Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002413.1 Hibiscus syriacus cultivar Beakdansim tig00004935_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: 57794
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:82 original size:20 final size:20
Alignment explanation
Indices: 45--87 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
35 ATTCTGTCGT
*
45 TTGAAGGGTAGCGGTTCCCC
1 TTGAAGGGTAGCGATTCCCC
65 TTGAATGGGTA-CGATTCCCC
1 TTGAA-GGGTAGCGATTCCCC
85 TTG
1 TTG
88 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.30
Consensus pattern (20 bp):
TTGAAGGGTAGCGATTCCCC
Found at i:16450 original size:23 final size:23
Alignment explanation
Indices: 16424--16471 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
16414 ATAAAGTACA
*
16424 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
16447 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
16470 AT
1 AT
16472 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:17145 original size:327 final size:334
Alignment explanation
Indices: 16511--17173 Score: 1205
Period size: 327 Copynumber: 2.0 Consensus size: 334
16501 TTATACCGAT
* * *
16511 AGCATTGTAAATTTTCCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAATGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
*
16576 TCGATATTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
16641 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
131 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
* *
16706 TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATT
196 TAAAATAATATTTAGAATTTTTAATTT-ATAATAATATATATCGTAACGAAAAAAATAAATCATT
16771 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
260 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
16836 TTCCACAGTG
325 TTCCACAGTG
16846 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
16911 TCGATACTTCTTTTAAAGTTATGTAA-TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
*
16974 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGA-TG-TTTGATATTTTG
131 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
17037 TAAAATAATATTTAGAA-TTTTAA-TT-TAATAATATATATCGTAACGAAAAAAATAAATCATTA
196 TAAAATAATATTTAGAATTTTTAATTTATAATAATATATATCGTAACGAAAAAAATAAATCATTA
17099 GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
261 GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
17164 TCCACAGTG
326 TCCACAGTG
17173 A
1 A
17174 AAAAAGTATG
Statistics
Matches: 321, Mismatches: 7, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
327 111 0.35
329 2 0.01
330 6 0.02
331 27 0.08
332 2 0.01
333 75 0.23
334 11 0.03
335 87 0.27
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (334 bp):
AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
TAAAATAATATTTAGAATTTTTAATTTATAATAATATATATCGTAACGAAAAAAATAAATCATTA
GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
TCCACAGTG
Found at i:17288 original size:23 final size:23
Alignment explanation
Indices: 17226--17288 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
17216 ATATAACCAC
* *
17226 TACCTATTACATTATACAAATGA
1 TACCTATTACATTATATAAACGA
* *
17249 TACCTATTACATTATATAAGCGT
1 TACCTATTACATTATATAAACGA
*
17272 TACCTATTACATCATAT
1 TACCTATTACATTATAT
17289 GTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:18400 original size:17 final size:18
Alignment explanation
Indices: 18378--18420 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
18368 CAATATCCGG
18378 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
18395 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
18415 TATCAT
1 TATCAT
18421 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:18576 original size:20 final size:20
Alignment explanation
Indices: 18550--18595 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
18540 CACTTTTAAA
18550 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
18569 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
18590 TTTACC
1 TTTACC
18596 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:24783 original size:28 final size:29
Alignment explanation
Indices: 24743--24817 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
24733 GAGGAGCAGG
*
24743 AGGAGTGCCTGGCGACCTTGTA-GTCGCC
1 AGGAGTGCATGGCGACCTTGTAGGTCGCC
24771 AGGAGTGCATGGCGACCTTGTAGGTCGCC
1 AGGAGTGCATGGCGACCTTGTAGGTCGCC
*
24800 CGGAGTGCATGGCGACCT
1 AGGAGTGCATGGCGACCT
24818 ATGCTGGGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 21 0.48
29 23 0.52
ACGTcount: A:0.16, C:0.27, G:0.37, T:0.20
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTTGTAGGTCGCC
Found at i:29608 original size:23 final size:25
Alignment explanation
Indices: 29567--29619 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 25
29557 ATAAATTTTA
29567 ATTTATAAAAAATTATCTATTTTAAG
1 ATTTATAAAAAATTATCTA-TTTAAG
29593 ATTTA-AAAAAA-T-TCTATTTAAG
1 ATTTATAAAAAATTATCTATTTAAG
*
29615 GTTTA
1 ATTTA
29620 GAATTTGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 10 0.38
23 4 0.15
24 1 0.04
25 6 0.23
26 5 0.19
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (25 bp):
ATTTATAAAAAATTATCTATTTAAG
Found at i:29714 original size:20 final size:21
Alignment explanation
Indices: 29689--29727 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29679 ATTAATATTT
29689 TAAAAA-TAAATTAAAAAAAG
1 TAAAAAGTAAATTAAAAAAAG
*
29709 TAAAAAGTAATTTAAAAAA
1 TAAAAAGTAAATTAAAAAA
29728 TTAAATAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (21 bp):
TAAAAAGTAAATTAAAAAAAG
Found at i:29732 original size:20 final size:20
Alignment explanation
Indices: 29688--29732 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
29678 GATTAATATT
29688 TTAAAAATAAATTAAAAAAA
1 TTAAAAATAAATTAAAAAAA
* *
29708 GTAAAAAGT-AATTTAAAAAA
1 TTAAAAA-TAAATTAAAAAAA
29728 TTAAA
1 TTAAA
29733 TAGACGGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (20 bp):
TTAAAAATAAATTAAAAAAA
Found at i:31665 original size:20 final size:20
Alignment explanation
Indices: 31642--31693 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
31632 TTAATATTAA
31642 TATAAATTAATCA-ATTATAT
1 TATAAATTAAT-ATATTATAT
31662 TATAATAATATAATATATTATAT
1 TAT-A-AAT-TAATATATTATAT
*
31685 AATAAATTA
1 TATAAATTA
31694 TTAATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
20 5 0.19
21 4 0.15
22 5 0.19
23 13 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAAATTAATATATTATAT
Found at i:31685 original size:25 final size:25
Alignment explanation
Indices: 31583--31685 Score: 65
Period size: 25 Copynumber: 4.1 Consensus size: 25
31573 AATTATTAAA
*
31583 ATATT-TAA-AATAT-ATTTATTA-
1 ATATTATAATAATATAATATATTAT
*
31604 ATATTTATAATAATATAATATAATAT
1 ATA-TTATAATAATATAATATATTAT
* * *
31630 -TTTTAATATTAATATAA-ATTAATCAATT
1 ATATT-ATAATAATATAATA-T-AT-TA-T
31658 ATATTATAATAATATAATATATTAT
1 ATATTATAATAATATAATATATTAT
31683 ATA
1 ATA
31686 ATAAATTATT
Statistics
Matches: 61, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
21 3 0.05
22 2 0.03
23 3 0.05
24 8 0.13
25 23 0.38
26 2 0.03
27 3 0.05
28 13 0.21
29 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATTATAATAATATAATATATTAT
Found at i:31704 original size:12 final size:12
Alignment explanation
Indices: 31649--31701 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
31639 TAATATAAAT
*
31649 TAATCAATTATA
1 TAATAAATTATA
* *
31661 TTAT-AATAATA
1 TAATAAATTATA
*
31672 TAATATATTATA
1 TAATAAATTATA
31684 TAATAAATTAT-
1 TAATAAATTATA
31695 TAATAAA
1 TAATAAA
31702 ATTTATATCA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 16 0.47
12 18 0.53
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATAAATTATA
Found at i:31776 original size:8 final size:7
Alignment explanation
Indices: 31763--31839 Score: 50
Period size: 8 Copynumber: 10.7 Consensus size: 7
31753 ATGAATATAT
31763 TATTTAAA
1 TATTT-AA
31771 TATTTAA
1 TATTTAA
31778 TA-TTAA
1 TATTTAA
*
31784 TATAATAA
1 TAT-TTAA
31792 TATTTTAA
1 TA-TTTAA
31800 TATTTTAA
1 TA-TTTAA
**
31808 TAAAT-A
1 TATTTAA
31814 TATTTAA
1 TATTTAA
* *
31821 AATATAA
1 TATTTAA
*
31828 TAATTAA
1 TATTTAA
31835 TATTT
1 TATTT
31840 TTAAAATATA
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
6 10 0.19
7 19 0.36
8 23 0.43
9 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (7 bp):
TATTTAA
Found at i:31807 original size:30 final size:34
Alignment explanation
Indices: 31731--31809 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 34
31721 TTCATAGAAA
31731 TAATATTATTAAATTATTAATAATGAATATATTATTT
1 TAATATT-TT-AA-TATTAATAATGAATATATTATTT
*
31768 AAATA-TTTAATATTAAT-AT-AATA-A-TATTT
1 TAATATTTTAATATTAATAATGAATATATTATTT
31797 TAATATTTTAATA
1 TAATATTTTAATA
31810 AATATATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 9 0.23
30 8 0.21
31 4 0.10
32 2 0.05
33 7 0.18
34 2 0.05
35 2 0.05
36 1 0.03
37 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (34 bp):
TAATATTTTAATATTAATAATGAATATATTATTT
Found at i:31814 original size:34 final size:33
Alignment explanation
Indices: 31776--31855 Score: 76
Period size: 35 Copynumber: 2.4 Consensus size: 33
31766 TTAAATATTT
*
31776 AATATTAATATAATAATATTTTAATATTTTAATAA
1 AATATTAATATAATAATA-ATTAATATTTTAA-AA
* *
31811 ATATATTTAAAAT-ATAATAATTAATATTTT-TAA
1 A-ATA-TTAATATAATAATAATTAATATTTTAAAA
31844 AATA-TAATATAA
1 AATATTAATATAA
31856 CACTATTACT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
30 5 0.13
31 1 0.03
32 3 0.08
33 3 0.08
35 11 0.29
36 9 0.24
37 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
AATATTAATATAATAATAATTAATATTTTAAAA
Found at i:31824 original size:23 final size:23
Alignment explanation
Indices: 31777--31849 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
31767 TAAATATTTA
*
31777 ATATTAATATAATAATATTT-TAAT
1 ATATTAATA-AAT-ATATTTAAAAT
*
31801 ATTTTAATAAATATATTTAAAAT
1 ATATTAATAAATATATTTAAAAT
* * *
31824 ATAATAATTAATATTTTTAAAAT
1 ATATTAATAAATATATTTAAAAT
31847 ATA
1 ATA
31850 ATATAACACT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 6 0.14
23 28 0.67
24 8 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTAATAAATATATTTAAAAT
Found at i:31850 original size:23 final size:23
Alignment explanation
Indices: 31805--31852 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
31795 TTTAATATTT
31805 TAATAAATATATTTAAAATATAA
1 TAATAAATATATTTAAAATATAA
* *
31828 TAATTAATATTTTTAAAATATAA
1 TAATAAATATATTTAAAATATAA
31851 TA
1 TA
31853 TAACACTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAA
Found at i:31852 original size:43 final size:43
Alignment explanation
Indices: 31770--31852 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
31760 TATTATTTAA
* * *
31770 ATATTTAATATTAATATAATAATATTTTAATATTTTAATAAAT
1 ATATTTAAAATTAATATAATAATATTTTAATAATATAATAAAT
*
31813 ATATTTAAAATATAATA-ATTAATATTTTTAA-AATATAATA
1 ATATTTAAAAT-TAATATAATAATA-TTTTAATAATATAATA
31853 TAACACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
43 23 0.68
44 11 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (43 bp):
ATATTTAAAATTAATATAATAATATTTTAATAATATAATAAAT
Found at i:32001 original size:21 final size:21
Alignment explanation
Indices: 31938--32001 Score: 56
Period size: 26 Copynumber: 2.8 Consensus size: 21
31928 TTTTTATTAA
* * *
31938 TAAAATTATAAAAATAATATT
1 TAAAATAATAATATTAATATT
31959 TAATAATAAATAAATTATTTAATATT
1 TAA-AAT-AAT-AA-TA-TTAATATT
31985 TAAAATAATAATATTAA
1 TAAAATAATAATATTAA
32002 GTTTATGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
21 7 0.20
22 5 0.14
23 4 0.11
24 5 0.14
25 4 0.11
26 10 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAATAATAATATTAATATT
Found at i:48830 original size:23 final size:23
Alignment explanation
Indices: 48800--48856 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
48790 GCTAAAGTCA
*
48800 GCACCGAAAGGTGCAAAATTAAT
1 GCACCGAAAAGTGCAAAATTAAT
48823 GCACCGAAAAGTGCAAAATTAAT
1 GCACCGAAAAGTGCAAAATTAAT
48846 GCACCGAAAAG
1 GCACCGAAAAG
48857 AAGCTGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (23 bp):
GCACCGAAAAGTGCAAAATTAAT
Found at i:49782 original size:14 final size:14
Alignment explanation
Indices: 49763--49801 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
49753 CTTAGCATAT
49763 AGTGATGGAATGCG
1 AGTGATGGAATGCG
49777 AGTGATGGAATGCG
1 AGTGATGGAATGCG
*
49791 AGTGATTGAAT
1 AGTGATGGAAT
49802 CAGGCAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.31, C:0.05, G:0.38, T:0.26
Consensus pattern (14 bp):
AGTGATGGAATGCG
Found at i:50849 original size:12 final size:13
Alignment explanation
Indices: 50828--50863 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
50818 GGATTTTTTA
50828 AAAAATAATAAAT
1 AAAAATAATAAAT
50841 AAAAA-AATAAAAT
1 AAAAATAAT-AAAT
50854 AAAAATAATA
1 AAAAATAATA
50864 TTGATTAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 15 0.71
14 3 0.14
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAATAATAAAT
Found at i:53452 original size:34 final size:35
Alignment explanation
Indices: 53409--53486 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 35
53399 AATGGATTAT
*
53409 GAATTTGGGATTGAGCATGTAA-TGAAGTATTTTG
1 GAATTTGGGATTGAGAATGTAATTGAAGTATTTTG
* *
53443 GAATTTGGGATTTAGAATGTAATTGAAGTATTTTT
1 GAATTTGGGATTGAGAATGTAATTGAAGTATTTTG
53478 GAATTTGGG
1 GAATTTGGG
53487 GTTTAGATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 20 0.50
35 20 0.50
ACGTcount: A:0.29, C:0.01, G:0.28, T:0.41
Consensus pattern (35 bp):
GAATTTGGGATTGAGAATGTAATTGAAGTATTTTG
Found at i:53482 original size:35 final size:34
Alignment explanation
Indices: 53408--53493 Score: 127
Period size: 35 Copynumber: 2.5 Consensus size: 34
53398 GAATGGATTA
* *
53408 TGAATTTGGGATTGAGCATGTAATGAAGTATTTT
1 TGAATTTGGGATTTAGAATGTAATGAAGTATTTT
*
53442 GGAATTTGGGATTTAGAATGTAATTGAAGTATTTT
1 TGAATTTGGGATTTAGAATGTAA-TGAAGTATTTT
*
53477 TGAATTTGGGGTTTAGA
1 TGAATTTGGGATTTAGA
53494 TATATTGACT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 20 0.43
35 26 0.57
ACGTcount: A:0.29, C:0.01, G:0.28, T:0.42
Consensus pattern (34 bp):
TGAATTTGGGATTTAGAATGTAATGAAGTATTTT
Found at i:53919 original size:14 final size:13
Alignment explanation
Indices: 53872--53919 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
53862 TTTTAAAAAA
53872 TTAAAATCATTTT
1 TTAAAATCATTTT
*
53885 TTACACAA-CACTTT
1 TTA-A-AATCATTTT
53899 TTAAAATCATTTT
1 TTAAAATCATTTT
53912 TTATAAAT
1 TTA-AAAT
53920 AATACCTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 2 0.07
13 12 0.41
14 13 0.45
15 2 0.07
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAAATCATTTT
Found at i:54130 original size:17 final size:18
Alignment explanation
Indices: 54110--54144 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
54100 AGGTTTTTAA
54110 GATTAACATGCT-TTTCC
1 GATTAACATGCTCTTTCC
54127 GATTAACATGCTCTTTCC
1 GATTAACATGCTCTTTCC
54145 TCTTTGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (18 bp):
GATTAACATGCTCTTTCC
Done.