Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004916.1 Hibiscus syriacus cultivar Beakdansim tig00011067_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: 77544
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:90 original size:20 final size:21
Alignment explanation
Indices: 65--120 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
55 CATACAAAAT
*
65 TTGTCCCAAAGGACCAC-GTA
1 TTGTCCCGAAGGACCACTGTA
85 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
106 TTGTCCCGAAGGACC
1 TTGTCCCGAAGGACC
121 TATGAAACCC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.21
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:446 original size:16 final size:15
Alignment explanation
Indices: 422--456 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
412 TCACATATGG
*
422 CATATCACATAAATCA
1 CATAGCACATAAA-CA
438 CATAGCACATAAACA
1 CATAGCACATAAACA
453 CATA
1 CATA
457 CCAGCTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.20
Consensus pattern (15 bp):
CATAGCACATAAACA
Found at i:2418 original size:2 final size:2
Alignment explanation
Indices: 2411--2461 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
2401 CAAACTATCC
*
2411 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT A- 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
2452 AT AT AT AT AT
1 AT AT AT AT AT
2462 TCTTTCCAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4153 original size:21 final size:19
Alignment explanation
Indices: 4109--4156 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
4099 ATATATGTTT
* *
4109 TATGAACAGTAAATTACGG
1 TATGAACAGTAAAGTACCG
4128 TATGAACAGTGAACAGTACCG
1 TATGAACAGT-AA-AGTACCG
4149 TATGAACA
1 TATGAACA
4157 TACGTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23
Consensus pattern (19 bp):
TATGAACAGTAAAGTACCG
Found at i:4276 original size:21 final size:22
Alignment explanation
Indices: 4238--4279 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4228 ATTATAATAG
*
4238 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATTACCCTGCTACA
4260 GGGAACCGA-TACCCTGCTAC
1 GGGAACCGATTACCCTGCTAC
4280 TATACTGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.17
Consensus pattern (22 bp):
GGGAACCGATTACCCTGCTACA
Found at i:7371 original size:16 final size:17
Alignment explanation
Indices: 7343--7374 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
7333 TTATACTTCA
7343 TCCATTCATTTCTTTAT
1 TCCATTCATTTCTTTAT
7360 TCCATT-ATTTCTTTA
1 TCCATTCATTTCTTTA
7375 AAATCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (17 bp):
TCCATTCATTTCTTTAT
Found at i:11151 original size:21 final size:21
Alignment explanation
Indices: 11127--11182 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
11117 CATATGAAAT
*
11127 TTGTCCTGAATGACCACTGTA
1 TTGTCCTGAAGGACCACTGTA
*
11148 TTGTCCCGAAGGACCACTGTA
1 TTGTCCTGAAGGACCACTGTA
11169 TTGTCCTGAAGGAC
1 TTGTCCTGAAGGAC
11183 TTATGAAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (21 bp):
TTGTCCTGAAGGACCACTGTA
Found at i:11541 original size:17 final size:16
Alignment explanation
Indices: 11508--11544 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
11498 TCACATATGG
*
11508 CATATCACATAAATCA
1 CATAGCACATAAATCA
11524 CATAGCACATATAATCA
1 CATAGCACATA-AATCA
11541 CATA
1 CATA
11545 CCATTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.24
Consensus pattern (16 bp):
CATAGCACATAAATCA
Found at i:14490 original size:18 final size:19
Alignment explanation
Indices: 14455--14491 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
14445 CATTTTTTCG
14455 GGGGGAATCGATACCCCCA
1 GGGGGAATCGATACCCCCA
14474 GGGGGAATCTG-TACCCCC
1 GGGGGAATC-GATACCCCC
14492 TACGTAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.14
Consensus pattern (19 bp):
GGGGGAATCGATACCCCCA
Found at i:17043 original size:21 final size:21
Alignment explanation
Indices: 17014--17057 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
17004 ATTATATAAT
17014 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
*
17035 ATAATTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
17056 AT
1 AT
17058 TTAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:17218 original size:37 final size:37
Alignment explanation
Indices: 17128--17232 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
17118 CCTTTTCGTC
*
17128 CTACAAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
17165 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** *
17202 CTACTATTACTT-AAACTCCTAAAGATAGGAT
1 CTACTAGGA-TTCAAACTCCTAAAAATAGGAT
17233 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 56 0.97
38 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:17740 original size:23 final size:24
Alignment explanation
Indices: 17704--17752 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
17694 TTTCTTTGCG
* *
17704 TTATATTATATTATTTTTTTATTA
1 TTATATTATATTATATTATTATTA
17728 TTATA-TATATTATATTATTATTA
1 TTATATTATATTATATTATTATTA
17751 TT
1 TT
17753 TTTATCTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTATATTATATTATATTATTATTA
Found at i:17969 original size:12 final size:11
Alignment explanation
Indices: 17951--18018 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
17941 ACATACATTT
17951 TTATATTTTTA
1 TTATATTTTTA
*
17962 TATATATTTTTT
1 T-TATATTTTTA
17974 TTAT-TATTTTA
1 TTATAT-TTTTA
*
17985 TTTATACTATTTA
1 -TTATA-TTTTTA
*
17998 TT-TATTTTCA
1 TTATATTTTTA
18008 TTATATTTTTA
1 TTATATTTTTA
18019 GTTTCTTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
10 7 0.16
11 17 0.38
12 16 0.36
13 4 0.09
14 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATATTTTTA
Found at i:17976 original size:45 final size:45
Alignment explanation
Indices: 17927--18017 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
17917 CTATTTAGTA
*
17927 TTTTATTATATTATACATAC-ATTT-TTATATTTTTATATATATTTT
1 TTTTATTATATTATACATACTATTTATT-TATTTTCAT-TATATTTT
* **
17972 TTTTATTATTTTATTTATACTATTTATTTATTTTCATTATATTTT
1 TTTTATTATATTATACATACTATTTATTTATTTTCATTATATTTT
18017 T
1 T
18018 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
45 26 0.65
46 12 0.30
47 2 0.05
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.68
Consensus pattern (45 bp):
TTTTATTATATTATACATACTATTTATTTATTTTCATTATATTTT
Found at i:17978 original size:21 final size:20
Alignment explanation
Indices: 17948--18017 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 20
17938 TATACATACA
*
17948 TTTTTATATTTTTATATATAT
1 TTTTTTTATTTTTAT-TATAT
17969 TTTTTTTATTATTTTATTTATACT
1 TTTTTTTA-T-TTTTA-TTATA-T
* *
17993 ATTTATTTATTTTCATTATAT
1 -TTTTTTTATTTTTATTATAT
18014 TTTT
1 TTTT
18018 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
20 3 0.08
21 8 0.20
22 6 0.15
23 13 0.32
24 3 0.08
25 7 0.17
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTTTATTTTTATTATAT
Found at i:18128 original size:19 final size:19
Alignment explanation
Indices: 18101--18155 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
18091 TTTTATCTTC
18101 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* *
18120 ATTTCTTTT-TTTTCATCCA
1 ATTTATTTTATTTT-ATTCA
18139 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
18156 ATTATTGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 10 0.34
19 16 0.55
20 3 0.10
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:18931 original size:20 final size:20
Alignment explanation
Indices: 18906--18951 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
18896 TTAAGGGTCT
18906 GGCAAGCCCAAGGGGGCACC
1 GGCAAGCCCAAGGGGGCACC
18926 GGCAAGCCCAAGGGGGCACC
1 GGCAAGCCCAAGGGGGCACC
*
18946 TGCAAG
1 GGCAAG
18952 GAGAACTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.33, G:0.39, T:0.02
Consensus pattern (20 bp):
GGCAAGCCCAAGGGGGCACC
Found at i:22408 original size:16 final size:16
Alignment explanation
Indices: 22384--22462 Score: 74
Period size: 16 Copynumber: 4.9 Consensus size: 16
22374 CAAAAAGGGC
22384 AAAA-ACAAAAAAGAA
1 AAAAGACAAAAAAGAA
22399 AAGAAG-CAAAAAAGAA
1 AA-AAGACAAAAAAGAA
*
22415 GAAAAGAAAAAAAAGAA
1 -AAAAGACAAAAAAGAA
*
22432 AAAAAATC-AAAAAGAA
1 AAAAGA-CAAAAAAGAA
*
22448 AAAGGGACAAAAAAG
1 AAA-AGACAAAAAAG
22463 CGCATGCAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
15 2 0.04
16 32 0.62
17 18 0.35
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.01
Consensus pattern (16 bp):
AAAAGACAAAAAAGAA
Found at i:22425 original size:14 final size:13
Alignment explanation
Indices: 22390--22437 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
22380 GGGCAAAAAC
*
22390 AAAAAAGAAAAGA
1 AAAAAAAAAAAGA
* *
22403 AGCAAAAAAGAAGA
1 A-AAAAAAAAAAGA
22417 AAAGAAAAAAAAGA
1 AAA-AAAAAAAAGA
22431 AAAAAAA
1 AAAAAAA
22438 TCAAAAAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:22460 original size:33 final size:33
Alignment explanation
Indices: 22384--22462 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
22374 CAAAAAGGGC
*
22384 AAAA-ACAAAAAAGAAAAGAAGCAAAAAAGAAG
1 AAAAGACAAAAAAGAAAAAAAGCAAAAAAGAAG
* *
22416 AAAAGAAAAAAAAGAAAAAAAATC-AAAAAGAA-
1 AAAAGACAAAAAAG-AAAAAAAGCAAAAAAGAAG
*
22448 AAAGGGACAAAAAAG
1 AAA-AGACAAAAAAG
22463 CGCATGCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 7 0.18
33 25 0.64
34 7 0.18
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.01
Consensus pattern (33 bp):
AAAAGACAAAAAAGAAAAAAAGCAAAAAAGAAG
Found at i:23083 original size:22 final size:22
Alignment explanation
Indices: 23055--23109 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
23045 GCTACCCCAT
*
23055 CAAACCTTTGAGCATTAAATGC
1 CAAACCTTTGAGCATCAAATGC
23077 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
23099 CAAACCTTTGA
1 CAAACCTTTGA
23110 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:24799 original size:106 final size:106
Alignment explanation
Indices: 23699--24798 Score: 1682
Period size: 106 Copynumber: 10.4 Consensus size: 106
23689 TGCAGCTTTT
* *
23699 AGAGTCAAGTTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 AGAGCCAA-TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
23764 ACGAAGGGACCGCTGGTTTTCAATAAACAATTTCCCAATTTC
65 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * *
23806 AAAGCCAATTGCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
23871 CGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
23912 ATAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
23977 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * *
24018 AGAGCCAATTTTAACTTCACAACAAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
24083 CGAAGGGACCCCTGGTTGTCAACAAAAAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
24124 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
24189 AGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
24230 GGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCGACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
24295 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
*
24336 -GAAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACG
1 AG-AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
24400 ACGAAGGGACTGCTGGTTGTCAACAAATAACTTCTCAATTTC
65 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
24442 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACACAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
24507 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
24548 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTTAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
24613 CGAAGGGACTGTTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * * * * *
24654 GGAGCCAATTTCAACTTCACAACAAAGTATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
24719 CGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
24760 ATAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
24799 GGAACAATGC
Statistics
Matches: 912, Mismatches: 78, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
105 1 0.00
106 904 0.99
107 7 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
Found at i:25601 original size:37 final size:37
Alignment explanation
Indices: 25548--25652 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
25538 CCTTTTCGTC
25548 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
25585 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
25622 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
25653 TCACAAGCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:26153 original size:25 final size:24
Alignment explanation
Indices: 26119--26169 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
26109 TTTCTTTGCG
* *
26119 TTATATTATATTATTTTTTTATTA
1 TTATATTATATTATATTATTATTA
26143 TTATATATATATTATATTATTATTA
1 TTATAT-TATATTATATTATTATTA
26168 TT
1 TT
26170 TTTTTCTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTATATTATATTATATTATTATTA
Found at i:26207 original size:14 final size:14
Alignment explanation
Indices: 26168--26214 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
26158 ATTATTATTA
26168 TTTTTTT-CTATGT
1 TTTTTTTACTATGT
26181 TTACTTATTTACTATGT
1 TT--TT-TTTACTATGT
*
26198 TTTTTTTACTATAT
1 TTTTTTTACTATGT
26212 TTT
1 TTT
26215 CCTAACGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 2 0.07
14 12 0.41
15 4 0.14
16 3 0.10
17 8 0.28
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (14 bp):
TTTTTTTACTATGT
Found at i:26374 original size:23 final size:23
Alignment explanation
Indices: 26338--26419 Score: 60
Period size: 25 Copynumber: 3.4 Consensus size: 23
26328 CTATTTAGTA
26338 TTTTATTATATTATACATACA-ATT
1 TTTTATT-T-TTATACATACATATT
* *
26362 TTTATATTTTTATATATATATATT
1 TTT-TATTTTTATACATACATATT
**
26386 TTTTATTATTTTATTTATAC-TATT
1 TTTTA-T-TTTTATACATACATATT
26410 TATTTATTTT
1 T-TTTATTTT
26420 CATTATATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
23 14 0.29
24 17 0.35
25 18 0.37
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTATTTTTATACATACATATT
Found at i:26377 original size:25 final size:26
Alignment explanation
Indices: 26349--26397 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
26339 TTTATTATAT
26349 TATACATACAATTTTTA-TATTTTTA
1 TATACATACAATTTTTATTATTTTTA
* * *
26374 TATATATATATTTTTTATTATTTT
1 TATACATACAATTTTTATTATTTT
26398 ATTTATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (26 bp):
TATACATACAATTTTTATTATTTTTA
Found at i:26394 original size:28 final size:30
Alignment explanation
Indices: 26363--26432 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
26353 CATACAATTT
26363 TTATATTTTTATA-TATATATATT-TTTT-A
1 TTATATTTTTATACTATATAT-TTATTTTCA
* *
26391 TTATTTTATTTATACTATTTATTTATTTTCA
1 TTATATT-TTTATACTATATATTTATTTTCA
26422 TTATATTTTTA
1 TTATATTTTTA
26433 GTTTCTTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 6 0.17
29 8 0.23
30 14 0.40
31 7 0.20
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (30 bp):
TTATATTTTTATACTATATATTTATTTTCA
Found at i:26398 original size:25 final size:25
Alignment explanation
Indices: 26338--26417 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 25
26328 CTATTTAGTA
* * *
26338 TTTTATTATATTATACATACA-A-T
1 TTTTATTATTTTATATATATATATT
26361 TTTTA-TATTTTTATATATATATATT
1 TTTTATTA-TTTTATATATATATATT
26386 TTTTATTATTTTAT-T-TATACTATT
1 TTTTATTATTTTATATATATA-TATT
26410 TATTTATT
1 T-TTTATT
26418 TTCATTATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
22 2 0.04
23 19 0.40
24 7 0.15
25 18 0.38
26 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTATTATTTTATATATATATATT
Found at i:26418 original size:48 final size:48
Alignment explanation
Indices: 26310--26427 Score: 123
Period size: 48 Copynumber: 2.4 Consensus size: 48
26300 ATTATTTTTC
* *
26310 ATTTATTTATTATTATTACTATTTAGTATTTTATTATATTATACATACA
1 ATTTATTTATTTTTATTA-TATATAGTATTTTATTATATTATACATACA
* * ** *
26359 ATTT-TTATATTTTTATATATATATA-TTTTTTATTATTTTATTTATACT
1 ATTTATT-TATTTTTAT-TATATATAGTATTTTATTATATTATACATACA
*
26407 ATTTATTTATTTTCATTATAT
1 ATTTATTTATTTTTATTATAT
26428 TTTTAGTTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
47 5 0.09
48 32 0.55
49 19 0.33
50 2 0.03
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (48 bp):
ATTTATTTATTTTTATTATATATAGTATTTTATTATATTATACATACA
Found at i:26544 original size:19 final size:19
Alignment explanation
Indices: 26517--26571 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
26507 TTTTATCTTC
26517 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* *
26536 ATTTCTTTT-TTTTCATCCA
1 ATTTATTTTATTTT-ATTCA
26555 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
26572 ATTAGAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 10 0.34
19 16 0.55
20 3 0.10
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:26763 original size:41 final size:41
Alignment explanation
Indices: 26718--26933 Score: 380
Period size: 41 Copynumber: 5.3 Consensus size: 41
26708 TTCGTGTTGT
26718 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
*
26759 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
26800 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
* *
26841 ATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCC
*
26882 ATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
26923 ATTTCGCGTTG
1 ATTTCGCGTTG
26934 TCGTTGCGAT
Statistics
Matches: 167, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
40 1 0.01
41 165 0.99
42 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.38
Consensus pattern (41 bp):
ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
Found at i:26963 original size:27 final size:27
Alignment explanation
Indices: 26909--26982 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
26899 TTGAAATTCG
* *
26909 CGTTGCGATTTTCC-ATTTCGCGTTGT
1 CGTTGCGATTTTCCAAATTCGCATTGT
26935 CGTTGCGATTTTCCAAATTCGCATTGT
1 CGTTGCGATTTTCCAAATTCGCATTGT
26962 CGTTGCGATTTTCCAAATTCG
1 CGTTGCGATTTTCCAAATTCG
26983 TTGCGATAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 14 0.31
27 31 0.69
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (27 bp):
CGTTGCGATTTTCCAAATTCGCATTGT
Found at i:27080 original size:6 final size:6
Alignment explanation
Indices: 27069--27137 Score: 138
Period size: 6 Copynumber: 11.5 Consensus size: 6
27059 GACACGTATT
27069 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
27117 ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACC
27138 CGAGACGAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:27661 original size:6 final size:6
Alignment explanation
Indices: 27645--27707 Score: 119
Period size: 6 Copynumber: 10.7 Consensus size: 6
27635 TCTCGTCTCG
27645 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
27692 GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTC
27708 ATACGTGTCT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.09
6 52 0.91
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:27844 original size:20 final size:20
Alignment explanation
Indices: 27791--27850 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
27781 TCAACGAATT
27791 TGGAAAATCGCAACGAC-AAA
1 TGGAAAATCGCAACG-CGAAA
**
27811 TGTAGACTATCGCAACGCGAAA
1 TG--GAAAATCGCAACGCGAAA
27833 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
27851 TCTCCAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 16 0.48
21 1 0.03
22 16 0.48
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:27921 original size:65 final size:65
Alignment explanation
Indices: 27839--27969 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
27829 GAAATGGAAA
27839 ATCGCAACGCGATCTCCAACTATCGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTG
1 ATCGCAACGCGATCTCCAACTATCGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTG
27904 ATCGCAACGCGATCTCCAACTATCGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTG
1 ATCGCAACGCGATCTCCAACTATCGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTG
27969 A
1 A
27970 ATTTGCGATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (65 bp):
ATCGCAACGCGATCTCCAACTATCGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTG
Found at i:27965 original size:21 final size:21
Alignment explanation
Indices: 27816--27965 Score: 140
Period size: 21 Copynumber: 7.1 Consensus size: 21
27806 ACAAATGTAG
* *
27816 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATATGCA
* * *
27837 A-AATCGCAACGCGATCTCCA
1 ACTATCGCAACGCGATATGCA
* *
27857 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATATGCA
* *
27878 ACTATCGCAATGCGAAATGCA
1 ACTATCGCAACGCGATATGCA
* *
27899 ACGTGATCGCAACGCGATCTCCA
1 AC-T-ATCGCAACGCGATATGCA
* *
27922 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATATGCA
* *
27943 ACTATCGCAATGCGAAATGCA
1 ACTATCGCAACGCGATATGCA
27964 AC
1 AC
27966 GTGAATTTGC
Statistics
Matches: 104, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
20 15 0.14
21 71 0.68
22 2 0.02
23 16 0.15
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGATATGCA
Found at i:28177 original size:19 final size:18
Alignment explanation
Indices: 28093--28182 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 18
28083 GTCACTGAAG
*
28093 TTATTTTCTCTTATTATTA
1 TTATTTTCTTTTATT-TTA
* *
28112 TT-TGTTTCATTTATTTTC
1 TTAT-TTTCTTTTATTTTA
* * *
28130 TTGGTTTACTCTTTAGTTTTG
1 TT-ATTTTCT-TTTA-TTTTA
*
28151 TTACTTTCTTTTATTATTA
1 TTATTTTCTTTTATT-TTA
28170 TTATTTTCTTTTA
1 TTATTTTCTTTTA
28183 AAATCTTATA
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
18 7 0.13
19 32 0.59
20 9 0.17
21 6 0.11
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.69
Consensus pattern (18 bp):
TTATTTTCTTTTATTTTA
Found at i:28540 original size:20 final size:20
Alignment explanation
Indices: 28509--28562 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
28499 GGTTGCGACA
28509 CCTTTC-TTCTTCTTCCTTT
1 CCTTTCTTTCTTCTTCCTTT
28528 CCTTTCTTTCTTCTTCCTTT
1 CCTTTCTTTCTTCTTCCTTT
28548 CCTTTCTTTCTTCTT
1 CCTTTCTTTCTTCTT
28563 ACCCCATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 6 0.18
20 28 0.82
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (20 bp):
CCTTTCTTTCTTCTTCCTTT
Found at i:35039 original size:2 final size:2
Alignment explanation
Indices: 35032--35056 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35022 TAATTTTTAA
35032 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35057 GCTTTTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35811 original size:23 final size:23
Alignment explanation
Indices: 35780--35870 Score: 157
Period size: 23 Copynumber: 4.0 Consensus size: 23
35770 TAATGTCTAT
*
35780 AATC-AACAAACTCTAAACATAA
1 AATCAAACAAACTCAAAACATAA
*
35802 CATCAAACAAACTCAAAACATAA
1 AATCAAACAAACTCAAAACATAA
35825 AATCAAACAAACTCAAAACATAA
1 AATCAAACAAACTCAAAACATAA
35848 AATCAAACAAACTCAAAACATAA
1 AATCAAACAAACTCAAAACATAA
35871 CACTTGTAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
22 3 0.05
23 62 0.95
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (23 bp):
AATCAAACAAACTCAAAACATAA
Found at i:39001 original size:3 final size:3
Alignment explanation
Indices: 38993--39074 Score: 76
Period size: 3 Copynumber: 27.3 Consensus size: 3
38983 AATTACTTAA
* ** * * * *
38993 ATT ATT ATT TTT AAA ATT ACT ATT ATT ATT -TA AAT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
39040 ATT ATA ATT ATT AATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT A
39075 AATAATTACA
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
2 1 0.02
3 57 0.93
4 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:42773 original size:43 final size:43
Alignment explanation
Indices: 42702--42786 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
42692 GGCTTTAGAA
* *
42702 AAGTTAGGAGAGAAAGTTATCCCATATATGTAAAGTTTTGTTG
1 AAGTTAGGACAGAAAGATATCCCATATATGTAAAGTTTTGTTG
* * *
42745 AAGTTAGGACTGAAAGATGTCCCCTATATGTAAAGTTTTGTT
1 AAGTTAGGACAGAAAGATATCCCATATATGTAAAGTTTTGTT
42787 TGATGCACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (43 bp):
AAGTTAGGACAGAAAGATATCCCATATATGTAAAGTTTTGTTG
Found at i:46207 original size:32 final size:32
Alignment explanation
Indices: 46167--46228 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
46157 TCTGGAAACA
* *
46167 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAGTATCTCTACCAGATAAGCATAACAACG
*
46199 AGAAGTATCTCTACCAGATAATCATAACAA
1 AGAAGTATCTCTACCAGATAAGCATAACAA
46229 TCATTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (32 bp):
AGAAGTATCTCTACCAGATAAGCATAACAACG
Found at i:51084 original size:45 final size:45
Alignment explanation
Indices: 51033--51438 Score: 616
Period size: 45 Copynumber: 9.0 Consensus size: 45
51023 CTTTTTGATA
*
51033 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCAGGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
*
51078 TTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
* * *
51123 TTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCATTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
*
51168 TTTTCAAAACCTTCAGGGTCATCTGTAAGCCCTTTAGTGCAGGATG
1 TTTTCAAAACCTTC-GGGTCATCTGTAAGCCCTTCAGTGCAGGATG
* *
51214 TTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
* * *
51259 TTTTCAAAACCTTCGGTTCATCTGTAAGTCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
*
51304 TTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCAGGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
* * *
51349 TTTTCAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
* * * *
51394 TTTTCAAACCCTTAGGGTCATCTGTAAGACCTAT-AGTGCAAGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCT-TCAGTGCAGGATG
51439 ATAGGACCTT
Statistics
Matches: 335, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
45 293 0.87
46 42 0.13
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (45 bp):
TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCAGGATG
Found at i:51292 original size:136 final size:134
Alignment explanation
Indices: 51028--51438 Score: 644
Period size: 136 Copynumber: 3.0 Consensus size: 134
51018 TGGAGCTTTT
* *
51028 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCAGGATGTTTTCAAAACCTTTG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCAGGATGTTTTCAAAACCTTCG
*
51093 GGTCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCA
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG-GTCATCTGTAAGCCCTTCA
*
51158 TTGCA
130 GTGCA
51163 TGATGTTTTCAAAACCTTCAGGGTCATCTGTAAGCCCTTTAGTGCAGGATGTTTTCAAAACCTTC
1 TGATGTTTTCAAAACCTTC-GGGTCATCTGTAAGCCCTTTAGTGCAGGATGTTTTCAAAACCTTC
* *
51228 AGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGTTCATCTGTAAGTCCTTC
65 GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG-TCATCTGTAAGCCCTTC
51293 AGTGCA
129 AGTGCA
* * *
51299 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCAGGATGTTTTCAAAGCCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCAGGATGTTTTCAAAACCTTCG
* * * *
51364 GGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAACCCTTAGGGTCATCTGTAAGACCTAT-
66 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT-CGGTCATCTGTAAGCCCT-TC
51428 AGTGCA
129 AGTGCA
*
51434 AGATG
1 TGATG
51439 ATAGGACCTT
Statistics
Matches: 257, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
135 126 0.49
136 131 0.51
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (134 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCAGGATGTTTTCAAAACCTTCG
GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGTCATCTGTAAGCCCTTCAG
TGCA
Found at i:51622 original size:3 final size:3
Alignment explanation
Indices: 51614--51689 Score: 64
Period size: 3 Copynumber: 25.3 Consensus size: 3
51604 AACTACTTAA
* ** * * * *
51614 ATT ATT ATT TTT AAA ATT ACT ATT ATT ATT -TA AAT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
51661 ATT ATA ATT ATT AATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT A
51690 AATAATTACA
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
2 1 0.02
3 51 0.93
4 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:51679 original size:16 final size:16
Alignment explanation
Indices: 51654--51690 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
51644 TAAATATTAG
51654 TATT-ATTATTATAAT
1 TATTAATTATTATAAT
*
51669 TATTAATTATTATTAT
1 TATTAATTATTATAAT
51685 TATTAA
1 TATTAA
51691 ATAATTACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTAATTATTATAAT
Found at i:59769 original size:36 final size:36
Alignment explanation
Indices: 59703--59911 Score: 214
Period size: 36 Copynumber: 6.0 Consensus size: 36
59693 AAAAACGAAC
* * * * * *
59703 ACTTGAAACGAAAGTG-CGATACATCTTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
* * *
59738 ACTTAAATCGGAAGTGTCGATGCTTCATTCCGTTCA
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
*
59774 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
* * *
59810 ACTTGAATCGGAAGTGTCGATGCCTCCTTTCGTTCA
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
*
59846 ACTTGAATCGGAAATGCCGATG----CTTCC-TTCA
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
* * * *
59877 ACTTGAATCGGAAGTACTGATGCTTTCTTTCGTTC
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTC
59912 TTCTTATTCA
Statistics
Matches: 146, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
31 23 0.16
32 4 0.03
35 17 0.12
36 102 0.70
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCA
Found at i:59819 original size:72 final size:72
Alignment explanation
Indices: 59703--59875 Score: 249
Period size: 72 Copynumber: 2.4 Consensus size: 72
59693 AAAAACGAAC
* * * * * *
59703 ACTTGAAACGAAAGTG-CGATACATCTTTCCGTTCGACTTAAATCGGAAGTGTCGATGCTTCATT
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGACTTAAATCGGAAGTGTCGATGCCTCATT
59767 CCGTTCA
66 CCGTTCA
* *
59774 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCCTCCTT
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGACTTAAATCGGAAGTGTCGATGCCTCATT
*
59839 TCGTTCA
66 CCGTTCA
*
59846 ACTTGAATCGGAAATGCCGATGCTTCCTTC
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTC
59876 AACTTGAATC
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 14 0.15
72 77 0.85
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (72 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGACTTAAATCGGAAGTGTCGATGCCTCATT
CCGTTCA
Found at i:59899 original size:31 final size:31
Alignment explanation
Indices: 59842--59901 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
59832 CCTCCTTTCG
*
59842 TTCAACTTGAATCGGAAATGCCGATGCTTCC
1 TTCAACTTGAATCGGAAATACCGATGCTTCC
* *
59873 TTCAACTTGAATCGGAAGTACTGATGCTT
1 TTCAACTTGAATCGGAAATACCGATGCTT
59902 TCTTTCGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (31 bp):
TTCAACTTGAATCGGAAATACCGATGCTTCC
Found at i:68042 original size:35 final size:35
Alignment explanation
Indices: 68003--68071 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
67993 TTACACAATC
68003 TTCAATTTCATTCTAAA-TCCCAAATTCCAAAATAA
1 TTCAATTTCATTCTAAACT-CCAAATTCCAAAATAA
* * *
68038 TTCAATTTCATTTTAAACTCTAAATTCTAAAATA
1 TTCAATTTCATTCTAAACTCCAAATTCCAAAATA
68072 GGGTTTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (35 bp):
TTCAATTTCATTCTAAACTCCAAATTCCAAAATAA
Found at i:68218 original size:19 final size:19
Alignment explanation
Indices: 68194--68232 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
68184 TTTGAGGTTT
68194 GTTGCATGCACATCCAACG
1 GTTGCATGCACATCCAACG
68213 GTTGCATGCACATCCAACG
1 GTTGCATGCACATCCAACG
68232 G
1 G
68233 CTGCCGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.21
Consensus pattern (19 bp):
GTTGCATGCACATCCAACG
Found at i:69881 original size:39 final size:36
Alignment explanation
Indices: 69781--69881 Score: 96
Period size: 39 Copynumber: 2.7 Consensus size: 36
69771 AATGTAATTT
* * *
69781 AAAATATT-ATTATTTTAATATTTTTGGTGGAATTA
1 AAAATATTAATTATTATAATATTTTAGGTGGAATAA
* *
69816 AAAATATTATATTTTTATAATAATTTTAGTTGGTAATAA
1 AAAATATTA-ATTATTATAAT-ATTTTAGGTGG-AATAA
*
69855 AAAATATTACATTATTCGTAATATTTT
1 AAAATATTA-ATTATT-ATAATATTTT
69882 TGGTTCAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
35 8 0.15
37 9 0.17
38 9 0.17
39 23 0.43
40 4 0.08
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.50
Consensus pattern (36 bp):
AAAATATTAATTATTATAATATTTTAGGTGGAATAA
Found at i:74888 original size:12 final size:12
Alignment explanation
Indices: 74873--74925 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
74863 AGCAGCACAA
*
74873 TCAGCATCATCC
1 TCAGCAACATCC
74885 TCAGCAACAAT-C
1 TCAGCAAC-ATCC
* * *
74897 TCAACAGCACCC
1 TCAGCAACATCC
74909 TCAGCAACATCC
1 TCAGCAACATCC
74921 TCAGC
1 TCAGC
74926 GACAGTTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 1 0.03
12 29 0.91
13 2 0.06
ACGTcount: A:0.32, C:0.42, G:0.09, T:0.17
Consensus pattern (12 bp):
TCAGCAACATCC
Found at i:76153 original size:33 final size:32
Alignment explanation
Indices: 76119--76182 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
76109 TTTTTTAATA
*
76119 AAAAT-CTGACGTGTAAAATTTCACGTCATCAT
1 AAAATACTGACGTG-AAAATTCCACGTCATCAT
*
76151 AAAATAGTGACGTGAAAATTCCACGTCATCAT
1 AAAATACTGACGTGAAAATTCCACGTCATCAT
76183 CAGTGACCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
AAAATACTGACGTGAAAATTCCACGTCATCAT
Found at i:76553 original size:3 final size:3
Alignment explanation
Indices: 76545--76581 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
76535 ATTGTAGCCT
76545 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
76582 GTTACCATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.