Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000865.1 Hibiscus syriacus cultivar Beakdansim tig00001671_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: 87587
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:7187 original size:38 final size:37
Alignment explanation
Indices: 7112--7188 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 37
7102 TTACTATGAT
* **
7112 TAATTTATATATTTTCTTTAAAAATTTTAAATTTAAA
1 TAATTTATATATTTTCTTTAAAAATTTAAAAGATAAA
7149 TAATTTATATAATTTT-TTTACAAAATTTAAAAGATAAA
1 TAATTTATAT-ATTTTCTTTA-AAAATTTAAAAGATAAA
7187 TA
1 TA
7189 GGTTTAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
37 14 0.40
38 21 0.60
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (37 bp):
TAATTTATATATTTTCTTTAAAAATTTAAAAGATAAA
Found at i:9359 original size:30 final size:30
Alignment explanation
Indices: 9277--9346 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
9267 TAAAACGGTT
9277 CGGTTCGATTCGGTTCGTATTTATCTTTTA
1 CGGTTCGATTCGGTTCGTATTTATCTTTTA
9307 CGGTTCGATTCGGTTCGTATTTATCTTTTA
1 CGGTTCGATTCGGTTCGTATTTATCTTTTA
*
9337 CGGTTTGATT
1 CGGTTCGATT
9347 TTGTGTTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (30 bp):
CGGTTCGATTCGGTTCGTATTTATCTTTTA
Found at i:12310 original size:24 final size:24
Alignment explanation
Indices: 12280--12346 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
12270 CAAGGCAGAG
*
12280 GTAGAGGTCATGGACGAGGTGGAA
1 GTAGAGGTCATGGACGAGGTGCAA
*
12304 GTCGAGGTCATGGACGAGGTGCAA
1 GTAGAGGTCATGGACGAGGTGCAA
**
12328 GTAGAGGTCGCGGACGAGG
1 GTAGAGGTCATGGACGAGG
12347 CTAGAATTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.25, C:0.13, G:0.46, T:0.15
Consensus pattern (24 bp):
GTAGAGGTCATGGACGAGGTGCAA
Found at i:39217 original size:2 final size:2
Alignment explanation
Indices: 39210--39263 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
39200 TTTCAATCTA
39210 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
39252 AT AT AT AT AT AT
1 AT AT AT AT AT AT
39264 TGAACTCATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39830 original size:39 final size:39
Alignment explanation
Indices: 39785--39886 Score: 116
Period size: 39 Copynumber: 2.6 Consensus size: 39
39775 TTGAACGTGA
** * *
39785 TACTAAAATGAAACAAAGTCTAAAGTTTTTGAATGTTGG
1 TACTAAAATGAAACAAAAACTAAAGTTTTTGAAGGTCGG
* * *
39824 TACTAAAATGGAAA-AAAAACTGACGTTTTTGACGGTCGG
1 TACTAAAAT-GAAACAAAAACTAAAGTTTTTGAAGGTCGG
*
39863 TACTAAAATGAAACAAAAATTAAA
1 TACTAAAATGAAACAAAAACTAAA
39887 CTTTAGGTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
38 4 0.08
39 43 0.84
40 4 0.08
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (39 bp):
TACTAAAATGAAACAAAAACTAAAGTTTTTGAAGGTCGG
Found at i:40307 original size:27 final size:27
Alignment explanation
Indices: 40269--40323 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
40259 GCGAAGTCAT
40269 GGGTGTTTATAATTCGGTTAAAATTTC
1 GGGTGTTTATAATTCGGTTAAAATTTC
40296 GGGTGTTTATAATTCGGTTAAAATTTC
1 GGGTGTTTATAATTCGGTTAAAATTTC
40323 G
1 G
40324 ATAGATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (27 bp):
GGGTGTTTATAATTCGGTTAAAATTTC
Found at i:44295 original size:24 final size:23
Alignment explanation
Indices: 44260--44304 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
44250 TGAATGATTT
44260 AATCAAATATAAACTTCAAAATCG
1 AATCAAATATAAACTT-AAAATCG
*
44284 AATCGAAA-ATAATCTTAAAAT
1 AATC-AAATATAAACTTAAAAT
44305 TTCTTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 11 0.58
25 3 0.16
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (23 bp):
AATCAAATATAAACTTAAAATCG
Found at i:46664 original size:38 final size:38
Alignment explanation
Indices: 46590--46668 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
46580 AATTAAATAG
*
46590 AGACTTGAAATTCGGAGATAAATACATAAATTTATGTT
1 AGACTTGAAATTCGGAGATAAATACATAAATGTATGTT
46628 AGACTTGAAATTCGGAGATAAATACATAAATGTATGTT
1 AGACTTGAAATTCGGAGATAAATACATAAATGTATGTT
46666 AGA
1 AGA
46669 GTGATTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.32
Consensus pattern (38 bp):
AGACTTGAAATTCGGAGATAAATACATAAATGTATGTT
Found at i:52360 original size:16 final size:16
Alignment explanation
Indices: 52339--52371 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52329 TTATTTTTTA
52339 TTATA-TTATATTTATT
1 TTATATTTA-ATTTATT
52355 TTATATTTAATTTATT
1 TTATATTTAATTTATT
52371 T
1 T
52372 GACTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATATTTAATTTATT
Found at i:53427 original size:102 final size:101
Alignment explanation
Indices: 53178--53433 Score: 237
Period size: 102 Copynumber: 2.5 Consensus size: 101
53168 GGCAACATCG
* * * * * * *
53178 CTTCCAGTTCAAGGGGAAGACATTCATCTGCCAATTTCTTTGACATTAATATGGAGATGCCCTCG
1 CTTCAAGTTCAAGGGGAAGACATTCAACTGCCAA-TTGTTAGACCTCAATATGGAGATGCCATCG
** * * *
53243 ACACAACAATTTGTTCAATACCCATTTGACACGGTGC
65 ACACAACAATAAGTTCAAAACCCATATGACACGATGC
* * * * *
53280 CTTCAAGTTCCAGGGGAAGACATTCAACTGCGAGA-TGCCTCGACCTCAATGTGGAGATG-CATG
1 CTTCAAGTTCAAGGGGAAGACATTCAACTGCCA-ATTG-TTAGACCTCAATATGGAGATGCCAT-
* * * *
53343 CGACACAACACTAAGTTGAAAACCCGTATGACACTATGC
63 CGACACAACAATAAGTTCAAAACCCATATGACACGATGC
* * *
53382 CTTCAAGTTCAAGGGGAAGGCATTCAACTACCAACTTGTTAGACCTAAATAT
1 CTTCAAGTTCAAGGGGAAGACATTCAACTGCCAA-TTGTTAGACCTCAATAT
53434 CGGTATCACA
Statistics
Matches: 121, Mismatches: 28, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
101 4 0.03
102 114 0.94
103 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (101 bp):
CTTCAAGTTCAAGGGGAAGACATTCAACTGCCAATTGTTAGACCTCAATATGGAGATGCCATCGA
CACAACAATAAGTTCAAAACCCATATGACACGATGC
Found at i:58249 original size:2 final size:2
Alignment explanation
Indices: 58242--58267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58232 CCTAACCATA
58242 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
58268 TCTTTCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58907 original size:146 final size:146
Alignment explanation
Indices: 58635--58914 Score: 420
Period size: 146 Copynumber: 1.9 Consensus size: 146
58625 TTAAAGGACT
* * *
58635 AAATTGAAAAATAAAAAATTTGTTATAAAAAAGAGGAATTGCAAGTACACATGTATTCTATTATG
1 AAATTGAAAAATAAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG
* * *
58700 GTTTAGGAGCATGTAGCTCAAATTTTGTAAAAAAACAGACTTAAAATAAATGACGAATTGAAGAA
66 GTTTAAGAGCATGCAGCTCAAATTTTGTAAAAAAACAGACTTAAAATAAAGGACGAATTGAAGAA
58765 ATAAGGAGATTATGAA
131 ATAAGGAGATTATGAA
*
58781 AAATTGAAAGATAAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG
1 AAATTGAAAAATAAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG
* * * * *
58846 GTTTAAGAGCATGCAGTTCAAA-TTTGATAAAAAAATATACTTAAAATGAAGGA-TAACTTGAAG
66 GTTTAAGAGCATGCAGCTCAAATTTTG-TAAAAAAACAGACTTAAAATAAAGGACGAA-TTGAAG
58909 AAATAA
129 AAATAA
58915 TGAAATCATG
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
145 6 0.05
146 114 0.95
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (146 bp):
AAATTGAAAAATAAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTACACATGTATTCTACTATG
GTTTAAGAGCATGCAGCTCAAATTTTGTAAAAAAACAGACTTAAAATAAAGGACGAATTGAAGAA
ATAAGGAGATTATGAA
Found at i:60066 original size:29 final size:29
Alignment explanation
Indices: 60005--60075 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
59995 CCCAACCCAT
** *
60005 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCAGCGACCAACG
** *
60034 AGGTCGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCCAGCGACCAACG
60063 AGGTCGCCATGCA
1 AGGTCGCCATGCA
60076 TGCCCGACGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.14
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCAGCGACCAACG
Found at i:60086 original size:29 final size:29
Alignment explanation
Indices: 60005--60090 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
59995 CCCAACCCAT
****
60005 AGGTCGCCATGCACTCCC-AGCGACCTCCT
1 AGGTCGCCATGCACTCCCGA-CGACCAAGG
* *
60034 AGGTCGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGACGACCAAGG
60063 AGGTCGCCATGCA-TGCCCGACGACCAAG
1 AGGTCGCCATGCACT-CCCGACGACCAAG
60091 CTTTTAACCC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
28 1 0.02
29 46 0.98
ACGTcount: A:0.21, C:0.38, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGACGACCAAGG
Found at i:60194 original size:51 final size:55
Alignment explanation
Indices: 60076--60223 Score: 207
Period size: 51 Copynumber: 2.7 Consensus size: 55
60066 TCGCCATGCA
*
60076 TGCCCGACGACCAAGCTTTTAACCCT-TGCACGCCCTGCATGTCATAACTGGGAGATTCC
1 TGCCCGACGACCAAGC-TTTAACCCTCT--ACTCCCT-CATGT-ATAACTGGGAGATTCC
60135 TGCCCGACGACCAAGCTTTAACCCTCTACTCCCTCATGT-T-A-T-GGAGATTCC
1 TGCCCGACGACCAAGCTTTAACCCTCTACTCCCTCATGTATAACTGGGAGATTCC
60186 TGCCCGACGACCAAGCTTTAACCCTCTACTCCCTCATG
1 TGCCCGACGACCAAGCTTTAACCCTCTACTCCCTCATG
60224 CATGCGTTGC
Statistics
Matches: 87, Mismatches: 1, Indels: 10
0.89 0.01 0.10
Matches are distributed among these distances:
51 47 0.54
52 1 0.01
53 1 0.01
54 1 0.01
56 5 0.06
57 6 0.07
58 9 0.10
59 17 0.20
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (55 bp):
TGCCCGACGACCAAGCTTTAACCCTCTACTCCCTCATGTATAACTGGGAGATTCC
Found at i:60328 original size:29 final size:29
Alignment explanation
Indices: 60296--60396 Score: 130
Period size: 29 Copynumber: 3.5 Consensus size: 29
60286 GTCGTCGGGC
*
60296 GTGCATGGCGACCTCTTTGGTCGCCCGGA
1 GTGCATGGCGACCTCCTTGGTCGCCCGGA
60325 GTGCATGGCGACCTCCTTGGTCGCCCGGA
1 GTGCATGGCGACCTCCTTGGTCGCCCGGA
* **** **
60354 GTGAATGGCGACCTAGGAGGTCGCTGGGA
1 GTGCATGGCGACCTCCTTGGTCGCCCGGA
60383 GTGCATGGCGACCT
1 GTGCATGGCGACCT
60397 ATGGGTTGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.21
Consensus pattern (29 bp):
GTGCATGGCGACCTCCTTGGTCGCCCGGA
Found at i:64946 original size:30 final size:31
Alignment explanation
Indices: 64912--64988 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
64902 TTAAAAAAAC
*
64912 TTAAGATTTGGTCACTTT-GGTTCTTTTTAA
1 TTAAGATTTGGTCACTTTCGGTTCGTTTTAA
* *
64942 TTAAGATTCGGTCACTTTCGTTTCGTTTTAA
1 TTAAGATTTGGTCACTTTCGGTTCGTTTTAA
* *
64973 TTAAGATGTGATCACT
1 TTAAGATTTGGTCACT
64989 CAAGGTTAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 17 0.43
31 23 0.57
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (31 bp):
TTAAGATTTGGTCACTTTCGGTTCGTTTTAA
Found at i:64974 original size:31 final size:30
Alignment explanation
Indices: 64912--64979 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
64902 TTAAAAAAAC
* *
64912 TTAAGATTTGGTCACTTTGGTTCTTTTTAA
1 TTAAGATTCGGTCACTTTGGTTCGTTTTAA
*
64942 TTAAGATTCGGTCACTTTCGTTTCGTTTTAA
1 TTAAGATTCGGTCACTTT-GGTTCGTTTTAA
64973 TTAAGAT
1 TTAAGAT
64980 GTGATCACTC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 17 0.50
31 17 0.50
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (30 bp):
TTAAGATTCGGTCACTTTGGTTCGTTTTAA
Found at i:65307 original size:13 final size:13
Alignment explanation
Indices: 65287--65318 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
65277 CATTATTGTT
65287 CATCTTCTCCCGA
1 CATCTTCTCCCGA
*
65300 CTTCTTCTCCCGA
1 CATCTTCTCCCGA
65313 CATCTT
1 CATCTT
65319 TGTTCCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.12, C:0.44, G:0.06, T:0.38
Consensus pattern (13 bp):
CATCTTCTCCCGA
Found at i:65887 original size:31 final size:31
Alignment explanation
Indices: 65849--65929 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
65839 ACCTCATTTT
65849 TAAGTGACCAAAACTTAATAAA-ATAATAACG
1 TAAGTGACCAAAACTTAATAAATATAA-AACG
* * * * *
65880 TAAGTGACCAAAAGTTTACAAATATGAAAGG
1 TAAGTGACCAAAACTTAATAAATATAAAACG
*
65911 AAAGTGACCAAAACTTAAT
1 TAAGTGACCAAAACTTAAT
65930 CCACGTATTA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 37 0.93
32 3 0.08
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAATATAAAACG
Found at i:67622 original size:11 final size:11
Alignment explanation
Indices: 67583--67624 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
67573 ACGATAAAAA
67583 TAAAATAAAATG
1 TAAAAT-AAATG
67595 TAAAAT-AATG
1 TAAAATAAATG
**
67605 TGTAATAAATG
1 TAAAATAAATG
67616 TAAAATAAA
1 TAAAATAAA
67625 AAATAGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 11 0.44
12 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (11 bp):
TAAAATAAATG
Found at i:70718 original size:2 final size:2
Alignment explanation
Indices: 70713--70745 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
70703 ACTCATCCAT
70713 TA 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 TA T
70746 GAGACGGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:74377 original size:2 final size:2
Alignment explanation
Indices: 74330--74359 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
74320 TATTCAATGA
74330 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
74360 CATGCATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77670 original size:3 final size:3
Alignment explanation
Indices: 77658--77746 Score: 151
Period size: 3 Copynumber: 29.7 Consensus size: 3
77648 TACAGAGGAG
*
77658 GAA GAG GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
77706 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GCA GCA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
77747 GAATTAAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:81507 original size:130 final size:130
Alignment explanation
Indices: 81263--81510 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
81253 ATTATTTATA
* *
81263 ATCAATTTGGTCCTAAATTAAATAAAATTTAATGAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
81328 TTAGCACATGATCATGACACGTGTCATTGGTGACACGCGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACACGTCACCACCTAATTATTTATATATGCT
81393 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * * *
81458 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACACGTCACCACCTAATTA
81511 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACACGTCACCACCTAATTATTTATATATGCT
Found at i:81541 original size:130 final size:129
Alignment explanation
Indices: 81277--81541 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
81267 ATTTGGTCCT
* * *
81277 AAATTAAATAAAATTTAATGAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
81342 TGACACGTGTCATTGGTGACACGCGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACACGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
81407 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * * *
81472 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACACGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
81536 -A
128 CA
81537 AAATT
1 AAATT
81542 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACACGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:82154 original size:21 final size:21
Alignment explanation
Indices: 82130--82172 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
82120 TATTACCTTA
82130 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
82151 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
82172 A
1 A
82173 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:82190 original size:35 final size:35
Alignment explanation
Indices: 82141--82226 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
82131 ATTGAAGTAT
** * *
82141 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
82176 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
82211 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
82227 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:85554 original size:16 final size:16
Alignment explanation
Indices: 85533--85565 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
85523 TAATAAATAA
85533 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
85549 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
85565 A
1 A
85566 AAATTTTTTT
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:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:85660 original size:16 final size:16
Alignment explanation
Indices: 85635--85699 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
85625 TAATAAATAA
*
85635 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
85651 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
85667 ACGAACACAAATGAAC
1 ACGAACATAAACGAAC
85683 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
85699 A
1 A
85700 TAAACGTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:85664 original size:10 final size:10
Alignment explanation
Indices: 85631--85705 Score: 54
Period size: 10 Copynumber: 7.7 Consensus size: 10
85621 CATTTAATAA
*
85631 ATAAACGAAT
1 ATAAACGAAC
85641 ATAAACGAAC
1 ATAAACGAAC
85651 ----ACGAAC
1 ATAAACGAAC
85657 ATAAACGAAC
1 ATAAACGAAC
*
85667 ACGAACAC-AA-
1 A-TAA-ACGAAC
85677 ATGAACACGAAC
1 AT-AA-ACGAAC
85689 ATAAACGAAC
1 ATAAACGAAC
85699 ATAAACG
1 ATAAACG
85706 TTGGAGATCC
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
6 6 0.11
10 35 0.66
11 8 0.15
12 4 0.08
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:86821 original size:14 final size:14
Alignment explanation
Indices: 86802--86830 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
86792 GAACATAAGA
86802 GAACATAACCGAAC
1 GAACATAACCGAAC
86816 GAACATAACCGAAC
1 GAACATAACCGAAC
86830 G
1 G
86831 TTCACGAACG
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:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (14 bp):
GAACATAACCGAAC
Done.