Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006553.1 Hibiscus syriacus cultivar Beakdansim tig00016016_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: 51149
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:619 original size:15 final size:15
Alignment explanation
Indices: 589--640 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 15
579 TTATTTAAGT
589 TTTTTTAATTTCATAAA
1 TTTTTT-ATTT-ATAAA
606 TTTTTTATTTAT-AA
1 TTTTTTATTTATAAA
*
620 -TTTTTATTTTTAAA
1 TTTTTTATTTATAAA
*
634 TATTTTA
1 TTTTTTA
641 GATGACGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 10 0.32
14 4 0.13
15 7 0.23
16 4 0.13
17 6 0.19
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTATTTATAAA
Found at i:3193 original size:2 final size:2
Alignment explanation
Indices: 3186--3218 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3176 TTCCGTAAAT
3186 TA TA 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 TA TA T
3219 TGTAGATTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9395 original size:21 final size:22
Alignment explanation
Indices: 9371--9411 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
9361 GTGAATTTAG
*
9371 GGGAGGAGGAGGA-GGAGAGGT
1 GGGACGAGGAGGAGGGAGAGGT
*
9392 GGGACGAGGCGGAGGGAGAG
1 GGGACGAGGAGGAGGGAGAG
9412 ATGGTGGCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.05, G:0.66, T:0.02
Consensus pattern (22 bp):
GGGACGAGGAGGAGGGAGAGGT
Found at i:10836 original size:25 final size:22
Alignment explanation
Indices: 10783--10837 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 22
10773 GCCTACAAAC
*
10783 TATCTAATTTAAAATATTTCTT
1 TATCTAATTCAAAATATTTCTT
*
10805 TATTCTAATTACAAATATATTTTTTT
1 TA-TCTAATT-CAAA-ATA-TTTCTT
10831 TATCTAA
1 TATCTAA
10838 AACATAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.07
23 7 0.26
24 3 0.11
25 8 0.30
26 7 0.26
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (22 bp):
TATCTAATTCAAAATATTTCTT
Found at i:11377 original size:12 final size:13
Alignment explanation
Indices: 11335--11390 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
11325 ATTTCAGAAC
* *
11335 TTTCATATTTCGT
1 TTTCACATTTCAT
*
11348 TTTCATC-TTTCAC
1 TTTCA-CATTTCAT
*
11361 ATTCACA-TTCAT
1 TTTCACATTTCAT
11373 TTTCACATTTCAT
1 TTTCACATTTCAT
11386 TTTCA
1 TTTCA
11391 TAACCAATAC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 11 0.32
13 23 0.68
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.54
Consensus pattern (13 bp):
TTTCACATTTCAT
Found at i:11469 original size:19 final size:19
Alignment explanation
Indices: 11437--11489 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
11427 TTTAGAAGTT
*
11437 ATTTCCAAACTCATAACCTA
1 ATTT-CAAATTCATAACCTA
* * * *
11457 TTTTCATATTCATAGCTTA
1 ATTTCAAATTCATAACCTA
11476 ATTTCAAATTCATA
1 ATTTCAAATTCATA
11490 GCCCAATGCA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 23 0.88
20 3 0.12
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTTCAAATTCATAACCTA
Found at i:14948 original size:20 final size:20
Alignment explanation
Indices: 14904--15171 Score: 207
Period size: 20 Copynumber: 13.2 Consensus size: 20
14894 AATGACCAAC
*
14904 AAAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
*
14923 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
14943 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
14963 AAAATCGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
14983 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
15005 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
15025 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
15047 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
15067 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
15087 AGAATCGCAATGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
15107 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
15127 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
15147 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
15167 AAAAT
1 AAAAT
15172 GAGTAAATTC
Statistics
Matches: 210, Mismatches: 18, Indels: 41
0.78 0.07 0.15
Matches are distributed among these distances:
18 3 0.01
19 22 0.10
20 145 0.69
21 7 0.03
22 29 0.14
23 2 0.01
25 1 0.00
26 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:15102 original size:40 final size:41
Alignment explanation
Indices: 14985--15164 Score: 235
Period size: 40 Copynumber: 4.4 Consensus size: 41
14975 GTCAAAAGAA
* *
14985 AATCGCAACGCGATATTCCAAGAATCGCAATGCGATT-AAGAG
1 AATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTCCAGAG
*
15027 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT-CAGAA
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCCAGAG
*
15069 AATCGCAACGCGATTCCAAGAATCGCAATGCGATTCCA-AG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAGAG
*
15109 AATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCCAGAG
15149 AATCGCAACGCGATTC
1 AATCGCAACGCGATTC
15165 AGAAAATGAG
Statistics
Matches: 126, Mismatches: 7, Indels: 11
0.88 0.05 0.08
Matches are distributed among these distances:
39 2 0.02
40 73 0.58
41 2 0.02
42 49 0.39
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (41 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAGAG
Found at i:15130 original size:60 final size:60
Alignment explanation
Indices: 14985--15164 Score: 256
Period size: 60 Copynumber: 2.9 Consensus size: 60
14975 GTCAAAAGAA
* * *
14985 AATCGCAACGCGATATTCCA-AGAATCGCAATGCGATT-AAGAGAATCGCAACGCGATCTTCCAA
1 AATCGCAACGCG--ATT-CAGAAAATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TTCCAA
15048 G
60 G
*
15049 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAATGCGATTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
15109 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
15165 AGAAAATGAG
Statistics
Matches: 109, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
60 62 0.57
61 2 0.02
62 32 0.29
63 1 0.01
64 12 0.11
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (60 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
Found at i:15278 original size:6 final size:6
Alignment explanation
Indices: 15267--15497 Score: 462
Period size: 6 Copynumber: 38.5 Consensus size: 6
15257 GACACGTATT
15267 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
15315 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
15363 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
15411 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
15459 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
15498 CGAGACGAGA
Statistics
Matches: 225, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 225 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:16003 original size:6 final size:6
Alignment explanation
Indices: 15992--16120 Score: 258
Period size: 6 Copynumber: 21.5 Consensus size: 6
15982 TCTCGTCTCG
15992 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
16040 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
16088 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
16121 AATACGTGTC
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 123 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:16576 original size:20 final size:20
Alignment explanation
Indices: 16216--16603 Score: 352
Period size: 20 Copynumber: 19.2 Consensus size: 20
16206 GAATTTACTC
16216 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
16236 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
16256 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
16276 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
16296 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
16316 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
* *
16336 ATTTTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
16356 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
16376 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
16396 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
16416 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
16436 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
16456 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
16478 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
16498 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
16520 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
** *
16540 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
16560 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
16580 ATTTT-T-ATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
16599 ATTTT
1 ATTTT
16604 GTTGGTCATT
Statistics
Matches: 304, Mismatches: 37, Indels: 55
0.77 0.09 0.14
Matches are distributed among these distances:
17 1 0.00
18 2 0.01
19 26 0.09
20 224 0.74
21 22 0.07
22 28 0.09
25 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:19877 original size:70 final size:70
Alignment explanation
Indices: 19764--20077 Score: 448
Period size: 70 Copynumber: 4.5 Consensus size: 70
19754 GATCAATAAT
* * * * *
19764 TAAATATTGAAGTTGATTAAGTTGTATTGTCTGTCTATAATGTAGTAGAAACAAGTTCAAATCCT
1 TAAATATTGAAGTTGACTAAGTGGTATTGTATGTCTATAATGTAGCAGAACCAAGTTCAAATCCT
19829 TCAAC
66 TCAAC
* * * *
19834 TAAATATGGAAGTTGACCAAATGGTATTGTATGTCTATAATGTAGCAGAACCAAGCTCAAATCCT
1 TAAATATTGAAGTTGACTAAGTGGTATTGTATGTCTATAATGTAGCAGAACCAAGTTCAAATCCT
*
19899 TCAAT
66 TCAAC
* * * *
19904 TAAATATTGAAGTTGATTAAGTTGTATTGTCTGTCTATAATGTAGTAGAACCAAGTTCAAATCCT
1 TAAATATTGAAGTTGACTAAGTGGTATTGTATGTCTATAATGTAGCAGAACCAAGTTCAAATCCT
19969 TCAAC
66 TCAAC
* * * *
19974 TAAAAATGGAAGTTGACCAAATGGTATTGTATGTCTATAATGTAGCAGAACCAAGTTCAAATCCT
1 TAAATATTGAAGTTGACTAAGTGGTATTGTATGTCTATAATGTAGCAGAACCAAGTTCAAATCCT
*
20039 TCAAT
66 TCAAC
*
20044 TAAATATTGAAGTTGACTGAGTGGTATTGTATGT
1 TAAATATTGAAGTTGACTAAGTGGTATTGTATGT
20078 TTATCAATTT
Statistics
Matches: 211, Mismatches: 33, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 211 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (70 bp):
TAAATATTGAAGTTGACTAAGTGGTATTGTATGTCTATAATGTAGCAGAACCAAGTTCAAATCCT
TCAAC
Found at i:20013 original size:140 final size:140
Alignment explanation
Indices: 19761--20073 Score: 572
Period size: 140 Copynumber: 2.2 Consensus size: 140
19751 GTCGATCAAT
19761 AATTAAATATTGAAGTTGATTAAGTTGTATTGTCTGTCTATAATGTAGTAGAAACAAGTTCAAAT
1 AATTAAATATTGAAGTTGATTAAGTTGTATTGTCTGTCTATAATGTAGTAGAAACAAGTTCAAAT
*
19826 CCTTCAACTAAATATGGAAGTTGACCAAATGGTATTGTATGTCTATAATGTAGCAGAACCAAGCT
66 CCTTCAACTAAAAATGGAAGTTGACCAAATGGTATTGTATGTCTATAATGTAGCAGAACCAAGCT
19891 CAAATCCTTC
131 CAAATCCTTC
*
19901 AATTAAATATTGAAGTTGATTAAGTTGTATTGTCTGTCTATAATGTAGTAGAACCAAGTTCAAAT
1 AATTAAATATTGAAGTTGATTAAGTTGTATTGTCTGTCTATAATGTAGTAGAAACAAGTTCAAAT
*
19966 CCTTCAACTAAAAATGGAAGTTGACCAAATGGTATTGTATGTCTATAATGTAGCAGAACCAAGTT
66 CCTTCAACTAAAAATGGAAGTTGACCAAATGGTATTGTATGTCTATAATGTAGCAGAACCAAGCT
20031 CAAATCCTTC
131 CAAATCCTTC
* * *
20041 AATTAAATATTGAAGTTGACTGAGTGGTATTGT
1 AATTAAATATTGAAGTTGATTAAGTTGTATTGT
20074 ATGTTTATCA
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 167 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (140 bp):
AATTAAATATTGAAGTTGATTAAGTTGTATTGTCTGTCTATAATGTAGTAGAAACAAGTTCAAAT
CCTTCAACTAAAAATGGAAGTTGACCAAATGGTATTGTATGTCTATAATGTAGCAGAACCAAGCT
CAAATCCTTC
Found at i:25711 original size:12 final size:11
Alignment explanation
Indices: 25689--25730 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 11
25679 GAAGTAAGAG
25689 TCTTTTTCTTT
1 TCTTTTTCTTT
25700 TCTTTTTGCTTT
1 TCTTTTT-CTTT
25712 TCTTCTTTCTTT
1 TCTT-TTTCTTT
25724 TGCTTTT
1 T-CTTTT
25731 GTTGCATCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.25
12 15 0.54
13 6 0.21
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.76
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:25972 original size:15 final size:16
Alignment explanation
Indices: 25929--25974 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
25919 TATGAAATAA
25929 GAAATGGAAGAAGAAAG
1 GAAATGG-AGAAGAAAG
*
25946 GAAAT-GATAAGAAAG
1 GAAATGGAGAAGAAAG
25961 GAAATGGA-AAGAAA
1 GAAATGGAGAAGAAA
25975 TGATATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 19 0.70
16 3 0.11
17 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (16 bp):
GAAATGGAGAAGAAAG
Found at i:32809 original size:15 final size:16
Alignment explanation
Indices: 32789--32822 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
32779 CCGACCCAAC
32789 CCGTTGACT-CGTTGA
1 CCGTTGACTCCGTTGA
32804 CCGTTGACTGCCGTTGA
1 CCGTTGACT-CCGTTGA
32821 CC
1 CC
32823 ACCATTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.32, G:0.26, T:0.29
Consensus pattern (16 bp):
CCGTTGACTCCGTTGA
Found at i:35670 original size:89 final size:88
Alignment explanation
Indices: 35529--35764 Score: 395
Period size: 89 Copynumber: 2.7 Consensus size: 88
35519 GGTAAGACCT
*
35529 TACGGACCTAAGGATA-CCTTGGGTAGG-CTATAGGCCCCAAGGCATATCCTTAGGTTGGTTTCA
1 TACGGACCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGG-ATATCCTTAGGTTGGTTTCA
*
35592 TTTATTGTATGCATAGGGTAACCC
65 TTTACTGTATGCATAGGGTAACCC
35616 TACGGACCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGTATATCCTTAGGTTGGTTTCA
1 TACGGACCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGG-ATATCCTTAGGTTGGTTTCA
* *
35681 TTTGCTGTGTGCATAGGGTAACCC
65 TTTACTGTATGCATAGGGTAACCC
35705 TACGGACCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGATTATCCTTAGGTTGG
1 TACGGACCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGA-TATCCTTAGGTTGG
35765 CTCCCTTTTG
Statistics
Matches: 141, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
87 16 0.11
88 12 0.09
89 113 0.80
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.28
Consensus pattern (88 bp):
TACGGACCTAAGGATACCCTTGGGTAGGCCCATAGGCCCCAAGGATATCCTTAGGTTGGTTTCAT
TTACTGTATGCATAGGGTAACCC
Found at i:40624 original size:40 final size:40
Alignment explanation
Indices: 40572--40650 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
40562 TGCAGGTTTA
40572 TAATACACTTCGGTATATATGGTGAGCACAACCTTATGTT
1 TAATACACTTCGGTATATATGGTGAGCACAACCTTATGTT
* * * *
40612 TAATACACTTCGGTGTATATGGTGGGTACGACCTTATGT
1 TAATACACTTCGGTATATATGGTGAGCACAACCTTATGT
40651 GTAGCATTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (40 bp):
TAATACACTTCGGTATATATGGTGAGCACAACCTTATGTT
Found at i:40736 original size:20 final size:20
Alignment explanation
Indices: 40711--40753 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
40701 AATATTGGGC
* *
40711 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
40731 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
40751 TAT
1 TAT
40754 GGAATAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:40884 original size:46 final size:44
Alignment explanation
Indices: 40750--40894 Score: 184
Period size: 44 Copynumber: 3.2 Consensus size: 44
40740 TGGTATATGG
** * *
40750 TTATGGAATAATGGCAAGTGTATTAGTAAAATAAGCTTACGAGC
1 TTATGGAATAATGATAAGTATATTGGTAAAATAAGCTTACGAGC
*
40794 TTATGGAATAATGATAAATATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAATGATAAGTATATTGGTAAAATAAGCTTACGAGC
* *
40838 TTATGGTATTAAATTG-TAAGTATATTGGTAAAATAAGCTTATGAGC
1 TTATGG-AAT-AA-TGATAAGTATATTGGTAAAATAAGCTTACGAGC
*
40884 TTATGGGATAA
1 TTATGGAATAA
40895 ATGGTAAAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
44 47 0.53
45 3 0.03
46 36 0.41
47 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (44 bp):
TTATGGAATAATGATAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:45555 original size:22 final size:21
Alignment explanation
Indices: 45487--45580 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 21
45477 GCCATTTTGC
* *
45487 ATCGATGTACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
45510 ATCGGTGCACCTTC-ATGTGT
1 ATCGATGCACATTCAAGGTGT
45530 ATCGATGCACATTCAAGGATGT
1 ATCGATGCACATTCAAGG-TGT
*
45552 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
45572 ATCGATGCA
1 ATCGATGCA
45581 TGAAGCACAA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
20 27 0.46
21 6 0.10
22 15 0.25
23 11 0.19
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:49260 original size:20 final size:20
Alignment explanation
Indices: 49223--49261 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
49213 GAAGCTTTAA
** *
49223 GATCATCATTTTCTTTTGAT
1 GATCATCATTGACCTTTGAT
49243 GATCATCATTGACCTTTGA
1 GATCATCATTGACCTTTGA
49262 AAGTAAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (20 bp):
GATCATCATTGACCTTTGAT
Done.