Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003497.1 Hibiscus syriacus cultivar Beakdansim tig00007395_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: 74679
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:428 original size:4 final size:4
Alignment explanation
Indices: 419--475 Score: 66
Period size: 4 Copynumber: 15.0 Consensus size: 4
409 TTCTCATTCC
* * *
419 ATGT ATGT ATGT A-GT ATAT ATGT ACGT ATGT ACGT ATGT A-GT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
465 A-GT ATGT ATGT
1 ATGT ATGT ATGT
476 TAATGTTGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 9 0.20
4 35 0.80
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.44
Consensus pattern (4 bp):
ATGT
Found at i:4221 original size:2 final size:2
Alignment explanation
Indices: 4209--4263 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
4199 TTTTACGGTT
*
4209 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TG 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
* *
4250 TG TA TA TG TA TA TA
1 TA TA TA TA TA TA TA
4264 AGGATGGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6006 original size:18 final size:18
Alignment explanation
Indices: 5983--6018 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5973 AATAGTCCTC
5983 TCATATCCATACCCATAT
1 TCATATCCATACCCATAT
6001 TCATATCCATACCCATAT
1 TCATATCCATACCCATAT
6019 GCATTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (18 bp):
TCATATCCATACCCATAT
Found at i:16802 original size:22 final size:22
Alignment explanation
Indices: 16774--16826 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
16764 TTCCATTTCG
16774 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
16796 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
16818 CGTTGCGAT
1 CGTTGCGAT
16827 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:16917 original size:41 final size:41
Alignment explanation
Indices: 16872--17011 Score: 239
Period size: 41 Copynumber: 3.5 Consensus size: 41
16862 ATTCGCGTTG
* * *
16872 CATTTCGCATTACGATAGTTGAAAATCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
16913 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
16954 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
16995 CATTT--CGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
17012 CTACAGTTGT
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
39 12 0.12
41 84 0.88
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:16943 original size:21 final size:21
Alignment explanation
Indices: 16884--16990 Score: 101
Period size: 21 Copynumber: 5.2 Consensus size: 21
16874 TTTCGCATTA
*
16884 CGATAGTTGAAAATCGCATTG
1 CGATAGTTGAAAATCGCGTTG
* ** **
16905 CGAT-TTTCCATTTCGCGTTG
1 CGATAGTTGAAAATCGCGTTG
16925 CGATAGTTGAAAATCGCGTTG
1 CGATAGTTGAAAATCGCGTTG
* ** **
16946 CGAT-TTTCCATTTCGCGTTG
1 CGATAGTTGAAAATCGCGTTG
16966 CGATAGTTGAAAATCGCGTTG
1 CGATAGTTGAAAATCGCGTTG
16987 CGAT
1 CGAT
16991 TTTCCATTTC
Statistics
Matches: 63, Mismatches: 21, Indels: 4
0.72 0.24 0.05
Matches are distributed among these distances:
20 29 0.46
21 34 0.54
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (21 bp):
CGATAGTTGAAAATCGCGTTG
Found at i:17026 original size:22 final size:22
Alignment explanation
Indices: 16999--17052 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
16989 ATTTTCCATT
16999 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
*
17021 TTGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
17043 TCGTTGCGAT
1 TCGTTGCGAT
17053 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:17179 original size:6 final size:6
Alignment explanation
Indices: 17168--17226 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
17158 ACGTATTACT
17168 ACGACC ACGACC ACGACC ACGACC A--ACC ACGACC ACG--- ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
17211 ACGACC ACGACC -CGAC
1 ACGACC ACGACC ACGAC
17227 GAGACGGACG
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.06
4 4 0.08
5 4 0.08
6 37 0.77
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:17232 original size:25 final size:25
Alignment explanation
Indices: 17168--17221 Score: 56
Period size: 28 Copynumber: 2.1 Consensus size: 25
17158 ACGTATTACT
*
17168 ACGACCACGACCACGACCACGACCAACC
1 ACGACCACGACCA--ACCACGACC-ACG
*
17196 ACGACCACGA-CGACCACGACCACG
1 ACGACCACGACCAACCACGACCACG
17220 AC
1 AC
17222 CCGACGAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
24 4 0.17
25 9 0.38
27 1 0.04
28 10 0.42
ACGTcount: A:0.35, C:0.48, G:0.17, T:0.00
Consensus pattern (25 bp):
ACGACCACGACCAACCACGACCACG
Found at i:17716 original size:5 final size:5
Alignment explanation
Indices: 17701--17731 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
17691 CCGCCGCCGC
17701 CGTCT -GTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
17732 GGTCGTGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.39, G:0.23, T:0.39
Consensus pattern (5 bp):
CGTCT
Found at i:17850 original size:21 final size:21
Alignment explanation
Indices: 17824--17895 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
17814 AAACGAATTT
17824 TCGCAACGAATTTGTAAACTA
1 TCGCAACGAATTTGTAAACTA
* ** *
17845 TCGCAACAACAACTGTAGACTA
1 TCGCAACGA-ATTTGTAAACTA
* *
17867 TCGCAACGCGATTT-TCAACTA
1 TCGCAACG-AATTTGTAAACTA
17888 TCGCAACG
1 TCGCAACG
17896 CGAAATGGAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (21 bp):
TCGCAACGAATTTGTAAACTA
Found at i:17896 original size:21 final size:21
Alignment explanation
Indices: 17863--17939 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
17853 ACAACTGTAG
17863 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
** **
17884 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTTCA
*
17905 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
17925 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
17940 AATGGAAAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:17912 original size:20 final size:20
Alignment explanation
Indices: 17887--17963 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
17877 ATTTTCAACT
17887 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
17907 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
17928 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
17948 ATCGCAATGCGAAATG
1 ATCGCAACGCGAAATG
17964 CAATTCGAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:17918 original size:41 final size:41
Alignment explanation
Indices: 17866--17959 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
17856 ACTGTAGACT
17866 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
17907 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
*
17948 ATCGCAATGCGA
1 ATCGCAACGCGA
17960 AATGCAATTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:24605 original size:76 final size:76
Alignment explanation
Indices: 24404--24607 Score: 279
Period size: 75 Copynumber: 2.7 Consensus size: 76
24394 CGTTGTACAA
* * * *
24404 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGC-ATACTGGAATTCTCGGAAC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAAT-CTGGAAATCTCGGAAC
** *
24467 AAAACTGTTTAG
65 AAAACCATTCAG
* * *
24479 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAACA
24543 AAACCATTCAG
66 AAACCATTCAG
*
24554 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAA
24608 TTTTTGTCTT
Statistics
Matches: 114, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
75 82 0.72
76 32 0.28
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAACA
AAACCATTCAG
Found at i:25222 original size:17 final size:17
Alignment explanation
Indices: 25200--25243 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
25190 ATTAAAAATC
25200 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
25217 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
25234 -AAATATCCAA
1 CAAA-ATCCAA
25244 AAAGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:25235 original size:9 final size:8
Alignment explanation
Indices: 25193--25246 Score: 58
Period size: 9 Copynumber: 6.6 Consensus size: 8
25183 TCACACTATT
25193 AAAAATCC
1 AAAAATCC
25201 -AAAATCC
1 AAAAATCC
*
25208 AACAATCC
1 AAAAATCC
25216 ACAAAAT-C
1 A-AAAATCC
25224 AAACAATCC
1 AAA-AATCC
25233 AAAATATCC
1 AAAA-ATCC
25242 AAAAA
1 AAAAA
25247 GTTGAAACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 9 0.23
8 14 0.36
9 16 0.41
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAATCC
Found at i:27197 original size:22 final size:21
Alignment explanation
Indices: 27163--27223 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
27153 AACAGAACCC
*
27163 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGGATCGATTCCCCT
** *
27184 GTGGGGGGGAATCGGTT-CCCT
1 CAGGGGGGG-ATCGATTCCCCT
27205 CAGGGGGGGATCGATTCCC
1 CAGGGGGGGATCGATTCCC
27224 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 6 0.19
21 19 0.61
22 6 0.19
ACGTcount: A:0.13, C:0.25, G:0.41, T:0.21
Consensus pattern (21 bp):
CAGGGGGGGATCGATTCCCCT
Found at i:27212 original size:20 final size:20
Alignment explanation
Indices: 27163--27225 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
27153 AACAGAACCC
*
27163 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATT-CCCT
** *
27184 GTGGGGGGGAATCGGTTCCCT
1 -CAGGGGGGAATCGATTCCCT
*
27205 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
27225 C
1 C
27226 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
20 17 0.52
21 4 0.12
22 12 0.36
ACGTcount: A:0.13, C:0.25, G:0.40, T:0.22
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:33168 original size:75 final size:76
Alignment explanation
Indices: 32998--33204 Score: 267
Period size: 74 Copynumber: 2.7 Consensus size: 76
32988 CCGTTGTACA
* * * * *
32998 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
** *
33062 CAAAACTGTTT
66 CAAAACCATTC
*
33073 A-GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
*
33136 CCAAACCATTC
66 CAAAACCATTC
* *
33147 AGGGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 AGGGGGGAATCGGTTCCTCCTAT--GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
33205 TTTTTGGCTT
Statistics
Matches: 115, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
74 62 0.54
75 23 0.20
78 30 0.26
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
CAAAACCATTC
Found at i:33441 original size:2 final size:2
Alignment explanation
Indices: 33434--33466 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
33424 ATGTTTCAAC
33434 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33467 ATACTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:34186 original size:27 final size:26
Alignment explanation
Indices: 34127--34194 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
34117 TAAACTGTTT
*
34127 TTAATTATAAAATATTTAATTTTTATA
1 TTAATTAGAAAAT-TTTAATTTTTATA
* * *
34154 TAAATTAGAAAATTTTAATTTTTTTTG
1 TTAATTAGAAAATTTTAA-TTTTTATA
*
34181 TTAATTCGAAAATT
1 TTAATTAGAAAATT
34195 AACCGAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 5 0.15
27 29 0.85
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (26 bp):
TTAATTAGAAAATTTTAATTTTTATA
Found at i:38709 original size:18 final size:18
Alignment explanation
Indices: 38686--38739 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
38676 AAAGGCGATG
*
38686 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGCT
38704 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
38722 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
38740 ACGGTGGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:40384 original size:111 final size:111
Alignment explanation
Indices: 40249--40581 Score: 585
Period size: 111 Copynumber: 3.0 Consensus size: 111
40239 ATTACAAAAA
* *
40249 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
40314 AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
40360 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
40425 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* *
40471 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAAATATTATTAATAATTTAAATTA
1 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
40536 AATTAAAACATTAAAATGTTACTGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
40582 ATGATTTCCA
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 212 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:40913 original size:50 final size:50
Alignment explanation
Indices: 40859--40964 Score: 151
Period size: 50 Copynumber: 2.1 Consensus size: 50
40849 AGATACCCAG
* * *
40859 GTATAGCGC-GGATCAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACC
1 GTATAGCGCGGGA-CAGGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
* *
40909 GTATATCTCGGGACAGGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
1 GTATAGCGCGGGACAGGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
40959 GTATAG
1 GTATAG
40965 TACGATTCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
50 46 0.94
51 3 0.06
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.16
Consensus pattern (50 bp):
GTATAGCGCGGGACAGGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
Found at i:41120 original size:4 final size:5
Alignment explanation
Indices: 41102--41135 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
41092 TTACATTTGA
41102 TTATT TTATT TTA-T TTATT TTA-T TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT T
41136 CGTTTTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:41214 original size:8 final size:9
Alignment explanation
Indices: 41106--41218 Score: 63
Period size: 9 Copynumber: 12.2 Consensus size: 9
41096 ATTTGATTAT
41106 TTTATTTTA
1 TTTATTTTA
41115 TTTATTTTA
1 TTTATTTTA
41124 TTTATTTTA
1 TTTATTTTA
*
41133 TTTCGTTTTTCA
1 TTT--ATTTT-A
*
41145 TTTGTTTT-
1 TTTATTTTA
*
41153 TTT-TTTAA
1 TTTATTTTA
41161 TTT-TTTTA
1 TTTATTTTA
** *
41169 CTCAATCTTA
1 -TTTATTTTA
41179 TTTATCTTTA
1 TTTAT-TTTA
* *
41189 TTTATCTAA
1 TTTATTTTA
41198 TTTA-TTTA
1 TTTATTTTA
41206 TTTTATTATTA
1 -TTTATT-TTA
41217 TT
1 TT
41219 ACATTAATTT
Statistics
Matches: 80, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
7 3 0.04
8 12 0.15
9 35 0.44
10 19 0.24
11 7 0.09
12 4 0.05
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTATTTTA
Found at i:41259 original size:23 final size:24
Alignment explanation
Indices: 41199--41259 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
41189 TTTATCTAAT
41199 TTATTTA-TTTTATTATTATTACA
1 TTATTTATTTTTATTATTATTACA
* *
41222 TTAATTT-TTTTTATTCTTTTTACA
1 TT-ATTTATTTTTATTATTATTACA
41246 -TATTTATTTTTATT
1 TTATTTATTTTTATT
41260 TTACAATCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 4 0.12
23 11 0.33
24 18 0.55
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (24 bp):
TTATTTATTTTTATTATTATTACA
Found at i:41807 original size:2 final size:2
Alignment explanation
Indices: 41800--41825 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41790 ATTAAAATTA
41800 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
41826 TGAATACAAG
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):
AT
Found at i:44754 original size:70 final size:70
Alignment explanation
Indices: 44641--44782 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
44631 AATGTTGTGT
44641 TACGATCACCATAGATGATCCAATTACACCGAGATTTCTGCATCCAAATACTTTCCTCTTGGTCT
1 TACGATCACCATAGATGATCCAATTACACCGAGATTTCTGCATCCAAATACTTTCCTCTTGGTCT
44706 AGAGG
66 AGAGG
*
44711 TACGATCACCATAGATGATCCAATTACACCGATATTTCTGCATCCAAATACTTTCCTCTTGGTCT
1 TACGATCACCATAGATGATCCAATTACACCGAGATTTCTGCATCCAAATACTTTCCTCTTGGTCT
44776 AGAGG
66 AGAGG
44781 TA
1 TA
44783 ATTCAAGTTC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (70 bp):
TACGATCACCATAGATGATCCAATTACACCGAGATTTCTGCATCCAAATACTTTCCTCTTGGTCT
AGAGG
Found at i:47583 original size:263 final size:263
Alignment explanation
Indices: 47116--47641 Score: 1025
Period size: 263 Copynumber: 2.0 Consensus size: 263
47106 GGTCAATGGA
47116 TTAATCATGCACATGATCAGAAAAATTGACAATTGGATAGGAACCACTACGATTCACAGTAAAGT
1 TTAATCATGCACATGATCAGAAAAATTGACAATTGGATAGGAACCACTACGATTCACAGTAAAGT
47181 CGCCTTCCTGAATTGTAACATCATTATCACCAAAAATCGGGATGACAGATTGTGGAAGTCCAGAT
66 CGCCTTCCTGAATTGTAACATCATTATCACCAAAAATCGGGATGACAGATTGTGGAAGTCCAGAT
*
47246 GAACCTGCTATCGTCTCAGCATAAGACTTCACTGGTTGAGCGGTGTCTAGATTCATTTGGAAAGC
131 GAACCTGCTATCGTCTCAGCATAAGACTTCACTGGTTGAGCGGTGTCCAGATTCATTTGGAAAGC
47311 GGGATCAGTTGGTGCAACATCTTCCTCCATTGGAGAGGAAGAGATCATAAGATCATTCTGATTCA
196 GGGATCAGTTGGTGCAACATCTTCCTCCATTGGAGAGGAAGAGATCATAAGATCATTCTGATTCA
47376 GGG
261 GGG
*
47379 TTAATCATGCACATGATCAGAAAAATTGACAATTGGATAGGGACCACTACGATTCACAGTAAAGT
1 TTAATCATGCACATGATCAGAAAAATTGACAATTGGATAGGAACCACTACGATTCACAGTAAAGT
*
47444 CGCCTTCCTGAATTTTAACATCATTATCACCAAAAATCGGGATGACAGATTGTGGAAGTCCAGAT
66 CGCCTTCCTGAATTGTAACATCATTATCACCAAAAATCGGGATGACAGATTGTGGAAGTCCAGAT
47509 GAACCTGCTATCGTCTCAGCATAAGACTTCACTGGTTGAGCGGTGTCCAGATTCATTTGGAAAGC
131 GAACCTGCTATCGTCTCAGCATAAGACTTCACTGGTTGAGCGGTGTCCAGATTCATTTGGAAAGC
47574 GGGATCAGTTGGTGCAACATCTTCCTCCATTGGAGAGGAAGAGATCATAAGATCATTCTGATTCA
196 GGGATCAGTTGGTGCAACATCTTCCTCCATTGGAGAGGAAGAGATCATAAGATCATTCTGATTCA
47639 GGG
261 GGG
47642 CTATGACATC
Statistics
Matches: 260, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
263 260 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (263 bp):
TTAATCATGCACATGATCAGAAAAATTGACAATTGGATAGGAACCACTACGATTCACAGTAAAGT
CGCCTTCCTGAATTGTAACATCATTATCACCAAAAATCGGGATGACAGATTGTGGAAGTCCAGAT
GAACCTGCTATCGTCTCAGCATAAGACTTCACTGGTTGAGCGGTGTCCAGATTCATTTGGAAAGC
GGGATCAGTTGGTGCAACATCTTCCTCCATTGGAGAGGAAGAGATCATAAGATCATTCTGATTCA
GGG
Found at i:48265 original size:21 final size:19
Alignment explanation
Indices: 48232--48271 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
48222 TATACGCTAC
48232 CTATAATTTAAACCCTAAA
1 CTATAATTTAAACCCTAAA
48251 CTATAAATCTTAAACCCTAAA
1 CTAT-AAT-TTAAACCCTAAA
48272 TCATAATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 12 0.63
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (19 bp):
CTATAATTTAAACCCTAAA
Found at i:48292 original size:22 final size:20
Alignment explanation
Indices: 48266--48315 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
48256 AATCTTAAAC
*
48266 CCTAAATCATAATACCATAAT
1 CCTAAACCATAA-ACCATAAT
* *
48287 CTCTAACCCATAAACCCTAAT
1 C-CTAAACCATAAACCATAAT
48308 CCTAAACC
1 CCTAAACC
48316 CTATCTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.25
21 9 0.38
22 9 0.38
ACGTcount: A:0.42, C:0.34, G:0.00, T:0.24
Consensus pattern (20 bp):
CCTAAACCATAAACCATAAT
Found at i:48316 original size:21 final size:22
Alignment explanation
Indices: 48273--48312 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
48263 AACCCTAAAT
48273 CATAATACCATAATCTCTAACC
1 CATAATACCATAATCTCTAACC
*
48295 CATAA-ACCCTAATC-CTAA
1 CATAATACCATAATCTCTAA
48313 ACCCTATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (22 bp):
CATAATACCATAATCTCTAACC
Found at i:54503 original size:18 final size:18
Alignment explanation
Indices: 54480--54517 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
54470 CACCCCCATC
54480 AAGTTATTTGATTTGATA
1 AAGTTATTTGATTTGATA
54498 AAGTTATTTGATTTGATA
1 AAGTTATTTGATTTGATA
54516 AA
1 AA
54518 TTGTAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (18 bp):
AAGTTATTTGATTTGATA
Found at i:60251 original size:23 final size:21
Alignment explanation
Indices: 60214--60260 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 21
60204 ACTTCCGAAT
60214 ATTTGAAACCAGAAAGGTTTA
1 ATTTGAAACCAGAAAGGTTTA
60235 ATTTGAATACCCAGAAAGGTTTA
1 ATTTGAA-A-CCAGAAAGGTTTA
60258 ATT
1 ATT
60261 ATGGAGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.29
22 1 0.04
23 16 0.67
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (21 bp):
ATTTGAAACCAGAAAGGTTTA
Found at i:61572 original size:12 final size:12
Alignment explanation
Indices: 61555--61584 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
61545 GATGTTCGGG
61555 TCGGGTCGAGTT
1 TCGGGTCGAGTT
61567 TCGGGTCGAGTT
1 TCGGGTCGAGTT
*
61579 TAGGGT
1 TCGGGT
61585 GAAAAATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.13, G:0.43, T:0.33
Consensus pattern (12 bp):
TCGGGTCGAGTT
Done.