Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002049.1 Hibiscus syriacus cultivar Beakdansim tig00004173_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: 111340
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:9194 original size:21 final size:23
Alignment explanation
Indices: 9168--9213 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
9158 TTTTACAGTT
* *
9168 TCGAAT-TTTACAA-CATTTTAA
1 TCGAATATTTAAAATCATATTAA
9189 TCGAATATTTAAAATCATATTAA
1 TCGAATATTTAAAATCATATTAA
9212 TC
1 TC
9214 AGGTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 9 0.43
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.41
Consensus pattern (23 bp):
TCGAATATTTAAAATCATATTAA
Found at i:11279 original size:5 final size:5
Alignment explanation
Indices: 11263--11304 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
11253 AACTGGGTAA
* * *
11263 TCTTT TATTT TCCTT TCCTT TCTTT TCTTT TCTTT TCTTT TC
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TC
11305 CTTCAAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (5 bp):
TCTTT
Found at i:11294 original size:15 final size:15
Alignment explanation
Indices: 11263--11307 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
11253 AACTGGGTAA
*
11263 TCTTTTATTTTCCTT
1 TCTTTTCTTTTCCTT
* *
11278 TCCTTTCTTTTCTTT
1 TCTTTTCTTTTCCTT
11293 TCTTTTCTTTTCCTT
1 TCTTTTCTTTTCCTT
11308 CAAGAAACGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (15 bp):
TCTTTTCTTTTCCTT
Found at i:19615 original size:29 final size:30
Alignment explanation
Indices: 19552--19620 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
19542 AAAAACTTGG
* *
19552 ATTTTGAAATAAGAAAATAGAGGGACTATA
1 ATTTTGAAATAAGAAAATAGAGAGACTAAA
* *
19582 TTTTTGGAAAT-A-AAAATAGATAGACTAAA
1 ATTTT-GAAATAAGAAAATAGAGAGACTAAA
*
19611 ATTTTAAAAT
1 ATTTTGAAAT
19621 CTATAGAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.12
29 18 0.56
30 5 0.16
31 5 0.16
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (30 bp):
ATTTTGAAATAAGAAAATAGAGAGACTAAA
Found at i:19799 original size:31 final size:31
Alignment explanation
Indices: 19764--19822 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
19754 GGTTGTCTCC
* * *
19764 GTTTTTATTTAATTAAGATTTTGTCACTTTA
1 GTTTTAATTTAATTAAGATGTAGTCACTTTA
*
19795 GTTTTAATTTAGTTAAGATGTAGTCACT
1 GTTTTAATTTAATTAAGATGTAGTCACT
19823 AAAGATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.53
Consensus pattern (31 bp):
GTTTTAATTTAATTAAGATGTAGTCACTTTA
Found at i:20098 original size:2 final size:2
Alignment explanation
Indices: 20091--20119 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20081 ATTTAAAAAG
20091 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
20120 TGAAAAATTA
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:25046 original size:3 final size:3
Alignment explanation
Indices: 25040--25151 Score: 143
Period size: 3 Copynumber: 37.0 Consensus size: 3
25030 TTTATCCATT
* * * *
25040 TTA TTA TCA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
25088 TCA TTA TTA TTT TTA TTA TTT TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
25134 TTA TTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
25152 AATATATTAA
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
3 89 0.97
4 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:25046 original size:12 final size:11
Alignment explanation
Indices: 25025--25149 Score: 62
Period size: 12 Copynumber: 10.9 Consensus size: 11
25015 TGAAGATACT
*
25025 ATTTTTTTATCC
1 ATTTTATTAT-C
25037 ATTTTATTATC
1 ATTTTATTATC
25048 ATTATTATTAAT-
1 ATT-TTATT-ATC
25060 ATTATTATTATC
1 ATT-TTATTATC
* *
25072 ATTATTAATATT
1 ATT-TTATTATC
* *
25084 ATTATCATTATT
1 ATT-TTATTATC
25096 ATTTTTATTAT-
1 A-TTTTATTATC
25107 -TTTTATTAT-
1 ATTTTATTATC
*
25116 -TTATTATTATT
1 ATT-TTATTATC
*
25127 ATTATTATTATT
1 ATT-TTATTATC
25139 ATTTTTATTAT
1 A-TTTTATTAT
25150 TAAATATATT
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
9 11 0.11
10 7 0.07
11 6 0.06
12 69 0.70
13 6 0.06
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTTTATTATC
Found at i:26492 original size:19 final size:20
Alignment explanation
Indices: 26468--26506 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
26458 AATAATTAGT
*
26468 AATTAGTT-TTATTTTTATA
1 AATTAGTTATTAATTTTATA
26487 AATTAGTTATTAATTTTATA
1 AATTAGTTATTAATTTTATA
26507 TGTCTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
AATTAGTTATTAATTTTATA
Found at i:26597 original size:22 final size:20
Alignment explanation
Indices: 26556--26600 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
26546 ATAGAATTAT
**
26556 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
26576 TATTTTGATATATATTCATAAA
1 TATTTT-AT-TATATTCATAAA
26598 TAT
1 TAT
26601 ATATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Found at i:37878 original size:1 final size:1
Alignment explanation
Indices: 37872--37931 Score: 75
Period size: 1 Copynumber: 60.0 Consensus size: 1
37862 CTTGAAGAAG
* * * * *
37872 AAAAAAAGAGAAAAAAGAAAAAAAAAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
37932 GAGGGGTCAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:37886 original size:11 final size:10
Alignment explanation
Indices: 37866--37931 Score: 84
Period size: 9 Copynumber: 6.7 Consensus size: 10
37856 ATTATGCTTG
37866 AAGAAGAAAAA
1 AAGAA-AAAAA
*
37877 AAG-AGAAAA
1 AAGAAAAAAA
37886 AAGAAAAAAA
1 AAGAAAAAAA
37896 AA-AAAAAAA
1 AAGAAAAAAA
37905 AAGAAAAAAAA
1 AAG-AAAAAAA
37916 AAGAAAAAAA
1 AAGAAAAAAA
37926 AA-AAAA
1 AAGAAAA
37932 GAGGGGTCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
9 20 0.40
10 17 0.34
11 13 0.26
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:37909 original size:26 final size:25
Alignment explanation
Indices: 37873--37933 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
37863 TTGAAGAAGA
*
37873 AAAAAAGAGAAAAAAGAAAAAAAAAA
1 AAAAAAAAGAAAAAA-AAAAAAAAAA
*
37899 AAAAAAAAGAAAAAAAAAAGAAAAA
1 AAAAAAAAGAAAAAAAAAAAAAAAA
37924 AAAAAAAAGA
1 AAAAAAAAGA
37934 GGGGTCAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (25 bp):
AAAAAAAAGAAAAAAAAAAAAAAAA
Found at i:38279 original size:16 final size:16
Alignment explanation
Indices: 38260--38302 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
38250 ATTTCAAGTG
*
38260 CAATTTATTTGAGATT
1 CAATTTATTTGAAATT
*
38276 CAATTCATTTTTGAAATT
1 CAATT--TATTTGAAATT
38294 CAATTTATT
1 CAATTTATT
38303 CTTTTCTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (16 bp):
CAATTTATTTGAAATT
Found at i:38939 original size:52 final size:52
Alignment explanation
Indices: 38861--39365 Score: 902
Period size: 52 Copynumber: 9.7 Consensus size: 52
38851 TATGTGCTCA
* * *
38861 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
38913 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
38965 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
*
39017 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTAATCTGGTTAGACAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
*
39069 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
39121 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
39173 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
* * *
39225 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
* *
39277 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
* *
39329 ATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGAT
39366 TTGATTGGAC
Statistics
Matches: 438, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 438 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGGTATCTGATCTGGTTAGACAGAAT
Found at i:40215 original size:119 final size:119
Alignment explanation
Indices: 40004--40574 Score: 1010
Period size: 119 Copynumber: 4.8 Consensus size: 119
39994 CAAAGATTCA
*
40004 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
40069 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
*
40123 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCATC
1 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
*
40188 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
40242 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
40307 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
40361 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
* *
40426 TGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * *
40480 AATTCATC-AGTTGATGGATCAACATTACCAG-GTAA-AGTTCATAATGAGAAGAA--C-TCATC
1 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
*
40539 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
66 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
40575 CATCAAGAGC
Statistics
Matches: 438, Mismatches: 14, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
113 38 0.09
114 1 0.00
116 18 0.04
117 3 0.01
118 20 0.05
119 358 0.82
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (119 bp):
AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:40831 original size:3 final size:3
Alignment explanation
Indices: 40825--40936 Score: 143
Period size: 3 Copynumber: 37.0 Consensus size: 3
40815 TTTATCCATT
* * * *
40825 TTA TTA TCA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
40873 TCA TTA TTA TTT TTA TTA TTT TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
40919 TTA TTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
40937 AATATATTAA
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
3 89 0.97
4 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:40831 original size:12 final size:11
Alignment explanation
Indices: 40810--40934 Score: 62
Period size: 12 Copynumber: 10.9 Consensus size: 11
40800 TGAAGATACT
*
40810 ATTTTTTTATCC
1 ATTTTATTAT-C
40822 ATTTTATTATC
1 ATTTTATTATC
40833 ATTATTATTAAT-
1 ATT-TTATT-ATC
40845 ATTATTATTATC
1 ATT-TTATTATC
* *
40857 ATTATTAATATT
1 ATT-TTATTATC
* *
40869 ATTATCATTATT
1 ATT-TTATTATC
40881 ATTTTTATTAT-
1 A-TTTTATTATC
40892 -TTTTATTAT-
1 ATTTTATTATC
*
40901 -TTATTATTATT
1 ATT-TTATTATC
*
40912 ATTATTATTATT
1 ATT-TTATTATC
40924 ATTTTTATTAT
1 A-TTTTATTAT
40935 TAAATATATT
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
9 11 0.11
10 7 0.07
11 6 0.06
12 69 0.70
13 6 0.06
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTTTATTATC
Found at i:42276 original size:19 final size:20
Alignment explanation
Indices: 42252--42290 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42242 AATAATTAGT
*
42252 AATTAGTT-TTATTTTTATA
1 AATTAGTTATTAATTTTATA
42271 AATTAGTTATTAATTTTATA
1 AATTAGTTATTAATTTTATA
42291 TGTCTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
AATTAGTTATTAATTTTATA
Found at i:46765 original size:14 final size:14
Alignment explanation
Indices: 46743--46799 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
46733 GGTTCGTGAA
*
46743 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
46757 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
46771 CG--T--TTATGTT
1 CGTTTGGTTATGTT
* *
46781 CGTTCGATTATGTT
1 CGTTTGGTTATGTT
46795 CGTTT
1 CGTTT
46800 ATGTTCATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.25
12 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:46771 original size:24 final size:24
Alignment explanation
Indices: 46744--46818 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
46734 GTTCGTGAAC
* * *
46744 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
46768 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
46792 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
46816 GTT
1 GTT
46819 TAACCCAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:47555 original size:10 final size:10
Alignment explanation
Indices: 47540--47597 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 10
47530 GGGTCTCCAA
47540 CGTTTATGTT
1 CGTTTATGTT
47550 CGTTTATGTT
1 CGTTTATGTT
47560 CG----TGTT
1 CGTTTATGTT
47566 CGTTTATGTT
1 CGTTTATGTT
47576 CG----TGTT
1 CGTTTATGTT
47582 C-TTTATGTT
1 CGTTTATGTT
47591 CGTTTAT
1 CGTTTAT
47598 TTATTAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 18
0.68 0.00 0.32
Matches are distributed among these distances:
6 11 0.28
9 5 0.13
10 23 0.59
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:47567 original size:16 final size:16
Alignment explanation
Indices: 47546--47593 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
47536 CCAACGTTTA
47546 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
47562 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
47578 TGTTC-TTTATGTTCG
1 TGTTCGTTTATGTTCG
47593 T
1 T
47594 TTATTTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 11 0.34
16 21 0.66
ACGTcount: A:0.06, C:0.12, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:47684 original size:16 final size:16
Alignment explanation
Indices: 47663--47695 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
47653 AAAAAAATTT
47663 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
47679 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
47695 T
1 T
47696 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:53365 original size:15 final size:17
Alignment explanation
Indices: 53328--53366 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
53318 ATTTTACAAT
53328 TAATTTA-AATAATATA
1 TAATTTATAATAATATA
53344 TAA-TTATAA-AATATA
1 TAATTTATAATAATATA
53359 -AATTTATA
1 TAATTTATA
53367 TATATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.10
15 14 0.67
16 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTATAATAATATA
Found at i:56919 original size:19 final size:18
Alignment explanation
Indices: 56888--56924 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
56878 CATTAAAAAC
*
56888 CCGATAAACCGAACCGAA
1 CCGAAAAACCGAACCGAA
56906 CCGAAAAACTCGAACCGAA
1 CCGAAAAAC-CGAACCGAA
56925 AAAACCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.32, G:0.16, T:0.05
Consensus pattern (18 bp):
CCGAAAAACCGAACCGAA
Found at i:69721 original size:2 final size:2
Alignment explanation
Indices: 69714--69803 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
69704 ACCGTAAACA
69714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69798 AT AT AT
1 AT AT AT
69804 GAAAAAATGA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72423 original size:27 final size:27
Alignment explanation
Indices: 72385--72438 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
72375 CTCGGTTCAT
*
72385 CTTCTTCAACCTGCCGTGACTCCATAG
1 CTTCTTCAACCTGCCATGACTCCATAG
72412 CTTCTTCAACCTGCCATGACTCCATAG
1 CTTCTTCAACCTGCCATGACTCCATAG
72439 TCAAGGTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.30
Consensus pattern (27 bp):
CTTCTTCAACCTGCCATGACTCCATAG
Found at i:78705 original size:29 final size:29
Alignment explanation
Indices: 78662--78722 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
78652 TTTGGATGAA
*
78662 TTTGTGGATGAAATTGGAA-GATTCAAAAG
1 TTTGGGGATGAAATTGGAATG-TTCAAAAG
* *
78691 TTTGGGGATGCAATTGGAATGTTTAAAAG
1 TTTGGGGATGAAATTGGAATGTTCAAAAG
78720 TTT
1 TTT
78723 AAGGATCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
TTTGGGGATGAAATTGGAATGTTCAAAAG
Found at i:78728 original size:29 final size:29
Alignment explanation
Indices: 78667--78733 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
78657 ATGAATTTGT
* **
78667 GGATGAAATTGGAAGATTCAAAAGTTTGG
1 GGATGCAATTGGAAGATTCAAAAGTTTAA
*
78696 GGATGCAATTGGAATG-TTTAAAAGTTTAA
1 GGATGCAATTGGAA-GATTCAAAAGTTTAA
78725 GGAT-CAATT
1 GGATGCAATT
78734 TAGAATGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.15
29 27 0.82
30 1 0.03
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.31
Consensus pattern (29 bp):
GGATGCAATTGGAAGATTCAAAAGTTTAA
Found at i:80301 original size:35 final size:34
Alignment explanation
Indices: 80242--80353 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 34
80232 AAAACATTCC
* *
80242 TCAATTTCATTATAAATCCCAAATTTCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCAAATTTCAAAATAAT
*
80277 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTTCAAAATAAT
* *
80312 TCAATTACATTCTAAACCCCAAA-TTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTTC-AAAATAAT
80347 TCAATTT
1 TCAATTT
80354 AAGGAGAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
34 5 0.07
35 59 0.88
36 3 0.04
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTTCAAAATAAT
Found at i:81618 original size:35 final size:34
Alignment explanation
Indices: 81569--81681 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
81559 AAAAAAGACA
* *
81569 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
81604 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
81639 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
81674 GAAATTGA
1 GAAATTGA
81682 GAATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:94109 original size:31 final size:32
Alignment explanation
Indices: 94020--94158 Score: 126
Period size: 32 Copynumber: 4.4 Consensus size: 32
94010 CCTCGGCAAT
* *
94020 TGTCCATAGGTCCCGAAGGAC-CTAGGTAA-AC
1 TGTCCATATGTCCCGAAAGACAC-AGGTAATAC
* ** * *
94051 TATCCATATGTTCCTTATA-ACATAGGT-ATAC
1 TGTCCATATG-TCCCGAAAGACACAGGTAATAC
*
94082 TGTCCATATGTCCCGAAAGACACAGGTAATTC
1 TGTCCATATGTCCCGAAAGACACAGGTAATAC
* *
94114 TGTCCATGTGTCCCGAAAGACATAGGTAATTA-
1 TGTCCATATGTCCCGAAAGACACAGGTAA-TAC
94146 TGTCCATATGTCC
1 TGTCCATATGTCC
94159 TGTAGAACAT
Statistics
Matches: 85, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
30 6 0.07
31 32 0.38
32 46 0.54
33 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAAGACACAGGTAATAC
Found at i:94126 original size:32 final size:32
Alignment explanation
Indices: 94081--94158 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
94071 CATAGGTATA
94081 CTGTCCATATGTCCCGAAAGACACAGGTAATT
1 CTGTCCATATGTCCCGAAAGACACAGGTAATT
* *
94113 CTGTCCATGTGTCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTCCCGAAAGACACAGGTAATT
*
94145 ATGTCCATATGTCC
1 CTGTCCATATGTCC
94159 TGTAGAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (32 bp):
CTGTCCATATGTCCCGAAAGACACAGGTAATT
Found at i:94174 original size:32 final size:32
Alignment explanation
Indices: 94070--94158 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
94060 GTTCCTTATA
94070 ACATAGGT-A-TACTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTA-TGTCCATATGTCCCGAAAG
* * *
94101 ACACAGGTAATTCTGTCCATGTGTCCCGAAAG
1 ACATAGGTAATTATGTCCATATGTCCCGAAAG
94133 ACATAGGTAATTATGTCCATATGTCC
1 ACATAGGTAATTATGTCCATATGTCC
94159 TGTAGAACAT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 7 0.14
32 42 0.84
33 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (32 bp):
ACATAGGTAATTATGTCCATATGTCCCGAAAG
Found at i:100378 original size:18 final size:18
Alignment explanation
Indices: 100341--100380 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
100331 TTTAATTTCG
100341 TTTAATCATCTAGTTATTT
1 TTTAATCATCTAG-TATTT
100360 TTTAATCATCATA-TATTT
1 TTTAATCATC-TAGTATTT
100378 TTT
1 TTT
100381 TTTATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 10 0.50
20 2 0.10
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTAATCATCTAGTATTT
Found at i:103289 original size:10 final size:10
Alignment explanation
Indices: 103274--103359 Score: 51
Period size: 10 Copynumber: 9.0 Consensus size: 10
103264 GGTAAAAATT
103274 ATAATAAAAA
1 ATAATAAAAA
*
103284 ATAATAAAAG
1 ATAATAAAAA
103294 ATAA-AATAAA
1 ATAATAA-AAA
*
103304 AT-A-AAATA
1 ATAATAAAAA
103312 AT-ATAATAAA
1 ATAATAA-AAA
*
103322 A-GA-AAAAA
1 ATAATAAAAA
*
103330 ATAACAAAAA
1 ATAATAAAAA
103340 A-AAGTAAAAA
1 ATAA-TAAAAA
*
103350 ATAACAAAAA
1 ATAATAAAAA
103360 CCAAAATCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
8 9 0.15
9 12 0.20
10 38 0.62
11 2 0.03
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.16
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:103321 original size:18 final size:18
Alignment explanation
Indices: 103298--103332 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
103288 TAAAAGATAA
* *
103298 AATAAAATAAAATAATAT
1 AATAAAAGAAAAAAATAT
103316 AATAAAAGAAAAAAATA
1 AATAAAAGAAAAAAATA
103333 ACAAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
AATAAAAGAAAAAAATAT
Found at i:103329 original size:20 final size:20
Alignment explanation
Indices: 103319--103359 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
103309 ATAATATAAT
103319 AAAAGAAAAAAATAACAAAA
1 AAAAGAAAAAAATAACAAAA
*
103339 AAAAGTAAAAAATAACAAAA
1 AAAAGAAAAAAATAACAAAA
103359 A
1 A
103360 CCAAAATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.83, C:0.05, G:0.05, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAAAATAACAAAA
Found at i:104044 original size:16 final size:16
Alignment explanation
Indices: 104023--104058 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
104013 TGTTAGTTTT
104023 TTTAATTATTTTATTA
1 TTTAATTATTTTATTA
*
104039 TTTAATTTTTTTATTA
1 TTTAATTATTTTATTA
104055 TTTA
1 TTTA
104059 TTTAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTAATTATTTTATTA
Found at i:104052 original size:13 final size:12
Alignment explanation
Indices: 104019--104070 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
104009 ATTTTGTTAG
*
104019 TTTTTTTAATTA
1 TTTTTTTATTTA
*
104031 TTTTATTATTTAA
1 TTTTTTTATTT-A
104044 TTTTTTTA-TTA
1 TTTTTTTATTTA
* *
104055 TTTATTTAATTA
1 TTTTTTTATTTA
104067 TTTT
1 TTTT
104071 ATTTTTTTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
11 8 0.24
12 17 0.52
13 8 0.24
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTTTATTTA
Found at i:104060 original size:28 final size:27
Alignment explanation
Indices: 104019--104078 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 27
104009 ATTTTGTTAG
*
104019 TTTTTTTAATTATTTTATTATTTAATT
1 TTTTTTTAATTATTTAATTATTTAATT
* *
104046 TTTTTATTATTTATTTAATTATTTTATT
1 TTTTT-TTAATTATTTAATTATTTAATT
104074 TTTTT
1 TTTTT
104079 GTAGTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTTTTTAATTATTTAATTATTTAATT
Found at i:104061 original size:20 final size:20
Alignment explanation
Indices: 104008--104073 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
103998 AATTTAATCA
* *
104008 TATTTTGTTAGTTTTTTTAAT
1 TATTTTATTA-TTTATTTAAT
104029 TA--TT-TTA-TTATTTAAT
1 TATTTTATTATTTATTTAAT
*
104045 TTTTTTATTATTTATTTAAT
1 TATTTTATTATTTATTTAAT
104065 TATTTTATT
1 TATTTTATT
104074 TTTTTGTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 9 0.24
18 5 0.13
19 5 0.13
20 17 0.45
21 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (20 bp):
TATTTTATTATTTATTTAAT
Found at i:104339 original size:8 final size:8
Alignment explanation
Indices: 104323--104361 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
104313 TATTACTGTA
*
104323 AAAAAAAT
1 AAAATAAT
104331 AAAATAAT
1 AAAATAAT
104339 AAAATAAT
1 AAAATAAT
*
104347 ACAATAAT
1 AAAATAAT
*
104355 TAAATAA
1 AAAATAA
104362 AATACTAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Done.