Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001235.1 Hibiscus syriacus cultivar Beakdansim tig00002430_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: 53565
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3450 original size:13 final size:13
Alignment explanation
Indices: 3432--3456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3422 CTTGATTGAA
3432 TAAAAATAAAAAG
1 TAAAAATAAAAAG
3445 TAAAAATAAAAA
1 TAAAAATAAAAA
3457 TTTAACAGAA
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAG
Found at i:8919 original size:18 final size:18
Alignment explanation
Indices: 8880--8921 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
8870 GTAAGAAAAT
*
8880 ATTAAATTAATAAAACCG
1 ATTAAATTAATAAAACCA
*
8898 ATTAAA-TAAGTAAAAGCA
1 ATTAAATTAA-TAAAACCA
8916 ATTAAA
1 ATTAAA
8922 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (18 bp):
ATTAAATTAATAAAACCA
Found at i:14345 original size:2 final size:2
Alignment explanation
Indices: 14338--14366 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14328 TTTTCAGTTT
14338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14367 GCTGATATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15166 original size:16 final size:17
Alignment explanation
Indices: 15145--15178 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
15135 ACTATTCACA
*
15145 TGAATAGT-GAATTTTG
1 TGAATAGTAAAATTTTG
15161 TGAATAGTAAAATTTTG
1 TGAATAGTAAAATTTTG
15178 T
1 T
15179 CGGTGATACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TGAATAGTAAAATTTTG
Found at i:19619 original size:71 final size:72
Alignment explanation
Indices: 19497--19633 Score: 206
Period size: 71 Copynumber: 1.9 Consensus size: 72
19487 AATGGGGCCC
* * *
19497 CACTAAATTACTATATTTTCGAGTTTTTAAAATAAAAAATGATGTTTAAAATA-TTTTTAATTAT
1 CACTAAATTACCATATTTTCAAGTATTTAAAATAAAAAATGATGTTTAAAATATTTTTTAATTAT
19561 TGGGGCA
66 TGGGGCA
* *
19568 CACTAAATTACCATATTTTCAAGTATTTAAAATAAAAAGT-TTGTTTAAAAATATTTTTTAATTA
1 CACTAAATTACCATATTTTCAAGTATTTAAAATAAAAAATGATGTTT-AAAATATTTTTTAATTA
19632 TT
65 TT
19634 AAACTTAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
70 5 0.08
71 42 0.71
72 12 0.20
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (72 bp):
CACTAAATTACCATATTTTCAAGTATTTAAAATAAAAAATGATGTTTAAAATATTTTTTAATTAT
TGGGGCA
Found at i:25175 original size:136 final size:134
Alignment explanation
Indices: 25012--25280 Score: 459
Period size: 136 Copynumber: 2.0 Consensus size: 134
25002 ACCATTTAAA
* *
25012 ACTCAATTAATAATTTAAGATCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-
1 ACTCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAT
*
25076 TTATATAAAATTTTTATTTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAAT
66 TTATATAAAATTTTTA-TTTTATAATTATATATTATTTAAATTAATTATAAAC--TTTTTTTAAT
25141 TAAAAAT
128 TAAAAAT
25148 ACTCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAT
1 ACTCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAT
* *
25213 TTATCTGAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAA
66 TTATATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAA
25278 AAA
131 AAA
25281 ACATTTAATT
Statistics
Matches: 127, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
134 16 0.13
136 97 0.76
137 14 0.11
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (134 bp):
ACTCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAT
TTATATAAAATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAA
AAAT
Found at i:26366 original size:29 final size:29
Alignment explanation
Indices: 26324--26380 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
26314 AGTGTTGGCC
*
26324 GTAGGTCGCCATGCACTCCGGGTGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
26353 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
26381 ACCCTCGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.32, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:26471 original size:29 final size:29
Alignment explanation
Indices: 26438--26552 Score: 194
Period size: 29 Copynumber: 4.0 Consensus size: 29
26428 GTCCCAACAC
*
26438 GTAGGTCGCCATGCCCTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
*
26467 GTAGGTCGCCATGCACTCCAGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
* *
26496 GTAGGTCGTCATGCACTCCGGGTGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
26525 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
26553 ACCCTCGCTC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 79 1.00
ACGTcount: A:0.14, C:0.34, G:0.30, T:0.22
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:26611 original size:14 final size:14
Alignment explanation
Indices: 26589--26621 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
26579 CCTCGCATAG
*
26589 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
26603 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
26617 CTCGG
1 CTCGG
26622 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:26707 original size:29 final size:29
Alignment explanation
Indices: 26664--26721 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
26654 ACAATCTCTT
*
26664 GTAGCTTGCCGGGAAGACATGGCGACCTA
1 GTAGCTTGCCGGGAAGACATGGCAACCTA
* * *
26693 GTAGGTTGCCTGGAAGGCATGGCAACCTA
1 GTAGCTTGCCGGGAAGACATGGCAACCTA
26722 TGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.34, T:0.19
Consensus pattern (29 bp):
GTAGCTTGCCGGGAAGACATGGCAACCTA
Found at i:29865 original size:25 final size:27
Alignment explanation
Indices: 29810--29865 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 27
29800 TTTATAAAGT
**
29810 TTAAAAAATTATTTATCTATTTAAAAA
1 TTAAAAAATTATTTATAAATTTAAAAA
29837 -TAAAAAA-TATTT-TAAATTTAAAAA
1 TTAAAAAATTATTTATAAATTTAAAAA
29861 TTAAA
1 TTAAA
29866 TATTAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 10 0.38
25 9 0.35
26 7 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
TTAAAAAATTATTTATAAATTTAAAAA
Found at i:29866 original size:13 final size:13
Alignment explanation
Indices: 29848--29904 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
29838 AAAAAATATT
29848 TTAAATTTAAAAA
1 TTAAATTTAAAAA
29861 TTAAATATT--AAA
1 TTAAAT-TTAAAAA
* *
29873 -CAAATTAAAAAA
1 TTAAATTTAAAAA
*
29885 TTAAATATAAAAA
1 TTAAATTTAAAAA
29898 TTAAATT
1 TTAAATT
29905 AAATTGCTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 6 0.18
13 21 0.62
14 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
TTAAATTTAAAAA
Found at i:30023 original size:16 final size:15
Alignment explanation
Indices: 30002--30031 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29992 ATTAAGAAAA
30002 TAATATATATTATATG
1 TAATATATA-TATATG
30018 TAATATATATATAT
1 TAATATATATATAT
30032 AAACACAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAATATATATATATG
Found at i:34685 original size:251 final size:249
Alignment explanation
Indices: 34244--34739 Score: 852
Period size: 251 Copynumber: 2.0 Consensus size: 249
34234 CTGCAGTATC
34244 CATGCCAATGCATACATTTTAACTTCATCATCAGAGGCTCTCGCTCAACTTCCGAAAATTGGCAT
1 CATGCCAATGCATACATTTTAACTTCATCATCAGAGGCTCTCGCTCAACTTCCGAAAATTGGCAT
* *
34309 CTAACCAATTTAACGGTATCTGACCACCGTTAAAATTTTCCAGGACATGTCCTAGACTAACCCGA
66 CTAACCAATTTAACAGTATCTGACCACCGTTAAAATTTTCCAGGACACGTCCTAGACTAACCCGA
34374 TACAAAGTAGTCCAAGAAACGGAAAATATCCATGATATCACACCTCCATCCACCGGAAGCCCCAG
131 TACAAAGTAGTCCAAGAAACGGAAAATATCCATGATATCACACCTCCATCCACCGGAAGCCCCAG
* *
34439 GTGCATAGAAACATCCTCAAGTGTAATCGTGCTCTCTCCGCACGGAAGATTATG
196 GTGCATAGAAACATCCTCAAGTGTAATCGTGCACTCTCCGCACAGAAGATTATG
*
34493 CATGCCAATGCATACATTTTAACTTCATCATCGGAGGCGTCTGCGCTCAACTTCCGAAAATTGGC
1 CATGCCAATGCATACATTTTAACTTCATCATCAGAGGC-TCT-CGCTCAACTTCCGAAAATTGGC
* *
34558 ATCTAACCAATTTAACAGTATTTGACCACCGTTAAAATTTTCTAGGACACGTCCTAGACTAACCC
64 ATCTAACCAATTTAACAGTATCTGACCACCGTTAAAATTTTCCAGGACACGTCCTAGACTAACCC
* *
34623 G-TCACAAAGTAGTCCAAGAACCGGAAGATATCTC-TGATATCACACCTCCATCCACCGGAAGCC
129 GAT-ACAAAGTAGTCCAAGAAACGGAAAATATC-CATGATATCACACCTCCATCCACCGGAAGCC
*
34686 CTAGGTGCATAGAAACATCCTCAAGTGTAATCGTGCACTCTCCGCACAGAAGAT
192 CCAGGTGCATAGAAACATCCTCAAGTGTAATCGTGCACTCTCCGCACAGAAGAT
34740 GAAATGTGGG
Statistics
Matches: 233, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
249 37 0.16
250 4 0.02
251 191 0.82
252 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (249 bp):
CATGCCAATGCATACATTTTAACTTCATCATCAGAGGCTCTCGCTCAACTTCCGAAAATTGGCAT
CTAACCAATTTAACAGTATCTGACCACCGTTAAAATTTTCCAGGACACGTCCTAGACTAACCCGA
TACAAAGTAGTCCAAGAAACGGAAAATATCCATGATATCACACCTCCATCCACCGGAAGCCCCAG
GTGCATAGAAACATCCTCAAGTGTAATCGTGCACTCTCCGCACAGAAGATTATG
Found at i:35136 original size:17 final size:16
Alignment explanation
Indices: 35110--35163 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
35100 AATTAAATAT
*
35110 AATATTAAATAATTTA
1 AATATTAAATAAATTA
35126 AATACTTAAATAAATTA
1 AATA-TTAAATAAATTA
*
35143 AATGTTAAATATAA-TA
1 AATATTAAATA-AATTA
35159 AATAT
1 AATAT
35164 ACCTTAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 17 0.52
17 16 0.48
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AATATTAAATAAATTA
Found at i:35139 original size:21 final size:18
Alignment explanation
Indices: 35090--35162 Score: 51
Period size: 21 Copynumber: 3.7 Consensus size: 18
35080 ATTTTCTATC
35090 TATAAA-AAATAATTAAA
1 TATAAATAAATAATTAAA
35107 TATAATATTAAATAATTTAAA
1 TATAA-A-TAAATAA-TTAAA
35128 TACTTAAATAAATTAAATGTTAAA
1 TA--TAAATAAA-T-AA--TTAAA
35152 TAT-AATAAATA
1 TATAAATAAATA
35163 TACCTTAAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
17 5 0.11
18 1 0.02
19 1 0.02
20 7 0.15
21 17 0.37
22 3 0.07
23 5 0.11
24 7 0.15
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (18 bp):
TATAAATAAATAATTAAA
Found at i:35161 original size:16 final size:16
Alignment explanation
Indices: 35114--35153 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
35104 AAATATAATA
* *
35114 TTAAATAATTTAAATAC
1 TTAAATAAATTAAAT-G
35131 TTAAATAAATTAAATG
1 TTAAATAAATTAAATG
35147 TTAAATA
1 TTAAATA
35154 TAATAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
TTAAATAAATTAAATG
Found at i:37860 original size:19 final size:19
Alignment explanation
Indices: 37818--37860 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
37808 TCACGGTCAA
* *
37818 CGGTCGGGTCGGGTCAGTC
1 CGGTCGGGACGGGTCAGAC
*
37837 GGGTCGGGACGGGTCAGAC
1 CGGTCGGGACGGGTCAGAC
37856 CGGTC
1 CGGTC
37861 AAACCGGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.09, C:0.26, G:0.49, T:0.16
Consensus pattern (19 bp):
CGGTCGGGACGGGTCAGAC
Found at i:43478 original size:35 final size:37
Alignment explanation
Indices: 43411--43482 Score: 121
Period size: 35 Copynumber: 2.0 Consensus size: 37
43401 CTTTTTCGTC
43411 CTACTAGGATTCAAACTCTCAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCTCAAAAATAGGATAGAATT
*
43448 CTACTAGGATTC-AACTC-CTAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCTCAAAAATAGGATAGAATT
43483 TTGCTATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 17 0.50
36 5 0.15
37 12 0.35
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCTCAAAAATAGGATAGAATT
Found at i:44063 original size:15 final size:16
Alignment explanation
Indices: 44038--44107 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 16
44028 ATTTTACTCA
44038 TTTATTTATC-TAT-T
1 TTTATTTATCTTATAT
44052 TTTATATTATCTTATAT
1 TTTAT-TTATCTTATAT
44069 TTTATGTT-T-TTATAT
1 TTTAT-TTATCTTATAT
* *
44084 TCT-TTTA-CTTATTTT
1 TTTATTTATCTTA-TAT
44099 TTTATTTAT
1 TTTATTTAT
44108 TTGCATTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
13 2 0.05
14 9 0.20
15 17 0.39
16 8 0.18
17 8 0.18
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.71
Consensus pattern (16 bp):
TTTATTTATCTTATAT
Found at i:44129 original size:57 final size:56
Alignment explanation
Indices: 44019--44130 Score: 127
Period size: 57 Copynumber: 2.0 Consensus size: 56
44009 TGCTTTTACT
** *
44019 TTTTTATATATTTTACTCATTTATTTATCTATTTTTATATTATCTTATATTTTATG
1 TTTTTATATATTTTACTCATTTATTTATCTATTTGCATATCATCTTATATTTTATG
* * * * *
44075 TTTTTATATTCTTTTACTTATTTTTTTATTTATTTGCATTATCATTTTAT-TTTTAT
1 TTTTTATA-TATTTTACTCATTTATTTATCTATTTGCA-TATCATCTTATATTTTAT
44131 TTAGTTGTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
56 8 0.17
57 29 0.63
58 9 0.20
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (56 bp):
TTTTTATATATTTTACTCATTTATTTATCTATTTGCATATCATCTTATATTTTATG
Found at i:46194 original size:13 final size:14
Alignment explanation
Indices: 46160--46192 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
46150 ACGGTCAACG
46160 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
46174 GTCGGGTC-GGTCA
1 GTCGGGTCGGGTCA
46187 GATCGG
1 G-TCGG
46193 TCAAATTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.09, C:0.21, G:0.48, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:46222 original size:19 final size:19
Alignment explanation
Indices: 46184--46223 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
46174 GTCGGGTCGG
**
46184 TCAGATCGGTCAAATTGGT
1 TCAGATCGGTCAAACCGGT
46203 TCAGATCGGTCAAACCGGT
1 TCAGATCGGTCAAACCGGT
46222 TC
1 TC
46224 GAACCGTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (19 bp):
TCAGATCGGTCAAACCGGT
Found at i:49476 original size:14 final size:14
Alignment explanation
Indices: 49457--49484 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49447 CGCTGGGCAT
49457 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
49471 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
49485 GAGCATCGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:49496 original size:19 final size:20
Alignment explanation
Indices: 49471--49523 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
49461 GGCCATCCGA
49471 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
*
49491 -CGAGGCCATCAGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
*
49510 CCAAGGCCATCCGA
1 CCGAGGCCATCCGA
49524 CCGAGGGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.28, C:0.34, G:0.28, T:0.09
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAGCAT
Found at i:49626 original size:29 final size:29
Alignment explanation
Indices: 49593--49673 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
49583 GAGGGTAGGT
* *
49593 CGCCCGGAGTGCATGGCGACCTACATGGC
1 CGCCCGGAGGGCATGGCGACCTACAAGGC
* *
49622 CGCCCGGAGGGCATGACGACCTACAAGGT
1 CGCCCGGAGGGCATGGCGACCTACAAGGC
49651 CGCCCGGAGGGCATGGCGACCTA
1 CGCCCGGAGGGCATGGCGACCTA
49674 TGTGTTGGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.20, C:0.33, G:0.36, T:0.11
Consensus pattern (29 bp):
CGCCCGGAGGGCATGGCGACCTACAAGGC
Found at i:49730 original size:40 final size:40
Alignment explanation
Indices: 49675--49754 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
49665 GGCGACCTAT
* *
49675 GTGTTGGGACGTGCATGTGCCATGCAACACGTTCATTCTC
1 GTGTTGGGACGTGCATATGCCATGCAACACATTCATTCTC
49715 GTGTTGGGACGTGCATATGCCATGCAACACATTCATTCTC
1 GTGTTGGGACGTGCATATGCCATGCAACACATTCATTCTC
49755 TCTGTTTGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (40 bp):
GTGTTGGGACGTGCATATGCCATGCAACACATTCATTCTC
Found at i:49775 original size:12 final size:12
Alignment explanation
Indices: 49758--49783 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49748 CATTCTCTCT
49758 GTTTGAGCAAGG
1 GTTTGAGCAAGG
49770 GTTTGAGCAAGG
1 GTTTGAGCAAGG
49782 GT
1 GT
49784 AGGTCGCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.42, T:0.27
Consensus pattern (12 bp):
GTTTGAGCAAGG
Found at i:49826 original size:29 final size:29
Alignment explanation
Indices: 49794--49869 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 29
49784 AGGTCGCCCT
*
49794 GAGTGCATGGCGACCTACAAGGTC-GTCTG
1 GAGTGCATGGCGACCTACAAGGTCGGTC-A
*
49823 GAGTGCATGGTGACCTACAAGGTCGGTCA
1 GAGTGCATGGCGACCTACAAGGTCGGTCA
49852 GAGTGCATGGCGACCTAC
1 GAGTGCATGGCGACCTAC
49870 GGCCAACACT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 40 0.93
30 3 0.07
ACGTcount: A:0.22, C:0.24, G:0.34, T:0.20
Consensus pattern (29 bp):
GAGTGCATGGCGACCTACAAGGTCGGTCA
Found at i:52195 original size:31 final size:31
Alignment explanation
Indices: 52160--52227 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
52150 TCGATAAAGT
*
52160 TTAAAAAATTATAAAA-TACTTATTAAATTTA
1 TTAAAAAATTATAAAATTA-TTAATAAATTTA
*
52191 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAATTATTAATAAATTTA
52222 TCTAAA
1 T-TAAA
52228 CTATAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 27 0.82
32 6 0.18
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (31 bp):
TTAAAAAATTATAAAATTATTAATAAATTTA
Found at i:53008 original size:2 final size:2
Alignment explanation
Indices: 53001--53033 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52991 ATTGAATTAA
53001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53034 ATAATGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53235 original size:2 final size:2
Alignment explanation
Indices: 53228--53252 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53218 AAGTGAATCT
53228 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
53253 GTAAGTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.