Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007140.1 Hibiscus syriacus cultivar Beakdansim tig00018675_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: 67449
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:752 original size:7 final size:7
Alignment explanation
Indices: 740--872 Score: 56
Period size: 7 Copynumber: 18.3 Consensus size: 7
730 AGGGAAACTG
740 TAAAAAA
1 TAAAAAA
747 T-AAAAA
1 TAAAAAA
753 TAAAGAAAA
1 T-AA-AAAA
762 TAATAAAA
1 TAA-AAAA
** *
770 GGATAAA
1 TAAAAAA
*
777 TCAAAAGA
1 T-AAAAAA
*
785 GAAAAAA
1 TAAAAAA
*
792 AATAAAAA
1 TA-AAAAA
800 TAAAAAA
1 TAAAAAA
*
807 -AAAGGAA
1 TAAA-AAA
*
814 -AATAAA
1 TAAAAAA
*
820 TAATAAA
1 TAAAAAA
827 TAAAATAA
1 TAAAA-AA
*
835 TAAATAA
1 TAAAAAA
*
842 TAATAAAG
1 TAA-AAAA
850 TAAAAAA
1 TAAAAAA
*
857 CAAAAAA
1 TAAAAAA
*
864 TATAAAA
1 TAAAAAA
871 TA
1 TA
873 TGTTAAAATA
Statistics
Matches: 94, Mismatches: 23, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
6 11 0.12
7 50 0.53
8 28 0.30
9 5 0.05
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:805 original size:16 final size:16
Alignment explanation
Indices: 741--870 Score: 70
Period size: 16 Copynumber: 8.1 Consensus size: 16
731 GGGAAACTGT
741 AAAAAATAAAAAT-AA
1 AAAAAATAAAAATAAA
* * *
756 AGAAAATAATAA-AAG
1 AAAAAATAAAAATAAA
* * * *
771 GATAAATCAAAAGAGAA
1 AAAAAATAAAAATA-AA
788 AAAAAATAAAAATAAA
1 AAAAAATAAAAATAAA
**
804 AAAAAAGGAAAATAAA
1 AAAAAATAAAAATAAA
* *
820 TAATAAAT-AAAATAAT
1 -AAAAAATAAAAATAAA
*
836 AAATAATAATAAAGTAAA
1 AAAAAATAA-AAA-TAAA
*
854 AAACAAA-AAATATAAA
1 AAA-AAATAAAAATAAA
870 A
1 A
871 TATGTTAAAA
Statistics
Matches: 84, Mismatches: 23, Indels: 15
0.69 0.19 0.12
Matches are distributed among these distances:
15 23 0.27
16 30 0.36
17 21 0.25
18 8 0.10
19 2 0.02
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAAAATAAAAATAAA
Found at i:831 original size:22 final size:22
Alignment explanation
Indices: 789--869 Score: 64
Period size: 22 Copynumber: 3.7 Consensus size: 22
779 AAAAGAGAAA
*
789 AAAAATAAA-AATAAAAAAAAAG
1 AAAAATAAATAAT-AAATAAAAG
* *
811 GAAAATAAATAATAAATAAAAT
1 AAAAATAAATAATAAATAAAAG
833 AATAAAT-AATAATAAAGTAAAA-
1 AA-AAATAAATAATAAA-TAAAAG
855 AACAAA-AAAT-ATAAA
1 AA-AAATAAATAATAAA
870 ATATGTTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
21 5 0.10
22 33 0.66
23 12 0.24
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (22 bp):
AAAAATAAATAATAAATAAAAG
Found at i:887 original size:7 final size:7
Alignment explanation
Indices: 788--872 Score: 59
Period size: 7 Copynumber: 12.1 Consensus size: 7
778 CAAAAGAGAA
788 AAAAAAT
1 AAAAAAT
795 -AAAAAT
1 AAAAAAT
801 AAAAAA-
1 AAAAAAT
*
807 AAAGGAA-
1 AAA-AAAT
*
814 AATAAAT
1 AAAAAAT
*
821 AATAAAT
1 AAAAAAT
828 AAAATAAT
1 AAAA-AAT
*
836 AAATAAT
1 AAAAAAT
*
843 AATAAAGT
1 AA-AAAAT
*
851 AAAAAAC
1 AAAAAAT
858 AAAAAAT
1 AAAAAAT
*
865 ATAAAAT
1 AAAAAAT
872 A
1 A
873 TGTTAAAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
6 11 0.18
7 40 0.65
8 11 0.18
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.18
Consensus pattern (7 bp):
AAAAAAT
Found at i:2177 original size:39 final size:37
Alignment explanation
Indices: 2033--2217 Score: 137
Period size: 37 Copynumber: 5.3 Consensus size: 37
2023 TATATATAAC
* * *
2033 TATATTATATATATTCTAAAAACAT-CTTT--AAACTA
1 TATATTATATA-ATTTTAAAAAAATGTTTTAAAAACTA
*
2068 TATATTAT-T--TTTTAAAAAAA-GTTTTCAAAAC--
1 TATATTATATAATTTTAAAAAAATGTTTTAAAAACTA
** * *
2099 TATATTATATAGCTTT-CAAAAATGATTT-AAAA--A
1 TATATTATATAATTTTAAAAAAATGTTTTAAAAACTA
* *
2132 -ATATTATATAAGTTTTAAAAAAATGTTTTTTAAAATTA
1 TATATTATATAA-TTTTAAAAAAATG-TTTTAAAAACTA
**
2170 TATATTATATAATTTTTCAAAAATGTTTTAAAAACTA
1 TATATTATATAATTTTAAAAAAATGTTTTAAAAACTA
2207 TATATTATATA
1 TATATTATATA
2218 TATATATTTA
Statistics
Matches: 121, Mismatches: 14, Indels: 28
0.74 0.09 0.17
Matches are distributed among these distances:
31 20 0.17
32 11 0.09
33 16 0.13
34 15 0.12
35 11 0.09
36 4 0.03
37 21 0.17
38 12 0.10
39 11 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (37 bp):
TATATTATATAATTTTAAAAAAATGTTTTAAAAACTA
Found at i:2218 original size:39 final size:38
Alignment explanation
Indices: 2066--2335 Score: 129
Period size: 34 Copynumber: 7.6 Consensus size: 38
2056 ATCTTTAAAC
* * * *
2066 TATATAT-TATTTTTTAAAAAAAGTTTTCAAAAC--TA
1 TATATATATAATTTTTCAAAAATGTTTTAAAAACTATA
** *
2101 TAT-TATAT-AGCTTTCAAAAATGATTTAAAAA--ATA
1 TATATATATAATTTTTCAAAAATGTTTTAAAAACTATA
* ** * *
2135 T-TATATA-AGTTTTAAAAAAATGTTTTTTAAAATTATA
1 TATATATATAATTTTTCAAAAATG-TTTTAAAAACTATA
2172 TAT-TATATAATTTTTCAAAAATGTTTTAAAAACTATA
1 TATATATATAATTTTTCAAAAATGTTTTAAAAACTATA
* * *
2209 TATTATATATATATATTT--AAAATGATTT-CAAAC----
1 TA-TATATATA-ATTTTTCAAAAATGTTTTAAAAACTATA
** **
2242 TATATATATAGGTTTTC-AAAATGTTTTAAAAACCCTA
1 TATATATATAATTTTTCAAAAATGTTTTAAAAACTATA
*
2279 T-TTTATAT-A-TTTTC-AAAATGTTTTTCTAAAAACTATA
1 TATATATATAATTTTTCAAAAATG--TTT-TAAAAACTATA
*
2316 TATAT-TAT-ATATTTCAAAAA
1 TATATATATAATTTTTCAAAAA
2336 CATTTGCAGA
Statistics
Matches: 178, Mismatches: 33, Indels: 44
0.70 0.13 0.17
Matches are distributed among these distances:
31 3 0.02
32 17 0.10
33 7 0.04
34 46 0.26
35 11 0.06
36 9 0.05
37 41 0.23
38 29 0.16
39 10 0.06
40 5 0.03
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (38 bp):
TATATATATAATTTTTCAAAAATGTTTTAAAAACTATA
Found at i:2242 original size:37 final size:36
Alignment explanation
Indices: 2062--2248 Score: 117
Period size: 37 Copynumber: 5.3 Consensus size: 36
2052 AAACATCTTT
* * * *
2062 AAACTATATATTAT-T--TTTTAAAAAAAGTTTTCA
1 AAACTATATATTATATAATTTTTAAAAATGATTTAA
** *
2095 AAAC--TATATTATATAGCTTTCAAAAATGATTT-A
1 AAACTATATATTATATAATTTTTAAAAATGATTTAA
* * *
2128 AAA--A-ATATTATATAAGTTTTAAAAAAATGTTTTTTA
1 AAACTATATATTATATAA-TTTT-TAAAAATG-ATTTAA
* *
2164 AAATTATATATTATATAATTTTTCAAAAATGTTTTAA
1 AAACTATATATTATATAATTTTT-AAAAATGATTTAA
*
2201 AAACTATATATTATATATATATATTT-AAAATGATTT-C
1 AAACTATATATTATATA-AT-T-TTTAAAAATGATTTAA
2238 AAACTATATAT
1 AAACTATATAT
2249 ATAGGTTTTC
Statistics
Matches: 126, Mismatches: 13, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
31 8 0.06
32 11 0.09
33 11 0.09
34 19 0.15
35 3 0.02
36 4 0.03
37 32 0.25
38 23 0.18
39 12 0.10
40 3 0.02
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (36 bp):
AAACTATATATTATATAATTTTTAAAAATGATTTAA
Found at i:2312 original size:70 final size:75
Alignment explanation
Indices: 2151--2320 Score: 182
Period size: 70 Copynumber: 2.4 Consensus size: 75
2141 AAGTTTTAAA
* *
2151 AAAATGTTTTT-TAAAATTA-TATATTATATAATTTTTCAAAAATGTTTTAAAAACTATATATTA
1 AAAATGTTTTTCTAAAA--ACTATA-TATATAAGTTTTCAAAAATGTTTTAAAAACCATATATTA
*
2214 TATATATATATTT
63 TATATATATATTC
* * *
2227 AAAATG-ATTTC---AAACTATATATATAGGTTTTC-AAAATGTTTTAAAAACCCTAT-TT-TAT
1 AAAATGTTTTTCTAAAAACTATATATATAAGTTTTCAAAAATGTTTTAAAAACCATATATTATAT
2285 ATAT-T-TTC
66 ATATATATTC
2293 AAAATGTTTTTCTAAAAACTATATATAT
1 AAAATGTTTTTCTAAAAACTATATATAT
2321 TATATATTTC
Statistics
Matches: 81, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
66 8 0.10
67 5 0.06
68 7 0.09
69 2 0.02
70 32 0.40
71 12 0.15
72 4 0.05
73 2 0.02
75 3 0.04
76 6 0.07
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (75 bp):
AAAATGTTTTTCTAAAAACTATATATATAAGTTTTCAAAAATGTTTTAAAAACCATATATTATAT
ATATATATTC
Found at i:2374 original size:15 final size:15
Alignment explanation
Indices: 2354--2384 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2344 GATTATATAT
2354 ATAATAAATAAATAA
1 ATAATAAATAAATAA
*
2369 ATAATAAATAGATAA
1 ATAATAAATAAATAA
2384 A
1 A
2385 ATCAGACGAA
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:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAATAAATAAATAA
Found at i:2712 original size:28 final size:29
Alignment explanation
Indices: 2666--2729 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
2656 TAAAGTTTGG
*
2666 AAAAGTTTAGGACCAAAAAG-GTAATTTC
1 AAAAGTTTAGGAACAAAAAGTGTAATTTC
* *
2694 AAAAGTTTATGGAAC-AAAAGTTTAATTTT
1 AAAAGTTTA-GGAACAAAAAGTGTAATTTC
2723 AAAAGTT
1 AAAAGTT
2730 AATTTTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (29 bp):
AAAAGTTTAGGAACAAAAAGTGTAATTTC
Found at i:5534 original size:19 final size:19
Alignment explanation
Indices: 5506--5549 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5496 GCTATGAACT
*
5506 TGAAAATAAGATACGAATA
1 TGAAATTAAGATACGAATA
* * *
5525 TGAAATTAAGTTATGAATC
1 TGAAATTAAGATACGAATA
5544 TGAAAT
1 TGAAAT
5550 ACGTTTTGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.30
Consensus pattern (19 bp):
TGAAATTAAGATACGAATA
Found at i:5750 original size:39 final size:37
Alignment explanation
Indices: 5702--5782 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 37
5692 AAAAAGAATA
5702 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
1 TGATATGACTATTAT-TATGATATT-TTTATCATGGCTT
* *
5741 TGATATGACTATTATTATGATATTTTTATTATGGTTT
1 TGATATGACTATTATTATGATATTTTTATCATGGCTT
5778 TGATA
1 TGATA
5783 AAATGATGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 16 0.40
38 9 0.22
39 15 0.38
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (37 bp):
TGATATGACTATTATTATGATATTTTTATCATGGCTT
Found at i:9310 original size:23 final size:23
Alignment explanation
Indices: 9283--9327 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9273 CAACTCGGTC
*
9283 GAGTCAAATCATTAACTTTGACA
1 GAGTCAAACCATTAACTTTGACA
* *
9306 GAGTCAACCCATTGACTTTGAC
1 GAGTCAAACCATTAACTTTGAC
9328 CAATCTGACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (23 bp):
GAGTCAAACCATTAACTTTGACA
Found at i:11846 original size:31 final size:31
Alignment explanation
Indices: 11808--11881 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
11798 TAAGGAGACC
*
11808 CTTGGGTAGG-CTCTGAT-GCCCCAAGATCTTT
1 CTTGGGTAGGCCT-TG-TGGCCCCAAGATCATT
*
11839 CTTGGGTAGGCCTTGTGGCCCCGAGATCATT
1 CTTGGGTAGGCCTTGTGGCCCCAAGATCATT
*
11870 CTTGGGCAGGCC
1 CTTGGGTAGGCC
11882 CCATGGCCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 1 0.03
31 35 0.92
32 2 0.05
ACGTcount: A:0.14, C:0.27, G:0.31, T:0.28
Consensus pattern (31 bp):
CTTGGGTAGGCCTTGTGGCCCCAAGATCATT
Found at i:11889 original size:31 final size:31
Alignment explanation
Indices: 11825--11895 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
11815 AGGCTCTGAT
* * * ***
11825 GCCCCAAGATCTTTCTTGGGTAGGCCTTGTG
1 GCCCCGAGATCATTCTTGGGCAGGCCCCATG
11856 GCCCCGAGATCATTCTTGGGCAGGCCCCATG
1 GCCCCGAGATCATTCTTGGGCAGGCCCCATG
*
11887 GCCCTGAGA
1 GCCCCGAGA
11896 AACTTTCTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.24
Consensus pattern (31 bp):
GCCCCGAGATCATTCTTGGGCAGGCCCCATG
Found at i:14272 original size:16 final size:13
Alignment explanation
Indices: 14245--14284 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 13
14235 CTGTTGACTG
14245 TTGACTTTGACCA
1 TTGACTTTGACCA
14258 GTATGACTGTTGACCA
1 -T-TGACT-TTGACCA
14274 TTGACTTTGAC
1 TTGACTTTGAC
14285 TTTGATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.21
14 6 0.25
15 6 0.25
16 7 0.29
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (13 bp):
TTGACTTTGACCA
Found at i:15985 original size:31 final size:32
Alignment explanation
Indices: 15947--16017 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
15937 AAGGCGACCA
*
15947 TTGGGTAGGCTCC-GAAGCCCCGAG-ATCTTTC
1 TTGGGTAGGC-CCTGAAGCCCCGAGAAACTTTC
**
15978 TTGGGTAGGCCCTGTGGCCCCGAGAAACTTTC
1 TTGGGTAGGCCCTGAAGCCCCGAGAAACTTTC
16010 TTGGGTAG
1 TTGGGTAG
16018 ACTTTTGGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 2 0.06
31 19 0.54
32 14 0.40
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.27
Consensus pattern (32 bp):
TTGGGTAGGCCCTGAAGCCCCGAGAAACTTTC
Found at i:17767 original size:23 final size:23
Alignment explanation
Indices: 17737--17792 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
17727 TAAGGGGAAA
17737 GAATTGTAACACCCCAAAATTTT
1 GAATTGTAACACCCCAAAATTTT
17760 GAATTGTAACACCCCAAAATTTT
1 GAATTGTAACACCCCAAAATTTT
**
17783 GGTTTGTAAC
1 GAATTGTAAC
17793 CAAAATGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (23 bp):
GAATTGTAACACCCCAAAATTTT
Found at i:21137 original size:19 final size:18
Alignment explanation
Indices: 21113--21175 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
21103 TGCATTGGGC
21113 TATGAACTTGAAAATAAGT
1 TATGAA-TTGAAAATAAGT
21132 TATGAATCTG-AAATAAGT
1 TATGAAT-TGAAAATAAGT
* * *
21150 TTTGAGTTTGAAAACAAGT
1 TATGA-ATTGAAAATAAGT
*
21169 TCTGAAT
1 TATGAAT
21176 CTGAGAATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
18 16 0.44
19 20 0.56
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (18 bp):
TATGAATTGAAAATAAGT
Found at i:21147 original size:18 final size:18
Alignment explanation
Indices: 21124--21179 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
21114 ATGAACTTGA
21124 AAATAAGTTATGAATCTG
1 AAATAAGTTATGAATCTG
* * *
21142 AAATAAGTTTTGAGTTTG
1 AAATAAGTTATGAATCTG
* *
21160 AAAACAAGTTCTGAATCTG
1 -AAATAAGTTATGAATCTG
21179 A
1 A
21180 GAATGAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (18 bp):
AAATAAGTTATGAATCTG
Found at i:21175 original size:37 final size:38
Alignment explanation
Indices: 21120--21192 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 38
21110 GGCTATGAAC
*
21120 TTGAAAATAAGTTATGAATCTGA-AAT-AAGTTTTGAGT
1 TTGAAAACAAGTTATGAATCTGAGAATGAA-TTTTGAGT
*
21157 TTGAAAACAAGTTCTGAATCTGAGAATGAATTTTGA
1 TTGAAAACAAGTTATGAATCTGAGAATGAATTTTGA
21193 AATGTGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 21 0.66
38 9 0.28
39 2 0.06
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (38 bp):
TTGAAAACAAGTTATGAATCTGAGAATGAATTTTGAGT
Found at i:21340 original size:21 final size:21
Alignment explanation
Indices: 21316--21381 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
21306 CTAATATGTA
21316 TGATATTGTTTATCATGGCTT
1 TGATATTGTTTATCATGGCTT
** * *
21337 TGATA-TGACTATTAT-G-TA
1 TGATATTGTTTATCATGGCTT
21355 TGATATTGTTTATCATGGCTT
1 TGATATTGTTTATCATGGCTT
21376 TGATAT
1 TGATAT
21382 AATCGTGAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 8 0.24
21 12 0.35
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (21 bp):
TGATATTGTTTATCATGGCTT
Found at i:26153 original size:19 final size:21
Alignment explanation
Indices: 26120--26158 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
26110 TTGAAATTAA
*
26120 TGTTAGAGTGATG-AATTTGG
1 TGTTAGAATGATGAAATTTGG
26140 TGTTAGAATG-TGAAATTTG
1 TGTTAGAATGATGAAATTTG
26159 ACTATTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (21 bp):
TGTTAGAATGATGAAATTTGG
Found at i:29602 original size:43 final size:43
Alignment explanation
Indices: 29541--29624 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
29531 TTGACTTCAT
* **
29541 GTTCTACGTAACATTGGGTTCCTGATATATTGAAACGTTTCGC
1 GTTCTACGTAACACTGGGTTCCCAATATATTGAAACGTTTCGC
*
29584 GTTCTACGTAACACTGGGTTCCCAATATATTGAAATGTTTC
1 GTTCTACGTAACACTGGGTTCCCAATATATTGAAACGTTTC
29625 TGCAATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (43 bp):
GTTCTACGTAACACTGGGTTCCCAATATATTGAAACGTTTCGC
Found at i:36221 original size:30 final size:30
Alignment explanation
Indices: 36187--36245 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
36177 TTTTGATAAA
**
36187 TTTTGATAAATTTGATTAAGT-CTAAAATCT
1 TTTTGATAAATTCAATTAAGTGC-AAAATCT
36217 TTTTGATAAATTCAATTAAGTGCAAAATC
1 TTTTGATAAATTCAATTAAGTGCAAAATC
36246 AAATTTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (30 bp):
TTTTGATAAATTCAATTAAGTGCAAAATCT
Found at i:37674 original size:14 final size:14
Alignment explanation
Indices: 37657--37696 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
37647 TTAATTTTCA
37657 CTTCTATCTCAGTC
1 CTTCTATCTCAGTC
*
37671 CTTCTATCTCGGTC
1 CTTCTATCTCAGTC
37685 CTTCTATCTCAG
1 CTTCTATCTCAG
37697 CTGCCTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.35, G:0.10, T:0.42
Consensus pattern (14 bp):
CTTCTATCTCAGTC
Found at i:46140 original size:24 final size:24
Alignment explanation
Indices: 46107--46152 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
46097 TGATTATCAG
*
46107 ACATCCAAAAATAATAAACGATTT
1 ACATCAAAAAATAATAAACGATTT
*
46131 ACATCAAAAAGTAATAAACGAT
1 ACATCAAAAAATAATAAACGAT
46153 AACTTAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.22
Consensus pattern (24 bp):
ACATCAAAAAATAATAAACGATTT
Done.