Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009049.1 Hibiscus syriacus cultivar Beakdansim tig00112460_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: 58721
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4438 original size:17 final size:18
Alignment explanation
Indices: 4410--4455 Score: 78
Period size: 16 Copynumber: 2.7 Consensus size: 18
4400 AATAAGGGAT
4410 CTAAGAAGAAGGGATAAA
1 CTAAGAAGAAGGGATAAA
4428 CTAAG-AGAA-GGATAAA
1 CTAAGAAGAAGGGATAAA
4444 CTAAGAAGAAGG
1 CTAAGAAGAAGG
4456 TATTTGTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 12 0.46
17 8 0.31
18 6 0.23
ACGTcount: A:0.54, C:0.07, G:0.28, T:0.11
Consensus pattern (18 bp):
CTAAGAAGAAGGGATAAA
Found at i:6161 original size:18 final size:18
Alignment explanation
Indices: 6135--6169 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6125 CTAGAAAGCA
6135 AAAGAGGTACCGATACTC
1 AAAGAGGTACCGATACTC
*
6153 AAAGGGGTACCGATACT
1 AAAGAGGTACCGATACT
6170 ACTTTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (18 bp):
AAAGAGGTACCGATACTC
Found at i:6295 original size:21 final size:22
Alignment explanation
Indices: 6258--6298 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
6248 TTAAATATTA
6258 TAAAGGAAGTACTGATACTCAT
1 TAAAGGAAGTACTGATACTCAT
6280 TAAAGG-AGTA-TCGATACTC
1 TAAAGGAAGTACT-GATACTC
6299 CCTGTCCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 11 0.61
22 6 0.33
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGAAGTACTGATACTCAT
Found at i:9918 original size:151 final size:152
Alignment explanation
Indices: 9630--10268 Score: 1135
Period size: 151 Copynumber: 4.2 Consensus size: 152
9620 GATGAAAATA
* * * *
9630 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGCTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGC
9695 T-CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
*
9759 CATCAAAAGGCTCCCGAAGGCTT
130 CATCAAAAAGCTCCCGAAGGCTT
9782 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
9846 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
9910 ATCAAAAAGCTCCCGAAGGATT
131 ATCAAAAAGCTCCCGAAGGCTT
*
9932 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
9997 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-TTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
10061 ATCAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
*
10083 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
10148 CCC-AAGGCTTTTTGGAAACATCATGAACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
10212 ATCAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
10234 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
10269 TGGGAAATAG
Statistics
Matches: 471, Mismatches: 13, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
150 141 0.30
151 290 0.62
152 40 0.08
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (152 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTT
Found at i:10035 original size:226 final size:227
Alignment explanation
Indices: 9630--10268 Score: 1158
Period size: 226 Copynumber: 2.8 Consensus size: 227
9620 GATGAAAATA
* * * *
9630 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGCTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGC
9695 T-CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
*
9759 CATCAAAAGGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAA
130 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAA
9824 GGTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
195 GGTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
9857 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
9921 CCCGAAGGATTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
* *
9986 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAG
10051 GTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
10083 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
10148 CCC-AAGGCTTTTTGGAAACATCATGAACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
10212 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
10269 TGGGAAATAG
Statistics
Matches: 398, Mismatches: 12, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
225 20 0.05
226 315 0.79
227 63 0.16
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (227 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAG
GTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:10294 original size:75 final size:76
Alignment explanation
Indices: 9630--10268 Score: 1137
Period size: 75 Copynumber: 8.5 Consensus size: 76
9620 GATGAAAATA
* * *
9630 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGA-CCTGAAGGCTTTTGAAAACATCAAAAAG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT-AAGGC-TTTGAAAACATCAAAAAG
9694 CT-CCGAAGGCTT
64 CTCCCGAAGGCTT
*
9706 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAGGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
9771 CCCGAAGGCTT
66 CCCGAAGGCTT
*
9782 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
9846 CCCGAAGGCTT
66 CCCGAAGGCTT
*
9857 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
9921 CCCGAAGGATT
66 CCCGAAGGCTT
9932 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
9997 CCCGAAGGCTT
66 CCCGAAGGCTT
*
10008 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
10072 CCCGAAGGCTT
66 CCCGAAGGCTT
10083 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
10148 CCC-AAGGCTT
66 CCCGAAGGCTT
*
10158 TTTGGAAACATCATGAACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
10223 CCCGAAGGCTT
66 CCCGAAGGCTT
10234 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
10269 TGGGAAATAG
Statistics
Matches: 545, Mismatches: 13, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
75 314 0.58
76 228 0.42
77 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:10978 original size:20 final size:21
Alignment explanation
Indices: 10940--10988 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
10930 CATAAAGCTT
*
10940 TCATCTTGAAAAGAGAATCTA
1 TCATCTTTAAAAGAGAATCTA
10961 TCATCTTTAAAA-AGAATCTA
1 TCATCTTTAAAAGAGAATCTA
10981 TCATCTTT
1 TCATCTTT
10989 GAAGAGTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (21 bp):
TCATCTTTAAAAGAGAATCTA
Found at i:11436 original size:54 final size:54
Alignment explanation
Indices: 11354--11463 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
11344 TCAGAATAAC
* * * *
11354 ATGTTCGTAAAACATTTGACAGCGCATTCATCCTTTCATGTGGCTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAG
* *
11408 ATGTTCGTAAAACATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCCCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAG
11462 AT
1 AT
11464 TTCTGGTCAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (54 bp):
ATGTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAG
Found at i:22312 original size:2 final size:2
Alignment explanation
Indices: 22305--22342 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
22295 GTAATTTGTA
22305 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
22343 TTTAATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27577 original size:10 final size:11
Alignment explanation
Indices: 27562--27587 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27552 TTCTTCTTCA
27562 TTTTTTTATTT
1 TTTTTTTATTT
27573 TTTTTTTATTT
1 TTTTTTTATTT
27584 TTTT
1 TTTT
27588 CCCTCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:28957 original size:78 final size:79
Alignment explanation
Indices: 28872--29031 Score: 252
Period size: 78 Copynumber: 2.0 Consensus size: 79
28862 TAAAATTATA
* * *
28872 TTAAAATTTTATTTAACGAATCAA-AAGTTACAAACACAATTTAAATCACAAGACAAATTTATAA
1 TTAAAATTTTATTTAACAAAACAATAA-TTACAAACACAACTTAAATCACAAGACAAATTTATAA
28936 TTCAAATCTT-AAAT
65 TTCAAATCTTAAAAT
* *
28950 TTAAAATTTTATTTAACAAAACAATAATTATAAGCACAACTTAAATCACAAGACAAATTTATAAT
1 TTAAAATTTTATTTAACAAAACAATAATTACAAACACAACTTAAATCACAAGACAAATTTATAAT
29015 TCAAATCTTAAAAT
66 TCAAATCTTAAAAT
29029 TTA
1 TTA
29032 TTTAAGATTT
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
78 66 0.88
79 9 0.12
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (79 bp):
TTAAAATTTTATTTAACAAAACAATAATTACAAACACAACTTAAATCACAAGACAAATTTATAAT
TCAAATCTTAAAAT
Found at i:31212 original size:49 final size:48
Alignment explanation
Indices: 31171--31263 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 48
31161 AATTTTAATT
* *
31171 TAATAATA-TATAATAAATTATATTATTTATTTTAGAAATAATATTTCAA
1 TAATAATATTA-AATAAATTATATTA-ATATTTTAAAAATAATATTTCAA
*
31220 TAATAATATTAAATAAATTATTTTAATATTTTAAAAATAATATT
1 TAATAATATTAAATAAATTATATTAATATTTTAAAAATAATATT
31264 ATTTTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
48 17 0.43
49 21 0.52
50 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (48 bp):
TAATAATATTAAATAAATTATATTAATATTTTAAAAATAATATTTCAA
Found at i:31280 original size:21 final size:20
Alignment explanation
Indices: 31248--31288 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
31238 TATTTTAATA
*
31248 TTTTAAAAATAATATTATTT
1 TTTTAAAAATAATAGTATTT
31268 TTTTAATAAATAATAGTATTT
1 TTTTAA-AAATAATAGTATTT
31289 ATTATATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTAAAAATAATAGTATTT
Found at i:31399 original size:12 final size:13
Alignment explanation
Indices: 31376--31400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31366 CAAATATCGT
31376 AAAATTATTTTTA
1 AAAATTATTTTTA
31389 AAAATTATTTTT
1 AAAATTATTTTT
31401 CACAAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AAAATTATTTTTA
Found at i:33907 original size:17 final size:17
Alignment explanation
Indices: 33887--33929 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
33877 TGTGCTTGCA
33887 GGTCACGGGTGCGAGCT
1 GGTCACGGGTGCGAGCT
*
33904 GGTCACGAGTGCGAGCT
1 GGTCACGGGTGCGAGCT
33921 GGTCACGGG
1 GGTCACGGG
33930 CTTCAGGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.14, C:0.23, G:0.47, T:0.16
Consensus pattern (17 bp):
GGTCACGGGTGCGAGCT
Found at i:34768 original size:55 final size:55
Alignment explanation
Indices: 34608--35294 Score: 945
Period size: 55 Copynumber: 12.6 Consensus size: 55
34598 CTCCATAGTC
* * * *
34608 CTTCAGAGAGTATAAGACCCGAACAATCTTTAACAGTCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * * * * * *
34663 CTTCAGAGAATATAAGAC-C-CACAATCCTCATCAATCACGTCTTCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * *
34716 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCGGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * * *
34771 CTGCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * *
34824 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * * *
34879 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTTCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * * *
34932 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCGGCTTCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * ** * *
34987 CTGCATAGAGTACGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATCT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* *
35042 CTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* *
35097 CTTCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * *
35152 CTTCAGAGAGTATGAGACTCGAACAATTTTCAACAATCGTGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
35207 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
*
35262 CTTCAGAGAGTATAAGACTCGATCAATCTTCAA
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAA
35295 TTATCGTTGG
Statistics
Matches: 567, Mismatches: 59, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
53 137 0.24
54 6 0.01
55 424 0.75
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
Found at i:39855 original size:8 final size:8
Alignment explanation
Indices: 39842--39869 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
39832 GAAAAAGAAG
39842 ATATATAC
1 ATATATAC
39850 ATATATAC
1 ATATATAC
39858 ATATATAC
1 ATATATAC
39866 ATAT
1 ATAT
39870 GGGAGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:49480 original size:17 final size:17
Alignment explanation
Indices: 49460--49502 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
49450 TGTGCTTGCA
49460 GGTCACGGGTGCGAGCT
1 GGTCACGGGTGCGAGCT
*
49477 GGTCACGAGTGCGAGCT
1 GGTCACGGGTGCGAGCT
49494 GGTCACGGG
1 GGTCACGGG
49503 CTTCAGGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.14, C:0.23, G:0.47, T:0.16
Consensus pattern (17 bp):
GGTCACGGGTGCGAGCT
Found at i:51176 original size:15 final size:15
Alignment explanation
Indices: 51156--51205 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
51146 AGACATTACC
51156 CGCCCCGCATCCGCT
1 CGCCCCGCATCCGCT
51171 CGCCCCGCATCCGCT
1 CGCCCCGCATCCGCT
* *
51186 CGCCCCACATCCGCC
1 CGCCCCGCATCCGCT
51201 CGCCC
1 CGCCC
51206 AGCTAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.64, G:0.18, T:0.10
Consensus pattern (15 bp):
CGCCCCGCATCCGCT
Found at i:52180 original size:36 final size:36
Alignment explanation
Indices: 52111--52215 Score: 133
Period size: 36 Copynumber: 2.9 Consensus size: 36
52101 TTGATAATAA
* *
52111 CTCAAATTAAG-TTTTCCAATTAGTATTGGAAATATG
1 CTCAAATTAGGTTTTTCC-ACTAGTATTGGAAATATG
*
52147 CT-AAATTAGGTTTTTTCCACTAGTATTGCAAATATG
1 CTCAAATTAGG-TTTTTCCACTAGTATTGGAAATATG
* *
52183 CTCAAATTAGGTTATCCCACTAGTATTGGAAAT
1 CTCAAATTAGGTTTTTCCACTAGTATTGGAAAT
52216 GATGATTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
35 7 0.12
36 39 0.65
37 14 0.23
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (36 bp):
CTCAAATTAGGTTTTTCCACTAGTATTGGAAATATG
Found at i:54227 original size:20 final size:20
Alignment explanation
Indices: 54198--54235 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54188 CAATTTATTC
54198 ATTGGCGCATCGATGCATGG
1 ATTGGCGCATCGATGCATGG
* *
54218 ATTGGTGCATCGGTGCAT
1 ATTGGCGCATCGATGCAT
54236 CCCTTTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
ATTGGCGCATCGATGCATGG
Done.