Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 110 of 133
Found at i:21419364 original size:2 final size:2
Alignment explanation
Indices: 21419351--21419389 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
21419341 TCTATATTAC
*
21419351 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21419390 AGGGAGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:21420901 original size:106 final size:110
Alignment explanation
Indices: 21420617--21420938 Score: 265
Period size: 110 Copynumber: 2.9 Consensus size: 110
21420607 TATATTATAA
21420617 ACTTTTATATTTTTAAACAAATATTTATTATACCAAATTTAATAATAAATTGTGTGTTTTTTTAA
1 ACTTTTATATTTTTAAACAAATATTTATTATACCAAATTTAATAATAAATTGTGTGTTTTTTT--
*
21420682 ACTTTTTTAATGTTATATATAATAAAATCTTTTACCTTTTAAATATATTT
64 ACTTTTTTAA--TTATATATAATAAAATCTTTTA-CATTTAAATATATTT
* * * * * * * *
21420732 AATTTTA-CTTTCTAATATAAATA--TA-TA-A--ATTATGTT-ATAATATAATCTTTCTAATAT
1 ACTTTTATATTTTTAA-ACAAATATTTATTATACCA-AAT-TTAATAATA-AAT-TGTGT-GT-T
* * **
21420789 AATTTTACTTTTTTAA-TATATTTAAT-TTA-CTTTCTA-ATTTAAATAT-TTT
59 -TTTTTACTTTTTTAATTATATATAATAAAATCTTT-TACATTTAAATATATTT
21420838 ACTTTTATATTTTTAAACAAATATTTATTATACCAAATTTAATAATAAATTGTGTGTTTTTTTAA
1 ACTTTTATATTTTTAAACAAATATTTATTATACCAAATTTAATAATAAATTGTGTGTTTTTTT--
21420903 ACTTTGTTTAATGTTATATATAATAAAATCTTTTAC
64 ACTTT-TTTAA--TTATATATAATAAAATCTTTTAC
21420939 TTTTTTTTAA
Statistics
Matches: 156, Mismatches: 25, Indels: 53
0.67 0.11 0.23
Matches are distributed among these distances:
106 19 0.12
107 16 0.10
108 12 0.08
109 14 0.09
110 23 0.15
111 14 0.09
112 15 0.10
113 16 0.10
114 11 0.07
115 16 0.10
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (110 bp):
ACTTTTATATTTTTAAACAAATATTTATTATACCAAATTTAATAATAAATTGTGTGTTTTTTTAC
TTTTTTAATTATATATAATAAAATCTTTTACATTTAAATATATTT
Found at i:21421016 original size:224 final size:223
Alignment explanation
Indices: 21420617--21421064 Score: 837
Period size: 224 Copynumber: 2.0 Consensus size: 223
21420607 TATATTATAA
21420617 ACTTTTATATTTTTAAACAAATATTTATTATACCAAATTTAATAATAAATTGTGTGTTTTTTTAA
1 ACTTTTATATTTTTAAACAAATATTTATTATACCAAATTTAATAATAAATTGTGTGTTTTTTTAA
21420682 ACTTTTTTAATGTTATATATAATAAAATCTTTTACCTTTTAAATATATTTAATTTTACTTTCTAA
66 ACTTTTTTAATGTTATATATAATAAAATCTTTTACCTTTTAAATATATTTAATTTTACTTTCTAA
21420747 TATAAATATATAAATTATGTTATAATATAATCTTTCTAATATAATTTTAC-TTTTTTAATATATT
131 TATAAATATATAAATTATGTTATAATATAATCTTTCTAATATAATTTTACTTTTTTTAATATATT
21420811 TAA-TTTACTTTCTAATTTAAATATTTT
196 TAATTTTACTTTCTAATTTAAATATTTT
21420838 ACTTTTATATTTTTAAACAAATATTTATTATACCAAATTTAATAATAAATTGTGTGTTTTTTTAA
1 ACTTTTATATTTTTAAACAAATATTTATTATACCAAATTTAATAATAAATTGTGTGTTTTTTTAA
* *
21420903 ACTTTGTTTAATGTTATATATAATAAAATCTTTTACTTTTTTTTAATATATTTAATTTTACTTTC
66 ACTTT-TTTAATGTTATATATAATAAAATCTTTTAC--CTTTTAAATATATTTAATTTTACTTTC
21420968 TAATATAAATATATAAATTATGTTATAATATAATCTTTCTAATATAATTTTACTTTTTTTAATAT
128 TAATATAAATATATAAATTATGTTATAATATAATCTTTCTAATATAATTTTACTTTTTTTAATAT
21421033 ATTTAATTTTACTTTCTAATTTAAATATTTT
193 ATTTAATTTTACTTTCTAATTTAAATATTTT
21421064 A
1 A
21421065 TTACATAATT
Statistics
Matches: 220, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
221 70 0.32
222 30 0.14
224 78 0.35
225 17 0.08
226 25 0.11
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.54
Consensus pattern (223 bp):
ACTTTTATATTTTTAAACAAATATTTATTATACCAAATTTAATAATAAATTGTGTGTTTTTTTAA
ACTTTTTTAATGTTATATATAATAAAATCTTTTACCTTTTAAATATATTTAATTTTACTTTCTAA
TATAAATATATAAATTATGTTATAATATAATCTTTCTAATATAATTTTACTTTTTTTAATATATT
TAATTTTACTTTCTAATTTAAATATTTT
Found at i:21421433 original size:17 final size:17
Alignment explanation
Indices: 21421413--21421445 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21421403 CCTAATAACA
21421413 AAATTA-CATTAATAATT
1 AAATTATCA-TAATAATT
21421430 AAATTATCATAATAAT
1 AAATTATCATAATAAT
21421446 AGTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTATCATAATAATT
Found at i:21422420 original size:15 final size:15
Alignment explanation
Indices: 21422400--21422432 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
21422390 CTTGGAAAGT
21422400 TTATCTCTTATTGAG
1 TTATCTCTTATTGAG
21422415 TTATCTCTTATTGAG
1 TTATCTCTTATTGAG
21422430 TTA
1 TTA
21422433 AATCTAGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (15 bp):
TTATCTCTTATTGAG
Found at i:21425563 original size:20 final size:20
Alignment explanation
Indices: 21425530--21425569 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21425520 TCCGGTGAAC
21425530 TTTCGACGAAAAAACCCAGA
1 TTTCGACGAAAAAACCCAGA
* *
21425550 TTTCGGCGACAAAACCCAGA
1 TTTCGACGAAAAAACCCAGA
21425570 ATCCGATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.28, G:0.17, T:0.15
Consensus pattern (20 bp):
TTTCGACGAAAAAACCCAGA
Found at i:21425989 original size:16 final size:15
Alignment explanation
Indices: 21425970--21426026 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 15
21425960 ATTTAATATT
21425970 TTTTATTTTTATCTTA
1 TTTTATTTTTAT-TTA
21425986 TTTTTATTTTTATTTA
1 -TTTTATTTTTATTTA
21426002 TTTTCACTTTTT-TTTA
1 TTTT-A-TTTTTATTTA
*
21426018 TTCTATTTT
1 TTTTATTTT
21426027 CTTTAAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 5 0.14
16 11 0.30
17 17 0.46
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTATTTA
Found at i:21425991 original size:17 final size:16
Alignment explanation
Indices: 21425918--21426019 Score: 70
Period size: 16 Copynumber: 6.4 Consensus size: 16
21425908 CATTTATTTG
21425918 TTTATTTGTT-TTTTTA
1 TTTATTT-TTATTTTTA
21425934 TTT-TTTTTATTTATTA
1 TTTATTTTTATTT-TTA
* ** *
21425950 GATTAGGTTTA-TTTAA
1 -TTTATTTTTATTTTTA
*
21425966 TAT-TTTTTATTTTTA
1 TTTATTTTTATTTTTA
21425981 TCTTATTTTTATTTTTA
1 T-TTATTTTTATTTTTA
*
21425998 TTTATTTTCACTTTTT-
1 TTTATTTTTA-TTTTTA
21426014 TTTATT
1 TTTATT
21426020 CTATTTTCTT
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
14 6 0.09
15 12 0.18
16 23 0.34
17 22 0.33
18 4 0.06
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.75
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:21426016 original size:21 final size:22
Alignment explanation
Indices: 21425988--21426027 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21425978 TTATCTTATT
21425988 TTTATTTTTATT-TATTTTCAC
1 TTTATTTTTATTCTATTTTCAC
21426009 TTT-TTTTTATTCTATTTTC
1 TTTATTTTTATTCTATTTTC
21426028 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTATTTTTATTCTATTTTCAC
Found at i:21426131 original size:57 final size:58
Alignment explanation
Indices: 21426053--21426266 Score: 299
Period size: 57 Copynumber: 3.7 Consensus size: 58
21426043 AAAGTTCCAA
* *
21426053 AAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
1 AAAAAATAGTTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
21426110 AAAAAATA-TTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAATAGTTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * * *
21426167 AAAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAGATAAATTTTA
1 AAAAAATA--GTTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
21426227 AAAAAATATTTTTTGGAGAAAAGTTGAAAGTATCAATTTT
1 AAAAAATAGTTTTTGGAGAAAAGTTGAAAGTATCAATTTT
21426267 TCCTACACAA
Statistics
Matches: 140, Mismatches: 12, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
57 60 0.43
58 28 0.20
59 4 0.03
60 48 0.34
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.36
Consensus pattern (58 bp):
AAAAAATAGTTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:21426783 original size:5 final size:5
Alignment explanation
Indices: 21426773--21426800 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
21426763 TTATAAGATT
21426773 TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT
21426801 ATAAGAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:21427887 original size:2 final size:2
Alignment explanation
Indices: 21427880--21427916 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
21427870 ATCAATTTAA
* *
21427880 AT AT AT AT AT AT AT AT AC AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21427917 CATACACACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:21428300 original size:29 final size:29
Alignment explanation
Indices: 21428267--21428331 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
21428257 TTTAAACATG
21428267 ATACAAATAAATAAGAATAACACAAATAT
1 ATACAAATAAATAAGAATAACACAAATAT
* * * * **
21428296 ATACAATTAGATACGATTAACATGAATAT
1 ATACAAATAAATAAGAATAACACAAATAT
21428325 ATACAAA
1 ATACAAA
21428332 CACGCGAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.25
Consensus pattern (29 bp):
ATACAAATAAATAAGAATAACACAAATAT
Found at i:21432266 original size:21 final size:21
Alignment explanation
Indices: 21432240--21432283 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
21432230 AACAAATTCC
21432240 ACTCTCATCATATCAGAAATT
1 ACTCTCATCATATCAGAAATT
21432261 ACTCTCATCATATCAGAAATT
1 ACTCTCATCATATCAGAAATT
21432282 AC
1 AC
21432284 ATCAACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (21 bp):
ACTCTCATCATATCAGAAATT
Found at i:21435225 original size:27 final size:27
Alignment explanation
Indices: 21435195--21435253 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
21435185 ATTTATCAAA
* *
21435195 TAAATTTTTTTTAAAAATTATTTAAAT
1 TAAATTATTTTGAAAAATTATTTAAAT
* *
21435222 TAAA-TATTTTGGATAATTATTTAAAT
1 TAAATTATTTTGAAAAATTATTTAAAT
21435248 TGAAAT
1 T-AAAT
21435254 CAAAATCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (27 bp):
TAAATTATTTTGAAAAATTATTTAAAT
Found at i:21435231 original size:26 final size:27
Alignment explanation
Indices: 21435202--21435253 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
21435192 AAATAAATTT
*
21435202 TTTTTAAAAATTATTTAAATT-AAATA
1 TTTTGAAAAATTATTTAAATTGAAATA
* *
21435228 TTTTGGATAATTATTTAAATTGAAAT
1 TTTTGAAAAATTATTTAAATTGAAAT
21435254 CAAAATCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (27 bp):
TTTTGAAAAATTATTTAAATTGAAATA
Found at i:21438351 original size:16 final size:16
Alignment explanation
Indices: 21438319--21438367 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
21438309 ATATTGAGAT
*
21438319 AATTATTAAAATATTAA
1 AATTATT-AATTATTAA
*
21438336 AATTATTCATTATT-A
1 AATTATTAATTATTAA
21438351 AATTATTAATT-TTAA
1 AATTATTAATTATTAA
21438366 AA
1 AA
21438368 AGTAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 2 0.07
15 14 0.50
16 5 0.18
17 7 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTATTAATTATTAA
Found at i:21438539 original size:24 final size:22
Alignment explanation
Indices: 21438491--21438539 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
21438481 ATTAATTTAA
*
21438491 TATTATTAAAAATAATAATATT
1 TATTATTAAAAATAAAAATATT
*
21438513 TATTATTCAAATATAAAAAATATT
1 TATTATT-AAAAAT-AAAAATATT
21438537 TAT
1 TAT
21438540 ACGATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 5 0.22
24 11 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTATTAAAAATAAAAATATT
Found at i:21439360 original size:18 final size:17
Alignment explanation
Indices: 21439323--21439364 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
21439313 ATATTATGTC
21439323 AATATTTTTTATAAAAA
1 AATATTTTTTATAAAAA
21439340 AATTATTTTTTAGT-AAAA
1 AA-TATTTTTTA-TAAAAA
21439358 AATATTT
1 AATATTT
21439365 AAATTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.30
18 15 0.65
19 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AATATTTTTTATAAAAA
Found at i:21440541 original size:22 final size:22
Alignment explanation
Indices: 21440516--21440560 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21440506 TCTCATTTTT
*
21440516 ATTACTTATTCTTAATTTATTA
1 ATTACTTATTATTAATTTATTA
* *
21440538 ATTACTTTTTATTATTTTATTA
1 ATTACTTATTATTAATTTATTA
21440560 A
1 A
21440561 AGAAATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTACTTATTATTAATTTATTA
Found at i:21441732 original size:10 final size:10
Alignment explanation
Indices: 21441717--21441750 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
21441707 GCTGCCAGAA
21441717 AAAAAAAAAG
1 AAAAAAAAAG
21441727 AAAAAAAAAG
1 AAAAAAAAAG
*
21441737 AAAAAAAAAT
1 AAAAAAAAAG
21441747 AAAA
1 AAAA
21441751 GGAATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:21447237 original size:16 final size:17
Alignment explanation
Indices: 21447215--21447263 Score: 82
Period size: 16 Copynumber: 2.9 Consensus size: 17
21447205 TATGCTTGAA
21447215 AAAAAAAAAGAAAAAAT
1 AAAAAAAAAGAAAAAAT
*
21447232 AAAAAAATA-AAAAAAT
1 AAAAAAAAAGAAAAAAT
21447248 AAAAAAAAAGAAAAAA
1 AAAAAAAAAGAAAAAA
21447264 AAATGAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.90, C:0.00, G:0.04, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAT
Found at i:21447257 original size:33 final size:32
Alignment explanation
Indices: 21447215--21447277 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
21447205 TATGCTTGAA
21447215 AAAAAAAAAGAAAAAATAAAAAAATAAAAAAAT
1 AAAAAAAAAGAAAAAA-AAAAAAATAAAAAAAT
**
21447248 AAAAAAAAAGAAAAAAAAATGAATAAAAAA
1 AAAAAAAAAGAAAAAAAAAAAAATAAAAAA
21447278 GGAAGACTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.87, C:0.00, G:0.05, T:0.08
Consensus pattern (32 bp):
AAAAAAAAAGAAAAAAAAAAAAATAAAAAAAT
Found at i:21447277 original size:1 final size:1
Alignment explanation
Indices: 21447213--21447266 Score: 63
Period size: 1 Copynumber: 54.0 Consensus size: 1
21447203 ACTATGCTTG
* * * * *
21447213 AAAAAAAAAAAGAAAAAATAAAAAAATAAAAAAATAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21447267 TGAATAAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.91, C:0.00, G:0.04, T:0.06
Consensus pattern (1 bp):
A
Found at i:21448339 original size:41 final size:41
Alignment explanation
Indices: 21448282--21448368 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
21448272 TCAATGAAGT
*
21448282 AATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGC
1 AATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGC
**
21448323 AATTTACTTTCCAAAGTTGTGGTGCCTCTGTTTAGAGGAGC
1 AATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGC
21448364 AATTT
1 AATTT
21448369 GGTGCCTCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (41 bp):
AATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGC
Found at i:21448371 original size:26 final size:26
Alignment explanation
Indices: 21448342--21448394 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
21448332 TCCAAAGTTG
21448342 TGGTGCCTCTGTTTAGAGGAGCAATT
1 TGGTGCCTCTGTTTAGAGGAGCAATT
21448368 TGGTGCCTCTGTTTAGAGGAGCAATT
1 TGGTGCCTCTGTTTAGAGGAGCAATT
21448394 T
1 T
21448395 ACTTTCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.36
Consensus pattern (26 bp):
TGGTGCCTCTGTTTAGAGGAGCAATT
Found at i:21448412 original size:67 final size:67
Alignment explanation
Indices: 21448301--21448435 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
21448291 TTCAAAGTCA
*
21448301 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAA
1 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
21448366 TT
66 TT
21448368 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
1 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
21448433 TT
66 TT
21448435 T
1 T
21448436 ACTTTTCAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.36
Consensus pattern (67 bp):
TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
TT
Found at i:21448425 original size:41 final size:41
Alignment explanation
Indices: 21448368--21448572 Score: 252
Period size: 41 Copynumber: 5.0 Consensus size: 41
21448358 AGGAGCAATT
21448368 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG
1 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG
* *
21448409 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGTTG
1 TGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCCAAAGTCG
* * **
21448451 TGGTGCCTCTGTTTATAGGAGCAATTTACATTT-CAAACTTT
1 TGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCCAAAGTCG
* * * *
21448492 TGTTGCCTCTTTTTAGAGGAGTAATTTACTTTTCAAAGTCG
1 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG
* *
21448533 TGGTGCCTCTGTTTAGA-TAGGCAATTTATTTTTCCAAAGT
1 TGGTGCCTCTGTTTAGAGGA-GCAATTTA-CTTTCCAAAGT
21448573 TGTTGAGCCT
Statistics
Matches: 140, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
40 4 0.03
41 86 0.61
42 50 0.36
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (41 bp):
TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG
Found at i:21448507 original size:83 final size:82
Alignment explanation
Indices: 21448368--21448549 Score: 267
Period size: 83 Copynumber: 2.2 Consensus size: 82
21448358 AGGAGCAATT
*
21448368 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
1 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAACTCGTGGTGCCTCTGTTTAGAGGAGCAA
*
21448433 TTTACTTTTCAAAAGTTG
66 TTTACTTTTC-AAAGTCG
* ** * * *
21448451 TGGTGCCTCTGTTTATAGGAGCAATTTACATTT-CAAACTTTTGTTGCCTCTTTTTAGAGGAGTA
1 TGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCCAAACTCGTGGTGCCTCTGTTTAGAGGAGCA
21448515 ATTTACTTTTCAAAGTCG
65 ATTTACTTTTCAAAGTCG
21448533 TGGTGCCTCTGTTTAGA
1 TGGTGCCTCTGTTTAGA
21448550 TAGGCAATTT
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
82 22 0.25
83 64 0.72
84 3 0.03
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (82 bp):
TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAACTCGTGGTGCCTCTGTTTAGAGGAGCAA
TTTACTTTTCAAAGTCG
Found at i:21448583 original size:83 final size:84
Alignment explanation
Indices: 21448368--21448585 Score: 261
Period size: 83 Copynumber: 2.6 Consensus size: 84
21448358 AGGAGCAATT
* * * *
21448368 TGGTGCCTCTGTTTAGA-GGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 TGGTGCCTCTGTTTAGATAGAGCAATTTAATTTCCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCA
*
21448432 ATTTACTTTTCAAAAGTTG
66 ATTTACTTTTCAAAAGTCG
* *
21448451 TGGTGCCTCTGTTT--ATAGGAGCAATTTACATTT-CAAACTT-TTGTTGCCTCTTTTTAGAGGA
1 TGGTGCCTCTGTTTAGATA-GAGCAATTTA-ATTTCCAAAGTTGTTG-TGCCTCTGTTTAGAGGA
*
21448512 GTAATTTACTTTTC-AAAGTCG
63 GCAATTTACTTTTCAAAAGTCG
* *
21448533 TGGTGCCTCTGTTTAGATAG-GCAATTTATTTTTCCAAAGTTGTTGAGCCTCTG
1 TGGTGCCTCTGTTTAGATAGAGCAATTTA-ATTTCCAAAGTTGTTGTGCCTCTG
21448586 ATTACAAGAG
Statistics
Matches: 114, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
81 1 0.01
82 33 0.29
83 71 0.62
84 9 0.08
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (84 bp):
TGGTGCCTCTGTTTAGATAGAGCAATTTAATTTCCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCA
ATTTACTTTTCAAAAGTCG
Found at i:21448602 original size:124 final size:124
Alignment explanation
Indices: 21448366--21448602 Score: 341
Period size: 124 Copynumber: 1.9 Consensus size: 124
21448356 AGAGGAGCAA
*
21448366 TTTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
1 TTTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAAGAGC
* * * *
21448431 AATTTACTTTTCAAAAGTTGTGGTGCCTCTGTTTATAGGAGCAATTTACATTTCAAACT
66 AATTTACTTTTCAAAAGTTGTGGAGCCTCTGATTACAAGAGCAATTTACATTTCAAACT
* * * *
21448490 TTTGTTGCCTCTTTTTAGAGGAGTAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGATAG-G
1 TTTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGA-AGAG
* * * *
21448554 CAATTTATTTTTCCAAAGTTGTTGAGCCTCTGATTACAAGAGCCATTTA
65 CAATTTACTTTTCAAAAGTTGTGGAGCCTCTGATTACAAGAGCAATTTA
21448603 TGTTTCTTAA
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
124 98 0.99
125 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (124 bp):
TTTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAAGAGC
AATTTACTTTTCAAAAGTTGTGGAGCCTCTGATTACAAGAGCAATTTACATTTCAAACT
Found at i:21448667 original size:8 final size:8
Alignment explanation
Indices: 21448656--21448685 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
21448646 CAAAAACAAA
21448656 AAAAAAAT
1 AAAAAAAT
*
21448664 AAAAAAAC
1 AAAAAAAT
21448672 AAAAAAAT
1 AAAAAAAT
21448680 AAAAAA
1 AAAAAA
21448686 TATCGAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.07
Consensus pattern (8 bp):
AAAAAAAT
Found at i:21448848 original size:13 final size:13
Alignment explanation
Indices: 21448832--21448929 Score: 74
Period size: 13 Copynumber: 7.4 Consensus size: 13
21448822 TCTATTTTCT
21448832 TTTTTTTTTTTTA
1 TTTTTTTTTTTTA
*
21448845 TTTTTATTTTTTA
1 TTTTTTTTTTTTA
***
21448858 TTTTACATTTTTA
1 TTTTTTTTTTTTA
*
21448871 --TTTTATTTTTA
1 TTTTTTTTTTTTA
21448882 TTTTTATTTTTATTA
1 TTTTT-TTTTT-TTA
* *
21448897 TTTTTTATATATATA
1 TTTTTT-T-TTTTTA
*
21448912 TTTTTTTCTTTTA
1 TTTTTTTTTTTTA
21448925 TTTTT
1 TTTTT
21448930 ATCTTAGGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
11 9 0.13
13 33 0.49
14 6 0.09
15 17 0.25
16 2 0.03
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTTTTA
Found at i:21448875 original size:31 final size:30
Alignment explanation
Indices: 21448834--21448891 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
21448824 TATTTTCTTT
*
21448834 TTTTTTTTTTATTTTTATTTTTTATTTTACA
1 TTTTTATTTTATTTTTA-TTTTTATTTTACA
21448865 TTTTTATTTTATTTTTATTTTTATTTT
1 TTTTTATTTTATTTTTATTTTTATTTT
21448892 TATTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.83
Consensus pattern (30 bp):
TTTTTATTTTATTTTTATTTTTATTTTACA
Found at i:21448924 original size:43 final size:40
Alignment explanation
Indices: 21448824--21448931 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 40
21448814 TAGGTAAGTC
*
21448824 TATTTTCTTTTTTTTTTTTTATTTTTATTTTTTATTTTACA
1 TATTTT-TTTTTTTATTTTTATTTTTATTTTTTATTTTACA
* *
21448865 TTTTTATTTTATTTTTATTTTTATTTTTATTATTTT-TTATATATA
1 -TATT-TTTT-TTTTTATTTTTATTTTTATT-TTTTATT-T-TACA
21448910 TATTTTTTTCTTTTATTTTTAT
1 TATTTTTTT-TTTTATTTTTAT
21448932 CTTAGGTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
42 6 0.11
43 39 0.70
44 8 0.14
45 3 0.05
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.80
Consensus pattern (40 bp):
TATTTTTTTTTTTATTTTTATTTTTATTTTTTATTTTACA
Found at i:21448929 original size:6 final size:6
Alignment explanation
Indices: 21448833--21448931 Score: 94
Period size: 6 Copynumber: 16.2 Consensus size: 6
21448823 CTATTTTCTT
* *
21448833 TTTTTT TTTTTA TTTTTA TTTTTTA TTTTACA TTTTTA -TTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTT-TA TTTTTA TTTTTA TTTTTA
* * * *
21448882 TTTTTA TTTTTA TTATTT- TTTATA TATATA TTTTTT TCTTTTA TTTTTA
1 TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA T-TTTTA TTTTTA
21448931 T
1 T
21448932 CTTAGGTATT
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
5 7 0.09
6 52 0.67
7 19 0.24
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:21449960 original size:5 final size:5
Alignment explanation
Indices: 21449895--21450006 Score: 52
Period size: 5 Copynumber: 21.6 Consensus size: 5
21449885 TTTTTTAAAA
* * * * * *
21449895 TTTA- TTTA- TTTA- TTTAT TTAAT TATTAG ATTAT GTTTAT TTAAT ATTCT
1 TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT TTTAT -TTTAT TTTAT TTTAT
* *
21449944 TTTAT CTTTAT TTTATT TTTATT TTTGT TTTACT TTT-T TTTAT TTGTTT
1 TTTAT -TTTAT TTTA-T TTTA-T TTTAT TTTA-T TTTAT TTTAT TT-TAT
21449993 TATTAT TTTAT TTT
1 T-TTAT TTTAT TTT
21450007 CTTTAGATAA
Statistics
Matches: 83, Mismatches: 16, Indels: 17
0.72 0.14 0.15
Matches are distributed among these distances:
4 16 0.19
5 35 0.42
6 31 0.37
7 1 0.01
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:21449974 original size:11 final size:10
Alignment explanation
Indices: 21449950--21450006 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 10
21449940 TTCTTTTATC
21449950 TTTATTTTATT
1 TTTATTTT-TT
21449961 TTTATTTTTGT
1 TTTATTTTT-T
*
21449972 TTTACTTTTT
1 TTTATTTTTT
21449982 TTTATTTGTTT
1 TTTATTT-TTT
21449993 TATTATTTTATT
1 T-TTATTTT-TT
21450005 TT
1 TT
21450007 CTTTAGATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 8 0.20
11 23 0.57
12 9 0.22
ACGTcount: A:0.14, C:0.02, G:0.04, T:0.81
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:21449989 original size:19 final size:17
Alignment explanation
Indices: 21449943--21450006 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
21449933 TTTAATATTC
* *
21449943 TTTTATCTTTATTTTAT
1 TTTTATTTTTGTTTTAT
21449960 TTTTATTTTTGTTTTACT
1 TTTTATTTTTGTTTTA-T
*
21449978 TTTTTTTATTTGTTTTATT
1 TTTTATT-TTTGTTTTA-T
21449997 ATTTTATTTT
1 -TTTTATTTT
21450007 CTTTAGATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
17 14 0.36
18 7 0.18
19 12 0.31
20 6 0.15
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTATTTTTGTTTTAT
Found at i:21450001 original size:27 final size:27
Alignment explanation
Indices: 21449933--21450011 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
21449923 ATTATGTTTA
* * *
21449933 TTTAATATTCTTTTATCTTTATTTTATT
1 TTTATTATTATTTTA-CTTTTTTTTATT
* *
21449961 TTTATTTTTGTTTTACTTTTTTTTATT
1 TTTATTATTATTTTACTTTTTTTTATT
*
21449988 TGTT-TTATTATTTTA-TTTTCTTTA
1 T-TTATTATTATTTTACTTTTTTTTA
21450012 GATAAAATCC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 8 0.19
27 21 0.49
28 14 0.33
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (27 bp):
TTTATTATTATTTTACTTTTTTTTATT
Found at i:21450149 original size:31 final size:31
Alignment explanation
Indices: 21450114--21450208 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
21450104 GAAAGTATCA
21450114 ATTTTTCTCGAAATTAAAGTTTCCAAAAATT
1 ATTTTTCTCGAAATTAAAGTTTCCAAAAATT
* * * *
21450145 A-TTTT-T-GAAA-AAAAG-TT-GAAAGTATCA
1 ATTTTTCTCGAAATTAAAGTTTCCAAA-AAT-T
* *
21450172 ATTTTCCTCGAAATTAAAGTTTCCAAAAAAT
1 ATTTTTCTCGAAATTAAAGTTTCCAAAAATT
21450203 ATTTTT
1 ATTTTT
21450209 GGAAAAAATT
Statistics
Matches: 45, Mismatches: 11, Indels: 16
0.62 0.15 0.22
Matches are distributed among these distances:
25 3 0.07
26 4 0.09
27 5 0.11
28 7 0.16
29 2 0.04
30 8 0.18
31 10 0.22
32 3 0.07
33 3 0.07
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (31 bp):
ATTTTTCTCGAAATTAAAGTTTCCAAAAATT
Found at i:21450167 original size:58 final size:58
Alignment explanation
Indices: 21450024--21450470 Score: 383
Period size: 58 Copynumber: 7.7 Consensus size: 58
21450014 TAAAATCCAA
* * ** * *
21450024 AAAAAATATTTTTGTGAAAAAA-TTGAAAGTATCAATTTTTCTTAAAAATAAA-TTT-T
1 AAAAATTATTTTTG-AAAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
* *** **
21450080 TAAAACGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
1 AAAAATTATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
*
21450138 AAAAATTATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCC
1 AAAAATTATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
* * * ** * * *
21450196 AAAAAATATTTTTGGAAAAAATTTGAAAGTATCAATTTTT-TAAAAAAATAAATTTTCA
1 AAAAATTATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCT-CGAAATTAAAGTTTCC
* * * * * * *
21450254 AAAAAGGTTTTTTTTTTTTGAGAAAAAGTTGAAAGTATCAA-TTTTCCCTAAAAATAAATTTTCA
1 AAAAA------TTATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTC-GAAATTAAAGTTTCC
**
21450318 AAAAAGTT-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTT-C
1 AAAAA-TTATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
* * * *
21450375 AAAAGA-TA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCGAGATTAAAATTTCT
1 AAAA-ATTATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
* * *
21450432 AAAAA-AATATTTTGGAAAAAAGTTGAATGTATCAATTTT
1 AAAAATTAT-TTTTGAAAAAAAGTTGAAAGTATCAATTTT
21450471 CCCTAAACAA
Statistics
Matches: 324, Mismatches: 49, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
55 4 0.01
56 84 0.26
57 12 0.04
58 167 0.52
59 8 0.02
63 4 0.01
64 45 0.14
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (58 bp):
AAAAATTATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
Found at i:21450175 original size:27 final size:27
Alignment explanation
Indices: 21450145--21450243 Score: 67
Period size: 27 Copynumber: 3.5 Consensus size: 27
21450135 TCCAAAAATT
21450145 ATTTTTGAAAAAAAGTTGAAAGTATCA
1 ATTTTTGAAAAAAAGTTGAAAGTATCA
* * **
21450172 ATTTTCCTCGAAATTAAAGTTTCCAAAAAAT--
1 ATTTT--T-GAAA-AAAAG-TT-GAAAGTATCA
* *
21450203 ATTTTTGGAAAAAATTTGAAAGTATCA
1 ATTTTTGAAAAAAAGTTGAAAGTATCA
*
21450230 ATTTTTTAAAAAAA
1 ATTTTTGAAAAAAA
21450244 TAAATTTTCA
Statistics
Matches: 52, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
25 5 0.10
26 2 0.04
27 20 0.38
28 3 0.06
29 2 0.04
30 4 0.08
31 9 0.17
32 2 0.04
33 5 0.10
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.36
Consensus pattern (27 bp):
ATTTTTGAAAAAAAGTTGAAAGTATCA
Found at i:21450322 original size:122 final size:114
Alignment explanation
Indices: 21450097--21450470 Score: 380
Period size: 122 Copynumber: 3.2 Consensus size: 114
21450087 GTTTTTGAGG
** * *
21450097 AAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCCAAAA-ATTATTTTTGAAAAAAAGT
1 AAAAGTTGAAAGTATCAATTTTTCTAAAAAATAAAGTTT-CAAAAGA-T-TTTTTGAGAAAAAGT
* *
21450161 TGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCCAAAAAATATTTTTGGAA
63 TGAAAGTATCAATTTTCCTCGAAATTAAAATTTCAAAAAAATATTTTTGGAA
* * *
21450213 AAAATTTGAAAGTATCAATTTTT-TAAAAAAATAAATTTTCAAAAAAGGTTTTTTTTTTTTGAGA
1 AAAAGTTGAAAGTATCAATTTTTCT-AAAAAATAAAGTTTC--AAAA-G-----ATTTTTTGAGA
* * * * * *
21450277 AAAAGTTGAAAGTATCAATTTTCC-CTAAAAATAAATTTTCAAAAAAGT-TTTTTTGAGG
57 AAAAGTTGAAAGTATCAATTTTCCTC-GAAATTAAAATTTCAAAAAAATATTTTTGGA-A
** * *
21450335 AAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCAAAAGATATTTTGAGAAAAAGTTGA
1 AAAAGTTGAAAGTATCAATTTTTCTAAAAAATAAAGTTTCAAAAGATTTTTTGAGAAAAAGTTGA
* *
21450400 AAGTATCAATTTTTCTCGAGATTAAAATTTCTAAAAAAATA-TTTTGGAA
66 AAGTATCAATTTTCCTCGAAATTAAAATTTC-AAAAAAATATTTTTGGAA
*
21450449 AAAAGTTGAATGTATCAATTTT
1 AAAAGTTGAAAGTATCAATTTT
21450471 CCCTAAACAA
Statistics
Matches: 212, Mismatches: 30, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
114 63 0.30
115 16 0.08
116 32 0.15
117 4 0.02
119 1 0.00
120 4 0.02
121 8 0.04
122 82 0.39
123 2 0.01
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (114 bp):
AAAAGTTGAAAGTATCAATTTTTCTAAAAAATAAAGTTTCAAAAGATTTTTTGAGAAAAAGTTGA
AAGTATCAATTTTCCTCGAAATTAAAATTTCAAAAAAATATTTTTGGAA
Found at i:21450342 original size:180 final size:178
Alignment explanation
Indices: 21450088--21450413 Score: 487
Period size: 180 Copynumber: 1.8 Consensus size: 178
21450078 TTTAAAACGG
* * * * *
21450088 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCCAAAAATTATTTTTGA
1 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAAAATTATTTTTGA
21450153 AAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCCAAAAAATATTTTTG-GAAAAAA
66 AAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTT-CAAAAAATA-TTTTGAG-AAAAA
*
21450217 TTTGAAAGTATCAATTTTTTAAAAAAATAAATTTTCAAAAAAGGTTTTTTT
128 GTTGAAAGTATCAATTTTTTAAAAAAATAAATTTTCAAAAAAGGTTTTTTT
*
21450268 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCC-CTAAAAATAAATTTTCAAAAAAGTT-TTTTT
1 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTC-AAAAATAAAGTTTCAAAAAA-TTATTTTT
** * *
21450331 GAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCAAAAGATATTTTGAGAAAAAG
64 GAAAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCAAAAAATATTTTGAGAAAAAG
21450396 TTGAAAGTATCAATTTTT
129 TTGAAAGTATCAATTTTT
21450414 CTCGAGATTA
Statistics
Matches: 132, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
178 28 0.21
179 10 0.08
180 92 0.70
181 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.38
Consensus pattern (178 bp):
TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAAAATTATTTTTGA
AAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCAAAAAATATTTTGAGAAAAAGTT
GAAAGTATCAATTTTTTAAAAAAATAAATTTTCAAAAAAGGTTTTTTT
Found at i:21450466 original size:236 final size:236
Alignment explanation
Indices: 21450032--21450470 Score: 688
Period size: 236 Copynumber: 1.9 Consensus size: 236
21450022 AAAAAAAATA
* * * * *
21450032 TTTTTGTGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTAAAACGGTTTTTGAGG
1 TTTTTGAGAAAAAATTGAAAGTATCAATTTTCCCTAAAAATAAATTTTAAAAAAGGTTTTTGAGG
21450097 AAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCCAAAAATTATTTTTGAAAAAAAGTT
66 AAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCCAAAAATTATTTTTGAAAAAAAGTT
* * *
21450162 GAAAGTATCAATTTTCCTCGAAATTAAAGTTTCCAAAAAATATTTTTGGAAAAAATTTGAAAGTA
131 GAAAGTATCAATTTTCCTCGAAATTAAAATTTCAAAAAAATATTTTTGGAAAAAAGTTGAAAGTA
21450227 TCAATTTTTTAAAAAAATAAATTTTCAAAAAAGGTTTTTTT
196 TCAATTTTTTAAAAAAATAAATTTTCAAAAAAGGTTTTTTT
* *
21450268 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCCTAAAAATAAATTTTCAAAAAAGTTTTTTTGA
1 TTTTTGAGAAAAAATTGAAAGTATCAATTTTCCCTAAAAATAAATTTT-AAAAAAG-GTTTTTGA
*
21450333 GGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTT-CAAAAGA-TA-TTTTGAGAAAAA
64 GGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCCAAAA-ATTATTTTTGAAAAAAA
* *
21450395 GTTGAAAGTATCAATTTTTCTCGAGATTAAAATTTCTAAAAAAATA-TTTTGGAAAAAAGTTGAA
128 GTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTC-AAAAAAATATTTTTGGAAAAAAGTTGAA
*
21450459 TGTATCAATTTT
192 AGTATCAATTTT
21450471 CCCTAAACAA
Statistics
Matches: 185, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
236 116 0.63
237 20 0.11
238 49 0.26
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (236 bp):
TTTTTGAGAAAAAATTGAAAGTATCAATTTTCCCTAAAAATAAATTTTAAAAAAGGTTTTTGAGG
AAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCCAAAAATTATTTTTGAAAAAAAGTT
GAAAGTATCAATTTTCCTCGAAATTAAAATTTCAAAAAAATATTTTTGGAAAAAAGTTGAAAGTA
TCAATTTTTTAAAAAAATAAATTTTCAAAAAAGGTTTTTTT
Found at i:21454641 original size:31 final size:30
Alignment explanation
Indices: 21454567--21454669 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
21454557 TAAAGTTTTA
* *
21454567 GGTTTTAGGGTTT-TTGTTTTAAGATTTTG
1 GGTTTTAGGGTTTATAGTTTTAAGATTTCG
* *
21454596 AGATTTTAGAGTTTATAGTTTTAAGATTTCG
1 -GGTTTTAGGGTTTATAGTTTTAAGATTTCG
* * *
21454627 GGTTTTAAGGGTTTAGAGTTTT-TGATTTCA
1 GGTTTT-AGGGTTTATAGTTTTAAGATTTCG
*
21454657 GGTTTTAGTGTTT
1 GGTTTTAGGGTTT
21454670 CAAAATTTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
29 6 0.10
30 28 0.46
31 27 0.44
ACGTcount: A:0.19, C:0.02, G:0.25, T:0.53
Consensus pattern (30 bp):
GGTTTTAGGGTTTATAGTTTTAAGATTTCG
Found at i:21454689 original size:15 final size:16
Alignment explanation
Indices: 21454666--21454700 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
21454656 AGGTTTTAGT
21454666 GTTTCAAAATTTAAAG
1 GTTTCAAAATTTAAAG
*
21454682 GTTT-AAAATTTTAAG
1 GTTTCAAAATTTAAAG
21454697 GTTT
1 GTTT
21454701 TAAGGGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (16 bp):
GTTTCAAAATTTAAAG
Found at i:21454701 original size:8 final size:8
Alignment explanation
Indices: 21454690--21454736 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
21454680 AGGTTTAAAA
21454690 TTTTAAGG
1 TTTTAAGG
21454698 TTTTAAGGG
1 TTTTAA-GG
21454707 TTTTAAGG
1 TTTTAAGG
* *
21454715 GTTT-CGAG
1 TTTTAAG-G
21454723 TTTTAAGG
1 TTTTAAGG
21454731 TTTTAA
1 TTTTAA
21454737 AATTTAGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
7 1 0.03
8 22 0.69
9 9 0.28
ACGTcount: A:0.23, C:0.02, G:0.26, T:0.49
Consensus pattern (8 bp):
TTTTAAGG
Found at i:21454702 original size:16 final size:16
Alignment explanation
Indices: 21454666--21454741 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
21454656 AGGTTTTAGT
* *
21454666 GTTTCAAAATTTAAAG
1 GTTTTAAAATTTTAAG
21454682 G-TTTAAAATTTTAAG
1 GTTTTAAAATTTTAAG
**
21454697 GTTTTAAGGGTTTTAAG
1 GTTTTAA-AATTTTAAG
* ** *
21454714 GGTTTCGAGTTTTAAG
1 GTTTTAAAATTTTAAG
21454730 GTTTTAAAATTT
1 GTTTTAAAATTT
21454742 AGGGTTTAGG
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
15 13 0.28
16 22 0.48
17 11 0.24
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.46
Consensus pattern (16 bp):
GTTTTAAAATTTTAAG
Found at i:21454710 original size:9 final size:9
Alignment explanation
Indices: 21454690--21454718 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
21454680 AGGTTTAAAA
21454690 TTTTAA-GG
1 TTTTAAGGG
21454698 TTTTAAGGG
1 TTTTAAGGG
21454707 TTTTAAGGG
1 TTTTAAGGG
21454716 TTT
1 TTT
21454719 CGAGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (9 bp):
TTTTAAGGG
Found at i:21455237 original size:3 final size:3
Alignment explanation
Indices: 21455229--21455286 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
21455219 TCATTTTCAT
21455229 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21455277 TTA TTA TTA T
1 TTA TTA TTA T
21455287 CTCGTTATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21456781 original size:20 final size:20
Alignment explanation
Indices: 21456756--21456797 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
21456746 TTATTATTTG
*
21456756 TATTT-ATTATTATATTTTAA
1 TATTTAATTATCA-ATTTTAA
21456776 TATTTAATTATCAATTTTAA
1 TATTTAATTATCAATTTTAA
21456796 TA
1 TA
21456798 AAATTAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTAATTATCAATTTTAA
Found at i:21459874 original size:12 final size:13
Alignment explanation
Indices: 21459824--21459904 Score: 62
Period size: 12 Copynumber: 6.4 Consensus size: 13
21459814 TTTAATATAA
21459824 ATATGAAATTAAAT
1 ATAT-AAATTAAAT
*
21459838 ATATATAAATAAAT
1 ATATA-AATTAAAT
*
21459852 ACATAAA-TAAAT
1 ATATAAATTAAAT
21459864 ATA-AAATTAAAT
1 ATATAAATTAAAT
*
21459876 A-ATTAATTAAA-
1 ATATAAATTAAAT
* * *
21459887 AAATAATTTATAT
1 ATATAAATTAAAT
21459900 ATATA
1 ATATA
21459905 TCGGATCAGG
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
11 5 0.09
12 27 0.50
13 7 0.13
14 15 0.28
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (13 bp):
ATATAAATTAAAT
Found at i:21461017 original size:30 final size:30
Alignment explanation
Indices: 21460978--21461052 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
21460968 ATTAATTATT
*
21460978 TAAT-TTTTTATTTATATATATTTATATAA
1 TAATATTTTTATTTATATATATTTATAAAA
* ** * *
21461007 TGATATTTTTAAATATTTATATTTTTAAAA
1 TAATATTTTTATTTATATATATTTATAAAA
21461037 TAATATTTTATATTTA
1 TAATATTTT-TATTTA
21461053 AAAAAATTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 3 0.09
30 28 0.80
31 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TAATATTTTTATTTATATATATTTATAAAA
Found at i:21461022 original size:18 final size:18
Alignment explanation
Indices: 21461001--21461040 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
21460991 ATATATATTT
21461001 ATATAATGATATTTTTAA
1 ATATAATGATATTTTTAA
*
21461019 ATAT--TTATATTTTTAA
1 ATATAATGATATTTTTAA
21461035 A-ATAAT
1 ATATAAT
21461041 ATTTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
15 2 0.11
16 12 0.63
17 1 0.05
18 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATATAATGATATTTTTAA
Found at i:21461043 original size:20 final size:19
Alignment explanation
Indices: 21461017--21461067 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
21461007 TGATATTTTT
21461017 AAATATTTATATTTTTAAA
1 AAATATTTATATTTTTAAA
*
21461036 ATAATATTT-TATATTTAAA
1 A-AATATTTATATTTTTAAA
21461055 AAA-A-TTATATTTT
1 AAATATTTATATTTT
21461068 ATTAATTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 2 0.07
19 11 0.39
20 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATATTTATATTTTTAAA
Found at i:21464546 original size:24 final size:21
Alignment explanation
Indices: 21464518--21464561 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
21464508 ATTGTTTTAA
21464518 TTTTAATAATAATAATAATAATAT
1 TTTTAATAA-AA-AATAA-AATAT
21464542 TTTTAATAAAAAATAAAATA
1 TTTTAATAAAAAATAAAATA
21464562 AAATAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 2 0.10
24 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTAATAAAAAATAAAATAT
Found at i:21464574 original size:27 final size:27
Alignment explanation
Indices: 21464525--21464591 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
21464515 TAATTTTAAT
*
21464525 AATAATAATAATAATATTTTTAATAAA-A
1 AATAA-AATAA-AATATTATTAATAAACA
21464553 AATAAAATAAAATAATTATTAATAAACA
1 AATAAAATAAAAT-ATTATTAATAAACA
*
21464581 AA-AAAAAAAAA
1 AATAAAATAAAA
21464592 CAAACAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 3 0.09
27 24 0.69
28 8 0.23
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (27 bp):
AATAAAATAAAATATTATTAATAAACA
Found at i:21464598 original size:17 final size:17
Alignment explanation
Indices: 21464576--21464610 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21464566 AATTATTAAT
21464576 AAACAAAAAAAAAAAAC
1 AAACAAAAAAAAAAAAC
* *
21464593 AAACAAACAAAAGAAAC
1 AAACAAAAAAAAAAAAC
21464610 A
1 A
21464611 GAAAACGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (17 bp):
AAACAAAAAAAAAAAAC
Found at i:21465142 original size:16 final size:16
Alignment explanation
Indices: 21465121--21465155 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21465111 TTGAGTTTTC
21465121 AAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAGA
* *
21465137 AAAAAAAAAGAACAGA
1 AAAAAAAAAAAAAAGA
21465153 AAA
1 AAA
21465156 CTTTGAACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGA
Found at i:21465728 original size:17 final size:16
Alignment explanation
Indices: 21465685--21465729 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
21465675 GAACTTTCTA
* *
21465685 ATTTTTTTATATTATT
1 ATTTTTTTATTTTAGT
21465701 ATTTTTGTTATTTTAAGT
1 ATTTTT-TTATTTT-AGT
21465719 ATTTTTTTATT
1 ATTTTTTTATT
21465730 GATGCATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.24
17 11 0.44
18 8 0.32
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (16 bp):
ATTTTTTTATTTTAGT
Found at i:21465823 original size:17 final size:16
Alignment explanation
Indices: 21465776--21465825 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
21465766 GTTTAATTGT
21465776 TTAAATAATAATAA-AA
1 TTAAA-AATAATAATAA
*
21465792 TTAAAAACAAGTAATAA
1 TTAAAAATAA-TAATAA
21465809 TTAAAAATATATAATAA
1 TTAAAAATA-ATAATAA
21465826 AAATGTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 8 0.28
17 16 0.55
18 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
TTAAAAATAATAATAA
Found at i:21466108 original size:19 final size:19
Alignment explanation
Indices: 21466084--21466121 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21466074 AACACTAATT
21466084 TTTAATTTTCAAAATCCTA
1 TTTAATTTTCAAAATCCTA
21466103 TTTAATTTTCAAAATCCTA
1 TTTAATTTTCAAAATCCTA
21466122 AGTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAATTTTCAAAATCCTA
Found at i:21466175 original size:16 final size:15
Alignment explanation
Indices: 21466156--21466204 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
21466146 AAAATCTCTT
21466156 AAATCCAAACCCCATA
1 AAATCCAAACCCC-TA
*
21466172 AAATTCGAAACCCCTA
1 AAA-TCCAAACCCCTA
* *
21466188 AAATTCAAACCCTTA
1 AAATCCAAACCCCTA
21466203 AA
1 AA
21466205 TCAAAACTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 11 0.39
16 8 0.29
17 9 0.32
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (15 bp):
AAATCCAAACCCCTA
Found at i:21466199 original size:15 final size:15
Alignment explanation
Indices: 21466156--21466204 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
21466146 AAAATCTCTT
*
21466156 AAATCCAAACCCCATA
1 AAATTCAAACCCC-TA
21466172 AAATTCGAAACCCCTA
1 AAATTC-AAACCCCTA
*
21466188 AAATTCAAACCCTTA
1 AAATTCAAACCCCTA
21466203 AA
1 AA
21466205 TCAAAACTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 10 0.33
16 13 0.43
17 7 0.23
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (15 bp):
AAATTCAAACCCCTA
Found at i:21471451 original size:17 final size:17
Alignment explanation
Indices: 21471431--21471463 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21471421 CCTAATAACA
21471431 AAATTA-CATTAATAATT
1 AAATTATCA-TAATAATT
21471448 AAATTATCATAATAAT
1 AAATTATCATAATAAT
21471464 AGTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTATCATAATAATT
Found at i:21472171 original size:16 final size:17
Alignment explanation
Indices: 21472150--21472182 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21472140 CTTAATCGAA
21472150 TTTTTA-TATTTAAATT
1 TTTTTATTATTTAAATT
*
21472166 TTTTTATTATTTTAATT
1 TTTTTATTATTTAAATT
21472183 AATAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTATTTAAATT
Found at i:21474391 original size:18 final size:18
Alignment explanation
Indices: 21474365--21474489 Score: 105
Period size: 18 Copynumber: 6.9 Consensus size: 18
21474355 CTTTGTTCTT
*
21474365 GATACATTTGAGGTTGAG
1 GATACATTTGAGGTGGAG
* *
21474383 GATATATTTGA---GGAT
1 GATACATTTGAGGTGGAG
*
21474398 GATACATTTGTGGTGGAG
1 GATACATTTGAGGTGGAG
* * * *
21474416 GGTACATTTGTGGT-AACT
1 GATACATTTGAGGTGGA-G
21474434 GATACATTTGAGGTGGAG
1 GATACATTTGAGGTGGAG
*
21474452 GATATATTTGAGGAGGTGGAG
1 GATACATTT---GAGGTGGAG
21474473 GATACATTTGAGGTGGA
1 GATACATTTGAGGTGGA
21474490 TAATAACCAT
Statistics
Matches: 84, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
15 11 0.13
17 1 0.01
18 54 0.64
19 1 0.01
21 17 0.20
ACGTcount: A:0.27, C:0.05, G:0.35, T:0.33
Consensus pattern (18 bp):
GATACATTTGAGGTGGAG
Found at i:21474440 original size:36 final size:33
Alignment explanation
Indices: 21474364--21474465 Score: 132
Period size: 36 Copynumber: 3.0 Consensus size: 33
21474354 CCTTTGTTCT
*
21474364 TGATACATTTGAGGTTGAGGATATATTTGAGGA
1 TGATACATTTGAGGTGGAGGATATATTTGAGGA
* * * *
21474397 TGATACATTTGTGGTGGAGGGTACATTTGTGGTAA
1 TGATACATTTGAGGTGGAGGATATATTTGAGG--A
21474432 CTGATACATTTGAGGTGGAGGATATATTTGAGGA
1 -TGATACATTTGAGGTGGAGGATATATTTGAGGA
21474466 GGTGGAGGAT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 27 0.47
34 1 0.02
35 1 0.02
36 28 0.49
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.35
Consensus pattern (33 bp):
TGATACATTTGAGGTGGAGGATATATTTGAGGA
Found at i:21474467 original size:21 final size:21
Alignment explanation
Indices: 21474443--21474485 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
21474433 TGATACATTT
*
21474443 GAGGTGGAGGATATATTTGAG
1 GAGGTGGAGGATACATTTGAG
21474464 GAGGTGGAGGATACATTTGAG
1 GAGGTGGAGGATACATTTGAG
21474485 G
1 G
21474486 TGGATAATAA
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:0.28, C:0.02, G:0.44, T:0.26
Consensus pattern (21 bp):
GAGGTGGAGGATACATTTGAG
Found at i:21478319 original size:26 final size:26
Alignment explanation
Indices: 21478270--21478318 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
21478260 TTTCAAAAAT
*
21478270 TAAAAGTTTTCAAACTTATATTTTAA
1 TAAAAGTTTTCAAACCTATATTTTAA
21478296 TAAAA-TTTTCAAACCTATATTTT
1 TAAAAGTTTTCAAACCTATATTTT
21478319 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (26 bp):
TAAAAGTTTTCAAACCTATATTTTAA
Found at i:21478574 original size:19 final size:20
Alignment explanation
Indices: 21478550--21478587 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21478540 AACAACAAAA
*
21478550 AAAATTA-AAATTCATATAC
1 AAAATTATAAATTAATATAC
21478569 AAAATTATAAATTAATATA
1 AAAATTATAAATTAATATA
21478588 TAACACAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTATAAATTAATATAC
Found at i:21481874 original size:2 final size:2
Alignment explanation
Indices: 21481867--21481905 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
21481857 ATCAATTTAA
* *
21481867 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21481906 CATACACACA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:21483822 original size:30 final size:30
Alignment explanation
Indices: 21483786--21483860 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
21483776 TTCAATTCTG
*
21483786 ATATCACTTGTTAGGATTACGACTA-CTCTA
1 ATATCACTTGTTAGGATCACGA-TAGCTCTA
* *
21483816 ATATCACTTATTAGGATCACGATAGTTCTA
1 ATATCACTTGTTAGGATCACGATAGCTCTA
*
21483846 ATATCACATGTTAGG
1 ATATCACTTGTTAGG
21483861 CAAAAAGGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 2 0.05
30 37 0.95
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (30 bp):
ATATCACTTGTTAGGATCACGATAGCTCTA
Found at i:21492321 original size:15 final size:14
Alignment explanation
Indices: 21492294--21492332 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
21492284 TAATTATCAA
21492294 AATATTAAAATTATTT
1 AATATT-AAATTA-TT
*
21492310 ATTATTAAATTATT
1 AATATTAAATTATT
21492324 AATATTAAA
1 AATATTAAA
21492333 AAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 10 0.48
15 6 0.29
16 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATATTAAATTATT
Found at i:21492505 original size:24 final size:22
Alignment explanation
Indices: 21492457--21492505 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
21492447 ATTAATTTAA
*
21492457 TATTATTAAAAATAATAATATT
1 TATTATTAAAAATAAAAATATT
*
21492479 TATTATTCAAATATAAAAAATATT
1 TATTATT-AAAAAT-AAAAATATT
21492503 TAT
1 TAT
21492506 ACGATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 5 0.22
24 11 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTATTAAAAATAAAAATATT
Found at i:21493447 original size:13 final size:13
Alignment explanation
Indices: 21493429--21493463 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
21493419 TTTAAGAAAA
*
21493429 TATTTTTTGTTTT
1 TATTTTTTATTTT
21493442 TATTTTTTATTTT
1 TATTTTTTATTTT
*
21493455 CATTTTTTA
1 TATTTTTTA
21493464 GAAAATAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:21494756 original size:13 final size:13
Alignment explanation
Indices: 21494738--21494769 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
21494728 TTATTATAAA
21494738 TTTTATTAATTAT
1 TTTTATTAATTAT
21494751 TTTTATTAATTAT
1 TTTTATTAATTAT
*
21494764 TATTAT
1 TTTTAT
21494770 AAAACAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATTAATTAT
Found at i:21495698 original size:1 final size:1
Alignment explanation
Indices: 21495692--21495716 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21495682 CCGTTGCCAG
21495692 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
21495717 GAGAAGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21496354 original size:34 final size:34
Alignment explanation
Indices: 21496313--21496377 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
21496303 CCAAATATAA
21496313 TTTTTAGAAAACAAAAATAAAAAATAAAAACTAT
1 TTTTTAGAAAACAAAAATAAAAAATAAAAACTAT
*
21496347 TTTTTAGAAAATAAAAATAAAAAATAAAAAC
1 TTTTTAGAAAACAAAAATAAAAAATAAAAAC
21496378 AAAAAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (34 bp):
TTTTTAGAAAACAAAAATAAAAAATAAAAACTAT
Found at i:21496372 original size:13 final size:13
Alignment explanation
Indices: 21496354--21496385 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
21496344 TATTTTTTAG
*
21496354 AAAATAAAAATAA
1 AAAATAAAAACAA
21496367 AAAATAAAAACAA
1 AAAATAAAAACAA
21496380 AAAATA
1 AAAATA
21496386 TTTTCTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAATAAAAACAA
Found at i:21503665 original size:9 final size:9
Alignment explanation
Indices: 21503651--21503680 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
21503641 GATATTTTAT
21503651 TAATTAAAA
1 TAATTAAAA
21503660 TAATTAAAA
1 TAATTAAAA
21503669 TATATTAAAA
1 TA-ATTAAAA
21503679 TA
1 TA
21503681 TAAAAGCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:21503677 original size:10 final size:10
Alignment explanation
Indices: 21503653--21503682 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21503643 TATTTTATTA
21503653 ATTAAAATA-
1 ATTAAAATAT
21503662 ATTAAAATAT
1 ATTAAAATAT
21503672 ATTAAAATAT
1 ATTAAAATAT
21503682 A
1 A
21503683 AAAGCTTGAT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:21507790 original size:28 final size:27
Alignment explanation
Indices: 21507758--21507817 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 27
21507748 TTGTATTTTT
21507758 AATTAAATTTAAATATT-AATTTTAATAA
1 AATTAAA-TT-AATATTAAATTTTAATAA
*
21507786 AATTAAATTAATATTAAAATTTTATTAA
1 AATTAAATTAATATT-AAATTTTAATAA
21507814 AATT
1 AATT
21507818 TTTTAATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.21
27 2 0.07
28 21 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AATTAAATTAATATTAAATTTTAATAA
Found at i:21507844 original size:25 final size:25
Alignment explanation
Indices: 21507816--21507863 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
21507806 TTTATTAAAA
* *
21507816 TTTTTTAATCATAATTACAATAATC
1 TTTTTAAATCAAAATTACAATAATC
* *
21507841 TTTTTAAATTAAAATTATAATAA
1 TTTTTAAATCAAAATTACAATAA
21507864 ATTTTATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTTAAATCAAAATTACAATAATC
Found at i:21515845 original size:19 final size:20
Alignment explanation
Indices: 21515811--21515869 Score: 102
Period size: 19 Copynumber: 3.0 Consensus size: 20
21515801 TGGAAATTAT
21515811 GCAATGAATAAAGAAATCAC
1 GCAATGAATAAAGAAATCAC
*
21515831 GCAATGAAT-AAGAAATCAT
1 GCAATGAATAAAGAAATCAC
21515850 GCAATGAATAAAGAAATCAC
1 GCAATGAATAAAGAAATCAC
21515870 CCAAGAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.54, C:0.14, G:0.15, T:0.17
Consensus pattern (20 bp):
GCAATGAATAAAGAAATCAC
Found at i:21516710 original size:32 final size:33
Alignment explanation
Indices: 21516649--21516717 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 33
21516639 TTAGTAATTA
21516649 AAAATAATAAAATAATTAATGAAAATATTTT-T
1 AAAATAATAAAATAATTAATGAAAATATTTTAT
21516681 AAAATAA-AAAATAA-T-ATAGAAAATTTATTTTAT
1 AAAATAATAAAATAATTAAT-GAAAA--TATTTTAT
21516714 AAAA
1 AAAA
21516718 AACCAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
29 2 0.06
30 6 0.18
31 7 0.21
32 13 0.39
33 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (33 bp):
AAAATAATAAAATAATTAATGAAAATATTTTAT
Found at i:21517232 original size:6 final size:6
Alignment explanation
Indices: 21517225--21517255 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
21517215 TCAATTTTTG
*
21517225 TCTCTG TCTCTT TCTCTT TCTCTT TCTCTT T
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT T
21517256 TTTTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (6 bp):
TCTCTT
Found at i:21517272 original size:16 final size:16
Alignment explanation
Indices: 21517251--21517281 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21517241 TTTCTCTTTC
*
21517251 TCTTTTTTTATTTTAT
1 TCTTTTTTTAATTTAT
21517267 TCTTTTTTTAATTTA
1 TCTTTTTTTAATTTA
21517282 CTTTTTCTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTTTTTTAATTTAT
Found at i:21517415 original size:19 final size:18
Alignment explanation
Indices: 21517375--21517426 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
21517365 ATTTTTCATT
* *
21517375 TTTTTTCCTTTATTATGTC
1 TTTTTT-CTTTTTTATATC
21517394 TTTTTTCTTTTTTATATAC
1 TTTTTTCTTTTTTATAT-C
*
21517413 TTTTCTCTTTTTTA
1 TTTTTTCTTTTTTA
21517427 ATTATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.12, C:0.13, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTTCTTTTTTATATC
Found at i:21518732 original size:92 final size:92
Alignment explanation
Indices: 21518575--21518761 Score: 347
Period size: 92 Copynumber: 2.0 Consensus size: 92
21518565 TCAAGTCTTA
21518575 AACTAGTTTACTGTAAAAAAACAAAGTTTAAGAGATTTATCTTCTTTTGAAAGTGAAAAGGAGAG
1 AACTAGTTTACTGTAAAAAAACAAAGTTTAAGAGATTTATCTTCTTTTGAAAGTGAAAAGGAGAG
21518640 AATTTGGCAGAATTTCTACACATTTTC
66 AATTTGGCAGAATTTCTACACATTTTC
*
21518667 AACTAGTTTATTGTAAAAAAACAAAGTTTAAGAGATTTATCTTCTTTTGAAAGTGAAAAGGAGAG
1 AACTAGTTTACTGTAAAAAAACAAAGTTTAAGAGATTTATCTTCTTTTGAAAGTGAAAAGGAGAG
* *
21518732 AGTTTGGTAGAATTTCTACACATTTTC
66 AATTTGGCAGAATTTCTACACATTTTC
21518759 AAC
1 AAC
21518762 ATTAAACAAC
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (92 bp):
AACTAGTTTACTGTAAAAAAACAAAGTTTAAGAGATTTATCTTCTTTTGAAAGTGAAAAGGAGAG
AATTTGGCAGAATTTCTACACATTTTC
Found at i:21523898 original size:31 final size:33
Alignment explanation
Indices: 21523838--21523914 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 33
21523828 TAGTAATTAA
21523838 AAATAATAAAATAATTAATGAAAAATATTTT-T
1 AAATAATAAAATAATTAATGAAAAATATTTTAT
*
21523870 AAATAA-AAAATAA-T-ATAGAAAATTTATTTTAT
1 AAATAATAAAATAATTAAT-GAAAA-ATATTTTAT
*
21523902 AAAAAACTAAAAT
1 AAATAA-TAAAAT
21523915 TTTAATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 2 0.05
30 6 0.16
31 13 0.34
32 12 0.32
34 5 0.13
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (33 bp):
AAATAATAAAATAATTAATGAAAAATATTTTAT
Found at i:21524038 original size:12 final size:12
Alignment explanation
Indices: 21524021--21524051 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
21524011 TTTATTTTTA
21524021 TTTTTTTTC-TC
1 TTTTTTTTCATC
21524032 TTTTTTTTCATC
1 TTTTTTTTCATC
21524044 TTTTTTTT
1 TTTTTTTT
21524052 TTAAATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTCATC
Found at i:21524433 original size:21 final size:21
Alignment explanation
Indices: 21524407--21524458 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
21524397 CACGTGTCAA
21524407 CTCTTTCATTTAATTTTTTTT
1 CTCTTTCATTTAATTTTTTTT
* *
21524428 CTCTTTCTCTTTCATTTTTTTT
1 CTCTTTC-ATTTAATTTTTTTT
*
21524450 -TATTTCATT
1 CTCTTTCATT
21524459 CTTTTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 12 0.46
22 12 0.46
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (21 bp):
CTCTTTCATTTAATTTTTTTT
Found at i:21524457 original size:15 final size:15
Alignment explanation
Indices: 21524437--21524466 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21524427 TCTCTTTCTC
*
21524437 TTTCATTTTTTTTTA
1 TTTCATTCTTTTTTA
21524452 TTTCATTCTTTTTTA
1 TTTCATTCTTTTTTA
21524467 AGTTACTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCATTCTTTTTTA
Found at i:21527544 original size:19 final size:19
Alignment explanation
Indices: 21527512--21527561 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
21527502 AAACAAATTG
21527512 AAACATTGAAATAATAAATA
1 AAACATT-AAATAATAAATA
*
21527532 AAACATTAAATAATAAATG
1 AAACATTAAATAATAAATA
21527551 AAACATTAAAT
1 AAACATTAAAT
21527562 GGATATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (19 bp):
AAACATTAAATAATAAATA
Found at i:21529154 original size:18 final size:19
Alignment explanation
Indices: 21529110--21529174 Score: 64
Period size: 18 Copynumber: 3.5 Consensus size: 19
21529100 AATTTTGAAA
21529110 ATTAAAAAA-ATCTAAAATT
1 ATTAAAAAATAT-TAAAATT
** *
21529129 -TTTTAAAATATT-AACTT
1 ATTAAAAAATATTAAAATT
21529146 ATTAAAAAATATTAAAATT
1 ATTAAAAAATATTAAAATT
*
21529165 TTTAAAAAAT
1 ATTAAAAAAT
21529175 TCTTAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
17 4 0.11
18 17 0.47
19 15 0.42
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAAAAATATTAAAATT
Found at i:21529518 original size:11 final size:11
Alignment explanation
Indices: 21529502--21529537 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
21529492 AAATATTTAA
21529502 TTTTTTAATTT
1 TTTTTTAATTT
*
21529513 TTTTTTACTTT
1 TTTTTTAATTT
*
21529524 TTTTTTTATTT
1 TTTTTTAATTT
21529535 TTT
1 TTT
21529538 AAAAGCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTAATTT
Found at i:21529519 original size:19 final size:19
Alignment explanation
Indices: 21529497--21529539 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
21529487 TTTAAAAATA
21529497 TTTAATTTTTTAATTT-TTT
1 TTTAATTTTTT-ATTTATTT
* *
21529516 TTTACTTTTTTTTTTATTT
1 TTTAATTTTTTATTTATTT
21529535 TTTAA
1 TTTAA
21529540 AAGCTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTAATTTTTTATTTATTT
Found at i:21544843 original size:3 final size:3
Alignment explanation
Indices: 21544835--21544866 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
21544825 TACATAAACA
*
21544835 AAG AAG AAG AAG AAG AAG TAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
21544867 AGAAAATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:21547076 original size:19 final size:20
Alignment explanation
Indices: 21547052--21547092 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
21547042 TGAATGTGTT
*
21547052 AAAGAATGA-GAGAGGATTA
1 AAAGAATCATGAGAGGATTA
*
21547071 AAAGAATCATTAGAGGATTA
1 AAAGAATCATGAGAGGATTA
21547091 AA
1 AA
21547093 TCAGCTGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.20
Consensus pattern (20 bp):
AAAGAATCATGAGAGGATTA
Found at i:21550647 original size:2 final size:2
Alignment explanation
Indices: 21550640--21550672 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
21550630 TTTTGATGAT
*
21550640 TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
21550673 GTCTGTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:21551685 original size:21 final size:20
Alignment explanation
Indices: 21551647--21551685 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
21551637 TTATATTATT
* *
21551647 AAATAATTTATATTATATAA
1 AAATAATATATATAATATAA
21551667 AAATAAATATATATAATAT
1 AAAT-AATATATATAATAT
21551686 TATAGTATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAATATATATAATATAA
Found at i:21554635 original size:14 final size:14
Alignment explanation
Indices: 21554607--21554645 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
21554597 AAGAAATGAA
21554607 AAAAAAAATAGAAAG
1 AAAAAAAA-AGAAAG
* *
21554622 GAAATAAAAGAAAG
1 AAAAAAAAAGAAAG
21554636 AAAAAAAAAG
1 AAAAAAAAAG
21554646 GGAGTATTCG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:21554752 original size:28 final size:29
Alignment explanation
Indices: 21554719--21554793 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
21554709 GAGAAAGAAA
21554719 AAAAAAAG-AGAATAA-AAAGAAAT-AAGG
1 AAAAAAAGAAGAATAAGAAAG-AATGAAGG
*
21554746 AAGAAAAGAAGAATAAGAAAGAATGAAGG
1 AAAAAAAGAAGAATAAGAAAGAATGAAGG
21554775 -AAAAAAGAA-AATCAAGAAA
1 AAAAAAAGAAGAAT-AAGAAA
21554794 AAAAACTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 10 0.24
28 24 0.57
29 8 0.19
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.07
Consensus pattern (29 bp):
AAAAAAAGAAGAATAAGAAAGAATGAAGG
Found at i:21554763 original size:25 final size:25
Alignment explanation
Indices: 21554735--21554783 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21554725 AGAGAATAAA
*
21554735 AAGAAATAAGGAA-GAAAAGAAGAAT
1 AAGAAAGAAGGAAGGAAAA-AAGAAT
*
21554760 AAGAAAGAATGAAGGAAAAAAGAA
1 AAGAAAGAAGGAAGGAAAAAAGAA
21554784 AATCAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.06
Consensus pattern (25 bp):
AAGAAAGAAGGAAGGAAAAAAGAAT
Found at i:21558239 original size:19 final size:19
Alignment explanation
Indices: 21558215--21558259 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
21558205 TCTTTATATT
*
21558215 TATGCTTTTGAAAGTGTCA
1 TATGCTTTTGAAAATGTCA
*
21558234 TATGCTTTTGAAAATGTCC
1 TATGCTTTTGAAAATGTCA
21558253 TATGCTT
1 TATGCTT
21558260 GCTTTGAATT
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:0.24, C:0.13, G:0.18, T:0.44
Consensus pattern (19 bp):
TATGCTTTTGAAAATGTCA
Found at i:21558591 original size:23 final size:22
Alignment explanation
Indices: 21558565--21558625 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
21558555 TATATTATAT
21558565 TTTATCTTTTTATTTTCACTTTA
1 TTTATCTTTTTATTTT-ACTTTA
* * *
21558588 TTTATCTATATATATTTATTTTA
1 TTTATCTTTTTAT-TTTACTTTA
*
21558611 TTTATCCTTTTATTT
1 TTTATCTTTTTATTT
21558626 AATTTAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 2 0.06
23 26 0.84
24 3 0.10
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATCTTTTTATTTTACTTTA
Found at i:21562426 original size:20 final size:20
Alignment explanation
Indices: 21562401--21562440 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
21562391 AATGACTCTA
*
21562401 CAAAATAATAGGCATGATAT
1 CAAAATAATAAGCATGATAT
21562421 CAAAATAATAAGCATGATAT
1 CAAAATAATAAGCATGATAT
21562441 TAGATGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (20 bp):
CAAAATAATAAGCATGATAT
Found at i:21564848 original size:12 final size:12
Alignment explanation
Indices: 21564833--21564862 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21564823 GATAAATGCT
21564833 TATATAAATAAA
1 TATATAAATAAA
*
21564845 TATATAAATATA
1 TATATAAATAAA
21564857 TATATA
1 TATATA
21564863 TAGTAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TATATAAATAAA
Found at i:21571100 original size:3 final size:3
Alignment explanation
Indices: 21571092--21571194 Score: 89
Period size: 3 Copynumber: 34.3 Consensus size: 3
21571082 GTAGGCTCAA
* * * * * * *
21571092 CTT CTT CTT CTA CTC CTC CTT CTT CTT CTA CTC CTT CTT CTT CTA CTC
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * *
21571140 CTC CTT CTT CTT CTT CTT CAT CTT CTA CTC CTC CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
21571188 CAT CTT C
1 CTT CTT C
21571195 AGACTTTTCA
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.06, C:0.41, G:0.00, T:0.53
Consensus pattern (3 bp):
CTT
Found at i:21571115 original size:15 final size:15
Alignment explanation
Indices: 21571095--21571180 Score: 100
Period size: 15 Copynumber: 5.5 Consensus size: 15
21571085 GGCTCAACTT
21571095 CTTCTTCTACTCCTCC
1 CTTCTTCTACTCCT-C
*
21571111 TTCTTCTTCTACTCCTT
1 --CTTCTTCTACTCCTC
21571128 CTTCTTCTACTCCTC
1 CTTCTTCTACTCCTC
* * *
21571143 CTTCTTCTTCTTCTT
1 CTTCTTCTACTCCTC
*
21571158 CATCTTCTACTCCTC
1 CTTCTTCTACTCCTC
21571173 CTTCTTCT
1 CTTCTTCT
21571181 TCTTCTTCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
15 44 0.76
18 14 0.24
ACGTcount: A:0.06, C:0.42, G:0.00, T:0.52
Consensus pattern (15 bp):
CTTCTTCTACTCCTC
Found at i:21571115 original size:18 final size:18
Alignment explanation
Indices: 21571092--21571183 Score: 112
Period size: 18 Copynumber: 5.6 Consensus size: 18
21571082 GTAGGCTCAA
21571092 CTTCTTCTTCTACTCCTC
1 CTTCTTCTTCTACTCCTC
21571110 CTTCTTCTTCTA---CTC
1 CTTCTTCTTCTACTCCTC
21571125 CTTCTTCTTCTACTCCTC
1 CTTCTTCTTCTACTCCTC
21571143 CTTCTTC-T-T-CT--T-
1 CTTCTTCTTCTACTCCTC
*
21571155 CTTCATCTTCTACTCCTC
1 CTTCTTCTTCTACTCCTC
21571173 CTTCTTCTTCT
1 CTTCTTCTTCT
21571184 TCTTCATCTT
Statistics
Matches: 63, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
12 6 0.10
13 2 0.03
14 1 0.02
15 19 0.30
16 1 0.02
17 2 0.03
18 32 0.51
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.53
Consensus pattern (18 bp):
CTTCTTCTTCTACTCCTC
Found at i:21571184 original size:30 final size:30
Alignment explanation
Indices: 21571092--21571194 Score: 161
Period size: 30 Copynumber: 3.3 Consensus size: 30
21571082 GTAGGCTCAA
*
21571092 CTTCTTCTTCTACTCCTCCTTCTTCTTCTACT
1 CTTCATCTTCTACTCCTCCTTCTTCTTCT--T
*
21571124 CCTTCTTCTTCTACTCCTCCTTCTTCTTCTT
1 -CTTCATCTTCTACTCCTCCTTCTTCTTCTT
21571155 CTTCATCTTCTACTCCTCCTTCTTCTTCTT
1 CTTCATCTTCTACTCCTCCTTCTTCTTCTT
21571185 CTTCATCTTC
1 CTTCATCTTC
21571195 AGACTTTTCA
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
30 39 0.57
31 1 0.01
33 29 0.42
ACGTcount: A:0.06, C:0.41, G:0.00, T:0.53
Consensus pattern (30 bp):
CTTCATCTTCTACTCCTCCTTCTTCTTCTT
Found at i:21571184 original size:33 final size:33
Alignment explanation
Indices: 21571092--21571194 Score: 149
Period size: 33 Copynumber: 3.2 Consensus size: 33
21571082 GTAGGCTCAA
* *
21571092 CTTCTTCTTCTACTCCTCCTTCTTCTTCTACTC
1 CTTCTTCTTCTACTCCTCCTTCTTCTTCTTCTT
21571125 CTTCTTCTTCTACTCCT-C--CTTCTTCTTCTT
1 CTTCTTCTTCTACTCCTCCTTCTTCTTCTTCTT
*
21571155 CTTCATCTTCTACTCCTCCTTCTTCTTCTTCTT
1 CTTCTTCTTCTACTCCTCCTTCTTCTTCTTCTT
*
21571188 CATCTTC
1 CTTCTTC
21571195 AGACTTTTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
30 26 0.42
31 1 0.02
32 1 0.02
33 34 0.55
ACGTcount: A:0.06, C:0.41, G:0.00, T:0.53
Consensus pattern (33 bp):
CTTCTTCTTCTACTCCTCCTTCTTCTTCTTCTT
Found at i:21575247 original size:2 final size:2
Alignment explanation
Indices: 21575240--21575268 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21575230 GCACATAGAA
21575240 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
21575269 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:21575273 original size:2 final size:2
Alignment explanation
Indices: 21575268--21575300 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21575258 TCTCTCTCTC
21575268 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21575301 CAAATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21578150 original size:23 final size:23
Alignment explanation
Indices: 21578124--21578168 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21578114 TATACTAAAT
21578124 AAAAAAATCT-AAAATAATATATC
1 AAAAAAA-CTGAAAATAATATATC
* *
21578147 AAAATAACTGATAATAATATAT
1 AAAAAAACTGAAAATAATATAT
21578169 ACTATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAAAAACTGAAAATAATATATC
Found at i:21583136 original size:17 final size:17
Alignment explanation
Indices: 21583116--21583150 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
21583106 TTGATTTTAG
*
21583116 ATCCATAAAAATTTAAT
1 ATCCATAAAAATCTAAT
21583133 ATCCATAAAAATCTAAT
1 ATCCATAAAAATCTAAT
21583150 A
1 A
21583151 AGTCTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (17 bp):
ATCCATAAAAATCTAAT
Done.