Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006947.1 Hibiscus syriacus cultivar Beakdansim tig00017852_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: 82810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7318 original size:24 final size:23
Alignment explanation
Indices: 7266--7320 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
7256 GGAATCAATA
7266 CCCCC-TTGAAGGGGAACTGATT
1 CCCCCTTTGAAGGGGAACTGATT
7288 CCCCCTTTGAATGGGG-ACTGATT
1 CCCCCTTTGAA-GGGGAACTGATT
7311 CCCTCCTTTG
1 CCC-CCTTTG
7321 GGGAATCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.17
23 15 0.50
24 10 0.33
ACGTcount: A:0.16, C:0.31, G:0.24, T:0.29
Consensus pattern (23 bp):
CCCCCTTTGAAGGGGAACTGATT
Found at i:12113 original size:93 final size:93
Alignment explanation
Indices: 11988--12181 Score: 275
Period size: 93 Copynumber: 2.1 Consensus size: 93
11978 TATAATATTA
* * * *
11988 TATATATACAATAAATCTTGAGTTGCCTCTCTAAA-ACAATTGGTTAAATGCCCCGACTTTATGG
1 TATA-ATACAATAAAGCTTGAGCTGCCTCTCTAAAGA-AATTGATTAAACGCCCCGACTTTATGG
12052 ATAAGATTCAGCTAGCCTGATAAAGGTGAT
64 ATAAGATTCAGCTAGCCTGATAAAGGTGAT
* *
12082 TATAATACAATAAAGCTTGAGCTGTCC-CTCTAAAGAAATTGATTAAACGGCCTGACTTTATGGA
1 TATAATACAATAAAGCTTGAGCTG-CCTCTCTAAAGAAATTGATTAAACGCCCCGACTTTATGGA
* *
12146 TAATATTCAGCTAGCCTGATAAAGGTTAT
65 TAAGATTCAGCTAGCCTGATAAAGGTGAT
12175 TATAATA
1 TATAATA
12182 GTGAGTTGTC
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
93 83 0.92
94 7 0.08
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (93 bp):
TATAATACAATAAAGCTTGAGCTGCCTCTCTAAAGAAATTGATTAAACGCCCCGACTTTATGGAT
AAGATTCAGCTAGCCTGATAAAGGTGAT
Found at i:13804 original size:31 final size:31
Alignment explanation
Indices: 13769--13858 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
13759 TCGACAACTA
* *
13769 TCCATAGGTCCCGAAGAACTTAGGTAAAATG
1 TCCATATGTCCCGAAGAACATAGGTAAAATG
* ** * *
13800 TCCATATGTTCCTTAGAACATAGGTATACTG
1 TCCATATGTCCCGAAGAACATAGGTAAAATG
*
13831 TCCATATGTCCCTAA-AGACATAGGTAAA
1 TCCATATGTCCCGAAGA-ACATAGGTAAA
13859 CCCTCGACTC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 47 0.98
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAAAATG
Found at i:16197 original size:83 final size:82
Alignment explanation
Indices: 16013--16370 Score: 332
Period size: 83 Copynumber: 4.3 Consensus size: 82
16003 AGCAAAACAT
* * * * *
16013 CTTCGAGTTCG---ACACTCAGCTCAAGGACATATCAAATTTACAGCATAGCTCAAGGTGAGAAG
1 CTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTAAAGCATAACTCAA-GCGAGAAG
* * *
16075 GGCTATCTGTCAACAAAAAC
65 GGTTATATG-CCA-AAAAAC
* ** * *
16095 CTTCGAGTTCGATTACATTCAGCTCAAGGGCTTATCAAATTTGCAGTATAACTC-A-CGAGAATG
1 CTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTAAAGCATAACTCAAGCGAGAAGG
*
16158 GTTATTTGCCAATAAAAAAC
66 GTTATATGCC---AAAAAAC
* * *
16178 CTTCGAGTTCGATTCCATTCAGCTCAAGGACATATCAAATTTAAAGCATAACTCAAGGCGAGCAG
1 CTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTAAAGCATAACTCAA-GCGAGAAG
* *
16243 GGTTATATGTCAACAAAC
65 GGTTATATGCCAAAAAAC
* **
16261 CTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATCTACAA-CATAGTTCAAGGCGAGAA
1 CTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTA-AAGCATAACTCAA-GCGAGAA
* * * *
16325 GGGCTATCTGTCAACAAAAA
64 GGGTTATATGCCAA-AAAAC
*
16345 CTGTCGAGTTCGATTCCATTCAGCTC
1 CT-TCGAGTTCGATTACATTCAGCTC
16371 GATATCAATC
Statistics
Matches: 231, Mismatches: 33, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
81 1 0.00
82 23 0.10
83 127 0.55
84 10 0.04
85 56 0.24
86 14 0.06
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (82 bp):
CTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTAAAGCATAACTCAAGCGAGAAGG
GTTATATGCCAAAAAAC
Found at i:16354 original size:168 final size:169
Alignment explanation
Indices: 15968--16370 Score: 516
Period size: 168 Copynumber: 2.4 Consensus size: 169
15958 AGGAACTATT
* * * *
15968 TACAACATAGCTCAAGGCGAGAAGAGCTATCTGCCAGCAAAACATCTTCGAGTTCGA---CACTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAA-ACCTTCGAGTTCGATTCCATTC
* * * *
16030 AGCTCAAGGACATATCAAATTTACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAAAC
65 AGCTCAAGGACATATCAAATTTAAAGCATAACTCAAGGCGAGAAGGGCTATATGTCAAC-AAAAC
* *
16095 CTTCGAGTTCGATTACATTCAGCTCAAGGGCTTATCAAATT
129 CTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATC
* ** * * * * *
16136 TGCAGTATAACTC-A--CGAGAATGGTTATTTGCCAATAAAAAACCTTCGAGTTCGATTCCATTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAA-CAAAAACCTTCGAGTTCGATTCCATTC
* *
16198 AGCTCAAGGACATATCAAATTTAAAGCATAACTCAAGGCGAGCAGGGTTATATGTCAAC-AAACC
65 AGCTCAAGGACATATCAAATTTAAAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAACC
16262 TTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATC
130 TTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATC
* *
16302 TACAACATAGTTCAAGGCGAGAAGGGCTATCTGTCAACAAAAA-CTGTCGAGTTCGATTCCATTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAACCT-TCGAGTTCGATTCCATTC
16366 AGCTC
65 AGCTC
16371 GATATCAATC
Statistics
Matches: 197, Mismatches: 30, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
165 28 0.14
166 55 0.28
167 4 0.02
168 94 0.48
169 16 0.08
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (169 bp):
TACAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAACCTTCGAGTTCGATTCCATTCA
GCTCAAGGACATATCAAATTTAAAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAACCT
TCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATC
Found at i:18206 original size:9 final size:9
Alignment explanation
Indices: 18192--18281 Score: 58
Period size: 9 Copynumber: 9.6 Consensus size: 9
18182 TAATTATTTA
18192 TTTTTTCTTT
1 TTTTTTC-TT
*
18202 TTTTTTGTT
1 TTTTTTCTT
18211 TTTGTTTCTT
1 TTT-TTTCTT
* * *
18221 ATTATTATT
1 TTTTTTCTT
*
18230 TTTCTTCTT
1 TTTTTTCTT
*
18239 TTTTCTCTT
1 TTTTTTCTT
18248 TTTTTAT-TT
1 TTTTT-TCTT
18257 TTTCTTT-TT
1 TTT-TTTCTT
18266 TTATTTTCTT
1 TT-TTTTCTT
18276 TGTTTT
1 T-TTTT
18282 ATTTGATTTG
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
9 39 0.62
10 23 0.37
11 1 0.02
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:18207 original size:10 final size:10
Alignment explanation
Indices: 18192--18281 Score: 56
Period size: 10 Copynumber: 8.4 Consensus size: 10
18182 TAATTATTTA
18192 TTTTTTCTTT
1 TTTTTTCTTT
*
18202 TTTTTTGTTTT
1 TTTTTT-CTTT
*
18213 TGTTTCTTATTAT
1 T-TTT-TTCTT-T
*
18226 TATTTTTCTTC
1 T-TTTTTCTTT
*
18237 TTTTTTCTCT
1 TTTTTTCTTT
*
18247 TTTTTTATTT
1 TTTTTTCTTT
18257 TTTCTTT-TTT
1 TTT-TTTCTTT
*
18267 TATTTTCTTT
1 TTTTTTCTTT
18277 GTTTT
1 -TTTT
18282 ATTTGATTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
9 3 0.05
10 32 0.52
11 11 0.18
12 9 0.15
13 7 0.11
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:18281 original size:14 final size:14
Alignment explanation
Indices: 18256--18295 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
18246 TTTTTTTATT
18256 TTTTCTTT-TTTTA
1 TTTTCTTTGTTTTA
18269 TTTTCTTTGTTTTA
1 TTTTCTTTGTTTTA
**
18283 TTTGATTTGTTTT
1 TTTTCTTTGTTTT
18296 TTTAATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.80
Consensus pattern (14 bp):
TTTTCTTTGTTTTA
Found at i:18339 original size:16 final size:17
Alignment explanation
Indices: 18318--18360 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
18308 AACTTATTTG
18318 ATTTTTATTT-TTTTAT
1 ATTTTTATTTATTTTAT
*
18334 ATTTTTTATTTATTTTCT
1 A-TTTTTATTTATTTTAT
18352 -TTTTTATTT
1 ATTTTTATTT
18361 CAGGATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 10 0.42
17 9 0.38
18 5 0.21
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (17 bp):
ATTTTTATTTATTTTAT
Found at i:18341 original size:17 final size:16
Alignment explanation
Indices: 18319--18360 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
18309 ACTTATTTGA
*
18319 TTTTTATTTTTTTATAT
1 TTTTTATTTATTT-TAT
*
18336 TTTTTATTTATTTTCT
1 TTTTTATTTATTTTAT
18352 TTTTTATTT
1 TTTTTATTT
18361 CAGGATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTATTTATTTTAT
Found at i:24507 original size:51 final size:51
Alignment explanation
Indices: 24443--24629 Score: 286
Period size: 52 Copynumber: 3.7 Consensus size: 51
24433 ACAAGTATAT
*
24443 GTGTAGCACTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAA
1 GTGTAGCATTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAA
*
24494 GTGTAACATTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAAA
1 GTGTAGCATTTAACACATACTTACACCGGTGTAAATGAATAAAAT-AAAAAA
* * *
24546 GTGTAGCATTTAACATATACTTACACCAGTGTAAATGAATAAAA-ATAAAA
1 GTGTAGCATTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAA
* **
24596 GTGTAGCAGTTAACACATACTTACATTGGTGTAA
1 GTGTAGCATTTAACACATACTTACACCGGTGTAA
24630 GTATGTACAT
Statistics
Matches: 124, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
50 34 0.27
51 43 0.35
52 47 0.38
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (51 bp):
GTGTAGCATTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAA
Found at i:24566 original size:52 final size:52
Alignment explanation
Indices: 24443--24629 Score: 281
Period size: 51 Copynumber: 3.7 Consensus size: 52
24433 ACAAGTATAT
*
24443 GTGTAGCACTTAACACATACTTACACCGGTGTAAATGAATAAAAT-AAAAAA
1 GTGTAGCATTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAAA
*
24494 GTGTAACATTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAAA
1 GTGTAGCATTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAAA
* * *
24546 GTGTAGCATTTAACATATACTTACACCAGTGTAAATGAAT-AAA-AATAAAA
1 GTGTAGCATTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAAA
* **
24596 GTGTAGCAGTTAACACATACTTACATTGGTGTAA
1 GTGTAGCATTTAACACATACTTACACCGGTGTAA
24630 GTATGTACAT
Statistics
Matches: 124, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
50 35 0.28
51 46 0.37
52 43 0.35
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (52 bp):
GTGTAGCATTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAAA
Found at i:24578 original size:103 final size:102
Alignment explanation
Indices: 24443--24629 Score: 293
Period size: 103 Copynumber: 1.8 Consensus size: 102
24433 ACAAGTATAT
* *
24443 GTGTAGCACTTAACACATACTTACACCGGTGTAAATGAATAAAATAAAAAAGTGTAACATTTAAC
1 GTGTAGCACTTAACACATACTTACACCAGTGTAAATGAATAAAA-AAAAAAGTGTAACAGTTAAC
24508 ACATACTTACACCGGTGTAAATGAATAAAATAAAAAAA
65 ACATACTTACACCGGTGTAAATGAATAAAATAAAAAAA
* * * *
24546 GTGTAGCATTTAACATATACTTACACCAGTGTAAATGAATAAAAATAAAAGTGTAGCAGTTAACA
1 GTGTAGCACTTAACACATACTTACACCAGTGTAAATGAATAAAAAAAAAAGTGTAACAGTTAACA
**
24611 CATACTTACATTGGTGTAA
66 CATACTTACACCGGTGTAA
24630 GTATGTACAT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
102 35 0.46
103 41 0.54
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (102 bp):
GTGTAGCACTTAACACATACTTACACCAGTGTAAATGAATAAAAAAAAAAGTGTAACAGTTAACA
CATACTTACACCGGTGTAAATGAATAAAATAAAAAAA
Found at i:28035 original size:19 final size:20
Alignment explanation
Indices: 28011--28050 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28001 TTAAGGGTGA
*
28011 TAAAAAGA-CCGAAAATGTG
1 TAAAAAGATACGAAAATGTG
28030 TAAAAAGATACGAAAATGTG
1 TAAAAAGATACGAAAATGTG
28050 T
1 T
28051 TATAAAGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (20 bp):
TAAAAAGATACGAAAATGTG
Found at i:35392 original size:15 final size:15
Alignment explanation
Indices: 35374--35405 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35364 AAGATATTTT
*
35374 TTAAGAAAAATAAAG
1 TTAAAAAAAATAAAG
35389 TTAAAAAAAATAAAG
1 TTAAAAAAAATAAAG
35404 TT
1 TT
35406 CACAGGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (15 bp):
TTAAAAAAAATAAAG
Found at i:37482 original size:7 final size:7
Alignment explanation
Indices: 37470--37500 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
37460 AGATAATGAT
37470 GGGGAAG
1 GGGGAAG
37477 GGGGAAG
1 GGGGAAG
37484 GGGGAAG
1 GGGGAAG
37491 GGGGAAG
1 GGGGAAG
37498 GGG
1 GGG
37501 AGGAGAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (7 bp):
GGGGAAG
Found at i:41725 original size:27 final size:27
Alignment explanation
Indices: 41695--41747 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
41685 CGGTGCCGAA
41695 CTCGACCGGAAGTAGGTGTAGTTGGTC
1 CTCGACCGGAAGTAGGTGTAGTTGGTC
**
41722 CTCGGGCGGAAGTAGGTGTAGTTGGT
1 CTCGACCGGAAGTAGGTGTAGTTGGT
41748 GCAGAACCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.42, T:0.26
Consensus pattern (27 bp):
CTCGACCGGAAGTAGGTGTAGTTGGTC
Found at i:47469 original size:11 final size:11
Alignment explanation
Indices: 47453--47478 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47443 CTGTCTTTGT
47453 TCATCACATTC
1 TCATCACATTC
47464 TCATCACATTC
1 TCATCACATTC
47475 TCAT
1 TCAT
47479 TGAAAATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (11 bp):
TCATCACATTC
Found at i:50150 original size:36 final size:36
Alignment explanation
Indices: 50095--50208 Score: 194
Period size: 36 Copynumber: 3.2 Consensus size: 36
50085 CTCATTCCTA
* *
50095 TTTTC-AACAAACATCTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
50130 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
*
50166 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
50202 TTTTCAA
1 TTTTCAA
50209 TGTTGGTTGC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 5 0.07
36 70 0.93
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.31
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAAACAT
Found at i:50912 original size:9 final size:9
Alignment explanation
Indices: 50898--50922 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
50888 AGCATAACAA
50898 CTTCATCAT
1 CTTCATCAT
50907 CTTCATCAT
1 CTTCATCAT
50916 CTTCATC
1 CTTCATC
50923 TACAAGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTCATCAT
Found at i:53610 original size:59 final size:59
Alignment explanation
Indices: 53506--53644 Score: 174
Period size: 64 Copynumber: 2.3 Consensus size: 59
53496 CTGTGATTAT
* *
53506 CAAGAACAGACACATACGCAAACGAATAACTGCAAACTTAAAAAAG-G-AAAAAAAAAA
1 CAAGAACAAACACATACGAAAACGAATAACTGCAAACTTAAAAAAGAGAAAAAAAAAAA
* * *
53563 CAAGAACAAACACATACGAAATTACGAATAACTGTATACTTAGAAAAGAAAAGAAAAAAAAAAA
1 CAAGAACAAACACATACGAAA--ACGAATAACTGCAAACTT--AAAA-AAGAGAAAAAAAAAAA
53627 CAAGAACAAACACATACG
1 CAAGAACAAACACATACG
53645 CACGAATTGT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
57 19 0.27
59 16 0.23
61 4 0.06
62 2 0.03
63 1 0.01
64 28 0.40
ACGTcount: A:0.61, C:0.17, G:0.12, T:0.11
Consensus pattern (59 bp):
CAAGAACAAACACATACGAAAACGAATAACTGCAAACTTAAAAAAGAGAAAAAAAAAAA
Found at i:54116 original size:21 final size:21
Alignment explanation
Indices: 54090--54129 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54080 TATAATGTAA
* *
54090 ATTTCAGAATAATTAAATTAG
1 ATTTCAAAATAAATAAATTAG
54111 ATTTCAAAATAAATAAATT
1 ATTTCAAAATAAATAAATT
54130 TAATTATTTT
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:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTTCAAAATAAATAAATTAG
Found at i:54581 original size:15 final size:15
Alignment explanation
Indices: 54561--54598 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
54551 CGCCTCGACT
54561 GAGCCTCGCGCCTCA
1 GAGCCTCGCGCCTCA
*
54576 GAGCCTCACGCCTCA
1 GAGCCTCGCGCCTCA
54591 GAGCCTCG
1 GAGCCTCG
54599 TTGCGCCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.45, G:0.26, T:0.13
Consensus pattern (15 bp):
GAGCCTCGCGCCTCA
Found at i:58071 original size:16 final size:16
Alignment explanation
Indices: 58052--58085 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58042 ACTTGATTTG
* *
58052 AACTTAAAAAAACTCA
1 AACTAAAAAAAAATCA
58068 AACTAAAAAAAAATCA
1 AACTAAAAAAAAATCA
58084 AA
1 AA
58086 AACTTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (16 bp):
AACTAAAAAAAAATCA
Found at i:58133 original size:23 final size:23
Alignment explanation
Indices: 58107--58152 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
58097 AACTCAAGAC
58107 TCAAACTCAATTAAAATTCAATT
1 TCAAACTCAATTAAAATTCAATT
* *
58130 TCAAACTCAATTCAAGTTCAATT
1 TCAAACTCAATTAAAATTCAATT
58153 CAAGCTCGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (23 bp):
TCAAACTCAATTAAAATTCAATT
Found at i:58156 original size:11 final size:11
Alignment explanation
Indices: 58107--58155 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
58097 AACTCAAGAC
*
58107 TCAAACTCAAT
1 TCAAATTCAAT
*
58118 TAAAATTCAATT
1 TCAAATTCAA-T
*
58130 TCAAACTCAAT
1 TCAAATTCAAT
*
58141 TCAAGTTCAAT
1 TCAAATTCAAT
58152 TCAA
1 TCAA
58156 GCTCGATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
11 22 0.71
12 9 0.29
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (11 bp):
TCAAATTCAAT
Found at i:59929 original size:17 final size:16
Alignment explanation
Indices: 59886--59925 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
59876 TAACAATAAT
59886 TTAAAAA-ATTAGTTA
1 TTAAAAATATTAGTTA
59901 TTAAAAATATTA-TTA
1 TTAAAAATATTAGTTA
*
59916 TTAGAAATAT
1 TTAAAAATAT
59926 ATTAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (16 bp):
TTAAAAATATTAGTTA
Found at i:59970 original size:11 final size:11
Alignment explanation
Indices: 59954--60014 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
59944 GATAAAGAAA
59954 TTTTAATATAT
1 TTTTAATATAT
59965 TTTTAA-A-AT
1 TTTTAATATAT
59974 TTTATAAT-TAT
1 TTT-TAATATAT
*** *
59985 CAATAATGTAT
1 TTTTAATATAT
59996 TTTTAATATAT
1 TTTTAATATAT
60007 TTTTAATA
1 TTTTAATA
60015 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 26 0.67
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:60033 original size:25 final size:25
Alignment explanation
Indices: 59986--60033 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
59976 TATAATTATC
* * *
59986 AATAATGTATTTTTAATATATTTTT
1 AATAATGTAATTTTAAAAAATTTTT
60011 AATAATGTAATTTTAAAAAATTT
1 AATAATGTAATTTTAAAAAATTT
60034 AAAATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
AATAATGTAATTTTAAAAAATTTTT
Found at i:60079 original size:20 final size:20
Alignment explanation
Indices: 60054--60102 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
60044 TATAACATTT
60054 TTTTCGAGTTGCTCACGAAC
1 TTTTCGAGTTGCTCACGAAC
*
60074 TTTTCGAGTTGCTCACGAGC
1 TTTTCGAGTTGCTCACGAAC
60094 TTTTCGAGT
1 TTTTCGAGT
60103 CGAATATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.39
Consensus pattern (20 bp):
TTTTCGAGTTGCTCACGAAC
Found at i:61305 original size:15 final size:17
Alignment explanation
Indices: 61285--61317 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
61275 ATCTCACTAA
61285 TTCAAT-TTATTT-TAT
1 TTCAATATTATTTGTAT
61300 TTCAATATTATTTGTAT
1 TTCAATATTATTTGTAT
61317 T
1 T
61318 AACTCATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTCAATATTATTTGTAT
Found at i:63643 original size:29 final size:29
Alignment explanation
Indices: 63601--63671 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
63591 GACATGCGAT
63601 AAATTTTAATATTTTATGCATTAACTTTG
1 AAATTTTAATATTTTATGCATTAACTTTG
63630 AAATTTTAATATTTTATGCATTAACTTTG
1 AAATTTTAATATTTTATGCATTAACTTTG
*
63659 AAATTGTAATATT
1 AAATTTTAATATT
63672 AATTATTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.51
Consensus pattern (29 bp):
AAATTTTAATATTTTATGCATTAACTTTG
Found at i:64861 original size:21 final size:21
Alignment explanation
Indices: 64837--64921 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
64827 GGAGTATTGA
*
64837 TACTCCTTTTATGGGTATCAG
1 TACTCCTTTTATGGGTATCGG
* *
64858 TACTTCTTTTATGGGTATCGA
1 TACTCCTTTTATGGGTATCGG
* *
64879 TACTCTTTTTATGAGTATCGG
1 TACTCCTTTTATGGGTATCGG
*
64900 TACTCC-CTT-TGGGTATCGG
1 TACTCCTTTTATGGGTATCGG
64919 TAC
1 TAC
64922 CTATTTTACA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.22
20 2 0.04
21 40 0.74
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.44
Consensus pattern (21 bp):
TACTCCTTTTATGGGTATCGG
Found at i:73155 original size:31 final size:28
Alignment explanation
Indices: 73114--73194 Score: 76
Period size: 31 Copynumber: 2.8 Consensus size: 28
73104 GAAATATATT
*
73114 TATACATTTTATTATTAATTTAATATAAAAA
1 TATATATTTTATT-TTAATTTAAT-T-AAAA
*
73145 TATATATTTTATTCTT-ATCTTAATTTAAA
1 TATATATTTTATT-TTAAT-TTAATTAAAA
*
73174 -ATATATTTTATTTTAAATTAA
1 TATATATTTTATTTTAATTTAA
73195 AAATATAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 6 0.14
28 13 0.30
29 3 0.07
30 3 0.07
31 19 0.43
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (28 bp):
TATATATTTTATTTTAATTTAATTAAAA
Found at i:73184 original size:22 final size:23
Alignment explanation
Indices: 73154--73207 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
73144 ATATATATTT
*
73154 TATTCTTATCTT-AATTTAAAATA
1 TATT-TTATCTTAAATTAAAAATA
*
73177 TATTTTATTTTAAATTAAAAATA
1 TATTTTATCTTAAATTAAAAATA
*
73200 TAGTTTAT
1 TATTTTAT
73208 TATTATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
TATTTTATCTTAAATTAAAAATA
Found at i:73215 original size:22 final size:22
Alignment explanation
Indices: 73159--73216 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
73149 TATTTTATTC
* * *
73159 TTATCTTAATTTAAAATATATT
1 TTATTTTAATTAAAAATATAGT
73181 TTATTTTAAATTAAAAATATAGT
1 TTATTTT-AATTAAAAATATAGT
73204 TTATTATT-ATTAA
1 TTATT-TTAATTAA
73217 TTATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 11 0.35
23 18 0.58
24 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATTTTAATTAAAAATATAGT
Found at i:73224 original size:28 final size:27
Alignment explanation
Indices: 73121--73231 Score: 90
Period size: 28 Copynumber: 4.1 Consensus size: 27
73111 ATTTATACAT
*
73121 TTTATTATTAATTTAATATAAAAATATATA
1 TTTATTATT-ATTTAAT-TTAAAA-ATATA
*
73151 TTTTATTCTTATCTTAATTT-AAAATATA
1 -TTTATTATTAT-TTAATTTAAAAATATA
*
73179 -TT-TTA-T-TTTAAATTAAAAATATA
1 TTTATTATTATTTAATTTAAAAATATA
73202 GTTTATTATTA-TTAATTATAAAAATATA
1 -TTTATTATTATTTAATT-TAAAAATATA
73230 TT
1 TT
73232 ATAATATATT
Statistics
Matches: 67, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
22 6 0.09
23 9 0.13
24 1 0.01
25 4 0.06
26 5 0.07
27 8 0.12
28 15 0.22
29 3 0.04
30 3 0.04
31 13 0.19
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (27 bp):
TTTATTATTATTTAATTTAAAAATATA
Found at i:73226 original size:51 final size:53
Alignment explanation
Indices: 73123--73233 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 53
73113 TTATACATTT
* *
73123 TATTATTAATTTAATATAAAAATATATATTTTATTCTTATCTTAATTTAAAATA
1 TATTATTAATTTAATATAAAAATATATAGTTTATTATTA-CTTAATTTAAAATA
* *
73177 TATT-TTATTTTAA-ATTAAAA-ATATAGTTTATTATTA-TTAATTATAAAAATA
1 TATTATTAATTTAATATAAAAATATATAGTTTATTATTACTTAATT-T-AAAATA
73228 TATTAT
1 TATTAT
73234 AATATATTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
49 6 0.12
50 1 0.02
51 24 0.48
52 7 0.14
53 8 0.16
54 4 0.08
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (53 bp):
TATTATTAATTTAATATAAAAATATATAGTTTATTATTACTTAATTTAAAATA
Found at i:73336 original size:29 final size:29
Alignment explanation
Indices: 73304--73392 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 29
73294 TTTTAGAAAC
73304 ATTTTTTAAAGTTAAAATAATAATAAAAT
1 ATTTTTTAAAGTTAAAATAATAATAAAAT
* * *
73333 A--TTTTGAAGTTAAAATAAGAGTAAAAT
1 ATTTTTTAAAGTTAAAATAATAATAAAAT
* * *
73360 ATATTTTTATA-TTAAACTAATAATAAGAT
1 AT-TTTTTAAAGTTAAAATAATAATAAAAT
73389 ATTT
1 ATTT
73393 AAATATATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
27 24 0.50
28 2 0.04
29 17 0.35
30 5 0.10
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.42
Consensus pattern (29 bp):
ATTTTTTAAAGTTAAAATAATAATAAAAT
Found at i:73455 original size:2 final size:2
Alignment explanation
Indices: 73448--73475 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
73438 TATAAAGATA
73448 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
73476 TTAAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74824 original size:10 final size:10
Alignment explanation
Indices: 74809--74840 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
74799 AATAATAATA
74809 TATTTATATT
1 TATTTATATT
74819 TATTTATATT
1 TATTTATATT
74829 TATTTATATT
1 TATTTATATT
74839 TA
1 TA
74841 AAATTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATTTATATT
Found at i:74828 original size:16 final size:16
Alignment explanation
Indices: 74807--74840 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
74797 CTAATAATAA
74807 TATATTTATATTTATT
1 TATATTTATATTTATT
74823 TATATTTAT-TTATATT
1 TATATTTATATT-TATT
74839 TA
1 TA
74841 AAATTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTTATATTTATT
Found at i:76457 original size:2 final size:2
Alignment explanation
Indices: 76450--76493 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
76440 GTACAACAAC
76450 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA -A T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76488 TA -A TA T
1 TA TA TA T
76494 CTTATTGTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
1 5 0.14
2 32 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76474 original size:15 final size:15
Alignment explanation
Indices: 76450--76493 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
76440 GTACAACAAC
76450 TATA-TATATATATA
1 TATATTATATATATA
76464 TATATTATATATATA
1 TATATTATATATATA
76479 -ATTATTATATA-ATA
1 TA-TATTATATATATA
76493 T
1 T
76494 CTTATTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:76490 original size:11 final size:12
Alignment explanation
Indices: 76456--76491 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
76446 CAACTATATA
76456 TATATATATATAT
1 TATATATATA-AT
76469 TATATATATAAT
1 TATATATATAAT
76481 TAT-TATATAAT
1 TATATATATAAT
76492 ATCTTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.35
12 5 0.22
13 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATATATATAAT
Found at i:76498 original size:15 final size:15
Alignment explanation
Indices: 76452--76499 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
76442 ACAACAACTA
76452 TATATATATATATATAT
1 TATATA-ATATAT-TAT
76469 TATAT-ATATAATTAT
1 TATATAATAT-ATTAT
*
76484 TATATAATATCTTAT
1 TATATAATATATTAT
76499 T
1 T
76500 GTAGGAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 17 0.61
16 6 0.21
17 5 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATAATATATTAT
Done.