Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012235.1 Kokia drynarioides strain JFW-HI SEQ_127236, 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: 288195
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 34 characters in sequence are not A, C, G, or T
Found at i:8999 original size:42 final size:42
Alignment explanation
Indices: 8934--9054 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 42
8924 AAACAATCTT
* * * *
8934 ATTCTC-TATCGAGTCATAAGTCTTCCTTTAATCATATTCCC
1 ATTCTCATCTCGAGACATGAGTCTTCCTTTAATCATATTACC
* *
8975 ATTCTCATCTCGAGACATGAGTCTTCCTTTAATCATAATATC
1 ATTCTCATCTCGAGACATGAGTCTTCCTTTAATCATATTACC
9017 ATTCTCATC-CTGAGACATGAGTCTTCCTTTAATCATAT
1 ATTCTCATCTC-GAGACATGAGTCTTCCTTTAATCATAT
9055 AAACTTTTCA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
41 7 0.10
42 64 0.90
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.40
Consensus pattern (42 bp):
ATTCTCATCTCGAGACATGAGTCTTCCTTTAATCATATTACC
Found at i:14336 original size:22 final size:22
Alignment explanation
Indices: 14288--14359 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 22
14278 ATTTTGTTTA
14288 AAATTTTTAACTTTTCTAAAAAAAT
1 AAATTTTT-A-TTTT-TAAAAAAAT
*
14313 AAATTTTTATTTTTAAAAATAT
1 AAATTTTTATTTTTAAAAAAAT
*
14335 AAACTTATTTTTTTTTAAAGAAAAT
1 AAA-TT-TTTATTTTTAAA-AAAAT
14360 TACTATTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 11 0.27
23 6 0.15
24 12 0.29
25 12 0.29
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (22 bp):
AAATTTTTATTTTTAAAAAAAT
Found at i:14429 original size:138 final size:138
Alignment explanation
Indices: 14177--14429 Score: 325
Period size: 138 Copynumber: 1.8 Consensus size: 138
14167 TAAAAACCAT
*
14177 ATTTTTATTTTTAAAAATATAAACTTTCTACTTTTTTAATGAAAATCACTACTTTCTTAAAAATC
1 ATTTTTATTTTTAAAAATATAAACTTTCTACTTTTTTAAAGAAAATCACTACTTTCTTAAAAATC
* * ***
14242 TAAATTTTTATTCCAAAATATTTAAAAAAAATCAAAATTTTGTTTAAAATTTTTAACTTTTCTAA
66 AAAACTTTTATTCCAAAATATTTAAAAAAAATCAAAATTTTGCCCAAAATTTTTAACTTTTCTAA
14307 AAAAATAA
131 AAAAATAA
* * *
14315 ATTTTTATTTTTAAAAATATAAACTTAT-T-TTTTTTTAAAGAAAATTACTATTTTACTTAAAAA
1 ATTTTTATTTTTAAAAATATAAACTT-TCTACTTTTTTAAAGAAAATCACTACTTT-CTTAAAAA
* * * *
14378 TCAAAACTTTTATTTCGAAAT-TGTTTAAAAAAATTAAAACTTTT-CCCAAAAT
64 TCAAAACTTTTATTCCAAAATAT-TTAAAAAAAATCAAAA-TTTTGCCCAAAAT
14430 CAAGTTATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
137 22 0.22
138 71 0.72
139 5 0.05
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (138 bp):
ATTTTTATTTTTAAAAATATAAACTTTCTACTTTTTTAAAGAAAATCACTACTTTCTTAAAAATC
AAAACTTTTATTCCAAAATATTTAAAAAAAATCAAAATTTTGCCCAAAATTTTTAACTTTTCTAA
AAAAATAA
Found at i:17465 original size:14 final size:16
Alignment explanation
Indices: 17441--17481 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
17431 GTCATGCCTC
*
17441 TTTAAAATTTA-CTTT
1 TTTATAATTTAGCTTT
*
17456 TTT-TAATTTAGGTTT
1 TTTATAATTTAGCTTT
17471 TTTATAATTTA
1 TTTATAATTTA
17482 AAATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 6 0.27
15 9 0.41
16 7 0.32
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (16 bp):
TTTATAATTTAGCTTT
Found at i:20374 original size:52 final size:53
Alignment explanation
Indices: 20303--20421 Score: 186
Period size: 52 Copynumber: 2.3 Consensus size: 53
20293 AATACTCTTG
* *
20303 ATGACACATAGTCATCGGACCTCTTAATCCATAAA-GGAATCATATACTCACA
1 ATGACACATAGTCAACGGACCTCATAATCCATAAAGGGAATCATATACTCACA
* * *
20355 ATGACACATAGTCAACGGACCTCATAATCCTTAAAGGGATTCATATACTCACG
1 ATGACACATAGTCAACGGACCTCATAATCCATAAAGGGAATCATATACTCACA
20408 ATGACACATAGTCA
1 ATGACACATAGTCA
20422 TCAAACCTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
52 32 0.52
53 29 0.48
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (53 bp):
ATGACACATAGTCAACGGACCTCATAATCCATAAAGGGAATCATATACTCACA
Found at i:27489 original size:52 final size:52
Alignment explanation
Indices: 27419--27649 Score: 363
Period size: 52 Copynumber: 4.4 Consensus size: 52
27409 TAATACTTAT
* *
27419 GATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGAATCATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
* *
27471 GATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCATATACTCAT
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
* * *
27523 GATGACATATAGTCATTGGACCTCATAATCCGTAAATGATTCATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
* *
27575 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATCCTCAT
1 GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
* *
27627 GATGACACATAGTTATCAGACCT
1 GATGACACATAGTCATCGGACCT
27650 TTTTCATTTA
Statistics
Matches: 164, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 164 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (52 bp):
GATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCAC
Found at i:29668 original size:31 final size:32
Alignment explanation
Indices: 29617--29689 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
29607 TCAGTTTAAC
* * *
29617 AAGTG-TTTGCATCTTTAATTATGTCTTGCATT
1 AAGTGTTTTGCA-CTTTAATTAAGTCATGCATA
29649 AAGTGTTTTGCA-TTTAATTAAGTCATGCATA
1 AAGTGTTTTGCACTTTAATTAAGTCATGCATA
29680 AAGTTGTTTT
1 AAG-TGTTTT
29690 TTTTTCTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 19 0.53
32 11 0.31
33 6 0.17
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (32 bp):
AAGTGTTTTGCACTTTAATTAAGTCATGCATA
Found at i:29839 original size:24 final size:24
Alignment explanation
Indices: 29764--29840 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
29754 CTTCATTAAG
29764 TGTTTTGTTTGTTAAATGCATCTT
1 TGTTTTGTTTGTTAAATGCATCTT
** * * * **
29788 TGTTTAATAAT-CTACAT-CATTCAG
1 TGTTTTGT-TTGTTAAATGCA-TCTT
29812 TGTTTTGTTTGTTAAATGCATCTT
1 TGTTTTGTTTGTTAAATGCATCTT
29836 TGTTT
1 TGTTT
29841 AATAATCTGC
Statistics
Matches: 35, Mismatches: 14, Indels: 8
0.61 0.25 0.14
Matches are distributed among these distances:
23 3 0.09
24 29 0.83
25 3 0.09
ACGTcount: A:0.21, C:0.10, G:0.14, T:0.55
Consensus pattern (24 bp):
TGTTTTGTTTGTTAAATGCATCTT
Found at i:29950 original size:48 final size:48
Alignment explanation
Indices: 29756--29935 Score: 288
Period size: 48 Copynumber: 3.8 Consensus size: 48
29746 TAATTATGCT
29756 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACA
* *
29804 TCATTCAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACA
* *
29852 TCATTAAGTGTTTTGTTTATTAAATGCATCTTTGTTTAGTAATCTACA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACA
* * * *
29900 TTATTAAATGTTTTGTTTGCTAAATGCATCTCTGTT
1 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTT
29936 AAATGTCTTA
Statistics
Matches: 121, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 121 1.00
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (48 bp):
TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTACA
Found at i:30469 original size:78 final size:76
Alignment explanation
Indices: 30351--30507 Score: 233
Period size: 78 Copynumber: 2.0 Consensus size: 76
30341 CAACCAATAA
* * * *
30351 ACACATTAAGGTTACATAAGTCTTCATTAAGGAGAAATGCCATGTCTTTTCAGCTACATCAAATC
1 ACACATTAAGGTAAAATAAGTCTTCATTAAGGAGAAATGCCATGCCTTTTCAACTACATCAAATC
30416 CTAAGGAAGAG
66 CTAAGGAAGAG
* *
30427 ACACATTAAGGATAAAATCAGTCTTCATTTAAGGAGAAATGCCATGCCTTTTCAACTACATCAGA
1 ACACATTAAGG-TAAAATAAGTCTTCA-TTAAGGAGAAATGCCATGCCTTTTCAACTACATCAAA
*
30492 TCCTAATGAAGAG
64 TCCTAAGGAAGAG
30505 ACA
1 ACA
30508 TGACTCATTG
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
76 11 0.15
77 12 0.17
78 49 0.68
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (76 bp):
ACACATTAAGGTAAAATAAGTCTTCATTAAGGAGAAATGCCATGCCTTTTCAACTACATCAAATC
CTAAGGAAGAG
Found at i:32270 original size:21 final size:21
Alignment explanation
Indices: 32246--32287 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
32236 AAAAGAGTGC
32246 AAGAGAGAAGAAA-AAGAAAGT
1 AAGAGAGAA-AAAGAAGAAAGT
**
32267 AAGATTGAAAAAGAAGAAAGT
1 AAGAGAGAAAAAGAAGAAAGT
32288 GATCAAGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (21 bp):
AAGAGAGAAAAAGAAGAAAGT
Found at i:34387 original size:80 final size:78
Alignment explanation
Indices: 34250--34408 Score: 228
Period size: 80 Copynumber: 2.0 Consensus size: 78
34240 CAACCAATAA
* * * * *
34250 ACACATTAAGGTTACATAAGTCTTCATTAAGGAGAAATGACATGTCTTTTTAGCTACATTAGATC
1 ACACATTAAGGATACATAAGTCTTCATTAAGGAGAAATGACATGCCTTTTCAACTACATCAGATC
*
34315 TTAATGAAGAGAC
66 CTAATGAAGAGAC
* *
34328 ACACATTAAGGATACAATAAGTCTTCATTTAAGGAGAAATGCCATGCCTTTTCAACTACATCGGA
1 ACACATTAAGGATAC-ATAAGTCTTCA-TTAAGGAGAAATGACATGCCTTTTCAACTACATCAGA
34393 TCCTAATGAAGAGAC
64 TCCTAATGAAGAGAC
34408 A
1 A
34409 TGACTCATTG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 14 0.20
79 11 0.15
80 46 0.65
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (78 bp):
ACACATTAAGGATACATAAGTCTTCATTAAGGAGAAATGACATGCCTTTTCAACTACATCAGATC
CTAATGAAGAGAC
Found at i:38387 original size:16 final size:14
Alignment explanation
Indices: 38365--38405 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
38355 AACTAAACCC
38365 AAAACCCTAAATTCA
1 AAAACCCTAAA-TCA
*
38380 ATAAACCCTACATCA
1 A-AAACCCTAAATCA
38395 AAAACCCTAAA
1 AAAACCCTAAA
38406 CGCAAACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 5 0.22
16 9 0.39
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAACCCTAAATCA
Found at i:39049 original size:22 final size:21
Alignment explanation
Indices: 39009--39049 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
38999 TTGAGTTTAA
**
39009 ATTATAAAAATTATTTGATAT
1 ATTATAAAAATTAAGTGATAT
39030 ATTATTAAAAATTAAGTGAT
1 ATTA-TAAAAATTAAGTGAT
39050 GAATATAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
ATTATAAAAATTAAGTGATAT
Found at i:40306 original size:86 final size:86
Alignment explanation
Indices: 40173--40339 Score: 262
Period size: 86 Copynumber: 1.9 Consensus size: 86
40163 GGAAGATAGG
40173 ACACCATCGACAAATTAGGCCGATGGTGGTGTGGGACCATCGAGAAGCATCAGCACATTGGTGCC
1 ACACCATCGACAAATTAGGCCGATGGTGGTGTGGGACCATCGAGAAGCATCAGCACATTGGTGCC
40238 TTGGATATGCGGGACCGTCGA
66 TTGGATATGCGGGACCGTCGA
** * * * * *
40259 ACACCATCGGTAACTTAGGCCGGTGGTGGTGTGGGACCATCGTGAAGCATTAGCACCTTGGTGCC
1 ACACCATCGACAAATTAGGCCGATGGTGGTGTGGGACCATCGAGAAGCATCAGCACATTGGTGCC
*
40324 TTGGATGTGCGGGACC
66 TTGGATATGCGGGACC
40340 ATTGAGAAGC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.22
Consensus pattern (86 bp):
ACACCATCGACAAATTAGGCCGATGGTGGTGTGGGACCATCGAGAAGCATCAGCACATTGGTGCC
TTGGATATGCGGGACCGTCGA
Found at i:40338 original size:43 final size:43
Alignment explanation
Indices: 40205--40377 Score: 140
Period size: 43 Copynumber: 4.0 Consensus size: 43
40195 ATGGTGGTGT
* *
40205 GGGACCATCGAGAAGCATCAG-CACATTGGTGCCTTGGATATGC
1 GGGACCATCGAGAAGCAT-AGACACCTTGGTGCCTTGGATGTGC
* * * ** * * * *
40248 GGGACCGTCGA-ACACCATCGGTAACTTAG-GCCGGTGG-TGGTGT
1 GGGACCATCGAGA-AGCATAGACACCTTGGTGCC-TTGGAT-GTGC
*
40291 GGGACCATCGTGAAGCATTAG-CACCTTGGTGCCTTGGATGTGC
1 GGGACCATCGAGAAGCA-TAGACACCTTGGTGCCTTGGATGTGC
* *
40334 GGGACCATTGAGAAGCATCGACACCTTGGTGCCTTGGATGTGC
1 GGGACCATCGAGAAGCATAGACACCTTGGTGCCTTGGATGTGC
40377 G
1 G
40378 AGAGCATGGG
Statistics
Matches: 99, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
42 8 0.08
43 84 0.85
44 7 0.07
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.23
Consensus pattern (43 bp):
GGGACCATCGAGAAGCATAGACACCTTGGTGCCTTGGATGTGC
Found at i:40435 original size:129 final size:129
Alignment explanation
Indices: 40205--40472 Score: 342
Period size: 129 Copynumber: 2.1 Consensus size: 129
40195 ATGGTGGTGT
* * **
40205 GGGACCATCGAGAAGCATCAGCACATTGGTGCCTTGGATATGCGGGACCGTCGAACACCATCGGT
1 GGGACCATCGAGAAGCATCAGCACATTGGTGCCTTGGATATGCGAGACCATCGAACACCATCGAC
* * * *
40270 AACTTAGGCCGGTGGTGGTGTGGGACCATCGTGAAGCATTAGCACCTTGGTGCCTTGGATGTGC
66 AACTTAGGCCAGTGGTGGTGTGGGACCATAGTGAAGCATCAGCACATTGGTGCCTTGGATGTGC
* * * * * * *
40334 GGGACCATTGAGAAGCATC-GACACCTTGGTGCCTTGGATGTGCGAGAGCATGGGACACCATTGA
1 GGGACCATCGAGAAGCATCAG-CACATTGGTGCCTTGGATATGCGAGACCATCGAACACCATCGA
* *
40398 CAACTTAGGCTAGTGGTGGTGTGGGACCATTAG-GAAGCATCGGCACATTGGTGCCTTGGATGTG
65 CAACTTAGGCCAGTGGTGGTGTGGGACCA-TAGTGAAGCATCAGCACATTGGTGCCTTGGATGTG
40462 C
129 C
*
40463 GGGAGCATCG
1 GGGACCATCG
40473 GACACTATCG
Statistics
Matches: 118, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
128 1 0.01
129 115 0.97
130 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.22
Consensus pattern (129 bp):
GGGACCATCGAGAAGCATCAGCACATTGGTGCCTTGGATATGCGAGACCATCGAACACCATCGAC
AACTTAGGCCAGTGGTGGTGTGGGACCATAGTGAAGCATCAGCACATTGGTGCCTTGGATGTGC
Found at i:40489 original size:86 final size:86
Alignment explanation
Indices: 40333--40965 Score: 562
Period size: 86 Copynumber: 7.3 Consensus size: 86
40323 CTTGGATGTG
* * * * * *
40333 CGGGACCATTGAGAAGCATCGACACCTTGGTGCCTTGGATGTGCGAGAGCATGGGACACCATTGA
1 CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGA
*
40398 CAACTTAGGCT-AGTGGTGGTG
66 CAACTTAGGCTGA-TGGTGGTA
* ** * * *
40419 TGGGACCATTAGGAAGCATCGGCACATTGGTGCCTTGGATGTGCGGGAGCATCGGACACTATCGG
1 CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGA
* * * * *
40484 TAACTTTGGCTGATAGTAGTG
66 CAACTTAGGCTGATGGTGGTA
* ** * *
40505 CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATGTACAAGAGCATCGAACACCATCAA
1 CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGA
* *
40570 TAACTTAGGCTGATGGTAGTA
66 CAACTTAGGCTGATGGTGGTA
* * * ** *
40591 CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATTTGCGGTAACATCAAACACCATCAA
1 CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGA
* * *
40656 CAA-TAAAGG-TCGATAGTGGTG
66 CAACT-TAGGCT-GATGGTGGTA
* * * *
40677 TGGGACCATCGGGAAGCATCGGTACCTTGGTGCCTTAGATGTGCGGGAGCATCAGACACCATC-A
1 CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGA
* *
40741 GTAACTTAGG-TCGATGGTGATA
66 -CAACTTAGGCT-GATGGTGGTA
* ** * ** * *
40763 TGGGACCATCGGGAAGCATCAACACCTTGGTGCCTAGGATGTATGGGAGCATCGAACACCATCGG
1 CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGA
* *
40828 CACCTT-GG-TGCCTTGGAT-GTA
66 CAACTTAGGCTG--ATGG-TGGTA
* * ** * * * * *
40849 CGAGAGCATTAGGTAGCATCGGTACCTTGGTGCCTTGGATGTGCGGGACCATTGGACACTATCGA
1 CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGA
* *
40914 CAACGTAGGCCGATGGTGGTA
66 CAACTTAGGCTGATGGTGGTA
* *
40935 CGGGACCATCGGGAAGCGTCGACACCATTGG
1 CGGGACCATCGGGAAGCATCGGCACC-TTGG
40966 GCTAAAAAAA
Statistics
Matches: 439, Mismatches: 95, Indels: 25
0.79 0.17 0.04
Matches are distributed among these distances:
84 1 0.00
85 7 0.02
86 421 0.96
87 9 0.02
88 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (86 bp):
CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATGTGCGGGAGCATCGGACACCATCGA
CAACTTAGGCTGATGGTGGTA
Found at i:40624 original size:258 final size:258
Alignment explanation
Indices: 40333--40825 Score: 627
Period size: 258 Copynumber: 1.9 Consensus size: 258
40323 CTTGGATGTG
* * *** **
40333 CGGGACCATTGAGAAGCATCGACACCTTGGTGCCTTGGATGTGCGAG-AGCATGGGACACCATTG
1 CGGGACCATCGAGAAGCATCGACACCTTGGTGCCTTGGATGTGCG-GTAACATCAAACACCATCA
* * * *
40397 ACAACT-TAGGCTAG-TGGTGGTGTGGGACCATTAGGAAGCATCGGCACATTGGTGCCTTGGATG
65 ACAA-TAAAGG-TAGATAGTGGTGTGGGACCATCAGGAAGCATCGGCACATTGGTGCCTTAGATG
* * * * *
40460 TGCGGGAGCATCGGACACTATCGGTAACTTTGG-CTGATAGT-AGTGCGGGACCATCGGGAAGCA
128 TGCGGGAGCATCAGACACCATCAGTAACTTAGGTC-GATAGTGA-TACGGGACCATCGGGAAGCA
** *
40523 TCGGCACCTTGGTGCCTTGGATGTACAAGAGCATCGAACACCATCAATAACTTAGGCTGATGGTA
191 TCAACACCTTGGTGCCTAGGATGTACAAGAGCATCGAACACCATCAATAACTTAGGCTGATGGTA
40588 GTA
256 GTA
* * *
40591 CGGGACCATCGGGAAGCATCGGCACCTTGGTGCCTTGGATTTGCGGTAACATCAAACACCATCAA
1 CGGGACCATCGAGAAGCATCGACACCTTGGTGCCTTGGATGTGCGGTAACATCAAACACCATCAA
* * * *
40656 CAATAAAGGTCGATAGTGGTGTGGGACCATCGGGAAGCATCGGTACCTTGGTGCCTTAGATGTGC
66 CAATAAAGGTAGATAGTGGTGTGGGACCATCAGGAAGCATCGGCACATTGGTGCCTTAGATGTGC
* *
40721 GGGAGCATCAGACACCATCAGTAACTTAGGTCGATGGTGATATGGGACCATCGGGAAGCATCAAC
131 GGGAGCATCAGACACCATCAGTAACTTAGGTCGATAGTGATACGGGACCATCGGGAAGCATCAAC
***
40786 ACCTTGGTGCCTAGGATGTATGGGAGCATCGAACACCATC
196 ACCTTGGTGCCTAGGATGTACAAGAGCATCGAACACCATC
40826 GGCACCTTGG
Statistics
Matches: 199, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
257 4 0.02
258 193 0.97
259 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (258 bp):
CGGGACCATCGAGAAGCATCGACACCTTGGTGCCTTGGATGTGCGGTAACATCAAACACCATCAA
CAATAAAGGTAGATAGTGGTGTGGGACCATCAGGAAGCATCGGCACATTGGTGCCTTAGATGTGC
GGGAGCATCAGACACCATCAGTAACTTAGGTCGATAGTGATACGGGACCATCGGGAAGCATCAAC
ACCTTGGTGCCTAGGATGTACAAGAGCATCGAACACCATCAATAACTTAGGCTGATGGTAGTA
Found at i:40809 original size:43 final size:43
Alignment explanation
Indices: 40761--40848 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
40751 TCGATGGTGA
* *
40761 TATGGGACCATCGGGA-AGCATCAACACCTTGGTGCCTAGGATG
1 TATGGGACCATC-GAACACCATCAACACCTTGGTGCCTAGGATG
* ** *
40804 TATGGGAGCATCGAACACCATCGGCACCTTGGTGCCTTGGATG
1 TATGGGACCATCGAACACCATCAACACCTTGGTGCCTAGGATG
40847 TA
1 TA
40849 CGAGAGCATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 2 0.05
43 36 0.95
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.23
Consensus pattern (43 bp):
TATGGGACCATCGAACACCATCAACACCTTGGTGCCTAGGATG
Found at i:40856 original size:43 final size:43
Alignment explanation
Indices: 40785--40890 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
40775 GAAGCATCAA
* * *
40785 CACCTTGGTGCCTAGGATGTATGGGAGCATCGA-ACACCATCGG
1 CACCTTGGTGCCTTGGATGTACGAGAGCAT-GAGACACCATCGG
* ** *
40828 CACCTTGGTGCCTTGGATGTACGAGAGCATTAGGTAGCATCGG
1 CACCTTGGTGCCTTGGATGTACGAGAGCATGAGACACCATCGG
*
40871 TACCTTGGTGCCTTGGATGT
1 CACCTTGGTGCCTTGGATGT
40891 GCGGGACCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 53 0.98
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (43 bp):
CACCTTGGTGCCTTGGATGTACGAGAGCATGAGACACCATCGG
Found at i:41115 original size:33 final size:33
Alignment explanation
Indices: 41069--41141 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
41059 AGCATCGAAC
41069 ACCATCG-GCACCTTGGTGCCTTGGATGTACGAG
1 ACCATCGAG-ACCTTGGTGCCTTGGATGTACGAG
* *
41102 AGCATCGAGACCTTGGTGCCTTGGATGTGCGAG
1 ACCATCGAGACCTTGGTGCCTTGGATGTACGAG
41135 ACCATCG
1 ACCATCG
41142 GACACTATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.19, C:0.26, G:0.32, T:0.23
Consensus pattern (33 bp):
ACCATCGAGACCTTGGTGCCTTGGATGTACGAG
Found at i:41232 original size:239 final size:244
Alignment explanation
Indices: 40734--41235 Score: 816
Period size: 239 Copynumber: 2.1 Consensus size: 244
40724 AGCATCAGAC
* *
40734 ACCATCAGTAACTTAGGTCGATGGTGATATGGGACCATCGGGAAGCATCAACACCTTGGTGCCTA
1 ACCATCGGTAACTTAGGTCGATGGTGATATGGGACCATCGGGAAGCACCAACACCTTGGTGCCTA
*
40799 GGATGTATGGGAGCATCGAACACCATCGGCACCTTGGTGCCTTGGATGTACGAGAGCATTAGGTA
66 GGATGTACGGGAGCATCGAACACCATCGGCACCTTGGTGCCTTGGATGTACGAGAGC--TA-GTA
* * *
40864 GCATCGGTACCTTGGTGCCTTGGATGTGCGGGACCATTGGACACTATCGACAACGTAGGCCGATG
128 GCA-C-GTACCTTGGTGCCTTGGATGTGCGAGACCATCGGACACTATCGACAACATAGGCCGATG
*
40929 GTGGTACGGGACCATCGGGAAGCGTCGACACCATTGGGCTAAAAAAAGCACGGG
191 GTGGTACGGGACCATCGGGAAGCATCGACACCATTGGGCTAAAAAAAGCACGGG
*
40983 ACCATCGGTAACTTAGGTCGATGGTGATATGGGACCATCGGGAAGCACCGACACCTTGGTGCCTA
1 ACCATCGGTAACTTAGGTCGATGGTGATATGGGACCATCGGGAAGCACCAACACCTTGGTGCCTA
*
41048 GGATGTACGGGAGCATCGAACACCATCGGCACCTTGGTGCCTTGGATGTACGAGAGC-A-TCG-A
66 GGATGTACGGGAGCATCGAACACCATCGGCACCTTGGTGCCTTGGATGTACGAGAGCTAGTAGCA
41110 -G-ACCTTGGTGCCTTGGATGTGCGAGACCATCGGACACTATCGACAACATAGGCCGATGGTGGT
131 CGTACCTTGGTGCCTTGGATGTGCGAGACCATCGGACACTATCGACAACATAGGCCGATGGTGGT
* * *
41173 GCGGGACCATCGGGAAGCATCGGCACCATTGGGCTAAAAAAAGCGCGGG
196 ACGGGACCATCGGGAAGCATCGACACCATTGGGCTAAAAAAAGCACGGG
41222 ACCATCGGTAACTT
1 ACCATCGGTAACTT
41236 GGCGCCAAAA
Statistics
Matches: 241, Mismatches: 12, Indels: 10
0.92 0.05 0.04
Matches are distributed among these distances:
239 118 0.49
240 1 0.00
243 1 0.00
244 2 0.01
246 1 0.00
249 118 0.49
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.20
Consensus pattern (244 bp):
ACCATCGGTAACTTAGGTCGATGGTGATATGGGACCATCGGGAAGCACCAACACCTTGGTGCCTA
GGATGTACGGGAGCATCGAACACCATCGGCACCTTGGTGCCTTGGATGTACGAGAGCTAGTAGCA
CGTACCTTGGTGCCTTGGATGTGCGAGACCATCGGACACTATCGACAACATAGGCCGATGGTGGT
ACGGGACCATCGGGAAGCATCGACACCATTGGGCTAAAAAAAGCACGGG
Found at i:48183 original size:33 final size:32
Alignment explanation
Indices: 48144--48219 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 32
48134 AGCATCGAAC
48144 ACCATCGGCACCTTGGTGCCTTGGATGTACGAG
1 ACCATCGG-ACCTTGGTGCCTTGGATGTACGAG
* *
48177 AGCATCGAGACCTTGGTGCCTTGGATGTGCGAG
1 ACCATCG-GACCTTGGTGCCTTGGATGTACGAG
48210 ACCATCGGAC
1 ACCATCGGAC
48220 ACTATCGACA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 3 0.08
33 35 0.90
34 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.32, T:0.22
Consensus pattern (32 bp):
ACCATCGGACCTTGGTGCCTTGGATGTACGAG
Found at i:55301 original size:129 final size:129
Alignment explanation
Indices: 55071--55324 Score: 463
Period size: 129 Copynumber: 2.0 Consensus size: 129
55061 TCTCTCCAAA
* ** *
55071 ATAGACTGACTTGGGATTTAATGGACAATTTTCGAAGGAATGACCATCCCCACAATATACATAGG
1 ATAGACTGACTTGGAATTTAATGGACAATTCACAAAGGAATGACCATCCCCACAATATACATAGG
55136 AAACAATATCAAATTGACTCGGTGGCTGAGCTGTAACATGATTCAAACCATTAGTAATAATATC
66 AAACAATATCAAATTGACTCGGTGGCTGAGCTGTAACATGATTCAAACCATTAGTAATAATATC
*
55200 ATAGACTGACTTGGAATTTGATGGACAATTCACAAAGGAATGACCATCCCCACAATATACATAGG
1 ATAGACTGACTTGGAATTTAATGGACAATTCACAAAGGAATGACCATCCCCACAATATACATAGG
55265 AAACAATATCAAATTGACTCGGTGGCTGAGCTGTAACATGATTCAAACCATTAGTAATAA
66 AAACAATATCAAATTGACTCGGTGGCTGAGCTGTAACATGATTCAAACCATTAGTAATAA
55325 AATGTTTCAA
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 120 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (129 bp):
ATAGACTGACTTGGAATTTAATGGACAATTCACAAAGGAATGACCATCCCCACAATATACATAGG
AAACAATATCAAATTGACTCGGTGGCTGAGCTGTAACATGATTCAAACCATTAGTAATAATATC
Found at i:58382 original size:23 final size:25
Alignment explanation
Indices: 58356--58401 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
58346 AAAAATCATA
58356 AAAAATTATAAAA-A-AATAAAAAT
1 AAAAATTATAAAATATAATAAAAAT
58379 AAAAATTATAAAATATAATAAAA
1 AAAAATTATAAAATATAATAAAA
58402 TATGGAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
24 1 0.05
25 7 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAATTATAAAATATAATAAAAAT
Found at i:58401 original size:10 final size:10
Alignment explanation
Indices: 58342--58404 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
58332 ATTCAAAATT
58342 TATAA-AAAA
1 TATAATAAAA
58351 TCATAA-AAAA
1 T-ATAATAAAA
*
58361 TTATAAAAAAA
1 -TATAATAAAA
*
58372 TAAAAATAAAA
1 T-ATAATAAAA
*
58383 -ATTATAAAA
1 TATAATAAAA
58392 TATAATAAAA
1 TATAATAAAA
58402 TAT
1 TAT
58405 GGAGTAAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
9 8 0.18
10 24 0.55
11 12 0.27
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
TATAATAAAA
Found at i:64782 original size:15 final size:15
Alignment explanation
Indices: 64757--64801 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
64747 GGTGGTAAGA
64757 AATTTTT-ATTT-TCT
1 AATTTTTAATTTAT-T
64771 AATTTTTAATTTATT
1 AATTTTTAATTTATT
64786 AACTTTTTAATTTATT
1 AA-TTTTTAATTTATT
64802 TTAAATTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.25
15 7 0.25
16 14 0.50
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTTTTAATTTATT
Found at i:64787 original size:8 final size:7
Alignment explanation
Indices: 64757--64798 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 7
64747 GGTGGTAAGA
64757 AATTTTT
1 AATTTTT
64764 -ATTTTCT
1 AATTTT-T
64771 AATTTTT
1 AATTTTT
64778 AATTTATT
1 AATTT-TT
64786 AACTTTTT
1 AA-TTTTT
64794 AATTT
1 AATTT
64799 ATTTTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 5 0.16
7 10 0.32
8 13 0.42
9 3 0.10
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (7 bp):
AATTTTT
Found at i:76621 original size:21 final size:21
Alignment explanation
Indices: 76597--76664 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
76587 AAGGTTGAAG
76597 ATATGTGGCCATTATTGGCAA
1 ATATGTGGCCATTATTGGCAA
* *
76618 ATATGTAG-CAGTATAATT-TCAA
1 ATATGTGGCCA-T-T-ATTGGCAA
*
76640 ATTATGTGGCCATTATTGGTAA
1 A-TATGTGGCCATTATTGGCAA
76662 ATA
1 ATA
76665 AATGGTGGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
20 2 0.06
21 13 0.36
22 9 0.25
23 10 0.28
24 2 0.06
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (21 bp):
ATATGTGGCCATTATTGGCAA
Found at i:81168 original size:21 final size:21
Alignment explanation
Indices: 81144--81217 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 21
81134 AAGGTGGAAG
81144 ATATGTGGTCGTTATTGGCAA
1 ATATGTGGTCGTTATTGGCAA
81165 ATATGTGG-CAGTTTATCT-GCAA
1 ATATGTGGTC-G-TTAT-TGGCAA
* *
81187 ATTATGTGGCCATTATTGGCAA
1 A-TATGTGGTCGTTATTGGCAA
81209 ATATGTGGT
1 ATATGTGGT
81218 GGCTTGTCCA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
20 1 0.02
21 17 0.38
22 18 0.40
23 8 0.18
24 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.38
Consensus pattern (21 bp):
ATATGTGGTCGTTATTGGCAA
Found at i:110263 original size:48 final size:48
Alignment explanation
Indices: 110207--110305 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
110197 AACATTTCAT
110207 TTAATGCATATAACCAAATATGCATAATACTTCCATTCCTTGTAATTC
1 TTAATGCATATAACCAAATATGCATAATACTTCCATTCCTTGTAATTC
110255 TTAATGCATATAACCAAATATGCATAATACTTCCATTCCTTGTAATTC
1 TTAATGCATATAACCAAATATGCATAATACTTCCATTCCTTGTAATTC
110303 TTA
1 TTA
110306 CTCCACAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.38
Consensus pattern (48 bp):
TTAATGCATATAACCAAATATGCATAATACTTCCATTCCTTGTAATTC
Found at i:110649 original size:80 final size:80
Alignment explanation
Indices: 110515--110665 Score: 212
Period size: 80 Copynumber: 1.9 Consensus size: 80
110505 ACCGCAAATG
* * *
110515 TGAGCCCAGCTCTAGTTGAATTAACCAACAATTATCCATAAAATCCTAGAACTCGGTGCATAGTA
1 TGAGCCCAGCTCAAGTTGAATTAACCAACAATTATACATAAAATCCTAGAACTCGATGCATAGTA
110580 GATAAATCGTGAATT
66 GATAAATCGTGAATT
* * * * * * *
110595 TGAGCCCAGCTCAAGTTGAATTAACCAACAATTATACGTCAAATCTTGGCACTCGATGCCTAGTG
1 TGAGCCCAGCTCAAGTTGAATTAACCAACAATTATACATAAAATCCTAGAACTCGATGCATAGTA
110660 GATAAA
66 GATAAA
110666 CCACGAATGT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (80 bp):
TGAGCCCAGCTCAAGTTGAATTAACCAACAATTATACATAAAATCCTAGAACTCGATGCATAGTA
GATAAATCGTGAATT
Found at i:124414 original size:17 final size:17
Alignment explanation
Indices: 124370--124414 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
124360 GCATGCATTT
* *
124370 ATTTTAATTCTCATTGC
1 ATTTTAATTGTCATTAC
*
124387 ATTTTAGTTGTCATTAC
1 ATTTTAATTGTCATTAC
*
124404 ATTTTATTTGT
1 ATTTTAATTGT
124415 TTAGCATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (17 bp):
ATTTTAATTGTCATTAC
Found at i:126630 original size:21 final size:21
Alignment explanation
Indices: 126592--126632 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
126582 ACAGCAATTC
*
126592 AATTTTATCTTAACTTGCTTT
1 AATTTTAACTTAACTTGCTTT
* *
126613 AATTTTAACTTTAGTTGCTT
1 AATTTTAACTTAACTTGCTT
126633 CGACAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.56
Consensus pattern (21 bp):
AATTTTAACTTAACTTGCTTT
Found at i:130476 original size:17 final size:17
Alignment explanation
Indices: 130454--130488 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
130444 TAGGTTCCTT
130454 AAACAAAATTTTATTTG
1 AAACAAAATTTTATTTG
130471 AAACAAAATTTTATTTG
1 AAACAAAATTTTATTTG
130488 A
1 A
130489 CTTACACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (17 bp):
AAACAAAATTTTATTTG
Found at i:143661 original size:26 final size:24
Alignment explanation
Indices: 143616--143669 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
143606 AAGAAAACAT
143616 AAATATAAATAGACATGAAAATAAA
1 AAATATAAATAGACATG-AAATAAA
143641 CAAATATGAAATAAGA-A-GAAATAAA
1 -AAATAT-AAAT-AGACATGAAATAAA
143666 AAAT
1 AAAT
143670 TATACAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
24 4 0.15
25 7 0.27
26 7 0.27
27 5 0.19
28 3 0.12
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.19
Consensus pattern (24 bp):
AAATATAAATAGACATGAAATAAA
Found at i:144351 original size:152 final size:154
Alignment explanation
Indices: 144185--144470 Score: 352
Period size: 152 Copynumber: 1.9 Consensus size: 154
144175 CGGTGGTCGG
* *
144185 AAATTTATTCTTTTTTTTAAAT-CAAA-AGT-TTTCTTTTGATTAAAACAAAATCACTACTTCAC
1 AAATTT-TTATTTTTTTAAAATCCAAACAGTCTTTCTTTT--TTAAAACAAAATCACTACTTCAC
* * *
144247 TTCAA-AA-TCAAAATTTTTATTTCGAAGTAGTT-AAAAAAATCAAAACTTTGTTTAAAAATTTA
63 TT-AAGAATTC-AAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGATTAAAAATTTA
144309 AA-TTTTTTCTCTAAAATTACTAAAAAAC
126 AACTTTTTTCTCTAAAATTACTAAAAAAC
** * ** * *
144337 AAATTTTTATTTTTTTAAAATCCAAACTTTCTTTCTTTTTTTAATGAAAATCATTACTTTACTTA
1 AAATTTTTATTTTTTTAAAATCCAAACAGTCTTTCTTTTTTAAAACAAAATCACTACTTCACTTA
* *
144402 AGAATTCAAACTTTTATTTTGAAATAGTTAAAAAAAATTAAAACTTTGATTAAAAATTTAAACTT
66 AGAATTCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGATTAAAAATTTAAACTT
144467 TTTT
131 TTTT
144471 TAAATCAAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
151 15 0.13
152 51 0.45
153 33 0.29
154 14 0.12
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.44
Consensus pattern (154 bp):
AAATTTTTATTTTTTTAAAATCCAAACAGTCTTTCTTTTTTAAAACAAAATCACTACTTCACTTA
AGAATTCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTGATTAAAAATTTAAACTT
TTTTCTCTAAAATTACTAAAAAAC
Found at i:144522 original size:268 final size:268
Alignment explanation
Indices: 144196--144737 Score: 987
Period size: 268 Copynumber: 2.0 Consensus size: 268
144186 AATTTATTCT
*
144196 TTTTTTTAAATCAAAAGTTTTCTTTTGATTAAAACAAAATCACTACTTCACTTCAAAATCAAAAT
1 TTTTTTTAAATCAAAAGTTTTCTTTTGATTAAAACAAAATCACTACTTCACTTCAAAATCAAAAC
*
144261 TTTTATTTCGAAGTAGTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAATTTTTTCTCTAAAAT
66 TTTTATTTCGAAGTAGTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTCTAAAAT
144326 TACTAAAAAACAAATTTTTATTTTTTTAAAATCCAAACTTTCTTTCTTTTTTTAATGAAAATCAT
131 TACTAAAAAACAAATTTTTATTTTTTTAAAATCCAAACTTTCTTTCTTTTTTTAATGAAAATCAT
*
144391 TACTTTACTTAAGAATTCAAACTTTTATTTTGAAATAGTTAAAAAAAATTAAAACTTTGATTAAA
196 TACTTTACTTAAAAATTCAAACTTTTATTTTGAAATAGTT-AAAAAAATTAAAACTTTGATTAAA
144456 AATTTAAAC
260 AATTTAAAC
* * *
144465 TTTTTTTAAATCAAAAGTTTT-TTTTTATTAAAATAAAATCACTACTTTACTTCAAAATCAAAAC
1 TTTTTTTAAATCAAAAGTTTTCTTTTGATTAAAACAAAATCACTACTTCACTTCAAAATCAAAAC
*
144529 TTTTATTTCGAAGTAGTTAAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTTCTCTAAAAT
66 TTTTATTTCGAAGTAGTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTCTAAAAT
144594 TACTAAAAAACAAATTTTTATTTTTTTAAAATCCAAACTTTCTTTCTTTTTTTAATGAAAATCAT
131 TACTAAAAAACAAATTTTTATTTTTTTAAAATCCAAACTTTCTTTCTTTTTTTAATGAAAATCAT
*
144659 TATTTTACTTAAAAATTCAAACTTTTATTTTGAAATAGTTAAAAAAATTAAAACTTTGATTAAAA
196 TACTTTACTTAAAAATTCAAACTTTTATTTTGAAATAGTTAAAAAAATTAAAACTTTGATTAAAA
*
144724 ATTTAGAC
261 ATTTAAAC
144732 TTTTTT
1 TTTTTT
144738 AAAAATGACT
Statistics
Matches: 264, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
267 38 0.14
268 205 0.78
269 21 0.08
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (268 bp):
TTTTTTTAAATCAAAAGTTTTCTTTTGATTAAAACAAAATCACTACTTCACTTCAAAATCAAAAC
TTTTATTTCGAAGTAGTTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTCTAAAAT
TACTAAAAAACAAATTTTTATTTTTTTAAAATCCAAACTTTCTTTCTTTTTTTAATGAAAATCAT
TACTTTACTTAAAAATTCAAACTTTTATTTTGAAATAGTTAAAAAAATTAAAACTTTGATTAAAA
ATTTAAAC
Found at i:144684 original size:152 final size:149
Alignment explanation
Indices: 144465--144981 Score: 559
Period size: 152 Copynumber: 3.5 Consensus size: 149
144455 AAATTTAAAC
* * ** * * * *
144465 TTTTTTT-AAATCAAAAGTTT-TTTTTTATTAAAAT-AAAATCACTACTTTACTTCAAAATCAAA
1 TTTTTTTAAAATCTAAACTTTCTTTTTT-TTTTAATGAAAATCATTATTTTACTTAAAAATCTAA
* * *
144527 ACTTTTATTTCGAAGTAGTTAAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTTCTCTAAA
65 ACTTTTATTTCGAAATAGTTAAAAAAATTAAAAATTTGTTTAAAAATTTAAACTTTTTCT-TAAA
*
144592 ATTACTAAAAAACAAATTTTT
129 ATAACTAAAAAACAAATTTTT
*
144613 ATTTTTTTAAAATCCAAACTTTCTTTCTTTTTTTAATGAAAATCATTATTTTACTTAAAAAT-TC
1 -TTTTTTTAAAATCTAAACTTTCTTT-TTTTTTTAATGAAAATCATTATTTTACTTAAAAATCT-
* * * * *
144677 AAACTTTTATTTTGAAATAGTTAAAAAAATTAAAACTTTGATTAAAAATTTAGACTTTTT-TAAA
63 AAACTTTTATTTCGAAATAGTTAAAAAAATTAAAAATTTGTTTAAAAATTTAAACTTTTTCTTAA
* *
144741 AATGACTAAAAAAC-AGTTTTT
128 AATAACTAAAAAACAAATTTTT
* *
144762 TTTTTTTTAAATCTAAA----C--TTTTTTTTAATGAAAATCATTATTTTATTTAAAAATCTAAA
1 TTTTTTTAAAATCTAAACTTTCTTTTTTTTTTAATGAAAATCATTATTTTACTTAAAAATCTAAA
* * *
144821 TTTTTATTTCAAAATAGTT-TAAAAATTAAAAATTTGTTT-AAAATTTAAAC-TTTTCTTTAAAA
66 CTTTTATTTCGAAATAGTTAAAAAAATTAAAAATTTGTTTAAAAATTTAAACTTTTTC-TTAAAA
* *
144883 TAATTAAAAAAACAGATTTTT
130 TAACT-AAAAAACAAATTTTT
* *
144904 TTTTTTGAAAATCTAAACATTCTCTTTTTTTTTT--T--AAATCATTATTTTTCTTAAAAATCTA
1 TTTTTTTAAAATCTAAAC-TT-TCTTTTTTTTTTAATGAAAATCATTATTTTACTTAAAAATCTA
144965 AACTTTTATTTCGAAAT
64 AACTTTTATTTCGAAAT
144982 TATTTTAAAA
Statistics
Matches: 312, Mismatches: 38, Indels: 39
0.80 0.10 0.10
Matches are distributed among these distances:
138 4 0.01
139 10 0.03
140 25 0.08
141 60 0.19
142 22 0.07
144 1 0.00
146 39 0.12
148 17 0.05
149 13 0.04
150 34 0.11
151 9 0.03
152 78 0.25
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (149 bp):
TTTTTTTAAAATCTAAACTTTCTTTTTTTTTTAATGAAAATCATTATTTTACTTAAAAATCTAAA
CTTTTATTTCGAAATAGTTAAAAAAATTAAAAATTTGTTTAAAAATTTAAACTTTTTCTTAAAAT
AACTAAAAAACAAATTTTT
Found at i:144733 original size:19 final size:18
Alignment explanation
Indices: 144701--144743 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
144691 AAATAGTTAA
144701 AAAAATTAAAACTTTGATT
1 AAAAATTAAAACTTT-ATT
* * *
144720 AAAAATTTAGACTTTTTT
1 AAAAATTAAAACTTTATT
144738 AAAAAT
1 AAAAAT
144744 GACTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (18 bp):
AAAAATTAAAACTTTATT
Found at i:144861 original size:19 final size:19
Alignment explanation
Indices: 144837--144892 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
144827 TTTCAAAATA
144837 GTTTAAAAATTAAAAATTT
1 GTTTAAAAATTAAAAATTT
* **
144856 GTTTAAAATTTAAACTTTT
1 GTTTAAAAATTAAAAATTT
*
144875 CTTTAAAATAATTAAAAA
1 GTTT-AAA-AATTAAAAA
144893 AACAGATTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 19 0.68
20 3 0.11
21 6 0.21
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (19 bp):
GTTTAAAAATTAAAAATTT
Found at i:146408 original size:19 final size:20
Alignment explanation
Indices: 146386--146423 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
146376 CCCGTTGATC
*
146386 GTTGACCA-TTGACTTTTTT
1 GTTGACCAGTTAACTTTTTT
146405 GTTGACCAGTTAACTTTTT
1 GTTGACCAGTTAACTTTTT
146424 CTGAGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (20 bp):
GTTGACCAGTTAACTTTTTT
Found at i:152248 original size:27 final size:27
Alignment explanation
Indices: 152215--152287 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
152205 GGAGTATTTC
*
152215 TGATTCTATCTCGAAAGAGCGTTATTA
1 TGATTCTAGCTCGAAAGAGCGTTATTA
* *
152242 TGATTCTGGCTCGAAAGAGCGTTATTC
1 TGATTCTAGCTCGAAAGAGCGTTATTA
* * *
152269 TAATTCTGGCTTGAAAGAG
1 TGATTCTAGCTCGAAAGAG
152288 TAATATTCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (27 bp):
TGATTCTAGCTCGAAAGAGCGTTATTA
Found at i:152294 original size:27 final size:28
Alignment explanation
Indices: 152224--152308 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 28
152214 CTGATTCTAT
** *
152224 CTCGAAAGAGCGTTATTAT-GATTCTGG
1 CTCGAAAGAGCAATATTCTAGATTCTGG
**
152251 CTCGAAAGAGCGTTATTCTA-ATTCTGG
1 CTCGAAAGAGCAATATTCTAGATTCTGG
* * *
152278 CTTGAAAGAGTAATATTCTAGACTCTGG
1 CTCGAAAGAGCAATATTCTAGATTCTGG
152306 CTC
1 CTC
152309 AATAAGAGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 41 0.84
28 8 0.16
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (28 bp):
CTCGAAAGAGCAATATTCTAGATTCTGG
Found at i:154342 original size:21 final size:21
Alignment explanation
Indices: 154317--154364 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
154307 GGTGTGAAAT
*
154317 TATGATATGTATTATGTGATA-
1 TATGATAAGTATTATGTGA-AC
*
154338 TATGATAAGTGTTATGTGAAC
1 TATGATAAGTATTATGTGAAC
154359 TATGAT
1 TATGAT
154365 GTGTGAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (21 bp):
TATGATAAGTATTATGTGAAC
Found at i:154700 original size:23 final size:24
Alignment explanation
Indices: 154667--154714 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
154657 GATGTGGCCA
*
154667 TTACTGGAAAA-TAGGTGACAGTT
1 TTACTGCAAAACTAGGTGACAGTT
* *
154690 TTACTGCAAAACTATGTGGCAGTT
1 TTACTGCAAAACTAGGTGACAGTT
154714 T
1 T
154715 GTTTGTCACG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.33
Consensus pattern (24 bp):
TTACTGCAAAACTAGGTGACAGTT
Found at i:156544 original size:21 final size:21
Alignment explanation
Indices: 156471--156544 Score: 80
Period size: 21 Copynumber: 3.4 Consensus size: 21
156461 AAGGTGGAAG
*
156471 ATATGTGGCCATTATTGGCAA
1 ATATGTGGTCATTATTGGCAA
*
156492 ATATGTTG-CAGTTTATT-GCAAA
1 ATATGTGGTCA--TTATTGGC-AA
156514 ATTATGTGGTCATTATTGGCAA
1 A-TATGTGGTCATTATTGGCAA
156536 ATATGTGGT
1 ATATGTGGT
156545 GGCTTGTCCA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
20 2 0.04
21 17 0.38
22 16 0.36
23 8 0.18
24 2 0.04
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.39
Consensus pattern (21 bp):
ATATGTGGTCATTATTGGCAA
Found at i:161375 original size:20 final size:21
Alignment explanation
Indices: 161335--161376 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
161325 CGTGATCTAA
161335 ATCAATAAATCATTCAATTTT
1 ATCAATAAATCATTCAATTTT
*
161356 ATCATTAAATCATT-AATTTT
1 ATCAATAAATCATTCAATTTT
161376 A
1 A
161377 AATAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (21 bp):
ATCAATAAATCATTCAATTTT
Found at i:165832 original size:43 final size:43
Alignment explanation
Indices: 165785--166810 Score: 925
Period size: 43 Copynumber: 23.7 Consensus size: 43
165775 GGAGCATCAA
* * *
165785 ACACCATAGACACCTTGGTGCCTTGGATGTGCGAGAGCCTCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* * * * *
165828 ACACCATAGGCACCTTGGTACCTTGGATGTGGGGGAAGCTCGGAGCCTCAG
1 ACACCATCGGCACCTTGGTGCCTTGGATGT--GCG-A-----GAGCGTCGG
* * * *
165879 ACACCATAGGCACCTTGGTACCTTGGATGTGCGGGAGCCTCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* *
165922 ACACCATCGGCACCTTGGTGCCTT-GATGTGCTG-GTGCATCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGC-GAGAGCGTCGG
* * * * *
165964 ATACCATCGGTACCTTGGTGCCCTGGATGTGCGAGAGCATCAG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* * *
166007 CCACCATCGACACCTTGGTGCCTTGGATGTGCGGGAGCGTCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* * *
166050 ACACCATCGACACCTTGGTGCCTTGGATGTGCGGGAGCATCAGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTC-GG
* * * * *
166094 -CAGCATCCGGTACCTTGGTGCCGTAGATGTGCGAGAGCGTCAG
1 ACACCAT-CGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* * *
166137 ACACCATTGGCACCTTGGTGCCTTGTATGTGCG-GAAGTGTCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAG-AGCGTCGG
* * * * * * *
166180 ACACCATCGGCATCTTGGTTCCTTAGATGTGTGGGAGTGTCAG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* * * *
166223 ACACCATCGACACCTTGGTGCCTTGGATGTGCGAAAGCCTCGA
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* * * ** *
166266 ACACCATAGGTACCTTAGTGCCTTGGATGTGTAAGAGCGTCAG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* ** * * **
166309 ATAGTATCGGTACCTTGGCGCCTTGGATGTGGCG-GAGAATCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGT-GCGAGAGCGTCGG
* * * *
166352 ACACCATCGGTACCATGGTGCCTTGTATGTGCGGGAGCGTCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* * * *
166395 ACACCATCGACACCTTAGTGCCTTGGATGTCCGGGAGCGTCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
**** * *
166438 ACACCATCAATTCCTTGGTGCCTTGGTTGTCCGAGAGCGTCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
** * ** * * * * *
166481 GTAGCATCGATACCTTGCTGGCTTAGATGTGCGAGAGCATTGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* *
166524 ACACCATCGGCACCTTGGTGCCTTGGATGTACG-GTAGCGTCAG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAG-AGCGTCGG
* * *
166567 ACACCATCGACACCTTGGTGCCTTGGATGTGCG-GAAGCCTCGA
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAG-AGCGTCGG
* * * *
166610 ACACCGTCGGCACCTTGGTG-CTTGGATGTGCGGGAGCATCGA
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* *
166652 ACACCATCGGTACCTTGGTGCCTTGGATGTGCGAGAGTGTCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* * *** * * *
166695 ACACTATTGGCACCTTAAAGCCTTGGATGTACGAGAGCCTCGA
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
* * * *
166738 ACACCATTGGCACCTTGGTGCCTTGGATGTACGGGAGCATCGG
1 ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
166781 ACACCATCGGCACCTTGGTGCCTTGGATGT
1 ACACCATCGGCACCTTGGTGCCTTGGATGT
166811 ACTGGAGCAT
Statistics
Matches: 804, Mismatches: 158, Indels: 42
0.80 0.16 0.04
Matches are distributed among these distances:
42 78 0.10
43 646 0.80
44 37 0.05
45 2 0.00
46 1 0.00
49 2 0.00
51 38 0.05
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (43 bp):
ACACCATCGGCACCTTGGTGCCTTGGATGTGCGAGAGCGTCGG
Found at i:165882 original size:51 final size:51
Alignment explanation
Indices: 165819--165922 Score: 174
Period size: 51 Copynumber: 2.0 Consensus size: 51
165809 GGATGTGCGA
* *
165819 GAGCCTCGGACACCATAGGCACCTTGGTACCTTGGATGTGGGGGAAG-CTCG
1 GAGCCTCAGACACCATAGGCACCTTGGTACCTTGGATGTGCGGG-AGCCTCG
165870 GAGCCTCAGACACCATAGGCACCTTGGTACCTTGGATGTGCGGGAGCCTCG
1 GAGCCTCAGACACCATAGGCACCTTGGTACCTTGGATGTGCGGGAGCCTCG
165921 GA
1 GA
165923 CACCATCGGC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
50 2 0.04
51 48 0.96
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.19
Consensus pattern (51 bp):
GAGCCTCAGACACCATAGGCACCTTGGTACCTTGGATGTGCGGGAGCCTCG
Found at i:170917 original size:18 final size:18
Alignment explanation
Indices: 170886--170923 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
170876 TCTAATAAAT
*
170886 AAAATGCAGAGACAATTA
1 AAAATGCAGAGACAACTA
170904 AAAATGCA-ATGACAACTA
1 AAAATGCAGA-GACAACTA
170922 AA
1 AA
170924 TGAAATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (18 bp):
AAAATGCAGAGACAACTA
Found at i:171365 original size:15 final size:14
Alignment explanation
Indices: 171341--171380 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
171331 CTTTTTCTTT
171341 TTCCTTCTCTTCTC
1 TTCCTTCTCTTCTC
171355 TTCCTTCCTCTTCTC
1 TTCCTT-CTCTTCTC
171370 TT--TTCTCTTCT
1 TTCCTTCTCTTCT
171381 TCCTCTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.28
13 2 0.08
14 6 0.24
15 10 0.40
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (14 bp):
TTCCTTCTCTTCTC
Found at i:192050 original size:22 final size:22
Alignment explanation
Indices: 192023--192079 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
192013 TGGCACAACA
* **
192023 AATCAATTTTATTAGTGCAATC
1 AATCAATTATATTAACGCAATC
* *
192045 AGTCAATTACATTAACGCAATC
1 AATCAATTATATTAACGCAATC
192067 AATCAATTATATT
1 AATCAATTATATT
192080 GGCATAATAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (22 bp):
AATCAATTATATTAACGCAATC
Found at i:195360 original size:21 final size:22
Alignment explanation
Indices: 195331--195383 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
195321 CAAAGAAGAG
*
195331 AAAAA-AAAAGTGAAAA-GAAC
1 AAAAAGAAAAGTGAAAACAAAC
*
195351 AAAAAGAAAA-TTAAAACAAAC
1 AAAAAGAAAAGTGAAAACAAAC
195372 ACAAAAGAAAAG
1 A-AAAAGAAAAG
195384 AGTAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 10 0.37
21 8 0.30
22 9 0.33
ACGTcount: A:0.75, C:0.08, G:0.11, T:0.06
Consensus pattern (22 bp):
AAAAAGAAAAGTGAAAACAAAC
Found at i:214262 original size:20 final size:20
Alignment explanation
Indices: 214223--214262 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
214213 AATTTATATG
*
214223 TAATTTTGAATTGAAGAGTT
1 TAATTTTGAATTGAAAAGTT
214243 TAATTATTGAATT-AAAAGTT
1 TAATT-TTGAATTGAAAAGTT
214263 AGCATAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
TAATTTTGAATTGAAAAGTT
Found at i:215621 original size:20 final size:21
Alignment explanation
Indices: 215596--215634 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
215586 AATTTCCTTA
215596 TTTATTTA-TTATTATTTTTG
1 TTTATTTATTTATTATTTTTG
215616 TTTATTTATTTATTATTTT
1 TTTATTTATTTATTATTTT
215635 ATGAATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTATTTATTTATTATTTTTG
Found at i:217066 original size:58 final size:59
Alignment explanation
Indices: 216978--217129 Score: 197
Period size: 58 Copynumber: 2.6 Consensus size: 59
216968 TCTTTATTTT
* *
216978 AAAATTA-TTTTTGA-CCTTAAACTATCTAAAAATTATGTTTTAA-CCATAAACTATCC
1 AAAATTATTTTTTGACCCCTAAACTTTCTAAAAATTATGTTTTAACCCATAAACTATCC
* * *
217034 AAAATTATTTTTTGACCCCTAAACTTTCTAAAAATTATGTTTTAACCCTTAAACTTTCT
1 AAAATTATTTTTTGACCCCTAAACTTTCTAAAAATTATGTTTTAACCCATAAACTATCC
217093 AAAA--ATTTGAATTTGACCCCTAAACTTTCTAAAAATT
1 AAAATTATTT---TTTGACCCCTAAACTTTCTAAAAATT
217130 CAAATTTGAC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
56 7 0.08
57 11 0.13
58 27 0.32
59 14 0.16
60 26 0.31
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.40
Consensus pattern (59 bp):
AAAATTATTTTTTGACCCCTAAACTTTCTAAAAATTATGTTTTAACCCATAAACTATCC
Found at i:217070 original size:30 final size:30
Alignment explanation
Indices: 216978--217129 Score: 170
Period size: 30 Copynumber: 5.2 Consensus size: 30
216968 TCTTTATTTT
* *
216978 AAAATTAT-TTTTGA-CCTTAAACTATCTA
1 AAAATTATGTTTTGACCCCTAAACTTTCTA
* * * *
217006 AAAATTATGTTTT-AACCATAAACTATC-C
1 AAAATTATGTTTTGACCCCTAAACTTTCTA
*
217034 AAAATTATTTTTTGACCCCTAAACTTTCTA
1 AAAATTATGTTTTGACCCCTAAACTTTCTA
* *
217064 AAAATTATGTTTTAACCCTTAAACTTTCTA
1 AAAATTATGTTTTGACCCCTAAACTTTCTA
*
217094 AAAATT-TGAATTTGACCCCTAAACTTTCTA
1 AAAATTATG-TTTTGACCCCTAAACTTTCTA
217124 AAAATT
1 AAAATT
217130 CAAATTTGAC
Statistics
Matches: 106, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
28 21 0.20
29 28 0.26
30 57 0.54
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.40
Consensus pattern (30 bp):
AAAATTATGTTTTGACCCCTAAACTTTCTA
Found at i:217136 original size:30 final size:29
Alignment explanation
Indices: 217044--217139 Score: 120
Period size: 30 Copynumber: 3.2 Consensus size: 29
217034 AAAATTATTT
**
217044 TTTGACCCCTAAACTTTCTAAAAATTATGT
1 TTTGACCCCTAAACTTTCTAAAAATTA-AA
* * *
217074 TTTAACCCTTAAACTTTCTAAAAATTTGAA
1 TTTGACCCCTAAACTTTCTAAAAA-TTAAA
217104 TTTGACCCCTAAACTTTCTAAAAATTCAAA
1 TTTGACCCCTAAACTTTCTAAAAATT-AAA
217134 TTTGAC
1 TTTGAC
217140 TCGGGTTTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.04
30 52 0.93
31 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (29 bp):
TTTGACCCCTAAACTTTCTAAAAATTAAA
Found at i:228182 original size:2 final size:2
Alignment explanation
Indices: 228175--228201 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
228165 CAACATTTAT
228175 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
228202 TCTTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:228857 original size:17 final size:17
Alignment explanation
Indices: 228813--228854 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
228803 AATGCAACTA
228813 AAATGAAAATGCGTGGAC
1 AAAT-AAAATGCGTGGAC
228831 AAATAAAATGCAGT-GAC
1 AAATAAAATGC-GTGGAC
228848 -AATAAAA
1 AAATAAAA
228855 ATGTGATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.30
17 10 0.43
18 6 0.26
ACGTcount: A:0.55, C:0.10, G:0.19, T:0.17
Consensus pattern (17 bp):
AAATAAAATGCGTGGAC
Found at i:240669 original size:39 final size:39
Alignment explanation
Indices: 240580--240728 Score: 156
Period size: 39 Copynumber: 3.7 Consensus size: 39
240570 CCTAATCAGA
* * * *
240580 GGGCAGATTGAAAACATCATCCGATCTCTTACCCCGACCATG
1 GGGCAGATTG-AAGCA--ATCCAATCTTTTACCCCAACCATG
*
240622 GGGCAGATTGAAGCAATCCAATCTTTTACACCAACCATG
1 GGGCAGATTGAAGCAATCCAATCTTTTACCCCAACCATG
* * *
240661 GGGAAGATT-AAGGACCATCCGATCTTTTACCCCAACCATG
1 GGGCAGATTGAA-G-CAATCCAATCTTTTACCCCAACCATG
* *
240701 GGGCAGATTGAGGCAGTCCAATCTTTTA
1 GGGCAGATTGAAGCAATCCAATCTTTTA
240729 TACCTAAAGC
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.02
39 41 0.46
40 32 0.36
41 5 0.06
42 10 0.11
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (39 bp):
GGGCAGATTGAAGCAATCCAATCTTTTACCCCAACCATG
Found at i:242651 original size:29 final size:29
Alignment explanation
Indices: 242628--242789 Score: 150
Period size: 29 Copynumber: 5.6 Consensus size: 29
242618 TTTTTGTCCT
242628 CAAACTATCTAAAAATTATGTTTTAA-CC
1 CAAACTATCTAAAAATTATGTTTTAACCC
* * *
242656 CTAACTATCCAAAAATTATGTTTAAACCC
1 CAAACTATCTAAAAATTATGTTTTAACCC
* *
242685 CAAACTAT-TCAAAAA-TATTTTTTTACCCC
1 CAAACTATCT-AAAAATTA-TGTTTTAACCC
* * *
242714 CAAATTTTCCAAAAATTATGTTTTAACCC
1 CAAACTATCTAAAAATTATGTTTTAACCC
* * *
242743 CAAACTTTTTAAAAATTATGTTTTGACCC
1 CAAACTATCTAAAAATTATGTTTTAACCC
* * *
242772 TTAAACTTTCAAAAAATT
1 -CAAACTATCTAAAAATT
242790 CAAATTGACA
Statistics
Matches: 108, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
28 25 0.23
29 67 0.62
30 16 0.15
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (29 bp):
CAAACTATCTAAAAATTATGTTTTAACCC
Found at i:242780 original size:30 final size:30
Alignment explanation
Indices: 242629--242937 Score: 194
Period size: 30 Copynumber: 10.5 Consensus size: 30
242619 TTTTGTCCTC
* * *
242629 AAACTATCTAAAAATTATGTTTTAACCC-T
1 AAACTTTCCAAAAATTATGTTTTGACCCTT
* ** *
242658 -AACTATCCAAAAATTATGTTTAAACCC-C
1 AAACTTTCCAAAAATTATGTTTTGACCCTT
* * **
242686 AAACTATT-CAAAAA-TATTTTTTTACCCCC
1 AAACT-TTCCAAAAATTATGTTTTGACCCTT
* * *
242715 AAATTTTCCAAAAATTATGTTTTAACCC-C
1 AAACTTTCCAAAAATTATGTTTTGACCCTT
**
242744 AAACTTTTTAAAAATTATGTTTTGACCCTT
1 AAACTTTCCAAAAATTATGTTTTGACCCTT
* ** *
242774 AAACTTTCAAAAAATTCA--AATTGACACTT
1 AAACTTTCCAAAAATT-ATGTTTTGACCCTT
* *
242803 -AACTTTCCAAAAATT-TGAATTTAACCCTT
1 AAACTTTCCAAAAATTATG-TTTTGACCCTT
*
242832 AAACTTTCCAAAAATT-TGAATTTGACCCTT
1 AAACTTTCCAAAAATTATG-TTTTGACCCTT
* * *
242862 AAACTTTCTAAAAATTCT-TATTTGACCCCT
1 AAACTTTCCAAAAATTATGT-TTTGACCCTT
* * *
242892 GAACTTTCTAAAAATTCT-TATTTGACCCTT
1 AAACTTTCCAAAAATTATGT-TTTGACCCTT
* *
242922 TAACTTTCTAAAAATT
1 AAACTTTCCAAAAATT
242938 CAAATTTGAC
Statistics
Matches: 236, Mismatches: 31, Indels: 25
0.81 0.11 0.09
Matches are distributed among these distances:
28 51 0.22
29 62 0.26
30 121 0.51
31 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (30 bp):
AAACTTTCCAAAAATTATGTTTTGACCCTT
Found at i:242785 original size:58 final size:57
Alignment explanation
Indices: 242628--242786 Score: 178
Period size: 58 Copynumber: 2.8 Consensus size: 57
242618 TTTTTGTCCT
* *
242628 CAAACTATCTAAAAATTATGTTTTAACCCT-AACTATCCAAAAATTATGTTTAAACCC
1 CAAACTATTTAAAAATTATGTTTTAACCCTAAACT-TTCAAAAATTATGTTTAAACCC
* * * * * *
242685 CAAACTATTCAAAAA-TATTTTTTTACCCCCAAATTTTCCAAAAATTATGTTTTAACCC
1 CAAACTATTTAAAAATTA-TGTTTTAACCCTAAACTTT-CAAAAATTATGTTTAAACCC
* *
242743 CAAACTTTTTAAAAATTATGTTTTGACCCTTAAACTTTCAAAAA
1 CAAACTATTTAAAAATTATGTTTTAACCC-TAAACTTTCAAAAA
242787 ATTCAAATTG
Statistics
Matches: 82, Mismatches: 15, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
56 2 0.02
57 23 0.28
58 49 0.60
59 8 0.10
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.36
Consensus pattern (57 bp):
CAAACTATTTAAAAATTATGTTTTAACCCTAAACTTTCAAAAATTATGTTTAAACCC
Found at i:242938 original size:30 final size:30
Alignment explanation
Indices: 242744--242948 Score: 220
Period size: 30 Copynumber: 6.9 Consensus size: 30
242734 TTTTAACCCC
* * **
242744 AAACTTTTTAAAAATTATGTTTTGACCCTT
1 AAACTTTCTAAAAATTCTAATTTGACCCTT
* * *
242774 AAACTTTCAAAAAATTC-AAATTGACACTT
1 AAACTTTCTAAAAATTCTAATTTGACCCTT
* *
242803 -AACTTTCCAAAAATT-TGAATTTAACCCTT
1 AAACTTTCTAAAAATTCT-AATTTGACCCTT
*
242832 AAACTTTCCAAAAATT-TGAATTTGACCCTT
1 AAACTTTCTAAAAATTCT-AATTTGACCCTT
* *
242862 AAACTTTCTAAAAATTCTTATTTGACCCCT
1 AAACTTTCTAAAAATTCTAATTTGACCCTT
* *
242892 GAACTTTCTAAAAATTCTTATTTGACCCTT
1 AAACTTTCTAAAAATTCTAATTTGACCCTT
* *
242922 TAACTTTCTAAAAATTCAAATTTGACC
1 AAACTTTCTAAAAATTCTAATTTGACC
242949 TGGTTTTAAT
Statistics
Matches: 151, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
28 14 0.09
29 17 0.11
30 119 0.79
31 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTTTCTAAAAATTCTAATTTGACCCTT
Found at i:244118 original size:16 final size:17
Alignment explanation
Indices: 244095--244129 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
244085 CTCATAGAAG
244095 GAAAAAAATCAGATTAT
1 GAAAAAAATCAGATTAT
244112 GAAAAAAATCAGATTAT
1 GAAAAAAATCAGATTAT
244129 G
1 G
244130 GGGCTTACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.23
Consensus pattern (17 bp):
GAAAAAAATCAGATTAT
Found at i:261632 original size:6 final size:6
Alignment explanation
Indices: 261590--261644 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
261580 TAAATATTTG
* **
261590 TTTATA -TTATT TGTTATA -TTATA TTTCATA TAAATA TTTATA TTTATA
1 TTTATA TTTATA T-TTATA TTTATA TTT-ATA TTTATA TTTATA TTTATA
261638 TTTATA T
1 TTTATA T
261645 GTATTCGCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
5 9 0.23
6 22 0.56
7 8 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:261889 original size:14 final size:14
Alignment explanation
Indices: 261870--261902 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
261860 TGTTTCATTG
261870 AAAAT-AATTTTCAA
1 AAAATAAATTTT-AA
261884 AAAATAAATTTTAA
1 AAAATAAATTTTAA
261898 AAAAT
1 AAAAT
261903 TATCAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAAATTTTAA
Found at i:263039 original size:13 final size:11
Alignment explanation
Indices: 263016--263065 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
263006 CCATACTTAT
* *
263016 TTCTCACAAAT
1 TTCTCTCAAAA
263027 TTCTCTCATAAA
1 TTCTCTCA-AAA
263039 -TCTCTCAAAA
1 TTCTCTCAAAA
263049 TTCTCTC-AAA
1 TTCTCTCAAAA
263059 TTCTCTC
1 TTCTCTC
263066 TTAAATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 13 0.37
11 20 0.57
12 2 0.06
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (11 bp):
TTCTCTCAAAA
Found at i:263240 original size:32 final size:30
Alignment explanation
Indices: 263162--263249 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 30
263152 TACCAAGTGA
*
263162 GTATTTGTTATCATTTCACAAAATTAAAGTT
1 GTATTTG-TATCATTTCACAAAATGAAAGTT
* *
263193 GTAACTTGTCATCATTCCACAAAATGAAAGTT
1 GT-ATTTGT-ATCATTTCACAAAATGAAAGTT
263225 GATATTTGTAGTCATTTCACAAAAT
1 G-TATTTGTA-TCATTTCACAAAAT
263250 CGATCATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
31 4 0.08
32 43 0.90
33 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (30 bp):
GTATTTGTATCATTTCACAAAATGAAAGTT
Found at i:268491 original size:18 final size:18
Alignment explanation
Indices: 268468--268527 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
268458 ATATAAATAA
268468 AACTCTTAAGTAAACTAG
1 AACTCTTAAGTAAACTAG
* *
268486 AACTC-TAATTCTAAA-TAA
1 AACTCTTAA--GTAAACTAG
268504 AACTCTTAAGTAAACTAG
1 AACTCTTAAGTAAACTAG
268522 AACTCT
1 AACTCT
268528 AATTAATCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 7 0.21
18 20 0.59
19 7 0.21
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (18 bp):
AACTCTTAAGTAAACTAG
Found at i:268508 original size:36 final size:36
Alignment explanation
Indices: 268461--268531 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
268451 TAAATAAATA
268461 TAAATAAAACTCTTAAGTAAACTAGAACTCTAATTC
1 TAAATAAAACTCTTAAGTAAACTAGAACTCTAATTC
268497 TAAATAAAACTCTTAAGTAAACTAGAACTCTAATT
1 TAAATAAAACTCTTAAGTAAACTAGAACTCTAATT
268532 AATCTAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (36 bp):
TAAATAAAACTCTTAAGTAAACTAGAACTCTAATTC
Found at i:274038 original size:2 final size:2
Alignment explanation
Indices: 274031--274056 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
274021 GTATTCTATT
274031 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
274057 TATATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:274690 original size:40 final size:40
Alignment explanation
Indices: 274635--274714 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
274625 GGATATTTAT
274635 CTCCGTAGTCCTTCCCCTTTTTTGACTTATTTCAATTAAG
1 CTCCGTAGTCCTTCCCCTTTTTTGACTTATTTCAATTAAG
274675 CTCCGTAGTCCTTCCCCTTTTTTGACTTATTTCAATTAAG
1 CTCCGTAGTCCTTCCCCTTTTTTGACTTATTTCAATTAAG
274715 TCCTTTAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.17, C:0.28, G:0.10, T:0.45
Consensus pattern (40 bp):
CTCCGTAGTCCTTCCCCTTTTTTGACTTATTTCAATTAAG
Found at i:274965 original size:30 final size:30
Alignment explanation
Indices: 274942--275147 Score: 209
Period size: 30 Copynumber: 6.9 Consensus size: 30
274932 TTTGACCATC
* *
274942 AAACTTTCTAGAAATTCGAATTTGACCCCT
1 AAACTTTCTAAAAATTCAAATTTGACCCCT
* *
274972 AAACTTTCCATAAATTCAAATTTGACCCCT
1 AAACTTTCTAAAAATTCAAATTTGACCCCT
* * *
275002 AAATTTTCTAAAAATTCAAATTT-AACCTT
1 AAACTTTCTAAAAATTCAAATTTGACCCCT
275031 AAAACTTTCTAAAAATTCAAATTTGACCCCT
1 -AAACTTTCTAAAAATTCAAATTTGACCCCT
* * * *
275062 AAATTTTCTAAAAATTCTAATTTAACCCTCG
1 AAACTTTCTAAAAATTCAAATTTGACCC-CT
** *** *
275093 AATTTTTC-AAAAATTTTGATTTGACCACT
1 AAACTTTCTAAAAATTCAAATTTGACCCCT
* *
275122 AAAGTTTCCAAAAATTCAAATTTGAC
1 AAACTTTCTAAAAATTCAAATTTGAC
275148 TTGGTTTTAA
Statistics
Matches: 146, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
29 11 0.08
30 123 0.84
31 12 0.08
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.36
Consensus pattern (30 bp):
AAACTTTCTAAAAATTCAAATTTGACCCCT
Found at i:275054 original size:90 final size:90
Alignment explanation
Indices: 274942--275147 Score: 236
Period size: 90 Copynumber: 2.3 Consensus size: 90
274932 TTTGACCATC
* * * * *
274942 AAACTTTCTAGAAATTCGAATTTGACCCCTAAACTTTCCATAAATTCAAATTTGACCC-CTAAAT
1 AAACTTTCTAAAAATTCAAATTTGACCCCTAAACTTTCCAAAAATTCAAATTTAACCCTCGAAAT
*
275006 TTTCTAAAAATTCAAATTTAACC-TT
66 TTTC-AAAAATTCAAATTTAACCACT
* * * *
275031 AAAACTTTCTAAAAATTCAAATTTGACCCCTAAATTTTCTAAAAATTCTAATTTAACCCTCGAAT
1 -AAACTTTCTAAAAATTCAAATTTGACCCCTAAACTTTCCAAAAATTCAAATTTAACCCTCGAAA
*** *
275096 TTTTCAAAAATTTTGATTTGACCACT
65 TTTTCAAAAATTCAAATTTAACCACT
* *
275122 AAAGTTTCCAAAAATTCAAATTTGAC
1 AAACTTTCTAAAAATTCAAATTTGAC
275148 TTGGTTTTAA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
90 89 0.91
91 9 0.09
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.36
Consensus pattern (90 bp):
AAACTTTCTAAAAATTCAAATTTGACCCCTAAACTTTCCAAAAATTCAAATTTAACCCTCGAAAT
TTTCAAAAATTCAAATTTAACCACT
Found at i:286790 original size:50 final size:49
Alignment explanation
Indices: 286643--286796 Score: 166
Period size: 50 Copynumber: 3.1 Consensus size: 49
286633 AATGATTCCT
* * * * * *
286643 ATACCCCTAAAGCTATAGAGGAACGGATTGAAGCCGCAATGGAAAATCTC
1 ATACACCTAAAGCTGTAAAGGGACAGATTGAAG-CGCAATGGAGAATCTC
*
286693 ATACACCTAAAGCTGTAAAGGGACAGATTGAAGCGACAATGGCGAATCTC
1 ATACACCTAAAGCTGTAAAGGGACAGATTGAAGCG-CAATGGAGAATCTC
* ** *
286743 ATTCACCTAAAGCTGTAAAGGGGTAGATTGAAGTCGCAA-GGATGAATCTT
1 ATACACCTAAAGCTGTAAAGGGACAGATTGAAG-CGCAATGGA-GAATCTC
286793 ATAC
1 ATAC
286797 TCTTGAAGCT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
49 4 0.05
50 82 0.93
51 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (49 bp):
ATACACCTAAAGCTGTAAAGGGACAGATTGAAGCGCAATGGAGAATCTC
Found at i:286935 original size:40 final size:40
Alignment explanation
Indices: 286821--286952 Score: 144
Period size: 39 Copynumber: 3.4 Consensus size: 40
286811 TGGAGCGAAA
* * *
286821 ACCATCCAATCTTTTACCTCGACCATGGGGCAAATTAAAG
1 ACCATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAG
* ** *
286861 -CAATCCAATCTTTTACCCTAACCA-GAGGGAAGATTGAAG
1 ACCATCCAATCTTTTACCCCGACCATG-GGGCAGATTGAAG
* *
286900 ACCATCCTATCTCTTACCCCGACCATGGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAG
*
286940 -CAATCCAATCTTT
1 ACCATCCAATCTTT
286953 CACCTCTAAA
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
38 1 0.01
39 40 0.55
40 31 0.42
41 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (40 bp):
ACCATCCAATCTTTTACCCCGACCATGGGGCAGATTGAAG
Found at i:287737 original size:21 final size:21
Alignment explanation
Indices: 287707--287747 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
287697 TTTATTTATT
*
287707 ATTTATAAATAAATAAATAAA
1 ATTTAAAAATAAATAAATAAA
287728 ATTTAAAAATAAATAAATAA
1 ATTTAAAAATAAATAAATAA
287748 TAAGAGCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTTAAAAATAAATAAATAAA
Found at i:288147 original size:2 final size:2
Alignment explanation
Indices: 288140--288181 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
288130 GTATTTTGTT
288140 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
288182 TATATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.