Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 6 of 126
Found at i:1535608 original size:17 final size:17
Alignment explanation
Indices: 1535576--1535609 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1535566 CGATCCGATC
**
1535576 AAAATACAAATTTTTTT
1 AAAATACAAAGATTTTT
1535593 AAAATACAAAGATTTTT
1 AAAATACAAAGATTTTT
1535610 GAAACAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (17 bp):
AAAATACAAAGATTTTT
Found at i:1535644 original size:18 final size:18
Alignment explanation
Indices: 1535622--1536126 Score: 334
Period size: 17 Copynumber: 28.5 Consensus size: 18
1535612 AACAATTATT
1535622 TTTTTGAAAACACGAAAAA
1 TTTTTGAAAACACG-AAAA
*
1535641 TTTTT-AAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
1535658 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
1535675 TTCTTAAAAATACGAAAA
1 TTTTTGAAAACACGAAAA
*
1535693 TTTTTGAAAACACG-ACA
1 TTTTTGAAAACACGAAAA
* * *
1535710 TTTTTTAAAACACGGGAAT
1 TTTTTGAAAACAC-GAAAA
* *
1535729 TTTTTG-AAACATTG-GAA
1 TTTTTGAAAACA-CGAAAA
*
1535746 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
1535764 TTTTTGAAACACAC-AAAA
1 TTTTTGAAA-ACACGAAAA
1535782 -TTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
1535799 TTTTTGAAATA-A-GAAAA
1 TTTTTGAAA-ACACGAAAA
* *
1535816 TTTTAG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
1535833 TTTTT-AAAACACGACAA
1 TTTTTGAAAACACGAAAA
* **
1535850 TTTTTGAAACACAAGAATT
1 TTTTTGAAA-ACACGAAAA
** **
1535869 TTTTTTTAAACATAAAAA
1 TTTTTGAAAACACGAAAA
*
1535887 ATTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
1535904 TTTGTG-AAACACGAGAA
1 TTTTTGAAAACACGAAAA
* * ***
1535921 TTGTTGAAAATA--ATTTT
1 TTTTTGAAAACACGA-AAA
* *
1535938 TTTTTGAAAATATGAAAA
1 TTTTTGAAAACACGAAAA
1535956 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
1535973 TTTTTG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
1535990 TTTTTAGAAAACACGAAAAA
1 TTTTT-GAAAACACG-AAAA
** * * *
1536010 AATTTGAAAA-ATGGAAT
1 TTTTTGAAAACACGAAAA
*
1536027 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* *
1536045 TTTTTGAAAATATGAAAA
1 TTTTTGAAAACACGAAAA
*
1536063 TTTTTG-AAACACCGGAAATT
1 TTTTTGAAAACA-C-GAAA-A
*
1536083 TTTTTGAAATAC-TG-AAA
1 TTTTTGAAA-ACACGAAAA
1536100 TTTTTGAAAACAC-AAAGA
1 TTTTTGAAAACACGAAA-A
*
1536118 TATTTGAAA
1 TTTTTGAAA
1536127 CTAGAATTTT
Statistics
Matches: 375, Mismatches: 78, Indels: 67
0.72 0.15 0.13
Matches are distributed among these distances:
15 1 0.00
16 10 0.03
17 179 0.48
18 123 0.33
19 45 0.12
20 13 0.03
21 2 0.01
22 2 0.01
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:1535644 original size:36 final size:34
Alignment explanation
Indices: 1535585--1535651 Score: 89
Period size: 36 Copynumber: 1.9 Consensus size: 34
1535575 CAAAATACAA
* * *
1535585 ATTTTTTTAAAATACAAAGATTTTTGAAACAATT
1 ATTTTTTTAAAACACAAAAATTTTTAAAACAATT
1535619 ATTTTTTTGAAAACACGAAAAATTTTTAAAACA
1 ATTTTTTT-AAAACAC-AAAAATTTTTAAAACA
1535652 CGAGAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 8 0.29
35 6 0.21
36 14 0.50
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.40
Consensus pattern (34 bp):
ATTTTTTTAAAACACAAAAATTTTTAAAACAATT
Found at i:1535674 original size:35 final size:34
Alignment explanation
Indices: 1535622--1536127 Score: 297
Period size: 35 Copynumber: 14.3 Consensus size: 34
1535612 AACAATTATT
*
1535622 TTTTTGAAAACACGAAAAATTTTTAAAACACGAGAA
1 TTTTTG-AAACACG-AAAATTTTTAAAACACGAAAA
* * *
1535658 TTTTAGAAACACGAAAATTCTTAAAAATACGAAAA
1 TTTTTGAAACACGAAAATT-TTTAAAACACGAAAA
* * * *
1535693 TTTTTGAAAACACGACATTTTTTAAAACACGGGAAT
1 TTTTTG-AAACACGAAAATTTTTAAAACAC-GAAAA
* * *
1535729 TTTTTGAAACATTG-GAATTTTTGAAAACACGAAGA
1 TTTTTGAAACA-CGAAAATTTTT-AAAACACGAAAA
* *
1535764 TTTTTGAAACACACAAAATTTTGAAAACACGAAAA
1 TTTTTGAAACAC-GAAAATTTTTAAAACACGAAAA
* * *
1535799 TTTTTGAAATAAGAAAA-TTTTAGAAACATGAAAA
1 TTTTTGAAACACGAAAATTTTTA-AAACACGAAAA
* * *
1535833 TTTTTAAAACACGACAATTTTTGAAACAC-AAGAA
1 TTTTTGAAACACGAAAATTTTTAAAACACGAA-AA
* ** *
1535867 TTTTTTTTTAAACATAAAAAATTTTAAAACACGAAAA
1 ---TTTTTGAAACACGAAAATTTTTAAAACACGAAAA
* * * * ***
1535904 TTTGTGAAACACGAGAATTGTTGAAAATA--ATTTT
1 TTTTTGAAACACGAAAATT-TTTAAAACACGA-AAA
* * *
1535938 TTTTTGAAAATATGAAAATTTTTGAAACACGAAAA
1 TTTTTG-AAACACGAAAATTTTTAAAACACGAAAA
*
1535973 TTTTTGAAACATGAAAATTTTTAGAAAACACGAAAAA
1 TTTTTGAAACACGAAAATTTTT--AAAACACG-AAAA
** * * * * *
1536010 AATTTGAAAAATGGAATTTTTTGAAAACACGAGAA
1 TTTTTGAAACACGAAAATTTTT-AAAACACGAAAA
* * * *
1536045 TTTTTGAAAATATGAAAATTTTTGAAACACCGGAAATT
1 TTTTTG-AAACACGAAAATTTTTAAAACA-C-GAAA-A
*
1536083 TTTTTGAAATACTG-AAATTTTTGAAAACAC-AAAGA
1 TTTTTGAAACAC-GAAAATTTTT-AAAACACGAAA-A
*
1536118 TATTTGAAAC
1 TTTTTGAAAC
1536128 TAGAATTTTT
Statistics
Matches: 360, Mismatches: 82, Indels: 57
0.72 0.16 0.11
Matches are distributed among these distances:
33 7 0.02
34 79 0.22
35 127 0.35
36 70 0.19
37 63 0.17
38 14 0.04
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (34 bp):
TTTTTGAAACACGAAAATTTTTAAAACACGAAAA
Found at i:1535750 original size:19 final size:18
Alignment explanation
Indices: 1535621--1535759 Score: 79
Period size: 18 Copynumber: 7.8 Consensus size: 18
1535611 AAACAATTAT
**
1535621 TTTTTTGAAAACACGAAAA
1 TTTTTT-AAAACACGGGAA
* *
1535640 ATTTTTAAAACACGAGAA
1 TTTTTTAAAACACGGGAA
**
1535658 --TTTTAGAAACACGAAAA
1 TTTTTTA-AAACACGGGAA
* * * **
1535675 TTCTTAAAAATACGAAAA
1 TTTTTTAAAACACGGGAA
*
1535693 TTTTTGAAAACAC--GACA
1 TTTTTTAAAACACGGGA-A
1535710 TTTTTTAAAACACGGGAA
1 TTTTTTAAAACACGGGAA
* **
1535728 TTTTTTGAAACATTGGAA
1 TTTTTTAAAACACGGGAA
*
1535746 TTTTTGAAAACACG
1 TTTTTTAAAACACG
1535760 AAGATTTTTG
Statistics
Matches: 96, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
16 6 0.06
17 23 0.24
18 57 0.59
19 10 0.10
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (18 bp):
TTTTTTAAAACACGGGAA
Found at i:1536088 original size:20 final size:19
Alignment explanation
Indices: 1536063--1536104 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1536053 AATATGAAAA
1536063 TTTTTGAAACACCGGAAATT
1 TTTTTGAAACA-CGGAAATT
* *
1536083 TTTTTGAAATACTGAAATT
1 TTTTTGAAACACGGAAATT
1536102 TTT
1 TTT
1536105 GAAAACACAA
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:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (19 bp):
TTTTTGAAACACGGAAATT
Found at i:1536124 original size:55 final size:51
Alignment explanation
Indices: 1535938--1536127 Score: 143
Period size: 55 Copynumber: 3.5 Consensus size: 51
1535928 AAATAATTTT
* * * *
1535938 TTTTTGAAAATATGAAAATTTTTGAAACAC-GAAAATTTTTG-AAACATGAAAA
1 TTTTTGAAAACA-CAAAATATTTGAAACACGGAAATTTTTTGAAAAC-TG-AAA
* * * *
1535990 TTTTTAGAAAACACGAAAAAAATTTGAAAAATGG-AATTTTTTGAAAACACGAGAA
1 TTTTT-GAAAACAC--AAAATATTTGAAACACGGAAATTTTTTGAAAAC-TGA-AA
* * *
1536045 TTTTTGAAAATATGAAAATTTTTGAAACACCGGAAATTTTTTTGAAATACTGAAA
1 TTTTTGAAAACA-CAAAATATTTGAAACA-CGGAAA-TTTTTTGAAA-ACTGAAA
1536100 TTTTTGAAAACACAAAGATATTTGAAAC
1 TTTTTGAAAACACAAA-ATATTTGAAAC
1536128 TAGAATTTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 21
0.73 0.12 0.14
Matches are distributed among these distances:
52 5 0.05
53 18 0.17
54 32 0.30
55 39 0.36
56 12 0.11
57 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (51 bp):
TTTTTGAAAACACAAAATATTTGAAACACGGAAATTTTTTGAAAACTGAAA
Found at i:1536374 original size:133 final size:133
Alignment explanation
Indices: 1536134--1536383 Score: 335
Period size: 133 Copynumber: 1.9 Consensus size: 133
1536124 AAACTAGAAT
* * * *
1536134 TTTTTTTAATTTTTTTGACTTTTTTTAAGGACGTATCGTATTTAGCACAAACCGGTGATATTCAC
1 TTTTTTGAATATTTTTGACTTTTTTAAAGGACGTATCGTATTTAACACAAACCGGTGATATTCAC
* ** * *
1536199 TCAACATAGCGATGAAATCATTGAATTAGTGTCGAATTGATTCGTTGCCTTAATTTTGAAAACAC
66 CCAACATAGCGATGAAATCAACGAATTAGTGTCAAATCGATTCGTTGCCTTAATTTTGAAAACAC
1536264 GAA
131 GAA
* *
1536267 TTTTTTGAATATTTTTGA-TTTTTTAAAAGGGCGTATCG-ATTTTAACGCAAACCGGTGATATTC
1 TTTTTTGAATATTTTTGACTTTTTT-AAAGGACGTATCGTA-TTTAACACAAACCGGTGATATTC
* *
1536330 ACCCAACATAGCGATGAAATCAACGATTTTA-TGTTAAATCGATTCGTTGCCTTA
64 ACCCAACATAGCGATGAAATCAACGA-ATTAGTGTCAAATCGATTCGTTGCCTTA
1536384 TTTATTAAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
132 7 0.07
133 91 0.90
134 3 0.03
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (133 bp):
TTTTTTGAATATTTTTGACTTTTTTAAAGGACGTATCGTATTTAACACAAACCGGTGATATTCAC
CCAACATAGCGATGAAATCAACGAATTAGTGTCAAATCGATTCGTTGCCTTAATTTTGAAAACAC
GAA
Found at i:1536616 original size:10 final size:10
Alignment explanation
Indices: 1536593--1536634 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
1536583 TGAACTTTTA
*
1536593 TTTTTTTCCT
1 TTTTTTTTCT
1536603 TTTTTCTTTCT
1 TTTTT-TTTCT
1536614 TTTTTTTTCT
1 TTTTTTTTCT
1536624 CTTTTTTTTCT
1 -TTTTTTTTCT
1536635 CCTCTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.34
11 19 0.66
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:1536617 original size:21 final size:21
Alignment explanation
Indices: 1536593--1536634 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1536583 TGAACTTTTA
1536593 TTTTTTTCCT-TTTTTCTTTCT
1 TTTTTTTCCTCTTTTT-TTTCT
*
1536614 TTTTTTTTCTCTTTTTTTTCT
1 TTTTTTTCCTCTTTTTTTTCT
1536635 CCTCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTTCCTCTTTTTTTTCT
Found at i:1536619 original size:14 final size:13
Alignment explanation
Indices: 1536602--1536645 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
1536592 ATTTTTTTCC
1536602 TTTTTTCTTTCTTT
1 TTTTTTC-TTCTTT
1536616 TTTTTTC-TCTTT
1 TTTTTTCTTCTTT
*
1536628 TTTTTCTCCTCTTT
1 TTTTT-TCTTCTTT
1536642 TTTT
1 TTTT
1536646 GGCCTGCTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.36
13 2 0.07
14 16 0.57
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTCTTCTTT
Found at i:1536635 original size:11 final size:11
Alignment explanation
Indices: 1536593--1536645 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 11
1536583 TGAACTTTTA
1536593 TTTTTTTC-CT
1 TTTTTTTCTCT
1536603 TTTTTCTT-TCTT
1 TTTTT-TTCTC-T
1536615 TTTTTTTCTCT
1 TTTTTTTCTCT
1536626 TTTTTTTCTCCT
1 TTTTTTTCT-CT
1536638 CTTTTTTT
1 -TTTTTTT
1536646 GGCCTGCTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 5 0.14
11 15 0.41
12 10 0.27
13 7 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:1536915 original size:10 final size:10
Alignment explanation
Indices: 1536902--1536949 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
1536892 TTATTTTTAA
1536902 TTTTTTTCTC
1 TTTTTTTCTC
1536912 TTTTTTTCT-
1 TTTTTTTCTC
1536921 TTTTCTTTCTTC
1 TTTT-TTTC-TC
*
1536933 TTTCTTTCTC
1 TTTTTTTCTC
1536943 TTTTTTT
1 TTTTTTT
1536950 TTCTCTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 4 0.12
10 21 0.64
11 5 0.15
12 3 0.09
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:1536933 original size:23 final size:23
Alignment explanation
Indices: 1536902--1536953 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1536892 TTATTTTTAA
1536902 TTTT-TTTC-TCTTT-TTT-TCT
1 TTTTCTTTCTTCTTTCTTTCTCT
1536921 TTTTCTTTCTTCTTTCTTTCTCT
1 TTTTCTTTCTTCTTTCTTTCTCT
*
1536944 TTTTTTTTCT
1 TTTTCTTTCT
1536954 CTTCTTCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 4 0.14
21 5 0.18
22 3 0.11
23 12 0.43
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTCTTTCTTCTTTCTTTCTCT
Found at i:1536940 original size:21 final size:21
Alignment explanation
Indices: 1536902--1536959 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
1536892 TTATTTTTAA
*
1536902 TTTTTTTC-TCTTTTTTTCT-
1 TTTTTTTCTTCTTTCTTTCTC
1536921 TTTTCTTTCTTCTTTCTTTCTC
1 TTTT-TTTCTTCTTTCTTTCTC
1536943 TTTTTTT-TTCTCTTCTT
1 TTTTTTTCTTCT-TTCTT
1536960 CTCCGTTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 4 0.12
20 8 0.24
21 18 0.53
22 4 0.12
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTTTCTTCTTTCTTTCTC
Found at i:1536958 original size:17 final size:16
Alignment explanation
Indices: 1536912--1536958 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
1536902 TTTTTTTCTC
*
1536912 TTTTTTTCTTTTTCTT
1 TTTTTTTCTTTCTCTT
*
1536928 TCTTCTTTCTTTCTCTT
1 T-TTTTTTCTTTCTCTT
1536945 TTTTTTTCTCTTCT
1 TTTTTTTCT-TTCT
1536959 TCTCCGTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTTTCTCTT
Found at i:1537336 original size:30 final size:30
Alignment explanation
Indices: 1537302--1537366 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
1537292 GCCAAAACAA
*
1537302 AATTTTGAGAAAA-CTTAGGGGTCAAAATGT
1 AATTTTCA-AAAAGCTTAGGGGTCAAAATGT
* *
1537332 AA-TTTCAAAAAGTTTATGGGTCAAAATGT
1 AATTTTCAAAAAGCTTAGGGGTCAAAATGT
1537361 AATTTT
1 AATTTT
1537367 TTATTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 4 0.13
29 21 0.70
30 5 0.17
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (30 bp):
AATTTTCAAAAAGCTTAGGGGTCAAAATGT
Found at i:1538282 original size:97 final size:97
Alignment explanation
Indices: 1538181--1538457 Score: 412
Period size: 97 Copynumber: 2.8 Consensus size: 97
1538171 CACATATCGG
** *
1538181 TGCCGATGCCATGTCTTAGACATGGTCTTACACTAGCACTCATCTCGAGCCGATGTCATGTCCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCGAGCCGATGCCATGTCCCA
*
1538246 GACAAGGTCTTACACTGACTCTTCTCTGTCCA
66 GACATGGTCTTACACTGACTCTTCTCTGTCCA
*
1538278 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCGAGCTGATGCCATGTCCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCGAGCCGATGCCATGTCCCA
*
1538343 GACATGGTC-TACACTGACTCTTCTCTGTCCG
66 GACATGGTCTTACACTGACTCTTCTCTGTCCA
* * * * * *
1538374 TGTCGATGCCATGTCCCAGACATGATCTTACACTAGCACTCGTCGGACTGTGTCGATGCCATGTC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATC--TC-GAGCCGATGCCATGTC
1538439 CCAGACATGGTCTTACACT
63 CCAGACATGGTCTTACACT
1538458 AGCACACTCA
Statistics
Matches: 163, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
96 62 0.38
97 69 0.42
98 1 0.01
99 25 0.15
100 6 0.04
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (97 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCGAGCCGATGCCATGTCCCA
GACATGGTCTTACACTGACTCTTCTCTGTCCA
Found at i:1538295 original size:50 final size:49
Alignment explanation
Indices: 1538181--1538462 Score: 296
Period size: 50 Copynumber: 5.8 Consensus size: 49
1538171 CACATATCGG
**
1538181 TGCCGATGCCATGTCTTAGACATGGTCTTACACTAGCACTCATCTCG-A
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCGCA
* * *
1538229 -GCCGATGTCATGTCCCAGACAAGGTCTTACACT-G-ACTCTTCTCTGTCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTC-G--CA
1538278 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCG-A
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCGCA
* * *
1538326 -GCTGATGCCATGTCCCAGACATGGTC-TACACT-G-ACTCTTCTCTGTCCG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTC-G--CA
* * * * *
1538374 TGTCGATGCCATGTCCCAGACATGATCTTACACTAGCACTCGTC-GGACTG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCG-C-A
*
1538424 TGTCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
1538463 ACTCACTGCC
Statistics
Matches: 200, Mismatches: 18, Indels: 30
0.81 0.07 0.12
Matches are distributed among these distances:
44 8 0.04
45 10 0.05
46 8 0.04
47 54 0.27
48 1 0.00
49 25 0.12
50 77 0.38
51 3 0.01
52 14 0.07
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (49 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCGCA
Found at i:1540622 original size:3 final size:3
Alignment explanation
Indices: 1540614--1540662 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1540604 GGTAATGAAT
1540614 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1540662 T
1 T
1540663 GAAGTGATTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1555212 original size:30 final size:30
Alignment explanation
Indices: 1555176--1555235 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1555166 TGCTCAGCGA
* *
1555176 CTTAAATAAAAACTTTTGACTAGTTCAGTG
1 CTTAAATAAAAAATTTTGAATAGTTCAGTG
*
1555206 CTTAAATAAAAAATTTTGAATAGTTTAGTG
1 CTTAAATAAAAAATTTTGAATAGTTCAGTG
1555236 ACCATTTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (30 bp):
CTTAAATAAAAAATTTTGAATAGTTCAGTG
Found at i:1555533 original size:14 final size:14
Alignment explanation
Indices: 1555514--1555545 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1555504 TTTTCTCCAA
*
1555514 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTCC
1555528 TTTTTCTTTTTTCC
1 TTTTTCTTTTTTCC
1555542 TTTT
1 TTTT
1555546 CAATACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTTCC
Found at i:1557722 original size:24 final size:24
Alignment explanation
Indices: 1557685--1557732 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1557675 CCTGATGAAA
* *
1557685 ACAATGCAATTGTTGAAACTAAAG
1 ACAATGCAAATGTTGAAAATAAAG
*
1557709 ACAATGGAAATGTTGAAAATAAAG
1 ACAATGCAAATGTTGAAAATAAAG
1557733 TCTCACTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (24 bp):
ACAATGCAAATGTTGAAAATAAAG
Found at i:1563207 original size:26 final size:25
Alignment explanation
Indices: 1563168--1563218 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
1563158 TAGGCTTTAA
*
1563168 ACTTGACAAATGTTTCTACATTGGG
1 ACTTGACAAATGTTTCCACATTGGG
* *
1563193 ACTTGAACAAGTGTTTCCATATTGGG
1 ACTTG-ACAAATGTTTCCACATTGGG
1563219 CCTTAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (25 bp):
ACTTGACAAATGTTTCCACATTGGG
Found at i:1564343 original size:15 final size:16
Alignment explanation
Indices: 1564316--1564348 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1564306 AATTAAACTA
1564316 AATATATAAAGTAATT
1 AATATATAAAGTAATT
1564332 AATATA-AAAGTAATT
1 AATATATAAAGTAATT
1564347 AA
1 AA
1564349 AATCTTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AATATATAAAGTAATT
Found at i:1567217 original size:11 final size:11
Alignment explanation
Indices: 1567201--1567230 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1567191 TTGATTTCTT
1567201 TCTCACCATTA
1 TCTCACCATTA
1567212 TCTCACCATTA
1 TCTCACCATTA
1567223 TCTCACCA
1 TCTCACCA
1567231 ATGTGATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.40, G:0.00, T:0.33
Consensus pattern (11 bp):
TCTCACCATTA
Found at i:1574554 original size:13 final size:14
Alignment explanation
Indices: 1574532--1574567 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
1574522 ACCGAGTGTG
1574532 AATAATAAAAAATA
1 AATAATAAAAAATA
1574546 AAT-AT-AAAAATA
1 AATAATAAAAAATA
1574558 AATAATAAAA
1 AATAATAAAA
1574568 TTTTGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 10 0.50
13 4 0.20
14 6 0.30
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAATAAAAAATA
Found at i:1581163 original size:40 final size:42
Alignment explanation
Indices: 1581072--1581174 Score: 131
Period size: 40 Copynumber: 2.5 Consensus size: 42
1581062 GAGAATGCTA
1581072 AAAATAATAAGAAAAATAATGAAATAACAAGAACATAAAAATG
1 AAAATAATAA-AAAAATAATGAAATAACAAGAACATAAAAATG
** *
1581115 ATGA-AATAAAATAATAA-GAAATAACAAGAACATAAAAAT-
1 AAAATAATAAAAAAATAATGAAATAACAAGAACATAAAAATG
1581154 AAAATAATAAAAGACAATAAT
1 AAAATAATAAAA-A-AATAAT
1581175 AAGCAAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
39 2 0.04
40 29 0.58
41 7 0.14
42 10 0.20
43 2 0.04
ACGTcount: A:0.70, C:0.05, G:0.08, T:0.17
Consensus pattern (42 bp):
AAAATAATAAAAAAATAATGAAATAACAAGAACATAAAAATG
Found at i:1581843 original size:26 final size:26
Alignment explanation
Indices: 1581797--1581849 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
1581787 CGCCATACGC
*
1581797 TGGGCCTTTAGTTTTATTTATTTATT
1 TGGGCCTTTAGTTTTATTTATTAATT
1581823 TGGGCCTGTTA-TTATTA-TTATTAATT
1 TGGGCCT-TTAGTT-TTATTTATTAATT
1581849 T
1 T
1581850 TTATTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.19, C:0.08, G:0.15, T:0.58
Consensus pattern (26 bp):
TGGGCCTTTAGTTTTATTTATTAATT
Found at i:1592836 original size:35 final size:35
Alignment explanation
Indices: 1592784--1592851 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
1592774 TATATCTATA
1592784 AATACAATTTTCATAATCCTAATTCAA-TTCTAACT
1 AATACAATTTTCATAATCCTAATT-AAGTTCTAACT
* *
1592819 AATATAATTTTCGTAATCCTAATTAAGTTCTAA
1 AATACAATTTTCATAATCCTAATTAAGTTCTAA
1592852 GATAGTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 2 0.07
35 28 0.93
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.41
Consensus pattern (35 bp):
AATACAATTTTCATAATCCTAATTAAGTTCTAACT
Found at i:1594443 original size:24 final size:24
Alignment explanation
Indices: 1594415--1594466 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1594405 TTAATAGGTC
* *
1594415 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1594439 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1594463 AAAT
1 AAAT
1594467 CTTCTGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1596004 original size:109 final size:109
Alignment explanation
Indices: 1595888--1596121 Score: 468
Period size: 109 Copynumber: 2.1 Consensus size: 109
1595878 GAAATCGAGT
1595888 CCCAATACGTTAGGGCACAACAAGTTAAGTTCCCAAAAATGATTTTTATACCTATGCATTTTGAA
1 CCCAATACGTTAGGGCACAACAAGTTAAGTTCCCAAAAATGATTTTTATACCTATGCATTTTGAA
1595953 TAAAGAATATTCTCGGTAATTTAAGCTTACAAAGAAAATCGGAA
66 TAAAGAATATTCTCGGTAATTTAAGCTTACAAAGAAAATCGGAA
1595997 CCCAATACGTTAGGGCACAACAAGTTAAGTTCCCAAAAATGATTTTTATACCTATGCATTTTGAA
1 CCCAATACGTTAGGGCACAACAAGTTAAGTTCCCAAAAATGATTTTTATACCTATGCATTTTGAA
1596062 TAAAGAATATTCTCGGTAATTTAAGCTTACAAAGAAAATCGGAA
66 TAAAGAATATTCTCGGTAATTTAAGCTTACAAAGAAAATCGGAA
1596106 CCCAATACGTTAGGGC
1 CCCAATACGTTAGGGC
1596122 TCAATTTCCC
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 125 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (109 bp):
CCCAATACGTTAGGGCACAACAAGTTAAGTTCCCAAAAATGATTTTTATACCTATGCATTTTGAA
TAAAGAATATTCTCGGTAATTTAAGCTTACAAAGAAAATCGGAA
Found at i:1596531 original size:35 final size:35
Alignment explanation
Indices: 1596470--1596536 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
1596460 GAAGAAAGAT
*
1596470 AAAATACAAAAATATGTATATGTGTATATATTTAC
1 AAAATACAAAAATATGTATATATGTATATATTTAC
*
1596505 AAAATA-AAAAA-ATGTATAAGTATGTATGTATT
1 AAAATACAAAAATATGTAT-A-TATGTATATATT
1596537 GAAAAATCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.21
34 6 0.21
35 16 0.57
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (35 bp):
AAAATACAAAAATATGTATATATGTATATATTTAC
Found at i:1596996 original size:3 final size:3
Alignment explanation
Indices: 1596962--1597017 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
1596952 GTAGAGATAG
* * *
1596962 TAA TAG TAA TAA TGA TAA TATA TAA T-A TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
1597007 TAAA TAA TAA T
1 T-AA TAA TAA T
1597018 TTAAAAAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1597000 original size:24 final size:22
Alignment explanation
Indices: 1596963--1597017 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 22
1596953 TAGAGATAGT
*
1596963 AATAGTAATAATGATAATATATA
1 AATAATAATAATGATAATA-ATA
1596986 ATATAATAATAATGATAATAATA
1 A-ATAATAATAATGATAATAATA
1597009 AATAATAAT
1 AATAATAAT
1597018 TTAAAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 8 0.27
23 5 0.17
24 17 0.57
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (22 bp):
AATAATAATAATGATAATAATA
Found at i:1597635 original size:5 final size:5
Alignment explanation
Indices: 1597616--1597655 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
1597606 TGTTTTAGGA
* *
1597616 AAAAT AAAAT GAAAAT AAAAG AAAAT AAAAG AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1597656 AATATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (5 bp):
AAAAT
Found at i:1597641 original size:10 final size:10
Alignment explanation
Indices: 1597616--1597655 Score: 71
Period size: 10 Copynumber: 3.9 Consensus size: 10
1597606 TGTTTTAGGA
1597616 AAAATAAAATG
1 AAAATAAAA-G
1597627 AAAATAAAAG
1 AAAATAAAAG
1597637 AAAATAAAAG
1 AAAATAAAAG
1597647 AAAATAAAA
1 AAAATAAAA
1597656 AATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (10 bp):
AAAATAAAAG
Found at i:1602459 original size:35 final size:35
Alignment explanation
Indices: 1602413--1602480 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
1602403 TATATATATA
1602413 AATATAATTTTCATAATCCTAATTCAA-TTCTAACT
1 AATATAATTTTCATAATCCTAATT-AAGTTCTAACT
*
1602448 AATATAATTTTCGTAATCCTAATTAAGTTCTAA
1 AATATAATTTTCATAATCCTAATTAAGTTCTAA
1602481 GATAGTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.43
Consensus pattern (35 bp):
AATATAATTTTCATAATCCTAATTAAGTTCTAACT
Found at i:1602469 original size:20 final size:19
Alignment explanation
Indices: 1602413--1602470 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
1602403 TATATATATA
1602413 AATATAATTTTCATAATCCT
1 AATATAATTTTC-TAATCCT
1602433 AAT-TCAA--TTCTAA--CT
1 AATAT-AATTTTCTAATCCT
1602448 AATATAATTTTCGTAATCCT
1 AATATAATTTTC-TAATCCT
1602468 AAT
1 AAT
1602471 TAAGTTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
15 7 0.23
16 1 0.03
17 6 0.19
18 6 0.19
19 1 0.03
20 10 0.32
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.43
Consensus pattern (19 bp):
AATATAATTTTCTAATCCT
Found at i:1609675 original size:23 final size:23
Alignment explanation
Indices: 1609631--1609675 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1609621 CTTTTTACAT
**
1609631 TTTTATAAATTTTATCTGTTTTC
1 TTTTATAAATTTTATCAATTTTC
1609654 TTTTATAAA-TTTATACAATTTT
1 TTTTATAAATTTTAT-CAATTTT
1609676 ATATTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTATAAATTTTATCAATTTTC
Found at i:1609710 original size:21 final size:21
Alignment explanation
Indices: 1609670--1609710 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1609660 AAATTTATAC
*
1609670 AATTTTATATTTGTTAAAAAG
1 AATTTTATATATGTTAAAAAG
1609691 AATTTTATATAT-TTAGAAAA
1 AATTTTATATATGTTA-AAAA
1609711 ACAGGTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (21 bp):
AATTTTATATATGTTAAAAAG
Found at i:1621453 original size:32 final size:30
Alignment explanation
Indices: 1621399--1621457 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
1621389 AATAAAAATG
* *
1621399 TATAAAATTATTAAACATTAAAATAATATAA
1 TATAAAATTATTAAAAAATAAAA-AATATAA
*
1621430 TATAAATATTTTTAAAAAATAAAAAATA
1 TATAAA-ATTATTAAAAAATAAAAAATA
1621458 CTATGAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 10 0.42
32 14 0.58
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (30 bp):
TATAAAATTATTAAAAAATAAAAAATATAA
Found at i:1626070 original size:20 final size:19
Alignment explanation
Indices: 1626047--1626126 Score: 65
Period size: 20 Copynumber: 4.1 Consensus size: 19
1626037 TTTTATATTC
1626047 TTTTTATACTTTTTAAATAA
1 TTTTTATA-TTTTTAAATAA
*
1626067 TTTTTA-ATTTTTAAAAATAT
1 TTTTTATATTTTT--AAATAA
*
1626087 TTTTTATAATTTTTTAAT-A
1 TTTTTAT-ATTTTTAAATAA
* * *
1626106 TTTTTAAAATTTTAAAAAA
1 TTTTTATATTTTTAAATAA
1626125 TT
1 TT
1626127 AGTTAAGTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
18 12 0.25
19 10 0.21
20 20 0.42
22 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTATATTTTTAAATAA
Found at i:1626094 original size:40 final size:40
Alignment explanation
Indices: 1626047--1626123 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
1626037 TTTTATATTC
* *
1626047 TTTTTATACTTTTTAAATAATTTTT-AATTTTTAAAAATAT
1 TTTTTATAATTTTTAAAT-ATTTTTAAAATTTTAAAAATAT
*
1626087 TTTTTATAATTTTTTAATATTTTTAAAATTTTAAAAA
1 TTTTTATAATTTTTAAATATTTTTAAAATTTTAAAAA
1626124 ATTAGTTAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 6 0.18
40 27 0.82
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (40 bp):
TTTTTATAATTTTTAAATATTTTTAAAATTTTAAAAATAT
Found at i:1629961 original size:15 final size:15
Alignment explanation
Indices: 1629929--1629984 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
1629919 CCATATTGAA
* *
1629929 ATTTTTTATATTATTT
1 ATTTTTAATA-TAATT
1629945 ATTTTTAATATAATT
1 ATTTTTAATATAATT
*
1629960 ATTCTTT-TTATAATT
1 ATT-TTTAATATAATT
1629975 ATATTTTAAT
1 AT-TTTTAAT
1629985 TTGTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 19 0.58
16 14 0.42
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTTAATATAATT
Found at i:1632838 original size:2 final size:2
Alignment explanation
Indices: 1632833--1632873 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1632823 TATATATATA
* *
1632833 TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1632874 ATGTATTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.02, C:0.02, G:0.46, T:0.49
Consensus pattern (2 bp):
TG
Found at i:1632846 original size:10 final size:10
Alignment explanation
Indices: 1632831--1632877 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
1632821 TATATATATA
1632831 TATGTGTGTG
1 TATGTGTGTG
1632841 TATGTGTGTG
1 TATGTGTGTG
*
1632851 TGTGTGTGTG
1 TATGTGTGTG
*
1632861 TGCGTGTGTGTG
1 T--ATGTGTGTG
1632873 TATGT
1 TATGT
1632878 ATTGACTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 23 0.70
12 10 0.30
ACGTcount: A:0.06, C:0.02, G:0.43, T:0.49
Consensus pattern (10 bp):
TATGTGTGTG
Found at i:1636312 original size:23 final size:21
Alignment explanation
Indices: 1636273--1636343 Score: 56
Period size: 23 Copynumber: 3.3 Consensus size: 21
1636263 ATGTTCAAAT
*
1636273 ATATATAATCTT--AGATATG
1 ATATGTAATCTTAGAGATATG
*
1636292 ATATGTAATCTTTAGAAGATACG
1 ATATGTAATC-TTAG-AGATATG
* *
1636315 ATTCTGTAATCTTAGAGATTTG
1 A-TATGTAATCTTAGAGATATG
*
1636337 ATTTGTA
1 ATATGTA
1636344 GATAGCTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 9 0.22
20 2 0.05
21 5 0.12
22 6 0.15
23 11 0.27
24 8 0.20
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (21 bp):
ATATGTAATCTTAGAGATATG
Found at i:1636339 original size:22 final size:23
Alignment explanation
Indices: 1636285--1636343 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
1636275 ATATAATCTT
* *
1636285 AGATATGATATGTAATCTTTAGA
1 AGATACGATTTGTAATCTTTAGA
1636308 AGATACGATTCTGTAATC-TTAG-
1 AGATACGATT-TGTAATCTTTAGA
**
1636330 AGATTTGATTTGTA
1 AGATACGATTTGTA
1636344 GATAGCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.13
22 8 0.26
23 12 0.39
24 7 0.23
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.41
Consensus pattern (23 bp):
AGATACGATTTGTAATCTTTAGA
Found at i:1637580 original size:17 final size:17
Alignment explanation
Indices: 1637554--1637586 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1637544 ACTCCGAGTT
1637554 TATAAATACAAATACAA
1 TATAAATACAAATACAA
*
1637571 TATAATTACAAATACA
1 TATAAATACAAATACA
1637587 TATTTAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (17 bp):
TATAAATACAAATACAA
Found at i:1640665 original size:26 final size:25
Alignment explanation
Indices: 1640636--1640685 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
1640626 TTTAAAAAAT
1640636 AAATTT-TATAATAAATAAGATTTACA
1 AAATTTATATAAT-AATAA-ATTTACA
1640662 AAATTTAATATAATAATAAATTTA
1 AAATTT-ATATAATAATAAATTTA
1640686 TTTAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 11 0.50
27 5 0.23
28 6 0.27
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
AAATTTATATAATAATAAATTTACA
Found at i:1640684 original size:17 final size:17
Alignment explanation
Indices: 1640662--1640711 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1640652 AAGATTTACA
1640662 AAATTTAATATAATAAT
1 AAATTTAATATAATAAT
*
1640679 AAATTT-AT-TTA-AAT
1 AAATTTAATATAATAAT
*
1640693 -AATTTAATATAATGAT
1 AAATTTAATATAATAAT
1640709 AAA
1 AAA
1640712 ATTTTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
13 5 0.19
14 5 0.19
15 4 0.15
16 4 0.15
17 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATTTAATATAATAAT
Found at i:1640689 original size:30 final size:31
Alignment explanation
Indices: 1640655--1640719 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
1640645 AATAAATAAG
1640655 ATTTACAA-AATTTAATATAATAAT-AAATTT
1 ATTTA-AATAATTTAATATAATAATAAAATTT
*
1640685 ATTTAAATAATTTAATATAATGATAAAATTT
1 ATTTAAATAATTTAATATAATAATAAAATTT
1640716 -TTTA
1 ATTTA
1640720 TAACTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 2 0.06
30 24 0.75
31 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (31 bp):
ATTTAAATAATTTAATATAATAATAAAATTT
Found at i:1642522 original size:27 final size:27
Alignment explanation
Indices: 1642492--1642546 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1642482 TAAAAATTTC
1642492 AATAAAAATATA-TTAAAATAATAAATA
1 AATAAAAAT-TACTTAAAATAATAAATA
**
1642519 AATAAAAATTACTTATCATAATAAATA
1 AATAAAAATTACTTAAAATAATAAATA
1642546 A
1 A
1642547 TAGGTTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (27 bp):
AATAAAAATTACTTAAAATAATAAATA
Found at i:1642827 original size:14 final size:14
Alignment explanation
Indices: 1642808--1642849 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
1642798 AATAAATATA
1642808 TATTTTTCT-ATTTT
1 TATTTTT-TAATTTT
1642822 TATTTTTTAATTTT
1 TATTTTTTAATTTT
*
1642836 TAATTTTTAATTTT
1 TATTTTTTAATTTT
1642850 AAAATACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 1 0.04
14 25 0.96
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:1642851 original size:6 final size:7
Alignment explanation
Indices: 1642817--1642849 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1642807 ATATTTTTCT
1642817 ATTTTTA
1 ATTTTTA
*
1642824 TTTTTTA
1 ATTTTTA
1642831 ATTTTTA
1 ATTTTTA
1642838 ATTTTTA
1 ATTTTTA
1642845 ATTTT
1 ATTTT
1642850 AAAATACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
ATTTTTA
Found at i:1642908 original size:26 final size:27
Alignment explanation
Indices: 1642857--1642911 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1642847 TTTAAAATAC
* *
1642857 TTTTAAAATAATTTTTTATTTTTTTAT
1 TTTTAAAATAATTTTTTATATGTTTAT
1642884 TTTTAAAATAATTTTTTA-ATGTTTAT
1 TTTTAAAATAATTTTTTATATGTTTAT
1642910 TT
1 TT
1642912 AAAAAATGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTTAAAATAATTTTTTATATGTTTAT
Found at i:1642917 original size:26 final size:27
Alignment explanation
Indices: 1642861--1642918 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
1642851 AAATACTTTT
* * **
1642861 AAAATAATTTTTTATTTTTTTATTTTT
1 AAAATAATTTTTTATATGTTTATTTAA
1642888 AAAATAATTTTTTA-ATGTTTATTTAA
1 AAAATAATTTTTTATATGTTTATTTAA
1642914 AAAAT
1 AAAAT
1642919 GGGCCGGGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
AAAATAATTTTTTATATGTTTATTTAA
Found at i:1649944 original size:98 final size:98
Alignment explanation
Indices: 1649775--1649970 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
1649765 CGAAAAGCGT
1649775 GAAGCATATGACAAGAGAGGGAAGACCAGAGTGATACCGTAAGTTTATATGCTATAAGTGTAATG
1 GAAGCATATGACAAGAGAGGGAAGACCAGAGTGATACCGTAAGTTTATATGCTATAAGTGTAATG
1649840 TTCATTATCTCGCATACTGTTTTGAAATGCATA
66 TTCATTATCTCGCATACTGTTTTGAAATGCATA
1649873 GAAGCATATGACAAGAGAGGGAAGACCAGAGTGATACCGTAAGTTTATATGCTATAAGTGTAATG
1 GAAGCATATGACAAGAGAGGGAAGACCAGAGTGATACCGTAAGTTTATATGCTATAAGTGTAATG
1649938 TTCATTATCTCGCATACTGTTTTGAAATGCATA
66 TTCATTATCTCGCATACTGTTTTGAAATGCATA
1649971 AAATGACATG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (98 bp):
GAAGCATATGACAAGAGAGGGAAGACCAGAGTGATACCGTAAGTTTATATGCTATAAGTGTAATG
TTCATTATCTCGCATACTGTTTTGAAATGCATA
Found at i:1652464 original size:31 final size:31
Alignment explanation
Indices: 1652421--1652481 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1652411 ATGATTACTA
1652421 AATTATTAGAAAGTT-TCTATTTAAGTCACTG
1 AATTATTAGAAAGTTCT-TATTTAAGTCACTG
*
1652452 AATTATTTGAAAGTTCTTATTTAAGTCACT
1 AATTATTAGAAAGTTCTTATTTAAGTCACT
1652482 CATGTGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (31 bp):
AATTATTAGAAAGTTCTTATTTAAGTCACTG
Found at i:1653127 original size:22 final size:22
Alignment explanation
Indices: 1653100--1653165 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 22
1653090 TATATTTTAA
1653100 CACATTCGAATATACGACTATG
1 CACATTCGAATATACGACTATG
*
1653122 CACATTCGAATTCACAACCGACTATG
1 CACATTCGAA-T-A-TA-CGACTATG
* *
1653148 TACATTCGAATCTACGAC
1 CACATTCGAATATACGAC
1653166 CTCCTACGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
22 14 0.39
23 2 0.06
24 1 0.03
25 2 0.06
26 17 0.47
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (22 bp):
CACATTCGAATATACGACTATG
Found at i:1653576 original size:30 final size:30
Alignment explanation
Indices: 1653540--1653616 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
1653530 TGATTTGAGA
*
1653540 GACGAACACGGCAACCCTATTCAACTCACC
1 GACGAACACGGCAACCCGATTCAACTCACC
* *
1653570 GACGAACACGGCAACCCGGTTCAACTCACT
1 GACGAACACGGCAACCCGATTCAACTCACC
*
1653600 GACGAACACGGTAACCC
1 GACGAACACGGCAACCC
1653617 CATTTATGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.32, C:0.38, G:0.18, T:0.12
Consensus pattern (30 bp):
GACGAACACGGCAACCCGATTCAACTCACC
Found at i:1660309 original size:2 final size:2
Alignment explanation
Indices: 1660304--1660340 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1660294 AATGTAAAAA
1660304 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1660341 CCAAATTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1668423 original size:13 final size:13
Alignment explanation
Indices: 1668407--1668448 Score: 68
Period size: 12 Copynumber: 3.2 Consensus size: 13
1668397 AAGAAGAAGG
1668407 AAAAACAAAAC-A
1 AAAAACAAAACAA
1668419 AAAAACAAAACAA
1 AAAAACAAAACAA
1668432 AAAAACAAAATCAA
1 AAAAACAAAA-CAA
1668446 AAA
1 AAA
1668449 TCAAAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 11 0.39
13 11 0.39
14 6 0.21
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.02
Consensus pattern (13 bp):
AAAAACAAAACAA
Found at i:1668453 original size:13 final size:12
Alignment explanation
Indices: 1668407--1668454 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
1668397 AAGAAGAAGG
1668407 AAAAACAAAACA
1 AAAAACAAAACA
1668419 AAAAACAAAACAA
1 AAAAACAAAAC-A
1668432 AAAAACAAAATCA
1 AAAAACAAAA-CA
*
1668445 AAAATCAAAA
1 AAAAACAAAA
1668455 AATCGAAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 11 0.33
13 21 0.64
14 1 0.03
ACGTcount: A:0.81, C:0.15, G:0.00, T:0.04
Consensus pattern (12 bp):
AAAAACAAAACA
Found at i:1668480 original size:13 final size:13
Alignment explanation
Indices: 1668464--1668499 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1668454 AAATCGAAGT
*
1668464 AAAAAAAAGGGAG
1 AAAAAAAAGGGAA
*
1668477 AAAAAAAAGAGAA
1 AAAAAAAAGGGAA
1668490 AAAAAAAAGG
1 AAAAAAAAGG
1668500 AGAGGTCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGGGAA
Found at i:1670086 original size:13 final size:13
Alignment explanation
Indices: 1670068--1670092 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1670058 CCCAATCAAT
1670068 TTCTTTATTATTC
1 TTCTTTATTATTC
1670081 TTCTTTATTATT
1 TTCTTTATTATT
1670093 TTTGGATAAT
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:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTTATTATTC
Found at i:1671044 original size:88 final size:88
Alignment explanation
Indices: 1670944--1671375 Score: 688
Period size: 88 Copynumber: 4.9 Consensus size: 88
1670934 GAAGTTACAA
* * * *
1670944 ATCTTTCCTTCCTGCATTGACAGTGAAGCAGGTCGAAAACAT-AAACATTGCCTCTCTCGGTTGT
1 ATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAC-TCAAACCTTGCCTCTCTCGGTTGT
1671008 GATGGAGCTGGTTGAAGACAAAAG
65 GATGGAGCTGGTTGAAGACAAAAG
* * * * *
1671032 ATCTTGCCTTCCTTCATTGGCGGTGAAGCAGATCGAAGACAT-AAACCTTGCCTCTCTCGGTTGT
1 ATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAC-TCAAACCTTGCCTCTCTCGGTTGT
*
1671096 GATGGAGCTAGTTGAAGACAAAAG
65 GATGGAGCTGGTTGAAGACAAAAG
*
1671120 ATCTTGCCTTCATGCATTGACAGCGAAGCAGGTCGAAGACTCAAACCTTGCCTCTCTCGGTTGTG
1 ATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACTCAAACCTTGCCTCTCTCGGTTGTG
1671185 ATGGAGCTGGTTGAAGACAAAAG
66 ATGGAGCTGGTTGAAGACAAAAG
* * *
1671208 ATCTTGCCTTCCTTCATTAACAGCGAAGCAGATCGAAGACTCAAACCTTGCCTCTCTCGGTTGTG
1 ATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACTCAAACCTTGCCTCTCTCGGTTGTG
* *
1671273 ATAGAGCTTGTTGAAGACAAAAG
66 ATGGAGCTGGTTGAAGACAAAAG
1671296 ATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACTCAAACCTTGCCTCTCTCGGTTGTG
1 ATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACTCAAACCTTGCCTCTCTCGGTTGTG
1671361 ATGGAGCTGGTTGAA
66 ATGGAGCTGGTTGAA
1671376 TCATTAGAAA
Statistics
Matches: 317, Mismatches: 26, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
87 1 0.00
88 316 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (88 bp):
ATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACTCAAACCTTGCCTCTCTCGGTTGTG
ATGGAGCTGGTTGAAGACAAAAG
Found at i:1671126 original size:44 final size:44
Alignment explanation
Indices: 1670991--1671304 Score: 170
Period size: 44 Copynumber: 7.1 Consensus size: 44
1670981 AACATAAACA
*
1670991 TTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATC
1 TTGCCTCTCTCGGTTGTGATGGAGCTAGTTGAAGACAAAAGATC
* * * * * * *
1671035 TTGCCT-TCCTTC-ATTGGCGGTGAAGC-AGATCGAAGACATAA-ACC
1 TTGCCTCT-C-TCGGTT-GTGATGGAGCTAG-TTGAAGACAAAAGATC
1671079 TTGCCTCTCTCGGTTGTGATGGAGCTAGTTGAAGACAAAAGATC
1 TTGCCTCTCTCGGTTGTGATGGAGCTAGTTGAAGACAAAAGATC
** * * ** *
1671123 TTGCCT-TCAT-GCAT-TGACAGCGAAGC-AGGTCGAAGACTCAA-ACC
1 TTGCCTCTC-TCGGTTGTGA-TG-G-AGCTA-GTTGAAGACAAAAGATC
*
1671167 TTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATC
1 TTGCCTCTCTCGGTTGTGATGGAGCTAGTTGAAGACAAAAGATC
* *** * ** *
1671211 TTGCCT-TCCTTC-ATTAACA-GCGAAGC-AGATCGAAGACTCAA-ACC
1 TTGCCTCT-C-TCGGTTGTGATG-G-AGCTAG-TTGAAGACAAAAGATC
* *
1671255 TTGCCTCTCTCGGTTGTGATAGAGCTTGTTGAAGACAAAAGATC
1 TTGCCTCTCTCGGTTGTGATGGAGCTAGTTGAAGACAAAAGATC
1671299 TTGCCT
1 TTGCCT
1671305 TCCTGCATTG
Statistics
Matches: 193, Mismatches: 49, Indels: 56
0.65 0.16 0.19
Matches are distributed among these distances:
42 3 0.02
43 54 0.28
44 80 0.41
45 53 0.27
46 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (44 bp):
TTGCCTCTCTCGGTTGTGATGGAGCTAGTTGAAGACAAAAGATC
Found at i:1671346 original size:44 final size:44
Alignment explanation
Indices: 1671122--1671348 Score: 137
Period size: 44 Copynumber: 5.2 Consensus size: 44
1671112 GACAAAAGAT
*
1671122 CTTGCCTTCATGCATTGACAGCGAAGCAGGTCGAAGACTCAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACTCAAAC
** * * * ** *
1671166 CTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACTCAA-AC
* * *
1671210 CTTGCCTTCCTTCATTAACAGCGAAGCAGATCGAAGACTCAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACTCAAAC
** * ** * ** *
1671254 CTTGCC-TCTCTCGGTTGTGATA--G-AGCTTGTTGAAGACAAAAGAT
1 CTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACTCAA-AC
1671298 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACTCAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACTCAAAC
1671342 CTTGCCT
1 CTTGCCT
1671349 CTCTCGGTTG
Statistics
Matches: 126, Mismatches: 41, Indels: 32
0.63 0.21 0.16
Matches are distributed among these distances:
42 6 0.05
43 34 0.27
44 46 0.37
45 34 0.27
46 6 0.05
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACTCAAAC
Found at i:1671886 original size:13 final size:13
Alignment explanation
Indices: 1671870--1671911 Score: 68
Period size: 12 Copynumber: 3.2 Consensus size: 13
1671860 AAGAAGAAGG
1671870 AAAAACAAAAC-A
1 AAAAACAAAACAA
1671882 AAAAACAAAACAA
1 AAAAACAAAACAA
1671895 AAAAACAAAATCAA
1 AAAAACAAAA-CAA
1671909 AAA
1 AAA
1671912 TCAAAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 11 0.39
13 11 0.39
14 6 0.21
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.02
Consensus pattern (13 bp):
AAAAACAAAACAA
Found at i:1671916 original size:13 final size:12
Alignment explanation
Indices: 1671870--1671917 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
1671860 AAGAAGAAGG
1671870 AAAAACAAAACA
1 AAAAACAAAACA
1671882 AAAAACAAAACAA
1 AAAAACAAAAC-A
1671895 AAAAACAAAATCA
1 AAAAACAAAA-CA
*
1671908 AAAATCAAAA
1 AAAAACAAAA
1671918 AATCGAAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 11 0.33
13 21 0.64
14 1 0.03
ACGTcount: A:0.81, C:0.15, G:0.00, T:0.04
Consensus pattern (12 bp):
AAAAACAAAACA
Found at i:1671943 original size:13 final size:13
Alignment explanation
Indices: 1671927--1671962 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1671917 AAATCGAAGT
*
1671927 AAAAAAAAGGGAG
1 AAAAAAAAGGGAA
*
1671940 AAAAAAAAGAGAA
1 AAAAAAAAGGGAA
1671953 AAAAAAAAGG
1 AAAAAAAAGG
1671963 AGAGGTCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGGGAA
Found at i:1673549 original size:13 final size:13
Alignment explanation
Indices: 1673531--1673555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1673521 CCCAATCAAT
1673531 TTCTTTATTATTC
1 TTCTTTATTATTC
1673544 TTCTTTATTATT
1 TTCTTTATTATT
1673556 TTTGGATAAT
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:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTTATTATTC
Found at i:1674507 original size:88 final size:88
Alignment explanation
Indices: 1674407--1675045 Score: 802
Period size: 88 Copynumber: 7.3 Consensus size: 88
1674397 GAAGTTACAA
* * *
1674407 ATCTTTCCTTCCTGCATTGACAGTGAAGCAGGTCGAAAACATAAACATTGCCTCTCTCGGTTGTG
1 ATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACATAAACCTTGCCTCTCTCGGTTGTG
1674472 ATGGAGCTGGTTGAAGACAAAAG
66 ATGGAGCTGGTTGAAGACAAAAG
* * * *
1674495 ATCTTGCCTTCCTTCATTGGCGGTGAAGCAGATCGAAGACATAAACCTTGCCTCTCTCGGTTGTG
1 ATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACATAAACCTTGCCTCTCTCGGTTGTG
*
1674560 ATGGAGCTAGTTGAAGACAAAAG
66 ATGGAGCTGGTTGAAGACAAAAG
* *
1674583 ATCTTGCCTTCATGCATTGAAAGTGAAGCAGGTCGAAGAC-TCAAACCTTGCCTCTCTCGGTTGT
1 ATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACAT-AAACCTTGCCTCTCTCGGTTGT
1674647 GATGGAGCTGGTTGAAGACAAAAG
65 GATGGAGCTGGTTGAAGACAAAAG
* * * *
1674671 ATCTTGCCTTCCTTCATTGGCGGTGAAGCAGATCGAAGACATAAACCTTGCCTCTCTCGGTTGTG
1 ATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACATAAACCTTGCCTCTCTCGGTTGTG
*
1674736 ATGGAGCTAGTTGAAGACAAAAG
66 ATGGAGCTGGTTGAAGACAAAAG
* *
1674759 ATCTTGCCTTCATGCATTGACAGCGAAGCAGGTCGAAGAC-TCAAACCTTGCCTCTCTCGGTTGT
1 ATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACAT-AAACCTTGCCTCTCTCGGTTGT
1674823 GATGGAGCTGGTTGAAGACAAAAG
65 GATGGAGCTGGTTGAAGACAAAAG
* * * * * * * *
1674847 ATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCGAAAATACAAACTTTACCTCCCTCGGTTGT-
1 ATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACATAAACCTTGCCTCTCTCGGTTGTG
* * ** * * **
1674911 AGGGAAGCAGGTAAAAAATAGCAG
66 ATGG-AGCTGGTTGAAGACAAAAG
* * * * *
1674935 ATCTTGCATTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTC-CATCGGTTGT
1 ATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACATAAACCTTGCCTCTC-TCGGTTGT
* * ** * *
1674999 -AGTCGAGCAGGTCAAAGATAACAG
65 GA-TGGAGCTGGTTGAAGACAAAAG
1675023 ATCTTGCCTTCCTGCATTGACAG
1 ATCTTGCCTTCCTGCATTGACAG
1675046 CGGAGCAGAC
Statistics
Matches: 484, Mismatches: 60, Indels: 14
0.87 0.11 0.03
Matches are distributed among these distances:
87 6 0.01
88 476 0.98
89 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (88 bp):
ATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACATAAACCTTGCCTCTCTCGGTTGTG
ATGGAGCTGGTTGAAGACAAAAG
Found at i:1674545 original size:44 final size:44
Alignment explanation
Indices: 1674497--1674723 Score: 128
Period size: 44 Copynumber: 5.2 Consensus size: 44
1674487 GACAAAAGAT
1674497 CTTGCCTTCCTTCATTGGCGGTGAAGCAGATCGAAGACATAAAC
1 CTTGCCTTCCTTCATTGGCGGTGAAGCAGATCGAAGACATAAAC
* * * * * * *
1674541 CTTGCC-T-CTCTCGGTT-GTGATGGAGCTAG-TTGAAGACAAAAGAT
1 CTTGCCTTCCT-TC-ATTGGCGGTGAAGC-AGATCGAAGACATAA-AC
* * *** *
1674585 CTTGCCTTCATGCATTGAAAGTGAAGCAGGTCGAAGAC-TCAAAC
1 CTTGCCTTCCTTCATTGGCGGTGAAGCAGATCGAAGACAT-AAAC
* * * * * * * * *
1674629 CTTGCC-T-CTCTCGGTT-GTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCT-TC-ATTGGCGGTGAAGCAGATCGAAGACATAA-AC
1674673 CTTGCCTTCCTTCATTGGCGGTGAAGCAGATCGAAGACATAAAC
1 CTTGCCTTCCTTCATTGGCGGTGAAGCAGATCGAAGACATAAAC
1674717 CTTGCCT
1 CTTGCCT
1674724 CTCTCGGTTG
Statistics
Matches: 128, Mismatches: 39, Indels: 32
0.64 0.20 0.16
Matches are distributed among these distances:
42 3 0.02
43 38 0.30
44 47 0.37
45 37 0.29
46 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (44 bp):
CTTGCCTTCCTTCATTGGCGGTGAAGCAGATCGAAGACATAAAC
Found at i:1675106 original size:44 final size:44
Alignment explanation
Indices: 1675056--1675141 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
1675046 CGGAGCAGAC
*
1675056 TGAAGATTGCAAATCCTATCTCCCTAAGCAGTAGTGGAGTAGGT
1 TGAAGATTGCAAATCATATCTCCCTAAGCAGTAGTGGAGTAGGT
* * *
1675100 TGAAGATTTCAGATCATGTCTCCCTAAGCAGTAGTGGAGTAG
1 TGAAGATTGCAAATCATATCTCCCTAAGCAGTAGTGGAGTAG
1675142 ATCAAGTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (44 bp):
TGAAGATTGCAAATCATATCTCCCTAAGCAGTAGTGGAGTAGGT
Found at i:1675255 original size:133 final size:132
Alignment explanation
Indices: 1675071--1675344 Score: 349
Period size: 133 Copynumber: 2.1 Consensus size: 132
1675061 ATTGCAAATC
* * * * *
1675071 CTATCTCCCTAAGCA-GTAGTGGAGTAGGTTGAAGATTTCAGATCATGTCTCCCTAAGCAGTAGT
1 CTATCTCCCT-AGTAGGCAGTGGAATAGATTGAAGATTTCAGATCATATCTCCCTAAGCAGTAGT
** * *
1675135 GGAGTAGATC-AAGTAATGGC-AGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAATCCA
65 GGAGTAGATCGAA-T-ATGGCGA-ATTTTACCTCCCTAAGATTACAATGGAGTACATTGAAGCCA
*
1675198 GTGATT
127 GTAATT
* *
1675204 TTATCTCCCTAGTAGGCAGTGGAATAGATTGAAGATTAT-AGATCTTATCTCCCTAAGCAGTAGT
1 CTATCTCCCTAGTAGGCAGTGGAATAGATTGAAGATT-TCAGATCATATCTCCCTAAGCAGTAGT
* *
1675268 GGAGTAGATCGAATATGGCGAATTTTACCTCCCTAAGGTTACAATGGAGTACTTTGAAGCCAGTA
65 GGAGTAGATCGAATATGGCGAATTTTACCTCCCTAAGATTACAATGGAGTACATTGAAGCCAGTA
1675333 ATT
130 ATT
1675336 CTATCTCCC
1 CTATCTCCC
1675345 CGGTGTTGCA
Statistics
Matches: 122, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
132 56 0.46
133 63 0.52
134 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (132 bp):
CTATCTCCCTAGTAGGCAGTGGAATAGATTGAAGATTTCAGATCATATCTCCCTAAGCAGTAGTG
GAGTAGATCGAATATGGCGAATTTTACCTCCCTAAGATTACAATGGAGTACATTGAAGCCAGTAA
TT
Found at i:1677047 original size:13 final size:13
Alignment explanation
Indices: 1677029--1677058 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1677019 TTAATAATAA
1677029 TATTATTATTATT
1 TATTATTATTATT
*
1677042 TATTATTATTGTT
1 TATTATTATTATT
1677055 TATT
1 TATT
1677059 TTGGTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:1678572 original size:29 final size:30
Alignment explanation
Indices: 1678532--1678605 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
1678522 ACAACATGAT
* **
1678532 AACATAAGTGACTAAAACGTAACAT-TTCA
1 AACAAAAGTGACTAAAACGTAACATAACCA
*
1678561 AACAAAAGTGACTAAAATGTAACATGAACCA
1 AACAAAAGTGACTAAAACGTAACAT-AACCA
1678592 AACAAAAGTGACTA
1 AACAAAAGTGACTA
1678606 TTTTAGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.59
31 16 0.41
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (30 bp):
AACAAAAGTGACTAAAACGTAACATAACCA
Found at i:1679865 original size:141 final size:140
Alignment explanation
Indices: 1679612--1679869 Score: 369
Period size: 141 Copynumber: 1.8 Consensus size: 140
1679602 GAACGGGATA
* *
1679612 AACTTTTCCACCTCCGTTAGAGGAGGAAAAGGGAAAGGCATACCGTACACTAAGTTTCTTCTCGA
1 AACTTTTCCACCTCCGTTAAAGGAGGAAAAGGGAAAGGCATACCGAACACTAAGTTTCTTCTCGA
* * * *
1679677 TACTTCATCACGATGAAACGATGCATCATCATGTGATGGATCATGATCATCATTATCATGATCAT
66 TAATTCATCACGATGAAACGATGCATCAACA-GTCATGCATCATGATCATCATTATCATGATCAT
1679742 GCATCAGGTTG
130 GCATCAGGTTG
*
1679753 AACTGTTT-CACCTCCGTTAAAGGGGGAAAAGGGAAAGGCATACCGAACACTAAGTTTCTTCTTC
1 AACT-TTTCCACCTCCGTTAAAGGAGGAAAAGGGAAAGGCATACCGAACACTAAG--T-TTCTTC
* *
1679817 TCGATAATTCATCACGATGAAATGATGCATCAACA-TCAT-CATCTTGATCATCA
62 TCGATAATTCATCACGATGAAACGATGCATCAACAGTCATGCATCATGATCATCA
1679870 GATCCATCAT
Statistics
Matches: 104, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
141 59 0.57
142 6 0.06
143 1 0.01
144 38 0.37
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (140 bp):
AACTTTTCCACCTCCGTTAAAGGAGGAAAAGGGAAAGGCATACCGAACACTAAGTTTCTTCTCGA
TAATTCATCACGATGAAACGATGCATCAACAGTCATGCATCATGATCATCATTATCATGATCATG
CATCAGGTTG
Found at i:1681385 original size:10 final size:10
Alignment explanation
Indices: 1681370--1681400 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1681360 TAATATTATG
1681370 AAAAACAAAA
1 AAAAACAAAA
1681380 AAAAACAAAA
1 AAAAACAAAA
1681390 AAAAACAAAA
1 AAAAACAAAA
1681400 A
1 A
1681401 CCAAATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:1691097 original size:16 final size:17
Alignment explanation
Indices: 1691076--1691110 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1691066 ATTAAAATTT
1691076 TAAAAATA-ATTAGTTA
1 TAAAAATATATTAGTTA
*
1691092 TAAAAATATTTTAGTTA
1 TAAAAATATATTAGTTA
1691109 TA
1 TA
1691111 TTATGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
TAAAAATATATTAGTTA
Found at i:1694183 original size:9 final size:9
Alignment explanation
Indices: 1694169--1694197 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1694159 TTCTTATGTG
1694169 ATTGTTATT
1 ATTGTTATT
1694178 ATTGTTATT
1 ATTGTTATT
1694187 ATTGTT-TT
1 ATTGTTATT
1694195 ATT
1 ATT
1694198 TTTTTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (9 bp):
ATTGTTATT
Found at i:1694999 original size:30 final size:30
Alignment explanation
Indices: 1694958--1695016 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1694948 ATTTTATTGA
*
1694958 TAATCTTGTTATTATTTTAAATGCATTTGT
1 TAATCTTGTTATTATTTTAAAGGCATTTGT
* *
1694988 TAATTTTGTTATTATTTTAGAGGCATTTG
1 TAATCTTGTTATTATTTTAAAGGCATTTG
1695017 CTTGTTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (30 bp):
TAATCTTGTTATTATTTTAAAGGCATTTGT
Found at i:1695760 original size:3 final size:3
Alignment explanation
Indices: 1695752--1695784 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1695742 GAAGCATTGA
1695752 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1695785 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1697923 original size:28 final size:28
Alignment explanation
Indices: 1697873--1697926 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1697863 TTTCTTGTAA
* *
1697873 AGACGTAATAAATTATTTTTAAAAAAAG
1 AGACATAATAAATTATTTATAAAAAAAG
1697901 AGACATAATAAATT-TTTAATAAAAAA
1 AGACATAATAAATTATTT-ATAAAAAA
1697927 CACTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.31
Consensus pattern (28 bp):
AGACATAATAAATTATTTATAAAAAAAG
Found at i:1702315 original size:14 final size:14
Alignment explanation
Indices: 1702292--1702323 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1702282 ACCTTAAACA
*
1702292 TGAACTCTAAATCT
1 TGAACCCTAAATCT
1702306 TGAACCCTAAATCT
1 TGAACCCTAAATCT
1702320 TGAA
1 TGAA
1702324 TTCTCTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (14 bp):
TGAACCCTAAATCT
Found at i:1702426 original size:21 final size:21
Alignment explanation
Indices: 1702385--1702446 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1702375 TGATTGAAAT
1702385 ATCATTAAATAATTGAAAAAA
1 ATCATTAAATAATTGAAAAAA
1702406 ATCA-TAAATAATAT-AATAAAA
1 ATCATTAAATAAT-TGAA-AAAA
* *
1702427 ATTCATTCAATAACTGAAAA
1 A-TCATTAAATAATTGAAAA
1702447 CCATCATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 10 0.29
21 10 0.29
22 6 0.18
23 8 0.24
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.29
Consensus pattern (21 bp):
ATCATTAAATAATTGAAAAAA
Found at i:1715189 original size:22 final size:22
Alignment explanation
Indices: 1715163--1715207 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1715153 AAAAGTCATA
* *
1715163 TATGCTTTTAGATTTTTGTATT
1 TATGCTTATAGATTTTTCTATT
*
1715185 TATGCTTATATATTTTTCTATT
1 TATGCTTATAGATTTTTCTATT
1715207 T
1 T
1715208 TTATAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.64
Consensus pattern (22 bp):
TATGCTTATAGATTTTTCTATT
Found at i:1715959 original size:12 final size:12
Alignment explanation
Indices: 1715942--1715967 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1715932 AATTATTCAT
1715942 GTCAGTAATGAA
1 GTCAGTAATGAA
1715954 GTCAGTAATGAA
1 GTCAGTAATGAA
1715966 GT
1 GT
1715968 ACAAGCAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.27
Consensus pattern (12 bp):
GTCAGTAATGAA
Found at i:1717442 original size:20 final size:20
Alignment explanation
Indices: 1717417--1717467 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1717407 GATAAAAAAT
1717417 AAAAATCAATAAAATTT-ATA
1 AAAAAT-AATAAAATTTAATA
* *
1717437 AAAAATATTAAATTTTAATA
1 AAAAATAATAAAATTTAATA
*
1717457 AAAAATTATAA
1 AAAAATAATAA
1717468 GAAATATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATAATAAAATTTAATA
Found at i:1717484 original size:31 final size:30
Alignment explanation
Indices: 1717427--1717501 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
1717417 AAAAATCAAT
*
1717427 AAAATTTATAAAAAATATTAAATTTTAATA
1 AAAAATTATAAAAAATATTAAATTTTAATA
* * * *
1717457 AAAAATTATAAGAAATATTTAATTTTTATT
1 AAAAATTATAAAAAATATTAAATTTTAATA
*
1717487 AAAAATTAGAAAAAA
1 AAAAATTATAAAAAA
1717502 AAAGTTATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAAATTATAAAAAATATTAAATTTTAATA
Found at i:1717673 original size:19 final size:21
Alignment explanation
Indices: 1717651--1717690 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1717641 TTCTATAACA
1717651 TTTATT-ATTTTTT-TTATTT
1 TTTATTAATTTTTTATTATTT
1717670 TTTATTAATTTTTTATTATTT
1 TTTATTAATTTTTTATTATTT
1717691 GTCGTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 7 0.37
21 6 0.32
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTATTAATTTTTTATTATTT
Found at i:1717680 original size:11 final size:10
Alignment explanation
Indices: 1717651--1717690 Score: 64
Period size: 11 Copynumber: 4.0 Consensus size: 10
1717641 TTCTATAACA
1717651 TTTATTATTT
1 TTTATTATTT
1717661 TTT-TTATTT
1 TTTATTATTT
1717670 TTTATTAATTT
1 TTTATT-ATTT
1717681 TTTATTATTT
1 TTTATTATTT
1717691 GTCGTTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.32
10 9 0.32
11 10 0.36
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTATTT
Found at i:1719637 original size:31 final size:32
Alignment explanation
Indices: 1719602--1719661 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
1719592 TTTTTAAGCT
1719602 AAATTTAGACCA-CAACCTTTT-AAAAAGAATC
1 AAATTT-GACCATCAACCTTTTGAAAAAGAATC
1719633 AAATTTGACCATCAACCTTTTGAAAAAGA
1 AAATTTGACCATCAACCTTTTGAAAAAGA
1719662 GTCGAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 5 0.19
31 15 0.56
32 7 0.26
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (32 bp):
AAATTTGACCATCAACCTTTTGAAAAAGAATC
Found at i:1721555 original size:34 final size:35
Alignment explanation
Indices: 1721511--1721577 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1721501 CAGTAAAATA
*
1721511 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
1721545 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
1721578 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:1726461 original size:301 final size:301
Alignment explanation
Indices: 1725919--1726519 Score: 1139
Period size: 301 Copynumber: 2.0 Consensus size: 301
1725909 ATATAAACAT
* *
1725919 TACACTCAATCATAGTCGCAAGCTAGTCTTTTTGAAGACTAACCACATGATAAACCATTTTAATA
1 TACACTCAACCATAGTCGCAAGCTAGTCTTTTTGAAGACTAACCACATGATAAACAATTTTAATA
*
1725984 AAGATTACAAACTTTAAACCTTACCACCCTTTTATGATTACAAGCATATTTCCATCTAGACATTT
66 AAGATTACAAACTTTAAACCTTACCACCCTTTTATGATCACAAGCATATTTCCATCTAGACATTT
*
1726049 ACCATCTCAATGCATAATTTTATAAATTTAATGTGGCGTAATCCAGCCACAACTTGGCCGAAGCC
131 ACCATCTCAATACATAATTTTATAAATTTAATGTGGCGTAATCCAGCCACAACTTGGCCGAAGCC
1726114 TAAGCATACACCACAAACATGCTAGCCAAATAAACATATAGTATAATAATTATAAGCATGGATAA
196 TAAGCATACACCACAAACATGCTAGCCAAATAAACATATAGTATAATAATTATAAGCATGGATAA
1726179 ACACCACATTTATTTATGTATCAAACTTATCAACATGAGTA
261 ACACCACATTTATTTATGTATCAAACTTATCAACATGAGTA
*
1726220 TACACTCAACCATAGTCGTAAGCTAGTCTTTTTGAAGACTAACCACATGATAAACAATTTTAATA
1 TACACTCAACCATAGTCGCAAGCTAGTCTTTTTGAAGACTAACCACATGATAAACAATTTTAATA
* *
1726285 AAGATTACAAACTTTAAACCTTACCACCCTTTTATGATCACAATCATATTTCTATCTAGACATTT
66 AAGATTACAAACTTTAAACCTTACCACCCTTTTATGATCACAAGCATATTTCCATCTAGACATTT
1726350 ACCATCTCAATACATAATTTTATAAATTTAATGTGGCGTAATCCAGCCACAACTTGGCCGAAGCC
131 ACCATCTCAATACATAATTTTATAAATTTAATGTGGCGTAATCCAGCCACAACTTGGCCGAAGCC
1726415 TAAGCATACACCACAAACATGCTAGCCAAATAAACATATAGTATAATAATTATAAGCATGGATAA
196 TAAGCATACACCACAAACATGCTAGCCAAATAAACATATAGTATAATAATTATAAGCATGGATAA
1726480 ACACCACATTTATTTATGTATCAAACTTATCAACATGAGT
261 ACACCACATTTATTTATGTATCAAACTTATCAACATGAGT
1726520 TAATTCATAA
Statistics
Matches: 293, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
301 293 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (301 bp):
TACACTCAACCATAGTCGCAAGCTAGTCTTTTTGAAGACTAACCACATGATAAACAATTTTAATA
AAGATTACAAACTTTAAACCTTACCACCCTTTTATGATCACAAGCATATTTCCATCTAGACATTT
ACCATCTCAATACATAATTTTATAAATTTAATGTGGCGTAATCCAGCCACAACTTGGCCGAAGCC
TAAGCATACACCACAAACATGCTAGCCAAATAAACATATAGTATAATAATTATAAGCATGGATAA
ACACCACATTTATTTATGTATCAAACTTATCAACATGAGTA
Found at i:1727505 original size:23 final size:22
Alignment explanation
Indices: 1727462--1727505 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
1727452 TTCTAAGTCG
1727462 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
1727485 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
1727506 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:1727614 original size:45 final size:45
Alignment explanation
Indices: 1727550--1727643 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
1727540 AACAGATACT
* *
1727550 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
* *
1727595 CGGTGGAATCAGCACATAGCAACCACTTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
1727640 CGGT
1 CGGT
1727644 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:1727707 original size:51 final size:50
Alignment explanation
Indices: 1727649--1727835 Score: 189
Period size: 51 Copynumber: 3.7 Consensus size: 50
1727639 TCGGTTCACA
* * * *
1727649 TAGTAGCCTGCACATAGTACTACATATGTGACCATTACTATTTGATACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACTATTTGGTACACG
* * * * * *
1727700 TAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATGTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACTATTTGGTACACG
* * * *
1727751 TAGTAGCCTGCACATAGTACTATACATGCGACC-TA-TCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACT-ATT-TGGTACACG
*
1727801 TAGTAGCCTGTACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1727836 GACTTTCACT
Statistics
Matches: 108, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 36 0.33
51 66 0.61
52 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACTATTTGGTACACG
Found at i:1727825 original size:101 final size:102
Alignment explanation
Indices: 1727647--1727831 Score: 259
Period size: 101 Copynumber: 1.8 Consensus size: 102
1727637 GTTCGGTTCA
* * * *
1727647 CATAGTAGCCTGCACATAGTACTACATATGTGACCATTACTATTTGATACATGTAGTAGCCTACA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATTACTATTCGATACACGTAGTAGCCTACA
1727712 CATAGTACTACACACGTGATCGAAACTATGTGGTACG
66 CATAGTACTACACACGTGATCGAAACTATGTGGTACG
* * *
1727749 CATAGTAGCCTGCACATAGTACTATACATGCGACC--TA-TCATTCCGGTACACGTAGTAGCCTG
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATTACT-ATT-CGATACACGTAGTAGCCTA
*
1727811 TACATAGTACTACACACGTGA
64 CACATAGTACTACACACGTGA
1727832 CCATGACTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
99 1 0.01
100 5 0.07
101 35 0.48
102 32 0.44
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATTACTATTCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAACTATGTGGTACG
Found at i:1729291 original size:15 final size:16
Alignment explanation
Indices: 1729273--1729305 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1729263 TTCTTTTATG
1729273 TTCTTTT-AATTTTCT
1 TTCTTTTCAATTTTCT
*
1729288 TTCTTTTCCATTTTCT
1 TTCTTTTCAATTTTCT
1729304 TT
1 TT
1729306 TGCTTCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (16 bp):
TTCTTTTCAATTTTCT
Found at i:1734125 original size:5 final size:5
Alignment explanation
Indices: 1734115--1734147 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
1734105 TAATTGATTC
1734115 AAATA AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
1734148 CCTGAGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:1742117 original size:16 final size:16
Alignment explanation
Indices: 1742096--1742127 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1742086 TGCATGTGAA
1742096 AAATAATAAATTAAAT
1 AAATAATAAATTAAAT
*
1742112 AAATAATACATTAAAT
1 AAATAATAAATTAAAT
1742128 TAAAAAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAATAAATTAAAT
Found at i:1747924 original size:21 final size:21
Alignment explanation
Indices: 1747894--1747960 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1747884 CTAATGTATG
1747894 ATAACTTTAAATAATATAATTA
1 ATAA-TTTAAATAATATAATTA
*
1747916 ATAATTTAAATGATA-ATATT-
1 ATAATTTAAATAATATA-ATTA
* *
1747936 ATATTTTAAATTATACTAA-TA
1 ATAATTTAAATAATA-TAATTA
1747957 ATAA
1 ATAA
1747961 GCTTAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
20 15 0.41
21 17 0.46
22 5 0.14
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (21 bp):
ATAATTTAAATAATATAATTA
Found at i:1752295 original size:166 final size:166
Alignment explanation
Indices: 1752021--1752341 Score: 525
Period size: 166 Copynumber: 1.9 Consensus size: 166
1752011 GTAATACTGA
** * * * *
1752021 TTTTTCTCTAAATCTTTTTTGTCTTGATTTTCTTTTAACCTTTGTTGTCACGTGAGGTTGCAGGG
1 TTTTTCTCTAAATCTTTTCGGTCTTGATTTTCTTTTAACATTTGTTGTCACATGAGGTTGCAAGA
* * *
1752086 ACGTGATACTATTTGATCGTGTCTTTTTGGAATAACCACTTGGTGCATTTGGAAAAACAAGAATT
66 ACGTGACACTATTTGATCGTGTCTTTTTAGAATAACCACTTGGTGCATCTGGAAAAACAAGAATT
1752151 TATTCATTTTCCAGAACATCCCTTGTTGTCACATGG
131 TATTCATTTTCCAGAACATCCCTTGTTGTCACATGG
1752187 TTTTTCTCTAAATCTTTTCGGTCTTGATTTTCTTTTAACATTTGTTGTCACATGAGGTTGCAAGA
1 TTTTTCTCTAAATCTTTTCGGTCTTGATTTTCTTTTAACATTTGTTGTCACATGAGGTTGCAAGA
* * *
1752252 ACGTGACACTATTTGGTCGTGTTTTTTTAGAATAATCACTTGGTGCATCTGGAAAAACAAGAATT
66 ACGTGACACTATTTGATCGTGTCTTTTTAGAATAACCACTTGGTGCATCTGGAAAAACAAGAATT
*
1752317 TATTCATTTTCCAGAACATCGCTTG
131 TATTCATTTTCCAGAACATCCCTTG
1752342 GACAACAATC
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
166 142 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (166 bp):
TTTTTCTCTAAATCTTTTCGGTCTTGATTTTCTTTTAACATTTGTTGTCACATGAGGTTGCAAGA
ACGTGACACTATTTGATCGTGTCTTTTTAGAATAACCACTTGGTGCATCTGGAAAAACAAGAATT
TATTCATTTTCCAGAACATCCCTTGTTGTCACATGG
Found at i:1755210 original size:20 final size:20
Alignment explanation
Indices: 1755185--1755224 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1755175 AAGACGATAC
1755185 TATTAAAAA-ATAATCATAAA
1 TATTAAAAATA-AATCATAAA
*
1755205 TATTAAACATAAATCATAAA
1 TATTAAAAATAAATCATAAA
1755225 ACAGATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
TATTAAAAATAAATCATAAA
Found at i:1758278 original size:46 final size:46
Alignment explanation
Indices: 1758211--1758418 Score: 332
Period size: 46 Copynumber: 4.6 Consensus size: 46
1758201 TTTGAGTACT
1758211 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
1758257 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAACTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
1758303 TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
1758349 TCTGATCAAGTAACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
1758394 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
1758419 ATCATATGTA
Statistics
Matches: 152, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
43 12 0.08
44 4 0.03
45 19 0.12
46 117 0.77
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:1760817 original size:3 final size:3
Alignment explanation
Indices: 1760802--1760844 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1760792 TTTTATATCG
* *
1760802 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1760845 ATTTATACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1768204 original size:22 final size:22
Alignment explanation
Indices: 1768162--1768234 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 22
1768152 GTGTTTTACT
*
1768162 AAAATAACACAAAAGAA-ATAAAA
1 AAAAT-AC-CAAAATAATATAAAA
1768185 AAAATACCAAAATAATATAAAAA
1 AAAATACCAAAATAATAT-AAAA
1768208 AAATATTTACCAAAATAATATAAAA
1 AAA-A--TACCAAAATAATATAAAA
1768233 AA
1 AA
1768235 TTATTTACAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
21 7 0.16
22 4 0.09
23 12 0.27
24 1 0.02
25 6 0.14
26 14 0.32
ACGTcount: A:0.73, C:0.08, G:0.01, T:0.18
Consensus pattern (22 bp):
AAAATACCAAAATAATATAAAA
Found at i:1768232 original size:25 final size:26
Alignment explanation
Indices: 1768189--1768249 Score: 97
Period size: 25 Copynumber: 2.4 Consensus size: 26
1768179 ATAAAAAAAA
1768189 TACCAAAATAATATAAAAAAAATATT
1 TACCAAAATAATATAAAAAAAATATT
*
1768215 TACCAAAATAATAT-AAAAAATTATT
1 TACCAAAATAATATAAAAAAAATATT
*
1768240 TACAAAAATA
1 TACCAAAATA
1768250 TACCAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (26 bp):
TACCAAAATAATATAAAAAAAATATT
Found at i:1768257 original size:25 final size:25
Alignment explanation
Indices: 1768193--1768260 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
1768183 AAAAAATACC
* *
1768193 AAAATAATATAAAAAAAATATTTACC
1 AAAATAATA-CAAAAAAATATTTACA
* *
1768219 AAAATAATATAAAAAATTATTTACA
1 AAAATAATACAAAAAAATATTTACA
1768244 AAAAT-ATACCAAAAAAA
1 AAAATAATA-CAAAAAAA
1768261 GAAAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.08
25 24 0.67
26 9 0.25
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAATAATACAAAAAAATATTTACA
Found at i:1769910 original size:166 final size:166
Alignment explanation
Indices: 1769634--1769957 Score: 524
Period size: 166 Copynumber: 2.0 Consensus size: 166
1769624 TCAATAATAC
* *
1769634 TGGTTTTTCTCTAAATCTTTTCGGTATTGATTTTCTTTTAACTTTTGTTGTCACATGAGGTTGCA
1 TGGTTTTTCTCTAAATCTTTTCGGTATTAATTTTCTTTTAACCTTTGTTGTCACATGAGGTTGCA
*
1769699 GGGACGTGACACTATTTGATCGTGTCTTTTTGAAATAACCACTTGGTGCACCTGGAAAAACAAGA
66 GGAACGTGACACTATTTGATCGTGTCTTTTTGAAATAACCACTTGGTGCACCTGGAAAAACAAGA
1769764 ATTTATTCATTTTCCAAAACATCGCTTGTTGTCACA
131 ATTTATTCATTTTCCAAAACATCGCTTGTTGTCACA
*
1769800 TGGTTTTTCTCTAAATCTTTTCGGTTTTAATTTTCTTTTAACCTTTGTTGTCACATGAGGTTGCA
1 TGGTTTTTCTCTAAATCTTTTCGGTATTAATTTTCTTTTAACCTTTGTTGTCACATGAGGTTGCA
* * * * * *
1769865 GGAATGTGACA-TGATTTGGTCGTGTTTTTTTGGAATAATCACTTGGTGCATCTGGAAAAACAAG
66 GGAACGTGACACT-ATTTGATCGTGTCTTTTTGAAATAACCACTTGGTGCACCTGGAAAAACAAG
* *
1769929 AATTTATTCATTTTTCAGAACATCGCTTG
130 AATTTATTCATTTTCCAAAACATCGCTTG
1769958 GACAACAATC
Statistics
Matches: 145, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
165 1 0.01
166 144 0.99
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (166 bp):
TGGTTTTTCTCTAAATCTTTTCGGTATTAATTTTCTTTTAACCTTTGTTGTCACATGAGGTTGCA
GGAACGTGACACTATTTGATCGTGTCTTTTTGAAATAACCACTTGGTGCACCTGGAAAAACAAGA
ATTTATTCATTTTCCAAAACATCGCTTGTTGTCACA
Found at i:1775141 original size:23 final size:23
Alignment explanation
Indices: 1775102--1775146 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1775092 GATTAGAGCA
*
1775102 TTATTTAATTAATAAAATATAAT
1 TTATTTAATTAATAAAAAATAAT
*
1775125 TTATTTGAATTTA-AAAAAATAA
1 TTATTT-AATTAATAAAAAATAA
1775147 CTAATTAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTATTTAATTAATAAAAAATAAT
Found at i:1777763 original size:21 final size:21
Alignment explanation
Indices: 1777721--1777763 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1777711 TTTTTAACAG
** **
1777721 TAGAAATGGGTAATTTTTTAT
1 TAGAAATGACTAATTTGCTAT
1777742 TAGAAATGACTAATTTGCTAT
1 TAGAAATGACTAATTTGCTAT
1777763 T
1 T
1777764 TGGTCTAACG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (21 bp):
TAGAAATGACTAATTTGCTAT
Found at i:1783971 original size:14 final size:14
Alignment explanation
Indices: 1783952--1783980 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1783942 CATAGTCCTG
1783952 ATTACTAAGAAATT
1 ATTACTAAGAAATT
1783966 ATTACTAAGAAATT
1 ATTACTAAGAAATT
1783980 A
1 A
1783981 AAAATTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (14 bp):
ATTACTAAGAAATT
Found at i:1784692 original size:17 final size:17
Alignment explanation
Indices: 1784670--1784741 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 17
1784660 ACTTTTTCAA
1784670 AATA-TTTTCTGTTGTAG
1 AATATTTTTCTGTTG-AG
*
1784687 AATATTTTTCAGTTGAGG
1 AATATTTTTCTGTTGA-G
*
1784705 AAAATTTTCTGACTGTTGCAG
1 AATATTTT-T--CTGTTG-AG
1784726 AATA-TTTTCTGTTGAG
1 AATATTTTTCTGTTGAG
1784742 GAAAATCCTC
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
16 2 0.04
17 11 0.24
18 17 0.38
19 2 0.04
20 3 0.07
21 9 0.20
22 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.46
Consensus pattern (17 bp):
AATATTTTTCTGTTGAG
Found at i:1790557 original size:17 final size:17
Alignment explanation
Indices: 1790535--1790606 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 17
1790525 ACTTTTTCAA
1790535 AATA-TTTTCTGTTGTAG
1 AATATTTTTCTGTTG-AG
*
1790552 AATATTTTTCAGTTGAGG
1 AATATTTTTCTGTTGA-G
*
1790570 AAAATTTTCTAACTGTTGCAG
1 AATATTTT-T--CTGTTG-AG
1790591 AATA-TTTTCTGTTGAG
1 AATATTTTTCTGTTGAG
1790607 GAAAATCCTC
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
16 2 0.04
17 11 0.24
18 17 0.38
19 2 0.04
20 3 0.07
21 9 0.20
22 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (17 bp):
AATATTTTTCTGTTGAG
Found at i:1795297 original size:39 final size:37
Alignment explanation
Indices: 1795238--1795323 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 37
1795228 AATAAATATA
1795238 TTTATTTTTTATTTTTTATTTTTAAAATAC-A-TTTT
1 TTTATTTTTTATTTTTTATTTTTAAAATACTATTTTT
*
1795273 TTTATTTTTTATTTTTAAAATATTTTTAGAATACT-TTTTT
1 TTTATTTTTTATTTTT----TATTTTTAAAATACTATTTTT
1795313 TTTATTTTTTA
1 TTTATTTTTTA
1795324 AAATTTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
35 16 0.36
39 13 0.30
40 15 0.34
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (37 bp):
TTTATTTTTTATTTTTTATTTTTAAAATACTATTTTT
Done.