Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_pilon, 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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 27
Found at i:3405640 original size:6 final size:6
Alignment explanation
Indices: 3405612--3405669 Score: 59
Period size: 6 Copynumber: 9.7 Consensus size: 6
3405602 CCTCTTTGTA
*
3405612 TCTATC TCTATGC T-TA-C TCCTATC TCTATC TCTATC CCTA-C TCCTATC
1 TCTATC TCTAT-C TCTATC T-CTATC TCTATC TCTATC TCTATC T-CTATC
3405660 TCTATC TCTA
1 TCTATC TCTA
3405670 CCCTTATCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 2 0.05
5 1 0.02
6 35 0.80
7 6 0.14
ACGTcount: A:0.17, C:0.36, G:0.02, T:0.45
Consensus pattern (6 bp):
TCTATC
Found at i:3405640 original size:24 final size:24
Alignment explanation
Indices: 3405612--3405673 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
3405602 CCTCTTTGTA
* *
3405612 TCTATCTCTATGCTTACTCCTATC
1 TCTATCTCTATCCCTACTCCTATC
3405636 TCTATCTCTATCCCTACTCCTATC
1 TCTATCTCTATCCCTACTCCTATC
3405660 TCTATCTCTA-CCCT
1 TCTATCTCTATCCCT
3405674 TATCCCTCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 4 0.11
24 32 0.89
ACGTcount: A:0.16, C:0.39, G:0.02, T:0.44
Consensus pattern (24 bp):
TCTATCTCTATCCCTACTCCTATC
Found at i:3409422 original size:20 final size:21
Alignment explanation
Indices: 3409393--3409432 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3409383 ATAAGGGTAA
*
3409393 ACTATGCG-TTTAGTACCTAG
1 ACTATCCGTTTTAGTACCTAG
3409413 ACTATCCGTTTTAGTACCTA
1 ACTATCCGTTTTAGTACCTA
3409433 AACAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
ACTATCCGTTTTAGTACCTAG
Found at i:3409703 original size:119 final size:119
Alignment explanation
Indices: 3409566--3409786 Score: 284
Period size: 119 Copynumber: 1.8 Consensus size: 119
3409556 AATGATAGTT
** * **
3409566 TAGGTACTAAACGCGTTAAGTTTTTAACGACGGGTACTAAAATGAA-ACAAAAACTAAATTTTAG
1 TAGGTACTAAACGCGTTAAGGCTTTAACGACGGGTACTAAAATGAACAAAAAAACTAAACATTAG
* *
3409630 GTATAATTTT-AAAAAATAAAAGTTTAGGTACTAAAACGAACAAAAACTAATAATA
66 ATAT-ATTTTAAAAAAATAAAAG-TTAGATACTAAAACGAACAAAAACTAATAATA
* * * **
3409685 TAGGTACTAAATGTGTTAAGGCTTTAATGGTGGGTACTAAAATGAACAAAAAAACTAAACATTAG
1 TAGGTACTAAACGCGTTAAGGCTTTAACGACGGGTACTAAAATGAACAAAAAAACTAAACATTAG
*
3409750 ATATGTTTTAAAAAAAATAAAAGTTAGATACTAAAAC
66 ATATATTTT-AAAAAAATAAAAGTTAGATACTAAAAC
3409787 AAACCAAAGC
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
119 43 0.50
120 31 0.36
121 12 0.14
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.28
Consensus pattern (119 bp):
TAGGTACTAAACGCGTTAAGGCTTTAACGACGGGTACTAAAATGAACAAAAAAACTAAACATTAG
ATATATTTTAAAAAAATAAAAGTTAGATACTAAAACGAACAAAAACTAATAATA
Found at i:3410456 original size:2 final size:2
Alignment explanation
Indices: 3410449--3410479 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3410439 CCACCAGTTA
3410449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3410480 ATTAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3410485 original size:4 final size:4
Alignment explanation
Indices: 3410478--3410503 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3410468 TATATATATA
3410478 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
3410504 TATTCCGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:3416706 original size:35 final size:34
Alignment explanation
Indices: 3416621--3416707 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
3416611 AAAATAATTT
*
3416621 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
3416655 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
3416693 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
3416708 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:3420079 original size:2 final size:2
Alignment explanation
Indices: 3420072--3420109 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3420062 ACTGACTATT
3420072 TA TA TA 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 TA TA TA
3420110 GTTCCTCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3426697 original size:12 final size:12
Alignment explanation
Indices: 3426682--3426733 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
3426672 ATTTAAACGA
3426682 GTATTGGGCCGG
1 GTATTGGGCCGG
*
3426694 GTATTGGGTCGG
1 GTATTGGGCCGG
3426706 GTATTGGGCCGG
1 GTATTGGGCCGG
* * *
3426718 GAATCGGGCCTG
1 GTATTGGGCCGG
3426730 GTAT
1 GTAT
3426734 ATATATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.12, C:0.15, G:0.46, T:0.27
Consensus pattern (12 bp):
GTATTGGGCCGG
Found at i:3428307 original size:22 final size:22
Alignment explanation
Indices: 3428282--3428339 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
3428272 CTCAGTGCTA
3428282 AGGCACTTTTGTATTAGTGATG
1 AGGCACTTTTGTATTAGTGATG
3428304 AGGCACTTTTGTATTAGTGATG
1 AGGCACTTTTGTATTAGTGATG
*
3428326 AGGCACTTTAGTAT
1 AGGCACTTTTGTAT
3428340 CAATGCTAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (22 bp):
AGGCACTTTTGTATTAGTGATG
Found at i:3428351 original size:22 final size:22
Alignment explanation
Indices: 3428275--3428339 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
3428265 TCTCTCCCTC
*
3428275 AGTGCTAAGGCACTTTTGTATT
1 AGTGATAAGGCACTTTTGTATT
*
3428297 AGTGATGAGGCACTTTTGTATT
1 AGTGATAAGGCACTTTTGTATT
* *
3428319 AGTGATGAGGCACTTTAGTAT
1 AGTGATAAGGCACTTTTGTAT
3428340 CAATGCTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (22 bp):
AGTGATAAGGCACTTTTGTATT
Found at i:3432022 original size:30 final size:29
Alignment explanation
Indices: 3431953--3432026 Score: 139
Period size: 29 Copynumber: 2.5 Consensus size: 29
3431943 GAATTTAAAT
3431953 ATTTAAAACTAAAAATATAAATTTAACCC
1 ATTTAAAACTAAAAATATAAATTTAACCC
3431982 ATTTAAAACTAAAAATATAAATTTAACCC
1 ATTTAAAACTAAAAATATAAATTTAACCC
3432011 ATTTAAAAACTAAAAA
1 ATTT-AAAACTAAAAA
3432027 GTACTACAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 33 0.75
30 11 0.25
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (29 bp):
ATTTAAAACTAAAAATATAAATTTAACCC
Found at i:3451430 original size:134 final size:136
Alignment explanation
Indices: 3451237--3451518 Score: 349
Period size: 134 Copynumber: 2.1 Consensus size: 136
3451227 AGAGCCTATT
*
3451237 ATGTTGTATATGTGATATTTCATGTCTTCTGTCTTATAGAGTTGATGATTACATGTCCCTATTC-
1 ATGTT-TATATGTGATATTTCATGTCTTCTGTCTGATAGAGTTGATGATTACATGTCCCTATTCA
* * * *
3451301 CATACAATAGTTATATTTTC-ATTTTTCACTT-G-TCTGTC-TTAGCAATTTATGATTTTATGCT
65 C-TACAACAATTATATTTTCGATTTTTC-CTTCGATCTGCCTTTA-CAATTTATGATTTTATACT
3451362 TAAGTTTGCA
127 TAAGTTTGCA
* * * *
3451372 ATGTTTATTTGTGATGTTTCATGTCTTCTGTCTGATAGAGTTGATGATTGCATTTCCCTATTCAC
1 ATGTTTATATGTGATATTTCATGTCTTCTGTCTGATAGAGTTGATGATTACATGTCCCTATTCAC
* *
3451437 TACACCAATTATATTTTCGTTTTTTCCTTGCGATTATCTGCCTTTACAATTTATGATTTTATACT
66 TACAACAATTATATTTTCGATTTTTCCTT-CG---ATCTGCCTTTACAATTTATGATTTTATACT
*
3451502 TCAGTTTGCA
127 TAAGTTTGCA
3451512 ATGTTTA
1 ATGTTTA
3451519 GGCCAGATTT
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
134 71 0.56
135 12 0.10
136 1 0.01
140 39 0.31
141 3 0.02
ACGTcount: A:0.22, C:0.15, G:0.14, T:0.49
Consensus pattern (136 bp):
ATGTTTATATGTGATATTTCATGTCTTCTGTCTGATAGAGTTGATGATTACATGTCCCTATTCAC
TACAACAATTATATTTTCGATTTTTCCTTCGATCTGCCTTTACAATTTATGATTTTATACTTAAG
TTTGCA
Found at i:3455550 original size:12 final size:12
Alignment explanation
Indices: 3455511--3455550 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3455501 CTGAAATGAT
*
3455511 TGCTGGATCTGG
1 TGCTGTATCTGG
* *
3455523 TTCCGTATCTGG
1 TGCTGTATCTGG
3455535 TGCTGTATCTGG
1 TGCTGTATCTGG
3455547 TGCT
1 TGCT
3455551 ACTAGCTCAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.07, C:0.20, G:0.33, T:0.40
Consensus pattern (12 bp):
TGCTGTATCTGG
Found at i:3470494 original size:15 final size:15
Alignment explanation
Indices: 3470474--3470503 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3470464 GATTAGTATC
3470474 TTTCCTAACTTAGAG
1 TTTCCTAACTTAGAG
*
3470489 TTTCCTAATTTAGAG
1 TTTCCTAACTTAGAG
3470504 ATATAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTCCTAACTTAGAG
Found at i:3483433 original size:23 final size:23
Alignment explanation
Indices: 3483381--3483427 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
3483371 CATAATTGTC
*
3483381 CCAAA-TGACCACCTAGGTTTGCA
1 CCAAAGTG-CCACATAGGTTTGCA
3483404 CCAAAGTGCCACATAGGTTTGCA
1 CCAAAGTGCCACATAGGTTTGCA
3483427 C
1 C
3483428 TGAAGTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (23 bp):
CCAAAGTGCCACATAGGTTTGCA
Found at i:3483439 original size:23 final size:23
Alignment explanation
Indices: 3483388--3483441 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
3483378 GTCCCAAATG
*
3483388 ACCACCTAGGTTTGCACCAAAGT
1 ACCACATAGGTTTGCACCAAAGT
* **
3483411 GCCACATAGGTTTGCACTGAAGT
1 ACCACATAGGTTTGCACCAAAGT
*
3483434 ATCACATA
1 ACCACATA
3483442 TTTGTCTTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (23 bp):
ACCACATAGGTTTGCACCAAAGT
Found at i:3484104 original size:20 final size:21
Alignment explanation
Indices: 3484079--3484158 Score: 78
Period size: 20 Copynumber: 3.9 Consensus size: 21
3484069 ATGTTTCAAG
*
3484079 GGTATCGATACCATCCTT-CA
1 GGTATCGATACCACCCTTACA
*
3484099 GGTATCGATACTACCCTTACA
1 GGTATCGATACCACCCTTACA
*
3484120 -GTATCGATA-C-CTCTTCAACA
1 GGTATCGATACCACCCTT--ACA
*
3484140 GGTATCGATACTACCCTTA
1 GGTATCGATACCACCCTTA
3484159 ATAATTTCCC
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
18 4 0.08
20 28 0.58
21 12 0.25
23 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.30
Consensus pattern (21 bp):
GGTATCGATACCACCCTTACA
Found at i:3498469 original size:16 final size:17
Alignment explanation
Indices: 3498450--3498482 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3498440 CATATAATAT
*
3498450 TATATTTTTA-TAAAAA
1 TATATATTTATTAAAAA
3498466 TATATATTTATTAAAAA
1 TATATATTTATTAAAAA
3498483 AATTCTTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATTTATTAAAAA
Found at i:3498483 original size:19 final size:19
Alignment explanation
Indices: 3498445--3498485 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3498435 GTTATCATAT
*
3498445 AATATTATATTTTTATAAA
1 AATATTATATTTTTAAAAA
3498464 AATA-TATATTTATTAAAAA
1 AATATTATATTT-TTAAAAA
3498483 AAT
1 AAT
3498486 TCTTAGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATTATATTTTTAAAAA
Found at i:3499009 original size:18 final size:18
Alignment explanation
Indices: 3498974--3499010 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3498964 ATTTTTTTTA
**
3498974 ATATATTTTTAATTATTT
1 ATATATTTTTAAAAATTT
3498992 ATATATTTTTAAAAATTT
1 ATATATTTTTAAAAATTT
3499010 A
1 A
3499011 ATAATATTCA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATATTTTTAAAAATTT
Found at i:3500552 original size:186 final size:184
Alignment explanation
Indices: 3500216--3500587 Score: 575
Period size: 186 Copynumber: 2.0 Consensus size: 184
3500206 AAATTAAATG
* * *
3500216 TTTTTAATTCAAACAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
* *
3500281 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTTAAAGTTATTAGACCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAATTATTAGACCTTAAATTATTAATT
* *
3500346 GAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATATAATAT
131 GAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATAT
3500400 TTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAAATTT
1 TTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT--AAAAATTT
* * * * *
3500465 -ATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTGGATCTTAAATTATTA
63 CAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAATTATTAGACCTTAAATTATTA
* * *
3500529 ATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
128 ATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATAT
3500586 TT
1 TT
3500588 AAAATTTAAT
Statistics
Matches: 170, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
184 14 0.08
185 37 0.22
186 111 0.65
187 8 0.05
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (184 bp):
TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAATTATTAGACCTTAAATTATTAATT
GAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATAT
Found at i:3504804 original size:21 final size:20
Alignment explanation
Indices: 3504773--3504811 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3504763 TTTAAAAATT
3504773 ATATTCAAATTTT-TTAAAA
1 ATATTCAAATTTTCTTAAAA
3504792 ATATTCACTAATTTTCTTAA
1 ATATTCA--AATTTTCTTAA
3504812 GGAATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTCAAATTTTCTTAAAA
Found at i:3505866 original size:19 final size:20
Alignment explanation
Indices: 3505830--3505868 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3505820 TGTTTGTGTG
3505830 TAAATTTATTAAAAAATATA
1 TAAATTTATTAAAAAATATA
* *
3505850 TAAA-TTATTTAATAATATA
1 TAAATTTATTAAAAAATATA
3505869 AAGTTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATTTATTAAAAAATATA
Found at i:3511698 original size:6 final size:6
Alignment explanation
Indices: 3511687--3511717 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3511677 TTGTTTTTAT
3511687 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA G
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA G
3511718 AGAGCTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:3513287 original size:24 final size:23
Alignment explanation
Indices: 3513250--3513303 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
3513240 TACCCATTTA
*
3513250 ATTATATTCCAATATTTATATACT
1 ATTATATTCCAATATATATATA-T
**
3513274 ATTATATTTTAATATATATATAT
1 ATTATATTCCAATATATATATAT
3513297 ATATATA
1 AT-TATA
3513304 ATTAAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATATTCCAATATATATATAT
Found at i:3514916 original size:2 final size:2
Alignment explanation
Indices: 3514880--3514904 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3514870 AATTCACTTT
3514880 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
3514905 TAATCTTATA
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
Found at i:3521544 original size:25 final size:27
Alignment explanation
Indices: 3521505--3521593 Score: 82
Period size: 26 Copynumber: 3.5 Consensus size: 27
3521495 TAACTTTAAA
3521505 AAATAT-TTTTA-TATTAGCTT-A-TT
1 AAATATATTTTATTATTAGCTTAATTT
**
3521528 AAATATATTTTATTATTAATTTAATTT
1 AAATATATTTTATTATTAGCTTAATTT
*
3521555 AAA-ATATTTTATT-TTAGTTTTAATTT
1 AAATATATTTTATTATTAG-CTTAATTT
* *
3521581 ATATATATATTAT
1 AAATATATTTTAT
3521594 GTCAAAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
23 6 0.11
24 5 0.09
25 10 0.18
26 21 0.38
27 13 0.24
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (27 bp):
AAATATATTTTATTATTAGCTTAATTT
Found at i:3521566 original size:26 final size:27
Alignment explanation
Indices: 3521526--3521593 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 27
3521516 TATTAGCTTA
3521526 TTAAATATATTTTATTATTA-ATTTAAT
1 TTAAATATATTTTATT-TTAGATTTAAT
*
3521553 TTAAA-ATATTTTATTTTAGTTTTAAT
1 TTAAATATATTTTATTTTAGATTTAAT
* *
3521579 TTATATATATATTAT
1 TTAAATATATTTTAT
3521594 GTCAAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 3 0.08
26 20 0.56
27 13 0.36
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
TTAAATATATTTTATTTTAGATTTAAT
Found at i:3521662 original size:30 final size:29
Alignment explanation
Indices: 3521612--3521722 Score: 102
Period size: 30 Copynumber: 3.8 Consensus size: 29
3521602 TATTTTGAAG
* *
3521612 TTAAGATAATAATAAAATATATTTAATAAT
1 TTAAGATAA-AATATAATATATTTAATAAA
*
3521642 TTAA-AGTGAAAATATAATATATTTAGTAAA
1 TTAAGA-T-AAAATATAATATATTTAATAAA
*
3521672 TTAAGATAAAATAT-ATATA-TTAAAAAA
1 TTAAGATAAAATATAATATATTTAATAAA
* * *
3521699 TTAAAATAGTAATAAAATATATTT
1 TTAAGATA-AAATATAATATATTT
3521723 TTAAAAGTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
27 13 0.19
28 9 0.13
29 13 0.19
30 29 0.43
31 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (29 bp):
TTAAGATAAAATATAATATATTTAATAAA
Found at i:3521737 original size:31 final size:31
Alignment explanation
Indices: 3521715--3521812 Score: 55
Period size: 28 Copynumber: 3.2 Consensus size: 31
3521705 TAGTAATAAA
* *
3521715 ATATATTTTTAAAAGTTTAAATAAGAATAAGACAT
1 ATAT-TTTTAAAAA-TTAAAATAAGAATAA-A-AT
*
3521750 ATATTTTT--AAATAAAAATAA-AACTAAAA-
1 ATATTTTTAAAAATTAAAATAAGAA-TAAAAT
* **
3521778 ATATTTTT--AAATTAAATTAATTATAAAAT
1 ATATTTTTAAAAATTAAAATAAGAATAAAAT
3521807 ATATTT
1 ATATTT
3521813 AATTAGTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
28 23 0.42
29 8 0.15
30 3 0.05
31 10 0.18
32 3 0.05
34 4 0.07
35 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (31 bp):
ATATTTTTAAAAATTAAAATAAGAATAAAAT
Found at i:3521804 original size:28 final size:27
Alignment explanation
Indices: 3521750--3521839 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 27
3521740 AATAAGACAT
* * *
3521750 ATATTTTTAAATAAAAATAAAACTAAAA
1 ATATTTTTAAATTAAATTAATA-TAAAA
3521778 ATATTTTTAAATTAAATTAAT-TATAAA
1 ATATTTTTAAATTAAATTAATATA-AAA
* *
3521805 ATATATTT-AATT-AGTTAATATAAAA
1 ATATTTTTAAATTAAATTAATATAAAA
3521830 ATATATTTTA
1 ATAT-TTTTA
3521840 GAAAACCGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 13 0.25
26 11 0.21
27 10 0.19
28 18 0.35
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
ATATTTTTAAATTAAATTAATATAAAA
Found at i:3521830 original size:25 final size:26
Alignment explanation
Indices: 3521773--3521837 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
3521763 AAAATAAAAC
*
3521773 TAAAAATATTTTTAAATTAAATTAAT
1 TAAAAATATATTTAAATTAAATTAAT
*
3521799 TATAAAATATATTT-AATT-AGTTAAT
1 TA-AAAATATATTTAAATTAAATTAAT
3521824 ATAAAAATATATTT
1 -TAAAAATATATTT
3521838 TAGAAAACCG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 17 0.49
26 8 0.23
27 10 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
TAAAAATATATTTAAATTAAATTAAT
Found at i:3522314 original size:23 final size:22
Alignment explanation
Indices: 3522282--3522325 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
3522272 GACCGAAAAC
3522282 TACCAAAAGGCAGAA-ATAAATT
1 TACCAAAAGGCA-AATATAAATT
3522304 TACCACAAAGGCAAATATAAAT
1 TACCA-AAAGGCAAATATAAAT
3522326 GTATAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (22 bp):
TACCAAAAGGCAAATATAAATT
Found at i:3522602 original size:2 final size:2
Alignment explanation
Indices: 3522595--3522622 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3522585 TTTTAAAGTT
3522595 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
3522623 ATTATGAATT
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):
TA
Found at i:3523466 original size:22 final size:22
Alignment explanation
Indices: 3523438--3523484 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3523428 TTCAGATGAC
3523438 GTAAGTGTTTGGGTTTGATATT
1 GTAAGTGTTTGGGTTTGATATT
3523460 GTAAGTGTTTGGGTTTGATATT
1 GTAAGTGTTTGGGTTTGATATT
3523482 GTA
1 GTA
3523485 TGCACTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (22 bp):
GTAAGTGTTTGGGTTTGATATT
Found at i:3531341 original size:2 final size:2
Alignment explanation
Indices: 3531334--3531379 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3531324 TTTATACTTT
3531334 TA TA TA TA TA 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 TA TA TA TA TA
3531376 TA TA
1 TA TA
3531380 GTGAAAATTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3531593 original size:2 final size:2
Alignment explanation
Indices: 3531586--3531628 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3531576 TTTATACTTT
3531586 TA TA TA TA TA 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 TA TA TA TA TA
3531628 T
1 T
3531629 CCATAATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3533387 original size:72 final size:72
Alignment explanation
Indices: 3533311--3533464 Score: 236
Period size: 72 Copynumber: 2.1 Consensus size: 72
3533301 GATAAAAAGC
*
3533311 ATAATGATGTGACATGTGTCATATGTATCCAAAGTGATAACATAACATATATCATGTGTACATAA
1 ATAATGATGTGACATGTGCCATATGTATCCAAAGTGATAACATAACATATATCATGTGTACATAA
3533376 ATATTAA
66 ATATTAA
* * * * * * *
3533383 ATAATGATGTGGCATGTGCCATATGTATTCAAAGTGATGACATGATATGTATTATGTGTACATAA
1 ATAATGATGTGACATGTGCCATATGTATCCAAAGTGATAACATAACATATATCATGTGTACATAA
3533448 ATATTAA
66 ATATTAA
3533455 ATAATGATGT
1 ATAATGATGT
3533465 AGCACATGCC
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (72 bp):
ATAATGATGTGACATGTGCCATATGTATCCAAAGTGATAACATAACATATATCATGTGTACATAA
ATATTAA
Found at i:3533475 original size:72 final size:72
Alignment explanation
Indices: 3533330--3533481 Score: 214
Period size: 72 Copynumber: 2.1 Consensus size: 72
3533320 TGACATGTGT
*
3533330 CATATGTATCCAAAGTGATAACATAACATATATCATGTGTACATAAATATTAAATAATGATGTGG
1 CATATGTATCCAAAGTGATAACATAACATATATCATGTGTACATAAATATTAAATAATGATGTAG
**
3533395 CATGTGC
66 CACATGC
* * * * * *
3533402 CATATGTATTCAAAGTGATGACATGATATGTATTATGTGTACATAAATATTAAATAATGATGTAG
1 CATATGTATCCAAAGTGATAACATAACATATATCATGTGTACATAAATATTAAATAATGATGTAG
3533467 CACATGC
66 CACATGC
*
3533474 CACATGTA
1 CATATGTA
3533482 AACAAGTGAT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (72 bp):
CATATGTATCCAAAGTGATAACATAACATATATCATGTGTACATAAATATTAAATAATGATGTAG
CACATGC
Found at i:3539519 original size:17 final size:18
Alignment explanation
Indices: 3539486--3539520 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3539476 CTCTTCTATT
3539486 CCAATGTTTCCAGTCTTC
1 CCAATGTTTCCAGTCTTC
3539504 CCAATGTTTCCA-TCTTC
1 CCAATGTTTCCAGTCTTC
3539521 GTATCTGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.17, C:0.34, G:0.09, T:0.40
Consensus pattern (18 bp):
CCAATGTTTCCAGTCTTC
Found at i:3542155 original size:14 final size:14
Alignment explanation
Indices: 3542136--3542163 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3542126 ACATGACAAG
3542136 TCATATGTATTCAA
1 TCATATGTATTCAA
3542150 TCATATGTATTCAA
1 TCATATGTATTCAA
3542164 AGTGATGACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TCATATGTATTCAA
Found at i:3557089 original size:8 final size:8
Alignment explanation
Indices: 3557076--3557101 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3557066 TCTCCCAATA
3557076 TATTTTAT
1 TATTTTAT
3557084 TATTTTAT
1 TATTTTAT
3557092 TATTTTAT
1 TATTTTAT
3557100 TA
1 TA
3557102 ATAAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TATTTTAT
Found at i:3557641 original size:32 final size:31
Alignment explanation
Indices: 3557578--3557648 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
3557568 TTAATTTTTA
* * *
3557578 TTTTAATAAGAATATAATTAAATCATGATTT
1 TTTTATTAAAAATATAATTAAATCATAATTT
* *
3557609 TTTTATTAAAAATCATAATTAATTTATAATTT
1 TTTTATTAAAAAT-ATAATTAAATCATAATTT
3557641 TATTTATT
1 T-TTTATT
3557649 TAATTCAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 11 0.33
32 16 0.48
33 6 0.18
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (31 bp):
TTTTATTAAAAATATAATTAAATCATAATTT
Found at i:3562595 original size:24 final size:24
Alignment explanation
Indices: 3562563--3562611 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3562553 GAGAAGGTCG
3562563 AGAATGGGCAGCTACAAGTGAATT
1 AGAATGGGCAGCTACAAGTGAATT
3562587 AGAATGGGCAGCTACAAGTGAATT
1 AGAATGGGCAGCTACAAGTGAATT
3562611 A
1 A
3562612 TGTTCCTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (24 bp):
AGAATGGGCAGCTACAAGTGAATT
Found at i:3566765 original size:11 final size:11
Alignment explanation
Indices: 3566749--3566775 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3566739 TCATATTCAT
3566749 TAATTTTAAAA
1 TAATTTTAAAA
3566760 TAATTTTAAAA
1 TAATTTTAAAA
3566771 TAATT
1 TAATT
3566776 ATCAACTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:3567603 original size:14 final size:14
Alignment explanation
Indices: 3567584--3567610 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3567574 GCAAATTATA
3567584 GCTTTTAAAAAGTG
1 GCTTTTAAAAAGTG
3567598 GCTTTTAAAAAGT
1 GCTTTTAAAAAGT
3567611 ATTGTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (14 bp):
GCTTTTAAAAAGTG
Found at i:3567790 original size:27 final size:27
Alignment explanation
Indices: 3567759--3567844 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
3567749 TTTAAATTAT
3567759 ATTTACACTTATATATGAATAATATCA
1 ATTTACACTTATATATGAATAATATCA
* *
3567786 ATTTAAAC-TATAATAAGAA-AA-AT-A
1 ATTTACACTTAT-ATATGAATAATATCA
* *
3567810 AGTTATCACTACTATATATGAATTATATCA
1 ATTTA-CACT--TATATATGAATAATATCA
3567840 ATTTA
1 ATTTA
3567845 AGCTATAACA
Statistics
Matches: 44, Mismatches: 7, Indels: 13
0.69 0.11 0.20
Matches are distributed among these distances:
24 5 0.11
25 4 0.09
26 5 0.11
27 19 0.43
28 4 0.09
29 2 0.05
30 5 0.11
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (27 bp):
ATTTACACTTATATATGAATAATATCA
Found at i:3570177 original size:25 final size:25
Alignment explanation
Indices: 3570149--3570198 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3570139 ATTGATCATC
3570149 TAATTTCGCACTCCC-AAAAATTTTA
1 TAATTTCGCAC-CCCTAAAAATTTTA
*
3570174 TAATTTCGCACCCCTAAAACTTTTA
1 TAATTTCGCACCCCTAAAAATTTTA
3570199 ATATAACTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (25 bp):
TAATTTCGCACCCCTAAAAATTTTA
Found at i:3586113 original size:22 final size:21
Alignment explanation
Indices: 3586087--3586127 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3586077 AAATAGTTTA
3586087 AATATTACATATATAATTATTT
1 AATATTACAT-TATAATTATTT
* *
3586109 AATATTTCATTTTAATTAT
1 AATATTACATTATAATTAT
3586128 AAAATATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATTACATTATAATTATTT
Found at i:3586133 original size:21 final size:22
Alignment explanation
Indices: 3586086--3586134 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
3586076 TAAATAGTTT
*
3586086 AAATATTACATATATAATTATT
1 AAATATTACATATATAATTATA
* * *
3586108 TAATATTTCAT-TTTAATTATA
1 AAATATTACATATATAATTATA
3586129 AAATAT
1 AAATAT
3586135 GTCAATATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATATTACATATATAATTATA
Found at i:3589751 original size:15 final size:14
Alignment explanation
Indices: 3589731--3589761 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3589721 TTAATTATCA
3589731 AATATTTGTATATAC
1 AATATTTGTAT-TAC
3589746 AATATTTGTATTAC
1 AATATTTGTATTAC
3589760 AA
1 AA
3589762 AGTAGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (14 bp):
AATATTTGTATTAC
Found at i:3595707 original size:12 final size:12
Alignment explanation
Indices: 3595690--3595732 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
3595680 AACTGCGCTA
3595690 TATTTTTTTTGT
1 TATTTTTTTTGT
3595702 TA-TTTTTTT-T
1 TATTTTTTTTGT
* *
3595712 AATTTCTTTTGT
1 TATTTTTTTTGT
3595724 TATTTTTTT
1 TATTTTTTT
3595733 AATTTCTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.08
11 13 0.52
12 10 0.40
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.81
Consensus pattern (12 bp):
TATTTTTTTTGT
Found at i:3595731 original size:21 final size:22
Alignment explanation
Indices: 3595691--3595742 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
3595681 ACTGCGCTAT
*
3595691 ATTTTTTTTGTTATTTTTTTTA
1 ATTTCTTTTGTTATTTTTTTTA
3595713 ATTTCTTTTGTTA-TTTTTTTA
1 ATTTCTTTTGTTATTTTTTTTA
3595734 ATTTCTTTT
1 ATTTCTTTT
3595743 CTTTGTTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (22 bp):
ATTTCTTTTGTTATTTTTTTTA
Found at i:3596637 original size:21 final size:23
Alignment explanation
Indices: 3596611--3596657 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
3596601 ATTATTGTTT
3596611 AATATT-TAGAGTAGAGAT-AGA
1 AATATTGTAGAGTAGAGATGAGA
*
3596632 AATATTGTAGAGTAGATATGAGA
1 AATATTGTAGAGTAGAGATGAGA
3596655 AAT
1 AAT
3596658 GGAGATAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.26
22 11 0.48
23 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (23 bp):
AATATTGTAGAGTAGAGATGAGA
Found at i:3597409 original size:2 final size:2
Alignment explanation
Indices: 3597404--3597431 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3597394 TTGGACACAC
3597404 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3597432 GGGGGGGGGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3599098 original size:50 final size:49
Alignment explanation
Indices: 3598970--3599110 Score: 126
Period size: 49 Copynumber: 2.8 Consensus size: 49
3598960 TTACAATAAC
* * *
3598970 TTGAAACTCGTCAAATTGATATGTAGAATTTTAAT-AAAATATATTTTTA
1 TTGAAACTTGTCACATTGATATG-AAAATTTTAATAAAAATATATTTTTA
* * * * *
3599019 TTAAAATTTATTATC-TTGATGTGATAAATTTTAATAAAAATTATATTTTT-
1 TTGAAACTTGTCA-CATTGATATGA-AAATTTTAATAAAAA-TATATTTTTA
3599069 TTGAAACTTGTCACATTGATATGACAAATTTTTGAATAAAAA
1 TTGAAACTTGTCACATTGATATGA-AAA-TTTT-AATAAAAA
3599111 ACTATTATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
48 1 0.01
49 25 0.35
50 24 0.34
51 13 0.18
52 8 0.11
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (49 bp):
TTGAAACTTGTCACATTGATATGAAAATTTTAATAAAAATATATTTTTA
Found at i:3602495 original size:19 final size:20
Alignment explanation
Indices: 3602468--3602507 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3602458 AATACAAATA
*
3602468 TAAAAATACATA-TAATAAT
1 TAAAAATACAAATTAATAAT
*
3602487 TAAATATACAAATTAATAAT
1 TAAAAATACAAATTAATAAT
3602507 T
1 T
3602508 TACTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAAATACAAATTAATAAT
Found at i:3603258 original size:14 final size:15
Alignment explanation
Indices: 3603226--3603272 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
3603216 TAATAAGTAA
3603226 AATTTCATATAATTAAT
1 AATTT-ATATAATT-AT
3603243 AATTTATATAA-TAT
1 AATTTATATAATTAT
*
3603257 AAATTAT-TAATTAT
1 AATTTATATAATTAT
3603271 AA
1 AA
3603273 AAAATATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.11
14 13 0.46
15 1 0.04
16 6 0.21
17 5 0.18
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTATATAATTAT
Found at i:3604625 original size:14 final size:14
Alignment explanation
Indices: 3604603--3604633 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3604593 AAGAAATTTT
*
3604603 AGTCGAGTTATTCG
1 AGTCAAGTTATTCG
3604617 AGTCAAGTTATTCG
1 AGTCAAGTTATTCG
3604631 AGT
1 AGT
3604634 TTTTATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (14 bp):
AGTCAAGTTATTCG
Found at i:3604783 original size:18 final size:19
Alignment explanation
Indices: 3604760--3604807 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
3604750 TTATAGTGTT
3604760 ATTTAATATAT-AAATATA
1 ATTTAATATATAAAATATA
3604778 ATTTAATATTATAAAATATA
1 ATTTAATA-TATAAAATATA
*
3604798 TTTATAATAT
1 ATT-TAATAT
3604808 TATATTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 3 0.12
20 10 0.38
21 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTAATATATAAAATATA
Found at i:3604805 original size:21 final size:20
Alignment explanation
Indices: 3604760--3604811 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
3604750 TTATAGTGTT
3604760 ATTTAATA-TAT-AAATATA
1 ATTTAATATTATAAAATATA
3604778 ATTTAATATTATAAAATATA
1 ATTTAATATTATAAAATATA
*
3604798 TTTATAATATTATA
1 ATT-TAATATTATA
3604812 TTTCAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.27
19 3 0.10
20 9 0.30
21 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAATATTATAAAATATA
Found at i:3604901 original size:18 final size:17
Alignment explanation
Indices: 3604861--3604904 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
3604851 AATTGTAGTC
*
3604861 AAAAATCAAA-TTAAGTA
1 AAAAAT-AAAGTTAAGGA
3604878 AAAAATAAAGTTAAGGA
1 AAAAATAAAGTTAAGGA
3604895 AATAAATAAA
1 AA-AAATAAA
3604905 AAAAGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 14 0.58
18 7 0.29
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.20
Consensus pattern (17 bp):
AAAAATAAAGTTAAGGA
Found at i:3606085 original size:84 final size:84
Alignment explanation
Indices: 3605981--3606149 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
3605971 TGAATCTCAG
3605981 AACTGAAACCAATGATTTATTGGATTTGATTTATACTGAAAAGTTAATATTGAATTTGTTTGTTT
1 AACTGAAACCAATGATTTATTGGATTTGATTTATACTGAAAAGTTAATATTGAATTTGTTTGTTT
3606046 ATTATTCCCACTCATTGAA
66 ATTATTCCCACTCATTGAA
3606065 AACTGAAACCAATGATTTATTGGATTTGATTTATACTGAAAAGTTAATATTGAATTTGTTTGTTT
1 AACTGAAACCAATGATTTATTGGATTTGATTTATACTGAAAAGTTAATATTGAATTTGTTTGTTT
3606130 ATTATTCCCACTCATTGAA
66 ATTATTCCCACTCATTGAA
3606149 A
1 A
3606150 CAAATTGAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (84 bp):
AACTGAAACCAATGATTTATTGGATTTGATTTATACTGAAAAGTTAATATTGAATTTGTTTGTTT
ATTATTCCCACTCATTGAA
Found at i:3611503 original size:60 final size:60
Alignment explanation
Indices: 3611418--3611530 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
3611408 TATATGATCC
* *
3611418 TACTTTATTAAGTCTCTCGACTATTAAAAGTTATAAAATAGTCA-TCCGACTATAGAATGT
1 TACTTTATTAAGTCCCTCGACTATTAAAAATTATAAAATAGTCACT-CGACTATAGAATGT
* * * *
3611478 TACTTTGTTATGTCCCTCGGCTATTAAAAATTATAAAGTAGTCACTCGACTAT
1 TACTTTATTAAGTCCCTCGACTATTAAAAATTATAAAATAGTCACTCGACTAT
3611531 TCATTATGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 45 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (60 bp):
TACTTTATTAAGTCCCTCGACTATTAAAAATTATAAAATAGTCACTCGACTATAGAATGT
Found at i:3613876 original size:14 final size:14
Alignment explanation
Indices: 3613857--3613911 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
3613847 CGTTCGTGAA
3613857 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
3613871 CGTTCG-GTATG-T
1 CGTTCGATTATGTT
*
3613883 --TT-GTTTATGTT
1 CGTTCGATTATGTT
3613894 CGTTCGATTATGTT
1 CGTTCGATTATGTT
3613908 CGTT
1 CGTT
3613912 TATGTTCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
9 1 0.03
10 6 0.18
11 1 0.03
12 1 0.03
13 6 0.18
14 18 0.55
ACGTcount: A:0.11, C:0.13, G:0.24, T:0.53
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:3613892 original size:23 final size:24
Alignment explanation
Indices: 3613858--3613918 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
3613848 GTTCGTGAAC
*
3613858 GTTCGATTATGTTCGTTCG-GTAT
1 GTTCGTTTATGTTCGTTCGAGTAT
* *
3613881 GTTTGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGAGTAT
3613905 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
3613919 ATTTATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.54
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGAGTAT
Found at i:3614663 original size:16 final size:16
Alignment explanation
Indices: 3614638--3614696 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
3614628 CCAACGTTTA
3614638 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
3614654 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
3614670 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3614686 TGTTCGTTTAT
1 TGTTCGTTTAT
3614697 TTATTAATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:3614781 original size:16 final size:16
Alignment explanation
Indices: 3614760--3614792 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3614750 AAAAAAATTT
3614760 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3614776 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3614792 T
1 T
3614793 CTATTTATTA
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:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:3615877 original size:15 final size:16
Alignment explanation
Indices: 3615857--3615888 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3615847 AAAGAACAAC
3615857 ATAATTTAA-ATTAAT
1 ATAATTTAATATTAAT
3615872 ATAATTTAATATTAAT
1 ATAATTTAATATTAAT
3615888 A
1 A
3615889 CTTTGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTTAATATTAAT
Found at i:3621134 original size:13 final size:14
Alignment explanation
Indices: 3621110--3621139 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3621100 AATGAACATT
*
3621110 ATTTTTTCAAAATA
1 ATTTTTTAAAAATA
3621124 ATTTTTTAAAAATA
1 ATTTTTTAAAAATA
3621138 AT
1 AT
3621140 CTCAAACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTTTTAAAAATA
Found at i:3625562 original size:23 final size:24
Alignment explanation
Indices: 3625514--3625563 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
3625504 ACCATAAATC
* *
3625514 AGAGAGGAGAACAAGATAAATAAA
1 AGAGAGGAGAACAAGAAAAACAAA
3625538 AGAGA-GAGAACAA-AAAAACACAA
1 AGAGAGGAGAACAAGAAAAACA-AA
3625561 AGA
1 AGA
3625564 AAAAAGAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 13 0.57
24 5 0.22
ACGTcount: A:0.66, C:0.08, G:0.22, T:0.04
Consensus pattern (24 bp):
AGAGAGGAGAACAAGAAAAACAAA
Found at i:3626840 original size:21 final size:20
Alignment explanation
Indices: 3626754--3626911 Score: 95
Period size: 21 Copynumber: 7.8 Consensus size: 20
3626744 AAATGACCAA
**
3626754 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3626773 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* **
3626793 CAGAATCGCAAATC-ATTTT
1 CAAAATCGCAACGCGATTTT
3626812 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGATT-TT
* * * *
3626834 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3626855 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3626875 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3626896 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3626912 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 17 0.16
20 37 0.36
21 48 0.46
22 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3626902 original size:20 final size:20
Alignment explanation
Indices: 3626878--3627125 Score: 241
Period size: 20 Copynumber: 12.5 Consensus size: 20
3626868 CGATTTTCCA
** *
3626878 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
3626898 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
3626918 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
3626938 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
3626958 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
** *
3626978 AAATCGCAGTGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3626998 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3627018 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
3627038 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3627058 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
3627078 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3627098 -AATCGCAACG-AAATCTGT
1 AAATCGCAACGCGAATCCGT
*
3627116 AAATCACAAC
1 AAATCGCAAC
3627126 ACTGAAATTT
Statistics
Matches: 197, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
18 6 0.03
19 18 0.09
20 172 0.87
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:3628038 original size:12 final size:12
Alignment explanation
Indices: 3628021--3628045 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3628011 ATATAATCCT
3628021 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3628033 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3628045 G
1 G
3628046 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3630165 original size:19 final size:19
Alignment explanation
Indices: 3630125--3630222 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
3630115 GATTCTCTCG
3630125 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3630145 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3630164 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3630178 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3630197 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3630216 TTGCGAT
1 TTGCGAT
3630223 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3630219 original size:52 final size:53
Alignment explanation
Indices: 3630106--3630222 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
3630096 GAAATGAAAA
3630106 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
3630159 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
3630211 TCGCATTGCGAT
1 TCGCATTGCGAT
3630223 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:3630348 original size:14 final size:14
Alignment explanation
Indices: 3630329--3630365 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3630319 CATCAATTAC
3630329 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3630343 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3630357 ACAAATCAA
1 ACAAATCAA
3630366 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3632364 original size:14 final size:14
Alignment explanation
Indices: 3632345--3632401 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3632335 GCGAAATGAA
*
3632345 AATCGCAACGACAG
1 AATCGCAACGAAAG
3632359 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
3632376 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3632392 AATCGCAACG
1 AATCGCAACG
3632402 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3632372 original size:33 final size:33
Alignment explanation
Indices: 3632326--3632418 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3632316 GCGAAACCAA
*
3632326 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3632359 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3632392 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3632419 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3632383 original size:19 final size:19
Alignment explanation
Indices: 3632289--3632423 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3632279 TAGTTTACTT
* *
3632289 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3632309 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3632328 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3632347 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3632361 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3632380 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3632394 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3632413 TCGCAATGCGA
1 TCGCAACGCGA
3632424 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3632441 original size:19 final size:19
Alignment explanation
Indices: 3632419--3632547 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3632409 AAAATCGCAA
3632419 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3632438 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3632452 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3632471 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3632485 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3632504 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3632523 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3632543 TGCGA
1 TGCGA
3632548 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3632461 original size:33 final size:33
Alignment explanation
Indices: 3632419--3632510 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3632409 AAAATCGCAA
3632419 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3632452 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3632485 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3632511 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3632750 original size:93 final size:93
Alignment explanation
Indices: 3632591--3633157 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
3632581 TTGAATGGAT
3632591 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3632656 AGTTTAGCAGAATTGGTAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
3632684 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3632749 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3632777 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3632842 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
3632870 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3632935 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3632963 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3633028 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3633056 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3633121 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3633149 AAATTTACT
1 AAATTTACT
3633158 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 468 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3634883 original size:14 final size:14
Alignment explanation
Indices: 3634864--3634953 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3634854 TTGAAATGAA
3634864 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3634878 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
3634895 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
3634911 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3634930 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3634944 AATCGCAACG
1 AATCGCAACG
3634954 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3634901 original size:33 final size:33
Alignment explanation
Indices: 3634856--3634970 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3634846 TCTTTTGGTT
3634856 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3634889 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3634922 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3634955 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3634971 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3634902 original size:19 final size:18
Alignment explanation
Indices: 3634863--3634975 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
3634853 GTTGAAATGA
3634863 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
3634878 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
3634895 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
3634911 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
3634928 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
3634944 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
3634961 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
3634976 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:3635008 original size:14 final size:14
Alignment explanation
Indices: 3634989--3635040 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
3634979 TGGTTTCGCA
3634989 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
3635003 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
3635022 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
3635036 TTGCG
1 TTGCG
3635041 CTTTTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 15 0.48
16 3 0.10
17 3 0.10
19 10 0.32
ACGTcount: A:0.08, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:3635019 original size:33 final size:33
Alignment explanation
Indices: 3634971--3635051 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
3634961 AAAATCGCAA
**
3634971 TGCGATTTTGGTTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
3635004 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
3635037 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
3635052 TCTCGTTGCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.09, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:3635087 original size:41 final size:41
Alignment explanation
Indices: 3635027--3635104 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
3635017 TCGCGTTGCG
* *
3635027 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
3635068 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
3635105 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:3635103 original size:21 final size:21
Alignment explanation
Indices: 3635028--3635103 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3635018 CGCGTTGCGA
*
3635028 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
3635049 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3635069 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
3635090 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
3635104 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3635230 original size:33 final size:33
Alignment explanation
Indices: 3635183--3635253 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
3635173 AATACTAACT
* *
3635183 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3635216 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3635249 TGAAA
1 TGAAA
3635254 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3635654 original size:20 final size:20
Alignment explanation
Indices: 3635629--3635822 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3635619 CTTTAAATAT
3635629 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3635649 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3635671 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3635690 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3635710 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3635730 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3635750 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3635770 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3635790 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3635810 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3635823 TGGCAAAACG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3635816 original size:60 final size:60
Alignment explanation
Indices: 3635629--3635822 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3635619 CTTTAAATAT
**
3635629 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3635690 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3635750 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3635810 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3635823 TGGCAAAACG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3636355 original size:28 final size:28
Alignment explanation
Indices: 3636298--3636369 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
3636288 ACTATACATA
* * *
3636298 TGTATATATTATATTTATATACTTATTT
1 TGTACATATTATATTTATATACATAGTT
3636326 TGTACATATTATATTTATATACATAGTT
1 TGTACATATTATATTTATATACATAGTT
*
3636354 TGCTACTTATTTATAT
1 TG-TACATA-TTATAT
3636370 ACTTTTCATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 27 0.71
29 5 0.13
30 6 0.16
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.56
Consensus pattern (28 bp):
TGTACATATTATATTTATATACATAGTT
Found at i:3636733 original size:5 final size:5
Alignment explanation
Indices: 3636723--3636773 Score: 61
Period size: 5 Copynumber: 10.4 Consensus size: 5
3636713 AACTATTATA
**
3636723 ATTTT ATTTT ATTTT A-TTT ATGCT ATTTT -TTATT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATT-TT ATTTT ATTTT ATTTT
3636772 AT
1 AT
3636774 GTTCATAGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 6 0.15
5 31 0.79
6 2 0.05
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:3637235 original size:12 final size:13
Alignment explanation
Indices: 3637212--3637237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3637202 AATTAATTCC
3637212 AAATCAAAAAAAA
1 AAATCAAAAAAAA
3637225 AAATCAAAAAAAA
1 AAATCAAAAAAAA
3637238 GTCATAATTA
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:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAATCAAAAAAAA
Found at i:3639719 original size:4 final size:4
Alignment explanation
Indices: 3639710--3639761 Score: 59
Period size: 4 Copynumber: 12.0 Consensus size: 4
3639700 CCCTTTCTCT
*
3639710 TTTC TTTC TTTC TTTC TTTCCC TTAC ATTTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTT--C TTTC --TTTC TTTC TTTC TTTC TTTC
3639758 TTTC
1 TTTC
3639762 CCTTACAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 36 0.86
6 6 0.14
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:3641336 original size:56 final size:56
Alignment explanation
Indices: 3641200--3641337 Score: 240
Period size: 56 Copynumber: 2.5 Consensus size: 56
3641190 TCGAACTTAC
* *
3641200 TGCATGAATCGCATTACTGCATTCATTCAAACTTCTGACCTCTCATGAAGACTTTT
1 TGCATGAATCACATTACCGCATTCATTCAAACTTCTGACCTCTCATGAAGACTTTT
*
3641256 TGCATGAATCACATTACCACATTCATTCAAACTTCTGACCTCTCATGAAGACTTTT
1 TGCATGAATCACATTACCGCATTCATTCAAACTTCTGACCTCTCATGAAGACTTTT
*
3641312 TGCATGAATCACATTACCGTATTCAT
1 TGCATGAATCACATTACCGCATTCAT
3641338 GAGTGCATTA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 77 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (56 bp):
TGCATGAATCACATTACCGCATTCATTCAAACTTCTGACCTCTCATGAAGACTTTT
Found at i:3650476 original size:3 final size:3
Alignment explanation
Indices: 3650468--3650493 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3650458 CATGAAGTAA
3650468 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3650494 AAAAGGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3657159 original size:29 final size:29
Alignment explanation
Indices: 3657117--3657175 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3657107 CTCCCATCAT
3657117 CTAGAACATGGGAGAAACCAACACCTATG
1 CTAGAACATGGGAGAAACCAACACCTATG
3657146 CTAGAACATGGGAGAAACCAACACCTATG
1 CTAGAACATGGGAGAAACCAACACCTATG
3657175 C
1 C
3657176 AAATGCCTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (29 bp):
CTAGAACATGGGAGAAACCAACACCTATG
Found at i:3676822 original size:16 final size:17
Alignment explanation
Indices: 3676798--3676837 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3676788 GGTATTGTAT
*
3676798 TTATGTTATTTT-TATA
1 TTATTTTATTTTATATA
*
3676814 TTATTTTATTTTATATT
1 TTATTTTATTTTATATA
3676831 TTATTTT
1 TTATTTT
3676838 TTATGCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (17 bp):
TTATTTTATTTTATATA
Found at i:3678618 original size:2 final size:2
Alignment explanation
Indices: 3678613--3678642 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3678603 GTTTCTCTCT
3678613 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3678643 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3678647 original size:2 final size:2
Alignment explanation
Indices: 3678642--3678686 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3678632 ACACACACAC
3678642 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3678683 AT AT
1 AT AT
3678687 TAGAATAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3684307 original size:35 final size:35
Alignment explanation
Indices: 3684249--3684395 Score: 167
Period size: 35 Copynumber: 4.2 Consensus size: 35
3684239 TGAAATTATT
***
3684249 AAAATGGTTTTC-AAGTTTGGTAAA-CAACTTTGAA
1 AAAATGGTTTTCAAAGTTTGGTAAAGTTTCTTTG-A
3684283 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-
1 AAAATGGTTTTCAAAGTTTGGTAAA-GTTTCTTTGA
3684318 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAAA-GTTTCTTTGA
* * *
3684354 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTA-AAGTTTCTTTGA
3684390 AAAATG
1 AAAATG
3684396 ATAATGGGAT
Statistics
Matches: 101, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
34 12 0.12
35 48 0.48
36 14 0.14
37 26 0.26
38 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.41
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAAGTTTCTTTGA
Found at i:3684308 original size:21 final size:21
Alignment explanation
Indices: 3684284--3684344 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3684274 AACTTTGAAA
3684284 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
3684305 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
3684319 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
3684340 AAATG
1 AAATG
3684345 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:3684375 original size:37 final size:37
Alignment explanation
Indices: 3684276--3684394 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
3684266 TGGTAAACAA
3684276 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
3684313 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
3684348 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
3684385 -GTTGAAAAAT
1 CTTTGAAAAAT
3684395 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:3684395 original size:72 final size:69
Alignment explanation
Indices: 3684249--3684392 Score: 184
Period size: 72 Copynumber: 2.1 Consensus size: 69
3684239 TGAAATTATT
3684249 AAAATGGTTTTCAAGTTTGGTAAACAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 AAAATGGTTTTCAAGTTTGGTAAACAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
*
3684314 TTTG
66 GTTG
*** * *
3684318 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-AAAAATAGTTTTTCAAAGTTTGGTAGATG
1 AAAATGGTTTTC-AAGTTTGGTAAA--CAACTTTGAAAAAAT-GGTTTTCAAAGTTTGGTAAATG
3684382 TTT-GTTG
62 TTTCGTTG
3684389 AAAA
1 AAAA
3684393 ATGATAATGG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
69 12 0.18
70 12 0.18
71 13 0.20
72 28 0.43
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (69 bp):
AAAATGGTTTTCAAGTTTGGTAAACAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
GTTG
Found at i:3688882 original size:21 final size:21
Alignment explanation
Indices: 3688858--3688918 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3688848 AACTTTGAAA
3688858 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
3688879 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
3688893 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
3688914 AAATG
1 AAATG
3688919 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:3688949 original size:37 final size:37
Alignment explanation
Indices: 3688850--3688968 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
3688840 TGGTAACCAA
3688850 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
3688887 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
3688922 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
3688959 -GTTGAAAAAT
1 CTTTGAAAAAT
3688969 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:3697075 original size:2 final size:2
Alignment explanation
Indices: 3697068--3697120 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3697058 TGAGACATGA
3697068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3697110 AT AT AT AT AT A
1 AT AT AT AT AT A
3697121 ATTAACAAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3710704 original size:68 final size:65
Alignment explanation
Indices: 3710621--3710784 Score: 222
Period size: 67 Copynumber: 2.5 Consensus size: 65
3710611 GAATTAAATT
* *
3710621 GAACATCGAATGCATTTCTTGCATCAAATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTA
1 GAACATCGAATGCATTTCATGCATC-AATGCACCAGCCATACATCGATGCACTCTGGCTA-TTT-
3710686 TGA
63 TGA
* * *
3710689 GAACATCGAATGCATTTGATGCATCAATGCACTAGCCATACATCGATGCACTTTGGCTATTTTGA
1 GAACATCGAATGCATTTCATGCATCAATGCACCAGCCATACATCGATGCACTCTGGCTATTTTGA
* * *
3710754 -AACATCGAATGCACTTGATGCATCGATGCAC
1 GAACATCGAATGCATTTCATGCATCAATGCAC
3710785 TAAGGGTTCA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
64 29 0.33
65 3 0.03
66 3 0.03
67 31 0.35
68 23 0.26
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (65 bp):
GAACATCGAATGCATTTCATGCATCAATGCACCAGCCATACATCGATGCACTCTGGCTATTTTGA
Found at i:3710740 original size:67 final size:65
Alignment explanation
Indices: 3710621--3710786 Score: 235
Period size: 64 Copynumber: 2.5 Consensus size: 65
3710611 GAATTAAATT
** * *
3710621 GAACATCGAATGCATTTCTTGCATCAAATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTA
1 GAACATCGAATGCATTTGATGCATC-AATGCACTAGCCATACATCGATGCACTCTGGCTA-TTT-
3710686 TGA
63 TGA
*
3710689 GAACATCGAATGCATTTGATGCATCAATGCACTAGCCATACATCGATGCACTTTGGCTATTTTGA
1 GAACATCGAATGCATTTGATGCATCAATGCACTAGCCATACATCGATGCACTCTGGCTATTTTGA
* *
3710754 -AACATCGAATGCACTTGATGCATCGATGCACTA
1 GAACATCGAATGCATTTGATGCATCAATGCACTA
3710787 AGGGTTCAAT
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
64 31 0.34
65 3 0.03
66 3 0.03
67 31 0.34
68 23 0.25
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (65 bp):
GAACATCGAATGCATTTGATGCATCAATGCACTAGCCATACATCGATGCACTCTGGCTATTTTGA
Found at i:3718038 original size:21 final size:21
Alignment explanation
Indices: 3717996--3718039 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3717986 ACCCCAGGAG
* *
3717996 CTAGCTTTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
3718017 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
3718038 CT
1 CT
3718040 CCTCCTCCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:3718634 original size:2 final size:2
Alignment explanation
Indices: 3718627--3718653 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3718617 AAGCTTAAGC
3718627 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 T
3718654 CAATGGGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3719267 original size:65 final size:64
Alignment explanation
Indices: 3719089--3719278 Score: 194
Period size: 65 Copynumber: 2.9 Consensus size: 64
3719079 TATCAAAGTG
* * * *
3719089 ATGCACCGATGCACCA-ATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCAT
1 ATGCATCGATGCA-CATA-CCATGCACCGATGCACTCA-GGATTATA-TGAAACATCGAATGCAT
3719151 TTC
62 TTC
* *
3719154 ATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTATATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACATACCATGCACCGATGCACTCAGGATTATATG-AAACATCGAATGCATTTC
* *
3719219 ATGCATCGATGCATCAT-CCATGCATCGATGCACTCTGGCTATT-T-TGAAACATCGAATGCA
1 ATGCATCGATGCA-CATACCATGCACCGATGCACTCAGG--ATTATATGAAACATCGAATGCA
3719279 CTCTTAGTGC
Statistics
Matches: 109, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
63 2 0.02
64 37 0.34
65 63 0.58
66 4 0.04
67 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACATACCATGCACCGATGCACTCAGGATTATATGAAACATCGAATGCATTTC
Found at i:3719298 original size:19 final size:19
Alignment explanation
Indices: 3719274--3719318 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
3719264 GAAACATCGA
3719274 ATGCACTCTTAGTGCACCG
1 ATGCACTCTTAGTGCACCG
3719293 ATGCACTCTTAGTGCACCG
1 ATGCACTCTTAGTGCACCG
3719312 ATGCACT
1 ATGCACT
3719319 AAGGGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (19 bp):
ATGCACTCTTAGTGCACCG
Found at i:3729321 original size:5 final size:5
Alignment explanation
Indices: 3729311--3729381 Score: 142
Period size: 5 Copynumber: 14.2 Consensus size: 5
3729301 ACATAGTTAT
3729311 ACAAC ACAAC ACAAC ACAAC ACAAC ACAAC ACAAC ACAAC ACAAC ACAAC
1 ACAAC ACAAC ACAAC ACAAC ACAAC ACAAC ACAAC ACAAC ACAAC ACAAC
3729361 ACAAC ACAAC ACAAC ACAAC A
1 ACAAC ACAAC ACAAC ACAAC A
3729382 TAATATAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 66 1.00
ACGTcount: A:0.61, C:0.39, G:0.00, T:0.00
Consensus pattern (5 bp):
ACAAC
Found at i:3731894 original size:13 final size:14
Alignment explanation
Indices: 3731867--3731893 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3731857 GATTTAAAAA
3731867 AATTAGATTTTTTT
1 AATTAGATTTTTTT
3731881 AATTAGATTTTTT
1 AATTAGATTTTTT
3731894 ATTTTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
AATTAGATTTTTTT
Found at i:3737328 original size:140 final size:140
Alignment explanation
Indices: 3737076--3737359 Score: 550
Period size: 140 Copynumber: 2.0 Consensus size: 140
3737066 GTATGTATGG
3737076 ATTTGACGGCAAGGGCGGTTGCATCCCATTATTTTGGGAAAATAATTAAATTTAACTTGATATGT
1 ATTTGACGGCAAGGGCGGTTGCATCCCATTATTTTGGGAAAATAATTAAATTTAACTTGATATGT
*
3737141 TAATGAAACAAGAAAAAATAAATATTTTGCATACCCATTATTTTTAAAAAGAGAAAATTAAAATT
66 TAAGGAAACAAGAAAAAATAAATATTTTGCATACCCATTATTTTTAAAAAGAGAAAATTAAAATT
3737206 TTAGACCCCA
131 TTAGACCCCA
*
3737216 ATTTGACGGCAAGGGCGGTTGCATTCCATTATTTTGGGAAAATAATTAAATTTAACTTGATATGT
1 ATTTGACGGCAAGGGCGGTTGCATCCCATTATTTTGGGAAAATAATTAAATTTAACTTGATATGT
3737281 TAAGGAAACAAGAAAAAATAAATATTTTGCATACCCATTATTTTTAAAAAGAGAAAATTAAAATT
66 TAAGGAAACAAGAAAAAATAAATATTTTGCATACCCATTATTTTTAAAAAGAGAAAATTAAAATT
3737346 TTAGACCCCA
131 TTAGACCCCA
3737356 ATTT
1 ATTT
3737360 TAAATTTCTA
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (140 bp):
ATTTGACGGCAAGGGCGGTTGCATCCCATTATTTTGGGAAAATAATTAAATTTAACTTGATATGT
TAAGGAAACAAGAAAAAATAAATATTTTGCATACCCATTATTTTTAAAAAGAGAAAATTAAAATT
TTAGACCCCA
Done.