Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001647.1 Hibiscus syriacus cultivar Beakdansim tig00003296_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: 85464
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3467 original size:28 final size:29
Alignment explanation
Indices: 3433--3491 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
3423 TTTTCTTAAT
*
3433 CTTATTTTATGCTA-GTATTAACTAAGTC
1 CTTATTTTATGCTAGGTATTAACTAACTC
3461 CTTATTTTATGCTAGGTATTAACTAACTC
1 CTTATTTTATGCTAGGTATTAACTAACTC
3490 CT
1 CT
3492 GTCTTTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (29 bp):
CTTATTTTATGCTAGGTATTAACTAACTC
Found at i:20417 original size:31 final size:31
Alignment explanation
Indices: 20382--20445 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
20372 TGATGAGCAC
*
20382 ATCTTAATTAAATAAAAATGATAGTGACCAT
1 ATCTTAATTAAATAAAAATGAAAGTGACCAT
* *
20413 ATCTTAATTAAATAAAATTGAAAGTGATCAT
1 ATCTTAATTAAATAAAAATGAAAGTGACCAT
20444 AT
1 AT
20446 ATTATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.34
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAATGAAAGTGACCAT
Found at i:23996 original size:25 final size:24
Alignment explanation
Indices: 23961--24022 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
23951 TTATTACAAC
* *
23961 AATAATAATTTATCATAAAACTTAA
1 AATAATTATTTATCA-AAAAATTAA
* *
23986 TATAATTATTT-TTAAAAAATTAA
1 AATAATTATTTATCAAAAAATTAA
24009 AATAATTTATTTAT
1 AATAA-TTATTTAT
24023 TATTAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 12 0.40
24 8 0.27
25 10 0.33
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (24 bp):
AATAATTATTTATCAAAAAATTAA
Found at i:24030 original size:25 final size:24
Alignment explanation
Indices: 23961--24035 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
23951 TTATTACAAC
* *
23961 AATAATAATTTATCATAAAACTTAA
1 AATAATTATTTATTATAAAA-TTAA
* *
23986 TATAATTATTT-TTAAAAAATTAA
1 AATAATTATTTATTATAAAATTAA
24009 AATAATTTATTTATTATTAAATATTAA
1 AATAA-TTATTTATTA-TAAA-ATTAA
24036 TTTTATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
23 8 0.20
24 12 0.30
25 12 0.30
26 3 0.08
27 5 0.12
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (24 bp):
AATAATTATTTATTATAAAATTAA
Found at i:24137 original size:43 final size:43
Alignment explanation
Indices: 24090--24221 Score: 127
Period size: 43 Copynumber: 3.1 Consensus size: 43
24080 TGAAACAAAA
24090 ATATTATAAATTATATTAATTTTTTTATTAAAGTAATAGTGTT
1 ATATTATAAATTATATTAATTTTTTTATTAAAGTAATAGTGTT
* * *
24133 ATATT-TAAA-AATATTAATTAGTATATTTTATTGAAA-CAA-A----A
1 ATATTATAAATTATATTAA-T--T-T-TTTTATT-AAAGTAATAGTGTT
24174 ATATTATAAATTATATTAATTTTTTTATTAAAGTAATAGTGTT
1 ATATTATAAATTATATTAATTTTTTTATTAAAGTAATAGTGTT
24217 ATATT
1 ATATT
24222 TTTAAAAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 28
0.67 0.06 0.27
Matches are distributed among these distances:
37 3 0.04
38 9 0.13
39 2 0.03
40 1 0.01
41 12 0.17
42 10 0.14
43 17 0.25
44 1 0.01
45 2 0.03
46 9 0.13
47 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (43 bp):
ATATTATAAATTATATTAATTTTTTTATTAAAGTAATAGTGTT
Found at i:24233 original size:43 final size:42
Alignment explanation
Indices: 24102--24237 Score: 115
Period size: 43 Copynumber: 3.2 Consensus size: 42
24092 ATTATAAATT
24102 ATATTAATTTTTTTATTAAAGTAATAGTGTTATA-TTTAAAA
1 ATATTAATTTTTTTATTAAAGTAATAGTGTTATATTTTAAAA
* * * *
24143 ATATTAATTAGTATATTTTATTGAAA-CAA-A----AATATTATAAATT
1 ATATTAA-T--T-T-TTTTATT-AAAGTAATAGTGTTATATTTTAAA-A
24186 ATATTAATTTTTTTATTAAAGTAATAGTGTTATATTTTTAAAA
1 ATATTAATTTTTTTATTAAAGTAATAGTGTTATA-TTTTAAAA
24229 ATATTAATT
1 ATATTAATT
24238 AGTATATTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 28
0.67 0.07 0.26
Matches are distributed among these distances:
37 3 0.04
38 9 0.12
39 2 0.03
40 1 0.01
41 10 0.14
42 7 0.10
43 19 0.26
44 7 0.10
45 2 0.03
46 9 0.12
47 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (42 bp):
ATATTAATTTTTTTATTAAAGTAATAGTGTTATATTTTAAAA
Found at i:24254 original size:86 final size:86
Alignment explanation
Indices: 24054--24335 Score: 448
Period size: 84 Copynumber: 3.3 Consensus size: 86
24044 TTTTATTAAT
*
24054 AAAATATTAATATTGGTATATTTTATTGAAACAAAAATATTATAAATTATATTAATTTTTTTATT
1 AAAATATT-A-ATTAGTATATTTTATTGAAACAAAAATATTATAAATTATATTAATTTTTTTATT
24119 AAAGTAATAGTGTTATA--TTTA
64 AAAGTAATAGTGTTATATTTTTA
24140 AAAATATTAATTAGTATATTTTATTGAAACAAAAATATTATAAATTATATTAATTTTTTTATTAA
1 AAAATATTAATTAGTATATTTTATTGAAACAAAAATATTATAAATTATATTAATTTTTTTATTAA
24205 AGTAATAGTGTTATATTTTTA
66 AGTAATAGTGTTATATTTTTA
* *
24226 AAAATATTAATTAGTATATTTTATTGAAAC-AAAA-ATCATAAATTATATTAA-TTATTTATTAA
1 AAAATATTAATTAGTATATTTTATTGAAACAAAAATATTATAAATTATATTAATTTTTTTATTAA
24288 AGTAATAGTGTTATATTATATTTTA
66 AGTAATAGTG-T-TA-TAT-TTTTA
24313 AAAATATTAATTAGTATATTTTA
1 AAAATATTAATTAGTATATTTTA
24336 AATATCTTTA
Statistics
Matches: 187, Mismatches: 3, Indels: 11
0.93 0.01 0.05
Matches are distributed among these distances:
83 20 0.11
84 87 0.47
85 7 0.04
86 45 0.24
87 28 0.15
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (86 bp):
AAAATATTAATTAGTATATTTTATTGAAACAAAAATATTATAAATTATATTAATTTTTTTATTAA
AGTAATAGTGTTATATTTTTA
Found at i:24354 original size:23 final size:23
Alignment explanation
Indices: 24305--24360 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
24295 GTGTTATATT
**
24305 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
24328 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
24351 ATATTATTAA
1 ATATT-TTAA
24361 TTAATATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:24359 original size:11 final size:12
Alignment explanation
Indices: 24343--24401 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
24333 TTAAATATCT
24343 TTATTAA-AATA
1 TTATTAATAATA
24354 TTATTAATTAATA
1 TTATTAA-TAATA
*
24367 -TATAAATAATA
1 TTATTAATAATA
*
24378 TTATTCAT--TA
1 TTATTAATAATA
*
24388 TTAATAATAATA
1 TTATTAATAATA
24400 TT
1 TT
24402 GTTTCTATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
10 8 0.21
11 12 0.32
12 14 0.37
13 4 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
TTATTAATAATA
Found at i:24377 original size:24 final size:22
Alignment explanation
Indices: 24350--24401 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
24340 TCTTTATTAA
24350 AATATTATTAATTAATATATAAAT
1 AATATTATTAATTAATA-AT-AAT
* *
24374 AATATTATTCATTATTAATAAT
1 AATATTATTAATTAATAATAAT
24396 AATATT
1 AATATT
24402 GTTTCTATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 9 0.35
23 2 0.08
24 15 0.58
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTATTAATTAATAATAAT
Found at i:24540 original size:31 final size:30
Alignment explanation
Indices: 24482--24560 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 30
24472 ATATTATTAT
* *
24482 AATATAATTGATTATTTTATTATAATATTAAA
1 AATATAATT--TTATATTATTAAAATATTAAA
*
24514 AATATAATTTTATATTATTAGAAATATTAAT
1 AATATAATTTTATATTATTA-AAATATTAAA
24545 AATAT-ATTTTAATATT
1 AATATAATTTT-ATATT
24561 TTCATAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 15 0.36
31 18 0.43
32 9 0.21
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
AATATAATTTTATATTATTAAAATATTAAA
Found at i:26243 original size:24 final size:21
Alignment explanation
Indices: 26216--26258 Score: 59
Period size: 24 Copynumber: 1.9 Consensus size: 21
26206 TTTTCGAGTA
26216 TAATGATATAATATATTATATTTT
1 TAATGATA-AA-AT-TTATATTTT
26240 TAATGATAAAATTTATATT
1 TAATGATAAAATTTATATT
26259 CGAACATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 2 0.11
24 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TAATGATAAAATTTATATTTT
Found at i:31988 original size:33 final size:33
Alignment explanation
Indices: 31948--32073 Score: 146
Period size: 33 Copynumber: 3.8 Consensus size: 33
31938 CTCTTGGATT
* *
31948 TACTGACTCGAATTATGGTGCTTCCCTTGGACC
1 TACTGACTCGAATGATGATGCTTCCCTTGGACC
* *
31981 TATTGACTCGAATGATGGTGCTTCTCC-TGGACC
1 TACTGACTCGAATGATGATGCTTC-CCTTGGACC
* * **
32014 TACTGACTCGCATGATGATGTTTTTCTTGGACC
1 TACTGACTCGAATGATGATGCTTCCCTTGGACC
* *
32047 TACTGCCTCGAATGATGATGTTTCCCT
1 TACTGACTCGAATGATGATGCTTCCCT
32074 ACACATTGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
32 1 0.01
33 76 0.96
34 2 0.03
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (33 bp):
TACTGACTCGAATGATGATGCTTCCCTTGGACC
Found at i:43252 original size:21 final size:21
Alignment explanation
Indices: 43215--43259 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
43205 GATTTCTGGG
*
43215 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
43236 CAAGGGGAA-CTGATACCCCTT
1 CAAGGGGAATC-GATACCCATT
43257 CAA
1 CAA
43260 ACGAACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:44650 original size:14 final size:14
Alignment explanation
Indices: 44631--44658 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44621 GAAAAGAAGC
44631 TATGTGATACGTGA
1 TATGTGATACGTGA
44645 TATGTGATACGTGA
1 TATGTGATACGTGA
44659 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:45029 original size:149 final size:149
Alignment explanation
Indices: 44759--45073 Score: 524
Period size: 149 Copynumber: 2.1 Consensus size: 149
44749 GAGTCGAGGG
* * *
44759 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCGTGAAAGACACAT
* *
44824 ACTTGATCTCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
44889 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
44908 TCTACGCGGTCCTTTGGGATATATATATATTCTGTGGAACATGTGTGAAGTCGTGAGAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCGTGAAAGACACAT
**
44973 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
45038 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
45057 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
45074 TGCAATTATA
Statistics
Matches: 154, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
148 1 0.01
149 153 0.99
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCGTGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:45074 original size:23 final size:23
Alignment explanation
Indices: 45041--45085 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
45031 ATCATTATAT
*
45041 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
45064 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
45086 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:48271 original size:21 final size:21
Alignment explanation
Indices: 48245--48289 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
48235 GATTTCTGGG
* *
48245 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
48266 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
48287 CAA
1 CAA
48290 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:49688 original size:14 final size:14
Alignment explanation
Indices: 49669--49696 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49659 GAAAAGAAGC
49669 TATGTGATACGTGA
1 TATGTGATACGTGA
49683 TATGTGATACGTGA
1 TATGTGATACGTGA
49697 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:49963 original size:23 final size:23
Alignment explanation
Indices: 49930--49974 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
49920 ATCATTATAT
*
49930 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
49953 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
49975 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:58828 original size:30 final size:30
Alignment explanation
Indices: 58788--58844 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
58778 CTCTTCCCAA
* *
58788 CCAACGGCTAGAGTAACCATTTAATTTCAT
1 CCAACAGCTAGAGTAAACATTTAATTTCAT
58818 CCAACAGCTAGAGTAAACATTTAATTT
1 CCAACAGCTAGAGTAAACATTTAATTT
58845 ACTTTCAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (30 bp):
CCAACAGCTAGAGTAAACATTTAATTTCAT
Found at i:61977 original size:37 final size:37
Alignment explanation
Indices: 61909--61979 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
61899 AATTCAAATA
* * * *
61909 AAATTAATATCGATTATTATAATCTATATGTATATAC
1 AAATTAATATCAATAATAATAATATATATGTATATAC
61946 AAATTAATATCAATAATAATAATA-ATAATGTATA
1 AAATTAATATCAATAATAATAATATAT-ATGTATA
61980 AGCATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 2 0.07
37 27 0.93
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (37 bp):
AAATTAATATCAATAATAATAATATATATGTATATAC
Found at i:67628 original size:3 final size:3
Alignment explanation
Indices: 67614--67664 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
67604 TTTTTCATTC
* * * *
67614 TAT TAT TTT TAT TAT TAT TAT TAT TAT TA- AAT AAA TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
67660 TAT TA
1 TAT TA
67665 AATTAAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 3 0.07
3 38 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:67657 original size:22 final size:23
Alignment explanation
Indices: 67629--67674 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
67619 TTTTTATTAT
67629 TATTATTATTATTAAA-TAAATA
1 TATTATTATTATTAAATTAAATA
67651 TATTATTATTATTAAATTAAATA
1 TATTATTATTATTAAATTAAATA
67674 T
1 T
67675 TAAAAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATTATTATTAAATTAAATA
Found at i:69043 original size:20 final size:19
Alignment explanation
Indices: 69018--69059 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
69008 CTATTTTATA
69018 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
69038 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
69057 AAT
1 AAT
69060 ATCGAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:69049 original size:119 final size:117
Alignment explanation
Indices: 68914--69150 Score: 280
Period size: 120 Copynumber: 2.0 Consensus size: 117
68904 ATTTTAATCC
* * * * **
68914 TGTTTTAATATTTATTTATTTTTCAATAT-TAA-GAAAGGGCAGTCTTAAAACAACTGGATTTTC
1 TGTTTTAATATTTATTTATTTTTCAATATCGAATAAAAGAGCAGTCTTAAAACAACTAGA-AGTC
* *
68977 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAA-TATATATAAAT
* * ** *
69032 TGTTTTAATTATTTATTTATTTTTTAATATCGAATAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATATCGAATAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* **
69097 CTTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
69150 T
1 T
69151 AATATTTTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 19 0.19
119 28 0.28
120 34 0.34
121 19 0.19
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (117 bp):
TGTTTTAATATTTATTTATTTTTCAATATCGAATAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
Found at i:69148 original size:29 final size:29
Alignment explanation
Indices: 69115--69171 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
69105 ATATTTCTAA
69115 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTT-TTTCATAAATATAT
* *
69144 ATAAATTAATATTTTTTTCATAATTATA
1 ATAAATAAATATTTTTTTCATAAATATA
69172 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTTTTCATAAATATAT
Found at i:72179 original size:15 final size:14
Alignment explanation
Indices: 72138--72178 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
72128 ATTTTAAATA
72138 ATTTACATTTTTGC
1 ATTTACATTTTTGC
72152 ATTTATGCA-TTTTGC
1 ATTTA--CATTTTTGC
72167 ATTTACATTTTT
1 ATTTACATTTTT
72179 TATTTGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (14 bp):
ATTTACATTTTTGC
Found at i:77233 original size:114 final size:114
Alignment explanation
Indices: 77033--77253 Score: 370
Period size: 114 Copynumber: 1.9 Consensus size: 114
77023 CCACGTTCTT
*
77033 ATAGTAGAAATAAGGAGGCCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 ATAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
** * *
77098 TGGTAGGAACCCTTAAACCAATCATTGGATTTGAAAGATGAATTTGCTC
66 TGGTAGGAACCCCAAAACCAATCATTGAATTTAAAAGATGAATTTGCTC
* *
77147 ATAGTAGAGATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 ATAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
*
77212 TGGTATGAACCCCAAAACCAATCATTGAATTTAAAAGATGAA
66 TGGTAGGAACCCCAAAACCAATCATTGAATTTAAAAGATGAA
77254 CATGATCATC
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
ATAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
TGGTAGGAACCCCAAAACCAATCATTGAATTTAAAAGATGAATTTGCTC
Found at i:79352 original size:54 final size:53
Alignment explanation
Indices: 79270--79427 Score: 205
Period size: 54 Copynumber: 3.0 Consensus size: 53
79260 TGATTGAGAA
*
79270 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGCCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATG-TTTACGAAC
* *
79324 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTT---TAC
1 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTACGAAC
* * * * *
79374 ATCTGAGCAGAAACCACATAAGATGATGCATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATG-TTTACGAAC
79428 CAGTTATTCT
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
50 40 0.44
51 3 0.03
53 3 0.03
54 44 0.49
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (53 bp):
ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTACGAAC
Found at i:79407 original size:50 final size:50
Alignment explanation
Indices: 79270--79423 Score: 191
Period size: 50 Copynumber: 3.0 Consensus size: 50
79260 TGATTGAGAA
* * *
79270 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGCCAAATGCTTTACGAAC
1 ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATG-TTT---TAC
* *
79324 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
1 ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTAC
* * * *
79374 ATCTGAGCAGAAACCACATAAGATGATGCATGTGTTGTCAAATGTTTTAC
1 ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTAC
79424 GAACCAGTTA
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
50 46 0.51
53 3 0.03
54 42 0.46
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (50 bp):
ATCTGAGCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:80604 original size:76 final size:76
Alignment explanation
Indices: 80505--80716 Score: 397
Period size: 76 Copynumber: 2.8 Consensus size: 76
80495 CTATTTCCCA
80505 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
80570 AGCCTTAGGGT
66 AGCCTTAGGGT
*
80581 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
80646 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
80657 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTT
80717 GTTATTTTGA
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 132 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:80906 original size:45 final size:45
Alignment explanation
Indices: 80842--81057 Score: 351
Period size: 45 Copynumber: 4.8 Consensus size: 45
80832 CTATTTCCCA
80842 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
* * *
80887 CATCTATAAGCCCTTCAGTGCAAGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
80932 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
* * *
80977 CATCTGTAAGCCCTTCAGTGCAAGATGTTTTCAAAGCCTTAGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
* * *
81022 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
81058 AGCCTTCAGG
Statistics
Matches: 157, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 157 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
Found at i:81126 original size:76 final size:76
Alignment explanation
Indices: 81000--81279 Score: 506
Period size: 76 Copynumber: 3.7 Consensus size: 76
80990 TTCAGTGCAA
81000 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
1 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
*
81065 AGGAGCTTTTT
66 GGGAGCTTTTT
81076 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
1 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
*
81141 GGGAGATTTTT
66 GGGAGCTTTTT
* *
81152 GATATTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTC
1 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
81217 GGGAGCTTTTT
66 GGGAGCTTTTT
* *
81228 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTT
1 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTT
81280 TTAAGACCTC
Statistics
Matches: 195, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 195 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTT
Found at i:81435 original size:3 final size:3
Alignment explanation
Indices: 81427--81499 Score: 87
Period size: 3 Copynumber: 24.7 Consensus size: 3
81417 TTTTTCATTC
* * *
81427 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- AAT AAA TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
81473 TAT TAT TCT ATAT TAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TA
81500 AATTAAATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
2 3 0.05
3 57 0.92
4 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:81473 original size:22 final size:22
Alignment explanation
Indices: 81445--81509 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
81435 TTATTATTAT
81445 TATTATTATTATTAAATAAATA
1 TATTATTATTATTAAATAAATA
* *
81467 TATTATTATTATT--CTATAT-
1 TATTATTATTATTAAATAAATA
81486 TATTATTATTATTAAATTAAATA
1 TATTATTATTATTAAA-TAAATA
81509 T
1 T
81510 TATAAAACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 13 0.37
20 4 0.11
22 17 0.49
23 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTATTATTATTAAATAAATA
Found at i:83095 original size:20 final size:19
Alignment explanation
Indices: 83070--83111 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
83060 CTATTTTATA
83070 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
83090 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
83109 AAT
1 AAT
83112 ATCGAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:83197 original size:27 final size:25
Alignment explanation
Indices: 83166--83218 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
83156 GATATTTCTA
*
83166 ATAATAAATATTTTATTTATAATATAT
1 ATAATAAATATTTT-TTCATAAT-TAT
*
83193 ATAATTAATATTTTTTCATAATTAT
1 ATAATAAATATTTTTTCATAATTAT
83218 A
1 A
83219 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 7 0.29
27 13 0.54
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
ATAATAAATATTTTTTCATAATTAT
Done.