Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005804.1 Hibiscus syriacus cultivar Beakdansim tig00013610_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: 25159
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:331 original size:29 final size:29
Alignment explanation
Indices: 294--439 Score: 177
Period size: 29 Copynumber: 5.1 Consensus size: 29
284 CCCCAACACC
*
294 CCTACAAGGTCGCCAAGCACTCCCAGCGA
1 CCTACAAGGTCGCCAAGCACTCCCGGCGA
* *
323 CCTACAAGGTCGCCAAACACTCCCAGCGA
1 CCTACAAGGTCGCCAAGCACTCCCGGCGA
*
352 CCTACAAGGTCGCCATGCACTCCCGGCGA
1 CCTACAAGGTCGCCAAGCACTCCCGGCGA
*** *
381 CCTTGTAGGTCGCCAAGCAAT-CCGGCGA
1 CCTACAAGGTCGCCAAGCACTCCCGGCGA
*** *
409 CCTTGTAGGTCGCCAAGCAATCCCGGCGA
1 CCTACAAGGTCGCCAAGCACTCCCGGCGA
438 CC
1 CC
440 AAGCCTCGAC
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
28 28 0.26
29 79 0.74
ACGTcount: A:0.24, C:0.39, G:0.23, T:0.14
Consensus pattern (29 bp):
CCTACAAGGTCGCCAAGCACTCCCGGCGA
Found at i:510 original size:32 final size:32
Alignment explanation
Indices: 474--534 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
464 AACTTAACCT
*
474 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
1 GCTCCCTCGTGCATGGGTTGCAACCATAGCTG
506 GCTCCCTCGTGCATGGGTTGCAACCATAG
1 GCTCCCTCGTGCATGGGTTGCAACCATAG
535 TGGGAGATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.15, C:0.31, G:0.28, T:0.26
Consensus pattern (32 bp):
GCTCCCTCGTGCATGGGTTGCAACCATAGCTG
Found at i:554 original size:22 final size:23
Alignment explanation
Indices: 524--566 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
514 GTGCATGGGT
524 TGCAACCATAG-TGGGAGATTCC
1 TGCAACCATAGCTGGGAGATTCC
*
546 TGCATCCATAGCTGGGAGATT
1 TGCAACCATAGCTGGGAGATT
567 GTAGCCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (23 bp):
TGCAACCATAGCTGGGAGATTCC
Found at i:1098 original size:44 final size:46
Alignment explanation
Indices: 1001--1099 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 46
991 TTTAAGTTAT
* * *
1001 ATTATATTAGTTTGTTAGTTAAGTTATATATTATATATATAAAAATTC
1 ATTA-ATTAGTTTCTTAGTTAAGTTATATA-TATATATAAAAAAATTA
*
1049 GTTAATTAGTTTCTTAGTTTAAGTTAT-TA-A-ATATAAAAAAATTA
1 ATTAATTAGTTTCTTAG-TTAAGTTATATATATATATAAAAAAATTA
1093 ATTAATT
1 ATTAATT
1100 TGTTAGTATC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
44 18 0.40
45 1 0.02
47 14 0.31
48 12 0.27
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.48
Consensus pattern (46 bp):
ATTAATTAGTTTCTTAGTTAAGTTATATATATATATAAAAAAATTA
Found at i:4523 original size:21 final size:21
Alignment explanation
Indices: 4496--4583 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 21
4486 AGATTTAGTA
*
4496 ATGATTAGTAATGATGAAATT
1 ATGATTAGTAATAATGAAATT
* * *
4517 ATTATTAATATTTAATG--ATT
1 ATGATTAGTA-ATAATGAAATT
* * * *
4537 -TGA-TAGTAATGATGTAGTA
1 ATGATTAGTAATAATGAAATT
4556 ATGATTAGTAATAATGAAATT
1 ATGATTAGTAATAATGAAATT
*
4577 ATTATTA
1 ATGATTA
4584 ATATTTAATG
Statistics
Matches: 47, Mismatches: 15, Indels: 10
0.65 0.21 0.14
Matches are distributed among these distances:
17 4 0.09
18 4 0.09
19 3 0.06
20 6 0.13
21 26 0.55
22 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (21 bp):
ATGATTAGTAATAATGAAATT
Found at i:4562 original size:60 final size:59
Alignment explanation
Indices: 4490--5046 Score: 655
Period size: 48 Copynumber: 10.1 Consensus size: 59
4480 TTTATAAGAT
*
4490 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
4549 TGTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 T-TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
4609 TTTAGTAATGA-TAGTAATAATG--ATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
4666 -TAG---T-A--A-TAAT-A--AAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
4714 TTAGTAATGATTAGTAATAATGAAATTATT-TTAATATTTAATGATTTTATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
4772 TTAGT-A--A-T-GTAAT-ATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
* *
4825 TTTAATAATGATTAGTAATAATGAAATT-CTATTAATATTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
* *
4884 TTTAGTAATGATTAGTAATAATAAAATTATTATTAAT-TTT--T-A----AT-G-ATTGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
4934 -TAGTAATGATTAGTAATAATGAAATTA-TATTAATTTTTAATGATTTG--A-T-A--A
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
4985 -T--T-ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
5040 TTA-TAAT
1 TTAGTAAT
5047 AATGAAATTA
Statistics
Matches: 438, Mismatches: 16, Indels: 89
0.81 0.03 0.16
Matches are distributed among these distances:
47 7 0.02
48 87 0.20
49 28 0.06
50 6 0.01
51 6 0.01
52 15 0.03
53 34 0.08
54 5 0.01
55 7 0.02
56 6 0.01
57 38 0.09
58 34 0.08
59 84 0.19
60 80 0.18
61 1 0.00
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
Found at i:4697 original size:48 final size:49
Alignment explanation
Indices: 4611--5186 Score: 561
Period size: 48 Copynumber: 11.3 Consensus size: 49
4601 ATTAATGATT
*
4611 TAGTAATGA-TAGTAATAAT--GATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
4657 TAGTAATGA-TAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
* * *
4705 TAGTAATGATTAGTAATGATTAGTAATAATGAAATTATTTTAATATTTAATGATTTTA
1 TAGTAATGATTAGTAAT-A--A-TAA-AAT--TATTA--TTAATTTTTAATGATTTGA
* *
4763 TAGTAATGATTAGTAATGTAATATGAAATTGTTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAA--TAATA--AAATTATTATTAATTTTTAATGATTTGA
* * *
4816 TAGTAATGATTTAATAATGATTAGTAATAATGAAATTCTATTAATATTTAATGATTTGATAGTAA
1 TAGTAATGA-TTAGTAAT-A--A-TAA-AAT--TA-T-TATTAAT-TTT--T-A-ATGAT--T--
4881 TGA
47 TGA
4884 TTTAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGA-TTGA
1 --TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
*
4934 TAGTAATGATTAGTAATAATGAAATTA-TATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
* * *
4982 TAATTATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
* *
5031 TAGTAATGATTA-TAATAAT-GAA--ATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
*
5076 TA--AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGA-TTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
* *
5122 TAGTAATGATTAGTAATAAT-AATTTATTATTAA-TATTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
*
5169 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
5187 GATTTGATAG
Statistics
Matches: 456, Mismatches: 27, Indels: 92
0.79 0.05 0.16
Matches are distributed among these distances:
43 8 0.02
44 7 0.02
45 26 0.06
46 33 0.07
47 59 0.13
48 121 0.27
49 38 0.08
50 4 0.01
52 3 0.01
53 31 0.07
54 10 0.02
55 10 0.02
56 9 0.02
57 5 0.01
58 35 0.08
59 11 0.02
60 10 0.02
61 1 0.00
62 2 0.00
63 1 0.00
64 7 0.02
65 3 0.01
66 2 0.00
68 4 0.01
69 7 0.02
70 9 0.02
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
Found at i:4718 original size:10 final size:10
Alignment explanation
Indices: 4705--4731 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
4695 AATGATTTGA
4705 TAGTAATGAT
1 TAGTAATGAT
4715 TAGTAATGAT
1 TAGTAATGAT
4725 TAGTAAT
1 TAGTAAT
4732 AATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:4754 original size:58 final size:59
Alignment explanation
Indices: 4657--5046 Score: 448
Period size: 59 Copynumber: 7.1 Consensus size: 59
4647 AATGATTTGA
* *
4657 TAGTAATGA-TAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGAT
*
4715 TAGTAATGATTAGTAATAATGAAATTATT-TTAATATTTAATGATTTTATAGTAATGAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGAT
*
4773 TAGT-A--A-T-GTAAT-ATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA-T
* *
4827 TAATAATGATTAGTAATAATGAAATT-CTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA-T
* *
4886 TAGTAATGATTAGTAATAATAAAATTATTATTAAT-TTT--T-A----AT-G-ATTGA-
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGAT
*
4934 TAGTAATGATTAGTAATAATGAAATTA-TATTAATTTTTAATGATTTG--A-T-A--A-
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGAT
*
4985 T--T-ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGAT
5041 TA-TAAT
1 TAGTAAT
5047 AATGAAATTA
Statistics
Matches: 289, Mismatches: 13, Indels: 60
0.80 0.04 0.17
Matches are distributed among these distances:
47 7 0.02
48 51 0.18
49 21 0.07
50 5 0.02
51 5 0.02
52 13 0.04
53 33 0.11
54 5 0.02
55 3 0.01
56 2 0.01
57 4 0.01
58 43 0.15
59 82 0.28
60 15 0.05
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (59 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGAT
Found at i:4881 original size:21 final size:20
Alignment explanation
Indices: 4798--4887 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 20
4788 AAATTGTTAT
4798 TAATATTTAATGATTTGATAG
1 TAATATTTAAT-ATTTGATAG
*
4819 TAATGATTTAATA-ATGATTAG
1 TAAT-ATTTAATATTTGA-TAG
* *
4840 TAATAATGAA-ATTCT-AT--
1 TAATATTTAATATT-TGATAG
4857 TAATATTTAATGATTTGATAG
1 TAATATTTAAT-ATTTGATAG
4878 TAATGATTTA
1 TAAT-ATTTA
4888 GTAATGATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 19
0.68 0.08 0.24
Matches are distributed among these distances:
17 8 0.15
18 1 0.02
19 7 0.13
20 8 0.15
21 17 0.32
22 12 0.23
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (20 bp):
TAATATTTAATATTTGATAG
Found at i:4974 original size:21 final size:21
Alignment explanation
Indices: 4950--5025 Score: 55
Period size: 22 Copynumber: 3.3 Consensus size: 21
4940 TGATTAGTAA
4950 TAATGAAATTATATTAATTTT
1 TAATGAAATTATATTAATTTT
* *
4971 TAATG-ATTTGATAATTATGATTAGTAA
1 TAATGAAATT-AT-ATTA--ATT--T-T
4998 TAATGAAATTATTATTAATTTT
1 TAATGAAATTA-TATTAATTTT
5020 TAATGA
1 TAATGA
5026 TTTGATAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 17
0.67 0.06 0.27
Matches are distributed among these distances:
20 3 0.07
21 7 0.17
22 10 0.24
23 1 0.02
24 3 0.07
25 3 0.07
26 1 0.02
27 10 0.24
28 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (21 bp):
TAATGAAATTATATTAATTTT
Found at i:5161 original size:20 final size:20
Alignment explanation
Indices: 5138--5175 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5128 TGATTAGTAA
5138 TAATAATTT-ATTATTAATAT
1 TAATAATTTGA-TATTAATAT
*
5158 TAATGATTTGATATTAAT
1 TAATAATTTGATATTAAT
5176 GATTTAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TAATAATTTGATATTAATAT
Found at i:5171 original size:14 final size:14
Alignment explanation
Indices: 5158--5205 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
5148 TTATTAATAT
*
5158 TAATGATTTGATAT
1 TAATGATTTGATAG
5172 TAATGA-TT--TAG
1 TAATGATTTGATAG
5183 TAATGATTTGATAG
1 TAATGATTTGATAG
5197 TAATGATTT
1 TAATGATTT
5206 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:5187 original size:25 final size:25
Alignment explanation
Indices: 5158--5206 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5148 TTATTAATAT
*
5158 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
5183 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
5207 CGACTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:5206 original size:140 final size:140
Alignment explanation
Indices: 4886--5188 Score: 436
Period size: 140 Copynumber: 2.1 Consensus size: 140
4876 AGTAATGATT
* *
4886 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTGATAGTAATGATTAGTAAT
1 TAGTAATGATTA-TAATAAT-GAA--ATTATTAATATTTAATGATTGATAG-AATGATTAGTAAT
*
4951 AATGAAATTATATTAATTTTTAATGATTTGATAATTATGATTAGTAATAATGAAATTATTATTAA
61 AATGAAATTATATTAATTTTTAATGATTTGATAATAATGATTAGTAATAATGAAATTATTATTAA
*
5016 TTTTTAATGATTTGA
126 TTATTAATGATTTGA
5031 TAGTAATGATTATAATAATGAAATTATTAATATTTAATGATTTGATA-AATGATTAGTAATAATG
1 TAGTAATGATTATAATAATGAAATTATTAATATTTAATGA-TTGATAGAATGATTAGTAATAATG
* *
5095 AAATTATTATTAATTTTTAATGA-TTGATAGTAATGATTAGTAATAAT-AATTTATTATTAA-TA
65 AAATTA-TATTAATTTTTAATGATTTGATAATAATGATTAGTAATAATGAAATTATTATTAATTA
5157 TTAATGATTTGA
129 TTAATGATTTGA
* *
5169 TATTAATGATT-TAGTAATGA
1 TAGTAATGATTATAATAATGA
5189 TTTGATAGTA
Statistics
Matches: 148, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
137 8 0.05
138 23 0.16
139 12 0.08
140 45 0.30
141 33 0.22
142 6 0.04
143 2 0.01
144 7 0.05
145 12 0.08
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (140 bp):
TAGTAATGATTATAATAATGAAATTATTAATATTTAATGATTGATAGAATGATTAGTAATAATGA
AATTATATTAATTTTTAATGATTTGATAATAATGATTAGTAATAATGAAATTATTATTAATTATT
AATGATTTGA
Found at i:7952 original size:26 final size:27
Alignment explanation
Indices: 7904--7964 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
7894 CCCTTTCTTT
*
7904 CTTTCTCTCGGCTGCAATTTCTTCT-CC
1 CTTTCT-TCGGCTGCAATCTCTTCTCCC
*
7931 CTTTCTTCTGCTGCAATCTCTTCTCCC
1 CTTTCTTCGGCTGCAATCTCTTCTCCC
7958 CTTTCTT
1 CTTTCTT
7965 TGTTTTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.07, C:0.38, G:0.08, T:0.48
Consensus pattern (27 bp):
CTTTCTTCGGCTGCAATCTCTTCTCCC
Found at i:8304 original size:29 final size:29
Alignment explanation
Indices: 8226--8307 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
8216 CTTGGTCGGC
* *** *
8226 GGGACTGCTTGGCGACCTACAAGGTCGCT
1 GGGAGTGCTTGGCGACCTTGTAGGTCACT
* *
8255 GGGAGTGCATGGCGACGTTGTAGGTCACT
1 GGGAGTGCTTGGCGACCTTGTAGGTCACT
8284 GGGAGTGCTTGGCGACCTTGTAGG
1 GGGAGTGCTTGGCGACCTTGTAGG
8308 GGTGTTGGGG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.16, C:0.21, G:0.40, T:0.23
Consensus pattern (29 bp):
GGGAGTGCTTGGCGACCTTGTAGGTCACT
Found at i:8705 original size:4 final size:4
Alignment explanation
Indices: 8685--11068 Score: 3288
Period size: 4 Copynumber: 596.8 Consensus size: 4
8675 CAAGTAGAAT
* *
8685 ATAC AAAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
8733 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
8781 ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATGC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
8829 ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATGC ATGC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
8877 ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
8925 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
8973 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
9021 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
9069 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
9117 ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATGC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
9165 ATGC ATAC ATAC ATAC ATAC ATGC ATAC ATGC ATGC ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * *
9213 ATGC ATAC ATAC ATAC ATGC ATGC ATAC ATTC ATGC ATGC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
9261 ATAC ATGC ATAC ATGC ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
9309 ATAC ATAC ATAC ATGC ATAC ATAC ATGC ATAC ATGC ATGC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
9357 ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
9405 ATAC ATAC ATAC ATAC ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
9453 ATGC ATAC ATGC ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
9501 ATGC ATGC ATAC ATGC ATAC ATGC ATAC ATAC ATAC ATGC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * * * *
9549 ATGC ATGC ATGC ATGC ATAC ATAC ATGC ATAC ATGC ATGC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
9597 ATAC ATGC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
9645 ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
9693 ATGC ATAC ATAC ATGC ATAC ATGC ATGC ATAC ATGC ATGC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
9741 ATAC ATAT ATAC ATAC ATGC ATAC ATGC ATGC ATAC ATGC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
9789 ATAA ATTC ATAC ATGC ATGC ATATGC ATGC ATGC ATGC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATA--C ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
9839 TATAC ATAC ATGC ATAC ATAC ATGC ATAC ATGC ATGC ATGC ATAC ATAC
1 -ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
9888 ATAC ATAC ATGC ATGC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
9936 ATAC ATAC ATAC ATAC ATAC -TAC ATAC ATAC ATAC ATGC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
9983 ATGC ATAC ATGC AT-C ATAC ATAC ATAC ATGC ATAC ATGC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
10030 ATGC ATAC ATGC ATAC ATAC ATAC ATGC ATAC ATAC ATGC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * ** * * * *
10078 ATGC ATAC ATAC ATGC ATAC ATGT ATGC ATGC ATGC ATAC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
10126 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATGC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
10174 ATAC ATAC ATGC ATAC ATGC ATAC ATGC ATGC ATAC ATGC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
10222 ATAC ATAC ATAC ATGC ATGC ATAC ATGC ATGC ATGC ATGC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
10270 ATGC ATAC ATGC ATGC ATGC ATGC ATAC ATGC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
10318 ATAC ATAC ATAC ATAC ATGC ATGC ATAC ATAC ATGC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
10366 ATAC ATAC ATAC ATGC ATAC ATAC ATGC ATAC ATGC ATGC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
10414 ATAC ATAC ATAC ATGC ATGC ATGC ATGC ATGC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
10462 ATGC ATGC ATGC ATGC ATAC ATAC ATAC ATAC -TAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
10509 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA- ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
10556 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
10604 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
10652 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
10700 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
10748 ATAC -TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
10795 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
10843 ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
10889 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
10937 ATAT ACTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC A-TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
10986 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
11034 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
11069 TACTTGCATG
Statistics
Matches: 2183, Mismatches: 186, Indels: 22
0.91 0.08 0.01
Matches are distributed among these distances:
2 2 0.00
3 15 0.01
4 2156 0.99
5 7 0.00
6 3 0.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:11744 original size:103 final size:100
Alignment explanation
Indices: 11607--11811 Score: 347
Period size: 103 Copynumber: 2.0 Consensus size: 100
11597 AATTGTAATG
* *
11607 GTGTATAAGTGATTAGTTCTTATGTAATAATAATTTTAAAAATTAAATTAAAGTAAAATGCATTG
1 GTGTATAAGTGATTAGTTATTATGTAATAATAATTTTAAAAATTAAATTAAAATAAAATGCATTG
11672 CATTTTATATTTATATTAGGATGAAATTTAATGTGTT
66 CATTTTATA-TTAT-TTAGGATGAAATTTAATGTGTT
* *
11709 GTGTATACGTGATTAGTTATTATTGTAATTATAATTTTAAAAATTAAATTAAAATAAAATGCATT
1 GTGTATAAGTGATTAGTTATTA-TGTAATAATAATTTTAAAAATTAAATTAAAATAAAATGCATT
11774 GCATTTTATATTATTTAGGATGAAATTTAATGTGTT
65 GCATTTTATATTATTTAGGATGAAATTTAATGTGTT
11810 GT
1 GT
11812 TGGTGTCTAT
Statistics
Matches: 98, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
101 24 0.24
102 24 0.24
103 50 0.51
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.45
Consensus pattern (100 bp):
GTGTATAAGTGATTAGTTATTATGTAATAATAATTTTAAAAATTAAATTAAAATAAAATGCATTG
CATTTTATATTATTTAGGATGAAATTTAATGTGTT
Found at i:12192 original size:12 final size:13
Alignment explanation
Indices: 12124--12209 Score: 56
Period size: 12 Copynumber: 6.6 Consensus size: 13
12114 ATTTAAAATT
12124 TAAT-TATATATA
1 TAATATATATATA
12136 T-ATATATATATA
1 TAATATATATATA
* *
12148 TAAT-TTTAATATTT
1 TAATATAT-ATA-TA
* *
12162 TAAAATTATTTAGTA
1 TAATA-TATATA-TA
12177 TAATATA-ATATA
1 TAATATATATATA
12189 TAAT-TATATATA
1 TAATATATATATA
12201 TGAATATAT
1 T-AATATAT
12210 TGATATATTA
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
11 4 0.07
12 24 0.43
13 10 0.18
14 9 0.16
15 7 0.12
16 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
TAATATATATATA
Found at i:20528 original size:16 final size:16
Alignment explanation
Indices: 20507--20538 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20497 TGGAGTTTTG
20507 TGTGACAAGAAGGTAC
1 TGTGACAAGAAGGTAC
20523 TGTGACAAGAAGGTAC
1 TGTGACAAGAAGGTAC
20539 CTCTAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.31, T:0.19
Consensus pattern (16 bp):
TGTGACAAGAAGGTAC
Done.