Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002205.1 Hibiscus syriacus cultivar Beakdansim tig00004495_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: 106020
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:1351 original size:40 final size:41
Alignment explanation
Indices: 1289--1367 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
1279 CTCGAACTGT
* *
1289 GGGAGAGACCTCTTGAACGATGACAGGGGCCT-TGAACGGC
1 GGGAGAGACCTCTTAAACGATGACAAGGGCCTCTGAACGGC
* *
1329 GGGAGA-AGCCTCTTAAAGGATGATAAGGGCCTCTGAACG
1 GGGAGAGA-CCTCTTAAACGATGACAAGGGCCTCTGAACG
1368 ATGACAGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.03
40 26 0.79
41 6 0.18
ACGTcount: A:0.28, C:0.20, G:0.35, T:0.16
Consensus pattern (41 bp):
GGGAGAGACCTCTTAAACGATGACAAGGGCCTCTGAACGGC
Found at i:3502 original size:19 final size:19
Alignment explanation
Indices: 3477--3523 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3467 TTCTGAAACT
3477 TAAAATCGCAACGC-AAAA
1 TAAAATCGCAACGCGAAAA
* *
3495 TGAAAATCGTAACGCGAAAC
1 T-AAAATCGCAACGCGAAAA
3515 TAAAATCGC
1 TAAAATCGC
3524 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.79
20 4 0.17
ACGTcount: A:0.49, C:0.21, G:0.15, T:0.15
Consensus pattern (19 bp):
TAAAATCGCAACGCGAAAA
Found at i:4115 original size:20 final size:20
Alignment explanation
Indices: 4092--4153 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
4082 GTGTTGCGAA
* *
4092 TTACAAATTCACGTTGTGAT
1 TTACAGATTCGCGTTGTGAT
*
4112 TTACAGATTCGCGTTGCGAT
1 TTACAGATTCGCGTTGTGAT
4132 TTACAGATTCGCGTTGTGAT
1 TTACAGATTCGCGTTGTGAT
4152 TT
1 TT
4154 TAAAATGAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (20 bp):
TTACAGATTCGCGTTGTGAT
Found at i:7712 original size:15 final size:15
Alignment explanation
Indices: 7694--7725 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7684 TATTTAAAAA
*
7694 AATACAATAAAAATT
1 AATAAAATAAAAATT
7709 AATAAAATAAAAATT
1 AATAAAATAAAAATT
7724 AA
1 AA
7726 GTGATCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
AATAAAATAAAAATT
Found at i:13880 original size:203 final size:203
Alignment explanation
Indices: 13531--13938 Score: 789
Period size: 203 Copynumber: 2.0 Consensus size: 203
13521 GTAGCATTTA
*
13531 TTATGTTGCACAACCGCCATAAACATGATGAAAATGTGGCTATGAGAGACTGAGACTCCTATGAC
1 TTATGTTGCACAACAGCCATAAACATGATGAAAATGTGGCTATGAGAGACTGAGACTCCTATGAC
*
13596 AATTTGAATCCCTTTATTTTAGGCGCTAAAGCTTGCATTTTCTGAGGTTATGTTTGGTTGCAGCT
66 AATTTGAATCCCTTTATTTTAGGCGCTAAAGCTTGCATTTTCTAAGGTTATGTTTGGTTGCAGCT
13661 TTGGTTACAGAAGTTAATGATATTTATCATTTTATAACATTATAGTAAATTTTTTGTAGTATAAA
131 TTGGTTACAGAAGTTAATGATATTTATCATTTTATAACATTATAGTAAATTTTTTGTAGTATAAA
13726 TGCATAAT
196 TGCATAAT
13734 TTATGTTGCACAACAGCCATAAACATGATGAAAATGTGGCTATGAGAGACTGAGACTCCTATGAC
1 TTATGTTGCACAACAGCCATAAACATGATGAAAATGTGGCTATGAGAGACTGAGACTCCTATGAC
*
13799 AATTTGAATCCCTTTATTTTTGGCGCTAAAGCTTGCATTTTCTAAGGTTATGTTTGGTTGCAGCT
66 AATTTGAATCCCTTTATTTTAGGCGCTAAAGCTTGCATTTTCTAAGGTTATGTTTGGTTGCAGCT
13864 TTGGTTACAGAAGTTAATGATATTTATCATTTTATAACATTATAGTAAATTTTTTGTAGTATAAA
131 TTGGTTACAGAAGTTAATGATATTTATCATTTTATAACATTATAGTAAATTTTTTGTAGTATAAA
13929 TGCATAAT
196 TGCATAAT
13937 TT
1 TT
13939 GACTTTTATA
Statistics
Matches: 202, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
203 202 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (203 bp):
TTATGTTGCACAACAGCCATAAACATGATGAAAATGTGGCTATGAGAGACTGAGACTCCTATGAC
AATTTGAATCCCTTTATTTTAGGCGCTAAAGCTTGCATTTTCTAAGGTTATGTTTGGTTGCAGCT
TTGGTTACAGAAGTTAATGATATTTATCATTTTATAACATTATAGTAAATTTTTTGTAGTATAAA
TGCATAAT
Found at i:18711 original size:23 final size:23
Alignment explanation
Indices: 18685--18735 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
18675 GAACATATAA
18685 ACGAACACTAAACAAACATGTTC
1 ACGAACACTAAACAAACATGTTC
** *
18708 ACGAACGTTAAACGAACATGTTC
1 ACGAACACTAAACAAACATGTTC
*
18731 GCGAA
1 ACGAA
18736 AAATAAGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (23 bp):
ACGAACACTAAACAAACATGTTC
Found at i:19759 original size:26 final size:26
Alignment explanation
Indices: 19730--19779 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
19720 TAATATACAT
*
19730 TAAACTTCTAAGTGAAATTAAACTTA
1 TAAACTTCCAAGTGAAATTAAACTTA
19756 TAAACTTCCAAGTGAAATTAAACT
1 TAAACTTCCAAGTGAAATTAAACT
19780 CCTAATTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (26 bp):
TAAACTTCCAAGTGAAATTAAACTTA
Found at i:27983 original size:37 final size:37
Alignment explanation
Indices: 27933--28009 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
27923 TGCAGCTCCA
* * *
27933 AGTTTAAACTTGGCTACGCCTTATCCCTACATGCTCT
1 AGTTTAAACTTGGCTACACCTAATCACTACATGCTCT
* *
27970 AGTTTATACTTGGCTACACCTAATCACTACATGCTTT
1 AGTTTAAACTTGGCTACACCTAATCACTACATGCTCT
28007 AGT
1 AGT
28010 ATCTAATTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (37 bp):
AGTTTAAACTTGGCTACACCTAATCACTACATGCTCT
Found at i:28758 original size:14 final size:14
Alignment explanation
Indices: 28739--28776 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
28729 TCTCTCACTA
28739 AAGCTTTTCTCTCT
1 AAGCTTTTCTCTCT
28753 AAGCTTTTCTCTCT
1 AAGCTTTTCTCTCT
28767 AAGCTTTTCT
1 AAGCTTTTCT
28777 TTGTGTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.16, C:0.26, G:0.08, T:0.50
Consensus pattern (14 bp):
AAGCTTTTCTCTCT
Found at i:30872 original size:23 final size:23
Alignment explanation
Indices: 30846--30914 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
30836 CACCACAGCT
*
30846 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * **
30869 CGTAGAATTGCACCGTAGTGCTG
1 CGTAGAAATGCACCGAAGTGCCA
*
30892 CGTAGAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
30915 TATAATATGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:42717 original size:17 final size:17
Alignment explanation
Indices: 42688--42733 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
42678 TTTTCATCTC
*
42688 TCATTTTTTTCTCTTTT
1 TCATTTTTTTCTCGTTT
42705 TC-TTTTCTTTCTCGTTT
1 TCATTTT-TTTCTCGTTT
42722 TCATTTTTTTCT
1 TCATTTTTTTCT
42734 TCATCGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.15
17 18 0.69
18 4 0.15
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (17 bp):
TCATTTTTTTCTCGTTT
Found at i:42764 original size:21 final size:21
Alignment explanation
Indices: 42707--42749 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
42697 TCTCTTTTTC
42707 TTTTCTTTC-TCGTTTTCATTT
1 TTTTC-TTCATCGTTTTCATTT
42728 TTTTCTTCATCGTTTTCATTT
1 TTTTCTTCATCGTTTTCATTT
42749 T
1 T
42750 CTTTTTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.07, C:0.19, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTCTTCATCGTTTTCATTT
Found at i:42780 original size:15 final size:16
Alignment explanation
Indices: 42761--42805 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
42751 TTTTTCCATT
42761 TTTTTTCTTCTTCTGG
1 TTTTTTCTTCTTCTGG
*
42777 TTTTTTTTTCTTCT-G
1 TTTTTTCTTCTTCTGG
42792 TTTTTTCTTCTTCT
1 TTTTTTCTTCTTCT
42806 TATAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.00, C:0.18, G:0.07, T:0.76
Consensus pattern (16 bp):
TTTTTTCTTCTTCTGG
Found at i:43901 original size:6 final size:6
Alignment explanation
Indices: 43890--43925 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
43880 ACACTTGTAT
43890 CATGAC CATGAC CATGAC CATGAC CATGAC CTATGA
1 CATGAC CATGAC CATGAC CATGAC CATGAC C-ATGA
43926 GTCTTCCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (6 bp):
CATGAC
Found at i:66486 original size:15 final size:15
Alignment explanation
Indices: 66462--66493 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
66452 TGGCAGATCG
*
66462 AAATCCAGAATGGGA
1 AAATCAAGAATGGGA
66477 AAATCAAGAATGGGA
1 AAATCAAGAATGGGA
66492 AA
1 AA
66494 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.25, T:0.12
Consensus pattern (15 bp):
AAATCAAGAATGGGA
Found at i:67916 original size:14 final size:14
Alignment explanation
Indices: 67897--67934 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
67887 GCTTGGGATT
67897 ATTGCACTTTAGTC
1 ATTGCACTTTAGTC
67911 ATTGCACTTTAGTC
1 ATTGCACTTTAGTC
*
67925 ATTGTACTTT
1 ATTGCACTTT
67935 GGGGTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.47
Consensus pattern (14 bp):
ATTGCACTTTAGTC
Found at i:73896 original size:183 final size:184
Alignment explanation
Indices: 73583--73969 Score: 640
Period size: 183 Copynumber: 2.1 Consensus size: 184
73573 AATTCTAATT
* *
73583 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
*
73647 TATAAAATAAAAATATTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAATATTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATT
*
73712 GGATCTTAAATTATTAATTGGGTTTGAAATGGTTTGGACTT-AACCCATATGTTA
131 GGATCTTAAATTATTAATTGGGTTTGAAATGATTTGG-CTTGAACCCATATGTTA
73766 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTATAATTAATTTAAATAATATATAA
*
73830 TTATAAAATAAAAA-ATT-TATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTA
65 TTATAAAATAAAAATATTAGATA-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTA
* * *
73893 TTGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
129 TTGGATCTTAAATTATTAATTGGGTTTGAAATGATTTGGCTTGAACCCATATGTTA
73949 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
73970 AAAATTTAAT
Statistics
Matches: 192, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
182 5 0.03
183 126 0.66
184 61 0.32
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
TATAAAATAAAAATATTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATT
GGATCTTAAATTATTAATTGGGTTTGAAATGATTTGGCTTGAACCCATATGTTA
Found at i:74132 original size:18 final size:18
Alignment explanation
Indices: 74111--74155 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
74101 AATTCGGTTC
74111 GATCGATTAACCGAATTA
1 GATCGATTAACCGAATTA
74129 GATC-AGTTAACCGAATTA
1 GATCGA-TTAACCGAATTA
*
74147 GTTCGATTA
1 GATCGATTA
74156 TTTGAACACC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (18 bp):
GATCGATTAACCGAATTA
Found at i:74979 original size:26 final size:28
Alignment explanation
Indices: 74950--75005 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
74940 AGACTGATGA
*
74950 ATTTTTAAAATTTCAT-AG-AAAAATAG
1 ATTTATAAAATTTCATGAGCAAAAATAG
*
74976 ATTTATAAAATTTTATGAGCAAAAATAG
1 ATTTATAAAATTTCATGAGCAAAAATAG
75004 AT
1 AT
75006 GAGTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 14 0.54
27 2 0.08
28 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (28 bp):
ATTTATAAAATTTCATGAGCAAAAATAG
Found at i:76531 original size:23 final size:23
Alignment explanation
Indices: 76499--76545 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
76489 CTTTTAGAAA
76499 TTAATATTTTCTT-ATTTTTATT
1 TTAATATTTTCTTAATTTTTATT
76521 TTAATATTTTTCTTAATTTTTATT
1 TTAATA-TTTTCTTAATTTTTATT
76545 T
1 T
76546 ATTTCTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.26
23 7 0.30
24 10 0.43
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (23 bp):
TTAATATTTTCTTAATTTTTATT
Found at i:81710 original size:2 final size:2
Alignment explanation
Indices: 81699--81731 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
81689 TTATTTTTTT
*
81699 TA TA TC TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81732 GTTTGCAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81761 original size:37 final size:36
Alignment explanation
Indices: 81720--82078 Score: 159
Period size: 38 Copynumber: 9.6 Consensus size: 36
81710 ATATATATAT
**
81720 ATATATTATATAG-TTTGCAAACAGTTTTTGAAGATAC
1 ATATATTATATAGTTTTTAAAACA-TTTTTGAA-ATAC
*
81757 ATATATAATATATAGTTTTTAAAACACTTTTGAAA-AC
1 ATATAT--TATATAGTTTTTAAAACATTTTTGAAATAC
* *
81794 TATATATTATATAGTTTTTAAAACATTTTAGAAAATAT
1 -ATATATTATATAGTTTTTAAAACATTTTTG-AAATAC
* * *
81832 ATATAATATATAGTTTTTAAAATGA-TTTTGAAAAAC
1 ATATATTATATAGTTTTTAAAA-CATTTTTGAAATAC
* * * *
81868 TTATATAATATATATTTTTTGAAAACATTTTTTAAAAAAAC
1 --ATATATTATATAGTTTTT-AAAACA-TTTTT-GAAATAC
* *
81909 TTATATAATATATAGTTTTTGAAAATACTTTTT-AAA-AC
1 --ATATATTATATAGTTTTT-AAAACA-TTTTTGAAATAC
* * **
81947 TTATATAATATATAATTTAAAAAAACATTTTT----TGA-
1 --ATATATTATATAGTTT-TTAAAACATTTTTGAAAT-AC
*
81982 A-A-ATTATATAGTTTTTAGAAAACATTTTTGAAA-AT
1 ATATATTATATAGTTTTT--AAAACATTTTTGAAATAC
* ** * * *
82017 TTATATGTAATATAGTTTTTTAAAATGTTTTTAAAAAAGT
1 ATATAT-T-ATATAG-TTTTTAAAACATTTTTGAAATA-C
*
82057 TTATATTATATAGTTTTTAAAA
1 ATATATTATATAGTTTTTAAAA
82079 AAATATATTT
Statistics
Matches: 263, Mismatches: 29, Indels: 60
0.75 0.08 0.17
Matches are distributed among these distances:
31 10 0.04
32 12 0.05
33 1 0.00
34 1 0.00
36 28 0.11
37 52 0.20
38 70 0.27
39 29 0.11
40 24 0.09
41 36 0.14
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
ATATATTATATAGTTTTTAAAACATTTTTGAAATAC
Found at i:81761 original size:39 final size:36
Alignment explanation
Indices: 81718--81969 Score: 141
Period size: 36 Copynumber: 6.6 Consensus size: 36
81708 ATATATATAT
* *
81718 ATATATATTATATAGTTTGCAAACAGTTTTTGAAGATAC
1 ATATATATTATATAGTTTGAAAACA-CTTTTGAA-A-AC
* *
81757 ATATATAATATATAGTTTTTAAAACACTTTTGAAAAC
1 ATATATATTATATAG-TTTGAAAACACTTTTGAAAAC
* *
81794 -TATATATTATATAGTTTTTAAAACA-TTTTAGAAAAT
1 ATATATATTATATAG-TTTGAAAACACTTTT-GAAAAC
* * *
81830 ATATATAATATATAGTTTTTAAAATGA-TTTTGAAAAAC
1 ATATATATTATATAG-TTTGAAAA-CACTTTTG-AAAAC
* ** * *
81868 TTATATAATATATATTTTTTGAAAACATTTTTTAAAAAAAC
1 ATATAT-AT-TATATAGTTTGAAAACA-CTTTT--GAAAAC
* * * *
81909 TTATATAATATATAGTTTTTGAAAATACTTTTTAAAAC
1 ATATATATTATATAG--TTTGAAAACACTTTTGAAAAC
* * * *
81947 TTATATAATATATAATTTAAAAA
1 ATATATATTATATAGTTTGAAAA
81970 AACATTTTTT
Statistics
Matches: 176, Mismatches: 24, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
35 4 0.02
36 36 0.20
37 25 0.14
38 35 0.20
39 34 0.19
40 22 0.12
41 20 0.11
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATATATTATATAGTTTGAAAACACTTTTGAAAAC
Found at i:81803 original size:75 final size:73
Alignment explanation
Indices: 81719--81984 Score: 257
Period size: 79 Copynumber: 3.5 Consensus size: 73
81709 TATATATATA
*
81719 TATATATTATATAGTTTGCAAACAGTTTTTGAAGATACATATATAATATATAGTTTTTAAAACAC
1 TATATATTATATAGTTTGAAAACA-TTTTTGAA-A-ACATATATAATATATAGTTTTTAAAACAC
81784 TTTTGAAAAC-
63 TTTTGAAAACT
* * * *
81794 TATATATTATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATGA-T
1 TATATATTATATAG-TTTGAAAACATTTTTGAAAACATATATAATATATAGTTTTTAAAA-CACT
81858 TTTGAAAAACT
64 TTTG-AAAACT
** * *
81869 TATATAATATATATTTTTTGAAAACATTTTTTAAAAAAACTTATATAATATATAGTTTTTGAAAA
1 TATAT-AT-TATATAGTTTGAAAACA-TTTTT--GAAAACATATATAATATATAGTTTTT-AAAA
* *
81934 TACTTTTTAAAACT
60 CACTTTTGAAAACT
* * *
81948 TATATAATATATAATTTAAAAAAACATTTTTTGAAAA
1 TATATATTATATAGTTT--GAAAACA-TTTTTGAAAA
81985 TTATATAGTT
Statistics
Matches: 159, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
73 30 0.19
74 7 0.04
75 26 0.16
76 19 0.12
77 21 0.13
78 1 0.01
79 47 0.30
80 8 0.05
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (73 bp):
TATATATTATATAGTTTGAAAACATTTTTGAAAACATATATAATATATAGTTTTTAAAACACTTT
TGAAAACT
Found at i:81928 original size:79 final size:76
Alignment explanation
Indices: 81757--81991 Score: 282
Period size: 79 Copynumber: 3.1 Consensus size: 76
81747 TTGAAGATAC
* * *
81757 ATATATAATATATAGTTTTTAAAACACTTTTGAAAAC-TATATATTATATAGTTTTTAAAACA--
1 ATATATAATATATAGTTTTTAAAATACTTTTGAAAACTTATATAATATATAATTTTTAAAACATT
*
81819 TTTTAGAAAAT
66 TTTTAAAAAAT
*
81830 ATATATAATATATAGTTTTTAAAATGA-TTTTGAAAAACTTATATAATATATATTTTTTGAAAAC
1 ATATATAATATATAGTTTTTAAAAT-ACTTTTG-AAAACTTATATAATATATAATTTTT-AAAAC
81894 ATTTTTTAAAAAA-
63 ATTTTTTAAAAAAT
* **
81907 ACTTATATAATATATAGTTTTTGAAAATACTTTTTAAAACTTATATAATATATAATTTAAAAAAA
1 A--TATATAATATATAGTTTTT-AAAATACTTTTGAAAACTTATATAATATATAATTT-TTAAAA
* *
81972 CATTTTTTGAAAATT
62 CATTTTTTAAAAAAT
81987 ATATA
1 ATATA
81992 GTTTTTAGAA
Statistics
Matches: 140, Mismatches: 10, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
73 29 0.21
74 6 0.04
75 17 0.12
76 6 0.04
77 1 0.01
78 13 0.09
79 58 0.41
80 10 0.07
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (76 bp):
ATATATAATATATAGTTTTTAAAATACTTTTGAAAACTTATATAATATATAATTTTTAAAACATT
TTTTAAAAAAT
Found at i:81979 original size:38 final size:38
Alignment explanation
Indices: 81758--82079 Score: 247
Period size: 38 Copynumber: 8.6 Consensus size: 38
81748 TGAAGATACA
* *
81758 TATATAATATATAGTTTTT-AAAACACTTTTGAAAAC-
1 TATATAATATATAGTTTTTAAAAACATTTTTTAAAACT
* **
81794 TATATATTATATAGTTTTT-AAAACATTTTAGAAAA-T
1 TATATAATATATAGTTTTTAAAAACATTTTTTAAAACT
** **
81830 ATATATAATATATAGTTTTTAAAATGATTTTGAAAAACT
1 -TATATAATATATAGTTTTTAAAAACATTTTTTAAAACT
* *
81869 TATATAATATATATTTTTTGAAAACATTTTTTAAAAAAACT
1 TATATAATATATAGTTTTTAAAAACATTTTTT---AAAACT
* * *
81910 TATATAATATATAGTTTTTGAAAATACTTTTTAAAACT
1 TATATAATATATAGTTTTTAAAAACATTTTTTAAAACT
* ** *
81948 TATATAATATATAATTTAAAAAAACATTTTTT-GAA--
1 TATATAATATATAGTTTTTAAAAACATTTTTTAAAACT
* *
81983 -A-AT--TATATAGTTTTTAGAAAACATTTTTGAAAATT
1 TATATAATATATAGTTTTTA-AAAACATTTTTTAAAACT
* * ** * *
82018 TATAT-GTAATATAGTTTTTTAAAATGTTTTTAAAAAAGT
1 TATATAAT-ATATAGTTTTTAAAAACATTTTT-TAAAACT
*
82057 T-TATATTATATAGTTTTTAAAAA
1 TATATAATATATAGTTTTTAAAAA
82080 AATATATTTT
Statistics
Matches: 233, Mismatches: 36, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
31 10 0.04
32 11 0.05
33 4 0.02
34 1 0.00
36 33 0.14
37 22 0.09
38 98 0.42
39 19 0.08
41 35 0.15
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (38 bp):
TATATAATATATAGTTTTTAAAAACATTTTTTAAAACT
Found at i:82104 original size:10 final size:10
Alignment explanation
Indices: 82089--82129 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
82079 AAATATATTT
82089 TTATTTTTTA
1 TTATTTTTTA
82099 TTATTTTTTA
1 TTATTTTTTA
82109 -T-TTTTTTA
1 TTATTTTTTA
82117 TTATTTTTTA
1 TTATTTTTTA
82127 TTA
1 TTA
82130 CTTATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.24
9 2 0.07
10 20 0.69
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTATTTTTTA
Found at i:82113 original size:18 final size:18
Alignment explanation
Indices: 82086--82128 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
82076 AAAAAATATA
82086 TTTTTA-TTTTTTATTAT
1 TTTTTATTTTTTTATTAT
82103 TTTTTATTTTTTTATTAT
1 TTTTTATTTTTTTATTAT
82121 TTTTTATT
1 TTTTTATT
82129 ACTTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTATTTTTTTATTAT
Found at i:83276 original size:25 final size:26
Alignment explanation
Indices: 83210--83279 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
83200 TTTCATCCCC
*
83210 TGTTTTACTATTATTCTAATTCATACA
1 TGTTTTA-TATTATTTTAATTCATACA
* * * *
83237 T-TTTTATGTTTTTTTTATT-ATATA
1 TGTTTTATATTATTTTAATTCATACA
83261 TGTTTTATATTATTTTAAT
1 TGTTTTATATTATTTTAAT
83280 ATTTTTTCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
24 5 0.15
25 23 0.68
26 5 0.15
27 1 0.03
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (26 bp):
TGTTTTATATTATTTTAATTCATACA
Found at i:84116 original size:2 final size:2
Alignment explanation
Indices: 84109--84161 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
84099 ATCAACGATC
84109 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
84151 AT AT AT AT AT A
1 AT AT AT AT AT A
84162 ATCAAATGCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:85476 original size:13 final size:13
Alignment explanation
Indices: 85458--85484 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
85448 TTACAGACGC
85458 GCATATGAAGACT
1 GCATATGAAGACT
85471 GCATATGAAGACT
1 GCATATGAAGACT
85484 G
1 G
85485 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:85504 original size:4 final size:4
Alignment explanation
Indices: 85495--85529 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
85485 TTCAACTATG
85495 TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
85530 ACATGCATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:86627 original size:3 final size:3
Alignment explanation
Indices: 86619--86648 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
86609 TAATTTACCT
*
86619 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
86649 GAGTGTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:87032 original size:21 final size:20
Alignment explanation
Indices: 86997--87035 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
86987 ACCACCAAGG
86997 ATAATCATAAAATTAAATAA
1 ATAATCATAAAATTAAATAA
*
87017 ATAATCAATTAAATTAAAT
1 ATAATC-ATAAAATTAAAT
87036 TAATCGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATCATAAAATTAAATAA
Found at i:87937 original size:20 final size:20
Alignment explanation
Indices: 87912--87961 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
87902 AATTTTGGTT
*
87912 TTGATTAATTCGGTTCGAAA
1 TTGATTAATTCGATTCGAAA
*
87932 TTGATTAATTCGATTCTAAA
1 TTGATTAATTCGATTCGAAA
*
87952 TTGGTTAATT
1 TTGATTAATT
87962 AACTGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (20 bp):
TTGATTAATTCGATTCGAAA
Found at i:91933 original size:25 final size:25
Alignment explanation
Indices: 91905--91992 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 25
91895 AAATCCAAAC
91905 CCGAAACTCAACTTTAAATCTGAAT
1 CCGAAACTCAACTTTAAATCTGAAT
* *
91930 CCGAACCCGACACTCAACTTTAAGTCTGAAC
1 CCG-A----A-ACTCAACTTTAAATCTGAAT
* *
91961 CCGAAGCTCAACTTCAAATCTGAAT
1 CCGAAACTCAACTTTAAATCTGAAT
*
91986 CTGAAAC
1 CCGAAAC
91993 CGACACTCAG
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
25 24 0.49
26 2 0.04
30 2 0.04
31 21 0.43
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (25 bp):
CCGAAACTCAACTTTAAATCTGAAT
Found at i:91958 original size:31 final size:31
Alignment explanation
Indices: 91870--92034 Score: 153
Period size: 31 Copynumber: 5.5 Consensus size: 31
91860 ACACATATTT
* * * *
91870 GAACCCAAAACTCAACTTTAAGTCTAAATCC
1 GAACCCGACACTCAACTTTAAATCTGAATCC
* *
91901 AAACCCGAAACTCAACTTTAAATCTGAATCC
1 GAACCCGACACTCAACTTTAAATCTGAATCC
* *
91932 GAACCCGACACTCAACTTTAAGTCTGAACCC
1 GAACCCGACACTCAACTTTAAATCTGAATCC
* *
91963 GAA---G---CTCAACTTCAAATCTGAATCT
1 GAACCCGACACTCAACTTTAAATCTGAATCC
* *
91988 GAAACCGACACTCAGAACTTTAAATCCGAATCC
1 GAACCCGACACTC--AACTTTAAATCTGAATCC
*
92021 AAACCCGACACTCA
1 GAACCCGACACTCA
92035 TGTCTAAATC
Statistics
Matches: 109, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
25 20 0.18
28 2 0.02
31 61 0.56
33 26 0.24
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.21
Consensus pattern (31 bp):
GAACCCGACACTCAACTTTAAATCTGAATCC
Found at i:91996 original size:56 final size:57
Alignment explanation
Indices: 91902--92010 Score: 166
Period size: 56 Copynumber: 1.9 Consensus size: 57
91892 TCTAAATCCA
* *
91902 AACCCGAAACTCAACTTTAAATCTGAATCCGAACCCGACACTC-AACTTTAAGTCTG
1 AACCCGAAACTCAACTTCAAATCTGAATCCGAAACCGACACTCAAACTTTAAGTCTG
* *
91958 AACCCGAAGCTCAACTTCAAATCTGAATCTGAAACCGACACTCAGAACTTTAA
1 AACCCGAAACTCAACTTCAAATCTGAATCCGAAACCGACACTCA-AACTTTAA
92011 ATCCGAATCC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
56 39 0.83
58 8 0.17
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (57 bp):
AACCCGAAACTCAACTTCAAATCTGAATCCGAAACCGACACTCAAACTTTAAGTCTG
Found at i:92013 original size:33 final size:33
Alignment explanation
Indices: 91970--92034 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
91960 CCCGAAGCTC
* *
91970 AACTTCAAATCTGAATCTGAAA-CCGACACTCAG
1 AACTTCAAATCCGAATC-CAAACCCGACACTCAG
*
92003 AACTTTAAATCCGAATCCAAACCCGACACTCA
1 AACTTCAAATCCGAATCCAAACCCGACACTCA
92035 TGTCTAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (33 bp):
AACTTCAAATCCGAATCCAAACCCGACACTCAG
Found at i:101075 original size:12 final size:12
Alignment explanation
Indices: 101058--101102 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
101048 AATTTAATAT
101058 ATATTTTTTATA
1 ATATTTTTTATA
*
101070 ATATTTTTTATC
1 ATATTTTTTATA
*
101082 ATATTTATTTTTA
1 ATATTT-TTTATA
*
101095 CTATTTTT
1 ATATTTTT
101103 AATCTTCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (12 bp):
ATATTTTTTATA
Found at i:101373 original size:29 final size:29
Alignment explanation
Indices: 101331--101397 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
101321 TTAAATTAAA
*
101331 AATATTTAATAAATTATGTTCATATTTAT
1 AATATTTAATAAATTATGTTAATATTTAT
101360 AATATTTAATAAATTATGTTAATATTTAT
1 AATATTTAATAAATTATGTTAATATTTAT
**
101389 TGTATTTAA
1 AATATTTAA
101398 CCTTACTGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (29 bp):
AATATTTAATAAATTATGTTAATATTTAT
Done.