Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008290.1 Hibiscus syriacus cultivar Beakdansim tig00110954_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: 1890093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:1026592 original size:17 final size:16
Alignment explanation
Indices: 1026565--1026596 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1026555 TAAATTTTAC
1026565 AAATATATTTTATATA
1 AAATATATTTTATATA
1026581 AAATATTATTTTATAT
1 AAATA-TATTTTATAT
1026597 TTTTAATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATATTTTATATA
Found at i:1051404 original size:20 final size:21
Alignment explanation
Indices: 1051352--1051405 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
1051342 CATTGAAAAG
1051352 GAGTATCGATACCATAATATA
1 GAGTATCGATACCATAATATA
* **
1051373 GAAGTATTGATACCATGGTAT-
1 G-AGTATCGATACCATAATATA
1051394 GAGTATCGATAC
1 GAGTATCGATAC
1051406 TATTGAGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.36
21 2 0.07
22 16 0.57
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (21 bp):
GAGTATCGATACCATAATATA
Found at i:1052056 original size:163 final size:161
Alignment explanation
Indices: 1051769--1052336 Score: 787
Period size: 163 Copynumber: 3.5 Consensus size: 161
1051759 ATTTATATTA
* * * *
1051769 TGAGTAAAAAAATTAAATGTCTAACTGTGCATTTGGAAGAAAGGTGCCAATCATGCTAGTTAGAT
1 TGAGT-AAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGAT
* * * * * * * *
1051834 GAAAGGTTAAATGCCTTTGAGTAAAAAATTAAATATCTAACTCTACATTTAGTAGAAATGTGTCA
65 GAAAGGTTAAATGCCTTTGGGTAAAAGATTAAATGTCTAAATGTGCATTTGGAAGAAATGTGTCA
1051899 ATCATGCTAGTTAGATGAAAGGTTAAAATGCCTT
130 ATCATGCTAGTTAGATGAAA-GTT-AAATGCCTT
** *
1051933 TGAGTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTAACAACCATGCTAGTTAGATG
1 TGAGTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
* * *
1051998 AAAGTTTAAATGCCTTTGGGTAAAAGATTAAATGCCTAATTGTGCATTTGGAAGAAATGTGTCAA
66 AAAGGTTAAATGCCTTTGGGTAAAAGATTAAATGTCTAAATGTGCATTTGGAAGAAATGTGTCAA
*
1052063 TCATGCTAGTTATATGAAATGTTAAATGCCTT
131 TCATGCTAGTTAGATGAAA-GTTAAATGCCTT
* * * * *
1052095 TGAGTAAAAGATTAAATGTCTAACTGTGTATTTGGCAGAAAGGTGTTAATCATGTTAGTTAG-TT
1 TGAGTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
* * * * *
1052159 AAAGGTTAAATACCTTTGGGTAAAAGATTAAATGTCTAAATGTGCATTTGGCATAAAGGTGCCAA
66 AAAGGTTAAATGCCTTTGGGTAAAAGATTAAATGTCTAAATGTGCATTTGGAAGAAATGTGTCAA
1052224 TCATGCTAGTTAGATGAAAGTTAAATGCCTT
131 TCATGCTAGTTAGATGAAAGTTAAATGCCTT
* * * * *
1052255 TGGGTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATAATGCAAGTTAAACG
1 TGAGTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
1052320 AAAGGTTAAATGCCTTT
66 AAAGGTTAAATGCCTTT
1052337 AGAGGAAAGA
Statistics
Matches: 357, Mismatches: 46, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
160 66 0.18
161 92 0.26
162 64 0.18
163 130 0.36
164 5 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (161 bp):
TGAGTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
AAAGGTTAAATGCCTTTGGGTAAAAGATTAAATGTCTAAATGTGCATTTGGAAGAAATGTGTCAA
TCATGCTAGTTAGATGAAAGTTAAATGCCTT
Found at i:1052193 original size:80 final size:81
Alignment explanation
Indices: 1051769--1052368 Score: 783
Period size: 81 Copynumber: 7.4 Consensus size: 81
1051759 ATTTATATTA
* * *
1051769 TGAGTAAAAAAATTAAATGTCTAACTGTGCATTTGGAAGAAAGGTGCCAATCATGCTAGTTAGAT
1 TGAGT-AAAAGATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGAT
1051834 GAAAGGTTAAATGCCTT
65 GAAAGGTTAAATGCCTT
* * * * * * *
1051851 TGAGTAAAAAATTAAATATCTAACTCTACATTTAGTAGAAATGTGTCAATCATGCTAGTTAGATG
1 TGAGTAAAAGATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
1051916 AAAGGTTAAAATGCCTT
66 AAAGGTT-AAATGCCTT
* ** *
1051933 TGAGTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTAACAACCATGCTAGTTAGATG
1 TGAGTAAAAGATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
*
1051998 AAAGTTTAAATGCCTT
66 AAAGGTTAAATGCCTT
* * * * * *
1052014 TGGGTAAAAGATTAAATGCCTAATTGTGCATTTGGAAGAAATGTGTCAATCATGCTAGTTATATG
1 TGAGTAAAAGATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
*
1052079 AAATGTTAAATGCCTT
66 AAAGGTTAAATGCCTT
* * * *
1052095 TGAGTAAAAGATTAAATGTCTAACTGTGTATTTGGCAGAAAGGTGTTAATCATGTTAGTTAG-TT
1 TGAGTAAAAGATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
*
1052159 AAAGGTTAAATACCTT
66 AAAGGTTAAATGCCTT
* * * *
1052175 TGGGTAAAAGATTAAATGTCTAAATGTGCATTTGGCATAAAGGTGCCAATCATGCTAGTTAGATG
1 TGAGTAAAAGATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
1052240 AAA-GTTAAATGCCTT
66 AAAGGTTAAATGCCTT
* * * * * *
1052255 TGGGTAAAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATAATGCAAGTTAAACG
1 TGAGTAAAAGATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
1052320 AAAGGTTAAATGCCTT
66 AAAGGTTAAATGCCTT
* * * *
1052336 TAGAG-GAAAGAATAAATGTTTAACAGTGCATTT
1 T-GAGTAAAAGATTAAATGTCTAACTGTGCATTT
1052369 TGACCTAAAA
Statistics
Matches: 450, Mismatches: 64, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
80 141 0.31
81 233 0.52
82 76 0.17
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (81 bp):
TGAGTAAAAGATTAAATGTCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGCTAGTTAGATG
AAAGGTTAAATGCCTT
Found at i:1055094 original size:31 final size:31
Alignment explanation
Indices: 1055056--1055149 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
1055046 AGGGTCGAGG
1055056 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1055087 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1055118 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1055149 G
1 G
1055150 GTCCTTCGGG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1055989 original size:66 final size:67
Alignment explanation
Indices: 1055867--1055991 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 67
1055857 CCATTCAACA
* * * ** *
1055867 GGTACTGATACCCTCTCAAACGAGAAGAATTACAGAATGTCATAAGGGTACCAATACCTCCCAGT
1 GGTACCGATACCCCCTCAAACGAGAAAAATTACAGAATACCATAAGGGTACAAATACCTCCCAGT
1055932 TG
66 TG
**
1055934 GGTACCGATACCCCCTTGAACGA-AAAAATTACAGAATACCATGAA-GGTACAAATACCT
1 GGTACCGATACCCCCTCAAACGAGAAAAATTACAGAATACCAT-AAGGGTACAAATACCT
1055992 TAAATAGGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
66 28 0.57
67 21 0.43
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (67 bp):
GGTACCGATACCCCCTCAAACGAGAAAAATTACAGAATACCATAAGGGTACAAATACCTCCCAGT
TG
Found at i:1056672 original size:23 final size:23
Alignment explanation
Indices: 1056623--1056678 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1056613 TCTTATATGG
* * *
1056623 CACTACGGTGCAATTCTATGCGG
1 CACTTCGGTGCAATTCTACGCGA
*
1056646 CACTTCGGTGCAATTCTACGTGA
1 CACTTCGGTGCAATTCTACGCGA
1056669 CACTTCGGTG
1 CACTTCGGTG
1056679 TATTTATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGA
Found at i:1063531 original size:23 final size:23
Alignment explanation
Indices: 1063463--1063523 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1063453 ACATCTTATA
*
1063463 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* **
1063486 CGAAACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1063509 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1063524 TTTATACGAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1069813 original size:23 final size:23
Alignment explanation
Indices: 1069787--1069834 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1069777 CACTACGATA
1069787 CAATTCTACGCGGCACTTCGGTG
1 CAATTCTACGCGGCACTTCGGTG
* *
1069810 CAATTCTACGTGGCACTTCTGTG
1 CAATTCTACGCGGCACTTCGGTG
1069833 CA
1 CA
1069835 TTTATACGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (23 bp):
CAATTCTACGCGGCACTTCGGTG
Found at i:1069842 original size:23 final size:23
Alignment explanation
Indices: 1069787--1069842 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1069777 CACTACGATA
*
1069787 CAATTCTACGCGGCACTTCGGTG
1 CAATTATACGCGGCACTTCGGTG
* * *
1069810 CAATTCTACGTGGCACTTCTGTG
1 CAATTATACGCGGCACTTCGGTG
*
1069833 CATTTATACG
1 CAATTATACG
1069843 AGTTGTGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (23 bp):
CAATTATACGCGGCACTTCGGTG
Found at i:1084835 original size:33 final size:33
Alignment explanation
Indices: 1084788--1084860 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
1084778 CCTCTGAAAA
*
1084788 TCTTCTGGTGTTGCAGACTTCACTGCTTTCAGC
1 TCTTGTGGTGTTGCAGACTTCACTGCTTTCAGC
1084821 TCTTGTGGTGTTGCAGACTTCACTGCTTTCAGC
1 TCTTGTGGTGTTGCAGACTTCACTGCTTTCAGC
1084854 T-TTGTGG
1 TCTTGTGG
1084861 AATAAGCTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 6 0.15
33 33 0.85
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.41
Consensus pattern (33 bp):
TCTTGTGGTGTTGCAGACTTCACTGCTTTCAGC
Found at i:1085661 original size:6 final size:6
Alignment explanation
Indices: 1085650--1085682 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1085640 TCTCGTCTCG
1085650 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1085683 AATACGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1085837 original size:40 final size:41
Alignment explanation
Indices: 1085778--1085985 Score: 223
Period size: 42 Copynumber: 5.1 Consensus size: 41
1085768 GAATTTACTC
*
1085778 ATTTTCTGAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGATATCGCGTTGCG
* *
1085818 ATTTTCTTAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-ATATCGCGTTGCG
* *
1085860 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-ATATCGCGTTGCG
* ** * *
1085902 ATTTTCTT--TTGACCGTTGCGATT-TT-CTTTTCAACGTTGCG
1 ATTTTCTTAATCG--CGTTGCGATTCTTGGATATC-GCGTTGCG
*
1085942 ATTTTCTAAATCGCGTTGCGATT-TT-GATATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGATATCGCGTTGCG
1085981 ATTTT
1 ATTTT
1085986 GTTGGTCATT
Statistics
Matches: 144, Mismatches: 17, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
39 15 0.10
40 57 0.40
41 3 0.02
42 69 0.48
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (41 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGATATCGCGTTGCG
Found at i:1085958 original size:20 final size:20
Alignment explanation
Indices: 1085778--1085985 Score: 138
Period size: 20 Copynumber: 10.2 Consensus size: 20
1085768 GAATTTACTC
*
1085778 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1085798 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
* *
1085818 ATTTTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1085838 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
1085860 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1085880 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
1085902 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
1085922 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
1085942 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* *
1085962 ATTTT-GATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
1085981 ATTTT
1 ATTTT
1085986 GTTGGTCATT
Statistics
Matches: 148, Mismatches: 29, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
18 2 0.01
19 19 0.13
20 86 0.58
21 15 0.10
22 26 0.18
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:1089597 original size:14 final size:14
Alignment explanation
Indices: 1089575--1089628 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
1089565 TACTTTTAAA
1089575 TTTTATAAATTCAT
1 TTTTATAAATTCAT
* **
1089589 TTTTCTAAATAAATT
1 TTTTATAAATTCA-T
1089604 TTTTATAAATTCAT
1 TTTTATAAATTCAT
*
1089618 TCTTTTTAAAT
1 T-TTTATAAAT
1089629 AAAAATATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTATAAATTCAT
Found at i:1089611 original size:29 final size:30
Alignment explanation
Indices: 1089575--1089631 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
1089565 TACTTTTAAA
1089575 TTTTATAAATTCATT-TTTCTAAATAAATT
1 TTTTATAAATTCATTCTTTCTAAATAAATT
*
1089604 TTTTATAAATTCATTCTTTTTAAATAAA
1 TTTTATAAATTCATTCTTTCTAAATAAA
1089632 AATATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTTATAAATTCATTCTTTCTAAATAAATT
Found at i:1089640 original size:30 final size:29
Alignment explanation
Indices: 1089572--1089640 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
1089562 CTTTACTTTT
1089572 AAATTTTATAAATTCATTTTTCTAAATAA
1 AAATTTTATAAATTCATTTTTCTAAATAA
** *
1089601 ATTTTTTATAAATTCATTCTTTTTAAATAA
1 AAATTTTATAAATTCATT-TTTCTAAATAA
*
1089631 AAATATTATA
1 AAATTTTATA
1089641 TTTATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (29 bp):
AAATTTTATAAATTCATTTTTCTAAATAA
Found at i:1090053 original size:24 final size:24
Alignment explanation
Indices: 1090024--1090075 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1090014 TGGTTTTTTT
1090024 AATATAACTTTATTTTTAAATTTA
1 AATATAACTTTATTTTTAAATTTA
1090048 AATATAACTTTATTTTTAAATTTA
1 AATATAACTTTATTTTTAAATTTA
1090072 AATA
1 AATA
1090076 CAATTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATAACTTTATTTTTAAATTTA
Found at i:1091409 original size:27 final size:26
Alignment explanation
Indices: 1091358--1091410 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1091348 AAAAATATTA
* * *
1091358 TTTATTTATTTATTATTATTATTTTT
1 TTTATTAAATTATTATTATAATTTTT
1091384 TTTATTAAATTATATATTATAATTTTT
1 TTTATTAAATTAT-TATTATAATTTTT
1091411 GCAGGCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTATTAAATTATTATTATAATTTTT
Found at i:1093393 original size:29 final size:30
Alignment explanation
Indices: 1093351--1093422 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
1093341 CCCGAAGGAC
*
1093351 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
* *
1093380 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
* *
1093410 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1093423 CCGAAGAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCCCGGTAA
Found at i:1093446 original size:31 final size:31
Alignment explanation
Indices: 1093408--1093472 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1093398 GATCCTCGGT
*
1093408 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
1093439 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
1093470 AAC
1 AAC
1093473 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:1094179 original size:64 final size:64
Alignment explanation
Indices: 1094073--1094215 Score: 173
Period size: 64 Copynumber: 2.2 Consensus size: 64
1094063 CAATGAAGGT
* * * *
1094073 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTAAAATG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTAAAATG
* * * *
1094137 ATGCATCGATGCATTA-TCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTT-AAAGG
1 ATGCATCGATGCACTACT-TATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTAAAATG
*
1094200 AATGTATCGATGCACT
1 -ATGCATCGATGCACT
1094216 TATGAATGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
63 5 0.07
64 62 0.93
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTAAAATG
Found at i:1096275 original size:30 final size:30
Alignment explanation
Indices: 1096233--1096365 Score: 146
Period size: 30 Copynumber: 4.5 Consensus size: 30
1096223 AAGTTTATGT
*
1096233 TTTTTGCTATTTTAGTCCGTTAAGTTTCTG
1 TTTTTGCTATTTTAGTCCGTTAAGTTTCTA
**
1096263 TGTTTT-CTATTTTAGTCATTTAAGTTTCTA
1 T-TTTTGCTATTTTAGTCCGTTAAGTTTCTA
** * *
1096293 TTTTTTATATTTTAGTCTGCTAAGTTTCTA
1 TTTTTGCTATTTTAGTCCGTTAAGTTTCTA
* * *
1096323 TTTTTGCTATTTCAGTCCTTTAACTTT-T-
1 TTTTTGCTATTTTAGTCCGTTAAGTTTCTA
1096351 TTTTTGCTATTTTAG
1 TTTTTGCTATTTTAG
1096366 CCCTTTAAAT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
28 14 0.16
29 5 0.06
30 63 0.73
31 4 0.05
ACGTcount: A:0.17, C:0.12, G:0.11, T:0.60
Consensus pattern (30 bp):
TTTTTGCTATTTTAGTCCGTTAAGTTTCTA
Found at i:1098744 original size:24 final size:24
Alignment explanation
Indices: 1098711--1098757 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1098701 TTTATTAGCT
*
1098711 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTATTAA
* *
1098735 TAATTAAATATTTAATATTATTA
1 TAATTAAATATATAAAATTATTA
1098758 TATATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATTAAATATATAAAATTATTAA
Found at i:1109527 original size:37 final size:36
Alignment explanation
Indices: 1109470--1109551 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 36
1109460 TGACAACCAA
1109470 CTTTG-AAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
1109505 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
1109542 -GTTGAAAAAT
1 CTTTGAAAAAT
1109552 TGTAATGGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 5 0.12
36 14 0.33
37 23 0.55
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:1109547 original size:36 final size:37
Alignment explanation
Indices: 1109482--1109551 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
1109472 TTGAAAATGA
*
1109482 TTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGGT
1 TTTTCAAAGTTTGGTAAATGTTTCGTTGAAAAATGGT
*
1109519 TTTTCAAAGTTTGGTAGATGTTT-GTTGAAAAAT
1 TTTTCAAAGTTTGGTAAATGTTTCGTTGAAAAAT
1109552 TGTAATGGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 9 0.29
37 22 0.71
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (37 bp):
TTTTCAAAGTTTGGTAAATGTTTCGTTGAAAAATGGT
Found at i:1113139 original size:48 final size:45
Alignment explanation
Indices: 1113042--1113166 Score: 155
Period size: 48 Copynumber: 2.8 Consensus size: 45
1113032 ATAAGTATGC
* *
1113042 AAATAAGCTTACGAGCTTAT-GAAT-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
* * *
1113085 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAATATTTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAATA-TATTGATA
*
1113133 AAATAAGCTTACGAGCTTATGGGATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA
1113167 TAGATTTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
43 19 0.27
44 3 0.04
46 11 0.16
47 9 0.13
48 28 0.40
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
Found at i:1114103 original size:28 final size:27
Alignment explanation
Indices: 1114064--1114117 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
1114054 CAAGTTTATC
*
1114064 TTTTTATCAAAATAAATACTTAAAATG
1 TTTTTATCAAAATAAATACATAAAATG
1114091 TTTTTAGTCAAAATAAATACATAAAAT
1 TTTTTA-TCAAAATAAATACATAAAAT
1114118 ATTCAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (27 bp):
TTTTTATCAAAATAAATACATAAAATG
Found at i:1124665 original size:84 final size:86
Alignment explanation
Indices: 1124558--1124724 Score: 225
Period size: 88 Copynumber: 1.9 Consensus size: 86
1124548 TAGCTCGATG
*
1124558 AAGATGATTATGTCCATATTAGGA-C-ACAAGTTTGGAAGTGGT-ATAATCACCAATAG-TCGAT
1 AAGATGATTATGTCAATATTAGGAGCTACAAGTTTGGAAGTGGTCA-AATCACCAAT-GCTCGAT
* *
1124619 ACCGAGCATATTGGTAGACTGTA
64 ACCAAGCATATTGATAGACTGTA
*
1124642 AAGATGATTTTGTCAATATTAGGATGCTTACAAGTTTGGAAGTGGTCAAATCACCAATGCTCGAT
1 AAGATGATTATGTCAATATTAGGA-GC-TACAAGTTTGGAAGTGGTCAAATCACCAATGCTCGAT
*
1124707 ATCAAGCATATTGATAGA
64 ACCAAGCATATTGATAGA
1124725 TTTTCCACTA
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
84 22 0.31
86 1 0.01
87 1 0.01
88 47 0.65
89 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (86 bp):
AAGATGATTATGTCAATATTAGGAGCTACAAGTTTGGAAGTGGTCAAATCACCAATGCTCGATAC
CAAGCATATTGATAGACTGTA
Found at i:1125218 original size:185 final size:185
Alignment explanation
Indices: 1124990--1125379 Score: 608
Period size: 185 Copynumber: 2.1 Consensus size: 185
1124980 TTAAATTTTT
*
1124990 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAATAA
1125055 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAA-TT
*
1125119 TTTATTTTATAATTATATATTATTTAAAATAATTGTAAACTGTTTTTTT-AATTAAA
130 TTTATTTTATAATTATATATTATTTAAAATAATTATAAA-TGTTTTTTTGAATTAAA
* * *
1125175 AAATATTAAATATATTATATATAACATTTGGACT-AAGCCCAAACTATTTAAAACTCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGACTCAA-CCCAAACCATTTAAAACCCAATTAATA
* * *
1125239 ATTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATT
* *
1125304 TTTATTTTATAATTATATATTATTTAAATTAATTATAAATTTTTTTTTGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAAATAATTATAAATGTTTTTTTGAATTAAA
* * *
1125360 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1125380 AATTAGAAAA
Statistics
Matches: 189, Mismatches: 13, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
184 18 0.10
185 168 0.89
186 3 0.02
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
TTATTTTATAATTATATATTATTTAAAATAATTATAAATGTTTTTTTGAATTAAA
Found at i:1132051 original size:17 final size:18
Alignment explanation
Indices: 1132029--1132062 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1132019 TCCGTTAATT
*
1132029 AAAAATATAT-ATTTTTA
1 AAAAATAAATAATTTTTA
1132046 AAAAATAAATAATTTTT
1 AAAAATAAATAATTTTT
1132063 TTTATCAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAATAAATAATTTTTA
Found at i:1133045 original size:41 final size:40
Alignment explanation
Indices: 1133000--1133096 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
1132990 ATTCGCGTTG
1133000 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGAT-GTTGAAAATCGCGTTGCGATTTTC
* ** ** *
1133041 CATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATGTTGAAAATCGCGTTGCGATTTTC
1133081 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1133097 TTTCCATTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 34 0.68
41 16 0.32
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.42
Consensus pattern (40 bp):
CATTTCGCGTTGCGATGTTGAAAATCGCGTTGCGATTTTC
Found at i:1133050 original size:20 final size:20
Alignment explanation
Indices: 1133025--1133116 Score: 166
Period size: 20 Copynumber: 4.6 Consensus size: 20
1133015 TAGTTGAAAA
1133025 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
1133045 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
*
1133065 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
1133085 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1133105 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1133117 AGTCTATAGT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1133834 original size:6 final size:6
Alignment explanation
Indices: 1133823--1133909 Score: 174
Period size: 6 Copynumber: 14.5 Consensus size: 6
1133813 TCTCGTCTCG
1133823 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1133871 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1133910 AATACGTGTC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1139553 original size:21 final size:21
Alignment explanation
Indices: 1139529--1139573 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1139519 GAAGAGCGTG
1139529 GAAATGAAGAAGAAATTGGGA
1 GAAATGAAGAAGAAATTGGGA
*
1139550 GAAATGACGAAGAAATTGGGA
1 GAAATGAAGAAGAAATTGGGA
1139571 GAA
1 GAA
1139574 GTTGAGGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.33, T:0.13
Consensus pattern (21 bp):
GAAATGAAGAAGAAATTGGGA
Found at i:1140506 original size:31 final size:31
Alignment explanation
Indices: 1140468--1140529 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1140458 TCATCCGATC
*
1140468 CAGCCCTAAGGCAAGCAGAGGATGGTAAATA
1 CAGCCCTAAAGCAAGCAGAGGATGGTAAATA
1140499 CAGCCCTAAAGCAAGCAGAGGATGGTAAATA
1 CAGCCCTAAAGCAAGCAGAGGATGGTAAATA
1140530 AAGATGCACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.13
Consensus pattern (31 bp):
CAGCCCTAAAGCAAGCAGAGGATGGTAAATA
Found at i:1141786 original size:28 final size:28
Alignment explanation
Indices: 1141746--1141801 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1141736 TTAATAATGG
1141746 GGATAAATCTCAAAATTTTATATGAACT
1 GGATAAATCTCAAAATTTTATATGAACT
1141774 GGATAAATCTCAAAATTTTATATGAACT
1 GGATAAATCTCAAAATTTTATATGAACT
1141802 TTGATTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (28 bp):
GGATAAATCTCAAAATTTTATATGAACT
Found at i:1147701 original size:88 final size:86
Alignment explanation
Indices: 1147465--1147771 Score: 289
Period size: 88 Copynumber: 3.5 Consensus size: 86
1147455 GGACTTTTAC
** ** *
1147465 TTTTTTTAAT-TCTACTTTTTATTTTTATAATTGAATCCCCTAATTTTTGTAATCTCACTTTTTA
1 TTTTTTTAATCTC-ACTTTTTACATTTATAATTGAGGCCCCTAATTTTTTTAATCTCACTTTTTA
* ***
1147529 CTTTTTATAATTGAGATTCCTAA
65 C-CTTTATAATTGAGGCCCCTAA
* * * * * *
1147552 TTTTTTTAATATCATTTTTTACATTTATAATTGAGGGCTCTAATTTTTTCAAT-T-ATGCTTTTA
1 TTTTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCCTAATTTTTTTAATCTCA--CTTTTT
* *
1147615 ACCTTTATATTTAAGGCCCCTAA
64 ACCTTTATAATTGAGGCCCCTAA
**
1147638 TTTATTTTCAATCTCACTTTCCA-ACTTTATAATTGAGGCCCCTAATTTTTTTAATCTCACTTTT
1 TTT-TTTT-AATCTCACTTTTTACA-TTTATAATTGAGGCCCCTAATTTTTTTAATCTCACTTTT
* * * *
1147702 TATCTTTTTAACTGATGCCCCTAA
63 TACCTTTATAATTGAGGCCCCTAA
* * *
1147726 TTTTTTTAATCTCACTTTTTACTTTTATAATTTAGGCCTCTAATTT
1 TTTTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCCTAATTT
1147772 AATTAATTTT
Statistics
Matches: 176, Mismatches: 35, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
85 1 0.01
86 52 0.30
87 57 0.32
88 64 0.36
89 1 0.01
90 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.53
Consensus pattern (86 bp):
TTTTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCCTAATTTTTTTAATCTCACTTTTTAC
CTTTATAATTGAGGCCCCTAA
Found at i:1147744 original size:131 final size:130
Alignment explanation
Indices: 1147532--1147772 Score: 290
Period size: 131 Copynumber: 1.8 Consensus size: 130
1147522 CTTTTTACTT
** * * * *
1147532 TTTATAATTGAGATTCCTAATTTTTTTAATATCATTTTTTACATTTATAATTGAGGGCTCTAATT
1 TTTATAATTGAGACCCCTAATTTTTTTAATATCACTTTTTACATTTATAACTGAGGCCCCTAATT
1147597 TTTTCAATTATGCTTTTAACCTTTAT-ATTTAAGGCCCCTAATTTATTTTCAATCTCACTTTCCA
66 TTTTCAATTA-GCTTTTAACCTTTATAATTT-AGGCCCCTAATTTATTTTCAATCTCACTTTCCA
1147661 AC
129 AC
* * * *
1147663 TTTATAATTGAGGCCCCTAATTTTTTTAATCTCACTTTTTATC-TTTTTAACTGATGCCCCTAAT
1 TTTATAATTGAGACCCCTAATTTTTTTAATATCACTTTTTA-CATTTATAACTGAGGCCCCTAAT
* * * *
1147727 TTTTTTAATCTCA-CTTTTTACTTTTATAATTTAGGCCTCTAATTTA
65 TTTTTCAAT-T-AGCTTTTAACCTTTATAATTTAGGCCCCTAATTTA
1147773 ATTAATTTTC
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
131 85 0.92
132 6 0.07
133 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.51
Consensus pattern (130 bp):
TTTATAATTGAGACCCCTAATTTTTTTAATATCACTTTTTACATTTATAACTGAGGCCCCTAATT
TTTTCAATTAGCTTTTAACCTTTATAATTTAGGCCCCTAATTTATTTTCAATCTCACTTTCCAAC
Found at i:1147778 original size:43 final size:43
Alignment explanation
Indices: 1147465--1147771 Score: 300
Period size: 43 Copynumber: 7.1 Consensus size: 43
1147455 GGACTTTTAC
* **
1147465 TTTTTTTAAT-TCTACTTTTTATTTTTATAATTGAATCCCCTAA
1 TTTTTTTAATCTC-ACTTTTTACTTTTATAATTGAGGCCCCTAA
* ***
1147508 TTTTTGTAATCTCACTTTTTACTTTTTATAATTGAGATTCCTAA
1 TTTTTTTAATCTCACTTTTTAC-TTTTATAATTGAGGCCCCTAA
* * * * *
1147552 TTTTTTTAATATCATTTTTTACATTTATAATTGAGGGCTCTAA
1 TTTTTTTAATCTCACTTTTTACTTTTATAATTGAGGCCCCTAA
* * * * *
1147595 TTTTTTCAAT-T-ATGCTTTTAACCTTTATATTTAAGGCCCCTAA
1 TTTTTTTAATCTCA--CTTTTTACTTTTATAATTGAGGCCCCTAA
**
1147638 TTTATTTTCAATCTCACTTTCCAAC-TTTATAATTGAGGCCCCTAA
1 TTT-TTTT-AATCTCACTTT-TTACTTTTATAATTGAGGCCCCTAA
* *
1147683 TTTTTTTAATCTCACTTTTTATCTTTT-TAACTGATGCCCCTAA
1 TTTTTTTAATCTCACTTTTTA-CTTTTATAATTGAGGCCCCTAA
* *
1147726 TTTTTTTAATCTCACTTTTTACTTTTATAATTTAGGCCTCTAA
1 TTTTTTTAATCTCACTTTTTACTTTTATAATTGAGGCCCCTAA
1147769 TTT
1 TTT
1147772 AATTAATTTT
Statistics
Matches: 218, Mismatches: 34, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
41 1 0.00
42 7 0.03
43 129 0.59
44 48 0.22
45 28 0.13
46 4 0.02
47 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.53
Consensus pattern (43 bp):
TTTTTTTAATCTCACTTTTTACTTTTATAATTGAGGCCCCTAA
Found at i:1151681 original size:3 final size:3
Alignment explanation
Indices: 1151665--1151723 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
1151655 TCTACAAAAA
1151665 TAT T-T TAT TA- TAT TAT TATT TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
1151708 TATT TAT T-T TAT TAT T
1 TA-T TAT TAT TAT TAT T
1151724 TTTGCAGGCC
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
2 8 0.16
3 36 0.72
4 6 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1151688 original size:15 final size:15
Alignment explanation
Indices: 1151668--1151723 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
1151658 ACAAAAATAT
1151668 TTTATTATATTATTA
1 TTTATTATATTATTA
1151683 TTTATTATATTATTA
1 TTTATTATATTATTA
1151698 -TTA-T-TATTATTA
1 TTTATTATATTATTA
*
1151710 TTTATTTTATTATT
1 TTTATTATATTATT
1151724 TTTGCAGGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.21
13 4 0.11
14 4 0.11
15 22 0.58
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTATATTATTA
Found at i:1152409 original size:23 final size:23
Alignment explanation
Indices: 1152371--1152419 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1152361 AAAAAGTTGA
*
1152371 TTTTATTTTTTAATTTTAGTATTT
1 TTTTATTATTTAATTTTA-TATTT
*
1152395 TTTTATTATTT-ATTTTATGTTT
1 TTTTATTATTTAATTTTATATTT
1152417 TTT
1 TTT
1152420 ACTTCTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 6 0.26
24 10 0.43
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTTATTATTTAATTTTATATTT
Found at i:1152410 original size:36 final size:38
Alignment explanation
Indices: 1152370--1152444 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 38
1152360 TAAAAAGTTG
1152370 ATTTTA-TTTTTTAATT-TTAGTATTTTT-TTATTATTT
1 ATTTTAGTTTTTTAATTCTTAGTATTTTTATT-TTATTT
* *
1152406 ATTTTATGTTTTTTACTTCTTATTATTTTTATTTTATTT
1 ATTTTA-GTTTTTTAATTCTTAGTATTTTTATTTTATTT
1152445 TATTACTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
36 6 0.18
38 9 0.27
39 16 0.48
40 2 0.06
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (38 bp):
ATTTTAGTTTTTTAATTCTTAGTATTTTTATTTTATTT
Found at i:1152432 original size:28 final size:28
Alignment explanation
Indices: 1152397--1152451 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
1152387 TAGTATTTTT
*
1152397 TTATTA-TTTATTTTATGTTTTTTACTTC
1 TTATTATTTTATTTTAT-TTTATTACTTC
1152425 TTATTATTTTTATTTTATTTTATTACT
1 TTATTA-TTTTATTTTATTTTATTACT
1152452 GTTAGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 8 0.33
30 10 0.42
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (28 bp):
TTATTATTTTATTTTATTTTATTACTTC
Found at i:1157186 original size:42 final size:42
Alignment explanation
Indices: 1157138--1157226 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
1157128 ATAATAAATT
1157138 AATATATTATCGATGAAGTTT-TATAGAAATAATTTTTATTTA
1 AATATATTATCGATGAA-TTTGTATAGAAATAATTTTTATTTA
1157180 AATATATTATCGATGAATTTGTATAGAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTGTATAGAAATAATTTTTATTTA
1157222 AATAT
1 AATAT
1157227 TTAGAATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 3 0.07
42 43 0.93
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (42 bp):
AATATATTATCGATGAATTTGTATAGAAATAATTTTTATTTA
Found at i:1168336 original size:23 final size:22
Alignment explanation
Indices: 1168302--1168360 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
1168292 ATCAGAATAA
* *
1168302 AAAAAC-CTTGTTTACCATAGTCG
1 AAAAACTC-TGTTTACCAGA-TCC
1168325 AAAAACTCTGTTTACCAGATCC
1 AAAAACTCTGTTTACCAGATCC
1168347 AGAAAACTCTGTTT
1 A-AAAACTCTGTTT
1168361 CTACATGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 3 0.09
23 28 0.88
24 1 0.03
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.31
Consensus pattern (22 bp):
AAAAACTCTGTTTACCAGATCC
Found at i:1174372 original size:21 final size:21
Alignment explanation
Indices: 1174296--1174373 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
1174286 CCTTCGTGAT
*
1174296 ATATATGTAATCCTTTGGAAC
1 ATATATGTGATCCTTTGGAAC
* * **
1174317 ATATATGCGGTTTTTCTGGACAC
1 ATATATGTGATCCTT-TGGA-AC
* *
1174340 ATAT-T-TGGTCCTTTGGAAT
1 ATATATGTGATCCTTTGGAAC
1174359 ATATATGTGATCCTT
1 ATATATGTGATCCTT
1174374 AAGGAGTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
19 5 0.12
20 5 0.12
21 22 0.51
22 5 0.12
23 6 0.14
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (21 bp):
ATATATGTGATCCTTTGGAAC
Found at i:1174457 original size:21 final size:21
Alignment explanation
Indices: 1174379--1174455 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
1174369 TCCTTAAGGA
1174379 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
* *
1174400 GTGGTCATTCGGGACATCTAT
1 GTGGTCCTTCGGGACATATAT
*
1174421 GTGGTCCTTCGGGATATATAT
1 GTGGTCCTTCGGGACATATAT
*
1174442 ATGGTCCTTCGGGA
1 GTGGTCCTTCGGGA
1174456 TAAATTCTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAT
Found at i:1176008 original size:23 final size:23
Alignment explanation
Indices: 1175958--1176008 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1175948 TTCAGAATAA
*
1175958 AAAAACCATGTTTACCATAACCG
1 AAAAACCATGTTTACCAGAACCG
* *
1175981 GAAAACTC-TGTTTACCAGAGCCG
1 AAAAAC-CATGTTTACCAGAACCG
1176004 AAAAA
1 AAAAA
1176009 ATGTGTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.20
Consensus pattern (23 bp):
AAAAACCATGTTTACCAGAACCG
Found at i:1176015 original size:23 final size:23
Alignment explanation
Indices: 1175957--1176016 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
1175947 TTTCAGAATA
* *
1175957 AAAAAACCATGTTTACCATAACCG
1 AAAAAATC-TGTTTACCAGAACCG
* * *
1175981 GAAAACTCTGTTTACCAGAGCCG
1 AAAAAATCTGTTTACCAGAACCG
*
1176004 AAAAAATGTGTTT
1 AAAAAATCTGTTT
1176017 CTACACGGTC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (23 bp):
AAAAAATCTGTTTACCAGAACCG
Found at i:1177748 original size:33 final size:33
Alignment explanation
Indices: 1177711--1177775 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1177701 TGGAAATTTC
*
1177711 ATCTTGATTGGTGGCCAACTTATTGAAAAATTA
1 ATCTTGATTGGTGGCCAACTCATTGAAAAATTA
* *
1177744 ATCTTGGTTGGTGGCCAACTCATTGGAAAATT
1 ATCTTGATTGGTGGCCAACTCATTGAAAAATT
1177776 CTTTGGTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (33 bp):
ATCTTGATTGGTGGCCAACTCATTGAAAAATTA
Found at i:1177788 original size:31 final size:33
Alignment explanation
Indices: 1177711--1177794 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
1177701 TGGAAATTTC
* * *
1177711 ATCTTGATTGGTGGCCAACTTATTGAAAAATTA
1 ATCTTGGTAGGTGGCCAACTCATTGAAAAATTA
* *
1177744 ATCTTGGTTGGTGGCCAACTCATTGGAAAATT-
1 ATCTTGGTAGGTGGCCAACTCATTGAAAAATTA
* *
1177776 CT-TTGGTAGGTGGCTAACT
1 ATCTTGGTAGGTGGCCAACT
1177795 TATTTTTCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 15 0.33
32 1 0.02
33 29 0.64
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (33 bp):
ATCTTGGTAGGTGGCCAACTCATTGAAAAATTA
Found at i:1180311 original size:20 final size:22
Alignment explanation
Indices: 1180286--1180343 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1180276 TTCCCCTTGA
1180286 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1180306 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1180329 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1180344 CTACTCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1185019 original size:33 final size:33
Alignment explanation
Indices: 1184982--1185046 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1184972 TGGAAATTTC
*
1184982 ATCTTGGGTGGTGGCCAACTTATTGAAAAATTA
1 ATCTTGGGTGGTGGCCAACTCATTGAAAAATTA
*
1185015 ATCTTGGTTGGTGGCCAACTCATTGAAAAATT
1 ATCTTGGGTGGTGGCCAACTCATTGAAAAATT
1185047 CTTTGGTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (33 bp):
ATCTTGGGTGGTGGCCAACTCATTGAAAAATTA
Found at i:1185059 original size:31 final size:30
Alignment explanation
Indices: 1184983--1185065 Score: 94
Period size: 33 Copynumber: 2.6 Consensus size: 30
1184973 GGAAATTTCA
* *
1184983 TCTTGGGTGGTGGCCAACTTATTGAAAAAT
1 TCTTTGGTGGTGGCCAACTCATTGAAAAAT
*
1185013 TAATCTTGGTTGGTGGCCAACTCATTGAAAAAT
1 T-CT-TTGG-TGGTGGCCAACTCATTGAAAAAT
*
1185046 TCTTTGGTAGGTGGCTAACT
1 TCTTTGGT-GGTGGCCAACT
1185066 TATTTTTCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 2 0.05
31 15 0.34
32 4 0.09
33 23 0.52
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (30 bp):
TCTTTGGTGGTGGCCAACTCATTGAAAAAT
Found at i:1204345 original size:64 final size:63
Alignment explanation
Indices: 1204234--1204396 Score: 229
Period size: 64 Copynumber: 2.6 Consensus size: 63
1204224 TAACCTAATT
* *
1204234 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTGCAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTAAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
*
1204297 TTAGCATTATCATTATCAAAATTAAAGCATTATCAAGAAATGGCAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATT-AAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
* * * *
1204361 TGAGCATTATACAATACTC-AATTTGAGCATTATCAA
1 TTAGCATTAT-CATTA-TCAAAATTAAGCATTATCAA
1204397 CATTCCCTCA
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
63 23 0.26
64 57 0.63
65 8 0.09
66 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTAAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
Found at i:1209791 original size:63 final size:63
Alignment explanation
Indices: 1209692--1209829 Score: 258
Period size: 63 Copynumber: 2.2 Consensus size: 63
1209682 TAACCTAATT
*
1209692 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGTTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
*
1209755 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTATAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1209818 TTAGCATTATCA
1 TTAGCATTATCA
1209830 AGAAATGACA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
Found at i:1209836 original size:41 final size:41
Alignment explanation
Indices: 1209774--1209950 Score: 327
Period size: 41 Copynumber: 4.3 Consensus size: 41
1209764 TCATTATCAA
*
1209774 AATTGAGCATTATCAAGAAATGACAATTTATAATGCTAGTTG
1 AATT-AGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1209816 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1209857 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1209898 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
*
1209939 AATGAGCATTAT
1 AATTAGCATTAT
1209951 ACAATACTCA
Statistics
Matches: 133, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
41 129 0.97
42 4 0.03
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (41 bp):
AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
Found at i:1217324 original size:21 final size:21
Alignment explanation
Indices: 1217298--1217339 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1217288 AGGCAAAGGT
1217298 AAAGCCTTTTTCGCACCCAAG
1 AAAGCCTTTTTCGCACCCAAG
1217319 AAAGCCTTTTTCGCACCCAAG
1 AAAGCCTTTTTCGCACCCAAG
1217340 TCAAAGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (21 bp):
AAAGCCTTTTTCGCACCCAAG
Found at i:1219295 original size:31 final size:30
Alignment explanation
Indices: 1219260--1219346 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
1219250 TCAATAAAGT
1219260 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
1219291 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
1219322 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
1219347 TATTATCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:1219322 original size:20 final size:20
Alignment explanation
Indices: 1219255--1219322 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
1219245 TTTCGTCAAT
*
1219255 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
1219273 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
1219294 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
1219313 ATAA-ATTTAT
1 A-AAGATTTAT
1219323 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:1219902 original size:23 final size:23
Alignment explanation
Indices: 1219858--1219903 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1219848 TGTTCTTTGC
*
1219858 CTTTATGACACGTTTATGTCTGT
1 CTTTATGACACGTTTATCTCTGT
* *
1219881 CTTTGTGACACGTTTTTCTCTGT
1 CTTTATGACACGTTTATCTCTGT
1219904 TTTTTGTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (23 bp):
CTTTATGACACGTTTATCTCTGT
Found at i:1220369 original size:38 final size:36
Alignment explanation
Indices: 1220298--1220710 Score: 397
Period size: 38 Copynumber: 11.1 Consensus size: 36
1220288 ATTAATATAG
* *
1220298 TATAGTTTTTGAAAA-TATTTTTGAAAAAAATATAATA
1 TATAG-TTTTGAAAACAATTTTTG-AAAATATATAATA
** *
1220335 TATAGTTTTTAGAAAACGGTTTTTGAAAACATATAATA
1 TATAG-TTTT-GAAAACAATTTTTGAAAATATATAATA
* *
1220373 TATACTTTTTACAAAATCAATTTTTGAAAAAATATATATATA
1 TATA-GTTTT-GAAAA-CAATTTTTG--AAAATATATA-ATA
* * * *
1220415 TATAATTTTAAAAATAATTTTTGAAAA-ATATATTA
1 TATAGTTTTGAAAACAATTTTTGAAAATATATAATA
1220450 TATAGTTTTGAAAACGAA-TTTTGAAAATATATATATTA
1 TATAGTTTTGAAAAC-AATTTTTGAAAATATATA-A-TA
** *
1220488 TATAGTTTTGAAAACGCTTTTTGAAAATATATATTA
1 TATAGTTTTGAAAACAATTTTTGAAAATATATAATA
*
1220524 TATAGCTTTGAAAACAATTTTTGAAAATATATATATTA
1 TATAGTTTTGAAAACAATTTTTGAAAATATATA-A-TA
* *
1220562 TATAGTTTTGAAAACAATTTTTGAACATATATGTATTA
1 TATAGTTTTGAAAACAATTTTTGAA-A-ATATATAATA
**
1220600 TATAGTTTTGAAAATGATTTTTGAAAATATAT--TA
1 TATAGTTTTGAAAACAATTTTTGAAAATATATAATA
*
1220634 TATAGTTTTGAAAATCAATTTTTGAAAACATATATATTA
1 TATAGTTTTGAAAA-CAATTTTTG-AAA-ATATATAATA
* * *
1220673 CATAGTTTCGAAAATAATTTTTGAAAATATAT-ATA
1 TATAGTTTTGAAAACAATTTTTGAAAATATATAATA
1220708 TAT
1 TAT
1220711 TATATAGTTT
Statistics
Matches: 319, Mismatches: 36, Indels: 44
0.80 0.09 0.11
Matches are distributed among these distances:
34 16 0.05
35 34 0.11
36 58 0.18
37 24 0.08
38 121 0.38
39 36 0.11
40 10 0.03
41 13 0.04
42 7 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
TATAGTTTTGAAAACAATTTTTGAAAATATATAATA
Found at i:1220482 original size:74 final size:74
Alignment explanation
Indices: 1220298--1220725 Score: 449
Period size: 74 Copynumber: 5.7 Consensus size: 74
1220288 ATTAATATAG
* * * **
1220298 TATAGTTTTTGAAAA-TATTTTTGAAAA-AAATATAATATATAGTTTTTAGAAAACGGTTTTTGA
1 TATAG-TTTTGAAAACAATTTTTGAAAATATATATATTATATAG-TTTTA-AAAACAATTTTTGA
* *
1220361 AAACATATAATA
63 AAATATATATTA
* * * * *
1220373 TATACTTTTTACAAAATCAATTTTTGAAAAAATATATATATATATAATTTTAAAAATAATTTTTG
1 TATA-GTTTT-GAAAA-CAATTTTTGAAAATATATATAT-TATATAGTTTTAAAAACAATTTTTG
1220438 AAAA-ATATATTA
62 AAAATATATATTA
* **
1220450 TATAGTTTTGAAAACGAA-TTTTGAAAATATATATATTATATAGTTTTGAAAACGCTTTTTGAAA
1 TATAGTTTTGAAAAC-AATTTTTGAAAATATATATATTATATAGTTTTAAAAACAATTTTTGAAA
1220514 ATATATATTA
65 ATATATATTA
* *
1220524 TATAGCTTTGAAAACAATTTTTGAAAATATATATATTATATAGTTTTGAAAACAATTTTTGAACA
1 TATAGTTTTGAAAACAATTTTTGAAAATATATATATTATATAGTTTTAAAAACAATTTTTGAA-A
*
1220589 TATATGTATTA
65 -ATATATATTA
** *
1220600 TATAGTTTTGAAAATGATTTTTG--AA-A-ATATATTATATAGTTTTGAAAATCAATTTTTGAAA
1 TATAGTTTTGAAAACAATTTTTGAAAATATATATATTATATAGTTTT-AAAAACAATTTTTG-AA
1220661 ACATATATATTA
64 A-ATATATATTA
* * *
1220673 CATAGTTTCGAAAATAATTTTTGAAAATATATATATATTATATAGTTTTAAAA
1 TATAGTTTTGAAAACAATTTTTG-AAA-ATATATATATTATATAGTTTTAAAA
1220726 TTGATTTTTT
Statistics
Matches: 302, Mismatches: 32, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
72 17 0.06
73 69 0.23
74 87 0.29
75 15 0.05
76 38 0.13
77 12 0.04
78 30 0.10
79 28 0.09
80 6 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (74 bp):
TATAGTTTTGAAAACAATTTTTGAAAATATATATATTATATAGTTTTAAAAACAATTTTTGAAAA
TATATATTA
Found at i:1225221 original size:2 final size:2
Alignment explanation
Indices: 1225216--1225257 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1225206 TTAAAAAAAT
1225216 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
1225258 AAAAAAACAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1225839 original size:29 final size:29
Alignment explanation
Indices: 1225797--1225868 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 29
1225787 GTCATAGAAT
* *
1225797 TAAACGTTAAGCACCAAAATGGAACGAAA
1 TAAACGCTAAGCACCAAAATAGAACGAAA
* * *
1225826 TAAACGCTAGGCACCAAACTAGAATGAAA
1 TAAACGCTAAGCACCAAAATAGAACGAAA
* *
1225855 TAAAGGTTAAGCAC
1 TAAACGCTAAGCAC
1225869 TAAATTGGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (29 bp):
TAAACGCTAAGCACCAAAATAGAACGAAA
Found at i:1232992 original size:31 final size:31
Alignment explanation
Indices: 1232922--1233037 Score: 169
Period size: 31 Copynumber: 3.7 Consensus size: 31
1232912 ATTTATGTAT
* * * **
1232922 TAAAATGAAATAAAAAGTTAACAATAAGGTAC
1 TAAAATGAAACAAAAAGTAAAC-GTCGGGTAC
*
1232954 TAGAATGAAACAAAAAGTAAACGTCGGGTAC
1 TAAAATGAAACAAAAAGTAAACGTCGGGTAC
1232985 TAAAATGAAACAAAAAGTAAACGTCGGGTAC
1 TAAAATGAAACAAAAAGTAAACGTCGGGTAC
1233016 TAAAATGAAACAAAAAGTAAAC
1 TAAAATGAAACAAAAAGTAAAC
1233038 ATTAGGTATG
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
31 58 0.75
32 19 0.25
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.17
Consensus pattern (31 bp):
TAAAATGAAACAAAAAGTAAACGTCGGGTAC
Found at i:1233396 original size:31 final size:33
Alignment explanation
Indices: 1233352--1233415 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 33
1233342 TCAAAAGGTA
*
1233352 AATTATATATTTAATATTTAAACTATTAGTTTT
1 AATTATATATTTAATATTTAAACTATTAATTTT
*
1233385 AATT-TAT-TTTAATATTTAAACTTTTAATTTT
1 AATTATATATTTAATATTTAAACTATTAATTTT
1233416 TTAAAATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 22 0.76
32 3 0.10
33 4 0.14
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (33 bp):
AATTATATATTTAATATTTAAACTATTAATTTT
Found at i:1245138 original size:21 final size:21
Alignment explanation
Indices: 1245096--1245138 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1245086 TTTCTGGGCT
* *
1245096 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1245117 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1245138 A
1 A
1245139 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1246126 original size:30 final size:30
Alignment explanation
Indices: 1246085--1246568 Score: 896
Period size: 30 Copynumber: 16.1 Consensus size: 30
1246075 AAGGAACATA
*
1246085 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1246115 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1246145 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1246175 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1246205 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1246235 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1246265 TGGACTGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1246295 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* *
1246325 TGGATAGTTACCAAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1246355 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1246385 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1246415 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1246445 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1246475 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1246505 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1246535 TGGACAATTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1246565 TGGA
1 TGGA
1246569 TAGGTCCTTC
Statistics
Matches: 440, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 440 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1249935 original size:21 final size:21
Alignment explanation
Indices: 1249893--1249935 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1249883 TTTCTGGGCT
* *
1249893 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1249914 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1249935 A
1 A
1249936 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1250924 original size:30 final size:30
Alignment explanation
Indices: 1250883--1251336 Score: 863
Period size: 30 Copynumber: 15.1 Consensus size: 30
1250873 AAGGAACATA
*
1250883 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1250913 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1250943 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1250973 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1251003 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1251033 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1251063 TGGACTGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1251093 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1251123 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1251153 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1251183 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1251213 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1251243 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1251273 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1251303 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1251333 TGGA
1 TGGA
1251337 TAGGTCCTTC
Statistics
Matches: 415, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 415 1.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1257079 original size:20 final size:20
Alignment explanation
Indices: 1256985--1257353 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1256975 GATTTTCCAT
* ** *
1256985 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1257005 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1257025 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1257045 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1257065 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1257085 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1257105 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1257125 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1257145 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1257165 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1257185 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1257205 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1257225 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1257245 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1257265 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1257285 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1257305 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1257325 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1257345 AATCACAAC
1 AATCGCAAC
1257354 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1258054 original size:24 final size:24
Alignment explanation
Indices: 1258027--1258073 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1258017 AAATTTAGTC
1258027 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
1258051 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
1258074 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:1258265 original size:12 final size:12
Alignment explanation
Indices: 1258248--1258272 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1258238 ATATAATCCT
1258248 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1258260 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1258272 G
1 G
1258273 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1260598 original size:19 final size:19
Alignment explanation
Indices: 1260576--1260843 Score: 291
Period size: 19 Copynumber: 15.4 Consensus size: 19
1260566 CGGAAAATAC
*
1260576 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1260595 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1260609 AATCGCAATGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
*
1260628 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1260642 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1260661 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1260680 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1260694 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1260713 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
1260732 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
1260746 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1260765 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1260784 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1260798 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1260817 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1260836 AATCGCAA
1 AATCGCAA
1260844 CGAGATAATC
Statistics
Matches: 212, Mismatches: 10, Indels: 54
0.77 0.04 0.20
Matches are distributed among these distances:
13 1 0.00
14 44 0.21
15 3 0.01
16 17 0.08
17 15 0.07
18 4 0.02
19 125 0.59
20 3 0.01
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1260631 original size:33 final size:32
Alignment explanation
Indices: 1260576--1260865 Score: 146
Period size: 33 Copynumber: 8.5 Consensus size: 32
1260566 CGGAAAATAC
*
1260576 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATG-AAATCCCAACGA-GAA
* *
1260609 AATCGCAATGCGGAAATGAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAATCCCAACGAGAA
*
1260642 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-AAATCCCAA--CG--A-GAA
* * * * *
1260680 AATCGCAACGAGAGAATCGCAATGCGAA--ATGAA
1 AATCGCAATGCGA-AAT-GAAATCCCAACGA-GAA
* * *
1260713 AATCGCAATGCGAAATGAAAAT-CGAACCGACAT
1 AATCGCAATGCGAAATG-AAATCCCAA-CGAGAA
*
1260746 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-AAATCCCAA--CG--A-GAA
*
1260784 AATCGCAA--CGAAA-G-AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAATCCCAA--CG--A-GAA
* *
1260817 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATG-AAATCCCAACGAGAA
1260850 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1260866 TATAAACGCA
Statistics
Matches: 212, Mismatches: 21, Indels: 48
0.75 0.07 0.17
Matches are distributed among these distances:
31 5 0.02
32 12 0.06
33 125 0.59
34 11 0.05
35 10 0.05
36 8 0.04
37 2 0.01
38 30 0.14
39 8 0.04
40 1 0.00
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (32 bp):
AATCGCAATGCGAAATGAAATCCCAACGAGAA
Found at i:1260881 original size:52 final size:52
Alignment explanation
Indices: 1260604--1260865 Score: 456
Period size: 52 Copynumber: 5.0 Consensus size: 52
1260594 AAATCCCAAC
1260604 ATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1260656 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1260708 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
*
1260760 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1260812 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1260864 AT
1 AT
1260866 TATAAACGCA
Statistics
Matches: 201, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
51 8 0.04
52 191 0.95
53 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1260981 original size:19 final size:19
Alignment explanation
Indices: 1260872--1260973 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1260862 AAATTATAAA
1260872 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1260891 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1260911 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1260927 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1260944 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1260963 CGCATTGCGAT
1 CGCATTGCGAT
1260974 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1261099 original size:14 final size:14
Alignment explanation
Indices: 1261080--1261116 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1261070 CATCAATTAC
1261080 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1261094 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1261108 ACAAATCAA
1 ACAAATCAA
1261117 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1263097 original size:14 final size:14
Alignment explanation
Indices: 1263078--1263133 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
1263068 GCGAAATGAA
*
1263078 AATCGCAACGACAG
1 AATCGCAACGAAAG
1263092 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1263109 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
1263124 AATCGCAACG
1 AATCGCAACG
1263134 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 1 0.03
16 9 0.24
17 1 0.03
18 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1263118 original size:32 final size:33
Alignment explanation
Indices: 1263059--1263150 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
1263049 GCGAAACCAA
*
1263059 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1263092 AATCGCAATGCGAAATG-AAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1263124 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1263151 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1263148 original size:19 final size:19
Alignment explanation
Indices: 1263022--1263155 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1263012 TAGTTTACTT
* *
1263022 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1263042 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1263061 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1263080 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1263094 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
1263112 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1263126 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1263145 TCGCAATGCGA
1 TCGCAACGCGA
1263156 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 19
0.78 0.06 0.15
Matches are distributed among these distances:
14 16 0.16
15 1 0.01
16 15 0.15
17 6 0.06
18 8 0.08
19 39 0.40
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1263173 original size:19 final size:19
Alignment explanation
Indices: 1263151--1263279 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1263141 AAAATCGCAA
1263151 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1263170 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1263184 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1263203 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1263217 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1263236 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1263255 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1263275 TGCGA
1 TGCGA
1263280 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1263193 original size:33 final size:33
Alignment explanation
Indices: 1263151--1263242 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1263141 AAAATCGCAA
1263151 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1263184 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1263217 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1263243 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1263487 original size:93 final size:93
Alignment explanation
Indices: 1263323--1263793 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
1263313 TTGAATGGAT
1263323 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1263387 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1263415 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1263480 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1263508 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1263573 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1263601 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1263664 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1263692 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1263757 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1263785 AAATTTACT
1 AAATTTACT
1263794 AAGCAATCTA
Statistics
Matches: 376, Mismatches: 0, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
91 89 0.24
92 46 0.12
93 241 0.64
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1263730 original size:184 final size:186
Alignment explanation
Indices: 1263323--1263793 Score: 921
Period size: 184 Copynumber: 2.5 Consensus size: 186
1263313 TTGAATGGAT
1263323 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1263387 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1263452 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1263508 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1263573 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1263638 TA-TA-TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1263692 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1263757 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1263794 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 152 0.53
185 44 0.15
186 89 0.31
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1265516 original size:14 final size:14
Alignment explanation
Indices: 1265497--1265586 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1265487 TTGAAATGAA
1265497 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1265511 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1265528 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1265544 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1265563 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1265577 AATCGCAACG
1 AATCGCAACG
1265587 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1265534 original size:33 final size:33
Alignment explanation
Indices: 1265489--1265603 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1265479 TCTTTTGGTT
1265489 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1265522 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1265555 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1265588 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1265604 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1265535 original size:19 final size:18
Alignment explanation
Indices: 1265496--1265608 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1265486 GTTGAAATGA
1265496 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1265511 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1265528 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1265544 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1265561 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1265577 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1265594 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1265609 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1265639 original size:14 final size:14
Alignment explanation
Indices: 1265620--1265674 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1265610 TTTGGTTTCG
1265620 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1265634 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
1265653 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1265667 CGTTGCGA
1 CGTTGCGA
1265675 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1265837 original size:33 final size:33
Alignment explanation
Indices: 1265795--1265865 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1265785 AATACTAACT
*
1265795 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1265828 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1265861 TGAAA
1 TGAAA
1265866 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1266098 original size:22 final size:22
Alignment explanation
Indices: 1266046--1266100 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1266036 TGGTTGTGAG
**
1266046 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1266068 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1266090 GGATTTCTTCG
1 GGATTTCTTCG
1266101 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1266271 original size:20 final size:20
Alignment explanation
Indices: 1266246--1266439 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1266236 CTTTAAATAT
1266246 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1266266 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1266288 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1266307 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1266327 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1266347 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1266367 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1266387 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1266407 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1266427 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1266440 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1266433 original size:60 final size:60
Alignment explanation
Indices: 1266246--1266439 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1266236 CTTTAAATAT
**
1266246 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1266307 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1266367 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1266427 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1266440 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1266456 original size:21 final size:20
Alignment explanation
Indices: 1266432--1266508 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
1266422 ATATTCGCGT
1266432 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
1266453 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
1266473 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
1266495 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
1266509 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:1266519 original size:20 final size:20
Alignment explanation
Indices: 1266494--1266545 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1266484 AAGAATCGCG
*
1266494 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1266514 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1266534 TTGCGATTCTGG
1 TTGCGATTCTGG
1266546 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1269032 original size:21 final size:21
Alignment explanation
Indices: 1269007--1269054 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1268997 CCTAATATTG
*
1269007 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTACAA
1269028 CAATGTCAAAATTAGGTACAA
1 CAATGTCAAAATTAGGTACAA
*
1269049 TAATGT
1 CAATGT
1269055 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTACAA
Found at i:1273673 original size:21 final size:21
Alignment explanation
Indices: 1273648--1273695 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1273638 CCTAATATTG
1273648 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
1273669 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
1273690 TAATGT
1 CAATGT
1273696 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:1277141 original size:19 final size:19
Alignment explanation
Indices: 1277117--1277158 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1277107 AAGCTGACAG
*
1277117 AGTTCCAAT-TGGAGATAAA
1 AGTTCCAATGTCG-GATAAA
1277136 AGTTCCAATGTCGGATAAA
1 AGTTCCAATGTCGGATAAA
1277155 AGTT
1 AGTT
1277159 ATTTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (19 bp):
AGTTCCAATGTCGGATAAA
Found at i:1278123 original size:182 final size:181
Alignment explanation
Indices: 1277693--1278641 Score: 1359
Period size: 182 Copynumber: 5.2 Consensus size: 181
1277683 GACACAAATG
* * * *
1277693 AAAAATGTATCGCTCCATAGCAATATTACAGGTAAAAATATGACAAAATCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
* *
1277758 AAACCGGT-AAAACGTTACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATTGACACTT
66 AAACCGGTAAAAAC--TACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
1277822 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGACACTTTAT
129 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * * * *
1277874 GAAAATGTATCGATCTATAACAATATAACAGCTAAAAATATGACAAACCCGATCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
* * * * *
1277939 AAACAGGTAAATAACTATCGGATATATTGAAAGTGCCGATACTTTAATATAAGTATCGACACTTT
66 AAACCGGTAAA-AACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* *
1278004 -TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAA
130 CT-GAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * *
1278056 AAAAATGTATCGATCTATAACAATATAATAGGTAAAAATATGATAAAACCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
* * *
1278121 AAACCGGTAAAATGCTACCGGATATATTGAAAGCGTCGATAATTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAA-ACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* *
1278186 CTGAATTTAAAAGAGAATAAGTTATAGCGCCTAAAAAGTGTCGACACTTTGT
130 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * **
1278238 GAACATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
* * * *
1278303 AAACAGGTAAATAACTACCGGATATGTTGAAAGTGTCAATACTTTAATATAAGTATCAACACTTT
66 AAACCGGTAAA-AACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
** * * *
1278368 AAGAATTTAAAAAAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA-
130 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * * *
1278419 AAAAATATATCGGTCCATAACAATATAACAAGTAAAAATATGACAAAATCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
*
1278484 AAACCGGT-AAAACGTTACTGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
66 AAACCGGTAAAAAC--TACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
1278548 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
129 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * * *
1278601 GAAAATGTATCGATCGATAACAATATAACAGCTAACAATAT
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATAT
1278642 AAGAAAATAG
Statistics
Matches: 680, Mismatches: 78, Indels: 19
0.88 0.10 0.02
Matches are distributed among these distances:
179 3 0.00
180 3 0.00
181 296 0.44
182 373 0.55
183 5 0.01
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
AAACCGGTAAAAACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTC
TGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
Found at i:1278424 original size:363 final size:364
Alignment explanation
Indices: 1277693--1278641 Score: 1569
Period size: 363 Copynumber: 2.6 Consensus size: 364
1277683 GACACAAATG
* * *
1277693 AAAAATGTATCGCTCCATAGCAATATTACAGGTAAAAATATGACAAAATCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAAATGACA
* *
1277758 AAACCGGTAAAACGTTACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATTGACACTTT
66 AAACCGGTAAAACGTTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
1277823 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGACACTTTATGAAAATGTATCGA
131 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGA
* *
1277887 TCTATAACAATATAACAGCTAAAAATATGACAAACCCGATCTCAAAATGACAAAACAGGTAAATA
196 TCCATAACAATATAACAGCTAAAAATATGACAAAACCGATCTCAAAATGACAAAACAGGTAAATA
* * * ** *
1277952 ACTATCGGATATATTGAAAGTGCCGATACTTTAATATAAGTATCGACACTTTTGGAATTTAAAAG
261 ACTACCGGATATATTGAAAGTGCCAATACTTTAATATAAGTATCAACACTTTAAGAATTTAAAAA
1278017 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAA
326 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAA
* * * *
1278056 AAAAATGTATCGATCTATAACAATATAATAGGTAAAAATATGATAAAACCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAAATGACA
* * * *
1278121 AAACCGGTAAAATGCTACCGGATATATTGAAAGCGTCGATAATTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAACGTTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* * *
1278186 CTGAATTTAAAAGAGAATAAGTTATAGCGCCTAAAAAGTGTCGACACTTTGTGAACATGTATCGA
131 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGA
* *
1278251 TCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAATA
196 TCCATAACAATATAACAGCTAAAAATATGACAAAACCGATCTCAAAATGACAAAACAGGTAAATA
* *
1278316 ACTACCGGATATGTTGAAAGTGTCAATACTTTAATATAAGTATCAACACTTTAAGAATTTAAAAA
261 ACTACCGGATATATTGAAAGTGCCAATACTTTAATATAAGTATCAACACTTTAAGAATTTAAAAA
*
1278381 AGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTT-A
326 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAA
* * *
1278419 AAAAATATATCGGTCCATAACAATATAACAAGTAAAAATATGACAAAATCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAAATGACA
*
1278484 AAACCGGTAAAACGTTACTGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAACGTTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
1278549 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGA
131 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGA
* *
1278614 TCGATAACAATATAACAGCTAACAATAT
196 TCCATAACAATATAACAGCTAAAAATAT
1278642 AAGAAAATAG
Statistics
Matches: 538, Mismatches: 47, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
363 354 0.66
364 184 0.34
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (364 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAAATGACA
AAACCGGTAAAACGTTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGA
TCCATAACAATATAACAGCTAAAAATATGACAAAACCGATCTCAAAATGACAAAACAGGTAAATA
ACTACCGGATATATTGAAAGTGCCAATACTTTAATATAAGTATCAACACTTTAAGAATTTAAAAA
AGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAA
Found at i:1279141 original size:23 final size:23
Alignment explanation
Indices: 1279091--1279135 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1279081 TGCCTATTTT
* * *
1279091 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAACGCTACCTAATAC
1279114 ATTATATAAACGCTACCTAATA
1 ATTATATAAACGCTACCTAATA
1279136 TGTTATTATG
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:0.40, C:0.18, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:1288341 original size:20 final size:20
Alignment explanation
Indices: 1288313--1288354 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1288303 TTAGTGTTTA
*
1288313 TATGTGTGATATGTTGACTT
1 TATGAGTGATATGTTGACTT
1288333 TATGAGTGATATGTTGACTT
1 TATGAGTGATATGTTGACTT
1288353 TA
1 TA
1288355 CGATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.48
Consensus pattern (20 bp):
TATGAGTGATATGTTGACTT
Found at i:1288801 original size:26 final size:27
Alignment explanation
Indices: 1288748--1288819 Score: 101
Period size: 26 Copynumber: 2.7 Consensus size: 27
1288738 AATTCTATAG
1288748 ATTGAAACTTAAACACTTTTTCCTAAC
1 ATTGAAACTTAAACACTTTTTCCTAAC
* * *
1288775 ATTTAAGCTTAAACACTTTTT-TTAAC
1 ATTGAAACTTAAACACTTTTTCCTAAC
*
1288801 ATTGAAACTTAAATACTTT
1 ATTGAAACTTAAACACTTT
1288820 AAAATTCCAC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 20 0.51
27 19 0.49
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (27 bp):
ATTGAAACTTAAACACTTTTTCCTAAC
Found at i:1289713 original size:19 final size:19
Alignment explanation
Indices: 1289689--1289794 Score: 194
Period size: 19 Copynumber: 5.6 Consensus size: 19
1289679 AATGCATTTT
1289689 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1289708 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
* *
1289727 ATGAATCGATGCAAATACC
1 ATGCATCGATGCACATACC
1289746 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1289765 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1289784 ATGCATCGATG
1 ATGCATCGATG
1289795 GACTCAGGCT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 83 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:1298451 original size:45 final size:46
Alignment explanation
Indices: 1298402--1298492 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
1298392 AAACATCGAA
* * *
1298402 TGCATTTTATGCATCGATGCA-TATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1298447 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1298493 GCTTTTTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 20 0.48
46 22 0.52
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:1300729 original size:21 final size:21
Alignment explanation
Indices: 1300703--1300743 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1300693 AATTATCTTG
*
1300703 GATTTT-ATTAATAATTATATA
1 GATTTTGATTAA-AATAATATA
1300724 GATTTTGATTAAAATAATAT
1 GATTTTGATTAAAATAATAT
1300744 CGACTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
GATTTTGATTAAAATAATATA
Found at i:1302860 original size:41 final size:42
Alignment explanation
Indices: 1302812--1302912 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 42
1302802 AATTGATACT
* * **
1302812 TTAGCGGCGTTTTTATAAAAAATGCCGCAATAGGGTGGTTTA
1 TTAGCGGCGTTTTTATAAAAAATGCCGCAATAGAGTGATAAA
* *
1302854 TT-GCGGCGTTTTTA-AACAAATGCCGTAATAGAGTGATAAA
1 TTAGCGGCGTTTTTATAAAAAATGCCGCAATAGAGTGATAAA
*
1302894 TTAGCGGCGTTTATATAAA
1 TTAGCGGCGTTTTTATAAA
1302913 CGCCGCAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 22 0.45
41 23 0.47
42 4 0.08
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (42 bp):
TTAGCGGCGTTTTTATAAAAAATGCCGCAATAGAGTGATAAA
Found at i:1303502 original size:40 final size:42
Alignment explanation
Indices: 1303430--1303523 Score: 129
Period size: 40 Copynumber: 2.3 Consensus size: 42
1303420 AATTGATACT
* **
1303430 TTAGCGGCGTTTTTATAAAAAATGCCGCAATAGGGTGGTTTA
1 TTAGCGGCGTTTTTATAAAAAATGCCGCAATAGAGTGGTAAA
* *
1303472 TT-GCGGCGTTTTTA-AACAAATGCCGTAATAGAGTGGTAAA
1 TTAGCGGCGTTTTTATAAAAAATGCCGCAATAGAGTGGTAAA
1303512 TTAGCGGCGTTT
1 TTAGCGGCGTTT
1303524 ATACCACAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 23 0.50
41 21 0.46
42 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.33
Consensus pattern (42 bp):
TTAGCGGCGTTTTTATAAAAAATGCCGCAATAGAGTGGTAAA
Found at i:1303540 original size:82 final size:82
Alignment explanation
Indices: 1303474--1303639 Score: 201
Period size: 82 Copynumber: 2.0 Consensus size: 82
1303464 GTGGTTTATT
* * *
1303474 GCGGCGTTTTTAAAC-AAATGCCGTAATAGAGT-GGTAAATTAGCGGCGTTTATACCACAAACGC
1 GCGGCG-TTTTAAACAAAACGCCGCAATAGA-TCGATAAATTAGCGGCGTTTATACCACAAACGC
*
1303537 CGCAATAGATTAACATATA
64 CGCAATAGAGTAACATATA
* ** *
1303556 GTGGCGTTTTAGCCAAAACGCCGCAATAGATCGATAAATTAGCAGCGTTTATACCACAAACGCCG
1 GCGGCGTTTTAAACAAAACGCCGCAATAGATCGATAAATTAGCGGCGTTTATACCACAAACGCCG
* *
1303621 CAATAAATTACACATATA
66 CAATAGAGTA-ACATATA
1303639 G
1 G
1303640 TGGCATTTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
81 7 0.10
82 58 0.79
83 8 0.11
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (82 bp):
GCGGCGTTTTAAACAAAACGCCGCAATAGATCGATAAATTAGCGGCGTTTATACCACAAACGCCG
CAATAGAGTAACATATA
Found at i:1303562 original size:41 final size:40
Alignment explanation
Indices: 1303517--1303809 Score: 165
Period size: 41 Copynumber: 7.1 Consensus size: 40
1303507 GTAAATTAGC
1303517 GGCGTTTATACCACAAACGCCGCAATAGATTAACATATAGT
1 GGCGTTTATACCACAAACGCCGCAATAGATTAACA-ATAGT
* *
1303558 GGCGTTT-TAGCCA-AAACGCCGCAATAGATCGATAA-ATTAGC
1 GGCGTTTATA-CCACAAACGCCGCAATAGAT---TAACAATAGT
* *
1303599 AGCGTTTATACCACAAACGCCGCAATAAATTACACATATAGT
1 GGCGTTTATACCACAAACGCCGCAATAGATTA-ACA-ATAGT
* * * * *
1303641 GGCATTTATTCTTA-AAACGCCACAATAG-TGATAATAAATAGT
1 GGCGTTTATAC-CACAAACGCCGCAATAGAT--TAA-CAATAGT
** * * * *
1303683 GGTTTTTTTA-GATAAACGCCGCAATAGTGTTAATCAATAGT
1 GGCGTTTATACCACAAACGCCGCAATAG-ATTAA-CAATAGT
* * * *
1303724 GGCGTTTTTA-GAAAAACGCCGCAATAGTTTTAATCAATAGT
1 GGCGTTTATACCACAAACGCCGCAATAG-ATTAA-CAATAGT
* *
1303765 GGCGTTTTTTA--ACAAACGCCACAATAG-TGTAATCAATAGT
1 GGCG-TTTATACCACAAACGCCGCAATAGAT-TAA-CAATAGT
1303805 GGCGT
1 GGCGT
1303810 GTTTTTTGTA
Statistics
Matches: 208, Mismatches: 26, Indels: 38
0.76 0.10 0.14
Matches are distributed among these distances:
39 4 0.02
40 35 0.17
41 102 0.49
42 59 0.28
43 8 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (40 bp):
GGCGTTTATACCACAAACGCCGCAATAGATTAACAATAGT
Found at i:1303674 original size:82 final size:80
Alignment explanation
Indices: 1303503--1303674 Score: 229
Period size: 82 Copynumber: 2.1 Consensus size: 80
1303493 GCCGTAATAG
* * * *
1303503 AGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATTAACATATAGTGGCGTTTTAG
1 AGTGATAAATTAGCAGCGTTTATACCACAAACGCCGCAATAAATTAACATATAGTGGCATTTTAG
*
1303568 CCAAAACGCCGCAAT
66 CCAAAACGCCACAAT
1303583 AGATCGATAAATTAGCAGCGTTTATACCACAAACGCCGCAATAAATTACACATATAGTGGCA-TT
1 AG-T-GATAAATTAGCAGCGTTTATACCACAAACGCCGCAATAAATTA-ACATATAGTGGCATTT
* *
1303647 TATTCTTAAAACGCCACAAT
63 TA-GC-CAAAACGCCACAAT
1303667 AGTGATAA
1 AGTGATAA
1303675 TAAATAGTGG
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
80 2 0.03
81 1 0.01
82 49 0.61
83 14 0.17
84 14 0.17
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (80 bp):
AGTGATAAATTAGCAGCGTTTATACCACAAACGCCGCAATAAATTAACATATAGTGGCATTTTAG
CCAAAACGCCACAAT
Found at i:1303764 original size:82 final size:82
Alignment explanation
Indices: 1303654--1303814 Score: 227
Period size: 82 Copynumber: 2.0 Consensus size: 82
1303644 ATTTATTCTT
* * *
1303654 AAAACGCCACAATAGTGATAATAAATAGTGG-TTTTTTTAGATAAACGCCGCAATAGTGTTAATC
1 AAAACGCCACAATAGTGATAATAAATAGTGGCGTTTTTTA-ACAAACGCCACAATAGTG-TAATC
1303718 AATAGTGGCGT-TTTTAGA
64 AATAGTGGCGTGTTTTAGA
* ** *
1303736 AAAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTTAACAAACGCCACAATAGTGTAATCAA
1 AAAACGCCACAATAGTGATAATAAATAGTGGCGTTTTTTAACAAACGCCACAATAGTGTAATCAA
1303801 TAGTGGCGTGTTTT
66 TAGTGGCGTGTTTT
1303815 TTGTATAAAC
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
81 16 0.23
82 47 0.67
83 7 0.10
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (82 bp):
AAAACGCCACAATAGTGATAATAAATAGTGGCGTTTTTTAACAAACGCCACAATAGTGTAATCAA
TAGTGGCGTGTTTTAGA
Found at i:1303809 original size:40 final size:42
Alignment explanation
Indices: 1303654--1303815 Score: 206
Period size: 41 Copynumber: 3.9 Consensus size: 42
1303644 ATTTATTCTT
* *
1303654 AAAACGCCACAATAGTGATAATAAATAGTGG-TTTTTTTAGA
1 AAAACGCCACAATAGTGATAATCAATAGTGGCGTTTTTTAGA
* * *
1303695 TAAACGCCGCAATAGTGTTAATCAATAGTGGCG-TTTTTAGA
1 AAAACGCCACAATAGTGATAATCAATAGTGGCGTTTTTTAGA
* **
1303736 AAAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTTA-A
1 AAAACGCCACAATAGTGATAATCAATAGTGGCGTTTTTTAGA
*
1303777 CAAACGCCACAATAGTG-TAATCAATAGTGGCGTGTTTTT
1 AAAACGCCACAATAGTGATAATCAATAGTGGCGT-TTTTT
1303816 TGTATAAACG
Statistics
Matches: 108, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
40 16 0.15
41 86 0.80
42 6 0.06
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (42 bp):
AAAACGCCACAATAGTGATAATCAATAGTGGCGTTTTTTAGA
Found at i:1305516 original size:41 final size:41
Alignment explanation
Indices: 1305191--1305538 Score: 289
Period size: 41 Copynumber: 8.4 Consensus size: 41
1305181 TATAGGTACG
* * * *
1305191 TACTTTAGTGGTGTTTTTATACAAACACCGCTATAGAATCG
1 TACTTTAGTGGCGTTTTTATATAAACACCGCTATAGACTCA
* * *
1305232 TACGTTAGTGGCGTTTTTATACAAACACCGCTATATACT-A
1 TACTTTAGTGGCGTTTTTATATAAACACCGCTATAGACTCA
* * * *
1305272 GTACTTTAGTGGCGTTTCTATACAAACGCCGCTATATACTCA
1 -TACTTTAGTGGCGTTTTTATATAAACACCGCTATAGACTCA
* * * * * *
1305314 TACTTTAGTGGTGTTTTGAATTTAAATGA-CGCTATAAACTCG
1 TACTTTAGTGGCGTTTT-TATATAAA-CACCGCTATAGACTCA
* * *
1305356 TAATTTAGTGGC-TTTTTGA-ATGAAA-ACTCAGCTAAAGACTCG
1 TACTTTAGTGGCGTTTTT-ATAT-AAACAC-C-GCTATAGACTCA
** *
1305398 TACTTTAGCAGCGTTTTTATATAAACGCCGCTATAGACT-A
1 TACTTTAGTGGCGTTTTTATATAAACACCGCTATAGACTCA
*
1305438 GTACTTTAGTGGCGTTTTTATACAAACGA-CGCTATAGACTCA
1 -TACTTTAGTGGCGTTTTTATATAAAC-ACCGCTATAGACTCA
* * * *
1305480 TACTTTAGTGGCGTTTTTAGATAAACACCGCAATAGATATAA
1 TACTTTAGTGGCGTTTTTATATAAACACCGCTATAGA-CTCA
*
1305522 TA-TTTTGTGGCGTTTTT
1 TACTTTAGTGGCGTTTTT
1305539 TCAGATAAAC
Statistics
Matches: 251, Mismatches: 39, Indels: 34
0.77 0.12 0.10
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 184 0.73
42 56 0.22
43 8 0.03
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (41 bp):
TACTTTAGTGGCGTTTTTATATAAACACCGCTATAGACTCA
Found at i:1305532 original size:82 final size:82
Alignment explanation
Indices: 1305190--1305538 Score: 327
Period size: 82 Copynumber: 4.2 Consensus size: 82
1305180 CTATAGGTAC
* * * * *
1305190 GTACTTTAGTGGTGTTTTTATACAAACACCGCTATAGAATCGTACGTTAGTGGCGTTTTTATACA
1 GTACTTTAGTGGCGTTTTTATACAAACA-CGCTATAGACTCATACTTTAGTGGCGTTTTTATATA
*
1305255 AACACCGCTATA-TACTA
65 AACACCGCTATAGAACTA
* * * * * *
1305272 GTACTTTAGTGGCGTTTCTATACAAACGCCGCTATATACTCATACTTTAGTGGTGTTTTGAATTT
1 GTACTTTAGTGGCGTTTTTATACAAAC-ACGCTATAGACTCATACTTTAGTGGCGTTTT-TATAT
* *
1305337 AAATGA-CGCTATA-AACTC
64 AAA-CACCGCTATAGAACTA
* * * * **
1305355 GTAATTTAGTGGC-TTTTTGAATGA-AAACTCAGCTAAAGACTCGTACTTTAGCAGCGTTTTTAT
1 GTACTTTAGTGGCGTTTTT--AT-ACAAACAC-GCTATAGACTCATACTTTAGTGGCGTTTTTAT
*
1305418 ATAAACGCCGCTATAG-ACTA
62 ATAAACACCGCTATAGAACTA
*
1305438 GTACTTTAGTGGCGTTTTTATACAAACGACGCTATAGACTCATACTTTAGTGGCGTTTTTAGATA
1 GTACTTTAGTGGCGTTTTTATACAAAC-ACGCTATAGACTCATACTTTAGTGGCGTTTTTATATA
*
1305503 AACACCGCAATAGATA-TA
65 AACACCGCTATAGA-ACTA
* *
1305521 ATA-TTTTGTGGCGTTTTT
1 GTACTTTAGTGGCGTTTTT
1305539 TCAGATAAAC
Statistics
Matches: 214, Mismatches: 39, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
81 1 0.00
82 115 0.54
83 61 0.29
84 36 0.17
85 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (82 bp):
GTACTTTAGTGGCGTTTTTATACAAACACGCTATAGACTCATACTTTAGTGGCGTTTTTATATAA
ACACCGCTATAGAACTA
Found at i:1305557 original size:43 final size:42
Alignment explanation
Indices: 1305487--1305581 Score: 138
Period size: 43 Copynumber: 2.3 Consensus size: 42
1305477 TCATACTTTA
*
1305487 GTGGCG-TTTTTAGATAAACACCGCAATAGATATAATATTTT
1 GTGGCGTTTTTTAGATAAACACCACAATAGATATAATATTTT
*
1305528 GTGGCGTTTTTTCAGATAAACTCCACAATAGATATAATATTTT
1 GTGGCGTTTTTT-AGATAAACACCACAATAGATATAATATTTT
* *
1305571 GCGGTGTTTTT
1 GTGGCGTTTTT
1305582 ATAAAAACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 6 0.12
42 5 0.10
43 37 0.77
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (42 bp):
GTGGCGTTTTTTAGATAAACACCACAATAGATATAATATTTT
Found at i:1311335 original size:3 final size:3
Alignment explanation
Indices: 1311327--1311371 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
1311317 TAAAATTAAA
* *
1311327 ATT ATT ATT TTT ATT ATT ATT ATT AAT ATAT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT AT
1311372 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.