Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005668.1 Hibiscus syriacus cultivar Beakdansim tig00013257_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: 65338
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:9325 original size:54 final size:54
Alignment explanation
Indices: 9176--9787 Score: 646
Period size: 54 Copynumber: 11.5 Consensus size: 54
9166 CTCTGCTGGG
* * * *
9176 GTATGGAACTCGAACAT-ATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGA
1 GTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGA
9229 GTATGGAACTCGAACA---TCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGA
1 GTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGA
* * ** * *
9280 GTATAGAACTCAAACATCTTCTTCTTACAGGTTCGCTCCCTCTTTC-TCTAGAGA
1 GTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGGA
* *
9334 GTATGGAACTCGAACATCTTCTTCAAACAGGTTCGCTCCCTCTTTC-TCTAGGAA
1 GTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGGA
* * ** *
9388 GTATAGAACTCGAAAATCTTCTTCTTACAGGTTCGCTCCCTCTTTC-TCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGGA
* * * * *
9442 GTATGGAACTCGAA-ACTCTTCTT-ATTAC-GGTTCTCTCCTTCTTTCTTTAAGGA
1 GTATGGAACTCGAACA-TCTTCTTCA-AACGGGTTCGCTCCCTCTTTCTTCAGGGA
* * * * *
9495 GTATGGAACTCGAACAT-ATCTTCAAACAGGTTCGCTCCTTCTTTCTTTAAGGA
1 GTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGA
* * * * *
9548 GTATGGAACTCGAACATCTTCTT-ATTACGGGTTCTCTCCTTCTTTCTTTAAGGA
1 GTATGGAACTCGAACATCTTCTTCA-AACGGGTTCGCTCCCTCTTTCTTCAGGGA
* ** * *
9602 GTATGGAACTCGAACAT-ATCTTCAAACGGGTTCGCTCATTCTTTCTTTAAGGA
1 GTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGA
*
9655 GTATGGAACTCGAACA---TCTTCAAACGGGTTCACTCCCTCTTTCTTCAGGGA
1 GTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGA
* * ** *
9706 GTATAGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTC-TCTAGAGA
1 GTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGGA
*
9760 GTATGAAACTCGAACATCTTCTTCAAAC
1 GTATGGAACTCGAACATCTTCTTCAAAC
9788 AGGTGGGGAT
Statistics
Matches: 489, Mismatches: 53, Indels: 33
0.85 0.09 0.06
Matches are distributed among these distances:
51 90 0.18
52 6 0.01
53 144 0.29
54 249 0.51
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (54 bp):
GTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGA
Found at i:10595 original size:16 final size:16
Alignment explanation
Indices: 10569--10606 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
10559 TCTACTAAAG
10569 CATGATTGGGTAGATAT
1 CATG-TTGGGTAGATAT
10586 CATGTTGGGTAGATAT
1 CATGTTGGGTAGATAT
10602 CATGT
1 CATGT
10607 GAATAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (16 bp):
CATGTTGGGTAGATAT
Found at i:20281 original size:21 final size:21
Alignment explanation
Indices: 20255--20299 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20245 GATTTCTGGG
* *
20255 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
20276 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
20297 CAA
1 CAA
20300 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:20781 original size:2 final size:2
Alignment explanation
Indices: 20774--20805 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20764 CATGAGTTAG
20774 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
20806 GAATTGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21619 original size:32 final size:32
Alignment explanation
Indices: 21578--21674 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
21568 GAGTCGAGGG
21578 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
21610 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
21641 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
21673 TT
1 TT
21675 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:21650 original size:31 final size:31
Alignment explanation
Indices: 21577--21677 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
21567 AGAGTCGAGG
21577 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
21608 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
21640 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
21671 GTTTACC
1 GTTTACC
21678 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:21709 original size:30 final size:30
Alignment explanation
Indices: 21665--21758 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
21655 AAGGAACATA
21665 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
21696 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * * *
21726 TTGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
21755 TGGA
1 TGGA
21759 TAGGTCCTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.28
30 34 0.60
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:23531 original size:20 final size:20
Alignment explanation
Indices: 23515--23560 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
23505 AAAAAAATAT
23515 AATAAAAAAAT-AAAAAATG
1 AATAAAAAAATGAAAAAATG
*
23534 AATGAAAAAATGAAAAAATG
1 AATAAAAAAATGAAAAAATG
23554 AA-AAAAA
1 AATAAAAA
23561 TGAGGGTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (20 bp):
AATAAAAAAATGAAAAAATG
Found at i:23549 original size:7 final size:8
Alignment explanation
Indices: 23534--23559 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
23524 ATAAAAAATG
23534 AATGAAAA
1 AATGAAAA
23542 AATGAAAA
1 AATGAAAA
23550 AATGAAAA
1 AATGAAAA
23558 AA
1 AA
23560 ATGAGGGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AATGAAAA
Found at i:24626 original size:55 final size:55
Alignment explanation
Indices: 24557--24925 Score: 499
Period size: 55 Copynumber: 6.7 Consensus size: 55
24547 AGGATTCCCA
*
24557 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGAAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
24612 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAGGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
24667 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * *
24722 GCGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
24777 ACGATTGTTGAAGATTGTTCGTGTCTCATACTCTCTGAACG-AATAGAGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAA-GAAATAGGGAGCAGAC
* * * * * *
24832 AAGATTATTAAAGATTGTTCGTGTCTCATACTCTCTGAAGAAATAGAGAGCATAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * *
24887 ACGATTCTT-AGAGATTATTCGAGTTTCATATTCCCTGAA
1 ACGATTGTTGA-AGATTGTTCGAGTCTCATACTCTCTGAA
24926 AGCAATACGG
Statistics
Matches: 283, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
54 2 0.01
55 280 0.99
56 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:29815 original size:72 final size:71
Alignment explanation
Indices: 29691--29839 Score: 253
Period size: 72 Copynumber: 2.1 Consensus size: 71
29681 TCTATGTCCA
* * *
29691 TATATTTAGCTTATTTAATGCATAGTTATGTTACACATTCCTTGCTTGTGTTATCATATCATTTG
1 TATATTTAGCTTAATTAATGCATAGTTATGTTACACATTCCTTACTTATGTTATCATATCATTTG
29756 CATCAT
66 CATCAT
*
29762 TATATTTAGCTTAATTCATGCATATGTTATGTTACACATTCCTTACTTATGTTATCATATCATTT
1 TATATTTAGCTTAATTAATGCATA-GTTATGTTACACATTCCTTACTTATGTTATCATATCATTT
29827 GCATCAT
65 GCATCAT
29834 TATATT
1 TATATT
29840 AGGCTTGGGA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 22 0.30
72 51 0.70
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.48
Consensus pattern (71 bp):
TATATTTAGCTTAATTAATGCATAGTTATGTTACACATTCCTTACTTATGTTATCATATCATTTG
CATCAT
Found at i:30536 original size:43 final size:43
Alignment explanation
Indices: 30442--30537 Score: 149
Period size: 43 Copynumber: 2.2 Consensus size: 43
30432 TAAGAGAATT
* * *
30442 CAAGTTCATGAAGGTAGTCGAACCATCATGTTCACATGGGATC
1 CAAGTTCATGAAGATAGTCAAACCATCATGTTCACATGGGAAC
30485 CTAA-TTCATGAAGATAGTCAAACCATCATGTTCACATGGGAAC
1 C-AAGTTCATGAAGATAGTCAAACCATCATGTTCACATGGGAAC
30528 CAAGTTCATG
1 CAAGTTCATG
30538 CAAGGAAGAC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
42 2 0.04
43 44 0.92
44 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (43 bp):
CAAGTTCATGAAGATAGTCAAACCATCATGTTCACATGGGAAC
Found at i:34928 original size:21 final size:22
Alignment explanation
Indices: 34870--34946 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 22
34860 GGCAGTGTGA
34870 ATCGATGCACATTCAAGGAGTGC
1 ATCGATGCACATTC-AGGAGTGC
* * *
34893 ATCGGTGCATC-TTCATGA-TGT
1 ATCGATGCA-CATTCAGGAGTGC
34914 ATCGATGCACATTCAAAGG-GATGC
1 ATCGATGCACATTC--AGGAG-TGC
34938 ATCGATGCA
1 ATCGATGCA
34947 TTATTTAGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
20 1 0.02
21 13 0.31
22 3 0.07
23 13 0.31
24 12 0.29
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
ATCGATGCACATTCAGGAGTGC
Found at i:34959 original size:44 final size:44
Alignment explanation
Indices: 34870--34966 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
34860 GGCAGTGTGA
* *
34870 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGT
1 ATCGATGCACATTCAAGGAGTGCATCGATGCATATTCATGATGT
*
34914 ATCGATGCACATTCAAAGG-GATGCATCGATGCATTATTTA-G-TGT
1 ATCGATGCACATTC-AAGGAG-TGCATCGATGCA-TATTCATGATGT
34958 ATCGATGCA
1 ATCGATGCA
34967 TTATGCACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 27 0.57
45 16 0.34
46 4 0.09
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGATGCATATTCATGATGT
Found at i:43946 original size:13 final size:13
Alignment explanation
Indices: 43928--43952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43918 ACATTCGCGG
43928 ATATGAAGACTGC
1 ATATGAAGACTGC
43941 ATATGAAGACTG
1 ATATGAAGACTG
43953 TTCAACGATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATATGAAGACTGC
Found at i:45036 original size:28 final size:27
Alignment explanation
Indices: 44996--45049 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
44986 TAAAATTATC
*
44996 AAATTACACAAAATAATTATTAAAAATA
1 AAATTACACAAAAGAA-TATTAAAAATA
* * *
45024 AAATTATATAAAAGAATGTTAAAAAT
1 AAATTACACAAAAGAATATTAAAAAT
45050 TCAACTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (27 bp):
AAATTACACAAAAGAATATTAAAAATA
Found at i:47347 original size:12 final size:12
Alignment explanation
Indices: 47332--47377 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
47322 CGGTTTTTTT
*
47332 ACCGGATAAAAA
1 ACCGGTTAAAAA
47344 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
47359 ACCGGTTAAAAA
1 ACCGGTTAAAAA
47371 ACCGGTT
1 ACCGGTT
47378 TTTATCTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:47359 original size:15 final size:13
Alignment explanation
Indices: 47338--47378 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
47328 TTTTACCGGA
47338 TAAAAAACCGGTT
1 TAAAAAACCGGTT
47351 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
47365 TAAAAAACCGGTT
1 TAAAAAACCGGTT
47378 T
1 T
47379 TTATCTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:49690 original size:21 final size:21
Alignment explanation
Indices: 49666--49705 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49656 TTTATTTTAT
49666 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
49687 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
49706 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:49741 original size:32 final size:33
Alignment explanation
Indices: 49700--49797 Score: 128
Period size: 32 Copynumber: 3.0 Consensus size: 33
49690 TTTGTTTCAA
*
49700 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTAAAT
49732 TTATCGAACTTGGAAG-TTTTAAGTATTTAAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTAAAT
** * * *
49764 TTATTAAACTTGGAAGTATTTAAATATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTAAAT
49797 T
1 T
49798 ATGTTGAGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
32 40 0.69
33 18 0.31
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTAAAT
Found at i:49826 original size:13 final size:13
Alignment explanation
Indices: 49808--49837 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
49798 ATGTTGAGTT
49808 AATTAAGTATTTC
1 AATTAAGTATTTC
*
49821 AATTAAGTATTTG
1 AATTAAGTATTTC
49834 AATT
1 AATT
49838 TATCGAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (13 bp):
AATTAAGTATTTC
Found at i:50083 original size:21 final size:21
Alignment explanation
Indices: 50033--50085 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
50023 TCGAGCGTGG
* *
50033 GGGAATCGATATCCTCTCATA
1 GGGAATCGGTTTCCTCTCATA
50054 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTTCCTCTCATA
50075 GGGAATCGGTT
1 GGGAATCGGTT
50086 CCCTAAGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (21 bp):
GGGAATCGGTTTCCTCTCATA
Found at i:50280 original size:15 final size:15
Alignment explanation
Indices: 50255--50311 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
50245 ATCTAGAATA
*
50255 TTAAAATCGATTTTT
1 TTAAAACCGATTTTT
*
50270 TTATAACCGATTTTT
1 TTAAAACCGATTTTT
*
50285 TAAAAAAACCGATTTTT
1 T--TAAAACCGATTTTT
50302 TTAAAACCGA
1 TTAAAACCGA
50312 AACCAGTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 22 0.63
17 13 0.37
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (15 bp):
TTAAAACCGATTTTT
Found at i:50294 original size:17 final size:18
Alignment explanation
Indices: 50274--50307 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
50264 ATTTTTTTAT
50274 AACCGA-TTTTTTAAAAA
1 AACCGATTTTTTTAAAAA
50291 AACCGATTTTTTTAAAA
1 AACCGATTTTTTTAAAA
50308 CCGAAACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (18 bp):
AACCGATTTTTTTAAAAA
Found at i:58405 original size:20 final size:21
Alignment explanation
Indices: 58366--58405 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
58356 GGATTCTACC
58366 TAAAAATCACAAATATATATA
1 TAAAAATCACAAATATATATA
58387 TAAAAAT-ACTAAATA-ATAT
1 TAAAAATCAC-AAATATATAT
58406 CATTTGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAATCACAAATATATATA
Found at i:58762 original size:19 final size:19
Alignment explanation
Indices: 58738--58788 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
58728 GTATATGACC
*
58738 GTTGAGGCTGTTAATGGTG
1 GTTGAGGTTGTTAATGGTG
58757 GTTGAGGTTGTTAATGGTG
1 GTTGAGGTTGTTAATGGTG
58776 GTTGAGGTTGTTA
1 GTTGAGGTTGTTA
58789 GAGTTGTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (19 bp):
GTTGAGGTTGTTAATGGTG
Found at i:59364 original size:3 final size:3
Alignment explanation
Indices: 59356--59427 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
59346 GAGAAAGTGG
59356 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
59404 ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
59428 TTGTGGGTCC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.