Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 23 of 120
Found at i:6023723 original size:48 final size:48
Alignment explanation
Indices: 6023664--6023803 Score: 163
Period size: 48 Copynumber: 2.9 Consensus size: 48
6023654 TTGAGCTTTA
* * *
6023664 CTTCATTGATTCGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCG
1 CTTCATTGATTCGATCCACTTCTCTGTATCTCATCAGGAAGATGACCG
* * * * *
6023712 CTTCATGGATTCAATCCACTTTTCTATATCTCATCAGAAAGATGACCG
1 CTTCATTGATTCGATCCACTTCTCTGTATCTCATCAGGAAGATGACCG
* * * * *
6023760 CTTTATTGCTTTGACCCACTTCTTTGTATCTCATCAGGAAGATG
1 CTTCATTGATTCGATCCACTTCTCTGTATCTCATCAGGAAGATG
6023804 GGGTTTGAAG
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 74 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (48 bp):
CTTCATTGATTCGATCCACTTCTCTGTATCTCATCAGGAAGATGACCG
Found at i:6023733 original size:123 final size:123
Alignment explanation
Indices: 6023530--6023755 Score: 319
Period size: 123 Copynumber: 1.8 Consensus size: 123
6023520 TTTCACCCGC
* * * *
6023530 ATTGAACTTTTCTTCATTAATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTTCTTTAT
1 ATTGAACTTTACTTCATTAATTCGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCAT
* * ** * *
6023595 TGCTTTGACCCACTTTTCTATATCTTATCAGGAAGATGGGGTTTGAAGTCTCATTCGT
66 GGATTCAACCCACTTTTCTATATCTCATCAGAAAGATGGGGTTTGAAGTCTCATTCGT
* *
6023653 ATTGAGCTTTACTTCATTGATTCGGTCTACTTCTCTGTATCTCATCAGGAAGATGA-TCGCTTCA
1 ATTGAACTTTACTTCATTAATTCGGTCTACTTCTCTGTATCTCATCAGGAAGATGACT-GCTTCA
*
6023717 TGGATTCAATCCACTTTTCTATATCTCATCAGAAAGATG
65 TGGATTCAACCCACTTTTCTATATCTCATCAGAAAGATG
6023756 ACCGCTTTAT
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
122 1 0.01
123 88 0.99
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (123 bp):
ATTGAACTTTACTTCATTAATTCGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCAT
GGATTCAACCCACTTTTCTATATCTCATCAGAAAGATGGGGTTTGAAGTCTCATTCGT
Found at i:6023772 original size:171 final size:171
Alignment explanation
Indices: 6023558--6023924 Score: 574
Period size: 171 Copynumber: 2.1 Consensus size: 171
6023548 AATTTGGTCT
** *
6023558 ACTTCTCTGTATCTCATCAGGAAGATGACTTCTTTATTGCTTTGACCCACTT-TTCTATATCTTA
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTT-TATATCTCA
* *
6023622 TCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTTACTTCATTGATTCGGTCTACTTCT
65 TCAGGAAGATGGGGTTTGAAGTCTCATTCGTATCGAGCTTCACTTCATTGATTCGGTCTACTTCT
*
6023687 CTGTATCTCATCAGGAAGATGATCGCTTCATGGATTCAATCC
130 CTGTATCTCATCAGGAAGATGACCGCTTCATGGATTCAATCC
* * * *
6023729 ACTTTTCTATATCTCATCAGAAAGATGACCGCTTTATTGCTTTGACCCACTTCTTTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTTTATATCTCAT
* *
6023794 CAGGAAGATGGGGTTTGAAGTCTCATTCGTATCGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
66 CAGGAAGATGGGGTTTGAAGTCTCATTCGTATCGAGCTTCACTTCATTGATTCGGTCTACTTCTC
* * * *
6023859 TGTATCTCATCAGGAAGATGACCGCTTCATTGTTTTAATCT
131 TGTATCTCATCAGGAAGATGACCGCTTCATGGATTCAATCC
6023900 ACTTCTCTGTATCTCATCAGGAAGA
1 ACTTCTCTGTATCTCATCAGGAAGA
6023925 CAAATTTGGT
Statistics
Matches: 176, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
171 174 0.99
172 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (171 bp):
ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTTTATATCTCAT
CAGGAAGATGGGGTTTGAAGTCTCATTCGTATCGAGCTTCACTTCATTGATTCGGTCTACTTCTC
TGTATCTCATCAGGAAGATGACCGCTTCATGGATTCAATCC
Found at i:6023887 original size:48 final size:48
Alignment explanation
Indices: 6023833--6023924 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
6023823 TATCGAGCTT
**
6023833 CGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGAC
1 CGCTTCATTGATTTAATCTACTTCTCTGTATCTCATCAGGAAGATGAC
*
6023881 CGCTTCATTGTTTTAATCTACTTCTCTGTATCTCATCAGGAAGA
1 CGCTTCATTGATTTAATCTACTTCTCTGTATCTCATCAGGAAGA
6023925 CAAATTTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (48 bp):
CGCTTCATTGATTTAATCTACTTCTCTGTATCTCATCAGGAAGATGAC
Found at i:6023989 original size:85 final size:85
Alignment explanation
Indices: 6023843--6024009 Score: 230
Period size: 85 Copynumber: 2.0 Consensus size: 85
6023833 CGCTTCATTG
** * * * *
6023843 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTTAATCTACTTCTCT
1 ATTTGGTCTACTTCTCTACATCTCATCAGGAAGATGACCACTTCATTGTCTTAACCCACTTCTCT
6023908 GTATCTCATCAGGAAGACAA
66 GTATCTCATCAGGAAGACAA
* *
6023928 ATTTGGT-TCACTTCTCTACATCTCGTCAGGAAGATGACCACTTTATTG-CTTAGACCCACTTCT
1 ATTTGGTCT-ACTTCTCTACATCTCATCAGGAAGATGACCACTTCATTGTCTTA-ACCCACTTCT
6023991 CTGTATCTCATCAGGAAGA
64 CTGTATCTCATCAGGAAGA
6024010 TGGGGTTTGA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
84 4 0.06
85 68 0.94
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (85 bp):
ATTTGGTCTACTTCTCTACATCTCATCAGGAAGATGACCACTTCATTGTCTTAACCCACTTCTCT
GTATCTCATCAGGAAGACAA
Found at i:6036549 original size:16 final size:18
Alignment explanation
Indices: 6036519--6036555 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
6036509 AAATGACACA
*
6036519 AAAAGAATAATTATAC-G
1 AAAAGAATAAATATACAG
6036536 AAAA-AATAAATATACAG
1 AAAAGAATAAATATACAG
6036553 AAA
1 AAA
6036556 TTAAGCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.19
Consensus pattern (18 bp):
AAAAGAATAAATATACAG
Found at i:6036765 original size:30 final size:30
Alignment explanation
Indices: 6036730--6037062 Score: 324
Period size: 30 Copynumber: 11.2 Consensus size: 30
6036720 TAATTTGGGA
* * *
6036730 TCAAAATGTAATTTTGGAAAAATTCAGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
*
6036760 TCAAAATGTAATTTTTGG--AAGTTT--GGC
1 TCAAAATGTAA-TTTTGGAAAAGTTTAAGGG
* *
6036787 TAACAAAATGTGATTTTGGCAAAG-TTAAGGAG
1 T--CAAAATGTAATTTTGGAAAAGTTTAAGG-G
*
6036819 TCAAAATGTGATTTTGG-AAAGTTT-AGGAG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGG-G
*
6036848 TCAAAATGTAATTTTGGAAAAGTTTAAGTG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* *
6036878 TCAAAATGTCATTTTGGAAAAGTTTAAAGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* * **
6036908 TTAAAATGCAATTTTGGAAAAGTTTGGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* *
6036938 TTAAAATGTAATTTTGGAGAAGTTTAAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* * *
6036968 T-TAAATGTAATTTTAGAGAAGTTT-AGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* * * *
6036996 CTCAAAATATAATTATGGAAAGGTTCAAGGG
1 -TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* *
6037027 TCAAAATGTAATTTTAGAAAAATTTAAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
6037057 TCAAAA
1 TCAAAA
6037063 CATGGTTTTT
Statistics
Matches: 254, Mismatches: 35, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
27 3 0.01
28 10 0.04
29 62 0.24
30 164 0.65
31 14 0.06
32 1 0.00
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (30 bp):
TCAAAATGTAATTTTGGAAAAGTTTAAGGG
Found at i:6036915 original size:60 final size:60
Alignment explanation
Indices: 6036730--6037062 Score: 324
Period size: 59 Copynumber: 5.6 Consensus size: 60
6036720 TAATTTGGGA
* * * *
6036730 TCAAAATGTAATTTTGGAAAAATTCAGGGGTCAAAATGTAATTTTTGG--AAGTTT--GGC
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAA-TTTTGGAAAAGTTTAAGGG
* * *
6036787 TAACAAAATGTGATTTTGGCAAAG-TTAAGGAGTCAAAATGTGATTTTGG-AAAGTTT-AGGAG
1 T--CAAAATGTAATTTTGGAAAAGTTTAAGG-GTCAAAATGTAATTTTGGAAAAGTTTAAGG-G
* * *
6036848 TCAAAATGTAATTTTGGAAAAGTTTAAGTGTCAAAATGTCATTTTGGAAAAGTTTAAAGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGG
* * ** * *
6036908 TTAAAATGCAATTTTGGAAAAGTTTGGGGGTTAAAATGTAATTTTGGAGAAGTTTAAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGG
* * * * * * *
6036968 T-TAAATGTAATTTTAGAGAAGTTT-AGGGCTCAAAATATAATTATGGAAAGGTTCAAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG-TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* *
6037027 TCAAAATGTAATTTTAGAAAAATTTAAGGGTCAAAA
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAA
6037063 CATGGTTTTT
Statistics
Matches: 229, Mismatches: 35, Indels: 21
0.80 0.12 0.07
Matches are distributed among these distances:
57 1 0.00
58 13 0.06
59 115 0.50
60 93 0.41
61 7 0.03
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (60 bp):
TCAAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGG
Found at i:6037003 original size:89 final size:90
Alignment explanation
Indices: 6036730--6037062 Score: 322
Period size: 89 Copynumber: 3.7 Consensus size: 90
6036720 TAATTTGGGA
* * *
6036730 TCAAAATGTAATTTTGGAAAAATTCAGGGGTCAAAATGTAATTTTTGG--AAGTTT--GGCTAAC
1 TCAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAA-TTTTGGAAAAGTTTAAGGGT--C
* * * *
6036791 AAAATGTGATTTTGGCAAAG-TTAAGGAG
63 AAAATGTAATTTTAGAAAAGTTTAAAG-G
* * *
6036819 TCAAAATGTGATTTTGG-AAAGTTTAGGAGTCAAAATGTAATTTTGGAAAAGTTTAAGTGTCAAA
1 TCAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTCAAA
* *
6036883 ATGTCATTTTGGAAAAGTTTAAAGG
66 ATGTAATTTTAGAAAAGTTTAAAGG
* * * * * *
6036908 TTAAAATGCAATTTTGGAAAAGTTTGGGGGTTAAAATGTAATTTTGGAGAAGTTTAAGGGT-TAA
1 TCAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTCAAA
* *
6036972 ATGTAATTTTAGAGAAGTTT-AGGG
66 ATGTAATTTTAGAAAAGTTTAAAGG
* * * * * * *
6036996 CTCAAAATATAATTATGGAAAGGTTCAAGGGTCAAAATGTAATTTTAGAAAAATTTAAGGGTCAA
1 -TCAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTCAA
6037061 AA
65 AA
6037063 CATGGTTTTT
Statistics
Matches: 201, Mismatches: 35, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
87 6 0.03
88 23 0.11
89 124 0.62
90 46 0.23
91 2 0.01
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (90 bp):
TCAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTCAAA
ATGTAATTTTAGAAAAGTTTAAAGG
Found at i:6037080 original size:119 final size:119
Alignment explanation
Indices: 6036811--6037082 Score: 275
Period size: 119 Copynumber: 2.3 Consensus size: 119
6036801 TTTGGCAAAG
* *
6036811 TTAAGGAGTCAAAATGTGATTTTGGAAAGTTT-AGGAGTCAAAATGTAATTTTGGAAAAGTTTAA
1 TTAAGG-GTAAAAATGT-ATTTTGGAAAGTTTAAGGAGTCAAAATGTAATTTTAGAAAAGTTTAA
* * * * * * * *
6036875 GTGTCAAAATGTCATTTTGGAAAAGTTTAAAGGTTAAAATGCAATTTTGGAAAAGT
64 GGGTCAAAATATAATTATGGAAAAGTTCAAAGGTCAAAATGCAATTTTAGAAAAAT
** * * *
6036931 TTGGGGGTTAAAATGTAATTTTGGAGAAGTTTAAGG-GT-TAAATGTAATTTTAGAGAAGTTT-A
1 TTAAGGGTAAAAATGT-ATTTTGGA-AAGTTTAAGGAGTCAAAATGTAATTTTAGAAAAGTTTAA
* * *
6036993 GGGCTCAAAATATAATTATGGAAAGGTTCAAGGGTCAAAATGTAATTTTAGAAAAAT
64 GGG-TCAAAATATAATTATGGAAAAGTTCAAAGGTCAAAATGCAATTTTAGAAAAAT
6037050 TTAAGGGTCAAAACATGGT-TTTTGGAAAGTTTA
1 TTAAGGGT-AAAA-AT-GTATTTTGGAAAGTTTA
6037083 GGGATCCCTT
Statistics
Matches: 125, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
118 3 0.02
119 93 0.74
120 22 0.18
121 5 0.04
122 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (119 bp):
TTAAGGGTAAAAATGTATTTTGGAAAGTTTAAGGAGTCAAAATGTAATTTTAGAAAAGTTTAAGG
GTCAAAATATAATTATGGAAAAGTTCAAAGGTCAAAATGCAATTTTAGAAAAAT
Found at i:6038779 original size:18 final size:17
Alignment explanation
Indices: 6038756--6038789 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
6038746 ATTTAAAATT
6038756 TAAATTTAAAATTTAAAG
1 TAAATTT-AAATTTAAAG
6038774 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
6038790 ATTTGTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:6038793 original size:7 final size:6
Alignment explanation
Indices: 6038746--6038789 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
6038736 TGTATTGAAC
*
6038746 ATTTAAA ATTTAA ATTTAAA ATTTAA A-GTAA ATTTAA ATTTAA A
1 ATTT-AA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA A
6038790 ATTTGTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 4 0.12
6 19 0.58
7 10 0.30
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:6044382 original size:23 final size:23
Alignment explanation
Indices: 6044356--6044400 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6044346 AAAATTGAAT
**
6044356 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
6044379 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
6044401 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:6044659 original size:58 final size:58
Alignment explanation
Indices: 6044609--6044730 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 58
6044599 AAACCCATCA
6044609 ACAAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTATTAAAAAACACTC
1 ACAAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTATTAAAAAACACTC
* * ** *
6044667 ATAAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTC
1 ACAAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTATTAAAAAACACTC
*
6044725 ATAAAC
1 ACAAAC
6044731 AATTCTTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.30
Consensus pattern (58 bp):
ACAAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTATTAAAAAACACTC
Found at i:6046780 original size:26 final size:26
Alignment explanation
Indices: 6046751--6046836 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 26
6046741 TATATTTTTC
6046751 ATATTTTATTAAAAATATTTATATTA
1 ATATTTTATTAAAAATATTTATATTA
* *
6046777 ATATTTTAATAATAAATATATATATTA
1 ATATTTTATTAA-AAATATTTATATTA
* *
6046804 A-ATTTT-TGTAAAAAT-TTAATAATAA
1 ATATTTTAT-TAAAAATATTTAT-ATTA
6046829 ATATTTTA
1 ATATTTTA
6046837 GAGTATAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
24 3 0.06
25 8 0.16
26 24 0.49
27 14 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (26 bp):
ATATTTTATTAAAAATATTTATATTA
Found at i:6046801 original size:27 final size:27
Alignment explanation
Indices: 6046737--6046809 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 27
6046727 ATTTTAAATT
* * *
6046737 TAAATATAT-TTTTCATATTTTATTAA
1 TAAATATATATATTAATATTTTAATAA
*
6046763 -AAATATTTATATTAATATTTTAATAA
1 TAAATATATATATTAATATTTTAATAA
6046789 TAAATATATATATTAA-ATTTT
1 TAAATATATATATTAATATTTT
6046810 TGTAAAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 7 0.17
26 19 0.47
27 14 0.35
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (27 bp):
TAAATATATATATTAATATTTTAATAA
Found at i:6046810 original size:27 final size:26
Alignment explanation
Indices: 6046738--6046836 Score: 87
Period size: 26 Copynumber: 3.8 Consensus size: 26
6046728 TTTTAAATTT
* * *
6046738 AAATATAT-TTTTCATATTTTATTAA
1 AAATATATATATTAATATTTTAATAA
*
6046763 AAATATTTATATTAATATTTTAATAA
1 AAATATATATATTAATATTTTAATAA
**
6046789 TAAATATATATATTAA-ATTTTTGTAA
1 -AAATATATATATTAATATTTTAATAA
* *
6046815 AAATTTA-ATAATAAATATTTTA
1 AAATATATAT-ATTAATATTTTA
6046837 GAGTATAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
24 2 0.03
25 17 0.28
26 27 0.45
27 14 0.23
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
AAATATATATATTAATATTTTAATAA
Found at i:6054154 original size:17 final size:17
Alignment explanation
Indices: 6054132--6054221 Score: 87
Period size: 17 Copynumber: 5.2 Consensus size: 17
6054122 GTGTTGAGAA
6054132 TTAAATTTATCTTAAAT
1 TTAAATTTATCTTAAAT
6054149 TTAAATTTATCTTAAAT
1 TTAAATTTATCTTAAAT
* *
6054166 TTAAATTTAAT-TTGAGT
1 TTAAATTT-ATCTTAAAT
*
6054183 TTAAATCTA-CTTTCAAAT
1 TTAAATTTATC-TT-AAAT
*
6054201 TTAAAATTAT-TATAAAT
1 TTAAATTTATCT-TAAAT
6054218 TTAA
1 TTAA
6054222 TTAAAATGTC
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
16 1 0.02
17 47 0.78
18 12 0.20
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (17 bp):
TTAAATTTATCTTAAAT
Found at i:6054243 original size:15 final size:15
Alignment explanation
Indices: 6054220--6054257 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
6054210 TTATAAATTT
6054220 AATTA-AAATGTCCA
1 AATTACAAATGTCCA
*
6054234 AATTACAAATGTCTA
1 AATTACAAATGTCCA
6054249 AATTACAAA
1 AATTACAAA
6054258 GGCCCAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (15 bp):
AATTACAAATGTCCA
Found at i:6057040 original size:43 final size:45
Alignment explanation
Indices: 6056981--6057075 Score: 133
Period size: 43 Copynumber: 2.2 Consensus size: 45
6056971 GAGAAAAAAG
*
6056981 AAAAAAA-GGGTTGAAAAGCCGTAAAAGGCA-TT-AAAAAAACTC
1 AAAAAAAGGGGTTGAAAAGCCGCAAAAGGCATTTAAAAAAAACTC
* * *
6057023 AAAAAAAGGGGTTGAAAATCCGCAAAAGGTATTTAAAAAAAACTT
1 AAAAAAAGGGGTTGAAAAGCCGCAAAAGGCATTTAAAAAAAACTC
6057068 AAAAAAAG
1 AAAAAAAG
6057076 AGTCAAGATG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
42 7 0.15
43 20 0.43
44 2 0.04
45 17 0.37
ACGTcount: A:0.57, C:0.09, G:0.18, T:0.16
Consensus pattern (45 bp):
AAAAAAAGGGGTTGAAAAGCCGCAAAAGGCATTTAAAAAAAACTC
Found at i:6059244 original size:50 final size:51
Alignment explanation
Indices: 6059164--6059269 Score: 171
Period size: 50 Copynumber: 2.1 Consensus size: 51
6059154 CTACAGGTCT
*
6059164 CAGTACCACGCAAAGACATAAGGGAAAGATCTAAGACCGCAACGATAGATC
1 CAGTACCACGCAAAGACATAAGGGAAAGATCTAAGACCGCAACGACAGATC
*
6059215 CAGTACCACG-AAA-ACATGACGGGAAAGATCTAAGACCGCAACGACAGATC
1 CAGTACCACGCAAAGACAT-AAGGGAAAGATCTAAGACCGCAACGACAGATC
6059265 CAGTA
1 CAGTA
6059270 TCGCAAAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
49 4 0.08
50 38 0.73
51 10 0.19
ACGTcount: A:0.42, C:0.25, G:0.22, T:0.11
Consensus pattern (51 bp):
CAGTACCACGCAAAGACATAAGGGAAAGATCTAAGACCGCAACGACAGATC
Found at i:6059448 original size:92 final size:92
Alignment explanation
Indices: 6059291--6060206 Score: 1408
Period size: 92 Copynumber: 10.0 Consensus size: 92
6059281 CAAAAAGGAA
*
6059291 AAGTCTTCATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
6059356 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
* *
6059383 AAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATCCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
**
6059448 CTTGAAACTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
* * * * *
6059475 AAGTCATTATCTCTCTGAAATTGTAGTAAGAGCTAGATGAAGCATCAAACATCATTTTCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
6059540 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
* * * *
6059567 AAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCTAGATGAAGCATCAAACATCATTTTCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
6059632 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
*
6059659 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATCCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
* * * *
6059724 -TGTGAAGTTGCAGTAAAGCTAGATAGT
66 CT-TGAAGTTGTAGTAAAGTTGGATAGC
* * *
6059751 AAGCCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAACATCAAACATCAATTTCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
*
6059816 CTTGAAGTTGTAGTAAAGTTGGATAAC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
* *
6059843 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAACATCAAACATCATTTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
6059908 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
* *
6059935 AAGTTTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATC-AACATCAATTCTTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
*
6059999 CTTGAAGTTATAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
* * * * *
6060026 GAA-CCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATTAATTCTTATCC
1 -AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
*
6060090 TCTTGAAGTTATAGTAAAGTTGGAT-GAC
65 TCTTGAAGTTGTAGTAAAGTTGGATAG-C
** * * * *
6060118 AAACCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATTAATTTCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
*
6060183 CTTGAAGTTGCAGTAAAGTTGGAT
66 CTTGAAGTTGTAGTAAAGTTGGAT
6060207 TAAAAACAAA
Statistics
Matches: 763, Mismatches: 55, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
91 85 0.11
92 677 0.89
93 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (92 bp):
AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCT
CTTGAAGTTGTAGTAAAGTTGGATAGC
Found at i:6060872 original size:17 final size:17
Alignment explanation
Indices: 6060849--6060971 Score: 117
Period size: 17 Copynumber: 7.3 Consensus size: 17
6060839 TCAAGCCCAT
6060849 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
6060867 -TTAAATTTGTTTGAAA
1 TTTAAATTTATTTTAAA
*
6060883 TTTAAATTTATCTTAAA
1 TTTAAATTTATTTTAAA
6060900 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
6060917 TTTAAATTTA--ATGAG
1 TTTAAATTTATTTTAAA
*
6060932 TTTAAATCTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
6060950 TTTAAAATTGTTATAAA
1 TTTAAATTTATTTTAAA
6060967 TTTAA
1 TTTAA
6060972 TTAAAATGTC
Statistics
Matches: 84, Mismatches: 17, Indels: 9
0.76 0.15 0.08
Matches are distributed among these distances:
15 11 0.13
16 1 0.01
17 61 0.73
18 11 0.13
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:6060889 original size:6 final size:6
Alignment explanation
Indices: 6060880--6060927 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
6060870 AATTTGTTTG
*
6060880 AAATTT AAATTT --ATCTT AAATTT AAATTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAAT-TT AAATTT AAATTT AAATTT AAATTT AAATTT
6060926 AA
1 AA
6060928 TGAGTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
4 2 0.06
5 6 0.17
6 26 0.72
7 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:6060995 original size:15 final size:15
Alignment explanation
Indices: 6060970--6061007 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
6060960 TTATAAATTT
6060970 AATTA-AAATGTCCA
1 AATTACAAATGTCCA
*
6060984 AATTACAAATGTCTA
1 AATTACAAATGTCCA
6060999 AATTACAAA
1 AATTACAAA
6061008 GGCCCAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (15 bp):
AATTACAAATGTCCA
Found at i:6062286 original size:13 final size:13
Alignment explanation
Indices: 6062268--6062303 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
6062258 GGTGAGATAT
6062268 GAGAAAGAAAGGA
1 GAGAAAGAAAGGA
*
6062281 GAGAAAGAAAGGG
1 GAGAAAGAAAGGA
*
6062294 GAAAAAGAAA
1 GAGAAAGAAA
6062304 TTTTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
GAGAAAGAAAGGA
Found at i:6062797 original size:30 final size:30
Alignment explanation
Indices: 6062757--6063112 Score: 287
Period size: 30 Copynumber: 11.9 Consensus size: 30
6062747 CTCTGAAAGT
*
6062757 CCCT-AAACTTTCTATAAATTATATTTTGA
1 CCCTAAAACTTTCTATAAATTACATTTTGA
* * *
6062786 CCCTAAAACTTTTTAAAAATTACATGTTGA
1 CCCTAAAACTTTCTATAAATTACATTTTGA
** * *
6062816 CCCTTGAACTTTTCTAT-AATTATATTTTAA
1 CCCTAAAAC-TTTCTATAAATTACATTTTGA
6062846 CCCTAAAACTTTCTATAAATTACATTTTGA
1 CCCTAAAACTTTCTATAAATTACATTTTGA
*
6062876 CCCTAAAACTTTCTATAAATTACATTTTAA
1 CCCTAAAACTTTCTATAAATTACATTTTGA
* * * *
6062906 CCCTTAAACTTTTTCA-AAATTATATTTTAA
1 CCCTAAAACTTTCT-ATAAATTACATTTTGA
* * ** * *
6062936 CCCTAAAATTTTTTGGAAATTGCATTTCGA
1 CCCTAAAACTTTCTATAAATTACATTTTGA
* **
6062966 CTCCT-AAACTTTTCCA-AAAGGACATTTTGA
1 C-CCTAAAAC-TTTCTATAAATTACATTTTGA
* * *
6062996 CCCTTAAACTTTTCCA-AAATTATATTTTGA
1 CCCTAAAAC-TTTCTATAAATTACATTTTGA
* * *
6063026 CCCCAAAACTTTTTGTAAATTACATTTTGA
1 CCCTAAAACTTTCTATAAATTACATTTTGA
** * * *
6063056 CCCTTGAGCTTTCT-TGAAATTATATTTTAA
1 CCCTAAAACTTTCTAT-AAATTACATTTTGA
* *
6063086 CCCCAAAACTTTCTA-AAATTATATTTT
1 CCCTAAAACTTTCTATAAATTACATTTT
6063113 TACCACCAAG
Statistics
Matches: 262, Mismatches: 54, Indels: 22
0.78 0.16 0.07
Matches are distributed among these distances:
29 30 0.11
30 220 0.84
31 12 0.05
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (30 bp):
CCCTAAAACTTTCTATAAATTACATTTTGA
Found at i:6062840 original size:60 final size:61
Alignment explanation
Indices: 6062760--6063112 Score: 328
Period size: 60 Copynumber: 5.9 Consensus size: 61
6062750 TGAAAGTCCC
* *
6062760 TAAAC-TTTCTATAAATTATATTTTGACCCTAAAACTTTTTAAAAATTACATGTTGACCCT
1 TAAACTTTTCTATAAATTATATTTTAACCCTAAAACTTTTTAAAAATTACATTTTGACCCT
* * *
6062820 TGAACTTTTCTAT-AATTATATTTTAACCCTAAAACTTTCTATAAATTACATTTTGACCCT
1 TAAACTTTTCTATAAATTATATTTTAACCCTAAAACTTTTTAAAAATTACATTTTGACCCT
* * * * * *
6062880 AAAAC-TTTCTATAAATTACATTTTAACCCTTAAACTTTTTCAAAATTATATTTTAACCC-
1 TAAACTTTTCTATAAATTATATTTTAACCCTAAAACTTTTTAAAAATTACATTTTGACCCT
* * ** ** ** ** **
6062939 TAAAATTTTTTGGAAATTGCATTTCGACTCCT-AAACTTTTCCAAAAGGACATTTTGACCCT
1 TAAACTTTTCTATAAATTATATTTTAAC-CCTAAAACTTTTTAAAAATTACATTTTGACCCT
* * * **
6063000 TAAACTTTTCCA-AAATTATATTTTGACCCCAAAACTTTTTGTAAATTACATTTTGACCCT
1 TAAACTTTTCTATAAATTATATTTTAACCCTAAAACTTTTTAAAAATTACATTTTGACCCT
* * * * *
6063060 TGAGC-TTTCT-TGAAATTATATTTTAACCCCAAAACTTTCT-AAAATTATATTTT
1 TAAACTTTTCTAT-AAATTATATTTTAACCCTAAAACTTTTTAAAAATTACATTTT
6063113 TACCACCAAG
Statistics
Matches: 238, Mismatches: 47, Indels: 17
0.79 0.16 0.06
Matches are distributed among these distances:
59 27 0.11
60 193 0.81
61 18 0.08
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (61 bp):
TAAACTTTTCTATAAATTATATTTTAACCCTAAAACTTTTTAAAAATTACATTTTGACCCT
Found at i:6062861 original size:90 final size:90
Alignment explanation
Indices: 6062757--6063112 Score: 380
Period size: 90 Copynumber: 4.0 Consensus size: 90
6062747 CTCTGAAAGT
* *
6062757 CCCT-AAACTTTCTATAAATTATATTTTGACCCTAAAACTTTTTAAAAATTACATGTTGACCCTT
1 CCCTAAAACTTTCTATAAATTACATTTTGACCCTAAAACTTTTTAAAAATTACATTTTGACCCTT
* *
6062821 GAACTTTTCTATAATTATATTTTAA
66 AAACTTTTCTAAAATTATATTTTAA
* * *
6062846 CCCTAAAACTTTCTATAAATTACATTTTGACCCTAAAACTTTCTATAAATTACATTTTAACCCTT
1 CCCTAAAACTTTCTATAAATTACATTTTGACCCTAAAACTTTTTAAAAATTACATTTTGACCCTT
6062911 AAACTTTT-TCAAAATTATATTTTAA
66 AAACTTTTCT-AAAATTATATTTTAA
* * ** * * ** **
6062936 CCCTAAAATTTTTTGGAAATTGCATTTCGACTCCT-AAACTTTTCCAAAAGGACATTTTGACCCT
1 CCCTAAAACTTTCTATAAATTACATTTTGAC-CCTAAAACTTTTTAAAAATTACATTTTGACCCT
* *
6063000 TAAACTTTTCCAAAATTATATTTTGA
65 TAAACTTTTCTAAAATTATATTTTAA
* * * ** * * * * *
6063026 CCCCAAAACTTTTTGTAAATTACATTTTGACCCTTGAGCTTTCTT-GAAATTATATTTTAACCCC
1 CCCTAAAACTTTCTATAAATTACATTTTGACCCTAAAACTTT-TTAAAAATTACATTTTGACCCT
*
6063090 AAAAC-TTTCTAAAATTATATTTT
65 TAAACTTTTCTAAAATTATATTTT
6063113 TACCACCAAG
Statistics
Matches: 223, Mismatches: 38, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
89 25 0.11
90 194 0.87
91 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (90 bp):
CCCTAAAACTTTCTATAAATTACATTTTGACCCTAAAACTTTTTAAAAATTACATTTTGACCCTT
AAACTTTTCTAAAATTATATTTTAA
Found at i:6063254 original size:86 final size:87
Alignment explanation
Indices: 6063079--6063261 Score: 205
Period size: 86 Copynumber: 2.1 Consensus size: 87
6063069 TTGAAATTAT
* * *
6063079 ATTTTAACCCCAAAACTTTCTAAAATTATATTTTTACCACCAAGTTCTCCATAATTCCATTTTGA
1 ATTTTAACCCCAAAACTTTCTAAAATTACATTTTTACCACCAAGTTCACCAAAATTCCATTTTGA
* *
6063144 ACCTAATTTTACCAAAATTACC
66 ACCAAACTTTACCAAAATTACC
* * *
6063166 ATTTT-ACCCCCAAACTTTCTAAAATTCCATTTTTACC-CTCAATTTCACCAAAATTACCATTTT
1 ATTTTAACCCCAAAACTTTCTAAAATTACATTTTTACCAC-CAAGTTCACCAAAATT-CCATTTT
*
6063229 -ACTCCCAAACTTT-CCAAAATT-CC
64 GA--ACCAAACTTTACCAAAATTACC
6063252 ATTTTTAACC
1 A-TTTTAACC
6063262 TCGATTTTAC
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
85 1 0.01
86 46 0.57
87 24 0.30
88 10 0.12
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.38
Consensus pattern (87 bp):
ATTTTAACCCCAAAACTTTCTAAAATTACATTTTTACCACCAAGTTCACCAAAATTCCATTTTGA
ACCAAACTTTACCAAAATTACC
Found at i:6063300 original size:59 final size:58
Alignment explanation
Indices: 6063126--6063345 Score: 295
Period size: 58 Copynumber: 3.8 Consensus size: 58
6063116 CACCAAGTTC
* * *
6063126 TCCATAATTCCATTTTGAACCT-AATTTTACCAAAATTACCATTTTACCCCCAAACTT
1 TCCAAAATTCCATTTTTAACCTCAATTTTACCAAAATTACCATTTTACTCCCAAACTT
* * *
6063183 TCTAAAATTCCATTTTTACCCTCAATTTCACCAAAATTACCATTTTACTCCCAAACTT
1 TCCAAAATTCCATTTTTAACCTCAATTTTACCAAAATTACCATTTTACTCCCAAACTT
*
6063241 TCCAAAATTCCATTTTTAACCTCGATTTTACCAAAAATTACCATTTTACTCCCAAACTT
1 TCCAAAATTCCATTTTTAACCTCAATTTTACC-AAAATTACCATTTTACTCCCAAACTT
* *
6063300 T-TACAAA-TCTCATTTTTGACC-CAATTTTAACCAAAATTACCATTTT
1 TCCA-AAATTC-CATTTTTAACCTCAATTTT-ACCAAAATTACCATTTT
6063346 GCCCCCAGGT
Statistics
Matches: 145, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
57 18 0.12
58 84 0.58
59 43 0.30
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.38
Consensus pattern (58 bp):
TCCAAAATTCCATTTTTAACCTCAATTTTACCAAAATTACCATTTTACTCCCAAACTT
Found at i:6063346 original size:29 final size:27
Alignment explanation
Indices: 6063131--6063350 Score: 128
Period size: 29 Copynumber: 7.6 Consensus size: 27
6063121 AGTTCTCCAT
* *
6063131 AATTCCATTTTGAACCTAATTTTACCAA
1 AATTCCATTTT-ACCCCAATTTTACCAA
* *
6063159 AATTACCATTTTACCCCCAAACTTT-CTAA
1 AATT-CCATTTTA-CCCC-AATTTTACCAA
*
6063188 AATTCCATTTTTACCCTCAATTTCACCAA
1 AATTCCA-TTTTACCC-CAATTTTACCAA
*
6063217 AATTACCATTTTACTCCCAAACTTT-CCAA
1 AATT-CCATTTTAC-CCC-AATTTTACCAA
* *
6063246 AATTCCATTTTTAACCTCGATTTTACCAAA
1 AATTCCA-TTTT-ACCCCAATTTTACC-AA
6063276 AATTACCATTTTACTCCCAAACTTTTA-C-A
1 AATT-CCATTTTAC-CCC-AA-TTTTACCAA
6063305 AA-TCTCATTTTTGA-CCCAATTTTAACCAA
1 AATTC-CA-TTTT-ACCCCAATTTT-ACCAA
*
6063334 AATTACCATTTTGCCCC
1 AATT-CCATTTTACCCC
6063351 CAGGTATCCA
Statistics
Matches: 151, Mismatches: 15, Indels: 51
0.70 0.07 0.24
Matches are distributed among these distances:
26 4 0.03
27 4 0.03
28 29 0.19
29 71 0.47
30 32 0.21
31 6 0.04
32 5 0.03
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (27 bp):
AATTCCATTTTACCCCAATTTTACCAA
Found at i:6068407 original size:15 final size:15
Alignment explanation
Indices: 6068384--6068420 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
6068374 GACGTGTAGA
*
6068384 TTATGTTTCTAATCT
1 TTATATTTCTAATCT
6068399 TTATATTTCTAATCT
1 TTATATTTCTAATCT
6068414 TT-TATTT
1 TTATATTT
6068421 TTAGTTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.65
Consensus pattern (15 bp):
TTATATTTCTAATCT
Found at i:6068591 original size:58 final size:56
Alignment explanation
Indices: 6068529--6068688 Score: 173
Period size: 58 Copynumber: 2.8 Consensus size: 56
6068519 ATGTTTCTAA
* *
6068529 TATTATATATTATAATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATAT
1 TATTAAATATTATAATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATAT
* * *
6068587 TATTAAAT-TCTATATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATAT
1 TATTAAATAT-TATAAT-TTTTATTAAATTATATTTAATAATAATTATATTAAAATAT
*
6068644 AATTAAATTAATTA-ATATTTTTATTAAATTATATTTAATAATAAT
1 TATTAAA-T-ATTATA-ATTTTTATTAAATTATATTTAATAATAAT
6068689 CGTTAAATTT
Statistics
Matches: 87, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
57 14 0.16
58 57 0.66
59 11 0.13
60 5 0.06
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (56 bp):
TATTAAATATTATAATTTTTATTAAATTATATTTAATAATAATTATATTAAAATAT
Found at i:6068850 original size:46 final size:46
Alignment explanation
Indices: 6068783--6068878 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
6068773 ATTACAGCAT
*
6068783 CATTCCATTCAACCAAACAATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACAATTGAATTACTGATTACAGCTCTATTC
6068829 CATTCCAATCAACCAAACAATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACAATTGAATTACTGATTACAGCTCTATTC
6068875 CATT
1 CATT
6068879 ACACCTCTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (46 bp):
CATTCCAATCAACCAAACAATTGAATTACTGATTACAGCTCTATTC
Found at i:6068881 original size:16 final size:16
Alignment explanation
Indices: 6068860--6068897 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
6068850 TGAATTACTG
*
6068860 ATTACAGCTCTATTCC
1 ATTACACCTCTATTCC
6068876 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
6068892 ATTACA
1 ATTACA
6068898 ACGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.32, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:6072327 original size:28 final size:28
Alignment explanation
Indices: 6072272--6072342 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
6072262 ATTTTTTAAA
* *
6072272 AAATAATTTTGTATTTTATTTTAATATT
1 AAATAATTTTATATATTATTTTAATATT
* *
6072300 TAATAATTTTATATATT-TTTTATTTATT
1 AAATAATTTTATATATTATTTTA-ATATT
**
6072328 AAATTTTTTTATATA
1 AAATAATTTTATATA
6072343 GTCATCTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
27 5 0.14
28 30 0.86
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (28 bp):
AAATAATTTTATATATTATTTTAATATT
Found at i:6075757 original size:27 final size:27
Alignment explanation
Indices: 6075657--6075752 Score: 120
Period size: 27 Copynumber: 3.6 Consensus size: 27
6075647 TGGCAGCTAT
* * * *
6075657 GAATTGCCTTTGTGGAGAAGTCTGAAA
1 GAATAGCCTTTGTGGCGAACTCTGAAG
* *
6075684 GAATAGCCTTTGCGACGAACTCTGAAG
1 GAATAGCCTTTGTGGCGAACTCTGAAG
* *
6075711 GAATAGCCTTTGTAGCGTACTCTGAAG
1 GAATAGCCTTTGTGGCGAACTCTGAAG
6075738 GAATAGCCTTTGTGG
1 GAATAGCCTTTGTGG
6075753 TGTACCATGA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GAATAGCCTTTGTGGCGAACTCTGAAG
Found at i:6081214 original size:30 final size:30
Alignment explanation
Indices: 6081175--6081425 Score: 235
Period size: 30 Copynumber: 8.3 Consensus size: 30
6081165 AAAGAATACG
6081175 GGGTTAAAATGTAATTTTGGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAA
*
6081205 GGGTAAAAATGTAATTTTTAGG-AAAGTTT-A
1 GGGTTAAAATGTAA-TTTT-GGAAAAGTTTAA
* *
6081235 GGGTTAAAATTTGATTTT-GAAGAAGTTT-A
1 GGGTTAAAATGTAATTTTGGAA-AAGTTTAA
* * * *
6081264 GGATCAAAATGTGATTTT-GAAAAGGTCTGAA
1 GGGTTAAAATGTAATTTTGGAAAA-GT-TTAA
* * **
6081295 GGGTCAAAATGTAATTTTGGAAAAAATTTGG
1 GGGTTAAAATGTAATTTTGG-AAAAGTTTAA
*
6081326 GGGTTAAAATATAATTTTGGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAA
* * * *
6081356 AGGTTAAAATGTAATTTAGAAAAAGTTT-G
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAA
* *
6081385 GGGTTTAAAATGTAATTTTGGAAATGTTAAA
1 GGG-TTAAAATGTAATTTTGGAAAAGTTTAA
6081416 GGGTTAAAAT
1 GGGTTAAAAT
6081426 TGGATTTTTA
Statistics
Matches: 180, Mismatches: 30, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
27 1 0.01
28 3 0.02
29 33 0.18
30 85 0.47
31 50 0.28
32 4 0.02
33 4 0.02
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.35
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTAA
Found at i:6081441 original size:60 final size:59
Alignment explanation
Indices: 6081316--6081443 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 59
6081306 TAATTTTGGA
* *
6081316 AAAAATTTGGGGGTTAAAATATAATTTTGGAAAAGTTTAAAGGTTAAAATGTAATTTAG
1 AAAAGTTTGGGGGTTAAAATATAATTTTGGAAAAGTTTAAAGGTTAAAATGGAATTTAG
* * * *
6081375 AAAAAGTTTGGGGTTTAAAATGTAATTTTGGAAATG-TTAAAGGGTTAAAATTGGATTTTTAG
1 -AAAAGTTTGGGGGTTAAAATATAATTTTGGAAAAGTTTAAA-GGTTAAAA-TGGA-ATTTAG
6081437 -AAAGTTT
1 AAAAGTTT
6081444 AGAGACCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
59 5 0.08
60 46 0.78
61 3 0.05
62 5 0.08
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (59 bp):
AAAAGTTTGGGGGTTAAAATATAATTTTGGAAAAGTTTAAAGGTTAAAATGGAATTTAG
Found at i:6083783 original size:49 final size:48
Alignment explanation
Indices: 6083697--6084416 Score: 488
Period size: 49 Copynumber: 14.6 Consensus size: 48
6083687 TAAGGTGCTA
* *
6083697 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTATCA
1 GGTTCGCCGTTGCGGCCTCAACC-TTCCCTTCATATCTTCATGGTATCG
* * * * * * * *
6083746 GATTCACCGTTGCGACCTCAATCCTTCCCATCGTATCTTTTAAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTCCCTTCATATC-TTCATGGTATCG
* * * * *
6083796 GGTTCGCTGTTTCGTCCTCAACCTTTCCTTTCATATCTTCGTGGTATCG
1 GGTTCGCCGTTGCGGCCTCAACC-TTCCCTTCATATCTTCATGGTATCG
* * * * **
6083845 GGTTCACCGTTACGGCCTCAACTTTTCCCATC-TCATCTTTTTAGGTATCG
1 GGTTCGCCGTTGCGGCCTCAAC-CTTCCCTTCAT-ATCTTCAT-GGTATCG
* *
6083895 GGTTCGCCGTTGCGGCCTCAACCTTCCCTTCGTATCTTCATGGTATCA
1 GGTTCGCCGTTGCGGCCTCAACCTTCCCTTCATATCTTCATGGTATCG
* * * * * * *
6083943 GGTTCGCCGTTGCGACCTCAACCTTTCCCATCACATCTTTTAAGGCACCG
1 GGTTCGCCGTTGCGGCCTCAACC-TTCCCTTCATATC-TTCATGGTATCG
* * *
6083993 GATTCGTCGTTGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTATCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTCCCTTCATATCTTCATGGTATCG
* * * * * *
6084042 GGTTCACCGTTGCGGCCTCAACCTTTCTCATCACATCTTTTAAGGTATCG
1 GGTTCGCCGTTGCGGCCTCAACC-TTCCCTTCATATC-TTCATGGTATCG
** * * * * * * *
6084092 AATTCGTCGTCGCGGTCTCAATCCTTCCTTTCAAATCTTCATGGTACCA
1 GGTTCGCCGTTGCGGCCTCAA-CCTTCCCTTCATATCTTCATGGTATCG
* * ** * * * *
6084141 GATTCGTCGTTGCAACCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACC-TTCCCTTCATATCTTC-ATGGTATCG
* * ** * *
6084191 GATTCGTCGACGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTCCCTTCATATCTTCATGGTATCG
* * ** * * * *
6084240 GGTTCGTCGTTGCGACCTCAAATTTTCTCATCACATCTTCTTAGGTATCG
1 GGTTCGCCGTTGCGGCCTC-AACCTTCCCTTCATATCTTCAT-GGTATCG
* * * * *
6084290 GGTTCGTCGTTACGGCCTCAACTTTTCCCTTCATATCTTCATGGTACCA
1 GGTTCGCCGTTGCGGCCTCAAC-CTTCCCTTCATATCTTCATGGTATCG
* * * * **
6084339 GGTTCACCGTTACGGCCTCAACCTTTCCCTTCATATCTTTAGGGTATTA
1 GGTTCGCCGTTGCGGCCTCAACC-TTCCCTTCATATCTTCATGGTATCG
* * * *
6084388 GATTTGTCGTTGCGGCCTCAATCTTCCCT
1 GGTTCGCCGTTGCGGCCTCAACCTTCCCT
6084417 GTCAAACCTC
Statistics
Matches: 523, Mismatches: 128, Indels: 41
0.76 0.18 0.06
Matches are distributed among these distances:
48 39 0.07
49 266 0.51
50 212 0.41
51 6 0.01
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (48 bp):
GGTTCGCCGTTGCGGCCTCAACCTTCCCTTCATATCTTCATGGTATCG
Found at i:6083821 original size:99 final size:98
Alignment explanation
Indices: 6083697--6084416 Score: 755
Period size: 99 Copynumber: 7.3 Consensus size: 98
6083687 TAAGGTGCTA
* * *
6083697 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTATCAGATTCACCGTTGCGAC
1 GGTTCGTCGTTGCGGCCTCAACC-TTCCCTTCATATCTTCATGGTATCAGGTTCACCGTTGCGAC
**
6083762 CTCAATCC-TTCCCATCGTATCTTTTAAGGTACCG
65 CTCAA-CCTTTCCCATCACATCTTTTAAGGTACCG
* * * * * * *
6083796 GGTTCG-CTGTTTCGTCCTCAACCTTTCCTTTCATATCTTCGTGGTATCGGGTTCACCGTTACGG
1 GGTTCGTC-GTTGCGGCCTCAACC-TTCCCTTCATATCTTCATGGTATCAGGTTCACCGTTGCGA
* * * *
6083860 CCTCAACTTTTCCCATCTCATCTTTTTAGGTATCG
64 CCTCAACCTTTCCCATCACATCTTTTAAGGTACCG
* * *
6083895 GGTTCGCCGTTGCGGCCTCAACCTTCCCTTCGTATCTTCATGGTATCAGGTTCGCCGTTGCGACC
1 GGTTCGTCGTTGCGGCCTCAACCTTCCCTTCATATCTTCATGGTATCAGGTTCACCGTTGCGACC
*
6083960 TCAACCTTTCCCATCACATCTTTTAAGGCACCG
66 TCAACCTTTCCCATCACATCTTTTAAGGTACCG
* * * *
6083993 GATTCGTCGTTGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTATCGGGTTCACCGTTGCGGC
1 GGTTCGTCGTTGCGGCCTCAA-CCTTCCCTTCATATCTTCATGGTATCAGGTTCACCGTTGCGAC
* *
6084058 CTCAACCTTTCTCATCACATCTTTTAAGGTATCG
65 CTCAACCTTTCCCATCACATCTTTTAAGGTACCG
** * * * * * * ** *
6084092 AATTCGTCGTCGCGGTCTCAATCCTTCCTTTCAAATCTTCATGGTACCAGATTCGTCGTTGCAAC
1 GGTTCGTCGTTGCGGCCTCAA-CCTTCCCTTCATATCTTCATGGTATCAGGTTCACCGTTGCGAC
*
6084157 CTCAACCTTTCCCATCACATCTTCTAAGGTACCG
65 CTCAACCTTTCCCATCACATCTTTTAAGGTACCG
* ** * * * **
6084191 GATTCGTCGACGCGGCCTCAATCCTTCCCTTCAAATCTTCATGGTACCGGGTTCGTCGTTGCGAC
1 GGTTCGTCGTTGCGGCCTCAA-CCTTCCCTTCATATCTTCATGGTATCAGGTTCACCGTTGCGAC
** * *
6084256 CTCAAATTTTCTCATCACATCTTCTT-AGGTATCG
65 CTCAACCTTTCCCATCACATCTT-TTAAGGTACCG
* * * * *
6084290 GGTTCGTCGTTACGGCCTCAACTTTTCCCTTCATATCTTCATGGTACCAGGTTCACCGTTACGGC
1 GGTTCGTCGTTGCGGCCTCAAC-CTTCCCTTCATATCTTCATGGTATCAGGTTCACCGTTGCGAC
* * * ***
6084355 CTCAACCTTTCCCTTCATATC-TTTAGGGTATTA
65 CTCAACCTTTCCCATCACATCTTTTAAGGTACCG
* * *
6084388 GATTTGTCGTTGCGGCCTCAATCTTCCCT
1 GGTTCGTCGTTGCGGCCTCAACCTTCCCT
6084417 GTCAAACCTC
Statistics
Matches: 526, Mismatches: 88, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
97 8 0.02
98 109 0.21
99 407 0.77
100 2 0.00
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (98 bp):
GGTTCGTCGTTGCGGCCTCAACCTTCCCTTCATATCTTCATGGTATCAGGTTCACCGTTGCGACC
TCAACCTTTCCCATCACATCTTTTAAGGTACCG
Found at i:6084194 original size:198 final size:196
Alignment explanation
Indices: 6083697--6084422 Score: 877
Period size: 198 Copynumber: 3.7 Consensus size: 196
6083687 TAAGGTGCTA
* * *
6083697 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATCTTCATGGTATCAGATTCACCGTTGCGAC
1 GGTTCGTCGTTGCGGCCTCAACC-TTCCCTTCATATCTTCATGGTACCAGATTCACCGTTGCGAC
** * * *
6083762 CTCAATCC-TTCCCATCGTATCTTTTAAGGTACCGGGTTCG-CTGTTTCGTCCTCAA-CCTTTCC
65 CTCAA-CCTTTCCCATCACATCTTTTAAGGTACCGGATTCGTC-GTTGCGGCCTCAATCC-TTCC
* * * * * *
6083824 TTTCATATCTTCGTGGTATCGGGTTCACCGTTACGGCCTCAACTTTTCCCATCTCATCTTTTTAG
127 CTTCAAATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACTTTTCTCATCACATC-TTTTAG
6083889 GTATCG
191 GTATCG
* * * * *
6083895 GGTTCGCCGTTGCGGCCTCAACCTTCCCTTCGTATCTTCATGGTATCAGGTTCGCCGTTGCGACC
1 GGTTCGTCGTTGCGGCCTCAACCTTCCCTTCATATCTTCATGGTACCAGATTCACCGTTGCGACC
*
6083960 TCAACCTTTCCCATCACATCTTTTAAGGCACCGGATTCGTCGTTGCGGCCTCAATCCTTCCCTTC
66 TCAACCTTTCCCATCACATCTTTTAAGGTACCGGATTCGTCGTTGCGGCCTCAATCCTTCCCTTC
*
6084025 AAATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACCTTTCTCATCACATCTTTTAAGGTAT
131 AAATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACTTTTCTCATCACATCTTTT-AGGTAT
6084090 CG
195 CG
** * * * * ** *
6084092 AATTCGTCGTCGCGGTCTCAATCCTTCCTTTCAAATCTTCATGGTACCAGATTCGTCGTTGCAAC
1 GGTTCGTCGTTGCGGCCTCAA-CCTTCCCTTCATATCTTCATGGTACCAGATTCACCGTTGCGAC
* **
6084157 CTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGTCGACGCGGCCTCAATCCTTCCCTT
65 CTCAACCTTTCCCATCACATCTTTTAAGGTACCGGATTCGTCGTTGCGGCCTCAATCCTTCCCTT
* ** * *
6084222 CAAATCTTCATGGTACCGGGTTCGTCGTTGCGACCTCAAATTTTCTCATCACATCTTCTTAGGTA
130 CAAATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACTTTTCTCATCACATCTT-TTAGGTA
6084287 TCG
194 TCG
* * * * *
6084290 GGTTCGTCGTTACGGCCTCAACTTTTCCCTTCATATCTTCATGGTACCAGGTTCACCGTTACGGC
1 GGTTCGTCGTTGCGGCCTCAAC-CTTCCCTTCATATCTTCATGGTACCAGATTCACCGTTGCGAC
* * * *** *
6084355 CTCAACCTTTCCCTTCATATC-TTTAGGGTATTAGATTTGTCGTTGCGGCCTCAAT-CTTCCCTG
65 CTCAACCTTTCCCATCACATCTTTTAAGGTACCGGATTCGTCGTTGCGGCCTCAATCCTTCCCT-
6084418 TCAAA
129 TCAAA
6084423 CCTCTATAAT
Statistics
Matches: 457, Mismatches: 63, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
196 13 0.03
197 192 0.42
198 250 0.55
199 2 0.00
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (196 bp):
GGTTCGTCGTTGCGGCCTCAACCTTCCCTTCATATCTTCATGGTACCAGATTCACCGTTGCGACC
TCAACCTTTCCCATCACATCTTTTAAGGTACCGGATTCGTCGTTGCGGCCTCAATCCTTCCCTTC
AAATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACTTTTCTCATCACATCTTTTAGGTATC
G
Found at i:6092729 original size:59 final size:60
Alignment explanation
Indices: 6092621--6092820 Score: 147
Period size: 59 Copynumber: 3.3 Consensus size: 60
6092611 CAGAGAATAC
* *
6092621 AGGGTTAAAATGTAATTTTGGGAAAGTTTGGGGGAAAAATATAATTTTTGGGAAAGTTT-
1 AGGGTTAAAATATAATTTTGGGAAAGTTTGGGGGAAAAATATAATTTTTGAGAAAGTTTG
* ** * * *
6092680 AGGGTTAAAATATGATTTT-GGAGAAGTTTGAGGGTCAAAATGTGA-TTTTGAGAAGGTTTGG
1 AGGGTTAAAATATAATTTTGGGA-AAGTTTG-GGGGAAAAATATAATTTTTGAGAAAGTTT-G
** * * ** * * * *
6092741 AGGGTTAAAATGCAATTTTGGAAAAAGTTTAAGGGTTAAAACATAATTTTAGA-AAAGCTTA
1 AGGGTTAAAATATAATTTTGG-GAAAGTTT-GGGGGAAAAATATAATTTTTGAGAAAGTTTG
* *
6092802 AGGGTCAAAATGTAATTTT
1 AGGGTTAAAATATAATTTT
6092821 AGAAAAATTT
Statistics
Matches: 110, Mismatches: 23, Indels: 14
0.75 0.16 0.10
Matches are distributed among these distances:
58 3 0.03
59 36 0.33
60 10 0.09
61 33 0.30
62 22 0.20
63 6 0.05
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (60 bp):
AGGGTTAAAATATAATTTTGGGAAAGTTTGGGGGAAAAATATAATTTTTGAGAAAGTTTG
Found at i:6092776 original size:31 final size:30
Alignment explanation
Indices: 6092621--6092864 Score: 174
Period size: 30 Copynumber: 8.1 Consensus size: 30
6092611 CAGAGAATAC
*
6092621 AGGGTTAAAATGTAATTTTGGGAAAGTTT-
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTA
* ** * *
6092650 GGGGGAAAAATATAATTTTTGGGAAAGTTT-
1 AGGGTTAAAATGTAA-TTTTGGAAAAGTTTA
* * * *
6092680 AGGGTTAAAATATGATTTTGGAGAAGTTTG
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTA
* * * *
6092710 AGGGTCAAAATGTGATTTT-GAGAAGGTTTGG
1 AGGGTTAAAATGTAATTTTGGA-AAAGTTT-A
*
6092741 AGGGTTAAAATGCAATTTTGGAAAAAGTTTA
1 AGGGTTAAAATGTAATTTTGG-AAAAGTTTA
** * *
6092772 AGGGTTAAAACATAATTTTAGAAAAGCTTA
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTA
* * *
6092802 AGGGTCAAAATGTAATTTTAGAAAAATTTGA
1 AGGGTTAAAATGTAATTTTGGAAAAGTTT-A
* * *
6092833 A-GGTTAAAATTTGATTTCTAG-AAAGTTTA
1 AGGGTTAAAATGTAATTT-TGGAAAAGTTTA
6092862 AGG
1 AGG
6092865 ACCAAAATAT
Statistics
Matches: 173, Mismatches: 33, Indels: 17
0.78 0.15 0.08
Matches are distributed among these distances:
29 27 0.16
30 99 0.57
31 39 0.23
32 7 0.04
33 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.34
Consensus pattern (30 bp):
AGGGTTAAAATGTAATTTTGGAAAAGTTTA
Found at i:6092855 original size:61 final size:60
Alignment explanation
Indices: 6092741--6092864 Score: 144
Period size: 61 Copynumber: 2.0 Consensus size: 60
6092731 GAAGGTTTGG
* *
6092741 AGGGTTAAAATGCAATTTTGGAAAAAGTTTAAGGGTTAAAACATAATTTTAGAAAAGCTTA
1 AGGGTCAAAATGCAATTTTAGAAAAAGTTTAAGGGTTAAAACATAATTTTAG-AAAGCTTA
* ** * *
6092802 AGGGTCAAAATGTAATTTTAGAAAAA-TTTGAA-GGTTAAAATTTGATTTCTAGAAAGTTTA
1 AGGGTCAAAATGCAATTTTAGAAAAAGTTT-AAGGGTTAAAACATAATTT-TAGAAAGCTTA
6092862 AGG
1 AGG
6092865 ACCAAAATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
60 26 0.48
61 28 0.52
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (60 bp):
AGGGTCAAAATGCAATTTTAGAAAAAGTTTAAGGGTTAAAACATAATTTTAGAAAGCTTA
Found at i:6092878 original size:30 final size:30
Alignment explanation
Indices: 6092838--6092897 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
6092828 TTTGAAGGTT
* *
6092838 AAAATTTGATTTCTAGAAAGTTTAAGGACC
1 AAAATATGATTTCTAGAAAGTTCAAGGACC
* *
6092868 AAAATATGATTTTTGGAAAGTTCAAGGACC
1 AAAATATGATTTCTAGAAAGTTCAAGGACC
6092898 TACTAGGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (30 bp):
AAAATATGATTTCTAGAAAGTTCAAGGACC
Found at i:6092880 original size:60 final size:61
Alignment explanation
Indices: 6092754--6092880 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 61
6092744 GTTAAAATGC
* ** *
6092754 AATTTTGGAAAAAGTTTAAGGGTTAAAACATAATTTTAGAAAAGCTTAAGGGTCAAAATGT
1 AATTTTAGAAAAAGTTTAAGGGTTAAAACATAATTTTAGAAAAGCTTAAGGACCAAAATAT
** * *
6092815 AATTTTAGAAAAA-TTTGAA-GGTTAAAATTTGATTTCTAG-AAAGTTTAAGGACCAAAATAT
1 AATTTTAGAAAAAGTTT-AAGGGTTAAAACATAATTT-TAGAAAAGCTTAAGGACCAAAATAT
*
6092875 GATTTT
1 AATTTT
6092881 TGGAAAGTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
60 38 0.69
61 17 0.31
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (61 bp):
AATTTTAGAAAAAGTTTAAGGGTTAAAACATAATTTTAGAAAAGCTTAAGGACCAAAATAT
Found at i:6093813 original size:7 final size:7
Alignment explanation
Indices: 6093803--6093846 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
6093793 AAACATAATA
6093803 AATAAAT
1 AATAAAT
6093810 AATAAAT
1 AATAAAT
*
6093817 -ATATATT
1 AATA-AAT
6093824 AATAAAT
1 AATAAAT
6093831 AATAAAT
1 AATAAAT
*
6093838 AGTAAAT
1 AATAAAT
6093845 AA
1 AA
6093847 ATATCTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 3 0.10
7 25 0.81
8 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (7 bp):
AATAAAT
Found at i:6101069 original size:12 final size:12
Alignment explanation
Indices: 6101052--6101094 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
6101042 AAACTATTAG
6101052 TATATTATATAA
1 TATATTATATAA
6101064 TATATTATATGATA
1 TATATTATAT-A-A
*
6101078 TAACATTATATAA
1 T-ATATTATATAA
6101091 TATA
1 TATA
6101095 GTAGGAGGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 12 0.46
13 3 0.12
14 3 0.12
15 8 0.31
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (12 bp):
TATATTATATAA
Found at i:6103976 original size:23 final size:22
Alignment explanation
Indices: 6103949--6104007 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
6103939 TACATTTCAT
*
6103949 ATGTTATCATATTGTAGCATAAC
1 ATGTTATCATATTG-AACATAAC
6103972 ATGTTAAGTCATATTGAACATAAC
1 ATGTT-A-TCATATTGAACATAAC
*
6103996 AT-ATATCATATT
1 ATGTTATCATATT
6104008 CTATTGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 7 0.22
22 1 0.03
23 6 0.19
24 10 0.31
25 8 0.25
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (22 bp):
ATGTTATCATATTGAACATAAC
Found at i:6104876 original size:21 final size:20
Alignment explanation
Indices: 6104838--6104876 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6104828 TAAGTTCTGA
*
6104838 TTATATCTAAATTTTTTACT
1 TTATATCTAAATTATTTACT
*
6104858 TTATATTTAAAATTATTTA
1 TTATATCT-AAATTATTTA
6104877 TAATCTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATATCTAAATTATTTACT
Found at i:6108932 original size:6 final size:6
Alignment explanation
Indices: 6108921--6108948 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6108911 ATGAAGTGAA
6108921 GAAGAG GAAGAG GAAGAG GAAGAG GAAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAG
6108949 TAGTGGGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:6109793 original size:18 final size:18
Alignment explanation
Indices: 6109722--6109783 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
6109712 TTTTTAAAAT
6109722 ATAAATTAAAGATAAGTG
1 ATAAATTAAAGATAAGTG
**
6109740 ATGATTTTAAA-A-AA-T-
1 AT-AAATTAAAGATAAGTG
6109755 ATAAATTAAAGATAAGTG
1 ATAAATTAAAGATAAGTG
6109773 ATAAATTAAAG
1 ATAAATTAAAG
6109784 TATATCGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 6 0.17
15 3 0.09
16 3 0.09
17 3 0.09
18 14 0.40
19 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (18 bp):
ATAAATTAAAGATAAGTG
Found at i:6110478 original size:15 final size:15
Alignment explanation
Indices: 6110455--6110498 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6110445 GTTTTTACAT
6110455 AAATAATACAAAAAA
1 AAATAATACAAAAAA
* **
6110470 AAATTATACACTAAA
1 AAATAATACAAAAAA
*
6110485 ATATAATACAAAAA
1 AAATAATACAAAAA
6110499 TTAAAATTAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAATACAAAAAA
Found at i:6110521 original size:30 final size:29
Alignment explanation
Indices: 6110453--6110522 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 29
6110443 TGGTTTTTAC
6110453 ATAAATAATACAAAAAAAAATTATACACT
1 ATAAATAATACAAAAAAAAATTATACACT
*
6110482 AAAATATAATACAAAAATTAAAATTAATA-ACT
1 ATAA-ATAATACAAAAA--AAAATT-ATACACT
6110514 -TAAATAATA
1 ATAAATAATA
6110523 TATATATATC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
29 3 0.09
30 18 0.51
31 2 0.06
32 9 0.26
33 3 0.09
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (29 bp):
ATAAATAATACAAAAAAAAATTATACACT
Found at i:6113861 original size:26 final size:26
Alignment explanation
Indices: 6113812--6113861 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
6113802 TCTGTTTAAA
**
6113812 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
6113838 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
6113862 GCAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:6113942 original size:10 final size:10
Alignment explanation
Indices: 6113924--6113965 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
6113914 AAAATATTTG
6113924 CATACATAAA
1 CATACATAAA
*
6113934 CATAAAT-AA
1 CATACATAAA
*
6113943 GA-ACATAAA
1 CATACATAAA
6113952 CATACATAAA
1 CATACATAAA
6113962 CATA
1 CATA
6113966 TTTAGTTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
8 3 0.12
9 6 0.23
10 17 0.65
ACGTcount: A:0.62, C:0.17, G:0.02, T:0.19
Consensus pattern (10 bp):
CATACATAAA
Found at i:6116924 original size:32 final size:33
Alignment explanation
Indices: 6116883--6116950 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
6116873 TATTTTAATT
* * *
6116883 TAAATTTTTTACATGATTAA-ATAATATTTAAA
1 TAAATTTTTTACAAGAATAATATAAAATTTAAA
*
6116915 TAAATTTTTTTCAAGAATAATATAAAATTTAAA
1 TAAATTTTTTACAAGAATAATATAAAATTTAAA
6116948 TAA
1 TAA
6116951 TAATCAAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (33 bp):
TAAATTTTTTACAAGAATAATATAAAATTTAAA
Found at i:6116925 original size:33 final size:32
Alignment explanation
Indices: 6116883--6116950 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
6116873 TATTTTAATT
* * *
6116883 TAAATTTTTTACATGATTAA-ATAATATTTAAA
1 TAAATTTTTT-CAAGAATAATATAAAATTTAAA
6116915 TAAATTTTTTTCAAGAATAATATAAAATTTAAA
1 TAAA-TTTTTTCAAGAATAATATAAAATTTAAA
6116948 TAA
1 TAA
6116951 TAATCAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (32 bp):
TAAATTTTTTCAAGAATAATATAAAATTTAAA
Found at i:6117905 original size:21 final size:20
Alignment explanation
Indices: 6117873--6117931 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
6117863 GTAACACATC
*
6117873 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
6117893 AAATTATTTTTAAAAATA-TA
1 AAATTA-TTTTAAAATTATTA
*
6117913 AAATTAATTTAAAATTATT
1 AAATTATTTTAAAATTATT
6117932 TTTTTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.27
20 14 0.42
21 10 0.30
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:6117925 original size:19 final size:21
Alignment explanation
Indices: 6117880--6117931 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
6117870 ATCAAATGAT
* *
6117880 TTTAAAATTATTAAAATTATT
1 TTTAAAAATATTAAAATTATA
6117901 TTTAAAAATA-TAAAATTA-A
1 TTTAAAAATATTAAAATTATA
*
6117920 TTTAAAATTATT
1 TTTAAAAATATT
6117932 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 9 0.33
21 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAAAAATATTAAAATTATA
Found at i:6117928 original size:31 final size:31
Alignment explanation
Indices: 6117882--6117955 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 31
6117872 CAAATGATTT
6117882 TAAAATT-ATTAAAATTA-TTTTTAAAAATA
1 TAAAATTAATTAAAATTATTTTTTAAAAATA
*
6117911 TAAAATTAATTTAAAATTATTTTTTTAAAATA
1 TAAAATTAA-TTAAAATTATTTTTTAAAAATA
6117943 TAAAATT-ATTAAA
1 TAAAATTAATTAAA
6117956 CTCATCATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 7 0.17
30 6 0.15
31 10 0.24
32 18 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TAAAATTAATTAAAATTATTTTTTAAAAATA
Found at i:6119056 original size:14 final size:14
Alignment explanation
Indices: 6119037--6119066 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6119027 TATACAAATG
*
6119037 AATAAATATACGAA
1 AATAAATATAAGAA
6119051 AATAAATATAAGAA
1 AATAAATATAAGAA
6119065 AA
1 AA
6119067 AAGAAATACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (14 bp):
AATAAATATAAGAA
Found at i:6119291 original size:29 final size:28
Alignment explanation
Indices: 6119259--6119331 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
6119249 TTTAGGAACC
6119259 AAATGGTAACTTTTGGATGTCCGAGGGCA
1 AAATGGTAA-TTTTGGATGTCCGAGGGCA
* * *
6119288 AAATGGTAATTTTGGATGTTCGGGGGTA
1 AAATGGTAATTTTGGATGTCCGAGGGCA
6119316 AAATGGTAATTTTGGA
1 AAATGGTAATTTTGGA
6119332 AATTCAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 32 0.78
29 9 0.22
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.33
Consensus pattern (28 bp):
AAATGGTAATTTTGGATGTCCGAGGGCA
Found at i:6119341 original size:28 final size:28
Alignment explanation
Indices: 6119287--6119346 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
6119277 GTCCGAGGGC
** *
6119287 AAAATGGTAATTTTGGATGTTCGGGGGT
1 AAAATGGTAATTTTGGAAATTCAGGGGT
6119315 AAAATGGTAATTTTGGAAATTCAGGGGT
1 AAAATGGTAATTTTGGAAATTCAGGGGT
6119343 AAAA
1 AAAA
6119347 ATATGATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAATGGTAATTTTGGAAATTCAGGGGT
Found at i:6119357 original size:29 final size:28
Alignment explanation
Indices: 6119297--6119561 Score: 180
Period size: 30 Copynumber: 9.1 Consensus size: 28
6119287 AAAATGGTAA
* * *
6119297 TTTTGGATGTTCGGGGGTAAAATG-GTAA
1 TTTTGGAAGTTCAGGGGTAAAATGTG-AT
* *
6119325 TTTTGGAAATTCAGGGGTAAAAATATGAT
1 TTTTGGAAGTTCAGGGGT-AAAATGTGAT
* * *
6119354 TTTTTGAAGTTCGGGGGCTAAAATGTGGT
1 TTTTGGAAGTTCAGGGG-TAAAATGTGAT
*
6119383 TTTTGGAAGTTTGAGGGG-AAAATGTGAT
1 TTTTGGAAG-TTCAGGGGTAAAATGTGAT
*
6119411 TTTTGAGAAGTTCAAGGGTCAAAATGTGAT
1 TTTTG-GAAGTTCAGGGGT-AAAATGTGAT
* *
6119441 TTTTGAGAAGTTTAGGGGCAAAAAATGTG-T
1 TTTTG-GAAGTTCAGGGG--TAAAATGTGAT
* ** *
6119471 TTTTTGAAGTTTGGGGGTAATAATGTAAT
1 TTTTGGAAGTTCAGGGGTAA-AATGTGAT
* * *
6119500 TTTTAAGAAGTT-TGAGGGTAAAAATGTAAT
1 TTTT-GGAAGTTCAG-GGGT-AAAATGTGAT
* *
6119530 TTTTGAGAAGTTTA-GGGTAAAATGTAAT
1 TTTTG-GAAGTTCAGGGGTAAAATGTGAT
6119558 TTTT
1 TTTT
6119562 TGAAAGTTTG
Statistics
Matches: 194, Mismatches: 27, Indels: 32
0.77 0.11 0.13
Matches are distributed among these distances:
27 2 0.01
28 54 0.28
29 61 0.31
30 67 0.35
31 10 0.05
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.38
Consensus pattern (28 bp):
TTTTGGAAGTTCAGGGGTAAAATGTGAT
Found at i:6119376 original size:30 final size:28
Alignment explanation
Indices: 6119338--6119621 Score: 187
Period size: 30 Copynumber: 9.7 Consensus size: 28
6119328 TGGAAATTCA
* * *
6119338 GGGGTAAAAATATGATTTTTTGAAGTTCG
1 GGGGT-AAAATGTGATTTTTAGAAGTTTG
* *
6119367 GGGGCTAAAATGTGGTTTTTGGAAGTTTG
1 GGGG-TAAAATGTGATTTTTAGAAGTTTG
**
6119396 AGGGG-AAAATGTGATTTTTGAGAAGTTCA
1 -GGGGTAAAATGTGATTTTT-AGAAGTTTG
*
6119425 AGGGTCAAAATGTGATTTTTGAGAAGTTTAG
1 GGGGT-AAAATGTGATTTTT-AGAAGTTT-G
** *
6119456 GGGCAAAAAATGTG-TTTTTTGAAGTTTG
1 GGG-GTAAAATGTGATTTTTAGAAGTTTG
*
6119484 GGGGTAATAATGTAATTTTTAAGAAGTTTG
1 GGGGTAA-AATGTGATTTTT-AGAAGTTTG
* *
6119514 AGGGTAAAAATGTAATTTTTGAGAAGTTT-
1 GGGGT-AAAATGTGATTTTT-AGAAGTTTG
* * *
6119543 AGGGTAAAATGTAATTTTTTGAAAGTTTG
1 GGGGTAAAATGTGATTTTTAG-AAGTTTG
* * ** * *
6119572 GGGATCAAGATGCAATTTTGGAAAAGTTTG
1 GGGGT-AAAATGTGATTTT-TAGAAGTTTG
*
6119602 GGGGTCAAAATATGATTTTT
1 GGGGT-AAAATGTGATTTTT
6119622 GGTCAGAGAC
Statistics
Matches: 205, Mismatches: 35, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.01
28 45 0.22
29 49 0.24
30 96 0.47
31 12 0.06
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.37
Consensus pattern (28 bp):
GGGGTAAAATGTGATTTTTAGAAGTTTG
Found at i:6119387 original size:58 final size:56
Alignment explanation
Indices: 6119305--6119496 Score: 158
Period size: 58 Copynumber: 3.3 Consensus size: 56
6119295 AATTTTGGAT
6119305 GTTCGGGGGTAAAA--TGGTAATTTTGGAAATTCAGGGGTAAAAATATGATTTTTTGAA
1 GTTCGGGGGTAAAATGTGGT--TTTTGGAAATTCAGGGG-AAAAATATGATTTTTTGAA
* * * *
6119362 GTTCGGGGGCTAAAATGTGGTTTTTGGAAGTTTGAGGGG-AAAATGTGATTTTTGAGAA
1 GTTCGGGGG-TAAAATGTGGTTTTTGGAA-ATTCAGGGGAAAAATATGATTTTT-TGAA
** * * * *
6119420 GTTCAAGGGTCAAAATGTGATTTTTGAGAAGTTTAGGGGCAAAAA-ATGTGTTTTTTGAA
1 GTTCGGGGGT-AAAATGTGGTTTTTG-GAAATTCAGGGG-AAAAATATG-ATTTTTTGAA
*
6119479 GTTTGGGGGTAATAATGT
1 GTTCGGGGGTAA-AATGT
6119497 AATTTTTAAG
Statistics
Matches: 109, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
57 23 0.21
58 46 0.42
59 27 0.25
60 13 0.12
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (56 bp):
GTTCGGGGGTAAAATGTGGTTTTTGGAAATTCAGGGGAAAAATATGATTTTTTGAA
Found at i:6119562 original size:29 final size:29
Alignment explanation
Indices: 6119372--6119622 Score: 192
Period size: 30 Copynumber: 8.6 Consensus size: 29
6119362 GTTCGGGGGC
**
6119372 TAAAATGTGGTTTTTG-GAAGTTTGAGGG
1 TAAAATGTAATTTTTGAGAAGTTTGAGGG
* * **
6119400 GAAAATGTGATTTTTGAGAAGTTCAAGGG
1 TAAAATGTAATTTTTGAGAAGTTTGAGGG
*
6119429 TCAAAATGTGATTTTTGAGAAGTTT-AGGGG
1 T-AAAATGTAATTTTTGAGAAGTTTGA-GGG
* * * *
6119459 CAAAAAATGT-GTTTTT-TGAAGTTTGGGGG
1 --TAAAATGTAATTTTTGAGAAGTTTGAGGG
*
6119488 TAATAATGTAATTTTTAAGAAGTTTGAGGG
1 TAA-AATGTAATTTTTGAGAAGTTTGAGGG
6119518 TAAAAATGTAATTTTTGAGAAGTTT-AGGG
1 T-AAAATGTAATTTTTGAGAAGTTTGAGGG
6119547 TAAAATGTAATTTTTTGA-AAGTTTG-GGG
1 TAAAATGTAA-TTTTTGAGAAGTTTGAGGG
* * * * *
6119575 ATCAAGATGCAATTTTGGAAAAGTTTGGGGG
1 -T-AAAATGTAATTTTTGAGAAGTTTGAGGG
* *
6119606 TCAAAATATGATTTTTG
1 T-AAAATGTAATTTTTG
6119623 GTCAGAGACC
Statistics
Matches: 184, Mismatches: 23, Indels: 30
0.78 0.10 0.13
Matches are distributed among these distances:
27 2 0.01
28 37 0.20
29 45 0.24
30 88 0.48
31 12 0.07
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.37
Consensus pattern (29 bp):
TAAAATGTAATTTTTGAGAAGTTTGAGGG
Found at i:6119589 original size:58 final size:60
Alignment explanation
Indices: 6119476--6119606 Score: 144
Period size: 58 Copynumber: 2.2 Consensus size: 60
6119466 TGTGTTTTTT
* * *
6119476 GAAGTTTGGGGGTAATAATGTAATTTTTAAGAAGTTTGAGGGTAAAAATGTAATTTTTGA
1 GAAGTTTGAGGGTAATAATGTAATTTTTAAGAAGTTTGAGGGTAAAAATGCAATTTTGGA
* * *
6119536 GAAGTTT-AGGGTAA-AATGTAATTTTT-TGAAAGTTTG-GGGATCAAGATGCAATTTTGGA
1 GAAGTTTGAGGGTAATAATGTAATTTTTAAG-AAGTTTGAGGG-TAAAAATGCAATTTTGGA
* *
6119594 AAAGTTTGGGGGT
1 GAAGTTTGAGGGT
6119607 CAAAATATGA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
57 4 0.07
58 39 0.65
59 10 0.17
60 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.37
Consensus pattern (60 bp):
GAAGTTTGAGGGTAATAATGTAATTTTTAAGAAGTTTGAGGGTAAAAATGCAATTTTGGA
Found at i:6120746 original size:2 final size:2
Alignment explanation
Indices: 6120739--6120778 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6120729 AATATGATTA
6120739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6120779 TAAAACGTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6121345 original size:20 final size:20
Alignment explanation
Indices: 6121322--6121359 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6121312 ATGTGGATGT
6121322 AATTGGGCTTGAGTTTGTAA
1 AATTGGGCTTGAGTTTGTAA
*
6121342 AATTGGGTTTGAGTTTGT
1 AATTGGGCTTGAGTTTGT
6121360 GATTTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.03, G:0.32, T:0.45
Consensus pattern (20 bp):
AATTGGGCTTGAGTTTGTAA
Found at i:6121407 original size:6 final size:6
Alignment explanation
Indices: 6121390--6121464 Score: 57
Period size: 6 Copynumber: 12.8 Consensus size: 6
6121380 GGACTTTTAA
* * * * *
6121390 TTAAATT TTAAAT TTAAAT TCAAA- ATAAAT TTAAAC TCAAA- TTAAGT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
6121437 TTAAAT TTAAA- ATAAAT TAAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
6121465 ATTGGGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
5 10 0.19
6 37 0.71
7 5 0.10
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:6121418 original size:17 final size:17
Alignment explanation
Indices: 6121398--6121466 Score: 84
Period size: 17 Copynumber: 4.1 Consensus size: 17
6121388 AATTAAATTT
6121398 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
* *
6121415 TAAATTTAAACTCAAAT
1 TAAATTTAAATTCAAAA
* *
6121432 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
* *
6121449 TAAATTAAAATTTAAAA
1 TAAATTTAAATTCAAAA
6121466 T
1 T
6121467 TGGGTTTAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:6121462 original size:23 final size:23
Alignment explanation
Indices: 6121390--6121464 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
6121380 GGACTTTTAA
*
6121390 TTAAATTTTAAATTTAAATTCAAAA-
1 TTAAA-TTTAAA-ATAAATT-AAAAT
* *
6121415 -TAAATTTAAACTCAAATT-AAGT
1 TTAAATTTAAAAT-AAATTAAAAT
6121437 TTAAATTTAAAATAAATTAAAAT
1 TTAAATTTAAAATAAATTAAAAT
6121460 TTAAA
1 TTAAA
6121465 ATTGGGTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 2 0.05
22 6 0.14
23 30 0.71
24 4 0.10
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (23 bp):
TTAAATTTAAAATAAATTAAAAT
Found at i:6121739 original size:6 final size:6
Alignment explanation
Indices: 6121728--6121770 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
6121718 TGCCATTGGA
*
6121728 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGA GAAGGG G
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG G
6121771 GGAAGGGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:6121959 original size:6 final size:6
Alignment explanation
Indices: 6121948--6121984 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
6121938 TGCCATTGGA
*
6121948 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGA GAAGGG G
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG G
6121985 GGAAGGGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:6122075 original size:11 final size:10
Alignment explanation
Indices: 6122056--6122088 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
6122046 ATATTTTAAA
6122056 AAATAATTTT
1 AAATAATTTT
6122066 AAAGTAATTTT
1 AAA-TAATTTT
6122077 -AATAATTTT
1 AAATAATTTT
6122086 AAA
1 AAA
6122089 ATCATCTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 7 0.33
10 7 0.33
11 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (10 bp):
AAATAATTTT
Found at i:6122521 original size:23 final size:20
Alignment explanation
Indices: 6122478--6122522 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
6122468 TAAAAATCTA
*
6122478 TAATTATATTATTTTTAATT
1 TAATTATATTATATTTAATT
6122498 TAATATATATATATATTTATATT
1 TAAT-TATAT-TATATTTA-ATT
6122521 TA
1 TA
6122523 TAGTCATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 5 0.24
22 7 0.33
23 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATTATATTATATTTAATT
Found at i:6136144 original size:5 final size:5
Alignment explanation
Indices: 6136134--6136160 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6136124 CATCTTCCCC
6136134 TCTTT TCTTT TCTTT TCTTT TCTTT TC
1 TCTTT TCTTT TCTTT TCTTT TCTTT TC
6136161 CTTCATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:6137302 original size:5 final size:5
Alignment explanation
Indices: 6137292--6137341 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
6137282 TGGAGGTAAT
* * * *
6137292 ATATG ATATG ATGTG ATATG ATATG ATACG ATATG TTATG ATACG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
6137342 CCATAAGATG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (5 bp):
ATATG
Found at i:6137312 original size:15 final size:15
Alignment explanation
Indices: 6137292--6137341 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
6137282 TGGAGGTAAT
**
6137292 ATATGATATGATGTG
1 ATATGATATGATACG
6137307 ATATGATATGATACG
1 ATATGATATGATACG
*
6137322 ATATGTTATGATACG
1 ATATGATATGATACG
6137337 ATATG
1 ATATG
6137342 CCATAAGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (15 bp):
ATATGATATGATACG
Found at i:6138981 original size:22 final size:23
Alignment explanation
Indices: 6138938--6138981 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
6138928 TAGCTTATTC
* *
6138938 AGTTTAATTAATAGTTTAATTTT
1 AGTTTAATAAATAATTTAATTTT
*
6138961 AGTTT-ATAAATAATTTTATTT
1 AGTTTAATAAATAATTTAATTT
6138982 GGAGTTGCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (23 bp):
AGTTTAATAAATAATTTAATTTT
Found at i:6147376 original size:581 final size:579
Alignment explanation
Indices: 6146274--6147430 Score: 1978
Period size: 581 Copynumber: 2.0 Consensus size: 579
6146264 TGAAAAAGAG
* * * * *
6146274 GATGATGTTCATCCTAGGAGTCCCGAATTCGAGCGCCTGTGCGTACAAGATGTATGTGCGTTGTC
1 GATGATGTTCATCCTAAGAGTCCCGAATTCGAGCGACTATACATACAAGA-GTATGTGCGTTGTC
6146339 AAAAAATTAAAAAAGTATGAACAAATATTATCATATAATCACATCAATCTATTCAAAAAAAATAT
65 AAAAAATTAAAAAAGTATGAACAAATATTATCATATAATCACATCAATCTATTCAAAAAAAATAT
*
6146404 GAAGAATTTGAATATAGAATATGAGTTACACATCTTTATTTTTGAAATTTCTTAATAAAAATAAA
130 GAAGAATTTGAATAGAGAATATGAGTTACACATCTTTATTTTTGAAATTTCTTAATAAAAATAAA
6146469 TTTTTTATTTAAATGCACTTTAAAATATTTGCAAATGGATTAAATATAATTTTGGCTTAATTCAC
195 TTTTTTATTTAAATGCACTTTAAAATATTTGCAAATGGATTAAATATAATTTTGGCTTAATTCAC
* *
6146534 AAATTGATATCTAAACTATATCTTTTTTTGTATTTAAACTTTTTTTATCAAAAGTGATACTTAAA
260 AAATTGATATCTAAACTATATCTTTTTTTATATTTAAACTTTTTTTATCAAAAGTGATACCTAAA
* * * * *
6146599 CTATTTTTTTCTCAAGTTGGTATATTCGTTAGTCAAACCGTTAAGTTTATTTAAGAAAAATGTTT
325 CTATTTTTTTCTCAAGTTGGTACATTCGTTAATCAAACCGTTAAGTCTATTTAAAAAAAATATTT
6146664 AACCCACAAATTGGTACCTAAACTATATCTTCTTTTTCCTATTTTGGTATTTAAACATTTTTTTA
390 AACCCACAAATTGGTACCTAAACTATATCTTCTTTTTCCTATTTTGGTATTTAAACATTTTTTTA
6146729 GTCACAAGTGGTACATTGTTATACCCCACCTCGACCTGGACATATGGATGACATCACAAGAAGCA
455 GTCACAAGTGGTACATTGTTATACCCCACCTCGACCTGGACATATGGATGACATCACAAGAAGCA
* *
6146794 ACTTTGAAGCACTCGATGAATGACCAACCACCCGCTAAATAGCGAACCCTCTATTACAAT
520 ACTTCGAAGCACTCGATGAATAACCAACCACCCGCTAAATAGCGAACCCTCTATTACAAT
* * * *
6146854 GATGATGTTCATCTTAAGAGTCCCGAGTTCGAGCGACTATATATACAAG-GTGTGTGCGTATTGT
1 GATGATGTTCATCCTAAGAGTCCCGAATTCGAGCGACTATACATACAAGAGTATGTGCG--TTGT
* * *
6146918 CAAAAAGTTAAAAAAGTATGAACAAATATTATCATATAGTCACATCAATCTATTC-AAAAAATTA
64 CAAAAAATTAAAAAAGTATGAACAAATATTATCATATAATCACATCAATCTATTCAAAAAAAATA
*
6146982 TGAAGAATTTGAATAGAGAATATGAGTTACACATCTTTATTTTTGAAATTTCTTAATAAAAATGA
129 TGAAGAATTTGAATAGAGAATATGAGTTACACATCTTTATTTTTGAAATTTCTTAATAAAAATAA
* *
6147047 ATTTTTTATTTAAATTCACTTTAAAATATTTGCAAATGGATTAAATATGATTTTGGCTTAATTCA
194 ATTTTTTATTTAAATGCACTTTAAAATATTTGCAAATGGATTAAATATAATTTTGGCTTAATTCA
*
6147112 CAAATTGATATCTAAATTATAT-TTTTTTCCTATATTTAAACTTTTTTTTATCAAAAGTGATACC
259 CAAATTGATATCTAAACTATATCTTTTTT--TATATTTAAAC-TTTTTTTATCAAAAGTGATACC
6147176 TAAACTATTTTTTTCTCAAGTTGGTACATTCGTTAATCAAACCGTTAAGTCTATTTAAAAAAAAT
321 TAAACTATTTTTTTCTCAAGTTGGTACATTCGTTAATCAAACCGTTAAGTCTATTTAAAAAAAAT
6147241 ATTTAACCCACAAATTGGTACCTAAACTATATCTTCTTTTTCCTATTTTGGTATTTAAACATTTT
386 ATTTAACCCACAAATTGGTACCTAAACTATATCTTCTTTTTCCTATTTTGGTATTTAAACATTTT
* *
6147306 TTTAGTCACAAGTGGTACATTGTTGTACCCCACCTCGACCTGGACATATGGATGGCATCACAAGA
451 TTTAGTCACAAGTGGTACATTGTTATACCCCACCTCGACCTGGACATATGGATGACATCACAAGA
*
6147371 AGCAACTTCGAAGCACTCGGTGAATAACCAACCACCCGCTAAATAGCGAACCCTCTATTA
516 AGCAACTTCGAAGCACTCGATGAATAACCAACCACCCGCTAAATAGCGAACCCTCTATTA
6147431 GGTCATTCAT
Statistics
Matches: 543, Mismatches: 29, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
578 14 0.03
579 155 0.29
580 108 0.20
581 266 0.49
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (579 bp):
GATGATGTTCATCCTAAGAGTCCCGAATTCGAGCGACTATACATACAAGAGTATGTGCGTTGTCA
AAAAATTAAAAAAGTATGAACAAATATTATCATATAATCACATCAATCTATTCAAAAAAAATATG
AAGAATTTGAATAGAGAATATGAGTTACACATCTTTATTTTTGAAATTTCTTAATAAAAATAAAT
TTTTTATTTAAATGCACTTTAAAATATTTGCAAATGGATTAAATATAATTTTGGCTTAATTCACA
AATTGATATCTAAACTATATCTTTTTTTATATTTAAACTTTTTTTATCAAAAGTGATACCTAAAC
TATTTTTTTCTCAAGTTGGTACATTCGTTAATCAAACCGTTAAGTCTATTTAAAAAAAATATTTA
ACCCACAAATTGGTACCTAAACTATATCTTCTTTTTCCTATTTTGGTATTTAAACATTTTTTTAG
TCACAAGTGGTACATTGTTATACCCCACCTCGACCTGGACATATGGATGACATCACAAGAAGCAA
CTTCGAAGCACTCGATGAATAACCAACCACCCGCTAAATAGCGAACCCTCTATTACAAT
Found at i:6155474 original size:17 final size:17
Alignment explanation
Indices: 6155452--6155485 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6155442 CTTTAATGAG
6155452 GGTTTAAAAGAGTTAGA
1 GGTTTAAAAGAGTTAGA
*
6155469 GGTTTAAAGGAGTTAGA
1 GGTTTAAAAGAGTTAGA
6155486 CATCCACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (17 bp):
GGTTTAAAAGAGTTAGA
Found at i:6157010 original size:36 final size:36
Alignment explanation
Indices: 6156959--6157031 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
6156949 ACCATACAAA
6156959 TAGGCTGTAACAACATCCATTAGACGCATGCAAAGT
1 TAGGCTGTAACAACATCCATTAGACGCATGCAAAGT
*
6156995 TAGGCTGTAATAACATCCATTAGACGCATGCAAAGT
1 TAGGCTGTAACAACATCCATTAGACGCATGCAAAGT
6157031 T
1 T
6157032 TTTCACGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (36 bp):
TAGGCTGTAACAACATCCATTAGACGCATGCAAAGT
Found at i:6161167 original size:21 final size:21
Alignment explanation
Indices: 6161129--6161168 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6161119 ACTAAATGTA
*
6161129 TTTAAAACATTTTTTTATTTT
1 TTTAAAACATTTTATTATTTT
6161150 TTTAAAA-ATTTTCATTATT
1 TTTAAAACATTTT-ATTATT
6161169 AATTTATGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTAAAACATTTTATTATTTT
Found at i:6161174 original size:21 final size:21
Alignment explanation
Indices: 6161128--6161174 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
6161118 CACTAAATGT
* *
6161128 ATTTAAAACATTTTTTTATTT
1 ATTTAAAACATTTTATTATTA
*
6161149 TTTTAAAA-ATTTTCATTATTA
1 ATTTAAAACATTTT-ATTATTA
6161170 ATTTA
1 ATTTA
6161175 TGCCTTTGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTAAAACATTTTATTATTA
Found at i:6161216 original size:13 final size:14
Alignment explanation
Indices: 6161198--6161227 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6161188 TTAAAGTAGT
6161198 TAAATTG-TTTAAC
1 TAAATTGATTTAAC
6161211 TAAATTGATTTAAC
1 TAAATTGATTTAAC
6161225 TAA
1 TAA
6161228 TAATTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TAAATTGATTTAAC
Found at i:6163269 original size:5 final size:5
Alignment explanation
Indices: 6163256--6163295 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
6163246 TTTTCTCTCT
*
6163256 GTTTT GTTTG GTTTG GTTTG GTTTTG GTTTG GTTTG GTTT
1 GTTTG GTTTG GTTTG GTTTG G-TTTG GTTTG GTTTG GTTT
6163296 AAATCTGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (5 bp):
GTTTG
Found at i:6163283 original size:16 final size:16
Alignment explanation
Indices: 6163262--6163295 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6163252 CTCTGTTTTG
6163262 TTTGGTTTGGTTTGGT
1 TTTGGTTTGGTTTGGT
6163278 TTTGGTTTGGTTTGGT
1 TTTGGTTTGGTTTGGT
6163294 TT
1 TT
6163296 AAATCTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (16 bp):
TTTGGTTTGGTTTGGT
Found at i:6164490 original size:10 final size:10
Alignment explanation
Indices: 6164477--6164516 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
6164467 TAATATTTAT
6164477 TATTTAAAAA
1 TATTTAAAAA
**
6164487 TATTTAATATT
1 TATTTAA-AAA
6164498 TATTTAAAAA
1 TATTTAAAAA
6164508 TATTTAAAA
1 TATTTAAAA
6164517 TTTATATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TATTTAAAAA
Found at i:6164490 original size:17 final size:18
Alignment explanation
Indices: 6164468--6164513 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 18
6164458 TTATAATATT
6164468 AATATTTA-TTATTTAAA
1 AATATTTATTTATTTAAA
6164485 AATATTTAATATTTATTTAAA
1 AATA-TT--TATTTATTTAAA
6164506 AATATTTA
1 AATATTTA
6164514 AAATTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 4 0.16
18 4 0.16
20 4 0.16
21 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATTTATTTATTTAAA
Found at i:6164502 original size:21 final size:21
Alignment explanation
Indices: 6164476--6164521 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
6164466 TTAATATTTA
*
6164476 TTATTTAAAAATATTTAATAT
1 TTATTTAAAAATATTTAAAAT
6164497 TTATTTAAAAATATTTAAAAT
1 TTATTTAAAAATATTTAAAAT
6164518 TTAT
1 TTAT
6164522 ATTTCATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTTAAAAATATTTAAAAT
Found at i:6167718 original size:57 final size:57
Alignment explanation
Indices: 6167630--6167741 Score: 224
Period size: 57 Copynumber: 2.0 Consensus size: 57
6167620 TACGTAAGAG
6167630 ACTGCAGGACATCATAATTTCACAAACATGGAAACGATAAAAATCACTCATTAGCTT
1 ACTGCAGGACATCATAATTTCACAAACATGGAAACGATAAAAATCACTCATTAGCTT
6167687 ACTGCAGGACATCATAATTTCACAAACATGGAAACGATAAAAATCACTCATTAGC
1 ACTGCAGGACATCATAATTTCACAAACATGGAAACGATAAAAATCACTCATTAGC
6167742 ATAAATGGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.23
Consensus pattern (57 bp):
ACTGCAGGACATCATAATTTCACAAACATGGAAACGATAAAAATCACTCATTAGCTT
Found at i:6171725 original size:14 final size:15
Alignment explanation
Indices: 6171706--6171735 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6171696 TCTGTTTTTC
6171706 TGAAAAAT-GATTAA
1 TGAAAAATAGATTAA
6171720 TGAAAAATAGATTAA
1 TGAAAAATAGATTAA
6171735 T
1 T
6171736 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (15 bp):
TGAAAAATAGATTAA
Found at i:6172596 original size:17 final size:17
Alignment explanation
Indices: 6172576--6172611 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6172566 CTTTTTTAGC
* *
6172576 TTTATTTTAAGTTTAAA
1 TTTATTCTAAATTTAAA
6172593 TTTATTCTAAATTTAAA
1 TTTATTCTAAATTTAAA
6172610 TT
1 TT
6172612 AATAATGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTATTCTAAATTTAAA
Found at i:6172707 original size:14 final size:15
Alignment explanation
Indices: 6172683--6172720 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
6172673 TACCCACCTA
6172683 AACCTAAACCCAATT
1 AACCTAAACCCAATT
6172698 AACC-AAACCCAATT
1 AACCTAAACCCAATT
6172712 AACCTAAAC
1 AACCTAAAC
6172721 TTGTGCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (15 bp):
AACCTAAACCCAATT
Found at i:6174449 original size:29 final size:28
Alignment explanation
Indices: 6174371--6174667 Score: 247
Period size: 29 Copynumber: 10.2 Consensus size: 28
6174361 AAACTTTTCT
6174371 AAAATCACATTTTTACCCTCGAACTTCCAA
1 AAAATCACATTTTTACCC-CGAACTTCC-A
*
6174401 AAAATCATATTTTTACCCCCGAACTTCTCA
1 AAAATCACATTTTTA-CCCCGAACTTC-CA
* * *
6174431 AAAATTACATTTTTGCCCCCGAACTTCCT
1 AAAATCACATTTTT-ACCCCGAACTTCCA
* * **
6174460 AAAGTCACATTTTTACTCCCAAACTTCTTG
1 AAAATCACATTTTTAC-CCCGAACTTC-CA
* **
6174490 AAAATTACATTTTTACCCTTAAACTTCCA
1 AAAATCACATTTTTACCC-CGAACTTCCA
* * *
6174519 AAAATTACA-TTTTACCCCAAACTTATCA
1 AAAATCACATTTTTACCCCGAACTT-CCA
* * *
6174547 AAAATTACATTTTTGCCCCGAACTTCAA
1 AAAATCACATTTTTACCCCGAACTTCCA
* *
6174575 AAAATCACGTTTTTGCCCTCGAACTTCCA
1 AAAATCACATTTTTACCC-CGAACTTCCA
* *
6174604 AAAATCACATTTTTACCTCGAATTTTTCC-
1 AAAATCACATTTTTACCCCGAA--CTTCCA
* *
6174633 AAAATGACATTTTTACCCCTAAAACTTCCA
1 AAAATCACATTTTTACCCC--GAACTTCCA
6174663 AAAAT
1 AAAAT
6174668 TTCATTTTAA
Statistics
Matches: 220, Mismatches: 33, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
27 6 0.03
28 41 0.19
29 91 0.41
30 76 0.35
31 6 0.03
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAATCACATTTTTACCCCGAACTTCCA
Found at i:6174495 original size:59 final size:59
Alignment explanation
Indices: 6174348--6174680 Score: 279
Period size: 59 Copynumber: 5.7 Consensus size: 59
6174338 TCCAAAATTG
* * * * * *
6174348 CATTTTAACTCCTAAACTTTTCTAAAATCACATTTTTACCCTCGAACTTCCAAAAAATCA
1 CATTTTTACTCCCAAACTTCTCAAAAATTACATTTTTACCCCCGAACTTCC-AAAAATCA
* * * * * *
6174408 TATTTTTACCCCCGAACTTCTCAAAAATTACATTTTTGCCCCCGAACTTCCTAAAGTCA
1 CATTTTTACTCCCAAACTTCTCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATCA
** *** *
6174467 CATTTTTACTCCCAAACTTCTTGAAAATTACATTTTTACCCTTAAACTTCCAAAAATTA
1 CATTTTTACTCCCAAACTTCTCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATCA
* * *
6174526 CA-TTTTAC-CCCAAACTTATCAAAAATTACATTTTT-GCCCCGAACTTCAAAAAATCA
1 CATTTTTACTCCCAAACTTCTCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATCA
* * * * * * *
6174582 CGTTTTTGC-CCTCGAACTTC-CAAAAATCACATTTTTA-CCTCGAATTTTTCC-AAAATGA
1 CATTTTTACTCC-CAAACTTCTCAAAAATTACATTTTTACCCCCGAA--CTTCCAAAAATCA
* *
6174640 CATTTTTAC-CCCTAAAACTTC-CAAAAATTTCATTTTAACCC
1 CATTTTTACTCCC--AAACTTCTCAAAAATTACATTTTTACCC
6174681 TAAATTCTCT
Statistics
Matches: 217, Mismatches: 48, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
56 16 0.07
57 53 0.24
58 27 0.12
59 78 0.36
60 43 0.20
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
CATTTTTACTCCCAAACTTCTCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATCA
Found at i:6174532 original size:28 final size:29
Alignment explanation
Indices: 6174332--6174681 Score: 239
Period size: 30 Copynumber: 12.0 Consensus size: 29
6174322 TTTGACCCCA
* *
6174332 AAACTTTCC-AAAATTGCATTTTAACTCCT-
1 AAAC-TTCCAAAAATTACATTTTTAC-CCTC
* * *
6174361 AAACTTTTCTAAAATCACATTTTTACCCTC
1 AAAC-TTCCAAAAATTACATTTTTACCCTC
* * * *
6174391 GAACTTCCAAAAAATCATATTTTTACCCCC
1 AAACTTCC-AAAAATTACATTTTTACCCTC
* * *
6174421 GAACTTCTCAAAAATTACATTTTTGCCCCC
1 AAACTTC-CAAAAATTACATTTTTACCCTC
* * * *
6174451 GAACTTCCTAAAGTCACATTTTTACTCC-C
1 AAACTTCCAAAAATTACATTTTTAC-CCTC
** *
6174480 AAACTTCTTGAAAATTACATTTTTACCCTT
1 AAACTTC-CAAAAATTACATTTTTACCCTC
6174510 AAACTTCCAAAAATTACA-TTTTACCC-C
1 AAACTTCCAAAAATTACATTTTTACCCTC
* *
6174537 AAACTTATCAAAAATTACATTTTTGCCC-C
1 AAACTT-CCAAAAATTACATTTTTACCCTC
* * * * *
6174566 GAACTTCAAAAAATCACGTTTTTGCCCTC
1 AAACTTCCAAAAATTACATTTTTACCCTC
* *
6174595 GAACTTCCAAAAATCACATTTTTA-CCTC
1 AAACTTCCAAAAATTACATTTTTACCCTC
** * *
6174623 GAATTTTTCC-AAAATGACATTTTTACCCCTA
1 -AA-ACTTCCAAAAATTACATTTTTA-CCCTC
* *
6174654 AAACTTCCAAAAATTTCATTTTAACCCT
1 AAACTTCCAAAAATTACATTTTTACCCT
6174682 AAATTCTCTG
Statistics
Matches: 261, Mismatches: 45, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
27 6 0.02
28 40 0.15
29 104 0.40
30 107 0.41
31 4 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCTC
Found at i:6174675 original size:29 final size:30
Alignment explanation
Indices: 6174311--6174684 Score: 188
Period size: 29 Copynumber: 12.8 Consensus size: 30
6174301 TGAACCATCT
* * *
6174311 AAAAATCATATTTTGACCCC-AAAACTTTCC
1 AAAAATTACATTTTTACCCCTAAAAC-TTCC
* * * *
6174341 -AAAATTGCATTTTAACTCCT-AAACTTTTC
1 AAAAATTACATTTTTACCCCTAAAAC-TTCC
* * **
6174370 TAAAATCACATTTTTA-CCCTCGAACTTCC
1 AAAAATTACATTTTTACCCCTAAAACTTCC
* * **
6174399 AAAAAATCATATTTTTACCCC-CGAACTTCTC
1 -AAAAATTACATTTTTACCCCTAAAACTTC-C
* **
6174430 AAAAATTACATTTTTGCCCC-CGAACTTCC
1 AAAAATTACATTTTTACCCCTAAAACTTCC
* * * *
6174459 TAAAGTCACATTTTTACTCCC--AAACTTCTT
1 AAAAATTACATTTTTAC-CCCTAAAACTTC-C
* *
6174489 GAAAATTACATTTTTA-CCCTTAAACTTCC
1 AAAAATTACATTTTTACCCCTAAAACTTCC
*
6174518 AAAAATTACA-TTTTACCCC--AAACTTATC
1 AAAAATTACATTTTTACCCCTAAAACTT-CC
* * *
6174546 AAAAATTACATTTTTGCCCC--GAACTTCA
1 AAAAATTACATTTTTACCCCTAAAACTTCC
* * * **
6174574 AAAAATCACGTTTTT-GCCCTCGAACTTCC
1 AAAAATTACATTTTTACCCCTAAAACTTCC
* * * ***
6174603 AAAAATCACATTTTTACCTCGAATTTTTCC
1 AAAAATTACATTTTTACCCCTAAAACTTCC
*
6174633 -AAAATGACATTTTTACCCCTAAAACTTCC
1 AAAAATTACATTTTTACCCCTAAAACTTCC
* *
6174662 AAAAATTTCA-TTTTAACCCTAAA
1 AAAAATTACATTTTTACCCCTAAA
6174685 TTCTCTGAAA
Statistics
Matches: 272, Mismatches: 55, Indels: 35
0.75 0.15 0.10
Matches are distributed among these distances:
27 9 0.03
28 32 0.12
29 129 0.47
30 98 0.36
31 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAAATTACATTTTTACCCCTAAAACTTCC
Found at i:6174703 original size:144 final size:145
Alignment explanation
Indices: 6174417--6174676 Score: 364
Period size: 144 Copynumber: 1.8 Consensus size: 145
6174407 ATATTTTTAC
* * * *
6174417 CCCCGAACTTCTCAAAAATTACATTTTTGCCCCCGAACTTCCTAAAGTCACATTTTTACTCCCAA
1 CCCCGAACTTCTAAAAAATCACATTTTTGCCCCCGAACTTCCAAAAATCACATTTTTACTCCCAA
* * *
6174482 ACTTCTTGAAAATTACATTTTTACCCTTAAACTTCCAAAAATTACATTTTACCCCAAACTTATCA
66 ACTTCTTCAAAATGACATTTTTACCCTAAAACTTCCAAAAATTACATTTTACCCCAAACTTATCA
6174547 AAAATTACATTTTTG
131 AAAATTACATTTTTG
* * * *
6174562 CCCCGAACTTC-AAAAAATCACGTTTTTGCCCTCGAACTTCCAAAAATCACATTTTTAC-CTCGA
1 CCCCGAACTTCTAAAAAATCACATTTTTGCCCCCGAACTTCCAAAAATCACATTTTTACTCCCAA
* *
6174625 A-TTTTTCCAAAATGACATTTTTACCCCTAAAACTTCCAAAAATTTCATTTTA
66 ACTTCTT-CAAAATGACATTTTTA-CCCTAAAACTTCCAAAAATTACATTTTA
6174677 ACCCTAAATT
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
142 4 0.04
143 18 0.18
144 67 0.67
145 11 0.11
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (145 bp):
CCCCGAACTTCTAAAAAATCACATTTTTGCCCCCGAACTTCCAAAAATCACATTTTTACTCCCAA
ACTTCTTCAAAATGACATTTTTACCCTAAAACTTCCAAAAATTACATTTTACCCCAAACTTATCA
AAAATTACATTTTTG
Found at i:6175865 original size:3 final size:3
Alignment explanation
Indices: 6175857--6175915 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
6175847 AAGAAATTAT
6175857 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6175905 ATA ATA ATA AT
1 ATA ATA ATA AT
6175916 TGTAAAATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6176614 original size:7 final size:7
Alignment explanation
Indices: 6176602--6176626 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6176592 TCGAAAAGCA
6176602 CATATTC
1 CATATTC
6176609 CATATTC
1 CATATTC
6176616 CATATTC
1 CATATTC
6176623 CATA
1 CATA
6176627 CCGTGAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (7 bp):
CATATTC
Found at i:6183662 original size:21 final size:21
Alignment explanation
Indices: 6183622--6183662 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6183612 GGATACTAGC
**
6183622 TTTTGATGTCGCGACATTGAA
1 TTTTGATGTCAAGACATTGAA
*
6183643 TTTTGATGTCAAGACTTTGA
1 TTTTGATGTCAAGACATTGA
6183663 TTGATGTCAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.41
Consensus pattern (21 bp):
TTTTGATGTCAAGACATTGAA
Found at i:6184875 original size:80 final size:78
Alignment explanation
Indices: 6184741--6184897 Score: 206
Period size: 80 Copynumber: 2.0 Consensus size: 78
6184731 TTGTACTAAT
* * * * * *
6184741 TATTTGGTTTCAAAGTTAGGTTTCCAATAGGACTTTGAGTATTTGGCTACAAAATTATGTTTTTT
1 TATTTGGATACAAAGTTAGGTTTCCAATAGGAATTTAAGTAATTGACTACAAAATTATG--TTTT
6184806 CACTAGAAATTTGAG
64 CACTAGAAATTTGAG
* * * *
6184821 TATTTGGATACAAAGTTGGGTTTCCAATAGGAATTTAAGTAATTGATTATAAAATTATGTTTTCC
1 TATTTGGATACAAAGTTAGGTTTCCAATAGGAATTTAAGTAATTGACTACAAAATTATGTTTTCA
6184886 CTAGAAATTTGA
66 CTAGAAATTTGA
6184898 ATAATTGTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
78 17 0.25
80 50 0.75
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (78 bp):
TATTTGGATACAAAGTTAGGTTTCCAATAGGAATTTAAGTAATTGACTACAAAATTATGTTTTCA
CTAGAAATTTGAG
Found at i:6186690 original size:31 final size:29
Alignment explanation
Indices: 6186655--6186730 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
6186645 ATTAACGCTC
*
6186655 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
***
6186686 AGTGACTAAAATGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
6186715 AGTGACTAAAATGTAA
1 AGTGACTAAAATGTAA
6186731 TCTGAGACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 22 0.54
30 1 0.02
31 18 0.44
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:6197169 original size:2 final size:2
Alignment explanation
Indices: 6197162--6197187 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6197152 TGATGTAAGG
6197162 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6197188 TCCCTCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6198345 original size:6 final size:6
Alignment explanation
Indices: 6198334--6198378 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
6198324 CCAAGACAAT
6198334 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GAT
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA GAT
6198379 TAAACGACAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.33, T:0.18
Consensus pattern (6 bp):
GATGAA
Found at i:6208188 original size:18 final size:19
Alignment explanation
Indices: 6208155--6208190 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6208145 AAAATCAAAT
*
6208155 AATAAAAATGTAATTATAC
1 AATAAAAATATAATTATAC
6208174 AATAAAAATAT-ATTATA
1 AATAAAAATATAATTATA
6208191 AATCATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
AATAAAAATATAATTATAC
Found at i:6215147 original size:14 final size:15
Alignment explanation
Indices: 6215128--6215160 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6215118 GAAATATTTC
6215128 AAATATAT-ATACAA
1 AAATATATAATACAA
*
6215142 AAATATATAATACTA
1 AAATATATAATACAA
6215157 AAAT
1 AAAT
6215161 TTACATCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATATAATACAA
Found at i:6219972 original size:14 final size:13
Alignment explanation
Indices: 6219953--6219992 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
6219943 AATAGTAGTA
6219953 TATTATATATTAAT
1 TATTATATATT-AT
6219967 TATTATATATTAT
1 TATTATATATTAT
6219980 TATT-TATTATTAT
1 TATTATA-TATTAT
6219993 ACTGGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.08
13 12 0.48
14 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:6219980 original size:10 final size:10
Alignment explanation
Indices: 6219951--6219993 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
6219941 ATAATAGTAG
6219951 TATATTA-TA
1 TATATTATTA
6219960 TATTAATTATTA
1 TA-T-ATTATTA
6219972 TATATTATTA
1 TATATTATTA
*
6219982 TTTATTATTA
1 TATATTATTA
6219992 TA
1 TA
6219994 CTGGTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 2 0.07
10 18 0.62
11 5 0.17
12 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATTATTA
Found at i:6220076 original size:250 final size:252
Alignment explanation
Indices: 6219703--6220363 Score: 881
Period size: 250 Copynumber: 2.6 Consensus size: 252
6219693 GTAGAGTAAT
*
6219703 ACATAATATATTAATTATTATCATA-TATTATTGTTTATTATACTGGTTGAAATATGCTCTAAGT
1 ACATTATATATTAATTATTAT-ATATTATTATT-TTTATTATACTGGTTGAAATATGCTCTAAGT
* * *
6219767 CCTATACTTTTCTTACATTTGAAAGTTAACCCTTTTACTATATTATATAATGCTATATCATATCA
64 CCTATACTTTTCATATATTTGAAAGTTAACCCTCTTACTATATTATATAATGCTATATCATATCA
* * * * * *
6219832 AATAGTATATAATCTATTAATAGTTTATATATATATATATCAATGATTAAATATTAT-A-AT-AT
129 TATAGTATATAATATATTAATAGTTTATATACATATACATCAATGAATAAACATTATAATATCAT
* * * * * *
6219894 -CAATACTATATATTCTATTATACTTTATAATTTAATAATAGTTGTATATAATAGTAGT
194 GCAATACTATATATTCTATTATAATCTATAATATAATAATAGTTATATAAAATAGTAGG
* * *
6219952 ATATTATATATTAATTATTATATATTATTATTTATTATTATACTGGTTGAAATATGTTCTACGCT
1 ACATTATATATTAATTATTATATATTATTATTT-TTATTATACTGGTTGAAATATGCTCTAAG-T
* * * *
6220017 CCAATACTTTTCATATATTTGAAAGTTAATCCTCCTACTATATTATATAATGTTATATCATATCA
64 CCTATACTTTTCATATATTTGAAAGTTAACCCTCTTACTATATTATATAATGCTATATCATATCA
* *
6220082 TGTAGTATATAATATATTAATAG--T-T-TACATATGCATCAATGAATAAACATTATAATATCAT
129 TATAGTATATAATATATTAATAGTTTATATACATATACATCAATGAATAAACATTATAATATCAT
* * *
6220143 GCAATACTGTATTTTTTATTATAATCTATAATATAATAATAGTTATATAAAATAGTAGG
194 GCAATACTATATATTCTATTATAATCTATAATATAATAATAGTTATATAAAATAGTAGG
* **
6220202 ACATTATATATTAATTATTATATATTATTGTTTGTTATTATACTATTTGAAATATGCTCTAAGTC
1 ACATTATATATTAATTATTATATATTATTATTT-TTATTATACTGGTTGAAATATGCTCTAAGT-
* * * * *
6220267 CCTATATTTTTCGTATATTTGAAAGTTAACCCTCTTACCATGTTATATAATGCTATATCATTTCA
64 CCTATACTTTTCATATATTTGAAAGTTAACCCTCTTACTATATTATATAATGCTATATCATATCA
6220332 TATAGTATATAATATATTAATAGTTTATATAC
129 TATAGTATATAATATATTAATAGTTTATATAC
6220364 TCATAATCCT
Statistics
Matches: 355, Mismatches: 45, Indels: 19
0.85 0.11 0.05
Matches are distributed among these distances:
246 23 0.06
247 2 0.01
248 7 0.02
249 56 0.16
250 262 0.74
252 1 0.00
253 1 0.00
254 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (252 bp):
ACATTATATATTAATTATTATATATTATTATTTTTATTATACTGGTTGAAATATGCTCTAAGTCC
TATACTTTTCATATATTTGAAAGTTAACCCTCTTACTATATTATATAATGCTATATCATATCATA
TAGTATATAATATATTAATAGTTTATATACATATACATCAATGAATAAACATTATAATATCATGC
AATACTATATATTCTATTATAATCTATAATATAATAATAGTTATATAAAATAGTAGG
Found at i:6220894 original size:33 final size:34
Alignment explanation
Indices: 6220852--6220917 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
6220842 TTTTAGATAG
6220852 TATAAATACAAATTTACCTTATTCTCA-AAAAAT
1 TATAAATACAAATTTACCTTATTCTCACAAAAAT
*
6220885 TATAAATACAAATTTACTTTATTCTCACAAAAA
1 TATAAATACAAATTTACCTTATTCTCACAAAAA
6220918 GTATGGTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (34 bp):
TATAAATACAAATTTACCTTATTCTCACAAAAAT
Found at i:6227816 original size:22 final size:22
Alignment explanation
Indices: 6227788--6227840 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
6227778 CACAAATGAA
**
6227788 CAGAGAGCACCGAGGAGCTAAT
1 CAGAGAGCACAAAGGAGCTAAT
* *
6227810 CAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACAAAGGAGCTAAT
6227832 CAGAGAGCA
1 CAGAGAGCA
6227841 TTACACGTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.28, T:0.11
Consensus pattern (22 bp):
CAGAGAGCACAAAGGAGCTAAT
Found at i:6242100 original size:24 final size:22
Alignment explanation
Indices: 6242052--6242101 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
6242042 ACAAATGAAT
* *
6242052 AGAGAGCACAGAGGTGCTAATC
1 AGAGAGCACAAAGATGCTAATC
*
6242074 AGAGAGCACAAATATGCTAATC
1 AGAGAGCACAAAGATGCTAATC
*
6242096 ACAGAG
1 AGAGAG
6242102 TATTACACGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.14
Consensus pattern (22 bp):
AGAGAGCACAAAGATGCTAATC
Found at i:6243987 original size:35 final size:35
Alignment explanation
Indices: 6243948--6244039 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
6243938 TAAGAGCTAA
* ** *
6243948 AAATTATTGGGAGTCTAGATGAGTTCGTATGAGTT
1 AAATTATTGGGAGTCTAGAAGAACTCCTATGAGTT
* * *
6243983 AAATTACTGGGAATCTTGAAGAACTCCTATGAGTT
1 AAATTATTGGGAGTCTAGAAGAACTCCTATGAGTT
* *
6244018 AAATTATTGGGAGACTTGAAGA
1 AAATTATTGGGAGTCTAGAAGA
6244040 GATCTACTAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.33
Consensus pattern (35 bp):
AAATTATTGGGAGTCTAGAAGAACTCCTATGAGTT
Done.