Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold171
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: 2364178
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 278680 characters in sequence are not A, C, G, or T
File 11 of 13
Found at i:1751945 original size:76 final size:77
Alignment explanation
Indices: 1751760--1751956 Score: 315
Period size: 76 Copynumber: 2.5 Consensus size: 77
1751750 GATTGTGGAG
* *
1751760 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATTCTCCTCAAAAATAACAGGGTTGGAGTA
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTA-TCCCCTCAAAAATAACAGGGTTGGAGTA
1751825 TCCCCGATTATGAAA
65 TCCCCG--TATGAAA
* *
1751840 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTAT
1751905 CCCCG-ATGAAA
66 CCCCGTATGAAA
*
1751916 AATTGATGTTTTAGAAATAAAACCAGGGTTGGAGTATCCCC
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1751957 GATTAAGAAA
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
76 46 0.41
79 31 0.28
80 35 0.31
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (77 bp):
AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTAT
CCCCGTATGAAA
Found at i:1754323 original size:20 final size:19
Alignment explanation
Indices: 1754274--1754329 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1754264 AATACATTTT
1754274 AAAATGTATCGATACAATG
1 AAAATGTATCGATACAATG
*
1754293 AGCAATGTATCGATACAATG
1 A-AAATGTATCGATACAATG
*
1754313 CAAAATCTATCGATACA
1 -AAAATGTATCGATACA
1754330 TCTGGGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (19 bp):
AAAATGTATCGATACAATG
Found at i:1754382 original size:20 final size:20
Alignment explanation
Indices: 1754356--1754412 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1754346 ATGTATTGAT
1754356 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
1754376 GCAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
1754396 ACAATGTATCGATACAA
1 ACAATGTATCGATACAA
1754413 ATTGTGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:1754393 original size:13 final size:13
Alignment explanation
Indices: 1754345--1754374 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1754335 GTAAAGCCAG
*
1754345 AATGTATTGATAC
1 AATGTATCGATAC
1754358 AATGTATCGATAC
1 AATGTATCGATAC
1754371 AATG
1 AATG
1754375 AGCAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1755234 original size:45 final size:44
Alignment explanation
Indices: 1755100--1755284 Score: 160
Period size: 42 Copynumber: 4.4 Consensus size: 44
1755090 AAAAAGAGTA
* * *
1755100 CGTCCTGCT-TTTCGAGGA-TAAAGGAAAA-AAGAAAATGAAATG
1 CGTCCTGCTCTTT-GAGGACAAAAGGAAAAGAAGGAAATGAAGTG
* **
1755142 CGTCCTGCTCTTTAAGGACAAAA-G-AAAG-AGGAAAACAAAGTG
1 CGTCCTGCTCTTTGAGGACAAAAGGAAAAGAAGG-AAATGAAGTG
*
1755184 CGTCCTGCTCTTTGAGGACAAAATGGAAAAGAAGGGAATGAAGTG
1 CGTCCTGCTCTTTGAGGACAAAA-GGAAAAGAAGGAAATGAAGTG
* * *
1755229 TGTCCTGCTCTTTGATGAC-AAAGGAGAA-AAGG-AA--AAG-G
1 CGTCCTGCTCTTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTG
*
1755267 CATCCTGCTCTTTGAGGA
1 CGTCCTGCTCTTTGAGGA
1755285 ATAAAAAGTG
Statistics
Matches: 119, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
38 16 0.13
39 3 0.03
41 7 0.06
42 47 0.39
43 11 0.09
44 4 0.03
45 28 0.24
46 3 0.03
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.21
Consensus pattern (44 bp):
CGTCCTGCTCTTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTG
Found at i:1755249 original size:87 final size:84
Alignment explanation
Indices: 1755100--1755264 Score: 199
Period size: 87 Copynumber: 1.9 Consensus size: 84
1755090 AAAAAGAGTA
*
1755100 CGTCCTGCTTTTCGAGGATAAAGGAAAAAAGAAAATGAAATGCGTCCTGCTCTTTAAGGACAAA-
1 CGTCCTGCTTTTCGAGGAAAAAGGAAAAAAGAAAATGAAATGCGTCCTGCTCTTTAAGGACAAAG
1755164 AGAAAGAGGAAAACAAAGTG
66 AGAAA-AGGAAAACAAAGTG
** * * * *
1755184 CGTCCTGCTCTTT-GAGGACAAAATGGAAAAGAAGGGAATGAAGTGTGTCCTGCTCTTTGATGAC
1 CGTCCTGCT-TTTCGAGGA-AAAA-GGAAAA-AAGAAAATGAAATGCGTCCTGCTCTTTAAGGAC
1755248 AAAGGAGAAAAGGAAAA
62 AAA-GAGAAAAGGAAAA
1755265 GGCATCCTGC
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
84 14 0.21
85 6 0.09
86 6 0.09
87 30 0.44
88 7 0.10
89 5 0.07
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.20
Consensus pattern (84 bp):
CGTCCTGCTTTTCGAGGAAAAAGGAAAAAAGAAAATGAAATGCGTCCTGCTCTTTAAGGACAAAG
AGAAAAGGAAAACAAAGTG
Found at i:1755437 original size:60 final size:59
Alignment explanation
Indices: 1755255--1755441 Score: 234
Period size: 61 Copynumber: 3.1 Consensus size: 59
1755245 GACAAAGGAG
* ** **
1755255 AAAAGGAAAAGGCATCCTGCTCTTTGAGGAATAAAAAGTGCCACCAACTCATGTGGGCTTT
1 AAAA-GAAAAGGCATCCTGCTCTTTGAGG-ACAGGAAGTGCCACCAACTTGTGTGGGCTTT
* *
1755316 GAAAAGAAAAGGCATCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
1 -AAAAGAAAAGGCATCCTGCTCTTTGAGGACAGGAA-GTGCCACCAACTTGTGTGGGCTTT
1755377 ACAAAGAGAAA-GCATCCTGCT-TCTTGAGGACAGGAAGTGCCACCAACTTGTGTGGGCTTT
1 A-AAAGA-AAAGGCATCCTGCTCT-TTGAGGACAGGAAGTGCCACCAACTTGTGTGGGCTTT
1755437 AAAAG
1 AAAAG
1755442 GCGTCCTGCT
Statistics
Matches: 112, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
59 4 0.04
60 30 0.27
61 71 0.63
62 7 0.06
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (59 bp):
AAAAGAAAAGGCATCCTGCTCTTTGAGGACAGGAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:1755699 original size:55 final size:55
Alignment explanation
Indices: 1755481--1755923 Score: 600
Period size: 55 Copynumber: 8.0 Consensus size: 55
1755471 AAAGGAGAGA
* * *** * * *
1755481 GCGTCCTACTCTTTGAGGATTGGGAAGTGCCACCAACTTGGGTGGGCTTCGAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* *
1755536 GCATCCTACTCTTTGAGGACTAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACT-AAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
*
1755592 GCGTCCTGCTCTTTGAGGACAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGAC-TAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* * * *
1755648 GCATCCTGCTTTTTGAGGACTGAAAAATGCCACCGACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* **
1755703 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
*
1755758 GCGTCCTGCTCTTTGAGGACTAAAAAATGCCACCGACTTGTGTGGG-TTTGGAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTT-GAAAG
* ** *
1755813 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTTTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* * ** *
1755868 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCGTCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1755923 G
1 G
1755924 AAAAAGCAAC
Statistics
Matches: 349, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
54 3 0.01
55 245 0.70
56 101 0.29
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (55 bp):
GCGTCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:1755976 original size:39 final size:40
Alignment explanation
Indices: 1755919--1755994 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
1755909 GTGGGCTTTA
1755919 AAAGGAAAAAGCAACCTGCTCTTTGAGGACTA-AAGGGTG
1 AAAGGAAAAAGCAACCTGCTCTTTGAGGACTAGAAGGGTG
* *
1755958 AAAGGAGAAAGCATCCTGCTCTTTGAGGACTAGAAGG
1 AAAGGAAAAAGCAACCTGCTCTTTGAGGACTAGAAGG
1755995 TGCCACCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 30 0.88
40 4 0.12
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (40 bp):
AAAGGAAAAAGCAACCTGCTCTTTGAGGACTAGAAGGGTG
Found at i:1756041 original size:100 final size:100
Alignment explanation
Indices: 1755863--1756268 Score: 636
Period size: 100 Copynumber: 4.0 Consensus size: 100
1755853 TGTGGGCTTT
1755863 GAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
1 GAAA-GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
*
1755928 -AGCAACCTGCTCTTTGAGGACTAAAGGGTGAAAGGA
65 GA-CATCCTGCTCTTTGAGGACTAAAGGGTGAAAGGA
1755964 GAAAGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GAAAGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
*
1756029 ACGTCCTGCTCTTTGAGGACTAAAGGGTGAAAGGA
66 ACATCCTGCTCTTTGAGGACTAAAGGGTGAAAGGA
* * * *
1756064 GAGATCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GAAAGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* *
1756129 GCGTCCTGCTCTTTGAGGACTAAAGGGTGAAAGGA
66 ACATCCTGCTCTTTGAGGACTAAAGGGTGAAAGGA
* * * *
1756164 GAGAGCGTCCTGCTCTTTGAGCACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAACG
1 GAAAGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * *
1756229 GCATCCTACTCTTTGAGGACTGAAA-AGTGAAAGGA
66 ACATCCTGCTCTTTGAGGACT-AAAGGGTGAAAGGA
1756264 GAAAG
1 GAAAG
1756269 TTTAGATACC
Statistics
Matches: 288, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
100 280 0.97
101 8 0.03
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (100 bp):
GAAAGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
ACATCCTGCTCTTTGAGGACTAAAGGGTGAAAGGA
Found at i:1756163 original size:39 final size:40
Alignment explanation
Indices: 1756119--1756194 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
1756109 GTGGGCTTTA
*
1756119 AAAGGAAA-AGGCGTCCTGCTCTTTGAGGACTA-AAGGGTG
1 AAAGGAAAGA-GCGTCCTGCTCTTTGAGCACTAGAAGGGTG
*
1756158 AAAGGAGAGAGCGTCCTGCTCTTTGAGCACTAGAAGG
1 AAAGGAAAGAGCGTCCTGCTCTTTGAGCACTAGAAGG
1756195 TGCCACCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 28 0.85
40 5 0.15
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.20
Consensus pattern (40 bp):
AAAGGAAAGAGCGTCCTGCTCTTTGAGCACTAGAAGGGTG
Found at i:1757265 original size:18 final size:18
Alignment explanation
Indices: 1757222--1757285 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
1757212 GTAGGTTCTT
* *
1757222 TTTTTTTTCTCTTTTTT-C
1 TTTTTTTTGT-TTTTTTGA
*
1757240 TTTGTTTTGTTTTTTTGA
1 TTTTTTTTGTTTTTTTGA
*
1757258 TTTTTTTTGTTGGTTTTTGG
1 TTTTTTTTGTT--TTTTTGA
1757278 TTTTTTTT
1 TTTTTTTT
1757286 TTGAAAAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
17 6 0.16
18 18 0.47
20 14 0.37
ACGTcount: A:0.02, C:0.05, G:0.12, T:0.81
Consensus pattern (18 bp):
TTTTTTTTGTTTTTTTGA
Found at i:1767546 original size:32 final size:33
Alignment explanation
Indices: 1767486--1767550 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1767476 CACACCCAGA
* *
1767486 TGTATCGATACATGCTGCTTTGTATTGATACAT
1 TGTATCAATACATGCTGCATTGTATTGATACAT
*
1767519 TGTATCAATACATG-TTCATTGTATTGATACAT
1 TGTATCAATACATGCTGCATTGTATTGATACAT
1767551 GGACAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCAATACATGCTGCATTGTATTGATACAT
Found at i:1767638 original size:13 final size:13
Alignment explanation
Indices: 1767617--1767647 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1767607 CGATACATGG
*
1767617 TACAATGTATCGA
1 TACATTGTATCGA
1767630 TACATTGTATCGA
1 TACATTGTATCGA
1767643 TACAT
1 TACAT
1767648 AAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1773688 original size:13 final size:13
Alignment explanation
Indices: 1773670--1773698 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1773660 ACAACATTCC
1773670 TTGTATCGATACA
1 TTGTATCGATACA
1773683 TTGTATCGATACA
1 TTGTATCGATACA
1773696 TTG
1 TTG
1773699 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1775555 original size:18 final size:19
Alignment explanation
Indices: 1775522--1775557 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1775512 AAATTTTTAT
*
1775522 ATATAAAAAGGGGGAGAAG
1 ATATAAAAAGGAGGAGAAG
1775541 ATATAAAAA-GAGGAGAA
1 ATATAAAAAGGAGGAGAA
1775558 TTTTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.11
Consensus pattern (19 bp):
ATATAAAAAGGAGGAGAAG
Found at i:1776164 original size:13 final size:13
Alignment explanation
Indices: 1776146--1776172 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1776136 ACATGCTGCT
1776146 TTGTATCGATACA
1 TTGTATCGATACA
1776159 TTGTATCGATACA
1 TTGTATCGATACA
1776172 T
1 T
1776173 GTTCATTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1776169 original size:33 final size:32
Alignment explanation
Indices: 1776127--1776191 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1776117 CACACCCAGA
*
1776127 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTGTATCGATACAT
* *
1776160 TGTATCGATACATGTTCATTGTGTCGATACAT
1 TGTATCGATACATGTGCATTGTATCGATACAT
1776192 GGACAAACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATACAT
Found at i:1778016 original size:21 final size:21
Alignment explanation
Indices: 1777991--1778077 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 21
1777981 TCCTCCACCA
1777991 AAAAAAAACAGAAGA-AAAAAAG
1 AAAAAAAACA-AA-ACAAAAAAG
1778013 AAAAAAAACAAAACAAAAAAG
1 AAAAAAAACAAAACAAAAAAG
1778034 AAAAAAAACAAACAACAAAAAA-
1 AAAAAAAAC-AA-AACAAAAAAG
1778056 AAAACAACAACAACAACAAAAA
1 AAAA-AA-AACAA-AACAAAAA
1778078 GGGTCCGGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.02
21 18 0.30
22 16 0.27
23 22 0.37
24 3 0.05
ACGTcount: A:0.83, C:0.13, G:0.05, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAACAAAAAAG
Found at i:1778016 original size:22 final size:20
Alignment explanation
Indices: 1777991--1778065 Score: 89
Period size: 21 Copynumber: 3.5 Consensus size: 20
1777981 TCCTCCACCA
1777991 AAAAAAAACAGAAGAAAAAAAG
1 AAAAAAAACA-AA-AAAAAAAG
1778013 AAAAAAAACAAAACAAAAAAG
1 AAAAAAAACAAAA-AAAAAAG
1778034 AAAAAAAACAAACAACAAAAA-
1 AAAAAAAACAAA-AA-AAAAAG
*
1778055 AAAAACAACAA
1 AAAAAAAACAA
1778066 CAACAACAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
20 1 0.02
21 32 0.65
22 16 0.33
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAAAAG
Found at i:1778025 original size:14 final size:14
Alignment explanation
Indices: 1778007--1778065 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
1777997 AACAGAAGAA
*
1778007 AAAAAGAAAAAAAAC
1 AAAAA-AAAAACAAC
*
1778022 AAAACAAAAAAGAA-
1 AAAA-AAAAAACAAC
*
1778036 AAAAAACAAACAAC
1 AAAAAAAAAACAAC
1778050 AAAAAAAAAACAAC
1 AAAAAAAAAACAAC
1778064 AA
1 AA
1778066 CAACAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
13 7 0.18
14 19 0.50
15 11 0.29
16 1 0.03
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAC
Found at i:1778067 original size:20 final size:20
Alignment explanation
Indices: 1778013--1778077 Score: 82
Period size: 20 Copynumber: 3.2 Consensus size: 20
1778003 AGAAAAAAAG
1778013 AAAAAAAACAA-AACAA-AA
1 AAAAAAAACAACAACAACAA
1778031 AAGAAAAAA-AACAAACAACAA
1 AA-AAAAAACAAC-AACAACAA
1778052 AAAAAAAACAACAACAACAA
1 AAAAAAAACAACAACAACAA
1778072 CAAAAA
1 -AAAAA
1778078 GGGTCCGGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.10
19 6 0.15
20 19 0.46
21 12 0.29
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAACAACAACAA
Found at i:1778076 original size:17 final size:18
Alignment explanation
Indices: 1778015--1778068 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
1778005 AAAAAAAGAA
1778015 AAAAAACAAAACAAA-AA-
1 AAAAAA-AAAACAAACAAC
*
1778032 AGAAAAAAAACAAACAAC
1 AAAAAAAAAACAAACAAC
1778050 AAAAAAAAAAC-AACAAC
1 AAAAAAAAAACAAACAAC
1778067 AA
1 AA
1778069 CAACAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 8 0.24
17 15 0.45
18 10 0.30
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAACAAACAAC
Found at i:1778077 original size:1 final size:1
Alignment explanation
Indices: 1777990--1778059 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
1777980 GTCCTCCACC
* * * * * * * * * *
1777990 AAAAAAAAACAGAAGAAAAAAAGAAAAAAAACAAAACAAAAAAGAAAAAAAACAAACAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1778055 AAAAA
1 AAAAA
1778060 CAACAACAAC
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.86, C:0.09, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:1779553 original size:29 final size:29
Alignment explanation
Indices: 1779514--1779687 Score: 208
Period size: 29 Copynumber: 6.0 Consensus size: 29
1779504 TCACCCTTCA
1779514 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1779543 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1779572 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1779599 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
1779629 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1779658 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1779688 TTTTGTAAGC
Statistics
Matches: 124, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
27 22 0.18
28 1 0.01
29 74 0.60
30 27 0.22
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:1779636 original size:86 final size:86
Alignment explanation
Indices: 1779508--1779678 Score: 254
Period size: 86 Copynumber: 2.0 Consensus size: 86
1779498 CATTCCTCAC
* * * *
1779508 CCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTCA
1 CCTTCAAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
*
1779573 AAGTCCACAAGTCAGTGGCAA
66 AAGTCCACAACTCAGTGGCAA
* *
1779594 CCTTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGCATCTTTTCC
1 CCTTCAAAAGCCCACAAATCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
*
1779658 AAAGTCCACAACTCCGTGGCA
65 AAAGTCCACAACTCAGTGGCA
1779679 CTCTTTTTCT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
85 20 0.26
86 56 0.74
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.23
Consensus pattern (86 bp):
CCTTCAAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
AAGTCCACAACTCAGTGGCAA
Found at i:1779737 original size:34 final size:35
Alignment explanation
Indices: 1779663--1779737 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1779653 TTTCCAAAGT
* *
1779663 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
*
1779698 TCACAACTCCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
1779732 CCACAA
1 CCACAA
1779738 GTTAGTGGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.35
Consensus pattern (35 bp):
CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
Found at i:1779754 original size:34 final size:35
Alignment explanation
Indices: 1779663--1779754 Score: 105
Period size: 35 Copynumber: 2.7 Consensus size: 35
1779653 TTTCCAAAGT
* *
1779663 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCAGTGGCACTCTTTTTCCTTTGTAAGC
* * *
1779698 TCACAACTCCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCAGTGGCACTCTTTTTCCTTTGTAAGC
* * *
1779732 CCACAAGTTAGTGGCACCCTTTT
1 CCACAACTCAGTGGCACTCTTTT
1779755 CTAAAGCCCA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
34 22 0.46
35 26 0.54
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.36
Consensus pattern (35 bp):
CCACAACTCAGTGGCACTCTTTTTCCTTTGTAAGC
Found at i:1779778 original size:32 final size:33
Alignment explanation
Indices: 1779733--1779851 Score: 179
Period size: 32 Copynumber: 3.6 Consensus size: 33
1779723 CTTTTAAGCC
**
1779733 CACAAGTTAGTGGC-ACCCTTTTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCTAAAGCCCA
*
1779765 CACAAGTCGGTGGCAACCC-TTCCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCTAAAGCCCA
*
1779797 CACAAGTCGGTGGCAACCTTTTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTT-TCTAAAGCCCA
1779831 CACAAGTCGGTGGCAACCCTT
1 CACAAGTCGGTGGCAACCCTT
1779852 CTAAGCCCAA
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
32 42 0.54
33 6 0.08
34 30 0.38
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.21
Consensus pattern (33 bp):
CACAAGTCGGTGGCAACCCTTTTCTAAAGCCCA
Found at i:1779845 original size:66 final size:62
Alignment explanation
Indices: 1779733--1779860 Score: 193
Period size: 66 Copynumber: 2.0 Consensus size: 62
1779723 CTTTTAAGCC
*
1779733 CACAAGTTAGTGGCACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCCTAAAGCCCA
1 CACAAGTCAGTGGCACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTT-CT-AAGCCCA
* *
1779797 CACAAGTCGGTGGCAACCTTTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAGCCCA
1 CACAAGTCAGTGGC-ACCCTTT-TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAGCCCA
1779861 ATATCGCTGG
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
64 19 0.32
65 8 0.14
66 32 0.54
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.20
Consensus pattern (62 bp):
CACAAGTCAGTGGCACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAGCCCA
Found at i:1779962 original size:43 final size:43
Alignment explanation
Indices: 1779899--1780168 Score: 351
Period size: 43 Copynumber: 6.0 Consensus size: 43
1779889 GCACCTTCAT
*
1779899 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
1779942 CTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C
*
1779986 TTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 -----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
1780034 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
*
1780081 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
1780126 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
1780169 ATTTTCCATC
Statistics
Matches: 199, Mismatches: 16, Indels: 24
0.83 0.07 0.10
Matches are distributed among these distances:
43 118 0.59
44 1 0.01
45 1 0.01
47 1 0.01
48 1 0.01
49 77 0.39
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1780015 original size:92 final size:92
Alignment explanation
Indices: 1779848--1780225 Score: 639
Period size: 92 Copynumber: 4.1 Consensus size: 92
1779838 CGGTGGCAAC
*
1779848 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1779913 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* *
1779941 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1780006 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
1780033 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1780098 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
1780125 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTTTAAGTCCAA
* *
1780190 TGTAGCTGGCTTTGAATCAGCACATTGACA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
1780220 TCCTTT
1 -CCTTT
1780226 TTCTCATCTT
Statistics
Matches: 271, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
92 218 0.80
93 4 0.01
94 2 0.01
95 42 0.15
96 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1780196 original size:52 final size:54
Alignment explanation
Indices: 1780126--1780343 Score: 179
Period size: 67 Copynumber: 3.8 Consensus size: 54
1780116 ACATTGGCAC
1780126 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
* * * * * *
1780178 CTTTAAGTTCAATGTAGCTGGCTTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * * *
1780233 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-----CA---TT-T--TC-TC
1780298 AT
53 AT
* *
1780300 CTTTAAGTCCAATATTGATGGCCTTGAATCAGCATATTGGCACC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1780344 TTCATCATCT
Statistics
Matches: 129, Mismatches: 22, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
52 37 0.29
54 6 0.05
55 37 0.29
60 1 0.01
61 1 0.01
63 2 0.02
64 1 0.01
66 3 0.02
67 41 0.32
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
Found at i:1780261 original size:55 final size:52
Alignment explanation
Indices: 1780126--1780263 Score: 159
Period size: 52 Copynumber: 2.6 Consensus size: 52
1780116 ACATTGGCAC
* *
1780126 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACATTTTCCAT
* * * *
1780178 CTTTAAGTTCAATGTAGCTGGCTTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA--CATTTTC-CAT
* * * *
1780233 CTTTAAGCCCAATATCGTTGGCCATGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
1780264 ACATATTGGC
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
52 37 0.53
54 6 0.09
55 27 0.39
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACATTTTCCAT
Found at i:1781171 original size:13 final size:13
Alignment explanation
Indices: 1781153--1781177 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1781143 CATAAAGTGT
1781153 TGTATCGATACAA
1 TGTATCGATACAA
1781166 TGTATCGATACA
1 TGTATCGATACA
1781178 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1781193 original size:32 final size:33
Alignment explanation
Indices: 1781133--1781198 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
1781123 TTCAATGATT
1781133 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
1781166 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1781198 T
1 T
1781199 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1781227 original size:33 final size:33
Alignment explanation
Indices: 1781185--1781262 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
1781175 ACATAAGTTT
1781185 TGTATCGATACAATTTAAGCTACTGCCAAAAAA
1 TGTATCGATACAATTTAAGCTACTGCCAAAAAA
1781218 TGTATCGATACAATTTAAGCTACTGCCAAAAAA
1 TGTATCGATACAATTTAAGCTACTGCCAAAAAA
1781251 TGTATCGATACA
1 TGTATCGATACA
1781263 TTACTCAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (33 bp):
TGTATCGATACAATTTAAGCTACTGCCAAAAAA
Found at i:1781290 original size:13 final size:13
Alignment explanation
Indices: 1781272--1781296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1781262 ATTACTCAAA
1781272 TGTATCGATACAT
1 TGTATCGATACAT
1781285 TGTATCGATACA
1 TGTATCGATACA
1781297 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1781435 original size:52 final size:52
Alignment explanation
Indices: 1781305--1781435 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 52
1781295 CACTGATCTT
* * *
1781305 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
*
1781357 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
*
1781409 TGTATCGATACATGCAGGCAACTTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
1781436 ATATTTCGGA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
Found at i:1781842 original size:21 final size:21
Alignment explanation
Indices: 1781818--1781894 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
1781808 AATTTATCCA
1781818 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1781839 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
1781860 AATGTATCGATACATCT-TACA
1 AATGTATCGATACATTTGTA-G
1781881 AATGTATCGATACA
1 AATGTATCGATACA
1781895 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 1 0.02
21 50 0.98
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1781954 original size:19 final size:19
Alignment explanation
Indices: 1781930--1781995 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
1781920 AATTCAACAA
1781930 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1781949 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1781964 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1781981 TTTGTATCGATACAT
1 TTTGTATCGATACAT
1781996 TGTATCGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.27
15 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1781973 original size:32 final size:32
Alignment explanation
Indices: 1781932--1782010 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
1781922 TTCAACAATT
1781932 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
1781964 TGTATCGATACATAAGTTTTGTATCGATACAT
1 TGTATCGATACATAAGTTTTGTATCGATACAA
1781996 TGTATCGATACATAA
1 TGTATCGATACATAA
1782011 TTAGCTACTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:1782008 original size:13 final size:13
Alignment explanation
Indices: 1781950--1782008 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 13
1781940 TACATAAGTT
1781950 TTGTATCGATACA
1 TTGTATCGATACA
*
1781963 ATGTATCGATACATAA
1 TTGTATCGATAC---A
1781979 GTTTTGTATCGATACA
1 ---TTGTATCGATACA
1781995 TTGTATCGATACA
1 TTGTATCGATACA
1782008 T
1 T
1782009 AATTAGCTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 25 0.66
16 2 0.05
19 11 0.29
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1782068 original size:13 final size:13
Alignment explanation
Indices: 1782050--1782075 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1782040 CATTTTTCTG
1782050 TGTATCGATACAT
1 TGTATCGATACAT
1782063 TGTATCGATACAT
1 TGTATCGATACAT
1782076 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1782072 original size:33 final size:33
Alignment explanation
Indices: 1782030--1782096 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1782020 GCCAAGTAAA
***
1782030 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1782063 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1782096 T
1 T
1782097 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1784570 original size:27 final size:28
Alignment explanation
Indices: 1784540--1784615 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
1784530 TTTCTTCACA
1784540 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1784567 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1784595 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
1784616 GTTTTATTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.56
28 20 0.44
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:1784650 original size:107 final size:104
Alignment explanation
Indices: 1784490--1784881 Score: 308
Period size: 107 Copynumber: 3.7 Consensus size: 104
1784480 TCTATAATCA
* * *
1784490 GGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCA
1 GGGATACTCCAACCCCGGTTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCCA
1784555 ACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAG
63 ACCCCGTTAATCATCGGGGATACTCCAACCCCGTTA-TTC-GAG
* * *
1784599 GGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCAAA
1 GGGATACTCCAACCCCGGTTTTATTCCAAAAACACCAATTTTT-CACAATCGGGGATACTCC-AA
** * ** * * * ** * *
1784664 CCTGGTTTTATTTTC---AAAACGCCAATTTTCCTTTAATC--G
64 CCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTCGAG
* * * * *
1784703 GGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCATAATCGAGGATACTCCAAC
1 GGGATACTCCAACCCCGGTTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
* * *
1784768 CTCGTTATTTCATCGGGGATAATCCAACCCCGTTACTTCCGAG
65 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTA-TT-CGAG
* * * *** * * *
1784811 GGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACC
1 GGGATACTCCAACCCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACC
1784876 CCGTTA
66 CCGTTA
1784882 TTTTCGAAGG
Statistics
Matches: 219, Mismatches: 50, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
102 2 0.01
103 9 0.04
104 43 0.20
105 17 0.08
106 16 0.07
107 72 0.33
108 34 0.16
109 26 0.12
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (104 bp):
GGGATACTCCAACCCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACC
CCGTTAATCATCGGGGATACTCCAACCCCGTTATTCGAG
Found at i:1784767 original size:52 final size:50
Alignment explanation
Indices: 1784434--1784768 Score: 194
Period size: 52 Copynumber: 6.4 Consensus size: 50
1784424 AATTCTCCAC
* * * *
1784434 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAA-TTTTCTAT
1 AATCGGGGATACTCCAAC-CCGGTTTTATTTCCAAAACACCAATTTTTC-AT
* * * *
1784485 AATCAGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAC
1 AATCGGGGATACTCCAAC-CCGGTTTTATTTCC--AAAACACCAATTT-TTCAT
* * * ** * *
1784539 AATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAACCCCGTTATTTC-T
1 AATCGGGGATACTCCAACCCGGTTTTAT-TTC--CAAAACACCAA-----TT-TTTCAT
* * * * *
1784596 GA--GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAA-CCCGGTTTTATTTCCAAAACACCAATTTTT-CAT
* * * * *
1784646 AATCGGGGATACTCCAAACCTGGTTTTATTTTCAAAACGCCAATTTTCCTTT
1 AATCGGGGATACTCC-AACCCGGTTTTATTTCCAAAACACCAATTTTTC-AT
* *
1784698 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCAT
1 AATCGGGGATACTCCAAC-CCGGTTTTATTTCC-AAAACACCAATTTTTCAT
*
1784750 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
1784769 TCGTTATTTC
Statistics
Matches: 215, Mismatches: 46, Indels: 46
0.70 0.15 0.15
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 1 0.00
51 34 0.16
52 82 0.38
53 35 0.16
54 25 0.12
55 16 0.07
56 5 0.02
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (50 bp):
AATCGGGGATACTCCAACCCGGTTTTATTTCCAAAACACCAATTTTTCAT
Found at i:1784787 original size:28 final size:28
Alignment explanation
Indices: 1784751--1784827 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1784741 ATTTTTCATA
* * *
1784751 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*
1784779 ATCGGGGATAATCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
1784807 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1784828 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:1784796 original size:212 final size:212
Alignment explanation
Indices: 1784429--1784835 Score: 613
Period size: 212 Copynumber: 1.9 Consensus size: 212
1784419 TTCTCAATTC
* *
1784429 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCAGGGA
1 TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGA
* *
1784494 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * * *
1784559 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATT
131 CGTTAATCATCGGGGATAATCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATT
1784624 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * * * *
1784641 TCCACAATCGGGGATACTCCAAAC-CTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCC-AACTCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCAGG
* *
1784705 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCATAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
1784768 CTCGTTATTTCATCGGGGATAATCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATAATCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
1784833 ATT
193 ATT
1784836 CCCAAAATAT
Statistics
Matches: 175, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
211 27 0.15
212 111 0.63
213 37 0.21
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATAATCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATT
GCTAAAACACTAATTTT
Found at i:1784930 original size:79 final size:79
Alignment explanation
Indices: 1784781--1784983 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
1784771 GTTATTTCAT
* * * * *
1784781 CGGGGATAATCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
1784846 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
1784860 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
1784924 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* *
1784939 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
1784984 TGTTATTATC
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
78 8 0.08
79 95 0.92
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:1797406 original size:11 final size:11
Alignment explanation
Indices: 1797389--1797420 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1797379 TTCTCTTCAA
1797389 AAAAAAAAGAGC
1 AAAAAAAA-AGC
1797401 AAAAAAAAAGC
1 AAAAAAAAAGC
1797412 AAAAAAAAA
1 AAAAAAAAA
1797421 AACAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGC
Found at i:1797406 original size:13 final size:12
Alignment explanation
Indices: 1797388--1797440 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
1797378 CTTCTCTTCA
1797388 AAAAAAAAAGAGC
1 AAAAAAAAA-AGC
1797401 -AAAAAAAAAGC
1 AAAAAAAAAAGC
*
1797412 AAAAAAAAAAAC
1 AAAAAAAAAAGC
*
1797424 AAAACAAAAAAAC
1 AAAA-AAAAAAGC
1797437 AAAA
1 AAAA
1797441 CAAAGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
11 3 0.08
12 22 0.59
13 12 0.32
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGC
Found at i:1797415 original size:8 final size:8
Alignment explanation
Indices: 1797403--1797450 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
1797393 AAAAGAGCAA
1797403 AAAAAAAGC
1 AAAAAAA-C
*
1797412 AAAAAAAA
1 AAAAAAAC
1797420 AAACAAAAC
1 AAA-AAAAC
1797429 AAAAAAAC
1 AAAAAAAC
*
1797437 AAAACAAAG
1 AAAA-AAAC
1797446 AAAAA
1 AAAAA
1797451 GAGAGAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 13 0.38
9 21 0.62
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1797420 original size:12 final size:12
Alignment explanation
Indices: 1797386--1797440 Score: 67
Period size: 13 Copynumber: 4.4 Consensus size: 12
1797376 ACCTTCTCTT
1797386 CAAAAAAAAAAGA
1 CAAAAAAAAAA-A
*
1797399 GC-AAAAAAAAAG
1 -CAAAAAAAAAAA
1797411 CAAAAAAAAAAA
1 CAAAAAAAAAAA
1797423 CAAAACAAAAAAA
1 CAAAA-AAAAAAA
1797436 CAAAA
1 CAAAA
1797441 CAAAGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 1 0.03
12 14 0.38
13 21 0.57
14 1 0.03
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:1797422 original size:18 final size:18
Alignment explanation
Indices: 1797401--1797450 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
1797391 AAAAAAGAGC
1797401 AAAAAAAAAGCAAAAAAA
1 AAAAAAAAAGCAAAAAAA
*
1797419 AAAACAAAA-CAAAAAAA
1 AAAAAAAAAGCAAAAAAA
* *
1797436 CAAAACAAAG-AAAAA
1 AAAAAAAAAGCAAAAA
1797451 GAGAGAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGCAAAAAAA
Found at i:1797441 original size:13 final size:13
Alignment explanation
Indices: 1797403--1797449 Score: 69
Period size: 13 Copynumber: 3.5 Consensus size: 13
1797393 AAAAGAGCAA
1797403 AAAAAAAGCAAAA-
1 AAAAAAA-CAAAAC
1797416 AAAAAAACAAAAC
1 AAAAAAACAAAAC
1797429 AAAAAAACAAAAC
1 AAAAAAACAAAAC
1797442 AAAGAAAA
1 AAA-AAAA
1797450 AGAGAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.16
13 23 0.72
14 4 0.12
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:1798593 original size:59 final size:54
Alignment explanation
Indices: 1798435--1798960 Score: 577
Period size: 55 Copynumber: 9.3 Consensus size: 54
1798425 TCTGCTTTTT
* * **
1798435 AGTCCTCAAAGAGCAAGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* *
1798490 AGTCCTCAGAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
1798544 AGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACAC-----CTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
1798603 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGAC-AC----CTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
**
1798662 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTC
* * * *
1798723 AGTCCCCGAAGAGCAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * **
1798778 AGTTCC-CAAAGAGTAGGACACCTTTTAAAGCCCACACAAGTTGATGGCATTTTCC
1 AG-TCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
*
1798833 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * * * * *
1798888 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCTACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
* *
1798943 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
1798961 TACACTTTAT
Statistics
Matches: 412, Mismatches: 42, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
54 25 0.06
55 223 0.54
56 9 0.02
59 110 0.27
60 25 0.06
61 20 0.05
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (54 bp):
AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:1798785 original size:29 final size:28
Alignment explanation
Indices: 1798698--1798785 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 28
1798688 CTTTTCAAAG
1798698 CCCACACAAGTTGGTGGCACCTTTCAGT
1 CCCACACAAGTTGGTGGCACCTTTCAGT
* * ** *
1798726 CCC-C-GAAG-AGCAGGACCCCTTTCAAAG-
1 CCCACACAAGTTGGTGG-CACCTTTC--AGT
1798753 CCCACACAAGTTGGTGGCACCTTTCAGTT
1 CCCACACAAGTTGGTGGCACCTTTCAG-T
1798782 CCCA
1 CCCA
1798786 AAGAGTAGGA
Statistics
Matches: 42, Mismatches: 10, Indels: 15
0.63 0.15 0.22
Matches are distributed among these distances:
25 3 0.07
26 10 0.24
27 6 0.14
28 6 0.14
29 14 0.33
30 3 0.07
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.20
Consensus pattern (28 bp):
CCCACACAAGTTGGTGGCACCTTTCAGT
Found at i:1799607 original size:19 final size:19
Alignment explanation
Indices: 1799583--1799650 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1799573 AATTCAACGA
1799583 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1799602 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1799617 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1799634 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1799651 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1799621 original size:32 final size:32
Alignment explanation
Indices: 1799585--1799647 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1799575 TTCAACGATT
*
1799585 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1799617 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1799648 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1799622 original size:13 final size:13
Alignment explanation
Indices: 1799604--1799628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1799594 ACATAAGTTT
1799604 TGTATCGATACAA
1 TGTATCGATACAA
1799617 TGTATCGATACA
1 TGTATCGATACA
1799629 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1802183 original size:27 final size:27
Alignment explanation
Indices: 1802153--1802228 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
1802143 TTTCTTCACA
*
1802153 ATCGGGGATACTCCAACCCTGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
* *
1802180 ATCGGGGATACTCCAACCCCGTTATTT
1 ATCGGGGATACTCCAACCCCGTTAATC
* *
1802207 TTGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
1802229 GTTTTATTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:1802278 original size:52 final size:51
Alignment explanation
Indices: 1802213--1802381 Score: 180
Period size: 52 Copynumber: 3.3 Consensus size: 51
1802203 ATTTTTGAGG
* * * *
1802213 GGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGG
1 GGATACTCCAACCCTGGTTTTATT-CTAAAACACCAATTTTTCCATAATCGA
* * *
1802265 GGATACTCCAACCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATCGA
1 GGATACTCCAACCCTGGTTTTATTCT-AAAACACCAATTTTTCC-ATAATCGA
* * * *
1802317 GGATACTCCAACTCTGATTTTATTTCCAAAAATACCAATTTTT-CATAATCGA
1 GGATACTCCAACCCTGGTTTTA-TT-CTAAAACACCAATTTTTCCATAATCGA
1802369 GGATACTCCAACC
1 GGATACTCCAACC
1802382 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
51 7 0.07
52 75 0.77
53 11 0.11
54 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
GGATACTCCAACCCTGGTTTTATTCTAAAACACCAATTTTTCCATAATCGA
Found at i:1802400 original size:28 final size:30
Alignment explanation
Indices: 1802364--1802440 Score: 108
Period size: 28 Copynumber: 2.7 Consensus size: 30
1802354 ATTTTTCATA
* *
1802364 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
1802392 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
1802422 A--GGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1802441 GCTTTATTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 40 0.89
29 4 0.09
30 1 0.02
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGTTACTTTCG
Found at i:1802409 original size:212 final size:211
Alignment explanation
Indices: 1802039--1802489 Score: 615
Period size: 212 Copynumber: 2.1 Consensus size: 211
1802029 AGTTTCTCAA
* *
1802039 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCAG
1 TTCTCCACAATCGGGGATACTCCAAC-CCGATTTTATTTTCAAAACACCAATTTTCTATAATCAG
* *
1802104 GGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAA
65 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* * *
1802169 CCCTGTTAATCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTTTT
130 CCCTGTTAATCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCGGCTTT
* *
1802234 ATTGCTAAAACACTAAT
195 ATTCCCAAAACACTAAT
* * * *
1802251 TTTTCCACAATCGGGGATACTCCAACCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC-
1 TTCTCCACAATCGGGGATACTCCAACCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCA
* * *
1802315 GAGGATACTCCAACTCTGATTTTATTTCC-AAAAATACCAATTT-TTCATAATCGAGGATACTCC
64 G-GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCC
*
1802378 AA-CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCGG
128 AACCCT-GTTA-ATCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCGG
* * *
1802442 CTTTATTCCCAAAATATTGAT
191 CTTTATTCCCAAAACACTAAT
* *
1802463 TTCT-CATAATTGGGGATACTCCAACCC
1 TTCTCCACAATCGGGGATACTCCAACCC
1802490 CGTTATTTTC
Statistics
Matches: 211, Mismatches: 23, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
210 3 0.01
211 47 0.22
212 129 0.61
213 32 0.15
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (211 bp):
TTCTCCACAATCGGGGATACTCCAACCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGG
GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
CCTGTTAATCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCGGCTTTA
TTCCCAAAACACTAAT
Found at i:1802540 original size:79 final size:79
Alignment explanation
Indices: 1802394--1802596 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
1802384 GTTATTTCAT
* * *
1802394 CGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* *
1802459 TGATTTCTCATAAT
66 TGATTTCTCACAAC
* * * * * ** *
1802473 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCTCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
1802537 TTGATTTCTCACAAC
65 TTGATTTCTCACAAC
* * * *
1802552 CGGGGATACTCCAGCCCCATTATTTTC-AAGGAAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGG-GATACTCCAACCC
1802597 TGTTATTATC
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
78 7 0.07
79 95 0.93
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.31
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
TGATTTCTCACAAC
Found at i:1803892 original size:80 final size:79
Alignment explanation
Indices: 1803790--1803992 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
1803780 AATAACAGGG
* * * * *
1803790 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTA
*
1803853 GAAAAAAAAAATCGGGA
64 G-AAAAAAAAACCGGGA
* * *
1803870 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * * *
1803935 GAATAAAGCCGGGG
66 AAAAAAAACCGGGA
* * *
1803949 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1803993 GAAATAACGA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
79 56 0.54
80 48 0.46
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAAACCGGGA
Found at i:1803984 original size:28 final size:28
Alignment explanation
Indices: 1803944--1804015 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1803934 GGAATAAAGC
** *
1803944 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1803972 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1804000 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1804016 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1804144 original size:52 final size:52
Alignment explanation
Indices: 1804004--1804173 Score: 168
Period size: 52 Copynumber: 3.3 Consensus size: 52
1803994 AAATAACGAG
* * * *
1804004 GTTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGT-GTTTTGAAAATAAAACCGGA
* ** *
1804056 GTTAGAGTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGGAAAAATTGGTGTTTTGAAAATAAAACC-GGA
* ** *
1804109 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCCGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGA-AAATAAAACCGGA
1804160 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1804174 TCGAAAATAA
Statistics
Matches: 96, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
51 5 0.05
52 79 0.82
53 11 0.11
54 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGAAAATAAAACCGGA
Found at i:1806664 original size:13 final size:13
Alignment explanation
Indices: 1806646--1806672 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1806636 ACAAAGATCC
1806646 ATGTATCGATACA
1 ATGTATCGATACA
1806659 ATGTATCGATACA
1 ATGTATCGATACA
1806672 A
1 A
1806673 AGAAAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1806667 original size:33 final size:33
Alignment explanation
Indices: 1806625--1806691 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1806615 AAAATTTCCA
***
1806625 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1806658 AATGTATCGATACAAAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1806691 A
1 A
1806692 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1807644 original size:55 final size:55
Alignment explanation
Indices: 1807560--1808720 Score: 1539
Period size: 55 Copynumber: 21.3 Consensus size: 55
1807550 ATAAACTGTA
* * * * * *
1807560 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1807615 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
1807670 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1807725 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1807780 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
1807835 TCCTGCTCTTTGAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1807890 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1807945 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
1808000 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTTTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1808055 TCCTGCTCTTTGGGGACTGAAAGGTGCCACC-ACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1808109 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1808164 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGG-TG
1808220 TCC-GCTCTTTGAGGACTGGAAA--TGCCACC-ACTTGTGTGGGCTTTGCAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT--AAGAGGTG
* * **
1808273 TTCC-GCT-TTTGAGGATTGGAACATGCCACCAAAACTTGTGT--GCTTTAAGAGGTG
1 -TCCTGCTCTTTGAGGACTGAAAGGTGCCACC--AACTTGTGTGGGCTTTAAGAGGTG
* *
1808327 TCCTGCT-TCTTGGGGACTGACAGGTGCCA-CAACTTGTGTGGGCTTTAAGATGGTG
1 TCCTGCTCT-TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGA-GGTG
**
1808382 TCCTGCTCTTTGA-GACTGGAAACATGCCACCCAACTTG-G-GGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCA-CCAACTTGTGTGGGCTTT-AAGAGGTG
* **
1808436 TCCTGCTCTTTGGGGACAAAAAGAGTGCCACCAACTTGTGT-GGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAG-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1808491 T-CTACTC-TTG-GGACTGAAAGGT-CCACC-AC-TGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1808540 TCCTGCTCTTTG-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1808594 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGT-GGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1808648 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1808703 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
1808721 AAAAAGCGGA
Statistics
Matches: 1007, Mismatches: 51, Indels: 96
0.87 0.04 0.08
Matches are distributed among these distances:
48 5 0.00
49 17 0.02
50 10 0.01
51 17 0.02
52 25 0.02
53 40 0.04
54 224 0.22
55 625 0.62
56 29 0.03
57 15 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:1807724 original size:29 final size:28
Alignment explanation
Indices: 1807634--1808217 Score: 135
Period size: 28 Copynumber: 21.2 Consensus size: 28
1807624 TTGAGGACTG
1807634 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * ** *
1807662 GAAAGGTGTCCTGC-TCTT-TG-GGGAATG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
1807689 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
1807717 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
*
1807745 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
1807772 GAAAGGTGTCCTGC-TCTT-TGAGGACTGG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
*
1807800 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * *
1807827 GAAAGGTGTCCTGC-TCTT-TG-AGGATTGG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTT-T
*
1807855 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
1807882 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
1807909 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
1807937 AAGAGGTGTCCTGC-TCTT-TGAGGACTAG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
1807965 AAA-ATGCCACCAACTTGGGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
1807992 GAAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGG-CTTT
*
1808019 AAAGGTGCCACCAACTTTTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
1808047 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
1808074 AAAGGTGCCACC-ACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
1808101 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
1808128 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
1808156 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
1808183 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
1808211 AAGAGGT
1 AA-AGGT
1808218 TGTCCGCTCT
Statistics
Matches: 378, Mismatches: 116, Indels: 122
0.61 0.19 0.20
Matches are distributed among these distances:
25 33 0.09
26 72 0.19
27 85 0.22
28 89 0.24
29 72 0.19
30 27 0.07
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (28 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:1809751 original size:12 final size:12
Alignment explanation
Indices: 1809702--1809758 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
1809692 CTTTTCTCTC
* *
1809702 TTTTTCTTTGTT
1 TTTTTTTTTGCT
1809714 TTGTTTTTTTG-T
1 TT-TTTTTTTGCT
*
1809726 TTTTTTTCCT-CT
1 TTTTTTT-TTGCT
1809738 TTTTTTTTTGCT
1 TTTTTTTTTGCT
1809750 TTTTTTTTT
1 TTTTTTTTT
1809759 TGAAGAGAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 6 0.16
12 25 0.66
13 7 0.18
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTGCT
Found at i:1809758 original size:13 final size:14
Alignment explanation
Indices: 1809725--1809760 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1809715 TGTTTTTTTG
*
1809725 TTTTTTTTCCTCTT
1 TTTTTTTTGCTCTT
1809739 TTTTTTTTGCT-TT
1 TTTTTTTTGCTCTT
1809752 TTTTTTTTG
1 TTTTTTTTG
1809761 AAGAGAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (14 bp):
TTTTTTTTGCTCTT
Found at i:1809758 original size:37 final size:38
Alignment explanation
Indices: 1809687--1809760 Score: 100
Period size: 36 Copynumber: 2.0 Consensus size: 38
1809677 TTAAGTAGGT
*
1809687 TTTTTCTTTTCTCTCTTTTTCTTTGTTTTGTTTTTTTG
1 TTTTTCTTTCCTCTCTTTTTCTTTGTTTTGTTTTTTTG
*
1809725 TTTTT-TTTCCTCT-TTTTTTTTTGCTTTT-TTTTTTTG
1 TTTTTCTTTCCTCTCTTTTTCTTTG-TTTTGTTTTTTTG
1809761 AAGAGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 17 0.52
37 11 0.33
38 5 0.15
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (38 bp):
TTTTTCTTTCCTCTCTTTTTCTTTGTTTTGTTTTTTTG
Found at i:1864932 original size:16 final size:17
Alignment explanation
Indices: 1864906--1864940 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1864896 TGGCCCTGAA
1864906 TCCGCAGCTTCTTGCCG
1 TCCGCAGCTTCTTGCCG
1864923 TCCG-AGCTTCTTGCCG
1 TCCGCAGCTTCTTGCCG
1864939 TC
1 TC
1864941 GATTCTGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.06, C:0.40, G:0.23, T:0.31
Consensus pattern (17 bp):
TCCGCAGCTTCTTGCCG
Found at i:1868983 original size:79 final size:79
Alignment explanation
Indices: 1868818--1869019 Score: 219
Period size: 79 Copynumber: 2.6 Consensus size: 79
1868808 GATAATAACA
* * ** * *
1868818 GGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCTATGAT
1 GGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGAT
*
1868882 TAGAAAAAAAAATCG
65 TAGAAAAAAAAACCG
*
1868897 GGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATT
1 GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA-T
* ** * *
1868961 TTGGGAATAAAGCCG
65 TAGAAAAAAAAACCG
* * * *
1868976 GGGTTGGAGTAACCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
1869020 GATGAAATAA
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
78 7 0.07
79 96 0.93
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGATT
AGAAAAAAAAACCG
Found at i:1869014 original size:28 final size:28
Alignment explanation
Indices: 1868974--1869042 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
1868964 GGAATAAAGC
** *
1868974 CGGGGTTGGAGTAACCCCTCGGAAGTAA
1 CGGGGTTGGAGTAACCCCGAGGAAATAA
* *
1869002 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTAACCCCGAGGAAATAA
*
1869030 CGAGGTTGGAGTA
1 CGGGGTTGGAGTA
1869043 TCCTCGATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.20
Consensus pattern (28 bp):
CGGGGTTGGAGTAACCCCGAGGAAATAA
Found at i:1869223 original size:28 final size:28
Alignment explanation
Indices: 1869191--1869263 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
1869181 TAAAACCCGA
1869191 GTTGGAGTATCCCCTCGA-AAATAACGGG
1 GTTGGAGTATCCCC-CGATAAATAACGGG
* *
1869219 GTTGGAGTA-CCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCCGATAAATAACGGG
*
1869246 GTTAGAGTATCCCCCGAT
1 GTTGGAGTATCCCCCGAT
1869264 TATAGAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
26 3 0.08
27 20 0.50
28 17 0.43
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (28 bp):
GTTGGAGTATCCCCCGATAAATAACGGG
Found at i:1871698 original size:13 final size:13
Alignment explanation
Indices: 1871680--1871705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1871670 ACAAAGATCC
1871680 ATGTATCGATACA
1 ATGTATCGATACA
1871693 ATGTATCGATACA
1 ATGTATCGATACA
1871706 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1871701 original size:33 final size:33
Alignment explanation
Indices: 1871659--1871725 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1871649 AAAATTTCCA
***
1871659 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1871692 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1871725 A
1 A
1871726 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1871769 original size:19 final size:19
Alignment explanation
Indices: 1871745--1871799 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
1871735 CAGTAGCTAA
*
1871745 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
1871764 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
1871783 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1871800 TTGTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:1872672 original size:55 final size:55
Alignment explanation
Indices: 1872588--1873012 Score: 644
Period size: 55 Copynumber: 7.7 Consensus size: 55
1872578 ATAAACTGTA
* * * * * *
1872588 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1872643 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
1872698 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1872753 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1872808 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
1872863 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1872918 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1872973 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGT
1873013 TGGCGCCCGG
Statistics
Matches: 344, Mismatches: 19, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
54 12 0.03
55 322 0.94
56 10 0.03
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:1872938 original size:26 final size:26
Alignment explanation
Indices: 1872909--1872998 Score: 85
Period size: 26 Copynumber: 3.3 Consensus size: 26
1872899 GGGTGGGCTT
1872909 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
1872935 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
1872962 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
1872990 TGAAAGGTG
1 TGAAAGGTG
1872999 CCACCAACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
25 3 0.06
26 17 0.35
27 9 0.18
28 9 0.18
29 8 0.16
30 3 0.06
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:1875719 original size:21 final size:21
Alignment explanation
Indices: 1875695--1875750 Score: 85
Period size: 24 Copynumber: 2.5 Consensus size: 21
1875685 CAGCCCATGA
1875695 TTCATGCATTTTGAGCTATGT
1 TTCATGCATTTTGAGCTATGT
1875716 TTCATGATGCATTTTGAGCTATGT
1 TTC---ATGCATTTTGAGCTATGT
1875740 TTCATGCATTT
1 TTCATGCATTT
1875751 ACAGCATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 11 0.34
24 21 0.66
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (21 bp):
TTCATGCATTTTGAGCTATGT
Found at i:1875725 original size:24 final size:24
Alignment explanation
Indices: 1875698--1875745 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1875688 CCCATGATTC
1875698 ATGCATTTTGAGCTATGTTTCATG
1 ATGCATTTTGAGCTATGTTTCATG
1875722 ATGCATTTTGAGCTATGTTTCATG
1 ATGCATTTTGAGCTATGTTTCATG
1875746 CATTTACAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (24 bp):
ATGCATTTTGAGCTATGTTTCATG
Found at i:1888753 original size:18 final size:16
Alignment explanation
Indices: 1888732--1888820 Score: 72
Period size: 18 Copynumber: 5.1 Consensus size: 16
1888722 CATCCTCCAC
1888732 AAAAAAAAAACAGAAGAA
1 AAAAAAAAAACA-AA-AA
1888750 AAAAAGAAAAA-AAAACA
1 AAAAA-AAAAACAAAA-A
* *
1888767 AAACAAAAAAGAAAAA
1 AAAAAAAAAACAAAAA
1888783 AAAAACAAACAACAAAAA
1 AAAAA-AAA-AACAAAAA
*
1888801 AAAAACAACAACAACAAA
1 AAAAA-AAAAACAA-AAA
1888819 AA
1 AA
1888821 GGGTACAGAT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
16 11 0.18
17 19 0.31
18 26 0.43
19 5 0.08
ACGTcount: A:0.84, C:0.11, G:0.04, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAAAAA
Found at i:1888763 original size:23 final size:22
Alignment explanation
Indices: 1888733--1888820 Score: 101
Period size: 22 Copynumber: 3.9 Consensus size: 22
1888723 ATCCTCCACA
1888733 AAAAAAAAACAGAAGA-AAAAAAG
1 AAAAAAAAACA-AA-ACAAAAAAG
1888756 AAAAAAAAACAAAACAAAAAAG
1 AAAAAAAAACAAAACAAAAAAG
1888778 AAAAAAAAA-ACAAACAACAAAA-
1 AAAAAAAAACA-AAACAA-AAAAG
*
1888800 AAAAAACAACAACAACAAAAA
1 AAAAAAAAACAA-AACAAAAA
1888821 GGGTACAGAT
Statistics
Matches: 59, Mismatches: 1, Indels: 11
0.83 0.01 0.15
Matches are distributed among these distances:
21 2 0.03
22 36 0.61
23 21 0.36
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (22 bp):
AAAAAAAAACAAAACAAAAAAG
Found at i:1888781 original size:30 final size:29
Alignment explanation
Indices: 1888735--1888805 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 29
1888725 CCTCCACAAA
1888735 AAAAAAACAGAAGAAAAAAAGAAA-AAAAAAC
1 AAAAAAA-A-AAGAAAAAAA-AAACAAAAAAC
*
1888766 AAAACAAAAAAGAAAAAAAAAACAAACAAC
1 AAAA-AAAAAAGAAAAAAAAAACAAAAAAC
1888796 AAAAAAAAAA
1 AAAAAAAAAA
1888806 CAACAACAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 9 0.24
30 20 0.54
31 5 0.14
32 3 0.08
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAGAAAAAAAAAACAAAAAAC
Found at i:1888811 original size:17 final size:18
Alignment explanation
Indices: 1888759--1888820 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
1888749 AAAAAAGAAA
* *
1888759 AAAAAACAAAACAAAAAAG
1 AAAAAA-AAAACAAACAAC
1888778 AAAAAAAAAACAAACAAC
1 AAAAAAAAAACAAACAAC
1888796 AAAAAAAAAAC-AACAAC
1 AAAAAAAAAACAAACAAC
1888813 AACAAAAA
1 AA-AAAAA
1888821 GGGTACAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.20
18 26 0.65
19 6 0.15
ACGTcount: A:0.84, C:0.15, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAACAAACAAC
Found at i:1888820 original size:1 final size:1
Alignment explanation
Indices: 1888732--1888805 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
1888722 CATCCTCCAC
* * * * * * * * * *
1888732 AAAAAAAAAACAGAAGAAAAAAAGAAAAAAAAACAAAACAAAAAAGAAAAAAAAAACAAACAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1888797 AAAAAAAAA
1 AAAAAAAAA
1888806 CAACAACAAC
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:1890296 original size:29 final size:29
Alignment explanation
Indices: 1890257--1890430 Score: 217
Period size: 29 Copynumber: 6.0 Consensus size: 29
1890247 TCACCCTTCA
1890257 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1890286 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1890315 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1890342 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* *
1890372 GAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1890401 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1890431 TTTTATAAGC
Statistics
Matches: 125, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
27 22 0.18
28 1 0.01
29 74 0.59
30 28 0.22
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:1890379 original size:86 final size:86
Alignment explanation
Indices: 1890251--1890421 Score: 263
Period size: 86 Copynumber: 2.0 Consensus size: 86
1890241 CATTCCTCAC
* * * *
1890251 CCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTCA
1 CCTTCAAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
*
1890316 AAGTCCACAAGTCAGTGGCAA
66 AAGTCCACAACTCAGTGGCAA
*
1890337 CCTTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCAGTGGCATCTTTTCC
1 CCTTCAAAAGCCCACAAATCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCC
*
1890401 AAAGTCCACAACTCCGTGGCA
65 AAAGTCCACAACTCAGTGGCA
1890422 CTCTTTTTCT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
85 20 0.26
86 57 0.74
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.23
Consensus pattern (86 bp):
CCTTCAAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
AAGTCCACAACTCAGTGGCAA
Found at i:1890480 original size:34 final size:35
Alignment explanation
Indices: 1890406--1890480 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1890396 TTTCCAAAGT
* *
1890406 CCACAACTCCGTGGCACTCTTTTTCTTTTATAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTATAAGC
*
1890441 TCACAACTCCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTATAAGC
1890475 CCACAA
1 CCACAA
1890481 GTTAGTGGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.23, C:0.33, G:0.09, T:0.35
Consensus pattern (35 bp):
CCACAACTCCGTAGCACTCTTTTTCCTTTATAAGC
Found at i:1890497 original size:34 final size:35
Alignment explanation
Indices: 1890373--1890497 Score: 111
Period size: 35 Copynumber: 3.8 Consensus size: 35
1890363 CCCTTTTCCG
*
1890373 AAGCCCACAAGTCAGTGGCA-TC-TTTTCC---A-
1 AAGCCCACAACTCAGTGGCACTCTTTTTCCTTTAT
* * *
1890402 AAGTCCACAACTCCGTGGCACTCTTTTTCTTTTAT
1 AAGCCCACAACTCAGTGGCACTCTTTTTCCTTTAT
* * *
1890437 AAGCTCACAACTCCGTAGCACTCTTTTTCCTTT-T
1 AAGCCCACAACTCAGTGGCACTCTTTTTCCTTTAT
* * *
1890471 AAGCCCACAAGTTAGTGGCACCCTTTT
1 AAGCCCACAACTCAGTGGCACTCTTTT
1890498 CTAAAGCCCA
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
29 17 0.22
30 2 0.03
31 5 0.07
34 23 0.30
35 29 0.38
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (35 bp):
AAGCCCACAACTCAGTGGCACTCTTTTTCCTTTAT
Found at i:1890521 original size:32 final size:33
Alignment explanation
Indices: 1890476--1890594 Score: 170
Period size: 32 Copynumber: 3.6 Consensus size: 33
1890466 CTTTTAAGCC
**
1890476 CACAAGTTAGTGGC-ACCCTTTTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCTAAAGCCCA
*
1890508 CACAAGTCGGTGGCAACCC-TTCCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTTTCTAAAGCCCA
*
1890540 CACAAGTCGGTGGCAACCTTTTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTT-TCTAAAGCCCA
*
1890574 CATAAGTCGGTGGCAACCCTT
1 CACAAGTCGGTGGCAACCCTT
1890595 CTAAGCCCAA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
32 42 0.55
33 6 0.08
34 29 0.38
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (33 bp):
CACAAGTCGGTGGCAACCCTTTTCTAAAGCCCA
Found at i:1890589 original size:66 final size:62
Alignment explanation
Indices: 1890476--1890603 Score: 184
Period size: 66 Copynumber: 2.0 Consensus size: 62
1890466 CTTTTAAGCC
*
1890476 CACAAGTTAGTGGCACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCCTAAAGCCCA
1 CACAAGTCAGTGGCACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTT-CT-AAGCCCA
* * *
1890540 CACAAGTCGGTGGCAACCTTTTCTCTAAAGCCCACATAAGTCGGTGGCAACCCTTCTAAGCCCA
1 CACAAGTCAGTGGC-ACCCTTT-TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAGCCCA
1890604 ATATCGTTGG
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
64 19 0.33
65 8 0.14
66 31 0.53
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.21
Consensus pattern (62 bp):
CACAAGTCAGTGGCACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAGCCCA
Found at i:1890654 original size:49 final size:49
Alignment explanation
Indices: 1890596--1891308 Score: 745
Period size: 49 Copynumber: 14.8 Consensus size: 49
1890586 GCAACCCTTC
* * *
1890596 TAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1890645 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1890688 TAAGTCCAATATCGCTTGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1890737 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
1890780 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
1890829 TAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * **
1890872 TAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1890921 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
1890970 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATATT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTT
* * * * * *
1891022 TAAGTCCAATGTCGCTGGCTTTGAATCAGCTTATTGACACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1891071 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTTTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
1891120 TAATTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
1891163 TAAGTCCAATATAGCTGGCCTTGAATCAGTATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * * * * *
1891215 TAAGTTCAATGTAGCTGGCTTTGAATTAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC----T-TCATCTT
* * * * *
1891270 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
1891309 TCTTTATCAC
Statistics
Matches: 552, Mismatches: 78, Indels: 62
0.80 0.11 0.09
Matches are distributed among these distances:
43 151 0.27
45 4 0.01
47 2 0.00
49 275 0.50
50 2 0.00
51 1 0.00
52 77 0.14
53 2 0.00
55 37 0.07
56 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:1890758 original size:92 final size:92
Alignment explanation
Indices: 1890591--1891259 Score: 942
Period size: 92 Copynumber: 7.1 Consensus size: 92
1890581 CGGTGGCAAC
* *
1890591 CCTTCTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1890656 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
*
1890684 CCTTTAAGTCCAATATCGCTTGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1890749 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
1890776 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
1890841 AGCTAGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* **
1890868 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1890933 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
1890960 CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATATTTAA
1 ----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAA
* * ** *
1891025 GTCCAATGTCGCTGGCTTTGAATCAGCTTATTGACACCTTCA
57 GTCCAATGTAGCTGGCCTTGAATCAGCACATTG------GCA
* * * *
1891067 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTTTTTAATTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1891132 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
1891159 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGTATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAA
* * *
1891224 TGTAGCTGGCTTTGAATTAGCACATTGACA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
1891254 TCCTTT
1 -CCTTT
1891260 TTCTCATCTT
Statistics
Matches: 520, Mismatches: 37, Indels: 35
0.88 0.06 0.06
Matches are distributed among these distances:
92 309 0.59
93 4 0.01
94 2 0.00
95 38 0.07
96 6 0.01
98 78 0.15
99 1 0.00
100 1 0.00
101 78 0.15
103 1 0.00
107 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (92 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1891141 original size:150 final size:150
Alignment explanation
Indices: 1890870--1891313 Score: 438
Period size: 150 Copynumber: 3.0 Consensus size: 150
1890860 CATTGGCACC
* *** *
1890870 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGACACCTTCACCTTTAAGTCCAATATAG
*
1890935 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
* *
1891000 ATATTGGCGCCTTTGTCATA
131 ACATTGGCACCTTTGTCATA
* * * *
1891020 TTTAAGTCCAATGTCGCTGGCTTTGAATCAGCTTATTGACACCTTCACCTTTAAGTCCAATATAG
1 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGACACCTTCACCTTTAAGTCCAATATAG
* * * * *
1891085 CTGGCCTTGAATCAGCATATTGGCACCTTCTTTTTTAATTCCAATGTAGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
1891150 ACATTGGCA-C-----C---
131 ACATTGGCACCTTTGTCATA
* * * * * * *
1891161 TTTAAGTCCAATATAGCTGGCCTTGAATCAGTATATTGGCACCTTTTCCATCTTTAAGTTCAATG
1 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGACACC--TT-CACCTTTAAGTCCAATA
* * * * * * *
1891226 TAGCTGGCTTTGAATTAGCACATTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCA
63 TAGCTGGCCTTGAATCAGCACATTGGCA-CC----T-TCATCTTTAAGTCCAATATAGCTGGCCT
* * *
1891291 TGAATCAACATATTGGCATCTTT
122 TGAATCAGCACATTGGCACCTTT
1891314 ATCACTTTTC
Statistics
Matches: 241, Mismatches: 40, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
141 37 0.15
143 2 0.01
144 39 0.16
145 2 0.01
149 2 0.01
150 158 0.66
151 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (150 bp):
TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGACACCTTCACCTTTAAGTCCAATATAG
CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
ACATTGGCACCTTTGTCATA
Found at i:1891371 original size:67 final size:68
Alignment explanation
Indices: 1891263--1891389 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
1891253 ATCCTTTTTC
* * *
1891263 TCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
1891327 TCA
66 TCA
* * * *
1891330 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTT
1891390 AAAACCCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCA
Found at i:1892206 original size:13 final size:13
Alignment explanation
Indices: 1892188--1892212 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1892178 CATAAAGCGT
1892188 TGTATCGATACAA
1 TGTATCGATACAA
1892201 TGTATCGATACA
1 TGTATCGATACA
1892213 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1892228 original size:32 final size:33
Alignment explanation
Indices: 1892168--1892233 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
1892158 TTCAACGATT
1892168 TGTATCGATACATAAAGCGTTGTATCGATACAA
1 TGTATCGATACATAAAGCGTTGTATCGATACAA
**
1892201 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGCGTTGTATCGATACAA
1892233 T
1 T
1892234 TTAAGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATAAAGCGTTGTATCGATACAA
Found at i:1892292 original size:13 final size:13
Alignment explanation
Indices: 1892274--1892298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1892264 ATTACTCAAA
1892274 TGTATCGATACAT
1 TGTATCGATACAT
1892287 TGTATCGATACA
1 TGTATCGATACA
1892299 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1892350 original size:52 final size:50
Alignment explanation
Indices: 1892287--1892431 Score: 191
Period size: 52 Copynumber: 2.8 Consensus size: 50
1892277 ATCGATACAT
*
1892287 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* * * *
1892339 TGTATCGATACATTATAAAATGTATCGATACATGCAAGTAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
1892391 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAA
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAA
1892432 CTTTTCATAT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1894611 original size:27 final size:27
Alignment explanation
Indices: 1894581--1894651 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
1894571 TATATTCATC
1894581 GGGGACACTCCAACCCCATTCCTCCGA
1 GGGGACACTCCAACCCCATTCCTCCGA
1894608 GGGGACACTCCAACCCCATTCCTCCGA
1 GGGGACACTCCAACCCCATTCCTCCGA
1894635 GGGGACACTCCAACCCC
1 GGGGACACTCCAACCCC
1894652 GTTTTCAATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.23, C:0.45, G:0.20, T:0.13
Consensus pattern (27 bp):
GGGGACACTCCAACCCCATTCCTCCGA
Found at i:1896135 original size:20 final size:20
Alignment explanation
Indices: 1896090--1896141 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1896080 GTAGCCAAAC
* **
1896090 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
1896110 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
1896129 TTGTATCGATACA
1 TTGTATCGATACA
1896142 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:1898762 original size:28 final size:27
Alignment explanation
Indices: 1898727--1898792 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 27
1898717 AGCTGGGGTA
1898727 GAGTATCCCC-TCAGAAATAACGGGGTTG
1 GAGTATCCCCAT-A-AAATAACGGGGTTG
1898755 GAGTATCCCCGATAAAATAACGGGGTTG
1 GAGTATCCCC-ATAAAATAACGGGGTTG
1898783 GAGTATCCCC
1 GAGTATCCCC
1898793 GATTGTGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
28 34 0.94
29 1 0.03
30 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (27 bp):
GAGTATCCCCATAAAATAACGGGGTTG
Found at i:1898793 original size:28 final size:28
Alignment explanation
Indices: 1898741--1898795 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1898731 ATCCCCTCAG
1898741 AAATAACGGGGTTGGAGTATCCCCGATA
1 AAATAACGGGGTTGGAGTATCCCCGATA
1898769 AAATAACGGGGTTGGAGTATCCCCGAT
1 AAATAACGGGGTTGGAGTATCCCCGAT
1898796 TGTGAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (28 bp):
AAATAACGGGGTTGGAGTATCCCCGATA
Found at i:1898834 original size:51 final size:51
Alignment explanation
Indices: 1898777--1898892 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
1898767 TAAAATAACG
* * *
1898777 GGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTGGAAATAAAATC-
1 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAACCA
* * * * *
1898827 GGAGTTGGAATATCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAACCA
1 GG-GTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAACCA
1898879 GGGTTGGAGTATCC
1 GGGTTGGAGTATCC
1898893 TCTCAAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
50 2 0.04
51 51 0.93
52 2 0.04
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAACCA
Found at i:1899004 original size:80 final size:79
Alignment explanation
Indices: 1898831--1899050 Score: 313
Period size: 79 Copynumber: 2.8 Consensus size: 79
1898821 AAAATCGGAG
* * * * *
1898831 TTGGAATATCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAACCA-GGGTTGGAGTATCCTC
1 TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAA-CAGGGGTTGGAGTATCCCC
*
1898895 TCAAAAATAACGGGG
65 TCAAAAATAACGGGA
1898910 TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCAGGGGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAA-CAGGGGTTGGAGTATCCCC
*
1898975 TCGAAAATAACGGGA
65 TCAAAAATAACGGGA
* *
1898990 TTGGAGTATCCCCGA-TA--AAAAATTGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCC
1 TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACAGGGGTTGGAGTATCCCC
1899051 GATTAAGAAA
Statistics
Matches: 130, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
76 18 0.14
77 24 0.18
79 45 0.35
80 43 0.33
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (79 bp):
TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACAGGGGTTGGAGTATCCCCT
CAAAAATAACGGGA
Found at i:1899009 original size:28 final size:27
Alignment explanation
Indices: 1898949--1899009 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
1898939 TGTTTTAGAA
* * *
1898949 ATAAAATCAGGGGTTGGAGTATCCCCT
1 ATAAAATAAGGGATTGGAGTATCCCCG
**
1898976 CGAAAATAACGGGATTGGAGTATCCCCG
1 ATAAAATAA-GGGATTGGAGTATCCCCG
1899004 ATAAAA
1 ATAAAA
1899010 AATTGATGTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (27 bp):
ATAAAATAAGGGATTGGAGTATCCCCG
Found at i:1901376 original size:20 final size:19
Alignment explanation
Indices: 1901351--1901438 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 19
1901341 AAAATGTCTG
1901351 AATGTATCGATACATTGTAA
1 AATGTATCGATACA-TGTAA
1901371 AATGTATCGATAC------
1 AATGTATCGATACATGTAA
*
1901384 AATGTATCGATACA-ATAA
1 AATGTATCGATACATGTAA
*
1901402 GCAATGTATCGATACAATGCAA
1 --AATGTATCGATAC-ATGTAA
1901424 AATGTATCGATACAT
1 AATGTATCGATACAT
1901439 TCTGGGTTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
13 13 0.23
19 2 0.04
20 39 0.68
21 1 0.02
22 2 0.04
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACATGTAA
Found at i:1901387 original size:13 final size:13
Alignment explanation
Indices: 1901371--1901399 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1901361 TACATTGTAA
1901371 AATGTATCGATAC
1 AATGTATCGATAC
1901384 AATGTATCGATAC
1 AATGTATCGATAC
1901397 AAT
1 AAT
1901400 AAGCAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1901388 original size:33 final size:32
Alignment explanation
Indices: 1901351--1901420 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 32
1901341 AAAATGTCTG
*
1901351 AATGTATCGATACATTGTAA-AATGTATCGATAC
1 AATGTATCGATACA--ATAACAATGTATCGATAC
1901384 AATGTATCGATACAATAAGCAATGTATCGATAC
1 AATGTATCGATACAATAA-CAATGTATCGATAC
1901417 AATG
1 AATG
1901421 CAAAATGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 3 0.09
33 31 0.91
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (32 bp):
AATGTATCGATACAATAACAATGTATCGATAC
Found at i:1901479 original size:20 final size:20
Alignment explanation
Indices: 1901454--1901508 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1901444 GTTTACCCAG
*
1901454 AATGTATCGATACAACGAGC
1 AATGTATCGATACAACGAAC
* *
1901474 AATGTATCAATACAATGAAC
1 AATGTATCGATACAACGAAC
1901494 AATGTATCGATACAA
1 AATGTATCGATACAA
1901509 ATTGTGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AATGTATCGATACAACGAAC
Found at i:1902056 original size:19 final size:19
Alignment explanation
Indices: 1902032--1902078 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1902022 AATATTCTAG
*
1902032 AATATCTTAAAAAATATAA
1 AATATCTAAAAAAATATAA
1902051 AATATCTAAAAAAATATAA
1 AATATCTAAAAAAATATAA
*
1902070 AATTTCTAA
1 AATATCTAA
1902079 GTGTATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (19 bp):
AATATCTAAAAAAATATAA
Found at i:1904570 original size:14 final size:15
Alignment explanation
Indices: 1904543--1904598 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
1904533 TATTTTTAAA
* *
1904543 AAAAATTTATAAATT
1 AAAAATATAAAAATT
1904558 AAAAATA-AAAAATT
1 AAAAATATAAAAATT
* *
1904572 ATAAATATTAAAATT
1 AAAAATATAAAAATT
* *
1904587 TAAAATTTAAAA
1 AAAAATATAAAA
1904599 TTATTTTATT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATATAAAAATT
Done.