Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002046.1 Hibiscus syriacus cultivar Beakdansim tig00004168_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: 83007
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:50315 original size:29 final size:29
Alignment explanation
Indices: 50273--50331 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
50263 ATTTTCACCT
50273 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
50302 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
50331 A
1 A
50332 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:54997 original size:29 final size:29
Alignment explanation
Indices: 54955--55013 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
54945 ATTTTCACCT
54955 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
54984 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
55013 A
1 A
55014 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:58038 original size:216 final size:216
Alignment explanation
Indices: 57572--58391 Score: 1314
Period size: 216 Copynumber: 3.8 Consensus size: 216
57562 ATTTAAGAAT
57572 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
57637 TGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAATACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * *
57702 CCATTTAAAAA-TTATGGGCCAGTTAAAAAATAGAATTAAGTAATAAGTATGGATCAATTTCATA
131 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
57766 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
*
57787 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAGATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
57852 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAGTACAAAAAAGTACTAAATTATAT
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
57917 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
131 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
*
57982 TGCAAAAAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
* *
58003 TAAATTGAATAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * * * * *
58068 GGATCAAATTGAAATAATTTTAAATTGTGATGTTAAAATTTATACAAAAGAGTACTATATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * *
58133 CCATTTAAAAAGTTATAGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGAGTTAATTTCATG
131 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
58198 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
* *
58219 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAAC-C-CA---A-AAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
58278 GGATCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* *
58343 TCATTTAAAAAGTTATGGGTCAA-TTAATAAATAGAAATAAGTAATAAGT
131 CCATTTAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGT
58392 TGAGAAAAAA
Statistics
Matches: 564, Mismatches: 39, Indels: 9
0.92 0.06 0.01
Matches are distributed among these distances:
209 4 0.01
210 100 0.18
211 1 0.00
214 2 0.00
215 136 0.24
216 321 0.57
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.30
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
TGCAAATAAAATTTGGAGGAC
Found at i:58443 original size:22 final size:22
Alignment explanation
Indices: 58415--58487 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
58405 AAACAACTAA
58415 TATATATATAAACTATATAG-T
1 TATATATATAAACTATATAGTT
*
58436 T-TATATATAAAGTATAT-GTAT
1 TATATATATAAACTATATAGT-T
* *
58457 TATATATAAAAATTATATAGTT
1 TATATATATAAACTATATAGTT
58479 TATATATAT
1 TATATATAT
58488 TATGTATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.02
20 15 0.34
21 3 0.07
22 23 0.52
23 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (22 bp):
TATATATATAAACTATATAGTT
Found at i:58509 original size:27 final size:28
Alignment explanation
Indices: 58479--58539 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
58469 TTATATAGTT
** *
58479 TATATATATTATGTATAAAGTATAA-AC
1 TATATATACAATGTATAAACTATAATAC
58506 TATATATACAATGTATAAACTATAATAC
1 TATATATACAATGTATAAACTATAATAC
58534 TATATA
1 TATATA
58540 GTTTATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (28 bp):
TATATATACAATGTATAAACTATAATAC
Found at i:58597 original size:11 final size:11
Alignment explanation
Indices: 58581--58618 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
58571 ACTACATAGT
58581 TTATATATAAA
1 TTATATATAAA
*
58592 TTATATATGAA
1 TTATATATAAA
58603 TTATATATAAA
1 TTATATATAAA
*
58614 CTATA
1 TTATA
58619 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:58709 original size:20 final size:20
Alignment explanation
Indices: 58417--58710 Score: 113
Period size: 20 Copynumber: 14.4 Consensus size: 20
58407 ACAACTAATA
*
58417 TATATATAAACTATATAGTT
1 TATATATAAATTATATAGTT
*
58437 TATATATAAAGTATAT-GTAT
1 TATATATAAATTATATAGT-T
58457 TATATATAAAAATTATATAGTT
1 TATATAT--AAATTATATAGTT
* * *
58479 TATATATATTATGTATAAAGTA
1 TATATATA-AAT-TATATAGTT
* * * *
58501 TAAACTATATA-TACA-ATGTA
1 TATA-TATAAATTATATA-GTT
* *
58521 TAAACTATAATACTATATAGTT
1 TATA-TATAA-ATTATATAGTT
* * **
58543 TATATATGAACTAT-T-GAAC
1 TATATATAAATTATATAG-TT
* *
58562 TATATATAAACTACATAGTT
1 TATATATAAATTATATAGTT
*
58582 TATATATAAATTATATATGAAT
1 TATATATAAATTATATA-G-TT
* * *
58604 TATATATAAACTATACAATT
1 TATATATAAATTATATAGTT
* * *
58624 TATATTTATA-TAGTAT-GTA
1 TATATATAAATTA-TATAGTT
* *
58643 TA-ATTATAAATAATATA-TA
1 TATA-TATAAATTATATAGTT
** *
58662 T-TGCATAAATTATATAATT
1 TATATATAAATTATATAGTT
58681 TATTAATATAAATTATATAGTT
1 TA-T-ATATAAATTATATAGTT
58703 TATATATA
1 TATATATA
58711 TAGTATATAT
Statistics
Matches: 209, Mismatches: 40, Indels: 50
0.70 0.13 0.17
Matches are distributed among these distances:
18 13 0.06
19 33 0.16
20 77 0.37
21 11 0.05
22 68 0.33
23 7 0.03
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (20 bp):
TATATATAAATTATATAGTT
Found at i:58781 original size:20 final size:20
Alignment explanation
Indices: 58756--58828 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 20
58746 TATAAACTAC
58756 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
*
58776 ATACTATATTTTATACTATTTAT
1 ATACTATA-ATT-TA-TATTTAT
* *
58799 ATAAATTATAGTTTATATTTAT
1 AT--ACTATAATTTATATTTAT
*
58821 ATAATATA
1 ATACTATA
58829 TATGAACTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
20 13 0.30
21 2 0.05
22 11 0.25
23 11 0.25
24 2 0.05
25 5 0.11
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:58792 original size:12 final size:13
Alignment explanation
Indices: 58767--58816 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
58757 TACTATAATT
58767 TATATTTATATAC
1 TATATTTATATAC
58780 TATATTT-TATAC
1 TATATTTATATAC
* *
58792 TAT-TTATATAAAT
1 TATATT-TATATAC
58805 TATAGTTTATAT
1 TATA-TTTATAT
58817 TTATATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
11 2 0.07
12 9 0.30
13 13 0.43
14 4 0.13
15 2 0.07
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:58831 original size:31 final size:31
Alignment explanation
Indices: 58796--58868 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
58786 TTATACTATT
* *
58796 TATATAAATTATAGTTTATAT-TTATATAATA
1 TATATAAATTATAGTTTACATATGA-ATAATA
* * *
58827 TATATGAACTATAGTTTACATATGAATTATA
1 TATATAAATTATAGTTTACATATGAATAATA
58858 TATATAAATTA
1 TATATAAATTA
58869 ATATACTAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (31 bp):
TATATAAATTATAGTTTACATATGAATAATA
Found at i:58907 original size:18 final size:18
Alignment explanation
Indices: 58886--59081 Score: 80
Period size: 24 Copynumber: 9.9 Consensus size: 18
58876 AAGGTTGATA
58886 TTTATATATGAACTATAG
1 TTTATATATGAACTATAG
* * * *
58904 TTTACATGTAAACTATATAA
1 TTTATATATGAAC--TATAG
58924 TTTATATACT-AACTATAG
1 TTTATATA-TGAACTATAG
* *
58942 TTTACATATAAACTATAG
1 TTTATATATGAACTATAG
58960 TTGATATTTACATATGAACTATAG
1 TT--TA--T--ATATGAACTATAG
58984 TTGATATTTACATATGAACTATAG
1 TT--TA--T--ATATGAACTATAG
59008 TTGATATTTACATATGAACTATAG
1 TT--TA--T--ATATGAACTATAG
59032 TTTATATATGAACTATA-
1 TTTATATATGAACTATAG
59049 --TATATA--AACTATATAG
1 TTTATATATGAAC--TATAG
*
59065 TTTACATATGAACTATA
1 TTTATATATGAACTATA
59082 TATATAGTTT
Statistics
Matches: 150, Mismatches: 11, Indels: 34
0.77 0.06 0.17
Matches are distributed among these distances:
13 3 0.02
15 10 0.07
17 1 0.01
18 52 0.35
20 19 0.13
21 1 0.01
22 2 0.01
24 62 0.41
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (18 bp):
TTTATATATGAACTATAG
Found at i:58928 original size:38 final size:41
Alignment explanation
Indices: 58881--59048 Score: 173
Period size: 48 Copynumber: 4.0 Consensus size: 41
58871 ATACTAAGGT
*
58881 TGATATTTATATATGAACTATAGTTTACATGTAAACTATA-
1 TGATATTTATATATGAACTATAGTTTACATATAAACTATAG
58921 T-A-ATTTATATACT-AACTATAGTTTACATATAAACTATAG
1 TGATATTTATATA-TGAACTATAGTTTACATATAAACTATAG
* *
58960 TTGATATTTACATATGAACTATAGTTGATATTTACATATGAACTATAG
1 -TGATATTTATATATGAACTATA---G---TTTACATATAAACTATAG
* * *
59008 TTGATATTTACATATGAACTATAGTTTATATATGAACTATA
1 -TGATATTTATATATGAACTATAGTTTACATATAAACTATA
59049 TATATAAACT
Statistics
Matches: 112, Mismatches: 4, Indels: 22
0.81 0.03 0.16
Matches are distributed among these distances:
38 33 0.29
39 2 0.02
40 2 0.02
41 2 0.02
42 31 0.28
45 2 0.02
48 40 0.36
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (41 bp):
TGATATTTATATATGAACTATAGTTTACATATAAACTATAG
Found at i:58973 original size:24 final size:24
Alignment explanation
Indices: 58942--59038 Score: 176
Period size: 24 Copynumber: 4.0 Consensus size: 24
58932 CTAACTATAG
*
58942 TTTACATATAAACTATAGTTGATA
1 TTTACATATGAACTATAGTTGATA
58966 TTTACATATGAACTATAGTTGATA
1 TTTACATATGAACTATAGTTGATA
58990 TTTACATATGAACTATAGTTGATA
1 TTTACATATGAACTATAGTTGATA
*
59014 TTTACATATGAACTATAGTTTATA
1 TTTACATATGAACTATAGTTGATA
59038 T
1 T
59039 ATGAACTATA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.43
Consensus pattern (24 bp):
TTTACATATGAACTATAGTTGATA
Found at i:59052 original size:13 final size:13
Alignment explanation
Indices: 59034--59063 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
59024 AACTATAGTT
*
59034 TATATATGAACTA
1 TATATATAAACTA
59047 TATATATAAACTA
1 TATATATAAACTA
59060 TATA
1 TATA
59064 GTTTACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:59059 original size:31 final size:32
Alignment explanation
Indices: 59019--59087 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
59009 TGATATTTAC
* *
59019 ATATGAAC-TATAGTTTATATATGAACTATAT
1 ATATAAACATATAGTTTACATATGAACTATAT
59050 ATATAAACTATATAGTTTACATATGAACTATAT
1 ATATAAAC-ATATAGTTTACATATGAACTATAT
59083 ATATA
1 ATATA
59088 GTTTATTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 7 0.21
33 27 0.79
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (32 bp):
ATATAAACATATAGTTTACATATGAACTATAT
Found at i:59116 original size:24 final size:25
Alignment explanation
Indices: 59061--59122 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
59051 TATAAACTAT
* *
59061 ATAGTTTACATA-TGAACTATATAT
1 ATAGTTTATATAGTGAACTATATAC
59085 ATAGTTTAT-TAGTGAACTATATAC
1 ATAGTTTATATAGTGAACTATATAC
59109 ACTA-TTTATATAGT
1 A-TAGTTTATATAGT
59123 ATATAGTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 2 0.06
24 25 0.76
25 6 0.18
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.44
Consensus pattern (25 bp):
ATAGTTTATATAGTGAACTATATAC
Found at i:59127 original size:9 final size:8
Alignment explanation
Indices: 59115--59218 Score: 61
Period size: 9 Copynumber: 12.4 Consensus size: 8
59105 ATACACTATT
59115 TATATAGTA
1 TATATA-TA
59124 TATAGTATA
1 TATA-TATA
59133 TAT-TATA
1 TATATATA
*
59140 TATATAAA
1 TATATATA
*
59148 CTATAGTTTA
1 -TATA-TATA
*
59158 TATTTATA
1 TATATATA
*
59166 TACTCTATA
1 TA-TATATA
59175 T-TATATA
1 TATATATA
*
59182 TATAAACTA
1 TATATA-TA
59191 TATATACTA
1 TATATA-TA
59200 TATAGTATA
1 TATA-TATA
*
59209 -ATTTATA
1 TATATATA
59216 TAT
1 TAT
59219 GAACTATATA
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
7 17 0.22
8 15 0.20
9 38 0.50
10 6 0.08
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (8 bp):
TATATATA
Found at i:59181 original size:7 final size:7
Alignment explanation
Indices: 59114--59218 Score: 58
Period size: 7 Copynumber: 15.1 Consensus size: 7
59104 TATACACTAT
59114 TTATATA
1 TTATATA
*
59121 GTATATA
1 TTATATA
*
59128 GTATATA
1 TTATATA
59135 TTATATA
1 TTATATA
*
59142 -TATAAA
1 TTATATA
*
59148 CTATAGT-
1 TTATA-TA
59155 TTATAT-
1 TTATATA
59161 TTATATA
1 TTATATA
* *
59168 CTCTATA
1 TTATATA
59175 TTATATA
1 TTATATA
*
59182 -TATAAA
1 TTATATA
59188 CTATATATA
1 -T-TATATA
*
59197 CTATATA
1 TTATATA
*
59204 GTATA-A
1 TTATATA
59210 TTTATATA
1 -TTATATA
59218 T
1 T
59219 GAACTATATA
Statistics
Matches: 76, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
6 18 0.24
7 52 0.68
8 1 0.01
9 5 0.07
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.49
Consensus pattern (7 bp):
TTATATA
Found at i:59230 original size:2 final size:2
Alignment explanation
Indices: 59115--59218 Score: 61
Period size: 2 Copynumber: 49.5 Consensus size: 2
59105 ATACACTATT
* *
59115 TA TA TA GTA TA TA GTA TA TA T- TA TA TA TA TA AA CTA TA GTT TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA
* * *
59158 TA TT TA TA TA CTC TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
*
59200 TA TA GTA TA -A TT TA TA TA T
1 TA TA -TA TA TA TA TA TA TA T
59219 GAACTATATA
Statistics
Matches: 79, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
1 3 0.04
2 64 0.81
3 12 0.15
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:59281 original size:33 final size:33
Alignment explanation
Indices: 59244--59398 Score: 170
Period size: 33 Copynumber: 4.5 Consensus size: 33
59234 TCCTAAACCC
*
59244 TAAACTATACATTATATAGTTTATTAGTATATA
1 TAAACTATACATTATATAGTTCATTAGTATATA
* *
59277 TAAACTATATGATATATATAG-AC-TATATGATATATA
1 TAAACTATA-CAT-TATATAGTTCAT-TA-G-TATATA
59313 TAAACTATACATTATATATAGTTCATTAGTATATA
1 TAAACTATACA-T-TATATAGTTCATTAGTATATA
* *
59348 TAAACTATATATTATATGGTTCATTAGTATATA
1 TAAACTATACATTATATAGTTCATTAGTATATA
* *
59381 TAAACTATATAGTATATA
1 TAAACTATACATTATATA
59399 TAAACTATAT
Statistics
Matches: 105, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
33 46 0.44
34 5 0.05
35 25 0.24
36 25 0.24
37 3 0.03
38 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (33 bp):
TAAACTATACATTATATAGTTCATTAGTATATA
Found at i:59294 original size:18 final size:18
Alignment explanation
Indices: 59268--59478 Score: 185
Period size: 18 Copynumber: 12.1 Consensus size: 18
59258 TATAGTTTAT
59268 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
*
59286 T-GATATATATAGACTATA
1 TAG-TATATATAAACTATA
59304 T-GATATATATAAACTATA
1 TAG-TATATATAAACTATA
* * **
59322 CATTATATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
59339 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
***
59357 TA-T-TATAT-GGTTCAT-
1 TAGTATATATAAACT-ATA
59372 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
59390 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
**
59408 TA-T-TATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
*
59423 TAGTATATATAACCTATA
1 TAGTATATATAAACTATA
*
59441 TAGTATATGTAAACTATA
1 TAGTATATATAAACTATA
59459 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
59477 TA
1 TA
59479 TTAATTTATT
Statistics
Matches: 155, Mismatches: 23, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
15 7 0.05
16 16 0.10
17 29 0.19
18 103 0.66
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:59302 original size:51 final size:51
Alignment explanation
Indices: 59244--59467 Score: 253
Period size: 51 Copynumber: 4.4 Consensus size: 51
59234 TCCTAAACCC
* *
59244 TAAACTATACATTATATAGTTTATTAGTATATATAAACTATAT-GATATATA
1 TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAG-TATATA
* * *
59295 TAGACTATATGATATATATAAACTATACATTA-TATATAGT--TC-AT-TAGTATATA
1 TAAACTATAT-AT-TATAT--AGT-T-CATTAGTATATA-TAAACTATATAGTATATA
*
59348 TAAACTATATATTATATGGTTCATTAGTATATATAAACTATATAGTATATA
1 TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATA
* *
59399 TAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
1 TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATA
*
59450 TAAACTATATAGTATATA
1 TAAACTATATATTATATA
59468 TAAACTATAT
Statistics
Matches: 147, Mismatches: 13, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
47 6 0.04
48 7 0.05
49 2 0.01
50 2 0.01
51 87 0.59
52 4 0.03
53 21 0.14
54 3 0.02
55 3 0.02
56 7 0.05
57 5 0.03
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (51 bp):
TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATA
Found at i:59468 original size:104 final size:103
Alignment explanation
Indices: 59244--59467 Score: 264
Period size: 104 Copynumber: 2.2 Consensus size: 103
59234 TCCTAAACCC
* * *
59244 TAAACTATACATTATATAGTTTATTAGTATATATAAACTATATGATATATATAGACTATATGATA
1 TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATGATATATATAAACTATATGATA
*
59309 TATATAAACTATACATTATATATAGTTCATTAGTATATA
66 TATAT-AACTATACATTATATATAGTCCATTAGTATATA
*
59348 TAAACTATATATTATATGGTTCATTAGTATATATAAACTATAT-AGTATATATAAACTATAT-AT
1 TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATGA-TATATATAAACTATATGAT
* *
59411 -TATAT-AGT-T-CATTAGTATATA-TAACCTATATAGTATATG
65 ATATATAACTATACATTA-TATATAGT--CC-AT-TAGTATATA
*
59450 TAAACTATATAGTATATA
1 TAAACTATATATTATATA
59468 TAAACTATAT
Statistics
Matches: 105, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
98 6 0.06
99 7 0.07
100 3 0.03
101 2 0.02
102 29 0.28
103 3 0.03
104 55 0.52
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (103 bp):
TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATGATATATATAAACTATATGATA
TATATAACTATACATTATATATAGTCCATTAGTATATA
Found at i:59502 original size:69 final size:69
Alignment explanation
Indices: 59372--59502 Score: 185
Period size: 69 Copynumber: 1.9 Consensus size: 69
59362 TATGGTTCAT
* * *
59372 TAGTATATATAAACTATATAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACC
1 TAGTATATATAAACTATATAGTATATATAAACTATATATTATATAGTTAATTAGAACATATAACC
59437 TATA
66 TATA
* *
59441 TAGTATATGTAAACTATATAGTATATATAAACTATATATTAATTTA-TTAATATA-AACATATA
1 TAGTATATATAAACTATATAGTATATATAAACTATATATT-ATATAGTTAAT-TAGAACATATA
59503 TATTAATTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
69 49 0.89
70 6 0.11
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (69 bp):
TAGTATATATAAACTATATAGTATATATAAACTATATATTATATAGTTAATTAGAACATATAACC
TATA
Found at i:59506 original size:26 final size:26
Alignment explanation
Indices: 59465--59536 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
59455 TATATAGTAT
59465 ATATAAAC-TATATATTAATTTATTA
1 ATATAAACATATATATTAATTTATTA
59490 ATATAAACATATATATTAATTTATTA
1 ATATAAACATATATATTAATTTATTA
59516 ATATAAACATATATATTAATT
1 ATATAAACATATATATTAATT
59537 GAAAGAATTG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 8 0.17
26 38 0.83
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATAAACATATATATTAATTTATTA
Found at i:59631 original size:61 final size:61
Alignment explanation
Indices: 59560--59700 Score: 176
Period size: 61 Copynumber: 2.3 Consensus size: 61
59550 AATATATAAT
* * * * *
59560 GATTAAATTGAACAAATTTTAATTATGAAGCTTAAATTAATAAATTGTAA-CATTAAATTTG
1 GATTAAATTGAAAAAATTTGAAATATAAAGCTTAAATTAATAAATT-AAATCATTAAATTTG
* * *
59621 GATTAAATTGAAAAAAATTGAAATATAAAGCTTAAATTAATATATTAAATCGTTAAATTTG
1 GATTAAATTGAAAAAATTTGAAATATAAAGCTTAAATTAATAAATTAAATCATTAAATTTG
* *
59682 GACTAAATTGAATAAATTT
1 GATTAAATTGAAAAAATTT
59701 AAAACTAAGA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 2 0.03
61 66 0.97
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (61 bp):
GATTAAATTGAAAAAATTTGAAATATAAAGCTTAAATTAATAAATTAAATCATTAAATTTG
Found at i:61511 original size:20 final size:20
Alignment explanation
Indices: 61473--61519 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
61463 GTTTAATAAG
**
61473 ATAATATTTAAATTTAATTT
1 ATAATATTTAAATAAAATTT
61493 AGTAAT-TTTAAATAAAATTT
1 A-TAATATTTAAATAAAATTT
61513 ATAATAT
1 ATAATAT
61520 AAGAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.17
20 15 0.65
21 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATAATATTTAAATAAAATTT
Found at i:61608 original size:18 final size:18
Alignment explanation
Indices: 61557--61608 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
61547 AATTAACATA
61557 AAAATTAAATTTATAATAT
1 AAAATTAAATTT-TAATAT
61576 ACAAATTATAA--TTAATAT
1 A-AAATTA-AATTTTAATAT
*
61594 AAAACTAAATTTTAA
1 AAAATTAAATTTTAA
61609 AAAAGTAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
16 2 0.07
17 5 0.18
18 11 0.39
19 2 0.07
20 6 0.21
21 2 0.07
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTAAATTTTAATAT
Found at i:61669 original size:51 final size:51
Alignment explanation
Indices: 61599--61697 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 51
61589 AATATAAAAC
* *
61599 TAAATTTTAAAAAAGTAATCATATTAATTTGATTATCATAATAATTTATGA
1 TAAAATTTAAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGA
*
61650 TAAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAATAATTTA
1 TAAAATTTAAAAAAGTAATCATATTAATTTAATTATCATAATAATTTA
61698 ATTATCATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.42
Consensus pattern (51 bp):
TAAAATTTAAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGA
Found at i:61689 original size:17 final size:17
Alignment explanation
Indices: 61667--61707 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
61657 TCAAAAAGTA
*
61667 ATCATATTAATTTAATT
1 ATCATAATAATTTAATT
61684 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
61701 ATCATAA
1 ATCATAA
61708 GTTTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
ATCATAATAATTTAATT
Found at i:63329 original size:2 final size:2
Alignment explanation
Indices: 63322--63353 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
63312 AACCAAACAT
63322 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
63354 AGTTTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:70472 original size:34 final size:34
Alignment explanation
Indices: 70424--70491 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
70414 AAAGATTTGC
*
70424 TTAACTGTATGGGTGATTTAGGGCTTTTGGATCA
1 TTAACTGTATGGGTGATTTAAGGCTTTTGGATCA
*
70458 TTAATTGTATGGGTGATTTAAGGCTTTTGGATCA
1 TTAACTGTATGGGTGATTTAAGGCTTTTGGATCA
70492 CTCTTTCTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (34 bp):
TTAACTGTATGGGTGATTTAAGGCTTTTGGATCA
Found at i:73592 original size:44 final size:44
Alignment explanation
Indices: 73541--73634 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
73531 TACCATTATA
* * * *
73541 AAGGAAGTATCGGTATTGTACCTTGAATACCGATACTACTTAAT
1 AAGGAAGTATCGGTACTATACCTTGAATAACAATACTACTTAAT
* **
73585 ATGGAAGTATCGGTACTATACCTTGGGTAACAATACTACTTAAT
1 AAGGAAGTATCGGTACTATACCTTGAATAACAATACTACTTAAT
73629 AAGGAA
1 AAGGAA
73635 AATGTGAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (44 bp):
AAGGAAGTATCGGTACTATACCTTGAATAACAATACTACTTAAT
Found at i:74151 original size:21 final size:23
Alignment explanation
Indices: 74112--74161 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
74102 GTCCTTCGGG
74112 ACATATATGTAATCCTTTG-GA-
1 ACATATATGTAATCCTTTGAGAC
** *
74133 ACATATATGTGGTCTTTTGAGAC
1 ACATATATGTAATCCTTTGAGAC
74156 ACATAT
1 ACATAT
74162 TTGGTCCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.67
22 2 0.08
23 6 0.25
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (23 bp):
ACATATATGTAATCCTTTGAGAC
Found at i:74161 original size:23 final size:21
Alignment explanation
Indices: 74103--74142 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
74093 GTCTACGTGG
* *
74103 TCCTTCGGGACATATATGTAA
1 TCCTTTGGAACATATATGTAA
74124 TCCTTTGGAACATATATGT
1 TCCTTTGGAACATATATGT
74143 GGTCTTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TCCTTTGGAACATATATGTAA
Found at i:74260 original size:23 final size:23
Alignment explanation
Indices: 74233--74297 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
74223 TTTATATGGC
*
74233 ACTTCAGTGCATTTCTACGCGGA
1 ACTTCGGTGCATTTCTACGCGGA
* * * *
74256 ACTTCGGTACAATTCTACGTGGC
1 ACTTCGGTGCATTTCTACGCGGA
*
74279 ACTTCGGTGCATTTATACG
1 ACTTCGGTGCATTTCTACG
74298 AGTTGTGGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGA
Found at i:78986 original size:18 final size:19
Alignment explanation
Indices: 78963--79025 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
78953 CTAGTAATCA
78963 TATTCT-CTGATAATCTTT
1 TATTCTACTGATAATCTTT
*
78981 TATTCTCACTGGTAATCTTT
1 TATTCT-ACTGATAATCTTT
* * *
79001 TATTCCCACTGGTAATCTTA
1 TATT-CTACTGATAATCTTT
79021 TATTC
1 TATTC
79026 CGTGAACCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 6 0.15
19 1 0.03
20 31 0.79
21 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.08, T:0.49
Consensus pattern (19 bp):
TATTCTACTGATAATCTTT
Found at i:78998 original size:20 final size:20
Alignment explanation
Indices: 78973--79026 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
78963 TATTCTCTGA
*
78973 TAATCTTTTATTCTCACTGG
1 TAATCTTTTATTCCCACTGG
78993 TAATCTTTTATTCCCACTGG
1 TAATCTTTTATTCCCACTGG
*
79013 TAATCTTATATTCC
1 TAATCTTTTATTCC
79027 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (20 bp):
TAATCTTTTATTCCCACTGG
Done.