Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002110.1 Hibiscus syriacus cultivar Beakdansim tig00004316_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: 71047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:5582 original size:30 final size:30
Alignment explanation
Indices: 5547--5606 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
5537 AAAATAGAGT
5547 AAGTATAAGATAATATATGTTCAAAAATAA
1 AAGTATAAGATAATATATGTTCAAAAATAA
5577 AAGTATAAGATAATATATGTTCAAAAATAA
1 AAGTATAAGATAATATATGTTCAAAAATAA
5607 CTATCAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (30 bp):
AAGTATAAGATAATATATGTTCAAAAATAA
Found at i:11019 original size:5 final size:5
Alignment explanation
Indices: 11009--11034 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
10999 TCAGTTGATA
11009 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
11035 AAAAGGGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:14090 original size:3 final size:3
Alignment explanation
Indices: 14082--14149 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
14072 AGCATATCTT
14082 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14130 -AA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
14150 AACTTGCTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:19672 original size:18 final size:18
Alignment explanation
Indices: 19649--19691 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
19639 GTGTCCGAAG
19649 CGTGAGATTCGTCTGAAA
1 CGTGAGATTCGTCTGAAA
*
19667 CGTGAGATTCGTCTGAAG
1 CGTGAGATTCGTCTGAAA
19685 CGTGAGA
1 CGTGAGA
19692 CTAATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.26
Consensus pattern (18 bp):
CGTGAGATTCGTCTGAAA
Found at i:23082 original size:8 final size:8
Alignment explanation
Indices: 23071--23625 Score: 476
Period size: 8 Copynumber: 71.8 Consensus size: 8
23061 ATTATTTAAC
23071 TTTAATGA
1 TTTAATGA
23079 TTTAAT-A
1 TTTAATGA
* *
23086 -ATAATTA
1 TTTAATGA
23093 CTTTAATGA
1 -TTTAATGA
*
23102 TTTAA--C
1 TTTAATGA
23108 TTTAATGA
1 TTTAATGA
23116 TTTAAT-A
1 TTTAATGA
* *
23123 -ATAATTA
1 TTTAATGA
23130 CTTTAATGA
1 -TTTAATGA
*
23139 TTTAATTA
1 TTTAATGA
23147 TTTAATGA
1 TTTAATGA
23155 TTTAAT-A
1 TTTAATGA
* *
23162 -ATAATTA
1 TTTAATGA
23169 TTTTAATGA
1 -TTTAATGA
23178 TTTAATGA
1 TTTAATGA
23186 TTTAATGA
1 TTTAATGA
23194 TTTAATGA
1 TTTAATGA
23202 TTTAAT-A
1 TTTAATGA
* *
23209 -ATAATTA
1 TTTAATGA
23216 CTTTAATGA
1 -TTTAATGA
23225 TTTAATGA
1 TTTAATGA
23233 TTTAATGA
1 TTTAATGA
23241 TTTAATGA
1 TTTAATGA
23249 TTTAATGA
1 TTTAATGA
23257 TTTAATGA
1 TTTAATGA
23265 TTTAAT-A
1 TTTAATGA
* *
23272 -ATAATTA
1 TTTAATGA
23279 CTTTAATGA
1 -TTTAATGA
23288 TTTAATGA
1 TTTAATGA
23296 TTTAATGA
1 TTTAATGA
23304 TTTAATGA
1 TTTAATGA
23312 TTTAATGA
1 TTTAATGA
23320 TTTAAT-A
1 TTTAATGA
*
23327 -TTAATTA
1 TTTAATGA
23334 CTTTAATGA
1 -TTTAATGA
*
23343 TTTAA--C
1 TTTAATGA
23349 TTTAATGA
1 TTTAATGA
23357 TTTAAT-A
1 TTTAATGA
* *
23364 -ATAATTA
1 TTTAATGA
23371 CTTTAATGA
1 -TTTAATGA
23380 TTTAATGA
1 TTTAATGA
23388 TTTAATGA
1 TTTAATGA
23396 TTTAAT-A
1 TTTAATGA
* *
23403 -ATAATTA
1 TTTAATGA
23410 TTTTAATGA
1 -TTTAATGA
23419 TTTAATGA
1 TTTAATGA
23427 TTTAATGA
1 TTTAATGA
23435 TTTAATGA
1 TTTAATGA
*
23443 TTTAATAA
1 TTTAATGA
23451 TAATTACTATGA
1 T--TTA--ATGA
23463 TTTAAT-A
1 TTTAATGA
* *
23470 -ATAATTA
1 TTTAATGA
23477 CTTTAATGA
1 -TTTAATGA
23486 TTTAATGA
1 TTTAATGA
23494 TTTAAT-A
1 TTTAATGA
* *
23501 -ATAATTA
1 TTTAATGA
23508 TTTTAATGA
1 -TTTAATGA
23517 TTTAATGA
1 TTTAATGA
23525 TTTAATGA
1 TTTAATGA
23533 TTTAATGA
1 TTTAATGA
23541 TTTAAT-A
1 TTTAATGA
* *
23548 -ATAATTA
1 TTTAATGA
23555 CTTTAATGA
1 -TTTAATGA
23564 TTTAAT--
1 TTTAATGA
*
23570 TTTAATAA
1 TTTAATGA
23578 TTTAAT-A
1 TTTAATGA
* *
23585 -ATAATTA
1 TTTAATGA
*
23592 CTTAAT--
1 TTTAATGA
23598 TTTAATGA
1 TTTAATGA
23606 TTTAAT--
1 TTTAATGA
23612 TTTAATGA
1 TTTAATGA
23620 TTTAAT
1 TTTAAT
23626 AATAATTACT
Statistics
Matches: 456, Mismatches: 42, Indels: 98
0.77 0.07 0.16
Matches are distributed among these distances:
6 76 0.17
7 24 0.05
8 290 0.64
9 56 0.12
10 6 0.01
12 4 0.01
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (8 bp):
TTTAATGA
Found at i:23162 original size:39 final size:39
Alignment explanation
Indices: 23071--23636 Score: 481
Period size: 39 Copynumber: 14.6 Consensus size: 39
23061 ATTATTTAAC
*
23071 TTTAATGATTTAATAATAATTACTTTAATGATTTAA--C
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
*
23108 TTTAATGATTTAATAATAATTACTTTAATGATTTAATTA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
*
23147 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGA
1 TTTAATGATTTAATAAT-A--A--TT-A--CTTTAATGATTTAATGA
23194 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
* *
23233 TTTAATGATTTAATGATTTAATGA-TTTAATGATTTAAT-A
1 TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGA
* * * *
23272 -ATAATTACTTTAATGATTTAATGA-TTTAATGATTTAATGA
1 TTTAATGA-TTTAAT-A-ATAATTACTTTAATGATTTAATGA
* *
23312 TTTAATGATTTAATATTAATTACTTTAATGATTTAA--C
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
23349 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
*
23388 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
* * *
23427 TTTAATGATTTAATGAT--TTA--ATAAT-AATTACTATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTA--ATGA
* * * *
23463 TTTAATAATAATTACT-TTAATGA-TTTAATGATTTAAT-A
1 TTTAATGAT--TTAATAATAATTACTTTAATGATTTAATGA
* * * *
23501 -ATAATTATTTTAATGATTTAATGA-TTTAATGA-TT--T--
1 TTTAATGA-TTTAAT-A-ATAATTACTTTAATGATTTAATGA
23536 ---AATGATTTAATAATAATTACTTTAATGATTTAAT--
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
*
23570 TTTAATAATTTAATAATAATTACTTAATTTTAATGATTTAAT--
1 TTTAATGATTTAATAATAATTAC-----TTTAATGATTTAATGA
23612 TTTAATGATTTAATAATAATTACTT
1 TTTAATGATTTAATAATAATTACTT
23637 GACTTTAATG
Statistics
Matches: 455, Mismatches: 32, Indels: 84
0.80 0.06 0.15
Matches are distributed among these distances:
30 5 0.01
31 9 0.02
32 8 0.02
33 4 0.01
34 5 0.01
35 4 0.01
36 17 0.04
37 101 0.22
38 19 0.04
39 165 0.36
40 27 0.06
41 15 0.03
42 39 0.09
44 3 0.01
45 1 0.00
46 1 0.00
47 32 0.07
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (39 bp):
TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
Found at i:23183 original size:47 final size:47
Alignment explanation
Indices: 23131--23625 Score: 536
Period size: 47 Copynumber: 10.5 Consensus size: 47
23121 TAATAATTAC
*
23131 TTTAATGATTTAATTATTTAATGATTTAATAATAATTATTTTAATGA
1 TTTAATGATTTAATGATTTAATGATTTAATAATAATTATTTTAATGA
*
23178 TTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGA
1 TTTAATGATTTAATGATTTAATGATTTAATAATAATTATTTTAATGA
* *
23225 TTTAATGATTTAATGATTTAATGATTTAATGATTTAATGA-TTTAAT-A
1 TTTAATGATTTAATGATTTAATGATTTAAT-A-ATAATTATTTTAATGA
* * * *
23272 -ATAATTACTTTAATGATTTAATGATTTAATGATTTAATGA-TTTAATGA
1 TTTAATGA-TTTAATGATTTAATGATTTAAT-A-ATAATTATTTTAATGA
* * ** *
23320 TTTAAT-A-TTAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTA
1 TTTAATGATTTAATGA-TTTAATGATTTAA---TAAT-AATT-ATTTTAATGA
23371 CTTTAATGATTTAATGATTTAATGATTTAATAATAATTATTTTAATGA
1 -TTTAATGATTTAATGATTTAATGATTTAATAATAATTATTTTAATGA
23419 TTTAATGATTTAATGATTTAATGATTTAATAATAATTACTATGATTTAAT-A
1 TTTAATGATTTAATGATTTAATGATTTAATAATAA-T--TAT--TTTAATGA
* *
23470 -ATAATTACTTTAATGATTTAATGATTTAATAATAATTATTTTAATGA
1 TTTAATGA-TTTAATGATTTAATGATTTAATAATAATTATTTTAATGA
*
23517 TTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGA
1 TTTAATGATTTAATGATTTAATGATTTAATAATAATTATTTTAATGA
* * *
23564 TTTAAT--TTTAATAATTTAAT-A-ATAAT--TACTTAATTTTAATGA
1 TTTAATGATTTAATGATTTAATGATTTAATAATAATT-ATTTTAATGA
23606 TTTAAT--TTTAATGATTTAAT
1 TTTAATGATTTAATGATTTAAT
23626 AATAATTACT
Statistics
Matches: 395, Mismatches: 29, Indels: 53
0.83 0.06 0.11
Matches are distributed among these distances:
41 4 0.01
42 28 0.07
43 4 0.01
44 1 0.00
45 13 0.03
46 17 0.04
47 207 0.52
48 26 0.07
49 15 0.04
50 15 0.04
51 33 0.08
52 12 0.03
53 14 0.04
54 6 0.02
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (47 bp):
TTTAATGATTTAATGATTTAATGATTTAATAATAATTATTTTAATGA
Found at i:26193 original size:172 final size:173
Alignment explanation
Indices: 25880--26238 Score: 560
Period size: 172 Copynumber: 2.1 Consensus size: 173
25870 CATCAAATAT
*
25880 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
25945 TATAAATACTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATACTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
* * *
26010 TTTTTATAATTTACTCTAATTTCTTAAATTCCTCAAATTTTGC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* * *
26053 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAGCAATTTAATC-CATAAAT
1 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * * *
26117 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
65 TTATAAATACTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
* *
26181 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
26225 AAAATGGTCCCTAA
1 AAAATGATCCCTAA
26239 AACTTTACAA
Statistics
Matches: 169, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
172 109 0.64
173 60 0.36
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (173 bp):
AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATACTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:26717 original size:23 final size:23
Alignment explanation
Indices: 26691--26734 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
26681 AGTTGCATGC
26691 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
26714 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
26735 CCTTGCAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:26779 original size:22 final size:22
Alignment explanation
Indices: 26751--26804 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
26741 AGGACCCAGG
26751 ACCCGTGATTTCTCCTTGCAGA
1 ACCCGTGATTTCTCCTTGCAGA
* *
26773 ACCCGTGCTCTCTCCTTGCAGA
1 ACCCGTGATTTCTCCTTGCAGA
26795 ACCCGTGATT
1 ACCCGTGATT
26805 CTCACGTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.35, G:0.19, T:0.30
Consensus pattern (22 bp):
ACCCGTGATTTCTCCTTGCAGA
Found at i:28248 original size:21 final size:22
Alignment explanation
Indices: 28219--28271 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
28209 ATTCTGACTA
28219 TCGCATTGCGATTTTCC-AAAT
1 TCGCATTGCGATTTTCCTAAAT
*
28240 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
*
28261 TCGCAATGCGA
1 TCGCATTGCGA
28272 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:29180 original size:24 final size:24
Alignment explanation
Indices: 29148--29201 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
29138 GTATTCGAAA
29148 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
29172 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
29196 TTTGAT
1 TTTGAT
29202 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:31660 original size:20 final size:21
Alignment explanation
Indices: 31635--31703 Score: 99
Period size: 20 Copynumber: 3.4 Consensus size: 21
31625 CAACGCGGAA
31635 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAATATGACT
*
31655 ATCGCAACACGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
*
31675 ATCTCAACGCGGAAT-TGACT
1 ATCGCAACGCGGAATATGACT
31695 ATCGCAACG
1 ATCGCAACG
31704 AGAGAATCGT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 40 0.93
21 3 0.07
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGGAATATGACT
Found at i:33366 original size:21 final size:18
Alignment explanation
Indices: 33342--33386 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
33332 GAACGGTGGG
33342 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGA---ATGAT
*
33363 AGGGGCCTCTTGAATGAT
1 AGGGGACTCTTGAATGAT
33381 AGGGGA
1 AGGGGA
33387 GGCCTCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
21 12 0.55
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.22
Consensus pattern (18 bp):
AGGGGACTCTTGAATGAT
Found at i:33403 original size:42 final size:42
Alignment explanation
Indices: 33296--33407 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 42
33286 TCTAGAATGT
* * * *
33296 TGGGAGAGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** * *
33338 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAATGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
33380 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
33408 TGAGTCGGGC
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
42 51 0.94
43 3 0.06
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:33975 original size:20 final size:20
Alignment explanation
Indices: 33895--33978 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
33885 AAATCGCAAC
* *
33895 GCGAAAATGACTATCGCAAC
1 GCGAAAATGACTATCACAAT
*
33915 GCGATAATGACTATCACAAT
1 GCGAAAATGACTATCACAAT
* **
33935 GCGAAAATAACTATCGTAAT
1 GCGAAAATGACTATCACAAT
33955 GCGAAAATGACTATCACAAT
1 GCGAAAATGACTATCACAAT
33975 GCGA
1 GCGA
33979 TAGTCATTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
GCGAAAATGACTATCACAAT
Found at i:33997 original size:20 final size:20
Alignment explanation
Indices: 33974--34019 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
33964 ACTATCACAA
33974 TGCGATAGTCATTTTCGCAT
1 TGCGATAGTCATTTTCGCAT
*
33994 TGCGATAGTCATTTTCGCGT
1 TGCGATAGTCATTTTCGCAT
34014 TGCGAT
1 TGCGAT
34020 TTTGTTGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
TGCGATAGTCATTTTCGCAT
Found at i:33998 original size:40 final size:40
Alignment explanation
Indices: 33895--33978 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
33885 AAATCGCAAC
* * *
33895 GCGAAAATGACTATCGCAACGCGATAATGACTATCACAAT
1 GCGAAAATAACTATCGCAATGCGAAAATGACTATCACAAT
*
33935 GCGAAAATAACTATCGTAATGCGAAAATGACTATCACAAT
1 GCGAAAATAACTATCGCAATGCGAAAATGACTATCACAAT
33975 GCGA
1 GCGA
33979 TAGTCATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (40 bp):
GCGAAAATAACTATCGCAATGCGAAAATGACTATCACAAT
Found at i:34029 original size:14 final size:14
Alignment explanation
Indices: 34012--34050 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
34002 TCATTTTCGC
34012 GTTGCGATTTTGTT
1 GTTGCGATTTTGTT
34026 GTTGCGATTTTGTT
1 GTTGCGATTTTGTT
34040 GTTGCGATTTT
1 GTTGCGATTTT
34051 CATTTCGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.08, C:0.08, G:0.28, T:0.56
Consensus pattern (14 bp):
GTTGCGATTTTGTT
Found at i:36021 original size:20 final size:20
Alignment explanation
Indices: 35973--36022 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
35963 GAAACTTTAA
*
35973 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
35993 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
36013 ATCGCAACGC
1 ATCGCAACGC
36023 AAGAATCGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:36061 original size:33 final size:34
Alignment explanation
Indices: 35993--36065 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
35983 GAAAATGACT
* **
35993 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
36027 ATCGCAACGCGAA-ATGAAAATCGCAACG-ACAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCA-AGA
36060 ATCGCA
1 ATCGCA
36066 TTGCGATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 21 0.60
34 13 0.37
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
Found at i:36654 original size:20 final size:20
Alignment explanation
Indices: 36631--36760 Score: 167
Period size: 20 Copynumber: 6.5 Consensus size: 20
36621 CGATAGTCAG
*
36631 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
36651 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
36671 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
36691 ATTCGCATTGCGAATTT-GGAA
1 ATTCGCATTGCG-ATTTACG-T
* *
36712 AATCGCAATGC--TTTACGT
1 ATTCGCATTGCGATTTACGT
*
36730 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
36750 ATTCGCATTGC
1 ATTCGCATTGC
36761 AAATTTGAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
18 11 0.12
19 1 0.01
20 69 0.73
21 13 0.14
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:36744 original size:59 final size:59
Alignment explanation
Indices: 36664--36781 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
36654 CGCATTGCGA
* * *
36664 TTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGAATTTGGAAAATCGCAATGC
1 TTTACGTATTCACATTGCGATTTACGTATTCGCATTGCAAATTTGAAAAATCGCAATGC
36723 TTTACGTATTCACATTGCGATTTACGTATTCGCATTGCAAATTTGAAAAATCGCAATGC
1 TTTACGTATTCACATTGCGATTTACGTATTCGCATTGCAAATTTGAAAAATCGCAATGC
36782 GATAGTCAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (59 bp):
TTTACGTATTCACATTGCGATTTACGTATTCGCATTGCAAATTTGAAAAATCGCAATGC
Found at i:36795 original size:79 final size:79
Alignment explanation
Indices: 36610--36796 Score: 200
Period size: 79 Copynumber: 2.3 Consensus size: 79
36600 GTCGCTATGT
* ** *
36610 AAATCGCATTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTC
1 AAATCGCATTGCGATAGTCAGAATCGCAATGC-ATTTACGTATTCACATTGCGATTTACGTATTC
* *
36675 GCATTGCGATTTACG
65 GCATTGCAATTTACA
* * * * *
36690 TATTCGCATTGCGA-ATTTGGAAAATCGCAATGC-TTTACGTATTCACATTGCGATTTACGTATT
1 AAATCGCATTGCGATA-GT-CAGAATCGCAATGCATTTACGTATTCACATTGCGATTTACGTATT
36753 CGCATTGCAAATTTGA-A
64 CGCATTGC-AATTT-ACA
*
36770 AAATCGCAATGCGATAGTCAGAATCGC
1 AAATCGCATTGCGATAGTCAGAATCGC
36797 GTTGTGAATC
Statistics
Matches: 85, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
79 45 0.53
80 29 0.34
81 11 0.13
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (79 bp):
AAATCGCATTGCGATAGTCAGAATCGCAATGCATTTACGTATTCACATTGCGATTTACGTATTCG
CATTGCAATTTACA
Found at i:39411 original size:7 final size:7
Alignment explanation
Indices: 39399--39678 Score: 560
Period size: 7 Copynumber: 40.0 Consensus size: 7
39389 CTACACACAT
39399 GTAAGCA
1 GTAAGCA
39406 GTAAGCA
1 GTAAGCA
39413 GTAAGCA
1 GTAAGCA
39420 GTAAGCA
1 GTAAGCA
39427 GTAAGCA
1 GTAAGCA
39434 GTAAGCA
1 GTAAGCA
39441 GTAAGCA
1 GTAAGCA
39448 GTAAGCA
1 GTAAGCA
39455 GTAAGCA
1 GTAAGCA
39462 GTAAGCA
1 GTAAGCA
39469 GTAAGCA
1 GTAAGCA
39476 GTAAGCA
1 GTAAGCA
39483 GTAAGCA
1 GTAAGCA
39490 GTAAGCA
1 GTAAGCA
39497 GTAAGCA
1 GTAAGCA
39504 GTAAGCA
1 GTAAGCA
39511 GTAAGCA
1 GTAAGCA
39518 GTAAGCA
1 GTAAGCA
39525 GTAAGCA
1 GTAAGCA
39532 GTAAGCA
1 GTAAGCA
39539 GTAAGCA
1 GTAAGCA
39546 GTAAGCA
1 GTAAGCA
39553 GTAAGCA
1 GTAAGCA
39560 GTAAGCA
1 GTAAGCA
39567 GTAAGCA
1 GTAAGCA
39574 GTAAGCA
1 GTAAGCA
39581 GTAAGCA
1 GTAAGCA
39588 GTAAGCA
1 GTAAGCA
39595 GTAAGCA
1 GTAAGCA
39602 GTAAGCA
1 GTAAGCA
39609 GTAAGCA
1 GTAAGCA
39616 GTAAGCA
1 GTAAGCA
39623 GTAAGCA
1 GTAAGCA
39630 GTAAGCA
1 GTAAGCA
39637 GTAAGCA
1 GTAAGCA
39644 GTAAGCA
1 GTAAGCA
39651 GTAAGCA
1 GTAAGCA
39658 GTAAGCA
1 GTAAGCA
39665 GTAAGCA
1 GTAAGCA
39672 GTAAGCA
1 GTAAGCA
39679 ATCATCATTT
Statistics
Matches: 273, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 273 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (7 bp):
GTAAGCA
Found at i:40523 original size:6 final size:6
Alignment explanation
Indices: 40512--40656 Score: 290
Period size: 6 Copynumber: 24.2 Consensus size: 6
40502 ACGGCACGGC
40512 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
40560 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
40608 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
40656 T
1 T
40657 AATACGTGTC
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 139 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:43815 original size:20 final size:20
Alignment explanation
Indices: 43790--43839 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
43780 TTTCATACTC
43790 TTGCCCAAAAACTCACAAAT
1 TTGCCCAAAAACTCACAAAT
*
43810 TTGCCCAAAAACTCACATAT
1 TTGCCCAAAAACTCACAAAT
43830 TTGCCCAAAA
1 TTGCCCAAAA
43840 CGAAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.06, T:0.22
Consensus pattern (20 bp):
TTGCCCAAAAACTCACAAAT
Found at i:44468 original size:16 final size:18
Alignment explanation
Indices: 44437--44470 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
44427 CTCACTTTAG
44437 GAAAGAATGAAGAAGATA
1 GAAAGAATGAAGAAGATA
44455 GAAAG-ATG-AGAAGATA
1 GAAAGAATGAAGAAGATA
44471 TGAAGAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (18 bp):
GAAAGAATGAAGAAGATA
Found at i:50241 original size:15 final size:15
Alignment explanation
Indices: 50201--50244 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
50191 TGTTATGTCC
50201 ATATTTTTTAAATAAA
1 ATATTTTTTAAA-AAA
* *
50217 ATATTATTTAAAAAT
1 ATATTTTTTAAAAAA
50232 ATATTTTTTAAAA
1 ATATTTTTTAAAA
50245 TATGGACGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTTTTTAAAAAA
Found at i:55970 original size:2 final size:2
Alignment explanation
Indices: 55950--55996 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
55940 ATCATAATCC
*
55950 TA TA TG TA T- TA TA -A TA TA TA TA 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
55990 TA TA TA T
1 TA TA TA T
55997 TGTTAAATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56254 original size:21 final size:21
Alignment explanation
Indices: 56225--56280 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
56215 ATTCTGACTA
56225 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
56246 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
**
56267 TCGCAACGCGATTT
1 TCGCATTGCGATTT
56281 AGTAAATCAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:56324 original size:20 final size:20
Alignment explanation
Indices: 56299--56350 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
56289 ACAACGCGAA
*
56299 TACGTATTCGCATTGCAATT
1 TACGTAATCGCATTGCAATT
* *
56319 TACGTAATCGCGTTGCGATT
1 TACGTAATCGCATTGCAATT
56339 TA-GTAAATCGCA
1 TACGT-AATCGCA
56351 ACGAGATTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
TACGTAATCGCATTGCAATT
Found at i:59856 original size:33 final size:33
Alignment explanation
Indices: 59806--59986 Score: 182
Period size: 33 Copynumber: 5.3 Consensus size: 33
59796 GGAAATTACT
* *
59806 ATCGCAATGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
* * * *
59839 ATCGTAACGTGAAAATCGCAACGCGAATATGAAT
1 ATCGCAACGAGAAAATCGCAATGCGAA-ATGAAA
*
59873 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAACG-AG-AA--A--ATCGCAATGCGAAATGAAA
* *
59912 ATCGCAACGAGAGAATCACAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
** * *
59945 ATCGCAACGAGGGAATCGCAAAGAGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
59978 ATCGCAACG
1 ATCGCAACG
59987 CGAATTTAGT
Statistics
Matches: 124, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
33 78 0.63
34 13 0.10
35 2 0.02
36 2 0.02
37 1 0.01
38 2 0.02
39 14 0.11
40 12 0.10
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:59871 original size:20 final size:19
Alignment explanation
Indices: 59819--59990 Score: 104
Period size: 19 Copynumber: 9.7 Consensus size: 19
59809 GCAATGAGAG
*
59819 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
59838 AATCGTAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
59852 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* *
59872 TATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* *
59892 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
59911 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
* *
59925 AATCACAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
**
59944 AATCGCAA--CG--A-GGG
1 AATCGCAACGCGAAATGAA
* *
59958 AATCGCAAAGAGAAATGAA
1 AATCGCAACGCGAAATGAA
59977 AATCGCAACGCGAA
1 AATCGCAACGCGAA
59991 TTTAGTTTCG
Statistics
Matches: 118, Mismatches: 18, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
14 29 0.25
15 2 0.02
16 5 0.04
17 6 0.05
18 2 0.02
19 43 0.36
20 28 0.24
21 3 0.03
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:59934 original size:106 final size:106
Alignment explanation
Indices: 59779--59988 Score: 278
Period size: 106 Copynumber: 2.0 Consensus size: 106
59769 CAATCATCTT
* * ** * * *
59779 AATGTCTATCGCAACGCGGAAATTACTATCGCAATGAGAGAATCGCAATGCGAAATGAAAATCGT
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGC
* * * *
59844 AACGTGAAAATCGCAACGCGAATATGAATATCGCAACGCGGA
66 AACGAGAAAATCGCAAAGAGAA-ATGAAAATCGCAACGCGGA
*
59886 AATGACTATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGC
**
59950 AACGAGGGAATCGCAAAGAGAAATGAAAATCGCAACGCG
66 AACGAGAAAATCGCAAAGAGAAATGAAAATCGCAACGCG
59989 AATTTAGTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 16 0.18
106 58 0.65
107 15 0.17
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (106 bp):
AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGC
AACGAGAAAATCGCAAAGAGAAATGAAAATCGCAACGCGGA
Found at i:60008 original size:19 final size:19
Alignment explanation
Indices: 59986--60060 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
59976 AAATCGCAAC
*
59986 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCA-TTTCGCATT
*
60005 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
*
60024 GCG-A-TTC-TCTCG--TT
1 GCGAATTTCATTTCGCATT
*
60038 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
60057 GCGA
1 GCGA
60061 TAGTCATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 5 0.11
16 7 0.16
17 7 0.16
19 24 0.55
20 1 0.02
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCATT
Found at i:60069 original size:19 final size:19
Alignment explanation
Indices: 59996--60061 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
59986 GCGAATTTAG
*
59996 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
60015 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
60031 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
60048 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
60062 AGTCATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 7 0.18
19 19 0.49
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:63532 original size:14 final size:14
Alignment explanation
Indices: 63513--63568 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
63503 GAGAATGACT
63513 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
63527 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
63546 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
63560 ATCGCAACG
1 ATCGCAACG
63569 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:63550 original size:19 final size:19
Alignment explanation
Indices: 63526--63587 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
63516 GCAACGAGAG
63526 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
63545 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
63559 AATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATGAA
*
63578 AATCACAACG
1 AATCGCAACG
63588 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.53
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:63550 original size:33 final size:33
Alignment explanation
Indices: 63492--63604 Score: 163
Period size: 33 Copynumber: 3.4 Consensus size: 33
63482 TTGAAATAAA
* **
63492 AATCGCAACGAGAGAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGAGAG
63526 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
63559 AATCGCAACGCGAAATTAAAATCACAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
63592 AATCGCAATGCGA
1 AATCGCAACGCGA
63605 TTTTGGTTTC
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 61 0.84
34 12 0.16
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:63622 original size:19 final size:19
Alignment explanation
Indices: 63600--63644 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
63590 AGAATCGCAA
**
63600 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAATTTCGCGT
63619 TGCGATTTTAATTTCGCGT
1 TGCGATTTTAATTTCGCGT
*
63638 TGTGATT
1 TGCGATT
63645 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.13, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTAATTTCGCGT
Found at i:63719 original size:20 final size:20
Alignment explanation
Indices: 63650--63721 Score: 101
Period size: 20 Copynumber: 3.5 Consensus size: 20
63640 TGATTCTCTC
63650 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
**
63670 CGTTGCGATAGTCATTTTCAT
1 -GTTGCGATTTTCATTTTCAT
63691 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
63711 GTTGCGATTTT
1 GTTGCGATTTT
63722 AAGTTTAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:64169 original size:27 final size:27
Alignment explanation
Indices: 64139--64204 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
64129 GAGATGGGAC
64139 TGAGTTGTGATTTTAGGTTTTAGGTTA
1 TGAGTTGTGATTTTAGGTTTTAGGTTA
64166 TGAGTTGTGATTTTAGGTTTTAGGTTA
1 TGAGTTGTGATTTTAGGTTTTAGGTTA
*
64193 TGAGTTGCGATT
1 TGAGTTGTGATT
64205 ACGGGATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.18, C:0.02, G:0.30, T:0.50
Consensus pattern (27 bp):
TGAGTTGTGATTTTAGGTTTTAGGTTA
Found at i:64334 original size:20 final size:20
Alignment explanation
Indices: 64309--64519 Score: 228
Period size: 20 Copynumber: 10.4 Consensus size: 20
64299 TAAAAATCGT
64309 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
64329 GTTGCGATTTTACGTAT-TGTC
1 GTTGCGA-TTTACGGATACG-C
64350 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * * *
64370 ATTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
*
64390 GTTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATACGC
* * *
64410 GTTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
64430 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
64450 ATTGCGATTTTACGTAT-TGTC
1 GTTGCGA-TTTACGGATACG-C
64471 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
64491 GTTGTGATTTTACGGATACTC
1 GTTGCGA-TTTACGGATACGC
64512 GTTGCGAT
1 GTTGCGAT
64520 AGTCAGAATC
Statistics
Matches: 155, Mismatches: 29, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
20 104 0.67
21 51 0.33
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:64392 original size:40 final size:41
Alignment explanation
Indices: 64309--64519 Score: 336
Period size: 41 Copynumber: 5.2 Consensus size: 41
64299 TAAAAATCGT
*
64309 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
*
64350 GTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
*
64390 GTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* *
64430 GTTGCGATTTACGGATACGCATTGCGATTTTACGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* * *
64471 GTTGCGATTTACGGATACGCGTTGTGATTTTACGGATACTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
64512 GTTGCGAT
1 GTTGCGAT
64520 AGTCAGAATC
Statistics
Matches: 157, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 75 0.48
41 82 0.52
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
Found at i:64659 original size:20 final size:19
Alignment explanation
Indices: 64610--64663 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
64600 ATTCTTCATA
64610 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
64629 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
64650 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
64664 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:70208 original size:15 final size:16
Alignment explanation
Indices: 70176--70208 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
70166 AATCTAAGCT
*
70176 TAAATATAAAATTCGA
1 TAAAAATAAAATTCGA
70192 TAAAAATAAAA-TCGA
1 TAAAAATAAAATTCGA
70207 TA
1 TA
70209 CTTGAATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (16 bp):
TAAAAATAAAATTCGA
Found at i:70244 original size:27 final size:27
Alignment explanation
Indices: 70188--70245 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
70178 AATATAAAAT
*
70188 TCGATAAAAATAAAATCGATACTTGAA
1 TCGATAAAAATAAAATCGATACTTCAA
*
70215 TCGATACAAAACT-AAATCG-TACTTCCA
1 TCGATA-AAAA-TAAAATCGATACTTCAA
70242 TCGA
1 TCGA
70246 AATTTCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 16 0.59
28 10 0.37
29 1 0.04
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (27 bp):
TCGATAAAAATAAAATCGATACTTCAA
Done.