Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007011.1 Hibiscus syriacus cultivar Beakdansim tig00018098_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: 50530
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:4117 original size:59 final size:59
Alignment explanation
Indices: 4018--4154 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 59
4008 GCAGCAGCTG
** * * *
4018 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAAATGGTGGACACGACCTTATGTAT
* ** *
4077 CATATTCGGGACTTTACTTAAGGATACCTAGTACAAATGGTGGACACGACCTTATGTAT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAAATGGTGGACACGACCTTATGTAT
4136 CATATTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
4155 CGGTGCTTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAAATGGTGGACACGACCTTATGTAT
Found at i:4245 original size:20 final size:20
Alignment explanation
Indices: 4208--4246 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4198 TATATTGGGC
* *
4208 TATTGTCTATTGTTTATGGA
1 TATTGTCTATGGTATATGGA
*
4228 TATTTTCTATGGTATATGG
1 TATTGTCTATGGTATATGG
4247 TTATGGAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.54
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGA
Found at i:4329 original size:46 final size:45
Alignment explanation
Indices: 4247--4355 Score: 150
Period size: 46 Copynumber: 2.4 Consensus size: 45
4237 TGGTATATGG
* *
4247 TTATGGAAT-AATGGTGAGTTTATTGATAAAATAAGCTTATGAGC
1 TTATGGAATAAATGGTAAGTTTATTGATAAAATAAGCTTACGAGC
*
4291 TTATGGAATTTAAATGGTAAGTTT-TTGGTAAAATAAGCTTACGAGC
1 TTATGGAA--TAAATGGTAAGTTTATTGATAAAATAAGCTTACGAGC
*
4337 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGGTAAG
4356 GGATTTTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
44 19 0.33
46 28 0.48
47 11 0.19
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTTTATTGATAAAATAAGCTTACGAGC
Found at i:10547 original size:16 final size:17
Alignment explanation
Indices: 10513--10557 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
10503 ACCGATTTGG
*
10513 TATTGACCCGA-CCTGA
1 TATTGACCCGATCCTAA
10529 TATTGACCCGATCC-AA
1 TATTGACCCGATCCTAA
*
10545 TATTGAACCGATC
1 TATTGACCCGATC
10558 TGAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 24 0.92
17 2 0.08
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (17 bp):
TATTGACCCGATCCTAA
Found at i:10995 original size:19 final size:19
Alignment explanation
Indices: 10971--11036 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
10961 TATGCATTGG
* *
10971 GCTATGAATTTGAAACTAA
1 GCTATGAATATGAAAATAA
* *
10990 GCTATGAATATGAAATTAT
1 GCTATGAATATGAAAATAA
* *
11009 GCAATGAATATGAAAATAC
1 GCTATGAATATGAAAATAA
*
11028 GTTATGAAT
1 GCTATGAAT
11037 TTGGAAATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.32
Consensus pattern (19 bp):
GCTATGAATATGAAAATAA
Found at i:11044 original size:19 final size:19
Alignment explanation
Indices: 10973--11055 Score: 58
Period size: 19 Copynumber: 4.4 Consensus size: 19
10963 TGCATTGGGC
* * * *
10973 TATGAATTTGAAACTAAGC
1 TATGAATATGAAAATACGT
* * *
10992 TATGAATATGAAATTATGC
1 TATGAATATGAAAATACGT
*
11011 AATGAATATGAAAATACGT
1 TATGAATATGAAAATACGT
* * *
11030 TATGAATTTGGAAATATGT
1 TATGAATATGAAAATACGT
*
11049 TCTGAAT
1 TATGAAT
11056 CGAGAATGAA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (19 bp):
TATGAATATGAAAATACGT
Found at i:11137 original size:13 final size:13
Alignment explanation
Indices: 11090--11145 Score: 62
Period size: 12 Copynumber: 4.5 Consensus size: 13
11080 GGTATTCATT
*
11090 ATGAAAATGAGAG
1 ATGAAAATGAAAG
* *
11103 -TTAAAATGAATG
1 ATGAAAATGAAAG
*
11115 -TGAAATTGAAAG
1 ATGAAAATGAAAG
11127 ATGAAAATGAAAG
1 ATGAAAATGAAAG
11140 ATGAAA
1 ATGAAA
11146 GTTTTTAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
12 18 0.51
13 17 0.49
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.21
Consensus pattern (13 bp):
ATGAAAATGAAAG
Found at i:11412 original size:2 final size:2
Alignment explanation
Indices: 11347--11392 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
11337 ATTTTTAAGT
11347 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
11389 TA TA
1 TA TA
11393 CACGCACACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17592 original size:19 final size:18
Alignment explanation
Indices: 17539--17596 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
17529 TGCATTGGTC
**
17539 TATGAATTTGAAATTAAAC
1 TATGAATTTGAAA-TAAGT
*
17558 TATGAATATGAGAATAAGT
1 TATGAATTTGA-AATAAGT
17577 TATGAATTTTGAAATAAGT
1 TATGAA-TTTGAAATAAGT
17596 T
1 T
17597 TTAAATTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 27 0.82
20 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.38
Consensus pattern (18 bp):
TATGAATTTGAAATAAGT
Found at i:22759 original size:49 final size:49
Alignment explanation
Indices: 22613--22884 Score: 332
Period size: 49 Copynumber: 5.6 Consensus size: 49
22603 GAATACCATG
* * * *
22613 AGTGGCACC-GTTATGCCAAAATACACTGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
* * * *
22661 AGTGGCACCTTTAATGCTG-AATGAACCGTTGTGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
* * * *
22709 AGTGGCACTTTTTATGCCGAAATGCATCGTTGTGCATTTAACATTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
* * **
22758 AGTGGCACCTTTTATGCCTAAATGCACCATTACACATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
* * * *
22807 ACTGGAACCTTTTATGTCGAAATGCACCGTTATGAATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
* *
22856 AGTGACACCTTTTATGCCGAAATACACCG
1 AGTGGCACCTTTTATGCCGAAATGCACCG
22885 CACCCTCGAT
Statistics
Matches: 187, Mismatches: 35, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
48 50 0.27
49 137 0.73
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
Found at i:31476 original size:15 final size:15
Alignment explanation
Indices: 31458--31488 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31448 GTGGTGGAGG
31458 TCTCACATCGACTGC
1 TCTCACATCGACTGC
*
31473 TCTCACATTGACTGC
1 TCTCACATCGACTGC
31488 T
1 T
31489 GATGGTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.35, G:0.13, T:0.32
Consensus pattern (15 bp):
TCTCACATCGACTGC
Found at i:34300 original size:16 final size:16
Alignment explanation
Indices: 34279--34312 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
34269 TTCTCTCTTC
*
34279 TTCCTTGCCCCCCTTT
1 TTCCTTGCCCCCATTT
34295 TTCCTTGCCCCCATTT
1 TTCCTTGCCCCCATTT
34311 TT
1 TT
34313 TTGCGACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.44, G:0.06, T:0.47
Consensus pattern (16 bp):
TTCCTTGCCCCCATTT
Found at i:34311 original size:15 final size:16
Alignment explanation
Indices: 34279--34311 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
34269 TTCTCTCTTC
*
34279 TTCCTTGCCCCCCTTT
1 TTCCTTGCCCCCCATT
34295 TTCCTTG-CCCCCATT
1 TTCCTTGCCCCCCATT
34310 TT
1 TT
34312 TTTGCGACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.03, C:0.45, G:0.06, T:0.45
Consensus pattern (16 bp):
TTCCTTGCCCCCCATT
Found at i:36998 original size:19 final size:20
Alignment explanation
Indices: 36974--37043 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 20
36964 GCAAAAATGT
*
36974 TATCGATACCATAATA-GGG
1 TATCGATACCATAGTAGGGG
*
36993 TATCGATACCATAGTATGGTAG
1 TATCGATACCATAGTA-GG-GG
*
37015 TATCGATACCATGGTAGGGG
1 TATCGATACCATAGTAGGGG
37035 TATCGATAC
1 TATCGATAC
37044 TGAGGAGCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
19 15 0.34
20 10 0.23
21 3 0.07
22 16 0.36
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
TATCGATACCATAGTAGGGG
Found at i:37523 original size:54 final size:55
Alignment explanation
Indices: 37383--37535 Score: 164
Period size: 55 Copynumber: 2.8 Consensus size: 55
37373 TAAGAGCACA
* * ** ***
37383 AAAACCTAAGAAATTCGTACTAAGGGTATGAATTTTGGTATGGGCACTTTGTGTGC
1 AAAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTACATGTGC
* * * *
37439 AAAAATAAGAAGTTTATACTAAGTGTATGAATTTCCGTATGGGTACTACATGTGC
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTACATGTGC
* * *
37494 -GAACTAAGAAATTCATACTAAGTGTATGAAGTTCTGTATGGG
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
37536 AAATATATGA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
54 36 0.45
55 40 0.50
56 4 0.05
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (55 bp):
AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTACATGTGC
Found at i:38152 original size:68 final size:68
Alignment explanation
Indices: 37747--38134 Score: 591
Period size: 68 Copynumber: 5.7 Consensus size: 68
37737 GTTTTCAGAA
*
37747 CTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
37812 GGC
66 GGC
* * *
37815 CTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCACTTAGATGAAAGGCTAAGTGCCTTTAA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
37880 GGC
66 GGC
* * * *
37883 CTAACTATGCATTTAACAGAATGGTGTCAATTAAGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
37948 GGC
66 GGC
* * * * *
37951 CTAACTTTGCATTTAATAGAAATGG-GTCAATTATGCCAGTTAGATGAAAGACTAACTGCCTTTG
1 CTAACTGTGCATTTGACAGAAA-GGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
38015 AGGC
65 AGGC
* * * *
38019 CTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGACATTTAGATGAAAGACTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
38084 GGC
66 GGC
38087 CTAACTGTGCATTTGGA-AGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 CTAACTGTGCATTT-GACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
38135 TGGTTAAATA
Statistics
Matches: 290, Mismatches: 27, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
67 2 0.01
68 285 0.98
69 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (68 bp):
CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
GGC
Found at i:38221 original size:81 final size:81
Alignment explanation
Indices: 38084--38564 Score: 545
Period size: 81 Copynumber: 5.9 Consensus size: 81
38074 GTGCCTTTGA
* * *
38084 GGCCTAACTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAATACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
*
38149 TGAGTAAAACATGAAT
66 TGAGTAAAAAATGAAT
* * * *
38165 GGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCATTTAGATGAACGGTTAAATATCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
*
38230 AGAGTAAAAAATGAAT
66 TGAGTAAAAAATGAAT
* * * * * *
38246 GGCCTAGCTGTGCATTTTGCAGAAAGGTGTTAATTATGTCAGTGAGATGAACAGTTAAATATCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
*
38311 TGAGTAAAAGATGAAT
66 TGAGTAAAAAATGAAT
* * * * * * *
38327 AGCCTAGCTGTGCATTTGGCAGAAAGATGTTAATTATGTCAGTTAGATGAATGGTTAAACAACGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
*
38392 TGAGTAAAAGATGAAT
66 TGAGTAAAAAATGAAT
* * * * * * *
38408 GACCTAGCTGGGAATTTGGCAGAAAGGTGTCAATTATGCCAGGTAGATGAACAGTTAAACACTGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
38473 TGAGTAAAAGAAT-AAT
66 TGAGTAAAA-AATGAAT
* * * * * * * * *
38489 GGACTAGCTGTGCATTTGACAAAAAAGTGGCAAATATGCAAGTTATATAGAA-GGCTAAATACCA
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGAT-GAACGGTTAAATACC-
*
38553 TTTG-GTAAAAAA
64 GTTGAGTAAAAAA
38565 AGGAATTATA
Statistics
Matches: 342, Mismatches: 55, Indels: 7
0.85 0.14 0.02
Matches are distributed among these distances:
80 2 0.01
81 332 0.97
82 8 0.02
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
TGAGTAAAAAATGAAT
Found at i:40548 original size:20 final size:21
Alignment explanation
Indices: 40511--40549 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40501 ATACTATGGG
40511 TAGTATCGATACCACAGGGGT
1 TAGTATCGATACCACAGGGGT
40532 TAGTATCGATACC-CAGGG
1 TAGTATCGATACCACAGGG
40550 TGAAAGTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (21 bp):
TAGTATCGATACCACAGGGGT
Found at i:40557 original size:21 final size:21
Alignment explanation
Indices: 40512--40564 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
40502 TACTATGGGT
**
40512 AGTATCGATACCACAGGGGTT
1 AGTATCGATACCACAGGGGAA
40533 AGTATCGATACC-CAGGGTGAA
1 AGTATCGATACCACAGGG-GAA
*
40554 AGTATCAATAC
1 AGTATCGATAC
40565 TCGTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (21 bp):
AGTATCGATACCACAGGGGAA
Found at i:40938 original size:22 final size:22
Alignment explanation
Indices: 40904--40968 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
40894 CAATCCCTGC
* *
40904 AGTGCTAAGGCACTTTAGTATT
1 AGTGCAAATGCACTTTAGTATT
40926 AGTGCAAATGCACTTTAGTATT
1 AGTGCAAATGCACTTTAGTATT
*
40948 AGTGCAAATGCACTTTCGTAT
1 AGTGCAAATGCACTTTAGTAT
40969 CAGTACTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (22 bp):
AGTGCAAATGCACTTTAGTATT
Found at i:41754 original size:17 final size:17
Alignment explanation
Indices: 41729--41771 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
41719 TGAAAGCATT
*
41729 TATAGATTTGAAAAAAA
1 TATATATTTGAAAAAAA
41746 TATATATTTTTGAAAAAAA
1 TATATA--TTTGAAAAAAA
41765 TATATAT
1 TATATAT
41772 AATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
19 17 0.74
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
TATATATTTGAAAAAAA
Found at i:41757 original size:19 final size:19
Alignment explanation
Indices: 41735--41771 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
41725 CATTTATAGA
41735 TTTGAAAAAAATATATATT
1 TTTGAAAAAAATATATATT
41754 TTTGAAAAAAATATATAT
1 TTTGAAAAAAATATATAT
41772 AATATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTGAAAAAAATATATATT
Found at i:41812 original size:18 final size:19
Alignment explanation
Indices: 41768--41813 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
41758 AAAAAAATAT
*
41768 ATATAATATATTTTTTGAAA
1 ATAT-ATATAGTTTTTGAAA
*
41788 A-ACATATAGTTTTT-AAA
1 ATATATATAGTTTTTGAAA
41805 ATATATATA
1 ATATATATA
41814 ATATATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 1 0.05
20 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATATATAGTTTTTGAAA
Found at i:41818 original size:46 final size:44
Alignment explanation
Indices: 41735--41850 Score: 107
Period size: 46 Copynumber: 2.6 Consensus size: 44
41725 CATTTATAGA
41735 TTTGAAAAAAATATATATTTTTGAAAAAAATATATATAATATATTT
1 TTTGAAAAAAATATATATTTTTGAAAAAAATATATAT-ATA-ATTT
* * *
41781 TTTGAAAAACATATA-GTTTTT-AAAATATATATAATATATAA--T
1 TTTGAAAAAAATATATATTTTTGAAAA-AAATAT-ATATATAATTT
*
41823 TTT-AAAAAAATTAATATAGTTTTGAAAA
1 TTTGAAAAAAA-T-ATATATTTTTGAAAA
41851 CATGTGTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
41 6 0.10
42 5 0.09
43 3 0.05
44 9 0.16
45 17 0.29
46 18 0.31
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (44 bp):
TTTGAAAAAAATATATATTTTTGAAAAAAATATATATATAATTT
Found at i:41832 original size:43 final size:42
Alignment explanation
Indices: 41739--41850 Score: 111
Period size: 41 Copynumber: 2.6 Consensus size: 42
41729 TATAGATTTG
*
41739 AAAAAAAT-ATATATTTTTGAAAAAAATATATATAATATATTTTT
1 AAAAAAATAATATAGTTTTG---AAAATATATATAATATATTTTT
** * *
41783 TGAAAAA-CATATAGTTTTTAAAATATATATAATATATAATTTT
1 AAAAAAATAATATAGTTTTGAAAATATATATAATATAT--TTTT
41826 AAAAAAATTAATATAGTTTTGAAAA
1 AAAAAAA-TAATATAGTTTTGAAAA
41851 CATGTGTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
41 18 0.33
43 9 0.16
44 14 0.25
45 14 0.25
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (42 bp):
AAAAAAATAATATAGTTTTGAAAATATATATAATATATTTTT
Found at i:41940 original size:16 final size:16
Alignment explanation
Indices: 41919--41964 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 16
41909 TTTCATTTTC
41919 TTCATTTATTTACTTT
1 TTCATTTATTTACTTT
41935 TTCA-TTA-TTA-TTT
1 TTCATTTATTTACTTT
*
41948 CT-ATTTATTTACTTT
1 TTCATTTATTTACTTT
41963 TT
1 TT
41965 TTCATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
12 1 0.04
13 7 0.28
14 6 0.24
15 7 0.28
16 4 0.16
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCATTTATTTACTTT
Found at i:46069 original size:21 final size:22
Alignment explanation
Indices: 46045--46086 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
46035 GGTGGTCTTG
46045 ATGGAAGATGGT-TGATGGTAT
1 ATGGAAGATGGTATGATGGTAT
46066 ATGGAAGATGGTAATGATGGT
1 ATGGAAGATGGT-ATGATGGT
46087 GTATCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (22 bp):
ATGGAAGATGGTATGATGGTAT
Found at i:47973 original size:59 final size:58
Alignment explanation
Indices: 47886--48176 Score: 377
Period size: 59 Copynumber: 4.9 Consensus size: 58
47876 CATATTTAGA
* *
47886 ATTGCACTAAAGGATACCTAGTGGATATGGTGGTCATGACCTTATGTGTCATATTCGGG
1 ATTGCACTAAA-GATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATATTCGGG
*
47945 ATTGCACTAAATGATACCTAGTGCATATGGTGGGCACGACCTTATGTGTCATATTCGGG
1 ATTGCACTAAA-GATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATATTCGGG
* * * * **
48004 ACTGCACTGAAAGATACCAAGTGCATATGGTGGGCATGACCTTTTGTGTAATATTTTAGG
1 ATTGCACT-AAAGATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATA-TTCGGG
* * *
48064 -TTGCACTAAAGAATGCCAAGTGTATATGGTGGGCATGACCTTATGTGTCATATTCGGG
1 ATTGCACTAAAG-ATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATATTCGGG
* ** *
48122 ATTGCATTAAAAGATACCTAGTAAATATGGTGGGCACGACCTTATGTGTCATATT
1 ATTGCACT-AAAGATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATATT
48177 TTGTTTAGCA
Statistics
Matches: 203, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
58 8 0.04
59 184 0.91
60 11 0.05
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (58 bp):
ATTGCACTAAAGATACCTAGTGCATATGGTGGGCATGACCTTATGTGTCATATTCGGG
Done.