Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 184 of 222
Found at i:58772205 original size:14 final size:15
Alignment explanation
Indices: 58772175--58772211 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
58772165 ATGAGAAGAG
58772175 AGAAAAATAAAAGGGA
1 AGAAAAA-AAAAGGGA
58772191 AGAAAAAAAAA-GGA
1 AGAAAAAAAAAGGGA
58772205 A-AAAAAA
1 AGAAAAAA
58772212 GAACAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 4 0.19
15 4 0.19
16 7 0.33
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AGAAAAAAAAAGGGA
Found at i:58774247 original size:11 final size:12
Alignment explanation
Indices: 58774187--58774245 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
58774177 CCTCCAAAGT
58774187 GAAAAAAAG-AA
1 GAAAAAAAGAAA
*
58774198 -AAAAAAAGATTCA
1 GAAAAAAAGA--AA
* *
58774211 GAAGAGAAGAAA
1 GAAAAAAAGAAA
58774223 GAAAAAAAGAAA
1 GAAAAAAAGAAA
*
58774235 GAAAAATAGAA
1 GAAAAAAAGAA
58774246 GATTAGTGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
10 8 0.22
12 21 0.57
13 1 0.03
14 7 0.19
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.05
Consensus pattern (12 bp):
GAAAAAAAGAAA
Found at i:58774423 original size:33 final size:34
Alignment explanation
Indices: 58774373--58774475 Score: 120
Period size: 33 Copynumber: 3.1 Consensus size: 34
58774363 GGTTTGAATT
* * *
58774373 AAAAAAGATAAAAGGGTTTTGATTAGGGTCTAAA
1 AAAAAAGATTAGAGGGTTTTGTTTAGGGTCTAAA
* * ***
58774407 AAAAGA-ATTAGGGGGTTTTGTTTAAAAT-TAAA
1 AAAAAAGATTAGAGGGTTTTGTTTAGGGTCTAAA
58774439 AAAAAAGATTAGAGGGTTTTGTTTAGGGTCTAAA
1 AAAAAAGATTAGAGGGTTTTGTTTAGGGTCTAAA
58774473 AAA
1 AAA
58774476 GGGCTAAAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
32 9 0.17
33 33 0.61
34 12 0.22
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (34 bp):
AAAAAAGATTAGAGGGTTTTGTTTAGGGTCTAAA
Found at i:58775018 original size:14 final size:14
Alignment explanation
Indices: 58775001--58775031 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
58774991 TGTAATGGTA
58775001 TTATTGTACTATAT
1 TTATTGTACTATAT
*
58775015 TTATTGTATTATAT
1 TTATTGTACTATAT
58775029 TTA
1 TTA
58775032 GGTGATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTGTACTATAT
Found at i:58776940 original size:96 final size:94
Alignment explanation
Indices: 58776810--58777107 Score: 355
Period size: 96 Copynumber: 3.1 Consensus size: 94
58776800 TAAACAAAGG
* * * * * *
58776810 ATTAGGGTTTAGGGTT-TCTTAATTAAATTGATTATAAAATTTTCAAAATTAGATTAGGGTTTCG
1 ATTAGGGTTTAGGGTTAT-TTGAGTAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAG
* * *
58776874 TGTTTATAGTTTTTAAGTAAAAAGTCAATTAA
65 TGTTTA-GGTTTTTAAG-AAAAAATCAAATAA
* * *
58776906 ATTAAGGTTTAGGGTTATTTGAGTAAATTAATTATAAATTTTTAAGAAATCAGATTAGAGTTTAG
1 ATTAGGGTTTAGGGTTATTTGAGTAAATTAATTATAAATTTTTAA-AAATTAGATTAGGGTTTAG
*
58776971 TGTTAAGGGTTTTTAAGAAAAAATCAAATAA
65 TGTTTA-GGTTTTTAAGAAAAAATCAAATAA
* * * *
58777002 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTAAAAAAATAAATTAGGGTTTAA
1 ATTAGGGTTTAGGGTTATTTGAGTAAATTAATTATAAATTTTT-AAAAATTAGATTAGGGTTTAG
* *
58777067 TGTTTAGGGTTTTAAGGAAAAACTCAAATAA
65 TGTTTAGGTTTTTAA-GAAAAAATCAAATAA
58777098 ATTAGGGTTT
1 ATTAGGGTTT
58777108 GGGATTTAGG
Statistics
Matches: 174, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
95 8 0.05
96 133 0.76
97 33 0.19
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.40
Consensus pattern (94 bp):
ATTAGGGTTTAGGGTTATTTGAGTAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGT
GTTTAGGTTTTTAAGAAAAAATCAAATAA
Found at i:58777400 original size:126 final size:126
Alignment explanation
Indices: 58777170--58777440 Score: 409
Period size: 126 Copynumber: 2.2 Consensus size: 126
58777160 ATGGATGTTT
* * *
58777170 TTTTACTACAGTAGTTAC-TGAAAAAATAATTTCGAGAAGACGTTTTTGAGTAAATAGTGGCAAA
1 TTTTGCTACAGTAGTT-CTTGAAAAAATAATTTCGAGAAGACGTTTCTGAGTAAATAGTGGAAAA
* * * *
58777234 AACGCTTTAAGCAGGATGCATTGTAAGCAAAAGTACTGAAAGAAGCTCCCACATAGACGCTC
65 AACGCTTTAAACAGGATACATTGTAAGCAAAAGTACTGAAAAAAGCTCCCACATAGACGCTA
* *
58777296 TTTTGCTACAGTGGTTCTTGAAAAAATAATTTCGAGAAGACGTTTCTGAGTAAATAGTGTAAAAA
1 TTTTGCTACAGTAGTTCTTGAAAAAATAATTTCGAGAAGACGTTTCTGAGTAAATAGTGGAAAAA
* * * *
58777361 ACGCTTTAAACAGGATACTTTGTCAGCAAAAGTACTGAAAAAAGCTCCCACGTAGACGTTA
66 ACGCTTTAAACAGGATACATTGTAAGCAAAAGTACTGAAAAAAGCTCCCACATAGACGCTA
58777422 TTTTGCTACAGTAGTTCTT
1 TTTTGCTACAGTAGTTCTT
58777441 ATTTGGCTGA
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
125 1 0.01
126 129 0.99
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (126 bp):
TTTTGCTACAGTAGTTCTTGAAAAAATAATTTCGAGAAGACGTTTCTGAGTAAATAGTGGAAAAA
ACGCTTTAAACAGGATACATTGTAAGCAAAAGTACTGAAAAAAGCTCCCACATAGACGCTA
Found at i:58778934 original size:61 final size:59
Alignment explanation
Indices: 58778749--58778937 Score: 176
Period size: 58 Copynumber: 3.2 Consensus size: 59
58778739 GTATTATTTA
*
58778749 TATTTT-TTAAAATTAAATAATATAGAAATATTCAAAATATTGTCTTATTTAAAAGAATTTC
1 TATTTTATT-AAA-TAAATAATATAGAAATATTCAAAATATTGTCTTA-TTAAAAGAAATTC
* * * * ** * * *
58778810 TATTTTATT-AA-AAATATTAAAGTAA-ATT-ACAAT-TACT-TTATTCAAAACAACGTTT
1 TATTTTATTAAATAAATAATATAGAAATATTCAAAATATTGTCTTATT-AAAAGAA-ATTC
58778865 TATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTCTTATGTAAAAGAAATTC
1 TATTTTATTAAAT-AAATAATATAGAAATATTCAAAATATTGTCTTAT-TAAAAGAAATTC
58778926 TATTTTATTAAA
1 TATTTTATTAAA
58778938 AATATAAAAG
Statistics
Matches: 99, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
53 2 0.02
54 9 0.09
55 13 0.13
56 6 0.06
57 3 0.03
58 22 0.22
59 3 0.03
60 6 0.06
61 22 0.22
62 12 0.12
63 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (59 bp):
TATTTTATTAAATAAATAATATAGAAATATTCAAAATATTGTCTTATTAAAAGAAATTC
Found at i:58779441 original size:18 final size:18
Alignment explanation
Indices: 58779400--58779442 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
58779390 GACTAGAAAA
* * *
58779400 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
*
58779418 ATGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
58779436 AGGATAC
1 AGGATAC
58779443 GCACCTGGCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:58780065 original size:7 final size:7
Alignment explanation
Indices: 58780053--58780182 Score: 260
Period size: 7 Copynumber: 18.6 Consensus size: 7
58780043 ATATAGTTAT
58780053 ATACTAA
1 ATACTAA
58780060 ATACTAA
1 ATACTAA
58780067 ATACTAA
1 ATACTAA
58780074 ATACTAA
1 ATACTAA
58780081 ATACTAA
1 ATACTAA
58780088 ATACTAA
1 ATACTAA
58780095 ATACTAA
1 ATACTAA
58780102 ATACTAA
1 ATACTAA
58780109 ATACTAA
1 ATACTAA
58780116 ATACTAA
1 ATACTAA
58780123 ATACTAA
1 ATACTAA
58780130 ATACTAA
1 ATACTAA
58780137 ATACTAA
1 ATACTAA
58780144 ATACTAA
1 ATACTAA
58780151 ATACTAA
1 ATACTAA
58780158 ATACTAA
1 ATACTAA
58780165 ATACTAA
1 ATACTAA
58780172 ATACTAA
1 ATACTAA
58780179 ATAC
1 ATAC
58780183 GAATCGACTA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 123 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACTAA
Found at i:58781398 original size:13 final size:13
Alignment explanation
Indices: 58781359--58781398 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
58781349 GAAAGGATTT
58781359 GAGATAAATATGA
1 GAGATAAATATGA
*
58781372 GAGA-ATAT-TG-
1 GAGATAAATATGA
58781382 GAGATAAATATGA
1 GAGATAAATATGA
58781395 GAGA
1 GAGA
58781399 ATTTGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.18
11 5 0.23
12 5 0.23
13 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.23
Consensus pattern (13 bp):
GAGATAAATATGA
Found at i:58781406 original size:21 final size:21
Alignment explanation
Indices: 58781355--58781406 Score: 86
Period size: 23 Copynumber: 2.4 Consensus size: 21
58781345 ATTTGAAAGG
58781355 ATTTGAGATAAATATGAGAGA
1 ATTTGAGATAAATATGAGAGA
58781376 ATATTGGAGATAAATATGAGAGA
1 AT-TT-GAGATAAATATGAGAGA
58781399 ATTTGAGA
1 ATTTGAGA
58781407 AAAAGGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.21
22 4 0.14
23 19 0.66
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (21 bp):
ATTTGAGATAAATATGAGAGA
Found at i:58782984 original size:5 final size:5
Alignment explanation
Indices: 58782974--58783003 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
58782964 AAATCCAAAG
58782974 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
58783004 ATAACTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:58792334 original size:28 final size:28
Alignment explanation
Indices: 58792301--58792357 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
58792291 AACCCGTAAT
* *
58792301 CCCAAATATTTAAACCTTGAACCCAAAC
1 CCCAAACACTTAAACCTTGAACCCAAAC
* * *
58792329 CCCAAACCCTTCAACCTTGAACTCAAAC
1 CCCAAACACTTAAACCTTGAACCCAAAC
58792357 C
1 C
58792358 TTCAACCTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.39, G:0.04, T:0.19
Consensus pattern (28 bp):
CCCAAACACTTAAACCTTGAACCCAAAC
Found at i:58792361 original size:20 final size:20
Alignment explanation
Indices: 58792331--58792393 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
58792321 ACCCAAACCC
58792331 CAAACCCTTCAACCTTGAACT
1 CAAA-CCTTCAACCTTGAACT
58792352 CAAACCTTCAACCTTGAATCCT
1 CAAACCTTCAACCTTGAA--CT
* *
58792374 TAAACCCTCAACC-TGAACT
1 CAAACCTTCAACCTTGAACT
58792393 C
1 C
58792394 CGAACCCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.05
20 14 0.38
21 8 0.22
22 13 0.35
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.24
Consensus pattern (20 bp):
CAAACCTTCAACCTTGAACT
Found at i:58792384 original size:22 final size:20
Alignment explanation
Indices: 58792331--58792393 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 20
58792321 ACCCAAACCC
58792331 CAAACCCTTCAACCTTGAACT
1 CAAACCC-TCAACCTTGAACT
*
58792352 CAAACCTTCAACCTTGAATCCT
1 CAAACCCTCAACCTTGAA--CT
*
58792374 TAAACCCTCAACC-TGAACT
1 CAAACCCTCAACCTTGAACT
58792393 C
1 C
58792394 CGAACCCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 10 0.28
22 13 0.36
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.24
Consensus pattern (20 bp):
CAAACCCTCAACCTTGAACT
Found at i:58805397 original size:29 final size:29
Alignment explanation
Indices: 58805355--58805613 Score: 150
Period size: 29 Copynumber: 8.9 Consensus size: 29
58805345 CGACCAAAAA
*
58805355 AAAAAGGATAGCTTCGGCTATCAATTATG
1 AAAAGGGATAGCTTCGGCTATCAATTATG
*
58805384 AAAAGGGATAGCTTCGGCTAT-AGATCATG
1 AAAAGGGATAGCTTCGGCTATCA-ATTATG
* * * * * *
58805413 AAAAGGGATTG-TGGCGACCATCTACTATG
1 AAAAGGGATAGCT-TCGGCTATCAATTATG
* * * * *
58805442 AAAAGGAAT-GGTGACGACCATCGAA-TATG
1 AAAAGGGATAGCT-TCGGCTATC-AATTATG
** * *
58805471 AAAAACGATAGCTTTGGCTATCAATGATG
1 AAAAGGGATAGCTTCGGCTATCAATTATG
* * *
58805500 AAAAGAGATAGCTTCAGCTATCGATTATG
1 AAAAGGGATAGCTTCGGCTATCAATTATG
* ** * * *
58805529 AAAAGGGATGGCAACGACCATCGAA-TACG
1 AAAAGGGATAGCTTCGGCTATC-AATTATG
* * *
58805558 AAAAGGGATATCTTCGGCTAACGATTATG
1 AAAAGGGATAGCTTCGGCTATCAATTATG
* * *
58805587 AAAAGGGATAGTTTTGGCTATCGATTA
1 AAAAGGGATAGCTTCGGCTATCAATTA
58805614 AAGAAAATGG
Statistics
Matches: 172, Mismatches: 49, Indels: 18
0.72 0.21 0.08
Matches are distributed among these distances:
28 6 0.03
29 162 0.94
30 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (29 bp):
AAAAGGGATAGCTTCGGCTATCAATTATG
Found at i:58805529 original size:87 final size:86
Alignment explanation
Indices: 58805438--58805640 Score: 217
Period size: 87 Copynumber: 2.3 Consensus size: 86
58805428 GACCATCTAC
* * * *
58805438 TATGAAAAGGAATGGTGACGACCATCGAATATGAAAAACGATAGCTTTGGCTATCAATGATGAAA
1 TATGAAAAGG-ATGGTAACGACCATCGAATACGAAAAACGATAGCTTCGGCTAACAATGATGAAA
58805503 AGAGATAGCTTCAGCTATCGAT
65 AGAGATAGCTTCAGCTATCGAT
* ** * * *
58805525 TATGAAAAGGGATGGCAACGACCATCGAATACGAAAAGGGATATCTTCGGCTAACGATTATGAAA
1 TATGAAAA-GGATGGTAACGACCATCGAATACGAAAAACGATAGCTTCGGCTAACAATGATGAAA
* * **
58805590 AGGGATAGTTTTGGCTATCGAT
65 AGAGATAGCTTCAGCTATCGAT
* **
58805612 TAAAGAAAATGGATGGTTTCGACCATCGA
1 T-ATGAAAA-GGATGGTAACGACCATCGA
58805641 CTAAAAAAAG
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
87 71 0.75
88 24 0.25
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (86 bp):
TATGAAAAGGATGGTAACGACCATCGAATACGAAAAACGATAGCTTCGGCTAACAATGATGAAAA
GAGATAGCTTCAGCTATCGAT
Found at i:58805561 original size:116 final size:116
Alignment explanation
Indices: 58805355--58805563 Score: 292
Period size: 116 Copynumber: 1.8 Consensus size: 116
58805345 CGACCAAAAA
* * * *
58805355 AAAAAGGATAGCTTCGGCTATCAATTATGAAAAGGGATAGCTTCGGCTATAGATCATGAAAAGGG
1 AAAAACGATAGCTTCGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATCATGAAAAGGG
* *** * * *
58805420 ATTGTGGCGACCATCTACTATGAAAAGGAATGGTGACGACCATCGAATATG
66 ATGGCAACGACCATCGAATACGAAAAGGAATGGTGACGACCATCGAATATG
* * *
58805471 AAAAACGATAGCTTTGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATCGATTATGAAAAGGG
1 AAAAACGATAGCTTCGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATCATGAAAAGGG
58805536 ATGGCAACGACCATCGAATACGAAAAGG
66 ATGGCAACGACCATCGAATACGAAAAGG
58805564 GATATCTTCG
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
116 79 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (116 bp):
AAAAACGATAGCTTCGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATCATGAAAAGGG
ATGGCAACGACCATCGAATACGAAAAGGAATGGTGACGACCATCGAATATG
Found at i:58805587 original size:116 final size:116
Alignment explanation
Indices: 58805355--58805608 Score: 278
Period size: 116 Copynumber: 2.2 Consensus size: 116
58805345 CGACCAAAAA
* * * *
58805355 AAAAAGGATAGCTTCGGCTATCAATTATGAAAAGGGATAGCTTCGGCTATAGATCATGAAAAGGG
1 AAAAAGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATCATGAAAAGGG
* *** * * * * *
58805420 ATTGTGGCGACCATCTACTATGAAAAGGAATGGTGACGACCATCGAATATG
66 ATGGCAACGACCATCGAATACGAAAAGGAATGCTGACGACCAACGAATATG
* * *
58805471 AAAAACGATAGCTTTGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATCGATTATGAAAAGGG
1 AAAAAGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATCATGAAAAGGG
* * * *
58805536 ATGGCAACGACCATCGAATACGAAAAGGGATAT-CT-TCGGCTAACGATTATG
66 ATGGCAACGACCATCGAATACGAAAA-GGA-ATGCTGACGACCAACGAATATG
* *
58805587 AAAAGGGATAGTTTTGGCTATC
1 AAAAAGGATAGCTTTGGCTATC
58805609 GATTAAAGAA
Statistics
Matches: 113, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
116 107 0.95
117 4 0.04
118 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.24
Consensus pattern (116 bp):
AAAAAGGATAGCTTTGGCTATCAATGATGAAAAGAGATAGCTTCAGCTATAGATCATGAAAAGGG
ATGGCAACGACCATCGAATACGAAAAGGAATGCTGACGACCAACGAATATG
Found at i:58811049 original size:21 final size:20
Alignment explanation
Indices: 58811025--58811063 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58811015 GGACTAATTT
58811025 AAAACAAATAAAAAATTTGGG
1 AAAA-AAATAAAAAATTTGGG
**
58811046 AAAAAGTTAAAAAATTTG
1 AAAAAAATAAAAAATTTG
58811064 AAAACAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.23
Consensus pattern (20 bp):
AAAAAAATAAAAAATTTGGG
Found at i:58816709 original size:79 final size:79
Alignment explanation
Indices: 58816568--58816732 Score: 213
Period size: 79 Copynumber: 2.1 Consensus size: 79
58816558 TGAAATTGTA
** * * * * * *
58816568 TTCTATTTGTAAATAGAAATCAATTGAACAATTCTATTTTAGGATTTTATTCTTGCTATTCAACA
1 TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTATTTTAGGATTCTATTCCTACCATTCAACA
* *
58816633 GAATTTGTTTGATT
66 AAATTTATTTGATT
* *
58816647 TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTGTTTTAGGATTCTATTCCTACCGTTCAACA
1 TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTATTTTAGGATTCTATTCCTACCATTCAACA
58816712 AAATTTATTTGATT
66 AAATTTATTTGATT
*
58816726 TTTTATT
1 TTCTATT
58816733 GTTAACGGTA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (79 bp):
TTCTATTTCCAAACAGAAATCAATTGAAAAATTCTATTTTAGGATTCTATTCCTACCATTCAACA
AAATTTATTTGATT
Found at i:58839392 original size:3 final size:3
Alignment explanation
Indices: 58839384--58839408 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
58839374 TATATGTAAG
58839384 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
58839409 ATGGGGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:58843838 original size:47 final size:48
Alignment explanation
Indices: 58843561--58843945 Score: 309
Period size: 49 Copynumber: 7.9 Consensus size: 48
58843551 TAAAAAAAAC
* * *
58843561 AAAAAAAAA-TTGGGTGCT-GCCTTGTTAATGGCCGGCACCAGTATACG
1 AAAAAAAAATTTTGGTGCTGGCC-TGTCAATGGCCGGCACCAGAATACG
** *
58843608 -AAAAAAAATTTTAGGTGCTGGATTGTCAATGGCCGGCACCACCAATACG
1 AAAAAAAAATTTT-GGTGCTGGCCTGTCAATGGCCGGCACCA-GAATACG
* * * * * *
58843657 -AAAAAAAATTTGTGATGCTGGCTTGTCAATGGTCGGTACAAGCAATATG
1 AAAAAAAAATTT-TGGTGCTGGCCTGTCAATGGCCGGCACCAG-AATACG
* *
58843706 AAAAAAAAATTTTGGTGCTGGCCTGTTAATGGCCGGCACCAGCAGTACGG
1 AAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCAG-AATAC-G
*** * * ** *
58843756 AAAAAATTTTTTTTTTGGTGTTGGCTTGTCAATGGCCAACACCAGTATACG
1 AAAAAA---AAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGAATACG
* * *
58843807 AAAAAAAAAATTT-GTGCTGGCCTGTCAATGGCCTGCACCAGTATAC-
1 AAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGAATACG
* * *
58843853 AAAAAAATAACTTTTTTGAGTGCTAGCCTGTCAATAGACGGCACCAGAAGTACG
1 AAAAAAA-AA---TTTTG-GTGCTGGCCTGTCAATGGCCGGCACCAGAA-TACG
*
58843907 -AAAAAAAA-TTTGGTGCTGGCCTGTCAATGGCTGGCACCA
1 AAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCA
58843946 AATTTATCAA
Statistics
Matches: 270, Mismatches: 49, Indels: 38
0.76 0.14 0.11
Matches are distributed among these distances:
46 15 0.06
47 56 0.21
48 30 0.11
49 73 0.27
50 22 0.08
51 7 0.03
52 30 0.11
53 37 0.14
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (48 bp):
AAAAAAAAATTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGAATACG
Found at i:58843927 original size:99 final size:99
Alignment explanation
Indices: 58843574--58843945 Score: 355
Period size: 99 Copynumber: 3.8 Consensus size: 99
58843564 AAAAAATTGG
* * * * **
58843574 GTGCTGCCTTGTTAATGGCCGGCACCAGTATACG-AAAAAAAATTTTAGGTGCTGGATTGTCAAT
1 GTGCTGGCTTGTCAATGGACGGCACCAGAATACGAAAAAAAAATTTT-GGTGCTGGCCTGTCAAT
* *
58843638 GGCCGGCACCACCAATACGAAAAAA-AA-TTTGTGA
65 GGCCGGCACCA-GAATACGAAAAAATAATTTTTTGA
* * * * *
58843672 -TGCTGGCTTGTCAATGGTCGGTACAAGCAATATGAAAAAAAAATTTTGGTGCTGGCCTGTTAAT
1 GTGCTGGCTTGTCAATGGACGGCACCAG-AATACGAAAAAAAAATTTTGGTGCTGGCCTGTCAAT
* **
58843736 GGCCGGCACCAGCAGTACGGAAAAAATTTTTTTTTTG-
65 GGCCGGCACCAG-AATAC-GAAAAAA-TAATTTTTTGA
* * ** * *
58843773 GTGTTGGCTTGTCAATGGCCAACACCAGTATACGAAAAAAAAAATTT-GTGCTGGCCTGTCAATG
1 GTGCTGGCTTGTCAATGGACGGCACCAGAATACGAAAAAAAAATTTTGGTGCTGGCCTGTCAATG
* * *
58843837 GCCTGCACCAGTATACAAAAAAATAACTTTTTTGA
66 GCCGGCACCAGAATACGAAAAAATAA-TTTTTTGA
* * *
58843872 GTGCTAGCCTGTCAATAGACGGCACCAGAAGTACG-AAAAAAAA-TTTGGTGCTGGCCTGTCAAT
1 GTGCTGGCTTGTCAATGGACGGCACCAGAA-TACGAAAAAAAAATTTTGGTGCTGGCCTGTCAAT
*
58843935 GGCTGGCACCA
65 GGCCGGCACCA
58843946 AATTTATCAA
Statistics
Matches: 221, Mismatches: 41, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
97 23 0.10
98 49 0.22
99 77 0.35
100 30 0.14
101 16 0.07
102 26 0.12
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (99 bp):
GTGCTGGCTTGTCAATGGACGGCACCAGAATACGAAAAAAAAATTTTGGTGCTGGCCTGTCAATG
GCCGGCACCAGAATACGAAAAAATAATTTTTTGA
Found at i:58844747 original size:13 final size:12
Alignment explanation
Indices: 58844728--58844752 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58844718 AATGCAGCAC
58844728 TAAAAAAAATTT
1 TAAAAAAAATTT
58844740 TAAAAAAAATTT
1 TAAAAAAAATTT
58844752 T
1 T
58844753 GTATACCAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAAAAATTT
Found at i:58856761 original size:70 final size:68
Alignment explanation
Indices: 58856547--58856762 Score: 151
Period size: 70 Copynumber: 3.1 Consensus size: 68
58856537 CAAGACATAT
*
58856547 CAATTAGCTCAAACATTCAAATGTCAACCTTCAACTATGCCATATCATATTGAATCAAGCTATTC
1 CAATTAGCTCAAACATTCAAATGTC-ACCTTCAACTATG-CATATCATATTGAATCAAGCCATTC
58856612 CATTA
64 CATTA
* * * * *
58856617 CAATTA-CAT-ACAA-ATT-TAAT-TCACTCATCATAACCTTCATGCACT-TGAT-TTAAAGCAA
1 CAATTAGC-TCA-AACATTCAAATGTCAC-CTTC--AA-C-T-ATGCA-TATCATATTGAATCAA
** ***
58856675 ATCAAGACA-TA
57 GCCATTCCATTA
58856686 TCAATTAGCTCAAACATTCAAATGTCGACCTTCAACTATGCTATATCATATTGAATCAAGCCATT
1 -CAATTAGCTCAAACATTCAAATGTC-ACCTTCAACTATGC-ATATCATATTGAATCAAGCCATT
58856751 CCATTA
63 CCATTA
58856757 CAATTA
1 CAATTA
58856763 CATACAAATT
Statistics
Matches: 105, Mismatches: 21, Indels: 40
0.63 0.13 0.24
Matches are distributed among these distances:
66 2 0.02
67 5 0.05
68 8 0.08
69 14 0.13
70 47 0.45
71 15 0.14
72 7 0.07
73 5 0.05
74 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.31
Consensus pattern (68 bp):
CAATTAGCTCAAACATTCAAATGTCACCTTCAACTATGCATATCATATTGAATCAAGCCATTCCA
TTA
Found at i:58856770 original size:140 final size:140
Alignment explanation
Indices: 58856518--58856805 Score: 533
Period size: 140 Copynumber: 2.1 Consensus size: 140
58856508 TTACTACATC
58856518 CACTTGATTTAAAGCAAATCAAGACATATCAATTAGCTCAAACATTCAAATGTCAACCTTCAACT
1 CACTTGATTTAAAGCAAATCAAGACATATCAATTAGCTCAAACATTCAAATGTCAACCTTCAACT
*
58856583 ATGCCATATCATATTGAATCAAGCTATTCCATTACAATTACATACAAATTTAATTCACTCATCAT
66 ATGCCATATCATATTGAATCAAGCCATTCCATTACAATTACATACAAATTTAATTCACTCATCAT
58856648 AACCTTCATG
131 AACCTTCATG
*
58856658 CACTTGATTTAAAGCAAATCAAGACATATCAATTAGCTCAAACATTCAAATGTCGACCTTCAACT
1 CACTTGATTTAAAGCAAATCAAGACATATCAATTAGCTCAAACATTCAAATGTCAACCTTCAACT
*
58856723 ATGCTATATCATATTGAATCAAGCCATTCCATTACAATTACATACAAATTTAATTCACTCATCAT
66 ATGCCATATCATATTGAATCAAGCCATTCCATTACAATTACATACAAATTTAATTCACTCATCAT
58856788 AACCTTCATG
131 AACCTTCATG
58856798 -ACCTTGAT
1 CA-CTTGAT
58856806 ATGAACCATA
Statistics
Matches: 144, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
139 1 0.01
140 143 0.99
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.32
Consensus pattern (140 bp):
CACTTGATTTAAAGCAAATCAAGACATATCAATTAGCTCAAACATTCAAATGTCAACCTTCAACT
ATGCCATATCATATTGAATCAAGCCATTCCATTACAATTACATACAAATTTAATTCACTCATCAT
AACCTTCATG
Found at i:58864138 original size:9 final size:9
Alignment explanation
Indices: 58864114--58864378 Score: 88
Period size: 9 Copynumber: 28.7 Consensus size: 9
58864104 TATTAGATTT
58864114 TTTTTATAAA
1 TTTTTAT-AA
58864124 TTTTTATAA
1 TTTTTATAA
*
58864133 TATTTAATAA
1 T-TTTTATAA
58864143 TCTTTTATAA
1 T-TTTTATAA
*
58864153 CTTTTATAA
1 TTTTTATAA
* *
58864162 GGTTATATCAA
1 -TTTTTAT-AA
*
58864173 TTTTAAT-A
1 TTTTTATAA
* *
58864181 TTTTTTTTA
1 TTTTTATAA
58864190 TTTTTATAA
1 TTTTTATAA
58864199 GTTTTTAATAA
1 -TTTTT-ATAA
*
58864210 -TTTTATATG
1 TTTTTATA-A
58864219 TTTTTATAAA
1 TTTTTAT-AA
* ** *
58864229 ATTCAAAATA
1 TTTTTATA-A
*
58864239 TGTTTTGTTAA
1 T-TTTT-ATAA
58864250 TTTGATTATAA
1 TTT--TTATAA
*
58864261 GTTTT-TAA
1 TTTTTATAA
58864269 -TTTT-T--
1 TTTTTATAA
*
58864274 TCTTTATAA
1 TTTTTATAA
58864283 TTTTTATAA
1 TTTTTATAA
*
58864292 GTTTATATCAA
1 -TTTTTAT-AA
*
58864303 -TTTTATTA
1 TTTTTATAA
58864311 TTTTT-TAAA
1 TTTTTAT-AA
58864320 TATTTT-TAA
1 T-TTTTATAA
58864329 TTTTTAATAA
1 TTTTT-ATAA
58864339 -TTTTATAA
1 TTTTTATAA
58864347 TTTTTAATAA
1 TTTTT-ATAA
*
58864357 -TTTTA-AT
1 TTTTTATAA
*
58864364 TTTTTATTA
1 TTTTTATAA
58864373 TTTTTA
1 TTTTTA
58864379 AGAGAAAATA
Statistics
Matches: 191, Mismatches: 35, Indels: 59
0.67 0.12 0.21
Matches are distributed among these distances:
6 3 0.02
7 7 0.04
8 28 0.15
9 66 0.35
10 66 0.35
11 18 0.09
12 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:58864152 original size:10 final size:10
Alignment explanation
Indices: 58864115--58864161 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
58864105 ATTAGATTTT
58864115 TTTTATAAAT-
1 TTTTAT-AATC
*
58864125 TTTTATAATA
1 TTTTATAATC
*
58864135 TTTAATAATC
1 TTTTATAATC
58864145 TTTTATAA-C
1 TTTTATAATC
58864154 TTTTATAA
1 TTTTATAA
58864162 GGTTATATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 12 0.36
10 21 0.64
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTTATAATC
Found at i:58864213 original size:19 final size:18
Alignment explanation
Indices: 58864115--58864361 Score: 95
Period size: 19 Copynumber: 13.3 Consensus size: 18
58864105 ATTAGATTTT
*
58864115 TTTTATAAATTTTTATAA
1 TTTTATAAGTTTTTATAA
58864133 TATTTAATAA-TCTTTTATAA
1 T-TTT-ATAAGT-TTTTATAA
* *
58864153 CTTTTATAAGGTTATATCAA
1 -TTTTATAAGTTTTTAT-AA
* * *
58864173 TTTTA-ATATTTTTTTTAT
1 TTTTATA-AGTTTTTATAA
58864191 TTTTATAAGTTTTTAATAA
1 TTTTATAAGTTTTT-ATAA
*
58864210 TTTTATATGTTTTTATAAAA
1 TTTTATAAGTTTTTAT--AA
** *
58864230 TTCAAAATATGTTTTGT-TAA
1 TT--TTATAAGTTTT-TATAA
58864250 TTTGATTATAAG-TTTT-TAA
1 -TT--TTATAAGTTTTTATAA
*
58864269 TTTT-T---TCTTTATAA
1 TTTTATAAGTTTTTATAA
*
58864283 TTTTTATAAGTTTATATCAA
1 -TTTTATAAGTTTTTAT-AA
* *
58864303 TTTTATTATTTTTTA-AA
1 TTTTATAAGTTTTTATAA
*
58864320 TATTTTTAA-TTTTTAATAA
1 T-TTTATAAGTTTTT-ATAA
58864339 TTTTATAA-TTTTTAATAA
1 TTTTATAAGTTTTT-ATAA
58864357 TTTTA
1 TTTTA
58864362 ATTTTTTATT
Statistics
Matches: 177, Mismatches: 26, Indels: 52
0.69 0.10 0.20
Matches are distributed among these distances:
13 3 0.02
14 3 0.02
15 5 0.03
16 3 0.02
17 8 0.05
18 45 0.25
19 63 0.36
20 28 0.16
21 8 0.05
22 10 0.06
23 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTATAAGTTTTTATAA
Found at i:58864334 original size:17 final size:16
Alignment explanation
Indices: 58864312--58864379 Score: 82
Period size: 17 Copynumber: 4.0 Consensus size: 16
58864302 ATTTTATTAT
58864312 TTTTTAAATATTTTTAA
1 TTTTT-AATATTTTTAA
58864329 TTTTTAATAATTTTATAA
1 TTTTTAAT-ATTTT-TAA
*
58864347 TTTTTAATAATTTTAA
1 TTTTTAATATTTTTAA
*
58864363 TTTTTTATTATTTTTAA
1 -TTTTTAATATTTTTAA
58864380 GAGAAAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
16 6 0.13
17 28 0.62
18 11 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTAATATTTTTAA
Found at i:58869525 original size:57 final size:57
Alignment explanation
Indices: 58869440--58869556 Score: 182
Period size: 57 Copynumber: 2.1 Consensus size: 57
58869430 ACAAATTTAA
*
58869440 AAAAAAATTCTTTTTTTTTGTGTCAGAATCAAATATAAATATAC-GAAAAAAATTTT
1 AAAAAAATTCTTTTTTTTTGTGTCAGAATCAAATATAAATATACAAAAAAAAATTTT
* * *
58869496 AAAAAAATTTTCTTTTTTTTGTGTTAGAATCAGATATAAATATACAAAAAAAAATTTT
1 AAAAAAATTCT-TTTTTTTTGTGTCAGAATCAAATATAAATATACAAAAAAAAATTTT
58869554 AAA
1 AAA
58869557 TTTGTACTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 10 0.18
57 31 0.56
58 14 0.25
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (57 bp):
AAAAAAATTCTTTTTTTTTGTGTCAGAATCAAATATAAATATACAAAAAAAAATTTT
Found at i:58869662 original size:97 final size:101
Alignment explanation
Indices: 58869550--58869815 Score: 328
Period size: 97 Copynumber: 2.6 Consensus size: 101
58869540 CAAAAAAAAA
* * *
58869550 TTTT-AAATTTGTACTGGATGCAGGCCATTGACAGGCCAGCACCTAAAATTTTTTTTATTTTTTT
1 TTTTAAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTTTT
*
58869614 CGTATATTTATATCT-AAT-T-AAAAAAG-AATTTT
66 CCTATATTTATATCTGAATCTAAAAAAAGAAATTTT
* * **
58869646 TTTTAAAATTTGTACTGGGTGCCGGCCATTAACAGGCTAGCACCCAAAATTTTTTTTAACTTTTT
1 TTTTAAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTTTT
*
58869711 CCTATATTTATATCTGATTCTAACACGAAAAAAAAAGAAATTTT
66 CCTATATTTATATCTGAATCT--------AAAAAAAGAAATTTT
*
58869755 TTTTAAAATTTGTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAAATTTTTTTT-TTTT
1 TTTTAAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTT
58869816 CGTTTTTCTT
Statistics
Matches: 143, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
96 4 0.03
97 67 0.47
98 2 0.01
99 1 0.01
108 9 0.06
109 60 0.42
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (101 bp):
TTTTAAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTTTT
CCTATATTTATATCTGAATCTAAAAAAAGAAATTTT
Found at i:58872141 original size:91 final size:91
Alignment explanation
Indices: 58872026--58872206 Score: 265
Period size: 91 Copynumber: 2.0 Consensus size: 91
58872016 ATTGTATATA
* * *
58872026 TATTAATATTGTTATTGATTGAGTTGGTGTCACAAATTAACTCGACACCAA-TTTAGAATTGATA
1 TATTAATAATGTTATTGATTGAGTTGGTATCACAAATTAACTCGACACCAACTTAAG-ATTGATA
* *
58872090 TATTTATTTAGTCCTCTTAATCTGATG
65 TAGTTATTTAGTACTCTTAATCTGATG
* * *
58872117 TATTAATAATGTTATTGATTGAGTTGGTATCACAAATTAACTTGACACCAACTTAAGATTTATGT
1 TATTAATAATGTTATTGATTGAGTTGGTATCACAAATTAACTCGACACCAACTTAAGATTGATAT
*
58872182 AGTTATTTAGTATTCTTAATCTGAT
66 AGTTATTTAGTACTCTTAATCTGAT
58872207 TTAAATTTCG
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 76 0.95
92 4 0.05
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (91 bp):
TATTAATAATGTTATTGATTGAGTTGGTATCACAAATTAACTCGACACCAACTTAAGATTGATAT
AGTTATTTAGTACTCTTAATCTGATG
Found at i:58873820 original size:30 final size:31
Alignment explanation
Indices: 58873752--58873826 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
58873742 AACTACATAA
58873752 TTAGTCAC-CAAACTATTAAGTTCTTTCTGTT
1 TTAGTCACTC-AACTATTAAGTTCTTTCTGTT
* * *
58873783 TTGGTCACTCAACTATTAA-TTTTTTTTGTT
1 TTAGTCACTCAACTATTAAGTTCTTTCTGTT
58873813 TTAGTCACTCAACT
1 TTAGTCACTCAACT
58873827 TTTCAAAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 22 0.56
31 16 0.41
32 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (31 bp):
TTAGTCACTCAACTATTAAGTTCTTTCTGTT
Found at i:58875415 original size:43 final size:43
Alignment explanation
Indices: 58875367--58875452 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
58875357 TATGTTATTG
* * *
58875367 ATATTGAAATGGAAAAGATGATAACTGAATATGAGATGAGAAA
1 ATATTGAAATGGAAAAGATGAGAAATGAATATGAAATGAGAAA
* * *
58875410 ATATTGAAATGGCAAATATGAGAAATGATTATGAAATGAGAAA
1 ATATTGAAATGGAAAAGATGAGAAATGAATATGAAATGAGAAA
58875453 TGAAATATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.22, T:0.24
Consensus pattern (43 bp):
ATATTGAAATGGAAAAGATGAGAAATGAATATGAAATGAGAAA
Found at i:58875450 original size:18 final size:19
Alignment explanation
Indices: 58875427--58875467 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
58875417 AATGGCAAAT
*
58875427 ATGAGAAATG-ATTATGAA
1 ATGAGAAATGAAATATGAA
58875445 ATGAGAAATGAAATATGAA
1 ATGAGAAATGAAATATGAA
58875464 ATGA
1 ATGA
58875468 TGAATTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (19 bp):
ATGAGAAATGAAATATGAA
Found at i:58876831 original size:49 final size:49
Alignment explanation
Indices: 58876759--58876855 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
58876749 TCAAGAAGGG
* *
58876759 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAGTTTAGAAATGT
* *
58876808 ATAAATAGTGATAAGTGTGTAGACAGTGGAAGACCAAGTTTAGAAATG
1 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAGTTTAGAAATG
58876856 CATAGCATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAGTTTAGAAATGT
Found at i:58881385 original size:16 final size:16
Alignment explanation
Indices: 58881364--58881398 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
58881354 AGCTAGAGGG
58881364 ATTAAATAGCTATGAA
1 ATTAAATAGCTATGAA
*
58881380 ATTAAATAGCTATGGA
1 ATTAAATAGCTATGAA
58881396 ATT
1 ATT
58881399 CAAACTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (16 bp):
ATTAAATAGCTATGAA
Found at i:58891670 original size:42 final size:42
Alignment explanation
Indices: 58891606--58891752 Score: 147
Period size: 42 Copynumber: 3.5 Consensus size: 42
58891596 CTTTCCATTT
* * * *
58891606 AGCTCTCACGAGCTTCTATTTAACTCATATGAGTTT-TCGTTC
1 AGCTCTTACGAGCTTCTGTTTAACCCATATGGGTTTCT-GTTC
** *
58891648 AGCTCTTTTGAGCTTCTGTTTAACCCTTATGGGTTTCTGTTC
1 AGCTCTTACGAGCTTCTGTTTAACCCATATGGGTTTCTGTTC
** * *
58891690 AGCTCTTACGAGCTTCTGTCCAACCCTTATGGGTTTCTGTTT
1 AGCTCTTACGAGCTTCTGTTTAACCCATATGGGTTTCTGTTC
58891732 AG--CTTACATGAGCTTCTGTTT
1 AGCTCTTAC--GAGCTTCTGTTT
58891753 GGCCTTCGAG
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 5 0.06
42 82 0.93
43 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (42 bp):
AGCTCTTACGAGCTTCTGTTTAACCCATATGGGTTTCTGTTC
Found at i:58891687 original size:21 final size:21
Alignment explanation
Indices: 58891661--58891730 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
58891651 TCTTTTGAGC
*
58891661 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
* * * * *
58891682 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAACCCTTATGGGT
*
58891703 TTCTGTCCAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
58891724 TTCTGTT
1 TTCTGTT
58891731 TAGCTTACAT
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (21 bp):
TTCTGTTCAACCCTTATGGGT
Found at i:58895929 original size:23 final size:23
Alignment explanation
Indices: 58895886--58895929 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
58895876 TTAATTAAAT
* *
58895886 TGTAATTTTTACAATAATAAAAA
1 TGTAATTTTTAAAAGAATAAAAA
*
58895909 TGTAATTTTTAAAAGATTAAA
1 TGTAATTTTTAAAAGAATAAA
58895930 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (23 bp):
TGTAATTTTTAAAAGAATAAAAA
Found at i:58900551 original size:25 final size:25
Alignment explanation
Indices: 58900518--58900569 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
58900508 AAACTCAAAT
58900518 AACTAATCTTTAATAATTGTTTACA
1 AACTAATCTTTAATAATTGTTTACA
*
58900543 AACTCATCTTTAATAATTGTTTACA
1 AACTAATCTTTAATAATTGTTTACA
58900568 AA
1 AA
58900570 ATCAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (25 bp):
AACTAATCTTTAATAATTGTTTACA
Found at i:58900579 original size:25 final size:25
Alignment explanation
Indices: 58900526--58900579 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
58900516 ATAACTAATC
* **
58900526 TTTAATAATTGTTTACAAACTCATC
1 TTTAATAATTGTTTACAAAATCAAA
58900551 TTTAATAATTGTTTACAAAATCAAA
1 TTTAATAATTGTTTACAAAATCAAA
58900576 TTTA
1 TTTA
58900580 TTTTTGACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (25 bp):
TTTAATAATTGTTTACAAAATCAAA
Found at i:58905884 original size:3 final size:3
Alignment explanation
Indices: 58905876--58905945 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
58905866 ACCAGATCTT
58905876 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
58905924 ATA ATA ATA ATA ATG ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
58905946 AAGGTAGATT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:58906064 original size:19 final size:19
Alignment explanation
Indices: 58906040--58906077 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
58906030 GATAGTTATC
58906040 ATATGGAAT-CTATTATTTG
1 ATATGGAATGC-ATTATTTG
*
58906059 ATATGGTATGCATTATTTG
1 ATATGGAATGCATTATTTG
58906078 TGGTATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47
Consensus pattern (19 bp):
ATATGGAATGCATTATTTG
Found at i:58908954 original size:28 final size:27
Alignment explanation
Indices: 58908911--58908968 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
58908901 TATATAGTAT
* *
58908911 CAGTACAGTGTGGGCCTTAACCCATTA
1 CAGTACAGTGTAGGCCTTAACCCAATA
*
58908938 CAGTAACAGTGTAGGCCTTAGCCCAATA
1 CAGT-ACAGTGTAGGCCTTAACCCAATA
58908966 CAG
1 CAG
58908969 AAATTAGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (27 bp):
CAGTACAGTGTAGGCCTTAACCCAATA
Found at i:58909133 original size:26 final size:26
Alignment explanation
Indices: 58909077--58909134 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
58909067 GCCAACACAC
58909077 CAATATCGCAGAAAAGCCGCCAGTAA
1 CAATATCGCAGAAAAGCCGCCAGTAA
* * * * *
58909103 TAATATCGCAGTAAAGCTGTCAGTGA
1 CAATATCGCAGAAAAGCCGCCAGTAA
58909129 CAATAT
1 CAATAT
58909135 ATGTGGCAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (26 bp):
CAATATCGCAGAAAAGCCGCCAGTAA
Found at i:58909481 original size:81 final size:81
Alignment explanation
Indices: 58909366--58909534 Score: 243
Period size: 81 Copynumber: 2.1 Consensus size: 81
58909356 TTATTTTGGG
* *
58909366 TAATTTTACCCTTTGAGGGTATTTTGGGAATTTTAACCTTCGAGGATATTTCTG-TAATTTTACC
1 TAATTTTACCCTTTGAGGGTATTTCGAGAATTTTAACCTTCGAGGATATTTC-GATAATTTTACC
*
58909430 CTTTGAGGGTATTTCAA
65 CTTTGAGGGCATTTCAA
* * *
58909447 TAATTTTACTCTTCT-AGGGTATTTCGATAATTTTAACCTTCGAGGGTATTTCGATAATTTTACC
1 TAATTTTACCCTT-TGAGGGTATTTCGAGAATTTTAACCTTCGAGGATATTTCGATAATTTTACC
*
58909511 CTTTGAGGGCATTTCAG
65 CTTTGAGGGCATTTCAA
58909528 TAATTTT
1 TAATTTT
58909535 TTGGCCTAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
80 1 0.01
81 77 0.97
82 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (81 bp):
TAATTTTACCCTTTGAGGGTATTTCGAGAATTTTAACCTTCGAGGATATTTCGATAATTTTACCC
TTTGAGGGCATTTCAA
Found at i:58909525 original size:27 final size:27
Alignment explanation
Indices: 58909328--58909534 Score: 197
Period size: 27 Copynumber: 7.6 Consensus size: 27
58909318 ACCTTACGGA
* *
58909328 GGTATTTCGATCATTTTACCTTTTTG-G
1 GGTATTTCGATAATTTTACC-CTTTGAG
* * *
58909355 GTTATTTTGGGTAATTTTACCCTTTGAG
1 GGTA-TTTCGATAATTTTACCCTTTGAG
* ** * *
58909383 GGTATTTTGGGAATTTTAACCTTCGAG
1 GGTATTTCGATAATTTTACCCTTTGAG
*
58909410 GATATTTCTG-TAATTTTACCCTTTGAG
1 GGTATTTC-GATAATTTTACCCTTTGAG
* *
58909437 GGTATTTCAATAATTTTACTCTTCT-AG
1 GGTATTTCGATAATTTTACCCTT-TGAG
* *
58909464 GGTATTTCGATAATTTTAACCTTCGAG
1 GGTATTTCGATAATTTTACCCTTTGAG
58909491 GGTATTTCGATAATTTTACCCTTTGAG
1 GGTATTTCGATAATTTTACCCTTTGAG
*
58909518 GGCATTTC-AGTAATTTT
1 GGTATTTCGA-TAATTTT
58909535 TTGGCCTAAG
Statistics
Matches: 148, Mismatches: 25, Indels: 14
0.79 0.13 0.07
Matches are distributed among these distances:
26 1 0.01
27 128 0.86
28 19 0.13
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (27 bp):
GGTATTTCGATAATTTTACCCTTTGAG
Found at i:58909900 original size:28 final size:27
Alignment explanation
Indices: 58909841--58910116 Score: 173
Period size: 27 Copynumber: 10.2 Consensus size: 27
58909831 TATAACAGTT
* * * * *
58909841 ATTTTAACCTATAGGGGTATTTCGGTT
1 ATTTTACCCTTTAAGGGTATTTTGGTA
*
58909868 ATTTTACCCTTT-GGGGTTATTTTGGGTA
1 ATTTTACCCTTTAAGGG-TATTTT-GGTA
58909896 ATTTTACCCTTTAAGGGTATTTTGGTA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
* ** ** * *
58909923 ATTTTAACCTTCGAGAATATTTCGATA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
* * **
58909950 ATTTTACCTTTTGAGGGTATTTCAGTA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
* * **
58909977 ATTTTACCCTTTTAGGATATTTCAGTA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
* * *
58910004 ATTTTACCCTTCGAA-GGTATTTCGATA
1 ATTTTACCCTT-TAAGGGTATTTTGGTA
** *
58910031 ATTTTACCCTTCGATGGTATTTCT-GTA
1 ATTTTACCCTTTAAGGGTATTT-TGGTA
** *
58910058 ATTTTACCCTTCGATGGTATTTCT-GTA
1 ATTTTACCCTTTAAGGGTATTT-TGGTA
** * *
58910085 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTTAAGGGTATTTTGGTA
58910112 ATTTT
1 ATTTT
58910117 CTAGCCCAAT
Statistics
Matches: 208, Mismatches: 34, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
26 5 0.02
27 178 0.86
28 22 0.11
29 3 0.01
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.46
Consensus pattern (27 bp):
ATTTTACCCTTTAAGGGTATTTTGGTA
Found at i:58909971 original size:54 final size:54
Alignment explanation
Indices: 58909855--58910116 Score: 278
Period size: 54 Copynumber: 4.8 Consensus size: 54
58909845 TAACCTATAG
* * * * * * **
58909855 GGGTATTTCGGTTATTTTACCCTTTGGGGTTATTTTGGGTAATTTTACCCTTTAA
1 GGGTATTTCGGTAATTTTACCCTTCGAGGATA-TTTCGATAATTTTACCCTTCGA
* * * * *
58909910 GGGTATTTTGGTAATTTTAACCTTCGAGAATATTTCGATAATTTTACCTTTTGA
1 GGGTATTTCGGTAATTTTACCCTTCGAGGATATTTCGATAATTTTACCCTTCGA
* **
58909964 GGGTATTTCAGTAATTTTACCCTTTTAGGATATTTC-AGTAATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGAGGATATTTCGA-TAATTTTACCCTTCGA
* *
58910018 AGGTATTTCGATAATTTTACCCTTCGATGG-TATTTCTG-TAATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA-GGATATTTC-GATAATTTTACCCTTCGA
* * *
58910072 TGGTATTTCTGTAATTTTACCCTTCGAGGGTATTTCGATAATTTT
1 GGGTATTTCGGTAATTTTACCCTTCGAGGATATTTCGATAATTTT
58910117 CTAGCCCAAT
Statistics
Matches: 174, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
53 4 0.02
54 143 0.82
55 27 0.16
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.47
Consensus pattern (54 bp):
GGGTATTTCGGTAATTTTACCCTTCGAGGATATTTCGATAATTTTACCCTTCGA
Found at i:58910005 original size:81 final size:80
Alignment explanation
Indices: 58909857--58910116 Score: 299
Period size: 81 Copynumber: 3.2 Consensus size: 80
58909847 ACCTATAGGG
* * ** **
58909857 GTATTTCGGTTATTTTACCCTTTG-GGGTTATTTTGGGTAATTTTACCCTTTAAGGGTATTTTGG
1 GTATTTCGATAATTTTACCCTTTGAGGG-TA-TTTCAGTAATTTTACCCTTTAA-GGTATTTCAG
*
58909921 TAATTTTAACCTTCGAGA
63 TAATTTTACCCTTCGAGA
* * *
58909939 ATATTTCGATAATTTTACCTTTTGAGGGTATTTCAGTAATTTTACCCTTTTAGGATATTTCAGTA
1 GTATTTCGATAATTTTACCCTTTGAGGGTATTTCAGTAATTTTACCCTTTAAGG-TATTTCAGTA
58910004 ATTTTACCCTTCGA-A
65 ATTTTACCCTTCGAGA
* * * * * *
58910019 GGTATTTCGATAATTTTACCCTTCGATGGTATTTCTGTAATTTTACCCTTCGATGGTATTTCTGT
1 -GTATTTCGATAATTTTACCCTTTGAGGGTATTTCAGTAATTTTACCCTT-TAAGGTATTTCAGT
*
58910084 AATTTTACCCTTCGAGG
64 AATTTTACCCTTCGAGA
58910101 GTATTTCGATAATTTT
1 GTATTTCGATAATTTT
58910117 CTAGCCCAAT
Statistics
Matches: 153, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.02
81 123 0.80
82 24 0.16
83 3 0.02
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.47
Consensus pattern (80 bp):
GTATTTCGATAATTTTACCCTTTGAGGGTATTTCAGTAATTTTACCCTTTAAGGTATTTCAGTAA
TTTTACCCTTCGAGA
Found at i:58915826 original size:28 final size:27
Alignment explanation
Indices: 58915787--58915844 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
58915777 TATACAGTAT
*
58915787 CAGTACAGTGTGGGCCTTAGCCCATTA
1 CAGTACAGTGTGGGCCTTAGCCCAATA
* *
58915814 CAGTAACAGTGTGGGCTTTATCCCAATA
1 CAGT-ACAGTGTGGGCCTTAGCCCAATA
58915842 CAG
1 CAG
58915845 AAATCAGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (27 bp):
CAGTACAGTGTGGGCCTTAGCCCAATA
Found at i:58915984 original size:26 final size:26
Alignment explanation
Indices: 58915948--58916015 Score: 136
Period size: 26 Copynumber: 2.6 Consensus size: 26
58915938 ACCCAACCAA
58915948 CGCAACAAAGCTGCCAATAATGATAT
1 CGCAACAAAGCTGCCAATAATGATAT
58915974 CGCAACAAAGCTGCCAATAATGATAT
1 CGCAACAAAGCTGCCAATAATGATAT
58916000 CGCAACAAAGCTGCCA
1 CGCAACAAAGCTGCCA
58916016 GTGACAGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.16
Consensus pattern (26 bp):
CGCAACAAAGCTGCCAATAATGATAT
Found at i:58916261 original size:27 final size:27
Alignment explanation
Indices: 58916219--58916423 Score: 234
Period size: 27 Copynumber: 7.6 Consensus size: 27
58916209 AACCTACGGA
* * *
58916219 GGTATTTTGGTCATTTTACCCTTTG-G
1 GGTATTTCGGTAATTTTACCCTTCGAG
* * *
58916245 GGTATTTAGGGTAATTTTACCTTTTGAG
1 GGTATTT-CGGTAATTTTACCCTTCGAG
* *
58916273 GGTTTTTCGGTAATTTTACCCTTCAAG
1 GGTATTTCGGTAATTTTACCCTTCGAG
* *
58916300 AG-ATTTCGATAATTTTACCCTTCGAG
1 GGTATTTCGGTAATTTTACCCTTCGAG
**
58916326 GGTATTTCAATAATTTTACCCTTCGAG
1 GGTATTTCGGTAATTTTACCCTTCGAG
* * *
58916353 GGTATTTTGGTAATTTAACCCTTCGTG
1 GGTATTTCGGTAATTTTACCCTTCGAG
*
58916380 GGTATTTCGGTAATTTTACCTTTCGAG
1 GGTATTTCGGTAATTTTACCCTTCGAG
*
58916407 GGTATTTCGATAATTTT
1 GGTATTTCGGTAATTTT
58916424 CTTACCCAAG
Statistics
Matches: 152, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
26 29 0.19
27 116 0.76
28 7 0.05
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (27 bp):
GGTATTTCGGTAATTTTACCCTTCGAG
Found at i:58918287 original size:46 final size:46
Alignment explanation
Indices: 58918231--58918377 Score: 186
Period size: 46 Copynumber: 3.2 Consensus size: 46
58918221 TTACCCGTTT
* **
58918231 GGGTTAAACCTACACGAATTGGATAATTGTGCATGGTCACCCATTA
1 GGGTTGAACCTACACGAATTGGATAATTGTGCATGGTCACCTGTTA
* *
58918277 GGGTTGAACCTACACGAATTGGGTAATTGTGCTTGGTCACCTGTTA
1 GGGTTGAACCTACACGAATTGGATAATTGTGCATGGTCACCTGTTA
* * * * * *
58918323 GGGTTGAACCTACATGAATCGAATAATAGTACATTGTCACCTGTTA
1 GGGTTGAACCTACACGAATTGGATAATTGTGCATGGTCACCTGTTA
*
58918369 GGATTGAAC
1 GGGTTGAAC
58918378 GTGCACAGGA
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (46 bp):
GGGTTGAACCTACACGAATTGGATAATTGTGCATGGTCACCTGTTA
Found at i:58919107 original size:20 final size:20
Alignment explanation
Indices: 58919082--58919119 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58919072 TCCATCAAAG
* *
58919082 ATTCAAAATCTACCATAAAC
1 ATTCAAAAACTACAATAAAC
58919102 ATTCAAAAACTACAATAA
1 ATTCAAAAACTACAATAA
58919120 TATCAATGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (20 bp):
ATTCAAAAACTACAATAAAC
Found at i:58921575 original size:10 final size:11
Alignment explanation
Indices: 58921557--58921588 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
58921547 TTTGCATAAG
58921557 ATATGAATTGA
1 ATATGAATTGA
58921568 AT-TGAATTGA
1 ATATGAATTGA
58921578 ATATGAATTGA
1 ATATGAATTGA
58921589 TGTTAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (11 bp):
ATATGAATTGA
Found at i:58922127 original size:24 final size:24
Alignment explanation
Indices: 58922100--58922191 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 24
58922090 ATCCCAATTA
58922100 ATTGGCTCTCCGGAGCTTCTCGAT
1 ATTGGCTCTCCGGAGCTTCTCGAT
* * * *
58922124 ATTGGCTCGCTTGAACCTTCAT-GAT
1 ATTGGCTCTC-CGGAGCTTC-TCGAT
*** *
58922149 ATTGGCTCTTATGAGCTTCTCGTT
1 ATTGGCTCTCCGGAGCTTCTCGAT
*
58922173 AATGGCTCTCCGGAGCTTC
1 ATTGGCTCTCCGGAGCTTC
58922192 CTATTACATA
Statistics
Matches: 50, Mismatches: 15, Indels: 6
0.70 0.21 0.08
Matches are distributed among these distances:
23 1 0.02
24 31 0.62
25 17 0.34
26 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (24 bp):
ATTGGCTCTCCGGAGCTTCTCGAT
Found at i:58924934 original size:3 final size:3
Alignment explanation
Indices: 58924926--58924955 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
58924916 TTGATTTGTT
58924926 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
58924956 CAAACCGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58937849 original size:13 final size:13
Alignment explanation
Indices: 58937827--58937858 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
58937817 TGGGATTTAT
*
58937827 CACACAGCCTGGA
1 CACACGGCCTGGA
58937840 CACACGGCCTGGA
1 CACACGGCCTGGA
58937853 CACACG
1 CACACG
58937859 ACCGTGTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.41, G:0.25, T:0.06
Consensus pattern (13 bp):
CACACGGCCTGGA
Found at i:58945667 original size:33 final size:33
Alignment explanation
Indices: 58945625--58945923 Score: 123
Period size: 33 Copynumber: 8.4 Consensus size: 33
58945615 CGGTGGATTT
*
58945625 AGCACTTAGCAACCACCAGTGATTCGGGGAATC
1 AGCACTTAGCAACCACCAATGATTCGGGGAATC
*
58945658 AGCACTTAGCAACCCCTTTCACATTCAATGATACGGTGGAATC
1 AGCACTTAGCAA---C---CAC---CAATGATTCGG-GGAATC
* *
58945701 AGCACTTAGCAACCACCAATGAATCAGGGAATC
1 AGCACTTAGCAACCACCAATGATTCGGGGAATC
* *
58945734 AGCACTTAGCAACCCCTTTCACATTTAAGATAT-GGTGGGATC
1 AGCACTTAGCAACCAC---CA-A--T--GAT-TCGG-GGAATC
*
58945776 AGCACTTAGCAACCACCAATGAATT-GGGGAATT
1 AGCACTTAGCAACCACCAATG-ATTCGGGGAATC
* *
58945809 AACACTTAGCAA-C-CC-----TTGGGGGAATC
1 AGCACTTAGCAACCACCAATGATTCGGGGAATC
* * *
58945835 -GACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATC
1 AG-CACTTAGCAA-CCAC--CA-A--T--GATTCGG-GGAATC
* *
58945877 AGCACTTAGCAATCACCAATGAATCGGGGAATC
1 AGCACTTAGCAACCACCAATGATTCGGGGAATC
58945910 AGCACTTAGCAACC
1 AGCACTTAGCAACC
58945924 CCCTTTATAT
Statistics
Matches: 203, Mismatches: 23, Indels: 80
0.66 0.08 0.26
Matches are distributed among these distances:
25 2 0.01
26 17 0.08
28 1 0.00
29 1 0.00
31 3 0.01
32 1 0.00
33 67 0.33
34 16 0.08
35 2 0.01
36 5 0.02
37 4 0.02
38 2 0.01
39 8 0.04
40 1 0.00
41 8 0.04
42 46 0.23
43 19 0.09
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (33 bp):
AGCACTTAGCAACCACCAATGATTCGGGGAATC
Found at i:58945799 original size:75 final size:76
Alignment explanation
Indices: 58945615--58945823 Score: 312
Period size: 76 Copynumber: 2.8 Consensus size: 76
58945605 TATCCGTTAT
* * * *
58945615 CGGTGGATTTAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
58945680 ATTCAATGATA
66 ATTCAATGATA
*
58945691 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCAGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
58945756 ATTTAA-GATA
66 ATTCAATGATA
* * * * *
58945766 TGGTGGGATCAGCACTTAGCAACCACCAATGAATTGGGGAATTAACACTTAGCAACCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCC
58945824 TTGGGGGAAT
Statistics
Matches: 121, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 56 0.46
76 65 0.54
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (76 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTCAATGATA
Found at i:58945878 original size:101 final size:101
Alignment explanation
Indices: 58945727--58945924 Score: 308
Period size: 101 Copynumber: 2.0 Consensus size: 101
58945717 CAATGAATCA
* * * *
58945727 GGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATATGGTGGGATCAGCACTTAGCAACCAC
1 GGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCAC
* *
58945792 CAATGAATTGGGGAATTAACACTTAGCAACCCTTGG
66 CAATGAATCGGGGAATCAACACTTAGCAACCCTTGG
*
58945828 GGGAATC-GACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAATCA
1 GGGAATCAG-CACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
*
58945892 CCAATGAATCGGGGAATCAGCACTTAGCAACCC
65 CCAATGAATCGGGGAATCAACACTTAGCAACCC
58945925 CCTTTATATT
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 1 0.01
101 87 0.99
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (101 bp):
GGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCAC
CAATGAATCGGGGAATCAACACTTAGCAACCCTTGG
Found at i:58947706 original size:24 final size:23
Alignment explanation
Indices: 58947679--58947726 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
58947669 TACCCATCAT
*
58947679 TGGCTCGCATGAGCTTTCTGATTA
1 TGGCTCGCATGAGCTTCCTG-TTA
**
58947703 TGGCTCTTATGAGCTTCCTGTTA
1 TGGCTCGCATGAGCTTCCTGTTA
58947726 T
1 T
58947727 ACAATCTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.42
Consensus pattern (23 bp):
TGGCTCGCATGAGCTTCCTGTTA
Found at i:58949353 original size:26 final size:26
Alignment explanation
Indices: 58949324--58949396 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
58949314 CCCGTTATTT
58949324 GGCTCTTCGTGAGCTTTCCGATTAAA
1 GGCTCTTCGTGAGCTTTCCGATTAAA
* *
58949350 GGCTCTTTGTGAGC-TTCCTGATTAAT
1 GGCTCTTCGTGAGCTTTCC-GATTAAA
* *
58949376 GGCTCTTC-AGAGTTTTCCGAT
1 GGCTCTTCGTGAGCTTTCCGAT
58949397 ATGGCTCTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 10 0.25
26 30 0.75
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTTCCGATTAAA
Found at i:58949423 original size:25 final size:25
Alignment explanation
Indices: 58949395--58949453 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
58949385 GAGTTTTCCG
*
58949395 ATATGGCTCTCTTGAACTTCCCGGT
1 ATATGGCTCTCTGGAACTTCCCGGT
* * *
58949420 ATATGGCTATCTGGAGCTTCCCGTT
1 ATATGGCTCTCTGGAACTTCCCGGT
58949445 A-ATGGCTCT
1 ATATGGCTCT
58949454 TCGGAGCTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (25 bp):
ATATGGCTCTCTGGAACTTCCCGGT
Found at i:58951604 original size:14 final size:14
Alignment explanation
Indices: 58951587--58951615 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58951577 TATACATCAA
58951587 AACATACCATCACT
1 AACATACCATCACT
58951601 AACATACCATCACT
1 AACATACCATCACT
58951615 A
1 A
58951616 GCCATTCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (14 bp):
AACATACCATCACT
Found at i:58952783 original size:27 final size:27
Alignment explanation
Indices: 58952743--58953379 Score: 731
Period size: 27 Copynumber: 23.6 Consensus size: 27
58952733 AATCGGCCTC
*
58952743 TAAAATGA-CTGAAATACCCTCGATGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
* *
58952770 TAAAATTATCGAAATACCCTCGATGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* *
58952797 TAAAATGATCGAAATACCATCAAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
58952824 TAAAATGA-CTGAAATACCCTCGAAGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
*
58952851 TAAAATGATCGAAATACCCTTGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
58952878 TAAAATGATCGAAATACCC-CTGTAGGG
1 TAAAATGATCGAAATACCCTC-GAAGGG
* * *
58952905 TAAAATGATCGAAAGACCCTTGAAGGA
1 TAAAATGATCGAAATACCCTCGAAGGG
58952932 TAAAATGA-CGGAAATACCCTCGAAGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
* *
58952959 TAAAATGACCGAAATACCC-CAAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
58952985 TAAAATGATCGAAATACCCTTGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* **
58953012 TAAAATGATCGAAATACTCTCGAAATG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
58953039 TAAAATGACCGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* * *
58953066 TAAAAT-AACTAAAATACTCAT-GAAGGG
1 TAAAATGATC-GAAATAC-CCTCGAAGGG
58953093 TAAAATGA-CTGAAATACCCTCGAAGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
58953120 TAAAATGATCGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* *
58953147 TAAAATGACCGAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* *
58953174 TAAAATGACCGAAATACCCTTGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* *
58953201 TAAAATGATAGAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
58953228 TAAAATGA-CTGAAATACCCTCGATA-GG
1 TAAAATGATC-GAAATACCCTCGA-AGGG
**
58953255 TAAAATGATCGAAATACCCTTTAATGGG
1 TAAAATGATCGAAATACCCTCGAA-GGG
* * * * *
58953283 TAAATTTA-CTAAAATACACTCGATGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
* ** *
58953310 TAAAATTATTAAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
*
58953337 TAAAATGA-CTGAAATACCCTCGATGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
*
58953364 TAAAATTATCGAAATA
1 TAAAATGATCGAAATA
58953380 TCCTTATATG
Statistics
Matches: 524, Mismatches: 64, Indels: 44
0.83 0.10 0.07
Matches are distributed among these distances:
26 31 0.06
27 466 0.89
28 27 0.05
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (27 bp):
TAAAATGATCGAAATACCCTCGAAGGG
Found at i:58953694 original size:26 final size:26
Alignment explanation
Indices: 58953597--58953692 Score: 113
Period size: 26 Copynumber: 3.7 Consensus size: 26
58953587 ACAAATATTG
58953597 TTACTGGCAGCTTTGCTGCGTTACTGA
1 TTACTGGCAGCTTTGCTGCGTTACT-A
* * * * *
58953624 -TACTGGCAACTCTGTTGCATTACTG
1 TTACTGGCAGCTTTGCTGCGTTACTA
* *
58953649 TTATTGGCAGCTTTGCTGTGTTACTA
1 TTACTGGCAGCTTTGCTGCGTTACTA
58953675 TTACTGGCAGCTTTGCTG
1 TTACTGGCAGCTTTGCTG
58953693 TGATATTGGT
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCGTTACTA
Found at i:58953839 original size:30 final size:30
Alignment explanation
Indices: 58953800--58953887 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
58953790 ACTGCATTTG
*
58953800 CACTATTACTGTATTGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGGCCCACA
* *
58953830 CTCTGTTACTGTATTGGGCTATGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGGCCCACA
* * * *
58953860 CAGTGCTACTGTATAGGGCTCAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
58953888 AATTGATTCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (30 bp):
CACTGTTACTGTATTGGGCTAAGGCCCACA
Found at i:58955030 original size:25 final size:25
Alignment explanation
Indices: 58954999--58955046 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
58954989 CAAGCGAACC
58954999 ATATCAGGA-AGCTCACAAAGAGCCT
1 ATATCAGGACA-CTCACAAAGAGCCT
*
58955024 ATATCAGGACACTCATAAAGAGC
1 ATATCAGGACACTCACAAAGAGC
58955047 TGTGGTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (25 bp):
ATATCAGGACACTCACAAAGAGCCT
Found at i:58962057 original size:25 final size:25
Alignment explanation
Indices: 58962026--58962073 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
58962016 CAAGCTAGCC
58962026 ATATCAGGA-AGCTCACAAAGAGCAT
1 ATATCAGGACA-CTCACAAAGAGCAT
*
58962051 ATATCAGGACACTCATAAAGAGC
1 ATATCAGGACACTCACAAAGAGC
58962074 TGTAGTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.17
Consensus pattern (25 bp):
ATATCAGGACACTCACAAAGAGCAT
Found at i:58962888 original size:25 final size:25
Alignment explanation
Indices: 58962859--58962911 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
58962849 TTTCATTTTC
58962859 TACCATAAATTTCAAAATTTCAACA
1 TACCATAAATTTCAAAATTTCAACA
58962884 TACCATAAATTTCAAAATTTCAACA
1 TACCATAAATTTCAAAATTTCAACA
58962909 TAC
1 TAC
58962912 TCATCCATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (25 bp):
TACCATAAATTTCAAAATTTCAACA
Found at i:58976109 original size:28 final size:29
Alignment explanation
Indices: 58976053--58976128 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
58976043 CCTGCAAAGA
***
58976053 CATCTCGCACTTCACCA-TTTCGTGGTGT
1 CATCTCGCACTTCACCACTTTCGCAATGT
58976081 CATCTCGCACTTCACCACTTT-GCAATGT
1 CATCTCGCACTTCACCACTTTCGCAATGT
*
58976109 CATCTCACAGC-TCACCACTT
1 CATCTCGCA-CTTCACCACTT
58976129 CTTGGTGTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 38 0.90
29 4 0.10
ACGTcount: A:0.20, C:0.37, G:0.12, T:0.32
Consensus pattern (29 bp):
CATCTCGCACTTCACCACTTTCGCAATGT
Found at i:58976137 original size:28 final size:28
Alignment explanation
Indices: 58976053--58976139 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
58976043 CCTGCAAAGA
* * *
58976053 CATCTCGCACTTCACCATTTCGTGGTGT
1 CATCTCACACTTCACCACTTCTTGGTGT
* *
58976081 CATCTCGCACTTCACCAC-T-TTGCAATGT
1 CATCTCACACTTCACCACTTCTTG--GTGT
58976109 CATCTCACAGC-TCACCACTTCTTGGTGT
1 CATCTCACA-CTTCACCACTTCTTGGTGT
58976137 CAT
1 CAT
58976140 TTTGCAGTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 41 0.84
29 2 0.04
30 3 0.06
ACGTcount: A:0.18, C:0.34, G:0.14, T:0.33
Consensus pattern (28 bp):
CATCTCACACTTCACCACTTCTTGGTGT
Found at i:58976189 original size:27 final size:27
Alignment explanation
Indices: 58976157--58976209 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
58976147 TTCATCTCAC
*
58976157 AGCTTGCCACTTGTGGAGACTTCTCGT
1 AGCTTGCCACTTGTGAAGACTTCTCGT
58976184 AGCTTGCCACTTGTGAAGACTTCTCG
1 AGCTTGCCACTTGTGAAGACTTCTCG
58976210 CAACTCGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (27 bp):
AGCTTGCCACTTGTGAAGACTTCTCGT
Found at i:58976221 original size:27 final size:27
Alignment explanation
Indices: 58976162--58976224 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
58976152 CTCACAGCTT
* * * *
58976162 GCCACTTGTGGAGACTTCTCGTAGCTT
1 GCCACTTGTGAAGACTTCTCGCAACTC
58976189 GCCACTTGTGAAGACTTCTCGCAACTC
1 GCCACTTGTGAAGACTTCTCGCAACTC
*
58976216 GTCACTTGT
1 GCCACTTGT
58976225 AGAGACATCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.32
Consensus pattern (27 bp):
GCCACTTGTGAAGACTTCTCGCAACTC
Found at i:58976230 original size:27 final size:26
Alignment explanation
Indices: 58976162--58976239 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
58976152 CTCACAGCTT
* * *
58976162 GCCACTTGTGGAGACTTCTCGTAGCTT
1 GCCACTTGT-GAGACTTCTCGCAACTC
58976189 GCCACTTGTGAAGACTTCTCGCAACTC
1 GCCACTTGTG-AGACTTCTCGCAACTC
* * *
58976216 GTCACTTGTAGAGACATCTTGCAA
1 GCCACTTGT-GAGACTTCTCGCAA
58976240 TTTACCATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.02
27 41 0.95
28 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (26 bp):
GCCACTTGTGAGACTTCTCGCAACTC
Found at i:58981756 original size:17 final size:17
Alignment explanation
Indices: 58981734--58981769 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
58981724 CACCCCAATC
58981734 ACTATAA-ACTAGAATAA
1 ACTATAATACTA-AATAA
58981751 ACTATAATACTAAATAA
1 ACTATAATACTAAATAA
58981768 AC
1 AC
58981770 ACTTATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (17 bp):
ACTATAATACTAAATAA
Found at i:58986519 original size:39 final size:40
Alignment explanation
Indices: 58986464--58986564 Score: 115
Period size: 39 Copynumber: 2.6 Consensus size: 40
58986454 ATCAACATTT
58986464 AATTAATTTTTAAAAATTTTAAAAATTCA-AAAA-AATAAAA
1 AATT-ATTTTTAAAAATTTTAAAAA-TCATAAAATAATAAAA
*
58986504 AATTATTTTTAAAAA--TTAAAAATCATTAAAATTATAAAA
1 AATTATTTTTAAAAATTTTAAAAATCA-TAAAATAATAAAA
*
58986543 AATCATTTTT--AAATTTTAAAAA
1 AATTATTTTTAAAAATTTTAAAAA
58986565 ATTAATTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
36 3 0.06
37 10 0.19
38 4 0.07
39 33 0.61
40 4 0.07
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (40 bp):
AATTATTTTTAAAAATTTTAAAAATCATAAAATAATAAAA
Found at i:58986523 original size:21 final size:21
Alignment explanation
Indices: 58986493--58986566 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
58986483 TAAAAATTCA
* *
58986493 AAAAAATAAAAAATTATTTTT
1 AAAAATTAAAAAATCATTTTT
58986514 AAAAATT-AAAAATCA---TT
1 AAAAATTAAAAAATCATTTTT
*
58986531 AAAATTATAAAAAATCATTTTT
1 AAAAAT-TAAAAAATCATTTTT
**
58986553 AAATTTTAAAAAAT
1 AAAAATTAAAAAAT
58986567 TAATTAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 7 0.16
18 1 0.02
19 8 0.18
20 7 0.16
21 14 0.32
22 7 0.16
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAATTAAAAAATCATTTTT
Found at i:58993073 original size:18 final size:18
Alignment explanation
Indices: 58993029--58993073 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
58993019 TAACCTTTAA
58993029 CCTTTAACCTTTCATCTT
1 CCTTTAACCTTTCATCTT
*
58993047 CCTTAAACCTTTCATC-T
1 CCTTTAACCTTTCATCTT
58993064 CCTTGTAACC
1 CCTT-TAACC
58993074 CTTTTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.20, C:0.36, G:0.02, T:0.42
Consensus pattern (18 bp):
CCTTTAACCTTTCATCTT
Found at i:58994224 original size:18 final size:18
Alignment explanation
Indices: 58994201--58994236 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
58994191 AAAAAAAGTG
*
58994201 CGATTGATAGTGTGATTT
1 CGATTGATAATGTGATTT
58994219 CGATTGATAATGTGATTT
1 CGATTGATAATGTGATTT
58994237 GGCTCCGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (18 bp):
CGATTGATAATGTGATTT
Found at i:58995262 original size:20 final size:22
Alignment explanation
Indices: 58995220--58995262 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
58995210 TCAATTTCAT
*
58995220 ACATATGCCATTTATACAATTC
1 ACATATGCAATTTATACAATTC
58995242 ACATATGCAATTT-TA-AATTC
1 ACATATGCAATTTATACAATTC
58995262 A
1 A
58995263 AACATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 2 0.10
22 12 0.60
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.37
Consensus pattern (22 bp):
ACATATGCAATTTATACAATTC
Found at i:58995267 original size:22 final size:23
Alignment explanation
Indices: 58995215--58995269 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
58995205 TGTGATCAAT
*
58995215 TTCATACATATGCCATTTATACAA
1 TTCA-ACATATGCAATTTATACAA
58995239 TTC-ACATATGCAATTT-TA-AA
1 TTCAACATATGCAATTTATACAA
58995259 TTCAAACATAT
1 TTC-AACATAT
58995270 AAATATACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.18
21 2 0.07
22 18 0.64
24 3 0.11
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (23 bp):
TTCAACATATGCAATTTATACAA
Found at i:59002835 original size:22 final size:21
Alignment explanation
Indices: 59002795--59002836 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
59002785 CAATTATCAT
*
59002795 TCAACCAAAAACTCACCTAAA
1 TCAACCAAAAACTAACCTAAA
59002816 TCAACCAAAAACTAAGCCTAA
1 TCAACCAAAAACTAA-CCTAA
59002837 GCTATATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.52, C:0.31, G:0.02, T:0.14
Consensus pattern (21 bp):
TCAACCAAAAACTAACCTAAA
Found at i:59004024 original size:29 final size:29
Alignment explanation
Indices: 59003991--59004233 Score: 118
Period size: 29 Copynumber: 8.4 Consensus size: 29
59003981 TTTCAATGTT
*
59003991 TTGCCACAAAGGCATTCTTTTAACGGAG-
1 TTGCCACAAAGGCATTCTTTTAACAGAGA
* * *
59004019 TCTG-C-CTATGGCATTCCTTTAACAGAGA
1 T-TGCCACAAAGGCATTCTTTTAACAGAGA
* * *
59004047 TGGCCACAAAGGCATCCTTTTGACAGAGA
1 TTGCCACAAAGGCATTCTTTTAACAGAGA
* * * * * *
59004076 TAGCCATAAAGACATCCTTTTGACAGAGG
1 TTGCCACAAAGGCATTCTTTTAACAGAGA
* * *
59004105 TTGCC-CTAAAATG-ATTCATTTAACTGAGA
1 TTGCCAC--AAAGGCATTCTTTTAACAGAGA
** ** * * *
59004134 AAGCCACAAAGATATTCGTTTAAAAAAGA
1 TTGCCACAAAGGCATTCTTTTAACAGAGA
* * * ** *
59004163 TAGCCATAAATGCAGCCTTTTAACAAAGA
1 TTGCCACAAAGGCATTCTTTTAACAGAGA
* * * *
59004192 TTGCTATAAAGGCTTTCTTATAACAGAGA
1 TTGCCACAAAGGCATTCTTTTAACAGAGA
*
59004221 TTGACACAAAGGC
1 TTGCCACAAAGGC
59004234 TTCCATTCAG
Statistics
Matches: 156, Mismatches: 51, Indels: 15
0.70 0.23 0.07
Matches are distributed among these distances:
27 19 0.12
28 7 0.04
29 126 0.81
30 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (29 bp):
TTGCCACAAAGGCATTCTTTTAACAGAGA
Found at i:59004064 original size:28 final size:28
Alignment explanation
Indices: 59004028--59004304 Score: 95
Period size: 29 Copynumber: 9.9 Consensus size: 28
59004018 GTCTGCCTAT
*
59004028 GGCATTCCTTTAACAGAGATGGCCACAAA
1 GGCA-TCCTTTAACAGAGATAGCCACAAA
* *
59004057 GGCATCCTTTTGACAGAGATAGCCATAAA
1 GGCATCC-TTTAACAGAGATAGCCACAAA
* * * *
59004086 GACATCCTTTTGACAGAGGTTGCC-CTAAAA
1 GGCATCC-TTTAACAGAGATAGCCAC--AAA
* * * *
59004116 TG-ATTCATTTAACTGAGAAAGCCACAAA
1 GGCA-TCCTTTAACAGAGATAGCCACAAA
** * * * *
59004144 GATATTCGTTTAAAAAAGATAGCCATAAA
1 GGCA-TCCTTTAACAGAGATAGCCACAAA
* * * * * *
59004173 TGCAGCCTTTTAACAAAGATTGCTATAAA
1 GGCATCC-TTTAACAGAGATAGCCACAAA
* * * *
59004202 GGCTTTCTTATAACAGAGATTGACACAAA
1 GGCATCCTT-TAACAGAGATAGCCACAAA
* * * *
59004231 GGCTTCCATT--CAGAGATAACTACAAA
1 GGCATCCTTTAACAGAGATAGCCACAAA
*
59004257 GGCTTCCATTT---AGAGATAGCCACAAA
1 GGCATCC-TTTAACAGAGATAGCCACAAA
* *
59004283 GGCTTCCTTT--TAGAGATAGCCA
1 GGCATCCTTTAACAGAGATAGCCA
59004305 TAAAAGTGTC
Statistics
Matches: 190, Mismatches: 48, Indels: 23
0.73 0.18 0.09
Matches are distributed among these distances:
25 3 0.02
26 50 0.26
27 2 0.01
28 10 0.05
29 119 0.63
30 6 0.03
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (28 bp):
GGCATCCTTTAACAGAGATAGCCACAAA
Found at i:59004301 original size:26 final size:26
Alignment explanation
Indices: 59004216--59004304 Score: 124
Period size: 26 Copynumber: 3.4 Consensus size: 26
59004206 TTCTTATAAC
* * *
59004216 AGAGATTGACACAAAGGCTTCCATTC
1 AGAGATAGCCACAAAGGCTTCCATTT
* *
59004242 AGAGATAACTACAAAGGCTTCCATTT
1 AGAGATAGCCACAAAGGCTTCCATTT
*
59004268 AGAGATAGCCACAAAGGCTTCCTTTT
1 AGAGATAGCCACAAAGGCTTCCATTT
59004294 AGAGATAGCCA
1 AGAGATAGCCA
59004305 TAAAAGTGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (26 bp):
AGAGATAGCCACAAAGGCTTCCATTT
Found at i:59004324 original size:52 final size:52
Alignment explanation
Indices: 59004215--59004326 Score: 118
Period size: 52 Copynumber: 2.2 Consensus size: 52
59004205 TTTCTTATAA
* * *
59004215 CAGAGATTGACACAAAGGCTTCCATTCAGAGATAACTACAAAGGCTTCCATT
1 CAGAGATAGACACAAAGGCTTCCATTCAGAGATAACCACAAAAGCTTCCATT
* * * * * * *
59004267 TAGAGATAGCCACAAAGGCTTCCTTTTAGAGATAGCCATAAAAG-TGTCTATT
1 CAGAGATAGACACAAAGGCTTCCATTCAGAGATAACCACAAAAGCT-TCCATT
59004319 CAGAGATA
1 CAGAGATA
59004327 ACCATAAAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
51 1 0.02
52 47 0.98
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (52 bp):
CAGAGATAGACACAAAGGCTTCCATTCAGAGATAACCACAAAAGCTTCCATT
Found at i:59014928 original size:14 final size:14
Alignment explanation
Indices: 59014893--59014931 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
59014883 CTCCAAACTG
*
59014893 AGGACTTAACACTA
1 AGGACTTAACTCTA
59014907 AGGACTTAACTCTA
1 AGGACTTAACTCTA
59014921 A-GAGCTTAACT
1 AGGA-CTTAACT
59014932 TTAAAGATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (14 bp):
AGGACTTAACTCTA
Found at i:59015389 original size:16 final size:17
Alignment explanation
Indices: 59015368--59015405 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
59015358 GTTTCTTACG
* *
59015368 ATATAAATTACATAAT-
1 ATATAAAATAAATAATA
59015384 ATATAAAATAAATAATA
1 ATATAAAATAAATAATA
59015401 ATATA
1 ATATA
59015406 TTAAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATAAATAATA
Found at i:59015413 original size:21 final size:21
Alignment explanation
Indices: 59015370--59015411 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 21
59015360 TTCTTACGAT
59015370 ATAAATTACATAATATATAAA
1 ATAAATTACATAATATATAAA
59015391 ATAAA-TA-ATAATATATTAAA
1 ATAAATTACATAATATA-TAAA
59015411 A
1 A
59015412 ATTTGAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATTACATAATATATAAA
Found at i:59022242 original size:50 final size:50
Alignment explanation
Indices: 59022116--59022364 Score: 266
Period size: 50 Copynumber: 4.8 Consensus size: 50
59022106 GATAATAACA
* * ** * *
59022116 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* * *
59022167 TGCCCATGCCATGTCCCAGATATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
59022217 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
59022267 TGCCCATGCTATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
59022322 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
59022365 TTACCCAAAT
Statistics
Matches: 166, Mismatches: 25, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 90 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:59022296 original size:100 final size:104
Alignment explanation
Indices: 59022115--59022364 Score: 339
Period size: 100 Copynumber: 2.4 Consensus size: 104
59022105 TGATAATAAC
**
59022115 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* * *
59022180 TCCCAGATATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
59022217 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCTATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
59022280 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
59022322 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
59022365 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 48 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:59022480 original size:13 final size:13
Alignment explanation
Indices: 59022459--59022490 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
59022449 GCTTGGATCA
*
59022459 TCATCAAATAAAT
1 TCATAAAATAAAT
59022472 TCATAAAATAAAT
1 TCATAAAATAAAT
59022485 TCATAA
1 TCATAA
59022491 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:59022737 original size:30 final size:30
Alignment explanation
Indices: 59022702--59022759 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
59022692 CCTCGACTCT
*
59022702 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
59022732 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
59022760 AAGGCTCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:59029830 original size:50 final size:50
Alignment explanation
Indices: 59029706--59029954 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
59029696 GATAATAACA
* * ** * *
59029706 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
59029757 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
59029807 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
59029857 TGCCCATGCCATGTCCTAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
59029912 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
59029955 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:59029885 original size:100 final size:104
Alignment explanation
Indices: 59029705--59029954 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
59029695 TGATAATAAC
**
59029705 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
59029770 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
59029807 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
59029870 TCCTAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
59029912 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
59029955 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:59030070 original size:13 final size:13
Alignment explanation
Indices: 59030049--59030080 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
59030039 GCTTGGATCA
*
59030049 TCATCAAATAAAT
1 TCATAAAATAAAT
59030062 TCATAAAATAAAT
1 TCATAAAATAAAT
59030075 TCATAA
1 TCATAA
59030081 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:59030328 original size:29 final size:30
Alignment explanation
Indices: 59030290--59030349 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
59030280 GCCCTCGACT
*
59030290 CTAAA-TTTTTCAAAATTACAATTTTGCCC
1 CTAAACTTTTACAAAATTACAATTTTGCCC
* *
59030319 CTAAACTTTTACATAATTACATTTTTGCCC
1 CTAAACTTTTACAAAATTACAATTTTGCCC
59030349 C
1 C
59030350 AAGGCTCGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (30 bp):
CTAAACTTTTACAAAATTACAATTTTGCCC
Found at i:59032853 original size:9 final size:9
Alignment explanation
Indices: 59032832--59032861 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
59032822 TAAAAATTAG
59032832 TTATAAGAAA
1 TTATAA-AAA
59032842 TTATAAAAA
1 TTATAAAAA
59032851 TTATAAAAA
1 TTATAAAAA
59032860 TT
1 TT
59032862 GGGTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (9 bp):
TTATAAAAA
Found at i:59034183 original size:9 final size:9
Alignment explanation
Indices: 59034109--59034281 Score: 61
Period size: 9 Copynumber: 18.2 Consensus size: 9
59034099 CTTTACCAAA
*
59034109 GTATGTTAT
1 GTATATTAT
59034118 GTATATTACT
1 GTATATTA-T
59034128 GT-TATGTAT
1 GTATAT-TAT
*
59034137 GTCTATTAT
1 GTATATTAT
*
59034146 GTTTAATGTAT
1 GTAT-AT-TAT
* * *
59034157 GTCTCTTTT
1 GTATATTAT
*
59034166 GTATGTTAT
1 GTATATTAT
59034175 GTATATTATT
1 GTATATTA-T
59034185 GT-TATGTAT
1 GTATAT-TAT
*
59034194 GAGATTATTAT
1 G-TA-TATTAT
*
59034205 GTGGTA-TAT
1 GT-ATATTAT
*
59034214 -TACTTTTAT
1 GTA-TATTAT
59034223 GCT-TCATGTAT
1 G-TAT-AT-TAT
59034234 GTATATTAT
1 GTATATTAT
*
59034243 GTATGTTAT
1 GTATATTAT
59034252 GTATATTACT
1 GTATATTA-T
59034262 GT-TATGTAT
1 GTATAT-TAT
*
59034271 GTATGTTAT
1 GTATATTAT
59034280 GT
1 GT
59034282 GGTATATTTG
Statistics
Matches: 125, Mismatches: 18, Indels: 42
0.68 0.10 0.23
Matches are distributed among these distances:
8 2 0.02
9 75 0.60
10 29 0.23
11 16 0.13
12 3 0.02
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (9 bp):
GTATATTAT
Found at i:59034233 original size:77 final size:75
Alignment explanation
Indices: 59034142--59034289 Score: 206
Period size: 77 Copynumber: 1.9 Consensus size: 75
59034132 TGTATGTCTA
* * * * *
59034142 TTATGTTTAATGTATGTCTCTTTTGTATGTTATGTATATTATTGTTATGTATGAGATTATTATGT
1 TTATGCTTAATGTATGTATATTATGTATGTTATGTATATTACTGTTATGTATG-GA-TATTATGT
59034207 GGTATATTACTT
64 GGTATATTACTT
* * *
59034219 TTATGCTTCATGTATGTATATTATGTATGTTATGTATATTACTGTTATGTATGTATGTTATGTGG
1 TTATGCTTAATGTATGTATATTATGTATGTTATGTATATTACTGTTATGTATGGATATTATGTGG
59034284 TATATT
66 TATATT
59034290 TGTAACATCC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 15 0.24
76 1 0.02
77 47 0.75
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.55
Consensus pattern (75 bp):
TTATGCTTAATGTATGTATATTATGTATGTTATGTATATTACTGTTATGTATGGATATTATGTGG
TATATTACTT
Found at i:59034900 original size:19 final size:20
Alignment explanation
Indices: 59034868--59034911 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
59034858 CATTATTGAA
* *
59034868 TTTATGAGA-TTTTTTAAGT
1 TTTATGAGAGTTTTGTAAGC
*
59034887 TTTATGATAGTTTTGTAAGC
1 TTTATGAGAGTTTTGTAAGC
59034907 TTTAT
1 TTTAT
59034912 AGTTAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (20 bp):
TTTATGAGAGTTTTGTAAGC
Found at i:59037030 original size:29 final size:29
Alignment explanation
Indices: 59036997--59037056 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
59036987 GTTTTTGTAA
*
59036997 GTATATTATGTATGTTATGTTTAATGCAT
1 GTATATTATGTATGTTATATTTAATGCAT
*
59037026 GTATATTATGTATGTTATATTTAATGTAT
1 GTATATTATGTATGTTATATTTAATGCAT
59037055 GT
1 GT
59037057 TATGTTTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (29 bp):
GTATATTATGTATGTTATATTTAATGCAT
Found at i:59037054 original size:16 final size:16
Alignment explanation
Indices: 59037004--59037064 Score: 74
Period size: 16 Copynumber: 4.0 Consensus size: 16
59036994 TAAGTATATT
*
59037004 ATGTATGTTATGTTTA
1 ATGTATGTTATATTTA
*
59037020 ATGCATG-TATA-TT-
1 ATGTATGTTATATTTA
59037033 ATGTATGTTATATTTA
1 ATGTATGTTATATTTA
*
59037049 ATGTATGTTATGTTTA
1 ATGTATGTTATATTTA
59037065 GCACTGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
13 6 0.16
14 6 0.16
15 5 0.13
16 21 0.55
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54
Consensus pattern (16 bp):
ATGTATGTTATATTTA
Found at i:59038993 original size:24 final size:25
Alignment explanation
Indices: 59038961--59039026 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
59038951 CAGCTCGAAA
* *
59038961 GAGCGTCCCGTTAT-TAGTTCTCAT
1 GAGCTTCCCATTATATAGTTCTCAT
* *
59038985 GAGCTTCCCATTATATGGTTCTTAT
1 GAGCTTCCCATTATATAGTTCTCAT
*
59039010 GAGCTTCTCATTA-ATAG
1 GAGCTTCCCATTATATAG
59039027 CTCTTTGGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 15 0.43
25 20 0.57
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (25 bp):
GAGCTTCCCATTATATAGTTCTCAT
Found at i:59039235 original size:25 final size:25
Alignment explanation
Indices: 59039207--59039284 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
59039197 TTCCTGATAT
* *
59039207 TGGCTTGTATGAGCTTTCTGTTACA
1 TGGCTTGAATGAGCTTCCTGTTACA
* * *
59039232 TGGC-TCACATGAACTTCCTGTTATA
1 TGGCTTGA-ATGAGCTTCCTGTTACA
* *
59039257 TGGCTTGAAAGAGCTTCCCGTTTACA
1 TGGCTTGAATGAGCTTCCTG-TTACA
59039283 TG
1 TG
59039285 TTTGCATAAG
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
24 1 0.03
25 31 0.77
26 8 0.20
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (25 bp):
TGGCTTGAATGAGCTTCCTGTTACA
Found at i:59040220 original size:26 final size:26
Alignment explanation
Indices: 59040184--59040236 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
59040174 CGGGCAAAGA
59040184 CACGGGTGTGTG-TCTCAGCCGTGTGT
1 CACGGGTGTGTGATCT-AGCCGTGTGT
*
59040210 CACGGGTGTGTGATCTGGCCGTGTGT
1 CACGGGTGTGTGATCTAGCCGTGTGT
59040236 C
1 C
59040237 CCTTGCATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.08, C:0.23, G:0.40, T:0.30
Consensus pattern (26 bp):
CACGGGTGTGTGATCTAGCCGTGTGT
Found at i:59042971 original size:24 final size:24
Alignment explanation
Indices: 59042924--59042979 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
59042914 CAATTGGAAT
** *
59042924 AGCTCCAATAGCTCCTTTTTCACC
1 AGCTCCAATAGCTCCTACTCCACC
*
59042948 AGCTCCAGTAGCTCCTACTCCACC
1 AGCTCCAATAGCTCCTACTCCACC
*
59042972 AGCCCCAA
1 AGCTCCAA
59042980 CAACTCCTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.43, G:0.11, T:0.23
Consensus pattern (24 bp):
AGCTCCAATAGCTCCTACTCCACC
Found at i:59047205 original size:42 final size:42
Alignment explanation
Indices: 59047098--59047218 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 42
59047088 GTTAAACTCA
* * * * *
59047098 TATGAGTTTCTGTTCAGCTCTTTTGAGCTTCTATTTAACCCT
1 TATGGGTTTCTGTTAAGCTCTTATGAGCTTCCATTCAACCCT
* *
59047140 TATAGGTTT-TCATTAAGCTCTTATGAGCTTCCATTCAACCCT
1 TATGGGTTTCT-GTTAAGCTCTTATGAGCTTCCATTCAACCCT
* * * *
59047182 TATGGGTTTCTGTTTAGCACTTATGTGCTTCCGTTCA
1 TATGGGTTTCTGTTAAGCTCTTATGAGCTTCCATTCA
59047219 GCCTTCGGGC
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 1 0.02
42 62 0.97
43 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (42 bp):
TATGGGTTTCTGTTAAGCTCTTATGAGCTTCCATTCAACCCT
Found at i:59054836 original size:42 final size:42
Alignment explanation
Indices: 59054786--59054918 Score: 158
Period size: 42 Copynumber: 3.2 Consensus size: 42
59054776 TAGCTCGCAC
* * * * *
59054786 GAGCTTCTGTTAAACTCATATGAGTTTTTGTTCAGCTCTTTT
1 GAGCTTCTGTTAAACCCTTATGGGTTTTTGTTAAGCTCTTAT
* **
59054828 GAGCTTCTGTTTAACCCTTATGGGTTTTCATTAAGCTCTTAT
1 GAGCTTCTGTTAAACCCTTATGGGTTTTTGTTAAGCTCTTAT
* * *
59054870 GAGCTTCTATTAAACCCTTATGGGTTTTTGTTTAGCACTTAT
1 GAGCTTCTGTTAAACCCTTATGGGTTTTTGTTAAGCTCTTAT
*
59054912 GTGCTTC
1 GAGCTTC
59054919 CGTTCAGCCT
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.46
Consensus pattern (42 bp):
GAGCTTCTGTTAAACCCTTATGGGTTTTTGTTAAGCTCTTAT
Found at i:59054838 original size:21 final size:21
Alignment explanation
Indices: 59054786--59054838 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
59054776 TAGCTCGCAC
59054786 GAGCTTCTGTTAAACTCATAT
1 GAGCTTCTGTTAAACTCATAT
* * * * * *
59054807 GAGTTTTTGTTCAGCTCTTTT
1 GAGCTTCTGTTAAACTCATAT
59054828 GAGCTTCTGTT
1 GAGCTTCTGTT
59054839 TAACCCTTAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (21 bp):
GAGCTTCTGTTAAACTCATAT
Found at i:59054868 original size:21 final size:22
Alignment explanation
Indices: 59054840--59054897 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
59054830 GCTTCTGTTT
59054840 AACCCTTATGGGTTTTC-ATTA
1 AACCCTTATGGGTTTTCTATTA
* * * *
59054861 AGCTCTTATGAG-CTTCTATTA
1 AACCCTTATGGGTTTTCTATTA
59054882 AACCCTTATGGGTTTT
1 AACCCTTATGGGTTTT
59054898 TGTTTAGCAC
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
20 3 0.11
21 22 0.81
22 2 0.07
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (22 bp):
AACCCTTATGGGTTTTCTATTA
Found at i:59057660 original size:31 final size:31
Alignment explanation
Indices: 59057599--59057675 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
59057589 AAAAATATTT
* *
59057599 TTTAAATGACTAAAATAAGAACTACCTAAAA
1 TTTAAATAACTAAAATAAGAAATACCTAAAA
*
59057630 TTTAAATAACTAAAATAA-AAATACATTAAAA
1 TTTAAATAACTAAAATAAGAAATAC-CTAAAA
* *
59057661 GTTAAATTAC-AAAAT
1 TTTAAATAACTAAAAT
59057676 TACAAAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 10 0.25
31 30 0.75
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (31 bp):
TTTAAATAACTAAAATAAGAAATACCTAAAA
Found at i:59066268 original size:16 final size:16
Alignment explanation
Indices: 59066237--59066267 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59066227 TTTATTTCCA
59066237 ATTCCCTTTTTGTTTT
1 ATTCCCTTTTTGTTTT
59066253 ATTCCCTTTTT-TTTT
1 ATTCCCTTTTTGTTTT
59066268 TCTTTTTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.71
Consensus pattern (16 bp):
ATTCCCTTTTTGTTTT
Found at i:59071128 original size:7 final size:7
Alignment explanation
Indices: 59071118--59071154 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
59071108 GCTCATTTCT
59071118 CATCATC
1 CATCATC
59071125 CATCATC
1 CATCATC
59071132 CATCATC
1 CATCATC
*
59071139 CCTCATC
1 CATCATC
59071146 TCATCATC
1 -CATCATC
59071154 C
1 C
59071155 CTCTCATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.24, C:0.46, G:0.00, T:0.30
Consensus pattern (7 bp):
CATCATC
Done.