Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005280.1 Hibiscus syriacus cultivar Beakdansim tig00011942_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: 58891
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:330 original size:21 final size:21
Alignment explanation
Indices: 292--331 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
282 CTATCTGCTA
*
292 CGAAGATCTGAAACCCATCGT
1 CGAAGATCTCAAACCCATCGT
* *
313 CGAAGATCTCCAATCCATC
1 CGAAGATCTCAAACCCATC
332 TCCATTTGCG
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:0.33, C:0.33, G:0.15, T:0.20
Consensus pattern (21 bp):
CGAAGATCTCAAACCCATCGT
Found at i:5142 original size:2 final size:2
Alignment explanation
Indices: 5137--5161 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5127 GAAATTAACA
5137 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5162 AATTAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6001 original size:34 final size:30
Alignment explanation
Indices: 5963--6031 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
5953 TTGATATAAC
5963 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
5997 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
6026 AATTTA
1 AATTTA
6032 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:6042 original size:29 final size:30
Alignment explanation
Indices: 5972--6031 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
5962 CAATTTAAGG
5972 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
6003 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
6032 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:6126 original size:8 final size:8
Alignment explanation
Indices: 6113--6232 Score: 58
Period size: 8 Copynumber: 17.0 Consensus size: 8
6103 GGTGTCAAAG
6113 TGCATCCA
1 TGCATCCA
*
6121 TGCATCCC
1 TGCATCCA
*
6129 TGCA---G
1 TGCATCCA
6134 TGCATCCA
1 TGCATCCA
*
6142 TGCATCCC
1 TGCATCCA
6150 TGCA---A
1 TGCATCCA
6155 TGCATCCA
1 TGCATCCA
*
6163 TACAT-C-
1 TGCATCCA
*
6169 TGCA-CTAA
1 TGCATC-CA
*
6177 TGCATCGA
1 TGCATCCA
6185 TGCAT-CA
1 TGCATCCA
6192 TGCA---A
1 TGCATCCA
6197 TGCATCCA
1 TGCATCCA
6205 TGCAT-CA
1 TGCATCCA
6212 TGCA---A
1 TGCATCCA
6217 TGCATCCA
1 TGCATCCA
6225 TGCATCCA
1 TGCATCCA
6233 AACATCGAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 32
0.67 0.08 0.25
Matches are distributed among these distances:
5 18 0.21
6 3 0.03
7 12 0.14
8 52 0.60
9 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:6137 original size:21 final size:20
Alignment explanation
Indices: 6113--6325 Score: 149
Period size: 20 Copynumber: 10.7 Consensus size: 20
6103 GGTGTCAAAG
*
6113 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCAT-CCTGCAA
6134 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCAT-CCTGCAA
*
6155 TGCATCCATACAT-CTGCACTAA
1 TGCATCCATGCATCCTG--C-AA
* *
6177 TGCATCGATGCATCATGCAA
1 TGCATCCATGCATCCTGCAA
*
6197 TGCATCCATGCATCATGCAA
1 TGCATCCATGCATCCTGCAA
6217 TGCATCCATGCAT-C--CAA
1 TGCATCCATGCATCCTGCAA
* * *
6234 -ACATCGAATGCAAT--T--AG
1 TGCATC-CATGC-ATCCTGCAA
* * *
6251 TGCATCGATGCATCTTGCTA
1 TGCATCCATGCATCCTGCAA
*
6271 TGCATCGATGCATCCTTGGC-A
1 TGCATCCATGCATCC-T-GCAA
* *
6292 TGCATCGATGCATCCTGCCA
1 TGCATCCATGCATCCTGCAA
6312 TGCATCCATGCATC
1 TGCATCCATGCATC
6326 AAGGCTGCAA
Statistics
Matches: 161, Mismatches: 16, Indels: 31
0.77 0.08 0.15
Matches are distributed among these distances:
16 6 0.04
17 12 0.07
18 7 0.04
19 5 0.03
20 63 0.39
21 51 0.32
22 15 0.09
23 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (20 bp):
TGCATCCATGCATCCTGCAA
Found at i:6208 original size:13 final size:12
Alignment explanation
Indices: 6184--6228 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
6174 TAATGCATCG
6184 ATGCATCATGCA
1 ATGCATCATGCA
6196 ATGCATC---C-
1 ATGCATCATGCA
6204 ATGCATCATGCA
1 ATGCATCATGCA
6216 ATGCATCCATGCA
1 ATGCAT-CATGCA
6229 TCCAAACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
8 7 0.25
9 1 0.04
11 1 0.04
12 13 0.46
13 6 0.21
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (12 bp):
ATGCATCATGCA
Found at i:6720 original size:34 final size:32
Alignment explanation
Indices: 6681--6750 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
6671 TTTTGTAAAG
*
6681 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
6715 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
6747 GGGA
1 GGGA
6751 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:9587 original size:30 final size:30
Alignment explanation
Indices: 9517--9574 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
9507 CAATTTAAGG
*
9517 CAAAATGGTTTTTGGACTTGAATTGAATTA
1 CAAAATGTTTTTTGGACTTGAATTGAATTA
9547 CAAAATGTTTTTTGGACTT-AATTGAATT
1 CAAAATGTTTTTTGGACTTGAATTGAATT
9575 TATTCAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTTGGACTTGAATTGAATTA
Found at i:9671 original size:8 final size:8
Alignment explanation
Indices: 9658--9757 Score: 55
Period size: 8 Copynumber: 14.0 Consensus size: 8
9648 GGTGTCAAAG
9658 TGCATCCA
1 TGCATCCA
*
9666 TGCATCCC
1 TGCATCCA
*
9674 TGCA---G
1 TGCATCCA
9679 TGCATCCA
1 TGCATCCA
*
9687 TGCATCCC
1 TGCATCCA
9695 TGCA---A
1 TGCATCCA
9700 TGCATCCA
1 TGCATCCA
9708 TGCAT-C-
1 TGCATCCA
*
9714 TGCA-CTAA
1 TGCATC-CA
*
9722 TGCATCGA
1 TGCATCCA
9730 TGCAT-CA
1 TGCATCCA
9737 TGCA---A
1 TGCATCCA
9742 TGCATCCA
1 TGCATCCA
9750 TGCATCCA
1 TGCATCCA
9758 AACATCGAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 26
0.68 0.08 0.25
Matches are distributed among these distances:
5 13 0.18
6 4 0.06
7 6 0.08
8 47 0.66
9 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:9682 original size:21 final size:21
Alignment explanation
Indices: 9658--9756 Score: 123
Period size: 21 Copynumber: 4.7 Consensus size: 21
9648 GGTGTCAAAG
*
9658 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCATCCCTGCAA
9679 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCATCCCTGCAA
9700 TGCATCCATGCAT--CTGCACTAA
1 TGCATCCATGCATCCCTG--C-AA
* *
9722 TGCATCGATGCAT-CATGCAA
1 TGCATCCATGCATCCCTGCAA
9742 TGCATCCATGCATCC
1 TGCATCCATGCATCC
9757 AAACATCGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
19 3 0.04
20 14 0.20
21 36 0.52
22 14 0.20
23 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.25
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAA
Found at i:9702 original size:13 final size:13
Alignment explanation
Indices: 9686--9753 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
9676 CAGTGCATCC
*
9686 ATGCATCCCTGCA
1 ATGCATCCATGCA
9699 ATGCATCCATGCA
1 ATGCATCCATGCA
* *
9712 TCTGCA-CTAATGCA
1 -ATGCATC-CATGCA
9726 TCGATGCAT-CATGCA
1 ---ATGCATCCATGCA
9741 ATGCATCCATGCA
1 ATGCATCCATGCA
9754 TCCAAACATC
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
12 6 0.14
13 19 0.44
14 9 0.21
15 5 0.12
16 4 0.09
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (13 bp):
ATGCATCCATGCA
Found at i:9726 original size:22 final size:20
Alignment explanation
Indices: 9658--9830 Score: 110
Period size: 20 Copynumber: 8.8 Consensus size: 20
9648 GGTGTCAAAG
* *
9658 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCAT-CATGCAA
*
9679 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCAT-CATGCAA
9700 TGCATCCATGCATC-TGCACTAA
1 TGCATCCATGCATCATG--C-AA
*
9722 TGCATCGATGCATCATGCAA
1 TGCATCCATGCATCATGCAA
9742 TGCATCCATGCATC---CAA
1 TGCATCCATGCATCATGCAA
* * * *
9759 -ACATCGAATGCA--AT-TAG
1 TGCATC-CATGCATCATGCAA
* * *
9776 TGCATCGATGCATCTTGCTA
1 TGCATCCATGCATCATGCAA
* * *
9796 TGCATCGATGCATCCTGCCA
1 TGCATCCATGCATCATGCAA
9816 TGCATCCATGCATCA
1 TGCATCCATGCATCA
9831 AGGCTGCAAC
Statistics
Matches: 124, Mismatches: 17, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.03
17 14 0.11
18 4 0.03
19 3 0.02
20 47 0.38
21 35 0.28
22 15 0.12
23 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (20 bp):
TGCATCCATGCATCATGCAA
Found at i:13050 original size:130 final size:129
Alignment explanation
Indices: 12816--13065 Score: 410
Period size: 130 Copynumber: 1.9 Consensus size: 129
12806 TTACTCTACG
* * * * *
12816 AAATTAAATATGTTCCTTAAATGTATCATATCTTTTTGAATATTCTGAATTTAAAAAATATTATA
1 AAATTAAATATGTTCCTTAAATATAGCATATATTTTTGAATATTCTAAATTAAAAAAATATTATA
* * *
12881 TGATTTTCTTTTAATTCAAATGTTAATATGGTATGACTTGCAGTTCACGAATATATCACTAAAA
66 CGATTTACTTTTAATTCAAATGTTAATATGATATGACTTGCAGTTCACGAATATATCACTAAAA
*
12945 AAATTAAATATTTTCCTTAAATATAGCATATATTTTTGAATATTCTAAATTAAAAAAGATATTAT
1 AAATTAAATATGTTCCTTAAATATAGCATATATTTTTGAATATTCTAAATTAAAAAA-ATATTAT
13010 ACGATTTACTTTTAATTCAAATGTTAATATGATATGACTTGCAGTTCACGAATATA
65 ACGATTTACTTTTAATTCAAATGTTAATATGATATGACTTGCAGTTCACGAATATA
13066 GTCTAATTAA
Statistics
Matches: 111, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 51 0.46
130 60 0.54
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.42
Consensus pattern (129 bp):
AAATTAAATATGTTCCTTAAATATAGCATATATTTTTGAATATTCTAAATTAAAAAAATATTATA
CGATTTACTTTTAATTCAAATGTTAATATGATATGACTTGCAGTTCACGAATATATCACTAAAA
Found at i:14602 original size:21 final size:21
Alignment explanation
Indices: 14527--14602 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 21
14517 TCTGCAATCG
* * *
14527 CAACGTGATTTTCCAAATTCA
1 CAACGCGAATTTCTAAATTCA
* * **
14548 TAACACGGAATTT-TAAATTTG
1 CAACGC-GAATTTCTAAATTCA
*
14569 CAACTCG-ATTTCTAAATTCA
1 CAACGCGAATTTCTAAATTCA
14589 CAACGCGAATTTCT
1 CAACGCGAATTTCT
14603 TTTTCGCAAC
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
19 4 0.10
20 13 0.32
21 18 0.45
22 5 0.12
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (21 bp):
CAACGCGAATTTCTAAATTCA
Found at i:14671 original size:20 final size:20
Alignment explanation
Indices: 14648--14712 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
14638 TTTCTAAATT
14648 GCAACACGAATTTTGTTTTC
1 GCAACACGAATTTTGTTTTC
* **
14668 GCAACTCG-ATTTTCGAATTC
1 GCAACACGAATTTT-GTTTTC
* *
14688 GCAACA--ACTTTTATTTTC
1 GCAACACGAATTTTGTTTTC
14706 GCAACAC
1 GCAACAC
14713 AAAAGTTTTG
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
18 9 0.26
19 9 0.26
20 16 0.47
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (20 bp):
GCAACACGAATTTTGTTTTC
Found at i:14692 original size:40 final size:40
Alignment explanation
Indices: 14605--14711 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 40
14595 GAATTTCTTT
**
14605 TTCGCAACACAAGTTTCCTTTTCGCAACAAGATTTTCTAAA
1 TTCGCAACACAA-TTTTATTTTCGCAACAAGATTTTCTAAA
* ** *
14646 TT-GCAACACGAATTTTGTTTTCGCAACTCGATTTTC-GAA
1 TTCGCAACAC-AATTTTATTTTCGCAACAAGATTTTCTAAA
*
14685 TTCGCAACA-ACTTTTATTTTCGCAACA
1 TTCGCAACACAATTTTATTTTCGCAACA
14712 CAAAAGTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
38 15 0.27
39 4 0.07
40 33 0.59
41 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.36
Consensus pattern (40 bp):
TTCGCAACACAATTTTATTTTCGCAACAAGATTTTCTAAA
Found at i:15655 original size:24 final size:24
Alignment explanation
Indices: 15619--15672 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
15609 GTATTCGAAA
*
15619 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTAGGTCAATACCCGGAC
* * *
15643 TTTGATCTAGGTCAGTACTCGGAT
1 TTTGATCTAGGTCAATACCCGGAC
15667 TTTGAT
1 TTTGAT
15673 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (24 bp):
TTTGATCTAGGTCAATACCCGGAC
Found at i:18271 original size:20 final size:20
Alignment explanation
Indices: 18228--18290 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
18218 CGATTGTTGT
* *
18228 GAAAGTCAAATTCGCAACGT
1 GAAAATCAAATTCGCAACGC
18248 GAAAATCAAATTCGTC-ACGC
1 GAAAATCAAATTCG-CAACGC
* *
18268 GAAAATAAAAATCGCAACGC
1 GAAAATCAAATTCGCAACGC
18288 GAA
1 GAA
18291 TTTGACTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.16
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACGC
Found at i:19855 original size:21 final size:21
Alignment explanation
Indices: 19829--19903 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
19819 GTGAATCGGG
* *
19829 CTCTTGAACGGTGGGAGAGGT
1 CTCTTGAACGATGGGAGAGGC
*
19850 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGGGAGAGGC
19871 CTCTTGAACGAT-GG-GAGGC
1 CTCTTGAACGATGGGAGAGGC
*
19890 CATCTTGAATGATG
1 C-TCTTGAACGATG
19904 ACAGGTGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 5 0.11
20 12 0.26
21 30 0.64
ACGTcount: A:0.21, C:0.17, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGAGGC
Found at i:20069 original size:4 final size:4
Alignment explanation
Indices: 20048--20089 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
20038 GGGCCGCTAA
* * *
20048 AAAT AAAT TAAT ACAT AAAT AAGT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
20090 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:20321 original size:21 final size:21
Alignment explanation
Indices: 20291--20337 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
20281 ACCATTTTCG
*
20291 TCACGTAAAGTAAC-GACCTCA
1 TCACGCAAAG-AACTGACCTCA
*
20312 TCACGCAAAGCACTGACCTCA
1 TCACGCAAAGAACTGACCTCA
20333 TCACG
1 TCACG
20338 TAACTCCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.17
Consensus pattern (21 bp):
TCACGCAAAGAACTGACCTCA
Found at i:21298 original size:20 final size:20
Alignment explanation
Indices: 21268--21346 Score: 108
Period size: 20 Copynumber: 4.0 Consensus size: 20
21258 CACTGAATAT
21268 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* * *
21288 TTATTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
21307 -TGTCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
21326 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
21346 T
1 T
21347 AATCCCTCGA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 14 0.29
19 1 0.02
20 34 0.69
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:21320 original size:38 final size:38
Alignment explanation
Indices: 21269--21343 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
21259 ACTGAATATT
*
21269 TGTCCCGAAGGACCACTGATTATTCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTGATTATCCCGAAGAACCACTA
* * *
21307 TGTCCCGAAGGACCACTGTTTGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACTGATTATCCCGAAGAACCACT
21344 GATAATCCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (38 bp):
TGTCCCGAAGGACCACTGATTATCCCGAAGAACCACTA
Found at i:26627 original size:31 final size:31
Alignment explanation
Indices: 26557--26728 Score: 140
Period size: 31 Copynumber: 5.5 Consensus size: 31
26547 GTCGAGGGTA
*
26557 TACCTATGTTCTACG-GAACATATGGACAGAAT
1 TACCTATGTT-TTCGAG-ACATATGGACAGAAT
*
26589 TACCTATGTCTTTCGAGACATATGGACAGTA-
1 TACCTATGT-TTTCGAGACATATGGACAGAAT
*
26620 TACCTATGTTCTACG-GAACATATGGACAGAAT
1 TACCTATGTT-TTCGAG-ACATATGGACAGAAT
*
26652 TACCTATGTGTTTCGAGACATATAGAC--AAT
1 TACCTATGT-TTTCGAGACATATGGACAGAAT
* ** *
26682 ATACCTATGTTCTAAAGAACATATGGACA-ATT
1 -TACCTATGTTTTCGAG-ACATATGGACAGAAT
*
26714 TACCTAGGTTCTTCG
1 TACCTATGTT-TTCG
26729 GAACCTATAG
Statistics
Matches: 114, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
30 9 0.08
31 52 0.46
32 49 0.43
33 4 0.04
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (31 bp):
TACCTATGTTTTCGAGACATATGGACAGAAT
Found at i:26632 original size:63 final size:63
Alignment explanation
Indices: 26554--26719 Score: 271
Period size: 63 Copynumber: 2.7 Consensus size: 63
26544 AGAGTCGAGG
*
26554 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
*
26617 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTGTTTCGAGACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
* ** *
26680 ATATACCTATGTTCTAAAGAACATATGGACA-ATTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
26720 GGTTCTTCGG
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
62 8 0.08
63 89 0.92
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
Found at i:30941 original size:32 final size:32
Alignment explanation
Indices: 30905--31085 Score: 175
Period size: 32 Copynumber: 5.8 Consensus size: 32
30895 GTTCTACGGA
*
30905 ACATATGGACATAATTACCTATGTCTTTTGAG
1 ACATATGGACATAATTACCTATGTCTTTCGAG
*
30937 ACATATGGACAGT-A-TACCTATGT-TCTACG-G
1 ACATATGGACA-TAATTACCTATGTCT-TTCGAG
*
30967 AACATATGGACAGAATTACCTATGTCTTTCGAG
1 -ACATATGGACATAATTACCTATGTCTTTCGAG
*
31000 ACATATGGAC--AATATACCTATGT-TCTACG-G
1 ACATATGGACATAAT-TACCTATGTCT-TTCGAG
*
31030 AACATATGGACAGAATTACCTATGTCTTTCGAG
1 -ACATATGGACATAATTACCTATGTCTTTCGAG
*
31063 ACATATAGACAGT-A-TACCTATGT
1 ACATATGGACA-TAATTACCTATGT
31086 TCTAAGGAAC
Statistics
Matches: 126, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
30 7 0.06
31 54 0.43
32 57 0.45
33 8 0.06
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (32 bp):
ACATATGGACATAATTACCTATGTCTTTCGAG
Found at i:30958 original size:31 final size:31
Alignment explanation
Indices: 30885--31141 Score: 238
Period size: 31 Copynumber: 8.2 Consensus size: 31
30875 AGAGTCGAGG
*
30885 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* *
30916 -TAATTACCTATG-TCTTTTGAGACATATGGACA
1 GT-A-TACCTATGTTCTATGGA-ACATATGGACA
*
30948 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * *
30979 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 GTA-TACCTATGTTCTATGGA-ACATATGGACA
* *
31011 ATATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * * *
31042 GAATTACCTATG-TCTTTCGAGACATATAGACA
1 GTA-TACCTATGTTCTATGGA-ACATATGGACA
*
31074 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * * *
31105 GTTTACCTAGGTTCT-TCGGAACCTATAGACA
1 GTATACCTATGTTCTAT-GGAACATATGGACA
31136 GT-TACC
1 GTATACC
31142 GATGATCTTT
Statistics
Matches: 183, Mismatches: 31, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
30 5 0.03
31 102 0.56
32 75 0.41
33 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTATGGAACATATGGACA
Found at i:30963 original size:63 final size:63
Alignment explanation
Indices: 30885--31113 Score: 397
Period size: 63 Copynumber: 3.7 Consensus size: 63
30875 AGAGTCGAGG
* *
30885 GTATACCTATGTTCTACGGAACATATGGACATAATTACCTATGTCTTTTGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
30948 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
31011 ATATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
31074 GTATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
31114 GGTTCTTCGG
Statistics
Matches: 159, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
62 7 0.04
63 152 0.96
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:35336 original size:32 final size:31
Alignment explanation
Indices: 35298--35478 Score: 190
Period size: 32 Copynumber: 5.7 Consensus size: 31
35288 GTTCTACGGA
35298 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAA-TACCTATGTCTTTCGAG
* * *
35330 AGATATGGACAGTATACCTATGT-TCTACG-G
1 ACATATGGACAGAATACCTATGTCT-TTCGAG
*
35360 AACATATGAACAGAATTACCTATGTCTTTCGAG
1 -ACATATGGACAGAA-TACCTATGTCTTTCGAG
* *
35393 ACATATGGACAGTATACCTATGT-TCTACG-G
1 ACATATGGACAGAATACCTATGTCT-TTCGAG
*
35423 AACATATGGACATAATTACCTATGTCTTTCGAG
1 -ACATATGGACAGAA-TACCTATGTCTTTCGAG
* *
35456 ACATATAGACAGTATACCTATGT
1 ACATATGGACAGAATACCTATGT
35479 TCTAAGGAAC
Statistics
Matches: 123, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
30 4 0.03
31 56 0.46
32 59 0.48
33 4 0.03
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (31 bp):
ACATATGGACAGAATACCTATGTCTTTCGAG
Found at i:35357 original size:63 final size:63
Alignment explanation
Indices: 35278--35506 Score: 388
Period size: 63 Copynumber: 3.7 Consensus size: 63
35268 AGAGTCGAGG
* *
35278 GTATATCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGAGATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
*
35341 GTATACCTATGTTCTACGGAACATATGAACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
35404 GTATACCTATGTTCTACGGAACATATGGACATAATTACCTATGTCTTTCGAGACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
35467 GTATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
35507 GGTTCTTCGG
Statistics
Matches: 157, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
62 7 0.04
63 150 0.96
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:35491 original size:31 final size:31
Alignment explanation
Indices: 35278--35534 Score: 233
Period size: 31 Copynumber: 8.2 Consensus size: 31
35268 AGAGTCGAGG
*
35278 GTATATCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
35309 GAATTACCTATG-TCTTTC-GAGAGATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
*
35341 GTATACCTATGTTCTACGGAACATATGAACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
35372 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
35404 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
35435 -TAATTACCTATG-TCTTTC-GAGACATATAGACA
1 GT-A-TACCTATGTTC-TACGGA-ACATATGGACA
*
35467 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * * *
35498 GTTTACCTAGGTTCTTCGGAACCTATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
35529 GT-TACC
1 GTATACC
35535 GAGGATCTTT
Statistics
Matches: 185, Mismatches: 24, Indels: 35
0.76 0.10 0.14
Matches are distributed among these distances:
30 5 0.03
31 103 0.56
32 76 0.41
33 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:37812 original size:18 final size:18
Alignment explanation
Indices: 37789--37881 Score: 87
Period size: 18 Copynumber: 4.9 Consensus size: 18
37779 ACTGAATATT
37789 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
37807 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* * *
37826 TTGTTCCAAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
* * *
37845 TGTCCCAAAAGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
*
37865 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
37882 GATAATCCCT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
18 31 0.51
19 2 0.03
20 28 0.46
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:37880 original size:38 final size:38
Alignment explanation
Indices: 37787--37881 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 38
37777 GCACTGAATA
* * *
37787 TTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
1 TTTGTCTCGAAGGACCACTATGTCCCAAAAGACCACTG
* * *
37825 ATTGT-TCCAAAGAACCACTATGTCCCAAAAGACCACTG
1 TTTGTCT-CGAAGGACCACTATGTCCCAAAAGACCACTG
37863 TTTGTCTCGAAGGACCACT
1 TTTGTCTCGAAGGACCACT
37882 GATAATCCCT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
38 45 0.98
39 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.23
Consensus pattern (38 bp):
TTTGTCTCGAAGGACCACTATGTCCCAAAAGACCACTG
Found at i:40014 original size:13 final size:13
Alignment explanation
Indices: 39996--40020 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39986 ACGGGAGGAG
39996 AGGAAGAAGAAGA
1 AGGAAGAAGAAGA
40009 AGGAAGAAGAAG
1 AGGAAGAAGAAG
40021 TTCTGGAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
AGGAAGAAGAAGA
Found at i:40412 original size:42 final size:42
Alignment explanation
Indices: 40314--40412 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
40304 GTGATGGAAT
* * * *
40314 AGGTGATGGCTCTCAGTGTGAAGATGTATAATCGGCTCGATT
1 AGGTGATGGCTCTCGGTGTCAAGATGTAGAATCGGCTCGATC
*
40356 AGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCAAGATGTAGAATCGGCTCGATC
40398 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
40413 AAGTGGGGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCAAGATGTAGAATCGGCTCGATC
Found at i:41900 original size:20 final size:20
Alignment explanation
Indices: 41877--41960 Score: 107
Period size: 20 Copynumber: 4.2 Consensus size: 20
41867 TTTGAAACTT
**
41877 AAATTCGCAACATGAAAATA
1 AAATTCGCAACGCGAAAATA
41897 AAATTCGCAACGCGAAAATCA
1 AAATTCGCAACGCGAAAAT-A
*
41918 AAA-TCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATA
* *
41937 AAATTCGCAACGTGAAACTA
1 AAATTCGCAACGCGAAAATA
41957 AAAT
1 AAAT
41961 CGCTTCGCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.05
20 49 0.88
21 4 0.07
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATA
Found at i:42306 original size:22 final size:22
Alignment explanation
Indices: 42278--42321 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
42268 CCCTCGGTGG
42278 TTGATTTTCCATTTGTGGCCGT
1 TTGATTTTCCATTTGTGGCCGT
* *
42300 TTGATTTTTCTTTTGTGGCCGT
1 TTGATTTTCCATTTGTGGCCGT
42322 GAATGGTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.16, G:0.23, T:0.55
Consensus pattern (22 bp):
TTGATTTTCCATTTGTGGCCGT
Found at i:42545 original size:19 final size:20
Alignment explanation
Indices: 42506--42548 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
42496 GTTTCGAATT
*
42506 CGAAAATAAAACTCGCATTG
1 CGAAAATAAAACGCGCATTG
*
42526 CGAAAAT-AAACGCGCGTTG
1 CGAAAATAAAACGCGCATTG
42545 CGAA
1 CGAA
42549 TTTGGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (20 bp):
CGAAAATAAAACGCGCATTG
Found at i:47620 original size:29 final size:29
Alignment explanation
Indices: 47542--47623 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
47532 CAGTGGTCGT
* ** *
47542 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAACG
* *
47571 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAACG
*
47600 AGGTCGCCATGCACTCGCGGCGAC
1 AGGTCGCCATGCACTCCCGGCGAC
47624 ATCCCCTGCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.18, C:0.40, G:0.29, T:0.12
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAACG
Found at i:47871 original size:29 final size:28
Alignment explanation
Indices: 47838--47895 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
47828 CATGCATGAA
47838 TCCTTGGTCGCCCCGAGTGCATGGCGACC
1 TCCTTGGTCG-CCCGAGTGCATGGCGACC
** *
47867 TCCTTGGTCGCGGGCGTGCATGGCGACC
1 TCCTTGGTCGCCCGAGTGCATGGCGACC
47895 T
1 T
47896 AGGAGGTCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.09, C:0.34, G:0.34, T:0.22
Consensus pattern (28 bp):
TCCTTGGTCGCCCGAGTGCATGGCGACC
Found at i:47892 original size:28 final size:29
Alignment explanation
Indices: 47852--47925 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
47842 TGGTCGCCCC
* **
47852 GAGTGCATGGCGACCTCCTTGGTCGC-GG
1 GAGTGCATGGCGACCTACGAGGTCGCTGG
* *
47880 GCGTGCATGGCGACCTAGGAGGTCGCTGG
1 GAGTGCATGGCGACCTACGAGGTCGCTGG
47909 GAGTGCATGGCGACCTA
1 GAGTGCATGGCGACCTA
47926 TGATTGGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 21 0.54
29 18 0.46
ACGTcount: A:0.15, C:0.26, G:0.41, T:0.19
Consensus pattern (29 bp):
GAGTGCATGGCGACCTACGAGGTCGCTGG
Found at i:49214 original size:23 final size:23
Alignment explanation
Indices: 49188--49247 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
49178 CGTGAATTCA
*
49188 GCTGTATTATTGCAACACTTATT
1 GCTGCATTATTGCAACACTTATT
* * *
49211 GCTGCATTATTACAGCCCTTATT
1 GCTGCATTATTGCAACACTTATT
49234 GCTGCATTATTGCA
1 GCTGCATTATTGCA
49248 CTCCTTCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (23 bp):
GCTGCATTATTGCAACACTTATT
Found at i:49701 original size:27 final size:27
Alignment explanation
Indices: 49639--49701 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
49629 ATATATTAAA
49639 AAATAATTAATTAGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTTAGTTAGTCT
** *
49666 -AATTTTTAATTAGTTTGTAGTTAGT-T
1 AAATAATTAATTAGTGT-TAGTTAGTCT
*
49692 AAATAGTTAA
1 AAATAATTAA
49702 GTTATATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.48
Consensus pattern (27 bp):
AAATAATTAATTAGTGTTAGTTAGTCT
Found at i:49884 original size:22 final size:23
Alignment explanation
Indices: 49849--49900 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
49839 AACAAAAATT
49849 AGTTA-ATTAGTTTGGTAGTTTA
1 AGTTATATTAGTTTGGTAGTTTA
*
49871 AGTTATATTA-TTTGTTAGTTTA
1 AGTTATATTAGTTTGGTAGTTTA
49893 AGTTATAT
1 AGTTATAT
49901 CATATAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (23 bp):
AGTTATATTAGTTTGGTAGTTTA
Found at i:50121 original size:29 final size:29
Alignment explanation
Indices: 50084--50161 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
50074 TAGTAATAAA
50084 TTATAATTAAAAATCA-TTTATTAGTTTAA-G
1 TTAT-ATTAAAAAT-AGTTTATTAG-TTAACG
50114 TTATATTAAAAAATAGTTTATTAGTTAACG
1 TTATATT-AAAAATAGTTTATTAGTTAACG
50144 TTATATTAAAGAATAGTT
1 TTATATTAAA-AATAGTT
50162 AAAGTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (29 bp):
TTATATTAAAAATAGTTTATTAGTTAACG
Found at i:50130 original size:22 final size:22
Alignment explanation
Indices: 50105--50185 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
50095 AATCATTTAT
*
50105 TAGTTTAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAGAA
50127 TAGTTTATTAGTTAACGTTATATTAAAGAA
1 TAGTTTA--AG-T----T-ATATTAAAGAA
*
50157 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
50179 TAGTTTA
1 TAGTTTA
50186 TTAGTTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 24 0.50
23 1 0.02
24 2 0.04
25 1 0.02
27 1 0.02
28 2 0.04
29 1 0.02
30 16 0.33
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:52631 original size:59 final size:59
Alignment explanation
Indices: 52496--52631 Score: 147
Period size: 59 Copynumber: 2.3 Consensus size: 59
52486 AATATTTAGT
* * *
52496 AATTCGACTATTTTAAATCATTAGTATCAAATAATTAAATATTAATAATAAATCATTATT
1 AATTTGACTATTATAAATCATTAGTATCAAATAATTAAATATT-ATAATAAATCATTATA
* *
52556 AA--T-AATAATTAGTAAATCATTAGTATCAAATCATTAAATATT-TAA-AAATCATTAATA
1 AATTTGACT-ATTA-TAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATT-ATA
52613 AATTTGACTATGTATAAAT
1 AATTTGACTAT-TATAAAT
52632 TTAAACTCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
56 8 0.13
57 9 0.14
58 3 0.05
59 37 0.59
60 6 0.10
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (59 bp):
AATTTGACTATTATAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATTATA
Found at i:52714 original size:14 final size:13
Alignment explanation
Indices: 52695--52907 Score: 69
Period size: 14 Copynumber: 16.2 Consensus size: 13
52685 TTAGTATAAT
52695 TATTAAATCATTAA
1 TATTAAATCATT-A
*
52709 TATTAAATTATTA
1 TATTAAATCATTA
*
52722 TTATAAAATCA-T-
1 -TATTAAATCATTA
* *
52734 TACTAAATAATTA
1 TATTAAATCATTA
52747 CTATTAAATCA-T-
1 -TATTAAATCATTA
* *
52759 TATTATCATTATTA
1 TATTA-AATCATTA
*
52773 TTATTAAATTA-T-
1 -TATTAAATCATTA
*
52785 TATT-CATCATTA
1 TATTAAATCATTA
52797 TTATTAAATCA-T-
1 -TATTAAATCATTA
52809 TATT--ATCATTA
1 TATTAAATCATTA
52820 TTATTAAATCA-T-
1 -TATTAAATCATTA
*
52832 TATTATAATGATTA
1 TATTA-AATCATTA
*
52846 TTATCAAATCATTA
1 -TATTAAATCATTA
52860 CTAAATCATCAAATCATTAAA
1 -T--AT--T-AAATCATT--A
52881 TATTTAAATCA-T-
1 TA-TTAAATCATTA
52893 TATTAAATCATTA
1 TATTAAATCATTA
52906 TA
1 TA
52908 ATGATTTACT
Statistics
Matches: 149, Mismatches: 19, Indels: 63
0.65 0.08 0.27
Matches are distributed among these distances:
9 4 0.03
10 4 0.03
11 34 0.23
12 15 0.10
13 14 0.09
14 47 0.32
15 10 0.07
16 8 0.05
17 1 0.01
18 1 0.01
19 9 0.06
20 1 0.01
21 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTAAATCATTA
Found at i:52762 original size:11 final size:11
Alignment explanation
Indices: 52693--53032 Score: 132
Period size: 11 Copynumber: 28.3 Consensus size: 11
52683 TATTAGTATA
52693 ATTATTAAATC
1 ATTATTAAATC
*
52704 ATTAATATTAAATT
1 A-T--TATTAAATC
52718 ATTATTATAAAATC
1 ATTA-T-T-AAATC
* *
52732 ATTACTAAATA
1 ATTATTAAATC
52743 ATTACTATTAAATC
1 A-T--TATTAAATC
*
52757 ATTATTATCATTATT
1 ATTATTA--A--ATC
*
52772 ATTATTAAATT
1 ATTATTAAATC
* *
52783 ATTATTCATCATT
1 ATTATT-A-AATC
52796 ATTATTAAATC
1 ATTATTAAATC
* *
52807 ATTATTATCATT
1 ATTATTA-AATC
52819 ATTATTAAATC
1 ATTATTAAATC
*
52830 ATTATTATAATG
1 ATTATTA-AATC
52842 ATTATTATCAAATC
1 ATTA-T-T-AAATC
*
52856 ATTACTAAATC
1 ATTATTAAATC
52867 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
52882 A-T-TTAAATC
1 ATTATTAAATC
52891 ATTATTAAATC
1 ATTATTAAATC
*
52902 ATTA-T-AATG
1 ATTATTAAATC
*
52911 ATTTACTAAATC
1 A-TTATTAAATC
*
52923 ATTATTATAATG
1 ATTATTA-AATC
52935 ATTATTATCAAATC
1 ATTA-T-T-AAATC
*
52949 ATTACTAAATC
1 ATTATTAAATC
* * * *
52960 ATCAAATAATTA
1 AT-TATTAAATC
* *
52972 AATATTAAATTT
1 ATTATTAAA-TC
*
52984 ATTATTAAATTT
1 ATTATTAAA-TC
52996 ATTATTAAATC
1 ATTATTAAATC
*
53007 ATTATTTAAATT
1 ATTA-TTAAATC
53019 ATTATTAAATC
1 ATTATTAAATC
53030 ATT
1 ATT
53033 TTTATGGTTA
Statistics
Matches: 254, Mismatches: 37, Indels: 76
0.69 0.10 0.21
Matches are distributed among these distances:
8 6 0.02
9 5 0.02
10 6 0.02
11 89 0.35
12 72 0.28
13 16 0.06
14 41 0.16
15 13 0.05
16 6 0.02
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.46
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:52772 original size:3 final size:3
Alignment explanation
Indices: 52757--52849 Score: 66
Period size: 3 Copynumber: 31.7 Consensus size: 3
52747 CTATTAAATC
* * *
52757 ATT ATT ATC ATT ATT ATT ATT A-A ATT ATT ATT CATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
* * * * * * *
52802 A-A ATC ATT ATT ATC ATT ATT ATT A-A ATC ATT ATT ATA ATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
52848 AT
1 AT
52850 CAAATCATTA
Statistics
Matches: 69, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
2 3 0.04
3 64 0.93
4 2 0.03
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (3 bp):
ATT
Found at i:52837 original size:23 final size:23
Alignment explanation
Indices: 52718--52848 Score: 145
Period size: 23 Copynumber: 5.4 Consensus size: 23
52708 ATATTAAATT
* * *
52718 ATTATTATAAAATCATTACTAAATA
1 ATTATTATTAAATCATTA-T-TATC
*
52743 ATTACTATTAAATCATTATTATC
1 ATTATTATTAAATCATTATTATC
*
52766 ATTATTATTATTAAATTATTATTCATC
1 ---ATTATTATTAAATCATTATT-ATC
52793 ATTATTATTAAATCATTATTATC
1 ATTATTATTAAATCATTATTATC
*
52816 ATTATTATTAAATCATTATTATA
1 ATTATTATTAAATCATTATTATC
*
52839 ATGATTATTA
1 ATTATTATTA
52849 TCAAATCATT
Statistics
Matches: 93, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
23 36 0.39
24 20 0.22
25 16 0.17
26 18 0.19
27 3 0.03
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTATTATTAAATCATTATTATC
Found at i:52872 original size:19 final size:19
Alignment explanation
Indices: 52848--52971 Score: 71
Period size: 19 Copynumber: 6.6 Consensus size: 19
52838 AATGATTATT
52848 ATCAAATCATTACTAAATC
1 ATCAAATCATTACTAAATC
52867 ATCAAATCA-T--TAAAT-
1 ATCAAATCATTACTAAATC
* *
52882 ATTTAAATCATTATTAAATC
1 A-TCAAATCATTACTAAATC
* *
52902 ATTATAATGATTTACTAAATC
1 ATCA-AATCA-TTACTAAATC
* * * * * *
52923 ATTATTATAATGA-T-TATT
1 ATCA-AATCATTACTAAATC
52941 ATCAAATCATTACTAAATC
1 ATCAAATCATTACTAAATC
*
52960 ATCAAATAATTA
1 ATCAAATCATTA
52972 AATATTAAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
15 1 0.01
16 12 0.15
17 6 0.07
18 7 0.09
19 31 0.38
20 7 0.09
21 17 0.21
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (19 bp):
ATCAAATCATTACTAAATC
Found at i:52932 original size:93 final size:95
Alignment explanation
Indices: 52796--53025 Score: 326
Period size: 93 Copynumber: 2.4 Consensus size: 95
52786 ATTCATCATT
* *
52796 ATTATTAAATCATTATTATCATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTAC
1 ATTATTAAATCATTATAATCATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAC
*
52861 TAAATCATCAAATCATTAAATATTTAAA-TC
66 TAAATCATCAAATAATTAAATA-TTAAATTC
*
52891 ATTATTAAATCATTATAATGA-T-TTACTAAATCATTATTATAATGATTATTATCAAATCATTAC
1 ATTATTAAATCATTATAATCATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAC
*
52954 TAAATCATCAAATAATTAAATATTAAATTT
66 TAAATCATCAAATAATTAAATATTAAATTC
* *
52984 ATTATTAAATTTATTATTAAATCATTATT--TAAATTATTATTA
1 ATTATTAAA-TCATTA-T-AATCATTATTACTAAATCATTATTA
53026 AATCATTTTT
Statistics
Matches: 121, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
92 5 0.04
93 71 0.59
94 6 0.05
95 20 0.17
96 16 0.13
97 1 0.01
98 2 0.02
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (95 bp):
ATTATTAAATCATTATAATCATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTAC
TAAATCATCAAATAATTAAATATTAAATTC
Found at i:52989 original size:12 final size:12
Alignment explanation
Indices: 52974--53028 Score: 78
Period size: 12 Copynumber: 4.7 Consensus size: 12
52964 AATAATTAAA
52974 TATTAAATTTAT
1 TATTAAATTTAT
52986 TATTAAATTTAT
1 TATTAAATTTAT
*
52998 TATTAAA-TCAT
1 TATTAAATTTAT
53009 TATTTAAA-TTAT
1 TA-TTAAATTTAT
53021 TATTAAAT
1 TATTAAAT
53029 CATTTTTATG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTAAATTTAT
Found at i:53043 original size:20 final size:22
Alignment explanation
Indices: 52996--53044 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
52986 TATTAAATTT
*
52996 ATTATTAAATCATTATTTAAATT
1 ATTATTAAATCATTATTT-AATG
53019 ATTATTAAATCATT-TTT-ATG
1 ATTATTAAATCATTATTTAATG
*
53039 GTTATT
1 ATTATT
53045 GAACCACACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.29
22 3 0.12
23 14 0.58
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTATTAAATCATTATTTAATG
Found at i:53044 original size:23 final size:23
Alignment explanation
Indices: 52704--53036 Score: 107
Period size: 24 Copynumber: 14.0 Consensus size: 23
52694 TTATTAAATC
* *
52704 ATTAATATTAAATTATTATTATAAA
1 ATTATTATTAAATCATTATT-T-AA
* * *
52729 ATCATTACTAAATAATTACTATTAA
1 ATTATTATTAAATCATTA-T-TTAA
* * *
52754 ATCATTATTATCATTATTATTATTAA
1 ATTATTATTA-AATCATTA-T-TTAA
*
52780 ATTATTATT-CATCATTATTATTAA
1 ATTATTATTAAATCATTA-T-TTAA
*
52804 ATCATTATT--ATCATTATTATTAA
1 ATTATTATTAAATCATTA-T-TTAA
* *
52827 ATCATTATTATAATGATTATTATCAA
1 ATTATTATTA-AATCATTATT-T-AA
* * *
52853 ATCATTACTAAATCATCAAATCATTAA
1 ATTATTATTAAATCAT--TAT--TTAA
52880 A-TA-T-TTAAATCATTA-TTAA
1 ATTATTATTAAATCATTATTTAA
* * *
52899 ATCATTA-T-AATGATT-TACTAA
1 ATTATTATTAAATCATTAT-TTAA
* *
52920 ATCATTATTATAATGATTATTATCAA
1 ATTATTATTA-AATCATTATT-T-AA
* * * **
52946 ATCATTACTAAATCATCAAAT-A
1 ATTATTATTAAATCATTATTTAA
* *
52968 ATTAAATATTAAATTTATTA-TTAA
1 ATT-ATTATTAAA-TCATTATTTAA
52992 ATTTATTATTAAATCATTATTTAA
1 A-TTATTATTAAATCATTATTTAA
53016 ATTATTATTAAATCATT-TTTA
1 ATTATTATTAAATCATTATTTA
53037 TGGTTATTGA
Statistics
Matches: 245, Mismatches: 35, Indels: 59
0.72 0.10 0.17
Matches are distributed among these distances:
19 5 0.02
20 7 0.03
21 12 0.05
22 9 0.04
23 52 0.21
24 58 0.24
25 43 0.18
26 51 0.21
27 6 0.02
28 1 0.00
29 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.47
Consensus pattern (23 bp):
ATTATTATTAAATCATTATTTAA
Found at i:53225 original size:17 final size:18
Alignment explanation
Indices: 53205--53239 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
53195 TATTAGTAAA
53205 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
53222 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
53240 ACTAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:53350 original size:93 final size:96
Alignment explanation
Indices: 53237--53464 Score: 369
Period size: 93 Copynumber: 2.4 Consensus size: 96
53227 ATTATTAATA
* *
53237 ATTACTAATCATTACTATCAAATAATTAAATATTAATAATAATTTCATTA-CTAATCATTACTAT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATATAATCATTACTAT
*
53301 CAAATCATT-AATATTAATAATAA-TTCATT
66 CAAATCATTAAATATTAATAATAATTTCATC
*
53330 ATTACTAATCATTACTATCAAATCTTTAAATATTAATAATAATTTCATTATTATAATCATTACTA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTA-TATAATCATTACTA
53395 TCAAATCATTAAATATTAATAATAATTTCATC
65 TCAAATCATTAAATATTAATAATAATTTCATC
53427 ATTACTAATCA-T--TATCAAATCATTAAATATTAATAATA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
53465 GATGGGTGCC
Statistics
Matches: 126, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
93 48 0.38
94 25 0.20
95 22 0.17
96 15 0.12
97 16 0.13
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (96 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATATAATCATTACTAT
CAAATCATTAAATATTAATAATAATTTCATC
Found at i:53364 original size:48 final size:49
Alignment explanation
Indices: 53237--53464 Score: 357
Period size: 48 Copynumber: 4.8 Consensus size: 49
53227 ATTATTAATA
*
53237 ATTACTAATCATTACTATCAAATAATTAAATATTAATAATAA-TT--TC
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
*
53283 ATTACTAATCATTACTATCAAATCATT-AATATTAATAATAA-TTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
* *
53330 ATTACTAATCATTACTATCAAATCTTTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
53379 ATTA-TAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
53427 ATTACTAATCA-T--TATCAAATCATTAAATATTAATAATA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
53465 GATGGGTGCC
Statistics
Matches: 172, Mismatches: 5, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
45 16 0.09
46 52 0.30
47 27 0.16
48 61 0.35
49 16 0.09
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
Found at i:56429 original size:14 final size:14
Alignment explanation
Indices: 56369--56429 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 14
56359 CTAATATTAC
56369 TAATAATGATTTAA
1 TAATAATGATTTAA
* *
56383 TAATTATTA-TTAA
1 TAATAATGATTTAA
* *
56396 T-CTAATGATTTGA
1 TAATAATGATTTAA
*
56409 TATTAATGATTTAA
1 TAATAATGATTTAA
56423 TAATAAT
1 TAATAAT
56430 ATGATTTAGT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
12 4 0.11
13 9 0.25
14 23 0.64
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.48
Consensus pattern (14 bp):
TAATAATGATTTAA
Found at i:56712 original size:17 final size:17
Alignment explanation
Indices: 56660--56716 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 17
56650 ACAATATAAA
*
56660 TTAAACAAAATATTTTT
1 TTAAACACAATATTTTT
*
56677 TTAAAACACTAA-ATATTT
1 TT-AAACAC-AATATTTTT
56695 TTAAACACAATA-TTTT
1 TTAAACACAATATTTTT
56711 TTAAAC
1 TTAAAC
56717 GGAAATTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 11 0.32
17 9 0.26
18 12 0.35
19 2 0.06
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:57165 original size:43 final size:49
Alignment explanation
Indices: 57108--57222 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 49
57098 GTTTAAAGAC
*
57108 ACTAACAAATTAATTAATATA-TTTTT-TAT-AT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAATATATTTTTTATATAATATATATATAACTTAA
*
57151 ACTAATAAACTAATTAACTA-ATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAA-TATATTTTTTATATAATAT-ATATATAACTTAA
57201 ACTAACAAACTAATATAATATA
1 ACTAACAAACTAAT-TAATATA
57223 ACTTAAACTA
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
43 16 0.27
44 7 0.12
45 3 0.05
46 2 0.03
47 1 0.02
49 2 0.03
50 24 0.41
51 4 0.07
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (49 bp):
ACTAACAAACTAATTAATATATTTTTTATATAATATATATATAACTTAA
Found at i:57221 original size:28 final size:31
Alignment explanation
Indices: 57181--57244 Score: 107
Period size: 28 Copynumber: 2.2 Consensus size: 31
57171 ATTTTTTATA
57181 TAATATAATATATAACTTAAACT-AACAAAC
1 TAATATAATATATAACTTAAACTAAACAAAC
57211 TAATAT-A-ATATAACTTAAACTAAACAAAC
1 TAATATAATATATAACTTAAACTAAACAAAC
57240 TAATA
1 TAATA
57245 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 14 0.42
29 13 0.39
30 6 0.18
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (31 bp):
TAATATAATATATAACTTAAACTAAACAAAC
Found at i:57245 original size:22 final size:21
Alignment explanation
Indices: 57220--57269 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
57210 CTAATATAAT
57220 ATAACTTAAACTAAACAAACTA
1 ATAACTTAAACT-AACAAACTA
* *
57242 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
57263 ATTAACT
1 A-TAACT
57270 AGATTTAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:57251 original size:29 final size:28
Alignment explanation
Indices: 57185--57251 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
57175 TTTATATAAT
57185 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
57213 AT-ATAATATAACTTAAACTAAACAAACTA
1 ATAAT-ATATAACTTAAACT-AACAAACTA
*
57242 ATAATTTATA
1 ATAATATATA
57252 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
27 2 0.06
28 16 0.46
29 15 0.43
30 2 0.06
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:57847 original size:29 final size:29
Alignment explanation
Indices: 57805--57860 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
57795 CGAGAACGTT
57805 GGACGCCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
57834 GGACGCCGGGCGTGCATGGCGACCTAT
1 GGACGCCGGGCGTGCATGGCGACCTAT
57861 GCTGGTTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.29, G:0.39, T:0.14
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGACCTATAA
Done.