Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001783.1 Hibiscus syriacus cultivar Beakdansim tig00003602_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: 105642
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2213 original size:20 final size:20
Alignment explanation
Indices: 2173--2215 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2163 GAAACCCTCA
*
2173 TCCTTTATCTTTTATGCGAG
1 TCCTTTATCTTTTACGCGAG
*
2193 TCCTTTATCTTTTACGTGAG
1 TCCTTTATCTTTTACGCGAG
2213 TCC
1 TCC
2216 ATGGATGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (20 bp):
TCCTTTATCTTTTACGCGAG
Found at i:2387 original size:33 final size:34
Alignment explanation
Indices: 2319--2387 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
2309 CAGTTTTGAT
* *
2319 TTACTTAAATTTTATGAGATCGTTACCTCTTAAAA
1 TTACTAAAATTATATGAGATCGTTA-CTCTTAAAA
2354 TTACTAAAATTATATGAGATCGTT-CTCTTAAAA
1 TTACTAAAATTATATGAGATCGTTACTCTTAAAA
2387 T
1 T
2388 GTTTAAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 10 0.31
35 22 0.69
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (34 bp):
TTACTAAAATTATATGAGATCGTTACTCTTAAAA
Found at i:19960 original size:22 final size:22
Alignment explanation
Indices: 19895--19963 Score: 120
Period size: 22 Copynumber: 3.1 Consensus size: 22
19885 CTTTTTTCGC
*
19895 CGGCAGTCACAGCCTCCATCGC
1 CGGCAGTCACAGCCTCCATCGT
19917 CGGCAGTCACAGCCTCCATCGT
1 CGGCAGTCACAGCCTCCATCGT
*
19939 CGGCAGTCACAGCTTCCATCGT
1 CGGCAGTCACAGCCTCCATCGT
19961 CGG
1 CGG
19964 GCGCTAACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.17, C:0.41, G:0.25, T:0.17
Consensus pattern (22 bp):
CGGCAGTCACAGCCTCCATCGT
Found at i:26158 original size:21 final size:22
Alignment explanation
Indices: 26128--26179 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
26118 ATTCTAATAA
*
26128 AAAATTAAACATTAAAAAAATT
1 AAAATTAAACAATAAAAAAATT
26150 AAAA-TAAACAATAAAAAAATT
1 AAAATTAAACAATAAAAAAATT
26171 AAACATTAA
1 AAA-ATTAA
26180 TAATTATCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 19 0.70
22 5 0.19
23 3 0.11
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAATTAAACAATAAAAAAATT
Found at i:27737 original size:31 final size:30
Alignment explanation
Indices: 27702--27775 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
27692 TTACAAGAAA
27702 AAAAAATCAGATTCATTTGATATAAAACAAT
1 AAAAAATCAGATTCATTT-ATATAAAACAAT
* *
27733 AAAAAAACAGATTCATTTATATAAAATAAT
1 AAAAAATCAGATTCATTTATATAAAACAAT
*
27763 AAAAATTCAGATT
1 AAAAAATCAGATT
27776 TATTATTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 22 0.56
31 17 0.44
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (30 bp):
AAAAAATCAGATTCATTTATATAAAACAAT
Found at i:39275 original size:33 final size:33
Alignment explanation
Indices: 39233--39320 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 33
39223 AACTCGAACC
* *
39233 GAAAGAAACCTGAACTAAATTTTAACCCAAACT
1 GAAAGAAACCTGAACCAAATTTTAAACCAAACT
** * *
39266 GAAAGAAACCCAAACGAAATTTTAAACCAATCT
1 GAAAGAAACCTGAACCAAATTTTAAACCAAACT
* *
39299 GAAAGCAACTTGAACCAAATTT
1 GAAAGAAACCTGAACCAAATTT
39321 AATCCGACCC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.20
Consensus pattern (33 bp):
GAAAGAAACCTGAACCAAATTTTAAACCAAACT
Found at i:42205 original size:28 final size:28
Alignment explanation
Indices: 42165--42223 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
42155 CGAGATTAAT
* *
42165 ATAAAAATTTGATAACAATTTCTAACAC
1 ATAAAAATTTGATAACAAATTATAACAC
*
42193 ATAAAATTTTGATAACAAATTATAACAC
1 ATAAAAATTTGATAACAAATTATAACAC
42221 ATA
1 ATA
42224 TTATAAGATC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (28 bp):
ATAAAAATTTGATAACAAATTATAACAC
Found at i:45985 original size:22 final size:22
Alignment explanation
Indices: 45957--45999 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
45947 ATTTAAGAAA
45957 AATATTAATATATAAAAAAATT
1 AATATTAATATATAAAAAAATT
45979 AATATTAATATATAAAAAAAT
1 AATATTAATATATAAAAAAAT
46000 CAATCTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AATATTAATATATAAAAAAATT
Found at i:47875 original size:12 final size:12
Alignment explanation
Indices: 47858--47887 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
47848 TGGTTCTGAC
*
47858 TCATCACTGTCA
1 TCATCACTATCA
47870 TCATCACTATCA
1 TCATCACTATCA
47882 TCATCA
1 TCATCA
47888 TCCTCGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.33
Consensus pattern (12 bp):
TCATCACTATCA
Found at i:49532 original size:21 final size:20
Alignment explanation
Indices: 49465--49534 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
49455 TTTAAAAAAG
*
49465 AATAAAAATATTTTTAAAATT
1 AATAAAAATATTATT-AAATT
* *
49486 AATGAAAATCTATATTAAA-T
1 AATAAAAATAT-TATTAAATT
49506 --TAAAAATATTATTAAATTT
1 AATAAAAATATTATTAAA-TT
49525 AATAAAAATA
1 AATAAAAATA
49535 AAATATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 7 0.18
18 7 0.18
19 1 0.03
20 1 0.03
21 20 0.51
22 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (20 bp):
AATAAAAATATTATTAAATT
Found at i:50031 original size:19 final size:16
Alignment explanation
Indices: 50008--50051 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
49998 TTAAGTCAAC
50008 AAATATTTAAGAAAAAT
1 AAATATTTAA-AAAAAT
*
50025 ATTAATATATAAAAAAAT
1 A--AATATTTAAAAAAAT
50043 AAATATTTA
1 AAATATTTA
50052 TATATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 7 0.30
17 1 0.04
18 7 0.30
19 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAATATTTAAAAAAAT
Found at i:50049 original size:22 final size:22
Alignment explanation
Indices: 50021--50086 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
50011 TATTTAAGAA
50021 AAATATTAATATATAAAAAAAT
1 AAATATTAATATATAAAAAAAT
*
50043 AAATATTTATATATAAAAAAAT
1 AAATATTAATATATAAAAAAAT
* * * *
50065 CAAT-CTCATTTATAAAAAAAT
1 AAATATTAATATATAAAAAAAT
50086 A
1 A
50087 TTCACTCTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
21 14 0.37
22 24 0.63
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATATTAATATATAAAAAAAT
Found at i:50874 original size:29 final size:30
Alignment explanation
Indices: 50824--50901 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 30
50814 ATAAATACAT
* * * *
50824 TCTCAACCCGTAAACAT-TCACAACAATCA
1 TCTCAACCTGTAAAAATCACACAACAAACA
*
50853 TCTCAACCTG-AAAAATCACACAACAAACC
1 TCTCAACCTGTAAAAATCACACAACAAACA
* *
50882 TTTCAACCTGTAAATATCAC
1 TCTCAACCTGTAAAAATCAC
50902 CCCGACAATC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 5 0.12
29 27 0.68
30 8 0.20
ACGTcount: A:0.42, C:0.32, G:0.04, T:0.22
Consensus pattern (30 bp):
TCTCAACCTGTAAAAATCACACAACAAACA
Found at i:53944 original size:20 final size:22
Alignment explanation
Indices: 53903--53943 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
53893 TATTTAAGAA
53903 AAATATTAATATATAAAAAAAT
1 AAATATTAATATATAAAAAAAT
53925 AAATATTAATATA-AAAAAA
1 AAATATTAATATATAAAAAA
53944 TCAATCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATATTAATATATAAAAAAAT
Found at i:55314 original size:17 final size:17
Alignment explanation
Indices: 55292--55326 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55282 CTTGATATAG
55292 TTAGAA-TATTATATTTA
1 TTAGAATTA-TATATTTA
55309 TTAGAATTATATATTTA
1 TTAGAATTATATATTTA
55326 T
1 T
55327 GTTTCAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAGAATTATATATTTA
Found at i:55941 original size:42 final size:42
Alignment explanation
Indices: 55880--55985 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
55870 GATGATGCCA
* * *
55880 CAAGGGTACGTGCCTAGCCCACCAGTTCAGATTCCATCTCCG
1 CAAGGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCG
* * *
55922 CAAGGGTATATGCCAAGCCCACCAGTTCATATGCCATCTCTG
1 CAAGGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCG
* *
55964 C-AGGGTTACATTCCTAGCCCAC
1 CAAGGG-TACATGCCAAGCCCAC
55986 AGAGGTACAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 4 0.07
42 50 0.93
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.23
Consensus pattern (42 bp):
CAAGGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCG
Found at i:56015 original size:21 final size:21
Alignment explanation
Indices: 55967--56033 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
55957 ATCTCTGCAG
* *
55967 GGTTACATTCCTAGCCCACAGA
1 GGTTACATACCTAGCCCGCA-A
55989 GG-TACATACCTAGCCCGCAA
1 GGTTACATACCTAGCCCGCAA
* * *
56009 GGTTACATGCCCAGCCCGCAG
1 GGTTACATACCTAGCCCGCAA
56030 GGTT
1 GGTT
56034 TTATGAAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 3 0.08
21 34 0.87
22 2 0.05
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (21 bp):
GGTTACATACCTAGCCCGCAA
Found at i:56108 original size:14 final size:14
Alignment explanation
Indices: 56089--56117 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56079 TGCATATGGT
56089 TCATATGCATCTTA
1 TCATATGCATCTTA
56103 TCATATGCATCTTA
1 TCATATGCATCTTA
56117 T
1 T
56118 TTGACTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (14 bp):
TCATATGCATCTTA
Found at i:56992 original size:20 final size:21
Alignment explanation
Indices: 56947--56993 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
56937 AAAAGAACCC
*
56947 AATTTC-ACATTCTAACATCA
1 AATTTCAACACTCTAACATCA
56967 AA-TTCAACACTCTAACAT-A
1 AATTTCAACACTCTAACATCA
56986 AATTTCAA
1 AATTTCAA
56994 GCATAATAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTTCAACACTCTAACATCA
Found at i:57245 original size:139 final size:139
Alignment explanation
Indices: 56995--57310 Score: 463
Period size: 139 Copynumber: 2.3 Consensus size: 139
56985 AAATTTCAAG
* * * * * * *
56995 CATAATAGGGCAATTATAACCTATTATCTGACAAAAAAAGGGAAGGTGCACCCCCTGAAATACGC
1 CATAATAGGGAAATTATAACATATTCTCTGACAAAGAAAGAGAAGGCGCACCCCCTGAAATACAC
* *
57060 TTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTACTAACATGAATAGTGCCACACCGGGA
66 TTTCACCACATTGTTGCATCCCATCAAACATGATAGGTACTAACATGAATAGTGCCACACCGGGA
57125 GACATCACA
131 GACATCACA
* ** *
57134 CATAATAGGGTAATTATAACATATTCTCTGACAAAGAAAGAGAAGGCGCGTCCCCTGAAATGCAC
1 CATAATAGGGAAATTATAACATATTCTCTGACAAAGAAAGAGAAGGCGCACCCCCTGAAATACAC
* * * *
57199 TTTCACCACTTTGTTGCATCCCATCAAACATGATAGGTACTGACATGAATAGTGCCACGCCGGGG
66 TTTCACCACATTGTTGCATCCCATCAAACATGATAGGTACTAACATGAATAGTGCCACACCGGGA
57264 GACATCACA
131 GACATCACA
*
57273 CATAATAGGGAAATTATAACATATTCTCTG-GAAAGAAA
1 CATAATAGGGAAATTATAACATATTCTCTGACAAAGAAA
57311 AAGGGGAATG
Statistics
Matches: 159, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
138 7 0.04
139 152 0.96
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (139 bp):
CATAATAGGGAAATTATAACATATTCTCTGACAAAGAAAGAGAAGGCGCACCCCCTGAAATACAC
TTTCACCACATTGTTGCATCCCATCAAACATGATAGGTACTAACATGAATAGTGCCACACCGGGA
GACATCACA
Found at i:64069 original size:31 final size:31
Alignment explanation
Indices: 64011--64069 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
64001 TCTTTATAGG
* *
64011 TTAAATTATGATTTCGGTCCCTCTATTATGC
1 TTAAATTATGATTTCAGTCCATCTATTATGC
* *
64042 TTAAATTATGGTTTCAGTCCATTTATTA
1 TTAAATTATGATTTCAGTCCATCTATTA
64070 CGTGGTAGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (31 bp):
TTAAATTATGATTTCAGTCCATCTATTATGC
Found at i:66587 original size:123 final size:121
Alignment explanation
Indices: 66359--66799 Score: 451
Period size: 123 Copynumber: 3.6 Consensus size: 121
66349 CAAAATGGGC
* * * * ** * *
66359 TTTTAGCGGCGTTTTTTGAACAAAGGCCGGTAAATACTCGTACTTTAGTAGCGTTTTTAT-ATAA
1 TTTTAGCGGCG-TTTTTGTACAAACGCCGCTAAAGACTCGTACTTTAGCGGCGTTTTAATCACAA
* ** **
66423 ACGCCGTTAAAGACTGTAGTTTAGTGGTATTTTCATATAAACGCCGCTAATTACTATA
65 A-GCCGCTAAAGACTGTACATTAGTGGCGTTTTCATATAAACGCCGCTAATTACTATA
* *
66481 TTTTAGCGGCGTTTTTGTACAAACGCCGCTAAAGACTCGTACTCTAGCGGTGTTTTAATCACAAA
1 TTTTAGCGGCGTTTTTGTACAAACGCCGCTAAAGACTCGTACTTTAGCGGCGTTTTAATCACAAA
* *
66546 GACCGCTAAAGGCCTGTACATTAGTGGCGTTTTCATATAAACGCTGCTAATTACTATA
66 G-CCGCTAAA-GACTGTACATTAGTGGCGTTTTCATATAAACGCCGCTAATTACTATA
* * *
66604 CTTTAGCGGCGTTTTTGTACAAACGTCGCT-AAGAACTCGTACTTTAGCGGCGTTTTAAGCACAA
1 TTTTAGCGGCGTTTTTGTACAAACGCCGCTAAAG-ACTCGTACTTTAGCGGCGTTTTAATCACAA
* * * * * *
66668 TCGCCGCTAAAGTCTCGTACATTAGCT-GCGTTTTAAGTACAAACGCCGCTAAAGTAGT-TA
65 -AGCCGCTAAAGACT-GTACATTAG-TGGCGTTTTCA-TATAAACGCCGCT-AATTACTATA
* * * * * *
66728 TATTTAGCTGCATTTTTATACAAACGCCGATAAAGACTCGTACTTTAGTGGCGTTTTTAT-ACAA
1 T-TTTAGCGGCGTTTTTGTACAAACGCCGCTAAAGACTCGTACTTTAGCGGCGTTTTAATCACAA
66792 ATGCCGCT
65 A-GCCGCT
66800 TTAGTGGCGT
Statistics
Matches: 268, Mismatches: 39, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
121 40 0.15
122 28 0.10
123 121 0.45
124 25 0.09
125 51 0.19
126 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (121 bp):
TTTTAGCGGCGTTTTTGTACAAACGCCGCTAAAGACTCGTACTTTAGCGGCGTTTTAATCACAAA
GCCGCTAAAGACTGTACATTAGTGGCGTTTTCATATAAACGCCGCTAATTACTATA
Found at i:66659 original size:41 final size:40
Alignment explanation
Indices: 66360--66799 Score: 273
Period size: 42 Copynumber: 10.7 Consensus size: 40
66350 AAAATGGGCT
* *
66360 TTTAGCGGCGTTTTT-TGAACAAAGGCCGGTAAATACTCGTAC
1 TTTAGCGGCGTTTTTAT--ACAAACGCCGCTAAA-ACTCGTAC
** * * *
66402 TTTAGTAGCGTTTTTATATAAACGCCGTTAAAGACT-GTAG
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAA-ACTCGTAC
* ** * * * * *
66442 TTTAGTGGTATTTTCATATAAACGCCGCTAATTACT-ATAT
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAA-AACTCGTAC
*
66482 TTTAGCGGCGTTTTTGTACAAACGCCGCTAAAGACTCGTAC
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAA-ACTCGTAC
* * * *
66523 TCTAGCGGTGTTTTAATCACAAA-GACCGCTAAAGGC-CTGTAC
1 TTTAGCGGCGTTTTTAT-ACAAACG-CCGCTAAA-ACTC-GTAC
* * * * * * *
66565 ATTAGTGGCGTTTTCATATAAACGCTGCTAATTACT-ATAC
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAA-AACTCGTAC
* *
66605 TTTAGCGGCGTTTTTGTACAAACGTCGCTAAGAACTCGTAC
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAA-AACTCGTAC
* * * *
66646 TTTAGCGGCGTTTTAAGCACAATCGCCGCTAAAGTCTCGTAC
1 TTTAGCGGCGTTTTTA-TACAAACGCCGCTAAA-ACTCGTAC
* * * * * *
66688 ATTAGCTGCGTTTTAAGTACAAACGCCGCT-AAAGTAGTTATA
1 TTTAGCGGCGTTTTTA-TACAAACGCCGCTAAAACTCG-TA-C
* * *
66730 TTTAGCTGCATTTTTATACAAACGCCGATAAAGACTCGTAC
1 TTTAGCGGCGTTTTTATACAAACGCCGCTAAA-ACTCGTAC
* *
66771 TTTAGTGGCGTTTTTATACAAATGCCGCT
1 TTTAGCGGCGTTTTTATACAAACGCCGCT
66800 TTAGTGGCGT
Statistics
Matches: 306, Mismatches: 75, Indels: 35
0.74 0.18 0.08
Matches are distributed among these distances:
40 94 0.31
41 101 0.33
42 107 0.35
43 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTATACAAACGCCGCTAAAACTCGTAC
Found at i:66802 original size:28 final size:28
Alignment explanation
Indices: 66770--66856 Score: 138
Period size: 28 Copynumber: 3.1 Consensus size: 28
66760 AAGACTCGTA
*
66770 CTTTAGTGGCGTTTTTATACAAATGCCG
1 CTTTAGTGGCGTTTTTATACAAACGCCG
66798 CTTTAGTGGCGTTTTTATACAAACGCCG
1 CTTTAGTGGCGTTTTTATACAAACGCCG
* *
66826 CTTTAGTGGCGTTTTAAGCACAAACGCCG
1 CTTTAGTGGCGTTTTTA-TACAAACGCCG
66855 CT
1 CT
66857 AAATAGATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 43 0.78
29 12 0.22
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (28 bp):
CTTTAGTGGCGTTTTTATACAAACGCCG
Found at i:69963 original size:43 final size:43
Alignment explanation
Indices: 69910--70022 Score: 172
Period size: 43 Copynumber: 2.6 Consensus size: 43
69900 ACAAATGACA
* * *
69910 TTAAATACACAGTCAATAGCGGCGTTTGTAAAGAAAAATGTCG
1 TTAAATACACAGTCAATAGCGGCGTTTATAAAGAAAAACGCCG
* *
69953 TTAAATACACAGTAAATAGCGGCGTTTATAAAGACAAACGCCG
1 TTAAATACACAGTCAATAGCGGCGTTTATAAAGAAAAACGCCG
*
69996 CTAAATACACAGTCAATAGCGGCGTTT
1 TTAAATACACAGTCAATAGCGGCGTTT
70023 TTTTTAAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (43 bp):
TTAAATACACAGTCAATAGCGGCGTTTATAAAGAAAAACGCCG
Found at i:73101 original size:2 final size:2
Alignment explanation
Indices: 73094--73118 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
73084 CTTCTGTATG
73094 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 T
73119 TAGAAACGCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:74809 original size:24 final size:22
Alignment explanation
Indices: 74768--74815 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
74758 ATATTATGAA
* *
74768 TTTTTAAATAAATCATTAATTT
1 TTTTTAAAAAAATCATTAAGTT
74790 TTTTTATAAAAAATCAATTAAGTT
1 TTTTTA-AAAAAATC-ATTAAGTT
74814 TT
1 TT
74816 GAGTTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 7 0.32
24 9 0.41
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTTAAAAAAATCATTAAGTT
Found at i:76163 original size:19 final size:18
Alignment explanation
Indices: 76135--76170 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
76125 AAATTATGTC
76135 AAATACAATTATAAATATT
1 AAATACAATT-TAAATATT
*
76154 AAATATAATTTAAATAT
1 AAATACAATTTAAATAT
76171 AATAAAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATACAATTTAAATATT
Found at i:79325 original size:16 final size:17
Alignment explanation
Indices: 79286--79326 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
79276 TTTTTTATTT
79286 GAGTTTAAAATTAATTG
1 GAGTTTAAAATTAATTG
*
79303 GATTTTAAATATTAA-TG
1 GAGTTTAAA-ATTAATTG
79320 G-GTTTAA
1 GAGTTTAA
79327 GGTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 11 0.52
18 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (17 bp):
GAGTTTAAAATTAATTG
Found at i:79397 original size:14 final size:14
Alignment explanation
Indices: 79378--79422 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
79368 GATTGGACTG
79378 AATATAAACAAACA
1 AATATAAACAAACA
** *
79392 AATATAAATGAACG
1 AATATAAACAAACA
*
79406 AACATAAACAAACA
1 AATATAAACAAACA
79420 AAT
1 AAT
79423 TATTGAACGC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.67, C:0.13, G:0.04, T:0.16
Consensus pattern (14 bp):
AATATAAACAAACA
Found at i:84346 original size:2 final size:2
Alignment explanation
Indices: 84339--84384 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
84329 ATAAACGTGA
84339 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
84381 AT AT
1 AT AT
84385 TGTTATATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91874 original size:48 final size:48
Alignment explanation
Indices: 91798--91893 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
91788 TCTTACATGT
*
91798 CTATTGAATCTATATAATTCTCTCTCGGGTCAATCAATAACTTCTAAC
1 CTATTAAATCTATATAATTCTCTCTCGGGTCAATCAATAACTTCTAAC
* * * *
91846 CTATTAAATTTATATAATTCTCTTTCGGGTCAATCCATAACTTTTAAC
1 CTATTAAATCTATATAATTCTCTCTCGGGTCAATCAATAACTTCTAAC
91894 TTGGGAATCG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (48 bp):
CTATTAAATCTATATAATTCTCTCTCGGGTCAATCAATAACTTCTAAC
Found at i:92758 original size:2 final size:2
Alignment explanation
Indices: 92746--92785 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
92736 TTAATAAGAA
92746 AT AT A- AT AT 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 AT AT AT AT AT A
92786 CACGCATATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:93273 original size:37 final size:36
Alignment explanation
Indices: 93198--93273 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
93188 TTTTTATATT
*
93198 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
93234 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
93271 TTT
1 TTT
93274 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:100934 original size:2 final size:2
Alignment explanation
Indices: 100921--100967 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
100911 TTATTTTATT
*
100921 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
100963 TA TA T
1 TA TA T
100968 TTAATCGCAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Done.