Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009297.1 Hibiscus syriacus cultivar Beakdansim tig00113008_pilon, whole genome shotgun sequence
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: 292623
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:14199 original size:23 final size:23
Alignment explanation
Indices: 14173--14219 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
14163 GTCACCACAG
*
14173 CTCGTATAAATGCACCGAAGTGC
1 CTCGTAGAAATGCACCGAAGTGC
* *
14196 CTCGTAGAATTGCACCGTAGTGC
1 CTCGTAGAAATGCACCGAAGTGC
14219 C
1 C
14220 ATATAATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (23 bp):
CTCGTAGAAATGCACCGAAGTGC
Found at i:14468 original size:149 final size:149
Alignment explanation
Indices: 14198--14501 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
14188 CGAAGTGCCT
*
14198 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
* *
14263 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATTCCAAAGAATATA
*
14328 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCA
14347 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
14412 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATTCCAAAGAATATA
14477 CATATGTCCCAAAGAACCA
131 CATATGTCCCAAAGAACCA
14496 CGTAGA
1 CGTAGA
14502 CCCTCTACCC
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATTCCAAAGAATATA
CATATGTCCCAAAGAACCA
Found at i:15020 original size:20 final size:21
Alignment explanation
Indices: 14979--15019 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
14969 TTTTTTCTCA
*
14979 TGGGGGAATCGGTTCCCCCCC
1 TGGGGGAATCGATTCCCCCCC
*
15000 TGGGGGTATCGATTCCCCCC
1 TGGGGGAATCGATTCCCCCC
15020 TAGCATTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.37, G:0.32, T:0.22
Consensus pattern (21 bp):
TGGGGGAATCGATTCCCCCCC
Found at i:15090 original size:67 final size:67
Alignment explanation
Indices: 14980--15131 Score: 268
Period size: 67 Copynumber: 2.3 Consensus size: 67
14970 TTTTTCTCAT
* *
14980 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAATTTCATATTCGT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAAATTCATATTCGT
15045 TGA
65 TGA
*
15048 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAAATTCATATTCGTT
15113 GA
66 GA
15115 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
15132 TTGAATGGGT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 69 0.85
68 12 0.15
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.30
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAAATTCATATTCGTT
GA
Found at i:25004 original size:21 final size:21
Alignment explanation
Indices: 24978--25020 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24968 TTTCTGGGTT
* *
24978 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
24999 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
25020 A
1 A
25021 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:25125 original size:68 final size:67
Alignment explanation
Indices: 25000--25151 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 67
24990 ACCCATTCAA
* * *
25000 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCAG
25065 GG
66 GG
* * * **
25067 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCA
25132 GGG
65 GGG
*
25135 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
25152 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 21 0.28
68 54 0.72
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCAG
GG
Found at i:25488 original size:29 final size:29
Alignment explanation
Indices: 25454--25519 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
25444 CATATTATGA
**
25454 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
25483 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
25512 TACATGAC
1 TACATGAC
25520 TTGATTATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:25581 original size:30 final size:31
Alignment explanation
Indices: 25539--25598 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
25529 CAGAAAAGTT
*
25539 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
25570 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
25599 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:25892 original size:22 final size:22
Alignment explanation
Indices: 25818--25884 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
25808 TTATGGACAT
25818 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
25840 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
25862 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
25884 A
1 A
25885 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:27674 original size:2 final size:2
Alignment explanation
Indices: 27667--27737 Score: 115
Period size: 2 Copynumber: 35.5 Consensus size: 2
27657 CACGCATTTC
27667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
27709 TA TA TA TA TA TA TG TC TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27738 CATACATAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30807 original size:30 final size:30
Alignment explanation
Indices: 30728--30812 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 30
30718 TTTGTGTACT
*
30728 GACTAAAAT-GTAATTTTTAAAAGTTTAGG
1 GACTTAAATAGTAATTTTTAAAAGTTTAGG
*
30757 G-C-TAAAGTA-TAAACTTTTAAAAGTTTAGG
1 GACTTAAA-TAGT-AATTTTTAAAAGTTTAGG
30786 GACTTAAATAGTAATTTTTAAAA-TTTA
1 GACTTAAATAGTAATTTTTAAAAGTTTA
30813 TATATTTTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
27 3 0.06
28 3 0.06
29 23 0.49
30 13 0.28
31 5 0.11
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (30 bp):
GACTTAAATAGTAATTTTTAAAAGTTTAGG
Found at i:34528 original size:19 final size:19
Alignment explanation
Indices: 34504--34543 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
34494 ACACTATCAG
34504 TCTCAGTGTGTTGATTCAC
1 TCTCAGTGTGTTGATTCAC
34523 TCTCAGTGTGTTGATTCAC
1 TCTCAGTGTGTTGATTCAC
34542 TC
1 TC
34544 CCACCAGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TCTCAGTGTGTTGATTCAC
Found at i:34595 original size:60 final size:60
Alignment explanation
Indices: 34520--34661 Score: 194
Period size: 60 Copynumber: 2.4 Consensus size: 60
34510 TGTGTTGATT
* *
34520 CACTCTCAGTGTGTTGATTCACTCCCACCAGGCTATCATTATGACTTCCACCAACACTAC
1 CACTCTCAGTATGTTGATTCACTCCCACCAAGCTATCATTATGACTTCCACCAACACTAC
* * * * * * *
34580 TACTTTCAGTATGTTGATTCTCTCCCACCAAGCTATTATTTTGGCTTTCACCAACACTAC
1 CACTCTCAGTATGTTGATTCACTCCCACCAAGCTATCATTATGACTTCCACCAACACTAC
*
34640 CACTCGCAGTATGTTGATTCAC
1 CACTCTCAGTATGTTGATTCAC
34662 CCTACTACTA
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (60 bp):
CACTCTCAGTATGTTGATTCACTCCCACCAAGCTATCATTATGACTTCCACCAACACTAC
Found at i:39282 original size:21 final size:21
Alignment explanation
Indices: 39256--39297 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39246 ATCTTAAATT
*
39256 TTTTTATATT-TTTAAAATATA
1 TTTTTA-ATTATTAAAAATATA
39277 TTTTTAATTATTAAAAATATA
1 TTTTTAATTATTAAAAATATA
39298 AAATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTAATTATTAAAAATATA
Found at i:40969 original size:27 final size:26
Alignment explanation
Indices: 40911--40980 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 26
40901 TTATGGGGTA
* *
40911 AATTTTTAAAATTTTAAAAAGATACG
1 AATTTATAAAATTTTAAAAAAATACG
* * *
40937 AGTTTATAAATTTTTATAAAAAATTCG
1 AATTTATAAAATTTTA-AAAAAATACG
*
40964 AATTTATAAAAATTTAA
1 AATTTATAAAATTTTAA
40981 GAGGGCAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 14 0.40
27 21 0.60
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (26 bp):
AATTTATAAAATTTTAAAAAAATACG
Found at i:41470 original size:24 final size:23
Alignment explanation
Indices: 41430--41474 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
41420 AATTGAGGGG
*
41430 AAAATTAAATTTTTAAAATTTTTA
1 AAAATTAAATTTAT-AAATTTTTA
41454 AAAATCTAAA-TTATAAATTTT
1 AAAAT-TAAATTTATAAATTTT
41475 CAAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 8 0.42
25 4 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATTAAATTTATAAATTTTTA
Found at i:45166 original size:88 final size:88
Alignment explanation
Indices: 45053--45229 Score: 282
Period size: 88 Copynumber: 2.0 Consensus size: 88
45043 TTAGTGAGCA
* * * *
45053 TCAACGTTCGTGCTCCTACAGTGCTCAAGCTCTACTGCATGCTGCATAGTGATTCTAGAAGATTG
1 TCAACGATCGTGCTCCTACACTGCTCAAGCTCAACTGCATACTGCATAGTGATTCTAGAAGATTG
45118 TTGTTAATGATTAGTTGAGGTTG
66 TTGTTAATGATTAGTTGAGGTTG
* * * *
45141 TCAACGATCGTGCTCCTACACTGCTCGAGCTCAAGTGCATATTGCATAGTGATTCTATAAGATTG
1 TCAACGATCGTGCTCCTACACTGCTCAAGCTCAACTGCATACTGCATAGTGATTCTAGAAGATTG
45206 TTGTTAATGATTAGTTGAGGTTG
66 TTGTTAATGATTAGTTGAGGTTG
45229 T
1 T
45230 TAATGTTTAG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.36
Consensus pattern (88 bp):
TCAACGATCGTGCTCCTACACTGCTCAAGCTCAACTGCATACTGCATAGTGATTCTAGAAGATTG
TTGTTAATGATTAGTTGAGGTTG
Found at i:46524 original size:21 final size:21
Alignment explanation
Indices: 46498--46542 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
46488 AATTTCTGGG
* *
46498 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
46519 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
46540 CAA
1 CAA
46543 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:47004 original size:20 final size:22
Alignment explanation
Indices: 46964--47020 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
46954 TGAATATGTG
*
46964 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
46986 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
47006 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
47021 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:47585 original size:31 final size:31
Alignment explanation
Indices: 47547--47624 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
47537 AGAGTCGAGG
* *
47547 GTTTACCTATG-TCTTTTGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
47578 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
* *
47609 GTTTACCGAGGATCTT
1 GTTTACCTAGGTTCTT
47625 TATGACCTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:47699 original size:29 final size:30
Alignment explanation
Indices: 47597--47696 Score: 148
Period size: 30 Copynumber: 3.3 Consensus size: 30
47587 GGTTCTTCGG
*
47597 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
47628 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
47658 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
47687 GACCTCTGGA
1 GACCTCTGGA
47697 TAGGTCCTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
29 18 0.28
30 35 0.54
31 12 0.18
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:51147 original size:21 final size:21
Alignment explanation
Indices: 51121--51165 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
51111 AATTTCTGGG
* *
51121 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
51142 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
51163 CAA
1 CAA
51166 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:51629 original size:20 final size:22
Alignment explanation
Indices: 51589--51645 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
51579 TGAATATGTG
*
51589 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
51611 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
51631 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
51646 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:52326 original size:29 final size:30
Alignment explanation
Indices: 52224--52323 Score: 148
Period size: 30 Copynumber: 3.3 Consensus size: 30
52214 GGTTCTTCGG
*
52224 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
52255 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
52285 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
52314 GACCTCTGGA
1 GACCTCTGGA
52324 TAGGTCCTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
29 18 0.28
30 35 0.54
31 12 0.18
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:54162 original size:35 final size:34
Alignment explanation
Indices: 54116--54218 Score: 152
Period size: 35 Copynumber: 2.9 Consensus size: 34
54106 TGAATAAGAA
*
54116 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATC-ACACTTTCGATTCAAGT
*
54151 GAACGGAAGGAAACATCAACACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATC-ACACTTTCGATTCAAGT
*
54186 AAACGGAAGGAAGCATCAGCACTTTCGATTCAA
1 GAACGGAAGGAAGCATCA-CACTTTCGATTCAA
54219 TTTTTTTCCT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
34 1 0.02
35 61 0.98
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (34 bp):
GAACGGAAGGAAGCATCACACTTTCGATTCAAGT
Found at i:62745 original size:3 final size:3
Alignment explanation
Indices: 62737--62796 Score: 95
Period size: 3 Copynumber: 20.0 Consensus size: 3
62727 AATTATTTTT
*
62737 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA CT-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
62782 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
62797 AATGAGTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 1 0.02
3 51 0.96
4 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:63282 original size:113 final size:113
Alignment explanation
Indices: 63140--64461 Score: 2147
Period size: 113 Copynumber: 11.7 Consensus size: 113
63130 ATAGGGTTAT
* ** * *
63140 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * *
63205 ATTATGAACTCTCTTCT-GAAAAGTTGATCTATCGAGTGATGAATTCGA
66 ATTATGAACT-TTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * * *
63253 GCGAAAA-ATTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
63317 CATTATGAATTTTTTCTGGAGAAGCTGATCCATCAAATGATGGATTTGA
65 CATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
63366 GCAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
63431 ATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
63479 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTC--A-GA-TTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
63540 ATTATGAACTTTTTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
63588 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
63653 ATTATGAACTTTTTCTGGAGAAGTTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
63701 GCAAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
63766 ATTATGAACTTTTTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
63814 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
63879 ATTATGAACTTCTTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
63927 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
63992 ATTATGAACTTTTTCTGGAGAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
64040 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * *
64105 ATTATGAACTTTTTCT-GATACTGTTGATCCATTGAA-TGATGGATTTGA
66 ATTATGAACTTTTTCTGGA-AAAGCTGATCCA-TCAAGTGATGGATTTGA
64153 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
64218 ATTATGAACTTTTTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
64266 GCAAAAAGGTTGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
64331 CATTATGAACTTTTTCTGGAGAAGCTGATCCATCAAGTGATGGATTTGA
65 CATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
64380 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
64445 ATTATGAACTTTTTCTG
66 ATTATGAACTTTTTCTG
64462 ACACTGTTGA
Statistics
Matches: 1135, Mismatches: 62, Indels: 24
0.93 0.05 0.02
Matches are distributed among these distances:
109 105 0.09
110 2 0.00
111 2 0.00
112 16 0.01
113 893 0.79
114 117 0.10
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:65345 original size:115 final size:115
Alignment explanation
Indices: 65179--65493 Score: 571
Period size: 115 Copynumber: 2.7 Consensus size: 115
65169 GATCATGCAG
* * *
65179 TTCATCTTT-TAATTCCAATGATTGGTTCTGTAG-TTCCTACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATT-CAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
65242 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
65 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
65293 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
65358 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
*
65408 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
65473 AACACTTCCAGAAGATGCTAT
66 AACACTTCCAGAAGATGCTAT
65494 GAGCACATTC
Statistics
Matches: 195, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
114 26 0.13
115 169 0.87
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (115 bp):
TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:66675 original size:22 final size:21
Alignment explanation
Indices: 66635--66710 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 21
66625 TGACCCCCCT
* *
66635 TTTTTCTTCTTCTTTTTTTCTC
1 TTTTTC-TCTTTTTTTTTTTTC
*
66657 TTTTTTTCTTTTTTCTTTTTTC
1 TTTTTCTCTTTTTT-TTTTTTC
66679 TTTTTCTCTTTTTTTTCTTTTC
1 TTTTTCTCTTTTTTTT-TTTTC
66701 TTTTTCTCTT
1 TTTTTCTCTT
66711 CAAGCATAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.19
22 39 0.81
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTCTCTTTTTTTTTTTTC
Found at i:66683 original size:30 final size:30
Alignment explanation
Indices: 66633--66710 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
66623 CTTGACCCCC
66633 CTTTTTTCTTCTTCTT-TTTTTCTCTTTTTTT
1 CTTTTTTCTT-TT-TTCTTTTTCTCTTTTTTT
66664 CTTTTTTCTTTTTTCTTTTTCTCTTTTTTT
1 CTTTTTTCTTTTTTCTTTTTCTCTTTTTTT
*
66694 -TCTTTTCTTTTTCTCTT
1 CTTTTTTCTTTTT-TCTT
66711 CAAGCATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 13 0.30
30 21 0.48
31 10 0.23
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (30 bp):
CTTTTTTCTTTTTTCTTTTTCTCTTTTTTT
Found at i:74063 original size:15 final size:15
Alignment explanation
Indices: 74040--74071 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
74030 TGAAATGAAT
74040 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
74055 AATGCATGTATGCAA
1 AATGAATGTATGCAA
74070 AA
1 AA
74072 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:79540 original size:3 final size:3
Alignment explanation
Indices: 79534--79573 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
79524 TATTATTATT
*
79534 ATA ATA ATA ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
79574 AATGAGTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:81740 original size:168 final size:168
Alignment explanation
Indices: 81449--81801 Score: 457
Period size: 170 Copynumber: 2.1 Consensus size: 168
81439 AATATAAAGA
* * * * * *
81449 AAAAACTTGATATAGTTTATTTTAATAGTGTTGAGTTATTATAAGGTAGTATATGTTCATAATTT
1 AAAAACTTGATATAGTTTATTTTAATACTCTTGAATGATTATAAGGTAGTATATGTTCAGAACTT
* *
81514 TCTTAACCTATTAATAACACACACACCATAAACGTAGTTACTCAAACTCAATACCTCTAAGAAGA
66 GCTTAACCTATTAATAACACACACACCACAAACGTAGTTACTCAAACTCAATACCTCTAAGAAGA
* *
81579 ACAATATTCTTTTTTATCATCGAAACCACTTGATGGGGTTT
131 ACAATA-TC-TTTTTACCATCGAAACCACTTGAT-GGATTT
81620 AAAAACTTGATATAGTTT-TTTTAATACTCTTGAATGATT-TCAAGGTAGTATATGTTCAGAACT
1 AAAAACTTGATATAGTTTATTTTAATACTCTTGAATGATTAT-AAGGTAGTATATGTTCAGAACT
* * * *
81683 TGCTTGACTTATTAA-CA-ACACACACCACAAACGTAGTTTA-TCAAACTCAGA-ACCTCTAAGG
65 TGCTTAACCTATTAATAACACACACACCACAAACGTAG-TTACTCAAACTCA-ATACCTCTAAGA
* *
81744 AGAATAATATCTTTTTACCATCGAAATCACTTGATGGATTT
128 AGAACAATATCTTTTTACCATCGAAACCACTTGATGGATTT
*
81785 AAAAACTTGATACAGTT
1 AAAAACTTGATATAGTT
81802 AATAACAAAT
Statistics
Matches: 162, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
165 21 0.13
166 22 0.14
167 2 0.01
168 44 0.27
169 6 0.04
170 49 0.30
171 18 0.11
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (168 bp):
AAAAACTTGATATAGTTTATTTTAATACTCTTGAATGATTATAAGGTAGTATATGTTCAGAACTT
GCTTAACCTATTAATAACACACACACCACAAACGTAGTTACTCAAACTCAATACCTCTAAGAAGA
ACAATATCTTTTTACCATCGAAACCACTTGATGGATTT
Found at i:85893 original size:16 final size:17
Alignment explanation
Indices: 85848--85894 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
85838 TATTTTTGAG
85848 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
*
85866 GGGATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
*
85882 GGAATTGAAATCT
1 GGAATTGGAATCT
85895 AAATCTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:86524 original size:34 final size:33
Alignment explanation
Indices: 86438--86520 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
86428 TTTTCACCAT
* *
86438 AAACCCGAACCCGACCCAAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGAATATCAAACTTAAAA
**
86472 AAACCCGACCCGACCCGAATATCAAACTTTTAA
1 AAACCCGACCCGACCCGAATATCAAACTTAAAA
*
86505 AAACCCGACCCAACCC
1 AAACCCGACCCGACCC
86521 CGAAATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 37 0.84
34 7 0.16
ACGTcount: A:0.42, C:0.39, G:0.07, T:0.12
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAATATCAAACTTAAAA
Found at i:86547 original size:31 final size:31
Alignment explanation
Indices: 86503--86577 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
86493 TCAAACTTTT
*
86503 AAAAACCCGACCCAACCCCGAAATTTTTAAA
1 AAAAATCCGACCCAACCCCGAAATTTTTAAA
* * ** *
86534 AAAAATCCAACCCAATCCCGATTTTTTTTAA
1 AAAAATCCGACCCAACCCCGAAATTTTTAAA
*
86565 AAACATCCGACCC
1 AAAAATCCGACCC
86578 GAATACCAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.21
Consensus pattern (31 bp):
AAAAATCCGACCCAACCCCGAAATTTTTAAA
Found at i:89037 original size:20 final size:20
Alignment explanation
Indices: 89012--89056 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
89002 GGTTAAAATA
89012 TTTTCCTTTTGGTCCTCTTT
1 TTTTCCTTTTGGTCCTCTTT
89032 TTTTCCTTTTGGTCCTCTTT
1 TTTTCCTTTTGGTCCTCTTT
89052 TTTTC
1 TTTTC
89057 TTCTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTTCCTTTTGGTCCTCTTT
Found at i:89038 original size:11 final size:11
Alignment explanation
Indices: 89024--89069 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
89014 TTCCTTTTGG
89024 TCCTCTTTTTT
1 TCCTCTTTTTT
**
89035 T-C-CTTTTGG
1 TCCTCTTTTTT
89044 TCCTCTTTTTT
1 TCCTCTTTTTT
*
89055 TCTTCTTTTTT
1 TCCTCTTTTTT
89066 TCCT
1 TCCT
89070 ATAGAATCCT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
9 6 0.22
10 2 0.07
11 19 0.70
ACGTcount: A:0.00, C:0.26, G:0.04, T:0.70
Consensus pattern (11 bp):
TCCTCTTTTTT
Found at i:95954 original size:2 final size:2
Alignment explanation
Indices: 95947--96007 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
95937 GAATGAAGAG
95947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
95989 TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
96008 ATAGGACGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:96435 original size:12 final size:12
Alignment explanation
Indices: 96418--96456 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
96408 TTCACGAGTA
96418 TTTTATTAATTT
1 TTTTATTAATTT
*
96430 TTTTATTATATAT
1 TTTTATTA-ATTT
96443 TTTTA-TAATTT
1 TTTTATTAATTT
96454 TTT
1 TTT
96457 AGTAATTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 10 0.42
13 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTAATTT
Found at i:96786 original size:10 final size:10
Alignment explanation
Indices: 96751--96790 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
96741 TAATTTCCTA
96751 AAAAAT-TAT
1 AAAAATATAT
96760 AAAAATATAT
1 AAAAATATAT
96770 AAAAATAT-T
1 AAAAATATAT
96779 AAATAATA-AT
1 AAA-AATATAT
96789 AA
1 AA
96791 TTAATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 10 0.36
10 18 0.64
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAATATAT
Found at i:97747 original size:2 final size:2
Alignment explanation
Indices: 97740--97771 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
97730 CGATAAAACA
97740 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
97772 TTTACCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100199 original size:43 final size:43
Alignment explanation
Indices: 100069--100403 Score: 557
Period size: 43 Copynumber: 7.8 Consensus size: 43
100059 AGGTCTTATA
* * * *
100069 CTTGCACATAGCAAA-AGAGCCTGTGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGA-CCTGGGGGAACTGTAAGGCTTACC
* * *
100112 CTTGCACACAACAAAGGAACCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
*
100154 CTTGCACACAACAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
100197 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
100240 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
*
100283 CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
100326 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
*
100369 CTTGCACACAACAAAGGGACCTGGGGGAACTGTAA
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAA
100404 CGGTAATTAA
Statistics
Matches: 279, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
42 40 0.14
43 238 0.85
44 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (43 bp):
CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
Found at i:103207 original size:13 final size:13
Alignment explanation
Indices: 103189--103220 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
103179 GGTCAACGTC
*
103189 GGTCAACGGGTCG
1 GGTCAACAGGTCG
103202 GGTCAACAGGTCG
1 GGTCAACAGGTCG
103215 GGTCAA
1 GGTCAA
103221 GTCAACGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.41, T:0.16
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:103228 original size:31 final size:31
Alignment explanation
Indices: 103190--103249 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
103180 GTCAACGTCG
*
103190 GTCAACGGGTCGGGTCAACAGGTCGGGTCAA
1 GTCAACGGGTCGGGTAAACAGGTCGGGTCAA
**
103221 GTCAACGGGTCGGGTAAATGGGTCGGGTC
1 GTCAACGGGTCGGGTAAACAGGTCGGGTC
103250 GGGTTATGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.42, T:0.18
Consensus pattern (31 bp):
GTCAACGGGTCGGGTAAACAGGTCGGGTCAA
Found at i:108160 original size:31 final size:30
Alignment explanation
Indices: 108118--108195 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
108108 TAATATATAT
*
108118 ATAATTATTTTATAGTATTTAGATAAATTTA
1 ATAA-TATTTTATAATATTTAGATAAATTTA
* * **
108149 TTAATAATTTTATAATCTTTTTATAAATTTA
1 ATAAT-ATTTTATAATATTTAGATAAATTTA
108180 ATAAGTATTTTATAAT
1 ATAA-TATTTTATAAT
108196 TTTTTAAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (30 bp):
ATAATATTTTATAATATTTAGATAAATTTA
Found at i:113468 original size:27 final size:27
Alignment explanation
Indices: 113431--113487 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
113421 AAATAACCAC
113431 GATGATTATAGACGGTTCATTCATTGT
1 GATGATTATAGACGGTTCATTCATTGT
113458 GATGATTATAGACGGTTCATTCATTGT
1 GATGATTATAGACGGTTCATTCATTGT
113485 GAT
1 GAT
113488 TTAGATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (27 bp):
GATGATTATAGACGGTTCATTCATTGT
Found at i:114663 original size:3 final size:3
Alignment explanation
Indices: 114655--114679 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
114645 AATCACCAAT
114655 AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC A
114680 TAAAAGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:115167 original size:2 final size:2
Alignment explanation
Indices: 115160--115207 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
115150 TTTAATTTAA
115160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
115202 AT AT AT
1 AT AT AT
115208 TAATGGTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115721 original size:22 final size:23
Alignment explanation
Indices: 115688--115735 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
115678 TTAATTTATA
*
115688 AAACGTTAAATTGTAAAGTA-TT
1 AAACGTTAAATTATAAAGTAGTT
*
115710 AAACG-TATAATTATAAATTAGTT
1 AAACGTTA-AATTATAAAGTAGTT
115733 AAA
1 AAA
115736 AATCTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 15 0.68
23 5 0.23
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.35
Consensus pattern (23 bp):
AAACGTTAAATTATAAAGTAGTT
Found at i:116120 original size:22 final size:22
Alignment explanation
Indices: 116095--116136 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
116085 TACATTGAAA
116095 ATGTTAACTAATTTATAATTAT
1 ATGTTAACTAATTTATAATTAT
* * *
116117 ATGTTTAGTACTTTATAATT
1 ATGTTAACTAATTTATAATT
116137 TAACGTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (22 bp):
ATGTTAACTAATTTATAATTAT
Found at i:117413 original size:2 final size:2
Alignment explanation
Indices: 117406--117467 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
117396 ATAATTGTTA
*
117406 AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117447 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
117468 ACTTGATCAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:117761 original size:60 final size:60
Alignment explanation
Indices: 117640--117770 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
117630 ATTATTATTT
* **
117640 TAAATT-GATCCTTAAACTTTTATAAATTTAAATTTCATCCTTAAACTATAATTCTCATTC
1 TAAATTAG-TCCTTAAACTTTTATAAATTTAAATTTCATCCCTAAACTATAACCCTCATTC
* * * *
117700 TATATTAGTCCTTAAACTTTTGAT-CA-TTATAATTTCATCCCTAAACTATGACCCTCCTTC
1 TAAATTAGTCCTTAAACTTTT-ATAAATTTA-AATTTCATCCCTAAACTATAACCCTCATTC
117760 TAAATTAGTCC
1 TAAATTAGTCC
117771 CCAAAATTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 3 0.05
60 54 0.90
61 3 0.05
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.43
Consensus pattern (60 bp):
TAAATTAGTCCTTAAACTTTTATAAATTTAAATTTCATCCCTAAACTATAACCCTCATTC
Found at i:117781 original size:60 final size:60
Alignment explanation
Indices: 117670--117800 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
117660 TATAAATTTA
* ** * ** * *
117670 AATTTCATCCTTAAACTATAATTCTCATTCTATATTAGTCCTTAAACTTTTG-ATCATTAT
1 AATTTCATCCCTAAACTATAACCCTCATTCTAAATTAGTCCCCAAAATTTTGAAT-ATTAC
* * *
117730 AATTTCATCCCTAAACTATGACCCTCCTTCTAAATTAGTCCCCAAAATTTTGAATATTCC
1 AATTTCATCCCTAAACTATAACCCTCATTCTAAATTAGTCCCCAAAATTTTGAATATTAC
117790 AATTTCATCCC
1 AATTTCATCCC
117801 CAAATTCATC
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 57 0.97
61 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.40
Consensus pattern (60 bp):
AATTTCATCCCTAAACTATAACCCTCATTCTAAATTAGTCCCCAAAATTTTGAATATTAC
Found at i:118103 original size:60 final size:59
Alignment explanation
Indices: 117922--118114 Score: 183
Period size: 60 Copynumber: 3.2 Consensus size: 59
117912 GTGTATATGT
* * * * * *
117922 ATAGTTTGGGATGAAATTGGAATATTTAGAAAGCTTGGGGACCAAATTATAATGAAGATC
1 ATAGTTTGGGATGAAATTGAAATATTTA-AAAGCTTGAGGATCAATTTAAAATGAAGGTC
* * * * *
117982 ATAGTTTGGGGGTGAAATTGAAATATTTAAAAGTTTGAGGATTAATTTAGAAT-AATAGTC
1 ATAGTTT-GGGATGAAATTGAAATATTTAAAAGCTTGAGGATCAATTTAAAATGAA-GGTC
* * *
118042 ATAGTTTATGGATGAAATTAAAATATTTAAAAG-TTGAAGGATCAATTTAAAATGAGGGTC
1 ATAGTTT-GGGATGAAATTGAAATATTTAAAAGCTTG-AGGATCAATTTAAAATGAAGGTC
*
118102 ATACTTTGAGGAT
1 ATAGTTTG-GGAT
118115 ATGTGATACA
Statistics
Matches: 108, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
59 5 0.05
60 83 0.77
61 20 0.19
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGAAATATTTAAAAGCTTGAGGATCAATTTAAAATGAAGGTC
Found at i:120282 original size:2 final size:2
Alignment explanation
Indices: 120275--120306 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
120265 ACAATACAAT
120275 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
120307 TTTATCAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:120299 original size:15 final size:15
Alignment explanation
Indices: 120275--120311 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
120265 ACAATACAAT
120275 TATA-TATATATATA
1 TATATTATATATATA
120289 TATATTATATATATA
1 TATATTATATATATA
*
120304 TATTTTAT
1 TATATTAT
120312 CAAAGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:121466 original size:2 final size:2
Alignment explanation
Indices: 121459--121496 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
121449 ATAACAATAC
121459 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
121497 TTATTTATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124779 original size:3 final size:3
Alignment explanation
Indices: 124773--124858 Score: 118
Period size: 3 Copynumber: 28.7 Consensus size: 3
124763 AAATATTAAT
* * * * *
124773 AAC AAC ACC AAC AAC AAC AAT AAA AAC AAC AAC ATC AAC AAA AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
*
124821 AAC AAC AAC AAC AAC AAC AAC AAC AAA AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
124859 TAATAATAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.69, C:0.29, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:127982 original size:45 final size:45
Alignment explanation
Indices: 127933--128066 Score: 150
Period size: 45 Copynumber: 3.0 Consensus size: 45
127923 GAACATCGAA
127933 TGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCTG
1 TGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCTG
* *
127978 TGCATTTGATGCATCGATGCACA-AGCCATGCATCGATGCACTTTG
1 TGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCTG
** **
128023 -GCTATTTTGAAACATCGAATGCAC-T-TGATGCATCGATGCACTCT
1 TGC-ATTTT-ATGCATCG-ATGCACATACCATGCATCGATGCACTCT
128067 TAGTGCACCG
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
44 3 0.04
45 61 0.80
46 6 0.08
47 6 0.08
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (45 bp):
TGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCTG
Found at i:142147 original size:23 final size:23
Alignment explanation
Indices: 142120--142167 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
142110 CATGGCTTCA
142120 AGCCATTTCTCAGAGTCTAGGCT
1 AGCCATTTCTCAGAGTCTAGGCT
142143 AGCCATTTCTCAGAGTCTAGGCT
1 AGCCATTTCTCAGAGTCTAGGCT
142166 AG
1 AG
142168 ACACTGCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (23 bp):
AGCCATTTCTCAGAGTCTAGGCT
Found at i:156942 original size:17 final size:16
Alignment explanation
Indices: 156901--156942 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
156891 AAATATAATT
156901 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
156917 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
156934 TAAAA-AATT
1 TAAAATAATT
156943 ACACGCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:159541 original size:18 final size:18
Alignment explanation
Indices: 159518--159564 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
159508 TTTATATCTA
*
159518 GAATAGGCACAACTCTTG
1 GAATAGTCACAACTCTTG
*
159536 GAATAGTCACAAGTCTTG
1 GAATAGTCACAACTCTTG
159554 GAATAGTCACA
1 GAATAGTCACA
159565 CTTGTATAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (18 bp):
GAATAGTCACAACTCTTG
Found at i:160653 original size:26 final size:26
Alignment explanation
Indices: 160624--160683 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
160614 GGGCCTCTTA
*
160624 TTTTGGGCTGTTAATTGGGTTTCTGG
1 TTTTGGGCTGTTAATTAGGTTTCTGG
*
160650 TTTTGGGCTGTTAATTAGGTTTTTGG
1 TTTTGGGCTGTTAATTAGGTTTCTGG
160676 TTTTGGGC
1 TTTTGGGC
160684 ATGTAACAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.08, C:0.07, G:0.33, T:0.52
Consensus pattern (26 bp):
TTTTGGGCTGTTAATTAGGTTTCTGG
Found at i:160876 original size:72 final size:73
Alignment explanation
Indices: 160725--160879 Score: 287
Period size: 72 Copynumber: 2.2 Consensus size: 73
160715 AATACCTTTT
160725 ATATATATATATATATAATCAATTTACTTATTTAATATATATTCATACATATAATAATCACATAC
1 ATATATATATATATATAATCAATTTACTTATTTAATATATATTCATACATATAATAATCACATAC
160790 ACCCATAC
66 ACCCATAC
*
160798 CT-TATATATATATATAATCAATTTACTTATTTAATATATATTCATACATATAATAATCACATAC
1 ATATATATATATATATAATCAATTTACTTATTTAATATATATTCATACATATAATAATCACATAC
160862 ACCCATA-
66 ACCCATAC
160869 ATATATATATA
1 ATATATATATA
160880 CAACCACACA
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
71 1 0.01
72 77 0.97
73 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (73 bp):
ATATATATATATATATAATCAATTTACTTATTTAATATATATTCATACATATAATAATCACATAC
ACCCATAC
Found at i:161101 original size:13 final size:13
Alignment explanation
Indices: 161083--161110 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
161073 CGAATTTAAA
161083 ATGATTCATGTAC
1 ATGATTCATGTAC
161096 ATGATTCATGTAC
1 ATGATTCATGTAC
161109 AT
1 AT
161111 TTTTACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATGATTCATGTAC
Found at i:164039 original size:2 final size:2
Alignment explanation
Indices: 164032--164062 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
164022 TATGTACACC
164032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
164063 GTATGTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:175282 original size:59 final size:60
Alignment explanation
Indices: 175159--175284 Score: 134
Period size: 59 Copynumber: 2.1 Consensus size: 60
175149 ATATGTACTT
* * * * *
175159 AAACTATGATATTCATTTCAAATTGGCCTCTAAAGTTTTGAACATTCTAATTTCATCCTT
1 AAACTATGATATTCATTTAAAATTGGCCTCTAAACTTTTGAACATCCAAATTTCATCCTC
* *
175219 AAACTATGCT-TTCATTTAAAATTAGTCC-CTAAACTTTTGAACATACCAAATTT-AT-CTCC
1 AAACTATGATATTCATTTAAAATT-GGCCTCTAAACTTTTGAACAT-CCAAATTTCATCCT-C
175278 AAACTAT
1 AAACTAT
175285 AACTCTCATT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
58 2 0.04
59 36 0.64
60 18 0.32
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (60 bp):
AAACTATGATATTCATTTAAAATTGGCCTCTAAACTTTTGAACATCCAAATTTCATCCTC
Found at i:180492 original size:14 final size:15
Alignment explanation
Indices: 180473--180501 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
180463 TTTTCAAGTG
180473 TTTAAATATA-ACTT
1 TTTAAATATACACTT
180487 TTTAAATATACACTT
1 TTTAAATATACACTT
180502 ATTGAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAAATATACACTT
Found at i:181945 original size:20 final size:22
Alignment explanation
Indices: 181920--181960 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
181910 ATGAGAAAAT
*
181920 GGCTAG-GAGCTCGA-ATTAGA
1 GGCTAGTGAGATCGACATTAGA
181940 GGCTAGTGAGATCGACATTAG
1 GGCTAGTGAGATCGACATTAG
181961 TAAATTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (22 bp):
GGCTAGTGAGATCGACATTAGA
Found at i:189966 original size:177 final size:177
Alignment explanation
Indices: 189664--190018 Score: 701
Period size: 177 Copynumber: 2.0 Consensus size: 177
189654 TACAGAAGCT
189664 TGTCCCCGGTTTTTCTACAGTATGGCATTATGACCCCCTTACATGTCCTCACACTTCTGAGCAGA
1 TGTCCCCGGTTTTTCTACAGTATGGCATTATGACCCCCTTACATGTCCTCACACTTCTGAGCAGA
189729 ATGGTGTAGTGGAGAAGAAGCATAGGCATGCCATTAAACTTGCTTTAGTTCTACTTGCTCAAGCC
66 ATGGTGTAGTGGAGAAGAAGCATAGGCATGCCATTAAACTTGCTTTAGTTCTACTTGCTCAAGCC
189794 TCTATGCCTGTTCAGTATTAGTTCTATGAAACCATGATTGCATTTTA
131 TCTATGCCTGTTCAGTATTAGTTCTATGAAACCATGATTGCATTTTA
*
189841 TGTCCTCGGTTTTTCTACAGTATGGCATTATGACCCCCTTACATGTCCTCACACTTCTGAGCAGA
1 TGTCCCCGGTTTTTCTACAGTATGGCATTATGACCCCCTTACATGTCCTCACACTTCTGAGCAGA
189906 ATGGTGTAGTGGAGAAGAAGCATAGGCATGCCATTAAACTTGCTTTAGTTCTACTTGCTCAAGCC
66 ATGGTGTAGTGGAGAAGAAGCATAGGCATGCCATTAAACTTGCTTTAGTTCTACTTGCTCAAGCC
189971 TCTATGCCTGTTCAGTATTAGTTCTATGAAACCATGATTGCATTTTA
131 TCTATGCCTGTTCAGTATTAGTTCTATGAAACCATGATTGCATTTTA
190018 T
1 T
190019 ACTATTAATC
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 177 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (177 bp):
TGTCCCCGGTTTTTCTACAGTATGGCATTATGACCCCCTTACATGTCCTCACACTTCTGAGCAGA
ATGGTGTAGTGGAGAAGAAGCATAGGCATGCCATTAAACTTGCTTTAGTTCTACTTGCTCAAGCC
TCTATGCCTGTTCAGTATTAGTTCTATGAAACCATGATTGCATTTTA
Found at i:195076 original size:5 final size:5
Alignment explanation
Indices: 195066--195125 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
195056 AATGGTCAAC
* * *
195066 GGTCG GGTCG GGTCG GGTCAAC GGTCG TGTCG GGTCG GGTC- GGTAG GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
*
195117 GGTCA GGTC
1 GGTCG GGTC
195126 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 3 0.07
5 38 0.84
7 4 0.09
ACGTcount: A:0.07, C:0.20, G:0.52, T:0.22
Consensus pattern (5 bp):
GGTCG
Found at i:195087 original size:22 final size:22
Alignment explanation
Indices: 195059--195126 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
195049 AACGGTCAAT
195059 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
195081 GGTCAACGGTCGTGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
* *
195103 GGT---CGGTAGGGTCGGGTCA
1 GGTCAACGGTCGGGTCGGGTCG
195122 GGTCA
1 GGTCA
195127 GACCGGTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.40
22 24 0.60
ACGTcount: A:0.10, C:0.21, G:0.49, T:0.21
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:202439 original size:17 final size:17
Alignment explanation
Indices: 202417--202449 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
202407 TCGGTCAACG
202417 GTCAACGGTCGGGTCGT
1 GTCAACGGTCGGGTCGT
202434 GTCAACGGTCGGGTCG
1 GTCAACGGTCGGGTCG
202450 GGTCGGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.24, G:0.42, T:0.21
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGT
Found at i:205496 original size:17 final size:17
Alignment explanation
Indices: 205471--205513 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
205461 GAATGACGAG
* * *
205471 TTTCATCTTTTTCTTCA
1 TTTCTTCTTTGTCATCA
205488 TTTCTTCTTTGTCATCA
1 TTTCTTCTTTGTCATCA
205505 TATTCTTCT
1 T-TTCTTCT
205514 AAAAAAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.12, C:0.23, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTCTTCTTTGTCATCA
Found at i:209422 original size:20 final size:20
Alignment explanation
Indices: 209392--209457 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
209382 ACGGGTCATA
* *
209392 CCGGTTCGGGTTGACACAAG
1 CCGGTTTGGGTTGACTCAAG
*
209412 CTGGTTTGGGTTGACTCAAG
1 CCGGTTTGGGTTGACTCAAG
*
209432 CCGATTTGGGTTGACTCAAG
1 CCGGTTTGGGTTGACTCAAG
*
209452 TCGGTT
1 CCGGTT
209458 CAGATTGGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (20 bp):
CCGGTTTGGGTTGACTCAAG
Found at i:210230 original size:2 final size:2
Alignment explanation
Indices: 210223--210248 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
210213 AGATAACTTA
210223 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
210249 TCAATAAAAT
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:210659 original size:21 final size:21
Alignment explanation
Indices: 210635--210710 Score: 134
Period size: 21 Copynumber: 3.6 Consensus size: 21
210625 TACCCCAAAA
210635 AAGAGTATCGATACTCTGGGT
1 AAGAGTATCGATACTCTGGGT
*
210656 AAGAGTATCAATACTCTGGGT
1 AAGAGTATCGATACTCTGGGT
*
210677 AAGATTATCGATACTCTGGGT
1 AAGAGTATCGATACTCTGGGT
210698 AAGAGTATCGATA
1 AAGAGTATCGATA
210711 TTGGATAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (21 bp):
AAGAGTATCGATACTCTGGGT
Found at i:212658 original size:17 final size:17
Alignment explanation
Indices: 212621--212657 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
212611 AGTGGTTTAG
212621 TTTGTTTGTTGTCTTAT
1 TTTGTTTGTTGTCTTAT
*
212638 TTTGTATTGTTGTGTTAT
1 TTTGT-TTGTTGTCTTAT
212656 TT
1 TT
212658 GATTTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.08, C:0.03, G:0.19, T:0.70
Consensus pattern (17 bp):
TTTGTTTGTTGTCTTAT
Found at i:220837 original size:85 final size:86
Alignment explanation
Indices: 220677--220837 Score: 220
Period size: 85 Copynumber: 1.9 Consensus size: 86
220667 ATTTTGCAGC
* * *
220677 GTTTGTTACAAATGTCGCTATAGATATAGAGCTTTTGCGGCGTTTGTATCCAAAAAACGCTGTTA
1 GTTTGTTAAAAATGCCGCTATAGATATAGAGCTTTTGCGGCGTTTGTATCCAAAAAACGCTATTA
*
220742 AATATCTCGACCTTTTACGAT
66 AATATATCGACCTTTTACGAT
* *
220763 GTTT-TTAAAAATGCCGCTATAGATATCGA-CATTTTGTGGCGTTTGTATCCAAAAAACG-TCAT
1 GTTTGTTAAAAATGCCGCTATAGATATAGAGC-TTTTGCGGCGTTTGTATCCAAAAAACGCT-AT
*
220825 TATATATATCGAC
64 TAAATATATCGAC
220838 AAACGTTGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
84 2 0.03
85 60 0.91
86 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (86 bp):
GTTTGTTAAAAATGCCGCTATAGATATAGAGCTTTTGCGGCGTTTGTATCCAAAAAACGCTATTA
AATATATCGACCTTTTACGAT
Found at i:220841 original size:22 final size:21
Alignment explanation
Indices: 220816--220858 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
220806 TGTATCCAAA
220816 AAACGTCATTATATATATCGAC
1 AAACGTCATTATATAT-TCGAC
**
220838 AAACGTTGTTATATATTCGAC
1 AAACGTCATTATATATTCGAC
220859 CTTTTGCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (21 bp):
AAACGTCATTATATATTCGAC
Found at i:221391 original size:36 final size:33
Alignment explanation
Indices: 221324--221407 Score: 80
Period size: 36 Copynumber: 2.5 Consensus size: 33
221314 ATGGCACATG
* * **
221324 TCATGTCACCCAAGATGATAATGTGGCATGTATGTA
1 TCATATCACCCAAGATAATAATGTGAAATGTA---A
* *
221360 TCATATCACCCAAGTTAATGATGTGAAATGTAA
1 TCATATCACCCAAGATAATAATGTGAAATGTAA
221393 -CATATCACCCAAGAT
1 TCATATCACCCAAGAT
221408 GATGGCGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
32 14 0.34
33 1 0.02
36 26 0.63
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (33 bp):
TCATATCACCCAAGATAATAATGTGAAATGTAA
Found at i:226353 original size:632 final size:632
Alignment explanation
Indices: 224068--226667 Score: 3498
Period size: 631 Copynumber: 4.1 Consensus size: 632
224058 ATGAATTAAT
* * *
224068 TTATATATTTTT-ATGTTAAACATGATTTA--TTTTTAAAACAAATGTAAGCTTAGTTTTAAAGG
1 TTATATTTTTTTGA-GTTAAACATAATTTATTTTTTTAAAACAAATGTAAGCTTAATTTTAAAGG
* * *
224130 CATAAT-AAAAAAATTAGTCCCTCAACT-TTTGCCCAAATGGTCATTTTGACACATATTCTTTTT
65 CATAATGCAAAAAATTAGTCCCCCAA-TGTTTGCCCAAATAGTCATTTTGACACA-ATTCTTTTT
* * * *
224193 TGCGAGCCCTTAGTCCTTAAACATTTTAATTTTTGGTCAAAATGACCACTTCTGGATGGAAATTG
128 TGGGAGCACTTAGTCCTTAAACATTTTAATTTTTGGTCAAAATGACCACTTCTAGATGGAAATCG
* ** * * **
224258 TTAGTTGACTAACTTTTAATGCATGATACTGATGTGATATTTCCACATGTGTTAAATTACTGACA
193 TTAGTTGACTAACTGTTAACACATGATGCTGATGTGATATTTTCACATGTACTAAATTACTGACA
* * *
224323 TAACACATACTACGTCACCCAAGGTCATAATTATTATATGTACCACGTCATCTAAGACAAAGATG
258 TGA-ACATACTACGTCACCCAAGGTCATAATTATGATATGTACCACATCATCTAAGACAAAGATG
* * * * ***
224388 TGACACGATCCACATTACTCAATATGATAACATGAAACATATATGTCATATAAGATGATATATTA
322 TGACATGATCCACGTCACTCAAGATGATAACATGAAACATATATGTCACCCAAGATGATATATTA
*
224453 AATTATTGTAATTAGCTCTTGTAGCTCAGTTGGTTAGAGCACCTGTTTAGTAAGCGGGAGGTCTT
387 AATTATTGTAATTAGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTT
* * *
224518 GAGTTCAACTCTCAACAAGAGCAATTGGATAAT-TTTCTTATCCATGAAAATTAGTTCTTCATGT
452 GAGTTAAACTCTCAACAAGAGC-ATTGGATAATATTT-TTATCCATGAAAATTAATTCTTCAGGT
* *
224582 AATCATAATTATTCTTGATAAGAATTTTTACACTTAATCAATTACTTGTTATTATATTCATTTTT
515 AATCATAATTATTCTTGATATGAATTTTTACACTTAATCAATTACTTGTTATTATATTCATTTAT
* * * *
224647 ATTATCTTCAATTATTTTCAATAAAAAAAAAGTAAA-CAGAATATAAATTGAA
580 ATTATCTTCAATAATTTTCAATAAAAAATAAGTAAATTAAAATATAAATTGAA
* * *
224699 TTATA-TTTTTTGATTTAAACATAATTTATTTTTTAAAAATAAATGTAAGCTTAATTTTAAAGGC
1 TTATATTTTTTTGAGTTAAACATAATTTATTTTTTTAAAACAAATGTAAGCTTAATTTTAAAGGC
* * * * * *
224763 ATAATG-AAAAAATTAGTCCCCCAACGTTTGTCCAAATTGTCATTTTAAGAC-ATTCATTTTTGG
66 ATAATGCAAAAAATTAGTCCCCCAATGTTTGCCCAAATAGTCATTTTGACACAATTCTTTTTTGG
* * *
224826 TAGCACTTAGTCCTTAAACATTTTAATTTTTAGTCAAAATGACCACTTCTAGATGGAAACCGTTA
131 GAGCACTTAGTCCTTAAACATTTTAATTTTTGGTCAAAATGACCACTTCTAGATGGAAATCGTTA
* * * * * * * *
224891 GTTTATTAATTGTTAACGCATGATGTTGATTTGAT-TTTTCCACATGTACTAAATTATTTACATG
196 GTTGACTAACTGTTAACACATGATGCTGATGTGATATTTT-CACATGTACTAAATTACTGACATG
* * * * *
224955 ACACATACTATGTCACCCATGGTCATAATTATGGTATGTGCCACATCATCTAAGACAAAGATATG
260 A-ACATACTACGTCACCCAAGGTCATAATTATGATATGTACCACATCATCTAAGACAAAGATGTG
* *
225020 ATATGATCCACGTCACTCAAGATGATAACATGAAACATATATGTCACCCAAGATGATATATTATA
324 ACATGATCCACGTCACTCAAGATGATAACATGAAACATATATGTCACCCAAGATGATATATTAAA
*
225085 TTGTTGTAATTAGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGGAGGTCTTG
389 TTATTGTAATTAGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGC-GGGAGGTCTTG
* *
225150 AGTTAAACTCTCAACAAGAGCATTGGATAATATTCTTATCCATGAAAATTAATTCTTTAGGTAAT
453 AGTTAAACTCTCAACAAGAGCATTGGATAATATTTTTATCCATGAAAATTAATTCTTCAGGTAAT
* * * * *
225215 CATAATTATTCATGATACGAATTTTTATACTTGATCAATTACTTGTTATTATATTCAGTTATATT
518 CATAATTATTCTTGATATGAATTTTTACACTTAATCAATTACTTGTTATTATATTCATTTATATT
*
225280 ATCTTCAATAATTTTCAATGAAAAAATAAGTTAATTAAAATATAAATTGAA
583 ATCTTCAATAATTTTCAAT-AAAAAATAAGTAAATTAAAATATAAATTGAA
* * * *
225331 TTTTATTTTCTTGAGTTAAACATAATTTATTTTTTTTAAACAAATGTAAGCTTAATTTTAAAGGT
1 TTATATTTTTTTGAGTTAAACATAATTTATTTTTTTAAAACAAATGTAAGCTTAATTTTAAAGGC
* * * ***
225396 ATAATGCAAAAAA-TAGTTCCCCGATATTTTTTCAAA-AGGTCATTTTGACACATATTCTTTTTT
66 ATAATGCAAAAAATTAGTCCCCCAATGTTTGCCCAAATA-GTCATTTTGACACA-ATTC--TTTT
* * *
225459 TTTGAAGCACTTAGTCCTTAAACATTTTAATTTTTTGTCAAAATGACCACTT-T---TGG--ATC
127 TTGGGAGCACTTAGTCCTTAAACATTTTAATTTTTGGTCAAAATGACCACTTCTAGATGGAAATC
* * * * *
225518 GTTAGTTGACTAAATGTTAACACATGATGCTAATGTGACATTTTCACATGTGCTAAATTACTAAC
192 GTTAGTTGACTAACTGTTAACACATGATGCTGATGTGATATTTTCACATGTACTAAATTACTGAC
* * * *
225583 ATGACACATACTACATCACCCAAGGTCATAATTATGGTATATACCACATCATCTAAGACGAAGAT
257 ATGA-ACATACTACGTCACCCAAGGTCATAATTATGATATGTACCACATCATCTAAGACAAAGAT
*
225648 GTGACATGATCCACGTCACTCAAGATGATAACGTGAAACATATATGTCACCCAAGATGATATATT
321 GTGACATGATCCACGTCACTCAAGATGATAACATGAAACATATATGTCACCCAAGATGATATATT
* *
225713 ATATTATTGTAATGAGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCAGGGAGGTC
386 AAATTATTGTAATTAGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGC-GGGAGGTC
* * *
225778 TTGAGTTAAACTCTCAACAAGTGCATTGGATAATATTTTTATCTATGAAAATTAAATTCTTCAGA
450 TTGAGTTAAACTCTCAACAAGAGCATTGGATAATATTTTTATCCATGAAAATT-AATTCTTCAGG
* *
225843 TAATCATAATTATTCTTTATATGAATTTTTACACTTAATCTATTACTTGTTATTATATTCATTTA
514 TAATCATAATTATTCTTGATATGAATTTTTACACTTAATCAATTACTTGTTATTATATTCATTTA
* * *
225908 TATTATCTTCAATAATTTTCAATAAAAAATAAGTAAATAAAAATATTAATTAAA
579 TATTATCTTCAATAATTTTCAATAAAAAATAAGTAAATTAAAATATAAATTGAA
**
225962 TTATATTTTTTTGAGTTAAACATAATTTATTTTTTTAAAACAAATGTAAATTTAATTTTAAAGGC
1 TTATATTTTTTTGAGTTAAACATAATTTATTTTTTTAAAACAAATGTAAGCTTAATTTTAAAGGC
226027 ATAATGCAAAAAA-TAGTCCCACCAATGTTTGCCCAAATAGTCATTTTGACAC-ATTCTTTTTTG
66 ATAATGCAAAAAATTAGTCCC-CCAATGTTTGCCCAAATAGTCATTTTGACACAATTCTTTTTTG
*
226090 GGAGCACTTAGTCCTTAAACATTTTAATTTTTGGTCAAAATGACCACTTCTAGATGAAAATCGTT
130 GGAGCACTTAGTCCTTAAACATTTTAATTTTTGGTCAAAATGACCACTTCTAGATGGAAATCGTT
* * * *
226155 AGTTGACTAACTGTTAATACATGATGCTGACGTAATATTTTCACATGTATTAAATTACTGACATG
195 AGTTGACTAACTGTTAACACATGATGCTGATGTGATATTTTCACATGTACTAAATTACTGACATG
* *
226220 -ACATACTACGTCACCCAAGGTCATAATTATCATATGTACCACATCATCTAAGACGAAGATGTGA
260 AACATACTACGTCACCCAAGGTCATAATTATGATATGTACCACATCATCTAAGACAAAGATGTGA
* * * *
226284 CATGATCCATGTCAGTCAAGATGATAACGTGAAACATATATGTCACCTAAGATGATATATTAAAT
325 CATGATCCACGTCACTCAAGATGATAACATGAAACATATATGTCACCCAAGATGATATATTAAAT
* *
226349 TATTGTAATTAGCTCTTGTAGCTTAGTTGGTTAGAGCACCCATTTAGTAAGCGGGAGGTCTTGAG
390 TATTGTAATTAGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAG
* * *
226414 TTCAACTCTCAACAAGAGTAATT-G--AATA--ATT-TCC-------TT-ATTCTTCAGGTAATC
455 TTAAACTCTCAACAAGAG-CATTGGATAATATTTTTATCCATGAAAATTAATTCTTCAGGTAATC
* * *
226465 ATAATTATTCCTGATATGATTTTTTTACACTTGATCAATTACTTGTTATTATATTCATTTATATT
519 ATAATTATTCTTGATATGA-ATTTTTACACTTAATCAATTACTTGTTATTATATTCATTTATATT
* * *
226530 ATCTTCAATAA-TTTGAATAAAAAATAAGTTAATTAAAATAAAAAATTGAA
583 ATCTTCAATAATTTTCAATAAAAAATAAGTAAATTAAAAT-ATAAATTGAA
* * * * * *
226580 TTATATTTTTTTAAGTTATACATAATTTA-CTTTTTAAAACAAATGTACGCTTAATTTAAAAGAC
1 TTATATTTTTTTGAGTTAAACATAATTTATTTTTTTAAAACAAATGTAAGCTTAATTTTAAAGGC
*
226644 ATAATGC-AAAAATCAG-CCCCCAAT
66 ATAATGCAAAAAATTAGTCCCCCAAT
226668 AATTTCTCAA
Statistics
Matches: 1748, Mismatches: 190, Indels: 78
0.87 0.09 0.04
Matches are distributed among these distances:
615 5 0.00
616 8 0.00
617 94 0.05
618 87 0.05
619 2 0.00
626 2 0.00
627 2 0.00
628 53 0.03
629 8 0.00
630 416 0.24
631 470 0.27
632 385 0.22
633 91 0.05
634 68 0.04
635 4 0.00
636 1 0.00
637 52 0.03
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (632 bp):
TTATATTTTTTTGAGTTAAACATAATTTATTTTTTTAAAACAAATGTAAGCTTAATTTTAAAGGC
ATAATGCAAAAAATTAGTCCCCCAATGTTTGCCCAAATAGTCATTTTGACACAATTCTTTTTTGG
GAGCACTTAGTCCTTAAACATTTTAATTTTTGGTCAAAATGACCACTTCTAGATGGAAATCGTTA
GTTGACTAACTGTTAACACATGATGCTGATGTGATATTTTCACATGTACTAAATTACTGACATGA
ACATACTACGTCACCCAAGGTCATAATTATGATATGTACCACATCATCTAAGACAAAGATGTGAC
ATGATCCACGTCACTCAAGATGATAACATGAAACATATATGTCACCCAAGATGATATATTAAATT
ATTGTAATTAGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGT
TAAACTCTCAACAAGAGCATTGGATAATATTTTTATCCATGAAAATTAATTCTTCAGGTAATCAT
AATTATTCTTGATATGAATTTTTACACTTAATCAATTACTTGTTATTATATTCATTTATATTATC
TTCAATAATTTTCAATAAAAAATAAGTAAATTAAAATATAAATTGAA
Found at i:230011 original size:59 final size:59
Alignment explanation
Indices: 229935--230055 Score: 174
Period size: 59 Copynumber: 2.1 Consensus size: 59
229925 CATACTAAAC
* * *
229935 AGTTGGGTGACTATTTTATAACTTTTAATAGTCAGGGGACT-AAACAAAGCAACACCCTAT
1 AGTTGGGTGACCATTTTATAACTTTTAATAGTCAAGAGACTCAAA-AAAGCAAC-CCCTAT
*
229995 AGTTGGG-GACCATTTTATAACTTTTAATAGTCAAGAGACTCAAAAAAGCATCCCCTAT
1 AGTTGGGTGACCATTTTATAACTTTTAATAGTCAAGAGACTCAAAAAAGCAACCCCTAT
230053 AGT
1 AGT
230056 CGAAAGACTA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
58 9 0.16
59 37 0.66
60 10 0.18
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (59 bp):
AGTTGGGTGACCATTTTATAACTTTTAATAGTCAAGAGACTCAAAAAAGCAACCCCTAT
Found at i:230069 original size:59 final size:59
Alignment explanation
Indices: 229943--230069 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 59
229933 ACAGTTGGGT
* * * **
229943 GACTATTTTATAACTTTTAATAGTCAGGGGACTAAACAAAGCAACACCCTATAGTTGGG
1 GACTATTTTATAACTTTTAATAGTCAAGAGACTAAACAAAGCAACACCCTATAGTCGAA
* *
230002 GACCATTTTATAACTTTTAATAGTCAAGAGACTCAAA-AAAGCATC-CCCTATAGTCGAAA
1 GACTATTTTATAACTTTTAATAGTCAAGAGACT-AAACAAAGCAACACCCTATAGTCG-AA
230061 GACTATTTT
1 GACTATTTT
230070 GTGTACTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 10 0.17
59 45 0.78
60 3 0.05
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (59 bp):
GACTATTTTATAACTTTTAATAGTCAAGAGACTAAACAAAGCAACACCCTATAGTCGAA
Found at i:238955 original size:33 final size:32
Alignment explanation
Indices: 238916--238986 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
238906 ATTAATCTAC
* ** * *
238916 TTTTCTCCATTTTTTTCCTTTTTTTCTTTTTT
1 TTTTCTCCAATTTTTTAATTTTTTTATTATTT
*
238948 TCTTTCTCTAATTTTTTAATTTTTTTATTATTT
1 T-TTTCTCCAATTTTTTAATTTTTTTATTATTT
238981 TTTTCT
1 TTTTCT
238987 TTTTTTATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTCTCCAATTTTTTAATTTTTTTATTATTT
Found at i:238980 original size:19 final size:19
Alignment explanation
Indices: 238958--238994 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
238948 TCTTTCTCTA
238958 ATTTTTTAATTTTTTTATT
1 ATTTTTTAATTTTTTTATT
**
238977 ATTTTTTTCTTTTTTTAT
1 ATTTTTTAATTTTTTTAT
238995 ATCCTATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (19 bp):
ATTTTTTAATTTTTTTATT
Found at i:239388 original size:44 final size:44
Alignment explanation
Indices: 239336--239421 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
239326 AAGTGGAGAC
*
239336 AATGTTGATCCAACTCCTTCTAAGATGGAATCGAGCAAAATGAA
1 AATGTTGATCCAACTCCTTCTAAGATGGAATCGAACAAAATGAA
* * **
239380 AATGTTGATCCACCTCTTTCTGTGATGGAATCGAACAAAATG
1 AATGTTGATCCAACTCCTTCTAAGATGGAATCGAACAAAATG
239422 TTGATGCGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (44 bp):
AATGTTGATCCAACTCCTTCTAAGATGGAATCGAACAAAATGAA
Found at i:239439 original size:44 final size:44
Alignment explanation
Indices: 239342--239463 Score: 120
Period size: 44 Copynumber: 2.8 Consensus size: 44
239332 AGACAATGTT
* * * **
239342 GATCCAACTCCTTCTAAGATGGAATCGAGCAAAATGAAAATGTT
1 GATCCACCTCCTTTTATGATGGAATCGAGCAAAATGAAAATGCG
* * ***
239386 GATCCACCT-CTTTCTGTGATGGAATCGAACAAAATGTTGATGCG
1 GATCCACCTCCTTT-TATGATGGAATCGAGCAAAATGAAAATGCG
* *
239430 GATCTACCTCCTTTTATGATAGAATCGAGCAAAA
1 GATCCACCTCCTTTTATGATGGAATCGAGCAAAA
239464 GGGTGAACAA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
43 3 0.05
44 55 0.89
45 4 0.06
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (44 bp):
GATCCACCTCCTTTTATGATGGAATCGAGCAAAATGAAAATGCG
Found at i:241886 original size:24 final size:23
Alignment explanation
Indices: 241853--241914 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
241843 TGAACCCTCC
*
241853 TTTTTATTTTTCTTTCTCTCTCT
1 TTTTTCTTTTTCTTTCTCTCTCT
* *
241876 TTTTT-TCTTTTCATTTTTCTTTCT
1 TTTTTCT-TTTTC-TTTCTCTCTCT
241900 TTTTTCTATTTTCTT
1 TTTTTCT-TTTTCTT
241915 CTTTTTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 1 0.03
23 10 0.30
24 16 0.48
25 6 0.18
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTCTTTTTCTTTCTCTCTCT
Found at i:241893 original size:7 final size:7
Alignment explanation
Indices: 241883--242010 Score: 58
Period size: 7 Copynumber: 18.4 Consensus size: 7
241873 TCTTTTTTTC
241883 TTTTCAT
1 TTTTCAT
241890 TTTTC--
1 TTTTCAT
*
241895 -TTTCTT
1 TTTTCAT
241901 TTTTCTATT
1 TTTTC-A-T
*
241910 TTCTTCTT
1 TT-TTCAT
241918 TTTTTCAT
1 TT-TTCAT
241926 TTTTCATT
1 TTTTCA-T
241934 TTTTCCACT
1 TTTT-CA-T
241943 TTTT-AT
1 TTTTCAT
*
241949 CTTTTCCT
1 -TTTTCAT
*
241957 CTTT--T
1 TTTTCAT
241962 -TTTC-T
1 TTTTCAT
*
241967 TTTTCTT
1 TTTTCAT
*
241974 TTTTCTT
1 TTTTCAT
241981 TTTTCAT
1 TTTTCAT
*
241988 TTTTCTT
1 TTTTCAT
241995 TTTTCAT
1 TTTTCAT
242002 TTTTC-T
1 TTTTCAT
242008 TTT
1 TTT
242011 CTCTCTTTTC
Statistics
Matches: 98, Mismatches: 10, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
4 7 0.07
5 2 0.02
6 9 0.09
7 52 0.53
8 15 0.15
9 10 0.10
10 3 0.03
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCAT
Found at i:241935 original size:6 final size:7
Alignment explanation
Indices: 241918--242010 Score: 63
Period size: 7 Copynumber: 13.6 Consensus size: 7
241908 TTTTCTTCTT
241918 TTTTTCA
1 TTTTTCA
241925 TTTTTCA
1 TTTTTCA
241932 TTTTTTCCA
1 -TTTTT-CA
241941 CTTTTT-A
1 -TTTTTCA
241948 TCTTTTC-
1 T-TTTTCA
* *
241955 CTCTT--
1 TTTTTCA
241960 TTTTTC-
1 TTTTTCA
*
241966 TTTTTCT
1 TTTTTCA
*
241973 TTTTTCT
1 TTTTTCA
241980 TTTTTCA
1 TTTTTCA
*
241987 TTTTTCT
1 TTTTTCA
241994 TTTTTCA
1 TTTTTCA
242001 TTTTTC-
1 TTTTTCA
242007 TTTT
1 TTTT
242011 CTCTCTTTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
5 3 0.04
6 14 0.19
7 43 0.60
8 5 0.07
9 7 0.10
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:242022 original size:14 final size:14
Alignment explanation
Indices: 241895--242010 Score: 99
Period size: 14 Copynumber: 7.6 Consensus size: 14
241885 TTCATTTTTC
241895 TTTCTTTTTTCTATTT
1 TTTCTTTTTTC-A-TT
241911 TCTTCTTTTTTTCATT
1 T-TTC-TTTTTTCATT
241927 TTTCATTTTTTCCACTTT
1 TTTC-TTTTTT-CA--TT
*
241945 TTATCTTTTCCTC-TT
1 TT-TCTTTT-TTCATT
* *
241960 TTTTTCTTTTTCTTT
1 TTTCT-TTTTTCATT
241975 TTTCTTTTTTCATT
1 TTTCTTTTTTCATT
241989 TTTCTTTTTTCATT
1 TTTCTTTTTTCATT
242003 TTTCTTTT
1 TTTCTTTT
242011 CTCTCTTTTC
Statistics
Matches: 85, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
14 34 0.40
15 22 0.26
16 6 0.07
17 4 0.05
18 16 0.19
19 3 0.04
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTTTTTCATT
Found at i:242033 original size:14 final size:14
Alignment explanation
Indices: 241959--242032 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 14
241949 CTTTTCCTCT
*
241959 TTTTTTCTT-TTTC
1 TTTTTTCTTATCTC
* *
241972 TTTTTTCTTTTTTC
1 TTTTTTCTTATCTC
* * *
241986 ATTTTTCTTTTTTC
1 TTTTTTCTTATCTC
* *
242000 ATTTTTCTTTTCTC
1 TTTTTTCTTATCTC
*
242014 TCTTTTCTTATCT-
1 TTTTTTCTTATCTC
242027 TTTTTT
1 TTTTTT
242033 TTCTTCAAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
13 14 0.26
14 40 0.74
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTCTTATCTC
Found at i:244062 original size:16 final size:17
Alignment explanation
Indices: 244023--244062 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
244013 GTTATGGAAT
244023 GAATG-AAAGAATAGAA
1 GAATGTAAAGAATAGAA
*
244039 -AATCTAAAGAATA-AA
1 GAATGTAAAGAATAGAA
244054 GAATGTAAA
1 GAATGTAAA
244063 ATAATGATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.62, C:0.03, G:0.17, T:0.17
Consensus pattern (17 bp):
GAATGTAAAGAATAGAA
Found at i:248150 original size:34 final size:34
Alignment explanation
Indices: 248107--248174 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
248097 GCAACCATTC
248107 AATATTTATGTTTTTTATTATTATTAATCTGGGG
1 AATATTTATGTTTTTTATTATTATTAATCTGGGG
248141 AATATTTATGTTTTTTATTATTATTAATCTGGGG
1 AATATTTATGTTTTTTATTATTATTAATCTGGGG
248175 TAAATATAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (34 bp):
AATATTTATGTTTTTTATTATTATTAATCTGGGG
Found at i:253252 original size:24 final size:25
Alignment explanation
Indices: 253207--253265 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
253197 CCTTAAAGTT
253207 TTATAAG-TTTTTATCCTCTAAAATC
1 TTATAAGTTTTTTAT-CTCTAAAATC
* *
253232 TTATAAGTTTTTTAT-TTTAAAATT
1 TTATAAGTTTTTTATCTCTAAAATC
253256 TTATAAGTTT
1 TTATAAGTTT
253266 GCTCATCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 17 0.55
25 7 0.23
26 7 0.23
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (25 bp):
TTATAAGTTTTTTATCTCTAAAATC
Found at i:255127 original size:15 final size:15
Alignment explanation
Indices: 255106--255148 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
255096 TATTTTACTC
255106 TTATTTTTA-AATTA
1 TTATTTTTATAATTA
*
255120 TGTATTTTTATTATTA
1 T-TATTTTTATAATTA
*
255136 TTATTTTCATAAT
1 TTATTTTTATAAT
255149 ATAGATTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATTTTTATAATTA
Found at i:256463 original size:12 final size:11
Alignment explanation
Indices: 256433--256457 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
256423 TTATATATTA
256433 TTTAAATTGAT
1 TTTAAATTGAT
256444 TTTAAATTGAT
1 TTTAAATTGAT
256455 TTT
1 TTT
256458 TGAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (11 bp):
TTTAAATTGAT
Found at i:265948 original size:25 final size:24
Alignment explanation
Indices: 265911--265958 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
265901 ATTACTATTT
*
265911 TATGTATGGTATGTACATTTTTATG
1 TATGTATGGTATGCA-ATTTTTATG
*
265936 TATGTATGTTATGCAATTTTTAT
1 TATGTATGGTATGCAATTTTTAT
265959 TTTATTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54
Consensus pattern (24 bp):
TATGTATGGTATGCAATTTTTATG
Found at i:277331 original size:25 final size:26
Alignment explanation
Indices: 277303--277354 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
277293 AAAGAATAAG
*
277303 AAAAAATGAGTG-AAAATGAAAAAAT
1 AAAAAATGAATGAAAAATGAAAAAAT
277328 AAAAAATGAATGAAAAAATGAAAAAAT
1 AAAAAATGAATG-AAAAATGAAAAAAT
277355 GAGGGTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 11 0.46
27 13 0.54
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.15
Consensus pattern (26 bp):
AAAAAATGAATGAAAAATGAAAAAAT
Found at i:277339 original size:19 final size:20
Alignment explanation
Indices: 277317--277356 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
277307 AATGAGTGAA
277317 AATGAAAAAAT-AAAAAATG
1 AATGAAAAAATGAAAAAATG
277336 AATGAAAAAATGAAAAAATG
1 AATGAAAAAATGAAAAAATG
277356 A
1 A
277357 GGGTTCAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (20 bp):
AATGAAAAAATGAAAAAATG
Found at i:278913 original size:108 final size:107
Alignment explanation
Indices: 278357--279046 Score: 1078
Period size: 108 Copynumber: 6.3 Consensus size: 107
278347 CGTTTGATGG
*
278357 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTT-TGAAGATTGTGGG
278422 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
65 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
* *
278465 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGACGCGATCGTTGAAGATTGTGTG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGAT-TTTGAAGA-T-TGTG
278530 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
63 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
*
278575 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGAT-TTTGAAGATTG-T-G
*
278640 AGTCTTATACTCTCTGAAGAAATA-GGGGCAGACGCGATCGTTGA
63 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
*
278684 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGTTGAAGATTGTTCG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-TTGAAGATTG-T-G
* * *
278749 AGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
63 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
* *
278794 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTT-TGAAGATTGTGGG
278859 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
65 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
*
278902 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-TTGAAGATTGTGGG
* * **
278967 TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGA
65 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
* * *
279010 AGATTGTCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
1 AGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
279047 AGCGAACCCG
Statistics
Matches: 547, Mismatches: 25, Indels: 20
0.92 0.04 0.03
Matches are distributed among these distances:
107 1 0.00
108 230 0.42
109 112 0.20
110 204 0.37
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (107 bp):
AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTTTGAAGATTGTGGGT
CTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
Found at i:279049 original size:55 final size:55
Alignment explanation
Indices: 278357--279046 Score: 1060
Period size: 55 Copynumber: 12.7 Consensus size: 55
278347 CGTTTGATGG
* *
278357 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGAT-TTATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGT-TGA
*
278412 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
*
278465 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGACGCGATCGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
*
278520 AGATTGTGT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
1 AGATTGT-TCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
278575 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
278630 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGCAGACGCGATCGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
* *
278684 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
* *
278739 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
* * *
278794 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGAT-TTATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGT-TGA
*
278849 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
* *
278902 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
* * * **
278957 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
* * *
279010 AGATTGTCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
1 AGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
279047 AGCGAACCCG
Statistics
Matches: 591, Mismatches: 31, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
53 141 0.24
54 64 0.11
55 385 0.65
56 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
Found at i:286248 original size:17 final size:19
Alignment explanation
Indices: 286204--286240 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
286194 ACGTGTAACT
*
286204 TAAAATGTTATATTTTTTC
1 TAAAATATTATATTTTTTC
286223 TAAAATATTATATTTTTT
1 TAAAATATTATATTTTTT
286241 ATAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TAAAATATTATATTTTTTC
Found at i:287166 original size:28 final size:30
Alignment explanation
Indices: 287106--287166 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
287096 TGGCCCCAAA
* **
287106 TTTAAAAAATTCTAATTGATCCTTAAATTT
1 TTTAAAAAATTCTAATTGATCCTCAAAAGT
287136 TTTAAAAAA-TC-AATTGATCCTCAAAAGT
1 TTTAAAAAATTCTAATTGATCCTCAAAAGT
287164 TTT
1 TTT
287167 GAAATTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 17 0.61
29 2 0.07
30 9 0.32
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (30 bp):
TTTAAAAAATTCTAATTGATCCTCAAAAGT
Found at i:287178 original size:28 final size:28
Alignment explanation
Indices: 287110--287175 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
287100 CCCAAATTTA
* **
287110 AAAAATTCTAATTGATCCTTAAATTTTTT
1 AAAAATTC-AATTGATCCTCAAAAGTTTT
*
287139 AAAAAATCAATTGATCCTCAAAAGTTTT
1 AAAAATTCAATTGATCCTCAAAAGTTTT
*
287167 -GAAATTCAA
1 AAAAATTCAA
287176 ATTAAAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 7 0.23
28 17 0.55
29 7 0.23
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (28 bp):
AAAAATTCAATTGATCCTCAAAAGTTTT
Found at i:291798 original size:20 final size:22
Alignment explanation
Indices: 291760--291800 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
291750 ATGAGAAAAT
291760 TAGCAAAAGAGAAGAAATTCAG
1 TAGCAAAAGAGAAGAAATTCAG
*
291782 TAGCATAAGA-AAG-AATTCA
1 TAGCAAAAGAGAAGAAATTCA
291801 TGTACACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.54, C:0.10, G:0.20, T:0.17
Consensus pattern (22 bp):
TAGCAAAAGAGAAGAAATTCAG
Done.