Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007367.1 Hibiscus syriacus cultivar Beakdansim tig00019760_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: 133275
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:12740 original size:21 final size:21
Alignment explanation
Indices: 12700--12741 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12690 CTTATATAAC
* * *
12700 TTAAGTATTTTTTTTTATTTT
1 TTAAGTATATTTTATAATTTT
12721 TTAAGTATATTTTATAATTTT
1 TTAAGTATATTTTATAATTTT
12742 ATATTCTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (21 bp):
TTAAGTATATTTTATAATTTT
Found at i:12757 original size:16 final size:15
Alignment explanation
Indices: 12726--12777 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 15
12716 ATTTTTTAAG
*
12726 TATATTTTATAATTT
1 TATATTTTAAAATTT
12741 TATATTCTTAAAATTT
1 TATATT-TTAAAATTT
12757 TAATATAATTTAAAATATT
1 T-ATAT--TTTAAAAT-TT
12776 TA
1 TA
12778 CGTTTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 6 0.19
16 9 0.29
17 4 0.13
18 8 0.26
19 4 0.13
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATTTTAAAATTT
Found at i:20057 original size:14 final size:15
Alignment explanation
Indices: 19976--20110 Score: 103
Period size: 15 Copynumber: 8.5 Consensus size: 15
19966 TAATAAGGCT
19976 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
19991 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
* *
20006 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
20025 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
20043 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
** * *
20057 ATTTATTAGTATGGATTG
1 ATTTATT--T-TAAAATA
20075 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
20090 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
20104 ATTTATT
1 ATTTATT
20111 AGTATGGATT
Statistics
Matches: 96, Mismatches: 13, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
14 24 0.25
15 41 0.43
16 5 0.05
17 3 0.03
18 10 0.10
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:20058 original size:94 final size:93
Alignment explanation
Indices: 19953--20136 Score: 241
Period size: 94 Copynumber: 2.0 Consensus size: 93
19943 TATTAAAATA
19953 ATTTTAAATAATTTA-A-TAAGG-CT-ATTTATTTTAAAATAATTTATTATAAAATAAATTATTA
1 ATTTTAAATAATTTATAGTAAGGACTGATTTATTTTAAAATAATTTATT-TAAAAT-AA-T-TTA
20014 TAAAATATGGATTGATTTATTTTAAAATAATTT
62 T-AAATATGGATTGATTTATTTTAAAATAATTT
* * * *
20047 ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAATTTATTTTAAATAATTTATTA
1 ATTTTAAATAATTTA-TAGTAAGGACTGATTTATTTTAAAATAATTTATTTAAAATAATTTATAA
*
20112 GTATGGATTGATTTATTTTAAAATA
65 ATATGGATTGATTTATTTTAAAATA
20137 TGAATTGATT
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
94 40 0.50
95 4 0.05
96 2 0.03
97 6 0.08
98 6 0.08
99 22 0.28
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (93 bp):
ATTTTAAATAATTTATAGTAAGGACTGATTTATTTTAAAATAATTTATTTAAAATAATTTATAAA
TATGGATTGATTTATTTTAAAATAATTT
Found at i:20073 original size:47 final size:47
Alignment explanation
Indices: 19976--20136 Score: 250
Period size: 47 Copynumber: 3.3 Consensus size: 47
19966 TAATAAGGCT
* * *
19976 ATTTATTTTAAAATAATTTATTATAAAATAAATTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATT-TTAAAT-AA-T-TTAT-TAGTATGGATTG
20028 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
20075 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
20122 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
20137 TGAATTGATT
Statistics
Matches: 106, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
47 72 0.68
48 4 0.04
49 1 0.01
50 2 0.02
51 5 0.05
52 22 0.21
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (47 bp):
ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:20138 original size:22 final size:22
Alignment explanation
Indices: 20113--20198 Score: 84
Period size: 22 Copynumber: 3.7 Consensus size: 22
20103 AATTTATTAG
*
20113 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
** *
20135 TATGAATTGATTTATTATTGTAG
1 TATGAATTGATTTATT-TTAAAA
20158 T-TGTATAGATTGATTTATTTTAAAA
1 TATG---A-ATTGATTTATTTTAAAA
20183 TATGAATTGATTTATT
1 TATGAATTGATTTATT
20199 ATTGTAGTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
22 28 0.55
23 5 0.10
25 5 0.10
26 13 0.25
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:20146 original size:26 final size:26
Alignment explanation
Indices: 20117--20279 Score: 83
Period size: 26 Copynumber: 6.3 Consensus size: 26
20107 TATTAGTATG
20117 GATTGATTTATTTTAAAATATGAATT
1 GATTGATTTATTTTAAAATATGAATT
* * * * *
20143 GATTTA-TTATTGT--AGT-TGTATA
1 GATTGATTTATTTTAAAATATGAATT
20165 GATTGATTTATTTTAAAATATGAATT
1 GATTGATTTATTTTAAAATATGAATT
* * * * *
20191 GATTTA-TTATTGT--AGT-TGTATA
1 GATTGATTTATTTTAAAATATGAATT
*
20213 GATTGATTTATTTTAAATAATTTATTAGTATAT
1 GATTGATTTATTTT-AA-AA--TA-T-GAAT-T
20246 -ATTGATTTATTTTAAAATATGAATT
1 GATTGATTTATTTTAAAATATGAATT
* *
20271 AATTTATTT
1 GATTGATTT
20280 TAAATAATTT
Statistics
Matches: 100, Mismatches: 21, Indels: 32
0.65 0.14 0.21
Matches are distributed among these distances:
22 18 0.18
23 16 0.16
25 15 0.15
26 24 0.24
27 2 0.02
28 2 0.02
29 1 0.01
30 2 0.02
31 3 0.03
32 17 0.17
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (26 bp):
GATTGATTTATTTTAAAATATGAATT
Found at i:20183 original size:48 final size:48
Alignment explanation
Indices: 20112--20229 Score: 227
Period size: 48 Copynumber: 2.5 Consensus size: 48
20102 TAATTTATTA
*
20112 GTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT
1 GTATAGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT
20160 GTATAGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT
1 GTATAGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT
20208 GTATAGATTGATTTATTTTAAA
1 GTATAGATTGATTTATTTTAAA
20230 TAATTTATTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (48 bp):
GTATAGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTT
Found at i:20216 original size:22 final size:22
Alignment explanation
Indices: 20143--20216 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
20133 AATATGAATT
20143 GATTTATTATTGTAGTTGTATA
1 GATTTATTATTGTAGTTGTATA
* * * * *
20165 GATTGATTTATTTTAAAATATGAATT
1 GATTTA-TTATTGT--AGT-TGTATA
20191 GATTTATTATTGTAGTTGTATA
1 GATTTATTATTGTAGTTGTATA
20213 GATT
1 GATT
20217 GATTTATTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
22 13 0.34
23 8 0.21
25 8 0.21
26 9 0.24
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (22 bp):
GATTTATTATTGTAGTTGTATA
Found at i:20357 original size:29 final size:30
Alignment explanation
Indices: 20308--20364 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
20298 AGTTGTATGG
*
20308 ATTATTTAAATTTCAGTATTGTAAAACTAA
1 ATTATTTAAATCTCAGTATTGTAAAACTAA
20338 ATTATTT-AATCTCAGTATTGTAAAACT
1 ATTATTTAAATCTCAGTATTGTAAAACT
20365 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (30 bp):
ATTATTTAAATCTCAGTATTGTAAAACTAA
Found at i:26072 original size:59 final size:59
Alignment explanation
Indices: 25970--26102 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 59
25960 ACTATTTTGT
25970 TACTTTTAATAGTCGAGAGACTCAATAAAGCAACACCTAATAGTCGGTAAATCATTTTATG
1 TACTTTTAATAGTCGAGAGACTCAATAAAGCAACACCTAATAGTCGGT-AATCA-TTTATG
* * * *
26031 -ATTTTTAATAGTTG-GAGACTCAATAAAG-AAGCACTCT-ATAGTTGGTGATCATTTATG
1 TACTTTTAATAGTCGAGAGACTCAATAAAGCAA-CAC-CTAATAGTCGGTAATCATTTATG
26088 TACTTTTAATAGTCG
1 TACTTTTAATAGTCG
26103 GATCATTCAG
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
57 6 0.10
58 18 0.29
59 25 0.40
60 14 0.22
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (59 bp):
TACTTTTAATAGTCGAGAGACTCAATAAAGCAACACCTAATAGTCGGTAATCATTTATG
Found at i:26453 original size:111 final size:111
Alignment explanation
Indices: 26259--26492 Score: 443
Period size: 111 Copynumber: 2.1 Consensus size: 111
26249 GTCTAGTGCC
*
26259 GGCTAGCCATACAAACTATTGGTGAACCATGGGTGCTATTGTGGAGAAGGTCTTCAAACTCAGGA
1 GGCTAGCCATGCAAACTATTGGTGAACCATGGGTGCTATTGTGGAGAAGGTCTTCAAACTCAGGA
26324 GGAGGGTCCCGGAAAGAACGAAATTCAAAAGACAGATTCCATGCGA
66 GGAGGGTCCCGGAAAGAACGAAATTCAAAAGACAGATTCCATGCGA
26370 GGCTAGCCATGCAAACTATTGGTGAACCATGGGTGCTATTGTGGAGAAGGTCTTCAAACTCAGGA
1 GGCTAGCCATGCAAACTATTGGTGAACCATGGGTGCTATTGTGGAGAAGGTCTTCAAACTCAGGA
26435 GGAGGGTCCCGGAAAGAACGAAATTCAAAAGACAGATTCCATGCGA
66 GGAGGGTCCCGGAAAGAACGAAATTCAAAAGACAGATTCCATGCGA
26481 -GCTTAGCCATGC
1 GGC-TAGCCATGC
26493 CATCTGCAAC
Statistics
Matches: 121, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
110 2 0.02
111 119 0.98
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (111 bp):
GGCTAGCCATGCAAACTATTGGTGAACCATGGGTGCTATTGTGGAGAAGGTCTTCAAACTCAGGA
GGAGGGTCCCGGAAAGAACGAAATTCAAAAGACAGATTCCATGCGA
Found at i:31290 original size:16 final size:16
Alignment explanation
Indices: 31269--31301 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31259 CGCTGGGCGT
31269 GCATGGCGACCTGGTA
1 GCATGGCGACCTGGTA
31285 GCATGGCGACCTGGTA
1 GCATGGCGACCTGGTA
31301 G
1 G
31302 GTCGCTGGGC
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:0.18, C:0.24, G:0.39, T:0.18
Consensus pattern (16 bp):
GCATGGCGACCTGGTA
Found at i:31319 original size:29 final size:29
Alignment explanation
Indices: 31285--31354 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
31275 CGACCTGGTA
31285 GCATGGCGACCTGGTAGGTCGCTGGGCGT
1 GCATGGCGACCTGGTAGGTCGCTGGGCGT
31314 GCATGGCGACCTGGTAGGTCGCTGGGCGT
1 GCATGGCGACCTGGTAGGTCGCTGGGCGT
31343 GCATGGCGACCT
1 GCATGGCGACCT
31355 ACCCCATCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.11, C:0.26, G:0.43, T:0.20
Consensus pattern (29 bp):
GCATGGCGACCTGGTAGGTCGCTGGGCGT
Found at i:34073 original size:23 final size:23
Alignment explanation
Indices: 34039--34105 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
34029 CACCACAGCT
*
34039 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
34062 CGTAGAATTGCATCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
34085 CGTAGAAATGCACCGAAGTGC
1 CGTAGAAATGCACCGAAGTGC
34106 TATATACGGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:36569 original size:2 final size:2
Alignment explanation
Indices: 36562--36599 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
36552 ATCTTATGTT
36562 CA CA CA CA 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 CA CA CA CA
36600 TATATATCAA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:37690 original size:17 final size:16
Alignment explanation
Indices: 37656--37687 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
37646 AGCTTTCCTT
37656 AAGCTTGTATAACCCC
1 AAGCTTGTATAACCCC
37672 AAGCTTGTATAACCCC
1 AAGCTTGTATAACCCC
37688 CAAAGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.25
Consensus pattern (16 bp):
AAGCTTGTATAACCCC
Found at i:40691 original size:34 final size:35
Alignment explanation
Indices: 40648--40717 Score: 115
Period size: 37 Copynumber: 2.0 Consensus size: 35
40638 TCTTAAGTCA
40648 TCTTTCTAACA-TGTAAGCAGATAATATGTTCCTG
1 TCTTTCTAACATTGTAAGCAGATAATATGTTCCTG
40682 TCTTTCTAACATTTTGTAAGCAGATAATATGTTCCT
1 TCTTTCTAACA--TTGTAAGCAGATAATATGTTCCT
40718 ATCATTTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 11 0.33
37 22 0.67
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (35 bp):
TCTTTCTAACATTGTAAGCAGATAATATGTTCCTG
Found at i:47207 original size:30 final size:30
Alignment explanation
Indices: 47154--47236 Score: 139
Period size: 30 Copynumber: 2.7 Consensus size: 30
47144 AAAAAAAAAT
*
47154 AATAGTTAAGTGACTATAATAGAAAGCAAAC
1 AATAGTTGAGTGACTA-AATAGAAAGCAAAC
*
47185 AATAGTTGAGTGACTAAATAGAAAGTAAAC
1 AATAGTTGAGTGACTAAATAGAAAGCAAAC
47215 AATAGTTGAGTGACTAAATAGA
1 AATAGTTGAGTGACTAAATAGA
47237 TAGTTTATCC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 35 0.70
31 15 0.30
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.24
Consensus pattern (30 bp):
AATAGTTGAGTGACTAAATAGAAAGCAAAC
Found at i:59096 original size:16 final size:17
Alignment explanation
Indices: 59070--59101 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
59060 AACAGTAGCA
59070 TTCCAACTGAACTCAAT
1 TTCCAACTGAACTCAAT
59087 TTCC-ACTGAACTCAA
1 TTCCAACTGAACTCAA
59102 CTGGGTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.28
Consensus pattern (17 bp):
TTCCAACTGAACTCAAT
Found at i:59618 original size:16 final size:17
Alignment explanation
Indices: 59593--59624 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
59583 TCACCGATCG
59593 AATTTCACTATTCACGA
1 AATTTCACTATTCACGA
59610 AATTT-ACTATTCACG
1 AATTTCACTATTCACG
59625 TGAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (17 bp):
AATTTCACTATTCACGA
Found at i:72918 original size:19 final size:18
Alignment explanation
Indices: 72872--72921 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
72862 CTATAAAAAG
*
72872 CTACTTTAATAAAGTACT
1 CTACTTTAATTAAGTACT
* *
72890 ATACTTTAATTAAGTTCT
1 CTACTTTAATTAAGTACT
72908 CTACATTTAATTAA
1 CTAC-TTTAATTAA
72922 ATTAGGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (18 bp):
CTACTTTAATTAAGTACT
Found at i:76127 original size:18 final size:18
Alignment explanation
Indices: 76106--76142 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
76096 ACATCCCCTT
76106 ACCCCATTACATATAGGA
1 ACCCCATTACATATAGGA
76124 ACCCCATTACATATAGGA
1 ACCCCATTACATATAGGA
76142 A
1 A
76143 TAGAGTCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.22
Consensus pattern (18 bp):
ACCCCATTACATATAGGA
Found at i:82204 original size:3 final size:3
Alignment explanation
Indices: 82196--82224 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
82186 CGGAGCCGCC
82196 AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
82225 AGCTGCTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:96170 original size:2 final size:2
Alignment explanation
Indices: 96163--96189 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
96153 TGCATGAACG
96163 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
96190 GCCGCGTGAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:99283 original size:41 final size:41
Alignment explanation
Indices: 99236--99400 Score: 158
Period size: 41 Copynumber: 4.0 Consensus size: 41
99226 ATTCGCGTTG
* *
99236 CATTTCGATTTGCGATAGTTGAAAACCGCGTTGCGATTTTC
1 CATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * * ** ** **
99277 CATTTCGCGTTGTGAT-TTTCCATTTCGCGTTGTAATTTTC
1 CATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
99317 CATTTC-ACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGA-GTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
99358 CATTTCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTC
1 CATTTCGAGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
99399 CA
1 CA
99401 AATTCGTTGG
Statistics
Matches: 97, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
40 30 0.31
41 66 0.68
42 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (41 bp):
CATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:99287 original size:20 final size:20
Alignment explanation
Indices: 99262--99373 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
99252 AGTTGAAAAC
99262 CGCGTTGCGATTTTCCATTT
1 CGCGTTGCGATTTTCCATTT
*
99282 CGCGTTGTGATTTTCCATTT
1 CGCGTTGCGATTTTCCATTT
**
99302 CGCGTTGTAATTTTCCATTT
1 CGCGTTGCGATTTTCCATTT
* * ** **
99322 CACGTTGCGATAGTTGAAAAT
1 CGCGTTGCGAT-TTTCCATTT
99343 CGCGTTGCGATTTTCCATTT
1 CGCGTTGCGATTTTCCATTT
99363 CGCGTTGCGAT
1 CGCGTTGCGAT
99374 AGTCTACAAT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 61 0.81
21 14 0.19
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.42
Consensus pattern (20 bp):
CGCGTTGCGATTTTCCATTT
Found at i:99409 original size:81 final size:79
Alignment explanation
Indices: 99245--99409 Score: 190
Period size: 81 Copynumber: 2.0 Consensus size: 79
99235 GCATTTCGAT
* * * * *
99245 TTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGTGATTTTCCATTTCGCGTTGT
1 TTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTACAATGTC-CGTTGC
*
99310 AATTTTCCATTTCACG
65 AATTTTCCAATT-ACG
*
99326 TTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAATGT-CGTT
1 TTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCGAT--T-TACAATGTCCGTT
*
99390 GCGATTTTCCAAATT-CG
63 GCAATTTTCC-AATTACG
99407 TTG
1 TTG
99410 GAAATAAGTG
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
81 51 0.71
82 12 0.17
83 4 0.06
84 5 0.07
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (79 bp):
TTGCGATAGTTGAAAACCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTACAATGTCCGTTGCA
ATTTTCCAATTACG
Found at i:99713 original size:19 final size:19
Alignment explanation
Indices: 99668--99714 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
99658 CAACGAATTT
*
99668 TCGCAACAAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
99687 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
99706 TCGCAACGA
1 TCGCAACGA
99715 CAACTGTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:99778 original size:21 final size:21
Alignment explanation
Indices: 99754--99807 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
99744 GAACTGGAAA
99754 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
99775 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
99796 ATCGCAACGCGA
1 ATCGCAACGCGA
99808 AATGCAACGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:106134 original size:24 final size:23
Alignment explanation
Indices: 106064--106157 Score: 107
Period size: 23 Copynumber: 4.0 Consensus size: 23
106054 AATTTTAAAT
* *
106064 AATGCGCCACAAAGACAAAGATA
1 AATGTGCCACAAAGACAGAGATA
* *
106087 AACGTGCCACAAAGATAGAGATA
1 AATGTGCCACAAAGACAGAGATA
*
106110 AATGTGCCATAAATGACAGAGATA
1 AATGTGCCACAAA-GACAGAGATA
* *
106134 AATGTGTCATAAAAGACAGAGATA
1 AATGTGCCA-CAAAGACAGAGATA
106158 CGCGTATCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
23 30 0.50
24 27 0.45
25 3 0.05
ACGTcount: A:0.49, C:0.15, G:0.20, T:0.16
Consensus pattern (23 bp):
AATGTGCCACAAAGACAGAGATA
Found at i:106167 original size:24 final size:24
Alignment explanation
Indices: 106074--106170 Score: 70
Period size: 24 Copynumber: 4.1 Consensus size: 24
106064 AATGCGCCAC
* ** *
106074 AAAGACAAAGATAAACGTGCCA-C
1 AAAGACAGAGATAAACGTATCATA
* * **
106097 AAAGATAGAGATAAATGTGCCATA
1 AAAGACAGAGATAAACGTATCATA
* * *
106121 AATGACAGAGATAAATGTGTCATA
1 AAAGACAGAGATAAACGTATCATA
**
106145 AAAGACAGAGATACGCGTATCATA
1 AAAGACAGAGATAAACGTATCATA
106169 AA
1 AA
106171 GGCAGAATTA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
23 19 0.31
24 42 0.69
ACGTcount: A:0.49, C:0.13, G:0.20, T:0.18
Consensus pattern (24 bp):
AAAGACAGAGATAAACGTATCATA
Found at i:106798 original size:20 final size:20
Alignment explanation
Indices: 106761--106799 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
106751 GTATTGTATG
**
106761 AATAGTAACGATGTTGTGTA
1 AATAGTAACGATACTGTGTA
*
106781 AATAGTATCGATACTGTGT
1 AATAGTAACGATACTGTGT
106800 GAACAGTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (20 bp):
AATAGTAACGATACTGTGTA
Found at i:107471 original size:31 final size:31
Alignment explanation
Indices: 107417--107508 Score: 103
Period size: 31 Copynumber: 3.0 Consensus size: 31
107407 CCCTAAGGAC
* * * *
107417 CAGTTCATATGTTCTGAAAAACATAGGTAAT
1 CAGTACATATGTCCCGAAGAACATAGGTAAT
* *
107448 TAGTACATATGTCCCTAAGAACATAGGTAAT
1 CAGTACATATGTCCCGAAGAACATAGGTAAT
* * *
107479 CAGTCCATATTTCCCGAATAACATAGGTAA
1 CAGTACATATGTCCCGAAGAACATAGGTAA
107509 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (31 bp):
CAGTACATATGTCCCGAAGAACATAGGTAAT
Found at i:109836 original size:32 final size:32
Alignment explanation
Indices: 109792--109879 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 32
109782 CTAAAAATTA
109792 ATTAACAA-AATTAATATTTTTGATAAAAAAAT
1 ATTAA-AATAATTAATATTTTTGATAAAAAAAT
*** *
109824 ATTATTTTAATTAAT-TTTTT-AT-CAAAAAT
1 ATTAAAATAATTAATATTTTTGATAAAAAAAT
*
109853 ATTAAAATATATTAATATTTATGATAA
1 ATTAAAATA-ATTAATATTTTTGATAA
109880 TTTTTTTAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
29 12 0.29
30 8 0.19
31 9 0.21
32 13 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (32 bp):
ATTAAAATAATTAATATTTTTGATAAAAAAAT
Found at i:111344 original size:206 final size:206
Alignment explanation
Indices: 110989--111402 Score: 819
Period size: 206 Copynumber: 2.0 Consensus size: 206
110979 AAATCGAGTC
110989 TAAATTATATATGGACAAATGAAATGACACATTTTTTAACAAGATTATATAAATATTCTATACAT
1 TAAATTATATATGGACAAATGAAATGACACATTTTTTAACAAGATTATATAAATATTCTATACAT
111054 ACATGTTAGGCTTGTCAACTCAACTTGAATTAAACCGAAGATAAAAAATTGACCCGATCCAAAAA
66 ACATGTTAGGCTTGTCAACTCAACTTGAATTAAACCGAAGATAAAAAATTGACCCGATCCAAAAA
*
111119 CTAATTGATACACTATTAACCCGAATTAAAAATCGATCAATCTAATATTAACCAACTAAAAAGTT
131 CTAATTGATACAATATTAACCCGAATTAAAAATCGATCAATCTAATATTAACCAACTAAAAAGTT
111184 AACTGATTTGA
196 AACTGATTTGA
111195 TAAATTATATATGGACAAATGAAATGACACATTTTTTAACAAGATTATATAAATATTCTATACAT
1 TAAATTATATATGGACAAATGAAATGACACATTTTTTAACAAGATTATATAAATATTCTATACAT
111260 ACATGTTAGGCTTGTCAACTCAACTTGAATTAAACCGAAGATAAAAAATTGACCCGATCCAAAAA
66 ACATGTTAGGCTTGTCAACTCAACTTGAATTAAACCGAAGATAAAAAATTGACCCGATCCAAAAA
111325 CTAATTGATACAATATTAACCCGAATTAAAAATCGATCAATCTAATATTAACCAACTAAAAAGTT
131 CTAATTGATACAATATTAACCCGAATTAAAAATCGATCAATCTAATATTAACCAACTAAAAAGTT
111390 AACTGATTTGA
196 AACTGATTTGA
111401 TA
1 TA
111403 TTCATCCAAC
Statistics
Matches: 207, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
206 207 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (206 bp):
TAAATTATATATGGACAAATGAAATGACACATTTTTTAACAAGATTATATAAATATTCTATACAT
ACATGTTAGGCTTGTCAACTCAACTTGAATTAAACCGAAGATAAAAAATTGACCCGATCCAAAAA
CTAATTGATACAATATTAACCCGAATTAAAAATCGATCAATCTAATATTAACCAACTAAAAAGTT
AACTGATTTGA
Found at i:117341 original size:23 final size:23
Alignment explanation
Indices: 117311--117364 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
117301 TTAACGCTAT
117311 TGTATGTTGTCTATCTTAGCAGA
1 TGTATGTTGTCTATCTTAGCAGA
117334 TGTATGTTGTCTATCTTAGCAGA
1 TGTATGTTGTCTATCTTAGCAGA
*
117357 TGTGTGTT
1 TGTATGTT
117365 CTACTTTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.11, G:0.24, T:0.46
Consensus pattern (23 bp):
TGTATGTTGTCTATCTTAGCAGA
Found at i:119239 original size:15 final size:17
Alignment explanation
Indices: 119219--119250 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
119209 GTTAAGTGTC
119219 CATGAT-ATATG-TATA
1 CATGATAATATGATATA
119234 CATGATAATATGATATA
1 CATGATAATATGATATA
119251 AGTTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
CATGATAATATGATATA
Found at i:119709 original size:32 final size:31
Alignment explanation
Indices: 119655--119839 Score: 230
Period size: 32 Copynumber: 5.9 Consensus size: 31
119645 AGTCGAGGGT
*
119655 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTTCGGAACATATGGACAG-A
* *
119687 TTACTTATG-TCTTTCGGGACATATGGACAGGA
1 TTACCTATGTTC-TTCGGAACATATGGACA-GA
*
119719 TTACCTATGTTCTTCGGAACATATGTACATGA
1 TTACCTATGTTCTTCGGAACATATGGACA-GA
*
119751 TTACCTATGTTCTTCGGAACATATGAACAGGA
1 TTACCTATGTTCTTCGGAACATATGGACA-GA
* * *
119783 TTTCTTATGTTCTCCGGAACATATGGACAG-
1 TTACCTATGTTCTTCGGAACATATGGACAGA
*
119813 TTACATATGTTCTTCGGAACATATGGA
1 TTACCTATGTTCTTCGGAACATATGGA
119840 TAGGTCATTT
Statistics
Matches: 134, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
30 24 0.18
31 3 0.02
32 104 0.78
33 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACAGA
Found at i:119805 original size:96 final size:94
Alignment explanation
Indices: 119655--119837 Score: 269
Period size: 96 Copynumber: 1.9 Consensus size: 94
119645 AGTCGAGGGT
* * *
119655 TTACCTATGTTCTACGGAACATATGGACAGAATTACTTATGTCTTTCGGGACATATGGACAGGAT
1 TTACCTATGTTCTACGGAACATATGAACAGAATTACTTATGTCTTCCGGAACATATGGACA-G-T
*
119720 TACCTATGTTCTTCGGAACATATGTACATGA
64 TACATATGTTCTTCGGAACATATGTACATGA
* * *
119751 TTACCTATGTTCTTCGGAACATATGAACAGGATTTCTTATGT-TCTCCGGAACATATGGACAGTT
1 TTACCTATGTTCTACGGAACATATGAACAGAATTACTTATGTCT-TCCGGAACATATGGACAGTT
119815 ACATATGTTCTTCGGAACATATG
65 ACATATGTTCTTCGGAACATATG
119838 GATAGGTCAT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 24 0.30
95 2 0.03
96 53 0.67
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (94 bp):
TTACCTATGTTCTACGGAACATATGAACAGAATTACTTATGTCTTCCGGAACATATGGACAGTTA
CATATGTTCTTCGGAACATATGTACATGA
Done.