Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007178.1 Hibiscus syriacus cultivar Beakdansim tig00018853_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: 100860
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6189 original size:2 final size:2
Alignment explanation
Indices: 6182--6206 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6172 ACTGCAAGTT
6182 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
6207 GGTTTATTAA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6543 original size:17 final size:18
Alignment explanation
Indices: 6518--6551 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6508 ATCTCAGGAG
*
6518 TTATGAAAT-TTTAAAAC
1 TTATAAAATATTTAAAAC
6535 TTATAAAATATTTAAAA
1 TTATAAAATATTTAAAA
6552 TACAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
TTATAAAATATTTAAAAC
Found at i:8910 original size:23 final size:23
Alignment explanation
Indices: 8880--8943 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
8870 TACTTCTGTG
* *
8880 CTGAATCATTCAACATTGTTTTA
1 CTGAATCAGTCAACACTGTTTTA
**
8903 CTGAATCAGTCGGCACTGTTTTA
1 CTGAATCAGTCAACACTGTTTTA
*
8926 CTGAATCAGTCAGCACTG
1 CTGAATCAGTCAACACTG
8944 AATCATTCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (23 bp):
CTGAATCAGTCAACACTGTTTTA
Found at i:10538 original size:21 final size:21
Alignment explanation
Indices: 10514--10562 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
10504 TTAATCCAGA
**
10514 AAAAAATTCGGTCTGGGGTTT
1 AAAAAATTCGGTCTGAAGTTT
* *
10535 -AAAAATCCGGTTTGAAGTTT
1 AAAAAATTCGGTCTGAAGTTT
10555 AAAAAATT
1 AAAAAATT
10563 GGATGGCCGG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (21 bp):
AAAAAATTCGGTCTGAAGTTT
Found at i:11114 original size:11 final size:11
Alignment explanation
Indices: 11098--11137 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
11088 TTATATACTA
11098 TAAAAATAAAT
1 TAAAAATAAAT
*
11109 TAAAAATATA-
1 TAAAAATAAAT
11119 TAAAAATAAAT
1 TAAAAATAAAT
11130 TATAAAAT
1 TA-AAAAT
11138 TACAACTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 11 0.44
12 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAAAATAAAT
Found at i:11121 original size:21 final size:22
Alignment explanation
Indices: 11096--11137 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
11086 TATTATATAC
11096 TATAAAAATAAATTA-AAAATA
1 TATAAAAATAAATTATAAAATA
11117 TATAAAAATAAATTATAAAAT
1 TATAAAAATAAATTATAAAAT
11138 TACAACTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
TATAAAAATAAATTATAAAATA
Found at i:11135 original size:13 final size:12
Alignment explanation
Indices: 11096--11136 Score: 52
Period size: 10 Copynumber: 3.6 Consensus size: 12
11086 TATTATATAC
11096 TATAAAAATAAA
1 TATAAAAATAAA
11108 T-TAAAAAT--A
1 TATAAAAATAAA
11117 TATAAAAATAAA
1 TATAAAAATAAA
11129 TTATAAAA
1 -TATAAAA
11137 TTACAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.08
10 7 0.28
11 7 0.28
12 2 0.08
13 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
TATAAAAATAAA
Found at i:12112 original size:20 final size:18
Alignment explanation
Indices: 12069--12109 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
12059 CTATGTTTGA
*
12069 TTTTCGCAACGTAATTGC
1 TTTTTGCAACGTAATTGC
12087 TTTTTGCAACGTAATTGC
1 TTTTTGCAACGTAATTGC
12105 TTTTT
1 TTTTT
12110 TTGGAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (18 bp):
TTTTTGCAACGTAATTGC
Found at i:14149 original size:22 final size:23
Alignment explanation
Indices: 14118--14165 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
14108 GTTTCTTAAG
14118 ATTCAAGTATAATACTAATGT-C
1 ATTCAAGTATAATACTAATGTAC
* *
14140 ATTCATGTATCATACTAATGTAC
1 ATTCAAGTATAATACTAATGTAC
14163 ATT
1 ATT
14166 TGTATGGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
ATTCAAGTATAATACTAATGTAC
Found at i:14248 original size:13 final size:13
Alignment explanation
Indices: 14232--14267 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
14222 ATGTTTATAT
14232 AATTTATATTCAA
1 AATTTATATTCAA
* *
14245 AATTAATATTCAT
1 AATTTATATTCAA
14258 AATTTATATT
1 AATTTATATT
14268 GTTAGAGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTATATTCAA
Found at i:29627 original size:21 final size:22
Alignment explanation
Indices: 29593--29633 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
29583 TGAACAAAAA
29593 ATATAAAAACAAAGAAAATAAT
1 ATATAAAAACAAAGAAAATAAT
*
29615 ATATAAAAA-AAAGCAAATA
1 ATATAAAAACAAAGAAAATA
29634 TGAGTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (22 bp):
ATATAAAAACAAAGAAAATAAT
Found at i:29965 original size:63 final size:63
Alignment explanation
Indices: 29866--29991 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
29856 AGGGGAATTA
29866 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATGA-AGTTTACCC
1 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAAT-ACAGTTTACCC
*
29929 AACCGATTTGGGGACCAAATTGAATGTTTTTCAAAACAGAGGGAGCCAAAATACAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATACAGTTTACCC
29992 CTTTTAGCAA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 1 0.02
63 60 0.98
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (63 bp):
AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATACAGTTTACCC
Found at i:29978 original size:31 final size:31
Alignment explanation
Indices: 29876--29978 Score: 88
Period size: 31 Copynumber: 3.3 Consensus size: 31
29866 AACCGATTTG
*
29876 GGGA-CCAAATTAAATGTTTTTCAAAACAGA
1 GGGAGCCAAATTGAATGTTTTTCAAAACAGA
* * ** *
29906 GGGAGCCAAAATGAA-G-TTTACCCAACCGA
1 GGGAGCCAAATTGAATGTTTTTCAAAACAGA
29935 TTTGGG-GACCAAATTGAATGTTTTTCAAAACAGA
1 ---GGGAG-CCAAATTGAATGTTTTTCAAAACAGA
29969 GGGAGCCAAA
1 GGGAGCCAAA
29979 ATACAGTTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
29 9 0.17
30 5 0.09
31 17 0.31
32 13 0.24
33 1 0.02
34 9 0.17
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (31 bp):
GGGAGCCAAATTGAATGTTTTTCAAAACAGA
Found at i:31359 original size:105 final size:105
Alignment explanation
Indices: 31177--31638 Score: 888
Period size: 105 Copynumber: 4.4 Consensus size: 105
31167 TGTTGTTTTC
31177 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
31242 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
31282 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
31347 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
31387 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
31452 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
31492 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
31557 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
31597 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
31639 TAAAACCTGC
Statistics
Matches: 354, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 354 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:43011 original size:21 final size:22
Alignment explanation
Indices: 42977--43017 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
42967 TGAACAAAAA
42977 ATATAAAAACAAAGAAAATAAT
1 ATATAAAAACAAAGAAAATAAT
*
42999 ATATAAAAA-AAAGCAAATA
1 ATATAAAAACAAAGAAAATA
43018 TGAGTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (22 bp):
ATATAAAAACAAAGAAAATAAT
Found at i:43347 original size:63 final size:63
Alignment explanation
Indices: 43248--43373 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
43238 AGGGGAATTA
43248 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATGA-AGTTTACCC
1 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAAT-ACAGTTTACCC
*
43311 AACCGATTTGGGGACCAAATTGAATGTTTTTCAAAACAGAGGGAGCCAAAATACAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATACAGTTTACCC
43374 CTTTTAGCAA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 1 0.02
63 60 0.98
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (63 bp):
AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATACAGTTTACCC
Found at i:43360 original size:31 final size:31
Alignment explanation
Indices: 43258--43360 Score: 88
Period size: 31 Copynumber: 3.3 Consensus size: 31
43248 AACCGATTTG
*
43258 GGGA-CCAAATTAAATGTTTTTCAAAACAGA
1 GGGAGCCAAATTGAATGTTTTTCAAAACAGA
* * ** *
43288 GGGAGCCAAAATGAA-G-TTTACCCAACCGA
1 GGGAGCCAAATTGAATGTTTTTCAAAACAGA
43317 TTTGGG-GACCAAATTGAATGTTTTTCAAAACAGA
1 ---GGGAG-CCAAATTGAATGTTTTTCAAAACAGA
43351 GGGAGCCAAA
1 GGGAGCCAAA
43361 ATACAGTTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
29 9 0.17
30 5 0.09
31 17 0.31
32 13 0.24
33 1 0.02
34 9 0.17
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (31 bp):
GGGAGCCAAATTGAATGTTTTTCAAAACAGA
Found at i:49424 original size:89 final size:89
Alignment explanation
Indices: 49309--49515 Score: 231
Period size: 89 Copynumber: 2.3 Consensus size: 89
49299 GTTGTAATTG
* * * *
49309 AAATTATTATCAATTGTGTAACTTTTTCGAGTA-AA-CACCTAATATTTTAGATTAAAACCCATT
1 AAATTATTATCAATTGTATAACTTTTT--AGTATAAGCAACTAACATTTTAGATTAAAACCCATC
* *
49372 GTAATATAACATTCTT-TATTTAATCA
64 GTAATATAACATT-TTAAATGTAATCA
* * * *
49398 AAATTATTATCAATTGTATAAATTTTTAGTATAAGCAAGTAACATTTTAGGTTAAAATCCATCGT
1 AAATTATTATCAATTGTATAACTTTTTAGTATAAGCAACTAACATTTTAGATTAAAACCCATCGT
*
49463 AATATAGCATTTTCAAATGTAATCA
66 AATATAACATTTT-AAATGTAATCA
* * *
49488 AAATTATAATAAATTATATAACTTTTTA
1 AAATTATTATCAATTGTATAACTTTTTA
49516 AGTTTGATAG
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
87 4 0.04
88 4 0.04
89 59 0.60
90 32 0.32
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (89 bp):
AAATTATTATCAATTGTATAACTTTTTAGTATAAGCAACTAACATTTTAGATTAAAACCCATCGT
AATATAACATTTTAAATGTAATCA
Found at i:49514 original size:90 final size:89
Alignment explanation
Indices: 49352--49515 Score: 213
Period size: 90 Copynumber: 1.8 Consensus size: 89
49342 AACACCTAAT
* * * * * *
49352 ATTTTAGATTAAAACCCATTGTAATATAACATTCTTTATTTAATCAAAATTATTATCAATTGTAT
1 ATTTTAGATTAAAACCCATCGTAATATAACATTCTTAATGTAATCAAAATTATAATAAATTATAT
49417 AAATTTTTAGTATAAGCAAGTAAC
66 AAATTTTTAGTATAAGCAAGTAAC
* * *
49441 ATTTTAGGTTAAAATCCATCGTAATATAGCATT-TTCAAATGTAATCAAAATTATAATAAATTAT
1 ATTTTAGATTAAAACCCATCGTAATATAACATTCTT--AATGTAATCAAAATTATAATAAATTAT
*
49505 ATAACTTTTTA
64 ATAAATTTTTA
49516 AGTTTGATAG
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
88 2 0.03
89 29 0.46
90 32 0.51
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (89 bp):
ATTTTAGATTAAAACCCATCGTAATATAACATTCTTAATGTAATCAAAATTATAATAAATTATAT
AAATTTTTAGTATAAGCAAGTAAC
Found at i:57807 original size:75 final size:75
Alignment explanation
Indices: 57696--57887 Score: 251
Period size: 75 Copynumber: 2.5 Consensus size: 75
57686 GATTGCTCAT
* * ** *
57696 AGGGAACCGATTCCCCCCCATAGGAGGAACCAATTCCCCCCTGAATGGTTTGGCTCCGAGATTTC
1 AGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTC
57761 CAGAATGCTCGG
64 CAGAATGCTCGG
* *
57773 AGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGTTCCGAGAATTCCA
1 AGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCA
*
57838 GTATGCTCGG
66 GAATGCTCGG
* * *
57848 AGGGAACCGATCCCCCCCAAAGG-GGTACCGATTCCCCCCT
1 AGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
57888 TGTACAACGG
Statistics
Matches: 103, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
75 82 0.80
76 9 0.09
77 12 0.12
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (75 bp):
AGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCA
GAATGCTCGG
Found at i:63710 original size:22 final size:22
Alignment explanation
Indices: 63676--63725 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
63666 ATCGATCCCC
*
63676 CCCCCTCTGA-GGGAACCGATT
1 CCCCCTCTGAGGGGAACCGATA
* *
63697 CCCCCTTTGCAGGGGAATCGATA
1 CCCCCTCTG-AGGGGAACCGATA
63720 CCCCCT
1 CCCCCT
63726 GGGGTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.18, C:0.40, G:0.22, T:0.20
Consensus pattern (22 bp):
CCCCCTCTGAGGGGAACCGATA
Found at i:66447 original size:75 final size:75
Alignment explanation
Indices: 66297--66503 Score: 263
Period size: 75 Copynumber: 2.7 Consensus size: 75
66287 CAAAGCCAAA
* ** * **
66297 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
66362 TTTGGCTCCGAG
64 TTTGGCTCCGAG
*
66374 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
66439 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
66449 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCC
66504 TTGTACAACG
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
75 84 0.73
76 6 0.05
77 25 0.22
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:77651 original size:21 final size:20
Alignment explanation
Indices: 77622--77661 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
77612 CTCTTTTTTC
*
77622 AATAATAGTATTTTTTGTTAA
1 AATAATAGTA-ATTTTGTTAA
*
77643 AATAGTAGTAATTTTGTTA
1 AATAATAGTAATTTTGTTA
77662 CCTCCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (20 bp):
AATAATAGTAATTTTGTTAA
Found at i:77878 original size:16 final size:17
Alignment explanation
Indices: 77843--77879 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
77833 CATGAGATAA
77843 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
77860 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
77876 AAAA
1 AAAA
77880 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:82683 original size:2 final size:2
Alignment explanation
Indices: 82676--82733 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
82666 GGTGCCTACG
82676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82718 AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
82734 AATAAAAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83211 original size:21 final size:19
Alignment explanation
Indices: 83182--83224 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 19
83172 AAGTTTTTCT
83182 TAAATAATATATTATTTTCTAA
1 TAAATAATAT-TT-TTTT-TAA
83204 TAAA-AATATTTTTTTTAA
1 TAAATAATATTTTTTTTAA
83222 TAA
1 TAA
83225 TTTCTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.29
19 4 0.19
20 2 0.10
21 5 0.24
22 4 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAATAATATTTTTTTTAA
Found at i:86810 original size:144 final size:144
Alignment explanation
Indices: 86333--87309 Score: 971
Period size: 144 Copynumber: 6.8 Consensus size: 144
86323 AACGGCGATT
* ** * * *
86333 GTGATCTTCTTGGT-TTCAGTGTGGGTTGGTCTCTTTCTTTAACATGATCATTATGTTCCTTACC
1 GTGATCTTCTTGGTCTT-AGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATC
* * * * * *
86397 TTGTTC-GAAATTCTCCATTTC--CG-ACTTCTTCATCATCACCAACGCGTTCTTTCT-A-C-CC
65 TTGCTCAG-AATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACC
* *
86455 AACGGTATCGGCGATG
129 ATCGGTATCGGTGATG
* * * *
86471 GTGATCTTCTTGTTCTTAGTATGGGTTGTTC-ACTTTCTTTATCTCGATCAATATGTTCCTTATC
1 GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGA-TTTCTTTATCACGATCATTATGTTCCTTATC
* * * *
86535 TTGCTCAGAATCCTCTATTTCGGAGTGCTGCTTCATCGTCACCAACGAGGCCTTTCTC--C-CCA
65 TTGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCA
86597 TCGGTATCGGTGATG
130 TCGGTATCGGTGATG
* * * * *
86612 GTGATCTTGTTGGTCTTAGTGTAGGTTGTTCGCTTTCTTTATCTCGATCATTATGTTCATTATCT
1 GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATCT
* ** * **** *
86677 TGCTCAGAATCCTCCATTTCGGGGCGCTGCTTCATTGTTGTTAATGCGGTCTTTCTCATCACCAT
66 TGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCAT
*
86742 CGGTATTGGTGATG
131 CGGTATCGGTGATG
* * * * * * * **
86756 GTGATCTTCTCGGTGTTAATGTGGGTTGTTCGATGTCTTTGTCCCGATCGTTATGTTCCCCATCT
1 GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATCT
* * * * * *
86821 TGTTCAGAATCATCTATTTCGGAGTACTGCTTCATTGTCACCACCGCAGTCTTTCTCATCACCAT
66 TGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCAT
86886 CGGTATCGGAT-ATG
131 CGGTATCGG-TGATG
** * * *
86900 GTGATCTTCTTGGTGC-TAGTGCAGGTTGTTCGCTTTCTTTATCAGGATCATTATGTTCCGTATC
1 GTGATCTTCTTGGT-CTTAGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATC
* ** * * * * *
86964 TTGTTCAGAATTTTCCATGTCCGAGTACTGCTTCACCGTTACCACCGCGGTCTTTCTCATCACCA
65 TTGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCA
87029 TCGGTATCGGTGATG
130 TCGGTATCGGTGATG
* * * * * * * *
87044 GTGTTCTTCTTGTTCTTTGTGTGAGTTCTTCGCTTTCTTTATCAGGATCATTATGTTCTTTATCT
1 GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATCT
* * * * *
87109 TGCTCAGAATCCTCCGTTTCGGAGTACTGCTTCACCGTCATCAATGCGGTCTTCCTCATCACCAT
66 TGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCAT
* *
87174 CGGAATCGGTAATG
131 CGGTATCGGTGATG
* *
87188 GTGATCTTCTCGGTCTTAGTGTGGG-TGTTTC-ACTTTCTATT-TCACGATCATTATGTTTCTTA
1 GTGATCTTCTTGGTCTTAGTGTGGGTTG-TTCGA-TTTCT-TTATCACGATCATTATGTTCCTTA
** ** * *
87250 TCTTGCTCAGAATCCTCCATTTCATAGTGTTGCTTCATCGTCATCAACGCGGTCCTTCTC
63 TCTTGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTC
87310 GCCGGTGATC
Statistics
Matches: 691, Mismatches: 130, Indels: 30
0.81 0.15 0.04
Matches are distributed among these distances:
138 67 0.10
139 3 0.00
140 1 0.00
141 145 0.21
143 4 0.01
144 468 0.68
145 3 0.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (144 bp):
GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATCT
TGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCAT
CGGTATCGGTGATG
Found at i:94967 original size:24 final size:24
Alignment explanation
Indices: 94939--94999 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
94929 TTTGGCTCAA
94939 TGAGAAAATAGAATGAATTTGGAG
1 TGAGAAAATAGAATGAATTTGGAG
94963 TGAGAAAATAGAATGAATTTGGAG
1 TGAGAAAATAGAATGAATTTGGAG
*
94987 TGAGAAAACAGAA
1 TGAGAAAATAGAA
95000 GGGTTAACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.49, C:0.02, G:0.28, T:0.21
Consensus pattern (24 bp):
TGAGAAAATAGAATGAATTTGGAG
Found at i:96073 original size:20 final size:20
Alignment explanation
Indices: 96050--96094 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
96040 GTTTCCAGAT
96050 TCGCAACGCGAATCTGACTA
1 TCGCAACGCGAATCTGACTA
*** *
96070 TCGCCTTGCGATTCTGACTA
1 TCGCAACGCGAATCTGACTA
96090 TCGCA
1 TCGCA
96095 TTGCGGTTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGAATCTGACTA
Found at i:96098 original size:20 final size:20
Alignment explanation
Indices: 96057--96099 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
96047 GATTCGCAAC
*
96057 GCGAATCTGACTATCGCCTT
1 GCGAATCTGACTATCGCATT
*
96077 GCGATTCTGACTATCGCATT
1 GCGAATCTGACTATCGCATT
96097 GCG
1 GCG
96100 GTTTATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (20 bp):
GCGAATCTGACTATCGCATT
Found at i:96157 original size:20 final size:20
Alignment explanation
Indices: 96132--96243 Score: 163
Period size: 20 Copynumber: 5.6 Consensus size: 20
96122 TTTTCCGACT
* *
96132 ATCGCAATGTGAATATATAA
1 ATCGCAATGCGAATATGTAA
96152 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
96172 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
96192 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* * *
96212 ATCACAATGCGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
96232 ATCGCAATGCGA
1 ATCGCAATGCGA
96244 TTCTGACTGT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
19 1 0.01
20 84 0.99
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:96244 original size:20 final size:20
Alignment explanation
Indices: 96128--96336 Score: 135
Period size: 20 Copynumber: 10.6 Consensus size: 20
96118 GCGATTTTCC
*
96128 GACTATCGCAATGTGAATAT
1 GACTATCGCAATGCGAATAT
96148 -A-TAAATCGCAATGCGAATAT
1 GACT--ATCGCAATGCGAATAT
*
96168 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
*
96188 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
* * *
96208 GTA-AATCACAATGCGATTAT
1 G-ACTATCGCAATGCGAATAT
* *
96228 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGAATAT
* * * *
96248 GACTGTCGCAACGCGATTCT
1 GACTATCGCAATGCGAATAT
* **
96268 GACTGTCGCAACACG-A-AT
1 GACTATCGCAATGCGAATAT
* * *
96286 GACTGTCGCAACGCGAAAAT
1 GACTATCGCAATGCGAATAT
* * *
96306 GGCTATCGCAACGCGAATTT
1 GACTATCGCAATGCGAATAT
96326 GACTATCGCAA
1 GACTATCGCAA
96337 CGAGAGAATC
Statistics
Matches: 164, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
18 16 0.10
19 3 0.02
20 144 0.88
22 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:96257 original size:60 final size:60
Alignment explanation
Indices: 96128--96263 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 60
96118 GCGATTTTCC
* *
96128 GACTATCGCAATGTGAATATATAAATCGCAATGCGAATATGTAAATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATATATAAATCACAATGCGAATATGTAAATCGCAATGCGAATAT
* * * * * *
96188 GTA-AATCGCAATGCGAATATGTAAATCACAATGCGATTATG-ACTATCGCAATGCGATTCT
1 G-ACTATCGCAATGCGAATATATAAATCACAATGCGAATATGTA-AATCGCAATGCGAATAT
* *
96248 GACTGTCGCAACGCGA
1 GACTATCGCAATGCGA
96264 TTCTGACTGT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
59 2 0.03
60 59 0.95
61 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (60 bp):
GACTATCGCAATGCGAATATATAAATCACAATGCGAATATGTAAATCGCAATGCGAATAT
Found at i:96315 original size:38 final size:39
Alignment explanation
Indices: 96226--96338 Score: 111
Period size: 38 Copynumber: 2.9 Consensus size: 39
96216 CAATGCGATT
** * **
96226 ATGACTATCGCAATGCGATTCTGACTGTCGCAACGCGATT
1 ATGACTATCGCAACACGAAT-TGACTGTCGCAACGCGAAA
* *
96266 CTGACTGTCGCAACACGAA-TGACTGTCGCAACGCGAAA
1 ATGACTATCGCAACACGAATTGACTGTCGCAACGCGAAA
* * *
96304 ATGGCTATCGCAACGCGAATTTGACTATCGCAACG
1 ATGACTATCGCAACACGAA-TTGACTGTCGCAACG
96339 AGAGAATCGC
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
38 32 0.54
40 27 0.46
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (39 bp):
ATGACTATCGCAACACGAATTGACTGTCGCAACGCGAAA
Found at i:96406 original size:20 final size:20
Alignment explanation
Indices: 96381--96448 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
96371 GCGATTCTTT
96381 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
96401 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
96421 CGTTACGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
96441 CGTTGCGA
1 CGTTGCGA
96449 AAGTAAACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:96619 original size:18 final size:18
Alignment explanation
Indices: 96596--96645 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
96586 TTTACTAAGC
*
96596 AATCTAAGTAAAATAGTT
1 AATCTAAGTGAAATAGTT
*
96614 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATAGTT
96632 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
96646 TACGAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATAGTT
Found at i:98376 original size:20 final size:20
Alignment explanation
Indices: 98353--98457 Score: 144
Period size: 19 Copynumber: 5.4 Consensus size: 20
98343 TCTGAAACTT
*
98353 AAAATCGTAACACGAAAATG
1 AAAATCGCAACACGAAAATG
98373 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
98393 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
98412 AAAATCGCAACTCG-AAATG
1 AAAATCGCAACACGAAAATG
* *
98431 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
98450 AAAATCGC
1 AAAATCGC
98458 GTTGCGATTC
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
19 44 0.56
20 35 0.44
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:98837 original size:22 final size:22
Alignment explanation
Indices: 98810--98851 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
98800 AGATAGACGG
*
98810 ATTTCGCCGGAGATGGGGACTA
1 ATTTCGCCGGAGATGAGGACTA
*
98832 ATTTCGTCGGAGATGAGGAC
1 ATTTCGCCGGAGATGAGGAC
98852 GGATGTCGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.24
Consensus pattern (22 bp):
ATTTCGCCGGAGATGAGGACTA
Found at i:99056 original size:20 final size:20
Alignment explanation
Indices: 99031--99121 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
99021 GAAAATCGCA
*
99031 TTGCGATAGTCAGCATAGCG
1 TTGCGATAGTCAGAATAGCG
* *
99051 TTGCGACAGTCAGAATCA-CA
1 TTGCGATAGTCAGAAT-AGCG
**
99071 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATAGCG
* *
99091 TTGTGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATAGCG
99111 TTGCGATAGTC
1 TTGCGATAGTC
99122 GAAAAATCGC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
20 59 0.98
21 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (20 bp):
TTGCGATAGTCAGAATAGCG
Found at i:99093 original size:40 final size:40
Alignment explanation
Indices: 99024--99121 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
99014 GCGCTTTGAA
*
99024 AATCGCATTGCGATAGTCAGCATAGCGTTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAGAATAGCGTTGCGACAGTCAG
* ** * *
99064 AATCACATTGCGATAGTCAGAATCTCGTTGTGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATAGCGTTGCGACAGTCAG
*
99104 AATCGCGTTGCGATAGTC
1 AATCGCATTGCGATAGTC
99122 GAAAAATCGC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAGAATAGCGTTGCGACAGTCAG
Found at i:99138 original size:22 final size:22
Alignment explanation
Indices: 99113--99164 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
99103 GAATCGCGTT
99113 GCGATAGTCGAAAAATCGCAAC
1 GCGATAGTCGAAAAATCGCAAC
* * * *
99135 GCGA-ATTTGGAAAATCGCAAT
1 GCGATAGTCGAAAAATCGCAAC
99156 GCGATAGTC
1 GCGATAGTC
99165 AGAATCGCGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (22 bp):
GCGATAGTCGAAAAATCGCAAC
Done.