Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 163 of 172
Found at i:53453458 original size:13 final size:13
Alignment explanation
Indices: 53453383--53453459 Score: 59
Period size: 13 Copynumber: 5.8 Consensus size: 13
53453373 TCATTTGCTT
53453383 TTCTTTTCTTTCTC
1 TTCTTTT-TTTCTC
*
53453397 TTTTTTGTTTTTCTC
1 -TTCTT-TTTTTCTC
* *
53453412 TTC-TTTTTCCTT
1 TTCTTTTTTTCTC
*
53453424 TTCCTTTTTTCTC
1 TTCTTTTTTTCTC
*
53453437 TT-TCCTTTTTCTC
1 TTCT-TTTTTTCTC
53453450 TTCTTTTTTT
1 TTCTTTTTTT
53453460 TTTTTGAAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
12 9 0.18
13 25 0.51
14 3 0.06
15 10 0.20
16 2 0.04
ACGTcount: A:0.00, C:0.23, G:0.01, T:0.75
Consensus pattern (13 bp):
TTCTTTTTTTCTC
Found at i:53459648 original size:126 final size:126
Alignment explanation
Indices: 53459488--53459731 Score: 470
Period size: 126 Copynumber: 1.9 Consensus size: 126
53459478 GTTTTAGCCT
53459488 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
1 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
*
53459553 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTTGAGAGTGAACTGG
66 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGTGAACTGG
*
53459614 TAAGAGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
1 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
53459679 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAG
66 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAG
53459732 AAGATCAATG
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 116 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (126 bp):
TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGTGAACTGG
Found at i:53459864 original size:13 final size:12
Alignment explanation
Indices: 53459832--53459881 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
53459822 AACCATATAT
53459832 AAATAA-TAA-A
1 AAATAATTAATA
53459842 AAATAA-TAATA
1 AAATAATTAATA
*
53459853 ATAGTAATTAATA
1 A-AATAATTAATA
53459866 GAAATAATTAATA
1 -AAATAATTAATA
53459879 AAA
1 AAA
53459882 CAACAGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.26
11 2 0.06
12 7 0.21
13 15 0.44
14 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (12 bp):
AAATAATTAATA
Found at i:53460636 original size:18 final size:18
Alignment explanation
Indices: 53460613--53460648 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53460603 ATAACAAGTA
*
53460613 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
53460631 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
53460649 ATGGTTTAGT
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:0.17, C:0.00, G:0.58, T:0.25
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:53461424 original size:25 final size:24
Alignment explanation
Indices: 53461385--53461443 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
53461375 TTTTTTTATT
* * *
53461385 AAATAAAAAAATTT-AAAATATAA
1 AAATAAATACATTTAAAAACATAA
53461408 TAAATCAAATACATTTAAAAACATAA
1 -AAAT-AAATACATTTAAAAACATAA
53461434 AAATAAATAC
1 AAATAAATAC
53461444 TAAAACAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.33
25 12 0.40
26 8 0.27
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (24 bp):
AAATAAATACATTTAAAAACATAA
Found at i:53476696 original size:21 final size:21
Alignment explanation
Indices: 53476671--53476773 Score: 93
Period size: 21 Copynumber: 4.8 Consensus size: 21
53476661 ACACACATAT
*
53476671 ATATAAATAATAGTATTAGAA
1 ATATAAATAATAATATTAGAA
53476692 ATATACAAT-ATAATATTAGAA
1 ATATA-AATAATAATATTAGAA
* **
53476713 ATATATATAATAGTATAAAAGAAAA
1 ATATAAATAATA--ATATTAG--AA
*
53476738 ATATAACTAATAATATTA-AA
1 ATATAAATAATAATATTAGAA
*
53476758 ATATATATAATAATAT
1 ATATAAATAATAATAT
53476774 ATGTGAAATA
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
20 18 0.27
21 24 0.36
22 3 0.05
23 9 0.14
25 12 0.18
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (21 bp):
ATATAAATAATAATATTAGAA
Found at i:53476696 original size:23 final size:23
Alignment explanation
Indices: 53476669--53476785 Score: 102
Period size: 23 Copynumber: 5.2 Consensus size: 23
53476659 ACACACACAT
*
53476669 ATATATAAATAATAGTATTAGAA
1 ATATATAAATAATAATATTAGAA
*
53476692 ATATA-CAAT-ATAATATTAGAA
1 ATATATAAATAATAATATTAGAA
* **
53476713 ATATATATAATAGT-ATAAAAGAA
1 ATATATA-AATAATAATATTAGAA
* *
53476736 AAATATAACTAATAATATTA-AA
1 ATATATAAATAATAATATTAGAA
53476758 ATATATATAATAAT-ATATGT-GAA
1 ATATATA-AATAATAATAT-TAGAA
53476781 ATATA
1 ATATA
53476786 ATATTAAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
21 16 0.22
22 19 0.26
23 38 0.51
24 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATATAAATAATAATATTAGAA
Found at i:53476758 original size:20 final size:20
Alignment explanation
Indices: 53476735--53476773 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
53476725 GTATAAAAGA
53476735 AAAATATA-ACTAATAATATT
1 AAAATATATA-TAATAATATT
53476755 AAAATATATATAATAATAT
1 AAAATATATATAATAATAT
53476774 ATGTGAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATATATATAATAATATT
Found at i:53477118 original size:12 final size:12
Alignment explanation
Indices: 53477086--53477119 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53477076 AATAATTAGT
53477086 ATATTAATAAAA
1 ATATTAATAAAA
**
53477098 ATAAAAATAAAA
1 ATATTAATAAAA
53477110 ATATTAATAA
1 ATATTAATAA
53477120 TATGTAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATATTAATAAAA
Found at i:53479104 original size:54 final size:54
Alignment explanation
Indices: 53479031--53479241 Score: 271
Period size: 54 Copynumber: 3.9 Consensus size: 54
53479021 CATATGACCT
* *
53479031 AAGGCTCAACTCACTTCTCGCAATATGATTTGATTTTTGAAAAACAAAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAA
* *
53479085 AAGG-TACAACTCACCTCTCGCAATATGAATTGCTTTTTGAAAAACAAAAATTAA
1 AAGGCT-CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAA
* *** * * *
53479139 AAGGCTCAACTCACCTCTCGCGATATGAGTTGATTTTTTTTTTTAAATATAAATTGA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAACAAAAATTAA
*
53479196 AAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
53479242 GGAATTGGAA
Statistics
Matches: 134, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
53 1 0.01
54 86 0.64
55 1 0.01
57 46 0.34
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAA
Found at i:53479222 original size:111 final size:108
Alignment explanation
Indices: 53479031--53479241 Score: 271
Period size: 111 Copynumber: 1.9 Consensus size: 108
53479021 CATATGACCT
* *
53479031 AAGGCTCAACTCACTTCTCGCAATATGATTTGATTTTTGAAAAACAAAAATTAAAAGGTACAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGTACAACT
*
53479096 CACCTCTCGCAATATGAATTGCTTTTTGAAAAACAAAAATTAA
66 CACCTCTCGCAATATGAATTGATTTTTGAAAAACAAAAATTAA
* *** * * *
53479139 AAGGCTCAACTCACCTCTCGCGATATGAGTTGATTTTTTTTTTTAAATATAAATTGAAAGGCT-C
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAACAAAAATTAAAAGG-TAC
* *
53479203 AACTTACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
62 AACTCACCTCTCGCAATATGAATTGATTTTTGAAAAACA
53479242 GGAATTGGAA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
108 30 0.34
111 56 0.64
112 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (108 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGTACAACT
CACCTCTCGCAATATGAATTGATTTTTGAAAAACAAAAATTAA
Found at i:53479373 original size:71 final size:71
Alignment explanation
Indices: 53479257--53479395 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 71
53479247 TGGAAAGTAG
* *
53479257 AAATTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTG
1 AAATTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGG
53479322 AAACAT
66 AAACAT
* * * **
53479328 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGG
1 AAATTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGG
53479393 AAA
66 AAA
53479396 AGTAAAAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (71 bp):
AAATTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGG
AAACAT
Found at i:53491178 original size:21 final size:21
Alignment explanation
Indices: 53491153--53491255 Score: 93
Period size: 21 Copynumber: 4.8 Consensus size: 21
53491143 ACACACATAT
*
53491153 ATATAAATAATAGTATTAGAA
1 ATATAAATAATAATATTAGAA
53491174 ATATACAAT-ATAATATTAGAA
1 ATATA-AATAATAATATTAGAA
* **
53491195 ATATATATAATAGTATAAAAGAAAA
1 ATATAAATAATA--ATATTAG--AA
*
53491220 ATATAACTAATAATATTA-AA
1 ATATAAATAATAATATTAGAA
*
53491240 ATATATATAATAATAT
1 ATATAAATAATAATAT
53491256 ATGTGAAATA
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
20 18 0.27
21 24 0.36
22 3 0.05
23 9 0.14
25 12 0.18
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (21 bp):
ATATAAATAATAATATTAGAA
Found at i:53491178 original size:23 final size:23
Alignment explanation
Indices: 53491151--53491267 Score: 102
Period size: 23 Copynumber: 5.2 Consensus size: 23
53491141 ACACACACAT
*
53491151 ATATATAAATAATAGTATTAGAA
1 ATATATAAATAATAATATTAGAA
*
53491174 ATATA-CAAT-ATAATATTAGAA
1 ATATATAAATAATAATATTAGAA
* **
53491195 ATATATATAATAGT-ATAAAAGAA
1 ATATATA-AATAATAATATTAGAA
* *
53491218 AAATATAACTAATAATATTA-AA
1 ATATATAAATAATAATATTAGAA
53491240 ATATATATAATAAT-ATATGT-GAA
1 ATATATA-AATAATAATAT-TAGAA
53491263 ATATA
1 ATATA
53491268 ATATTAAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
21 16 0.22
22 19 0.26
23 38 0.51
24 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATATAAATAATAATATTAGAA
Found at i:53491240 original size:20 final size:20
Alignment explanation
Indices: 53491217--53491255 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
53491207 GTATAAAAGA
53491217 AAAATATA-ACTAATAATATT
1 AAAATATATA-TAATAATATT
53491237 AAAATATATATAATAATAT
1 AAAATATATATAATAATAT
53491256 ATGTGAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATATATATAATAATATT
Found at i:53491602 original size:25 final size:27
Alignment explanation
Indices: 53491554--53491612 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 27
53491544 AATAATACCT
53491554 TAAAAATAATTAGTATATTAATAAAAAG
1 TAAAAATAATTAG-ATATTAATAAAAAG
* *
53491582 TAAAAATAA-TA-ATATTAATAATATG
1 TAAAAATAATTAGATATTAATAAAAAG
53491607 TAAAAA
1 TAAAAA
53491613 AATGAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 18 0.62
27 2 0.07
28 9 0.31
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (27 bp):
TAAAAATAATTAGATATTAATAAAAAG
Found at i:53496999 original size:14 final size:14
Alignment explanation
Indices: 53496982--53497035 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
53496972 AATATTTTCC
53496982 GGAAAATGATTTTT
1 GGAAAATGATTTTT
53496996 GGAAAATGATTTTT
1 GGAAAATGATTTTT
* *
53497010 AGAAAATGATTTCT
1 GGAAAATGATTTTT
*
53497024 GAAAAATGATTT
1 GGAAAATGATTT
53497036 ACTTTTCTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.39
Consensus pattern (14 bp):
GGAAAATGATTTTT
Found at i:53497002 original size:28 final size:28
Alignment explanation
Indices: 53496970--53497035 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
53496960 GTTTGCAGGT
* * *
53496970 AAAAT-ATTTTCCGGAAAATGATTTTTGG
1 AAAATGATTTT-CAGAAAATGATTTCTGA
*
53496998 AAAATGATTTTTAGAAAATGATTTCTGA
1 AAAATGATTTTCAGAAAATGATTTCTGA
53497026 AAAATGATTT
1 AAAATGATTT
53497036 ACTTTTCTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (28 bp):
AAAATGATTTTCAGAAAATGATTTCTGA
Found at i:53497164 original size:18 final size:18
Alignment explanation
Indices: 53497126--53497165 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
53497116 CTGTTTTTAC
*
53497126 ATATATATTAATATATAT
1 ATATATATTAATAAATAT
*
53497144 ATATATATTAATAAATTT
1 ATATATATTAATAAATAT
53497162 ATAT
1 ATAT
53497166 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATTAATAAATAT
Found at i:53500616 original size:38 final size:37
Alignment explanation
Indices: 53500532--53500626 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
53500522 TATACGTACT
*
53500532 TATACATACTTAAATATATTTTTCATATTTCATAATTC
1 TATACATACTTAAATATATTTTGCATATTT-ATAATTC
* *
53500570 T-TATATACTTACATATATTTATGCATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TGCATATTTATA-ATTC
*
53500606 ATATACATACTTATATATATT
1 -TATACATACTTAAATATATT
53500627 CTTTATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.08
37 19 0.40
38 25 0.52
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTGCATATTTATAATTC
Found at i:53502736 original size:19 final size:20
Alignment explanation
Indices: 53502696--53502739 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
53502686 GTTTCTTTTG
* *
53502696 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
53502715 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
53502734 GCATTA
1 GCATTA
53502740 GACTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:53507010 original size:44 final size:44
Alignment explanation
Indices: 53506887--53507150 Score: 214
Period size: 44 Copynumber: 6.0 Consensus size: 44
53506877 TGAAGTCATT
* * *
53506887 AAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTGGATCGACG
1 AAAGCAGATCTTATCTTCATATATTGGCGTGAAGTAGATCGAAG
* * ** * * *
53506931 -ATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
1 AAAGCAGATCTTATCTTCATATATTGG-CGTGAAGTAGATCGAAG
*
53506975 AAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAG
1 AAAGCAGATCTTATCTTCATATATTGGCGTGAAGTAGATCGAAG
* * * * * *
53507019 ATAA-CAGGTCCTATCTTCCTATATTGGTAG-GAAGTGGATCGATG
1 A-AAGCAGATCTTATCTTCATATATTGG-CGTGAAGTAGATCGAAG
* * ** **
53507063 -ATGCAGATCTTGTCTTCCCATATTAGTAG-GAAGTAGATCGAAG
1 AAAGCAGATCTTATCTTCATATATT-GGCGTGAAGTAGATCGAAG
* * * *
53507106 AAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAG
1 AAAGCAGATCTTATCTTCATATATTGGCGTGAAGTAGATCGAAG
53507150 A
1 A
53507151 TAACATGTCC
Statistics
Matches: 171, Mismatches: 41, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
42 1 0.01
43 53 0.31
44 94 0.55
45 23 0.13
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (44 bp):
AAAGCAGATCTTATCTTCATATATTGGCGTGAAGTAGATCGAAG
Found at i:53507053 original size:88 final size:88
Alignment explanation
Indices: 53506887--53507079 Score: 246
Period size: 88 Copynumber: 2.2 Consensus size: 88
53506877 TGAAGTCATT
* * * * *
53506887 AAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTGGATCGACGATGCAGATCTTGTCTTCCCAT
1 AAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGATACAGATCCTATCTTCCCAT
*
53506952 ACTGGTGGCGAAGTAGATCGAAG
66 ACTGGTAGCGAAGTAGATCGAAG
* *
53506975 AAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGGTCCTATCTTCCTA
1 AAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGAT-ACAGATCCTATCTTCCCA
* * *
53507040 TATTGGTAG-GAAGTGGATCGATG
65 TACTGGTAGCGAAGTAGATCGAAG
* *
53507063 -ATGCAGATCTTGTCTTC
1 AAAGCAGATCTTATCTTC
53507080 CCATATTAGT
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
87 15 0.16
88 56 0.62
89 20 0.22
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (88 bp):
AAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGATACAGATCCTATCTTCCCAT
ACTGGTAGCGAAGTAGATCGAAG
Found at i:53507123 original size:87 final size:88
Alignment explanation
Indices: 53507005--53507215 Score: 198
Period size: 87 Copynumber: 2.4 Consensus size: 88
53506995 GTATTGGCGT
* * * * * * *
53507005 GAAGTAGATCGAAGATAA-CAGGTCCTATCTTCCTATATTGGTAG-GAAGTGGATCGATGAT-GC
1 GAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCCTATATTGG-AGTGAAGTAGATCAAAGATAAC
**
53507067 A-GATCTTGTCTTCCCATATTAGTAG
64 ATG-TCCGGTCTTCCCATATTAGTAG
* * * *
53507092 GAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGGAGTGAAGTAGATCAAAGATAACAT
* *
53507157 GTCCGGTCTTCCTATATTGGTAG
66 GTCCGGTCTTCCCATATTAGTAG
* * *
53507180 GAAGTGGATCGACG-ATGCAGATCTTGTCTTCCTATA
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCTATA
53507216 NNNNNNNNNN
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
86 3 0.03
87 63 0.64
88 32 0.32
89 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (88 bp):
GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCTATATTGGAGTGAAGTAGATCAAAGATAACAT
GTCCGGTCTTCCCATATTAGTAG
Found at i:53507141 original size:131 final size:132
Alignment explanation
Indices: 53506917--53507211 Score: 493
Period size: 131 Copynumber: 2.2 Consensus size: 132
53506907 GTATTGGCGT
* *
53506917 GAAGTGGATCGACGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAG
1 GAAGTGGATCGACGATGCAGATCTTGTCTTCCCATACTAGTAGCGAAGTAGATCGAAGAAAGCAG
* *
53506982 ATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGGTCCTATCTTCCTATATTGGT
66 ATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGGTCCGATCTTCCTATATTGGT
53507047 AG
131 AG
* * *
53507049 GAAGTGGATCGATGATGCAGATCTTGTCTTCCCATATTAGTAG-GAAGTAGATCGAAGAAAGTAG
1 GAAGTGGATCGACGATGCAGATCTTGTCTTCCCATACTAGTAGCGAAGTAGATCGAAGAAAGCAG
* * *
53507113 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACATGTCCGGTCTTCCTATATTGGT
66 ATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGGTCCGATCTTCCTATATTGGT
53507178 AG
131 AG
53507180 GAAGTGGATCGACGATGCAGATCTTGTCTTCC
1 GAAGTGGATCGACGATGCAGATCTTGTCTTCC
53507212 TATANNNNNN
Statistics
Matches: 152, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
131 113 0.74
132 39 0.26
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (132 bp):
GAAGTGGATCGACGATGCAGATCTTGTCTTCCCATACTAGTAGCGAAGTAGATCGAAGAAAGCAG
ATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGGTCCGATCTTCCTATATTGGT
AG
Found at i:53507184 original size:44 final size:45
Alignment explanation
Indices: 53506936--53507215 Score: 179
Period size: 44 Copynumber: 6.4 Consensus size: 45
53506926 CGACGATGCA
* * * *
53506936 GATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA-AAGCA-
1 GATCCTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAA-CAT
* * * * *
53506981 GATCTTATCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAACA-
1 GATCCTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAACAT
* * * * *
53507025 GGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGATGAT-GCA-
1 GATCCTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGATAACAT
* * * *
53507068 GATCTTGTCTTCCCATATTAGTAGGAAGTAGATCGAAGA-AA-GT
1 GATCCTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGATAACAT
* * * * *
53507111 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGATAACAT
1 -GATCCTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAACAT
* * * *
53507157 G-TCCGGTCTTCCTATATTGGTAGGAAGTGGATCGACGAT-GCA-
1 GATCCTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGATAACAT
*
53507199 GATCTTGTCTTCCTATA
1 GATCCTGTCTTCCTATA
53507216 NNNNNNNNNN
Statistics
Matches: 183, Mismatches: 42, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.01
43 50 0.27
44 108 0.59
45 23 0.13
46 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (45 bp):
GATCCTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGATAACAT
Found at i:53507820 original size:40 final size:40
Alignment explanation
Indices: 53507772--53507927 Score: 199
Period size: 40 Copynumber: 3.9 Consensus size: 40
53507762 AAACCACAGA
*
53507772 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGTATCAAG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAATCAAG
* * * *
53507812 TCTTATCTCCCTAAACAGTAGTGGAGCAGA-CAAAACCATAG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATC-GAATCA-AG
*
53507853 ATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAATCAAG
* *
53507894 TCTTATCTCCCTAAGCAGTAGCGGAGCAGA-CGAA
1 TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAA
53507928 ACNNNNNNNN
Statistics
Matches: 99, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
39 4 0.04
40 59 0.60
41 4 0.04
42 31 0.31
43 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAATCAAG
Found at i:53507865 original size:42 final size:39
Alignment explanation
Indices: 53507751--53507929 Score: 187
Period size: 40 Copynumber: 4.4 Consensus size: 39
53507741 NNNNNNNNNN
53507751 TGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAG
1 TGGAGCAGAC-AAACCA-AG-TCTTATCTCCCTAAGCAATAG
** * * *
53507793 TGGAGCAGATCGTATCAAGTCTTATCTCCCTAAACAGTAG
1 TGGAGCAGA-CAAACCAAGTCTTATCTCCCTAAGCAATAG
53507833 TGGAGCAGACAAAACCATAGATCTTATCTCCCTAAGCAATAG
1 TGGAGCAGAC-AAACCA-AG-TCTTATCTCCCTAAGCAATAG
** * *
53507875 TGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
1 TGGAGCAGA-CAAACCAAGTCTTATCTCCCTAAGCAATAG
*
53507915 CGGAGCAGACGAAAC
1 TGGAGCAGAC-AAAC
53507930 NNNNNNNNNN
Statistics
Matches: 113, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
39 2 0.02
40 60 0.53
41 6 0.05
42 43 0.38
43 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (39 bp):
TGGAGCAGACAAACCAAGTCTTATCTCCCTAAGCAATAG
Found at i:53507892 original size:82 final size:82
Alignment explanation
Indices: 53507751--53507929 Score: 313
Period size: 82 Copynumber: 2.2 Consensus size: 82
53507741 NNNNNNNNNN
*
53507751 TGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGTATCAAGTCTT
1 TGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTT
53507816 ATCTCCCTAAACAGTAG
66 ATCTCCCTAAACAGTAG
*
53507833 TGGAGCAGACAAAACCATAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTT
1 TGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTT
*
53507898 ATCTCCCTAAGCAGTAG
66 ATCTCCCTAAACAGTAG
* *
53507915 CGGAGCAGACGAAAC
1 TGGAGCAGACAAAAC
53507930 NNNNNNNNNN
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 92 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (82 bp):
TGGAGCAGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTT
ATCTCCCTAAACAGTAG
Found at i:53510747 original size:18 final size:18
Alignment explanation
Indices: 53510721--53510784 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
53510711 ATTGAAACTT
*
53510721 CAACTTATAAATGAACAA
1 CAACATATAAATGAACAA
53510739 CAACATATAAATGAACAA
1 CAACATATAAATGAACAA
*
53510757 CAAC-TCCCTAAA-GAACAA
1 CAACAT--ATAAATGAACAA
53510775 CAACATATAA
1 CAACATATAA
53510785 CTTATTTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.10
18 31 0.77
19 5 0.12
ACGTcount: A:0.56, C:0.22, G:0.05, T:0.17
Consensus pattern (18 bp):
CAACATATAAATGAACAA
Found at i:53511580 original size:48 final size:48
Alignment explanation
Indices: 53511466--53511559 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
53511456 TTCAGATCAG
* *
53511466 TCAGGGAAAAGAAGAAGAAGAAGAAAAAGCCGTACCCAAAAACTAATT
1 TCAGAGAAAAGAAGAAGAAGAAGAAAAAGCCGTACCCAAAAACCAATT
* *
53511514 TCAGGGAAAAGAAGAAGAAGAAGAAAAAGCCGTA-CCTAAAACCAAT
1 TCAGAGAAAAGAAGAAGAAGAAGAAAAAGCCGTACCCAAAAACCAAT
53511560 CTTATAGAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 10 0.23
48 34 0.77
ACGTcount: A:0.54, C:0.15, G:0.21, T:0.10
Consensus pattern (48 bp):
TCAGAGAAAAGAAGAAGAAGAAGAAAAAGCCGTACCCAAAAACCAATT
Found at i:53512039 original size:60 final size:60
Alignment explanation
Indices: 53511975--53512089 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
53511965 TCATGTTTTA
* *
53511975 TTATTAATTAATTCCAAACAATACTTTTCATTATTTATTGTATGTTATCTTTAAACACAT
1 TTATTAATTAATTCCAAACAATACTTTTCATTATATATTATATGTTATCTTTAAACACAT
* * *
53512035 TTATTAATTAATTTCAAATAATACTTTTCCTTATATATTATATGTTATCTTTAAA
1 TTATTAATTAATTCCAAACAATACTTTTCATTATATATTATATGTTATCTTTAAA
53512090 GATATTTTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (60 bp):
TTATTAATTAATTCCAAACAATACTTTTCATTATATATTATATGTTATCTTTAAACACAT
Found at i:53518070 original size:17 final size:17
Alignment explanation
Indices: 53518037--53518071 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
53518027 TAAAACGTAT
53518037 TTAATAATTAAAATAAA
1 TTAATAATTAAAATAAA
53518054 TTAA-AATTAAAATTAAA
1 TTAATAATTAAAA-TAAA
53518071 T
1 T
53518072 ATGAGTGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAATAATTAAAATAAA
Found at i:53518203 original size:15 final size:15
Alignment explanation
Indices: 53518183--53518212 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53518173 TTACAAAAAT
53518183 TAAATTAATTATTAA
1 TAAATTAATTATTAA
*
53518198 TAAATTTATTATTAA
1 TAAATTAATTATTAA
53518213 ATAAGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATTAATTATTAA
Found at i:53519478 original size:218 final size:218
Alignment explanation
Indices: 53519185--53519613 Score: 840
Period size: 218 Copynumber: 2.0 Consensus size: 218
53519175 CGCTCCACTC
53519185 TTTTTTTTTTTAGTTTCGTCGTTTTCTTTCCGCTTCGGCTCTCGAGATTCTCTCTTTTCAATTCC
1 TTTTTTTTTTTAGTTTCGTCGTTTTCTTTCCGCTTCGGCTCTCGAGATTCTCTCTTTTCAATTCC
53519250 TTTTTTTTCACTTTTTCGTGAGATTATCTCCGATATTTTTGAGATCGTCAACGCTTCTTGCTTTG
66 TTTTTTTTCACTTTTTCGTGAGATTATCTCCGATATTTTTGAGATCGTCAACGCTTCTTGCTTTG
53519315 ATTAAAATAATCTCCCAAGGTATGGAACAACCAACAACTCGCATTCTAAGCCGGACATCTGTCAG
131 ATTAAAATAATCTCCCAAGGTATGGAACAACCAACAACTCGCATTCTAAGCCGGACATCTGTCAG
53519380 CAAAACCACCTTGTCTCCCCTTT
196 CAAAACCACCTTGTCTCCCCTTT
**
53519403 TTTTTTTTTTTTTTTTCGTCGTTTTCTTTCCGCTTCGGCTCTCGAGATTCTCTCTTTTCAATTCC
1 TTTTTTTTTTTAGTTTCGTCGTTTTCTTTCCGCTTCGGCTCTCGAGATTCTCTCTTTTCAATTCC
53519468 TTTTTTTTCACTTTTTCGTGAGATTATCTCCGATATTTTTGAGATCGTCAACGCTTCTTGCTTTG
66 TTTTTTTTCACTTTTTCGTGAGATTATCTCCGATATTTTTGAGATCGTCAACGCTTCTTGCTTTG
53519533 ATTAAAATAATCTCCCAAGGTATGGAACAACCAACAACTCGCATTCTAAGCCGGACATCTGTCAG
131 ATTAAAATAATCTCCCAAGGTATGGAACAACCAACAACTCGCATTCTAAGCCGGACATCTGTCAG
53519598 CAAAACCACCTTGTCT
196 CAAAACCACCTTGTCT
53519614 GTCACGTGGC
Statistics
Matches: 209, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
218 209 1.00
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (218 bp):
TTTTTTTTTTTAGTTTCGTCGTTTTCTTTCCGCTTCGGCTCTCGAGATTCTCTCTTTTCAATTCC
TTTTTTTTCACTTTTTCGTGAGATTATCTCCGATATTTTTGAGATCGTCAACGCTTCTTGCTTTG
ATTAAAATAATCTCCCAAGGTATGGAACAACCAACAACTCGCATTCTAAGCCGGACATCTGTCAG
CAAAACCACCTTGTCTCCCCTTT
Found at i:53529381 original size:16 final size:16
Alignment explanation
Indices: 53529362--53529421 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
53529352 AAATATTTAG
*
53529362 AAATCAAAATAAAAAT
1 AAATCAAAATAAAAAA
* * *
53529378 AAATTAAAATGAAAAC
1 AAATCAAAATAAAAAA
53529394 AAATACTAAAATAAAAAA
1 AAAT-C-AAAATAAAAAA
53529412 AAATTCAAAA
1 AAA-TCAAAA
53529422 AAATAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
16 17 0.49
17 4 0.11
18 13 0.37
19 1 0.03
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (16 bp):
AAATCAAAATAAAAAA
Found at i:53529486 original size:21 final size:21
Alignment explanation
Indices: 53529442--53529483 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53529432 AAATGGAAAG
*
53529442 ATATAAGGGAAATAATTGAAA
1 ATATAAGGGAAATAATTAAAA
*
53529463 ATATAAGGGAAAT-TTTAAAA
1 ATATAAGGGAAATAATTAAAA
53529483 A
1 A
53529484 ATAGAAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26
Consensus pattern (21 bp):
ATATAAGGGAAATAATTAAAA
Found at i:53529513 original size:22 final size:22
Alignment explanation
Indices: 53529482--53529539 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
53529472 AAATTTTAAA
* *
53529482 AAATAGAAATGTAAATGAAATG
1 AAATTGAAATGTAAAGGAAATG
* * *
53529504 -AATTGAAAATATAAGGGTAATG
1 AAATTG-AAATGTAAAGGAAATG
53529526 AAATTGAAATGTAA
1 AAATTGAAATGTAA
53529540 TATAAATAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
21 4 0.14
22 19 0.68
23 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (22 bp):
AAATTGAAATGTAAAGGAAATG
Found at i:53529749 original size:21 final size:21
Alignment explanation
Indices: 53529725--53529770 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
53529715 ATTTTAATGG
* *
53529725 AAATACATTTTAAATTGCAAA
1 AAATAAATGTTAAATTGCAAA
*
53529746 AAATAAATGTTAAATTTCAAA
1 AAATAAATGTTAAATTGCAAA
53529767 AAAT
1 AAAT
53529771 TTAATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (21 bp):
AAATAAATGTTAAATTGCAAA
Found at i:53529779 original size:21 final size:20
Alignment explanation
Indices: 53529733--53529781 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
53529723 GGAAATACAT
53529733 TTTAAATTGCAAAAAATAAA
1 TTTAAATTGCAAAAAATAAA
* *
53529753 TGTTAAATTTCAAAAAATTTAA
1 T-TTAAATTGCAAAAAA-TAAA
53529775 TTTAAAT
1 TTTAAAT
53529782 GAAATGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.80
22 4 0.16
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (20 bp):
TTTAAATTGCAAAAAATAAA
Found at i:53529833 original size:23 final size:24
Alignment explanation
Indices: 53529773--53529833 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
53529763 CAAAAAATTT
*
53529773 AATTTAAATGAAA-TGAAAATAAA
1 AATTGAAATGAAATTGAAAATAAA
* * *
53529796 AATAGAAATTAAATTGGAAAT-AA
1 AATTGAAATGAAATTGAAAATAAA
53529819 AATTGAAATGAAATT
1 AATTGAAATGAAATT
53529834 AAATTGGAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (24 bp):
AATTGAAATGAAATTGAAAATAAA
Found at i:53529853 original size:28 final size:29
Alignment explanation
Indices: 53529795--53529854 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
53529785 ATGAAAATAA
*
53529795 AAATAGAAATTAAATTGGAAATAAAATTG
1 AAATAGAAATTAAATTGGAAAGAAAATTG
*
53529824 AAAT-GAAATTAAATTGGAGAGAGAAA-TG
1 AAATAGAAATTAAATTGGAAAGA-AAATTG
53529852 AAA
1 AAA
53529855 AAAAAAGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.23
Consensus pattern (29 bp):
AAATAGAAATTAAATTGGAAAGAAAATTG
Found at i:53530081 original size:15 final size:17
Alignment explanation
Indices: 53530063--53530099 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
53530053 TTTTTAATGG
53530063 AAATATT-AAATGAAA-
1 AAATATTAAAATGAAAT
53530078 AAAT-TTAAAATGAAAT
1 AAATATTAAAATGAAAT
53530094 AAATAT
1 AAATAT
53530100 ATATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.11
15 12 0.63
16 4 0.21
17 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
AAATATTAAAATGAAAT
Found at i:53530217 original size:21 final size:21
Alignment explanation
Indices: 53530193--53530235 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
53530183 ATTTTAATAG
*
53530193 AAATAAATTTTAAATTGCAAA
1 AAATAAATGTTAAATTGCAAA
*
53530214 AAATAAATGTTAAATTTCAAA
1 AAATAAATGTTAAATTGCAAA
53530235 A
1 A
53530236 CATTTGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
AAATAAATGTTAAATTGCAAA
Found at i:53530540 original size:32 final size:32
Alignment explanation
Indices: 53530504--53530572 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
53530494 TTTAGATAAT
53530504 TTAATGAAAATAAAT-TATAAAATGAAAAAAAA
1 TTAATGAAAATAAATCT-TAAAATGAAAAAAAA
* * * *
53530536 TTAATGGAAATAAATCTTAAATTTAAAAAAAT
1 TTAATGAAAATAAATCTTAAAATGAAAAAAAA
53530568 TTAAT
1 TTAAT
53530573 TTAAATGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (32 bp):
TTAATGAAAATAAATCTTAAAATGAAAAAAAA
Found at i:53530632 original size:468 final size:464
Alignment explanation
Indices: 53529588--53530547 Score: 1381
Period size: 468 Copynumber: 2.0 Consensus size: 464
53529578 TGAATTTTTT
* * *
53529588 TTAATGGAAATGTTAAATGAAAAAAATTAAAATGAAATAAATATATATAAACTAAAATAATAGAT
1 TTAATGGAAATATTAAATGAAAAAATTTAAAA-GAAAT-AATATATATAAAATAAAATAATAGA-
* * *
53529653 AAAATTAAATGAAC-CAAAAAAAATAATGAAATAGTAAATTAAAAAAACTTAAATTATAGATAAT
63 CAAATGAAATGAACAC-AAAAAAAGAATGAAATAGTAAA-TAAAAAAACTTAAATTATAGATAAT
* *
53529717 TTTAATGGAAATACATTTTAAATTGCAAAAAATAAATGTTAAATTTCAAAAAATTTAATTTAAAT
126 TTTAATAGAAATAAATTTTAAATTGCAAAAAATAAATGTTAAATTTCAAAAAATTTAATTTAAAT
*
53529782 GAAATGAAAATAAAAATAGAAATTAAATTGGAAATAAAATTGAAATGAAATTAAATTGGAGAGAG
191 GAAATGAAAATAAAAATAGAAATTAAATTGGAAATAAAATTGAAATGAAATTAAATTGGAGAAAG
* * *
53529847 AAATGAAAAAAAAAGGTGAAAAAATGCGAAGTAATTTCTCAAATAGGCCTGTGTGTTAGGCCTAG
256 AAATGAAAAAAAAAGGTGAAAAAATGCGAAGTAATGTCTCAAACAGGCCTGCGTGTTAGGCCTAG
*
53529912 GCCTGCCTTGCCAAATTAATTTTAATAGCCGAATCAATGGCCAGCCACACTATGCTTTTTTTTTT
321 GCCTGCCTTGCCAAATTAATTTTAATAGCCAAATCAATGGCCAGCCACACTATGCTTTTTTTTTT
53529977 TCTATTCAATTGAAATTTAAATAAAAAAACTTAAATTCTAGATAATTTTAATGAAAATTAAATAT
386 TCTATTCAATTGAAATTTAAATAAAAAAACTTAAATTCTAGATAATTTTAATGAAAATTAAATAT
*****
53530042 AAAATGAAATTTTT
451 AAAATGAAAAAAAA
53530056 TTAATGGAAATATTAAATGAAAAAATTTAAAATGAAATAAATATATATAAAATAAAATAATAGAT
1 TTAATGGAAATATTAAATGAAAAAATTTAAAA-GAAAT-AATATATATAAAATAAAATAATAGA-
*
53530121 CAAATTAAATGAACCACAAAAAAAGAATGAAATAGTAAATAAAAAAACTTAAATTATAGATAATT
63 CAAATGAAATGAA-CACAAAAAAAGAATGAAATAGTAAATAAAAAAACTTAAATTATAGATAATT
* *
53530186 TTAATAGAAATAAATTTTAAATTGCAAAAAATAAATGTTAAATTTCAAAACATTTGATTTAAATG
127 TTAATAGAAATAAATTTTAAATTGCAAAAAATAAATGTTAAATTTCAAAAAATTTAATTTAAATG
** *
53530251 AAATTCAAGTAAAAATAGAAATTAAATTAAATTGGAAATAAAATT-AACATGAAATTAAATTGGA
192 AAATGAAAATAAAAATAG-----AAATTAAATTGGAAATAAAATTGAA-ATGAAATTAAATTGGA
* * *
53530315 TGGAAAGAAATGAAAAAAAAAGGTGAAAAAATGTGAAGTAATGTCTTAAACAGGTCTGCGTGTTA
251 --GAAAGAAATGAAAAAAAAAGGTGAAAAAATGCGAAGTAATGTCTCAAACAGGCCTGCGTGTTA
* *
53530380 GGCCTAGGCCTGGCC-TGCCAAATTTATTTTAATGGCCAAATCAATGGCCAGCCACACTATGCTT
314 GGCCTAGGCCT-GCCTTGCCAAATTAATTTTAATAGCCAAATCAATGGCCAGCCACACTATGCTT
* *
53530444 TTTTTTTGTTCTATTCAATTGAAATTTAAATAAAAAAATAAAACTTGAATTTTAGATAA-TTTAA
378 TTTTTTT-TTCTATTCAATTGAAATTTAAAT----AAA-AAAACTTAAATTCTAGATAATTTTAA
53530508 TGAAAA-TAAATTATAAAATGAAAAAAAA
437 TGAAAATTAAA-TATAAAATGAAAAAAAA
53530536 TTAATGGAAATA
1 TTAATGGAAATA
53530548 AATCTTAAAT
Statistics
Matches: 445, Mismatches: 29, Indels: 24
0.89 0.06 0.05
Matches are distributed among these distances:
468 176 0.40
469 22 0.05
470 1 0.00
472 2 0.00
473 38 0.09
475 120 0.27
476 26 0.06
479 4 0.01
480 38 0.09
481 18 0.04
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.31
Consensus pattern (464 bp):
TTAATGGAAATATTAAATGAAAAAATTTAAAAGAAATAATATATATAAAATAAAATAATAGACAA
ATGAAATGAACACAAAAAAAGAATGAAATAGTAAATAAAAAAACTTAAATTATAGATAATTTTAA
TAGAAATAAATTTTAAATTGCAAAAAATAAATGTTAAATTTCAAAAAATTTAATTTAAATGAAAT
GAAAATAAAAATAGAAATTAAATTGGAAATAAAATTGAAATGAAATTAAATTGGAGAAAGAAATG
AAAAAAAAAGGTGAAAAAATGCGAAGTAATGTCTCAAACAGGCCTGCGTGTTAGGCCTAGGCCTG
CCTTGCCAAATTAATTTTAATAGCCAAATCAATGGCCAGCCACACTATGCTTTTTTTTTTTCTAT
TCAATTGAAATTTAAATAAAAAAACTTAAATTCTAGATAATTTTAATGAAAATTAAATATAAAAT
GAAAAAAAA
Found at i:53530644 original size:11 final size:11
Alignment explanation
Indices: 53530592--53530649 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
53530582 GTGCACATAA
53530592 AAATAGAAATT-
1 AAATA-AAATTG
*
53530603 AAATTAAA-TG
1 AAATAAAATTG
*
53530613 AAATGAAATTGG
1 AAATAAAATT-G
53530625 AAATAAAATTG
1 AAATAAAATTG
*
53530636 AAATCAAATT-
1 AAATAAAATTG
53530646 AAAT
1 AAAT
53530650 TGGAAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 1 0.03
10 14 0.35
11 15 0.38
12 10 0.25
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.28
Consensus pattern (11 bp):
AAATAAAATTG
Found at i:53530644 original size:23 final size:22
Alignment explanation
Indices: 53530603--53530645 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
53530593 AATAGAAATT
* *
53530603 AAATTAAATGAAATGAAATTGG
1 AAATAAAATGAAATCAAATTGG
53530625 AAATAAAATTGAAATCAAATT
1 AAATAAAA-TGAAATCAAATT
53530646 AAATTGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.28
Consensus pattern (22 bp):
AAATAAAATGAAATCAAATTGG
Found at i:53530649 original size:28 final size:27
Alignment explanation
Indices: 53530597--53530655 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
53530587 CATAAAAATA
* *
53530597 GAAATTAAATTAAATGAAATGAAATTG
1 GAAATAAAATTAAATCAAATGAAATTG
*
53530624 GAAATAAAATTGAAATCAAATTAAATTG
1 GAAATAAAATT-AAATCAAATGAAATTG
53530652 GAAA
1 GAAA
53530656 GAAATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.58, C:0.02, G:0.14, T:0.27
Consensus pattern (27 bp):
GAAATAAAATTAAATCAAATGAAATTG
Found at i:53534719 original size:28 final size:27
Alignment explanation
Indices: 53534669--53534733 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
53534659 TTCGATTGTA
*
53534669 CACTACAAATAACTCCTATATACAATC
1 CACTACAAAAAACTCCTATATACAATC
53534696 CACTACAAACAAACTTCCT-TATACAATC
1 CACTACAAA-AAAC-TCCTATATACAATC
53534724 CACTA-AAAAA
1 CACTACAAAAA
53534734 CTCATTTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 2 0.06
27 12 0.34
28 17 0.49
29 4 0.11
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (27 bp):
CACTACAAAAAACTCCTATATACAATC
Found at i:53534983 original size:57 final size:58
Alignment explanation
Indices: 53534902--53535329 Score: 233
Period size: 57 Copynumber: 7.6 Consensus size: 58
53534892 ATTTTTGTAC
*
53534902 TGGTGCCGGCCATTA-AAAGACCAGCACCAAAAAAATTTTGAATTTTTTTTACTACAG
1 TGGTGCCGACCATTAGAAAGACCAGCACCAAAAAAATTTTGAATTTTTTTTACTACAG
* * * *
53534959 TGGTACCGACCATTAGAAAG-CCAGCACAAAAAAAAATTTCT-AA-TATTTTT-GTAC--
1 TGGTGCCGACCATTAGAAAGACCAGCAC-CAAAAAAATTT-TGAATTTTTTTTACTACAG
* *
53535013 TGGTGCC-AGCCATTAG-AAGACTAGCACCCAAAAAAA-TTTGAATTTTTTTTATTACAG
1 TGGTGCCGA-CCATTAGAAAGACCAGCA-CCAAAAAAATTTTGAATTTTTTTTACTACAG
* * * *** **
53535070 TGGTGCCGACCATTAG-AAGGCCAG---CATAAAATTTTTTTTTTCCTGATATTTTTGTAC--
1 TGGTGCCGACCATTAGAAAGACCAGCACCAAAAAAATTTTGAATT--T--T-TTTTACTACAG
* * * * *
53535127 TAGTGCCGACCATTAG-AAGACTAGCACCTAAAAAATTTT-AAATTTTTTTATTACAG
1 TGGTGCCGACCATTAGAAAGACCAGCACCAAAAAAATTTTGAATTTTTTTTACTACAG
* * * * * *
53535183 TGGTGCCGGCCATTAG-AAGGCCAGCACCAAGAAAAAAAATTCCT-CA-TATTTTT-GTAC--
1 TGGTGCCGACCATTAGAAAGACCAGCACC----AAAAAAATT-TTGAATTTTTTTTACTACAG
* * ** * *
53535240 TGGTGCCGGCCATTAG-AAGACCAACACCCGAAAAATTTTGAATTTTTTTTTCCTAGAG
1 TGGTGCCGACCATTAGAAAGACCAGCACCAAAAAAATTTTGAA-TTTTTTTTACTACAG
* *
53535298 TGGTGCCGGCCATTAG-AAGGCCAGCACCAAAA
1 TGGTGCCGACCATTAGAAAGACCAGCACCAAAA
53535330 TTTTTTTTTC
Statistics
Matches: 285, Mismatches: 52, Indels: 67
0.71 0.13 0.17
Matches are distributed among these distances:
52 2 0.01
53 22 0.08
54 43 0.15
55 11 0.04
56 30 0.11
57 94 0.33
58 46 0.16
59 12 0.04
60 23 0.08
61 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (58 bp):
TGGTGCCGACCATTAGAAAGACCAGCACCAAAAAAATTTTGAATTTTTTTTACTACAG
Found at i:53535053 original size:111 final size:110
Alignment explanation
Indices: 53534847--53535329 Score: 588
Period size: 111 Copynumber: 4.3 Consensus size: 110
53534837 ATATAAGGTT
*
53534847 TGGTGCCGGCCATTAGAAGGTCAGCACCAAAAAAAAATTCCTAATATTTTTGTACTGGTGCCGGC
1 TGGTGCCGGCCATTAGAAGGCCAGCA-CAAAAAAAAATTCCTAATATTTTTGTACTGGTGCCGGC
*
53534912 CATTAAAAGACCAGCACCAAAAAAATTTTGAATTTTTTTTACTACAG
65 CATTAGAAGACCAGCACCAAAAAAA-TTTGAATTTTTTTTACTACAG
* * * * *
53534959 TGGTACCGACCATTAGAAAGCCAGCACAAAAAAAAATTTCTAATATTTTTGTACTGGTGCCAGCC
1 TGGTGCCGGCCATTAGAAGGCCAGCACAAAAAAAAATTCCTAATATTTTTGTACTGGTGCCGGCC
* *
53535024 ATTAGAAGACTAGCACCCAAAAAAATTTGAATTTTTTTTATTACAG
66 ATTAGAAGACCAGCA-CCAAAAAAATTTGAATTTTTTTTACTACAG
* * ***** * *
53535070 TGGTGCCGACCATTAGAAGGCCAGCATAAAATTTTTTTTTTCCTGATATTTTTGTACTAGTGCCG
1 TGGTGCCGGCCATTAGAAGGCCAGCACAAAA---AAAAATTCCTAATATTTTTGTACTGGTGCCG
* * * * * *
53535135 ACCATTAGAAGACTAGCACCTAAAAAATTTTAAATTTTTTTATTACAG
63 GCCATTAGAAGACCAGCACCAAAAAAATTTGAATTTTTTTTACTACAG
*
53535183 TGGTGCCGGCCATTAGAAGGCCAGCACCAAGAAAAAAAATTCCTCATATTTTTGTACTGGTGCCG
1 TGGTGCCGGCCATTAGAAGGCCAGCA-C-A-AAAAAAAATTCCTAATATTTTTGTACTGGTGCCG
* * * * *
53535248 GCCATTAGAAGACCAACACCCGAAAAATTTTGAATTTTTTTTTCCTAGAG
63 GCCATTAGAAGACCAGCA-CCAAAAAAATTTGAA-TTTTTTTTACTACAG
*
53535298 TGGTGCCGGCCATTAGAAGGCCAGCACCAAAA
1 TGGTGCCGGCCATTAGAAGGCCAGCACAAAAA
53535330 TTTTTTTTTC
Statistics
Matches: 317, Mismatches: 45, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
111 98 0.31
112 35 0.11
113 91 0.29
114 52 0.16
115 38 0.12
116 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (110 bp):
TGGTGCCGGCCATTAGAAGGCCAGCACAAAAAAAAATTCCTAATATTTTTGTACTGGTGCCGGCC
ATTAGAAGACCAGCACCAAAAAAATTTGAATTTTTTTTACTACAG
Found at i:53535226 original size:113 final size:112
Alignment explanation
Indices: 53534847--53535329 Score: 571
Period size: 113 Copynumber: 4.3 Consensus size: 112
53534837 ATATAAGGTT
* *
53534847 TGGTGCCGGCCATTAGAAGGTCAGCACC-AAAAAAAAATTCCTAATATTTTTGTACTGGTGCCGG
1 TGGTGCCGGCCATTAGAAGGCCAGCACCAAAAAAAAAATTCCTAATATTTTTGTACTGGTGCCGA
* * *
53534911 CCATTAAAAGACCAGCACCAAAAAAATTTTGAATTTTTTTTACTACAG
66 CCATTAGAAGACCAGCACCAAAAAAATTTT-AAATTTTTTTATTACAG
* * * *
53534959 TGGTACCGACCATTAGAAAGCCAGCA-C-AAAAAAAAATTTCTAATATTTTTGTACTGGTGCC-A
1 TGGTGCCGGCCATTAGAAGGCCAGCACCAAAAAAAAAATTCCTAATATTTTTGTACTGGTGCCGA
* * *
53535021 GCCATTAGAAGACTAGCACCCAAAAAAATTTGAATTTTTTTTATTACAG
66 -CCATTAGAAGACCAGCA-CCAAAAAAATTTTAAATTTTTTTATTACAG
* * ****** * *
53535070 TGGTGCCGACCATTAGAAGGCCAGCA-TAAAATTTTTTTTTTCCTGATATTTTTGTACTAGTGCC
1 TGGTGCCGGCCATTAGAAGGCCAGCACCAAAA--AAAAAATTCCTAATATTTTTGTACTGGTGCC
* *
53535134 GACCATTAGAAGACTAGCACCTAAAAAATTTTAAATTTTTTTATTACAG
64 GACCATTAGAAGACCAGCACCAAAAAAATTTTAAATTTTTTTATTACAG
*
53535183 TGGTGCCGGCCATTAGAAGGCCAGCACCAAGAAAAAAAATTCCTCATATTTTTGTACTGGTGCCG
1 TGGTGCCGGCCATTAGAAGGCCAGCACCAA-AAAAAAAATTCCTAATATTTTTGTACTGGTGCCG
* * ** * * *
53535248 GCCATTAGAAGACCAACACCCGAAAAATTTTGAATTTTTTTTTCCTAGAG
65 ACCATTAGAAGACCAGCACCAAAAAAATTTTAAATTTTTTTAT--TACAG
53535298 TGGTGCCGGCCATTAGAAGGCCAGCACCAAAA
1 TGGTGCCGGCCATTAGAAGGCCAGCACCAAAA
53535330 TTTTTTTTTC
Statistics
Matches: 318, Mismatches: 43, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
111 89 0.28
112 37 0.12
113 112 0.35
114 43 0.14
115 37 0.12
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (112 bp):
TGGTGCCGGCCATTAGAAGGCCAGCACCAAAAAAAAAATTCCTAATATTTTTGTACTGGTGCCGA
CCATTAGAAGACCAGCACCAAAAAAATTTTAAATTTTTTTATTACAG
Found at i:53536755 original size:9 final size:9
Alignment explanation
Indices: 53536738--53536792 Score: 83
Period size: 9 Copynumber: 6.1 Consensus size: 9
53536728 TATAGTTTAA
*
53536738 TATTGGAAT
1 TATTCGAAT
53536747 TATTCGAAT
1 TATTCGAAT
*
53536756 TATTCGAGT
1 TATTCGAAT
53536765 TATTCGAAT
1 TATTCGAAT
*
53536774 TATTCGAGT
1 TATTCGAAT
53536783 TATTCGAAT
1 TATTCGAAT
53536792 T
1 T
53536793 CGAAAACTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.45
Consensus pattern (9 bp):
TATTCGAAT
Found at i:53536767 original size:18 final size:18
Alignment explanation
Indices: 53536746--53536792 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
53536736 AATATTGGAA
53536746 TTATTCGAATTATTCGAG
1 TTATTCGAATTATTCGAG
53536764 TTATTCGAATTATTCGAG
1 TTATTCGAATTATTCGAG
53536782 TTATTCGAATT
1 TTATTCGAATT
53536793 CGAAAACTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.47
Consensus pattern (18 bp):
TTATTCGAATTATTCGAG
Found at i:53536856 original size:9 final size:9
Alignment explanation
Indices: 53536842--53536874 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
53536832 ATTCGAGTTG
53536842 ACTCGAATA
1 ACTCGAATA
*
53536851 ACTCGATTA
1 ACTCGAATA
53536860 ACTCGAATA
1 ACTCGAATA
53536869 ACTCGA
1 ACTCGA
53536875 TTCGTTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (9 bp):
ACTCGAATA
Found at i:53536865 original size:18 final size:18
Alignment explanation
Indices: 53536842--53536876 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
53536832 ATTCGAGTTG
53536842 ACTCGAATAACTCGATTA
1 ACTCGAATAACTCGATTA
53536860 ACTCGAATAACTCGATT
1 ACTCGAATAACTCGATT
53536877 CGTTAAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:53545344 original size:9 final size:9
Alignment explanation
Indices: 53545332--53545362 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
53545322 AATAATAATA
53545332 ATAATGATG
1 ATAATGATG
53545341 ATAATGATG
1 ATAATGATG
*
53545350 ATGATGATG
1 ATAATGATG
53545359 ATAA
1 ATAA
53545363 AATAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (9 bp):
ATAATGATG
Found at i:53547054 original size:18 final size:20
Alignment explanation
Indices: 53547031--53547068 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
53547021 ACGTGACAGT
53547031 CCAAC-TAGATTT-TAAATG
1 CCAACTTAGATTTCTAAATG
53547049 CCAACTTAGATTTCTAAATG
1 CCAACTTAGATTTCTAAATG
53547069 GGATGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (20 bp):
CCAACTTAGATTTCTAAATG
Found at i:53551593 original size:17 final size:17
Alignment explanation
Indices: 53551571--53551603 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53551561 GATATGATAC
53551571 TAAAAT-TATTAAAAAAT
1 TAAAATATA-TAAAAAAT
53551588 TAAAATATATAAAAAA
1 TAAAATATATAAAAAA
53551604 AATCAGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATATATAAAAAAT
Found at i:53551604 original size:18 final size:17
Alignment explanation
Indices: 53551571--53551604 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
53551561 GATATGATAC
*
53551571 TAAAATTATTAAAAAAT
1 TAAAATTATAAAAAAAT
53551588 TAAAATATATAAAAAAA
1 TAAAAT-TATAAAAAAA
53551605 ATCAGGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATTATAAAAAAAT
Found at i:53551895 original size:22 final size:21
Alignment explanation
Indices: 53551860--53551935 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
53551850 AAAAGGTATC
* *
53551860 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
53551881 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
53551904 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
53551923 TGC-AATCATATCT
1 TACAAATCATATCT
53551936 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:53551952 original size:35 final size:37
Alignment explanation
Indices: 53551889--53551967 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
53551879 ATTACAAAAT
53551889 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
53551925 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
53551960 CATATCAT
1 CATATCAT
53551968 TGAAGATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:53551965 original size:14 final size:15
Alignment explanation
Indices: 53551910--53551965 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
53551900 AGATTGCATA
53551910 TCATATCTAAGATTG
1 TCATATCTAAGATTG
53551925 CAATCATATCTAAGATTG
1 ---TCATATCTAAGATTG
53551943 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
53551960 -CATATC
1 TCATATC
53551966 ATTGAAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 6 0.16
17 16 0.43
18 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:53551975 original size:17 final size:19
Alignment explanation
Indices: 53551896--53551967 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
53551886 AATCATATCT
53551896 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53551915 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
53551933 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
53551950 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
53551968 TGAAGATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:53552381 original size:45 final size:45
Alignment explanation
Indices: 53552317--53552516 Score: 278
Period size: 45 Copynumber: 4.5 Consensus size: 45
53552307 GGAAGGTGAT
* * *
53552317 ATCTGCTATCTTTGATCTGCTCTCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
53552362 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * *
53552407 ATCTGCT-TCTTCAATCTGCTCCCTGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
53552451 ATCTGTTATC-TCTGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTC-GATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
53552496 ATCTGTCATCTTGGATCTGCT
1 ATCTGTTATCTTCGATCTGCT
53552517 TCGATGTAAA
Statistics
Matches: 138, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
44 42 0.30
45 95 0.69
46 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.33
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:53552482 original size:89 final size:90
Alignment explanation
Indices: 53552317--53552500 Score: 284
Period size: 89 Copynumber: 2.1 Consensus size: 90
53552307 GGAAGGTGAT
**
53552317 ATCTGCTATCTTTGATCTGCTCTCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTGC
1 ATCTGCTATCTTCAATCTGCTCTCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTGC
53552382 TCCCCGTCTAATACAGAGACGCCAA
66 TCCCCGTCTAATACAGAGACGCCAA
* *
53552407 ATCTGCT-TCTTCAATCTGCTC-CCTGTCTAATACAGAGATGCCAAATCTGTTATC-TCTGATTT
1 ATCTGCTATCTTCAATCTGCTCTCC-GTCTAATACAGAGACGCCAAATCTGTTATCTTC-GATCT
*
53552469 GCTCCCCGTCTAATACAGAGATGCCAA
64 GCTCCCCGTCTAATACAGAGACGCCAA
53552496 ATCTG
1 ATCTG
53552501 TCATCTTGGA
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
88 4 0.05
89 76 0.87
90 7 0.08
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (90 bp):
ATCTGCTATCTTCAATCTGCTCTCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTGC
TCCCCGTCTAATACAGAGACGCCAA
Found at i:53552670 original size:78 final size:78
Alignment explanation
Indices: 53552530--53553136 Score: 812
Period size: 78 Copynumber: 7.8 Consensus size: 78
53552520 ATGTAAACAC
* *
53552530 ATGAAGG-TCAGATCTGCTATGTCTCCGATCTGCTCCCCGTCTAATACAGATATGCCAAATCATC
1 ATGAAGGTTCA-ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
53552594 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * * * *
53552608 ATGACGGTTCAATCTGTTATGTCTTTGATCTGTTCCCTGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTTCAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
*
53552673 TGGACCTGCTTCA
66 TGGATCTGCTTCA
* * *
53552686 ATGAAGG-TCAGATCTGCTGTGTCTTCGATCTGCTCCCCATCTAATACAGAGATGTCAAATCATC
1 ATGAAGGTTCA-ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
53552750 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * * ** *
53552764 ATAAAGGTT-AGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATTCCAAATCATC
1 ATGAAGGTTCA-ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
53552828 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * **
53552842 ATGAAGG-TCAAATCTGCTGTGTCTTCGATCTGCTCCCCGTCGAATATGGAGATGCCAAATCATC
1 ATGAAGGTTC-AATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
53552906 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * * * *
53552920 ATGAA-TTTCCAATCTGTTGTGTCTTCGATCTACTCCCCGTCTAATATAGAGATGCCAAATCATC
1 ATGAAGGTT-CAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
53552984 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * *
53552998 ATAAAGGTCCAATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTTCAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
53553063 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * **
53553076 ATGAAGG-TCAGATCTGCTATGTCTTTGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTTCA-ATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
53553137 TGTTTCTTCG
Statistics
Matches: 471, Mismatches: 49, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
77 6 0.01
78 458 0.97
79 7 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (78 bp):
ATGAAGGTTCAATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:53552948 original size:234 final size:234
Alignment explanation
Indices: 53552533--53553136 Score: 908
Period size: 234 Copynumber: 2.6 Consensus size: 234
53552523 TAAACACATG
* *
53552533 AAGGTCAGATCTGCTATGTCTCCGATCTGCTCCCCGTCTAATACAGATATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
* * * * * **
53552598 ATCTGCTTCAATGACGGTTC-AATCTGTTATGTCTTTGATCTGTTCCCTGTCTAATACAGAGATG
66 ATCTGCTTCAATGAAGG-TCAAATCTGCTATGTCTTTGATCTGCTCCCCGTCGAATATGGAGATG
*
53552662 CCAAATCATCTTGGACCTGCTTCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCATC
130 CCAAATCATCTTGGACCTGCTTCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTACTCCCCATC
*
53552727 TAATACAGAGATGTCAAATCATCTTGGATCTGCTTCAATA
195 TAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATA
* * * ** *
53552767 AAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATTCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
* *
53552832 ATCTGCTTCAATGAAGGTCAAATCTGCTGTGTCTTCGATCTGCTCCCCGTCGAATATGGAGATGC
66 ATCTGCTTCAATGAAGGTCAAATCTGCTATGTCTTTGATCTGCTCCCCGTCGAATATGGAGATGC
* ** * *
53552897 CAAATCATCTTGGATCTGCTTCAATGAATTTCCA-ATCTGTTGTGTCTTCGATCTACTCCCCGTC
131 CAAATCATCTTGGACCTGCTTCAATGAAGGT-CAGATCTGCTGTGTCTTCGATCTACTCCCCATC
*
53552961 TAATATAGAGATGCCAAATCATCTTGGATCTGCTTCAATA
195 TAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATA
*
53553001 AAGGTCCA-ATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTG
1 AAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTG
* *
53553065 GATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTTGATCTGCTCTCCGTCGAATATGGAGATG
65 GATCTGCTTCAATGAAGGTCAAATCTGCTATGTCTTTGATCTGCTCCCCGTCGAATATGGAGATG
53553130 CCAAATC
130 CCAAATC
53553137 TGTTTCTTCG
Statistics
Matches: 331, Mismatches: 36, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
233 2 0.01
234 326 0.98
235 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (234 bp):
AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
ATCTGCTTCAATGAAGGTCAAATCTGCTATGTCTTTGATCTGCTCCCCGTCGAATATGGAGATGC
CAAATCATCTTGGACCTGCTTCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTACTCCCCATCT
AATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATA
Found at i:53553263 original size:87 final size:89
Alignment explanation
Indices: 53553169--53553330 Score: 240
Period size: 89 Copynumber: 1.8 Consensus size: 89
53553159 ACAGTACAGA
* *
53553169 GATGCCAAATCATCTTAGATCTGCTTC-A-GCGTAAACA-CCTGAAGGTCAAATCTGCTATGTCT
1 GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATCC-GAAGGTCAAATCTGCTATGTCT
53553231 TCGATCTGCTCCTTGTAAACGTAAG
65 TCGATCTGCTCCTTGTAAACGTAAG
* * * *
53553256 GATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCCGAAGGTTAGATCTGCTATGTCTT
1 GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATCCGAAGGTCAAATCTGCTATGTCTT
53553321 CGATCTGCTC
66 CGATCTGCTC
53553331 TCCGTCGAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
87 25 0.38
88 1 0.02
89 38 0.58
90 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATCCGAAGGTCAAATCTGCTATGTCTT
CGATCTGCTCCTTGTAAACGTAAG
Found at i:53553484 original size:220 final size:220
Alignment explanation
Indices: 53553078--53553887 Score: 1332
Period size: 220 Copynumber: 3.7 Consensus size: 220
53553068 CTGCTTCAAT
* * *
53553078 GAAGGTCAGATCTGCTATGTCTTTGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTC
* *
53553143 TTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACC
66 TTCGATTTGTTCTCTGACAATACAGAGATGTCAAATCATCTTAGATCTGCTTCAGCGTAAACACC
* * *
53553208 TGAAGGTCAAATCTGCTATGTCTTCGATCTGCTCCTTGTAAACGTAAGGATGCCAAATCATCTTG
131 TGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTG
53553273 GATCTACTTCGATGTGAAAACATCC
196 GATCTACTTCGATGTGAAAACATCC
53553298 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTC
* * * * * * *
53553363 TTTGATTTGTTCTCTGATAATACAGAGATGTTAAATCATCTTGGATCTACTTCAGTGTAAACACG
66 TTCGATTTGTTCTCTGACAATACAGAGATGTCAAATCATCTTAGATCTGCTTCAGCGTAAACACC
* * * *
53553428 TGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTATATACGCAAGGTTGCCAAATCATCTTA
131 TGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTG
*
53553493 GATCTACTTCGATGTGAAATCATCC
196 GATCTACTTCGATGTGAAAACATCC
* * *
53553518 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATAGGGAGATACCAAATCTTTTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTC
* * * *
53553583 TTCGATTTGTTCTCTGATAGTGCAGAGATGTCAAATCATCTTAGATCTGCTTCAGCGTAAACACG
66 TTCGATTTGTTCTCTGACAATACAGAGATGTCAAATCATCTTAGATCTGCTTCAGCGTAAACACC
53553648 TGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTG
131 TGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTG
53553713 GATCTACTTCGATGTGAAAACATCC
196 GATCTACTTCGATGTGAAAACATCC
53553738 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTC
1 GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTC
* * *
53553803 TTCGATTTGTTCTCTGACAATACAGAGATGTTAAATCATCTTGGATCCGCTTCAGCGTAAACACC
66 TTCGATTTGTTCTCTGACAATACAGAGATGTCAAATCATCTTAGATCTGCTTCAGCGTAAACACC
* *
53553868 TGAAGGTCAAATCTGCTATG
131 TGAAAGCCAAATCTGCTATG
53553888 CTTTAGCCTG
Statistics
Matches: 543, Mismatches: 47, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
220 543 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (220 bp):
GAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTC
TTCGATTTGTTCTCTGACAATACAGAGATGTCAAATCATCTTAGATCTGCTTCAGCGTAAACACC
TGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTG
GATCTACTTCGATGTGAAAACATCC
Found at i:53556816 original size:30 final size:30
Alignment explanation
Indices: 53556782--53556840 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
53556772 TATGAATCCT
*
53556782 AGGTCTCGATACCTCGTTTTCAACCCAATG
1 AGGTCTCGATACCTCATTTTCAACCCAATG
53556812 AGGTCTCGATACCTCATTTTCAACCCAAT
1 AGGTCTCGATACCTCATTTTCAACCCAAT
53556841 TTACCTGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.31
Consensus pattern (30 bp):
AGGTCTCGATACCTCATTTTCAACCCAATG
Found at i:53559807 original size:22 final size:24
Alignment explanation
Indices: 53559781--53559930 Score: 164
Period size: 25 Copynumber: 6.2 Consensus size: 24
53559771 TAATGAACAA
*
53559781 AGAGCACTGACGTGCT-ACA-CAG
1 AGAGCACTGACGTGCTAATATCAG
** *
53559803 AGAGCACAAATGTGCT-A-ATCAG
1 AGAGCACTGACGTGCTAATATCAG
*
53559825 AGAGCACTGACGTGCTAAATATTAG
1 AGAGCACTGACGTGCT-AATATCAG
* *
53559850 AGAGCACTGGCATGCTAATAATCAG
1 AGAGCACTGACGTGCTAAT-ATCAG
*
53559875 AGAGCACTGGCGTGCTAATATTCAG
1 AGAGCACTGACGTGCTAATA-TCAG
53559900 AGAGCACTGACGTGCTAATAATCAG
1 AGAGCACTGACGTGCTAAT-ATCAG
53559925 AGAGCA
1 AGAGCA
53559931 TGCTGAGGTC
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
21 1 0.01
22 30 0.28
24 5 0.05
25 72 0.66
26 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.19
Consensus pattern (24 bp):
AGAGCACTGACGTGCTAATATCAG
Found at i:53559854 original size:25 final size:25
Alignment explanation
Indices: 53559818--53559930 Score: 165
Period size: 25 Copynumber: 4.5 Consensus size: 25
53559808 ACAAATGTGC
53559818 TAATCAGAGAGCACTGACGTGCTAA
1 TAATCAGAGAGCACTGACGTGCTAA
* * *
53559843 -ATATTAGAGAGCACTGGCATGCTAA
1 TA-ATCAGAGAGCACTGACGTGCTAA
*
53559868 TAATCAGAGAGCACTGGCGTGCTAA
1 TAATCAGAGAGCACTGACGTGCTAA
*
53559893 TATTCAGAGAGCACTGACGTGCTAA
1 TAATCAGAGAGCACTGACGTGCTAA
53559918 TAATCAGAGAGCA
1 TAATCAGAGAGCA
53559931 TGCTGAGGTC
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
24 1 0.01
25 76 0.97
26 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (25 bp):
TAATCAGAGAGCACTGACGTGCTAA
Found at i:53559883 original size:50 final size:50
Alignment explanation
Indices: 53559818--53559930 Score: 183
Period size: 50 Copynumber: 2.3 Consensus size: 50
53559808 ACAAATGTGC
*
53559818 TAATCAGAGAGCACTGACGTGCTAAATATT-AGAGAGCACTGGCATGCTAA
1 TAATCAGAGAGCACTGACGTGCT-AATATTCAGAGAGCACTGACATGCTAA
* *
53559868 TAATCAGAGAGCACTGGCGTGCTAATATTCAGAGAGCACTGACGTGCTAA
1 TAATCAGAGAGCACTGACGTGCTAATATTCAGAGAGCACTGACATGCTAA
53559918 TAATCAGAGAGCA
1 TAATCAGAGAGCA
53559931 TGCTGAGGTC
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
49 6 0.10
50 53 0.90
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (50 bp):
TAATCAGAGAGCACTGACGTGCTAATATTCAGAGAGCACTGACATGCTAA
Found at i:53561802 original size:25 final size:25
Alignment explanation
Indices: 53561766--53561859 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
53561756 GACGTGCTAC
53561766 TGCTAA-ATATCAGAGAGCACTGGCG
1 TGCTAATA-ATCAGAGAGCACTGGCG
53561791 TGCTAATAATCAGAGAGCACTGGCG
1 TGCTAATAATCAGAGAGCACTGGCG
* *
53561816 TGCTAATATTCAGAGAGCACTGACG
1 TGCTAATAATCAGAGAGCACTGGCG
53561841 TGCTAATAATCAGAGAGCA
1 TGCTAATAATCAGAGAGCA
53561860 TGCTGAGGTC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
25 64 0.98
26 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (25 bp):
TGCTAATAATCAGAGAGCACTGGCG
Found at i:53570583 original size:44 final size:48
Alignment explanation
Indices: 53570466--53570585 Score: 155
Period size: 44 Copynumber: 2.6 Consensus size: 48
53570456 ATGATACTAA
*
53570466 AATTATTGAAAAATTAAAATATATAAAAAAATCCGAGAAACATGGTTG
1 AATTATTGAAAAATTAAAATATATAAAAAAATCCGAGAAACATGATTG
* * *
53570514 AA--A--AAAAAATTAAAATATATAAAAAAATCCG-G-GA-ATGATTT
1 AATTATTGAAAAATTAAAATATATAAAAAAATCCGAGAAACATGATTG
53570555 AATTATTGAAAAATTAAAATATATAAAAAAA
1 AATTATTGAAAAATTAAAATATATAAAAAAA
53570586 ATTAAAAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
41 7 0.11
42 1 0.02
43 2 0.03
44 27 0.43
45 23 0.37
46 1 0.02
48 2 0.03
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (48 bp):
AATTATTGAAAAATTAAAATATATAAAAAAATCCGAGAAACATGATTG
Found at i:53570610 original size:7 final size:7
Alignment explanation
Indices: 53570600--53570685 Score: 82
Period size: 7 Copynumber: 12.0 Consensus size: 7
53570590 AAAATAAGAT
53570600 CCCTAAA
1 CCCTAAA
53570607 CCCTAAA
1 CCCTAAA
*
53570614 CCTTAAA
1 CCCTAAA
53570621 CCCTAAA
1 CCCTAAA
* *
53570628 TCTTAAA
1 CCCTAAA
*
53570635 TCCTAAAA
1 CCCT-AAA
53570643 CCCTAAA
1 CCCTAAA
*
53570650 TCCTAAA
1 CCCTAAA
* *
53570657 TCTTAAA
1 CCCTAAA
*
53570664 TCCTAAAA
1 CCCT-AAA
53570672 CCCTAAA
1 CCCTAAA
53570679 CCCTAAA
1 CCCTAAA
53570686 TCAAAATAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
7 55 0.82
8 12 0.18
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (7 bp):
CCCTAAA
Found at i:53570643 original size:29 final size:29
Alignment explanation
Indices: 53570603--53570687 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
53570593 ATAAGATCCC
* *
53570603 TAAACCCT-AAACCTTAAACCCTAAATCT
1 TAAATCCTAAAACCCTAAACCCTAAATCT
*
53570631 TAAATCCTAAAACCCTAAATCCTAAATCT
1 TAAATCCTAAAACCCTAAACCCTAAATCT
53570660 TAAATCCTAAAACCCTAAACCCTAAATC
1 TAAATCCTAAAACCCTAAACCCTAAATC
53570688 AAAATAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 7 0.13
29 45 0.87
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.25
Consensus pattern (29 bp):
TAAATCCTAAAACCCTAAACCCTAAATCT
Found at i:53570646 original size:22 final size:21
Alignment explanation
Indices: 53570601--53570685 Score: 89
Period size: 22 Copynumber: 4.0 Consensus size: 21
53570591 AAATAAGATC
53570601 CCTAAACCCTAAACCTTAAAC
1 CCTAAACCCTAAACCTTAAAC
* * *
53570622 CCTAAATCTTAAATCCTAAAAC
1 CCTAAACCCTAAA-CCTTAAAC
* * *
53570644 CCTAAATCCTAAATCTTAAAT
1 CCTAAACCCTAAACCTTAAAC
*
53570665 CCTAAAACCCTAAACCCTAAA
1 CCT-AAACCCTAAACCTTAAA
53570686 TCAAAATAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 19 0.37
22 33 0.63
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
CCTAAACCCTAAACCTTAAAC
Found at i:53571017 original size:17 final size:19
Alignment explanation
Indices: 53570956--53571009 Score: 94
Period size: 17 Copynumber: 2.9 Consensus size: 19
53570946 AATCATATAT
53570956 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53570975 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
53570992 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
53571010 TGAAGATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 17 0.52
19 16 0.48
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:53572775 original size:28 final size:30
Alignment explanation
Indices: 53572729--53572787 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
53572719 ATTCATAAAT
**
53572729 AAATTATAAAAATCATTTTTTAAAAATTAA
1 AAATTATAAAAATCATTTTAAAAAAATTAA
*
53572759 AAATTAT-AATAT-ATTTTAAAAAAATTAA
1 AAATTATAAAAATCATTTTAAAAAAATTAA
53572787 A
1 A
53572788 TGTTGACATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 15 0.58
29 4 0.15
30 7 0.27
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (30 bp):
AAATTATAAAAATCATTTTAAAAAAATTAA
Found at i:53575343 original size:21 final size:22
Alignment explanation
Indices: 53575317--53575363 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
53575307 CTCTGCTCAA
*
53575317 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
53575338 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
53575360 ACTC
1 ACTC
53575364 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:53578767 original size:17 final size:18
Alignment explanation
Indices: 53578740--53578773 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53578730 TCATAAGATG
*
53578740 AATTATTAAATATATTAA
1 AATTATTAAATAAATTAA
53578758 AATT-TTAAATAAATTA
1 AATTATTAAATAAATTA
53578774 TTTTATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTATTAAATAAATTAA
Found at i:53580660 original size:19 final size:20
Alignment explanation
Indices: 53580628--53580670 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
53580618 TGATTGCTAC
53580628 AAAACTTATAAAAT-TTAATA
1 AAAACTTATAAAATATT-ATA
53580648 AAAACTTAT-AAATATTATA
1 AAAACTTATAAAATATTATA
53580667 AAAA
1 AAAA
53580671 TCTAATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAACTTATAAAATATTATA
Found at i:53580750 original size:22 final size:23
Alignment explanation
Indices: 53580703--53580750 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
53580693 AATAAATTAT
**
53580703 AAATTTTAATAAAAAAATATTTA
1 AAATTTTAATAAAAAAATATAAA
*
53580726 AAATTTT-ATAAAAACATATAAA
1 AAATTTTAATAAAAAAATATAAA
53580748 AAA
1 AAA
53580751 ATCTCAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATTTTAATAAAAAAATATAAA
Found at i:53580776 original size:10 final size:9
Alignment explanation
Indices: 53580763--53580818 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
53580753 CTCAAAAATT
53580763 TTATTAACAA
1 TTATTAA-AA
53580773 TTATTAAAA
1 TTATTAAAA
*
53580782 ATATTAAAA
1 TTATTAAAA
*
53580791 TTGATATAAAC
1 TT-AT-TAAAA
*
53580802 TTATAAAAA
1 TTATTAAAA
53580811 TTA-TAAAA
1 TTATTAAAA
53580819 AGATCATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 4 0.11
9 17 0.45
10 11 0.29
11 6 0.16
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (9 bp):
TTATTAAAA
Found at i:53582282 original size:23 final size:22
Alignment explanation
Indices: 53582239--53582295 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
53582229 TTGAACTATT
* *
53582239 TTTTTTTAGTATACAT-TTTTT
1 TTTTTTTAATATACATATTTTA
*
53582260 TTAGTTTTTAATATATATATTTTA
1 TT--TTTTTAATATACATATTTTA
53582284 TTTTTTTAATAT
1 TTTTTTTAATAT
53582296 TTTATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 2 0.07
22 10 0.33
23 12 0.40
24 6 0.20
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (22 bp):
TTTTTTTAATATACATATTTTA
Found at i:53582308 original size:16 final size:16
Alignment explanation
Indices: 53582266--53582308 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
53582256 TTTTTTAGTT
53582266 TTTAATATATATATTTTA
1 TTTAAT-TA-ATATTTTA
**
53582284 TTTTTTTAATATTTTA
1 TTTAATTAATATTTTA
53582300 TTTAATTAA
1 TTTAATTAA
53582309 ATTGGAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 15 0.71
17 2 0.10
18 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAATTAATATTTTA
Found at i:53582668 original size:10 final size:10
Alignment explanation
Indices: 53582653--53582753 Score: 50
Period size: 10 Copynumber: 10.2 Consensus size: 10
53582643 CTAGCTCATG
*
53582653 TTTTTATGAT
1 TTTTTATAAT
53582663 TTTTTATAAT
1 TTTTTATAAT
*
53582673 TTTATATCAA-
1 TTTTTAT-AAT
*
53582683 TTTTAAT-AT
1 TTTTTATAAT
* *
53582692 TTTTAATAAG
1 TTTTTATAAT
*
53582702 TTTTTAT-TT
1 TTTTTATAAT
*
53582711 TTTCTTATAAA
1 TTT-TTATAAT
*
53582722 TTTTTA-AGAA
1 TTTTTATA-AT
53582732 TTTTTAT-AT
1 TTTTTATAAT
*
53582741 GTTTTATTAAT
1 TTTTTA-TAAT
53582752 TT
1 TT
53582754 GATAAAGTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
8 1 0.01
9 17 0.25
10 43 0.62
11 8 0.12
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:53590033 original size:48 final size:48
Alignment explanation
Indices: 53589976--53590067 Score: 175
Period size: 48 Copynumber: 1.9 Consensus size: 48
53589966 TATTTATATT
53589976 TCAACTTTGTTTGGTTGGTTAATATAATAACATGGGTATAAGTTTATC
1 TCAACTTTGTTTGGTTGGTTAATATAATAACATGGGTATAAGTTTATC
*
53590024 TCAACTTTGTTTGGTTGGTTAATATGATAACATGGGTATAAGTT
1 TCAACTTTGTTTGGTTGGTTAATATAATAACATGGGTATAAGTT
53590068 AATTCAGTAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (48 bp):
TCAACTTTGTTTGGTTGGTTAATATAATAACATGGGTATAAGTTTATC
Found at i:53595136 original size:3 final size:3
Alignment explanation
Indices: 53595128--53595207 Score: 51
Period size: 3 Copynumber: 27.0 Consensus size: 3
53595118 TTCGGGAACA
* * * * *
53595128 AAG AAG AAG GAG AAA AAG AA- AAG GAG AATG AGG AA- AGAG GAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG A-AG AAG AAG
*
53595173 AAG AA- AAG AAG -AG AAG AAG AAG AAAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG
53595208 GGGAGGAGGA
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
2 7 0.12
3 46 0.79
4 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:53595174 original size:19 final size:17
Alignment explanation
Indices: 53595132--53595200 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 17
53595122 GGAACAAAGA
* * *
53595132 AGAAGGAGAAAAAGAAA
1 AGAAGAAGAGAAAGAAG
* *
53595149 AGGAGAATGAGGAAAGAGG
1 AGAAGAA-GA-GAAAGAAG
53595168 AGAAGAAGA-AAAGAAG
1 AGAAGAAGAGAAAGAAG
53595184 AGAAGAAGAAGAAAGAA
1 AGAAGAAG-AGAAAGAA
53595201 AAAGAAGGGG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
16 14 0.34
17 6 0.15
18 10 0.24
19 11 0.27
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (17 bp):
AGAAGAAGAGAAAGAAG
Found at i:53595180 original size:16 final size:16
Alignment explanation
Indices: 53595135--53595193 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
53595125 ACAAAGAAGA
*
53595135 AGGAGAAAAAG-AAA-
1 AGGAGAAGAAGAAAAG
*
53595149 AGGAGAATG-AGGAAAG
1 AGGAGAA-GAAGAAAAG
53595165 AGGAGAAGAAGAAAAG
1 AGGAGAAGAAGAAAAG
*
53595181 AAGAGAAGAAGAA
1 AGGAGAAGAAGAA
53595194 GAAAGAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 9 0.24
15 4 0.11
16 25 0.66
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.02
Consensus pattern (16 bp):
AGGAGAAGAAGAAAAG
Found at i:53595189 original size:13 final size:13
Alignment explanation
Indices: 53595131--53595207 Score: 52
Period size: 13 Copynumber: 5.9 Consensus size: 13
53595121 GGGAACAAAG
*
53595131 AAGAAGGAGAA-A
1 AAGAAGAAGAAGA
*
53595143 AAGAA-AAGGAGA
1 AAGAAGAAGAAGA
* * *
53595155 ATGAGGAAAGAGGA
1 AAGAAG-AAGAAGA
53595169 GAAGAAGAA-AAGA
1 -AAGAAGAAGAAGA
53595182 AGAGAAGAAGAAGA
1 A-AGAAGAAGAAGA
*
53595196 AAGAAAAAGAAG
1 AAGAAGAAGAAG
53595208 GGGAGGAGGA
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
11 3 0.06
12 10 0.20
13 20 0.41
14 12 0.24
15 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:53595206 original size:19 final size:19
Alignment explanation
Indices: 53595128--53595207 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 19
53595118 TTCGGGAACA
*
53595128 AAGAAGAAG-GAGAAAAAG
1 AAGAAGAAGAAAGAAAAAG
* *
53595146 AA-AAGGAGAATGAGGAAAGAG
1 AAGAAGAAGAA--A-GAAAAAG
* *
53595167 GAGAAGAAGAAA-AGAAGAG
1 AAGAAGAAGAAAGA-AAAAG
53595186 AAGAAGAAGAAAGAAAAAG
1 AAGAAGAAGAAAGAAAAAG
53595205 AAG
1 AAG
53595208 GGGAGGAGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
17 5 0.10
18 3 0.06
19 23 0.48
20 3 0.06
21 7 0.15
22 7 0.15
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (19 bp):
AAGAAGAAGAAAGAAAAAG
Found at i:53595929 original size:133 final size:130
Alignment explanation
Indices: 53595791--53596486 Score: 399
Period size: 146 Copynumber: 4.9 Consensus size: 130
53595781 TATAAAAAAA
* *
53595791 TAAAAT-AT-GAAAATAATATATTTTAAAAAATAAAATCCGAAAATAAAAAAATACGAACAAGGT
1 TAAAATAATAGAAAATAATATATTTTAAAAAAT--AAT---AAAAGAAAAAAATACGAACAAAGT
* **
53595854 GCCAAAGTCAGGGTTATTTATTAAATTAATATAAAAAAAACTTAAATAATACATTTGAAAGATTT
61 GCCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAAACTTAAATAATACATTTGAAAGATTT
53595919 TATGC
126 TATGC
* * *
53595924 TAAAATAAAATACGAAAATAATATATTTTAAAAAATAATAGACGAAAAAAATACGAATAAAGTGC
1 TAAAAT--AATA-GAAAATAATATATTTTAAAAAATAATAAAAGAAAAAAATACGAACAAAGTGC
* * * * * *
53595989 TAAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTTAAATATTATG
63 CAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAAACTTAAATAATACATTTGAAAGATTTTA
*
53596054 TAC
128 TGC
* *
53596057 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAACAAA
1 TAAAAT-A-AT--AG----AAAAT-----AAT-ATAT-TTTAAAA-AAT-A-AT---AAAAGAAA
* * * ** *
53596122 AAAATACGAAGAAAGTGCCAAACTCAGGGTTATGTATTAAATTAATATAAAAAAAACACTTACAT
45 AAAATACGAACAAAGTGCCAAAATCAGGGTTATTTATTAAAAAAATAT-AAAAAAA-ACTTAAAT
* *
53596187 AATACATTTGAAACATTTTTTGC
108 AATACATTTGAAAGATTTTATGC
* * * *
53596210 TAAAATAATATAAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAAT
1 TAAAAT-A-AT------AGAAAAT-----AAT-ATAT-TTTAAAA-AATAATAAAAGAAAAAAAT
* * * *
53596275 ACGAATAAAGTGCTAAAATTAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACAT
50 ACGAACAAAGTGCCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAAACTTAAATAATACAT
* * * **
53596340 TTGAAATATTATGTAA
115 TTGAAAGATTTTATGC
**
53596356 TAAAATAATATAAAGAAATAAAATATGAAAATAATATTTTTTAAAA-AATAAGATACGAAAAAAA
1 TAAAAT-A-AT--AG-----AAA-AT---AAT-ATATTTTAAAAAATAATAA-A-A-GAAAAAAA
** * *
53596420 TACGAATTAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACA
49 TACGAACAAAGTGCCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAAACTTAAATAATACA
53596485 TT
114 TT
53596487 GTAAATAGTA
Statistics
Matches: 467, Mismatches: 56, Indels: 67
0.79 0.09 0.11
Matches are distributed among these distances:
132 2 0.00
133 93 0.20
134 1 0.00
135 1 0.00
136 5 0.01
138 28 0.06
142 3 0.01
143 7 0.01
144 7 0.01
145 12 0.03
146 123 0.26
147 10 0.02
148 50 0.11
151 49 0.10
152 7 0.01
153 66 0.14
157 3 0.01
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.29
Consensus pattern (130 bp):
TAAAATAATAGAAAATAATATATTTTAAAAAATAATAAAAGAAAAAAATACGAACAAAGTGCCAA
AATCAGGGTTATTTATTAAAAAAATATAAAAAAAACTTAAATAATACATTTGAAAGATTTTATGC
Found at i:53596099 original size:146 final size:146
Alignment explanation
Indices: 53595926--53596686 Score: 1026
Period size: 146 Copynumber: 5.1 Consensus size: 146
53595916 TTTTATGCTA
53595926 AAATAAAATACGAAAATAATATATTTTAAAAAATAATAGACGAAAAAAATACGAATAAAGTGCTA
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAATAGACGAAAAAAATACGAATAAAGTGCTA
*
53595991 AAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTTAAATATTATGTA
66 AAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTGAAATATTATGTA
53596056 CTAAAATAATATAAAG
131 CTAAAATAATATAAAG
*
53596072 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAC-AAAAAAATACGAAGAAA
1 AAATAAAATACGAAAATAATATATTTTAAAAAAT-A-ATA-G---ACGAAAAAAATACGAATAAA
* * * * * * *
53596136 GTGCCAAACTCAGGGTTATGTATTAAATTAATATAAAAAAAACACTTACATAATACATTTGAAAC
60 GTGCTAAAATCAGGGTTATTTATTAAA--AAAATATAAAAAACACTTAAATAATACATTTGAAAT
* * * *
53596201 ATTTTTTGCTAAAATAATATAAAA
123 ATTATGTACTAAAATAATATAAAG
*
53596225 AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTA
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAATAGACGAAAAAAATACGAATAAAGTGCTA
*
53596290 AAATTAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTGAAATATTATGTA
66 AAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTGAAATATTATGTA
*
53596355 ATAAAATAATATAAAG
131 CTAAAATAATATAAAG
* * * * *
53596371 AAATAAAATATGAAAATAATATTTTTTAAAAAATAAGATACGAAAAAAATACGAATTAAGTGCTA
1 AAATAAAATACGAAAATAATATATTTTAAAAAATAATAGACGAAAAAAATACGAATAAAGTGCTA
*
53596436 AAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACA-TTGTAAATAGTATGT
66 AAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTG-AAATATTATGT
*
53596500 ACTGAAATAATATAAAG
130 ACTAAAATAATATAAAG
*
53596517 AAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAC-AAAAAAATACGAAGAAA
1 AAATAAAATACGAAAATAATATATTTTAAAAAAT-A-ATA-G---ACGAAAAAAATACGAATAAA
* * * * * * *
53596581 GTGCCAAACTCAGGGTTATGTATTAAATTAATATAAAAAAAACACTTACATAATACATTTGAAAC
60 GTGCTAAAATCAGGGTTATTTATTAAA--AAAATATAAAAAACACTTAAATAATACATTTGAAAT
* * *
53596646 ATTTTTTGCTAAAATAATATAAA-
123 ATTATGTACTAAAATAATATAAAG
*
53596669 AAATAATATACGAAAATA
1 AAATAAAATACGAAAATA
53596687 TTTTACTTAT
Statistics
Matches: 541, Mismatches: 55, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
145 3 0.01
146 251 0.46
147 4 0.01
148 44 0.08
149 1 0.00
151 82 0.15
152 22 0.04
153 131 0.24
154 3 0.01
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (146 bp):
AAATAAAATACGAAAATAATATATTTTAAAAAATAATAGACGAAAAAAATACGAATAAAGTGCTA
AAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTGAAATATTATGTA
CTAAAATAATATAAAG
Found at i:53596241 original size:299 final size:292
Alignment explanation
Indices: 53595925--53596686 Score: 1062
Period size: 299 Copynumber: 2.6 Consensus size: 292
53595915 ATTTTATGCT
53595925 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATAGACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATAGACGAAAAAAATACGAATAAAGTGCT
*
53595990 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTTAAATATTATGT
66 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTGAAATATTATGT
53596055 ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAACA
131 ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACG-----A
* * *
53596120 AAAAAATACGAAGAAAGTGCCAAACTCAGGGTTATGTATTAAATTAATATAAAAAAAACACTTAC
191 AAAAAATACGAAGAAAGTGCCAAAATCAGGGTTATGTATTAAA--AAAATAAAAAAAACACTTAA
* * * *
53596185 ATAATACATT-TGAAACATTTTTTGCTAAAATAATATAAA
254 ATAATACATTGT-AAACAGTATGTACTAAAATAATATAAA
*
53596224 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATAGACGAAAAAAATACGAATAAAGTGCT
*
53596289 AAAATTAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTGAAATATTATGT
66 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTGAAATATTATGT
* * *
53596354 AATAAAATAATATAAAGAAATAAAATATGAAAATAATATTTTTTAAAAAATAAGATACGAAAAAA
131 ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAA
** * * *
53596419 ATACGAATTAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATAC
196 ATACGAAGAAAGTGCCAAAATCAGGGTTATGTATTAAAAAAATAAAAAAAACACTTAAATAATAC
* *
53596484 ATTGTAAATAGTATGTACTGAAATAATATAAA
261 ATTGTAAACAGTATGTACTAAAATAATATAAA
* *
53596516 GAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAC-AAAAAAATACGAAGAA
1 AAAATAAAATACGAAAATAATATATTTTAAAAAAT-A-ATA-G---ACGAAAAAAATACGAATAA
* * * * * *
53596580 AGTGCCAAACTCAGGGTTATGTATTAAATTAATATAAAAAAAACACTTACATAATACATTTGAAA
60 AGTGCTAAAATCAGGGTTATTTATTAAA--AAAATATAAAAAACACTTAAATAATACATTTGAAA
* * * * *
53596645 CATTTTTTGCTAAAATAATATAAA-AAATAATATACGAAAATA
123 TATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATA
53596687 TTTTACTTAT
Statistics
Matches: 417, Mismatches: 37, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
292 82 0.20
293 2 0.00
294 42 0.10
297 39 0.09
298 18 0.04
299 234 0.56
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (292 bp):
AAAATAAAATACGAAAATAATATATTTTAAAAAATAATAGACGAAAAAAATACGAATAAAGTGCT
AAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAATAATACATTTGAAATATTATGT
ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAA
ATACGAAGAAAGTGCCAAAATCAGGGTTATGTATTAAAAAAATAAAAAAAACACTTAAATAATAC
ATTGTAAACAGTATGTACTAAAATAATATAAA
Found at i:53596586 original size:445 final size:433
Alignment explanation
Indices: 53595765--53596686 Score: 1461
Period size: 445 Copynumber: 2.1 Consensus size: 433
53595755 GCTGAAGAGT
* * *
53595765 TTTTTTGTTAAAATAATATAAAAAAATAAAATATGAAAATAATATATTTTAAAAAATAAAATCCG
1 TTTTTTGCTAAAATAATATAAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACG
* * **
53595830 AAAATAAAAAAATACGAACAAGGTGCCAAAGTCAGGGTTATTTATTAAATTAATATAAAAAAAAC
66 ---A-AAAAAAATACGAACAAAGTGCCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAAAC
*
53595895 TTAAATAATACATTTGAAAGATTTTATGCTAAAATAAAATACGAAAATAATATATTTTAAAAAAT
127 TTAAATAATACATTTGAAAGATTTTATGATAAAATAAAATACGAAAATAATATATTTTAAAAAAT
*
53595960 AATAGACGAAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAA
192 AAGAGACGAAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAA
* *
53596025 CACTTAAATAATACATTTTAAATATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATA
257 CACTTAAATAATACATTGTAAATAGTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATA
53596090 ATATATTTTAAAAAATAAGATACGAAAACAAAAAAATACGAAGAAAGTGCCAAACTCAGGGTTAT
322 ATATATTTTAAAAAATAAGATACGAAAACAAAAAAATACGAAGAAAGTGCCAAACTCAGGGTTAT
53596155 GTATTAAATTAATATAAAAAAAACACTTACATAATACATTTGAAACA
387 GTATTAAATTAATATAAAAAAAACACTTACATAATACATTTGAAACA
*
53596202 TTTTTTGCTAAAATAATATAAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACG
1 TTTTTTGCTAAAATAATATAAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACG
* * * *
53596267 -AAAAAAATACGAATAAAGTGCTAAAATTAGGGTTATTTATTAAAAAAATATAAAAAACACTTAA
66 AAAAAAAATACGAACAAAGTGCCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAAACTTAA
* * * *
53596331 ATAATACATTTGAAATATTATGTAATAAAATAATATAAAGAAATAAAATATGAAAATAATATTTT
131 ATAATACATTTGAAAGA-T-T-T--T---AT--GAT--A-AAATAAAATACGAAAATAATATATT
* *
53596396 TTAAAAAATAAGATACGAAAAAAATACGAATTAAGTGCTAAAATCAGGGTTATTTATTAAAAAAA
183 TTAAAAAATAAGAGACGAAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAA
*
53596461 TATAAAAAACACTTAAATAATACATTGTAAATAGTATGTACTGAAATAATATAAAGAAATAAAAT
248 TATAAAAAACACTTAAATAATACATTGTAAATAGTATGTACTAAAATAATATAAAGAAATAAAAT
53596526 ACGAAAATAATATATTTTAAAAAATAAGATACGAAAACAAAAAAATACGAAGAAAGTGCCAAACT
313 ACGAAAATAATATATTTTAAAAAATAAGATACGAAAACAAAAAAATACGAAGAAAGTGCCAAACT
53596591 CAGGGTTATGTATTAAATTAATATAAAAAAAACACTTACATAATACATTTGAAACA
378 CAGGGTTATGTATTAAATTAATATAAAAAAAACACTTACATAATACATTTGAAACA
*
53596647 TTTTTTGCTAAAATAATAT-AAAAAATAATATACGAAAATA
1 TTTTTTGCTAAAATAATATAAAAAAATAAAATACGAAAATA
53596687 TTTTACTTAT
Statistics
Matches: 448, Mismatches: 24, Indels: 19
0.91 0.05 0.04
Matches are distributed among these distances:
432 72 0.16
433 1 0.00
434 1 0.00
435 1 0.00
437 62 0.14
440 2 0.00
442 1 0.00
444 21 0.05
445 287 0.64
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.29
Consensus pattern (433 bp):
TTTTTTGCTAAAATAATATAAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACG
AAAAAAAATACGAACAAAGTGCCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAAACTTAA
ATAATACATTTGAAAGATTTTATGATAAAATAAAATACGAAAATAATATATTTTAAAAAATAAGA
GACGAAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACT
TAAATAATACATTGTAAATAGTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATAT
ATTTTAAAAAATAAGATACGAAAACAAAAAAATACGAAGAAAGTGCCAAACTCAGGGTTATGTAT
TAAATTAATATAAAAAAAACACTTACATAATACATTTGAAACA
Found at i:53596843 original size:18 final size:17
Alignment explanation
Indices: 53596817--53596858 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
53596807 TATAAGTTAT
*
53596817 TCTAATAAATATTTAAAA
1 TCTAATAAACA-TTAAAA
*
53596835 TCTATTAAACATTAAAA
1 TCTAATAAACATTAAAA
53596852 T-TAATAA
1 TCTAATAA
53596859 TTGAAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 9 0.43
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (17 bp):
TCTAATAAACATTAAAA
Found at i:53598668 original size:72 final size:72
Alignment explanation
Indices: 53598546--53598686 Score: 246
Period size: 72 Copynumber: 2.0 Consensus size: 72
53598536 AGTCCGAGTG
* *
53598546 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACTATTTTTCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTTCCGG
53598611 GCTCGTC
66 GCTCGTC
* *
53598618 ATCGCATTCACATTCGGCTGATACTTCTTATCATCCGGATTTGGCGGGCAATGACAATTTTCCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTTCCGG
53598683 GCTC
66 GCTC
53598687 ATCGGGAGGC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (72 bp):
ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTTCCGG
GCTCGTC
Found at i:53604037 original size:20 final size:20
Alignment explanation
Indices: 53604012--53604058 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
53604002 CTAACAATGT
53604012 TAATAACAAA-CAACAAAAAA
1 TAATAACAAATCAAC-AAAAA
*
53604032 TAATAA-AAATCAACAATAA
1 TAATAACAAATCAACAAAAA
53604051 TAATAACA
1 TAATAACA
53604059 GCAAAAACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (20 bp):
TAATAACAAATCAACAAAAA
Found at i:53604131 original size:16 final size:17
Alignment explanation
Indices: 53604110--53604164 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
53604100 AAATTATACC
* *
53604110 TTCTTTTTT-CTTTTCT
1 TTCTTTTTTCCTTCTCG
53604126 TTCTTTTTTCCTTCTCG
1 TTCTTTTTTCCTTCTCG
53604143 TTCTTTTTCTTCCTTCTC-
1 TTC-TTTT-TTCCTTCTCG
53604161 TTCT
1 TTCT
53604165 CCTTTCTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 9 0.26
17 9 0.26
18 7 0.21
19 9 0.26
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (17 bp):
TTCTTTTTTCCTTCTCG
Found at i:53604157 original size:19 final size:17
Alignment explanation
Indices: 53604109--53604164 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
53604099 AAAATTATAC
*
53604109 CTTC-TTTTTT-CTTTT
1 CTTCTTTTTTTCCTTCT
53604124 CTT-TCTTTTTTCCTTCT
1 CTTCT-TTTTTTCCTTCT
53604141 CGTTCTTTTTCTTCCTTCT
1 C-TTCTTTTT-TTCCTTCT
53604160 CTTCT
1 CTTCT
53604165 CCTTTCTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 3 0.09
16 6 0.18
17 5 0.15
18 10 0.29
19 10 0.29
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.70
Consensus pattern (17 bp):
CTTCTTTTTTTCCTTCT
Found at i:53604170 original size:19 final size:19
Alignment explanation
Indices: 53604127--53604172 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
53604117 TTCTTTTCTT
*
53604127 TCTTTTTTCCTTCTCGTTC
1 TCTTTCTTCCTTCTCGTTC
*
53604146 TTTTTCTTCCTTCTC-TTC
1 TCTTTCTTCCTTCTCGTTC
53604164 TCCTTTCTT
1 T-CTTTCTT
53604173 TCCCTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (19 bp):
TCTTTCTTCCTTCTCGTTC
Found at i:53604335 original size:19 final size:18
Alignment explanation
Indices: 53604311--53604353 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
53604301 CCATTTTTTA
53604311 TTTTTTTTCGTTTTCAGT
1 TTTTTTTTCGTTTTCAGT
*
53604329 GTTTTTTTTCTTTTTCAGT
1 -TTTTTTTTCGTTTTCAGT
53604348 TTTTTT
1 TTTTTT
53604354 ACTGTTGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.05, C:0.09, G:0.09, T:0.77
Consensus pattern (18 bp):
TTTTTTTTCGTTTTCAGT
Found at i:53608798 original size:18 final size:18
Alignment explanation
Indices: 53608749--53608824 Score: 91
Period size: 18 Copynumber: 4.2 Consensus size: 18
53608739 TCCCAACTAT
*
53608749 TGTATACGTGAACAGTAC
1 TGTATACGTGAATAGTAC
*
53608767 TGTATACGTAAATAGTAC
1 TGTATACGTGAATAGTAC
*
53608785 TGTATACGTGAATAGT-G
1 TGTATACGTGAATAGTAC
* *
53608802 TCATATACGTGAATAGTGC
1 T-GTATACGTGAATAGTAC
53608821 TGTA
1 TGTA
53608825 AATGGTCGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
17 1 0.02
18 47 0.96
19 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (18 bp):
TGTATACGTGAATAGTAC
Found at i:53619446 original size:24 final size:24
Alignment explanation
Indices: 53619400--53619448 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
53619390 TCTTTAATTC
* *
53619400 AGAATTTAATTTTTTATTATTTTA
1 AGAATTTAATTTTATAATATTTTA
*
53619424 AGAATTTAATTTCTATAATTTTTTA
1 AGAATTTAATTT-TATAATATTTTA
53619449 TTAATCTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (24 bp):
AGAATTTAATTTTATAATATTTTA
Found at i:53622411 original size:116 final size:118
Alignment explanation
Indices: 53622303--53622522 Score: 374
Period size: 118 Copynumber: 1.9 Consensus size: 118
53622293 AAATCTATTT
*
53622303 TTTAGTTATTTTAAAAGAAAGTTTAAATTTTT-AAATAAAGTTTTGA-TTTTTTTCAACTATTTC
1 TTTAGTTATTTTAAAAGAAAGTTTAAATTTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTC
*
53622366 AAATTAA-AAGCTTTAATCTTTAAGAAAAATAGTATTTTTAAAAAAAAATAAAG
66 AAAGTAAGAA-CTTTAATCTTTAAGAAAAATAGTATTTTTAAAAAAAAATAAAG
*
53622419 TTTAGTTATTTTAAAGGAAAGTTTAAATTTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTC
1 TTTAGTTATTTTAAAAGAAAGTTTAAATTTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTC
*
53622484 AAAGTAAGAACTTTAATCTTTAAGAAAAATAGTGTTTTT
66 AAAGTAAGAACTTTAATCTTTAAGAAAAATAGTATTTTT
53622523 TTTAAAAGGA
Statistics
Matches: 97, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
116 31 0.32
117 13 0.13
118 51 0.53
119 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (118 bp):
TTTAGTTATTTTAAAAGAAAGTTTAAATTTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTC
AAAGTAAGAACTTTAATCTTTAAGAAAAATAGTATTTTTAAAAAAAAATAAAG
Found at i:53627167 original size:18 final size:17
Alignment explanation
Indices: 53627115--53627230 Score: 53
Period size: 16 Copynumber: 6.6 Consensus size: 17
53627105 CGTGATCCAA
*
53627115 TTGAAACACGAGA-ATT
1 TTGAAACACGAAATATT
* *
53627131 TTGAAACAC-AACCTTTT
1 TTGAAACACGAA-ATATT
53627148 TTCGAAACACGAAATATT
1 TT-GAAACACGAAATATT
* *
53627166 TTAAAATAC-AAGA-ATT
1 TTGAAACACGAA-ATATT
* *
53627182 TTAGAAACACGAATTTTTT
1 TT-GAAACACGAA-ATATT
*
53627201 TTAAAAAAACACGAAA-ATT
1 TT---GAAACACGAAATATT
53627220 TTGAAACACGA
1 TTGAAACACGA
53627231 GAATTTTTTT
Statistics
Matches: 74, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
15 1 0.01
16 24 0.32
17 15 0.20
18 14 0.19
19 10 0.14
21 10 0.14
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (17 bp):
TTGAAACACGAAATATT
Found at i:53627228 original size:16 final size:16
Alignment explanation
Indices: 53627207--53627237 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53627197 TTTTTTAAAA
53627207 AAACACGAAAATTTTG
1 AAACACGAAAATTTTG
*
53627223 AAACACGAGAATTTT
1 AAACACGAAAATTTT
53627238 TTTTTTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (16 bp):
AAACACGAAAATTTTG
Found at i:53627249 original size:39 final size:38
Alignment explanation
Indices: 53627178--53627301 Score: 110
Period size: 39 Copynumber: 3.2 Consensus size: 38
53627168 AAAATACAAG
***
53627178 AATTTTAGAAACAC-GAATTTTTTTTAAAAAAACACGAA
1 AATTTT-GAAACACAGAATTTTTTTTTTGAAAACACGAA
53627216 AATTTTGAAACACGAGAATTTTTTTTTTGAAAACACGAA
1 AATTTTGAAACAC-AGAATTTTTTTTTTGAAAACACGAA
* * * * *
53627255 TTTTATTTTTAAA-ACACAA-TTTTATTTTGAAAACACAAA
1 ---AATTTTGAAACACAGAATTTTTTTTTTGAAAACACGAA
53627294 AATTTTGA
1 AATTTTGA
53627302 TAAATTATGA
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
36 6 0.08
37 7 0.10
38 6 0.08
39 39 0.55
40 3 0.04
41 2 0.03
42 8 0.11
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (38 bp):
AATTTTGAAACACAGAATTTTTTTTTTGAAAACACGAA
Found at i:53627255 original size:21 final size:21
Alignment explanation
Indices: 53627218--53627290 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
53627208 AACACGAAAA
53627218 TTTTG-AAACACGAGAATTTTTT
1 TTTTGAAAACAC--GAATTTTTT
*
53627240 TTTTGAAAACACGAATTTTAT
1 TTTTGAAAACACGAATTTTTT
*
53627261 TTTT-AAAACAC-AA-TTTTA
1 TTTTGAAAACACGAATTTTTT
53627279 TTTTGAAAACAC
1 TTTTGAAAACAC
53627291 AAAAATTTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 7 0.15
19 9 0.20
20 7 0.15
21 12 0.26
22 5 0.11
23 6 0.13
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (21 bp):
TTTTGAAAACACGAATTTTTT
Found at i:53627257 original size:37 final size:36
Alignment explanation
Indices: 53627146--53627259 Score: 99
Period size: 39 Copynumber: 3.1 Consensus size: 36
53627136 ACACAACCTT
* * * * *
53627146 TTTTCGAAACACGAA-ATATTTT-AAAATACAAGAA
1 TTTTAGAAACACGAATTTTTTTTAAAAAAACACGAA
53627180 TTTTAGAAACACGAATTTTTTTTAAAAAAACACGAAAA
1 TTTTAGAAACACGAATTTTTTTTAAAAAAACACG--AA
***
53627218 TTTT-GAAACACGAGAATTTTTTTTTTGAAAACACGAA
1 TTTTAGAAACAC--GAATTTTTTTTAAAAAAACACGAA
53627255 TTTTA
1 TTTTA
53627260 TTTTTAAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
34 14 0.22
35 5 0.08
36 8 0.12
37 13 0.20
38 6 0.09
39 19 0.29
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.35
Consensus pattern (36 bp):
TTTTAGAAACACGAATTTTTTTTAAAAAAACACGAA
Found at i:53627258 original size:19 final size:19
Alignment explanation
Indices: 53627235--53627292 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
53627225 ACACGAGAAT
*
53627235 TTTTTTTTTGAAAACACGAA
1 TTTTATTTTGAAAACAC-AA
*
53627255 TTTTATTTTTAAAACACAA
1 TTTTATTTTGAAAACACAA
53627274 TTTTATTTTGAAAACACAA
1 TTTTATTTTGAAAACACAA
53627293 AAATTTTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (19 bp):
TTTTATTTTGAAAACACAA
Found at i:53627379 original size:18 final size:17
Alignment explanation
Indices: 53627361--53627755 Score: 143
Period size: 17 Copynumber: 21.9 Consensus size: 17
53627351 CAATGTCAAT
53627361 TTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
* *
53627378 TTTTTTGAAAGTCGA-GAAT
1 -TTTTTGAAA-AC-ACGAAA
*
53627397 TTTTTGAAAACACGGAGA
1 TTTTTGAAAACAC-GAAA
* *
53627415 TTTAT-AAAACACGGAAGTTTT
1 TTTTTGAAAACAC-GAA----A
* **
53627436 TTTTTGAAAAAAAAAAA
1 TTTTTGAAAACACGAAA
*
53627453 TTTTTG-AAATACGAGAA
1 TTTTTGAAAACACGA-AA
*
53627470 TTTTTGAAAACAGGGGAAA
1 TTTTTGAAAACA--CGAAA
*
53627489 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACG-AAA
*
53627507 TTTTTG-AAACACTAGAA
1 TTTTTGAAAACACGA-AA
53627524 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAA-A
*
53627541 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGA-AA
*
53627558 TTTTTGAAAACACGAGGAT
1 TTTTTGAAAACACGA--AA
*
53627577 TTTTTG-AAATACGAACA
1 TTTTTGAAAACACGAA-A
* *
53627594 TTTTAG-AAACATGAAAA
1 TTTTTGAAAACACG-AAA
*
53627611 TTTTT-AAAACATGACAA
1 TTTTTGAAAACACGA-AA
53627628 TTTTTG-AAACACGAGAAATTTA
1 TTTTTGAAAACAC--G-AA---A
* **
53627650 TTTTTTAAAACATAAAAAA
1 TTTTTGAAAAC--ACGAAA
*
53627669 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-TGAAAACACG-AAA
*
53627690 TTTTTG-AAACACTAGAA
1 TTTTTGAAAACACGA-AA
53627707 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAA-A
*
53627724 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGA-AA
53627741 TTTTT-AAAAGCACGA
1 TTTTTGAAAA-CACGA
53627756 GGATTATTGA
Statistics
Matches: 289, Mismatches: 42, Indels: 92
0.68 0.10 0.22
Matches are distributed among these distances:
16 22 0.08
17 120 0.42
18 71 0.25
19 33 0.11
20 6 0.02
21 13 0.04
22 19 0.07
23 4 0.01
25 1 0.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (17 bp):
TTTTTGAAAACACGAAA
Found at i:53627471 original size:17 final size:17
Alignment explanation
Indices: 53627451--53627767 Score: 167
Period size: 17 Copynumber: 17.6 Consensus size: 17
53627441 GAAAAAAAAA
*
53627451 AATTTTTGAAATACGAG
1 AATTTTTGAAACACGAG
* *
53627468 AATTTTTGAAAACAGGGG
1 AATTTTTG-AAACACGAG
* *
53627486 AAATTTTTGAAAACATGAA
1 -AATTTTTG-AAACACGAG
*
53627505 AATTTTTGAAACACTAG
1 AATTTTTGAAACACGAG
53627522 AA-TTTTGAAAACACGA-
1 AATTTTTG-AAACACGAG
*
53627538 AGATTTTTGAAACATGAG
1 A-ATTTTTGAAACACGAG
53627556 AATTTTTGAAAACACGAGG
1 AATTTTTG-AAACACGA-G
* *
53627575 ATTTTTTGAAATACGA-
1 AATTTTTGAAACACGAG
* * *
53627591 ACATTTTAGAAACATGAA
1 A-ATTTTTGAAACACGAG
* * *
53627609 AATTTTTAAAACATGAC
1 AATTTTTGAAACACGAG
53627626 AATTTTTGAAACACGAG
1 AATTTTTGAAACACGAG
* ** *
53627643 AAATTTATTTTTTAAAACATAAAA
1 --A---A-TTTTTGAAACA-CGAG
* *
53627667 AATTTTTTCTGAAAACAAGAA
1 AA--TTTT-TG-AAACACGAG
*
53627688 AATTTTTGAAACACTAG
1 AATTTTTGAAACACGAG
53627705 AA-TTTTGAAAACACGA-
1 AATTTTTG-AAACACGAG
*
53627721 AGATTTTTGAAACATGAG
1 A-ATTTTTGAAACACGAG
*
53627739 AATTTTTAAAAGCACGAG
1 AATTTTTGAAA-CACGAG
* *
53627757 GATTATTGAAA
1 AATTTTTGAAA
53627768 TTACAATTTT
Statistics
Matches: 235, Mismatches: 40, Indels: 49
0.73 0.12 0.15
Matches are distributed among these distances:
16 13 0.06
17 108 0.46
18 56 0.24
19 29 0.12
20 5 0.02
21 6 0.03
22 7 0.03
23 10 0.04
24 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (17 bp):
AATTTTTGAAACACGAG
Found at i:53627712 original size:16 final size:16
Alignment explanation
Indices: 53627691--53627744 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
53627681 ACAAGAAAAT
53627691 TTTTGAAACACTAGAA
1 TTTTGAAACACTAGAA
* *
53627707 TTTTGAAAACACGAAGAT
1 TTTTG-AAACAC-TAGAA
53627725 TTTTGAAACA-TGAGAA
1 TTTTGAAACACT-AGAA
53627741 TTTT
1 TTTT
53627745 TAAAAGCACG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 12 0.39
17 11 0.35
18 8 0.26
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (16 bp):
TTTTGAAACACTAGAA
Found at i:53628118 original size:10 final size:9
Alignment explanation
Indices: 53628103--53628155 Score: 63
Period size: 10 Copynumber: 5.7 Consensus size: 9
53628093 ATTGAACCCC
53628103 TTTTTTCTT
1 TTTTTTCTT
53628112 GTTTTTTC-T
1 -TTTTTTCTT
53628121 TTTTTTCTT
1 TTTTTTCTT
*
53628130 TTTCTCTCTT
1 TTT-TTTCTT
53628140 TTTTTTCTCT
1 TTTTTTCT-T
53628150 TTTTTT
1 TTTTTT
53628156 TCTGCTGGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 7 0.18
9 9 0.24
10 22 0.58
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTCTT
Done.