Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001197.1 Hibiscus syriacus cultivar Beakdansim tig00002371_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: 51409
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2167 original size:36 final size:35
Alignment explanation
Indices: 2014--2232 Score: 186
Period size: 36 Copynumber: 6.2 Consensus size: 35
2004 TTGAATTTGT
* *
2014 TTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGACAA
1 TTTCTCTTAAAACAAA--TTTGTCTCTCTTGAGACAG
2050 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACAG
* * * *
2086 TTTCCCTTGAAACAAA-----ATCT-TTGA-ATATG
1 TTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA-G
2115 TTT-TCCTTAAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCT-CTTAAAACAAATTT-GTCTCTCTTGAGACAG
*
2151 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGG
1 TTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACAG
* * *
2187 TTTCCCTTGAAACAAAGTTTTTAGCTCTCTTGAGACAG
1 TTTCTCTTAAAACAAA-TTTGT--CTCTCTTGAGACAG
*
2225 TTTATCTT
1 TTTCTCTT
2233 GAAGCACCAA
Statistics
Matches: 150, Mismatches: 18, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
28 2 0.01
29 18 0.12
30 3 0.02
35 3 0.02
36 89 0.59
37 16 0.11
38 19 0.13
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (35 bp):
TTTCTCTTAAAACAAATTTGTCTCTCTTGAGACAG
Found at i:2180 original size:101 final size:101
Alignment explanation
Indices: 1927--2202 Score: 446
Period size: 101 Copynumber: 2.7 Consensus size: 101
1917 GCTCAAGACT
* * * *
1927 AATTTTGTCTATCTTGAGACATTTTCTCTTAAAA-AAATTTCGTCTCTCTTAAGACGGTTTCCCT
1 AATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCT
* *
1991 TGAAACAAAAACTTTGAATTTGTTTTCCTTGAAACA
66 TGAAACAAAAACTTTGAATATGTTTTCCTTAAAACA
*
2027 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
1 AA-TTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCC
*
2092 TTGAAACAAAATCTTTGAATATGTTTTCCTTAAAACA
65 TTGAAACAAAAACTTTGAATATGTTTTCCTTAAAACA
* *
2129 AATTTCGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCT
1 AATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCT
2194 TGAAACAAA
66 TGAAACAAA
2203 GTTTTTAGCT
Statistics
Matches: 163, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
100 2 0.01
101 99 0.61
102 62 0.38
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (101 bp):
AATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCT
TGAAACAAAAACTTTGAATATGTTTTCCTTAAAACA
Found at i:2315 original size:33 final size:34
Alignment explanation
Indices: 2245--2336 Score: 150
Period size: 33 Copynumber: 2.7 Consensus size: 34
2235 AGCACCAATA
*
2245 TTTGAAATTGTTTCCCTTGAAACACAAAAAAAAC
1 TTTGAAATTGTTTCTCTTGAAACACAAAAAAAAC
*
2279 TTTGAAATTGTTTCTCTTGAAACAC-AAAAAACC
1 TTTGAAATTGTTTCTCTTGAAACACAAAAAAAAC
*
2312 TTTGAAAATGTTTCTCTTGAAACAC
1 TTTGAAATTGTTTCTCTTGAAACAC
2337 CAAACCTTCG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (34 bp):
TTTGAAATTGTTTCTCTTGAAACACAAAAAAAAC
Found at i:5525 original size:14 final size:13
Alignment explanation
Indices: 5493--5545 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
5483 AATAAAAAAG
5493 ATAAAATATAAAT
1 ATAAAATATAAAT
5506 ATAAAAT-TAAAT
1 ATAAAATATAAAT
**
5518 ACATAAAA-ATATGT
1 --ATAAAATATAAAT
5532 ATAAAATATAAAT
1 ATAAAATATAAAT
5545 A
1 A
5546 ATTAATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 11 0.34
13 12 0.38
14 9 0.28
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (13 bp):
ATAAAATATAAAT
Found at i:5583 original size:21 final size:20
Alignment explanation
Indices: 5541--5593 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
5531 TATAAAATAT
* *
5541 AAATAATTA-ATAATTTAAA
1 AAATATTTATATAATTAAAA
5560 AAATATTTATATAATTAAAAA
1 AAATATTTATATAATT-AAAA
*
5581 AAATATATATATA
1 AAATATTTATATA
5594 TATATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 8 0.28
20 6 0.21
21 15 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATTTATATAATTAAAA
Found at i:9213 original size:29 final size:29
Alignment explanation
Indices: 9177--9232 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
9167 ATTAATTTAT
*
9177 TTTTTGTTATTTATAATTT-TGCCTTTAAA
1 TTTTTGTTATTT-TAATTTATGCATTTAAA
9206 TTTTTGTTATTTTAATTTATGCATTTA
1 TTTTTGTTATTTTAATTTATGCATTTA
9233 CTTTCAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.64
Consensus pattern (29 bp):
TTTTTGTTATTTTAATTTATGCATTTAAA
Found at i:12954 original size:16 final size:17
Alignment explanation
Indices: 12923--12958 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
12913 TACATATATT
*
12923 TTTTACTATTTATTTTA
1 TTTTACTATATATTTTA
12940 TTTTA-TATATATTTTA
1 TTTTACTATATATTTTA
12956 TTT
1 TTT
12959 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:13217 original size:2 final size:2
Alignment explanation
Indices: 13210--13245 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13200 CAACATTTGA
13210 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
13246 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16736 original size:21 final size:21
Alignment explanation
Indices: 16712--16755 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
16702 CCAAATTGCA
16712 TACATCATACATTACATATTT
1 TACATCATACATTACATATTT
** **
16733 TACATTTTACATTTTATATTT
1 TACATCATACATTACATATTT
16754 TA
1 TA
16756 TATTTGTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (21 bp):
TACATCATACATTACATATTT
Found at i:16776 original size:7 final size:7
Alignment explanation
Indices: 16727--16760 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
16717 CATACATTAC
16727 ATATTTT
1 ATATTTT
*
16734 ACATTTT
1 ATATTTT
*
16741 ACATTTT
1 ATATTTT
16748 ATATTTT
1 ATATTTT
16755 ATATTT
1 ATATTT
16761 GTTTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (7 bp):
ATATTTT
Found at i:24737 original size:105 final size:105
Alignment explanation
Indices: 24555--25713 Score: 1888
Period size: 105 Copynumber: 11.0 Consensus size: 105
24545 TTTTTCAAGT
* * * *
24555 TCTAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAATTTCTCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
24620 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* *
24660 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAATTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
24725 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* *
24765 TCTAGACAACGCAAGTTCAACTTCATGAAGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
24830 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
24870 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
24935 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * *
24975 TCTAGACAACGCAAGTTCAACTTCACGATGAATGGACCGCTGCTTGTCAACAATAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
25040 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * *
25080 TCTAGACAACGCAAGTTCAACTTCACGATGAAGGGACTGTTGCTTGTCAACAACAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
25145 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
25185 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAATAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
*
25250 CTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
25290 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAATAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
* * *
25355 CTCAGATCTAATTTCAACTTCACAGCGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
25395 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
* *
25460 CTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
66 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * * * * *
25500 TCAAGATAGCACAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAGCAA-TCTCCCA
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-CAACT-TCCCA
*
25564 ATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGAC
64 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * * * * * * *
25606 TCAAGGCAGCACAAGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAATAAACAATTTCCCAG
1 TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACAACTTCCCAA
* * *
25671 TTTCAGAGCCAACTTCAACTTCACAGCGGATGATATTGGAC
65 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
25712 TC
1 TC
25714 AGAACAATAC
Statistics
Matches: 1002, Mismatches: 48, Indels: 7
0.95 0.05 0.01
Matches are distributed among these distances:
105 857 0.86
106 142 0.14
107 3 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
TCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAAT
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
Found at i:27430 original size:11 final size:11
Alignment explanation
Indices: 27393--27430 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
27383 TTTTTTACTA
27393 TTTATTT-TAT
1 TTTATTTATAT
*
27403 TTTATATATAT
1 TTTATTTATAT
27414 TTTATTTATAT
1 TTTATTTATAT
*
27425 GTTATT
1 TTTATT
27431 ACATATATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
TTTATTTATAT
Found at i:27430 original size:16 final size:16
Alignment explanation
Indices: 27385--27430 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
27375 TACATATATT
27385 TTTTACTATTTATTTTA
1 TTTTA-TATTTATTTTA
*
27402 TTTTATATATATTTTA
1 TTTTATATTTATTTTA
27418 -TTTATATGTTATT
1 TTTTATAT-TTATT
27431 ACATATATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 7 0.27
16 14 0.54
17 5 0.19
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTTATATTTATTTTA
Found at i:27673 original size:2 final size:2
Alignment explanation
Indices: 27666--27709 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
27656 CAACATTTGA
*
27666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27708 AT
1 AT
27710 TTTATTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29922 original size:29 final size:29
Alignment explanation
Indices: 29887--29968 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
29877 AAACTAAATT
*
29887 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
29916 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
*
29945 GATGTCATTGCTTGCATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
29969 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:34684 original size:29 final size:29
Alignment explanation
Indices: 34649--34730 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
34639 AAACTAAATT
*
34649 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
* *
34678 GATGTCATTGCTTACATAATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
34707 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
34731 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:35301 original size:19 final size:19
Alignment explanation
Indices: 35279--35318 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
35269 TAAAATATTA
35279 ATATTTGATTTATTAATCG
1 ATATTTGATTTATTAATCG
35298 ATATTTGATTTATTAATCG
1 ATATTTGATTTATTAATCG
35317 AT
1 AT
35319 TAATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (19 bp):
ATATTTGATTTATTAATCG
Found at i:36533 original size:29 final size:30
Alignment explanation
Indices: 36488--36561 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
36478 TAACCGTTGA
36488 GTGACTAAAA-A-ATAAATTTTAAAAGCTA-
1 GTGACTAAAATAGA-AAATTTTAAAAGCTAT
*
36516 GATGA-TAAAATTGAAAATTTTAAAAGCTAT
1 G-TGACTAAAATAGAAAATTTTAAAAGCTAT
36546 GTGACTAAAATAGAAA
1 GTGACTAAAATAGAAA
36562 CACAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 6 0.15
29 21 0.54
30 12 0.31
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (30 bp):
GTGACTAAAATAGAAAATTTTAAAAGCTAT
Found at i:41548 original size:23 final size:23
Alignment explanation
Indices: 41518--41587 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
41508 GACACTTGAT
41518 TATGGTTTAGTATTTCGCAAGGC
1 TATGGTTTAGTATTTCGCAAGGC
41541 TATGGTTTAGTATTTCGCAAGGC
1 TATGGTTTAGTATTTCGCAAGGC
*
41564 TATGGTTTAATATTTCGCAAGGC
1 TATGGTTTAGTATTTCGCAAGGC
41587 T
1 T
41588 GGATTGGGCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (23 bp):
TATGGTTTAGTATTTCGCAAGGC
Found at i:42998 original size:32 final size:31
Alignment explanation
Indices: 42934--43021 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 31
42924 TAGGAGAGTT
42934 GCAGGGAACAAAGTGCGTCTTCCGGGAAGAC
1 GCAGGGAACAAAGTGCGTCTTCCGGGAAGAC
* * *
42965 GCAGGGAACATAGTGTGTCTTCTGGGGAAGAC
1 GCAGGGAACAAAGTGCGTCTTC-CGGGAAGAC
*
42997 GCCAGGGGAACACAA-TGCATCTTCC
1 G-CA-GGGAACA-AAGTGCGTCTTCC
43022 TCGTTTTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
31 20 0.43
32 9 0.20
33 2 0.04
34 14 0.30
35 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.33, T:0.17
Consensus pattern (31 bp):
GCAGGGAACAAAGTGCGTCTTCCGGGAAGAC
Found at i:44505 original size:19 final size:18
Alignment explanation
Indices: 44431--44525 Score: 97
Period size: 18 Copynumber: 5.3 Consensus size: 18
44421 ATTATTTTTG
* *
44431 AAATAAAAGATTAGAATA
1 AAATAAAAGATAAGGATA
*
44449 AAATAAAAGATAAAGATA
1 AAATAAAAGATAAGGATA
* * *
44467 AAATAAATAAAT-A--TTT
1 AAATAAA-AGATAAGGATA
44483 AAATAAAAGATAAGGATAA
1 AAATAAAAGATAAGGAT-A
44502 AAATAAAAGATAAGGATA
1 AAATAAAAGATAAGGATA
44520 AAATAA
1 AAATAA
44526 TTAAATAGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
15 3 0.05
16 9 0.14
18 31 0.49
19 20 0.32
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAGGATA
Found at i:44520 original size:53 final size:52
Alignment explanation
Indices: 44431--44532 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 52
44421 ATTATTTTTG
*
44431 AAATAAAAGATTAGAATAAAATAAAAGATAAAGATAAAATAAATAAATATTT
1 AAATAAAAGATAAGAATAAAATAAAAGATAAAGATAAAATAAATAAATATTT
* * *
44483 AAATAAAAGATAAGGATAAAAATAAAAGATAAGGATAAAATAATTAAATA
1 AAATAAAAGATAAGAAT-AAAATAAAAGATAAAGATAAAATAAATAAATA
44533 GATAAATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 15 0.33
53 30 0.67
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (52 bp):
AAATAAAAGATAAGAATAAAATAAAAGATAAAGATAAAATAAATAAATATTT
Found at i:47198 original size:11 final size:11
Alignment explanation
Indices: 47182--47214 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
47172 AAAGTACGCT
47182 AAAAATAAAAC
1 AAAAATAAAAC
*
47193 AAAAATAAAAT
1 AAAAATAAAAC
47204 AAAAATAAAAC
1 AAAAATAAAAC
47215 GAAATGGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (11 bp):
AAAAATAAAAC
Found at i:48034 original size:65 final size:63
Alignment explanation
Indices: 47957--48079 Score: 162
Period size: 63 Copynumber: 1.9 Consensus size: 63
47947 AATGCATTTT
*
47957 ATGCATCAATGCACTCAGG-TT-TTATGAAAAACATCGAATGT-GTTTTATGCATCGATGCACAG
1 ATGCATCAATGCACTCAGGCTTGTT-TG---AACATCGAAT-TCATTTTATGCATCGATGCACAG
48019 ACC
61 ACC
*
48022 ATGCATCGATGCACTCAGGCTTGTTTGAACATCGAATTCATTTTATGCATCGATGCAC
1 ATGCATCAATGCACTCAGGCTTGTTTGAACATCGAATTCATTTTATGCATCGATGCAC
48080 TCTTAGTGCA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
62 1 0.02
63 28 0.53
65 18 0.34
66 4 0.08
67 2 0.04
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (63 bp):
ATGCATCAATGCACTCAGGCTTGTTTGAACATCGAATTCATTTTATGCATCGATGCACAGACC
Done.