Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001708.1 Hibiscus syriacus cultivar Beakdansim tig00003430_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: 120919
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1365 original size:3 final size:3
Alignment explanation
Indices: 1357--1399 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
1347 AAATTGTATA
1357 TAT TAT TAT TAT TAT TAT TATT TAT TA- TAT TAT TAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT T-AT TAT
1400 CAATTGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1387 original size:18 final size:19
Alignment explanation
Indices: 1358--1399 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1348 AATTGTATAT
1358 ATTATTATTATTATTATTA
1 ATTATTATTATTATTATTA
*
1377 TTTATTA-TATTATTATTA
1 ATTATTATTATTATTATTA
1395 ATTAT
1 ATTAT
1400 CAATTGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:1722 original size:38 final size:40
Alignment explanation
Indices: 1679--1757 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
1669 ACTTAACATT
* * *
1679 AAATTTGAAC-GATG-GTACTAAAATGAAACAAAAATTAA
1 AAATTTGAACAGAGGAGTACTAAAATAAAACAAAAACTAA
* *
1717 AAATTTTAACAGCGGAGTACTAAAATAAAACAAAAACTAA
1 AAATTTGAACAGAGGAGTACTAAAATAAAACAAAAACTAA
1757 A
1 A
1758 CTTAGGTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 9 0.26
39 2 0.06
40 23 0.68
ACGTcount: A:0.57, C:0.10, G:0.11, T:0.22
Consensus pattern (40 bp):
AAATTTGAACAGAGGAGTACTAAAATAAAACAAAAACTAA
Found at i:6304 original size:15 final size:15
Alignment explanation
Indices: 6284--6313 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6274 AACAAAACAA
6284 TGCTGAATGATTCAG
1 TGCTGAATGATTCAG
*
6299 TGCTGACTGATTCAG
1 TGCTGAATGATTCAG
6314 CAAAACAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (15 bp):
TGCTGAATGATTCAG
Found at i:6318 original size:38 final size:38
Alignment explanation
Indices: 6249--6372 Score: 187
Period size: 38 Copynumber: 3.3 Consensus size: 38
6239 TTTTGCATCT
* *
6249 CTGAATGATTCAGTGCT-ACTGATTCAACAAAACAATG
1 CTGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTG
6286 CTGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTG
1 CTGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTG
* * *
6324 CTGACTGATTCAATGCTGACTGATTCAGCAAAGCAGTG
1 CTGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTG
*
6362 CTGGATGATTC
1 CTGAATGATTC
6373 GCACAAAAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
37 17 0.22
38 62 0.78
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (38 bp):
CTGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTG
Found at i:6342 original size:15 final size:15
Alignment explanation
Indices: 6322--6350 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6312 AGCAAAACAG
6322 TGCTGACTGATTCAA
1 TGCTGACTGATTCAA
6337 TGCTGACTGATTCA
1 TGCTGACTGATTCA
6351 GCAAAGCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (15 bp):
TGCTGACTGATTCAA
Found at i:13565 original size:38 final size:38
Alignment explanation
Indices: 13514--13613 Score: 182
Period size: 38 Copynumber: 2.6 Consensus size: 38
13504 AGAGAATTCT
13514 GTTAAAGACTGATATTAGAGGTCTAGGTTATGAACTTA
1 GTTAAAGACTGATATTAGAGGTCTAGGTTATGAACTTA
*
13552 GTTAAAGACTGATATTAGAGGTCTAGGTTATGAATTTA
1 GTTAAAGACTGATATTAGAGGTCTAGGTTATGAACTTA
*
13590 GTTAAAGACTGGTATTAGAGGTCT
1 GTTAAAGACTGATATTAGAGGTCT
13614 TGATTTTGAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (38 bp):
GTTAAAGACTGATATTAGAGGTCTAGGTTATGAACTTA
Found at i:21556 original size:23 final size:25
Alignment explanation
Indices: 21530--21584 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
21520 ATAATAATAA
* *
21530 AAATAATATT-TAA-ATATATAAAC
1 AAATAATATTAAAACATAAATAAAC
*
21553 AAATAAAATTAAAACATAAATAAAC
1 AAATAATATTAAAACATAAATAAAC
21578 -AATAATA
1 AAATAATA
21585 AAAATACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.35
24 8 0.31
25 9 0.35
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.27
Consensus pattern (25 bp):
AAATAATATTAAAACATAAATAAAC
Found at i:21662 original size:28 final size:26
Alignment explanation
Indices: 21630--21684 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
21620 TGAAAATATT
*
21630 TAAAATTAATTACTAAATTATAATCTAA
1 TAAAATTAAATACTAAATT-TAAT-TAA
*
21658 TAAAATTAAATACTTAATTTAATTAA
1 TAAAATTAAATACTAAATTTAATTAA
21684 T
1 T
21685 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 17 0.68
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAAATTAAATACTAAATTTAATTAA
Found at i:23008 original size:3 final size:3
Alignment explanation
Indices: 23002--23047 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
22992 ATTTATTATT
23002 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23048 AATGAGAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:23420 original size:124 final size:124
Alignment explanation
Indices: 23245--23965 Score: 1178
Period size: 124 Copynumber: 5.8 Consensus size: 124
23235 GATGATAATT
* * * * * *
23245 TATCTTCTTCTGTGAT-GTAATT-TGGAAAAAGGTTGAACAAGTTCTTCTCATTATAAAATTCTT
1 TATCTCCTTCTGTGATAG-AATTAT-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTT
* * *
23308 CTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTC-CTTGGAAAAGTTGATGTTGACC
64 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC-TGGAAAAGTTGATGCTGATC
* * * * * * * *
23369 TATTTCCTTCTATGATAGAGTCATTCAAAAGGTTGAATAAACTCTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
*
23434 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATGCTGATC
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
23493 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
*
23558 TCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
23617 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
*
23682 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAAGTTGATGCTGATC
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
*
23741 TATCTCCTTCTGTGATAGAATTATGCAAAATGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
23806 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
* *
23865 TATCTCCTTCTGTGATAGAATTATGCAAAAGTTTGAACAAGCTCTTCTCATTATAAACTTTTTCT
1 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
*
23930 TCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTT
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
23966 TTCTTCCTTC
Statistics
Matches: 560, Mismatches: 34, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
124 557 0.99
125 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (124 bp):
TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
Found at i:23962 original size:40 final size:40
Alignment explanation
Indices: 23907--24003 Score: 185
Period size: 40 Copynumber: 2.4 Consensus size: 40
23897 TTGAACAAGC
23907 TCTTCTCATTATAAACTTTTTCTTCCTTCTTCAGATGAGT
1 TCTTCTCATTATAAACTTTTTCTTCCTTCTTCAGATGAGT
23947 TCTTCTCATTATAAACTTTTTCTTCCTTCTTCAGATGAGT
1 TCTTCTCATTATAAACTTTTTCTTCCTTCTTCAGATGAGT
*
23987 TCTTCTCATTATGAACT
1 TCTTCTCATTATAAACT
24004 CGACCTGGTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49
Consensus pattern (40 bp):
TCTTCTCATTATAAACTTTTTCTTCCTTCTTCAGATGAGT
Found at i:24466 original size:22 final size:22
Alignment explanation
Indices: 24441--24495 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
24431 GATAAAGCTT
*
24441 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* * *
24463 TCATCTTTAAAAAGGGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
24485 TCATTTTTGAA
1 TCATCTTTGAA
24496 GAGTGTAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:27274 original size:115 final size:114
Alignment explanation
Indices: 27106--27335 Score: 408
Period size: 115 Copynumber: 2.0 Consensus size: 114
27096 GATCATGCAG
* * *
27106 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAATTCCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGA
27171 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
27220 TTCATCTTTCAAATT-CAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTT-AAATTCCAATGATTGGTTCTGTGG-TTCATACCAAACCAGATCAGATAACTCAAA
27284 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
64 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
27335 T
1 T
27336 GAAACTTGCT
Statistics
Matches: 111, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
114 27 0.24
115 84 0.76
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (114 bp):
TTCATCTTTAAATTCCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACA
Found at i:28067 original size:28 final size:26
Alignment explanation
Indices: 28035--28089 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
28025 TGAAAATATT
*
28035 TAAAATTAATTACTAAATTATAATCTAA
1 TAAAATTAAATACTAAATT-TAAT-TAA
*
28063 TAAAATTAAATACTTAATTTAATTAA
1 TAAAATTAAATACTAAATTTAATTAA
28089 T
1 T
28090 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 17 0.68
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAAATTAAATACTAAATTTAATTAA
Found at i:29414 original size:3 final size:3
Alignment explanation
Indices: 29408--29462 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
29398 ATTTATTATT
* *
29408 TAA TAA TAA TATA TCA TCA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29454 TAA TAA TAA
1 TAA TAA TAA
29463 AATGAGAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 47 0.96
4 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:32089 original size:6 final size:6
Alignment explanation
Indices: 32078--32106 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
32068 TGATAGCTTT
32078 ATGCAC ATGCAC ATGCAC ATGCAC ATGCA
1 ATGCAC ATGCAC ATGCAC ATGCAC ATGCA
32107 TAAAGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGCAC
Found at i:32654 original size:20 final size:21
Alignment explanation
Indices: 32622--32660 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
32612 AAGTATTTTG
32622 ACAAGAGGTTTCGAAACTTCT
1 ACAAGAGGTTTCGAAACTTCT
32643 ACAAGA-GTTTCGAAACTT
1 ACAAGAGGTTTCGAAACTT
32661 TCCAAGACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (21 bp):
ACAAGAGGTTTCGAAACTTCT
Found at i:34387 original size:2 final size:2
Alignment explanation
Indices: 34380--34411 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34370 GTGTTTTCTT
34380 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
34412 ATTTTTTAAT
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:38653 original size:3 final size:3
Alignment explanation
Indices: 38645--38673 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38635 TCCCCCAGAA
38645 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
38674 CATAATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42491 original size:23 final size:24
Alignment explanation
Indices: 42465--42509 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
42455 CAGCATTATG
42465 ATCAAGGAT-ATC-AGATTTCACAT
1 ATCAA-GATGATCAAGATTTCACAT
*
42488 ATCAATATGATCAAGATTTCAC
1 ATCAAGATGATCAAGATTTCAC
42510 CATAATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 8 0.42
24 9 0.47
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (24 bp):
ATCAAGATGATCAAGATTTCACAT
Found at i:46069 original size:25 final size:24
Alignment explanation
Indices: 46023--46069 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
46013 GAAATTTACC
*
46023 CTTTAAAATAAAACAAAGATAAAG
1 CTTTAAAATAAAACAAAAATAAAG
46047 CTTTAAAAATGAAAA-AAAAATAA
1 CTTT-AAAAT-AAAACAAAAATAA
46070 TTCTCATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 12 0.60
26 4 0.20
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.21
Consensus pattern (24 bp):
CTTTAAAATAAAACAAAAATAAAG
Found at i:68890 original size:17 final size:16
Alignment explanation
Indices: 68852--68889 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
68842 TTTTATTCAA
68852 TAAAATAAAAATTTAAT
1 TAAAATAAAAA-TTAAT
68869 TAAAATAAAAA-TAAT
1 TAAAATAAAAATTAAT
68884 ATAAAA
1 -TAAAA
68890 AATATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAATAAAAATTAAT
Found at i:70681 original size:21 final size:20
Alignment explanation
Indices: 70657--70704 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
70647 TAAAAATATT
* *
70657 TATTTTAGATAATGAAATTAA
1 TATTTTAGATAA-AAAAATAA
*
70678 TATTTTTGATAAAAAAATAA
1 TATTTTAGATAAAAAAATAA
70698 TATTTTA
1 TATTTTA
70705 AATATCATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
TATTTTAGATAAAAAAATAA
Found at i:71821 original size:18 final size:18
Alignment explanation
Indices: 71798--71852 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
71788 GTCACAATCC
*
71798 TATATCTATATCTATATT
1 TATATCTATATTTATATT
71816 TATATCTATATTTATATT
1 TATATCTATATTTATATT
71834 TATAT-TATATTTATATT
1 TATATCTATATTTATATT
71851 TA
1 TA
71853 GATATATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
17 14 0.39
18 22 0.61
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATCTATATTTATATT
Found at i:71850 original size:6 final size:6
Alignment explanation
Indices: 71798--71852 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
71788 GTCACAATCC
* * *
71798 TATATC TATATC TATATT TATATC TATATT TATATT TATA-T TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
71845 TATATT TA
1 TATATT TA
71853 GATATATGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
5 5 0.11
6 40 0.89
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (6 bp):
TATATT
Found at i:72366 original size:3 final size:3
Alignment explanation
Indices: 72358--72430 Score: 105
Period size: 3 Copynumber: 24.3 Consensus size: 3
72348 TTTCAGTTTA
*
72358 AAT AAT AAT -AT CAAT CA- AAT TAAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
72403 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
72431 GGATCGTTCA
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 3 0.05
3 56 0.88
4 5 0.08
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:81003 original size:24 final size:23
Alignment explanation
Indices: 80971--81018 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
80961 TCCTCCAACT
80971 TCTTTTTCCTATTCC-TCTCCTCC
1 TCTTTTTCCT-TTCCATCTCCTCC
80994 TCTTTCTTCCTTTCCATCTCCTCC
1 TCTTT-TTCCTTTCCATCTCCTCC
81018 T
1 T
81019 TCCTCTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.04, C:0.44, G:0.00, T:0.52
Consensus pattern (23 bp):
TCTTTTTCCTTTCCATCTCCTCC
Found at i:81025 original size:24 final size:24
Alignment explanation
Indices: 80976--81026 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
80966 CAACTTCTTT
*
80976 TTCCTATTCCTCTCCTCCTCTTTC
1 TTCCTATTCCTCTCCTCCTCTCTC
81000 TTCCT-TTCCATCTCCTCCT-TCCTC
1 TTCCTATTCC-TCTCCTCCTCT-CTC
81024 TTC
1 TTC
81027 ACACCCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (24 bp):
TTCCTATTCCTCTCCTCCTCTCTC
Found at i:82150 original size:28 final size:28
Alignment explanation
Indices: 82118--82176 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
82108 CAAATCTCCT
82118 AATTATAATACAAATATATACACTATAC
1 AATTATAATACAAATATATACACTATAC
*
82146 AATTATAATACAAATCTATACACTATAC
1 AATTATAATACAAATATATACACTATAC
82174 AAT
1 AAT
82177 AAGGTGGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (28 bp):
AATTATAATACAAATATATACACTATAC
Found at i:82416 original size:30 final size:31
Alignment explanation
Indices: 82382--82439 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
82372 ATTCATAAAA
*
82382 TCTTAATTCTAAT-TAAATATATTTATAGTT
1 TCTTAATTCTAATATAAATATATATATAGTT
* *
82412 TCTTAATTTTAATATAACTATATATATA
1 TCTTAATTCTAATATAAATATATATATA
82440 TAAATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.52
Consensus pattern (31 bp):
TCTTAATTCTAATATAAATATATATATAGTT
Found at i:82641 original size:16 final size:17
Alignment explanation
Indices: 82611--82643 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
82601 ATGAAAGTAC
*
82611 TATCTATTTATTAAATA
1 TATCTATTTAATAAATA
82628 TATCT-TTTAATAAATA
1 TATCTATTTAATAAATA
82644 GATAGTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TATCTATTTAATAAATA
Found at i:87327 original size:39 final size:38
Alignment explanation
Indices: 87279--87388 Score: 141
Period size: 39 Copynumber: 2.8 Consensus size: 38
87269 TTATTTATAA
* **
87279 TTCTCAAATTATTTCATTTTAACATTCTAAATTCTTAAT
1 TTCTTAAATT-TTTCACATTAACATTCTAAATTCTTAAT
*
87318 TTCTTAAATTTTATCACCA-TAACATTTTAAATTCTTAAT
1 TTCTTAAATTTT-TCA-CATTAACATTCTAAATTCTTAAT
*
87357 TTCTTAAAATTTTCACATTAACATTCTAAATT
1 TTCTTAAATTTTTCACATTAACATTCTAAATT
87389 ATTTTTAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
37 2 0.03
38 18 0.29
39 42 0.68
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.49
Consensus pattern (38 bp):
TTCTTAAATTTTTCACATTAACATTCTAAATTCTTAAT
Found at i:94649 original size:42 final size:42
Alignment explanation
Indices: 94602--94729 Score: 136
Period size: 42 Copynumber: 3.0 Consensus size: 42
94592 GTTTTTAGAC
94602 AAACGCCAC-ATAAAGGTTAAACA-ATAGCGGCGTTTATAGTAA
1 AAACGCCACAATAAA-G-TAAACATATAGCGGCGTTTATAGTAA
* * * *
94644 AAACGCCGCAATATAGTAGACATGTAGCGGCGTTTATAGTAA
1 AAACGCCACAATAAAGTAAACATATAGCGGCGTTTATAGTAA
* * * *
94686 AAACGCCGCAATATAGTAGACATGTAGCGGCGTTT-TAGCTAA
1 AAACGCCACAATAAAGTAAACATATAGCGGCGTTTATAG-TAA
94728 AA
1 AA
94730 CATGTGATAT
Statistics
Matches: 79, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
41 8 0.10
42 67 0.85
43 4 0.05
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (42 bp):
AAACGCCACAATAAAGTAAACATATAGCGGCGTTTATAGTAA
Found at i:95846 original size:52 final size:52
Alignment explanation
Indices: 95781--95939 Score: 291
Period size: 52 Copynumber: 3.1 Consensus size: 52
95771 TACTGAACAA
95781 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
* *
95833 TATGTTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCCAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
*
95885 TATGGTGAAGACTGTTTATGAATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
95937 TAT
1 TAT
95940 TTTGTTGTTA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 102 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (52 bp):
TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
Found at i:96159 original size:43 final size:43
Alignment explanation
Indices: 96066--96163 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
96056 ATAAAGGTAT
* * * *
96066 TTAGCGGCGTTTGTATCTAAAAACGCCGCTATATATCTATCCT
1 TTAGCGGCGTTTATATCTAAAAACGCCGCTATATATCAATACA
*
96109 TTTGCGGCGTTTATATCTAAAAACGCCGCTA-ATGAT-AAGTACA
1 TTAGCGGCGTTTATATCTAAAAACGCCGCTATAT-ATCAA-TACA
96152 TTAGCGGCGTTT
1 TTAGCGGCGTTT
96164 TGTTACAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 3 0.06
43 44 0.94
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (43 bp):
TTAGCGGCGTTTATATCTAAAAACGCCGCTATATATCAATACA
Found at i:99404 original size:21 final size:21
Alignment explanation
Indices: 99366--99405 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
99356 TTCATTTTTC
* *
99366 TTGTTATGGATTTTAAGTTAG
1 TTGTTATGGATGTCAAGTTAG
99387 TTGTTATGGATGTCAAGTT
1 TTGTTATGGATGTCAAGTT
99406 TATTGGAAAA
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:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (21 bp):
TTGTTATGGATGTCAAGTTAG
Found at i:99624 original size:45 final size:45
Alignment explanation
Indices: 99534--99624 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 45
99524 TTTATATCTT
* *
99534 AAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTATAAAA
1 AAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTGAGAAAA
* * * * *
99579 AAAACGCTGCTATATACTA-GATCTTTTGCGGTGTTTGTGGGAAAA
1 AAAACGCCGCTATAGA-TATGACCTTTTGCGGCGTTTGTGAGAAAA
99624 A
1 A
99625 TGCTGCTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 36 0.95
46 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (45 bp):
AAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTGAGAAAA
Found at i:99658 original size:43 final size:43
Alignment explanation
Indices: 99611--99786 Score: 226
Period size: 43 Copynumber: 4.1 Consensus size: 43
99601 CTTTTGCGGT
* * *
99611 GTTTGTGGGAAAAATGCTGCTAAATCTCAAGACCTATTGCGAC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGAC
** * *
99654 GTTTGTGAAAAAAACGCCGTTAAATCTCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGAC
*
99697 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGAC
* * * * **
99740 GTTTGTTGGACAAACGCCGCTATATATCATTACCTATTGCGAC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGAC
99783 GTTT
1 GTTT
99787 TTTGTTACCA
Statistics
Matches: 116, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 116 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (43 bp):
GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGAC
Found at i:101668 original size:19 final size:19
Alignment explanation
Indices: 101644--101680 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
101634 ATGACCAACA
* *
101644 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
101663 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
101681 CATTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:102001 original size:22 final size:22
Alignment explanation
Indices: 101976--102048 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
101966 CTACGGTGAC
101976 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
101998 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
102020 ATCCATCCCCATCTCTGACAAA
1 ATCCGTCCCCATCTCCGACGAA
102042 ATCCGTC
1 ATCCGTC
102049 TATCTCCATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.25, C:0.42, G:0.11, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:102452 original size:14 final size:14
Alignment explanation
Indices: 102433--102488 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
102423 ACAAAATTCG
102433 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
102447 CGTTGCGATAGCTATTTCG
1 CGTTGCGAT---TA--TCT
102466 CGTTGCGATTATCT
1 CGTTGCGATTATCT
102480 CGTTGCGAT
1 CGTTGCGAT
102489 AGTCAAATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:102471 original size:33 final size:34
Alignment explanation
Indices: 102426--102508 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 34
102416 CGCAACAACA
102426 AAATTCGCGTTGCGATTATCTCGTTGCGATAG-C
1 AAATTCGCGTTGCGATTATCTCGTTGCGATAGTC
* *
102459 TATTTCGCGTTGCGATTATCTCGTTGCGATAGTC
1 AAATTCGCGTTGCGATTATCTCGTTGCGATAGTC
*
102493 AAATTCGTGTTGCGAT
1 AAATTCGCGTTGCGAT
102509 AATCATTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 30 0.68
34 14 0.32
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (34 bp):
AAATTCGCGTTGCGATTATCTCGTTGCGATAGTC
Found at i:102506 original size:20 final size:20
Alignment explanation
Indices: 102481--102528 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
102471 CGATTATCTC
*
102481 GTTGCGATAGTCAAATTCGT
1 GTTGCGATAATCAAATTCGT
**
102501 GTTGCGATAATCATTTTCGT
1 GTTGCGATAATCAAATTCGT
102521 GTTGCGAT
1 GTTGCGAT
102529 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGATAATCAAATTCGT
Found at i:102538 original size:20 final size:20
Alignment explanation
Indices: 102496--102538 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
102486 GATAGTCAAA
* *
102496 TTCGTGTTGCGATAATCATT
1 TTCGTGTTGCGATAATAAGT
**
102516 TTCGTGTTGCGATTTTAAGT
1 TTCGTGTTGCGATAATAAGT
102536 TTC
1 TTC
102539 AGAAACTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.16, C:0.14, G:0.21, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATAATAAGT
Found at i:104069 original size:21 final size:21
Alignment explanation
Indices: 104021--104070 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
104011 GTTAGGGGAG
* *
104021 TTACGTGATGAGGTCAATGCC
1 TTACGTGAGGAGGTCAATACC
* * *
104042 TTGCGTGAGGAGGTCAGTACT
1 TTACGTGAGGAGGTCAATACC
104063 TTACGTGA
1 TTACGTGA
104071 TGACAATGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACC
Found at i:104378 original size:31 final size:31
Alignment explanation
Indices: 104322--104383 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
104312 TTGTCTTTGT
*
104322 TTTGTCTTTTGGTTGAAGTTAGTAAATTCATA
1 TTTGTCTTTTGGTTG-ACTTAGTAAATTCATA
104354 TTTGTCTTTTGGATTG-CTTAGTAAATTCAT
1 TTTGTCTTTTGG-TTGACTTAGTAAATTCAT
104384 TCGGTAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.52
Consensus pattern (31 bp):
TTTGTCTTTTGGTTGACTTAGTAAATTCATA
Found at i:104543 original size:20 final size:19
Alignment explanation
Indices: 104502--104661 Score: 115
Period size: 20 Copynumber: 8.6 Consensus size: 19
104492 AGAAGAATAG
* *
104502 TCGCAACACGAAAATGATTA
1 TCGCAACGCG-AAATGACTA
*
104522 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAA-ATGACTA
*
104542 TCACAACGCG--AT-A--A
1 TCGCAACGCGAAATGACTA
*
104556 TCGCAATGCGAAAATGACTA
1 TCGCAACGCG-AAATGACTA
*
104576 TCGCAACGTGGAAATGACTA
1 TCGCAACG-CGAAATGACTA
*
104596 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAA-ATGACTA
*
104616 TCGCAACG-G-GAT-A--A
1 TCGCAACGCGAAATGACTA
*
104630 TCGCAATGCGAAAATGACTA
1 TCGCAACGCG-AAATGACTA
104650 TCGCAACGCGAA
1 TCGCAACGCGAA
104662 TTTAGTTTCG
Statistics
Matches: 109, Mismatches: 16, Indels: 31
0.70 0.10 0.20
Matches are distributed among these distances:
14 17 0.16
15 1 0.01
16 2 0.02
17 6 0.06
18 2 0.02
19 8 0.07
20 72 0.66
21 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:104623 original size:74 final size:74
Alignment explanation
Indices: 104513--104657 Score: 263
Period size: 74 Copynumber: 2.0 Consensus size: 74
104503 CGCAACACGA
*
104513 AAATGATTATCGCAACGCGAATTTGACTATCACAACGCGATAATCGCAATGCGAAAATGACTATC
1 AAATGACTATCGCAACGCGAATTTGACTATCACAACGCGATAATCGCAATGCGAAAATGACTATC
104578 GCAACGTGG
66 GCAACGTGG
* *
104587 AAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAATGACTATC
1 AAATGACTATCGCAACGCGAATTTGACTATCACAACGCGATAATCGCAATGCGAAAATGACTATC
104652 GCAACG
66 GCAACG
104658 CGAATTTAGT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (74 bp):
AAATGACTATCGCAACGCGAATTTGACTATCACAACGCGATAATCGCAATGCGAAAATGACTATC
GCAACGTGG
Found at i:104688 original size:19 final size:19
Alignment explanation
Indices: 104666--104702 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
104656 CGCGAATTTA
104666 GTTTCGCGTTGCAATTTTG
1 GTTTCGCGTTGCAATTTTG
*
104685 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCAATTTT
104703 CTCGTTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCAATTTTG
Found at i:104745 original size:20 final size:20
Alignment explanation
Indices: 104705--104812 Score: 137
Period size: 20 Copynumber: 5.5 Consensus size: 20
104695 GCGATTTTCT
* *
104705 CGTTGCAATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
104724 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
104744 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
104764 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
104784 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
104804 TGTTGCGAT
1 CGTTGCGAT
104813 TTTAAGTTTC
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
19 12 0.15
20 66 0.85
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:104776 original size:40 final size:40
Alignment explanation
Indices: 104705--104812 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 40
104695 GCGATTTTCT
* *
104705 CGTTGCAATAGTC-ATTTCGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCGTGTTGCGATAGTCAAATTCG
* *
104744 CGTTGTGATAGTCAAATTCGTGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCGTGTTGCGATAGTCAAATTCG
* *
104784 CGTTGCGATAATCATTTTCGTGTTGCGAT
1 CGTTGCGATAGTCAATTTCGTGTTGCGAT
104813 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 11 0.18
40 49 0.82
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCAATTTCGTGTTGCGATAGTCAAATTCG
Found at i:104822 original size:20 final size:20
Alignment explanation
Indices: 104799--104842 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
104789 CGATAATCAT
104799 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
104819 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
104839 TTTC
1 TTTC
104843 AGAAACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:105413 original size:21 final size:21
Alignment explanation
Indices: 105322--105420 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
105312 GACTCACCTG
* *
105322 TCATCATTCAAGAGGCCTCT-
1 TCATCGTTCAAGAGGCCCCTA
*
105342 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCCCTA
** * * *
105364 TCATCCCTCATGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* *
105385 CCACCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
*
105406 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
105421 TCCTTCCCAA
Statistics
Matches: 58, Mismatches: 19, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:105429 original size:42 final size:42
Alignment explanation
Indices: 105329--105410 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
105319 CTGTCATCAT
* * * *
105329 TCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
*
105371 TCATGAGTCCCCTCCCACCGTTCAAGAGGCCCCTATCATC
1 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTATCATC
105411 GTTGAAGAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.21, C:0.40, G:0.16, T:0.23
Consensus pattern (42 bp):
TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:106884 original size:36 final size:30
Alignment explanation
Indices: 106804--106869 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
106794 ATAAGAGTTG
*
106804 ATTTGTTTAATTAATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
106834 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
106864 ATTTGT
1 ATTTGT
106870 GCTTGTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:106956 original size:54 final size:54
Alignment explanation
Indices: 106842--106956 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
106832 TTATTTGTTT
* * *
106842 AATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTTTAT
1 AATTGATGTGTAAATAATTCTTATTTGTGCTTGTGTAATTGATTAAAAGTGTAA
* *
106896 TATTGATGTGTAAATAATTCTTATTTGTGCTTGTGTAATTGATTGAAA-TGTAA
1 AATTGATGTGTAAATAATTCTTATTTGTGCTTGTGTAATTGATTAAAAGTGTAA
106949 AAGTTGAT
1 AA-TTGAT
106957 TTGTTGATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 4 0.07
54 50 0.93
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.48
Consensus pattern (54 bp):
AATTGATGTGTAAATAATTCTTATTTGTGCTTGTGTAATTGATTAAAAGTGTAA
Found at i:107045 original size:34 final size:34
Alignment explanation
Indices: 106985--107235 Score: 135
Period size: 34 Copynumber: 6.9 Consensus size: 34
106975 ATCATATTCG
* * * *
106985 CGTTGCGATAGTCTAATACACTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* *
107019 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCT
* * * *
107059 CATTGCGATAGTC-ATTTCGCGTAGCGATTATCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
*
107092 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCG--A-TT---TTCT
* * *
107132 CGTTACGATAGTCATATTCGCGTTGCGATAGTCATTTTTT
1 CGTTGCGATAGTCAAATTCGCGTTGC----G--ATTTTCT
** ** * * *
107172 GCGTTGCGATAGTCATTTTCGAATTGCAATTATCC
1 -CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
107207 CGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT
107236 AGTCATTTTC
Statistics
Matches: 164, Mismatches: 35, Indels: 36
0.70 0.15 0.15
Matches are distributed among these distances:
33 14 0.09
34 60 0.37
35 4 0.02
36 2 0.01
37 3 0.02
39 12 0.07
40 43 0.26
41 22 0.13
43 2 0.01
44 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:107100 original size:73 final size:74
Alignment explanation
Indices: 107009--107160 Score: 234
Period size: 73 Copynumber: 2.1 Consensus size: 74
106999 AATACACTTT
* *
107009 GCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCATTGCGATAGTCAT
1 GCGATTATCTCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCATTACGATAGTCAT
107074 -TTCGCGTA
66 ATTCGCGTA
* * * *
107082 GCGATTATCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTACGATAGTCAT
1 GCGATTATCTCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCATTACGATAGTCAT
*
107147 ATTCGCGTT
66 ATTCGCGTA
107156 GCGAT
1 GCGAT
107161 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 59 0.83
74 12 0.17
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (74 bp):
GCGATTATCTCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCATTACGATAGTCAT
ATTCGCGTA
Found at i:107177 original size:21 final size:20
Alignment explanation
Indices: 107019--107255 Score: 194
Period size: 20 Copynumber: 12.4 Consensus size: 20
107009 GCGATTTTCT
* *
107019 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCATATTCG
* *
107039 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCATATTCG
*
107059 CATTGCGATAGTCAT-TTCG
1 CGTTGCGATAGTCATATTCG
* *
107078 CGTAGCG--A-T--TA-TCT
1 CGTTGCGATAGTCATATTCG
*
107092 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATATTCG
* *
107112 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCATATTCG
*
107132 CGTTACGATAGTCATATTCG
1 CGTTGCGATAGTCATATTCG
* *
107152 CGTTGCGATAGTCATTTTTTG
1 CGTTGCGATAGTCA-TATTCG
*
107173 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATATTCG
** *
107193 AATTGC-A-A-T--TA-TCC
1 CGTTGCGATAGTCATATTCG
*
107207 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATATTCG
*
107227 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATATTCG
*
107247 CATTGCGAT
1 CGTTGCGAT
107256 TATCCCGTTG
Statistics
Matches: 173, Mismatches: 30, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
14 15 0.09
15 2 0.01
16 3 0.02
17 4 0.02
18 1 0.01
19 12 0.07
20 118 0.68
21 18 0.10
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATATTCG
Found at i:107228 original size:95 final size:92
Alignment explanation
Indices: 107019--107255 Score: 273
Period size: 95 Copynumber: 2.5 Consensus size: 92
107009 GCGATTTTCT
* * *
107019 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCATTGCGATAGTCATTTCGCGTAGC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTGCGATAGTCATTTCGCGTAGC
*
107084 GATTATCTCGTTGCGATAGTCAAATTCG
66 GATTATCTC-TTGCGATAGTCAAATTCC
* * * * *
107112 CGTTGCGATAGTTAAATTCGCGTTACGATAGTCATATTCGCGTTGCGATAGTCATTTTTTGCGTT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTGCGATAGTCA--TTTCGCGTA
* * *
107177 GCGA-TAGTCAT-TTTCGA-ATTGCAATTATCC
64 GCGATTA-TC-TCTTGCGATAGT-CAAAT-TCC
*
107207 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTGCGAT
107256 TATCCCGTTG
Statistics
Matches: 122, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
93 50 0.41
94 11 0.09
95 60 0.49
96 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (92 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCATTGCGATAGTCATTTCGCGTAGC
GATTATCTCTTGCGATAGTCAAATTCC
Found at i:107496 original size:18 final size:18
Alignment explanation
Indices: 107473--107507 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
107463 AAGCTGGTTG
*
107473 TGATTGGGATTTTGATTC
1 TGATTGCGATTTTGATTC
107491 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
107508 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.26, T:0.51
Consensus pattern (18 bp):
TGATTGCGATTTTGATTC
Found at i:114326 original size:20 final size:20
Alignment explanation
Indices: 114272--114330 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
114262 ATTCGAAACA
* *
114272 CGATTTTGACTATCGCAATG
1 CGATTATGACTATCGCAACG
* *
114292 CGAATATGTA-AATCGCAACG
1 CGATTATG-ACTATCGCAACG
*
114312 CGATTCTGACTATCGCAAC
1 CGATTATGACTATCGCAAC
114331 ACTGAATTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (20 bp):
CGATTATGACTATCGCAACG
Found at i:116148 original size:20 final size:21
Alignment explanation
Indices: 116109--116165 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
116099 TCTGAAACTT
116109 AAAATCACAACACGAAAAATG
1 AAAATCACAACACGAAAAATG
*
116130 AAAATCGCAACAC-AAAAATG
1 AAAATCACAACACGAAAAATG
**
116150 ACTATCACAACACGAA
1 AAAATCACAACACGAA
116166 TTTGACTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.58, C:0.23, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAATCACAACACGAAAAATG
Found at i:116827 original size:21 final size:21
Alignment explanation
Indices: 116803--116871 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
116793 GAAAATCACA
116803 TTGCGATTTTGTATTATCGCG
1 TTGCGATTTTGTATTATCGCG
* **
116824 TTGCGA--TAGTCAGAATCGCG
1 TTGCGATTTTGT-ATTATCGCG
116844 TTGCGATTTTGTATTATCGCG
1 TTGCGATTTTGTATTATCGCG
116865 TTGCGAT
1 TTGCGAT
116872 AGTTAGAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.08
20 13 0.33
21 20 0.51
22 3 0.08
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTGTATTATCGCG
Found at i:116843 original size:20 final size:20
Alignment explanation
Indices: 116818--116931 Score: 88
Period size: 20 Copynumber: 5.6 Consensus size: 20
116808 ATTTTGTATT
*
116818 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
* **
116838 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAAA
* *
116859 ATCGCGTTGCGATAGTTAGA
1 ATCGCGTTGCGATAGTCAAA
*
116879 ATCGCGTTGCGA-ATTTCGAAA
1 ATCGCGTTGCGATA-GTC-AAA
** *
116900 ATCGCAATGTGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
116920 ATCGCGTTGCGA
1 ATCGCGTTGCGA
116932 ATCTGAAAAC
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
19 4 0.06
20 38 0.53
21 26 0.36
22 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:116860 original size:41 final size:41
Alignment explanation
Indices: 116803--116931 Score: 170
Period size: 41 Copynumber: 3.1 Consensus size: 41
116793 GAAAATCACA
116803 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
*
116844 TTGCGATTTTGTATTATCGCGTTGCGATAGTTAGAATCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
* ** ** * *
116885 TTGCGAATTTCG-AAAATCGCAATGTGATAGTCAAAATCGCG
1 TTGCG-ATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
116926 TTGCGA
1 TTGCGA
116932 ATCTGAAAAC
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 72 0.92
42 5 0.06
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (41 bp):
TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCG
Done.