Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 87 of 100
Found at i:17539708 original size:59 final size:58
Alignment explanation
Indices: 17539632--17540042 Score: 393
Period size: 59 Copynumber: 7.0 Consensus size: 58
17539622 TAAACAAGAG
* *
17539632 AATTGATACTTTTAACTTTTTCTCAAAATTATTTTTTGAAATTTTTATTTTCAAGAAA
1 AATTGATACTTTCAACTTTTTCTCAAAATTATTTTTTGAAAATTTTATTTTCAAGAAA
* * * *
17539690 AATTGATAACTTTCAACTTTTCCTTAAAAATATTTTTTGAAAATTTTATTTTCAAGGAA
1 AATTGAT-ACTTTCAACTTTTTCTCAAAATTATTTTTTGAAAATTTTATTTTCAAGAAA
* *
17539749 AATTGATACTTTCAACTTTTTCTCAAAAATTCCTTTTTTTG-AAATCTTTATTTTTAAGAAA
1 AATTGATACTTTCAACTTTTTCTC-AAAATT--ATTTTTTGAAAAT-TTTATTTTCAAGAAA
* * * * * *
17539810 AAAT-AAACTCTCAACTTTTCCTC--AATAATTTTTTGAAAATTTTATTTTCAAGGAA
1 AATTGATACTTTCAACTTTTTCTCAAAATTATTTTTTGAAAATTTTATTTTCAAGAAA
* * * * *
17539865 AATTGATATTTTTAA-TTTTTCCTCAAAAATGA-TTTTTGAAAATTTTATTTTTAAGGAA
1 AATTGATACTTTCAACTTTTT-CTC-AAAATTATTTTTTGAAAATTTTATTTTCAAGAAA
* * * * * * *
17539923 AATTGGTACTTTCAAATTTTTCTCAAAAATATTTCTTTTAAAAATTGTATTTTTATGAAA
1 AATTGATACTTTCAACTTTTTCTCAAAATTA-TT-TTTTGAAAATTTTATTTTCAAGAAA
* * * * * **
17539983 AATTGATAATTTTAACTTTTCCTTAAAAATGATTTTTTTTAAATTTTATTTTCAAGAAA
1 AATTGATACTTTCAACTTTTTC-TCAAAATTATTTTTTGAAAATTTTATTTTCAAGAAA
17540042 A
1 A
17540043 TCATTGAAAA
Statistics
Matches: 287, Mismatches: 50, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
55 27 0.09
56 13 0.05
57 8 0.03
58 62 0.22
59 88 0.31
60 60 0.21
61 29 0.10
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (58 bp):
AATTGATACTTTCAACTTTTTCTCAAAATTATTTTTTGAAAATTTTATTTTCAAGAAA
Found at i:17539868 original size:116 final size:118
Alignment explanation
Indices: 17539632--17540042 Score: 437
Period size: 118 Copynumber: 3.5 Consensus size: 118
17539622 TAAACAAGAG
* *
17539632 AATTGATACTTTTAACTTTTTCTC-AAAATTATTTTTTGAAATTTTTATTTTCAAGAAAAATTGA
1 AATTGATACTTTTAACTTTTTCTCAAAAATTATTTTTTGAAATCTTTATTTTCAAGAAAAAATGA
*
17539696 TAACTTTCAACTTTTCCTTAAAAATATTTTTTGAAAATTTTATTTTCAAGGAA
66 TAACTCTCAACTTTTCCTTAAAAATATTTTTTGAAAATTTTATTTTCAAGGAA
* * *
17539749 AATTGATACTTTCAACTTTTTCTCAAAAATTCCTTTTTTTGAAATCTTTATTTTTAAGAAAAAAT
1 AATTGATACTTTTAACTTTTTCTCAAAAATT--ATTTTTTGAAATCTTTATTTTCAAGAAAAAAT
* *
17539814 -A-AACTCTCAACTTTTCC-TCAATA-ATTTTTTGAAAATTTTATTTTCAAGGAA
64 GATAACTCTCAACTTTTCCTTAAAAATATTTTTTGAAAATTTTATTTTCAAGGAA
* * * * *
17539865 AATTGATATTTTTAA-TTTTTCCTCAAAAATGA-TTTTTGAAAAT-TTTATTTTTAAGGAAAATT
1 AATTGATACTTTTAACTTTTT-CTCAAAAATTATTTTTTG-AAATCTTTATTTTCAAGAAAAAAT
* * * * * * * * * *
17539927 GGT-ACTTTCAAATTTTTCTCAAAAATATTTCTTTTAAAAATTGTATTTTTATGAAA
64 GATAACTCTCAACTTTTCCTTAAAAATA-TT-TTTTGAAAATTTTATTTTCAAGGAA
* * * * *
17539983 AATTGATAATTTTAACTTTTCCTTAAAAATGATTTTTTTTAAAT-TTTATTTTCAAGAAAA
1 AATTGATACTTTTAACTTTTTCTCAAAAATTA-TTTTTTGAAATCTTTATTTTCAAGAAAA
17540043 TCATTGAAAA
Statistics
Matches: 248, Mismatches: 32, Indels: 26
0.81 0.10 0.08
Matches are distributed among these distances:
113 23 0.09
114 16 0.06
115 8 0.03
116 51 0.21
117 29 0.12
118 65 0.26
119 23 0.09
120 33 0.13
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (118 bp):
AATTGATACTTTTAACTTTTTCTCAAAAATTATTTTTTGAAATCTTTATTTTCAAGAAAAAATGA
TAACTCTCAACTTTTCCTTAAAAATATTTTTTGAAAATTTTATTTTCAAGGAA
Found at i:17540130 original size:27 final size:24
Alignment explanation
Indices: 17540097--17540160 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 24
17540087 TAATTTAATC
17540097 AATAAATACATAAGCAAAAAAAATCA
1 AATAAATACATAAG-AAAAAAAAT-A
* * *
17540123 TAATAAATAAATAAGTAAATAAATA
1 -AATAAATACATAAGAAAAAAAATA
17540148 AAT-AATACATAAG
1 AATAAATACATAAG
17540161 TAGAGAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 9 0.27
24 3 0.09
25 1 0.03
26 7 0.21
27 13 0.39
ACGTcount: A:0.67, C:0.06, G:0.05, T:0.22
Consensus pattern (24 bp):
AATAAATACATAAGAAAAAAAATA
Found at i:17543638 original size:3 final size:3
Alignment explanation
Indices: 17543632--17543683 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
17543622 ATTATTATTA
* * * * * *
17543632 TTG TTG TTG TTG TTG TTG TTA TTT TTA TTG TTG TTA TTA TTG TTA TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
17543680 TTG T
1 TTG T
17543684 CGTATTTGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:17543644 original size:9 final size:9
Alignment explanation
Indices: 17543629--17543683 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
17543619 ACTATTATTA
17543629 TTATTGTTG
1 TTATTGTTG
*
17543638 TTGTTGTTG
1 TTATTGTTG
* * *
17543647 TTGTTATTT
1 TTATTGTTG
17543656 TTATTGTTG
1 TTATTGTTG
*
17543665 TTATTATTG
1 TTATTGTTG
17543674 TTATTGTTG
1 TTATTGTTG
17543683 T
1 T
17543684 CGTATTTGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.11, C:0.00, G:0.20, T:0.69
Consensus pattern (9 bp):
TTATTGTTG
Found at i:17543664 original size:18 final size:18
Alignment explanation
Indices: 17543641--17543696 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
17543631 ATTGTTGTTG
17543641 TTGTTGTTGTTATTTTTA
1 TTGTTGTTGTTATTTTTA
* *
17543659 TTGTTGTTATTATTGTTA
1 TTGTTGTTGTTATTTTTA
*
17543677 TTGTTGTCG-TATTTGTTA
1 TTGTTGTTGTTATTT-TTA
17543695 TT
1 TT
17543697 AATTTTCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 4 0.12
18 28 0.88
ACGTcount: A:0.12, C:0.02, G:0.18, T:0.68
Consensus pattern (18 bp):
TTGTTGTTGTTATTTTTA
Found at i:17548105 original size:16 final size:16
Alignment explanation
Indices: 17548067--17548117 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
17548057 AAAAAATCAG
17548067 ATTATTTTAAATTGTA
1 ATTATTTTAAATTGTA
* *
17548083 ATCATTTTAAGTT-TA
1 ATTATTTTAAATTGTA
* *
17548098 AGTTATTTTTAATTTTA
1 A-TTATTTTAAATTGTA
17548115 ATT
1 ATT
17548118 TTTCTAATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 3 0.11
16 22 0.79
17 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTATTTTAAATTGTA
Found at i:17550578 original size:37 final size:35
Alignment explanation
Indices: 17550537--17550608 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
17550527 ATAAAACGTG
* * *
17550537 AAATATTTTTACTTAATATTATTACATATAAAATTTA
1 AAATATATTTACTGAATATTACT--ATATAAAATTTA
*
17550574 AAATATATTTAGTGAATATTACTATATAAAATTTA
1 AAATATATTTACTGAATATTACTATATAAAATTTA
17550609 TTTTGGGGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 12 0.39
37 19 0.61
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (35 bp):
AAATATATTTACTGAATATTACTATATAAAATTTA
Found at i:17550925 original size:26 final size:26
Alignment explanation
Indices: 17550889--17550940 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17550879 TAATTAGGAG
17550889 ATTAGCTTGTGTCATCATAGATATTA
1 ATTAGCTTGTGTCATCATAGATATTA
17550915 ATTAGCTTGTGTCATCATAGATATTA
1 ATTAGCTTGTGTCATCATAGATATTA
17550941 TCATGTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (26 bp):
ATTAGCTTGTGTCATCATAGATATTA
Found at i:17552308 original size:23 final size:23
Alignment explanation
Indices: 17552282--17552325 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17552272 TACTTTCAAA
* *
17552282 TTTTTTTAAAAAAATCTTTTTTC
1 TTTTCTTAAAAAAATCATTTTTC
*
17552305 TTTTCTTAAAATAATCATTTT
1 TTTTCTTAAAAAAATCATTTT
17552326 GTTTAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTCTTAAAAAAATCATTTTTC
Found at i:17553089 original size:5 final size:5
Alignment explanation
Indices: 17553048--17553121 Score: 57
Period size: 5 Copynumber: 14.8 Consensus size: 5
17553038 TCTTTCCCTA
** *
17553048 TTTTG TTTT- TTTT- TTTTG TTTGTG ATACT- TTTT- TTTTA TTTTG TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTT-TG -TTTTG TTTTG TTTTG TTTTG TTTTG
17553096 TTTTG TTTTTTG TTTTG TTTTG TTTT
1 TTTTG --TTTTG TTTTG TTTTG TTTT
17553122 TGCTACTAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
4 14 0.24
5 35 0.60
6 3 0.05
7 6 0.10
ACGTcount: A:0.04, C:0.01, G:0.14, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:17553099 original size:17 final size:17
Alignment explanation
Indices: 17553086--17553122 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
17553076 TTTTTTTTTA
17553086 TTTTGTTTTGTTTTGTT
1 TTTTGTTTTGTTTTGTT
17553103 TTTTGTTTTGTTTTGTT
1 TTTTGTTTTGTTTTGTT
17553120 TTT
1 TTT
17553123 GCTACTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (17 bp):
TTTTGTTTTGTTTTGTT
Found at i:17553104 original size:22 final size:22
Alignment explanation
Indices: 17553048--17553121 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 22
17553038 TCTTTCCCTA
*
17553048 TTTTGTTTTTTTTTTTTGTTTGTG
1 TTTTG-TTTTTTATTTTGTTT-TG
17553072 ATACTTT-TTTTTTATTTTGTTTTG
1 -T--TTTGTTTTTTATTTTGTTTTG
*
17553096 TTTTGTTTTTTGTTTTGTTTTG
1 TTTTGTTTTTTATTTTGTTTTG
17553118 TTTT
1 TTTT
17553122 TGCTACTAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
21 3 0.07
22 20 0.45
23 1 0.02
24 2 0.05
25 15 0.34
27 3 0.07
ACGTcount: A:0.04, C:0.01, G:0.14, T:0.81
Consensus pattern (22 bp):
TTTTGTTTTTTATTTTGTTTTG
Found at i:17554158 original size:16 final size:17
Alignment explanation
Indices: 17554129--17554162 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17554119 TCAGTTACTC
*
17554129 TTTTTTTTTATTTTTTG
1 TTTTGTTTTATTTTTTG
17554146 TTTTGTTTT-TTTTTTG
1 TTTTGTTTTATTTTTTG
17554162 T
1 T
17554163 GTGCATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (17 bp):
TTTTGTTTTATTTTTTG
Found at i:17554161 original size:11 final size:11
Alignment explanation
Indices: 17554129--17554162 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
17554119 TCAGTTACTC
*
17554129 TTTTTTTTTAT
1 TTTTTTTTTGT
17554140 TTTTTGTTTTGT
1 TTTTT-TTTTGT
17554152 TTTTTTTTTGT
1 TTTTTTTTTGT
17554163 GTGCATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:17554171 original size:11 final size:11
Alignment explanation
Indices: 17554157--17554182 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17554147 TTTGTTTTTT
17554157 TTTTGTGTGCA
1 TTTTGTGTGCA
17554168 TTTTGTGTGCA
1 TTTTGTGTGCA
17554179 TTTT
1 TTTT
17554183 TCTTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (11 bp):
TTTTGTGTGCA
Found at i:17554231 original size:18 final size:19
Alignment explanation
Indices: 17554204--17554240 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17554194 TTATTAAAAA
17554204 TAAAAGTG-AAATTGGGTT
1 TAAAAGTGAAAATTGGGTT
*
17554222 TAAAATTGAAAATTGGGTT
1 TAAAAGTGAAAATTGGGTT
17554241 CTATTAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (19 bp):
TAAAAGTGAAAATTGGGTT
Found at i:17555225 original size:38 final size:41
Alignment explanation
Indices: 17555151--17555254 Score: 117
Period size: 39 Copynumber: 2.6 Consensus size: 41
17555141 TAAAGTCTTG
17555151 GAAATCATTT-AAAAATTTAAAATTTTGCTTGAAGGTC-TTA
1 GAAATC-TTTCAAAAATTTAAAATTTTGCTTGAAGGTCTTTA
* * * *
17555191 -AAATCTTTCAAAATTTTAAGATTTT-TTTGGAGGTCTTTA
1 GAAATCTTTCAAAAATTTAAAATTTTGCTTGAAGGTCTTTA
* *
17555230 GAAATCATTCAAAAATCTAAAATTT
1 GAAATCTTTCAAAAATTTAAAATTT
17555255 GCTCGGGAGG
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
38 11 0.21
39 22 0.42
40 20 0.38
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (41 bp):
GAAATCTTTCAAAAATTTAAAATTTTGCTTGAAGGTCTTTA
Found at i:17555406 original size:40 final size:41
Alignment explanation
Indices: 17555307--17555416 Score: 127
Period size: 41 Copynumber: 2.7 Consensus size: 41
17555297 CCTGAAAGTC
* * *
17555307 TTTGAAAATCATTAAAAAATTTGAAATTTCACTCGGAGATG
1 TTTGAAAATCATTTAAAAATTTAAAATTTCACTCAGAGATG
* * *
17555348 TTTGAAAATC-TTTCAAAAATTCAAAATTTGAC-CA-AGAGG
1 TTTGAAAATCATTT-AAAAATTTAAAATTTCACTCAGAGATG
17555387 TTTTGAAAATCATTTAAAAATTTAAAATTT
1 -TTTGAAAATCATTTAAAAATTTAAAATTT
17555417 TGCACGGATG
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
39 4 0.07
40 27 0.46
41 28 0.47
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (41 bp):
TTTGAAAATCATTTAAAAATTTAAAATTTCACTCAGAGATG
Found at i:17555433 original size:40 final size:40
Alignment explanation
Indices: 17555020--17555436 Score: 219
Period size: 40 Copynumber: 10.4 Consensus size: 40
17555010 AATTTTTATC
* * * * *
17555020 CGGAGGTCTT-AAGAAGACATTTAAAATTTTGAAGTTTTAC-
1 CGGAGGTCTTGAA-AA-TCATTTAAAAATTTAAAATTTTGCT
* *
17555060 CGGAGGTCTTGAAAATCCTTTAAAAATTTTAAATTTTG-T
1 CGGAGGTCTTGAAAATCATTTAAAAATTTAAAATTTTGCT
** * * * * * * * *
17555099 CCAAAGGTTTTGGAGATCATTCAAAATTTTCAGATTTTGCC
1 -CGGAGGTCTTGAAAATCATTTAAAAATTTAAAATTTTGCT
** * *
17555140 CTAAAGTCTTGGAAATCATTTAAAAATTTAAAATTTTGCT
1 CGGAGGTCTTGAAAATCATTTAAAAATTTAAAATTTTGCT
* * * * *
17555180 TGAAGGTCTT-AAAATC-TTTCAAAATTTTAAGATTTT-TT
1 CGGAGGTCTTGAAAATCATTT-AAAAATTTAAAATTTTGCT
* * * *
17555218 TGGAGGTCTTTAGAAATCATTCAAAAATCTAAAA-TTTGCT
1 CGGAGGTCTTGA-AAATCATTTAAAAATTTAAAATTTTGCT
* * * * *
17555258 CGGGAGGCCTTGAAAATTATTTAGAAATTTAAGATTTTTC-
1 C-GGAGGTCTTGAAAATCATTTAAAAATTTAAAATTTTGCT
* * * * **
17555298 CTGAAAGTCTTTGAAAATCATTAAAAAATTTGAAATTTCACT
1 C-GGAGGTC-TTGAAAATCATTTAAAAATTTAAAATTTTGCT
*
17555340 CGGAGATGT-TTGAAAATC-TTTCAAAAATTCAAAA-TTTGAC-
1 CGGAG--GTCTTGAAAATCATTT-AAAAATTTAAAATTTTG-CT
* * *
17555380 CAAGAGGTTTTGAAAATCATTTAAAAATTTAAAATTTTGCA
1 C-GGAGGTCTTGAAAATCATTTAAAAATTTAAAATTTTGCT
*
17555421 CGGATGTCTTGAAAAT
1 CGGAGGTCTTGAAAAT
17555437 TTTACTTGAA
Statistics
Matches: 284, Mismatches: 71, Indels: 44
0.71 0.18 0.11
Matches are distributed among these distances:
38 13 0.05
39 42 0.15
40 152 0.54
41 74 0.26
42 1 0.00
43 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (40 bp):
CGGAGGTCTTGAAAATCATTTAAAAATTTAAAATTTTGCT
Found at i:17556243 original size:6 final size:6
Alignment explanation
Indices: 17556210--17556242 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
17556200 CTCTATTTGC
*
17556210 TTTTCT TTTTCT TTTTCT CTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
17556243 TAAATTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:17556396 original size:3 final size:3
Alignment explanation
Indices: 17556388--17556427 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
17556378 CAAATGTCTC
* *
17556388 TAT TAT TAT TAA TAT TAA TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17556428 TAAATAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:17559712 original size:21 final size:22
Alignment explanation
Indices: 17559677--17559717 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
17559667 TGTTTTTTTC
*
17559677 TATTTTTTATTCTTTGTTGTTT
1 TATTTTTTATACTTTGTTGTTT
*
17559699 TATTTTTT-TACTTTTTTGT
1 TATTTTTTATACTTTGTTGT
17559718 GCTTTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (22 bp):
TATTTTTTATACTTTGTTGTTT
Found at i:17559714 original size:30 final size:30
Alignment explanation
Indices: 17559666--17559744 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
17559656 TTCAGTTGTC
*
17559666 TTGTT-TTTTTCTATTTTTTAT-T-CTTTGTT
1 TTGTTATTTTTTTA-TTTTTATGTGCTTT-TT
17559695 GTT-TTATTTTTTTACTTTTT-TGTGCTTTTT
1 -TTGTTATTTTTTTA-TTTTTATGTGCTTTTT
17559725 TTGTTATTTTTTTATTTTTA
1 TTGTTATTTTTTTATTTTTA
17559745 ATTAATAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
29 10 0.24
30 28 0.67
31 4 0.10
ACGTcount: A:0.09, C:0.05, G:0.08, T:0.78
Consensus pattern (30 bp):
TTGTTATTTTTTTATTTTTATGTGCTTTTT
Found at i:17565812 original size:106 final size:106
Alignment explanation
Indices: 17565627--17565836 Score: 411
Period size: 106 Copynumber: 2.0 Consensus size: 106
17565617 TAAATTGAAA
17565627 ATTGATACTTTAGTTGTCTTTGCAATATGGTCATAGAGGTTTGGGTTTTATTTTTAGCATAAAAA
1 ATTGATACTTTAGTTGTCTTTGCAATATGGTCATAGAGGTTTGGGTTTTATTTTTAGCATAAAAA
17565692 AGAAAAAAAATCCTATTCACTCTTAAAATGTAAAAAAAAGT
66 AGAAAAAAAATCCTATTCACTCTTAAAATGTAAAAAAAAGT
*
17565733 ATTGATACTTTAGTTGTCTTTGCAATCTGGTCATAGAGGTTTGGGTTTTATTTTTAGCATAAAAA
1 ATTGATACTTTAGTTGTCTTTGCAATATGGTCATAGAGGTTTGGGTTTTATTTTTAGCATAAAAA
17565798 AGAAAAAAAATCCTATTCACTCTTAAAATGTAAAAAAAA
66 AGAAAAAAAATCCTATTCACTCTTAAAATGTAAAAAAAA
17565837 AAAAAAGTAT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (106 bp):
ATTGATACTTTAGTTGTCTTTGCAATATGGTCATAGAGGTTTGGGTTTTATTTTTAGCATAAAAA
AGAAAAAAAATCCTATTCACTCTTAAAATGTAAAAAAAAGT
Found at i:17567344 original size:24 final size:24
Alignment explanation
Indices: 17567311--17567363 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
17567301 ACTATGGTTC
17567311 AAATA-CACATAATTAAAAGCTTA
1 AAATAGCACATAATTAAAAGCTTA
*
17567334 AAATAGCACATAATTAAAAGTTTA
1 AAATAGCACATAATTAAAAGCTTA
17567358 AAATAG
1 AAATAG
17567364 TATAATAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.57, C:0.09, G:0.08, T:0.26
Consensus pattern (24 bp):
AAATAGCACATAATTAAAAGCTTA
Found at i:17570455 original size:71 final size:69
Alignment explanation
Indices: 17570332--17570506 Score: 176
Period size: 71 Copynumber: 2.5 Consensus size: 69
17570322 AATGTAGTAG
* **
17570332 ATGTTGAAACTATATTTTTGAAATTTTAAAATTTTAATAAAGACAGTATTTTTAA-AACAAAAAC
1 ATGTTAAAACTATATTTTCAAAATTTTAAAATTTTAATAAAGACAG-ATTTTTAAGAACAAAAA-
* *
17570396 TTAGTGA
64 -AAATGA
**
17570403 ATGTTAAAACTATATTTTCAAAATTTTAAAATTTTAACT-AAGACTACG-TTTTTAAGATTAAAA
1 ATGTTAAAACTATATTTTCAAAATTTTAAAATTTTAA-TAAAGAC-A-GATTTTTAAGAACAAAA
*
17570466 AAAATGG
63 AAAATGA
* * *
17570473 ATGTTAAAATTTTATTTTCAAATTTTTAAAATTT
1 ATGTTAAAACTATATTTTCAAAATTTTAAAATTT
17570507 CAACAAAAAG
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
70 34 0.38
71 46 0.52
72 8 0.09
73 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (69 bp):
ATGTTAAAACTATATTTTCAAAATTTTAAAATTTTAATAAAGACAGATTTTTAAGAACAAAAAAA
ATGA
Found at i:17570536 original size:70 final size:70
Alignment explanation
Indices: 17570403--17570536 Score: 171
Period size: 70 Copynumber: 1.9 Consensus size: 70
17570393 AACTTAGTGA
* * * *
17570403 ATGTTAAAACTATATTTTCAAAATTTTAAAATTTTAACTAAGACTACGTTTTTAAGATTAAAAAA
1 ATGTTAAAACTATATTTTCAAAATTTTAAAATTTCAACAAAAACTACGTTTTTAAGATAAAAAAA
17570468 AATGG
66 AATGG
* * * **
17570473 ATGTTAAAATTTTATTTTCAAATTTTTAAAATTTCAACAAAAAGCTGTGTTTTT-AGATAAAAAA
1 ATGTTAAAACTATATTTTCAAAATTTTAAAATTTCAACAAAAA-CTACGTTTTTAAGATAAAAAA
17570537 CGTAGTCCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
70 46 0.85
71 8 0.15
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (70 bp):
ATGTTAAAACTATATTTTCAAAATTTTAAAATTTCAACAAAAACTACGTTTTTAAGATAAAAAAA
AATGG
Found at i:17571125 original size:10 final size:10
Alignment explanation
Indices: 17571099--17571135 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
17571089 ACTTACCTTT
17571099 TTAA-TAAAA
1 TTAATTAAAA
17571108 TT--TTAAAA
1 TTAATTAAAA
17571116 TTAATTAAAA
1 TTAATTAAAA
17571126 TTAATTAAAA
1 TTAATTAAAA
17571136 AATAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 2 0.08
10 16 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TTAATTAAAA
Found at i:17572323 original size:22 final size:23
Alignment explanation
Indices: 17572293--17572335 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
17572283 ACTCTCAAAT
* *
17572293 TTTTTTTAAAA-AATCCTTTTTC
1 TTTTCTTAAAACAATCATTTTTC
17572315 TTTTCTTAAAACAATCATTTT
1 TTTTCTTAAAACAATCATTTT
17572336 GATTAATTCT
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:0.30, C:0.14, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTCTTAAAACAATCATTTTTC
Found at i:17574682 original size:12 final size:11
Alignment explanation
Indices: 17574666--17574696 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
17574656 TTTTTTGAAG
17574666 ATTTTTTTGGT
1 ATTTTTTTGGT
17574677 ATTTTTTTGGT
1 ATTTTTTTGGT
17574688 ATTTTTTTG
1 ATTTTTTTG
17574697 TCGTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.16, T:0.74
Consensus pattern (11 bp):
ATTTTTTTGGT
Found at i:17574725 original size:17 final size:17
Alignment explanation
Indices: 17574706--17574737 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17574696 GTCGTTTTGT
17574706 TTTTCTT-ATTTTTGGA
1 TTTTCTTGATTTTTGGA
17574722 TTTTCTTGATTTTTGG
1 TTTTCTTGATTTTTGG
17574738 TTTCTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.06, G:0.16, T:0.69
Consensus pattern (17 bp):
TTTTCTTGATTTTTGGA
Found at i:17574765 original size:10 final size:10
Alignment explanation
Indices: 17574667--17574768 Score: 53
Period size: 11 Copynumber: 9.5 Consensus size: 10
17574657 TTTTTGAAGA
17574667 TTTTTTTGGT
1 TTTTTTTGGT
17574677 ATTTTTTTGGT
1 -TTTTTTTGGT
17574688 ATTTTTTTGTCGT
1 -TTTTTTTG--GT
**
17574701 TTTGTTTTTCT
1 TTT-TTTTGGT
* *
17574712 TATTTTTGGA
1 TTTTTTTGGT
* *
17574722 TTTTCTTGAT
1 TTTTTTTGGT
*
17574732 TTTTGGTTT-CT
1 TTTT--TTTGGT
*
17574743 TTTTGTTGTGT
1 TTTTTTTG-GT
17574754 TTTTTTTGGT
1 TTTTTTTGGT
17574764 TTTTT
1 TTTTT
17574769 ATTTTTTATT
Statistics
Matches: 69, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
9 2 0.03
10 21 0.30
11 35 0.51
12 5 0.07
13 6 0.09
ACGTcount: A:0.05, C:0.04, G:0.17, T:0.75
Consensus pattern (10 bp):
TTTTTTTGGT
Found at i:17575029 original size:78 final size:78
Alignment explanation
Indices: 17574933--17575084 Score: 241
Period size: 78 Copynumber: 1.9 Consensus size: 78
17574923 TTAGAAATGG
** * * * *
17574933 CCGGAGGTTTTACAAATCTCAACATTTACAAAAGCTCTTCTAATCGCAAGCATTGAAACTTTAAA
1 CCGGAGGCCTTACAAATCTCAACATTTACAAAAACTCCTCTAATCACAAGCATTAAAACTTTAAA
17574998 AATTTAAAAATAC
66 AATTTAAAAATAC
*
17575011 CCGGAGGCCTTACAAATCTCAACATTTACAAAAACTCCTCTAATCACAGGCATTAAAACTTTAAA
1 CCGGAGGCCTTACAAATCTCAACATTTACAAAAACTCCTCTAATCACAAGCATTAAAACTTTAAA
17575076 AATTTAAAA
66 AATTTAAAA
17575085 TGTTTTGCTC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (78 bp):
CCGGAGGCCTTACAAATCTCAACATTTACAAAAACTCCTCTAATCACAAGCATTAAAACTTTAAA
AATTTAAAAATAC
Found at i:17575238 original size:104 final size:104
Alignment explanation
Indices: 17575019--17575226 Score: 256
Period size: 104 Copynumber: 2.0 Consensus size: 104
17575009 ACCCGGAGGC
* * *
17575019 CTTACAAATC-TCAACATTTACAAAAACTCCTCTAATCACAGGCATTAAAACTTTAAAAATTTAA
1 CTTACAAATCAT-GACATTTACAAAAACTCCTATAATCACAAGCATTAAAACTTTAAAAATTTAA
* * * *
17575083 AATGTTTTGCTCAAAAAACTTAAAGATTATGCTTGAAGGT
65 AATATTTTACCCAAAAAACTGAAAGATTATGCTTGAAGGT
** * * *
17575123 CTTACAAATCATGACATTTATGAAAACTCTTATAATCAGAAGCATTAAAACTTTAAAGATTTAAA
1 CTTACAAATCATGACATTTACAAAAACTCCTATAATCACAAGCATTAAAACTTTAAAAATTTAAA
* * * *
17575188 ATATTTTACCCAGAAGACTGAGAGATTATGTTTGAAGGT
66 ATATTTTACCCAAAAAACTGAAAGATTATGCTTGAAGGT
17575227 TTTATGAATC
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
104 86 0.99
105 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (104 bp):
CTTACAAATCATGACATTTACAAAAACTCCTATAATCACAAGCATTAAAACTTTAAAAATTTAAA
ATATTTTACCCAAAAAACTGAAAGATTATGCTTGAAGGT
Found at i:17575539 original size:40 final size:37
Alignment explanation
Indices: 17575352--17575625 Score: 119
Period size: 41 Copynumber: 6.8 Consensus size: 37
17575342 AGATCATTCC
* *
17575352 AAAATTTAAGATTTTAGCCTAAAGT-TTTGGAAATCATTT
1 AAAATTTAA-ATTTT-GCTTGAAGTCTTT-GAAATCATTT
* ** * *
17575391 AAATATTTAAAATTTTGCTCGAAGGGTTTAAAATTC-TTC
1 AAA-ATTT-AAATTTTGCTTGAAGTCTTTGAAA-TCATTT
* * *
17575430 AAAATTTTAAGATTTTGGTTGGAGATCTTTAGAAATCATTCA
1 AAAA-TTTAA-ATTTTGCTTGAAG-TCTTT-GAAATCATT-T
** *
17575472 AAAATCCAAAATTTT-CTAGAGAGGTC-TTGAATATCATTT
1 AAAAT-TTAAATTTTGCTTGA-A-GTCTTTGAA-ATCATTT
17575511 AGAAATTTAAGATTTTGCTTGAAAGTCTTTGGAAATCATTT
1 A-AAATTTAA-ATTTTGCTTG-AAGTCTTT-GAAATCATTT
** *
17575552 AAAATTTTGAAATTTCACCTGAAGATCTTTGAAAATC-TTT
1 AAAA-TTT-AAATTTTGCTTGAAG-TCTTTG-AAATCATTT
17575592 CAAAAATTTAAAATTTTGCTTGGAAGTC-TTGAAA
1 --AAAATTT-AAATTTTGCTT-GAAGTCTTTGAAA
17575626 ATTTTGTCCG
Statistics
Matches: 179, Mismatches: 29, Indels: 54
0.68 0.11 0.21
Matches are distributed among these distances:
38 3 0.02
39 38 0.21
40 54 0.30
41 63 0.35
42 21 0.12
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.39
Consensus pattern (37 bp):
AAAATTTAAATTTTGCTTGAAGTCTTTGAAATCATTT
Found at i:17575565 original size:81 final size:79
Alignment explanation
Indices: 17575351--17575566 Score: 194
Period size: 81 Copynumber: 2.7 Consensus size: 79
17575341 GAGATCATTC
* *
17575351 CAAAATTTAAGATTTTAGCCT-AAAGT-TTTGGAAATCATTT-AAATATTTAAAATTTTGCTCGA
1 CAAAATTTAAGATTTT-GCTTGAAAGTCTTTGGAAATCATTTAAAAT-TTTAAAATTTTGCTAGA
17575413 AGGGTTTAAAATTCTT
64 AGGGTTTAAAATTCTT
* * * * * **
17575429 CAAAATTTTAAGATTTTGGTTG-GAGATCTTTAGAAATCATTCAAAAATCCAAAATTTT-CTAG-
1 CAAAA-TTTAAGATTTTGCTTGAAAG-TCTTTGGAAATCATTTAAAATTTTAAAATTTTGCTAGA
*
17575491 AGAGGTCTT-GAATATCATT
64 AG-GGT-TTAAAAT-TC-TT
* *
17575510 TAGAAATTTAAGATTTTGCTTGAAAGTCTTTGGAAATCATTTAAAATTTTGAAATTT
1 CA-AAATTTAAGATTTTGCTTGAAAGTCTTTGGAAATCATTTAAAATTTTAAAATTT
17575567 CACCTGAAGA
Statistics
Matches: 108, Mismatches: 19, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
78 11 0.10
79 21 0.19
80 25 0.23
81 46 0.43
82 5 0.05
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (79 bp):
CAAAATTTAAGATTTTGCTTGAAAGTCTTTGGAAATCATTTAAAATTTTAAAATTTTGCTAGAAG
GGTTTAAAATTCTT
Found at i:17576162 original size:32 final size:31
Alignment explanation
Indices: 17576078--17576163 Score: 111
Period size: 31 Copynumber: 2.7 Consensus size: 31
17576068 GATAAGGTGC
*
17576078 CAGCTAAACTAGGCTTATAA-CATGATTGATA
1 CAGCTAAACTAGGCTTAAAATC-TGATTGATA
* *
17576109 CAACTAAACTAGGCTTGAAATCTGATTGATGA
1 CAGCTAAACTAGGCTTAAAATCTGATTGAT-A
*
17576141 CAGCAAAACTAGGCTTAAAATCT
1 CAGCTAAACTAGGCTTAAAATCT
17576164 TATCTCATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 25 0.53
32 22 0.47
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (31 bp):
CAGCTAAACTAGGCTTAAAATCTGATTGATA
Found at i:17576388 original size:18 final size:18
Alignment explanation
Indices: 17576365--17576401 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17576355 ATTCCATCCC
17576365 TCTTTTTGCT-TTTTTTTT
1 TCTTTTT-CTCTTTTTTTT
17576383 TCTTTTTCTCTTTTTTTT
1 TCTTTTTCTCTTTTTTTT
17576401 T
1 T
17576402 TAAATTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (18 bp):
TCTTTTTCTCTTTTTTTT
Found at i:17576557 original size:3 final size:3
Alignment explanation
Indices: 17576549--17576586 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
17576539 CAAATGTCTC
17576549 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17576587 ATGAGAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:17579938 original size:18 final size:19
Alignment explanation
Indices: 17579911--17579947 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17579901 TTAATAAAAA
17579911 TAAAAGTG-AAATTGGATT
1 TAAAAGTGAAAATTGGATT
*
17579929 TAAAATTGAAAATTGGATT
1 TAAAAGTGAAAATTGGATT
17579948 ATATTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (19 bp):
TAAAAGTGAAAATTGGATT
Found at i:17580919 original size:16 final size:18
Alignment explanation
Indices: 17580900--17580936 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
17580890 TATAATACGG
17580900 TGATAC-AATAAAAAA-A
1 TGATACAAATAAAAAACA
17580916 TGATACAAATAAAAAACA
1 TGATACAAATAAAAAACA
17580934 TGA
1 TGA
17580937 AGTTGATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (18 bp):
TGATACAAATAAAAAACA
Found at i:17585933 original size:26 final size:25
Alignment explanation
Indices: 17585881--17585938 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
17585871 AAATTTAATG
17585881 ATTTAAAATATTAAATATAAAAATA
1 ATTTAAAATATTAAATATAAAAATA
**
17585906 ATTTAAAATACTTTAAA-ATAAATGTA
1 ATTTAAAATA--TTAAATATAAAAATA
17585932 ATTTAAA
1 ATTTAAA
17585939 CAAATATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 10 0.34
26 14 0.48
27 5 0.17
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTTAAAATATTAAATATAAAAATA
Found at i:17590266 original size:161 final size:161
Alignment explanation
Indices: 17589911--17590796 Score: 819
Period size: 161 Copynumber: 5.5 Consensus size: 161
17589901 CATTTTGGTC
* ** *
17589911 TTTCACACATATCAATCATG--AAAACCAAATTCAATCATTTGGATAAA-TTTAATATCATGTAT
1 TTTCACACATATCAA-C-TGTAAAAACCAAGTTCAATCA-TTCAAAAAAGTTTAATATCATGTAT
* * * * * * * *
17589973 TGAAGCTATTCAAACTATTAAAACAGAACAATAACAGTAACTTTGTATTTTTGCCTTTTAATGAC
63 TAAAGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGAC
* * *
17590038 AAAAAAAAGTCCTCAAC-AGAGGTAAACAACAACTT
128 ATAAAAAA-TCCTAAACTA-AGGTAAACAATAACTT
* * * *
17590073 TTTCACATATATCAACTATGAAAACCAAGTTCAATCATTCAAAAAAGTTTAATATCACGTATTAA
1 TTTCACACATATCAACTGTAAAAACCAAGTTCAATCATTCAAAAAAGTTTAATATCATGTATTAA
* * * * * * * *
17590138 AGCTCTCTAAATTGTTAAAATAAAACAATAATAGCAAATTTATATTTTTACCTTTTAACAACACA
66 AGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGACATA
*
17590203 AAAAATCCTAAACTAAGGTAAACAACAACTT
131 AAAAATCCTAAACTAAGGTAAACAATAACTT
*** * * *
17590234 TTTCACTTGTATCAACTGCAAAAACCAAGTTCAATTATTCGAAAAAA-TTTAATATCATGTATTG
1 TTTCACACATATCAACTGTAAAAACCAAGTTCAATCATTC-AAAAAAGTTTAATATCATGTATTA
* * * *
17590298 AAGCCATCCAAACTGTTAAAATAGAATAATAATAGCAATTTTGTATTTTTGCCTTTTAACGGCA-
65 AAGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGACAT
*
17590362 AAAATAGTCCTAAA-T-AGGCATAAACAATAACTT
130 AAAA-AATCCTAAACTAAGG--TAAACAATAACTT
* * *** *
17590395 TTTCATACATATCAA-TAGTAGAAACCAAGTTCAATCATTTGGATAAGTTTAATATCATGTATTA
1 TTTCACACATATCAACT-GTAAAAACCAAGTTCAATCATTCAAAAAAGTTTAATATCATGTATTA
** ** * * *
17590459 AAGCTATCCAATTTGTTAAAATAGAACAATAATATTAAACTTGCA-TTTGGCCTTTTAACGGA-A
65 AAGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAAC-GACA
* * * ** *
17590522 TAAAAAGTCCTAAACAAACGTAAACGTTAGCTT
129 TAAAAAATCCTAAACTAAGGTAAACAATAACTT
** * * * *
17590555 TTTCACACATATCAACTGTGGAAATCAAGTTCAATTATTTC-AACAAGTTTAATATCATATATTA
1 TTTCACACATATCAACTGTAAAAACCAAGTTCAATCA-TTCAAAAAAGTTTAATATCATGTATTA
* * * * * * * *
17590619 AAGCTATGCAAACTATTAAAATAGAACAATAACAACAATTTTGCATTTTTGCCTGTTAA-AAGCA
65 AAGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGA-CA
* * *
17590683 TAAAAAATCTTAAA-TAGATGTAAACGATAACTT
129 TAAAAAATCCTAAACTA-AGGTAAACAATAACTT
* * * * **
17590716 TTTCACACATATCAACTGTAAAAATCAAGTTCAATCATTCAGACAAGTTTGATATCATGTATTGG
1 TTTCACACATATCAACTGTAAAAACCAAGTTCAATCATTCAAAAAAGTTTAATATCATGTATTAA
17590781 AGCTATCCAAACTGTT
66 AGCTATCCAAACTGTT
17590797 CAATCGATTC
Statistics
Matches: 594, Mismatches: 109, Indels: 43
0.80 0.15 0.06
Matches are distributed among these distances:
159 4 0.01
160 134 0.23
161 346 0.58
162 110 0.19
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (161 bp):
TTTCACACATATCAACTGTAAAAACCAAGTTCAATCATTCAAAAAAGTTTAATATCATGTATTAA
AGCTATCCAAACTGTTAAAATAGAACAATAATAGCAAATTTGTATTTTTGCCTTTTAACGACATA
AAAAATCCTAAACTAAGGTAAACAATAACTT
Found at i:17590670 original size:321 final size:320
Alignment explanation
Indices: 17589785--17590796 Score: 941
Period size: 321 Copynumber: 3.1 Consensus size: 320
17589775 AAATTGGAAT
* * * * * *
17589785 AAGTTTAATATCATGTATTTAATCTATCTAAATTGTTAAAATATAAA-TATAACTA-TAAAATTA
1 AAGTTTAATATCATGTATTAAAGCTATCCAAATTGTTAAAATA-AAACAATAA-TAGCAAACTTA
* * * * * * *
17589848 TATTTTTACCCTTTAACAGCAC-AAAAGTCTTCAACAAACGTAAACAATACAAGCATTTTGGTCT
64 CATTTTGACCTTTTAACAACACAAAAAATCCTAAACAAACGTAAAC-A-ACAA-C----T--T-T
* * * * *
17589912 TTCACACATATCAA-T-CATGAAAACCAAATTCAATCATTTGGATAAATTTAATATCATGTATTG
119 TTCACACATATCAACTGCA--AAAACCAAGTTCAATTATTCGAAAAAATTTAATATCATGTATTG
* * * * * *
17589975 AAGCTATTCAAACTATTAAAACAGAACAATAACAGTAACTTTGTATTTTTGCCTTTTAATGACAA
182 AAGCTATCCAAACTATTAAAATAGAACAATAACAGCAATTTTGTATTTTTGCCTTTTAAAGGC--
* * *
17590040 AAAAAAGTCCTCAACAGAGGTAAACAACAACTTTTTCACATATATCAACTA-T-GAAAACCAAGT
245 AAAAAAGTCCT-AA-ATAGGTAAACAATAACTTTTTCACACATATCAACTAGTAG-AAACCAAGT
*
17590103 TCAATCATTCAAAA
307 TCAATCATTCAGAA
* * * * *
17590117 AAGTTTAATATCACGTATTAAAGCTCTCTAAATTGTTAAAATAAAACAATAATAGCAAATTTATA
1 AAGTTTAATATCATGTATTAAAGCTATCCAAATTGTTAAAATAAAACAATAATAGCAAACTTACA
* * * ***
17590182 TTTTTACCTTTTAACAACACAAAAAATCCTAAACTAAGGTAAACAACAACTTTTTCACTTGTATC
66 TTTTGACCTTTTAACAACACAAAAAATCCTAAACAAACGTAAACAACAACTTTTTCACACATATC
*
17590247 AACTGCAAAAACCAAGTTCAATTATTCGAAAAAATTTAATATCATGTATTGAAGCCATCCAAACT
131 AACTGCAAAAACCAAGTTCAATTATTCGAAAAAATTTAATATCATGTATTGAAGCTATCCAAACT
* * * *
17590312 GTTAAAATAGAATAATAATAGCAATTTTGTATTTTTGCCTTTTAACGGCAAAAATAGTCCTAAAT
196 ATTAAAATAGAACAATAACAGCAATTTTGTATTTTTGCCTTTTAAAGGCAAAAA-AGTCCTAAAT
* ** *
17590377 AGGCATAAACAATAACTTTTTCATACATATCAA-TAGTAGAAACCAAGTTCAATCATTTGGAT
260 AGG--TAAACAATAACTTTTTCACACATATCAACTAGTAGAAACCAAGTTCAATCATTCAGAA
* * ** *
17590439 AAGTTTAATATCATGTATTAAAGCTATCCAATTTGTTAAAATAGAACAATAATATTAAACTTGCA
1 AAGTTTAATATCATGTATTAAAGCTATCCAAATTGTTAAAATAAAACAATAATAGCAAACTTACA
* * * * *** *
17590504 -TTTGGCCTTTTAACGGA-ATAAAAAGTCCTAAACAAACGTAAACGTTAGCTTTTTCACACATAT
66 TTTTGACCTTTTAAC-AACACAAAAAATCCTAAACAAACGTAAACAACAACTTTTTCACACATAT
*** * * * * * *
17590567 CAACTGTGGAAATCAAGTTCAATTATTTC-AACAAGTTTAATATCATATATTAAAGCTATGCAAA
130 CAACTGCAAAAACCAAGTTCAATTA-TTCGAAAAAATTTAATATCATGTATTGAAGCTATCCAAA
* * * * * *
17590631 CTATTAAAATAGAACAATAACAACAATTTTGCATTTTTGCCTGTTAAAAGCATAAAAAATCTTAA
194 CTATTAAAATAGAACAATAACAGCAATTTTGTATTTTTGCCTTTTAAAGGCA-AAAAAGTCCTAA
* * * *
17590696 ATAGATGTAAACGATAACTTTTTCACACATATCAACT-GTAAAAATCAAGTTCAATCATTCAGAC
258 ATAG--GTAAACAATAACTTTTTCACACATATCAACTAGTAGAAACCAAGTTCAATCATTCAGAA
* ** *
17590760 AAGTTTGATATCATGTATTGGAGCTATCCAAACTGTT
1 AAGTTTAATATCATGTATTAAAGCTATCCAAATTGTT
17590797 CAATCGATTC
Statistics
Matches: 568, Mismatches: 96, Indels: 43
0.80 0.14 0.06
Matches are distributed among these distances:
320 4 0.01
321 240 0.42
322 115 0.20
323 106 0.19
324 2 0.00
325 2 0.00
326 1 0.00
330 1 0.00
331 9 0.02
332 70 0.12
333 18 0.03
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (320 bp):
AAGTTTAATATCATGTATTAAAGCTATCCAAATTGTTAAAATAAAACAATAATAGCAAACTTACA
TTTTGACCTTTTAACAACACAAAAAATCCTAAACAAACGTAAACAACAACTTTTTCACACATATC
AACTGCAAAAACCAAGTTCAATTATTCGAAAAAATTTAATATCATGTATTGAAGCTATCCAAACT
ATTAAAATAGAACAATAACAGCAATTTTGTATTTTTGCCTTTTAAAGGCAAAAAAGTCCTAAATA
GGTAAACAATAACTTTTTCACACATATCAACTAGTAGAAACCAAGTTCAATCATTCAGAA
Found at i:17590717 original size:482 final size:484
Alignment explanation
Indices: 17589911--17590796 Score: 1108
Period size: 482 Copynumber: 1.8 Consensus size: 484
17589901 CATTTTGGTC
*
17589911 TTTCACACATATCAATCATGAAAACCAAATTCAATCATTTGGATAAATTTAATATCATGTATTGA
1 TTTCACACATATCAATCATGAAAACCAAATTCAATCATTTGGATAAATTTAATATCATGTATTAA
* * * *
17589976 AGCTATTCAAACTATTAAAACAGAACAATAACAGTAACTTTGTATTTTTGCCTTTTAATGACAAA
66 AGCTATCCAAACTATTAAAACAGAACAATAACAGTAACTTTGCATTTTGGCCTTTTAACGACAAA
* * * *
17590041 AAAAAGTCCTCAACAGAGGTAAACAACAACTTTTTCACATATATCAACTATGAAAACCAAGTTCA
131 AAAAAGTCCTAAACAAACGTAAACAACAACTTTTTCACACATATCAACTATGAAAACCAAGTTCA
* * * * *
17590106 ATCATTCAAAAAAGTTTAATATCACGTATTAAAGCTCTCTAAATTGTTAAAATAAAACAATAATA
196 ATCATTCAAAAAAGTTTAATATCACATATTAAAGCTATCTAAACTATTAAAATAAAACAATAACA
* * *
17590171 GCAAATTTATATTTTTACCTTTTAACAACACAAAAAATCCTAAACTAAGGTAAACAACAACTTTT
261 ACAAATTTACATTTTTACCTGTTAACAACACAAAAAATCCTAAACTAAGGTAAACAACAACTTTT
*** *
17590236 TCACTTGTATCAACTGCAAAAACCAAGTTCAATTATTC-GAAAAAATTTAATATCATGTATTGAA
326 TCACACATATCAACTGCAAAAACCAAGTTCAATCATTCAG-AAAAATTTAATATCATGTATTGAA
17590300 GCCATCCAAACTGTTAAAATAGAATAATAATAGCAATTTTGTATTTTTGCCTTTTAACGGCAAAA
390 GCCATCCAAACTGTTAAAATAGAATAATAATAGCAATTTTGTATTTTTGCCTTTTAACGGCAAAA
17590365 ATAGTCCTAAATAGGCATAAACAATAACTT
455 ATAGTCCTAAATAGGCATAAACAATAACTT
* * *
17590395 TTTCATACATATCAAT-A-GTAGAAACCAAGTTCAATCATTTGGATAAGTTTAATATCATGTATT
1 TTTCACACATATCAATCATG-A-AAACCAAATTCAATCATTTGGATAAATTTAATATCATGTATT
** * * * * *
17590458 AAAGCTATCCAATTTGTTAAAATAGAACAATAATATTAAAC-TTGCA-TTTGGCCTTTTAACG-G
64 AAAGCTATCCAAACTATTAAAACAGAACAATAACAGT-AACTTTGCATTTTGGCCTTTTAACGAC
* *** * * * *
17590520 AATAAAAAGTCCTAAACAAACGTAAACGTTAGCTTTTTCACACATATCAACTGTGGAAATCAAGT
128 AAAAAAAAGTCCTAAACAAACGTAAACAACAACTTTTTCACACATATCAACTATGAAAACCAAGT
* * * *
17590585 TCAATTATTTC-AACAAGTTTAATATCATATATTAAAGCTATGC-AAACTATTAAAATAGAACAA
193 TCAATCA-TTCAAAAAAGTTTAATATCACATATTAAAGCTAT-CTAAACTATTAAAATAAAACAA
* * * * * * * *
17590648 TAACAACAATTTTGCATTTTTGCCTGTTAA-AAGCATAAAAAATCTTAAA-TAGATGTAAACGAT
256 TAACAACAAATTTACATTTTTACCTGTTAACAA-CACAAAAAATCCTAAACTA-AGGTAAACAAC
* * * * *
17590711 AACTTTTTCACACATATCAACTGTAAAAATCAAGTTCAATCATTCAGACAAGTTTGATATCATGT
319 AACTTTTTCACACATATCAACTGCAAAAACCAAGTTCAATCATTCAGAAAAATTTAATATCATGT
* *
17590776 ATTGGAGCTATCCAAACTGTT
384 ATTGAAGCCATCCAAACTGTT
17590797 CAATCGATTC
Statistics
Matches: 336, Mismatches: 58, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
481 4 0.01
482 221 0.66
483 20 0.06
484 88 0.26
485 3 0.01
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (484 bp):
TTTCACACATATCAATCATGAAAACCAAATTCAATCATTTGGATAAATTTAATATCATGTATTAA
AGCTATCCAAACTATTAAAACAGAACAATAACAGTAACTTTGCATTTTGGCCTTTTAACGACAAA
AAAAAGTCCTAAACAAACGTAAACAACAACTTTTTCACACATATCAACTATGAAAACCAAGTTCA
ATCATTCAAAAAAGTTTAATATCACATATTAAAGCTATCTAAACTATTAAAATAAAACAATAACA
ACAAATTTACATTTTTACCTGTTAACAACACAAAAAATCCTAAACTAAGGTAAACAACAACTTTT
TCACACATATCAACTGCAAAAACCAAGTTCAATCATTCAGAAAAATTTAATATCATGTATTGAAG
CCATCCAAACTGTTAAAATAGAATAATAATAGCAATTTTGTATTTTTGCCTTTTAACGGCAAAAA
TAGTCCTAAATAGGCATAAACAATAACTT
Found at i:17591636 original size:13 final size:13
Alignment explanation
Indices: 17591601--17591637 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
17591591 ATAAAAGCGA
*
17591601 ATATATAAAAAAC
1 ATATATAAAGAAC
*
17591614 ATATGTAAAGAAC
1 ATATATAAAGAAC
17591627 ATATATAAAGA
1 ATATATAAAGA
17591638 CATTGATAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.24
Consensus pattern (13 bp):
ATATATAAAGAAC
Found at i:17592336 original size:25 final size:22
Alignment explanation
Indices: 17592289--17592332 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
17592279 AGCACTAGTA
17592289 TAGTAGTTGATGAAATAACAAC
1 TAGTAGTTGATGAAATAACAAC
17592311 TAGTAGTTGATGAAATAACAAC
1 TAGTAGTTGATGAAATAACAAC
17592333 AACTCCTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (22 bp):
TAGTAGTTGATGAAATAACAAC
Found at i:17593922 original size:21 final size:21
Alignment explanation
Indices: 17593898--17593940 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
17593888 CATCACTTTA
*
17593898 AATATCAAGATCACTAACTTG
1 AATATCAAGATCACCAACTTG
*
17593919 AATATCAATATCACCAACTTG
1 AATATCAAGATCACCAACTTG
17593940 A
1 A
17593941 GTAATACGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (21 bp):
AATATCAAGATCACCAACTTG
Found at i:17607504 original size:62 final size:62
Alignment explanation
Indices: 17607437--17607692 Score: 193
Period size: 62 Copynumber: 4.1 Consensus size: 62
17607427 AATCCCCTCT
**
17607437 AATTTTTTAAAAGAAATTATTGAAGGCATTTTTTTGTAGAAAACGCCTTCAATAATCTC-TTC
1 AATTTTTTAAAAGAAATTATTGAAGGCATTTTTTTGTA-AAAATACCTTCAATAATCTCTTTC
* * * ** * * * * *
17607499 CA-TTTTTATTAGGGGATTATTAAAGGC-GTTTTCTGTCAAAAATACCTTTAATAATCTCCTT-
1 AATTTTTTA-AAAGAAATTATTGAAGGCATTTTTTTGT-AAAAATACCTTCAATAATCTCTTTC
* * * * * *
17607560 AAATTTTGACAAGAAGATTATTGAATGCATTTTTTAT-TAAAAATACCTTCAATAATCCCTTTT
1 AATTTTTTAAAAGAA-ATTATTGAAGGCATTTTTT-TGTAAAAATACCTTCAATAATCTCTTTC
* * * * *
17607623 AATTTTTTAAAGGAAATTATTGAAGCCA-TTTTTTATAGAAAATGCCTTTAATAATC-CTTTC
1 AATTTTTTAAAAGAAATTATTGAAGGCATTTTTTTGTA-AAAATACCTTCAATAATCTCTTTC
*
17607684 CATTTTTTA
1 AATTTTTTA
17607693 TAGGGATTAT
Statistics
Matches: 150, Mismatches: 34, Indels: 21
0.73 0.17 0.10
Matches are distributed among these distances:
60 1 0.01
61 52 0.35
62 80 0.53
63 16 0.11
64 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (62 bp):
AATTTTTTAAAAGAAATTATTGAAGGCATTTTTTTGTAAAAATACCTTCAATAATCTCTTTC
Found at i:17608045 original size:49 final size:49
Alignment explanation
Indices: 17607949--17608053 Score: 126
Period size: 49 Copynumber: 2.1 Consensus size: 49
17607939 GGCATAACAC
**
17607949 GCCTTGAATTTTTTGTAATAGAATATTCAAGGCATTTTTGGTGAAAAAT
1 GCCTTGAATTTTTTGTAATAGAATATTCAAGGCATTTTTGAAGAAAAAT
* *
17607998 GCCTTTAATTTTTTGTAAT-GAAATATTCAA-G-ATGTTTTTAAGCAAAAAT
1 GCCTTGAATTTTTTGTAATAG-AATATTCAAGGCAT-TTTTGAAG-AAAAAT
17608047 GCCTTGA
1 GCCTTGA
17608054 CTAATCTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
47 2 0.04
48 7 0.15
49 39 0.81
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (49 bp):
GCCTTGAATTTTTTGTAATAGAATATTCAAGGCATTTTTGAAGAAAAAT
Found at i:17614961 original size:16 final size:16
Alignment explanation
Indices: 17614942--17614977 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17614932 TTTATATAAT
*
17614942 TTTAACTTTCATGCCC
1 TTTAAATTTCATGCCC
*
17614958 TTTAAATTTCATGTCC
1 TTTAAATTTCATGCCC
17614974 TTTA
1 TTTA
17614978 TGTTTATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTAAATTTCATGCCC
Found at i:17615037 original size:32 final size:31
Alignment explanation
Indices: 17615001--17615079 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
17614991 TTAAATTTCA
* *
17615001 TAATTTCGATGTTATTCAAATTTGTGTATCTT
1 TAATTTCCATGATATTCAAATTTGTGT-TCTT
** * *
17615033 TAATTTCCATGCCATTTACATTTGTGTTCTT
1 TAATTTCCATGATATTCAAATTTGTGTTCTT
17615064 TAATTTCCATGATATT
1 TAATTTCCATGATATT
17615080 GTGTATTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 18 0.45
32 22 0.55
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (31 bp):
TAATTTCCATGATATTCAAATTTGTGTTCTT
Found at i:17616951 original size:28 final size:28
Alignment explanation
Indices: 17616882--17616956 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 28
17616872 TCGATTTGAT
* *
17616882 TGGGC-CCTAGGCCCGATTTTGGCTCAAC
1 TGGGCTCC-AGGCCTGATTTTGACTCAAC
* *
17616910 TGGGCTCCATGCCTGATTTTGACTCAAT
1 TGGGCTCCAGGCCTGATTTTGACTCAAC
* * *
17616938 TGGGTTTCAGGCCTAATTT
1 TGGGCTCCAGGCCTGATTT
17616957 GATCCAACCA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (28 bp):
TGGGCTCCAGGCCTGATTTTGACTCAAC
Found at i:17617026 original size:17 final size:17
Alignment explanation
Indices: 17617004--17617040 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
17616994 GTCAAAAACA
17617004 TATTTATATTTT-AT-TT
1 TATTT-TATTTTAATATT
17617020 TATTTTATTTTAATATT
1 TATTTTATTTTAATATT
17617037 TATT
1 TATT
17617041 AATTAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 7 0.37
17 6 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTTTATTTTAATATT
Found at i:17618099 original size:3 final size:3
Alignment explanation
Indices: 17618093--17618162 Score: 61
Period size: 3 Copynumber: 22.7 Consensus size: 3
17618083 TTCAAACTTT
* * * *
17618093 TTA TTA TTA TTT TTA TTG TTA TATA TTA TTTA TT- TATA TCA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA T-TA TTA TTA TTA
*
17618140 ATA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
17618163 TATGCATGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 1 0.02
3 45 0.85
4 7 0.13
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17618129 original size:15 final size:13
Alignment explanation
Indices: 17618093--17618165 Score: 68
Period size: 12 Copynumber: 6.1 Consensus size: 13
17618083 TTCAAACTTT
17618093 TTATTATTATTT-
1 TTATTATTATTTA
* *
17618105 TTATTGTTATATA
1 TTATTATTATTTA
17618118 TTA-T-TTATTTA
1 TTATTATTATTTA
*
17618129 -TATCATT-TTTA
1 TTATTATTATTTA
*
17618140 ATATTATTA-TTA
1 TTATTATTATTTA
17618152 TTATTATTATTTA
1 TTATTATTATTTA
17618165 T
1 T
17618166 GCATGTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
10 2 0.04
11 10 0.20
12 30 0.61
13 7 0.14
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:17618680 original size:22 final size:21
Alignment explanation
Indices: 17618654--17618697 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
17618644 AATCAAAACC
*
17618654 CTAAACCCTTCAAACCTTAAAA
1 CTAAACCC-TAAAACCTTAAAA
*
17618676 CTAAACCCTAAAACCTTTAAA
1 CTAAACCCTAAAACCTTAAAA
17618697 C
1 C
17618698 CCTGAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (21 bp):
CTAAACCCTAAAACCTTAAAA
Found at i:17618692 original size:29 final size:30
Alignment explanation
Indices: 17618628--17618698 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
17618618 CTTAAATCGT
*
17618628 AAACC-TCAAACATTAAAATCAAAACCCTA
1 AAACCTTCAAACCTTAAAATCAAAACCCTA
* *
17618657 AACCCTTCAAACCTTAAAA-CTAAACCCTA
1 AAACCTTCAAACCTTAAAATCAAAACCCTA
*
17618686 AAACCTTTAAACC
1 AAACCTTCAAACC
17618699 CTGAAATTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (30 bp):
AAACCTTCAAACCTTAAAATCAAAACCCTA
Found at i:17618712 original size:30 final size:29
Alignment explanation
Indices: 17618649--17618718 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
17618639 ATTAAAATCA
* *
17618649 AAACCCTAAACCCTTCAAACCTTAAAACT
1 AAACCCTAAAACCTTCAAACCCTAAAACT
* * *
17618678 AAACCCTAAAACCTTTAAACCCTGAAATT
1 AAACCCTAAAACCTTCAAACCCTAAAACT
*
17618707 GAAACCTTAAAA
1 -AAACCCTAAAA
17618719 TCTAAAATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.47, C:0.29, G:0.03, T:0.21
Consensus pattern (29 bp):
AAACCCTAAAACCTTCAAACCCTAAAACT
Found at i:17618733 original size:22 final size:21
Alignment explanation
Indices: 17618707--17618769 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 21
17618697 CCCTGAAATT
17618707 GAAACCTTAAAATCTAAAATTCC
1 GAAACC-TAAAATCTAAAA-TCC
17618730 -AAACCCTAAAATCTAAAATCC
1 GAAA-CCTAAAATCTAAAATCC
17618751 GAAATCCTAAAAGTCTAAA
1 GAAA-CCTAAAA-TCTAAA
17618770 CCCCAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 3 0.08
22 25 0.69
23 8 0.22
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (21 bp):
GAAACCTAAAATCTAAAATCC
Found at i:17618777 original size:22 final size:22
Alignment explanation
Indices: 17618714--17618777 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
17618704 ATTGAAACCT
** *
17618714 TAAAATCTAAAATTCCAAACCC
1 TAAAATCTAAAACCCCAAATCC
* *
17618736 TAAAATCTAAAATCCGAAATCC
1 TAAAATCTAAAACCCCAAATCC
17618758 TAAAAGTCT-AAACCCCAAAT
1 TAAAA-TCTAAAACCCCAAAT
17618778 TTAGCACAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 33 0.92
23 3 0.08
ACGTcount: A:0.50, C:0.25, G:0.03, T:0.22
Consensus pattern (22 bp):
TAAAATCTAAAACCCCAAATCC
Found at i:17631584 original size:35 final size:35
Alignment explanation
Indices: 17631545--17631667 Score: 131
Period size: 35 Copynumber: 3.5 Consensus size: 35
17631535 CTCGCCATTT
**
17631545 AATCTCGATCATCATTATTTTATGACTCGTGGTTC
1 AATCTCGATCATCATTATTTTATGACTCACGGTTC
* * * * *
17631580 AATCTCGATC-TCATTATTCTCTGATTCACGATTT
1 AATCTCGATCATCATTATTTTATGACTCACGGTTC
* *
17631614 AATCTCGGTCATCATTATTTTATGACTTACGGTTC
1 AATCTCGATCATCATTATTTTATGACTCACGGTTC
* * *
17631649 ATTCCCAATCATCATTATT
1 AATCTCGATCATCATTATT
17631668 CCTTAACTTG
Statistics
Matches: 69, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
34 26 0.38
35 43 0.62
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (35 bp):
AATCTCGATCATCATTATTTTATGACTCACGGTTC
Found at i:17631618 original size:34 final size:34
Alignment explanation
Indices: 17631492--17631633 Score: 117
Period size: 34 Copynumber: 4.2 Consensus size: 34
17631482 CTAGCCGTTC
* * * *
17631492 TTATTTCTAAATCCCGATTCAATCTCGATC-TCT
1 TTATTTCTGACTCGCGATTCAATCTCGATCATCA
* * * *
17631525 TTAATTCTAACTCGCCATTTAATCTCGATCATCA
1 TTATTTCTGACTCGCGATTCAATCTCGATCATCA
* * *
17631559 TTATTTTATGACTCGTGGTTCAATCTCGATC-TCA
1 TTA-TTTCTGACTCGCGATTCAATCTCGATCATCA
* * * *
17631593 TTATTCTCTGATTCACGATTTAATCTCGGTCATCA
1 TTATT-TCTGACTCGCGATTCAATCTCGATCATCA
17631628 TTATTT
1 TTATTT
17631634 TATGACTTAC
Statistics
Matches: 85, Mismatches: 20, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
33 27 0.32
34 30 0.35
35 28 0.33
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (34 bp):
TTATTTCTGACTCGCGATTCAATCTCGATCATCA
Found at i:17631626 original size:69 final size:68
Alignment explanation
Indices: 17631509--17631640 Score: 192
Period size: 69 Copynumber: 1.9 Consensus size: 68
17631499 TAAATCCCGA
* *
17631509 TTCAATCTCGATCTCTTTAATTCTAACTCGCCATTTAATCTCGATCATCATTATTTTATGACTCG
1 TTCAATCTCGATCTCATTAATTCTAACTCACCATTTAATCTCGATCATCATTATTTTATGACTCG
17631574 TGG
66 TGG
* * * * *
17631577 TTCAATCTCGATCTCATTATTCTCTGATTCACGATTTAATCTCGGTCATCATTATTTTATGACT
1 TTCAATCTCGATCTCATTAAT-TCTAACTCACCATTTAATCTCGATCATCATTATTTTATGACT
17631641 TACGGTTCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
68 19 0.34
69 37 0.66
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (68 bp):
TTCAATCTCGATCTCATTAATTCTAACTCACCATTTAATCTCGATCATCATTATTTTATGACTCG
TGG
Found at i:17631648 original size:69 final size:69
Alignment explanation
Indices: 17631509--17631668 Score: 187
Period size: 69 Copynumber: 2.3 Consensus size: 69
17631499 TAAATCCCGA
* * *
17631509 TTCAATCTCGATCTCTTTAAT-TCTAACTCGCCATTTAATCTCGATCATCATTATTTTATGACTC
1 TTCAATCTCGATCTCATTATTCTCTAACTCACCATTTAATCTCGATCATCATTATTTTATGACTC
**
17631573 GTGG
66 ACGG
* * * * *
17631577 TTCAATCTCGATCTCATTATTCTCTGATTCACGATTTAATCTCGGTCATCATTATTTTATGACTT
1 TTCAATCTCGATCTCATTATTCTCTAACTCACCATTTAATCTCGATCATCATTATTTTATGACTC
17631642 ACGG
66 ACGG
* * *
17631646 TTCATTCCCAATCATCATTATTC
1 TTCAATCTCGATC-TCATTATTC
17631669 CTTAACTTGC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
68 19 0.25
69 49 0.64
70 9 0.12
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (69 bp):
TTCAATCTCGATCTCATTATTCTCTAACTCACCATTTAATCTCGATCATCATTATTTTATGACTC
ACGG
Found at i:17631682 original size:35 final size:34
Alignment explanation
Indices: 17631622--17631703 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 34
17631612 TTAATCTCGG
*
17631622 TCATCATTATTTTATGACTTACGGTTCATTCCCAA
1 TCATCATTATTTTA-GACTTACGGTTCAATCCCAA
* * *
17631657 TCATCATTATTCCTTA-ACTTGCGGTTCAATCCTAG
1 TCATCATTATT--TTAGACTTACGGTTCAATCCCAA
*
17631692 TCATCGTTATTT
1 TCATCATTATTT
17631704 ATTGACTAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 1 0.03
35 36 0.90
37 3 0.08
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (34 bp):
TCATCATTATTTTAGACTTACGGTTCAATCCCAA
Found at i:17632672 original size:28 final size:27
Alignment explanation
Indices: 17632605--17632675 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
17632595 ACCTGATCTT
*
17632605 ATCAGATCCAACCACCCCACCCAGTCCC
1 ATCAGAT-CAGCCACCCCACCCAGTCCC
* * *
17632633 ATTA-AACTAGCCACCCCTACCCAGTCTC
1 ATCAGATC-AGCCACCCC-ACCCAGTCCC
17632661 ATCAGATCAGCCACC
1 ATCAGATCAGCCACC
17632676 TTCACCTACC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.03
27 9 0.26
28 22 0.65
29 2 0.06
ACGTcount: A:0.30, C:0.46, G:0.08, T:0.15
Consensus pattern (27 bp):
ATCAGATCAGCCACCCCACCCAGTCCC
Found at i:17633044 original size:10 final size:11
Alignment explanation
Indices: 17633024--17633052 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
17633014 AAATATATAT
17633024 AAAAAAGAAAG
1 AAAAAAGAAAG
17633035 AAAAAA-AAAG
1 AAAAAAGAAAG
17633045 AAAAAAGA
1 AAAAAAGA
17633053 GAATCAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:17633616 original size:12 final size:12
Alignment explanation
Indices: 17633601--17633625 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17633591 TTCCAAATTC
17633601 TTTTTATTATTA
1 TTTTTATTATTA
17633613 TTTTTATTATTA
1 TTTTTATTATTA
17633625 T
1 T
17633626 ATATTATTTA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:17633622 original size:15 final size:15
Alignment explanation
Indices: 17633604--17633664 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
17633594 CAAATTCTTT
17633604 TTATTATTATTTTTA
1 TTATTATTATTTTTA
17633619 TTATTATATATTATTTA
1 TTATTAT-TATT-TTTA
*
17633636 TT-TATATCATTTTTA
1 TTAT-TATTATTTTTA
**
17633651 ACATTATTATTTTT
1 TTATTATTATTTTT
17633665 GTTTTTTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 20 0.53
16 9 0.24
17 9 0.24
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTATTATTTTTA
Found at i:17634142 original size:28 final size:28
Alignment explanation
Indices: 17634102--17634198 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 28
17634092 CTTTAACCCT
*
17634102 AAAATCCTAAACC-TCAAACACTAAAATC
1 AAAACCCTAAACCTTCAAAC-CTAAAATC
*
17634130 AAAACCCTAAACCTTTCAAACCTTAAA-C
1 AAAACCCTAAACC-TTCAAACCTAAAATC
* *
17634158 TAAACCCTATAACCTTTAAACCCTAAAATC
1 AAAACCCTA-AACCTTCAAA-CCTAAAATC
*
17634188 AAAACCTTAAA
1 AAAACCCTAAA
17634199 ATCCAAAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
28 26 0.46
29 17 0.30
30 14 0.25
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (28 bp):
AAAACCCTAAACCTTCAAACCTAAAATC
Found at i:17634179 original size:16 final size:16
Alignment explanation
Indices: 17634131--17634182 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
17634121 ACTAAAATCA
17634131 AAACCCTA-AACCTTT
1 AAACCCTATAACCTTT
*
17634146 CAAA-CCT-TAAAC--T
1 -AAACCCTATAACCTTT
17634159 AAACCCTATAACCTTT
1 AAACCCTATAACCTTT
17634175 AAACCCTA
1 AAACCCTA
17634183 AAATCAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 3 0.10
13 4 0.14
14 4 0.14
15 6 0.21
16 12 0.41
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (16 bp):
AAACCCTATAACCTTT
Found at i:17634195 original size:22 final size:22
Alignment explanation
Indices: 17634168--17634221 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
17634158 TAAACCCTAT
*
17634168 AACCTTTAAACCCTAAAAT-CAA
1 AACCTTAAAACCC-AAAATCCAA
*
17634190 AACCTTAAAATCCAAAATCCAA
1 AACCTTAAAACCCAAAATCCAA
17634212 AATCC-TAAAA
1 AA-CCTTAAAA
17634222 GTCTAAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.18
22 21 0.75
23 2 0.07
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (22 bp):
AACCTTAAAACCCAAAATCCAA
Found at i:17634198 original size:14 final size:15
Alignment explanation
Indices: 17634175--17634221 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
17634165 TATAACCTTT
17634175 AAACCCTAAAAT-CA
1 AAACCCTAAAATCCA
*
17634189 AAACCTTAAAATCCA
1 AAACCCTAAAATCCA
*
17634204 AAATCC-AAAATCCTA
1 AAACCCTAAAATCC-A
17634219 AAA
1 AAA
17634222 GTCTAAACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACCCTAAAATCCA
Found at i:17635463 original size:20 final size:20
Alignment explanation
Indices: 17635427--17635464 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17635417 ATGAAAATTA
*
17635427 TGAAATTGATGTTGAATTTG
1 TGAAATTGATGTAGAATTTG
17635447 TGAAATTAGA-GTAGAATT
1 TGAAATT-GATGTAGAATT
17635465 ATTGTGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
TGAAATTGATGTAGAATTTG
Found at i:17635633 original size:44 final size:44
Alignment explanation
Indices: 17635580--17635669 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
17635570 AATCATTATG
*
17635580 TACATTGTCAAAATTGGTGTTGAATTTGTGAAATAGGTATGAAA
1 TACATTGTCAAAATTGGTGTTAAATTTGTGAAATAGGTATGAAA
*
17635624 TACATTGTCAAAATTGGTGTTAAATTTGTGAAATGGGTATGAAA
1 TACATTGTCAAAATTGGTGTTAAATTTGTGAAATAGGTATGAAA
17635668 TA
1 TA
17635670 GGTATTCTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (44 bp):
TACATTGTCAAAATTGGTGTTAAATTTGTGAAATAGGTATGAAA
Found at i:17635668 original size:20 final size:20
Alignment explanation
Indices: 17635602--17635668 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 20
17635592 ATTGGTGTTG
17635602 AATTTGTGAAATAGGTATGA
1 AATTTGTGAAATAGGTATGA
* * * *
17635622 AATACATTGTCAAAATTGGTGTTA
1 AAT---TTGT-GAAATAGGTATGA
*
17635646 AATTTGTGAAATGGGTATGA
1 AATTTGTGAAATAGGTATGA
17635666 AAT
1 AAT
17635669 AGGTATTCTT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
20 15 0.43
21 4 0.11
23 4 0.11
24 12 0.34
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (20 bp):
AATTTGTGAAATAGGTATGA
Found at i:17639480 original size:15 final size:16
Alignment explanation
Indices: 17639445--17639492 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
17639435 CATATCAAAT
17639445 AATTTTT-ATATTATA
1 AATTTTTAATATTATA
17639460 AA--TTTAATATT-TA
1 AATTTTTAATATTATA
* *
17639473 AATTTTTAAAATTAAA
1 AATTTTTAATATTATA
17639489 AATT
1 AATT
17639493 CAATTCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 7 0.26
14 5 0.19
15 10 0.37
16 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTTTAATATTATA
Found at i:17639502 original size:29 final size:28
Alignment explanation
Indices: 17639445--17639517 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
17639435 CATATCAAAT
* * *
17639445 AATTTTTATATTATAAATTTAATATTTA
1 AATTTTTAAATTAAAAATTCAATATTTA
17639473 AATTTTTAAAATTAAAAATTCAAT-TCTTA
1 AATTTTT-AAATTAAAAATTCAATAT-TTA
*
17639502 ACA-TTTTAATTTAAAA
1 A-ATTTTTAAATTAAAA
17639518 TTTTGAACAG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 16 0.42
29 21 0.55
30 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
AATTTTTAAATTAAAAATTCAATATTTA
Found at i:17640974 original size:13 final size:13
Alignment explanation
Indices: 17640934--17640974 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
17640924 GTAATGTTAT
17640934 TTTAAAATTAAAAA
1 TTTAAAA-TAAAAA
17640948 TTTAAAA-AAAAA
1 TTTAAAATAAAAA
*
17640960 TTTAAAATAATAA
1 TTTAAAATAAAAA
17640973 TT
1 TT
17640975 ATGTATTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 12 0.48
13 6 0.24
14 7 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TTTAAAATAAAAA
Found at i:17641010 original size:19 final size:19
Alignment explanation
Indices: 17640968--17641012 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
17640958 AATTTAAAAT
* *
17640968 AATAATTATGTATTGAATA
1 AATAATTATATACTGAATA
* *
17640987 TATAATTATATACTGTATA
1 AATAATTATATACTGAATA
17641006 AATAATT
1 AATAATT
17641013 GAAATTAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (19 bp):
AATAATTATATACTGAATA
Found at i:17642038 original size:9 final size:9
Alignment explanation
Indices: 17642021--17642089 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
17642011 ACAAAAAACC
*
17642021 TTTTAAAAA
1 TTTTTAAAA
17642030 TTTTTAAAAA
1 TTTTT-AAAA
* **
17642040 ATTAAAAAA
1 TTTTTAAAA
17642049 TTTTTAAAA
1 TTTTTAAAA
17642058 TTTTTCTAAAA
1 -TTTT-TAAAA
* *
17642069 ATTTTAAAG
1 TTTTTAAAA
17642078 TTTTTAAAA
1 TTTTTAAAA
17642087 TTT
1 TTT
17642090 ATAAGAAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
9 28 0.61
10 13 0.28
11 5 0.11
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:17642068 original size:20 final size:20
Alignment explanation
Indices: 17642044--17642082 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17642034 TAAAAAATTA
17642044 AAAAATTTTTAAAATTTTTCT
1 AAAAA-TTTTAAAATTTTTCT
*
17642065 AAAAATTTTAAAGTTTTT
1 AAAAATTTTAAAATTTTT
17642083 AAAATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
AAAAATTTTAAAATTTTTCT
Found at i:17642070 original size:29 final size:28
Alignment explanation
Indices: 17642021--17642100 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
17642011 ACAAAAAACC
*
17642021 TTTTAAAAATTTTTAAAAAATTAAAAAA
1 TTTTTAAAATTTTTAAAAAATTAAAAAA
* ** *
17642049 TTTTTAAAATTTTTCTAAAAATTTTAAAG
1 TTTTTAAAATTTTT-AAAAAATTAAAAAA
*
17642078 TTTTTAAAATTTATAAGAAAATT
1 TTTTTAAAATTTTTAA-AAAATT
17642101 TGTAATTTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 14 0.33
29 29 0.67
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (28 bp):
TTTTTAAAATTTTTAAAAAATTAAAAAA
Found at i:17642136 original size:9 final size:9
Alignment explanation
Indices: 17642112--17642154 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
17642102 GTAATTTCAA
*
17642112 AAAAATTAT
1 AAAAATTCT
17642121 AAAAAATTCT
1 -AAAAATTCT
* *
17642131 ACAAATTAT
1 AAAAATTCT
17642140 AAAAATTCT
1 AAAAATTCT
17642149 AAAAAT
1 AAAAAT
17642155 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATTCT
Found at i:17642145 original size:18 final size:19
Alignment explanation
Indices: 17642112--17642154 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
17642102 GTAATTTCAA
17642112 AAAAATTATAAAAAATTCT
1 AAAAATTATAAAAAATTCT
*
17642131 ACAAATTAT-AAAAATTCT
1 AAAAATTATAAAAAATTCT
17642149 AAAAAT
1 AAAAAT
17642155 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATTATAAAAAATTCT
Found at i:17642180 original size:21 final size:22
Alignment explanation
Indices: 17642145--17642185 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17642135 ATTATAAAAA
17642145 TTCTAAAAATATTTTTTAAATG
1 TTCTAAAAATATTTTTTAAATG
17642167 TTCTAAAAAT-TTTTTTAAA
1 TTCTAAAAATATTTTTTAAA
17642186 AAATTCCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
TTCTAAAAATATTTTTTAAATG
Found at i:17642224 original size:21 final size:22
Alignment explanation
Indices: 17642145--17642227 Score: 68
Period size: 22 Copynumber: 4.0 Consensus size: 22
17642135 ATTATAAAAA
*
17642145 TTCTAAAAATATTTTTTAAA-T
1 TTCTAAAAATATTTTTAAAACT
* **
17642166 GTTCTAAAAATTTTTTTAAAAAA
1 -TTCTAAAAATATTTTTAAAACT
* *
17642189 TTC-CACAA-A-TTTTAAAACT
1 TTCTAAAAATATTTTTAAAACT
17642208 TTCTAAAAA-ATTTTTAAAAC
1 TTCTAAAAATATTTTTAAAAC
17642228 ATAAAAAATC
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.23
20 4 0.08
21 12 0.25
22 21 0.44
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (22 bp):
TTCTAAAAATATTTTTAAAACT
Found at i:17642266 original size:22 final size:22
Alignment explanation
Indices: 17642139--17642266 Score: 67
Period size: 22 Copynumber: 6.2 Consensus size: 22
17642129 CTACAAATTA
17642139 TAAA-AATTCTAAAAATATTTTT
1 TAAACAATTCTAAAAAT-TTTTT
**
17642161 TAAA-TGTTCTAAAAATTTTTT
1 TAAACAATTCTAAAAATTTTTT
* * *
17642182 TAAAAAATTCCACAAA--TTTT
1 TAAACAATTCTAAAAATTTTTT
* * *
17642202 AAAAC-TTTCTAAAAAATTTTT
1 TAAACAATTCTAAAAATTTTTT
* * * **
17642223 AAAAC-A---TAAAAAATCTAC
1 TAAACAATTCTAAAAATTTTTT
17642241 TAAACAATTCTAAAAATTTTTT
1 TAAACAATTCTAAAAATTTTTT
17642263 TAAA
1 TAAA
17642267 ATTCTGAAAA
Statistics
Matches: 79, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
18 13 0.16
19 8 0.10
20 7 0.09
21 18 0.23
22 33 0.42
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (22 bp):
TAAACAATTCTAAAAATTTTTT
Found at i:17642298 original size:11 final size:11
Alignment explanation
Indices: 17642284--17642312 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
17642274 AAAAAAATTC
17642284 TAAAATTTTTT
1 TAAAATTTTTT
17642295 TAAAA-TTTTT
1 TAAAATTTTTT
17642305 TAAAATTT
1 TAAAATTT
17642313 ATAAAACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TAAAATTTTTT
Found at i:17642648 original size:10 final size:9
Alignment explanation
Indices: 17642625--17642767 Score: 103
Period size: 9 Copynumber: 15.4 Consensus size: 9
17642615 TTCCTTAATT
*
17642625 ATTTTTTAA
1 ATTTTTAAA
*
17642634 CTTTTTAAAA
1 ATTTTT-AAA
17642644 ATTTTCTAAA
1 ATTTT-TAAA
17642654 ATTTTTGAAA
1 ATTTTT-AAA
*
17642664 A-TTTAATAA
1 ATTTTTA-AA
*
17642673 ATTTTAAAAA
1 ATTTT-TAAA
*
17642683 AATTTTAAA
1 ATTTTTAAA
*
17642692 AATTTTAAA
1 ATTTTTAAA
*
17642701 ATTTTTTAGA
1 A-TTTTTAAA
17642711 A-TTTTAAA
1 ATTTTTAAA
*
17642719 ATTTTTTAA
1 ATTTTTAAA
17642728 ATTTTT-AA
1 ATTTTTAAA
*
17642736 ATTTTTGAA
1 ATTTTTAAA
*
17642745 AGTTTTAAA
1 ATTTTTAAA
*
17642754 AGTTTTTAGA
1 A-TTTTTAAA
17642764 ATTT
1 ATTT
17642768 CTATTTTTTA
Statistics
Matches: 110, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
8 16 0.15
9 50 0.45
10 41 0.37
11 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:17642659 original size:11 final size:10
Alignment explanation
Indices: 17642635--17642761 Score: 78
Period size: 10 Copynumber: 13.6 Consensus size: 10
17642625 ATTTTTTAAC
17642635 TTTTTAAAAA
1 TTTTTAAAAA
17642645 TTTTCT-AAAA
1 TTTT-TAAAAA
*
17642655 TTTTTGAAAA
1 TTTTTAAAAA
17642665 --TTTAATAAA
1 TTTTTAA-AAA
*
17642674 TTTTAAAAAA
1 TTTTTAAAAA
*
17642684 ATTTTAAAAA
1 TTTTTAAAAA
17642694 -TTTT-AAAA
1 TTTTTAAAAA
* *
17642702 TTTTTTAGAA
1 TTTTTAAAAA
17642712 -TTTT-AAAA
1 TTTTTAAAAA
*
17642720 TTTTT-TAAA
1 TTTTTAAAAA
17642729 TTTTT--AAA
1 TTTTTAAAAA
*
17642737 TTTTT-GAAA
1 TTTTTAAAAA
* *
17642746 GTTTTAAAAG
1 TTTTTAAAAA
17642756 TTTTTA
1 TTTTTA
17642762 GAATTTCTAT
Statistics
Matches: 96, Mismatches: 11, Indels: 20
0.76 0.09 0.16
Matches are distributed among these distances:
8 19 0.20
9 35 0.36
10 37 0.39
11 5 0.05
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (10 bp):
TTTTTAAAAA
Found at i:17642701 original size:8 final size:8
Alignment explanation
Indices: 17642681--17642759 Score: 59
Period size: 8 Copynumber: 9.0 Consensus size: 8
17642671 AAATTTTAAA
17642681 AAAATTTT
1 AAAATTTT
17642689 AAAAATTTT
1 -AAAATTTT
17642698 AAAATTTTTT
1 AAAA--TTTT
*
17642708 AGAATTTT
1 AAAATTTT
17642716 AAAATTTTTT
1 AAAA--TTTT
*
17642726 AAATTTTT
1 AAAATTTT
*
17642734 AAATTTTT
1 AAAATTTT
*
17642742 GAAAGTTTT
1 -AAAATTTT
17642751 AAAAGTTTT
1 AAAA-TTTT
17642760 TAGAATTTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
8 26 0.44
9 19 0.32
10 14 0.24
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (8 bp):
AAAATTTT
Found at i:17642836 original size:29 final size:30
Alignment explanation
Indices: 17642780--17642842 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
17642770 ATTTTTTATT
17642780 TTTTTTCAATTTTCAAAAAATTGTTTAGAAA
1 TTTTTTCAATTTTCAAAAAATTGTTTAG-AA
**
17642811 TTTTTT-AATTTTCAAAATTTTG-TTAGAA
1 TTTTTTCAATTTTCAAAAAATTGTTTAGAA
17642839 TTTT
1 TTTT
17642843 CAAATAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 6 0.20
29 4 0.13
30 14 0.47
31 6 0.20
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (30 bp):
TTTTTTCAATTTTCAAAAAATTGTTTAGAA
Found at i:17642856 original size:20 final size:20
Alignment explanation
Indices: 17642817--17642857 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17642807 GAAATTTTTT
*
17642817 AATTTTCAAAATTTTGTTAG
1 AATTTTCAAAAGTTTGTTAG
17642837 AATTTTCAAATAGTTT-TTAG
1 AATTTTCAAA-AGTTTGTTAG
17642857 A
1 A
17642858 TTGTTTTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (20 bp):
AATTTTCAAAAGTTTGTTAG
Found at i:17642919 original size:19 final size:20
Alignment explanation
Indices: 17642884--17642921 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17642874 TACAATTTTT
*
17642884 AAAAAAATTTTGGGAATATC
1 AAAAAAATTTTGAGAATATC
17642904 AAAAAAATTTT-AGAATAT
1 AAAAAAATTTTGAGAATAT
17642922 TTAGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAAAAATTTTGAGAATATC
Found at i:17642950 original size:9 final size:9
Alignment explanation
Indices: 17642911--17643028 Score: 60
Period size: 9 Copynumber: 12.4 Consensus size: 9
17642901 ATCAAAAAAA
17642911 TTTTAGAAT
1 TTTTAGAAT
*
17642920 ATTTAG-AT
1 TTTTAGAAT
17642928 TTTTATTTGAAT
1 TTTTA---GAAT
17642940 TTTTAGAATT
1 TTTTAGAA-T
17642950 TTTTAGAAT
1 TTTTAGAAT
* *
17642959 TTCATAAAAT
1 TT-TTAGAAT
**
17642969 TATTTTCAATT
1 T-TTTAGAA-T
*
17642980 TTTTAGATT
1 TTTTAGAAT
*
17642989 TTTTA-ATT
1 TTTTAGAAT
*
17642997 TTTTAAAAT
1 TTTTAGAAT
*
17643006 TTTTAAAATT
1 TTTTAGAA-T
*
17643016 TTTTAAAAT
1 TTTTAGAAT
17643025 TTTT
1 TTTT
17643029 TTGAAAAATT
Statistics
Matches: 88, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
8 14 0.16
9 32 0.36
10 31 0.35
11 4 0.05
12 7 0.08
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTAGAAT
Found at i:17642954 original size:10 final size:10
Alignment explanation
Indices: 17642911--17643029 Score: 81
Period size: 10 Copynumber: 12.4 Consensus size: 10
17642901 ATCAAAAAAA
17642911 TTTTAGAA-T
1 TTTTAGAATT
* *
17642920 ATTTAGATTT
1 TTTTAGAATT
*
17642930 TTATTTGAA-T
1 TT-TTAGAATT
17642940 TTTTAGAATT
1 TTTTAGAATT
17642950 TTTTAGAATT
1 TTTTAGAATT
** *
17642960 TCATAAAATT
1 TTTTAGAATT
*
17642970 ATTTT-CAATT
1 -TTTTAGAATT
17642980 TTTTAG-ATT
1 TTTTAGAATT
17642989 TTTT--AATT
1 TTTTAGAATT
*
17642997 TTTTA-AAAT
1 TTTTAGAATT
*
17643006 TTTTAAAATT
1 TTTTAGAATT
*
17643016 TTTTAAAATT
1 TTTTAGAATT
17643026 TTTT
1 TTTT
17643030 TGAAAAATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
8 7 0.08
9 30 0.34
10 44 0.51
11 6 0.07
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.61
Consensus pattern (10 bp):
TTTTAGAATT
Found at i:17642996 original size:17 final size:17
Alignment explanation
Indices: 17642970--17643028 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
17642960 TCATAAAATT
* *
17642970 ATTTTCAATTTTTTAGA
1 ATTTTTAATTTTTTAAA
*
17642987 TTTTTTAATTTTTTAAA
1 ATTTTTAATTTTTTAAA
17643004 ATTTTTAAAATTTTTTAAA
1 ATTTTT--AATTTTTTAAA
17643023 ATTTTT
1 ATTTTT
17643029 TTGAAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 19 0.53
19 17 0.47
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
ATTTTTAATTTTTTAAA
Found at i:17644564 original size:21 final size:22
Alignment explanation
Indices: 17644531--17644572 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
17644521 AACTAACAAA
* *
17644531 TTAATATATAATTAAA-TAAAT
1 TTAACATAAAATTAAACTAAAT
17644552 TTAACATAAAATTAAACTAAA
1 TTAACATAAAATTAAACTAAA
17644573 ACAATACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAACATAAAATTAAACTAAAT
Found at i:17644792 original size:20 final size:21
Alignment explanation
Indices: 17644764--17644819 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
17644754 AATTAATTAA
17644764 ATTTTAAATTTTAA-AAT-AT
1 ATTTTAAATTTTAATAATAAT
*
17644783 ATTTTAAAATATTAATAATAAT
1 ATTTT-AAATTTTAATAATAAT
*
17644805 ATTTTGATATTTTAA
1 ATTTT-AAATTTTAA
17644820 GCCTATTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 5 0.17
20 8 0.27
21 3 0.10
22 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTTAAATTTTAATAATAAT
Found at i:17645190 original size:14 final size:14
Alignment explanation
Indices: 17645173--17645206 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17645163 TTCATTTAAT
17645173 TTAAAAATTAATTA
1 TTAAAAATTAATTA
**
17645187 TTAAATTTTAATTA
1 TTAAAAATTAATTA
17645201 TTAAAA
1 TTAAAA
17645207 TTCAATAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAAAAATTAATTA
Found at i:17651102 original size:21 final size:21
Alignment explanation
Indices: 17651029--17651105 Score: 66
Period size: 25 Copynumber: 3.5 Consensus size: 21
17651019 ATCCATAACC
* * * *
17651029 CTCCCTTTCTACCCTTAGCTC
1 CTCCCTTTCAACCCTCAGTTT
17651050 CT-CCTTTCAACCCTCAGTGGGTT
1 CTCCCTTTCAACCCTCAGT---TT
*
17651073 CTTCACTTTCAACCCTCAGTTT
1 C-TCCCTTTCAACCCTCAGTTT
17651095 CTCCCTTTCAA
1 CTCCCTTTCAA
17651106 ACTCCCTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
20 13 0.29
21 11 0.24
22 3 0.07
23 2 0.04
24 1 0.02
25 15 0.33
ACGTcount: A:0.14, C:0.40, G:0.08, T:0.38
Consensus pattern (21 bp):
CTCCCTTTCAACCCTCAGTTT
Found at i:17656862 original size:2 final size:2
Alignment explanation
Indices: 17656855--17656882 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17656845 ATTATGAACA
17656855 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
17656883 GAAATAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17660920 original size:22 final size:22
Alignment explanation
Indices: 17660892--17660935 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17660882 CTAAATCTTC
*
17660892 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
17660914 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
17660936 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:17664404 original size:18 final size:18
Alignment explanation
Indices: 17664378--17664412 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17664368 TAATCCATGA
*
17664378 GAACCAGAAGCTTTACCT
1 GAACCAGAAACTTTACCT
*
17664396 GAACTAGAAACTTTACC
1 GAACCAGAAACTTTACC
17664413 CAAAGAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (18 bp):
GAACCAGAAACTTTACCT
Found at i:17664639 original size:23 final size:23
Alignment explanation
Indices: 17664584--17664668 Score: 125
Period size: 23 Copynumber: 3.6 Consensus size: 23
17664574 TTGAAAGGGT
* *
17664584 TCGGCAATGAAGGCCTAAACAGGAT
1 TCGGCAATGAAGGCCTAAA-A-AAG
17664609 TCGGCAATGAAGGCCTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
17664632 TCGGCAATGAAGGCCTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
*
17664655 TCAGCAATGAAGGC
1 TCGGCAATGAAGGC
17664669 TGAAAATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 37 0.65
24 1 0.02
25 19 0.33
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (23 bp):
TCGGCAATGAAGGCCTAAAAAAG
Found at i:17664844 original size:22 final size:22
Alignment explanation
Indices: 17664816--17664859 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17664806 CTAAATCTTC
*
17664816 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
17664838 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
17664860 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:17681306 original size:27 final size:26
Alignment explanation
Indices: 17681252--17681306 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
17681242 GGTGCACAAG
*
17681252 ATTATGATAGGATAAGATAATATGAT
1 ATTATGATAGGATAAGATAATATAAT
*
17681278 ATTATGAATAGGATTAGATTAA-ATAAT
1 ATTATG-ATAGGATAAGA-TAATATAAT
17681305 AT
1 AT
17681307 CATCCTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 16 0.64
28 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.36
Consensus pattern (26 bp):
ATTATGATAGGATAAGATAATATAAT
Found at i:17684888 original size:19 final size:20
Alignment explanation
Indices: 17684864--17684912 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
17684854 CTAACTGGAG
17684864 GAATAAATAGGAATGC-AAT
1 GAATAAATAGGAATGCAAAT
*
17684883 GAATAATTAGGAATGCAAAT
1 GAATAAATAGGAATGCAAAT
17684903 GAATAAATAG
1 GAATAAATAG
17684913 ATAGAGCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (20 bp):
GAATAAATAGGAATGCAAAT
Found at i:17686780 original size:11 final size:11
Alignment explanation
Indices: 17686752--17686784 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
17686742 ACTATTGAAA
*
17686752 AAATTAACTTG
1 AAATTAAATTG
17686763 AAA-TAAATTG
1 AAATTAAATTG
17686773 AAATTAAATTG
1 AAATTAAATTG
17686784 A
1 A
17686785 TTCAACTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (11 bp):
AAATTAAATTG
Found at i:17686870 original size:22 final size:22
Alignment explanation
Indices: 17686826--17686875 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
17686816 AACTCACGAT
*
17686826 TAAAATTCAAATAATTATAATA
1 TAAAATTCAAAAAATTATAATA
* *
17686848 TCAAATTTAAAAAATT-TACATA
1 TAAAATTCAAAAAATTATA-ATA
17686870 TAAAAT
1 TAAAAT
17686876 AATCTGAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAATTCAAAAAATTATAATA
Found at i:17687106 original size:64 final size:64
Alignment explanation
Indices: 17686998--17687122 Score: 191
Period size: 64 Copynumber: 2.0 Consensus size: 64
17686988 ACTTGAAAAG
* *
17686998 CTTAAAAAGAGGGCAACGATGGCACCCAAGTAAAAGTCTTCATCTAAAGCATGATTTACGCAAA
1 CTTAAAAAGAGGGCAACAATGGCACCCAAGTAAAAGTCTTCATCTAAAACATGATTTACGCAAA
*
17687062 CTTAAAAACG-GGGCAACAATGGCACCCAAGTAAAAGT-TTCCATCTAAAACGTGATTTACGC
1 CTTAAAAA-GAGGGCAACAATGGCACCCAAGTAAAAGTCTT-CATCTAAAACATGATTTACGC
17687123 TTCTTTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
63 2 0.04
64 53 0.95
65 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (64 bp):
CTTAAAAAGAGGGCAACAATGGCACCCAAGTAAAAGTCTTCATCTAAAACATGATTTACGCAAA
Found at i:17690098 original size:95 final size:95
Alignment explanation
Indices: 17689881--17690079 Score: 389
Period size: 95 Copynumber: 2.1 Consensus size: 95
17689871 TGATAGAAGG
17689881 GATCGATCCTGTCCTTTACCAGATCGATCCTTTAGTAAAAAGAATCGATCCTATTTTCAACCAGA
1 GATCGATCCTGTCCTTTACCAGATCGATCCTTTAGTAAAAAGAATCGATCCTATTTTCAACCAGA
17689946 ACCGAAAGTTCTCAAGATTTGACAAAAATT
66 ACCGAAAGTTCTCAAGATTTGACAAAAATT
*
17689976 GATCGATCCTGTCCTTTACCAGATCGATCCTTTAGTAAAAAGGATCGATCCTATTTTCAACCAGA
1 GATCGATCCTGTCCTTTACCAGATCGATCCTTTAGTAAAAAGAATCGATCCTATTTTCAACCAGA
17690041 ACCGAAAGTTCTCAAGATTTGACAAAAATT
66 ACCGAAAGTTCTCAAGATTTGACAAAAATT
17690071 GATCGATCC
1 GATCGATCC
17690080 CTTCCTTGTA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 103 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.29
Consensus pattern (95 bp):
GATCGATCCTGTCCTTTACCAGATCGATCCTTTAGTAAAAAGAATCGATCCTATTTTCAACCAGA
ACCGAAAGTTCTCAAGATTTGACAAAAATT
Found at i:17690218 original size:20 final size:20
Alignment explanation
Indices: 17690193--17690249 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
17690183 TTTTTTAGAA
*
17690193 AAGGGATTGATCCCCTACAT
1 AAGGGATCGATCCCCTACAT
17690213 AAGGGATCGATCCCCTACAT
1 AAGGGATCGATCCCCTACAT
*
17690233 AAGGGATCGATCACCTA
1 AAGGGATCGATCCCCTA
17690250 AGGCAAGGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
AAGGGATCGATCCCCTACAT
Found at i:17699516 original size:18 final size:18
Alignment explanation
Indices: 17699468--17699510 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
17699458 ATTAGCATTC
* *
17699468 TTGCATTCATATCAACAT
1 TTGCATTCACATCGACAT
17699486 TTGCATTCACATCGACAT
1 TTGCATTCACATCGACAT
17699504 TTGCATT
1 TTGCATT
17699511 TGCATCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (18 bp):
TTGCATTCACATCGACAT
Found at i:17700050 original size:49 final size:50
Alignment explanation
Indices: 17699966--17700064 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 50
17699956 TTAATAGGTC
* * *
17699966 AAAGTTTCACAGCCTCTGTTTAGGGGGAGCAATTTTCAAACAAG-ATTTT
1 AAAGTTTCAAAACCTCTATTTAGGGGGAGCAATTTTCAAACAAGAATTTT
* * *
17700015 AAAGTTTCAAAACTTCTATTTAGGGGGAGTC-ATTTTGAAATAAGAATTTT
1 AAAGTTTCAAAACCTCTATTTAGGGGGAG-CAATTTTCAAACAAGAATTTT
17700065 TTTTTCCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
49 36 0.86
50 6 0.14
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (50 bp):
AAAGTTTCAAAACCTCTATTTAGGGGGAGCAATTTTCAAACAAGAATTTT
Found at i:17700463 original size:5 final size:6
Alignment explanation
Indices: 17700450--17700478 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
17700440 ATTGTTATAG
17700450 TTAAAA TT-AAA TTAAAA TTAAAA TTAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
17700479 CAACAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TTAAAA
Found at i:17702797 original size:3 final size:3
Alignment explanation
Indices: 17702789--17702833 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
17702779 ATTCATATGC
17702789 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17702834 TATACTGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.