Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003493.1 Hibiscus syriacus cultivar Beakdansim tig00007389_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: 83730
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:18820 original size:20 final size:20
Alignment explanation
Indices: 18795--18838 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
18785 TTCACAACTT
*
18795 GTTTTTATATGTTTGAATGA
1 GTTTTTATATGTTGGAATGA
18815 GTTTTTATATGTTGGAATGA
1 GTTTTTATATGTTGGAATGA
18835 GTTT
1 GTTT
18839 GTGGCCGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (20 bp):
GTTTTTATATGTTGGAATGA
Found at i:22346 original size:19 final size:19
Alignment explanation
Indices: 22322--22377 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
22312 GTGTTTTAAT
22322 CATATGTATAATCATATTC
1 CATATGTATAATCATATTC
** *
22341 CATATG--TGCTC-TAAT-
1 CATATGTATAATCATATTC
22356 CATATGTATAATCATATTC
1 CATATGTATAATCATATTC
22375 CAT
1 CAT
22378 TTGCATCCCA
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
15 6 0.22
16 3 0.11
17 6 0.22
18 3 0.11
19 9 0.33
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (19 bp):
CATATGTATAATCATATTC
Found at i:22458 original size:2 final size:2
Alignment explanation
Indices: 22451--22511 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
22441 TTAATTCAAC
22451 TA TA TA TA TA 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 TA TA TA TA TA
22493 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
22512 CATCTAATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22720 original size:23 final size:23
Alignment explanation
Indices: 22649--22720 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
22639 AAGATAAAAA
22649 ATAATATTTAAATAGTGAGAATT
1 ATAATATTTAAATAGTGAGAATT
* * * *
22672 ATATTCA-TAAAATAAT-ATTTAA-T
1 ATAAT-ATTTAAATAGTGA--GAATT
22695 ATAATATTTAAATAGTGAGAATT
1 ATAATATTTAAATAGTGAGAATT
22718 ATA
1 ATA
22721 TTAAAGAGAG
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
22 4 0.11
23 27 0.77
24 4 0.11
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.40
Consensus pattern (23 bp):
ATAATATTTAAATAGTGAGAATT
Found at i:24252 original size:2 final size:2
Alignment explanation
Indices: 24245--24319 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
24235 ATGAACATGG
24245 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
24287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24320 CTCCCATGGT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26876 original size:23 final size:21
Alignment explanation
Indices: 26826--26879 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 21
26816 ATTAACGTGA
26826 TATAAAT-TATTAAATGTATTT
1 TATAAATATA-TAAATGTATTT
26847 T-TAAATATATAAATGATATGTT
1 TATAAATATATAAATG-TAT-TT
26869 TATAAATATAT
1 TATAAATATAT
26880 TGTACTAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 11 0.38
21 6 0.21
22 3 0.10
23 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (21 bp):
TATAAATATATAAATGTATTT
Found at i:26877 original size:21 final size:20
Alignment explanation
Indices: 26826--26878 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
26816 ATTAACGTGA
*
26826 TATAAATTATTAAATGTATTTT
1 TATAAA-TA-TAAATGTATGTT
26848 TA-AATATATAAATGATATGTT
1 TATAA-ATATAAATG-TATGTT
26869 TATAAATATA
1 TATAAATATA
26879 TTGTACTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 6 0.22
21 16 0.59
22 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (20 bp):
TATAAATATAAATGTATGTT
Found at i:31510 original size:1 final size:1
Alignment explanation
Indices: 31506--31537 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
31496 TCAAGGGGGC
31506 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31538 TCAGTGTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44619 original size:14 final size:14
Alignment explanation
Indices: 44593--44693 Score: 58
Period size: 15 Copynumber: 7.4 Consensus size: 14
44583 CTATGCTTGA
44593 AGAAAAA-AAAAAG
1 AGAAAAATAAAAAG
44606 -GAACAAATAAAAAG
1 AGAA-AAATAAAAAG
44620 ATGAAAAATAAAAA-
1 A-GAAAAATAAAAAG
*
44634 A-AAATGA-AAAAAG
1 AGAAA-AATAAAAAG
44647 -GAAAAAATGAAAAATG
1 AG-AAAAAT-AAAAA-G
*
44663 A-AAAAA-AGAAATG
1 AGAAAAATA-AAAAG
44676 A-AAAAATAAAAAG
1 AGAAAAATAAAAAG
44689 AGAAA
1 AGAAA
44694 GGAGGGTTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 29
0.68 0.04 0.28
Matches are distributed among these distances:
12 11 0.16
13 18 0.26
14 17 0.25
15 19 0.28
16 4 0.06
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (14 bp):
AGAAAAATAAAAAG
Found at i:44628 original size:15 final size:13
Alignment explanation
Indices: 44594--44693 Score: 57
Period size: 14 Copynumber: 7.3 Consensus size: 13
44584 TATGCTTGAA
44594 GAAAAA-AAAAAG
1 GAAAAATAAAAAG
44606 GAACAAATAAAAAG
1 GAA-AAATAAAAAG
44620 ATGAAAAAT-AAAA-
1 --GAAAAATAAAAAG
44633 -AAAAATGAAAAAAG
1 GAAAAAT--AAAAAG
*
44647 GAAAAAATGAAAAAT
1 G-AAAAAT-AAAAAG
44662 GAAAAA-AAGAAATG
1 GAAAAATAA-AAA-G
*
44676 AAAAAATAAAAAG
1 GAAAAATAAAAAG
44689 AGAAA
1 -GAAA
44694 GGAGGGTTTG
Statistics
Matches: 69, Mismatches: 5, Indels: 26
0.69 0.05 0.26
Matches are distributed among these distances:
10 6 0.09
12 5 0.07
13 11 0.16
14 26 0.38
15 12 0.17
16 9 0.13
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (13 bp):
GAAAAATAAAAAG
Found at i:44637 original size:33 final size:34
Alignment explanation
Indices: 44595--44693 Score: 123
Period size: 33 Copynumber: 2.9 Consensus size: 34
44585 ATGCTTGAAG
* *
44595 AAAAAAAAAAGGAACAAATAAAAAGATGAAAAAT
1 AAAAAAAAAATGAAAAAATAAAAAGATGAAAAAT
*
44629 -AAAAAAAAATGAAAAAAGGAAAAA-ATGAAAAAT
1 AAAAAAAAAATGAAAAAA-TAAAAAGATGAAAAAT
44662 GAAAAAAAGAAATGAAAAAATAAAAAGA-GAAA
1 -AAAAAAA-AAATGAAAAAATAAAAAGATGAAA
44694 GGAGGGTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
33 24 0.43
34 5 0.09
35 15 0.27
36 12 0.21
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.08
Consensus pattern (34 bp):
AAAAAAAAAATGAAAAAATAAAAAGATGAAAAAT
Found at i:44692 original size:20 final size:20
Alignment explanation
Indices: 44651--44693 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
44641 AAAAAGGAAA
44651 AAATGAAAAATGAAAAAAAG
1 AAATGAAAAATGAAAAAAAG
*
44671 AAATGAAAAAAT-AAAAAGAG
1 AAATG-AAAAATGAAAAAAAG
44691 AAA
1 AAA
44694 GGAGGGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
AAATGAAAAATGAAAAAAAG
Found at i:45811 original size:136 final size:136
Alignment explanation
Indices: 45562--45914 Score: 555
Period size: 136 Copynumber: 2.6 Consensus size: 136
45552 GGAGGTGAAC
45562 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
* * *
45627 ATGAGAAGAGCTTGTTCGACCTATCACTAGATTCACGACATTTTGAATCAGTGACACCTTGCTTG
66 ATGAGAAGAGCTTGTTCGACCTATCACTAGATTCACAACATTTCGAATCAGTGACACCTCGCTTG
45692 AAGGAT
131 AAGGAT
** *
45698 CAGTATTTCCAATGGATAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
* *
45763 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACACCTCGCTTG
66 ATGAGAAGAGCTTGTTCGACCTATCACTAGATTCACAACATTTCGAATCAGTGACACCTCGCTTG
*
45828 AGGGAT
131 AAGGAT
* * ** * *
45834 CAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCAAAC-GAAGAAGAAGAAGTTCATA
1 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
*
45898 ATGAGAAGAACTTGTTC
66 ATGAGAAGAGCTTGTTC
45915 AACTTCGCAT
Statistics
Matches: 198, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
135 33 0.17
136 165 0.83
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (136 bp):
CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCGACCTATCACTAGATTCACAACATTTCGAATCAGTGACACCTCGCTTG
AAGGAT
Found at i:45951 original size:91 final size:87
Alignment explanation
Indices: 45832--46001 Score: 234
Period size: 91 Copynumber: 1.9 Consensus size: 87
45822 CGCTTGAGGG
* *
45832 ATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCAAACGAAGAAGA-AGAAGTTCA
1 ATCAACATTTCCAATGAAGAGCTCATAATGAGAAGAACTCATC---CGAA-AAGATA-AAGTTCA
45896 TAATGAGAAGAACTTGTTCAACTTCGC
61 TAATGAGAAGAACTTGTTCAACTTCGC
* * * *
45923 ATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCTAAAGGATAAAGTTCATAATG
1 ATCAACATTTCCAATGAAGAGCTCATAATGAGAAGAACTCATCCGAAAAGATAAAGTTCATAATG
45988 AGAAGAACTTGTTC
66 AGAAGAACTTGTTC
46002 CTTTCAAATC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
87 29 0.40
88 4 0.06
91 39 0.54
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (87 bp):
ATCAACATTTCCAATGAAGAGCTCATAATGAGAAGAACTCATCCGAAAAGATAAAGTTCATAATG
AGAAGAACTTGTTCAACTTCGC
Found at i:46112 original size:20 final size:20
Alignment explanation
Indices: 46049--46113 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
46039 TTCAGTGAAG
46049 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
46069 CA-TCCA-AA-GAGGAAGAAGA
1 -AGTTCATAATGA-GAAGAACT
46088 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
46108 TGTTCA
1 AGTTCA
46114 ACCTTGGTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:46176 original size:117 final size:113
Alignment explanation
Indices: 45923--46231 Score: 416
Period size: 117 Copynumber: 2.7 Consensus size: 113
45913 TCAACTTCGC
* * * * *
45923 ATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCATCCTAAAGG-A-TA-AAGTTCATA
1 ATCAACATTTTCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAAAGGAAGAAGAAGTTCATA
45985 ATGAGAAGAACTTGTT---CCTTTCAAATCCATCACAGAAAGAGATGG
66 ATGAGAAGAACTTGTTCAACCTTTCAAATCCATCACAGAAAGAGATGG
*
46030 GTCAACATTTTCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTTCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAA-AGGAAGAAGAAGTTCAT
* * * * *
46095 AATGAGAAGAACTTGTTCAACCTTGGTTCGATTTCATCACAGAAGGAGGTGG
65 AATGAGAAGAACTTGTTCAACC-T--TTCAAATCCATCACAGAAAGAGATGG
46147 ATCAACATTTTCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAACAA-GAGAGAAGAAGTTCA
1 ATCAACATTTTCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAA-AAGGA-AGAAGAAGTTCA
46211 TAATGAGAAGAACTTGTTCAA
64 TAATGAGAAGAACTTGTTCAA
46232 TCCAACGCTT
Statistics
Matches: 178, Mismatches: 12, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
107 42 0.24
108 3 0.02
109 1 0.01
110 1 0.01
111 25 0.14
114 2 0.01
115 1 0.01
116 2 0.01
117 100 0.56
118 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (113 bp):
ATCAACATTTTCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAAAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTCAAATCCATCACAGAAAGAGATGG
Found at i:46772 original size:1 final size:1
Alignment explanation
Indices: 46768--46801 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
46758 TCAAGGGGGC
46768 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
46802 TCAGTGTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:49825 original size:129 final size:129
Alignment explanation
Indices: 49595--49844 Score: 412
Period size: 129 Copynumber: 1.9 Consensus size: 129
49585 TATCCTATGC
* * *
49595 ATTAAGGAAGAAGAAGATCCTATGAGAATATTGAATTCCCTTTCAGCTTCTAAATTAATTTCAAT
1 ATTAAGGAAGAAGAAGACCCTACGAGAATATTGAATTCCCTTTCAGCATCTAAATTAATTTCAAT
* * *
49660 CCCCGCTGTGTTTTTCATACTTTCCAATGATATCCGAGCAGATTCTCTATCTCTCTTCCGATGG
66 CCCAGCTGTGTTTTTCATACTTTCCAATGACATCCGAGAAGATTCTCTATCTCTCTTCCGATGG
49724 ATTAAGGAAGAAGAAGACCCTACGAGGAA-ATTGAATTCCCTTTCAGCATCTAAATTAATTTCAA
1 ATTAAGGAAGAAGAAGACCCTACGA-GAATATTGAATTCCCTTTCAGCATCTAAATTAATTTCAA
* *
49788 TCCCAGCTGTGTTTTTCATACTTTCCAATGCCATCCGAGAAGCTTCTCTATCTCTCT
65 TCCCAGCTGTGTTTTTCATACTTTCCAATGACATCCGAGAAGATTCTCTATCTCTCT
49845 CCCGTTGTAT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
129 109 0.97
130 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (129 bp):
ATTAAGGAAGAAGAAGACCCTACGAGAATATTGAATTCCCTTTCAGCATCTAAATTAATTTCAAT
CCCAGCTGTGTTTTTCATACTTTCCAATGACATCCGAGAAGATTCTCTATCTCTCTTCCGATGG
Found at i:50820 original size:16 final size:16
Alignment explanation
Indices: 50792--50841 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
50782 ACTCGAACCG
*
50792 AAAA-TAACACAAACT
1 AAAAGTAACTCAAACT
50807 AAAAGTAACTCAAACT
1 AAAAGTAACTCAAACT
* * *
50823 GAAAGAAACTCGAACT
1 AAAAGTAACTCAAACT
50839 AAA
1 AAA
50842 TATAAACCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 4 0.14
16 25 0.86
ACGTcount: A:0.60, C:0.18, G:0.08, T:0.14
Consensus pattern (16 bp):
AAAAGTAACTCAAACT
Found at i:52047 original size:12 final size:12
Alignment explanation
Indices: 52030--52084 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
52020 TCTAAAATGT
52030 TGCTTCTCTCTC
1 TGCTTCTCTCTC
**
52042 TGCTTCTCTCGA
1 TGCTTCTCTCTC
52054 TGC-TCTCT-T-
1 TGCTTCTCTCTC
*
52063 TGCTTCTGTCTC
1 TGCTTCTCTCTC
52075 TGCTTCTCTC
1 TGCTTCTCTC
52085 GCTTCAGCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 3 0.09
10 4 0.11
11 6 0.17
12 22 0.63
ACGTcount: A:0.02, C:0.36, G:0.13, T:0.49
Consensus pattern (12 bp):
TGCTTCTCTCTC
Found at i:53143 original size:17 final size:17
Alignment explanation
Indices: 53103--53136 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53093 TCCAATTATC
53103 ACCCGACCCGAAAATTG
1 ACCCGACCCGAAAATTG
*
53120 ACCCGACCTGAAAATTG
1 ACCCGACCCGAAAATTG
53137 GCTCGACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (17 bp):
ACCCGACCCGAAAATTG
Found at i:53669 original size:15 final size:15
Alignment explanation
Indices: 53649--53682 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
53639 CTTTCCGTTG
* *
53649 TGATGATTATGATTA
1 TGATGATAATGATAA
53664 TGATGATAATGATAA
1 TGATGATAATGATAA
53679 TGAT
1 TGAT
53683 AATAGTATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (15 bp):
TGATGATAATGATAA
Found at i:55134 original size:16 final size:16
Alignment explanation
Indices: 55115--55176 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
55105 AAATAACACA
*
55115 AACTAAAAGTAACTCG
1 AACTAAAAGTAACCCG
*
55131 AACTGAAAGTAACCCG
1 AACTAAAAGTAACCCG
*
55147 AACTAAATA-TAAACCG
1 AACTAAA-AGTAACCCG
* *
55163 ATCCAAAAGTAACC
1 AACTAAAAGTAACC
55177 TGGACTGATG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 1 0.03
16 35 0.95
17 1 0.03
ACGTcount: A:0.50, C:0.23, G:0.11, T:0.16
Consensus pattern (16 bp):
AACTAAAAGTAACCCG
Found at i:55574 original size:22 final size:22
Alignment explanation
Indices: 55535--55576 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55525 ATAAAAGAAT
*
55535 ATATATTATTATTATTATATTG
1 ATATATAATTATTATTATATTG
* *
55557 ATATATAATTTTTTTTATAT
1 ATATATAATTATTATTATAT
55577 AAATGAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATATATAATTATTATTATATTG
Found at i:56329 original size:32 final size:32
Alignment explanation
Indices: 56293--56365 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
56283 TCAACCAATA
56293 TGATATTGAT-TCAACCCGAAAACTAAACGATT
1 TGATATTGATAT-AACCCGAAAACTAAACGATT
* * * *
56325 TGATATTAATATGACCCGAAAATTAATCGATT
1 TGATATTGATATAACCCGAAAACTAAACGATT
56357 TGATATTGA
1 TGATATTGA
56366 CCTAACCTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 34 0.97
33 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (32 bp):
TGATATTGATATAACCCGAAAACTAAACGATT
Found at i:56378 original size:32 final size:32
Alignment explanation
Indices: 56305--56378 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
56295 ATATTGATTC
* * **
56305 AACCCGAAAACTAAACGATTTGATATTAATAT
1 AACCCGAAAATTAAACGATTTGATATTGACCT
* *
56337 GACCCGAAAATTAATCGATTTGATATTGACCT
1 AACCCGAAAATTAAACGATTTGATATTGACCT
*
56369 AACCTGAAAA
1 AACCCGAAAA
56379 AATCTGATCT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (32 bp):
AACCCGAAAATTAAACGATTTGATATTGACCT
Found at i:56683 original size:21 final size:21
Alignment explanation
Indices: 56658--56705 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
56648 CCTAATATTG
56658 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
56679 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
56700 TAATGT
1 CAATGT
56706 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:61332 original size:21 final size:21
Alignment explanation
Indices: 61307--61354 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
61297 CCTAATATTG
61307 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
61328 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
61349 TAATGT
1 CAATGT
61355 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:62998 original size:16 final size:15
Alignment explanation
Indices: 62975--63013 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
62965 ACTCGAACCG
62975 AAAATAACTCAAACT
1 AAAATAACTCAAACT
*
62990 AAAAGTAACTCGAACT
1 AAAA-TAACTCAAACT
63006 AAATATAA
1 AAA-ATAA
63014 ACCGATCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 16 0.76
17 1 0.05
ACGTcount: A:0.59, C:0.15, G:0.05, T:0.21
Consensus pattern (15 bp):
AAAATAACTCAAACT
Found at i:64194 original size:12 final size:12
Alignment explanation
Indices: 64177--64252 Score: 65
Period size: 12 Copynumber: 6.8 Consensus size: 12
64167 TCTAAAATGT
64177 TGCTTCTCTCTC
1 TGCTTCTCTCTC
64189 TGC-T-TCTCTC
1 TGCTTCTCTCTC
* *
64199 -GATGCTCTCTC
1 TGCTTCTCTCTC
**
64210 TGCTTCTCTCGA
1 TGCTTCTCTCTC
64222 TGC-TCTCT-T-
1 TGCTTCTCTCTC
*
64231 TGCTTCTGTCTC
1 TGCTTCTCTCTC
64243 TGCTTCTCTC
1 TGCTTCTCTC
64253 GCTTCAGCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
9 4 0.08
10 10 0.20
11 13 0.27
12 22 0.45
ACGTcount: A:0.03, C:0.37, G:0.13, T:0.47
Consensus pattern (12 bp):
TGCTTCTCTCTC
Found at i:64246 original size:21 final size:21
Alignment explanation
Indices: 64182--64237 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
64172 AATGTTGCTT
64182 CTCTCTCTGCTTCTCTCGATG
1 CTCTCTCTGCTTCTCTCGATG
64203 CTCTCTCTGCTTCTCTCGATG
1 CTCTCTCTGCTTCTCTCGATG
*
64224 CTCTCTTTGCTTCT
1 CTCTCTCTGCTTCT
64238 GTCTCTGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.04, C:0.38, G:0.12, T:0.46
Consensus pattern (21 bp):
CTCTCTCTGCTTCTCTCGATG
Found at i:65228 original size:17 final size:17
Alignment explanation
Indices: 65206--65241 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
65196 TCCAATTATC
65206 ACCCGACCCGAAAATTG
1 ACCCGACCCGAAAATTG
*
65223 ACCCGACCTGAAAATTG
1 ACCCGACCCGAAAATTG
65240 AC
1 AC
65242 TAGACTCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.33, G:0.17, T:0.14
Consensus pattern (17 bp):
ACCCGACCCGAAAATTG
Found at i:66323 original size:129 final size:129
Alignment explanation
Indices: 66093--66342 Score: 421
Period size: 129 Copynumber: 1.9 Consensus size: 129
66083 TATCCTATGC
* *
66093 ATTAAGGAAGAAGAAGATCCTATGAGAATATTGAATTCCCTTTCAGCTTCTAAATTAATTTCAAT
1 ATTAAGGAAGAAGAAGATCCTACGAGAATATTGAATTCCCTTTCAGCATCTAAATTAATTTCAAT
*
66158 CCCCGCTGTGTTTTTCATACTTTCCAATGCCATCCGAGCAGCTTCTCTATCTCTCTTCCGATGG
66 CCCAGCTGTGTTTTTCATACTTTCCAATGCCATCCGAGCAGCTTCTCTATCTCTCTTCCGATGG
66222 ATTAAGGAAGAAGAAGATCCTACGAGGAA-ATTGAATTCCCTTTCAGCATCTAAATTAATTTCAA
1 ATTAAGGAAGAAGAAGATCCTACGA-GAATATTGAATTCCCTTTCAGCATCTAAATTAATTTCAA
* * * *
66286 TTCCAGCTGTGTTTTTCATACTTTTCACTGCGATCCGAGCAGCTTCTCTATCTCTCT
65 TCCCAGCTGTGTTTTTCATACTTTCCAATGCCATCCGAGCAGCTTCTCTATCTCTCT
66343 CCCTTTGTTT
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
129 110 0.97
130 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (129 bp):
ATTAAGGAAGAAGAAGATCCTACGAGAATATTGAATTCCCTTTCAGCATCTAAATTAATTTCAAT
CCCAGCTGTGTTTTTCATACTTTCCAATGCCATCCGAGCAGCTTCTCTATCTCTCTTCCGATGG
Found at i:67065 original size:21 final size:21
Alignment explanation
Indices: 67040--67084 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
67030 TTAAATAATT
*
67040 ATTTT-ATTTTTGAATATTTTA
1 ATTTTCATATTTGAAT-TTTTA
67061 ATTTTCATATTTGAATTTTTA
1 ATTTTCATATTTGAATTTTTA
67082 ATT
1 ATT
67085 AACAAGACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (21 bp):
ATTTTCATATTTGAATTTTTA
Found at i:67300 original size:16 final size:16
Alignment explanation
Indices: 67281--67342 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
67271 AAATAACACA
*
67281 AACTAAAAGTAACTCG
1 AACTAAAAGTAACCCG
*
67297 AACTGAAAGTAACCCG
1 AACTAAAAGTAACCCG
*
67313 AACTAAATA-TAAACCG
1 AACTAAA-AGTAACCCG
* *
67329 ATCCAAAAGTAACC
1 AACTAAAAGTAACC
67343 TGGACTGATG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 1 0.03
16 35 0.95
17 1 0.03
ACGTcount: A:0.50, C:0.23, G:0.11, T:0.16
Consensus pattern (16 bp):
AACTAAAAGTAACCCG
Found at i:68479 original size:32 final size:32
Alignment explanation
Indices: 68438--68515 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
68428 TAAAATCAAC
*
68438 CGATATGATATTGAT-TCAACCCGAAAACTAAA
1 CGATTTGATATTGATAT-AACCCGAAAACTAAA
* * * * *
68470 CTATTTGATATTAATATGACCCGAAAATTAAT
1 CGATTTGATATTGATATAACCCGAAAACTAAA
68502 CGATTTGATATTGA
1 CGATTTGATATTGA
68516 CCTAACCTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
32 36 0.97
33 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATTTGATATTGATATAACCCGAAAACTAAA
Found at i:68850 original size:19 final size:18
Alignment explanation
Indices: 68826--68861 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
68816 CGCAAATCGG
68826 GAGAAAAGGAGAAAAAAAA
1 GAGAAAAGGA-AAAAAAAA
*
68845 GAGAAAATGAAAAAAAA
1 GAGAAAAGGAAAAAAAA
68862 GGAATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (18 bp):
GAGAAAAGGAAAAAAAAA
Found at i:70356 original size:16 final size:16
Alignment explanation
Indices: 70328--70377 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
70318 ACTCGAACCG
*
70328 AAAA-TAACACAAACT
1 AAAAGTAACTCAAACT
70343 AAAAGTAACTCAAACT
1 AAAAGTAACTCAAACT
* *
70359 GAAAGTAACTCGAACT
1 AAAAGTAACTCAAACT
70375 AAA
1 AAA
70378 TATAAACCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 4 0.13
16 26 0.87
ACGTcount: A:0.58, C:0.18, G:0.08, T:0.16
Consensus pattern (16 bp):
AAAAGTAACTCAAACT
Found at i:71582 original size:12 final size:11
Alignment explanation
Indices: 71545--71637 Score: 69
Period size: 10 Copynumber: 9.0 Consensus size: 11
71535 TTCTAAAATG
71545 TTGCTTCTCTC
1 TTGCTTCTCTC
71556 -TGCTTCTCTC
1 TTGCTTCTCTC
71566 --GC-TCTCTC
1 TTGCTTCTCTC
71574 -TGCTTCTCTC
1 TTGCTTCTCTC
*
71584 GATGC-TCTCT-
1 -TTGCTTCTCTC
71594 TTGCTTCTCTC
1 TTGCTTCTCTC
*
71605 GATGC-TCTCT-
1 -TTGCTTCTCTC
*
71615 TTGCTTCTGTC
1 TTGCTTCTCTC
71626 TCTGCTTCTCTC
1 T-TGCTTCTCTC
71638 GCTTCAGCTT
Statistics
Matches: 67, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
8 6 0.09
9 10 0.15
10 25 0.37
11 11 0.16
12 15 0.22
ACGTcount: A:0.02, C:0.37, G:0.13, T:0.48
Consensus pattern (11 bp):
TTGCTTCTCTC
Found at i:71631 original size:21 final size:21
Alignment explanation
Indices: 71550--71622 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
71540 AAATGTTGCT
*
71550 TCTCTCTGCTTCTCTC---GC
1 TCTCTTTGCTTCTCTCGATGC
*
71568 TCTCTCTGCTTCTCTCGATGC
1 TCTCTTTGCTTCTCTCGATGC
71589 TCTCTTTGCTTCTCTCGATGC
1 TCTCTTTGCTTCTCTCGATGC
71610 TCTCTTTGCTTCT
1 TCTCTTTGCTTCT
71623 GTCTCTGCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
18 16 0.31
21 35 0.69
ACGTcount: A:0.03, C:0.37, G:0.12, T:0.48
Consensus pattern (21 bp):
TCTCTTTGCTTCTCTCGATGC
Found at i:72674 original size:17 final size:17
Alignment explanation
Indices: 72652--72696 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
72642 TCCAATTATC
72652 ACCCGACCCGAAAATTA
1 ACCCGACCCGAAAATTA
* *
72669 ACCCGACCTGAAAATTG
1 ACCCGACCCGAAAATTA
*
72686 ACTCGACCCGA
1 ACCCGACCCGA
72697 CTCGACCCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.36, C:0.36, G:0.16, T:0.13
Consensus pattern (17 bp):
ACCCGACCCGAAAATTA
Found at i:74370 original size:139 final size:140
Alignment explanation
Indices: 74212--74489 Score: 452
Period size: 139 Copynumber: 2.0 Consensus size: 140
74202 CATATGTACA
* *
74212 TATATAAAAAAATGTAAAATAATAGCGTATAAAGTAGAATAAATAAAATTAATAAGAACATATAA
1 TATATAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAATTAATAAAAACATATAA
* *
74277 GAATATCAATACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAATATATATA-ATAAT
66 GAATATCAACACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAATATATATATAAT
74341 AATAGAAAAAT
131 AA-AGAAAAAT
* *
74352 TATA-AAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAGTTAGTAAAAACATATAA
1 TATATAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAATTAATAAAAACATATAA
* * *
74416 TAATATTAACACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAATATGTATATAAT
66 GAATATCAACACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAATATATATATAAT
74481 AAAGAAAAA
131 AAAGAAAAA
74490 AAAACTAAAT
Statistics
Matches: 128, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
139 117 0.91
140 11 0.09
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.26
Consensus pattern (140 bp):
TATATAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAATTAATAAAAACATATAA
GAATATCAACACCATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAAATATATATATAAT
AAAGAAAAAT
Found at i:76399 original size:105 final size:104
Alignment explanation
Indices: 76006--76559 Score: 823
Period size: 105 Copynumber: 5.3 Consensus size: 104
75996 TGTTTCGAGG
* * * *
76006 CCAATATCTTTCGTTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGAGAAA-TGTTTGTTGACAACCAG
* **
76071 CAGTCCCTTCGTTTTGAAGTTGAACTTGCGTTGTCTGGAGT
64 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * *
76112 CCAATATCTTTCGTTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGAGAAA-TGTTTGTTGACAACCAG
76177 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
64 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
76218 CCAATATCTTTCG-T-T----TTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATT-GAGAAATGTTTGTTGACAACCAGC
* *
76277 GGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGT
65 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
** *
76317 CCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAT-TGAGAAATGTTTGTTGACAACCAGC
*
76382 GGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
76422 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAT-TGAGAAATGTTTGTTGACAACCAGC
76487 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
76527 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
76560 ATGGGTAAAA
Statistics
Matches: 421, Mismatches: 19, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
99 70 0.17
100 20 0.05
101 1 0.00
104 1 0.00
105 212 0.50
106 117 0.28
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (104 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAGAAATGTTTGTTGACAACCAGCG
GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:77405 original size:60 final size:61
Alignment explanation
Indices: 77296--77414 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 61
77286 CTCTTCTTTT
* * *
77296 GTTCTTTTTTCCTCTTTTTCTTTCTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAAC
1 GTTCTTTTTTCCTCTTTTTCTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAAC
*
77357 GTTCTTTTCTTTCCT-TTTTT-TTT-TCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 GTTC-TTT-TTTCCTCTTTTTCTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
77415 GCGAAGTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
60 31 0.60
61 7 0.13
62 8 0.15
63 6 0.12
ACGTcount: A:0.12, C:0.27, G:0.13, T:0.49
Consensus pattern (61 bp):
GTTCTTTTTTCCTCTTTTTCTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAAC
Done.