Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 8 of 135
Found at i:2377932 original size:122 final size:118
Alignment explanation
Indices: 2377675--2378033 Score: 363
Period size: 122 Copynumber: 3.0 Consensus size: 118
2377665 TTCGAGAAAA
* * * * * *
2377675 AAAATT-TGAAATTTTTTTCGAGAAAAGGAGGTGTCAACCATTTGATGACCAACACCAAAAAAAA
1 AAAATTGT-AAATTTTTTTCAAAAAAAGGGGGTGTCGACCATTTGATGGCCAACACC-AAAAAAT
* * * * * **
2377739 TTTGAAATTTTTTTCTCTAGAAAAGGGGGTGTCGGTCATGCAATGACCAACACCAA
64 TTTG-AATTTTTTTTTCGAGAAAAGGGAGTGTCGGCCATTCAATGACCAACACCCC
* *
2377795 AAAATTTTGAATTTTTTTCTTAAAAAAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAA
1 AAAATTGTAAATTTTTTTC---AAAAAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAA
* * *
2377860 TTTTGAATTTCTTTTTTCGAGAATAGGGAGTGTCGGCCATTTAATGGCCAACACCCC
63 TTTTGAATTT-TTTTTTCGAGAAAAGGGAGTGTCGGCCATTCAATGACCAACACCCC
* * *
2377917 AAAA-TGTAAATTTTTTTCGAGAAAAGGGCGTGTCGACCATTT-A--GCCAACACCAAAAAATTT
1 AAAATTGTAAATTTTTTTCAAAAAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAATTT
* * **
2377978 TAAATTTTTTTTT-GACAAAAAAGAGGTGTCGGCCATTGC-ATGACCAACACCCC
66 TGAATTTTTTTTTCGAGAAAAGGGA-GTGTCGGCCATT-CAATGACCAACACCCC
2378031 AAA
1 AAA
2378034 TTTTTTTTTC
Statistics
Matches: 203, Mismatches: 29, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
113 7 0.03
114 34 0.17
115 24 0.12
117 1 0.00
118 21 0.10
120 16 0.08
121 18 0.09
122 50 0.25
123 32 0.16
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (118 bp):
AAAATTGTAAATTTTTTTCAAAAAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAATTT
TGAATTTTTTTTTCGAGAAAAGGGAGTGTCGGCCATTCAATGACCAACACCCC
Found at i:2379940 original size:37 final size:37
Alignment explanation
Indices: 2379899--2379978 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
2379889 AGAAGCAAAA
2379899 AAGAAAAAACAAAATACAGAATAAGGTAGCAAGATGC
1 AAGAAAAAACAAAATACAGAATAAGGTAGCAAGATGC
* **** *
2379936 AAGAAATATTTTAATACAGAATAAGGTAGTAAGATGC
1 AAGAAAAAACAAAATACAGAATAAGGTAGCAAGATGC
2379973 AAGAAA
1 AAGAAA
2379979 TATTTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.17
Consensus pattern (37 bp):
AAGAAAAAACAAAATACAGAATAAGGTAGCAAGATGC
Found at i:2379979 original size:37 final size:37
Alignment explanation
Indices: 2379911--2379984 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
2379901 GAAAAAACAA
2379911 AATACAGAATAAGGTAGCAAGATGCAAGAAATATTTT
1 AATACAGAATAAGGTAGCAAGATGCAAGAAATATTTT
*
2379948 AATACAGAATAAGGTAGTAAGATGCAAGAAATATTTT
1 AATACAGAATAAGGTAGCAAGATGCAAGAAATATTTT
2379985 TATTTGCTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (37 bp):
AATACAGAATAAGGTAGCAAGATGCAAGAAATATTTT
Found at i:2383725 original size:19 final size:18
Alignment explanation
Indices: 2383681--2383726 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2383671 GAGTTAAACA
* *
2383681 AATTGAGTTATTAGAGTT
1 AATTGAATTATTAGAGTC
*
2383699 AATTGAATTATTCGAGTC
1 AATTGAATTATTAGAGTC
2383717 AACTTGAATT
1 AA-TTGAATT
2383727 TTTTTTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (18 bp):
AATTGAATTATTAGAGTC
Found at i:2383749 original size:13 final size:13
Alignment explanation
Indices: 2383731--2383763 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2383721 TGAATTTTTT
2383731 TTCGAATTTCGAG
1 TTCGAATTTCGAG
2383744 TTCGAATTTCGAG
1 TTCGAATTTCGAG
2383757 TTCGAAT
1 TTCGAAT
2383764 CGAGTTTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.39
Consensus pattern (13 bp):
TTCGAATTTCGAG
Found at i:2395929 original size:129 final size:129
Alignment explanation
Indices: 2395780--2396033 Score: 427
Period size: 129 Copynumber: 2.0 Consensus size: 129
2395770 TACAAATTTG
* * *
2395780 TCTCAAAGTTTGAATATTTAAAACCTATTAACCCAAATATTTAAGATTTTTTATTCCAATATCTT
1 TCTCAAAGCTTGAATATTTAAAACCCATTAACCCAAATATTCAAGATTTTTTATTCCAATATCTT
*
2395845 CTTCCCTTTAAGTTTTTTTGGGTTAATGGGTTTCAAATATTCAAGCTTTGAGACAGATTTGTAA
66 CTTCCCTTTAAGTTTCTTTGGGTTAATGGGTTTCAAATATTCAAGCTTTGAGACAGATTTGTAA
* * *
2395909 TCTCAAAGCTTGAATCTTTAAAACCCATTAACCCAAATATTCAATATTTTTTATTCCAATATTTT
1 TCTCAAAGCTTGAATATTTAAAACCCATTAACCCAAATATTCAAGATTTTTTATTCCAATATCTT
* *
2395974 CTTCCCTTTAAGTTTCTTTGGGTTCATGGGTTTCAAATATTCAAGCTTTGAGTCAGATTT
66 CTTCCCTTTAAGTTTCTTTGGGTTAATGGGTTTCAAATATTCAAGCTTTGAGACAGATTT
2396034 ATAACTAAAG
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 116 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (129 bp):
TCTCAAAGCTTGAATATTTAAAACCCATTAACCCAAATATTCAAGATTTTTTATTCCAATATCTT
CTTCCCTTTAAGTTTCTTTGGGTTAATGGGTTTCAAATATTCAAGCTTTGAGACAGATTTGTAA
Found at i:2400097 original size:37 final size:37
Alignment explanation
Indices: 2400056--2400135 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 37
2400046 AGAAGCAAAA
2400056 AAGAAAAAACAAAATACAGAATAAGGTAGCAAGATGC
1 AAGAAAAAACAAAATACAGAATAAGGTAGCAAGATGC
****** *
2400093 AAGAAATTTTTTAATACAGAATAAGGTAGTAAGATGC
1 AAGAAAAAACAAAATACAGAATAAGGTAGCAAGATGC
2400130 AAGAAA
1 AAGAAA
2400136 TATTTTTTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.55, C:0.07, G:0.19, T:0.19
Consensus pattern (37 bp):
AAGAAAAAACAAAATACAGAATAAGGTAGCAAGATGC
Found at i:2400136 original size:37 final size:38
Alignment explanation
Indices: 2400068--2400142 Score: 134
Period size: 37 Copynumber: 2.0 Consensus size: 38
2400058 GAAAAAACAA
2400068 AATACAGAATAAGGTAGCAAGATGCAAGAAAT-TTTTT
1 AATACAGAATAAGGTAGCAAGATGCAAGAAATATTTTT
*
2400105 AATACAGAATAAGGTAGTAAGATGCAAGAAATATTTTT
1 AATACAGAATAAGGTAGCAAGATGCAAGAAATATTTTT
2400143 TCTTGCTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 31 0.86
38 5 0.14
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (38 bp):
AATACAGAATAAGGTAGCAAGATGCAAGAAATATTTTT
Found at i:2402690 original size:11 final size:11
Alignment explanation
Indices: 2402659--2402700 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2402649 CCCAATTTGG
2402659 ATTTTAAATTA
1 ATTTTAAATTA
* *
2402670 AGTTTGAATTA
1 ATTTTAAATTA
*
2402681 ATTTTAAATTT
1 ATTTTAAATTA
2402692 A-TTTAAATT
1 ATTTTAAATT
2402701 TAAATTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:2402703 original size:22 final size:23
Alignment explanation
Indices: 2402659--2402708 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
2402649 CCCAATTTGG
*
2402659 ATTTTAAATTAAGTTTGAATT-A
1 ATTTTAAATTAAGTTTAAATTAA
*
2402681 ATTTTAAATTTA-TTTAAATTTAA
1 ATTTTAAATTAAGTTTAAA-TTAA
2402704 ATTTT
1 ATTTT
2402709 TTTAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 13 0.54
23 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
ATTTTAAATTAAGTTTAAATTAA
Found at i:2402730 original size:16 final size:16
Alignment explanation
Indices: 2402678--2402721 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
2402668 TAAGTTTGAA
*
2402678 TTAATTTTAAATTTAT
1 TTAAATTTAAATTTAT
*
2402694 TTAAATTTAAATTTTT
1 TTAAATTTAAATTTAT
2402710 TTAAATTTAAAT
1 TTAAATTTAAAT
2402722 ACATTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:2403568 original size:15 final size:15
Alignment explanation
Indices: 2403550--2403604 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
2403540 ATTATTAATA
*
2403550 AATAATATTAACATT
1 AATAATAATAACATT
* *
2403565 AATATTAATAACATA
1 AATAATAATAACATT
2403580 ACAGTAATAAT-A-ATT
1 A-A-TAATAATAACATT
2403595 AATAATAATA
1 AATAATAATA
2403605 GTGACTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
13 7 0.22
14 1 0.03
15 16 0.50
16 2 0.06
17 6 0.19
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (15 bp):
AATAATAATAACATT
Found at i:2404033 original size:11 final size:11
Alignment explanation
Indices: 2404011--2404052 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
2404001 TAAAATTTTC
2404011 AAGAAGAAGAGA
1 AAGAA-AAGAGA
*
2404023 AGGAAAAGAGA
1 AAGAAAAGAGA
2404034 AAGAAAAGAGA
1 AAGAAAAGAGA
2404045 AAGAAAAG
1 AAGAAAAG
2404053 GAAGGGACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 24 0.86
12 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (11 bp):
AAGAAAAGAGA
Found at i:2406117 original size:28 final size:28
Alignment explanation
Indices: 2406086--2406353 Score: 156
Period size: 29 Copynumber: 9.2 Consensus size: 28
2406076 AATCGGGCCG
* * *
2406086 AAAATGAAATTTTGGAAAATTTAGGGGT
1 AAAATGGAATTTTGGGAAATTCAGGGGT
*
2406114 AAAATGGTAATTTTGGTGAAA-TCAGGGTT
1 AAAATGG-AATTTTGG-GAAATTCAGGGGT
*
2406143 AAAAATGGAATTTT-GGAAAGTTCGGGGGT
1 -AAAATGGAATTTTGGGAAA-TTCAGGGGT
* *
2406172 AAAATGGCAATTTTGGTGAAATTGA-GGTT
1 AAAATGG-AATTTTGG-GAAATTCAGGGGT
* **
2406201 AAAAATGGAATTTTGGGAAGTTTGGGGGT
1 -AAAATGGAATTTTGGGAAATTCAGGGGT
2406230 AAAATGGTAATTTTTGGTGAAA-TC-GGGGTT
1 AAAATGG-AA-TTTTGG-GAAATTCAGGGG-T
* *
2406260 AAAAATGGAATTTT-GGAATGTTCGGGGGT
1 -AAAATGGAATTTTGGGAA-ATTCAGGGGT
* * * *
2406289 AAATTGGTCATTTTTGGTG-AAGTCAGGGTT
1 AAAATGG--AATTTTGG-GAAATTCAGGGGT
**
2406319 AAAAATGGAATTTT-GGAAAGTTTTGGGGT
1 -AAAATGGAATTTTGGGAAA-TTCAGGGGT
2406348 AAAATG
1 AAAATG
2406354 ATAATTTTTG
Statistics
Matches: 187, Mismatches: 28, Indels: 50
0.71 0.11 0.19
Matches are distributed among these distances:
27 8 0.04
28 42 0.22
29 69 0.37
30 45 0.24
31 22 0.12
32 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGGAAATTCAGGGGT
Found at i:2406274 original size:59 final size:59
Alignment explanation
Indices: 2406051--2406364 Score: 420
Period size: 59 Copynumber: 5.4 Consensus size: 59
2406041 GGACTTGCGA
* *** * * *
2406051 GGGGCAAAATGGTAATTTTTGGTGAAATC-GGGCCGAAAATGAAATTTTGGAAAATTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
*
2406109 GGGGTAAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
* * *
2406167 GGGGTAAAATGGCAA-TTTTGGTGAAAT-TGAGGTTAAAAATGGAATTTTGGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAG-GGTTAAAAATGGAATTTTGGAAAGTTTG
* * *
2406225 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAATGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
* * * *
2406284 GGGGTAAATTGGTCATTTTTGGTGAAGTCAGGGTTAAAAATGGAATTTTGGAAAGTTTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
*
2406343 GGGGTAAAATGATAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
2406365 ACAGTCCAGG
Statistics
Matches: 225, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
57 14 0.06
58 102 0.45
59 108 0.48
60 1 0.00
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
Found at i:2406375 original size:59 final size:58
Alignment explanation
Indices: 2406051--2406363 Score: 387
Period size: 58 Copynumber: 5.4 Consensus size: 58
2406041 GGACTTGCGA
* *** * * *
2406051 GGGGCAAAATGGTAATTTTTGGTGAAATC-GGGCCGAAAATGAAATTTTGGAAAATTTA
1 GGGGTAAAATGGTAATTTTT-GTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
* *
2406109 GGGGTAAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
* * * *
2406167 GGGGTAAAATGGCAATTTTGGTGAAAT-TGAGGTTAAAAATGGAATTTTGGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGTGAAATCAG-GGTTAAAAATGGAATTTTGGAAAGTTTG
* * *
2406225 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAATGTTCG
1 GGGGTAAAATGGTAATTTTT-GTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
* * * *
2406284 GGGGTAAATTGGTCATTTTTGGTGAAGTCAGGGTTAAAAATGGAATTTTGGAAAGTTTT
1 GGGGTAAAATGGTAATTTTT-GTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
*
2406343 GGGGTAAAATGATAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
2406364 GACAGTCCAG
Statistics
Matches: 222, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
57 9 0.04
58 111 0.50
59 101 0.45
60 1 0.00
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.33
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
Found at i:2406621 original size:162 final size:162
Alignment explanation
Indices: 2406435--2406772 Score: 559
Period size: 162 Copynumber: 2.1 Consensus size: 162
2406425 AGCATCCAGA
** *
2406435 AGTCAAAGGACGAATTTGTAAATCTTGAAAAATTCTCAGGCCAATTTTGTAATTAAGCAGAAGTT
1 AGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTCAGGCCAATTTTGTAATTAAGCAGAAGTT
*
2406500 GATTTGAAGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACGTAAAAAAACTAAAAA
66 GATTTGAAGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACGTAAAAAAACCAAAAA
* *
2406565 GTGACACGTGGCGACCTCTGGTGCAGTTAAAC
131 GTGACACATGGCGACCTCTGGTGCAGTCAAAC
**
2406597 AGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAGCAGAAGTT
1 AGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTCAGGCCAATTTTGTAATTAAGCAGAAGTT
* * *
2406662 GATTTGAGGATTAGATTAAAACAAATTAAAAATGACAGGGACTAGATACGTAAATAAACCAAAAA
66 GATTTGAAGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACGTAAAAAAACCAAAAA
*
2406727 GTGACACATGGCGGCCTCTGGTGCAGTCAAAC
131 GTGACACATGGCGACCTCTGGTGCAGTCAAAC
*
2406759 AGTCAAAAGATTAA
1 AGTCAAAGGATTAA
2406773 ATTGAAAACT
Statistics
Matches: 163, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 163 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (162 bp):
AGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTCAGGCCAATTTTGTAATTAAGCAGAAGTT
GATTTGAAGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACGTAAAAAAACCAAAAA
GTGACACATGGCGACCTCTGGTGCAGTCAAAC
Found at i:2407584 original size:21 final size:20
Alignment explanation
Indices: 2407525--2407584 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
2407515 TTCTTTTTTT
*
2407525 TTATTAAATATTTATTATTA
1 TTATTAAAAATTTATTATTA
*
2407545 TTATTAAAAATGTATTTATTA
1 TTATTAAAAATTTA-TTATTA
*
2407566 TTATTAAAACCTTTATTAT
1 TTATTAAAA-ATTTATTAT
2407585 CATAACTGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.35
21 19 0.56
22 3 0.09
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATTAAAAATTTATTATTA
Found at i:2408429 original size:12 final size:12
Alignment explanation
Indices: 2408403--2408460 Score: 61
Period size: 11 Copynumber: 5.2 Consensus size: 12
2408393 TATAATAATA
*
2408403 TTAAATTTAAA-
1 TTAAAATTAAAT
*
2408414 TTAAAATTGAAT
1 TTAAAATTAAAT
2408426 TTAAAA-TAAAT
1 TTAAAATTAAAT
2408437 TTAAAATTAAA-
1 TTAAAATTAAAT
*
2408448 AT-AAATTAAAT
1 TTAAAATTAAAT
2408459 TT
1 TT
2408461 CAAAGTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 8 0.21
11 21 0.54
12 10 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
TTAAAATTAAAT
Found at i:2408469 original size:17 final size:16
Alignment explanation
Indices: 2408389--2408460 Score: 81
Period size: 17 Copynumber: 4.3 Consensus size: 16
2408379 TTCTTTTTTT
*
2408389 AATTTATAATAATATTA
1 AATTTAAAATAA-ATTA
* *
2408406 AATTTAAATTAAAATTG
1 AATTTAAAAT-AAATTA
2408423 AATTTAAAATAAATTTA
1 AATTTAAAATAAA-TTA
*
2408440 AAATTAAAATAAATTA
1 AATTTAAAATAAATTA
2408456 AATTT
1 AATTT
2408461 CAAAGTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
16 10 0.22
17 34 0.74
18 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (16 bp):
AATTTAAAATAAATTA
Found at i:2408469 original size:22 final size:22
Alignment explanation
Indices: 2408427--2408470 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2408417 AAATTGAATT
*
2408427 TAAAATAAATTTAAAATTAAAA
1 TAAAATAAATTTAAAAGTAAAA
* *
2408449 TAAATTAAATTTCAAAGTAAAA
1 TAAAATAAATTTAAAAGTAAAA
2408471 ATGGTTTGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
TAAAATAAATTTAAAAGTAAAA
Found at i:2408597 original size:58 final size:58
Alignment explanation
Indices: 2408506--2408678 Score: 208
Period size: 58 Copynumber: 2.9 Consensus size: 58
2408496 GCTCCAACAT
* *
2408506 TTCCAAAATTCTATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACC
1 TTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTA-CATTTTACCCCCGAACC
* * *
2408565 TTCCAAAATTCCA-TTTTAACCCCAATTTCACCATAAATTATCATTTTACCCTCGAATC
1 TTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTA-CATTTTACCCCCGAACC
* * *
2408623 TTCTAAAATCCCATTTTTAACCCCGAATTTTC-CC-AAAATTACATTTTTGCCCCCGA
1 TTCCAAAATTCCATTTTTAACCCC-AA-TTTCACCAAAAATTACA-TTTTACCCCCGA
2408679 GAATCAAAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
58 53 0.54
59 38 0.38
60 4 0.04
61 4 0.04
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.35
Consensus pattern (58 bp):
TTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACATTTTACCCCCGAACC
Found at i:2408670 original size:30 final size:28
Alignment explanation
Indices: 2408504--2408669 Score: 112
Period size: 30 Copynumber: 5.7 Consensus size: 28
2408494 GGGCTCCAAC
2408504 ATTT-CCAAAATT-CTATTTTTAACCCCG-
1 ATTTCCCAAAATTAC-A-TTTTAACCCCGA
*
2408531 ATTTCACCAAAAATTACCATTTTACCCCCGA
1 ATTTC-CC-AAAATTA-CATTTTAACCCCGA
* *
2408562 ACCTT-CCAAAATTCCATTTTAACCCC-A
1 A-TTTCCCAAAATTACATTTTAACCCCGA
2408589 ATTTCACCATAAATTATCATTTT-ACCCTCGA
1 ATTTC-CCA-AAATTA-CATTTTAACCC-CGA
* **
2408620 ATCTT-CTAAAATCCCATTTTTAACCCCGA
1 AT-TTCCCAAAATTACA-TTTTAACCCCGA
2408649 ATTTTCCCAAAATTACATTTT
1 A-TTTCCCAAAATTACATTTT
2408670 TGCCCCCGAG
Statistics
Matches: 109, Mismatches: 12, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
26 2 0.02
27 6 0.06
28 16 0.15
29 35 0.32
30 40 0.37
31 5 0.05
32 5 0.05
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (28 bp):
ATTTCCCAAAATTACATTTTAACCCCGA
Found at i:2408675 original size:29 final size:28
Alignment explanation
Indices: 2408506--2408675 Score: 93
Period size: 29 Copynumber: 5.8 Consensus size: 28
2408496 GCTCCAACAT
2408506 TTCCAAAATT-CTATTTTTAACCCCG-AT-
1 TTCCAAAATTAC-ATTTTT-ACCCCGAATC
*
2408533 TTCACCAAAAATTACCA-TTTTACCCCCGAACC
1 TT--CC-AAAATTA-CATTTTTA-CCCCGAATC
* *
2408565 TTCCAAAATTCCATTTTAACCCC-AAT-
1 TTCCAAAATTACATTTTTACCCCGAATC
2408591 TTCACCATAAATTATCA-TTTTACCCTCGAATC
1 TT--CCA-AAATTA-CATTTTTACCC-CGAATC
* ** *
2408623 TTCTAAAATCCCATTTTTAACCCCGAATT
1 TTCCAAAATTACATTTTT-ACCCCGAATC
*
2408652 TTCCCAAAATTACATTTTTGCCCC
1 TT-CCAAAATTACATTTTTACCCC
2408676 CGAGAATCAA
Statistics
Matches: 110, Mismatches: 14, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
26 2 0.02
27 4 0.04
28 11 0.10
29 44 0.40
30 39 0.35
31 5 0.05
32 5 0.05
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.35
Consensus pattern (28 bp):
TTCCAAAATTACATTTTTACCCCGAATC
Found at i:2413382 original size:5 final size:5
Alignment explanation
Indices: 2413372--2413401 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2413362 TTTAGAGAAT
*
2413372 GTTGG GTTGG GTTGG GTTGG GTTAG GTTGG
1 GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG
2413402 ATTTAAGGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.00, G:0.57, T:0.40
Consensus pattern (5 bp):
GTTGG
Found at i:2421182 original size:23 final size:23
Alignment explanation
Indices: 2421152--2421209 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
2421142 CTGACGTAGC
* *
2421152 ATCCAGTCAGCAGCTTCTAGAAG
1 ATCCAGTCAGCAGCTTCCAAAAG
2421175 ATCCAGTCAGCAGCTTCCAAAAG
1 ATCCAGTCAGCAGCTTCCAAAAG
* *
2421198 GTCTAGTCAGCA
1 ATCCAGTCAGCA
2421210 AGGATGGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (23 bp):
ATCCAGTCAGCAGCTTCCAAAAG
Found at i:2427582 original size:16 final size:14
Alignment explanation
Indices: 2427551--2427597 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
2427541 TTTATTTTGA
*
2427551 TTATTTATATTATT
1 TTATTTTTATTATT
2427565 TTATTTTTACTTATTT
1 TTATTTTTA-TTA-TT
*
2427581 TTATTTTTGTTATT
1 TTATTTTTATTATT
2427595 TTA
1 TTA
2427598 GGTATGCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 13 0.45
15 6 0.21
16 10 0.34
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (14 bp):
TTATTTTTATTATT
Found at i:2427597 original size:24 final size:22
Alignment explanation
Indices: 2427536--2427597 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
2427526 TTTTTTCGTC
*
2427536 ATTAATTTATTTTGATTATTTAT
1 ATTATTTTATTTT-ATTATTTAT
*
2427559 ATTATTTTATTTTTACTTATTTTT
1 ATTATTTTA-TTTTA-TTATTTAT
*
2427583 ATTTTTGTTATTTTA
1 ATTATT-TTATTTTA
2427598 GGTATGCGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 9 0.27
24 21 0.64
25 3 0.09
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (22 bp):
ATTATTTTATTTTATTATTTAT
Found at i:2428506 original size:8 final size:8
Alignment explanation
Indices: 2428495--2428538 Score: 56
Period size: 7 Copynumber: 5.5 Consensus size: 8
2428485 AAAAGGTAAT
2428495 AAAAGAAA
1 AAAAGAAA
2428503 AAAA-AAA
1 AAAAGAAA
2428510 AAAA-AAA
1 AAAAGAAA
2428517 AAAGAGAAA
1 AAA-AGAAA
2428526 AAGAAGAAA
1 AA-AAGAAA
2428535 AAAA
1 AAAA
2428539 ATGGTTGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 13 0.39
8 7 0.21
9 12 0.36
10 1 0.03
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:2428519 original size:21 final size:21
Alignment explanation
Indices: 2428495--2428539 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2428485 AAAAGGTAAT
2428495 AAAAGAAAAAAAAAAAAAAAA
1 AAAAGAAAAAAAAAAAAAAAA
* * *
2428516 AAAAGAGAAAAAGAAGAAAAA
1 AAAAGAAAAAAAAAAAAAAAA
2428537 AAA
1 AAA
2428540 TGGTTGCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAAAAAAAAAAA
Found at i:2431024 original size:33 final size:33
Alignment explanation
Indices: 2430987--2431052 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2430977 GAAAAAGATA
* *
2430987 AAATTGAATAATTGGGTAGACATTTTATAACTT
1 AAATTGAATAATTAGATAGACATTTTATAACTT
*
2431020 AAATTGAATAATTAGATAGTCATTTTATAACTT
1 AAATTGAATAATTAGATAGACATTTTATAACTT
2431053 TTCATAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (33 bp):
AAATTGAATAATTAGATAGACATTTTATAACTT
Found at i:2440177 original size:33 final size:33
Alignment explanation
Indices: 2440140--2440205 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2440130 GAAAAAGATA
* *
2440140 AAATTGAATAATTGGGTAGACATTTTATAACTT
1 AAATTGAATAATTAGGTAGACATATTATAACTT
*
2440173 AAATTGAATAATTAGGTAGTCATATTATAACTT
1 AAATTGAATAATTAGGTAGACATATTATAACTT
2440206 TTCATAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (33 bp):
AAATTGAATAATTAGGTAGACATATTATAACTT
Found at i:2440584 original size:4 final size:4
Alignment explanation
Indices: 2440575--2440612 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
2440565 AAAAATTGAG
2440575 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
2440613 GGGAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2442979 original size:8 final size:8
Alignment explanation
Indices: 2442966--2443003 Score: 67
Period size: 8 Copynumber: 4.6 Consensus size: 8
2442956 TATTGGTGCT
2442966 CATCTCAA
1 CATCTCAA
2442974 CATCTCAA
1 CATCTCAA
2442982 CATCTCAA
1 CATCTCAA
2442990 CATCGTCAA
1 CATC-TCAA
2442999 CATCT
1 CATCT
2443004 TATGTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (8 bp):
CATCTCAA
Found at i:2448747 original size:6 final size:6
Alignment explanation
Indices: 2448733--2448763 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2448723 TGTGTTGTTG
*
2448733 TGTCTT TGTCGT TGTCTT TGTCTT TGTCTT T
1 TGTCTT TGTCTT TGTCTT TGTCTT TGTCTT T
2448764 CACTTTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.16, G:0.19, T:0.65
Consensus pattern (6 bp):
TGTCTT
Found at i:2448785 original size:2 final size:2
Alignment explanation
Indices: 2448778--2448811 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2448768 TTCTGACTCC
* *
2448778 CT CT CT CT CT GT CT CT CT CT TT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2448812 TCCATTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2449049 original size:17 final size:17
Alignment explanation
Indices: 2449027--2449086 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 17
2449017 ATATTCATTA
2449027 TATGTAAATTTTAATTT
1 TATGTAAATTTTAATTT
*
2449044 TATGT-AATTTT-A-TA
1 TATGTAAATTTTAATTT
*
2449058 TAT-TAAATATTAATTT
1 TATGTAAATTTTAATTT
* *
2449074 AATTTAAATTTTA
1 TATGTAAATTTTA
2449087 TAAATTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
13 1 0.03
14 9 0.26
15 2 0.06
16 9 0.26
17 13 0.38
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TATGTAAATTTTAATTT
Found at i:2449084 original size:31 final size:30
Alignment explanation
Indices: 2449025--2449110 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
2449015 TAATATTCAT
* *
2449025 TATATGTAAATTTTAATTTTATGTAATTTTA
1 TATAT-TAAATATTAATTTAATGTAATTTTA
*
2449056 TATATTAAATATTAATTTAATTTAAATTTTA
1 TATATTAAATATTAATTTAATGT-AATTTTA
* *
2449087 TAAATTATTAATA-TAATTTTATGT
1 TATATTA--AATATTAATTTAATGT
2449111 GAACATATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
30 15 0.33
31 18 0.39
32 9 0.20
33 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (30 bp):
TATATTAAATATTAATTTAATGTAATTTTA
Found at i:2450531 original size:30 final size:30
Alignment explanation
Indices: 2450491--2450580 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
2450481 TTTTTAATAC
*
2450491 ATAT-AATTAAATTA-AAATTAAATTTTTAT
1 ATATAAATTAAATTACAAA-TAAAATTTTAT
*
2450520 CTATAAATTAAATTACAAATAAAATTTTAT
1 ATATAAATTAAATTACAAATAAAATTTTAT
*
2450550 ATAT-AATT--A-TACAAAATAAAAATTTAT
1 ATATAAATTAAATTAC-AAATAAAATTTTAT
2450577 ATAT
1 ATAT
2450581 TCACGTTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.06
27 18 0.33
29 7 0.13
30 23 0.43
31 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
ATATAAATTAAATTACAAATAAAATTTTAT
Found at i:2450550 original size:26 final size:27
Alignment explanation
Indices: 2450521--2450577 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
2450511 AATTTTTATC
*
2450521 TATAAATTAAAT-TAC-AAATAAAATTT
1 TATAAA-TAAATATACAAAATAAAAATT
* *
2450547 TATATATAATTATACAAAATAAAAATT
1 TATAAATAAATATACAAAATAAAAATT
2450574 TATA
1 TATA
2450578 TATTCACGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 4 0.15
26 8 0.31
27 14 0.54
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (27 bp):
TATAAATAAATATACAAAATAAAAATT
Found at i:2452595 original size:17 final size:17
Alignment explanation
Indices: 2452573--2452606 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2452563 TTTAAGTGTA
*
2452573 ATTTATCTATATAATAT
1 ATTTATATATATAATAT
*
2452590 ATTTATATATATTATAT
1 ATTTATATATATAATAT
2452607 GTTATTTGCA
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:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATATATATAATAT
Found at i:2454792 original size:24 final size:24
Alignment explanation
Indices: 2454765--2454817 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2454755 TAGGGGTAGG
*
2454765 ATCTGTGTCTACATTTATATCTGA
1 ATCTGTGTCTACATTTACATCTGA
* *
2454789 ATCTGTGTCTGCATTTGCATCTGA
1 ATCTGTGTCTACATTTACATCTGA
2454813 ATCTG
1 ATCTG
2454818 AATATGCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (24 bp):
ATCTGTGTCTACATTTACATCTGA
Found at i:2456869 original size:19 final size:18
Alignment explanation
Indices: 2456845--2456885 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2456835 AAAAGAAGCA
2456845 TTTTATAGTTTTTATTGAT
1 TTTTATAGTTTTTATT-AT
**
2456864 TTTTATTTTTTTTATTAT
1 TTTTATAGTTTTTATTAT
2456882 TTTT
1 TTTT
2456886 CGCTACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTATAGTTTTTATTAT
Found at i:2457047 original size:19 final size:20
Alignment explanation
Indices: 2457004--2457058 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2456994 ATTTTTTTAC
* *
2457004 TATTTTTAATATATTTAATA
1 TATTTTTATTAAATTTAATA
2457024 TATTTTTATTAAATTTAATA
1 TATTTTTATTAAATTTAATA
*
2457044 -ATTTTTATTGAATTT
1 TATTTTTATTAAATTT
2457059 TTTTAATCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTTTATTAAATTTAATA
Found at i:2457301 original size:91 final size:87
Alignment explanation
Indices: 2457192--2457374 Score: 226
Period size: 91 Copynumber: 2.1 Consensus size: 87
2457182 TTGCATTTTA
* *
2457192 AAAGTTCAATTACTCAATTGAGTGAAAAAAAAGATCAAGGG-TTTAATTGCATTTTTTCAAAAAA
1 AAAGTTCAAATACTCAATTAAGTGAAAAAAAAG-T--AGGGATTTAATTGCATTTTTT-AAAAAA
* *
2457256 GTTT-GAGAGCCTTTTTTATGTATTATG
62 -TTTAAAGA-CCTTTTTGATGTATTATG
* *
2457283 AAAGTTCAAATACTCAATTAAGTGTAAAAAAAGTAGGGATTTAATTGTATTTTTTAAAAAATTTA
1 AAAGTTCAAATACTCAATTAAGTGAAAAAAAAGTAGGGATTTAATTGCATTTTTTAAAAAATTTA
* *
2457348 AAGATCTTTTTGATGTATTTTG
66 AAGACCTTTTTGATGTATTATG
2457370 AAAGT
1 AAAGT
2457375 ATAAGTATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
87 23 0.28
88 13 0.16
89 15 0.18
90 1 0.01
91 30 0.37
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (87 bp):
AAAGTTCAAATACTCAATTAAGTGAAAAAAAAGTAGGGATTTAATTGCATTTTTTAAAAAATTTA
AAGACCTTTTTGATGTATTATG
Found at i:2458722 original size:34 final size:34
Alignment explanation
Indices: 2458674--2458748 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
2458664 ATTTCTTCAA
*
2458674 ATTTCAGACATAATAAATTACGAAAACAGA-AGCC
1 ATTTTAGACATAATAAATTACGAAAACA-ACAGCC
* *
2458708 ATTTTAGACATAATAAATTATGAAAACAACGGCC
1 ATTTTAGACATAATAAATTACGAAAACAACAGCC
2458742 ATTTTAG
1 ATTTTAG
2458749 GCAATCATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 1 0.03
34 36 0.97
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (34 bp):
ATTTTAGACATAATAAATTACGAAAACAACAGCC
Found at i:2461905 original size:59 final size:57
Alignment explanation
Indices: 2461736--2461999 Score: 397
Period size: 57 Copynumber: 4.6 Consensus size: 57
2461726 ACCATAACAG
* * * * *
2461736 AACAGCAGCCGTTTTAGACAACCATTTCTTCAAATGTC--ACAGAATAAATTCTGGA
1 AACAGCAGCCATTTTAGACAACCATTTCTTCAAATTTCAGACATAATAAATTGTGAA
2461791 AACAGCAGCCATTTTAGACAACCATTTCTTCAAATTTCAGACATAATAAATTGTGAA
1 AACAGCAGCCATTTTAGACAACCATTTCTTCAAATTTCAGACATAATAAATTGTGAA
*
2461848 AACAGCAGCCATTTTAGACAACCATTTGAATTCAAATTTCAGACATAATAAATTGTGAA
1 AACAGCAGCCATTTTAGACAACCATTT--CTTCAAATTTCAGACATAATAAATTGTGAA
* * *
2461907 AACAGCAGCCATTTTAGACAATCATTTCTTCAAATTTCTGACATAATAAATTATGAA
1 AACAGCAGCCATTTTAGACAACCATTTCTTCAAATTTCAGACATAATAAATTGTGAA
* *
2461964 AACAACAGCCATTTTAGACAATCATTTCTTCAAATT
1 AACAGCAGCCATTTTAGACAACCATTTCTTCAAATT
2462000 CTAGCACGTT
Statistics
Matches: 194, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
55 36 0.19
57 103 0.53
59 55 0.28
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (57 bp):
AACAGCAGCCATTTTAGACAACCATTTCTTCAAATTTCAGACATAATAAATTGTGAA
Found at i:2461936 original size:116 final size:112
Alignment explanation
Indices: 2461736--2461998 Score: 382
Period size: 116 Copynumber: 2.3 Consensus size: 112
2461726 ACCATAACAG
* * *
2461736 AACAGCAGCCGTTTTAGACAACCATTTCTTCAAATGTCACAGAATAAATTCTGGAAACAGCAGCC
1 AACAGCAGCCATTTTAGACAACCATTTATTCAAATGTCACAGAATAAATTCTGAAAACAGCAGCC
*
2461801 ATTTTAGACAACCATTTCTTCAAATTTCAGACATAATAAATTGTGAA
66 ATTTTAGACAACCATTTCTTCAAATTTCAGACATAATAAATTATGAA
* * *
2461848 AACAGCAGCCATTTTAGACAACCATTTGAATTCAAATTTCAGACATAATAAATTGTGAAAACAGC
1 AACAGCAGCCATTTTAGACAACCATTT--ATTCAAATGTC--ACAGAATAAATTCTGAAAACAGC
* *
2461913 AGCCATTTTAGACAATCATTTCTTCAAATTTCTGACATAATAAATTATGAA
62 AGCCATTTTAGACAACCATTTCTTCAAATTTCAGACATAATAAATTATGAA
* * *
2461964 AACAACAGCCATTTTAGACAATCATTTCTTCAAAT
1 AACAGCAGCCATTTTAGACAACCATTTATTCAAAT
2461999 TCTAGCACGT
Statistics
Matches: 135, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
112 26 0.19
114 16 0.12
116 93 0.69
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (112 bp):
AACAGCAGCCATTTTAGACAACCATTTATTCAAATGTCACAGAATAAATTCTGAAAACAGCAGCC
ATTTTAGACAACCATTTCTTCAAATTTCAGACATAATAAATTATGAA
Found at i:2466655 original size:10 final size:10
Alignment explanation
Indices: 2466640--2466799 Score: 72
Period size: 10 Copynumber: 16.6 Consensus size: 10
2466630 TGGCATGTGG
2466640 TAAAAAATTA
1 TAAAAAATTA
2466650 TAAAAAA--A
1 TAAAAAATTA
*
2466658 T--AAAATCA
1 TAAAAAATTA
*
2466666 -ATAAAAGTTA
1 TA-AAAAATTA
2466676 T-AAAAATTA
1 TAAAAAATTA
* **
2466685 TTAAATTTTAA
1 TAAAAAATT-A
2466696 TAAAAAATTA
1 TAAAAAATTA
2466706 TAAAAAA-T-
1 TAAAAAATTA
2466714 T-AAAAATTA
1 TAAAAAATTA
*
2466723 TTAAAAATTA
1 TAAAAAATTA
*
2466733 GAAAAAA-TA
1 TAAAAAATTA
*
2466742 TAAAAATTGTA
1 TAAAAAAT-TA
*
2466753 AAAAAAATTA
1 TAAAAAATTA
** * *
2466763 CGAAAATTTT
1 TAAAAAATTA
*
2466773 TATAAAAATTG
1 TA-AAAAATTA
2466784 T-AAAAATATA
1 TAAAAAAT-TA
2466794 TAAAAA
1 TAAAAA
2466800 TATATAGAAA
Statistics
Matches: 111, Mismatches: 23, Indels: 31
0.67 0.14 0.19
Matches are distributed among these distances:
6 4 0.04
7 5 0.05
8 5 0.05
9 23 0.21
10 48 0.43
11 26 0.23
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:2466678 original size:9 final size:9
Alignment explanation
Indices: 2466666--2466756 Score: 76
Period size: 9 Copynumber: 9.8 Consensus size: 9
2466656 AATAAAATCA
*
2466666 ATAAAAGTT
1 ATAAAAATT
2466675 ATAAAAATT
1 ATAAAAATT
**
2466684 ATTAAATTTT
1 A-TAAAAATT
2466694 AATAAAAAATT
1 -AT-AAAAATT
*
2466705 ATAAAAAAT
1 ATAAAAATT
2466714 -TAAAAATT
1 ATAAAAATT
2466722 ATTAAAAATT
1 A-TAAAAATT
* *
2466732 AGAAAAAAT
1 ATAAAAATT
2466741 ATAAAAATT
1 ATAAAAATT
*
2466750 GTAAAAA
1 ATAAAAA
2466757 AAATTACGAA
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
8 7 0.11
9 34 0.52
10 18 0.28
11 6 0.09
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:2466720 original size:17 final size:18
Alignment explanation
Indices: 2466696--2466757 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 18
2466686 TAAATTTTAA
2466696 TAAAAAATTATAAAAAAT
1 TAAAAAATTATAAAAAAT
*
2466714 T-AAAAATTATTAAAAAT
1 TAAAAAATTATAAAAAAT
* *
2466731 TAGAAAAAATATAAAAATT
1 TA-AAAAATTATAAAAAAT
2466750 GTAAAAAA
1 -TAAAAAA
2466758 AATTACGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 16 0.43
18 1 0.03
19 18 0.49
20 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (18 bp):
TAAAAAATTATAAAAAAT
Found at i:2466720 original size:57 final size:57
Alignment explanation
Indices: 2466640--2466762 Score: 151
Period size: 57 Copynumber: 2.2 Consensus size: 57
2466630 TGGCATGTGG
* * * * *
2466640 TAAAAAATTATAAAAAAATAAAATCAATAAAAGTTATAAAAATTAT-TAAATTTTAA
1 TAAAAAATTATAAAAAAATAAAATCAATAAAAATTAGAAAAAATATAAAAATTGTAA
* * *
2466696 TAAAAAATTATAAAAAATTAAAAATTATTAAAAATTAGAAAAAATATAAAAATTGTAA
1 TAAAAAATTATAAAAAAAT-AAAATCAATAAAAATTAGAAAAAATATAAAAATTGTAA
2466754 -AAAAAATTA
1 TAAAAAATTA
2466763 CGAAAATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
56 18 0.32
57 31 0.54
58 8 0.14
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (57 bp):
TAAAAAATTATAAAAAAATAAAATCAATAAAAATTAGAAAAAATATAAAAATTGTAA
Found at i:2466800 original size:10 final size:10
Alignment explanation
Indices: 2466642--2466819 Score: 64
Period size: 9 Copynumber: 18.5 Consensus size: 10
2466632 GCATGTGGTA
2466642 AAAAAT-TAT
1 AAAAATATAT
2466651 AAAAA-A-AT
1 AAAAATATAT
2466659 -AAAATCA-AT
1 AAAAAT-ATAT
*
2466668 AAAAGT-TAT
1 AAAAATATAT
2466677 AAAAAT-TAT
1 AAAAATATAT
* * *
2466686 TAAATTTTAAT
1 AAAAATAT-AT
2466697 AAAAA-ATTAT
1 AAAAATA-TAT
2466707 AAAAA-AT-T
1 AAAAATATAT
2466715 AAAAAT-TATT
1 AAAAATATA-T
*
2466725 AAAAAT-TAG
1 AAAAATATAT
2466734 AAAAA-ATAT
1 AAAAATATAT
*
2466743 AAAAAT-TGT
1 AAAAATATAT
*
2466752 AAAAA-AAATT
1 AAAAATATA-T
*
2466762 ACGAAAATTTTTAT
1 A--AAAA--TATAT
*
2466776 AAAAAT-TGT
1 AAAAATATAT
2466785 AAAAATATAT
1 AAAAATATAT
2466795 AAAAATATAT
1 AAAAATATAT
* *
2466805 AGAAATATAG
1 AAAAATATAT
2466815 AAAAA
1 AAAAA
2466820 AATTTATAAA
Statistics
Matches: 129, Mismatches: 19, Indels: 41
0.68 0.10 0.22
Matches are distributed among these distances:
7 4 0.03
8 9 0.07
9 50 0.39
10 49 0.38
11 6 0.05
12 8 0.06
14 2 0.02
15 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (10 bp):
AAAAATATAT
Found at i:2466830 original size:10 final size:10
Alignment explanation
Indices: 2466668--2466830 Score: 61
Period size: 10 Copynumber: 16.3 Consensus size: 10
2466658 TAAAATCAAT
*
2466668 AAAAGTTATA
1 AAAATTTATA
*
2466678 AAAA-TTATT
1 AAAATTTATA
*
2466687 AAATTTTAATA
1 AAAATTT-ATA
*
2466698 AAAAATTATA
1 AAAATTTATA
*
2466708 AAAA-AT-TA
1 AAAATTTATA
2466716 AAAA-TTATTA
1 AAAATTTA-TA
*
2466726 AAAA-TTAGA
1 AAAATTTATA
*
2466735 AAAA-ATATA
1 AAAATTTATA
*
2466744 AAAATTGTAAA
1 AAAATT-TATA
* *
2466755 AAAAATTACGA
1 AAAATTTA-TA
*
2466766 AAATTTTTATA
1 AAA-ATTTATA
*
2466777 AAAA-TTGTA
1 AAAATTTATA
*
2466786 AAAATATATA
1 AAAATTTATA
*
2466796 AAAATATATA
1 AAAATTTATA
** *
2466806 GAAATATAGAAA
1 -AAA-ATTTATA
2466818 AAAATTTATA
1 AAAATTTATA
2466828 AAA
1 AAA
2466831 TTTTCATATC
Statistics
Matches: 116, Mismatches: 26, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
8 7 0.06
9 28 0.24
10 44 0.38
11 29 0.25
12 8 0.07
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (10 bp):
AAAATTTATA
Found at i:2476668 original size:3 final size:3
Alignment explanation
Indices: 2476660--2476690 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2476650 CTAAGTAACT
2476660 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2476691 AAATCAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2479125 original size:24 final size:24
Alignment explanation
Indices: 2479064--2479126 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
2479054 TAGAGTAATA
* *
2479064 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
2479088 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
2479112 CGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
2479127 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:2488200 original size:17 final size:16
Alignment explanation
Indices: 2488180--2488255 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 16
2488170 TTTGAAATTA
2488180 AATTTATTTTAATTTTG
1 AATTTATTTTAA-TTTG
* *
2488197 AATTTATTTTAAATTC
1 AATTTATTTTAATTTG
2488213 AATTTTAATTTTAATTTG
1 AA-TTT-ATTTTAATTTG
*
2488231 AATTTAATTTAAATTT-
1 AATTT-ATTTTAATTTG
2488247 AATATTATT
1 AAT-TTATT
2488256 ATAAATTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
16 10 0.20
17 30 0.59
18 11 0.22
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (16 bp):
AATTTATTTTAATTTG
Found at i:2488206 original size:34 final size:33
Alignment explanation
Indices: 2488168--2488264 Score: 106
Period size: 34 Copynumber: 2.8 Consensus size: 33
2488158 GGCCCAAACC
2488168 ATTTTGAAATTAAATTTATTTTAATTTTGAATTT
1 ATTTT-AAATTAAATTTATTTTAATTTTGAATTT
*
2488202 ATTTTAAATTCAATTTTAATTTTAA-TTTGAATTT
1 ATTTTAAATT-AAATTT-ATTTTAATTTTGAATTT
* * *
2488236 AATTTAAATTTAATATTATTATAAATTTT
1 ATTTTAAATTAAAT-TTATT-TTAATTTT
2488265 TTTAAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
33 10 0.19
34 33 0.62
35 10 0.19
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (33 bp):
ATTTTAAATTAAATTTATTTTAATTTTGAATTT
Found at i:2488224 original size:6 final size:6
Alignment explanation
Indices: 2488185--2488246 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
2488175 AATTAAATTT
* * *
2488185 ATTTTA ATTTTGA A-TTT- ATTTTA AATTCA ATTTTA ATTTTA ATTTGA
1 ATTTTA ATTTT-A ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
*
2488232 A-TTTA ATTTAA ATTT
1 ATTTTA ATTTTA ATTT
2488247 AATATTATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
4 1 0.02
5 7 0.16
6 35 0.78
7 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (6 bp):
ATTTTA
Found at i:2488225 original size:23 final size:23
Alignment explanation
Indices: 2488190--2488246 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
2488180 AATTTATTTT
*
2488190 AATTTTGAA-TTTATTTTAAATTC
1 AATTTT-AATTTTAATTTAAATTC
* *
2488213 AATTTTAATTTTAATTTGAATTT
1 AATTTTAATTTTAATTTAAATTC
*
2488236 AATTTAAATTT
1 AATTTTAATTT
2488247 AATATTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
AATTTTAATTTTAATTTAAATTC
Found at i:2488248 original size:11 final size:11
Alignment explanation
Indices: 2488174--2488249 Score: 64
Period size: 11 Copynumber: 6.8 Consensus size: 11
2488164 AACCATTTTG
*
2488174 AAATTAAATTT
1 AAATTTAATTT
*
2488185 -ATTTTAATTTT
1 AAATTTAA-TTT
* *
2488196 GAATTTATTTT
1 AAATTTAATTT
*
2488207 AAATTCAATTTT
1 AAATTTAA-TTT
*
2488219 AATTTTAATTT
1 AAATTTAATTT
*
2488230 GAATTTAATTT
1 AAATTTAATTT
2488241 AAATTTAAT
1 AAATTTAAT
2488250 ATTATTATAA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
10 5 0.10
11 31 0.62
12 14 0.28
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:2490357 original size:29 final size:30
Alignment explanation
Indices: 2490196--2490350 Score: 195
Period size: 30 Copynumber: 5.2 Consensus size: 30
2490186 AAACTGTCCA
* *
2490196 AAAATTACATTTTGACTCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* * *
2490226 AAAATTACATTTTAACACTAAAACTTTTCT
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* * * *
2490256 AATATTACATTTTGACCCTAAAACTTTTAC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
2490286 AATATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
*
2490316 AAAATTACATTTTAACCCCCAAAC-TTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
2490345 AAAATT
1 AAAATT
2490351 CTATTTTTGA
Statistics
Matches: 111, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
29 11 0.10
30 100 0.90
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCAAAACTTTTCC
Found at i:2490387 original size:60 final size:58
Alignment explanation
Indices: 2490310--2490444 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 58
2490300 ACCCCAAAAC
* *
2490310 TTTTCCAAAATTA-CATTTTAACCCCC-AAACTTTCCAAAATTCTATTTTT-GACCTCGA
1 TTTTCCAAAATTACCATTTT-ACCCCCTAAACTTTCAAAAATTCCATTTTTAG-CCTCGA
* *
2490367 TTTTTCCAAAATTTACCATTTTACCCCCTGAACTTTCAAAAATTCCCTTTTTAGCCTCGA
1 -TTTTCCAAAA-TTACCATTTTACCCCCTAAACTTTCAAAAATTCCATTTTTAGCCTCGA
*
2490427 TTTTACAAAATTACCATT
1 TTTTCCAAAATTACCATT
2490445 CTGCCCCCGA
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
58 18 0.26
59 18 0.26
60 31 0.46
61 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (58 bp):
TTTTCCAAAATTACCATTTTACCCCCTAAACTTTCAAAAATTCCATTTTTAGCCTCGA
Found at i:2491814 original size:16 final size:18
Alignment explanation
Indices: 2491779--2491815 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2491769 TATTACTTTT
*
2491779 AAAAAGTATTTTTGAGAC
1 AAAAAGTATTTTTGAAAC
2491797 AAAAA-TATTTTT-AAAC
1 AAAAAGTATTTTTGAAAC
2491813 AAA
1 AAA
2491816 TTACTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (18 bp):
AAAAAGTATTTTTGAAAC
Found at i:2492622 original size:24 final size:21
Alignment explanation
Indices: 2492577--2492630 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
2492567 AACTAGTACG
2492577 ATATTATTAATACGAAACGAA
1 ATATTATTAATACGAAACGAA
*
2492598 ATATTATAATAATATCGAAATGAA
1 ATATTAT--TAATA-CGAAACGAA
*
2492622 ATACTATTA
1 ATATTATTA
2492631 CAGCAAGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 7 0.25
22 2 0.07
23 5 0.18
24 14 0.50
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
ATATTATTAATACGAAACGAA
Found at i:2494100 original size:21 final size:21
Alignment explanation
Indices: 2494075--2494118 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2494065 ATTTGCATCA
2494075 AAAATGTTTGCTCTGTACCGC
1 AAAATGTTTGCTCTGTACCGC
2494096 AAAATGTTTGCTCTGTACCGC
1 AAAATGTTTGCTCTGTACCGC
2494117 AA
1 AA
2494119 TATAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (21 bp):
AAAATGTTTGCTCTGTACCGC
Found at i:2498951 original size:6 final size:6
Alignment explanation
Indices: 2498940--2498992 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
2498930 TTGCATGTGA
* * *
2498940 CCACCG CCACCG CCACCG CCACCT CCACCT CCACCT CCACCT CCACCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
2498988 CCACC
1 CCACC
2498993 AAAATGCATG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.17, C:0.68, G:0.06, T:0.09
Consensus pattern (6 bp):
CCACCT
Found at i:2498986 original size:66 final size:66
Alignment explanation
Indices: 2498910--2499034 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
2498900 CTTAAATCCA
* *
2498910 CCACCACCACCACCACCAAATTGCATGTGACCACCGCCACCGCCACCGCCACCTCCACCTCCACC
1 CCACCACCACCACCACCAAAATGCATGTGACCACCGCCACCGCCACCGCCACCACCACCTCCACC
2498975 T
66 T
* * * *
2498976 CCACCTCCACCTCCACCAAAATGCATGTGACCACTGCCACCGCCACCTCCACCACCACC
1 CCACCACCACCACCACCAAAATGCATGTGACCACCGCCACCGCCACCGCCACCACCACC
2499035 AAAATGCATG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.25, C:0.55, G:0.09, T:0.11
Consensus pattern (66 bp):
CCACCACCACCACCACCAAAATGCATGTGACCACCGCCACCGCCACCGCCACCACCACCTCCACC
T
Found at i:2499053 original size:3 final size:3
Alignment explanation
Indices: 2499047--2499113 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
2499037 AATGCATGTG
* * *
2499047 ACC ACC ACT ACC ACC ACC ACC GCC ACC ACC ACC AAC ACC ACC ACC ACC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
*
2499095 ACC ACT ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC A
2499114 AAATGCATGT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.61, G:0.01, T:0.03
Consensus pattern (3 bp):
ACC
Found at i:2499064 original size:78 final size:78
Alignment explanation
Indices: 2498982--2499260 Score: 283
Period size: 78 Copynumber: 3.5 Consensus size: 78
2498972 ACCTCCACCT
* ** *
2498982 CCACCTCCACCAAAATGCATGTGACCACTGCCACCGCCACCTCCACCACCACCAAAATGCATGTG
1 CCACCACCACCAAAATGCATGTGACCACCACCACCACCACCTCCACCACCACCAAAATGCATGTG
2499047 ACCACCACTACCA
66 ACCACCACTACCA
* ** * ****
2499060 CCACCACCGCCACCA-CCACCAACACCACCACCACCACCA-CTACCACCACCACCAAAATGCATG
1 CCACCACCACCAAAATGCA-TGTGACCACCACCACCACCACCT-CCACCACCACCAAAATGCATG
2499123 TGACCACTACCACTACCTTCA
64 TGA-C-C-ACCACTA-C--CA
** * *
2499144 CCACCACCAGTAAAATGCATGTGACCACCACCACTACCTCCTCCACCACCACCAAAATGCATGTG
1 CCACCACCACCAAAATGCATGTGACCACCACCACCACCACCTCCACCACCACCAAAATGCATGTG
* *
2499209 AGCACCACCACCA
66 ACCACCACTACCA
* * *
2499222 CCACCACCAGCAAAATGCATGTGACCGCCACCTCCACCA
1 CCACCACCACCAAAATGCATGTGACCACCACCACCACCA
2499261 TGCCTTTCAA
Statistics
Matches: 160, Mismatches: 31, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
77 4 0.03
78 84 0.52
79 1 0.01
80 2 0.01
81 13 0.08
82 2 0.01
84 50 0.31
85 4 0.03
ACGTcount: A:0.32, C:0.47, G:0.09, T:0.11
Consensus pattern (78 bp):
CCACCACCACCAAAATGCATGTGACCACCACCACCACCACCTCCACCACCACCAAAATGCATGTG
ACCACCACTACCA
Found at i:2499215 original size:120 final size:120
Alignment explanation
Indices: 2498939--2499247 Score: 324
Period size: 120 Copynumber: 2.6 Consensus size: 120
2498929 ATTGCATGTG
* * * * * * *
2498939 ACCACCGCCACCGCCACCGCCACC---TCCACCTCCACCTCCACCTCCACCTCCACCAAAATGCA
1 ACCACCACCACCGCCACCACCACCAAAACCACCACCACCACCACCACCACCACCACCAAAATGCA
* * *
2499001 TGTGACCACTGCCACCGCCACCTCCACCACCACCAAAATGCATGTGACCACCACT
66 TGTGACCACTACCACCACCACCACCACCACCACCAAAATGCATGTGACCACCACT
* *
2499056 ACCACCACCACCGCCACCACCACCAACACCACCACCACCACCACTACCACCACCACCAAAATGCA
1 ACCACCACCACCGCCACCACCACCAAAACCACCACCACCACCACCACCACCACCACCAAAATGCA
* ** **
2499121 TGTGACCACTACCACTACCTTCACCACCACCAGTAAAATGCATGTGACCA-C-C-
66 TGTGACCACTACCACCACCACCACCACCACCACCAAAATGCATGTGACCACCACT
* * * * ** * *
2499173 ACCACTACCTCCTCCACCACCACCAAAATGCATGTGAGCACCACCACCACCACCACCAGCAAAAT
1 ACCACCACCACCGCCACCACCACCAAAA-CCA--CCACCACCACCACCACCACCACCACCAAAAT
2499238 GCATGTGACC
63 GCATGTGACC
2499248 GCCACCTCCA
Statistics
Matches: 160, Mismatches: 26, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
117 46 0.29
118 3 0.02
119 1 0.01
120 110 0.69
ACGTcount: A:0.31, C:0.49, G:0.09, T:0.11
Consensus pattern (120 bp):
ACCACCACCACCGCCACCACCACCAAAACCACCACCACCACCACCACCACCACCACCAAAATGCA
TGTGACCACTACCACCACCACCACCACCACCACCAAAATGCATGTGACCACCACT
Found at i:2499253 original size:36 final size:36
Alignment explanation
Indices: 2499186--2499260 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
2499176 ACTACCTCCT
*
2499186 CCACCACCACCAAAATGCATGTGAGCACCACCACCA
1 CCACCACCACCAAAATGCATGTGACCACCACCACCA
* * *
2499222 CCACCACCAGCAAAATGCATGTGACCGCCACCTCCA
1 CCACCACCACCAAAATGCATGTGACCACCACCACCA
2499258 CCA
1 CCA
2499261 TGCCTTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.45, G:0.12, T:0.09
Consensus pattern (36 bp):
CCACCACCACCAAAATGCATGTGACCACCACCACCA
Found at i:2499260 original size:42 final size:42
Alignment explanation
Indices: 2498964--2499230 Score: 278
Period size: 42 Copynumber: 6.5 Consensus size: 42
2498954 ACCGCCACCT
* * * *
2498964 CCACCTCCACCTCCACCTCCACCTCCACCAAAATGCATGTGA
1 CCACCACCACCACCACCACCACCACCACCAAAATGCATGTGA
** * *
2499006 CCACTGCCACCGCCACCTCCACCACCACCAAAATGCATGTGA
1 CCACCACCACCACCACCACCACCACCACCAAAATGCATGTGA
* * *
2499048 CCACCACTACCACCACCACCGCCACCACCACCAA--C-----A
1 CCACCACCACCACCACCACCACCACCACCA-AAATGCATGTGA
*
2499084 CCACCACCACCACCACTACCACCACCACCAAAATGCATGTGA
1 CCACCACCACCACCACCACCACCACCACCAAAATGCATGTGA
* * ** **
2499126 CCACTACCACTACCTTCACCACCACCAGTAAAATGCATGTGA
1 CCACCACCACCACCACCACCACCACCACCAAAATGCATGTGA
* * *
2499168 CCACCACCACTACCTCCTCCACCACCACCAAAATGCATGTGA
1 CCACCACCACCACCACCACCACCACCACCAAAATGCATGTGA
*
2499210 GCACCACCACCACCACCACCA
1 CCACCACCACCACCACCACCA
2499231 GCAAAATGCA
Statistics
Matches: 186, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
35 2 0.01
36 28 0.15
37 1 0.01
41 1 0.01
42 152 0.82
43 2 0.01
ACGTcount: A:0.31, C:0.49, G:0.07, T:0.12
Consensus pattern (42 bp):
CCACCACCACCACCACCACCACCACCACCAAAATGCATGTGA
Found at i:2499363 original size:12 final size:12
Alignment explanation
Indices: 2499345--2499459 Score: 77
Period size: 12 Copynumber: 9.6 Consensus size: 12
2499335 TATTTTTCCT
2499345 TTAGCTTCAGCA
1 TTAGCTTCAGCA
* *
2499357 TTGGCTTCAGCC
1 TTAGCTTCAGCA
* *
2499369 TTAACTTCAGCC
1 TTAGCTTCAGCA
*
2499381 TTAGCTTTAGCA
1 TTAGCTTCAGCA
** *
2499393 TCCGCTTCAGCC
1 TTAGCTTCAGCA
*
2499405 TTAGCTTTAGCA
1 TTAGCTTCAGCA
** *
2499417 TCCGCTTCAGCC
1 TTAGCTTCAGCA
* *
2499429 TTTGCTTTAGCA
1 TTAGCTTCAGCA
** *
2499441 TCCGCTTCAGCT
1 TTAGCTTCAGCA
2499453 TTAGCTT
1 TTAGCTT
2499460 TTGCTTCGGC
Statistics
Matches: 74, Mismatches: 29, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
12 74 1.00
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.37
Consensus pattern (12 bp):
TTAGCTTCAGCA
Found at i:2499455 original size:18 final size:18
Alignment explanation
Indices: 2499444--2499707 Score: 159
Period size: 18 Copynumber: 15.0 Consensus size: 18
2499434 TTTAGCATCC
* * *
2499444 GCTTCAGCTTTAGCTTTT
1 GCTTCCGCTTCAGCTTTA
* *
2499462 GCTTCGGCTTTAGCTTTA
1 GCTTCCGCTTCAGCTTTA
*
2499480 GCTTCGGCTTCAGCTTTA
1 GCTTCCGCTTCAGCTTTA
* *
2499498 GCTTCTGCTTCTGCTTTA
1 GCTTCCGCTTCAGCTTTA
*
2499516 GCATCCGCTTCAGCCTTT-
1 GCTTCCGCTTCAG-CTTTA
*
2499534 GC-T----TT-AGCATCT-
1 GCTTCCGCTTCAGC-TTTA
* * *
2499546 GCTTCAGCTTTAGCTTTT
1 GCTTCCGCTTCAGCTTTA
* *
2499564 GCTTCAGCTTTAGCTTTA
1 GCTTCCGCTTCAGCTTTA
*
2499582 GCTTCGGCTTCAGCTTTA
1 GCTTCCGCTTCAGCTTTA
* * *
2499600 GCTTCTGCTTCTGCTTCA
1 GCTTCCGCTTCAGCTTTA
** * *
2499618 GCTTTAGCTTCGGCTTCA
1 GCTTCCGCTTCAGCTTTA
* * *
2499636 GCCTCAGCTTTAGCTTTA
1 GCTTCCGCTTCAGCTTTA
* *
2499654 GCTTCCGCTTTAGCTTCA
1 GCTTCCGCTTCAGCTTTA
* *
2499672 GCTTCAGCCTT-AGCATTA
1 GCTTCCG-CTTCAGCTTTA
*
2499690 GCTTCGGCTTCAGCTTTA
1 GCTTCCGCTTCAGCTTTA
2499708 ACTTGATCTT
Statistics
Matches: 203, Mismatches: 32, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
11 1 0.00
12 6 0.03
13 3 0.01
17 8 0.04
18 178 0.88
19 7 0.03
ACGTcount: A:0.12, C:0.28, G:0.19, T:0.42
Consensus pattern (18 bp):
GCTTCCGCTTCAGCTTTA
Found at i:2499460 original size:24 final size:24
Alignment explanation
Indices: 2499373--2499675 Score: 238
Period size: 24 Copynumber: 12.6 Consensus size: 24
2499363 TCAGCCTTAA
* *
2499373 CTTCAGCCTTAGCTTTAGCATCCG
1 CTTCAGCTTTAGCTTTAGCTTCCG
* *
2499397 CTTCAGCCTTAGCTTTAGCATCCG
1 CTTCAGCTTTAGCTTTAGCTTCCG
*
2499421 CTTCAGCCTTT-GCTTTAGCATCCG
1 CTTCAG-CTTTAGCTTTAGCTTCCG
* *
2499445 CTTCAGCTTTAGCTTTTGCTTCGG
1 CTTCAGCTTTAGCTTTAGCTTCCG
* ** *
2499469 CTTTAGCTTTAGCTTCGGCTTCAG
1 CTTCAGCTTTAGCTTTAGCTTCCG
* **
2499493 CTTTAGCTTCT-GCTTCT-GCTTTAG
1 CTTCAGCTT-TAGCTT-TAGCTTCCG
* * * **
2499517 CATCCGCTTCAGCCTTT-GCTTTAG
1 CTTCAGCTTTAG-CTTTAGCTTCCG
* * * **
2499541 CATCTGCTTCAGCTTTAGCTTTTG
1 CTTCAGCTTTAGCTTTAGCTTCCG
*
2499565 CTTCAGCTTTAGCTTTAGCTTCGG
1 CTTCAGCTTTAGCTTTAGCTTCCG
*
2499589 CTTCAGCTTTAGCTTCT-GCTTCTG
1 CTTCAGCTTTAGCTT-TAGCTTCCG
** *
2499613 CTTCAGCTTTAGCTTCGGCTTCAG
1 CTTCAGCTTTAGCTTTAGCTTCCG
*
2499637 CCTCAGCTTTAGCTTTAGCTTCCG
1 CTTCAGCTTTAGCTTTAGCTTCCG
* *
2499661 CTTTAGCTTCAGCTT
1 CTTCAGCTTTAGCTT
2499676 CAGCCTTAGC
Statistics
Matches: 239, Mismatches: 31, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
23 8 0.03
24 223 0.93
25 8 0.03
ACGTcount: A:0.12, C:0.29, G:0.18, T:0.41
Consensus pattern (24 bp):
CTTCAGCTTTAGCTTTAGCTTCCG
Found at i:2499466 original size:42 final size:42
Alignment explanation
Indices: 2499373--2499707 Score: 259
Period size: 42 Copynumber: 7.8 Consensus size: 42
2499363 TCAGCCTTAA
* * *
2499373 CTTCAGCCTTAGCTTTAGCATCCGCTTCAGCCTTAGCTTTAGCATCCG
1 CTTCAGCCTTTGCTTTAGCTTCCGCTTCAGCTTTAGC-TT--C-T--G
* *
2499421 CTTCAGCCTTTGCTTTAGCATCCGCTTCAGCTTTAGCTTTTG
1 CTTCAGCCTTTGCTTTAGCTTCCGCTTCAGCTTTAGCTTCTG
* *
2499463 CTTC-GGCTTTAGCTTTAGCTTCGGCTTCAGCTTTAGCTTCTG
1 CTTCAGCCTTT-GCTTTAGCTTCCGCTTCAGCTTTAGCTTCTG
* * ** * * *
2499505 CTTCTG-CTTTAGCATCCGCTTCAGCCTT-TGCTTTAGCATCTG
1 CTTCAGCCTTT-GCTTTAGCTTCCG-CTTCAGCTTTAGCTTCTG
* * * *
2499547 CTTCAG-CTTTAGCTTTTGCTTCAGCTTTAGCTTTAGCTTCGG
1 CTTCAGCCTTT-GCTTTAGCTTCCGCTTCAGCTTTAGCTTCTG
* *
2499589 CTTCAG-CTTTAGCTTCT-GCTTCTGCTTCAGCTTTAGCTTCGG
1 CTTCAGCCTTT-GCTT-TAGCTTCCGCTTCAGCTTTAGCTTCTG
** ** * *
2499631 CTTCAGCCTCAGCTTTAGCTTTAGCTTCCGCTTTAGCTTCAG
1 CTTCAGCCTTTGCTTTAGCTTCCGCTTCAGCTTTAGCTTCTG
* * *
2499673 CTTCAGCCTTAGCATTAGCTTCGGCTTCAGCTTTA
1 CTTCAGCCTTTGCTTTAGCTTCCGCTTCAGCTTTA
2499708 ACTTGATCTT
Statistics
Matches: 247, Mismatches: 33, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
41 9 0.04
42 193 0.78
43 7 0.03
44 1 0.00
47 2 0.01
48 35 0.14
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (42 bp):
CTTCAGCCTTTGCTTTAGCTTCCGCTTCAGCTTTAGCTTCTG
Found at i:2499901 original size:27 final size:27
Alignment explanation
Indices: 2499871--2499922 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2499861 CCAAATCCTG
* * *
2499871 CACCTGCACCTCCATCACCGCCACCGT
1 CACCTACACCTCCACCACCACCACCGT
2499898 CACCTACACCTCCACCACCACCACC
1 CACCTACACCTCCACCACCACCACC
2499923 ACCACCACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.60, G:0.06, T:0.12
Consensus pattern (27 bp):
CACCTACACCTCCACCACCACCACCGT
Found at i:2499917 original size:3 final size:3
Alignment explanation
Indices: 2499904--2499934 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2499894 CCGTCACCTA
*
2499904 CAC CTC CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
2499935 TTCTTGCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.68, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:2499928 original size:27 final size:27
Alignment explanation
Indices: 2499871--2499928 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2499861 CCAAATCCTG
* * * **
2499871 CACCTGCACCTCCATCACCGCCACCGT
1 CACCTACACCTCCACCACCACCACCAC
2499898 CACCTACACCTCCACCACCACCACCAC
1 CACCTACACCTCCACCACCACCACCAC
2499925 CACC
1 CACC
2499929 ACCACCTTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.60, G:0.05, T:0.10
Consensus pattern (27 bp):
CACCTACACCTCCACCACCACCACCAC
Found at i:2500301 original size:3 final size:3
Alignment explanation
Indices: 2500295--2500329 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2500285 CAGCCATACT
* *
2500295 ACC ACC ACC ACC ACC ACC ACC ACT ACC ACC GCC AC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
2500330 TTGCACTTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.63, G:0.03, T:0.03
Consensus pattern (3 bp):
ACC
Found at i:2500330 original size:12 final size:12
Alignment explanation
Indices: 2500292--2500330 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2500282 CAGCAGCCAT
2500292 ACTACCACCACC
1 ACTACCACCACC
*
2500304 ACCACCACCACC
1 ACTACCACCACC
*
2500316 ACTACCACCGCC
1 ACTACCACCACC
2500328 ACT
1 ACT
2500331 TGCACTTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.31, C:0.59, G:0.03, T:0.08
Consensus pattern (12 bp):
ACTACCACCACC
Found at i:2500354 original size:6 final size:6
Alignment explanation
Indices: 2500331--2500522 Score: 116
Period size: 6 Copynumber: 30.0 Consensus size: 6
2500321 CACCGCCACT
* * * *
2500331 TGCACT TGCACT TGCACC TGCACCAC CGCCACC TGCACC TGCACCAC CGCCACC
1 TGCACC TGCACC TGCACC TGCA-C-C TG-CACC TGCACC TGCA-C-C TG-CACC
* * * * *
2500385 TGCACT TGCACT TGCACC TGCACC TGCACT TGCACT TGCACT TGCACC
1 TGCACC TGCACC TGCACC TGCACC TGCACC TGCACC TGCACC TGCACC
** *
2500433 TGCACC TGCATT TGCACC -GCCACC TGCACC TGCACCAC CGCCACC TGCACC
1 TGCACC TGCACC TGCACC TG-CACC TGCACC TGCA-C-C TG-CACC TGCACC
* * **
2500484 TGCACCAC CGCCACC TGCACC TACACC TATACC TGCACC
1 TGCA-C-C TG-CACC TGCACC TGCACC TGCACC TGCACC
2500523 ACCGCCATCG
Statistics
Matches: 151, Mismatches: 21, Indels: 28
0.75 0.10 0.14
Matches are distributed among these distances:
5 1 0.01
6 117 0.77
7 13 0.09
8 12 0.08
9 8 0.05
ACGTcount: A:0.19, C:0.48, G:0.15, T:0.18
Consensus pattern (6 bp):
TGCACC
Found at i:2500368 original size:21 final size:21
Alignment explanation
Indices: 2500343--2500510 Score: 178
Period size: 21 Copynumber: 7.6 Consensus size: 21
2500333 CACTTGCACT
2500343 TGCACCTGCACCACCGCCACC
1 TGCACCTGCACCACCGCCACC
2500364 TGCACCTGCACCACCGCCACC
1 TGCACCTGCACCACCGCCACC
*
2500385 TGCACTTGCACTTGCACCTG-CACC
1 TGCACCTGCAC---CACC-GCCACC
* *
2500409 TGCACTTGCACTTGCACTTG-CACC
1 TGCACCTGCAC---CAC-CGCCACC
*
2500433 TGCACCTGCATTTGCACCGCCACC
1 TGCACCTGCA---CCACCGCCACC
2500457 TGCACCTGCACCACCGCCACC
1 TGCACCTGCACCACCGCCACC
2500478 TGCACCTGCACCACCGCCACC
1 TGCACCTGCACCACCGCCACC
*
2500499 TGCACCTACACC
1 TGCACCTGCACC
2500511 TATACCTGCA
Statistics
Matches: 131, Mismatches: 7, Indels: 18
0.84 0.04 0.12
Matches are distributed among these distances:
21 73 0.56
23 1 0.01
24 56 0.43
25 1 0.01
ACGTcount: A:0.18, C:0.50, G:0.15, T:0.17
Consensus pattern (21 bp):
TGCACCTGCACCACCGCCACC
Found at i:2500485 original size:27 final size:27
Alignment explanation
Indices: 2500453--2500529 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 27
2500443 TTTGCACCGC
*
2500453 CACCTGCACCTGCACCACCGCCACCTG
1 CACCTGCACCTGCACCACCGCCACCTA
** *
2500480 CACCTGCACCACCGCCACCTG-CACCTA
1 CACCTGCACCTGCACCACC-GCCACCTA
**
2500507 CACCTATACCTGCACCACCGCCA
1 CACCTGCACCTGCACCACCGCCA
2500530 TCGCTGCCAC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.03
27 37 0.95
28 1 0.03
ACGTcount: A:0.22, C:0.55, G:0.12, T:0.12
Consensus pattern (27 bp):
CACCTGCACCTGCACCACCGCCACCTA
Found at i:2500503 original size:54 final size:54
Alignment explanation
Indices: 2500319--2500529 Score: 187
Period size: 54 Copynumber: 3.8 Consensus size: 54
2500309 CACCACCACT
* * *
2500319 ACCACCGCCACTTGCACTTGCACTTGCACCTGCACCACCGCCACCTGCACCTGC
1 ACCACCGCCACCTGCACTCGCACCTGCACCTGCACCACCGCCACCTGCACCTGC
* * * * *
2500373 ACCACCGCCACCTGCACTTGCACTTGCACCTGCACCTGCACTTG-CACTTGCACTTGC
1 ACCACCGCCACCTGCACTCGCACCTGCACCTGCA-C--CAC-CGCCACCTGCACCTGC
**
2500430 ACCTGCACCTG-CATTTGCAC-CGCCACCTGCACCTGCACCACCGCCACCTGCACCTGC
1 A-C--CACC-GCCACCTGCACTCG-CACCTGCACCTGCACCACCGCCACCTGCACCTGC
* **
2500487 ACCACCGCCACCTGCAC-CTACACCTATACCTGCACCACCGCCA
1 ACCACCGCCACCTGCACTC-GCACCTGCACCTGCACCACCGCCA
2500530 TCGCTGCCAC
Statistics
Matches: 129, Mismatches: 16, Indels: 24
0.76 0.09 0.14
Matches are distributed among these distances:
53 1 0.01
54 66 0.51
55 1 0.01
56 2 0.02
57 30 0.23
58 2 0.02
59 2 0.02
60 24 0.19
61 1 0.01
ACGTcount: A:0.19, C:0.49, G:0.14, T:0.17
Consensus pattern (54 bp):
ACCACCGCCACCTGCACTCGCACCTGCACCTGCACCACCGCCACCTGCACCTGC
Found at i:2503493 original size:36 final size:36
Alignment explanation
Indices: 2503453--2503530 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
2503443 AGGAGCAGGT
* *
2503453 GGTGGTGCCTATGGTGGAGGTGCAGGTGTAGGAGGC
1 GGTGGTGCCTATGGTAGAGGTGCAGGTGCAGGAGGC
* *
2503489 GGTGGTGGCTATGGTAGAGGTGTAGGTGCAGGAGGC
1 GGTGGTGCCTATGGTAGAGGTGCAGGTGCAGGAGGC
2503525 GGTGGT
1 GGTGGT
2503531 ATGGCTGCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.14, C:0.09, G:0.54, T:0.23
Consensus pattern (36 bp):
GGTGGTGCCTATGGTAGAGGTGCAGGTGCAGGAGGC
Found at i:2503626 original size:33 final size:32
Alignment explanation
Indices: 2503579--2503700 Score: 149
Period size: 33 Copynumber: 3.7 Consensus size: 32
2503569 CGGTGGTGGA
*
2503579 GGTGCAGGTGCAGGTGTAAGTGGCAGTGGCAAT
1 GGTGGAGGTGCAGGTGTAAGTGGCAGTGG-AAT
*
2503612 GGTGAAGGTGCAGGTGTAAGTGGCGATAGTGG--T
1 GGTGGAGGTGCAGGTGTAAGTGGC---AGTGGAAT
*
2503645 GGTGGAGGTGCAGGTGTAAGTGGCGGTGGAAAT
1 GGTGGAGGTGCAGGTGTAAGTGGCAGTGG-AAT
*
2503678 GGTGGAGGTGCAGGTGCAAGTGG
1 GGTGGAGGTGCAGGTGTAAGTGG
2503701 AGGTGGTGGT
Statistics
Matches: 79, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
30 4 0.05
33 70 0.89
36 5 0.06
ACGTcount: A:0.20, C:0.08, G:0.50, T:0.21
Consensus pattern (32 bp):
GGTGGAGGTGCAGGTGTAAGTGGCAGTGGAAT
Found at i:2503710 original size:66 final size:66
Alignment explanation
Indices: 2503570--2503710 Score: 201
Period size: 66 Copynumber: 2.1 Consensus size: 66
2503560 GTTTAGAGGC
* * *
2503570 GGTGGTGGAGGTGCAGGTGCAGGTGTAAGTGGCAGTGGCAATGGTGAAGGTGCAGGTGTAAGTGG
1 GGTGGTGGTGGTGCAGGTGCAGGTGTAAGTGGCAGTGGAAATGGTGAAGGTGCAGGTGCAAGTGG
*
2503635 C
66 A
* * * * *
2503636 GATAGTGGTGGTGGAGGTGCAGGTGTAAGTGGCGGTGGAAATGGTGGAGGTGCAGGTGCAAGTGG
1 GGTGGTGGTGGTGCAGGTGCAGGTGTAAGTGGCAGTGGAAATGGTGAAGGTGCAGGTGCAAGTGG
2503701 A
66 A
2503702 GGTGGTGGT
1 GGTGGTGGT
2503711 ATGGCTGCTG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.19, C:0.07, G:0.52, T:0.22
Consensus pattern (66 bp):
GGTGGTGGTGGTGCAGGTGCAGGTGTAAGTGGCAGTGGAAATGGTGAAGGTGCAGGTGCAAGTGG
A
Found at i:2503711 original size:180 final size:179
Alignment explanation
Indices: 2503464--2503829 Score: 499
Period size: 180 Copynumber: 2.0 Consensus size: 179
2503454 GTGGTGCCTA
* ** *
2503464 TGGTGGAGGTGCAGGTGTAGGAGGCGGTGGTGGCTATGGTAGAGGTGTAGGTGCAGGAGGCGGTG
1 TGGTGGAGGTGCAGGTGTA-GAGGCGGCGGTGGAAATGGTAGAGGTGCAGGTGCAGGAGGCGGTG
*
2503529 GTATGGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGTGGTGGAGGTGCAGGTGCAGGT
65 GTATGGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGTGGTGGAGGTGCAGGTGCAAGT
*
2503594 GTA-AGTGGCAGTGG-CAATGGTGAAGGTGCAGGTGTAAGTGGC-GATAGTGG
130 G-ACAGTGGCAGTGGTCAA-GGTGAAGGTGCAGGTGCAAGTGGCAG-TAGTGG
* * *
2503644 TGGTGGAGGTGCAGGTGTA-A-GTGGCGGTGGAAATGGTGGAGGTGCAGGTGCAAGTGGAGGTGG
1 TGGTGGAGGTGCAGGTGTAGAGGCGGCGGTGGAAATGGTAGAGGTGCAGGTGC-A--GGAGGCGG
*
2503707 TGGTATGGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGTGGTGGAGGTGCAGGTGTAA
63 TGGTATGGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGTGGTGGAGGTGCAGGTGCAA
* ** * *
2503772 GTGACGGTGGCAGTGGTGGAGGTGCAGGTGCAGGTGCAAGTGGCAGTGGTGG
128 GTGACAGTGGCAGTGGTCAAGGTGAAGGTGCAGGTGCAAGTGGCAGTAGTGG
2503824 TGGTGG
1 TGGTGG
2503830 TATGGCTGCT
Statistics
Matches: 165, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
177 25 0.15
178 2 0.01
179 1 0.01
180 135 0.82
181 2 0.01
ACGTcount: A:0.16, C:0.08, G:0.51, T:0.25
Consensus pattern (179 bp):
TGGTGGAGGTGCAGGTGTAGAGGCGGCGGTGGAAATGGTAGAGGTGCAGGTGCAGGAGGCGGTGG
TATGGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGTGGTGGAGGTGCAGGTGCAAGTG
ACAGTGGCAGTGGTCAAGGTGAAGGTGCAGGTGCAAGTGGCAGTAGTGG
Found at i:2503793 original size:33 final size:33
Alignment explanation
Indices: 2503751--2503828 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
2503741 TTTAGAGGCG
* *
2503751 GTGGTGGAGGTGCAGGTGTAAGTG-ACGGTGGCA
1 GTGGTGGAGGTGCAGGTGCAAGTGCA-AGTGGCA
*
2503784 GTGGTGGAGGTGCAGGTGCAGGTGCAAGTGGCA
1 GTGGTGGAGGTGCAGGTGCAAGTGCAAGTGGCA
*
2503817 GTGGTGGTGGTG
1 GTGGTGGAGGTG
2503829 GTATGGCTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 39 0.98
34 1 0.03
ACGTcount: A:0.15, C:0.09, G:0.54, T:0.22
Consensus pattern (33 bp):
GTGGTGGAGGTGCAGGTGCAAGTGCAAGTGGCA
Found at i:2503827 original size:39 final size:39
Alignment explanation
Indices: 2503753--2503829 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
2503743 TAGAGGCGGT
* * *
2503753 GGTGGAGGTGCAGGTGTAAGTGACGGTGGCAGTGGTGGA
1 GGTGCAGGTGCAGGTGCAAGTGACAGTGGCAGTGGTGGA
* **
2503792 GGTGCAGGTGCAGGTGCAAGTGGCAGTGGTGGTGGTGG
1 GGTGCAGGTGCAGGTGCAAGTGACAGTGGCAGTGGTGG
2503830 TATGGCTGCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.16, C:0.09, G:0.55, T:0.21
Consensus pattern (39 bp):
GGTGCAGGTGCAGGTGCAAGTGACAGTGGCAGTGGTGGA
Found at i:2504299 original size:423 final size:423
Alignment explanation
Indices: 2503791--2504626 Score: 1184
Period size: 423 Copynumber: 2.0 Consensus size: 423
2503781 GCAGTGGTGG
** *
2503791 AGGTGCAGGTGCAGGTGCAAGTGGCAGTGGTGGTGGTGGTATGGCTGCTGAGGGTGGTTTTAAGT
1 AGGTGCAGGTGCAGGTGCAAGTGGCAGTGGCAGTGGTGGTATAGCTGCTGAGGGTGGTTTTAAGT
* * * ** * **
2503856 TTGGGATTAGAGGTGGAATAAGAG-GAGGATTTGGTGGAAATAGTGCTA-GAAGTGGTGGCACTA
66 TTGGGATTAGAGGCGGAATAAAAGCAAGG-GCTGGTGGAAATAGTG-GAGGAAGTGGTGAAACTA
* * *
2503919 ATGTTGGTGGTGGGGCAGGAGGCCATGTCGAAGGTATTGGTAGTGGTGCAACTAGTACA-AGTGG
129 ATGTTGGTGGAGGGGCAGGAGGCCATGTCGAAAGTATTGATAGTGGTGCAACTAGTACACA-TGG
* * * *
2503983 TAGTCTTAGCGGAGCAAAGAGTAGTGA-GGACAAAGCTAGTGATACTAGTAAGAGTGAGGCTAAA
193 TAGTCTCAGCGGAGCAAAGAGTAGTGATAGA-AAAGCTAGTGATACTAGTAAAAGTAAGGCTAAA
* * *
2504047 GCTAGTTTTGAAGGTAAAGTAAGAGGGA-AAGGAGAGGTTGGTGGAAATAGTGGTGGAAGTGGTA
257 GCTAGTTTTGAAGGTAAAGTAAGA-GGACAAGGAGAGGTCGGTGGAAATAGCGATGGAAGTGGTA
* ** * * *
2504111 GCACTAATGTTGATGGTAAGGTAGGAGGGCAAGGTGGAGGTGTTGGTAGTGGTAGTACTGATGCA
321 ACACTAATGTTGATAATAAGGTAGGAGGGCAAAGTGGAGGTGTTGGCAGTGATAGTACTGATGCA
2504176 AATGGTA-GTCATAGCAGTGAAAAAGATAGTGGAATTAA
386 AATGGTACG-CATAGCAGTGAAAAAGATAGTGGAATTAA
* *
2504214 AGGTGCAGGTGGC-GGTGCAAGT-GTAGGTGGCAGTGGTGGTATAGCTGCTGGGGGTGGTTTTAA
1 AGGTGCAGGT-GCAGGTGCAAGTGGCA-GTGGCAGTGGTGGTATAGCTGCTGAGGGTGGTTTTAA
*
2504277 GTTTGGGTTTAGAGGCGGAATAAAAGCAAGGGCTGGTGGAAATAGTGGAGGAAGTGGTGAAACTA
64 GTTTGGGATTAGAGGCGGAATAAAAGCAAGGGCTGGTGGAAATAGTGGAGGAAGTGGTGAAACTA
* *
2504342 ATGTTGGTGGAGGGGCAGGAGGCCATGTTGAAAGTGTTGATAGTGGTGCAACTAGTACACATGGT
129 ATGTTGGTGGAGGGGCAGGAGGCCATGTCGAAAGTATTGATAGTGGTGCAACTAGTACACATGGT
*
2504407 AGTCTCAGCGGAGCAAAGAGTAGTGATAGAAAAGCTAGTGATACTAGTAAAAGTAAGGGTAAAGC
194 AGTCTCAGCGGAGCAAAGAGTAGTGATAGAAAAGCTAGTGATACTAGTAAAAGTAAGGCTAAAGC
* *
2504472 TGGTTTTGAAGGTAAAGTAGGAGGACAAGGAGAGGTCGGTGGAAATAGCGATGGAAGTGGTAACA
259 TAGTTTTGAAGGTAAAGTAAGAGGACAAGGAGAGGTCGGTGGAAATAGCGATGGAAGTGGTAACA
* ** *
2504537 CTAGTGTTTCTAATAAGGTAGGAGGGCAAAGTGGAGGTGTTGGCAGTGATAGTACTGATGCAAGT
324 CTAATGTTGATAATAAGGTAGGAGGGCAAAGTGGAGGTGTTGGCAGTGATAGTACTGATGCAAAT
*
2504602 GGTACGCATAGCGGTGAAAAAGATA
389 GGTACGCATAGCAGTGAAAAAGATA
2504627 ATGATGGAAA
Statistics
Matches: 365, Mismatches: 40, Indels: 16
0.87 0.10 0.04
Matches are distributed among these distances:
422 6 0.02
423 350 0.96
424 9 0.02
ACGTcount: A:0.29, C:0.08, G:0.39, T:0.24
Consensus pattern (423 bp):
AGGTGCAGGTGCAGGTGCAAGTGGCAGTGGCAGTGGTGGTATAGCTGCTGAGGGTGGTTTTAAGT
TTGGGATTAGAGGCGGAATAAAAGCAAGGGCTGGTGGAAATAGTGGAGGAAGTGGTGAAACTAAT
GTTGGTGGAGGGGCAGGAGGCCATGTCGAAAGTATTGATAGTGGTGCAACTAGTACACATGGTAG
TCTCAGCGGAGCAAAGAGTAGTGATAGAAAAGCTAGTGATACTAGTAAAAGTAAGGCTAAAGCTA
GTTTTGAAGGTAAAGTAAGAGGACAAGGAGAGGTCGGTGGAAATAGCGATGGAAGTGGTAACACT
AATGTTGATAATAAGGTAGGAGGGCAAAGTGGAGGTGTTGGCAGTGATAGTACTGATGCAAATGG
TACGCATAGCAGTGAAAAAGATAGTGGAATTAA
Found at i:2505425 original size:15 final size:16
Alignment explanation
Indices: 2505397--2505426 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2505387 TCTTAGCGGA
2505397 GCAAAGAGTAGTGATG
1 GCAAAGAGTAGTGATG
2505413 GCAAAGA-TAGTGAT
1 GCAAAGAGTAGTGAT
2505427 ATTAGTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (16 bp):
GCAAAGAGTAGTGATG
Found at i:2505449 original size:486 final size:484
Alignment explanation
Indices: 2504239--2506141 Score: 2400
Period size: 486 Copynumber: 4.0 Consensus size: 484
2504229 TGCAAGTGTA
*
2504239 GGTGGC-AGTGGTGGTAT-AGCTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGAATAAAA
1 GGTGGCGA-TGGTGGTATGA-CTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGAATAAGA
* *
2504302 GCAAGGGCTGGTGGAAATAGTGGAGGAAGTGGTGAAACTAATGTTGGTGGAGGGGCAGGAGGCCA
64 GCAGGGGCTGGTGGAAATAGTGGAGGAAGTGGTGAAACTAATGTTGGTGGAGGGGTAGGAGGCCA
** * *
2504367 TGTTGAAAGTGTTGATAGTGGTGCAACTAGTACACA-TGGTAGTCTCAGCGGAGCAAAGAGTAGT
129 TGCCGAAAGTGTTGGTAGTGGTGCAACTAGTACA-AGTGGTAGTCTTAGCGGAGCAAAGAGTAGT
* * * * * * * *
2504431 GATAGAAAAGCTAGTGATACTAGTAAAAGTAAGGGTAAAGCTGGTTTTGAAGGTAAAGTAGGAGG
193 GATGGCAAAGATAGTGATACTAGTAAGAGTGAGGCTAAAGATAGTTTTGAAGGTAAAGTAGGAGG
* * * * * * * **
2504496 ACAAGGAGAGGTCGGTGGAAATAGCGATGGAAGTGGTAACACTAGTGTTTCTAATAAGGTAGGAG
258 AAAAGGAGAAGTTGGTGGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAG
* *
2504561 GGCAAA-GTGGAGGTGTTGGCAGTGATAGTACTGATGCAAGTGGTACGCATAGCGGTGAAAAAGA
323 GG-AAAGGTGGAGGTGTTGGCAGTGGTAGTACTGATGCAAGTGGTACTCATAGCGGTGAAAAAGA
* * *
2504625 TAATGATGGAAAAACTAGTGTTACTAGTAAGGGTGAAGCTAAAGATGGATTTAAAGGTATAGTAG
387 TAGTGATGGAAAAACTAGTGTTACTAGTAAGGGTGAAGCTAAAGATGGATTTGAAGGTAAAGTAG
* * *
2504690 GAGGG-AAAGGAGGTGATGGTAGCGGTGGTGGTGCAGGT
452 GAGGGCAAA-GA-G-G-TGGTAGTGG-GGAGGAG-AGGT
* * *
2504728 GCAAGTGGCGATGGTGGTATGGCTGTTGGGGGTGGTTTTAAGTTTGGGTTTAAAGGCGGAATAAG
1 G---GTGGCGATGGTGGTATGACTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGAATAAG
* * *
2504793 AGCAGGGGCTGGTGCAAATAGTGGTGGAAGTGGTGAAACTAATGTTGGTAGAGGGGTAGGAGGCC
63 AGCAGGGGCTGGTGGAAATAGTGGAGGAAGTGGTGAAACTAATGTTGGTGGAGGGGTAGGAGGCC
*
2504858 ATGCCGAAAGTGTTGGTAGTGGTGCAACTAGTACAAGTGGTAATCTTAGCGGAGCAAAGAGTAGT
128 ATGCCGAAAGTGTTGGTAGTGGTGCAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGT
* * ** * *
2504923 GATGACAAAGCTAGTGATACTAGTAAGAGTGATACTAAAGATGGTTTTGATGGTAAAGTAGGAGG
193 GATGGCAAAGATAGTGATACTAGTAAGAGTGAGGCTAAAGATAGTTTTGAAGGTAAAGTAGGAGG
* *
2504988 AAAAGGAGAAGTTGGTGGAAATAGTGGTGGAAGTGGTAGCACTAGTGCTACTGGTAAGGTAGGAG
258 AAAAGGAGAAGTTGGTGGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAG
* *
2505053 GGAAAGGTGGAGCTGTTGGCAGTAGTAGTACTGATGCAAGTGGTACTCATAGCGGTGAAAAAGAT
323 GGAAAGGTGGAGGTGTTGGCAGTGGTAGTACTGATGCAAGTGGTACTCATAGCGGTGAAAAAGAT
*
2505118 AGTGATGGAAAAACTAGTGTTACTAGTAAGGGTGAAGCTAAAGATGGATTTGAAGGTAAAGTAGA
388 AGTGATGGAAAAACTAGTGTTACTAGTAAGGGTGAAGCTAAAGATGGATTTGAAGGTAAAGTAGG
2505183 AGGGCAAAGAGGTGGTAGTGGAGGAGGAAGAGGT
453 AGGGCAAAGAGGTGGTAGTGG-GGAGG-AGAGGT
* * *
2505217 GGTGGCGATGGTGGTATGACTGCTAGGGGTGATTTTAAGTTTGGGTTTAGAGGAGGAATAAGAGC
1 GGTGGCGATGGTGGTATGACTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGAATAAGAGC
* * * * *
2505282 AGGGGCTGGTGGAAACAGTGGTGGAAGTGGTGGAACTAATGTTGGTGGAAGGGTAAGAGGCCATG
66 AGGGGCTGGTGGAAATAGTGGAGGAAGTGGTGAAACTAATGTTGGTGGAGGGGTAGGAGGCCATG
* * *
2505347 CCGAAGGTGTTGCTAGTGGTGTAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGTGAT
131 CCGAAAGTGTTGGTAGTGGTGCAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGTGAT
* * * *
2505412 GGCAAAGATAGTGATATTAGTAAGAGTGATGCTAAAGATAGTTTTGAAGGTAAAGTAAGAGGACA
196 GGCAAAGATAGTGATACTAGTAAGAGTGAGGCTAAAGATAGTTTTGAAGGTAAAGTAGGAGGAAA
*
2505477 AGGAGAGGTTGGTGGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAGGGA
261 AGGAGAAGTTGGTGGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAGGGA
* * * *
2505542 AAGGTGGAGGTGTTGGAAGTGGTAGTACTGATGCAAGTGCTTCTCATAGCGATGAAAAAGATAGT
326 AAGGTGGAGGTGTTGGCAGTGGTAGTACTGATGCAAGTGGTACTCATAGCGGTGAAAAAGATAGT
2505607 GATGGAAAAACTAGTGCTT-CTAGTAAGGGTGAAGCTAAAGATGTG-TTTGAAGGTAAAGTAGGA
391 GATGGAAAAACTAGTG-TTACTAGTAAGGGTGAAGCTAAAGATG-GATTTGAAGGTAAAGTAGGA
2505670 GGGCAAAGA----G--GT----A-GAGA---
454 GGGCAAAGAGGTGGTAGTGGGGAGGAGAGGT
* * * * *
2505687 --T-G-G-TGGT-ATA-G-CTGGTGAGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGAATAGGATC
1 GGTGGCGATGGTGGTATGACTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGAATAAGAGC
* *** * * * ** *
2505744 TGGCTTTGGTGGAAATAATAGAGGAAGTGTTGGCACTAATGTTGGTGGAGGGGTTGGAGGCCATG
66 AGGGGCTGGTGGAAATAGTGGAGGAAGTGGTGAAACTAATGTTGGTGGAGGGGTAGGAGGCCATG
* * ** *
2505809 CCGAAAGTGTTGGTAGTGGTGCAACTAGTACAAGTGGTAGTCGTAACAAAGTAAAGAGTAGTGAT
131 CCGAAAGTGTTGGTAGTGGTGCAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGTGAT
* * * *
2505874 GG-AAAAACTAGTGATATTAGTAAGAGTGAGGATAAA-ACAAGTTTTGAAGGTAAAGTAGGAGGA
196 GGCAAAGA-TAGTGATACTAGTAAGAGTGAGGCTAAAGA-TAGTTTTGAAGGTAAAGTAGGAGGA
* * *
2505937 AAAGGA-AAG--GTTGGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGTTGGTAAGGTAGAAGG
259 AAAGGAGAAGTTGGTGGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAGG
* * **
2505999 GCAAGGTGGAGGTGTTGGCAGTGGTAGTACTGATGCTAGTGGTAC-CAATAATGGTGAAAAAGAT
324 GAAAGGTGGAGGTGTTGGCAGTGGTAGTACTGATGCAAGTGGTACTC-ATAGCGGTGAAAAAGAT
* * * * * * *
2506063 AGTGATGGAAAAGCAAGTGCTACTAGTAAGGGTGAAGCTAATGATGGGTTTGAGGGTAAAATAGG
388 AGTGATGGAAAAACTAGTGTTACTAGTAAGGGTGAAGCTAAAGATGGATTTGAAGGTAAAGTAGG
*
2506128 AGGGCAAGGAGGTG
453 AGGGCAAAGAGGTG
2506142 CAAGTGGTGG
Statistics
Matches: 1260, Mismatches: 134, Indels: 66
0.86 0.09 0.05
Matches are distributed among these distances:
458 3 0.00
459 168 0.13
461 7 0.01
462 204 0.16
463 1 0.00
464 2 0.00
465 4 0.00
466 1 0.00
467 1 0.00
468 1 0.00
473 3 0.00
474 1 0.00
475 1 0.00
480 2 0.00
482 1 0.00
486 422 0.33
487 3 0.00
489 18 0.01
490 2 0.00
491 5 0.00
492 406 0.32
493 4 0.00
ACGTcount: A:0.31, C:0.07, G:0.38, T:0.24
Consensus pattern (484 bp):
GGTGGCGATGGTGGTATGACTGCTGGGGGTGGTTTTAAGTTTGGGTTTAGAGGCGGAATAAGAGC
AGGGGCTGGTGGAAATAGTGGAGGAAGTGGTGAAACTAATGTTGGTGGAGGGGTAGGAGGCCATG
CCGAAAGTGTTGGTAGTGGTGCAACTAGTACAAGTGGTAGTCTTAGCGGAGCAAAGAGTAGTGAT
GGCAAAGATAGTGATACTAGTAAGAGTGAGGCTAAAGATAGTTTTGAAGGTAAAGTAGGAGGAAA
AGGAGAAGTTGGTGGAAATAGTGGTGGAAGTGGTAGCACTAGTGTTGCTGGTAAGGTAGGAGGGA
AAGGTGGAGGTGTTGGCAGTGGTAGTACTGATGCAAGTGGTACTCATAGCGGTGAAAAAGATAGT
GATGGAAAAACTAGTGTTACTAGTAAGGGTGAAGCTAAAGATGGATTTGAAGGTAAAGTAGGAGG
GCAAAGAGGTGGTAGTGGGGAGGAGAGGT
Found at i:2506291 original size:24 final size:24
Alignment explanation
Indices: 2506264--2506315 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2506254 TTTTGAGACT
2506264 TCTCAT-AGCAATGAAACTAAATCA
1 TCTCATAAG-AATGAAACTAAATCA
*
2506288 TCTCATAAGAGTGAAACTAAATCA
1 TCTCATAAGAATGAAACTAAATCA
2506312 TCTC
1 TCTC
2506316 GTGAGAGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (24 bp):
TCTCATAAGAATGAAACTAAATCA
Found at i:2506322 original size:24 final size:24
Alignment explanation
Indices: 2506275--2506326 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
2506265 CTCATAGCAA
2506275 TGAAACTAAATCATCTCATAAGAG
1 TGAAACTAAATCATCTCATAAGAG
* *
2506299 TGAAACTAAATCATCTCGTGAGAG
1 TGAAACTAAATCATCTCATAAGAG
2506323 TGAA
1 TGAA
2506327 CACAAAGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (24 bp):
TGAAACTAAATCATCTCATAAGAG
Found at i:2506540 original size:6 final size:6
Alignment explanation
Indices: 2506523--2506645 Score: 79
Period size: 6 Copynumber: 20.5 Consensus size: 6
2506513 AGTAAAGATG
* * * * *
2506523 AAGCTG AAGCTA AAGCTA AGGCTA AAGC-A GAAGAC-A AAGCTA AGGTTG
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA -AAG-CTA AAGCTA AAGCTA
* * * * * **
2506571 AAGCTA AAGGTA AAGTTG AAGCCA AAGCTA AAGCTA AAGCAA AAGGAA
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA
* * *
2506619 AAACTG AAGCTG AAGCTA AAGCTA AAG
1 AAGCTA AAGCTA AAGCTA AAGCTA AAG
2506646 ATGAAGCTGA
Statistics
Matches: 90, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
5 2 0.02
6 86 0.96
7 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (6 bp):
AAGCTA
Found at i:2506550 original size:24 final size:24
Alignment explanation
Indices: 2506523--2506653 Score: 88
Period size: 24 Copynumber: 5.5 Consensus size: 24
2506513 AGTAAAGATG
2506523 AAGCTGAAGCTAAAGCTAAGGCTA
1 AAGCTGAAGCTAAAGCTAAGGCTA
* * *
2506547 AAGCAGAAGAC-AAAGCTAAGGTTG
1 AAGCTGAAG-CTAAAGCTAAGGCTA
* * * *
2506571 AAGCTAAAGGTAAAGTTGAA-GCCA
1 AAGCTGAAGCTAAAGCT-AAGGCTA
* * *
2506595 AAGCTAAAGCTAAAGCAAAAGG-AA
1 AAGCTGAAGCTAAAGC-TAAGGCTA
* * *
2506619 AAACTGAAGCTGAAGCTAAAGCTA
1 AAGCTGAAGCTAAAGCTAAGGCTA
*
2506643 AAGATGAAGCT
1 AAGCTGAAGCT
2506654 GAAGGAAAAG
Statistics
Matches: 79, Mismatches: 22, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
23 3 0.04
24 72 0.91
25 4 0.05
ACGTcount: A:0.47, C:0.14, G:0.24, T:0.15
Consensus pattern (24 bp):
AAGCTGAAGCTAAAGCTAAGGCTA
Found at i:2506616 original size:36 final size:35
Alignment explanation
Indices: 2506523--2506645 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 35
2506513 AGTAAAGATG
* * * *
2506523 AAGCTGAAGCTAAAGCTAAGGCTAAAGCAGAAGACA
1 AAGCTAAAGCTAAAGCAAAGG-TAAAGCTGAAGCCA
* * * *
2506559 AAGCTAAGGTTGAAGCTAAAGGTAAAGTTGAAGCCA
1 AAGCTAAAGCTAAAGC-AAAGGTAAAGCTGAAGCCA
* * **
2506595 AAGCTAAAGCTAAAGCAAAAGGAAAAACTGAAGCTG
1 AAGCTAAAGCTAAAGC-AAAGGTAAAGCTGAAGCCA
2506631 AAGCTAAAGCTAAAG
1 AAGCTAAAGCTAAAG
2506646 ATGAAGCTGA
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
36 65 0.94
37 4 0.06
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (35 bp):
AAGCTAAAGCTAAAGCAAAGGTAAAGCTGAAGCCA
Found at i:2506659 original size:42 final size:42
Alignment explanation
Indices: 2506587--2506681 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 42
2506577 AAGGTAAAGT
* * *
2506587 TGAAGCCAAAGCTAAAGCTAAAGCAAAAGGAAAAACTGAAGC
1 TGAAGCTAAAGCTAAAGATAAAGCAAAAGGAAAAACTGAAGA
* ** **
2506629 TGAAGCTAAAGCTAAAGATGAAGCTGAAGGAAAAGTTGAAGA
1 TGAAGCTAAAGCTAAAGATAAAGCAAAAGGAAAAACTGAAGA
*
2506671 TGGAGCTAAAG
1 TGAAGCTAAAG
2506682 GTGGAATAGA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.48, C:0.12, G:0.26, T:0.14
Consensus pattern (42 bp):
TGAAGCTAAAGCTAAAGATAAAGCAAAAGGAAAAACTGAAGA
Found at i:2506663 original size:24 final size:24
Alignment explanation
Indices: 2506623--2506682 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2506613 AAGGAAAAAC
**
2506623 TGAAGCTGAAGCTAAAGCTAAAGA
1 TGAAGCTGAAGGAAAAGCTAAAGA
* *
2506647 TGAAGCTGAAGGAAAAGTTGAAGA
1 TGAAGCTGAAGGAAAAGCTAAAGA
* *
2506671 TGGAGCTAAAGG
1 TGAAGCTGAAGG
2506683 TGGAATAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.43, C:0.08, G:0.32, T:0.17
Consensus pattern (24 bp):
TGAAGCTGAAGGAAAAGCTAAAGA
Found at i:2506800 original size:24 final size:24
Alignment explanation
Indices: 2506771--2506928 Score: 210
Period size: 24 Copynumber: 6.6 Consensus size: 24
2506761 ATTTAGCACT
2506771 TCTCATA-GTAGTGAAACTAAATCA
1 TCTCATATG-AGTGAAACTAAATCA
* * *
2506795 TTTCATAAGAGTGAAACTAGATCA
1 TCTCATATGAGTGAAACTAAATCA
** **
2506819 TCTCATAAAAGTGAAAGAAAATCA
1 TCTCATATGAGTGAAACTAAATCA
*
2506843 TCTCATATGGGTGAAACTAAATCA
1 TCTCATATGAGTGAAACTAAATCA
2506867 TCTCATATGAGTGAAACTAAATCA
1 TCTCATATGAGTGAAACTAAATCA
*
2506891 TCTCATATGAGTGAAAGTAAATCA
1 TCTCATATGAGTGAAACTAAATCA
*
2506915 TCTCATAAGAGTGA
1 TCTCATATGAGTGA
2506929 GCACAAAGCT
Statistics
Matches: 118, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
24 117 0.99
25 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (24 bp):
TCTCATATGAGTGAAACTAAATCA
Found at i:2507331 original size:24 final size:24
Alignment explanation
Indices: 2507304--2507355 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
2507294 TTCATAGCAA
2507304 TGAAACTAAATCATCTCACAAGAG
1 TGAAACTAAATCATCTCACAAGAG
**
2507328 TGAAACTAAATCATCTCGTAAGAG
1 TGAAACTAAATCATCTCACAAGAG
2507352 TGAA
1 TGAA
2507356 CACAAAGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.23
Consensus pattern (24 bp):
TGAAACTAAATCATCTCACAAGAG
Found at i:2507592 original size:24 final size:24
Alignment explanation
Indices: 2507556--2507772 Score: 221
Period size: 24 Copynumber: 9.0 Consensus size: 24
2507546 AAGATGAAGT
2507556 TAAAGCTGAAGCAGAAGCTAAAGC
1 TAAAGCTGAAGCAGAAGCTAAAGC
*
2507580 TAAGGCTGAAGCAGAAGCTAAAGC
1 TAAAGCTGAAGCAGAAGCTAAAGC
*
2507604 TAAGGCTGAAGCAGAAGCTAAAGC
1 TAAAGCTGAAGCAGAAGCTAAAGC
* *
2507628 TGAAGCTGAGGCTA-AAGCTAAAGC
1 TAAAGCTGAAGC-AGAAGCTAAAGC
* *
2507652 TGAAGCTAAAGCTA-AAGCTAAAGC
1 TAAAGCTGAAGC-AGAAGCTAAAGC
* * *
2507676 -AGAAGCTAAAGCTA-AAGATGAAGC
1 TA-AAGCTGAAGC-AGAAGCTAAAGC
*
2507700 TAAAGCTAAAGCAGAAGC-AGAAGC
1 TAAAGCTGAAGCAGAAGCTA-AAGC
*
2507724 TAAAGCTAAAG-ATGAAGCTAAAGC
1 TAAAGCTGAAGCA-GAAGCTAAAGC
**
2507748 TAAAGCTGAAGTTGAAGCTAAAGC
1 TAAAGCTGAAGCAGAAGCTAAAGC
2507772 T
1 T
2507773 GGAATAGGGG
Statistics
Matches: 172, Mismatches: 13, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
23 2 0.01
24 167 0.97
25 3 0.02
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (24 bp):
TAAAGCTGAAGCAGAAGCTAAAGC
Found at i:2507602 original size:42 final size:42
Alignment explanation
Indices: 2507551--2507772 Score: 288
Period size: 42 Copynumber: 5.3 Consensus size: 42
2507541 TAGTAAAGAT
* * *
2507551 GAAGTTAAAGCTGAAGCAGAAGCTAAAGCTAAGGCTGAAGCA
1 GAAGCTAAAGCTAAAGCAGAAGCTAAAGCTAAAGCTGAAGCA
* * *
2507593 GAAGCTAAAGCTAAGGCTGAAGC-AGAAGCTAAAGCTGAAGCT
1 GAAGCTAAAGCTAAAGCAGAAGCTA-AAGCTAAAGCTGAAGCA
* * *
2507635 GAGGCTAAAGCTAAAGCTGAAGCTAAAGCTAAAGCTAAAGCA
1 GAAGCTAAAGCTAAAGCAGAAGCTAAAGCTAAAGCTGAAGCA
*
2507677 GAAGCTAAAGCTAAAG-ATGAAGCTAAAGCTAAAGCAGAAGCA
1 GAAGCTAAAGCTAAAGCA-GAAGCTAAAGCTAAAGCTGAAGCA
**
2507719 GAAGCTAAAGCTAAAG-ATGAAGCTAAAGCTAAAGCTGAAGTT
1 GAAGCTAAAGCTAAAGCA-GAAGCTAAAGCTAAAGCTGAAGCA
2507761 GAAGCTAAAGCT
1 GAAGCTAAAGCT
2507773 GGAATAGGGG
Statistics
Matches: 160, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
41 1 0.01
42 158 0.99
43 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.26, T:0.15
Consensus pattern (42 bp):
GAAGCTAAAGCTAAAGCAGAAGCTAAAGCTAAAGCTGAAGCA
Found at i:2507765 original size:18 final size:18
Alignment explanation
Indices: 2507570--2507773 Score: 198
Period size: 18 Copynumber: 11.3 Consensus size: 18
2507560 GCTGAAGCAG
* * *
2507570 AAGCTAAAGCTAAGGCTG
1 AAGCTGAAGCTAAAGCTA
*
2507588 AAGCAGAAGCTAAAGCTA
1 AAGCTGAAGCTAAAGCTA
*
2507606 AGGCTGAAGC-AGAAGCTA
1 AAGCTGAAGCTA-AAGCTA
* *
2507624 AAGCTGAAGCTGAGGCTA
1 AAGCTGAAGCTAAAGCTA
* *
2507642 AAGCTAAAGCTGAAGCTA
1 AAGCTGAAGCTAAAGCTA
*
2507660 AAGCTAAAGCTAAAGC-A
1 AAGCTGAAGCTAAAGCTA
* * *
2507677 GAAGCTAAAGCTAAAGATG
1 -AAGCTGAAGCTAAAGCTA
*
2507696 AAGCTAAAGCTAAAGC-A
1 AAGCTGAAGCTAAAGCTA
*
2507713 GAAGCAGAAGCTAAAGCTA
1 -AAGCTGAAGCTAAAGCTA
*
2507732 AAGATGAAGCTAAAGCTA
1 AAGCTGAAGCTAAAGCTA
* *
2507750 AAGCTGAAGTTGAAGCTA
1 AAGCTGAAGCTAAAGCTA
2507768 AAGCTG
1 AAGCTG
2507774 GAATAGGGGG
Statistics
Matches: 157, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.01
18 154 0.98
19 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (18 bp):
AAGCTGAAGCTAAAGCTA
Found at i:2507869 original size:33 final size:33
Alignment explanation
Indices: 2507832--2507945 Score: 156
Period size: 33 Copynumber: 3.4 Consensus size: 33
2507822 GCAATAATGT
*
2507832 TGCTGGTGGTGGTGGTGGTCACATGCATTTTGC
1 TGCTGGTGGTGGTGGTGGTCACATGCATTTTGG
* *
2507865 TGCTGGCGGTGGTGGTGGTCACATTCATTTTGG
1 TGCTGGTGGTGGTGGTGGTCACATGCATTTTGG
*
2507898 TGGTGGTGGGGGTGGTGGTGGTCACATGCATTTTGG
1 TGCTGGT---GGTGGTGGTGGTCACATGCATTTTGG
*
2507934 TGGTGGTGGTGG
1 TGCTGGTGGTGG
2507946 CGGATTTAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
33 40 0.56
36 32 0.44
ACGTcount: A:0.08, C:0.11, G:0.46, T:0.35
Consensus pattern (33 bp):
TGCTGGTGGTGGTGGTGGTCACATGCATTTTGG
Found at i:2507933 original size:36 final size:36
Alignment explanation
Indices: 2507839--2507942 Score: 151
Period size: 36 Copynumber: 3.0 Consensus size: 36
2507829 TGTTGCTGGT
* *
2507839 GGTGGTGGTGGTCACATGCA-TTT--TGCTGCTGGC
1 GGTGGTGGTGGTCACATGCATTTTGGTGGTGGTGGC
* *
2507872 GGTGGTGGTGGTCACATTCATTTTGGTGGTGGTGGG
1 GGTGGTGGTGGTCACATGCATTTTGGTGGTGGTGGC
2507908 GGTGGTGGTGGTCACATGCATTTTGGTGGTGGTGG
1 GGTGGTGGTGGTCACATGCATTTTGGTGGTGGTGG
2507943 TGGCGGATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
33 19 0.30
34 3 0.05
36 41 0.65
ACGTcount: A:0.09, C:0.12, G:0.45, T:0.35
Consensus pattern (36 bp):
GGTGGTGGTGGTCACATGCATTTTGGTGGTGGTGGC
Found at i:2509240 original size:70 final size:70
Alignment explanation
Indices: 2509144--2509303 Score: 284
Period size: 70 Copynumber: 2.3 Consensus size: 70
2509134 TTAGGATATA
* *
2509144 AGGATGTCCTAAACATATACTAGATAATGATGCAAAGAAGTTGGATTCACGGATAAAATTGTACA
1 AGGATGTCC-AAAAAGA-ACTAGATAATGATGCAAAGAAGTTGGATTCACGGATAAAATTGTACA
2509209 TATTTGT
64 TATTTGT
2509216 AGGATGTCCAAAAAGAACTAGATAATGATGCAAAGAAGTTGGATTCACGGATAAAATTGTACATA
1 AGGATGTCCAAAAAGAACTAGATAATGATGCAAAGAAGTTGGATTCACGGATAAAATTGTACATA
2509281 TTTGT
66 TTTGT
2509286 AGGATGTCCAAAAAGAAC
1 AGGATGTCCAAAAAGAAC
2509304 GAAGGGCGAA
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
70 72 0.84
71 5 0.06
72 9 0.10
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (70 bp):
AGGATGTCCAAAAAGAACTAGATAATGATGCAAAGAAGTTGGATTCACGGATAAAATTGTACATA
TTTGT
Found at i:2510590 original size:20 final size:19
Alignment explanation
Indices: 2510561--2510601 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2510551 TGTAGGGAGC
*
2510561 AATTTTTCAATCGATTTAA
1 AATTTTTCAATCGAATTAA
*
2510580 AATTGTTTCAATTGAATTAA
1 AATT-TTTCAATCGAATTAA
2510600 AA
1 AA
2510602 CCATTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (19 bp):
AATTTTTCAATCGAATTAA
Found at i:2510770 original size:2 final size:2
Alignment explanation
Indices: 2510763--2510798 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2510753 AATTAGTTTA
2510763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2510799 GTTTTCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2515277 original size:12 final size:12
Alignment explanation
Indices: 2515262--2515349 Score: 122
Period size: 12 Copynumber: 7.3 Consensus size: 12
2515252 TTTCGCCTTT
2515262 TGCTCCGGCTTG
1 TGCTCCGGCTTG
2515274 TGCTCCGGCTTG
1 TGCTCCGGCTTG
*
2515286 TGCTCCTGCTTG
1 TGCTCCGGCTTG
*
2515298 TGCTCCAGCTTG
1 TGCTCCGGCTTG
* *
2515310 TGCTCCAGCTTT
1 TGCTCCGGCTTG
*
2515322 TGCTCCGGCTTT
1 TGCTCCGGCTTG
*
2515334 TGCTCCGGCTTT
1 TGCTCCGGCTTG
2515346 TGCT
1 TGCT
2515350 TCAGCCTCAG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 72 1.00
ACGTcount: A:0.02, C:0.33, G:0.26, T:0.39
Consensus pattern (12 bp):
TGCTCCGGCTTG
Found at i:2515382 original size:12 final size:12
Alignment explanation
Indices: 2515356--2515403 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
2515346 TGCTTCAGCC
**
2515356 TCAGCTTTTCCT
1 TCAGCTTTAGCT
*
2515368 TCAGCTTTAGTT
1 TCAGCTTTAGCT
*
2515380 TCAGCTTCAGCT
1 TCAGCTTTAGCT
*
2515392 TCACCTTTAGCT
1 TCAGCTTTAGCT
2515404 CCGGCTTCAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.15, C:0.29, G:0.12, T:0.44
Consensus pattern (12 bp):
TCAGCTTTAGCT
Found at i:2515493 original size:3 final size:3
Alignment explanation
Indices: 2515487--2515513 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2515477 AATGCATGTT
2515487 ACC ACC ACC ACC ACC ACC ACC ACC ACC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC
2515514 TACCTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:2515584 original size:18 final size:18
Alignment explanation
Indices: 2515563--2515627 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
2515553 TTGTGCTCCG
2515563 GCTTCAGCTTTTCCTTCA
1 GCTTCAGCTTTTCCTTCA
* *
2515581 GCTTTAGCTTTACCTTCA
1 GCTTCAGCTTTTCCTTCA
* *
2515599 GCTTTAG-TTTTAGCTTCA
1 GCTTCAGCTTTT-CCTTCA
*
2515617 GCTTCACCTTT
1 GCTTCAGCTTT
2515628 AGCTCTAGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
17 3 0.08
18 33 0.85
19 3 0.08
ACGTcount: A:0.14, C:0.28, G:0.12, T:0.46
Consensus pattern (18 bp):
GCTTCAGCTTTTCCTTCA
Found at i:2515589 original size:6 final size:6
Alignment explanation
Indices: 2515580--2515638 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
2515570 CTTTTCCTTC
* * * * * *
2515580 AGCTTT AGCTTT ACCTTC AGCTTT AGTTTT AGCTTC AGCTTC ACCTTT
1 AGCTTT AGCTTT AGCTTT AGCTTT AGCTTT AGCTTT AGCTTT AGCTTT
*
2515628 AGCTCT AGCTT
1 AGCTTT AGCTT
2515639 CACTAAACCC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (6 bp):
AGCTTT
Found at i:2515610 original size:24 final size:24
Alignment explanation
Indices: 2515575--2515641 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
2515565 TTCAGCTTTT
* *
2515575 CCTTCAGCTTTAGCTTTACCTTCA
1 CCTTTAGCTTTAGCTTCACCTTCA
* * *
2515599 GCTTTAGTTTTAGCTTCAGCTTCA
1 CCTTTAGCTTTAGCTTCACCTTCA
*
2515623 CCTTTAGCTCTAGCTTCAC
1 CCTTTAGCTTTAGCTTCAC
2515642 TAAACCCTCC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.16, C:0.30, G:0.12, T:0.42
Consensus pattern (24 bp):
CCTTTAGCTTTAGCTTCACCTTCA
Found at i:2515628 original size:18 final size:18
Alignment explanation
Indices: 2515576--2515641 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
2515566 TCAGCTTTTC
* * *
2515576 CTTCAGCTTTAGCTTTAC
1 CTTCAGCTTCACCTTTAG
* **
2515594 CTTCAGCTTTAGTTTTAG
1 CTTCAGCTTCACCTTTAG
2515612 CTTCAGCTTCACCTTTAG
1 CTTCAGCTTCACCTTTAG
2515630 C-TCTAGCTTCAC
1 CTTC-AGCTTCAC
2515642 TAAACCCTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
17 2 0.05
18 40 0.95
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.42
Consensus pattern (18 bp):
CTTCAGCTTCACCTTTAG
Found at i:2515631 original size:12 final size:12
Alignment explanation
Indices: 2515563--2515640 Score: 57
Period size: 12 Copynumber: 6.5 Consensus size: 12
2515553 TTGTGCTCCG
*
2515563 GCTTCAGCTTTT
1 GCTTCAGCTTTA
*
2515575 CCTTCAGCTTTA
1 GCTTCAGCTTTA
* * *
2515587 GCTTTACCTTCA
1 GCTTCAGCTTTA
* *
2515599 GCTTTAGTTTTA
1 GCTTCAGCTTTA
*
2515611 GCTTCAGCTTCA
1 GCTTCAGCTTTA
* * *
2515623 CCTTTAGCTCTA
1 GCTTCAGCTTTA
2515635 GCTTCA
1 GCTTCA
2515641 CTAAACCCTC
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.15, C:0.28, G:0.13, T:0.44
Consensus pattern (12 bp):
GCTTCAGCTTTA
Done.