Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002057.1 Hibiscus syriacus cultivar Beakdansim tig00004191_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: 105188
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4187 original size:8 final size:8
Alignment explanation
Indices: 4175--5062 Score: 1456
Period size: 8 Copynumber: 112.5 Consensus size: 8
4165 TAAAACTATT
*
4175 ATGTATGT
1 ATGTATGC
*
4183 ATGTATGT
1 ATGTATGC
*
4191 ATGTATGT
1 ATGTATGC
*
4199 ATGTATGT
1 ATGTATGC
*
4207 ATGTATGT
1 ATGTATGC
4215 ATGTAT--
1 ATGTATGC
*
4221 ATGTATGTGT
1 ATGTA--TGC
4231 ATGTATGC
1 ATGTATGC
*
4239 ATGTAGGC
1 ATGTATGC
4247 ATGTATGC
1 ATGTATGC
4255 ATGTATGC
1 ATGTATGC
4263 ATGTATGC
1 ATGTATGC
4271 ATGTATGC
1 ATGTATGC
4279 ATGTATGC
1 ATGTATGC
4287 ATGTATGC
1 ATGTATGC
4295 ATGTATGC
1 ATGTATGC
*
4303 ATTTATGC
1 ATGTATGC
4311 ATGTATGC
1 ATGTATGC
4319 ATGTATGC
1 ATGTATGC
4327 ATGTATGC
1 ATGTATGC
*
4335 ATGTATTC
1 ATGTATGC
4343 ATGTATGC
1 ATGTATGC
4351 ATGTATGC
1 ATGTATGC
4359 ATGTATGC
1 ATGTATGC
4367 ATGTATGC
1 ATGTATGC
4375 ATGTATGC
1 ATGTATGC
4383 ATGTATGC
1 ATGTATGC
4391 ATGTATGC
1 ATGTATGC
4399 ATGTATGC
1 ATGTATGC
4407 ATGTATGC
1 ATGTATGC
4415 -TGTATGC
1 ATGTATGC
4422 ATGTATGC
1 ATGTATGC
4430 ATGTATGC
1 ATGTATGC
*
4438 ATG-GTGC
1 ATGTATGC
4445 ATGTATGC
1 ATGTATGC
4453 ATGTATGC
1 ATGTATGC
4461 ATGTATGC
1 ATGTATGC
4469 ATGTATGC
1 ATGTATGC
4477 ATGTATGC
1 ATGTATGC
4485 ATGTATGC
1 ATGTATGC
4493 ATGTATGC
1 ATGTATGC
4501 ATGTATGC
1 ATGTATGC
4509 ATGTATGC
1 ATGTATGC
4517 ATGTATGC
1 ATGTATGC
4525 ATGTATGC
1 ATGTATGC
4533 ATGTA-GC
1 ATGTATGC
4540 ATGTATGC
1 ATGTATGC
4548 ATGTATGC
1 ATGTATGC
4556 ATGTATTGC
1 ATGTA-TGC
4565 ATGTATGC
1 ATGTATGC
4573 ATGTATGC
1 ATGTATGC
4581 ATGTATGC
1 ATGTATGC
4589 -TGTATGC
1 ATGTATGC
4596 ATGTATGC
1 ATGTATGC
4604 ATGTATGC
1 ATGTATGC
4612 ATGTATGC
1 ATGTATGC
4620 ATTGTATGC
1 A-TGTATGC
4629 ATGTATGC
1 ATGTATGC
4637 ATGTATGC
1 ATGTATGC
4645 ATGTATGC
1 ATGTATGC
4653 --GTATGC
1 ATGTATGC
4659 ATGTATGC
1 ATGTATGC
4667 ATGTATGC
1 ATGTATGC
4675 ATGTATGC
1 ATGTATGC
4683 ATGTATGC
1 ATGTATGC
4691 ATGTATGC
1 ATGTATGC
4699 ATGTATGC
1 ATGTATGC
*
4707 ATGGATGC
1 ATGTATGC
4715 ATG--T--
1 ATGTATGC
4719 ATGTATGC
1 ATGTATGC
4727 ATGTATGC
1 ATGTATGC
4735 A-GTATGGC
1 ATGTAT-GC
4743 ATGTATGC
1 ATGTATGC
*
4751 ATTTATGC
1 ATGTATGC
4759 ATGTATGC
1 ATGTATGC
4767 ATGTATGC
1 ATGTATGC
4775 ATGTATGC
1 ATGTATGC
4783 ATGTATGC
1 ATGTATGC
4791 -TGTATGC
1 ATGTATGC
4798 ATGTATGC
1 ATGTATGC
4806 ATGTATGC
1 ATGTATGC
4814 ATGTATGC
1 ATGTATGC
4822 ATGTATGC
1 ATGTATGC
4830 ATGTATGC
1 ATGTATGC
4838 ATGTATGC
1 ATGTATGC
4846 ATGTATGC
1 ATGTATGC
4854 ATGTATGC
1 ATGTATGC
4862 ATGTAT-C
1 ATGTATGC
4869 ATGTATGC
1 ATGTATGC
4877 ATGTATGC
1 ATGTATGC
4885 A-GTATGC
1 ATGTATGC
4892 ATGTATGC
1 ATGTATGC
4900 ATGTATG-
1 ATGTATGC
4907 ATG--TGC
1 ATGTATGC
4913 ATGTATGC
1 ATGTATGC
4921 ATGTATGC
1 ATGTATGC
4929 ATGTATGC
1 ATGTATGC
4937 ATGTATGC
1 ATGTATGC
4945 ATGTATGC
1 ATGTATGC
4953 ATGTATGC
1 ATGTATGC
4961 ATGTATGC
1 ATGTATGC
4969 ATGTATGC
1 ATGTATGC
4977 ATGTATGC
1 ATGTATGC
4985 ATG-ATGC
1 ATGTATGC
4992 ATGGTATGC
1 AT-GTATGC
5001 ATGTATGC
1 ATGTATGC
5009 ATGTATGC
1 ATGTATGC
5017 ATGTATGC
1 ATGTATGC
5025 ATGTATATGC
1 ATG--TATGC
5035 ATGTATGC
1 ATGTATGC
5043 ATGTATGC
1 ATGTATGC
5051 ATGTATGC
1 ATGTATGC
5059 ATGT
1 ATGT
5063 CATGTATATA
Statistics
Matches: 840, Mismatches: 12, Indels: 56
0.93 0.01 0.06
Matches are distributed among these distances:
4 3 0.00
5 2 0.00
6 16 0.02
7 61 0.07
8 719 0.86
9 26 0.03
10 13 0.02
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (8 bp):
ATGTATGC
Found at i:11290 original size:22 final size:22
Alignment explanation
Indices: 11253--11309 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
11243 CATTTTAATC
11253 AAAATATTAATTATTAAAATATT-T
1 AAAATA-T-ATTATTAAAAT-TTCT
*
11277 AAAATATATTATTAATATTTCT
1 AAAATATATTATTAAAATTTCT
11299 AAAA-ATATTAT
1 AAAATATATTAT
11310 ATTTTAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 9 0.29
22 15 0.48
23 1 0.03
24 6 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATATATTATTAAAATTTCT
Found at i:11432 original size:27 final size:26
Alignment explanation
Indices: 11386--11476 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 26
11376 TATATAATAA
* *
11386 ATTATTAATAA-AATTTATATTATTT
1 ATTATTAATAAGAAATAATATTATTT
* *
11411 ATTAATTTCAT-AGAAATAATATTATTAA
1 ATT-A-TTAATAAGAAATAATATTATT-T
*
11439 ATTATTAATAATAAATAATATTATTT
1 ATTATTAATAAGAAATAATATTATTT
11465 ATATATTTAATA
1 AT-TA-TTAATA
11477 TTAATATAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
25 3 0.06
26 8 0.15
27 32 0.62
28 9 0.17
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
ATTATTAATAAGAAATAATATTATTT
Found at i:11463 original size:19 final size:19
Alignment explanation
Indices: 11439--11507 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
11429 ATATTATTAA
11439 ATTATTAATAATAAATAAT
1 ATTATTAATAATAAATAAT
* **
11458 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATAAATAAT
*
11476 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAAT-AAATAAT
11498 ATT-TTAATAA
1 ATTATTAATAA
11508 AGATATTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 10 0.26
19 16 0.41
20 4 0.10
21 2 0.05
22 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTATTAATAATAAATAAT
Found at i:11482 original size:27 final size:27
Alignment explanation
Indices: 11402--11487 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 27
11392 AATAAAATTT
* *
11402 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
*
11429 ATATTA-TTAAAT-TATTAATAATAAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
11456 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
11485 ATA
1 ATA
11488 ATCTAATAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 20 0.42
28 13 0.27
29 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:11528 original size:23 final size:23
Alignment explanation
Indices: 11502--11546 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11492 AATAATATTT
11502 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
11525 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
11547 ATATAAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:11660 original size:91 final size:86
Alignment explanation
Indices: 11515--11683 Score: 200
Period size: 91 Copynumber: 1.9 Consensus size: 86
11505 TAAAGATATT
* * * *
11515 TAAAATATACTAATTAATATTTTTAAAATATAATATAAAACTATTACTTTAATAA-ATAATTAAT
1 TAAAATATACAAATTAATATTTTTAAAATATAATATAAAAATAATACTTTAATAATA-AATAAAT
11579 ATACTTTATAATATTTTTATTTCAA
65 -TA-TTT-TAATATTTTTATTTCAA
*
11604 TAAAATATACCAATATTAATATTTTTATTAATA-AATTATAAAAATAATA-TTTAATAATAAATA
1 TAAAATATA-CAA-ATTAATATTTTTA-AAATATAA-TATAAAAATAATACTTTAATAATAAATA
11667 AATTATTTTAATATTTT
62 AATTATTTTAATATTTT
11684 AAAAATAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
88 9 0.13
89 12 0.17
90 4 0.06
91 29 0.41
92 16 0.23
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTAAAATATAATATAAAAATAATACTTTAATAATAAATAAATT
ATTTTAATATTTTTATTTCAA
Found at i:11675 original size:47 final size:48
Alignment explanation
Indices: 11623--11723 Score: 118
Period size: 47 Copynumber: 2.1 Consensus size: 48
11613 CCAATATTAA
*
11623 TATTTT-TATTAATAAATTATAAAAATAATAT-TTAATAATAAATAA-AT
1 TATTTTATATT-ATAAA-AATAAAAATAATATGTTAATAATAAATAATAT
* * *
11670 TATTTTAATATTTTAAAAATAAAAATAATATGTTTATGATAAATAATAT
1 TATTTT-ATATTATAAAAATAAAAATAATATGTTAATAATAAATAATAT
11719 TATTT
1 TATTT
11724 ATTGTATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
47 19 0.41
48 16 0.35
49 11 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (48 bp):
TATTTTATATTATAAAAATAAAAATAATATGTTAATAATAAATAATAT
Found at i:17908 original size:12 final size:13
Alignment explanation
Indices: 17888--17914 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17878 TCAAGTGAGG
17888 CATTTTTTTGTAT
1 CATTTTTTTGTAT
17901 CATTTTTTTGTAT
1 CATTTTTTTGTAT
17914 C
1 C
17915 TAAATCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.11, G:0.07, T:0.67
Consensus pattern (13 bp):
CATTTTTTTGTAT
Found at i:20048 original size:29 final size:29
Alignment explanation
Indices: 20005--20087 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
19995 CTCACCTAAC
20005 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
20035 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
20064 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
20088 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:24817 original size:29 final size:29
Alignment explanation
Indices: 24774--24856 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
24764 CTCACCTAAC
24774 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
24804 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
24833 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
24857 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:34691 original size:21 final size:21
Alignment explanation
Indices: 34665--34709 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34655 GATTTCTGGG
* *
34665 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
34686 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
34707 CAA
1 CAA
34710 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:35314 original size:23 final size:24
Alignment explanation
Indices: 35271--35317 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
35261 ATATGGCATG
*
35271 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
35295 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
35318 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:35533 original size:31 final size:31
Alignment explanation
Indices: 35495--35650 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
35485 AGGGTCGAGG
35495 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
35526 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
35557 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
35588 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
35619 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
35650 G
1 G
35651 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:39242 original size:70 final size:70
Alignment explanation
Indices: 39152--39315 Score: 217
Period size: 70 Copynumber: 2.3 Consensus size: 70
39142 TGAAATTATT
*
39152 AAAATGGTTTTC-AAGTTTGGTAA-CCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTT
1 AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG--AAAATGGTTTTCAAAGTTTGGTAAATATT
39215 TCTTTG-
64 TCTTTGA
****
39221 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAATGGTTTTCAAAGTTTGGTAAATATTT
1 AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTGAAAATGGTTTTCAAAGTTTGGTAAATATTT
39286 CTTTGA
65 CTTTGA
*
39292 AAAATAGTTTTTCAAAGTTTGGTA
1 AAAAT-GGTTTTCAAAGTTTGGTA
39316 GATGTTTGTT
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
69 12 0.14
70 43 0.51
71 8 0.10
72 21 0.25
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (70 bp):
AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTGAAAATGGTTTTCAAAGTTTGGTAAATATTTC
TTTGA
Found at i:39328 original size:36 final size:36
Alignment explanation
Indices: 39179--39333 Score: 235
Period size: 35 Copynumber: 4.3 Consensus size: 36
39169 TGGTAACCAA
39179 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
39216 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
39251 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
39286 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
39323 -GTTGAAAAATG
1 CTTTGAAAAATG
39334 ATAATGAGAT
Statistics
Matches: 111, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
35 70 0.63
36 14 0.13
37 27 0.24
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:42647 original size:31 final size:31
Alignment explanation
Indices: 42575--42654 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
42565 CAGTTTGATA
* * *
42575 AATTTCGAT-AATTTAAAAATTATTTTATAAT
1 AATTT-GATAAATTTAATAACTATTTTATAAC
**
42606 AATTCAATAAATTTAATAACTATTTTATAAC
1 AATTTGATAAATTTAATAACTATTTTATAAC
42637 AATTTGATAAACTTTAAT
1 AATTTGATAAA-TTTAAT
42655 CAGCATTTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 2 0.05
31 32 0.80
32 6 0.15
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (31 bp):
AATTTGATAAATTTAATAACTATTTTATAAC
Found at i:59119 original size:51 final size:51
Alignment explanation
Indices: 59040--59141 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
59030 GATAATCAAT
59040 CATCTGAACTATTTTCTTTCAAGGTATTTCACATGGTGACCTCAAATACTA
1 CATCTGAACTATTTTCTTTCAAGGTATTTCACATGGTGACCTCAAATACTA
*
59091 CATCTGAACTATTTTCTTTCAAGTTATTTCACATGGTGACCTCAAATACTA
1 CATCTGAACTATTTTCTTTCAAGGTATTTCACATGGTGACCTCAAATACTA
59142 TGTACCTCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (51 bp):
CATCTGAACTATTTTCTTTCAAGGTATTTCACATGGTGACCTCAAATACTA
Found at i:70371 original size:16 final size:16
Alignment explanation
Indices: 70350--70381 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
70340 TGTGAACGCC
70350 ATGGTTCCTCTCAGAT
1 ATGGTTCCTCTCAGAT
70366 ATGGTTCCTCTCAGAT
1 ATGGTTCCTCTCAGAT
70382 TTTCATCCAG
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:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (16 bp):
ATGGTTCCTCTCAGAT
Found at i:75268 original size:4 final size:4
Alignment explanation
Indices: 75259--75288 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
75249 CAAACATGAA
*
75259 ATGT ATGT ATGC ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
75289 TTCACCTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:78395 original size:25 final size:25
Alignment explanation
Indices: 78344--78396 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
78334 AGTTCTTAGG
* *
78344 TTAATTCACGATTTATATTCTATAT
1 TTAATTCACCATTTATATTCTAAAT
*
78369 TTAATTTACCATTTATATTC-AGAAT
1 TTAATTCACCATTTATATTCTA-AAT
78394 TTA
1 TTA
78397 TAATTATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (25 bp):
TTAATTCACCATTTATATTCTAAAT
Found at i:78439 original size:19 final size:19
Alignment explanation
Indices: 78381--78439 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
78371 AATTTACCAT
*
78381 TTATATTCAGAATTTATAA
1 TTATATTCAAAATTTATAA
* *
78400 TTAT-TGT-TACATTTATGAA
1 TTATAT-TCAAAATTTAT-AA
78419 TTATATTCAAAATTTATAA
1 TTATATTCAAAATTTATAA
78438 TT
1 TT
78440 TTTATTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 7 0.23
19 16 0.52
20 8 0.26
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
TTATATTCAAAATTTATAA
Found at i:79660 original size:35 final size:35
Alignment explanation
Indices: 79614--79694 Score: 162
Period size: 35 Copynumber: 2.3 Consensus size: 35
79604 AACTAGATGG
79614 AACAATCATAGATTAATTACACCAAGTGATCCTCA
1 AACAATCATAGATTAATTACACCAAGTGATCCTCA
79649 AACAATCATAGATTAATTACACCAAGTGATCCTCA
1 AACAATCATAGATTAATTACACCAAGTGATCCTCA
79684 AACAATCATAG
1 AACAATCATAG
79695 TTTTGAAGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (35 bp):
AACAATCATAGATTAATTACACCAAGTGATCCTCA
Found at i:95266 original size:20 final size:20
Alignment explanation
Indices: 95241--95298 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
95231 TTTGGTTCAC
* *
95241 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTACCAGTG
95261 GGAATAAAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
*
95281 AGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
95299 GGAATATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.22
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:95521 original size:36 final size:37
Alignment explanation
Indices: 95446--95521 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
95436 ACAAGTTGGA
* *
95446 AAATATTTATATATTTCTTTAAAAAATTTAAATTCAT
1 AAATATTTATATATTTCTTTAAAAAATTGAAAATCAT
* *
95483 AAAT-TTTATATAATTTTTTTACAAAATTGAAAAT-AT
1 AAATATTTATAT-ATTTCTTTAAAAAATTGAAAATCAT
95519 AAA
1 AAA
95522 AAGGTTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
AAATATTTATATATTTCTTTAAAAAATTGAAAATCAT
Found at i:99281 original size:23 final size:23
Alignment explanation
Indices: 99244--99312 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
99234 CACCACAACT
*
99244 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
99267 CGTAGAATTGTACCGAAGTTCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
99290 CGTAGAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
99313 TATAAAATGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:99414 original size:21 final size:23
Alignment explanation
Indices: 99380--99429 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
99370 AAAGGACCAA
99380 ATATGTGTCTCAAAAGACCACAT
1 ATATGTGTCTCAAAAGACCACAT
* **
99403 ATATGT-TC-CAAAGGATTACAT
1 ATATGTGTCTCAAAAGACCACAT
99424 ATATGT
1 ATATGT
99430 CCCGAAGGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.67
22 2 0.08
23 6 0.25
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (23 bp):
ATATGTGTCTCAAAAGACCACAT
Found at i:99437 original size:21 final size:21
Alignment explanation
Indices: 99399--99438 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
99389 TCAAAAGACC
*
99399 ACATATATGTTCCAAAGGATT
1 ACATATATGTCCCAAAGGATT
*
99420 ACATATATGTCCCGAAGGA
1 ACATATATGTCCCAAAGGA
99439 CCACGTAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
ACATATATGTCCCAAAGGATT
Found at i:99978 original size:44 final size:44
Alignment explanation
Indices: 99903--99994 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
99893 TTATTCACTT
* * * * * *
99903 TTCCTTATTAAGTAGTATTGTTACCCGAGGTATAGTACCGATAC
1 TTCCATATTAAGTAGTATCGGTACCCAAGGTACAATACCGATAC
**
99947 TTCCATATTAAGTAGTATCGGTATTCAAGGTACAATACCGATAC
1 TTCCATATTAAGTAGTATCGGTACCCAAGGTACAATACCGATAC
99991 TTCC
1 TTCC
99995 TTTATAATGG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (44 bp):
TTCCATATTAAGTAGTATCGGTACCCAAGGTACAATACCGATAC
Found at i:103047 original size:33 final size:34
Alignment explanation
Indices: 102996--103062 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
102986 CGAGAAAGAG
*
102996 TGATCCAAAAGCCTTAAATCACCCATACAATTAA
1 TGATCCAAAAGCCCTAAATCACCCATACAATTAA
*
103030 TGATCC-AAAGCCCTAAATCACCCATACAGTTAA
1 TGATCCAAAAGCCCTAAATCACCCATACAATTAA
103063 GCAAATCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.22
Consensus pattern (34 bp):
TGATCCAAAAGCCCTAAATCACCCATACAATTAA
Done.