Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005731.1 Hibiscus syriacus cultivar Beakdansim tig00013392_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: 96564
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:82 original size:19 final size:21
Alignment explanation
Indices: 58--97 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48 AGTTTATTTT
58 TAAA-TTTATTT-AATTATCG
1 TAAATTTTATTTCAATTATCG
*
77 TAAATTTTGTTTCAATTATCG
1 TAAATTTTATTTCAATTATCG
98 AACTTAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
TAAATTTTATTTCAATTATCG
Found at i:145 original size:30 final size:32
Alignment explanation
Indices: 92--191 Score: 118
Period size: 30 Copynumber: 3.2 Consensus size: 32
82 TTTGTTTCAA
* *
92 TTATCGAACTT-AAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAG-ATTTAAGTATTTGAAT
124 TTATCGAA-TTGGAAG-TTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGATTTAAGTATTTGAAT
* *
154 TTATCAAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAG-ATTTAAGTATTTGAAT
186 TTATCG
1 TTATCG
192 TAAACTTTGT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
30 22 0.37
31 9 0.15
32 16 0.27
33 13 0.22
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (32 bp):
TTATCGAACTTGGAAGATTTAAGTATTTGAAT
Found at i:277 original size:17 final size:17
Alignment explanation
Indices: 251--283 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
241 GTTTTTTTAT
*
251 AACCGTTTTTTAAAAAA
1 AACCGATTTTTAAAAAA
268 AACCGATTTTTAAAAA
1 AACCGATTTTTAAAAA
284 CCGAAACCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (17 bp):
AACCGATTTTTAAAAAA
Found at i:2496 original size:14 final size:14
Alignment explanation
Indices: 2463--2504 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
2453 AAGCTTGTAG
2463 CTGTAGAAAACAGA
1 CTGTAGAAAACAGA
2477 -TGTAGAAAACAGA
1 CTGTAGAAAACAGA
2490 CTGTAGAAAACAGA
1 CTGTAGAAAACAGA
2504 C
1 C
2505 AAGTCTGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.48
14 14 0.52
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
CTGTAGAAAACAGA
Found at i:4465 original size:36 final size:36
Alignment explanation
Indices: 4408--4504 Score: 167
Period size: 36 Copynumber: 2.7 Consensus size: 36
4398 CTGTTTAGAT
*
4408 GCAACAGGATCTGAATCTGGTTCTTGGCTTTCAGAG
1 GCAACAGGATCCGAATCTGGTTCTTGGCTTTCAGAG
* *
4444 GTAACAGGATCCGAATATGGTTCTTGGCTTTCAGAG
1 GCAACAGGATCCGAATCTGGTTCTTGGCTTTCAGAG
4480 GCAACAGGATCCGAATCTGGTTCTT
1 GCAACAGGATCCGAATCTGGTTCTT
4505 AGCGAATGCT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (36 bp):
GCAACAGGATCCGAATCTGGTTCTTGGCTTTCAGAG
Found at i:15970 original size:26 final size:26
Alignment explanation
Indices: 15922--15972 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
15912 ATTATCTTAT
* * **
15922 AATGTTGCTTGTGGAACTTAGCAAAA
1 AATGTTACTTGTCGAACCCAGCAAAA
15948 AATGTTACTTGTCGAACCCAGCAAA
1 AATGTTACTTGTCGAACCCAGCAAA
15973 TGCATTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (26 bp):
AATGTTACTTGTCGAACCCAGCAAAA
Found at i:16094 original size:38 final size:40
Alignment explanation
Indices: 16020--16111 Score: 134
Period size: 38 Copynumber: 2.3 Consensus size: 40
16010 ATGGCATTCC
*
16020 GGGCCAAAATACATTTCCAGGTGAAGTAAAGGAGCTCTACTT
1 GGGCGAAAATACATTTCCAGGT--AGTAAAGGAGCTCTACTT
*
16062 TGGCGAAAATACATTT-CAGGT-GTAAAGGAGCTCTACTT
1 GGGCGAAAATACATTTCCAGGTAGTAAAGGAGCTCTACTT
16100 GGGCGAAAATAC
1 GGGCGAAAATAC
16112 GTTTTCGAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
38 28 0.60
41 5 0.11
42 14 0.30
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (40 bp):
GGGCGAAAATACATTTCCAGGTAGTAAAGGAGCTCTACTT
Found at i:18589 original size:23 final size:22
Alignment explanation
Indices: 18551--18601 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
18541 ATTGCACTAA
*
18551 AGTGCCGATAGAATTGCATCGG
1 AGTGCCGATAGAATTGCACCGG
* *
18573 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCG-ATAGAATTGCACCGG
18596 AGTGCC
1 AGTGCC
18602 ATATAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.22
Consensus pattern (22 bp):
AGTGCCGATAGAATTGCACCGG
Found at i:23849 original size:2 final size:2
Alignment explanation
Indices: 23842--23895 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
23832 CATGTAGCAA
23842 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
*
23884 AT AT AC AT AT AT
1 AT AT AT AT AT AT
23896 GTCATTATCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24229 original size:23 final size:23
Alignment explanation
Indices: 24203--24280 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
24193 CACCACAGCT
24203 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
24226 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
24249 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
24272 TATAATAAT
1 CAT-ATAAT
24281 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:25146 original size:2 final size:2
Alignment explanation
Indices: 25139--25169 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25129 ATACTGATAA
25139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25170 GACACCCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25258 original size:25 final size:25
Alignment explanation
Indices: 25230--25281 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
25220 TTATTAATAA
25230 TAATAATAATAATATTAATTATTAC
1 TAATAATAATAATATTAATTATTAC
* *
25255 TAATAATATTATTATTAATTATTAC
1 TAATAATAATAATATTAATTATTAC
25280 TA
1 TA
25282 TACCACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATAATAATAATATTAATTATTAC
Found at i:25260 original size:19 final size:18
Alignment explanation
Indices: 25236--25271 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
25226 ATAATAATAA
25236 TAATAATATTAATTATTAC
1 TAATAATATT-ATTATTAC
25255 TAATAATATTATTATTA
1 TAATAATATTATTATTA
25272 ATTATTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATATTATTATTAC
Found at i:25261 original size:22 final size:24
Alignment explanation
Indices: 25218--25281 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
25208 ATATTATTAC
* *
25218 TATTATTAA-TAATAATAATAATA
1 TATTATTAATTATTACTAATAATA
25241 -A-TATTAATTATTACTAATAATA
1 TATTATTAATTATTACTAATAATA
25263 TTATTATTAATTATTACTA
1 -TATTATTAATTATTACTA
25282 TACCACAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 6 0.17
22 13 0.37
24 1 0.03
25 15 0.43
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTATTAATTATTACTAATAATA
Found at i:25952 original size:145 final size:142
Alignment explanation
Indices: 25607--26079 Score: 450
Period size: 144 Copynumber: 3.3 Consensus size: 142
25597 AGACTATCAA
* * *
25607 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGATGGCGGTGGATCGGAGAAAATAAGCC
1 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGGCGGTGAATCGGAGAAAATAAGTC
* * * * * * *
25672 GAACGATTTTTGGCCTCTTGCCTGCGATCGGGATCTCTGATTAACATTCTGAACGATTAAAGTTT
66 GAACGATTTTTGGCCTCTTGCCGGCGATCGGGATCTCCGATCAATATTCGGAACG-TAAAAGTTG
*
25737 TGAGA-G-ACCATCAC
130 TGA-ATGTA--AACAC
* ** *
25751 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGACGGCAAATCAGAGAAAATAAGTC
1 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGGCGGTGAATCGGAGAAAATAAGTC
* * * * *
25816 GAACGGTTTTTAGCCTTTTTCCGGCGATCGGGATCTCCGATCAATACTTC-AAACAGTGAAAAGT
66 GAACGATTTTTGGCCTCTTGCCGGCGATCGGGATCTCCGATCAATA-TTCGGAAC-GT-AAAAGT
25880 TGTGTAATGTAAACAC
128 TGTG-AATGTAAACAC
* * * * * * *
25896 GAACAGCATACTGAAATTTCATGACGATCAGACGGTAGACGGTGGTGAATCGGAGAAAACAAATC
1 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGGCGGTGAATCGGAGAAAATAAGTC
* * * * *
25961 CAGACGATATTTGGCCTCTCGCCGGTGATC-GGAACATCCGATCAATATTCGGAACGGTCAAAAG
66 GA-ACGATTTTTGGCCTCTTGCCGGCGATCGGGATC-TCCGATCAATATTCGGAAC-GT-AAAAG
* *
26025 TTGCGCGATGTAAACAC
127 TTGTG-AATGTAAACAC
* * * * *
26042 GAACATCATACTGAAATTTCAGAACAATCGGACGGTGG
1 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGG
26080 CACGACAGCG
Statistics
Matches: 269, Mismatches: 51, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
144 100 0.37
145 79 0.29
146 89 0.33
147 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (142 bp):
GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGGCGGTGAATCGGAGAAAATAAGTC
GAACGATTTTTGGCCTCTTGCCGGCGATCGGGATCTCCGATCAATATTCGGAACGTAAAAGTTGT
GAATGTAAACAC
Found at i:26045 original size:146 final size:145
Alignment explanation
Indices: 25748--26077 Score: 349
Period size: 146 Copynumber: 2.3 Consensus size: 145
25738 GAGAGACCAT
* * *
25748 CACGAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGACGGCAAATCAGAGAAAATAA
1 CACGAACAACATACTGAAATTTCAGGACGATCAGACGGTAGACGACGGCAAATCAGAGAAAACAA
* * * * * ** * *
25813 GTCGAACGGTTTTTAGCCTTTTTCCGGCGATCGGGATCTCCGATCAATACTTCAAACAGTGAAAA
66 ATCCAACGATATTTAGCCTCTCGCCGGCGATCGGGAACTCCGATCAATACTTCAAACAGTCAAAA
* *
25878 GTTGTGTAATGTAAA
131 GTTGCGCAATGTAAA
* * ** ** *
25893 CACGAACAGCATACTGAAATTTCATGACGATCAGACGGTAGACGGTGGTGAATCGGAGAAAACAA
1 CACGAACAACATACTGAAATTTCAGGACGATCAGACGGTAGACGACGGCAAATCAGAGAAAACAA
* * * *
25958 ATCCAGACGATATTTGGCCTCTCGCCGGTGATC-GGAACATCCGATCAATA-TTCGGAACGGTCA
66 ATCCA-ACGATATTTAGCCTCTCGCCGGCGATCGGGAAC-TCCGATCAATACTTC-AAACAGTCA
*
26021 AAAGTTGCGCGATGTAAA
128 AAAGTTGCGCAATGTAAA
* * * *
26039 CACGAACATCATACTGAAATTTCAGAACAATCGGACGGT
1 CACGAACAACATACTGAAATTTCAGGACGATCAGACGGT
26078 GGCACGACAG
Statistics
Matches: 151, Mismatches: 31, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
145 65 0.43
146 86 0.57
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.22
Consensus pattern (145 bp):
CACGAACAACATACTGAAATTTCAGGACGATCAGACGGTAGACGACGGCAAATCAGAGAAAACAA
ATCCAACGATATTTAGCCTCTCGCCGGCGATCGGGAACTCCGATCAATACTTCAAACAGTCAAAA
GTTGCGCAATGTAAA
Found at i:28828 original size:55 final size:55
Alignment explanation
Indices: 28764--28905 Score: 205
Period size: 55 Copynumber: 2.6 Consensus size: 55
28754 ACATTCAAGT
** * *
28764 GATTCATGAAGAAGGACGCCCGATGAATGAAGAAATTTGAACCTGATTGAAGAAC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
* *
28819 GATTCATGAAGATGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGACC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
*
28874 GATCCATGAAGAAAGG-CATCCGATGAATGAAG
1 GATTCATGAAG-AAGGACATCCGATGAATGAAG
28906 TTTGAAGTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
55 75 0.96
56 3 0.04
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (55 bp):
GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
Found at i:34390 original size:15 final size:15
Alignment explanation
Indices: 34370--34403 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
34360 GGTCAACTCC
*
34370 GGTCAACGGTCAACG
1 GGTCAACAGTCAACG
34385 GGTCAACAGTCAACG
1 GGTCAACAGTCAACG
34400 GGTC
1 GGTC
34404 GGGTCGGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.15
Consensus pattern (15 bp):
GGTCAACAGTCAACG
Found at i:34435 original size:32 final size:31
Alignment explanation
Indices: 34396--34457 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
34386 GTCAACAGTC
34396 AACGGGTCGGGTCGGGTCAAACGGGTCGGGTA
1 AACGGGTCGGGTCGGGT-AAACGGGTCGGGTA
*
34428 AACGGGTCTGGTCGGGTAAACGGGTCGGGT
1 AACGGGTCGGGTCGGGTAAACGGGTCGGGT
34458 CGGGCTGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.18, C:0.18, G:0.47, T:0.18
Consensus pattern (31 bp):
AACGGGTCGGGTCGGGTAAACGGGTCGGGTA
Found at i:34442 original size:18 final size:18
Alignment explanation
Indices: 34417--34461 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
34407 TCGGGTCAAA
34417 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
34435 CTGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
34453 CGGGTCGGG
1 CGGGTCGGG
34462 CTGTGACCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.18, G:0.51, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:34457 original size:13 final size:14
Alignment explanation
Indices: 34403--34440 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
34393 GTCAACGGGT
34403 CGGGTCGGGTCAAA
1 CGGGTCGGGTCAAA
34417 CGGGTCGGGT-AAA
1 CGGGTCGGGTCAAA
*
34430 CGGGTCTGGTC
1 CGGGTCGGGTC
34441 GGGTAAACGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (14 bp):
CGGGTCGGGTCAAA
Found at i:36889 original size:7 final size:7
Alignment explanation
Indices: 36875--36963 Score: 53
Period size: 7 Copynumber: 12.7 Consensus size: 7
36865 CAGAGCCAAA
36875 AAAAAAG
1 AAAAAAG
*
36882 AGAAAAG
1 AAAAAAG
36889 AAAAAAG
1 AAAAAAG
36896 AAATTAAAG
1 AAA--AAAG
36905 CAAAGAAA-
1 -AAA-AAAG
*
36913 AAAAGAG
1 AAAAAAG
*
36920 CAACAAAG
1 -AAAAAAG
*
36928 -AACAA-
1 AAAAAAG
36933 AAAAAAG
1 AAAAAAG
36940 -AAAAAG
1 AAAAAAG
36946 AAAAAA-
1 AAAAAAG
*
36952 AACAAAG
1 AAAAAAG
36959 AAAAA
1 AAAAA
36964 GGGACGATAA
Statistics
Matches: 62, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
6 20 0.32
7 27 0.44
8 5 0.08
9 7 0.11
10 3 0.05
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:36892 original size:14 final size:13
Alignment explanation
Indices: 36848--36896 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
36838 CAATCAGAAC
36848 AAAAAGAGAAAAA
1 AAAAAGAGAAAAA
*
36861 AAAACAGAGCCAAAA
1 AAAA-AGAG-AAAAA
36876 AAAAAGAGAAAAGA
1 AAAAAGAGAAAA-A
36890 AAAAAGA
1 AAAAAGA
36897 AATTAAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 7 0.23
14 16 0.52
15 8 0.26
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:36893 original size:18 final size:18
Alignment explanation
Indices: 36872--36962 Score: 64
Period size: 17 Copynumber: 4.9 Consensus size: 18
36862 AAACAGAGCC
36872 AAAAAAAAAGAGAAAAG-
1 AAAAAAAAAGAGAAAAGA
* **
36889 AAAAAAGAA-ATTAAAGCA
1 AAAAAAAAAGAGAAAAG-A
36907 AAGAAAAAAAGAGCAACAAAGA
1 AA-AAAAAAAGAG--A-AAAGA
36929 ACAAAAAAAAGA-AAAAGA
1 A-AAAAAAAAGAGAAAAGA
36947 AAAAAAACAA-AGAAAA
1 AAAAAAA-AAGAGAAAA
36963 AGGGACGATA
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
16 5 0.09
17 15 0.26
18 14 0.24
19 7 0.12
20 1 0.02
22 11 0.19
23 5 0.09
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAGAGAAAAGA
Found at i:38036 original size:32 final size:32
Alignment explanation
Indices: 38000--38073 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
37990 GCATCGTTAA
* *
38000 AGATTCAACAACAAATGTTGGGGCATATTTGG
1 AGATTCAACAACAAATATTGGGGCATATATGG
***
38032 AGATTCAACATTGAATATTGGGGCATATATGG
1 AGATTCAACAACAAATATTGGGGCATATATGG
*
38064 GGATTCAACA
1 AGATTCAACA
38074 TCCTGATGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (32 bp):
AGATTCAACAACAAATATTGGGGCATATATGG
Found at i:38398 original size:43 final size:43
Alignment explanation
Indices: 38349--38472 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
38339 ACGAAGGCGC
**
38349 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAATG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
38392 GATCCACGATTTCAACTCCACGACGGAGGATATTGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
38435 CATCCACGGTTTCAACTTCACGACGAAGGAAATCGTAC
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTAC
38473 ACACAAGCAG
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
Found at i:38733 original size:43 final size:43
Alignment explanation
Indices: 38684--38807 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
38674 ACGAAGGTGC
* **
38684 CATCCACGATATCAACTCCACGACGGAGGATATCGTACCAATG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * *
38727 GATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
38770 CATCCACGGTTTCAACTTCACGACGAAGGAAATCGTAC
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTAC
38808 ACACAAGCAA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
Found at i:38844 original size:335 final size:335
Alignment explanation
Indices: 38234--39345 Score: 1730
Period size: 335 Copynumber: 3.3 Consensus size: 335
38224 TGCAGCTTTT
* *
38234 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAGCACAAGCTTGGATTTTAAC
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
* * *
38299 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCATGACGAAGGCGCCATCCACGATTTCAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGTGCCATCCACGATATCAA
*
38364 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATTGTG
131 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
38429 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
196 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
*
38494 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGACGGAGTGTCTGTCAATAAACT
261 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
*
38559 TTTCAGTTTC
326 TTCCAGTTTC
*
38569 AGAGCCAATTTTAACTTCACGACGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
* *
38634 TTCACGACGAAGGATATTCAAGTTAAGGCTCAATTTCACGACGAAGGTGCCATCCACGATATCAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGTGCCATCCACGATATCAA
38699 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
131 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
*
38764 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAACATTCATCTCT
196 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
38829 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
261 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
38894 TTCCAGTTTC
326 TTCCAGTTTC
* * *
38904 AGAGCCAATTTTAACTTCACGGCGAAGGATATTGGACTCGAAACAGCACAAGCTTGGATTTCAAC
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
** * *
38969 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAA--TGATATTCAAG-TCAAGG
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGTGCCATCCACGAT--A--
* *
39031 CTCAACTTCACGACGAAGG----CG--CC-----ATCCACGATTTCAACTCCACGACGGAGGATA
127 -TCAACTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATA
* * * *
39085 TCGTGCCCACACATCCACGATTTCAACTTCACGACGAAGGGAATCGTACACACAAGCAGTATCCA
191 TCGTGCCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCA
* *
39150 TCTCTAGATTGGATTTCAACTTCACGACGAATGATATCCAACTCGAAGAAGGAGTGTCTGTCAAT
256 TCTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAAT
39215 AAACTTTCCAGTTTC
321 AAACTTTCCAGTTTC
* * * *
39230 AGAGTCAATTTCAACTTCACGTCGAAGGATATTGGCCTCGAAACAACACAACTTAACTTGGATTT
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAACAC-A---AGCTTGGATTT
* * * *
39295 CAACTTCACGACTAAGGATATCCAATTCAAGGTTCAACTTCACGACGAAGG
62 CAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGG
39346 GAATCGTACC
Statistics
Matches: 727, Mismatches: 39, Indels: 25
0.92 0.05 0.03
Matches are distributed among these distances:
326 213 0.29
327 1 0.00
330 55 0.08
331 2 0.00
332 1 0.00
333 9 0.01
334 1 0.00
335 429 0.59
337 16 0.02
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (335 bp):
AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGTGCCATCCACGATATCAA
CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
TTCCAGTTTC
Found at i:39007 original size:34 final size:34
Alignment explanation
Indices: 38964--39049 Score: 163
Period size: 34 Copynumber: 2.5 Consensus size: 34
38954 AGCTTGGATT
38964 TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
1 TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
*
38998 TCAACTTCACGACGAATGATATTCAAGTCAAGGC
1 TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
39032 TCAACTTCACGACGAAGG
1 TCAACTTCACGACGAAGG
39050 CGCCATCCAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (34 bp):
TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
Found at i:39476 original size:36 final size:36
Alignment explanation
Indices: 39436--39514 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
39426 AATGAGCCAT
* *
39436 CCTTGAAACAAATTTTGTCTCTCATGAGACAGTTTC
1 CCTTGAAACAAATTTTATCTCTCATGAGACAATTTC
**
39472 CCTTGAAACAAATTTTATCTCTTTTGAGACAATTTC
1 CCTTGAAACAAATTTTATCTCTCATGAGACAATTTC
*
39508 TCTTGAA
1 CCTTGAA
39515 GCATCATTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.39
Consensus pattern (36 bp):
CCTTGAAACAAATTTTATCTCTCATGAGACAATTTC
Found at i:39808 original size:3 final size:3
Alignment explanation
Indices: 39792--39874 Score: 58
Period size: 3 Copynumber: 26.7 Consensus size: 3
39782 GTCGAAAAAA
* * * * * *
39792 TAT TAT TAAA TAT TAT TAT TAC TAT TAT TTT TAA TAA TAA TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
39838 TAT TAAT TAT TAC TAA TAA TAT TAT TAT TAAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA
39875 CTATACCACA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
3 58 0.88
4 8 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:39825 original size:25 final size:27
Alignment explanation
Indices: 39792--39867 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 27
39782 GTCGAAAAAA
39792 TATTATTA-AATATTATTATTACT-AT
1 TATTATTATAATATTATTATTACTAAT
* * *
39817 TATTTTTAATAATAATATTATTATTAAT
1 TATTATT-ATAATATTATTATTACTAAT
*
39845 TATTACTAATAATATTATTATTA
1 TATTA-TTATAATATTATTATTA
39868 ATTATTACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
25 6 0.15
26 1 0.02
27 13 0.32
28 20 0.49
29 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTATTATAATATTATTATTACTAAT
Found at i:39855 original size:28 final size:27
Alignment explanation
Indices: 39800--39879 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 27
39790 AATATTATTA
**
39800 AATATTATTATTACTATTATTTTTAATAAT
1 AATATTATTATTA--ATTATTACT-ATAAT
39830 AATATTATTATTAATTATTAC--TAAT
1 AATATTATTATTAATTATTACTATAAT
39855 AATATTATTATTAATTATTACTATA
1 AATATTATTATTAATTATTACTATA
39880 CCACAAAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
25 25 0.54
27 2 0.04
28 6 0.13
30 13 0.28
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
AATATTATTATTAATTATTACTATAAT
Found at i:39868 original size:25 final size:25
Alignment explanation
Indices: 39808--39877 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
39798 TAAATATTAT
* * *
39808 TATTACTATT-ATTTTTAATAATAA
1 TATTATTATTAATTATTACTAATAA
39832 TATTATTATTAATTATTACTAATAA
1 TATTATTATTAATTATTACTAATAA
39857 TATTATTATTAATTATTACTA
1 TATTATTATTAATTATTACTA
39878 TACCACAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 9 0.21
25 33 0.79
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTATTATTAATTATTACTAATAA
Found at i:40310 original size:145 final size:145
Alignment explanation
Indices: 40149--40670 Score: 480
Period size: 145 Copynumber: 3.6 Consensus size: 145
40139 GTTGATCGAA
* *
40149 ATCTCCGATCACCATTCCGAACGGTCAAAAGTTGTGCAAGACCATCACGAACAACATACTAAAAA
1 ATCTCCGATCAACATTCCGAACGGTCAAAAGTTGTGCAAGACCATCACGAACAACATACTGAAAA
* *
40214 TTCAGGACGATCAGACGGTGGACGGCGGTGGATCGGAGAAAATAAGCCAAACGGTTTTTGGCCTC
66 TTCAAGACGATCAGACGGTGGACGGCGGTGGATCGGAGAAAATAAGACAAACGGTTTTTGGCCTC
*
40279 TTGCCTGCGATCGGG
131 TTGCCGGCGATCGGG
* * * * * * *
40294 ATCTACGATTAACATTCTGAATGGTCAAAAGTTGCGCGAGACCATCAAGAACAACATACTGAAAA
1 ATCTCCGATCAACATTCCGAACGGTCAAAAGTTGTGCAAGACCATCACGAACAACATACTGAAAA
* ** * * * * *
40359 TTCAAGACGATCAGACGGTGGACGACGGCAGATCAGAGAAAATAAGTCGAACGGTTTTTAGCCTT
66 TTCAAGACGATCAGACGGTGGACGGCGGTGGATCGGAGAAAATAAGACAAACGGTTTTTGGCCTC
40424 TTGCCGGCGATCGGG
131 TTGCCGGCGATCGGG
* * * * * * *
40439 ATCTCCGATCAATACTT-CAAACAGTGAAAAGTTGTGTAATGTA--AACACGAACAGCATACTGA
1 ATCTCCGATCAACA-TTCCGAACGGTCAAAAGTTGTGCAA-G-ACCATCACGAACAACATACTGA
* * * * * * * * * * * *
40501 AATTTTATGAGGATCAGACGGTAGACGGTGGTGAATCGGAGAAAACAAATACAGACGATATTTGG
63 AAATTCAAGACGATCAGACGGTGGACGGCGGTGGATCGGAGAAAA-TAAGACAAACGGTTTTTGG
* *
40566 CCTCTCGCCGGTGATC-GG
127 CCTCTTGCCGGCGATCGGG
* * * * * * *
40584 AACATCCGATCAATATTCCGAACGGTCAAAAGTTGCGCGATG-TCAACACGAACATCATACTGAA
1 ATC-TCCGATCAACATTCCGAACGGTCAAAAGTTGTGC-AAGACCATCACGAACAACATACTGAA
* * *
40648 ATTTC-AGAACAATCGGACGGTGG
64 AATTCAAG-ACGATCAGACGGTGG
40671 CACGACAGCG
Statistics
Matches: 298, Mismatches: 69, Indels: 19
0.77 0.18 0.05
Matches are distributed among these distances:
145 208 0.70
146 88 0.30
147 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (145 bp):
ATCTCCGATCAACATTCCGAACGGTCAAAAGTTGTGCAAGACCATCACGAACAACATACTGAAAA
TTCAAGACGATCAGACGGTGGACGGCGGTGGATCGGAGAAAATAAGACAAACGGTTTTTGGCCTC
TTGCCGGCGATCGGG
Found at i:42294 original size:2 final size:2
Alignment explanation
Indices: 42289--42319 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
42279 CGTTTCGACA
42289 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42320 TACTTCTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:44151 original size:16 final size:16
Alignment explanation
Indices: 44112--44154 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
44102 AGCATCAGTT
*
44112 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
44128 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
44145 CTTATCAATC
1 CTTATCAATC
44155 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:45981 original size:2 final size:2
Alignment explanation
Indices: 45946--45970 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45936 CATGTAGCAA
45946 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
45971 CATGCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46322 original size:23 final size:23
Alignment explanation
Indices: 46296--46373 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
46286 CACCACAACT
46296 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
46319 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
46342 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
46365 TATAATAAT
1 CAT-ATAAT
46374 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:46551 original size:103 final size:103
Alignment explanation
Indices: 46380--46700 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
46370 TAATGTCCAT
* * *
46380 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
46445 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
46483 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
46548 GACTTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
46586 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGCATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
46651 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
46689 AAGGACCACATA
1 AAGGACCACATA
46701 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:51131 original size:23 final size:23
Alignment explanation
Indices: 51105--51163 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
51095 CACCACATCT
* *
51105 CGTATAATTGCACC-GAAGTGCTA
1 CGTAGAATTGCACCAG-AGTGCCA
* *
51128 CGTAGAATTACACCAGAGTGCCG
1 CGTAGAATTGCACCAGAGTGCCA
51151 CGTAGAATTGCAC
1 CGTAGAATTGCAC
51164 TGTAGTGCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCAGAGTGCCA
Found at i:58481 original size:15 final size:15
Alignment explanation
Indices: 58450--58490 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
58440 TTTGATTTAA
*
58450 TTATTTCAAGTTTGTT
1 TTATTT-AAGTTAGTT
*
58466 TTTTTTAAGTTAGTT
1 TTATTTAAGTTAGTT
58481 TTATTTAAGT
1 TTATTTAAGT
58491 CTATTATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.63
Consensus pattern (15 bp):
TTATTTAAGTTAGTT
Found at i:62238 original size:92 final size:92
Alignment explanation
Indices: 62081--62261 Score: 299
Period size: 92 Copynumber: 2.0 Consensus size: 92
62071 CATAGTAACA
* * *
62081 CCCGTTAATATTGAGTGATCGATTTATTACAAATCGATAACGTTAGCGACTAATTTGTTATTTTT
1 CCCGTTAATATTGAGTGACCGATTTATTACAAATCGATAACGTTAGCGACCAATTTGTTACTTTT
* *
62146 AAAACTTTAATAGGAAAAACAAAATTG
66 AAAACTTCAATAAGAAAAACAAAATTG
* *
62173 CCCGTTAATATTGAGTGACCGATTTATTACAAATCGATAACGTTAGTGACCAATTTGTTGCTTTT
1 CCCGTTAATATTGAGTGACCGATTTATTACAAATCGATAACGTTAGCGACCAATTTGTTACTTTT
62238 AAAACTTCAATAAGAAAAACAAAA
66 AAAACTTCAATAAGAAAAACAAAA
62262 ACTTACTCAA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 82 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (92 bp):
CCCGTTAATATTGAGTGACCGATTTATTACAAATCGATAACGTTAGCGACCAATTTGTTACTTTT
AAAACTTCAATAAGAAAAACAAAATTG
Found at i:64364 original size:28 final size:28
Alignment explanation
Indices: 64324--64386 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
64314 CCAACCTCAA
64324 GTTCCATTAGATGAAAGTGATCTGCTTT
1 GTTCCATTAGATGAAAGTGATCTGCTTT
64352 GTTCCATTAGATGAAAGTGATCTGCTTT
1 GTTCCATTAGATGAAAGTGATCTGCTTT
64380 GTTCCAT
1 GTTCCAT
64387 CTCCAAATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (28 bp):
GTTCCATTAGATGAAAGTGATCTGCTTT
Found at i:71313 original size:31 final size:31
Alignment explanation
Indices: 71275--71333 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
71265 TGTTAACACA
*
71275 AGACATCTAAAGTGGTAACATTTGTAATGTC
1 AGACATCTAAAGTGGTAACATTTATAATGTC
*
71306 AGACATCTAAAGTGGTAACGTTTATAAT
1 AGACATCTAAAGTGGTAACATTTATAAT
71334 TTAGGCACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (31 bp):
AGACATCTAAAGTGGTAACATTTATAATGTC
Found at i:72206 original size:16 final size:16
Alignment explanation
Indices: 72185--72217 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
72175 CCTCACCAAA
72185 ACAACGTCATTTTGGC
1 ACAACGTCATTTTGGC
72201 ACAACGTCATTTTGGC
1 ACAACGTCATTTTGGC
72217 A
1 A
72218 TGACTGTATT
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:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (16 bp):
ACAACGTCATTTTGGC
Found at i:72847 original size:16 final size:18
Alignment explanation
Indices: 72826--72858 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
72816 ATTAAATAAT
72826 AATAATA-AT-TTTTTTC
1 AATAATATATGTTTTTTC
72842 AATAATATATGTTTTTT
1 AATAATATATGTTTTTT
72859 TTGGAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
AATAATATATGTTTTTTC
Found at i:76851 original size:31 final size:31
Alignment explanation
Indices: 76785--76843 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
76775 AATTTAAGGT
*
76785 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAATGGTATTTGGACTTGAATTGAATTTAC
76816 AAAAT-GTATTTGGACTT-AATTGAATTTA
1 AAAATGGTATTTGGACTTGAATTGAATTTA
76844 TTCAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAATGGTATTTGGACTTGAATTGAATTTAC
Found at i:77069 original size:21 final size:21
Alignment explanation
Indices: 77043--77084 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
77033 ATTTGAATAT
*
77043 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
77064 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
77085 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:77401 original size:34 final size:32
Alignment explanation
Indices: 77362--77431 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
77352 TTTTGTAAAG
* *
77362 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
77396 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
77428 GGGA
1 GGGA
77432 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:79104 original size:21 final size:21
Alignment explanation
Indices: 79078--79127 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
79068 CCTATAATCG
79078 AGAAATCATTTTGCAACTTTT
1 AGAAATCATTTTGCAACTTTT
79099 AGAAATCATTTTGCAACTTTT
1 AGAAATCATTTTGCAACTTTT
*
79120 AGTAATCA
1 AGAAATCA
79128 ACGAACTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
AGAAATCATTTTGCAACTTTT
Found at i:84895 original size:90 final size:88
Alignment explanation
Indices: 84751--84916 Score: 206
Period size: 90 Copynumber: 1.9 Consensus size: 88
84741 AAAATAGTCC
* * * * * * * *
84751 TAACTAAATAGTCATTTTGGTCTTTTTTTTTTTTTTTGAGCATTTTGTCTCTCAACATTTTATTT
1 TAACAAAATAGTCATTTTGGTCATATTCTTTGTTTTTGAGCATTTTGGCCCTCAACATTTCATTT
*
84816 TAGGGTAAAAAAACCCTAATGTT
66 TAGGGCAAAAAAACCCTAATGTT
* **
84839 TAACAAAATAGTCATTTTAGTTCATATTCTTTGTTTTTGAAGCATTTTGGCCCTCAATGTTTCAT
1 TAACAAAATAGTCATTTT-GGTCATATTCTTTGTTTTTG-AGCATTTTGGCCCTCAACATTTCAT
84904 TTTAGGGCAAAAA
64 TTTAGGGCAAAAA
84917 GATCCCTATT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
88 17 0.27
89 15 0.23
90 32 0.50
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (88 bp):
TAACAAAATAGTCATTTTGGTCATATTCTTTGTTTTTGAGCATTTTGGCCCTCAACATTTCATTT
TAGGGCAAAAAAACCCTAATGTT
Found at i:89734 original size:149 final size:150
Alignment explanation
Indices: 89455--89746 Score: 380
Period size: 149 Copynumber: 2.0 Consensus size: 150
89445 GGTCCAAAAA
* *
89455 GGATAGGAATTTATCTTGATTAAGAAGTCGACTTATCAACCACACCAAATTGTCCCCATAAACTG
1 GGATAGGAATTTATCTTGATTAAGAAGTCCACTTATCAACCACACCAAAGTGTCCCCATAAACTG
* *
89520 GAACAAACAGAAAAACAACGGGCATTTGCGGGCTTCTCAGAACAGTAACATAAAAGGAAGGAAAA
66 GAACAAACAGAAAAACAACGGACATTTGCGGGCTTCTCAGAACAGTAACATAAAAGGAAGAAAAA
*
89585 GGGAA-GCAAAATCATCCTG
131 GAGAATGCAAAATCATCCTG
*
89604 GGATAGGAATTTATCTTGA-TAAGAAG-CACACTTATCAACCATACCAAAGTGTGCCCC-TAAAC
1 GGATAGGAATTTATCTTGATTAAGAAGTC-CACTTATCAACCACACCAAAGTGT-CCCCATAAAC
* * * * * * *
89666 TGGAAGAAGCAGAAACAAGAACTGACGTTTG-TGGCATTCTCAGAACAGTAACAT-AAAGAGATG
64 TGGAACAAACAGAAA-AACAACGGACATTTGCGGGC-TTCTCAGAACAGTAACATAAAAG-GAAG
89729 AAAAAGAGAATGCAAAAT
126 AAAAAGAGAATGCAAAAT
89747 TCAATTTCAA
Statistics
Matches: 124, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
147 1 0.01
148 53 0.43
149 63 0.51
150 7 0.06
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (150 bp):
GGATAGGAATTTATCTTGATTAAGAAGTCCACTTATCAACCACACCAAAGTGTCCCCATAAACTG
GAACAAACAGAAAAACAACGGACATTTGCGGGCTTCTCAGAACAGTAACATAAAAGGAAGAAAAA
GAGAATGCAAAATCATCCTG
Done.