Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012131.1 Kokia drynarioides strain JFW-HI SEQ_127130, 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: 63649
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:65 original size:17 final size:17
Alignment explanation
Indices: 34--66 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24 CAAACACTTA
34 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
51 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
67 AATCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:1384 original size:16 final size:17
Alignment explanation
Indices: 1365--1402 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1355 TAATATTAAA
1365 TAAATAAATA-ATTATT
1 TAAATAAATATATTATT
*
1381 TAAAT-AATATATTTTT
1 TAAATAAATATATTATT
1397 TAAATA
1 TAAATA
1403 CTGATACGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATAAATATATTATT
Found at i:1788 original size:17 final size:17
Alignment explanation
Indices: 1766--1799 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1756 AAAAAAATTC
1766 ATTTAAA-AGTTATTTAA
1 ATTTAAATA-TTATTTAA
1783 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
1800 TTATGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:4784 original size:6 final size:6
Alignment explanation
Indices: 4766--4818 Score: 65
Period size: 6 Copynumber: 8.8 Consensus size: 6
4756 TAGAATTAAA
*
4766 TATGTT TAGGTT TATGTT TATGTT TATGTT TATGTACT TA--TT TATGTT
1 TATGTT TATGTT TATGTT TATGTT TATGTT TATGT--T TATGTT TATGTT
4814 TATGT
1 TATGT
4819 ATGAAAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 3 0.07
6 35 0.85
8 3 0.07
ACGTcount: A:0.19, C:0.02, G:0.17, T:0.62
Consensus pattern (6 bp):
TATGTT
Found at i:4947 original size:26 final size:26
Alignment explanation
Indices: 4892--4947 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
4882 GCTAAACCTC
**
4892 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
4918 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
4944 ATTA
1 ATTA
4948 TTTCCAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:4960 original size:28 final size:28
Alignment explanation
Indices: 4925--4982 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
4915 ATTATTAAAT
*
4925 AAATTCAAATT-TAAACAGAATTATTTCC
1 AAATTC-AATTATAAACAGAATTAATTCC
**
4953 AAATTCAATTATAAACTTAATTAATTCC
1 AAATTCAATTATAAACAGAATTAATTCC
4981 AA
1 AA
4983 CATAAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (28 bp):
AAATTCAATTATAAACAGAATTAATTCC
Found at i:10325 original size:27 final size:27
Alignment explanation
Indices: 10246--10339 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
10236 CCTACTTAAT
* *
10246 AGACGACACAAAAGGTGCCTACCTGAC
1 AGACGGCACCAAAGGTGCCTACCTGAC
* * * * *
10273 AGGCGGTACCAAAAGTGTCTATCTGAC
1 AGACGGCACCAAAGGTGCCTACCTGAC
* * *
10300 AGACGGCACCGATGGTGCCTACCTGAA
1 AGACGGCACCAAAGGTGCCTACCTGAC
10327 ATG-CGGCACCAAA
1 A-GACGGCACCAAA
10340 ACCCAATTTA
Statistics
Matches: 49, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
27 48 0.98
28 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.26, T:0.15
Consensus pattern (27 bp):
AGACGGCACCAAAGGTGCCTACCTGAC
Found at i:10911 original size:22 final size:23
Alignment explanation
Indices: 10869--10912 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
10859 ATTTTTTAAG
10869 AAGGAAATGAAGCAAAATTTTTT
1 AAGGAAATGAAGCAAAATTTTTT
10892 AAGGAAA-GAAAGC-AAATTTTT
1 AAGGAAATG-AAGCAAAATTTTT
10913 GAAAAGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (23 bp):
AAGGAAATGAAGCAAAATTTTTT
Found at i:14032 original size:5 final size:5
Alignment explanation
Indices: 14022--14048 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
14012 CGATGAAGTC
14022 AACAA AACAA AACAA AACAA AACAA AA
1 AACAA AACAA AACAA AACAA AACAA AA
14049 TTAACTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:16032 original size:14 final size:14
Alignment explanation
Indices: 16015--16075 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
16005 GGTTCTAGTT
16015 TTTAGGGTTTAAGA
1 TTTAGGGTTTAAGA
* *
16029 TTTAGAGTTTTAGA
1 TTTAGGGTTTAAGA
* * *
16043 TATAAGGTTTAAGG
1 TTTAGGGTTTAAGA
* * *
16057 TTTAAGATTTAAGG
1 TTTAGGGTTTAAGA
16071 TTTAG
1 TTTAG
16076 TGTAATTAGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTTAGGGTTTAAGA
Found at i:16053 original size:21 final size:22
Alignment explanation
Indices: 16024--16075 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
16014 TTTTAGGGTT
* *
16024 TAAGATTTAGA-GTTTTAGATA
1 TAAGGTTTAGAGGTTTAAGATA
*
16045 TAAGGTTTA-AGGTTTAAGATT
1 TAAGGTTTAGAGGTTTAAGATA
16066 TAAGGTTTAG
1 TAAGGTTTAG
16076 TGTAATTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (22 bp):
TAAGGTTTAGAGGTTTAAGATA
Found at i:16088 original size:35 final size:35
Alignment explanation
Indices: 16015--16129 Score: 99
Period size: 35 Copynumber: 3.3 Consensus size: 35
16005 GGTTCTAGTT
* * * *
16015 TTTAGGGTTTAAGATTTAGAGTTTTAGATATAA--GG
1 TTTAAGGTTTAAGATTTA-AGGTTTAG-TGTAATTAG
16050 TTTAAGGTTTAAGATTTAAGGTTTAGTGTAATTAG
1 TTTAAGGTTTAAGATTTAAGGTTTAGTGTAATTAG
* * * * * *
16085 TTTAAGGTTTAGGGTTAAAGGATTAGGGTAATTAA
1 TTTAAGGTTTAAGATTTAAGGTTTAGTGTAATTAG
*
16120 TTTACGGTTT
1 TTTAAGGTTT
16130 TGGGTTTTAA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
33 4 0.06
34 7 0.10
35 56 0.84
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.43
Consensus pattern (35 bp):
TTTAAGGTTTAAGATTTAAGGTTTAGTGTAATTAG
Found at i:16135 original size:35 final size:35
Alignment explanation
Indices: 16050--16135 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
16040 AGATATAAGG
* * * * * *
16050 TTTAAGGTTTAAGATTTAAGGTTTAGTGTAATTAG
1 TTTAAGGTTTAGGGTTAAAGGATTAGGGTAATTAA
16085 TTTAAGGTTTAGGGTTAAAGGATTAGGGTAATTAA
1 TTTAAGGTTTAGGGTTAAAGGATTAGGGTAATTAA
* *
16120 TTTACGGTTTTGGGTT
1 TTTAAGGTTTAGGGTT
16136 TTAAATACAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.44
Consensus pattern (35 bp):
TTTAAGGTTTAGGGTTAAAGGATTAGGGTAATTAA
Found at i:18348 original size:23 final size:25
Alignment explanation
Indices: 18322--18368 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
18312 TTGAGATTAT
18322 CAATTTGT-C-AGAAGTAATTAATA
1 CAATTTGTACTAGAAGTAATTAATA
*
18345 CAATTTTTAACTAGAAGTAATTAA
1 CAATTTGT-ACTAGAAGTAATTAA
18369 AATTCTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
25 1 0.05
26 12 0.60
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (25 bp):
CAATTTGTACTAGAAGTAATTAATA
Found at i:19238 original size:10 final size:10
Alignment explanation
Indices: 19225--19256 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
19215 ACAACTTACC
19225 TTTCTTTTTT
1 TTTCTTTTTT
19235 TTTCTTTTTTT
1 TTTC-TTTTTT
19246 TTTCTTTTTT
1 TTTCTTTTTT
19256 T
1 T
19257 CTTCCTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:19245 original size:11 final size:11
Alignment explanation
Indices: 19225--19256 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
19215 ACAACTTACC
19225 TTTC-TTTTTT
1 TTTCTTTTTTT
19235 TTTCTTTTTTT
1 TTTCTTTTTTT
19246 TTTCTTTTTTT
1 TTTCTTTTTTT
19257 CTTCCTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:19575 original size:13 final size:12
Alignment explanation
Indices: 19552--19590 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
19542 ACCAGTTTTC
19552 TTTTTTT-AATA
1 TTTTTTTAAATA
19563 TTATTTTTAAATA
1 TT-TTTTTAAATA
19576 -TTTTTTAAATA
1 TTTTTTTAAATA
19587 TTTT
1 TTTT
19591 AATATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 12 0.48
12 9 0.36
13 4 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTTTAAATA
Found at i:21312 original size:29 final size:28
Alignment explanation
Indices: 21255--21320 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
21245 GAAAAAAAAG
* *
21255 GGGTCAAAATGAAGTTTTGGAGAGTTTA
1 GGGTTAAAATGAAGTTTTGGAAAGTTTA
* *
21283 GGGTTAAAATGTAGTTTTGGAAAATTTTA
1 GGGTTAAAATGAAGTTTTGG-AAAGTTTA
*
21312 GGGATAAAA
1 GGGTTAAAA
21321 ATGTCATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (28 bp):
GGGTTAAAATGAAGTTTTGGAAAGTTTA
Found at i:21361 original size:30 final size:28
Alignment explanation
Indices: 21336--21593 Score: 171
Period size: 29 Copynumber: 8.9 Consensus size: 28
21326 ATTTTGGGAG
* *
21336 AGTTCGGGGTAAAAATATGATTTTTGGA
1 AGTTCGGGGTAAAAATATAATTTTTAGA
* * *
21364 AGTTAAGGGGCAAAAATGTAACTTTTTGAGA
1 AGTT-CGGGGTAAAAATATAA-TTTTT-AGA
* * *
21395 AGTTCGAGGGTAAAAATGT-GTTTTTTGAA
1 AGTTCG-GGGTAAAAATATAATTTTTAG-A
* *
21424 AGTTTAGGGGTAAAAATATAATTTTTGGA
1 AG-TTCGGGGTAAAAATATAATTTTTAGA
** * *
21453 AGTTTAGGGCAAAAATGTAATTTTTGAGA
1 AGTTCGGGGTAAAAATATAATTTTT-AGA
* *
21482 AGTTTGAGCGTAAAAATA-AGATTTTTAGA
1 AGTTCG-GGGTAAAAATATA-ATTTTTAGA
*
21511 AGTTCGAGGGT-AAAATATAATTTTTAATA
1 AGTTCG-GGGTAAAAATATAATTTTT-AGA
* * *
21540 AGTTTGAGGGTAAAAATGTAATTTTGTAAA
1 AGTTCG-GGGTAAAAATATAATTTT-TAGA
* * *
21570 AGTTTGGGGTCAAAATATGATTTT
1 AGTTCGGGGTAAAAATATAATTTT
21594 CGGAAAGTTT
Statistics
Matches: 185, Mismatches: 31, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
28 36 0.19
29 82 0.44
30 49 0.26
31 18 0.10
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (28 bp):
AGTTCGGGGTAAAAATATAATTTTTAGA
Found at i:21391 original size:60 final size:58
Alignment explanation
Indices: 21327--21485 Score: 176
Period size: 60 Copynumber: 2.7 Consensus size: 58
21317 AAAAATGTCA
* *
21327 TTTTGGGAGAGTTCGGGGTAAAAATATGATTTTTGGAAGTTAAGGGGCAAAAATGTAACT
1 TTTTGGGA-AGTTCGGGGTAAAAATGTGATTTTTGGAAGTTAAGGGGCAAAAATATAA-T
* * * * *
21387 TTTTGAGAAGTTCGAGGGTAAAAATGTGTTTTTTGAAAGTTTAGGGGTAAAAATATAAT
1 TTTTGGGAAGTTCG-GGGTAAAAATGTGATTTTTGGAAGTTAAGGGGCAAAAATATAAT
** * *
21446 TTTT-GGAAGTTTAGGGCAAAAATGTAATTTTTGAGAAGTT
1 TTTTGGGAAGTTCGGGGTAAAAATGTGATTTTTG-GAAGTT
21486 TGAGCGTAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
57 17 0.20
58 11 0.13
59 11 0.13
60 44 0.53
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (58 bp):
TTTTGGGAAGTTCGGGGTAAAAATGTGATTTTTGGAAGTTAAGGGGCAAAAATATAAT
Found at i:21486 original size:58 final size:58
Alignment explanation
Indices: 21253--21564 Score: 244
Period size: 58 Copynumber: 5.3 Consensus size: 58
21243 AAGAAAAAAA
* * * * * * * *
21253 AGGGGTCAAAATG-AAGTTTTGGAGAGTTTAGGGTTAAAATGTAGTTTTGGAAAATTTT
1 AGGGGTAAAAATGTAATTTTTGGA-AGTTGAGGGTAAAAATGTAATTTTTGAGAAGTTT
* * * * * *
21311 AGGGATAAAAATGTCATTTTGGGAGAGTTCG-GGGTAAAAATATGATTTTTG-GAAGTTA
1 AGGGGTAAAAATGTAATTTTTGGA-AGTT-GAGGGTAAAAATGTAATTTTTGAGAAGTTT
* **
21369 AGGGGCAAAAATGTAACTTTTTGAGAAGTTCGAGGGTAAAAATGTGTTTTTTGA-AAGTTT
1 AGGGGTAAAAATGTAA-TTTTTG-GAAGTT-GAGGGTAAAAATGTAATTTTTGAGAAGTTT
* * *
21429 AGGGGTAAAAATATAATTTTTGGAAGTTTAGGGCAAAAATGTAATTTTTGAGAAGTTT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTGAGGGTAAAAATGTAATTTTTGAGAAGTTT
* * * * * *
21487 -GAGCGTAAAAAT-AAGATTTTTAGAAGTTCGAGGGT-AAAATATAATTTTTAATAAGTTT
1 AG-GGGTAAAAATGTA-ATTTTTGGAAGTT-GAGGGTAAAAATGTAATTTTTGAGAAGTTT
21545 -GAGGGTAAAAATGTAATTTT
1 AG-GGGTAAAAATGTAATTTT
21565 GTAAAAGTTT
Statistics
Matches: 206, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
57 21 0.10
58 97 0.47
59 49 0.24
60 39 0.19
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (58 bp):
AGGGGTAAAAATGTAATTTTTGGAAGTTGAGGGTAAAAATGTAATTTTTGAGAAGTTT
Found at i:21507 original size:87 final size:87
Alignment explanation
Indices: 21269--21607 Score: 305
Period size: 87 Copynumber: 3.9 Consensus size: 87
21259 CAAAATGAAG
** * * * * * * *
21269 TTTTGGAGAGTTTAGGGTTAAAATGTAGTTTTGGA-AAATTTTAGGGATAAAAATGTCATTTTGG
1 TTTTGGA-AGTTTAGGGCAAAAATGTAATTTTTGAGAAGTTTGAGGG-TAAAAATATGATTTT-T
* * *
21333 GAGAG-TTCGGGGTAAAAATATGAT
63 GAAAGTTTAGGGGTAAAAATATAAT
* * * *
21357 TTTTGGAAGTTAAGGGGCAAAAATGTAACTTTTTGAGAAGTTCGAGGGTAAAAATGTGTTTTTTG
1 TTTTGGAAGTTTA-GGGCAAAAATGTAA-TTTTTGAGAAGTTTGAGGGTAAAAATATGATTTTTG
21422 AAAGTTTAGGGGTAAAAATATAAT
64 AAAGTTTAGGGGTAAAAATATAAT
* *
21446 TTTTGGAAGTTTAGGGCAAAAATGTAATTTTTGAGAAGTTTGAGCGTAAAAATAAGATTTTT-AG
1 TTTTGGAAGTTTAGGGCAAAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATATGATTTTTGA-
*
21510 AAG-TTCGAGGGT-AAAATATAAT
65 AAGTTTAG-GGGTAAAAATATAAT
** * * *
21532 TTTTAATAAGTTTGAGGGTAAAAATGTAA-TTTTGTAAAAGTTTG-GGGTCAAAATATGATTTTC
1 TTTT-GGAAGTTT-AGGGCAAAAATGTAATTTTTG-AGAAGTTTGAGGGTAAAAATATGATTTT-
*
21595 GGAAAGTTTAGGG
62 TGAAAGTTTAGGG
21608 ACCTTCTAAC
Statistics
Matches: 209, Mismatches: 30, Indels: 24
0.79 0.11 0.09
Matches are distributed among these distances:
86 18 0.09
87 68 0.33
88 63 0.30
89 52 0.25
90 8 0.04
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (87 bp):
TTTTGGAAGTTTAGGGCAAAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATATGATTTTTGAA
AGTTTAGGGGTAAAAATATAAT
Found at i:21579 original size:29 final size:28
Alignment explanation
Indices: 21277--21585 Score: 163
Period size: 29 Copynumber: 10.6 Consensus size: 28
21267 AGTTTTGGAG
* * * *
21277 AGTTTAGGGTTAAAATGTAGTTTTGGAAA
1 AGTTTGGGGTAAAAATGTAATTTT-TAAA
* * * ** *
21306 ATTTTAGGGATAAAAATGTCATTTTGGGAG
1 AGTTT-GGGGTAAAAATGTAATTTT-TAAA
* * * **
21336 AGTTCGGGGTAAAAATATGATTTTTGGA
1 AGTTTGGGGTAAAAATGTAATTTTTAAA
* * *
21364 AGTTAAGGGGCAAAAATGTAACTTTTTGAGA
1 AGTT-TGGGGTAAAAATGTAA-TTTTT-AAA
* ** *
21395 AGTTCGAGGGTAAAAATGTGTTTTTTGAA
1 AGTTTG-GGGTAAAAATGTAATTTTTAAA
* **
21424 AGTTTAGGGGTAAAAATATAATTTTTGGA
1 AGTTT-GGGGTAAAAATGTAATTTTTAAA
* * *
21453 AGTTTAGGGCAAAAATGTAATTTTTGAGA
1 AGTTTGGGGTAAAAATGTAATTTTT-AAA
* * *
21482 AGTTTGAGCGTAAAAAT-AAGATTTTTAGA
1 AGTTTG-GGGTAAAAATGTA-ATTTTTAAA
* *
21511 AGTTCGAGGGT-AAAATATAATTTTTAATA
1 AGTTTG-GGGTAAAAATGTAATTTTTAA-A
21540 AGTTTGAGGGTAAAAATGTAATTTTGTAAA
1 AGTTTG-GGGTAAAAATGTAATTTT-TAAA
*
21570 AGTTTGGGGTCAAAAT
1 AGTTTGGGGTAAAAAT
21586 ATGATTTTCG
Statistics
Matches: 220, Mismatches: 47, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
28 34 0.15
29 101 0.46
30 65 0.30
31 20 0.09
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
AGTTTGGGGTAAAAATGTAATTTTTAAA
Found at i:22675 original size:26 final size:26
Alignment explanation
Indices: 22601--22676 Score: 66
Period size: 30 Copynumber: 2.8 Consensus size: 26
22591 TGTTTCGAAT
* *
22601 AATATTAA-ATAAATA-ATTAATAAA
1 AATATTAATATATATATATAAATAAA
* *
22625 TATATTAATGTATAATAATGGATAAATAAA
1 AATATTAATATAT-AT-AT--ATAAATAAA
22655 AATATTAATATATATATATAAA
1 AATATTAATATATATATATAAA
22677 CGCTTTGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
24 7 0.17
25 2 0.05
26 7 0.17
27 1 0.03
28 2 0.05
29 2 0.05
30 19 0.47
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (26 bp):
AATATTAATATATATATATAAATAAA
Found at i:31462 original size:20 final size:20
Alignment explanation
Indices: 31437--31474 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31427 ATAGAATAGA
31437 AAAATAAT-TAAAATATTATT
1 AAAATAATAT-AAATATTATT
31457 AAAATAATATAAATATTA
1 AAAATAATATAAATATTA
31475 CGTATAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATAATATAAATATTATT
Found at i:32441 original size:44 final size:44
Alignment explanation
Indices: 32356--32441 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
32346 TTTGATTTTT
* * * **
32356 TAAAATAAAATTTTTTATTTAAATTTTAAAAAATTTTAAATTAA
1 TAAAATAAAATTATATATTTAAATTTTAAAAAAATAAAAATTAA
*
32400 TAAAATAAAATTATAT-TTTAATTTTTAAAAATAATAAAAATT
1 TAAAATAAAATTATATATTTAAATTTTAAAAA-AATAAAAATT
32442 TAATTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 14 0.40
44 21 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (44 bp):
TAAAATAAAATTATATATTTAAATTTTAAAAAAATAAAAATTAA
Found at i:33328 original size:24 final size:26
Alignment explanation
Indices: 33300--33351 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
33290 ATATTATTGT
*
33300 ATTAATCA-CATAAATAATTTT-AAA
1 ATTAACCATCATAAATAATTTTGAAA
**
33324 ATTAACCATTTTAAATAATTTTGAAA
1 ATTAACCATCATAAATAATTTTGAAA
33350 AT
1 AT
33352 ATACGAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 11 0.48
26 5 0.22
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (26 bp):
ATTAACCATCATAAATAATTTTGAAA
Found at i:34726 original size:39 final size:39
Alignment explanation
Indices: 34664--34738 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
34654 GGGAAACAAA
*
34664 GAGCACACACAATGCTAAACAGAGAGTACACAAAATACT
1 GAGCACACACAATGCTAAACAGAGAGCACACAAAATACT
* * *
34703 GAGCACACA-AAGTGTTAATCAGAGAGCACACGAAAT
1 GAGCACACACAA-TGCTAAACAGAGAGCACACAAAAT
34739 GCTAATCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.06
39 29 0.94
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (39 bp):
GAGCACACACAATGCTAAACAGAGAGCACACAAAATACT
Found at i:34733 original size:23 final size:23
Alignment explanation
Indices: 34703--34767 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
34693 ACAAAATACT
*
34703 GAGCACACAAAGTGTTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
*
34726 GAGCACACGAAA-TGCTAATCATA
1 GAGCACAC-AAAGTGCTAATCAGA
*
34749 GAGCACACGAAGTGCTAAT
1 GAGCACACAAAGTGCTAAT
34768 AACGAAGAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.05
23 32 0.86
24 3 0.08
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:35184 original size:16 final size:16
Alignment explanation
Indices: 35151--35188 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
35141 TTTTCATCAT
35151 AATTAATAAAACATTAA
1 AATT-ATAAAACATTAA
35168 AATTATAAACACA-TAA
1 AATTATAAA-ACATTAA
35184 AATTA
1 AATTA
35189 ATTATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTATAAAACATTAA
Found at i:37294 original size:26 final size:26
Alignment explanation
Indices: 37265--37319 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
37255 ATCTCGACCC
37265 ACAGCTCGTGTGAGCAGGCCCATTTT
1 ACAGCTCGTGTGAGCAGGCCCATTTT
37291 ACAGCTCGTGTGAGCAGGCCCATTTT
1 ACAGCTCGTGTGAGCAGGCCCATTTT
37317 ACA
1 ACA
37320 TGGGTGCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (26 bp):
ACAGCTCGTGTGAGCAGGCCCATTTT
Found at i:40014 original size:69 final size:69
Alignment explanation
Indices: 39903--40040 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 69
39893 AAATTTAATA
*
39903 TCAAAATAATACATTCTCCCTATTATTTACTAAAATAGTATATTTGGGGGAGTGATACTTCCTAG
1 TCAAAATAATACATTCTCCCCATTATTTACTAAAATAGTATATTTGGGGGAGTGATACTTCCTAG
39968 ATAG
66 ATAG
*
39972 TCAAAATAATACATTCTCCCCATTATTTATTAAAATAGTATATTTGGGGGAGTGATACTTCCTAG
1 TCAAAATAATACATTCTCCCCATTATTTACTAAAATAGTATATTTGGGGGAGTGATACTTCCTAG
40037 ATAG
66 ATAG
40041 ACATCACCAC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (69 bp):
TCAAAATAATACATTCTCCCCATTATTTACTAAAATAGTATATTTGGGGGAGTGATACTTCCTAG
ATAG
Found at i:49908 original size:97 final size:97
Alignment explanation
Indices: 49736--49929 Score: 279
Period size: 97 Copynumber: 2.0 Consensus size: 97
49726 AACTTTGAAA
* *
49736 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCGCACCTAGTCAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
49801 AAATCAGAAAT-AAAGAAACATTGCCTTGATTT
66 AAATCAGAAATAAAAG-AACATTGCCTTGATTT
* *
49833 AAGGGTATTCGATTAT-TCCGATTTGAAGAAAAATCG-AGCCTAGTAAGTTAAGGCAGAAATTTT
1 AAGGATATTCGATTATCT-CGATTTGAAGAAAAATCGCA-CCTAGTAAGTTAAGGCACAAATTTT
*
49896 CAAAACTC-GAAATAAAAGAATATTGCCTTGATTT
64 CAAAA-TCAGAAATAAAAGAACATTGCCTTGATTT
49930 TAAAGTTTTC
Statistics
Matches: 88, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
96 2 0.02
97 80 0.91
98 6 0.07
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAATCAGAAATAAAAGAACATTGCCTTGATTT
Found at i:49956 original size:97 final size:97
Alignment explanation
Indices: 49756--49952 Score: 215
Period size: 97 Copynumber: 2.0 Consensus size: 97
49746 GATTATCTCG
* *
49756 ATTTGAAGAAAAGTCGCACCTAGTCAGTTAAGGCACAAATTTTCAAAATCAGAAATAAAGAAACA
1 ATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAGAAATAAAGAAACA
* * *** *
49821 TTGCCTTGATTTAAGGGTATTCGATTATTCCG
66 TTGCCTTGATTTAAGAGTATTCGATGAAGACA
*
49853 ATTTGAAGAAAAATCG-AGCCTAGTAAGTTAAGGCAGAAATTTTCAAAACTC-GAAATAAA-AGA
1 ATTTGAAGAAAAATCGCA-CCTAGTAAGTTAAGGCACAAATTTTCAAAA-TCAGAAATAAAGA-A
* * *
49915 ATATTGCCTTGATTTTAA-AGTTTTC-ATGAAGATA
63 ACATTGCCTTGA-TTTAAGAGTATTCGATGAAGACA
49949 ATTT
1 ATTT
49953 TGAAAACAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
96 9 0.11
97 68 0.81
98 7 0.08
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (97 bp):
ATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAGAAATAAAGAAACA
TTGCCTTGATTTAAGAGTATTCGATGAAGACA
Found at i:50177 original size:28 final size:28
Alignment explanation
Indices: 50146--50207 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
50136 AAAATGTGAT
*
50146 TTTTGGATACCCGAGGGAAAAATGATAA
1 TTTTGGACACCCGAGGGAAAAATGATAA
* * * * *
50174 TTTTAGACACTCGGGGGTAAAATGGTAA
1 TTTTGGACACCCGAGGGAAAAATGATAA
50202 TTTTGG
1 TTTTGG
50208 GAAAGTTCGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (28 bp):
TTTTGGACACCCGAGGGAAAAATGATAA
Found at i:50239 original size:59 final size:58
Alignment explanation
Indices: 50174--50324 Score: 205
Period size: 60 Copynumber: 2.5 Consensus size: 58
50164 AAAATGATAA
*
50174 TTTTAGACACTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAACGGAAT
1 TTTTAGACA-TCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAACGGAAC
* **
50233 TTTTAGACATCCGGGGGTAAAATGGTAATTTTTTGGAAAGTTCGAGGTCAAAAGTGGAAC
1 TTTTAGACAT-CGGGGGTAAAATGGTAA-TTTTGGGAAAGTTCGAGGTCAAAAACGGAAC
*
50293 TTTTGGA-AGTTCGGGGGTAAAATGGTAATTTT
1 TTTTAGACA--TCGGGGGTAAAATGGTAATTTT
50325 TGAAAAAAAT
Statistics
Matches: 83, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
58 1 0.01
59 31 0.37
60 50 0.60
61 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (58 bp):
TTTTAGACATCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAACGGAAC
Found at i:50262 original size:29 final size:29
Alignment explanation
Indices: 50164--50265 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 29
50154 ACCCGAGGGA
*
50164 AAAATGATAA-TTTTAGACA-CTCGGGGGT
1 AAAATGGTAATTTTTAGACATC-CGGGGGT
** * * *
50192 AAAATGGTAATTTTGGGAAAGTTC-GAGGT
1 AAAATGGTAATTTTTAGACA-TCCGGGGGT
*
50221 CAAAAACGG-AATTTTTAGACATCCGGGGGT
1 --AAAATGGTAATTTTTAGACATCCGGGGGT
50251 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
50266 TGGAAAGTTC
Statistics
Matches: 54, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
28 15 0.28
29 19 0.35
30 14 0.26
31 6 0.11
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.30
Consensus pattern (29 bp):
AAAATGGTAATTTTTAGACATCCGGGGGT
Found at i:50308 original size:60 final size:59
Alignment explanation
Indices: 50184--50476 Score: 294
Period size: 59 Copynumber: 5.0 Consensus size: 59
50174 TTTTAGACAC
* * * *
50184 TCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAACGGAATTTTTAGACA-T
1 TCGGGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGGAACTTTTGGA-AGT
* *
50243 CCGGGGGTAAAATGGTAATTTTTTGGAAAGTTCGAGGTCAAAAGTGGAACTTTTGGAAGT
1 TCGGGGGTAAAATGGTAA-TTTTTGGAAAGTTCGAGGTCAAAAATGGAACTTTTGGAAGT
* * *
50303 TCGGGGGTAAAATGGTAATTTTTGAAAAAAATTAG-GGTCAAAAAT-G-ACATTTTGGAAGT
1 TCGGGGGTAAAATGGTAATTTTTG--GAAAGTTCGAGGTCAAAAATGGAAC-TTTTGGAAGT
** * * *
50362 TTAGGGGTAAAATGGTAATTTTTGGAAAGTTTGAGGTCAAAAAT-GAAATTTTGAAAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGGAACTTTTG-GAAGT
** * * * *
50421 TTAGGGGTAAAATTGTAATTTCTAGAAAGTTTG-GTGTCAAAAATGGAA-TTTTGGAA
1 TCGGGGGTAAAATGGTAATTTTTGGAAAGTTCGAG-GTCAAAAATGGAACTTTTGGAA
50477 AAGTTCAAGG
Statistics
Matches: 202, Mismatches: 22, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
57 6 0.03
58 21 0.10
59 106 0.52
60 63 0.31
61 6 0.03
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (59 bp):
TCGGGGGTAAAATGGTAATTTTTGGAAAGTTCGAGGTCAAAAATGGAACTTTTGGAAGT
Found at i:50314 original size:29 final size:31
Alignment explanation
Indices: 50184--50326 Score: 108
Period size: 30 Copynumber: 4.8 Consensus size: 31
50174 TTTTAGACAC
*
50184 TCGGGGGTAAAATGGTAAT-TTTGGGAAAGT
1 TCGGGGGTAAAATGGTAATCTTTTGGAAAGT
* * * *
50214 TC-GAGGTCAAAAACGG-AAT-TTTTAGACA-T
1 TCGGGGGT--AAAATGGTAATCTTTTGGAAAGT
* *
50243 CCGGGGGTAAAATGGTAATTTTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATCTTTTGGAAAGT
*
50274 TC-GAGGTCAAAAGTGG-AA-CTTTTGG-AAGT
1 TCGGGGGT-AAAA-TGGTAATCTTTTGGAAAGT
50303 TCGGGGGTAAAATGGTAAT-TTTTG
1 TCGGGGGTAAAATGGTAATCTTTTG
50327 AAAAAAATTA
Statistics
Matches: 88, Mismatches: 14, Indels: 23
0.70 0.11 0.18
Matches are distributed among these distances:
28 9 0.10
29 26 0.30
30 36 0.41
31 14 0.16
32 3 0.03
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (31 bp):
TCGGGGGTAAAATGGTAATCTTTTGGAAAGT
Found at i:50385 original size:29 final size:29
Alignment explanation
Indices: 50246--50441 Score: 104
Period size: 29 Copynumber: 6.6 Consensus size: 29
50236 TAGACATCCG
*
50246 GGGGTAAAATGGTAATTTTTTGGAAAG-TTC
1 GGGGTAAAATGGTAA-TTTTTGG-AAGTTTA
* * **
50276 GAGGTCAAAAGTGG-AACTTTTGGAAGTTCG
1 GGGGT-AAAA-TGGTAATTTTTGGAAGTTTA
* **
50306 GGGGTAAAATGGTAATTTTTGAAAAAAATTA
1 GGGGTAAAATGGTAATTTTTG--GAAGTTTA
50337 -GGGTCAAAAAT-G-ACA-TTTTGGAAGTTTA
1 GGGGT--AAAATGGTA-ATTTTTGGAAGTTTA
50365 GGGGTAAAATGGTAATTTTTGGAAAGTTT-
1 GGGGTAAAATGGTAATTTTTGG-AAGTTTA
* * *
50394 GAGGTCAAAAAT-G-AAATTTTGAAAAGTTTA
1 GGGGT--AAAATGGTAATTTTTG-GAAGTTTA
*
50424 GGGGTAAAATTGTAATTT
1 GGGGTAAAATGGTAATTT
50442 CTAGAAAGTT
Statistics
Matches: 127, Mismatches: 19, Indels: 40
0.68 0.10 0.22
Matches are distributed among these distances:
27 5 0.04
28 15 0.12
29 43 0.34
30 40 0.31
31 16 0.13
32 8 0.06
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAGTTTA
Found at i:50412 original size:30 final size:30
Alignment explanation
Indices: 50337--50516 Score: 140
Period size: 29 Copynumber: 6.1 Consensus size: 30
50327 AAAAAAATTA
*
50337 GGGTCAAAAATGACATTTTGG-AAGTTTAG
1 GGGTCAAAAATGAAATTTTGGAAAGTTTAG
*
50366 GGGT--AAAATGGTAATTTTTGGAAAGTTT-G
1 GGGTCAAAAAT-G-AAATTTTGGAAAGTTTAG
* *
50395 AGGTCAAAAATGAAATTTTGAAAAGTTTAG
1 GGGTCAAAAATGAAATTTTGGAAAGTTTAG
* * *
50425 GGGT-AAAATTGTAATTTCTAGAAAGTTT-G
1 GGGTCAAAAATGAAATTT-TGGAAAGTTTAG
* * * *
50454 GTGTCAAAAATGGAATTTTGGAAAAGTTCAA
1 GGGTCAAAAATGAAATTTTGG-AAAGTTTAG
* * *
50485 GGGTCAAAATATG-ACTTTTAGATAGTTTAG
1 GGGTCAAAA-ATGAAATTTTGGAAAGTTTAG
50515 GG
1 GG
50517 ACCTTTATGG
Statistics
Matches: 118, Mismatches: 22, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
27 5 0.04
28 1 0.01
29 46 0.39
30 44 0.37
31 19 0.16
32 3 0.03
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (30 bp):
GGGTCAAAAATGAAATTTTGGAAAGTTTAG
Found at i:51505 original size:9 final size:9
Alignment explanation
Indices: 51444--51510 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 9
51434 TTTTACTTAT
*
51444 TATTATTAT
1 TATTATTAA
51453 TATTAATTAA
1 TATT-ATTAA
* *
51463 TGTCATTAA
1 TATTATTAA
51472 TATTA-T-A
1 TATTATTAA
*
51479 T-TTATTAT
1 TATTATTAA
*
51487 TATTAATAA
1 TATTATTAA
51496 TATTATTAA
1 TATTATTAA
*
51505 TGTTAT
1 TATTAT
51511 CAAAATCATT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 2 0.05
9 30 0.68
10 6 0.14
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (9 bp):
TATTATTAA
Found at i:52360 original size:17 final size:17
Alignment explanation
Indices: 52281--52360 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
52271 TAAATAAATT
*
52281 TAAATTTAATATTTATAA
1 TAAATTTAA-ATTTAAAA
* **
52299 TAAATTTAAACTCCAAA
1 TAAATTTAAATTTAAAA
** *
52316 TGGATTTAAATTTAATA
1 TAAATTTAAATTTAAAA
* *
52333 TAAACTGAAATTTAAAA
1 TAAATTTAAATTTAAAA
52350 TAAATTTAAAT
1 TAAATTTAAAT
52361 CTGTTGGGCC
Statistics
Matches: 45, Mismatches: 17, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
17 36 0.80
18 9 0.20
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:52819 original size:49 final size:49
Alignment explanation
Indices: 52766--53152 Score: 279
Period size: 49 Copynumber: 7.9 Consensus size: 49
52756 GTGTTTTCAT
* * * *
52766 GGTACCAGATTCGCCTTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGA
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATGCTTCTGA
* * * * *
52815 GGTACAAGGTTTGCCGTTGCGACTTAAACCTTTCTCC-TCGTGTCTT-TGC
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTC-CCTTCATG-CTTCTGA
* * * * *
52864 GGTACTGGATTCGCCGTTACGGCTTAAATCC-TTCACTTCATGTTTCTGA
1 GGTACTAGATTCGCCGTTGCGACTTAAA-CCTTTCCCTTCATGCTTCTGA
* * * * *
52913 GGTATTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTATGCTTTTGA
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATGCTTCTGA
* * *
52962 GGTAC-ACGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC--A
1 GGTACTA-GATTCGCCGTTGCGACTTAAACCTTTCCCTTCAT-GCTTCTGA
* * * * **
53010 TGGTACTGGATTTGCCGTTGCGGCTTAAATCTTTCCCTTTGTGTCTTCTGA
1 -GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATG-CTTCTGA
* * * * * **
53061 GGTA-TAAAGTTTGCCATTACGACTTAAACCTTTTCCTTTTGTGTCTTC-GA
1 GGTACTAGA-TTCGCCGTTGCGACTTAAACC-TTTCCCTTCATG-CTTCTGA
* *
53111 GGTA-TAGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
1 GGTACTA-GATTCGCCGTTGCGACTTAAACCTTTCCCTTCATG
53153 TTTTTGTGGT
Statistics
Matches: 263, Mismatches: 59, Indels: 32
0.74 0.17 0.09
Matches are distributed among these distances:
48 7 0.03
49 183 0.70
50 55 0.21
51 18 0.07
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (49 bp):
GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATGCTTCTGA
Found at i:53027 original size:147 final size:146
Alignment explanation
Indices: 52775--53147 Score: 428
Period size: 147 Copynumber: 2.5 Consensus size: 146
52765 TGGTACCAGA
* * * * * *
52775 TTCGCCTTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTTGCCGTTGCGACTT
1 TTCGCCATTGCGACTTAAACCTTTCCCTTTATGCTTTTGAGGTAC-AGGTTCGCCGTTGCGACTT
* * **
52840 AAACCTTTCTCCTCGTGTCTTTGCGGTACTGGATTCGCCGTTACGGCTTAAATCCTTCACTTCAT
65 AAACCTTTC-CCTCATATCTTCACGGTACTGGATTCGCCGTTACGGCTTAAATCCTTCACTTCAT
* *
52905 GT-TTCTGAGGTATTAGG
129 GTCTTCTGAGGTATAAAG
52922 TTCGCCATTGCGACTTAAACCTTTCCCTTTATGCTTTTGAGGTACACGGTTCGCCGTTGCGACTT
1 TTCGCCATTGCGACTTAAACCTTTCCCTTTATGCTTTTGAGGTACA-GGTTCGCCGTTGCGACTT
* * * * * **
52987 AAACCTTTCCCTCCATATCTTCATGGTACTGGATTTGCCGTTGCGGCTTAAATCTTTCCCTTTGT
65 AAACCTTTCCCT-CATATCTTCACGGTACTGGATTCGCCGTTACGGCTTAAATCCTTCACTTCAT
53052 GTCTTCTGAGGTATAAAG
129 GTCTTCTGAGGTATAAAG
* * * * *
53070 TTTGCCATTACGACTTAAACCTTTTCCTTT-TG-TGTCTTCGAGGTATAGGATTCGCCGTTGCGG
1 TTCGCCATTGCGACTTAAACCTTTCCCTTTATGCT-T-TT-GAGGTACAGG-TTCGCCGTTGCGA
*
53133 CTTAAATCTTTCCCT
62 CTTAAACCTTTCCCT
53148 TCATGTTTTT
Statistics
Matches: 194, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
146 5 0.03
147 112 0.58
148 44 0.23
149 33 0.17
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.39
Consensus pattern (146 bp):
TTCGCCATTGCGACTTAAACCTTTCCCTTTATGCTTTTGAGGTACAGGTTCGCCGTTGCGACTTA
AACCTTTCCCTCATATCTTCACGGTACTGGATTCGCCGTTACGGCTTAAATCCTTCACTTCATGT
CTTCTGAGGTATAAAG
Found at i:62015 original size:41 final size:42
Alignment explanation
Indices: 61970--62097 Score: 117
Period size: 41 Copynumber: 3.1 Consensus size: 42
61960 ATGGCATTTT
*
61970 TAGCGGCGTTTGGATAGAAAACGCTGCAAAAGG-TAGGGCAA
1 TAGCGGCGTTTGGATAGAAAACGCTGCTAAAGGTTAGGGCAA
* * *
62011 TAGCGACGCTTATGG---GAAAGCGCCGCTAAAGGTTAGGGCAA
1 TAGCGGCG-TT-TGGATAGAAAACGCTGCTAAAGGTTAGGGCAA
* *
62052 TAGCGGCGCTT--ATAGGAAA-GCGTCGCTAAAGGTTAGGGCAA
1 TAGCGGCGTTTGGATAGAAAACGC-T-GCTAAAGGTTAGGGCAA
62093 TAGCG
1 TAGCG
62098 ACGCTTATAG
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
39 3 0.04
40 18 0.26
41 44 0.63
42 2 0.03
43 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.34, T:0.18
Consensus pattern (42 bp):
TAGCGGCGTTTGGATAGAAAACGCTGCTAAAGGTTAGGGCAA
Found at i:62061 original size:24 final size:24
Alignment explanation
Indices: 62029--62102 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 24
62019 CTTATGGGAA
*
62029 AGCGCCGCTAAAGGTTAGGGCAAT
1 AGCGACGCTAAAGGTTAGGGCAAT
* *
62053 AGCGGCGCT-TA---TA-GG-AA-
1 AGCGACGCTAAAGGTTAGGGCAAT
*
62070 AGCGTCGCTAAAGGTTAGGGCAAT
1 AGCGACGCTAAAGGTTAGGGCAAT
62094 AGCGACGCT
1 AGCGACGCT
62103 TATAGGAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
17 8 0.21
18 3 0.08
19 2 0.05
20 2 0.05
21 2 0.05
22 2 0.05
23 3 0.08
24 16 0.42
ACGTcount: A:0.28, C:0.20, G:0.34, T:0.18
Consensus pattern (24 bp):
AGCGACGCTAAAGGTTAGGGCAAT
Found at i:62103 original size:41 final size:41
Alignment explanation
Indices: 61998--62400 Score: 430
Period size: 41 Copynumber: 9.6 Consensus size: 41
61988 AAACGCTGCA
* *
61998 AAAGG-TAGGGCAATAGCGACGCTTATGGGAAAGCGCCGCT
1 AAAGGTTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
* * *
62038 AAAGGTTAGGGCAATAGCGGCGCTTATAGGAAAGCGTCGCT
1 AAAGGTTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
* * * *
62079 AAAGGTTAGGGCAATAGCGACGCTTATAGGAAAGCGCCACT
1 AAAGGTTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
* * * * * * *
62120 AAAGGTCAGATCAATAACGGCGCTTATGAGAATGCGTCGTT
1 AAAGGTTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
* ** *
62161 AAAGGTTAGAGCAATAGCGACGCTTATGAAAAAGCGCTGCT
1 AAAGGTTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
62202 AAAGGTCAGAGCAATTTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
1 -AA----AG-G----TTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
* *
62253 AAAGGTCAGATCAATAGCGGCGCTTATGGGAAAGCGCCGCT
1 AAAGGTTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
* *
62294 AAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGCGCCGCT
1 AAAGGTTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
* * * * * *
62335 AAAGGTCAGAGCAATAGTGGCGCTTATGGGTAATCACCGTT
1 AAAGGTTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
*
62376 AAAGGTCAGAGCAATAGCGGCGCTT
1 AAAGGTTAGAGCAATAGCGGCGCTT
62401 TCAGGACAAT
Statistics
Matches: 311, Mismatches: 41, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
40 5 0.02
41 264 0.85
42 2 0.01
45 1 0.00
46 4 0.01
47 1 0.00
50 2 0.01
51 32 0.10
ACGTcount: A:0.32, C:0.19, G:0.31, T:0.19
Consensus pattern (41 bp):
AAAGGTTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
Found at i:62226 original size:51 final size:51
Alignment explanation
Indices: 62166--62267 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
62156 TCGTTAAAGG
*
62166 TTAGAGCAATAGCGACGCTTATGAAAAAGCGCTGCTAAAGGTCAGAGCAAT
1 TTAGAGCAATAGCGACGCTTATGAAAAAGCGCCGCTAAAGGTCAGAGCAAT
* ** *
62217 TTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAAT
1 TTAGAGCAATAGCGACGCTTATGAAAAAGCGCCGCTAAAGGTCAGAGCAAT
62268 AGCGGCGCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (51 bp):
TTAGAGCAATAGCGACGCTTATGAAAAAGCGCCGCTAAAGGTCAGAGCAAT
Found at i:62328 original size:133 final size:133
Alignment explanation
Indices: 62084--62349 Score: 415
Period size: 133 Copynumber: 2.0 Consensus size: 133
62074 TCGCTAAAGG
*
62084 TTAGGGCAATAGCGACGCTTATAGGAAAGCGCCACTAAAGGTCAGATCAATAACGGCGCTTATGA
1 TTAGAGCAATAGCGACGCTTATAGGAAAGCGCCACTAAAGGTCAGATCAATAACGGCGCTTATGA
* * * * *
62149 GAATGCGTCGTTAAAGGTTAGAGCAATAGCGACGCTTATGAAAAAGCGCTGCTAAAGGTCAGAGC
66 GAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGAAAAAGCGCCGCTAAAGGTCAGAGC
62214 AAT
131 AAT
* * * * *
62217 TTAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGGCGCTTATGG
1 TTAGAGCAATAGCGACGCTTATAGGAAAGCGCCACTAAAGGTCAGATCAATAACGGCGCTTATGA
**
62282 GAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGC
66 GAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGAAAAAGCGCCGCTAAAGGTCAGAGC
62347 AAT
131 AAT
62350 AGTGGCGCTT
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
133 120 1.00
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (133 bp):
TTAGAGCAATAGCGACGCTTATAGGAAAGCGCCACTAAAGGTCAGATCAATAACGGCGCTTATGA
GAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGAAAAAGCGCCGCTAAAGGTCAGAGC
AAT
Found at i:62340 original size:174 final size:176
Alignment explanation
Indices: 62047--62489 Score: 518
Period size: 174 Copynumber: 2.5 Consensus size: 176
62037 TAAAGGTTAG
* * * *
62047 GGCAATAGCGGCGCTTATAGGAAAGCGTCGCTAAAGGTTAGGGCAATAGCGACGCTTATAGGAAA
1 GGCAATAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATAGGAAA
* * * * * * *
62112 GCGCCACTAAAGGTCAGATCAATAACGGCGCTTATGAGAATGCGTCGTTAAAGGTTAGAGCAATA
66 GCGCCGCTAAAGGTCAGAGCAATAACGACGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCAATA
* *
62177 GCGACGCTTATGAAAAAGCGCTGCTAAAGGTCAGAGC-A-A-TTTA
131 GCGACGCTTATGAAAAAGCACCGCTAAAGGTCAGAGCAATAGTTTA
* * *
62220 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGGCGCTTATGGGAA
1 G-GCAATAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATAGGAA
* *
62285 AGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAAT
65 AGCGCCGCTAAAGGTCAGAGCAATAACGACGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCAAT
* * *** * *
62350 AGTGGCGCTTATGGGTAATCACCGTTAAAGGTCAGAGCAATAGCGGCGCTTTCA
130 AGCGACGCTTATGAAAAAGCACCGCTAAAGGTCAGAGCAATA-----G-TTT-A
*
62404 GGACAATAGCAGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATTA-GA
1 GG-CAATAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTA-TAGGA
*
62468 AAGCACCG-TAAAGGTCAGAGCA
64 AAGCGCCGCTAAAGGTCAGAGCA
62490 TTAGAAGCGC
Statistics
Matches: 227, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
173 1 0.00
174 141 0.62
175 1 0.00
176 1 0.00
183 18 0.08
184 64 0.28
185 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (176 bp):
GGCAATAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATAGGAAA
GCGCCGCTAAAGGTCAGAGCAATAACGACGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCAATA
GCGACGCTTATGAAAAAGCACCGCTAAAGGTCAGAGCAATAGTTTA
Found at i:62378 original size:215 final size:215
Alignment explanation
Indices: 62007--62400 Score: 610
Period size: 215 Copynumber: 1.8 Consensus size: 215
61997 AAAAGGTAGG
* *
62007 GCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTTAGGGCAATAGCGGCGCTTATAGGAAAG
1 GCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATAGGAAAG
* * * *
62072 CGTCGCTAAAGGTTAGGGCAATAGCGACGCTTATAGGAAAGCGCCACTAAAGGTCAGATCAATAA
66 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATAGGAAAGCGCCACTAAAGGTCAGAGCAATAA
** *
62137 CGGCGCTTATGAGAATGCGTCGTTAAAGGTTAGAGCAATAGCGACGCTTATGAAAAAGCGCTGCT
131 CGGCGCTTATGAGAATGCACCGTTAAAGGTCAGAGCAATAGCGACGCTTATGAAAAAGCGCTGCT
62202 AAAGGTCAGAGCAATTTAGA
196 AAAGGTCAGAGCAATTTAGA
* * *
62222 GCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGGCGCTTATGGGAAAG
1 GCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATAGGAAAG
* * *
62287 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAG
66 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATAGGAAAGCGCCACTAAAGGTCAGAGCAATAA
* * *
62352 TGGCGCTTATGGGTAAT-CACCGTTAAAGGTCAGAGCAATAGCGGCGCTT
131 CGGCGCTTATGAG-AATGCACCGTTAAAGGTCAGAGCAATAGCGACGCTT
62401 TCAGGACAAT
Statistics
Matches: 160, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
215 157 0.98
216 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (215 bp):
GCAATAGCGACGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATAGGAAAG
CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATAGGAAAGCGCCACTAAAGGTCAGAGCAATAA
CGGCGCTTATGAGAATGCACCGTTAAAGGTCAGAGCAATAGCGACGCTTATGAAAAAGCGCTGCT
AAAGGTCAGAGCAATTTAGA
Found at i:62470 original size:41 final size:40
Alignment explanation
Indices: 62407--62499 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
62397 GCTTTCAGGA
*
62407 CAATAGCAGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGAG
1 CAATAGCAGCGCTTATAGGAAAGCACCG-TAAAGGTCAGAG
*
62448 CAATAGCGGCGCTTATTA-GAAAGCACCGTAAAGGTCAGAG
1 CAATAGCAGCGCTTA-TAGGAAAGCACCGTAAAGGTCAGAG
* *
62488 CATTAGAAGCGC
1 CAATAGCAGCGC
62500 CGCTAAAGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 21 0.46
41 23 0.50
42 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.28, T:0.16
Consensus pattern (40 bp):
CAATAGCAGCGCTTATAGGAAAGCACCGTAAAGGTCAGAG
Found at i:62612 original size:19 final size:19
Alignment explanation
Indices: 62590--62629 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
62580 TATATAAACT
*
62590 AAAAAAATTTAAAA-TTTA
1 AAAAAAAATTAAAATTTTA
62608 AAAAAAAATTAAAATTTTA
1 AAAAAAAATTAAAATTTTA
62627 AAA
1 AAA
62630 CTAAACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAAAAATTAAAATTTTA
Done.