Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024099.1 Corchorus olitorius cultivar O-4 contig24132, 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: 113875
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:232 original size:20 final size:20
Alignment explanation
Indices: 207--244 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
197 ACTGAGGCGG
* *
207 TCGGTTTTTGGCGGTTTTGT
1 TCGGTTGTTGACGGTTTTGT
227 TCGGTTGTTGACGGTTTT
1 TCGGTTGTTGACGGTTTT
245 TAATAGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.11, G:0.34, T:0.53
Consensus pattern (20 bp):
TCGGTTGTTGACGGTTTTGT
Found at i:327 original size:11 final size:11
Alignment explanation
Indices: 311--419 Score: 57
Period size: 11 Copynumber: 10.4 Consensus size: 11
301 AAATAATTTA
311 TTATATATATT
1 TTATATATATT
* *
322 TTATATGTATC
1 TTATATATATT
* * *
333 ATAAATATA-A
1 TTATATATATT
*
343 TT-CATATATT
1 TTATATATATT
*
353 TTACATATATT
1 TTATATATATT
364 TTATATATA--
1 TTATATATATT
* * *
373 TCATAAATA-A
1 TTATATATATT
*
383 TTAAATATATT
1 TTATATATATT
*
394 TTATATATATC
1 TTATATATATT
* *
405 ATAAATATATT
1 TTATATATATT
416 TTAT
1 TTAT
420 TTAAATAGCA
Statistics
Matches: 71, Mismatches: 23, Indels: 8
0.70 0.23 0.08
Matches are distributed among these distances:
9 12 0.17
10 9 0.13
11 50 0.70
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (11 bp):
TTATATATATT
Found at i:375 original size:42 final size:41
Alignment explanation
Indices: 315--403 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 41
305 AATTTATTAT
* *
315 ATATATTTTATATGTATCATAAATATAATT-CATATATTTTAC
1 ATATATTTTATATATATCAT-AA-ATAATTAAATATATTTTAC
*
357 ATATATTTTATATATATCATAAATAATTAAATATATTTTAT
1 ATATATTTTATATATATCATAAATAATTAAATATATTTTAC
398 ATATAT
1 ATATAT
404 CATAAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 6 0.14
41 18 0.42
42 19 0.44
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (41 bp):
ATATATTTTATATATATCATAAATAATTAAATATATTTTAC
Found at i:431 original size:24 final size:22
Alignment explanation
Indices: 384--432 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
374 CATAAATAAT
* *
384 TAAATATATTTTATATATATCA
1 TAAATATATTTTATAAATAGCA
406 TAAATATATTTTATTTAAATAGCA
1 TAAATATATTTTA--TAAATAGCA
430 TAA
1 TAA
433 TCGGTCGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 13 0.57
24 10 0.43
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAATATATTTTATAAATAGCA
Found at i:531 original size:17 final size:18
Alignment explanation
Indices: 498--531 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
488 CGGTGGCAGT
498 TTAAACCACCTAAACCGA
1 TTAAACCACCTAAACCGA
516 TTAAACCACC-AAACCG
1 TTAAACCACCTAAACCG
532 CCTTATCTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.44, C:0.35, G:0.06, T:0.15
Consensus pattern (18 bp):
TTAAACCACCTAAACCGA
Found at i:8963 original size:37 final size:37
Alignment explanation
Indices: 8921--9096 Score: 301
Period size: 37 Copynumber: 4.9 Consensus size: 37
8911 TGGTTTTGGT
8921 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAATGC
1 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAATGC
8958 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAATGC
1 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAATGC
8995 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAA-G-
1 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAATGC
*
9030 ----GCATAACCATGTGTGAGTTTTGTTAGTTAATGC
1 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAATGC
9063 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAA
1 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAA
9097 GACTTAACCC
Statistics
Matches: 131, Mismatches: 2, Indels: 12
0.90 0.01 0.08
Matches are distributed among these distances:
31 29 0.22
32 1 0.01
36 1 0.01
37 100 0.76
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (37 bp):
CAACGTATAACCATGTGTGAGTTTTGTTAGTTAATGC
Found at i:9105 original size:68 final size:68
Alignment explanation
Indices: 8921--9110 Score: 299
Period size: 68 Copynumber: 2.7 Consensus size: 68
8911 TGGTTTTGGT
8921 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAATGCCAACGTATAACCATGTGTGAGTTTTGTT
1 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAA-G---AC-T-TAACCATGTGTGAGTTTTGTT
8986 AGTTAATGC
60 AGTTAATGC
* *
8995 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAAGGCATAACCATGTGTGAGTTTTGTTAGTTAA
1 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAAGACTTAACCATGTGTGAGTTTTGTTAGTTAA
9060 TGC
66 TGC
9063 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAAGACTTAACCCATGT
1 CAACGTATAACCATGTGTGAGTTTTGTTAGTTAAGACTTAA-CCATGT
9111 TCCCTTTGTG
Statistics
Matches: 111, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
68 69 0.62
69 6 0.05
70 1 0.01
73 1 0.01
74 34 0.31
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (68 bp):
CAACGTATAACCATGTGTGAGTTTTGTTAGTTAAGACTTAACCATGTGTGAGTTTTGTTAGTTAA
TGC
Found at i:15285 original size:219 final size:219
Alignment explanation
Indices: 14439--15440 Score: 1454
Period size: 218 Copynumber: 4.6 Consensus size: 219
14429 GTATATATAT
* *
14439 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACTTTTTAAAACCAATTTTGGGT
1 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACAC-GTTTAAAGCCAATTTTGGGT
* * * *
14504 ATATAAGAAAAAATGTCAATCTCTAATGAATTTTGGGTGACGGTGCTTATAATTATTTGGGGATG
65 ATATAA-AAAAAATGTCAATCTCTAAAGAA-TTTGGG-GATGGTGCATATGATTATTTGGGGATG
* *
14569 ATGAGAAATGATTT--G------GTATATCAGTTTGGGGATACAGAATATTGCATTTTGTTTAAT
127 ATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGAATACTGAATATTGCATTTTGTTTAAT
*
14626 TATTAGATGACACAAAATTCATATGGAC
192 TATTAGATGACACAAAATTCATATAGAC
*
14654 GGGGTTTATTC-A--AATTAGGATGAAAAATATGGATTAAAACACGTTTGAAGCCAATTTTGGGT
1 GGGGTTTATTCAATTAATTAGGATG-AAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGT
* * *
14716 ATATAAAAAAAAATGTCAATCTCTAAAGAATTTGAGGATGTTGCACATGATTATTTGGGGATGAT
65 ATAT-AAAAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
* * *
14781 GAGAAATGATTTGGGTATAAAGTATATCATTTTGGGGATATTGAATATTGCATTTTGTTTAATTA
129 GAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGAATACTGAATATTGCATTTTGTTTAATTA
* *
14846 TTAGATGGCACAAAATTCATATGGAC
194 TTAGATGACACAAAATTCATATAGAC
*
14872 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGTCAATTTTGGGTA
1 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTA
* *
14937 TAT-AAAAAAATATCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGA
66 TATAAAAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGA
* *
15001 GAAATGATTTGGGTATAAAGTATATCAGTTT-GAAGATACTGAATTTTGCATTTTGTTTAATTAT
131 GAAATGATTTGGGTATAAAGTATATCAGTTTGGGA-ATACTGAATATTGCATTTTGTTTAATTAT
15065 TAGATGACACAAAATTCATATAGAC
195 TAGATGACACAAAATTCATATAGAC
** * *
15090 ATGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAACCCAGTTTTGGGTA
1 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTA
* *
15155 TATAAAAAAAATGTCAATCTCTAAAAAATTTGGGGATGGTGCATATGATTATGTGGGGATGATGA
66 TATAAAAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGA
* * * *
15220 GAAATGATTTGGGTATAAAGTATATCACTTTGGGAATACTGAATTTTGCATGTTGTTTGATTATT
131 GAAATGATTTGGGTATAAAGTATATCAGTTTGGGAATACTGAATATTGCATTTTGTTTAATTATT
* * * *
15285 AAATGGCACTAAATTCATGTAGAC
196 AGATGACACAAAATTCATATAGAC
* * *
15309 TGGGTTTATTCAATTAATTATGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGTA
1 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTA
* * *
15374 TATAAGAAAAAATGTCAATGTCTAATGAATTTGGGGATGGTGCTTATGATTATTTGGGGATGATG
66 TATAA-AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATG
15439 AG
130 AG
15441 TAATATCAAG
Statistics
Matches: 716, Mismatches: 54, Indels: 29
0.90 0.07 0.04
Matches are distributed among these distances:
210 36 0.05
211 5 0.01
212 54 0.08
213 21 0.03
214 1 0.00
215 11 0.02
217 1 0.00
218 276 0.39
219 202 0.28
220 99 0.14
221 10 0.01
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.35
Consensus pattern (219 bp):
GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTA
TATAAAAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGA
GAAATGATTTGGGTATAAAGTATATCAGTTTGGGAATACTGAATATTGCATTTTGTTTAATTATT
AGATGACACAAAATTCATATAGAC
Found at i:15285 original size:437 final size:430
Alignment explanation
Indices: 14439--15440 Score: 1508
Period size: 437 Copynumber: 2.3 Consensus size: 430
14429 GTATATATAT
* *
14439 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACTTTTTAAAACCAATTTTGGGT
1 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACAC-GTTTAAAGCCAATTTTGGGT
* *
14504 ATATAAGAAAAAATGTCAATCTCTAATGAATTTTGGGTGACGGTGCTTATAATTATTTGGGGATG
65 ATATAAGAAAAAATGTCAATCTCTAATGAA-TTTGGG-GATGGTGCTTATGATTATTTGGGGATG
**
14569 ATGAGAAATGATTTGGTATATCAGTTTGGGGATACAGAATATTGCATTTTGTTTAATTATTAGAT
128 ATGAGAAATGATTTGGTATATCAGTTTGAAGATACAGAATATTGCATTTTGTTTAATTATTAGAT
* *
14634 GACACAAAATTCATATGGACGGGGTTTATTCAAATTAGGATGAAAAATATGGATTAAAACACGTT
193 GACACAAAATTCATATAGACAGGGTTTATTCAAATTAGGATGAAAAATATGGATTAAAACACGTT
* * * *
14699 TGAAGCCAATTTTGGGTATATAAAAAAAAATGTCAATCTCTAAAGAATTTGAGGATGTTGCACAT
258 TAAACCCAATTTTGGGTATATAAAAAAAAATGTCAATCTCTAAAAAATTTGAGGATGGTGCACAT
* * * *
14764 GATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCATTTTGGGGATATTGAATAT
323 GATTATGTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCACTTTGGGAATACTGAATAT
* * *
14829 TGCATTTTGTTTAATTATTAGATGGCACAAAATTCATATGGAC
388 TGCATGTTGTTTAATTATTAAATGGCACAAAATTCATATAGAC
*
14872 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGTCAATTTTGGGTA
1 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTA
* * * *
14937 TAT-A-AAAAAATATCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATGTGGGGATGATG
66 TATAAGAAAAAATGTCAATCTCTAATGAATTTGGGGATGGTGCTTATGATTATTTGGGGATGATG
* *
15000 AGAAATGATTTGGGTATAAAGTATATCAGTTTGAAGATACTGAATTTTGCATTTTGTTTAATTAT
131 AGAAATGATTT--G------GTATATCAGTTTGAAGATACAGAATATTGCATTTTGTTTAATTAT
*
15065 TAGATGACACAAAATTCATATAGACATGGTTTATTCAATTAATTAGGATG-AAAATATGGATTAA
188 TAGATGACACAAAATTCATATAGACAGGGTTTATTC-A--AATTAGGATGAAAAATATGGATTAA
* *
15129 AACACGTTTAAACCCAGTTTTGGGTATAT-AAAAAAAATGTCAATCTCTAAAAAATTTGGGGATG
250 AACACGTTTAAACCCAATTTTGGGTATATAAAAAAAAATGTCAATCTCTAAAAAATTTGAGGATG
*
15193 GTGCATATGATTATGTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCACTTTGGGAATA
315 GTGCACATGATTATGTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCACTTTGGGAATA
* * * *
15258 CTGAATTTTGCATGTTGTTTGATTATTAAATGGCACTAAATTCATGTAGAC
380 CTGAATATTGCATGTTGTTTAATTATTAAATGGCACAAAATTCATATAGAC
* * *
15309 TGGGTTTATTCAATTAATTATGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGGTA
1 GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTA
*
15374 TATAAGAAAAAATGTCAATGTCTAATGAATTTGGGGATGGTGCTTATGATTATTTGGGGATGATG
66 TATAAGAAAAAATGTCAATCTCTAATGAATTTGGGGATGGTGCTTATGATTATTTGGGGATGATG
15439 AG
131 AG
15441 TAATATCAAG
Statistics
Matches: 513, Mismatches: 43, Indels: 20
0.89 0.07 0.03
Matches are distributed among these distances:
428 37 0.07
429 6 0.01
430 22 0.04
431 1 0.00
432 21 0.04
433 44 0.09
436 74 0.14
437 201 0.39
438 41 0.08
439 66 0.13
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.35
Consensus pattern (430 bp):
GGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTA
TATAAGAAAAAATGTCAATCTCTAATGAATTTGGGGATGGTGCTTATGATTATTTGGGGATGATG
AGAAATGATTTGGTATATCAGTTTGAAGATACAGAATATTGCATTTTGTTTAATTATTAGATGAC
ACAAAATTCATATAGACAGGGTTTATTCAAATTAGGATGAAAAATATGGATTAAAACACGTTTAA
ACCCAATTTTGGGTATATAAAAAAAAATGTCAATCTCTAAAAAATTTGAGGATGGTGCACATGAT
TATGTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCACTTTGGGAATACTGAATATTGC
ATGTTGTTTAATTATTAAATGGCACAAAATTCATATAGAC
Found at i:16301 original size:215 final size:215
Alignment explanation
Indices: 15920--16592 Score: 917
Period size: 215 Copynumber: 3.2 Consensus size: 215
15910 TGAGGCATGC
* * * *
15920 GCAAAATTCAGCATCCCCAAAGTGATATACTCTATACCCAAATCA-TTCTCATCATTCCCAAATA
1 GCAAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
* * *
15984 ATCATAAGC-ACAATCCCCAAATTCATTAGAGATTGACATCTATCTTATATACCCAAAATTGGCT
66 ATCATATGCAAC-ATCCCCAAATT--TTAGAGATTGACAT-TTTTTTATATACCCAAAATTGGCT
* * *
16048 TTAAACATGTTTTAATCCATATTATCATCCTGATTAATTGAATAAACCCCGTCCATATGAATTTA
127 TTAAACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAA-CCCGTCCATATGAATTTA
*
16113 GTGTCGTCTAATAATTAAACAAAAT
191 GTGTCATCTAATAATTAAACAAAAT
16138 GCAAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
1 GCAAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
* *
16203 ATCATATGCAACATCCCCAAA-TTTAGAGATTGACATTTTTTTATATGCCCAAAATTGACTTTAA
66 ATCATATGCAACATCCCCAAATTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTTAA
* * *
16267 ACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCATGTCTATATGAATTTAATGT
131 ACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC-CGTCCATATGAATTTAGTGT
*
16332 CAT-TAAATAGTTAAACAAAAT
195 CATCT-AATAATTAAACAAAAT
* * *
16353 ACAAAATTCAGTATCCCCAAACTGATATACTTTATACACAACTCATTTCTCATCATCCCCAAATA
1 GCAAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
* * *
16418 ATCATTTGCACCATCCCCAAATTCTTTCGAGATTGACATTTTTTTATATACCCAAAATTGGCTTT
66 ATCATATGCAACATCCCCAAA-T-TTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTT
* *
16483 AAACGTGCTTTAATCCATATTTTCATCTTAATTAATTGAATAAA--C--CC--A-G----TAGTG
129 AAACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCGTCCATATGAATTTAGTG
*
16537 TCATCTAATAATTAAACAACAT
194 TCATCTAATAATTAAACAAAAT
*
16559 GCAAAATTCAGTATCCCCAAAGTGATATACTTTA
1 GCAAAATTCAGTATCCCCAAACTGATATACTTTA
16593 GGGGCCGTTT
Statistics
Matches: 413, Mismatches: 34, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
206 54 0.13
207 1 0.00
210 1 0.00
211 1 0.00
213 1 0.00
214 3 0.01
215 178 0.43
216 14 0.03
218 123 0.30
219 35 0.08
220 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.34
Consensus pattern (215 bp):
GCAAAATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
ATCATATGCAACATCCCCAAATTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTTAA
ACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCGTCCATATGAATTTAGTGTC
ATCTAATAATTAAACAAAAT
Found at i:17532 original size:51 final size:51
Alignment explanation
Indices: 17403--17533 Score: 129
Period size: 51 Copynumber: 2.5 Consensus size: 51
17393 GGCTGCTTGG
* *
17403 TTAATCTTTGGTTTGATTTGTGAATGGCAGCAATACAAATATGCAATTTTGG
1 TTAATATTTGGTTTGA-TTGTGAATGGCAGCAATACAAATATGCAATTTTGC
** ** ** **
17455 TTAATATTTGGTTTGATTAGCAAATGGCAGC-ATGGATTTATGCCTTTTTGC
1 TTAATATTTGGTTTGATT-GTGAATGGCAGCAATACAAATATGCAATTTTGC
*
17506 TTAATATTTGGTTGGATGTGTGAATGGC
1 TTAATATTTGGTTTGAT-TGTGAATGGC
17534 TTAGGTTGAT
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
51 38 0.59
52 26 0.41
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (51 bp):
TTAATATTTGGTTTGATTGTGAATGGCAGCAATACAAATATGCAATTTTGC
Found at i:19607 original size:24 final size:24
Alignment explanation
Indices: 19579--19625 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
19569 TTGGTGTAAA
*
19579 TTATGTTGAACTTGAATTATGTTT
1 TTATGTTGAACATGAATTATGTTT
*
19603 TTATGTTGGACATGAATTATGTT
1 TTATGTTGAACATGAATTATGTT
19626 GCATTTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (24 bp):
TTATGTTGAACATGAATTATGTTT
Found at i:19621 original size:40 final size:40
Alignment explanation
Indices: 19577--19710 Score: 171
Period size: 40 Copynumber: 3.4 Consensus size: 40
19567 GTTTGGTGTA
19577 AATTATGTTGAACTTGAATTATGTTTTTATGTTGGACATG
1 AATTATGTTGAACTTGAATTATGTTTTTATGTTGGACATG
* * * *
19617 AATTATGTTGCATTTGAATGATGTTTTTATGTTTGACATG
1 AATTATGTTGAACTTGAATTATGTTTTTATGTTGGACATG
* * * ** *
19657 AAATATGTTGCACTTTAATTATG-AATCATGTTGGACATG
1 AATTATGTTGAACTTGAATTATGTTTTTATGTTGGACATG
19696 AATTATGTTGAACTT
1 AATTATGTTGAACTT
19711 TATTAATTGA
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 25 0.31
40 55 0.69
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.46
Consensus pattern (40 bp):
AATTATGTTGAACTTGAATTATGTTTTTATGTTGGACATG
Found at i:21113 original size:217 final size:217
Alignment explanation
Indices: 20484--21212 Score: 1104
Period size: 217 Copynumber: 3.4 Consensus size: 217
20474 AAACGGCCCC
*
20484 TTATATCCAAATCATTTCTCATCATCCCCACATAATCATATGCACCATCCCCAAATT-TTTAGAG
1 TTATACCCAAATCATTTCTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAG
* * * *
20548 ATTGACATTTTTTTATATGCCCAAAATTGACTTTAAACGTGTTTTAATCCATATTTTCATCCTGA
66 ATTGACA-ATTTTTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCATATTTTCATCCTAA
* * *
20613 TTAATTGAATAAACTCTGTCTATATAAATTTAGTGTCATTTAATAATTAAACAAAATACAAAATT
130 TTAATTGAATAAACCCTGTCTATATGAATTTAGTGTCATCTAATAATTAAACAAAATACAAAATT
20678 CAGTATCCCCAAACTGATATACT
195 CAGTATCCCCAAACTGATATACT
* * * * *
20701 TTATACCCAACTTATTTCTCATCATCCCCAAATAATCATTTGCACCATCCCCAAATTCTTTCGAG
1 TTATACCCAAATCATTTCTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAG
*
20766 A-TCAGCAATTTTTTTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCATATTTTCATCCT
66 ATTGA-CAA--TTTTTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCATATTTTCATCCT
* * * *
20830 AATTAATTGAATAAACCCAGTCTAAATGAATTTAGTGTCATCTAACAATTAAACAACATACAAAA
128 AATTAATTGAATAAACCCTGTCTATATGAATTTAGTGTCATCTAATAATTAAACAAAATACAAAA
*
20895 TTCAGTATCCCCAAAGTGATATACT
193 TTCAGTATCCCCAAACTGATATACT
*
20920 TTATACCCAAATCATTTCTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGGG
1 TTATACCCAAATCATTTCTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAG
*
20985 ATTGACAATTTTTATATACCCAAAATTGGGTTTAAACGTGTTTTAATCCATATTTTCATCCTAAT
66 ATTGACAATTTTTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCATATTTTCATCCTAAT
* * * *
21050 TAATTGAATAATCCCTGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAAAATTC
131 TAATTGAATAAACCCTGTCTATATGAATTTAGTGTCATCTAATAATTAAACAAAATACAAAATTC
* **
21115 AGTGTCTTCAAACTGATATACT
196 AGTATCCCCAAACTGATATACT
* * * * *
21137 TTATACTCAAATTATTTCTCATCATCCCCACATAATCCTATGCACCTTCCCCAAATTCTTTCGAG
1 TTATACCCAAATCATTTCTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAG
21202 ATTGAC-ATTTT
66 ATTGACAATTTT
21213 ATGTACTTAC
Statistics
Matches: 462, Mismatches: 45, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
216 5 0.01
217 250 0.54
218 9 0.02
219 196 0.42
220 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.36
Consensus pattern (217 bp):
TTATACCCAAATCATTTCTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAG
ATTGACAATTTTTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCATATTTTCATCCTAAT
TAATTGAATAAACCCTGTCTATATGAATTTAGTGTCATCTAATAATTAAACAAAATACAAAATTC
AGTATCCCCAAACTGATATACT
Found at i:21298 original size:64 final size:64
Alignment explanation
Indices: 21197--21325 Score: 224
Period size: 64 Copynumber: 2.0 Consensus size: 64
21187 CCAAATTCTT
*
21197 TCGAGATTGACATTTTATGTACTTACTTTTCAAGATTATATCTATATTTGAAGAGACTTTCTGG
1 TCGAGATTGACATTTTATGTACTTAATTTTCAAGATTATATCTATATTTGAAGAGACTTTCTGG
*
21261 TCGAGATTGACAATTTT-TGTACTTAATTTTCAAGATTATATCTATATTTGAAGAGACTTTTTGG
1 TCGAGATTGAC-ATTTTATGTACTTAATTTTCAAGATTATATCTATATTTGAAGAGACTTTCTGG
21325 T
1 T
21326 AGACTATTAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 57 0.92
65 5 0.08
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (64 bp):
TCGAGATTGACATTTTATGTACTTAATTTTCAAGATTATATCTATATTTGAAGAGACTTTCTGG
Found at i:30813 original size:15 final size:15
Alignment explanation
Indices: 30793--30826 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
30783 TTTGCTGTTC
30793 TAATCAATTTTTCAT
1 TAATCAATTTTTCAT
*
30808 TAATCAATTTTTCGT
1 TAATCAATTTTTCAT
30823 TAAT
1 TAAT
30827 GGTGGTCGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (15 bp):
TAATCAATTTTTCAT
Found at i:38511 original size:2 final size:2
Alignment explanation
Indices: 38504--38531 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38494 TCTTATGTAC
38504 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
38532 TATTTTTTCT
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:47432 original size:62 final size:62
Alignment explanation
Indices: 47354--47476 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
47344 CTGAACTTAA
** * *
47354 TGTTATTCTGCATGCAACAAA-TCCAACATATCATCTCTTCATGGTAACA-AAAGCTAAAGCAG
1 TGTTATTCAACATGCAACAAATTCC-ACATATCATCTCTTCATAGCAA-AGAAAGCTAAAGCAG
*
47416 TGTTATTCAACATGCAATAAATTCCACATATCATCTCTTCATAGCAAAGAAAGCTAAAGCA
1 TGTTATTCAACATGCAACAAATTCCACATATCATCTCTTCATAGCAAAGAAAGCTAAAGCA
47477 ACTATTCCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
61 1 0.02
62 50 0.93
63 3 0.06
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (62 bp):
TGTTATTCAACATGCAACAAATTCCACATATCATCTCTTCATAGCAAAGAAAGCTAAAGCAG
Found at i:50894 original size:29 final size:27
Alignment explanation
Indices: 50862--50922 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
50852 TTTTAGTGAC
*
50862 TATATATATAGTGTGGCTATGGGCCGT
1 TATATATATAGTGTGGCTATGAGCCGT
*
50889 TATATATATAGTGTGGCTTTGAGCCGT
1 TATATATATAGTGTGGCTATGAGCCGT
*
50916 TTTATAT
1 TATATAT
50923 GGGCTCAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.43
Consensus pattern (27 bp):
TATATATATAGTGTGGCTATGAGCCGT
Found at i:57989 original size:14 final size:14
Alignment explanation
Indices: 57951--57993 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
57941 CTTCTCTTTT
57951 AATCGGTAATTTCC
1 AATCGGTAATTTCC
** *
57965 AATATGCAATTTCC
1 AATCGGTAATTTCC
57979 AATCGGTAATTTCC
1 AATCGGTAATTTCC
57993 A
1 A
57994 GGTATTTGTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (14 bp):
AATCGGTAATTTCC
Found at i:70996 original size:21 final size:23
Alignment explanation
Indices: 70962--71020 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
70952 ACAGGGAGGT
*
70962 TATCAAAA-ATCATAGAAAGAT-
1 TATCAAAATTTCATAGAAAGATG
* *
70983 TA-CAAAATTTCATATAAAGGTG
1 TATCAAAATTTCATAGAAAGATG
*
71005 TATTAAAATTTCATAG
1 TATCAAAATTTCATAG
71021 TTAGACTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 5 0.17
21 12 0.40
22 2 0.07
23 11 0.37
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.32
Consensus pattern (23 bp):
TATCAAAATTTCATAGAAAGATG
Found at i:71096 original size:22 final size:22
Alignment explanation
Indices: 71009--71129 Score: 88
Period size: 22 Copynumber: 5.5 Consensus size: 22
70999 AAGGTGTATT
* *
71009 AAAATTTCATAG-TTAGACTATC
1 AAAATTTCATAGCGTAG-TTATC
*
71031 AAAGTTTCATATG-G-AGTTTATC
1 AAAATTTCATA-GCGTAG-TTATC
* **
71053 ACAATTTCATAG-GTAAAATATC
1 AAAATTTCATAGCGT-AGTTATC
* *
71075 AAAATTCCATAGCGTGGTTATC
1 AAAATTTCATAGCGTAGTTATC
* *
71097 AAAATTTAATAGGGTAGTTATC
1 AAAATTTCATAGCGTAGTTATC
71119 AAAATTTCATA
1 AAAATTTCATA
71130 AAATATTCAA
Statistics
Matches: 77, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
21 2 0.03
22 71 0.92
23 4 0.05
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGCGTAGTTATC
Found at i:71721 original size:22 final size:22
Alignment explanation
Indices: 71669--71833 Score: 120
Period size: 22 Copynumber: 7.5 Consensus size: 22
71659 ATACCCTCTT
* *
71669 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* * * *
71691 TGTGGAATTTTAAGAACCTCAC
1 TATGAAATTTTGATAACCTCAC
*
71713 TATGAAATTTTGATAACC-CCC
1 TATGAAATTTTGATAACCTCAC
* * *
71734 AATGAAATTTTGATAAACACAC
1 TATGAAATTTTGATAACCTCAC
* *
71756 TATTACATTTTGATAACCTTC-C
1 TATGAAATTTTGATAACC-TCAC
* *
71778 TATGAAATTTTAACAACC-CGATCC
1 TATGAAATTTTGATAACCTC-A--C
* * *
71802 AATGAAATTTTGATAACCACTC
1 TATGAAATTTTGATAACCTCAC
71824 TATGAAATTT
1 TATGAAATTT
71834 GGCTAATTGC
Statistics
Matches: 108, Mismatches: 28, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
20 1 0.01
21 18 0.17
22 71 0.66
23 1 0.01
24 16 0.15
25 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:72030 original size:44 final size:44
Alignment explanation
Indices: 71980--72121 Score: 144
Period size: 44 Copynumber: 3.2 Consensus size: 44
71970 TCGTGAGATT
* *
71980 TCAAAATTTCATAGCGAGGTTATTAGATTTTCATAGTGTGGTTA
1 TCAAAATTTCATAGCGAGGTTATTAAAATTTCATAGTGTGGTTA
* * * *
72024 TCAAAATTCCATAAG-AAGGTTACTAAAATTTCATAG-GAAGGTTA
1 TCAAAATTTCAT-AGCGAGGTTATTAAAATTTCATAGTG-TGGTTA
* * * * *
72068 TCAAAATGTCATAGCGTGCTTATCAAAATTTCGTAGTGTGGTTA
1 TCAAAATTTCATAGCGAGGTTATTAAAATTTCATAGTGTGGTTA
*
72112 CCAAAATTTC
1 TCAAAATTTC
72122 GTATGAAAGT
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
43 3 0.04
44 71 0.92
45 3 0.04
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (44 bp):
TCAAAATTTCATAGCGAGGTTATTAAAATTTCATAGTGTGGTTA
Found at i:72036 original size:22 final size:21
Alignment explanation
Indices: 71980--72121 Score: 106
Period size: 22 Copynumber: 6.5 Consensus size: 21
71970 TCGTGAGATT
*
71980 TCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATAG-GTGGTTA
* * *
72002 TTAGATTTTCATAGTGTGGTTA
1 TCAAAATTTCATAG-GTGGTTA
* **
72024 TCAAAATTCCATAAGAAGGTTA
1 TCAAAATTTCAT-AGGTGGTTA
*
72046 -CTAAAATTTCATAGGAAGGTTA
1 TC-AAAATTTCATAGG-TGGTTA
* *
72068 TCAAAATGTCATAGCGTGCTTA
1 TCAAAATTTCATAG-GTGGTTA
*
72090 TCAAAATTTCGTAGTGTGGTTA
1 TCAAAATTTCATAG-GTGGTTA
*
72112 CCAAAATTTC
1 TCAAAATTTC
72122 GTATGAAAGT
Statistics
Matches: 94, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
21 3 0.03
22 87 0.93
23 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (21 bp):
TCAAAATTTCATAGGTGGTTA
Found at i:72133 original size:22 final size:22
Alignment explanation
Indices: 72091--72133 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
72081 GCGTGCTTAT
**
72091 CAAAATTTCGTAGTGTGGTTAC
1 CAAAATTTCGTAGTGAAGTTAC
72113 CAAAATTTCGTA-TGAAAGTTA
1 CAAAATTTCGTAGTG-AAGTTA
72134 TAAAAATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (22 bp):
CAAAATTTCGTAGTGAAGTTAC
Found at i:72164 original size:26 final size:26
Alignment explanation
Indices: 72130--72198 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
72120 TCGTATGAAA
*
72130 GTTAT-AAAAATCTCAATTTCATGAG
1 GTTATCAAAAATCTCAATTTCACGAG
72155 GTTATCAAAAATCTCAATTTCACGAG
1 GTTATCAAAAATCTCAATTTCACGAG
* *
72181 CTTATCAGAAATCTCAAT
1 GTTATCAAAAATCTCAAT
72199 CTCAATGCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 5 0.12
26 35 0.88
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (26 bp):
GTTATCAAAAATCTCAATTTCACGAG
Found at i:85141 original size:22 final size:22
Alignment explanation
Indices: 85116--85161 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
85106 ATTTTTTATG
*
85116 ACCTCCTTATAAAATTTTAATA
1 ACCTCCTTATAAAACTTTAATA
* *
85138 ACCTTCTTATGAAACTTTAATA
1 ACCTCCTTATAAAACTTTAATA
85160 AC
1 AC
85162 GATATTATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (22 bp):
ACCTCCTTATAAAACTTTAATA
Found at i:85335 original size:22 final size:22
Alignment explanation
Indices: 85310--85369 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
85300 TGAGATGTTG
*
85310 ATAACCTCCATATG-ATATATTA
1 ATAACCTCCATATGAAAAT-TTA
* **
85332 ATAACCACGTTATGAAAATTTA
1 ATAACCTCCATATGAAAATTTA
*
85354 AAAACCTCCATATGAA
1 ATAACCTCCATATGAA
85370 TTGTTAGTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (22 bp):
ATAACCTCCATATGAAAATTTA
Found at i:85605 original size:22 final size:22
Alignment explanation
Indices: 85580--85625 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
85570 ATTTTTTATG
*
85580 ACCTCCTTATAAAATTTTAATA
1 ACCTCCTTATAAAACTTTAATA
* *
85602 ACCTTCTTATGAAACTTTAATA
1 ACCTCCTTATAAAACTTTAATA
85624 AC
1 AC
85626 GATATTATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (22 bp):
ACCTCCTTATAAAACTTTAATA
Found at i:85668 original size:20 final size:22
Alignment explanation
Indices: 85645--85690 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
85635 GAATTTCGAG
*
85645 AACCCTT-TTAT-AATTTTTTT
1 AACCCTTCTTATAAATTTTGTT
85665 AA-CCTTCTTATGAAATTTTGTT
1 AACCCTTCTTAT-AAATTTTGTT
85687 AACC
1 AACC
85691 TCCCTAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 4 0.19
20 6 0.29
22 10 0.48
23 1 0.05
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.50
Consensus pattern (22 bp):
AACCCTTCTTATAAATTTTGTT
Found at i:85936 original size:22 final size:21
Alignment explanation
Indices: 85664--86141 Score: 226
Period size: 22 Copynumber: 22.0 Consensus size: 21
85654 ATAATTTTTT
* *
85664 TAACCTTCTTATGAAATTTTGT
1 TAACC-TCCTATGAAATTTTGA
* *
85686 TAACCTCCCTAAGGAATTTTGA
1 TAACCT-CCTATGAAATTTTGA
85708 -AGACCTCACTATGAAATTTTGA
1 TA-ACCTC-CTATGAAATTTTGA
* *
85730 TAA-TTTCTGAGTGAAATTTTGA
1 TAACCTCCT-A-TGAAATTTTGA
* * *
85752 TAACCAACACTATGAGATGTTGA
1 TAACC-TC-CTATGAAATTTTGA
* * *
85775 TAACCTCCATATGATATATTAA
1 TAACCTCC-TATGAAATTTTGA
* * *
85797 TAA-CTACGTTATGAAAATTTAA
1 TAACCT-C-CTATGAAATTTTGA
*
85819 AAACCTCCATATG-AATTGTT-A
1 TAACCTCC-TATGAAATT-TTGA
* * *
85840 GTAATCATACTCTGAAATTTTGA
1 -TAA-CCTCCTATGAAATTTTGA
* * *
85863 TAATCACACTATGAAATTGTGA
1 TAACCTC-CTATGAAATTTTGA
* * *
85885 -AATCTTGCTATAAAATTTTGA
1 TAA-CCTCCTATGAAATTTTGA
*
85906 TAAACCTCCTTATAAAATTTTGA
1 T-AACCTCC-TATGAAATTTTGA
* *
85929 TAACCTCCTTATGAAATCTTAA
1 TAACCTCC-TATGAAATTTTGA
*
85951 TAA----CTA-AAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
**
85967 TAACCTCCCTATGATTTTTTGA
1 TAACCT-CCTATGAAATTTTGA
**
85989 TAACCTCCCTATGATTTTTTGA
1 TAACCT-CCTATGAAATTTTGA
*
86011 TAACCTCCCTATGAAATTTTGT
1 TAACCT-CCTATGAAATTTTGA
* *
86033 TAATCTCGCTATGGAATTTTGA
1 TAACCTC-CTATGAAATTTTGA
*
86055 TAACCCTCTTATGAAATTTTGA
1 TAA-CCTCCTATGAAATTTTGA
* * *
86077 -AAACTAAACTATGAAAATTTGA
1 TAACCT--CCTATGAAATTTTGA
*
86099 TAACCTTCATATGAAATTTTGA
1 TAACC-TCCTATGAAATTTTGA
* *
86121 TATCCTCC-CTGAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
86141 T
1 T
86142 TACTCCATAT
Statistics
Matches: 349, Mismatches: 71, Indels: 74
0.71 0.14 0.15
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
20 16 0.05
21 34 0.10
22 235 0.67
23 47 0.13
24 2 0.01
25 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGA
Found at i:86021 original size:44 final size:44
Alignment explanation
Indices: 85664--86895 Score: 203
Period size: 44 Copynumber: 28.6 Consensus size: 44
85654 ATAATTTTTT
* * * *
85664 TAACCTTCTTATGAAATTTTGTTAACCTCCCTAAGGAATTTTGA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* ** *
85708 -AGACCTCACTATGAAATTTTGATAA--TTTCTGAGTGAAATTTTGA
1 TA-ACCTCCCTATGAAATTTTGATAACCTCCCT-A-TGGAATTTTGA
* * * * * * *
85752 TAACCAACACTATGAGATGTTGATAACCTCCATAT-GATATATTAA
1 TAACC-TCCCTATGAAATTTTGATAACCTCCCTATGGA-ATTTTGA
** * * * *
85797 TAA-CTACGTTATGAAAATTTAAAAACCTCCATAT-GAATTGTT-A
1 TAACCT-CCCTATGAAATTTTGATAACCTCCCTATGGAATT-TTGA
* * * * * * * *
85840 GTAATCAT-ACTCTGAAATTTTGATAATCACACTATGAAATTGTGA
1 -TAA-CCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* ** * * **
85885 -AATCTTGCTATAAAATTTTGATAAACCTCCTTATAAAATTTTGA
1 TAACCTCCCTATGAAATTTTGAT-AACCTCCCTATGGAATTTTGA
* * * **
85929 TAACCTCCTTATGAAATCTTAATAA-----CTA-AAAATTTTGA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
** *
85967 TAACCTCCCTATGATTTTTTGATAACCTCCCTAT-GATTTTTTGA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGA-ATTTTGA
* * *
86011 TAACCTCCCTATGAAATTTTGTTAATCTCGCTATGGAATTTTGA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * ** * *
86055 TAACC-CTCTTATGAAATTTTGA-AAACTAAACTATGAAAATTTGA
1 TAACCTC-CCTATGAAATTTTGATAACCT-CCCTATGGAATTTTGA
* * * *
86099 TAACCTTCATATGAAATTTTGATATCCTCCC--TGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * * * * * *
86141 TTA-CTCCATATTAAAAGTTTAATAACCTTCC-A---AA-TTTGG
1 TAACCTCCCTA-TGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * * *
86180 TAACCAT-ACTATAAAATTTTGATTACTTTCCC-AT--AA-----A
1 TAACC-TCCCTATGAAATTTTGATAAC-CTCCCTATGGAATTTTGA
* * * * ** * * *
86217 T-A-C-CACTATGAAATTTTGGTAATCACATTTTGAAAATTTGA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
** * ** * ** *
86258 TAACCTCTTTATGAAATTTTGAAAATTTCTCTATAAAATTTTGT
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * *** ** * *
86302 TGACC-CCTCTATGAAATTTTAATATTTTCATTACGTAATTTTGA
1 TAACCTCC-CTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * ** *
86346 TAACCTCGCTTTGAAATTTTGATAACAACACTAT-GAGATTTTGA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGA-ATTTTGA
* * ** * *
86390 TAATCTTCCTAT-AAATTTTGATAATCCAATTTCTATGAAATTTCGA
1 TAACCTCCCTATGAAATTTTGATAA-CC--TCCCTATGGAATTTTGA
* * * * * ** *
86436 TAATCACTCTATGAGA-TTTGATAACCT-TCTATAAAATTTTGG
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * * * *
86478 T-A-CTCCTTATGAAATTAAGACTTTTATAACCTTCATATGAAATTTTGA
1 TAACCTCCCTATGAAA-T-----TTTGATAACCTCCCTATGGAATTTTGA
* * ** * * * *
86526 TAACCACACTAAAAAATTTTAATAACCACACTATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * * *
86570 TAACCTCCCTATGAAATATT-AGTAACCTCCTTATGAAATTTTGT
1 TAACCTCCCTATGAAATTTTGA-TAACCTCCCTATGGAATTTTGA
* * *
86614 TAACCACACTATGAAATTCTT-ATAACCTCGCTAT-GACATTTTGA
1 TAACCTCCCTATGAAATT-TTGATAACCTCCCTATGGA-ATTTTGA
* ** ** *
86658 TAA--T--C--T----CTTTGATAACCTTTCTATAAAATTGTGA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * ** * * *** *
86692 TAACCACACTATGAAATTTCAATAAACTTCCTAAAAAATTTTAA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * * * *
86736 TAACCTGATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGA
1 TAACCT--CCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * * * * *
86782 TAACCTTTCC-ATGAAATTTTGATAACTTTCATATGAAATTTTGG
1 TAACC-TCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
* * * * * *
86826 TAACC-CACTATGGAATTTTGATAA-TTTCCTCATGAAATTATGA
1 TAACCTCCCTATGAAATTTTGATAACCTCCCT-ATGGAATTTTGA
*
86869 TAACCAT-CTTATGAAATTTTGATAACC
1 TAACC-TCCCTATGAAATTTTGATAACC
86896 ACATAGAGAC
Statistics
Matches: 856, Mismatches: 243, Indels: 177
0.67 0.19 0.14
Matches are distributed among these distances:
33 3 0.00
34 37 0.04
35 2 0.00
36 3 0.00
37 1 0.00
38 32 0.04
39 20 0.02
40 19 0.02
41 12 0.01
42 51 0.06
43 76 0.09
44 442 0.52
45 61 0.07
46 60 0.07
47 16 0.02
48 12 0.01
49 2 0.00
50 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (44 bp):
TAACCTCCCTATGAAATTTTGATAACCTCCCTATGGAATTTTGA
Found at i:86528 original size:22 final size:22
Alignment explanation
Indices: 86338--86660 Score: 111
Period size: 22 Copynumber: 14.5 Consensus size: 22
86328 TTCATTACGT
* *
86338 AATTTTGATAACC-TCGCTTTGA
1 AATTTTGATAACCTTC-ATATGA
**
86360 AATTTTGATAA-CAACACTATGA
1 AATTTTGATAACCTTCA-TATGA
* * *
86382 GATTTTGATAATCTTCCTAT-A
1 AATTTTGATAACCTTCATATGA
86403 AATTTTGATAATCCAATTTC-TATGA
1 AATTTTGATAA-CC---TTCATATGA
*
86428 AATTTCGATAATCAC-TC-TATGA
1 AATTTTGATAA-C-CTTCATATGA
* *
86450 GA-TTTGATAACCTTC-TATAA
1 AATTTTGATAACCTTCATATGA
* * *
86470 AATTTTGGTACTCCTT-ATGAAATTA
1 AATTTTGATA-ACCTTCAT---ATGA
86495 AGACTTTT-ATAACCTTCATATGA
1 A-A-TTTTGATAACCTTCATATGA
* **
86518 AATTTTGATAACC-ACACTAAAA
1 AATTTTGATAACCTTCA-TATGA
* *
86540 AATTTTAATAACC-ACACTATGA
1 AATTTTGATAACCTTCA-TATGA
* *
86562 AATTTTGATAACCTCCCTATGA
1 AATTTTGATAACCTTCATATGA
* * *
86584 AATATT-AGTAACCTCCTTATGA
1 AATTTTGA-TAACCTTCATATGA
* *
86606 AATTTTGTTAACC-ACACTATGA
1 AATTTTGATAACCTTCA-TATGA
*
86628 AATTCTT-ATAACC-TCGCTATGA
1 AATT-TTGATAACCTTC-ATATGA
*
86650 CATTTTGATAA
1 AATTTTGATAA
86661 TCTCTTTGAT
Statistics
Matches: 234, Mismatches: 39, Indels: 56
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.00
20 8 0.03
21 35 0.15
22 144 0.62
23 9 0.04
24 3 0.01
25 24 0.10
26 6 0.03
27 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTTCATATGA
Found at i:86583 original size:66 final size:65
Alignment explanation
Indices: 86499--86660 Score: 184
Period size: 66 Copynumber: 2.5 Consensus size: 65
86489 AAATTAAGAC
* *
86499 TTTTATAACCTTCATATGAAATTTTGATAACCACAC-TAAAAAATTTTAATAACCACACTATGAA
1 TTTTATAACCTCCCTATGAAATTTTGATAACCAC-CTTAAAAAATTTTAATAACCACACTATGAA
86563 A
65 A
* * ** **
86564 TTTTGATAACCTCCCTATGAAATATT-AGTAACCTCCTTATGAAATTTTGTTAACCACACTATGA
1 TTTT-ATAACCTCCCTATGAAATTTTGA-TAACCACCTTAAAAAATTTTAATAACCACACTATGA
86628 AA
64 AA
* *
86630 TTCTTATAACCTCGCTATGACATTTTGATAA
1 TT-TTATAACCTCCCTATGAAATTTTGATAA
86661 TCTCTTTGAT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
65 6 0.07
66 72 0.89
67 3 0.04
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (65 bp):
TTTTATAACCTCCCTATGAAATTTTGATAACCACCTTAAAAAATTTTAATAACCACACTATGAAA
Found at i:86716 original size:22 final size:21
Alignment explanation
Indices: 86691--86897 Score: 76
Period size: 22 Copynumber: 9.4 Consensus size: 21
86681 TAAAATTGTG
*
86691 ATAACCACACTATGAAATTTCA
1 ATAACCAC-CTATGAAATTTTA
** **
86713 ATAAACTTCCTAAAAAATTTTA
1 AT-AACCACCTATGAAATTTTA
*
86735 ATAACCTGATCCTATGAAATTTTG
1 ATAACC--A-CCTATGAAATTTTA
* *
86759 GTAACCACACTATGAAATTTTG
1 ATAACCAC-CTATGAAATTTTA
* *
86781 ATAACCTTTCC-ATGAAATTTTG
1 ATAACC--ACCTATGAAATTTTA
** * *
86803 ATAACTTTCATATGAAATTTTG
1 ATAAC-CACCTATGAAATTTTA
* * *
86825 GTAACC-CACTATGGAATTTTG
1 ATAACCAC-CTATGAAATTTTA
*** * *
86846 ATAATTTCCTCATGAAATTATG
1 ATAACCACCT-ATGAAATTTTA
* *
86868 ATAACCATCTTATGAAATTTTG
1 ATAACCA-CCTATGAAATTTTA
86890 ATAACCAC
1 ATAACCAC
86898 ATAGAGACAA
Statistics
Matches: 143, Mismatches: 29, Indels: 27
0.72 0.15 0.14
Matches are distributed among these distances:
20 1 0.01
21 23 0.16
22 95 0.66
23 7 0.05
24 17 0.12
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (21 bp):
ATAACCACCTATGAAATTTTA
Found at i:86776 original size:68 final size:66
Alignment explanation
Indices: 86678--86843 Score: 183
Period size: 68 Copynumber: 2.5 Consensus size: 66
86668 GATAACCTTT
* * *
86678 CTATAAAATTGTGATAACCACACTATGAAATTTCAATAAAC-TTCCTAAAAAATTTTAATAACCT
1 CTATGAAATTTTGGTAACCACACTATGAAATTTCAATAAACTTTCC-AAAAAATTTTAATAA-CT
86742 GATC
64 -ATC
** * ** * *
86746 CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTTCCATGAAATTTTGATAACTTT
1 CTATGAAATTTTGGTAACCACACTATGAAATTTCAATAAACTTTCCAAAAAATTTTAATAACTAT
86811 C
66 C
* *
86812 ATATGAAATTTTGGTAACC-CACTATGGAATTT
1 CTATGAAATTTTGGTAACCACACTATGAAATTT
86844 TGATAATTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 12 0.14
66 20 0.24
67 2 0.02
68 47 0.55
69 4 0.05
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (66 bp):
CTATGAAATTTTGGTAACCACACTATGAAATTTCAATAAACTTTCCAAAAAATTTTAATAACTAT
C
Found at i:86849 original size:65 final size:66
Alignment explanation
Indices: 86683--86898 Score: 215
Period size: 65 Copynumber: 3.3 Consensus size: 66
86673 CCTTTCTATA
* * ** * ** * * *
86683 AAATTGTGATAACCACACTATGAAATTTCAATAAACTTCCT-AAAAAATTTTAATAACCTGATCC
1 AAATTTTGGTAACCACACTATGAAATTTTGAT-AATTTCCTCATGAAATTATGATAACC--ATCA
86747 TATG
63 TATG
* **
86751 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTT-C-CATGAAATTTTGATAACTTTCAT
1 AAATTTTGGTAACCACACTATGAAATTTTGATAA--TTTCCTCATGAAATTATGATAACCATCAT
86814 ATG
64 ATG
* *
86817 AAATTTTGGTAACC-CACTATGGAATTTTGATAATTTCCTCATGAAATTATGATAACCATCTTAT
1 AAATTTTGGTAACCACACTATGAAATTTTGATAATTTCCTCATGAAATTATGATAACCATCATAT
86881 G
66 G
*
86882 AAATTTTGATAACCACA
1 AAATTTTGGTAACCACA
86899 TAGAGACAAG
Statistics
Matches: 125, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
63 3 0.02
64 1 0.01
65 53 0.42
66 22 0.18
67 2 0.02
68 42 0.34
69 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (66 bp):
AAATTTTGGTAACCACACTATGAAATTTTGATAATTTCCTCATGAAATTATGATAACCATCATAT
G
Found at i:88409 original size:238 final size:238
Alignment explanation
Indices: 87981--88452 Score: 892
Period size: 238 Copynumber: 2.0 Consensus size: 238
87971 GCATCGGATT
* *
87981 TGTTTATCACTTCAATCTTCATCGCTTCATTTTATTTTCTCTGTTCATTTCTTCAATTCTTCTTG
1 TGTTCATCACTTCAATCTTCATCGCTTCATTTTATTGTCTCTGTTCATTTCTTCAATTCTTCTTG
*
88046 CTTGTTGTTCGATTCGACTCCACCAACTCAATCGATTCAAAAAGAAGCGCAAAAGGTTTGTTGGT
66 CTTGTTGTTCGATTCGACTCCACCAACTCAATAGATTCAAAAAGAAGCGCAAAAGGTTTGTTGGT
88111 TTTTAGTTTTCATTTTCTCTACTTTTCTTCCAAAGTTTCTGACAAACCAAACGAAATTTTGGGTC
131 TTTTAGTTTTCATTTTCTCTACTTTTCTTCCAAAGTTTCTGACAAACCAAACGAAATTTTGGGTC
88176 TGTTGATGGGTTTATTATTTATGTTCTCTGATGTTATCAGATC
196 TGTTGATGGGTTTATTATTTATGTTCTCTGATGTTATCAGATC
88219 TGTTCATCACTTCAATCTTCATCGCTTCATTTTATTGTCTCTGTTCATTTCTTCAATTCTTCTTG
1 TGTTCATCACTTCAATCTTCATCGCTTCATTTTATTGTCTCTGTTCATTTCTTCAATTCTTCTTG
88284 CTTGTTGTTCGATTCGACTCCACCAACTCAATAGATTCAAAAAGAAGCGCAAAAGGTTTGTTGGT
66 CTTGTTGTTCGATTCGACTCCACCAACTCAATAGATTCAAAAAGAAGCGCAAAAGGTTTGTTGGT
88349 TTTTAGTTTTCATTTTCTCTACTTTTCTTCCAAAGTTTCTGACAAACCAAAC-AGAATTTTGGGT
131 TTTTAGTTTTCATTTTCTCTACTTTTCTTCCAAAGTTTCTGACAAACCAAACGA-AATTTTGGGT
*
88413 CTGTTGATGGGTTTATTATTTATGTTCTTTGATGTTATCA
195 CTGTTGATGGGTTTATTATTTATGTTCTCTGATGTTATCA
88453 TTTCAATTAA
Statistics
Matches: 229, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
237 1 0.00
238 228 1.00
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.44
Consensus pattern (238 bp):
TGTTCATCACTTCAATCTTCATCGCTTCATTTTATTGTCTCTGTTCATTTCTTCAATTCTTCTTG
CTTGTTGTTCGATTCGACTCCACCAACTCAATAGATTCAAAAAGAAGCGCAAAAGGTTTGTTGGT
TTTTAGTTTTCATTTTCTCTACTTTTCTTCCAAAGTTTCTGACAAACCAAACGAAATTTTGGGTC
TGTTGATGGGTTTATTATTTATGTTCTCTGATGTTATCAGATC
Found at i:89651 original size:16 final size:16
Alignment explanation
Indices: 89626--89662 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
89616 ATGTAATTTG
*
89626 AATTCAGTTCCCTCTT
1 AATTCAGTTCCCTCTA
*
89642 AATTCGGTTCCCTCTA
1 AATTCAGTTCCCTCTA
89658 AATTC
1 AATTC
89663 CCCCTCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.30, G:0.08, T:0.41
Consensus pattern (16 bp):
AATTCAGTTCCCTCTA
Found at i:89823 original size:2 final size:2
Alignment explanation
Indices: 89816--89951 Score: 220
Period size: 2 Copynumber: 67.5 Consensus size: 2
89806 TATAAAACCT
89816 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * *
89858 AT TC AA ATC GA- AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC A-C -AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
89901 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
89943 AC AC AC AC A
1 AC AC AC AC A
89952 TCAAATCGAA
Statistics
Matches: 125, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.01
2 123 0.98
4 1 0.01
ACGTcount: A:0.50, C:0.47, G:0.01, T:0.02
Consensus pattern (2 bp):
AC
Found at i:89976 original size:13 final size:13
Alignment explanation
Indices: 89955--89985 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
89945 ACACACATCA
*
89955 AATCGAATTTATC
1 AATCAAATTTATC
89968 AATCAAATTTATC
1 AATCAAATTTATC
89981 AATCA
1 AATCA
89986 CGTAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.35
Consensus pattern (13 bp):
AATCAAATTTATC
Found at i:92750 original size:51 final size:51
Alignment explanation
Indices: 92685--92806 Score: 154
Period size: 51 Copynumber: 2.4 Consensus size: 51
92675 AATTAAAGAT
* * * ***
92685 CCAACCTTTGAATTAAAGACTCAATTTTTGGGTTAACTTTAACCTAAAAAC
1 CCAAACTTTAAATTAAAGAATCAATTTTCAAGTTAACTTTAACCTAAAAAC
*
92736 CCAAACTTTAAATTAAAGAATCAATTTTCAAGTTAACTTTAACCTAAAAAT
1 CCAAACTTTAAATTAAAGAATCAATTTTCAAGTTAACTTTAACCTAAAAAC
*
92787 CAAAACTTTAATACTTAAAG
1 CCAAACTTTAA-A-TTAAAG
92807 CCATCTTTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 54 0.89
52 1 0.02
53 6 0.10
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (51 bp):
CCAAACTTTAAATTAAAGAATCAATTTTCAAGTTAACTTTAACCTAAAAAC
Found at i:92848 original size:70 final size:70
Alignment explanation
Indices: 92741--92876 Score: 177
Period size: 70 Copynumber: 1.9 Consensus size: 70
92731 AAAACCCAAA
* *
92741 CTTTAAATTAAAGAATCAATTTTCAAGTTAACTTTAACCTAAAAATCAAAACTTTAATACTT-AA
1 CTTTAAATTAAAGAATCAATTTTCAAGCTAACCTTAACCTAAAAATCAAAACTTTAAT-CTTGAA
92805 AGCCAT
65 AGCCAT
* ** **
92811 CTTTCAATTAAAGGGTCAACTTTT-AAGCTAACCTTAACCTAAAAATTTAAACTTTAATCTTGAA
1 CTTTAAATTAAAGAATCAA-TTTTCAAGCTAACCTTAACCTAAAAATCAAAACTTTAATCTTGAA
92875 AG
65 AG
92877 TTAATATCTT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
69 3 0.05
70 50 0.88
71 4 0.07
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.35
Consensus pattern (70 bp):
CTTTAAATTAAAGAATCAATTTTCAAGCTAACCTTAACCTAAAAATCAAAACTTTAATCTTGAAA
GCCAT
Found at i:93923 original size:71 final size:71
Alignment explanation
Indices: 93840--93988 Score: 298
Period size: 71 Copynumber: 2.1 Consensus size: 71
93830 AAGCCAATTT
93840 TAATGTTTTGATTCTAAAAAATGCTTCCGAAATTGTGTGGTTTCGATTGTCGATCTATTAAATAT
1 TAATGTTTTGATTCTAAAAAATGCTTCCGAAATTGTGTGGTTTCGATTGTCGATCTATTAAATAT
93905 TCTAAA
66 TCTAAA
93911 TAATGTTTTGATTCTAAAAAATGCTTCCGAAATTGTGTGGTTTCGATTGTCGATCTATTAAATAT
1 TAATGTTTTGATTCTAAAAAATGCTTCCGAAATTGTGTGGTTTCGATTGTCGATCTATTAAATAT
93976 TCTAAA
66 TCTAAA
93982 TAATGTT
1 TAATGTT
93989 GCTTCCGAAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (71 bp):
TAATGTTTTGATTCTAAAAAATGCTTCCGAAATTGTGTGGTTTCGATTGTCGATCTATTAAATAT
TCTAAA
Found at i:98708 original size:6 final size:6
Alignment explanation
Indices: 98697--98725 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
98687 AGTGCAAATC
98697 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
98726 TTAACGCAAT
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:100302 original size:22 final size:21
Alignment explanation
Indices: 100250--100303 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
100240 TGCTTCTTGA
100250 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
100271 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
100290 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
100304 CACGAACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:103265 original size:17 final size:17
Alignment explanation
Indices: 103243--103278 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
103233 TTGGTGTTTC
103243 GGTGGGAGAAATAATGG
1 GGTGGGAGAAATAATGG
103260 GGTGGGAGAAATAATGG
1 GGTGGGAGAAATAATGG
103277 GG
1 GG
103279 CCGCTGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.50, T:0.17
Consensus pattern (17 bp):
GGTGGGAGAAATAATGG
Found at i:103644 original size:13 final size:13
Alignment explanation
Indices: 103622--103683 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
103612 TTTTGCATTG
*
103622 CATTAACATATCA
1 CATTAGCATATCA
*
103635 TATTAGCATATCA
1 CATTAGCATATCA
* **
103648 CGTTAAAATATCA
1 CATTAGCATATCA
*
103661 GATTAGCATATCA
1 CATTAGCATATCA
*
103674 CATTTGCATA
1 CATTAGCATA
103684 GTATGTTTGC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (13 bp):
CATTAGCATATCA
Found at i:103653 original size:26 final size:26
Alignment explanation
Indices: 103624--103674 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
103614 TTGCATTGCA
* *
103624 TTAACATATCATATTAGCATATCACG
1 TTAAAATATCAGATTAGCATATCACG
103650 TTAAAATATCAGATTAGCATATCAC
1 TTAAAATATCAGATTAGCATATCAC
103675 ATTTGCATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (26 bp):
TTAAAATATCAGATTAGCATATCACG
Found at i:107458 original size:42 final size:42
Alignment explanation
Indices: 107399--107480 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
107389 CATGAGAAAT
* * *
107399 AAAAAGGGTGAATTAAAA-AGAGAAGTGAAAATTAGTTTTTTA
1 AAAAAGGGGGAAATAAAAGAGA-AAATGAAAATTAGTTTTTTA
* *
107441 AAAAAGGGGGAAATAAAAGGGAAAATGAAAATTTGTTTTT
1 AAAAAGGGGGAAATAAAAGAGAAAATGAAAATTAGTTTTT
107481 CTAGACAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (42 bp):
AAAAAGGGGGAAATAAAAGAGAAAATGAAAATTAGTTTTTTA
Found at i:112969 original size:11 final size:11
Alignment explanation
Indices: 112953--112977 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
112943 TATTCATAAT
112953 CAATCCAAAAA
1 CAATCCAAAAA
112964 CAATCCAAAAA
1 CAATCCAAAAA
112975 CAA
1 CAA
112978 ACAATTTTCT
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:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (11 bp):
CAATCCAAAAA
Found at i:112974 original size:85 final size:84
Alignment explanation
Indices: 112864--113033 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 84
112854 AAATTGGAGA
112864 ATAATCAATCCAAAACAATCCAAAAACAAACAATTTTCTATCCTAAGTTCTCATACAAATAAATA
1 ATAATCAATCCAAAACAATCCAAAAACAAACAATTTTCTATCCTAAGTTCTCATACAAATAAATA
112929 GCATATGACTCAATTATTC
66 GCATATGACTCAATTATTC
112948 ATAATCAATCCAAAAACAATCCAAAAACAAACAATTTTCTATCCTAAGTTCTCATACAAATAAAT
1 ATAATCAATCC-AAAACAATCCAAAAACAAACAATTTTCTATCCTAAGTTCTCATACAAATAAAT
113013 AGCATATGACTCAATTATTC
65 AGCATATGACTCAATTATTC
113033 A
1 A
113034 AGCAATAAAC
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 11 0.13
85 74 0.87
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (84 bp):
ATAATCAATCCAAAACAATCCAAAAACAAACAATTTTCTATCCTAAGTTCTCATACAAATAAATA
GCATATGACTCAATTATTC
Done.