Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000330.1 Hibiscus syriacus cultivar Beakdansim tig00000613_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: 63511
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:8860 original size:30 final size:30
Alignment explanation
Indices: 8826--8883 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
8816 TGATCTCTTC
*
8826 TTTTTCTCGTTGGAGAAGGATTATTTTATT
1 TTTTTCTCGTTGCAGAAGGATTATTTTATT
8856 TTTTTCTCGTTGCAGAAGGATTATTTTA
1 TTTTTCTCGTTGCAGAAGGATTATTTTA
8884 ACTTGTCTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.52
Consensus pattern (30 bp):
TTTTTCTCGTTGCAGAAGGATTATTTTATT
Found at i:9012 original size:27 final size:27
Alignment explanation
Indices: 8982--9039 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
8972 TTAAACATAC
*
8982 AGATGTACATGATTTTTTAATTTAATA
1 AGATGTACATGATTTCTTAATTTAATA
9009 AGATGTACATGATTTCTTAATTTAATA
1 AGATGTACATGATTTCTTAATTTAATA
9036 AGAT
1 AGAT
9040 ATAATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (27 bp):
AGATGTACATGATTTCTTAATTTAATA
Found at i:16403 original size:13 final size:13
Alignment explanation
Indices: 16385--16419 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
16375 TTTTGTTCTC
16385 AATTTAATATTTA
1 AATTTAATATTTA
16398 AATTTAATATTTA
1 AATTTAATATTTA
16411 ATATTTAAT
1 A-ATTTAAT
16420 TTGATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTAATATTTA
Found at i:16411 original size:20 final size:20
Alignment explanation
Indices: 16386--16459 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
16376 TTTGTTCTCA
16386 ATTTAATATTTAAATTTAAT
1 ATTTAATATTTAAATTTAAT
*
16406 ATTTAATATTT-AATTTGATT
1 ATTTAATATTTAAATTT-AAT
* * *
16426 TTTTAAT-TTTTAATTAAAT
1 ATTTAATATTTAAATTTAAT
16445 ATTTAA-A-TTAAATTT
1 ATTTAATATTTAAATTT
16460 TAGTGGTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
18 6 0.14
19 15 0.34
20 23 0.52
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
ATTTAATATTTAAATTTAAT
Found at i:16439 original size:7 final size:7
Alignment explanation
Indices: 16386--16419 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
16376 TTTGTTCTCA
16386 ATTTAAT
1 ATTTAAT
16393 ATTTAA-
1 ATTTAAT
16399 ATTTAAT
1 ATTTAAT
16406 ATTTAAT
1 ATTTAAT
16413 ATTTAAT
1 ATTTAAT
16420 TTGATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTTAAT
Found at i:27345 original size:22 final size:20
Alignment explanation
Indices: 27308--27348 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
27298 ATCATATCAA
*
27308 AATATAATATCCTTTATAAC
1 AATATAATATCATTTATAAC
27328 AATATTAATTATCATTTATAA
1 AATA-TAA-TATCATTTATAA
27349 AAACTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATAATATCATTTATAAC
Found at i:29189 original size:2 final size:2
Alignment explanation
Indices: 29184--29235 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
29174 CATTTTTTAA
29184 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
29226 AT AT AT AT AT
1 AT AT AT AT AT
29236 GCAACTTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29524 original size:26 final size:25
Alignment explanation
Indices: 29478--29528 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
29468 TATTATATCT
* **
29478 ACTTTAATTTTTATTTTTATTTTTA
1 ACTTTAATTTATATTGCTATTTTTA
29503 ACTTTAACTTTATATTGCTATTTTTA
1 ACTTTAA-TTTATATTGCTATTTTTA
29529 TGTTACGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (25 bp):
ACTTTAATTTATATTGCTATTTTTA
Found at i:34605 original size:40 final size:41
Alignment explanation
Indices: 34550--34637 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 41
34540 CTTTCGAACT
34550 CTTTTTTAGGCTTTTAGCTGATTTT-CCCCACAATCAAAGG
1 CTTTTTTAGGCTTTTAGCTGATTTTCCCCCACAATCAAAGG
*
34590 CTTTTTTAGGCTTTTAGCTGATTTTCCCCCATAATCAAAGG
1 CTTTTTTAGGCTTTTAGCTGATTTTCCCCCACAATCAAAGG
34631 CTTTTTT
1 CTTTTTT
34638 TTTTTCTCGA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 25 0.54
41 21 0.46
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (41 bp):
CTTTTTTAGGCTTTTAGCTGATTTTCCCCCACAATCAAAGG
Found at i:35074 original size:17 final size:18
Alignment explanation
Indices: 35035--35076 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35025 AATATTATGT
*
35035 TTTTAATTTATTTAAGCA
1 TTTTACTTTATTTAAGCA
*
35053 TTTTACTTTATTTAA-TA
1 TTTTACTTTATTTAAGCA
35070 TTTTACT
1 TTTTACT
35077 AATATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTACTTTATTTAAGCA
Found at i:36782 original size:18 final size:18
Alignment explanation
Indices: 36759--36802 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
36749 AACAGCTATT
36759 TATGATGCCGCAACCATA
1 TATGATGCCGCAACCATA
* *
36777 TATGATGTCGCAGCCATA
1 TATGATGCCGCAACCATA
36795 TATGATGC
1 TATGATGC
36803 TGCCGTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (18 bp):
TATGATGCCGCAACCATA
Found at i:37433 original size:35 final size:34
Alignment explanation
Indices: 37394--37480 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
37384 GTATTTCAGT
37394 TAATTTTGTTT-A-TTACCATTTAATATCAGTTATTG
1 TAATTTTGTTTCATTTACCATTTAAT-TC--TTATTG
*
37429 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTT-TCATTTACCATTTAATTCTTATTG
* *
37464 TAAGTTTGTTTTATTTA
1 TAATTTTGTTTCATTTA
37481 AAATTATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 6 0.13
35 23 0.51
36 1 0.02
37 3 0.07
38 12 0.27
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.56
Consensus pattern (34 bp):
TAATTTTGTTTCATTTACCATTTAATTCTTATTG
Found at i:40810 original size:12 final size:13
Alignment explanation
Indices: 40793--40821 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40783 TATAATAAAA
40793 AAAATTTATAAC-
1 AAAATTTATAACG
40805 AAAATTTATAACG
1 AAAATTTATAACG
40818 AAAA
1 AAAA
40822 AATCGTACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (13 bp):
AAAATTTATAACG
Found at i:41204 original size:51 final size:50
Alignment explanation
Indices: 41104--41222 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 50
41094 CTACGTGGCG
* * **
41104 TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGTAAGTCATGTCAGCA
1 TATAGCGCGGA-CAGGGGGCACGCTATACCCACGTGTAAGCCAAATCAGCA
**
41155 TATAGCGCGGTACAGGGGGCACGCTATACCCCACGTG-GCGCCAAATCAGCA
1 TATAGCGCGG-ACAGGGGGCACGCTATA-CCCACGTGTAAGCCAAATCAGCA
*
41206 TATAACGCAGGACAGGG
1 TATAGCGC-GGACAGGG
41223 AACGCGCTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
51 47 0.81
52 11 0.19
ACGTcount: A:0.26, C:0.27, G:0.31, T:0.16
Consensus pattern (50 bp):
TATAGCGCGGACAGGGGGCACGCTATACCCACGTGTAAGCCAAATCAGCA
Found at i:41996 original size:24 final size:23
Alignment explanation
Indices: 41962--42008 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
41952 TATTTGAATA
41962 TTTTTTCCATATTTTTTTGCAAGC
1 TTTTTTCCATA-TTTTTTGCAAGC
*
41986 TTTTTTTCATATTTTTTGCAAGC
1 TTTTTTCCATATTTTTTGCAAGC
42009 CAACATATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.60
Consensus pattern (23 bp):
TTTTTTCCATATTTTTTGCAAGC
Found at i:45346 original size:37 final size:37
Alignment explanation
Indices: 45296--45388 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
45286 ACTAGAATTC
* *
45296 AAACTCCTAAAAATAGGATAGAATTTTGCTATGATTT
1 AAACTCCTAAAAATAGGATAGAATTCTACTATGATTT
* * * *
45333 AAACTCTTAAAAATATGATAGAGTTCTATTATGATTT
1 AAACTCCTAAAAATAGGATAGAATTCTACTATGATTT
*
45370 AAACTCCTAAAGATAGGAT
1 AAACTCCTAAAAATAGGAT
45389 CCACAAGCAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (37 bp):
AAACTCCTAAAAATAGGATAGAATTCTACTATGATTT
Found at i:45988 original size:20 final size:20
Alignment explanation
Indices: 45942--45980 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
45932 CTTTGCGTTT
*
45942 TTATTATTACTATTATATTA
1 TTATTTTTACTATTATATTA
45962 TTATTTTTACTATTATATT
1 TTATTTTTACTATTATATT
45981 TTCCTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTTTACTATTATATTA
Found at i:46038 original size:13 final size:12
Alignment explanation
Indices: 46017--46050 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
46007 TATATGTATA
46017 TTTTTTTATTTT
1 TTTTTTTATTTT
46029 TTTTTATTATTATT
1 TTTTT-TTATT-TT
46043 TTTTTTTA
1 TTTTTTTA
46051 CTTTCTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 8 0.40
14 7 0.35
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTATTTT
Found at i:46088 original size:12 final size:11
Alignment explanation
Indices: 46066--46105 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
46056 TCTTTCTTTT
46066 TATTATTCTTG
1 TATTATTCTTG
46077 TATTATTACTTG
1 TATTATT-CTTG
*
46089 TATTATT-TTA
1 TATTATTCTTG
46099 TATTATT
1 TATTATT
46106 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 11 0.41
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:46602 original size:12 final size:11
Alignment explanation
Indices: 46585--46703 Score: 53
Period size: 11 Copynumber: 10.2 Consensus size: 11
46575 AATTTATATA
46585 TATTTACTTTTT
1 TATTTA-TTTTT
*
46597 TATTTATTTTA
1 TATTTATTTTT
* * *
46608 TATATATATAT
1 TATTTATTTTT
*
46619 TATTCGTACTTTGT
1 TATT--TA-TTTTT
46633 TA-TTATTATTT
1 TATTTATT-TTT
*
46644 TGTTTATGTGTTT
1 TATTTAT-T-TTT
46657 TATTTATTTTCT
1 TATTTATTTT-T
* *
46669 T-TTTCTTTTA
1 TATTTATTTTT
*
46679 TATATATTTTAT
1 TATTTATTTT-T
*
46691 TATTTGTTTTT
1 TATTTATTTTT
46702 TA
1 TA
46704 CTTACTATTT
Statistics
Matches: 79, Mismatches: 19, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
10 3 0.04
11 37 0.47
12 21 0.27
13 13 0.16
14 5 0.06
ACGTcount: A:0.21, C:0.04, G:0.05, T:0.70
Consensus pattern (11 bp):
TATTTATTTTT
Found at i:50411 original size:22 final size:22
Alignment explanation
Indices: 50337--50411 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
50327 GCTACCCCAT
*
50337 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
50359 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
50381 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
50403 CAAACCTTT
1 CAAACCTTT
50412 AACCAAACAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:51441 original size:106 final size:106
Alignment explanation
Indices: 51229--52496 Score: 1802
Period size: 106 Copynumber: 12.0 Consensus size: 106
51219 ATATCGTGCC
* * * * * * * *
51229 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAATAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
51293 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
51334 ACTCCAGACAACGCAAGTTCCACTTCACGACGAAGGGCCCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
51399 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
51440 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
51505 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
51546 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
51611 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
51652 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
51717 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
51758 ACTCCAGACAACGCAAGTTCAACTTCACAAAGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
51823 AATTTCAGAGCCAATTTCAACTTCATAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
51864 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
51929 AATTTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
51970 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
52035 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
52076 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTAGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
52141 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
52182 ACTCAAAACAAAGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
52247 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
52288 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAAGAGG-CGGCTGATTGTCAA-AAA-AA-AT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG-GGACCGCTGGTTGTCAATAAACAACTTC
* *
52347 -C-A-TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
52387 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * * * *
52452 AGTTCCATAGCCAATTTCAATTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
52493 ACTC
1 ACTC
52497 AGAACAATGC
Statistics
Matches: 1044, Mismatches: 106, Indels: 25
0.89 0.09 0.02
Matches are distributed among these distances:
98 2 0.00
99 75 0.07
100 5 0.00
101 3 0.00
102 1 0.00
103 1 0.00
104 3 0.00
105 50 0.05
106 902 0.86
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:53289 original size:37 final size:37
Alignment explanation
Indices: 53227--53331 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
53217 CCTTTTCGTC
* *
53227 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * * *
53264 TTGCTAGGATTTAAACTCTTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * *
53301 CTATTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
53332 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:54016 original size:12 final size:11
Alignment explanation
Indices: 53994--54023 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
53984 CTCTTCTTTT
53994 TATTATTCTTG
1 TATTATTCTTG
54005 TATTATTACTTG
1 TATTATT-CTTG
54017 TATTATT
1 TATTATT
54024 TTTATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:54040 original size:23 final size:24
Alignment explanation
Indices: 53990--54040 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
53980 CTTTCTCTTC
53990 TTTT-TATTATTCTTGTATTATTA
1 TTTTGTATTATTCTTGTATTATTA
*
54013 -CTTGTATTATT-TT-TATATATTA
1 TTTTGTATTATTCTTGTAT-TATTA
54035 TTTTGT
1 TTTTGT
54041 TATATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
21 3 0.13
22 9 0.39
23 11 0.48
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.69
Consensus pattern (24 bp):
TTTTGTATTATTCTTGTATTATTA
Found at i:54046 original size:2 final size:2
Alignment explanation
Indices: 54041--54073 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54031 ATTATTTTGT
54041 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 T
54074 GCATATGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54634 original size:26 final size:26
Alignment explanation
Indices: 54506--54634 Score: 69
Period size: 26 Copynumber: 5.1 Consensus size: 26
54496 AATTTATTAA
* *
54506 TTTATATATATTTACTT-TTTATTTAT
1 TTTATATATATTTA-TTATTTGTTTTT
*
54532 TTTATATATA--TATTATTCGTACTTTGT
1 TTTATATATATTTATTATTTGT--TTT-T
* *
54559 TATTAT-TAT-TTTGTTTATTTGTTTTA
1 T-TTATATATATTT-ATTATTTGTTTTT
* * *
54585 TTTAT-T-TCTTT-TTCTTT-TTCTT
1 TTTATATATATTTATTATTTGTTTTT
54607 TTTATATATATTTATTATTTGTTTTT
1 TTTATATATATTTATTATTTGTTTTT
54633 TT
1 TT
54635 ACTTACTATT
Statistics
Matches: 78, Mismatches: 12, Indels: 26
0.67 0.10 0.22
Matches are distributed among these distances:
22 8 0.10
23 8 0.10
24 10 0.13
25 13 0.17
26 19 0.24
27 8 0.10
28 5 0.06
29 7 0.09
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTATATATATTTATTATTTGTTTTT
Found at i:57738 original size:23 final size:24
Alignment explanation
Indices: 57712--57760 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
57702 AAAAAATTTA
57712 AATTATATACT-TTTAATT-TTCAT
1 AATTATATA-TATTTAATTATTCAT
* *
57735 AATTTTATATATTTATTTATTCAT
1 AATTATATATATTTAATTATTCAT
57759 AA
1 AA
57761 AATTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 1 0.05
23 14 0.64
24 7 0.32
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTATATATATTTAATTATTCAT
Found at i:59402 original size:2 final size:2
Alignment explanation
Indices: 59395--59446 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
59385 TAATATTTGT
59395 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
59437 TA TA T- TA TA T
1 TA TA TA TA TA T
59447 TTTCATAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60062 original size:23 final size:23
Alignment explanation
Indices: 60013--60062 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
60003 AATATTGTAT
* * *
60013 TTTAATTAAATTATATTTAGATT
1 TTTAACTAAATTATAATTAGATG
* *
60036 TTTAACTAATTTATAATTATATG
1 TTTAACTAAATTATAATTAGATG
60059 TTTA
1 TTTA
60063 GTATTTTGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTAACTAAATTATAATTAGATG
Done.