Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001714.1 Hibiscus syriacus cultivar Beakdansim tig00003470_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: 69236
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:159 original size:20 final size:20
Alignment explanation
Indices: 131--171 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
121 TATAGGTTCC
*
131 GAAGCGTTGTTTGCAGATTT
1 GAAGAGTTGTTTGCAGATTT
151 GAAGAGTTGTTTGCAGATTT
1 GAAGAGTTGTTTGCAGATTT
171 G
1 G
172 GGTCATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.07, G:0.32, T:0.39
Consensus pattern (20 bp):
GAAGAGTTGTTTGCAGATTT
Found at i:1552 original size:39 final size:40
Alignment explanation
Indices: 1498--1577 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
1488 ACCCTCATTT
* * * *
1498 TAAATTGGTCTTTAAACT-TTTAAAATTCCAATTTCATCC
1 TAAATTAGTCCTTAAACTATTGAAAATTCCAATTCCATCC
* *
1537 TAAATTAGTCCTTAAACTATTGAACATTCTAATTCCATCC
1 TAAATTAGTCCTTAAACTATTGAAAATTCCAATTCCATCC
1577 T
1 T
1578 TAAACTATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 16 0.47
40 18 0.53
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (40 bp):
TAAATTAGTCCTTAAACTATTGAAAATTCCAATTCCATCC
Found at i:2677 original size:21 final size:21
Alignment explanation
Indices: 2651--2690 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2641 TAAACAATAA
* *
2651 TTAAAACATTATTATTTTTAT
1 TTAAAACATCAATATTTTTAT
2672 TTAAAACATCAATATTTTT
1 TTAAAACATCAATATTTTT
2691 TAATATTTCT
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:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAAACATCAATATTTTTAT
Found at i:6020 original size:18 final size:18
Alignment explanation
Indices: 5982--6036 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
5972 ACTTAAATAC
*
5982 TTAAAAA-TTTTGTTTTAT
1 TTAAAAAGTTTT-TTTTCT
*
6000 TTAATAA-TTTTTTTATCT
1 TTAAAAAGTTTTTTT-TCT
6018 TTAAAAAGTTTTTTTTCT
1 TTAAAAAGTTTTTTTTCT
6036 T
1 T
6037 AATCATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 3 0.09
18 22 0.69
19 7 0.22
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (18 bp):
TTAAAAAGTTTTTTTTCT
Found at i:7010 original size:18 final size:18
Alignment explanation
Indices: 6984--7064 Score: 71
Period size: 17 Copynumber: 4.7 Consensus size: 18
6974 TCTACGTTTA
* *
6984 ATAATTGTAAAACATCTT
1 ATAACTGTAAAACATCTG
7002 ATAACTGT-AAACATCTG
1 ATAACTGTAAAACATCTG
* *
7019 ATAAAT-AAAAATCATCTG
1 ATAACTGTAAAA-CATCTG
* *
7037 ATAACTGT-AAATATTTG
1 ATAACTGTAAAACATCTG
7054 ATAACT-TAAAA
1 ATAACTGTAAAA
7065 TCATATGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
16 1 0.02
17 29 0.57
18 21 0.41
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (18 bp):
ATAACTGTAAAACATCTG
Found at i:7015 original size:17 final size:17
Alignment explanation
Indices: 6993--7063 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
6983 AATAATTGTA
*
6993 AAACATCTTATAACTGT
1 AAACATCTGATAACTGT
* **
7010 AAACATCTGATAAATAA
1 AAACATCTGATAACTGT
7027 AAATCATCTGATAACTGT
1 AAA-CATCTGATAACTGT
* *
7045 AAATATTTGATAACT-T
1 AAACATCTGATAACTGT
7061 AAA
1 AAA
7064 ATCATATGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
16 4 0.09
17 26 0.59
18 14 0.32
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (17 bp):
AAACATCTGATAACTGT
Found at i:7035 original size:35 final size:35
Alignment explanation
Indices: 6992--7082 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
6982 TAATAATTGT
*
6992 AAAA-CATCTTATAACTGTAAACATCTGATAAATA
1 AAAATCATCTGATAACTGTAAACATCTGATAAATA
* * * *
7026 AAAATCATCTGATAACTGTAAATATTTGATAACTT
1 AAAATCATCTGATAACTGTAAACATCTGATAAATA
* * *
7061 AAAATCATATGAAAATTGTAAA
1 AAAATCATCTGATAACTGTAAA
7083 TATTTAGAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 4 0.08
35 44 0.92
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (35 bp):
AAAATCATCTGATAACTGTAAACATCTGATAAATA
Found at i:7083 original size:35 final size:35
Alignment explanation
Indices: 7004--7087 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
6994 AACATCTTAT
* * * *
7004 AACTGTAAACATCTGATAAATAAAAATCATCTGAT
1 AACTGTAAATATTTGATAAATAAAAATCATATGAA
* *
7039 AACTGTAAATATTTGATAACTTAAAATCATATGAA
1 AACTGTAAATATTTGATAAATAAAAATCATATGAA
*
7074 AATTGTAAATATTT
1 AACTGTAAATATTT
7088 AGAATTCATC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.35
Consensus pattern (35 bp):
AACTGTAAATATTTGATAAATAAAAATCATATGAA
Found at i:16030 original size:2 final size:2
Alignment explanation
Indices: 16023--16048 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16013 ATATTTCTAA
16023 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
16049 CCATACCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16350 original size:14 final size:14
Alignment explanation
Indices: 16331--16359 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16321 ACCGGTCCGA
16331 ACATGTACATCTCT
1 ACATGTACATCTCT
16345 ACATGTACATCTCT
1 ACATGTACATCTCT
16359 A
1 A
16360 TTTAAAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (14 bp):
ACATGTACATCTCT
Found at i:17204 original size:39 final size:39
Alignment explanation
Indices: 17161--17271 Score: 118
Period size: 39 Copynumber: 2.8 Consensus size: 39
17151 TAAAATAAAT
17161 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
** ** * *
17200 AATTTAGAATCCT-ATGGTGGTACAATTTAAGAAATTAGG
1 AATTTAGAATGTTAAT-GTGAAATAATTTAAGAAATTAAG
* *
17239 AATTTTGAATGTTAGA-GTGAAATAATTTGAGAA
1 AATTTAGAATGTTA-ATGTGAAATAATTTAAGAA
17272 TTCTAAATAA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
38 2 0.04
39 53 0.95
41 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
Found at i:22843 original size:21 final size:24
Alignment explanation
Indices: 22804--22850 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
22794 ATTAAATTAA
22804 TTTAAAAATAATTATGA-TTTTAT
1 TTTAAAAATAATTATGATTTTTAT
*
22827 TTTAAAAA-ATTTA-GATTTTTAT
1 TTTAAAAATAATTATGATTTTTAT
22849 TT
1 TT
22851 AATTTGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 2 0.09
22 12 0.55
23 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTAAAAATAATTATGATTTTTAT
Found at i:24098 original size:35 final size:35
Alignment explanation
Indices: 24058--24133 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
24048 AAAACAGTCC
* *
24058 TCAATTTCATTCTAAAACCC-AATTTCCAAACTAAT
1 TCAATTTCATTCT-AAACCCTAAATTCCAAAATAAT
24093 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
24128 TCAATT
1 TCAATT
24134 AAATTCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 6 0.16
35 32 0.84
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
Found at i:24672 original size:130 final size:130
Alignment explanation
Indices: 24531--24778 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
24521 TATTTATATA
* * **
24531 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATATG
1 ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* *
24596 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGAT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGAT
*
24661 ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
24726 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
24779 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCATAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGAT
Found at i:25270 original size:16 final size:18
Alignment explanation
Indices: 25249--25282 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
25239 ATTTTTTATT
25249 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
25265 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
25283 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:29123 original size:81 final size:82
Alignment explanation
Indices: 29018--29181 Score: 296
Period size: 81 Copynumber: 2.0 Consensus size: 82
29008 ACTCTGTTAG
29018 ACCTAGAACCAAAAAGGGCTAAAACTATCAAAACGTGGCCCAAAAAATACCTCGAAG-CGAGGGG
1 ACCTAGAACCAAAAAGGGCTAAAACTATCAAAACGT-GCCCAAAAAATACCTCGAAGACGAGGGG
29082 TCGGAGTCCAATGGTTTA
65 TCGGAGTCCAATGGTTTA
29100 ACCTAGAACC-AAAAGGGCTAAAACTATCAAAACGTGCCCAAAAAATACCTCGAAGACGAGGGGT
1 ACCTAGAACCAAAAAGGGCTAAAACTATCAAAACGTGCCCAAAAAATACCTCGAAGACGAGGGGT
*
29164 CGGCGTCCAATGGTTTA
66 CGGAGTCCAATGGTTTA
29181 A
1 A
29182 AAAAATTATC
Statistics
Matches: 80, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
80 20 0.25
81 50 0.62
82 10 0.12
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (82 bp):
ACCTAGAACCAAAAAGGGCTAAAACTATCAAAACGTGCCCAAAAAATACCTCGAAGACGAGGGGT
CGGAGTCCAATGGTTTA
Found at i:32455 original size:2 final size:2
Alignment explanation
Indices: 32448--32472 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32438 TAAAGCTTTT
32448 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
32473 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40261 original size:27 final size:28
Alignment explanation
Indices: 40207--40265 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
40197 CCGACCTGAT
40207 CCGAATATCACACTTTAAAAAACCCGAC
1 CCGAATATCACACTTTAAAAAACCCGAC
**
40235 CCGAATATCACAC-TTAAAAAATTCGAC
1 CCGAATATCACACTTTAAAAAACCCGAC
40262 CCGA
1 CCGA
40266 CTCGAACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (28 bp):
CCGAATATCACACTTTAAAAAACCCGAC
Found at i:42694 original size:200 final size:200
Alignment explanation
Indices: 42345--42744 Score: 593
Period size: 200 Copynumber: 2.0 Consensus size: 200
42335 ACAACAAATT
** * * *
42345 ATAGGAGAGATGGTGAGAGCCTATGATATTCGGACTTGGGATGCAAGTCTGGACACATGTATTCG
1 ATAGGAGAGATGGTGAGAGCCTATGATATTCGGACTCAGGATGCAAGTCTCGACACATATATGCG
* * * * * * *
42410 GAGGATCTTTAAGGGGTGATATTCCCGGATCCATGTTCGTTGAATACGAGTTACCTGAGCATGGA
66 GAGGACCATGAAAGGGTAATATTCCCGGATCCATGTTCGCTGAATACGAGTTACCTGAGCATAGA
** * *
42475 TTTTTTATGCTCACATGATGTGAGAATCAGTCCAGAGAATGGTGTACTGATGGAAATCTTCAGCG
131 TTTTAGATGCTCACATGATGTGAGAATCAGTCCAGAGAATGGTGTACTGATGGAAATCATCAGCA
42540 GGATC
196 GGATC
*
42545 ATAGGGGAGATGGTGAGAGCCTATGATATTCGGACTCAGGATGCAAGTCTCGACACATATATGCG
1 ATAGGAGAGATGGTGAGAGCCTATGATATTCGGACTCAGGATGCAAGTCTCGACACATATATGCG
* * * *
42610 GAGGACCATGAAAGGGTAATCTTCTCGTATCCATGTTCGCTGAATACGAGTTACGTGAGCATAGA
66 GAGGACCATGAAAGGGTAATATTCCCGGATCCATGTTCGCTGAATACGAGTTACCTGAGCATAGA
* *
42675 TTTTAGATGCTTACATGATGTGTGAATCAGTCCAGAGAATGGTGTACTGATGGAAATCATCAGCA
131 TTTTAGATGCTCACATGATGTGAGAATCAGTCCAGAGAATGGTGTACTGATGGAAATCATCAGCA
42740 GGATC
196 GGATC
42745 GAACCAAAGA
Statistics
Matches: 177, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
200 177 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (200 bp):
ATAGGAGAGATGGTGAGAGCCTATGATATTCGGACTCAGGATGCAAGTCTCGACACATATATGCG
GAGGACCATGAAAGGGTAATATTCCCGGATCCATGTTCGCTGAATACGAGTTACCTGAGCATAGA
TTTTAGATGCTCACATGATGTGAGAATCAGTCCAGAGAATGGTGTACTGATGGAAATCATCAGCA
GGATC
Found at i:44229 original size:18 final size:18
Alignment explanation
Indices: 44206--44250 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
44196 TATCGGGTCG
44206 GGTCGTGGTAATACGTGT
1 GGTCGTGGTAATACGTGT
44224 GGTCGTGGTAATACGTGT
1 GGTCGTGGTAATACGTGT
44242 GGTCGTGGT
1 GGTCGTGGT
44251 CGTGGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.11, G:0.42, T:0.33
Consensus pattern (18 bp):
GGTCGTGGTAATACGTGT
Found at i:44362 original size:21 final size:21
Alignment explanation
Indices: 44336--44498 Score: 101
Period size: 21 Copynumber: 7.9 Consensus size: 21
44326 TTTTTAATTT
44336 ACTGTAGACTATCGCAACGAC
1 ACTGTAGACTATCGCAACGAC
*
44357 ACTGTAGATTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* **
44377 GAAATG--GAAAATCGCAACGAC
1 --ACTGTAGACTATCGCAACGAC
*
44398 ACTGTACACTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* **
44418 GAAATG-A-AAAATCGCAACGAC
1 --ACTGTAGACTATCGCAACGAC
44439 ACTGTAGACTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* ** *
44459 GAAATG-A-AAAATAGCAACGAC
1 --ACTGTAGACTATCGCAACGAC
44480 ACTGTAGACTATCGCAACG
1 ACTGTAGACTATCGCAACG
44499 CGATTTTCAA
Statistics
Matches: 105, Mismatches: 22, Indels: 30
0.67 0.14 0.19
Matches are distributed among these distances:
19 9 0.09
20 35 0.33
21 52 0.50
22 9 0.09
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.17
Consensus pattern (21 bp):
ACTGTAGACTATCGCAACGAC
Found at i:44392 original size:20 final size:20
Alignment explanation
Indices: 44367--44477 Score: 68
Period size: 20 Copynumber: 5.5 Consensus size: 20
44357 ACTGTAGATT
*
44367 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
* **
44387 ATCGCAA--CGACACTGTACACT
1 ATCGCAACGCGA-AATG-A-AAA
44408 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
* **
44428 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG-A-AAA
44449 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
44469 ATAGCAACG
1 ATCGCAACG
44478 ACACTGTAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
18 6 0.09
19 6 0.09
20 25 0.37
21 18 0.27
22 6 0.09
23 6 0.09
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:44403 original size:41 final size:41
Alignment explanation
Indices: 44346--44501 Score: 276
Period size: 41 Copynumber: 3.8 Consensus size: 41
44336 ACTGTAGACT
* *
44346 ATCGCAACGACACTGTAGATTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGAAAA
*
44387 ATCGCAACGACACTGTACACTATCGCAACGCGAAATGAAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGAAAA
44428 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGAAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGAAAA
*
44469 ATAGCAACGACACTGTAGACTATCGCAACGCGA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGA
44502 TTTTCAACTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 110 1.00
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (41 bp):
ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGAAAA
Found at i:52027 original size:21 final size:20
Alignment explanation
Indices: 52001--52042 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
51991 TTTTAATAAG
52001 TATGTTTGCATGACACATTTT
1 TATGTTT-CATGACACATTTT
* *
52022 TATGTTTTATGGCACATTTT
1 TATGTTTCATGACACATTTT
52042 T
1 T
52043 TAATATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.52
Consensus pattern (20 bp):
TATGTTTCATGACACATTTT
Found at i:59865 original size:4 final size:4
Alignment explanation
Indices: 59856--59893 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
59846 TAGGCGAGTT
*
59856 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATAC ATCC AT
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
59894 ACACAGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.29, C:0.45, G:0.00, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:62066 original size:9 final size:9
Alignment explanation
Indices: 62052--62079 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
62042 AAATGTAAAT
62052 CGGTTACAC
1 CGGTTACAC
62061 CGGTTACAC
1 CGGTTACAC
62070 CGGTTACAC
1 CGGTTACAC
62079 C
1 C
62080 ATCAGACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (9 bp):
CGGTTACAC
Found at i:62556 original size:2 final size:2
Alignment explanation
Indices: 62549--62576 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62539 TTTTTCAAAT
62549 TA 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
62577 ACGTTGATGA
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):
TA
Found at i:62648 original size:19 final size:20
Alignment explanation
Indices: 62610--62649 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
62600 ACTGAGATCA
62610 ATAGTAAAAAATGTGAAGATAT
1 ATAGTAAAAAA--TGAAGATAT
62632 ATAGTAAAAAA-GAAGATA
1 ATAGTAAAAAATGAAGATA
62650 AAAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
22 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (20 bp):
ATAGTAAAAAATGAAGATAT
Found at i:63271 original size:16 final size:17
Alignment explanation
Indices: 63240--63273 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
63230 CCTTATTTTT
*
63240 TTATTTATTATTTTAAA
1 TTATTTATTATATTAAA
63257 TTATTT-TTATATTAAA
1 TTATTTATTATATTAAA
63273 T
1 T
63274 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTATTATATTAAA
Found at i:66571 original size:60 final size:59
Alignment explanation
Indices: 66467--66616 Score: 144
Period size: 60 Copynumber: 2.5 Consensus size: 59
66457 TGTGTCATAT
* * * * **
66467 ATCCTTAAACTATGATTCTCGTTTTAAATAAGTTTCTAGATTTTTAAATGTTTTAATTTC
1 ATCCTTAAACTATGACT-TCATTCTAAATTAGTTTCTAGATTTTTAAACATTTTAATTTC
* *
66527 ATCCTTAAACTATGACTATCATTCTAAATTAGTCTTC-A-ATTTTTTGAACATTTTAGTTTC
1 ATCCTTAAACTATGACT-TCATTCTAAATTAGT-TTCTAGA-TTTTTAAACATTTTAATTTC
*
66587 ATCCTCAAACTAT-ATCCTTCATTCTAAATT
1 ATCCTTAAACTATGA--CTTCATTCTAAATT
66617 GGTCCCCACA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
59 2 0.03
60 69 0.91
61 5 0.07
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (59 bp):
ATCCTTAAACTATGACTTCATTCTAAATTAGTTTCTAGATTTTTAAACATTTTAATTTC
Done.