Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 56 of 64
Found at i:8986325 original size:16 final size:16
Alignment explanation
Indices: 8986288--8986325 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
8986278 TCTTCCTCTT
*
8986288 TAAAAAAAAACCAAAA
1 TAAAAAAAAAACAAAA
8986304 -AGAAAAAAAAACAAAA
1 TA-AAAAAAAAACAAAA
8986320 TAAAAA
1 TAAAAA
8986326 GGGTTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
15 1 0.05
16 17 0.89
17 1 0.05
ACGTcount: A:0.84, C:0.08, G:0.03, T:0.05
Consensus pattern (16 bp):
TAAAAAAAAAACAAAA
Found at i:8986378 original size:23 final size:23
Alignment explanation
Indices: 8986336--8986390 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
8986326 GGGTTAGAAT
*
8986336 AAAATAAAATAAATCCAAATCA-A
1 AAAATAAAATAAATCAAAAT-AGA
8986359 AAAATAAAATAAAAT-AAAATAGA
1 AAAATAAAAT-AAATCAAAATAGA
8986382 AAAA-AAAAT
1 AAAATAAAAT
8986391 GAGATCGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.21
23 19 0.66
24 4 0.14
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAATAAAATAAATCAAAATAGA
Found at i:8986388 original size:28 final size:28
Alignment explanation
Indices: 8986333--8986389 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
8986323 AAAGGGTTAG
* *
8986333 AATAAAATAAAATAAATCCAAATCAAAA
1 AATAAAATAAAATAAATACAAATAAAAA
*
8986361 AATAAAATAAAATAAAATAGAAA-AAAAA
1 AATAAAATAAAAT-AAATACAAATAAAAA
8986389 A
1 A
8986390 TGAGATCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (28 bp):
AATAAAATAAAATAAATACAAATAAAAA
Found at i:8987206 original size:22 final size:22
Alignment explanation
Indices: 8987164--8987206 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
8987154 AGTGAAATAA
* *
8987164 AAAAGGAAATAGGAGAAAAAAC
1 AAAAGGAAATAGAAAAAAAAAC
8987186 AAAAGGAAA-AGAAAAATAAAA
1 AAAAGGAAATAGAAAAA-AAAA
8987207 ATAAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (22 bp):
AAAAGGAAATAGAAAAAAAAAC
Found at i:8987365 original size:16 final size:17
Alignment explanation
Indices: 8987333--8987366 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
8987323 ACCTAATCAA
*
8987333 GCCTAGACTTCAAATGG
1 GCCTAGACATCAAATGG
8987350 GCCTAGACAT-AAATGG
1 GCCTAGACATCAAATGG
8987366 G
1 G
8987367 TGTCTACAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (17 bp):
GCCTAGACATCAAATGG
Found at i:8987417 original size:3 final size:3
Alignment explanation
Indices: 8987409--8987466 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
8987399 TTAGACAAAG
8987409 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8987457 ATA ATA ATA A
1 ATA ATA ATA A
8987467 GTTATCTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8987647 original size:246 final size:244
Alignment explanation
Indices: 8987200--8987649 Score: 765
Period size: 246 Copynumber: 1.8 Consensus size: 244
8987190 GGAAAAGAAA
*
8987200 AATAAAAATAAAAAATAATAAGTTATCCCTTTGGGCCCAAATGGTCCTAATTGGGCTTGAACATT
1 AATAAAAATAAAAAATAATAAGTTATCCCTTTGGGCCCAAATGGTCCTAATTGGGCCTGAACATT
8987265 GATGGGCCCAATTGGACTTGGATCTCAATAGGTCCAATCGAGCCCGAACCTAATGTGGACCTAAT
66 GATGGGCCCAATTGGACTTGGATCTCAATAGGTCCAATCGAGCCCGAACCTAATGTGGACCTAAT
* * * * *
8987330 CAAGCCTAGACTTCAAATGGGCCTAGACATAAATGGGTGTCTACAGTTGTCCCTTTTTGTATATC
131 CAAGCCTAGACTTAAAATGGGCCCAAACATAAATGGGTGTCTACAGCTGTCCCTCTTTGTATATC
8987395 TTTGTTAGACAAAGATAATAATAATAATAATAATAATAATAATAATAAT
196 TTTGTTAGACAAAGATAATAATAATAATAATAATAATAATAATAATAAT
* **
8987444 AATAATAATAATAATAATAATAAGTTATCTTTTTGGGCCCAAATGGTCCTAATTGGGCCTGAACA
1 AATAAAAATAA-AA-AATAATAAGTTATCCCTTTGGGCCCAAATGGTCCTAATTGGGCCTGAACA
*
8987509 TTGATGGGCCCAATTGGACTTGGATCTCAATGGGTCCAATCGAGCCCGAACCTAATGTGGACCTA
64 TTGATGGGCCCAATTGGACTTGGATCTCAATAGGTCCAATCGAGCCCGAACCTAATGTGGACCTA
* * *
8987574 ATCAGGCTTGGACTTAAAATGGGCCCAAACATAAATGGGTGTCTACAGCTGTCCCTCTTTGTATA
129 ATCAAGCCTAGACTTAAAATGGGCCCAAACATAAATGGGTGTCTACAGCTGTCCCTCTTTGTATA
8987639 TCTTTGTTAGA
194 TCTTTGTTAGA
8987650 TAAATATGAT
Statistics
Matches: 191, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
244 10 0.05
245 2 0.01
246 179 0.94
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (244 bp):
AATAAAAATAAAAAATAATAAGTTATCCCTTTGGGCCCAAATGGTCCTAATTGGGCCTGAACATT
GATGGGCCCAATTGGACTTGGATCTCAATAGGTCCAATCGAGCCCGAACCTAATGTGGACCTAAT
CAAGCCTAGACTTAAAATGGGCCCAAACATAAATGGGTGTCTACAGCTGTCCCTCTTTGTATATC
TTTGTTAGACAAAGATAATAATAATAATAATAATAATAATAATAATAAT
Found at i:8988119 original size:117 final size:117
Alignment explanation
Indices: 8987959--8988444 Score: 686
Period size: 117 Copynumber: 4.2 Consensus size: 117
8987949 CCGCAAGTAA
* * * *
8987959 AAAATGAAACGACCAGGATCGAGTCGAGGTTGAAAATAAATGATCGGACTAGTGTTATGAGTCTA
1 AAAATGAAATGACCAAGATCGAGTCGAGGTTGAAGATAAATGATCGGACTAGTGTCATGAGTCTA
**
8988024 AATATGATCTGACATGAGTTAAGATCGGGTGATTGGGATAATGTCATAAGTC
66 AATATGATCTGACATGAGTCGAGATCGGGTGATTGGGATAATGTCATAAGTC
8988076 AAAATGAAATGACCAAGATCGAGTCGAGGTTGAAGATAAATGATCGGACTAGTGTCATGAGTCTA
1 AAAATGAAATGACCAAGATCGAGTCGAGGTTGAAGATAAATGATCGGACTAGTGTCATGAGTCTA
* * * *
8988141 AATATGATCTGACATGAGTTGAGATCAGGTGATTGAGATAATGTCACAAGTC
66 AATATGATCTGACATGAGTCGAGATCGGGTGATTGGGATAATGTCATAAGTC
* *
8988193 AAAATAAAATGACCAAGATCGAGTCAAGGTTGAAGATAAATGATCGGACTAGTGTCATGAGTCTA
1 AAAATGAAATGACCAAGATCGAGTCGAGGTTGAAGATAAATGATCGGACTAGTGTCATGAGTCTA
* * * *
8988258 AATATAATCTGACATGAGTCGAGATTGGGTGACTGGGATAATGTCGTAAGTC
66 AATATGATCTGACATGAGTCGAGATCGGGTGATTGGGATAATGTCATAAGTC
* * * * * * * *
8988310 AAAATGAAATGATCAAAATCGAGTCGAGGTCGAAGATAAATGATC-AAATTGATGTCACGTGTCT
1 AAAATGAAATGACCAAGATCGAGTCGAGGTTGAAGATAAATGATCGGACTAG-TGTCATGAGTCT
* ** *
8988374 AAATATGATCTGACCTGAGTCGAGATCGAATGATTGGGATAATGTCGTAAGTC
65 AAATATGATCTGACATGAGTCGAGATCGGGTGATTGGGATAATGTCATAAGTC
* *
8988427 AAAATAAAATGACTAAGA
1 AAAATGAAATGACCAAGA
8988445 CTGAATTGAA
Statistics
Matches: 330, Mismatches: 38, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
116 3 0.01
117 327 0.99
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.26
Consensus pattern (117 bp):
AAAATGAAATGACCAAGATCGAGTCGAGGTTGAAGATAAATGATCGGACTAGTGTCATGAGTCTA
AATATGATCTGACATGAGTCGAGATCGGGTGATTGGGATAATGTCATAAGTC
Found at i:8988273 original size:234 final size:231
Alignment explanation
Indices: 8987857--8988444 Score: 741
Period size: 234 Copynumber: 2.5 Consensus size: 231
8987847 AAGTAACTTG
* * * *
8987857 GATCGGGTCGAGGTCGAAAATAAATGATCAGACTGATGTC-GCAGGTCTAAAGATGATCTGATAT
1 GATCGAGTCGAGGTCGAAGATAAATGATC-GACTGATGTCAG-A-GTCTAAATATGATCTGACAT
* ** * * * * * *
8987921 GAGTCGAGATCAAATGACTTGGACGATGCCGCAAGTAAAAAATGAAACGACCAGGATCGAGTCGA
63 GAGTCGAGATCAGATGA-TTGGATAATGTCGCAAGT-CAAAATAAAATGACCAAGATCGAGTCAA
* * *
8987986 GGTTGAAAATAAATGATCGGACTAGTGTTATGAGTCTAAATATGATCTGACATGAGTTAAGATCG
126 GGTTGAAAATAAATGATCGGACTAGTGTCATGAGTCTAAATATAATCTGACATGAGTCAAGATCG
*
8988051 GGTGATTGGGATAATGTCATAAGTCAAAATGAAATGACCAA
191 GGTGACTGGGATAATGTCATAAGTCAAAATGAAATGACCAA
*
8988092 GATCGAGTCGAGGTTGAAGATAAATGATCGGACT-AGTGTCATGAGTCTAAATATGATCTGACAT
1 GATCGAGTCGAGGTCGAAGATAAATGATC-GACTGA-TGTCA-GAGTCTAAATATGATCTGACAT
* * *
8988156 GAGTTGAGATCAGGTGATTGAGATAATGTCACAAGTCAAAATAAAATGACCAAGATCGAGTCAAG
63 GAGTCGAGATCAGATGATTG-GATAATGTCGCAAGTCAAAATAAAATGACCAAGATCGAGTCAAG
* * *
8988221 GTTGAAGATAAATGATCGGACTAGTGTCATGAGTCTAAATATAATCTGACATGAGTCGAGATTGG
127 GTTGAAAATAAATGATCGGACTAGTGTCATGAGTCTAAATATAATCTGACATGAGTCAAGATCGG
* *
8988286 GTGACTGGGATAATGTCGTAAGTCAAAATGAAATGATCAA
192 GTGACTGGGATAATGTCATAAGTCAAAATGAAATGACCAA
* * * * *
8988326 AATCGAGTCGAGGTCGAAGATAAATGATCAAATTGATGTCACGTGTCTAAATATGATCTGACCTG
1 GATCGAGTCGAGGTCGAAGATAAATGATC-GACTGATGTCA-GAGTCTAAATATGATCTGACATG
* *
8988391 AGTCGAGATC-GAATGATTGGGATAATGTCGTAAGTCAAAATAAAATGACTAAGA
64 AGTCGAGATCAG-ATGATT-GGATAATGTCGCAAGTCAAAATAAAATGACCAAGA
8988445 CTGAATTGAA
Statistics
Matches: 306, Mismatches: 40, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
233 1 0.00
234 224 0.73
235 79 0.26
236 1 0.00
237 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (231 bp):
GATCGAGTCGAGGTCGAAGATAAATGATCGACTGATGTCAGAGTCTAAATATGATCTGACATGAG
TCGAGATCAGATGATTGGATAATGTCGCAAGTCAAAATAAAATGACCAAGATCGAGTCAAGGTTG
AAAATAAATGATCGGACTAGTGTCATGAGTCTAAATATAATCTGACATGAGTCAAGATCGGGTGA
CTGGGATAATGTCATAAGTCAAAATGAAATGACCAA
Found at i:8988463 original size:117 final size:117
Alignment explanation
Indices: 8987864--8988475 Score: 572
Period size: 117 Copynumber: 5.2 Consensus size: 117
8987854 TTGGATCGGG
* * * * *
8987864 TCGAGGTCGAAAATAAATGATCAGACT-GATGTCGC-AGGTCTAAAGATGATCTGATATGAGTCG
1 TCGAAGTCGAAGATAAATGATCAGACTAG-TGTCACGA-GTCTAAATATGATCTGACATGAGTCG
* * ** * ** * * * * *
8987927 AGATCAAATGACTT-GGACGATGCCGCAAGTAAAAAATGAAACGACCAGGATCGAG
64 AGATCGAGTGA-TTGGGATAATGTCATAAGT-CAAAATAAAATGACCAAGATCGAA
* * * * * * **
8987982 TCGAGGTTGAAAATAAATGATCGGACTAGTGTTATGAGTCTAAATATGATCTGACATGAGTTAAG
1 TCGAAGTCGAAGATAAATGATCAGACTAGTGTCACGAGTCTAAATATGATCTGACATGAGTCGAG
* * *
8988047 ATCGGGTGATTGGGATAATGTCATAAGTCAAAATGAAATGACCAAGATCGAG
66 ATCGAGTGATTGGGATAATGTCATAAGTCAAAATAAAATGACCAAGATCGAA
* * * * *
8988099 TCGAGGTTGAAGATAAATGATCGGACTAGTGTCATGAGTCTAAATATGATCTGACATGAGTTGAG
1 TCGAAGTCGAAGATAAATGATCAGACTAGTGTCACGAGTCTAAATATGATCTGACATGAGTCGAG
* * *
8988164 ATC-AGGTGATTGAGATAATGTCACAAGTCAAAATAAAATGACCAAGATCGAG
66 ATCGA-GTGATTGGGATAATGTCATAAGTCAAAATAAAATGACCAAGATCGAA
* * * *
8988216 TC-AAGGTTGAAGATAAATGATCGGACTAGTGTCATGAGTCTAAATATAATCTGACATGAGTCGA
1 TCGAA-GTCGAAGATAAATGATCAGACTAGTGTCACGAGTCTAAATATGATCTGACATGAGTCGA
* * * * * * * *
8988280 GATTGGGTGACTGGGATAATGTCGTAAGTCAAAATGAAATGATCAAAATCGAG
65 GATCGAGTGATTGGGATAATGTCATAAGTCAAAATAAAATGACCAAGATCGAA
* * * * *
8988333 TCGAGGTCGAAGATAAATGATCA-AATTGATGTCACGTGTCTAAATATGATCTGACCTGAGTCGA
1 TCGAAGTCGAAGATAAATGATCAGACTAG-TGTCACGAGTCTAAATATGATCTGACATGAGTCGA
* * *
8988397 GATCGAATGATTGGGATAATGTCGTAAGTCAAAATAAAATGACTAAGA-CTGAA
65 GATCGAGTGATTGGGATAATGTCATAAGTCAAAATAAAATGACCAAGATC-GAA
* * *
8988450 TTGAAGCCAAAGATAAATGATCAGAC
1 TCGAAGTCGAAGATAAATGATCAGAC
8988476 CGACATTACG
Statistics
Matches: 422, Mismatches: 62, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
116 5 0.01
117 344 0.82
118 71 0.17
119 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (117 bp):
TCGAAGTCGAAGATAAATGATCAGACTAGTGTCACGAGTCTAAATATGATCTGACATGAGTCGAG
ATCGAGTGATTGGGATAATGTCATAAGTCAAAATAAAATGACCAAGATCGAA
Found at i:8988493 original size:234 final size:234
Alignment explanation
Indices: 8987858--8988517 Score: 647
Period size: 234 Copynumber: 2.8 Consensus size: 234
8987848 AGTAACTTGG
* * * * * *
8987858 ATCGGGTCGAGGTCGAAAATAAATGATCAGACT-GATGTCGC-AGGTCTAAAGATGATCTGATAT
1 ATCGAGTCGAGGTCGAAGATAAATGATCAAACTAG-TGTCACGA-GTCTAAATATGATCTGACAT
* ** * * * * * * *
8987921 GAGTCGAGATCAAATGACTTG-GACGATGCCGCAAGTAAAAAATGAAACGACCAGGATCGAGTCG
64 GAGTCGAGATCAGATGA-TTGAGATAATGTCACAAGT-CAAAATAAAATGACCAAGATCGAGTCA
** * * * * * * *
8987985 AGGTTGAAA-ATAAATGATCGGACTAGTGTTATGAGTCTAAATATGATCTGACATGAGTTAAGAT
127 AGG-CCAAAGATAAATGATCAGACGAATGTCACGAGTCTAAATATAATCTGACATGAGTCAAGAT
* *
8988049 CGGGTGATTGGGATAATGTCATAAGTCAAAATGAAATGACCAAG
191 CGGGTGACTGGGATAATGTCATAAGTCAAAATGAAATGACCAAA
* ** *
8988093 ATCGAGTCGAGGTTGAAGATAAATGATCGGACTAGTGTCATGAGTCTAAATATGATCTGACATGA
1 ATCGAGTCGAGGTCGAAGATAAATGATCAAACTAGTGTCACGAGTCTAAATATGATCTGACATGA
* * *
8988158 GTTGAGATCAGGTGATTGAGATAATGTCACAAGTCAAAATAAAATGACCAAGATCGAGTCAAGGT
66 GTCGAGATCAGATGATTGAGATAATGTCACAAGTCAAAATAAAATGACCAAGATCGAGTCAAGGC
** * * * * * *
8988223 TGAAGATAAATGATCGGACTAGTGTCATGAGTCTAAATATAATCTGACATGAGTCGAGATTGGGT
131 CAAAGATAAATGATCAGACGAATGTCACGAGTCTAAATATAATCTGACATGAGTCAAGATCGGGT
* *
8988288 GACTGGGATAATGTCGTAAGTCAAAATGAAATGATCAAA
196 GACTGGGATAATGTCATAAGTCAAAATGAAATGACCAAA
* * *
8988327 ATCGAGTCGAGGTCGAAGATAAATGATCAAA-TTGATGTCACGTGTCTAAATATGATCTGACCTG
1 ATCGAGTCGAGGTCGAAGATAAATGATCAAACTAG-TGTCACGAGTCTAAATATGATCTGACATG
* ** * * *
8988391 AGTCGAGATC-GAATGATTGGGATAATGTCGTAAGTCAAAATAAAATGACTAAGA-CTGAATTGA
65 AGTCGAGATCAG-ATGATTGAGATAATGTCACAAGTCAAAATAAAATGACCAAGATC-G-AGTCA
* * *
8988454 A-GCCAAAGATAAATGATCAGACCGACAT-T-ACGGGTCTAAATATAATCTGACCTGAGTTAAGA
127 AGGCCAAAGATAAATGATCAGA-CGA-ATGTCACGAGTCTAAATATAATCTGACATGAGTCAAGA
8988516 TC
190 TC
8988518 AAATAAGTGG
Statistics
Matches: 357, Mismatches: 58, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
233 7 0.02
234 264 0.74
235 83 0.23
236 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (234 bp):
ATCGAGTCGAGGTCGAAGATAAATGATCAAACTAGTGTCACGAGTCTAAATATGATCTGACATGA
GTCGAGATCAGATGATTGAGATAATGTCACAAGTCAAAATAAAATGACCAAGATCGAGTCAAGGC
CAAAGATAAATGATCAGACGAATGTCACGAGTCTAAATATAATCTGACATGAGTCAAGATCGGGT
GACTGGGATAATGTCATAAGTCAAAATGAAATGACCAAA
Found at i:8999439 original size:5 final size:5
Alignment explanation
Indices: 8999429--8999473 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
8999419 AAATAAAGGT
*
8999429 TAAAA TAAAA TAAAA T-AAA TCAAAA T-CAA -AAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TA
8999474 GAAAAAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
4 8 0.24
5 22 0.65
6 4 0.12
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:8999478 original size:18 final size:17
Alignment explanation
Indices: 8999387--8999488 Score: 58
Period size: 18 Copynumber: 6.2 Consensus size: 17
8999377 CATCTTTTTA
8999387 AAAATAAAAAATAAAACT
1 AAAATAAAAAATAAAA-T
* *
8999405 -AGA-AAGAAA-AAAAT
1 AAAATAAAAAATAAAAT
***
8999419 -AAATAAAGGTTAAAAT
1 AAAATAAAAAATAAAAT
8999435 AAAAT--AAAAT-AAAT
1 AAAATAAAAAATAAAAT
8999449 CAAAATCAAAAAATAAAAT
1 -AAAAT-AAAAAATAAAAT
*
8999468 AAAATAGAAAAAGAAAA-
1 AAAATA-AAAAATAAAAT
8999485 AAAA
1 AAAA
8999489 AAAGAAAAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
14 7 0.11
15 13 0.20
16 10 0.16
17 11 0.17
18 19 0.30
19 4 0.06
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAATAAAAAATAAAAT
Found at i:8999487 original size:28 final size:27
Alignment explanation
Indices: 8999430--8999490 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 27
8999420 AATAAAGGTT
**
8999430 AAAATAAAATAAAATAAATCAAAATCAA
1 AAAATAAAATAAAATAAA-CAAAAAAAA
*
8999458 AAAATAAAATAAAATAGAAAAAGAAAAAA
1 AAAATAAAATAAAATA-AACAA-AAAAAA
8999487 AAAA
1 AAAA
8999491 AGAAAAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.13
Consensus pattern (27 bp):
AAAATAAAATAAAATAAACAAAAAAAA
Found at i:8999489 original size:18 final size:18
Alignment explanation
Indices: 8999457--8999497 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
8999447 ATCAAAATCA
* * *
8999457 AAAAATAAAATAAAATAG
1 AAAAAGAAAAAAAAAAAG
8999475 AAAAAGAAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAAG
8999493 AAAAA
1 AAAAA
8999498 CTTGTGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAAG
Found at i:8999874 original size:11 final size:11
Alignment explanation
Indices: 8999858--8999889 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
8999848 CATAAAACCC
8999858 AAAAAAATTCA
1 AAAAAAATTCA
*
8999869 AAAAAAATCCA
1 AAAAAAATTCA
8999880 AAAAAAATTC
1 AAAAAAATTC
8999890 CTAGATTATC
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:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:9002268 original size:13 final size:12
Alignment explanation
Indices: 9002250--9002295 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
9002240 TTTAATAAAA
9002250 TATATTTAATTGT
1 TATATTTAATT-T
9002263 TATATTTAATTT
1 TATATTTAATTT
* *
9002275 TAAATTTAATTA
1 TATATTTAATTT
*
9002287 TATGTTTAA
1 TATATTTAA
9002296 ACTCAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (12 bp):
TATATTTAATTT
Found at i:9002464 original size:32 final size:30
Alignment explanation
Indices: 9002421--9002491 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 30
9002411 TTAATTAAAT
* **
9002421 ATTAAAATATTTAAAATTAATTCTTTCAATAA
1 ATTAAATTATTTAAAATTAATTCAAT-AAT-A
*
9002453 ATTAAATTATTTAAATTTAATTCAATAATA
1 ATTAAATTATTTAAAATTAATTCAATAATA
9002483 ATTAAATTA
1 ATTAAATTA
9002492 AATTCGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 10 0.29
31 3 0.09
32 22 0.63
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (30 bp):
ATTAAATTATTTAAAATTAATTCAATAATA
Found at i:9004205 original size:13 final size:15
Alignment explanation
Indices: 9004177--9004239 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
9004167 AAAATTTGAT
9004177 ATATTTATTAAATAA
1 ATATTTATTAAATAA
*
9004192 ATATTT-TTAATAAAA
1 ATATTTATTAA-ATAA
* **
9004207 ATATTGA-TAAATTT
1 ATATTTATTAAATAA
*
9004221 TTA-TTATTAAATAA
1 ATATTTATTAAATAA
9004235 ATATT
1 ATATT
9004240 GATCAATTTA
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
13 2 0.06
14 14 0.41
15 18 0.53
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATATTTATTAAATAA
Found at i:9004225 original size:29 final size:28
Alignment explanation
Indices: 9004193--9004248 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
9004183 ATTAAATAAA
*
9004193 TATTTTTAATAAAAATATTGATAAATTTT
1 TATTATTAA-AAAAATATTGATAAATTTT
* *
9004222 TATTATTAAATAAATATTGATCAATTT
1 TATTATTAAAAAAATATTGATAAATTT
9004249 AAAATATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (28 bp):
TATTATTAAAAAAATATTGATAAATTTT
Found at i:9004425 original size:24 final size:24
Alignment explanation
Indices: 9004393--9004444 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
9004383 CAGTTTAAAA
* *
9004393 TTTTTTAATAACAACTATATTAAT
1 TTTTTTAATAACAACTACAATAAT
* *
9004417 TTTTTTAATTACAATTACAATAAT
1 TTTTTTAATAACAACTACAATAAT
9004441 TTTT
1 TTTT
9004445 ATTATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTTTAATAACAACTACAATAAT
Found at i:9011387 original size:29 final size:29
Alignment explanation
Indices: 9011322--9011400 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
9011312 AATTTTGTTC
* * * *
9011322 AATTAAAAGTTTAATTAAATCGAAATAAAA
1 AATTAAAAATTTAAAT-AATTGCAATAAAA
*
9011352 AATTAAAAATTTAAGTAATTGCAATAAAA
1 AATTAAAAATTTAAATAATTGCAATAAAA
* *
9011381 TATTAAATATTTAAATAATT
1 AATTAAAAATTTAAATAATT
9011401 ATTAAATTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 28 0.67
30 14 0.33
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (29 bp):
AATTAAAAATTTAAATAATTGCAATAAAA
Found at i:9012512 original size:2 final size:2
Alignment explanation
Indices: 9012507--9012539 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9012497 CAGGCGCGCT
9012507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9012540 TAAGGATATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9013002 original size:17 final size:18
Alignment explanation
Indices: 9012972--9013008 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
9012962 AAAATATCCG
*
9012972 ATAAATATAGATATAAAA
1 ATAAAAATAGATATAAAA
9012990 ATAAAAATA-ATATAAAA
1 ATAAAAATAGATATAAAA
9013007 AT
1 AT
9013009 TTAAAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (18 bp):
ATAAAAATAGATATAAAA
Found at i:9023329 original size:2 final size:2
Alignment explanation
Indices: 9023311--9023345 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
9023301 ATGATGAGTT
* *
9023311 TA TA TA AA TA TA AA 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 T
9023346 CATTGCTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9038370 original size:14 final size:13
Alignment explanation
Indices: 9038350--9038398 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
9038340 TAAATATTAA
9038350 TTTTAATAAAATT
1 TTTTAATAAAATT
9038363 TATTTAATATAAAATT
1 T-TTT-A-ATAAAATT
9038379 TTTT-ATGAAAATT
1 TTTTAAT-AAAATT
9038392 TTTTAAT
1 TTTTAAT
9038399 CATAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 11 0.35
14 5 0.16
15 4 0.13
16 9 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
TTTTAATAAAATT
Found at i:9039957 original size:54 final size:54
Alignment explanation
Indices: 9039875--9039981 Score: 178
Period size: 54 Copynumber: 2.0 Consensus size: 54
9039865 TTGAGAAAAC
* * *
9039875 AAGCACATGAATTATCGAGATTAATGTTTGCTCATAGTCAAAGTGAAGTTTGCA
1 AAGCACATGAATTAACAAGATTAATGTTTGCCCATAGTCAAAGTGAAGTTTGCA
*
9039929 AAGCACATGAATTAACAAGATTAATGTTTGCCCATGGTCAAAGTGAAGTTTGC
1 AAGCACATGAATTAACAAGATTAATGTTTGCCCATAGTCAAAGTGAAGTTTGC
9039982 TTTTCACTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (54 bp):
AAGCACATGAATTAACAAGATTAATGTTTGCCCATAGTCAAAGTGAAGTTTGCA
Found at i:9040383 original size:18 final size:18
Alignment explanation
Indices: 9040357--9040411 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
9040347 TTAAAAATCA
9040357 TTAAATTTTAATATAAAT
1 TTAAATTTTAATATAAAT
* *
9040375 TTTAATTTT-ATAAAAAAT
1 TTAAATTTTAAT-ATAAAT
*
9040393 TTAAAATTTAATATTAAAT
1 TTAAATTTTAATA-TAAAT
9040412 ACATTACAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 2 0.07
18 21 0.72
19 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAATTTTAATATAAAT
Found at i:9041060 original size:8 final size:8
Alignment explanation
Indices: 9041047--9041077 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
9041037 CAAGAAGGTT
9041047 GACATGTA
1 GACATGTA
9041055 GACATGTA
1 GACATGTA
9041063 GACATGTA
1 GACATGTA
9041071 GACATGT
1 GACATGT
9041078 TTTATAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (8 bp):
GACATGTA
Found at i:9041341 original size:25 final size:25
Alignment explanation
Indices: 9041301--9041354 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
9041291 TTTATGAATT
9041301 TTTTTTTCAATCGTAGTTACAATATA
1 TTTTTTTCAATCGTAGTTACAATA-A
* *
9041327 TTTTTTT-AATTGTAGTTATAATAA
1 TTTTTTTCAATCGTAGTTACAATAA
9041351 TTTT
1 TTTT
9041355 AATTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 5 0.19
25 14 0.54
26 7 0.27
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.57
Consensus pattern (25 bp):
TTTTTTTCAATCGTAGTTACAATAA
Found at i:9045217 original size:2 final size:2
Alignment explanation
Indices: 9045210--9045241 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9045200 TATCTTGTAA
9045210 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
9045242 CAGCAGCCAA
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):
AT
Found at i:9045727 original size:20 final size:19
Alignment explanation
Indices: 9045702--9045766 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
9045692 TATATATAAA
9045702 TAATTTTTTAATAATTTATT
1 TAATTTTTTAAT-ATTTATT
*
9045722 TAATTTTATAAT-TATT-TT
1 TAATTTTTTAATAT-TTATT
*
9045740 TATATATTTTT-ATATATATT
1 TA-AT-TTTTTAATATTTATT
9045760 TAATTTT
1 TAATTTT
9045767 ATATTTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
18 8 0.22
19 9 0.24
20 20 0.54
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATTTTTTAATATTTATT
Found at i:9045769 original size:12 final size:12
Alignment explanation
Indices: 9045718--9045773 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
9045708 TTTAATAATT
9045718 TATTTAATTTTA
1 TATTTAATTTTA
* *
9045730 TAATTATTTTTA
1 TATTTAATTTTA
*
9045742 TATATT-TTTATATA
1 TAT-TTAATT-T-TA
9045756 TATTTAATTTTA
1 TATTTAATTTTA
9045768 TATTTA
1 TATTTA
9045774 TATTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 23 0.64
13 6 0.17
14 7 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTTAATTTTA
Found at i:9057840 original size:22 final size:21
Alignment explanation
Indices: 9057803--9057849 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
9057793 GTTTTTACTT
* *
9057803 TTTTTTAAATTATTTTCTGTTA
1 TTTTTTAAATGATTTTATG-TA
*
9057825 TTTTTTAAATGCTTTTATGTA
1 TTTTTTAAATGATTTTATGTA
9057846 TTTT
1 TTTT
9057850 ATTGATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.68
Consensus pattern (21 bp):
TTTTTTAAATGATTTTATGTA
Found at i:9062131 original size:3 final size:3
Alignment explanation
Indices: 9062117--9062154 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
9062107 AGTCCTGATT
*
9062117 CAG CAT CAG CAG CAG CAG CAG CAG CAG -AGG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CA-G CAG CAG CA
9062155 TATAAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 29 0.94
4 1 0.03
ACGTcount: A:0.34, C:0.32, G:0.32, T:0.03
Consensus pattern (3 bp):
CAG
Found at i:9066131 original size:28 final size:27
Alignment explanation
Indices: 9066100--9066164 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
9066090 ATTTTATTAT
* *
9066100 ATTATTAAAAATTATAATAGTAATTTAA
1 ATTATTAAAAATTA-AAAAATAATTTAA
* *
9066128 ATTATATAAAATTTAAAAAATAATTTTA
1 ATTAT-TAAAAATTAAAAAATAATTTAA
*
9066156 ATTAATAAA
1 ATTATTAAA
9066165 TAAAATTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 4 0.13
28 19 0.61
29 8 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
ATTATTAAAAATTAAAAAATAATTTAA
Found at i:9067023 original size:30 final size:30
Alignment explanation
Indices: 9066989--9067046 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
9066979 TCTATGAAAG
* *
9066989 TAAAAATAAATATTTAAAAGTTTAATTAGA
1 TAAAAATAAATATTTAAAAATTCAATTAGA
9067019 TAAAAATAAATATTTAAAAATTCAATTA
1 TAAAAATAAATATTTAAAAATTCAATTA
9067047 ATCTGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (30 bp):
TAAAAATAAATATTTAAAAATTCAATTAGA
Found at i:9075934 original size:2 final size:2
Alignment explanation
Indices: 9075929--9075967 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
9075919 ATATATATAT
* *
9075929 AG AG AG AG AG AG AG AG AG AG AG AG A- AG GG GG 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
9075968 GAGGGATCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9080978 original size:14 final size:14
Alignment explanation
Indices: 9080954--9080992 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
9080944 CAAATTTAAA
9080954 TTATAAATATTTTTT
1 TTAT-AATATTTTTT
9080969 TTATAATATTTTTT
1 TTATAATATTTTTT
* *
9080983 ATATATTATT
1 TTATAATATT
9080993 AATTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATAATATTTTTT
Found at i:9084666 original size:20 final size:21
Alignment explanation
Indices: 9084641--9084679 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9084631 TTCAATAAAT
9084641 ATTT-AAAAAATAAAAAATTA
1 ATTTAAAAAAATAAAAAATTA
9084661 ATTTAAAAAAATAAAAAAT
1 ATTTAAAAAAATAAAAAAT
9084680 GTGTGTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTTAAAAAAATAAAAAATTA
Found at i:9098123 original size:27 final size:27
Alignment explanation
Indices: 9098093--9098146 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9098083 TTAGTTTTTA
9098093 TTGGTTGGAGAAAGTAGAAAGAAAGGG
1 TTGGTTGGAGAAAGTAGAAAGAAAGGG
9098120 TTGGTTGGAGAAAGTAGAAAGAAAGGG
1 TTGGTTGGAGAAAGTAGAAAGAAAGGG
9098147 ATTAAGGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (27 bp):
TTGGTTGGAGAAAGTAGAAAGAAAGGG
Found at i:9104324 original size:31 final size:30
Alignment explanation
Indices: 9104267--9104332 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
9104257 TTTAAATTGC
* *
9104267 ATTAATAATAAAGTATTATGTCATTAAATA
1 ATTAATAATAAAGTATAATGTAATTAAATA
* *
9104297 ATTAATTAATAAATTATAATTTAATTAAATA
1 ATTAA-TAATAAAGTATAATGTAATTAAATA
9104328 ATTAA
1 ATTAA
9104333 ACCCACACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (30 bp):
ATTAATAATAAAGTATAATGTAATTAAATA
Found at i:9112979 original size:28 final size:28
Alignment explanation
Indices: 9112924--9112998 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
9112914 AAAAAATTCA
*
9112924 ATAATCATTTAAATATTTAATATTTTATT
1 ATAATCAATTAAAT-TTTAATATTTTATT
9112953 ATAATCAATTAAATTTTAA-ATATTTATT
1 ATAATCAATTAAATTTTAATAT-TTTATT
* *
9112981 TTTATCAATTAAAATTTT
1 ATAATCAATT-AAATTTT
9112999 TTTATATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (28 bp):
ATAATCAATTAAATTTTAATATTTTATT
Found at i:9119121 original size:13 final size:13
Alignment explanation
Indices: 9119103--9119146 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
9119093 TATGTTAATG
9119103 GAGAAACCAAATT
1 GAGAAACCAAATT
** *
9119116 GAGAAA-TTAATA
1 GAGAAACCAAATT
9119128 GAGAAACCAAATT
1 GAGAAACCAAATT
9119141 GAGAAA
1 GAGAAA
9119147 TGAGAATCAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.57, C:0.09, G:0.18, T:0.16
Consensus pattern (13 bp):
GAGAAACCAAATT
Found at i:9119131 original size:25 final size:25
Alignment explanation
Indices: 9119097--9119147 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
9119087 TGGTATTATG
*
9119097 TTAATGGAGAAACCAAATTGAGAAA
1 TTAATAGAGAAACCAAATTGAGAAA
9119122 TTAATAGAGAAACCAAATTGAGAAA
1 TTAATAGAGAAACCAAATTGAGAAA
9119147 T
1 T
9119148 GAGAATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.22
Consensus pattern (25 bp):
TTAATAGAGAAACCAAATTGAGAAA
Found at i:9120471 original size:19 final size:17
Alignment explanation
Indices: 9120436--9120475 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 17
9120426 TTTCACTAAT
9120436 TAAACAATAAAAATAAA
1 TAAACAATAAAAATAAA
9120453 TAAACAAATAAATAATAAA
1 TAAAC-AATAAA-AATAAA
9120472 TAAA
1 TAAA
9120476 ATACTTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 10 0.48
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (17 bp):
TAAACAATAAAAATAAA
Found at i:9123063 original size:2 final size:2
Alignment explanation
Indices: 9123056--9123086 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
9123046 CGCCATGATG
9123056 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9123087 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9123354 original size:22 final size:22
Alignment explanation
Indices: 9123301--9123350 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
9123291 CATTTTCCTA
* *
9123301 TCATATTCATAATTTTGTTCTAT
1 TCATAATC-TAATCTTGTTCTAT
*
9123324 TCGTAATCTAATCTTGTTCTA-
1 TCATAATCTAATCTTGTTCTAT
9123345 TCATAA
1 TCATAA
9123351 ATCTTATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 12 0.52
23 6 0.26
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (22 bp):
TCATAATCTAATCTTGTTCTAT
Found at i:9126179 original size:2 final size:2
Alignment explanation
Indices: 9126174--9126207 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
9126164 TTTTTATGAA
* *
9126174 AT AT AT AT AT AT AT AT TT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9126208 GACTGATGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9126589 original size:22 final size:22
Alignment explanation
Indices: 9126576--9126620 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
9126566 ATCATATTCA
9126576 TAATTTTGTTCTATCTATAATC
1 TAATTTTGTTCTATCTATAATC
*
9126598 TAATTTTGTTCTATCCATAATC
1 TAATTTTGTTCTATCTATAATC
9126620 T
1 T
9126621 TATAATATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.53
Consensus pattern (22 bp):
TAATTTTGTTCTATCTATAATC
Found at i:9127200 original size:2 final size:2
Alignment explanation
Indices: 9127193--9127218 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9127183 CATCAAAAGA
9127193 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
9127219 GTTAGACACC
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:9128751 original size:13 final size:13
Alignment explanation
Indices: 9128709--9128751 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
9128699 TCAATTGTAA
*
9128709 ATTTTTTTTTCAT
1 ATTTTTATTTCAT
* * *
9128722 TTTTTTATTTTAG
1 ATTTTTATTTCAT
9128735 ATTTTTATTTCAT
1 ATTTTTATTTCAT
9128748 ATTT
1 ATTT
9128752 ATCATTTTTT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (13 bp):
ATTTTTATTTCAT
Found at i:9131399 original size:15 final size:15
Alignment explanation
Indices: 9131365--9131407 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
9131355 ATATCAATTT
*
9131365 TTTTTAAAAATAAGTA
1 TTTTTAAAAA-AAATA
9131381 -TTTTAAAAAAAATA
1 TTTTTAAAAAAAATA
9131395 TTTTTAAAGAAAA
1 TTTTTAAA-AAAA
9131408 GTTGAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
TTTTTAAAAAAAATA
Found at i:9131466 original size:27 final size:27
Alignment explanation
Indices: 9131436--9131527 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 27
9131426 CTTCGAAATT
9131436 AAAGTTTTCAAAAAATATTTTTGAGGA
1 AAAGTTTTCAAAAAATATTTTTGAGGA
*** *
9131463 AAAGTTGAAAATATCAAAT-TTTCTTCGA-AA
1 AAAGTTTTCAA-A--AAATATTT-TT-GAGGA
9131493 TTAAAGTTTTCAAAAAATATTTTTGAGGA
1 --AAAGTTTTCAAAAAATATTTTTGAGGA
9131522 AAAGTT
1 AAAGTT
9131528 GAAAATATCA
Statistics
Matches: 48, Mismatches: 8, Indels: 18
0.65 0.11 0.24
Matches are distributed among these distances:
27 14 0.29
28 3 0.06
29 10 0.21
30 10 0.21
31 3 0.06
32 8 0.17
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (27 bp):
AAAGTTTTCAAAAAATATTTTTGAGGA
Found at i:9131467 original size:58 final size:58
Alignment explanation
Indices: 9131333--9131599 Score: 342
Period size: 59 Copynumber: 4.6 Consensus size: 58
9131323 GCTGAGGTCC
* * * * ** *
9131333 TATTTTTGAGAAAAAATTAAAAATATCAATTTTTTTTAAAAAT-AAGTATTTTAAAAAAAA
1 TATTTTTGAGGAAAAGTTGAAAATATCAATTTTCTTCGAAATTAAAG--TTTT-AAAAAAA
* * *
9131393 TATTTTTAAAGAAAAGTTGAAAATATCAATTTTCTTCGAAATTAAAGTTTTCAAAAAA
1 TATTTTTGAGGAAAAGTTGAAAATATCAATTTTCTTCGAAATTAAAGTTTTAAAAAAA
*
9131451 TATTTTTGAGGAAAAGTTGAAAATATCAAATTTTCTTCGAAATTAAAGTTTTCAAAAAA
1 TATTTTTGAGGAAAAGTTGAAAATATC-AATTTTCTTCGAAATTAAAGTTTTAAAAAAA
*
9131510 TATTTTTGAGGAAAAGTTGAAAATATCAAATTTTC-TCGAAATTAAAATTTTAAAAAAA
1 TATTTTTGAGGAAAAGTTGAAAATATC-AATTTTCTTCGAAATTAAAGTTTTAAAAAAA
* *
9131568 TATTTTT-AGGAAAAATTGAAAGTATCAATTTT
1 TATTTTTGAGGAAAAGTTGAAAATATCAATTTT
9131600 TTCTGCACAA
Statistics
Matches: 189, Mismatches: 16, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
56 6 0.03
57 17 0.09
58 59 0.31
59 70 0.37
60 34 0.18
61 3 0.02
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (58 bp):
TATTTTTGAGGAAAAGTTGAAAATATCAATTTTCTTCGAAATTAAAGTTTTAAAAAAA
Found at i:9131491 original size:59 final size:59
Alignment explanation
Indices: 9131387--9131600 Score: 344
Period size: 59 Copynumber: 3.7 Consensus size: 59
9131377 AGTATTTTAA
* *
9131387 AAAAAATATTTTTAAAGAAAAGTTGAAAATATC-AATTTTCTTCGAAATTAAAGTTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAAATTTTCTTCGAAATTAAAGTTTTC
9131445 AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAAATTTTCTTCGAAATTAAAGTTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAAATTTTCTTCGAAATTAAAGTTTTC
* *
9131504 AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAAATTTTC-TCGAAATTAAAATTTTA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAAATTTTCTTCGAAATTAAAGTTTTC
* * *
9131562 AAAAAATATTTTT-AGGAAAAATTGAAAGTATCAATTTTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAAATTTT
9131601 TCTGCACAAA
Statistics
Matches: 148, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
57 23 0.16
58 59 0.40
59 66 0.45
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (59 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAATATCAAATTTTCTTCGAAATTAAAGTTTTC
Found at i:9131602 original size:58 final size:59
Alignment explanation
Indices: 9131333--9131603 Score: 318
Period size: 58 Copynumber: 4.6 Consensus size: 59
9131323 GCTGAGGTCC
* * * ** * *
9131333 TATTTTTGAGAAAAAATTAAAAATATCAATTTTTT-TTAAAAATAAGTATTTTAAAAAAAA
1 TATTTTTGAGGAAAAGTTGAAAATATCAATTTTTTCTCGAAATTAA-AATTTT-AAAAAAA
* * * * *
9131393 TATTTTTAAAGAAAAGTTGAAAATATCAATTTTCT-TCGAAATTAAAGTTTTCAAAAAA
1 TATTTTTGAGGAAAAGTTGAAAATATCAATTTTTTCTCGAAATTAAAATTTTAAAAAAA
* * *
9131451 TATTTTTGAGGAAAAGTTGAAAATATCAA-ATTTTCTTCGAAATTAAAGTTTTCAAAAAA
1 TATTTTTGAGGAAAAGTTGAAAATATCAATTTTTTC-TCGAAATTAAAATTTTAAAAAAA
*
9131510 TATTTTTGAGGAAAAGTTGAAAATATCAA-ATTTTCTCGAAATTAAAATTTTAAAAAAA
1 TATTTTTGAGGAAAAGTTGAAAATATCAATTTTTTCTCGAAATTAAAATTTTAAAAAAA
* *
9131568 TATTTTT-AGGAAAAATTGAAAGTATCAATTTTTTCT
1 TATTTTTGAGGAAAAGTTGAAAATATCAATTTTTTCT
9131604 GCACAAAAAC
Statistics
Matches: 187, Mismatches: 21, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
57 22 0.12
58 67 0.36
59 62 0.33
60 36 0.19
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.39
Consensus pattern (59 bp):
TATTTTTGAGGAAAAGTTGAAAATATCAATTTTTTCTCGAAATTAAAATTTTAAAAAAA
Found at i:9131603 original size:117 final size:117
Alignment explanation
Indices: 9131333--9131600 Score: 346
Period size: 117 Copynumber: 2.3 Consensus size: 117
9131323 GCTGAGGTCC
* * * ** * *
9131333 TATTTTTGAGAAAAAATTAAAAATATC-AATTTTTTTTAAAAAT-AAGTATTTTAAAAAAAATAT
1 TATTTTTGAGGAAAAATTGAAAATATCAAATTTTCTTCGAAATTAAAG--TTTT-CAAAAAATAT
* *
9131396 TTTTAAAGAAAAGTTGAAAATATCAATTTTCTTCGAAATTAAAGTTTTCAAAAAA
63 TTTTAAAGAAAAGTTGAAAATATCAATTTTCTTCGAAATTAAAATTTTAAAAAAA
*
9131451 TATTTTTGAGGAAAAGTTGAAAATATCAAATTTTCTTCGAAATTAAAGTTTTCAAAAAATATTTT
1 TATTTTTGAGGAAAAATTGAAAATATCAAATTTTCTTCGAAATTAAAGTTTTCAAAAAATATTTT
* *
9131516 TGAGGAAAAGTTGAAAATATCAAATTTTC-TCGAAATTAAAATTTTAAAAAAA
66 TAAAGAAAAGTTGAAAATATC-AATTTTCTTCGAAATTAAAATTTTAAAAAAA
* *
9131568 TATTTTT-AGGAAAAATTGAAAGTATCAATTTTT
1 TATTTTTGAGGAAAAATTGAAAATATCAAATTTT
9131601 TCTGCACAAA
Statistics
Matches: 132, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
116 23 0.17
117 59 0.45
118 35 0.27
119 12 0.09
120 3 0.02
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (117 bp):
TATTTTTGAGGAAAAATTGAAAATATCAAATTTTCTTCGAAATTAAAGTTTTCAAAAAATATTTT
TAAAGAAAAGTTGAAAATATCAATTTTCTTCGAAATTAAAATTTTAAAAAAA
Found at i:9135268 original size:31 final size:31
Alignment explanation
Indices: 9135230--9135292 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
9135220 TTGTTTTCGC
*
9135230 TATCTTTGTTGCTGAAAGAATACATAACGAT
1 TATCTTTGTTGCTAAAAGAATACATAACGAT
*
9135261 TATCTTTGTTGCTAAAAGAATGCATAACGAT
1 TATCTTTGTTGCTAAAAGAATACATAACGAT
9135292 T
1 T
9135293 TTCATTGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (31 bp):
TATCTTTGTTGCTAAAAGAATACATAACGAT
Found at i:9139445 original size:18 final size:17
Alignment explanation
Indices: 9139403--9139445 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
9139393 TGTAGATTCT
9139403 TGGAAATTCGCAATATG
1 TGGAAATTCGCAATATG
* *
9139420 TAGAAATTTGCAATATG
1 TGGAAATTCGCAATATG
9139437 CTGGAAATT
1 -TGGAAATT
9139446 GTCTATTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (17 bp):
TGGAAATTCGCAATATG
Found at i:9139558 original size:12 final size:12
Alignment explanation
Indices: 9139541--9139565 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9139531 TTTGACACGA
9139541 AACAAATATGAT
1 AACAAATATGAT
9139553 AACAAATATGAT
1 AACAAATATGAT
9139565 A
1 A
9139566 TGAATATACA
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:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AACAAATATGAT
Found at i:9139995 original size:12 final size:12
Alignment explanation
Indices: 9139962--9140004 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
9139952 ATTATTTTTA
9139962 ATATAAATATA-
1 ATATAAATATAT
* *
9139973 AAATTAA-ATAT
1 ATATAAATATAT
9139984 ATATAAATATAT
1 ATATAAATATAT
9139996 ATATAAATA
1 ATATAAATA
9140005 AATAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 3 0.12
11 10 0.38
12 13 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATAAATATAT
Found at i:9139999 original size:16 final size:16
Alignment explanation
Indices: 9139962--9140008 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
9139952 ATTATTTTTA
*
9139962 ATATAAATATA-AAAT
1 ATATATATATATAAAT
*
9139977 -TAAATATATATAAAT
1 ATATATATATATAAAT
*
9139992 ATATATATAAATAAAT
1 ATATATATATATAAAT
9140008 A
1 A
9140009 ATTAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 8 0.31
15 4 0.15
16 14 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATATATATATAAAT
Found at i:9140346 original size:2 final size:2
Alignment explanation
Indices: 9140339--9140364 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9140329 AGTTCAACCA
9140339 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
9140365 TTTAAGAAAA
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:9143146 original size:27 final size:26
Alignment explanation
Indices: 9143089--9143146 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
9143079 AATATGAATG
* *
9143089 TTATATATTTTAAAAAATTTATAAAAT
1 TTATATATTTTAAAAAA-TTAAAAAAA
9143116 TTATATATATTTAATAAAA-TAAAAAAA
1 TTATATAT-TTTAA-AAAATTAAAAAAA
9143143 TTAT
1 TTAT
9143147 TTCATTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 18 0.67
28 5 0.19
29 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TTATATATTTTAAAAAATTAAAAAAA
Found at i:9144871 original size:20 final size:20
Alignment explanation
Indices: 9144833--9144885 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
9144823 GATATAAAAA
9144833 TAATAT-AATT-TAAAATTT
1 TAATATAAATTATAAAATTT
*
9144851 TAATATAAATTATATAATTT
1 TAATATAAATTATAAAATTT
9144871 TAATA-AAATTA-AAAA
1 TAATATAAATTATAAAA
9144886 AATATATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 9 0.29
19 10 0.32
20 12 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATATAAATTATAAAATTT
Found at i:9157287 original size:9 final size:9
Alignment explanation
Indices: 9157261--9157303 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
9157251 TTAAATCGAA
9157261 TTATATATTT
1 TTATA-ATTT
9157271 TTATTAATTT
1 TTA-TAATTT
9157281 TTATAATTT
1 TTATAATTT
*
9157290 TTA-AGTTT
1 TTATAATTT
9157298 TTATAA
1 TTATAA
9157304 AATAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 7 0.24
9 10 0.34
10 10 0.34
11 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TTATAATTT
Found at i:9157817 original size:17 final size:15
Alignment explanation
Indices: 9157791--9157841 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 15
9157781 GGTAGATTTA
9157791 ATAATTTTAAATATAAT
1 ATAA-TTTAAATAT-AT
9157808 ATAATATTAAATATAT
1 ATAAT-TTAAATATAT
9157824 ATAATTTAAA-AT-T
1 ATAATTTAAATATAT
9157837 ATAAT
1 ATAAT
9157842 AAAAAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.18
14 2 0.06
15 5 0.15
16 8 0.24
17 12 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTTAAATATAT
Found at i:9157826 original size:21 final size:22
Alignment explanation
Indices: 9157801--9157842 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
9157791 ATAATTTTAA
*
9157801 ATATAATATAATATTA-AATAT
1 ATATAATATAAAATTATAATAT
*
9157822 ATATAATTTAAAATTATAATA
1 ATATAATATAAAATTATAATA
9157843 AAAAATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATAATATAAAATTATAATAT
Found at i:9157859 original size:33 final size:33
Alignment explanation
Indices: 9157791--9157864 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 33
9157781 GGTAGATTTA
* * * *
9157791 ATAATTTTAAATATAATATAATATTAAATATAT
1 ATAATTTAAAATATAATAAAAAATTAAATACAT
*
9157824 ATAATTTAAAATTATAATAAAAAATTATA-ACAT
1 ATAATTTAAAA-TATAATAAAAAATTAAATACAT
*
9157857 ATATTTTA
1 ATAATTTA
9157865 TATTTAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 20 0.59
34 14 0.41
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
ATAATTTAAAATATAATAAAAAATTAAATACAT
Found at i:9158136 original size:2 final size:2
Alignment explanation
Indices: 9158129--9158153 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9158119 ATCACTTGAG
9158129 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 A
9158154 ACACCTATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9173320 original size:24 final size:23
Alignment explanation
Indices: 9173263--9173323 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
9173253 CATACTATTA
* *
9173263 ATTTTAATT-TCATTACTATAAT
1 ATTTTTATTATCATTACAATAAT
9173285 ATTTAATT-TTATCATTACAATAATT
1 ATTT--TTATTATCATTACAATAA-T
9173310 ATTTTTATTATCAT
1 ATTTTTATTATCAT
9173324 CATTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
22 4 0.12
23 4 0.12
24 19 0.59
25 5 0.16
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTTATTATCATTACAATAAT
Found at i:9173341 original size:18 final size:18
Alignment explanation
Indices: 9173307--9173343 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9173297 CATTACAATA
*
9173307 ATTATTTTTATTATCATC
1 ATTATTTTTAATATCATC
*
9173325 ATTATTTTTAATCTCATC
1 ATTATTTTTAATATCATC
9173343 A
1 A
9173344 AAATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATTTTTAATATCATC
Found at i:9180281 original size:28 final size:27
Alignment explanation
Indices: 9180218--9180283 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
9180208 TTTTTTTGGA
9180218 ATTAA-AAACATTAAAATTTAAATTTTG
1 ATTAATAAA-ATTAAAATTTAAATTTTG
* *
9180245 ATCATTAAAATTAAAAATTTAACATTTT-
1 ATTAATAAAATT-AAAATTTAA-ATTTTG
9180273 ATTAATAAAAT
1 ATTAATAAAAT
9180284 ATATTGCAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 6 0.19
28 21 0.66
29 5 0.16
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTAATAAAATTAAAATTTAAATTTTG
Found at i:9181111 original size:12 final size:12
Alignment explanation
Indices: 9181075--9181114 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
9181065 ATTTTAAATC
9181075 ATATTA-TTTTT
1 ATATTATTTTTT
*
9181086 ATA-T-TTTTTA
1 ATATTATTTTTT
9181096 ATATTATTTTTT
1 ATATTATTTTTT
9181108 ATATTAT
1 ATATTAT
9181115 ATTATTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
10 8 0.33
11 4 0.17
12 12 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:9182075 original size:1 final size:1
Alignment explanation
Indices: 9182069--9182093 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
9182059 ATCATTTGTG
9182069 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
9182094 CCTGATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9192896 original size:30 final size:30
Alignment explanation
Indices: 9192862--9192933 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
9192852 ATTCTTTTTT
*
9192862 TAATTA-ATTATTTAATTATATATATTTATA
1 TAATTATATT-TTTAAATATATATATTTATA
* *
9192892 TAATTATATTTTTAAATATTTATATTTAAA
1 TAATTATATTTTTAAATATATATATTTATA
* *
9192922 AAATAATATTTT
1 TAATTATATTTT
9192934 ATATTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 33 0.92
31 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TAATTATATTTTTAAATATATATATTTATA
Found at i:9192905 original size:16 final size:16
Alignment explanation
Indices: 9192869--9192918 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
9192859 TTTTAATTAA
*
9192869 TTATTTAATTATATATAT
1 TTATATAATTATAT-T-T
9192887 TTATATAATTATATTT
1 TTATATAATTATATTT
* *
9192903 TTAAATATTTATATTT
1 TTATATAATTATATTT
9192919 AAAAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 15 0.52
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATAATTATATTT
Found at i:9192921 original size:14 final size:14
Alignment explanation
Indices: 9192870--9192921 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
9192860 TTTAATTAAT
* *
9192870 TATTTAATTATATA
1 TATTTAAATATTTA
*
9192884 TATTTATATAATTATA
1 TATTTAAAT-ATT-TA
*
9192900 TTTTTAAATATTTA
1 TATTTAAATATTTA
9192914 TATTTAAA
1 TATTTAAA
9192922 AAATAATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 16 0.53
15 5 0.17
16 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTTAAATATTTA
Found at i:9192936 original size:21 final size:20
Alignment explanation
Indices: 9192906--9192955 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
9192896 TATATTTTTA
9192906 AATA-TTTATATTTAAAAAAT
1 AATATTTTATA-TTAAAAAAT
9192926 AATATTTTATATTAAAAAAT
1 AATATTTTATATTAAAAAAT
9192946 AATATTTTAT
1 AATATTTTAT
9192956 TAATTTCGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATTTTATATTAAAAAAT
Found at i:9193551 original size:25 final size:25
Alignment explanation
Indices: 9193458--9193548 Score: 110
Period size: 25 Copynumber: 3.6 Consensus size: 25
9193448 GTAGTATCAA
*
9193458 AGCTGAAGGTTCGAGACGTGAAAAA
1 AGCTGAAGGTTCGAGACGTGAAAAG
* * * *
9193483 AGTTGAAAGTTTGAGACGTGATAAG
1 AGCTGAAGGTTCGAGACGTGAAAAG
* * *
9193508 AGCTAAAGGTTCAAGATGTGAAAAG
1 AGCTGAAGGTTCGAGACGTGAAAAG
9193533 AGCTGAAGGTTCGAGA
1 AGCTGAAGGTTCGAGA
9193549 TGTAAGAAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (25 bp):
AGCTGAAGGTTCGAGACGTGAAAAG
Found at i:9193966 original size:52 final size:52
Alignment explanation
Indices: 9193864--9193968 Score: 124
Period size: 52 Copynumber: 2.0 Consensus size: 52
9193854 TGGACAAATA
* * *
9193864 GACTTGCAAAATAAAAATTCTAAAGGAAAGATGATTCTTAATAAGCAAGTTT
1 GACTTGCAAAAGAAAAATTCTAAAGGAAAGATAATTCTTAATAAGAAAGTTT
* * *
9193916 GACTTGCAAGAGAAGAATTCTAAAAGGAAATA-AATTCTTAAT-AGAAAAGTTT
1 GACTTGCAAAAGAAAAATTCT-AAAGGAAAGATAATTCTTAATAAG-AAAGTTT
9193968 G
1 G
9193969 TATGGTTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 2 0.04
52 34 0.76
53 9 0.20
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.28
Consensus pattern (52 bp):
GACTTGCAAAAGAAAAATTCTAAAGGAAAGATAATTCTTAATAAGAAAGTTT
Found at i:9194214 original size:6 final size:6
Alignment explanation
Indices: 9194205--9194270 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
9194195 TTTTTTTAAT
* * *
9194205 TTTATA TTTA-A TTTTATA TTTAATTA TATATA TTTTTA TATATA TTTA-A
1 TTTATA TTTATA -TTTATA TTT-A-TA TTTATA TTTATA TTTATA TTTATA
9194254 TTTTATA TTTATA TTTA
1 -TTTATA TTTATA TTTA
9194271 AAATAATATT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
5 2 0.04
6 38 0.79
7 4 0.08
8 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTATA
Found at i:9194214 original size:12 final size:12
Alignment explanation
Indices: 9194199--9194269 Score: 83
Period size: 12 Copynumber: 5.7 Consensus size: 12
9194189 AAATTATTTT
9194199 TTTAATTTTATA
1 TTTAATTTTATA
9194211 TTTAATTTTATA
1 TTTAATTTTATA
9194223 TTTAATTATATATA
1 TTTAATT-T-TATA
9194237 TTT--TTATATATA
1 TTTAATT-T-TATA
9194249 TTTAATTTTATA
1 TTTAATTTTATA
9194261 TTTATATTT
1 TTTA-ATTT
9194270 AAAATAATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
12 39 0.72
13 6 0.11
14 9 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTAATTTTATA
Found at i:9194241 original size:22 final size:22
Alignment explanation
Indices: 9194206--9194271 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
9194196 TTTTTTAATT
*
9194206 TTATATTTAATTTTATATTTAA
1 TTATATTTATTTTTATATTTAA
* * *
9194228 TTATATATATTTTTATATATAT
1 TTATATTTATTTTTATATTTAA
*
9194250 TTA-ATTTTATATTTATATTTAA
1 TTATA-TTTATTTTTATATTTAA
9194272 AATAATATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATATTTATTTTTATATTTAA
Found at i:9194248 original size:16 final size:16
Alignment explanation
Indices: 9194229--9194267 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9194219 TATATTTAAT
*
9194229 TATATATATTTTTATA
1 TATATATAATTTTATA
*
9194245 TATATTTAATTTTATA
1 TATATATAATTTTATA
*
9194261 TTTATAT
1 TATATAT
9194268 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATATAATTTTATA
Found at i:9197619 original size:2 final size:2
Alignment explanation
Indices: 9197612--9197643 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9197602 CTCTAGATTC
9197612 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
9197644 AACACTAACT
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:9197784 original size:7 final size:7
Alignment explanation
Indices: 9197774--9197803 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
9197764 ATATTTAATT
9197774 TTTAAAA
1 TTTAAAA
9197781 TTTAAAA
1 TTTAAAA
9197788 TTTAAAA
1 TTTAAAA
*
9197795 TGTAAAA
1 TTTAAAA
9197802 TT
1 TT
9197804 ATTTCAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (7 bp):
TTTAAAA
Found at i:9198385 original size:23 final size:23
Alignment explanation
Indices: 9198359--9198428 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
9198349 GTTCAATTAA
9198359 ATTAAATAAATTTATTTATAAAT
1 ATTAAATAAATTTATTTATAAAT
* * *
9198382 ATTAAATAAATATATTCACGAACAT
1 ATTAAATAAATTTATTTA-TAA-AT
*
9198407 ATATAAATAAA-TAATTTATAAA
1 AT-TAAATAAATTTATTTATAAA
9198429 CAATAAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
23 17 0.46
24 4 0.11
25 8 0.22
26 8 0.22
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (23 bp):
ATTAAATAAATTTATTTATAAAT
Found at i:9199425 original size:18 final size:19
Alignment explanation
Indices: 9199355--9199426 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
9199345 TGATATAAAT
9199355 TATAATATATAAT-TTTTA
1 TATAATATATAATATTTTA
* **
9199373 TATAAAATATAATATAACTA
1 TATAATATATAATAT-TTTA
9199393 TATAA-ATTATTAATATTTTA
1 TATAATA-TA-TAATATTTTA
9199413 TATAATATA-AATAT
1 TATAATATATAATAT
9199427 ACGAACTATC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.39
19 2 0.05
20 18 0.41
21 7 0.16
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (19 bp):
TATAATATATAATATTTTA
Found at i:9205126 original size:2 final size:2
Alignment explanation
Indices: 9205119--9205144 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9205109 TCGTGTAAAC
9205119 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
9205145 CAAAATCATA
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:9219184 original size:15 final size:14
Alignment explanation
Indices: 9219164--9219212 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
9219154 AAATTTAGAT
9219164 AAAATTTATCACCTA
1 AAAATTT-TCACCTA
9219179 AAAATTTT-A--TA
1 AAAATTTTCACCTA
9219190 AAAATTTTTCACCTA
1 AAAA-TTTTCACCTA
*
9219205 GAAATTTT
1 AAAATTTT
9219213 GTAAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
11 6 0.21
12 4 0.14
13 2 0.07
14 5 0.17
15 12 0.41
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (14 bp):
AAAATTTTCACCTA
Found at i:9219193 original size:26 final size:26
Alignment explanation
Indices: 9219164--9219223 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
9219154 AAATTTAGAT
9219164 AAAATTTATCACCTAAAAATTTTATA
1 AAAATTTATCACCTAAAAATTTTATA
* * *
9219190 AAAATTTTTCACCTAGAAATTTTGTA
1 AAAATTTATCACCTAAAAATTTTATA
9219216 AAAATTTA
1 AAAATTTA
9219224 CTATTTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (26 bp):
AAAATTTATCACCTAAAAATTTTATA
Found at i:9223947 original size:2 final size:2
Alignment explanation
Indices: 9223940--9224002 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
9223930 CGTGTAAACG
* *
9223940 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TC TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
9223982 TA CA TA TA TA TC TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
9224003 CATAATGAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:9223969 original size:22 final size:22
Alignment explanation
Indices: 9223941--9224002 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
9223931 GTGTAAACGT
*
9223941 ATATATATATATATATATATAC
1 ATATATATCTATATATATATAC
9223963 ATATATATCTATATATATATAC
1 ATATATATCTATATATATATAC
9223985 ATATATATCTATATATAT
1 ATATATATCTATATATAT
9224003 CATAATGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATATCTATATATATATAC
Found at i:9227721 original size:19 final size:19
Alignment explanation
Indices: 9227694--9227740 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
9227684 TAGTGAGATT
*
9227694 CATCATTCATTCATTCATA
1 CATCCTTCATTCATTCATA
9227713 CATCCTTCATTCATTCATA
1 CATCCTTCATTCATTCATA
9227732 CATCCTTCA
1 CATCCTTCA
9227741 GACGAAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (19 bp):
CATCCTTCATTCATTCATA
Found at i:9230422 original size:25 final size:24
Alignment explanation
Indices: 9230394--9230442 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
9230384 TATTAAATAA
9230394 ATTAAAATATTTGTAAAAATAATTT
1 ATTAAAATATTT-TAAAAATAATTT
** *
9230419 ATTAGTATATTTTAAAATTAATTT
1 ATTAAAATATTTTAAAAATAATTT
9230443 TAATAACCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
ATTAAAATATTTTAAAAATAATTT
Found at i:9231733 original size:43 final size:43
Alignment explanation
Indices: 9231667--9231755 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
9231657 GACCAATTTG
* *
9231667 ATTTGGTTTTGATTTAATGACCCTTTTGTATTTATTTTTATTA
1 ATTTAGTTTTGATTTAATGACCCTTGTGTATTTATTTTTATTA
9231710 ATTTAGTTTTG-TTTAAATGACCCTTGTGTATTTATTTTTATTA
1 ATTTAGTTTTGATTT-AATGACCCTTGTGTATTTATTTTTATTA
9231753 ATT
1 ATT
9231756 GTAAGAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 3 0.07
43 40 0.93
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.60
Consensus pattern (43 bp):
ATTTAGTTTTGATTTAATGACCCTTGTGTATTTATTTTTATTA
Found at i:9236071 original size:11 final size:11
Alignment explanation
Indices: 9236030--9236096 Score: 53
Period size: 13 Copynumber: 5.6 Consensus size: 11
9236020 GATAAAATCG
*
9236030 ATAATTTAAAA
1 ATAATATAAAA
*
9236041 TATAATATAATGAT
1 -ATAATATAA--AA
9236055 ATAATATAAAA
1 ATAATATAAAA
9236066 ATAATATAAATAA
1 ATAATAT-AA-AA
*
9236079 ATTATATAAAA
1 ATAATATAAAA
*
9236090 ATGATAT
1 ATAATAT
9236097 GAAATAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
11 16 0.35
12 12 0.26
13 17 0.37
14 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:9236074 original size:24 final size:24
Alignment explanation
Indices: 9236030--9236105 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
9236020 GATAAAATCG
* *
9236030 ATAATTTAAAATATAATAT-AATGAT
1 ATAATATAAAA-ATAATATAAAT-AA
9236055 ATAATATAAAAATAATATAAATAA
1 ATAATATAAAAATAATATAAATAA
* *
9236079 ATTATATAAAAATGATATGAAATAA
1 ATAATATAAAAATAATAT-AAATAA
9236104 AT
1 AT
9236106 TTTTAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
24 24 0.53
25 21 0.47
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (24 bp):
ATAATATAAAAATAATATAAATAA
Found at i:9236130 original size:24 final size:24
Alignment explanation
Indices: 9236058--9236132 Score: 91
Period size: 24 Copynumber: 3.0 Consensus size: 24
9236048 TAATGATATA
9236058 ATATAAAAATAATATAAATAAA-TT
1 ATATAAAAAT-ATATAAATAAATTT
9236082 ATATAAAAATGATATGAAATAAATTT
1 ATATAAAAAT-ATAT-AAATAAATTT
*
9236108 TTAATAAAAAT-TATAAATAAATTT
1 AT-ATAAAAATATATAAATAAATTT
9236132 A
1 A
9236133 AAAATATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
24 24 0.53
25 10 0.22
26 3 0.07
27 8 0.18
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (24 bp):
ATATAAAAATATATAAATAAATTT
Found at i:9236147 original size:45 final size:50
Alignment explanation
Indices: 9236060--9236153 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 50
9236050 ATGATATAAT
*
9236060 ATAAAAATAATATAAATAAATTATATAAAAATGATATGAAATAAATTTTTA
1 ATAAAAAT-ATATAAATAAATTATATAAAAATGATATAAAATAAATTTTTA
* *
9236111 ATAAAAAT-TATAAATAAA-T-T-TAAAAAT-ATTTAAAATATATTTT
1 ATAAAAATATATAAATAAATTATATAAAAATGATATAAAATAAATTTT
9236154 ATATTTGTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
45 13 0.32
46 7 0.17
47 1 0.03
48 1 0.03
49 10 0.25
51 8 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (50 bp):
ATAAAAATATATAAATAAATTATATAAAAATGATATAAAATAAATTTTTA
Found at i:9236445 original size:41 final size:40
Alignment explanation
Indices: 9236400--9236506 Score: 96
Period size: 41 Copynumber: 2.6 Consensus size: 40
9236390 TATATATATT
*
9236400 ATTTTATTTTTATTAATAGAATTAAATTTGTTAATTTTA-AA
1 ATTTTATTTTTATTAATA-AATTAAATTT-TGAATTTTATAA
* * *
9236441 ATTTTA-ATTAATTAATTAAAATTATATTTTGAATTTTATAA
1 ATTTTATTTTTATTAA-T-AAATTAAATTTTGAATTTTATAA
*
9236482 TTTTTATATTTTA--AATAAATTAAAT
1 ATTTTAT-TTTTATTAATAAATTAAAT
9236507 AAATTCATCT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
39 8 0.15
40 16 0.30
41 25 0.47
42 1 0.02
43 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (40 bp):
ATTTTATTTTTATTAATAAATTAAATTTTGAATTTTATAA
Found at i:9240182 original size:2 final size:2
Alignment explanation
Indices: 9240175--9240202 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9240165 ATCATGAAGA
9240175 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
9240203 TTGTACACGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9243687 original size:1 final size:1
Alignment explanation
Indices: 9243681--9243708 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
9243671 ATGTTCAAGG
9243681 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
9243709 AAGATTTACC
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:9249003 original size:6 final size:6
Alignment explanation
Indices: 9248992--9249030 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
9248982 ATGCAGTGAA
* *
9248992 CTGTTG CTGTTG TTGTGG CTGTTG CTGTTG CTGTTG CTG
1 CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTG
9249031 CTGCAAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.15, G:0.36, T:0.49
Consensus pattern (6 bp):
CTGTTG
Found at i:9260121 original size:16 final size:16
Alignment explanation
Indices: 9260100--9260132 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
9260090 ATCAGTAGCT
9260100 AAACAATGTAACGTAG
1 AAACAATGTAACGTAG
9260116 AAACAATGTAACGTAG
1 AAACAATGTAACGTAG
9260132 A
1 A
9260133 CCCTAATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (16 bp):
AAACAATGTAACGTAG
Found at i:9260690 original size:14 final size:14
Alignment explanation
Indices: 9260671--9260703 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
9260661 AAATAATTTC
9260671 TTTTTAGTTTTTTA
1 TTTTTAGTTTTTTA
9260685 TTTTTAGTTTTTTA
1 TTTTTAGTTTTTTA
9260699 TTTTT
1 TTTTT
9260704 CTGCGCATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (14 bp):
TTTTTAGTTTTTTA
Found at i:9261283 original size:39 final size:39
Alignment explanation
Indices: 9261207--9261292 Score: 88
Period size: 39 Copynumber: 2.2 Consensus size: 39
9261197 ATTTCTAAAC
*
9261207 TTATTAAAATGAATATCAATTTGAAGATATAAAAAATTA
1 TTATTAAAATGAATATCAATTTGAAGAGATAAAAAATTA
* *
9261246 TTATCTAAAAT-AATTAT-AATTTTAAGAGA-AAATAAATTT
1 TTAT-TAAAATGAA-TATCAATTTGAAGAGATAAA-AAATTA
9261285 TTAATTAA
1 TT-ATTAA
9261293 TTTTATATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
38 3 0.08
39 26 0.65
40 11 0.28
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (39 bp):
TTATTAAAATGAATATCAATTTGAAGAGATAAAAAATTA
Found at i:9272790 original size:2 final size:2
Alignment explanation
Indices: 9272783--9272818 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9272773 TATGTTTCTA
9272783 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
9272819 CGATTTCATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9273224 original size:10 final size:10
Alignment explanation
Indices: 9273173--9273225 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
9273163 ACATAATCTC
9273173 ATAAATATAT
1 ATAAATATAT
*
9273183 ATTAAATGTAT
1 A-TAAATATAT
9273194 ATAAATAATAT
1 ATAAAT-ATAT
9273205 ATAGAAATATAT
1 AT--AAATATAT
*
9273217 ATAGATATA
1 ATAAATATA
9273226 ATATCTATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 12 0.33
11 14 0.39
12 6 0.17
13 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (10 bp):
ATAAATATAT
Found at i:9274430 original size:53 final size:53
Alignment explanation
Indices: 9274367--9274468 Score: 204
Period size: 53 Copynumber: 1.9 Consensus size: 53
9274357 TTAGGCACTA
9274367 GCCCAGCTCTCTCAGTCTTTGATTACTTGTTGGTGTGTCTTTCTTGGTTGACT
1 GCCCAGCTCTCTCAGTCTTTGATTACTTGTTGGTGTGTCTTTCTTGGTTGACT
9274420 GCCCAGCTCTCTCAGTCTTTGATTACTTGTTGGTGTGTCTTTCTTGGTT
1 GCCCAGCTCTCTCAGTCTTTGATTACTTGTTGGTGTGTCTTTCTTGGTT
9274469 TCTTTTTATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (53 bp):
GCCCAGCTCTCTCAGTCTTTGATTACTTGTTGGTGTGTCTTTCTTGGTTGACT
Found at i:9282423 original size:13 final size:13
Alignment explanation
Indices: 9282405--9282430 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9282395 TAATTTATCG
9282405 ATTTTAATTTTTA
1 ATTTTAATTTTTA
9282418 ATTTTAATTTTTA
1 ATTTTAATTTTTA
9282431 TTTACTCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTAATTTTTA
Found at i:9284914 original size:119 final size:119
Alignment explanation
Indices: 9284702--9285027 Score: 372
Period size: 119 Copynumber: 2.8 Consensus size: 119
9284692 TATCTTTCTC
* * * * * * *
9284702 ATGCATTACTTCTTTGTTTGCTCTGCTTTAGTGAAGGATTTTCAGTTTGTCTCTACATCTATTGT
1 ATGCATTGCTTCTCTATTTTCTCTACTTTTGTGAAGGATTTTTAGTTTGTCTCTACATCTATTGT
* * ** *
9284767 TGGTTTCTTTTCTTTTTTCAGTCTATTCTTTTCAATATTTTTGATATTTTTCTT
66 GGGTTTCTTTTCTTATTTCAGTCTATTCTTTTCAATATTTTCCATATTTTTCAT
* * * *
9284821 ATGGATTGCTTCTCTATTTTCTCTACTTTTGTGAAGGATTTTTAGTTTGTTTCTACATTTGTTGT
1 ATGCATTGCTTCTCTATTTTCTCTACTTTTGTGAAGGATTTTTAGTTTGTCTCTACATCTATTGT
* *
9284886 GGGTTTTTTTTCTTATTTCAAT-TCATTCTTTTCAATATTTTCCATATTTTTCAT
66 GGGTTTCTTTTCTTATTTCAGTCT-ATTCTTTTCAATATTTTCCATATTTTTCAT
* ** *
9284940 ATGCATTGCTTCTCTTTTTTCT-TACTTTCT-TGAAAAATTTTTAGTTTG-CTCTACATCTATTT
1 ATGCATTGCTTCTCTATTTTCTCTACTTT-TGTGAAGGATTTTTAGTTTGTCTCTACATCTATTG
* * * *
9285002 TAGTTTTCTTTTCTTGTTTCAATCTA
65 TGGGTTTCTTTTCTTATTTCAGTCTA
9285028 AAATAGGGAA
Statistics
Matches: 174, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
117 30 0.17
118 24 0.14
119 120 0.69
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (119 bp):
ATGCATTGCTTCTCTATTTTCTCTACTTTTGTGAAGGATTTTTAGTTTGTCTCTACATCTATTGT
GGGTTTCTTTTCTTATTTCAGTCTATTCTTTTCAATATTTTCCATATTTTTCAT
Found at i:9286434 original size:30 final size:30
Alignment explanation
Indices: 9286399--9286457 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
9286389 TTGTAAGGGG
*
9286399 TCATGACAGCAT-TGACATTACTTGTTAAGA
1 TCATGACAGC-TCTGACACTACTTGTTAAGA
* *
9286429 TCATGATAGCTCTGATACTACTTGTTAAG
1 TCATGACAGCTCTGACACTACTTGTTAAG
9286458 CTAAAAAGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (30 bp):
TCATGACAGCTCTGACACTACTTGTTAAGA
Found at i:9291246 original size:103 final size:104
Alignment explanation
Indices: 9291058--9291259 Score: 275
Period size: 103 Copynumber: 1.9 Consensus size: 104
9291048 CAATAAGTAA
* * * * *
9291058 ATTTTAAATATAATCATGCTTTTATAGTCTCATTTTAAGATTTTTTTTATGTTAATTCATAAATA
1 ATTTCAAATATAATCATGATTTTATAGTCTCATTTTAAGA--TCTTTTATATCAATTCATAAATA
* * *
9291123 TTTATATGAATCTATTTCATCATGGACACTATTAATAACAT
64 CTTACATGAATCTATCTCATCATGGACACTATTAATAACAT
9291164 ATTTCAAATATAATCAT-ATTTATATAGTCTTC-TTTTAAGA-CTTTTATATCAATTCATAAATA
1 ATTTCAAATATAATCATGATTT-TATAGTC-TCATTTTAAGATCTTTTATATCAATTCATAAATA
9291226 CTTACATGAATCTATCTCATCATGGACACTATTA
64 CTTACATGAATCTATCTCATCATGGACACTATTA
9291260 TAATTTTTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
103 50 0.58
105 3 0.03
106 31 0.36
107 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.46
Consensus pattern (104 bp):
ATTTCAAATATAATCATGATTTTATAGTCTCATTTTAAGATCTTTTATATCAATTCATAAATACT
TACATGAATCTATCTCATCATGGACACTATTAATAACAT
Found at i:9294542 original size:25 final size:25
Alignment explanation
Indices: 9294514--9294574 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
9294504 TCTTTCATCC
9294514 ATGCCAAATTTCCTTGATGTACATT
1 ATGCCAAATTTCCTTGATGTACATT
9294539 ATGCCAAATTTCCTTGATGTACATT
1 ATGCCAAATTTCCTTGATGTACATT
9294564 ATGCCAAATTT
1 ATGCCAAATTT
9294575 TCCTACAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (25 bp):
ATGCCAAATTTCCTTGATGTACATT
Found at i:9296404 original size:60 final size:60
Alignment explanation
Indices: 9296246--9296407 Score: 252
Period size: 60 Copynumber: 2.7 Consensus size: 60
9296236 ATTCCTTTCA
* * * * *
9296246 GCCTCCTAGGCCTCCAACTAGGGCTCGACCTCCATCTACAAGCTCCCGCTCCAATTCTCT
1 GCCTCCTAGGCCTCCAACCAGCGCTCGAACTCCATCTATAAGCCCCCGCTCCAATTCTCT
* *
9296306 GCCTCCTAGGCCTCCAACCAGCGCTCAAACTCCATCTATAGGCCCCCGCTCCAATTCTCT
1 GCCTCCTAGGCCTCCAACCAGCGCTCGAACTCCATCTATAAGCCCCCGCTCCAATTCTCT
*
9296366 GCCTCCTAGGCCTCCAACCAGCGTTCGAACTCCATCTATAAG
1 GCCTCCTAGGCCTCCAACCAGCGCTCGAACTCCATCTATAAG
9296408 AATCCGCTTC
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.20, C:0.43, G:0.15, T:0.22
Consensus pattern (60 bp):
GCCTCCTAGGCCTCCAACCAGCGCTCGAACTCCATCTATAAGCCCCCGCTCCAATTCTCT
Found at i:9297917 original size:6 final size:6
Alignment explanation
Indices: 9297906--9297934 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9297896 ATCGACTAAA
9297906 ATTCAG ATTCAG ATTCAG ATTCAG ATTCA
1 ATTCAG ATTCAG ATTCAG ATTCAG ATTCA
9297935 TCATAGGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (6 bp):
ATTCAG
Found at i:9299755 original size:2 final size:2
Alignment explanation
Indices: 9299748--9299772 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9299738 CTGTAGAATT
9299748 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 T
9299773 TTGTTTTCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.