Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002895.1 Hibiscus syriacus cultivar Beakdansim tig00005982_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: 83010
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:473 original size:23 final size:22
Alignment explanation
Indices: 426--474 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
416 TTGTGTTGTC
* *
426 AAAATTATATCTAAGAATTACT
1 AAAATTATATCAAAGAATTAAT
448 AAAATTAT-TCAAATGATATTAAT
1 AAAATTATATCAAA-GA-ATTAAT
471 AAAA
1 AAAA
475 AAATCCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
22 10 0.43
23 9 0.39
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAATTATATCAAAGAATTAAT
Found at i:1365 original size:23 final size:23
Alignment explanation
Indices: 1335--1391 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
1325 TCATAGATGC
1335 CAAG-GGTATGAGCGTTCAATGT
1 CAAGAGGTATGAGCGTTCAATGT
1357 CAAGAGGTATGAGCGTTCAATGT
1 CAAGAGGTATGAGCGTTCAATGT
1380 CAAGAGGT-TGAG
1 CAAGAGGTATGAG
1392 AGTTATCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 8 0.24
23 26 0.76
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (23 bp):
CAAGAGGTATGAGCGTTCAATGT
Found at i:16732 original size:41 final size:42
Alignment explanation
Indices: 16622--16737 Score: 101
Period size: 44 Copynumber: 2.7 Consensus size: 42
16612 AATAAACAAT
* ** *
16622 TTAAGTCCTTCGGGACCATCGC-TAAGTCTTTCGAGCATGATGA
1 TTAAGTCCTTCGGG-CCATC-CATAAGCCTTTAAAGCAAGATGA
* ** *
16665 TTAAAAATCCTTCGGGTTATCTATAAGCCTTTAAAGCAAGATGA
1 TT--AAGTCCTTCGGGCCATCCATAAGCCTTTAAAGCAAGATGA
16709 -TAAGTCCTTCGGGCCATCCATAAGACCTT
1 TTAAGTCCTTCGGGCCATCCATAAG-CCTT
16738 CAGGTAGTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
41 19 0.33
42 4 0.07
43 3 0.05
44 20 0.35
45 11 0.19
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (42 bp):
TTAAGTCCTTCGGGCCATCCATAAGCCTTTAAAGCAAGATGA
Found at i:16893 original size:42 final size:42
Alignment explanation
Indices: 16846--16942 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
16836 TCGCACTTAG
* * *
16846 TAAATCTTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGAT
*
16888 TAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGAT
1 TAAATCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGAT
16930 TAAATCCTTAGGG
1 TAAATCCTTAGGG
16943 TAATTGGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (42 bp):
TAAATCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGAT
Found at i:16953 original size:42 final size:42
Alignment explanation
Indices: 16846--17073 Score: 154
Period size: 42 Copynumber: 5.2 Consensus size: 42
16836 TCGCACTTAG
* * * * *
16846 TAAATCTTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTAGGGCAATCAGTAAGTCTTTCGAGCATGATGAT
*
16888 TAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGAT
1 TAAATCCTTAGGGCAATCAGTAAGTCTTTCGAGCATGATGAT
* ** * * *
16930 TAAATCCTTAGGGTAATTGGTAAGCCTTGACGGAAG-A-GTAGTGAAG
1 TAAATCCTTAGGGCAATCAGTAAGTCTT-TC-G-AGCATG-A-TG-AT
* * * *
16976 CAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGAT
1 TAAATCC-T---T-AGGGCAATCAGTAAGTCTTTCGAGCATGATGAT
* * * * *
17023 GAAGTTCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGAT
1 TAAATCCTTAGGGCAATCAGTAAGTCTTTCGAGCATGATGAT
17065 TAAATCCTT
1 TAAATCCTT
17074 CGGGTAATTT
Statistics
Matches: 142, Mismatches: 31, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
42 97 0.68
43 3 0.02
44 3 0.02
45 4 0.03
46 7 0.05
47 5 0.04
48 4 0.03
49 3 0.02
50 3 0.02
51 13 0.09
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (42 bp):
TAAATCCTTAGGGCAATCAGTAAGTCTTTCGAGCATGATGAT
Found at i:16999 original size:13 final size:13
Alignment explanation
Indices: 16981--17005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16971 TGAAGCAAAC
16981 CCATCAGTAAGTG
1 CCATCAGTAAGTG
16994 CCATCAGTAAGT
1 CCATCAGTAAGT
17006 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:17075 original size:42 final size:42
Alignment explanation
Indices: 16996--17199 Score: 144
Period size: 42 Copynumber: 5.0 Consensus size: 42
16986 AGTAAGTGCC
* *
16996 ATCAGTAAGTCTTTCGAGCATGATGATGAAGTTCTTCGGGCT
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCT
*
17038 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG-T
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCT
** * * *
17079 AATTTGTAAGCCTTCATCGAAG-A-GTAGTGAAGAAA---ATC---C-
1 -ATCAGTAAGTCTT--TCG-AGCATG-A-TGATGAAATCCTTCGGGCT
17118 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG-T
1 ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCT
** * * *
17159 CATTTGTAAGTCTTTCGAGCAAGATGAT-AAGTCATTCGGGC
1 -ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
17200 CATTTTAAGC
Statistics
Matches: 125, Mismatches: 19, Indels: 36
0.69 0.11 0.20
Matches are distributed among these distances:
35 9 0.07
36 5 0.04
37 1 0.01
38 12 0.10
41 11 0.09
42 73 0.58
43 1 0.01
44 5 0.04
45 8 0.06
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (42 bp):
ATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCT
Found at i:17101 original size:135 final size:135
Alignment explanation
Indices: 16858--17127 Score: 416
Period size: 135 Copynumber: 2.0 Consensus size: 135
16848 AATCTTTCGG
* *
16858 GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCA
1 GCCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCA
* *
16923 TGATGATTAAATCCTTAGGGTAATTGGTAAGCCTTGACGGAAGAGTAGTGAAGCAAACCCATCAG
66 TGATGATTAAATCCTTAGGGTAATTGGTAAGCCTTCACGGAAGAGTAGTGAAGAAAACCCATCAG
16988 TAAGT
131 TAAGT
* * * * *
16993 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTTCTTCGGGCTATCAGTAAGTCTTTCGAGCA
1 GCCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCA
* * *
17058 TGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCATC-GAAGAGTAGTGAAGAAAATCCATCA
66 TGATGATTAAATCCTTAGGGTAATTGGTAAGCCTTCA-CGGAAGAGTAGTGAAGAAAACCCATCA
17122 GTAAGT
130 GTAAGT
17128 CTTTCGAGCA
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
135 121 0.99
136 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (135 bp):
GCCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCA
TGATGATTAAATCCTTAGGGTAATTGGTAAGCCTTCACGGAAGAGTAGTGAAGAAAACCCATCAG
TAAGT
Found at i:17683 original size:55 final size:55
Alignment explanation
Indices: 17581--17896 Score: 374
Period size: 55 Copynumber: 5.8 Consensus size: 55
17571 GAATCACACC
* * * ** *
17581 AGAAGATTGTTCGAGTTC--TACTC-CTTGAAGCAAGAGGGAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTATACTCTC-TGAAGGAATAGAGAGCGAACCCGTTTGT
17634 AGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTGT
1 AGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTGT
* *
17689 TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT
1 AGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTGT
* * *
17744 TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAACGGACCCGTTT-T
1 AGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTGT
* * * *
17798 ATGAATATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACCCGTTTAT
1 A-GAAGATTGTTCGAGTTCTATACTCTCTGAA-GGAATAGAGAGCGAACCCGTTTGT
* * * * *
17854 TGAAGATTGATCGAG-TCTTATACTCCCTGAAGAAATAGGGAGC
1 AGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGC
17897 AGACTTATCA
Statistics
Matches: 236, Mismatches: 19, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
53 18 0.08
54 4 0.02
55 210 0.89
56 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (55 bp):
AGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTGT
Found at i:22690 original size:18 final size:19
Alignment explanation
Indices: 22646--22696 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
22636 TCATATTAGG
*
22646 GAGTATCGATACTCTACCCT
1 GAGTATCGATACTCTA-CAT
*
22666 CAGTATCGATACTCT-CAT
1 GAGTATCGATACTCTACAT
*
22684 GAGTATCGGTACT
1 GAGTATCGATACT
22697 AAAATTGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 13 0.48
20 14 0.52
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (19 bp):
GAGTATCGATACTCTACAT
Found at i:25207 original size:37 final size:37
Alignment explanation
Indices: 25127--25207 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
25117 TCGGGTCGGG
* * * *
25127 TCGGATTTTTTAAGTGTGATATTTGGGTCGAGTCGGG
1 TCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTAGGA
* * *
25164 TTGGGTTTTTTAAGTGTGATATTCGGGTTGGGTAGGA
1 TCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTAGGA
25201 TCGGGTT
1 TCGGGTT
25208 CGGGTTTAGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.15, C:0.06, G:0.37, T:0.42
Consensus pattern (37 bp):
TCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTAGGA
Found at i:25207 original size:42 final size:37
Alignment explanation
Indices: 25121--25191 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
25111 TTTTGTTCGG
* * *
25121 GTCGGGTCGGATTTTTTAAGTGTGATATTTGGGTCGA
1 GTCGGGTTGGGTTTTTTAAGTGTGATATTCGGGTCGA
25158 GTCGGGTTGGGTTTTTTAAGTGTGATATTCGGGT
1 GTCGGGTTGGGTTTTTTAAGTGTGATATTCGGGT
25192 TGGGTAGGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.14, C:0.07, G:0.37, T:0.42
Consensus pattern (37 bp):
GTCGGGTTGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:25256 original size:18 final size:18
Alignment explanation
Indices: 25235--25269 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
25225 AAACCGGACC
25235 GACCCGAAAAAAAAATAT
1 GACCCGAAAAAAAAATAT
25253 GACCCGAAAAAAAAATA
1 GACCCGAAAAAAAAATA
25270 ATTTTACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.17, G:0.11, T:0.09
Consensus pattern (18 bp):
GACCCGAAAAAAAAATAT
Found at i:25837 original size:18 final size:18
Alignment explanation
Indices: 25800--25850 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
25790 TATGGAATTG
*
25800 GATTCCAA-TTCCTGACA
1 GATTCCAATTTCCTCACA
*
25817 GATTCCAATTTCTTCACA
1 GATTCCAATTTCCTCACA
*
25835 GATTCCAATTCCCTCA
1 GATTCCAATTTCCTCA
25851 TAAACATTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.33
Consensus pattern (18 bp):
GATTCCAATTTCCTCACA
Found at i:26569 original size:22 final size:19
Alignment explanation
Indices: 26539--26589 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 19
26529 TTATTTAAAA
*
26539 ATATAAATTTAATATACTAATT
1 ATATTAATTT-ATATA-T-ATT
26561 ATATTAA-TTATATATATT
1 ATATTAATTTATATATATT
26579 ATATGTAATTT
1 ATAT-TAATTT
26590 CTCCTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.27
19 4 0.15
20 7 0.27
21 2 0.08
22 6 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATTAATTTATATATATT
Found at i:38868 original size:7 final size:7
Alignment explanation
Indices: 38856--38882 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38846 AATATAATAC
38856 AGATAAA
1 AGATAAA
38863 AGATAAA
1 AGATAAA
38870 AGATAAA
1 AGATAAA
38877 AGATAA
1 AGATAA
38883 TTATGTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AGATAAA
Found at i:39526 original size:23 final size:24
Alignment explanation
Indices: 39500--39547 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
39490 TTTTTGTAAA
*
39500 CAATTA-AGTTTTATTTTAAAAAT
1 CAATTAGAGTTTTATTTGAAAAAT
*
39523 CAATTATGATTTTTATTTGAAAAAT
1 CAATTA-GAGTTTTATTTGAAAAAT
39548 TGGGGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
25 15 0.71
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (24 bp):
CAATTAGAGTTTTATTTGAAAAAT
Found at i:40491 original size:59 final size:59
Alignment explanation
Indices: 40376--40625 Score: 248
Period size: 59 Copynumber: 4.2 Consensus size: 59
40366 ACCAAAATGG
* * * * * * * *
40376 AAAAATAGAAACTTAAAGGACCAAAATAGTACAAACAGGAATTTAAAGGTCCAAATAGA
1 AAAAATAGAAACTTAAAGGACTAAAATAGCAAAAACAGAAACTTAAAGGACTAAATAGC
* * *
40435 AAAAATAGAAACTTAAGGGACTAAAATAGCAAAAATAGAAACTTAAGGGACTAAATAGC
1 AAAAATAGAAACTTAAAGGACTAAAATAGCAAAAACAGAAACTTAAAGGACTAAATAGC
* * * * * * *
40494 AAAAACATACATTTAAAGGACTAAAATAGGAAAAAACATAAACTTAAGGGACTAAAATAGC
1 AAAAATAGAAACTTAAAGGACTAAAATA-GCAAAAACAGAAACTTAAAGGACT-AAATAGC
* * * * * * *
40555 AAAAACATAAAGTTAAAGGACTAAAATAACAAAAATAGAAACTTAAAGGACTTAAACAGT
1 AAAAATAGAAACTTAAAGGACTAAAATAGCAAAAACAGAAACTTAAAGGAC-TAAATAGC
40615 AAAAATAGAAA
1 AAAAATAGAAA
40626 TTCGAATGGC
Statistics
Matches: 158, Mismatches: 30, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
59 71 0.45
60 53 0.34
61 34 0.22
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.17
Consensus pattern (59 bp):
AAAAATAGAAACTTAAAGGACTAAAATAGCAAAAACAGAAACTTAAAGGACTAAATAGC
Found at i:40606 original size:30 final size:30
Alignment explanation
Indices: 40362--40625 Score: 246
Period size: 30 Copynumber: 8.9 Consensus size: 30
40352 ATTTAATTAC
* *
40362 AAGGACCAAAAT-GGAAAAATAGAAACTTA
1 AAGGACTAAAATAGCAAAAATAGAAACTTA
* * * * * *
40391 AAGGACCAAAATAGTACAAACAGGAATTTA
1 AAGGACTAAAATAGCAAAAATAGAAACTTA
* * *
40421 AAGGTC-CAAATAGAAAAAATAGAAACTTA
1 AAGGACTAAAATAGCAAAAATAGAAACTTA
*
40450 AGGGACTAAAATAGCAAAAATAGAAACTTA
1 AAGGACTAAAATAGCAAAAATAGAAACTTA
* * * * *
40480 AGGGACT-AAATAGCAAAAACATACATTTA
1 AAGGACTAAAATAGCAAAAATAGAAACTTA
* * *
40509 AAGGACTAAAATAGGAAAAAACATAAACTTA
1 AAGGACTAAAATA-GCAAAAATAGAAACTTA
* * * *
40540 AGGGACTAAAATAGCAAAAACATAAAGTTA
1 AAGGACTAAAATAGCAAAAATAGAAACTTA
*
40570 AAGGACTAAAATAACAAAAATAGAAACTTA
1 AAGGACTAAAATAGCAAAAATAGAAACTTA
* * *
40600 AAGGACTTAAACAGTAAAAATAGAAA
1 AAGGACTAAAATAGCAAAAATAGAAA
40626 TTCGAATGGC
Statistics
Matches: 195, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
29 57 0.29
30 112 0.57
31 26 0.13
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.17
Consensus pattern (30 bp):
AAGGACTAAAATAGCAAAAATAGAAACTTA
Found at i:41618 original size:149 final size:149
Alignment explanation
Indices: 41446--41762 Score: 607
Period size: 149 Copynumber: 2.1 Consensus size: 149
41436 TTCTCTCTTT
41446 TCTTTCTTGGGTTTTCTTTCTCTCTGACTCCTCTGCCTTTTTTTCTCTCAACCCCCTCACCGAAT
1 TCTTTCTTGGGTTTTCTTTCTCTCTGACTCCTCTGCCTTTTTTTCTCTCAACCCCCTCACCGAAT
*
41511 GGCCCCCTATCTCCTCTGTCTTCCTTTTCTTTTATTGATGCATGTTGATTGATCCATTTGCCTCT
66 GGCCCCCTATCTCATCTGTCTTCCTTTTCTTTTATTGATGCATGTTGATTGATCCATTTGCCTCT
41576 ACTCGAGGAGATTCATTGA
131 ACTCGAGGAGATTCATTGA
41595 TCTTTCTTGGGTTTTCTTTCTCTCTGACTCCTCTGCCTTTTTTTCTCTCAACCCCCTCACCGAAT
1 TCTTTCTTGGGTTTTCTTTCTCTCTGACTCCTCTGCCTTTTTTTCTCTCAACCCCCTCACCGAAT
41660 GGCCCCCTATCTCATCTGTCTTCCTTTTCTTTTATTGATGCATGTTGATTGATCCATTTGCCTCT
66 GGCCCCCTATCTCATCTGTCTTCCTTTTCTTTTATTGATGCATGTTGATTGATCCATTTGCCTCT
41725 ACTCGAGGAGATTCATTGA
131 ACTCGAGGAGATTCATTGA
* *
41744 TCTTTCTTGGATTTGCTTT
1 TCTTTCTTGGGTTTTCTTT
41763 GGATATATTA
Statistics
Matches: 165, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 165 1.00
ACGTcount: A:0.13, C:0.29, G:0.14, T:0.45
Consensus pattern (149 bp):
TCTTTCTTGGGTTTTCTTTCTCTCTGACTCCTCTGCCTTTTTTTCTCTCAACCCCCTCACCGAAT
GGCCCCCTATCTCATCTGTCTTCCTTTTCTTTTATTGATGCATGTTGATTGATCCATTTGCCTCT
ACTCGAGGAGATTCATTGA
Found at i:42386 original size:21 final size:21
Alignment explanation
Indices: 42360--42407 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
42350 TGCTCGCAAA
42360 AAAAAAGTGCTTATTTTTAAT
1 AAAAAAGTGCTTATTTTTAAT
42381 AAAAAAGTGCTTATTTTTAAT
1 AAAAAAGTGCTTATTTTTAAT
42402 AAAAAA
1 AAAAAA
42408 ATAATCTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (21 bp):
AAAAAAGTGCTTATTTTTAAT
Found at i:43954 original size:52 final size:52
Alignment explanation
Indices: 43875--43979 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
43865 TGGAGAAGAA
43875 AGACCCCATCTCAACAAGCTCTAGGTCCTTGTGTTAAAGTTGGCAGGTTCGG
1 AGACCCCATCTCAACAAGCTCTAGGTCCTTGTGTTAAAGTTGGCAGGTTCGG
*
43927 AGACCCCATCTCAACAAGCTCTTGGTCCTTGTGTTAAAGTTGGCAGGTTCGG
1 AGACCCCATCTCAACAAGCTCTAGGTCCTTGTGTTAAAGTTGGCAGGTTCGG
43979 A
1 A
43980 CTAGAAGAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (52 bp):
AGACCCCATCTCAACAAGCTCTAGGTCCTTGTGTTAAAGTTGGCAGGTTCGG
Found at i:54563 original size:80 final size:80
Alignment explanation
Indices: 54367--54563 Score: 306
Period size: 80 Copynumber: 2.5 Consensus size: 80
54357 TCTTTCGGGC
54367 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCAAGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCAAGGAAGA
*
54432 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATA
* * * * *
54447 CATCAATAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCAAGGAAGA
54512 GTAGTGAAGC-AATCA
66 GTAGTGAAGCAAAT-A
* *
54527 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
54564 TGGGCCATTC
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 3 0.03
80 103 0.97
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (80 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCAAGGAAGA
GTAGTGAAGCAAATA
Found at i:54929 original size:53 final size:53
Alignment explanation
Indices: 54810--55121 Score: 416
Period size: 53 Copynumber: 5.9 Consensus size: 53
54800 TAATCACACC
* * *
54810 AGAAGATTGTTTGAGTTTTACTCCCTGAAGCAAGAGGGAG-G-A-CCGTAAGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
*
54860 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
*
54913 AGAAGATTGTTCGAGTTCTACTCCCTGAAACAAGAGGGAGCGAACCCGTAAGT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
* * * *
54966 AGAAGATTATTCGAGTTCTACCCCCTGAAGCAAAAGGGAGCGAACCCGTAAGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
* * * ***
55019 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCATTTTT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
* * *
55072 AGAAGATTGTTCGAGTTCCTTAATCCCGGAA-CAAGAGGGAGCGGACCCGT
1 AGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCCGT
55122 CATTTGATGA
Statistics
Matches: 233, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
50 38 0.16
51 1 0.00
52 1 0.00
53 167 0.72
54 17 0.07
55 9 0.04
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (53 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
Found at i:65605 original size:80 final size:80
Alignment explanation
Indices: 65409--65605 Score: 315
Period size: 80 Copynumber: 2.5 Consensus size: 80
65399 TCTTTCGGGC
65409 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
*
65474 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATA
* * * *
65489 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCTTCGCGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
65554 GTAGTGAAGC-AATCA
66 GTAGTGAAGCAAAT-A
* *
65569 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
65606 TGGGCCATTC
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
79 3 0.03
80 105 0.97
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (80 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
GTAGTGAAGCAAATA
Found at i:65971 original size:53 final size:53
Alignment explanation
Indices: 65852--66163 Score: 407
Period size: 53 Copynumber: 5.9 Consensus size: 53
65842 TAATCACACC
* *
65852 AGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAG-G-A-CCGTAAGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
*
65902 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
*
65955 AGAAGATTGTTCGAGTTCTACTCCCTGAAACAAGAGGGAGCGAACCCGTAAGT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
* * * * *
66008 AGAAGATTATTCGAGTTCTACCCCCTGAAGCAAAAGGGAGCGAAGCCGTAAGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
* * * * ***
66061 AGAAGATTATTCGAGTTCTACTCCCTAAAGCAATAGGGAGCGAACCCATTTTT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
* * *
66114 AGAAGATTGTTCGAGTTCCTTAATCCCGGAA-CAAGAGGGAGCGGACCCGT
1 AGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCCGT
66164 CATTTGATGA
Statistics
Matches: 230, Mismatches: 27, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
50 39 0.17
51 1 0.00
52 1 0.00
53 164 0.71
54 17 0.07
55 8 0.03
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (53 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGT
Found at i:73842 original size:3 final size:3
Alignment explanation
Indices: 73836--73875 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
73826 AATATTTTAT
73836 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA T
73876 CAAATGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:74321 original size:113 final size:113
Alignment explanation
Indices: 74198--74482 Score: 471
Period size: 113 Copynumber: 2.5 Consensus size: 113
74188 AGAATCAAAC
*
74198 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTAATT
* * **
74263 ATGAACTTTACCTGGCAATGCTGATCCATCAAGTGATGGATTTGAGCA
66 ATGAACTTTACCTGGCAATGCTAATCCATCAAGTGATGAATTAAAGCA
* * *
74311 AAAGGTTGAACAAGTTCTTCTTATTATGAATTTCCTCTTCCTTCTTCAGATGAGTTCTTCTAATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTAATT
* **
74376 ATGAACTTTATCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGCA
66 ATGAACTTTACCTGGCAATGCTAATCCATCAAGTGATGAATTAAAGCA
74424 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
74483 GTTAACTTCC
Statistics
Matches: 158, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 158 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTAATT
ATGAACTTTACCTGGCAATGCTAATCCATCAAGTGATGAATTAAAGCA
Found at i:75865 original size:17 final size:16
Alignment explanation
Indices: 75834--75867 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
75824 CACGTGAGGA
75834 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
75850 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
75867 T
1 T
75868 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Done.