Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007141.1 Hibiscus syriacus cultivar Beakdansim tig00018678_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: 48465
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2808 original size:18 final size:18
Alignment explanation
Indices: 2787--2829 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2777 GGAAAGAAGT
*
2787 AAAAAAGAAGAAAACA-AA
1 AAAAAAGAACAAAA-ATAA
2805 AAAAAAGAACAAAAATAA
1 AAAAAAGAACAAAAATAA
2823 AAAAAAG
1 AAAAAAG
2830 GGATAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (18 bp):
AAAAAAGAACAAAAATAA
Found at i:2809 original size:19 final size:19
Alignment explanation
Indices: 2763--2829 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 19
2753 ACAAAAAGGG
* *
2763 CAAAAAAAAAAAAAGGAAA
1 CAAAAAAAAAAGAAGAAAA
* **
2782 GAAGTAAAAAAGAAGAAAA
1 CAAAAAAAAAAGAAGAAAA
*
2801 C-AAAAAAAAAGAACAAAA
1 CAAAAAAAAAAGAAGAAAA
*
2819 -ATAAAAAAAAG
1 CAAAAAAAAAAG
2830 GGATAAAAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
18 23 0.62
19 14 0.38
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.03
Consensus pattern (19 bp):
CAAAAAAAAAAGAAGAAAA
Found at i:4521 original size:106 final size:106
Alignment explanation
Indices: 4403--5677 Score: 1899
Period size: 106 Copynumber: 12.0 Consensus size: 106
4393 ATATCGTGCC
* * * *
4403 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
4468 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
4509 ATTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
4574 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* ** * * * *
4615 ACTCGAGACAACACAAGTTCAACAACACAACGAAGGGACGGCTGGTTGTCAATAAACAATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
4680 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
4721 ACTCAAGACTACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
4786 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
4827 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
4892 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
4933 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
4998 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
5039 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-TATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
5103 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
5144 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGATTTTCAACAAACAATTTCTC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
5209 AATTTCGGAGCCAATTTCAACTTAACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
5250 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5315 AATTTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
5356 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
5421 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
5462 ACTTGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
5526 AATTTCGGAGCCAATTTCAACTTCACAACAAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
5567 ACTCGAGACAACACAAGTTTAACTTCACAACAAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* * * * * *
5631 CGATTCCATAGCCAATTTCAACTTCACGACGGAGGATATTAG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
5673 ACTCG
1 ACTCG
5678 GAACAATGCT
Statistics
Matches: 1074, Mismatches: 92, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
104 2 0.00
105 188 0.18
106 884 0.82
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:5328 original size:423 final size:422
Alignment explanation
Indices: 4403--5676 Score: 1976
Period size: 423 Copynumber: 3.0 Consensus size: 422
4393 ATATCGTGCC
* * * * *
4403 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * * *
4468 AATTT-TAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCGAGACAACACAAGTTCAAC
66 AATTTCT-GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* *
4532 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTT
130 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTT
* * * ** * *
4597 CACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAACAACACAACGAAGGGACGGCTGGTT
195 CACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
* * * *
4662 GTCAATAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCAA
260 GTCAA-CAA-AATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCAA
* * * * *
4727 GACTACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
323 GACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAATTTCCCAATTTC
* *
4792 AGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
388 AGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
4827 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * *
4892 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGTAAGTTCAACT
66 AATTTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
4957 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
5022 ACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
196 ACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* *
5087 TCAACAAATATTTCCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCTAGA
261 TCAACAAA-ATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCAAGA
* * * *
5152 CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGATTTTCAACAAACAATTTCTCAATTTCGG
325 CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAATTTCCCAATTTCAG
*
5217 AGCCAATTTCAACTTAACAACGAAGGATATTGG
390 AGCCAATTTCAACTTCACAACGAAGGATATTGG
5250 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
5315 AATTTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
5380 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* *
5445 ACAGTGAAGGATATTGGACTTGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
196 ACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
*
5510 TCAACAACAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAAC-AAAGAATATTGGACTCGAG
261 TCAACAA-AATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAAG-ATATTGGACTCAAG
* * * * * * *
5574 ACAACACAAGTTTAACTTCACAACAAAGGGACGACTGGTTGTCAACAAACAATTTCCCGATTCCA
324 ACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAATTTCCCAATTTCA
* * * *
5639 TAGCCAATTTCAACTTCACGACGGAGGATATTAG
389 GAGCCAATTTCAACTTCACAACGAAGGATATTGG
5673 ACTC
1 ACTC
5677 GGAACAATGC
Statistics
Matches: 778, Mismatches: 68, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
422 5 0.01
423 533 0.69
424 240 0.31
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (422 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
AATTTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
TCAACAAAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCAAGAC
AACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAATTTCCCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:7139 original size:35 final size:32
Alignment explanation
Indices: 7098--7182 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 32
7088 TTCCTAACGT
* *
7098 TATATATATATATTCTTACTTTATTTTATATTATA
1 TATATATATATATT-TT--TTTAGTTAATATTATA
*
7133 TTTATATGATTACTATTTTTTTAGTTAATATTATA
1 TATATAT-A-TA-TATTTTTTTAGTTAATATTATA
7168 TATATATATAT-TTTT
1 TATATATATATATTTT
7183 CATTTATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
31 4 0.09
32 1 0.02
33 2 0.05
34 1 0.02
35 26 0.60
36 1 0.02
37 4 0.09
38 4 0.09
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (32 bp):
TATATATATATATTTTTTTAGTTAATATTATA
Found at i:7265 original size:9 final size:8
Alignment explanation
Indices: 7238--7267 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
7228 TTATACATAC
7238 ATTTTTAT
1 ATTTTTAT
7246 ATTTTTAT
1 ATTTTTAT
7254 ATTTTTATT
1 ATTTTTA-T
7263 ATTTT
1 ATTTT
7268 ATTTATACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
ATTTTTAT
Found at i:18525 original size:17 final size:18
Alignment explanation
Indices: 18498--18531 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
18488 AGATTACATG
18498 ATAATTAATAAATTTGAT
1 ATAATTAATAAATTTGAT
18516 ATAA-TAATAAATTTGA
1 ATAATTAATAAATTTGA
18532 CATTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
ATAATTAATAAATTTGAT
Found at i:27111 original size:50 final size:50
Alignment explanation
Indices: 27041--27149 Score: 182
Period size: 50 Copynumber: 2.2 Consensus size: 50
27031 TGACCGGTTT
* * * *
27041 GACCGGTTTTGGTGCATAGTTGACCGGTTTGACCGGTCATAACCCGACCG
1 GACCCGTTTTGATGCATAGTTGACCGGTTTGACCGATCATAACCCGACCC
27091 GACCCGTTTTGATGCATAGTTGACCGGTTTGACCGATCATAACCCGACCC
1 GACCCGTTTTGATGCATAGTTGACCGGTTTGACCGATCATAACCCGACCC
27141 GACCCGTTT
1 GACCCGTTT
27150 ATCCGACCCG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (50 bp):
GACCCGTTTTGATGCATAGTTGACCGGTTTGACCGATCATAACCCGACCC
Found at i:29685 original size:24 final size:24
Alignment explanation
Indices: 29658--29748 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
29648 TCAAATTTGA
* *
29658 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
29682 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
29705 ATTCTGATCTGATACATGACCAGG
1 ATTCTGATATGATACTTGACCTGG
*
29729 ATTCTTATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
29749 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:29718 original size:47 final size:48
Alignment explanation
Indices: 29658--29748 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
29648 TCAAATTTGA
* * *
29658 ATTCTGTTATGATACCTGACCTGGATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACATGACCAGGATTCTGATATGATACTTGACATGG
* *
29705 ATTCTGATCTGATACATGACCAGGATTCTTATATGATACTTGAC
1 ATTCTGATATGATACATGACCAGGATTCTGATATGATACTTGAC
29749 TTGAATTATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCAGGATTCTGATATGATACTTGACATGG
Found at i:29973 original size:2 final size:2
Alignment explanation
Indices: 29966--30029 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
29956 GGGATGGGGG
29966 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30007 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
30030 GTTTTAAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34082 original size:3 final size:3
Alignment explanation
Indices: 34074--34117 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
34064 TGACGACAAC
*
34074 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
34118 CAGCGTGGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:34275 original size:15 final size:14
Alignment explanation
Indices: 34245--34278 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
34235 TTTTTAGTTG
34245 TTTATTGAACTTTT
1 TTTATTGAACTTTT
34259 TTTATTGTAA-TTTT
1 TTTATTG-AACTTTT
34273 TTTATT
1 TTTATT
34279 ACTTATCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTATTGAACTTTT
Found at i:34339 original size:32 final size:34
Alignment explanation
Indices: 34299--34380 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 34
34289 TAATACTTAC
*
34299 TTTATTTTGTTAATTTCGTT-GGATTTTTTTTAA
1 TTTATTTTGTTAATTTCGTTAGGATTTTTGTTAA
* *
34332 TTT-TTTTGTTAATTTTGTTAGGCTTTTTGTTAA
1 TTTATTTTGTTAATTTCGTTAGGATTTTTGTTAA
*
34365 TTTATTTTGTTGATTT
1 TTTATTTTGTTAATTT
34381 TGTTTATTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 15 0.35
33 17 0.40
34 11 0.26
ACGTcount: A:0.16, C:0.02, G:0.13, T:0.68
Consensus pattern (34 bp):
TTTATTTTGTTAATTTCGTTAGGATTTTTGTTAA
Found at i:34347 original size:21 final size:21
Alignment explanation
Indices: 34323--34372 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
34313 TTCGTTGGAT
**
34323 TTTTTTTAATTTTTTTGTTAA
1 TTTTTTTAAGCTTTTTGTTAA
* *
34344 TTTTGTTAGGCTTTTTGTTAA
1 TTTTTTTAAGCTTTTTGTTAA
34365 TTTATTTT
1 TTT-TTTT
34373 GTTGATTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.72
Consensus pattern (21 bp):
TTTTTTTAAGCTTTTTGTTAA
Found at i:38488 original size:30 final size:30
Alignment explanation
Indices: 38454--38510 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
38444 CAAGCGTTTG
38454 GAGAAAATTTAGGAAGTGATAAGGCTGTGA
1 GAGAAAATTTAGGAAGTGATAAGGCTGTGA
38484 GAGAAAATTTAGGAAGTGATAAGGCTG
1 GAGAAAATTTAGGAAGTGATAAGGCTG
38511 CAGGATAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.33, T:0.23
Consensus pattern (30 bp):
GAGAAAATTTAGGAAGTGATAAGGCTGTGA
Found at i:42062 original size:17 final size:17
Alignment explanation
Indices: 42021--42056 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
42011 CCTAGGACCT
42021 AGTGGTCAGTATTAGTA
1 AGTGGTCAGTATTAGTA
42038 AGTGGTCAGTATTAGTA
1 AGTGGTCAGTATTAGTA
42055 AG
1 AG
42057 GTGTCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.33
Consensus pattern (17 bp):
AGTGGTCAGTATTAGTA
Found at i:45223 original size:40 final size:39
Alignment explanation
Indices: 45179--45279 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 39
45169 TCAGGCCAAG
*
45179 AGTATTGATATGTTTCAAGAGCATCGATACTTTACCTCAA
1 AGTATCGATAT-TTTCAAGAGCATCGATACTTTACCTCAA
*
45219 AGTATCGATAATTTTCAAGAGCATCGATACTTTACCTTAA
1 AGTATCGAT-ATTTTCAAGAGCATCGATACTTTACCTCAA
45259 AGTATCGATATTTTCCAAGAG
1 AGTATCGATATTTT-CAAGAG
45280 TATTGATATT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
39 5 0.09
40 50 0.88
41 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (39 bp):
AGTATCGATATTTTCAAGAGCATCGATACTTTACCTCAA
Found at i:45225 original size:21 final size:21
Alignment explanation
Indices: 45201--45268 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
45191 TTTCAAGAGC
45201 ATCGATACTTTACCTCAAAGT
1 ATCGATACTTTACCTCAAAGT
* *
45222 ATCGATAATTT---TCAAGAGC
1 ATCGATACTTTACCTCAA-AGT
*
45241 ATCGATACTTTACCTTAAAGT
1 ATCGATACTTTACCTCAAAGT
45262 ATCGATA
1 ATCGATA
45269 TTTTCCAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
18 4 0.11
19 12 0.32
21 19 0.50
22 3 0.08
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (21 bp):
ATCGATACTTTACCTCAAAGT
Found at i:45287 original size:19 final size:19
Alignment explanation
Indices: 45174--45291 Score: 82
Period size: 19 Copynumber: 6.0 Consensus size: 19
45164 GGATTTCAGG
*
45174 CCAAGAGTATTGATATGTTT
1 CCAAGAGTATCGATAT-TTT
* *
45194 -CAAGAGCATCGATACTTTAC
1 CCAAGAGTATCGATA-TTT-T
45214 CTCAA-AGTATCGATAATTTT
1 C-CAAGAGTATCGAT-ATTTT
* *
45234 -CAAGAGCATCGATACTTTA
1 CCAAGAGTATCGATA-TTTT
45253 CCTTAA-AGTATCGATATTTT
1 CC--AAGAGTATCGATATTTT
*
45273 CCAAGAGTATTGATATTTT
1 CCAAGAGTATCGATATTTT
45292 TCGCATCAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
18 6 0.08
19 38 0.49
20 7 0.09
21 20 0.26
22 6 0.08
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (19 bp):
CCAAGAGTATCGATATTTT
Done.