Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, 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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 6 of 22
Found at i:2189298 original size:20 final size:21
Alignment explanation
Indices: 2189270--2189312 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2189260 TAACAAATTA
* *
2189270 TTAAAAAATAAATATTTTAAT
1 TTAAAAATTAAATATTATAAT
2189291 TTAAAAATTAAATATTATAAT
1 TTAAAAATTAAATATTATAAT
2189312 T
1 T
2189313 AATGGTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAAAATTAAATATTATAAT
Found at i:2190589 original size:31 final size:31
Alignment explanation
Indices: 2190523--2190622 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
2190513 TCATAAAAAT
* * * * *
2190523 TAAATTAAACAAAATTGTA-AAGTACAAGAAT
1 TAAATTGAACAAAACTCTATAA-TACATGAAC
* *
2190554 TAAATTGAACAAAACTCTATGATATATGAAC
1 TAAATTGAACAAAACTCTATAATACATGAAC
* * * *
2190585 TAAATTGAATAAAATTTTATAATACATGAAT
1 TAAATTGAACAAAACTCTATAATACATGAAC
2190616 TAAATTG
1 TAAATTG
2190623 GGTACTTTTA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (31 bp):
TAAATTGAACAAAACTCTATAATACATGAAC
Found at i:2193369 original size:17 final size:17
Alignment explanation
Indices: 2193349--2193381 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2193339 TTATTTTTTC
2193349 TTTATCAAATATTAAAT
1 TTTATCAAATATTAAAT
*
2193366 TTTATTAAATATTAAA
1 TTTATCAAATATTAAA
2193382 GTGAGATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATCAAATATTAAAT
Found at i:2200887 original size:5 final size:6
Alignment explanation
Indices: 2200869--2200896 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2200859 TCTCTATTAT
2200869 AATAAA AATAAA AATAAA AATAAA AATA
1 AATAAA AATAAA AATAAA AATAAA AATA
2200897 CTTAGTTGAA
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:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:2200965 original size:23 final size:23
Alignment explanation
Indices: 2200935--2200979 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2200925 TTATAACGAT
2200935 TTAGGATTCTTAAAATCTGGAAA
1 TTAGGATTCTTAAAATCTGGAAA
* *
2200958 TTAGGATTCTTCAAGTCTGGAA
1 TTAGGATTCTTAAAATCTGGAA
2200980 GTTGATGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (23 bp):
TTAGGATTCTTAAAATCTGGAAA
Found at i:2201087 original size:23 final size:23
Alignment explanation
Indices: 2201057--2201106 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
2201047 ATTCTTAATT
2201057 CAAAAGTAAAATGTGATTTTAGA
1 CAAAAGTAAAATGTGATTTTAGA
2201080 CAAAAGTAAAATGTGATTTTAGA
1 CAAAAGTAAAATGTGATTTTAGA
2201103 CAAA
1 CAAA
2201107 TTGCTTCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (23 bp):
CAAAAGTAAAATGTGATTTTAGA
Found at i:2201727 original size:25 final size:21
Alignment explanation
Indices: 2201681--2201723 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2201671 GACCCTGGTA
2201681 TCTCTCAAAACAAAATTTAAG
1 TCTCTCAAAACAAAATTTAAG
2201702 TCTCTCAAAACAAAATTTAAG
1 TCTCTCAAAACAAAATTTAAG
2201723 T
1 T
2201724 AAGTTTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30
Consensus pattern (21 bp):
TCTCTCAAAACAAAATTTAAG
Found at i:2210840 original size:252 final size:252
Alignment explanation
Indices: 2210166--2211826 Score: 1532
Period size: 252 Copynumber: 6.6 Consensus size: 252
2210156 TGTGGGAGAT
* * * * * *
2210166 TGAATGAATAATAGTAAGGATAAGAATAATTATAGTAAAAATTAGTAATTGAAAACT-TTAATAT
1 TGAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAATAGTTGAAAAATGTTGATAT
* * * *
2210230 AAAATAGTAAGAATTAACT-TAAAAACTTATAAAGGTGGAACACGGATTATCAAAATATTAACGT
66 AAAGTAGTAAGAATTAA-TGTAAAAAATTATAAAGGTGGAACAAGGATTATCAAAATATTGACGT
* * *
2210294 AAATATGTTAGATTTAACATAACAAGTCAATTA-AGTCAAATAAATATAATTTTTTGAAAAAATT
130 AAATGTGTGAGATTTAACATAACAAGTCAATTATA-TCAAATAAATATAATTTTTAG-AAAAATT
* ** * *
2210358 AAACATTTAAATTTTTATTCTTGAGTTTATAGTATGCAACAACTTATAAATTTTAATTTA
193 AAACATTTAAATTTTTATTCTTGAGTTTAAAGTATGTTACAGCTTATAAATTTTAATCTA
* * * * * ** *
2210418 TAAATGAATAATAGTAGGGATAAAAAT-ATTGTAGTAAAAATTAATAGTTGAAAGACCTTGACAT
1 TGAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAATAGTTGAAAAATGTTGATAT
* * *
2210482 AAA-TAGTAAGAATTAATGTAAAAAATTATAAAGGTGGAATAAGTATTATCAAAATATTGACATA
66 AAAGTAGTAAGAATTAATGTAAAAAATTATAAAGGTGGAACAAGGATTATCAAAATATTGACGTA
* * *
2210546 AATGTGTGAAATTTAACATAACAAGTCAATTATATCAAATAAATATAATTTTTAGAGAAATTACA
131 AATGTGTGAGATTTAACATAACAAGTCAATTATATCAAATAAATATAATTTTTAGAAAAATTAAA
** *
2210611 CATTTAAATTTTTATTCTTGAGTTTAAAGTACT-TTATGGTTTATAAATTTTAATCTA
196 CATTTAAATTTTTATTCTTGAGTTTAAAGTA-TGTTACAGCTTATAAATTTTAATCTA
* * **
2210668 TCAATGAATAATAGTAAGGATAAAAATAATTATAATGAAAATTAATAGTTGAAAAATGTTGACGT
1 TGAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAATAGTTGAAAAATGTTGATAT
* * * * *
2210733 AAAGTAGTAAGAATTAATATAAAAAATTATAAAAGTAGAATAAGGATTATCAAAATATTGACTTA
66 AAAGTAGTAAGAATTAATGTAAAAAATTATAAAGGTGGAACAAGGATTATCAAAATATTGACGTA
* ** * * * * *
2210798 AATATGTGAGATTTAATGTAACAAGTCAATTCTGTTAAATAAACT-TAATATTTAGGAAAATTAA
131 AATGTGTGAGATTTAACATAACAAGTCAATTATATCAAATAAA-TATAATTTTTAGAAAAATTAA
* * * * *
2210862 ATATTAAAATTTTTATTCTCGAGTTTAAAGTATCTTACGGCTTATAAATTTTAATCTA
195 ACATTTAAATTTTTATTCTTGAGTTTAAAGTATGTTACAGCTTATAAATTTTAATCTA
* * ** ** * * * *** * *
2210920 TGAATAAATAGTAACAAAAATAAAAATGATTATAGCGAAAATTAGTAGTTGAAAACCATTAATGT
1 TGAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAATAGTTGAAAAATGTTGATAT
* * * * * * *
2210985 AAAGCAATAAGAATTAATGTACAAAATTATAAAGATGGAACAAGGTTTGTCAAAATATTGAAGTA
66 AAAGTAGTAAGAATTAATGTAAAAAATTATAAAGGTGGAACAAGGATTATCAAAATATTGACGTA
* * * * * * *
2211050 AATGTATGAGGTTTAACGTAACAAGTTATTTATATCAAATAAACATAATTTTCA-AAAAAGTTAA
131 AATGTGTGAGATTTAACATAACAAGTCAATTATATCAAATAAATATAATTTTTAGAAAAA-TTAA
* * * *
2211114 ACATTTAAATTTTTATT-TTCGAGTTTAGAGTATGTAACAACTTACAAATTTTAATCTA
195 ACATTTAAATTTTTATTCTT-GAGTTTAAAGTATGTTACAGCTTATAAATTTTAATCTA
* * * * *
2211172 T-AGATAAATAATAATAAGAATAAAAATAATTATAGTGAAAATTAATAGTTAAAAAACGTTGATA
1 TGA-ATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAATAGTTGAAAAATGTTGATA
* * * * * * * * *
2211236 TAAAGTAGTAAGAATTAAGGTAAAAAATTATAAAGGTTGAACAAGCAGTGTTAAAATTTTAACAT
65 TAAAGTAGTAAGAATTAATGTAAAAAATTATAAAGGTGGAACAAGGATTATCAAAATATTGACGT
* * * * * *
2211301 AAATGTGTGAGATATAAAATAATAAGTCAATTACATCAAATAAACATAATTTTT-G--AGA--AA
130 AAATGTGTGAGATTTAACATAACAAGTCAATTATATCAAATAAATATAATTTTTAGAAAAATTAA
* * * * * * * *
2211361 A-ATTTGAACTTGTGTTCTTAAGTTTAATGTAATTTTACAG-TTGA-ATAATTTTGATCTA
195 ACATTTAAATTTTTATTCTTGAGTTTAAAGT-ATGTTACAGCTT-ATA-AATTTTAATCTA
* * * * *
2211419 TGAATGAATAATAGTATGGATAAACATAATTATAGTAAAAATTAGTAGTTAAAAAATG-T-A-A-
1 TGAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAATAGTTGAAAAATGTTGATAT
* * ** * ** * *
2211480 ACA-TCAGTAAAAATTAACATAAAATATTATAAAGGTGGAACAAATATTGTCAAAATGTT-ACCG
66 AAAGT-AGTAAGAATTAATGTAAAAAATTATAAAGGTGGAACAAGGATTATCAAAATATTGA-CG
* ** *
2211543 TAAATGTGTAAGATTTAATGTAATAAGTCAATTA-AGTCAAATAAATATAATTTTTA-AAAAATT
129 TAAATGTGTGAGATTTAACATAACAAGTCAATTATA-TCAAATAAATATAATTTTTAGAAAAATT
* * *
2211606 AAACATTTAAATTTTTATTCTTGAGTTTAAAGTAT-TTA-ATGGTT-TACAAATTTAATATA
193 AAACATTTAAATTTTTATTCTTGAGTTTAAAGTATGTTACA-GCTTATA-AATTTTAATCTA
* * *
2211665 TGAATGTATAATAATAAGGATAAAAATAATTATAGTGAAAA-TAAGTAGATGAAAAAT-TCTGAT
1 TGAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAA-TAGTTGAAAAATGT-TGAT
* * * * * * * * * *
2211728 GTAAAACT-GTAAGAATTAATGTAAAAGATTATAAAGATGAAACTAGTAATATCAAAATATTAAT
64 AT-AAAGTAGTAAGAATTAATGTAAAAAATTATAAAGGTGGAACAAGGATTATCAAAATATTGAC
* * * *
2211792 GTTAATGTGTGAAATTTAACGTAATAAGTCAATTA
128 GTAAATGTGTGAGATTTAACATAACAAGTCAATTA
2211827 ATAAAAATTT
Statistics
Matches: 1150, Mismatches: 220, Indels: 80
0.79 0.15 0.06
Matches are distributed among these distances:
242 3 0.00
243 95 0.08
244 1 0.00
245 6 0.01
246 83 0.07
247 79 0.07
248 25 0.02
250 156 0.14
251 169 0.15
252 532 0.46
253 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (252 bp):
TGAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAATAGTTGAAAAATGTTGATAT
AAAGTAGTAAGAATTAATGTAAAAAATTATAAAGGTGGAACAAGGATTATCAAAATATTGACGTA
AATGTGTGAGATTTAACATAACAAGTCAATTATATCAAATAAATATAATTTTTAGAAAAATTAAA
CATTTAAATTTTTATTCTTGAGTTTAAAGTATGTTACAGCTTATAAATTTTAATCTA
Found at i:2211585 original size:243 final size:243
Alignment explanation
Indices: 2211160--2211605 Score: 553
Period size: 243 Copynumber: 1.8 Consensus size: 243
2211150 ACAACTTACA
*
2211160 AATTTTAATCTATAGATAAATAATAATAAGAATAAAAATAATTATAGTGAAAATTAATAGTTAAA
1 AATTTTAATCTATAGATAAATAATAATAAGAATAAAAATAATTATAGTAAAAATTAATAGTTAAA
* ** * * *
2211225 AAACGTTGATATAAAGTAGTAAGAATTAAGGTAAAAAATTATAAAGGTTGAACAAGCAGTGTTAA
66 AAAC--TGATATAAAGTAGTAAAAATTAACATAAAAAATTATAAAGGTGGAACAAACAGTGTCAA
* *
2211290 AATTTTAACATAAATGTGTGAGATATAAAATAATAAGTCAATTACATCAAATAAACATAATTTTT
129 AATGTTAACATAAATGTGTAAGATATAAAATAATAAGTCAATTACATCAAATAAACATAATTTTT
2211355 GAGAAAAATTTGAACTTGTGTTCTTAAGTTTAATGTAATTTTACAGTTGAAT
194 -A-AAAAATTTGAACTTGTGTTCTTAAGTTTAATGTAATTTTACAGTTGAAT
* * * * * * *
2211407 AATTTTGATCTAT-GAATGAATAATAGTATGGATAAACATAATTATAGTAAAAATTAGTAGTTAA
1 AATTTTAATCTATAG-ATAAATAATAATAAGAATAAAAATAATTATAGTAAAAATTAATAGTTAA
* * *
2211471 AAAA-TG-TA-AACA-TCAGTAAAAATTAACATAAAATATTATAAAGGTGGAACAAATATTGTCA
65 AAAACTGATATAA-AGT-AGTAAAAATTAACATAAAAAATTATAAAGGTGGAACAAACAGTGTCA
* * * ** *
2211532 AAATGTTACCGTAAATGTGTAAGATTTAATGTAATAAGTCAATTA-AGTCAAATAAATATAATTT
128 AAATGTTAACATAAATGTGTAAGATATAAAATAATAAGTCAATTACA-TCAAATAAACATAATTT
2211596 TTAAAAAATT
192 TTAAAAAATT
2211606 AAACATTTAA
Statistics
Matches: 170, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
241 7 0.04
242 5 0.03
243 97 0.57
244 2 0.01
246 1 0.01
247 58 0.34
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.34
Consensus pattern (243 bp):
AATTTTAATCTATAGATAAATAATAATAAGAATAAAAATAATTATAGTAAAAATTAATAGTTAAA
AAACTGATATAAAGTAGTAAAAATTAACATAAAAAATTATAAAGGTGGAACAAACAGTGTCAAAA
TGTTAACATAAATGTGTAAGATATAAAATAATAAGTCAATTACATCAAATAAACATAATTTTTAA
AAAATTTGAACTTGTGTTCTTAAGTTTAATGTAATTTTACAGTTGAAT
Found at i:2224728 original size:2 final size:2
Alignment explanation
Indices: 2224723--2224752 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2224713 GATCTCTCCT
2224723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2224753 GATACACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2232158 original size:9 final size:9
Alignment explanation
Indices: 2232144--2232169 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2232134 CCAAGAATGA
2232144 TGATGATGC
1 TGATGATGC
2232153 TGATGATGC
1 TGATGATGC
2232162 TGATGATG
1 TGATGATG
2232170 AGGAAAGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.35, T:0.35
Consensus pattern (9 bp):
TGATGATGC
Found at i:2249677 original size:21 final size:21
Alignment explanation
Indices: 2249639--2249679 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2249629 AAGTGAATTA
*
2249639 TTTTAATTTTATATTTATTTC
1 TTTTAATTTGATATTTATTTC
2249660 TTTTAATTTGAT-TATTATTT
1 TTTTAATTTGATAT-TTATTT
2249680 ATTAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTAATTTGATATTTATTTC
Found at i:2262155 original size:19 final size:19
Alignment explanation
Indices: 2262133--2262214 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 19
2262123 TATTTAAAAT
2262133 TAAATTACAATTTTAATTA
1 TAAATTACAATTTTAATTA
***
2262152 TAAATTACAA-AAGAATTA
1 TAAATTACAATTTTAATTA
** **
2262170 -ATAATTTTAATTTTAAAAA
1 TA-AATTACAATTTTAATTA
*
2262189 TTAAATTAAAATTTTAATTA
1 -TAAATTACAATTTTAATTA
2262209 TAAATT
1 TAAATT
2262215 TTTAATATTT
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
17 1 0.02
18 11 0.24
19 19 0.42
20 13 0.29
21 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (19 bp):
TAAATTACAATTTTAATTA
Found at i:2262390 original size:92 final size:88
Alignment explanation
Indices: 2262204--2262391 Score: 204
Period size: 92 Copynumber: 2.1 Consensus size: 88
2262194 TTAAAATTTT
** * * *
2262204 AATTATAAATTTTTAATATTTTAAAATAAAAATAAAAGAAAATAATCATATTAATATTTTAATTA
1 AATTATAAATTAATAATATTTAAAAATAAAAATAAAAGAAAATAATCATATTAAAATTTTAATAA
* *
2262269 TAAACTATTAATATTTTAAATGA
66 TAAACTAATAATATTGTAAATGA
2262292 AA-TATAAATTAATAATATTCTAAAAAT-AAAATAAAAGTAAACTAGATAATCATATTAAAATTT
1 AATTATAAATTAATAATATT-TAAAAATAAAAATAAAAG--AA--A-ATAATCATATTAAAATTT
**
2262355 TAAATAATAATTTAATAATATTGT-AAT-A
60 T-AATAATAAACTAATAATATTGTAAATGA
2262383 AATTATAAA
1 AATTATAAA
2262392 AAATAAATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
87 25 0.30
88 8 0.10
89 2 0.02
91 4 0.05
92 27 0.33
93 17 0.20
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (88 bp):
AATTATAAATTAATAATATTTAAAAATAAAAATAAAAGAAAATAATCATATTAAAATTTTAATAA
TAAACTAATAATATTGTAAATGA
Found at i:2263416 original size:26 final size:25
Alignment explanation
Indices: 2263387--2263439 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
2263377 TATCACGACG
*
2263387 TGTAAACTGGTGAGGCAACATCAACA
1 TGTAAACTAGTGAGGCAACAT-AACA
* *
2263413 TGTAAACTAGTGAGTCATCATAACA
1 TGTAAACTAGTGAGGCAACATAACA
2263438 TG
1 TG
2263440 GTGAAATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (25 bp):
TGTAAACTAGTGAGGCAACATAACA
Found at i:2275037 original size:2 final size:2
Alignment explanation
Indices: 2275030--2275056 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2275020 TTAGAGGCCG
2275030 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2275057 GCGTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2278927 original size:15 final size:15
Alignment explanation
Indices: 2278907--2278940 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2278897 AATAAGTATT
*
2278907 AAATATAGTAATTTA
1 AAATATAGTAATATA
*
2278922 AAATATATTAATATA
1 AAATATAGTAATATA
2278937 AAAT
1 AAAT
2278941 TATTTTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATATAGTAATATA
Found at i:2282379 original size:17 final size:17
Alignment explanation
Indices: 2282357--2282392 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2282347 CGGTGATTGG
* *
2282357 ACTGAGCGGTGTGGCGA
1 ACTGAGCAGCGTGGCGA
2282374 ACTGAGCAGCGTGGCGA
1 ACTGAGCAGCGTGGCGA
2282391 AC
1 AC
2282393 GACAAGGGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.42, T:0.14
Consensus pattern (17 bp):
ACTGAGCAGCGTGGCGA
Found at i:2286096 original size:25 final size:25
Alignment explanation
Indices: 2286068--2286119 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
2286058 TGAGGGGGAG
*
2286068 TAATGGAAGAGATTTGATTTGAGAT
1 TAATGGAAGAGATTTGACTTGAGAT
*
2286093 TAATGGAGGAGATTTGACTTGAGAT
1 TAATGGAAGAGATTTGACTTGAGAT
2286118 TA
1 TA
2286120 TCCTATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.35
Consensus pattern (25 bp):
TAATGGAAGAGATTTGACTTGAGAT
Found at i:2288043 original size:21 final size:21
Alignment explanation
Indices: 2288019--2288060 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2288009 TTTACTAAAC
* *
2288019 CTAAACCTTCTTGTTTTTGCA
1 CTAAACCTTCCTATTTTTGCA
*
2288040 CTAAATCTTCCTATTTTTGCA
1 CTAAACCTTCCTATTTTTGCA
2288061 TTGATAACAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.07, T:0.48
Consensus pattern (21 bp):
CTAAACCTTCCTATTTTTGCA
Found at i:2299093 original size:3 final size:3
Alignment explanation
Indices: 2299085--2299116 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2299075 CATCAACATC
2299085 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2299117 CTTTGACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2299281 original size:20 final size:20
Alignment explanation
Indices: 2299256--2299301 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2299246 ACCTCCCTTG
*
2299256 TTTTCTCCATTGTTCTACAT
1 TTTTCTACATTGTTCTACAT
** *
2299276 TTTTCTATGTTGTTCTTCAT
1 TTTTCTACATTGTTCTACAT
2299296 TTTTCT
1 TTTTCT
2299302 TGTTTCATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.20, G:0.07, T:0.63
Consensus pattern (20 bp):
TTTTCTACATTGTTCTACAT
Found at i:2306930 original size:30 final size:30
Alignment explanation
Indices: 2306894--2306955 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
2306884 TATTAGTCAC
*
2306894 AAAAACTTGTTTGACTCAAAATAAAAATAT
1 AAAAACTTATTTGACTCAAAATAAAAATAT
**
2306924 AAAAACTTATTTGGGTCAAAATAAAAATAT
1 AAAAACTTATTTGACTCAAAATAAAAATAT
2306954 AA
1 AA
2306956 TGGCTTGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (30 bp):
AAAAACTTATTTGACTCAAAATAAAAATAT
Found at i:2312131 original size:4 final size:4
Alignment explanation
Indices: 2312124--2312165 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
2312114 GCTATATATA
* *
2312124 TATG TATG TATG TATG CATG CATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
2312166 CAAACGCACG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:2324447 original size:14 final size:15
Alignment explanation
Indices: 2324423--2324453 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2324413 TTCTATATTC
2324423 TTTTTATTCTTTTCA
1 TTTTTATTCTTTTCA
2324438 TTTTTA-TCTTTTCA
1 TTTTTATTCTTTTCA
2324452 TT
1 TT
2324454 ATTCATCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTCTTTTCA
Found at i:2324611 original size:25 final size:25
Alignment explanation
Indices: 2324573--2324667 Score: 75
Period size: 25 Copynumber: 3.8 Consensus size: 25
2324563 ATCCATCCAC
* *
2324573 TTCTAGTGGCAAAATTATCCTAAGA
1 TTCTAATGGTAAAATTATCCTAAGA
* *
2324598 TTCTAATGGTAAAATTATCCATCCA-C
1 TTCTAATGGTAAAATTATCC-T-AAGA
* * * *
2324624 TTTTGATGGTAAAATTATTCTTAGA
1 TTCTAATGGTAAAATTATCCTAAGA
* *
2324649 TTCTGATAGTAAAATTATC
1 TTCTAATGGTAAAATTATC
2324668 TATTCACTTC
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
24 1 0.02
25 35 0.64
26 18 0.33
27 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (25 bp):
TTCTAATGGTAAAATTATCCTAAGA
Found at i:2324638 original size:26 final size:26
Alignment explanation
Indices: 2324537--2324692 Score: 133
Period size: 26 Copynumber: 6.1 Consensus size: 26
2324527 GGGTTACAAC
*
2324537 ATCCATCCACTTCTTG-TGCTAAAATT
1 ATCCATCCACTTC-TGATGGTAAAATT
*
2324563 ATCCATCCACTTCT-AGTGGCAAAATT
1 ATCCATCCACTTCTGA-TGGTAAAATT
* * *
2324589 ATCC-T-AAGATTCTAATGGTAAAATT
1 ATCCATCCA-CTTCTGATGGTAAAATT
*
2324614 ATCCATCCACTTTTGATGGTAAAATT
1 ATCCATCCACTTCTGATGGTAAAATT
* * ** *
2324640 ATTCTTAGA-TTCTGATAGTAAAATT
1 ATCCATCCACTTCTGATGGTAAAATT
* *
2324665 ATCTATTCACTTCTGATGGTAAAATT
1 ATCCATCCACTTCTGATGGTAAAATT
2324691 AT
1 AT
2324693 TCTTAAAATT
Statistics
Matches: 102, Mismatches: 21, Indels: 14
0.74 0.15 0.10
Matches are distributed among these distances:
24 1 0.01
25 37 0.36
26 63 0.62
27 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (26 bp):
ATCCATCCACTTCTGATGGTAAAATT
Found at i:2324693 original size:51 final size:51
Alignment explanation
Indices: 2324556--2324697 Score: 196
Period size: 51 Copynumber: 2.8 Consensus size: 51
2324546 CTTCTTGTGC
* * * *
2324556 TAAAATTATCCATCCACTTCT-AGTGGCAAAATTATCCTAAGATTCTAATGG
1 TAAAATTATCCATCCACTTCTGA-TGGTAAAATTATTCTTAGATTCTAATAG
* *
2324607 TAAAATTATCCATCCACTTTTGATGGTAAAATTATTCTTAGATTCTGATAG
1 TAAAATTATCCATCCACTTCTGATGGTAAAATTATTCTTAGATTCTAATAG
* *
2324658 TAAAATTATCTATTCACTTCTGATGGTAAAATTATTCTTA
1 TAAAATTATCCATCCACTTCTGATGGTAAAATTATTCTTA
2324698 AAATTAAAAC
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 80 0.99
52 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (51 bp):
TAAAATTATCCATCCACTTCTGATGGTAAAATTATTCTTAGATTCTAATAG
Found at i:2330100 original size:20 final size:19
Alignment explanation
Indices: 2330061--2330100 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2330051 TACTAAACCC
* *
2330061 TAAATAAAATAAGTTTTAA
1 TAAATAAAATAAGGTATAA
2330080 TAAATTAAAATAAGGTATAA
1 TAAA-TAAAATAAGGTATAA
2330100 T
1 T
2330101 GTTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (19 bp):
TAAATAAAATAAGGTATAA
Found at i:2331332 original size:28 final size:28
Alignment explanation
Indices: 2331247--2331321 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
2331237 GACTCTAAGC
* *
2331247 ATAACTTTACCTTCTAAAAGGTGGATGG
1 ATAACTTTACCTACTAAAAGGTGGATGT
* *
2331275 ATAACTTTCCCTATTAAAAGGTGGATGT
1 ATAACTTTACCTACTAAAAGGTGGATGT
2331303 ATAACTTTACCTACTAAAA
1 ATAACTTTACCTACTAAAA
2331322 AATAGATGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (28 bp):
ATAACTTTACCTACTAAAAGGTGGATGT
Found at i:2333765 original size:12 final size:12
Alignment explanation
Indices: 2333748--2333775 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2333738 ATACTAACCT
2333748 TAAATTATGTGA
1 TAAATTATGTGA
2333760 TAAATTATGTGA
1 TAAATTATGTGA
2333772 TAAA
1 TAAA
2333776 ACACGTAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (12 bp):
TAAATTATGTGA
Found at i:2336099 original size:13 final size:14
Alignment explanation
Indices: 2336066--2336092 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2336056 GTAAAATTAT
2336066 AACTTATAAAAAAG
1 AACTTATAAAAAAG
2336080 AACTTATAAAAAA
1 AACTTATAAAAAA
2336093 AATTTATCAA
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:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
AACTTATAAAAAAG
Found at i:2342200 original size:15 final size:15
Alignment explanation
Indices: 2342180--2342214 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2342170 TTGCAAAGCA
2342180 TTTATGTCATTTATT
1 TTTATGTCATTTATT
*
2342195 TTTATGTCATTTCTT
1 TTTATGTCATTTATT
2342210 TTTAT
1 TTTAT
2342215 TTAAACTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.09, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTATGTCATTTATT
Found at i:2342506 original size:38 final size:37
Alignment explanation
Indices: 2342441--2342520 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 37
2342431 CAAGGGCAAC
* * *
2342441 ATAATGAAAAGGAAAAATAGAAAAAACATTATAATAA
1 ATAATGAAAAGGAAAAAGAAAAAAAACATTATAAGAA
*
2342478 ATAA-GAAAAGAGAAAAAGAAAAGAAAACATTATGAGAA
1 ATAATGAAAAG-GAAAAAGAAAA-AAAACATTATAAGAA
2342516 ATAAT
1 ATAAT
2342521 CTTACGAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 6 0.17
37 13 0.36
38 17 0.47
ACGTcount: A:0.68, C:0.03, G:0.14, T:0.16
Consensus pattern (37 bp):
ATAATGAAAAGGAAAAAGAAAAAAAACATTATAAGAA
Found at i:2343382 original size:29 final size:30
Alignment explanation
Indices: 2343334--2343392 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
2343324 TTTCCAACTG
*
2343334 TAACAATATTTTTTTGAACATAGCATGTAA
1 TAACAATATTTTTTTAAACATAGCATGTAA
* *
2343364 TAACGATA-TTTTTTAAACATAGCGTGTAA
1 TAACAATATTTTTTTAAACATAGCATGTAA
2343393 CTTATTCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (30 bp):
TAACAATATTTTTTTAAACATAGCATGTAA
Found at i:2343452 original size:48 final size:48
Alignment explanation
Indices: 2343377--2343477 Score: 150
Period size: 48 Copynumber: 2.1 Consensus size: 48
2343367 CGATATTTTT
*
2343377 TAAACATAGCGTGTAACTTATTCTCTATCTTTGTATTTCACTAGGACA
1 TAAACATAGCGTGTAACTTATTCTCTATCTTTGTATTTCACTAAGACA
* * *
2343425 TAAACATGGCGTGTAACTTGGTT-TCTATCTTTGTATTTGACTAAGACA
1 TAAACATAGCGTGTAACTT-ATTCTCTATCTTTGTATTTCACTAAGACA
2343473 TAAAC
1 TAAAC
2343478 TCTTGGAGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 46 0.96
49 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (48 bp):
TAAACATAGCGTGTAACTTATTCTCTATCTTTGTATTTCACTAAGACA
Found at i:2346315 original size:11 final size:11
Alignment explanation
Indices: 2346301--2346325 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2346291 TATTATATAA
2346301 TTTTTATTAAT
1 TTTTTATTAAT
2346312 TTTTTATTAAT
1 TTTTTATTAAT
2346323 TTT
1 TTT
2346326 AAAAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTATTAAT
Found at i:2354060 original size:15 final size:16
Alignment explanation
Indices: 2354040--2354074 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2354030 TTCACTCAAA
2354040 TTTTTTCTCA-TAAGGT
1 TTTTTTCT-AGTAAGGT
2354056 TTTTTTCTAGTAAGGT
1 TTTTTTCTAGTAAGGT
2354072 TTT
1 TTT
2354075 AACAAGGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.17, C:0.09, G:0.14, T:0.60
Consensus pattern (16 bp):
TTTTTTCTAGTAAGGT
Found at i:2354695 original size:18 final size:18
Alignment explanation
Indices: 2354672--2354711 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2354662 AGTTCCACAA
* *
2354672 ATAATTTATAAGTAACAC
1 ATAATTCATAAATAACAC
*
2354690 ATAATTCATAAATAACTC
1 ATAATTCATAAATAACAC
2354708 ATAA
1 ATAA
2354712 ATTAACCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (18 bp):
ATAATTCATAAATAACAC
Found at i:2363660 original size:12 final size:12
Alignment explanation
Indices: 2363643--2363667 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2363633 CAAGTATACA
2363643 CGTGGGCTAAGG
1 CGTGGGCTAAGG
2363655 CGTGGGCTAAGG
1 CGTGGGCTAAGG
2363667 C
1 C
2363668 CAAATGATAG
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:0.20, G:0.48, T:0.16
Consensus pattern (12 bp):
CGTGGGCTAAGG
Found at i:2368129 original size:17 final size:17
Alignment explanation
Indices: 2368103--2368135 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2368093 CACACCTTAG
2368103 ACTTCTTTA-TATTTTC
1 ACTTCTTTATTATTTTC
2368119 ACTTGCTTTATTATTTT
1 ACTT-CTTTATTATTTT
2368136 TTCATTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (17 bp):
ACTTCTTTATTATTTTC
Found at i:2368147 original size:19 final size:20
Alignment explanation
Indices: 2368109--2368148 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2368099 TTAGACTTCT
2368109 TTATATTTTCACTTGCTTTA
1 TTATATTTTCACTTGCTTTA
* *
2368129 TTATTTTTTCATTTG-TTTA
1 TTATATTTTCACTTGCTTTA
2368148 T
1 T
2368149 CAAATTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (20 bp):
TTATATTTTCACTTGCTTTA
Found at i:2373510 original size:38 final size:38
Alignment explanation
Indices: 2373459--2373536 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
2373449 ACAATCTCTA
* * *
2373459 AATTTTTTTAAAATAATTATCTAATTTTTTTCTTCAAT
1 AATTTTTTAAAAATAAATAACTAATTTTTTTCTTCAAT
2373497 AATTTTTTAAAAATAAATAACTAATTTTTTTCTTCAAT
1 AATTTTTTAAAAATAAATAACTAATTTTTTTCTTCAAT
2373535 AA
1 AA
2373537 AAATCAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.53
Consensus pattern (38 bp):
AATTTTTTAAAAATAAATAACTAATTTTTTTCTTCAAT
Found at i:2374107 original size:111 final size:107
Alignment explanation
Indices: 2373938--2374139 Score: 255
Period size: 111 Copynumber: 1.9 Consensus size: 107
2373928 TAAATTCGGA
* * * * *
2373938 TTTTATCTTTAAATTATCTTAATTTATTTAGTGATAAATTGAATGATTCATAGATGAATTTTAAT
1 TTTTATCTATAAATTATCTTAATTTATGTAGAGATAAATTGAATAATTCATAGATGAA-TATAA-
2374003 TGGTCAAAATATGAGCTTTTGAGATTTAATGGGCTAAATTTGGGTG
64 T--TCAAAATATGAGCTTTTGAGATTTAATGGGCTAAATTTGGGTG
* * *
2374049 TTTTATCTATAAATTATCTTAATTTATGTAGAGATGAATT-ACATAACTT-GTAGGTGAATATAA
1 TTTTATCTATAAATTATCTTAATTTATGTAGAGATAAATTGA-ATAA-TTCATAGATGAATATAA
*
2374112 TTCAAAATATGAGTTTTTGAGATTTAAT
64 TTCAAAATATGAGCTTTTGAGATTTAAT
2374140 TAATCAAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
107 26 0.32
109 1 0.01
110 5 0.06
111 46 0.57
112 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (107 bp):
TTTTATCTATAAATTATCTTAATTTATGTAGAGATAAATTGAATAATTCATAGATGAATATAATT
CAAAATATGAGCTTTTGAGATTTAATGGGCTAAATTTGGGTG
Found at i:2383801 original size:3 final size:3
Alignment explanation
Indices: 2383793--2383823 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2383783 GATTATAAAT
2383793 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2383824 TCTACCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2388294 original size:23 final size:23
Alignment explanation
Indices: 2388237--2388294 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
2388227 AATTAAAAAA
*
2388237 AAATTAAAAAATATAATTTTAAGT
1 AAATT-AAATATATAATTTTAAGT
* * *
2388261 AGATGATATATATAATTATTAA-T
1 AAATTAAATATATAATT-TTAAGT
2388284 AAATTAAATAT
1 AAATTAAATAT
2388295 TTAAATATAA
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (23 bp):
AAATTAAATATATAATTTTAAGT
Found at i:2398115 original size:2 final size:2
Alignment explanation
Indices: 2398108--2398133 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2398098 CTTTTAAGTC
2398108 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2398134 TAAAAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2401510 original size:20 final size:23
Alignment explanation
Indices: 2401473--2401517 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
2401463 TATTTAATTA
2401473 TTTATATTTTATGTATTAT-AGT
1 TTTATATTTTATGTATTATAAGT
2401495 TTTATA-TTTA-GTATTATAAGT
1 TTTATATTTTATGTATTATAAGT
2401516 TT
1 TT
2401518 AGATAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 6 0.27
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (23 bp):
TTTATATTTTATGTATTATAAGT
Found at i:2415085 original size:20 final size:20
Alignment explanation
Indices: 2415032--2415086 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
2415022 TCTGTCAGTG
*
2415032 ATTCCATAGGTAACTA-ATGA
1 ATTCCATTGGTAA-TAGATGA
*
2415052 ATTCCATTGTTAATAGATGA
1 ATTCCATTGGTAATAGATGA
* *
2415072 ATTTCGTTGGTAATA
1 ATTCCATTGGTAATA
2415087 CTTGCAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (20 bp):
ATTCCATTGGTAATAGATGA
Found at i:2418886 original size:15 final size:14
Alignment explanation
Indices: 2418855--2418899 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
2418845 GATTATAATT
2418855 GAAAACAGAAAAAG
1 GAAAACAGAAAAAG
*
2418869 GAAAATAGAAAGAAG
1 GAAAACAGAAA-AAG
*
2418884 GAAAGCAGAAAAAG
1 GAAAACAGAAAAAG
2418898 GA
1 GA
2418900 GAGTTTTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.67, C:0.04, G:0.27, T:0.02
Consensus pattern (14 bp):
GAAAACAGAAAAAG
Found at i:2419816 original size:13 final size:14
Alignment explanation
Indices: 2419795--2419824 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2419785 CTTCAAATAT
*
2419795 AATTTTTTTTTTAA
1 AATTTTTTTTATAA
2419809 AATTTTTTTTATAA
1 AATTTTTTTTATAA
2419823 AA
1 AA
2419825 AGAGTATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTTTTTTATAA
Found at i:2419953 original size:31 final size:29
Alignment explanation
Indices: 2419899--2419963 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
2419889 TCAAGTAAAA
* *
2419899 AAATATTTATATATATATTTTTAACATTAT
1 AAATATTTATATATAAATATTTAAC-TTAT
*
2419929 AAATATTTTATATTTAAATATTTAACTTAT
1 AAATA-TTTATATATAAATATTTAACTTAT
*
2419959 TAATA
1 AAATA
2419964 AGTATATCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (29 bp):
AAATATTTATATATAAATATTTAACTTAT
Found at i:2431200 original size:16 final size:16
Alignment explanation
Indices: 2431150--2431204 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
2431140 TTTTTTTTTT
2431150 AAATTAATAAAAAATTA
1 AAATTAATAAAAAA-TA
***
2431167 ATAA-TAATAAATTTTA
1 A-AATTAATAAAAAATA
2431183 AAATTAATAAAAAATA
1 AAATTAATAAAAAATA
2431199 AAATTA
1 AAATTA
2431205 TTTTTTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 2 0.07
16 18 0.60
17 8 0.27
18 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTAATAAAAAATA
Found at i:2433675 original size:51 final size:51
Alignment explanation
Indices: 2433520--2433761 Score: 177
Period size: 51 Copynumber: 4.7 Consensus size: 51
2433510 TGGGGTGCAT
** * * * *
2433520 GGCACAGGCCCCCGGGCGAGCCAGCTCGGCAGGGA-GCCAACAAGGGCGCAC
1 GGCACAGGCCCTTGGGCGAGCCAGCCCGACA-GGATGCTAGCAAGGGCGCAC
** * * * * **
2433571 ATCACAGGCCCTTGGGCTAGCC-GTCCCGAC-GGAATGCCAGGAGGGGCAAAC
1 GGCACAGGCCCTTGGGCGAGCCAG-CCCGACAGG-ATGCTAGCAAGGGCGCAC
* *
2433622 GGCACAGGCCCTTGGGCGAGCTAGCTCGACAGGATGCTAGCAAGGGCGCAC
1 GGCACAGGCCCTTGGGCGAGCCAGCCCGACAGGATGCTAGCAAGGGCGCAC
* * * * * * * * *
2433673 GGCTCGGGCCCATGAGCGAGCCAGCCCGACCGAAGGCTAGCAGGGGCGCAA
1 GGCACAGGCCCTTGGGCGAGCCAGCCCGACAGGATGCTAGCAAGGGCGCAC
* *
2433724 GGCGCAGGACCC-TGGGCGAGCCAGCCCGACGGGATGCT
1 GGCACAGG-CCCTTGGGCGAGCCAGCCCGACAGGATGCT
2433762 GGTAAGGGTG
Statistics
Matches: 146, Mismatches: 39, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
49 2 0.01
50 2 0.01
51 136 0.93
52 6 0.04
ACGTcount: A:0.21, C:0.33, G:0.38, T:0.08
Consensus pattern (51 bp):
GGCACAGGCCCTTGGGCGAGCCAGCCCGACAGGATGCTAGCAAGGGCGCAC
Found at i:2433683 original size:102 final size:101
Alignment explanation
Indices: 2433520--2433804 Score: 229
Period size: 102 Copynumber: 2.8 Consensus size: 101
2433510 TGGGGTGCAT
* * * * *
2433520 GGCACAGGCCCCCGGGCGAGCCAGCTCGGCAGGGA-GCCAACAAGGGCGCACATCACAGGCCCTT
1 GGCACAGG-CCCTGGGCGAGCCAGCTCGACA-GGATGCTAACAAGGGCGCACAGCACAGGCCCAT
* * * * *
2433584 GGGCTAGCC-GTCCCGACGGAATGCCAGGAGGGGC-AAA
64 GAGCGAGCCAG-CCCGACCGAAGGCCAGCAGGGGCGAAA
* * * * *
2433621 CGGCACAGGCCCTTGGGCGAGCTAGCTCGACAGGATGCTAGCAAGGGCGCACGGCTCGGGCCCAT
1 -GGCACAGGCCC-TGGGCGAGCCAGCTCGACAGGATGCTAACAAGGGCGCACAGCACAGGCCCAT
* *
2433686 GAGCGAGCCAGCCCGACCGAAGGCTAGCAGGGGCGCAA
64 GAGCGAGCCAGCCCGACCGAAGGCCAGCAGGGGCGAAA
* * * *** *
2433724 GGCGCAGGACCCTGGGCGAGCCAGCCCGACGGGATGCTGGTAAGGGTGCACAGCA-ACGGCTCC-
1 GGCACAGG-CCCTGGGCGAGCCAGCTCGACAGGATGCTAACAAGGGCGCACAGCACA-GGC-CCA
* *
2433787 TAAGCGAGCCAGCTCGAC
63 TGAGCGAGCCAGCCCGAC
2433805 AGAACAGGCA
Statistics
Matches: 147, Mismatches: 29, Indels: 14
0.77 0.15 0.07
Matches are distributed among these distances:
101 6 0.04
102 133 0.90
103 8 0.05
ACGTcount: A:0.22, C:0.33, G:0.37, T:0.08
Consensus pattern (101 bp):
GGCACAGGCCCTGGGCGAGCCAGCTCGACAGGATGCTAACAAGGGCGCACAGCACAGGCCCATGA
GCGAGCCAGCCCGACCGAAGGCCAGCAGGGGCGAAA
Found at i:2434095 original size:15 final size:16
Alignment explanation
Indices: 2434077--2434121 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
2434067 CACGAAGGCG
2434077 CGCGGCACGCCAG-TA
1 CGCGGCACGCCAGATA
*
2434092 CGCGGCACG-CAGATG
1 CGCGGCACGCCAGATA
*
2434107 CGCGGCACGCGAGAT
1 CGCGGCACGCCAGAT
2434122 GGCTCGGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 3 0.12
15 19 0.73
16 4 0.15
ACGTcount: A:0.20, C:0.36, G:0.38, T:0.07
Consensus pattern (16 bp):
CGCGGCACGCCAGATA
Found at i:2434384 original size:15 final size:14
Alignment explanation
Indices: 2434348--2434404 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
2434338 CCAAATGGGT
*
2434348 TTTGGAGGGAAAAC
1 TTTGGAGGGAAATC
2434362 TTTCGGAGGGAAATCC
1 TTT-GGAGGGAAAT-C
*
2434378 TTTGGAGAGAAAGT-
1 TTTGGAGGGAAA-TC
2434392 TTTGGAGGGAAAT
1 TTTGGAGGGAAAT
2434405 GGGTGGGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 1 0.03
14 14 0.38
15 17 0.46
16 5 0.14
ACGTcount: A:0.32, C:0.07, G:0.35, T:0.26
Consensus pattern (14 bp):
TTTGGAGGGAAATC
Found at i:2434401 original size:29 final size:30
Alignment explanation
Indices: 2434348--2434404 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
2434338 CCAAATGGGT
*
2434348 TTTGGAGGGAAAACTTTCGGAGGGAAATCC
1 TTTGGAGAGAAAACTTTCGGAGGGAAATCC
* *
2434378 TTTGGAGAG-AAAGTTTTGGAGGGAAAT
1 TTTGGAGAGAAAACTTTCGGAGGGAAAT
2434405 GGGTGGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.32, C:0.07, G:0.35, T:0.26
Consensus pattern (30 bp):
TTTGGAGAGAAAACTTTCGGAGGGAAATCC
Found at i:2446175 original size:28 final size:29
Alignment explanation
Indices: 2446121--2446175 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
2446111 ATGTATCAAC
*
2446121 ATAAGAATATTATATTTTATTTTAATTAA
1 ATAAGAATATTATATTTTATTTAAATTAA
*
2446150 ATAATAAT-TTATATATTT-TTTAAATT
1 ATAAGAATATTATAT-TTTATTTAAATT
2446176 CTAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
ATAAGAATATTATATTTTATTTAAATTAA
Found at i:2453600 original size:7 final size:7
Alignment explanation
Indices: 2453588--2453619 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
2453578 AAAAAGGGAA
2453588 TTTTTAT
1 TTTTTAT
2453595 TTTTTAT
1 TTTTTAT
2453602 TTTTTAT
1 TTTTTAT
2453609 TTTTTAT
1 TTTTTAT
2453616 TTTT
1 TTTT
2453620 GTAATTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:2453627 original size:21 final size:21
Alignment explanation
Indices: 2453588--2453627 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2453578 AAAAAGGGAA
*
2453588 TTTTTATTTTTTATTTTTTAT
1 TTTTTATTTTTTATATTTTAT
2453609 TTTTTATTTTTGTA-ATTTT
1 TTTTTATTTTT-TATATTTT
2453628 GCAGAGACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (21 bp):
TTTTTATTTTTTATATTTTAT
Found at i:2472094 original size:27 final size:27
Alignment explanation
Indices: 2472055--2472108 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2472045 TCCCTTCTTC
2472055 TTTTATCTCTATCATGTTGAATTGTTG
1 TTTTATCTCTATCATGTTGAATTGTTG
*
2472082 TTTTATCTTTATCATGTTGAATTGTTG
1 TTTTATCTCTATCATGTTGAATTGTTG
2472109 AGTGTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.09, G:0.15, T:0.57
Consensus pattern (27 bp):
TTTTATCTCTATCATGTTGAATTGTTG
Found at i:2472444 original size:2 final size:2
Alignment explanation
Indices: 2472437--2472473 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2472427 TAATATAACT
2472437 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 T
2472474 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2477231 original size:23 final size:23
Alignment explanation
Indices: 2477201--2477247 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2477191 TTATGAAAAT
2477201 ATAACTTAAAAAAACAAATAAAG
1 ATAACTTAAAAAAACAAATAAAG
* *
2477224 ATAACTTAAAAGAACAATTAAAG
1 ATAACTTAAAAAAACAAATAAAG
2477247 A
1 A
2477248 GATGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (23 bp):
ATAACTTAAAAAAACAAATAAAG
Found at i:2477751 original size:16 final size:17
Alignment explanation
Indices: 2477722--2477757 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2477712 TTTTCTTTCA
2477722 ATTTATATTATTTAACT
1 ATTTATATTATTTAACT
*
2477739 ATTTATA-TATTTAATT
1 ATTTATATTATTTAACT
2477755 ATT
1 ATT
2477758 ATGTGAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATATTATTTAACT
Found at i:2480677 original size:2 final size:2
Alignment explanation
Indices: 2480672--2480703 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2480662 TATAACACAC
2480672 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
2480704 CTCCTTCAAT
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:2493700 original size:12 final size:12
Alignment explanation
Indices: 2493683--2493708 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2493673 TGTCTGTGGC
2493683 TGGACTGGATGT
1 TGGACTGGATGT
2493695 TGGACTGGATGT
1 TGGACTGGATGT
2493707 TG
1 TG
2493709 AAGCCATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.42, T:0.35
Consensus pattern (12 bp):
TGGACTGGATGT
Found at i:2497417 original size:10 final size:10
Alignment explanation
Indices: 2497393--2497426 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2497383 TGTTATTAAT
2497393 GTATATAACAA
1 GTATATAA-AA
*
2497404 GTATTTAAAA
1 GTATATAAAA
2497414 GTATATAAAA
1 GTATATAAAA
2497424 GTA
1 GTA
2497427 AAGTATGCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (10 bp):
GTATATAAAA
Found at i:2503345 original size:27 final size:27
Alignment explanation
Indices: 2503279--2503345 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
2503269 ATAGTATTTT
* * *
2503279 AAAATTTAATTATTACACGTTAAGTTG
1 AAAATTTAATTGTTACAAGTTAAGTTA
* * *
2503306 AAAATATACTTGTTACAAGTTATGTTA
1 AAAATTTAATTGTTACAAGTTAAGTTA
2503333 AAAATTTAATTGT
1 AAAATTTAATTGT
2503346 CATACTTCAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (27 bp):
AAAATTTAATTGTTACAAGTTAAGTTA
Found at i:2503357 original size:27 final size:27
Alignment explanation
Indices: 2503327--2503395 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
2503317 GTTACAAGTT
*
2503327 ATGTTAAAAATTTAATTGTCATACTTC
1 ATGTTAAAAATTTAATTATCATACTTC
* * * *
2503354 ATGTTAAAATTTTAGTTATTATATTTC
1 ATGTTAAAAATTTAATTATCATACTTC
*
2503381 ATATTAAAAATTTAA
1 ATGTTAAAAATTTAA
2503396 AATCCATATC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (27 bp):
ATGTTAAAAATTTAATTATCATACTTC
Found at i:2509989 original size:30 final size:31
Alignment explanation
Indices: 2509955--2510015 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2509945 TATATCATTA
2509955 TAAAAATAAAT-TAAAAATTTTAAAAAAATT
1 TAAAAATAAATATAAAAATTTTAAAAAAATT
* * * *
2509985 TAAAACTAAATATTAATATTTTTAAAAAATT
1 TAAAAATAAATATAAAAATTTTAAAAAAATT
2510016 ACATAAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAATAAATATAAAAATTTTAAAAAAATT
Found at i:2522765 original size:15 final size:15
Alignment explanation
Indices: 2522745--2522783 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
2522735 ATAGAATGAG
2522745 TTTGACTTTTTAATT
1 TTTGACTTTTTAATT
2522760 TTTGACTTTTTAATT
1 TTTGACTTTTTAATT
2522775 TTTGACTTT
1 TTTGACTTT
2522784 CTTCAAGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.67
Consensus pattern (15 bp):
TTTGACTTTTTAATT
Found at i:2524578 original size:7 final size:7
Alignment explanation
Indices: 2524555--2524645 Score: 58
Period size: 6 Copynumber: 14.1 Consensus size: 7
2524545 TATATTTTAA
2524555 AAAAT-T
1 AAAATAT
2524561 AAAA-AT
1 AAAATAT
*
2524567 TAAATAT
1 AAAATAT
2524574 AAAATAT
1 AAAATAT
*
2524581 -AGA-AT
1 AAAATAT
*
2524586 AATATATT
1 AAAATA-T
2524594 AAAA-AT
1 AAAATAT
2524600 -AAATAT
1 AAAATAT
2524606 AAAATAT
1 AAAATAT
2524613 AAAA-ATT
1 AAAATA-T
*
2524620 ATAATA-
1 AAAATAT
2524626 AAAA-AT
1 AAAATAT
2524632 AAAA-AT
1 AAAATAT
2524638 AAAATAT
1 AAAATAT
2524645 A
1 A
2524646 TGACATTAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
5 6 0.09
6 29 0.43
7 27 0.40
8 5 0.07
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (7 bp):
AAAATAT
Found at i:2524607 original size:32 final size:32
Alignment explanation
Indices: 2524557--2524645 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
2524547 TATTTTAAAA
2524557 AATTAAAAATTAAATATAAAATATAGAATAA-TAT
1 AATTAAAAA-TAAATATAAAATATA-AA-AATTAT
2524591 -ATTAAAAATAAATATAAAATATAAAAATTAT
1 AATTAAAAATAAATATAAAATATAAAAATTAT
* *
2524622 AATAAAAAATAAAAATAAAATATA
1 AATTAAAAATAAATATAAAATATA
2524646 TGACATTAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
30 2 0.04
31 5 0.10
32 36 0.71
33 8 0.16
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (32 bp):
AATTAAAAATAAATATAAAATATAAAAATTAT
Found at i:2524626 original size:39 final size:38
Alignment explanation
Indices: 2524554--2524645 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 38
2524544 TTATATTTTA
* * * *
2524554 AAAAATTAAAAATTAAATATAAAATATAGAATAATATATT
1 AAAAA-TAAATATAAAATATAAAATATAGAATAA-AAAAT
*
2524594 AAAAATAAATATAAAATATAAAA-ATTATAATAAAAAAT
1 AAAAATAAATATAAAATATAAAATA-TAGAATAAAAAAT
2524632 AAAAATAAAATATA
1 AAAAAT-AAATATA
2524646 TGACATTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 10 0.22
39 30 0.67
40 5 0.11
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (38 bp):
AAAAATAAATATAAAATATAAAATATAGAATAAAAAAT
Found at i:2525244 original size:33 final size:33
Alignment explanation
Indices: 2525185--2525268 Score: 102
Period size: 31 Copynumber: 2.6 Consensus size: 33
2525175 TTTTACTGTC
*
2525185 ATATATTTTATTTTTATTTTATT-ATA-AGT-TT
1 ATATATTTTATTTTTATTTT-TTAATATAATATT
*
2525216 ATATGTTTTATTTTTATTTTTTAATATAATATT
1 ATATATTTTATTTTTATTTTTTAATATAATATT
* *
2525249 CTATATTTTATATTTATTTT
1 ATATATTTTATTTTTATTTT
2525269 AATTTTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
30 2 0.04
31 22 0.49
32 2 0.04
33 19 0.42
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTTTTAATATAATATT
Found at i:2527882 original size:2 final size:2
Alignment explanation
Indices: 2527875--2527900 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2527865 TTAATCTTCG
2527875 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
2527901 TTCGCTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2531462 original size:2 final size:2
Alignment explanation
Indices: 2531424--2531449 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2531414 TTATTTTTCA
2531424 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2531450 TGATTTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2538280 original size:14 final size:14
Alignment explanation
Indices: 2538246--2538281 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2538236 AGCATAAATC
*
2538246 TTAAAAATATTTTT
1 TTAAAAATATTTTA
2538260 TTAAAAATATTTTA
1 TTAAAAATATTTTA
2538274 TTGAAAAA
1 TT-AAAAA
2538282 CAAATTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TTAAAAATATTTTA
Found at i:2540431 original size:2 final size:2
Alignment explanation
Indices: 2540424--2540448 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2540414 AAGTTTTATA
2540424 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2540449 ATGTATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2540453 original size:4 final size:4
Alignment explanation
Indices: 2540446--2540474 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2540436 TGTGTGTGTG
2540446 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
2540475 AACTTATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:2547637 original size:2 final size:2
Alignment explanation
Indices: 2547630--2547655 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2547620 CTTAATTTGA
2547630 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2547656 GAAGGCAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2547734 original size:17 final size:17
Alignment explanation
Indices: 2547712--2547748 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2547702 GAAAATTTAC
2547712 GTATATAACAAGCCCAA
1 GTATATAACAAGCCCAA
2547729 GTATATAACAAGCCCAA
1 GTATATAACAAGCCCAA
2547746 GTA
1 GTA
2547749 GATTATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.22, G:0.14, T:0.19
Consensus pattern (17 bp):
GTATATAACAAGCCCAA
Found at i:2555456 original size:19 final size:19
Alignment explanation
Indices: 2555432--2555488 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
2555422 ATAAATTAAT
2555432 TAAAAACAAAAGACAAATG
1 TAAAAACAAAAGACAAATG
* *
2555451 TAAAAA-ATAAATAAACAAT-
1 TAAAAACA-AAAGACA-AATG
2555470 TAAAAACAAAAGACAAATG
1 TAAAAACAAAAGACAAATG
2555489 ACGAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
18 4 0.13
19 22 0.73
20 4 0.13
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (19 bp):
TAAAAACAAAAGACAAATG
Found at i:2555480 original size:38 final size:39
Alignment explanation
Indices: 2555407--2555501 Score: 140
Period size: 39 Copynumber: 2.4 Consensus size: 39
2555397 ATAATAGAAA
* *
2555407 AAATGTAATAAATAAATAAATTAATTAAAAACAAAAGAC
1 AAATGTAAAAAATAAATAAATCAATTAAAAACAAAAGAC
2555446 AAATGTAAAAAATAAATAAA-CAATTAAAAACAAAAGAC
1 AAATGTAAAAAATAAATAAATCAATTAAAAACAAAAGAC
2555484 AAATG-ACGAAAAATAAAT
1 AAATGTA--AAAAATAAAT
2555502 TATAAAACCA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
37 1 0.02
38 22 0.42
39 29 0.56
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (39 bp):
AAATGTAAAAAATAAATAAATCAATTAAAAACAAAAGAC
Found at i:2556986 original size:16 final size:15
Alignment explanation
Indices: 2556961--2556994 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2556951 TGATCATTTG
2556961 ATTTTAAATATTAAT
1 ATTTTAAATATTAAT
*
2556976 ATTTATAAATATTATT
1 ATTT-TAAATATTAAT
2556992 ATT
1 ATT
2556995 GTGATTACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTAAATATTAAT
Found at i:2557499 original size:51 final size:51
Alignment explanation
Indices: 2557435--2557539 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 51
2557425 AAAACTCCTA
*
2557435 CCCATCGCAGACCTAACTCCTTCCCCC-CCTCTCGAATCCCG-CCTAATTCCC
1 CCCATCGCAGACCTAACTCCTTCCCCCTCCGCT--AATCCCGACCTAATTCCC
*
2557486 CCCATCGCCGACCTAACTCCTTCCCCCTCCGCTAATCCCGACCTAATTCCC
1 CCCATCGCAGACCTAACTCCTTCCCCCTCCGCTAATCCCGACCTAATTCCC
2557537 CCC
1 CCC
2557540 GGCCCCCCTC
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
50 7 0.14
51 39 0.78
52 4 0.08
ACGTcount: A:0.17, C:0.54, G:0.08, T:0.21
Consensus pattern (51 bp):
CCCATCGCAGACCTAACTCCTTCCCCCTCCGCTAATCCCGACCTAATTCCC
Found at i:2567303 original size:30 final size:29
Alignment explanation
Indices: 2567251--2567339 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
2567241 TTACTTAATG
* * *
2567251 TAAAATAAAAATACAAAGACTTATTTGAT
1 TAAAATAAAAATATAAAGACTTAATTGAA
2567280 TCAAAATAAAAATAT-AAGAACTTAATTGAA
1 T-AAAATAAAAATATAAAG-ACTTAATTGAA
* * * *
2567310 TACAATAAAATTATAAAGATTTACTTGAA
1 TAAAATAAAAATATAAAGACTTAATTGAA
2567339 T
1 T
2567340 TTTTTTAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 25 0.50
30 25 0.50
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (29 bp):
TAAAATAAAAATATAAAGACTTAATTGAA
Found at i:2572261 original size:23 final size:22
Alignment explanation
Indices: 2572220--2572262 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2572210 GGGCTCTTTG
*
2572220 GTTTGTTTTTTTACTTAGTTTT
1 GTTTGTTTTTTTACCTAGTTTT
*
2572242 GTTTGTTTTTTATCCCTAGTT
1 GTTTGTTTTTT-TACCTAGTT
2572263 ACTGTAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.09, C:0.09, G:0.14, T:0.67
Consensus pattern (22 bp):
GTTTGTTTTTTTACCTAGTTTT
Found at i:2583166 original size:41 final size:41
Alignment explanation
Indices: 2583093--2583175 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
2583083 TCAACTAAGC
2583093 ATATCAAATTTCAAATGGCCATAAGAACTAATCAAAATGAA
1 ATATCAAATTTCAAATGGCCATAAGAACTAATCAAAATGAA
* * * *
2583134 ATATGAAATTTCAAATGGCTATAGGAATTAATCAAAATGAA
1 ATATCAAATTTCAAATGGCCATAAGAACTAATCAAAATGAA
2583175 A
1 A
2583176 ATCTTACATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.27
Consensus pattern (41 bp):
ATATCAAATTTCAAATGGCCATAAGAACTAATCAAAATGAA
Found at i:2611220 original size:2 final size:2
Alignment explanation
Indices: 2611213--2611244 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2611203 AGGGTAAAAT
2611213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2611245 CCGTAGCTCT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2615652 original size:2 final size:2
Alignment explanation
Indices: 2615645--2615684 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2615635 AAGAAAACTT
* * *
2615645 GA GA GA GA GA GA AA GC GA GA GA GA GG GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2615685 AAACACTCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2616095 original size:21 final size:21
Alignment explanation
Indices: 2616053--2616102 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2616043 ATGATGTTGA
*
2616053 TGATGCTCTTGTATTTGATGC
1 TGATGCTGTTGTATTTGATGC
*
2616074 TGATGCTGTTGT-TGTTGCTGC
1 TGATGCTGTTGTAT-TTGATGC
*
2616095 TGCTGCTG
1 TGATGCTG
2616103 ATTTTGATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.08, C:0.16, G:0.30, T:0.46
Consensus pattern (21 bp):
TGATGCTGTTGTATTTGATGC
Found at i:2619061 original size:10 final size:10
Alignment explanation
Indices: 2619045--2619082 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2619035 ATTAAAATAA
2619045 ATTTAATTAT
1 ATTTAATTAT
*
2619055 TTTTAATTAT
1 ATTTAATTAT
2619065 ATTTAATTAT
1 ATTTAATTAT
2619075 AATTTAAT
1 -ATTTAAT
2619083 AAAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTTAATTAT
Found at i:2619092 original size:24 final size:24
Alignment explanation
Indices: 2619008--2619092 Score: 63
Period size: 24 Copynumber: 3.7 Consensus size: 24
2618998 GAATAAATTT
**
2619008 TTTAATAAAAATATTTTAAAAATAA
1 TTTAATAAAAATA-TTTAATTATAA
* *
2619033 -TTATTAAAATAAATTTAATTAT--
1 TTTAATAAAA-ATATTTAATTATAA
**
2619055 TTT--TAATTATATTTAATTATAA
1 TTTAATAAAAATATTTAATTATAA
2619077 TTTAATAAAAATATTT
1 TTTAATAAAAATATTT
2619093 TTAAAATTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 13
0.67 0.13 0.19
Matches are distributed among these distances:
20 11 0.24
21 3 0.07
22 3 0.07
23 2 0.04
24 24 0.53
25 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTAATAAAAATATTTAATTATAA
Found at i:2619667 original size:29 final size:30
Alignment explanation
Indices: 2619624--2619706 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
2619614 TGTAAAATTT
* * * *
2619624 TTTTTTTGAATATGACATGTAATGATAACA
1 TTTTTTTCAACATGACATGTAATAACAACA
* *
2619654 TTTTTTT-AACATGA-AGTATAATAACAATA
1 TTTTTTTCAACATGACA-TGTAATAACAACA
2619683 TTTTTTTCAACATGACATGTAATA
1 TTTTTTTCAACATGACATGTAATA
2619707 TATTTTTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 22 0.50
30 20 0.45
31 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (30 bp):
TTTTTTTCAACATGACATGTAATAACAACA
Found at i:2619794 original size:26 final size:26
Alignment explanation
Indices: 2619738--2619787 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2619728 ACAACAAGAT
* *
2619738 TTTTTTTCAACATTACGTGTAATAAC
1 TTTTTTTCAACATGACGTGTAACAAC
2619764 TTTTTTT-AACTATGACGTGTAACA
1 TTTTTTTCAAC-ATGACGTGTAACA
2619788 TGTTTTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (26 bp):
TTTTTTTCAACATGACGTGTAACAAC
Found at i:2619950 original size:163 final size:164
Alignment explanation
Indices: 2619674--2619989 Score: 388
Period size: 163 Copynumber: 1.9 Consensus size: 164
2619664 ATGAAGTATA
* * ** *
2619674 ATAACAATATTTTTTTCAACATGACATGTAATATATTTTTGTACATAACTTGTAACAACAAGATT
1 ATAACAATATTTTTTTCAACATGACATATAACATATTTTTGTACATAACGAGCAACAACAAGATT
* * * *
2619739 TTTTTTCAACATTACGTGTAATAACTTTTTTTAACTATGACGTGTAACATGTTTTTGTACATGAC
66 TTTTTTCAACATGACGTGTAATAAATTTTTTTAACCATGACGTGTAACATATTTTTGTACATGAC
* *
2619804 ATATACCAATAATAATTTTTTTTTTAACACGGCGT
131 ATATAACAATAAT-ATTTTCTTTTTAACACGGCGT
* * **
2619839 ATAACAATA-TTTTTT-AACCATGTCATATAACATATTTTTGTACATAACGAGCAACAATAATTT
1 ATAACAATATTTTTTTCAA-CATGACATATAACATATTTTTGTACATAACGAGCAACAACAAGAT
* ** *
2619902 TTTTTTTC-ATATGGTGTGTAATAAATTTTTTTAACCATGAAC-TGTAACATATTTTTGTATATG
65 TTTTTTTCAACATGACGTGTAATAAATTTTTTTAACCATG-ACGTGTAACATATTTTTGTACATG
* *
2619965 ACGTATAATAATAATATTTTCTTTT
129 ACATATAACAATAATATTTTCTTTT
2619990 AATATGACGT
Statistics
Matches: 128, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
162 9 0.07
163 58 0.45
164 52 0.41
165 9 0.07
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (164 bp):
ATAACAATATTTTTTTCAACATGACATATAACATATTTTTGTACATAACGAGCAACAACAAGATT
TTTTTTCAACATGACGTGTAATAAATTTTTTTAACCATGACGTGTAACATATTTTTGTACATGAC
ATATAACAATAATATTTTCTTTTTAACACGGCGT
Found at i:2619978 original size:80 final size:80
Alignment explanation
Indices: 2619682--2620028 Score: 272
Period size: 80 Copynumber: 4.3 Consensus size: 80
2619672 TAATAACAAT
* * * * * * * *
2619682 ATTTTTTTCAA-CATGACATGTAATATATTTTTGTACATAACTTGTAACAACAAGATTTTTTTTC
1 ATTTTTTT-AACCATGACATGTAACATATTTTTGTACATGACGTATAATAATAA-TTTTTTTTTT
* **
2619746 AACATTACGTGTAATAA
64 AATATGGCGTGTAATAA
* * * * *
2619763 CTTTTTTTAACTATGACGTGTAACATGTTTTTGTACATGACATATACCAATAATAATTTTTTTTT
1 ATTTTTTTAACCATGACATGTAACATATTTTTGTACATGACGTAT---AATAATAATTTTTTTTT
* * * *
2619828 TAACACGGCGTATAA-CA
63 TAATATGGCGTGTAATAA
* * * * *
2619845 ATATTTTTTAACCATGTCATATAACATATTTTTGTACATAACG-AGCAACAATAATTTTTTTTTT
1 AT-TTTTTTAACCATGACATGTAACATATTTTTGTACATGACGTA-TAATAATAATTTTTTTTTT
* *
2619909 CATATGGTGTGTAATAA
64 AATATGGCGTGTAATAA
* *
2619926 ATTTTTTTAACCATGA-ACTGTAACATATTTTTGTATATGACGTATAATAATAATATTTTCTTTT
1 ATTTTTTTAACCATGACA-TGTAACATATTTTTGTACATGACGTATAATAATAAT-TTTTTTTTT
*
2619990 AATATGACGTGTAAT-A
64 AATATGGCGTGTAATAA
** * *
2620006 ACCTTTTTAATCATGACGTGTAA
1 ATTTTTTTAACCATGACATGTAA
2620029 TAATAAATTT
Statistics
Matches: 208, Mismatches: 47, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
79 1 0.00
80 89 0.43
81 58 0.28
82 3 0.01
83 51 0.25
84 6 0.03
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (80 bp):
ATTTTTTTAACCATGACATGTAACATATTTTTGTACATGACGTATAATAATAATTTTTTTTTTAA
TATGGCGTGTAATAA
Found at i:2619998 original size:218 final size:219
Alignment explanation
Indices: 2619767--2620183 Score: 467
Period size: 218 Copynumber: 1.9 Consensus size: 219
2619757 TAATAACTTT
* ** *
2619767 TTTTAACTATGACGTGTAA-CATGTTTTT-GTACATGACATATACCAATAAT-AATTTTTTTTTT
1 TTTTAACTATGACGTGTAATAACCTTTTTAAT-CATGACATAT---AATAATAAATTTTTTTTTT
* ** *
2619829 -AACACGGCGTATAACAA-TATTTTTTAACCATGTCATATAACATATTTTTGTACATAACGAGCA
62 AAACACAGCGTATAACAACT-TTTTTTAACCATAACATACAACATATTTTTGTACATAACGAGCA
* *
2619892 ACAATAATTTTTTTTTTC-ATATGGTGTGTAATAAAT-TTTTTTAACC-ATGA-ACTGTAACATA
126 ACAATAA-TATTTTTTTCAATATGGCGTGTAA-AAATCTTTTTTAACCAAT-ACA-TGTAACATA
*
2619953 TTTTTGTATATGACGTATAATAATAATATTTTC
187 TTTTTGTACATGACGTATAATAATAATATTTTC
* *
2619986 TTTTAA-TATGACGTGTAATAACCTTTTTAATCATGACGTGTAATAATAAATTTTTTTTTTAAAC
1 TTTTAACTATGACGTGTAATAACCTTTTTAATCATGACATATAATAATAAATTTTTTTTTTAAAC
* * * * *** * *
2620050 ATAGCGTGTAACAACTTTTTTTAACCATAACGTACAACATATTTTTGTATATGGTGTGTAACAAT
66 ACAGCGTATAACAACTTTTTTTAACCATAACATACAACATATTTTTGTACATAACGAGCAACAAT
* *
2620115 AATATTTTTTTCAATATTGCGTGTAACAATCTTTTTTAACCAATACATGTAACATATTTTTGTAC
131 AATATTTTTTTCAATATGGCGTGTAAAAATCTTTTTTAACCAATACATGTAACATATTTTTGTAC
2620180 ATGA
196 ATGA
2620184 AGTTGTAGCA
Statistics
Matches: 165, Mismatches: 24, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
216 6 0.04
217 24 0.15
218 110 0.67
219 24 0.15
220 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (219 bp):
TTTTAACTATGACGTGTAATAACCTTTTTAATCATGACATATAATAATAAATTTTTTTTTTAAAC
ACAGCGTATAACAACTTTTTTTAACCATAACATACAACATATTTTTGTACATAACGAGCAACAAT
AATATTTTTTTCAATATGGCGTGTAAAAATCTTTTTTAACCAATACATGTAACATATTTTTGTAC
ATGACGTATAATAATAATATTTTC
Found at i:2620068 original size:56 final size:56
Alignment explanation
Indices: 2619962--2620070 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
2619952 ATTTTTGTAT
* *
2619962 ATGACGTATAATAATAATATTTTCTTTTAATATGACGTGTAATAACCTTTTTAATC
1 ATGACGTATAATAATAATATTTTCTTTTAACATGACGTGTAACAACCTTTTTAATC
* * *
2620018 ATGACGTGTAATAATAA-ATTTTTTTTTTAAACAT-AGCGTGTAACAACTTTTTT
1 ATGACGTATAATAATAATA-TTTTCTTTT-AACATGA-CGTGTAACAACCTTTTT
2620071 TAACCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
55 1 0.02
56 25 0.56
57 19 0.42
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (56 bp):
ATGACGTATAATAATAATATTTTCTTTTAACATGACGTGTAACAACCTTTTTAATC
Found at i:2620095 original size:26 final size:26
Alignment explanation
Indices: 2620039--2620088 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
2620029 TAATAAATTT
* **
2620039 TTTTTTTAAACATAGCGTGTAACAAC
1 TTTTTTTAAACATAACGTACAACAAC
*
2620065 TTTTTTTAACCATAACGTACAACA
1 TTTTTTTAAACATAACGTACAACA
2620089 TATTTTTGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (26 bp):
TTTTTTTAAACATAACGTACAACAAC
Found at i:2620166 original size:138 final size:138
Alignment explanation
Indices: 2619917--2620166 Score: 321
Period size: 138 Copynumber: 1.8 Consensus size: 138
2619907 TTCATATGGT
* *
2619917 GTGTAATAAATTTTTTTAACCATGAACTGTAACATATTTTTGTATATGACGTATAATAATAATAT
1 GTGTAACAAATTTTTTTAACCATGAACTGTAACATATTTTTGTATATGACGTATAACAATAATAT
* * * *
2619982 TTTCTTTTAATATGACGTGTAATAACCTTTTTAATCATGACGTGTAATAATAAATTTTTTTTTTA
66 TTTCTTTCAATATGACGTGTAACAACCTTTTTAACCATGACATGTAATAATAAATTTTTTTTTTA
2620047 AACATAGC
131 AACATAGC
* ** *
2620055 GTGTAACAACTTTTTTTAACCAT-AAC-GTACAACATATTTTTGTATATGGTGTGTAACAATAAT
1 GTGTAACAAATTTTTTTAACCATGAACTGT--AACATATTTTTGTATATGACGTATAACAATAAT
*
2620118 ATTTT-TTTCAATATTG-CGTGTAACAATCTTTTTTAACCAAT-ACATGTAA
64 ATTTTCTTTCAATA-TGACGTGTAACAA-CCTTTTTAACC-ATGACATGTAA
2620167 CATATTTTTG
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
136 2 0.02
137 19 0.20
138 73 0.76
139 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (138 bp):
GTGTAACAAATTTTTTTAACCATGAACTGTAACATATTTTTGTATATGACGTATAACAATAATAT
TTTCTTTCAATATGACGTGTAACAACCTTTTTAACCATGACATGTAATAATAAATTTTTTTTTTA
AACATAGC
Found at i:2620222 original size:80 final size:79
Alignment explanation
Indices: 2620053--2620211 Score: 191
Period size: 80 Copynumber: 2.0 Consensus size: 79
2620043 TTTAAACATA
* *
2620053 GCGTGTAACAACTTTTTTTAACCATAACGTACAACATATTTTTGTATATGGTGTGTAACAATAAT
1 GCGTGTAACAACTTTTTTTAACCATAACGTA-AACATATTTTTGTACATGGTGTGTAACAATAAC
*
2620118 ATTTTTTTCAATATT
65 ATTCTTTTCAATATT
* *
2620133 GCGTGTAACAA-TCTTTTTTAACCAATACATGT-AACATATTTTTGTACATGAAGT-TGTAGCAA
1 GCGTGTAACAACT-TTTTTTAACC-ATA-ACGTAAACATATTTTTGTACATG--GTGTGTAACAA
2620195 TAACA-TCTTTTCAATAT
61 TAACATTCTTTTCAATAT
2620212 GATGTGTAAC
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
79 1 0.01
80 49 0.71
81 14 0.20
82 5 0.07
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (79 bp):
GCGTGTAACAACTTTTTTTAACCATAACGTAAACATATTTTTGTACATGGTGTGTAACAATAACA
TTCTTTTCAATATT
Found at i:2621622 original size:26 final size:26
Alignment explanation
Indices: 2621564--2621615 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2621554 CAAATTATTC
*
2621564 AAATTGTGATACACATGAATGATACT
1 AAATTGTGATACAAATGAATGATACT
2621590 AAATTGTGATACAAATGAATGATACT
1 AAATTGTGATACAAATGAATGATACT
2621616 GACTTGTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (26 bp):
AAATTGTGATACAAATGAATGATACT
Found at i:2631883 original size:10 final size:10
Alignment explanation
Indices: 2631868--2631896 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2631858 AAAAAAAACC
2631868 TTAAATTTAA
1 TTAAATTTAA
2631878 TTAAATTTAA
1 TTAAATTTAA
2631888 TTAAATTTA
1 TTAAATTTA
2631897 TTTTTTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAAATTTAA
Found at i:2639619 original size:17 final size:16
Alignment explanation
Indices: 2639597--2639650 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
2639587 AAAAAATTAT
2639597 TTTAATTAATTTAATAA
1 TTTAA-TAATTTAATAA
2639614 TTTAATATATTTAACT-A
1 TTTAATA-ATTTAA-TAA
*
2639631 TGTAA-AA-TTAATAA
1 TTTAATAATTTAATAA
2639645 TTTAAT
1 TTTAAT
2639651 TACCAATGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
13 1 0.03
14 9 0.29
15 1 0.03
16 3 0.10
17 16 0.52
18 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTAATAATTTAATAA
Found at i:2639625 original size:9 final size:8
Alignment explanation
Indices: 2639597--2639650 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
2639587 AAAAAATTAT
2639597 TTTAATTAA
1 TTTAA-TAA
2639606 TTTAATAA
1 TTTAATAA
2639614 TTTAATATA
1 TTTAATA-A
2639623 TTTAACT-A
1 TTTAA-TAA
*
2639631 TGTAA-AA
1 TTTAATAA
2639638 -TTAATAA
1 TTTAATAA
2639645 TTTAAT
1 TTTAAT
2639651 TACCAATGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
8 20 0.53
9 11 0.29
10 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (8 bp):
TTTAATAA
Found at i:2643463 original size:3 final size:3
Alignment explanation
Indices: 2643455--2643481 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2643445 GTAAATATGG
2643455 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
2643482 AGCATTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2644216 original size:2 final size:2
Alignment explanation
Indices: 2644209--2644245 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2644199 TACATGTATG
2644209 TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2644246 ATTTGTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2653161 original size:31 final size:33
Alignment explanation
Indices: 2653126--2653197 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
2653116 ATACTATATA
** *
2653126 AATTTTTATTTCTTATATT-T-TATTTTATTTT
1 AATTTTTAAGTCTTATATTATATATTTTATTGT
*
2653157 AATTTCTAAGTCTTATATTATATATTTTATTGT
1 AATTTTTAAGTCTTATATTATATATTTTATTGT
2653190 AATATTTT
1 AAT-TTTT
2653198 TTATTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
31 16 0.48
32 1 0.03
33 13 0.39
34 3 0.09
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (33 bp):
AATTTTTAAGTCTTATATTATATATTTTATTGT
Found at i:2654871 original size:90 final size:90
Alignment explanation
Indices: 2654767--2655133 Score: 267
Period size: 90 Copynumber: 4.0 Consensus size: 90
2654757 TTTCGAATAT
*
2654767 TAATAATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATAAAT
1 TAATGATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATAAAT
*
2654832 TATAAATTATTAATATTTTTTAAAA
66 TATAAATTATTAATATTTATTAAAA
* * * * * *
2654857 AAAT-AGTTAAATTATAAATAAAATATTAAAAATTTTAAAAT-ATTAATGATT-AGATTAT-AAT
1 TAATGA-TTAAATTATAAATAAAATATT-AATA-TTT-AAATGATCAATTATTAATATTTTAAAT
* * *
2654918 AAAATATTAATATTTAAATT-ATCAATTATTAATA
62 AAATTA-TAA-A-TT--ATTAAT-ATTTATTAAAA
* * *
2654952 TAATGATTAAATTATAAAT----TATTAATATTTAAA-AATAAATAATCATAATAATATTTAAAT
1 TAATGATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTAT--TAAT-AT-TTTAAA-
* ***
2655012 TTTAAA-TA-AAA-TATTAATACTTTATGATGT
61 --TAAATTATAAATTATTAATA-TTTATTAAAA
*
2655042 TAATGATTAAATTATAAATAAAATATTAATATTTCAATGATCAATTATTAATATTTTAAATAAAT
1 TAATGATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATAAAT
** * *
2655107 TGCAAATTATAAATATTTA-AAAAA
66 TATAAATTATTAATATTTATTAAAA
2655131 TAA
1 TAA
2655134 AATAAAATAA
Statistics
Matches: 215, Mismatches: 31, Indels: 63
0.70 0.10 0.20
Matches are distributed among these distances:
88 14 0.07
89 13 0.06
90 69 0.32
91 30 0.14
92 16 0.07
93 13 0.06
94 19 0.09
95 34 0.16
96 3 0.01
97 4 0.02
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.43
Consensus pattern (90 bp):
TAATGATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATAAAT
TATAAATTATTAATATTTATTAAAA
Found at i:2654884 original size:41 final size:42
Alignment explanation
Indices: 2654833--2654932 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
2654823 TAAATAAATT
*
2654833 ATAAATTATTAATATTTTTTAAAA-A-AAT-AGTTAAATTATAA
1 ATAAAATATTAATATTTTTTAAAATATAATGA-TTAAATTAT-A
** *
2654874 ATAAAATATTAA-AAATTTTAAAATATTAATGATTAGATTATA
1 ATAAAATATTAATATTTTTTAAAATA-TAATGATTAAATTATA
2654916 ATAAAATATTAATATTT
1 ATAAAATATTAATATTT
2654933 AAATTATCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
40 9 0.19
41 12 0.25
42 13 0.27
43 13 0.27
44 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (42 bp):
ATAAAATATTAATATTTTTTAAAATATAATGATTAAATTATA
Found at i:2654921 original size:25 final size:26
Alignment explanation
Indices: 2654891--2654968 Score: 90
Period size: 25 Copynumber: 3.0 Consensus size: 26
2654881 ATTAAAAATT
*
2654891 TTAAAATATTAATGATTAGATTATAA
1 TTAAAATATTAATGATTAAATTATAA
2654917 -TAAAATATTAAT-ATTTAAATTATCAA
1 TTAAAATATTAATGA-TTAAATTAT-AA
*
2654943 TTATTAATA-TAATGATTAAATTATAA
1 TTA-AAATATTAATGATTAAATTATAA
2654969 ATTATTAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
24 1 0.02
25 20 0.44
26 4 0.09
27 15 0.33
28 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (26 bp):
TTAAAATATTAATGATTAAATTATAA
Found at i:2654950 original size:22 final size:22
Alignment explanation
Indices: 2654764--2654984 Score: 93
Period size: 27 Copynumber: 9.6 Consensus size: 22
2654754 AACTTTCGAA
*
2654764 TATTAATAATTAAATTATAAAT
1 TATTAATATTTAAATTATAAAT
* *
2654786 AAAATATTAATATTTAAATGATCAAT
1 ----TATTAATATTTAAATTATAAAT
2654812 TATTAATATTTTAAATAAATTATAAAT
1 TATTAATA--TT---TAAATTATAAAT
2654839 TATTAATATTT---TT-TAAA-
1 TATTAATATTTAAATTATAAAT
* *
2654856 -A-AAATAGTTAAATTATAAA-
1 TATTAATATTTAAATTATAAAT
* * * *
2654875 TA-AAATATTAAAAATTTTAAAA
1 TATTAATATT-TAAATTATAAAT
* *
2654897 TATTAATGA-TTAGATTATAATAAAA
1 TATTAAT-ATTTA-A--ATTATAAAT
*
2654922 TATTAATATTTAAATTATCAAT
1 TATTAATATTTAAATTATAAAT
2654944 TATTAATATAATGATTAAATTATAAAT
1 TATT-A-AT-AT--TTAAATTATAAAT
2654971 TATTAATATTTAAA
1 TATTAATATTTAAA
2654985 AATAAATAAT
Statistics
Matches: 154, Mismatches: 18, Indels: 50
0.69 0.08 0.23
Matches are distributed among these distances:
15 6 0.04
16 1 0.01
18 6 0.04
19 6 0.04
20 7 0.05
21 9 0.06
22 27 0.18
23 6 0.04
24 9 0.06
25 23 0.15
26 20 0.13
27 34 0.22
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTAATATTTAAATTATAAAT
Found at i:2654984 original size:15 final size:16
Alignment explanation
Indices: 2654916--2654984 Score: 63
Period size: 15 Copynumber: 4.3 Consensus size: 16
2654906 TTAGATTATA
*
2654916 ATAAAATATTAATATT
1 ATAAATTATTAATATT
*
2654932 -TAAATTATCAATTATT
1 ATAAATTATTAA-TATT
*
2654948 AATATAATGATTAA-ATT
1 -ATA-AATTATTAATATT
2654965 ATAAATTATTAATATT
1 ATAAATTATTAATATT
2654981 -TAAA
1 ATAAA
2654985 AATAAATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
15 21 0.49
16 10 0.23
17 3 0.07
18 2 0.05
19 7 0.16
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
ATAAATTATTAATATT
Found at i:2655018 original size:143 final size:139
Alignment explanation
Indices: 2654762--2655527 Score: 500
Period size: 132 Copynumber: 5.7 Consensus size: 139
2654752 ACAACTTTCG
*
2654762 AATATTAATAATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAA
1 AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAA
*
2654827 TAAATTATAAATTATTAATATTT-----T--TTAAAAAAATAGTTAAATTATAAATAAAATATTA
66 TAAATTATAAATTATTAATATTTAAAAATAAATAAAAAAATAGTTAAATTATAAATAAAATATT-
*
2654885 AAAATTTTAA
130 AAAACTTTAA
* * ** * *
2654895 AATATTAATGATTAGATTAT-AATAAAATATTAATATTTAAATTATCAATTATTAATATAATGAT
1 AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAA
* *
2654959 TAAATTATAAATTATTAATATTTAAAAATAAATAATCATAATAATATTTAAATTTTAAATAAAAT
66 TAAATTATAAATTATTAATATTTAAAAATAAATAA--A-AA-AATAGTTAAATTATAAATAAAAT
* *
2655024 ATTAATACTTTAT
127 ATTAAAACTTTAA
* * *
2655037 GATGTTAATGATTAAATTATAAATAAAATATTAATATTTCAATGATCAATTATTAATATTTTAAA
1 AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAA
** * * **
2655102 TAAATTGCAAATTATAAATATTTAAAAAATAAAATAAAATAAA-A-TAAAAACA-AACATAATAA
66 TAAATTATAAATTATTAATATTT-AAAAAT-AAATAAAA-AAATAGTTAAATTATAA-ATAA-AA
* ** *
2655164 CATTTGAA--TTAT
126 TATTAAAACTTTAA
* * * * *
2655176 AATA-AAAT-ATTAATATT-T---TATAATATTAAT-TGTTAAATTATAAATTAATAATATTATT
1 AATATTAATGATTAA-ATTATAAATAAAATATTAATAT-TTAAATGATCAATTATTAATATT-TT
* *
2655234 ---TAAATTATAAATTATTATTATTT--AAA-AAATAAAATAAA-A--TAAAATA-AAATAAAAT
63 AAATAAATTATAAATTATTAATATTTAAAAATAAATAAAA-AAATAGTTAAATTATAAATAAAAT
2655289 A--AAAAC---AA
127 ATTAAAACTTTAA
* * * * *
2655297 TCATAATAA-CATTTGAATTAT-AATAAAATATTAATATTT---T-AT-AA-TATT-A-ATTGT-
1 -AATATTAATGA-TTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTA
* *
2655351 --TAAATTATAAATTATTACTATTTAAAAATAAAATAAAAATATAATAATATTTAAATTAT-AAT
64 AATAAATTATAAATTATTAATATTTAAAAAT-AAAT---AA-A-AA-AATAGTTAAATTATAAAT
* *
2655413 AAAATATT-ATA-TTATAT
122 AAAATATTAAAACTT-TAA
** * * * *
2655430 AATGCTAATTATTCAATTATAAATAAAATATTAAAATTTAAATTATCAATTATTAATATTTTAAA
1 AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAA
* *
2655495 CAAATTATAAATTACTAATATTTAAAAAATAAA
66 TAAATTATAAATTATTAATATTT-AAAAATAAA
2655528 AATAAATAAT
Statistics
Matches: 499, Mismatches: 71, Indels: 115
0.73 0.10 0.17
Matches are distributed among these distances:
117 23 0.05
118 3 0.01
119 4 0.01
120 3 0.01
121 7 0.01
122 7 0.01
123 7 0.01
124 9 0.02
125 6 0.01
126 23 0.05
127 15 0.03
129 18 0.04
130 2 0.00
132 94 0.19
133 38 0.08
134 30 0.06
135 2 0.00
136 1 0.00
137 9 0.02
138 8 0.02
139 15 0.03
140 9 0.02
141 12 0.02
142 29 0.06
143 84 0.17
144 29 0.06
145 12 0.02
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (139 bp):
AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAA
TAAATTATAAATTATTAATATTTAAAAATAAATAAAAAAATAGTTAAATTATAAATAAAATATTA
AAACTTTAA
Found at i:2655029 original size:26 final size:25
Alignment explanation
Indices: 2654965--2655035 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
2654955 TGATTAAATT
*
2654965 ATAAATTATTAATATTTAAAAATAA
1 ATAAAATATTAATATTTAAAAATAA
* * **
2654990 ATAATCATAATAATATTTAAATTTTAA
1 ATAA-AATATTAATATTTAAA-AATAA
2655017 ATAAAATATTAATACTTTA
1 ATAAAATATTAATA-TTTA
2655036 TGATGTTAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
25 4 0.11
26 21 0.58
27 11 0.31
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAAAATATTAATATTTAAAAATAA
Found at i:2655224 original size:25 final size:26
Alignment explanation
Indices: 2655196--2655253 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
2655186 TAATATTTTA
2655196 TAATATTAATT-GTTAAATTATAAAT
1 TAATATTAATTAGTTAAATTATAAAT
* *
2655221 TAATAAT-ATTATTTAAATTATAAAT
1 TAATATTAATTAGTTAAATTATAAAT
*
2655246 TATTATTA
1 TAATATTA
2655254 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 3 0.11
25 24 0.89
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TAATATTAATTAGTTAAATTATAAAT
Found at i:2655239 original size:18 final size:16
Alignment explanation
Indices: 2655216--2655249 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
2655206 TGTTAAATTA
2655216 TAAATTAATAATATTATT
1 TAAATT-ATAA-ATTATT
2655234 TAAATTATAAATTATT
1 TAAATTATAAATTATT
2655250 ATTATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATTATAAATTATT
Done.