Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007007.1 Hibiscus syriacus cultivar Beakdansim tig00018084_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: 83544
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1846 original size:31 final size:32
Alignment explanation
Indices: 1791--1858 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 32
1781 GCCTTAAAGT
* *
1791 CTACCCAAAGGAGTACCTTGGGGCCTAGGAGC
1 CTACCCAAAGGAGTACCTTAGGGCCTAAGAGC
**
1823 CTACCC-AAGGAGTAGTTTAGGGCCTAAGAGC
1 CTACCCAAAGGAGTACCTTAGGGCCTAAGAGC
*
1854 ATACC
1 CTACC
1859 TAAGCATCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (32 bp):
CTACCCAAAGGAGTACCTTAGGGCCTAAGAGC
Found at i:9258 original size:16 final size:16
Alignment explanation
Indices: 9237--9299 Score: 101
Period size: 16 Copynumber: 4.0 Consensus size: 16
9227 TACTAATGAG
9237 GCATCAGGTGAGTGCA
1 GCATCAGGTGAGTGCA
9253 GCATCAGGTGAGTGCA
1 GCATCAGGTGAGTGCA
*
9269 GCATCAGGTGAGTACA
1 GCATCAGGTGAGTGCA
*
9285 -CATCATGTGAGTGCA
1 GCATCAGGTGAGTGCA
9300 TCTTACTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
15 13 0.30
16 31 0.70
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (16 bp):
GCATCAGGTGAGTGCA
Found at i:14506 original size:13 final size:13
Alignment explanation
Indices: 14479--14518 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
14469 TTGGTTATGT
*
14479 AAATGAATG-TGA
1 AAATGAAAGATGA
14491 AAATGAAAGATGA
1 AAATGAAAGATGA
*
14504 AAATGAAATATGA
1 AAATGAAAGATGA
14517 AA
1 AA
14519 GTTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (13 bp):
AAATGAAAGATGA
Found at i:16807 original size:16 final size:17
Alignment explanation
Indices: 16762--16807 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
16752 TGTTTATGAG
16762 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
**
16780 GGAATTATAATCTGT-A
1 GGAATTGGAATCTGTAA
16796 GGAATTGGAATC
1 GGAATTGGAATC
16808 CAATTCCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 11 0.46
18 13 0.54
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:17936 original size:27 final size:28
Alignment explanation
Indices: 17877--17938 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
17867 CCGACCCGAT
*
17877 CCGACCCGAATATCACACTTAAAAAAAC
1 CCGACCCAAATATCACACTTAAAAAAAC
*
17905 TCGACCCAAATATCACACTT-AAAAAAC
1 CCGACCCAAATATCACACTTAAAAAAAC
17932 CCGACCC
1 CCGACCC
17939 GACCTGAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.44, C:0.35, G:0.06, T:0.15
Consensus pattern (28 bp):
CCGACCCAAATATCACACTTAAAAAAAC
Found at i:18031 original size:248 final size:248
Alignment explanation
Indices: 17408--18160 Score: 1081
Period size: 248 Copynumber: 3.0 Consensus size: 248
17398 GACCTGTCCT
* *
17408 GACCCGAATATCACACTTAAAAAACCCGACTCGACCTGAACAAAATAAAGTTTCAT-----CCGA
1 GACCCAAATATCACACTTAAAAAACCCGACCCGACCTGAACAAAATAAAGTTTCATCCGACCCGA
* * *
17468 CCCGAATATATGAATTAGAAATCTGACCCGACCCTACCCGAAATAATAAAAAATTATTTTTATTT
66 CCCGAATATATGAATTAGAAATCCGACCCGACCCGACCTGAAATAATAAAAAATTATTTTTATTT
* * *
17533 AATAAAAACAGTGACTTAATCCGA-TCCGACCCGAATTATATATATTTTTGGGTCGATCC-GGTT
131 AATAAAAACAGTGACTTAATCCGACT-CGACCCGAATTATATATATTTTCGGGTCGGTCCAGATT
* *
17596 TTTTCACCCTAAACCAGACCCGATCCGACCCGAATATCGCACTTAAAAAAACCC
195 TTTTCACCCTAAACCCGACCCGATCCGACCCGAATATCACACTTAAAAAAACCC
* *
17650 GACCCAACTCGAGCCGAATATCACACTTAAAAAACCCGA-CTGACCCGAACAAAATAAAGTTTCA
1 GA--C--C-C-A----AATATCACACTTAAAAAACCCGACCCGACCTGAACAAAATAAAGTTTCA
** * *
17714 TCCGACCCGACTAGAATATATGAATTAGAAATCCAACCCGACCCGACTTGAAATAATAAAAAATT
56 TCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCGACCCGACCTGAAATAATAAAAAATT
17779 ATTTTTATTTAATAAAAACAGTGACTTAATCCGACTCGACCCGAATTATATATATTTTCGGGTCG
121 ATTTTTATTTAATAAAAACAGTGACTTAATCCGACTCGACCCGAATTATATATATTTTCGGGTCG
* *
17844 GTCCAGTTTTTTTCACCCTAAACCCGACCCGATCCGACCCGAATATCACACTTAAAAAAACTC
186 GTCCAGATTTTTTCACCCTAAACCCGACCCGATCCGACCCGAATATCACACTTAAAAAAACCC
17907 GACCCAAATATCACACTTAAAAAACCCGACCCGACCTGAACAAAATAAAGTTTCATCCGACCCGA
1 GACCCAAATATCACACTTAAAAAACCCGACCCGACCTGAACAAAATAAAGTTTCATCCGACCCGA
*
17972 CCCGAATATATGAATTAGAAATCCGACCCAACCCGACCTGAAATAATAAAAAATTATTTTTATTT
66 CCCGAATATATGAATTAGAAATCCGACCCGACCCGACCTGAAATAATAAAAAATTATTTTTATTT
* * * *
18037 AATAAAAACAATGACTTAATCCGACCCGACCTGAATTATATATATTTTCAGGTCGGTCCAGATTT
131 AATAAAAACAGTGACTTAATCCGACTCGACCCGAATTATATATATTTTCGGGTCGGTCCAGATTT
*
18102 TTTCACCCTAAACCCGAACCTGACCCGACCCGACCCGAATATCACACTTAAAAAAACCC
196 TTTCACCCTAAA--C---CC-GACCCGATCCGACCCGAATATCACACTTAAAAAAACCC
18161 AATCCGACCC
Statistics
Matches: 456, Mismatches: 31, Indels: 36
0.87 0.06 0.07
Matches are distributed among these distances:
242 2 0.00
244 1 0.00
246 1 0.00
247 24 0.05
248 165 0.36
250 1 0.00
251 24 0.05
252 24 0.05
253 3 0.01
254 36 0.08
255 1 0.00
256 117 0.26
257 57 0.12
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.24
Consensus pattern (248 bp):
GACCCAAATATCACACTTAAAAAACCCGACCCGACCTGAACAAAATAAAGTTTCATCCGACCCGA
CCCGAATATATGAATTAGAAATCCGACCCGACCCGACCTGAAATAATAAAAAATTATTTTTATTT
AATAAAAACAGTGACTTAATCCGACTCGACCCGAATTATATATATTTTCGGGTCGGTCCAGATTT
TTTCACCCTAAACCCGACCCGATCCGACCCGAATATCACACTTAAAAAAACCC
Found at i:20115 original size:24 final size:24
Alignment explanation
Indices: 20085--20157 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
20075 ATACATTACC
* *
20085 TGAATTCTGTTCTAATTTCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
* * *
20109 TGGATTCTATTTTGATATCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
20133 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
20157 T
1 T
20158 CTTTGTTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTTTGATTTCTGATA
Found at i:20125 original size:48 final size:48
Alignment explanation
Indices: 20051--20157 Score: 110
Period size: 48 Copynumber: 2.2 Consensus size: 48
20041 ATTTTATATT
* * *
20051 ATTTCTGACT-TGAATTCTGTTATGATA-CATTACCTGAATTCTGTTCTA
1 ATTTCTGA-TATGAATTCTATTATGATATC-TGACATGAATTCTGTTCTA
* * * * *
20099 ATTTCTGATATGGATTCTATTTTGATATCTGATATGAATTCTGTTTTG
1 ATTTCTGATATGAATTCTATTATGATATCTGACATGAATTCTGTTCTA
20147 ATTTCTGATAT
1 ATTTCTGATAT
20158 CTTTGTTTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
47 1 0.02
48 47 0.96
49 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (48 bp):
ATTTCTGATATGAATTCTATTATGATATCTGACATGAATTCTGTTCTA
Found at i:21095 original size:19 final size:19
Alignment explanation
Indices: 21071--21116 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
21061 AAATTAACAT
*
21071 TTTTGGAATCTAATGTTTA
1 TTTTGGAATCTAATGTTGA
21090 TTTTGGAATCTAATGTTGA
1 TTTTGGAATCTAATGTTGA
21109 TTTTGGAA
1 TTTTGGAA
21117 AGTTTGAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (19 bp):
TTTTGGAATCTAATGTTGA
Found at i:22542 original size:2 final size:2
Alignment explanation
Indices: 22535--22565 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22525 GTTATGTCCG
22535 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22566 TTTTTATATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23508 original size:29 final size:30
Alignment explanation
Indices: 23476--23544 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
23466 CATTTTACAG
*
23476 AAATAACACCCT-TTTTAAATTAATTACTA
1 AAATAACACCCTATTTCAAATTAATTACTA
* *
23505 AAATAGCA-CCTATTTCGAATTAATTACTA
1 AAATAACACCCTATTTCAAATTAATTACTA
23534 AAATAACACCC
1 AAATAACACCC
23545 GGTCAACGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.09
29 29 0.85
30 2 0.06
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATAACACCCTATTTCAAATTAATTACTA
Found at i:33465 original size:29 final size:30
Alignment explanation
Indices: 33423--33497 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 30
33413 GTCAACCATT
*
33423 TTACAAAAATAGCACCCT-TTTTAAATTAA
1 TTACTAAAATAGCACCCTATTTTAAATTAA
*
33452 TTACTAAAATAGCA-CCTATTTTGAATTAA
1 TTACTAAAATAGCACCCTATTTTAAATTAA
*
33481 TTACTAAAATAACACCC
1 TTACTAAAATAGCACCC
33498 GATCAACGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 3 0.07
29 36 0.88
30 2 0.05
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (30 bp):
TTACTAAAATAGCACCCTATTTTAAATTAA
Found at i:33536 original size:12 final size:12
Alignment explanation
Indices: 33500--33595 Score: 78
Period size: 12 Copynumber: 8.2 Consensus size: 12
33490 TAACACCCGA
*
33500 TCAACGGTTGGG
1 TCAACGGTCGGG
* *
33512 TTAACATGTCGGG
1 TCAAC-GGTCGGG
33525 TCAACGGTCGGG
1 TCAACGGTCGGG
*
33537 TC--GGGTC-GG
1 TCAACGGTCGGG
33546 TCAACGGGTCGGG
1 TCAAC-GGTCGGG
*
33559 TCAACGATCGGG
1 TCAACGGTCGGG
33571 TC-A-GGTC-GG
1 TCAACGGTCGGG
33580 TCAACGGGTCGGG
1 TCAAC-GGTCGGG
33593 TCA
1 TCA
33596 GGTTGGAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
9 8 0.12
10 8 0.12
11 1 0.02
12 28 0.42
13 21 0.32
ACGTcount: A:0.17, C:0.22, G:0.41, T:0.21
Consensus pattern (12 bp):
TCAACGGTCGGG
Found at i:33541 original size:17 final size:17
Alignment explanation
Indices: 33519--33577 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
33509 GGGTTAACAT
33519 GTCGGGTCAACGGTCGG
1 GTCGGGTCAACGGTCGG
33536 GTCGGGT---CGGTCAACGG
1 GTCGGGTCAACGGT---CGG
*
33553 GTCGGGTCAACGATCGG
1 GTCGGGTCAACGGTCGG
*
33570 GTCAGGTC
1 GTCGGGTC
33578 GGTCAACGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 4 0.12
17 27 0.79
20 3 0.09
ACGTcount: A:0.14, C:0.24, G:0.44, T:0.19
Consensus pattern (17 bp):
GTCGGGTCAACGGTCGG
Found at i:33562 original size:34 final size:34
Alignment explanation
Indices: 33519--33595 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
33509 GGGTTAACAT
* *
33519 GTCGGGTCAACGGTCGGGTCGGGTCGGTCAACGG
1 GTCGGGTCAACGATCGGGTCAGGTCGGTCAACGG
33553 GTCGGGTCAACGATCGGGTCAGGTCGGTCAACGG
1 GTCGGGTCAACGATCGGGTCAGGTCGGTCAACGG
33587 GTCGGGTCA
1 GTCGGGTCA
33596 GGTTGGAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.14, C:0.23, G:0.44, T:0.18
Consensus pattern (34 bp):
GTCGGGTCAACGATCGGGTCAGGTCGGTCAACGG
Found at i:33577 original size:22 final size:22
Alignment explanation
Indices: 33552--33598 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
33542 TCGGTCAACG
33552 GGTCGGGTCAAC-GATCGGGTCA
1 GGTC-GGTCAACGGATCGGGTCA
*
33574 GGTCGGTCAACGGGTCGGGTCA
1 GGTCGGTCAACGGATCGGGTCA
33596 GGT
1 GGT
33599 TGGAATAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19
Consensus pattern (22 bp):
GGTCGGTCAACGGATCGGGTCA
Found at i:33587 original size:17 final size:17
Alignment explanation
Indices: 33533--33594 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
33523 GGTCAACGGT
33533 CGGGTCGGGTCGGTCAA
1 CGGGTCGGGTCGGTCAA
** *
33550 CGGGTCGGGTC-AACGAT
1 CGGGTCGGGTCGGTC-AA
*
33567 CGGGTCAGGTCGGTCAA
1 CGGGTCGGGTCGGTCAA
33584 CGGGTCGGGTC
1 CGGGTCGGGTC
33595 AGGTTGGAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
16 1 0.03
17 33 0.94
18 1 0.03
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
CGGGTCGGGTCGGTCAA
Found at i:48426 original size:22 final size:21
Alignment explanation
Indices: 48384--48423 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48374 GAGTTTGTTT
*
48384 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
48405 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
48424 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:53414 original size:14 final size:14
Alignment explanation
Indices: 53380--53422 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
53370 CCGAAATACA
53380 GAAATCAGATATCAG
1 GAAATCA-ATATCAG
53395 GAAATCAATATTCAG
1 GAAATCAATA-TCAG
53410 G-AATCAAGTATCA
1 GAAATCAA-TATCA
53423 TGTATCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (14 bp):
GAAATCAATATCAG
Found at i:54195 original size:29 final size:30
Alignment explanation
Indices: 54153--54227 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 30
54143 GTCAACCATT
*
54153 TTACAAAAATAGCACCCT-TTTTAAATTAA
1 TTACTAAAATAGCACCCTATTTTAAATTAA
*
54182 TTACTAAAATAGCA-CATATTTTAAATTAA
1 TTACTAAAATAGCACCCTATTTTAAATTAA
54211 TTACTAAAATAGCACCC
1 TTACTAAAATAGCACCC
54228 GGTTAACAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 2 0.05
29 38 0.93
30 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.33
Consensus pattern (30 bp):
TTACTAAAATAGCACCCTATTTTAAATTAA
Found at i:54275 original size:12 final size:12
Alignment explanation
Indices: 54258--54309 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
54248 GGTCGGGTCT
54258 GGTCGGTCAACG
1 GGTCGGTCAACG
54270 GGTCGGGTCAACG
1 GGTC-GGTCAACG
* *
54283 GTTGGGT---CG
1 GGTCGGTCAACG
54292 GGTCGGTCAACG
1 GGTCGGTCAACG
54304 GGTCGG
1 GGTCGG
54310 GTCGGGTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 7 0.22
12 15 0.47
13 10 0.31
ACGTcount: A:0.12, C:0.21, G:0.48, T:0.19
Consensus pattern (12 bp):
GGTCGGTCAACG
Found at i:54293 original size:22 final size:22
Alignment explanation
Indices: 54268--54316 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
54258 GGTCGGTCAA
*
54268 CGGGTCGGGTCAAC-GGTTGGGT
1 CGGGTC-GGTCAACGGGTCGGGT
54290 CGGGTCGGTCAACGGGTCGGGT
1 CGGGTCGGTCAACGGGTCGGGT
54312 CGGGT
1 CGGGT
54317 TGGAACCGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.08, C:0.20, G:0.51, T:0.20
Consensus pattern (22 bp):
CGGGTCGGTCAACGGGTCGGGT
Found at i:54306 original size:17 final size:17
Alignment explanation
Indices: 54251--54314 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
54241 GCTAACGGGT
*
54251 CGGGTCTGGTCGGTCAA
1 CGGGTCGGGTCGGTCAA
54268 CGGGTCGGGTCAACGGT---
1 CGGGTCGGGT---CGGTCAA
*
54285 TGGGTCGGGTCGGTCAA
1 CGGGTCGGGTCGGTCAA
54302 CGGGTCGGGTCGG
1 CGGGTCGGGTCGG
54315 GTTGGAACCG
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
14 4 0.11
17 30 0.79
20 4 0.11
ACGTcount: A:0.09, C:0.22, G:0.48, T:0.20
Consensus pattern (17 bp):
CGGGTCGGGTCGGTCAA
Found at i:58666 original size:19 final size:19
Alignment explanation
Indices: 58632--58676 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
58622 AATAAGCACC
**
58632 TTGCATTTTATTTTTCACA
1 TTGCATTTTACCTTTCACA
*
58651 TTGCATTTTACCTTTCGCA
1 TTGCATTTTACCTTTCACA
*
58670 TTACATT
1 TTGCATT
58677 ATATTCATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (19 bp):
TTGCATTTTACCTTTCACA
Found at i:65767 original size:9 final size:10
Alignment explanation
Indices: 65748--65782 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
65738 ACTTTGTCTG
65748 AAAGAAAAAA
1 AAAGAAAAAA
65758 AAAGAAAAAA
1 AAAGAAAAAA
*
65768 AAATAAGAAAA
1 AAAGAA-AAAA
65779 AAAG
1 AAAG
65783 TTAAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:69121 original size:13 final size:13
Alignment explanation
Indices: 69103--69136 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
69093 GATGATGGTC
69103 TTGATGAAGGATG
1 TTGATGAAGGATG
*
69116 TTGATGATGGATG
1 TTGATGAAGGATG
*
69129 ATGATGAA
1 TTGATGAA
69137 ATGGCAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:74659 original size:13 final size:13
Alignment explanation
Indices: 74641--74674 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
74631 GATGATGGTC
74641 TTGATGAAGGATG
1 TTGATGAAGGATG
*
74654 TTGATGATGGATG
1 TTGATGAAGGATG
*
74667 ATGATGAA
1 TTGATGAA
74675 ATGGCAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Done.