Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000956.1 Hibiscus syriacus cultivar Beakdansim tig00001912_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: 67320
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:3793 original size:95 final size:95
Alignment explanation
Indices: 3674--3881 Score: 263
Period size: 95 Copynumber: 2.2 Consensus size: 95
3664 GGATTCAATC
* * * * * * *
3674 AGTACCGATACCATGATAATGGTATCAATACCAAGCAACATCGAATCTAAATTTTGTATCGATAC
1 AGTATCGATACCATGGTAAGGGTATCAATACCAAGAAACATCGAACCTAAATTTGGTATCAATAC
* * * *
3739 TAGAAGGGGGTATCGGTACCATAGTATTGT
66 CAGAAAGGGGTATCGGTACCATAGTATGGA
** *
3769 AGTATCGATACCATGGTAAGGGTATTGATACCAGGAAACATCGAACCTAAATTTGGTATCAATAC
1 AGTATCGATACCATGGTAAGGGTATCAATACCAAGAAACATCGAACCTAAATTTGGTATCAATAC
*
3834 CAGAAAGGGGTATTGGTACCATAGTATGGA
66 CAGAAAGGGGTATCGGTACCATAGTATGGA
* *
3864 AGTATCGGTACCAGGGTA
1 AGTATCGATACCATGGTA
3882 GCAGTATCGA
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (95 bp):
AGTATCGATACCATGGTAAGGGTATCAATACCAAGAAACATCGAACCTAAATTTGGTATCAATAC
CAGAAAGGGGTATCGGTACCATAGTATGGA
Found at i:4311 original size:59 final size:59
Alignment explanation
Indices: 4219--4904 Score: 1023
Period size: 59 Copynumber: 11.8 Consensus size: 59
4209 TTGACACTAA
*
4219 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTGTGAATTTCCATATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
*
4278 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGTACTTC
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
* * * * *
4337 GTGTACTAAACTGTTAAGGATTTCATACTAAGTGTATGAATTTTCGTGTAGGGCACTTC
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
* *
4396 GTGTGCTAAAA---T---GATTTCATACTAAGCGTATGAATTTCCATATAGGGCACTTT
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
*
4449 GTGTGCTAAATTGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
*
4508 GTGTGCTACAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTTC
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCAC-TTC
* *
4568 -TGTGCTGAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCTATATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
*
4626 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCCTATAGGGCACTTC
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
* *
4685 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTT
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
* * * * *
4744 ATGTGCTAAAATGTTAAGGATTTCATGCTATGTGTATGAATTTCCATATAGGACACTTT
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
* * ** * *
4803 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTG--TGAATTTCTGTATAGGACACTTT
1 GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
* *
4860 GTGTGCTAAAATGTT-AGGAAATTCATACTAAGTTTATGAATTTCC
1 GTGTGCTAAAATGTTAAGG-ATTTCATACTAAGTGTATGAATTTCC
4905 GTATGAGAAA
Statistics
Matches: 573, Mismatches: 43, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
53 46 0.08
56 4 0.01
57 50 0.09
58 3 0.01
59 467 0.82
60 3 0.01
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGGATTTCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
Found at i:5357 original size:29 final size:29
Alignment explanation
Indices: 5315--5375 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
5305 TATGCTAGTT
5315 AGATGAACAGTTAAAAAATGTTGAGTAAA
1 AGATGAACAGTTAAAAAATGTTGAGTAAA
* * *
5344 AGATGAACGGTTAAACATTGTTGAGTAAA
1 AGATGAACAGTTAAAAAATGTTGAGTAAA
5373 AGA
1 AGA
5376 ATAATGGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.05, G:0.23, T:0.25
Consensus pattern (29 bp):
AGATGAACAGTTAAAAAATGTTGAGTAAA
Found at i:6893 original size:83 final size:81
Alignment explanation
Indices: 6718--6904 Score: 214
Period size: 83 Copynumber: 2.3 Consensus size: 81
6708 ACATACCAAA
* * * * * * * *
6718 CTATTGCGGCGTTTATA-AAAAACGTCGCTAAAGTAATACTTTGTTATGGCATTTTTTAAAAAAG
1 CTATTACGGCATTTATATAAAAACGACGCTAAAGTAATACTATATTACGGCATTTTTGAAAAAAA
* *
6782 CCACTATAGATTAACC
66 CCACCATAGATGAACC
* * * *
6798 CTATTATGGCATTTATATAAAAATGACGCTAAAGTACTACTATATTGCGGCATTTGTTGAAAAAA
1 CTATTACGGCATTTATATAAAAACGACGCTAAAGTAATACTATATTACGGCATTT-TTGAAAAAA
6863 TACCACCATAGATGAACC
65 -ACCACCATAGATGAACC
*
6881 CTATTACGGCATTTGTATAAAAAC
1 CTATTACGGCATTTATATAAAAAC
6905 ACCACTTTTG
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
80 14 0.16
81 30 0.34
82 8 0.09
83 35 0.40
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (81 bp):
CTATTACGGCATTTATATAAAAACGACGCTAAAGTAATACTATATTACGGCATTTTTGAAAAAAA
CCACCATAGATGAACC
Found at i:7033 original size:153 final size:152
Alignment explanation
Indices: 6775--7060 Score: 398
Period size: 153 Copynumber: 1.9 Consensus size: 152
6765 GGCATTTTTT
6775 AAAAAAGCCACTATAGATTAACCCTATTATGGCATTTATATAAAAATGACGCTAAAGTACTACTA
1 AAAAAAGCCACTATAGATTAACCCTATTATGGCATTTATATAAAAATGACGCTAAAGTACTACTA
* * * * * * *
6840 TATTGCGGCATTTGTTGAAAAAATACCACCATAGATGAACCCTATTACGGCATTTGTATAAAAAC
66 TATTACGACATTTGTTAAAAAAATACCACCATAAAGGAACCCTATTACAGCATTTATATAAAAAC
6905 ACCACTTTTGCAGTATTTGTTA
131 ACCACTTTTGCAGTATTTGTTA
* *
6927 AAAAAATGCCATTATAGATTAACCCTATTATGGCGATTGTATA-AAAAA-G-CGCTAAAGTTCTA
1 AAAAAA-GCCACTATAGATTAACCCTATTATGGC-ATT-TATATAAAAATGACGCTAAAGTACTA
* ** *
6989 CTCTATTACGACATTTGTTAAAAACAATGTCACTATAAAGGAACCCTATTACAGCATTTATATAA
63 CTATATTACGACATTTGTTAAAAA-AATACCACCATAAAGGAACCCTATTACAGCATTTATATAA
7054 AAACACC
127 AAACACC
7061 GCTAAAGTAT
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
152 38 0.32
153 67 0.57
154 8 0.07
155 4 0.03
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (152 bp):
AAAAAAGCCACTATAGATTAACCCTATTATGGCATTTATATAAAAATGACGCTAAAGTACTACTA
TATTACGACATTTGTTAAAAAAATACCACCATAAAGGAACCCTATTACAGCATTTATATAAAAAC
ACCACTTTTGCAGTATTTGTTA
Found at i:7137 original size:82 final size:84
Alignment explanation
Indices: 6919--7151 Score: 228
Period size: 82 Copynumber: 2.8 Consensus size: 84
6909 CTTTTGCAGT
* * ** ** *
6919 ATTTGTTAAAAA-AATGCCATTATAGATTAACCCTATTATGGCGA-TTGTATAAAAA-AGCGCTA
1 ATTTGTTAAAAACAATGCCACTATAAAGGAACCCTATTACAGC-ATTTGTATAAAAACACCGCTA
6981 AAGTTCTACTCTATTACGAC
65 AAGTTCTACTCTATTACGAC
* *
7001 ATTTGTTAAAAACAATGTCACTATAAAGGAACCCTATTACAGCATTTATATAAAAACACCGCTAA
1 ATTTGTTAAAAACAATGCCACTATAAAGGAACCCTATTACAGCATTTGTATAAAAACACCGCTAA
*
7066 AGTAT-TACTCTATTACGGC
66 AGT-TCTACTCTATTACGAC
* * * * * * * *
7085 GTTTGTTGAAAA-AA-GCCTCTATAGATGAACTCTATTGC-GACATTTGTATAAAAACGCCGCTA
1 ATTTGTTAAAAACAATGCCACTATAAAGGAACCCTATTACAG-CATTTGTATAAAAACACCGCTA
7147 AAGTT
65 AAGTT
7152 ACCATTTTAT
Statistics
Matches: 126, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
81 2 0.02
82 55 0.44
83 35 0.28
84 33 0.26
85 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (84 bp):
ATTTGTTAAAAACAATGCCACTATAAAGGAACCCTATTACAGCATTTGTATAAAAACACCGCTAA
AGTTCTACTCTATTACGAC
Found at i:11596 original size:26 final size:26
Alignment explanation
Indices: 11550--11630 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
11540 ATACAATCTT
* * *
11550 CTTTTTCTTTCTAGTTT-TTTTTAAAG
1 CTTTCTCTTT-TATTTTATTTTTCAAG
11576 CTTTCTCTTTTATTTTATTTTTCAAG
1 CTTTCTCTTTTATTTTATTTTTCAAG
* *
11602 TTTTCAT-TTTTCTTTTA-TTTTCAAG
1 CTTTC-TCTTTTATTTTATTTTTCAAG
11627 CTTT
1 CTTT
11631 GTTTTTAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
25 16 0.34
26 30 0.64
27 1 0.02
ACGTcount: A:0.15, C:0.14, G:0.05, T:0.67
Consensus pattern (26 bp):
CTTTCTCTTTTATTTTATTTTTCAAG
Found at i:20401 original size:18 final size:18
Alignment explanation
Indices: 20375--20441 Score: 125
Period size: 18 Copynumber: 3.7 Consensus size: 18
20365 GCGTAGAATT
*
20375 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
20393 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
20411 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
20429 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
20442 TATATAGAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:20477 original size:28 final size:28
Alignment explanation
Indices: 20427--20507 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
20417 GAAGGACCAC
* * **
20427 TATGTCCCGAAGGACTATATAGAACACA
1 TATGTCCCGAATGACCACGTAGAACACA
20455 TATGTCCCGAATGACCACGTAGAACACA
1 TATGTCCCGAATGACCACGTAGAACACA
20483 TATGTCCCGAATGACCACGTAGAAC
1 TATGTCCCGAATGACCACGTAGAAC
20508 CCTCGACTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (28 bp):
TATGTCCCGAATGACCACGTAGAACACA
Found at i:21919 original size:2 final size:2
Alignment explanation
Indices: 21912--21937 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21902 ATGCATAAGT
21912 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
21938 CATAGGATTT
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):
TA
Found at i:22196 original size:22 final size:22
Alignment explanation
Indices: 22166--22232 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
22156 AGATGAGGGT
*
22166 TACATAGGTCCTTCGGGAAAAA
1 TACATAGGTCCTTCGGGACAAA
* *
22188 TACAAAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACAAA
22210 TACATAGGTCCTTCGGGACAAA
1 TACATAGGTCCTTCGGGACAAA
22232 T
1 T
22233 TTCACATGCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACAAA
Found at i:26651 original size:13 final size:13
Alignment explanation
Indices: 26633--26657 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26623 TACAGACACG
26633 CATATGAAGACTT
1 CATATGAAGACTT
26646 CATATGAAGACT
1 CATATGAAGACT
26658 GTTCAACTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
CATATGAAGACTT
Found at i:27410 original size:20 final size:20
Alignment explanation
Indices: 27385--27436 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
27375 AATATTTCCC
27385 TGGTATCGATACCTCCATTA
1 TGGTATCGATACCTCCATTA
27405 TGGTATCGATACCTCCATTA
1 TGGTATCGATACCTCCATTA
27425 TGGTATCGATAC
1 TGGTATCGATAC
27437 TACCTTCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (20 bp):
TGGTATCGATACCTCCATTA
Found at i:30068 original size:21 final size:22
Alignment explanation
Indices: 30019--30074 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
30009 TTAATGCATG
30019 GGGTATCGATA-CAATATGGAA
1 GGGTATCGATACCAATATGGAA
*
30040 GAGGTATCGATACCTATAT-GAA
1 G-GGTATCGATACCAATATGGAA
*
30062 GGGTATCAATACC
1 GGGTATCGATACC
30075 CGGGAAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.39
22 14 0.45
23 5 0.16
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (22 bp):
GGGTATCGATACCAATATGGAA
Found at i:30677 original size:18 final size:19
Alignment explanation
Indices: 30648--30685 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
30638 AAGAACTGTT
30648 ATATGAAATGTGACATGTG
1 ATATGAAATGTGACATGTG
*
30667 ATATG-AATGTGATATGTG
1 ATATGAAATGTGACATGTG
30685 A
1 A
30686 ACATAAGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (19 bp):
ATATGAAATGTGACATGTG
Found at i:33962 original size:21 final size:21
Alignment explanation
Indices: 33938--33977 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
33928 GACCATTATA
33938 CTTCAATTCAGAATCAAGGAG
1 CTTCAATTCAGAATCAAGGAG
* * *
33959 CTTCACTTCATAGTCAAGG
1 CTTCAATTCAGAATCAAGG
33978 CGCCTTACTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (21 bp):
CTTCAATTCAGAATCAAGGAG
Found at i:38543 original size:14 final size:14
Alignment explanation
Indices: 38524--38564 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
38514 TTTCTCTCTC
38524 ATTTTTAACTTTTT
1 ATTTTTAACTTTTT
*
38538 ATTTTT--CTCTTTC
1 ATTTTTAACT-TTTT
38551 ATTTTTAACTTTTT
1 ATTTTTAACTTTTT
38565 CTCTTTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
12 2 0.09
13 9 0.41
14 9 0.41
15 2 0.09
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTTAACTTTTT
Found at i:38552 original size:27 final size:26
Alignment explanation
Indices: 38514--38602 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 26
38504 CTATCACCCA
38514 TTTCTCTCTCATTTTTAACTTTTTATT
1 TTTCTCTCTCATTTTTAACTTTTT-TT
*
38541 TTTCTCTTTCATTTTTAAC-----TT
1 TTTCTCTCTCATTTTTAACTTTTTTT
*
38562 TTTCTCTTTCATTTTTAACTTTTTCTT
1 TTTCTCTCTCATTTTTAACTTTTT-TT
*
38589 CTTCTCTCTCATTT
1 TTTCTCTCTCATTT
38603 CTTCATCTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
21 21 0.40
27 32 0.60
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTCTCTCTCATTTTTAACTTTTTTT
Found at i:38565 original size:21 final size:21
Alignment explanation
Indices: 38539--38587 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
38529 TAACTTTTTA
38539 TTTTTCTCTTTCATTTTTAAC
1 TTTTTCTCTTTCATTTTTAAC
38560 TTTTTCTCTTTCATTTTTAAC
1 TTTTTCTCTTTCATTTTTAAC
38581 TTTTTCT
1 TTTTTCT
38588 TCTTCTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTCTCTTTCATTTTTAAC
Found at i:38621 original size:48 final size:48
Alignment explanation
Indices: 38515--38624 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
38505 TATCACCCAT
* * * *
38515 TTCTCTCTCATTTTTAACTTTTTATTTTTCTCTTTCATTTTTAACTTT
1 TTCTCTTTCATTTTTAACTTTTTATTCTTCTCTCTCATTTTTAACTTC
* *
38563 TTCTCTTTCATTTTTAACTTTTTCTTCTTCTCTCTCATTTCTTCATCTTC
1 TTCTCTTTCATTTTTAACTTTTTATTCTTCTCTCTCATTT-TT-AACTTC
38613 TTC-C-TTCATTTT
1 TTCTCTTTCATTTT
38625 CCCCATAGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
48 44 0.81
49 3 0.06
50 7 0.13
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (48 bp):
TTCTCTTTCATTTTTAACTTTTTATTCTTCTCTCTCATTTTTAACTTC
Found at i:43822 original size:21 final size:22
Alignment explanation
Indices: 43772--43824 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
43762 TGTATGAACA
43772 GTATCGATACCATATGGATGAG
1 GTATCGATACCATATGGATGAG
** *
43794 GTGCCGATACCTATGTGGA-G-G
1 GTATCGATACC-ATATGGATGAG
43815 GTATCGATAC
1 GTATCGATAC
43825 ACGAGGAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 9 0.36
22 10 0.40
23 6 0.24
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (22 bp):
GTATCGATACCATATGGATGAG
Found at i:44674 original size:28 final size:28
Alignment explanation
Indices: 44634--44714 Score: 135
Period size: 28 Copynumber: 2.9 Consensus size: 28
44624 AGAGTCGAGG
44634 GTTCTATGTGGTCCTTTGGGACATATGT
1 GTTCTATGTGGTCCTTTGGGACATATGT
*
44662 GTTCTACGTGGTCCTTTGGGACATATGT
1 GTTCTATGTGGTCCTTTGGGACATATGT
* *
44690 GTTCTATGTGGTTCTTCGGGACATA
1 GTTCTATGTGGTCCTTTGGGACATA
44715 GTGGTCCTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.15, C:0.16, G:0.28, T:0.41
Consensus pattern (28 bp):
GTTCTATGTGGTCCTTTGGGACATATGT
Found at i:45732 original size:20 final size:20
Alignment explanation
Indices: 45707--45751 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
45697 TATTTTTGTT
45707 TTATACATTTATTATATCAC
1 TTATACATTTATTATATCAC
45727 TTATACATTTATTATATCAC
1 TTATACATTTATTATATCAC
45747 TTATA
1 TTATA
45752 GACGATGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATACATTTATTATATCAC
Found at i:54673 original size:3 final size:3
Alignment explanation
Indices: 54665--54694 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
54655 TCGAAACCAA
54665 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
54695 CTTTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:64483 original size:132 final size:132
Alignment explanation
Indices: 64150--64722 Score: 549
Period size: 132 Copynumber: 4.3 Consensus size: 132
64140 GCAAATCGAA
* **
64150 CTCGATTCAATCTTCCCTG-AGTAACAGTAGAATGAATCAAAATCCCCAGATTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAG-AACAGTAGAATGAATCAACATTTCCAGATTGATTTTCCCTCA
** * * *
64214 AGAAGAAGCAAAACAGATCCATCTCTTTCAAGATTTGATAT-TCTATGAGTAACAGTGGAACAAC
65 AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATCCCTA--AGTAACAGTGGAACAAG
64278 TCTAC
128 TCTAC
* ** * * **
64283 CTCAATTCAATCTT-CCTG-AG-TTAGTGGAATGAATCAAAATCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTAGAATGAATCAACATTTCCAGAT-TGATTTTCCCTCA
* * * *
64345 TA-AAGAAGTGTAACAGATCCTTCTCTTTCAAGATTTGATAT-CCTCAAGTAACAGTGGAATAAG
65 -AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATCCCT-AAGTAACAGTGGAACAAG
*
64408 TCTGC
128 TCTAC
* * *
64413 CTCGATTCAAT-TTCCCTGAGGAACAGTAGAATTAATCAACATTTCCAGATCTAATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTAGAATGAATCAACATTTCCAGAT-TGATTTTCCCTCA
*** * * * *
64477 AGAAGAAGCGGAATTTATCCCTCTCTTTCAAGATTTGATATACCCTGAGTGATAGTAGAACAAGT
65 AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATAT-CCCTAAGTAACAGTGGAACAAGT
64542 CTAC
129 CTAC
* * * * * * * * *
64546 C-CGATTTAATCTTCCCTAAAGAACAGTAGAATAAATAAAC-GTTCAAAGATTTATTTTTCCTTA
1 CTCGATTCAATCTTCCCTGAAGAACAGTAGAATGAATCAACATTTC-CAGATTGATTTTCCCTCA
* * *
64609 TGAAGAAGTGGAACAGATCCCTCGT-TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAC-AG
65 AGAAGAAGCGGAACAGATCCCTC-TCTTTCAAGATTTGATA-TCCCTAAGTAACAGTGGAACAAG
64672 TCTAC
128 TCTAC
* * * *
64677 CCCGATTCAATCTTCCCTGAAAAACAGTGGAATGAATCAACGTTTC
1 CTCGATTCAATCTTCCCTGAAGAACAGTAGAATGAATCAACATTTC
64723 TCGATCTGAT
Statistics
Matches: 366, Mismatches: 59, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
129 2 0.01
130 58 0.16
131 60 0.16
132 178 0.49
133 65 0.18
134 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (132 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTAGAATGAATCAACATTTCCAGATTGATTTTCCCTCAA
GAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATCCCTAAGTAACAGTGGAACAAGTCT
AC
Found at i:65473 original size:19 final size:20
Alignment explanation
Indices: 65449--65487 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
65439 ATTTGCTCTA
*
65449 ATTTGA-CTACGTATGATTT
1 ATTTGATCTAAGTATGATTT
*
65468 ATTTGATTTAAGTATGATTT
1 ATTTGATCTAAGTATGATTT
65488 TTGATTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.51
Consensus pattern (20 bp):
ATTTGATCTAAGTATGATTT
Found at i:65492 original size:18 final size:20
Alignment explanation
Indices: 65459--65495 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
65449 ATTTGACTAC
65459 GTATGATTTATTTGATTTAA
1 GTATGATTTATTTGATTTAA
65479 GTATGA-TT-TTTGATTTA
1 GTATGATTTATTTGATTTA
65496 CTGTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.57
Consensus pattern (20 bp):
GTATGATTTATTTGATTTAA
Done.