Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 5 of 74
Found at i:1115543 original size:14 final size:13
Alignment explanation
Indices: 1115519--1115651 Score: 76
Period size: 11 Copynumber: 10.9 Consensus size: 13
1115509 TTAAAACTTC
1115519 TTAAAGATTCTCAT
1 TTAAA-ATTCTCAT
1115533 TTAAAATT-TC--
1 TTAAAATTCTCAT
1115543 TTAAAGATTCTCAT
1 TTAAA-ATTCTCAT
1115557 TTAAAATTC-C-T
1 TTAAAATTCTCAT
*
1115568 TAAAAATTCTCAT
1 TTAAAATTCTCAT
**
1115581 TTAAAA--C-CCC
1 TTAAAATTCTCAT
*
1115591 TTAACAATTTTCAT
1 TTAA-AATTCTCAT
*
1115605 TTAAAACT-TC--
1 TTAAAATTCTCAT
1115615 TTAAAGATTCTCAT
1 TTAAA-ATTCTCAT
1115629 TTAAAA--CTCAT
1 TTAAAATTCTCAT
* *
1115640 TGAAGATTCTCA
1 TTAAAATTCTCA
1115652 CTTAGAACTC
Statistics
Matches: 92, Mismatches: 11, Indels: 33
0.68 0.08 0.24
Matches are distributed among these distances:
10 15 0.16
11 26 0.28
12 10 0.11
13 21 0.23
14 20 0.22
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41
Consensus pattern (13 bp):
TTAAAATTCTCAT
Found at i:1115674 original size:96 final size:96
Alignment explanation
Indices: 1115409--1115675 Score: 383
Period size: 96 Copynumber: 2.8 Consensus size: 96
1115399 ACAAAGATTC
** * *
1115409 TCATTTAAAACACCTTAAAAATTCTCATTTAAAATTTCTTAAAGATTCTAATTTAAAACTCCTTA
1 TCATTTAAAACTTCTTAAAGATTCTCATTTAAAATTTCTTAAAGATTCTCATTTAAAACTCCTTA
* * * **
1115474 ATGATTCTAATTTAAAACTCCTTAATGATTT
66 AAGATTCTCATTTAAAACCCCTTAACAATTT
*
1115505 TCATTTAAAACTTCTTAAAGATTCTCATTTAAAATTTCTTAAAGATTCTCATTTAAAATTCCTTA
1 TCATTTAAAACTTCTTAAAGATTCTCATTTAAAATTTCTTAAAGATTCTCATTTAAAACTCCTTA
*
1115570 AAAATTCTCATTTAAAACCCCTTAACAATTT
66 AAGATTCTCATTTAAAACCCCTTAACAATTT
* * * *
1115601 TCATTTAAAACTTCTTAAAGATTCTCATTTAAAA-CTCATTGAAGATTCTCACTTAGAACTCCTT
1 TCATTTAAAACTTCTTAAAGATTCTCATTTAAAATTTC-TTAAAGATTCTCATTTAAAACTCCTT
1115665 AAAGATTCTCA
65 AAAGATTCTCA
1115676 AAATTTTTAA
Statistics
Matches: 153, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
95 2 0.01
96 151 0.99
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (96 bp):
TCATTTAAAACTTCTTAAAGATTCTCATTTAAAATTTCTTAAAGATTCTCATTTAAAACTCCTTA
AAGATTCTCATTTAAAACCCCTTAACAATTT
Found at i:1119054 original size:22 final size:22
Alignment explanation
Indices: 1118954--1119308 Score: 218
Period size: 22 Copynumber: 16.1 Consensus size: 22
1118944 AATTAAAAGC
*
1118954 AAATCAAT-ATAACTTAATAGT
1 AAATCAATAATAATTTAATAGT
* * *
1118975 -AA-CATTGATAAATTAATAGT
1 AAATCAATAATAATTTAATAGT
* *
1118995 TAATCAATAATAGTTTAGTATAGT
1 AAATCAATAATAATTTA--ATAGT
* * * *
1119019 AAATTAGTGATAATTTAATAAT
1 AAATCAATAATAATTTAATAGT
*
1119041 ATATCAATAATAATTTAATAGT
1 AAATCAATAATAATTTAATAGT
* *
1119063 AAAT-AATTGATAATTTAGTAGT
1 AAATCAA-TAATAATTTAATAGT
*
1119085 AAATCAATAATAATATAATAGT
1 AAATCAATAATAATTTAATAGT
*
1119107 AAATGC-ATAATAACTTAATAGT
1 AAAT-CAATAATAATTTAATAGT
* ** *
1119129 AAATCAATTATAACATAATTGT
1 AAATCAATAATAATTTAATAGT
** *
1119151 AAATGC-ATAATAACATATTAGT
1 AAAT-CAATAATAATTTAATAGT
* * **
1119173 AAATCAAATGATAACTTAATAAAA
1 AAATC-AATAATAATTTAAT-AGT
* *
1119197 AAATAAATAATAACTTAATAGT
1 AAATCAATAATAATTTAATAGT
* * * *
1119219 TAATCATTGATAATTTAGTAGT
1 AAATCAATAATAATTTAATAGT
* * * *
1119241 AAATAAATAAAAACTTAGTAGT
1 AAATCAATAATAATTTAATAGT
* * *
1119263 AAATTAGTTATAATTTAATAGT
1 AAATCAATAATAATTTAATAGT
* ** *
1119285 AAATCTATTTTAGTTTAATAGT
1 AAATCAATAATAATTTAATAGT
1119307 AA
1 AA
1119309 TTAAATTATA
Statistics
Matches: 258, Mismatches: 63, Indels: 25
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 6 0.02
22 186 0.72
23 27 0.10
24 22 0.09
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (22 bp):
AAATCAATAATAATTTAATAGT
Found at i:1119343 original size:156 final size:154
Alignment explanation
Indices: 1119046--1119398 Score: 329
Period size: 156 Copynumber: 2.3 Consensus size: 154
1119036 ATAATATATC
* * * * *
1119046 AATAATAATTTAATAGTAAATAATTGATAATTTAGTAGTAAATCAATAATAATATAATAGTAAAT
1 AATAATAACTTAATAGTTAATCATTGATAATTTAGTAGTAAATAAATAAAAATATAATAGTAAAT
* ** ** *
1119111 GCATAATAACTTAATAGTAAATCAATTATAACATAATTGTAAATGCATAATAACATATTAGTAAA
66 GCATAATAACTTAATAGTAAATCAATTATAACATAATAGTAAATAAATAATAACATAGCAATAAA
*
1119176 TCAAATGATAACTTAATAAAAAAATA
131 TCAAA-GATAACTT-AGAAAAAAATA
*
1119202 AATAATAACTTAATAGTTAATCATTGATAATTTAGTAGTAAATAAATAAAAACT-TAGTAGTAAA
1 AATAATAACTTAATAGTTAATCATTGATAATTTAGTAGTAAATAAATAAAAA-TATAATAGTAAA
* * * * * *** * * *
1119266 T-TAGTTATAATTTAATAGTAAATCTATTTTAGTTTAATAGTAATTAAATTATAAACTTAGCAAT
65 TGCA-TAATAACTTAATAGTAAATCAATTATAACATAATAGTAAATAAATAAT-AACATAGCAAT
* * *
1119330 AAATCATAA-ATAACTTAGCAATAAATT
128 AAATCA-AAGATAACTTAGAAAAAAATA
* * * *
1119357 AATGAT-ACTTTAGTAGTTAATCATTGA-AACTTAGTAGCAAAT
1 AATAATAAC-TTAATAGTTAATCATTGATAATTTAGTAGTAAAT
1119399 CAATGATAAC
Statistics
Matches: 161, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
154 15 0.09
155 30 0.19
156 100 0.62
157 14 0.09
158 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (154 bp):
AATAATAACTTAATAGTTAATCATTGATAATTTAGTAGTAAATAAATAAAAATATAATAGTAAAT
GCATAATAACTTAATAGTAAATCAATTATAACATAATAGTAAATAAATAATAACATAGCAATAAA
TCAAAGATAACTTAGAAAAAAATA
Found at i:1119399 original size:21 final size:22
Alignment explanation
Indices: 1119352--1119420 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
1119342 ACTTAGCAAT
* *
1119352 AAATTAATGAT-ACTTTAGTAGT
1 AAATCAATGATAAC-TTAGTAGC
* *
1119374 TAATCATTGA-AACTTAGTAGC
1 AAATCAATGATAACTTAGTAGC
*
1119395 AAATCAATGATAACATAGTAGC
1 AAATCAATGATAACTTAGTAGC
1119417 AAAT
1 AAAT
1119421 ACATAGCAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 15 0.39
22 23 0.61
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (22 bp):
AAATCAATGATAACTTAGTAGC
Found at i:1119461 original size:21 final size:21
Alignment explanation
Indices: 1119437--1119484 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1119427 CAGTGTATAA
*
1119437 TAAATACTTGAT-TTTTAATAG
1 TAAATA-TTGATAATTTAATAG
*
1119458 TAAATTATTGATAATTTAGTAG
1 TAAA-TATTGATAATTTAATAG
1119480 TAAAT
1 TAAAT
1119485 CGTTAATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (21 bp):
TAAATATTGATAATTTAATAG
Found at i:1119480 original size:22 final size:22
Alignment explanation
Indices: 1119450--1119574 Score: 85
Period size: 22 Copynumber: 5.7 Consensus size: 22
1119440 ATACTTGATT
*
1119450 TTTAATAGTAAATTATTGATAA
1 TTTAGTAGTAAATTATTGATAA
** *
1119472 TTTAGTAGTAAATCGTTAATAA
1 TTTAGTAGTAAATTATTGATAA
* * *
1119494 CGTCA-TAGTAAATCATTGATAA
1 -TTTAGTAGTAAATTATTGATAA
* *
1119516 CTTAGTTA-TAAATTAGTGATAA
1 TTTAG-TAGTAAATTATTGATAA
* * *
1119538 TTTAGCTA-TACATTAATGCTAA
1 TTTAG-TAGTAAATTATTGATAA
*
1119560 TTTAGTTGTAAATTA
1 TTTAGTAGTAAATTA
1119575 GTTAATTATT
Statistics
Matches: 80, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
21 3 0.04
22 73 0.91
23 4 0.05
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (22 bp):
TTTAGTAGTAAATTATTGATAA
Found at i:1119603 original size:22 final size:22
Alignment explanation
Indices: 1119573--1119689 Score: 76
Period size: 22 Copynumber: 5.4 Consensus size: 22
1119563 AGTTGTAAAT
* *
1119573 TAGTTAATTATTAATAACTTCA
1 TAGTAAATTATTAATAACTTAA
* * *
1119595 TAGTAAATTAGTAATAATTTTA
1 TAGTAAATTATTAATAACTTAA
* **
1119617 TAATAAAAGATCT-ATAACTTAA
1 TAGTAAATTAT-TAATAACTTAA
* * *
1119639 TAGTAAATTATCAATAATTTAG
1 TAGTAAATTATTAATAACTTAA
* * * *
1119661 TAGT-AATTGTTTATAATTTAG
1 TAGTAAATTATTAATAACTTAA
1119682 TAGTAAAT
1 TAGTAAAT
1119690 CTTCTATAAC
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
21 18 0.25
22 54 0.74
23 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (22 bp):
TAGTAAATTATTAATAACTTAA
Found at i:1120267 original size:22 final size:20
Alignment explanation
Indices: 1120241--1120338 Score: 79
Period size: 22 Copynumber: 4.5 Consensus size: 20
1120231 AATTTTGTAG
1120241 TAAATTATTGATAACTTCATAA
1 TAAATTATT-ATAACTT-ATAA
* *
1120263 AAAATTAGTTATAATTTTATAA
1 TAAATTA-TTATAA-CTTATAA
*
1120285 TAAATTATCAATAACTTAGTAA
1 TAAATTAT-TATAACTTA-TAA
*
1120307 TAAATTATTTATAACTTAATAG
1 TAAATTA-TTATAACTT-ATAA
*
1120329 TAAATCATTA
1 TAAATTATTA
1120339 AAAATTTAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
21 7 0.11
22 49 0.79
23 6 0.10
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (20 bp):
TAAATTATTATAACTTATAA
Found at i:1120292 original size:44 final size:44
Alignment explanation
Indices: 1120229--1120320 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
1120219 TTAATCATTG
* * **
1120229 ATAATTTTGTAGTAAATTATTGATAACTTCA-TAAAAAATTAGTT
1 ATAATTTTATAATAAATTATCAATAACTT-AGTAAAAAATTAGTT
* *
1120273 ATAATTTTATAATAAATTATCAATAACTTAGTAATAAATTATTT
1 ATAATTTTATAATAAATTATCAATAACTTAGTAAAAAATTAGTT
1120317 ATAA
1 ATAA
1120321 CTTAATAGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (44 bp):
ATAATTTTATAATAAATTATCAATAACTTAGTAAAAAATTAGTT
Found at i:1120333 original size:44 final size:44
Alignment explanation
Indices: 1120238--1120333 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
1120228 GATAATTTTG
** * *
1120238 TAGTAAATTATTGATAACTTCATAAAAAATTAGTTATAATTTTA
1 TAGTAAATTATCAATAACTTCATAAAAAATTAGTTATAACTTAA
* * *
1120282 TAATAAATTATCAATAACTT-AGTAATAAATTATTTATAACTTAA
1 TAGTAAATTATCAATAACTTCA-TAAAAAATTAGTTATAACTTAA
1120326 TAGTAAAT
1 TAGTAAAT
1120334 CATTAAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.02
44 42 0.98
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (44 bp):
TAGTAAATTATCAATAACTTCATAAAAAATTAGTTATAACTTAA
Found at i:1120352 original size:44 final size:44
Alignment explanation
Indices: 1120253--1120355 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 44
1120243 AATTATTGAT
* * * * * *
1120253 AACTTCATAAAAAATTAGTTATAATTTTATAATAAATTATCAAT
1 AACTTAATAATAAATTAGTTATAACTTAATAATAAATCATCAAA
* * * *
1120297 AACTTAGTAATAAATTATTTATAACTTAATAGTAAATCATTAAA
1 AACTTAATAATAAATTAGTTATAACTTAATAATAAATCATCAAA
*
1120341 AATTTAATAATAAAT
1 AACTTAATAATAAAT
1120356 CACTGTTAAC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (44 bp):
AACTTAATAATAAATTAGTTATAACTTAATAATAAATCATCAAA
Found at i:1120387 original size:22 final size:22
Alignment explanation
Indices: 1120348--1120489 Score: 82
Period size: 22 Copynumber: 6.8 Consensus size: 22
1120338 AAAAATTTAA
* *
1120348 TAATAAATCACTGTTAACATAG
1 TAATAAATCAGTGATAACATAG
*
1120370 TAATAAATCAGTGATAACTTAG
1 TAATAAATCAGTGATAACATAG
* * *
1120392 TTATCAATC-G-G-TTA-ATAG
1 TAATAAATCAGTGATAACATAG
* * * ** *
1120410 ---TAAATCATTAAAAATTTAA
1 TAATAAATCAGTGATAACATAG
*
1120429 TAATAAATCACTGATAACATAG
1 TAATAAATCAGTGATAACATAG
*
1120451 TAATAAATCAGTGATAACTTAG
1 TAATAAATCAGTGATAACATAG
* * *
1120473 TTATCAATCGGTGATAA
1 TAATAAATCAGTGATAA
1120490 GTTTTTTTAT
Statistics
Matches: 88, Mismatches: 25, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
15 5 0.06
18 4 0.05
19 4 0.05
20 1 0.01
21 1 0.01
22 73 0.83
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (22 bp):
TAATAAATCAGTGATAACATAG
Found at i:1120413 original size:81 final size:81
Alignment explanation
Indices: 1120322--1120484 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
1120312 TATTTATAAC
*
1120322 TTAATAGTAAATCATTAAAAATTTAATAATAAATCACTGTTAACATAGTAATAAATCAGTGATAA
1 TTAATAGTAAATCATTAAAAATTTAATAATAAATCACTGATAACATAGTAATAAATCAGTGATAA
1120387 CTTAGTTATCAATCGG
66 CTTAGTTATCAATCGG
1120403 TTAATAGTAAATCATTAAAAATTTAATAATAAATCACTGATAACATAGTAATAAATCAGTGATAA
1 TTAATAGTAAATCATTAAAAATTTAATAATAAATCACTGATAACATAGTAATAAATCAGTGATAA
1120468 CTTAGTTATCAATCGG
66 CTTAGTTATCAATCGG
1120484 T
1 T
1120485 GATAAGTTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (81 bp):
TTAATAGTAAATCATTAAAAATTTAATAATAAATCACTGATAACATAGTAATAAATCAGTGATAA
CTTAGTTATCAATCGG
Found at i:1120760 original size:22 final size:22
Alignment explanation
Indices: 1120718--1120760 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1120708 TATGAAAAAC
*
1120718 TTAATAATAAATTATTCATATT
1 TTAATAATAAATTAATCATATT
* *
1120740 TTAATAGTAAATTAATGATAT
1 TTAATAATAAATTAATCATAT
1120761 AACTTAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
TTAATAATAAATTAATCATATT
Found at i:1123242 original size:25 final size:25
Alignment explanation
Indices: 1123214--1123264 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1123204 TTTTGAGATT
1123214 TTCTCCAACTTCTTTCACCTGGTCA
1 TTCTCCAACTTCTTTCACCTGGTCA
*
1123239 TTCTCCAACTTCTTTCTCCTGGTCA
1 TTCTCCAACTTCTTTCACCTGGTCA
1123264 T
1 T
1123265 GTGTAGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.14, C:0.35, G:0.08, T:0.43
Consensus pattern (25 bp):
TTCTCCAACTTCTTTCACCTGGTCA
Found at i:1123621 original size:13 final size:14
Alignment explanation
Indices: 1123585--1123611 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1123575 CAATTTCATT
1123585 AAAATTATTTTATC
1 AAAATTATTTTATC
1123599 AAAATTATTTTAT
1 AAAATTATTTTAT
1123612 TAATTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
AAAATTATTTTATC
Found at i:1124205 original size:81 final size:81
Alignment explanation
Indices: 1124119--1124281 Score: 254
Period size: 81 Copynumber: 2.0 Consensus size: 81
1124109 TATTTATAAC
*
1124119 TTAATAGTAAATCATTAAAAATTTAATAATAAATCACTGATAACATAGTAATAAATCAATGACAA
1 TTAATAGTAAATCATTAAAAATTTAATAATAAATCACTGATAACATAATAATAAATCAATGACAA
1124184 CTTAATTATCAATCGG
66 CTTAATTATCAATCGG
* * * * *
1124200 TTAATAGTAAATCATTGAAAATTTAATAATAAATCACTGATAACATAATAATGAATTAGTGATAA
1 TTAATAGTAAATCATTAAAAATTTAATAATAAATCACTGATAACATAATAATAAATCAATGACAA
* *
1124265 CTTAGTTATCAGTCGG
66 CTTAATTATCAATCGG
1124281 T
1 T
1124282 GATAAGTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 74 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.34
Consensus pattern (81 bp):
TTAATAGTAAATCATTAAAAATTTAATAATAAATCACTGATAACATAATAATAAATCAATGACAA
CTTAATTATCAATCGG
Found at i:1124248 original size:22 final size:22
Alignment explanation
Indices: 1124223--1124265 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1124213 ATTGAAAATT
1124223 TAATAATAAATCACTGATAACA
1 TAATAATAAATCACTGATAACA
* * *
1124245 TAATAATGAATTAGTGATAAC
1 TAATAATAAATCACTGATAAC
1124266 TTAGTTATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (22 bp):
TAATAATAAATCACTGATAACA
Found at i:1124557 original size:22 final size:22
Alignment explanation
Indices: 1124515--1124557 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1124505 TACGGATAAC
*
1124515 TTAATAATAAATTATTCATATT
1 TTAATAATAAATTAATCATATT
* *
1124537 TTAATAGTAAATTAATGATAT
1 TTAATAATAAATTAATCATAT
1124558 AACTTAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
TTAATAATAAATTAATCATATT
Found at i:1129792 original size:2 final size:2
Alignment explanation
Indices: 1129785--1129835 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
1129775 GATAGGTATC
* * *
1129785 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TG CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1129827 TA TA TA TA T
1 TA TA TA TA T
1129836 GCATCAAGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1133457 original size:44 final size:46
Alignment explanation
Indices: 1133391--1133489 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 46
1133381 AAGATTTTTT
*
1133391 ATTTTTTTATTTTTAAATTTTTC-ACCATTTGGGTCAATTT-AAAA
1 ATTTTTTTATTTCTAAATTTTTCTACCATTTGGGTCAATTTAAAAA
*
1133435 ATTTTTTTAATTTCTAAA-TTTTCTACCATTTGGGTCTATTTAAAAAA
1 ATTTTTTT-ATTTCTAAATTTTTCTACCATTTGGGTCAATTT-AAAAA
1133482 ATTTTTTT
1 ATTTTTTT
1133490 TATCTTTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
44 13 0.27
45 24 0.49
47 12 0.24
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (46 bp):
ATTTTTTTATTTCTAAATTTTTCTACCATTTGGGTCAATTTAAAAA
Found at i:1135421 original size:21 final size:21
Alignment explanation
Indices: 1135386--1135425 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1135376 AACTTTAGGA
1135386 TTTCATCCAAAGTTTTAAAGCT
1 TTTCATCCAAAG-TTTAAAGCT
*
1135408 TTTCATTC-AAGTTTAAAG
1 TTTCATCCAAAGTTTAAAG
1135426 ATTCATATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 3 0.18
22 7 0.41
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTCATCCAAAGTTTAAAGCT
Found at i:1135501 original size:108 final size:107
Alignment explanation
Indices: 1135364--1135654 Score: 379
Period size: 108 Copynumber: 2.7 Consensus size: 107
1135354 CCATCGATAT
* * * * *
1135364 TTCTCATTTAAAAACTTTAGGATT-TCATCCAAAGTTTTAAAGCTTTTCATTCAAGTTTAAAGAT
1 TTCTCATTCAAAAAATTTAGGGTTCACATCCAAAG-TTTAAAGCTTTTCATTCAAGTTCAAAGAT
* **
1135428 TCATATTCGATAGATTTTAGAGTTTTACATCTAAATTCAAAGG
65 TCACATTCGATAGATCGTAGAGTTTTACATCTAAATTCAAAGG
* * * *
1135471 TTCTCTTTCAAAAAATTTGGGGTTCACATCCAAGAGTTCAAAGCTTCTCATTCAAGTTCAAAGAT
1 TTCTCATTCAAAAAATTTAGGGTTCACATCCAA-AGTTTAAAGCTTTTCATTCAAGTTCAAAGAT
** *
1135536 TCACATTTAATATATCGTAGAGTTTTACATCTAAATTCAAAGG
65 TCACATTCGATAGATCGTAGAGTTTTACATCTAAATTCAAAGG
* *
1135579 TTCTCATTCAAAAAATTTAGGGTTCACATCTAAAAGTTTAAAACTTCTT-ATTCAAGTTCAAAGA
1 TTCTCATTCAAAAAATTTAGGGTTCACATC-CAAAGTTTAAAGCTT-TTCATTCAAGTTCAAAGA
1135643 TTCACATTCGAT
64 TTCACATTCGAT
1135655 GCTTCAAATA
Statistics
Matches: 157, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
107 19 0.12
108 133 0.85
109 5 0.03
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (107 bp):
TTCTCATTCAAAAAATTTAGGGTTCACATCCAAAGTTTAAAGCTTTTCATTCAAGTTCAAAGATT
CACATTCGATAGATCGTAGAGTTTTACATCTAAATTCAAAGG
Found at i:1135542 original size:20 final size:20
Alignment explanation
Indices: 1135505--1135542 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1135495 CACATCCAAG
* *
1135505 AGTTCAAAGCTTCTCATTCA
1 AGTTCAAAGATTCACATTCA
1135525 AGTTCAAAGATTCACATT
1 AGTTCAAAGATTCACATT
1135543 TAATATATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
AGTTCAAAGATTCACATTCA
Found at i:1135747 original size:14 final size:13
Alignment explanation
Indices: 1135729--1135850 Score: 74
Period size: 14 Copynumber: 10.0 Consensus size: 13
1135719 ACTCAAAAAC
1135729 AAAGATTCTCATT
1 AAAGATTCTCATT
1135742 CAAAGATTCTCATTT
1 -AAAGATTCTCA-TT
1135757 AAA-ACTT-T--TT
1 AAAGA-TTCTCATT
1135767 AAAGATTCTCATTT
1 AAAGATTCTCA-TT
1135781 AAA-ATT-TC-TT
1 AAAGATTCTCATT
1135791 AAAGATTCTCATTT
1 AAAGATTCTCA-TT
*
1135805 AAA-ACT-TC-TT
1 AAAGATTCTCATT
1135815 AAA-ATTCTCATTT
1 AAAGATTCTCA-TT
1135828 AAA-ATT-TC-TT
1 AAAGATTCTCATT
*
1135838 AAAAATTCTCATT
1 AAAGATTCTCATT
1135851 TAAAACTCTT
Statistics
Matches: 89, Mismatches: 2, Indels: 35
0.71 0.02 0.28
Matches are distributed among these distances:
10 24 0.27
11 10 0.11
12 10 0.11
13 17 0.19
14 26 0.29
15 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.03, T:0.43
Consensus pattern (13 bp):
AAAGATTCTCATT
Found at i:1135775 original size:24 final size:24
Alignment explanation
Indices: 1135743--1135940 Score: 267
Period size: 24 Copynumber: 8.3 Consensus size: 24
1135733 ATTCTCATTC
1135743 AAAGATTCTCATTTAAAACTTTTT
1 AAAGATTCTCATTTAAAACTTTTT
1135767 AAAGATTCTCATTTAAAA-TTTCTT
1 AAAGATTCTCATTTAAAACTTT-TT
*
1135791 AAAGATTCTCATTTAAAACTTCTT
1 AAAGATTCTCATTTAAAACTTTTT
1135815 AAA-ATTCTCATTTAAAA-TTTCTT
1 AAAGATTCTCATTTAAAACTTT-TT
* *
1135838 AAAAATTCTCATTTAAAACTCTTT
1 AAAGATTCTCATTTAAAACTTTTT
* * *
1135862 AACGATTTTCATTTAAAACTTCTT
1 AAAGATTCTCATTTAAAACTTTTT
*
1135886 AAAGATTCTCATTTAAAACTTATT
1 AAAGATTCTCATTTAAAACTTTTT
* **
1135910 GAAGATTCTCATTTAAAACTCCTT
1 AAAGATTCTCATTTAAAACTTTTT
1135934 AAAGATT
1 AAAGATT
1135941 TTCAAAATTT
Statistics
Matches: 154, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
22 2 0.01
23 22 0.14
24 126 0.82
25 4 0.03
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAGATTCTCATTTAAAACTTTTT
Found at i:1135797 original size:48 final size:48
Alignment explanation
Indices: 1135743--1135940 Score: 299
Period size: 48 Copynumber: 4.1 Consensus size: 48
1135733 ATTCTCATTC
*
1135743 AAAGATTCTCATTTAAAACTTTTTAAAGATTCTCATTTAAAATTTCTT
1 AAAGATTCTCATTTAAAACTTTTTAAAGATTCTCATTTAAAACTTCTT
* *
1135791 AAAGATTCTCATTTAAAACTTCTTAAA-ATTCTCATTTAAAATTTCTT
1 AAAGATTCTCATTTAAAACTTTTTAAAGATTCTCATTTAAAACTTCTT
* * * *
1135838 AAAAATTCTCATTTAAAACTCTTTAACGATTTTCATTTAAAACTTCTT
1 AAAGATTCTCATTTAAAACTTTTTAAAGATTCTCATTTAAAACTTCTT
* * *
1135886 AAAGATTCTCATTTAAAACTTATTGAAGATTCTCATTTAAAACTCCTT
1 AAAGATTCTCATTTAAAACTTTTTAAAGATTCTCATTTAAAACTTCTT
1135934 AAAGATT
1 AAAGATT
1135941 TTCAAAATTT
Statistics
Matches: 135, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
47 43 0.32
48 92 0.68
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (48 bp):
AAAGATTCTCATTTAAAACTTTTTAAAGATTCTCATTTAAAACTTCTT
Found at i:1135816 original size:10 final size:10
Alignment explanation
Indices: 1135779--1135846 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 10
1135769 AGATTCTCAT
1135779 TTAAAATTTC
1 TTAAAATTTC
1135789 TTAAAGATTCTC
1 TTAAA-ATT-TC
*
1135801 ATTTAAAACTTC
1 --TTAAAATTTC
1135813 TTAAAATTCTC
1 TTAAAATT-TC
1135824 ATTTAAAATTTC
1 --TTAAAATTTC
*
1135836 TTAAAAATTC
1 TTAAAATTTC
1135846 T
1 T
1135847 CATTTAAAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
10 22 0.46
11 5 0.10
12 6 0.12
13 10 0.21
14 5 0.10
ACGTcount: A:0.40, C:0.13, G:0.01, T:0.46
Consensus pattern (10 bp):
TTAAAATTTC
Found at i:1135874 original size:95 final size:96
Alignment explanation
Indices: 1135747--1135936 Score: 301
Period size: 95 Copynumber: 2.0 Consensus size: 96
1135737 TCATTCAAAG
* *
1135747 ATTCTCATTTAAAACTTTTTAAAGATTCTCATTTAAAATTTCTTAAAGATTCTCATTTAAAACTT
1 ATTCTCATTTAAAACTCTTTAAAGATTCTCATTTAAAACTTCTTAAAGATTCTCATTTAAAACTT
* * *
1135812 CTT-AAAATTCTCATTTAAAATTTCTTAAAA
66 ATTGAAAATTCTCATTTAAAACTCCTTAAAA
* *
1135842 ATTCTCATTTAAAACTCTTTAACGATTTTCATTTAAAACTTCTTAAAGATTCTCATTTAAAACTT
1 ATTCTCATTTAAAACTCTTTAAAGATTCTCATTTAAAACTTCTTAAAGATTCTCATTTAAAACTT
*
1135907 ATTGAAGATTCTCATTTAAAACTCCTTAAA
66 ATTGAAAATTCTCATTTAAAACTCCTTAAA
1135937 GATTTTCAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
95 63 0.73
96 23 0.27
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (96 bp):
ATTCTCATTTAAAACTCTTTAAAGATTCTCATTTAAAACTTCTTAAAGATTCTCATTTAAAACTT
ATTGAAAATTCTCATTTAAAACTCCTTAAAA
Found at i:1136660 original size:79 final size:79
Alignment explanation
Indices: 1136468--1136661 Score: 226
Period size: 79 Copynumber: 2.5 Consensus size: 79
1136458 TTATCAATTC
* *** * ** *
1136468 ATCCATATTATTTTCATCATTTGATCATAACTTGCAAGCTTCTCAGTACTAGTAATTTCAGAACA
1 ATCCATATTATTTCCATCATTTGATCATAACTCATAAGCTTCTCAGTACGAACAATATCAGAACA
** *
1136533 AATTTCGTCCACTG
66 AATTTCACCCACTA
* * * * * * *
1136547 ATCCACATTACTTCTATCATTTGATCACAACTCATAAGTTTTTTAGTACGAACAATATCAGAACA
1 ATCCATATTATTTCCATCATTTGATCATAACTCATAAGCTTCTCAGTACGAACAATATCAGAACA
1136612 AATTTCACCCACTA
66 AATTTCACCCACTA
1136626 ATCCATATTATTTCCATCATTTGATCATAACTCATA
1 ATCCATATTATTTCCATCATTTGATCATAACTCATA
1136662 GGTTATATCG
Statistics
Matches: 93, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
79 93 1.00
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.37
Consensus pattern (79 bp):
ATCCATATTATTTCCATCATTTGATCATAACTCATAAGCTTCTCAGTACGAACAATATCAGAACA
AATTTCACCCACTA
Found at i:1137327 original size:19 final size:20
Alignment explanation
Indices: 1137300--1137349 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1137290 ACCTTTTCAG
*
1137300 TTTTCTTCATTTCTTCATT-
1 TTTTTTTCATTTCTTCATTC
*
1137319 TTTTTTTCATTTTTTCATTC
1 TTTTTTTCATTTCTTCATTC
1137339 TTTTTCTTCAT
1 TTTTT-TTCAT
1137350 CTATTATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 5 0.19
21 5 0.19
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTTCATTTCTTCATTC
Found at i:1140848 original size:109 final size:109
Alignment explanation
Indices: 1140657--1140877 Score: 442
Period size: 109 Copynumber: 2.0 Consensus size: 109
1140647 AATACAAATG
1140657 CATATGATAGTGTGTGTGAAGAAACATAAAATTTTCAATCCCATAAATTAAGACAAAAAAGAAAA
1 CATATGATAGTGTGTGTGAAGAAACATAAAATTTTCAATCCCATAAATTAAGACAAAAAAGAAAA
1140722 AAAAATGTTAGTAAACAAATAACATAATCATTACATTTTAAAAC
66 AAAAATGTTAGTAAACAAATAACATAATCATTACATTTTAAAAC
1140766 CATATGATAGTGTGTGTGAAGAAACATAAAATTTTCAATCCCATAAATTAAGACAAAAAAGAAAA
1 CATATGATAGTGTGTGTGAAGAAACATAAAATTTTCAATCCCATAAATTAAGACAAAAAAGAAAA
1140831 AAAAATGTTAGTAAACAAATAACATAATCATTACATTTTAAAAC
66 AAAAATGTTAGTAAACAAATAACATAATCATTACATTTTAAAAC
1140875 CAT
1 CAT
1140878 TAGATCAGAG
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 112 1.00
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (109 bp):
CATATGATAGTGTGTGTGAAGAAACATAAAATTTTCAATCCCATAAATTAAGACAAAAAAGAAAA
AAAAATGTTAGTAAACAAATAACATAATCATTACATTTTAAAAC
Found at i:1142490 original size:2 final size:2
Alignment explanation
Indices: 1142483--1142518 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1142473 AAATTTTCTT
1142483 TC TC TC TC TC TC TC TC TC TC T- TC TC TC -C TC T- TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1142519 TTTTCTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1143021 original size:13 final size:12
Alignment explanation
Indices: 1143003--1143032 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
1142993 TTCACTTAAT
1143003 TTTTTGTTTTTTA
1 TTTTTG-TTTTTA
1143016 TTTTTGTTTTTA
1 TTTTTGTTTTTA
1143028 TTTTT
1 TTTTT
1143033 ATTAACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.87
Consensus pattern (12 bp):
TTTTTGTTTTTA
Found at i:1144562 original size:14 final size:15
Alignment explanation
Indices: 1144535--1144564 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1144525 GAGATCATTT
1144535 GAAACCTGAAAAAAA
1 GAAACCTGAAAAAAA
1144550 GAAACCT-AAAAAAA
1 GAAACCTGAAAAAAA
1144564 G
1 G
1144565 TCCAGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.67, C:0.13, G:0.13, T:0.07
Consensus pattern (15 bp):
GAAACCTGAAAAAAA
Found at i:1153238 original size:2 final size:2
Alignment explanation
Indices: 1153231--1153261 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1153221 ACCAATGTAA
1153231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1153262 ATCAAGGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1155594 original size:5 final size:5
Alignment explanation
Indices: 1155584--1155609 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1155574 GATGACTCAT
1155584 TTCTC TTCTC TTCTC TTCTC TTCTC T
1 TTCTC TTCTC TTCTC TTCTC TTCTC T
1155610 CTTCCTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TTCTC
Found at i:1157589 original size:16 final size:16
Alignment explanation
Indices: 1157552--1157591 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1157542 TGTGTTAAGG
1157552 GTATTTTCGGTCAATA
1 GTATTTTCGGTCAATA
* *
1157568 GT-TTTTTGGTTAATA
1 GTATTTTCGGTCAATA
1157583 GTATTTTCG
1 GTATTTTCG
1157592 AAATTGACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (16 bp):
GTATTTTCGGTCAATA
Found at i:1172514 original size:2 final size:2
Alignment explanation
Indices: 1172509--1172549 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1172499 GCTCATCCAG
1172509 TA TA TA TA 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 TA TA TA TA T
1172550 GATCTTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1182082 original size:6 final size:6
Alignment explanation
Indices: 1182071--1182095 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1182061 GTGCTACCCT
1182071 CTTTCA CTTTCA CTTTCA CTTTCA C
1 CTTTCA CTTTCA CTTTCA CTTTCA C
1182096 AATCACTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (6 bp):
CTTTCA
Found at i:1186024 original size:11 final size:10
Alignment explanation
Indices: 1186008--1186047 Score: 53
Period size: 11 Copynumber: 3.7 Consensus size: 10
1185998 ATGGTACAAT
1186008 ATAAAATTTCA
1 ATAAAATTT-A
1186019 ATAAAATTTA
1 ATAAAATTTA
1186029 TATATAAATTTA
1 -ATA-AAATTTA
1186041 ATAAAAT
1 ATAAAAT
1186048 AAAAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.19
11 15 0.56
12 7 0.26
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (10 bp):
ATAAAATTTA
Found at i:1186043 original size:22 final size:22
Alignment explanation
Indices: 1186006--1186047 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1185996 AAATGGTACA
1186006 ATATAAAATTTCAATAAAATTT
1 ATATAAAATTTCAATAAAATTT
1186028 ATATATAAATTT-AATAAAAT
1 ATATA-AAATTTCAATAAAAT
1186048 AAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAAAATTTCAATAAAATTT
Found at i:1186055 original size:22 final size:23
Alignment explanation
Indices: 1186005--1186061 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
1185995 AAAATGGTAC
**
1186005 AATATAAAATTTCAATAAAATTTA
1 AATAT-AAATTTCAATAAAATAAA
*
1186029 TATATAAATTT-AATAAAATAAA
1 AATATAAATTTCAATAAAATAAA
*
1186051 AATATATATTT
1 AATATAAATTT
1186062 TATATTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 18 0.64
23 6 0.21
24 4 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AATATAAATTTCAATAAAATAAA
Found at i:1186122 original size:18 final size:18
Alignment explanation
Indices: 1186077--1186128 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1186067 TTTTATATCG
* *
1186077 ATATAACTATAATATATA
1 ATATAAATATAAAATATA
* **
1186095 ATTTTTATATAAAATATA
1 ATATAAATATAAAATATA
1186113 ATATAAATATATAAAT
1 ATATAAATATA-AAAT
1186129 TATCATTTAC
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAAATATAAAATATA
Found at i:1192290 original size:120 final size:120
Alignment explanation
Indices: 1192069--1192304 Score: 400
Period size: 120 Copynumber: 2.0 Consensus size: 120
1192059 CAATCCATTT
* * *
1192069 TTTTCGTTCTACCTTCCTTATTTATTTTATATAATTCTTATATAATTAGAATTCTAAAAAATACT
1 TTTTAGTTCTACCTTCCTTATTTATTTTATAAAATTCTTATATAATTAAAATTCTAAAAAATACT
* * * *
1192134 AAATATAATTATTTCTTATAGAATTATAATTCTAAAAACAACTAAAGTCAAAGGG
66 AAATAGAATTATTTCTTAAAAAATTATAATTATAAAAACAACTAAAGTCAAAGGG
*
1192189 TTTTAGTTCTACCTTCCTTATTTATTTTATAAAATTCTTATATAATTAAAATTCTAAAAAATGCT
1 TTTTAGTTCTACCTTCCTTATTTATTTTATAAAATTCTTATATAATTAAAATTCTAAAAAATACT
1192254 AAATAGAATTATTTCTTAAAAAATTATAATTATAAAAACAACTAAAGTCAA
66 AAATAGAATTATTTCTTAAAAAATTATAATTATAAAAACAACTAAAGTCAA
1192305 GGGGAGCGAG
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (120 bp):
TTTTAGTTCTACCTTCCTTATTTATTTTATAAAATTCTTATATAATTAAAATTCTAAAAAATACT
AAATAGAATTATTTCTTAAAAAATTATAATTATAAAAACAACTAAAGTCAAAGGG
Found at i:1194022 original size:180 final size:180
Alignment explanation
Indices: 1193707--1194060 Score: 548
Period size: 180 Copynumber: 2.0 Consensus size: 180
1193697 TGCTACATGA
* * * * *
1193707 TGGTCTGGTGTGATCTTGGTCCTGTGGATGGACGTCAAGCATTAAAGGTAGAGAAATTGTAATGC
1 TGGTCTGGTGTGATCTTGGTCATGTGGATAGACATCAAGCATTAAAGATAGAGAAATTATAATGC
* * * *
1193772 CCCCAATCCCACATCAGAAGGATGTATGTAGAGACTTAATCCTAAACTTGCGAGGTTCTTTTTGT
66 CCCCAATCCCACATCAGAAAGATGTATATAGAGACTTAATCCAAAACTTGCGAGGTTCTTTTTAT
* * *
1193837 GGGATAAAATCGTGAGACTTTCGGGTCAAAGCGGACAATACCTCTCAGGT
131 GGGATAAAATCGTGAAACCTTCGGATCAAAGCGGACAATACCTCTCAGGT
* * *
1193887 TGGTCTGGTGTGATCTTGGTCATGTGGATAGACATCAAGCATTAAAGATGGGGAGATTATAATGC
1 TGGTCTGGTGTGATCTTGGTCATGTGGATAGACATCAAGCATTAAAGATAGAGAAATTATAATGC
*
1193952 CCCTAATCCCACATCAGAAAGATGTATATAGAGACTTAATCCAAAACTTGCGAGG-TCTTTTTTA
66 CCCCAATCCCACATCAGAAAGATGTATATAGAGACTTAATCCAAAACTTGCGAGGTTC-TTTTTA
1194016 TGGGATAAAATCGTGAAACCTTCGGATCAAAGCGGACAATACCTC
130 TGGGATAAAATCGTGAAACCTTCGGATCAAAGCGGACAATACCTC
1194061 GTAAGTTGGG
Statistics
Matches: 157, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
179 2 0.01
180 155 0.99
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (180 bp):
TGGTCTGGTGTGATCTTGGTCATGTGGATAGACATCAAGCATTAAAGATAGAGAAATTATAATGC
CCCCAATCCCACATCAGAAAGATGTATATAGAGACTTAATCCAAAACTTGCGAGGTTCTTTTTAT
GGGATAAAATCGTGAAACCTTCGGATCAAAGCGGACAATACCTCTCAGGT
Found at i:1201850 original size:26 final size:23
Alignment explanation
Indices: 1201788--1201851 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
1201778 ATATTTGAAT
*
1201788 AATTATTTTAAT-TTTTTAAAAA
1 AATTATTTTAATAATTTTAAAAA
*
1201810 AATTATTTAAGATAATTTTACAAAA
1 AATTATTTTA-ATAATTTTA-AAAA
1201835 AATATACTTTTAATAAT
1 AAT-TA-TTTTAATAAT
1201852 CTACTCCGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 9 0.26
23 2 0.06
24 5 0.15
25 7 0.21
26 7 0.21
27 4 0.12
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTATTTTAATAATTTTAAAAA
Found at i:1203902 original size:93 final size:93
Alignment explanation
Indices: 1203743--1203929 Score: 356
Period size: 93 Copynumber: 2.0 Consensus size: 93
1203733 TCTTAATTGG
* *
1203743 ATATGGTAGAACGTATGAATCTTAGGCCAAGTAAATTATCTTCAGAATCTTGCCCTGATGCCCTT
1 ATATGGTAGAAAGTATGAATCTTAGGCCAAGTAAATTATCTTCAGAATCTTGCCCCGATGCCCTT
1203808 CTGGCACCCTTTTTTGTTTTCGCAAGTC
66 CTGGCACCCTTTTTTGTTTTCGCAAGTC
1203836 ATATGGTAGAAAGTATGAATCTTAGGCCAAGTAAATTATCTTCAGAATCTTGCCCCGATGCCCTT
1 ATATGGTAGAAAGTATGAATCTTAGGCCAAGTAAATTATCTTCAGAATCTTGCCCCGATGCCCTT
1203901 CTGGCACCCTTTTTTGTTTTCGCAAGTC
66 CTGGCACCCTTTTTTGTTTTCGCAAGTC
1203929 A
1 A
1203930 ATTGGTGGAG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (93 bp):
ATATGGTAGAAAGTATGAATCTTAGGCCAAGTAAATTATCTTCAGAATCTTGCCCCGATGCCCTT
CTGGCACCCTTTTTTGTTTTCGCAAGTC
Found at i:1205721 original size:24 final size:24
Alignment explanation
Indices: 1205694--1205739 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1205684 TGATGATCTT
*
1205694 GATGGTGAAGATGACAGTGGTGAA
1 GATGATGAAGATGACAGTGGTGAA
* * *
1205718 GATGATGATGGTGATAGTGGTG
1 GATGATGAAGATGACAGTGGTG
1205740 GTCATGAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.02, G:0.43, T:0.26
Consensus pattern (24 bp):
GATGATGAAGATGACAGTGGTGAA
Found at i:1205729 original size:15 final size:15
Alignment explanation
Indices: 1205693--1205731 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1205683 ATGATGATCT
1205693 TGATGGTGAAGATGA
1 TGATGGTGAAGATGA
*
1205708 -CAGTGGTGAAGATGA
1 TGA-TGGTGAAGATGA
1205723 TGATGGTGA
1 TGATGGTGA
1205732 TAGTGGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.05
15 18 0.90
16 1 0.05
ACGTcount: A:0.31, C:0.03, G:0.41, T:0.26
Consensus pattern (15 bp):
TGATGGTGAAGATGA
Found at i:1214339 original size:3 final size:3
Alignment explanation
Indices: 1214331--1214356 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1214321 TAAAGAAAAG
1214331 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
1214357 GAGGTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1217550 original size:8 final size:8
Alignment explanation
Indices: 1217530--1217570 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1217520 TATTATTTTT
1217530 TAAA-ATA
1 TAAATATA
*
1217537 TAAATATT
1 TAAATATA
1217545 TAAATATA
1 TAAATATA
*
1217553 TAATTATA
1 TAAATATA
1217561 TAAATATA
1 TAAATATA
1217569 TA
1 TA
1217571 TAAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAATATA
Found at i:1217576 original size:26 final size:24
Alignment explanation
Indices: 1217534--1217585 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
1217524 ATTTTTTAAA
* *
1217534 ATATAAATATTTAAATATATAATT
1 ATATAAATATTTAAATAAAAAATT
1217558 ATATAAATATATATAAATAAAAAATT
1 ATATAAATAT-T-TAAATAAAAAATT
1217584 AT
1 AT
1217586 TTTTATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
25 1 0.04
26 13 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATAAATATTTAAATAAAAAATT
Found at i:1218516 original size:29 final size:28
Alignment explanation
Indices: 1218470--1218534 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
1218460 CAATAATCAT
*
1218470 TTAAATTTATGATATTTTA-TTACAATTAA
1 TTAAA-TTATGATATTTTATTTA-AACTAA
*
1218499 TTAAATTATGAATCTTTTATTTAAACTAA
1 TTAAATTATG-ATATTTTATTTAAACTAA
1218528 TTAAATT
1 TTAAATT
1218535 TTTAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.16
29 24 0.75
30 3 0.09
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.51
Consensus pattern (28 bp):
TTAAATTATGATATTTTATTTAAACTAA
Found at i:1237247 original size:20 final size:22
Alignment explanation
Indices: 1237224--1237275 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
1237214 TAATTATTAT
*
1237224 ATATATAAA-TTTATTTAAA-A
1 ATATATAAATTTTATTAAAATA
1237244 ATAT-TAAAGATTTTATTAAAATA
1 ATATAT-AA-ATTTTATTAAAATA
1237267 ATATATAAA
1 ATATATAAA
1237276 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
19 1 0.04
20 6 0.23
21 1 0.04
22 10 0.38
23 7 0.27
24 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATATAAATTTTATTAAAATA
Found at i:1261018 original size:40 final size:43
Alignment explanation
Indices: 1260947--1261048 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 43
1260937 TTAAAATGAC
* *
1260947 TTTTTATTATTAAATTTCTATTGAAATAAATTATAATTTGAACTT
1 TTTTTATTATTAAACTTC-ATT-AAATAAATTATAATTTAAACTT
*
1260992 TTTTTATTATTAAACTTC-TT-AA-AAATTGTAATTTAAACTT
1 TTTTTATTATTAAACTTCATTAAATAAATTATAATTTAAACTT
*
1261032 TTTTTATTATTAGACTT
1 TTTTTATTATTAAACTT
1261049 TTATACAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
40 32 0.60
41 2 0.04
43 2 0.04
45 17 0.32
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (43 bp):
TTTTTATTATTAAACTTCATTAAATAAATTATAATTTAAACTT
Found at i:1263964 original size:42 final size:42
Alignment explanation
Indices: 1263903--1263987 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
1263893 AAAGCACATT
* *
1263903 AAATCTTACAATAGTATGTTTTCATTCACATCATTTGGAGTG
1 AAATCTTACAATAGGATGTTCTCATTCACATCATTTGGAGTG
1263945 AAATCTTACAATAGGATGTTCTCATTCACATCATTTGGAGTG
1 AAATCTTACAATAGGATGTTCTCATTCACATCATTTGGAGTG
1263987 A
1 A
1263988 GGTTAGATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (42 bp):
AAATCTTACAATAGGATGTTCTCATTCACATCATTTGGAGTG
Found at i:1265027 original size:12 final size:12
Alignment explanation
Indices: 1265012--1265050 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1265002 TCACTTTATA
1265012 TATATATATAAT
1 TATATATATAAT
1265024 TATATA-AGTAAT
1 TATATATA-TAAT
*
1265036 TATTTATATAAT
1 TATATATATAAT
1265048 TAT
1 TAT
1265051 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
TATATATATAAT
Found at i:1270224 original size:11 final size:11
Alignment explanation
Indices: 1270208--1270236 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1270198 AATAATTTAA
1270208 AATATAAAAAT
1 AATATAAAAAT
1270219 AATATAAAAAT
1 AATATAAAAAT
1270230 AATATAA
1 AATATAA
1270237 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:1271108 original size:136 final size:137
Alignment explanation
Indices: 1270932--1271188 Score: 444
Period size: 136 Copynumber: 1.9 Consensus size: 137
1270922 AATCAAAACT
*
1270932 GAACTTTTCTAATATTACTTTCTATATTGATTAGATTAAGAGATTTTAGATCTAATATCTTGTTT
1 GAACTTTTCTAAAATTACTTTCTATATTGATTAGATTAAGAGATTTTAGATCTAATATCTTGTTT
1270997 AACAAGTGAATAATAACGAAATTAACGATTATCGTTATAATAGTTAAATTGAATTTGTTTTGAGT
66 AACAAGTGAATAATAACGAAATTAACGATTATCGTTATAATAGTTAAATTGAATTTGTTTTGAGT
1271062 TAGAACC
131 TAGAACC
*
1271069 GAACTTTT-TAAAATTACTTTCTATATTGATTAGATTAAGAGATTTTGGATCTAATATCTTGTTT
1 GAACTTTTCTAAAATTACTTTCTATATTGATTAGATTAAGAGATTTTAGATCTAATATCTTGTTT
** * * *
1271133 AATGAGTGAATAATAACGAAATTAACTATTATCGTTATGATAGTTGAATTGAATTT
66 AACAAGTGAATAATAACGAAATTAACGATTATCGTTATAATAGTTAAATTGAATTT
1271189 ATTTGATTAA
Statistics
Matches: 113, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
136 105 0.93
137 8 0.07
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (137 bp):
GAACTTTTCTAAAATTACTTTCTATATTGATTAGATTAAGAGATTTTAGATCTAATATCTTGTTT
AACAAGTGAATAATAACGAAATTAACGATTATCGTTATAATAGTTAAATTGAATTTGTTTTGAGT
TAGAACC
Found at i:1273839 original size:2 final size:2
Alignment explanation
Indices: 1273832--1273874 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1273822 TTTCCAAATG
* * * *
1273832 AC AC AC AC AC AC AC AC AC AT AT AT AT AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1273874 A
1 A
1273875 AGCAAAACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.40, G:0.00, T:0.09
Consensus pattern (2 bp):
AC
Found at i:1274066 original size:20 final size:19
Alignment explanation
Indices: 1274013--1274066 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
1274003 GGAATTTATA
* *
1274013 TATAGAAGAATTTAACTTC
1 TATATAAGAATTTAATTTC
* *
1274032 TATAT-ACATTTTAATTTC
1 TATATAAGAATTTAATTTC
1274050 TATATCAAGAATTTAAT
1 TATAT-AAGAATTTAAT
1274067 ACTAAAAGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 15 0.56
19 4 0.15
20 8 0.30
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (19 bp):
TATATAAGAATTTAATTTC
Found at i:1287288 original size:24 final size:24
Alignment explanation
Indices: 1287260--1287308 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
1287250 TAATTATGTA
1287260 ATTTTTT--AAATATATTAATATTT
1 ATTTTTTAAAAATATATTAAT-TTT
1287283 ATTTTTTAAAAAATATATTAATTTT
1 ATTTTTT-AAAAATATATTAATTTT
1287308 A
1 A
1287309 ATTAATCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.30
25 4 0.17
26 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTTTAAAAATATATTAATTTT
Found at i:1288720 original size:34 final size:33
Alignment explanation
Indices: 1288659--1288724 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
1288649 ATGTATTTCT
* *
1288659 AATTAATTTTACAATTAAAATTTTAATAATTTTA
1 AATTAATTATAAAATTAAAATTTTAAT-ATTTTA
*
1288693 AATTAATTATAAAATT-AATTTTATAATATTTT
1 AATTAATTATAAAATTAAAATTT-TAATATTTT
1288725 GTGTAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (33 bp):
AATTAATTATAAAATTAAAATTTTAATATTTTA
Found at i:1300368 original size:2 final size:2
Alignment explanation
Indices: 1300361--1300392 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1300351 GTTTTGCAGC
1300361 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1300393 CAGAAAGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1302059 original size:28 final size:28
Alignment explanation
Indices: 1302002--1302059 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1301992 CCAAACAAAT
* **
1302002 ATTGACGTACACAGAGGCAGTTAGGGCA
1 ATTGACGTACACAGAGGCAATTAGCCCA
1302030 ATTGACGTACACAGAGGCAATT-GACCCA
1 ATTGACGTACACAGAGGCAATTAG-CCCA
1302058 AT
1 AT
1302060 GAAAGCTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (28 bp):
ATTGACGTACACAGAGGCAATTAGCCCA
Found at i:1306116 original size:30 final size:31
Alignment explanation
Indices: 1306061--1306134 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
1306051 ATTATTTAAA
* ** *
1306061 TTTTAAAATTTAATTCGAATTTGAATTGATTT
1 TTTTTAAA-TTAATTCGAATTTGAATCAAATT
*
1306093 TTTTTAAATTAATTC-ATTTTGAATCAAATT
1 TTTTTAAATTAATTCGAATTTGAATCAAATT
*
1306123 TTATTAAATTAA
1 TTTTTAAATTAA
1306135 ATTTTTTGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 22 0.61
31 7 0.19
32 7 0.19
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (31 bp):
TTTTTAAATTAATTCGAATTTGAATCAAATT
Found at i:1322534 original size:13 final size:14
Alignment explanation
Indices: 1322503--1322535 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1322493 ATAAAATTAT
*
1322503 TTAAAGTTATTTAA
1 TTAAATTTATTTAA
1322517 TTAAATTTATTT-A
1 TTAAATTTATTTAA
1322530 TTAAAT
1 TTAAAT
1322536 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TTAAATTTATTTAA
Found at i:1322746 original size:48 final size:47
Alignment explanation
Indices: 1322634--1322751 Score: 121
Period size: 48 Copynumber: 2.4 Consensus size: 47
1322624 ATAATTTTTT
* * *
1322634 AATTAAACTAATAAAATTATAAAAATATAAAAATTTAATTAGATTCGTA
1 AATTAAATTAATTAAATT-T-AAAATATAAAAATTTAATTACATTCGTA
** * *
1322683 AATTATTTTAATTAAATATTAAAATATTAAAATTTGATT-CATTCGATA
1 AATTAAATTAATTAAAT-TTAAAATATAAAAATTTAATTACATTCG-TA
*
1322731 AATTAAATTATTTAAATTTAA
1 AATTAAATTAATTAAATTTAA
1322752 TTTAATAATA
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
47 9 0.16
48 33 0.58
49 14 0.25
50 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (47 bp):
AATTAAATTAATTAAATTTAAAATATAAAAATTTAATTACATTCGTA
Found at i:1323937 original size:36 final size:36
Alignment explanation
Indices: 1323885--1323957 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1323875 CTTGGCGGGC
1323885 CCTACTTTCACTGTTCCATTGTTGCTTACAGAACCA
1 CCTACTTTCACTGTTCCATTGTTGCTTACAGAACCA
*
1323921 CCTAGTTTCACTGTTCCATTGTTGCTTACAGAACCA
1 CCTACTTTCACTGTTCCATTGTTGCTTACAGAACCA
1323957 C
1 C
1323958 TGAATCACCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (36 bp):
CCTACTTTCACTGTTCCATTGTTGCTTACAGAACCA
Found at i:1326092 original size:23 final size:24
Alignment explanation
Indices: 1326059--1326103 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1326049 AAAAAATTAA
1326059 AATTTGTTAAATGAATTTAAATAT
1 AATTTGTTAAATGAATTTAAATAT
**
1326083 AATTT-TTAAATTTATTTAAAT
1 AATTTGTTAAATGAATTTAAAT
1326104 TTTAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
AATTTGTTAAATGAATTTAAATAT
Found at i:1326172 original size:13 final size:13
Alignment explanation
Indices: 1326151--1326191 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1326141 AATTCGATTC
1326151 AAATAAAATATAT
1 AAATAAAATATAT
*
1326164 AATTAAAATAT-T
1 AAATAAAATATAT
*
1326176 AAATCAAATATAT
1 AAATAAAATATAT
1326189 AAA
1 AAA
1326192 CTATTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATAAAATATAT
Found at i:1335661 original size:22 final size:22
Alignment explanation
Indices: 1335633--1335676 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1335623 AGGGATTGTC
1335633 CTTAATTCTAG-GAATACAAATA
1 CTTAATTCTAGAG-ATACAAATA
1335655 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
1335677 TAAATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:1339603 original size:22 final size:22
Alignment explanation
Indices: 1339578--1339621 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1339568 ATTTTTTGTC
*
1339578 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
1339600 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
1339622 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:1341718 original size:18 final size:20
Alignment explanation
Indices: 1341675--1341718 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1341665 TAAATTAAAA
*
1341675 AATAAATTTTAAATTTATTT
1 AATAAATTTTAAATTTATAT
*
1341695 ATTAAA-TTT-AATTTATAT
1 AATAAATTTTAAATTTATAT
1341713 AATAAA
1 AATAAA
1341719 AAATTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 13 0.62
19 3 0.14
20 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAAATTTTAAATTTATAT
Found at i:1341904 original size:14 final size:14
Alignment explanation
Indices: 1341885--1341911 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1341875 TAAATTTATA
1341885 TTTTTCAAAATTTT
1 TTTTTCAAAATTTT
1341899 TTTTTCAAAATTT
1 TTTTTCAAAATTT
1341912 AGATAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTCAAAATTTT
Found at i:1343690 original size:52 final size:52
Alignment explanation
Indices: 1343633--1343735 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
1343623 GCCATTGTTA
* *
1343633 AAATTCTATGTAGACAAGGTTAACATACAAGATTACGTGTATCAGATGCCAG
1 AAATTCTATGTAGACAAGGATAACATACAAGATTACCTGTATCAGATGCCAG
*
1343685 AAATTCTATGTAGAGAAGGATAACATACAAGATTACCTGTATCAGATGCCA
1 AAATTCTATGTAGACAAGGATAACATACAAGATTACCTGTATCAGATGCCA
1343736 TGCACAATAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (52 bp):
AAATTCTATGTAGACAAGGATAACATACAAGATTACCTGTATCAGATGCCAG
Found at i:1345758 original size:21 final size:21
Alignment explanation
Indices: 1345732--1345773 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1345722 TAAACAATCC
1345732 GATCCTTTTTGCAAGAATAAA
1 GATCCTTTTTGCAAGAATAAA
1345753 GATCCTTTTTGCAAGAATAAA
1 GATCCTTTTTGCAAGAATAAA
1345774 AATTCCAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
GATCCTTTTTGCAAGAATAAA
Found at i:1352945 original size:33 final size:33
Alignment explanation
Indices: 1352906--1352969 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
1352896 ATTATTTTTT
1352906 ATAAAAAAAGGATTAAATCAAATAAGATTTCTA
1 ATAAAAAAAGGATTAAATCAAATAAGATTTCTA
1352939 ATAAAAAAAGGATTAAATCAAATAAGATTTC
1 ATAAAAAAAGGATTAAATCAAATAAGATTTC
1352970 ATTAATTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (33 bp):
ATAAAAAAAGGATTAAATCAAATAAGATTTCTA
Found at i:1354471 original size:31 final size:32
Alignment explanation
Indices: 1354422--1354505 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 32
1354412 ATAGGGTAAA
**
1354422 ATATAAATAATTTATATATTTAT-A-TTATATTTT
1 ATATAAA-AA-TTATATATTTATAATTTATA-TCG
1354455 ATATAAAAATTATATA-TTATAATTTATATCG
1 ATATAAAAATTATATATTTATAATTTATATCG
1354486 ATATAAAAATATATATATTT
1 ATATAAAAAT-TATATATTT
1354506 TTAAAATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
30 4 0.09
31 19 0.42
32 13 0.29
33 9 0.20
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (32 bp):
ATATAAAAATTATATATTTATAATTTATATCG
Found at i:1354521 original size:19 final size:19
Alignment explanation
Indices: 1354489--1354528 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1354479 TATATCGATA
1354489 TAAAAATATATAT-ATTTT
1 TAAAAATATATATAATTTT
*
1354507 TAAAATATATTTATAATTTT
1 TAAAA-ATATATATAATTTT
1354527 TA
1 TA
1354529 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 7 0.37
20 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAAAATATATATAATTTT
Found at i:1357991 original size:54 final size:54
Alignment explanation
Indices: 1357863--1358283 Score: 319
Period size: 54 Copynumber: 7.8 Consensus size: 54
1357853 TCTTATCATT
* * * *
1357863 AGCAGAGGTTGCTTCCCTTCTAGAAAATTGATTTCTAGAAATGATCCTATCAGA
1 AGCAGAGGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCTATCAGA
*** * * * * * *
1357917 AATGGAAGTCGATTCACTTCTAGTAATTTGGTTTCCAGTAATGATCCCATCAGA
1 AGCAGAGGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCTATCAGA
* *
1357971 AGCAGAGGTTGGTTCCCTTCTAGAAATTTGATTTCCAGTAACGATACC-A-CTAGA
1 AGCAGAGGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGAT-CCTATC-AGA
* * * * * *
1358025 TGCAGAGCTTGATTCCTTTCTAGAAATTTGATTTACAGTAATGATACTATGAG-
1 AGCAGAGGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCTATCAGA
* ** * * * * * * *
1358078 GGGTGAAGGTTGATTCCTTTCGAGAATTTTGATCTCCAGTAATCAACCTATCAGG
1 AGCAG-AGGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCTATCAGA
* * * * * * *
1358133 GGCAAAGGTTGATTCCTTTCTAGAATTTTGATTTCCAGCAATCATTCTATCAG-
1 AGCAGAGGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCTATCAGA
* ** * * *
1358186 GGGTGAGGGTTAATTCCCTTCTAGAAATTTGATCTCCAGTAATGATCCCATCAGA
1 AGCAGA-GGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCTATCAGA
** * * * * *
1358241 AGTGGGGGTTGATTCCCTTCTAGGAATCTGACTTCCAATAATG
1 AGCAGAGGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATG
1358284 CCTCCCTCAC
Statistics
Matches: 287, Mismatches: 72, Indels: 16
0.77 0.19 0.04
Matches are distributed among these distances:
53 7 0.02
54 274 0.95
55 6 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (54 bp):
AGCAGAGGTTGATTCCCTTCTAGAAATTTGATTTCCAGTAATGATCCTATCAGA
Found at i:1364215 original size:16 final size:15
Alignment explanation
Indices: 1364194--1364237 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 15
1364184 CAAAAGCAAC
1364194 TATTAAATTCTATTAA
1 TATTAAATT-TATTAA
*
1364210 TATTAAATTTA-AAA
1 TATTAAATTTATTAA
1364224 T-TTAAATTTATTAA
1 TATTAAATTTATTAA
1364238 CTTATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 9 0.36
14 5 0.20
15 2 0.08
16 9 0.36
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAAATTTATTAA
Found at i:1365169 original size:12 final size:12
Alignment explanation
Indices: 1365152--1365176 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1365142 ATTTAACCAA
1365152 GTTGCTACATGT
1 GTTGCTACATGT
1365164 GTTGCTACATGT
1 GTTGCTACATGT
1365176 G
1 G
1365177 GAAGTCTTAA
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:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (12 bp):
GTTGCTACATGT
Found at i:1380279 original size:117 final size:116
Alignment explanation
Indices: 1380064--1380297 Score: 369
Period size: 117 Copynumber: 2.0 Consensus size: 116
1380054 CTAAACTAAG
* * * * *
1380064 ATAGTTCACCTAAATTGCCTTATTATCTCCCATACTGAAAGTGCATCACGCATAATCTCATTATC
1 ATAGGTCACCTAAATCGCCTTATCATCTCCAATACTGAAAGTGCATCACGCATAATCCCATTATC
*
1380129 CACGGAATCCATGGGTCAAGTATCATAATGAAGTTTAACAGAGTGCACATTA
66 CACAGAATCCATGGGTCAAGTATCATAATGAAG-TTAACAGAGTGCACATTA
* *
1380181 ATAGGTCATCTAAATCGCCTTATCATCTCCAATACTGAAAGTGCATCACGCATAATCCCATTTTC
1 ATAGGTCACCTAAATCGCCTTATCATCTCCAATACTGAAAGTGCATCACGCATAATCCCATTATC
* *
1380246 CACAGAATCCATGGGTCAATTATCATAATGAAGTTAACATAGTGCACATTA
66 CACAGAATCCATGGGTCAAGTATCATAATGAAGTTAACAGAGTGCACATTA
1380297 A
1 A
1380298 GCACTGAAGA
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
116 18 0.17
117 89 0.83
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (116 bp):
ATAGGTCACCTAAATCGCCTTATCATCTCCAATACTGAAAGTGCATCACGCATAATCCCATTATC
CACAGAATCCATGGGTCAAGTATCATAATGAAGTTAACAGAGTGCACATTA
Found at i:1382394 original size:2 final size:2
Alignment explanation
Indices: 1382387--1382424 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1382377 CATTCCCCTC
1382387 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1382425 TGCTACTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1385029 original size:23 final size:25
Alignment explanation
Indices: 1384992--1385038 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
1384982 ATCATATATA
* *
1384992 TATATATATATTTTTTTCAAAAATC
1 TATATATATATTTTTATAAAAAATC
1385017 TATAT-TATA-TTTTATAAAAAAT
1 TATATATATATTTTTATAAAAAAT
1385039 ATCGCAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 4 0.20
25 5 0.25
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
TATATATATATTTTTATAAAAAATC
Found at i:1386989 original size:33 final size:33
Alignment explanation
Indices: 1386941--1387003 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1386931 ATCTAGCATT
* *
1386941 TCAGATCAGTTTGATCGTCACAGTTCACACATC
1 TCAGATCAATCTGATCGTCACAGTTCACACATC
* *
1386974 TCAGATCAATCTGATCGTTATAGTTCACAC
1 TCAGATCAATCTGATCGTCACAGTTCACAC
1387004 TTTTATGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (33 bp):
TCAGATCAATCTGATCGTCACAGTTCACACATC
Found at i:1394122 original size:17 final size:20
Alignment explanation
Indices: 1394091--1394129 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1394081 CAATGCTAAC
1394091 AAAAGACAAATTAAAA-AAA
1 AAAAGACAAATTAAAAGAAA
1394110 AAAAGA-AAA-TAAAAGAAA
1 AAAAGACAAATTAAAAGAAA
1394128 AA
1 AA
1394130 TATATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 8 0.42
19 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAAGACAAATTAAAAGAAA
Found at i:1394344 original size:41 final size:44
Alignment explanation
Indices: 1394298--1394380 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
1394288 TTGATTTTCA
*
1394298 TAAGT-AAAA-AAAAA-ATGATATTCAACGTTTAATATGAATCG
1 TAAGTAAAAAGAAAAATATGATAATCAACGTTTAATATGAATCG
**
1394339 TAAGTAAAAAGAAAAATATGATAATCAATTTTTAATATGAAT
1 TAAGTAAAAAGAAAAATATGATAATCAACGTTTAATATGAAT
1394381 TATTAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 5 0.14
42 4 0.11
43 5 0.14
44 22 0.61
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.31
Consensus pattern (44 bp):
TAAGTAAAAAGAAAAATATGATAATCAACGTTTAATATGAATCG
Found at i:1394682 original size:12 final size:12
Alignment explanation
Indices: 1394662--1394691 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1394652 TAAAAATTAA
1394662 AAATATAAAATT
1 AAATATAAAATT
*
1394674 AAATTTAAAATT
1 AAATATAAAATT
1394686 AAATAT
1 AAATAT
1394692 TTTTTTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATATAAAATT
Found at i:1394819 original size:28 final size:28
Alignment explanation
Indices: 1394775--1394830 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1394765 ATTCAGATAC
* * *
1394775 AAATTTAAATATTTTTAATTATTTAATA
1 AAATTTAAATATATTTAAATATTAAATA
1394803 AAATTTAAATGA-ATTTAAATATTAAATA
1 AAATTTAAAT-ATATTTAAATATTAAATA
1394831 TCTAACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
AAATTTAAATATATTTAAATATTAAATA
Found at i:1395141 original size:30 final size:30
Alignment explanation
Indices: 1395089--1395159 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
1395079 ATCCGATTCG
* * *
1395089 ATATATATAAATAATTATATTT-ATTTATTT
1 ATATATATTAATAATTAAATTTAATTT-TAT
1395119 ATATATATTAAT-ATATAAATTTAATTTTAT
1 ATATATATTAATAAT-TAAATTTAATTTTAT
*
1395149 ATTTATATTAA
1 ATATATATTAA
1395160 AAATAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 2 0.06
30 29 0.83
31 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
ATATATATTAATAATTAAATTTAATTTTAT
Found at i:1395149 original size:24 final size:23
Alignment explanation
Indices: 1395122--1395169 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1395112 TTTATTTATA
**
1395122 TATATTAATATATAAATTTAATTT
1 TATATTAATAT-TAAAAATAATTT
*
1395146 TATATTTATATTAAAAATAATTT
1 TATATTAATATTAAAAATAATTT
1395169 T
1 T
1395170 TTATATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATTAATATTAAAAATAATTT
Found at i:1395181 original size:20 final size:20
Alignment explanation
Indices: 1395150--1395210 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
1395140 TAATTTTATA
*
1395150 TTTATA-TTAAAAATAATTT
1 TTTATATTTAAAAATAATAT
*
1395169 TTTATATTTAAAATTAATAT
1 TTTATATTTAAAAATAATAT
* * *
1395189 TTTACATTAAAAAATTATAT
1 TTTATATTTAAAAATAATAT
1395209 TT
1 TT
1395211 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
19 6 0.17
20 29 0.83
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTATATTTAAAAATAATAT
Found at i:1404628 original size:18 final size:18
Alignment explanation
Indices: 1404589--1404641 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1404579 AGTTATTAGG
**
1404589 AATCTGTC-ATATATCTTT
1 AATCTGTCTATA-ATCTAC
1404607 AATCTGTCTATAATCTAC
1 AATCTGTCTATAATCTAC
* *
1404625 AATCTATCTACAATCTA
1 AATCTGTCTATAATCTA
1404642 TAACTATAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 27 0.90
19 3 0.10
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.42
Consensus pattern (18 bp):
AATCTGTCTATAATCTAC
Found at i:1404660 original size:29 final size:30
Alignment explanation
Indices: 1404628--1404686 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1404618 AATCTACAAT
1404628 CTATCTACAATCTATAA-CTATAGATTAAA
1 CTATCTACAATCTATAATCTATAGATTAAA
* *
1404657 CTATTTATAATCTATAATCTATAGATTAAA
1 CTATCTACAATCTATAATCTATAGATTAAA
1404687 ACTACCCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (30 bp):
CTATCTACAATCTATAATCTATAGATTAAA
Found at i:1404813 original size:22 final size:22
Alignment explanation
Indices: 1404787--1404830 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1404777 TCTATAATCA
1404787 TCAATAACTATAGATTAAAATT
1 TCAATAACTATAGATTAAAATT
*
1404809 TCAATAATTATAGATTAAAATT
1 TCAATAACTATAGATTAAAATT
1404831 GTCTCTTAAG
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:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (22 bp):
TCAATAACTATAGATTAAAATT
Found at i:1405026 original size:6 final size:6
Alignment explanation
Indices: 1405015--1405042 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1405005 TTTATTTGTT
1405015 TAATTA TAATTA TAATTA TAATTA TAAT
1 TAATTA TAATTA TAATTA TAATTA TAAT
1405043 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:1405217 original size:20 final size:20
Alignment explanation
Indices: 1405180--1405218 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1405170 TAAATAACTT
*
1405180 ACACAAAATCAACTAAAAAC
1 ACACAAAATCAACAAAAAAC
1405200 ACACAAAAAT-AACAAAAAA
1 ACAC-AAAATCAACAAAAAA
1405219 TTCTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.72, C:0.21, G:0.00, T:0.08
Consensus pattern (20 bp):
ACACAAAATCAACAAAAAAC
Found at i:1407040 original size:26 final size:28
Alignment explanation
Indices: 1406999--1407060 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
1406989 TTTTATTTTG
1406999 TATAT-TTAA-ATAA-TTTTT-ATAAATA
1 TATATATTAATATAATTTTTTAATAAA-A
1407024 TATATATTAATAT-ATTTTTTAATAAAA
1 TATATATTAATATAATTTTTTAATAAAA
1407051 -ATATATTAAT
1 TATATATTAAT
1407061 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
25 5 0.15
26 15 0.45
27 8 0.24
28 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TATATATTAATATAATTTTTTAATAAAA
Found at i:1407094 original size:22 final size:22
Alignment explanation
Indices: 1407061--1407121 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 22
1407051 ATATATTAAT
*
1407061 TTTA-ATTAATTTAAAATAATAA
1 TTTATATT-ATTTAAAATAAAAA
1407083 TTTATATTATTT--AATAAAAA
1 TTTATATTATTTAAAATAAAAA
1407103 TTTAT-TTA-TTAAATATAAA
1 TTTATATTATTTAAA-ATAAA
1407122 TAAATAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 13 0.38
21 5 0.15
22 8 0.24
23 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTATATTATTTAAAATAAAAA
Found at i:1407117 original size:19 final size:20
Alignment explanation
Indices: 1407074--1407122 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1407064 AATTAATTTA
*
1407074 AAATAATAATTTATATTATT
1 AAATAAAAATTTATATTATT
*
1407094 TAATAAAAATTTAT-TTATT
1 AAATAAAAATTTATATTATT
*
1407113 AAATATAAAT
1 AAATAAAAAT
1407123 AAATAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAAAAATTTATATTATT
Found at i:1410876 original size:36 final size:36
Alignment explanation
Indices: 1410829--1410900 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1410819 TCAAGAGAAT
* *
1410829 GATTCAAGATGAGGCTTGTCAGAATCAGATTTTTGG
1 GATTCAAGATGAGCCTTATCAGAATCAGATTTTTGG
*
1410865 GATTCACGATGAGCCTTATCAGAATCAGATTTTTGG
1 GATTCAAGATGAGCCTTATCAGAATCAGATTTTTGG
1410901 TCAATGGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (36 bp):
GATTCAAGATGAGCCTTATCAGAATCAGATTTTTGG
Found at i:1416293 original size:174 final size:177
Alignment explanation
Indices: 1415982--1416342 Score: 557
Period size: 174 Copynumber: 2.0 Consensus size: 177
1415972 TCTGTAACTT
* *
1415982 ACATTATCCTATAGTATAATATCAATGTCAGAGGAATTTCTCATGACTTAATTCTAGTCCTTTTT
1 ACATTATCCTATAATATAATATCAATGTCAGAGGAATTTCTCATGACTTAATTCTAGTCCATTTT
1416047 TTTTTTTTGGGGGGGGGGGGGGGGAGGTATAATTTCCTTTATTCCATATTATTGCTCTTCCATTA
66 TTTTTTTT---------GGGGGGGAGGTATAATTTCCTTTATTCCATATTATTGCTCTTCCATTA
*
1416112 ATGTCTGTGACAAAGCTTTGATATGATGGTTTCATGAACCTTATCAGATGCCAAGG
122 ATGTCTGTGACAAAGCTTTGATATGATGGTTTCATGAACCTTACCAGATGCCAAGG
*
1416168 ACATTATCCTATAATATAATATCAATGTCAGAGGAATTTCTCATGACTTAATTCTTGT-CATTTT
1 ACATTATCCTATAATATAATATCAATGTCAGAGGAATTTCTCATGACTTAATTCTAGTCCATTTT
* *
1416232 TTTTTTTT-GGTGGG-GGTATAATTTCCTTTATTCCATGTTATTGCTCTTCCATTAATGTCTGTG
66 TTTTTTTTGGGGGGGAGGTATAATTTCCTTTATTCCATATTATTGCTCTTCCATTAATGTCTGTG
*
1416295 ACAAAGTTTTGATATGATGGTTTCATGAACCTTACCAGATGCCAAGG
131 ACAAAGCTTTGATATGATGGTTTCATGAACCTTACCAGATGCCAAGG
1416342 A
1 A
1416343 TTTTGGGTGG
Statistics
Matches: 168, Mismatches: 7, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
174 94 0.56
175 5 0.03
185 13 0.08
186 56 0.33
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (177 bp):
ACATTATCCTATAATATAATATCAATGTCAGAGGAATTTCTCATGACTTAATTCTAGTCCATTTT
TTTTTTTTGGGGGGGAGGTATAATTTCCTTTATTCCATATTATTGCTCTTCCATTAATGTCTGTG
ACAAAGCTTTGATATGATGGTTTCATGAACCTTACCAGATGCCAAGG
Found at i:1423772 original size:19 final size:19
Alignment explanation
Indices: 1423725--1423778 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1423715 TATAAATAAC
* *
1423725 TAATTTATTAATTTAATTT
1 TAATTTATTAATTAAATAT
*
1423744 TAATTAATTATATTAAATAT
1 TAATTTATTA-ATTAAATAT
*
1423764 T-ATTTATTAAATAAA
1 TAATTTATTAATTAAA
1423779 ATAAAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 5 0.17
19 16 0.55
20 8 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTTATTAATTAAATAT
Found at i:1424506 original size:17 final size:18
Alignment explanation
Indices: 1424474--1424511 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1424464 GGAAATAATT
*
1424474 AAATTAGTAATGTAAA-A
1 AAATTAGTAATATAAATA
*
1424491 AAATTAGTATTATAAATA
1 AAATTAGTAATATAAATA
1424509 AAA
1 AAA
1424512 AATAATCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
AAATTAGTAATATAAATA
Found at i:1424543 original size:223 final size:220
Alignment explanation
Indices: 1424112--1424570 Score: 482
Period size: 223 Copynumber: 2.1 Consensus size: 220
1424102 AAAATGTGAT
* *
1424112 AATAATCATAAAATTGATGTCATTTAACGTAAAATGAATTAAAAGTATCGTAACACCTTAACAAA
1 AATAATCATAAAATTAATATCATTTAACGTAAAATGAATTAAAAGTATCGTAACACCTTAACAAA
* * * * * *
1424177 AAGTTGTAATAACTATAAATGTAATGAAAAGTAACAACAGATATAAAAAGATATTATTATAACAA
66 AAGTTGTAATAACTATAAATGTAACGAAAAGTAACAACAAATATAAAAAAAAAGTATTAAAACAA
* * ** *
1424242 TAATAATTAAGTTGATAACATAAAAGAAATATTATTACAAATAAAAAAATAATTTTAAACTAAAA
131 TAATAATTAAATTGATAACATAAAAGAAATAGTATTACAAATAAAAAAATAATCCTAAACCAAAA
1424307 AATTAAAGTTAATGTAAAAAATTAATGAG
196 AATTAAAGTTAATGTAAAAAA-T-A-G-G
* * * * * * *
1424336 AATAATCATAAAATTAATATTATTTGACTTAAAATG-ATTACAAGTATTGTTACACCTTAATAAA
1 AATAATCATAAAATTAATATCATTTAACGTAAAATGAATTAAAAGTATCGTAACACCTTAACAAA
* * * * * *
1424400 ATA-TTGTGATAATTCTAAATTTAACGAAAAGTAACAATAAATGTAAAAAAAAAAGTATTAAAAT
66 A-AGTTGTAATAACTATAAATGTAACGAAAAGTAACAACAAATAT-AAAAAAAAAGTATTAAAA-
** ** * *
1424464 GGA-AATAATTAAATT-AGTAATGTAAAA-AAATTAGTATTATAAAT-AAAAAATAATCCTATAC
128 CAATAATAATTAAATTGA-TAACATAAAAGAAA-TAGTATTACAAATAAAAAAATAATCCTAAAC
*
1424525 CAAAAAA-TAAATGTTAATGTAAAATATAGG
191 CAAAAAATTAAA-GTTAATGTAAAAAATAGG
1424555 AATAATCATAAAATTA
1 AATAATCATAAAATTA
1424571 TTTTTTTTTT
Statistics
Matches: 196, Mismatches: 33, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
219 17 0.09
220 1 0.01
221 1 0.01
222 5 0.03
223 95 0.48
224 76 0.39
225 1 0.01
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.31
Consensus pattern (220 bp):
AATAATCATAAAATTAATATCATTTAACGTAAAATGAATTAAAAGTATCGTAACACCTTAACAAA
AAGTTGTAATAACTATAAATGTAACGAAAAGTAACAACAAATATAAAAAAAAAGTATTAAAACAA
TAATAATTAAATTGATAACATAAAAGAAATAGTATTACAAATAAAAAAATAATCCTAAACCAAAA
AATTAAAGTTAATGTAAAAAATAGG
Found at i:1429322 original size:408 final size:408
Alignment explanation
Indices: 1428313--1429544 Score: 2231
Period size: 408 Copynumber: 3.0 Consensus size: 408
1428303 ATATTGATTT
1428313 ATAATCTATGAAATGTTTGATATAATGATGATTTTTAAAATGTTTTGACATTATGATTTAACGAA
1 ATAATCTATGAAATGTTTGATATAATGATGATTTTTAAAATGTTTTGACATTATGATTTAACGAA
1428378 TATTTTGAACGATCTATATGATATGTATAAAAATGATACTTGATCCAGTAAGG-GTGTGAGCTTA
66 TATTTTGAACGATCTATATGATATGTATAAAAATGATACTTGATCCAGTAAGGTGTGTGAGCTTA
1428442 TAC-TACTAAGCTGTTGATTTGCTTATTCTCATTTTATTTATTTTTTTTACAGATGAGTAAAGTG
131 TACTTACTAAGCTG-TGATTTGCTTATTCTCATTTTATTTA-TTTTTTTACAGATGAGT-AAGTG
1428506 ATAAGTTTGCTTAGTTTTGTGAAAAGCTAGAAGATTAAATTGAGAAAAAATTACTTAGACGTCGG
193 ATAAGTTTGCTTAGTTTTGTGAAAAGCTAGAAGATTAAA-TGAG-AAAAATTACTTAGACGTCGG
*
1428571 AGACAATGTTGGCCAATGAGATCTTATGAAATGTTTTTATATTTTTATATGATTTATATTTAGAT
256 AGACAATGTTGGCCAATGAGATCTTATGAAAT-TTTTTATAGTTTTATATGATTTATATTTAGAT
1428636 ATATAGAGATGTATCATTTAGTTAGATTTAAAAATATATATTTTATTTGATAGATTATATCAATT
320 ATATAGAGATGTATCA-TTAGTTAGA-TTAAAAATATATATTTTATTTGATAGATTATATCAATT
1428701 TA-T-AAGAATTTTTAGAATAGTTAAA
383 TATTAAAGAA-TTTTAGAATAGTTAAA
*
1428726 AGTAATCTTATTGGAAATGTTTGATATAATGATGATTTTTAAAATGTTTTGACATTAGGATTTAA
1 A-TAATC-TA-T-GAAATGTTTGATATAATGATGATTTTTAAAATGTTTTGACATTATGATTTAA
*
1428791 TGAATATTTTGAACGATCTATATGATATGTAT-AAAATGATACTTGATCCAGTAAGGTGTGTGAG
62 CGAATATTTTGAACGATCTATATGATATGTATAAAAATGATACTTGATCCAGTAAGGTGTGTGAG
* *
1428855 CTTATACTTACTACGCTGCGATTTGCTTATTCTCATTTTATTTATTTTTTTACAGATGAGTAAGT
127 CTTATACTTACTAAGCTGTGATTTGCTTATTCTCATTTTATTTATTTTTTTACAGATGAGTAAGT
1428920 GATAAGTTTGCTTAGTTTTGTGAAAAGCTAGAAGATTAAATGAGAAAAATTACTTAGACGTCGGA
192 GATAAGTTTGCTTAGTTTTGTGAAAAGCTAGAAGATTAAATGAGAAAAATTACTTAGACGTCGGA
1428985 GACAATGTTGGCCAATGAGATCTTATGAAATTTTTTATAGTTTTATATGATTTATATTTAGATAT
257 GACAATGTTGGCCAATGAGATCTTATGAAATTTTTTATAGTTTTATATGATTTATATTTAGATAT
1429050 ATAGAGATGTATCATTAGTTAGATTAAAAATATATATTTTATTTGATAGATTATATCAATTTATT
322 ATAGAGATGTATCATTAGTTAGATTAAAAATATATATTTTATTTGATAGATTATATCAATTTATT
1429115 AAAGAATTTTAGAATAGTTAAA
387 AAAGAATTTTAGAATAGTTAAA
1429137 ATAATCTATGAAATGTTTGATATAATGATGATTTTTAAAATGTTTTGACATTATGATTTAACGAA
1 ATAATCTATGAAATGTTTGATATAATGATGATTTTTAAAATGTTTTGACATTATGATTTAACGAA
1429202 TATTTTGAACGATCTATATGATATGTATAAAAATGATACTTGATCCAGTAAGGTGTGTGAGCTTA
66 TATTTTGAACGATCTATATGATATGTATAAAAATGATACTTGATCCAGTAAGGTGTGTGAGCTTA
1429267 TACTTACTAAGCTGTGATTTGCTTATTCTCATTTTATTTATTTTTTTACAGATGAGTAAGTGATA
131 TACTTACTAAGCTGTGATTTGCTTATTCTCATTTTATTTATTTTTTTACAGATGAGTAAGTGATA
* *
1429332 AGTTTGCTTAGTTTTGTGAAAAACTAGAAGATTAAATGAGAAAAATTACTTAAACGTCGGAGACA
196 AGTTTGCTTAGTTTTGTGAAAAGCTAGAAGATTAAATGAGAAAAATTACTTAGACGTCGGAGACA
1429397 ATGTTGGCCAATGAGATCTTATGAAATTTTTTTATAGTTTTATATGATTTATATTTAGATATATA
261 ATGTTGGCCAATGAGATCTTATGAAA-TTTTTTATAGTTTTATATGATTTATATTTAGATATATA
*
1429462 GAGATGTATCATTAGTTAGATTAAAAATATTTATTTTATTTGATAGATTATATCAATTTATTAAA
325 GAGATGTATCATTAGTTAGATTAAAAATATATATTTTATTTGATAGATTATATCAATTTATTAAA
1429527 GAATTTTAGAATAGTTAA
390 GAATTTTAGAATAGTTAA
1429545 GAAAGAAGGC
Statistics
Matches: 797, Mismatches: 12, Indels: 24
0.96 0.01 0.03
Matches are distributed among these distances:
407 82 0.10
408 189 0.24
409 122 0.15
410 45 0.06
411 27 0.03
412 52 0.07
413 53 0.07
414 9 0.01
415 46 0.06
416 42 0.05
417 121 0.15
418 9 0.01
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (408 bp):
ATAATCTATGAAATGTTTGATATAATGATGATTTTTAAAATGTTTTGACATTATGATTTAACGAA
TATTTTGAACGATCTATATGATATGTATAAAAATGATACTTGATCCAGTAAGGTGTGTGAGCTTA
TACTTACTAAGCTGTGATTTGCTTATTCTCATTTTATTTATTTTTTTACAGATGAGTAAGTGATA
AGTTTGCTTAGTTTTGTGAAAAGCTAGAAGATTAAATGAGAAAAATTACTTAGACGTCGGAGACA
ATGTTGGCCAATGAGATCTTATGAAATTTTTTATAGTTTTATATGATTTATATTTAGATATATAG
AGATGTATCATTAGTTAGATTAAAAATATATATTTTATTTGATAGATTATATCAATTTATTAAAG
AATTTTAGAATAGTTAAA
Found at i:1440084 original size:18 final size:19
Alignment explanation
Indices: 1440061--1440097 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1440051 TTGATACACC
1440061 AACATACATCA-TTTGAAA
1 AACATACATCATTTTGAAA
1440079 AACATACATCATTTTGAAA
1 AACATACATCATTTTGAAA
1440098 TATGTAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (19 bp):
AACATACATCATTTTGAAA
Found at i:1448103 original size:52 final size:52
Alignment explanation
Indices: 1448002--1448103 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
1447992 ATAAGAAGAT
*
1448002 TTGTAGAAGAAGAATTCTAAAAGGAAAAAGATTCTTAATAAGTAAGTTTGAC
1 TTGTAGAAGAAGAATTCTAAAAGGAAAAAGATTCTTAATAAGCAAGTTTGAC
* * * *
1448054 TTGTAGAAGAAGAATTTTAAAAGTAAAAAGATTCTTAATAGGCATGTTTG
1 TTGTAGAAGAAGAATTCTAAAAGGAAAAAGATTCTTAATAAGCAAGTTTG
1448104 TATGGTTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (52 bp):
TTGTAGAAGAAGAATTCTAAAAGGAAAAAGATTCTTAATAAGCAAGTTTGAC
Found at i:1449833 original size:6 final size:6
Alignment explanation
Indices: 1449819--1449848 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1449809 TTTTCCATTG
*
1449819 TTTCTT TTTCAT TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
1449849 CCCTCAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:1454325 original size:20 final size:21
Alignment explanation
Indices: 1454289--1454347 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
1454279 TAATTAAATA
*
1454289 GTTATTTATTTACTTAT-TAT
1 GTTATTTATTTTCTTATCTAT
*
1454309 GTTATTTATTTTGTTATCTAT
1 GTTATTTATTTTCTTATCTAT
*
1454330 TTTATTTTATTTTTCTTA
1 GTTA-TTTA-TTTTCTTA
1454348 GATTTTATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 15 0.47
21 6 0.19
22 4 0.12
23 7 0.22
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.69
Consensus pattern (21 bp):
GTTATTTATTTTCTTATCTAT
Found at i:1455810 original size:53 final size:53
Alignment explanation
Indices: 1455712--1455819 Score: 130
Period size: 53 Copynumber: 2.0 Consensus size: 53
1455702 AATTTTTTTT
* * *
1455712 TAAATAAGCCCAAATTGTGAAAATTTTAGAAATGCCACAAAAAAAAGA-ATTTC
1 TAAATAAGCCCAAATTATGAAAAATTTAGAAATGCCA-AAAAAAAAAATATTTC
* * *
1455765 TAAATAGGCTCAAATTATGAAAAATTTAGAAAT-TCAAAAAGAAAAAATATTTC
1 TAAATAAGCCCAAATTATGAAAAATTTAGAAATGCCAAAAA-AAAAAATATTTC
1455818 TA
1 TA
1455820 GTTTGACCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 4 0.09
52 7 0.15
53 36 0.77
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (53 bp):
TAAATAAGCCCAAATTATGAAAAATTTAGAAATGCCAAAAAAAAAAATATTTC
Found at i:1456913 original size:12 final size:13
Alignment explanation
Indices: 1456898--1456934 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
1456888 TCCATTATCA
1456898 CATCATTTT-ATG
1 CATCATTTTCATG
1456910 CATCATTTTCATG
1 CATCATTTTCATG
1456923 C-TCATTTTCATG
1 CATCATTTTCATG
1456935 TTCATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.49
Consensus pattern (13 bp):
CATCATTTTCATG
Found at i:1456939 original size:12 final size:12
Alignment explanation
Indices: 1456900--1456939 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1456890 CATTATCACA
1456900 TCATTTT-ATGC
1 TCATTTTCATGC
1456911 ATCATTTTCATGC
1 -TCATTTTCATGC
*
1456924 TCATTTTCATGT
1 TCATTTTCATGC
1456936 TCAT
1 TCAT
1456940 ATTTTAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (12 bp):
TCATTTTCATGC
Found at i:1459426 original size:15 final size:17
Alignment explanation
Indices: 1459387--1459425 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1459377 CAAACCCAGT
*
1459387 CCACACAAGATATGTCA
1 CCACACAAAATATGTCA
1459404 CCACACAAAATATGTCA
1 CCACACAAAATATGTCA
1459421 CCACA
1 CCACA
1459426 ACAATTCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.33, G:0.08, T:0.15
Consensus pattern (17 bp):
CCACACAAAATATGTCA
Found at i:1467369 original size:44 final size:44
Alignment explanation
Indices: 1467316--1467723 Score: 452
Period size: 44 Copynumber: 9.3 Consensus size: 44
1467306 GATTGTCGAT
*
1467316 GAGC-TTGTTTATTTTTTCAAAGTCGTTGAGTCTCTGATTAGAG
1 GAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
*
1467359 GAGCTTTGTTTATTTTTTTCAAAGTCGTT-AACCTCTGATTAGAG
1 GAGCTTTGTTTA-TTTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
* *
1467403 GAGCTTTGTTTATTTTTTCAAAGTCGTTGATCCTCTAATTAGAG
1 GAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
* * *
1467447 GAGCTTTGTTTATTTTTTTCAAAGTCATTAAGCCTTTGATTAGAG
1 GAGCTTTGTTTA-TTTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
* * *
1467492 GAGCTTTGTTTATTTTTTCCAAAGTCATTGAGCCTCTAATTAGAT
1 GAGCTTTGTTTATTTTTT-CAAAGTCGTTGAGCCTCTGATTAGAG
* *
1467537 GAGCTTTATTTA-TTTTTCAAAAGTTGTTGAGCCTCT-ATTTAGAG
1 GAGCTTTGTTTATTTTTTC-AAAGTCGTTGAGCCTCTGA-TTAGAG
* * * * *
1467581 GAGCTTCGTTTA-TTTTTCAAAATCGTTAAGCCTCTGATTAAAA
1 GAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
* * * * * *
1467624 GAGCTTTGTTTA-TTTTCCAAAAGTCATTAAACATCTTATTAGAG
1 GAGCTTTGTTTATTTTTTC-AAAGTCGTTGAGCCTCTGATTAGAG
* * * *
1467668 GAGCTTTATTTATTTTTTAAAAGTTGTTGAACCTCT-ATTTAGAG
1 GAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTGA-TTAGAG
*
1467712 GAACTTTGTTTA
1 GAGCTTTGTTTA
1467724 CAAACCTCTG
Statistics
Matches: 312, Mismatches: 42, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
43 57 0.18
44 163 0.52
45 92 0.29
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (44 bp):
GAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
Found at i:1474033 original size:57 final size:57
Alignment explanation
Indices: 1473970--1474154 Score: 232
Period size: 57 Copynumber: 3.2 Consensus size: 57
1473960 ATTGCCGCGG
* * * * * *
1473970 CCACCACCACCTCCAACCCCATGGAAGTCAAATGTAGCGGCGACAGGATCAACCTTT
1 CCACCACCACCTCCAACCCCATTGCAGTCAAAAGTAGTGGCGACAGGAACAACCCTT
* *
1474027 CCACCACCACCTCCAGA-TCCATTGCAGTCAAAAGTAGTGGCGACACGAACAACCCTT
1 CCACCACCACCTCCA-ACCCCATTGCAGTCAAAAGTAGTGGCGACAGGAACAACCCTT
* *
1474084 CCACCACCACCTCCAGCCCCATTGCAGTCAAAAGTAGTGGC-AGCAGG-GCAACCACTT
1 CCACCACCACCTCCAACCCCATTGCAGTCAAAAGTAGTGGCGA-CAGGAACAACC-CTT
1474141 CCACCACCACCTCC
1 CCACCACCACCTCC
1474155 TCCTGGAAGT
Statistics
Matches: 112, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
56 6 0.05
57 105 0.94
58 1 0.01
ACGTcount: A:0.29, C:0.40, G:0.16, T:0.15
Consensus pattern (57 bp):
CCACCACCACCTCCAACCCCATTGCAGTCAAAAGTAGTGGCGACAGGAACAACCCTT
Done.