Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002833.1 Hibiscus syriacus cultivar Beakdansim tig00005828_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: 66737
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:987 original size:192 final size:194
Alignment explanation
Indices: 522--1022 Score: 721
Period size: 196 Copynumber: 2.6 Consensus size: 194
512 TATTTAAATT
* *
522 AGTATCGACACAATATTAAAAAATTGTCGATACATG-TGTAGACCTATTCTCTCATAAAACCAGT
1 AGTATCGACACAAAATTAAAAAATTGTCGATACATGTTGTAGACCTA-T-TCTCAT-AAACTAGT
** *
586 ATATTTATACTTGTTACATTGAAAATTTACTTATTACATTATAA-TATGGGTTTCGATGTTTTTG
63 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
*
650 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTGGCATCCATTCTGGA
128 GGATCGACACTTTTTGAAAATGTATCGACACTTTA---GTTAACCCTTTTGGCATCCATTCTGGA
715 CCAAA
190 CCAAA
** * * *
720 AGTA-CGACACAAAATTAAAAACGTATCGATACATGTTGTTAGACCT-TTCTCATAAAATCGGTA
1 AGTATCGACACAAAATTAAAAAATTGTCGATACATGTTG-TAGACCTATTCTCATAAACT-AGTA
* *
783 TATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTTT-G
64 TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
* *
847 GATCTACAC-TTTTGAAAATGTATCGACACTTTA-TTAACCCTTTTTGGCGTCCATTCTGGACCA
129 GATCGACACTTTTTGAAAATGTATCGACACTTTAGTTAACCC-TTTTGGCATCCATTCTGGACCA
910 AA
193 AA
912 AGTATCGACACAAAATTAAAAAATTGTCGATACATGTTGTAGACCTATTCTCATAAACTAGTATA
1 AGTATCGACACAAAATTAAAAAATTGTCGATACATGTTGTAGACCTATTCTCATAAACTAGTATA
*
977 TTTATACCGG-TACATTGAAAATTTACCTATTACATTATACTTATGG
66 TTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGG
1023 ATGCATATGT
Statistics
Matches: 274, Mismatches: 22, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
191 40 0.15
192 49 0.18
193 42 0.15
195 27 0.10
196 57 0.21
197 46 0.17
198 6 0.02
199 7 0.03
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (194 bp):
AGTATCGACACAAAATTAAAAAATTGTCGATACATGTTGTAGACCTATTCTCATAAACTAGTATA
TTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGA
TCGACACTTTTTGAAAATGTATCGACACTTTAGTTAACCCTTTTGGCATCCATTCTGGACCAAA
Found at i:5981 original size:31 final size:30
Alignment explanation
Indices: 5932--5991 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
5922 TTATATAAGC
*
5932 TATGTGATACAATGATGGAACATGATATGTT
1 TATGTGATACAAGGATGGAA-ATGATATGTT
*
5963 TATGTGATA-AAGGTATGGAAATTATATGT
1 TATGTGATACAAGG-ATGGAAATGATATGT
5992 CTATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TATGTGATACAAGGATGGAAATGATATGTT
Found at i:6256 original size:21 final size:21
Alignment explanation
Indices: 6208--6256 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
6198 AGGGACAAGC
*
6208 TTATATGGCACTACAGTGCAA
1 TTATACGGCACTACAGTGCAA
* * * *
6229 TTCTACGGCACTTCGGTGCAT
1 TTATACGGCACTACAGTGCAA
6250 TTATACG
1 TTATACG
6257 AACTGTGGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (21 bp):
TTATACGGCACTACAGTGCAA
Found at i:12436 original size:64 final size:63
Alignment explanation
Indices: 12361--12480 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 63
12351 ATTGTTCAAG
* * * **
12361 GTGTATCGATGCACATGAAGTGCATCGATTCACTCTTTTAAATTACAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAA-TACAAACATCGAATGCCATCA
* * *
12425 GTGTATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAATATAAACATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATACAAACATCGAAT
12481 AGGATTTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 13 0.27
64 35 0.73
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATGCCATCA
Found at i:12815 original size:25 final size:25
Alignment explanation
Indices: 12760--12821 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
12750 ATAAGTCTAG
*
12760 ATTCAATATTTTGATACATGATCGCA
1 ATTC-ATATTATGATACATGATCGCA
* *
12786 TTTCATATTATGATACATGA-CGTGA
1 ATTCATATTATGATACATGATCG-CA
12811 ATTCATATTAT
1 ATTCATATTAT
12822 ATGCATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 26 0.84
26 3 0.10
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCGCA
Found at i:12913 original size:31 final size:30
Alignment explanation
Indices: 12864--12923 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
12854 TTATATAAGC
*
12864 TATGTGATACAATGATGGAACATGATATGTT
1 TATGTGATACAAGGATGGAA-ATGATATGTT
*
12895 TATGTGATA-AAGGTATGGAAATTATATGT
1 TATGTGATACAAGG-ATGGAAATGATATGT
12924 CTATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TATGTGATACAAGGATGGAAATGATATGTT
Found at i:13173 original size:23 final size:23
Alignment explanation
Indices: 13147--13216 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
13137 AAGCTTATAT
* *
13147 GGCACTACGGTGCAATTCTATGA
1 GGCACTTCGGTGCAATTCTACGA
* *
13170 GGCACTTTGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGA
* *
13193 GGCACTTCGGTGCATTTATACGA
1 GGCACTTCGGTGCAATTCTACGA
13216 G
1 G
13217 CTGTGGTGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGA
Found at i:13424 original size:13 final size:13
Alignment explanation
Indices: 13390--13417 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13380 ATTTCGTCTC
13390 ATTCCATTTAATT
1 ATTCCATTTAATT
13403 ATTCCATTTAATT
1 ATTCCATTTAATT
13416 AT
1 AT
13418 GTCATTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTCCATTTAATT
Found at i:14665 original size:20 final size:19
Alignment explanation
Indices: 14611--14656 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
14601 CCGGTAGCGC
14611 TTTACCGGTTTTATCATTT
1 TTTACCGGTTTTATCATTT
*
14630 TGATACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCAT-TT
14651 TTTACC
1 TTTACC
14657 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:15515 original size:20 final size:20
Alignment explanation
Indices: 15492--15579 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
15482 AACTCCAATT
*
15492 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
** * ** *
15512 TCGCATTGCGATTTTCCAATT
1 TCGCAACGCGAATTTGTAA-A
* *
15533 TTGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATTTGTAAA
*
15553 TCGCAACGCAAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
15573 TCGCAAC
1 TCGCAAC
15580 ACAGAAGTCA
Statistics
Matches: 49, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 37 0.76
21 12 0.24
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:15596 original size:20 final size:20
Alignment explanation
Indices: 15573--15641 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
15563 AATTTGTAAA
15573 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
15593 TCGCAAC-GTGATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
15613 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
15633 TCGCAACAC
1 TCGCAACAC
15642 GAATTTAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 39 0.93
21 1 0.02
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:16561 original size:24 final size:24
Alignment explanation
Indices: 16534--16587 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
16524 GTATTCGAAA
16534 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
16558 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
16582 TTTGAT
1 TTTGAT
16588 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:16780 original size:12 final size:12
Alignment explanation
Indices: 16762--16794 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
16752 ATATAACCTT
16762 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
16774 TAAGAAGAAAAA
1 GAAGAAGAAAAA
16786 GAAGAAGAA
1 GAAGAAGAA
16795 GAAGTCCCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:18881 original size:18 final size:18
Alignment explanation
Indices: 18855--18890 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18845 AAGCAAAAGG
*
18855 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
*
18873 AAATTAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
18891 CAAACGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:19659 original size:39 final size:39
Alignment explanation
Indices: 19616--19702 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
19606 TCCGATGCTC
*
19616 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
19655 ATCAAAATCAAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
19694 ATCAAAATC
1 ATCAAAATC
19703 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:19956 original size:20 final size:20
Alignment explanation
Indices: 19876--19959 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
19866 ATGTTGTGAT
19876 CAATGCGAAAGTCAAATTCG
1 CAATGCGAAAGTCAAATTCG
*
19896 CAACGCGAAAGTCAAATTCG
1 CAATGCGAAAGTCAAATTCG
19916 CAATGCGAAA-T--AA---G
1 CAATGCGAAAGTCAAATTCG
* *
19930 CATTGCGATAGTCAAATTCG
1 CAATGCGAAAGTCAAATTCG
19950 CAATGCGAAA
1 CAATGCGAAA
19960 TCGCAAACCG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
17 4 0.08
19 1 0.02
20 37 0.71
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.19
Consensus pattern (20 bp):
CAATGCGAAAGTCAAATTCG
Found at i:20098 original size:25 final size:25
Alignment explanation
Indices: 20063--20117 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
20053 TCAATTAAAT
*
20063 ATTGTTGTGGGTACATTATTTGAAC
1 ATTGTTATGGGTACATTATTTGAAC
20088 ATTGTTATGGGTACATTATTTGAAC
1 ATTGTTATGGGTACATTATTTGAAC
20113 ATTGT
1 ATTGT
20118 ATGTATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.45
Consensus pattern (25 bp):
ATTGTTATGGGTACATTATTTGAAC
Found at i:20404 original size:39 final size:39
Alignment explanation
Indices: 20361--20447 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
20351 TCCGATGCTC
*
20361 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
20400 ATCAAAATCAAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
20439 ATCAAAATC
1 ATCAAAATC
20448 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:22286 original size:21 final size:21
Alignment explanation
Indices: 22245--22342 Score: 63
Period size: 21 Copynumber: 4.7 Consensus size: 21
22235 GCGGGCGGGA
* *
22245 CCTCTTGAACGATGACG-GGGG
1 CCTCTTAAACGATG-GGAGGGG
*
22266 CCTCTTAAACGGTGGGAGGGG
1 CCTCTTAAACGATGGGAGGGG
* ** * * *
22287 CTTCTTCGATGATGAGAGAGG
1 CCTCTTAAACGATGGGAGGGG
* * *
22308 CCTCTTGAACGATAGGAGGCG
1 CCTCTTAAACGATGGGAGGGG
*
22329 CCTCTTAAATGATG
1 CCTCTTAAACGATG
22343 ATAGGTGCAT
Statistics
Matches: 55, Mismatches: 21, Indels: 2
0.71 0.27 0.03
Matches are distributed among these distances:
20 1 0.02
21 54 0.98
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.23
Consensus pattern (21 bp):
CCTCTTAAACGATGGGAGGGG
Found at i:24800 original size:22 final size:22
Alignment explanation
Indices: 24772--24819 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
24762 GGAGATAGAT
24772 GGATTTCGTCGGAAATGGGGAC
1 GGATTTCGTCGGAAATGGGGAC
*
24794 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGTCGGAAATGGGGAC
24816 GGAT
1 GGAT
24820 ATCGCCGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.44, T:0.23
Consensus pattern (22 bp):
GGATTTCGTCGGAAATGGGGAC
Found at i:24972 original size:20 final size:20
Alignment explanation
Indices: 24947--24995 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
24937 GCGTAAAAAC
*
24947 ATTTGACTTTCGCTTTGCAA
1 ATTTGACTTTCGCGTTGCAA
* *
24967 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCAA
24987 ATTTGACTT
1 ATTTGACTT
24996 CTGTGTTGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCAA
Found at i:25063 original size:20 final size:20
Alignment explanation
Indices: 25014--25087 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
25004 TGATTTACAT
*
25014 ATTCGCGTTGCGATATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
25034 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
25054 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
*
25074 ATTCGTGTTGCGAA
1 ATTCGCGTTGCGAA
25088 TTTGTTGGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:29108 original size:20 final size:22
Alignment explanation
Indices: 29083--29128 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
29073 GAGTTTTGTG
29083 AAAATATTTTTT-AAAT-TTTA
1 AAAATATTTTTTGAAATATTTA
*
29103 AAAATATTTTTTGATATATTTA
1 AAAATATTTTTTGAAATATTTA
29125 AAAA
1 AAAA
29129 AAATAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.52
21 3 0.13
22 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAATATTTTTTGAAATATTTA
Found at i:31094 original size:23 final size:21
Alignment explanation
Indices: 31059--31106 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 21
31049 AATAAAGATA
31059 AGAAAGTAAAGAAGATTAAAG
1 AGAAAGTAAAGAAGATTAAAG
*
31080 AGAACAGTAAAAGAAGATTAAGG
1 AGAA-AGT-AAAGAAGATTAAAG
31103 AGAA
1 AGAA
31107 GATTTAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.17
22 3 0.12
23 17 0.71
ACGTcount: A:0.60, C:0.02, G:0.25, T:0.12
Consensus pattern (21 bp):
AGAAAGTAAAGAAGATTAAAG
Found at i:31118 original size:12 final size:11
Alignment explanation
Indices: 31066--31118 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
31056 ATAAGAAAGT
31066 AAAGAAGATTA
1 AAAGAAGATTA
* *
31077 AAGAGAACAGTA
1 AA-AGAAGATTA
31089 AAAGAAGATTA
1 AAAGAAGATTA
*
31100 AGGAGAAGATTTA
1 A-AAGAAGA-TTA
31113 AAAGAA
1 AAAGAA
31119 AAAAAATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
11 10 0.30
12 19 0.58
13 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.23, T:0.15
Consensus pattern (11 bp):
AAAGAAGATTA
Found at i:32363 original size:36 final size:36
Alignment explanation
Indices: 32303--32515 Score: 268
Period size: 36 Copynumber: 5.9 Consensus size: 36
32293 AGATGAACAA
* *
32303 TTGAGTCGAAAGTGCTGATGCTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
*
32339 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* *
32375 TTGAATCGAAAGTGCCGATACTTCCTTCCTTTCA-T
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* * * *
32410 TATGAATCGAAAGTGGCGACGCTTCCTTTCATTCTAC-
1 T-TGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-ACT
* *
32447 TTGAATCAAAAGTGCCGATGCTTCATTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
** *
32483 TTGAATCGAAAGTGTTGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
32516 TTCTTATTCA
Statistics
Matches: 153, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
35 4 0.03
36 147 0.96
37 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
Found at i:33989 original size:36 final size:36
Alignment explanation
Indices: 33929--34141 Score: 275
Period size: 36 Copynumber: 5.9 Consensus size: 36
33919 AGATGAACAA
* **
33929 TTGAGTCGAAAGTGCTAATGCTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
*
33965 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
*
34001 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* * * * * *
34037 ATGAATCGAAAGTGGCGACGCTTTCTTTCGTTC-TT
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* *
34072 CTTGAATCGAAAGTGTCGATGCTTCCTTCCATTCACT
1 -TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* *
34109 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
34142 TTCTTATTCA
Statistics
Matches: 153, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
35 1 0.01
36 151 0.99
37 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
Found at i:35631 original size:36 final size:36
Alignment explanation
Indices: 35560--35772 Score: 230
Period size: 36 Copynumber: 5.9 Consensus size: 36
35550 AGATGAACAA
* * * *
35560 TTGAGTCGAAATTGCTGATGCTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
* * * *
35596 TTGAATTGAATGTGTCGATACTTTCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
*
35632 TTGAATCGAAAGTGCCGATACTTTCTTCCGTTCACT
1 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
* ** * * *
35668 ATGAATCGAAAGTGGTGACACTTCCTTTCGTTC-TT
1 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
* *
35703 CTTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACT
1 -TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
* * *
35740 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCGATACTTCCTTCCGTTC
35773 TTCTTATTCA
Statistics
Matches: 150, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
35 1 0.01
36 148 0.99
37 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATACTTCCTTCCGTTCACT
Found at i:35700 original size:72 final size:72
Alignment explanation
Indices: 35560--35777 Score: 260
Period size: 72 Copynumber: 3.0 Consensus size: 72
35550 AGATGAACAA
* * * * * * *
35560 TTGAGTCGAAATTGCTGATGCTTCCTTCCGTTCACTTTGAATTGAATGT-GTCGATACTTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGGT-GATACTTCCTTT
35624 CGTTCACT-
65 CGTTC-CTC
* * * *
35632 TTGAATCGAAAGTGCCGATACTTTCTTCCGTTCACTATGAATCGAAAGTGGTGACACTTCCTTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGGTGATACTTCCTTTC
*
35697 GTTCTTC
66 GTTCCTC
* * *
35704 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGGTGATACTTCCTTTC
*
35769 GTTCTTC
66 GTTCCTC
35776 TT
1 TT
35778 ATTCAACTTC
Statistics
Matches: 125, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
71 1 0.01
72 122 0.98
73 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.39
Consensus pattern (72 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGGTGATACTTCCTTTC
GTTCCTC
Found at i:39680 original size:18 final size:17
Alignment explanation
Indices: 39626--39674 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
39616 TTGGACCCTT
* *
39626 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
39644 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
39662 AGTGCATTCGATG
1 AGTGCA-TCGATG
39675 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:39714 original size:64 final size:63
Alignment explanation
Indices: 39646--39855 Score: 219
Period size: 65 Copynumber: 3.3 Consensus size: 63
39636 TGCACTAAGA
* *
39646 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
* ** *
39710 GTGCATCGATGCATCAAATGCATTCGATATTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGAT-GTTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
39774 T
63 G
* ** * *
39775 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GCGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG--
39838 TG
62 TG
39840 GTGCATCGATGCATCA
1 GTGCATCGATGCATCA
39856 CTCTGAAAAA
Statistics
Matches: 120, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 45 0.38
65 66 0.55
66 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:40314 original size:2 final size:2
Alignment explanation
Indices: 40307--40340 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40297 GCCAATTGAT
40307 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
40341 GCTTAAGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48341 original size:64 final size:64
Alignment explanation
Indices: 48272--48430 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 64
48262 GGACCCTTAA
* *
48272 TGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAATGCATCGATGCATGGT-TG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-AGCCACAATGCATCGATGCATGGTAT-
48335 G
64 G
* * * *
48336 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTATG
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAGCCACAATGCATCGATGCATGGTATG
* *
48401 TACATCGATGCATGAAATGCATTCGATGTT
1 TGCATCGATGCATCAAATGCATTCGATGTT
48431 CAATTTAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
64 29 0.35
65 51 0.61
66 4 0.05
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAGCCACAATGCATCGATGCATGGTATG
Found at i:49718 original size:21 final size:22
Alignment explanation
Indices: 49688--49730 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
49678 AAGTTGATAT
49688 AGTGAATTTTC-GGGCATGAAC
1 AGTGAATTTTCTGGGCATGAAC
* *
49709 AGTGATTTTTCTGGGCTTGAAC
1 AGTGAATTTTCTGGGCATGAAC
49731 GAAATTCCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (22 bp):
AGTGAATTTTCTGGGCATGAAC
Found at i:51556 original size:2 final size:2
Alignment explanation
Indices: 51549--51594 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
51539 GTTTTAAACG
51549 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
51591 TA TA
1 TA TA
51595 CATAGATGAA
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:58224 original size:17 final size:17
Alignment explanation
Indices: 58183--58225 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
58173 TTTCCACCTC
58183 ATTCTTT-TTCTTATTT
1 ATTCTTTCTTCTTATTT
*
58199 A-TCTCTTCTTCTTCTTT
1 ATTCT-TTCTTCTTATTT
58216 ATTCTTTCTT
1 ATTCTTTCTT
58226 TGGAGCTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 3 0.13
16 3 0.13
17 14 0.61
18 3 0.13
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTCTTTCTTCTTATTT
Found at i:63635 original size:21 final size:21
Alignment explanation
Indices: 63609--63648 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
63599 CAGAACCCCA
*
63609 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
63630 GGGGGGAATCGATTCCCCT
1 GGGGGGAATCGATTCCCCT
63649 TCAAAGGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:63689 original size:20 final size:22
Alignment explanation
Indices: 63608--63691 Score: 59
Period size: 21 Copynumber: 3.9 Consensus size: 22
63598 CCAGAACCCC
* **
63608 AGGGGGGTATCGATTCCC-CTG
1 AGGGGGGAATCGATTCCCTCAA
*
63629 TGGGGGGAATCGATTCCCCTTCAA
1 AGGGGGGAATCGATT-CCC-TCAA
* **
63653 A-GGAGGAATCGGCTCCCTC-A
1 AGGGGGGAATCGATTCCCTCAA
63673 AGGGGGG-ATCGATTCCCTC
1 AGGGGGGAATCGATTCCCTC
63692 TGCACCAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
20 12 0.25
21 19 0.40
22 6 0.12
23 10 0.21
24 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.21
Consensus pattern (22 bp):
AGGGGGGAATCGATTCCCTCAA
Done.