Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005445.1 Hibiscus syriacus cultivar Beakdansim tig00012478_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: 58120
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:965 original size:29 final size:29
Alignment explanation
Indices: 933--1012 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 29
923 GCTCTTTAAG
933 GTATATTTTATTATATTTAATATTTGTTA
1 GTATATTTTATTATATTTAATATTTGTTA
*
962 GTAT-TTTT-TTAACTATTTAA-ATTTTTTA
1 GTATATTTTATT-A-TATTTAATATTTGTTA
*
990 --ATATTTTATT-TAATTAAT-TTTGT
1 GTATATTTTATTATATTTAATATTTGT
1013 AGTTATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
25 10 0.23
26 2 0.05
27 6 0.14
28 14 0.33
29 11 0.26
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (29 bp):
GTATATTTTATTATATTTAATATTTGTTA
Found at i:4683 original size:35 final size:35
Alignment explanation
Indices: 4641--4711 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
4631 GATTTTTCTC
*
4641 GAATATCCACATCACAATGAATTCGAGTAGATTTT
1 GAATATCCACATCACAATGAATTCGAGTAGACTTT
4676 GAATATCCACATCACAATGAATTCGAGTAGACTTT
1 GAATATCCACATCACAATGAATTCGAGTAGACTTT
4711 G
1 G
4712 GATGACCACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (35 bp):
GAATATCCACATCACAATGAATTCGAGTAGACTTT
Found at i:13196 original size:22 final size:23
Alignment explanation
Indices: 13171--13214 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13161 GTATATGATT
*
13171 CTTAAGGA-ATTTCTATGTGGCC
1 CTTAAGGACATTTCTACGTGGCC
*
13193 CTTATGGACATTTCTACGTGGC
1 CTTAAGGACATTTCTACGTGGC
13215 ACTTCGGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (23 bp):
CTTAAGGACATTTCTACGTGGCC
Found at i:13227 original size:23 final size:23
Alignment explanation
Indices: 13201--13289 Score: 124
Period size: 23 Copynumber: 3.9 Consensus size: 23
13191 CCCTTATGGA
*
13201 CATTTCTACGTGGCACTTCGGTG
1 CATTTCTACGCGGCACTTCGGTG
*
13224 CATTTCTACGCGGCACTTCAGTG
1 CATTTCTACGCGGCACTTCGGTG
13247 CATTTCTACGCGGCACTTCGGTG
1 CATTTCTACGCGGCACTTCGGTG
* * * *
13270 CAATCCTACGTGGTACTTCG
1 CATTTCTACGCGGCACTTCG
13290 CATTTATACG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (23 bp):
CATTTCTACGCGGCACTTCGGTG
Found at i:21019 original size:26 final size:27
Alignment explanation
Indices: 20969--21019 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
20959 TAATTTTCTT
**
20969 TAAAAAACCCTAAAATTCTTTAAATAC
1 TAAAAAACCCTAAAATTCTCGAAATAC
20996 TAAAAAACCC-AAAATTCTCGAAAT
1 TAAAAAACCCTAAAATTCTCGAAAT
21020 TCCCCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.53, C:0.20, G:0.02, T:0.25
Consensus pattern (27 bp):
TAAAAAACCCTAAAATTCTCGAAATAC
Found at i:21058 original size:20 final size:20
Alignment explanation
Indices: 21020--21058 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21010 TTCTCGAAAT
* *
21020 TCCCCAAAAAAACCCTAAAA
1 TCCCAAAAAAAACCATAAAA
*
21040 TCCCAAAAAAAACTATAAA
1 TCCCAAAAAAAACCATAAA
21059 CCTTGAATCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.13
Consensus pattern (20 bp):
TCCCAAAAAAAACCATAAAA
Found at i:21459 original size:2 final size:2
Alignment explanation
Indices: 21440--21496 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
21430 ATTATAAATC
* * *
21440 AT AT AT AA AA AT AT -T AT AT AT AT AT -T AT A- AT GT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21478 A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
21497 TACTTTAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
1 5 0.11
2 41 0.89
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21477 original size:10 final size:10
Alignment explanation
Indices: 21450--21498 Score: 62
Period size: 10 Copynumber: 4.6 Consensus size: 10
21440 ATATATAAAA
21450 ATATTATATAT
1 ATATTATA-AT
21461 ATATTATAAT
1 ATATTATAAT
*
21471 GTATTATAAT
1 ATATTATAAT
21481 ATATATATATAT
1 ATAT-TATA-AT
21493 ATATTA
1 ATATTA
21499 CTTTAGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 14 0.41
11 14 0.41
12 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (10 bp):
ATATTATAAT
Found at i:21497 original size:22 final size:22
Alignment explanation
Indices: 21429--21498 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
21419 ATATTATTTT
* *
21429 TATTATAA-ATCATATATAAAAA
1 TATTATAATAT-ATATATATATA
*
21451 TATTAT-ATATATAT-TATAATG
1 TATTATAATATATATATAT-ATA
21472 TATTATAATATATATATATATA
1 TATTATAATATATATATATATA
21494 TATTA
1 TATTA
21499 CTTTAGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.05
21 12 0.30
22 23 0.57
23 3 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (22 bp):
TATTATAATATATATATATATA
Found at i:24353 original size:2 final size:2
Alignment explanation
Indices: 24342--24370 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
24332 TAAAGACACC
24342 AT AT -T 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 AT
24371 CCCATTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:26379 original size:10 final size:10
Alignment explanation
Indices: 26364--26396 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
26354 AACCCAATCA
*
26364 CCCTTATCGT
1 CCCTTATTGT
26374 CCCTTATTGT
1 CCCTTATTGT
26384 CCCTTATTGT
1 CCCTTATTGT
26394 CCC
1 CCC
26397 ATTTATGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.09, C:0.39, G:0.09, T:0.42
Consensus pattern (10 bp):
CCCTTATTGT
Found at i:28188 original size:16 final size:16
Alignment explanation
Indices: 28152--28195 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
28142 ATATATATAC
28152 ATATA-TTT-TTTAAT
1 ATATATTTTATTTAAT
* *
28166 ATTTATTTTATTTTAT
1 ATATATTTTATTTAAT
28182 ATATATTTTATTTA
1 ATATATTTTATTTA
28196 TACGTTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 4 0.17
15 3 0.12
16 17 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATATTTTATTTAAT
Found at i:28196 original size:20 final size:19
Alignment explanation
Indices: 28155--28194 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
28145 TATATACATA
*
28155 TATTTTTTAATATTTATTT
1 TATTTTATAATATTTATTT
28174 TATTTTATATATATTTTATTT
1 TATTTTATA-ATA-TTTATTT
28195 ATACGTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTATAATATTTATTT
Found at i:39024 original size:105 final size:105
Alignment explanation
Indices: 38842--40209 Score: 2202
Period size: 105 Copynumber: 13.0 Consensus size: 105
38832 TTTTTCAAGT
* * * * *
38842 TCTAGACAATGCAAGTTCAACTTCACGACGAATGGACCGCTGGTTATCAACAACAATTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
38907 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
38947 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
* *
39012 TTCAGAACCAATTTCAACTTCACAGTGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* *
39052 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCACAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
39117 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * *
39157 TCTAGACAACTCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAATAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
39222 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * *
39262 TCTAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAAA
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
39327 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
39367 TCTAG-CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTTTCAACAACAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
39431 TTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
39471 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
39536 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
39576 TCTAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
39641 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* *
39681 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTACTAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
39746 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* *
39786 TCTAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAATAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
* * *
39851 CTCAGAGCCAATTTCAAATTCACAACGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* *
39891 TCTAGATAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
39956 CTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * * * *
39996 TCAAGACAGCACAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAGCAA-TCTCCCA
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-CAACT-TCCCA
* *
40060 ATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGAC
64 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * * * *
40102 TCAAGGA-AGCACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCA
1 TCTA-GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACAACTTCCCA
* * * *
40166 GTTTCAGAGCCAACTTCAACTTCACAGCGGATGATATTGGAC
64 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
40208 TC
1 TC
40210 GGAACAATAC
Statistics
Matches: 1182, Mismatches: 75, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
104 98 0.08
105 938 0.79
106 141 0.12
107 5 0.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
Found at i:41915 original size:16 final size:17
Alignment explanation
Indices: 41884--41919 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
41874 TACATATATT
*
41884 TTTTACTATTTATTTTA
1 TTTTACTATATATTTTA
41901 TTTTA-TATATATTTTA
1 TTTTACTATATATTTTA
41917 TTT
1 TTT
41920 ATACGTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTACTATATATTTTA
Found at i:42177 original size:2 final size:2
Alignment explanation
Indices: 42170--42251 Score: 155
Period size: 2 Copynumber: 41.0 Consensus size: 2
42160 CAACATTCGA
42170 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
*
42212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42252 TTATTTAATT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45654 original size:105 final size:105
Alignment explanation
Indices: 45472--46128 Score: 1019
Period size: 105 Copynumber: 6.2 Consensus size: 105
45462 AGCCCGTCAT
45472 CTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
1 CTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
45537 CTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTAAA
66 CTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAA
* * *
45577 CTTCACATCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTA
1 CTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
45642 CTTGTCAACAACAACTTCCCAATTTCAGAACCAATTTCAA
66 CTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAA
45682 CTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
1 CTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
* *
45747 CTTGTCAACAATAACTTCCCAATCTCAGAGCCAATTTCAA
66 CTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAA
*
45787 ATTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
1 CTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
*
45852 CTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAA
66 CTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAA
* * * *
45892 CTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGTTCAACTTCACGACGAAGGGACCGCTA
1 CTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
* *
45957 ATTGTCAATAAGCAA-TCTCCCAATTTCAGAGCCAATTTCAA
66 CTTGTCAACAA-CAACT-TCCCAATTTCAGAGCCAATTTCAA
* * * * * *
45998 CTTCACAGCGAATGATATTGGACTCAAGGCAGCACAAGTTCAACTTCACGACGAAGGGATCGCTG
1 CTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
* * * * *
46063 GTTGTCAATAAACAATTTCCCAGTTTCAGAGCCAACTTCAA
66 CTTGTCAA-CAACAACTTCCCAATTTCAGAGCCAATTTCAA
* * *
46104 CTTCACACCGGATGATATTGGACTC
1 CTTCACAGCGAAGGATATTGGACTC
46129 GGAACAATAC
Statistics
Matches: 517, Mismatches: 31, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
105 372 0.72
106 142 0.27
107 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
CTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAA
Found at i:48094 original size:2 final size:2
Alignment explanation
Indices: 48087--48144 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
48077 CAACATTTGA
48087 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
48129 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
48145 TTATTTAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48203 original size:4 final size:4
Alignment explanation
Indices: 48194--48225 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
48184 TGCTTTCCTC
48194 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
48226 TTCCGTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:49544 original size:2 final size:2
Alignment explanation
Indices: 49537--49628 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
49527 TAATAGATCA
49537 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
49579 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
49621 AT AT AT AT
1 AT AT AT AT
49629 GTGGTTATAC
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51763 original size:2 final size:2
Alignment explanation
Indices: 51756--51828 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
51746 CTTGATCTAA
51756 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
51798 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51829 CTATGAGAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52904 original size:2 final size:2
Alignment explanation
Indices: 52899--52939 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
52889 TATCTAATGC
52899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52940 TTTTATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54116 original size:16 final size:16
Alignment explanation
Indices: 54079--54117 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
54069 CGATAATGAT
*
54079 GGGGAATAAGTAGACA
1 GGGGAAGAAGTAGACA
*
54095 -GGGAAGAAGTAGATA
1 GGGGAAGAAGTAGACA
54110 GGGGAAGA
1 GGGGAAGA
54118 TACCAGCGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.44, C:0.03, G:0.44, T:0.10
Consensus pattern (16 bp):
GGGGAAGAAGTAGACA
Done.