Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007450.1 Hibiscus syriacus cultivar Beakdansim tig00020387_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: 46788
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:3319 original size:31 final size:31
Alignment explanation
Indices: 3281--3350 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
3271 CCTGAGAGCA
* *
3281 TACCCAAG-AAAGTTCTCAGGGCCACGGGGCC
1 TACCCAAGTAAA-ATCTCAGGGCCACAGGGCC
** *
3312 TACCCAAGTAAAATCTCAGGGTTACAGTGCC
1 TACCCAAGTAAAATCTCAGGGCCACAGGGCC
3343 TACCCAAG
1 TACCCAAG
3351 GGTTGCCTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (31 bp):
TACCCAAGTAAAATCTCAGGGCCACAGGGCC
Found at i:7712 original size:16 final size:16
Alignment explanation
Indices: 7691--7750 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
7681 GAATATTTAA
7691 TTTTTATATTTAATAT
1 TTTTTATATTTAATAT
7707 TTTTTATATTTAAT-T
1 TTTTTATATTTAATAT
*
7722 TTTTGAATATTTGAATA-
1 TTTT-TATATTT-AATAT
*
7739 ATTTTATATTTA
1 TTTTTATATTTA
7751 TAATTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.16
16 26 0.68
17 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTTATATTTAATAT
Found at i:7744 original size:32 final size:29
Alignment explanation
Indices: 7683--7750 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 29
7673 TCTAATATGA
*
7683 ATATTTAATTTTTATATTTAATATTTTTT
1 ATATTTAATTTTTATATTTAATATATTTT
7712 ATATTTAATTTTTTGAATATTTGAATA-ATTTT
1 ATATTTAA-TTTTT--ATATTT-AATATATTTT
7744 ATATTTA
1 ATATTTA
7751 TAATTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 8 0.24
30 5 0.15
32 17 0.50
33 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (29 bp):
ATATTTAATTTTTATATTTAATATATTTT
Found at i:7764 original size:48 final size:45
Alignment explanation
Indices: 7680--7772 Score: 107
Period size: 48 Copynumber: 2.0 Consensus size: 45
7670 ATTTCTAATA
***
7680 TGAATATTTAATTTTTATATTTAATATTTTTTATATTTAATTTTT
1 TGAATATTTAATTTTTATATTTAATATTTAAAATATTTAATTTTT
*
7725 TGAATATTTGAATAATTTTATATTT-ATAATTTAAAATATTTTATTTTT
1 TGAATATTT-AAT--TTTTATATTTAAT-ATTTAAAATATTTAATTTTT
7773 AAAATAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 9 0.22
46 3 0.08
47 2 0.05
48 26 0.65
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (45 bp):
TGAATATTTAATTTTTATATTTAATATTTAAAATATTTAATTTTT
Found at i:9306 original size:24 final size:24
Alignment explanation
Indices: 9101--9297 Score: 313
Period size: 24 Copynumber: 8.2 Consensus size: 24
9091 AAACATAATT
* * *
9101 CAGGTCAAGTAGCAGATCAGAATC
1 CAGGTCAAGTATCATATCAAAATC
* *
9125 CATGTCAAGTATCATATAAAAATC
1 CAGGTCAAGTATCATATCAAAATC
*
9149 CAGGTCAAGTATCATATAAAAATC
1 CAGGTCAAGTATCATATCAAAATC
9173 CAGGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATCAAAATC
*
9197 CAAGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATCAAAATC
9221 CAGGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATCAAAATC
*
9245 CAAGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATCAAAATC
*
9269 CAGGTCAAGTATCATATCAAAATT
1 CAGGTCAAGTATCATATCAAAATC
9293 CAGGT
1 CAGGT
9298 TAAAAATCAG
Statistics
Matches: 161, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 161 1.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAAAATC
Found at i:10106 original size:28 final size:29
Alignment explanation
Indices: 10065--10121 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
10055 AAAATATCAT
* *
10065 TTTTTAAAAAAATTA-TAAAATAACACCA
1 TTTTCAAAAAAATTACCAAAATAACACCA
* *
10093 TTTTCAAAATAATTACCAAAATATCACCA
1 TTTTCAAAAAAATTACCAAAATAACACCA
10122 GGTCAACAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (29 bp):
TTTTCAAAAAAATTACCAAAATAACACCA
Found at i:10144 original size:17 final size:18
Alignment explanation
Indices: 10122--10162 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
10112 AATATCACCA
10122 GGTCAAC-AGTCAGGTCG
1 GGTCAACGAGTCAGGTCG
* *
10139 GGTCAACGGGTCGGGTCG
1 GGTCAACGAGTCAGGTCG
10157 GGTCAA
1 GGTCAA
10163 TGGGTTGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.17
Consensus pattern (18 bp):
GGTCAACGAGTCAGGTCG
Found at i:10157 original size:18 final size:18
Alignment explanation
Indices: 10134--10187 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
10124 TCAACAGTCA
10134 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
* *
10152 GGTCGGGTCAATGGGTTG
1 GGTCGGGTCAACGGGTCG
*
10170 GGTCGGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCG
10188 AGTTGGAACC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.13, C:0.17, G:0.50, T:0.20
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:16552 original size:24 final size:24
Alignment explanation
Indices: 16419--16543 Score: 214
Period size: 24 Copynumber: 5.2 Consensus size: 24
16409 AAACATAATT
16419 CAGGTCAAGTATCATATAAAAATC
1 CAGGTCAAGTATCATATAAAAATC
16443 CAGGTCAAGTATCATATAAAAATC
1 CAGGTCAAGTATCATATAAAAATC
16467 CAGGTCAAGTATCATATAAAAATC
1 CAGGTCAAGTATCATATAAAAATC
* *
16491 CAGGTCAAGTATCATATCAAAATT
1 CAGGTCAAGTATCATATAAAAATC
* *
16515 CAGGTCAAGTATCATATCAAAATT
1 CAGGTCAAGTATCATATAAAAATC
16539 CAGGT
1 CAGGT
16544 TAAAAATCAG
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 99 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (24 bp):
CAGGTCAAGTATCATATAAAAATC
Found at i:16558 original size:72 final size:72
Alignment explanation
Indices: 16419--16558 Score: 208
Period size: 72 Copynumber: 1.9 Consensus size: 72
16409 AAACATAATT
** *
16419 CAGGTCAAGTATCATATAAAAATCCAGGTCAAGTATCATATAAAAATCCAGGTCAAGTATCATAT
1 CAGGTCAAGTATCATATAAAAATCCAGGTCAAGTATCATATAAAAATCCAGGTCAAAAATCAGAT
16484 AAAAATC
66 AAAAATC
* * * * *
16491 CAGGTCAAGTATCATATCAAAATTCAGGTCAAGTATCATATCAAAATTCAGGTTAAAAATCAGAT
1 CAGGTCAAGTATCATATAAAAATCCAGGTCAAGTATCATATAAAAATCCAGGTCAAAAATCAGAT
16556 AAA
66 AAA
16559 CTATTTATGT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.26
Consensus pattern (72 bp):
CAGGTCAAGTATCATATAAAAATCCAGGTCAAGTATCATATAAAAATCCAGGTCAAAAATCAGAT
AAAAATC
Found at i:17303 original size:29 final size:29
Alignment explanation
Indices: 17271--17351 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
17261 CAATTTTTAA
* *
17271 AAAAAAATTACAAAAATAGCACCATTTCC
1 AAAATAATTACAAAAATACCACCATTTCC
* * *
17300 AAAATAATTACCAAAATACCATCATTTTC
1 AAAATAATTACAAAAATACCACCATTTCC
*
17329 AAAATAATTACAAAAATATCACC
1 AAAATAATTACAAAAATACCACC
17352 TAAAATTACG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.54, C:0.20, G:0.01, T:0.25
Consensus pattern (29 bp):
AAAATAATTACAAAAATACCACCATTTCC
Found at i:17448 original size:18 final size:18
Alignment explanation
Indices: 17425--17477 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
17415 AATATCACCA
17425 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
17443 GGTCAACGGGTTGGGTCG
1 GGTCAACGGGTCGGGTCG
*
17461 GGTAAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
17478 AGGTTGGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.13, C:0.19, G:0.49, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:22744 original size:27 final size:27
Alignment explanation
Indices: 22706--22770 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
22696 TTTCTGCAGC
* *
22706 CTGAAAATGAACAAACTCAAAATTAAA
1 CTGAAACTGAACAAACTCAAAATCAAA
*
22733 CTGAAACTGAACAAACTCGAAATCAAA
1 CTGAAACTGAACAAACTCAAAATCAAA
*
22760 TTGAAACTGAA
1 CTGAAACTGAA
22771 ATGAAGAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.54, C:0.17, G:0.11, T:0.18
Consensus pattern (27 bp):
CTGAAACTGAACAAACTCAAAATCAAA
Found at i:24306 original size:87 final size:86
Alignment explanation
Indices: 24160--24421 Score: 346
Period size: 87 Copynumber: 3.0 Consensus size: 86
24150 ATATTATTTA
* * *
24160 ACTAGAAATATTATCAAGCACAATAATATATTAAGTACCACTTATATAATGTAATAGGTATGACT
1 ACTAGAAATATTATCAAGCACAATAACATATTAGGTACAACTTATATAATGTAATAGGTATG-CT
24225 TATATAATAAAAT-TGGTTAATT
65 TATATAATAAAATAT-GTTAATT
* * *
24247 ACTAGAAACATTATCAAACACAATAACATATTAGGTACAACTTATATAATGTAATAGGTAGCGCT
1 ACTAGAAATATTATCAAGCACAATAACATATTAGGTACAACTTATATAATGTAATAGGTA-TGCT
24312 TATATAATAAAATATGTTAATT
65 TATATAATAAAATATGTTAATT
* * *** * *
24334 ACCATAAATATTATCAAGCACAATAACATATTAGGTATTTCTTATATAACGTAATAGGTAGTGGT
1 ACTAGAAATATTATCAAGCACAATAACATATTAGGTACAACTTATATAATGTAATAGGTA-TGCT
* *
24399 TAGATAATAAAATATATTAATT
65 TATATAATAAAATATGTTAATT
24421 A
1 A
24422 TTTAATTTGT
Statistics
Matches: 155, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
87 153 0.99
88 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (86 bp):
ACTAGAAATATTATCAAGCACAATAACATATTAGGTACAACTTATATAATGTAATAGGTATGCTT
ATATAATAAAATATGTTAATT
Found at i:24827 original size:23 final size:23
Alignment explanation
Indices: 24797--24875 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
24787 AACATGTTTT
* **
24797 ATTATATAAGCGTTATTTATTAC
1 ATTATATAAGCGCTACCTATTAC
*
24820 ATTATATAAACGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
*
24843 ATTATATAAGTGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
24866 ATTATATAAG
1 ATTATATAAG
24876 TGATATCTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTATTAC
Found at i:24893 original size:23 final size:23
Alignment explanation
Indices: 24817--24887 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
24807 CGTTATTTAT
** * *
24817 TACATTATATAAACGCTACCTAT
1 TACATTATATAAGTGATACCTAA
* *
24840 TACATTATATAAGTGCTACCTAT
1 TACATTATATAAGTGATACCTAA
*
24863 TACATTATATAAGTGATATCTAA
1 TACATTATATAAGTGATACCTAA
24886 TA
1 TA
24888 TGTTATTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.38
Consensus pattern (23 bp):
TACATTATATAAGTGATACCTAA
Found at i:24972 original size:23 final size:23
Alignment explanation
Indices: 24921--24974 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
24911 CCAATAATTA
** * *
24921 ATCTATTTTATTATATAAGCGCT
1 ATCTATTAGATTATATAAACACT
*
24944 ACCTATTAGATTATATAAACACT
1 ATCTATTAGATTATATAAACACT
24967 ATCTATTA
1 ATCTATTA
24975 CATCATATTT
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:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (23 bp):
ATCTATTAGATTATATAAACACT
Found at i:28707 original size:22 final size:21
Alignment explanation
Indices: 28682--28724 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
28672 TAGATTAGTT
28682 TTAAAATATAAACATATAAATA
1 TTAAAATATAAACATA-AAATA
* * *
28704 TTAAGATTTAAACCTAAAATA
1 TTAAAATATAAACATAAAATA
28725 ATACCAAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAACATAAAATA
Found at i:30541 original size:11 final size:12
Alignment explanation
Indices: 30522--30560 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
30512 TTAATAGTGT
30522 AATTTATCTTAA
1 AATTTATCTTAA
30534 AA-TTATCTTAAAA
1 AATTTATCTT--AA
30547 AATTTATCTTAA
1 AATTTATCTTAA
30559 AA
1 AA
30561 ATTTTGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 7 0.29
12 6 0.25
13 4 0.17
14 7 0.29
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTTATCTTAA
Found at i:30555 original size:14 final size:14
Alignment explanation
Indices: 30522--30561 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
30512 TTAATAGTGT
30522 AATTTATCTT--AA
1 AATTTATCTTAAAA
30534 AA-TTATCTTAAAA
1 AATTTATCTTAAAA
30547 AATTTATCTTAAAA
1 AATTTATCTTAAAA
30561 A
1 A
30562 TTTTGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.28
12 2 0.08
13 4 0.16
14 12 0.48
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTTATCTTAAAA
Found at i:30575 original size:13 final size:13
Alignment explanation
Indices: 30522--30564 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
30512 TTAATAGTGT
30522 AATTTATCTT-AA
1 AATTTATCTTAAA
30534 AA-TTATCTTAAAA
1 AATTTATCTT-AAA
30547 AATTTATCTTAAA
1 AATTTATCTTAAA
30560 AATTT
1 AATTT
30565 TGTTGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.25
12 2 0.07
13 12 0.43
14 7 0.25
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTATCTTAAA
Found at i:31683 original size:23 final size:23
Alignment explanation
Indices: 31657--31719 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
31647 ATATAACCAC
31657 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
31680 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
31703 TACCTATTACATCATAT
1 TACCTATTACATTATAT
31720 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:32099 original size:431 final size:431
Alignment explanation
Indices: 31296--32352 Score: 1947
Period size: 431 Copynumber: 2.5 Consensus size: 431
31286 TATTACATTA
*
31296 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGACACTTCTTTTAAAGTTATGTAAT
*
31361 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTA
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
* *
31426 ATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATATTAAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
31491 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAAGAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAAGAT
31556 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACT
31621 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
326 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
*
31686 TTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TTACATTATATAAGCGCTACCTATCACATCATATTTTTACC
31727 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGACACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGACACTTCTTTTAAAGTTATGTAAT
31792 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
* * *
31857 AGTTGCACAAAAAATTATTTGATTGTTGTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
* * *
31922 AATAATAATATATATTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAAGAT
* *
31987 CTTAAAACTCACTCAAAGGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACT
*
32052 TTTATAAAAAGGATAGATACTTTACAATATAATCACTACCTATTACATTATATAAACGATACCTA
326 TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
32117 TTACATTATATAAGCGCTACCTATCACATCATATTTTTACC
391 TTACATTATATAAGCGCTACCTATCACATCATATTTTTACC
*
32158 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAAGATCGACACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGACACTTCTTTTAAAGTTATGTAAT
*
32223 TTATGTTTCAA-TTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
32287 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
32351 AA
196 AA
32353 CAACATTAAC
Statistics
Matches: 606, Mismatches: 20, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
429 10 0.02
430 104 0.17
431 492 0.81
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (431 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGACACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTT
AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACCTATAATTACTAAATTAAGAT
CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACT
TTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
TTACATTATATAAGCGCTACCTATCACATCATATTTTTACC
Found at i:32114 original size:23 final size:23
Alignment explanation
Indices: 32088--32150 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
32078 ATATAATCAC
32088 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
32111 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
* *
32134 TACCTATCACATCATAT
1 TACCTATTACATTATAT
32151 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:32622 original size:39 final size:39
Alignment explanation
Indices: 32568--32654 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
32558 TCAAGTTGTA
*
32568 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
32607 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
32646 GATTTTGAT
1 GATTTTGAT
32655 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:32950 original size:18 final size:18
Alignment explanation
Indices: 32927--32963 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
32917 CGAAATATAT
32927 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
32945 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
32963 A
1 A
32964 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:33397 original size:24 final size:25
Alignment explanation
Indices: 33349--33397 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
33339 ATTATTTTTC
* *
33349 CAAATAATGTACCCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
33374 CAAATAATATA-CCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
33398 TAATTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:33707 original size:23 final size:23
Alignment explanation
Indices: 33681--33743 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
33671 ATATAACCAC
33681 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
33704 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
33727 TACCTATTACATCATAT
1 TACCTATTACATTATAT
33744 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:34144 original size:25 final size:25
Alignment explanation
Indices: 34087--34152 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
34077 CAATCAAAAG
*
34087 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
34112 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
34137 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
34153 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:37320 original size:183 final size:183
Alignment explanation
Indices: 36619--37287 Score: 1156
Period size: 183 Copynumber: 3.7 Consensus size: 183
36609 TTAAAATTAC
*
36619 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
36684 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACC-G------TATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
36742 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
*
36795 TGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
36860 ATTAAAATGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
36925 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
*
36978 CGACATTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
37043 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAATCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
37108 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
* * *
37161 CGATACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
37225 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
37288 ATAGCATTGC
Statistics
Matches: 469, Mismatches: 16, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
176 108 0.23
177 1 0.00
183 357 0.76
184 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
Found at i:37685 original size:20 final size:21
Alignment explanation
Indices: 37625--37684 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
37615 TCCACAGTGA
* *
37625 AAAAAGTATATACACTTTTAT
1 AAAAAGGATAGACACTTTTAT
37646 AAAAAGGATAGACACTTTTAT
1 AAAAAGGATAGACACTTTTAT
*
37667 AAAAAGGATAGATACTTT
1 AAAAAGGATAGACACTTT
37685 ACAATATAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (21 bp):
AAAAAGGATAGACACTTTTAT
Found at i:37724 original size:23 final size:23
Alignment explanation
Indices: 37698--37760 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
37688 ATATAACCAC
37698 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
37721 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
37744 TACCTATTACATCATAT
1 TACCTATTACATTATAT
37761 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:37801 original size:21 final size:22
Alignment explanation
Indices: 37776--37817 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
37766 CCTATTATAT
*
37776 TAAAAGTG-TCCATACTTTTTA
1 TAAAAATGATCCATACTTTTTA
*
37797 TAAAAATGATCGATACTTTTT
1 TAAAAATGATCCATACTTTTT
37818 TTTAAAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (22 bp):
TAAAAATGATCCATACTTTTTA
Found at i:38155 original size:23 final size:23
Alignment explanation
Indices: 38129--38191 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
38119 ATATAACCAC
38129 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
38152 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
38175 TACCTATTACATCATAT
1 TACCTATTACATTATAT
38192 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:38284 original size:32 final size:32
Alignment explanation
Indices: 38244--38371 Score: 82
Period size: 32 Copynumber: 4.3 Consensus size: 32
38234 GGATCGATAC
38244 TTTTTTTAAAGATATGTAATTTATGTTTCAAT
1 TTTTTTTAAAGATATGTAATTTATGTTTCAAT
* *
38276 TTTTTTT-AAG-TATGT--TTCATGTTTTCCA-
1 TTTTTTTAAAGATATGTAATTTATG-TTTCAAT
** * * *
38304 ----CCTACA-ATAT-TAATTTAATAATTTCACT
1 TTTTTTTAAAGATATGTAATTT-AT-GTTTCAAT
38332 -TTTTTTAAAGATATGTAATTTATGTTTCAAT
1 TTTTTTTAAAGATATGTAATTTATGTTTCAAT
38363 TTTTTTTAA
1 TTTTTTTAA
38372 GTATGTTTCA
Statistics
Matches: 68, Mismatches: 14, Indels: 28
0.62 0.13 0.25
Matches are distributed among these distances:
24 2 0.03
25 4 0.06
26 2 0.03
27 6 0.09
28 5 0.07
29 5 0.07
30 5 0.07
31 12 0.18
32 21 0.31
33 6 0.09
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.55
Consensus pattern (32 bp):
TTTTTTTAAAGATATGTAATTTATGTTTCAAT
Found at i:38335 original size:87 final size:87
Alignment explanation
Indices: 38242--38416 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
38232 AAGGATCGAT
38242 ACTTTTTTTAAAGATATGTAATTTATGTTTCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCT
1 ACTTTTTTTAAAGATATGTAATTTATGTTTCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCT
38307 ACAATATTAATTTAATAATTTC
66 ACAATATTAATTTAATAATTTC
38329 ACTTTTTTTAAAGATATGTAATTTATGTTTCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCT
1 ACTTTTTTTAAAGATATGTAATTTATGTTTCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCT
38394 ACAATATTAATTTAATAATTTC
66 ACAATATTAATTTAATAATTTC
38416 A
1 A
38417 TTTGCACAAA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (87 bp):
ACTTTTTTTAAAGATATGTAATTTATGTTTCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCT
ACAATATTAATTTAATAATTTC
Found at i:38673 original size:23 final size:23
Alignment explanation
Indices: 38647--38709 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
38637 ATATAACCAC
38647 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
38670 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
38693 TACCTATTACATCATAT
1 TACCTATTACATTATAT
38710 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:38788 original size:518 final size:516
Alignment explanation
Indices: 37814--38846 Score: 1969
Period size: 518 Copynumber: 2.0 Consensus size: 516
37804 GATCGATACT
37814 TTTTTTTAAAGATATGTAATTTATGTTTCAATTTTTTTAAGTATGTTTCATGTTTTCCACCTACA
1 TTTTTTTAAAGATATGTAATTTATGTTTCAATTTTTTTAAGTATGTTTCATGTTTTCCACCTACA
*
37879 ATATTAATTTAATAATTTAATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAA
66 ATATTAATTTAATAATTTAATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAA
37944 TATTAAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACCT
131 TATTAAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACCT
38009 ATAATTACTAAATTAAGATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAG
196 ATAATTACTAAATTAAGATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAG
38074 TGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTAC
261 TGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTAC
38139 ATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTA
326 ATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTA
*
38204 TATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATG
391 TATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGATATGTAATTTATG
*
38269 TTTCAATTTTTTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCAC
456 TTTCAA-TTTTTTTAA-TAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCAC
38331 TTTTTTTAAAGATATGTAATTTATGTTTCAATTTTTTTTAAGTATGTTTCATGTTTTCCACCTAC
1 TTTTTTTAAAGATATGTAATTTATGTTTCAA-TTTTTTTAAGTATGTTTCATGTTTTCCACCTAC
*
38396 AATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATA
65 AATATTAATTTAATAATTTAATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATA
*
38461 ATATTAAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCC
130 ATATTAAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACC
*
38526 TATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACA
195 TATAATTACTAAATTAAGATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACA
38591 GTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTA
260 GTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTA
38656 CATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATT
325 CATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATT
*
38721 ATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTAT
390 ATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGATATGTAATTTAT
38786 GTTTCAATTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCA
455 GTTTCAATTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCA
38847 TTTGCACAAA
Statistics
Matches: 507, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
516 2 0.00
517 81 0.16
518 424 0.84
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (516 bp):
TTTTTTTAAAGATATGTAATTTATGTTTCAATTTTTTTAAGTATGTTTCATGTTTTCCACCTACA
ATATTAATTTAATAATTTAATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAA
TATTAAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACACCT
ATAATTACTAAATTAAGATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAG
TGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTAC
ATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTA
TATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGATATGTAATTTATG
TTTCAATTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCAC
Found at i:40312 original size:9 final size:9
Alignment explanation
Indices: 40298--40377 Score: 54
Period size: 9 Copynumber: 8.6 Consensus size: 9
40288 CTTGTTTGGA
40298 TCATCATCT
1 TCATCATCT
40307 TCATCATCAT
1 TCATCATC-T
*
40317 CATCATCATCG
1 --TCATCATCT
40328 TCATCATCT
1 TCATCATCT
* *
40337 TCATCGTCA
1 TCATCATCT
* *
40346 GCTTCAT-T
1 TCATCATCT
*
40354 GTCATCATCA
1 -TCATCATCT
*
40364 TCGTCATCT
1 TCATCATCT
40373 TCATC
1 TCATC
40378 GTCAGCTTCA
Statistics
Matches: 52, Mismatches: 14, Indels: 10
0.68 0.18 0.13
Matches are distributed among these distances:
9 43 0.83
10 1 0.02
12 8 0.15
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.39
Consensus pattern (9 bp):
TCATCATCT
Found at i:40314 original size:12 final size:12
Alignment explanation
Indices: 40301--40389 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
40291 GTTTGGATCA
* *
40301 TCATCTTCATCA
1 TCATCGTCATCT
* *
40313 TCATCATCATCA
1 TCATCGTCATCT
* *
40325 TCGTCATCATCT
1 TCATCGTCATCT
*
40337 TCATCGTCAGCT
1 TCATCGTCATCT
* *
40349 TCATTGTCATCA
1 TCATCGTCATCT
40361 TCATCGTCATCT
1 TCATCGTCATCT
*
40373 TCATCGTCAGCT
1 TCATCGTCATCT
40385 TCATC
1 TCATC
40390 TTCTGCGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:40316 original size:6 final size:6
Alignment explanation
Indices: 40297--40377 Score: 72
Period size: 6 Copynumber: 13.5 Consensus size: 6
40287 ACTTGTTTGG
* * * *
40297 ATCATC ATCTTC ATCATC ATCATC ATCATC GTCATC ATCTTC ATCGTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * ** * *
40345 AGCTTC ATTGTC ATCATC ATCGTC ATCTTC ATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATC
40378 GTCAGCTTCA
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.38
Consensus pattern (6 bp):
ATCATC
Found at i:40320 original size:18 final size:18
Alignment explanation
Indices: 40301--40392 Score: 78
Period size: 18 Copynumber: 5.1 Consensus size: 18
40291 GTTTGGATCA
* *
40301 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
40319 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
* * *
40337 TCATCGTCAGCTTCAT-T
1 TCATCATCATCATCATCT
*
40354 GTCATCATCATCGTCATCT
1 -TCATCATCATCATCATCT
* * *
40373 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
40391 TC
1 TC
40393 TGCGACCGCT
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
17 1 0.02
18 57 0.97
19 1 0.02
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.39
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:40359 original size:36 final size:36
Alignment explanation
Indices: 40319--40388 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
40309 ATCATCATCA
*
40319 TCATCATCGTCATCATCTTCATCGTCAGCTTCATTG
1 TCATCATCATCATCATCTTCATCGTCAGCTTCATTG
*
40355 TCATCATCATCGTCATCTTCATCGTCAGCTTCAT
1 TCATCATCATCATCATCTTCATCGTCAGCTTCAT
40389 CTTCTGCGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.20, C:0.31, G:0.10, T:0.39
Consensus pattern (36 bp):
TCATCATCATCATCATCTTCATCGTCAGCTTCATTG
Found at i:40392 original size:6 final size:6
Alignment explanation
Indices: 40301--40392 Score: 69
Period size: 6 Copynumber: 15.3 Consensus size: 6
40291 GTTTGGATCA
* * * * * * *
40301 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
40349 TCAT-T GTCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT -TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
40393 TGCGACCGCT
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
5 1 0.01
6 68 0.99
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:42400 original size:197 final size:196
Alignment explanation
Indices: 41832--42590 Score: 1295
Period size: 197 Copynumber: 3.9 Consensus size: 196
41822 TTTAAATTAG
41832 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
41897 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
* *
41962 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTCCATTCA-T-TGG-ACCAA
131 GACACTTTTTATATATGGATCGACAC-TTATGGTTGCACCCTGTTTCCATTCATTCTGGAACAAA
42024 AA
195 AA
* *
42026 TATCGACACCAACT-AAAAGTGTCGACACATTAGTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
42090 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
42155 GACACTTTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTCCATTCATTCTGGAACAAAA
131 GACACTTTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTCCATTCATTCTGGAACAAAA
42220 A
196 A
*
42221 TATCGACACAAACTAAAATAGCGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
42286 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
*
42351 CGACAC-TTTT-TATATGGATCGACATTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
130 CGACACTTTTTATATATGGATCGACA-CTTATGGTTGCACCCTG-TTTCCATTCATTCTGGAACA
42414 AAAA
193 AAAA
* *
42418 TATCGACACAAACTAAAATTGTGTCGACACA-TATTTAGACATA-TCTCTTATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
42481 CTTGTACCGGTTAGATTGAAAAAATTACATA-TACATTATACTTTTGGTTTTCGATGTTTTTGGG
65 CTTGTACCGGTTAGATTG-AAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTTTTGGG
*
42545 ATCGATACTTTTTATATATGGATCGACACTTATGGTTGCA-CCTGTT
128 ATCGACACTTTTTATATATGGATCGACACTTATGGTTGCACCCTGTT
42591 GGCCATATTG
Statistics
Matches: 540, Mismatches: 14, Indels: 21
0.94 0.02 0.04
Matches are distributed among these distances:
192 25 0.05
193 141 0.26
194 16 0.03
195 88 0.16
196 73 0.14
197 183 0.34
198 14 0.03
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (196 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
GACACTTTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTCCATTCATTCTGGAACAAAA
A
Found at i:42755 original size:19 final size:19
Alignment explanation
Indices: 42709--42757 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
42699 TTATATTCAC
*
42709 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
42728 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
42747 ATACAAAATTA
1 ATACAAAATTA
42758 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:44573 original size:33 final size:33
Alignment explanation
Indices: 44536--44601 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
44526 CATCTTAATA
*
44536 TCACCCCTTAACACCCCAACTTATTTCACCACT
1 TCACCCCTCAACACCCCAACTTATTTCACCACT
* * *
44569 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTATTTCACCACT
44602 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTATTTCACCACT
Found at i:44685 original size:21 final size:21
Alignment explanation
Indices: 44634--44694 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
44624 CCCCTTATGC
* *
44634 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
44655 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
44676 CTCTCAAGTTTCTTTTCGA
1 CTCTCAAGTTTCTCTTCGA
44695 TCTTGATTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.16, C:0.30, G:0.11, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Done.