Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001192.1 Hibiscus syriacus cultivar Beakdansim tig00002364_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: 54659
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:4668 original size:2 final size:2
Alignment explanation
Indices: 4663--4698 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4653 TAAAAAATTC
4663 AT AT AT A- AT -T 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
4699 TAAGCGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5097 original size:22 final size:23
Alignment explanation
Indices: 5071--5113 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
5061 TTAAAGTATA
5071 TTTT-ATTATATTTAA-TATTTTG
1 TTTTAATT-TATTTAAGTATTTTG
5093 TTTTAATTTATTTAAGTATTT
1 TTTTAATTTATTTAAGTATTT
5114 AAATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
TTTTAATTTATTTAAGTATTTTG
Found at i:5123 original size:17 final size:17
Alignment explanation
Indices: 5097--5129 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
5087 ATTTTGTTTT
5097 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
5115 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
5130 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:5131 original size:17 final size:19
Alignment explanation
Indices: 5093--5131 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
5083 TAATATTTTG
5093 TTTT-AATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
5111 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
5127 TTTTA
1 TTTTA
5132 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.11
17 12 0.63
18 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:7452 original size:23 final size:23
Alignment explanation
Indices: 7404--7452 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
7394 TAATACTTAC
* **
7404 TTTATTTCATTAATTTTGTTGGA
1 TTTATTTAATTAATTTTGTTAAA
*
7427 TTTATTTAATTTATTTTGTTAAA
1 TTTATTTAATTAATTTTGTTAAA
7450 TTT
1 TTT
7453 GTTGGACTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.65
Consensus pattern (23 bp):
TTTATTTAATTAATTTTGTTAAA
Found at i:9499 original size:51 final size:51
Alignment explanation
Indices: 9402--9500 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
9392 GCGCTTTAGA
* * * *
9402 CACGTGTGTCCATGTCAGCGTAAAGCGCACTGCAGGGGGCGTGCCTTACCC
1 CACGTGTGTCCATATCAGCGTAAAGCACACTGCAGGGAGCGCGCCTTACCC
* *
9453 CACGTG-GTTCCATATCAGCGTAAAGCACGCTGCAGGGAGTGCGCCTTA
1 CACGTGTG-TCCATATCAGCGTAAAGCACACTGCAGGGAGCGCGCCTTA
9501 TTGCAAATGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 1 0.02
51 40 0.98
ACGTcount: A:0.20, C:0.29, G:0.30, T:0.20
Consensus pattern (51 bp):
CACGTGTGTCCATATCAGCGTAAAGCACACTGCAGGGAGCGCGCCTTACCC
Found at i:11214 original size:6 final size:6
Alignment explanation
Indices: 11203--11237 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
11193 CAGTCAACAG
11203 CCATCT CCATCT CCATCT CCATCT CCATCT CCATC
1 CCATCT CCATCT CCATCT CCATCT CCATCT CCATC
11238 ATCATTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.51, G:0.00, T:0.31
Consensus pattern (6 bp):
CCATCT
Found at i:26145 original size:23 final size:23
Alignment explanation
Indices: 26119--26203 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
26109 TATGGAACTA
*
26119 CGGTGCAATTCTATGTGGCACTT
1 CGGTGCAATTCTACGTGGCACTT
* * *
26142 CGGTGCATTTCTACGCAGTC-CTT
1 CGGTGCAATTCTACG-TGGCACTT
26165 CGG-GACAATTTCTACGTGGCACTT
1 CGGTG-CAA-TTCTACGTGGCACTT
*
26189 CGGTGCAATTATACG
1 CGGTGCAATTCTACG
26204 AGCTGTGGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
22 1 0.02
23 29 0.59
24 18 0.37
25 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
CGGTGCAATTCTACGTGGCACTT
Found at i:26197 original size:24 final size:24
Alignment explanation
Indices: 26119--26198 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
26109 TATGGAACTA
*
26119 CGGTGCAA-TTCTATGTGGCACTT
1 CGGTGCAATTTCTACGTGGCACTT
* *
26142 CGGTGC-ATTTCTACGCAGTC-CTT
1 CGGTGCAATTTCTACG-TGGCACTT
26165 CGG-GACAATTTCTACGTGGCACTT
1 CGGTG-CAATTTCTACGTGGCACTT
26189 CGGTGCAATT
1 CGGTGCAATT
26199 ATACGAGCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
22 2 0.04
23 21 0.46
24 22 0.48
25 1 0.02
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (24 bp):
CGGTGCAATTTCTACGTGGCACTT
Found at i:28693 original size:2 final size:2
Alignment explanation
Indices: 28686--28761 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
28676 ATTAGAAAGA
28686 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
28728 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
28762 GGATAGTTTG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32753 original size:23 final size:23
Alignment explanation
Indices: 32716--32779 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
32706 CAGCTCATAT
*
32716 AATTGCATCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
32739 AATTGCACCGGAGTGTCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
32762 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
32780 TATAATAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:32966 original size:103 final size:103
Alignment explanation
Indices: 32795--33012 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
32785 TAATGTCCAT
* *
32795 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
32860 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
32898 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
32963 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
33001 AAGGACCACATA
1 AAGGACCACATA
33013 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:33872 original size:64 final size:64
Alignment explanation
Indices: 33764--33984 Score: 236
Period size: 64 Copynumber: 3.5 Consensus size: 64
33754 TAATGAAGGT
* * * * *
33764 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
33827 G
64 G
*
33828 ATGCATCGATGCA-TAACTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
** * * **
33892 AAACATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAATGGG
**
33955 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
33985 ACACCTTCAA
Statistics
Matches: 134, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
63 4 0.03
64 124 0.93
65 6 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:38455 original size:23 final size:23
Alignment explanation
Indices: 38418--38481 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
38408 CAGCTCATAT
*
38418 AATTGCATCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
38441 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
38464 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
38482 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:39558 original size:64 final size:64
Alignment explanation
Indices: 39356--39566 Score: 257
Period size: 64 Copynumber: 3.3 Consensus size: 64
39346 TCTTTTAATG
* * * * * * *
39356 ATGGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGTATTATTA
1 ATGGGATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTTATTATTA
* * **
39420 CTGGGATGCATCGATGCA-TGACTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTA
1 ATGGGATGCATCGATGCACT-ACTTATGCATCGATGCACAAATTGCATTCGATGTTTTATTATTA
39484 ATGGGATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTA
1 ATGGGATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTTATTATTA
**
39548 A-AAGAGTGCATCGATGCAC
1 ATGGGA-TGCATCGATGCAC
39567 AAATTGCATT
Statistics
Matches: 126, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
63 3 0.02
64 118 0.94
65 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGGGATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTTATTATTA
Found at i:39559 original size:45 final size:45
Alignment explanation
Indices: 39509--39611 Score: 206
Period size: 45 Copynumber: 2.3 Consensus size: 45
39499 GCACTACTTA
39509 TGCATCGATGCACAAATTGCATTCGATGTATTTATTTTAAAAGAG
1 TGCATCGATGCACAAATTGCATTCGATGTATTTATTTTAAAAGAG
39554 TGCATCGATGCACAAATTGCATTCGATGTATTTATTTTAAAAGAG
1 TGCATCGATGCACAAATTGCATTCGATGTATTTATTTTAAAAGAG
39599 TGCATCGATGCAC
1 TGCATCGATGCAC
39612 TACCAATGCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (45 bp):
TGCATCGATGCACAAATTGCATTCGATGTATTTATTTTAAAAGAG
Found at i:52568 original size:17 final size:16
Alignment explanation
Indices: 52527--52590 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
52517 GAAGAATAAA
52527 AGAAAAAATGAGAAAATG
1 AGAAAAAA--AGAAAATG
52545 AGAAAAAAAGAAAATG
1 AGAAAAAAAGAAAATG
* *
52561 ATGGAAAAACGAAAA-G
1 A-GAAAAAAAGAAAATG
52577 -GAAAAAGAAGAAAA
1 AGAAAAA-AAGAAAA
52591 AATGGAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 5 0.12
15 6 0.15
16 10 0.25
17 11 0.28
18 8 0.20
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.06
Consensus pattern (16 bp):
AGAAAAAAAGAAAATG
Found at i:52599 original size:18 final size:18
Alignment explanation
Indices: 52572--52611 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
52562 TGGAAAAACG
52572 AAAA-GGAAAAAGAAGAA
1 AAAATGGAAAAAGAAGAA
* *
52589 AAAATGGAAAAGGGAGAA
1 AAAATGGAAAAAGAAGAA
52607 AAAAT
1 AAAAT
52612 AAAAGAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (18 bp):
AAAATGGAAAAAGAAGAA
Found at i:54023 original size:51 final size:51
Alignment explanation
Indices: 53962--54461 Score: 927
Period size: 51 Copynumber: 9.9 Consensus size: 51
53952 AAATTCGTTT
53962 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
54013 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATA-GGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
54063 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
54114 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
54165 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATA-GGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
54215 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGC-GACAAG-TC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
54264 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
54315 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* *
54366 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* *
54417 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
54462 CTGTTTTTGA
Statistics
Matches: 439, Mismatches: 6, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
49 42 0.10
50 112 0.26
51 285 0.65
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
Found at i:54188 original size:152 final size:152
Alignment explanation
Indices: 53962--54461 Score: 932
Period size: 152 Copynumber: 3.3 Consensus size: 152
53952 AAATTCGTTT
*
53962 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
54027 CCTATACTCTCTGAATGAATAGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAA
66 CCTATACTCTCTGAATGAATAGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAA
54092 TGAATAGGGAGCGGACAAGTTC
131 TGAATAGGGAGCGGACAAGTTC
*
54114 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
54179 CCTATACTCTCTGAATGAATAGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAA
66 CCTATACTCTCTGAATGAATAGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAA
54244 TGAATAGGGAGC-GACAAG-TC
131 TGAATAGGGAGCGGACAAGTTC
54264 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
54329 CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGA
66 CCTATACTCTCTGAATGAATA-GGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGA
* *
54394 AGGAATAGGGAGCGGACTAGTTC
130 ATGAATAGGGAGCGGACAAGTTC
*
54417 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGAC
54462 CTGTTTTTGA
Statistics
Matches: 341, Mismatches: 4, Indels: 5
0.97 0.01 0.01
Matches are distributed among these distances:
150 87 0.26
151 61 0.18
152 147 0.43
153 46 0.13
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (152 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
CCTATACTCTCTGAATGAATAGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAA
TGAATAGGGAGCGGACAAGTTC
Found at i:54408 original size:252 final size:254
Alignment explanation
Indices: 53962--54461 Score: 925
Period size: 252 Copynumber: 2.0 Consensus size: 254
53952 AAATTCGTTT
53962 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
*
54027 CCTATACTCTCTGAATGAATAGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAA
66 CCTATACTCTCTGAAAGAATAGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAA
*
54092 TGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
131 TGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
* *
54157 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATA-GGAGCGGACAAGTTC
196 ACAAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACAAGTTC
54215 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGC-GACAAG-TCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
54278 CCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGA
66 CCTATACTCTCTGAAAGAATA-GGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGA
54343 ATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCG
130 ATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCG
*
54408 GACTAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC
195 GACAAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC
54462 CTGTTTTTGA
Statistics
Matches: 240, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
251 36 0.15
252 154 0.64
253 50 0.21
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (254 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
CCTATACTCTCTGAAAGAATAGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAA
TGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
ACAAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACAAGTTC
Found at i:54510 original size:52 final size:52
Alignment explanation
Indices: 54286--54627 Score: 215
Period size: 51 Copynumber: 6.5 Consensus size: 52
54276 GTCCTATACT
** * *
54286 CTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCCTATA
1 CTCTGAAAGAATAGGGAGCGGACCCGTT-TTTGAAGATTGTTCGAGTCTTATA
* ** * *
54335 CTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCCTATA
1 --CTCTGAAAGAATAGGGAGCGGACCCGTT-TTTGAAGATTGTTCGAGTCTTATA
* ** * *
54386 CTCTCTGAAGGAATAGGGAGCGGACTAGTTCGTTGAAGA---TT-GAGTCCTATA
1 --CTCTGAAAGAATAGGGAGCGGACCCGTT-TTTGAAGATTGTTCGAGTCTTATA
* *
54437 CTCCCTGAAAGAATAGGGAGCGGACCTGTTTTTGAAGATTTTTCGAGT-TCTATA
1 CT--CTGAAAGAATAGGGAGCGGACCCGTTTTTGAAGATTGTTCGAGTCT-TATA
* * * *
54491 CTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAAGATTGTTCAAGTCTTATA
1 CTCTGAAAGAATAGGGAGCGGACCCG-TTT-TTGAAGATTGTTCGAGTCTTATA
* * * *
54545 CTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTGTTCGAGTCTTATA
1 --CTCTGAAAGAATAGGGAGCGGACCCGTTTT-TGAAGATTGTTCGAGTCTTATA
*
54600 CTCAATGAAAGAATAGGGAGCAGACCCG
1 CTC--TGAAAGAATAGGGAGCGGACCCG
54628 CCATTTGAAG
Statistics
Matches: 254, Mismatches: 22, Indels: 26
0.84 0.07 0.09
Matches are distributed among these distances:
49 2 0.01
50 7 0.03
51 120 0.47
52 21 0.08
53 8 0.03
54 29 0.11
55 44 0.17
56 23 0.09
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (52 bp):
CTCTGAAAGAATAGGGAGCGGACCCGTTTTTGAAGATTGTTCGAGTCTTATA
Found at i:54561 original size:56 final size:56
Alignment explanation
Indices: 54427--54627 Score: 216
Period size: 55 Copynumber: 3.7 Consensus size: 56
54417 GTTGAAGATT
* * * * * *
54427 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTG-TTT-TTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAAGAATAGAGAGCAGACCCGTTTTATTGAAGATTGTTC
* * *
54481 GAGT-TCTATA--CTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAAGAATAGAGAGCAGACCCGTTTTATTGAAGATTGTTC
* * *
54535 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAAGAATAGAGAGCAGACCCGTTTTATTGAAGATTGTTC
** *
54590 GAGTCTTATACTCAATGAAAGAATAGGGAGCAGACCCG
1 GAGTCTTATACTCTCTGAAAGAATAGAGAGCAGACCCG
54628 CCATTTGAAG
Statistics
Matches: 123, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
52 22 0.18
53 3 0.02
54 26 0.21
55 44 0.36
56 28 0.23
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (56 bp):
GAGTCTTATACTCTCTGAAAGAATAGAGAGCAGACCCGTTTTATTGAAGATTGTTC
Done.