Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000292.1 Hibiscus syriacus cultivar Beakdansim tig00000537_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: 68501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:174 original size:89 final size:83
Alignment explanation
Indices: 1--186 Score: 241
Period size: 89 Copynumber: 2.2 Consensus size: 83
* *
1 AAATGCATATGGGTGCATTATCAGAAAAGTATGCTACATAATGCATATGGGTGCATATCAACAGA
1 AAATGCATATGGGTGCATTATCAGAAAAATATGCTACATAATGCATATGGGTACATATCAACAGA
*
66 AAAGTATGCTACAGTTG-
66 AAAGTATGCTACAGCTGA
83 AAATGCATATGGGTGCATTATCAACAGAAAAATATGCTACAGTTGAAATGCATATGGGTACATTA
1 AAATGCATATGGGTGCATTAT---CAGAAAAATATGCTACA--T--AATGCATATGGGTACA-TA
*
148 TCAACAG-AAAGTATGCTATAGCTGA
58 TCAACAGAAAAGTATGCTACAGCTGA
173 AAATGCATAATGGG
1 AAATGCAT-ATGGG
187 CATTATAAAC
Statistics
Matches: 90, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
82 21 0.23
85 16 0.18
87 1 0.01
89 30 0.33
90 17 0.19
91 5 0.06
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (83 bp):
AAATGCATATGGGTGCATTATCAGAAAAATATGCTACATAATGCATATGGGTACATATCAACAGA
AAAGTATGCTACAGCTGA
Found at i:192 original size:44 final size:45
Alignment explanation
Indices: 1--186 Score: 255
Period size: 45 Copynumber: 4.3 Consensus size: 45
1 AAATGCATATGGGTGCATTAT---CAGAAAAGTATGCTACA--T-
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTACAGTTG
40 -AATGCATATGGGTGCA-TATCAACAGAAAAGTATGCTACAGTTG
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTACAGTTG
*
83 AAATGCATATGGGTGCATTATCAACAGAAAAATATGCTACAGTTG
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTACAGTTG
* * *
128 AAATGCATATGGGTACATTATCAACAG-AAAGTATGCTATAGCTG
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTACAGTTG
172 AAAATGCATAATGGG
1 -AAATGCAT-ATGGG
187 CATTATAAAC
Statistics
Matches: 132, Mismatches: 5, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
37 3 0.02
38 16 0.12
40 17 0.13
42 1 0.01
44 30 0.23
45 60 0.45
46 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (45 bp):
AAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTACAGTTG
Found at i:3059 original size:10 final size:10
Alignment explanation
Indices: 3044--3071 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3034 GTCATTAGCT
3044 GTTTCAACTG
1 GTTTCAACTG
3054 GTTTCAACTG
1 GTTTCAACTG
3064 GTTTCAAC
1 GTTTCAAC
3072 CATTTTCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (10 bp):
GTTTCAACTG
Found at i:7558 original size:3 final size:3
Alignment explanation
Indices: 7550--7577 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
7540 CAAAAACTCT
7550 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
7578 GCCGCCGCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:8622 original size:2 final size:2
Alignment explanation
Indices: 8615--8661 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
8605 TTTTTAAATA
*
8615 AT AT AT AT A- AT ACT -T AT AT AC AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8655 AT AT AT A
1 AT AT AT A
8662 ATTATTGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.08
2 35 0.90
3 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:8641 original size:17 final size:17
Alignment explanation
Indices: 8619--8661 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
8609 TAAATAATAT
8619 ATATAATACT-TATATAC
1 ATATAATA-TATATATAC
*
8636 ATATAATATATATATAT
1 ATATAATATATATATAC
8653 ATAT-ATATA
1 ATATAATATA
8662 ATTATTGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATATATATATAC
Found at i:9369 original size:2 final size:2
Alignment explanation
Indices: 9362--9401 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9352 ATTATAACTA
9362 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
9402 TCTTATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12095 original size:20 final size:20
Alignment explanation
Indices: 12067--12114 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
12057 ATGTGACACT
*
12067 TTGACCAATATTTTTCGTTA
1 TTGACCAATATTTTCCGTTA
* *
12087 TTGATCAATGTTTTCCGTTA
1 TTGACCAATATTTTCCGTTA
12107 TTGACCAA
1 TTGACCAA
12115 CGGAGTCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (20 bp):
TTGACCAATATTTTCCGTTA
Found at i:20411 original size:2 final size:2
Alignment explanation
Indices: 20404--20429 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20394 CAAGAGATCA
20404 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
20430 CCCCTTACCA
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:22024 original size:18 final size:20
Alignment explanation
Indices: 21989--22026 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
21979 TAAGTTTTTA
*
21989 TCAATTTTTTATCTAAACTT
1 TCAATTTTTTATCAAAACTT
22009 TCAA-TTTTT-TCAAAACTT
1 TCAATTTTTTATCAAAACTT
22027 AACGTTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (20 bp):
TCAATTTTTTATCAAAACTT
Found at i:23110 original size:3 final size:3
Alignment explanation
Indices: 23104--23151 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
23094 TCGAAAAAAA
* *
23104 TAT TAT TAAA TAT TAT TAT TAA TA- TAT TAT ATAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
23150 TA
1 TA
23152 ATTAAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.82
4 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:23132 original size:21 final size:22
Alignment explanation
Indices: 23102--23161 Score: 86
Period size: 21 Copynumber: 2.7 Consensus size: 22
23092 AGTCGAAAAA
23102 AATATTATTAAATATTATTATT
1 AATATTATTAAATATTATTATT
*
23124 AATA-TATTATATATTATTATT
1 AATATTATTAAATATTATTATT
*
23145 ATTATTAATTAAATATT
1 AATATT-ATTAAATATT
23162 TTACATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.58
22 5 0.15
23 9 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATTATTAAATATTATTATT
Found at i:24293 original size:34 final size:34
Alignment explanation
Indices: 24245--24311 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
24235 TGATGGTGTT
*
24245 TTTCTAAAAGCAAATTTTGTCTCACTTGAGACAA
1 TTTCTAAAAGCAAATTTCGTCTCACTTGAGACAA
*
24279 TTTCTCAAAA-CAAATTTCGTCTCGCTTGAGACA
1 TTTCT-AAAAGCAAATTTCGTCTCACTTGAGACA
24312 TTTTTCCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (34 bp):
TTTCTAAAAGCAAATTTCGTCTCACTTGAGACAA
Found at i:24621 original size:71 final size:66
Alignment explanation
Indices: 24523--24655 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 66
24513 TTGAAACTAA
* *
24523 TTTTGTCTCTTGAGACAATTTCTTTTGAAACAAAAATCATCTTTGAGTCTGTTTCTTTGGAAACA
1 TTTTCTCTCTTGAGACAATTTCTTTTG--A-AAAAA--ATCTTTGAGTCTGTTTCATTGGAAACA
24588 AAGTTT
61 AAGTTT
* *
24594 TTTTCTCTCTTGAGATAATTTAC-TTTGAAAAAAATCTTTGAGTTTGTTTCATTGGAAACAAA
1 TTTTCTCTCTTGAGACAATTT-CTTTTGAAAAAAATCTTTGAGTCTGTTTCATTGGAAACAAA
24656 ATTTATAATC
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
66 27 0.47
68 5 0.09
69 1 0.02
71 23 0.40
72 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.44
Consensus pattern (66 bp):
TTTTCTCTCTTGAGACAATTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCATTGGAAACAAAGTT
T
Found at i:24848 original size:36 final size:35
Alignment explanation
Indices: 24808--24934 Score: 98
Period size: 36 Copynumber: 3.6 Consensus size: 35
24798 TGACCAAACT
24808 TTGAGATTATTTCTCTTGAAACATATCTTATTTTCC
1 TTGAGATTATTTCTCTTGAAACA-ATCTTATTTTCC
*** * * ** *
24844 TTGAGACCGTTTCTCATGAAACAA-C-AATCATCT
1 TTGAGATTATTTCTCTTGAAACAATCTTATTTTCC
* *
24877 TTGAGATTTGTTTCTCTTGAAACAAATATTATTTTCC
1 TTGAGA-TTATTTCTCTTGAAAC-AATCTTATTTTCC
*
24914 TTGAGA-TATTTTCTCGTGAAA
1 TTGAGATTA-TTTCTCTTGAAA
24935 TATCTCTATT
Statistics
Matches: 68, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
33 10 0.15
34 14 0.21
35 4 0.06
36 30 0.44
37 10 0.15
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (35 bp):
TTGAGATTATTTCTCTTGAAACAATCTTATTTTCC
Found at i:24927 original size:70 final size:70
Alignment explanation
Indices: 24665--24934 Score: 267
Period size: 70 Copynumber: 3.8 Consensus size: 70
24655 AATTTATAAT
* * * * * *
24665 CTTTGAG-TCTGTTTCTCTTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTTATGAAACAACA
1 CTTTGAGAT-TGTTTCTCTTGAAACAAATATTATTTTCCTTGAGACAGTTTCTCATGAAACAACA
24729 ACCAAA
65 ACCAAA
* * * * * * * *
24735 CTTTGATATTGTTTCCCTTGAAAC-AATATCAAAGTTTCCTTGAGACTGTCTCTAATGAAACAAT
1 CTTTGAGATTGTTTCTCTTGAAACAAATAT--TATTTTCCTTGAGACAGTTTCTCATGAAACAAC
*
24799 GACCAAA
64 AACCAAA
* * * *
24806 CTTTGAGATTATTTCTCTTGAAACATATCTTATTTTCCTTGAGACCGTTTCTCATGAAACAACAA
1 CTTTGAGATTGTTTCTCTTGAAACAAATATTATTTTCCTTGAGACAGTTTCTCATGAAACAACAA
* *
24871 TC-AT
66 CCAAA
* * *
24875 CTTTGAGATTTGTTTCTCTTGAAACAAATATTATTTTCCTTGAGATATTTTCTCGTGAAA
1 CTTTGAGA-TTGTTTCTCTTGAAACAAATATTATTTTCCTTGAGACAGTTTCTCATGAAA
24935 TATCTCTATT
Statistics
Matches: 160, Mismatches: 35, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
69 13 0.08
70 93 0.58
71 51 0.32
72 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (70 bp):
CTTTGAGATTGTTTCTCTTGAAACAAATATTATTTTCCTTGAGACAGTTTCTCATGAAACAACAA
CCAAA
Found at i:25324 original size:43 final size:43
Alignment explanation
Indices: 25209--25339 Score: 185
Period size: 43 Copynumber: 3.1 Consensus size: 43
25199 CATAGGAACC
* *
25209 GTGTTATCACCCTTATATGACCAAGACTCGTCGCATATGAGCA
1 GTGTTATCACCCTTAGATGACCAAGACTCATCGCATATGAGCA
* * * *
25252 GTGTCA--ACCCCTAGATAACCAGGACTCATCGCATATGAGCA
1 GTGTTATCACCCTTAGATGACCAAGACTCATCGCATATGAGCA
*
25293 GTGTTATCACCCTTAGATGGCCAAGACTCATCGCATATGAGCA
1 GTGTTATCACCCTTAGATGACCAAGACTCATCGCATATGAGCA
25336 GTGT
1 GTGT
25340 CATCCCTGAC
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
41 35 0.47
43 40 0.53
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (43 bp):
GTGTTATCACCCTTAGATGACCAAGACTCATCGCATATGAGCA
Found at i:25327 original size:84 final size:85
Alignment explanation
Indices: 25132--25341 Score: 298
Period size: 84 Copynumber: 2.5 Consensus size: 85
25122 TTGAAACTAT
* * *
25132 CCCTTATATGACCAAGACTCATTGCATATGAGCTGTGTCAACCCCAGATAACCAGCCGTCCTCAT
1 CCCTTATATGACCAAGACTCATCGCATATGAGCAGTGTCAACCCCAGATAACCAG-CGTACTCAT
*
25197 CACATAGGAACCGTGTTATCA
65 CACATAGGAACAGTGTTATCA
*
25218 CCCTTATATGACCAAGACTCGTCGCATATGAGCAGTGTCAACCCCTAGATAACCAG-G-ACTCAT
1 CCCTTATATGACCAAGACTCATCGCATATGAGCAGTGTCAACCCC-AGATAACCAGCGTACTCAT
* * *
25281 CGCATATGAGCAGTGTTATCA
65 CACATAGGAACAGTGTTATCA
* *
25302 CCCTTAGATGGCCAAGACTCATCGCATATGAGCAGTGTCA
1 CCCTTATATGACCAAGACTCATCGCATATGAGCAGTGTCA
25342 TCCCTGACCA
Statistics
Matches: 112, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
84 59 0.53
85 1 0.01
86 42 0.38
87 10 0.09
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (85 bp):
CCCTTATATGACCAAGACTCATCGCATATGAGCAGTGTCAACCCCAGATAACCAGCGTACTCATC
ACATAGGAACAGTGTTATCA
Found at i:27257 original size:21 final size:21
Alignment explanation
Indices: 27210--27257 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
27200 AGTTATAATT
*
27210 TATTTAAAATTGTTGTTTTAG
1 TATTTAAAATTGTTGTTTTAC
*
27231 TCATTT-AAATTTTTGTTTTTAC
1 T-ATTTAAAATTGTTG-TTTTAC
27253 TATTT
1 TATTT
27258 TAGTCCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.62
Consensus pattern (21 bp):
TATTTAAAATTGTTGTTTTAC
Found at i:27295 original size:30 final size:29
Alignment explanation
Indices: 27225--27298 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
27215 AAAATTGTTG
*
27225 TTTTAGTCATTTAAATTTTTGTTTTTACTA
1 TTTTAGTCCTTT-AATTTTTGTTTTTACTA
*
27255 TTTTAGTCCTTTAATTTTCTGTTTTTTCTA
1 TTTTAGTCCTTTAATTTT-TGTTTTTACTA
27285 TTTT-GATCCTTTAA
1 TTTTAG-TCCTTTAA
27299 GTTTATGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 7 0.17
30 33 0.82
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.64
Consensus pattern (29 bp):
TTTTAGTCCTTTAATTTTTGTTTTTACTA
Found at i:32776 original size:38 final size:38
Alignment explanation
Indices: 32731--32806 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
32721 AGATGAAAAC
32731 TACGTTAAGGTTCTAGCGGAAAGACCATGGATCATATA
1 TACGTTAAGGTTCTAGCGGAAAGACCATGGATCATATA
32769 TACGTTAAGGTTCTAGCGGAAAGACCATGGATCATATA
1 TACGTTAAGGTTCTAGCGGAAAGACCATGGATCATATA
32807 CGACCAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (38 bp):
TACGTTAAGGTTCTAGCGGAAAGACCATGGATCATATA
Found at i:33763 original size:15 final size:16
Alignment explanation
Indices: 33730--33766 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
33720 TAAACTTATT
33730 ACAATAAAATATTTGTC
1 ACAATAAAATA-TTGTC
33747 ACAATAAAATA-TGTC
1 ACAATAAAATATTGTC
33762 ACAAT
1 ACAAT
33767 CAATTAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (16 bp):
ACAATAAAATATTGTC
Found at i:34447 original size:196 final size:196
Alignment explanation
Indices: 34101--34474 Score: 511
Period size: 196 Copynumber: 1.9 Consensus size: 196
34091 TTACTATAAC
* ** *
34101 TAAATAATTTTGTTACAATTTTTTATTGTAAAAAATATTATTTGTCACAATTTTTTTATAATGAA
1 TAAATAAATTTGTTACAATTGATTATTGTAAAAAATATTATTTGTCACAATCTTTTTATAATGAA
* * * *
34166 AAATTAATATTTATTATACATTTTTATTTTAATTAAATAAATTTGTCAAAAGTTGTTATTTTGAA
66 AAATTAATACTTATTATACATTTTTATTATAACTAAATAAATTTATCAAAAGTTGTTATTTTGAA
*
34231 AAAATATTGTGATGAAATAAATTTCACATAAATTTTTTATTTTGACTAAATTTAATGTTATTGTG
131 AAAATATTGTGATGAAATAAATTTCACAT-AATTTTTTATTTTAACTAAATTTAATGTTATTGTG
34296 AT
195 AT
* * * * *
34298 TAAATAAATTTGTTATAATTGATTATTGTGAAAAATATTATTTGTCATAA-CTTTTTATATTGAG
1 TAAATAAATTTGTTACAATTGATTATTGTAAAAAATATTATTTGTCACAATCTTTTTATAATGAA
** * *
34362 AAATTAATACTTATTATA-ATTTGTTATTATAACTATTTAAATTTATCATAATTTGTTATTTTGA
66 AAATTAATACTTATTATACATTT-TTATTATAACTAAATAAATTTATCAAAAGTTGTTATTTTGA
* * *
34426 TAAAATATTTTGACT-AAATAAATTTGACATAATTTTTTATTTTAACTAA
130 AAAAATATTGTGA-TGAAATAAATTTCACATAATTTTTTATTTTAACTAA
34475 GGGGCTGTTT
Statistics
Matches: 154, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
195 22 0.14
196 87 0.56
197 45 0.29
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (196 bp):
TAAATAAATTTGTTACAATTGATTATTGTAAAAAATATTATTTGTCACAATCTTTTTATAATGAA
AAATTAATACTTATTATACATTTTTATTATAACTAAATAAATTTATCAAAAGTTGTTATTTTGAA
AAAATATTGTGATGAAATAAATTTCACATAATTTTTTATTTTAACTAAATTTAATGTTATTGTGA
T
Found at i:35684 original size:78 final size:78
Alignment explanation
Indices: 35560--35792 Score: 369
Period size: 78 Copynumber: 3.0 Consensus size: 78
35550 AAAGGGGCTA
*
35560 CAAATGTTTCGGAACAACAAAAAGAAGACAATGCTGAGGATTAAGGGAAAAGAAACGAGGCAAAA
1 CAAATGTTTCGGAACAACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAA
35625 CAAAAAGAGACTG
66 CAAAAAGAGACTG
* * * *
35638 CAAGTGTTTCGGAGCGACAAAAAGAAGACAATGCTGAAGATCAAGGGAAAAGAAACGAGGCAAAA
1 CAAATGTTTCGGAACAACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAA
35703 CAAAAAGAGACTG
66 CAAAAAGAGACTG
** * *
35716 CAAATGTTTCCAAACCAA-AAAAAGAAGACAATGCTGAGGATCAAGGGAAAGGAAATGAGGCAAA
1 CAAATGTTTCGGAA-CAACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAA
35780 ACAAAAAGAGACT
65 ACAAAAAGAGACT
35793 ATATTTTTCG
Statistics
Matches: 141, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
78 139 0.99
79 2 0.01
ACGTcount: A:0.51, C:0.14, G:0.24, T:0.11
Consensus pattern (78 bp):
CAAATGTTTCGGAACAACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAA
CAAAAAGAGACTG
Found at i:37494 original size:23 final size:21
Alignment explanation
Indices: 37435--37515 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 21
37425 GTTAGATTGT
*
37435 AAAATAAAAAAAAT-ATGAAA
1 AAAATAAATAAAATAATGAAA
*
37455 AAAATATTAATATAATAATGATAA
1 AAAATA--AATAAAATAATGA-AA
*
37479 TAAAATAAATAAAATAGATAACAA
1 -AAAATAAATAAAATA-ATGA-AA
37503 AAAATAAATAAAA
1 AAAATAAATAAAA
37516 GTTAATAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.12
22 6 0.12
23 25 0.50
24 7 0.14
25 6 0.12
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (21 bp):
AAAATAAATAAAATAATGAAA
Found at i:37527 original size:21 final size:23
Alignment explanation
Indices: 37435--37527 Score: 70
Period size: 23 Copynumber: 4.2 Consensus size: 23
37425 GTTAGATTGT
*
37435 AAAATAAAAAAAATATGA-AA-AA
1 AAAATAAATAAAATA-GATAATAA
* * * *
37457 AATATTAATATAATA-ATGATAA
1 AAAATAAATAAAATAGATAATAA
*
37479 TAAAATAAATAAAATAGATAACAA
1 -AAAATAAATAAAATAGATAATAA
*
37503 AAAATAAAT-AAA-AGTTAATAA
1 AAAATAAATAAAATAGATAATAA
37524 AAAA
1 AAAA
37528 GAAAAATAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.02
21 12 0.22
22 16 0.29
23 21 0.38
24 5 0.09
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (23 bp):
AAAATAAATAAAATAGATAATAA
Found at i:39441 original size:34 final size:34
Alignment explanation
Indices: 39323--39443 Score: 122
Period size: 33 Copynumber: 3.5 Consensus size: 34
39313 CTCGAAGGTC
*
39323 TTTGTGTTTCAAGAGAAAAAATTTCAAAAGGTTTTT
1 TTTGTGTTTCAAGAGAAAAAACTTCAAAA-G-TTTT
* *
39359 TTTGTGTTTCAAGAGAAACAACTT-TAAAGTTATT
1 TTTGTGTTTCAAGAGAAAAAACTTCAAAAGTT-TT
* ** *
39393 TTT-TGTTTCGAGAGAAATGA-TTCCAAAGATTTT
1 TTTGTGTTTCAAGAGAAAAAACTTCAAAAG-TTTT
39426 TTTGTGTTTCAAGAGAAA
1 TTTGTGTTTCAAGAGAAA
39444 CTGTCTCAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
32 2 0.03
33 25 0.34
34 21 0.29
35 3 0.04
36 22 0.30
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAAAAACTTCAAAAGTTTT
Found at i:39454 original size:34 final size:33
Alignment explanation
Indices: 39323--39454 Score: 101
Period size: 34 Copynumber: 3.9 Consensus size: 33
39313 CTCGAAGGTC
** *
39323 TTTGTGTTTCAAGAGAAAAAATTTCAAAAGGTTTTT
1 TTTGTGTTTCAAGAGAAACTATCTC-AAA-G-TTTT
* *
39359 TTTGTGTTTCAAGAGAAAC-AACTTTAAAGTTATT
1 TTTGTGTTTCAAGAGAAACTATC-TCAAAGTT-TT
*
39393 TTT-TGTTTCGAGAGAAA-TGAT-TCCAAAGATTTT
1 TTTGTGTTTCAAGAGAAACT-ATCT-CAAAG-TTTT
*
39426 TTTGTGTTTCAAGAGAAACTGTCTCAAAG
1 TTTGTGTTTCAAGAGAAACTATCTCAAAG
39455 GAGGCAAAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
32 1 0.01
33 24 0.31
34 28 0.36
35 6 0.08
36 19 0.24
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.40
Consensus pattern (33 bp):
TTTGTGTTTCAAGAGAAACTATCTCAAAGTTTT
Found at i:39539 original size:36 final size:36
Alignment explanation
Indices: 39499--39569 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
39489 AAGATTGGTG
39499 TTTCAAGGGAAACTGTCTCAAGAAAGAAAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAAAGAAAAAATTTA
* *
39535 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTT
1 TTTCAAGGGAAACTGTCTCAAGAAAGAAAAAATTT
39570 GTCTCAAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAAAGAAAAAATTTA
Found at i:39574 original size:21 final size:21
Alignment explanation
Indices: 39548--39614 Score: 107
Period size: 21 Copynumber: 3.1 Consensus size: 21
39538 CAAGGGAAAC
39548 TGTCTCAAGAGAGATAAAATT
1 TGTCTCAAGAGAGATAAAATT
39569 TGTCTCAAGAGAGATAAAATT
1 TGTCTCAAGAGAGATAAAATT
* *
39590 TGTTTCAAGAGAGACAAAACTT
1 TGTCTCAAGAGAGATAAAA-TT
39612 TGT
1 TGT
39615 TTTGAGTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
21 38 0.88
22 5 0.12
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTCTCAAGAGAGATAAAATT
Found at i:39577 original size:36 final size:36
Alignment explanation
Indices: 39501--39577 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
39491 GATTGGTGTT
*
39501 TCAAGGGAAACTGTCTCAAGAAAGAAAAAATTTATT
1 TCAAGGGAAACTGTCTCAAGAAAGAAAAAATTTATC
* * *
39537 TCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTC
1 TCAAGGGAAACTGTCTCAAGAAAGAAAAAATTTATC
39573 TCAAG
1 TCAAG
39578 AGAGATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (36 bp):
TCAAGGGAAACTGTCTCAAGAAAGAAAAAATTTATC
Found at i:39909 original size:116 final size:115
Alignment explanation
Indices: 39721--40047 Score: 512
Period size: 116 Copynumber: 2.8 Consensus size: 115
39711 GCTGGTGGGT
*
39721 ACGATTCCCTTCGTCGTGAAGTTAAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAACCTTAAA
1 ACGATTCCTTTCGTCGTGAAGTTAAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAACCTT-AA
39786 TTAGATATCCTTCGTCGTGAAGTTGAAATCTAATTAATGTTATTGGTGAGC
65 TTAGATATCCTTCGTCGTGAAGTTGAAATCTAATTAATGTTATTGGTGAGC
* *
39837 ACGATTCCTTTCGTCGTGAGGTTAAAACCGTGGATGTCCCCTTCGTTGTGAAGTTGAACCTTGAA
1 ACGATTCCTTTCGTCGTGAAGTTAAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAACCTT-AA
* * *
39902 TTAGATATCTTTCGCCGTGAAGTTGAAATCTAATTAATGTTGTTGGTGAGC
65 TTAGATATCCTTCGTCGTGAAGTTGAAATCTAATTAATGTTATTGGTGAGC
* * * * *
39953 ACGATTCCTTTCGTCGTGAAGTTGAAACCGTAGATGGCCCTTTCATTGTGAAGTTGAGCCTTAAC
1 ACGATTCCTTTCGTCGTGAAGTTAAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAACCTTAA-
40018 TT-GAATATCCTTCGTCGTGAAGTTGAAATC
65 TTAG-ATATCCTTCGTCGTGAAGTTGAAATC
40048 GAAGTATTTG
Statistics
Matches: 193, Mismatches: 16, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
115 3 0.02
116 190 0.98
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (115 bp):
ACGATTCCTTTCGTCGTGAAGTTAAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAACCTTAAT
TAGATATCCTTCGTCGTGAAGTTGAAATCTAATTAATGTTATTGGTGAGC
Found at i:40699 original size:3 final size:3
Alignment explanation
Indices: 40680--40768 Score: 134
Period size: 3 Copynumber: 31.3 Consensus size: 3
40670 GTCTGTAAAA
*
40680 AAT AA- AAT AAA AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40725 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40769 TATTATTTTG
Statistics
Matches: 79, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
2 10 0.13
3 69 0.87
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:40714 original size:20 final size:20
Alignment explanation
Indices: 40680--40768 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
40670 GTCTGTAAAA
*
40680 AATAAAATAAAAATAATAAT
1 AATAAAATAATAATAATAAT
40700 AA-AATAATAATAATAATAAT
1 AATAA-AATAATAATAATAAT
40720 AATAAAATAATAATAATAAT
1 AATAAAATAATAATAATAAT
*
40740 AATATAATAATAATAATAAT
1 AATAAAATAATAATAATAAT
*
40760 AATATAATA
1 AATAAAATA
40769 TATTATTTTG
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.94
21 2 0.03
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AATAAAATAATAATAATAAT
Found at i:40768 original size:17 final size:17
Alignment explanation
Indices: 40680--40760 Score: 116
Period size: 17 Copynumber: 4.9 Consensus size: 17
40670 GTCTGTAAAA
40680 AATAA-AATAA-AA-AT
1 AATAATAATAATAATAT
40694 AATAATAA-AATAATAAT
1 AATAATAATAATAAT-AT
*
40711 AATAATAATAATAAAAT
1 AATAATAATAATAATAT
40728 AATAATAATAATAATAT
1 AATAATAATAATAATAT
40745 AATAATAATAATAATA
1 AATAATAATAATAATA
40761 ATATAATATA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
14 7 0.12
15 4 0.07
17 44 0.73
18 5 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAATAATAATAATAT
Found at i:42652 original size:17 final size:17
Alignment explanation
Indices: 42632--42672 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
42622 TGATTTATAC
*
42632 AAATTATTTACGTAATT
1 AAATTATTTACATAATT
42649 AAATTATTTACATAATT
1 AAATTATTTACATAATT
42666 ATAATTA
1 A-AATTA
42673 AGAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (17 bp):
AAATTATTTACATAATT
Found at i:45606 original size:41 final size:41
Alignment explanation
Indices: 45561--45640 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
45551 CCTGAATAAA
45561 AAATAAGTTGTTATTTGGTTGTTATGGATAGTATTCCAGAC
1 AAATAAGTTGTTATTTGGTTGTTATGGATAGTATTCCAGAC
45602 AAATAAGTTGTTATTTGGTTGTTATGGATAGTATTCCAG
1 AAATAAGTTGTTATTTGGTTGTTATGGATAGTATTCCAG
45641 CAAGGCAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (41 bp):
AAATAAGTTGTTATTTGGTTGTTATGGATAGTATTCCAGAC
Found at i:51502 original size:15 final size:15
Alignment explanation
Indices: 51478--51507 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
51468 CCCAAAACAG
*
51478 AGGTATCGATACCAT
1 AGGTACCGATACCAT
51493 AGGTACCGATACCAT
1 AGGTACCGATACCAT
51508 CAAGCATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (15 bp):
AGGTACCGATACCAT
Found at i:54391 original size:23 final size:24
Alignment explanation
Indices: 54351--54400 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
54341 CCACTAGGGG
54351 CTATGAAATTTGTCCCGAAGGACCA
1 CTATGAAA-TTGTCCCGAAGGACCA
54376 CTATGAAA-TGTCCCGAAGGACCA
1 CTATGAAATTGTCCCGAAGGACCA
54399 CT
1 CT
54401 GTGTCCTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 17 0.68
25 8 0.32
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (24 bp):
CTATGAAATTGTCCCGAAGGACCA
Found at i:58781 original size:23 final size:24
Alignment explanation
Indices: 58735--58787 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
58725 CCACTAGGGG
*
58735 CTATGAAATTTGTCCTTAAAGACCA
1 CTATGAAA-TTGTCCTGAAAGACCA
*
58760 CTATGAAA-TGTCCTGAATGACCA
1 CTATGAAATTGTCCTGAAAGACCA
58783 CTATG
1 CTATG
58788 TCCCGAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 18 0.69
25 8 0.31
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (24 bp):
CTATGAAATTGTCCTGAAAGACCA
Found at i:65225 original size:15 final size:15
Alignment explanation
Indices: 65201--65230 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
65191 CCCAAAGCAG
*
65201 AGGTATCGATACCAT
1 AGGTACCGATACCAT
65216 AGGTACCGATACCAT
1 AGGTACCGATACCAT
65231 CAAGCATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (15 bp):
AGGTACCGATACCAT
Found at i:65980 original size:23 final size:23
Alignment explanation
Indices: 65953--66003 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
65943 TGGCACTACG
*
65953 GTGCAATTCTACGCGACACTTCA
1 GTGCAAATCTACGCGACACTTCA
* * *
65976 TTGCAAATCTACGTGGCACTTCA
1 GTGCAAATCTACGCGACACTTCA
65999 GTGCA
1 GTGCA
66004 TTTATACGAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (23 bp):
GTGCAAATCTACGCGACACTTCA
Found at i:66460 original size:21 final size:23
Alignment explanation
Indices: 66427--66472 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 23
66417 TGTATAACCT
66427 ATGTATAATATCGTATTTTCTTA
1 ATGTATAATATCGTATTTTCTTA
66450 ATGTAT-A-ATCGTATTTTCTTA
1 ATGTATAATATCGTATTTTCTTA
66471 AT
1 AT
66473 ATAAGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 16 0.70
22 1 0.04
23 6 0.26
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (23 bp):
ATGTATAATATCGTATTTTCTTA
Done.