Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 45 of 182
Found at i:14228111 original size:30 final size:29
Alignment explanation
Indices: 14228071--14228186 Score: 117
Period size: 30 Copynumber: 3.9 Consensus size: 29
14228061 TAAAAAATAA
* *
14228071 AAATTGCATTTTGACACCTAAACTTTTC-CT
1 AAATTTCATTTTGAC-CCTAAAC-TTTCATT
*
14228101 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCC-TAAACTTTCATT
* *
14228131 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGA-CCCTAAACTTTCATT
* * *
14228161 AAATTTCATTTTAATCCTAAATTTTC
1 AAATTTCATTTTGACCCTAAACTTTC
14228187 TAAAAATTAC
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
29 16 0.22
30 54 0.74
31 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTGACCCTAAACTTTCATT
Found at i:14228453 original size:10 final size:10
Alignment explanation
Indices: 14228434--14228483 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
14228424 TTTTTCGAAG
*
14228434 GAAAAAAGAA
1 GAAAAGAGAA
14228444 GAAAAGAGAA
1 GAAAAGAGAA
14228454 GAAAAGAGAA
1 GAAAAGAGAA
* *
14228464 -AGAGGAGAA
1 GAAAAGAGAA
14228473 GAAAAGA-AA
1 GAAAAGAGAA
14228482 GA
1 GA
14228484 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:14228484 original size:17 final size:19
Alignment explanation
Indices: 14228437--14228479 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
14228427 TTCGAAGGAA
14228437 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
14228455 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
14228474 AAAAGA
1 AAAAGA
14228480 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:14228545 original size:3 final size:3
Alignment explanation
Indices: 14228539--14228584 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
14228529 GCTAGACTTT
*
14228539 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
14228585 AGAAAGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:14228557 original size:10 final size:10
Alignment explanation
Indices: 14228542--14228570 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
14228532 AGACTTTGAA
14228542 GAAGAAGAAG
1 GAAGAAGAAG
14228552 GAAGAAGAAG
1 GAAGAAGAAG
14228562 GAAGAAGAA
1 GAAGAAGAA
14228571 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:14228557 original size:13 final size:13
Alignment explanation
Indices: 14228539--14228584 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
14228529 GCTAGACTTT
14228539 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
14228552 GAAGAAGAAGGAA-
1 GAAGAAGAA-GAAG
14228565 GAAGAA-AAG-AG
1 GAAGAAGAAGAAG
14228576 GAAGAAGAA
1 GAAGAAGAA
14228585 AGAAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.23
12 4 0.13
13 15 0.50
14 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:14228596 original size:24 final size:24
Alignment explanation
Indices: 14228539--14228597 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 24
14228529 GCTAGACTTT
*
14228539 GAAGAAGAAGAAGGAAGAAGAAGGAA
1 GAAGAA-AAG-AGGAAGAAGAAGAAA
14228565 GAAGAAAAGAGGAAGAAGAAAGAAA
1 GAAGAAAAGAGGAAGAAG-AAGAAA
*
14228590 GAAAAAAA
1 GAAGAAAA
14228598 AAAGAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 9 0.30
25 15 0.50
26 6 0.20
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (24 bp):
GAAGAAAAGAGGAAGAAGAAGAAA
Found at i:14228701 original size:19 final size:21
Alignment explanation
Indices: 14228677--14228717 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14228667 CCAGCAGCCC
14228677 AAGAAA-AAA-CAAAAAAAAA
1 AAGAAACAAACCAAAAAAAAA
*
14228696 AAGAAACAAACCCAAAAAAAA
1 AAGAAACAAACCAAAAAAAAA
14228717 A
1 A
14228718 TCAAAGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 3 0.16
21 10 0.53
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (21 bp):
AAGAAACAAACCAAAAAAAAA
Found at i:14228722 original size:17 final size:17
Alignment explanation
Indices: 14228680--14228831 Score: 71
Period size: 17 Copynumber: 8.6 Consensus size: 17
14228670 GCAGCCCAAG
14228680 AAAAAACAAA--AAAAA
1 AAAAAACAAACCAAAAA
*
14228695 AAAGAAACAAACCCAAAA
1 AAA-AAACAAACCAAAAA
* *
14228713 AAAAATCAAAGCAAAAA
1 AAAAAACAAACCAAAAA
* *
14228730 AAAAAGCAAA-AAAAAGA
1 AAAAAACAAACCAAAA-A
*
14228747 AGGGAAAGAAGC-AGCC-AAAA
1 A---AAA-AA-CAAACCAAAAA
*
14228767 AAAAAACAAAACAAAAAAA
1 AAAAAAC-AAAC-CAAAAA
* *
14228786 AAAGAAACAAGCCCAAAA
1 AAA-AAACAAACCAAAAA
* *
14228804 AAAAATCAAAGCAAAAA
1 AAAAAACAAACCAAAAA
14228821 AAAAAAGCAAA
1 AAAAAA-CAAA
14228832 AAAAAGAAGG
Statistics
Matches: 102, Mismatches: 19, Indels: 29
0.68 0.13 0.19
Matches are distributed among these distances:
15 4 0.04
16 13 0.13
17 42 0.41
18 18 0.18
19 10 0.10
20 9 0.09
21 5 0.05
22 1 0.01
ACGTcount: A:0.76, C:0.13, G:0.09, T:0.01
Consensus pattern (17 bp):
AAAAAACAAACCAAAAA
Found at i:14228786 original size:18 final size:18
Alignment explanation
Indices: 14228763--14228836 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
14228753 AGAAGCAGCC
14228763 AAAAAAAAAACAAAACAA
1 AAAAAAAAAACAAAACAA
* **
14228781 AAAAAAAAGAA-ACAAGCCC
1 AAAAAAAA-AACA-AAACAA
* *
14228800 AAAAAAAAATCAAAGCAA
1 AAAAAAAAAACAAAACAA
*
14228818 AAAAAAAAAGCAAAA-AA
1 AAAAAAAAAACAAAACAA
14228835 AA
1 AA
14228837 GAAGGGAAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
17 4 0.09
18 27 0.60
19 14 0.31
ACGTcount: A:0.81, C:0.12, G:0.05, T:0.01
Consensus pattern (18 bp):
AAAAAAAAAACAAAACAA
Found at i:14228788 original size:20 final size:20
Alignment explanation
Indices: 14228763--14228826 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
14228753 AGAAGCAGCC
14228763 AAAAAAAAAACAAAACAAAA
1 AAAAAAAAAACAAAACAAAA
* **
14228783 AAAAAAGAAACAAGCCCAAAA
1 AAAAAAAAAACAA-AACAAAA
* *
14228804 AAAAATCAAAGCAAAA-AAAA
1 AAAAA-AAAAACAAAACAAAA
14228824 AAA
1 AAA
14228827 GCAAAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 19 0.56
21 10 0.29
22 5 0.15
ACGTcount: A:0.81, C:0.12, G:0.05, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAACAAAACAAAA
Found at i:14228793 original size:15 final size:16
Alignment explanation
Indices: 14228680--14228825 Score: 71
Period size: 16 Copynumber: 8.4 Consensus size: 16
14228670 GCAGCCCAAG
14228680 AAAAAACAAAA-AAAA
1 AAAAAACAAAACAAAA
*
14228695 AAAGAAACAAACCCAAAA
1 AAA-AAACAAA-ACAAAA
* *
14228713 AAAAATCAAAGCAAAA
1 AAAAAACAAAACAAAA
*
14228729 AAAAAAGCAAAAAAAAGA
1 AAAAAA-CAAAACAAA-A
**
14228747 AGGGAAAGAAGC-AGCCAAAA
1 A---AAA-AA-CAAAACAAAA
14228767 AAAAAACAAAACAAAA
1 AAAAAACAAAACAAAA
*
14228783 AAAAAAGAAACAAGCCCAAAA
1 AAAAAA-CAA-AA---CAAAA
* *
14228804 AAAAATCAAAGCAAAA
1 AAAAAACAAAACAAAA
14228820 AAAAAA
1 AAAAAA
14228826 AGCAAAAAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
15 4 0.04
16 41 0.41
17 18 0.18
18 11 0.11
19 1 0.01
20 4 0.04
21 17 0.17
22 4 0.04
ACGTcount: A:0.77, C:0.13, G:0.09, T:0.01
Consensus pattern (16 bp):
AAAAAACAAAACAAAA
Found at i:14228804 original size:36 final size:36
Alignment explanation
Indices: 14228690--14228825 Score: 109
Period size: 37 Copynumber: 3.8 Consensus size: 36
14228680 AAAAAACAAA
* * * **
14228690 AAAAAAAAGAAACAAACCCAAAAAAAAATCAA-AG-C
1 AAAAAAAA-AATCAAAACAAAAAAAAAAGAAACAGCC
* * *
14228725 AAAAAAAAAAGCAAAA-AAAAGAAGGGAAAGAAGCAGCC
1 AAAAAAAAAATCAAAACAAAA-AA--AAAAGAAACAGCC
14228763 AAAAAAAAAA-CAAAACAAAAAAAAAAGAAACAAGCC
1 AAAAAAAAAATCAAAACAAAAAAAAAAGAAAC-AGCC
* *
14228799 CAAAAAAAAATCAAAGCAAAAAAAAAA
1 AAAAAAAAAATCAAAACAAAAAAAAAA
14228826 AGCAAAAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
33 3 0.04
34 8 0.10
35 15 0.18
36 17 0.21
37 24 0.29
38 15 0.18
ACGTcount: A:0.76, C:0.13, G:0.10, T:0.01
Consensus pattern (36 bp):
AAAAAAAAAATCAAAACAAAAAAAAAAGAAACAGCC
Found at i:14228820 original size:91 final size:94
Alignment explanation
Indices: 14228682--14228865 Score: 338
Period size: 92 Copynumber: 2.0 Consensus size: 94
14228672 AGCCCAAGAA
14228682 AAAACAAAAAAAAAAAGAAACAAACCCAAAAAAAAATCAAAGC-AAAAAAAAAAGCAAAAAAAAG
1 AAAACAAAAAAAAAAAGAAACAAACCCAAAAAAAAATCAAAGCAAAAAAAAAAAGCAAAAAAAAG
14228746 AAGGGAAAGAAGCAGC-CAAAAAAAAAAC
66 AAGGGAAAGAAGCAGCACAAAAAAAAAAC
*
14228774 AAAAC-AAAAAAAAAAGAAACAAGCCCAAAAAAAAATCAAAGCAAAAAAAAAAAGCAAAAAAAAG
1 AAAACAAAAAAAAAAAGAAACAAACCCAAAAAAAAATCAAAGCAAAAAAAAAAAGCAAAAAAAAG
14228838 AAGGGAAAGAAGCAGCACAAAAAAAAAA
66 AAGGGAAAGAAGCAGCACAAAAAAAAAA
14228866 AAGGGCAGGC
Statistics
Matches: 89, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
91 36 0.40
92 42 0.47
93 11 0.12
ACGTcount: A:0.75, C:0.12, G:0.11, T:0.01
Consensus pattern (94 bp):
AAAACAAAAAAAAAAAGAAACAAACCCAAAAAAAAATCAAAGCAAAAAAAAAAAGCAAAAAAAAG
AAGGGAAAGAAGCAGCACAAAAAAAAAAC
Found at i:14228821 original size:14 final size:13
Alignment explanation
Indices: 14228801--14228836 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
14228791 AACAAGCCCA
14228801 AAAAAAAATCAAAGC
1 AAAAAAAA--AAAGC
14228816 AAAAAAAAAAAGC
1 AAAAAAAAAAAGC
14228829 AAAAAAAA
1 AAAAAAAA
14228837 GAAGGGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
15 8 0.38
ACGTcount: A:0.83, C:0.08, G:0.06, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAAGC
Found at i:14228822 original size:39 final size:39
Alignment explanation
Indices: 14228725--14228826 Score: 104
Period size: 39 Copynumber: 2.6 Consensus size: 39
14228715 AAATCAAAGC
** *
14228725 AAAAAAA-AAAGCAAAAAAAAGAAGGGAAAGAAGCAGCCAAA
1 AAAAAAACAAAGCAAAAAAAA-AAAAGAAACAAGCA-CC-AA
*
14228766 AAAAAAACAAA--ACAAAAAAAAAAGAAACAAGC-CCAA
1 AAAAAAACAAAGCAAAAAAAAAAAAGAAACAAGCACCAA
14228802 AAAAAAATCAAAGCAAAAAAAAAAA
1 AAAAAAA-CAAAGCAAAAAAAAAAA
14228827 GCAAAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
36 9 0.17
37 6 0.12
39 20 0.38
40 7 0.13
41 7 0.13
42 3 0.06
ACGTcount: A:0.76, C:0.12, G:0.11, T:0.01
Consensus pattern (39 bp):
AAAAAAACAAAGCAAAAAAAAAAAAGAAACAAGCACCAA
Found at i:14228926 original size:57 final size:58
Alignment explanation
Indices: 14228827--14228942 Score: 216
Period size: 59 Copynumber: 2.0 Consensus size: 58
14228817 AAAAAAAAAA
14228827 GCAAAAAAAAGAAGGGAAAGAAGCAGCACAAAAAAAAAAAAGGGCAGGCCAACAATAGG
1 GCAAAAAAAAGAAGGGAAAGAAGCAGCAC-AAAAAAAAAAAGGGCAGGCCAACAATAGG
14228886 GCAAAAAAAAGAAGGGAAAGAAGCAGCAC-AAAAAAAAAAGGGCAGGCCAACAATAGG
1 GCAAAAAAAAGAAGGGAAAGAAGCAGCACAAAAAAAAAAAGGGCAGGCCAACAATAGG
14228943 CCCAATTCCA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
57 28 0.49
59 29 0.51
ACGTcount: A:0.59, C:0.14, G:0.26, T:0.02
Consensus pattern (58 bp):
GCAAAAAAAAGAAGGGAAAGAAGCAGCACAAAAAAAAAAAGGGCAGGCCAACAATAGG
Found at i:14228969 original size:57 final size:58
Alignment explanation
Indices: 14228828--14228944 Score: 155
Period size: 57 Copynumber: 2.0 Consensus size: 58
14228818 AAAAAAAAAG
** * *
14228828 CAAAAAAAAGAAGGGAAAGAAGCAGCACAAAAAAAAAAAAGGGCAGGCCAACAATAGGG
1 CAAAAAAAAGAAGCCAAACAAGCAGCAC-AAAAAAAAAAAGGGCAGGCCAACAATAGGC
** *
14228887 CAAAAAAAAGAAGGGAAAGAAGCAGCAC-AAAAAAAAAAGGGCAGGCCAACAATAGGC
1 CAAAAAAAAGAAGCCAAACAAGCAGCACAAAAAAAAAAAGGGCAGGCCAACAATAGGC
14228944 C
1 C
14228945 CAATTCCAGC
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 29 0.51
59 28 0.49
ACGTcount: A:0.58, C:0.15, G:0.25, T:0.02
Consensus pattern (58 bp):
CAAAAAAAAGAAGCCAAACAAGCAGCACAAAAAAAAAAAGGGCAGGCCAACAATAGGC
Found at i:14229044 original size:14 final size:14
Alignment explanation
Indices: 14229025--14229092 Score: 82
Period size: 15 Copynumber: 4.6 Consensus size: 14
14229015 GCAGCCCAGC
**
14229025 AGAAAAAAGAAGGA
1 AGAAAAAAGAAAAA
14229039 AGAAAAAGAAGAAAAA
1 AG-AAAA-AAGAAAAA
14229055 AGAAAAAAGAAAAA
1 AGAAAAAAGAAAAA
14229069 AGGAAAAAAGAAAAAA
1 A-GAAAAAAG-AAAAA
14229085 AGAAAAAA
1 AGAAAAAA
14229093 AGAAGAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
14 11 0.23
15 23 0.48
16 14 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAAAGAAAAA
Found at i:14229051 original size:23 final size:22
Alignment explanation
Indices: 14229025--14229101 Score: 100
Period size: 23 Copynumber: 3.4 Consensus size: 22
14229015 GCAGCCCAGC
**
14229025 AGAAAAAAGAAGGAAGAAAAAGA
1 AGAAAAAAGAAAAAAGAAAAA-A
14229048 AGAAAAAAGAAAAAAGAAAAAA
1 AGAAAAAAGAAAAAAGAAAAAA
*
14229070 GGAAAAAAGAAAAAAAGAAAAAA
1 AGAAAAAAG-AAAAAAGAAAAAA
14229093 AGAAGAAAA
1 AGAA-AAAA
14229102 AGGGGGTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
22 9 0.19
23 35 0.73
24 4 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AGAAAAAAGAAAAAAGAAAAAA
Found at i:14229057 original size:7 final size:7
Alignment explanation
Indices: 14229025--14229092 Score: 82
Period size: 7 Copynumber: 9.1 Consensus size: 7
14229015 GCAGCCCAGC
14229025 AGAAAAA
1 AGAAAAA
**
14229032 AGAAGGA
1 AGAAAAA
14229039 AGAAAAAGA
1 AG-AAAA-A
14229048 AGAAAAA
1 AGAAAAA
14229055 AGAAAAA
1 AGAAAAA
14229062 AGAAAAA
1 AGAAAAA
14229069 AGGAAAAA
1 A-GAAAAA
14229077 AGAAAAAA
1 AG-AAAAA
14229085 AGAAAAA
1 AGAAAAA
14229092 A
1 A
14229093 AGAAGAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
7 30 0.57
8 20 0.38
9 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:14229057 original size:16 final size:15
Alignment explanation
Indices: 14229027--14229101 Score: 89
Period size: 16 Copynumber: 4.9 Consensus size: 15
14229017 AGCCCAGCAG
**
14229027 AAAAAAGAAGGAAGA
1 AAAAAAGAAAAAAGA
14229042 AAAAGAAGAAAAAAG-
1 AAAA-AAGAAAAAAGA
*
14229057 AAAAAAGAAAAAAGG
1 AAAAAAGAAAAAAGA
14229072 AAAAAAGAAAAAAAGA
1 AAAAAAG-AAAAAAGA
14229088 AAAAAAGAAGAAAA
1 AAAAAAGAA-AAAA
14229102 AGGGGGTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.19
15 17 0.32
16 26 0.49
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAGA
Found at i:14229061 original size:8 final size:8
Alignment explanation
Indices: 14229038--14229103 Score: 84
Period size: 8 Copynumber: 8.4 Consensus size: 8
14229028 AAAAAGAAGG
14229038 AAGAAAAA
1 AAGAAAAA
14229046 GAAG-AAAA
1 -AAGAAAAA
14229054 AAG-AAAA
1 AAGAAAAA
14229061 AAG-AAAA
1 AAGAAAAA
*
14229068 AAGGAAAA
1 AAGAAAAA
14229076 AAGAAAAA
1 AAGAAAAA
14229084 AAGAAAAA
1 AAGAAAAA
14229092 AAGAAGAAA
1 AAGAA-AAA
14229101 AAG
1 AAG
14229104 GGGGTTCAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
7 17 0.31
8 28 0.52
9 9 0.17
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:14229685 original size:19 final size:18
Alignment explanation
Indices: 14229643--14229916 Score: 62
Period size: 17 Copynumber: 14.9 Consensus size: 18
14229633 GAAATTTTCG
* **
14229643 AATTTTCGCGTTTTCAAA
1 AATTTTCGTGTTTAAAAA
*
14229661 AGTTTTCGTGTTTGAAAAA
1 AATTTTCGTGTTT-AAAAA
*
14229680 AATTTTCGCGTTT-AAAA
1 AATTTTCGTGTTTAAAAA
* *
14229697 AATTTCTCGTATTT-CAAA
1 AATTT-TCGTGTTTAAAAA
* ** *
14229715 AATTGTCGT-TTTTTATA
1 AATTTTCGTGTTTAAAAA
* * *
14229732 AATCTTCGTGCTTT-CAAT
1 AATTTTCGTG-TTTAAAAA
** *
14229750 AATCCTCGTGCTTT-TAAA
1 AATTTTCGTG-TTTAAAAA
* * *
14229768 AATTCTCATGTTT-CAAA
1 AATTTTCGTGTTTAAAAA
* **
14229785 AATCTTCGTGTTT-TCAA
1 AATTTTCGTGTTTAAAAA
* * *
14229802 AATTCTAGTGTTT-CAAA
1 AATTTTCGTGTTTAAAAA
*
14229819 AATTTTCTTGTTTTCAAAAAAAA
1 AATTTTCGTG-TTT----AAAAA
*
14229842 AAATTTCGTGTTTTAAAAAAA
1 AATTTTCGTG-TTT--AAAAA
*
14229863 AATATTTCCGTGTTTTAAAA
1 AAT-TTT-CGTGTTTAAAAA
* *
14229883 ATTTTTCGTGTTT-TAAA
1 AATTTTCGTGTTTAAAAA
* *
14229900 AATTCTCGTATTTAAAA
1 AATTTTCGTGTTTAAAA
14229917 TTTTTTTTTT
Statistics
Matches: 195, Mismatches: 47, Indels: 28
0.72 0.17 0.10
Matches are distributed among these distances:
16 3 0.02
17 72 0.37
18 60 0.31
19 20 0.10
20 6 0.03
21 9 0.05
22 6 0.03
23 19 0.10
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (18 bp):
AATTTTCGTGTTTAAAAA
Found at i:14229716 original size:37 final size:37
Alignment explanation
Indices: 14229643--14229716 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
14229633 GAAATTTTCG
* * * *
14229643 AATTTTCGCGTTTTCAAAAGTTTTCGTGTTTGAAAAA
1 AATTTTCGCGTTTTAAAAAATTTTCGTATTTCAAAAA
14229680 AATTTTCGCG-TTTAAAAAATTTCTCGTATTTCAAAAA
1 AATTTTCGCGTTTTAAAAAATTT-TCGTATTTCAAAAA
14229717 TTGTCGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (37 bp):
AATTTTCGCGTTTTAAAAAATTTTCGTATTTCAAAAA
Found at i:14229758 original size:18 final size:18
Alignment explanation
Indices: 14229731--14229821 Score: 80
Period size: 17 Copynumber: 5.2 Consensus size: 18
14229721 CGTTTTTTAT
*
14229731 AAATCTTCGTGCTTTCAA
1 AAATCCTCGTGCTTTCAA
* *
14229749 TAATCCTCGTGCTTTTAA
1 AAATCCTCGTGCTTTCAA
* *
14229767 AAATTCTCATG-TTTCAA
1 AAATCCTCGTGCTTTCAA
* *
14229784 AAATCTTCGTGTTTTC-A
1 AAATCCTCGTGCTTTCAA
* *
14229801 AAATTCTAGTG-TTTCAA
1 AAATCCTCGTGCTTTCAA
14229818 AAAT
1 AAAT
14229822 TTTCTTGTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
16 4 0.07
17 27 0.47
18 27 0.47
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.42
Consensus pattern (18 bp):
AAATCCTCGTGCTTTCAA
Found at i:14229787 original size:17 final size:18
Alignment explanation
Indices: 14229761--14229838 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 18
14229751 ATCCTCGTGC
14229761 TTTT-AAAAATTCTCATG
1 TTTTCAAAAATTCTCATG
*
14229778 -TTTCAAAAA-TCTTCGTG
1 TTTTCAAAAATTC-TCATG
14229795 TTTTC-AAAATTCT-A-G
1 TTTTCAAAAATTCTCATG
* *
14229810 TGTTTCAAAAATTTTCTTG
1 T-TTTCAAAAATTCTCATG
14229829 TTTTCAAAAA
1 TTTTCAAAAA
14229839 AAAAAATTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
15 2 0.04
16 9 0.18
17 21 0.43
18 15 0.31
19 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (18 bp):
TTTTCAAAAATTCTCATG
Found at i:14229814 original size:34 final size:34
Alignment explanation
Indices: 14229743--14229837 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 34
14229733 ATCTTCGTGC
* * *
14229743 TTTCAATAATCCTCGTGCTTTTAAAAATTCTCATG
1 TTTCAAAAATCTTCGTG-TTTTCAAAATTCTCATG
14229778 TTTCAAAAATCTTCGTGTTTTCAAAATTCT-AGTG
1 TTTCAAAAATCTTCGTGTTTTCAAAATTCTCA-TG
* *
14229812 TTTCAAAAATTTTCTTGTTTTCAAAA
1 TTTCAAAAATCTTCGTGTTTTCAAAA
14229838 AAAAAAATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
33 1 0.02
34 38 0.70
35 15 0.28
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (34 bp):
TTTCAAAAATCTTCGTGTTTTCAAAATTCTCATG
Found at i:14229817 original size:16 final size:16
Alignment explanation
Indices: 14229766--14229819 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
14229756 CGTGCTTTTA
14229766 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
14229782 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
14229800 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
14229816 AAAA
1 AAAA
14229820 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:14229835 original size:18 final size:18
Alignment explanation
Indices: 14229643--14230093 Score: 140
Period size: 18 Copynumber: 25.1 Consensus size: 18
14229633 GAAATTTTCG
*
14229643 AATTTTCGCGTTTTCAAA
1 AATTTTCGTGTTTTCAAA
* **
14229661 AGTTTTCGTGTTTGAAAAA
1 AATTTTCGTGTTT-TCAAA
* *
14229680 AATTTTCGCG-TTTAAAA
1 AATTTTCGTGTTTTCAAA
*
14229697 AATTTCTCGT-ATTTCAAA
1 AATTT-TCGTGTTTTCAAA
* * *
14229715 AATTGTCGT-TTTTTATA
1 AATTTTCGTGTTTTCAAA
* * *
14229732 AATCTTCGTGCTTTCAAT
1 AATTTTCGTGTTTTCAAA
**
14229750 AATCCTCGTGCTTTT-AAA
1 AATTTTCGTG-TTTTCAAA
* *
14229768 AATTCTCATG-TTTCAAA
1 AATTTTCGTGTTTTCAAA
*
14229785 AATCTTCGTGTTTTC-AA
1 AATTTTCGTGTTTTCAAA
* *
14229802 AATTCTAGTG-TTTCAAA
1 AATTTTCGTGTTTTCAAA
*
14229819 AATTTTCTTGTTTTCAAAAAAAA
1 AATTTTCGTGTTTTC-----AAA
* *
14229842 AAATTTCGTGTTTTAAAAAAA
1 AATTTTCGTGTTTT---CAAA
14229863 AATATTTCCGTGTTTT-AAA
1 AAT-TTT-CGTGTTTTCAAA
14229882 AATTTTTCGTGTTTT-AAA
1 AA-TTTTCGTGTTTTCAAA
* *
14229900 AATTCTCGT-ATTT--AA
1 AATTTTCGTGTTTTCAAA
* *
14229915 AATTTT--TTTTTTAAGAAA
1 AATTTTCGTGTTTT--CAAA
*
14229933 AAATTT--TG-TTTCAAAA
1 AATTTTCGTGTTTTC-AAA
* * *
14229949 AAATGTCTTGTTTT-AAA
1 AATTTTCGTGTTTTCAAA
**
14229966 AATTCCCGTG-TTTCAAAAAA
1 AATTTTCGTGTTTTC---AAA
* *
14229986 AAATGTCGTGTTTT-AAGA
1 AATTTTCGTGTTTTCAA-A
* *
14230004 AAATTTCGTTTTTTTCCAAA
1 AATTTTCG-TGTTTT-CAAA
*
14230024 AATTTTCGTG-TTTCTAA
1 AATTTTCGTGTTTTCAAA
* *
14230041 AATATTCGTG-TTT-ACA
1 AATTTTCGTGTTTTCAAA
*
14230057 AATTCTCGTGTTTTCAAA
1 AATTTTCGTGTTTTCAAA
* *
14230075 AATTCTCGTATTTT-AAA
1 AATTTTCGTGTTTTCAAA
14230092 AA
1 AA
14230094 AAAAAACTTT
Statistics
Matches: 329, Mismatches: 64, Indels: 81
0.69 0.14 0.17
Matches are distributed among these distances:
13 1 0.00
14 3 0.01
15 7 0.02
16 30 0.09
17 96 0.29
18 106 0.32
19 31 0.09
20 19 0.06
21 10 0.03
22 3 0.01
23 23 0.07
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (18 bp):
AATTTTCGTGTTTTCAAA
Found at i:14229859 original size:22 final size:22
Alignment explanation
Indices: 14229816--14229883 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 22
14229806 CTAGTGTTTC
* *
14229816 AAAAATTTTCTTGTTTTCAAAAA
1 AAAAAATTTCGTGTTTT-AAAAA
14229839 AAAAAATTTCGTGTTTTAAAAA
1 AAAAAATTTCGTGTTTTAAAAA
*
14229861 AAAATATTTCCGTGTTTTAAAAA
1 AAAAAATTT-CGTGTTTTAAAAA
14229884 TTTTTCGTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.32
23 28 0.68
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (22 bp):
AAAAAATTTCGTGTTTTAAAAA
Found at i:14233435 original size:16 final size:18
Alignment explanation
Indices: 14233409--14233441 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
14233399 ATAAACATCA
14233409 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
14233426 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
14233442 CCTTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:14236428 original size:21 final size:19
Alignment explanation
Indices: 14236378--14236452 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
14236368 AATCTTCAAG
*
14236378 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
14236397 GATACGCAATCTTAGATTT
1 GATATGCAATCTTAGATAT
14236416 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
14236437 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
14236453 AGATATGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 32 0.65
21 17 0.35
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:14236478 original size:22 final size:22
Alignment explanation
Indices: 14236431--14236475 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
14236421 ATGCAATCTT
*
14236431 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATATTAGA
* *
14236453 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
14236476 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Found at i:14236703 original size:23 final size:23
Alignment explanation
Indices: 14236659--14236703 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
14236649 TCTTATTTTG
*
14236659 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTGTATAATTGATTTA
**
14236682 TTGATTTGTGTATTGTTGATTT
1 TTGATTTGTGTATAATTGATTT
14236704 CAAATTTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.62
Consensus pattern (23 bp):
TTGATTTGTGTATAATTGATTTA
Found at i:14236937 original size:7 final size:6
Alignment explanation
Indices: 14236917--14236948 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
14236907 TCTTGTATCA
14236917 TTATTAT TTATTT TTATTT TTATTT TTATTT T
1 TTATT-T TTATTT TTATTT TTATTT TTATTT T
14236949 CATGCACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTATTT
Found at i:14241621 original size:43 final size:43
Alignment explanation
Indices: 14241574--14241665 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
14241564 AACGTTTGTA
* *
14241574 GCGCTTACAGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCG
1 GCGCTTACAGAAAAAACGCCGCTAAAGAACATGATCTTTAGCG
** ** *
14241617 GCGCTTTTATCACAAACGCCGCTAAAGAACATGATCTTTAGCG
1 GCGCTTACAGAAAAAACGCCGCTAAAGAACATGATCTTTAGCG
14241660 GCGCTT
1 GCGCTT
14241666 TTATCTCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (43 bp):
GCGCTTACAGAAAAAACGCCGCTAAAGAACATGATCTTTAGCG
Found at i:14241666 original size:43 final size:43
Alignment explanation
Indices: 14241587--14241757 Score: 188
Period size: 43 Copynumber: 3.9 Consensus size: 43
14241577 CTTACAGAAA
* *
14241587 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
*
14241630 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCTC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
* * *
14241673 AAACGCCG-TAAA-AAAAGTAAAGTTATTTAGCGGCGCTTTCT-TCAC
1 AAACGCCGCTAAAGAACA-T---GATCTTTAGCGGCGCTTT-TATCAC
* *
14241718 AAACGCTGCTAGAGAACATGAGT-TTTAGCGGCGCTTTTAT
1 AAACGCCGCTAAAGAACATGA-TCTTTAGCGGCGCTTTTAT
14241758 GAAAAATGCC
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
41 3 0.03
42 6 0.06
43 64 0.59
44 1 0.01
45 26 0.24
46 5 0.05
47 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
Found at i:14242181 original size:21 final size:21
Alignment explanation
Indices: 14242156--14242203 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
14242146 GCTTCTCTCA
14242156 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
14242177 TTGCTTCTCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
14242198 CTGCTT
1 CTGCTT
14242204 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.42, G:0.19, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:14243116 original size:37 final size:36
Alignment explanation
Indices: 14243075--14243181 Score: 127
Period size: 37 Copynumber: 3.1 Consensus size: 36
14243065 TAGAAATTGA
14243075 TATGTAATTAGAAATTGTATCTTAATATTATATAAGT
1 TATGTAATTAGAAATT-TATCTTAATATTATATAAGT
*
14243112 TATGTAATGAG-AA---A--TTAATATTATATAAGT
1 TATGTAATTAGAAATTTATCTTAATATTATATAAGT
* *
14243142 TATGTAATTCGAAATTTTATCTTAATATTGTATAAGT
1 TATGTAATTAGAAA-TTTATCTTAATATTATATAAGT
14243179 TAT
1 TAT
14243182 CTAAAATATA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
30 25 0.42
31 2 0.03
32 1 0.02
35 1 0.02
36 2 0.03
37 28 0.47
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (36 bp):
TATGTAATTAGAAATTTATCTTAATATTATATAAGT
Found at i:14243296 original size:20 final size:20
Alignment explanation
Indices: 14243255--14243422 Score: 118
Period size: 20 Copynumber: 8.7 Consensus size: 20
14243245 TCCAAATTTA
* * *
14243255 ATCTTAAAATAATATAACTT
1 ATCTTAATATTATATAAGTT
* *
14243275 ATATTAATATTATAGAAGTT
1 ATCTTAATATTATATAAGTT
* * *
14243295 AT-GT-A-ATTAGA-AATTTT
1 ATCTTAATATTATATAA-GTT
14243312 ATCTTAATATTATATAAGTT
1 ATCTTAATATTATATAAGTT
14243332 ATCTTAATATTTATATAAGTT
1 ATCTTAATA-TTATATAAGTT
* * *
14243353 AT-GT-A-ATTAGA-AATTTT
1 ATCTTAATATTATATAA-GTT
* * *
14243370 GTCTTAATACTATATAAGTA
1 ATCTTAATATTATATAAGTT
14243390 ATCTTAATATTATATAAGTT
1 ATCTTAATATTATATAAGTT
*
14243410 ATCTTAATTTTAT
1 ATCTTAATATTAT
14243423 GTTATTTCCA
Statistics
Matches: 113, Mismatches: 24, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
16 4 0.04
17 16 0.14
18 4 0.04
19 4 0.04
20 68 0.60
21 17 0.15
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (20 bp):
ATCTTAATATTATATAAGTT
Found at i:14243367 original size:58 final size:57
Alignment explanation
Indices: 14243221--14243411 Score: 265
Period size: 57 Copynumber: 3.3 Consensus size: 57
14243211 AAATTACAAT
* ** * * * * *
14243221 TTAATATTATATAATTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATA
1 TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
*
14243278 TTAATATTATAGAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
1 TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
* * *
14243335 TTAATATTTATATAAGTTATGTAATTAGAAATTTTGTCTTAATACTATATAAGTAATC
1 TTAATA-TTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
14243393 TTAATATTATATAAGTTAT
1 TTAATATTATATAAGTTAT
14243412 CTTAATTTTA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
57 67 0.56
58 53 0.44
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (57 bp):
TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
Found at i:14245604 original size:6 final size:6
Alignment explanation
Indices: 14245595--14245768 Score: 348
Period size: 6 Copynumber: 29.0 Consensus size: 6
14245585 TTTAGTTTTA
14245595 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
14245643 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
14245691 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
14245739 ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT
14245769 CAACGAGATT
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 168 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:14247028 original size:7 final size:7
Alignment explanation
Indices: 14247016--14247086 Score: 63
Period size: 7 Copynumber: 10.1 Consensus size: 7
14247006 AATCGTAGAT
14247016 CCTAAAC
1 CCTAAAC
14247023 CCTAAAC
1 CCTAAAC
**
14247030 TATAAAC
1 CCTAAAC
14247037 CCTAAAC
1 CCTAAAC
14247044 CCTAAAC
1 CCTAAAC
*
14247051 CCCAAATC
1 CCTAAA-C
*
14247059 CC-AAAT
1 CCTAAAC
* *
14247065 CGTAAAA
1 CCTAAAC
*
14247072 CTTAAAC
1 CCTAAAC
14247079 CCTAAAC
1 CCTAAAC
14247086 C
1 C
14247087 TGTCAATTAA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
6 1 0.02
7 47 0.92
8 3 0.06
ACGTcount: A:0.45, C:0.37, G:0.01, T:0.17
Consensus pattern (7 bp):
CCTAAAC
Found at i:14247289 original size:13 final size:14
Alignment explanation
Indices: 14247254--14247294 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
14247244 CAAACCCCTA
*
14247254 AAGT-CTAAACCGT
1 AAGTCCTAAACCAT
*
14247267 AAGTCATAAACCAT
1 AAGTCCTAAACCAT
14247281 AA-TCCTAAACCAT
1 AAGTCCTAAACCAT
14247294 A
1 A
14247295 TCTTTGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (14 bp):
AAGTCCTAAACCAT
Found at i:14248026 original size:228 final size:229
Alignment explanation
Indices: 14247629--14248045 Score: 558
Period size: 228 Copynumber: 1.8 Consensus size: 229
14247619 AAAGTTACTC
* * * **
14247629 TATAGCGGCGTTTCTAAATAAGCGCCGCTAATGAATCTATACGTGAAGCCGAAACGATGTGTTTT
1 TATAGCGGCGTTTCTAAATAAGCGCCACTAATGAATCTATACGTCAAACCGAAACGATGCATTTT
* * *
14247694 GGTCAAAATTTTTGCGGCGCTTAAGCAGAAGCGCCACTAAAAGCTGATATATAACGGCGTTTATG
66 GGTCAAAATATTTGCGGCGATTAAGCAGAAGCGCCACTAAAAGCTAATATATAACGGCGTTTATG
*
14247759 GATAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCGCTTCGGTTT-AAAATTTTTC
131 GATAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCGCTTCAGTTTCAAAATTTTTC
14247823 GGCGTTTTTTAGTTAAACGCCGCTATTTATGGGA
196 GGCGTTTTTTAGTTAAACGCCGCTATTTATGGGA
** ** *
14247857 TATAGCGGCGTTTGC-AGGTAAGCGCCACTAATGCCTTTATACGTCAAACTCG-AACGATGCATT
1 TATAGCGGCGTTT-CTAAATAAGCGCCACTAATGAATCTATACGTCAAAC-CGAAACGATGCATT
* * * *
14247920 TTGTTCAAAATATTTGCGGCGATTCAGGA-ACAGCGCCA-TGAAAAGCTAATATATAGCGGCGTT
64 TTGGTCAAAATATTTGCGGCGATTAAGCAGA-AGCGCCACT-AAAAGCTAATATATAACGGCGTT
* * *
14247983 T-TCGGCTAAGCGCCGCTAAAGGCGCTATAGCTCAAGACGAAACGTTGCGTTTCAGTTTCAAAA
127 TAT-GGATAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCGCTTCAGTTTCAAAA
14248046 GTTCCGGCAT
Statistics
Matches: 162, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
227 3 0.02
228 152 0.94
229 7 0.04
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (229 bp):
TATAGCGGCGTTTCTAAATAAGCGCCACTAATGAATCTATACGTCAAACCGAAACGATGCATTTT
GGTCAAAATATTTGCGGCGATTAAGCAGAAGCGCCACTAAAAGCTAATATATAACGGCGTTTATG
GATAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCGCTTCAGTTTCAAAATTTTTC
GGCGTTTTTTAGTTAAACGCCGCTATTTATGGGA
Found at i:14248767 original size:21 final size:22
Alignment explanation
Indices: 14248742--14248790 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
14248732 AATTTCATTC
14248742 TATTTTGATC-ATTTAACTATTA
1 TATTTT-ATCGATTTAACTATTA
* *
14248764 -ATTTTTTCGATTTAATTATTA
1 TATTTTATCGATTTAACTATTA
14248785 TATTTT
1 TATTTT
14248791 TTAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 16 0.70
22 5 0.22
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (22 bp):
TATTTTATCGATTTAACTATTA
Found at i:14248791 original size:21 final size:21
Alignment explanation
Indices: 14248752--14248792 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
14248742 TATTTTGATC
14248752 ATTTAACTATTAATTTTTTCG
1 ATTTAACTATTAATTTTTTCG
*
14248773 ATTTAATTATTATATTTTTT
1 ATTTAACTATTA-ATTTTTT
14248793 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTAACTATTAATTTTTTCG
Found at i:14249499 original size:9 final size:9
Alignment explanation
Indices: 14249485--14249535 Score: 77
Period size: 9 Copynumber: 5.8 Consensus size: 9
14249475 TTTGGTTAAA
14249485 AATTACCCG
1 AATTACCCG
14249494 AATTACCCG
1 AATTACCCG
*
14249503 -ATTAACCG
1 AATTACCCG
*
14249511 AATTAACCG
1 AATTACCCG
14249520 AATTACCCG
1 AATTACCCG
14249529 AATTACC
1 AATTACC
14249536 TGAAAATTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
8 7 0.18
9 32 0.82
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:14249511 original size:17 final size:18
Alignment explanation
Indices: 14249485--14249535 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 18
14249475 TTTGGTTAAA
14249485 AATTACCCGAATTACCCG
1 AATTACCCGAATTACCCG
* *
14249503 -ATTAACCGAATTAACCG
1 AATTACCCGAATTACCCG
14249520 AATTACCCGAATTACC
1 AATTACCCGAATTACC
14249536 TGAAAATTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.24
Consensus pattern (18 bp):
AATTACCCGAATTACCCG
Found at i:14250493 original size:20 final size:20
Alignment explanation
Indices: 14250468--14250505 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14250458 CGTAAAATGA
14250468 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
*
14250488 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
14250506 TTGGAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:14250497 original size:34 final size:33
Alignment explanation
Indices: 14250454--14250518 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
14250444 AGTAAAATAT
14250454 TTTTCGTAAAATGATTT-CTGGAAAATGATTTAC
1 TTTTCGTAAAATGATTTACTGGAAAAT-ATTTAC
*
14250487 TTTTCTGTAAAATGATTTATTGGAAAATATTT
1 TTTTC-GTAAAATGATTTACTGGAAAATATTT
14250519 TTTGGTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 16 0.55
35 8 0.28
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (33 bp):
TTTTCGTAAAATGATTTACTGGAAAATATTTAC
Found at i:14252038 original size:21 final size:21
Alignment explanation
Indices: 14252014--14252054 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
14252004 CTTAAAAGTT
14252014 TGGTCCTCCATGAAAGAACAC
1 TGGTCCTCCATGAAAGAACAC
14252035 TGGTCCTCCATGAAAGAACA
1 TGGTCCTCCATGAAAGAACA
14252055 AAAGCAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
TGGTCCTCCATGAAAGAACAC
Found at i:14252066 original size:32 final size:32
Alignment explanation
Indices: 14252030--14252094 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
14252020 TCCATGAAAG
14252030 AACACTGGTCCTCCATGAAAGAACAAAAGCAA
1 AACACTGGTCCTCCATGAAAGAACAAAAGCAA
*
14252062 AACACTGGTCCTCCATGAAAGAACAGAAGCAA
1 AACACTGGTCCTCCATGAAAGAACAAAAGCAA
14252094 A
1 A
14252095 GAATTCCCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.25, G:0.17, T:0.12
Consensus pattern (32 bp):
AACACTGGTCCTCCATGAAAGAACAAAAGCAA
Found at i:14255109 original size:23 final size:23
Alignment explanation
Indices: 14255083--14255128 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
14255073 ATTGTTAGGG
14255083 TTAAAAATTAAGATTAGGGTTTT
1 TTAAAAATTAAGATTAGGGTTTT
* * *
14255106 TTAAGAATTAGGGTTAGGGTTTT
1 TTAAAAATTAAGATTAGGGTTTT
14255129 AGGAGTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (23 bp):
TTAAAAATTAAGATTAGGGTTTT
Found at i:14256263 original size:41 final size:41
Alignment explanation
Indices: 14256202--14256352 Score: 178
Period size: 41 Copynumber: 3.7 Consensus size: 41
14256192 CATAATTTAA
14256202 CATATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CATA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * *
14256244 CATATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
** ** * **
14256285 CCGATCACCGGCACTTAGCCTGCTAGATTTATAGTCTGAAA
1 CATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
14256326 AAT-TCACCGGCATTTAGCCTGCTAGGC
1 CATATCACCGGCACTTAGCCTGCTAGGC
14256353 GCTTAGCCTG
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 21 0.23
41 67 0.73
42 4 0.04
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
CATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:14256364 original size:40 final size:40
Alignment explanation
Indices: 14256205--14256371 Score: 117
Period size: 41 Copynumber: 4.1 Consensus size: 40
14256195 AATTTAACAT
***
14256205 ATTCACCGGCACTTAGCCTGCTAG-GCTTATAGCCTGATTC
1 ATTCACCGGCACTTAGCCTGCTAGAGC-TATAGCCTGAAAA
* * * ***
14256245 ATATCACCGGCACGTAGCCTGCTAG-GTTTATAACCTGATTCCG
1 AT-TCACCGGCACTTAGCCTGCTAGAG-CTATAGCCTGA--AAA
** *
14256288 A-TCACCGGCACTTAGCCTGCTAGATTTATAGTCTGAAAA
1 ATTCACCGGCACTTAGCCTGCTAGAGCTATAGCCTGAAAA
* *
14256327 ATTCACCGGCATTTAGCCTGCTAGGCGCT-TAGCCTGAAAA
1 ATTCACCGGCACTTAGCCTGCTA-GAGCTATAGCCTGAAAA
*
14256367 TTTCA
1 ATTCA
14256372 ATTTCACAGA
Statistics
Matches: 101, Mismatches: 19, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
39 1 0.01
40 36 0.36
41 63 0.62
43 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (40 bp):
ATTCACCGGCACTTAGCCTGCTAGAGCTATAGCCTGAAAA
Found at i:14278111 original size:12 final size:12
Alignment explanation
Indices: 14278094--14278123 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
14278084 GTAGGCTTCC
14278094 AAAATGGAAATG
1 AAAATGGAAATG
14278106 AAAATGGAAATG
1 AAAATGGAAATG
*
14278118 GAAATG
1 AAAATG
14278124 ATCCATTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:14278226 original size:47 final size:46
Alignment explanation
Indices: 14278169--14278263 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 46
14278159 TGATCGGAAG
* * *
14278169 AATGAGTTTATGTTTTTAAACTGTTTTGAAGCCCGAAAAT-GCAAAT
1 AATGAGTTTATGTTTTTAAACTATTTTGAAACCCAAAAATAG-AAAT
*
14278215 AANTGAGTTTATGTTTTTAGACTATTTTGAAACCCAAAAATAGAAAT
1 AA-TGAGTTTATGTTTTTAAACTATTTTGAAACCCAAAAATAGAAAT
14278262 AA
1 AA
14278264 ATCATTCTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
46 2 0.05
47 40 0.93
48 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (46 bp):
AATGAGTTTATGTTTTTAAACTATTTTGAAACCCAAAAATAGAAAT
Found at i:14279326 original size:22 final size:22
Alignment explanation
Indices: 14279284--14279328 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
14279274 AATTAGCTAA
* *
14279284 TAAATTAATAAGTTAATTTAAG
1 TAAATTAATAACTAAATTTAAG
14279306 TAAATTAA-AACTAAATATTAAG
1 TAAATTAATAACTAAAT-TTAAG
14279328 T
1 T
14279329 TATTTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (22 bp):
TAAATTAATAACTAAATTTAAG
Found at i:14297201 original size:16 final size:18
Alignment explanation
Indices: 14297171--14297208 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
14297161 ATCAGTTTTC
14297171 TTTATTTTTTAAATATTT
1 TTTATTTTTTAAATATTT
14297189 TTTA-TTTTT-AATATTT
1 TTTATTTTTTAAATATTT
14297205 TTTA
1 TTTA
14297209 AGAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
17 5 0.25
18 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTTTAAATATTT
Found at i:14297590 original size:168 final size:161
Alignment explanation
Indices: 14297344--14297647 Score: 423
Period size: 168 Copynumber: 1.8 Consensus size: 161
14297334 CAGCTTGGAG
* * *
14297344 AAAAATAGTTTATGTACCACTTGTGACAAAAAAATGTTTAAGTACCAAAATGAGAAAAATAACAT
1 AAAAATAGTTTAGGTAACACTTGTGACAAAAAAATATTTAAGTACCAAAATGAGAAAAATAACAT
* * *
14297409 AGTTTAGGTACCAATTTATGGGTTAATCCATTTTTTTTAAAAAAATAGACTTAATACTTTAACTA
66 AATTTAAGTACCAATTTATGGGTTAAT-C-TTTTTTTT---AAAATAGA--TAACACTTTAACTA
*
14297474 ATGGTTTGACTAATGAAGATATATCATGAACTTGGAAA
124 ATGGTCTGACTAATGAAGATATATCATGAACTTGGAAA
* *
14297512 AAAAATAGTTTAGGTAATACTTGTGACCAAAAAAATATTT-AGATACCAAAATGA-AAAAATGAC
1 AAAAATAGTTTAGGTAACACTTGTGA-CAAAAAAATATTTAAG-TACCAAAATGAGAAAAATAAC
*
14297575 ATAATTTAAGTACCAATTTATGGGTTAATCTTTTTTTTAAAATAGATAACATTTTAACTAATGGT
64 ATAATTTAAGTACCAATTTATGGGTTAATCTTTTTTTTAAAATAGATAACACTTTAACTAATGGT
14297640 CTGACTAA
129 CTGACTAA
14297648 CAAAAATGCC
Statistics
Matches: 124, Mismatches: 10, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
161 24 0.19
163 8 0.06
166 8 0.06
167 1 0.01
168 60 0.48
169 23 0.19
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (161 bp):
AAAAATAGTTTAGGTAACACTTGTGACAAAAAAATATTTAAGTACCAAAATGAGAAAAATAACAT
AATTTAAGTACCAATTTATGGGTTAATCTTTTTTTTAAAATAGATAACACTTTAACTAATGGTCT
GACTAATGAAGATATATCATGAACTTGGAAA
Found at i:14299590 original size:14 final size:15
Alignment explanation
Indices: 14299563--14299596 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
14299553 AACAATCACA
14299563 TATATTATTAATTTT
1 TATATTATTAATTTT
14299578 TATATTA-TAATTTT
1 TATATTATTAATTTT
14299592 TATAT
1 TATAT
14299597 GACATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTATTAATTTT
Found at i:14299899 original size:13 final size:13
Alignment explanation
Indices: 14299881--14299917 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
14299871 AAATAATAAA
*
14299881 AATATTTTTAATT
1 AATATTTATAATT
14299894 AATATTTATAATT
1 AATATTTATAATT
14299907 AA-ATTTA-AATT
1 AATATTTATAATT
14299918 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 4 0.17
12 5 0.22
13 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTTATAATT
Found at i:14306531 original size:3 final size:3
Alignment explanation
Indices: 14306523--14306578 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
14306513 GGAGAACTTA
* *
14306523 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT GAT GAC GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
14306571 GAT GAT GA
1 GAT GAT GA
14306579 AGCTCCAGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.32, C:0.02, G:0.36, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:14321028 original size:44 final size:45
Alignment explanation
Indices: 14320951--14321040 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 45
14320941 AAGGGACTAG
*
14320951 TTTGCAAATCTATAAAAAAACGAGGTTTAGGACTAAACTGTAGAA
1 TTTGCAAATCTATAAAAAAACAAGGTTTAGGACTAAACTGTAGAA
14320996 TTTGCAAATCTAT-AAAAAACAAGGTTTAGGACTAAACTGTAGAA
1 TTTGCAAATCTATAAAAAAACAAGGTTTAGGACTAAACTGTAGAA
14321040 T
1 T
14321041 AAGAAAATCT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 31 0.70
45 13 0.30
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (45 bp):
TTTGCAAATCTATAAAAAAACAAGGTTTAGGACTAAACTGTAGAA
Found at i:14321049 original size:44 final size:45
Alignment explanation
Indices: 14320956--14321052 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 45
14320946 ACTAGTTTGC
* ** *
14320956 AAATCTATAAAAAAACGAGGTTTAGGACTAAACTGTAGAATTTGC
1 AAATCTATAAAAAAACAAGGTTTAGGACTAAACTGTAGAATAAGA
14321001 AAATCTAT-AAAAAACAAGGTTTAGGACTAAACTGTAGAATAAGA
1 AAATCTATAAAAAAACAAGGTTTAGGACTAAACTGTAGAATAAGA
14321045 AAATCTAT
1 AAATCTAT
14321053 TTTTGAGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
44 40 0.83
45 8 0.17
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.26
Consensus pattern (45 bp):
AAATCTATAAAAAAACAAGGTTTAGGACTAAACTGTAGAATAAGA
Found at i:14321431 original size:17 final size:17
Alignment explanation
Indices: 14321405--14321442 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
14321395 CAAAAAGACC
14321405 TTAT-ATTAAAATATTA
1 TTATAATTAAAATATTA
14321421 TTATAATTAAAATATTA
1 TTATAATTAAAATATTA
*
14321438 ATATA
1 TTATA
14321443 TGATATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATAATTAAAATATTA
Found at i:14332270 original size:13 final size:13
Alignment explanation
Indices: 14332252--14332276 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14332242 TTGGTACCAC
14332252 ATTTATATTATCT
1 ATTTATATTATCT
14332265 ATTTATATTATC
1 ATTTATATTATC
14332277 AAAAAATCAT
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:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTATATTATCT
Found at i:14335493 original size:57 final size:59
Alignment explanation
Indices: 14335391--14335505 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 59
14335381 GTAAAAAGGA
14335391 TCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTGAAAAAGC
1 TCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-GAAAAAGC
14335453 TCTAGCCCGGACGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGGAAAA
1 TCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGGAAAA
14335506 TAGATTTAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
56 5 0.09
57 27 0.51
59 1 0.02
61 1 0.02
62 19 0.36
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (59 bp):
TCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGGAAAAAGC
Found at i:14335759 original size:67 final size:67
Alignment explanation
Indices: 14335651--14335782 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 67
14335641 AGTTTAATTA
14335651 CAGGGGATTTAGCCTAGACTGATAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTAGACTGATAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
14335716 TG
66 TG
* * *
14335718 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTAGACTGATAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
14335783 GAATTGAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (67 bp):
CAGGGGATTTAGCCTAGACTGATAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
TG
Found at i:14337332 original size:11 final size:11
Alignment explanation
Indices: 14337309--14337343 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
14337299 CTAGCTTTGG
14337309 TCTTTCTCTTTT
1 TCTTTC-CTTTT
14337321 TCTTTCCTTTT
1 TCTTTCCTTTT
14337332 TCTTT-CTTTT
1 TCTTTCCTTTT
14337342 TC
1 TC
14337344 CCTTCTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.30
11 10 0.43
12 6 0.26
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TCTTTCCTTTT
Found at i:14339185 original size:20 final size:20
Alignment explanation
Indices: 14339160--14339231 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
14339150 ATTATTTTTA
14339160 AATAAATTTATAAAACTTAT
1 AATAAATTTATAAAACTTAT
* *
14339180 AATAAAATAATAAAACCTTAT
1 AATAAATTTATAAAA-CTTAT
* * *
14339201 AA-ATATTT-TTAAA-TTCT
1 AATAAATTTATAAAACTTAT
14339218 AATAAA-TTATAAAA
1 AATAAATTTATAAAA
14339232 AAAATAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
17 7 0.17
18 6 0.15
19 4 0.10
20 16 0.40
21 7 0.17
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAATTTATAAAACTTAT
Found at i:14339834 original size:19 final size:20
Alignment explanation
Indices: 14339812--14339865 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
14339802 GTTTAAATGA
14339812 TTTTTATAATTTTTAATA-T
1 TTTTTATAATTTTTAATAGT
*
14339831 TTTTTAT-ATTGTTTATTAGT
1 TTTTTATAATT-TTTAATAGT
14339851 TTTTT-TAAGTTTTTA
1 TTTTTATAA-TTTTTA
14339866 TAGAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.10
19 14 0.47
20 11 0.37
21 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (20 bp):
TTTTTATAATTTTTAATAGT
Found at i:14339906 original size:10 final size:10
Alignment explanation
Indices: 14339891--14339923 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
14339881 TCAAATATAT
14339891 TTTTTAATAA
1 TTTTTAATAA
14339901 TTTTT-ATAA
1 TTTTTAATAA
14339910 GTTTTTAATAA
1 -TTTTTAATAA
14339921 TTT
1 TTT
14339924 CTTTTACGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.19
10 13 0.62
11 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:14340033 original size:19 final size:19
Alignment explanation
Indices: 14339943--14340049 Score: 78
Period size: 18 Copynumber: 5.6 Consensus size: 19
14339933 TTTTGTAAAA
14339943 TTTTATATATTTTA-AATTT
1 TTTTATA-ATTTTATAATTT
* *
14339962 GTTTTATTAATTTTAAAAATT
1 -TTTTA-TAATTTTATAATTT
* * * *
14339983 TATTAGAA-TTTATTATAT
1 TTTTATAATTTTATAATTT
* *
14340001 TTTTATAA-TATATAGTTT
1 TTTTATAATTTTATAATTT
14340019 TTATTAT-ATTTTATAATTT
1 TT-TTATAATTTTATAATTT
14340038 TTTTATAATTTT
1 TTTTATAATTTT
14340050 GTGTCAATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
18 25 0.37
19 21 0.31
20 15 0.22
21 6 0.09
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTATAATTT
Found at i:14340088 original size:11 final size:11
Alignment explanation
Indices: 14340072--14340113 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
14340062 ATAAATTCAA
14340072 TATATTTTTAT
1 TATATTTTTAT
14340083 TATA-TTTTAT
1 TATATTTTTAT
14340093 TA-ATTTTTAT
1 TATATTTTTAT
*
14340103 GAT-TTTTTAT
1 TATATTTTTAT
14340113 T
1 T
14340114 GAAAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 1 0.04
10 22 0.81
11 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:14340098 original size:20 final size:20
Alignment explanation
Indices: 14340016--14340113 Score: 69
Period size: 20 Copynumber: 4.9 Consensus size: 20
14340006 TAATATATAG
14340016 TTTTTATTATATTTTA-TAA
1 TTTTTATTATATTTTATTAA
*
14340035 TTTTT-TTATAATTTTGTGTCAA
1 TTTTTATTAT-ATTTTAT-T-AA
* * * *
14340057 -TTTTAATA-AATTCAATATA
1 TTTTTATTATATTTTATTA-A
14340076 TTTTTATTATATTTTATTAA
1 TTTTTATTATATTTTATTAA
* *
14340096 TTTTTATGATTTTTTATT
1 TTTTTATTATATTTTATT
14340114 GAAAATATTA
Statistics
Matches: 59, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
18 5 0.08
19 12 0.20
20 27 0.46
21 11 0.19
22 4 0.07
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTTTATTATATTTTATTAA
Found at i:14344442 original size:19 final size:19
Alignment explanation
Indices: 14344418--14344509 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
14344408 AATCACATCT
14344418 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
14344437 TCTAAGATTACATATTATA
1 TCTAAGATTGCATATCATA
14344456 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
14344475 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
14344494 TCCAAGATTGCATATC
1 TCTAAGATTGCATATC
14344510 CTTGAAAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:14344467 original size:38 final size:38
Alignment explanation
Indices: 14344418--14344509 Score: 166
Period size: 38 Copynumber: 2.4 Consensus size: 38
14344408 AATCACATCT
*
14344418 TCTAAGATTGCATATCATATCTAAGATTACATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTACATATCATA
14344456 TCTAAGATTGCATATCATATCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTACATATCATA
*
14344494 TCCAAGATTGCATATC
1 TCTAAGATTGCATATC
14344510 CTTGAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTACATATCATA
Found at i:14345120 original size:45 final size:45
Alignment explanation
Indices: 14345067--14345442 Score: 190
Period size: 44 Copynumber: 8.6 Consensus size: 45
14345057 TTAGTCTGCC
* * *
14345067 CCACTGCAATTTCAGGGGGATAAGACTTGATTTCTTGAGTATGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTATGCT
* * *
14345112 CCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTATGCT
* * * *
14345157 CCACTACAACTTCAGGGAGATAAGACCCGA-TGC--GA-TCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTATGCT
* * * * ***
14345198 -CTCTGCAACTTCAGAGAGATAAGATCTGTGA-TT-TT-AATCCACT
1 CCACTGCAACTTCAGGGAGATAAGA-CT-CGATTTCTTGAGTATGCT
* *** * *
14345241 CCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGC-
1 CCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTATGCT
* * * * * * *
14345285 CTCACTACAAATTCA-GGAGAATAAGGCTTGCTTACTT-AGTCTGCT
1 C-CACTGCAACTTCAGGGAG-ATAAGACTCGATTTCTTGAGTATGCT
* * * * *
14345330 CCATTGCAACTTCAGGGAGATAA-AATCTG-TTAT-TTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTC-GATT-TCTTGAGTATGCT
* * * * * * * *
14345374 CCACTACGACTTCAGGGAGAT-AGAAT-TATTGGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCGATT-TCTTGAGTATGCT
14345418 CCACTGCAACTTCAGGGAGATAAGA
1 CCACTGCAACTTCAGGGAGATAAGA
14345443 TTCGCCATCT
Statistics
Matches: 259, Mismatches: 52, Indels: 40
0.74 0.15 0.11
Matches are distributed among these distances:
40 21 0.08
41 7 0.03
42 6 0.02
43 14 0.05
44 111 0.43
45 100 0.39
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTATGCT
Found at i:14345256 original size:129 final size:132
Alignment explanation
Indices: 14345110--14345395 Score: 323
Period size: 129 Copynumber: 2.2 Consensus size: 132
14345100 CTTGAGTATG
** ** *
14345110 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGGTCTG-CTCCACTACAACTTCAGG-
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGCCATCTTCAGTCTGCCT-CACTACAAATTCAGGA
* *
14345173 GAGATAAGACCCG-ATGC-GA-TCTGCTCTC-TGCAACTTCAGAGAGATAAGATCTGTGATTTTA
65 GA-ATAAGACCCGCATACTGAGTCTGCTC-CATGCAACTTCAGAGAGATAAAATCTGTGATTTTA
14345234 ATCCA
128 ATCCA
*
14345239 CTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAAATTCAGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGCCATCTTCAGTCTGCCTCACTACAAATTCAGGAG
* ** * * * *
14345304 AATAAGGCTTGCTTACTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAAATCTGTTATTTTAAT
66 AATAAGACCCGCATACTGAGTCTGCTCCA-TGCAACTTCAGAGAGATAAAATCTGTGATTTTAAT
**
14345369 CTG
130 CCA
* *
14345372 CTCCACTACGACTTCAGGGAGATA
1 CTCCACTGCAACTTCAGGGAGATA
14345396 GAATTATTGG
Statistics
Matches: 131, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
129 61 0.47
130 6 0.05
131 2 0.02
132 7 0.05
133 55 0.42
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (132 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTCGCCATCTTCAGTCTGCCTCACTACAAATTCAGGAG
AATAAGACCCGCATACTGAGTCTGCTCCATGCAACTTCAGAGAGATAAAATCTGTGATTTTAATC
CA
Found at i:14352197 original size:71 final size:71
Alignment explanation
Indices: 14352117--14352257 Score: 273
Period size: 71 Copynumber: 2.0 Consensus size: 71
14352107 AAAAATCGAA
14352117 ATCTAGTAAGTTAAGACACAATTTTTCTCGAGAATCATGAATACCAAATATTTTAAAAATTACGA
1 ATCTAGTAAGTTAAGACACAATTTTTCTCGAGAATCATGAATACCAAATATTTTAAAAATTACGA
14352182 AATAAG
66 AATAAG
*
14352188 ATCTAGTAAGTTAAGACACAATTTTTCTCGAGAATCATGAATACCAAATATTTTGAAAATTACGA
1 ATCTAGTAAGTTAAGACACAATTTTTCTCGAGAATCATGAATACCAAATATTTTAAAAATTACGA
14352253 AATAA
66 AATAA
14352258 TATGATTTTC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (71 bp):
ATCTAGTAAGTTAAGACACAATTTTTCTCGAGAATCATGAATACCAAATATTTTAAAAATTACGA
AATAAG
Found at i:14352769 original size:14 final size:14
Alignment explanation
Indices: 14352745--14352796 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
14352735 ATGAAGATAT
*
14352745 ATATATGTGTAAAA
1 ATATATATGTAAAA
*
14352759 ATATGTATGTATACAA
1 ATATATATGTA-A-AA
* *
14352775 ATGTATATATAAAA
1 ATATATATGTAAAA
14352789 ATATATAT
1 ATATATAT
14352797 ATATATAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 18 0.60
15 2 0.07
16 10 0.33
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (14 bp):
ATATATATGTAAAA
Found at i:14352776 original size:16 final size:16
Alignment explanation
Indices: 14352743--14352801 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
14352733 CCATGAAGAT
*
14352743 ATATATATGTGTAAAA
1 ATATATATGTATAAAA
* *
14352759 ATATGTATGTATACAA
1 ATATATATGTATAAAA
*
14352775 ATGTATA--TATAAAA
1 ATATATATGTATAAAA
*
14352789 ATATATATATATA
1 ATATATATGTATA
14352802 TAGAAAGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
14 12 0.35
16 22 0.65
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (16 bp):
ATATATATGTATAAAA
Found at i:14352854 original size:32 final size:31
Alignment explanation
Indices: 14352789--14352855 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
14352779 ATATATAAAA
* * *
14352789 ATATATATATATATAGAAAGAAAATGTAAGT
1 ATATATATAAATATAAAAACAAAATGTAAGT
* *
14352820 ATATATATAAACTATAAAAACAATATGTACGT
1 ATATATATAAA-TATAAAAACAAAATGTAAGT
14352852 ATAT
1 ATAT
14352856 TTCAAATGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (31 bp):
ATATATATAAATATAAAAACAAAATGTAAGT
Found at i:14354616 original size:50 final size:50
Alignment explanation
Indices: 14354547--14354874 Score: 242
Period size: 50 Copynumber: 6.6 Consensus size: 50
14354537 CAGGGAGGTA
* * *
14354547 AGATTCGCCATTGTGGCTTCAATCTATTTAACTACAATGTTAGGGAAACC
1 AGATCCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTAGGGAAACC
* * ** ** * ***
14354597 AGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCTAGGGAAGTA
1 AGATCCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTAGGGAAACC
* * * * **
14354647 AGATCAGCCGTTGTGGCGTCAATCTTTTTAATTGCAATGTCGGGGAAACC
1 AGATCCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTAGGGAAACC
* ** * ** ** **
14354697 AGATCCGCCGTTGTGGCTTCAATCTGTTCCACTACACCGCCAGGGAAATA
1 AGATCCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTAGGGAAACC
* * *
14354747 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAACC
1 AGATCCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTAGGGAAACC
* * * * ** * ** ** ***
14354797 AGATCCGCTGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTA
1 AGATCCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTAGGGAAACC
14354847 AGATCCGCCGTTGTGGCTTCAATCTATT
1 AGATCCGCCGTTGTGGCTTCAATCTATT
14354875 CTACTGTAAT
Statistics
Matches: 204, Mismatches: 74, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 204 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (50 bp):
AGATCCGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTAGGGAAACC
Found at i:14354648 original size:100 final size:100
Alignment explanation
Indices: 14354513--14354874 Score: 544
Period size: 100 Copynumber: 3.6 Consensus size: 100
14354503 ACCGTTGTGA
* * * * *
14354513 CTTCAATTTGTTCCACTACACCACCAGGGAGGTAAGATTCGCCATTGTGGCTTCAATCTATTTAA
1 CTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTATTTAA
* * *
14354578 CTACAATGTTAGGGAAACCAGATCCGCCGTCGTAG
66 TTGCAATGTTGGGGAAACCAGATCCGCCGTCGTAG
* * * * * *
14354613 CTTCAATCTATTCCACTGCACCGCTAGGGAAGTAAGATCAGCCGTTGTGGCGTCAATCTTTTTAA
1 CTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTATTTAA
* * *
14354678 TTGCAATGTCGGGGAAACCAGATCCGCCGTTGTGG
66 TTGCAATGTTGGGGAAACCAGATCCGCCGTCGTAG
* *
14354713 CTTCAATCTGTTCCACTACACCGCCAGGGAAATAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTATTTAA
*
14354778 TTGCAATGTTGGGGAAACCAGATCCGCTGTCGTAG
66 TTGCAATGTTGGGGAAACCAGATCCGCCGTCGTAG
14354813 CTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTATT
1 CTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTATT
14354875 CTACTGTAAT
Statistics
Matches: 233, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 233 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (100 bp):
CTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTATTTAA
TTGCAATGTTGGGGAAACCAGATCCGCCGTCGTAG
Found at i:14355066 original size:50 final size:49
Alignment explanation
Indices: 14354960--14355066 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 49
14354950 ACGCCAGGGA
* * *
14354960 GATAAGATCCGCCGTCGTGGCTTCAATCTACTCCGCTGCAACGTCATGG
1 GATAAGATCCGCCGTCGTGGCTTCAATCTACTCCACTACAACGTCAAGG
* * * * * *
14355009 AAGTAAGATTCGCCGTTGTGGCTTTAATCTATTCCATTACAACGTCAAGG
1 GA-TAAGATCCGCCGTCGTGGCTTCAATCTACTCCACTACAACGTCAAGG
14355059 CGATAAGA
1 -GATAAGA
14355067 CGAGTATCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.02
50 44 0.96
51 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (49 bp):
GATAAGATCCGCCGTCGTGGCTTCAATCTACTCCACTACAACGTCAAGG
Found at i:14361719 original size:12 final size:12
Alignment explanation
Indices: 14361704--14361733 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
14361694 AATATGTATG
*
14361704 TATATAAATGTA
1 TATATAAATATA
14361716 TATATAAATATA
1 TATATAAATATA
14361728 TATATA
1 TATATA
14361734 TAAAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (12 bp):
TATATAAATATA
Found at i:14361833 original size:15 final size:15
Alignment explanation
Indices: 14361813--14361841 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14361803 AAATGCATGG
14361813 TTATAATAATAATAA
1 TTATAATAATAATAA
14361828 TTATAATAATAATA
1 TTATAATAATAATA
14361842 GTGTAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTATAATAATAATAA
Found at i:14363517 original size:110 final size:107
Alignment explanation
Indices: 14363140--14363591 Score: 748
Period size: 107 Copynumber: 4.2 Consensus size: 107
14363130 GGCACCAGGG
* * * * *
14363140 TACGAAAAAAGT--AAAAAAAATTTGGGGGCTGGCCTGTTAATGGCCGGCACCCAGTATAGTAAA
1 TACGAAAAAAGTAAAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
** *
14363203 AAATTATTTTAC-TTTTTTCGTGTCAGTATCAGGTATCAGTA
66 ATTTTTTTTTACTTTTTTTCGTGTCAGTATCAGGTATCAGTA
14363244 TACGAAAAAAGTAAAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
1 TACGAAAAAAGTAAAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
14363309 ATTTTTTTTTACTTTTTTTCGTGTCAGTATCAGGTATCAGTA
66 ATTTTTTTTTACTTTTTTTCGTGTCAGTATCAGGTATCAGTA
14363351 TACGAAAAAAGTAAAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
1 TACGAAAAAAGTAAAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
14363416 ATTTTTTTTTACTTTTTTTCGTGTCAGTATCAGGTATCAGTA
66 ATTTTTTTTTACTTTTTTTCGTGTCAGTATCAGGTATCAGTA
*
14363458 TACGAAAAAAGTAAAAAAAAAAATTTTTGGGTGCTGGCCTGTCAATCGCCGGCACCCAGCACAGT
1 TACGAAAAAAGT-AAAAAAAAAA-TTTT-GGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
* * *
14363523 AAATTTTTTTTTTACTTTTTTTCTTGTTAGTATCAGGTATCAGTA
63 AAAATTTTTTTTTACTTTTTTTCGTGTCAGTATCAGGTATCAGTA
14363568 TACGAAAAAAGTAAAAAAAAAATT
1 TACGAAAAAAGTAAAAAAAAAATT
14363592 CGTGTCATCA
Statistics
Matches: 330, Mismatches: 12, Indels: 8
0.94 0.03 0.02
Matches are distributed among these distances:
104 12 0.04
106 55 0.17
107 148 0.45
108 12 0.04
109 14 0.04
110 89 0.27
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (107 bp):
TACGAAAAAAGTAAAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
ATTTTTTTTTACTTTTTTTCGTGTCAGTATCAGGTATCAGTA
Found at i:14363545 original size:217 final size:213
Alignment explanation
Indices: 14363140--14363591 Score: 746
Period size: 217 Copynumber: 2.1 Consensus size: 213
14363130 GGCACCAGGG
* * *
14363140 TACGAAAAAAGT--AAAAAAAATTTGGGGGCTGGCCTGTTAATGGCCGGCACCCAGTATAGTAAA
1 TACGAAAAAAGTAAAAAAAAAATTTGGGGGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
14363203 AAATTATTTTACTTTTTTCGTGTCAGTATCAGGTATCAGTATACGAAAAAAGTAAAAAAAAAATT
66 AAATTATTTTACTTTTTTCGTGTCAGTATCAGGTATCAGTATACGAAAAAAGTAAAAAAAAAATT
*
14363268 TTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAATTTTTTTTTACTTTTTTTCGTGT
131 TTGGTGCTGGCCTGTCAATCGCCGGCACCCAGCACAGTAAAATTTTTTTTTACTTTTTTTCGTGT
14363333 CAGTATCAGGTATCAGTA
196 CAGTATCAGGTATCAGTA
* *
14363351 TACGAAAAAAGTAAAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
1 TACGAAAAAAGTAAAAAAAAAATTTGGGGGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
** *
14363416 ATTTTTTTTTACTTTTTTTCGTGTCAGTATCAGGTATCAGTATACGAAAAAAGTAAAAAAAAAAA
66 AAATTATTTTAC-TTTTTTCGTGTCAGTATCAGGTATCAGTATACGAAAAAAGT-AAAAAAAAAA
*
14363481 TTTTTGGGTGCTGGCCTGTCAATCGCCGGCACCCAGCACAGTAAATTTTTTTTTTACTTTTTTTC
129 -TTTT-GGTGCTGGCCTGTCAATCGCCGGCACCCAGCACAGTAAAATTTTTTTTTACTTTTTTTC
* *
14363546 TTGTTAGTATCAGGTATCAGTA
192 GTGTCAGTATCAGGTATCAGTA
14363568 TACGAAAAAAGTAAAAAAAAAATT
1 TACGAAAAAAGTAAAAAAAAAATT
14363592 CGTGTCATCA
Statistics
Matches: 223, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
211 12 0.05
213 55 0.25
214 41 0.18
215 10 0.04
216 4 0.02
217 101 0.45
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (213 bp):
TACGAAAAAAGTAAAAAAAAAATTTGGGGGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAA
AAATTATTTTACTTTTTTCGTGTCAGTATCAGGTATCAGTATACGAAAAAAGTAAAAAAAAAATT
TTGGTGCTGGCCTGTCAATCGCCGGCACCCAGCACAGTAAAATTTTTTTTTACTTTTTTTCGTGT
CAGTATCAGGTATCAGTA
Found at i:14363985 original size:13 final size:13
Alignment explanation
Indices: 14363967--14363991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14363957 GATCACGACA
14363967 ATTTTAATTTTTT
1 ATTTTAATTTTTT
14363980 ATTTTAATTTTT
1 ATTTTAATTTTT
14363992 ACTTTCTTAA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTAATTTTTT
Found at i:14364055 original size:19 final size:18
Alignment explanation
Indices: 14364015--14364057 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
14364005 TTATTATGTA
14364015 AATATTTCTTTTATTTTT
1 AATATTTCTTTTATTTTT
* *
14364033 -ATATTTTTTTCTTTTTTT
1 AATATTTCTTT-TATTTTT
14364051 AATATTT
1 AATATTT
14364058 ATTTAATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
18 6 0.29
19 6 0.29
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
AATATTTCTTTTATTTTT
Found at i:14364506 original size:104 final size:103
Alignment explanation
Indices: 14364320--14364649 Score: 452
Period size: 103 Copynumber: 3.2 Consensus size: 103
14364310 GATATAAAAA
* *
14364320 TTTTTTTACTTTTTTTGTATATTGATACCTGATACTGACACGAAAAAAAGT-AAAAAAAATTTAC
1 TTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACG-AAAAAAGTAAAAAAAAATTTAC
* * *
14364384 TGTGCTGGGTGTCGGCCATTGACAGACCAGCAACAAATT
65 TGTGCTGGGTGCCGGCCATTGACAGGCCAGCACCAAATT
*
14364423 TTTTTTTACTTTTTTCGTATACTGATACCTGATATTGACACGAAAAAAGTAAAAAAAAATTTTAC
1 TTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAGTAAAAAAAAA-TTTAC
* * *
14364488 TGTGCTAGGTGCCGGCCATTGACAGGCCAGTACCAATTT
65 TGTGCTGGGTGCCGGCCATTGACAGGCCAGCACCAAATT
*
14364527 TTTTTTTACTTTTTT-GTATACTGATACCTGATACTGACAC-AAAAAAGTAAAAAAAAA-ATACT
1 TTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAGTAAAAAAAAATTTACT
* * *
14364589 GTACTGGGTGCCGACCATTGACAGGCTAGCACCCAAAATTT
66 GTGCTGGGTGCCGGCCATTGACAGGCCAGCA-CC-AAA-TT
*
14364630 TTTTTTTCCTTCTTTTCGTA
1 TTTTTTTACTT-TTTTCGTA
14364650 CTGGGTGCCG
Statistics
Matches: 202, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
100 30 0.15
101 2 0.01
102 27 0.13
103 83 0.41
104 57 0.28
105 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (103 bp):
TTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAGTAAAAAAAAATTTACT
GTGCTGGGTGCCGGCCATTGACAGGCCAGCACCAAATT
Found at i:14367153 original size:87 final size:86
Alignment explanation
Indices: 14366980--14367322 Score: 296
Period size: 87 Copynumber: 3.9 Consensus size: 86
14366970 AGATACCTCA
* * * * *
14366980 CTTTCTCAAGCATCGAGCCTTTTAAAGCTCTTGACATTTTCAGGTCACGT-GCTTTTTAGGTATC
1 CTTT-TCAAGCGTCGAG-CTTTTAAAGCTCTTGACCTTTTCAGGTCACATACCTTTTAAGGTATC
* * * *
14367044 GTATCTTTTAATATATACATTGC
64 ATATCTCTTAAGATACACATTGC
* * * * *
14367067 CTTTTCAAGCGTCGAGCTTTTCAAAGCTCTTGACCTTTTTATGACACATGCCTATTAAGGTATCA
1 CTTTTCAAGCGTCGAGCTTTT-AAAGCTCTTGACCTTTTCAGGTCACATACCTTTTAAGGTATCA
*
14367132 TATCTTTTAAGATACACATTGC
65 TATCTCTTAAGATACACATTGC
* ** * * *
14367154 CTTTTCACGCGTTAAGCTTTTTAAAGCT-TTTAGCCTTTTCAGGTCACGTACCTCTTAAGGTATC
1 CTTTTCAAGCGTCGAGC-TTTTAAAGCTCTTGA-CCTTTTCAGGTCACATACCTTTTAAGGTATC
* * *
14367218 ATATCTCTCAAGATACACCTCGC
64 ATATCTCTTAAGATACACATTGC
* * * * * * * *
14367241 CTTCTGAAGTGTTGAGCTTTTGAAAGCTGTT-AGCTTTTTCAAGTCACATACCTTTTAAGGTATT
1 CTTTTCAAGCGTCGAGCTTTT-AAAGCTCTTGA-CCTTTTCAGGTCACATACCTTTTAAGGTATC
* *
14367305 GTCTCTCTTAAGATACAC
64 ATATCTCTTAAGATACAC
14367323 CTCATATCTT
Statistics
Matches: 211, Mismatches: 39, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
85 5 0.02
86 40 0.19
87 160 0.76
88 6 0.03
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (86 bp):
CTTTTCAAGCGTCGAGCTTTTAAAGCTCTTGACCTTTTCAGGTCACATACCTTTTAAGGTATCAT
ATCTCTTAAGATACACATTGC
Found at i:14367462 original size:108 final size:107
Alignment explanation
Indices: 14367227--14367519 Score: 333
Period size: 108 Copynumber: 2.7 Consensus size: 107
14367217 CATATCTCTC
* * * * *
14367227 AAGATACACCTCGCCTTCTGAAGTGTTGAGCTTTT-GAAAGCTGTTAGCTTTTTCAAGTCACATA
1 AAGATACACCTCGCCTTCTCAAGTGTTGAG-TTTTCGAAAGCTTTTGGCATTTTCAGGTCACATA
* *
14367291 CCTTTTAAGGTATTGTCTCTCTTAAGATACACCTCATATCTTTT
65 TC-TTTAAGGTATTGTCTCTCTTAAGATACACCTCATATCATTT
*
14367335 AAGATACACCTCGCCTTCTCAAGGGTTGAGTTTTCGAAAGCTTTTGGTC-TTTTCAGGTCACATA
1 AAGATACACCTCGCCTTCTCAAGTGTTGAGTTTTCGAAAGCTTTTGG-CATTTTCAGGTCACATA
**
14367399 TCGTTTAAGGTATTG-CATCTCTTAAGATACACCTTGTATCATTT
65 TC-TTTAAGGTATTGTC-TCTCTTAAGATACACCTCATATCATTT
** * ** * * *
14367443 AAGATACACCTTACATTCTCAAGTGTCAAGCTTTCCAAAGCTTTTGACCATTTT-AGGTCACATA
1 AAGATACACCTCGCCTTCTCAAGTGTTGAGTTTTCGAAAGCTTTTG-GCATTTTCAGGTCACATA
14367507 TCTCTTAAGGTAT
65 TCT-TTAAGGTAT
14367520 CTTTGAACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
107 6 0.04
108 149 0.93
109 5 0.03
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (107 bp):
AAGATACACCTCGCCTTCTCAAGTGTTGAGTTTTCGAAAGCTTTTGGCATTTTCAGGTCACATAT
CTTTAAGGTATTGTCTCTCTTAAGATACACCTCATATCATTT
Found at i:14367734 original size:86 final size:86
Alignment explanation
Indices: 14367584--14367743 Score: 214
Period size: 86 Copynumber: 1.9 Consensus size: 86
14367574 TTTTCAAGTT
* * * *
14367584 ACATATCTTTTAATGTATCATATCTCTTAAGATACATCTCACCTCATCAAGTGTGAAACTTTTTA
1 ACATATCTCTTAAGGTATCATATCTCTTAAGATACACCTCACCTCATCAAGTGTGAAACCTTTTA
14367649 AAGCTTTTGGCTTATCAAGAC
66 AAGCTTTTGGCTTATCAAGAC
* * * ** *
14367670 ACATATCTCTTAAGGTATCGTATCTCTTAAGATACACCTCGCCTTATCTGGTGCT-AAGCCTTTT
1 ACATATCTCTTAAGGTATCATATCTCTTAAGATACACCTCACCTCATCAAGTG-TGAAACCTTTT
14367734 AAAGCTTTTG
65 AAAGCTTTTG
14367744 ACCTTTCTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
86 62 0.98
87 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (86 bp):
ACATATCTCTTAAGGTATCATATCTCTTAAGATACACCTCACCTCATCAAGTGTGAAACCTTTTA
AAGCTTTTGGCTTATCAAGAC
Found at i:14369223 original size:66 final size:68
Alignment explanation
Indices: 14369116--14369332 Score: 219
Period size: 66 Copynumber: 3.2 Consensus size: 68
14369106 CATTCCCAAA
* * ** * * *
14369116 CACTTAGCTTTTCAAATCGTGTAACCTTTCCAGATCACATACTTCTTAAAGTACCTTGCCTTCTT
1 CACTTAACTTTTCAAAGCACGTAACCTTCCCAAATCACATACTTCTTAAAGTACCTTACCTTCTT
14369181 AAG
66 AAG
* * ** * * *
14369184 CA-TTGAGTTTTCAAAGCACGT-GTCTTCCCAAGTCACATACTTCTTAGAGTACCTCACCTTCTT
1 CACTTAACTTTTCAAAGCACGTAACCTTCCCAAATCACATACTTCTTAAAGTACCTTACCTTCTT
14369247 AAG
66 AAG
** * *
14369250 CACTTAACTTTTCAAAGTTCGTAACCTTCCCAAATCACGTACTTCTTAAAGTGCCTTACCTT-TT
1 CACTTAACTTTTCAAAGCACGTAACCTTCCCAAATCACATACTTCTTAAAGTACCTTACCTTCTT
*
14369314 CAAA
66 -AAG
14369318 CAC--AACTTTTCAAAG
1 CACTTAACTTTTCAAAG
14369333 TTCATGACCT
Statistics
Matches: 120, Mismatches: 26, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
66 51 0.43
67 30 0.25
68 39 0.32
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (68 bp):
CACTTAACTTTTCAAAGCACGTAACCTTCCCAAATCACATACTTCTTAAAGTACCTTACCTTCTT
AAG
Found at i:14376231 original size:22 final size:23
Alignment explanation
Indices: 14376193--14376237 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
14376183 GCACGATTAA
14376193 TAAAATTTAAATTTATTTATTTTC
1 TAAAATTT-AATTTATTTATTTTC
14376217 TAAAATTT-ATTTATTTATTTT
1 TAAAATTTAATTTATTTATTTT
14376238 TATATAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.62
24 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TAAAATTTAATTTATTTATTTTC
Found at i:14376477 original size:16 final size:16
Alignment explanation
Indices: 14376432--14376480 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
14376422 TTGAAATGGT
* *
14376432 TTTTATTAATTTTTAA
1 TTTTATAAATTTTAAA
*
14376448 TTTTTTGAACATTTTAAA
1 TTTTAT-AA-ATTTTAAA
14376466 TTTTATAAATTTTAA
1 TTTTATAAATTTTAA
14376481 TTATGTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 12 0.44
17 3 0.11
18 12 0.44
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTTATAAATTTTAAA
Found at i:14377284 original size:14 final size:15
Alignment explanation
Indices: 14377245--14377285 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 15
14377235 AATATATTAT
14377245 AAATTCAACACTTATAA
1 AAATTCAACAC-T-TAA
14377262 AAATT-AACAC-TAA
1 AAATTCAACACTTAA
14377275 AAATTCAACAC
1 AAATTCAACAC
14377286 CTAATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.35
14 5 0.22
16 5 0.22
17 5 0.22
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATTCAACACTTAA
Found at i:14386440 original size:5 final size:5
Alignment explanation
Indices: 14386403--14386456 Score: 60
Period size: 5 Copynumber: 11.4 Consensus size: 5
14386393 TATATTTCAT
* * *
14386403 ATATA AAATA TTATA A-ATA ATA-C ATAT- ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
14386450 ATATA AT
1 ATATA AT
14386457 TATTTTAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
4 11 0.27
5 30 0.73
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:14402990 original size:151 final size:151
Alignment explanation
Indices: 14402718--14403012 Score: 554
Period size: 151 Copynumber: 2.0 Consensus size: 151
14402708 CAACGCAAAA
14402718 CTTGTTAATAAATCAATATGTTGTTACCTTAAATTGCTTGTTTGCTTAATATGAAAACTGTAATG
1 CTTGTTAATAAATCAATATGTTGTTACCTTAAATTGCTTGTTTGCTTAATATGAAAACTGTAATG
*
14402783 GAAGTGTGTGATGGCAGTGGCCATTACGGCTTCACACTGTGAAAAATTGTGGAAACAAAACTAAA
66 GAAGTGTGTGATGGCAGTGGCCATTACGGCTTCACACTGTGAAAAATTGTGCAAACAAAACTAAA
14402848 TAACACCAATGATTCGCAACG
131 TAACACCAATGATTCGCAACG
14402869 CTTGTTAATAAATCAATATGTTGTTACCTTAAATTGCTTGTTTGCTTAATATGAAAACTGTAATG
1 CTTGTTAATAAATCAATATGTTGTTACCTTAAATTGCTTGTTTGCTTAATATGAAAACTGTAATG
* * *
14402934 GAAGTGTTTGATGGCAGTGGCCATTACGGCTTGACACTGTGAAAAATTGTGCAAACAAAACTATA
66 GAAGTGTGTGATGGCAGTGGCCATTACGGCTTCACACTGTGAAAAATTGTGCAAACAAAACTAAA
14402999 TAACACCAATGATT
131 TAACACCAATGATT
14403013 TGTTTACGCA
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
151 140 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (151 bp):
CTTGTTAATAAATCAATATGTTGTTACCTTAAATTGCTTGTTTGCTTAATATGAAAACTGTAATG
GAAGTGTGTGATGGCAGTGGCCATTACGGCTTCACACTGTGAAAAATTGTGCAAACAAAACTAAA
TAACACCAATGATTCGCAACG
Found at i:14404853 original size:31 final size:31
Alignment explanation
Indices: 14404796--14404854 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
14404786 AAGAGAAAGT
*
14404796 GTGAGAAAATAAAAGAAATTTGAAAAAAAAA
1 GTGAGAAAATAAAAGAAATATGAAAAAAAAA
14404827 GTGAGAAATATTAAAAGAAA-AT-AAAAAA
1 GTGAGAAA-A-TAAAAGAAATATGAAAAAA
14404855 TGGAGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 14 0.56
32 2 0.08
33 9 0.36
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (31 bp):
GTGAGAAAATAAAAGAAATATGAAAAAAAAA
Found at i:14406099 original size:24 final size:26
Alignment explanation
Indices: 14406072--14406120 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
14406062 GAAAAACTAG
14406072 GAAAA-AAGTGAAAA-AAA-AAGAAAT
1 GAAAAGAA-TGAAAATAAATAAGAAAT
14406096 GAAAAGAATGAAAATAAATAAGAAA
1 GAAAAGAATGAAAATAAATAAGAAA
14406121 ATAAATGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.50
25 5 0.23
26 6 0.27
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.10
Consensus pattern (26 bp):
GAAAAGAATGAAAATAAATAAGAAAT
Found at i:14416818 original size:25 final size:28
Alignment explanation
Indices: 14416784--14416834 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
14416774 CATTAAATGA
14416784 ATTTGAAAATA-TAATATAT-AAAATTC
1 ATTTGAAAATATTAATATATCAAAATTC
*
14416810 ATTTG-AAATATTATTATATCAAAAT
1 ATTTGAAAATATTAATATATCAAAAT
14416835 CTTGAAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 12 0.55
27 5 0.23
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (28 bp):
ATTTGAAAATATTAATATATCAAAATTC
Found at i:14425065 original size:74 final size:74
Alignment explanation
Indices: 14424944--14425118 Score: 260
Period size: 74 Copynumber: 2.4 Consensus size: 74
14424934 AATAAATAAT
* * *
14424944 TATTTATTCGTCGGTTTATCCGACTAGCACTGGGCACAAATATCGTTGGTGTATCGAACTAGAGC
1 TATTTATTCGTCGGTTTATCCGACTAGCACTAGGCACAAATATCGTTGGTATATCCAACTAGAGC
14425009 TGGGCTCAC
66 TGGGCTCAC
* ** *
14425018 TATTTATTCGTCGGCTTATCCGACTAGCGTTAGGCGCAAATATCGTTGGTATATCCAACTAGAGC
1 TATTTATTCGTCGGTTTATCCGACTAGCACTAGGCACAAATATCGTTGGTATATCCAACTAGAGC
14425083 TGGGCTCAC
66 TGGGCTCAC
* * *
14425092 TATTTATTTGTCGATTTATCTGACTAG
1 TATTTATTCGTCGGTTTATCCGACTAG
14425119 TGCTAGGTGC
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 90 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (74 bp):
TATTTATTCGTCGGTTTATCCGACTAGCACTAGGCACAAATATCGTTGGTATATCCAACTAGAGC
TGGGCTCAC
Found at i:14425152 original size:74 final size:74
Alignment explanation
Indices: 14424944--14425169 Score: 222
Period size: 74 Copynumber: 3.1 Consensus size: 74
14424934 AATAAATAAT
** * * * ** * *
14424944 TATTTATTCGTCGGTTTATCCGACTAGCACTGGGCACAAATATCGTTGGTGTATCGAACTAGAGC
1 TATTTATTCGTCGACTTATCCGACTAGCGCTAGGCGCAAATATCGTCAGTATATCCAACTAGAGC
14425009 TGGGCTCAC
66 TGGGCTCAC
* * **
14425018 TATTTATTCGTCGGCTTATCCGACTAGCGTTAGGCGCAAATATCGTTGGTATATCCAACTAGAGC
1 TATTTATTCGTCGACTTATCCGACTAGCGCTAGGCGCAAATATCGTCAGTATATCCAACTAGAGC
14425083 TGGGCTCAC
66 TGGGCTCAC
* * * * * * * * *
14425092 TATTTATTTGTCGATTTATCTGACTAGTGCTAGGTGCAACT-TCCGTCAGTTTATCTAACTAGTG
1 TATTTATTCGTCGACTTATCCGACTAGCGCTAGGCGCAAATAT-CGTCAGTATATCCAACTAGAG
*
14425156 CTGGGCGCAC
65 CTGGGCTCAC
14425166 -ATTT
1 TATTT
14425170 GTCGCACAAC
Statistics
Matches: 130, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
73 5 0.04
74 125 0.96
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (74 bp):
TATTTATTCGTCGACTTATCCGACTAGCGCTAGGCGCAAATATCGTCAGTATATCCAACTAGAGC
TGGGCTCAC
Found at i:14430529 original size:51 final size:51
Alignment explanation
Indices: 14430453--14430618 Score: 287
Period size: 51 Copynumber: 3.3 Consensus size: 51
14430443 ACTTCTGATC
* *
14430453 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACA
1 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
14430504 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * *
14430555 AGTGACAAGTGATGTGTGGTAGCTTTAGCTACACTTATCTAATCAGGGACA
1 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
14430606 AGTGACAAGTGAT
1 AGTGACAAGTGAT
14430619 AAATGTGATC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 110 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:14436473 original size:25 final size:26
Alignment explanation
Indices: 14436423--14436474 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
14436413 TTTGCATCAA
14436423 TTAATTATTTAAATATATAATAATTT
1 TTAATTATTTAAATATATAATAATTT
14436449 TTAATT-TTTGAAATGATA-AAT-ATTT
1 TTAATTATTT-AAAT-ATATAATAATTT
14436474 T
1 T
14436475 ATAAGAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 8 0.33
26 13 0.54
27 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
TTAATTATTTAAATATATAATAATTT
Found at i:14441233 original size:7 final size:7
Alignment explanation
Indices: 14441223--14441280 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
14441213 TGAATATCTG
14441223 AAATTAA
1 AAATTAA
*
14441230 AAATT-G
1 AAATTAA
14441236 AAATTAA
1 AAATTAA
*
14441243 AAATTGA
1 AAATTAA
14441250 AAATTAA
1 AAATTAA
*
14441257 AAATTGA
1 AAATTAA
* *
14441264 AGATTGA
1 AAATTAA
14441271 AAATATAA
1 AAAT-TAA
14441279 AA
1 AA
14441281 TCAGAAATTG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
6 5 0.12
7 32 0.78
8 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (7 bp):
AAATTAA
Found at i:14441239 original size:13 final size:13
Alignment explanation
Indices: 14441221--14441274 Score: 81
Period size: 14 Copynumber: 4.0 Consensus size: 13
14441211 ATTGAATATC
14441221 TGAAATTAAAAAT
1 TGAAATTAAAAAT
14441234 TGAAATTAAAAAT
1 TGAAATTAAAAAT
14441247 TGAAAATTAAAAAT
1 TG-AAATTAAAAAT
*
14441261 TGAAGATTGAAAAT
1 TGAA-ATTAAAAAT
14441275 ATAAAATCAG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
13 17 0.45
14 21 0.55
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (13 bp):
TGAAATTAAAAAT
Found at i:14441269 original size:21 final size:22
Alignment explanation
Indices: 14441236--14441280 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
14441226 TTAAAAATTG
14441236 AAATTAAAAATTGAAAAT-TAA
1 AAATTAAAAATTGAAAATATAA
* *
14441257 AAATTGAAGATTGAAAATATAA
1 AAATTAAAAATTGAAAATATAA
14441279 AA
1 AA
14441281 TCAGAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (22 bp):
AAATTAAAAATTGAAAATATAA
Found at i:14441290 original size:21 final size:20
Alignment explanation
Indices: 14441222--14441290 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
14441212 TTGAATATCT
* * *
14441222 GAAATTAAAAATTGAAATTA
1 GAAATTGAAAATTAAAAATA
* *
14441242 AAAATTGAAAATTAAAAATT
1 GAAATTGAAAATTAAAAATA
14441262 GAAGATTGAAAA-TATAAAATCA
1 GAA-ATTGAAAATTA-AAAAT-A
14441284 GAAATTG
1 GAAATTG
14441291 GGGATTGAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 19 0.49
21 17 0.44
22 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.12, T:0.28
Consensus pattern (20 bp):
GAAATTGAAAATTAAAAATA
Found at i:14441402 original size:15 final size:15
Alignment explanation
Indices: 14441378--14441420 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
14441368 AAGGTGGAAT
14441378 AGTTACCGTTGAAAA
1 AGTTACCGTTGAAAA
* * *
14441393 AGTTATCGTTGGAAT
1 AGTTACCGTTGAAAA
14441408 AGTTACCGTTGAA
1 AGTTACCGTTGAA
14441421 CGGAGAATAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTTACCGTTGAAAA
Found at i:14441851 original size:9 final size:9
Alignment explanation
Indices: 14441837--14441870 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
14441827 TGAATTGAAT
14441837 TTTATAAAA
1 TTTATAAAA
14441846 TTTATAAAA
1 TTTATAAAA
14441855 TTTATTAATAA
1 TTTA-TAA-AA
14441866 TTTAT
1 TTTAT
14441871 TTGTTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.57
10 4 0.17
11 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTATAAAA
Found at i:14443293 original size:16 final size:17
Alignment explanation
Indices: 14443272--14443308 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
14443262 TTGAATAGCC
14443272 AAAAGAAAAGAAAAAA-
1 AAAAGAAAAGAAAAAAG
14443288 AAAAGAAAAGAAAAAAG
1 AAAAGAAAAGAAAAAAG
14443305 AAAA
1 AAAA
14443309 TCGAAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAGAAAAAAG
Found at i:14443301 original size:12 final size:11
Alignment explanation
Indices: 14443272--14443308 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
14443262 TTGAATAGCC
*
14443272 AAAAGAAAAGA
1 AAAAAAAAAGA
14443283 AAAAAAAAAGA
1 AAAAAAAAAGA
14443294 AAAGAAAAAAGA
1 AAA-AAAAAAGA
14443306 AAA
1 AAA
14443309 TCGAAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Done.