Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004812.1 Hibiscus syriacus cultivar Beakdansim tig00010842_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: 68273
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:70 original size:33 final size:32
Alignment explanation
Indices: 18--113 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 32
8 TGCGAAATGA
* *
18 AAATCACAACGCGAAATGAAAATCGCAACGAG
1 AAATCGCAATGCGAAATGAAAATCGCAACGAG
* **
50 AGAATCGCAATGCGAAATGAAAATTGCAACGCT
1 A-AATCGCAATGCGAAATGAAAATCGCAACGAG
*
83 AATTTCGCAATGCGAAATGAAAATCGCAACG
1 AA-ATCGCAATGCGAAATGAAAATCGCAACG
114 CGAATTTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.16
Consensus pattern (32 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAG
Found at i:111 original size:19 final size:19
Alignment explanation
Indices: 1--117 Score: 92
Period size: 19 Copynumber: 6.7 Consensus size: 19
1 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
20 ATCACAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
39 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
53 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* * *
72 ATTGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
86 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
105 ATCGCAACGCGAA
1 ATCGCAATGCGAA
118 TTTAATTTCG
Statistics
Matches: 74, Mismatches: 14, Indels: 20
0.69 0.13 0.19
Matches are distributed among these distances:
14 17 0.23
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 45 0.61
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:114 original size:33 final size:33
Alignment explanation
Indices: 28--120 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
18 AAATCACAAC
* *
28 GCGAAATGAAAATCGCAACGAGAGA-ATCGCAAT
1 GCGAAATGAAAATCGCAACGCGA-ATTTCGCAAT
* *
61 GCGAAATGAAAATTGCAACGCTAATTTCGCAAT
1 GCGAAATGAAAATCGCAACGCGAATTTCGCAAT
94 GCGAAATGAAAATCGCAACGCGAATTT
1 GCGAAATGAAAATCGCAACGCGAATTT
121 AATTTCGCGT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 1 0.02
33 52 0.98
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGCGAATTTCGCAAT
Found at i:135 original size:19 final size:19
Alignment explanation
Indices: 113--175 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
103 AAATCGCAAC
*
113 GCGAATTTAATTTCGCGTT
1 GCGATTTTAATTTCGCGTT
*
132 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AATTTCGCGTT
* *
152 GCGATTTTCATTTCGCATT
1 GCGATTTTAATTTCGCGTT
171 GCGAT
1 GCGAT
176 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 20 0.53
20 18 0.47
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (19 bp):
GCGATTTTAATTTCGCGTT
Found at i:148 original size:20 final size:19
Alignment explanation
Indices: 122--175 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
112 CGCGAATTTA
122 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
141 ATTTTCGCGTTGCGATTTTC
1 A-TTTCGCGTTGCGATTTTC
*
161 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
176 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:308 original size:14 final size:14
Alignment explanation
Indices: 282--318 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
272 CATCAATTAA
282 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
296 ACATATCACCTTTT
1 ACAAATCAACTTTT
310 ACAAATCAA
1 ACAAATCAA
319 TTAAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1728 original size:21 final size:21
Alignment explanation
Indices: 1662--1728 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1652 CCATGTCGGG
*
1662 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1682 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1704 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1725 CTCT
1 CTCT
1729 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1747 original size:42 final size:41
Alignment explanation
Indices: 1662--1784 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1652 CCATGTCGGG
* * * *
1662 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1704 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1746 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1785 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:3869 original size:33 final size:33
Alignment explanation
Indices: 3812--3899 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
3802 ACGAGATAAT
*
3812 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
3846 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
3879 GACAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
3900 AAATCACAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 37 0.73
34 14 0.27
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:3904 original size:19 final size:19
Alignment explanation
Indices: 3787--3946 Score: 124
Period size: 19 Copynumber: 8.8 Consensus size: 19
3777 TCTTTTGGTT
*
3787 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3806 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3826 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
3844 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
3860 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
3878 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3893 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
* *
3912 GAAATGAAAATCACAATGC
1 GAAATGAAAATCGCAACGC
3931 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3947 TGTGATTTTT
Statistics
Matches: 114, Mismatches: 15, Indels: 24
0.75 0.10 0.16
Matches are distributed among these distances:
14 19 0.17
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.04
19 56 0.49
20 27 0.24
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3974 original size:19 final size:19
Alignment explanation
Indices: 3952--3988 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3942 CGCAATGTGA
*
3952 TTTTTGTTTCGCGTTGCGT
1 TTTTTATTTCGCGTTGCGT
3971 TTTTTATTTCGCGTTGCG
1 TTTTTATTTCGCGTTGCG
3989 ATTCTCTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.24, T:0.57
Consensus pattern (19 bp):
TTTTTATTTCGCGTTGCGT
Found at i:4566 original size:20 final size:20
Alignment explanation
Indices: 4541--4593 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
4531 GCGCTATGTA
4541 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
4561 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
4581 TATCTCGTTGCGA
1 AATCGCGTTGCGA
4594 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:4627 original size:20 final size:20
Alignment explanation
Indices: 4602--4655 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
4592 GATTTTGTAT
4602 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
4622 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
4642 TATCGCATTGCGAT
1 TATCGCATTGCGAT
4656 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:4640 original size:61 final size:61
Alignment explanation
Indices: 4542--4658 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
4532 CGCTATGTAA
* * * * *
4542 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
4603 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
4659 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:4674 original size:61 final size:61
Alignment explanation
Indices: 4542--4676 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
4532 CGCTATGTAA
* * * * * ** *
4542 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
4603 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
4665 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
4677 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:5818 original size:7 final size:7
Alignment explanation
Indices: 5806--5830 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5796 TTAAATAATA
5806 TTTTGAT
1 TTTTGAT
5813 TTTTGAT
1 TTTTGAT
5820 TTTTGAT
1 TTTTGAT
5827 TTTT
1 TTTT
5831 TATAAACACA
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:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTGAT
Found at i:6967 original size:13 final size:14
Alignment explanation
Indices: 6951--6982 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
6941 ATAAACATTT
6951 AATATAAAAT-AAA
1 AATATAAAATAAAA
6964 AATA-AAAATAAAA
1 AATATAAAATAAAA
6977 AATATA
1 AATATA
6983 TATAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.29
13 11 0.65
14 1 0.06
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATATAAAATAAAA
Found at i:8305 original size:2 final size:2
Alignment explanation
Indices: 8298--8323 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8288 TTTAAATGAA
8298 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
8324 CGAAAAGCAT
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:9096 original size:17 final size:17
Alignment explanation
Indices: 9054--9108 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
9044 TAGATATTAT
9054 ATAAATCAAAG--GAAA
1 ATAAATCAAAGAAGAAA
* **
9069 AAAAAGAAAAGAAGAAA
1 ATAAATCAAAGAAGAAA
9086 ATAAATCAAAGGAA-AAA
1 ATAAATCAAA-GAAGAAA
9103 ATAAAT
1 ATAAAT
9109 GATATTAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 8 0.26
17 20 0.65
18 3 0.10
ACGTcount: A:0.73, C:0.04, G:0.13, T:0.11
Consensus pattern (17 bp):
ATAAATCAAAGAAGAAA
Found at i:9133 original size:32 final size:32
Alignment explanation
Indices: 9033--9140 Score: 121
Period size: 32 Copynumber: 3.3 Consensus size: 32
9023 AAAAATCGAA
* *
9033 AAAATAATAAATAGATATTATATAAATCAAAGGAA
1 AAAA-AATAAAT-GATATTAAATAAATCAAA-GAG
* * **
9068 AAAAAAGAAAAGA-AGAAAATAAATCAAAG-G
1 AAAAAATAAATGATATTAAATAAATCAAAGAG
9098 AAAAAATAAATGATATTAAATAAATCAAAGAG
1 AAAAAATAAATGATATTAAATAAATCAAAGAG
9130 AAAAAATAAAT
1 AAAAAATAAAT
9141 AATAATAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
30 11 0.18
31 15 0.25
32 24 0.39
33 2 0.03
34 5 0.08
35 4 0.07
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.19
Consensus pattern (32 bp):
AAAAAATAAATGATATTAAATAAATCAAAGAG
Found at i:9200 original size:23 final size:24
Alignment explanation
Indices: 9159--9210 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
9149 TAATAATAAT
9159 AAAATAAATCAAAGGAAAAA-GATA
1 AAAATAAATCAAAGGAAAAAGGA-A
* *
9183 AAAATAAATTAAA-TAAAAAGGAA
1 AAAATAAATCAAAGGAAAAAGGAA
9206 AAAAT
1 AAAAT
9211 TAAAAAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (24 bp):
AAAATAAATCAAAGGAAAAAGGAA
Found at i:9205 original size:30 final size:28
Alignment explanation
Indices: 9150--9280 Score: 83
Period size: 29 Copynumber: 4.6 Consensus size: 28
9140 TAATAATAAT
* *
9150 AATAATAATAAAATAAATCAAAGGAAAA
1 AATAAAAATAAAATAAATAAAAGGAAAA
*
9178 AGATAAAAATAAATTAAATAAAAAGGAAAA
1 A-ATAAAAATAAAATAAAT-AAAAGGAAAA
*** *
9208 AATTAAAAA-ATGTTAAAT-AAAGTAATAA
1 AA-TAAAAATAAAATAAATAAAAGGAA-AA
* *
9236 AATAAAAATAATAAGAAGTAAAA--AAATA
1 AATAAAAATAA-AATAAATAAAAGGAAA-A
9264 AA-AATAAATAAAATAAA
1 AATAA-AAATAAAATAAA
9281 AACCACTAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 19
0.72 0.12 0.17
Matches are distributed among these distances:
27 19 0.23
28 17 0.21
29 26 0.32
30 19 0.23
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.20
Consensus pattern (28 bp):
AATAAAAATAAAATAAATAAAAGGAAAA
Found at i:9227 original size:76 final size:77
Alignment explanation
Indices: 9083--9282 Score: 189
Period size: 81 Copynumber: 2.5 Consensus size: 77
9073 AGAAAAGAAG
* *
9083 AAAATAAATCAAAGGAAAAAATAAATGATATTAAA-TAAAT-CAAAGAGAAAAAATAAATAATAA
1 AAAATAAATCAAAGGAAAAAATAAA--A-A-TAAATTAAATAAAAAGAGAAAAAATAAAAAATAA
9146 TAAT-AA-TAAT-AAT
62 TAATAAAGTAATAAAT
**
9159 AAAATAAATCAAAGGAAAAAGATAAAAATAAATTAAATAAAAAG-GAAAAAATTAAAAAATGTTA
1 AAAATAAATCAAAGGAAAAA-ATAAAAATAAATTAAATAAAAAGAGAAAAAA-TAAAAAATAAT-
9223 AATAAAGTAATAAAAT
63 AATAAAGTAAT-AAAT
* * *
9239 AAAA-ATAATAAGAAGTAAAAAAATAAAAATAAATAAAATAAAAA
1 AAAATA-AATCA-AAG-GAAAAAATAAAAATAAATTAAATAAAAA
9283 CCACTAAAAC
Statistics
Matches: 105, Mismatches: 7, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
73 4 0.04
74 13 0.12
75 13 0.12
76 23 0.22
77 7 0.07
78 4 0.04
79 1 0.01
80 11 0.10
81 24 0.23
82 5 0.05
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.20
Consensus pattern (77 bp):
AAAATAAATCAAAGGAAAAAATAAAAATAAATTAAATAAAAAGAGAAAAAATAAAAAATAATAAT
AAAGTAATAAAT
Found at i:9261 original size:24 final size:24
Alignment explanation
Indices: 9221--9282 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
9211 TAAAAAATGT
*
9221 TAAAT-AAAGTAATAAAATAAAAA
1 TAAATAAAAGTAAAAAAATAAAAA
9244 T-AATAAGAAGTAAAAAAATAAAAA
1 TAAATAA-AAGTAAAAAAATAAAAA
9268 TAAATAAAA-TAAAAA
1 TAAATAAAAGTAAAAA
9283 CCACTAAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
22 3 0.09
23 8 0.23
24 19 0.54
25 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (24 bp):
TAAATAAAAGTAAAAAAATAAAAA
Found at i:9263 original size:15 final size:14
Alignment explanation
Indices: 9234--9282 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 14
9224 ATAAAGTAAT
9234 AAAATAAAAATAATA
1 AAAATAAAAA-AATA
*
9249 AGAAGTAAAAAAATA
1 A-AAATAAAAAAATA
9264 AAAATAAATAAAATA
1 AAAATAAA-AAAATA
9279 AAAA
1 AAAA
9283 CCACTAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 6 0.20
15 16 0.53
16 8 0.27
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:9297 original size:39 final size:40
Alignment explanation
Indices: 9231--9307 Score: 95
Period size: 39 Copynumber: 1.9 Consensus size: 40
9221 TAAATAAAGT
* * *
9231 AATAAAATAAAAATAATAAGAAGTAAAAA-AATAAAAATA
1 AATAAAATAAAAACAATAAGAACTAAAAAGAAAAAAAATA
*
9270 AATAAAATAAAAACCACTAA-AACTAAAAAGAAAAAAAA
1 AATAAAATAAAAA-CAATAAGAACTAAAAAGAAAAAAAA
9308 ATGAATAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 21 0.66
40 11 0.34
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (40 bp):
AATAAAATAAAAACAATAAGAACTAAAAAGAAAAAAAATA
Found at i:9298 original size:81 final size:81
Alignment explanation
Indices: 9149--9298 Score: 187
Period size: 81 Copynumber: 1.8 Consensus size: 81
9139 ATAATAATAA
* * * ** *
9149 TAATAATAATAAAATAAATCAAAGGAAAAAGATAAAAATAAATTAAATAAAAAGGAAAAAATTAA
1 TAATAATAATAAAATAAATAAAAGGAAAAAAATAAAAATAAATAAAATAAAAACCAAAAAACTAA
9214 AAAATGTTAAATAAAG
66 AAAATGTTAAATAAAG
* *
9230 TAATAA-AATAAAA-ATAATAAGAAGTAAAAAAATAAAAATAAATAAAATAAAAACCACTAAAAC
1 TAATAATAATAAAATA-AATAA-AAGGAAAAAAATAAAAATAAATAAAATAAAAACCA-AAAAAC
9293 TAAAAA
63 TAAAAA
9299 GAAAAAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
79 1 0.02
80 11 0.19
81 36 0.62
82 10 0.17
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (81 bp):
TAATAATAATAAAATAAATAAAAGGAAAAAAATAAAAATAAATAAAATAAAAACCAAAAAACTAA
AAAATGTTAAATAAAG
Found at i:12017 original size:28 final size:26
Alignment explanation
Indices: 11981--12049 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 26
11971 TGTGTATTTA
* *
11981 AAAACGTTTTCAAAACCTATATATTTT
1 AAAA-GTTTTCAAAAACTATATATTAT
* *
12008 CAAAATGTTTTAAAAAACTATGTATTAT
1 -AAAA-GTTTTCAAAAACTATATATTAT
*
12036 ATAAGTTTTCAAAA
1 AAAAGTTTTCAAAA
12050 TGTTTTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 9 0.26
27 3 0.09
28 22 0.65
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (26 bp):
AAAAGTTTTCAAAAACTATATATTAT
Found at i:12132 original size:38 final size:36
Alignment explanation
Indices: 12004--12264 Score: 332
Period size: 38 Copynumber: 7.1 Consensus size: 36
11994 AACCTATATA
*
12004 TTTTCAAAATGTTTTAAAAAACTATGTATTATATAAG
1 TTTTCAAAATGTTTT-AAAAACTATATATTATATAAG
12041 TTTTCAAAATGTTTTAAAAAC--TATATTATATAAG
1 TTTTCAAAATGTTTTAAAAACTATATATTATATAAG
*
12075 TTTTCAAAATATTTTAAAAACTATATATTATATATA-
1 TTTTCAAAATGTTTTAAAAACTATATATTATATA-AG
*
12111 TTTTCAAAATGTTTTAAAAAAATTATATATTATATAAG
1 TTTTCAAAATGTTTT--AAAAACTATATATTATATAAG
12149 TTTTCAAAATGTTTTAAAAACTATATATTATATACAAG
1 TTTTCAAAATGTTTTAAAAACTATATATTATAT--AAG
* *
12187 TTTTCAATATGATTTAAAAACTATATATTATATATA-
1 TTTTCAAAATGTTTTAAAAACTATATATTATATA-AG
** * *
12223 TTTTCAAAATGATATAAAAAAATTATATATTATATAAA
1 TTTTCAAAATG-T-TTTAAAAACTATATATTATATAAG
12261 TTTT
1 TTTT
12265 TTCAAAAAAA
Statistics
Matches: 200, Mismatches: 12, Indels: 23
0.85 0.05 0.10
Matches are distributed among these distances:
34 32 0.16
36 59 0.29
37 19 0.09
38 90 0.45
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTCAAAATGTTTTAAAAACTATATATTATATAAG
Found at i:12156 original size:74 final size:72
Alignment explanation
Indices: 12004--12271 Score: 319
Period size: 74 Copynumber: 3.6 Consensus size: 72
11994 AACCTATATA
* * *
12004 TTTTCAAAATGTTTTAAAAAACTATGTATTATAT-AAGTTTTCAAAATGTTTTAAAAA-CTATAT
1 TTTTCAAAATATTTT-AAAAACTATATATTATATAAAGTTTTCAAAATGTTTTAAAAATATATAT
12067 TATATAAG
65 TATATAAG
*
12075 TTTTCAAAATATTTTAAAAACTATATATTATATATA-TTTTCAAAATGTTTTAAAAAAATTATAT
1 TTTTCAAAATATTTTAAAAACTATATATTATATAAAGTTTTCAAAATGTTTT--AAAAA-TATAT
12139 ATTATATAAG
63 ATTATATAAG
* * *
12149 TTTTCAAAATGTTTTAAAAACTATATATTATATACAAGTTTTCAATATGATTTAAAAACTATATA
1 TTTTCAAAATATTTTAAAAACTATATATTATATA-AAGTTTTCAAAATGTTTTAAAAA-TATATA
12214 TTATATATA-
64 TTATATA-AG
** * *
12223 TTTTCAAAATGATATAAAAAAATTATATATTATATAAATTTTTTCAAAA
1 TTTTCAAAAT-AT-TTTAAAAACTATATATTATATAAA-GTTTTCAAAA
12272 AAATTTTTTA
Statistics
Matches: 171, Mismatches: 15, Indels: 17
0.84 0.07 0.08
Matches are distributed among these distances:
70 32 0.19
71 15 0.09
72 5 0.03
74 74 0.43
75 5 0.03
76 40 0.23
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (72 bp):
TTTTCAAAATATTTTAAAAACTATATATTATATAAAGTTTTCAAAATGTTTTAAAAATATATATT
ATATAAG
Found at i:12284 original size:13 final size:14
Alignment explanation
Indices: 12258--12286 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12248 TATATTATAT
12258 AAATTTTTTCAAAA
1 AAATTTTTTCAAAA
12272 AAATTTTTT-AAAA
1 AAATTTTTTCAAAA
12285 AA
1 AA
12287 CACAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTTTTTCAAAA
Found at i:21398 original size:23 final size:23
Alignment explanation
Indices: 21372--21435 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
21362 ACTTTGGTGA
21372 AATTAATTTTAAAATATTAAATT
1 AATTAATTTTAAAATATTAAATT
* * *
21395 AATTTTATTTT-AAATTTTATATT
1 AA-TTAATTTTAAAATATTAAATT
21418 AATTATATTTTAAAATAT
1 AATTA-ATTTTAAAATAT
21436 ATGAAATGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
22 2 0.06
23 19 0.58
24 12 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTAATTTTAAAATATTAAATT
Found at i:21762 original size:9 final size:9
Alignment explanation
Indices: 21748--21785 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
21738 GATTGGAGAA
21748 AAATAAAAT
1 AAATAAAAT
21757 AAATAAAAT
1 AAATAAAAT
*
21766 AATTAAAAT
1 AAATAAAAT
*
21775 TAATAAAAT
1 AAATAAAAT
21784 AA
1 AA
21786 CTTCCAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AAATAAAAT
Found at i:22877 original size:16 final size:16
Alignment explanation
Indices: 22853--22888 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
22843 ATGTTGTCCC
* *
22853 TAAATTCTTAAATCTT
1 TAAAATCTTAAATATT
22869 TAAAATCTTAAATATT
1 TAAAATCTTAAATATT
22885 TAAA
1 TAAA
22889 TTTTAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATCTTAAATATT
Found at i:23062 original size:2 final size:2
Alignment explanation
Indices: 23055--23085 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23045 CGGATTTATT
23055 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 T
23086 TCATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29195 original size:44 final size:45
Alignment explanation
Indices: 29132--29227 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 45
29122 GTGTTAAAAT
* * *
29132 TTCTGGCGGTACAGATGGTGGCAGTGGGATTCCCGG-CTTGGAAG
1 TTCTGGCAGTACAGATGGTGACAGAGGGATTCCCGGTCTTGGAAG
* * *
29176 TTCTGGCAGTACAGATGGTGACGGAGGGATTCCTGGTGTTGGAAG
1 TTCTGGCAGTACAGATGGTGACAGAGGGATTCCCGGTCTTGGAAG
29221 TTCTGGC
1 TTCTGGC
29228 GGCAGATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
44 31 0.69
45 14 0.31
ACGTcount: A:0.17, C:0.17, G:0.40, T:0.27
Consensus pattern (45 bp):
TTCTGGCAGTACAGATGGTGACAGAGGGATTCCCGGTCTTGGAAG
Found at i:30432 original size:27 final size:27
Alignment explanation
Indices: 30402--30459 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
30392 ACATAAGCAA
30402 TAATTATTAAATATGTCATTATATATT
1 TAATTATTAAATATGTCATTATATATT
30429 TAATTATTAAATATGTCATTATATATT
1 TAATTATTAAATATGTCATTATATATT
30456 TAAT
1 TAAT
30460 AATTTAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (27 bp):
TAATTATTAAATATGTCATTATATATT
Found at i:30449 original size:15 final size:15
Alignment explanation
Indices: 30404--30450 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
30394 ATAAGCAATA
30404 ATTATTAAATATGTC
1 ATTATTAAATATGTC
* *
30419 ATTA-T--ATATTTA
1 ATTATTAAATATGTC
30431 ATTATTAAATATGTC
1 ATTATTAAATATGTC
30446 ATTAT
1 ATTAT
30451 ATATTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
12 9 0.36
13 1 0.04
14 1 0.04
15 14 0.56
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTATTAAATATGTC
Found at i:46581 original size:2 final size:2
Alignment explanation
Indices: 46570--47152 Score: 240
Period size: 2 Copynumber: 293.0 Consensus size: 2
46560 TTCAAACAAT
*
46570 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
46610 TA AA CTA TA TA GTT TA TA TA TA TA -A TA TA TA TA AA CTA CA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
46652 GTT TA TA TT TA TA T- TA T- TA TA TA CTA TC TA CA AA CTA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
* * * * *
46693 TA TA T- TA TG TA TA AA T- TA TA TA TA CCA TG TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
* * * *
46735 GTT TA TA TA TA AA T- TA TA TA TGA -A T- TA TA TT TA AA TA TA T-
1 -TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
** * * *
46775 TCA CC T- TA TA TT TA TA TA T- TA TG TA TA -A T- TA TA CA T- TA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
46813 TA TA GTT TA TA TA GTT TA AA TA TA AA GTA TA TA -A GTA TA TA TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
* * *
46856 AA CTT TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
46899 TA TA TA TA TA TA TA TA TA TA TA CTC TA -A T- TA TA AA GA CTA -A
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* * * **
46940 AA TA TA TA -A GTA TA TA -A TA TA AA GTA TA TA TA CA TA TA -A CG
1 TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
46981 TA TA -A GTA TG TA TA -A T- TA TA TA TA AA CTA TA AA GTA -A AA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * * *
47020 GTA TA TA TA TA TA AA GT- TT TA CTA TA AA GCA TA TA TA CA TA TA
1 -TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA
*
47063 TA -A TA -A TA TA AA GTA TA -A GTA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
47103 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47145 TA TA TA TA
1 TA TA TA TA
47153 AAGTGTAATT
Statistics
Matches: 430, Mismatches: 90, Indels: 122
0.67 0.14 0.19
Matches are distributed among these distances:
1 32 0.07
2 370 0.86
3 28 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:47373 original size:131 final size:137
Alignment explanation
Indices: 47128--47482 Score: 316
Period size: 131 Copynumber: 2.7 Consensus size: 137
47118 ATATATATAT
*
47128 ATATATATATATATATATATATATAAAGTGTAATTATAAAGACAAAAGTATATAAGTATATAATA
1 ATATATACATATATATATATATATAAAGTGTAATTATAAAGACAAAAG-ATATAAGTATATAATA
* * *
47193 TAAAGTATAAGTATGTATATATATATAAACTATAAAGTATGTATATATATATATATAAAGTTTTA
65 TAAAGTATAAGTATGTATATATATAAAAACTATAAAGTA-GCAAATATATATATATAAAGTTTTA
47258 CTATAAAGC
129 CTATAAAGC
* *
47267 ATATATACATATATA-ATA-ATA-AAAGGTGTAA-TATAAAGACTAAAG-TAT-A-TATA-CATA
1 ATATATACATATATATATATATATAAA-GTGTAATTATAAAGACAAAAGATATAAGTATATAATA
* ** * * **
47324 TAAAGTATAAGTACGTGTATATATATAAAAAGT-TTTAGTA-CAAAGTATATATACATATA-TAA
65 TAAAGTATAAGTA--TGTATATATATAAAAACTATAAAGTAGCAAA-TATATATATATAAAGTTT
*
47386 TAATAT-AAG-
127 TACTATAAAGC
* * * * * *
47395 -TATA-A-GTATAT-TATATCTATAAAGTATAATTATAAAGACTAAAGTATATAAGCATGTAATA
1 ATATATACATATATATATATATATAAAGTGTAATTATAAAGACAAAAG-ATATAAGTATATAATA
*
47456 TAAAGTAT-A-TAAGTATATAATATAAAA
65 TAAAGTATAAGTATGTATAT-ATATAAAA
47483 TATATAAGTA
Statistics
Matches: 181, Mismatches: 21, Indels: 38
0.75 0.09 0.16
Matches are distributed among these distances:
125 8 0.04
126 8 0.04
127 21 0.12
128 6 0.03
129 14 0.08
130 11 0.06
131 31 0.17
132 20 0.11
133 17 0.09
134 3 0.02
136 16 0.09
137 9 0.05
138 3 0.02
139 14 0.08
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (137 bp):
ATATATACATATATATATATATATAAAGTGTAATTATAAAGACAAAAGATATAAGTATATAATAT
AAAGTATAAGTATGTATATATATAAAAACTATAAAGTAGCAAATATATATATATAAAGTTTTACT
ATAAAGC
Found at i:47401 original size:217 final size:210
Alignment explanation
Indices: 46886--47410 Score: 493
Period size: 217 Copynumber: 2.5 Consensus size: 210
46876 ATATATATAT
* * ** * * * *
46886 ATATATATATATATATATATATATATATATATATACTCTAATTATAAAGACTAAA-ATATATAAG
1 ATATATATACATATAAATATATATATATATATATA-TAAAAATATATATAC-AAATATATATAAA
* *
46950 TATATAAT-ATA-AAGTAT-A-TATA-CATATAACGTATAAGTATGTATAATTATATATAAACTA
64 TATATAATAATATAAGTATAAGTATATAATATAAAGTATAAGTATGTATAATTATATATAAACTA
47010 TAAAGTAAAAGTATATATATATAAAGTTTTACTATAAAGCATATATACATATATAATAATATAAA
129 TAAAGTAAAAGTATATATATATAAAGTTTTACTATAAAGCATATATACATATATAATAATATAAA
** *
47075 GTATAAGTATATTATAT
194 GTATAAGTATAAGATAA
* * * * * *
47092 ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAAAGT
1 ATATATATACATATAAATATATATATATATATATATAAAAATATATATACAAATATATATAAA--
* *
47157 GTAATTATAA-AGACAAAAGTATATAAGTATATAATATAAAGTATAAGTATGTAT-A-TATATAT
64 -T-A-TATAATA-ATATAAG--TATAAGTATATAATATAAAGTATAAGTATGTATAATTATATAT
*
47219 AAACTATAAAGTATGTATA-TATATATATATAAAGTTTTACTATAAAGCATATATACATATATAA
123 AAACTATAAAGTA---AAAGTATATATATATAAAGTTTTACTATAAAGCATATATACATATATAA
*
47283 TAATA-AAAGGTGTAA-TATAAAGACTAA
185 TAATATAAA-GTATAAGTAT-AAGA-TAA
* *
47310 AGTATATATACATATAAAGTATA-AGTACGTGTATATATATAAAAAGT-TTTAGTACAAAGTATA
1 A-TATATATACATATAAA-TATATA-TA--TATATATATATAAAAA-TATATA-TACAAA-TATA
* *
47373 TATACATATATAATAATATAAGTATAAGTATATTATAT
58 TATAAATATATAATAATATAAGTATAAGTATATAATAT
47411 CTATAAAGTA
Statistics
Matches: 262, Mismatches: 28, Indels: 47
0.78 0.08 0.14
Matches are distributed among these distances:
204 2 0.01
205 17 0.06
206 35 0.13
208 1 0.00
209 1 0.00
210 5 0.02
211 2 0.01
212 3 0.01
214 3 0.01
215 21 0.08
216 11 0.04
217 92 0.35
218 5 0.02
219 25 0.10
220 8 0.03
221 1 0.00
222 16 0.06
223 5 0.02
224 9 0.03
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (210 bp):
ATATATATACATATAAATATATATATATATATATATAAAAATATATATACAAATATATATAAATA
TATAATAATATAAGTATAAGTATATAATATAAAGTATAAGTATGTATAATTATATATAAACTATA
AAGTAAAAGTATATATATATAAAGTTTTACTATAAAGCATATATACATATATAATAATATAAAGT
ATAAGTATAAGATAA
Found at i:47431 original size:103 final size:101
Alignment explanation
Indices: 47207--47404 Score: 263
Period size: 103 Copynumber: 1.9 Consensus size: 101
47197 GTATAAGTAT
* * * *
47207 GTATATATATATAAACTATAAAGTATGTATATATATATATATAAAGTTTTACTATAAAGCATATA
1 GTATATATATATAAAGTAT-AAGTACGTGTATATATATA-A-AAAGTTTTACTACAAAGCATATA
*
47272 TACATATATAATAATAAAAGGTGTAATATAAAGACTAAA
63 TACATATATAATAATAAAAGGTATAATATAAAGACTAAA
* *
47311 GTATATATACATATAAAGTATAAGTACGTGTATATATATAAAAAGTTTTAGTACAAAGTATATAT
1 GTATATAT--ATATAAAGTATAAGTACGTGTATATATATAAAAAGTTTTACTACAAAGCATATAT
*
47376 ACATATATAATAATATAA-GTATAAGTATA
64 ACATATATAATAATAAAAGGTATAA-TATA
47405 TTATATCTAT
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
102 5 0.06
103 42 0.51
104 9 0.11
105 17 0.20
106 10 0.12
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (101 bp):
GTATATATATATAAAGTATAAGTACGTGTATATATATAAAAAGTTTTACTACAAAGCATATATAC
ATATATAATAATAAAAGGTATAATATAAAGACTAAA
Found at i:47471 original size:8 final size:8
Alignment explanation
Indices: 47436--47493 Score: 61
Period size: 8 Copynumber: 7.8 Consensus size: 8
47426 ATAAAGACTA
47436 AAGTATAT
1 AAGTATAT
* *
47444 AAGCATGT
1 AAGTATAT
47452 AA-TATA-
1 AAGTATAT
47458 AAGTATAT
1 AAGTATAT
47466 AAGTATAT
1 AAGTATAT
47474 AA-TATA-
1 AAGTATAT
*
47480 AAATATAT
1 AAGTATAT
47488 AAGTAT
1 AAGTAT
47494 TATATACGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
6 4 0.10
7 14 0.34
8 23 0.56
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.34
Consensus pattern (8 bp):
AAGTATAT
Found at i:47491 original size:22 final size:22
Alignment explanation
Indices: 47434--47493 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
47424 TTATAAAGAC
* *
47434 TAAAGTATATAAGCATGTAATA
1 TAAAGTATATAAGTATATAATA
47456 TAAAGTATATAAGTATATAATA
1 TAAAGTATATAAGTATATAATA
*
47478 TAAAATATATAAGTAT
1 TAAAGTATATAAGTAT
47494 TATATACGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (22 bp):
TAAAGTATATAAGTATATAATA
Found at i:49511 original size:28 final size:27
Alignment explanation
Indices: 49472--49533 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 27
49462 AAAAAAACCG
49472 ATTTTTTCCAAAATCCGAT-TTCGGAT
1 ATTTTTTCCAAAATCCGATGTTCGGAT
*
49498 ATTTTTTACACAAAATCGGATGTTCGGAT
1 ATTTTTT-C-CAAAATCCGATGTTCGGAT
*
49527 TTTTTTT
1 ATTTTTT
49534 TATACATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.23
27 1 0.03
28 10 0.32
29 13 0.42
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.47
Consensus pattern (27 bp):
ATTTTTTCCAAAATCCGATGTTCGGAT
Found at i:54534 original size:109 final size:109
Alignment explanation
Indices: 54399--54598 Score: 294
Period size: 109 Copynumber: 1.8 Consensus size: 109
54389 TCCACGATGC
* * * * *
54399 ATTTTTGAAAGCAATATAAACTTGGAATGTTTTCCATTATTTTCATATTACTTTTAATTATTCCC
1 ATTTTTGAAAACAATAAAAAATTGGAAGGTTTTCCATTATTTTAATATTACTTTTAATTATTCCC
* * *
54464 CGTATATTAACATAATAATTCTTTAAAAATATTTTTTCACAGAA
66 CATATATTAACAGAATAATTCCTTAAAAATATTTTTTCACAGAA
* *
54508 ATTTTT-AAAACAATAAAAAATATGGAAGGTTTTCTATTATTTTAATATTACTTTTAATTATTCT
1 ATTTTTGAAAACAATAAAAAAT-TGGAAGGTTTTCCATTATTTTAATATTACTTTTAATTATTCC
54572 CCATATATTAACAGAATAATTCCTTAA
65 CCATATATTAACAGAATAATTCCTTAA
54599 TTATTCCTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 12 0.15
109 68 0.85
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.45
Consensus pattern (109 bp):
ATTTTTGAAAACAATAAAAAATTGGAAGGTTTTCCATTATTTTAATATTACTTTTAATTATTCCC
CATATATTAACAGAATAATTCCTTAAAAATATTTTTTCACAGAA
Found at i:54963 original size:25 final size:25
Alignment explanation
Indices: 54935--54985 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
54925 CACCCAAATC
*
54935 ATGGTGCCATTATTGGGCACTAATA
1 ATGGTGCCATTATTGGGCACCAATA
* *
54960 ATGGTGTCATTATTGTGCACCAATA
1 ATGGTGCCATTATTGGGCACCAATA
54985 A
1 A
54986 AGCATGTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (25 bp):
ATGGTGCCATTATTGGGCACCAATA
Found at i:55299 original size:111 final size:108
Alignment explanation
Indices: 55183--55593 Score: 344
Period size: 111 Copynumber: 3.9 Consensus size: 108
55173 TATTGTTTCA
* * * * *
55183 TTTTTATTTTAAATATAAATTAATTATATTATTTATTTTGATTTTACAAATTAAATTGTATTTGC
1 TTTTTATTGTAAATATAAATT-ATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGA
*
55248 GTGATTTGGTAAGTTTAATTTAAATTTTTGTGTAATTTTTA---
65 GTGATTTAGTAAGTTTAATTTAAATTTTTGTGTAATTTTTATTT
* * * * *
55289 TTTTTATTTTAAATA-ATAATTATTAGATTGTTTATTTTGATTTTACATATTAAGTTGTATTTAA
1 TTTTTATTGTAAATATA-AATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGA
* * *
55353 AT-AGTTTAGTAAG-TTAGTTTAAA--TTT-T-T-ATTTTT-TAT
65 GTGA-TTTAGTAAGTTTAATTTAAATTTTTGTGTAATTTTTATTT
* * * * *
55390 TTTTTATTG-AGTAATATAAATTATTAGACTAATTATTTTTATTTTATAGATTAAATCGTATTTG
1 TTTTTATTGTA--AATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTG
* * * * * *** * ***
55454 AGTGGTTTGGTAAGTTTAGTGTAAAATTTATTGTTTAGGGTTGAGGG
64 AGTGATTTAGTAAGTTTAAT-TTAAATTT-TTGTGTAATTTTTATTT
* * *
55501 TTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGATATTACATATTAAACTGTATTCGA
1 TTTTTATTGTAAATATAAATT-ATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGA
*
55566 GTGATTTAGTAAGTTTAATTTATATTTT
65 GTGATTTAGTAAGTTTAATTTAAATTTT
55594 CACGGTTTTA
Statistics
Matches: 242, Mismatches: 43, Indels: 37
0.75 0.13 0.11
Matches are distributed among these distances:
99 6 0.02
100 2 0.01
101 9 0.04
102 54 0.22
103 6 0.02
104 14 0.06
105 47 0.19
106 20 0.08
107 2 0.01
108 1 0.00
109 2 0.01
110 18 0.07
111 60 0.25
112 1 0.00
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (108 bp):
TTTTTATTGTAAATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGAG
TGATTTAGTAAGTTTAATTTAAATTTTTGTGTAATTTTTATTT
Found at i:55484 original size:102 final size:102
Alignment explanation
Indices: 55306--55490 Score: 219
Period size: 102 Copynumber: 1.8 Consensus size: 102
55296 TTTAAATAAT
* ** * * *
55306 AATTATTAGATTGTTTATTTTGATTTTACATATTAAGTTGTATTTAAATAGTTTAGTAAGTTAGT
1 AATTATTAGACTAATTATTTTGATTTTACAGATTAAATCGTATTTAAATAGTTTAGTAAGTTAGT
* * *
55371 TTAAATTTTTATTTTTTATTTTTTATTGAGTAATATA
66 GTAAATATTTATTGTTTATTTTTTATTGAGTAATATA
* * * * * *
55408 AATTATTAGACTAATTATTTTTATTTTATAGATTAAATCGTATTTGAGTGGTTTGGTAAGTTTAG
1 AATTATTAGACTAATTATTTTGATTTTACAGATTAAATCGTATTTAAATAGTTTAGTAAG-TTAG
55473 TGTAAA-ATTTATTGTTTA
65 TGTAAATATTTATTGTTTA
55491 GGGTTGAGGG
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
102 58 0.87
103 9 0.13
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.54
Consensus pattern (102 bp):
AATTATTAGACTAATTATTTTGATTTTACAGATTAAATCGTATTTAAATAGTTTAGTAAGTTAGT
GTAAATATTTATTGTTTATTTTTTATTGAGTAATATA
Found at i:55633 original size:96 final size:98
Alignment explanation
Indices: 55499--55736 Score: 265
Period size: 96 Copynumber: 2.6 Consensus size: 98
55489 TAGGGTTGAG
*
55499 GGTTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGA-TATTACATATTAAACTGTATT
1 GGTTTTAATTGTAAATATAAATTAATTAGACTATTTATTTTGATTA-TACATATTAAACTGTATT
55563 CGAGT-GATTTAGTAAGTTTAATTTATATTTTCAC
65 CGAGTAG-TTTAGTAAGTTTAATTTATATTTTCAC
**
55597 GGTTTTAATT-TAAAT-TATAATT-ATTAGACTATTTATTTTGATTATACATATTAAGTTGTATT
1 GGTTTTAATTGTAAATATA-AATTAATTAGACTATTTATTTTGATTATACATATTAAACTGTATT
* * * *
55659 TGAGTAGTTTTGTAAGTTTAATTTAAATTAT-A-
65 CGAGTAGTTTAGTAAGTTTAATTTATATTTTCAC
55691 ---TTT--TT-T--ATATAAATTAATTAGACTATTTATTTTGATT-TAACATATT
1 GGTTTTAATTGTAAATATAAATTAATTAGACTATTTATTTTGATTAT-ACATATT
55737 TTTTGTTTAA
Statistics
Matches: 127, Mismatches: 7, Indels: 22
0.81 0.04 0.14
Matches are distributed among these distances:
87 7 0.06
88 30 0.24
89 3 0.02
91 3 0.02
95 1 0.01
96 62 0.49
97 12 0.09
98 9 0.07
ACGTcount: A:0.34, C:0.04, G:0.10, T:0.52
Consensus pattern (98 bp):
GGTTTTAATTGTAAATATAAATTAATTAGACTATTTATTTTGATTATACATATTAAACTGTATTC
GAGTAGTTTAGTAAGTTTAATTTATATTTTCAC
Found at i:56935 original size:19 final size:19
Alignment explanation
Indices: 56913--56950 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
56903 ATTTAGTTGA
* *
56913 ATTTTATAATTATTTAATT
1 ATTTAATAATTATATAATT
56932 ATTTAATAATTATATAATT
1 ATTTAATAATTATATAATT
56951 TTGTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTAATAATTATATAATT
Found at i:60074 original size:18 final size:19
Alignment explanation
Indices: 60047--60082 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
60037 AAAACAAATG
*
60047 AAAAAGAAAAGAAAATTGC
1 AAAAAGAAAAAAAAATTGC
60066 AAAAA-AAAAAAAAATTG
1 AAAAAGAAAAAAAAATTG
60083 AAAGCACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAAAGAAAAAAAAATTGC
Done.