Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004649.1 Hibiscus syriacus cultivar Beakdansim tig00010420_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: 86001
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:4897 original size:3 final size:3
Alignment explanation
Indices: 4889--4938 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
4879 CAAGCACTTC
4889 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
4937 CC
1 CC
4939 AGTGCAGGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:6491 original size:21 final size:22
Alignment explanation
Indices: 6460--6500 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
6450 CTTAGACTTA
6460 AGGGGATGAACTAAAATTCTTG
1 AGGGGATGAACTAAAATTCTTG
6482 AGGGG-TGAACTAAAATTCT
1 AGGGGATGAACTAAAATTCT
6501 AGTGGTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (22 bp):
AGGGGATGAACTAAAATTCTTG
Found at i:10652 original size:19 final size:19
Alignment explanation
Indices: 10616--10655 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
10606 AATCAAAACC
*
10616 AAGAGAAAAGAAGCAAAGA
1 AAGAGAAAAGAAGAAAAGA
10635 AAGAGCAAAA-AAGAAAAGA
1 AAGAG-AAAAGAAGAAAAGA
10654 AA
1 AA
10656 ATAGATGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (19 bp):
AAGAGAAAAGAAGAAAAGA
Found at i:11713 original size:33 final size:33
Alignment explanation
Indices: 11665--11732 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
11655 AGAATCAGCG
* *
11665 TTGAAGCAATTAACATCGAATATTGAGGCATCT
1 TTGAAGAAATCAACATCGAATATTGAGGCATCT
* *
11698 TTGAAGAAATCAACATCGAATGTTGGGGCATCT
1 TTGAAGAAATCAACATCGAATATTGAGGCATCT
11731 TT
1 TT
11733 AGGGATTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (33 bp):
TTGAAGAAATCAACATCGAATATTGAGGCATCT
Found at i:11942 original size:37 final size:37
Alignment explanation
Indices: 11886--11965 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
11876 TCTTTAGTTT
* *
11886 GTTTCCTTTGAAATAAAATTGTGTCTCATTTGAGACA
1 GTTTCCTTCGAAATAAAATTGTGTCTCACTTGAGACA
* *
11923 GTTTCCTTCGAAA-ACAAATTTTGTCTCGCTTGAGACA
1 GTTTCCTTCGAAATA-AAATTGTGTCTCACTTGAGACA
*
11960 TTTTCC
1 GTTTCC
11966 CTTTGAGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (37 bp):
GTTTCCTTCGAAATAAAATTGTGTCTCACTTGAGACA
Found at i:12057 original size:36 final size:37
Alignment explanation
Indices: 12012--12131 Score: 122
Period size: 36 Copynumber: 3.3 Consensus size: 37
12002 ACAAAGTTGA
**
12012 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGATCAATTTCTCTAAAAACAAACTTTG
* *
12048 TCTCGCTTGAGA-CAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGATCAATTTCTCTAAAAACAAACTTTG
* * * * *
12084 TCTCTCTTAAGAT-AATTTCTCTCAAAGCAAA-TTTCA
1 TCTCACTTGAGATCAATTTCTCTAAAAACAAACTTT-G
12120 TCTCACTTGAGA
1 TCTCACTTGAGA
12132 CATTTTTTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
35 10 0.14
36 60 0.86
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (37 bp):
TCTCACTTGAGATCAATTTCTCTAAAAACAAACTTTG
Found at i:12433 original size:26 final size:26
Alignment explanation
Indices: 12387--12453 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
12377 GAGACAATTT
12387 CTTTTGAAATAAATCTTTGAGTATGTTC
1 CTTTTG-AA-AAATCTTTGAGTATGTTC
* *
12415 CTTTTGAAAAATCTTTGAGTTTGTTT
1 CTTTTGAAAAATCTTTGAGTATGTTC
* *
12441 CTCTTAAAAAATC
1 CTTTTGAAAAATC
12454 ATCTTTGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 27 0.77
27 2 0.06
28 6 0.17
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (26 bp):
CTTTTGAAAAATCTTTGAGTATGTTC
Found at i:13385 original size:20 final size:19
Alignment explanation
Indices: 13345--13386 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
13335 CGAAAGAAAG
*
13345 AGAAAATAAAAAACAACAA
1 AGAAAATAAAAAACAAAAA
*
13364 AGAAAATCAAAAAATAAAAA
1 AGAAAAT-AAAAAACAAAAA
13384 AGA
1 AGA
13387 GAGAAGGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (19 bp):
AGAAAATAAAAAACAAAAA
Found at i:14399 original size:29 final size:29
Alignment explanation
Indices: 14335--14407 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
14325 TCTGAGTTTC
*
14335 TGTTTTTGCTATTTTAATCCTTTAAATGTT
1 TGTTTTT-CTATTTTAAGCCTTTAAATGTT
*
14365 TTTTTTTCTATTTT-AGCCTTTTAAAT-TT
1 TGTTTTTCTATTTTAAGCC-TTTAAATGTT
14393 ATGTTTTGT-TATTTT
1 -TGTTTT-TCTATTTT
14408 GGGTCCTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 5 0.14
29 25 0.68
30 7 0.19
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.66
Consensus pattern (29 bp):
TGTTTTTCTATTTTAAGCCTTTAAATGTT
Found at i:17609 original size:25 final size:26
Alignment explanation
Indices: 17556--17617 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
17546 TTTCTTTACA
* *
17556 ATTTACTTTTC-TTATTTTTAATTTT
1 ATTTACTTTACTTTAATTTTAATTTT
17581 -TTTACTTTACTTTAATTTT-ATTTT
1 ATTTACTTTACTTTAATTTTAATTTT
17605 ATTTACTTTACTT
1 ATTTACTTTACTT
17618 GATTATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (26 bp):
ATTTACTTTACTTTAATTTTAATTTT
Found at i:17611 original size:20 final size:19
Alignment explanation
Indices: 17572--17614 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
17562 TTTTCTTATT
17572 TTTAATTTTTTTACTTTAC
1 TTTAATTTTTTTACTTTAC
17591 TTTAATTTTATTTTA-TTTAC
1 TTTAA-TTT-TTTTACTTTAC
17611 TTTA
1 TTTA
17615 CTTGATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.23
20 12 0.55
21 5 0.23
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTAATTTTTTTACTTTAC
Found at i:29937 original size:14 final size:15
Alignment explanation
Indices: 29908--29940 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29898 CTATTTTTAC
*
29908 TATTTACTTTATTTT
1 TATTTACTTCATTTT
29923 TATTTA-TTCATTTT
1 TATTTACTTCATTTT
29937 TATT
1 TATT
29941 GTTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTACTTCATTTT
Found at i:31289 original size:14 final size:13
Alignment explanation
Indices: 31272--31315 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
31262 ATATTTTTAC
31272 TATTTAATTTTTTT
1 TATTT-ATTTTTTT
**
31286 TATTTATTCATTT
1 TATTTATTTTTTT
31299 TATTGTATTTTTTT
1 TATT-TATTTTTTT
31313 TAT
1 TAT
31316 AAATTTAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (13 bp):
TATTTATTTTTTT
Found at i:35616 original size:18 final size:18
Alignment explanation
Indices: 35573--35622 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
35563 AACGAAGAAA
*
35573 AAGGCAAAACCCTAAGCG
1 AAGGCAAAACCCTAAACG
*
35591 -AGGACAAAGCCCTAAACG
1 AAGG-CAAAACCCTAAACG
35609 AAGGCAAAACCCTA
1 AAGGCAAAACCCTA
35623 CTACAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.46, C:0.28, G:0.20, T:0.06
Consensus pattern (18 bp):
AAGGCAAAACCCTAAACG
Found at i:41738 original size:18 final size:19
Alignment explanation
Indices: 41715--41750 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41705 GCGGGCGGTG
41715 GTGTCTAGATCTA-GTTAA
1 GTGTCTAGATCTATGTTAA
*
41733 GTGTCTAGGTCTATGTTA
1 GTGTCTAGATCTATGTTA
41751 CATAAAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (19 bp):
GTGTCTAGATCTATGTTAA
Found at i:42799 original size:3 final size:3
Alignment explanation
Indices: 42791--42815 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42781 AAATAGGATT
42791 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
42816 AAGTTGGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:43058 original size:20 final size:19
Alignment explanation
Indices: 43023--43062 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
43013 ATATTTTTTA
* *
43023 ATTTTTAATAATAAAATATT
1 ATTTTTAAAAAGAAAA-ATT
43043 ATTTTTAAAAAGAAAAATT
1 ATTTTTAAAAAGAAAAATT
43062 A
1 A
43063 AAAAGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTTTTAAAAAGAAAAATT
Found at i:43065 original size:13 final size:13
Alignment explanation
Indices: 43047--43071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43037 AATATTATTT
43047 TTAAAAAGAAAAA
1 TTAAAAAGAAAAA
43060 TTAAAAAGAAAA
1 TTAAAAAGAAAA
43072 TCAACCTTGC
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
TTAAAAAGAAAAA
Found at i:43800 original size:20 final size:20
Alignment explanation
Indices: 43772--43809 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43762 ATGCATACCA
43772 TAAAGTTATTTATTTATATT
1 TAAAGTTATTTATTTATATT
* *
43792 TAAATTTATTTTTTTATA
1 TAAAGTTATTTATTTATA
43810 ATTATAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TAAAGTTATTTATTTATATT
Found at i:46018 original size:6 final size:6
Alignment explanation
Indices: 46007--46067 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
45997 GACACGTATT
* * *
46007 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
46055 ACCACG ACCACG A
1 ACCACG ACCACG A
46068 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:46075 original size:5 final size:5
Alignment explanation
Indices: 46065--46113 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
46055 ACCACGACCA
* * * *
46065 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
46114 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:51860 original size:6 final size:6
Alignment explanation
Indices: 51849--51909 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
51839 GACACGTATT
* * *
51849 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
51897 ACCACG AACACG A
1 ACCACG ACCACG A
51910 GCCGAGCCGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.31, C:0.48, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:51917 original size:5 final size:5
Alignment explanation
Indices: 51907--51955 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
51897 ACCACGAACA
* * * *
51907 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
51956 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:55937 original size:116 final size:115
Alignment explanation
Indices: 55741--56030 Score: 343
Period size: 116 Copynumber: 2.5 Consensus size: 115
55731 CTCTTTATAC
* * * * * * *
55741 GAGTTTTTATCATTATGAACTATTCCAATAGAAATGATGATCCAACTCCTTATGTGATGGACGAA
1 GAGTTATTCTCATTATGAACCATTCCACTAAAAATGCTGATCCAACTCCTTATGTGATGAACGAA
* * * *
55806 CCACGTTCAAACAAGTTCTTC-CGATTAGGAACTTCTTCTCCCTCATTGGAT
66 CCAAGGTCAAACAAGTTCTTCTC-ATTAGGAACTT-TCCCCCCTCATTGGAT
* *
55857 TAGTTATTCTCATTATGAACCATTCCACTAAAAATGCTGATCCAACTCTTTATGTGATGAAAC-A
1 GAGTTATTCTCATTATGAACCATTCCACTAAAAATGCTGATCCAACTCCTTATGTGATG-AACGA
* *
55921 GCCAAGGTCAATCAAGTTCTTCTCATTAGGAACTTTCCCCCCTCATTGGAT
65 ACCAAGGTCAAACAAGTTCTTCTCATTAGGAACTTTCCCCCCTCATTGGAT
* * ** *
55972 GAGTTCTTCTCATTATGAACCCTTCCACTGTAAATGAC-GATCTAACTCCTTATGTGATG
1 GAGTTATTCTCATTATGAACCATTCCACTAAAAATG-CTGATCCAACTCCTTATGTGATG
56031 GAATTAAGCG
Statistics
Matches: 149, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
115 64 0.43
116 82 0.55
117 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (115 bp):
GAGTTATTCTCATTATGAACCATTCCACTAAAAATGCTGATCCAACTCCTTATGTGATGAACGAA
CCAAGGTCAAACAAGTTCTTCTCATTAGGAACTTTCCCCCCTCATTGGAT
Found at i:56422 original size:17 final size:18
Alignment explanation
Indices: 56400--56441 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
56390 TGCTTCATTC
56400 TCTTTG-ATGAGTCTTTA
1 TCTTTGCATGAGTCTTTA
*
56417 TCTTTGCTTGAGTCTTTA
1 TCTTTGCATGAGTCTTTA
56435 TCTTTGC
1 TCTTTGC
56442 CTGGATCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.55
Consensus pattern (18 bp):
TCTTTGCATGAGTCTTTA
Found at i:56430 original size:18 final size:18
Alignment explanation
Indices: 56407--56441 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
56397 TTCTCTTTGA
56407 TGAGTCTTTATCTTTGCT
1 TGAGTCTTTATCTTTGCT
56425 TGAGTCTTTATCTTTGC
1 TGAGTCTTTATCTTTGC
56442 CTGGATCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.54
Consensus pattern (18 bp):
TGAGTCTTTATCTTTGCT
Found at i:56450 original size:18 final size:18
Alignment explanation
Indices: 56408--56455 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
56398 TCTCTTTGAT
*
56408 GAGTCTTTATCTTTGCTT
1 GAGTCTTTATCTTTGCTG
56426 GAGTCTTTATCTTTGCCTG
1 GAGTCTTTATCTTTG-CTG
*
56445 GA-TCTTCATCT
1 GAGTCTTTATCT
56456 CATGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.12, C:0.21, G:0.17, T:0.50
Consensus pattern (18 bp):
GAGTCTTTATCTTTGCTG
Found at i:57331 original size:114 final size:114
Alignment explanation
Indices: 57122--57331 Score: 280
Period size: 114 Copynumber: 1.8 Consensus size: 114
57112 TCAATTTAAT
* * * *
57122 TTGCCTTTGTTTGGCTAGCTGAAGGAAATTATCCATAAAGTTAGGGCTTTCAACCAATTACTTTA
1 TTGCCTTTATTTGGCTAGCTGAAGGAAATTATCCATAAAGTCAGAGCTTTCAACCAATTAATTTA
* * * * *
57187 GCGGAATTGCTCAGCTTTGTTATATGTATATGCATATATGTATATATTA
66 GAGAAATAGCTCAGCTTTATTATATATATATGCATATATGTATATATTA
* *
57236 TTGCCTTTATTTGGCTAGTTG-AGGGAATCTATCCATAAA-TCCAGAGCTTTCAACCAATTAATT
1 TTGCCTTTATTTGGCTAGCTGAAGGAAAT-TATCCATAAAGT-CAGAGCTTTCAACCAATTAATT
*
57299 TAGAGAAATAGCTCAGCTTTATTGTATATATAT
64 TAGAGAAATAGCTCAGCTTTATTATATATATAT
57332 AATTATATTA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
113 7 0.09
114 75 0.91
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (114 bp):
TTGCCTTTATTTGGCTAGCTGAAGGAAATTATCCATAAAGTCAGAGCTTTCAACCAATTAATTTA
GAGAAATAGCTCAGCTTTATTATATATATATGCATATATGTATATATTA
Found at i:61908 original size:15 final size:15
Alignment explanation
Indices: 61804--61915 Score: 58
Period size: 14 Copynumber: 7.7 Consensus size: 15
61794 AAATAAAGTT
*
61804 TAAATGTAAATAACA
1 TAAATATAAATAACA
61819 -AAA-ATGAAATAACA
1 TAAATAT-AAATAACA
*
61833 TAAATA-AAATAAGA
1 TAAATATAAATAACA
**
61847 TAAA-ATAAAGGGA-A
1 TAAATATAAA-TAACA
*
61861 -AAATGTAAATAACA
1 TAAATATAAATAACA
* * * *
61875 GAAAAATAAA-ATGCG
1 TAAATATAAATA-ACA
61890 TAAATATAAATAACA
1 TAAATATAAATAACA
*
61905 TAAATGTAAAT
1 TAAATATAAAT
61916 TGAATAAAGA
Statistics
Matches: 71, Mismatches: 16, Indels: 20
0.66 0.15 0.19
Matches are distributed among these distances:
13 6 0.08
14 32 0.45
15 31 0.44
16 2 0.03
ACGTcount: A:0.64, C:0.04, G:0.10, T:0.21
Consensus pattern (15 bp):
TAAATATAAATAACA
Found at i:62345 original size:116 final size:114
Alignment explanation
Indices: 61938--62337 Score: 451
Period size: 116 Copynumber: 3.4 Consensus size: 114
61928 AAAAGCTACA
* * *
61938 AGTTCTTCTCATTATGAACACTTCCATTGAAAGTGCTT-ATCCAACTCCTTATGTGATGGATGAG
1 AGTTCTTCTCATTATGAACCCTTCAATGGAAA-TG-TTGATCCAACTCCTTATGTGATGGATGAG
* * * * * ** * *
62002 CTAAGGTTGAACAAGCTCTTCTCATTAAGATCTTCTTCTCATTCTTTAGACG
64 CCAAGGTCGAACAAGTTCTTCTCATT-AGAACTTATTCTCCCTCATTAGATG
* * * * * ** * *
62054 AGTTCTTCTTATTATGAACCCTTCCATTAGAAATGTTGATTCTACTCCTTATGTGATTCAAGATC
1 AGTTCTTCTCATTATGAACCCTT-CAATGGAAATGTTGATCCAACTCCTTATGTGATGGATGAGC
* * * * *
62119 CAAGGTCAAACAAGTTCTCCTTATTAGTAACTTATTCTTCCTCATTGGATG
65 CAAGGTCGAACAAGTTCTTCTCATTAG-AACTTATTCTCCCTCATTAGATG
*
62170 AGTTCTTCTCATTATGAACCCTTCAACTGGAAATGTTGATCCAACTCCTTGTGTGATGGATGAGC
1 AGTTCTTCTCATTATGAACCCTTCAA-TGGAAATGTTGATCCAACTCCTTATGTGATGGATGAGC
*
62235 CAAGGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATTAGATG
65 CAAGGTCGAACAAGTTCTTCTCATTA-GAACTTATTCTCCCTCATTAGATG
* *
62286 AGTTCTTCTCATTATGAACCCTTGCAATGGAAATGTAGATCTAACTCCTTAT
1 AGTTCTTCTCATTATGAACCCTT-CAATGGAAATGTTGATCCAACTCCTTAT
62338 ATAATGGAAT
Statistics
Matches: 234, Mismatches: 44, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
115 6 0.03
116 218 0.93
117 10 0.04
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (114 bp):
AGTTCTTCTCATTATGAACCCTTCAATGGAAATGTTGATCCAACTCCTTATGTGATGGATGAGCC
AAGGTCGAACAAGTTCTTCTCATTAGAACTTATTCTCCCTCATTAGATG
Found at i:63475 original size:6 final size:6
Alignment explanation
Indices: 63261--63473 Score: 327
Period size: 6 Copynumber: 35.5 Consensus size: 6
63251 ATATATGTAT
* * * * * * * *
63261 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC
*
63309 ATGTGT ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC
1 ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC
63357 ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC
1 ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC
63405 ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC
1 ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC
* *
63453 ATGCGC ATGTGC ATGCGC ATG
1 ATGTGC ATGTGC ATGTGC ATG
63474 CGTATACGTA
Statistics
Matches: 203, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 203 1.00
ACGTcount: A:0.17, C:0.13, G:0.33, T:0.37
Consensus pattern (6 bp):
ATGTGC
Found at i:63498 original size:18 final size:18
Alignment explanation
Indices: 63474--63559 Score: 90
Period size: 18 Copynumber: 5.0 Consensus size: 18
63464 CATGCGCATG
*
63474 CGTATACGTATACGTATA
1 CGTATACGTATATGTATA
*
63492 TGTATACGTATATGTATA
1 CGTATACGTATATGTATA
*
63510 CATATACGTATA--TAT-
1 CGTATACGTATATGTATA
63525 -GTATACGTATATGTATA
1 CGTATACGTATATGTATA
** *
63542 AATATATGTATATGTATA
1 CGTATACGTATATGTATA
63560 TTAACTTCCA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
14 10 0.18
16 6 0.11
18 41 0.72
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (18 bp):
CGTATACGTATATGTATA
Found at i:63525 original size:20 final size:20
Alignment explanation
Indices: 63500--63541 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
63490 TATGTATACG
63500 TATATGTATACATATACGTA
1 TATATGTATACATATACGTA
* *
63520 TATATGTATACGTATATGTA
1 TATATGTATACATATACGTA
63540 TA
1 TA
63542 AATATATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (20 bp):
TATATGTATACATATACGTA
Found at i:63553 original size:6 final size:6
Alignment explanation
Indices: 63475--63560 Score: 73
Period size: 6 Copynumber: 14.0 Consensus size: 6
63465 ATGCGCATGC
* * * * * *
63475 GTATAC GTATAC GTATAT GTATAC GTATAT GTATAC ATATACGT ATATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATA--T GTATAT
* * *
63525 GTATAC GTATAT GTATAA ATATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
63561 TAACTTCCAG
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
6 60 0.92
8 5 0.08
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (6 bp):
GTATAT
Found at i:63885 original size:19 final size:18
Alignment explanation
Indices: 63861--63908 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
63851 GTTAAAATGC
*
63861 AATAAAATAAAATACAGTA
1 AATAAAATAAAATA-AATA
*
63880 AATAAATTCAAAATAAATA
1 AATAAAAT-AAAATAAATA
63899 AAT-AAATAAA
1 AATAAAATAAA
63909 CAAAAAAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 3 0.12
18 3 0.12
19 13 0.52
20 6 0.24
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (18 bp):
AATAAAATAAAATAAATA
Found at i:69406 original size:13 final size:13
Alignment explanation
Indices: 69388--69417 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
69378 TCTTAAGAGC
69388 AAATAAAATAAAA
1 AAATAAAATAAAA
*
69401 AAATAATATAAAA
1 AAATAAAATAAAA
69414 AAAT
1 AAAT
69418 CGATTCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:70520 original size:10 final size:11
Alignment explanation
Indices: 70492--70520 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
70482 AATCATGTAT
70492 TTATTTTTATA
1 TTATTTTTATA
70503 TTATTTTTATA
1 TTATTTTTATA
70514 TTATTTT
1 TTATTTT
70521 CAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:73118 original size:31 final size:31
Alignment explanation
Indices: 73080--73142 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
73070 AAACTGATGA
**
73080 TTTTTTTTACTATTTAAATGCTTTAAACACT
1 TTTTTTTTACTATGAAAATGCTTTAAACACT
** *
73111 TTTTTTTTTGTGTGAAAATGCTTTAAACACT
1 TTTTTTTTACTATGAAAATGCTTTAAACACT
73142 T
1 T
73143 AATTTTGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (31 bp):
TTTTTTTTACTATGAAAATGCTTTAAACACT
Found at i:78086 original size:18 final size:18
Alignment explanation
Indices: 78063--78100 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
78053 AGGCCAAGTA
78063 ACATGATCAGAGGAATTT
1 ACATGATCAGAGGAATTT
78081 ACATGATCAGAGGAATTT
1 ACATGATCAGAGGAATTT
78099 AC
1 AC
78101 GTGCATCGGA
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:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (18 bp):
ACATGATCAGAGGAATTT
Found at i:79265 original size:21 final size:21
Alignment explanation
Indices: 79203--79265 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
79193 ATGTAAGATT
* *
79203 TGTCCCGAAGGATCTCATGTA
1 TGTCCCGAAGGACCTCATATA
* *
79224 TATCCCAAAGGACCT-AGTATA
1 TGTCCCGAAGGACCTCA-TATA
*
79245 TGTCCTGAAGGACCTCATATA
1 TGTCCCGAAGGACCTCATATA
79266 ATAACTCGAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (21 bp):
TGTCCCGAAGGACCTCATATA
Found at i:85735 original size:21 final size:21
Alignment explanation
Indices: 85709--85765 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
85699 GATTTGTCCC
*
85709 GAAGGACCTCATGTATGCCCT
1 GAAGGACCTCATATATGCCCT
* *
85730 GAAGGACCTCGTATATGTCCT
1 GAAGGACCTCATATATGCCCT
*
85751 GAAGAACCTCATATA
1 GAAGGACCTCATATA
85766 ATCCCTCGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (21 bp):
GAAGGACCTCATATATGCCCT
Done.