Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002467.1 Hibiscus syriacus cultivar Beakdansim tig00005046_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: 66470
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2539 original size:25 final size:25
Alignment explanation
Indices: 2505--2553 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2495 ATATAATTAT
2505 TGGGATCATAAATGACATGATGAAA
1 TGGGATCATAAATGACATGATGAAA
*
2530 TGGGATCATAAATGACGTGATGAA
1 TGGGATCATAAATGACATGATGAA
2554 TTAAGACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (25 bp):
TGGGATCATAAATGACATGATGAAA
Found at i:4986 original size:13 final size:14
Alignment explanation
Indices: 4959--4993 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
4949 AAAAATATCT
4959 AATATTAATTAATA
1 AATATTAATTAATA
*
4973 AATCTTAA-TAATA
1 AATATTAATTAATA
4986 AATATTAA
1 AATATTAA
4994 CCTAATGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATTAATTAATA
Found at i:6512 original size:22 final size:23
Alignment explanation
Indices: 6480--6522 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
6470 GACCGACCCG
*
6480 ATTCAAATAAAAAAGTTATTTTT
1 ATTCAAATAAAAAAGTGATTTTT
*
6503 ATTC-AATAAAATAGTGATTT
1 ATTCAAATAAAAAAGTGATTT
6523 AATTGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (23 bp):
ATTCAAATAAAAAAGTGATTTTT
Found at i:13961 original size:2 final size:2
Alignment explanation
Indices: 13949--13995 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
13939 CAACTTTTAC
*
13949 TA TA AA 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
13991 TA TA T
1 TA TA T
13996 CCCTAAACCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15482 original size:9 final size:9
Alignment explanation
Indices: 15468--15496 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
15458 AAAATTTTAT
15468 TTCGGTTAA
1 TTCGGTTAA
15477 TTCGGTTAA
1 TTCGGTTAA
15486 TTCGGTTAA
1 TTCGGTTAA
15495 TT
1 TT
15497 AACCGATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:19739 original size:14 final size:15
Alignment explanation
Indices: 19720--19753 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
19710 AATAAAAAAT
19720 ATTTTTTAT-TGAAA
1 ATTTTTTATCTGAAA
*
19734 ATTTTTTATCTTAAA
1 ATTTTTTATCTGAAA
19749 ATTTT
1 ATTTT
19754 ATAAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTTTTATCTGAAA
Found at i:27159 original size:6 final size:6
Alignment explanation
Indices: 27148--27175 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
27138 GCCGCTTTGG
27148 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
27176 CCTTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:28910 original size:180 final size:180
Alignment explanation
Indices: 28608--28972 Score: 721
Period size: 180 Copynumber: 2.0 Consensus size: 180
28598 TTTTTTTATG
28608 GTATAAATTATTTTGTTTTAAGATTTATTATGTATTATTAAACTTTTTTCAATTATGTTTGTAAA
1 GTATAAATTATTTTGTTTTAAGATTTATTATGTATTATTAAACTTTTTTCAATTATGTTTGTAAA
28673 ATATTTATGGATTGTTAGTTTGTTACTTTGATGTTTAAACTGTGAAATTGATTCACATAATATTT
66 ATATTTATGGATTGTTAGTTTGTTACTTTGATGTTTAAACTGTGAAATTGATTCACATAATATTT
28738 TGTTATTTTTTAATTTGTTAATTTATATTAAGTTTTATATATTATTGTTA
131 TGTTATTTTTTAATTTGTTAATTTATATTAAGTTTTATATATTATTGTTA
28788 GTATAAATTATTTTGTTTTAAGATTTATTATGTATTATTAAACTTTTTTCAATTATGTTTGTAAA
1 GTATAAATTATTTTGTTTTAAGATTTATTATGTATTATTAAACTTTTTTCAATTATGTTTGTAAA
28853 ATATTTATGGATTGTTAGTTTGTTACTTTGATGTTTAAACTGTGAAATTGATTCACATAATATTT
66 ATATTTATGGATTGTTAGTTTGTTACTTTGATGTTTAAACTGTGAAATTGATTCACATAATATTT
28918 TGTTATTTTTTAATTTGTTAATTTATATTAAGTTTTATATATTATTGTTA
131 TGTTATTTTTTAATTTGTTAATTTATATTAAGTTTTATATATTATTGTTA
*
28968 TTATA
1 GTATA
28973 TTAAAAAAAG
Statistics
Matches: 184, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 184 1.00
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (180 bp):
GTATAAATTATTTTGTTTTAAGATTTATTATGTATTATTAAACTTTTTTCAATTATGTTTGTAAA
ATATTTATGGATTGTTAGTTTGTTACTTTGATGTTTAAACTGTGAAATTGATTCACATAATATTT
TGTTATTTTTTAATTTGTTAATTTATATTAAGTTTTATATATTATTGTTA
Found at i:30862 original size:24 final size:24
Alignment explanation
Indices: 30835--30898 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
30825 ACGAAGATAT
* *
30835 CAGAAATCAAAACATAATTCAGAA
1 CAGAAATCAAAACAGAATCCAGAA
* * *
30859 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAAAACAGAATCCAGAA
*
30883 CAGAAATCAAATCAGA
1 CAGAAATCAAAACAGA
30899 TATCATTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.53, C:0.19, G:0.12, T:0.16
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATCCAGAA
Found at i:30868 original size:12 final size:12
Alignment explanation
Indices: 30853--30903 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
30843 AAAACATAAT
30853 TCAGAACAGATA
1 TCAGAACAGATA
30865 TCAGAACAGA-A
1 TCAGAACAGATA
* *
30876 TCCAGATCAGAAA
1 T-CAGAACAGATA
30889 TCA-AATCAGATA
1 TCAGAA-CAGATA
30901 TCA
1 TCA
30904 TTAAACGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.09
12 28 0.85
13 2 0.06
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.18
Consensus pattern (12 bp):
TCAGAACAGATA
Found at i:30985 original size:43 final size:43
Alignment explanation
Indices: 30919--31004 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
30909 CGGTATTTCA
* **
30919 ATCTTTTTCCTCCATTCGGTCTTATTATTTAATTCCAAT-TTAT
1 ATCTTTTTCCTCCATCCAATCTTATTATTTAATT-CAATCTTAT
30962 ATCTTTTTCCTCCATCCAATCTTATTATTTAATTCAATCTTAT
1 ATCTTTTTCCTCCATCCAATCTTATTATTTAATTCAATCTTAT
31005 CATTTACTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 4 0.10
43 35 0.90
ACGTcount: A:0.23, C:0.22, G:0.02, T:0.52
Consensus pattern (43 bp):
ATCTTTTTCCTCCATCCAATCTTATTATTTAATTCAATCTTAT
Found at i:32368 original size:13 final size:14
Alignment explanation
Indices: 32328--32373 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
32318 GTCAACTCCA
*
32328 GTCAACGATCAACGA
1 GTCAACG-TCAACGG
32343 GTCAACGGTCAACGG
1 GTCAAC-GTCAACGG
32358 GTCAA-GTCAACGG
1 GTCAACGTCAACGG
32371 GTC
1 GTC
32374 GGGTCGGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 11 0.38
15 17 0.59
16 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.15
Consensus pattern (14 bp):
GTCAACGTCAACGG
Found at i:32378 original size:18 final size:18
Alignment explanation
Indices: 32355--32393 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
32345 CAACGGTCAA
*
32355 CGGGTCAAGTCAACGGGT
1 CGGGTCAAGTAAACGGGT
**
32373 CGGGTCGGGTAAACGGGT
1 CGGGTCAAGTAAACGGGT
32391 CGG
1 CGG
32394 TTCGGGTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.46, T:0.15
Consensus pattern (18 bp):
CGGGTCAAGTAAACGGGT
Found at i:32398 original size:18 final size:18
Alignment explanation
Indices: 32366--32400 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32356 GGGTCAAGTC
32366 AACGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCGGGTA
*
32384 AACGGGTCGGTTCGGGT
1 AACGGGTCGGGTCGGGT
32401 TGTGACCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.17, G:0.49, T:0.20
Consensus pattern (18 bp):
AACGGGTCGGGTCGGGTA
Found at i:35932 original size:12 final size:12
Alignment explanation
Indices: 35915--35939 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35905 GGGTTAGTTG
35915 GTTATTATCGAA
1 GTTATTATCGAA
35927 GTTATTATCGAA
1 GTTATTATCGAA
35939 G
1 G
35940 GTTCGTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTATTATCGAA
Found at i:38801 original size:19 final size:20
Alignment explanation
Indices: 38772--38809 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
38762 CAGAAATTGT
38772 TGAAGGTGTATCGATGCACA
1 TGAAGGTGTATCGATGCACA
38792 TGAA-GTGTATCGATGCAC
1 TGAAGGTGTATCGATGCAC
38810 TCTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGTATCGATGCACA
Found at i:38917 original size:63 final size:63
Alignment explanation
Indices: 38777--38943 Score: 181
Period size: 63 Copynumber: 2.6 Consensus size: 63
38767 ATTGTTGAAG
* * * ** *
38777 GTGTATCGATGCACATGAAGTGTATCGATGCACTCTTTTAAAATAAAAACATCGAATGTCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCAC-CCCTTAAAATAAAAACATCGAATGGCATCA
* ** * **
38841 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTAATATTCAAACATCGAATGGGATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTAAAATAAAAACATCGAATGGCATCA
* * * *
38904 GTGTACCGATGCACAGGTAGTGCATAGATGCACCCGTTAA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTAA
38944 GGGATGCATC
Statistics
Matches: 87, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
63 57 0.66
64 30 0.34
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (63 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCTTAAAATAAAAACATCGAATGGCATCA
Found at i:39513 original size:22 final size:22
Alignment explanation
Indices: 39485--39619 Score: 179
Period size: 22 Copynumber: 6.3 Consensus size: 22
39475 GAGGGTTTAT
39485 AGTGGTCATTCGGGACGTATCC
1 AGTGGTCATTCGGGACGTATCC
* *
39507 AGTGGTCCTTCGGGAAGTATCC
1 AGTGGTCATTCGGGACGTATCC
39529 AGTGGTCATTCGGGACGTATCC
1 AGTGGTCATTCGGGACGTATCC
*
39551 AGTGGTCATTCGGGACATATCC
1 AGTGGTCATTCGGGACGTATCC
* *
39573 ACTGGTCATTCGGGA--TGT--
1 AGTGGTCATTCGGGACGTATCC
* *
39591 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCATTCGGGACGTATCC
39613 AGTGGTC
1 AGTGGTC
39620 CTTAGGGATG
Statistics
Matches: 99, Mismatches: 10, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
18 13 0.13
20 4 0.04
22 82 0.83
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (22 bp):
AGTGGTCATTCGGGACGTATCC
Found at i:39548 original size:44 final size:44
Alignment explanation
Indices: 39485--39619 Score: 199
Period size: 44 Copynumber: 3.2 Consensus size: 44
39475 GAGGGTTTAT
39485 AGTGGTCATTCGGGACGTATCCAGTGGTCCTTCGGGA-AGTATCC
1 AGTGGTCATTCGGGACGTATCCAGTGGTCCTTCGGGACA-TATCC
*
39529 AGTGGTCATTCGGGACGTATCCAGTGGTCATTCGGGACATATCC
1 AGTGGTCATTCGGGACGTATCCAGTGGTCCTTCGGGACATATCC
* *
39573 ACTGGTCATTCGGGA--TGT--AGTGGTCCTTCGGGACATATCC
1 AGTGGTCATTCGGGACGTATCCAGTGGTCCTTCGGGACATATCC
39613 AGTGGTC
1 AGTGGTC
39620 CTTAGGGATG
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
40 27 0.32
42 2 0.02
44 55 0.65
45 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (44 bp):
AGTGGTCATTCGGGACGTATCCAGTGGTCCTTCGGGACATATCC
Found at i:39606 original size:40 final size:40
Alignment explanation
Indices: 39507--39631 Score: 153
Period size: 40 Copynumber: 3.0 Consensus size: 40
39497 GGACGTATCC
*
39507 AGTGGTCCTTCGGGA-AGTATCCAGTGGTCATTCGGGACGTAT
1 AGTGGTCCTTCGGGACA-TATCCAGTGGTCATTCGGGA--TGT
* *
39549 CCAGTGGTCATTCGGGACATATCCACTGGTCATTCGGGATGT
1 --AGTGGTCCTTCGGGACATATCCAGTGGTCATTCGGGATGT
* *
39591 AGTGGTCCTTCGGGACATATCCAGTGGTCCTTAGGGATGT
1 AGTGGTCCTTCGGGACATATCCAGTGGTCATTCGGGATGT
39631 A
1 A
39632 ATGATCATTC
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
40 37 0.51
42 2 0.03
44 33 0.45
45 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (40 bp):
AGTGGTCCTTCGGGACATATCCAGTGGTCATTCGGGATGT
Found at i:39647 original size:40 final size:40
Alignment explanation
Indices: 39556--39647 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
39546 TATCCAGTGG
* * *
39556 TCATTCGGGACATATCCACTGGTCATTCGGGATGTAGTGG
1 TCATTCGGGACATATCCACTGGTCATTAGGGATGTAATGA
* * *
39596 TCCTTCGGGACATATCCAGTGGTCCTTAGGGATGTAATGA
1 TCATTCGGGACATATCCACTGGTCATTAGGGATGTAATGA
*
39636 TCATTCAGGACA
1 TCATTCGGGACA
39648 AATATTCACT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
TCATTCGGGACATATCCACTGGTCATTAGGGATGTAATGA
Found at i:40785 original size:21 final size:21
Alignment explanation
Indices: 40732--40787 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
40722 TTTTAATCTT
* *
40732 AGTATCGATACGCTGATGTAG
1 AGTATTGATACTCTGATGTAG
40753 AGTATTGATACTCTGATGTAG
1 AGTATTGATACTCTGATGTAG
40774 AGTATTGATACTCT
1 AGTATTGATACTCT
40788 CCCAATGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (21 bp):
AGTATTGATACTCTGATGTAG
Found at i:43060 original size:17 final size:17
Alignment explanation
Indices: 43038--43072 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
43028 TAAATAATAA
*
43038 TTAAAATAAATATTACT
1 TTAAAATAAATATAACT
43055 TTAAAATAAATATAACT
1 TTAAAATAAATATAACT
43072 T
1 T
43073 AATAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAATAAATATAACT
Found at i:47968 original size:21 final size:21
Alignment explanation
Indices: 47944--47992 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
47934 CATGACATCT
47944 ATAATAACAAACTTGAAATCC
1 ATAATAACAAACTTGAAATCC
* *
47965 ATAACAACCAACTTGAAATCC
1 ATAATAACAAACTTGAAATCC
47986 ATAATAA
1 ATAATAA
47993 TAAATCAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.22
Consensus pattern (21 bp):
ATAATAACAAACTTGAAATCC
Found at i:49932 original size:24 final size:25
Alignment explanation
Indices: 49905--49955 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
49895 TTTGATTGCT
*
49905 AACGTGAAAGT-ATAAAAATATTAA
1 AACGTGAAAGTAAAAAAAATATTAA
49929 AACGTGAAAGTAAAAAAAATATTAA
1 AACGTGAAAGTAAAAAAAATATTAA
49954 AA
1 AA
49956 AAATATCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.63, C:0.04, G:0.12, T:0.22
Consensus pattern (25 bp):
AACGTGAAAGTAAAAAAAATATTAA
Found at i:50806 original size:22 final size:23
Alignment explanation
Indices: 50745--50806 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
50735 CAAATGATCA
50745 AAAATATACTATAAAGA-TAGAG
1 AAAATATACTATAAAGACTAGAG
*
50767 AAAATATACTACAAAGACT-GAG
1 AAAATATACTATAAAGACTAGAG
* *
50789 AAAATATACCATACAGAC
1 AAAATATACTATAAAGAC
50807 AATATTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.56, C:0.13, G:0.11, T:0.19
Consensus pattern (23 bp):
AAAATATACTATAAAGACTAGAG
Found at i:63923 original size:75 final size:76
Alignment explanation
Indices: 63815--63955 Score: 205
Period size: 75 Copynumber: 1.9 Consensus size: 76
63805 CGTATGGGCA
*
63815 GACACAAATAAATTTTAAGAGTGAACACCTTTAGTAAAATGAACAACTAATATAAAGAAATCCGA
1 GACACAAATAAATTTTAAGAGTGAACACATTTAGTAAAATGAACAACTAATATAAAGAAATCCGA
63880 ATTCCAGGATG
66 ATTCCAGGATG
* * * * *
63891 GACA-AAATAAAATTTTATGATTG-ACACATTTAGTAAAATGAACCACTAATATAAAGTAATTCG
1 GACACAAAT-AAATTTTAAGAGTGAACACATTTAGTAAAATGAACAACTAATATAAAGAAATCCG
63954 AA
65 AA
63956 ATCTAGAATG
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
75 42 0.72
76 16 0.28
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (76 bp):
GACACAAATAAATTTTAAGAGTGAACACATTTAGTAAAATGAACAACTAATATAAAGAAATCCGA
ATTCCAGGATG
Found at i:65103 original size:35 final size:32
Alignment explanation
Indices: 65039--65105 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 32
65029 TAACTCAATC
65039 TATTTTGTCATTTAAACCTAGTTCGTAAGATT
1 TATTTTGTCATTTAAACCTAGTTCGTAAGATT
* *
65071 TATTTTGTCTCATTTATAACCTATTTCTTAAGATT
1 TATTTTG--TCATTTA-AACCTAGTTCGTAAGATT
65106 GATTAATCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 7 0.23
34 7 0.23
35 16 0.53
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (32 bp):
TATTTTGTCATTTAAACCTAGTTCGTAAGATT
Done.