Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007058.1 Hibiscus syriacus cultivar Beakdansim tig00018312_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: 64206
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2035 original size:11 final size:11
Alignment explanation
Indices: 2019--2048 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2009 TTCTGTTTCT
2019 TATTATTATTA
1 TATTATTATTA
2030 TATTATTATTA
1 TATTATTATTA
2041 TGATTATT
1 T-ATTATT
2049 TTCTTTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
TATTATTATTA
Found at i:3913 original size:5 final size:5
Alignment explanation
Indices: 3899--3930 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
3889 TGATTATATC
3899 ATTTT A-TTT ATTTT ATTTT ATTTT A-TTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
3931 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.32
5 17 0.68
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:3933 original size:8 final size:9
Alignment explanation
Indices: 3899--3930 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
3889 TGATTATATC
3899 ATTTTATTT
1 ATTTTATTT
3908 ATTTTATTTT
1 ATTTTA-TTT
3918 ATTTTATTT
1 ATTTTATTT
3927 ATTT
1 ATTT
3931 ATTCATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
ATTTTATTT
Found at i:9659 original size:105 final size:104
Alignment explanation
Indices: 9477--9682 Score: 297
Period size: 105 Copynumber: 2.0 Consensus size: 104
9467 AAAGAAAATT
* * * * * *
9477 CTGCACACTCATTTTTTGATGTTGTGTTGTTTAAGATGCATGAGAAGTTTGTATTGATTAAAATA
1 CTGCACAATCATTTTTTGATGTTATGTTGTTTAAGATGAATGAGAAGCTTATAATGATTAAAATA
*
9542 TTATTTACTTTTAACTTTTGCATCATCATTTCTTCAATG
66 TTATTTACTTTTAACTTTTACATCATCATTTCTTCAATG
9581 CTGCACAATCATTTTTTGAGTGTTATGTTGTTTAACG-TGAATGAGAAGCTTATAATGATTAAAA
1 CTGCACAATCATTTTTTGA-TGTTATGTTGTTTAA-GATGAATGAGAAGCTTATAATGATTAAAA
* * *
9645 TATTATTTATTTTTAGCTTTTACATTATCATTTCTTCA
64 TATTATTTACTTTTAACTTTTACATCATCATTTCTTCA
9683 CCTTTTTAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
104 18 0.20
105 71 0.79
106 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.47
Consensus pattern (104 bp):
CTGCACAATCATTTTTTGATGTTATGTTGTTTAAGATGAATGAGAAGCTTATAATGATTAAAATA
TTATTTACTTTTAACTTTTACATCATCATTTCTTCAATG
Found at i:9958 original size:30 final size:29
Alignment explanation
Indices: 9924--9980 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
9914 TCTCTTATTC
9924 TTTTAAATAAAGTTAAATTTATTTTTTAGT
1 TTTTAAAT-AAGTTAAATTTATTTTTTAGT
***
9954 TTTTAAATTTTTTAAATTTATTTTTTA
1 TTTTAAATAAGTTAAATTTATTTTTTA
9981 ATTTGAGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (29 bp):
TTTTAAATAAGTTAAATTTATTTTTTAGT
Found at i:10187 original size:25 final size:23
Alignment explanation
Indices: 10133--10189 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
10123 AAATTATATT
* *
10133 AAATTTGTGTAATTTAAATTATG
1 AAATTTGTCTAATTAAAATTATG
10156 AATATTTGTCTAATTAATAATTATTG
1 AA-ATTTGTCTAATTAA-AATTA-TG
*
10182 TAATTTGT
1 AAATTTGT
10190 AAATTTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 2 0.07
24 12 0.43
25 11 0.39
26 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.51
Consensus pattern (23 bp):
AAATTTGTCTAATTAAAATTATG
Found at i:12003 original size:2 final size:2
Alignment explanation
Indices: 11996--12037 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
11986 ATTATGACTG
11996 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
12038 TTCATAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12060 original size:14 final size:14
Alignment explanation
Indices: 12041--12072 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
12031 TATATATTTC
12041 ATAATCTTATTAAG
1 ATAATCTTATTAAG
12055 ATAATCTTATTAAG
1 ATAATCTTATTAAG
12069 ATAA
1 ATAA
12073 GACTTTTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (14 bp):
ATAATCTTATTAAG
Found at i:15140 original size:20 final size:20
Alignment explanation
Indices: 15115--15157 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
15105 AGAAAATTTC
**
15115 ATTCTAAAGTTTTTATGTTT
1 ATTCTAAACATTTTATGTTT
*
15135 ATTCTAAACATTTTGTGTTT
1 ATTCTAAACATTTTATGTTT
15155 ATT
1 ATT
15158 TTAATGATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.58
Consensus pattern (20 bp):
ATTCTAAACATTTTATGTTT
Found at i:15613 original size:18 final size:18
Alignment explanation
Indices: 15590--15627 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
15580 TAGTCACAAT
*
15590 AAAATAATAAATTTAGTC
1 AAAATAAGAAATTTAGTC
*
15608 AAAATAAGAAATTTTGTC
1 AAAATAAGAAATTTAGTC
15626 AA
1 AA
15628 TTTTATTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (18 bp):
AAAATAAGAAATTTAGTC
Found at i:15728 original size:33 final size:33
Alignment explanation
Indices: 15681--15757 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
15671 ATTTGGTGAT
* * *
15681 AATAGAAATTTATGAAAAATATTAATT-TTTCA-
1 AATAAAAAATTATGAAAAATAAT-ATTCTTTCAC
*
15713 ATATAAAAAATTATGATAAATAATATTCTTTCAC
1 A-ATAAAAAATTATGAAAAATAATATTCTTTCAC
15747 AATAAAAAATT
1 AATAAAAAATT
15758 GTAACAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
32 4 0.11
33 33 0.87
34 1 0.03
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (33 bp):
AATAAAAAATTATGAAAAATAATATTCTTTCAC
Found at i:15772 original size:192 final size:191
Alignment explanation
Indices: 15488--15851 Score: 545
Period size: 192 Copynumber: 1.9 Consensus size: 191
15478 TTATTTAATT
15488 ATAATAAAATTTTATAAAACAAATAAATTTCTTAATATAAAAAATTATGACAAATAATATTTTTC
1 ATAATAAAATTTTATAAAACAAATAAATTTCTTAATATAAAAAATTATGACAAATAATATTTTTC
* * * **
15553 ACAATAATAAATTGTAACAATTTTATTTAGTCACAATAAAATAATAAATTTAGTCAAAATAAGAA
66 ACAATAAAAAATTGTAACAAATTTATTTAGTAACAATAAAATAATAAATGAAGTCAAAATAAGAA
* * *
15618 ATTTTGTCAATTTTATTTAGTCACAATATTTTCTGAAAATAAAAAAATTTGATATTTGGTG
131 ATTTTGTCAAATATATTTAGTCACAATATTTTCTCAAAATAAAAAAATTTGATATTTGGTG
* * *
15679 ATAATAGAAA-TTTATGAAAA-ATATTAATTT-TTCAATATAAAAAATTATGATAAATAATATTC
1 ATAATA-AAATTTTAT-AAAACAAATAAATTTCTT-AATATAAAAAATTATGACAAATAATATT-
** *
15741 TTTCACAATAAAAAATTGTAACAAATTTATTTAGTAACAATAACCTATTAAATGAAGTCAAAATA
62 TTTCACAATAAAAAATTGTAACAAATTTATTTAGTAACAATAAAATAATAAATGAAGTCAAAATA
15806 AGAAATTTTGTCAAATATATTTAGTCACAATATTTTCTCAAAATAA
127 AGAAATTTTGTCAAATATATTTAGTCACAATATTTTCTCAAAATAA
15852 CAAATTATGA
Statistics
Matches: 155, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
190 2 0.01
191 46 0.30
192 107 0.69
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.38
Consensus pattern (191 bp):
ATAATAAAATTTTATAAAACAAATAAATTTCTTAATATAAAAAATTATGACAAATAATATTTTTC
ACAATAAAAAATTGTAACAAATTTATTTAGTAACAATAAAATAATAAATGAAGTCAAAATAAGAA
ATTTTGTCAAATATATTTAGTCACAATATTTTCTCAAAATAAAAAAATTTGATATTTGGTG
Found at i:20606 original size:19 final size:21
Alignment explanation
Indices: 20568--20607 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20558 CTGAAATTAT
*
20568 TGTAGCAGTGTACTGATACAC
1 TGTAGCAGTATACTGATACAC
20589 TGTAGCAGTAT-C-GATACAC
1 TGTAGCAGTATACTGATACAC
20608 ATTTTACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
TGTAGCAGTATACTGATACAC
Found at i:20711 original size:19 final size:20
Alignment explanation
Indices: 20652--20714 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
20642 TTCATTATTG
*
20652 TTCACACAGTATCGATACTA
1 TTCATACAGTATCGATACTA
* *
20672 TTTATACAGTACCGATACTA
1 TTCATACAGTATCGATACTA
*
20692 TTCATACAGTATAG-TACTA
1 TTCATACAGTATCGATACTA
20711 TTCA
1 TTCA
20715 CAAAAACATT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 9 0.24
20 28 0.76
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35
Consensus pattern (20 bp):
TTCATACAGTATCGATACTA
Found at i:27739 original size:16 final size:16
Alignment explanation
Indices: 27708--27756 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
27698 GAATTTAATT
*
27708 TTATATTTGA-TAAAG
1 TTATATTTTATTAAAG
27723 TTATATTTTATTAAAG
1 TTATATTTTATTAAAG
* *
27739 TTAAATTTCTATTTAAG
1 TTATATTT-TATTAAAG
27756 T
1 T
27757 AGTTTTTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 9 0.31
16 12 0.41
17 8 0.28
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (16 bp):
TTATATTTTATTAAAG
Found at i:28909 original size:20 final size:20
Alignment explanation
Indices: 28770--28906 Score: 213
Period size: 20 Copynumber: 6.8 Consensus size: 20
28760 TTTTACGACT
28770 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
28790 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
28810 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
28830 ATCGCAATGTGAATATATAA
1 ATCGCAATGCGAATATGTAA
28850 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
28870 ATCGCAATGCGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
*
28890 ATCGCAATGCGATTATG
1 ATCGCAATGCGAATATG
28907 ACTGTCGCAA
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
19 1 0.01
20 109 0.99
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:29766 original size:24 final size:24
Alignment explanation
Indices: 29738--29791 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
29728 GTATTTGAAA
29738 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
29762 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
29786 TTTGAT
1 TTTGAT
29792 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:30010 original size:14 final size:14
Alignment explanation
Indices: 29981--30016 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
29971 AGAAAAAGAA
29981 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
29996 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
30010 GAAGAAA
1 GAAGAAA
30017 TGCCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.50, C:0.22, G:0.22, T:0.06
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:32047 original size:6 final size:6
Alignment explanation
Indices: 32031--32069 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
32021 AAGAAAATGG
* * *
32031 CAATCA AAATCA CAATCA CAATCA AAATCC CAATCA CAA
1 CAATCA CAATCA CAATCA CAATCA CAATCA CAATCA CAA
32070 CCGGCTTCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (6 bp):
CAATCA
Found at i:32054 original size:18 final size:18
Alignment explanation
Indices: 32031--32069 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
32021 AAGAAAATGG
32031 CAATCAAAATCACAATCA
1 CAATCAAAATCACAATCA
*
32049 CAATCAAAATCCCAATCA
1 CAATCAAAATCACAATCA
32067 CAA
1 CAA
32070 CCGGCTTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (18 bp):
CAATCAAAATCACAATCA
Found at i:32381 original size:140 final size:140
Alignment explanation
Indices: 32126--32395 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
32116 AAACGTTGTA
*
32126 TTATGTGTAAACTTTTAACATTTTTAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
32191 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATTGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
32256 TATGTGTATT
131 TATGTGTATT
32266 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
32331 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
32396 CGCAACATGA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:32391 original size:20 final size:20
Alignment explanation
Indices: 32366--32570 Score: 173
Period size: 20 Copynumber: 10.8 Consensus size: 20
32356 TTACACATTC
*
32366 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
**
32386 ATTTGACTATCGCAACATGA
1 ATTTGACTATCGCAACGCGA
*
32406 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
** *
32425 A----AAAATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
32441 ATTTGTCTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
32461 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
32481 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
32495 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
32515 ATTTGAGTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
32535 ATTTGATTATCACAACGGGT
1 ATTTGACTATCGCAACGCGA
32555 ATTTGACTATCGCAAC
1 ATTTGACTATCGCAAC
32571 AAGAAAATCG
Statistics
Matches: 148, Mismatches: 24, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
14 12 0.08
15 10 0.07
16 3 0.02
18 1 0.01
19 3 0.02
20 118 0.80
21 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:32468 original size:55 final size:53
Alignment explanation
Indices: 32374--32531 Score: 199
Period size: 54 Copynumber: 2.9 Consensus size: 53
32364 TCATTTGAAT
*
32374 ATCGCAACGCGAATTTGACTATCGCAACATGAATATGACTATCGCAACGCAAAAA
1 ATCGCAACGCGAATTTGACTATCGCAAC-GGAATATGACTATCGCAACG-AAAAA
* * * * *
32429 ATCGCAACACGAATTTGTCTATCGCAACGGCTATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGG-AATATGACTATCGCAACGAAAAA
* * *
32483 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGAGTATCACAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG-GAATATGACTATCGCAACG
32532 CGAATTTGAT
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
54 47 0.52
55 43 0.48
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (53 bp):
ATCGCAACGCGAATTTGACTATCGCAACGGAATATGACTATCGCAACGAAAAA
Found at i:32562 original size:94 final size:94
Alignment explanation
Indices: 32433--32611 Score: 279
Period size: 94 Copynumber: 1.9 Consensus size: 94
32423 CAAAAAATCG
* * *
32433 CAACACGAATTTGTCTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAACGCGAATT
1 CAACACGAATTTGTCTATCACAACGGCTATTTGACTATCGCAACAAGAAAATCGCAAAGCGAATT
*
32498 TGACTATCGCAACGCGAATTTGAGTATCA
66 AGACTATCGCAACGCGAATTTGAGTATCA
* * *
32527 CAACGCGAATTTGAT-TATCACAACGGGTATTTGACTATCGCAACAAGAAAATCGCAAAGCGTAT
1 CAACACGAATTTG-TCTATCACAACGGCTATTTGACTATCGCAACAAGAAAATCGCAAAGCGAAT
32591 TAGACTATCGCAACGCGAATT
65 TAGACTATCGCAACGCGAATT
32612 GACTTTCGCG
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 76 0.99
95 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (94 bp):
CAACACGAATTTGTCTATCACAACGGCTATTTGACTATCGCAACAAGAAAATCGCAAAGCGAATT
AGACTATCGCAACGCGAATTTGAGTATCA
Found at i:32639 original size:20 final size:20
Alignment explanation
Indices: 32614--32672 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
32604 CGCGAATTGA
* *
32614 CTTTCGCGTTGTGATTTTGT
1 CTTTCGCATTGCGATTTTGT
32634 CTTTCGCATTGCGATTTTGT
1 CTTTCGCATTGCGATTTTGT
*
32654 TTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
32673 AGTTTAGCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.08, C:0.17, G:0.22, T:0.53
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Found at i:32846 original size:14 final size:14
Alignment explanation
Indices: 32786--32847 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
32776 CACAAATAAG
*
32786 AATTATTTACACATC
1 AATT-TTTACAAATC
**
32801 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
32816 AACTTTTACAAATC
1 AATTTTTACAAATC
*
32830 AATTTTTATAAATC
1 AATTTTTACAAATC
32844 AATT
1 AATT
32848 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:34351 original size:42 final size:42
Alignment explanation
Indices: 34253--34363 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 42
34243 TCTAGAATGT
* * *
34253 TGGGAG-GGACCTCTTTAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGA-CTCTTGAACGATGATAGTGGCCTCTTGAACGA
* **
34295 TGGGAGGGGACTCTTGAGGGATGATAGTGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGATAGTGGCCTCTTGAACGA
*
34337 TAGGG-GAGGCCTCTTGAACGATGATAG
1 T-GGGAGAGGACTCTTGAACGATGATAG
34364 GTGAGTCGGG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
42 52 0.90
43 6 0.10
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGATAGTGGCCTCTTGAACGA
Found at i:34867 original size:18 final size:19
Alignment explanation
Indices: 34844--34889 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
34834 GAAACTTAAA
34844 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
34862 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
34882 ATCGCAAC
1 ATCGCAAC
34890 GAGAGAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.40
20 15 0.60
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:34989 original size:20 final size:20
Alignment explanation
Indices: 34933--35000 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
34923 GCGATTCTTT
**
34933 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
34953 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
34973 TGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
*
34993 CATTGCGA
1 CGTTGCGA
35001 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:35160 original size:18 final size:18
Alignment explanation
Indices: 35137--35186 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
35127 TTTACTAAGC
35137 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
35155 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
35173 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
35187 TACGATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:36880 original size:20 final size:20
Alignment explanation
Indices: 36857--36924 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
36847 TCTGAAACTT
*
36857 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
36877 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
36897 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
36916 AAAATCGCA
1 AAAATCGCA
36925 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 7 0.17
20 34 0.83
ACGTcount: A:0.50, C:0.22, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:37336 original size:22 final size:22
Alignment explanation
Indices: 37306--37352 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
37296 GATGGAGATA
*
37306 GACTGATTTCGCCGGAGATGGG
1 GACTAATTTCGCCGGAGATGGG
*
37328 GACTAATTTCGTCGGAGATGGG
1 GACTAATTTCGCCGGAGATGGG
37350 GAC
1 GAC
37353 GGATGTCGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.23
Consensus pattern (22 bp):
GACTAATTTCGCCGGAGATGGG
Found at i:37595 original size:20 final size:20
Alignment explanation
Indices: 37532--37626 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 20
37522 GCTTTGAAAA
*
37532 TCGCATTGCGATAGTCA-GC
1 TCGCATTGCGATAGTCATAC
* * * *
37551 ATCGCGTTACGATAGTCAGAA
1 -TCGCATTGCGATAGTCATAC
*
37572 TCGCGTTGCGATAGTCATAC
1 TCGCATTGCGATAGTCATAC
* *
37592 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGT-CATAC
37612 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
37627 TGGAAAATCG
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
19 1 0.02
20 59 0.97
21 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATAC
Found at i:39201 original size:2 final size:2
Alignment explanation
Indices: 39194--39219 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39184 AGAGTCTATC
39194 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
39220 GTTTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45274 original size:21 final size:21
Alignment explanation
Indices: 45226--45275 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
45216 AGGATAAATA
*
45226 ATTTGATTTGATTATTGGATG
1 ATTTGATTTGAATATTGGATG
**
45247 ACCTGATTTGAATATTTGGAT-
1 ATTTGATTTGAATA-TTGGATG
45268 ATTTGATT
1 ATTTGATT
45276 CGATTTTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (21 bp):
ATTTGATTTGAATATTGGATG
Found at i:49616 original size:41 final size:41
Alignment explanation
Indices: 49571--49652 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
49561 ATCCTAGTAT
49571 TCATTTCAACTTAACCAATTCAGAATGGGATTGAACAATTA
1 TCATTTCAACTTAACCAATTCAGAATGGGATTGAACAATTA
49612 TCATTTCAACTTAACCAATTCAGAATGGGATTGAACAATTA
1 TCATTTCAACTTAACCAATTCAGAATGGGATTGAACAATTA
49653 GGGTTTGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (41 bp):
TCATTTCAACTTAACCAATTCAGAATGGGATTGAACAATTA
Found at i:50084 original size:17 final size:17
Alignment explanation
Indices: 50062--50136 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
50052 TTTTTAATAT
50062 TTTAATAATATTATTAA
1 TTTAATAATATTATTAA
*
50079 TTTAATAAGTA--ATTGA
1 TTTAATAA-TATTATTAA
*
50095 TATTAATAATAATATATTAT
1 T-TTAATAAT-AT-TATTAA
*
50115 TTTAATAA-ATAATTAA
1 TTTAATAATATTATTAA
*
50131 TATAAT
1 TTTAAT
50137 TTATAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
16 15 0.33
17 18 0.39
18 2 0.04
19 7 0.15
20 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAATATTATTAA
Found at i:50113 original size:36 final size:37
Alignment explanation
Indices: 50055--50163 Score: 109
Period size: 36 Copynumber: 3.0 Consensus size: 37
50045 TATACTATTT
* *
50055 TTAATATT-TTAATAATATTATTAATTTAATAAGTAA
1 TTAATATTAATAATAATATTATTAATTTAATAAATAA
* *
50091 TTGATATTAATAATAATA-TATTATTTTAATAAATAA
1 TTAATATTAATAATAATATTATTAATTTAATAAATAA
* *
50127 TTAATA-TAATTTATAATAATT-TTATTTTAATGAAATA
1 TTAATATTAA-TAATAAT-ATTATTAATTTAAT-AAATA
50164 TGATAATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
35 3 0.05
36 34 0.55
37 19 0.31
38 6 0.10
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.50
Consensus pattern (37 bp):
TTAATATTAATAATAATATTATTAATTTAATAAATAA
Found at i:50121 original size:19 final size:19
Alignment explanation
Indices: 50059--50177 Score: 78
Period size: 19 Copynumber: 6.5 Consensus size: 19
50049 CTATTTTTAA
50059 TATTTTAATAAT-ATT-AT
1 TATTTTAATAATAATTGAT
*
50076 TAATTTAATAAGTAATTGA-
1 TATTTTAATAA-TAATTGAT
50095 TA--TTAATAATAATAT-AT
1 TATTTTAATAATAAT-TGAT
*
50112 TATTTTAATAAATAATTAAT
1 TATTTTAAT-AATAATTGAT
*
50132 ATAATTT-ATAATAATT--T
1 -TATTTTAATAATAATTGAT
*
50149 TATTTTAATGA-AATATGAT
1 TATTTTAATAATAAT-TGAT
*
50168 AATTTTAATA
1 TATTTTAATA
50178 TTTTTATTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
16 13 0.16
17 25 0.30
18 1 0.01
19 27 0.33
20 11 0.13
21 5 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TATTTTAATAATAATTGAT
Found at i:50143 original size:23 final size:22
Alignment explanation
Indices: 50099--50145 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
50089 AATTGATATT
50099 AATAATAATATATTATTTTAATA
1 AATAATAATATA-TATTTTAATA
50122 AATAATTAATATA-ATTTATAATA
1 AATAA-TAATATATATTT-TAATA
50145 A
1 A
50146 TTTTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.18
23 11 0.50
24 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATAATATATATTTTAATA
Found at i:50453 original size:47 final size:47
Alignment explanation
Indices: 50375--50496 Score: 145
Period size: 47 Copynumber: 2.5 Consensus size: 47
50365 TTGTAAAATG
* * * ***
50375 ATTTTCAAAACATATTTTCCATGAAATGTAATTTAGTTTATGGAATTT
1 ATTTTTAAAAAATATTTT-CATGAAATGTAATTTACTTTACAAAATTT
50423 ATTTTTAAAAAATATTTTCATGAAATGTAATTTACTTTACAAAATTT
1 ATTTTTAAAAAATATTTTCATGAAATGTAATTTACTTTACAAAATTT
* *
50470 ATTTTTCGAAATATAATTTTCATGAAA
1 ATTTTT-AAAAAAT-ATTTTCATGAAA
50497 CAAACATAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
47 31 0.48
48 21 0.33
49 12 0.19
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (47 bp):
ATTTTTAAAAAATATTTTCATGAAATGTAATTTACTTTACAAAATTT
Found at i:50795 original size:25 final size:21
Alignment explanation
Indices: 50738--50783 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
50728 TTTGTTAACG
50738 AAATTATTTTATATGTAGAAC
1 AAATTATTTTATATGTAGAAC
50759 AAATTATTTTATATGTAGAAC
1 AAATTATTTTATATGTAGAAC
50780 AAAT
1 AAAT
50784 GTAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (21 bp):
AAATTATTTTATATGTAGAAC
Found at i:54400 original size:13 final size:13
Alignment explanation
Indices: 54384--54410 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54374 AAAAACTAAA
54384 AGATGAATAAGTT
1 AGATGAATAAGTT
54397 AGATGAATAAGTT
1 AGATGAATAAGTT
54410 A
1 A
54411 TGAGTGATTA
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:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (13 bp):
AGATGAATAAGTT
Found at i:55548 original size:28 final size:27
Alignment explanation
Indices: 55495--55553 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
55485 TATTGAATAC
* * *
55495 ATGTCTATGTGATATAAGCTACGTGACA
1 ATGTCTATGTGATACAAACCACGTGA-A
*
55523 ATGTCTATGTGATACAAACCATGTGAA
1 ATGTCTATGTGATACAAACCACGTGAA
55550 ATGT
1 ATGT
55554 GTAAATGGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (27 bp):
ATGTCTATGTGATACAAACCACGTGAA
Found at i:55712 original size:24 final size:24
Alignment explanation
Indices: 55677--55723 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
55667 ATTTCTATGT
55677 GGCATTTCGGTGCATATTT-TACAC
1 GGCATTTCGGTGCA-ATTTATACAC
55701 GGCACTTT-GGTGCAATTTATACA
1 GGCA-TTTCGGTGCAATTTATACA
55724 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 14 0.67
25 3 0.14
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (24 bp):
GGCATTTCGGTGCAATTTATACAC
Found at i:60305 original size:3 final size:3
Alignment explanation
Indices: 60297--60361 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
60287 CATCCATTTG
*
60297 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TT- TTA TTTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
60341 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
60362 AAAAATACTA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.07
3 50 0.88
4 3 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:60586 original size:22 final size:22
Alignment explanation
Indices: 60560--60618 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
60550 ATGTCGAGCT
60560 CTATGGTGAGTCACCACCATAG
1 CTATGGTGAGTCACCACCATAG
60582 CTATGGTGAGTCACCACCATAG
1 CTATGGTGAGTCACCACCATAG
*
60604 CTATGGTGACTCACC
1 CTATGGTGAGTCACC
60619 TAGGGTTACC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (22 bp):
CTATGGTGAGTCACCACCATAG
Found at i:62049 original size:2 final size:2
Alignment explanation
Indices: 62042--62069 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62032 TATCTTATTA
62042 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
62070 TAATAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.