Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005126.1 Hibiscus syriacus cultivar Beakdansim tig00011528_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: 78069
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:751 original size:13 final size:14
Alignment explanation
Indices: 733--763 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
723 TAGTCATTGT
733 AATTTAA-TTAATA
1 AATTTAACTTAATA
746 AATTTAACTTAATA
1 AATTTAACTTAATA
760 AATT
1 AATT
764 AGTCATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTTAACTTAATA
Found at i:5546 original size:51 final size:53
Alignment explanation
Indices: 5449--5556 Score: 193
Period size: 52 Copynumber: 2.1 Consensus size: 53
5439 CTTTTGTAAG
5449 CTAACTAAATATTTTCTTCTTCCTTGTAGTTGAGTGTACCTGGATGTAC-AAA
1 CTAACTAAATATTTTCTTCTTCCTTGTAGTTGAGTGTACCTGGATGTACAAAA
*
5501 CTAACTAAATATTTTTTTCTTCC-TGTAGTTGAGTGTACCTGGATGTACAAAA
1 CTAACTAAATATTTTCTTCTTCCTTGTAGTTGAGTGTACCTGGATGTACAAAA
5553 CTAA
1 CTAA
5557 GTGTCGATGG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
51 25 0.46
52 29 0.54
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (53 bp):
CTAACTAAATATTTTCTTCTTCCTTGTAGTTGAGTGTACCTGGATGTACAAAA
Found at i:13069 original size:43 final size:43
Alignment explanation
Indices: 13022--13103 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
13012 TTTAACCCTT
*
13022 TAATTTTATTTAAT-TTAATTTTTATATTTATAATTGAGGTCTC
1 TAATTTT-TGTAATCTTAATTTTTATATTTATAATTGAGGTCTC
* *
13065 TAATTTTTGTAATCTTACTTTTTATCTTTATAATTGAGG
1 TAATTTTTGTAATCTTAATTTTTATATTTATAATTGAGG
13104 CCCTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 5 0.14
43 30 0.86
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (43 bp):
TAATTTTTGTAATCTTAATTTTTATATTTATAATTGAGGTCTC
Found at i:13225 original size:42 final size:42
Alignment explanation
Indices: 13048--13374 Score: 292
Period size: 42 Copynumber: 7.7 Consensus size: 42
13038 AATTTTTATA
* * *
13048 TTTATAATTGAGGTCTCTAATTTTTGT-AATCTTACTTTTTATC
1 TTTATAATTGAGG-CCCTAATTTTT-TCAATCTCACTTTTTACC
* *
13091 TTTATAATTGAGGCCCTTAATTTTTTCAATCCCATTTTTTTACC
1 TTTATAATTGAGGCCC-TAATTTTTTCAATCTCA-CTTTTTACC
*** * * *
13135 TTTATAATTGATTATCCTAAGTTTTTCAATC-C-CTTTGTGCC
1 TTTATAATTGA-GGCCCTAATTTTTTCAATCTCACTTTTTACC
* ** * *
13176 TTTATAATTAAGTTCCTGATTTTTTCAATATCACTTTTTACC
1 TTTATAATTGAGGCCCTAATTTTTTCAATCTCACTTTTTACC
*
13218 TTTATAATTGAAGCCACTAATTTTTTCAATCTCA-TTTTTA-C
1 TTTATAATTGAGGCC-CTAATTTTTTCAATCTCACTTTTTACC
* *
13259 TTATATAATTTAGGCCACTAATTTTTT-AATCTCAC-TTTTAAC
1 TT-TATAATTGAGGCC-CTAATTTTTTCAATCTCACTTTTTACC
* * * *
13301 ATTAAAATCGAGACCCCTAATTTTTT-AATCTCACTTTTTACC
1 TTTATAATTGAG-GCCCTAATTTTTTCAATCTCACTTTTTACC
13343 TTTATAATTGAGGTCCCTAATTTTTTTCAATC
1 TTTATAATTGAGG-CCCTAA-TTTTTTCAATC
13375 ATAATTTTAC
Statistics
Matches: 231, Mismatches: 38, Indels: 29
0.78 0.13 0.10
Matches are distributed among these distances:
40 14 0.06
41 57 0.25
42 74 0.32
43 49 0.21
44 35 0.15
45 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (42 bp):
TTTATAATTGAGGCCCTAATTTTTTCAATCTCACTTTTTACC
Found at i:13298 original size:83 final size:82
Alignment explanation
Indices: 13048--13402 Score: 283
Period size: 83 Copynumber: 4.2 Consensus size: 82
13038 AATTTTTATA
* * * *
13048 TTTATAATTGAGGTCTCTAATTTTTGTAATCTTACTTTTTATCTTTATAATTGAGGCCCTTAATT
1 TTTATAATTGAAG-CCCTAATTTTT-TAATCTCACTTTTTACCTTTATAATTGAGGCCC-TAATT
* *
13113 TTTTCAATCCCATTTTTTTACC
63 TTTTCAATCTCA--CTTTTACC
* * * * * ** *
13135 TTTATAATTGATTA-TCCTAAGTTTTTCAATC-C-CTTTGTGCCTTTATAATTAAGTTCCTGATT
1 TTTATAATTGA--AGCCCTAA-TTTTTTAATCTCACTTTTTACCTTTATAATTGAGGCCCTAATT
*
13197 TTTTCAATATCACTTTTTACC
63 TTTTCAATCTCAC-TTTTACC
*
13218 TTTATAATTGAAGCCACTAATTTTTTCAATCTCA-TTTTTA-CTTATATAATTTAGGCCACTAAT
1 TTTATAATTGAAGCC-CTAATTTTTT-AATCTCACTTTTTACCTT-TATAATTGAGGCC-CTAAT
*
13281 TTTTT-AATCTCACTTTTAAC
62 TTTTTCAATCTCACTTTTACC
* * * *
13301 ATTAAAATCGAGACCCCTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAGGTCCCTAATTT
1 TTTATAATTGA-AGCCCTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAGG-CCCTAA-TT
* *
13366 TTTTCAATCAT-AATTTTACT
63 TTTTCAATC-TCACTTTTACC
* *
13386 TTTATAGTTTAAGCCCT
1 TTTATAATTGAAGCCCT
13403 TGATTTAACC
Statistics
Matches: 211, Mismatches: 39, Indels: 39
0.73 0.13 0.13
Matches are distributed among these distances:
81 1 0.00
82 13 0.06
83 73 0.35
84 55 0.26
85 44 0.21
86 1 0.00
87 19 0.09
88 5 0.02
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.49
Consensus pattern (82 bp):
TTTATAATTGAAGCCCTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAGGCCCTAATTTTT
TCAATCTCACTTTTACC
Found at i:13911 original size:41 final size:40
Alignment explanation
Indices: 13865--13945 Score: 92
Period size: 41 Copynumber: 2.0 Consensus size: 40
13855 CAGACCGTTA
* * *
13865 TTTAAGTAATTGTTCC-TAATAACAAGTGTTGAAAAATAAAT
1 TTTAAG-AATAGTTCCATAATAACAAATATTGAAAAA-AAAT
**
13906 TTTAAGGGTAGTTCCATAATAACAAATATTGAAAAAAAAT
1 TTTAAGAATAGTTCCATAATAACAAATATTGAAAAAAAAT
13946 GACCCCTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
40 10 0.29
41 24 0.71
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (40 bp):
TTTAAGAATAGTTCCATAATAACAAATATTGAAAAAAAAT
Found at i:15709 original size:15 final size:15
Alignment explanation
Indices: 15688--15743 Score: 76
Period size: 15 Copynumber: 3.5 Consensus size: 15
15678 AATGATGTCA
15688 ATAAAAACTATTAAAT
1 ATAAAAA-TATTAAAT
15704 ATAAAAATATTAATTAT
1 ATAAAAATATTAA--AT
*
15721 AAAAAAATATTAAAT
1 ATAAAAATATTAAAT
15736 ATAAAAAT
1 ATAAAAAT
15744 GAAGAAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
15 15 0.42
16 7 0.19
17 14 0.39
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAAATATTAAAT
Found at i:15710 original size:17 final size:16
Alignment explanation
Indices: 15688--15742 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
15678 AATGATGTCA
*
15688 ATAAAAACTATTAAAT
1 ATAAAAAATATTAAAT
*
15704 AT-AAAAATATTAATT
1 ATAAAAAATATTAAAT
15719 ATAAAAAAATATTAAAT
1 AT-AAAAAATATTAAAT
15736 ATAAAAA
1 ATAAAAA
15743 TGAAGAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.38
16 7 0.21
17 14 0.41
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAAAATATTAAAT
Found at i:15864 original size:40 final size:40
Alignment explanation
Indices: 15816--15893 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
15806 ATAAAAACCT
*
15816 TTATCTCTGTCGAGTGAGACGCTTTACAAAATGATAAAAA
1 TTATCTCTGTCGAATGAGACGCTTTACAAAATGATAAAAA
* *
15856 TTATCTCTGTCGAATGAGATGCTTTACGAAATGATAAA
1 TTATCTCTGTCGAATGAGACGCTTTACAAAATGATAAA
15894 GAAGTGGAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (40 bp):
TTATCTCTGTCGAATGAGACGCTTTACAAAATGATAAAAA
Found at i:17130 original size:14 final size:15
Alignment explanation
Indices: 17104--17132 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17094 AATATAGTAA
17104 ATAATTAATAATATT
1 ATAATTAATAATATT
17119 ATAATT-ATAATATT
1 ATAATTAATAATATT
17133 TTGAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATTAATAATATT
Found at i:20165 original size:44 final size:44
Alignment explanation
Indices: 20102--20198 Score: 176
Period size: 44 Copynumber: 2.2 Consensus size: 44
20092 GAAAAAAATA
20102 TAAATTATATTGTAATGAATCGTTATCATAAAAGCAATATTAAC
1 TAAATTATATTGTAATGAATCGTTATCATAAAAGCAATATTAAC
* *
20146 TAAATTATATTGTAATGAATCGTTATCTTAAAAGCAATCTTAAC
1 TAAATTATATTGTAATGAATCGTTATCATAAAAGCAATATTAAC
20190 TAAATTATA
1 TAAATTATA
20199 ATGCCTTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.38
Consensus pattern (44 bp):
TAAATTATATTGTAATGAATCGTTATCATAAAAGCAATATTAAC
Found at i:22280 original size:21 final size:21
Alignment explanation
Indices: 22254--22306 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
22244 TTAGCTGAGT
22254 AGTATCGATATTGATTCAATC
1 AGTATCGATATTGATTCAATC
*
22275 AGTATCGATATTGATTCAATT
1 AGTATCGATATTGATTCAATC
*
22296 AATATCGATAT
1 AGTATCGATAT
22307 CGACGAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (21 bp):
AGTATCGATATTGATTCAATC
Found at i:23475 original size:68 final size:68
Alignment explanation
Indices: 23133--23456 Score: 459
Period size: 68 Copynumber: 4.8 Consensus size: 68
23123 CTAAAATAAA
* * * * *
23133 AGGCCTAACTATGCATTTTACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCT
1 AGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
23198 TTG
66 TTG
* * *
23201 AGGCCTAATTGTGCATTTGACAGAAAGGTGTCAAATATGCCAATTAGATGAAAGACTAAGTGCCT
1 AGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
23266 TTG
66 TTG
* * *
23269 AGGCCTAATTGTGCATTTGACAGAAATGTGTCAATTATTCCAGTTAGATGAAAGGCTAAATGCCT
1 AGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
23334 TTG
66 TTG
** * *
23337 AGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAATTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
23402 TTG
66 TTG
* * * * * *
23405 AGTCCTAGTTGTGGATTTGGCAGAAAGGTGTCAAGTATTCCAGTTAGATGAA
1 AGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
23457 TGGTTAAAGA
Statistics
Matches: 227, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 227 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (68 bp):
AGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:23544 original size:81 final size:80
Alignment explanation
Indices: 23408--23728 Score: 403
Period size: 81 Copynumber: 4.0 Consensus size: 80
23398 GCCTTTGAGT
* * *
23408 CCTAGTTGTGGATTTGGCAGAAAGGTGTCAAGTATTCCAGTTAGATGAATGGTTAAAGACCGTTG
1 CCTAGCTGTGCATTTGGCAGAAA-GTGTCAATTATTCCAGTTAGATGAATGGTTAAAGACCGTTG
23473 AGTAAAAGATAAATGG
65 AGTAAAAGATAAATGG
* * * *
23489 CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTTTTCCAGTTAGACGAATAGTTAAAAACCGTTG
1 CCTAGCTGTGCATTTGGCAGAAA-GTGTCAATTATTCCAGTTAGATGAATGGTTAAAGACCGTTG
23554 AGTAAAAGA-AAATGG
65 AGTAAAAGATAAATGG
* * * * *
23569 CCTAGCTGTGCATTTGGCAGAACAATGTCAATTATGCTAGTTAGGTGAATGGTTAAAGATCGTTG
1 CCTAGCTGTGCATTTGGCAGAA-AGTGTCAATTATTCCAGTTAGATGAATGGTTAAAGACCGTTG
23634 AGTAAAAGATAAATGG
65 AGTAAAAGATAAATGG
* * * * * *
23650 CCTAGATGTGCATTTGGCAGACAAGTGTCAATCATGCAAGTTAGATGAAAGGTTAAATG-CCTTT
1 CCTAGCTGTGCATTTGGCAGA-AAGTGTCAATTATTCCAGTTAGATGAATGGTTAAA-GACCGTT
*
23714 GGGTAAAAGACTAAA
64 GAGTAAAAGA-TAAA
23729 GGAATTATAA
Statistics
Matches: 210, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
80 69 0.33
81 135 0.64
82 6 0.03
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (80 bp):
CCTAGCTGTGCATTTGGCAGAAAGTGTCAATTATTCCAGTTAGATGAATGGTTAAAGACCGTTGA
GTAAAAGATAAATGG
Found at i:30800 original size:15 final size:15
Alignment explanation
Indices: 30777--30853 Score: 72
Period size: 15 Copynumber: 5.4 Consensus size: 15
30767 CGCCCCGCAT
*
30777 CCGCACCGCATCCAC
1 CCGCCCCGCATCCAC
30792 CCGCCCCGCAT----
1 CCGCCCCGCATCCAC
*
30803 CCGCACCGCATCCAC
1 CCGCCCCGCATCCAC
*
30818 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCAC
* * *
30833 CCTCCCCACATCCGC
1 CCGCCCCGCATCCAC
30848 CCGCCC
1 CCGCCC
30854 AACTAAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
11 10 0.20
15 41 0.80
ACGTcount: A:0.13, C:0.65, G:0.14, T:0.08
Consensus pattern (15 bp):
CCGCCCCGCATCCAC
Found at i:30849 original size:26 final size:26
Alignment explanation
Indices: 30764--30832 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
30754 TTGAGACCTT
30764 ACCCGCCCCGCATCCGCACCGCATCC
1 ACCCGCCCCGCATCCGCACCGCATCC
30790 ACCCGCCCCGCATCCGCACCGCATCC
1 ACCCGCCCCGCATCCGCACCGCATCC
30816 ACCCGCCCCGCATCCGC
1 ACCCGCCCCGCATCCGC
30833 CCTCCCCACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.14, C:0.62, G:0.16, T:0.07
Consensus pattern (26 bp):
ACCCGCCCCGCATCCGCACCGCATCC
Found at i:41306 original size:35 final size:35
Alignment explanation
Indices: 41267--41337 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
41257 CTATTTGAAT
**
41267 AACTTTAACCAAATATTATCCAAAAAGGTCTATGA
1 AACTTTAACCAAATATTATCCAAAAAGAACTATGA
*
41302 AACTTTAACCTAATATTATCCAAAAAGAACTATGA
1 AACTTTAACCAAATATTATCCAAAAAGAACTATGA
41337 A
1 A
41338 TGACGACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (35 bp):
AACTTTAACCAAATATTATCCAAAAAGAACTATGA
Found at i:42418 original size:2 final size:2
Alignment explanation
Indices: 42411--42470 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
42401 AACCCTATTT
42411 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
42453 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
42471 AAATATCAAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43258 original size:20 final size:20
Alignment explanation
Indices: 43233--43273 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
43223 GTAGGTCAGA
43233 TATGGTGGCGCACATTAGTT
1 TATGGTGGCGCACATTAGTT
43253 TATGGTGGCGCACATTAGTT
1 TATGGTGGCGCACATTAGTT
43273 T
1 T
43274 GAGTTTGGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.37
Consensus pattern (20 bp):
TATGGTGGCGCACATTAGTT
Found at i:43590 original size:17 final size:17
Alignment explanation
Indices: 43564--43600 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
43554 TTAATTTAAT
*
43564 TTTTTTAAATAGAAGTG
1 TTTTTAAAATAGAAGTG
*
43581 TTTTTAAAATTGAAGTG
1 TTTTTAAAATAGAAGTG
43598 TTT
1 TTT
43601 GTGATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (17 bp):
TTTTTAAAATAGAAGTG
Found at i:51584 original size:13 final size:14
Alignment explanation
Indices: 51563--51623 Score: 76
Period size: 13 Copynumber: 4.6 Consensus size: 14
51553 AGTGGCGAGG
*
51563 AGAAG-AAAAGTGA
1 AGAAGAAAAAATGA
51576 A-AAGAAAAAATGA
1 AGAAGAAAAAATGA
*
51589 AGAAG-AAAAGTGA
1 AGAAGAAAAAATGA
51602 A-AAGAAAAAATGA
1 AGAAGAAAAAATGA
51615 AGAAGAAAA
1 AGAAGAAAA
51624 GAAGAAAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 6 0.15
13 25 0.61
14 10 0.24
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (14 bp):
AGAAGAAAAAATGA
Found at i:51598 original size:26 final size:26
Alignment explanation
Indices: 51563--51624 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
51553 AGTGGCGAGG
51563 AGAAGAAAAGTGAAAAGAAAAAATGA
1 AGAAGAAAAGTGAAAAGAAAAAATGA
51589 AGAAGAAAAGTGAAAAGAAAAAATGA
1 AGAAGAAAAGTGAAAAGAAAAAATGA
51615 AGAAGAAAAG
1 AGAAGAAAAG
51625 AAGAAAAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.06
Consensus pattern (26 bp):
AGAAGAAAAGTGAAAAGAAAAAATGA
Found at i:51638 original size:13 final size:13
Alignment explanation
Indices: 51563--51642 Score: 75
Period size: 13 Copynumber: 6.5 Consensus size: 13
51553 AGTGGCGAGG
51563 AGAAGAAAAGTGA
1 AGAAGAAAAGTGA
*
51576 A-AAGAAAAAATGA
1 AGAAG-AAAAGTGA
51589 AGAAGAAAAGTGA
1 AGAAGAAAAGTGA
*
51602 A-AAGAAAAAATGA
1 AGAAG-AAAAGTGA
51615 AGAAG--AA---A
1 AGAAGAAAAGTGA
51623 AGAAGAAAAGTGA
1 AGAAGAAAAGTGA
51636 AGAAGAA
1 AGAAGAA
51643 GATGGGAACG
Statistics
Matches: 55, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
8 6 0.11
10 2 0.04
11 2 0.04
12 6 0.11
13 33 0.60
14 6 0.11
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (13 bp):
AGAAGAAAAGTGA
Found at i:56947 original size:20 final size:20
Alignment explanation
Indices: 56922--56982 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
56912 CATTTCTGGT
* * *
56922 CCTTTATAGAAAATATAGAC
1 CCTTTACAGAGAATACAGAC
56942 CCTTTACAGAGAATACAGAC
1 CCTTTACAGAGAATACAGAC
*
56962 CCTTTAGAGAGAATACAGAC
1 CCTTTACAGAGAATACAGAC
56982 C
1 C
56983 ATAGCTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (20 bp):
CCTTTACAGAGAATACAGAC
Found at i:64759 original size:22 final size:21
Alignment explanation
Indices: 64733--64813 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 21
64723 ATAGGGCAGA
*
64733 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTT-AAG
*
64755 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATACCCCC-TT-AAG
* *
64778 GGGAACCGATTCCCCCAT-AG
1 GGGAACCGATACCCCCTTAAG
*
64798 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
64814 CTGGGGTTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 16 0.31
22 15 0.29
23 21 0.40
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCCCTTAAG
Found at i:64778 original size:23 final size:22
Alignment explanation
Indices: 64733--64793 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
64723 ATAGGGCAGA
* * *
64733 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTAAAG
64755 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCC-TTAAAG
64778 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
64794 ATAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTAAAG
Found at i:73490 original size:13 final size:12
Alignment explanation
Indices: 73474--73517 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
73464 AGTGGCGAGG
73474 AGAAGAAAGTGAA
1 AGAAGAAAGTG-A
*
73487 AGAA-AAAATGA
1 AGAAGAAAGTGA
73498 AGAAGAAAAGTGA
1 AGAAG-AAAGTGA
73511 AGAAGAA
1 AGAAGAA
73518 GATGGGAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 5 0.19
12 7 0.26
13 15 0.56
ACGTcount: A:0.66, C:0.00, G:0.27, T:0.07
Consensus pattern (12 bp):
AGAAGAAAGTGA
Done.