Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002345.1 Hibiscus syriacus cultivar Beakdansim tig00004787_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: 72833
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:11584 original size:10 final size:10
Alignment explanation
Indices: 11569--11595 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
11559 GGAGAAAGAA
11569 ATGATTTGGG
1 ATGATTTGGG
11579 ATGATTTGGG
1 ATGATTTGGG
11589 ATGATTT
1 ATGATTT
11596 TGAAGCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (10 bp):
ATGATTTGGG
Found at i:16308 original size:162 final size:163
Alignment explanation
Indices: 16041--16526 Score: 852
Period size: 162 Copynumber: 3.0 Consensus size: 163
16031 AAGTGTTTAC
* * *
16041 AAAACACTCACTACTCACAAGAAA--ACTTCTAGTATTGGGAGAAAGAAATGATTTGTGATGATT
1 AAAACACTCACTACTCACAAGAAAGTTCTT-TAGTATTGAGAGAAAGAAATGATTTGGGATGATT
16104 TGAAGGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGAGACTAATCTTGTAAATACCCTAAA
65 TGAAGGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGAGACTAATCTTGTAAATACCCTAAA
*
16169 GTATGCAGGGACTAAAGTGTAATTAACCCTATTA
130 GTATGTAGGGACTAAAGTGTAATTAACCCTATTA
16203 AAAACACTCACTACTCACAAGAAAGTTCTTTAGTATTGAGAGAAAGAAATGATTTGGGATGATTT
1 AAAACACTCACTACTCACAAGAAAGTTCTTTAGTATTGAGAGAAAGAAATGATTTGGGATGATTT
16268 GAAGGTAAAT-GGTTAGGGTATTTATAGTTGAAGCTTAGAGACTAATCTTGTAAATACCCTAAAG
66 GAAGGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGAGACTAATCTTGTAAATACCCTAAAG
16332 TATGTAGGGACTAAAGTGTAATTAACCCTATTA
131 TATGTAGGGACTAAAGTGTAATTAACCCTATTA
*
16365 AAAACACTCACTACTCACAAGAAAGTTCTTTAGTATTGAGAGAAAGAAATGATTTGGCATGATTT
1 AAAACACTCACTACTCACAAGAAAGTTCTTTAGTATTGAGAGAAAGAAATGATTTGGGATGATTT
* * * *
16430 GAATGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGGGACTAATCTTATAAATACCCTAAAA
66 GAAGGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGAGACTAATCTTGTAAATACCCTAAAG
*
16495 TATATAGGGACTAAAGTGTAATTAACCCTATT
131 TATGTAGGGACTAAAGTGTAATTAACCCTATT
16527 GTAATTGTAA
Statistics
Matches: 311, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
162 183 0.59
163 125 0.40
164 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (163 bp):
AAAACACTCACTACTCACAAGAAAGTTCTTTAGTATTGAGAGAAAGAAATGATTTGGGATGATTT
GAAGGTAAATGGGTTAGGGTATTTATAGTTGAAGCTTAGAGACTAATCTTGTAAATACCCTAAAG
TATGTAGGGACTAAAGTGTAATTAACCCTATTA
Found at i:17415 original size:258 final size:259
Alignment explanation
Indices: 16942--17723 Score: 1415
Period size: 258 Copynumber: 3.0 Consensus size: 259
16932 AAGGAACTGC
* * *
16942 AATCATTCTGCTGCTCAAAATGAATGCAATTTTCCACCACTCATAGGCTTTCCTAGTGCGAAACC
1 AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
17007 AATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAC
66 AATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAC
* * *
17072 TGTTGTACACCCATAACTAATAGAGATTGTAGTTTTCAAATTTCAATTACAATAATGCTCTTAAC
131 TGTTGCACACCCATAACTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
17137 ATCATACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTAGA
196 ATCATACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTAGA
17201 AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
1 AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
* *
17266 AATGGCATATGATTAATTGTAGATAATTTTCTTACATA-TTTAGAATAGTAATCATTGCAAGTAT
66 AATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAC
17330 TGTTGCACACCCATAACTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
131 TGTTGCACACCCATAACTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
* *
17395 ATCATACTATATCATATTGTGATTGATAATATCACCATACTTTCTATTTTAGTGTTTAGTTAGA
196 ATCATACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTAGA
17459 AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
1 AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
17524 AATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAC
66 AATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAC
*
17589 TG-TGCACACCCATAATTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
131 TGTTGCACACCCATAACTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
17653 ATCATAGTACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTA
196 ATC--A-TACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTA
*
17718 GT
258 GA
17720 AATC
1 AATC
17724 TTGTCAAATA
Statistics
Matches: 503, Mismatches: 16, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
258 315 0.63
259 126 0.25
260 1 0.00
261 61 0.12
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (259 bp):
AATCATTATGCTGCTCAAAATGAATGCAATTTTCCACCGCTCATAGGCTTTCCTAGTGCGGAACC
AATGGCATATGATTGATTGTAGATAATTTTCTTACATATTTTAGAATAGTAATCATTGCAAGTAC
TGTTGCACACCCATAACTGATAGAGATTGTAGTTTTCAAATTTCAATTACAATAAAGCTCTTAAC
ATCATACTATATCGTATTGTGATTGATAATATCACCATACTTTCTATTTTACTGTTTAGTTAGA
Found at i:23285 original size:141 final size:142
Alignment explanation
Indices: 22833--23398 Score: 1019
Period size: 141 Copynumber: 4.0 Consensus size: 142
22823 ATCTCACTTC
* * *
22833 TTGATCATTCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTTCCTGATATTCACCCTTTATT
1 TTGATCATCCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTGCCTCATATTCACCCTTTATT
*
22898 CCTCCATTAACTTTATACAATTTATAGAAG-AAAAAAAACCTTTATACAATTATTTTTGGACGCT
66 CCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTATTTTTGGACGCT
22962 TATGTGGGTAGA
131 TATGTGGGTAGA
* *
22974 TTGATCATCCTTTCCTTCCCTCATTATACTCTTCCTTTCAGGTTGCCTCATATTTACCCTTTATT
1 TTGATCATCCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTGCCTCATATTCACCCTTTATT
23039 CCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTATTTTTGGACGCT
66 CCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTATTTTTGGACGCT
23104 TATGTGGGTAGA
131 TATGTGGGTAGA
* *
23116 TTGATCATCCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTTCCTGATATTCACCCTTTATT
1 TTGATCATCCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTGCCTCATATTCACCCTTTATT
*
23181 CCTCCATTAACTTTATACAATTTATAGAAG-AAAAAAAACCTTTATACAATTATTTTTGGACGCT
66 CCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTATTTTTGGACGCT
23245 TATGTGGGTAGA
131 TATGTGGGTAGA
*
23257 TTGATCATCCTTTCCTTCCCTCATTATACTCTTCCTTTCAGGTTGCCTCATATTCACCCTTTATT
1 TTGATCATCCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTGCCTCATATTCACCCTTTATT
*
23322 CCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTATTTTTGGACGTT
66 CCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTATTTTTGGACGCT
23387 TATGTGGGTAGA
131 TATGTGGGTAGA
23399 CTGGAGTACT
Statistics
Matches: 407, Mismatches: 16, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
141 226 0.56
142 181 0.44
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (142 bp):
TTGATCATCCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTGCCTCATATTCACCCTTTATT
CCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTATTTTTGGACGCT
TATGTGGGTAGA
Found at i:23340 original size:283 final size:283
Alignment explanation
Indices: 22833--23398 Score: 1105
Period size: 283 Copynumber: 2.0 Consensus size: 283
22823 ATCTCACTTC
*
22833 TTGATCATTCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTTCCTGATATTCACCCTTTATT
1 TTGATCATCCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTTCCTGATATTCACCCTTTATT
22898 CCTCCATTAACTTTATACAATTTATAGAAGAAAAAAAACCTTTATACAATTATTTTTGGACGCTT
66 CCTCCATTAACTTTATACAATTTATAGAAGAAAAAAAACCTTTATACAATTATTTTTGGACGCTT
22963 ATGTGGGTAGATTGATCATCCTTTCCTTCCCTCATTATACTCTTCCTTTCAGGTTGCCTCATATT
131 ATGTGGGTAGATTGATCATCCTTTCCTTCCCTCATTATACTCTTCCTTTCAGGTTGCCTCATATT
*
23028 TACCCTTTATTCCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTAT
196 CACCCTTTATTCCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTAT
23093 TTTTGGACGCTTATGTGGGTAGA
261 TTTTGGACGCTTATGTGGGTAGA
23116 TTGATCATCCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTTCCTGATATTCACCCTTTATT
1 TTGATCATCCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTTCCTGATATTCACCCTTTATT
23181 CCTCCATTAACTTTATACAATTTATAGAAGAAAAAAAACCTTTATACAATTATTTTTGGACGCTT
66 CCTCCATTAACTTTATACAATTTATAGAAGAAAAAAAACCTTTATACAATTATTTTTGGACGCTT
23246 ATGTGGGTAGATTGATCATCCTTTCCTTCCCTCATTATACTCTTCCTTTCAGGTTGCCTCATATT
131 ATGTGGGTAGATTGATCATCCTTTCCTTCCCTCATTATACTCTTCCTTTCAGGTTGCCTCATATT
23311 CACCCTTTATTCCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTAT
196 CACCCTTTATTCCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTAT
*
23376 TTTTGGACGTTTATGTGGGTAGA
261 TTTTGGACGCTTATGTGGGTAGA
23399 CTGGAGTACT
Statistics
Matches: 280, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
283 280 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (283 bp):
TTGATCATCCTTTCCTTCCCTCAGTATACTCTTCCTTTCAGGTTTCCTGATATTCACCCTTTATT
CCTCCATTAACTTTATACAATTTATAGAAGAAAAAAAACCTTTATACAATTATTTTTGGACGCTT
ATGTGGGTAGATTGATCATCCTTTCCTTCCCTCATTATACTCTTCCTTTCAGGTTGCCTCATATT
CACCCTTTATTCCTCCAATAACTTTATACAATTTATAGAAGAAAAAAAAACCTTTATACAATTAT
TTTTGGACGCTTATGTGGGTAGA
Found at i:28944 original size:31 final size:31
Alignment explanation
Indices: 28909--28985 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
28899 TCAATAAAAG
* *
28909 AGATAAAATTTTAATTTGACTCTTAAATTTT
1 AGATAAAATATTAATTTGACTCCTAAATTTT
*
28940 AGATAAAATACTAATTTGACTCCTAAATTTT
1 AGATAAAATATTAATTTGACTCCTAAATTTT
28971 AGATAAAATATTAAT
1 AGATAAAATATTAAT
28986 ATCTTTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (31 bp):
AGATAAAATATTAATTTGACTCCTAAATTTT
Found at i:29394 original size:29 final size:30
Alignment explanation
Indices: 29324--29383 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
29314 CAATTTAAGG
29324 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
29355 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
29384 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:29489 original size:21 final size:20
Alignment explanation
Indices: 29463--29561 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
29453 AGGGTCTCAA
29463 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
29484 AGTGCATCCATACATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
29505 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
29526 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
29547 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
29562 TCAAACACTG
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.21
21 34 0.50
22 13 0.19
23 3 0.04
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:29518 original size:13 final size:14
Alignment explanation
Indices: 29496--29561 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 14
29486 TGCATCCATA
*
29496 CATCCCTGCA-GTG
1 CATCCATGCACGTG
*
29509 CATCCATGCACCTG
1 CATCCATGCACGTG
*
29523 CA-CTAGTGCATCGATG
1 CATCCA-TGCA-CG-TG
29539 CA-CCATGCA-GTG
1 CATCCATGCACGTG
29551 CATCCATGCAC
1 CATCCATGCAC
29562 TCAAACACTG
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
12 4 0.10
13 19 0.45
14 8 0.19
15 5 0.12
16 6 0.14
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (14 bp):
CATCCATGCACGTG
Found at i:29607 original size:20 final size:20
Alignment explanation
Indices: 29582--29636 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
29572 AATGCAATTA
29582 GTGCATCGATGCATCC-TACT
1 GTGCATCGATGCATCCTTA-T
29602 GTGCATCGATGCATCCTTAT
1 GTGCATCGATGCATCCTTAT
29622 GTGCATCGATGCATC
1 GTGCATCGATGCATC
29637 AAGGAGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 32 0.94
21 2 0.06
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTAT
Found at i:37088 original size:29 final size:30
Alignment explanation
Indices: 37018--37077 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
37008 CAATTTAAGG
37018 CAAAATGGTTTTTGGACTTGAATTAAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTAAATTTA
* *
37049 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
37078 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:37220 original size:20 final size:21
Alignment explanation
Indices: 37167--37221 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
37157 AGTGCATCCA
37167 TGCATCCATGCACCTGCACTAG
1 TGCATCCATGCACCTG-ACTAG
**
37189 TGCATCGGTGCACCATG-C-AG
1 TGCATCCATGCACC-TGACTAG
37209 TGCATCCATGCAC
1 TGCATCCATGCAC
37222 TCAAACACCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 13 0.46
21 1 0.04
22 12 0.43
23 2 0.07
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCATCCATGCACCTGACTAG
Found at i:37437 original size:21 final size:21
Alignment explanation
Indices: 37408--37447 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
37398 TTTGAGTAGA
37408 AAAATCATCCTCAAACGGCTCC
1 AAAATCATCC-CAAACGGCTCC
*
37430 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
37448 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:40700 original size:29 final size:29
Alignment explanation
Indices: 40602--40690 Score: 142
Period size: 29 Copynumber: 3.0 Consensus size: 29
40592 CAATTTAAGG
*
40602 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTATGGACTT-AATTGAATTTA
*
40633 CAAAATGTTTCTGGACTTAATTGAATTTA
1 CAAAATGTTTATGGACTTAATTGAATTTA
40662 CAAAATGTTTATGGACTTAATTGAATTTA
1 CAAAATGTTTATGGACTTAATTGAATTTA
40691 TTCAAAGTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
29 39 0.70
30 11 0.20
31 6 0.11
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.42
Consensus pattern (29 bp):
CAAAATGTTTATGGACTTAATTGAATTTA
Found at i:40913 original size:21 final size:21
Alignment explanation
Indices: 40887--40943 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
40877 AATGCAATTA
40887 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
40908 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
40929 GTGCATCGATGCATC
1 GTGCATCGATGCATC
40944 CTGTTGTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:41102 original size:20 final size:21
Alignment explanation
Indices: 41065--41103 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41055 TTTAGTAGAA
41065 AAAACATCCCCAAACGGCTCC
1 AAAACATCCCCAAACGGCTCC
41086 AAAACATCCCC-AACGGCT
1 AAAACATCCCCAAACGGCT
41104 ACATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.41, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAACATCCCCAAACGGCTCC
Found at i:41357 original size:34 final size:32
Alignment explanation
Indices: 41318--41387 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
41308 TTTTGTAAAG
* *
41318 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
41352 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
41384 GGGA
1 GGGA
41388 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:41683 original size:30 final size:31
Alignment explanation
Indices: 41623--41747 Score: 137
Period size: 30 Copynumber: 4.1 Consensus size: 31
41613 AAATCCCAAC
* *
41623 AAATTTCAATGGTCAAGTTAATATTTTATCT
1 AAATTTCAAGGGTCAAGTTGATATTTTATCT
*
41654 AAGTTTCAAGGGTCAAGTTGATA-TTTATCT
1 AAATTTCAAGGGTCAAGTTGATATTTTATCT
* * *
41684 AAATTTTAAGGATCAAATTGATATTTTATCT
1 AAATTTCAAGGGTCAAGTTGATATTTTATCT
* ** * *
41715 AAATTTGAA-GGTCAAAATAATATTCTATCT
1 AAATTTCAAGGGTCAAGTTGATATTTTATCT
41745 AAA
1 AAA
41748 ATTTAGAGGT
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
30 46 0.57
31 35 0.43
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (31 bp):
AAATTTCAAGGGTCAAGTTGATATTTTATCT
Found at i:41744 original size:61 final size:61
Alignment explanation
Indices: 41633--41760 Score: 152
Period size: 61 Copynumber: 2.1 Consensus size: 61
41623 AAATTTCAAT
* * * ** * *
41633 GGTCAAGTTAATATTTTATCTAAGTTTCAAGGGTCAAGTTGATATTTATCTAAATTTTA-A
1 GGTCAAATTGATATTTTATCTAAATTTCAAGGGTCAAAATAATATTTATCTAAAATTTAGA
*
41693 GGATCAAATTGATATTTTATCTAAATTTGAA-GGTCAAAATAATATTCTATCTAAAATTTAGA
1 GG-TCAAATTGATATTTTATCTAAATTTCAAGGGTCAAAATAATATT-TATCTAAAATTTAGA
41755 GGTCAA
1 GGTCAA
41761 TTTAAAATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
60 14 0.25
61 40 0.70
62 3 0.05
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (61 bp):
GGTCAAATTGATATTTTATCTAAATTTCAAGGGTCAAAATAATATTTATCTAAAATTTAGA
Found at i:41750 original size:31 final size:28
Alignment explanation
Indices: 41623--41760 Score: 96
Period size: 31 Copynumber: 4.5 Consensus size: 28
41613 AAATCCCAAC
**
41623 AAATTTCAATGGTCAAGTTAATATTTTATCT
1 AAATTT-AA-GGTCAAAATAATA-TTTATCT
* ** *
41654 AAGTTTCAAGGGTCAAGTTGATATTTATCT
1 AAATTT-AA-GGTCAAAATAATATTTATCT
* *
41684 AAATTTTAAGGATCAAATTGATATTTTATCT
1 AAA-TTTAAGG-TCAAAATAATA-TTTATCT
41715 AAATTTGAAGGTCAAAATAATATTCTATCT
1 AAATTT-AAGGTCAAAATAATATT-TATCT
41745 AAAATTTAGAGGTCAA
1 -AAATTTA-AGGTCAA
41761 TTTAAAATTT
Statistics
Matches: 93, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.04
30 39 0.42
31 50 0.54
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (28 bp):
AAATTTAAGGTCAAAATAATATTTATCT
Found at i:44859 original size:74 final size:72
Alignment explanation
Indices: 44761--44901 Score: 210
Period size: 74 Copynumber: 1.9 Consensus size: 72
44751 AAAACCTTAA
* * * * **
44761 GCAAGCAAAAGATACTATGCTTTGACCTAAACTTGTAACCCGATTGTTGAACAAGAATATGGAAT
1 GCAAACAAAAGATACCATACTTTGACCTAAAATTGTAACCCGATTGTCAAACAAG-A-ATGGAAT
44826 TAGCCATAG
64 TAGCCATAG
44835 GCAAACAAAAGATACCATACTTTGACCTAAAATTGTAACCCGATTGTCAAACAAGAATGGAATTA
1 GCAAACAAAAGATACCATACTTTGACCTAAAATTGTAACCCGATTGTCAAACAAGAATGGAATTA
44900 GC
66 GC
44902 AGGATATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 11 0.18
73 1 0.02
74 49 0.80
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.24
Consensus pattern (72 bp):
GCAAACAAAAGATACCATACTTTGACCTAAAATTGTAACCCGATTGTCAAACAAGAATGGAATTA
GCCATAG
Done.