Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005429.1 Hibiscus syriacus cultivar Beakdansim tig00012446_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: 158755
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:9633 original size:30 final size:31
Alignment explanation
Indices: 9588--9652 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
9578 AAATAGGATG
*
9588 AATTATGTATTTAGTCATCTAATTATTTTTT
1 AATTATGTATTTAGTCATCTAATTATTTTAT
* *
9619 AATTCTGT-TTTAGTCATTTAATTATTTTAT
1 AATTATGTATTTAGTCATCTAATTATTTTAT
9649 AATT
1 AATT
9653 TAGTAGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (31 bp):
AATTATGTATTTAGTCATCTAATTATTTTAT
Found at i:12025 original size:17 final size:16
Alignment explanation
Indices: 11991--12038 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 16
11981 AGGGGGCTAG
11991 TTTTTAAAAAAAATAT
1 TTTTTAAAAAAAATAT
12007 TTTTTAAACATAATAATTTAT
1 TTTTTAAA-A-AA-AA--TAT
12028 TTTTTAAAAAA
1 TTTTTAAAAAA
12039 TCTTAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 8 0.30
17 1 0.04
18 2 0.07
19 4 0.15
20 1 0.04
21 11 0.41
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTTAAAAAAAATAT
Found at i:21805 original size:8 final size:8
Alignment explanation
Indices: 21792--21841 Score: 91
Period size: 8 Copynumber: 6.2 Consensus size: 8
21782 TTTAAGTTTT
21792 ATACATGC
1 ATACATGC
21800 ATACATGC
1 ATACATGC
21808 ATACATGC
1 ATACATGC
21816 ATACATGC
1 ATACATGC
21824 ATACATGC
1 ATACATGC
*
21832 ATGCATGC
1 ATACATGC
21840 AT
1 AT
21842 TAATAAGTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (8 bp):
ATACATGC
Found at i:21836 original size:4 final size:4
Alignment explanation
Indices: 21795--21841 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
21785 AAGTTTTATA
* * * *
21795 CATG CATA CATG CATA CATG CATA CATG CATA CATG CATG CATG CAT
1 CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG CAT
21842 TAATAAGTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (4 bp):
CATG
Found at i:27301 original size:15 final size:14
Alignment explanation
Indices: 27274--27308 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
27264 TATTATTTTA
27274 AAATATTTAAAATTT
1 AAAT-TTTAAAATTT
27289 AAATTTTATAAATTT
1 AAATTTTA-AAATTT
27304 AAATT
1 AAATT
27309 CAAATTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTTTAAAATTT
Found at i:27313 original size:21 final size:23
Alignment explanation
Indices: 27268--27316 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
27258 TCAAAATATT
*
27268 ATTTTAAAATATTTAAAATTTAA
1 ATTTTAAAATATTTAAAATTCAA
*
27291 ATTTTATAA-ATTT-AAATTCAA
1 ATTTTAAAATATTTAAAATTCAA
27312 ATTTT
1 ATTTT
27317 GTATTGACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.50
22 4 0.17
23 8 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTAAAATATTTAAAATTCAA
Found at i:30527 original size:7 final size:7
Alignment explanation
Indices: 30515--30568 Score: 108
Period size: 7 Copynumber: 7.7 Consensus size: 7
30505 ACAAAGACCT
30515 CTAAACC
1 CTAAACC
30522 CTAAACC
1 CTAAACC
30529 CTAAACC
1 CTAAACC
30536 CTAAACC
1 CTAAACC
30543 CTAAACC
1 CTAAACC
30550 CTAAACC
1 CTAAACC
30557 CTAAACC
1 CTAAACC
30564 CTAAA
1 CTAAA
30569 ACTCTAACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:30575 original size:8 final size:8
Alignment explanation
Indices: 30517--30575 Score: 67
Period size: 7 Copynumber: 8.1 Consensus size: 8
30507 AAAGACCTCT
30517 AAACCCT-
1 AAACCCTA
30524 AAACCCT-
1 AAACCCTA
30531 AAACCCT-
1 AAACCCTA
30538 AAACCCT-
1 AAACCCTA
30545 AAACCCT-
1 AAACCCTA
30552 AAACCCT-
1 AAACCCTA
30559 AAACCCTA
1 AAACCCTA
*
30567 AAACTCTA
1 AAACCCTA
30575 A
1 A
30576 CAAATTCTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
7 42 0.84
8 8 0.16
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (8 bp):
AAACCCTA
Found at i:33448 original size:20 final size:22
Alignment explanation
Indices: 33423--33466 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
33413 CACCCGCGGC
33423 ATCCATCCACCCAT-TA-ATAT
1 ATCCATCCACCCATATATATAT
*
33443 ATCCATCCATCCATATATATAT
1 ATCCATCCACCCATATATATAT
33465 AT
1 AT
33467 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (22 bp):
ATCCATCCACCCATATATATAT
Found at i:33460 original size:2 final size:2
Alignment explanation
Indices: 33455--33496 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
33445 CCATCCATCC
33455 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
33497 TAAAAAAAAT
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:33843 original size:17 final size:17
Alignment explanation
Indices: 33794--33843 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
33784 TTGTTCATGT
33794 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
33811 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
33825 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
33842 TT
1 TT
33844 CACAAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:37937 original size:29 final size:30
Alignment explanation
Indices: 37875--37946 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
37865 GGGCCATAGC
* * * *
37875 TGTAAAGATTAAAAGAGTGGGAGTCCTAAT
1 TGTAAATATTAAAAGAATGGGAGCCCTAAA
*
37905 TGTAAATATTAAAATAAT-GGAGCCCTAAA
1 TGTAAATATTAAAAGAATGGGAGCCCTAAA
37934 TGTAAATATTAAA
1 TGTAAATATTAAA
37947 GGAGCAGGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (30 bp):
TGTAAATATTAAAAGAATGGGAGCCCTAAA
Found at i:41090 original size:76 final size:76
Alignment explanation
Indices: 40998--41155 Score: 316
Period size: 76 Copynumber: 2.1 Consensus size: 76
40988 AGTTAATGAT
40998 CAAGCTGGGTTTAATTTCTTGTGTAGAGCTTTCTTCGATTCGAACCCGGCTGATACTAAGCTAGG
1 CAAGCTGGGTTTAATTTCTTGTGTAGAGCTTTCTTCGATTCGAACCCGGCTGATACTAAGCTAGG
41063 AGATGACGGTC
66 AGATGACGGTC
41074 CAAGCTGGGTTTAATTTCTTGTGTAGAGCTTTCTTCGATTCGAACCCGGCTGATACTAAGCTAGG
1 CAAGCTGGGTTTAATTTCTTGTGTAGAGCTTTCTTCGATTCGAACCCGGCTGATACTAAGCTAGG
41139 AGATGACGGTC
66 AGATGACGGTC
41150 CAAGCT
1 CAAGCT
41156 TGATTAGTAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 82 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (76 bp):
CAAGCTGGGTTTAATTTCTTGTGTAGAGCTTTCTTCGATTCGAACCCGGCTGATACTAAGCTAGG
AGATGACGGTC
Found at i:42303 original size:6 final size:6
Alignment explanation
Indices: 42259--42301 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
42249 ATTTTAGAAG
*
42259 ATTTAA ATTTAA ATTTAA ATTTAAA TATTTAA ATTTAT ATTTA
1 ATTTAA ATTTAA ATTTAA ATTT-AA -ATTTAA ATTTAA ATTTA
42302 TAAAATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
6 26 0.76
7 4 0.12
8 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:43550 original size:28 final size:30
Alignment explanation
Indices: 43502--43568 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
43492 CGACCCACGA
* * * *
43502 TGCTATTTTTGTAATTAATTT-TAAAAGGG
1 TGCTATTTTGGGAATTAATTTCGAAAAAGG
43531 TGCTATTTTGGGAATT-ATTTCGAAAAAGG
1 TGCTATTTTGGGAATTAATTTCGAAAAAGG
*
43560 TGTTATTTT
1 TGCTATTTT
43569 CGTAATAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.48
Consensus pattern (30 bp):
TGCTATTTTGGGAATTAATTTCGAAAAAGG
Found at i:44585 original size:62 final size:63
Alignment explanation
Indices: 44463--44585 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 63
44453 CTAATGTGAC
* * * * *
44463 TCTTAGGTAGGCTCTACGGCCCTGAGATCATTCTCGGGTAGGCCCTGCGACCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCATACTCGGGTAGGCCCTGCGACCCTAAGATGTGT
* * *
44526 TCTTAGGTAGGCCCCACGGCCCCGAAATC-TACTTGGGTAGGCTCT-CAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCATACTCGGGTAGGCCCTGC-GACCCTAAGATGT
44586 TCCCTTAGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
61 1 0.02
62 25 0.49
63 25 0.49
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCATACTCGGGTAGGCCCTGCGACCCTAAGATGTGT
Found at i:44654 original size:25 final size:25
Alignment explanation
Indices: 44602--44654 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
44592 AGGGTAACTC
* *
44602 TTTTATGGGATTTACTGCAGTATAA
1 TTTTATGAGATTTACTGCACTATAA
* *
44627 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATAA
44652 TTT
1 TTT
44655 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATAA
Found at i:45449 original size:60 final size:60
Alignment explanation
Indices: 45313--45430 Score: 139
Period size: 60 Copynumber: 2.0 Consensus size: 60
45303 ATAGTTGGGT
** * * * *
45313 GATCATTTTATAACTTTTAATAGTTGGGGGACTCAACAAAGCAACATCCTATAGTCGAAG
1 GATCATTTCGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATCCTATAGCCGAAG
* * *
45373 GATCATTTTGTAACTTTTAATAGTCGAGAGATTCAACAAAGCATCA-CCATATAGCCGA
1 GATCATTTCGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATCC-TATAGCCGA
45431 GGGACTATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.04
60 48 0.96
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (60 bp):
GATCATTTCGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACATCCTATAGCCGAAG
Found at i:46391 original size:60 final size:60
Alignment explanation
Indices: 46280--46411 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
46270 TCAGATGAGG
* * * *
46280 ATCATAGTTTGGGGATGAAATTGGAATGTTAAAAATTTGAAGGACTGATTTAAAATAAAA
1 ATCATAGTTTGGAGATGAAATTAGAATATTAAAAATTTGAAGGACTAATTTAAAATAAAA
* * * **
46340 ATCATAGTTTGGAGATGAAATTAGAATATTCAAAAGTTT-AA-GATCTAATTTAATATGAGG
1 ATCATAGTTTGGAGATGAAATTAGAATATT-AAAAATTTGAAGGA-CTAATTTAAAATAAAA
46400 ATCATAGTTTGG
1 ATCATAGTTTGG
46412 GGACATACGA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 2 0.03
60 52 0.85
61 7 0.11
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (60 bp):
ATCATAGTTTGGAGATGAAATTAGAATATTAAAAATTTGAAGGACTAATTTAAAATAAAA
Found at i:68998 original size:22 final size:23
Alignment explanation
Indices: 68948--68990 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
68938 AATTATAATT
*
68948 TAAAAAAAAAATTAATATTAAAA
1 TAAAATAAAAATTAATATTAAAA
68971 TAAAATAAAAA-TAAT-TTAAA
1 TAAAATAAAAATTAATATTAAA
68991 TATTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 4 0.21
23 10 0.53
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAAAATTAATATTAAAA
Found at i:72870 original size:7 final size:7
Alignment explanation
Indices: 72860--72904 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
72850 TCGAATTTTT
72860 AATTAAA
1 AATTAAA
72867 AATTAAA
1 AATTAAA
72874 AATTAAA
1 AATTAAA
72881 AATTAAA
1 AATTAAA
*
72888 GTATTAAA
1 -AATTAAA
72896 AA-TAAA
1 AATTAAA
72902 AAT
1 AAT
72905 GACTATTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 6 0.18
7 22 0.65
8 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (7 bp):
AATTAAA
Found at i:73237 original size:21 final size:21
Alignment explanation
Indices: 73213--73252 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
73203 TGGTAGAATA
* *
73213 TTACTTAAAATGTTAATTTCG
1 TTACCTAAAATATTAATTTCG
*
73234 TTACCTAATATATTAATTT
1 TTACCTAAAATATTAATTT
73253 TTTAACGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (21 bp):
TTACCTAAAATATTAATTTCG
Found at i:74745 original size:8 final size:7
Alignment explanation
Indices: 74727--74779 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
74717 GATTTAAAGT
*
74727 TTTATGA
1 TTTATGG
*
74734 TTTATGTT
1 TTTATG-G
74742 TTTATGG
1 TTTATGG
74749 TTTATGG
1 TTTATGG
*
74756 TTTATGT
1 TTTATGG
*
74763 TTTAGGG
1 TTTATGG
*
74770 TTTAAGG
1 TTTATGG
74777 TTT
1 TTT
74780 TAATGTTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
7 33 0.85
8 6 0.15
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (7 bp):
TTTATGG
Found at i:74752 original size:22 final size:21
Alignment explanation
Indices: 74698--74773 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 21
74688 AAGTTTGAGG
* *
74698 TTTAGGGTTTATAATTTAGGAT
1 TTTAGGGTTTATGATTTATG-T
* * *
74720 TTAAAGTTTTATGATTTATGTT
1 TTTAGGGTTTATGATTTATG-T
* *
74742 TTTATGGTTTATGGTTTATGT
1 TTTAGGGTTTATGATTTATGT
74763 TTTAGGGTTTA
1 TTTAGGGTTTA
74774 AGGTTTTAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 11 0.26
22 32 0.74
ACGTcount: A:0.22, C:0.00, G:0.21, T:0.57
Consensus pattern (21 bp):
TTTAGGGTTTATGATTTATGT
Found at i:75125 original size:7 final size:7
Alignment explanation
Indices: 75113--75137 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
75103 TTTAAGATGT
75113 TAGGGTC
1 TAGGGTC
75120 TAGGGTC
1 TAGGGTC
75127 TAGGGTC
1 TAGGGTC
75134 TAGG
1 TAGG
75138 TTTTAAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.44, T:0.28
Consensus pattern (7 bp):
TAGGGTC
Found at i:75298 original size:22 final size:21
Alignment explanation
Indices: 75270--75311 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
75260 CGTAAATATT
75270 TTATAATTTATAAAATATTTTG
1 TTATAATTTATAAAAT-TTTTG
*
75292 TTATAATTTTTAAAATTTTT
1 TTATAATTTATAAAATTTTT
75312 AATGATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATAATTTATAAAATTTTTG
Found at i:76004 original size:58 final size:58
Alignment explanation
Indices: 75939--76057 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
75929 AAATCTAACG
75939 ATAAACATGTTATATTTATTTATTCTGTTATAACTCAAAGTTTGACCCTAAAAGATCA
1 ATAAACATGTTATATTTATTTATTCTGTTATAACTCAAAGTTTGACCCTAAAAGATCA
75997 ATAAACATGTTATATTTATTTATTCTGTTATAACTCAAAGTTTGACCCTAAAAGATCA
1 ATAAACATGTTATATTTATTTATTCTGTTATAACTCAAAGTTTGACCCTAAAAGATCA
76055 ATA
1 ATA
76058 TATAAACTCT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (58 bp):
ATAAACATGTTATATTTATTTATTCTGTTATAACTCAAAGTTTGACCCTAAAAGATCA
Found at i:93535 original size:29 final size:29
Alignment explanation
Indices: 93492--93574 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
93482 CTCACCTAAC
93492 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
93522 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
93551 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
93575 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:98307 original size:29 final size:29
Alignment explanation
Indices: 98264--98346 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
98254 CTCACCTAAC
98264 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
98294 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
98323 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
98347 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:111359 original size:33 final size:33
Alignment explanation
Indices: 111297--111359 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
111287 TATTCTCTCT
* *
111297 AAAAAAAAATTAGAATTAAATTTAGAATTTACC
1 AAAAAAAAATTAGAATTAAATTCACAATTTACC
111330 AAAAAAAAATT--AATATAAATATCACAATTT
1 AAAAAAAAATTAGAAT-TAAAT-TCACAATTT
111360 TAATCTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 3 0.12
32 5 0.19
33 18 0.69
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.30
Consensus pattern (33 bp):
AAAAAAAAATTAGAATTAAATTCACAATTTACC
Found at i:112196 original size:27 final size:27
Alignment explanation
Indices: 112156--112210 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
112146 GGTGTTTTGG
*
112156 ATTTGGAACTATGTCCTCGAAAGGCCA
1 ATTTGGAACAATGTCCTCGAAAGGCCA
112183 ATTTGGAACAATGTCCTCGAAAGGCCA
1 ATTTGGAACAATGTCCTCGAAAGGCCA
112210 A
1 A
112211 CATCAACCCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
ATTTGGAACAATGTCCTCGAAAGGCCA
Found at i:115812 original size:129 final size:130
Alignment explanation
Indices: 115567--115812 Score: 386
Period size: 129 Copynumber: 1.9 Consensus size: 130
115557 AAAACAATCC
* **
115567 TCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGT
1 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGT
* * * *
115632 TAGCACATGATCATGACACGTGTCATTGTTGACACATGTCACCACCTAATTATTTATATATGCTA
66 TAACACATGATCATGACACATGTCATTGGTGACACAAGTCACCACCTAATTATTTATATATGCTA
115697 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA-GATCTGACATGTGT
1 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGT
* * * *
115761 TAACACATGATCATGATATATGTTATTGGTGACACAAGTCATCACCTAATTA
66 TAACACATGATCATGACACATGTCATTGGTGACACAAGTCACCACCTAATTA
115813 GAAGAAAATT
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
129 58 0.55
130 47 0.45
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGT
TAACACATGATCATGACACATGTCATTGGTGACACAAGTCACCACCTAATTATTTATATATGCTA
Found at i:115843 original size:129 final size:129
Alignment explanation
Indices: 115580--115843 Score: 273
Period size: 129 Copynumber: 2.0 Consensus size: 129
115570 ATTTGGTCCT
* ** *
115580 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *** * * **** *
115645 TGACACGTGTCATTGTTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACAAGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
115710 AAATTAAATAAAATTTAATAAATTAATCATTTAACCA-GATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
115774 TGATATATGTTATTGGTGACACAAGTCATCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACAAGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
115838 -A
128 CA
115839 AAATT
1 AAATT
115844 TGGGTCTTGG
Statistics
Matches: 109, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
129 62 0.57
130 34 0.31
131 8 0.07
132 5 0.05
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACAAGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:116174 original size:28 final size:27
Alignment explanation
Indices: 116143--116205 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
116133 AGTTGATACA
*
116143 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
116171 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
116199 ATATTTT
1 ATATTTT
116206 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:130279 original size:16 final size:16
Alignment explanation
Indices: 130260--130290 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
130250 AATATTTCTA
*
130260 TTTTTTACTTTATAAC
1 TTTTTTACTTAATAAC
130276 TTTTTTACTTAATAA
1 TTTTTTACTTAATAA
130291 TTATATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTTACTTAATAAC
Found at i:131947 original size:3 final size:3
Alignment explanation
Indices: 131932--131988 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
131922 ATTTAATTTA
* * * *
131932 ATT ATT GTT ATT ATT A-T ATT ATT ATT ATC GTT A-T ATT ATT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
131978 ATT AAT ATT AT
1 ATT ATT ATT AT
131989 ATTTTTACAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:131954 original size:17 final size:17
Alignment explanation
Indices: 131932--131988 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
131922 ATTTAATTTA
*
131932 ATTATTGTTATTATTAT
1 ATTATTATTATTATTAT
**
131949 ATTATTATTATCGTTAT
1 ATTATTATTATTATTAT
*
131966 ATTATTATTTTTATTAAT
1 ATTATTATTATTATT-AT
131984 ATTAT
1 ATTAT
131989 ATTTTTACAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 26 0.79
18 7 0.21
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (17 bp):
ATTATTATTATTATTAT
Found at i:138308 original size:2 final size:2
Alignment explanation
Indices: 138301--138332 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
138291 ATATTAAATC
138301 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
138333 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142345 original size:20 final size:20
Alignment explanation
Indices: 142322--142361 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
142312 TTTATCTGTT
142322 GTGAATTTTGGTTGTCCTTC
1 GTGAATTTTGGTTGTCCTTC
142342 GTGAATTTTGGTTGTCCTTC
1 GTGAATTTTGGTTGTCCTTC
142362 AGAAAAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.50
Consensus pattern (20 bp):
GTGAATTTTGGTTGTCCTTC
Found at i:143205 original size:43 final size:42
Alignment explanation
Indices: 143155--143275 Score: 161
Period size: 44 Copynumber: 2.8 Consensus size: 42
143145 CAGAAATAGG
* *
143155 ACGGGATTTTGCCCTCCATAGAGGATCCCATACAGAATCAGA
1 ACGGGATTTTTCCCTCCGTAGAGGATCCCATACAGAATCAGA
* * * *
143197 ACAGGGATTTTTTTCCTCCGTAGAGGATCTCATGCAGAATCAGG
1 AC-GGGA-TTTTTCCCTCCGTAGAGGATCCCATACAGAATCAGA
143241 ACGAGGATTTTTCCCTCCGTAGAGGATCCCATACA
1 ACG-GGATTTTTCCCTCCGTAGAGGATCCCATACA
143276 TATGGCAGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.03
43 30 0.45
44 35 0.52
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (42 bp):
ACGGGATTTTTCCCTCCGTAGAGGATCCCATACAGAATCAGA
Found at i:152986 original size:31 final size:31
Alignment explanation
Indices: 152974--153031 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
152964 TTATTTTCTA
152974 TCTTTATGATTAATTATATTTTATCCTTCAT
1 TCTTTATGATTAATTATATTTTATCCTTCAT
*
153005 TCTTTATGATTAATTATACTTTA-CCTT
1 TCTTTATGATTAATTATATTTTATCCTT
153032 TTTTTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.26, C:0.14, G:0.03, T:0.57
Consensus pattern (31 bp):
TCTTTATGATTAATTATATTTTATCCTTCAT
Found at i:158102 original size:2 final size:2
Alignment explanation
Indices: 158095--158127 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
158085 AACATATTTG
158095 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
158128 TAGAAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.