Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005896.1 Hibiscus syriacus cultivar Beakdansim tig00013847_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: 65753
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5886 original size:9 final size:10
Alignment explanation
Indices: 5837--5937 Score: 59
Period size: 9 Copynumber: 10.2 Consensus size: 10
5827 TATTTTTATT
5837 TTAAT-ATAA
1 TTAATAATAA
5846 -TAATAATAA
1 TTAATAATAA
*
5855 -TAATAATAT
1 TTAATAATAA
*
5864 TTTATAATTAA
1 TTAATAA-TAA
5875 TTAAT-ATAA
1 TTAATAATAA
*
5884 TTAATAAAATA
1 TTAATAATA-A
** *
5895 TTAATCGTATT
1 TTAATAATA-A
5906 TTAATAAATAA
1 TTAAT-AATAA
*
5917 TTAGT-ATAA
1 TTAATAATAA
*
5926 TTTATAATAA
1 TTAATAATAA
5936 TT
1 TT
5938 TTATTTTAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 13
0.71 0.15 0.13
Matches are distributed among these distances:
8 4 0.06
9 27 0.39
10 14 0.20
11 23 0.33
12 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (10 bp):
TTAATAATAA
Found at i:5890 original size:20 final size:19
Alignment explanation
Indices: 5837--5937 Score: 71
Period size: 20 Copynumber: 5.1 Consensus size: 19
5827 TATTTTTATT
5837 TTAATATAA-TAATAATAA
1 TTAATATAATTAATAATAA
* *
5855 -TAATAATATTTTATAATTAA
1 TTAAT-ATAATTAATAA-TAA
*
5875 TTAATATAATTAATAAAATA
1 TTAATATAATTAATAATA-A
* *
5895 TTAATCGTATTTTAATAAATAA
1 TTAAT-ATA-ATTAAT-AATAA
* *
5917 TTAGTATAATTTATAATAA
1 TTAATATAATTAATAATAA
5936 TT
1 TT
5938 TTATTTTAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
17 4 0.06
18 3 0.05
19 13 0.21
20 22 0.35
21 8 0.13
22 10 0.16
23 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (19 bp):
TTAATATAATTAATAATAA
Found at i:5918 original size:42 final size:39
Alignment explanation
Indices: 5837--5936 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 39
5827 TATTTTTATT
*
5837 TTAATATAA-TAATAATAATAATAATATTTTATAATTAA
1 TTAATATAATTAATAATAATAATAATATTTTATAAATAA
*
5875 TTAATATAATTAATAA-AATATTAATCGTATTTTAATAAATAA
1 TTAATATAATTAATAATAATAATAA---TATTTT-ATAAATAA
* *
5917 TTAGTATAATTTATAATAAT
1 TTAATATAATTAATAATAAT
5937 TTTATTTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
38 16 0.31
39 6 0.12
41 6 0.12
42 21 0.40
43 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (39 bp):
TTAATATAATTAATAATAATAATAATATTTTATAAATAA
Found at i:5962 original size:27 final size:27
Alignment explanation
Indices: 5931--5996 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
5921 TATAATTTAT
5931 AATAA-TTTTATTTTAATAAAATAATA-A
1 AATAATTTTTA-TTT-ATAAAATAATAGA
*
5958 AATAATATTTTATTTATAAAATTATAGA
1 AATAAT-TTTTATTTATAAAATAATAGA
*
5986 TATAATTTTTA
1 AATAATTTTTA
5997 ATAATAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 20 0.59
28 9 0.26
29 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
AATAATTTTTATTTATAAAATAATAGA
Found at i:6003 original size:27 final size:27
Alignment explanation
Indices: 5944--6020 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
5934 AATTTTATTT
*
5944 TAATAAAATAATAAAATAATATTTTAT
1 TAATAAAATAATAAAATAATATTTTAA
* * *
5971 TTATAAAATTATAGATATAAT-TTTTAA
1 TAATAAAATAATA-AAATAATATTTTAA
* *
5998 TAATAATAT-TTCAAAATAATATT
1 TAATAAAATAAT-AAAATAATATT
6021 ATTATTTTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 7 0.18
27 26 0.67
28 6 0.15
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
TAATAAAATAATAAAATAATATTTTAA
Found at i:9082 original size:24 final size:24
Alignment explanation
Indices: 9055--9100 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
9045 ATTATAATAA
9055 TTTTAAAATTTTAATAAATTTATT
1 TTTTAAAATTTTAATAAATTTATT
* *
9079 TTTTAACATTTTGATAAATTTA
1 TTTTAAAATTTTAATAAATTTA
9101 ATGATTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTAAAATTTTAATAAATTTATT
Found at i:12172 original size:16 final size:15
Alignment explanation
Indices: 12151--12180 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12141 GTGTGAATAA
12151 AAGATTACTAGGGAAC
1 AAGATTACT-GGGAAC
12167 AAGATTACTGGGAA
1 AAGATTACTGGGAA
12181 TGTTGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.10, G:0.27, T:0.20
Consensus pattern (15 bp):
AAGATTACTGGGAAC
Found at i:12306 original size:18 final size:18
Alignment explanation
Indices: 12283--12330 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
12273 AAATTGTCCT
* *
12283 TATTATATATTTGTATAA
1 TATTATATATTTATAAAA
*
12301 TATTATA-AATTATAAAA
1 TATTATATATTTATAAAA
12318 TATTTATATATTT
1 TA-TTATATATTT
12331 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTATATATTTATAAAA
Found at i:12346 original size:36 final size:37
Alignment explanation
Indices: 12306--12390 Score: 106
Period size: 36 Copynumber: 2.3 Consensus size: 37
12296 TATAATATTA
12306 TAAATTATAAAATATTTATAT-ATTTTCTTTA-AAAAT
1 TAAATTATAAAATATTTATATAATTTT-TTTATAAAAT
12342 TAAATTCAT--AATATTTATATAATTTTTTTATAAAAT
1 TAAATT-ATAAAATATTTATATAATTTTTTTATAAAAT
*
12378 TAAAAATATAAAA
1 T-AAATTATAAAA
12391 AATGCTTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
35 15 0.36
36 19 0.45
37 6 0.14
38 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (37 bp):
TAAATTATAAAATATTTATATAATTTTTTTATAAAAT
Found at i:12386 original size:31 final size:31
Alignment explanation
Indices: 12303--12386 Score: 84
Period size: 35 Copynumber: 2.6 Consensus size: 31
12293 TTGTATAATA
12303 TTAT-AAATTATAAAATATTTATATATTTTCT
1 TTATAAAATTA-AAAATATTTATATATTTTCT
12334 TTA-AAAATTAAATTCATAATATTTATATAATTTT-T
1 TTATAAAATT-AA---A-AATATTTATAT-ATTTTCT
12369 TTATAAAATTAAAAATAT
1 TTATAAAATTAAAAATAT
12387 AAAAAATGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
31 14 0.31
32 2 0.04
34 1 0.02
35 17 0.38
36 11 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (31 bp):
TTATAAAATTAAAAATATTTATATATTTTCT
Found at i:14038 original size:14 final size:14
Alignment explanation
Indices: 14019--14047 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
14009 TCACTGTTAA
14019 TAACGATTAATCGT
1 TAACGATTAATCGT
14033 TAACGATTAATCGT
1 TAACGATTAATCGT
14047 T
1 T
14048 TCTTAATGAT
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:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (14 bp):
TAACGATTAATCGT
Found at i:14069 original size:89 final size:89
Alignment explanation
Indices: 13918--14092 Score: 332
Period size: 89 Copynumber: 2.0 Consensus size: 89
13908 TAACCAATAT
* *
13918 CTTCACTGTTAATAATGATTAATCGTTAACGATTAATTGTTTCTTAATGATTAGGTAATAATTAG
1 CTTCACTGTTAATAACGATTAATCGTTAACGATTAATCGTTTCTTAATGATTAGGTAATAATTAG
13983 TAAAATTTAGTAATTGTTAAATTG
66 TAAAATTTAGTAATTGTTAAATTG
14007 CTTCACTGTTAATAACGATTAATCGTTAACGATTAATCGTTTCTTAATGATTAGGTAATAATTAG
1 CTTCACTGTTAATAACGATTAATCGTTAACGATTAATCGTTTCTTAATGATTAGGTAATAATTAG
14072 TAAAATTTAGTAATTGTTAAA
66 TAAAATTTAGTAATTGTTAAA
14093 CTGATTAACC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (89 bp):
CTTCACTGTTAATAACGATTAATCGTTAACGATTAATCGTTTCTTAATGATTAGGTAATAATTAG
TAAAATTTAGTAATTGTTAAATTG
Found at i:17179 original size:13 final size:14
Alignment explanation
Indices: 17145--17191 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
17135 AGGGTTAGGA
17145 TTTAGGGTTTATA-
1 TTTAGGGTTTATAG
17158 TATAATAGGG-TTATAG
1 T-T--TAGGGTTTATAG
17174 TTTAGGGTTTATAG
1 TTTAGGGTTTATAG
17188 TTTA
1 TTTA
17192 TAATTTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 6 0.21
14 11 0.38
15 6 0.21
16 6 0.21
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTATAG
Found at i:22955 original size:2 final size:2
Alignment explanation
Indices: 22950--23014 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
22940 ATCAACACAC
*
22950 AT AT AT AC 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
22992 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
23015 GTTTGAGGCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24164 original size:18 final size:19
Alignment explanation
Indices: 24129--24165 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
24119 CACAAAATGT
24129 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
24149 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
24166 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:26522 original size:23 final size:23
Alignment explanation
Indices: 26496--26547 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
26486 ATGTATCAGG
* * *
26496 ATGAATGGATGTAAGTATTCATC
1 ATGAATGAATATAACTATTCATC
*
26519 ATGAATGAATATAACTATTCATG
1 ATGAATGAATATAACTATTCATC
26542 ATGAAT
1 ATGAAT
26548 AGACATAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (23 bp):
ATGAATGAATATAACTATTCATC
Found at i:26555 original size:23 final size:23
Alignment explanation
Indices: 26511--26568 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
26501 TGGATGTAAG
* *
26511 TATTCATCATGAATGAATATAAC
1 TATTCATGATGAATGAACATAAC
26534 TATTCATGATGAAT-AGACATAAC
1 TATTCATGATGAATGA-ACATAAC
26557 -ATGT-ATGATGAA
1 TAT-TCATGATGAA
26569 AAGGTGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (23 bp):
TATTCATGATGAATGAACATAAC
Found at i:53786 original size:16 final size:16
Alignment explanation
Indices: 53765--53816 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
53755 TTGCAAAACG
53765 CAAAATATGATTTTAA
1 CAAAATATGATTTTAA
* ** *
53781 CAAAATATTATCATAT
1 CAAAATATGATTTTAA
* *
53797 GAAAACATGATTTTAA
1 CAAAATATGATTTTAA
53813 CAAA
1 CAAA
53817 CTAAACCGCA
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (16 bp):
CAAAATATGATTTTAA
Found at i:57401 original size:81 final size:81
Alignment explanation
Indices: 57325--57965 Score: 1032
Period size: 81 Copynumber: 7.9 Consensus size: 81
57315 TCACAATGAT
* *
57325 ATTAAAAGCATGAGGCGACA-TAGGAGGAAAATTGTGATGAAGAGGATTTGGACCTTCCAGGGTT
1 ATTAAAAGCATGAGGCGA-AGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTT
*
57389 TCTCTCTTCACAATAGC
65 TCTCTATTCACAATAGC
* *
57406 ATTAAAAGCATGAGGTGACGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
1 ATTAAAAGCATGAGGCGAAGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
*
57471 CTCTCTTCACAATAGC
66 CTCTATTCACAATAGC
*
57487 ATTAAAAGCATGAGGCGAAGTTGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
1 ATTAAAAGCATGAGGCGAAGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
*
57552 CTCTATTCACAATAGA
66 CTCTATTCACAATAGC
* * * * *
57568 ATTAAAAGCATGAGGCGAAGTTGGAGGAAAATTGTGATGAAGGGGATTTGGCCCCTCTGGCGTTT
1 ATTAAAAGCATGAGGCGAAGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
*
57633 CTCTCTTCACAATAGC
66 CTCTATTCACAATAGC
*
57649 ATTAAAAGCATGAGGCGACGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
1 ATTAAAAGCATGAGGCGAAGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
57714 CTCTATTCACAATAGC
66 CTCTATTCACAATAGC
*
57730 ATTAAAAGCATGAGGCGAAGTTGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
1 ATTAAAAGCATGAGGCGAAGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
57795 CTCTATTCACAATAGC
66 CTCTATTCACAATAGC
* * * * *
57811 ATTAAAAGCATGAGGCGAAGTTGGAGGAAAATTGTGATGAAGGGGATTTGGCCCCTCTGGCGTTT
1 ATTAAAAGCATGAGGCGAAGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
*
57876 CTCTCTTCACAATAGC
66 CTCTATTCACAATAGC
* * * *
57892 ATCAAAAGCATGAGGCGACGTAGGAGGAAAATTGTTATGAAGGGGATTTGGCCCTTCCGGGGTTT
1 ATTAAAAGCATGAGGCGAAGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
57957 CTCTATTCA
66 CTCTATTCA
57966 ACGTAGGAGG
Statistics
Matches: 522, Mismatches: 37, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
81 522 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (81 bp):
ATTAAAAGCATGAGGCGAAGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTT
CTCTATTCACAATAGC
Found at i:57715 original size:243 final size:243
Alignment explanation
Indices: 57287--57965 Score: 1159
Period size: 243 Copynumber: 2.8 Consensus size: 243
57277 GTGACGATGA
* * * * *
57287 GGATTTGGTCTTTCCGGTGTATT-TCTTTTCACAAT-GATATTAAAAGCATGAGGCGACA-TAGG
1 GGATTTGGACCTTCCGGGGT-TTCTCTATTCACAATAGA-ATTAAAAGCATGAGGCGA-AGTTGG
* * * *
57349 AGGAAAATTGTGATGAAGAGGATTTGGACCTTCCAGG-GTTTCTCTCTTCACAATAGCATTAAAA
63 AGGAAAATTGTGATGAAGGGGATTTGGCCCCT-CTGGCGTTTCTCTCTTCACAATAGCATTAAAA
* *
57413 GCATGAGGTGACGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTTCTCTCTT
127 GCATGAGGCGACGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTTCTCTATT
57478 CACAATAGCATTAAAAGCATGAGGCGAAGTTGGAGGAAAATTGTGATGAAGG
192 CACAATAGCATTAAAAGCATGAGGCGAAGTTGGAGGAAAATTGTGATGAAGG
57530 GGATTTGGACCTTCCGGGGTTTCTCTATTCACAATAGAATTAAAAGCATGAGGCGAAGTTGGAGG
1 GGATTTGGACCTTCCGGGGTTTCTCTATTCACAATAGAATTAAAAGCATGAGGCGAAGTTGGAGG
57595 AAAATTGTGATGAAGGGGATTTGGCCCCTCTGGCGTTTCTCTCTTCACAATAGCATTAAAAGCAT
66 AAAATTGTGATGAAGGGGATTTGGCCCCTCTGGCGTTTCTCTCTTCACAATAGCATTAAAAGCAT
57660 GAGGCGACGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTTCTCTATTCACA
131 GAGGCGACGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTTCTCTATTCACA
57725 ATAGCATTAAAAGCATGAGGCGAAGTTGGAGGAAAATTGTGATGAAGG
196 ATAGCATTAAAAGCATGAGGCGAAGTTGGAGGAAAATTGTGATGAAGG
*
57773 GGATTTGGACCTTCCGGGGTTTCTCTATTCACAATAGCATTAAAAGCATGAGGCGAAGTTGGAGG
1 GGATTTGGACCTTCCGGGGTTTCTCTATTCACAATAGAATTAAAAGCATGAGGCGAAGTTGGAGG
*
57838 AAAATTGTGATGAAGGGGATTTGGCCCCTCTGGCGTTTCTCTCTTCACAATAGCATCAAAAGCAT
66 AAAATTGTGATGAAGGGGATTTGGCCCCTCTGGCGTTTCTCTCTTCACAATAGCATTAAAAGCAT
* *
57903 GAGGCGACGTAGGAGGAAAATTGTTATGAAGGGGATTTGGCCCTTCCGGGGTTTCTCTATTCA
131 GAGGCGACGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTTCTCTATTCA
57966 ACGTAGGAGG
Statistics
Matches: 417, Mismatches: 15, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
242 6 0.01
243 409 0.98
244 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (243 bp):
GGATTTGGACCTTCCGGGGTTTCTCTATTCACAATAGAATTAAAAGCATGAGGCGAAGTTGGAGG
AAAATTGTGATGAAGGGGATTTGGCCCCTCTGGCGTTTCTCTCTTCACAATAGCATTAAAAGCAT
GAGGCGACGTAGGAGGAAAATTGTGATGAAGGGGATTTGGACCTTCCGGGGTTTCTCTATTCACA
ATAGCATTAAAAGCATGAGGCGAAGTTGGAGGAAAATTGTGATGAAGG
Found at i:61906 original size:78 final size:78
Alignment explanation
Indices: 61428--62847 Score: 947
Period size: 78 Copynumber: 18.3 Consensus size: 78
61418 TTAGTATTTA
* * * ** * * * *
61428 TCTCTTCAC-ATTGAACTCATTAAAGAC-AGAAGGACTGACAGGAGTATTATAAAGAGGATCTGG
1 TCTCTTCACGA-TGAACTCATTAGAGACAAG-AGGGCTGAGAGGTTTATTGTGAATAGGATCTGA
*
61491 TCCTCC-CGGTGTTTA
64 TCCTCCTC-GTGTTTG
** * * * * * * *
61506 TCTCTTCACGGCGAACTCATTAGAGATAGGAGGGTTGAGAGGCTTATTATGAAGAGGATCTGGTC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
61571 CTCC-CGATGTTTGG
66 CTCCTCG-TGTTT-G
* * *
61585 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGTTTAGAGGTTTATTATGAATAGGATCTGATC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
* * *
61650 CTCATGGTATTTG
66 CTCCTCGTGTTTG
* * * * * * *
61663 TCTCTTCACGATGAACTCATTAGAGGCAAGAGGGCTAAAAGGTTTATTGTTATTAAGATCGGATC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
** *
61728 CTTTTGGTGTTTG
66 CTCCTCGTGTTTG
* * * * * * * * *
61741 TCTCTTCACAACGAACTCATTAGAGGCAAGAAGACTGTGATGTTTATTGTGAATAGGATCCGGTC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
61806 CTCC-CGATGTTTG
66 CTCCTCG-TGTTTG
* * * *
61819 TTTCTTCACGATGAACTCATTAGAGACAAGAGGACTGATAGGTTTATTGTAAATAGGATCTGATC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
*
61884 CTCCTCGTGTTTA
66 CTCCTCGTGTTTG
** * * *
61897 TCTCTTCACGGCGAACTCATTAAAGGCAAGAGGG-TGGAGAGGTTTACT-TGAATAGGATCTGAT
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCT-GAGAGGTTTATTGTGAATAGGATCTGAT
*
61960 CCT-CACGATGTTTG
65 CCTCCTCG-TGTTTG
* * * * * * * * * * *
61974 TCTTTTCACGACGAACTCATTAAAGAAAAAAGTGTTGAAAGTTTTACTATGAATAGGATCTTG-T
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATC-TGAT
* *
62038 CCTCCTGGCGTTTG
65 CCTCCTCGTGTTTG
* * * *
62052 TTTCTTCACGAAGAACTCATTATAGACATGAGGGCTGAGAGGTTTATTGTGAATAGGATCT-AGT
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGA-T
*
62116 CCT-CTCGGTGTTTT
65 CCTCCTC-GTGTTTG
* * * * * * * *
62130 TCTTTTCACGACGAACTCATTAGAG-CAAAAGGGCTTAGAGGTTTATTGTAAAGAGGATCTAACC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
* *
62194 CTCCTAGTGTTAG
66 CTCCTCGTGTTTG
* *
62207 TCTCTTCACGATGAACTCATTAGAGACATGAGGGCT-AGAAGGTTTATTGTGAAGAGGAT-TGAT
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAG-AGGTTTATTGTGAATAGGATCTGAT
*
62270 CCTAC-CGATGTTAT-
65 CCTCCTCG-TGTT-TG
* * * * * * **
62284 TCTATTCACGAAGAACTCATTAGCGGCAAGAGGGCTGAGAGGTTTATTGTGAAGAGAATAAGATC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
* * * *
62349 CTTCTGGAGTTAG
66 CTCCTCGTGTTTG
* * * * * **
62362 TCTCTTCACAATGAACTCATTAGAGGCATGAGGGCTAAGAGGTTTATTGTGAATAAGATCCAATC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
*
62427 CT-CTCGATGTTTA
66 CTCCTCG-TGTTTG
* ** * * * * * * *
62440 TCTATTCACGACAAACTCATTAGAGGCAAGAGGGCTAAAAAG----TTGTGAATAAGATATGGTC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
*
62501 CTCCTGGTGTTTG
66 CTCCTCGTGTTTG
* * * * * * ** * *
62514 TCTCTTCACGA-AAATCTCATTA-AAAGTAAGATGACTAAGAAATTTATTATGAATAGGATTTGA
1 TCTCTTCACGATGAA-CTCATTAGAGA-CAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGA
62577 TCCT-CTCGATGTTTG
64 TCCTCCTCG-TGTTTG
* * * * * * * * * *
62592 TCTCTTCATGATGAATTCATTAGAGACATGAGGGTTAAAAGGCTTATTGTGAAGAGAATCTGGTC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
* * *
62657 CTCC-CAATATTTT
66 CTCCTC-GTGTTTG
* * *** * ** * * *
62670 TCTCTTTACGATGAACTCATTAGAGACAGGATAACTGAAATATTTATTGTGCATGGGATCTGGTC
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
*
62735 CACC-CGATGTTTG
66 CTCCTCG-TGTTTG
* * * * * * * *
62748 TCTCTTCATGACGAA--CATTAAAGACAAGAGGACTAACAGATTTATTGTGAATATGATCT-AGT
1 TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGA-T
* * *
62810 CCTCAC-GGTATTTA
65 CCTC-CTCGTGTTTG
* *
62824 TCTCTTTACGATTAACTCATTAGA
1 TCTCTTCACGATGAACTCATTAGA
62848 AGGAGGAGGA
Statistics
Matches: 1057, Mismatches: 241, Indels: 88
0.76 0.17 0.06
Matches are distributed among these distances:
73 4 0.00
74 50 0.05
75 3 0.00
76 57 0.05
77 197 0.19
78 668 0.63
79 77 0.07
80 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (78 bp):
TCTCTTCACGATGAACTCATTAGAGACAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATC
CTCCTCGTGTTTG
Found at i:62097 original size:233 final size:231
Alignment explanation
Indices: 61482--62847 Score: 922
Period size: 233 Copynumber: 5.9 Consensus size: 231
61472 TATTATAAAG
* * * * * * * * *
61482 AGGATCTGGTCCTCCCGGTGTTTATCTCTTCACGGCGAACTCATTAGAGATAGGAGGGTTGAGAG
1 AGGATCTGATCCT-CCGATGTTTGTCTCTTCACGACGAACTCATTAAAGAAAAGAGTGTTGA-AA
* * *
61547 GCTTATTATGAAGAGGATCTGGTCCTCCCGATGTTTGGTCTCTTCACGATGAACTCATTAGAGAC
64 GTTTATTATGAATAGGATCTGGTCCTCCCGATGTTT-GTTTCTTCACGATGAACTCATTAGAGAC
* * * * * * * *
61612 AAGAGGGTTTAGAGGTTTATTATGAATAGGATCTGATCCTCATGGTATTTGTCTCTTCACGATGA
128 AAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATCCTCCTCGTGTTTATCTCTTCACGACGA
* *
61677 ACTCATTAGAGGCAAGAGGGCTAAAAGGTTTATTGTTATT
193 ACTCATTAGAGGCAAGAGGGCTAAGAGGTTTATTG-TAAT
* * ** * * * *
61717 AAGATCGGATCCTTTTGGTGTTTGTCTCTTCACAACGAACTCATTAGAGGCAAGAAGACTG-TG-
1 AGGATCTGATCC-TCCGATGTTTGTCTCTTCACGACGAACTCATTA-AAG-AA-AAGAGTGTTGA
* * *
61780 ATGTTTATTGTGAATAGGATCCGGTCCTCCCGATGTTTGTTTCTTCACGATGAACTCATTAGAGA
62 AAGTTTATTATGAATAGGATCTGGTCCTCCCGATGTTTGTTTCTTCACGATGAACTCATTAGAGA
* * * *
61845 CAAGAGGACTGATAGGTTTATTGTAAATAGGATCTGATCCTCCTCGTGTTTATCTCTTCACGGCG
127 CAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATCCTCCTCGTGTTTATCTCTTCACGACG
* *
61910 AACTCATTAAAGGCAAGAGGG-TGGAGAGGTTTACTTG-AAT
192 AACTCATTAGAGGCAAGAGGGCT-AAGAGGTTTA-TTGTAAT
* *
61950 AGGATCTGATCCTCACGATGTTTGTCTTTTCACGACGAACTCATTAAAGAAAAAAGTGTTGAAAG
1 AGGATCTGATCCTC-CGATGTTTGTCTCTTCACGACGAACTCATTAAAGAAAAGAGTGTTGAAAG
* * * ** * *
62015 TTTTACTATGAATAGGATCTTGTCCTCCTGGCGTTTGTTTCTTCACGAAGAACTCATTATAGACA
65 -TTTATTATGAATAGGATCTGGTCCTCCCGATGTTTGTTTCTTCACGATGAACTCATTAGAGACA
* * *
62080 TGAGGGCTGAGAGGTTTATTGTGAATAGGATCT-AGTCCT-CTCGGTGTTTTTCTTTTCACGACG
129 AGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGA-TCCTCCTC-GTGTTTATCTCTTCACGACG
* * *
62143 AACTCATTAGA-GCAAAAGGGCTTAGAGGTTTATTGTAAAG
192 AACTCATTAGAGGCAAGAGGGCTAAGAGGTTTATTGT-AAT
* * * * * * * * * * *
62183 AGGATCTAACCCTCCTAGTGTTAGTCTCTTCACGATGAACTCATTAGAGACATGAGGGCTAGAAG
1 AGGATCTGATCCTCCGA-TGTTTGTCTCTTCACGACGAACTCATTAAAGAAAAGAGTG-TTGAAA
* * * * * * * * *
62248 GTTTATTGTGAAGAGGAT-TGATCCTACCGATGTTAT-TCTATTCACGAAGAACTCATTAGCGGC
64 GTTTATTATGAATAGGATCTGGTCCTCCCGATGTT-TGTTTCTTCACGATGAACTCATTAGAGAC
* * ** * * * * *
62311 AAGAGGGCTGAGAGGTTTATTGTGAAGAGAATAAGATCCTTCTGGAG-TTAGTCTCTTCACAATG
128 AAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATCCTCCTCGTGTTTA-TCTCTTCACGACG
*
62375 AACTCATTAGAGGCATGAGGGCTAAGAGGTTTATTGTGAAT
192 AACTCATTAGAGGCAAGAGGGCTAAGAGGTTTATTGT-AAT
* ** * * * * ** * *
62416 AAGATCCAATCCTCTCGATGTTTATCTATTCACGACAAACTCATTAGAGGCAAGAGGGCT-AAA-
1 AGGATCTGATCCTC-CGATGTTTGTCTCTTCACGACGAACTCATTAAAGAAAAGAGTGTTGAAAG
* * * * * * * * *
62479 --AAGTTGTGAATAAGATATGGTCCTCCTGGTGTTTGTCTCTTCACGA-AAATCTCATTA-AAAG
65 TTTA-TTATGAATAGGATCTGGTCCTCCCGATGTTTGTTTCTTCACGATGAA-CTCATTAGAGA-
* * * * ** * * * * *
62540 TAAGATGACTAAGAAATTTATTATGAATAGGATTTGATCCT-CTCGATGTTTGTCTCTTCATGAT
127 CAAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGATCCTCCTCG-TGTTTATCTCTTCACGAC
* * * * * * *
62604 GAATTCATTAGAGACATGAGGGTTAAAAGGCTTATTGTGAAG
191 GAACTCATTAGAGGCAAGAGGGCTAAGAGGTTTATTGT-AAT
* * * * * * * * * * **
62646 AGAATCTGGTCCTCCCAATATTTTTCTCTTTACGATGAACTCATTAGAGACAGGA-TAACTGAAA
1 AGGATCTGATCCT-CCGATGTTTGTCTCTTCACGACGAACTCATTAAAGAAAAGAGT-GTTGAAA
* * * * * * * * *
62710 TATTTATTGTGCATGGGATCTGGTCCACCCGATGTTTGTCTCTTCATGACGAA--CATTAAAGAC
64 -GTTTATTATGAATAGGATCTGGTCCTCCCGATGTTTGTTTCTTCACGATGAACTCATTAGAGAC
* * * * * * * * *
62773 AAGAGGACTAACAGATTTATTGTGAATATGATCT-AGTCCTCAC-GGTATTTATCTCTTTACGAT
128 AAGAGGGCTGAGAGGTTTATTGTGAATAGGATCTGA-TCCTC-CTCGTGTTTATCTCTTCACGAC
*
62836 TAACTCATTAGA
191 GAACTCATTAGA
62848 AGGAGGAGGA
Statistics
Matches: 890, Mismatches: 199, Indels: 87
0.76 0.17 0.07
Matches are distributed among these distances:
228 1 0.00
229 17 0.02
230 152 0.17
231 18 0.02
232 177 0.20
233 291 0.33
234 150 0.17
235 75 0.08
236 2 0.00
237 3 0.00
238 4 0.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (231 bp):
AGGATCTGATCCTCCGATGTTTGTCTCTTCACGACGAACTCATTAAAGAAAAGAGTGTTGAAAGT
TTATTATGAATAGGATCTGGTCCTCCCGATGTTTGTTTCTTCACGATGAACTCATTAGAGACAAG
AGGGCTGAGAGGTTTATTGTGAATAGGATCTGATCCTCCTCGTGTTTATCTCTTCACGACGAACT
CATTAGAGGCAAGAGGGCTAAGAGGTTTATTGTAAT
Found at i:63028 original size:16 final size:16
Alignment explanation
Indices: 63007--63049 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
62997 GATTAAGCGT
63007 TGAATGATTCAAATGC
1 TGAATGATTCAAATGC
63023 TGAATGATTCAAATGC
1 TGAATGATTCAAATGC
63039 TGAATGATTCA
1 TGAATGATTCA
63050 GAGGCTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (16 bp):
TGAATGATTCAAATGC
Found at i:63179 original size:23 final size:22
Alignment explanation
Indices: 63130--63190 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
63120 CTTCAGTGCT
*
63130 GAATCATTCAACACTGTTTGCT
1 GAATCATTCAACACTGTTTGCC
* * *
63152 AAATCATTCAACATTATTTTGCC
1 GAATCATTCAACACT-GTTTGCC
*
63175 GAATCAGTCAACACTG
1 GAATCATTCAACACTG
63191 AATCATTCAG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (22 bp):
GAATCATTCAACACTGTTTGCC
Found at i:65696 original size:77 final size:77
Alignment explanation
Indices: 65385--65722 Score: 283
Period size: 77 Copynumber: 4.4 Consensus size: 77
65375 CTTCCGGAGT
* ** * * * * * **
65385 TTGTCTTTTCACGATGAATTCATTAGAGGCAGAAAGACTAAGAGGTTTATTGTGTA-TCGATCTG
1 TTGTCTCTTCACGACAAACTCATTAGAGGCAG-GAGACTGAGAGGTATATTGTGAAGAGGATCTG
65449 GTCCACTCGGTAC
65 GTCCACTCGGTAC
** * * *
65462 TTGTCTCTTCACGATGAACTCATTAGAGGTAGGAGGCTGAGAGGTTTATTGTGGAAGAGGATCTG
1 TTGTCTCTTCACGACAAACTCATTAGAGGCAGGAGACTGAGAGGTATATTGT-GAAGAGGATCTG
*
65527 GTCCACTC-GTAT
65 GTCCACTCGGTAC
* * * * ** * * *
65539 TTGTCTCTTAATGACAAA-TCATTAAAGGCAGGAGGGCCCAGAGGAATA-TATGAAGAGGATTTG
1 TTGTCTCTTCACGACAAACTCATTAGAGGCAGGA-GACTGAGAGGTATATTGTGAAGAGGATCTG
* **
65602 GTCCTCGT-GGTGT
65 GTCCAC-TCGGTAC
*
65615 TTGTCTCTTCACGACAAACTCATTAGAGGTA-GATGACTGAGAGGTATATTGTGAAGAGGATCTG
1 TTGTCTCTTCACGACAAACTCATTAGAGGCAGGA-GACTGAGAGGTATATTGTGAAGAGGATCTG
*
65679 ATCCACTCGGTAC
65 GTCCACTCGGTAC
* * * *
65692 TTGTCTCTTAATGAAAAACTCATTAAAGGCA
1 TTGTCTCTTCACGACAAACTCATTAGAGGCA
65723 CGAGGGTCGA
Statistics
Matches: 209, Mismatches: 44, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
75 16 0.08
76 65 0.31
77 114 0.55
78 14 0.07
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (77 bp):
TTGTCTCTTCACGACAAACTCATTAGAGGCAGGAGACTGAGAGGTATATTGTGAAGAGGATCTGG
TCCACTCGGTAC
Done.