Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007700.1 Corchorus capsularis cultivar CVL-1 contig07721, 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: 36378
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:156 original size:24 final size:24
Alignment explanation
Indices: 123--169 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
113 CAAAAACACA
*
123 AGAATGTTTTTAATTAGTAATTTT
1 AGAATATTTTTAATTAGTAATTTT
147 AGAATATTTTTAATTAGTAATTT
1 AGAATATTTTTAATTAGTAATTT
170 AGCATTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (24 bp):
AGAATATTTTTAATTAGTAATTTT
Found at i:3775 original size:26 final size:26
Alignment explanation
Indices: 3691--3776 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
3681 AGCAGTAATT
3691 AAGTAAAAAGAGATTAATCAGAGTCA
1 AAGTAAAAAGAGATTAATCAGAGTCA
* * *
3717 AAGTAATAGAA-ATCAGTAAATC-G-GTAA
1 AAGTAA-A-AAGA-GA-TTAATCAGAGTCA
3744 TTAAGTAAAAAGAGATTAATCAGAGTCA
1 --AAGTAAAAAGAGATTAATCAGAGTCA
3772 AAGTA
1 AAGTA
3777 GTAGTAATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
26 16 0.36
27 9 0.20
28 9 0.20
29 11 0.24
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (26 bp):
AAGTAAAAAGAGATTAATCAGAGTCA
Found at i:3779 original size:29 final size:29
Alignment explanation
Indices: 3692--3779 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
3682 GCAGTAATTA
3692 AGTAAAAAGAGATTAATCAGAGTCAAAGT
1 AGTAAAAAGAGATTAATCAGAGTCAAAGT
* ** * *
3721 AATAGAAATCAG-TAAATC-G-GT--AATT
1 AGTA-AAAAGAGATTAATCAGAGTCAAAGT
3746 AAGTAAAAAGAGATTAATCAGAGTCAAAGT
1 -AGTAAAAAGAGATTAATCAGAGTCAAAGT
3776 AGTA
1 AGTA
3780 GTAATCAGTA
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 8 0.19
26 8 0.19
27 3 0.07
28 3 0.07
29 12 0.29
30 8 0.19
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (29 bp):
AGTAAAAAGAGATTAATCAGAGTCAAAGT
Found at i:3834 original size:111 final size:103
Alignment explanation
Indices: 3631--3859 Score: 305
Period size: 111 Copynumber: 2.1 Consensus size: 103
3621 CATCAAGGGC
* * *
3631 AAATCAGTAATTAAGTAAGAAGAGATTAATCAGAGTTAAGGTAATAGTAAAGCAGTAATTAAGTA
1 AAATCGGTAATTAAGTAAAAAGAGATTAATCAGAGTAAAGGTAATAGTAAAGCAGTAATTAAGTA
*
3696 AAAAGAGATTAATCAGAGTCAAAGTAATAGAAATCAGT
66 AAAAAAGATTAATCAGAGTCAAAGTAATAGAAATCAGT
*
3734 AAATCGGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAATCAGTAAATCAGTAA
1 AAATCGGTAATTAAGTAAAAAGAGATTAATCAGAGT--AA--AG--GTAAT-AGTAAAGCAGTAA
* **
3799 TTAAGTAAAAAAAAGATTAATCAGAGTCAAGGTAATATTAATCAGT
59 TTAAGT-AAAAAAAGATTAATCAGAGTCAAAGTAATAGAAATCAGT
*
3845 AAATCGATAATTAAG
1 AAATCGGTAATTAAG
3860 AGTTAAAATG
Statistics
Matches: 109, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
103 34 0.31
105 1 0.01
107 2 0.02
109 5 0.05
110 18 0.17
111 49 0.45
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (103 bp):
AAATCGGTAATTAAGTAAAAAGAGATTAATCAGAGTAAAGGTAATAGTAAAGCAGTAATTAAGTA
AAAAAAGATTAATCAGAGTCAAAGTAATAGAAATCAGT
Found at i:3841 original size:56 final size:55
Alignment explanation
Indices: 3631--3859 Score: 303
Period size: 55 Copynumber: 4.3 Consensus size: 55
3621 CATCAAGGGC
* *
3631 AAATCAGTAATTAAGTAAGAAGAGATTAATCAGAGT-----TAA-GGTAAT-AGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* *
3679 AAAGCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGAAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* *
3734 AAATCGGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* * *
3789 AAATCAGTAATTAAGTAAAAAAAAGATTAATCAGAGTCAAGGTAATATTAATCAGT
1 AAATCAGTAATTAAGT-AAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
3845 AAATC-GATAATTAAG
1 AAATCAG-TAATTAAG
3860 AGTTAAAATG
Statistics
Matches: 159, Mismatches: 13, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
48 34 0.21
53 3 0.02
54 4 0.03
55 70 0.44
56 48 0.30
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (55 bp):
AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
Found at i:4165 original size:22 final size:21
Alignment explanation
Indices: 4091--4325 Score: 104
Period size: 22 Copynumber: 10.8 Consensus size: 21
4081 AATGGTAATT
*
4091 AGTAATCAATAAAAAGTAAGAA
1 AGTAATCAGTAAAAAGTAA-AA
* *
4113 GGTAATCA--ACAAGAGTAAAA
1 AGTAATCAGTA-AAAAGTAAAA
* **
4133 TAATAGGCAGTAAAAAGTAAAA
1 -AGTAATCAGTAAAAAGTAAAA
**
4155 TAGTAATCAGT-ATGAGTAAAAA
1 -AGTAATCAGTAAAAAGT-AAAA
* *
4177 AGGTAATAAGTAAGAAGT-AAA
1 A-GTAATCAGTAAAAAGTAAAA
* *
4198 AGTAAAATCAGT-AAGAGTAAGA
1 AGT--AATCAGTAAAAAGTAAAA
* * *
4220 AGATGATTAGTAAAGAGTAAAAAA
1 AG-TAATCAGTAAAAAGT--AAAA
**
4244 AGCTAATCAACAAGAAA-TAAAA
1 AG-TAATCAGTAA-AAAGTAAAA
*
4266 AGGTAATCAGTAAAAAGCAAAA
1 A-GTAATCAGTAAAAAGTAAAA
* *
4288 GGCAATCAGTAAAAAGTAAAA
1 AGTAATCAGTAAAAAGTAAAA
*
4309 GAGCAATCAGTAAAAAG
1 -AGTAATCAGTAAAAAG
4326 GAGCAGAAAA
Statistics
Matches: 160, Mismatches: 35, Indels: 36
0.69 0.15 0.16
Matches are distributed among these distances:
20 5 0.03
21 50 0.31
22 84 0.52
23 7 0.04
24 12 0.08
25 2 0.01
ACGTcount: A:0.57, C:0.06, G:0.19, T:0.17
Consensus pattern (21 bp):
AGTAATCAGTAAAAAGTAAAA
Found at i:4289 original size:21 final size:21
Alignment explanation
Indices: 4263--4325 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
4253 ACAAGAAATA
*
4263 AAAAGGTAATCAGTAAAAAGC
1 AAAAGGCAATCAGTAAAAAGC
*
4284 AAAAGGCAATCAGTAAAAAGT
1 AAAAGGCAATCAGTAAAAAGC
4305 AAAAGAGCAATCAGTAAAAAG
1 AAAAG-GCAATCAGTAAAAAG
4326 GAGCAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 24 0.62
22 15 0.38
ACGTcount: A:0.59, C:0.10, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAAGGCAATCAGTAAAAAGC
Found at i:8948 original size:18 final size:18
Alignment explanation
Indices: 8925--8960 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8915 CCCAAAAGAT
*
8925 TCTTCTGTCTTCAACTTC
1 TCTTCTGCCTTCAACTTC
*
8943 TCTTCTGCCTTCACCTTC
1 TCTTCTGCCTTCAACTTC
8961 ACCTTCTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.39, G:0.06, T:0.47
Consensus pattern (18 bp):
TCTTCTGCCTTCAACTTC
Found at i:12428 original size:131 final size:131
Alignment explanation
Indices: 12199--12834 Score: 610
Period size: 131 Copynumber: 4.8 Consensus size: 131
12189 TTTCAAAAGT
* *
12199 AAAATTATTTACAACC-AAATAATGTTGTTGTTGTGTAAGCATTTTGGCAACAACATTTTG-TCA
1 AAAAGTATTTACAACCAAAATAA--TT-TTGTTGTGTAAACATTTT-G--ACAACATTTTGCT-A
* * * * ** * * *
12262 TTTTAAAAAGTAATTTGTAACTAATTTGATGTCGTTTTAAAAAACTTTACACAA-TATTAAAATA
59 TTTTAAAAAGTTATTTGCAACCAACTAAATATCGTTATAAAAAACTTTACACAACCA-TAAAATA
* * *
12326 TCGTT-ACAT
123 TTGTTGTC-G
* * * *
12335 AAAAGTATTTACAACTAAAATGATATTATTGTGTAAACATTTTGACAACATTTTGCTATTTTAAA
1 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACATTTTGCTATTTTAAA
* * * * * * ** *
12400 ATGTTATTTGTAACCAACTAGATATCGTTGT-AAATATTATTACGTAATCATAAAATATTGTTGT
66 AAGTTATTTGCAACCAACTAAATATCGTTATAAAAAACT-TTACACAACCATAAAATATTGTTGT
12464 CG
130 CG
* * * **
12466 AAAAGTGTTTACAACCAAAATAATTTTGTTGTGCAAACATTTTGACAACAACAGTTTGCCGTTTT
1 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTG---ACAACATTTTGCTATTTT
* *
12531 AAAAAAATT-TTTCGCAACCAACTAAATATCGTTATAAAAAACTTTACACAACCAAAAAATATTG
63 -AAAAAGTTATTT-GCAACCAACTAAATATCGTTATAAAAAACTTTACACAACCATAAAATATTG
12595 TTGTCG
126 TTGTCG
* *
12601 ACAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAATAATTTG-TCGTTT
1 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAAC-AT--TTTGCT-ATTT
* * *
12665 TAAAAAGTTATTCGCAACCAACTAAATATTGTTATAAAAAACATTACACAACCA-ATAAATATTG
62 TAAAAAGTTATTTGCAACCAACTAAATATCGTTATAAAAAACTTTACACAACCATA-AAATATTG
12729 TTGTC-
126 TTGTCG
*
12734 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACATTTTTTCGT-TTTT-
1 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACA-TTTTGC-TATTTTA
* * *
12797 AAAAGCTATTCGCAACCAACTAAATATCGTTGTAAAAA
64 AAAAGTTATTTGCAACCAACTAAATATCGTTATAAAAA
12835 TTTTTAGTAA
Statistics
Matches: 425, Mismatches: 55, Indels: 46
0.81 0.10 0.09
Matches are distributed among these distances:
130 40 0.09
131 105 0.25
132 9 0.02
133 53 0.12
134 93 0.22
135 101 0.24
136 19 0.04
137 5 0.01
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (131 bp):
AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACATTTTGCTATTTTAAA
AAGTTATTTGCAACCAACTAAATATCGTTATAAAAAACTTTACACAACCATAAAATATTGTTGTC
G
Found at i:12612 original size:135 final size:134
Alignment explanation
Indices: 12199--12834 Score: 646
Period size: 135 Copynumber: 4.8 Consensus size: 134
12189 TTTCAAAAGT
* * * * *
12199 AAAATTATTTACAACC-AAATAATGTTGTTGTTGTGTAAGCATTTTGGCAACAACATTTTGTCAT
1 AAAAGTATTTACAACCAAAATAA--TT-TTGTTGTGTAAACATTTTGACAACAACAATTTGTCGT
* * * * * ** * * * * *
12263 TTTAAAAAGTAATTTGTAACTAATTTGATGTCGTTTTAAAAAACTTTACACAA-TATTAAAATAT
63 TTTAAAAAGTTATTCGCAACCAACTAAATATCGTTATAAAAAACATTACACAACCA-AAAAATAT
* * *
12327 CGTT-ACAT
127 TGTTGTC-G
* * * * * *
12335 AAAAGTATTTACAACTAAAATGATATTATTGTGTAAACATTTTG---ACAACATTTTG-CTATTT
1 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAACAATTTGTC-GTTT
* * * * * * ** ** * *
12396 TAAAATGTTATTTGTAACCAACTAGATATCGTTGTAAATATTATTACGTAATCATAAAATATTGT
65 TAAAAAGTTATTCGCAACCAACTAAATATCGTTATAAAAAACATTACACAACCAAAAAATATTGT
12461 TGTCG
130 TGTCG
* * * *
12466 AAAAGTGTTTACAACCAAAATAATTTTGTTGTGCAAACATTTTGACAACAACAGTTTGCCGTTTT
1 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAACAATTTGTCGTTTT
* * *
12531 AAAAAAATTTTTCGCAACCAACTAAATATCGTTATAAAAAACTTTACACAACCAAAAAATATTGT
66 -AAAAAGTTATTCGCAACCAACTAAATATCGTTATAAAAAACATTACACAACCAAAAAATATTGT
12596 TGTCG
130 TGTCG
* *
12601 ACAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAATAATTTGTCGTTTT
1 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAACAATTTGTCGTTTT
* *
12666 AAAAAGTTATTCGCAACCAACTAAATATTGTTATAAAAAACATTACACAACCAATAAATATTGTT
66 AAAAAGTTATTCGCAACCAACTAAATATCGTTATAAAAAACATTACACAACCAAAAAATATTGTT
12731 GTC-
131 GTCG
* *
12734 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTG---ACAACATTTTTTCGTTTT
1 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAACAATTTGTCGTTTT
* * *
12796 TAAAAGCTATTCGCAACCAACTAAATATCGTTGTAAAAA
66 AAAAAGTTATTCGCAACCAACTAAATATCGTTATAAAAA
12835 TTTTTAGTAA
Statistics
Matches: 426, Mismatches: 65, Indels: 24
0.83 0.13 0.05
Matches are distributed among these distances:
130 51 0.12
131 102 0.24
132 2 0.00
133 43 0.10
134 94 0.22
135 115 0.27
136 14 0.03
137 5 0.01
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (134 bp):
AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAACAATTTGTCGTTTT
AAAAAGTTATTCGCAACCAACTAAATATCGTTATAAAAAACATTACACAACCAAAAAATATTGTT
GTCG
Found at i:12649 original size:34 final size:33
Alignment explanation
Indices: 12611--12782 Score: 76
Period size: 33 Copynumber: 5.2 Consensus size: 33
12601 ACAAGTATTT
12611 ACAACCAAAATAATTTTGTTGTGTAAACATTTTG
1 ACAACCAAAATAATTTTGTTGT-TAAACATTTTG
*
12645 ACAA-C--AATAATTTGTCGTT-TTAAAAAGTTATTCG
1 ACAACCAAAATAATTT-T-GTTGTTAAACA-TT-TT-G
* * * * **
12679 -CAACC-AACTAAATATTGTTATAAAAAACA-TTAC
1 ACAACCAAAAT-AATTTTGTTGT--TAAACATTTTG
* * *
12712 ACAACCAATA-AATATTGTTGTCAAA-AGTATTT-
1 ACAACCAAAATAATTTTGTTGTTAAACA-T-TTTG
12744 ACAACCAAAATAATTTTGTTGTGTAAACATTTTG
1 ACAACCAAAATAATTTTGTTGT-TAAACATTTTG
12778 ACAAC
1 ACAAC
12783 ATTTTTTCGT
Statistics
Matches: 103, Mismatches: 15, Indels: 40
0.65 0.09 0.25
Matches are distributed among these distances:
30 1 0.01
31 16 0.16
32 13 0.13
33 34 0.33
34 24 0.23
35 7 0.07
36 4 0.04
37 4 0.04
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.34
Consensus pattern (33 bp):
ACAACCAAAATAATTTTGTTGTTAAACATTTTG
Found at i:13079 original size:30 final size:30
Alignment explanation
Indices: 13038--13098 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
13028 TATAGGGTTG
*
13038 TTGCGTGAAATAAAATTCTTTTAACAACAA
1 TTGCGTAAAATAAAATTCTTTTAACAACAA
*
13068 TTGCGTAAAATACAATTCTTTTAACAACAA
1 TTGCGTAAAATAAAATTCTTTTAACAACAA
13098 T
1 T
13099 AAAATGACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (30 bp):
TTGCGTAAAATAAAATTCTTTTAACAACAA
Found at i:13269 original size:17 final size:17
Alignment explanation
Indices: 13247--13280 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13237 GACTTTTTAC
13247 GTTGGTAAAAGTCACTT
1 GTTGGTAAAAGTCACTT
13264 GTTGGTAAAAGTCACTT
1 GTTGGTAAAAGTCACTT
13281 TTCTTGTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (17 bp):
GTTGGTAAAAGTCACTT
Found at i:13544 original size:18 final size:18
Alignment explanation
Indices: 13521--13555 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13511 TCTCCCGTAT
*
13521 TCTTCTTCTTAATTTTTC
1 TCTTCTCCTTAATTTTTC
*
13539 TCTTCTCCTTGATTTTT
1 TCTTCTCCTTAATTTTT
13556 TTTTTAAGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.23, G:0.03, T:0.66
Consensus pattern (18 bp):
TCTTCTCCTTAATTTTTC
Found at i:16087 original size:115 final size:115
Alignment explanation
Indices: 15885--16110 Score: 425
Period size: 115 Copynumber: 2.0 Consensus size: 115
15875 CAACAAGTGA
*
15885 TTGGTTCAAGTGATTTGACACTTATTCGTCTTACGTAAGAATGTATATATATATCTTGTATGAGG
1 TTGGTTCAAGTGATTTGACACTTATTCGTCTTACGTAAGAATGTATATATATATCTTGTATGAGA
*
15950 GTTGGGCCTTTGATGGGCCTCTGTGGCTAGTGAACCTGATTAGGCCCTTG
66 GTTGGGCCTTTGATGGACCTCTGTGGCTAGTGAACCTGATTAGGCCCTTG
*
16000 TTGGTTTAAGTGATTTGACACTTATTCGTCTTACGTAAGAATGTATATATATATCTTGTATGAGA
1 TTGGTTCAAGTGATTTGACACTTATTCGTCTTACGTAAGAATGTATATATATATCTTGTATGAGA
16065 GTTGGGCCTTTGATGGACCTCTGTGGCTAGTGAACCTGATTAGGCC
66 GTTGGGCCTTTGATGGACCTCTGTGGCTAGTGAACCTGATTAGGCC
16111 TTTTGGGCCT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 108 1.00
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (115 bp):
TTGGTTCAAGTGATTTGACACTTATTCGTCTTACGTAAGAATGTATATATATATCTTGTATGAGA
GTTGGGCCTTTGATGGACCTCTGTGGCTAGTGAACCTGATTAGGCCCTTG
Found at i:19586 original size:30 final size:31
Alignment explanation
Indices: 19550--19609 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
19540 TTTTTCAAAT
* *
19550 ATATTTCTA-AATTGCCATTATT-AAATAATA
1 ATATTTCAATAATT-CCACTATTAAAATAATA
19580 ATATTTCAATAATTCCACTATTAAAATAAT
1 ATATTTCAATAATTCCACTATTAAAATAAT
19610 GGAAATTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.42
Consensus pattern (31 bp):
ATATTTCAATAATTCCACTATTAAAATAATA
Found at i:20739 original size:22 final size:22
Alignment explanation
Indices: 20711--20944 Score: 149
Period size: 22 Copynumber: 10.5 Consensus size: 22
20701 TGTCTCTTTG
**
20711 TGGTTATCAAAATTTCATAACA
1 TGGTTATCAAAATTTCATAGGA
* *
20733 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* * *
20756 AGTTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
20778 TGGTTA-CTAAAATTTCATATGGA
1 TGGTTATC-AAAATTTCATA-GGA
*
20801 -AGTTATCAAAATTTCAT-GAGA
1 TGGTTATCAAAATTTCATAG-GA
* *
20822 AGATTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
20844 TAGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* *
20866 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* **
20890 AGGTTATTGAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
20912 TGATTATCACAAATTT-ATAGAA
1 TGGTTATCA-AAATTTCATAGGA
*
20934 AGGTTATCAAA
1 TGGTTATCAAA
20945 GAGATTATCA
Statistics
Matches: 163, Mismatches: 34, Indels: 31
0.71 0.15 0.14
Matches are distributed among these distances:
20 1 0.01
21 6 0.04
22 112 0.69
23 27 0.17
24 17 0.10
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:20782 original size:45 final size:44
Alignment explanation
Indices: 20713--20813 Score: 123
Period size: 45 Copynumber: 2.3 Consensus size: 44
20703 TCTCTTTGTG
* * *
20713 GTTATCAAAATTTCATAACATGGTTATTATAATTTCATGA-GGAA
1 GTTATCAAAATTCCATAACATGGTTACTAAAATTTCAT-ATGGAA
***
20757 GTTTATCAAAATTCCATAGTGTGGTTACTAAAATTTCATATGGAA
1 G-TTATCAAAATTCCATAACATGGTTACTAAAATTTCATATGGAA
20802 GTTATCAAAATT
1 GTTATCAAAATT
20814 TCATGAGAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 13 0.27
45 36 0.73
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (44 bp):
GTTATCAAAATTCCATAACATGGTTACTAAAATTTCATATGGAA
Found at i:20856 original size:66 final size:68
Alignment explanation
Indices: 20713--20944 Score: 230
Period size: 66 Copynumber: 3.5 Consensus size: 68
20703 TCTCTTTGTG
* * * * *
20713 GTTATCAAAATTTCATA--ACATGGTTATTATAATTTCATGAGGAAGTTTATCAAAATTCCATAG
1 GTTACCAAAATTTCATAGGACA-GGTTATCAAAATTTCATGAGGAAGATTATCAAAATTTCATAG
*
20776 TGTG
65 TGTA
*
20780 GTTACTAAAATTTCATATGGA-A-GTTATCAAAATTTCATGA-GAAGATTATCAAAATTTCATAG
1 GTTACCAAAATTTCATA-GGACAGGTTATCAAAATTTCATGAGGAAGATTATCAAAATTTCATAG
20842 TGTA
65 TGTA
* * * **
20846 GTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC-TTAGGAAGGTTATTGAAATTTCATAG
1 GTTACCAAAATTTCATAGGA-CAGGTTATCAAAATTTCATGAGGAAGATTATCAAAATTTCATAG
20910 TGT-
65 TGTA
* *
20913 GATTATCACAAATTT-ATA-GAAAGGTTATCAAA
1 G-TTACCA-AAATTTCATAGGACAGGTTATCAAA
20945 GAGATTATCA
Statistics
Matches: 140, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
65 3 0.02
66 49 0.35
67 37 0.26
68 43 0.31
69 7 0.05
70 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (68 bp):
GTTACCAAAATTTCATAGGACAGGTTATCAAAATTTCATGAGGAAGATTATCAAAATTTCATAGT
GTA
Found at i:20994 original size:22 final size:21
Alignment explanation
Indices: 20968--21108 Score: 90
Period size: 22 Copynumber: 6.5 Consensus size: 21
20958 TGTCATACGA
20968 GGTTATAAGAATTTCATAGTAT
1 GGTTATAA-AATTTCATAGTAT
*
20990 GGTTAACAAAATTTCATATGTA-
1 GGTT-ATAAAATTTCATA-GTAT
* * *
21012 GGTTACTAATATTTCATGGGGA-
1 GGTTA-TAAAATTTCAT-AGTAT
*
21034 GGTTATCAAAATTTCATAGTGT
1 GGTTAT-AAAATTTCATAGTAT
* ** *
21056 GGTTAATAACATTTTTTAGTGT
1 GGTT-ATAAAATTTCATAGTAT
* *
21078 GGTTATCAAATTTCATA-TGAA
1 GGTTATAAAATTTCATAGT-AT
21099 GGTTATAAAA
1 GGTTATAAAA
21109 GTCTCAATTT
Statistics
Matches: 92, Mismatches: 19, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.01
21 21 0.23
22 62 0.67
23 8 0.09
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (21 bp):
GGTTATAAAATTTCATAGTAT
Found at i:21016 original size:44 final size:43
Alignment explanation
Indices: 20949--21108 Score: 148
Period size: 44 Copynumber: 3.7 Consensus size: 43
20939 ATCAAAGAGA
* *
20949 TTATCAAAATGTCATACG-AGGTTATAAGAATTTCATAGTATGG
1 TTATCAAAATTTCATATGTAGGTTATAA-AATTTCATAGTATGG
* * * *
20992 TTAACAAAATTTCATATGTAGGTTACTAATATTTCATGGGGA-GG
1 TTATCAAAATTTCATATGTAGGTTA-TAAAATTTCAT-AGTATGG
* ** *
21036 TTATCAAAATTTCATAGTGT-GGTTAATAACATTTTTTAGTGTGG
1 TTATCAAAATTTCATA-TGTAGGTT-ATAAAATTTCATAGTATGG
*
21080 TTATC-AAATTTCATATGAAGGTTATAAAA
1 TTATCAAAATTTCATATGTAGGTTATAAAA
21109 GTCTCAATTT
Statistics
Matches: 95, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
42 7 0.07
43 30 0.32
44 49 0.52
45 9 0.09
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (43 bp):
TTATCAAAATTTCATATGTAGGTTATAAAATTTCATAGTATGG
Found at i:21255 original size:22 final size:22
Alignment explanation
Indices: 21194--21380 Score: 82
Period size: 22 Copynumber: 8.6 Consensus size: 22
21184 AAAGATCGGA
* *
21194 TTATCAAAATTT-ATAG-GAAG
1 TTATCAAAATTTCAAAGTGATG
* * * *
21214 ATTATTAAAATTTTATAGTGTTG
1 -TTATCAAAATTTCAAAGTGATG
*
21237 TTATCAAAATTTCAAAGTGAAG
1 TTATCAAAATTTCAAAGTGATG
*
21259 TTATCAAAATTACATAA-T-ATG
1 TTATCAAAATTTCA-AAGTGATG
* * **
21280 ATTATCAAAATTTCATAGAGGGG
1 -TTATCAAAATTTCAAAGTGATG
* * * * * *
21303 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCAAAGTGATG
*
21325 TTATCAAAATTTCATAA-AGA-G
1 TTATCAAAATTTCA-AAGTGATG
* *
21346 TTATCAAATTTTCAAAATG-TG
1 TTATCAAAATTTCAAAGTGATG
*
21367 ATTACCAAAATTTC
1 -TTATCAAAATTTC
21381 GTAGTGGTAT
Statistics
Matches: 129, Mismatches: 27, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
20 2 0.02
21 30 0.23
22 91 0.71
23 6 0.05
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCAAAGTGATG
Found at i:21292 original size:66 final size:64
Alignment explanation
Indices: 21194--21357 Score: 152
Period size: 66 Copynumber: 2.5 Consensus size: 64
21184 AAAGATCGGA
* * * ** * * *
21194 TTATCAAAATT-TATAGGAAGATTATTAAAATTTTATAGTGTTGTTATCAAAATTTCAAAGTGAA
1 TTATCAAAATTACATA--AAGATTATCAAAATTTTATAGAGGGGTCAACAAAATTTCAAAGAGAA
21258 G
64 G
* * * *
21259 TTATCAAAATTACATAATATGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAG
1 TTATCAAAATTACATAA-A-GATTATCAAAATTTTATAGAGGGGTCAACAAAATTTCAAAGAGAA
21324 G
64 G
*
21325 TTATCAAAATTTCATAAAGAGTTATC-AAATTTT
1 TTATCAAAATTACATAAAGA-TTATCAAAATTTT
21358 CAAAATGTGA
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
64 9 0.11
65 18 0.22
66 54 0.67
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (64 bp):
TTATCAAAATTACATAAAGATTATCAAAATTTTATAGAGGGGTCAACAAAATTTCAAAGAGAAG
Found at i:21356 original size:20 final size:22
Alignment explanation
Indices: 21169--21359 Score: 108
Period size: 22 Copynumber: 8.6 Consensus size: 22
21159 CATAGAGTAA
*
21169 TTATCGAAATTTCATAAAGATCGG
1 TTATCAAAATTTCATAAAGA--GG
21193 ATTATCAAAATTT-ATAGGAAGA--
1 -TTATCAAAATTTCATA--AAGAGG
* * ** **
21215 TTATTAAAATTTTATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
* *
21237 TTATCAAAATTTCA-AAGTGAAG
1 TTATCAAAATTTCATAA-AGAGG
*
21259 TTATCAAAATTACATAATATGA--
1 TTATCAAAATTTCATAA-A-GAGG
* *
21281 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAAAGAGG
* * * *
21303 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAAAGAGG
21325 TTATCAAAATTTCATAAAGA-G
1 TTATCAAAATTTCATAAAGAGG
*
21346 TTATCAAATTTTCA
1 TTATCAAAATTTCA
21360 AAATGTGATT
Statistics
Matches: 131, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
20 2 0.02
21 27 0.21
22 80 0.61
23 2 0.02
24 5 0.04
25 11 0.08
26 4 0.03
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:21426 original size:22 final size:22
Alignment explanation
Indices: 21400--21623 Score: 114
Period size: 22 Copynumber: 10.5 Consensus size: 22
21390 TTTCTGGGGA
21400 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* * *
21422 GGTTA-CCAAA--T--TAGGAA
1 GGTTATCAAAATTTCATAGTAT
* * *
21439 GGTTATTAAACTTT--TATTAT
1 GGTTATCAAAATTTCATAGTAT
* *
21459 GGAGTAATCAAAATTTCA-AGGA-
1 GG-TTA-TCAAAATTTCATAGTAT
* *
21481 GGATATCAAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAGT-AT
*
21503 GGTTATCAAAATTTCATAGTTT
1 GGTTATCAAAATTTCATAGTAT
* * * *
21525 AGTTTTCAAATTTTCATAAG-AG
1 GGTTATCAAAATTTCAT-AGTAT
21547 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* * *
21569 -GTAGATCAAAATTTCATAGGAA
1 GGT-TATCAAAATTTCATAGTAT
* * *
21591 GATTAACAAAATTTCATAATGA-
1 GGTTATCAAAATTTCATAGT-AT
21613 GGTTATCAAAA
1 GGTTATCAAAA
21624 AATCATAGGG
Statistics
Matches: 148, Mismatches: 38, Indels: 32
0.68 0.17 0.15
Matches are distributed among these distances:
17 9 0.06
18 2 0.01
19 1 0.01
20 17 0.11
21 14 0.09
22 98 0.66
23 7 0.05
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:21606 original size:66 final size:65
Alignment explanation
Indices: 21467--21623 Score: 167
Period size: 66 Copynumber: 2.4 Consensus size: 65
21457 ATGGAGTAAT
* * * ** **
21467 CAAAATTTCA-AGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTT
1 CAAAATTTCATAAGAGGTTATCAAAATTTCATATGAAGGTGATCAAAATTTCATAGTGAAGTTAA
* * *
21531 CAAATTTTCATAAGAGGGTTATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAG-GAAGAT
1 CAAAATTTCATAAGA-GGTTATCAAAATTTCATATGAAGGT-GATCAAAATTTCATAGTGAAG-T
21594 TAA
63 TAA
21597 CAAAATTTCATAATGAGGTTATCAAAA
1 CAAAATTTCATAA-GAGGTTATCAAAA
21624 AATCATAGGG
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
64 9 0.12
65 9 0.12
66 57 0.74
67 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (65 bp):
CAAAATTTCATAAGAGGTTATCAAAATTTCATATGAAGGTGATCAAAATTTCATAGTGAAGTTAA
Found at i:21621 original size:44 final size:44
Alignment explanation
Indices: 21465--22012 Score: 178
Period size: 44 Copynumber: 12.3 Consensus size: 44
21455 TTATGGAGTA
* * *
21465 ATCAAAATTTC--AAGGAGGATATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGGAAGGTT
* * * * * *
21507 ATCAAAATTTCATAGTTTA-GTTTTCAAATTTTCATAAGAGGGTT
1 ATCAAAATTTCATA-ATGAGGTTATCAAAATTTCATAGGAAGGTT
* * * *
21551 ATCAAAATTTCATAGT-ATGTAGATCAAAATTTCATAGGAAGATT
1 ATCAAAATTTCATAATGAGGT-TATCAAAATTTCATAGGAAGGTT
* ** * *
21595 AACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGCTT
1 ATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGGAAGGTT
* * * * * *
21639 ATCAAAATTTGTAGTTATCAAGATT-TCATAAGGAGGTT-ATATGAAGGTTT
1 ATCAAAATTT-CA-TAAT-GAGGTTATCA-AA--A-TTTCATAGGAAGG-TT
* * * * * *
21689 ATCAAAATTTCATAGCTAGCGGGGTTATCACAATTTCATAGTATGATT
1 ATCAAAATTTCATA---A-TGAGGTTATCAAAATTTCATAGGAAGGTT
* * * * * *
21737 ATCAAAATTTTAGAGTGTGATTA-CTAACAA-TTCATATGG-ATGTT
1 ATCAAAATTTCATAATGAGGTTATC-AA-AATTTCATA-GGAAGGTT
* * * * * *
21781 TTTAAATTTTCATAA-CATGGTTATCAATATATCATATGG-AGGTT
1 ATCAAAATTTCATAATGA-GGTTATCAAAATTTCATA-GGAAGGTT
* * * * *
21825 ATCAACATCTCATAGTGTCGGTTATCAAAATTTCATTGGGAA-GTT
1 ATCAAAATTTCATAATG-AGGTTATCAAAATTTCA-TAGGAAGGTT
* * * * *
21870 ATCAAAATTTCATAGTGAAGTCT-TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAATGAGGT-TATCAAAATTTCATAGGAAGGTT
* * **
21914 AACAAAATTTCATAA-GA--TTA--AAAATATTTATAAAAAGGTT
1 ATCAAAATTTCATAATGAGGTTATCAAAAT-TTCATAGGAAGGTT
* * * *** * * *
21954 CTCGAAATTTCATAGTTTCGTTATTAGAATTTCATAGAAAGGTT
1 ATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGGAAGGTT
21998 ATCAAAATTTCATAA
1 ATCAAAATTTCATAA
22013 ATAGATCATC
Statistics
Matches: 360, Mismatches: 107, Indels: 76
0.66 0.20 0.14
Matches are distributed among these distances:
39 5 0.01
40 20 0.06
41 1 0.00
42 12 0.03
43 14 0.04
44 194 0.54
45 48 0.13
46 8 0.02
47 6 0.02
48 17 0.05
49 14 0.04
50 13 0.04
51 5 0.01
52 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAATGAGGTTATCAAAATTTCATAGGAAGGTT
Found at i:21629 original size:22 final size:22
Alignment explanation
Indices: 21604--21645 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21594 TAACAAAATT
* *
21604 TCATAATGAGGTTATCAAAAAA
1 TCATAAGGAGCTTATCAAAAAA
*
21626 TCATAGGGAGCTTATCAAAA
1 TCATAAGGAGCTTATCAAAA
21646 TTTGTAGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (22 bp):
TCATAAGGAGCTTATCAAAAAA
Found at i:21745 original size:22 final size:22
Alignment explanation
Indices: 21687--21885 Score: 75
Period size: 22 Copynumber: 8.8 Consensus size: 22
21677 ATATGAAGGT
*
21687 TTATCAAAATTTCATAGCTAGCGGGG
1 TTATCAAAATTTCATAG-TA---TGG
* *
21713 TTATCACAATTTCATAGTATGA
1 TTATCAAAATTTCATAGTATGG
* * * *
21735 TTATCAAAATTTTAGAGTGTGA
1 TTATCAAAATTTCATAGTATGG
*
21757 TTA-CTAACAA-TTCATATGGAT-G
1 TTATC-AA-AATTTCATA-GTATGG
* * * **
21779 TTTTTAAATTTTCATAACATGG
1 TTATCAAAATTTCATAGTATGG
* * *
21801 TTATCAATATATCATATGGA-GG
1 TTATCAAAATTTCATA-GTATGG
* * *
21823 TTATCAACATCTCATAGTGTCGG
1 TTATCAAAATTTCATAGTAT-GG
* * *
21846 TTATCAAAATTTCATTGGGA-AG
1 TTATCAAAATTTCA-TAGTATGG
21868 TTATCAAAATTTCATAGT
1 TTATCAAAATTTCATAGT
21886 GAAGTCTTCA
Statistics
Matches: 127, Mismatches: 36, Indels: 25
0.68 0.19 0.13
Matches are distributed among these distances:
21 7 0.06
22 81 0.64
23 19 0.15
24 2 0.02
25 2 0.02
26 16 0.13
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTATGG
Found at i:21871 original size:45 final size:45
Alignment explanation
Indices: 21799--21886 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
21789 TTCATAACAT
* * *
21799 GGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTC
1 GGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGTC
* *
21844 GGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGTG
1 GGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGTG
21887 AAGTCTTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (45 bp):
GGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGTC
Found at i:21889 original size:22 final size:22
Alignment explanation
Indices: 21799--21927 Score: 100
Period size: 22 Copynumber: 5.8 Consensus size: 22
21789 TTCATAACAT
* *
21799 GGTTATCAATATATCATA-TGGA
1 GGTTATCAAAATTTCATAGT-GA
* * *
21821 GGTTATCAACATCTCATAGTGTC
1 GGTTATCAAAATTTCATAGTG-A
* *
21844 GGTTATCAAAATTTCATTGGGA
1 GGTTATCAAAATTTCATAGTGA
*
21866 AGTTATCAAAATTTCATAGTGA
1 GGTTATCAAAATTTCATAGTGA
* * * *
21888 AGTCT-TCAAAATTCCTTAGGGA
1 GGT-TATCAAAATTTCATAGTGA
*
21910 GGTTAACAAAATTTCATA
1 GGTTATCAAAATTTCATA
21928 AGATTAAAAA
Statistics
Matches: 85, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
21 1 0.01
22 65 0.76
23 19 0.22
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGA
Found at i:22023 original size:22 final size:22
Alignment explanation
Indices: 21981--22026 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
21971 TCGTTATTAG
* *
21981 AATTTCATAGAAAGGTTATCAA
1 AATTTCATAGAAAGATCATCAA
22003 AATTTCATA-AATAGATCATCAA
1 AATTTCATAGAA-AGATCATCAA
22025 AA
1 AA
22027 ATAGTGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (22 bp):
AATTTCATAGAAAGATCATCAA
Found at i:22203 original size:31 final size:31
Alignment explanation
Indices: 22168--22231 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
22158 AACTTTATGT
* *
22168 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGCACCCTTATTTTTAAAACATA
*
22199 TTTCCAATTGCACCCTTTTTTTTAAAACATA
1 TTTCCAATTGCACCCTTATTTTTAAAACATA
22230 TT
1 TT
22232 ACTAAATTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGCACCCTTATTTTTAAAACATA
Found at i:22380 original size:30 final size:31
Alignment explanation
Indices: 22327--22391 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
22317 AACTTTATGT
* * *
22327 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGCACCATTATTTTTAAAACATA
22358 TTTCCAATTGCACCATT-TTTTTAAAACATA
1 TTTCCAATTGCACCATTATTTTTAAAACATA
22388 TTTC
1 TTTC
22392 TAACTTGACA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGCACCATTATTTTTAAAACATA
Found at i:23552 original size:16 final size:16
Alignment explanation
Indices: 23531--23562 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
23521 CACAATTCAG
23531 AAAGCAGAAAAGCTCT
1 AAAGCAGAAAAGCTCT
23547 AAAGCAGAAAAGCTCT
1 AAAGCAGAAAAGCTCT
23563 GAAATATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
AAAGCAGAAAAGCTCT
Found at i:24432 original size:19 final size:20
Alignment explanation
Indices: 24405--24442 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
24395 TACTATTATT
24405 TTTTGAA-TTCAATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
24425 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
24443 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:24615 original size:22 final size:22
Alignment explanation
Indices: 24589--24738 Score: 63
Period size: 22 Copynumber: 6.7 Consensus size: 22
24579 TGTCTCTATG
24589 TGGTTATCAAAATTTCATAATA
1 TGGTTATCAAAATTTCATAATA
* * * **
24611 TGGTTCTTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AATA
* ** * *
24634 -GGTTAGCAAAATTTTGTAGTG
1 TGGTTATCAAAATTTCATAATA
* *
24655 TAGTTACCAAAATTTCAT-ATGGA
1 TGGTTATCAAAATTTCATAAT--A
* * *
24678 -AGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAATA
* * *
24699 TGATTACCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAATA
*
24721 TCAGGTTATTAAAATTTC
1 T--GGTTATCAAAATTTC
24739 TTAGGTTGGT
Statistics
Matches: 89, Mismatches: 31, Indels: 14
0.66 0.23 0.10
Matches are distributed among these distances:
21 3 0.03
22 71 0.80
23 3 0.03
24 12 0.13
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAATA
Found at i:24669 original size:44 final size:44
Alignment explanation
Indices: 24621--24717 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
24611 TGGTTCTTAT
* **
24621 AATTTCATGA-GGAGGTTAGCAAAATTTTGTAGTGT-AGTTACCAA
1 AATTTCAT-ATGGAAGTTAGCAAAATTTCATAGTGTGA-TTACCAA
*
24665 AATTTCATATGGAAGTTATCAAAATTTCATAGTGTGATTACCAA
1 AATTTCATATGGAAGTTAGCAAAATTTCATAGTGTGATTACCAA
24709 AATTTCATA
1 AATTTCATA
24718 AGATCAGGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
43 1 0.02
44 45 0.96
45 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
AATTTCATATGGAAGTTAGCAAAATTTCATAGTGTGATTACCAA
Found at i:24856 original size:22 final size:22
Alignment explanation
Indices: 24828--25083 Score: 87
Period size: 22 Copynumber: 11.5 Consensus size: 22
24818 ATCATAGAAG
* *
24828 AATTTCATAGTGTGATTAACAA
1 AATTTCATAGTGTGGTTATCAA
* * *
24850 AATTTCATGGGGAGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
*
24872 AATTTTATAGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * *
24894 AATTCCATA-TGAAGGTTATAAAA
1 AATTTCATAGTG-TGGTTAT-CAA
* *
24917 GTCTCAATTTCATA-AG-GAG-TACCAA
1 -----AATTTCATAGTGTG-GTTATCAA
* * **
24942 AAATTGATAG-AAGGTTATC-A
1 AATTTCATAGTGTGGTTATCAA
* * *
24962 AATCTT-ATA-AGTGATTATCGA
1 AAT-TTCATAGTGTGGTTATCAA
* *
24983 AATTTCATAGAGGTCAGATTATCAA
1 AATTTCATAG-TGT--GGTTATCAA
* *
25008 AATTCCATAGTGTTGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * *
25030 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * * *
25052 AATTACATAATGTGATTATCAG
1 AATTTCATAGTGTGGTTATCAA
25074 AATTTCATAG
1 AATTTCATAG
25084 AGGGGTCAAC
Statistics
Matches: 170, Mismatches: 45, Indels: 38
0.67 0.18 0.15
Matches are distributed among these distances:
20 22 0.13
21 15 0.09
22 95 0.56
23 4 0.02
24 2 0.01
25 19 0.11
26 3 0.02
27 1 0.01
28 9 0.05
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTATCAA
Found at i:24910 original size:44 final size:43
Alignment explanation
Indices: 24828--24916 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 43
24818 ATCATAGAAG
* * *
24828 AATTTCATAGTGTGATTAACAAAATTTCATGGGGAGGTTATCAA
1 AATTTCATAGTGTGATTAACAAAATTCCATAGGAAGGTTAT-AA
* * * *
24872 AATTTTATAGTGTGGTTATCAAAATTCCATATGAAGGTTATAA
1 AATTTCATAGTGTGATTAACAAAATTCCATAGGAAGGTTATAA
24915 AA
1 AA
24917 GTCTCAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 4 0.11
44 34 0.89
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (43 bp):
AATTTCATAGTGTGATTAACAAAATTCCATAGGAAGGTTATAA
Found at i:25097 original size:44 final size:44
Alignment explanation
Indices: 25005--25099 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 44
24995 GTCAGATTAT
* * * * *
25005 CAAAATTCCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTAT
1 CAAAATTACATAATGTTGTTATCAAAATTTCAAAGAGAGGTCAA
* * *
25049 CAAAATTACATAATG-TGATTATCAGAATTTCATAGAGGGGTCAA
1 CAAAATTACATAATGTTG-TTATCAAAATTTCAAAGAGAGGTCAA
25093 CAAAATT
1 CAAAATT
25100 TTACAAAAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (44 bp):
CAAAATTACATAATGTTGTTATCAAAATTTCAAAGAGAGGTCAA
Found at i:25139 original size:22 final size:22
Alignment explanation
Indices: 24974--25169 Score: 85
Period size: 22 Copynumber: 8.8 Consensus size: 22
24964 TCTTATAAGT
* *
24974 GATTATCGAAATTTCATAGAGGTCA
1 GATTATCAAAATTTCATA-AAG--A
* ** *
24999 GATTATCAAAATTCCATAGTGTT
1 GATTATCAAAATTTCATAAAG-A
*
25022 G-TTATCAAAATTTCA-AAGCGA
1 GATTATCAAAATTTCATAA-AGA
* * * *
25043 GGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAAAGA
* * *
25065 GATTATCAGAATTTCATAGAGG
1 GATTATCAAAATTTCATAAAGA
* * * * * *
25087 GGTCAACAAAATTTTACAAAAA
1 GATTATCAAAATTTCATAAAGA
* *
25109 GGTTTTCAAAATTTCATAAAGA
1 GATTATCAAAATTTCATAAAGA
* *
25131 GATTATCAAATTTTCA-AAATGT
1 GATTATCAAAATTTCATAAA-GA
25153 GATTA-CAAAAATTTCAT
1 GATTATC-AAAATTTCAT
25170 TGTGGTATTT
Statistics
Matches: 126, Mismatches: 39, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
21 6 0.05
22 100 0.79
23 3 0.02
24 1 0.01
25 16 0.13
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (22 bp):
GATTATCAAAATTTCATAAAGA
Found at i:25301 original size:20 final size:20
Alignment explanation
Indices: 25252--25304 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
25242 TTATTGCGTA
*
25252 ATCAAAATTTCATGGAGGAT
1 ATCAAAATTTCATGGAGAAT
* *
25272 ATTAATATTTC-TGGGAGAAT
1 ATCAAAATTTCAT-GGAGAAT
25292 ATCAAAATTTCAT
1 ATCAAAATTTCAT
25305 ATGAAGGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (20 bp):
ATCAAAATTTCATGGAGAAT
Found at i:25317 original size:22 final size:22
Alignment explanation
Indices: 25291--25432 Score: 110
Period size: 22 Copynumber: 6.5 Consensus size: 22
25281 TCTGGGAGAA
25291 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
25313 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
25335 TTTCAAAACTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* * *
25357 TATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGT
* *
25379 TAACAAAATTTCACAATG-AGGT
1 TATCAAAATTTCA-TATGAAGGT
** * *
25401 TATCAAAAAAT-ATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
25422 TATCAAAATTT
1 TATCAAAATTT
25433 GTAGTTATCA
Statistics
Matches: 91, Mismatches: 25, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
20 2 0.02
21 14 0.15
22 71 0.78
23 4 0.04
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:25386 original size:44 final size:43
Alignment explanation
Indices: 25252--25505 Score: 161
Period size: 44 Copynumber: 6.0 Consensus size: 43
25242 TTATTGCGTA
* * * * *
25252 ATCAAAATTTCAT-GGAGGATATTAATATTTC-T-GGGAGAAT
1 ATCAAAATTTCATAAGAGGTTATCAAAATTTCATAGGGAGATT
* **
25292 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAG-TT
1 ATCAAAATTTCATAAG-AGGTTATCAAAATTTCATAG-GGAGATT
* *
25336 TTCAAAACTTCATAAGAGGGTTATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAAGA-GGTTATCAAAATTTCATAGGGAGATT
* * ** *
25380 AACAAAATTTCACAATGAGGTTATCAAAAAAT-ATAGGGAGGTT
1 ATCAAAATTTCATAA-GAGGTTATCAAAATTTCATAGGGAGATT
* * * *
25423 ATCAAAATTT-GT---A-GTTATCAAGATTTCATA-AGAAAGTT
1 ATCAAAATTTCATAAGAGGTTATCAAAATTTCATAGGGAGA-TT
* * * *
25461 ATCAAAGTTTTATAAGGAGGTTTATCAAAATTTTATAGGAAGATT
1 ATCAAAATTTCATAA-GAGG-TTATCAAAATTTCATAGGGAGATT
25506 TCATAGCGAG
Statistics
Matches: 161, Mismatches: 35, Indels: 31
0.71 0.15 0.14
Matches are distributed among these distances:
37 12 0.07
38 15 0.09
39 1 0.01
40 13 0.08
41 1 0.01
42 13 0.08
43 24 0.15
44 60 0.37
45 20 0.12
46 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.35
Consensus pattern (43 bp):
ATCAAAATTTCATAAGAGGTTATCAAAATTTCATAGGGAGATT
Found at i:25475 original size:22 final size:22
Alignment explanation
Indices: 25435--25497 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
25425 CAAAATTTGT
*
25435 AGTTATC-AAGATTTCATAAGAA
1 AGTTATCAAAG-TTTTATAAGAA
*
25457 AGTTATCAAAGTTTTATAAGGA
1 AGTTATCAAAGTTTTATAAGAA
* *
25479 GGTTTATCAAAATTTTATA
1 AG-TTATCAAAGTTTTATA
25498 GGAAGATTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.38
Consensus pattern (22 bp):
AGTTATCAAAGTTTTATAAGAA
Found at i:25561 original size:20 final size:21
Alignment explanation
Indices: 25517--25561 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
25507 CATAGCGAGG
*
25517 TTATCACAATTTCATAGTGTAA
1 TTATCAAAATTTCA-AGTGTAA
*
25539 TTATCAAAATTTC-AGTGTGA
1 TTATCAAAATTTCAAGTGTAA
25559 TTA
1 TTA
25562 CTAACAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
TTATCAAAATTTCAAGTGTAA
Found at i:25663 original size:45 final size:44
Alignment explanation
Indices: 25592--25676 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
25582 TTTTAAATTT
*
25592 TCATAATGTGGTTATCAATATATCATATGGAGGTTATCAACATC
1 TCATAATGTGGTTATCAAAATATCATATGGAGGTTATCAACATC
* * * *
25636 TCATAGTGTTGGTTATCAAAATTTCATATTGAGGTTTTCAA
1 TCATAATG-TGGTTATCAAAATATCATATGGAGGTTATCAA
25677 AATTCCTTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 7 0.20
45 28 0.80
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (44 bp):
TCATAATGTGGTTATCAAAATATCATATGGAGGTTATCAACATC
Found at i:25680 original size:22 final size:22
Alignment explanation
Indices: 25590--25680 Score: 83
Period size: 22 Copynumber: 4.1 Consensus size: 22
25580 GTTTTTAAAT
* * *
25590 TTTCATAATGTGGTTATCAATA
1 TTTCATATTGAGGTTATCAAAA
* * *
25612 TATCATATGGAGGTTATCAACA
1 TTTCATATTGAGGTTATCAAAA
* * *
25634 TCTCATAGTGTTGGTTATCAAAA
1 TTTCATATTG-AGGTTATCAAAA
*
25657 TTTCATATTGAGGTTTTCAAAA
1 TTTCATATTGAGGTTATCAAAA
25679 TT
1 TT
25681 CCTTGGTTAA
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
22 36 0.67
23 18 0.33
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (22 bp):
TTTCATATTGAGGTTATCAAAA
Found at i:25918 original size:2 final size:2
Alignment explanation
Indices: 25911--25940 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25901 CTAAAACTAG
25911 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
25941 AGTGAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28744 original size:46 final size:48
Alignment explanation
Indices: 28684--28781 Score: 173
Period size: 46 Copynumber: 2.1 Consensus size: 48
28674 TCTAAATTAA
*
28684 ACTAACCATACCTACATGAAACTATA-TT-TAATCTAATGTAATTAGC
1 ACTAACCATACCTACATGAAACCATATTTATAATCTAATGTAATTAGC
28730 ACTAACCATACCTACATGAAACCATATTTATAATCTAATGTAATTAGC
1 ACTAACCATACCTACATGAAACCATATTTATAATCTAATGTAATTAGC
28778 ACTA
1 ACTA
28782 GGAATTGGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 25 0.51
47 2 0.04
48 22 0.45
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (48 bp):
ACTAACCATACCTACATGAAACCATATTTATAATCTAATGTAATTAGC
Found at i:29955 original size:31 final size:31
Alignment explanation
Indices: 29920--29979 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
29910 ATTTTTTTCG
*
29920 ATTGTACCCCTATT-TTTAAAATATATTTCCA
1 ATTGTA-CCCTATTCTTTAAAACATATTTCCA
*
29951 ATTGTACCCTTTTCTTTAAAACATATTTC
1 ATTGTACCCTATTCTTTAAAACATATTTC
29980 TAAATTGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTGTACCCTATTCTTTAAAACATATTTCCA
Found at i:30309 original size:19 final size:19
Alignment explanation
Indices: 30294--30331 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
30284 TACTATTATT
30294 TTTTGAATTTAATATTTTA
1 TTTTGAATTTAATATTTTA
*
30313 TTTTTAATTTCAAT-TTTTA
1 TTTTGAATTT-AATATTTTA
30332 AATTTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTGAATTTAATATTTTA
Found at i:30330 original size:14 final size:14
Alignment explanation
Indices: 30312--30340 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30302 TTAATATTTT
30312 ATTTTT-AATTTCA
1 ATTTTTAAATTTCA
30325 ATTTTTAAATTTCA
1 ATTTTTAAATTTCA
30339 AT
1 AT
30341 AAAAAGATTA
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:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTTTAAATTTCA
Found at i:30560 original size:22 final size:21
Alignment explanation
Indices: 30532--30587 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
30522 TTATCATTCT
*
30532 AATTTCATCAGGAGGTTATCAA
1 AATTTCAT-AGGAGGTTACCAA
*
30554 AATTTCATAGTGTGGTTACCAA
1 AATTTCATAG-GAGGTTACCAA
30576 AATTTCATAGGA
1 AATTTCATAGGA
30588 TCAGGTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (21 bp):
AATTTCATAGGAGGTTACCAA
Found at i:30616 original size:46 final size:46
Alignment explanation
Indices: 30544--30632 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
30534 TTTCATCAGG
*
30544 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATC
1 AGGTTATCAAAATCTCATAGTGTGGTTACCAAAATTTCATAGGATC
* * ***
30590 AGGTTATTAAAATCTCTTAG-GTTGGTTATTGAAATTTCATAGG
1 AGGTTATCAAAATCTCATAGTG-TGGTTACCAAAATTTCATAGG
30633 GTGGTTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
45 1 0.03
46 35 0.97
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (46 bp):
AGGTTATCAAAATCTCATAGTGTGGTTACCAAAATTTCATAGGATC
Found at i:30619 original size:22 final size:22
Alignment explanation
Indices: 30545--30639 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 22
30535 TTCATCAGGA
* * *
30545 GGTTATCAAAATTTCATAGTGT
1 GGTTATTAAAATCTCATAGGGT
** * *
30567 GGTTACCAAAATTTCATAGGAT
1 GGTTATTAAAATCTCATAGGGT
* *
30589 CAGGTTATTAAAATCTCTTAGGTT
1 --GGTTATTAAAATCTCATAGGGT
* *
30613 GGTTATTGAAATTTCATAGGGT
1 GGTTATTAAAATCTCATAGGGT
30635 GGTTA
1 GGTTA
30640 ATTATCACAA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
22 42 0.71
24 17 0.29
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (22 bp):
GGTTATTAAAATCTCATAGGGT
Found at i:30959 original size:22 final size:22
Alignment explanation
Indices: 30863--31081 Score: 117
Period size: 22 Copynumber: 9.9 Consensus size: 22
30853 CTAATGAAGT
* *
30863 GATTATCGAAATTTCATTGAGA
1 GATTATCAAAATTTCATAGAGA
*
30885 TCGGATTATCAAAATTT-ATAGAAA
1 ---GATTATCAAAATTTCATAGAGA
* *
30909 GATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAGAG-A
* * *
30932 G-GTATCAAAATTTCAAAGCGA
1 GATTATCAAAATTTCATAGAGA
* *
30953 GATTATCAAAATTACATA-ATGT
1 GATTATCAAAATTTCATAGA-GA
* *
30975 GATTATCAGAATTTCATAGAGG
1 GATTATCAAAATTTCATAGAGA
* * * * * *
30997 GGTCAACAAAATTTTATAAAAA
1 GATTATCAAAATTTCATAGAGA
*
31019 TG-TTATCAAAATTTCATAAAGA
1 -GATTATCAAAATTTCATAGAGA
* * * *
31041 GGTTATCAAATTTTCAGA-ATGT
1 GATTATCAAAATTTCATAGA-GA
31063 GATTA-CAAAAATTTCATAG
1 GATTATC-AAAATTTCATAG
31082 TGGTATTTCT
Statistics
Matches: 148, Mismatches: 36, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
21 18 0.12
22 109 0.74
23 3 0.02
24 5 0.03
25 13 0.09
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
GATTATCAAAATTTCATAGAGA
Found at i:31187 original size:20 final size:20
Alignment explanation
Indices: 31162--31212 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
31152 TTATGGAGTA
31162 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
31182 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
31201 ATCAAAATTTCA
1 ATCAAAATTTCA
31213 TATGAAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:31229 original size:22 final size:21
Alignment explanation
Indices: 31195--31333 Score: 68
Period size: 22 Copynumber: 6.4 Consensus size: 21
31185 AAAATTCAGG
* *
31195 GAGGATATCAAAATTTCATAT
1 GAGGTTATTAAAATTTCATAT
31216 GAAGGTTATTAAAATTTCATAGTT
1 G-AGGTTATTAAAATTTCATA--T
* * *
31240 TA-GTT-TTCAAAATTTCACAA
1 GAGGTTATT-AAAATTTCATAT
*
31260 GAGGTTATCAAAATTTCATAGT
1 GAGGTTATTAAAATTTCATA-T
* * * *
31282 G-TGTAGATCAAAATTTCATAGG
1 GAGGT-TATTAAAATTTCATA-T
* **
31304 GAGATTAACAAAATTTCATAAT
1 GAGGTTATTAAAATTTCAT-AT
31326 GAGGTTAT
1 GAGGTTAT
31334 CGAAAAATCA
Statistics
Matches: 89, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
20 1 0.01
21 18 0.20
22 66 0.74
23 3 0.03
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
GAGGTTATTAAAATTTCATAT
Found at i:31293 original size:43 final size:42
Alignment explanation
Indices: 31200--31323 Score: 133
Period size: 44 Copynumber: 2.9 Consensus size: 42
31190 TCAGGGAGGA
* *
31200 TATCAAAATTTCATATGAAGGTTATTAAAATTTCATAGTTTAG
1 TATCAAAATTTCATAAG-AGGTTATCAAAATTTCATAGTTTAG
* *
31243 TTTTCAAAATTTCACAAGAGGTTATCAAAATTTCATAGTGTGTAG
1 -TATCAAAATTTCATAAGAGGTTATCAAAATTTCATAGT-T-TAG
* * *
31288 -ATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
1 TATCAAAATTTCATA-AGAGGTTATCAAAATTTCATA
31324 ATGAGGTTAT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 32 0.47
44 33 0.49
45 3 0.04
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (42 bp):
TATCAAAATTTCATAAGAGGTTATCAAAATTTCATAGTTTAG
Found at i:31344 original size:22 final size:21
Alignment explanation
Indices: 31319--31360 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
31309 TAACAAAATT
*
31319 TCATAATGAGGTTATCGAAAAA
1 TCATAAGGAGGTTATC-AAAAA
*
31341 TCATAGGGAGGTTATCAAAA
1 TCATAAGGAGGTTATCAAAA
31361 TTTGTAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (21 bp):
TCATAAGGAGGTTATCAAAAA
Found at i:31420 original size:23 final size:22
Alignment explanation
Indices: 31390--31493 Score: 88
Period size: 23 Copynumber: 4.6 Consensus size: 22
31380 CATAAGAAAA
31390 TTATCAAAATTTTATAAGGAGGT
1 TTATCAAAATTTTAT-AGGAGGT
*
31413 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGG-AGGT
*
31436 TTAT-AAGAATTTCATAGCGAGG-
1 TTATCAA-AATTTTATAG-GAGGT
* * * *
31458 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAG-GAGGT
31480 TTATCAAAATTTTA
1 TTATCAAAATTTTA
31494 GAGTGTGATT
Statistics
Matches: 68, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
21 1 0.01
22 32 0.47
23 34 0.50
24 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGAGGT
Found at i:31483 original size:22 final size:22
Alignment explanation
Indices: 31443--31517 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
31433 GATTTATAAG
* * *
31443 AATTTCATAGCGAGGTTATCAC
1 AATTTCATAGTGTGATTATCAC
*
31465 AATTTCATAGTGTGATTATCAA
1 AATTTCATAGTGTGATTATCAC
* * *
31487 AATTTTAGAGTGTGATTACTAAC
1 AATTTCATAGTGTGATTA-TCAC
31510 AA-TTCATA
1 AATTTCATA
31518 TGGAGGTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
22 38 0.90
23 4 0.10
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
AATTTCATAGTGTGATTATCAC
Found at i:33339 original size:35 final size:35
Alignment explanation
Indices: 33300--33366 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
33290 ACATACAAGA
33300 ATATAAGATAAT-CTAAACAAAAAAAAACAGTCTAC
1 ATATAAGATAATACTAAA-AAAAAAAAACAGTCTAC
* *
33335 ATATAAGATAATATTTAAAAAAAAAAACAGTC
1 ATATAAGATAATACTAAAAAAAAAAAACAGTC
33367 CACCAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 26 0.90
36 3 0.10
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.22
Consensus pattern (35 bp):
ATATAAGATAATACTAAAAAAAAAAAACAGTCTAC
Done.