Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000284.1 Hibiscus syriacus cultivar Beakdansim tig00000526_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: 75887
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:6299 original size:21 final size:21
Alignment explanation
Indices: 6275--6318 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
6265 GTGTGAGGGG
6275 TGAAGGAAAACAAGTTTATGA
1 TGAAGGAAAACAAGTTTATGA
6296 TGAAGGAAAACAAGTTTATGA
1 TGAAGGAAAACAAGTTTATGA
6317 TG
1 TG
6319 TTGAAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.25, T:0.25
Consensus pattern (21 bp):
TGAAGGAAAACAAGTTTATGA
Found at i:6622 original size:14 final size:14
Alignment explanation
Indices: 6603--6636 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6593 ACCCAAACCA
6603 AACCAGTATAGTCG
1 AACCAGTATAGTCG
*
6617 AACCAGTCTAGTCG
1 AACCAGTATAGTCG
*
6631 ACCCAG
1 AACCAG
6637 CCAAGCCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (14 bp):
AACCAGTATAGTCG
Found at i:11449 original size:47 final size:47
Alignment explanation
Indices: 11379--11470 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
11369 GTATGAATGT
* *
11379 GAGTTTCACAGGCTAAGTTGATTTGCATCGAAGTTGTTTCCAACCGA
1 GAGTTTCACAGGATAAGTCGATTTGCATCGAAGTTGTTTCCAACCGA
* *
11426 GAGTTTTACAGGATAAGTCGATTTGCATTGAAGTTGTTTCCAACC
1 GAGTTTCACAGGATAAGTCGATTTGCATCGAAGTTGTTTCCAACC
11471 TAGAAAGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (47 bp):
GAGTTTCACAGGATAAGTCGATTTGCATCGAAGTTGTTTCCAACCGA
Found at i:26043 original size:18 final size:18
Alignment explanation
Indices: 26020--26054 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
26010 ACACTAGAGG
*
26020 ATATTGATATTCAACTAT
1 ATATTGAGATTCAACTAT
26038 ATATTGAGATTCAACTA
1 ATATTGAGATTCAACTA
26055 GATCTGAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (18 bp):
ATATTGAGATTCAACTAT
Found at i:30350 original size:66 final size:66
Alignment explanation
Indices: 30212--30969 Score: 1331
Period size: 66 Copynumber: 11.5 Consensus size: 66
30202 GCTGCCACCC
* * * * * * * *
30212 AGGGAATATCACAT-ATGGGGATGTTGATCCGTTGAATCGAAGCAAACTT-TTCCACTTACTTTA
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30275 A
66 A
* *
30276 AGGGAATATCAAATCTTGGAGAAGTTAATCCATTGAATCGAAGCAAACTTGTTCCACTTACTCTG
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30341 A
66 A
* * * *
30342 ATGGAATATCAAATCTTGGAGAAATTGATCCATTGAATCGAAACAGATTTGTTCCACTTACTCTG
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30407 A
66 A
* *
30408 AGGGAATATCAAATCTTAGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTATTCTG
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30473 A
66 A
30474 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30539 A
66 A
30540 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30605 A
66 A
*
30606 AGGGAATATCAAATCCTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30671 A
66 A
30672 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30737 A
66 A
*
30738 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTAAATCGAAGCAGACTTGTTCCACTTACTCTG
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30803 A
66 A
30804 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30869 A
66 A
*
30870 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTATTCCACTTACTCTG
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
30935 A
66 A
30936 AGGGAATATCAAATCTTGGAGAAGTTGATCCATT
1 AGGGAATATCAAATCTTGGAGAAGTTGATCCATT
30970 AAATTGGGAT
Statistics
Matches: 665, Mismatches: 27, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
64 13 0.02
65 30 0.05
66 622 0.94
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (66 bp):
AGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGACTTGTTCCACTTACTCTG
A
Found at i:32187 original size:12 final size:12
Alignment explanation
Indices: 32172--32213 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
32162 TTTTTCTTTC
32172 TTTTTT-TTCAT
1 TTTTTTATTCAT
32183 TTTTTTCCATTCAT
1 TTTTTT--ATTCAT
*
32197 TTTTCTATTCAT
1 TTTTTTATTCAT
32209 TTTTT
1 TTTTT
32214 CAGGCGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 6 0.23
12 10 0.38
14 10 0.38
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTATTCAT
Found at i:32188 original size:22 final size:23
Alignment explanation
Indices: 32139--32213 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
32129 CCTTCTTTTA
**
32139 TTTTTCTTTTCTTTTTTCCTCA-T
1 TTTTTC-TTTCTTTTTTATTCATT
32162 TTTTTCTTTCTTTTTT-TTCATT
1 TTTTTCTTTCTTTTTTATTCATT
*
32184 TTTTTCCATTCATTTTTCTATTCATT
1 TTTTT-CTTTC-TTTTT-TATTCATT
32210 TTTT
1 TTTT
32214 CAGGCGAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 3 0.07
22 16 0.36
23 10 0.22
24 5 0.11
25 1 0.02
26 10 0.22
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTTCTTTCTTTTTTATTCATT
Found at i:32214 original size:34 final size:33
Alignment explanation
Indices: 32150--32215 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
32140 TTTTCTTTTC
*
32150 TTTTTTCCTCATTTTTTCTTTCTTTTTTTTCAT
1 TTTTTTCCTCATTTTTTCTTTCTATTTTTTCAT
32183 TTTTTTCCATTCA-TTTTTCTATTC-ATTTTTTCA
1 TTTTTTCC--TCATTTTTTCT-TTCTATTTTTTCA
32216 GGCGAAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 8 0.28
34 15 0.52
35 6 0.21
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (33 bp):
TTTTTTCCTCATTTTTTCTTTCTATTTTTTCAT
Found at i:35756 original size:25 final size:25
Alignment explanation
Indices: 35718--35788 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
35708 AATCTATCCC
*
35718 ATATCAAAATAGAATGAAAT-AATAA
1 ATAT-AAAAAAGAATGAAATAAATAA
35743 TATATAAAAAAGAAAT-AAATAAATAA
1 -ATATAAAAAAG-AATGAAATAAATAA
35769 ATA-AATAAAAGAATGGAAAT
1 ATATAA-AAAAGAAT-GAAAT
35789 GATGATATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
24 5 0.13
25 18 0.46
26 16 0.41
ACGTcount: A:0.68, C:0.01, G:0.08, T:0.23
Consensus pattern (25 bp):
ATATAAAAAAGAATGAAATAAATAA
Found at i:35764 original size:4 final size:4
Alignment explanation
Indices: 35724--35777 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
35714 TCCCATATCA
* *
35724 AAAT AGAAT GAAAT -AAT -AAT ATAT AAA- AAAG AAAT AAAT AAAT AAAT
1 AAAT A-AAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
35771 AAAT AAA
1 AAAT AAA
35778 AGAATGGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
3 9 0.21
4 27 0.63
5 6 0.14
6 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:45221 original size:26 final size:26
Alignment explanation
Indices: 45161--45221 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
45151 ATTTTTTCTG
* *
45161 ATTTAAAAATGAGATTGATTTCTCTT
1 ATTTAAAAACGAGATTGATTTCTCTA
* *
45187 ATATAAAAACGAGATTGGTTTCTCTA
1 ATTTAAAAACGAGATTGATTTCTCTA
*
45213 ATTTTAAAA
1 ATTTAAAAA
45222 GTATGACTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (26 bp):
ATTTAAAAACGAGATTGATTTCTCTA
Found at i:45432 original size:39 final size:38
Alignment explanation
Indices: 45389--45469 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 38
45379 TCCTTATAGT
* * * *
45389 AGGCTCCTCTGCTTCTTGCATAGGTTAAGTCTTTACCGC
1 AGGCTCCTCTGCTTCGTGCACAGGATAAGTCCTTACC-C
45428 AGGCTCCTCTGCTTCGTGCACAGGATAAGTCCTTACCC
1 AGGCTCCTCTGCTTCGTGCACAGGATAAGTCCTTACCC
45466 AGGC
1 AGGC
45470 ATTTATGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
38 5 0.13
39 33 0.87
ACGTcount: A:0.17, C:0.31, G:0.22, T:0.30
Consensus pattern (38 bp):
AGGCTCCTCTGCTTCGTGCACAGGATAAGTCCTTACCC
Found at i:50570 original size:15 final size:15
Alignment explanation
Indices: 50550--50578 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
50540 ATTATTTAAA
50550 TCTTAAAAATAATAT
1 TCTTAAAAATAATAT
50565 TCTTAAAAATAATA
1 TCTTAAAAATAATA
50579 ATCATAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TCTTAAAAATAATAT
Found at i:50589 original size:15 final size:15
Alignment explanation
Indices: 50548--50591 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
50538 ATATTATTTA
*
50548 AATCTTAAAAATAAT
1 AATCATAAAAATAAT
* *
50563 ATTCTTAAAAATAAT
1 AATCATAAAAATAAT
*
50578 AATCATAGAAATAA
1 AATCATAAAAATAA
50592 ATATAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (15 bp):
AATCATAAAAATAAT
Found at i:51759 original size:2 final size:2
Alignment explanation
Indices: 51748--51776 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
51738 GTCCATACAA
51748 AT AT AT -T 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
51777 TACTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:52921 original size:21 final size:21
Alignment explanation
Indices: 52892--52935 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
52882 TTTAATTTTT
* *
52892 TTATTTTTTATTATTTAAATG
1 TTATATTTTATTATATAAATG
*
52913 TTATATTTTATTATATATATG
1 TTATATTTTATTATATAAATG
52934 TT
1 TT
52936 TTTTTCTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
TTATATTTTATTATATAAATG
Found at i:52989 original size:2 final size:2
Alignment explanation
Indices: 52982--53023 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
52972 TTTTTCATTA
52982 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
53024 TTAGTTTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53173 original size:8 final size:8
Alignment explanation
Indices: 53160--53201 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
53150 TATATAAATA
53160 TTTTTATT
1 TTTTTATT
*
53168 TTTTTATA
1 TTTTTATT
*
53176 TATTTATT
1 TTTTTATT
53184 TATTTT-TT
1 T-TTTTATT
53192 TTTTTATT
1 TTTTTATT
53200 TT
1 TT
53202 GGCTTTTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 4 0.14
8 21 0.75
9 3 0.11
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTATT
Found at i:53900 original size:31 final size:31
Alignment explanation
Indices: 53862--53922 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
53852 CGGCTTTGCC
*
53862 AAAATAATCTTC-AACTGTTGATAATTTTACT
1 AAAATAATCTTCTAA-TGTCGATAATTTTACT
*
53893 AAAATAATCTTCTAATGTCGATGATTTTAC
1 AAAATAATCTTCTAATGTCGATAATTTTAC
53923 CAATATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (31 bp):
AAAATAATCTTCTAATGTCGATAATTTTACT
Found at i:55441 original size:20 final size:18
Alignment explanation
Indices: 55393--55443 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
55383 GCTTGATTAA
55393 TTTTTCAATAA-TTAAAAT
1 TTTTTC-ATAATTTAAAAT
*
55411 TTTTTATATAATTTATAATAT
1 TTTTT-CATAATTTA-AA-AT
55432 TTTTTCATAATT
1 TTTTTCATAATT
55444 CTGATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 9 0.33
19 3 0.11
20 8 0.30
21 7 0.26
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTCATAATTTAAAAT
Found at i:59900 original size:29 final size:30
Alignment explanation
Indices: 59846--59984 Score: 115
Period size: 30 Copynumber: 4.7 Consensus size: 30
59836 TAAGATTAAC
*
59846 AGAAACTT-GAGGACT-AAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
*
59874 AGAAACTTAAAGGACTATAATAG-AAAAAGGT
1 AGAAACTTAAAGGACTAAAATAGCAAAAA--T
*
59905 -GAAACTTAAAGGACTAAAATAGTAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* *** * **
59934 GGACTTTTAAAGGACTAAAATAGTAAAAGC
1 AGAAACTTAAAGGACTAAAATAGCAAAAAT
* * *
59964 AAAAATTTAAGGGACTAAAAT
1 AGAAACTTAAAGGACTAAAAT
59985 GGTATTAACA
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.09
29 12 0.13
30 66 0.72
31 6 0.07
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.21
Consensus pattern (30 bp):
AGAAACTTAAAGGACTAAAATAGCAAAAAT
Found at i:59933 original size:60 final size:58
Alignment explanation
Indices: 59847--59962 Score: 142
Period size: 60 Copynumber: 2.0 Consensus size: 58
59837 AAGATTAACA
* *
59847 GAAACTTGAGGACTAAATAGCAAAAATAGAAACTTAAAGGACTATAATAGAAAAAGGT
1 GAAACTTAAGGACTAAATAGCAAAAATAGAAACTTAAAGGACTAAAATAGAAAAAGGT
* * *** *
59905 GAAACTTAAAGGACTAAAATAGTAAAAATGGACTTTTAAAGGACTAAAATAGTAAAAG
1 GAAACTT-AAGGACT-AAATAGCAAAAATAGAAACTTAAAGGACTAAAATAGAAAAAG
59963 CAAAAATTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 7 0.15
59 6 0.12
60 35 0.73
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.21
Consensus pattern (58 bp):
GAAACTTAAGGACTAAATAGCAAAAATAGAAACTTAAAGGACTAAAATAGAAAAAGGT
Found at i:61489 original size:17 final size:17
Alignment explanation
Indices: 61467--61500 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
61457 AATAATAATA
61467 ATAATATTATTATTATT
1 ATAATATTATTATTATT
61484 ATAATATTATTATTATT
1 ATAATATTATTATTATT
61501 GTAGACCCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAATATTATTATTATT
Found at i:61848 original size:43 final size:42
Alignment explanation
Indices: 61787--61892 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 42
61777 AAGAGCGATA
* * *
61787 ACACGGTTCCTATGTGATGAGGACGACTGGT-TA-TCTAGGGGTG
1 ACACGGTTCCTACGTGATGAGGA-GA--GGTCTACTCGAGGGATG
*
61830 ACACGGCTCCTACGTGATGA-G-GAGGTCTACTCGAGGGATG
1 ACACGGTTCCTACGTGATGAGGAGAGGTCTACTCGAGGGATG
61870 ACACGGTTCCTACGTGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
61893 TGATATACCA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
38 3 0.06
39 2 0.04
40 29 0.54
41 1 0.02
42 1 0.02
43 18 0.33
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.24
Consensus pattern (42 bp):
ACACGGTTCCTACGTGATGAGGAGAGGTCTACTCGAGGGATG
Found at i:62038 original size:129 final size:131
Alignment explanation
Indices: 61802--62038 Score: 309
Period size: 129 Copynumber: 1.8 Consensus size: 131
61792 GTTCCTATGT
* * * *
61802 GATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTACTCGAGGG
1 GATGAGGACGACTGGTTATCTAGAGGTGACACGGCTCCTACGCGATGAAGAAGTCTACTCGAGGG
** * * *
61867 ATGACACGGTTCCTACGTGATGAGGATGATATACCATCTTTAGGGATGCCATCATGGTTCCTGCG
66 ATGACACAATTCCTACGTGATGAGGACGACATACAATCTTTAGGGATGCCATCATGGTTCCTGCG
61932 C
131 C
* **
61933 GATGAGGACGACTGGTTATCTA-AGGTGACACGGTTCCTACGCGATGAAGACAGT-TGGTCG-GG
1 GATGAGGACGACTGGTTATCTAGAGGTGACACGGCTCCTACGCGATGAAGA-AGTCTACTCGAGG
* * *
61995 GATGATACAATTTCTACGTGATGAGGACGGCATACAATCTTTAG
65 GATGACACAATTCCTACGTGATGAGGACGACATACAATCTTTAG
62039 TGATTTTGGT
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
129 38 0.42
130 28 0.31
131 24 0.27
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.25
Consensus pattern (131 bp):
GATGAGGACGACTGGTTATCTAGAGGTGACACGGCTCCTACGCGATGAAGAAGTCTACTCGAGGG
ATGACACAATTCCTACGTGATGAGGACGACATACAATCTTTAGGGATGCCATCATGGTTCCTGCG
C
Found at i:62153 original size:35 final size:35
Alignment explanation
Indices: 62113--62204 Score: 159
Period size: 35 Copynumber: 2.6 Consensus size: 35
62103 ATAAAATTCT
62113 TTTCAAGGGAAACGATCTCAAAGATGTTTATTTTG
1 TTTCAAGGGAAACGATCTCAAAGATGTTTATTTTG
*
62148 TTTCAAGGGAAACGATCTCAAAGATGTTTGTTTTG
1 TTTCAAGGGAAACGATCTCAAAGATGTTTATTTTG
62183 TTTCAAGGGAAACAGA-CTCAAA
1 TTTCAAGGGAAAC-GATCTCAAA
62205 AGTAGGTGTT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
35 53 0.96
36 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (35 bp):
TTTCAAGGGAAACGATCTCAAAGATGTTTATTTTG
Found at i:62247 original size:65 final size:63
Alignment explanation
Indices: 62178--62322 Score: 157
Period size: 63 Copynumber: 2.3 Consensus size: 63
62168 AAGATGTTTG
* * * *
62178 TTTTGTTTCAAGGGAAACAGACTCAAAAGTAGGTGTTTCAAGAGAAACTGTCTCGAAAAACAAAA
1 TTTTGTTTCAAAGAAAACAAACTC-AAAG-AGGTGTTTCAAAAGAAACTGTCTCGAAAAACAAAA
** * * * *
62243 TTTTGTTTCAAAGAAAACAAACTCAAAGATTTTTTTTAAAAGAAACTGTCTCGAGAGACAAAA
1 TTTTGTTTCAAAGAAAACAAACTCAAAGAGGTGTTTCAAAAGAAACTGTCTCGAAAAACAAAA
**
62306 -TTTGTTTTTAAGAAAAC
1 TTTTGTTTCAAAGAAAAC
62323 TGTCTCTAGC
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
62 15 0.22
63 28 0.41
64 4 0.06
65 21 0.31
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (63 bp):
TTTTGTTTCAAAGAAAACAAACTCAAAGAGGTGTTTCAAAAGAAACTGTCTCGAAAAACAAAA
Found at i:63539 original size:11 final size:12
Alignment explanation
Indices: 63519--63607 Score: 69
Period size: 13 Copynumber: 7.2 Consensus size: 12
63509 TTGTCCAATA
63519 TTTT-TCTTTGT
1 TTTTCTCTTTGT
63530 TTTTCT-TTTGT
1 TTTTCTCTTTGT
*
63541 TCTTTTTCTTTGCT
1 T-TTTCTCTTTG-T
63555 TTTTCTCTTTGTT
1 TTTTCTCTTTG-T
63568 TATGTTCTCTTTGCT
1 T-T-TTCTCTTTG-T
* *
63583 CTTTGT-TTT-T
1 TTTTCTCTTTGT
63593 TTTTCTCTTTGT
1 TTTTCTCTTTGT
63605 TTT
1 TTT
63608 GATTGGATCT
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
10 5 0.08
11 13 0.21
12 12 0.19
13 18 0.29
14 4 0.06
15 10 0.16
ACGTcount: A:0.01, C:0.15, G:0.09, T:0.75
Consensus pattern (12 bp):
TTTTCTCTTTGT
Found at i:65038 original size:14 final size:14
Alignment explanation
Indices: 64983--65039 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
64973 AAAAATTGTA
64983 ATAA-AATAATTATT
1 ATAATAATAA-TATT
* **
64997 ATTATTAATAATAAG
1 A-TAATAATAATATT
65012 ATAATAATAATATT
1 ATAATAATAATATT
*
65026 ATAATATTAATATT
1 ATAATAATAATATT
65040 TTTGTAGACC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
14 24 0.71
15 5 0.15
16 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
ATAATAATAATATT
Found at i:68710 original size:62 final size:61
Alignment explanation
Indices: 68607--68725 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 61
68597 ACTCGATGTA
* *
68607 ATCCCTATCTTTAATCCTACTATCCATCCACAAGATCATGGATAGAAATGACCCAATGGTCC
1 ATCCCTACCTTTAATCCGACTATCCATCCACAAGATCATGGA-AGAAATGACCCAATGGTCC
* *
68669 ATCCCTACCTTTAATCCGACTATCCATCCACATGATTATGGAAGAAATGACCCAATG
1 ATCCCTACCTTTAATCCGACTATCCATCCACAAGATCATGGAAGAAATGACCCAATG
68726 TCATTGAGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
61 15 0.28
62 38 0.72
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (61 bp):
ATCCCTACCTTTAATCCGACTATCCATCCACAAGATCATGGAAGAAATGACCCAATGGTCC
Found at i:69515 original size:30 final size:30
Alignment explanation
Indices: 69478--69565 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 30
69468 ATAATTATGA
69478 TTAATAATAAATATTAAAAAAA-TAAAACC
1 TTAATAATAAATATTAAAAAAATTAAAACC
* *
69507 TATAATAATAAGTATTAGAAAAAAATTAAATCC
1 T-TAATAATAAATATT--AAAAAAATTAAAACC
*
69540 TTAATAATACATATTAAAAATAATTA
1 TTAATAATAAATATTAAAAA-AATTA
69566 GACTTTGTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
29 1 0.02
30 18 0.36
31 5 0.10
32 19 0.38
33 7 0.14
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (30 bp):
TTAATAATAAATATTAAAAAAATTAAAACC
Found at i:72872 original size:3 final size:3
Alignment explanation
Indices: 72864--72993 Score: 121
Period size: 3 Copynumber: 44.7 Consensus size: 3
72854 TTGTAATGTA
72864 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
72910 AAT AAT AAT -AT AAT TAT AA- AAT AAAT AAT AGT AAT AA- ATT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT
* * * *
72954 AA- AAT AA- AAT ATT AAT ATT AAT ATT AAT AAA AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
72994 CAAATGGATA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
2 13 0.12
3 83 0.80
4 8 0.08
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:73853 original size:118 final size:118
Alignment explanation
Indices: 73353--73922 Score: 715
Period size: 118 Copynumber: 4.7 Consensus size: 118
73343 GAATTAAGGC
73353 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * ** *
73417 TGAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGAT-AGAGTC-ATGCAA
66 TGAACTCTTCTGGAAATGTTGATGCTGATC-A-AT-C--GAGTGATGA-ATTCGA-GCAA
** * * *
73475 AAGACTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAAATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* ** * * *
73539 TGAACT-TTCTATAGAAAAT-TTGATGCTGATTTATCTCTTTCTA-TGATAGAA-TCAAGAAA
66 TGAACTCTTC--T-GGAAATGTTGATGCTG----A--TCAATCGAGTGAT-GAATTCGAGCAA
*
73598 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
73663 TGAACTTTCTCTGGAAAAGTTGATGCTGATCCATCGAGTGATGAATTCGAGCAA
66 TGAACTCT-TCTGGAAATGTTGATGCTGATCAATCGAGTGATGAATTCGAGCAA
*
73717 AAGGTTGATCAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
73782 TGAACTCTTCTGGAAATGTTGATGCTGATCAATCGAGTGATGAATTCGAGCAA
66 TGAACTCTTCTGGAAATGTTGATGCTGATCAATCGAGTGATGAATTCGAGCAA
*
73835 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
73900 TGAACTCTTCCGGAAATGTTGAT
66 TGAACTCTTCTGGAAATGTTGAT
73923 CCATTGAGTG
Statistics
Matches: 398, Mismatches: 31, Indels: 42
0.85 0.07 0.09
Matches are distributed among these distances:
118 136 0.34
119 80 0.20
120 1 0.00
121 3 0.01
122 59 0.15
123 64 0.16
124 46 0.12
125 2 0.01
126 3 0.01
127 2 0.01
129 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (118 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTTCTGGAAATGTTGATGCTGATCAATCGAGTGATGAATTCGAGCAA
Found at i:74138 original size:22 final size:22
Alignment explanation
Indices: 74113--74170 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
74103 AAATCCAATA
* * *
74113 AATCTTTCTTCTTTGAAAAGAT
1 AATCTATCATCTTTGAAAAGAG
*
74135 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAAAGAG
74157 AATCTATCATCTTT
1 AATCTATCATCTTT
74171 AAAGAATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:74565 original size:20 final size:20
Alignment explanation
Indices: 74518--74565 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
74508 ATTGCAACAT
*
74518 TGGTTCAACACCATAATTAC
1 TGGTTCATCACCATAATTAC
*
74538 TGGTTCATCACCATACTTAC
1 TGGTTCATCACCATAATTAC
74558 TGGTTCAT
1 TGGTTCAT
74566 AAACATTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (20 bp):
TGGTTCATCACCATAATTAC
Found at i:75203 original size:13 final size:14
Alignment explanation
Indices: 75184--75216 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
75174 ATTTTCTCTC
75184 TCATTTTTT-ATTT
1 TCATTTTTTCATTT
75197 T-ATTTTTTCATTT
1 TCATTTTTTCATTT
75210 TCATTTT
1 TCATTTT
75217 CATTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 6 0.33
14 5 0.28
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (14 bp):
TCATTTTTTCATTT
Found at i:75207 original size:20 final size:20
Alignment explanation
Indices: 75188--75224 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
75178 TCTCTCTCAT
*
75188 TTTTTATTTT-ATTTTTTCA
1 TTTTCATTTTCATTTTTTCA
75207 TTTTCATTTTCATTTTTT
1 TTTTCATTTTCATTTTTT
75225 TCTTCTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCATTTTCATTTTTTCA
Done.