Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005955.1 Hibiscus syriacus cultivar Beakdansim tig00013989_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: 130909
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5194 original size:10 final size:10
Alignment explanation
Indices: 5179--5204 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5169 TTCAACTTTC
5179 TTTCTTTCCT
1 TTTCTTTCCT
5189 TTTCTTTCCT
1 TTTCTTTCCT
5199 TTTCTT
1 TTTCTT
5205 CTTTTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTTTCCT
Found at i:21263 original size:21 final size:22
Alignment explanation
Indices: 21216--21264 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
21206 TTCTTTGCTT
*
21216 TTCTTCTTTTTGAGTGCTGGAAA
1 TTCTTCTTTTGGAGTGCT-GAAA
*
21239 TTCTTCTTTTGGAGTGCT-TAA
1 TTCTTCTTTTGGAGTGCTGAAA
21260 TTCTT
1 TTCTT
21265 TTTCTGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
23 17 0.71
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.53
Consensus pattern (22 bp):
TTCTTCTTTTGGAGTGCTGAAA
Found at i:31445 original size:19 final size:19
Alignment explanation
Indices: 31421--31466 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
31411 GATAATGAAT
31421 AGAAATGATGAAAGAAAAA
1 AGAAATGATGAAAGAAAAA
31440 AGAAATGATGAAAGAAAAA
1 AGAAATGATGAAAGAAAAA
*
31459 GGAAATGA
1 AGAAATGA
31467 AGATAACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.11
Consensus pattern (19 bp):
AGAAATGATGAAAGAAAAA
Found at i:35517 original size:19 final size:20
Alignment explanation
Indices: 35493--35532 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
35483 TATCCTTTCT
35493 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
35512 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
35532 T
1 T
35533 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:35803 original size:29 final size:30
Alignment explanation
Indices: 35749--35829 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
35739 GCGTGCAAAG
*
35749 CAAAAGAAAAATAAAAAAAGAAAGAAAA-GA
1 CAAAAG-AAAAGAAAAAAAGAAAGAAAACGA
* *
35779 CAAAAGGAAGAGAAAAAAAG-CAGAAAACGA
1 CAAAA-GAAAAGAAAAAAAGAAAGAAAACGA
* *
35809 GAAAAGAAAAGAAAAAGAGAA
1 CAAAAGAAAAGAAAAAAAGAA
35830 GTTCAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
29 18 0.44
30 22 0.54
31 1 0.02
ACGTcount: A:0.74, C:0.05, G:0.20, T:0.01
Consensus pattern (30 bp):
CAAAAGAAAAGAAAAAAAGAAAGAAAACGA
Found at i:35818 original size:21 final size:22
Alignment explanation
Indices: 35767--35824 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
35757 AAATAAAAAA
*
35767 AGAAAGAAAAGACAAAAGGAAG
1 AGAAAGAAAAGACAAAACGAAG
*
35789 AGAAA-AAAAGCAGAAAACG-AG
1 AGAAAGAAAAG-ACAAAACGAAG
35810 A-AAAGAAAAGA-AAAA
1 AGAAAGAAAAGACAAAA
35825 GAGAAGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 13 0.41
22 11 0.34
ACGTcount: A:0.72, C:0.05, G:0.22, T:0.00
Consensus pattern (22 bp):
AGAAAGAAAAGACAAAACGAAG
Found at i:39408 original size:21 final size:21
Alignment explanation
Indices: 39384--39434 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
39374 CACTTATTGG
*
39384 TCTCAATCCAAGCCCAAATTC
1 TCTCAAACCAAGCCCAAATTC
***
39405 TCTCAAACTTGGCCCAAATTC
1 TCTCAAACCAAGCCCAAATTC
39426 TCTCAAACC
1 TCTCAAACC
39435 TGGCCCAAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.37, G:0.06, T:0.25
Consensus pattern (21 bp):
TCTCAAACCAAGCCCAAATTC
Found at i:39438 original size:21 final size:21
Alignment explanation
Indices: 39395--39442 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
39385 CTCAATCCAA
*
39395 GCCCAAATTCTCTCAAACTTG
1 GCCCAAATTCTCTCAAACCTG
39416 GCCCAAATTCTCTCAAACCTG
1 GCCCAAATTCTCTCAAACCTG
39437 GCCCAA
1 GCCCAA
39443 GGCTTCCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.38, G:0.10, T:0.23
Consensus pattern (21 bp):
GCCCAAATTCTCTCAAACCTG
Found at i:39656 original size:34 final size:34
Alignment explanation
Indices: 39610--39683 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
39600 AAAGCACGAC
* *
39610 AAGCTAGCTAAAGTGTTTTTACTATAAATATATA
1 AAGCTAGATAAAGTATTTTTACTATAAATATATA
* *
39644 AAGCTAGATAAAGTATTTTTACTATAGATATATG
1 AAGCTAGATAAAGTATTTTTACTATAAATATATA
39678 AAGCTA
1 AAGCTA
39684 ACTACCCAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (34 bp):
AAGCTAGATAAAGTATTTTTACTATAAATATATA
Found at i:60737 original size:23 final size:23
Alignment explanation
Indices: 60709--60767 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
60699 AAAAATCAGA
* *
60709 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
60732 AAAGAAAAATCCAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
60756 -AAGAAAAATCAA
1 AAAG-AAAATCAA
60768 AGAAAAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.61, C:0.15, G:0.15, T:0.08
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:60747 original size:24 final size:23
Alignment explanation
Indices: 60720--60765 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
60710 AAGAAAGTGA
60720 AGCACTCAAAAGAAAGAAAAATCC
1 AGCACTCAAAAG-AAGAAAAATCC
60744 AGCACTCAAAAGAAGAAAAATC
1 AGCACTCAAAAGAAGAAAAATC
60766 AAAGAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.59, C:0.20, G:0.13, T:0.09
Consensus pattern (23 bp):
AGCACTCAAAAGAAGAAAAATCC
Found at i:61959 original size:23 final size:23
Alignment explanation
Indices: 61928--62004 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 23
61918 ATGCTCAAAG
61928 AAGAACCAATGCTATAGAGAGCA
1 AAGAACCAATGCTATAGAGAGCA
* * * ** *
61951 AAGACCCAAT-CTTTATATTG-T
1 AAGAACCAATGCTATAGAGAGCA
**
61972 TTGAACCAATGCTATAGAGAGCA
1 AAGAACCAATGCTATAGAGAGCA
*
61995 AAGACCCAAT
1 AAGAACCAAT
62005 CTTTATATTG
Statistics
Matches: 35, Mismatches: 17, Indels: 4
0.62 0.30 0.07
Matches are distributed among these distances:
21 7 0.20
22 12 0.34
23 16 0.46
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (23 bp):
AAGAACCAATGCTATAGAGAGCA
Found at i:61993 original size:44 final size:44
Alignment explanation
Indices: 61930--62031 Score: 204
Period size: 44 Copynumber: 2.3 Consensus size: 44
61920 GCTCAAAGAA
61930 GAACCAATGCTATAGAGAGCAAAGACCCAATCTTTATATTGTTT
1 GAACCAATGCTATAGAGAGCAAAGACCCAATCTTTATATTGTTT
61974 GAACCAATGCTATAGAGAGCAAAGACCCAATCTTTATATTGTTT
1 GAACCAATGCTATAGAGAGCAAAGACCCAATCTTTATATTGTTT
62018 GAACCAATGCTATA
1 GAACCAATGCTATA
62032 AAGGGTGGTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (44 bp):
GAACCAATGCTATAGAGAGCAAAGACCCAATCTTTATATTGTTT
Found at i:62560 original size:19 final size:20
Alignment explanation
Indices: 62521--62556 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
62511 GGATAATAAT
62521 ATAAGAAATGAAAATGAATA
1 ATAAGAAATGAAAATGAATA
62541 ATAAG-AATG-AAATGAA
1 ATAAGAAATGAAAATGAA
62557 ATAAATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 4 0.25
20 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (20 bp):
ATAAGAAATGAAAATGAATA
Found at i:62563 original size:20 final size:21
Alignment explanation
Indices: 62515--62564 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
62505 TAAAGGGGAT
62515 AATAATATAAGAAATGAAAATG
1 AATAA-ATAAGAAATGAAAATG
62537 AAT-AATAAG-AATG-AAATG
1 AATAAATAAGAAATGAAAATG
62555 AAATAAATAA
1 -AATAAATAA
62565 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.19
19 7 0.27
20 10 0.38
21 1 0.04
22 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (21 bp):
AATAAATAAGAAATGAAAATG
Found at i:67707 original size:18 final size:17
Alignment explanation
Indices: 67686--67753 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 17
67676 GAACTTCTAT
67686 TTTTCTTTTATTTTCTTC
1 TTTT-TTTTATTTTCTTC
67704 TTTTCTGATTT-TTTCTCTTC
1 TTTT-T--TTTATTT-TCTTC
* *
67724 -TTTTTGTCTTTTCTTTC
1 TTTTTTTTATTTTC-TTC
67741 TTTTTTTTATTTT
1 TTTTTTTTATTTT
67754 TCTTTTGCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
16 4 0.10
17 6 0.15
18 17 0.41
19 6 0.15
20 8 0.20
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTTTTATTTTCTTC
Found at i:67741 original size:17 final size:18
Alignment explanation
Indices: 67696--67745 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
67686 TTTTCTTTTA
*
67696 TTTTC-TTCTTTTCTGATT
1 TTTTCTTTCTTTT-TGATC
67714 TTTTCTCTTCTTTTTG-TC
1 TTTTCT-TTCTTTTTGATC
67732 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
67746 TTTATTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.28
18 12 0.41
19 2 0.07
20 7 0.24
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTCTTTCTTTTTGATC
Found at i:67747 original size:20 final size:19
Alignment explanation
Indices: 67697--67758 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
67687 TTTCTTTTAT
67697 TTTCTTCTTTTCTGATTTTT-
1 TTTCTTCTTTT-T-ATTTTTC
* *
67717 TCTCTTCTTTTTGTCTTTTC
1 TTTCTTCTTTTTAT-TTTTC
*
67737 TTTCTTTTTTTTATTTTTC
1 TTTCTTCTTTTTATTTTTC
67756 TTT
1 TTT
67759 TGCTTTGCAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.03
19 13 0.37
20 21 0.60
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTCTTCTTTTTATTTTTC
Found at i:69912 original size:22 final size:22
Alignment explanation
Indices: 69887--69931 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
69877 CTCCTCCAGC
69887 TGAATCGAGCTTCCCTTAGTGT
1 TGAATCGAGCTTCCCTTAGTGT
69909 TGAATCGAGCTTCCCTTAGTGT
1 TGAATCGAGCTTCCCTTAGTGT
69931 T
1 T
69932 CCATGAGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (22 bp):
TGAATCGAGCTTCCCTTAGTGT
Found at i:73380 original size:36 final size:36
Alignment explanation
Indices: 73328--73440 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
73318 TATACTATTT
*
73328 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
73364 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
73400 TCATCACCATATTCCATCACCA-TATCATGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
73435 ACATCA
1 TCATCA
73441 TCCTTCCATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:73383 original size:13 final size:11
Alignment explanation
Indices: 73328--73427 Score: 69
Period size: 13 Copynumber: 8.4 Consensus size: 11
73318 TATACTATTT
73328 TCATCACCATAA
1 TCATCACCAT-A
*
73340 TCCATCTCCATTA
1 T-CATCACCA-TA
*
73353 TCA-CGCCTATA
1 TCATCACC-ATA
73364 TCATCACCATA
1 TCATCACCATA
73375 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
73389 TCA-CGCCTATA
1 TCATCACC-ATA
73400 TCATCACCATA
1 TCATCACCATA
73411 TTCCATCACCATA
1 -T-CATCACCATA
73424 TCAT
1 TCAT
73428 GCCAATAACA
Statistics
Matches: 72, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 25 0.35
12 16 0.22
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:73859 original size:17 final size:19
Alignment explanation
Indices: 73816--73862 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
73806 ACAAAGTGCT
*
73816 ACAAAAAAAAACCAACAAG
1 ACAAAAGAAAACCAACAAG
73835 A-AAGAAGAAAA-CAA-AAG
1 ACAA-AAGAAAACCAACAAG
73852 ACAAAAGAAAA
1 ACAAAAGAAAA
73863 AGGCTCATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 11 0.44
18 7 0.28
19 7 0.28
ACGTcount: A:0.77, C:0.13, G:0.11, T:0.00
Consensus pattern (19 bp):
ACAAAAGAAAACCAACAAG
Found at i:77794 original size:36 final size:36
Alignment explanation
Indices: 77742--77854 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
77732 GATACTATTT
*
77742 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
77778 TCATCACCATAGTCCATCACCATTATCACACCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
77814 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
77849 ACATCA
1 TCATCA
77855 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.34, C:0.36, G:0.03, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:77815 original size:11 final size:11
Alignment explanation
Indices: 77742--77840 Score: 76
Period size: 13 Copynumber: 8.3 Consensus size: 11
77732 GATACTATTT
77742 TCATCACCATAA
1 TCATCACCAT-A
*
77754 TCCATCTCCATTA
1 T-CATCACCA-TA
*
77767 TCA-CGCCTATA
1 TCATCACC-ATA
77778 TCATCACCATA
1 TCATCACCATA
77789 GTCCATCACCATTA
1 -T-CATCACCA-TA
77803 TCA-CACCTATA
1 TCATCACC-ATA
77814 TCATCACCATA
1 TCATCACCATA
77825 TTCCATCACCATA
1 -T-CATCACCATA
77838 TCA
1 TCA
77841 CGCCAATAAC
Statistics
Matches: 73, Mismatches: 3, Indels: 23
0.74 0.03 0.23
Matches are distributed among these distances:
11 25 0.34
12 17 0.23
13 28 0.38
14 3 0.04
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:77869 original size:33 final size:33
Alignment explanation
Indices: 77825--77893 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
77815 CATCACCATA
*
77825 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
77858 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
77891 TTC
1 TTC
77894 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:84079 original size:18 final size:19
Alignment explanation
Indices: 84027--84080 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
84017 TTTTGAATTA
84027 TTTTTCTTTTCTTTTCT-TC
1 TTTTTCTTTTCTTTT-TGTC
84046 -TTTTCTTCTTCTTTTTGTC
1 TTTTTCTT-TTCTTTTTGTC
84065 TTTTTC-TTTCTTTTTG
1 TTTTTCTTTTCTTTTTG
84081 CACTCCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 17 0.53
19 10 0.31
20 5 0.16
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTTCTTTTTGTC
Found at i:91517 original size:2 final size:2
Alignment explanation
Indices: 91510--91534 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91500 ATCACCAACT
91510 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 T
91535 CGCTAGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:95055 original size:2 final size:2
Alignment explanation
Indices: 95048--95076 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
95038 ATCAACAAAT
95048 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 T
95077 TATGCTACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:97845 original size:9 final size:10
Alignment explanation
Indices: 97821--97863 Score: 70
Period size: 10 Copynumber: 4.3 Consensus size: 10
97811 ATTGGAGTGC
97821 AAAAAGAAAAG
1 AAAAA-AAAAG
97832 AAAAAAAAAG
1 AAAAAAAAAG
97842 AAAAAAAAAG
1 AAAAAAAAAG
97852 -AAAAAAAAG
1 AAAAAAAAAG
97861 AAA
1 AAA
97864 TTCAAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.29
10 17 0.55
11 5 0.16
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:97870 original size:20 final size:20
Alignment explanation
Indices: 97821--97863 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 20
97811 ATTGGAGTGC
97821 AAAAAGAAAAGAAAAAAAAAG
1 AAAAA-AAAAGAAAAAAAAAG
97842 AAAAAAAAAG-AAAAAAAAG
1 AAAAAAAAAGAAAAAAAAAG
97861 AAA
1 AAA
97864 TTCAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 12 0.55
20 5 0.23
21 5 0.23
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAAAAAG
Found at i:108472 original size:15 final size:16
Alignment explanation
Indices: 108454--108486 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
108444 AAATTTTGGC
108454 TTTTTT-TG-CTTTTT
1 TTTTTTGTGCCTTTTT
108468 TTTTTTGTGCCTTTTT
1 TTTTTTGTGCCTTTTT
108484 TTT
1 TTT
108487 ACATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 2 0.12
16 9 0.53
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (16 bp):
TTTTTTGTGCCTTTTT
Found at i:108482 original size:12 final size:11
Alignment explanation
Indices: 108467--108507 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
108457 TTTTGCTTTT
*
108467 TTTTTTTGTGCC
1 TTTTTTT-TACC
*
108479 TTTTTTTTACA
1 TTTTTTTTACC
108490 TTTTTTTTACC
1 TTTTTTTTACC
108501 TTTTTTT
1 TTTTTTT
108508 GTTTTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 19 0.73
12 7 0.27
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTTTTTTACC
Found at i:114728 original size:17 final size:17
Alignment explanation
Indices: 114706--114738 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
114696 CTATCCTAGT
114706 TTTACCATAACCATTTA
1 TTTACCATAACCATTTA
*
114723 TTTACCCTAACCATTT
1 TTTACCATAACCATTT
114739 CTTTTAGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTACCATAACCATTTA
Done.