Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, 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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 12 of 84
Found at i:2084293 original size:16 final size:17
Alignment explanation
Indices: 2084272--2084315 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2084262 TAAATAGAAT
2084272 AAAAAATAAA-A-CTAA
1 AAAAAATAAAGACCTAA
2084287 AATAAAATAAAGACCTAA
1 AA-AAAATAAAGACCTAA
2084305 AAAAATATAAA
1 AAAAA-ATAAA
2084316 TAAAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.08
16 8 0.32
17 4 0.16
18 11 0.44
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAAATAAAGACCTAA
Found at i:2084465 original size:19 final size:19
Alignment explanation
Indices: 2084431--2084472 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
2084421 TTTTGCTAAA
*
2084431 AAATAAATAAAAATTG-TT
1 AAATAAAAAAAAATTGTTT
2084449 AAATAAAAAATAAATTGTTT
1 AAATAAAAAA-AAATTGTTT
2084469 AAAT
1 AAAT
2084473 GAATCTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
AAATAAAAAAAAATTGTTT
Found at i:2092786 original size:15 final size:15
Alignment explanation
Indices: 2092766--2092795 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2092756 AAGAAAATTA
*
2092766 TTATTATTATTATTG
1 TTATTATTATCATTG
2092781 TTATTATTATCATTG
1 TTATTATTATCATTG
2092796 ATAAATTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (15 bp):
TTATTATTATCATTG
Found at i:2099241 original size:2 final size:2
Alignment explanation
Indices: 2099227--2099263 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
2099217 GAACCAAATT
2099227 TC TC TC T- TAC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC T
2099264 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2099268 original size:2 final size:2
Alignment explanation
Indices: 2099263--2099292 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2099253 TCTCTCTCTC
2099263 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
2099293 AGACAAGCTC
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:2099357 original size:2 final size:2
Alignment explanation
Indices: 2099350--2099382 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2099340 TATTCAAAAC
2099350 AT 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 AT A
2099383 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2105025 original size:2 final size:2
Alignment explanation
Indices: 2105020--2105051 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2105010 TGTGTGTGTG
2105020 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
2105052 AGACAAGCTC
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:2108758 original size:14 final size:14
Alignment explanation
Indices: 2108735--2108767 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2108725 CTCTTAAAAT
*
2108735 ATTTTATTTGTTTG
1 ATTTTTTTTGTTTG
2108749 ATTTTTTTTGTTTG
1 ATTTTTTTTGTTTG
2108763 -TTTTT
1 ATTTTT
2108768 GGGTGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.09, C:0.00, G:0.12, T:0.79
Consensus pattern (14 bp):
ATTTTTTTTGTTTG
Found at i:2111151 original size:35 final size:38
Alignment explanation
Indices: 2111072--2111152 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 38
2111062 ATTCCAATTT
* *
2111072 CGAAATGATTATTATTTTATATATATAGTATTAATCATTT
1 CGAAATGATTATTA-TCTATATATATAG-ATTAATCATTC
2111112 CGAAATGATTATTA-CTATATATATA-ATT-ATCATTC
1 CGAAATGATTATTATCTATATATATAGATTAATCATTC
2111147 CGAAAT
1 CGAAAT
2111153 TGGAATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
35 12 0.31
36 3 0.08
38 10 0.26
40 14 0.36
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (38 bp):
CGAAATGATTATTATCTATATATATAGATTAATCATTC
Found at i:2111254 original size:2 final size:2
Alignment explanation
Indices: 2111249--2111303 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2111239 ATATATATAA
2111249 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2111291 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
2111304 AATTTGGTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2120217 original size:24 final size:21
Alignment explanation
Indices: 2120188--2120234 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
2120178 TTTAAAATAA
2120188 TTAAATTAAAGGATATAAAATTTT
1 TTAAATTAAA--AT-TAAAATTTT
*
2120212 TTAAATTATAATTAAAATTTT
1 TTAAATTAAAATTAAAATTTT
2120233 TT
1 TT
2120235 TTAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 2 0.09
24 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TTAAATTAAAATTAAAATTTT
Found at i:2136751 original size:2 final size:2
Alignment explanation
Indices: 2136739--2136781 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2136729 GCTAATCATA
*
2136739 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2136780 AT
1 AT
2136782 GTACACCCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2145799 original size:40 final size:40
Alignment explanation
Indices: 2145755--2145834 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
2145745 TTATATATAT
* * *
2145755 ACCTTCACCATATTTGTAACAAATTTCCAGGTTTGGTTTC
1 ACCTTCACCAGATTTGCAACAAATTTCCAGCTTTGGTTTC
*
2145795 ACCTTCACCAGATTTGCAACACATTTCCAGCTTTGGTTTC
1 ACCTTCACCAGATTTGCAACAAATTTCCAGCTTTGGTTTC
2145835 TATTCTGGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (40 bp):
ACCTTCACCAGATTTGCAACAAATTTCCAGCTTTGGTTTC
Found at i:2146388 original size:24 final size:25
Alignment explanation
Indices: 2146361--2146411 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
2146351 GCATCCAAGC
2146361 ATTTATCTAAGTA-A-TTAATGCATG
1 ATTTATCTAA-TAGAGTTAATGCATG
* *
2146385 ATTTTTCTAATAGAGTTGATGCATG
1 ATTTATCTAATAGAGTTAATGCATG
2146410 AT
1 AT
2146412 ATTTGCTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 2 0.09
24 10 0.43
25 11 0.48
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (25 bp):
ATTTATCTAATAGAGTTAATGCATG
Found at i:2164188 original size:18 final size:18
Alignment explanation
Indices: 2164155--2164216 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
2164145 ATTAAAAGAA
2164155 ATAAATTTTCAATTTATTTG
1 ATAAA-TTT-AATTTATTTG
* *
2164175 ATAAATTTAATTTATATA
1 ATAAATTTAATTTATTTG
*
2164193 ATAAAAATTAATTT-TTTAG
1 AT-AAATTTAATTTATTT-G
2164212 ATAAA
1 ATAAA
2164217 ATATAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 15 0.43
19 15 0.43
20 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (18 bp):
ATAAATTTAATTTATTTG
Found at i:2171565 original size:11 final size:11
Alignment explanation
Indices: 2171551--2171575 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2171541 TTTCCAAAAT
2171551 TTTAAAATATA
1 TTTAAAATATA
2171562 TTTAAAATATA
1 TTTAAAATATA
2171573 TTT
1 TTT
2171576 TCGTACCATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATATA
Found at i:2172395 original size:1 final size:1
Alignment explanation
Indices: 2172389--2172416 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2172379 CTTTCATAGC
2172389 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
2172417 CAATTATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2184253 original size:2 final size:2
Alignment explanation
Indices: 2184246--2184285 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2184236 TGCAGTTGAC
2184246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2184286 TACAAAACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2192179 original size:11 final size:11
Alignment explanation
Indices: 2192162--2192193 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2192152 AAATCACATA
2192162 AGAGATTTGTT
1 AGAGATTTGTT
*
2192173 TGAGATTTGTT
1 AGAGATTTGTT
2192184 AGAGATTTGT
1 AGAGATTTGT
2192194 CAGATATTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (11 bp):
AGAGATTTGTT
Found at i:2192284 original size:52 final size:52
Alignment explanation
Indices: 2192218--2192374 Score: 217
Period size: 52 Copynumber: 3.0 Consensus size: 52
2192208 TGGACAAGAA
* * *
2192218 GACTTGCAAAAGAAGAATTCTAAGA-GAAAGAAGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAG-AGATTCTTAATAGGCAAGTTT
*
2192270 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
* ** * *
2192322 GACTTACAAGAGAAGAATTCTAAAAGGAGTGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
2192374 G
1 G
2192375 TATGGTTATA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
52 91 0.95
53 5 0.05
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:2192587 original size:108 final size:108
Alignment explanation
Indices: 2192465--2192662 Score: 387
Period size: 108 Copynumber: 1.8 Consensus size: 108
2192455 GACACCCCAT
2192465 GTGTGTATGTTTGTTTGTGAGTGGACTAGAGGAGATTGAAAGGGTCCACATAGGTATGATGTATG
1 GTGTGTATGTTTGTTTGTGAGTGGACTAGAGGAGATTGAAAGGGTCCACATAGGTATGATGTATG
*
2192530 GGAGCATATGTGTATGTGTTTGGTTTTGGGGCTCTACGTCTGG
66 GGAGCATATGGGTATGTGTTTGGTTTTGGGGCTCTACGTCTGG
2192573 GTGTGTATGTTTGTTTGTGAGTGGACTAGAGGAGATTGAAAGGGTCCACATAGGTATGATGTATG
1 GTGTGTATGTTTGTTTGTGAGTGGACTAGAGGAGATTGAAAGGGTCCACATAGGTATGATGTATG
2192638 GGAGCATATGGGTATGTGTTTGGTT
66 GGAGCATATGGGTATGTGTTTGGTT
2192663 ATGTTGAAAG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 89 1.00
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (108 bp):
GTGTGTATGTTTGTTTGTGAGTGGACTAGAGGAGATTGAAAGGGTCCACATAGGTATGATGTATG
GGAGCATATGGGTATGTGTTTGGTTTTGGGGCTCTACGTCTGG
Found at i:2197059 original size:30 final size:28
Alignment explanation
Indices: 2197025--2197081 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
2197015 TTTTTTACAA
*
2197025 ATTGATCCATGATTTGATGACATGTTTGAT
1 ATTGATCCATGATAT-ATGA-ATGTTTGAT
**
2197055 ATTGATTTATGATATATGAATGTTTGA
1 ATTGATCCATGATATATGAATGTTTGA
2197082 CAGAATGCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.33
29 4 0.17
30 12 0.50
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (28 bp):
ATTGATCCATGATATATGAATGTTTGAT
Found at i:2203608 original size:55 final size:55
Alignment explanation
Indices: 2203520--2203679 Score: 212
Period size: 55 Copynumber: 2.9 Consensus size: 55
2203510 CAACGTGCGT
* * **
2203520 AACTGAGTAATTAAATATTAATTCCTTAGTTAGTGGAATGGGTTATTTTATGGGC
1 AACTGAGTAATTAAATATTAATTTCTTAATTAGTGGAATGGGAAATTTTATGGGC
* * *
2203575 AACTGAGTAATTAAATATCAATTTCTTAATTAGTGGAACGGGAAATTTTATGGGT
1 AACTGAGTAATTAAATATTAATTTCTTAATTAGTGGAATGGGAAATTTTATGGGC
* * * * *
2203630 AACCGAGTAATTAAATTTTAATTTCTTATTTACTGGAATGGGAGATTTTA
1 AACTGAGTAATTAAATATTAATTTCTTAATTAGTGGAATGGGAAATTTTA
2203680 ATCTAACTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.39
Consensus pattern (55 bp):
AACTGAGTAATTAAATATTAATTTCTTAATTAGTGGAATGGGAAATTTTATGGGC
Found at i:2204873 original size:18 final size:18
Alignment explanation
Indices: 2204833--2204880 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2204823 ATATTAACTA
2204833 AAAATTATATAAAAAATTT
1 AAAATTATAT-AAAAATTT
* *
2204852 -AAATTATATAATATTTT
1 AAAATTATATAAAAATTT
2204869 AAAATTA-ATAAA
1 AAAATTATATAAA
2204881 TAGTTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTATATAAAAATTT
Found at i:2211757 original size:16 final size:16
Alignment explanation
Indices: 2211732--2211778 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
2211722 TTGGGGTTCG
2211732 AAAGAGAAAGAGAGAGA
1 AAAGA-AAAGAGAGAGA
*
2211749 AAAGAAAAGAGGAAAGA
1 AAAGAAAAGA-GAGAGA
2211766 AAA-AAAAGAGAGA
1 AAAGAAAAGAGAGA
2211779 AATTTAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 13 0.48
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAGAGAGA
Found at i:2216777 original size:7 final size:8
Alignment explanation
Indices: 2216761--2216858 Score: 114
Period size: 8 Copynumber: 12.4 Consensus size: 8
2216751 TATAAATGAT
2216761 AAATGAAA
1 AAATGAAA
2216769 AAATGAAA
1 AAATGAAA
2216777 AAATGAAA
1 AAATGAAA
*
2216785 AAAGGGAAA
1 AAA-TGAAA
2216794 AAAT-AAA
1 AAATGAAA
2216801 AAATGAAA
1 AAATGAAA
2216809 AAAT-AAA
1 AAATGAAA
2216816 AAA-GAAA
1 AAATGAAA
2216823 AAA-GAAAAA
1 AAATG--AAA
2216832 AAATGAAA
1 AAATGAAA
* *
2216840 CAATAAAA
1 AAATGAAA
2216848 AAATGAAA
1 AAATGAAA
2216856 AAA
1 AAA
2216859 AATGTAAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
7 20 0.26
8 44 0.56
9 13 0.17
10 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.11, T:0.09
Consensus pattern (8 bp):
AAATGAAA
Found at i:2218283 original size:40 final size:40
Alignment explanation
Indices: 2218223--2218392 Score: 182
Period size: 40 Copynumber: 4.2 Consensus size: 40
2218213 AGAAACCTTA
* * * *
2218223 TTTATTTTTCAAAA-TCGTTGA-CTCTCTGTTTAGAGGAGT
1 TTTATTTTTTAAAAGTTGTTGAGC-CTCTATTTAGAGGAGC
2218262 TTTATTTTTTAAAAGTTGTTGAGCCTCTATTTAGAGGAGC
1 TTTATTTTTTAAAAGTTGTTGAGCCTCTATTTAGAGGAGC
* * * *
2218302 CTTATTTACATTTTAAAAGTTGTCGAGCCTTTGTTTAGAGGAGC
1 TTTA-TT---TTTTAAAAGTTGTTGAGCCTCTATTTAGAGGAGC
* * *
2218346 CTTATTTTTTAAAAGTTGTTGAGTCTTTATTTAGAGGAGC
1 TTTATTTTTTAAAAGTTGTTGAGCCTCTATTTAGAGGAGC
2218386 TTTATTT
1 TTTATTT
2218393 ATTTTTCAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 13 0.12
40 60 0.53
41 3 0.03
43 2 0.02
44 35 0.31
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (40 bp):
TTTATTTTTTAAAAGTTGTTGAGCCTCTATTTAGAGGAGC
Found at i:2218330 original size:44 final size:42
Alignment explanation
Indices: 2218251--2218397 Score: 185
Period size: 40 Copynumber: 3.5 Consensus size: 42
2218241 TGACTCTCTG
** *
2218251 TTTAGAGGAGTTTTA-TT-TTTTAAAAGTTGTTGAGCCTCTA
1 TTTAGAGGAGCCTTATTTATTTTAAAAGTTGTTGAGCCTTTA
* *
2218291 TTTAGAGGAGCCTTATTTACATTTTAAAAGTTGTCGAGCCTTTG
1 TTTAGAGGAGCCTTATTT--ATTTTAAAAGTTGTTGAGCCTTTA
*
2218335 TTTAGAGGAGCCTTA-TT-TTTTAAAAGTTGTTGAGTCTTTA
1 TTTAGAGGAGCCTTATTTATTTTAAAAGTTGTTGAGCCTTTA
*
2218375 TTTAGAGGAGCTTTATTTATTTT
1 TTTAGAGGAGCCTTATTTATTTT
2218398 TCAAAATCAT
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
40 47 0.51
41 4 0.04
42 4 0.04
43 2 0.02
44 35 0.38
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (42 bp):
TTTAGAGGAGCCTTATTTATTTTAAAAGTTGTTGAGCCTTTA
Found at i:2218862 original size:14 final size:13
Alignment explanation
Indices: 2218839--2218896 Score: 61
Period size: 12 Copynumber: 4.8 Consensus size: 13
2218829 AGTAAGCAAC
2218839 AAAGACACA-AAG
1 AAAGACACACAAG
2218851 AAAGACACACAAG
1 AAAGACACACAAG
*
2218864 -AAGACATAC-AG
1 AAAGACACACAAG
*
2218875 AAATACACACAA-
1 AAAGACACACAAG
*
2218887 AGAGACACAC
1 AAAGACACAC
2218897 GTAAAAGAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 2 0.05
12 32 0.84
13 4 0.11
ACGTcount: A:0.60, C:0.22, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAGACACACAAG
Found at i:2218867 original size:24 final size:23
Alignment explanation
Indices: 2218839--2218895 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
2218829 AGTAAGCAAC
2218839 AAAGACACAAAGAAAGACACACA
1 AAAGACACAAAGAAAGACACACA
* * *
2218862 AGAAGACATACAGAAATACACACA
1 A-AAGACACAAAGAAAGACACACA
2218886 AAGAGACACA
1 AA-AGACACA
2218896 CGTAAAAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.61, C:0.21, G:0.14, T:0.04
Consensus pattern (23 bp):
AAAGACACAAAGAAAGACACACA
Found at i:2219519 original size:16 final size:16
Alignment explanation
Indices: 2219491--2219524 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2219481 TGGTTTTTTT
2219491 TTTTAATTTTTATTTA
1 TTTTAATTTTTATTTA
2219507 TTTT-ATTTGTTATTTA
1 TTTTAATTT-TTATTTA
2219523 TT
1 TT
2219525 GTTTAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTAATTTTTATTTA
Found at i:2221353 original size:28 final size:28
Alignment explanation
Indices: 2221300--2221354 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2221290 GAAAAATTAT
**
2221300 AAAAAAAGAAGTAGAAAAAAGTAAAAAA
1 AAAAAAAGAAGTAGAAAAAACAAAAAAA
*
2221328 AAAAAAAGAAGT-GAATCAAACAAAAAA
1 AAAAAAAGAAGTAGAA-AAAACAAAAAA
2221355 TATGTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (28 bp):
AAAAAAAGAAGTAGAAAAAACAAAAAAA
Found at i:2231136 original size:94 final size:90
Alignment explanation
Indices: 2231014--2231181 Score: 221
Period size: 94 Copynumber: 1.8 Consensus size: 90
2231004 TTGACGTGAA
* * **
2231014 CCCTTTTTTTTTTTTTCGTCGGATGCTTATCACCTTTC-CTTTTCTCATTTGCTATTTTTATATA
1 CCCTTTTTATTTTTTTCGTCGGATGCTTATAACCTTTCTCTTTTCTCATTTAAT-TTTTTATA-A
2231078 TTTTTTGGAAGCATAATCCGACATCAT
64 TTTTTTGGAAGCATAATCCGACATCAT
* * *
2231105 CCCTTTTTATTTTTTTCTTCACTGGATGCTTATAACCTTTCTTTTTTCTCGTTTAATTTTTTATA
1 CCCTTTTTATTTTTTTCGT--C-GGATGCTTATAACCTTTCTCTTTTCTCATTTAATTTTTTATA
2231170 ATTTTTTGGAAG
63 ATTTTTTGGAAG
2231182 AATATGCCGA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
91 17 0.26
93 13 0.20
94 25 0.38
95 11 0.17
ACGTcount: A:0.17, C:0.18, G:0.10, T:0.55
Consensus pattern (90 bp):
CCCTTTTTATTTTTTTCGTCGGATGCTTATAACCTTTCTCTTTTCTCATTTAATTTTTTATAATT
TTTTGGAAGCATAATCCGACATCAT
Found at i:2231205 original size:93 final size:93
Alignment explanation
Indices: 2231017--2231210 Score: 220
Period size: 93 Copynumber: 2.1 Consensus size: 93
2231007 ACGTGAACCC
* * **
2231017 TTTTTTTTTTT-TTC-GTCGGATGCTTATCACCTTTCCTTTTCTCATTTGCTATTTTTATATATT
1 TTTTTTTTTTTCTTCACT-GGATGCTTATAACCTTTCCTTTTCTCATTTAATATTTTTATATATT
* * *
2231080 TTTTGGAAGCATAATCCGACATCATCCCT
65 TTTTGGAAGAATAATCCGAAATCATCACT
* *
2231109 TTTTATTTTTTTCTTCACTGGATGCTTATAACCTTTCTTTTTTCTCGTTTAAT-TTTTTATA-AT
1 TTTT-TTTTTTTCTTCACTGGATGCTTATAACCTTTC-CTTTTCTCATTTAATATTTTTATATAT
*
2231172 TTTTTGGAAGAAT-ATGCCGAAATGATCA-T
64 TTTTTGGAAGAATAAT-CCGAAATCATCACT
2231201 TTTTTTTTTT
1 TTTTTTTTTT
2231211 GTTTTCATCT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
91 6 0.07
92 11 0.13
93 30 0.34
94 28 0.32
95 12 0.14
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (93 bp):
TTTTTTTTTTTCTTCACTGGATGCTTATAACCTTTCCTTTTCTCATTTAATATTTTTATATATTT
TTTGGAAGAATAATCCGAAATCATCACT
Found at i:2231259 original size:13 final size:13
Alignment explanation
Indices: 2231241--2231265 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2231231 TTCTATTTTT
2231241 TAAAAAATAAAAC
1 TAAAAAATAAAAC
2231254 TAAAAAATAAAA
1 TAAAAAATAAAA
2231266 AAAAAATGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAAATAAAAC
Found at i:2238073 original size:95 final size:95
Alignment explanation
Indices: 2237901--2238182 Score: 317
Period size: 95 Copynumber: 2.9 Consensus size: 95
2237891 TCATAGCCAT
* * * *
2237901 TGGATGCTTATCA-CTTTTCCTTCTCCCCTTTAAAATTTTTATATATATTTTTGGAAGCATATGC
1 TGGATGCTTATCACCTTTCCCTT-TCTCATTTAATATTTTTATATAT-TTTTTGGAAGCATATGC
* *
2237965 CGACATGA-ACCTTTTTTTTTGTTTTTTTC-C
64 CGACATGATCCCTTTTTTTTTGTTTTCTTCAC
*
2237995 TCGGATGCTTATCACCTTTCCCTTTCTCATTTGATATTTTTATATATTTTTTGGAAGCATAAT-C
1 T-GGATGCTTATCACCTTTCCCTTTCTCATTTAATATTTTTATATATTTTTTGGAAGCAT-ATGC
*
2238059 CGACATGATCCCTTTTTATTT-TTTTCTTCAC
64 CGACATGATCCCTTTTTTTTTGTTTTCTTCAC
** * *
2238090 TGGATGCTTATCACCTTTCTTTTTTCTCGTTTAAT-TTTTTAATATATTTTTTGGAAGAATATGC
1 TGGATGCTTATCACCTTTC-CCTTTCTCATTTAATATTTTT-ATATATTTTTTGGAAGCATATGC
*
2238154 CGGA-ATGATCACTTTTCTTTTTTGTTTTC
64 C-GACATGATC-CCTTT-TTTTTTGTTTTC
2238183 ATCTCAAATA
Statistics
Matches: 161, Mismatches: 15, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
94 55 0.34
95 82 0.51
96 14 0.09
97 5 0.03
98 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.51
Consensus pattern (95 bp):
TGGATGCTTATCACCTTTCCCTTTCTCATTTAATATTTTTATATATTTTTTGGAAGCATATGCCG
ACATGATCCCTTTTTTTTTGTTTTCTTCAC
Found at i:2240358 original size:17 final size:17
Alignment explanation
Indices: 2240324--2240384 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 17
2240314 AAAAAAATCA
*
2240324 AAATAT-AAAACATATT
1 AAATATAAAAAAATATT
*
2240340 AAATATAAAAAAATGTT
1 AAATATAAAAAAATATT
*
2240357 -AATAGAAAAAAA-A-T
1 AAATATAAAAAAATATT
2240371 AAATA-AAAATAAAT
1 AAATATAAAA-AAAT
2240385 GACTTGACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 5 0.14
15 7 0.19
16 17 0.46
17 8 0.22
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (17 bp):
AAATATAAAAAAATATT
Found at i:2251448 original size:16 final size:16
Alignment explanation
Indices: 2251407--2251457 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2251397 GTCAAGTCAT
* *
2251407 TTTCGAGTTTAAATTTG
1 TTTCGAGTTCAAA-TTA
*
2251424 TTTAG-GTTCAAATTA
1 TTTCGAGTTCAAATTA
*
2251439 TTTCGAGTTCGAATTA
1 TTTCGAGTTCAAATTA
2251455 TTT
1 TTT
2251458 TGAATTTAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 6 0.21
16 18 0.64
17 4 0.14
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (16 bp):
TTTCGAGTTCAAATTA
Found at i:2264431 original size:14 final size:14
Alignment explanation
Indices: 2264412--2264455 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
2264402 AAAAGTTTGG
*
2264412 TATAATCTTAGTTA
1 TATAATCTTAGATA
*
2264426 TATAATTTTAGATA
1 TATAATCTTAGATA
2264440 TATAATCTTAGATA
1 TATAATCTTAGATA
2264454 TA
1 TA
2264456 ATTATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (14 bp):
TATAATCTTAGATA
Found at i:2271462 original size:28 final size:28
Alignment explanation
Indices: 2271417--2271473 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2271407 ACTACCATTC
**
2271417 CTTAGCAAAGGTTGTAATCTAGATTACT
1 CTTAGCAAAGGTCATAATCTAGATTACT
*
2271445 CTTATCAAAGGTCATAATCTAGATTACT
1 CTTAGCAAAGGTCATAATCTAGATTACT
2271473 C
1 C
2271474 ACCCATGAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (28 bp):
CTTAGCAAAGGTCATAATCTAGATTACT
Found at i:2271553 original size:23 final size:23
Alignment explanation
Indices: 2271527--2271580 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
2271517 CAATGAAATT
*
2271527 TTAACATTGGCTTAAGCATTTGC
1 TTAACATCGGCTTAAGCATTTGC
*
2271550 TTAACATCGGCTTAAGCATTTGG
1 TTAACATCGGCTTAAGCATTTGC
2271573 TTAACATC
1 TTAACATC
2271581 ACTTGCAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (23 bp):
TTAACATCGGCTTAAGCATTTGC
Found at i:2271564 original size:11 final size:11
Alignment explanation
Indices: 2271527--2271579 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
2271517 CAATGAAATT
2271527 TTAACATTGGC
1 TTAACATTGGC
*
2271538 TTAAGCATTTGC
1 TTAA-CATTGGC
*
2271550 TTAACATCGGC
1 TTAACATTGGC
2271561 TTAAGCATTTGG-
1 TTAA-CA-TTGGC
2271573 TTAACAT
1 TTAACAT
2271580 CACTTGCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 1 0.03
11 15 0.43
12 16 0.46
13 3 0.09
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (11 bp):
TTAACATTGGC
Found at i:2277530 original size:21 final size:21
Alignment explanation
Indices: 2277488--2277535 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2277478 ATTTAGATTT
* * *
2277488 TTCT-TTTTTTTTTTTTGTTA
1 TTCTCTTTTTATTTTTGGATA
2277508 TTCTCTTTTTATTTTTGGATA
1 TTCTCTTTTTATTTTTGGATA
*
2277529 TTTTCTT
1 TTCTCTT
2277536 GATTAACTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.08, C:0.08, G:0.06, T:0.77
Consensus pattern (21 bp):
TTCTCTTTTTATTTTTGGATA
Found at i:2293476 original size:19 final size:19
Alignment explanation
Indices: 2293452--2293489 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2293442 TAGGGTTACC
2293452 TGAGTC-GGATGAGAAGCGG
1 TGAGTCAGGA-GAGAAGCGG
2293471 TGAGTCAGGAGAGAAGCGG
1 TGAGTCAGGAGAGAAGCGG
2293490 AAGGGGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.29, C:0.11, G:0.47, T:0.13
Consensus pattern (19 bp):
TGAGTCAGGAGAGAAGCGG
Found at i:2300687 original size:26 final size:22
Alignment explanation
Indices: 2300634--2300678 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2300624 TTTATAACAT
2300634 TATAAAATAAATATTATATTTG
1 TATAAAATAAATATTATATTTG
2300656 TATAAAATAAATATTATATTTG
1 TATAAAATAAATATTATATTTG
2300678 T
1 T
2300679 CTATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TATAAAATAAATATTATATTTG
Found at i:2300692 original size:26 final size:23
Alignment explanation
Indices: 2300634--2300688 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
2300624 TTTATAACAT
2300634 TATA-AAATAAATATTATATTTG
1 TATATAAATAAATATTATATTTG
2300656 TATA-AAATAAATATTATATTTG
1 TATATAAATAAATATTATATTTG
2300678 TCTATATAAAT
1 --TATATAAAT
2300689 TAAAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 22 0.73
24 4 0.13
25 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (23 bp):
TATATAAATAAATATTATATTTG
Found at i:2302188 original size:24 final size:25
Alignment explanation
Indices: 2302156--2302203 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
2302146 TATTGATTTT
2302156 AATTTAAATAA-TTATAAAAAATTC
1 AATTTAAATAATTTATAAAAAATTC
*
2302180 AATTTAAATAATTTATTAAAAATT
1 AATTTAAATAATTTATAAAAAATT
2302204 TTATTTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
AATTTAAATAATTTATAAAAAATTC
Found at i:2303040 original size:33 final size:33
Alignment explanation
Indices: 2303003--2303073 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
2302993 GTTTAGACAG
* *
2303003 AATTTAAACTTGACTAGTTCTTTATTGTTACAT
1 AATTTAAACTTAACTAGTTCTTTATTATTACAT
* ** *
2303036 AATTTTATTTTAACTTGTTCTTTATTATTACAT
1 AATTTAAACTTAACTAGTTCTTTATTATTACAT
2303069 AATTT
1 AATTT
2303074 TATTTTAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.55
Consensus pattern (33 bp):
AATTTAAACTTAACTAGTTCTTTATTATTACAT
Found at i:2303044 original size:16 final size:15
Alignment explanation
Indices: 2303023--2303080 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
2303013 TGACTAGTTC
2303023 TTTATTGTTACATAAT
1 TTTATT-TTACATAAT
* **
2303039 TTTATTTTAACTTGTT
1 TTTATTTT-ACATAAT
2303055 CTTTATTATTACATAAT
1 -TTTATT-TTACATAAT
2303072 TTTATTTTA
1 TTTATTTTA
2303081 ACATTTTGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
15 5 0.15
16 16 0.48
17 10 0.30
18 2 0.06
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTATTTTACATAAT
Found at i:2303074 original size:33 final size:33
Alignment explanation
Indices: 2303019--2303082 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
2303009 AACTTGACTA
*
2303019 GTTCTTTATTGTTACATAATTTTATTTTAACTT
1 GTTCTTTATTATTACATAATTTTATTTTAACTT
2303052 GTTCTTTATTATTACATAATTTTATTTTAAC
1 GTTCTTTATTATTACATAATTTTATTTTAAC
2303083 ATTTTGACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (33 bp):
GTTCTTTATTATTACATAATTTTATTTTAACTT
Found at i:2308132 original size:9 final size:9
Alignment explanation
Indices: 2308118--2308143 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2308108 CATTCACACC
2308118 AAAAAAAAG
1 AAAAAAAAG
2308127 AAAAAAAAG
1 AAAAAAAAG
2308136 AAAAAAAA
1 AAAAAAAA
2308144 AGAACTAGAG
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:2308133 original size:10 final size:10
Alignment explanation
Indices: 2308118--2308147 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2308108 CATTCACACC
2308118 AAAAAAAAG-
1 AAAAAAAAGA
2308127 AAAAAAAAGA
1 AAAAAAAAGA
2308137 AAAAAAAAGA
1 AAAAAAAAGA
2308147 A
1 A
2308148 CTAGAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:2311648 original size:2 final size:2
Alignment explanation
Indices: 2311641--2311676 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2311631 CCTCTGCATC
2311641 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
2311677 GTGCAAAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2323087 original size:12 final size:12
Alignment explanation
Indices: 2323070--2323103 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2323060 TAGAGTGATG
*
2323070 AATTTTTTATTT
1 AATTTTTTAATT
*
2323082 AATTTTGTAATT
1 AATTTTTTAATT
2323094 AATTTTTTAA
1 AATTTTTTAA
2323104 ATTTTTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
AATTTTTTAATT
Found at i:2326489 original size:18 final size:18
Alignment explanation
Indices: 2326445--2326547 Score: 79
Period size: 18 Copynumber: 5.9 Consensus size: 18
2326435 GATTATTATT
* *
2326445 CACCTCAAATGTATCTTC
1 CACCACAAATGTATCATC
* * *
2326463 CATCTCAAATGTATCATT
1 CACCACAAATGTATCATC
* *
2326481 TACCACAAATGGATTC-TC
1 CACCACAAATGTA-TCATC
2326499 CACCACAAATGTATCAT-
1 CACCACAAATGTATCATC
* *
2326516 CA--TCAAATATATCATC
1 CACCACAAATGTATCATC
*
2326532 CACCTCAAATGTATCA
1 CACCACAAATGTATCA
2326548 AGAACAAAAG
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
15 11 0.16
16 2 0.03
17 4 0.06
18 48 0.72
19 2 0.03
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (18 bp):
CACCACAAATGTATCATC
Found at i:2326490 original size:36 final size:33
Alignment explanation
Indices: 2326449--2326547 Score: 94
Period size: 33 Copynumber: 2.9 Consensus size: 33
2326439 ATTATTCACC
*
2326449 TCAAATGTATCTTCCATCTCAAATGTATCATTTACCA
1 TCAAATGTATCTTCCACCTCAAATGTATCA--T--CA
* *
2326486 -CAAATGGAT-TCTCCACCACAAATGTATCATCA
1 TCAAATGTATCT-TCCACCTCAAATGTATCATCA
* *
2326518 TCAAATATATCATCCACCTCAAATGTATCA
1 TCAAATGTATCTTCCACCTCAAATGTATCA
2326548 AGAACAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
32 2 0.04
33 24 0.46
34 1 0.02
35 1 0.02
36 24 0.46
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.31
Consensus pattern (33 bp):
TCAAATGTATCTTCCACCTCAAATGTATCATCA
Found at i:2342699 original size:8 final size:8
Alignment explanation
Indices: 2342686--2342710 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2342676 ATCGAATTTG
2342686 ATTTTAAT
1 ATTTTAAT
2342694 ATTTTAAT
1 ATTTTAAT
2342702 ATTTTAAT
1 ATTTTAAT
2342710 A
1 A
2342711 ATATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTAAT
Found at i:2357402 original size:36 final size:37
Alignment explanation
Indices: 2357351--2357425 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 37
2357341 GAGTATACTC
**
2357351 ATTTCTTTCTGGTCTGCATTGACTATTTTATGCC-AA
1 ATTTCTTTCCAGTCTGCATTGACTATTTTATGCCTAA
*
2357387 ATTTCTTTCCAGTCTGCATTGACTGTTTTATGCCTAA
1 ATTTCTTTCCAGTCTGCATTGACTATTTTATGCCTAA
2357424 AT
1 AT
2357426 GGAATCTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 31 0.89
37 4 0.11
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (37 bp):
ATTTCTTTCCAGTCTGCATTGACTATTTTATGCCTAA
Found at i:2358429 original size:25 final size:23
Alignment explanation
Indices: 2358380--2358429 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
2358370 CGTTAGAATG
*
2358380 ATTCTTTTCTCCAATTTTATTTT
1 ATTCTTTTCTCCAATTTTAATTT
2358403 ATTCTTTTCTCCAATAATTTAATTT
1 ATTCTTTTCTCCAAT--TTTAATTT
2358428 AT
1 AT
2358430 CCACAAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 15 0.62
25 9 0.38
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTCTTTTCTCCAATTTTAATTT
Found at i:2363024 original size:15 final size:16
Alignment explanation
Indices: 2362977--2363040 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
2362967 ACTAGTTTGG
2362977 TAAATAATATTATCTTTTT
1 TAAAT-ATATTA--TTTTT
*
2362996 TAACTA-ATTCATTTTT
1 TAAATATATT-ATTTTT
*
2363012 TATAT-TATTA-TTTT
1 TAAATATATTATTTTT
2363026 TAAATATATTATTTT
1 TAAATATATTATTTT
2363041 ATGATATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
14 8 0.22
15 6 0.16
16 14 0.38
17 3 0.08
18 2 0.05
19 4 0.11
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (16 bp):
TAAATATATTATTTTT
Found at i:2363025 original size:14 final size:15
Alignment explanation
Indices: 2363008--2363040 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2362998 ACTAATTCAT
*
2363008 TTTTTATAT-TATTA
1 TTTTTAAATATATTA
2363022 TTTTTAAATATATTA
1 TTTTTAAATATATTA
2363037 TTTT
1 TTTT
2363041 ATGATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAAATATATTA
Found at i:2363040 original size:30 final size:30
Alignment explanation
Indices: 2362983--2363040 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
2362973 TTGGTAAATA
*
2362983 ATATTATCTTTTTTAACTAATTCATTTTTT
1 ATATTATCTTTTTTAAATAATTCATTTTTT
2363013 ATATTAT-TATTTTTAAATATATT-ATTTT
1 ATATTATCT-TTTTTAAATA-ATTCATTTT
2363041 ATGATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 1 0.04
30 21 0.84
31 3 0.12
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (30 bp):
ATATTATCTTTTTTAAATAATTCATTTTTT
Found at i:2367946 original size:19 final size:19
Alignment explanation
Indices: 2367922--2367960 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2367912 TAAGGAAAAA
2367922 ATAACCAGGAATGAGTAAC
1 ATAACCAGGAATGAGTAAC
2367941 ATAACCAGGAATGAGTAAC
1 ATAACCAGGAATGAGTAAC
2367960 A
1 A
2367961 AGGCAACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.15
Consensus pattern (19 bp):
ATAACCAGGAATGAGTAAC
Found at i:2369643 original size:64 final size:65
Alignment explanation
Indices: 2369560--2369690 Score: 228
Period size: 64 Copynumber: 2.0 Consensus size: 65
2369550 GCGGGTAGGG
* *
2369560 TAAAATCCTTGATTTAAGTGGTAGTACTCCTTGTACCAAAATTTCACAAGTAATATGATATT-TT
1 TAAAATCCTTGATTCAAGTGGTAGTACTCCTTGTACCAAAATTTCACAAGCAATATGATATTGTT
*
2369624 TAAAATCCTTGATTCAAGTGTTAGTACTCCTTGTACCAAAATTTCACAAGCAATATGATATTGTT
1 TAAAATCCTTGATTCAAGTGGTAGTACTCCTTGTACCAAAATTTCACAAGCAATATGATATTGTT
2369689 TA
1 TA
2369691 TAAACATATC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
64 59 0.94
65 4 0.06
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (65 bp):
TAAAATCCTTGATTCAAGTGGTAGTACTCCTTGTACCAAAATTTCACAAGCAATATGATATTGTT
Found at i:2373335 original size:2 final size:2
Alignment explanation
Indices: 2373328--2373374 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
2373318 CCCTCTCCAC
* *
2373328 AT AT AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2373370 AT AT A
1 AT AT A
2373375 AAGTAGTGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2373718 original size:7 final size:8
Alignment explanation
Indices: 2373670--2373715 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
2373660 TAATTCAATA
2373670 TTTAAAAT
1 TTTAAAAT
2373678 TTTAAAAT
1 TTTAAAAT
*
2373686 ATTT--ATT
1 -TTTAAAAT
2373693 TTTAAGAAT
1 TTTAA-AAT
2373702 TTTAAAAT
1 TTTAAAAT
2373710 TTTAAA
1 TTTAAA
2373716 TTTGCTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
6 3 0.09
7 2 0.06
8 17 0.53
9 10 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (8 bp):
TTTAAAAT
Found at i:2382018 original size:30 final size:30
Alignment explanation
Indices: 2381960--2382041 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
2381950 CTAGTCAAGA
* * *
2381960 GTTTAATTGTGATGAAAATATACGTTTAAG
1 GTTTAATTGAGATGAAAATAAACATTTAAG
*
2381990 GATTTAATTGAG-TGAAAATAAATATTTAAG
1 G-TTTAATTGAGATGAAAATAAACATTTAAG
* *
2382020 GTTTCAATTAATAT-AAAATAAA
1 GTTT-AATTGAGATGAAAATAAA
2382042 AAATTCAGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 3 0.07
30 30 0.70
31 10 0.23
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (30 bp):
GTTTAATTGAGATGAAAATAAACATTTAAG
Found at i:2382894 original size:36 final size:36
Alignment explanation
Indices: 2382854--2382959 Score: 88
Period size: 36 Copynumber: 3.2 Consensus size: 36
2382844 ATTTTAATTT
*
2382854 ATTATACATTATGTAACAATATACTTTTTTTAGAGA
1 ATTATACATTATATAACAATATACTTTTTTTAGAGA
*
2382890 ATTATAC-TTA-CT-A-AATATA-TTTTAATTT-----
1 ATTATACATTATATAACAATATACTTTT--TTTAGAGA
* *
2382918 ATTATACATTATATAACGATATACTCTTTTTAGAGA
1 ATTATACATTATATAACAATATACTTTTTTTAGAGA
2382954 ATTATA
1 ATTATA
2382960 TAAGAATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 24
0.66 0.05 0.29
Matches are distributed among these distances:
28 7 0.13
29 3 0.06
30 1 0.02
31 8 0.15
32 11 0.20
33 7 0.13
34 1 0.02
35 3 0.06
36 13 0.24
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (36 bp):
ATTATACATTATATAACAATATACTTTTTTTAGAGA
Found at i:2382903 original size:64 final size:64
Alignment explanation
Indices: 2382832--2382959 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
2382822 ATAACAATTT
* *
2382832 CTTACTAAATATATTTTAATTTATTATACATTATGTAACAATATACTTTTTTTAGAGAATTATA
1 CTTACTAAATATATTTTAATTTATTATACATTATATAACAATATACTCTTTTTAGAGAATTATA
*
2382896 CTTACTAAATATATTTTAATTTATTATACATTATATAACGATATACTCTTTTTAGAGAATTATA
1 CTTACTAAATATATTTTAATTTATTATACATTATATAACAATATACTCTTTTTAGAGAATTATA
2382960 TAAGAATATA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.48
Consensus pattern (64 bp):
CTTACTAAATATATTTTAATTTATTATACATTATATAACAATATACTCTTTTTAGAGAATTATA
Found at i:2384176 original size:21 final size:20
Alignment explanation
Indices: 2384140--2384178 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2384130 CACACGTAAT
*
2384140 TAAAATTTTGAATTTAAACA
1 TAAAATTTTAAATTTAAACA
2384160 TAAAATATTTAAATTTAAA
1 TAAAAT-TTTAAATTTAAA
2384179 AATTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
TAAAATTTTAAATTTAAACA
Found at i:2386757 original size:30 final size:30
Alignment explanation
Indices: 2386720--2386784 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
2386710 CCCGAAATTA
* *
2386720 ATAAAAATATTATTTTTTAAATATAAATAT
1 ATAAAAATATTATTATATAAATATAAATAT
* *
2386750 TTAAAAATATTATTATATAAATATATATAT
1 ATAAAAATATTATTATATAAATATAAATAT
2386780 ATAAA
1 ATAAA
2386785 TAAATAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
ATAAAAATATTATTATATAAATATAAATAT
Found at i:2388121 original size:16 final size:16
Alignment explanation
Indices: 2388100--2388130 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2388090 AAAACTGCTG
2388100 TCCACTAACTAAAGTA
1 TCCACTAACTAAAGTA
*
2388116 TCCACTAATTAAAGT
1 TCCACTAACTAAAGT
2388131 TTTTCTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.29
Consensus pattern (16 bp):
TCCACTAACTAAAGTA
Found at i:2388543 original size:12 final size:12
Alignment explanation
Indices: 2388526--2388550 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2388516 GCATGGGGAC
2388526 AATAATATATAT
1 AATAATATATAT
2388538 AATAATATATAT
1 AATAATATATAT
2388550 A
1 A
2388551 GTTTTATTCA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAATATATAT
Found at i:2395880 original size:20 final size:18
Alignment explanation
Indices: 2395851--2395891 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
2395841 TTTTATATCT
*
2395851 AAATTGATTTATGTACAATA
1 AAATTAATTTATG-A-AATA
2395871 AAATTAATTTATGAAATA
1 AAATTAATTTATGAAATA
2395889 AAA
1 AAA
2395892 AACTCTTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 1 0.05
20 12 0.60
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (18 bp):
AAATTAATTTATGAAATA
Found at i:2396376 original size:13 final size:13
Alignment explanation
Indices: 2396355--2396387 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2396345 TTTTTATATC
2396355 ATATA-AATTATA
1 ATATATAATTATA
2396367 ATATATAATTATA
1 ATATATAATTATA
2396380 ATATATAA
1 ATATATAA
2396388 CATGATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATATAATTATA
Found at i:2396378 original size:27 final size:31
Alignment explanation
Indices: 2396355--2396416 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
2396345 TTTTTATATC
2396355 ATATAA-AT-TAT-AATATAT-AATTATAAT
1 ATATAACATATATAAATATATAAATTATAAT
2396382 ATATAACATGATATAAATATATAAATTATTAAT
1 ATATAACAT-ATATAAATATATAAATTA-TAAT
2396415 AT
1 AT
2396417 TTTATAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 6 0.21
28 2 0.07
30 3 0.10
31 7 0.24
32 5 0.17
33 6 0.21
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
ATATAACATATATAAATATATAAATTATAAT
Found at i:2396397 original size:10 final size:8
Alignment explanation
Indices: 2396355--2396416 Score: 55
Period size: 7 Copynumber: 8.2 Consensus size: 8
2396345 TTTTTATATC
2396355 ATATAAAT
1 ATATAAAT
2396363 -TAT-AAT
1 ATATAAAT
2396369 ATAT-AAT
1 ATATAAAT
2396376 -TAT-AAT
1 ATATAAAT
2396382 ATATAACAT
1 ATATAA-AT
2396391 GATATAAAT
1 -ATATAAAT
2396400 ATATAAAT
1 ATATAAAT
*
2396408 -TATTAAT
1 ATATAAAT
2396415 AT
1 AT
2396417 TTTATAAAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
6 9 0.19
7 18 0.38
8 10 0.21
9 4 0.09
10 6 0.13
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (8 bp):
ATATAAAT
Found at i:2412688 original size:20 final size:21
Alignment explanation
Indices: 2412665--2412703 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2412655 ACTCTTTTTC
*
2412665 TCTTGATT-TTTCTAATTGAT
1 TCTTGATTGTCTCTAATTGAT
2412685 TCTTGATTGTCTCTAATTG
1 TCTTGATTGTCTCTAATTG
2412704 GTCTTAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.56
Consensus pattern (21 bp):
TCTTGATTGTCTCTAATTGAT
Found at i:2412708 original size:20 final size:20
Alignment explanation
Indices: 2412665--2412708 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2412655 ACTCTTTTTC
* *
2412665 TCTTGATTTTTCTAATTGAT
1 TCTTGATTTCTCTAATTGAG
2412685 TCTTGATTGTCTCTAATTG-G
1 TCTTGATT-TCTCTAATTGAG
2412705 TCTT
1 TCTT
2412709 AATAGGGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (20 bp):
TCTTGATTTCTCTAATTGAG
Found at i:2413407 original size:19 final size:19
Alignment explanation
Indices: 2413371--2413436 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
2413361 CAAGATTCAT
* * * *
2413371 AAAAGATTCAAAGGTTTGT
1 AAAAAATTCCAAGATTTGC
*
2413390 AAAAAATTTCAAGATTTGC
1 AAAAAATTCCAAGATTTGC
*
2413409 AAAAGATTCCAAGATTTGC
1 AAAAAATTCCAAGATTTGC
*
2413428 AAAAGATTC
1 AAAAAATTC
2413437 TTGCAAAGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (19 bp):
AAAAAATTCCAAGATTTGC
Found at i:2413731 original size:16 final size:17
Alignment explanation
Indices: 2413695--2413737 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
2413685 AGGATTAAAG
* *
2413695 ATTCGCAAGAATTTTAG
1 ATTCGTAAGAATTTTAA
2413712 ATTCGTAAGAA-TTTAA
1 ATTCGTAAGAATTTTAA
2413728 ATTCGTAAGA
1 ATTCGTAAGA
2413738 TTTCAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (17 bp):
ATTCGTAAGAATTTTAA
Found at i:2414216 original size:109 final size:107
Alignment explanation
Indices: 2414058--2414327 Score: 364
Period size: 109 Copynumber: 2.5 Consensus size: 107
2414048 AGTGTTTCAC
* * *
2414058 ATTCAATAT-TTCTTATTTAAAAACTTTAAGATTTCATCTAAAATTTCAAA-CCTTCTCATTCGA
1 ATTCAA-ATGTTCTCATTCAAAAACTTTAAGAGTTCATCTAAAATTTCAAAGCCTT-TCATTCGA
*
2414121 GTTTAAAGATTCACATTCGATAAATTTTAAAGTTTCACATCTAA
64 GTTCAAAGATTCACATTCGATAAATTTTAAAGTTTCACATCTAA
* * *
2414165 ATTCAAATGTTCTCATTCAAAAACTTTAGGAGTTCATATCTAAAATTTCAAAGCGTTTTATTCGA
1 ATTCAAATGTTCTCATTCAAAAACTTTAAGAGTTC--ATCTAAAATTTCAAAGCCTTTCATTCGA
*
2414230 GTTCAAAGATTCACATTCGATAAATTTTAGAGTTTCACATCTAA
64 GTTCAAAGATTCACATTCGATAAATTTTAAAGTTTCACATCTAA
* * * *
2414274 ATTCAAAGGTTCTCATTCAAAAACTTTAAGGGTTCGTATACATAATTTCAAAGC
1 ATTCAAATGTTCTCATTCAAAAACTTTAAGAGTTCATCTA-A-AATTTCAAAGC
2414328 TCAAAGGTTC
Statistics
Matches: 144, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
106 2 0.01
107 31 0.22
108 1 0.01
109 107 0.74
110 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (107 bp):
ATTCAAATGTTCTCATTCAAAAACTTTAAGAGTTCATCTAAAATTTCAAAGCCTTTCATTCGAGT
TCAAAGATTCACATTCGATAAATTTTAAAGTTTCACATCTAA
Found at i:2414338 original size:52 final size:52
Alignment explanation
Indices: 2414276--2414380 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
2414266 ACATCTAAAT
2414276 TCAAAGGTTCTCATTCAAAAACTTTAAGGGTTCGTATACATAATTTCAAAGC
1 TCAAAGGTTCTCATTCAAAAACTTTAAGGGTTCGTATACATAATTTCAAAGC
2414328 TCAAAGGTTCTCATTCAAAAACTTTAAGGGTTCGTATACATAATTTCAAAGC
1 TCAAAGGTTCTCATTCAAAAACTTTAAGGGTTCGTATACATAATTTCAAAGC
2414380 T
1 T
2414381 TCTCATTCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (52 bp):
TCAAAGGTTCTCATTCAAAAACTTTAAGGGTTCGTATACATAATTTCAAAGC
Found at i:2414348 original size:161 final size:162
Alignment explanation
Indices: 2414167--2414488 Score: 418
Period size: 161 Copynumber: 2.0 Consensus size: 162
2414157 ACATCTAAAT
* * *
2414167 TCAAATGTTCTCATTCAAAAACTTT-AGGAGTTCATAT-CTAAAATTTCAAAGCGTT-TTATTCG
1 TCAAAGGTTCTCATTCAAAAACTTTAAGG-GTTCATATAC-AAAATTTCAAAGC-TTCTCATTCA
* * *
2414229 AGTTCAAAGATTCACATTCGATAAATTTTAGAGTTTCACATCTAAATTCAAAGGTTCTCATTC-A
63 AGTTCAAAAATTCACATTCAATAAATTTTAGAATTTCACATCTAAATTCAAAGGTTCTCATTCAA
* * *
2414293 AAAACTTTAAGGGTTCGTATACATAATTTCAAAGC
128 AAAAATTTAAGGGTTCATATACAAAATTTCAAAGC
* *
2414328 TCAAAGGTTCTCATTCAAAAACTTTAAGGGTTCGTATACATAATTTCAAAGCTTCTCATTCAAGT
1 TCAAAGGTTCTCATTCAAAAACTTTAAGGGTTCATATACAAAATTTCAAAGCTTCTCATTCAAGT
* * * * * *
2414393 TTAAAAATTCACATTCAATAAATTTTAGAATTTTACGTCTAAATTGAAAGGTTTTTATTCAAAAA
66 TCAAAAATTCACATTCAATAAATTTTAGAATTTCACATCTAAATTCAAAGGTTCTCATTCAAAAA
* *
2414458 AATTTAGGGGTTCATATCCAAAATTTCAAAG
131 AATTTAAGGGTTCATATACAAAATTTCAAAG
2414489 TTTCTCATTC
Statistics
Matches: 138, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
160 2 0.01
161 102 0.74
162 34 0.25
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (162 bp):
TCAAAGGTTCTCATTCAAAAACTTTAAGGGTTCATATACAAAATTTCAAAGCTTCTCATTCAAGT
TCAAAAATTCACATTCAATAAATTTTAGAATTTCACATCTAAATTCAAAGGTTCTCATTCAAAAA
AATTTAAGGGTTCATATACAAAATTTCAAAGC
Found at i:2414543 original size:109 final size:109
Alignment explanation
Indices: 2414328--2414565 Score: 289
Period size: 109 Copynumber: 2.2 Consensus size: 109
2414318 ATTTCAAAGC
* * *
2414328 TCAAAGGTTCTCATTCAAAAACTTTAAGGGTTCGTATACATAATTTCAAAGCTTCTCATTCAAGT
1 TCAAAGGTTCTCATTCAAAAAATTTAAGGGTTCATATACAAAATTTCAAAGCTTCTCATTCAAGT
* * *
2414393 TTAAAAATTCACATTCAATAAATTTTAGAATTTTACGTCTAAAT
66 TCAAAAATTCACATTCAATAAATTTTAGAATTTCACATCTAAAT
* * * * * * *
2414437 TGAAAGGTTTTTATTCAAAAAAATTTAGGGGTTCATATCCAAAATTTCAAAGTTTCTCATTCGAG
1 TCAAAGGTTCTCATTC-AAAAAATTTAAGGGTTCATATACAAAATTTCAAAGCTTCTCATTCAAG
* * * * *
2414502 -TCAAAGATTTATATTTAATAAATTTTAGAGTTTCACATCTAAAT
65 TTCAAAAATTCACATTCAATAAATTTTAGAATTTCACATCTAAAT
*
2414546 TCAAAGGTTCTCATTTAAAA
1 TCAAAGGTTCTCATTCAAAA
2414566 CTTCTTAAAG
Statistics
Matches: 106, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
108 4 0.04
109 61 0.58
110 41 0.39
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (109 bp):
TCAAAGGTTCTCATTCAAAAAATTTAAGGGTTCATATACAAAATTTCAAAGCTTCTCATTCAAGT
TCAAAAATTCACATTCAATAAATTTTAGAATTTCACATCTAAAT
Found at i:2414580 original size:24 final size:22
Alignment explanation
Indices: 2414547--2414820 Score: 116
Period size: 24 Copynumber: 12.3 Consensus size: 22
2414537 CATCTAAATT
* *
2414547 CAAAGGTTCTCATTTAAAACTT
1 CAAAGATTCTCATTTAAAACTA
* *
2414569 CTTAAAGATTCTAATTTAAAA-GA
1 C--AAAGATTCTCATTTAAAACTA
2414592 CAAAGATTCTCATTTAAAACTA
1 CAAAGATTCTCATTTAAAACTA
* * ** * * *
2414614 -AAA-AAT-TAAGGT-CATCATT
1 CAAAGATTCTCATTTAAAAC-TA
* *
2414633 CAAAGATTATCATTTAAAACTTTT
1 CAAAGATTCTCATTTAAAAC--TA
* * *
2414657 TAAA-ATTTTCATTTAAAA-GA
1 CAAAGATTCTCATTTAAAACTA
* * * * *
2414677 TAAATATTCTAATTCAAAACTC
1 CAAAGATTCTCATTTAAAACTA
*
2414699 CTTAAAGATTCTCATTTAAAACTT
1 C--AAAGATTCTCATTTAAAACTA
*
2414723 CTTAAAGATTCTCATTTAAAACTC
1 C--AAAGATTCTCATTTAAAACTA
* *
2414747 CTTAAATATTCTCATTTAAAA-GA
1 C--AAAGATTCTCATTTAAAACTA
* *
2414770 CAAAGATTCTCATTCAAAACTC
1 CAAAGATTCTCATTTAAAACTA
*
2414792 CTTAAAGATTCTCATTCAAAACT-
1 C--AAAGATTCTCATTTAAAACTA
2414815 CAAAGA
1 CAAAGA
2414821 CAAAGATTCT
Statistics
Matches: 194, Mismatches: 42, Indels: 33
0.72 0.16 0.12
Matches are distributed among these distances:
18 2 0.01
19 4 0.02
20 9 0.05
21 54 0.28
22 6 0.03
23 18 0.09
24 101 0.52
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.35
Consensus pattern (22 bp):
CAAAGATTCTCATTTAAAACTA
Found at i:2414602 original size:45 final size:45
Alignment explanation
Indices: 2414547--2414812 Score: 229
Period size: 45 Copynumber: 6.0 Consensus size: 45
2414537 CATCTAAATT
* * *
2414547 CAAAGGTTCTCATTTAAAACTTCTTAAAGATTCTAATTTAAAAGA
1 CAAAGATTCTCATTTAAAACTCCTTAAAGATTCTCATTTAAAAGA
* * * * * ** **
2414592 CAAAGATTCTCATTTAAAA---C-TAAAAAAT-TAAGGTCATCATT
1 CAAAGATTCTCATTTAAAACTCCTTAAAGATTCTCA-TTTAAAAGA
* ** *
2414633 CAAAGATTATCATTTAAAACTTTTTAAA-ATTTTCATTTAAAAGA
1 CAAAGATTCTCATTTAAAACTCCTTAAAGATTCTCATTTAAAAGA
* * * * **
2414677 TAAATATTCTAATTCAAAACTCCTTAAAGATTCTCATTTAAAACTT
1 CAAAGATTCTCATTTAAAACTCCTTAAAGATTCTCATTTAAAA-GA
*
2414723 CTTAAAGATTCTCATTTAAAACTCCTTAAATATTCTCATTTAAAAGA
1 C--AAAGATTCTCATTTAAAACTCCTTAAAGATTCTCATTTAAAAGA
* *
2414770 CAAAGATTCTCATTCAAAACTCCTTAAAGATTCTCATTCAAAA
1 CAAAGATTCTCATTTAAAACTCCTTAAAGATTCTCATTTAAAA
2414813 CTCAAAGACA
Statistics
Matches: 172, Mismatches: 39, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
40 3 0.02
41 27 0.16
42 1 0.01
44 26 0.15
45 76 0.44
47 1 0.01
48 38 0.22
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (45 bp):
CAAAGATTCTCATTTAAAACTCCTTAAAGATTCTCATTTAAAAGA
Found at i:2414778 original size:69 final size:70
Alignment explanation
Indices: 2414633--2414815 Score: 205
Period size: 69 Copynumber: 2.7 Consensus size: 70
2414623 GGTCATCATT
* * * *
2414633 CAAAGATTATCATTTAAAACTTTTTAAA-ATTTTCATTTAAAA---GATAAATATTCTAATTCAA
1 CAAAGATTCTCATTTAAAACTTCTTAAAGATTCTCATTTAAAACTCCATAAATATTCTAATTCAA
**
2414694 AACTC
66 AACGA
* * *
2414699 CTTAAAGATTCTCATTTAAAACTTCTTAAAGATTCTCATTTAAAACTCCTTAAATATTCTCATTT
1 C--AAAGATTCTCATTTAAAACTTCTTAAAGATTCTCATTTAAAACTCCATAAATATTCTAATTC
2414764 AAAA-GA
64 AAAACGA
* * *
2414770 CAAAGATTCTCATTCAAAACTCCTTAAAGATTCTCATTCAAAACTC
1 CAAAGATTCTCATTTAAAACTTCTTAAAGATTCTCATTTAAAACTC
2414816 AAAGACAAAG
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
66 1 0.01
68 25 0.25
69 55 0.56
71 1 0.01
72 17 0.17
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (70 bp):
CAAAGATTCTCATTTAAAACTTCTTAAAGATTCTCATTTAAAACTCCATAAATATTCTAATTCAA
AACGA
Found at i:2414792 original size:93 final size:92
Alignment explanation
Indices: 2414634--2414814 Score: 281
Period size: 93 Copynumber: 2.0 Consensus size: 92
2414624 GTCATCATTC
** * * *
2414634 AAAGATTATCATTTAAAACTTTTTAAAATTTTCATTTAAAAGATAAATATTCTAATTCAAAACTC
1 AAAGATTATCATTTAAAACTCCTTAAAATTCTCATTTAAAAGACAAAGATTCTAATTCAAAACTC
*
2414699 CTTAAAGATTCTCATTTAAAACTTCTT
66 CTTAAAGATTCTCATTCAAAACTTCTT
* *
2414726 AAAGATTCTCATTTAAAACTCCTTAAATATTCTCATTTAAAAGACAAAGATTCTCATTCAAAACT
1 AAAGATTATCATTTAAAACTCCTTAAA-ATTCTCATTTAAAAGACAAAGATTCTAATTCAAAACT
2414791 CCTTAAAGATTCTCATTCAAAACT
65 CCTTAAAGATTCTCATTCAAAACT
2414815 CAAAGACAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 24 0.30
93 56 0.70
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (92 bp):
AAAGATTATCATTTAAAACTCCTTAAAATTCTCATTTAAAAGACAAAGATTCTAATTCAAAACTC
CTTAAAGATTCTCATTCAAAACTTCTT
Found at i:2415801 original size:15 final size:15
Alignment explanation
Indices: 2415781--2415809 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2415771 ATGGTATAAC
2415781 AATATTCAGACAATG
1 AATATTCAGACAATG
2415796 AATATTCAGACAAT
1 AATATTCAGACAAT
2415810 ATTTAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (15 bp):
AATATTCAGACAATG
Found at i:2416046 original size:18 final size:17
Alignment explanation
Indices: 2416023--2416101 Score: 99
Period size: 18 Copynumber: 4.6 Consensus size: 17
2416013 TTCTCTTTTT
2416023 TTTTTTCATTTCTTTTCA
1 TTTTTTCATTT-TTTTCA
*
2416041 TTTTTTCACTTTTTTCA
1 TTTTTTCATTTTTTTCA
*
2416058 TTTTTTCATTTTTTTTTA
1 TTTTTTCA-TTTTTTTCA
*
2416076 TTTTTTTATTTTTTT-A
1 TTTTTTCATTTTTTTCA
2416092 TTTTTT-ATTT
1 TTTTTTCATTT
2416102 ATTATTGATA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
15 4 0.07
16 7 0.12
17 21 0.38
18 24 0.43
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTCATTTTTTTCA
Found at i:2416055 original size:9 final size:8
Alignment explanation
Indices: 2416023--2416101 Score: 79
Period size: 8 Copynumber: 9.4 Consensus size: 8
2416013 TTCTCTTTTT
2416023 TTTTTTCA
1 TTTTTTCA
2416031 TTTCTTTTCA
1 -TT-TTTTCA
2416041 TTTTTTCA
1 TTTTTTCA
2416049 CTTTTTTCA
1 -TTTTTTCA
2416058 TTTTTTCA
1 TTTTTTCA
*
2416066 TTTTTTTTTA
1 --TTTTTTCA
*
2416076 TTTTTTTA
1 TTTTTTCA
*
2416084 TTTTTTTA
1 TTTTTTCA
2416092 TTTTTT-A
1 TTTTTTCA
2416099 TTT
1 TTT
2416102 ATTATTGATA
Statistics
Matches: 65, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
7 4 0.06
8 36 0.55
9 12 0.18
10 13 0.20
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCA
Found at i:2416079 original size:7 final size:7
Alignment explanation
Indices: 2416035--2416107 Score: 53
Period size: 7 Copynumber: 10.1 Consensus size: 7
2416025 TTTTCATTTC
*
2416035 TTTTCAT
1 TTTTTAT
2416042 TTTTTCACT
1 TTTTT-A-T
2416051 TTTTTCAT
1 TTTTT-AT
2416059 TTTTTCA-
1 TTTTT-AT
2416066 TTTTT-T
1 TTTTTAT
*
2416072 TTTAT-T
1 TTTTTAT
2416078 TTTTTATT
1 TTTTTA-T
2416086 TTTTTAT
1 TTTTTAT
2416093 TTTTTAT
1 TTTTTAT
*
2416100 TTATTAT
1 TTTTTAT
2416107 T
1 T
2416108 GATATCTCCA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
6 9 0.16
7 24 0.42
8 16 0.28
9 8 0.14
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTAT
Found at i:2416102 original size:27 final size:26
Alignment explanation
Indices: 2416007--2416104 Score: 92
Period size: 26 Copynumber: 3.6 Consensus size: 26
2415997 AATTTAAGTA
*
2416007 TTCATTTTCTCTTTTTTTTTTTCATTTCTT
1 TTCATTTT-T-TTTTATTTTTTCA-TT-TT
*
2416037 TTCA--TTTTTTCACTTTTTTCATTTT
1 TTCATTTTTTTTTA-TTTTTTCATTTT
*
2416062 TTCATTTTTTTTTATTTTTTTATTTT
1 TTCATTTTTTTTTATTTTTTCATTTT
*
2416088 TTTATTTTTTATTTATT
1 TTCATTTTTT-TTTATT
2416105 ATTGATATCT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
25 6 0.10
26 25 0.42
27 22 0.37
28 2 0.03
30 4 0.07
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (26 bp):
TTCATTTTTTTTTATTTTTTCATTTT
Found at i:2420759 original size:4 final size:4
Alignment explanation
Indices: 2420728--2420781 Score: 56
Period size: 4 Copynumber: 13.2 Consensus size: 4
2420718 AAATATTTAC
* * *
2420728 AAAT AAAC AAAT ACAT AAAT -AAT CAAAT AAAT AAAAT AAAC AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT
2420777 AAAT A
1 AAAT A
2420782 GAGAATTATG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
3 3 0.07
4 31 0.76
5 7 0.17
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:2421442 original size:49 final size:48
Alignment explanation
Indices: 2421388--2421481 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 48
2421378 CTATATATAT
*
2421388 TTATATAAAAAACTGTATTTACAATCCCATA-AAAAAAGAAAAAAGATTA
1 TTATATAAAAAACTATATTTACAATCCCA-AGAAAAAA-AAAAAAGATTA
*
2421437 TTATATATAAAACTATATTTACAATCCCAAGAAAAAAAAAAAAGA
1 TTATATAAAAAACTATATTTACAATCCCAAGAAAAAAAAAAAAGA
2421482 AAAACAAGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
48 9 0.21
49 33 0.79
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.26
Consensus pattern (48 bp):
TTATATAAAAAACTATATTTACAATCCCAAGAAAAAAAAAAAAGATTA
Found at i:2421876 original size:15 final size:15
Alignment explanation
Indices: 2421856--2421885 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2421846 ATACAAAAGG
2421856 AAAATACTTCAATTC
1 AAAATACTTCAATTC
2421871 AAAATACTTCAATTC
1 AAAATACTTCAATTC
2421886 GTTTAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATACTTCAATTC
Found at i:2423784 original size:29 final size:28
Alignment explanation
Indices: 2423746--2423808 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
2423736 TAAAAAGTGC
* *
2423746 CCATGACATAATATATATCTTTAGGCATGG
1 CCAT-ACATAATAAATATCTTT-GACATGG
*
2423776 CCATACATAATAAATGTCTTTGACATGG
1 CCATACATAATAAATATCTTTGACATGG
2423804 CCATA
1 CCATA
2423809 TGTTAAGCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 11 0.37
29 15 0.50
30 4 0.13
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (28 bp):
CCATACATAATAAATATCTTTGACATGG
Found at i:2425759 original size:36 final size:36
Alignment explanation
Indices: 2425712--2425793 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 36
2425702 ATATATTTAC
* ** *
2425712 TTATGTTATGTATGGTCATGTTTAAACACATATCGA
1 TTATGTTATGTATGATCATGCCTAAACACATATAGA
**
2425748 TTATGTTATGTATGATCATGCCTAATGACATATAGA
1 TTATGTTATGTATGATCATGCCTAAACACATATAGA
2425784 TTATGTTATG
1 TTATGTTATG
2425794 GGCCATGTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (36 bp):
TTATGTTATGTATGATCATGCCTAAACACATATAGA
Found at i:2426779 original size:29 final size:30
Alignment explanation
Indices: 2426741--2426799 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
2426731 TAAGATGTTT
*
2426741 AATATTATATTTAAATT-TTAAAATTTTAA
1 AATATAATATTTAAATTATTAAAATTTTAA
*
2426770 AATATAATATTTGAATTATTAAAATTTTAA
1 AATATAATATTTAAATTATTAAAATTTTAA
2426800 TTAATATCAT
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:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (30 bp):
AATATAATATTTAAATTATTAAAATTTTAA
Found at i:2426858 original size:21 final size:22
Alignment explanation
Indices: 2426819--2426859 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2426809 TAATTTCTCT
*
2426819 TAATATAATTAATTTTAAATGA
1 TAATATAATTAATTATAAATGA
*
2426841 TAATAT-ATTACTTATAAAT
1 TAATATAATTAATTATAAAT
2426860 AATTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
TAATATAATTAATTATAAATGA
Found at i:2426899 original size:21 final size:20
Alignment explanation
Indices: 2426874--2426925 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2426864 TTTTAATATT
2426874 TATTAATTAATAAATTTATAA
1 TATTAATTAA-AAATTTATAA
*
2426895 TATTATATTAAAAATTTTTAA
1 TATTA-ATTAAAAATTTATAA
*
2426916 AATTCAATTA
1 TATT-AATTA
2426926 TTTGTAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTAATTAAAAATTTATAA
Found at i:2443763 original size:2 final size:2
Alignment explanation
Indices: 2443756--2443787 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2443746 AAGAACAAAT
2443756 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2443788 TATGTCACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2459107 original size:2 final size:2
Alignment explanation
Indices: 2459102--2459179 Score: 94
Period size: 2 Copynumber: 41.5 Consensus size: 2
2459092 TGAATTAATT
* * *
2459102 TA TA TA TA -A T- TA -A TA TA TA TA AA TA AA TA -A TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2459140 -A 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
2459180 GAATTTGATC
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
1 5 0.08
2 60 0.92
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2462486 original size:21 final size:21
Alignment explanation
Indices: 2462455--2462505 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2462445 CCTCTAATCT
2462455 TATATATAAGAACTTATATAAA
1 TATA-ATAAGAACTTATATAAA
** *
2462477 TATAATAAGAGTTTATTTAAA
1 TATAATAAGAACTTATATAAA
2462498 TATAATAA
1 TATAATAA
2462506 AAAGATAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (21 bp):
TATAATAAGAACTTATATAAA
Found at i:2471123 original size:2 final size:2
Alignment explanation
Indices: 2471116--2471141 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2471106 GAAGGAAGGC
2471116 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
2471142 GGAGTTTGTT
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):
TA
Found at i:2473326 original size:6 final size:6
Alignment explanation
Indices: 2473309--2473338 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2473299 AATAAAATAT
*
2473309 TTCGAG TCCGAG TTCGAG TTCGAG TTCGAG
1 TTCGAG TTCGAG TTCGAG TTCGAG TTCGAG
2473339 CATGAATAAT
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:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (6 bp):
TTCGAG
Found at i:2479385 original size:24 final size:23
Alignment explanation
Indices: 2479358--2479402 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2479348 GTGTCAAGTC
* *
2479358 TCTTTTTTAGAGCTTCTAGTATTA
1 TCTTATTTACAGCTT-TAGTATTA
2479382 TCTTATTTACAGCTTTAGTAT
1 TCTTATTTACAGCTTTAGTAT
2479403 GCCCATCGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (23 bp):
TCTTATTTACAGCTTTAGTATTA
Found at i:2484451 original size:39 final size:39
Alignment explanation
Indices: 2484408--2484501 Score: 152
Period size: 39 Copynumber: 2.4 Consensus size: 39
2484398 TATTGGATGG
* *
2484408 GGTGGGGAGGGATTGGGTGTGGTGGGGCGTTGGGGGGAA
1 GGTGGGGAGGGATTGGGTGTGGTGGGACGTTGGGAGGAA
*
2484447 GGTGGGGAGGGATTGGGTGTGGTGGGATGTTGGGAGGAA
1 GGTGGGGAGGGATTGGGTGTGGTGGGACGTTGGGAGGAA
*
2484486 GGTGGAGAGGGATTGG
1 GGTGGGGAGGGATTGG
2484502 ATTGGGGTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.14, C:0.01, G:0.64, T:0.21
Consensus pattern (39 bp):
GGTGGGGAGGGATTGGGTGTGGTGGGACGTTGGGAGGAA
Found at i:2487170 original size:13 final size:13
Alignment explanation
Indices: 2487130--2487171 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2487120 ATGTCATTGT
*
2487130 TTTAAAATATTAA
1 TTTAAAATATTTA
2487143 TTTAAAATATATTA
1 TTTAAAATAT-TTA
2487157 TTCTAAAA-ATTTA
1 TT-TAAAATATTTA
2487170 TT
1 TT
2487172 GATGAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 15 0.58
14 6 0.23
15 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAAATATTTA
Found at i:2488870 original size:18 final size:18
Alignment explanation
Indices: 2488847--2488971 Score: 105
Period size: 18 Copynumber: 6.9 Consensus size: 18
2488837 ATGGTTATTA
2488847 TCCACCTCAAATGTATCC
1 TCCACCTCAAATGTATCC
*
2488865 TCCACCTCCTCAAATATATCC
1 TCCA---CCTCAAATGTATCC
**
2488886 TCCACCTCAAATGTATAAG
1 TCCACCTCAAATGTAT-CC
* * *
2488905 T-TACCACAAATGTACCC
1 TCCACCTCAAATGTATCC
* *
2488922 TCCACCACAAATGTATCA
1 TCCACCTCAAATGTATCC
*
2488940 T---CCTCAAATATATCC
1 TCCACCTCAAATGTATCC
2488955 TCCACCTCAAATGTATC
1 TCCACCTCAAATGTATC
2488972 AAGAACAAAG
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
15 12 0.14
17 1 0.01
18 52 0.63
19 1 0.01
21 17 0.20
ACGTcount: A:0.33, C:0.35, G:0.05, T:0.27
Consensus pattern (18 bp):
TCCACCTCAAATGTATCC
Found at i:2488877 original size:21 final size:21
Alignment explanation
Indices: 2488851--2488893 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2488841 TTATTATCCA
*
2488851 CCTCAAATGTATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
2488872 CCTCAAATATATCCTCCACCT
1 CCTCAAATATATCCTCCACCT
2488893 C
1 C
2488894 AAATGTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.44, G:0.02, T:0.28
Consensus pattern (21 bp):
CCTCAAATATATCCTCCACCT
Found at i:2488957 original size:33 final size:34
Alignment explanation
Indices: 2488871--2488972 Score: 134
Period size: 33 Copynumber: 3.0 Consensus size: 34
2488861 ATCCTCCACC
*
2488871 TCCTCAAATATATCCTCCACCTCAAATGTATAAG
1 TCCTCAAATATATCCTCCACCTCAAATGTATCAG
* * * *
2488905 TTACCACAAATGTACCCTCCACCACAAATGTATCA-
1 -T-CCTCAAATATATCCTCCACCTCAAATGTATCAG
2488940 TCCTCAAATATATCCTCCACCTCAAATGTATCA
1 TCCTCAAATATATCCTCCACCTCAAATGTATCA
2488973 AGAACAAAGG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 28 0.49
34 1 0.02
35 1 0.02
36 27 0.47
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.27
Consensus pattern (34 bp):
TCCTCAAATATATCCTCCACCTCAAATGTATCAG
Found at i:2498281 original size:32 final size:32
Alignment explanation
Indices: 2498245--2498309 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
2498235 GGTAATTAGT
2498245 GAATATATTTACAAGTATGCAAAGGTAGCAGC
1 GAATATATTTACAAGTATGCAAAGGTAGCAGC
2498277 GAATATATTTACAAGTATGCAAAGGTAGCAGC
1 GAATATATTTACAAGTATGCAAAGGTAGCAGC
2498309 G
1 G
2498310 GAGTTAGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (32 bp):
GAATATATTTACAAGTATGCAAAGGTAGCAGC
Found at i:2501625 original size:17 final size:17
Alignment explanation
Indices: 2501599--2501632 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2501589 TTAAAGTAAT
* *
2501599 TACATGAATAATAAATA
1 TACATAAATAAAAAATA
2501616 TACATAAATAAAAAATA
1 TACATAAATAAAAAATA
2501633 AAAAAACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (17 bp):
TACATAAATAAAAAATA
Found at i:2502962 original size:22 final size:21
Alignment explanation
Indices: 2502935--2502984 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
2502925 ATAATTATTA
2502935 ATAAATTTTAAAAAAATCAAAT
1 ATAAATTTTAAAAAAA-CAAAT
**
2502957 ATAAATTTTTGTAAAAACAAAT
1 ATAAA-TTTTAAAAAAACAAAT
2502979 ATAAAT
1 ATAAAT
2502985 CTTATTCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.60
23 9 0.36
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (21 bp):
ATAAATTTTAAAAAAACAAAT
Found at i:2503348 original size:22 final size:23
Alignment explanation
Indices: 2503322--2503377 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
2503312 AAGTTTAACC
*
2503322 AACAAAAACT-TAACAAATATAT
1 AACAAAAAATATAACAAATATAT
*
2503344 AACAAAAAAATATAACAAATCTAT
1 AAC-AAAAAATATAACAAATATAT
2503368 AACAAAAAAT
1 AACAAAAAAT
2503378 TTGACAGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 3 0.10
23 13 0.43
24 14 0.47
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (23 bp):
AACAAAAAATATAACAAATATAT
Found at i:2504733 original size:64 final size:62
Alignment explanation
Indices: 2504648--2504843 Score: 175
Period size: 62 Copynumber: 3.1 Consensus size: 62
2504638 TAAAAACACC
*
2504648 TTAATAATCCAGT-CAATAAATTTTTATGA-GCGATTATTGAAGGTGGTTTTGGTCCAAAATGCC
1 TTAATAATCCA-TACAA-AAAATTTTA-GATG-GATTATTGAAGGTGGTTTTGGTCCAAAATGCC
2504711 T
62 T
* * * * * *
2504712 TTAATAATCCATACAAAAAATTTGAAATGGATTCTTGAAGG-CGTTTTTGACCTAAAATGCCT
1 TTAATAATCCATACAAAAAATTTTAGATGGATTATTGAAGGTGGTTTTGGTCC-AAAATGCCT
* * * * ** *
2504774 TTAATAATGCACACAATAAAAATTTAGATGGGATTATTGAAGGTGATTTTGGTAAAAAACGCC-
1 TTAATAATCCATACAA-AAAATTTTAGAT-GGATTATTGAAGGTGGTTTTGGTCCAAAATGCCT
2504837 TTAATAA
1 TTAATAA
2504844 CACTTTGTTA
Statistics
Matches: 106, Mismatches: 20, Indels: 13
0.76 0.14 0.09
Matches are distributed among these distances:
61 8 0.08
62 35 0.33
63 25 0.24
64 33 0.31
65 5 0.05
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (62 bp):
TTAATAATCCATACAAAAAATTTTAGATGGATTATTGAAGGTGGTTTTGGTCCAAAATGCCT
Found at i:2504741 original size:125 final size:125
Alignment explanation
Indices: 2504563--2504843 Score: 316
Period size: 126 Copynumber: 2.2 Consensus size: 125
2504553 AATTGTGGAT
* * ** *
2504563 GGTGTTTTTAGTAGAAAAACGCCCTTAATAATCCATAGGAAAAATATGGAATGGATTCTTGAAGG
1 GGTGATTTTGGTA-AAAAACG-CCTTAATAATCCATACAAAAAATATGAAATGGATTCTTGAAGG
* ** **
2504628 CATTTTTG-GCTAAAA-ACACCTTAATAATCCAGTCAATAAATTTTTATGA-GCGATTATTGAA
64 CATTTTTGACCTAAAATAC-CCTTAATAATCCACACAATAAAAATTTA-GATGCGATTATTGAA
* ** * *
2504689 GGTGGTTTTGGTCCAAAATGCCTTTAATAATCCATACAAAAAATTTGAAATGGATTCTTGAAGGC
1 GGTGATTTTGGTAAAAAACGCC-TTAATAATCCATACAAAAAATATGAAATGGATTCTTGAAGGC
* * * * *
2504754 GTTTTTGACCTAAAATGCCTTTAATAATGCACACAATAAAAATTTAGATGGGATTATTGAA
65 ATTTTTGACCTAAAATACCCTTAATAATCCACACAATAAAAATTTAGATGCGATTATTGAA
2504815 GGTGATTTTGGTAAAAAACGCCTTAATAA
1 GGTGATTTTGGTAAAAAACGCCTTAATAA
2504844 CACTTTGTTA
Statistics
Matches: 128, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
124 2 0.02
125 58 0.45
126 67 0.52
127 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (125 bp):
GGTGATTTTGGTAAAAAACGCCTTAATAATCCATACAAAAAATATGAAATGGATTCTTGAAGGCA
TTTTTGACCTAAAATACCCTTAATAATCCACACAATAAAAATTTAGATGCGATTATTGAA
Found at i:2504769 original size:62 final size:61
Alignment explanation
Indices: 2504578--2504816 Score: 164
Period size: 64 Copynumber: 3.8 Consensus size: 61
2504568 TTTTAGTAGA
* ** ** * * *
2504578 AAAACGCCCTTAATAATCCATAGGAAAAATATGGAAT-GGATTCTTGAAGGCATTTTTGGCT
1 AAAATGCCCTTAATAATCCATACAAAAAAT-TTAAATGGGATTATTGAAGGCGTTTTTGCCT
* * ** * *
2504639 AAAA-ACACCTTAATAATCCAGT-CAATAAATTTTTATGAGCGATTATTGAAGGTGGTTTTGGTC
1 AAAATGC-CCTTAATAATCCA-TACAAAAAATTTAAATG-G-GATTATTGAAGG-CGTTTTTG-C
2504702 C-
60 CT
* *
2504703 AAAATGCCTTTAATAATCCATACAAAAAATTTGAAAT-GGATTCTTGAAGGCGTTTTTGACCT
1 AAAATGCCCTTAATAATCCATACAAAAAATTT-AAATGGGATTATTGAAGGCGTTTTTG-CCT
* * * *
2504765 AAAATGCCTTTAATAATGCACACAATAAAAATTTAGATGGGATTATTGAAGG
1 AAAATGCCCTTAATAATCCATAC-A-AAAAATTTAAATGGGATTATTGAAGG
2504817 TGATTTTGGT
Statistics
Matches: 139, Mismatches: 25, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
60 4 0.03
61 30 0.22
62 34 0.24
63 17 0.12
64 50 0.36
65 4 0.03
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (61 bp):
AAAATGCCCTTAATAATCCATACAAAAAATTTAAATGGGATTATTGAAGGCGTTTTTGCCT
Done.