13738 AGAAAATA-AAAAAGGA
1 AAAAAATATAAAAAGGA
13754 AAAAAAT
1 AAAAAAT
13761 TGAAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAAATATAAAAAGGA
Found at i:14476 original size:12 final size:12
Alignment explanation
Indices: 14447--14502 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
14437 GGAAAAAGAT
14447 ATAAAAAATCAAA
1 ATAAAAAAT-AAA
14460 GATAAAAAATAAA
1 -ATAAAAAATAAA
* *
14473 AT-AAAAGT-TA
1 ATAAAAAATAAA
14483 ATAAAAAATATAA
1 ATAAAAAATA-AA
14496 ATAAAAA
1 ATAAAAA
14503 CAAAAGAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 3 0.09
11 10 0.29
12 2 0.06
13 11 0.31
14 9 0.26
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:14479 original size:19 final size:20
Alignment explanation
Indices: 14451--14501 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
14441 AAAGATATAA
*
14451 AAAATCAAAG-ATAAAAAAT
1 AAAATAAAAGTATAAAAAAT
14470 AAAATAAAAGTTAATAAAAAAT
1 AAAATAAAAG-T-ATAAAAAAT
14492 ATAAATAAAA
1 A-AAATAAAA
14502 ACAAAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 9 0.33
22 10 0.37
23 8 0.30
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAATAAAAGTATAAAAAAT
Found at i:15198 original size:26 final size:27
Alignment explanation
Indices: 15137--15198 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
15127 AAGGGATTAC
* * * *
15137 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
15164 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
15190 AAAATGAAA
1 AAAATGAAA
15199 GATAAAAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (27 bp):
AAAATGAAAAAAAGTAATTAAGAAAAA
Found at i:15916 original size:12 final size:12
Alignment explanation
Indices: 15877--15918 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
15867 GAAAATTTAT
15877 AAAATAGA-ACAA
1 AAAATAGACA-AA
15889 AAAATAG-CAAGA
1 AAAATAGACAA-A
15901 AAAATAGACAAA
1 AAAATAGACAAA
15913 AAAATA
1 AAAATA
15919 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:15932 original size:16 final size:15
Alignment explanation
Indices: 15911--15940 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
15901 AAAATAGACA
15911 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
15927 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
15941 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:15990 original size:12 final size:11
Alignment explanation
Indices: 15963--15997 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
15953 AAAAAATTTT
*
15963 TAAAATATAAA
1 TAAAAAATAAA
15974 TAAAAAATAAA
1 TAAAAAATAAA
15985 TGAAAAAATAAA
1 T-AAAAAATAAA
15997 T
1 T
15998 TAAGAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:16022 original size:17 final size:16
Alignment explanation
Indices: 15978--16035 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
15968 TATAAATAAA
* *
15978 AAATAAATGAAAAAAT
1 AAATAAAAGAAAAATT
* *
15994 AAATTAAGAGAAATATT
1 AAA-TAAAAGAAAAATT
16011 AATATAAAAGAAAAATT
1 AA-ATAAAAGAAAAATT
16028 AAATAAAA
1 AAATAAAA
16036 TACGAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 9 0.26
17 24 0.71
18 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (16 bp):
AAATAAAAGAAAAATT
Found at i:16240 original size:19 final size:18
Alignment explanation
Indices: 16218--16269 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
16208 ACAATAAAGG
16218 AAAAGATGAAAAATAAAAT
1 AAAAGAT-AAAAATAAAAT
* *
16237 AAAAGTTAATAA-AAAAT
1 AAAAGATAAAAATAAAAT
*
16254 ACAA-ATAAAAATAAAA
1 AAAAGATAAAAATAAAA
16270 GAATGTGCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 4 0.15
19 6 0.22
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAAGATAAAAATAAAAT
Found at i:16385 original size:23 final size:22
Alignment explanation
Indices: 16359--16401 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
16349 AAAAAGCAAG
16359 AAAAAAATAAAAAATGAAAATAC
1 AAAAAAATAAAAAAT-AAAATAC
* *
16382 AAAAATATATAAAATAAAAT
1 AAAAAAATAAAAAATAAAAT
16402 TTGAGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
AAAAAAATAAAAAATAAAATAC
Found at i:16439 original size:19 final size:20
Alignment explanation
Indices: 16407--16445 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
16397 AAAATTTGAG
*
16407 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
16427 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
16446 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:16478 original size:67 final size:67
Alignment explanation
Indices: 16347--16478 Score: 162
Period size: 67 Copynumber: 2.0 Consensus size: 67
16337 AAAAGATTTA
* * *
16347 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAATACAAAAATATATAAAATAAAATTTGAGAAAAA
1 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAAATATATAAAATAAAA-TAGAAAAAAA
16412 ATG
65 ATG
* *
16415 AGAAAAAG-AAGAAAAAAATAAAAAATGAAGAGGCAAAAATATGAAATAAAA-AAAA-AGAAAAA
1 AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAAATAT---ATAAAATAAAATAGAAAAA
16477 AA
63 AA
16479 TTTATAGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
67 38 0.68
68 8 0.14
69 4 0.07
70 6 0.11
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (67 bp):
AGAAAAAGCAAGAAAAAAATAAAAAATGAAAAGACAAAAATATATAAAATAAAATAGAAAAAAAA
TG
Found at i:16731 original size:22 final size:21
Alignment explanation
Indices: 16692--16747 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
16682 GAAACTATAA
*
16692 AAAAGAAAAA-AAATTAAAGC
1 AAAAGAAAAAGAAAATAAAGC
16712 AAAAGAAAAAGATAAATAAAGC
1 AAAAGAAAAAGA-AAATAAAGC
*
16734 ACAA-AAAAAGAAAA
1 AAAAGAAAAAGAAAA
16748 AAAATACAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.41
21 8 0.25
22 11 0.34
ACGTcount: A:0.77, C:0.05, G:0.11, T:0.07
Consensus pattern (21 bp):
AAAAGAAAAAGAAAATAAAGC
Found at i:16759 original size:22 final size:21
Alignment explanation
Indices: 16690--16762 Score: 58
Period size: 24 Copynumber: 3.2 Consensus size: 21
16680 ATGAAACTAT
16690 AAAAAAGAAAAAAAATTAAAGCA
1 AAAAAAGAAAAAAAA-TAAA-CA
* *
16713 AAAGAAA-AAGATAAATAAAGCACA
1 AAA-AAAGAAAAAAAAT-AA--ACA
16737 AAAAAAGAAAAAAAATACAACA
1 AAAAAAGAAAAAAAATA-AACA
16759 AAAA
1 AAAA
16763 TATAAAAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
22 8 0.20
23 15 0.38
24 16 0.40
25 1 0.03
ACGTcount: A:0.78, C:0.07, G:0.08, T:0.07
Consensus pattern (21 bp):
AAAAAAGAAAAAAAATAAACA
Found at i:16794 original size:15 final size:16
Alignment explanation
Indices: 16758--16795 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16748 AAAATACAAC
*
16758 AAAAATATAAAAAGTA
1 AAAAATATAAAAAGGA
16774 AGAAAATA-AAAAAGGA
1 A-AAAATATAAAAAGGA
16790 AAAAAT
1 AAAAAT
16796 TGAAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 9 0.45
17 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (16 bp):
AAAAATATAAAAAGGA
Found at i:18112 original size:20 final size:20
Alignment explanation
Indices: 18087--18125 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18077 ATTAGTTTAT
18087 AAAATACGAACAAA-AATAAA
1 AAAATA-GAACAAATAATAAA
*
18107 AAAATATAACAAATAATAA
1 AAAATAGAACAAATAATAA
18126 GAAATAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (20 bp):
AAAATAGAACAAATAATAAA
Found at i:18933 original size:12 final size:12
Alignment explanation
Indices: 18894--18935 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
18884 GAAAATTTAT
18894 AAAATAGA-ACAA
1 AAAATAGACA-AA
18906 AAAATAG-CAAGA
1 AAAATAGACAA-A
18918 AAAATAGACAAA
1 AAAATAGACAAA
18930 AAAATA
1 AAAATA
18936 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:18949 original size:16 final size:15
Alignment explanation
Indices: 18928--18957 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18918 AAAATAGACA
18928 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
18944 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
18958 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:19007 original size:12 final size:11
Alignment explanation
Indices: 18980--19014 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
18970 AAAAAAATTT
*
18980 TAAAATATAAA
1 TAAAAAATAAA
18991 TAAAAAATAAA
1 TAAAAAATAAA
19002 TGAAAAAATAAA
1 T-AAAAAATAAA
19014 T
1 T
19015 TAAGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:19416 original size:22 final size:21
Alignment explanation
Indices: 19382--19422 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
19372 AAAAGCAAGA
19382 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
19404 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
19423 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:19431 original size:24 final size:23
Alignment explanation
Indices: 19404--19457 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
19394 ATGAAAATAC
*
19404 AAAATATATAAAATAAAATTTGAG
1 AAAAAATAT-AAATAAAATTTGAG
* *
19428 AAAAAATATATATAAAGTTTGAG
1 AAAAAATATAAATAAAATTTGAG
19451 AAAAAAT
1 AAAAAAT
19458 GAGAAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (23 bp):
AAAAAATATAAATAAAATTTGAG
Found at i:19483 original size:19 final size:20
Alignment explanation
Indices: 19451--19489 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
19441 AAAGTTTGAG
*
19451 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
19471 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
19490 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:19692 original size:21 final size:21
Alignment explanation
Indices: 19645--19691 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
19635 AAAATGCAAT
* *
19645 AAAAAATAAAAAACGAGAATG
1 AAAAAATAAAAAAAGAGAAAG
*
19666 ATAAAATAAAAAAAGA-AAAG
1 AAAAAATAAAAAAAGAGAAAG
19686 AAAAAA
1 AAAAAA
19692 AGATAGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.09
Consensus pattern (21 bp):
AAAAAATAAAAAAAGAGAAAG
Found at i:19856 original size:16 final size:17
Alignment explanation
Indices: 19818--19857 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
19808 AAAATACAAC
*
19818 AAAAAATATAAAAAGTA
1 AAAAAATATAAAAAGGA
*
19835 AGAAAATA-AAAAAGGA
1 AAAAAATATAAAAAGGA
19851 AAAAAAT
1 AAAAAAT
19858 TGAAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAAATATAAAAAGGA
Found at i:21978 original size:16 final size:15
Alignment explanation
Indices: 21957--21986 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21947 AAAATAGACA
21957 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
21973 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
21987 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:22024 original size:12 final size:12
Alignment explanation
Indices: 22009--22042 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21999 AAAAAATTTT
*
22009 AAAATATAAAT-
1 AAAAAATAAATG
22020 AAAAAATAAATG
1 AAAAAATAAATG
22032 AAAAAATAAAT
1 AAAAAATAAAT
22043 TAAGAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAAAATAAATG
Found at i:22028 original size:11 final size:11
Alignment explanation
Indices: 22008--22042 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
21998 TAAAAAATTT
*
22008 TAAAATATAAA
1 TAAAAAATAAA
22019 TAAAAAATAAA
1 TAAAAAATAAA
22030 TGAAAAAATAAA
1 T-AAAAAATAAA
22042 T
1 T
22043 TAAGAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:22067 original size:17 final size:16
Alignment explanation
Indices: 22023--22080 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
22013 TATAAATAAA
* *
22023 AAATAAATGAAAAAAT
1 AAATAAAAGAAAAATT
* *
22039 AAATTAAGAGAAATATT
1 AAA-TAAAAGAAAAATT
22056 AATATAAAAGAAAAATT
1 AA-ATAAAAGAAAAATT
22073 AAATAAAA
1 AAATAAAA
22081 TACGAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 9 0.26
17 24 0.71
18 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (16 bp):
AAATAAAAGAAAAATT
Found at i:22421 original size:13 final size:14
Alignment explanation
Indices: 22404--22441 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
22394 AAAGCAAGAA
22404 AAAAATAAAAA-AT
1 AAAAATAAAAATAT
*
22417 GAAAATACAAAATAT
1 AAAAATA-AAAATAT
22432 AAAAATAAAA
1 AAAAATAAAA
22442 TTTGAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 6 0.29
14 7 0.33
15 8 0.38
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (14 bp):
AAAAATAAAAATAT
Found at i:22428 original size:20 final size:20
Alignment explanation
Indices: 22405--22442 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22395 AAGCAAGAAA
22405 AAAATA-AAAAATGAAAATAC
1 AAAATATAAAAAT-AAAATAC
22425 AAAATATAAAAATAAAAT
1 AAAATATAAAAATAAAAT
22443 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAATATAAAAATAAAATAC
Found at i:22451 original size:23 final size:23
Alignment explanation
Indices: 22425--22477 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
22415 ATGAAAATAC
*
22425 AAAATATAAAAATAAAATTTGAG
1 AAAAAATAAAAATAAAATTTGAG
* * *
22448 AAAAAATATATATAAAGTTTGAG
1 AAAAAATAAAAATAAAATTTGAG
22471 AAAAAAT
1 AAAAAAT
22478 GAGAAAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.26
Consensus pattern (23 bp):
AAAAAATAAAAATAAAATTTGAG
Found at i:22503 original size:19 final size:20
Alignment explanation
Indices: 22471--22509 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
22461 AAAGTTTGAG
*
22471 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
22491 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
22510 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:22874 original size:16 final size:17
Alignment explanation
Indices: 22836--22875 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
22826 AAAATACAAC
*
22836 AAAAAATATAAAAAGTA
1 AAAAAATATAAAAAGGA
*
22853 AGAAAATA-AAAAAGGA
1 AAAAAATATAAAAAGGA
22869 AAAAAAT
1 AAAAAAT
22876 TGAAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAAATATAAAAAGGA
Found at i:24308 original size:26 final size:27
Alignment explanation
Indices: 24247--24308 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
24237 AAGGGATTAC
* * * *
24247 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
24274 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
24300 AAAATGAAA
1 AAAATGAAA
24309 GATAAAAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (27 bp):
AAAATGAAAAAAAGTAATTAAGAAAAA
Found at i:24492 original size:16 final size:17
Alignment explanation
Indices: 24459--24505 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
24449 GAATATTTTG
24459 AAACAAAGAAAAAGTGA
1 AAACAAAGAAAAAGTGA
24476 AAACAAA-AAAATA-TGA
1 AAACAAAGAAAA-AGTGA
*
24492 AAAGCAATGAAAAA
1 AAA-CAAAGAAAAA
24506 ATAAGTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.38
17 12 0.46
18 4 0.15
ACGTcount: A:0.72, C:0.06, G:0.13, T:0.09
Consensus pattern (17 bp):
AAACAAAGAAAAAGTGA
Found at i:25000 original size:12 final size:12
Alignment explanation
Indices: 24983--25023 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
24973 GAAAATTTAT
24983 AAAATAGAACAA
1 AAAATAGAACAA
*
24995 AAAATAGCAA-GA
1 AAAATAG-AACAA
25007 AAAATAG-ACAA
1 AAAATAGAACAA
25018 AAAATA
1 AAAATA
25024 AGAAAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 1 0.04
11 7 0.28
12 15 0.60
13 2 0.08
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGAACAA
Found at i:25037 original size:16 final size:15
Alignment explanation
Indices: 25016--25045 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25006 AAAAATAGAC
25016 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
25032 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
25046 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:25095 original size:12 final size:11
Alignment explanation
Indices: 25068--25102 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
25058 AAAAAATTTT
*
25068 TAAAATATAAA
1 TAAAAAATAAA
25079 TAAAAAATAAA
1 TAAAAAATAAA
25090 TGAAAAAATAAA
1 T-AAAAAATAAA
25102 T
1 T
25103 TAAGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:25506 original size:22 final size:21
Alignment explanation
Indices: 25472--25512 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
25462 AAAAGCAAGA
25472 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
25494 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
25513 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:25521 original size:24 final size:23
Alignment explanation
Indices: 25494--25547 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
25484 ATGAAAATAC
*
25494 AAAATATATAAAATAAAATTTGAG
1 AAAAAATAT-AAATAAAATTTGAG
* *
25518 AAAAAATATATATAAAGTTTGAG
1 AAAAAATATAAATAAAATTTGAG
25541 AAAAAAT
1 AAAAAAT
25548 GAGAAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (23 bp):
AAAAAATATAAATAAAATTTGAG
Found at i:25573 original size:19 final size:20
Alignment explanation
Indices: 25541--25579 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
25531 AAAGTTTGAG
*
25541 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
25561 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
25580 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:26446 original size:22 final size:23
Alignment explanation
Indices: 26416--26458 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
26406 AAAATTTTTT
26416 AAAATATAAATAAAAATAAATGG
1 AAAATATAAATAAAAATAAATGG
* *
26439 AAAA-ATAAATTAAGATAAAT
1 AAAATATAAATAAAAATAAAT
26459 ATTAATATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (23 bp):
AAAATATAAATAAAAATAAATGG
Found at i:28046 original size:12 final size:12
Alignment explanation
Indices: 28029--28069 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
28019 GAAAATTTAT
28029 AAAATAGAACAA
1 AAAATAGAACAA
*
28041 AAAATAGCAA-GA
1 AAAATAG-AACAA
28053 AAAATAG-ACAA
1 AAAATAGAACAA
28064 AAAATA
1 AAAATA
28070 AGAAAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 1 0.04
11 7 0.28
12 15 0.60
13 2 0.08
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGAACAA
Found at i:28083 original size:16 final size:15
Alignment explanation
Indices: 28062--28091 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28052 AAAAATAGAC
28062 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
28078 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
28092 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:28555 original size:23 final size:24
Alignment explanation
Indices: 28517--28568 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
28507 AAGCAAGAAA
28517 AAAAAATATAAAATAAAATTTGAG
1 AAAAAATATAAAATAAAATTTGAG
* *
28541 AAAAAATAT-ATATAAAGTTTGAG
1 AAAAAATATAAAATAAAATTTGAG
28564 AAAAA
1 AAAAA
28569 TGAGAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (24 bp):
AAAAAATATAAAATAAAATTTGAG
Found at i:28911 original size:27 final size:25
Alignment explanation
Indices: 28867--28943 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 25
28857 AAATTAAAGC
*
28867 AAAAGAAAAA-AGATAAATAAAGCACAA
1 AAAAGAAAAAGA-AAAAATAAA-CA-AA
28894 AAAAGAAAAAGAAAAAATACAACAAA
1 AAAAGAAAAAGAAAAAATA-AACAAA
*
28920 AAATATAAAAAGTAAGAAAATAAA
1 AAA-AGAAAAAG-AA-AAAATAAA
28944 AAAGGAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
26 5 0.12
27 25 0.58
28 7 0.16
29 6 0.14
ACGTcount: A:0.77, C:0.05, G:0.09, T:0.09
Consensus pattern (25 bp):
AAAAGAAAAAGAAAAAATAAACAAA
Found at i:28955 original size:16 final size:17
Alignment explanation
Indices: 28917--28956 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
28907 AAAATACAAC
*
28917 AAAAAATATAAAAAGTA
1 AAAAAATATAAAAAGGA
*
28934 AGAAAATA-AAAAAGGA
1 AAAAAATATAAAAAGGA
28950 AAAAAAT
1 AAAAAAT
28957 TGAAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAAATATAAAAAGGA
Found at i:30396 original size:26 final size:27
Alignment explanation
Indices: 30335--30396 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
30325 AAGGGATTAC
* * * *
30335 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
30362 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
30388 AAAATGAAA
1 AAAATGAAA
30397 GATAAAAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (27 bp):
AAAATGAAAAAAAGTAATTAAGAAAAA
Found at i:30751 original size:15 final size:15
Alignment explanation
Indices: 30701--30751 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
30691 AAAATACAAT
30701 AAAAATATAAAAAGTAA
1 AAAAATA-AAAAAG-AA
* *
30718 GAAAATAAAAAAGAC
1 AAAAATAAAAAAGAA
*
30733 AAAAATGAAAAA-AA
1 AAAAATAAAAAAGAA
30747 AAAAA
1 AAAAA
30752 GTTCAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 6 0.21
15 11 0.38
16 6 0.21
17 6 0.21
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (15 bp):
AAAAATAAAAAAGAA
Found at i:31121 original size:12 final size:12
Alignment explanation
Indices: 31082--31123 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
31072 GAAAATTTAT
31082 AAAATAGA-ACAA
1 AAAATAGACA-AA
31094 AAAATAG-CAAGA
1 AAAATAGACAA-A
31106 AAAATAGACAAA
1 AAAATAGACAAA
31118 AAAATA
1 AAAATA
31124 AGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAATAGACAAA
Found at i:31137 original size:16 final size:15
Alignment explanation
Indices: 31116--31145 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31106 AAAATAGACA
31116 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
31132 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
31146 TTTGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:31597 original size:21 final size:20
Alignment explanation
Indices: 31573--31611 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
31563 AAGCAAGAGA
31573 AAAAATAAAAAATGAAAATAC
1 AAAAATAAAAAAT-AAAATAC
* *
31594 AAAATTATAAAATAAAAT
1 AAAAATAAAAAATAAAAT
31612 TTGAGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAAATAAAAAATAAAATAC
Found at i:31644 original size:20 final size:21
Alignment explanation
Indices: 31604--31643 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31594 AAAATTATAA
31604 AATAAAATTTGAGAAAAAAAT
1 AATAAAATTTGAGAAAAAAAT
*
31625 AATAAAGTTTGAGAAAAAA
1 AATAAAATTTGAGAAAAAA
31644 TGAGAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (21 bp):
AATAAAATTTGAGAAAAAAAT
Found at i:31670 original size:19 final size:20
Alignment explanation
Indices: 31638--31676 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
31628 AAAGTTTGAG
*
31638 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
31658 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
31677 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:31921 original size:20 final size:20
Alignment explanation
Indices: 31885--31931 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
31875 AAGATAGAAA
31885 AATAAAAATTTCAAAACT-T
1 AATAAAAATTTCAAAACTAT
31904 AATAAAAATTT-ATGAAACTAT
1 AATAAAAATTTCA--AAACTAT
31925 AA-AAAAA
1 AATAAAAA
31932 GAAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.04
19 11 0.44
20 10 0.40
21 3 0.12
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (20 bp):
AATAAAAATTTCAAAACTAT
Found at i:31980 original size:24 final size:24
Alignment explanation
Indices: 31925--31987 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
31915 ATGAAACTAT
31925 AAAAAAAGAAAAAAAATTAAAGCA
1 AAAAAAAGAAAAAAAATTAAAGCA
*
31949 AAAGAAAA-AAAGATAAA-TAAAGCA
1 AAA-AAAAGAAA-AAAAATTAAAGCA
31973 CAAAAAAAGAAAAAA
1 -AAAAAAAGAAAAAA
31988 TACAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
24 19 0.58
25 14 0.42
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.06
Consensus pattern (24 bp):
AAAAAAAGAAAAAAAATTAAAGCA
Found at i:32039 original size:15 final size:15
Alignment explanation
Indices: 32002--32040 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
31992 AAAATACAAC
*
32002 AAAAAATATAAAAAGT
1 AAAAAA-ATAAAAAGG
*
32018 AAGAAAATAAAAAGG
1 AAAAAAATAAAAAGG
32033 AAAAAAAT
1 AAAAAAAT
32041 TGAAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAAAAATAAAAAGG
Found at i:32743 original size:19 final size:19
Alignment explanation
Indices: 32707--32770 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
32697 AAATATAGGA
*
32707 AAAAGAATAATAAAAAAAT
1 AAAAGAATAAAAAAAAAAT
*
32726 CAAAG-ATAAAAAATAAAAT
1 AAAAGAATAAAAAA-AAAAT
*
32745 AAAAGTAATGAAAAATATAAAT
1 AAAAG-AAT-AAAAA-AAAAAT
32767 AAAA
1 AAAA
32771 ACAAAAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 7 0.19
19 13 0.36
21 2 0.06
22 13 0.36
23 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAAGAATAAAAAAAAAAT
Done.