Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 3 of 50
Found at i:1514299 original size:99 final size:99
Alignment explanation
Indices: 1514178--1514368 Score: 301
Period size: 99 Copynumber: 1.9 Consensus size: 99
1514168 TCTTGACACT
* *
1514178 GAACTGGACAGAGAGAGGAGGAAACCATAGATAATCCATAGCCAACCGCCACTAGATATTTGGTA
1 GAACCGGACAGAGAGAGGAGGAAACCAGAGATAATCCATAGCCAACCGCCACTAGATATTTGGTA
* * *
1514243 TCTTCATTTTAAATCATATTACATGTATGAGACC
66 TATACAGTTTAAATCATATTACATGTATGAGACC
* *
1514277 GAACCGGACAGAGAGAGGAGGAAACTAGAGATAATCCATAGCCAACCGCCACTTGATATTTGGTA
1 GAACCGGACAGAGAGAGGAGGAAACCAGAGATAATCCATAGCCAACCGCCACTAGATATTTGGTA
* *
1514342 TATACAGTTTAATTCATTTTACATGTA
66 TATACAGTTTAAATCATATTACATGTA
1514369 GAAGTTGTCA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 83 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (99 bp):
GAACCGGACAGAGAGAGGAGGAAACCAGAGATAATCCATAGCCAACCGCCACTAGATATTTGGTA
TATACAGTTTAAATCATATTACATGTATGAGACC
Found at i:1519209 original size:13 final size:13
Alignment explanation
Indices: 1519191--1519221 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1519181 AATTTCCTTT
*
1519191 TTTTTACAATTTG
1 TTTTTACAATTTA
1519204 TTTTTACAATTTA
1 TTTTTACAATTTA
1519217 TTTTT
1 TTTTT
1519222 TTTTTCCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (13 bp):
TTTTTACAATTTA
Found at i:1519221 original size:14 final size:13
Alignment explanation
Indices: 1519188--1519222 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1519178 TTGAATTTCC
1519188 TTTTTTTTACAAT
1 TTTTTTTTACAAT
*
1519201 TTGTTTTTACAAT
1 TTTTTTTTACAAT
1519214 TTATTTTTT
1 TT-TTTTTT
1519223 TTTTCCAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTTTTTTACAAT
Found at i:1527977 original size:17 final size:17
Alignment explanation
Indices: 1527955--1527990 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1527945 TTTTTTATAG
1527955 TATCATGTAACTACCAC
1 TATCATGTAACTACCAC
*
1527972 TATCATGTAACTATCAC
1 TATCATGTAACTACCAC
1527989 TA
1 TA
1527991 GATGAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (17 bp):
TATCATGTAACTACCAC
Found at i:1537273 original size:92 final size:92
Alignment explanation
Indices: 1537116--1537301 Score: 363
Period size: 92 Copynumber: 2.0 Consensus size: 92
1537106 GGAAAAAGAA
1537116 TACCTCCAACTTATTGATGGTGCAATGATGAATGTAACCCGAAGTGTAATTGAAGAACTTATATC
1 TACCTCCAACTTATTGATGGTGCAATGATGAATGTAACCCGAAGTGTAATTGAAGAACTTATATC
1537181 TGACAAAAGTTCCATCAGCACGATTCT
66 TGACAAAAGTTCCATCAGCACGATTCT
*
1537208 TACCTCCAACTTATTGATGGTGCAATGATGAATGTAACCCGAAGTGTAATTGAAGAACTTGTATC
1 TACCTCCAACTTATTGATGGTGCAATGATGAATGTAACCCGAAGTGTAATTGAAGAACTTATATC
1537273 TGACAAAAGTTCCATCAGCACGATTCT
66 TGACAAAAGTTCCATCAGCACGATTCT
1537300 TA
1 TA
1537302 TGCTTGCTAT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (92 bp):
TACCTCCAACTTATTGATGGTGCAATGATGAATGTAACCCGAAGTGTAATTGAAGAACTTATATC
TGACAAAAGTTCCATCAGCACGATTCT
Found at i:1554755 original size:2 final size:2
Alignment explanation
Indices: 1554748--1554856 Score: 118
Period size: 2 Copynumber: 53.5 Consensus size: 2
1554738 TATTATACAT
1554748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
1554791 TA -A CTA CTA CT- TA CT- TNN NA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA -TA -TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
1554832 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1554857 GTCAACATCA
Statistics
Matches: 97, Mismatches: 2, Indels: 16
0.84 0.02 0.14
Matches are distributed among these distances:
1 4 0.04
2 84 0.87
3 9 0.09
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1556614 original size:38 final size:38
Alignment explanation
Indices: 1556566--1556643 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
1556556 TCATATATTT
*
1556566 ATACAAAGGTGATTTTGATCCATGAAGATATGGTGGCG
1 ATACAAAGGTGATTTTGATCCAAGAAGATATGGTGGCG
*
1556604 ATACCAAGGTGATTTTGATCCAAGAAGATATGGTGGCG
1 ATACAAAGGTGATTTTGATCCAAGAAGATATGGTGGCG
1556642 AT
1 AT
1556644 GCCGCAGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (38 bp):
ATACAAAGGTGATTTTGATCCAAGAAGATATGGTGGCG
Found at i:1569404 original size:34 final size:34
Alignment explanation
Indices: 1569361--1569428 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1569351 GAGAGGTTAC
1569361 AAAATTCAGATTGCTC-TTCATTTGACAAGAAAAG
1 AAAATTCAGATTGCTCATT-ATTTGACAAGAAAAG
1569395 AAAATTCAGATTGCTCATTATTTGACAAGAAAAG
1 AAAATTCAGATTGCTCATTATTTGACAAGAAAAG
1569429 CATAAAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 31 0.94
35 2 0.06
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (34 bp):
AAAATTCAGATTGCTCATTATTTGACAAGAAAAG
Found at i:1580116 original size:2 final size:2
Alignment explanation
Indices: 1580109--1580136 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1580099 CAGCTCTGTT
1580109 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1580137 GTTCTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1580239 original size:2 final size:2
Alignment explanation
Indices: 1580228--1580265 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1580218 TGAGTAATGA
1580228 AG AG -G AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1580266 CAAACAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1580250 original size:17 final size:17
Alignment explanation
Indices: 1580228--1580265 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1580218 TGAGTAATGA
1580228 AGAGGAGAGAGAGAGAG
1 AGAGGAGAGAGAGAGAG
1580245 AGAGGAGAGAGAGAGAG
1 AGAGGAGAGAGAGAGAG
1580262 AGAG
1 AGAG
1580266 CAAACAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (17 bp):
AGAGGAGAGAGAGAGAG
Found at i:1580252 original size:15 final size:15
Alignment explanation
Indices: 1580234--1580263 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1580224 ATGAAGAGGA
1580234 GAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAG
1580249 GAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAG
1580264 AGCAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (15 bp):
GAGAGAGAGAGAGAG
Found at i:1581392 original size:12 final size:12
Alignment explanation
Indices: 1581354--1581396 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
1581344 ATTTAAATAC
1581354 ATTTGACGGTATT
1 ATTT-ACGGTATT
*
1581367 ATTTAC-ATACTT
1 ATTTACGGTA-TT
1581379 ATTTACGGTATT
1 ATTTACGGTATT
1581391 ATTTAC
1 ATTTAC
1581397 TTATTACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.08
12 18 0.69
13 6 0.23
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.49
Consensus pattern (12 bp):
ATTTACGGTATT
Found at i:1591948 original size:22 final size:22
Alignment explanation
Indices: 1591908--1591950 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1591898 CTTCTTTGTC
* * *
1591908 CTTTTTCCTGTTTTTCTTTTTT
1 CTTTTTCCAGTTCTACTTTTTT
1591930 CTTTTTCCAGTTCTACTTTTT
1 CTTTTTCCAGTTCTACTTTTT
1591951 AGTAATTTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.05, C:0.21, G:0.05, T:0.70
Consensus pattern (22 bp):
CTTTTTCCAGTTCTACTTTTTT
Found at i:1593137 original size:29 final size:29
Alignment explanation
Indices: 1593104--1593195 Score: 161
Period size: 29 Copynumber: 3.2 Consensus size: 29
1593094 AACGAAGTTC
1593104 AGCGACAGCGAAGTTCATGATCAAGATCA
1 AGCGACAGCGAAGTTCATGATCAAGATCA
1593133 AGCGACAGCGAAGTTCATGATCAAGATCA
1 AGCGACAGCGAAGTTCATGATCAAGATCA
*
1593162 AGCGACAGCGAAGTTCGTGATC-AGAT-A
1 AGCGACAGCGAAGTTCATGATCAAGATCA
1593189 AGCGACA
1 AGCGACA
1593196 TCAAGAGACG
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
27 8 0.13
28 4 0.06
29 50 0.81
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (29 bp):
AGCGACAGCGAAGTTCATGATCAAGATCA
Found at i:1593199 original size:37 final size:37
Alignment explanation
Indices: 1593158--1593290 Score: 161
Period size: 37 Copynumber: 3.7 Consensus size: 37
1593148 CATGATCAAG
* *
1593158 ATCAAGCGACAGCGAAGTTCGTGATCAGATAAGCGAC
1 ATCAAGAGACAGCGAAGTTCATGATCAGATAAGCGAC
*
1593195 ATCAAGAGACGGCGAAGTTCATGATC--ATCAA--G--
1 ATCAAGAGACAGCGAAGTTCATGATCAGAT-AAGCGAC
* *
1593227 ATCAAGCGACAGCGAAGTTCGTGATCAGATAAGCGAC
1 ATCAAGAGACAGCGAAGTTCATGATCAGATAAGCGAC
*
1593264 ATCAAGAGACGGCGAAGTTCATGATCA
1 ATCAAGAGACAGCGAAGTTCATGATCA
1593291 TCAAGATCAA
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
32 23 0.29
33 2 0.03
34 3 0.04
35 3 0.04
36 2 0.03
37 47 0.59
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.17
Consensus pattern (37 bp):
ATCAAGAGACAGCGAAGTTCATGATCAGATAAGCGAC
Found at i:1593242 original size:69 final size:69
Alignment explanation
Indices: 1593129--1593322 Score: 315
Period size: 69 Copynumber: 2.9 Consensus size: 69
1593119 CATGATCAAG
* *
1593129 ATCAAGCGACAGCGAAGTTCATG---ATCAAGATCAAGCGACAGCGAAGTTCGTGATCAGATAAG
1 ATCAAGAGACGGCGAAGTTCATGATCATCAAGATCAAGCGACAGCGAAGTTCGTGATCAGATAAG
1593191 CGAC
66 CGAC
1593195 ATCAAGAGACGGCGAAGTTCATGATCATCAAGATCAAGCGACAGCGAAGTTCGTGATCAGATAAG
1 ATCAAGAGACGGCGAAGTTCATGATCATCAAGATCAAGCGACAGCGAAGTTCGTGATCAGATAAG
1593260 CGAC
66 CGAC
* *
1593264 ATCAAGAGACGGCGAAGTTCATGATCATCAAGATCAAGTGGCAGCGAAGGTT-GTGATCA
1 ATCAAGAGACGGCGAAGTTCATGATCATCAAGATCAAGCGACAGCGAA-GTTCGTGATCA
1593323 AAATCAGTAT
Statistics
Matches: 120, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
66 21 0.17
69 96 0.80
70 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.18
Consensus pattern (69 bp):
ATCAAGAGACGGCGAAGTTCATGATCATCAAGATCAAGCGACAGCGAAGTTCGTGATCAGATAAG
CGAC
Found at i:1593381 original size:67 final size:67
Alignment explanation
Indices: 1593296--1593462 Score: 307
Period size: 67 Copynumber: 2.5 Consensus size: 67
1593286 GATCATCAAG
1593296 ATCAAGTGGCAGCGAAGGTTGTGATCAAAATCAGTATATCAAGTATTCATGATCAAAATCAAGGG
1 ATCAAGTGGCAGCGAAGGTTGTGATCAAAATCAGTATATCAAGTATTCATGATCAAAATCAAGGG
1593361 TT
66 TT
1593363 ATCAAGTGGCAGCGAAGGTTGTGATCAAAATCAGTATATCAAGTATTCATGATCAAAATCAAGGG
1 ATCAAGTGGCAGCGAAGGTTGTGATCAAAATCAGTATATCAAGTATTCATGATCAAAATCAAGGG
1593428 TT
66 TT
* * *
1593430 ATCAAGTGGCAGCAAAGTTTGTGATCAAGATCA
1 ATCAAGTGGCAGCGAAGGTTGTGATCAAAATCA
1593463 AGCGGTAGCG
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 97 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (67 bp):
ATCAAGTGGCAGCGAAGGTTGTGATCAAAATCAGTATATCAAGTATTCATGATCAAAATCAAGGG
TT
Found at i:1593476 original size:29 final size:29
Alignment explanation
Indices: 1593444--1593549 Score: 103
Period size: 29 Copynumber: 3.7 Consensus size: 29
1593434 AGTGGCAGCA
* *
1593444 AAGTTTGTGATCAAGATCAAGCGGTAGCG
1 AAGTTCGTGATCAAGATCAAGCGATAGCG
* * *
1593473 AAGTTCGTGATTAAGATGAA-C-ATGATC-
1 AAGTTCGTGATCAAGATCAAGCGAT-AGCG
*
1593500 AAGATCAG-GATCAAGATCAAGCGATAGCG
1 AAGTTC-GTGATCAAGATCAAGCGATAGCG
*
1593529 AAGTTCATGATCAAGATCAAG
1 AAGTTCGTGATCAAGATCAAG
1593550 ATCCAACGGC
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
27 16 0.27
28 7 0.12
29 37 0.62
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
AAGTTCGTGATCAAGATCAAGCGATAGCG
Found at i:1593548 original size:35 final size:35
Alignment explanation
Indices: 1593502--1593583 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
1593492 ACATGATCAA
* * *
1593502 GATCAGGATCAAGAT-CAAGCGATAGCGAAGTTCAT
1 GATCAAGATCAAGATCCAA-CGACAACGAAGTTCAT
* * *
1593537 GATCAAGATCAAGATCCAACGGCAATGAAGTTTAT
1 GATCAAGATCAAGATCCAACGACAACGAAGTTCAT
1593572 GATCAAGATCAA
1 GATCAAGATCAA
1593584 CGTGTTCAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 37 0.93
36 3 0.08
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (35 bp):
GATCAAGATCAAGATCCAACGACAACGAAGTTCAT
Found at i:1593613 original size:21 final size:21
Alignment explanation
Indices: 1593572--1593614 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1593562 TGAAGTTTAT
*
1593572 GATCAAGATCAACGTGTTCAA
1 GATCAAGATCAACGTGATCAA
*
1593593 GATCAAGATTAAGCG-GATCAA
1 GATCAAGATCAA-CGTGATCAA
1593614 G
1 G
1593615 CGGCAACGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (21 bp):
GATCAAGATCAACGTGATCAA
Found at i:1593779 original size:35 final size:35
Alignment explanation
Indices: 1593733--1593802 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
1593723 TTACGAATAC
1593733 CAAGATAAAGCGGCAGT-GAAGTT-TGTGATCAAGAT
1 CAAGATAAAGCGGCA-TCGAAGTTCT-TGATCAAGAT
*
1593768 CAAGATTAAGCGGCATCGAAGTTCTTGATCAAGAT
1 CAAGATAAAGCGGCATCGAAGTTCTTGATCAAGAT
1593803 TAACGTGATC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 1 0.03
35 30 0.94
36 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (35 bp):
CAAGATAAAGCGGCATCGAAGTTCTTGATCAAGAT
Found at i:1593854 original size:29 final size:29
Alignment explanation
Indices: 1593819--1593887 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
1593809 GATCGTGATG
**
1593819 AAGATCAAGTGACAGTGAAGTTTGTAATC
1 AAGATCAAGTGACAACGAAGTTTGTAATC
*** *
1593848 AAGATCAAACAACAACGAAGTTTGTGATC
1 AAGATCAAGTGACAACGAAGTTTGTAATC
*
1593877 AAAATCAAGTG
1 AAGATCAAGTG
1593888 TTTGTGATCA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.23
Consensus pattern (29 bp):
AAGATCAAGTGACAACGAAGTTTGTAATC
Found at i:1593892 original size:20 final size:20
Alignment explanation
Indices: 1593867--1593904 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1593857 CAACAACGAA
1593867 GTTTGTGATCAAAATCAAGT
1 GTTTGTGATCAAAATCAAGT
*
1593887 GTTTGTGATCAAGATCAA
1 GTTTGTGATCAAAATCAA
1593905 TAAAATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
GTTTGTGATCAAAATCAAGT
Found at i:1594010 original size:32 final size:32
Alignment explanation
Indices: 1593974--1594043 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
1593964 TCGTGATTAA
* * *
1593974 GATCAACAAAATCGAGCAGCAATGAAGTTTGT
1 GATCAACAAAATCAAGCAGCAACGAAGGTTGT
* * * *
1594006 GATCATCAAGATCAAGCGGTAACGAAGGTTGT
1 GATCAACAAAATCAAGCAGCAACGAAGGTTGT
1594038 GATCAA
1 GATCAA
1594044 AATCAAGATA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (32 bp):
GATCAACAAAATCAAGCAGCAACGAAGGTTGT
Found at i:1594155 original size:35 final size:35
Alignment explanation
Indices: 1594106--1594187 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
1594096 TGAAGTTCGT
*
1594106 GATCAGGATCAAGCGGCAACAAAGTTCATGATCAA
1 GATCAAGATCAAGCGGCAACAAAGTTCATGATCAA
* * *
1594141 GATCAAGATTAAGCGGCAACGAAGTTCGTGATCAA
1 GATCAAGATCAAGCGGCAACAAAGTTCATGATCAA
1594176 GATCAAGATCAA
1 GATCAAGATCAA
1594188 ACGAATCAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (35 bp):
GATCAAGATCAAGCGGCAACAAAGTTCATGATCAA
Found at i:1594173 original size:29 final size:29
Alignment explanation
Indices: 1594097--1594182 Score: 91
Period size: 35 Copynumber: 2.8 Consensus size: 29
1594087 AAGTGGTAGT
*
1594097 GAAGTTCGTGATCAGGATCAAGCGGCAAC
1 GAAGTTCGTGATCAAGATCAAGCGGCAAC
* *
1594126 AAAGTTCATGATCAAGATCAAGATTAAGCGGCAAC
1 GAAGTTC--G-T---GATCAAGATCAAGCGGCAAC
1594161 GAAGTTCGTGATCAAGATCAAG
1 GAAGTTCGTGATCAAGATCAAG
1594183 ATCAAACGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
29 18 0.39
31 1 0.02
32 2 0.04
33 1 0.02
35 24 0.52
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (29 bp):
GAAGTTCGTGATCAAGATCAAGCGGCAAC
Found at i:1594206 original size:44 final size:44
Alignment explanation
Indices: 1594135--1594276 Score: 155
Period size: 44 Copynumber: 3.2 Consensus size: 44
1594125 CAAAGTTCAT
*
1594135 GATCAAGATC-AA-G-ATTAAGCGGCAACGAAGTTCGTGATCAA
1 GATCAAGATCAAACGAATCAAGCGGCAACGAAGTTCGTGATCAA
1594176 GATCAAGATCAAACGAATCAAGCGGCAACGAAGTTCGTGATCAA
1 GATCAAGATCAAACGAATCAAGCGGCAACGAAGTTCGTGATCAA
* * * * *
1594220 AATCAATATGATCAAGATCAAGATCAAGCGGCAGCGAAGTTTGTGATCGA
1 GATC-A-A-GATCAA-A-CGA-ATCAAGCGGCAACGAAGTTCGTGATCAA
1594270 GATCAAG
1 GATCAAG
1594277 CAGCAGCGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
41 10 0.12
42 2 0.02
43 1 0.01
44 30 0.35
45 1 0.01
46 1 0.01
47 7 0.08
48 2 0.02
49 3 0.04
50 28 0.33
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (44 bp):
GATCAAGATCAAACGAATCAAGCGGCAACGAAGTTCGTGATCAA
Found at i:1594272 original size:29 final size:29
Alignment explanation
Indices: 1594235--1594305 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
1594225 ATATGATCAA
* *
1594235 GATCAAGATCAAGCGGCAGCGAAGTTTGT
1 GATCAAGATCAAGCAGCAGCGAAGTTCGT
*
1594264 GATCGAGATCAAGCAGCAGCGAAGTTCGT
1 GATCAAGATCAAGCAGCAGCGAAGTTCGT
1594293 GATCAAGATCAAG
1 GATCAAGATCAAG
1594306 ATCAAGAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (29 bp):
GATCAAGATCAAGCAGCAGCGAAGTTCGT
Found at i:1594274 original size:35 final size:33
Alignment explanation
Indices: 1594228--1594311 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 33
1594218 AAAATCAATA
*
1594228 TGATCAAGATCAAGATCAAGCGGCAGCGAAGTTTG
1 TGATCAAGATCAAGATCAA--GGCAGCGAAGTTCG
*
1594263 TGATCGAGATCAAG--C-A-GCAGCGAAGTTCG
1 TGATCAAGATCAAGATCAAGGCAGCGAAGTTCG
1594292 TGATCAAGATCAAGATCAAG
1 TGATCAAGATCAAGATCAAG
1594312 AAGATCAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
29 25 0.60
31 1 0.02
32 2 0.05
33 1 0.02
35 13 0.31
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (33 bp):
TGATCAAGATCAAGATCAAGGCAGCGAAGTTCG
Found at i:1594275 original size:79 final size:79
Alignment explanation
Indices: 1594192--1594354 Score: 227
Period size: 79 Copynumber: 2.1 Consensus size: 79
1594182 GATCAAACGA
* * * * *
1594192 ATCAAGCGGCAACGAAGTTCGTGATCAAAATCAATATGATCAAGATCAAGATCAAGCGGCAGCGA
1 ATCAAGCAGCAACGAAGTTCGTGATCAAAATCAAGATCAACAAGATCAAGATCAAGCGGCAACGA
* *
1594257 AGTTTGTGATCGAG
66 AGTTCGTGATCAAG
* * * *
1594271 ATCAAGCAGCAGCGAAGTTCGTGATCAAGATCAAGATCAAGAAGATCAAGATTAAGCGGCAACGA
1 ATCAAGCAGCAACGAAGTTCGTGATCAAAATCAAGATCAACAAGATCAAGATCAAGCGGCAACGA
1594336 AGTTCGTGATCAAG
66 AGTTCGTGATCAAG
1594350 ATCAA
1 ATCAA
1594355 CATGATCGTG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.19
Consensus pattern (79 bp):
ATCAAGCAGCAACGAAGTTCGTGATCAAAATCAAGATCAACAAGATCAAGATCAAGCGGCAACGA
AGTTCGTGATCAAG
Found at i:1594303 original size:129 final size:127
Alignment explanation
Indices: 1594106--1594434 Score: 351
Period size: 129 Copynumber: 2.6 Consensus size: 127
1594096 TGAAGTTCGT
* * * * *
1594106 GATCAGGATCAAGCGGCAACAAAGTTCATGATCAAGATCAAGATTAAGCGGCAACGAAGTTCGTG
1 GATCAAGATCAAGCGACAACGAAGTTCATGATCAAGATC---A--AA-CAGCAACGAAGTTCATG
* *
1594171 ATCAAGATCAAGATC-AA-A-CGA-ATCAAGCGGCAACGAAGTTCGTGATCAAAATCAATATGAT
60 ATCAAGATCAAGATCAAAGATCAAGATCAAGCGGCAACGAAGTTCGTGATCAAAATCAACATGAT
1594232 CAA
125 CAA
* * ** * * * *
1594235 GATCAAGATCAAGCGGCAGCGAAGTTTGTGATCGAGATCAAGCAGCAGCGAAGTTCGTGATCAAG
1 GATCAAGATCAAGCGACAACGAAGTTCATGATCAAGATCAAACAGCAACGAAGTTCATGATCAAG
* * **
1594300 ATCAAGATCAAGAAGATCAAGATTAAGCGGCAACGAAGTTCGTGATCAAGATCAACATGATCGT
66 ATCAAGATC-A-AAGATCAAGATCAAGCGGCAACGAAGTTCGTGATCAAAATCAACATGATCAA
* * * *
1594364 GATCAAGATCAAGTGACAACGAAGTTCATGATCAAGATCAAACGGCAACGAAGTTTATGCTCAAG
1 GATCAAGATCAAGCGACAACGAAGTTCATGATCAAGATCAAACAGCAACGAAGTTCATGATCAAG
1594429 ATCAAG
66 ATCAAG
1594435 TGGCAGTGAA
Statistics
Matches: 167, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
123 30 0.18
124 1 0.01
126 3 0.02
127 1 0.01
128 2 0.01
129 130 0.78
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.19
Consensus pattern (127 bp):
GATCAAGATCAAGCGACAACGAAGTTCATGATCAAGATCAAACAGCAACGAAGTTCATGATCAAG
ATCAAGATCAAAGATCAAGATCAAGCGGCAACGAAGTTCGTGATCAAAATCAACATGATCAA
Found at i:1594319 original size:21 final size:21
Alignment explanation
Indices: 1594293--1594376 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
1594283 CGAAGTTCGT
1594293 GATCAAGATCAAGATCAAGAA
1 GATCAAGATCAAGATCAAGAA
* **
1594314 GATCAAGATTAAGCGGCAACGAA
1 GATCAAGATCAAG-ATCAA-GAA
* ** * *
1594337 GTTCGTGATCAAGATCAACAT
1 GATCAAGATCAAGATCAAGAA
**
1594358 GATCGTGATCAAGATCAAG
1 GATCAAGATCAAGATCAAG
1594377 TGACAACGAA
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
21 30 0.62
22 6 0.12
23 12 0.25
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.19
Consensus pattern (21 bp):
GATCAAGATCAAGATCAAGAA
Found at i:1594340 original size:50 final size:50
Alignment explanation
Indices: 1594264--1594404 Score: 167
Period size: 50 Copynumber: 2.8 Consensus size: 50
1594254 CGAAGTTTGT
* * * *
1594264 GATCGAGATCAAGCAGCAGCGAAGTTCGTGATCAAGATCAAGATCA-AGAA
1 GATCAAGATCAAGCGGCAACGAAGTTCGTGATCAAGATCAACATCATAG-A
* * * *
1594314 GATCAAGATTAAGCGGCAACGAAGTTCGTGATCAAGATCAACATGATCGT
1 GATCAAGATCAAGCGGCAACGAAGTTCGTGATCAAGATCAACATCATAGA
* * *
1594364 GATCAAGATCAAGTGACAACGAAGTTCATGATCAAGATCAA
1 GATCAAGATCAAGCGGCAACGAAGTTCGTGATCAAGATCAA
1594405 ACGGCAACGA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
50 77 0.99
51 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (50 bp):
GATCAAGATCAAGCGGCAACGAAGTTCGTGATCAAGATCAACATCATAGA
Found at i:1594439 original size:29 final size:29
Alignment explanation
Indices: 1594363--1594463 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 29
1594353 AACATGATCG
* *
1594363 TGATCAAGATCAAGTGACAACGAAGTTCA
1 TGATCAAGATCAAGTGGCAACGAAGTTTA
**
1594392 TGATCAAGATCAAACGGCAACGAAGTTTA
1 TGATCAAGATCAAGTGGCAACGAAGTTTA
* ** *
1594421 TGCTCAAGATCAAGTGGCAGTGAAGTTTG
1 TGATCAAGATCAAGTGGCAACGAAGTTTA
* *
1594450 TAATCAAAATCAAG
1 TGATCAAGATCAAG
1594464 ATATTCGTGA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.23
Consensus pattern (29 bp):
TGATCAAGATCAAGTGGCAACGAAGTTTA
Found at i:1619508 original size:2 final size:2
Alignment explanation
Indices: 1619503--1619550 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1619493 ACACACACAC
1619503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1619543 AT AT AT AT
1 AT AT AT AT
1619551 NGAAAGCTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1626123 original size:27 final size:27
Alignment explanation
Indices: 1626084--1626151 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
1626074 ATACCAACCA
*
1626084 CCACCTCCTCCTCCCCATCCCCATCCC
1 CCACCTCCACCTCCCCATCCCCATCCC
* * * *
1626111 CCACCTCCCCCTCCCCCTCCCCCTCCT
1 CCACCTCCACCTCCCCATCCCCATCCC
*
1626138 CCACCACCACCTCC
1 CCACCTCCACCTCC
1626152 TCCACCTCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.10, C:0.74, G:0.00, T:0.16
Consensus pattern (27 bp):
CCACCTCCACCTCCCCATCCCCATCCC
Found at i:1626162 original size:15 final size:15
Alignment explanation
Indices: 1626120--1626163 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1626110 CCCACCTCCC
* *
1626120 CCTCCCCCTCCCCCT
1 CCTCCACCTCCACCT
*
1626135 CCTCCACCACCACCT
1 CCTCCACCTCCACCT
1626150 CCTCCACCTCCACC
1 CCTCCACCTCCACC
1626164 CCATCCCCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.11, C:0.73, G:0.00, T:0.16
Consensus pattern (15 bp):
CCTCCACCTCCACCT
Found at i:1626171 original size:45 final size:43
Alignment explanation
Indices: 1626111--1626249 Score: 120
Period size: 45 Copynumber: 3.2 Consensus size: 43
1626101 TCCCCATCCC
*
1626111 CCACCT-C-CCCCTCCCCCTCCCCCTCCTCCACCACCACCTCCT
1 CCACCTCCACCCCTCCCCCT-CCCCACCTCCACCACCACCTCCT
* ** * *
1626153 CCACCTCCACCCCATCCCCATCCAAAACTGCCACCACCACCACCT
1 CCACCTCCACCCC-TCCCCCTCCCCACCT-CCACCACCACCTCCT
* * * *
1626198 CCTCCTCCACCCGCCTCCACCACCCCACCACCACCACCACCTCCT
1 CCACCTCCA-CC-CCTCCCCCTCCCCACCTCCACCACCACCTCCT
*
1626243 CCTCCTC
1 CCACCTC
1626250 TATAATATGG
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
42 6 0.08
43 1 0.01
44 8 0.11
45 49 0.64
46 10 0.13
47 2 0.03
ACGTcount: A:0.17, C:0.68, G:0.01, T:0.14
Consensus pattern (43 bp):
CCACCTCCACCCCTCCCCCTCCCCACCTCCACCACCACCTCCT
Found at i:1626176 original size:21 final size:21
Alignment explanation
Indices: 1626090--1626176 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
1626080 ACCACCACCT
*
1626090 CCTCCTCCCCATCCCCATCCC
1 CCTCCTCCCCATCCCCATCCA
* * * *
1626111 CCACCTCCCCCTCCCCCTCCC
1 CCTCCTCCCCATCCCCATCCA
* *
1626132 CCTCCTCCACCACCACCTCCTCCA
1 CCTCCTCC-CCATC-CC-CATCCA
*
1626156 CCTCCACCCCATCCCCATCCA
1 CCTCCTCCCCATCCCCATCCA
1626177 AAACTGCCAC
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 30 0.57
22 5 0.09
23 6 0.11
24 12 0.23
ACGTcount: A:0.13, C:0.71, G:0.00, T:0.16
Consensus pattern (21 bp):
CCTCCTCCCCATCCCCATCCA
Found at i:1626191 original size:3 final size:3
Alignment explanation
Indices: 1626183--1626238 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
1626173 TCCAAAACTG
* * * * *
1626183 CCA CCA CCA CCA CCT CCT CCT CCA CCCG CCT CCA CCA CC- CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA -CCA CCA CCA CCA CCA CCA CCA
1626228 CCA CCA CCA CC
1 CCA CCA CCA CC
1626239 TCCTCCTCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.91
4 2 0.04
ACGTcount: A:0.21, C:0.70, G:0.02, T:0.07
Consensus pattern (3 bp):
CCA
Found at i:1636237 original size:2 final size:2
Alignment explanation
Indices: 1636230--1636291 Score: 85
Period size: 2 Copynumber: 32.5 Consensus size: 2
1636220 ATAAAACTTA
* *
1636230 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AN CT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1636269 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1636292 AGATGATTAC
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
1 3 0.05
2 52 0.95
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1638734 original size:11 final size:11
Alignment explanation
Indices: 1638718--1638755 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
1638708 ATAGAAATTT
1638718 ATTTTTAGTAA
1 ATTTTTAGTAA
*
1638729 ATTTTTAAT-A
1 ATTTTTAGTAA
1638739 ATTTTTAGTAA
1 ATTTTTAGTAA
1638750 CATTTT
1 -ATTTT
1638756 ATAGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 9 0.39
11 9 0.39
12 5 0.22
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (11 bp):
ATTTTTAGTAA
Found at i:1644332 original size:24 final size:24
Alignment explanation
Indices: 1644295--1644341 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1644285 ACTTGAATTT
1644295 AATAATATATTATTTTTTAATAAAG
1 AATAATATATTATTTTTT-ATAAAG
*
1644320 AATAA-ATTTTATTTTTTATAAA
1 AATAATATATTATTTTTTATAAA
1644342 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
AATAATATATTATTTTTTATAAAG
Found at i:1661648 original size:16 final size:16
Alignment explanation
Indices: 1661627--1661659 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1661617 TTCCTTCCCT
1661627 CCAACTGTAGAAAAAC
1 CCAACTGTAGAAAAAC
1661643 CCAACTGTAGAAAAAC
1 CCAACTGTAGAAAAAC
1661659 C
1 C
1661660 TGAGAGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.12, T:0.12
Consensus pattern (16 bp):
CCAACTGTAGAAAAAC
Found at i:1664652 original size:26 final size:26
Alignment explanation
Indices: 1664616--1664667 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1664606 AGACACAAAC
1664616 CTAACAACCTAACAACTTGAAGTTAT
1 CTAACAACCTAACAACTTGAAGTTAT
*
1664642 CTAACAACCTAATAACTTGAAGTTAT
1 CTAACAACCTAACAACTTGAAGTTAT
1664668 GACTAGTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (26 bp):
CTAACAACCTAACAACTTGAAGTTAT
Found at i:1677771 original size:6 final size:6
Alignment explanation
Indices: 1677750--1677784 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1677740 GCCTAGGGAA
* *
1677750 AGAGAT AAAGAT AGAGAG AGAGAT AGAGAT AGAGA
1 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGA
1677785 ACAAACCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.34, T:0.11
Consensus pattern (6 bp):
AGAGAT
Found at i:1677773 original size:18 final size:18
Alignment explanation
Indices: 1677750--1677784 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1677740 GCCTAGGGAA
1677750 AGAGATAAAGATAGAGAG
1 AGAGATAAAGATAGAGAG
*
1677768 AGAGATAGAGATAGAGA
1 AGAGATAAAGATAGAGA
1677785 ACAAACCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.34, T:0.11
Consensus pattern (18 bp):
AGAGATAAAGATAGAGAG
Found at i:1679184 original size:17 final size:17
Alignment explanation
Indices: 1679158--1679192 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1679148 AATGGCATTG
1679158 ATTTGGCAACTACCTTA
1 ATTTGGCAACTACCTTA
* *
1679175 ATTTGTCAACTACTTTA
1 ATTTGGCAACTACCTTA
1679192 A
1 A
1679193 AGGAAAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (17 bp):
ATTTGGCAACTACCTTA
Found at i:1679258 original size:19 final size:18
Alignment explanation
Indices: 1679215--1679258 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
1679205 TATTAGTAAC
1679215 AAATTACCTAATTAAGAA
1 AAATTACCTAATTAAGAA
1679233 AATATTA-CTAATATAAGAGA
1 AA-ATTACCTAAT-TAAGA-A
1679253 AAATTA
1 AAATTA
1679259 TTGGATTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 7 0.30
19 13 0.57
20 3 0.13
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (18 bp):
AAATTACCTAATTAAGAA
Found at i:1693093 original size:111 final size:111
Alignment explanation
Indices: 1692933--1693132 Score: 262
Period size: 111 Copynumber: 1.8 Consensus size: 111
1692923 TCACGTCATA
* * * * *
1692933 TACAAAAATATGTAACACGCTATGGTTAGGTTGTTATATGGTATATACAAAAACACGTAACACAA
1 TACAAAAACATGTAACACGCGATAGTTAGGTTGTTACATCGTATATACAAAAACACGTAACAC-A
1692998 C-AT-GTCTAGATTGTTATACACCATGGTTAGATTGTTATACACTATT
65 CTATGGT-TAGATTGTTATACACCATGGTTAGATTGTTATACACTATT
* * * * *
1693044 TACAAAAACATGTGACATGCGATAGTTAGGTTGTTACA-CGTCATGTACAAAAACATGTAACACG
1 TACAAAAACATGTAACACGCGATAGTTAGGTTGTTACATCGT-ATATACAAAAACACGTAACACA
1693108 CTATGGTTAGATTGTTATACACCAT
65 CTATGGTTAGATTGTTATACACCAT
1693133 ATTGAAAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
110 3 0.04
111 71 0.93
112 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (111 bp):
TACAAAAACATGTAACACGCGATAGTTAGGTTGTTACATCGTATATACAAAAACACGTAACACAC
TATGGTTAGATTGTTATACACCATGGTTAGATTGTTATACACTATT
Found at i:1693141 original size:45 final size:44
Alignment explanation
Indices: 1693020--1693141 Score: 118
Period size: 45 Copynumber: 2.7 Consensus size: 44
1693010 GTTATACACC
* * *
1693020 ATGGTTAGATTGTTATACACTATTTACAAAAACATGTGACATGCG
1 ATGGTTAGATTGTTATACACCATTT-CAAAAACATGTAACACGCG
* * * ** * *
1693065 ATAGTTAGGTTGTTACACGTCATGTACAAAAACATGTAACACGCT
1 ATGGTTAGATTGTTATACACCAT-TTCAAAAACATGTAACACGCG
*
1693110 ATGGTTAGATTGTTATACACCATATTGAAAAA
1 ATGGTTAGATTGTTATACACCAT-TTCAAAAA
1693142 AAAATATTAT
Statistics
Matches: 58, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
45 57 0.98
46 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (44 bp):
ATGGTTAGATTGTTATACACCATTTCAAAAACATGTAACACGCG
Found at i:1693633 original size:23 final size:23
Alignment explanation
Indices: 1693589--1693633 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1693579 CTTAGTGTCT
* *
1693589 TGAAAGCGTAAAAGAGAGAAATC
1 TGAAAACGTAAAAGAGAAAAATC
1693612 TGAAAACGTAAGAA-AGAAAAAT
1 TGAAAACGTAA-AAGAGAAAAAT
1693634 TGATAGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.58, C:0.07, G:0.22, T:0.13
Consensus pattern (23 bp):
TGAAAACGTAAAAGAGAAAAATC
Found at i:1718533 original size:30 final size:30
Alignment explanation
Indices: 1718497--1718581 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
1718487 TCAAATAGAG
*
1718497 GTTTCTATACCTATAAGATATATTTAAGAC
1 GTTTCTACACCTATAAGATATATTTAAGAC
* *
1718527 GTTTCTACACCTATCAGATATATTTAAGAG
1 GTTTCTACACCTATAAGATATATTTAAGAC
* *
1718557 GTTTCTACATCTATTAGATATATTT
1 GTTTCTACACCTATAAGATATATTT
1718582 CTTCTAGTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (30 bp):
GTTTCTACACCTATAAGATATATTTAAGAC
Found at i:1723072 original size:19 final size:20
Alignment explanation
Indices: 1723035--1723072 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1723025 AGTTGTCCTG
1723035 TTATTTTATGCTGTTATTTT
1 TTATTTTATGCTGTTATTTT
*
1723055 TTATTTTGTGCT-TTATTT
1 TTATTTTATGCTGTTATTT
1723073 GAAGTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.13, C:0.05, G:0.11, T:0.71
Consensus pattern (20 bp):
TTATTTTATGCTGTTATTTT
Found at i:1729295 original size:2 final size:2
Alignment explanation
Indices: 1729290--1729336 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1729280 TAAAAGCATG
1729290 AT AT AT 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 AT AT AT
1729332 AT AT A
1 AT AT A
1729337 GTAGTANNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1731002 original size:2 final size:2
Alignment explanation
Indices: 1730990--1731026 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1730980 NNNNNNNNNN
*
1730990 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1731027 GATGCAGACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1731728 original size:85 final size:87
Alignment explanation
Indices: 1731568--1731734 Score: 232
Period size: 85 Copynumber: 1.9 Consensus size: 87
1731558 ATTAAACATA
* * *
1731568 TTTAAATTGATGATGTCCTGATAGATTATATATTATAAAATTAATTAGAAGGAGAATTTGAATAT
1 TTTAAATTGATGATCTCCTGACAGATTATATATTATAAAATTAATTAGAAGGAGAACTTGAATAT
1731633 GAACACGTTTTAAGTAAACACG
66 GAACACGTTTTAAGTAAACACG
* * **
1731655 TTTAAATTGATGATCTCCTGACCGA-T-TATATTATGAAATTAATTA-AATGGAGAACTTGGGTA
1 TTTAAATTGATGATCTCCTGACAGATTATATATTATAAAATTAATTAGAA-GGAGAACTTGAATA
*
1731717 TGAACATGTTTTAAGTAA
65 TGAACACGTTTTAAGTAA
1731735 TTCATCTTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
84 2 0.03
85 46 0.65
86 1 0.01
87 22 0.31
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.37
Consensus pattern (87 bp):
TTTAAATTGATGATCTCCTGACAGATTATATATTATAAAATTAATTAGAAGGAGAACTTGAATAT
GAACACGTTTTAAGTAAACACG
Found at i:1733006 original size:2 final size:2
Alignment explanation
Indices: 1733001--1733043 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1732991 ATGAAGAAAT
1733001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1733043 T
1 T
1733044 TAAAGGTGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1735368 original size:236 final size:236
Alignment explanation
Indices: 1734950--1735418 Score: 821
Period size: 236 Copynumber: 2.0 Consensus size: 236
1734940 GAAAGGTGAA
*
1734950 AACTTGCAGGCTTGCAGCTGTGTCGAAACGTTGATGAGGTGGTTATGCTCCAGCCGTCCAGTCCA
1 AACTTGCAGGCTCGCAGCTGTGTCGAAACGTTGATGAGGTGGTTATGCTCCAGCCGTCCAGTCCA
*
1735015 AGATAGCCTTTACAATATTTAAGGTCCTTGTCAGCTTTTTGATGATTAAGCACCAAATTAAGATG
66 AGATAGCCTTTACAATATATAAGGTCCTTGTCAGCTTTTTGATGATTAAGCACCAAATTAAGATG
*
1735080 AAACATGTTTAAATTGATAATCTCCTAACAAATTATATATTATGAGATTAATTAGATGGAGAACT
131 AAACATGTTTAAATTGATAATCTCCTAACAAATTATATATTATGACATTAATTAGATGGAGAACT
*
1735145 TGGCTGTGATCACATTTAACATATTTTTTAAGTAATTTGAC
196 TGGCTGTGAACACATTTAACATATTTTTTAAGTAATTTGAC
* *
1735186 AACTTGCAGGCTCGCAGCTGTGTCGAAACTTTGATGAGGTGGTTATGCTCCAGCCGTTCAGTCCA
1 AACTTGCAGGCTCGCAGCTGTGTCGAAACGTTGATGAGGTGGTTATGCTCCAGCCGTCCAGTCCA
* * * *
1735251 AGCTAGCCTTTACACTATATAAGGTCCTTGTCGGCTTTTTGATGATTAAGCACTAAATTAAGATG
66 AGATAGCCTTTACAATATATAAGGTCCTTGTCAGCTTTTTGATGATTAAGCACCAAATTAAGATG
* *
1735316 AAACATGTTTATATTGATAATCTCCTAACAGATTATATATTATGACATTAATTAGATGGAGAACT
131 AAACATGTTTAAATTGATAATCTCCTAACAAATTATATATTATGACATTAATTAGATGGAGAACT
*
1735381 TGGTTGTGAACACATTTAACATATTTTTTAAGTAATTT
196 TGGCTGTGAACACATTTAACATATTTTTTAAGTAATTT
1735419 ATCTTTGATT
Statistics
Matches: 220, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
236 220 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (236 bp):
AACTTGCAGGCTCGCAGCTGTGTCGAAACGTTGATGAGGTGGTTATGCTCCAGCCGTCCAGTCCA
AGATAGCCTTTACAATATATAAGGTCCTTGTCAGCTTTTTGATGATTAAGCACCAAATTAAGATG
AAACATGTTTAAATTGATAATCTCCTAACAAATTATATATTATGACATTAATTAGATGGAGAACT
TGGCTGTGAACACATTTAACATATTTTTTAAGTAATTTGAC
Found at i:1739895 original size:27 final size:27
Alignment explanation
Indices: 1739857--1739941 Score: 143
Period size: 27 Copynumber: 3.1 Consensus size: 27
1739847 TTTAATAAGA
*
1739857 ATTAATGATCAGATTCATATGGTTGAT
1 ATTAATGATCAGATTCATATGGCTGAT
*
1739884 ATTAATAATCAGATTCATATGGCTGAT
1 ATTAATGATCAGATTCATATGGCTGAT
*
1739911 ATTAATGATCATATTCATATGGCTGAT
1 ATTAATGATCAGATTCATATGGCTGAT
1739938 ATTA
1 ATTA
1739942 TCCCGCCAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.40
Consensus pattern (27 bp):
ATTAATGATCAGATTCATATGGCTGAT
Found at i:1744937 original size:27 final size:27
Alignment explanation
Indices: 1744899--1744983 Score: 152
Period size: 27 Copynumber: 3.1 Consensus size: 27
1744889 TTTAATAAAA
*
1744899 ATTAATGATCAGATTCATATGGCTGAT
1 ATTAATGATCAGATTCATATGGTTGAT
1744926 ATTAATGATCAGATTCATATGGTTGAT
1 ATTAATGATCAGATTCATATGGTTGAT
*
1744953 ATTAATGATCAGATCCATATGGTTGAT
1 ATTAATGATCAGATTCATATGGTTGAT
1744980 ATTA
1 ATTA
1744984 TCTCGCCAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (27 bp):
ATTAATGATCAGATTCATATGGTTGAT
Found at i:1755040 original size:35 final size:35
Alignment explanation
Indices: 1754994--1755063 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1754984 TAACTGCCAA
1754994 AGTCTCTTTGAGCAGCTTGATCTTTGTAATTTGAT
1 AGTCTCTTTGAGCAGCTTGATCTTTGTAATTTGAT
1755029 AGTCTCTTTGAGCAGCTTGATCTTTGTAATTTGAT
1 AGTCTCTTTGAGCAGCTTGATCTTTGTAATTTGAT
1755064 TTGTTTCCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (35 bp):
AGTCTCTTTGAGCAGCTTGATCTTTGTAATTTGAT
Found at i:1757933 original size:11 final size:11
Alignment explanation
Indices: 1757919--1757950 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1757909 ATTTTCAATG
1757919 GATTTGCAACA
1 GATTTGCAACA
1757930 GATTTGCAACA
1 GATTTGCAACA
*
1757941 GATTTCCAAC
1 GATTTGCAAC
1757951 GGAGTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (11 bp):
GATTTGCAACA
Found at i:1757999 original size:11 final size:11
Alignment explanation
Indices: 1757980--1758014 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1757970 TAAATGCTTG
*
1757980 TTTCGATGGAT
1 TTTCAATGGAT
1757991 TTTCAATGGAT
1 TTTCAATGGAT
*
1758002 TTCCAATGGAT
1 TTTCAATGGAT
1758013 TT
1 TT
1758015 ATATTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (11 bp):
TTTCAATGGAT
Found at i:1771855 original size:22 final size:23
Alignment explanation
Indices: 1771830--1771873 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1771820 ACAATTGGGC
1771830 GAAAA-CAAGGATAAGAAGAGTT
1 GAAAATCAAGGATAAGAAGAGTT
**
1771852 GAAAATCTGGGATAAGAAGAGT
1 GAAAATCAAGGATAAGAAGAGT
1771874 AAGCCACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.50, C:0.05, G:0.30, T:0.16
Consensus pattern (23 bp):
GAAAATCAAGGATAAGAAGAGTT
Found at i:1771888 original size:75 final size:75
Alignment explanation
Indices: 1771799--1771948 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
1771789 ATCTACAGGG
1771799 AAGCCACCAACCAACAAGCTGACAATTGGGCGAAAACAAGGATAAGAAGAGTTGAAAATCTGGGA
1 AAGCCACCAACCAACAAGCTGACAATTGGGCGAAAACAAGGATAAGAAGAGTTGAAAATCTGGGA
1771864 TAAGAAGAGT
66 TAAGAAGAGT
*
1771874 AAGCCACCAACCAACAAGCTGACAATTTGGCGAAAACAAGGATAAGAAGAGTTGAAAATCTGGGA
1 AAGCCACCAACCAACAAGCTGACAATTGGGCGAAAACAAGGATAAGAAGAGTTGAAAATCTGGGA
1771939 TAAGAAGAGT
66 TAAGAAGAGT
1771949 TGAAAACCTG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.45, C:0.16, G:0.25, T:0.14
Consensus pattern (75 bp):
AAGCCACCAACCAACAAGCTGACAATTGGGCGAAAACAAGGATAAGAAGAGTTGAAAATCTGGGA
TAAGAAGAGT
Found at i:1771930 original size:22 final size:22
Alignment explanation
Indices: 1771905--1771955 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
1771895 ACAATTTGGC
1771905 GAAAACAAGGATAAGAAGAGTT
1 GAAAACAAGGATAAGAAGAGTT
**
1771927 GAAAATCTGGGATAAGAAGAGTT
1 GAAAA-CAAGGATAAGAAGAGTT
1771950 GAAAAC
1 GAAAAC
1771956 CTGCTCAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.51, C:0.06, G:0.27, T:0.16
Consensus pattern (22 bp):
GAAAACAAGGATAAGAAGAGTT
Found at i:1776169 original size:29 final size:25
Alignment explanation
Indices: 1776127--1776184 Score: 62
Period size: 29 Copynumber: 2.2 Consensus size: 25
1776117 AGTGTGACAA
*
1776127 AATATTTTTAAATATGGCATGTAATAAC
1 AATATTTTTAAATACGGC--GT-ATAAC
*
1776155 AATATTTTTTCAATACGGCGTATAAC
1 AATA-TTTTTAAATACGGCGTATAAC
1776181 AATA
1 AATA
1776185 AAAATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 9 0.33
27 2 0.07
28 4 0.15
29 12 0.44
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (25 bp):
AATATTTTTAAATACGGCGTATAAC
Found at i:1776194 original size:30 final size:32
Alignment explanation
Indices: 1776149--1776212 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 32
1776139 TATGGCATGT
*
1776149 AATAACAATATTTTTTCAATACGGCGTATAAC
1 AATAACAATATTTTTTCAATACAGCGTATAAC
**
1776181 AATAA-AA-ATTTTTTCAATGTAGCGTATAAC
1 AATAACAATATTTTTTCAATACAGCGTATAAC
1776211 AA
1 AA
1776213 CCTAACCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 22 0.76
31 2 0.07
32 5 0.17
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.34
Consensus pattern (32 bp):
AATAACAATATTTTTTCAATACAGCGTATAAC
Found at i:1776308 original size:45 final size:45
Alignment explanation
Indices: 1776207--1776312 Score: 133
Period size: 45 Copynumber: 2.4 Consensus size: 45
1776197 ATGTAGCGTA
* * * *
1776207 TAACAACCTAACCATGACGTGTCATATGTTTTTATACATAGCGTG
1 TAACAACCTAATCATGACGTATCACATGTTTTTATACATAGCGCG
* *
1776252 TAATAACCTAATCATGACGTATCACATGTTTTTGTACAT-GTCGCG
1 TAACAACCTAATCATGACGTATCACATGTTTTTATACATAG-CGCG
*
1776297 TAACAATCTAATCATG
1 TAACAACCTAATCATG
1776313 GTGTGTAACA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 1 0.02
45 51 0.98
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (45 bp):
TAACAACCTAATCATGACGTATCACATGTTTTTATACATAGCGCG
Found at i:1776390 original size:24 final size:24
Alignment explanation
Indices: 1776330--1776391 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
1776320 ACAACCTAAC
* *
1776330 CATAACGTGTTACATATTTTTATA
1 CATAGCGTGTAACATATTTTTATA
*
1776354 CATAGCG-GATAACATGTTTTTATA
1 CATAGCGTG-TAACATATTTTTATA
* *
1776378 TATGGCGTGTAACA
1 CATAGCGTGTAACA
1776392 ACCTAATCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 1 0.03
24 29 0.94
25 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (24 bp):
CATAGCGTGTAACATATTTTTATA
Found at i:1776437 original size:44 final size:45
Alignment explanation
Indices: 1776365--1776523 Score: 178
Period size: 45 Copynumber: 3.6 Consensus size: 45
1776355 ATAGCGGATA
* * ** *
1776365 ACATGTTTTTATATATGGCGTGTAACAACCTAATCATGCCGTGTC
1 ACATATTTTTGTATATAACGTGTAACAACCTAATCATGACGTGTC
* * * * *
1776410 ACAT-GTTTTGTACATAACTTGTAACAACCTAA-CTATAACATGTC
1 ACATATTTTTGTATATAACGTGTAACAACCTAATC-ATGACGTGTC
** *
1776454 ACATATTTTTGTATATGGCGTGTAACAACCTAATCATGACGTGTA
1 ACATATTTTTGTATATAACGTGTAACAACCTAATCATGACGTGTC
1776499 ACATATTTTTGTATATAACGTGTAA
1 ACATATTTTTGTATATAACGTGTAA
1776524 ACACCATTAC
Statistics
Matches: 92, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
43 1 0.01
44 33 0.36
45 57 0.62
46 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (45 bp):
ACATATTTTTGTATATAACGTGTAACAACCTAATCATGACGTGTC
Found at i:1784863 original size:39 final size:39
Alignment explanation
Indices: 1784804--1784985 Score: 204
Period size: 39 Copynumber: 4.7 Consensus size: 39
1784794 CATTGAATAT
* * *
1784804 ACTGAAGAGAAACCTCAGTTGCTGACACCGAAAGAGTTC
1 ACTGAAGAAAAATCTCAGTTGCTGACACCGAAAGAGTAC
* * * *
1784843 ATTGAAGAAAAACCTGAGTTGCTGGCACCGAAAGAGTAC
1 ACTGAAGAAAAATCTCAGTTGCTGACACCGAAAGAGTAC
* * * * *
1784882 ACTGAAGAAAAATCTGAATTGCTGGCACCAAAAGAGTAT
1 ACTGAAGAAAAATCTCAGTTGCTGACACCGAAAGAGTAC
* * *
1784921 GCAGAAGAAAAATCTCAGTTGCTGACACC-AATAGAATAC
1 ACTGAAGAAAAATCTCAGTTGCTGACACCGAA-AGAGTAC
*
1784960 ACTGAAGAAAAATCTCAGTTGTTGAC
1 ACTGAAGAAAAATCTCAGTTGCTGAC
1784986 CCCAGAGGAC
Statistics
Matches: 122, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
38 2 0.02
39 120 0.98
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (39 bp):
ACTGAAGAAAAATCTCAGTTGCTGACACCGAAAGAGTAC
Found at i:1789648 original size:16 final size:16
Alignment explanation
Indices: 1789629--1789668 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1789619 AAATGAAAAC
*
1789629 AGAAGAAAGGAAAAGG
1 AGAAGAAAAGAAAAGG
1789645 AGAAGAAAAGAAAA-G
1 AGAAGAAAAGAAAAGG
*
1789660 AAAAGAAAA
1 AGAAGAAAA
1789669 AACTGTGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
AGAAGAAAAGAAAAGG
Found at i:1789655 original size:5 final size:5
Alignment explanation
Indices: 1789612--1789668 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
1789602 ACCCAAAAAT
* * * * *
1789612 AAGAA AA-AA ATGAA AACAG AAGAA AGGAA AAGGAG AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA-GAA AAGAA AAGAA AAGAA
1789662 AAGAA AA
1 AAGAA AA
1789669 AACTGTGGTC
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
4 3 0.08
5 33 0.82
6 4 0.10
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:1794301 original size:45 final size:47
Alignment explanation
Indices: 1794229--1794319 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 47
1794219 AAAGATATGA
* * * *
1794229 GTAAGGCCAGAGCCTAAAAGCCCATATATAAAGCACAAAA-AGATGC
1 GTAAGGCCAAAGCCCAAAAGCCAATATATAAAACACAAAACAGATGC
1794275 GTAAGG-CAAAGCCCAAAAGCCAATATATAAAACACAAAACAGATG
1 GTAAGGCCAAAGCCCAAAAGCCAATATATAAAACACAAAACAGATG
1794320 ATTGGGTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 29 0.73
46 11 0.28
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (47 bp):
GTAAGGCCAAAGCCCAAAAGCCAATATATAAAACACAAAACAGATGC
Found at i:1794411 original size:46 final size:46
Alignment explanation
Indices: 1794356--1794444 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 46
1794346 ATGAGTGGGT
* *
1794356 AAATCCCAGTGGAGTGAA-ATAACAGGACTGCAACAAAGACAAAGAC
1 AAATCCCAGTAGAGTGAAGA-AACAAGACTGCAACAAAGACAAAGAC
1794402 AAATCCCAGTAGAGTGAAGAAACAAGACTGCAACAAAGACAAA
1 AAATCCCAGTAGAGTGAAGAAACAAGACTGCAACAAAGACAAA
1794445 AAGGAAGCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
46 39 0.98
47 1 0.03
ACGTcount: A:0.51, C:0.19, G:0.20, T:0.10
Consensus pattern (46 bp):
AAATCCCAGTAGAGTGAAGAAACAAGACTGCAACAAAGACAAAGAC
Found at i:1799625 original size:24 final size:21
Alignment explanation
Indices: 1799568--1799627 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
1799558 AGACCGAGAC
* *
1799568 AGGGACAGAGACAGAGATAGG
1 AGGGATAGAGATAGAGATAGG
1799589 AGGGATAGAGATAGAGATAGG
1 AGGGATAGAGATAGAGATAGG
1799610 AGTAGGCATAGAGATAGA
1 AG--GG-ATAGAGATAGA
1799628 TATAAAGAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 21 0.62
23 2 0.06
24 11 0.32
ACGTcount: A:0.43, C:0.05, G:0.40, T:0.12
Consensus pattern (21 bp):
AGGGATAGAGATAGAGATAGG
Found at i:1802907 original size:48 final size:49
Alignment explanation
Indices: 1802836--1802932 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 49
1802826 CAACAAGCCA
1802836 GACTTCCTTGATCTCTCTCTTTCATCTGTTTGAA-TTGTTTTGTTCACT
1 GACTTCCTTGATCTCTCTCTTTCATCTGTTTGAATTTGTTTTGTTCACT
1802884 GACTTCCTTGATCTCTCTCTTTCATCTGTTTGAATTTGTTTTGTTCACT
1 GACTTCCTTGATCTCTCTCTTTCATCTGTTTGAATTTGTTTTGTTCACT
1802933 AGTAGATGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 34 0.71
49 14 0.29
ACGTcount: A:0.12, C:0.23, G:0.12, T:0.53
Consensus pattern (49 bp):
GACTTCCTTGATCTCTCTCTTTCATCTGTTTGAATTTGTTTTGTTCACT
Found at i:1813651 original size:2 final size:2
Alignment explanation
Indices: 1813644--1813688 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
1813634 ATTTGAGTAG
* *
1813644 CT CT CT CT CT CT CT CT CT CT -T CT CT CT -T TT CT CT CT TT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1813684 CT CT C
1 CT CT C
1813689 CCTCAAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
CT
Found at i:1817167 original size:3 final size:3
Alignment explanation
Indices: 1817161--1817186 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1817151 GGCTTCTTCT
1817161 CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CT
1817187 TCAACCTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:1819032 original size:29 final size:30
Alignment explanation
Indices: 1818990--1819052 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1818980 TTAATTATTA
*
1818990 ATAATAAAATATTT-ATTTAAAATAAAAAT
1 ATAATAAAATATTTGATTCAAAATAAAAAT
**
1819019 ATAATAACTTATTTGATTCAAAATAAAAAT
1 ATAATAAAATATTTGATTCAAAATAAAAAT
1819049 ATAA
1 ATAA
1819053 AATTTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (30 bp):
ATAATAAAATATTTGATTCAAAATAAAAAT
Found at i:1853197 original size:3 final size:3
Alignment explanation
Indices: 1853189--1853214 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1853179 ATACACTTAA
1853189 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
1853215 TTATTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1855722 original size:2 final size:2
Alignment explanation
Indices: 1855717--1855743 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1855707 GAAGTGTGTG
1855717 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1855744 TTGGATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1869722 original size:165 final size:166
Alignment explanation
Indices: 1869437--1869778 Score: 562
Period size: 165 Copynumber: 2.1 Consensus size: 166
1869427 GATGTTATTA
1869437 AACTTACATTATTATCATGATTTCATAATTTAATTGATTTACTATATAATAAAACATAAAAAAAT
1 AACTTACATTATTATCATGATTTCATAATTTAATTGATTTACTATATAATAAAACATAAAAAAAT
* * *
1869502 GAATCTAAAACAAAATATAAGATATGTGACCCAAATAATTCACATAATTTGATAAACCGAACTTT
66 GAATCTAAAACAAAATATAAGATATGTGACCCAAAAAATTCACATAATTTGATAAACAGAACTCT
*
1869567 GGATCGATTTGGTTAATTTTCGCAACATATTCAATT
131 AGATCGATTTGGTTAATTTTCGCAACATATTCAATT
* *
1869603 AACTTACATTGTTATCATGATTTCATAATTTAATTGATTTACTATATAAT-CAACATAAAAAAAT
1 AACTTACATTATTATCATGATTTCATAATTTAATTGATTTACTATATAATAAAACATAAAAAAAT
* * * *
1869667 GAATCTAAAACAAAATATAAGATCTGTGACTCAAAAAATTCATATAATTTGATAAACAGAAGTCT
66 GAATCTAAAACAAAATATAAGATATGTGACCCAAAAAATTCACATAATTTGATAAACAGAACTCT
*
1869732 AGATCGATTTGGTTAATTTTCGCAACATATTCCATT
131 AGATCGATTTGGTTAATTTTCGCAACATATTCAATT
*
1869768 AATTTA-ATTAT
1 AACTTACATTAT
1869779 ACATTTTTTA
Statistics
Matches: 163, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
164 4 0.02
165 110 0.67
166 49 0.30
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (166 bp):
AACTTACATTATTATCATGATTTCATAATTTAATTGATTTACTATATAATAAAACATAAAAAAAT
GAATCTAAAACAAAATATAAGATATGTGACCCAAAAAATTCACATAATTTGATAAACAGAACTCT
AGATCGATTTGGTTAATTTTCGCAACATATTCAATT
Found at i:1880645 original size:13 final size:13
Alignment explanation
Indices: 1880627--1880652 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1880617 TTAAAAATAC
1880627 ATATATATATATA
1 ATATATATATATA
1880640 ATATATATATATA
1 ATATATATATATA
1880653 TTTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:1880702 original size:2 final size:2
Alignment explanation
Indices: 1880686--1880722 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1880676 TGCAATCACN
* *
1880686 TA TA TA AA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1880723 TATTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1905428 original size:19 final size:20
Alignment explanation
Indices: 1905392--1905429 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1905382 ACCTTCTCTA
**
1905392 TAAAAAATAATTTTATAAAT
1 TAAAAAATAATTCAATAAAT
1905412 TAAAAAAT-ATTCAATAAA
1 TAAAAAATAATTCAATAAA
1905430 AGAGAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAAATAATTCAATAAAT
Found at i:1907480 original size:26 final size:25
Alignment explanation
Indices: 1907421--1907480 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
1907411 AAAAATATAT
*
1907421 AAATAAATTTTAAAAATTATTTAAA
1 AAATAAATTTTAAAAATTACTTAAA
* * *
1907446 CAATCAATTTTAATAATATACTTAAA
1 AAATAAATTTTAAAAAT-TACTTAAA
*
1907472 AAATTAATT
1 AAATAAATT
1907481 AGTATAATCT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (25 bp):
AAATAAATTTTAAAAATTACTTAAA
Found at i:1911372 original size:48 final size:48
Alignment explanation
Indices: 1911316--1911411 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1911306 TCTGTTATAT
1911316 TAGAGAGCAGTATAGATTAGCATCCACTGGTTTTCCTGTCAGATAGAC
1 TAGAGAGCAGTATAGATTAGCATCCACTGGTTTTCCTGTCAGATAGAC
1911364 TAGAGAGCAGTATAGATTAGCATCCACTGGTTTTCCTGTCAGATAGAC
1 TAGAGAGCAGTATAGATTAGCATCCACTGGTTTTCCTGTCAGATAGAC
1911412 CTTCAAACCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (48 bp):
TAGAGAGCAGTATAGATTAGCATCCACTGGTTTTCCTGTCAGATAGAC
Found at i:1913968 original size:25 final size:24
Alignment explanation
Indices: 1913930--1913977 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1913920 AATCAATTGA
*
1913930 GTTTGGTTTAATTTTATTTAATTT
1 GTTTGGTTTAATTTTAATTAATTT
*
1913954 GTTTGGTTTTGATTTTAATTAATT
1 GTTTGG-TTTAATTTTAATTAATT
1913978 ATTTGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (24 bp):
GTTTGGTTTAATTTTAATTAATTT
Found at i:1915609 original size:6 final size:6
Alignment explanation
Indices: 1915598--1915637 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
1915588 TAATTGGCCA
1915598 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTT
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTT
1915638 TTTTTCTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CCTTCC
Found at i:1931542 original size:40 final size:40
Alignment explanation
Indices: 1931487--1931566 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1931477 AAATTATACC
1931487 ATCAAACTGAAACATATAGAGATATTGCATGATATTCTTT
1 ATCAAACTGAAACATATAGAGATATTGCATGATATTCTTT
1931527 ATCAAACTGAAACATATAGAGATATTGCATGATATTCTTT
1 ATCAAACTGAAACATATAGAGATATTGCATGATATTCTTT
1931567 CTCTCCCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (40 bp):
ATCAAACTGAAACATATAGAGATATTGCATGATATTCTTT
Found at i:1941314 original size:53 final size:53
Alignment explanation
Indices: 1941251--1941358 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
1941241 AACTTAAGAA
* *
1941251 ACTTTGATATAATTAATTAAGCCCAAAGCAAGTAACTATAACCATGCTTTTTT
1 ACTTTGATATAATTAAATAAGCCCAAAGCAAGTAACTATAACCACGCTTTTTT
*
1941304 ACTTTGATATAATTAAATAAGGCCAAAGCAAGTAACTATAACCACGCTTTTTT
1 ACTTTGATATAATTAAATAAGCCCAAAGCAAGTAACTATAACCACGCTTTTTT
1941357 AC
1 AC
1941359 ATTGCGATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (53 bp):
ACTTTGATATAATTAAATAAGCCCAAAGCAAGTAACTATAACCACGCTTTTTT
Found at i:1949673 original size:16 final size:16
Alignment explanation
Indices: 1949652--1949686 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1949642 TCAAAACCCA
1949652 AAAGCAAATTGAGTGG
1 AAAGCAAATTGAGTGG
1949668 AAAGCAAATTGAGTGG
1 AAAGCAAATTGAGTGG
1949684 AAA
1 AAA
1949687 TGATACCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.06, G:0.29, T:0.17
Consensus pattern (16 bp):
AAAGCAAATTGAGTGG
Found at i:1962010 original size:2 final size:2
Alignment explanation
Indices: 1962003--1962038 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1961993 CATTATCTTC
* *
1962003 CT CT CT CT CT CT CT CT CT CT CT CT CG CT CG CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1962039 GTTTCAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.06, T:0.44
Consensus pattern (2 bp):
CT
Found at i:1985526 original size:24 final size:24
Alignment explanation
Indices: 1985499--1985548 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1985489 CTGATTAGCT
* *
1985499 AGCTTACTGAAAATCCCGGATTTA
1 AGCTTACTGAAAATACAGGATTTA
*
1985523 AGCTTACTGAAGATACAGGATTTA
1 AGCTTACTGAAAATACAGGATTTA
1985547 AG
1 AG
1985549 AACCCTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (24 bp):
AGCTTACTGAAAATACAGGATTTA
Found at i:1990001 original size:32 final size:32
Alignment explanation
Indices: 1989949--1990016 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1989939 TAAACCATAT
*
1989949 AATATTAAAATATTCTAACAAACATGATTAAA
1 AATATTAAAATATTCTAACAAACATGAATAAA
* **
1989981 AATATTAAAATGTT-TCAACAAGTATGAATAAA
1 AATATTAAAATATTCT-AACAAACATGAATAAA
1990013 AATA
1 AATA
1990017 CACTAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 1 0.03
32 30 0.97
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (32 bp):
AATATTAAAATATTCTAACAAACATGAATAAA
Found at i:1992187 original size:25 final size:25
Alignment explanation
Indices: 1992151--1992205 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
1992141 AAAATTGAGT
**
1992151 ATTAATTATTTC-ATTGGTTAATTGA
1 ATTAATTATTTCGATT-ACTAATTGA
1992176 ATTAGATT-TTTCGATTACTAATTGA
1 ATTA-ATTATTTCGATTACTAATTGA
1992201 ATTAA
1 ATTAA
1992206 CTAAATTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.04
25 19 0.73
26 6 0.23
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (25 bp):
ATTAATTATTTCGATTACTAATTGA
Found at i:2004593 original size:26 final size:27
Alignment explanation
Indices: 2004551--2004610 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
2004541 GATATGTATA
*
2004551 ATGAAGCATGAGCGAACCCTAAGTA-G
1 ATGAAGCAAGAGCGAACCCTAAGTAGG
2004577 ATGAAGCAAGAAG-GAACCCTAAGTAGG
1 ATGAAGCAAG-AGCGAACCCTAAGTAGG
2004604 ATGAAGC
1 ATGAAGC
2004611 GCACTCATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.42, C:0.17, G:0.28, T:0.13
Consensus pattern (27 bp):
ATGAAGCAAGAGCGAACCCTAAGTAGG
Found at i:2004707 original size:13 final size:14
Alignment explanation
Indices: 2004674--2004708 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2004664 CATTTCATCT
2004674 AATTTTATTAAAAA
1 AATTTTATTAAAAA
*
2004688 AAATTTATT-AAAA
1 AATTTTATTAAAAA
2004701 AATTTTAT
1 AATTTTAT
2004709 CAACTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTTTATTAAAAA
Found at i:2005356 original size:29 final size:30
Alignment explanation
Indices: 2005324--2005389 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
2005314 TTACTATGTC
2005324 ATTAATAAA-AAAATAAATATA-TTAAAAAT
1 ATTAA-AAACAAAATAAATATATTTAAAAAT
* *
2005353 ATTAAAAACTAAATAATTATATTTAAAAA-
1 ATTAAAAACAAAATAAATATATTTAAAAAT
*
2005382 CTTAAAAA
1 ATTAAAAA
2005390 AATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 3 0.09
29 22 0.69
30 7 0.22
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (30 bp):
ATTAAAAACAAAATAAATATATTTAAAAAT
Found at i:2006022 original size:28 final size:28
Alignment explanation
Indices: 2005982--2006037 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2005972 ATAAATATCT
2005982 AAGGTTTGATCTAATAGACCATACAATC
1 AAGGTTTGATCTAATAGACCATACAATC
2006010 AAGGTTTGATCTAATAGACCATACAATC
1 AAGGTTTGATCTAATAGACCATACAATC
2006038 TTCACTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (28 bp):
AAGGTTTGATCTAATAGACCATACAATC
Found at i:2006106 original size:33 final size:33
Alignment explanation
Indices: 2006049--2006113 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
2006039 TCACTTTCAC
* * *
2006049 CAGCAATCTCACCTTCGACGGTAACTGAGGCAG
1 CAGCAAGCTCACCTACGACGGTAACCGAGGCAG
* *
2006082 CAGCAAGCTTACCTACGACTGTAACCGAGGCA
1 CAGCAAGCTCACCTACGACGGTAACCGAGGCA
2006114 ATAGCAACCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (33 bp):
CAGCAAGCTCACCTACGACGGTAACCGAGGCAG
Found at i:2009744 original size:155 final size:154
Alignment explanation
Indices: 2009559--2009873 Score: 555
Period size: 155 Copynumber: 2.0 Consensus size: 154
2009549 TTGAAATTTA
2009559 AAAAAGATGTGAAGCAATAAAAATGACAAGATTCGATTGCATTTTATTATTGTCATGTGCAATTG
1 AAAAAGATGTGAAGCAATAAAAATGACAAGATTCGATTGCATTTTATTATTGTCATGTGCAATTG
2009624 AAATGACAATAACAATAAAACAGT-ACGATTAAATATAAATTTTAAAAAGTTATTAAAAAAAGTT
66 AAATGACAATAACAATAAAACAGTCA-GATTAAATATAAATTTTAAAAAGTTATTAAAAAAAG-T
2009688 AA-TTTTTTT-AAAAATAAAATTTTTC
129 AATTTTTTTTAAAAAATAAAA-TTTTC
2009713 AAAAAGATGTAGAAGCAATAAAAATGACAAGATTCGATTGCATTTTATTATTGTCATGTGCAATT
1 AAAAAGATGT-GAAGCAATAAAAATGACAAGATTCGATTGCATTTTATTATTGTCATGTGCAATT
*
2009778 GAAATGACAATAACAATAAAACAGTCAGATTAAATATAAATTTTGAAAAGTTATTAAAAAAAGTA
65 GAAATGACAATAACAATAAAACAGTCAGATTAAATATAAATTTTAAAAAGTTATTAAAAAAAGTA
2009843 ATTTTTTTTAAAAAAATAAAATTTTC
130 ATTTTTTTT-AAAAAATAAAATTTTC
2009869 AAAAA
1 AAAAA
2009874 AAAACTTCCT
Statistics
Matches: 155, Mismatches: 1, Indels: 8
0.95 0.01 0.05
Matches are distributed among these distances:
154 13 0.08
155 121 0.78
156 11 0.07
157 10 0.06
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (154 bp):
AAAAAGATGTGAAGCAATAAAAATGACAAGATTCGATTGCATTTTATTATTGTCATGTGCAATTG
AAATGACAATAACAATAAAACAGTCAGATTAAATATAAATTTTAAAAAGTTATTAAAAAAAGTAA
TTTTTTTTAAAAAATAAAATTTTC
Found at i:2017411 original size:38 final size:38
Alignment explanation
Indices: 2017329--2017411 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
2017319 ATATTCACAT
* * *
2017329 AGAAATTCTCCATTTACATGCTCATTTTATAGCATTAT
1 AGAAATTCTACATTCACATGCTCATTTTATAGCATTAC
*
2017367 AAAAATTCTACATTCACATGCTCATTTTATAGCATTAC
1 AGAAATTCTACATTCACATGCTCATTTTATAGCATTAC
2017405 AGAAATT
1 AGAAATT
2017412 GTCCTTGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (38 bp):
AGAAATTCTACATTCACATGCTCATTTTATAGCATTAC
Found at i:2018336 original size:66 final size:66
Alignment explanation
Indices: 2018247--2018411 Score: 226
Period size: 66 Copynumber: 2.5 Consensus size: 66
2018237 GACACCACCT
* * *
2018247 TGGTCATCAACTGCAAGTGGGTCACGAACATTCAAGATTGCCCCGTCGTCAG-TCGCATTGTAGA
1 TGGTCACCAACTGCAAGTGGGTCACGAACATTCAAGACTGCCCCGTCATCAGCT-GCATTGTAGA
2018311 TG
65 TG
* * *
2018313 TGGTCACCAACTACAAGTGGGTCACGAACATTCAAGACTGCCCCGTCATCAGCTGCATTGTCGGT
1 TGGTCACCAACTGCAAGTGGGTCACGAACATTCAAGACTGCCCCGTCATCAGCTGCATTGTAGAT
2018378 G
66 G
* *
2018379 -GTGTCACCAATTGCAAGTGGGTCATGAACATTC
1 TG-GTCACCAACTGCAAGTGGGTCACGAACATTC
2018412 GGGGCTACCC
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 86 0.98
67 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (66 bp):
TGGTCACCAACTGCAAGTGGGTCACGAACATTCAAGACTGCCCCGTCATCAGCTGCATTGTAGAT
G
Found at i:2019168 original size:218 final size:218
Alignment explanation
Indices: 2018778--2019188 Score: 691
Period size: 218 Copynumber: 1.9 Consensus size: 218
2018768 ACTTTGGTAA
* * *
2018778 AAAATAAATCTTTCTTGTTTTTGGTTGACAACAAGAATATTTGAGTGAATATCAAAATGGGGGTA
1 AAAATAAATCTTTCTTGTTTTTGATTGACAACAAGAATATTTGAGTAAATATCAAAATGGAGGTA
* *
2018843 ATAAGAAGAATATAATGATTGAAAAACTTCAAAATGCGACGAATGATGTTTGCATCCATTAGGGT
66 ATAAGAAGAATAGAATGATTGAAAAACTTCAAAATGCGACGAATGATGTTTGCATCCATTAGGGC
* *
2018908 TTAAGAAATTTGTTTTGAACGTAAATTTTTTGAATTAAAAGCTAAAATGCCATAACAAATCTAGC
131 TTAAGAAATTTGTTTTGAACGTAAATTTCTTGAATCAAAAGCTAAAATGCCATAACAAATCTAGC
2018973 ATAAAAAACTGGTGGTTTGGCAG
196 ATAAAAAACTGGTGGTTTGGCAG
*
2018996 AAAATAAATCTTTCTTGTTTTTGATTGACAACAAGAATATTTGAGTAAATATCATAATGGAGGTA
1 AAAATAAATCTTTCTTGTTTTTGATTGACAACAAGAATATTTGAGTAAATATCAAAATGGAGGTA
2019061 ATAAGAAGAATAGAATGATTGAAAAACTTC-AAATGCGACGAATGATGTTTGCATCCATTAGGGC
66 ATAAGAAGAATAGAATGATTGAAAAACTTCAAAATGCGACGAATGATGTTTGCATCCATTAGGGC
* * *
2019125 TTAAGAAATTTTTTTTGAA-GATTAATTTCTTGATATCAAAAGCTAAAATGCCATAACAAGTCTA
131 TTAAGAAATTTGTTTTGAACG-TAAATTTCTTGA-ATCAAAAGCTAAAATGCCATAACAAATCTA
2019189 ACATCCGAAA
Statistics
Matches: 180, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
216 1 0.01
217 61 0.34
218 118 0.66
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (218 bp):
AAAATAAATCTTTCTTGTTTTTGATTGACAACAAGAATATTTGAGTAAATATCAAAATGGAGGTA
ATAAGAAGAATAGAATGATTGAAAAACTTCAAAATGCGACGAATGATGTTTGCATCCATTAGGGC
TTAAGAAATTTGTTTTGAACGTAAATTTCTTGAATCAAAAGCTAAAATGCCATAACAAATCTAGC
ATAAAAAACTGGTGGTTTGGCAG
Found at i:2019634 original size:32 final size:33
Alignment explanation
Indices: 2019598--2019674 Score: 84
Period size: 37 Copynumber: 2.2 Consensus size: 33
2019588 TAAAAATTAT
2019598 ATTAAAATCATGCGAAGTCACA-ATATATAAAG
1 ATTAAAATCATGCGAAGTCACACATATATAAAG
*
2019630 ATTAAACTGAAATCGTGCGAAGTCACAGCATATATAAAG
1 ATT--A---AAATCATGCGAAGTCACA-CATATATAAAG
2019669 ATTAAA
1 ATTAAA
2019675 CTGAAATCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
32 3 0.08
34 3 0.08
37 18 0.49
39 13 0.35
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (33 bp):
ATTAAAATCATGCGAAGTCACACATATATAAAG
Found at i:2019674 original size:39 final size:38
Alignment explanation
Indices: 2019602--2019734 Score: 205
Period size: 39 Copynumber: 3.5 Consensus size: 38
2019592 AATTATATTA
*
2019602 AAATCATGCGAAGTCACA-ATATATAAAGATTAAACTG
1 AAATCGTGCGAAGTCACACATATATAAAGATTAAACTG
2019639 AAATCGTGCGAAGTCACAGCATATATAAAGATTAAACTG
1 AAATCGTGCGAAGTCACA-CATATATAAAGATTAAACTG
* *
2019678 AAATCGTGCGAAGTCACAACATATTTAAAAATTAAACTG
1 AAATCGTGCGAAGTCAC-ACATATATAAAGATTAAACTG
*
2019717 AAATCGTGCGAAATCACA
1 AAATCGTGCGAAGTCACA
2019735 ACTTATGCCT
Statistics
Matches: 89, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
37 17 0.19
38 1 0.01
39 70 0.79
40 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (38 bp):
AAATCGTGCGAAGTCACACATATATAAAGATTAAACTG
Found at i:2019735 original size:39 final size:39
Alignment explanation
Indices: 2019588--2019736 Score: 203
Period size: 39 Copynumber: 3.9 Consensus size: 39
2019578 ATTGAGAAAC
* * * *
2019588 TAAAAATTATATTAAAATCATGCGAAGTCAC-A-ATATA
1 TAAAAATTAAACTGAAATCGTGCGAAGTCACAACATATA
* *
2019625 TAAAGATTAAACTGAAATCGTGCGAAGTCACAGCATATA
1 TAAAAATTAAACTGAAATCGTGCGAAGTCACAACATATA
* *
2019664 TAAAGATTAAACTGAAATCGTGCGAAGTCACAACATATT
1 TAAAAATTAAACTGAAATCGTGCGAAGTCACAACATATA
*
2019703 TAAAAATTAAACTGAAATCGTGCGAAATCACAAC
1 TAAAAATTAAACTGAAATCGTGCGAAGTCACAAC
2019737 TTATGCCTTT
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
37 26 0.26
39 74 0.74
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (39 bp):
TAAAAATTAAACTGAAATCGTGCGAAGTCACAACATATA
Found at i:2035957 original size:2 final size:2
Alignment explanation
Indices: 2035950--2035991 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2035940 ATTTTAAATA
2035950 AT AT AT 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 AT AT AT
2035992 GTAGAGTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2042727 original size:21 final size:20
Alignment explanation
Indices: 2042701--2042740 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2042691 TTCAAATGCA
*
2042701 ATCCTTTTTTTCTTTTTCTTC
1 ATCCTTTTTTT-TATTTCTTC
2042722 ATCCTTTTTTTTATTTCTT
1 ATCCTTTTTTTTATTTCTT
2042741 AAGCTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (20 bp):
ATCCTTTTTTTTATTTCTTC
Found at i:2042729 original size:20 final size:21
Alignment explanation
Indices: 2042701--2042740 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2042691 TTCAAATGCA
2042701 ATCCTTTTTTTCTT-TTTCTTC
1 ATCCTTTTTTT-TTATTTCTTC
2042722 ATCC-TTTTTTTTATTTCTT
1 ATCCTTTTTTTTTATTTCTT
2042741 AAGCTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (21 bp):
ATCCTTTTTTTTTATTTCTTC
Found at i:2056748 original size:23 final size:22
Alignment explanation
Indices: 2056731--2056785 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
2056721 ATAATATTTG
2056731 ATATATAAATAAAGTAATTATTAAA
1 ATATATAAA-AAA-TAA-TATTAAA
*
2056756 ATATATAAAAAATAATATTATA
1 ATATATAAAAAATAATATTAAA
2056778 ATAT-TAAA
1 ATATATAAA
2056786 TTTATAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 4 0.14
22 10 0.34
23 3 0.10
24 3 0.10
25 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATATAAAAAATAATATTAAA
Found at i:2056764 original size:25 final size:25
Alignment explanation
Indices: 2056731--2056812 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 25
2056721 ATAATATTTG
2056731 ATATATAAATAAAGTAATTATTAAA
1 ATATATAAATAAAGTAATTATTAAA
*
2056756 ATATATAAA-AAA-TAA-TATTATA
1 ATATATAAATAAAGTAATTATTAAA
*
2056778 ATAT-TAAATTTATAAGTATTTTATTAAA
1 ATATATAAA--TA-AAGTA-ATTATTAAA
2056806 A-ATATAA
1 ATATATAA
2056813 TATTAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
21 4 0.09
22 10 0.22
23 3 0.07
24 4 0.09
25 11 0.24
26 2 0.04
27 2 0.04
28 10 0.22
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATATAAATAAAGTAATTATTAAA
Found at i:2056992 original size:34 final size:33
Alignment explanation
Indices: 2056922--2057007 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 33
2056912 TTTTAACATC
*
2056922 ATATATTTTA--TTTATTTTTTATTATAATTTT
1 ATATATTTTATTTTTATTTTTTAATATAATTTT
2056953 ATATATTTTATTTTTATTTCTTTAATATAATTTT
1 ATATATTTTATTTTTATTT-TTTAATATAATTTT
* *
2056987 TTATATTATATATTTTATTTT
1 ATATATTTTAT-TTTTATTTT
2057008 AATTTCTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
31 10 0.21
33 7 0.15
34 23 0.48
35 8 0.17
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTTTTAATATAATTTT
Found at i:2057018 original size:29 final size:28
Alignment explanation
Indices: 2056983--2057104 Score: 101
Period size: 28 Copynumber: 4.3 Consensus size: 28
2056973 TTTAATATAA
*
2056983 TTTTTTATATTATATATTTTATTTTAAT
1 TTTTTTATATTATATATTATATTTTAAT
*
2057011 TTCTTTTA-CTTATAT-TATATAATTTTTAA-
1 TT-TTTTATATTATATAT-TAT-A-TTTTAAT
*
2057040 TTTATTATACTATATTATATTATATTTTAA-
1 TTTTTTATA-T-TA-TATATTATATTTTAAT
*
2057070 -TTATTATATTATATATTATATTTTAAT
1 TTTTTTATATTATATATTATATTTTAAT
*
2057097 ATTTTTAT
1 TTTTTTAT
2057105 TTTAATTATA
Statistics
Matches: 78, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
26 15 0.19
27 3 0.04
28 21 0.27
29 16 0.21
30 13 0.17
31 3 0.04
32 6 0.08
33 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTTTATATTATATATTATATTTTAAT
Found at i:2057040 original size:30 final size:30
Alignment explanation
Indices: 2056988--2057096 Score: 111
Period size: 29 Copynumber: 3.7 Consensus size: 30
2056978 TATAATTTTT
* * *
2056988 TATATTATATATTTTATTTTAATTTCTTTTAC
1 TATATTATATA--ATATTTTAATTTATTATAC
2057020 TTATATTATATAAT-TTTTAATTTATTATAC
1 -TATATTATATAATATTTTAATTTATTATAC
*
2057050 TATATTATATTATATTTTAA-TTATTATA-
1 TATATTATATAATATTTTAATTTATTATAC
*
2057078 T-TA-TATATTATATTTTAAT
1 TATATTATATAATATTTTAAT
2057097 ATTTTTATTT
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
26 15 0.21
27 2 0.03
28 1 0.01
29 20 0.29
30 20 0.29
31 1 0.01
33 11 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TATATTATATAATATTTTAATTTATTATAC
Done.