Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002789.1 Hibiscus syriacus cultivar Beakdansim tig00005747_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: 101783
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2625 original size:66 final size:66
Alignment explanation
Indices: 2519--2652 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
2509 GATATTGCTC
2519 TTCTGATTGGAAAGCACTCAGAGAGAACTCACAGAGAGAACTGTAGAAAACACTTTTGTAAGTGA
1 TTCTGATTGGAAAGCACTCAGAGAGAACTCACAGAGAGAACTGTAGAAAACACTTTTGTAAGTGA
2584 A
66 A
*
2585 TTCTGATTGGAAAGCACTCAGAGAGAACTCACAGAGAGAACTGTAGAAAACACTTTTTTAAGTGA
1 TTCTGATTGGAAAGCACTCAGAGAGAACTCACAGAGAGAACTGTAGAAAACACTTTTGTAAGTGA
2650 A
66 A
2651 TT
1 TT
2653 GTGAATGTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.25
Consensus pattern (66 bp):
TTCTGATTGGAAAGCACTCAGAGAGAACTCACAGAGAGAACTGTAGAAAACACTTTTGTAAGTGA
A
Found at i:2866 original size:22 final size:22
Alignment explanation
Indices: 2832--2873 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2822 TCAGCTGTTA
* *
2832 TAACTCCTAAAATTATATCATG
1 TAACCCCTAAAATTAAATCATG
*
2854 TAACCCCTGAAATTAAATCA
1 TAACCCCTAAAATTAAATCA
2874 AATAACTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (22 bp):
TAACCCCTAAAATTAAATCATG
Found at i:2879 original size:22 final size:22
Alignment explanation
Indices: 2831--2879 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2821 TTCAGCTGTT
* * *
2831 ATAACTCCTAAAATTATATCAT
1 ATAACCCCTAAAATTAAATCAA
* *
2853 GTAACCCCTGAAATTAAATCAA
1 ATAACCCCTAAAATTAAATCAA
2875 ATAAC
1 ATAAC
2880 TCTTGTAACT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (22 bp):
ATAACCCCTAAAATTAAATCAA
Found at i:3189 original size:5 final size:5
Alignment explanation
Indices: 3179--3222 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
3169 ACCACGACTA
* * * *
3179 CGAGC CGAGC CGAGC CGTGC CGTGC CGTGT CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
3223 ATGGACAGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.14, C:0.36, G:0.41, T:0.09
Consensus pattern (5 bp):
CGAGC
Found at i:8806 original size:22 final size:22
Alignment explanation
Indices: 8753--8806 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
8743 TTCAGCTGTT
* *
8753 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* *
8775 GTAA-TCCCTGGAATTAAATCAA
1 ATAACT-CCTGAAATTAAATCAA
8797 ATAACTCCTG
1 ATAACTCCTG
8807 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:9109 original size:5 final size:5
Alignment explanation
Indices: 9099--9137 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
9089 ACCACGACCA
*
9099 CGAGC CGAGC CGAGC CGAGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
9138 ACGGACGGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.18, C:0.38, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:11099 original size:27 final size:28
Alignment explanation
Indices: 11057--11124 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
11047 CTTTATTTTG
11057 TTCGGGTCGGG-CTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCTTTTTAAGTGTGATA
* *
11084 TTCGGGTCTGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCTTTTTAAGTGTGATA
11112 TTCGGGTCGGGTC
1 TTCGGGTCGGGTC
11125 GGGTTTAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 10 0.28
28 26 0.72
ACGTcount: A:0.12, C:0.12, G:0.34, T:0.43
Consensus pattern (28 bp):
TTCGGGTCGGGTCTTTTTAAGTGTGATA
Found at i:11193 original size:238 final size:238
Alignment explanation
Indices: 10855--11583 Score: 991
Period size: 238 Copynumber: 3.0 Consensus size: 238
10845 GTCGGATCAT
* * * * *
10855 GTTTTTTTAAGTGTGATATTCGGGTCAGGTTCAGGTTTAGGGTGAAAAAAACCGGACCGACCCGA
1 GTTTTTTTAAGTGTGATATTCGGGTC-GGGTCGGGTTTAGGATAAAAAAAACCGGATCGACCCGA
* * *
10920 AATTATATATAATTCAGGTCGGGTCGGAATAAGTCACTGTTTTTATTAAATAAAAATAATTTTTT
65 AAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTT
* * *
10985 ATTATTTCTGGTCAGGTCGGGTCGGATTTTTAATTCATATATTCGGGTCGGGTCGGATGAAACTT
130 ATTATTTCAGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTT
11050 TATTTTGTTCGGGTCGGGCTTTTTAAGTGTGATATTCGGGTCTG
195 TATTTTGTTCGGGTCGGGCTTTTTAAGTGTGATATTCGGGTCTG
*
11094 GTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTTAGGATAAAAAAAACCGGATCGACTCGAA
1 GTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTTAGGATAAAAAAAACCGGATCGACCCGAA
* *
11159 AATATATATAATTCGGGTCGCGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTA
66 AATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTA
* * * *
11224 TTATTTCGGGCCGGGTCAGGTCGGATTTCTAATTCATATA-T----TCGGGTCGAATGAAACTTT
131 TTATTTCAGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTT
11284 ATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTCTG
196 ATTTTGTTCGGGTCGGG-C----TTTTTAAGTGTGATA-T----TCGGGTCTG
* * * * *
11337 GTTATTTTAAGTGCGATATTCGGGTCGGGTCGGGTTTGGGTTTAGGGTGAAAAAACCGGATCGAC
1 GTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTTAGG-ATA----AAAAAAACCGGATCGAC
11402 CCGAAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATT
61 CCG-AAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATT
11467 TTTTTATTATTTCAGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGA
125 TTTTTATTATTTCAGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGA
* * *
11532 AACTTTATTTTGTTCAGGTTGGGTTGGGTTTTTTAAGTGTGATATTTGGGTC
190 AACTTTATTTTGTTC-----GGGTCGGGCTTTTTAAGTGTGATATTCGGGTC
11584 GAGTCGGGTC
Statistics
Matches: 432, Mismatches: 32, Indels: 42
0.85 0.06 0.08
Matches are distributed among these distances:
233 35 0.08
234 1 0.00
237 1 0.00
238 143 0.33
239 27 0.06
243 46 0.11
244 2 0.00
248 18 0.04
249 108 0.25
250 1 0.00
253 1 0.00
254 42 0.10
259 7 0.02
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (238 bp):
GTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTTAGGATAAAAAAAACCGGATCGACCCGAA
AATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTA
TTATTTCAGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTT
ATTTTGTTCGGGTCGGGCTTTTTAAGTGTGATATTCGGGTCTG
Found at i:11355 original size:33 final size:32
Alignment explanation
Indices: 11290--11373 Score: 141
Period size: 33 Copynumber: 2.6 Consensus size: 32
11280 CTTTATTTTG
*
11290 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTAAGTGCGATA
*
11322 TTCGGGTCGGGTCTGGTTATTTTAAGTGCGATA
1 TTCGGGTCGGGTCGGGTT-TTTTAAGTGCGATA
11355 TTCGGGTCGGGTCGGGTTT
1 TTCGGGTCGGGTCGGGTTT
11374 GGGTTTAGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
32 18 0.38
33 30 0.62
ACGTcount: A:0.11, C:0.12, G:0.38, T:0.39
Consensus pattern (32 bp):
TTCGGGTCGGGTCGGGTTTTTTAAGTGCGATA
Found at i:11636 original size:37 final size:37
Alignment explanation
Indices: 11545--11636 Score: 123
Period size: 38 Copynumber: 2.5 Consensus size: 37
11535 TTTATTTTGT
* * **
11545 TCAGGTTGGGTTGGGTTTTTTAAGTGTGATATTTGGG
1 TCAGGTCGGGTCGGGTTTTTTAAGTGTGATATTCAGG
11582 TC-GAGTCGGGTCGGGGTTTTTTAAGTGTGATATTCAGG
1 TCAG-GTCGGGTC-GGGTTTTTTAAGTGTGATATTCAGG
11620 TCAGGTCGGGTCGGGTT
1 TCAGGTCGGGTCGGGTT
11637 CGGGTTTAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
36 1 0.02
37 13 0.27
38 33 0.69
39 1 0.02
ACGTcount: A:0.13, C:0.09, G:0.39, T:0.39
Consensus pattern (37 bp):
TCAGGTCGGGTCGGGTTTTTTAAGTGTGATATTCAGG
Found at i:12199 original size:16 final size:18
Alignment explanation
Indices: 12174--12219 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
12164 TATGAAATTG
*
12174 GATTCCAATTCC-T-ACA
1 GATTCTAATTCCTTCACA
12190 GATTCTAATTCCTTCACA
1 GATTCTAATTCCTTCACA
12208 GATTCTAATTCC
1 GATTCTAATTCC
12220 CTCATAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.41
17 1 0.04
18 15 0.56
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (18 bp):
GATTCTAATTCCTTCACA
Found at i:13120 original size:4 final size:4
Alignment explanation
Indices: 13111--13137 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13101 CTGAAAGGTA
13111 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
13138 AGTTTAGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:13200 original size:7 final size:7
Alignment explanation
Indices: 13190--13223 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
13180 ATATTTTATA
13190 TAAAATT
1 TAAAATT
13197 TAAAATT
1 TAAAATT
13204 TAAAATT
1 TAAAATT
13211 T-AAATT
1 TAAAATT
*
13217 AAAAATT
1 TAAAATT
13224 AATCATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAAAATT
Found at i:13221 original size:13 final size:14
Alignment explanation
Indices: 13191--13223 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
13181 TATTTTATAT
*
13191 AAAATTTAAAATTT
1 AAAATTTAAAATTA
13205 AAAATTT-AAATTA
1 AAAATTTAAAATTA
13218 AAAATT
1 AAAATT
13224 AATCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATTTAAAATTA
Found at i:19492 original size:23 final size:23
Alignment explanation
Indices: 19464--19521 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
19454 ATCAAGCACA
* *
19464 ATAATATATTAGGTACCGCTTAT
1 ATAATATAATAGGTACCACTTAT
* *
19487 ATAATATAATATGTATCACTTAT
1 ATAATATAATAGGTACCACTTAT
*
19510 ATAATAAAATAG
1 ATAATATAATAG
19522 ATCAATTACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTACCACTTAT
Found at i:19509 original size:87 final size:87
Alignment explanation
Indices: 19359--19610 Score: 324
Period size: 87 Copynumber: 2.9 Consensus size: 87
19349 CATTTAACCG
* * * *
19359 GAAATATTATTAAGTACAATAACATATTAAGTACTGCTTATATAATGTAATATGTAAGGCTTATA
1 GAAATATTATCAAGCACAATAACATATTAAGTACCGCTTATATAATGTAATATGTAACGCTTATA
*
19424 TAATAAAATAGGTTAATTACTA
66 TAATAAAATAGGTCAATTACTA
* * * * *
19446 GAAATATTATCAAGCACAATAATATATTAGGTACCGCTTATATAATATAATATGTATCACTTATA
1 GAAATATTATCAAGCACAATAACATATTAAGTACCGCTTATATAATGTAATATGTAACGCTTATA
* *
19511 TAATAAAATAGATCAATTACTG
66 TAATAAAATAGGTCAATTACTA
* * * * * * * *
19533 GAAACATTATCAAACACAATAACATATTATGTAGCACTTATATAATGTAATAAGTAGCGCTTGTA
1 GAAATATTATCAAGCACAATAACATATTAAGTACCGCTTATATAATGTAATATGTAACGCTTATA
19598 TAATAAAATAGGT
66 TAATAAAATAGGT
19611 AGCGCTTATA
Statistics
Matches: 141, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 141 1.00
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (87 bp):
GAAATATTATCAAGCACAATAACATATTAAGTACCGCTTATATAATGTAATATGTAACGCTTATA
TAATAAAATAGGTCAATTACTA
Found at i:19594 original size:110 final size:110
Alignment explanation
Indices: 19480--19720 Score: 347
Period size: 110 Copynumber: 2.2 Consensus size: 110
19470 TATTAGGTAC
* * * *
19480 CGCTTATATAATATAATATGTATCACTTATATAATAAAATAGATCAATTACTGGAAACATTATCA
1 CGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGATCAATTACTAGAAACATTATCA
* * *
19545 AACACAATAACATATTATGTAGCACTTATATAATGTAATAAGTAG
66 AACACAATAACATATTAGGTACCACTTATATAATGTAATAAGTAA
* * * * *
19590 CGCTTGTATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTATAAACATTATCA
1 CGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGATCAATTACTAGAAACATTATCA
* *
19655 AGCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAA
66 AACACAATAACATATTAGGTACCACTTATATAATGTAATAAGTAA
*
19700 CACTTATATAATAAAATAGGT
1 CGCTTATATAATAAAATAGGT
19721 TAATTACTGG
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 115 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.33
Consensus pattern (110 bp):
CGCTTATATAATAAAATAGGTAGCACTTATATAATAAAATAGATCAATTACTAGAAACATTATCA
AACACAATAACATATTAGGTACCACTTATATAATGTAATAAGTAA
Found at i:19631 original size:23 final size:23
Alignment explanation
Indices: 19563--19633 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
19553 AACATATTAT
* ** *
19563 GTAGCACTTATATAATGTAATAA
1 GTAGCGCTTATATAATAAAATAG
*
19586 GTAGCGCTTGTATAATAAAATAG
1 GTAGCGCTTATATAATAAAATAG
19609 GTAGCGCTTATATAATAAAATAG
1 GTAGCGCTTATATAATAAAATAG
19632 GT
1 GT
19634 TAATTACTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.32
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAG
Found at i:19687 original size:23 final size:23
Alignment explanation
Indices: 19661--19720 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
19651 ATCAAGCACA
* *
19661 ATAACATATTAGGTACCACTTAT
1 ATAACATAATAGGTAACACTTAT
**
19684 ATAATGTAATAGGTAACACTTAT
1 ATAACATAATAGGTAACACTTAT
* *
19707 ATAATAAAATAGGT
1 ATAACATAATAGGT
19721 TAATTACTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACACTTAT
Found at i:19687 original size:87 final size:87
Alignment explanation
Indices: 19604--19815 Score: 370
Period size: 87 Copynumber: 2.4 Consensus size: 87
19594 TGTATAATAA
* *
19604 AATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTATAAACATTATCAAGCACAATAACATA
1 AATAGGTAACGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCACAATAACATA
19669 TTAGGTACCACTTATATAATGT
66 TTAGGTACCACTTATATAATGT
* *
19691 AATAGGTAACACTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAGCACAATAACATA
1 AATAGGTAACGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCACAATAACATA
* *
19756 TTAGGTAGCACTTATATAACGT
66 TTAGGTACCACTTATATAATGT
19778 AATAGGTAACGCTTATATAATAAAATAGGTTAATTACT
1 AATAGGTAACGCTTATATAATAAAATAGGTTAATTACT
19816 TAATTTGTTA
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 118 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (87 bp):
AATAGGTAACGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCACAATAACATA
TTAGGTACCACTTATATAATGT
Found at i:19752 original size:197 final size:197
Alignment explanation
Indices: 19377--19807 Score: 650
Period size: 197 Copynumber: 2.2 Consensus size: 197
19367 ATTAAGTACA
* * ** *
19377 ATAACATATTAAGT-ACTGCTTATATAATGTAATATGTAAG-GCTTATATAATAAAATAGGTTAA
1 ATAACGTAATAAGTAAC-GCTTATATAATAAAATAGGT-AGCGCTTATATAATAAAATAGGTTAA
* * * * *
19440 TTACTAGAAATATTATCAAGCACAATAATATATTAGGTACCGCTTATATAATATAATATGTATCA
64 TTACTAGAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATATAATAGGTAACA
*
19505 CTTATATAATAAAATAGATCAATTACTGGAAACATTATCAAACACAATAACATATTATGTAGCAC
129 CTTATATAATAAAATAGATCAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCAC
19570 TTAT
194 TTAT
* * *
19574 ATAATGTAATAAGTAGCGCTTGTATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
1 ATAACGTAATAAGTAACGCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
* *
19639 ACTATAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATGTAATAGGTAACACT
66 ACTAGAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATATAATAGGTAACACT
* * *
19704 TATATAATAAAATAGGTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCACTT
131 TATATAATAAAATAGATCAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCACTT
19769 AT
196 AT
*
19771 ATAACGTAATAGGTAACGCTTATATAATAAAATAGGT
1 ATAACGTAATAAGTAACGCTTATATAATAAAATAGGT
19808 TAATTACTTA
Statistics
Matches: 209, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
196 2 0.01
197 206 0.99
198 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (197 bp):
ATAACGTAATAAGTAACGCTTATATAATAAAATAGGTAGCGCTTATATAATAAAATAGGTTAATT
ACTAGAAACATTATCAAGCACAATAACATATTAGGTACCACTTATATAATATAATAGGTAACACT
TATATAATAAAATAGATCAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCACTT
AT
Found at i:19783 original size:23 final size:23
Alignment explanation
Indices: 19748--19807 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
19738 ATCAAGCACA
* *
19748 ATAACATATTAGGTAGCACTTAT
1 ATAACATAATAGGTAACACTTAT
* *
19771 ATAACGTAATAGGTAACGCTTAT
1 ATAACATAATAGGTAACACTTAT
* *
19794 ATAATAAAATAGGT
1 ATAACATAATAGGT
19808 TAATTACTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAACACTTAT
Found at i:20779 original size:200 final size:197
Alignment explanation
Indices: 20370--20811 Score: 602
Period size: 200 Copynumber: 2.2 Consensus size: 197
20360 TTTAAAATAA
*
20370 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGATACAATTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
* * *
20435 TAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACA
66 TAATGTATCAACACTTTATACGTGCACCTCGTTGGGCATTCATTCTAGAAAAAAGTATCGACACA
* *
20500 AACTTAAAATGTGTCGATACATTATGTAGACATATTTTCTCATAAAACCGGTATATTTATACCGA
131 AACTTAAAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACAGA
20565 GT
196 GT
* **
20567 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATA-TTTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
* * *
20631 AATAAATGTATCAACACTTTATATGTGCACCTCGTTTGGCATTCATTCTAGACAAAATGTATCGA
66 --T-AATGTATCAACACTTTATACGTGCACCTCGTTGGGCATTCATTCTAGA-AAAAAGTATCGA
*** * * ** *
20696 CAC-TTTTTAAATTTGTGTCGATACATTATGTTGATTTATTCTCTCATAAAATCGGTATATTTAT
127 CACAAACTTAAA-ATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTAT
20760 ACAG-GTT
191 ACAGAG-T
* * *
20767 ACATTATAAATTTACCTATTACATTATAATTATCGATTTCTATGT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
20812 AACATATGTG
Statistics
Matches: 215, Mismatches: 24, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
196 3 0.01
197 57 0.27
198 1 0.00
199 49 0.23
200 105 0.49
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (197 bp):
ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT
TAATGTATCAACACTTTATACGTGCACCTCGTTGGGCATTCATTCTAGAAAAAAGTATCGACACA
AACTTAAAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACAGA
GT
Found at i:21094 original size:24 final size:25
Alignment explanation
Indices: 21026--21094 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
21016 TAAATAATAT
*
21026 TAAATAA-ATTATTCTAATATT-TTAA
1 TAAATAATATTA-T-TATTATTGTTAA
21051 -AAATAATATTATTATT-TTGTTAA
1 TAAATAATATTATTATTATTGTTAA
21074 TAAATAATATTATT-TTATTGT
1 TAAATAATATTATTATTATTGT
21095 ATTTGATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 9 0.23
24 24 0.62
25 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (25 bp):
TAAATAATATTATTATTATTGTTAA
Found at i:21535 original size:32 final size:32
Alignment explanation
Indices: 21494--21558 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
21484 TTATGCACAA
*
21494 CAATAACAAAATCGATA-CAACTTTTTTTTAGC
1 CAATAACAAAACCGATATC-ACTTTTTTTTAGC
21526 CAATAACAAAACCGATATCACTTTTTTTTAGC
1 CAATAACAAAACCGATATCACTTTTTTTTAGC
21558 C
1 C
21559 GTATATTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (32 bp):
CAATAACAAAACCGATATCACTTTTTTTTAGC
Found at i:30329 original size:28 final size:28
Alignment explanation
Indices: 30289--30345 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
30279 CACCATTAAC
30289 ATAGCCTCTAAATGGGATGCTTCTATGA
1 ATAGCCTCTAAATGGGATGCTTCTATGA
30317 ATAGCCTCTAAATGGGATGCTTCTATGA
1 ATAGCCTCTAAATGGGATGCTTCTATGA
30345 A
1 A
30346 CCAGTTTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (28 bp):
ATAGCCTCTAAATGGGATGCTTCTATGA
Found at i:39037 original size:24 final size:25
Alignment explanation
Indices: 39010--39081 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 25
39000 ATTCATTTAT
39010 GTTCGTG-AACGTTCGGTTATGTTC
1 GTTCGTGTAACGTTCGGTTATGTTC
* * *
39034 GTTC-TGTTATGTTCGTTTATGTTC
1 GTTCGTGTAACGTTCGGTTATGTTC
* * *
39058 GTTCG-GTTATGTTCGTTTATGTTC
1 GTTCGTGTAACGTTCGGTTATGTTC
39082 ATTCATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.10, C:0.14, G:0.25, T:0.51
Consensus pattern (25 bp):
GTTCGTGTAACGTTCGGTTATGTTC
Found at i:39042 original size:14 final size:14
Alignment explanation
Indices: 39019--39074 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
39009 TGTTCGTGAA
39019 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
39033 CGTTCTGTTATGTT
1 CGTTCGGTTATGTT
39047 CG-T---TTATGTT
1 CGTTCGGTTATGTT
39057 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
39071 CGTT
1 CGTT
39075 TATGTTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.07, C:0.14, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:39091 original size:24 final size:23
Alignment explanation
Indices: 39020--39094 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
39010 GTTCGTGAAC
*
39020 GTTCGGTTATGTTCGTTCTGTTAT
1 GTTCGTTTATGTTCGTTCT-TTAT
*
39044 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-TTTAT
*
39068 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTC-TTTAT
39092 GTT
1 GTT
39095 TAACCTAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.56
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCTTTAT
Found at i:39922 original size:12 final size:11
Alignment explanation
Indices: 39894--39934 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
39884 TGGGGCAATG
39894 TCGAGCTTGAA
1 TCGAGCTTGAA
39905 TCGAGCTTAGAA
1 TCGAGCTT-GAA
*
39917 TTGAGCTTGAA
1 TCGAGCTTGAA
39928 TCGAGCT
1 TCGAGCT
39935 CAAGTCTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:40200 original size:32 final size:32
Alignment explanation
Indices: 40159--40219 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
40149 GGGTCTCCAA
**
40159 CGTTTATGTTCGTGTTCATTTATGTTCATGTT
1 CGTTTATGTTCGTGCGCATTTATGTTCATGTT
*
40191 CGTTTATGTTCGTGCGCGTTTATGTTCAT
1 CGTTTATGTTCGTGCGCATTTATGTTCAT
40220 TTAATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.11, C:0.15, G:0.21, T:0.52
Consensus pattern (32 bp):
CGTTTATGTTCGTGCGCATTTATGTTCATGTT
Found at i:40210 original size:16 final size:16
Alignment explanation
Indices: 40159--40217 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
40149 GGGTCTCCAA
40159 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
* *
40175 CATTTATGTTCATGTT
1 CGTTTATGTTCGTGTT
**
40191 CGTTTATGTTCGTGCG
1 CGTTTATGTTCGTGTT
40207 CGTTTATGTTC
1 CGTTTATGTTC
40218 ATTTAATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.10, C:0.15, G:0.22, T:0.53
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:42610 original size:76 final size:77
Alignment explanation
Indices: 42479--42622 Score: 191
Period size: 76 Copynumber: 1.9 Consensus size: 77
42469 TTATAGTACA
* * * * * *
42479 TTTATATTATTTAGTATAAATATATTGTATGTTTATATGGTATAGCATAC-CTATATTATATTAT
1 TTTATACTATATAGTATAAATATACTATATGTTTATATGATATAGCATACAATATATTATATTAT
42543 ATAGTGCATATG
66 ATAGTGCATATG
* * *
42555 TTTATACTATATAGTATAAATATACTATATGTTTATATGATGTAGCCTTCATATATATTATATTA
1 TTTATACTATATAGTATAAATATACTATATGTTTATATGATATAGCATACA-ATATATTATATTA
42620 TAT
65 TAT
42623 TGTAGATACG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
76 42 0.74
78 15 0.26
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (77 bp):
TTTATACTATATAGTATAAATATACTATATGTTTATATGATATAGCATACAATATATTATATTAT
ATAGTGCATATG
Found at i:42758 original size:15 final size:16
Alignment explanation
Indices: 42721--42750 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42711 CATCAATATA
42721 TATTATTATATCTTAC
1 TATTATTATATCTTAC
42737 TATTATTAT-TCTTA
1 TATTATTATATCTTA
42751 TTTTTATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTATTATATCTTAC
Found at i:46058 original size:18 final size:19
Alignment explanation
Indices: 46027--46069 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
46017 GAACATTATA
46027 AAAATAAGTAA-TTTTAAT
1 AAAATAAGTAATTTTTAAT
* * *
46045 AAAATAATTTATTTTTATT
1 AAAATAAGTAATTTTTAAT
46064 AAAATA
1 AAAATA
46070 TCAAGTTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AAAATAAGTAATTTTTAAT
Found at i:48980 original size:2 final size:2
Alignment explanation
Indices: 48973--49048 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
48963 TATAGTATTG
48973 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
49015 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
49049 CATTTTCGCT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51759 original size:19 final size:19
Alignment explanation
Indices: 51735--51774 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
51725 ACACTTCTCC
51735 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
51754 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
51773 CA
1 CA
51775 CTTAAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
CATTTATCATTTTAAAACA
Found at i:54055 original size:21 final size:21
Alignment explanation
Indices: 54029--54068 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54019 CAGAACCCCA
*
54029 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
54050 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
54069 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:54097 original size:20 final size:22
Alignment explanation
Indices: 54051--54110 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
54041 TTCCCCTGTG
*
54051 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTGCAAA
54074 GGGGGAATCGGTTCCC-GC-AA
1 GGGGGAATCGGTTCCCTGCAAA
* *
54094 GGGGGGATCGATTCCCT
1 GGGGGAATCGGTTCCCT
54111 CTGCACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 16 0.48
21 1 0.03
22 3 0.09
23 13 0.39
ACGTcount: A:0.18, C:0.25, G:0.37, T:0.20
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTGCAAA
Found at i:71080 original size:27 final size:27
Alignment explanation
Indices: 71022--71085 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
71012 ATTTAAAATT
** *
71022 AAAATTTAAATAATACCTTAATTTTTT
1 AAAATTTAAATAATACCTTAAACTTTC
*
71049 TAAATTTAAATAAGT-CCTTAAACTTTC
1 AAAATTTAAATAA-TACCTTAAACTTTC
71076 AAAATATTAA
1 AAAAT-TTAA
71086 TTAGGCCCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (27 bp):
AAAATTTAAATAATACCTTAAACTTTC
Found at i:72018 original size:29 final size:31
Alignment explanation
Indices: 71984--72060 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
71974 CCCAAATTTT
*
71984 GTTTAGTGACCAAAATGTAAAATT-TGAA-A
1 GTTTAGTGACCAAAATGTAAAATTAGGAAGA
* * *
72013 GTTTAGTGGCCAAAGTATAAAATTAGGAAGA
1 GTTTAGTGACCAAAATGTAAAATTAGGAAGA
*
72044 GTTTAGGGACCAAAATG
1 GTTTAGTGACCAAAATG
72061 GTAATTTTAC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 3 0.08
31 14 0.37
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (31 bp):
GTTTAGTGACCAAAATGTAAAATTAGGAAGA
Found at i:72485 original size:23 final size:23
Alignment explanation
Indices: 72458--72522 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
72448 TGGTATGAAT
*
72458 GTAATTATCAAGTTTCATTAATG
1 GTAATTATCAAATTTCATTAATG
*
72481 GTAATTATCAATTTTCATTAATG
1 GTAATTATCAAATTTCATTAATG
72504 GTAATTATCAAATTTCATT
1 GTAATTATCAAATTTCATT
72523 TAAGCTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.46
Consensus pattern (23 bp):
GTAATTATCAAATTTCATTAATG
Found at i:74117 original size:39 final size:39
Alignment explanation
Indices: 74059--74181 Score: 201
Period size: 39 Copynumber: 3.2 Consensus size: 39
74049 ATGAAACCTA
* *
74059 GTGCATATGATGGGCACGACTTTATGTGTAAGCACTTCG
1 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
* *
74098 GTGCATATGGTGGGTACGACCTTATGTGTAAGCACTTTG
1 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
*
74137 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCA
1 GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
74176 GTGCAT
1 GTGCAT
74182 GTTTGACTTG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (39 bp):
GTGCATATGGTGGGCACGACCTTATGTGTAAGCACTTCG
Found at i:77573 original size:52 final size:52
Alignment explanation
Indices: 77506--77615 Score: 177
Period size: 52 Copynumber: 2.1 Consensus size: 52
77496 CTGGACGTGG
*
77506 GAAATCACGGGTTGAGCATG-GAGATGTTGCTCCATGTCCCAGGGTGAGCACA
1 GAAAGCACGGGTTGAGCA-GAGAGATGTTGCTCCATGTCCCAGGGTGAGCACA
* *
77558 GAAAGCACGGGTTGAGCAGAGAGATGTTGTTGCATGTCCCAGGGTGAGCACA
1 GAAAGCACGGGTTGAGCAGAGAGATGTTGCTCCATGTCCCAGGGTGAGCACA
77610 GAAAGC
1 GAAAGC
77616 TGCATGTGGG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 1 0.02
52 53 0.98
ACGTcount: A:0.27, C:0.19, G:0.35, T:0.19
Consensus pattern (52 bp):
GAAAGCACGGGTTGAGCAGAGAGATGTTGCTCCATGTCCCAGGGTGAGCACA
Found at i:78337 original size:17 final size:19
Alignment explanation
Indices: 78303--78339 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
78293 TTAGGGATCA
78303 TTTTATATTTGATATTTAT
1 TTTTATATTTGATATTTAT
*
78322 TTTTAT-TTTTAT-TTTAT
1 TTTTATATTTGATATTTAT
78339 T
1 T
78340 AAAGTAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTATATTTGATATTTAT
Found at i:81510 original size:32 final size:32
Alignment explanation
Indices: 81465--81525 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
81455 TCTCGCACCC
* *
81465 TTTCTTTTACTTTTGCTTTGTTTTCAATCCCA
1 TTTCTTTTACTTTTGATTTGTTTTAAATCCCA
*
81497 TTTCTTTTGCTTTTGATTTGTTTTAAATC
1 TTTCTTTTACTTTTGATTTGTTTTAAATC
81526 AAATAAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.13, C:0.16, G:0.08, T:0.62
Consensus pattern (32 bp):
TTTCTTTTACTTTTGATTTGTTTTAAATCCCA
Found at i:85807 original size:31 final size:31
Alignment explanation
Indices: 85772--85869 Score: 144
Period size: 31 Copynumber: 3.2 Consensus size: 31
85762 CTTAGGCCTC
*
85772 AGTGATCACATCTTAATTAAATAAAAATGAA
1 AGTGATCAAATCTTAATTAAATAAAAATGAA
*
85803 AGTGA-CAAAATCTTAATTAAATAAAAACGAA
1 AGTGATC-AAATCTTAATTAAATAAAAATGAA
*
85834 AGTGATCAAATCTTAATTAAACAAAAATGAA
1 AGTGATCAAATCTTAATTAAATAAAAATGAA
*
85865 CGTGA
1 AGTGA
85870 CTAAATATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
30 1 0.02
31 58 0.97
32 1 0.02
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.26
Consensus pattern (31 bp):
AGTGATCAAATCTTAATTAAATAAAAATGAA
Found at i:87191 original size:34 final size:34
Alignment explanation
Indices: 87140--87227 Score: 158
Period size: 34 Copynumber: 2.6 Consensus size: 34
87130 CTCGACTCGA
*
87140 CTCGACTCGTTGCTCGTTAATTCGTTAAAATTTTG
1 CTCGACTC-ATGCTCGTTAATTCGTTAAAATTTTG
87175 CTCGACTCATGCTCGTTAATTCGTTAAAATTTTG
1 CTCGACTCATGCTCGTTAATTCGTTAAAATTTTG
87209 CTCGACTCATGCTCGTTAA
1 CTCGACTCATGCTCGTTAA
87228 GAAAACTCGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 44 0.85
35 8 0.15
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.40
Consensus pattern (34 bp):
CTCGACTCATGCTCGTTAATTCGTTAAAATTTTG
Found at i:93763 original size:31 final size:31
Alignment explanation
Indices: 93728--93787 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
93718 GTCAAACGGT
*
93728 CGGTTATATCGGGAACCATACTGCAAACGAA
1 CGGTTATATCGGGAACCATACTACAAACGAA
* * *
93759 CGGTTATGTCGGGGACCATATTACAAACG
1 CGGTTATATCGGGAACCATACTACAAACG
93788 GATTAAATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (31 bp):
CGGTTATATCGGGAACCATACTACAAACGAA
Found at i:95281 original size:2 final size:2
Alignment explanation
Indices: 95274--95320 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
95264 GCATAACAAG
95274 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
95316 GA GA G
1 GA GA G
95321 CTCCAATTCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.