Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 14 of 127
Found at i:3301773 original size:22 final size:23
Alignment explanation
Indices: 3301736--3301779 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3301726 TTAATTAAAA
3301736 TTTTAATTTATACAAA-AAATAT
1 TTTTAATTTATACAAACAAATAT
* *
3301758 TTTTAATTTTTGCAAACAAATA
1 TTTTAATTTATACAAACAAATA
3301780 CAATTTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTTAATTTATACAAACAAATAT
Found at i:3306463 original size:32 final size:32
Alignment explanation
Indices: 3306427--3306487 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
3306417 TCATTAAATA
* *
3306427 TGATTTCATTTGGTAAAATATTAATGCACGTT
1 TGATTTCATTTGATAAAATATTAACGCACGTT
3306459 TGATTTCATTTGATAAAATATTAACGCAC
1 TGATTTCATTTGATAAAATATTAACGCAC
3306488 ATGGATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (32 bp):
TGATTTCATTTGATAAAATATTAACGCACGTT
Found at i:3306501 original size:31 final size:32
Alignment explanation
Indices: 3306428--3306501 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
3306418 CATTAAATAT
* * * *
3306428 GATTTCATTTGGTAAAATATTAATGCACGTTT
1 GATTTCATTTGATAAAATATTAACGCACGATG
3306460 GATTTCATTTGATAAAATATTAACGCAC-ATG
1 GATTTCATTTGATAAAATATTAACGCACGATG
*
3306491 GATTTTATTTG
1 GATTTCATTTG
3306502 TAACGTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 11 0.30
32 26 0.70
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.43
Consensus pattern (32 bp):
GATTTCATTTGATAAAATATTAACGCACGATG
Found at i:3314122 original size:3 final size:3
Alignment explanation
Indices: 3314093--3314164 Score: 103
Period size: 3 Copynumber: 24.3 Consensus size: 3
3314083 TGTAGTATAC
* *
3314093 TAT TA- TAT TAT ATGT TAT TAT CA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3314137 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3314165 TATTCCCTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 3 0.05
3 57 0.92
4 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3314915 original size:13 final size:13
Alignment explanation
Indices: 3314899--3314979 Score: 60
Period size: 13 Copynumber: 6.3 Consensus size: 13
3314889 GGTTTTTTTA
3314899 TTTTAATTTTATT
1 TTTTAATTTTATT
* *
3314912 TTTTGATTTCA--
1 TTTTAATTTTATT
*
3314923 TTTT-ATTTTAAT
1 TTTTAATTTTATT
*
3314935 TTTTATATTTTATA
1 TTTTA-ATTTTATT
* *
3314949 TTTTGATTTTATA
1 TTTTAATTTTATT
*
3314962 TTTTAGTTTTAGTT
1 TTTTAATTTTA-TT
3314976 TTTT
1 TTTT
3314980 TATCTTACTA
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
10 5 0.09
11 4 0.07
12 4 0.07
13 26 0.48
14 15 0.28
ACGTcount: A:0.21, C:0.01, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTTAATTTTATT
Found at i:3314966 original size:7 final size:7
Alignment explanation
Indices: 3314922--3314966 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
3314912 TTTTGATTTC
3314922 ATTTTAT
1 ATTTTAT
*
3314929 -TTTAAT
1 ATTTTAT
3314935 -TTTTAT
1 ATTTTAT
3314941 ATTTTAT
1 ATTTTAT
*
3314948 ATTTT-G
1 ATTTTAT
3314954 ATTTTAT
1 ATTTTAT
3314961 ATTTTA
1 ATTTTA
3314967 GTTTTAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 15 0.47
7 17 0.53
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (7 bp):
ATTTTAT
Found at i:3315085 original size:36 final size:36
Alignment explanation
Indices: 3315044--3315117 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
3315034 ATTGTTTGGC
3315044 AAAAAAGAAAAATAAAAAC-AAATCTTTTT-TAAAATA
1 AAAAAAG-AAAATAAAAACAAAAT-TTTTTATAAAATA
* * *
3315080 AAAAAAGATATTAAAAACAAAATTTTTTATGAAATA
1 AAAAAAGAAAATAAAAACAAAATTTTTTATAAAATA
3315116 AA
1 AA
3315118 TCCATTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 14 0.42
36 19 0.58
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (36 bp):
AAAAAAGAAAATAAAAACAAAATTTTTTATAAAATA
Found at i:3320764 original size:54 final size:55
Alignment explanation
Indices: 3320660--3320798 Score: 228
Period size: 54 Copynumber: 2.5 Consensus size: 55
3320650 ATTTTAGCTT
3320660 AGTCCAGATCATTTTTTAGACTTGTGGTTTCACCTCGGTCACTTTATCTTGGCTC
1 AGTCCAGATCATTTTTTAGACTTGTGGTTTCACCTCGGTCACTTTATCTTGGCTC
* *
3320715 AGTCCAGATCATTTTTTAGACTTGTGGTTTCATCTTGGT-ACTTTATCTTGGCTC
1 AGTCCAGATCATTTTTTAGACTTGTGGTTTCACCTCGGTCACTTTATCTTGGCTC
*
3320769 AGTCCAGATCATTTTCCT-GACTTGTGGTTT
1 AGTCCAGATCATTTT-TTAGACTTGTGGTTT
3320799 AATCCTAATC
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
54 42 0.52
55 38 0.47
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.44
Consensus pattern (55 bp):
AGTCCAGATCATTTTTTAGACTTGTGGTTTCACCTCGGTCACTTTATCTTGGCTC
Found at i:3320817 original size:54 final size:55
Alignment explanation
Indices: 3320631--3320817 Score: 195
Period size: 54 Copynumber: 3.4 Consensus size: 55
3320621 TAAATTCACA
* * * *
3320631 GTTTCATCCCAATCA-TTCGATTTTAGCTTAGTCCAGATCATTTTTTAGACTTGTG
1 GTTTCATCCTAATCACTTC-ATCTTGGCTCAGTCCAGATCATTTTTTAGACTTGTG
** *
3320686 GTTTCA-CCTCGGTCACTTTATCTTGGCTCAGTCCAGATCATTTTTTAGACTTGTG
1 GTTTCATCCT-AATCACTTCATCTTGGCTCAGTCCAGATCATTTTTTAGACTTGTG
* ** * *
3320741 GTTTCATCTTGGT-ACTTTATCTTGGCTCAGTCCAGATCATTTTCCT-GACTTGTG
1 GTTTCATCCTAATCACTTCATCTTGGCTCAGTCCAGATCATTTT-TTAGACTTGTG
*
3320795 GTTTAATCCTAATCA-TTCATCTT
1 GTTTCATCCTAATCACTTCATCTT
3320818 CAATCTCAAC
Statistics
Matches: 113, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
54 56 0.50
55 53 0.47
56 4 0.04
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.44
Consensus pattern (55 bp):
GTTTCATCCTAATCACTTCATCTTGGCTCAGTCCAGATCATTTTTTAGACTTGTG
Found at i:3321118 original size:18 final size:19
Alignment explanation
Indices: 3321058--3321140 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 19
3321048 TTATTGTTTC
3321058 ATTATAAT-TAGTATTATT
1 ATTATAATATAGTATTATT
* *
3321076 ACTATAGTATAGTATGTTATTTT
1 ATTATAATATAGTA--TTA--TT
3321099 ATTATAATATAG-ATTATT
1 ATTATAATATAGTATTATT
*
3321117 ATTATAGTATAGTATTA-T
1 ATTATAATATAGTATTATT
3321135 ATTATA
1 ATTATA
3321141 GGTTATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
18 26 0.48
19 9 0.17
20 3 0.06
21 3 0.06
22 1 0.02
23 12 0.22
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.52
Consensus pattern (19 bp):
ATTATAATATAGTATTATT
Found at i:3321150 original size:18 final size:17
Alignment explanation
Indices: 3321058--3321170 Score: 59
Period size: 18 Copynumber: 6.3 Consensus size: 17
3321048 TTATTGTTTC
3321058 ATTATAATTAGTA-TTATT
1 ATTAT-ATTA-TAGTTATT
* * *
3321076 ACTATAGTATAGTATGTT
1 ATTATATTATAGT-TATT
* * *
3321094 ATTTTATTATA-ATATAG
1 ATTATATTATAGTTAT-T
*
3321111 ATTATTATTATAGTATAGT
1 ATTA-TATTATAGT-TATT
3321130 ATTATATTATAGGTTATT
1 ATTATATTATA-GTTATT
* *
3321148 ATTACATTATATGTCATT
1 ATTATATTATA-GTTATT
3321166 ATTAT
1 ATTAT
3321171 TACAATTTAT
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
16 4 0.06
17 7 0.10
18 51 0.73
19 6 0.09
20 2 0.03
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (17 bp):
ATTATATTATAGTTATT
Found at i:3322423 original size:18 final size:18
Alignment explanation
Indices: 3322389--3322422 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3322379 TGAGAGATTT
3322389 AATAAACATTTTCAAAAG
1 AATAAACATTTTCAAAAG
3322407 AATAAA-ATTTTCAAAA
1 AATAAACATTTTCAAAA
3322423 ATATTTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
AATAAACATTTTCAAAAG
Found at i:3322464 original size:74 final size:73
Alignment explanation
Indices: 3322365--3322535 Score: 272
Period size: 74 Copynumber: 2.3 Consensus size: 73
3322355 CTAAATTATG
*
3322365 TCTTATCAAACTATT-GAGAGATTTAATAAACATTTTCAAAAGAATAAAATTTTCAAAAATATTT
1 TCTTACCAAACTATTAG-GAGATTTAATAAACATTTTCAAAAGAATAAAATTTTCAAAAATATTT
3322429 TAGAATAAAA
65 T-GAATAAAA
*
3322439 TCTTACCAAATTATTAGGAGATTTAATAAACATTTTCAAAAGAATAAAATTTTCAAAAATATTTT
1 TCTTACCAAACTATTAGGAGATTTAATAAACATTTTCAAAAGAATAAAATTTTCAAAAATATTTT
3322504 GAATAAAA
66 GAATAAAA
* * *
3322512 TCTCACTAAACTATTAGAAGATTT
1 TCTTACCAAACTATTAGGAGATTT
3322536 GTCTCAAAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
73 28 0.31
74 61 0.68
75 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (73 bp):
TCTTACCAAACTATTAGGAGATTTAATAAACATTTTCAAAAGAATAAAATTTTCAAAAATATTTT
GAATAAAA
Found at i:3322497 original size:18 final size:18
Alignment explanation
Indices: 3322463--3322496 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3322453 TAGGAGATTT
3322463 AATAAACATTTTCAAAAG
1 AATAAACATTTTCAAAAG
3322481 AATAAA-ATTTTCAAAA
1 AATAAACATTTTCAAAA
3322497 ATATTTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
AATAAACATTTTCAAAAG
Found at i:3323841 original size:14 final size:15
Alignment explanation
Indices: 3323822--3323854 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3323812 TCATCAATTT
3323822 ATTTATTT-ATTTAA
1 ATTTATTTAATTTAA
*
3323836 ATTTATTTAATTTTA
1 ATTTATTTAATTTAA
3323851 ATTT
1 ATTT
3323855 GTTATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTATTTAATTTAA
Found at i:3323900 original size:18 final size:18
Alignment explanation
Indices: 3323844--3323905 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
3323834 AAATTTATTT
* *
3323844 AATTTTAATTTGTTATTAA
1 AATTATAATATGTT-TTAA
* *
3323863 AATATATAAAATTATTTTAA
1 AAT-TATAATA-TGTTTTAA
3323883 AATTATAATATGTTTTAA
1 AATTATAATATGTTTTAA
3323901 AATTA
1 AATTA
3323906 AAATGTAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 12 0.34
19 9 0.26
20 11 0.31
21 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTATAATATGTTTTAA
Found at i:3329614 original size:21 final size:21
Alignment explanation
Indices: 3329590--3329630 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3329580 ACATGAAAAC
*
3329590 TTATGAAGA-AAATACTTATAT
1 TTATCAAGATAAAT-CTTATAT
3329611 TTATCAAGATAAATCTTATA
1 TTATCAAGATAAATCTTATA
3329631 ATCATGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (21 bp):
TTATCAAGATAAATCTTATAT
Found at i:3331475 original size:55 final size:60
Alignment explanation
Indices: 3331366--3331486 Score: 180
Period size: 61 Copynumber: 2.1 Consensus size: 60
3331356 TTCTCTTTTC
3331366 TTTTACTTTTTGTCCTCCATTTATATATACATATATATATATATATATAGCTTTTGTAATA
1 TTTTACTTTTTGTCCTCCATTTATATATA-ATATATATATATATATATAGCTTTTGTAATA
* *
3331427 TTTTACTTTTTGTCCTCTATTTATATAT-ATATATATA-A-ATATA-A-CTTTTGTAATT
1 TTTTACTTTTTGTCCTCCATTTATATATAATATATATATATATATATAGCTTTTGTAATA
3331482 TTTTA
1 TTTTA
3331487 TACATAAATC
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
55 15 0.26
56 1 0.02
57 5 0.09
58 1 0.02
59 9 0.16
61 27 0.47
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (60 bp):
TTTTACTTTTTGTCCTCCATTTATATATAATATATATATATATATATAGCTTTTGTAATA
Found at i:3335742 original size:21 final size:23
Alignment explanation
Indices: 3335718--3335769 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3335708 TTATATCATG
3335718 TAATTATATT-AT-TAAAAATTT
1 TAATTATATTAATATAAAAATTT
3335739 TAATTAT-TTAGATATAAAAATTT
1 TAATTATATTA-ATATAAAAATTT
*
3335762 TTATTATA
1 TAATTATA
3335770 CTAAAAAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 7 0.27
22 2 0.08
23 15 0.58
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TAATTATATTAATATAAAAATTT
Found at i:3338197 original size:18 final size:18
Alignment explanation
Indices: 3338176--3338215 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3338166 ATTTTAATTT
3338176 ATTATTAAAATA-TTTAAA
1 ATTA-TAAAATATTTTAAA
*
3338194 ATTATAATATATTTTAAA
1 ATTATAAAATATTTTAAA
3338212 ATTA
1 ATTA
3338216 AAATATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATAAAATATTTTAAA
Found at i:3338220 original size:18 final size:18
Alignment explanation
Indices: 3338188--3338222 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3338178 TATTAAAATA
*
3338188 TTTAAAATTATAATATAT
1 TTTAAAATTAAAATATAT
3338206 TTTAAAATTAAAATATA
1 TTTAAAATTAAAATATA
3338223 ATAAAACTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAAAATTAAAATATAT
Found at i:3345872 original size:21 final size:20
Alignment explanation
Indices: 3345849--3345889 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
3345839 TTATATTATT
3345849 AAATCTTAAATATAAATAAATA
1 AAAT-TTAAATATAAA-AAATA
*
3345871 AAATTTAATTATAAAAAAT
1 AAATTTAAATATAAAAAAT
3345890 TTTAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTTAAATATAAAAAATA
Found at i:3360010 original size:2 final size:2
Alignment explanation
Indices: 3360003--3360065 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
3359993 TCAGGAGGGG
3360003 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3360045 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
3360066 CTATCATGAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3363132 original size:16 final size:15
Alignment explanation
Indices: 3363113--3363165 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
3363103 TCCCCTCGCG
3363113 TTTTGTTTTGCTATAC
1 TTTT-TTTTGCTATAC
*
3363129 TTTTTATTTGCT-TAA
1 TTTTT-TTTGCTATAC
3363144 TTATTCTTTTGCTATAC
1 TT-TT-TTTTGCTATAC
3363161 TTTTT
1 TTTTT
3363166 AGTTTCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 6 0.19
16 20 0.65
17 5 0.16
ACGTcount: A:0.15, C:0.11, G:0.08, T:0.66
Consensus pattern (15 bp):
TTTTTTTTGCTATAC
Found at i:3375871 original size:4 final size:4
Alignment explanation
Indices: 3375862--3375904 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
3375852 AATATATAGG
* * * *
3375862 TATA TATA TATA TATA TATA TATA CATA CATA CATA CATA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
3375905 GAAAAGGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:3375882 original size:12 final size:12
Alignment explanation
Indices: 3375863--3375904 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3375853 ATATATAGGT
*
3375863 ATATATATATAT
1 ATATATATATAC
3375875 ATATATATATAC
1 ATATATATATAC
* *
3375887 ATACATACATAC
1 ATATATATATAC
3375899 ATATAT
1 ATATAT
3375905 GAAAAGGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATATAC
Found at i:3376330 original size:2 final size:2
Alignment explanation
Indices: 3376323--3376349 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3376313 ATTATATCTT
3376323 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3376350 TTGAATTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3376977 original size:47 final size:47
Alignment explanation
Indices: 3376903--3376999 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 47
3376893 TCTTTTTTGG
* * *
3376903 TTATTTGTGATTGGTCACCTATTAAAACATATCCTCTTAATGATATC
1 TTATGTGTGATTGATCACCTATTAAAACATATCATCTTAATGATATC
* *
3376950 TTATGTGTGATTGATCACTTATTAAAACATATCATTTTAATGATATC
1 TTATGTGTGATTGATCACCTATTAAAACATATCATCTTAATGATATC
3376997 TTA
1 TTA
3377000 AAATTTATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (47 bp):
TTATGTGTGATTGATCACCTATTAAAACATATCATCTTAATGATATC
Found at i:3378050 original size:14 final size:15
Alignment explanation
Indices: 3378020--3378052 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
3378010 TAACATGCAT
3378020 AAATATTAATAATAA
1 AAATATTAATAATAA
3378035 AAAT-TTAA-AATAA
1 AAATATTAATAATAA
3378048 AAATA
1 AAATA
3378053 ATATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATTAATAATAA
Found at i:3379296 original size:48 final size:48
Alignment explanation
Indices: 3379141--3379570 Score: 361
Period size: 48 Copynumber: 8.7 Consensus size: 48
3379131 ATTTAATCAA
* *** * *
3379141 AGGCTCAACAACTTTAAAATTTATCATCTTGGGAAAGCTCCTATAAGTAG
1 AGGCTCAACAACTTTAAAAATT-T-ATCTTAAAAAAGCTCCTCTAAGCAG
* *
3379191 AGGCTCAACAACTTT-AAAATTCATCATCTCAGAAAAGCTCCTCTAAGCAG
1 AGGCTCAACAACTTTAAAAATT--T-ATCTTAAAAAAGCTCCTCTAAGCAG
*
3379241 AGACTCAACAACTTTAAAAATTTATCTTAAAAAAGCTCCTCTAAGTAGAGGCTCAAG
1 AGGCTCAACAACTTTAAAAATTTATCTTAAAAAAGCTCCTC----TA-A-G--C-AG
* * * *
3379298 AGGTTCAACAACTGTAAAAATTTATCTTACAAAAGCTTCTCTAAGCAG
1 AGGCTCAACAACTTTAAAAATTTATCTTAAAAAAGCTCCTCTAAGCAG
* * * * *
3379346 AGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCATCTCAGTAG
1 AGGCTCAACAACTTTAAAAATTTATCTTAAAAAAGCTCCTCTAAGCAG
* * *
3379394 AGGCTCAACAA-TTTTAAAATTCATCTTAAAAAAGCTCCTCTCAGCAG
1 AGGCTCAACAACTTTAAAAATTTATCTTAAAAAAGCTCCTCTAAGCAG
* * * *
3379441 AGGTTCAACAACTTTAAAAATCTATCTTGAAAAAA-TTTCTCTCAA-CAG
1 AGGCTCAACAACTTTAAAAATTTATCTT-AAAAAAGCTCCTCT-AAGCAG
* * * * *
3379489 AGGCTCAACAACTTT--AAATTCTCATATTGAAAAAGCTCCTATAAGTAA
1 AGGCTCAACAACTTTAAAAATT-T-ATCTTAAAAAAGCTCCTCTAAGCAG
*
3379537 AGGCTCAACAACTTT-AAAATTTCAGCTTAAAAAA
1 AGGCTCAACAACTTTAAAAATTT-ATCTTAAAAAA
3379571 TAACTTCAAA
Statistics
Matches: 315, Mismatches: 46, Indels: 40
0.79 0.11 0.10
Matches are distributed among these distances:
46 4 0.01
47 50 0.16
48 137 0.43
49 19 0.06
50 52 0.17
51 7 0.02
52 3 0.01
53 3 0.01
54 1 0.00
56 1 0.00
57 38 0.12
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (48 bp):
AGGCTCAACAACTTTAAAAATTTATCTTAAAAAAGCTCCTCTAAGCAG
Found at i:3379333 original size:57 final size:57
Alignment explanation
Indices: 3379245--3379353 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
3379235 AAGCAGAGAC
* *
3379245 TCAACAACTTTAAAAATTTATCTTAAAAAAGCTCCTCTAAGTAGAGGCTCAAGAGGT
1 TCAACAACTGTAAAAATTTATCTTAAAAAAGCTCCTCTAAGCAGAGGCTCAAGAGGT
* *
3379302 TCAACAACTGTAAAAATTTATCTTACAAAAGCTTCTCTAAGCAGAGGCTCAA
1 TCAACAACTGTAAAAATTTATCTTAAAAAAGCTCCTCTAAGCAGAGGCTCAA
3379354 CAACTTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (57 bp):
TCAACAACTGTAAAAATTTATCTTAAAAAAGCTCCTCTAAGCAGAGGCTCAAGAGGT
Found at i:3379554 original size:143 final size:144
Alignment explanation
Indices: 3379296--3379570 Score: 387
Period size: 143 Copynumber: 1.9 Consensus size: 144
3379286 TAGAGGCTCA
* *
3379296 AGAGGTTCAACAACTGTAAAAATTTATCTTACAAAAGCTTCTCTAAGCAGAGGCTCAACAACTTT
1 AGAGGTTCAACAACTGTAAAAATCTATCTTACAAAAACTTCTCTAAGCAGAGGCTCAACAACTTT
* * * * * *
3379361 AAAAATTCATCTTGAAAAAGCTCATCTCAGTAGAGGCTCAACAATTTTAAAA-TTCATCTTAAAA
66 AAAAATTCATATTGAAAAAGCTCATATAAGTAAAGGCTCAACAACTTTAAAATTTCAGCTTAAAA
3379425 AAGCTCCTCTCAGC
131 AAGCTCCTCTCAGC
* *
3379439 AGAGGTTCAACAACTTTAAAAATCTATCTTGA-AAAAATTTCTCTCAA-CAGAGGCTCAACAACT
1 AGAGGTTCAACAACTGTAAAAATCTATCTT-ACAAAAACTTCTCT-AAGCAGAGGCTCAACAACT
* *
3379502 TT-AAATTCTCATATTGAAAAAGCTCCTATAAGTAAAGGCTCAACAACTTTAAAATTTCAGCTTA
64 TTAAAAAT-TCATATTGAAAAAGCTCATATAAGTAAAGGCTCAACAACTTTAAAATTTCAGCTTA
3379566 AAAAA
128 AAAAA
3379571 TAACTTCAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
142 4 0.03
143 96 0.83
144 16 0.14
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (144 bp):
AGAGGTTCAACAACTGTAAAAATCTATCTTACAAAAACTTCTCTAAGCAGAGGCTCAACAACTTT
AAAAATTCATATTGAAAAAGCTCATATAAGTAAAGGCTCAACAACTTTAAAATTTCAGCTTAAAA
AAGCTCCTCTCAGC
Found at i:3379571 original size:95 final size:94
Alignment explanation
Indices: 3379189--3379571 Score: 336
Period size: 95 Copynumber: 3.9 Consensus size: 94
3379179 TCCTATAAGT
* *
3379189 AGAGGCTCAACAACTTTAAAATTCATCATCTCAGAAAAGCTCCTCTAAGCAGAGACTCAACAACT
1 AGAGGCTCAACAACTTTAAAATTCAT-AT-T-AAAAAAGCTCCTCTAAGCAGAGGCTCAACAACT
* * * *
3379254 TTAAAAATTTATCTTAAAAAAGCTCCTCTAAGTAGAGGCTC
63 TT-AAAATTCATCTTAAAAAATCTCATCT---CA-A----C
* * * * * *
3379295 AAGAGGTTCAACAACTGTAAAAATTTATCTTACAAAAGCTTCTCTAAGCAGAGGCTCAACAACTT
1 -AGAGGCTCAACAACT-TTAAAATTCATATTAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTT
* * **
3379360 TAAAAATTCATCTTGAAAAAGCTCATCTCAGT
64 T-AAAATTCATCTTAAAAAATCTCATCTCAAC
* * * *
3379392 AGAGGCTCAACAATTTTAAAATTCATCTTAAAAAAGCTCCTCTCAGCAGAGGTTCAACAACTTTA
1 AGAGGCTCAACAACTTTAAAATTCATATTAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTA
* *
3379457 AAAATCTATCTTGAAAAAATTTC-TCTCAAC
66 AAATTC-ATCTT-AAAAAATCTCATCTCAAC
* * * * *
3379487 AGAGGCTCAACAACTTTAAATTCTCATATTGAAAAAGCTCCTATAAGTAAAGGCTCAACAACTTT
1 AGAGGCTCAACAACTTTAAAAT-TCATATTAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTT
*
3379552 AAAATTTCAGCTTAAAAAAT
65 AAAA-TTCATCTTAAAAAAT
3379572 AACTTCAAAT
Statistics
Matches: 233, Mismatches: 38, Indels: 22
0.80 0.13 0.08
Matches are distributed among these distances:
94 6 0.03
95 80 0.34
96 63 0.27
97 2 0.01
102 1 0.00
105 56 0.24
106 1 0.00
107 15 0.06
108 9 0.04
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (94 bp):
AGAGGCTCAACAACTTTAAAATTCATATTAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTA
AAATTCATCTTAAAAAATCTCATCTCAAC
Found at i:3380078 original size:57 final size:56
Alignment explanation
Indices: 3379988--3380113 Score: 153
Period size: 57 Copynumber: 2.2 Consensus size: 56
3379978 ATTACCACTG
* * * *
3379988 AAAATATACAAATGACTTCGGATATCGCCACCGAAGGAAACTCAAATATCACTATAA
1 AAAAAATACAAATAACTTCGGATATCACCACCGAA-GAAACTCAAATATCACCATAA
* * * **
3380045 AAAAAATACAAATAACTTTGGATATCATCACCGAAGAAACTCGAATATCACCATCG
1 AAAAAATACAAATAACTTCGGATATCACCACCGAAGAAACTCAAATATCACCATAA
*
3380101 AAAAAATATAAAT
1 AAAAAATACAAAT
3380114 TCAGAGAAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
56 29 0.49
57 30 0.51
ACGTcount: A:0.49, C:0.19, G:0.10, T:0.21
Consensus pattern (56 bp):
AAAAAATACAAATAACTTCGGATATCACCACCGAAGAAACTCAAATATCACCATAA
Found at i:3380261 original size:97 final size:97
Alignment explanation
Indices: 3380135--3380383 Score: 270
Period size: 97 Copynumber: 2.5 Consensus size: 97
3380125 ATGTAAATTC
* *
3380135 AAACTTTAA-ACTCGGATATCACCACCGAGAAGATGCAAATAATTTTGGATATTACCA-TCGAAG
1 AAACTTTAACACTC-GATATCACCATCGAGAAGATGCAAATAATTTTGGATATCACCACT-GAAG
** *
3380198 AAAACTTGAATATCACCATCGAGAAACTACAAAT
64 AAAACTCAAATATCACCATCGAAAAACTACAAAT
* * * * * *
3380232 -AACTTTAACACTCAGATATCACCATCGAGAAAATGTAAATGATTTAGGATATCATCACTGAAGG
1 AAACTTTAACACTC-GATATCACCATCGAGAAGATGCAAATAATTTTGGATATCACCACTGAAGA
*
3380296 AAACTCAAATATCACCATCGAAAAACTATAAAT
65 AAACTCAAATATCACCATCGAAAAACTACAAAT
* * * * * *
3380329 AAAGCCTTAGCACTCGAATATCACCATCAAAAAGATGCAAGTAACTTTGGATATC
1 AAA-CTTTAACACTCG-ATATCACCATCGAGAAGATGCAAATAATTTTGGATATC
3380384 GTCATCAAAA
Statistics
Matches: 124, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
96 8 0.06
97 73 0.59
98 4 0.03
99 39 0.31
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (97 bp):
AAACTTTAACACTCGATATCACCATCGAGAAGATGCAAATAATTTTGGATATCACCACTGAAGAA
AACTCAAATATCACCATCGAAAAACTACAAAT
Found at i:3380565 original size:30 final size:30
Alignment explanation
Indices: 3380531--3380590 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
3380521 CCATCGAGAG
3380531 AATGTAATTCATACTTTAATACTCGGATAT
1 AATGTAATTCATACTTTAATACTCGGATAT
3380561 AATGTAATTCATACTTTAATACTCGGATAT
1 AATGTAATTCATACTTTAATACTCGGATAT
3380591 CACCATCGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (30 bp):
AATGTAATTCATACTTTAATACTCGGATAT
Found at i:3380847 original size:34 final size:34
Alignment explanation
Indices: 3380809--3380906 Score: 124
Period size: 34 Copynumber: 2.9 Consensus size: 34
3380799 GAACACCATT
* *
3380809 ATGATGCAAATGAAATGCAAATTTCTTTTCTTAA
1 ATGATGCACATGAAATGCAAATATCTTTTCTTAA
** * * *
3380843 ATGATGTTCATGAGATGAAAATGTCTTTTCTTAA
1 ATGATGCACATGAAATGCAAATATCTTTTCTTAA
*
3380877 AAGATGCACATGAAATGCAAATATCTTTTC
1 ATGATGCACATGAAATGCAAATATCTTTTC
3380907 AAAAAATACT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (34 bp):
ATGATGCACATGAAATGCAAATATCTTTTCTTAA
Found at i:3381744 original size:18 final size:18
Alignment explanation
Indices: 3381721--3381763 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
3381711 GAATCATTGG
3381721 TTGCAATGAGTTTTCATA
1 TTGCAATGAGTTTTCATA
*
3381739 TTGCAATGAGTTTTCATG
1 TTGCAATGAGTTTTCATA
3381757 TTGCAAT
1 TTGCAAT
3381764 CTCATTCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.44
Consensus pattern (18 bp):
TTGCAATGAGTTTTCATA
Found at i:3382522 original size:11 final size:11
Alignment explanation
Indices: 3382507--3382535 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
3382497 TTTTTATCAC
3382507 CTTTTTTTTC-
1 CTTTTTTTTCT
3382517 CTTTTTTTTCT
1 CTTTTTTTTCT
3382528 CTTTTTTT
1 CTTTTTTT
3382536 GGGATCGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
CTTTTTTTTCT
Found at i:3385463 original size:5 final size:5
Alignment explanation
Indices: 3385453--3385478 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3385443 TTTAGAGATT
3385453 TTTTG TTTTG TTTTG TTTTG TTTTG T
1 TTTTG TTTTG TTTTG TTTTG TTTTG T
3385479 ATAAGACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:3387260 original size:11 final size:11
Alignment explanation
Indices: 3387232--3387266 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3387222 AAATAATATA
3387232 TAAAAAAATCTT
1 TAAAAAAAT-TT
*
3387244 TTAAAAAATTT
1 TAAAAAAATTT
3387255 TAAAAAAATTT
1 TAAAAAAATTT
3387266 T
1 T
3387267 TTACCTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAAAAAATTT
Found at i:3389478 original size:2 final size:2
Alignment explanation
Indices: 3389471--3389514 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3389461 TCAGGTCCCT
3389471 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3389513 TC
1 TC
3389515 AAGTTTCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3390275 original size:7 final size:7
Alignment explanation
Indices: 3390252--3390288 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
3390242 TAAACAAGTG
3390252 ATATTTA
1 ATATTTA
3390259 ATAAATTTA
1 AT--ATTTA
3390268 ATATTTA
1 ATATTTA
3390275 ATATTTA
1 ATATTTA
3390282 ATATTTA
1 ATATTTA
3390289 TAACTTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 21 0.75
9 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
ATATTTA
Found at i:3391280 original size:22 final size:23
Alignment explanation
Indices: 3391245--3391287 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3391235 TTCTATTTTT
*
3391245 TATTTTTCATAAATTTTAATTAA
1 TATTTTTCATAAATTTAAATTAA
*
3391268 TATTTTTTA-AAATTTAAATT
1 TATTTTTCATAAATTTAAATT
3391288 TTGTGTGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTTTTCATAAATTTAAATTAA
Found at i:3391969 original size:17 final size:17
Alignment explanation
Indices: 3391947--3391987 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
3391937 AATAAATAAA
3391947 ATAAAATAATTATTTT-T
1 ATAAAATAA-TATTTTGT
3391964 ATAAAAT-ATATTTTGT
1 ATAAAATAATATTTTGT
3391980 A-AAAATAA
1 ATAAAATAA
3391988 GAGATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.50
16 4 0.18
17 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
ATAAAATAATATTTTGT
Found at i:3393403 original size:9 final size:9
Alignment explanation
Indices: 3393391--3393452 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 9
3393381 CAGTTTTAGA
3393391 ATTTTGAAG
1 ATTTTGAAG
*
3393400 ATTTTAAAG
1 ATTTTGAAG
3393409 -TTTT-AAGG
1 ATTTTGAA-G
*
3393417 GTTTTG-AG
1 ATTTTGAAG
3393425 ATTTTGAAG
1 ATTTTGAAG
3393434 A-TTT-AAG
1 ATTTTGAAG
3393441 ATTTTG-AG
1 ATTTTGAAG
3393449 ATTT
1 ATTT
3393453 AGAATTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
7 6 0.13
8 23 0.51
9 16 0.36
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (9 bp):
ATTTTGAAG
Found at i:3393405 original size:34 final size:34
Alignment explanation
Indices: 3393367--3393437 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
3393357 ATTTTAAGGG
*
3393367 TTTTAGAG-TTTAGACAGTTTT-AGAATTTTGAAGA
1 TTTTAAAGTTTTA-ACAGTTTTGAG-ATTTTGAAGA
**
3393401 TTTTAAAGTTTTAAGGGTTTTGAGATTTTGAAGA
1 TTTTAAAGTTTTAACAGTTTTGAGATTTTGAAGA
3393435 TTT
1 TTT
3393438 AAGATTTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 26 0.81
35 6 0.19
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.48
Consensus pattern (34 bp):
TTTTAAAGTTTTAACAGTTTTGAGATTTTGAAGA
Found at i:3393410 original size:25 final size:24
Alignment explanation
Indices: 3393382--3393452 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
3393372 GAGTTTAGAC
3393382 AGTTTTAGAATTTTGAAGATTTTAA
1 AGTTTTAGAATTTTG-AGATTTTAA
** *
3393407 AGTTTTAAGGGTTTTGAGATTTTGA
1 AGTTTT-AGAATTTTGAGATTTTAA
*
3393432 AGATTTA-AGATTTTGAGATTT
1 AGTTTTAGA-ATTTTGAGATTT
3393453 AGAATTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 12 0.32
25 19 0.50
26 7 0.18
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (24 bp):
AGTTTTAGAATTTTGAGATTTTAA
Found at i:3393526 original size:17 final size:17
Alignment explanation
Indices: 3393391--3393526 Score: 54
Period size: 17 Copynumber: 8.2 Consensus size: 17
3393381 CAGTTTTAGA
3393391 ATTTTGAAGATTTTAAAG
1 ATTTT-AAGATTTTAAAG
* *
3393409 -TTTTAAGGGTTTT-GAG
1 ATTTTAA-GATTTTAAAG
3393425 ATTTTGAAGA-TTT-AAG
1 ATTTT-AAGATTTTAAAG
* *
3393441 ATTTTGAGA-TTTAGA-
1 ATTTTAAGATTTTAAAG
* * *
3393456 ATTTAAAAATCTT-AAG
1 ATTTTAAGATTTTAAAG
* * * *
3393472 GTTTTGAGGGTTTTAAGG
1 ATTTT-AAGATTTTAAAG
* *
3393490 A-TTTAAGATTTGAAAT
1 ATTTTAAGATTTTAAAG
*
3393506 ATTTTATGATTTTAAAG
1 ATTTTAAGATTTTAAAG
3393523 ATTT
1 ATTT
3393527 AAGGTTTATA
Statistics
Matches: 82, Mismatches: 27, Indels: 19
0.64 0.21 0.15
Matches are distributed among these distances:
15 13 0.16
16 28 0.34
17 37 0.45
18 4 0.05
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (17 bp):
ATTTTAAGATTTTAAAG
Found at i:3396052 original size:2 final size:2
Alignment explanation
Indices: 3396039--3396084 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
3396029 GTTGACAATC
* *
3396039 AT AT AA AT AT AT AT AT AT AT AT AT AT AT -T AT AT A- AC A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3396078 AT AT AT A
1 AT AT AT A
3396085 AACAAGTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3396165 original size:21 final size:23
Alignment explanation
Indices: 3396139--3396192 Score: 76
Period size: 21 Copynumber: 2.4 Consensus size: 23
3396129 TAAGATATAG
3396139 GATAATTTTTTTAA-A-AAATAA
1 GATAATTTTTTTAATACAAATAA
*
3396160 GATAATTTTTTTAATTACAAATTA
1 GATAATTTTTTTAA-TACAAATAA
3396184 GATAATTTT
1 GATAATTTT
3396193 AAATTTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 14 0.48
23 1 0.03
24 14 0.48
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (23 bp):
GATAATTTTTTTAATACAAATAA
Found at i:3398362 original size:10 final size:10
Alignment explanation
Indices: 3398347--3398376 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3398337 ATCAAGTTTT
3398347 TATATTTTAA
1 TATATTTTAA
3398357 TATATTTTAA
1 TATATTTTAA
3398367 T-TATTTTAA
1 TATATTTTAA
3398376 T
1 T
3398377 TGATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:3402304 original size:2 final size:2
Alignment explanation
Indices: 3402297--3402353 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
3402287 GGCCGATTGG
* * * * *
3402297 AT AT AT AT AC AT AC AT AT AT CT AT AT AT AT AT AT AC AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3402339 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
3402354 GTTTTCTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:3402331 original size:26 final size:26
Alignment explanation
Indices: 3402297--3402353 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
3402287 GGCCGATTGG
*
3402297 ATATATATACATACATATATCTATAT
1 ATATATATACATACATATATATATAT
3402323 ATATATATACATACATATATATATAT
1 ATATATATACATACATATATATATAT
3402349 ATATA
1 ATATA
3402354 GTTTTCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATATATACATACATATATATATAT
Found at i:3406137 original size:21 final size:22
Alignment explanation
Indices: 3406111--3406154 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3406101 GATAAAACTA
*
3406111 TTTTTTT-TCTTTTTGACTTAT
1 TTTTTTTATCTTTTAGACTTAT
*
3406132 TTTTTTTATCTTTTAGATTTAT
1 TTTTTTTATCTTTTAGACTTAT
3406154 T
1 T
3406155 GAAATCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.75
Consensus pattern (22 bp):
TTTTTTTATCTTTTAGACTTAT
Found at i:3407333 original size:52 final size:52
Alignment explanation
Indices: 3407271--3407426 Score: 181
Period size: 52 Copynumber: 3.0 Consensus size: 52
3407261 TGGACAAGAA
* * *
3407271 GACTTGCAAAAGAAGAATTATAAGAG-AATGATGATTCTTAATAGGTAAGTTT
1 GACTTGCAAAAGAAGAATTATAAAAGAAAAGA-GATTCTTAATAGGCAAGTTT
* *
3407323 GACTTGCAAAAGAAGAATTCTAAAAGAAAAGAGATTTTTAATAGGCAAGTTT
1 GACTTGCAAAAGAAGAATTATAAAAGAAAAGAGATTCTTAATAGGCAAGTTT
* * * * * *
3407375 GACTTACAAGATAAGAATTTTAAAAGGAGAAG-GATTCTTAATGGGCAAGTTT
1 GACTTGCAAAAGAAGAATTATAAAA-GAAAAGAGATTCTTAATAGGCAAGTTT
3407427 ATATAGTTAT
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
52 81 0.90
53 9 0.10
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (52 bp):
GACTTGCAAAAGAAGAATTATAAAAGAAAAGAGATTCTTAATAGGCAAGTTT
Found at i:3408758 original size:2 final size:2
Alignment explanation
Indices: 3408751--3408780 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3408741 TCAGGTCCCT
3408751 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3408781 AAGTTTTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3410175 original size:19 final size:19
Alignment explanation
Indices: 3410151--3410215 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 19
3410141 TTAAAAATTT
*
3410151 TTAAATTTTAATTATCATA
1 TTAAATTTTAATTATAATA
*
3410170 TTAAATATTTTATTATAAT-
1 TTAAAT-TTTAATTATAATA
* ** *
3410189 TTAAAATTTGTTTATGATA
1 TTAAATTTTAATTATAATA
3410208 TT-AATTTT
1 TTAAATTTT
3410216 GTAAAATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 14 0.38
19 13 0.35
20 10 0.27
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (19 bp):
TTAAATTTTAATTATAATA
Found at i:3410582 original size:22 final size:23
Alignment explanation
Indices: 3410548--3410590 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3410538 TATCTTTTTT
*
3410548 TATTTTTCAAAAATTTTAATTAA
1 TATTTTTCAAAAATTTAAATTAA
*
3410571 TATTTTT-TAAAATTTAAATT
1 TATTTTTCAAAAATTTAAATT
3410591 TTGTACGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTTTCAAAAATTTAAATTAA
Found at i:3412517 original size:24 final size:24
Alignment explanation
Indices: 3412472--3412517 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3412462 TTTAAGCTTT
*
3412472 AAATTACAAAATAGTATTTAAAAA
1 AAATTACAAAATAGTATGTAAAAA
*
3412496 AAATTAC-ATATAGTAATGTAAA
1 AAATTACAAAATAGT-ATGTAAA
3412518 TGATATTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (24 bp):
AAATTACAAAATAGTATGTAAAAA
Found at i:3415876 original size:13 final size:12
Alignment explanation
Indices: 3415863--3415892 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
3415853 ATAAAAAATA
3415863 AAATTTATATAT
1 AAATTTATATAT
3415875 AAA-TTATATAT
1 AAATTTATATAT
3415886 AAATTTA
1 AAATTTA
3415893 ACAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AAATTTATATAT
Found at i:3422728 original size:38 final size:40
Alignment explanation
Indices: 3422686--3422766 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
3422676 CCTGGAAAAG
3422686 AAAATGGCTATAAA-C-CAAGTCATTCTTATCATCATTTT
1 AAAATGGCTATAAATCGCAAGTCATTCTTATCATCATTTT
* *
3422724 AAAATGGCTATAAATCGTTAAGTCATTCTTATCATTATTTT
1 AAAATGGCTATAAATCG-CAAGTCATTCTTATCATCATTTT
3422765 AA
1 AA
3422767 GGAACAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 14 0.37
39 1 0.03
41 23 0.61
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (40 bp):
AAAATGGCTATAAATCGCAAGTCATTCTTATCATCATTTT
Found at i:3422998 original size:22 final size:21
Alignment explanation
Indices: 3422962--3423002 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3422952 GCACATAAAT
*
3422962 AAATAATTTTTAATTTTTATC
1 AAATAATCTTTAATTTTTATC
3422983 AAATAAATCTTTAATTTTTA
1 AAAT-AATCTTTAATTTTTA
3423003 ATTTGTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATAATCTTTAATTTTTATC
Found at i:3427002 original size:2 final size:2
Alignment explanation
Indices: 3426997--3427026 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3426987 GTGCGTGTGA
3426997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3427027 TTGATCGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3428548 original size:19 final size:19
Alignment explanation
Indices: 3428524--3428567 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3428514 TAATTTTATA
3428524 TTTATA-TTAAAAATAATAT
1 TTTATATTTAAAAA-AATAT
3428543 TTTATATTTTAAAAAAATAT
1 TTTATA-TTTAAAAAAATAT
3428563 TTTAT
1 TTTAT
3428568 TAATTTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTATATTTAAAAAAATAT
Found at i:3428568 original size:25 final size:27
Alignment explanation
Indices: 3428509--3428568 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 27
3428499 ATATTTATAT
* *
3428509 ATATTTAATTTTATATTTATATTAAAA
1 ATATTTTATTTTATATTTATATAAAAA
*
3428536 ATA--ATATTTTATATTT-TA-AAAAA
1 ATATTTTATTTTATATTTATATAAAAA
3428559 ATATTTTATT
1 ATATTTTATT
3428569 AATTTTGAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
23 7 0.26
24 2 0.07
25 15 0.56
27 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATTTTATTTTATATTTATATAAAAA
Found at i:3430161 original size:31 final size:30
Alignment explanation
Indices: 3430074--3430164 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 30
3430064 CGATTCAATA
*
3430074 TTTTA-ATAAAATAAAAAATAAAT-TATATAT
1 TTTTATATAAAAT-AAATATAAATATATA-AT
* *
3430104 TTTTATATTAACATAAAT-TATGATATATAAT
1 TTTTATA-TAAAATAAATATA-AATATATAAT
3430135 TTTTATATAAAATATAATATAAATATATAA
1 TTTTATATAAAATA-AATATAAATATATAA
3430165 ATTATTAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
30 13 0.26
31 26 0.52
32 11 0.22
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
TTTTATATAAAATAAATATAAATATATAAT
Found at i:3432922 original size:2 final size:2
Alignment explanation
Indices: 3432917--3432958 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3432907 TGTAAAATAC
3432917 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3432959 TAGACAAAGT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3437992 original size:11 final size:11
Alignment explanation
Indices: 3437976--3438015 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
3437966 TCTCATAAAA
3437976 GATTTGTTTGG
1 GATTTGTTTGG
* *
3437987 GATTTGTTAGA
1 GATTTGTTTGG
*
3437998 AATTTGTTTGG
1 GATTTGTTTGG
3438009 GATTTGT
1 GATTTGT
3438016 CAGATATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (11 bp):
GATTTGTTTGG
Found at i:3438097 original size:52 final size:52
Alignment explanation
Indices: 3438040--3438164 Score: 169
Period size: 52 Copynumber: 2.4 Consensus size: 52
3438030 TGAATAAGAA
* * * *
3438040 GACTTGTAAAAGAAAAATTTTAAGAGAAAAATGATTCTTAATAGATAAGTTT
1 GACTTGCAAAAGAAAAATTCTAAAAGAAAAATGATTCTTAATAGACAAGTTT
* *
3438092 GACTTGCAAGAGAAAAATTCTAAAAGAAAAATGATTCTTAATAGGCAAGTTT
1 GACTTGCAAAAGAAAAATTCTAAAAGAAAAATGATTCTTAATAGACAAGTTT
* * *
3438144 GACTTACAGAAGAAGAATTCT
1 GACTTGCAAAAGAAAAATTCT
3438165 GAGAGTAAAG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (52 bp):
GACTTGCAAAAGAAAAATTCTAAAAGAAAAATGATTCTTAATAGACAAGTTT
Found at i:3438327 original size:89 final size:89
Alignment explanation
Indices: 3438172--3438352 Score: 272
Period size: 89 Copynumber: 2.0 Consensus size: 89
3438162 TCTGAGAGTA
* * * * *
3438172 AAGGGATTTTTAATGAGCAAGTTTGTATGGTTATAAATAGGTGAAGTCTCTATAGGGTTAGAGAT
1 AAGGGATTCTTAATGAGCAAGTTTATATGGTTATAAATAAGTGAAGTCTCTACAGGATTAGAGAT
3438237 GAGAAAAAGATGTAAGAGAGTTCT
66 GAGAAAAAGATGTAAGAGAGTTCT
* * * *
3438261 AAGGGATTCTTAATGGGTAAGTTTATATGGTTATAAATAAGTGAAGTCTTTACAGGATTAGGGAT
1 AAGGGATTCTTAATGAGCAAGTTTATATGGTTATAAATAAGTGAAGTCTCTACAGGATTAGAGAT
*
3438326 GAGAAAAAGATGTAAGAGAGTTGT
66 GAGAAAAAGATGTAAGAGAGTTCT
3438350 AAG
1 AAG
3438353 ATTTTGTGAG
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 82 1.00
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (89 bp):
AAGGGATTCTTAATGAGCAAGTTTATATGGTTATAAATAAGTGAAGTCTCTACAGGATTAGAGAT
GAGAAAAAGATGTAAGAGAGTTCT
Found at i:3439371 original size:52 final size:52
Alignment explanation
Indices: 3439282--3439438 Score: 174
Period size: 52 Copynumber: 3.0 Consensus size: 52
3439272 TAGACAAAAA
* * *
3439282 GACTTGTAAAAGAAGAATTTTAAGAGAAAA-AGAATTCTTAATAGGTAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAAAGAAAATAG-ATTCTTAATAGGTAAGTTT
* * * *
3439334 GACTTGCAAAAAAAAAATTCTAAAAGAAAATAGATTCTTAATATGCAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAAAGAAAATAGATTCTTAATAGGTAAGTTT
* * * * *
3439386 GACTTACAGAAGAAGAATTCTAAGAGGAAATTA-ATTCTTAATGGGTAAGTTT
1 GACTTGCAAAAGAAGAATTCTAA-AAGAAAATAGATTCTTAATAGGTAAGTTT
3439438 G
1 G
3439439 TATGGTTATA
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
52 78 0.90
53 9 0.10
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (52 bp):
GACTTGCAAAAGAAGAATTCTAAAAGAAAATAGATTCTTAATAGGTAAGTTT
Found at i:3445937 original size:20 final size:20
Alignment explanation
Indices: 3445905--3445955 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
3445895 TTTTTATCAA
3445905 AATAAAAAGTTAATTAAA-TAT
1 AATAAAAA-TTAA-TAAATTAT
3445926 AATAAAAATTAATAAATTAT
1 AATAAAAATTAATAAATTAT
3445946 AATAAAAATT
1 AATAAAAATT
3445956 TAAATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.14
20 17 0.59
21 8 0.28
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAAAAATTAATAAATTAT
Found at i:3445971 original size:21 final size:20
Alignment explanation
Indices: 3445905--3445964 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
3445895 TTTTTATCAA
* *
3445905 AATAAAAAGTTAATTAAATAT
1 AATAAAAA-TTAAATAATTAT
3445926 AATAAAAATT-AATAAATTAT
1 AATAAAAATTAAAT-AATTAT
3445946 AATAAAAATTTAAATAATT
1 AATAAAAA-TTAAATAATT
3445965 TAAATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.06
20 15 0.44
21 14 0.41
22 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AATAAAAATTAAATAATTAT
Found at i:3446376 original size:21 final size:21
Alignment explanation
Indices: 3446358--3446400 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3446348 TCTGTTTGTC
*
3446358 TCCTTCTCAAAACCTTTTGCT
1 TCCTTCTCAAAACCCTTTGCT
3446379 TCCTTCTCAAAACCCTTTGCT
1 TCCTTCTCAAAACCCTTTGCT
3446400 T
1 T
3446401 TTCTCTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.35, G:0.05, T:0.42
Consensus pattern (21 bp):
TCCTTCTCAAAACCCTTTGCT
Found at i:3449468 original size:4 final size:4
Alignment explanation
Indices: 3449459--3449483 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3449449 AGACAGCAAA
3449459 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
3449484 CTAATACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3450247 original size:19 final size:20
Alignment explanation
Indices: 3450211--3450252 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 20
3450201 TCGAGTTCAT
*
3450211 AAATATAAATATTTTATTTAA
1 AAATATAAATATTATA-TTAA
3450232 AAATAT-AATA-TATATTAA
1 AAATATAAATATTATATTAA
3450250 AAA
1 AAA
3450253 AAACATGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 7 0.35
19 3 0.15
20 4 0.20
21 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATATAAATATTATATTAA
Found at i:3450253 original size:19 final size:21
Alignment explanation
Indices: 3450211--3450253 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
3450201 TCGAGTTCAT
* *
3450211 AAATATAAATATTTTATTTAA
1 AAATATAAATATTATATTAAA
3450232 AAATAT-AATA-TATATTAAA
1 AAATATAAATATTATATTAAA
3450251 AAA
1 AAA
3450254 AACATGACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 4 0.20
21 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATATAAATATTATATTAAA
Found at i:3451804 original size:16 final size:16
Alignment explanation
Indices: 3451785--3451835 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
3451775 TATATAATTT
3451785 TTATTAAAAATTTTAA
1 TTATTAAAAATTTTAA
*
3451801 TTA-TAAATATTTTAA
1 TTATTAAAAATTTTAA
* *
3451816 TTTTTATATAATTTT-A
1 TTATTA-AAAATTTTAA
3451832 TTAT
1 TTAT
3451836 ATTTAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
16 9 0.32
17 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTAAAAATTTTAA
Found at i:3451812 original size:15 final size:15
Alignment explanation
Indices: 3451770--3451817 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3451760 TTTTTTATTA
*
3451770 AATTATATATAATTTT
1 AATTATAAAT-ATTTT
*
3451786 TATTA-AAA-ATTTT
1 AATTATAAATATTTT
3451799 AATTATAAATATTTT
1 AATTATAAATATTTT
3451814 AATT
1 AATT
3451818 TTTATATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 9 0.33
14 3 0.11
15 11 0.41
16 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTATAAATATTTT
Found at i:3453067 original size:22 final size:21
Alignment explanation
Indices: 3453003--3453071 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
3452993 TTATAATTTA
3453003 ATTTTAAAAATATATAAAATATT
1 ATTTTAAAAATA-ATAAAATA-T
* * * **
3453026 AGTATAAAAATATTTTAATAT
1 ATTTTAAAAATAATAAAATAT
3453047 ATTTTAAACAATAATAAAATAT
1 ATTTTAAA-AATAATAAAATAT
3453069 ATT
1 ATT
3453072 CAAATTTGAT
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
21 7 0.20
22 18 0.51
23 10 0.29
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (21 bp):
ATTTTAAAAATAATAAAATAT
Found at i:3460250 original size:19 final size:19
Alignment explanation
Indices: 3460223--3460267 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3460213 ATGATGGCTG
* *
3460223 GGGTAGCTTGGCAGGGCGT
1 GGGTGGCTTGGCAGGGCAT
3460242 GGGTGGCTTGGCAGGGCAT
1 GGGTGGCTTGGCAGGGCAT
3460261 GGGTGGC
1 GGGTGGC
3460268 CAGCGGTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.56, T:0.20
Consensus pattern (19 bp):
GGGTGGCTTGGCAGGGCAT
Found at i:3460631 original size:36 final size:39
Alignment explanation
Indices: 3460588--3460683 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 39
3460578 ATTAACGATA
* *
3460588 ACTGGGATTGAATCGCAAGTCAGAGAAA-TA-A-AAATG
1 ACTGGGATTAAACCGCAAGTCAGAGAAACTATAGAAATG
* *
3460624 ACTGGGATTAAACCACAAGT-TGAGAAACTATAGAAATG
1 ACTGGGATTAAACCGCAAGTCAGAGAAACTATAGAAATG
*
3460662 ACTGAGATTAAACCGCAAGTCA
1 ACTGGGATTAAACCGCAAGTCA
3460684 AAAAGCAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
35 6 0.12
36 19 0.39
37 1 0.02
38 23 0.47
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (39 bp):
ACTGGGATTAAACCGCAAGTCAGAGAAACTATAGAAATG
Found at i:3460890 original size:34 final size:35
Alignment explanation
Indices: 3460815--3460909 Score: 106
Period size: 34 Copynumber: 2.7 Consensus size: 35
3460805 TGAGGAGAGT
*
3460815 GGGATTAAACCACGAGTAAAAGAAATACTAAAGATC
1 GGGATTAAACCACGAATAAAAGAAATAC-AAAGATC
* * *
3460851 AGGATTAAATCACGAATAAGAG-AATA-AAGAGATC
1 GGGATTAAACCACGAATAAAAGAAATACAA-AGATC
*
3460885 GGGATTAAACCGCGAATAAAA-AAAT
1 GGGATTAAACCACGAATAAAAGAAAT
3460910 GATGTTAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
33 2 0.04
34 25 0.51
35 4 0.08
36 18 0.37
ACGTcount: A:0.52, C:0.12, G:0.20, T:0.17
Consensus pattern (35 bp):
GGGATTAAACCACGAATAAAAGAAATACAAAGATC
Found at i:3461498 original size:172 final size:171
Alignment explanation
Indices: 3460853--3461596 Score: 875
Period size: 171 Copynumber: 4.3 Consensus size: 171
3460843 TAAAGATCAG
* * * * *
3460853 GATTAAATCACGAATAAGAGAATAAAGAGATCGGGATTAAACCGCGAATAAAAAAATGATGTTAA
1 GATTGAATCACGAATCAGAGAATAAAGAGATCGGGATTAAATCGTGAATAAAAAAATGACGTTAA
* * * * * ** * *
3460918 CTTGGATTGAATCACAAGTCAGAAAATAAA-ATGACCAAAAATAAACCACGAATCGTAGGTTAAT
66 CTTGGATTGAATCACAAGTCAGAAAATAAAGA-GATCGAGATTAAACCACGAGTCAAAGGATAAC
* * *
3460982 GACAACCGAGATTAAACTATGATTTTAAATTAAAGCGATCGA
130 AACAACCGAGATTAAACTACGATTTTAAATTAAAGAGATCGA
* * *
3461024 GATTGAATCACGAATCAAAGAATAAAGAGATCGGGATTAAATCGTGAGTCAAAAAATGACGTTAA
1 GATTGAATCACGAATCAGAGAATAAAGAGATCGGGATTAAATCGTGAATAAAAAAATGACGTTAA
* * * *
3461089 CTTGGATTGAATCACAAGTCCA-AAAATAAGGAGATCGAGATTAGACCATGAGTCAAAGGTTAAC
66 CTTGGATTGAATCACAAGT-CAGAAAATAAAGAGATCGAGATTAAACCACGAGTCAAAGGATAAC
* * *
3461153 AACAATCGAGGTTAAACTACGATTTTACATTAAAGAGATCGA
130 AACAACCGAGATTAAACTACGATTTTAAATTAAAGAGATCGA
** * * * * *
3461195 GATTGAATCACGAATTGGAGAATAAAGAGACCAGGATCAAACCGT-AATAAAAAAAATGACATTA
1 GATTGAATCACGAATCAGAGAATAAAGAGATCGGGATTAAATCGTGAAT-AAAAAAATGACGTTA
* * * *
3461259 ACTTGGATTGAATCACAAGTTAGAAAATAAGGAGATTGGGATTAAACCACGAGTCAAAGGATAAC
65 ACTTGGATTGAATCACAAGTCAGAAAATAAAGAGATCGAGATTAAACCACGAGTCAAAGGATAAC
* * *
3461324 AACAACCGATATTAAACTATGATTTTAAATTAAAGAGATCGG
130 AACAACCGAGATTAAACTACGATTTTAAATTAAAGAGATCGA
* ** ** ** *
3461366 GATTGAACCGTGAATTGGAGAATAAAGAGATCGGGATTAAATTATGAATAAAAAAAATGATGTTA
1 GATTGAATCACGAATCAGAGAATAAAGAGATCGGGATTAAATCGTGAAT-AAAAAAATGACGTTA
* *
3461431 ACTTGGATTGAATCACAAGTAAGAAAATAAAGAGATCGAGATTGAACCACGAGTCAAAGGATAAC
65 ACTTGGATTGAATCACAAGTCAGAAAATAAAGAGATCGAGATTAAACCACGAGTCAAAGGATAAC
* * * * *
3461496 AACAATCAAGATTAAATTACGATTTTGAATTAAAGAGAT-TA
130 AACAACCGAGATTAAACTACGATTTTAAATTAAAGAGATCGA
* * * *
3461537 GGATTGAATCATGAATCAGAGAATAAAGAGATCGGGATTAAATCGCGAGTCAAAAAATGA
1 -GATTGAATCACGAATCAGAGAATAAAGAGATCGGGATTAAATCGTGAATAAAAAAATGA
3461597 AATGATCGAG
Statistics
Matches: 487, Mismatches: 80, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
170 3 0.01
171 330 0.68
172 154 0.32
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.23
Consensus pattern (171 bp):
GATTGAATCACGAATCAGAGAATAAAGAGATCGGGATTAAATCGTGAATAAAAAAATGACGTTAA
CTTGGATTGAATCACAAGTCAGAAAATAAAGAGATCGAGATTAAACCACGAGTCAAAGGATAACA
ACAACCGAGATTAAACTACGATTTTAAATTAAAGAGATCGA
Found at i:3476518 original size:654 final size:654
Alignment explanation
Indices: 3475258--3477880 Score: 3914
Period size: 654 Copynumber: 4.0 Consensus size: 654
3475248 TTCGTAGATT
* * * * * **
3475258 TGTTT-TTTTTTTGTTTGGGTATTTGGGGGGTTGTTTAGATTTTTTTTTTATCTGAGAGGTTAAT
1 TGTTTGTTTTTTTGTTTGGGTATTTGAGGGGTTGTTT-GAATTTTTTTTTGTCTAAGAAGTTGTT
* * * *
3475322 GGTAGGGGTGCGTGTTTTTTGGTGATCTGGTGAGGGGATATCCGAACATTTTAGGGAAGAAAGAT
65 GGTAGGAGTGCGTGTTTTTTGGTGTTCTGGTGAGGGGATATCCGAACATTTTAGAGAAGAGAGAT
* *
3475387 CAAGTATTTTATAAGGTTAGAAATGGTGGTTACATGTGCTGATGGAGTGAAGGAACTGGACGAGA
130 CAAGTATTTTATAAGGTTAGAAACGGTGGTTACATGTGCTGATGGAGTGAAGAAACTGGACGAGA
* * * * *
3475452 GGTGGTATGATGGCTGGGGTAGCTTGGCAGGGCGTGGGTGGCCA-ACGGTACCGTGCACGACACC
195 GGTGGTATGATGACTGGGGTAGCTTGACAGGGCGTGGGTGACCAGA-GGTACCATGCACGGCACC
* * * *
3475516 CGCTAGTACCAACCCTTTCCATTTTATTTTTTCTATTTAGATTTTTCGTTTATCTTTTTTTTTTC
259 CACTGGTACCAACCCTTTCCATTTTGTTTCTTCTATTTAGATTTTTCGTTTATC-----TTTTTC
* * **
3475581 TTTTTATTTAAAAGTTTAATTTTTTTGGATTATAAAAAATGTAGACCTGGATAAAATCTAGTGTT
319 TTTTTATTTAAAATTTTAATTTTTTTGGATTATAAAAAATGTAGACTTGGATAAAATCCGGTGTT
* * *
3475646 TACACCTATAGGCCCCACCCAATCATCCCTGATC-AGAATTCTTTGCTGTCCTCAATAACCTCTC
384 TACACCTATAGGGCCCACCCAATCATCCCTGACCGA-AATTCTCTGCTGTCCTCAATAACCTCTC
* * * * * * *
3475710 AACAACCGACTACTTCAATTTCCTCTATGCTTCAAAAGAGTTTGCGACGGTTGCTTCGGAGTTCC
448 AACAACCGGCTACTTCAATTCCCCCCATGCTTCAAAAGAGTTCGCGACGGCTGCTTCGGAGTTCT
* * * * *
3475775 CAGAAGAGTTTTCAGGCCTTCTTAATGCGTGCTTGATGTTTGCACGTGATAGAACAGACCCTTTA
513 CGGAAGAGTTTCCAGGCCTTCTTAATGCGTGCTTGATGTTCGCACGTGACAGAACAGACCTTTTA
3475840 AGTTAACAAAAAAAAAGAAATTTTGCTTAAATTATAACGTTTTCTTCGATGTTTTGAGTTTTGTA
578 AGTTAAC-AAAAAAAAGAAATTTTGCTTAAATTATAACGTTTTCTTCGATGTTTTGAGTTTTGTA
3475905 TGTTGGTTTATTC
642 TGTTGGTTTATTC
* *
3475918 TGTTTGTTTTTTTGTTTGGGTATTTGGGGGGTTGTTTGGATTTTTTTTTCGTCTAAGAAGTTGTT
1 TGTTTGTTTTTTTGTTTGGGTATTTGAGGGGTTGTTTGAATTTTTTTTT-GTCTAAGAAGTTGTT
* * *
3475983 GGTAGGGGTGCGTGTTTTTTGGTGTTCTGGTGAGGGGATATCCGAACATTTTAAAGAAGGGAGAT
65 GGTAGGAGTGCGTGTTTTTTGGTGTTCTGGTGAGGGGATATCCGAACATTTTAGAGAAGAGAGAT
* * * *
3476048 CAAGTATTTTATAAGGTTAGAAACGGTGATTACATGTGCTGATGGAATGAAGGAACTGGATGAGA
130 CAAGTATTTTATAAGGTTAGAAACGGTGGTTACATGTGCTGATGGAGTGAAGAAACTGGACGAGA
** * *
3476113 GGTGGTATGATGGTTGGGGTAGCTTGGCAGGGCGTGGGTGACCAGAGGTACCATGCACAGCACCC
195 GGTGGTATGATGACTGGGGTAGCTTGACAGGGCGTGGGTGACCAGAGGTACCATGCACGGCACCC
** *
3476178 GTTGGTACCAACCCTTTCCATTTTGTTTCTTCTATTTAGATTTTTTGTTTATC-TTTT-TTTTTA
260 ACTGGTACCAACCCTTTCCATTTTGTTTCTTCTATTTAGATTTTTCGTTTATCTTTTTCTTTTTA
3476241 TTTAAAATTTTAATTTTTTTGGATTATAAAAAATGTAGACTTGGATAAAATCCGGTGTTTACACC
325 TTTAAAATTTTAATTTTTTTGGATTATAAAAAATGTAGACTTGGATAAAATCCGGTGTTTACACC
* * *
3476306 TATA-GGCCTCACCCAATCATCCCTGATCGAAATTCTCTGCTATCCTCAATAACCTCTCAACAAT
390 TATAGGGCC-CACCCAATCATCCCTGACCGAAATTCTCTGCTGTCCTCAATAACCTCTCAACAAC
*
3476370 CGGCTACTTCAATTCCCCCCATGCTTCAAAAGAGTTCGCGACGGTTGCTTCGGAGTTCTCGGAAG
454 CGGCTACTTCAATTCCCCCCATGCTTCAAAAGAGTTCGCGACGGCTGCTTCGGAGTTCTCGGAAG
*
3476435 AGTTTTCAGGCCTTCTTAATGCGTGCTTGATGTTCGCACGTGACAGAACAGACCTTTTAAGTTAA
519 AGTTTCCAGGCCTTCTTAATGCGTGCTTGATGTTCGCACGTGACAGAACAGACCTTTTAAGTTAA
*
3476500 CAAAAAAAAAGAAATTTTGCTTAAATTATAACGTTTTCTTCAATGTTTTGAGTTTTGTATGTTGG
584 C-AAAAAAAAGAAATTTTGCTTAAATTATAACGTTTTCTTCGATGTTTTGAGTTTTGTATGTTGG
3476565 TTTATTC
648 TTTATTC
3476572 TGTTTGTTTTTTTTGTTTGGGTATTTGAGGGGTTGTTTGAATTTTTTTTTGTCTGAA-AAGTTGT
1 TGTTTG-TTTTTTTGTTTGGGTATTTGAGGGGTTGTTTGAATTTTTTTTTGTCT-AAGAAGTTGT
* * * * * *
3476636 TGGTAGGAGTGTGTGTTTTTTGGTGTTATGATGAGGGGATATTCAAACATTTTAGAGAAGGGAGA
64 TGGTAGGAGTGCGTGTTTTTTGGTGTTCTGGTGAGGGGATATCCGAACATTTTAGAGAAGAGAGA
* *
3476701 TCAAGTATTTTATAAGGTTAGAAATGGTGGTTACATGTACTGATGGAGTGAAGAAACTGGACGAG
129 TCAAGTATTTTATAAGGTTAGAAACGGTGGTTACATGTGCTGATGGAGTGAAGAAACTGGACGAG
* * * * * *
3476766 AGGTGGTATGATGACTGAGGTAGCTTGACAGGGCGTAGGTGACCAGCGATATCATGTACGGCACC
194 AGGTGGTATGATGACTGGGGTAGCTTGACAGGGCGTGGGTGACCAGAGGTACCATGCACGGCACC
*
3476831 TACTGGTACCAACCCTTTCCATTTTGTTTCTTCTATTTAGATTTTTCGTTTATCTTTTTATATTC
259 CACTGGTACCAACCCTTTCCATTTTGTTTCTTCTATTTAGATTTTTCGTTTATC---TT-T-TTC
* * *
3476896 TTTTTATTTAAAATTTTAATTTTTTTGGATTTTAAAAAATGTATAACTTGGATAAAATTCGGTGT
319 TTTTTATTTAAAATTTTAATTTTTTTGGATTATAAAAAATGTA-GACTTGGATAAAATCCGGTGT
* * *
3476961 TTACACCTATAGGGCCCACCCAATCATCCCCGACCGGAATTCTCTGCTGTCTTCAATAACCTCTC
383 TTACACCTATAGGGCCCACCCAATCATCCCTGACCGAAATTCTCTGCTGTCCTCAATAACCTCTC
3477026 AACAACCGGCTACTTCAATTCCCCCCATGCTTCAAAAGAGTTCGCGACGGCTGCTTCGGAGTTCT
448 AACAACCGGCTACTTCAATTCCCCCCATGCTTCAAAAGAGTTCGCGACGGCTGCTTCGGAGTTCT
*
3477091 C-GAAGGAGTTTCCAGGCCTTCTTAATGCGTGCTTGATGTTCGCACGTGACAGAATAGACCTTTT
513 CGGAA-GAGTTTCCAGGCCTTCTTAATGCGTGCTTGATGTTCGCACGTGACAGAACAGACCTTTT
*
3477155 AAGTTAACAAAAAAAAGAAATTTTGCTTAAATTATAACGTTTTCTTTGATGTTTTGAGTTTTGTA
577 AAGTTAACAAAAAAAAGAAATTTTGCTTAAATTATAACGTTTTCTTCGATGTTTTGAGTTTTGTA
* *
3477220 TATTGGTTTATTT
642 TGTTGGTTTATTC
* * *
3477233 TGTTTGTTTTTTTATTTGGGTATTTGAGAGGTTGTTTGAATTTTTTTTTGTCTGAGAAGTTGTTG
1 TGTTTGTTTTTTTGTTTGGGTATTTGAGGGGTTGTTTGAATTTTTTTTTGTCTAAGAAGTTGTTG
* *
3477298 GTAGGAGT--GTGTTTTTTGGTG---T--TGAGGGGATATTCGAACATTTTAGAGAAGAGAGATT
66 GTAGGAGTGCGTGTTTTTTGGTGTTCTGGTGAGGGGATATCCGAACATTTTAGAGAAGAGAGATC
*
3477356 AAGTATTTTATAAGGTTAGAAACGGTGGTTACATGTGCTGATGGAGTGAAAAAACTGGACGAGAG
131 AAGTATTTTATAAGGTTAGAAACGGTGGTTACATGTGCTGATGGAGTGAAGAAACTGGACGAGAG
* * * * * * *
3477421 GTGGTATGATGACTGGGATAGCTTGACAGGGAGTGGGTAATCAGCGGTACCGTGCACGGCACCTA
196 GTGGTATGATGACTGGGGTAGCTTGACAGGGCGTGGGTGACCAGAGGTACCATGCACGGCACCCA
* *
3477486 CTGGTACCAACCCTTTCCATTTTGTTTCTTTTATTTAGATTTTTCGTTTATCTTTTTATTTTTTT
261 CTGGTACCAACCCTTTCCATTTTGTTTCTTCTATTTAGATTTTTCGTTTATC---TT-TTTCTTT
* *
3477551 TTATTTAAATTTTTAATTTTTTT-TATTATAAAAAATGTAGACTTGGATAAAATCCGGTGTTTAC
322 TTATTTAAAATTTTAATTTTTTTGGATTATAAAAAATGTAGACTTGGATAAAATCCGGTGTTTAC
* *
3477615 ACCTATAGGGCCCACCCAATCATCCC-GGCCGGAATTCTCTGCTGTCCTCAATAACCTCTCAACA
387 ACCTATAGGGCCCACCCAATCATCCCTGACCGAAATTCTCTGCTGTCCTCAATAACCTCTCAACA
3477679 ACCGGCTACTTCAATTCCCCCCATGCTTCAAAAGAGTTCGCGACGGCTGCTTCGGAGTT-TCCGG
452 ACCGGCTACTTCAATTCCCCCCATGCTTCAAAAGAGTTCGCGACGGCTGCTTCGGAGTTCT-CGG
*
3477743 AGGAGTTTCCAGGCCTTCTTAATGCGTGCTTGATGTTCGCACGTGACAGAACAGACCTTTTAAGT
516 AAGAGTTTCCAGGCCTTCTTAATGCGTGCTTGATGTTCGCACGTGACAGAACAGACCTTTTAAGT
3477808 TAACAAAAAAAAGAAATTTTGCTTAAATTATAACGTTTTCTTCGATGTTTTGAGTTTTGTATGTT
581 TAACAAAAAAAAGAAATTTTGCTTAAATTATAACGTTTTCTTCGATGTTTTGAGTTTTGTATGTT
3477873 GGTTTATT
646 GGTTTATT
3477881 TATGGTCAGA
Statistics
Matches: 1821, Mismatches: 122, Indels: 51
0.91 0.06 0.03
Matches are distributed among these distances:
648 1 0.00
649 229 0.13
650 51 0.03
651 14 0.01
652 27 0.01
653 211 0.12
654 551 0.30
655 49 0.03
658 14 0.01
659 2 0.00
660 79 0.04
661 385 0.21
662 204 0.11
663 4 0.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (654 bp):
TGTTTGTTTTTTTGTTTGGGTATTTGAGGGGTTGTTTGAATTTTTTTTTGTCTAAGAAGTTGTTG
GTAGGAGTGCGTGTTTTTTGGTGTTCTGGTGAGGGGATATCCGAACATTTTAGAGAAGAGAGATC
AAGTATTTTATAAGGTTAGAAACGGTGGTTACATGTGCTGATGGAGTGAAGAAACTGGACGAGAG
GTGGTATGATGACTGGGGTAGCTTGACAGGGCGTGGGTGACCAGAGGTACCATGCACGGCACCCA
CTGGTACCAACCCTTTCCATTTTGTTTCTTCTATTTAGATTTTTCGTTTATCTTTTTCTTTTTAT
TTAAAATTTTAATTTTTTTGGATTATAAAAAATGTAGACTTGGATAAAATCCGGTGTTTACACCT
ATAGGGCCCACCCAATCATCCCTGACCGAAATTCTCTGCTGTCCTCAATAACCTCTCAACAACCG
GCTACTTCAATTCCCCCCATGCTTCAAAAGAGTTCGCGACGGCTGCTTCGGAGTTCTCGGAAGAG
TTTCCAGGCCTTCTTAATGCGTGCTTGATGTTCGCACGTGACAGAACAGACCTTTTAAGTTAACA
AAAAAAAGAAATTTTGCTTAAATTATAACGTTTTCTTCGATGTTTTGAGTTTTGTATGTTGGTTT
ATTC
Found at i:3477550 original size:22 final size:23
Alignment explanation
Indices: 3477538--3477582 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3477528 TTCGTTTATC
*
3477538 TTTTT-ATTTTTTTTTATTTAAA
1 TTTTTAATTTTTTTTCATTTAAA
3477560 TTTTTAATTTTTTTT-ATTATAAA
1 TTTTTAATTTTTTTTCATT-TAAA
3477583 AAATGTAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTAATTTTTTTTCATTTAAA
Found at i:3477564 original size:23 final size:23
Alignment explanation
Indices: 3477538--3477582 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3477528 TTCGTTTATC
*
3477538 TTTTTATTTTTTTTTATT-TAAA
1 TTTTTAATTTTTTTTATTATAAA
3477560 TTTTTAATTTTTTTTATTATAAA
1 TTTTTAATTTTTTTTATTATAAA
3477583 AAATGTAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTAATTTTTTTTATTATAAA
Found at i:3482173 original size:18 final size:18
Alignment explanation
Indices: 3482143--3482185 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
3482133 GATCAGTGAG
3482143 AATGGGAGCAATG-GGAA
1 AATGGGAGCAATGAGGAA
3482160 AATGGGAGGCAATGAGGAA
1 AATGGGA-GCAATGAGGAA
*
3482179 ATTGGGA
1 AATGGGA
3482186 TGTCAGAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 6 0.26
19 10 0.43
ACGTcount: A:0.40, C:0.05, G:0.42, T:0.14
Consensus pattern (18 bp):
AATGGGAGCAATGAGGAA
Found at i:3483390 original size:18 final size:17
Alignment explanation
Indices: 3483339--3483390 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
3483329 TTAAATAAGC
* *
3483339 TATCTTATACTAAATTT
1 TATCTTATACTAAAATA
* *
3483356 TAGCTTAATACTTAAATA
1 TATCTT-ATACTAAAATA
3483374 TATCTTATACTACAAAT
1 TATCTTATACTA-AAAT
3483391 GTTAGTTCTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (17 bp):
TATCTTATACTAAAATA
Found at i:3490349 original size:15 final size:15
Alignment explanation
Indices: 3490332--3490408 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 15
3490322 AATTTTTGTT
*
3490332 TAATAAAAATTTAAT
1 TAATAAAAATTTAAA
*
3490347 TAATGAAAA--TAAA
1 TAATAAAAATTTAAA
* *
3490360 TATTTAAAAATTTAAT
1 TA-ATAAAAATTTAAA
* * *
3490376 TGATAATAA-TAAAA
1 TAATAAAAATTTAAA
3490390 TAATAAAAATTTAAA
1 TAATAAAAATTTAAA
3490405 TAAT
1 TAAT
3490409 TATTAAAATT
Statistics
Matches: 45, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
13 5 0.11
14 15 0.33
15 21 0.47
16 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
TAATAAAAATTTAAA
Found at i:3490368 original size:29 final size:29
Alignment explanation
Indices: 3490332--3490408 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
3490322 AATTTTTGTT
3490332 TAATAAAAATTTAATTAATGAA-AAT-AAA
1 TAATAAAAATTTAATTAAT-AATAATAAAA
* *
3490360 TATTTAAAAATTTAATTGATAATAATAAAA
1 TA-ATAAAAATTTAATTAATAATAATAAAA
*
3490390 TAATAAAAATTTAAATAAT
1 TAATAAAAATTTAATTAAT
3490409 TATTAAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 4 0.10
29 32 0.78
30 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
TAATAAAAATTTAATTAATAATAATAAAA
Found at i:3490576 original size:28 final size:25
Alignment explanation
Indices: 3490507--3490578 Score: 63
Period size: 28 Copynumber: 2.6 Consensus size: 25
3490497 ATATTATATA
*
3490507 AAAAATTATATTTTATATAAAACTAT
1 AAAATTTA-ATTTTATATAAAACTAT
*
3490533 AAAATTAATAATTTTTATATAAAAAATTAT
1 AAAATT--TAA-TTTTATAT--AAAACTAT
3490563 CAAAATTTAATTTTAT
1 -AAAATTTAATTTTAT
3490579 TACTACAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 5 0.13
27 1 0.03
28 16 0.42
29 3 0.08
30 7 0.18
31 6 0.16
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAATTTAATTTTATATAAAACTAT
Found at i:3499456 original size:66 final size:66
Alignment explanation
Indices: 3499340--3499463 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
3499330 TATTTTGAAC
* * * * *
3499340 CCTCTCAATCTCCTGCAAGACAAACAGTTAAATGTTAGTAATGGGATTTTAAAGGCCATTCAATT
1 CCTCCCAATCTCCTGCAAAACAAACAATTAAATGTCAGAAATGGGATTTTAAAGGCCATTCAATT
3499405 A
66 A
*
3499406 CCTCCCAATTTCCTGCAAAACAAACAATTAGAA-GTCAGAAATGGGATTTTAAAGGCCA
1 CCTCCCAATCTCCTGCAAAACAAACAATTA-AATGTCAGAAATGGGATTTTAAAGGCCA
3499464 ACCAATTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
66 49 0.96
67 2 0.04
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (66 bp):
CCTCCCAATCTCCTGCAAAACAAACAATTAAATGTCAGAAATGGGATTTTAAAGGCCATTCAATT
A
Found at i:3518540 original size:21 final size:22
Alignment explanation
Indices: 3518511--3518551 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3518501 ATTATTTTAT
**
3518511 AAAATTTATTTCAAATTTTAGC
1 AAAATTTATTAAAAATTTTAGC
3518533 AAAA-TTATTAAAAATTTTA
1 AAAATTTATTAAAAATTTTA
3518552 ACATATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAATTTATTAAAAATTTTAGC
Found at i:3519581 original size:3 final size:3
Alignment explanation
Indices: 3519575--3519599 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3519565 GATGTAAAAA
3519575 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
3519600 TGGATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3519885 original size:2 final size:2
Alignment explanation
Indices: 3519878--3519902 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3519868 TATGATCTAA
3519878 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
3519903 GATCTAGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3521396 original size:170 final size:171
Alignment explanation
Indices: 3521111--3521450 Score: 542
Period size: 170 Copynumber: 2.0 Consensus size: 171
3521101 AACTTTTGCG
* *
3521111 GCCTTTGCTATATTTGTTATAGTACTGTAATTCTCGGAGATTGGTTTATAGAGCAGCTGACAAGA
1 GCCTTTGCTATATTTGTTATAGTACTGTAATTCTCGGAGATCGGTTTATAGA-CAGCAGACAAGA
* *
3521176 GCAAAGTTGTGGCAATTGAATTTTCACCAGACTTATCTGCAGAAATTTATGGGAAATTATTTGAG
65 GCAAAGTTGTGGCAACTGAATTTTCACCAGACTTATCTGCAGAAATTTAT-GGAAATTATTTAAG
* * *
3521241 GTTTTTGAGAGAGGCTTAGTTCTCTTCCTGGTACAAAAAAAAT
129 GTTTTTGAGACAGGCTTAGATCTCTTCCTGGAACAAAAAAAAT
* *
3521284 GCCTTTGCTATATTTGTTATAGTACTGTTATTC-CTGGAGATCGGTTTGT-GA-AGCAGACAAGA
1 GCCTTTGCTATATTTGTTATAGTACTGTAATTCTC-GGAGATCGGTTTATAGACAGCAGACAAGA
*
3521346 GCAAAGTTGTGGCCACTGAATTTTCACCAGACTTATCTGCAGAAATTTATGGAAATTATTTAAGG
65 GCAAAGTTGTGGCAACTGAATTTTCACCAGACTTATCTGCAGAAATTTATGGAAATTATTTAAGG
3521411 TTTTTGAGACAGGCTTAGATCTCTTCCTGGAACAAAAAAA
130 TTTTTGAGACAGGCTTAGATCTCTTCCTGGAACAAAAAAA
3521451 TTTAAATGAG
Statistics
Matches: 156, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
169 51 0.33
170 58 0.37
172 3 0.02
173 44 0.28
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (171 bp):
GCCTTTGCTATATTTGTTATAGTACTGTAATTCTCGGAGATCGGTTTATAGACAGCAGACAAGAG
CAAAGTTGTGGCAACTGAATTTTCACCAGACTTATCTGCAGAAATTTATGGAAATTATTTAAGGT
TTTTGAGACAGGCTTAGATCTCTTCCTGGAACAAAAAAAAT
Found at i:3523647 original size:38 final size:37
Alignment explanation
Indices: 3523576--3523647 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
3523566 CTCTTTATTT
*
3523576 CTAGAAATATCATCCAATATGTTGGTAATATTTTCTA
1 CTAGAAATATCATCCAATATGTTGGTAAGATTTTCTA
* * *
3523613 CTAGAAATTATCCTCTAATATGTTGGTAGGATTTT
1 CTAGAAA-TATCATCCAATATGTTGGTAAGATTTT
3523648 ATGAAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 7 0.23
38 23 0.77
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (37 bp):
CTAGAAATATCATCCAATATGTTGGTAAGATTTTCTA
Found at i:3523689 original size:17 final size:18
Alignment explanation
Indices: 3523651--3523691 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3523641 GGATTTTATG
3523651 AAAATTATATATTTTTTA
1 AAAATTATATATTTTTTA
*
3523669 AAAATTA-ATTTTTATTTA
1 AAAATTATATATTT-TTTA
3523687 AAAAT
1 AAAAT
3523692 CATAAGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATTATATATTTTTTA
Found at i:3523946 original size:4 final size:4
Alignment explanation
Indices: 3523937--3523989 Score: 61
Period size: 4 Copynumber: 13.2 Consensus size: 4
3523927 AAATATTTAC
* ** **
3523937 AAAT AAAT AAAT ACAT AAAT AGTT AAAT AACC AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
3523985 AAAT A
1 AAAT A
3523990 CACAATTATG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:3525114 original size:22 final size:21
Alignment explanation
Indices: 3525089--3525150 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
3525079 TCACAATTTA
3525089 AAATTCAAGAATTCTCAACTTG
1 AAATTCAAGAATTCTCAA-TTG
*
3525111 AAATTC-AGAAATTCGCAA-TG
1 AAATTCAAG-AATTCTCAATTG
*
3525131 AAAGTCAA-AGATTCTCAATT
1 AAATTCAAGA-ATTCTCAATT
3525151 TGAATTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 1 0.03
20 14 0.42
21 4 0.12
22 14 0.42
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (21 bp):
AAATTCAAGAATTCTCAATTG
Found at i:3525262 original size:18 final size:18
Alignment explanation
Indices: 3525233--3525403 Score: 90
Period size: 18 Copynumber: 9.7 Consensus size: 18
3525223 AAAAAATTCA
3525233 CAAAAG-TTCAAGATTTG
1 CAAAAGATTCAAGATTTG
3525250 CAAAAGATTCAAGATTT-
1 CAAAAGATTCAAGATTTG
3525267 -AAAA-ATTCAAGA-TT-
1 CAAAAGATTCAAGATTTG
*
3525281 CATAAA-ATTTCAAAAATTTG
1 CA-AAAGA-TTC-AAGATTTG
* * *
3525301 TAAGAGATTCCAGATTTG
1 CAAAAGATTCAAGATTTG
** * *
3525319 CAAGTGATCCAAGACTTG
1 CAAAAGATTCAAGATTTG
* *
3525337 CAAAAAATTTTAAAGATTTG
1 CAAAAGA--TTCAAGATTTG
* *
3525357 C-AAATATTCAAAAATTTG
1 CAAAAGATTC-AAGATTTG
* *
3525375 CAAAAGATTTAATATTTG
1 CAAAAGATTCAAGATTTG
*
3525393 -TAAAGATTCAA
1 CAAAAGATTCAA
3525404 AAATTCACAA
Statistics
Matches: 118, Mismatches: 24, Indels: 24
0.71 0.14 0.14
Matches are distributed among these distances:
14 2 0.02
15 9 0.08
16 8 0.07
17 20 0.17
18 51 0.43
19 17 0.14
20 11 0.09
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.32
Consensus pattern (18 bp):
CAAAAGATTCAAGATTTG
Found at i:3525276 original size:15 final size:16
Alignment explanation
Indices: 3525233--3525289 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
3525223 AAAAAATTCA
*
3525233 CAAAAGTTCAAGATTT
1 CAAAAATTCAAGATTT
3525249 GCAAAAGATTCAAGATTT
1 -CAAAA-ATTCAAGATTT
3525267 -AAAAATTCAAGA-TT
1 CAAAAATTCAAGATTT
3525281 CATAAAATT
1 CA-AAAATT
3525290 TCAAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 2 0.06
15 9 0.25
16 10 0.28
17 5 0.14
18 10 0.28
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (16 bp):
CAAAAATTCAAGATTT
Found at i:3525286 original size:17 final size:17
Alignment explanation
Indices: 3525228--3525293 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 17
3525218 TAATTAAAAA
* *
3525228 ATTCACAAAAGTTCAAG
1 ATTCATAAAAATTCAAG
*
3525245 ATTTGCA-AAAGATTCAAG
1 A-TT-CATAAAAATTCAAG
3525263 ATT--TAAAAATTCAAG
1 ATTCATAAAAATTCAAG
*
3525278 ATTCATAAAATTTCAA
1 ATTCATAAAAATTCAA
3525294 AAATTTGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
15 13 0.32
17 13 0.32
18 12 0.30
19 2 0.05
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (17 bp):
ATTCATAAAAATTCAAG
Found at i:3525402 original size:36 final size:36
Alignment explanation
Indices: 3525224--3525504 Score: 107
Period size: 36 Copynumber: 7.8 Consensus size: 36
3525214 AATTTAATTA
** *
3525224 AAAAATTCACAAAAG-TTCAAGATTTGCAAAAGATTC
1 AAAAATTTGCAAAAGATTTAAGATTTGC-AAAGATTC
* * *
3525260 -AAGATTT--AAAA-ATTCAAGA-TT-CATAAAATTTC
1 AAAAATTTGCAAAAGATTTAAGATTTGCA-AAGA-TTC
* * ** *
3525292 AAAAATTTGTAAGAGATTCCAGATTTGCAAGTGA-TC
1 AAAAATTTGCAAAAGATTTAAGATTTGCAA-AGATTC
* * * * *
3525328 CAAGACTTGCAAAAAATTTTAAAGATTTGCAAATATTC
1 AAAAATTTGCAAAAGA-TTT-AAGATTTGCAAAGATTC
* *
3525366 AAAAATTTGCAAAAGATTTAATATTTGTAAAGATTC
1 AAAAATTTGCAAAAGATTTAAGATTTGCAAAGATTC
** * ** *
3525402 AAAAATTCACAAAAG-TTTAAAAATTCACAAAAAATTC
1 AAAAATTTGCAAAAGATTT-AAGATTTGC-AAAGATTC
* * ** * *
3525439 ACAGATTCACAAGAGATTCAAAGA-TTGCAAATGATTC
1 AAAAATTTGCAAAAGATT-TAAGATTTGCAAA-GATTC
**
3525476 AAAAATTCACAAAA-ATTTAAGATTTGCAA
1 AAAAATTTGCAAAAGATTTAAGATTTGCAA
3525505 TGAATTTCAA
Statistics
Matches: 182, Mismatches: 44, Indels: 38
0.69 0.17 0.14
Matches are distributed among these distances:
30 1 0.01
31 4 0.02
32 5 0.03
33 17 0.09
35 15 0.08
36 63 0.35
37 45 0.25
38 32 0.18
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (36 bp):
AAAAATTTGCAAAAGATTTAAGATTTGCAAAGATTC
Found at i:3525446 original size:19 final size:19
Alignment explanation
Indices: 3525398--3525490 Score: 73
Period size: 19 Copynumber: 5.0 Consensus size: 19
3525388 ATTTGTAAAG
*
3525398 ATTCAAAAATTCAC-AAAA
1 ATTCAAAGATTCACAAAAA
* * *
3525416 GTTTAAAAATTCACAAAAA
1 ATTCAAAGATTCACAAAAA
* * *
3525435 ATTCACAGATTCACAAGAG
1 ATTCAAAGATTCACAAAAA
* **
3525454 ATTCAAAGATT-GCAAATG
1 ATTCAAAGATTCACAAAAA
*
3525472 ATTCAAAAATTCACAAAAA
1 ATTCAAAGATTCACAAAAA
3525491 TTTAAGATTT
Statistics
Matches: 57, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
18 26 0.46
19 31 0.54
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.24
Consensus pattern (19 bp):
ATTCAAAGATTCACAAAAA
Found at i:3525514 original size:37 final size:37
Alignment explanation
Indices: 3525339--3525594 Score: 136
Period size: 37 Copynumber: 7.0 Consensus size: 37
3525329 AAGACTTGCA
* * **
3525339 AAAAATTTTAAAGATTTGCAAA-TA-TTCAAAAATTTGC
1 AAAAA-TTT-AAGATTTGCAAAGAATTTCAAAGATTCAC
* * *
3525376 AAAAGATTTAATATTTGTAAAG-A-TTCAAAAATTCAC
1 AAAA-ATTTAAGATTTGCAAAGAATTTCAAAGATTCAC
* * * * * *
3525412 AAAAGTTTAAAAATT-CACAAAAAATTCACAGATTCAC
1 AAAAATTTAAGATTTGCA-AAGAATTTCAAAGATTCAC
* * *
3525449 AAGAGATTCAAAGA-TTGCAAATG-A-TTCAAAAATTCAC
1 AA-AAATT-TAAGATTTGCAAA-GAATTTCAAAGATTCAC
* * *
3525486 AAAAATTTAAGATTTGCAATGAATTTCAAAGTTTCAG
1 AAAAATTTAAGATTTGCAAAGAATTTCAAAGATTCAC
** * * * *
3525523 AATTA-TAAATATTTGGCAAAAAAATTC-AAGATTCAC
1 AAAAATTTAAGATTT-GCAAAGAATTTCAAAGATTCAC
*
3525559 AAAATTTTAAGATTTGCAAAGAATTTCAAAGATTCA
1 AAAAATTTAAGATTTGCAAAGAATTTCAAAGATTCA
3525595 AATATTTGCA
Statistics
Matches: 164, Mismatches: 40, Indels: 30
0.70 0.17 0.13
Matches are distributed among these distances:
34 1 0.01
35 15 0.09
36 64 0.39
37 70 0.43
38 9 0.05
39 5 0.03
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.31
Consensus pattern (37 bp):
AAAAATTTAAGATTTGCAAAGAATTTCAAAGATTCAC
Found at i:3525609 original size:29 final size:28
Alignment explanation
Indices: 3525570--3525626 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
3525560 AAATTTTAAG
*
3525570 ATTTGCAAAGAATT-TCAAAGATTCAAAT
1 ATTTGCAAAG-ATTCTCAAAGAATCAAAT
*
3525598 ATTTGCAAAAGATTCTTAAAGAATCAAAT
1 ATTTGC-AAAGATTCTCAAAGAATCAAAT
3525627 CCAAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (28 bp):
ATTTGCAAAGATTCTCAAAGAATCAAAT
Found at i:3525953 original size:42 final size:43
Alignment explanation
Indices: 3525824--3526001 Score: 121
Period size: 43 Copynumber: 4.1 Consensus size: 43
3525814 TATATATAAA
* * * *
3525824 AAAAAGCTCATCTTATCAAAG-TTCAACAACTTTGAAAAAAATAT
1 AAAAAGCTCCTCTAAACAAAGCTTCAACAA-TTT-TAAAAAATAT
* * * * * * *
3525868 AACAGGCTCCTCTCAATAGAGGC-TCAACAACTTTT-GAAGATAT
1 AAAAAGCTCCTCTAAACA-AAGCTTCAACAA-TTTTAAAAAATAT
* * * *
3525911 AAAAAGTTCTTCTAAACAAAGCTT-AACAATTTTTATAAATAT
1 AAAAAGCTCCTCTAAACAAAGCTTCAACAATTTTAAAAAATAT
* * * *
3525953 AAAAAACTCCTCTCAACAAAGGTTCTACAATTTTAAAAAATAT
1 AAAAAGCTCCTCTAAACAAAGCTTCAACAATTTTAAAAAATAT
3525996 AAAAAG
1 AAAAAG
3526002 AGATTCTTAT
Statistics
Matches: 100, Mismatches: 29, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
41 4 0.04
42 32 0.32
43 39 0.39
44 12 0.12
45 13 0.13
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (43 bp):
AAAAAGCTCCTCTAAACAAAGCTTCAACAATTTTAAAAAATAT
Found at i:3527443 original size:3 final size:3
Alignment explanation
Indices: 3527437--3527480 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
3527427 TTTTTAAATT
*
3527437 TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3527481 CAGTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3528547 original size:15 final size:15
Alignment explanation
Indices: 3528527--3528557 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3528517 ATAGAATTAT
3528527 CAGAACTGGTGATGG
1 CAGAACTGGTGATGG
3528542 CAGAACTGGTGATGG
1 CAGAACTGGTGATGG
3528557 C
1 C
3528558 TGCTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.39, T:0.19
Consensus pattern (15 bp):
CAGAACTGGTGATGG
Found at i:3531506 original size:20 final size:21
Alignment explanation
Indices: 3531462--3531511 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
3531452 TGATTGTTTT
*
3531462 ATTTTATTTATAAATTAATTG
1 ATTTTATTTACAAATTAATTG
*
3531483 A-TTTATTTACGAATTAA-TG
1 ATTTTATTTACAAATTAATTG
3531502 AATTTTATTT
1 -ATTTTATTT
3531512 TTTAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 8 0.32
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (21 bp):
ATTTTATTTACAAATTAATTG
Found at i:3540487 original size:31 final size:31
Alignment explanation
Indices: 3540452--3540520 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
3540442 AATAAAGCTG
*
3540452 AAAATAAAGTTAAAAAGCTGAAAGCAAAGAA
1 AAAATAAAGTTAAAAAGCTGAAAACAAAGAA
3540483 AAAATAAAGTTAAAAAGCTGAAAACAAAGAA
1 AAAATAAAGTTAAAAAGCTGAAAACAAAGAA
3540514 AAAATAA
1 AAAATAA
3540521 CAAAATGACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.68, C:0.06, G:0.13, T:0.13
Consensus pattern (31 bp):
AAAATAAAGTTAAAAAGCTGAAAACAAAGAA
Found at i:3541179 original size:18 final size:18
Alignment explanation
Indices: 3541158--3541194 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3541148 ATTCACATAT
3541158 ACATAAAAATTTAAAATA
1 ACATAAAAATTTAAAATA
3541176 ACATAAAAATTTAAAATA
1 ACATAAAAATTTAAAATA
3541194 A
1 A
3541195 AAATTAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
ACATAAAAATTTAAAATA
Found at i:3543058 original size:20 final size:20
Alignment explanation
Indices: 3543033--3543077 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3543023 AAAAGTTGAG
3543033 TTTTTTATTTT-TATTATAAT
1 TTTTTTATTTTATATT-TAAT
* *
3543053 TTTTTTCTTTTATATTTTAT
1 TTTTTTATTTTATATTTAAT
3543073 TTTTT
1 TTTTT
3543078 CAAACCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTATTTTATATTTAAT
Found at i:3543282 original size:13 final size:13
Alignment explanation
Indices: 3543264--3543289 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3543254 TATCTTGAAA
3543264 ATTTTTTGATATT
1 ATTTTTTGATATT
3543277 ATTTTTTGATATT
1 ATTTTTTGATATT
3543290 TTAAAACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (13 bp):
ATTTTTTGATATT
Found at i:3548770 original size:8 final size:8
Alignment explanation
Indices: 3548757--3548783 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3548747 AAGAAATATC
3548757 ATTTAAAA
1 ATTTAAAA
3548765 ATTTAAAA
1 ATTTAAAA
3548773 ATTTAAAA
1 ATTTAAAA
3548781 ATT
1 ATT
3548784 ATCGTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTTAAAA
Found at i:3549552 original size:33 final size:31
Alignment explanation
Indices: 3549505--3549582 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 31
3549495 ATTGAATTTG
* *
3549505 ATAATTTATATATTTGTGTTATATAAAATATTA
1 ATAA-TTATGTATTTGTATTATATAAAATA-TA
* *
3549538 ATAATTAATGTATTTGTATTGTATATAATATA
1 ATAATT-ATGTATTTGTATTATATAAAATATA
*
3549570 AAAATTATGTATT
1 ATAATTATGTATT
3549583 CTAATTTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 7 0.18
32 9 0.23
33 23 0.59
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (31 bp):
ATAATTATGTATTTGTATTATATAAAATATA
Found at i:3553000 original size:6 final size:6
Alignment explanation
Indices: 3552985--3553014 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3552975 AGAGGTGCTT
*
3552985 GGTTCG GGTTCA GGTTCA GGTTCA GGTTCA
1 GGTTCA GGTTCA GGTTCA GGTTCA GGTTCA
3553015 AGTATTAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.17, G:0.37, T:0.33
Consensus pattern (6 bp):
GGTTCA
Done.