Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016401.1 Corchorus capsularis cultivar CVL-1 contig16422, 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: 150454
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:234 original size:11 final size:11
Alignment explanation
Indices: 214--243 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
204 AAAGCAAAGG
*
214 AAATCAAATCT
1 AAATCTAATCT
225 AAATCTAATCT
1 AAATCTAATCT
236 AAATCTAA
1 AAATCTAA
244 AGCAGATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATCTAATCT
Found at i:258 original size:12 final size:13
Alignment explanation
Indices: 241--285 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
231 AATCTAAATC
241 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
253 TAAAGCAAATTAA
1 TAAAGCAGATTAA
266 TAAAGCAGATTAA
1 TAAAGCAGATTAA
279 TAAAGCA
1 TAAAGCA
286 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:292 original size:25 final size:25
Alignment explanation
Indices: 241--293 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
231 AATCTAAATC
*
241 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
266 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
291 TAA
1 TAA
294 TTAAAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Found at i:5296 original size:19 final size:18
Alignment explanation
Indices: 5272--5308 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5262 TTGAAGATTT
5272 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
5291 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
5309 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:5443 original size:10 final size:10
Alignment explanation
Indices: 5428--5452 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5418 ATTACTCAGC
5428 CCATATAAGT
1 CCATATAAGT
5438 CCATATAAGT
1 CCATATAAGT
5448 CCATA
1 CCATA
5453 ATTGGAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (10 bp):
CCATATAAGT
Found at i:7130 original size:22 final size:22
Alignment explanation
Indices: 7102--7150 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
7092 AGCGTGCTGA
7102 TGTCAGAAAGAGAATCACTACT
1 TGTCAGAAAGAGAATCACTACT
7124 TGTCAGAAAGAGAATCACTACT
1 TGTCAGAAAGAGAATCACTACT
7146 TGTCA
1 TGTCA
7151 ACAACTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (22 bp):
TGTCAGAAAGAGAATCACTACT
Found at i:13685 original size:19 final size:18
Alignment explanation
Indices: 13661--13697 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
13651 TTGAAGATTT
13661 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
13680 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
13698 ATAATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:13832 original size:10 final size:10
Alignment explanation
Indices: 13817--13841 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13807 ATTACTCAGC
13817 CCATATAAGT
1 CCATATAAGT
13827 CCATATAAGT
1 CCATATAAGT
13837 CCATA
1 CCATA
13842 ATTGGAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (10 bp):
CCATATAAGT
Found at i:19366 original size:30 final size:30
Alignment explanation
Indices: 19330--19386 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
19320 AAATTAACTA
* *
19330 AATGATGCGCCCAAGGCTTATCATGGAGGG
1 AATGATGCGCCAAAGACTTATCATGGAGGG
* *
19360 AATGATGTGCCAAAGACTTATTATGGA
1 AATGATGCGCCAAAGACTTATCATGGA
19387 CTTGAAGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (30 bp):
AATGATGCGCCAAAGACTTATCATGGAGGG
Found at i:23738 original size:19 final size:18
Alignment explanation
Indices: 23701--23740 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
23691 TTCTTGAAAT
*
23701 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
23719 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
23738 AAT
1 AAT
23741 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:35600 original size:21 final size:21
Alignment explanation
Indices: 35533--35600 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
35523 AATGTGCAAA
*
35533 TCTTGGAATCGGTTGGAATAT
1 TCTTGGAATCGATTGGAATAT
* * * * *
35554 TCCTAGAATCGATTGTAAGAA
1 TCTTGGAATCGATTGGAATAT
*
35575 GCTTGGAATCGATTGGAATAT
1 TCTTGGAATCGATTGGAATAT
35596 TCTTG
1 TCTTG
35601 CACAAAACAT
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (21 bp):
TCTTGGAATCGATTGGAATAT
Found at i:42700 original size:6 final size:6
Alignment explanation
Indices: 42691--42715 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42681 CCTAAAAACA
42691 AAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT A
42716 GGTTGCCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:44347 original size:13 final size:13
Alignment explanation
Indices: 44329--44354 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44319 CAATCAAGAA
44329 AATTAAAGAAAAC
1 AATTAAAGAAAAC
44342 AATTAAAGAAAAC
1 AATTAAAGAAAAC
44355 CCTCCAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AATTAAAGAAAAC
Found at i:61919 original size:12 final size:12
Alignment explanation
Indices: 61898--61929 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
61888 GCCACGCAAC
*
61898 ACCGGTCACATG
1 ACCGGCCACATG
61910 ACCGGCCACATG
1 ACCGGCCACATG
61922 ACCGGCCA
1 ACCGGCCA
61930 TCGCATGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (12 bp):
ACCGGCCACATG
Found at i:62827 original size:22 final size:22
Alignment explanation
Indices: 62797--62840 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
62787 CTTTCCCACA
*
62797 ACAACTTCTGTCCCGAAGTTGT
1 ACAACTTCTGGCCCGAAGTTGT
* *
62819 ACAAGTTCTGGGCCGAAGTTGT
1 ACAACTTCTGGCCCGAAGTTGT
62841 CCTGAAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (22 bp):
ACAACTTCTGGCCCGAAGTTGT
Found at i:68546 original size:16 final size:17
Alignment explanation
Indices: 68519--68553 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
68509 CGTTTGTTAC
68519 TTTCCATGGGAGAGTGA
1 TTTCCATGGGAGAGTGA
68536 TTTCC-TGGGAGAGTGA
1 TTTCCATGGGAGAGTGA
68552 TT
1 TT
68554 CTATGGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.20, C:0.11, G:0.34, T:0.34
Consensus pattern (17 bp):
TTTCCATGGGAGAGTGA
Found at i:72656 original size:22 final size:22
Alignment explanation
Indices: 72631--72737 Score: 60
Period size: 22 Copynumber: 4.9 Consensus size: 22
72621 GAGAATCTTT
*
72631 TTAT-AAATTTTTTTTAACCTTC
1 TTATGAAA-TTTTGTTAACCTTC
*
72653 TTATGAAATTTTGTTAACCTCC
1 TTATGAAATTTTGTTAACCTTC
* * * *
72675 CTAAGGAATTTTG-AAGACC-TC
1 TTATGAAATTTTGTTA-ACCTTC
* *
72696 AATATGAAATTTTGATAA-CTTCC
1 -TTATGAAATTTTGTTAACCTT-C
* *
72719 TAATGAAATTTTGATAACC
1 TTATGAAATTTTGTTAACC
72738 AACACTATGA
Statistics
Matches: 65, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
21 3 0.05
22 56 0.86
23 6 0.09
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
TTATGAAATTTTGTTAACCTTC
Found at i:72756 original size:45 final size:45
Alignment explanation
Indices: 72698--72783 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
72688 AAGACCTCAA
* *
72698 TATGAAATTTTGATAA-CTTCC-TAATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAATC-TCCAT-ATGAAATATTGATAACCAACAC
* *
72743 TATGACATGTTGATAATCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAATCTCCATATGAAATATTGATAACCA
72784 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
45 33 0.94
46 2 0.06
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (45 bp):
TATGAAATGTTGATAATCTCCATATGAAATATTGATAACCAACAC
Found at i:72884 original size:23 final size:22
Alignment explanation
Indices: 72835--72937 Score: 93
Period size: 23 Copynumber: 4.5 Consensus size: 22
72825 TCACACTCTT
* *
72835 AAATTTTGATAATCA-CACTCTA
1 AAATTTTGATAAACATC-CTATA
* *
72857 AAATTGTGAT-AACCTCGCTATGA
1 AAATTTTGATAAACATC-CTAT-A
* *
72880 AAATTCTGATAAATCTTCCTATA
1 AAATTTTGATAAA-CATCCTATA
72903 AAATTTTGATAAACATCCCTATA
1 AAATTTTGATAAACAT-CCTATA
72926 AAATTTTGATAA
1 AAATTTTGATAA
72938 CTTTCGTATG
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
21 2 0.03
22 15 0.22
23 41 0.61
24 6 0.09
25 3 0.04
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAAACATCCTATA
Found at i:72913 original size:46 final size:44
Alignment explanation
Indices: 72855--72960 Score: 113
Period size: 46 Copynumber: 2.3 Consensus size: 44
72845 AATCACACTC
* * *
72855 TAAAATTGTGATAACCTCGCTATGAAAATTCTGATAAATCTTCCTA
1 TAAAATTTTGATAACATCCCTAT-AAAATTCTGATAAAT-TTCCTA
* * *
72901 TAAAATTTTGATAAACATCCCTATAAAATTTTGATAACTTTCGTA
1 TAAAATTTTGAT-AACATCCCTATAAAATTCTGATAAATTTCCTA
* *
72946 TGAAATCTTGATAAC
1 TAAAATTTTGATAAC
72961 TACAAATTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 3 0.06
45 15 0.29
46 24 0.47
47 9 0.18
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (44 bp):
TAAAATTTTGATAACATCCCTATAAAATTCTGATAAATTTCCTA
Found at i:73014 original size:22 final size:22
Alignment explanation
Indices: 72654--73144 Score: 227
Period size: 22 Copynumber: 22.6 Consensus size: 22
72644 TTAACCTTCT
* *
72654 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
72676 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTCAC
*
72698 TATGAAATTTTGATAACTTC-C
1 TATGAAATTTTGATAACCTCAC
*
72719 TAATGAAATTTTGATAACCAACAC
1 T-ATGAAATTTTGATAACC-TCAC
* * *
72743 TATGACATGTTGATAATCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * **
72764 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCAC
* * *
72787 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
72808 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* * * *
72831 TCTTAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* * * *
72853 TCTAAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
* *
72875 TATGAAAATTCTGATAAATCTTC-C
1 TATG-AAATTTTGAT-AA-CCTCAC
* * *
72899 TATAAAATTTTGATAAACATCCC
1 TATGAAATTTTGAT-AACCTCAC
* * *
72922 TATAAAATTTTGATAACTTTC-G
1 TATGAAATTTTGATAAC-CTCAC
*
72944 TATGAAATCTTGATAA-CT-AC
1 TATGAAATTTTGATAACCTCAC
72964 ----AAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
** *
72981 GTATGATTTTTTGATAACCTCAT
1 -TATGAAATTTTGATAACCTCAC
* * *
73004 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
73026 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
* *
73048 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
73070 TATGAAATTTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
*
73092 TATGAAATTTTGATATCCTCAC
1 TATGAAATTTTGATAACCTCAC
*
73114 --TG-AATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
*
73132 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
73145 TACTCCATAA
Statistics
Matches: 362, Mismatches: 72, Indels: 72
0.72 0.14 0.14
Matches are distributed among these distances:
16 11 0.03
17 3 0.01
18 1 0.00
19 17 0.05
20 14 0.04
21 10 0.03
22 228 0.63
23 66 0.18
24 9 0.02
25 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:73141 original size:20 final size:20
Alignment explanation
Indices: 73072--73144 Score: 94
Period size: 19 Copynumber: 3.6 Consensus size: 20
73062 AACTAAACTA
* *
73072 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATATCC-TCA-C
73094 TGAAATTTTGATATCCTCAC
1 TGAAATTTTGATATCCTCAC
*
73114 TG-AATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCAC
73133 TGAAATTTTGAT
1 TGAAATTTTGAT
73145 TACTCCATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
19 18 0.38
20 11 0.23
21 3 0.06
22 15 0.32
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCAC
Found at i:74202 original size:30 final size:29
Alignment explanation
Indices: 74137--74203 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 29
74127 GAAGGAAGCA
74137 AATTCAAGGACAAATCAAGAAGAGCAAAAG
1 AATTCAAGGACAAATCAAGAAGAGC-AAAG
*
74167 GATTCAAGGAAGCAAAGTCAAGAA-AGC-AAG
1 AATTCAAGG-A-CAAA-TCAAGAAGAGCAAAG
74197 AATTCAA
1 AATTCAA
74204 AATAATAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 17 0.53
31 1 0.03
32 7 0.22
33 7 0.22
ACGTcount: A:0.54, C:0.13, G:0.21, T:0.12
Consensus pattern (29 bp):
AATTCAAGGACAAATCAAGAAGAGCAAAG
Found at i:74416 original size:70 final size:69
Alignment explanation
Indices: 74339--74697 Score: 487
Period size: 67 Copynumber: 5.2 Consensus size: 69
74329 AATGCTTCGA
* * *
74339 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGGT-AGTTCAAGTTTTGGTTCCAGCCAAGCATA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGA-GTCAGTTCAAGCTTTGGTTCCATCCAAGCA-A
*
74403 TAGGGG
64 CAGGGG
*
74409 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTT-TAGCTTT-GTTCCATCCAAGCAACA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCAACA
*
74472 GAGG
66 GGGG
* * * *
74476 CTTTTCCACAAGCCAATCTCGTTTCCATACGAGTCAGTT-TAGC-CTGGTTCCATCCAAGCAACA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCAACA
*
74539 GAGG
66 GGGG
** * *
74543 CTTTTCCACGAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTACATCCAAGCATT
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAG-TCAGTTCAAGCTTTGGTTCCATCCAAGCA-A
74607 CAGGGG
64 CAGGGG
*
74613 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCAACA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCAACA
*
74678 TGGG
66 GGGG
74682 CTTTTCCATAAGCCAA
1 CTTTTCCATAAGCCAA
74698 GATCAATGAG
Statistics
Matches: 260, Mismatches: 22, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
66 1 0.00
67 102 0.39
68 17 0.07
69 44 0.17
70 96 0.37
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (69 bp):
CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCAACA
GGGG
Found at i:75138 original size:90 final size:91
Alignment explanation
Indices: 74911--75398 Score: 513
Period size: 90 Copynumber: 5.5 Consensus size: 91
74901 GGGGGGGGGG
* *
74911 GGTGCCTTACTTCTACAAAGATAGAATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAATTCAA
1 GGTGCCTTACTTCTTCAAAGATAGAATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAA
*
74976 GATCATCCGGTGAATCAAGTT-GGTGC
66 GATCATTCGGTGAATCAAGTTAGG-GC
* *
75002 AGTG-C---CTTCTTCAAAG-TCAG-ATTCGGTGAGCTCGGTGCAGCAGATTTTCAAGCAGTTCA
1 GGTGCCTTACTTCTTCAAAGAT-AGAATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCA
75061 AGATCATTCGGTGAATCAAGTTAGGGC
65 AGATCATTCGGTGAATCAAGTTAGGGC
* * *
75088 GGTGCCTTACTTCTTCAAAG-TCAG-ATTCGTTGAGCTCGATGCAGCAGATTTTCAAGCAGTTCA
1 GGTGCCTTACTTCTTCAAAGAT-AGAATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCA
*
75151 AGATCATTCGGTGAATCAAGTTGGGGC
65 AGATCATTCGGTGAATCAAGTTAGGGC
* * * * * * *
75178 GGTGCCTTATTTCTTCAAAGATAGAATTCGGTGAGCTCGGAGCAGCATAGTTTCAAACAATAC-T
1 GGTGCCTTACTTCTTCAAAGATAGAATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAA
* * **
75242 GGTGATTCGGTGAATCAAGTTAATGC
66 GATCATTCGGTGAATCAAGTTAGGGC
* * * * * *
75268 GGTG-CAT-C-TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAACACATTTTCAAATAGATCA
1 GGTGCCTTACTTCTTCAAAGA-TAGAATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCA
* * * **
75330 TGGTGATTCGGTGAATCAAGTTAATGC
65 AGATCATTCGGTGAATCAAGTTAGGGC
* * *
75357 AGTG-CAT-C-TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCA
1 GGTGCCTTACTTCTTCAAAGA-TAGAATTCGGTGAGCTCGGTGCA
75399 ACACATTGAT
Statistics
Matches: 351, Mismatches: 36, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
86 64 0.18
87 25 0.07
88 33 0.09
89 70 0.20
90 125 0.36
91 34 0.10
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (91 bp):
GGTGCCTTACTTCTTCAAAGATAGAATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAA
GATCATTCGGTGAATCAAGTTAGGGC
Found at i:75760 original size:21 final size:21
Alignment explanation
Indices: 75734--75786 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
75724 GCACTGGAGT
* * *
75734 ACATGGGTCGCGAGGAAAACC
1 ACATGGGGCGCCAAGAAAACC
*
75755 ACATGGGGCGCCAAGCAAACC
1 ACATGGGGCGCCAAGAAAACC
75776 ACAT-GGGCGCC
1 ACATGGGGCGCC
75787 CAGCGCTAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.30, C:0.30, G:0.32, T:0.08
Consensus pattern (21 bp):
ACATGGGGCGCCAAGAAAACC
Found at i:86632 original size:24 final size:24
Alignment explanation
Indices: 86605--86650 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
86595 CATTTTTGCA
*
86605 CATTTTTATTTAGTAATTTAGTTG
1 CATTTTCATTTAGTAATTTAGTTG
*
86629 CATTTTCGTTTAGTAATTTAGT
1 CATTTTCATTTAGTAATTTAGT
86651 ATTGTTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.13, T:0.57
Consensus pattern (24 bp):
CATTTTCATTTAGTAATTTAGTTG
Found at i:95983 original size:43 final size:42
Alignment explanation
Indices: 95795--95982 Score: 186
Period size: 43 Copynumber: 4.5 Consensus size: 42
95785 CAACTTCAAC
** **
95795 GTGACAACTTCCAGTGTCAAA--TAATAATTTAA-TTTACCGGA
1 GTGACAACTTCTGGTGTCAAAGGTAAT--TTTAATTTTACCAAA
* * *
95836 GCGACAACTTCTAGTGTCAAAGGTAATTTTAA-TTTACCAAG
1 GTGACAACTTCTGGTGTCAAAGGTAATTTTAATTTTACCAAA
* *
95877 GTAACAACTTCTGGTGTTAAAGGTAATTTTAATTTTTACCAAA
1 GTGACAACTTCTGGTGTCAAAGGTAATTTTAA-TTTTACCAAA
* * * * *
95920 GTGACAACTTCTTGTGTCAATGGTAGATTTTAATTTTATCTAT
1 GTGACAACTTCTGGTGTCAAAGGTA-ATTTTAATTTTACCAAA
95963 GTGACAACTTCTGGTGTCAA
1 GTGACAACTTCTGGTGTCAA
95983 TTAAATTTTC
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 58 0.47
43 59 0.48
44 7 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (42 bp):
GTGACAACTTCTGGTGTCAAAGGTAATTTTAATTTTACCAAA
Found at i:96078 original size:94 final size:94
Alignment explanation
Indices: 95964--96367 Score: 627
Period size: 93 Copynumber: 4.3 Consensus size: 94
95954 TTTATCTATG
* * * * *
95964 TGACAACTTCTGGTGTCAATTAAATTTTCTTAAGTAAAAATTTAATTTGACAACTTCTTGTGTCA
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCA
* *
96029 ATTATGTTTACTAAAGTAAGCTTTTAATT
66 ATTATGTTTACTAAAATAAGATTTTAATT
* *
96058 TGACAACTTCTAGTGTCAATTAAATTTACGAAAGTAAAATTTTAATTTGACAACTTCTTGTGTCA
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCA
*
96123 ATTATGTTTACTAAAGTAAGATTTTAATT
66 ATTATGTTTACTAAAATAAGATTTTAATT
96152 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGT-AAATTTTAATTTGACAACTTCTAGTGTCA
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCA
* ** *
96216 AGTAAATTTACTAAAATAAAATTTTAATT
66 ATTATGTTTACTAAAATAAGATTTTAATT
*
96245 TGACAACTTCTAGTGTCAATTACATTTACT-AAGTAAAATTTTAATTTGACAACTTCTAGTGTCA
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCA
96309 ATTAAT-TTTACTAAAATAA-ATTTTAATT
66 ATT-ATGTTTACTAAAATAAGATTTTAATT
*
96337 TGACAACTTCTGGTGTCAATTAAATTTACTA
1 TGACAACTTCTAGTGTCAATTAAATTTACTA
96368 GAGCTCTCGT
Statistics
Matches: 289, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
92 41 0.14
93 125 0.43
94 123 0.43
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (94 bp):
TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCA
ATTATGTTTACTAAAATAAGATTTTAATT
Found at i:96210 original size:46 final size:47
Alignment explanation
Indices: 95964--96367 Score: 607
Period size: 47 Copynumber: 8.7 Consensus size: 47
95954 TTTATCTATG
* * * *
95964 TGACAACTTCTGGTGTCAATTAAATTTTCTTAAGTAAAAATTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
* ** **
96011 TGACAACTTCTTGTGTCAATTATGTTTACTAAAGTAAGCTTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
*
96058 TGACAACTTCTAGTGTCAATTAAATTTACGAAAGTAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
* ** *
96105 TGACAACTTCTTGTGTCAATTATGTTTACTAAAGTAAGATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
96152 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGT-AAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
* *
96198 TGACAACTTCTAGTGTCAAGTAAATTTACTAAAATAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
*
96245 TGACAACTTCTAGTGTCAATTACATTTACT-AAGTAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
* *
96291 TGACAACTTCTAGTGTCAATTAATTTTACTAAAAT-AAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
*
96337 TGACAACTTCTGGTGTCAATTAAATTTACTA
1 TGACAACTTCTAGTGTCAATTAAATTTACTA
96368 GAGCTCTCGT
Statistics
Matches: 322, Mismatches: 33, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
46 126 0.39
47 196 0.61
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (47 bp):
TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
Found at i:97142 original size:38 final size:37
Alignment explanation
Indices: 97053--97149 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 37
97043 ATTTATGTCC
* *
97053 AAATAGGACGTTGGAGACAAAGACAAAAAGCAAAATT
1 AAATAGGACATTGGAAACAAAGACAAAAAGCAAAATT
** * *
97090 AAATATAAGGATTGGAAACAAAGACAAAAAGGCGAAATT
1 AAATAGGA-CATTGGAAACAAAGACAAAAA-GCAAAATT
97129 AAATAGGACATTGGAAACAAA
1 AAATAGGACATTGGAAACAAA
97150 AAACCAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
37 6 0.12
38 30 0.61
39 13 0.27
ACGTcount: A:0.56, C:0.09, G:0.21, T:0.14
Consensus pattern (37 bp):
AAATAGGACATTGGAAACAAAGACAAAAAGCAAAATT
Found at i:97983 original size:7 final size:7
Alignment explanation
Indices: 97962--98029 Score: 57
Period size: 7 Copynumber: 9.3 Consensus size: 7
97952 TAATATACGT
97962 ATTATATA
1 ATTA-ATA
97970 ATATAATA
1 AT-TAATA
97978 ATTAATA
1 ATTAATA
97985 ATTAATA
1 ATTAATA
*
97992 ATGGAATA
1 AT-TAATA
*
98000 ATTTATA
1 ATTAATA
98007 ATTAA-A
1 ATTAATA
**
98013 AAAAATA
1 ATTAATA
98020 ATTGAATA
1 ATT-AATA
98028 AT
1 AT
98030 GAAAATATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 4 0.08
7 23 0.48
8 19 0.40
9 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (7 bp):
ATTAATA
Found at i:110899 original size:54 final size:54
Alignment explanation
Indices: 110816--111362 Score: 736
Period size: 54 Copynumber: 10.1 Consensus size: 54
110806 CCGAATTTCA
* *
110816 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTCTAAGTTCATCTTC
1 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTC
* * *
110870 GAGTGATCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGTATTAAGTTTATCTTC
1 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGT-TTAAGTTTATCTTC
* * * *
110925 AAGTGATCCAGTGCGGTCACTCAAGAAAGTTTGCAGTGGTCTAAGTTCATCTTC
1 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTC
* * * * *
110979 GAGTGGTCCAGTGCGATCAGTCAAGAAAGTTTCCAGTGGTATTAAGTTTACCTTC
1 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGT-TTAAGTTTATCTTC
* * *
111034 AAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTACTGTGGTTTAAGTTTATCTTC
1 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTC
* * * * * *
111088 AAGTGATTCAGTACGGTCAATCAAGCAAGTTACTAATGGTTTAAGTTTATCTTC
1 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTC
*
111142 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTGATCTTC
1 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTC
* *
111196 AAGTGATCCAGTGTGGTCAATCAAGAAAGTTTCCAGTGGTTTAAATTTATCTTC
1 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTC
* *
111250 AAGTGATCCAGTGCGGTTAATCAAGGAAGTTTCCAGTGGTTT-AGATTTATCTTC
1 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAG-TTTATCTTC
* * * * * * * *
111304 AAGTGATCCAGTGCGGTTATTCGAGGAAGTTTTCAGTGATTTGAGTATATCTTC
1 AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTC
111358 AAGTG
1 AAGTG
111363 GTTCGGTGAA
Statistics
Matches: 436, Mismatches: 53, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
53 1 0.00
54 339 0.78
55 96 0.22
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (54 bp):
AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCTTC
Found at i:111261 original size:29 final size:29
Alignment explanation
Indices: 111227--111316 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
111217 CAAGAAAGTT
111227 TCCAGTGGTTTAAATTTATCTTCAAGTGA
1 TCCAGTGGTTTAAATTTATCTTCAAGTGA
* * *** *
111256 TCCAGTGCGGTT-AA-TCA--AGGAAGT-T
1 TCCAGTG-GTTTAAATTTATCTTCAAGTGA
*
111281 TCCAGTGGTTTAGATTTATCTTCAAGTGA
1 TCCAGTGGTTTAAATTTATCTTCAAGTGA
111310 TCCAGTG
1 TCCAGTG
111317 CGGTTATTCG
Statistics
Matches: 42, Mismatches: 13, Indels: 12
0.63 0.19 0.18
Matches are distributed among these distances:
24 3 0.07
25 8 0.19
26 6 0.14
28 6 0.14
29 16 0.38
30 3 0.07
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (29 bp):
TCCAGTGGTTTAAATTTATCTTCAAGTGA
Found at i:111766 original size:43 final size:43
Alignment explanation
Indices: 111352--111758 Score: 529
Period size: 43 Copynumber: 9.5 Consensus size: 43
111342 ATTTGAGTAT
* * *
111352 ATCTTC-AAG-TGG-TTCGGTGAATCAGACGACTCGGAGAAGC
1 ATCTTCAAAGTTGGATTCGGTGAATCAGATGACTCGGTGTAGC
* * * *
111392 ATCTTCTAAGTTGGATTCGGTGAATCAGATGACTTGGTGAAAC
1 ATCTTCAAAGTTGGATTCGGTGAATCAGATGACTCGGTGTAGC
* * * *
111435 ATCTTCTAATTTGGATTTGGTGAACCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGGATTCGGTGAATCAGATGACTCGGTGTAGC
* *
111478 ATCTTCTAAGTTGGATTTGGTGAA-CATGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGGATTCGGTGAATCA-GATGACTCGGTGTAGC
*
111521 ATCTTCAAAGTTGGATTTGGTGAATCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGGATTCGGTGAATCAGATGACTCGGTGTAGC
**
111564 ATCTTCAAAGTTGGATTTAGTGAATCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGGATTCGGTGAATCAGATGACTCGGTGTAGC
111607 ATCTTC-AAGTTGGATTCGG-GAAAATCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGGATTCGGTG--AATCAGATGACTCGGTGTAGC
* * *
111650 ATCTTCAAAGTTGGATTCGGTGAGTCAGATGACTCAGTGGAGC
1 ATCTTCAAAGTTGGATTCGGTGAATCAGATGACTCGGTGTAGC
* * **
111693 ATCTTCAAAGTTGGATTCGGTGAATCCGGTGACTCAATGTAGC
1 ATCTTCAAAGTTGGATTCGGTGAATCAGATGACTCGGTGTAGC
*
111736 ATCTTCAAAGTTAGATTCGGTGA
1 ATCTTCAAAGTTGGATTCGGTGA
111759 GCTCGGTGCA
Statistics
Matches: 334, Mismatches: 24, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
40 6 0.02
41 4 0.01
42 16 0.05
43 292 0.87
44 15 0.04
45 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (43 bp):
ATCTTCAAAGTTGGATTCGGTGAATCAGATGACTCGGTGTAGC
Found at i:111843 original size:90 final size:90
Alignment explanation
Indices: 111737--112535 Score: 874
Period size: 90 Copynumber: 9.2 Consensus size: 90
111727 CAATGTAGCA
* * * * *
111737 TCTTCAAAGTTAGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGACGATTCGGTG
1 TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATGATTCGGTG
111802 AATCAAGTTAATGCGGTGCATTATT
66 AATCAAGTTAATGCGGTGCATTATT
* * *
111827 TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCATATTTTCAAATAGTTCAGGACGATTCGGTG
1 TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATGATTCGGTG
111892 AATCAAGTTAATGCGGTGCATTATT
66 AATCAAGTTAATGCGGTGCATTATT
* * * *
111917 TGTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTGAGGACGATTCGGTG
1 TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATGATTCGGTG
111982 AATCAAGTTAATGCGGTGC---A--
66 AATCAAGTTAATGCGGTGCATTATT
* *
112002 --TT---A-TTGGATTCGGTGAGCTCGGTGCAGCACATTCTCAAACAGTTAAAGG-TGATTCGGT
1 TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTT-CAGGATGATTCGGT
*
112060 GAATCAAGTTAATGCAGTGCATTA--
65 GAATCAAGTTAATGCGGTGCATTATT
* * *
112084 --TT---A----GATTCGGTGAGCTCGGTGCAGCACATTCTCAAACAGTTAAGGGTGATTCGGTG
1 TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATGATTCGGTG
* *
112140 AATCAAGTTATTGTGGTGC---A--
66 AATCAAGTTAATGCGGTGCATTATT
** * * *
112160 --TT---A-TTGGATTCGGTGAGCTCGGTGTTGCATATTCTCAAACAGTTCAGAATGATTCGGTG
1 TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATGATTCGGTG
* * * *
112219 AATTAAGTTGAGGCGGTGCCTTATT
66 AATCAAGTTAATGCGGTGCATTATT
* * * * *
112244 TCTTCAAAGTCGGATTCAGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTGATGATGATTCGGTG
1 TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATGATTCGGTG
* *
112309 AATCAAGTTACTGCGGTGCTTTATT
66 AATCAAGTTAATGCGGTGCATTATT
* * * *
112334 TCTTCAAAGTCGGATTCAGTGAGCTCAGTGCAGCAGATTTTCAAACAGTTCAGGATGATTCGGTG
1 TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATGATTCGGTG
* * * *
112399 AATCAAGTTGAGGCAGTGCCTTATT
66 AATCAAGTTAATGCGGTGCATTATT
* * * * *
112424 TCTTCAAAGTCGGATTCAGTGAGTTCGGTGCAGCAAATTTCCAAACAGTTCAGGATGATTCGGTG
1 TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATGATTCGGTG
* *
112489 AATTAAGTTACTGCGGTGCATTATT
66 AATCAAGTTAATGCGGTGCATTATT
**
112514 TCTTCAAAGTTTTATTCGGTGA
1 TCTTCAAAGTTGGATTCGGTGA
112536 ATCAGATTGG
Statistics
Matches: 629, Mismatches: 61, Indels: 38
0.86 0.08 0.05
Matches are distributed among these distances:
76 4 0.01
78 4 0.01
79 191 0.30
80 4 0.01
82 5 0.01
83 2 0.00
86 2 0.00
87 1 0.00
89 1 0.00
90 415 0.66
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (90 bp):
TCTTCAAAGTTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAACAGTTCAGGATGATTCGGTG
AATCAAGTTAATGCGGTGCATTATT
Found at i:112057 original size:79 final size:79
Alignment explanation
Indices: 111926--112333 Score: 453
Period size: 79 Copynumber: 5.0 Consensus size: 79
111916 TTGTTCAAAG
* * * *
111926 TTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTT-GAGGACGATTCGGTGAATCAAGT
1 TTGGATTCGGTGAGCTCGGTGCAGCACATTCTCAAACAGTTAAAGG-TGATTCGGTGAATCAAGT
111990 TAATGCGGTGCATTA
65 TAATGCGGTGCATTA
112005 TTGGATTCGGTGAGCTCGGTGCAGCACATTCTCAAACAGTTAAAGGTGATTCGGTGAATCAAGTT
1 TTGGATTCGGTGAGCTCGGTGCAGCACATTCTCAAACAGTTAAAGGTGATTCGGTGAATCAAGTT
*
112070 AATGCAGTGCATTA
66 AATGCGGTGCATTA
* *
112084 TTAGATTCGGTGAGCTCGGTGCAGCACATTCTCAAACAGTTAAGGGTGATTCGGTGAATCAAGTT
1 TTGGATTCGGTGAGCTCGGTGCAGCACATTCTCAAACAGTTAAAGGTGATTCGGTGAATCAAGTT
* *
112149 ATTGTGGTGCATTA
66 AATGCGGTGCATTA
** * *
112163 TTGGATTCGGTGAGCTCGGTGTTGCATATTCTCAAACAGTTCAGAA--TGATTCGGTGAATTAAG
1 TTGGATTCGGTGAGCTCGGTGCAGCACATTCTCAAACAGTT-A-AAGGTGATTCGGTGAATCAAG
* *
112226 TTGAGGCGGTGCCTTATTTCTTCAAA
64 TTAATGCGGTG-C--A----TT---A
* * * * * * *
112252 GTCGGATTCAGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTGATGATGATTCGGTGAATCAAGT
1 -TTGGATTCGGTGAGCTCGGTGCAGCACATTCTCAAACAGTTAAAGGTGATTCGGTGAATCAAGT
* *
112317 TACTGCGGTGCTTTA
65 TAATGCGGTGCATTA
112332 TT
1 TT
112334 TCTTCAAAGT
Statistics
Matches: 279, Mismatches: 34, Indels: 32
0.81 0.10 0.09
Matches are distributed among these distances:
79 205 0.73
80 6 0.02
81 1 0.00
82 1 0.00
83 2 0.01
86 2 0.01
88 1 0.00
89 2 0.01
90 59 0.21
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (79 bp):
TTGGATTCGGTGAGCTCGGTGCAGCACATTCTCAAACAGTTAAAGGTGATTCGGTGAATCAAGTT
AATGCGGTGCATTA
Found at i:124436 original size:18 final size:18
Alignment explanation
Indices: 124413--124448 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
124403 ACACACATGA
124413 TACCTAC-ATATATGACTT
1 TACCTACTATATAT-ACTT
124431 TACCTACTATATATACTT
1 TACCTACTATATATACTT
124449 CCATTCTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TACCTACTATATATACTT
Found at i:130860 original size:24 final size:24
Alignment explanation
Indices: 130809--130860 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
130799 CTAATTTAAG
*
130809 TGTTGTTTGCAATGACACTAAAAG
1 TGTTGTTTGCAATGACACTAAAAC
** * *
130833 TGTTGTTTGTGATGATACTAAATC
1 TGTTGTTTGCAATGACACTAAAAC
130857 TGTT
1 TGTT
130861 TTGGATGCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (24 bp):
TGTTGTTTGCAATGACACTAAAAC
Found at i:130948 original size:30 final size:33
Alignment explanation
Indices: 130878--130960 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
130868 CTAATTGTGA
* *
130878 TGAAAATAATTTTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATCTTGTTTTGGTAGATCATAGCAT
*
130911 TGCAAATAATCTTGTTTTGGTAGAT-A-A-CAT
1 TGAAAATAATCTTGTTTTGGTAGATCATAGCAT
130941 TGAAAATAAATC-TGTTTTGG
1 TGAAAAT-AATCTTGTTTTGG
130961 GTGACGAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
30 17 0.38
31 5 0.11
32 1 0.02
33 22 0.49
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (33 bp):
TGAAAATAATCTTGTTTTGGTAGATCATAGCAT
Found at i:132864 original size:30 final size:32
Alignment explanation
Indices: 132783--132864 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
132773 TCACATGGGG
*
132783 CAACCGGCCACAACCGGCCATCGATTGGCGCAC
1 CAACCGGACACAACCGGCCATCGATTGGCG-AC
*
132816 CAACCGGCCACAACCGGCCATCGATTGG-G-C
1 CAACCGGACACAACCGGCCATCGATTGGCGAC
*
132846 CATCCGGACA-AGACCGGCC
1 CAACCGGACACA-ACCGGCC
132865 TTTTGATCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 1 0.02
30 16 0.35
32 1 0.02
33 28 0.61
ACGTcount: A:0.24, C:0.41, G:0.26, T:0.09
Consensus pattern (32 bp):
CAACCGGACACAACCGGCCATCGATTGGCGAC
Found at i:137499 original size:13 final size:14
Alignment explanation
Indices: 137469--137505 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
137459 AGAGTCATGG
137469 TTTTCAAAAATGCTT
1 TTTTCAAAAATGC-T
137484 TTTTCAAAAATG-T
1 TTTTCAAAAATGCT
137497 TTTTCAAAA
1 TTTTCAAAA
137506 GAGAGTCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.45
15 12 0.55
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (14 bp):
TTTTCAAAAATGCT
Found at i:138288 original size:16 final size:17
Alignment explanation
Indices: 138269--138305 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
138259 AAAAAAAAGG
138269 ATGAAAAAAAT-AAAAA
1 ATGAAAAAAATGAAAAA
*
138285 ATG-AGAAAATGAAAAA
1 ATGAAAAAAATGAAAAA
138301 ATGAA
1 ATGAA
138306 TGGAAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 11 0.61
17 1 0.06
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (17 bp):
ATGAAAAAAATGAAAAA
Found at i:138293 original size:8 final size:8
Alignment explanation
Indices: 138273--138305 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
138263 AAAAGGATGA
138273 AAAAAAT-
1 AAAAAATG
138280 AAAAAATG
1 AAAAAATG
*
138288 AGAAAATG
1 AAAAAATG
138296 AAAAAATG
1 AAAAAATG
138304 AA
1 AA
138306 TGGAAAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:139103 original size:23 final size:23
Alignment explanation
Indices: 139073--139120 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
139063 GTCATACATA
**
139073 ATTGCATCATCATCCATTTTTGC
1 ATTGCATCATCAAACATTTTTGC
*
139096 ATTGCATCATGAAACATTTTTGC
1 ATTGCATCATCAAACATTTTTGC
139119 AT
1 AT
139121 CAAAGTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (23 bp):
ATTGCATCATCAAACATTTTTGC
Found at i:139329 original size:8 final size:8
Alignment explanation
Indices: 139307--139726 Score: 118
Period size: 8 Copynumber: 53.0 Consensus size: 8
139297 AGTAATCTCT
139307 TTCTTCAA
1 TTCTTCAA
* *
139315 CTATTCAA
1 TTCTTCAA
*
139323 TGCTTCAA
1 TTCTTCAA
* *
139331 ATCTTCTA
1 TTCTTCAA
*
139339 TTATTCAA
1 TTCTTCAA
139347 TTCTTCAA
1 TTCTTCAA
*
139355 TACTTCAA
1 TTCTTCAA
*
139363 -T-TT-AT
1 TTCTTCAA
139368 TTCTTCAA
1 TTCTTCAA
139376 TTCTTCAA
1 TTCTTCAA
* *
139384 TTATT-TA
1 TTCTTCAA
139391 TTGCTTCAA
1 TT-CTTCAA
*
139400 TTTTTCAA
1 TTCTTCAA
139408 TTAC-TCAA
1 TT-CTTCAA
*
139416 TGCTTCAA
1 TTCTTCAA
139424 TTCTTCAA
1 TTCTTCAA
*
139432 TTATTCAA
1 TTCTTCAA
*
139440 TGCTTCAA
1 TTCTTCAA
139448 TTTGCTTCAA
1 -TT-CTTCAA
* * *
139458 TGAC-CCAGG
1 T-TCTTCA-A
* **
139467 GTGGTC--
1 TTCTTCAA
139473 TTGCTTCAA
1 TT-CTTCAA
139482 TTCTTCAA
1 TTCTTCAA
*
139490 TTATTCAA
1 TTCTTCAA
*
139498 TACTTCAA
1 TTCTTCAA
*
139506 TTTACTTCTGATC
1 -TT-CTTC--A-A
139519 TTGCTTCAA
1 TT-CTTCAA
139528 -T-TTCAA
1 TTCTTCAA
139534 TTTCAAATTCAA
1 -TTC---TTCAA
*
139546 TCCTTCAA
1 TTCTTCAA
*
139554 TGCTT-AA
1 TTCTTCAA
*
139561 AT-TTCAA
1 TTCTTCAA
139568 -T-TTCAA
1 TTCTTCAA
139574 TTCTTCAA
1 TTCTTCAA
139582 TTCTTCAA
1 TTCTTCAA
139590 TTCTTCAA
1 TTCTTCAA
*
139598 -T-ATCAA
1 TTCTTCAA
139604 TTCTTCAA
1 TTCTTCAA
** *
139612 TGGTCCAA
1 TTCTTCAA
139620 TTTCAATTCAA
1 -TTC--TTCAA
* *
139631 TCCTTCAG
1 TTCTTCAA
139639 TGT-TTCAA
1 T-TCTTCAA
139647 -T-TTCAA
1 TTCTTCAA
*
139653 TTATTCAA
1 TTCTTCAA
139661 TGT-TTCAA
1 T-TCTTCAA
139669 -T-TTCAA
1 TTCTTCAA
* *
139675 TTATTCAG
1 TTCTTCAA
*
139683 TGCTTCAA
1 TTCTTCAA
139691 -T-TTCAA
1 TTCTTCAA
*
139697 TCCTTCAA
1 TTCTTCAA
*
139705 TGCTTCAA
1 TTCTTCAA
139713 -T-TTCAA
1 TTCTTCAA
139719 TTCTTCAA
1 TTCTTCAA
139727 ATGTTTCGAT
Statistics
Matches: 299, Mismatches: 69, Indels: 88
0.66 0.15 0.19
Matches are distributed among these distances:
5 1 0.00
6 43 0.14
7 18 0.06
8 194 0.65
9 12 0.04
10 13 0.04
11 6 0.02
12 12 0.04
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.45
Consensus pattern (8 bp):
TTCTTCAA
Found at i:139335 original size:24 final size:24
Alignment explanation
Indices: 139307--139726 Score: 186
Period size: 22 Copynumber: 17.7 Consensus size: 24
139297 AGTAATCTCT
*
139307 TTCTTCAACTATTCAATGCTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
* * *
139331 ATCTTCTATTATTCAATTCTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
*
139355 TACTTCAATTTATT---T-CTTCAA
1 TTCTTCAA-TTATTCAATGCTTCAA
* *
139376 TTCTTCAATTATTTATTGCTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
* *
139400 TTTTTCAATTACTCAATGCTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
139424 TTCTTCAATTATTCAATGCTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
* ** *
139448 TTTGCTTCAATGACCCAGGGTGGTCTTGCTTCAA
1 -TT-CTTCAATTATTCA--------ATGCTTCAA
*
139482 TTCTTCAATTATTCAATACTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
* *
139506 TTTACTTC--TGA-TC-TTGCTTCAA
1 -TT-CTTCAATTATTCAATGCTTCAA
*
139528 -T-TTCAATTTCAAATTCAATCCTTCAA
1 TTCTTCAA-TT---ATTCAATGCTTCAA
* *
139554 TGCTT-AAAT-TTCAAT--TTCAA
1 TTCTTCAATTATTCAATGCTTCAA
* *
139574 TTCTTCAATTCTTCAATTCTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
* * * *
139598 -T-ATCAATTCTTCAATGGTCCAA
1 TTCTTCAATTATTCAATGCTTCAA
** * *
139620 TTTCAATTCAATCCTTCAGTGTTTCAA
1 -TTC--TTCAATTATTCAATGCTTCAA
*
139647 -T-TTCAATTATTCAATGTTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
*
139669 -T-TTCAATTATTCAGTGCTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
**
139691 -T-TTCAATCCTTCAATGCTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
*
139713 -T-TTCAATTCTTCAA
1 TTCTTCAATTATTCAA
139727 ATGTTTCGAT
Statistics
Matches: 309, Mismatches: 51, Indels: 74
0.71 0.12 0.17
Matches are distributed among these distances:
18 3 0.01
20 15 0.05
21 17 0.06
22 107 0.35
23 4 0.01
24 89 0.29
25 12 0.04
26 22 0.07
27 18 0.06
28 2 0.01
32 10 0.03
33 2 0.01
34 8 0.03
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.45
Consensus pattern (24 bp):
TTCTTCAATTATTCAATGCTTCAA
Found at i:139373 original size:21 final size:20
Alignment explanation
Indices: 139347--139389 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
139337 TATTATTCAA
139347 TTCTTCAATACTTCAATTTAT
1 TTCTTCAATACTTCAA-TTAT
*
139368 TTCTTCAATTCTTCAATTAT
1 TTCTTCAATACTTCAATTAT
139388 TT
1 TT
139390 ATTGCTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.56
Consensus pattern (20 bp):
TTCTTCAATACTTCAATTAT
Found at i:139621 original size:30 final size:27
Alignment explanation
Indices: 139531--139654 Score: 113
Period size: 28 Copynumber: 4.4 Consensus size: 27
139521 GCTTCAATTT
* *
139531 CAATTTCAAATTCAATCCTTCAATGCTT
1 CAATTTC-AATTCAATTCTTCAATGCTC
* * *
139559 AAATTTCAATTTCAATTCTTCAATTCTT
1 CAATTTCAA-TTCAATTCTTCAATGCTC
*
139587 CAATTCTTCAATATCAATTCTTCAATGGTC
1 CAA-T-TTCAAT-TCAATTCTTCAATGCTC
* * * *
139617 CAATTTCAATTCAATCCTTCAGTGTTT
1 CAATTTCAATTCAATTCTTCAATGCTC
139644 CAATTTCAATT
1 CAATTTCAATT
139655 ATTCAATGTT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
27 26 0.32
28 30 0.37
29 3 0.04
30 22 0.27
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.44
Consensus pattern (27 bp):
CAATTTCAATTCAATTCTTCAATGCTC
Found at i:141152 original size:18 final size:18
Alignment explanation
Indices: 141129--141164 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
141119 ACACACATGA
141129 TACCTAC-ATATATGACTT
1 TACCTACTATATAT-ACTT
141147 TACCTACTATATATACTT
1 TACCTACTATATATACTT
141165 CCATTCTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TACCTACTATATATACTT
Found at i:145432 original size:67 final size:68
Alignment explanation
Indices: 145204--145643 Score: 479
Period size: 67 Copynumber: 6.6 Consensus size: 68
145194 TTATTTTCAC
* * * * **
145204 TTTCCAGAAATATCCTTTCGGTCAAAGGGCCATTTTTTTCTTTTCGCATTTAAGTTTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTCGCATTTAAGTTTAGTATTTT
145269 GTT
66 GTT
* *
145272 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTCGCATTTAAATTTAGTAGTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTCGCATTTAAGTTTAGTATTTT
145337 GTTT
66 G-TT
* * *
145341 TTTCCAAAAATACCCTTTCGGTGGAAGGATCATTTTCATCTTTT-GCATTTAGGTTTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTCGCATTTAAGTTTAGTATTTT
145405 GTT
66 GTT
* * * * * *
145408 TTTCCAAAAATACCCTTTCAGTGGAAGGATCATTTTCGTCTTTT-GCATTCAGGTTTAG--TTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTCGCATTTAAGTTTAGTATTTT
**
145470 -AC
66 GTT
* * * * * *
145472 TTTCCAAAAATACCCTTCCGGTCGAAAGGTCAGTTTT-GTCTTTTTGCATTCAATTTTAGTATTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCA-TTTTCATCTTTTCGCATTTAAGTTTAGTATTT
145536 TCG--
65 T-GTT
* * * * *
145539 TTTCCAGAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTGGCATTTAGGTTTAG--TTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTCGCATTTAAGTTTAGTATTTT
*
145602 -AT
66 GTT
* *
145604 TTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATC
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATC
145644 AGGTTGTTGC
Statistics
Matches: 326, Mismatches: 36, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
64 34 0.10
65 61 0.19
66 3 0.01
67 108 0.33
68 76 0.23
69 44 0.13
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.43
Consensus pattern (68 bp):
TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTCGCATTTAAGTTTAGTATTTT
GTT
Found at i:145619 original size:132 final size:131
Alignment explanation
Indices: 145204--145691 Score: 513
Period size: 132 Copynumber: 3.7 Consensus size: 131
145194 TTATTTTCAC
* * * * * * *
145204 TTTCCAGAAATATCCTTTCGGTC-AAAGGGCCATTTTTTTCTTTTCGCATTTAAGTTTAGTATTT
1 TTTCCAAAAATACCCTTCCGGTCGAAA-GGTCAGTTTTATCTTTTTGCATTTAAGTTTAGTATTT
* **
145268 TGTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCTTTTCGCATTTAAATTTAGTA
65 TG-TTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTT-GCATTT-AGGTT--TA
*
145333 GTTTGTTT
125 GTTT-TAT
* * *
145341 TTTCCAAAAATACCCTTTCGGT-GGAAGGATCA-TTTTCATC-TTTTGCATTTAGGTTTAGTATT
1 TTTCCAAAAATACCCTTCCGGTCGAAAGG-TCAGTTTT-ATCTTTTTGCATTTAAGTTTAGTATT
* * * *
145403 TTGTTTTTCCAAAAATACCCTTTCAGTGGAAGGATCATTTTCGTCTTTTGCATTCAGGTTTAGTT
64 TTG-TTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAGGTTTAGTT
*
145468 TTAC
128 TTAT
* * *
145472 TTTCCAAAAATACCCTTCCGGTCGAAAGGTCAGTTTTGTCTTTTTGCATTCAATTTTAGTATTTT
1 TTTCCAAAAATACCCTTCCGGTCGAAAGGTCAGTTTTATCTTTTTGCATTTAAGTTTAGTATTTT
* *
145537 CG-TTTCCAGAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTGGCATTTAGGTTTAGTTT
66 -GTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTT-GCATTTAGGTTTAGTTT
145601 TAT
129 TAT
* * * * *
145604 TTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATCAGGTTGTTGCATTTAAGTCTAGT-C
1 TTTCCAAAAATACCCTTCCGGTCGAAAGGTCAGTTTTATC---TTTTTGCATTTAAGTTTAGTAT
*
145668 TTT-CTTTCCAAAGAATACCCTTTC
63 TTTGTTTTCCAAA-AATACCCTTTC
145692 TGATACGAAT
Statistics
Matches: 300, Mismatches: 38, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
131 66 0.22
132 91 0.30
133 8 0.03
134 17 0.06
135 21 0.07
136 71 0.24
137 26 0.09
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.43
Consensus pattern (131 bp):
TTTCCAAAAATACCCTTCCGGTCGAAAGGTCAGTTTTATCTTTTTGCATTTAAGTTTAGTATTTT
GTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAGGTTTAGTTTTA
T
Found at i:148381 original size:39 final size:40
Alignment explanation
Indices: 148305--148387 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 40
148295 TTATCATGAT
* * * *
148305 ATTCATTTGTATATGTTCATGCATCGATCATACATTATCC
1 ATTCATATGTATATGTTCATGCATCCATCACACATTATAC
**
148345 ATTCATATGTATATG-TCATGCATCCATCACGTATTATAC
1 ATTCATATGTATATGTTCATGCATCCATCACACATTATAC
148384 ATTC
1 ATTC
148388 CGCCGTATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 23 0.62
40 14 0.38
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (40 bp):
ATTCATATGTATATGTTCATGCATCCATCACACATTATAC
Done.