Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010871.1 Kokia drynarioides strain JFW-HI SEQ_125839, 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: 230448
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 83 characters in sequence are not A, C, G, or T
Found at i:4218 original size:6 final size:6
Alignment explanation
Indices: 4209--4286 Score: 72
Period size: 6 Copynumber: 13.3 Consensus size: 6
4199 ATTGATTTTG
* ** *
4209 AATTTA AATTT- ATTTTA AATTTA AATTT- GTTTTA ATATTTG AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA A-ATTTA AATTTA
* *
4255 AATTTA AATTTA GATTTA TATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AA
4287 ACTTATTATA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
5 12 0.21
6 42 0.72
7 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
AATTTA
Found at i:4237 original size:29 final size:29
Alignment explanation
Indices: 4205--4286 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 29
4195 TTAAATTGAT
4205 TTTGAATTTAAATTTATTTTAAATTTAAA
1 TTTGAATTTAAATTTATTTTAAATTTAAA
* *
4234 TTTG--TTTTAA--TA-TTTGAATTT-AA
1 TTTGAATTTAAATTTATTTTAAATTTAAA
* *
4257 TTTAAATTTAGATTTATATTTAAATTTAAA
1 TTTGAATTTAAATTTAT-TTTAAATTTAAA
4287 ACTTATTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
23 5 0.12
24 8 0.20
25 6 0.15
27 7 0.17
29 12 0.30
30 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (29 bp):
TTTGAATTTAAATTTATTTTAAATTTAAA
Found at i:4260 original size:18 final size:17
Alignment explanation
Indices: 4182--4286 Score: 95
Period size: 17 Copynumber: 6.1 Consensus size: 17
4172 CCATTTTGAG
*
4182 ATTTATTTTAAGA-TTAA
1 ATTTAATTTAA-ATTTAA
* * *
4199 ATTGATTTTGAATTTAA
1 ATTTAATTTAAATTTAA
*
4216 ATTTATTTTAAATTTAA
1 ATTTAATTTAAATTTAA
** *
4233 ATTTGTTTTAATATTTGA
1 ATTTAATTTAA-ATTTAA
*
4251 ATTTAATTTAAATTTAG
1 ATTTAATTTAAATTTAA
4268 ATTTATATTTAAATTTAA
1 ATTTA-ATTTAAATTTAA
4286 A
1 A
4287 ACTTATTATA
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
16 1 0.01
17 47 0.64
18 26 0.35
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTAATTTAAATTTAA
Found at i:4261 original size:35 final size:35
Alignment explanation
Indices: 4176--4283 Score: 116
Period size: 35 Copynumber: 3.1 Consensus size: 35
4166 TTAAACCCAT
*
4176 TTTGAGATTTATTTTAAGA-TTAAA-TTGATTTTGAA
1 TTTGA-ATTTATTTTAA-ATTTAAATTTGATTTTAAA
*
4211 TTTAAATTTATTTTAAATTTAAATTTG-TTTTAATA
1 TTTGAATTTATTTTAAATTTAAATTTGATTTTAA-A
* *
4246 TTTGAATTTAATTTAAATTTAGATTT-ATATTTAAA
1 TTTGAATTTATTTTAAATTTAAATTTGAT-TTTAAA
4281 TTT
1 TTT
4284 AAAACTTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
33 1 0.02
34 21 0.33
35 36 0.57
36 5 0.08
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (35 bp):
TTTGAATTTATTTTAAATTTAAATTTGATTTTAAA
Found at i:4277 original size:12 final size:11
Alignment explanation
Indices: 4209--4286 Score: 59
Period size: 11 Copynumber: 6.7 Consensus size: 11
4199 ATTGATTTTG
4209 AATTTAAATTT
1 AATTTAAATTT
*
4220 ATTTTAAATTT
1 AATTTAAATTT
**
4231 AAATTT-GTTTT
1 -AATTTAAATTT
*
4242 AATATTTGAATTT
1 -A-ATTTAAATTT
4255 AATTTAAATTT
1 AATTTAAATTT
*
4266 AGATTTATATTT
1 A-ATTTAAATTT
4278 AAATTTAAA
1 -AATTTAAA
4287 ACTTATTATA
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
11 25 0.47
12 24 0.45
13 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:4999 original size:13 final size:13
Alignment explanation
Indices: 4965--5002 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
4955 TTAATACCTT
4965 CAGTAATAAT-AA
1 CAGTAATAATAAA
*
4977 CATTAATAATAAA
1 CAGTAATAATAAA
*
4990 CAGTAGTAATAAA
1 CAGTAATAATAAA
5003 TGACATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (13 bp):
CAGTAATAATAAA
Found at i:5053 original size:37 final size:39
Alignment explanation
Indices: 5012--5086 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 39
5002 ATGACATTAA
*
5012 TAATATTAATAATAA-CTGTTTCAAT-AATAAAAATAAT
1 TAATATTAATAATAATATGTTTCAATAAATAAAAATAAT
* * *
5049 TAATATTAATATTAATATTTTTTAATAAATAAAAATAA
1 TAATATTAATAATAATATGTTTCAATAAATAAAAATAA
5087 AAAGGAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 14 0.44
38 7 0.22
39 11 0.34
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (39 bp):
TAATATTAATAATAATATGTTTCAATAAATAAAAATAAT
Found at i:6208 original size:29 final size:29
Alignment explanation
Indices: 6163--6407 Score: 176
Period size: 29 Copynumber: 8.3 Consensus size: 29
6153 CCCTGTAGAT
*
6163 CCCT-AAACTATCAAAAAATTACATTTTTA
1 CCCTCAAACT-TCCAAAAATTACATTTTTA
* * *
6192 CCCTCGAACTTCCAAAAATTCCATTTTGA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* *
6221 -CCTCAAAACTTCTAAAAATTACATTTTAA
1 CCCTC-AAACTTCCAAAAATTACATTTTTA
* *
6250 CCCTTAAACTTCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACATTTTT-A
* *
6280 CCCTAAAACTTCTAAAAATTACATTTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* * * * *
6309 CCCCCATACCTCTAAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACATTTTT-A
* **
6339 -CCTCAAAAATTTAAAAAATTACCA-TTTTA
1 CCCTC-AAACTTCCAAAAATTA-CATTTTTA
* * * *
6368 CCCCCGAA-TGTCCAAAAACTCCATTTTTGA
1 CCCTCAAACT-TCCAAAAATTACATTTTT-A
*
6398 CCCTAAAACT
1 CCCTCAAACT
6408 CTAAAATTTT
Statistics
Matches: 168, Mismatches: 36, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
28 7 0.04
29 101 0.60
30 57 0.34
31 3 0.02
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACATTTTTA
Found at i:6288 original size:59 final size:59
Alignment explanation
Indices: 6163--6413 Score: 284
Period size: 59 Copynumber: 4.3 Consensus size: 59
6153 CCCTGTAGAT
* * *
6163 CCCT-AAACTATCAAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGA
1 CCCTAAAACT-TCTAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGA
* **
6221 -CCTCAAAACTTCTAAAAATTACATTTTAACCCTTAAACTTCCAAAAATTCCATTTTTGA
1 CCCT-AAAACTTCTAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGA
* * *
6280 CCCTAAAACTTCTAAAAATTACATTTTTACCCCCATACCTCTAAAAATTCCATTTTTGA
1 CCCTAAAACTTCTAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGA
* * *
6339 -CCTCAAAAATT-TAAAAAATTACCA-TTTTACCCCCGAA-TGTCCAAAAACTCCATTTTTGA
1 CCCT-AAAACTTCT-AAAAATTA-CATTTTTACCCCCAAACT-TCCAAAAATTCCATTTTTGA
6398 CCCTAAAAC-TCTAAAA
1 CCCTAAAACTTCTAAAA
6414 TTTTTTCCCA
Statistics
Matches: 166, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
57 3 0.02
58 47 0.28
59 108 0.65
60 8 0.05
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.33
Consensus pattern (59 bp):
CCCTAAAACTTCTAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGA
Found at i:15368 original size:115 final size:114
Alignment explanation
Indices: 15194--15400 Score: 344
Period size: 115 Copynumber: 1.8 Consensus size: 114
15184 GGCTCAAAAC
* * *
15194 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGTAATAAAATGG
1 GAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAA-GG
15259 TTAGCTTCCTGATGAGATACAAAGAAGTATACCAACTCAGGGCTCGATGT
65 TTAGCTTCCTGATGAGATACAAAGAAGTATACCAACTCAGGGCTCGATGT
*
15309 GAGCAAATCTTCGAATCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAA-CAATAAAAGG
1 GAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGC-AAAGCAATAAAAGG
*
15373 TTAGCTTCCTGATGAGATACTAAGAAGT
65 TTAGCTTCCTGATGAGATACAAAGAAGT
15401 GGACCAAATT
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
114 29 0.34
115 54 0.63
116 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (114 bp):
GAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAAGGT
TAGCTTCCTGATGAGATACAAAGAAGTATACCAACTCAGGGCTCGATGT
Found at i:15667 original size:206 final size:205
Alignment explanation
Indices: 15300--15714 Score: 634
Period size: 206 Copynumber: 2.0 Consensus size: 205
15290 CCAACTCAGG
* *
15300 GCTCGATGTGAGCAAATCTTCGAATCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAACA
1 GCTCGATATGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAACA
**
15365 ATAAAAGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATAAGGTAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATAAGAAAC
* * * *
15430 AGAGAAGTAGATTTAAACAAACGATGCGGTCATCTTTCTGATGAGATACTAAGAAGAAGACCAAA
131 AGAGAAGCAGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAA
15495 TCAAACACAC
196 TCAAACACAC
* * *
15505 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
1 GCTCGATATGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAACA
* * * *
15570 ATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGATCAAATTCGTTTTCCTGA-AGAGAA
66 ATAAAA-GGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATA-AGAA
* * *
15634 ACTGAGAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
129 ACAGAGAAGCAGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCA
*
15699 AATCAAACCCAC
194 AATCAAACACAC
15711 GCTC
1 GCTC
15715 AATNNNNNNN
Statistics
Matches: 189, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
205 67 0.35
206 122 0.65
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (205 bp):
GCTCGATATGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAACA
ATAAAAGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATAAGAAAC
AGAGAAGCAGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAA
TCAAACACAC
Found at i:16113 original size:192 final size:194
Alignment explanation
Indices: 15768--16325 Score: 705
Period size: 192 Copynumber: 2.8 Consensus size: 194
15758 NNNNNNNNNN
*
15768 ATCTTCGAACCCCAGCTTCCTGTTGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCT
1 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAAT-AAAAGGTTAGCT
* *
15833 TCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCTTGATGAGGTACAGAGAAGCGGATTG
65 TCCTGATGAGACACTGAGAAGTAGACCAAATTCGTCTTCTTGATGAGGTACAGAGAAGAGGATTG
* ** * *
15898 AAACAAGTGAGATGGTCATCTTCCTGATAAGATACAGAGAAGTATACCAACTCA-ATGCGA-CAA
130 AAACAAGCGAGGCGGTTATCTTCCTGATAAGACACAGAGAAGTATACCAACTCAGATGCGAGCAA
*
15961 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCGGGGCGAAGCAATAAAAGGTTAG-TT
1 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAGGTTAGCTT
* * * *
16025 CCTTGATGAGACACTAAGATGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGAGGATTG
66 CC-TGATGAGACACTGAGAAGTAGACCAAATTCGTCTTCTTGATGAGGTACAGAGAAGAGGATTG
* * *
16090 AAACAAACGGGGCGGTTATCTTCCTGATAAGACACAGAGAAGTATACCAACTCAGGGCTCGATGT
130 AAACAAGCGAGGCGGTTATCTTCCTGATAAGACACAGAGAAGTATACCAACTCA------GATGC
16155 GAGCAA
189 GAGCAA
* * * * *
16161 ATCTTCGAATCCCAGCTTGCTGATGAAATACTGAGAAGCAGGTCGAACCAATAAAATGGTTAGCT
1 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAA-GGTTAGCT
* * * * * * *
16226 TCCTGATCAAATC-CTGAGAAGTAGACCAAATTCATCCTCTTGATAAGATACAAAGAAGCA-GAT
65 TCCTGATGAGA-CACTGAGAAGTAGACCAAATTCGTCTTCTTGATGAGGTACAGAGAAG-AGGAT
*
16289 TGAAACAAGCGATGC-GTTCATCTTCCTGATAAGACAC
128 TGAAACAAGCGAGGCGGTT-ATCTTCCTGATAAGACAC
16326 TAAAAAGTAG
Statistics
Matches: 315, Mismatches: 36, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
191 4 0.01
192 113 0.36
193 50 0.16
199 5 0.02
200 56 0.18
201 81 0.26
202 6 0.02
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (194 bp):
ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAGGTTAGCTT
CCTGATGAGACACTGAGAAGTAGACCAAATTCGTCTTCTTGATGAGGTACAGAGAAGAGGATTGA
AACAAGCGAGGCGGTTATCTTCCTGATAAGACACAGAGAAGTATACCAACTCAGATGCGAGCAA
Found at i:16677 original size:17 final size:17
Alignment explanation
Indices: 16649--16759 Score: 125
Period size: 17 Copynumber: 6.4 Consensus size: 17
16639 TTAAACCCAT
16649 TTTAAGATTTATTTTAAGA
1 TTTAA-ATTTATTTTAA-A
*
16668 -TTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
*
16684 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
*
16701 TTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
*
16719 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
* *
16736 TTTAGATTTATAATTAAA
1 TTTAAATTTAT-TTTAAA
16754 TTTAAA
1 TTTAAA
16760 ACTTATTATA
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
16 1 0.01
17 48 0.62
18 29 0.37
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:16693 original size:6 final size:6
Alignment explanation
Indices: 16668--16759 Score: 86
Period size: 6 Copynumber: 15.8 Consensus size: 6
16658 TATTTTAAGA
* * **
16668 TTAAAT TT-ATT TTGAAT TTAAAT TT-AAT TTAAAT TTAAAT TT-GTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
16713 TTAAAAT TTAAAT TT-AAT TTAAAT TTAGAT TTATAA- TTAAAT TTAAA
1 TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT TTAAA
16760 ACTTATTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
5 19 0.27
6 47 0.67
7 4 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:16735 original size:35 final size:34
Alignment explanation
Indices: 16649--16759 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
16639 TTAAACCCAT
* *
16649 TTTAAGATTTATTTTAAGA-TTAAATTTATTTTGAA
1 TTTAA-ATTTAATTTAA-ATTTAAATTTATTTTAAA
*
16684 TTTAAATTTAATTTAAATTTAAATTTGTTTTAAAA
1 TTTAAATTTAATTTAAATTTAAATTTATTTT-AAA
* *
16719 TTTAAATTTAATTTAAATTTAGATTTATAATTAAA
1 TTTAAATTTAATTTAAATTTAAATTTAT-TTTAAA
16754 TTTAAA
1 TTTAAA
16760 ACTTATTATA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
33 1 0.01
34 22 0.33
35 42 0.63
36 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (34 bp):
TTTAAATTTAATTTAAATTTAAATTTATTTTAAA
Found at i:17453 original size:12 final size:12
Alignment explanation
Indices: 17438--17523 Score: 75
Period size: 12 Copynumber: 7.0 Consensus size: 12
17428 TTAATACCTT
17438 CATTAATAATAA
1 CATTAATAATAA
17450 CATTAATAATAA
1 CATTAATAATAA
* **
17462 TATTTCTAATAA
1 CATTAATAATAA
17474 CATTAATAATAAA
1 CATTAATAAT-AA
* *
17487 CAGTAGTAATAA
1 CATTAATAATAA
*
17499 -ATGACATTAATAA
1 CATTA-A-TAATAA
*
17512 TATTAATAATAA
1 CATTAATAATAA
17524 TTGTTTCAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
11 2 0.03
12 36 0.62
13 17 0.29
14 3 0.05
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (12 bp):
CATTAATAATAA
Found at i:17524 original size:12 final size:12
Alignment explanation
Indices: 17439--17562 Score: 74
Period size: 12 Copynumber: 10.1 Consensus size: 12
17429 TAATACCTTC
*
17439 ATTAATAATAAC
1 ATTAATAATAAT
17451 ATTAATAATAAT
1 ATTAATAATAAT
** *
17463 ATTTCTAATAAC
1 ATTAATAATAAT
*
17475 ATTAATAATAAAC
1 ATTAATAAT-AAT
* *
17488 AGTAGTAATAA-
1 ATTAATAATAAT
*
17499 ATGACATTAATAAT
1 ATTA-A-TAATAAT
17513 ATTAATAATAAT
1 ATTAATAATAAT
*
17525 -TGT-TTCAATAAT
1 AT-TAAT-AATAAT
*
17537 AATAATAATAAAT
1 ATTAATAAT-AAT
*
17550 ATTAATATTAAT
1 ATTAATAATAAT
17562 A
1 A
17563 ATTTTTAATA
Statistics
Matches: 86, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
11 4 0.05
12 51 0.59
13 28 0.33
14 3 0.03
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:17555 original size:16 final size:16
Alignment explanation
Indices: 17531--17582 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
17521 TAATTGTTTC
*
17531 AATAATAATAATAATA
1 AATATTAATAATAATA
*
17547 AATATTAATATTAATA
1 AATATTAATAATAATA
* *
17563 ATTTTTAATAAATAA-A
1 AATATTAAT-AATAATA
17579 AATA
1 AATA
17583 AAAAGGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 24 0.86
17 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATTAATAATAATA
Found at i:18688 original size:29 final size:29
Alignment explanation
Indices: 18654--18902 Score: 188
Period size: 29 Copynumber: 8.5 Consensus size: 29
18644 TAAACTGTTC
18654 AAAAATTACATTTTTACACTC-AAACTTCT
1 AAAAATTACATTTTTAC-CTCAAAACTTCT
* * *
18683 AAAAATTCCATTTTGACCCCAAAACTTCT
1 AAAAATTACATTTTTACCTCAAAACTTCT
* * * *
18712 AAAAATTCCATTTTTACCCCTAAACTTCC
1 AAAAATTACATTTTTACCTCAAAACTTCT
* *
18741 AAAAATTTCATTTTTAACCCCAAAACTT-T
1 AAAAATTACATTTTT-ACCTCAAAACTTCT
* * *
18770 CAAAAATTACATTTTTACCTCTAAACCTCC
1 -AAAAATTACATTTTTACCTCAAAACTTCT
* *
18800 AAAAATTCCATTTTGACCTCAAAACTT-T
1 AAAAATTACATTTTTACCTCAAAACTTCT
* *
18828 CAAAAATTACCA-TTTTACCCTC-GAA-TGTCC
1 -AAAAATTA-CATTTTTA-CCTCAAAACT-TCT
* * *
18858 AAAAACTCCATTTTTAACCTCGAAAC-TCTT
1 AAAAATTACATTTTT-ACCTCAAAACTTC-T
18888 AAAAATTACCATTTT
1 AAAAATTA-CATTTT
18903 ACCCTCGAAT
Statistics
Matches: 176, Mismatches: 29, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
28 5 0.03
29 125 0.71
30 40 0.23
31 6 0.03
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTTACCTCAAAACTTCT
Found at i:18844 original size:117 final size:118
Alignment explanation
Indices: 18645--18930 Score: 336
Period size: 117 Copynumber: 2.4 Consensus size: 118
18635 GGAGATCCCT
* * *
18645 AAACTGTTCAAAAATTACATTTTTACACTCAAACTTCTAAAAATTCCATTTTGACCCCAAAACTT
1 AAACTCTTCAAAAATTACATTTTTACACTCAAACCTCCAAAAATTCCATTTTGACCCCAAAACTT
* *
18710 CTAAAAATTCCATTTTTACCC-CTAAACT-TCCAAAAATTTCATTTTTAACCCCA
66 CTAAAAATTCCATTTTTACCCTC-AAA-TGTCCAAAAACTCCATTTTTAACCCCA
*
18763 AAACT-TTCAAAAATTACATTTTTAC-CTCTAAACCTCCAAAAATTCCATTTTGACCTCAAAACT
1 AAACTCTTCAAAAATTACATTTTTACACTC-AAACCTCCAAAAATTCCATTTTGACCCCAAAACT
* * *
18826 T-TCAAAAATTACCA-TTTTACCCTCGAATGTCCAAAAACTCCATTTTTAACCTCG
65 TCT-AAAAATT-CCATTTTTACCCTCAAATGTCCAAAAACTCCATTTTTAACCCCA
* * ** *
18880 AAACTCTT-AAAAATTACCA-TTTTACCCTCGAATGTCCAAAAATTCCGTTTT
1 AAACTCTTCAAAAATTA-CATTTTTACACTCAAACCTCCAAAAATTCCATTTT
18931 TTATCCCGAT
Statistics
Matches: 148, Mismatches: 12, Indels: 17
0.84 0.07 0.10
Matches are distributed among these distances:
116 5 0.03
117 127 0.86
118 16 0.11
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (118 bp):
AAACTCTTCAAAAATTACATTTTTACACTCAAACCTCCAAAAATTCCATTTTGACCCCAAAACTT
CTAAAAATTCCATTTTTACCCTCAAATGTCCAAAAACTCCATTTTTAACCCCA
Found at i:18931 original size:59 final size:59
Alignment explanation
Indices: 18645--19027 Score: 292
Period size: 59 Copynumber: 6.5 Consensus size: 59
18635 GGAGATCCCT
* * * * *
18645 AAACTGTTCAAAAATTA-CATTTTTACACTCAAACT-TCTAAAAATTCCA-TTTTGACCCCA
1 AAACT-TTCAAAAATTACCA-TTTTACCCTCGAA-TGTCCAAAAATTCCATTTTTAACCTCA
* * *
18704 AAAC-TTCTAAAAATT-CCATTTTTACCC-CTAAACT-TCCAAAAATTTCATTTTTAACCCCA
1 AAACTTTC-AAAAATTACCA-TTTTACCCTC-GAA-TGTCCAAAAATTCCATTTTTAACCTCA
* ** *
18763 AAACTTTCAAAAATTA-CATTTTTA-CCTCTAAACCTCCAAAAATTCCA-TTTTGACCTCA
1 AAACTTTCAAAAATTACCA-TTTTACCCTC-GAATGTCCAAAAATTCCATTTTTAACCTCA
* *
18821 AAACTTTCAAAAATTACCATTTTACCCTCGAATGTCCAAAAACTCCATTTTTAACCTCG
1 AAACTTTCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCTCA
* *
18880 AAACTCTT-AAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCGTTTTTTATCC-C-
1 AAACT-TTCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCC-ATTTTTAACCTCA
* ** * * * * * *
18938 GATTTTTCTAAAAATTACCATTTAACCCTCGGATAT-CTAAAATTCCA-TTTTAAACTCC
1 AAACTTTC-AAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCTCA
* * *
18996 AAATTTTCCTAAAATTACCATTTTGCCCTCGA
1 AAACTTT-CAAAAATTACCATTTTACCCTCGA
19028 GAATCCAAAA
Statistics
Matches: 273, Mismatches: 33, Indels: 37
0.80 0.10 0.11
Matches are distributed among these distances:
56 6 0.02
57 7 0.03
58 114 0.42
59 133 0.49
60 13 0.05
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (59 bp):
AAACTTTCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTCCATTTTTAACCTCA
Found at i:18933 original size:30 final size:28
Alignment explanation
Indices: 18828--18931 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 28
18818 TCAAAACTTT
*
18828 CAAAAATTACCATTTTACCCTCGAATGTC
1 CAAAAATT-CCTTTTTACCCTCGAATGTC
* * **
18857 CAAAAACTCCATTTTTAACCTCGAAACTC
1 CAAAAATTCC-TTTTTACCCTCGAATGTC
* *
18886 TTAAAAATTACCATTTTACCCTCGAATGTC
1 -CAAAAATT-CCTTTTTACCCTCGAATGTC
18916 CAAAAATTCCGTTTTT
1 CAAAAATTCC-TTTTT
18932 TATCCCGATT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
28 4 0.07
29 32 0.55
30 20 0.34
31 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.34
Consensus pattern (28 bp):
CAAAAATTCCTTTTTACCCTCGAATGTC
Found at i:19061 original size:28 final size:28
Alignment explanation
Indices: 19006--19063 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
18996 AAATTTTCCT
* *
19006 AAAATTACCATTTTGCCCTCGAGAATCC
1 AAAATTACCATTTTGCCCCCAAGAATCC
*
19034 AAAATTACCATTTTGCCCCCAAGTATCC
1 AAAATTACCATTTTGCCCCCAAGAATCC
19062 AA
1 AA
19064 TAAGTCTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCCAAGAATCC
Found at i:22836 original size:31 final size:30
Alignment explanation
Indices: 22801--22881 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
22791 GTGATTTGTG
* *
22801 AAAATTGA-ATCAAAATTAAAATTTTATATAT
1 AAAATTGACAT-AAAATCAAAA-TTCATATAT
22832 AAAATT-ACATAAAATCAAAATTCATATAT
1 AAAATTGACATAAAATCAAAATTCATATAT
* *
22861 AACATTGCACATTAAAT-AAAA
1 AAAATTG-ACATAAAATCAAAA
22882 GTTACTCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 13 0.30
30 14 0.33
31 16 0.37
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAATTGACATAAAATCAAAATTCATATAT
Found at i:27370 original size:13 final size:13
Alignment explanation
Indices: 27352--27376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27342 ATCGAAAACA
27352 TTTAGCTTTTCTC
1 TTTAGCTTTTCTC
27365 TTTAGCTTTTCT
1 TTTAGCTTTTCT
27377 TTCCTCTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.20, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTAGCTTTTCTC
Found at i:29908 original size:25 final size:27
Alignment explanation
Indices: 29880--29950 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 27
29870 TATTAATCAC
29880 ATTTAATCACA-TTAGTCACATGA-AT
1 ATTTAATCACATTTAGTCACATGACAT
* * *
29905 ATTT-TTAACATTTA-TCACATTACAT
1 ATTTAATCACATTTAGTCACATGACAT
29930 A-TTAATCACATTTAGTCACAT
1 ATTTAATCACATTTAGTCACAT
29951 TTTGTAAGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 13 0.35
25 18 0.49
26 6 0.16
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41
Consensus pattern (27 bp):
ATTTAATCACATTTAGTCACATGACAT
Found at i:31413 original size:39 final size:39
Alignment explanation
Indices: 31367--31560 Score: 226
Period size: 39 Copynumber: 5.0 Consensus size: 39
31357 CCACAACAGG
** *
31367 GATATACTGAACTGATAGTGACACTATAAACACTGCAAT
1 GATATACTGAACTGGCAGTGACACTGTAAACACTGCAAT
* *
31406 GATATACTGAACTGGTAGTGACACTGTAAACACTGTAAT
1 GATATACTGAACTGGCAGTGACACTGTAAACACTGCAAT
* * * * *
31445 GCTATCCTCAACTGGCAGTGACACTGTAAACACCGTAAT
1 GATATACTGAACTGGCAGTGACACTGTAAACACTGCAAT
* * *
31484 GCTATACTAAACTGGCAATGACACTGTAAACACTGCAAT
1 GATATACTGAACTGGCAGTGACACTGTAAACACTGCAAT
* * * * *
31523 GTTATACTGAACTGGCGGTGATACCGTAAACACCGCAA
1 GATATACTGAACTGGCAGTGACACTGTAAACACTGCAA
31561 CATTATACTG
Statistics
Matches: 135, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 135 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (39 bp):
GATATACTGAACTGGCAGTGACACTGTAAACACTGCAAT
Found at i:31475 original size:78 final size:78
Alignment explanation
Indices: 31369--31595 Score: 233
Period size: 78 Copynumber: 2.9 Consensus size: 78
31359 ACAACAGGGA
* ** * * *
31369 TATACTGAACTGATAGTGACACTATAAACACTGCAATGATATACTGAACTGGTAGTGACACTGTA
1 TATACTCAACTGGCAGTGACACTGTAAACACCGCAATGATATACTGAACTGGTAATGACACTGTA
*
31434 AACACTGTAATGC
66 AACACTGCAATGC
* * * * *
31447 TATCCTCAACTGGCAGTGACACTGTAAACACCGTAATGCTATACTAAACTGGCAATGACACTGTA
1 TATACTCAACTGGCAGTGACACTGTAAACACCGCAATGATATACTGAACTGGTAATGACACTGTA
*
31512 AACACTGCAATGT
66 AACACTGCAATGC
* * * * * * * *
31525 TATACTGAACTGGCGGTGATACCGTAAACACCGCAA-CATTATACTGAGGC-AGTATTGACACTG
1 TATACTCAACTGGCAGTGACACTGTAAACACCGCAATGA-TATACTGA-ACTGGTAATGACACTG
31588 TAAACACT
64 TAAACACT
31596 ACTAGTCTAT
Statistics
Matches: 121, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
78 120 0.99
79 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (78 bp):
TATACTCAACTGGCAGTGACACTGTAAACACCGCAATGATATACTGAACTGGTAATGACACTGTA
AACACTGCAATGC
Found at i:32110 original size:23 final size:23
Alignment explanation
Indices: 32084--32131 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
32074 ATTTCATCAC
*
32084 AAATCACATTAATAGTTAAGCAT
1 AAATCACATTAACAGTTAAGCAT
* *
32107 AAATCATATTAACATTTAAGCAT
1 AAATCACATTAACAGTTAAGCAT
32130 AA
1 AA
32132 GTTGTTGGAA
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:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (23 bp):
AAATCACATTAACAGTTAAGCAT
Found at i:36317 original size:23 final size:23
Alignment explanation
Indices: 36289--36395 Score: 133
Period size: 23 Copynumber: 4.6 Consensus size: 23
36279 TATTTTCCAA
36289 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
36312 CATAAATAACATTAAAATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
36335 CATAAATCATATTAACATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
36358 CTTAAGTCACATTAATATTTAACA
1 CATAAATCACATTAATATTTAA-G
36382 CATATAATCACATT
1 CATA-AATCACATT
36396 TAATCACATA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
23 59 0.84
24 3 0.04
25 8 0.11
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.35
Consensus pattern (23 bp):
CATAAATCACATTAATATTTAAG
Found at i:36399 original size:10 final size:10
Alignment explanation
Indices: 36374--36521 Score: 96
Period size: 10 Copynumber: 15.2 Consensus size: 10
36364 TCACATTAAT
36374 ATTTAA-CAC
1 ATTTAATCAC
*
36383 ATATAATCAC
1 ATTTAATCAC
36393 ATTTAATCAC
1 ATTTAATCAC
* * *
36403 ATATAGTCAT
1 ATTTAATCAC
*
36413 ATTTAACCAC
1 ATTTAATCAC
*
36423 ATATAATCAC
1 ATTTAATCAC
36433 ATTTAATCAC
1 ATTTAATCAC
*
36443 A-TTAGTCAC
1 ATTTAATCAC
*
36452 A-TGAAT-AC
1 ATTTAATCAC
*
36460 -TTCAAT-A-
1 ATTTAATCAC
*
36467 TTTATCACATCAC
1 ATT-T-A-ATCAC
*
36480 ATATTAATCAT
1 AT-TTAATCAC
*
36491 ATTTAGTCAC
1 ATTTAATCAC
36501 A-TTAATCAC
1 ATTTAATCAC
36510 ATTTAATCAC
1 ATTTAATCAC
36520 AT
1 AT
36522 GAATATTTCA
Statistics
Matches: 107, Mismatches: 22, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
8 9 0.08
9 24 0.22
10 61 0.57
11 8 0.07
12 2 0.02
13 2 0.02
14 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.36
Consensus pattern (10 bp):
ATTTAATCAC
Found at i:36405 original size:20 final size:20
Alignment explanation
Indices: 36374--36521 Score: 116
Period size: 20 Copynumber: 7.6 Consensus size: 20
36364 TCACATTAAT
36374 ATTTAA-CACATATAATCAC
1 ATTTAATCACATATAATCAC
* *
36393 ATTTAATCACATATAGTCAT
1 ATTTAATCACATATAATCAC
*
36413 ATTTAACCACATATAATCAC
1 ATTTAATCACATATAATCAC
*
36433 ATTTAATCACAT-TAGTCAC
1 ATTTAATCACATATAATCAC
*
36452 A-TGAAT-AC-T-TCAAT-A-
1 ATTTAATCACATAT-AATCAC
* *
36467 TTTATCACATCACATATTAATCAT
1 ATT-T-A-ATCACATA-TAATCAC
*
36491 ATTTAGTCACAT-TAATCAC
1 ATTTAATCACATATAATCAC
36510 ATTTAATCACAT
1 ATTTAATCACAT
36522 GAATATTTCA
Statistics
Matches: 102, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.04
17 4 0.04
18 5 0.05
19 32 0.31
20 41 0.40
21 7 0.07
22 4 0.04
23 3 0.03
24 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.36
Consensus pattern (20 bp):
ATTTAATCACATATAATCAC
Found at i:36424 original size:40 final size:38
Alignment explanation
Indices: 36372--36450 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 38
36362 AGTCACATTA
36372 ATATTTAACACATATAATCACATTTAATCACATATAGTC
1 ATATTTAACACATATAATCACATTTAATCACAT-TAGTC
36411 ATATTTAACCACATATAATCACATTTAATCACATTAGTC
1 ATATTTAA-CACATATAATCACATTTAATCACATTAGTC
36450 A
1 A
36451 CATGAATACT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 14 0.36
40 25 0.64
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (38 bp):
ATATTTAACACATATAATCACATTTAATCACATTAGTC
Found at i:36506 original size:19 final size:19
Alignment explanation
Indices: 36482--36521 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
36472 CACATCACAT
* *
36482 ATTAATCATATTTAGTCAC
1 ATTAATCACATTTAATCAC
36501 ATTAATCACATTTAATCAC
1 ATTAATCACATTTAATCAC
36520 AT
1 AT
36522 GAATATTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (19 bp):
ATTAATCACATTTAATCAC
Found at i:36520 original size:68 final size:67
Alignment explanation
Indices: 36415--36570 Score: 204
Period size: 68 Copynumber: 2.3 Consensus size: 67
36405 ATAGTCATAT
* * * * * *
36415 TTAACCACATATAATCACATTTAATCACATTAGTCACATGAATACTTCAATATTTATCACATCAC
1 TTAATCACATTTAATCACA-TTAATCACATTAATCACATGAATACTTCAACAATTATCACATCAA
36480 ATA
65 ATA
* * * *
36483 TTAATCATATTTAGTCACATTAATCACATTTAATCACATGAATATTTCAACAATTATTACATCAA
1 TTAATCACATTTAATCACATTAATCACA-TTAATCACATGAATACTTCAACAATTATCACATCAA
36548 ATA
65 ATA
36551 TTAATCACATTTAATCACAT
1 TTAATCACATTTAATCACAT
36571 GAATGTTTCA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
67 9 0.12
68 66 0.88
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.37
Consensus pattern (67 bp):
TTAATCACATTTAATCACATTAATCACATTAATCACATGAATACTTCAACAATTATCACATCAAA
TA
Found at i:36558 original size:49 final size:49
Alignment explanation
Indices: 36501--36619 Score: 184
Period size: 49 Copynumber: 2.4 Consensus size: 49
36491 ATTTAGTCAC
*
36501 ATTAATCACATTTAATCACATGAATATTTCAACAATTATTACATCAAAT
1 ATTAATCACATTTAATCACATGAATATTTCAACAATTATCACATCAAAT
* * *
36550 ATTAATCACATTTAATCACATGAATGTTTCAACATTTATCACATCACAT
1 ATTAATCACATTTAATCACATGAATATTTCAACAATTATCACATCAAAT
* *
36599 ATTAATAACATTTAGTCACAT
1 ATTAATCACATTTAATCACAT
36620 TTAACCACAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 64 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (49 bp):
ATTAATCACATTTAATCACATGAATATTTCAACAATTATCACATCAAAT
Found at i:36568 original size:59 final size:58
Alignment explanation
Indices: 36488--36685 Score: 218
Period size: 59 Copynumber: 3.5 Consensus size: 58
36478 ACATATTAAT
* * *
36488 CATATTTAGTCACATTAATCACATTTAATCACATGAATATTTCAACAATTATTACAT--
1 CATA-TTAATCACATTAATCACATTTAATCACATGAATATTTCAACATTTATCACATCA
*
36545 C--A--AAT---ATTAATCACATTTAATCACATGAATGTTTCAACATTTATCACATCA
1 CATATTAATCACATTAATCACATTTAATCACATGAATATTTCAACATTTATCACATCA
* * * *
36596 CATATTAATAACATTTAGTCACATTTAACCACATGAATATTTCAGCATTTATCACATCA
1 CATATTAATCACA-TTAATCACATTTAATCACATGAATATTTCAACATTTATCACATCA
36655 CATATTAATCACATATAATCAC-TTATAATCA
1 CATATTAATCACAT-TAATCACATT-TAATCA
36686 TATTTTATGA
Statistics
Matches: 118, Mismatches: 11, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
49 41 0.35
51 1 0.01
52 2 0.02
53 1 0.01
55 4 0.03
57 1 0.01
58 4 0.03
59 64 0.54
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (58 bp):
CATATTAATCACATTAATCACATTTAATCACATGAATATTTCAACATTTATCACATCA
Found at i:36584 original size:24 final size:23
Alignment explanation
Indices: 36508--36619 Score: 84
Period size: 24 Copynumber: 4.6 Consensus size: 23
36498 CACATTAATC
36508 ACATTTAATCACATGAATATTTCA
1 ACATTT-ATCACATGAATATTTCA
* * *
36532 ACAATTATTACATCAAATATTAATC-
1 ACATTTATCACAT-GAATATT--TCA
*
36557 ACATTTAATCACATGAATGTTTCA
1 ACATTT-ATCACATGAATATTTCA
*
36581 ACATTTATCACATCACATATTAAT-A
1 ACATTTATCACATGA-ATATT--TCA
36606 ACATTTAGTCACAT
1 ACATTTA-TCACAT
36620 TTAACCACAT
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
23 16 0.23
24 21 0.30
25 18 0.26
26 15 0.21
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.37
Consensus pattern (23 bp):
ACATTTATCACATGAATATTTCA
Found at i:36675 original size:10 final size:10
Alignment explanation
Indices: 36651--36685 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
36641 CATTTATCAC
36651 ATCACATATTA
1 ATCACATA-TA
36662 ATCACATATA
1 ATCACATATA
*
36672 ATCACTTATA
1 ATCACATATA
36682 ATCA
1 ATCA
36686 TATTTTATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (10 bp):
ATCACATATA
Found at i:36896 original size:66 final size:66
Alignment explanation
Indices: 36760--36888 Score: 150
Period size: 66 Copynumber: 2.0 Consensus size: 66
36750 AATACATGGA
* * * ** * *
36760 TCTCCAAACACACCAAATGACTCATAGAGTCGAACATATCCCATAAGTGAATTATATAGCTAAAA
1 TCTCCAAACACACCAAAAGACTCATAGAGTCAAACATATCCCAAAAGTGAAGCACAAAGCTAAAA
36825 C
66 C
* * * * *
36826 TCTCCAAACATACCAAAAGACTCGTAGAGTTAAACATGTCCCAAAAGTGGAGCACAAAGCTAA
1 TCTCCAAACACACCAAAAGACTCATAGAGTCAAACATATCCCAAAAGTGAAGCACAAAGCTAA
36889 TAGTCTCCTT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.20
Consensus pattern (66 bp):
TCTCCAAACACACCAAAAGACTCATAGAGTCAAACATATCCCAAAAGTGAAGCACAAAGCTAAAA
C
Found at i:37199 original size:36 final size:36
Alignment explanation
Indices: 37152--37516 Score: 523
Period size: 36 Copynumber: 10.1 Consensus size: 36
37142 ATAATCACTA
* *
37152 TCACATGGCATGAAAAACATACCCACATATTTACTC
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * *
37188 TCACATGGCATGAATAACACACCCATATATTTACTA
1 TCACATGGCATGAATAACATACCCACATATTTACTG
** *
37224 TCACATTACATGAATAACATACCCACATATTTACTA
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* *
37260 TCTCATGGCATGAATAACATACTCACATATTTACTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * * *
37296 TCACATGACATGAATAACATACCCACGTACTTATTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
37332 TCACATGGCATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
*
37368 TCTCATGGCATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* *
37404 TCACATGACATGAATAACATACCCACATATTTATTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * *
37440 TCACATGCCATGAATAACATACACACATATTTGCTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * *
37476 TCAAATGACATGAATAACATACCCACATATTTACTT
1 TCACATGGCATGAATAACATACCCACATATTTACTG
37512 TCACA
1 TCACA
37517 ACAATCATCA
Statistics
Matches: 292, Mismatches: 37, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 292 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.29
Consensus pattern (36 bp):
TCACATGGCATGAATAACATACCCACATATTTACTG
Found at i:43511 original size:13 final size:13
Alignment explanation
Indices: 43493--43519 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43483 ACCGAAAACA
43493 TTTAGCTTTTCTC
1 TTTAGCTTTTCTC
43506 TTTAGCTTTTCTC
1 TTTAGCTTTTCTC
43519 T
1 T
43520 CATCTCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.22, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTAGCTTTTCTC
Found at i:44201 original size:14 final size:14
Alignment explanation
Indices: 44184--44216 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
44174 AAACATAATA
44184 AATGTGGACCTTTT
1 AATGTGGACCTTTT
44198 AATGTGGACCTTTT
1 AATGTGGACCTTTT
44212 AATGT
1 AATGT
44217 TCCATCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.42
Consensus pattern (14 bp):
AATGTGGACCTTTT
Found at i:44227 original size:15 final size:15
Alignment explanation
Indices: 44207--44244 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
44197 TAATGTGGAC
44207 CTTTTAATGTTCCAT
1 CTTTTAATGTTCCAT
44222 CTTTTAATGTTCCAT
1 CTTTTAATGTTCCAT
44237 CTTTTAAT
1 CTTTTAAT
44245 ACACATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (15 bp):
CTTTTAATGTTCCAT
Found at i:45647 original size:52 final size:52
Alignment explanation
Indices: 45565--45953 Score: 541
Period size: 52 Copynumber: 7.5 Consensus size: 52
45555 TTCCCATTTA
* * ** * * *
45565 ATACTCACAATGACACAAAGTCATTGGACCTTA-AATCTGTAATAGGATCCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAA-AGGATTCAT
45617 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
45669 ATACTTACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
45721 ATACTCACGATGGCACATAGTCATC-GAACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAG-ACCTCATAATCCGTAAAGGATTCAT
* * *
45773 ATACTCACGATGACATATAGTCATCAGACCTCATAATTCGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
**
45825 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* * * * *
45877 ATACTCATGAGGACACACAGTCATCAAACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
45929 ATACTCACGACT-ACACATAGTCATC
1 ATACTCACGA-TGACACATAGTCATC
45954 GGATCTTTTT
Statistics
Matches: 301, Mismatches: 32, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
51 1 0.00
52 291 0.97
53 9 0.03
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
Found at i:48437 original size:2 final size:2
Alignment explanation
Indices: 48430--48464 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48420 AGTAGTCGAT
48430 TA TA TA TA 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 TA TA TA TA T
48465 TTCAATCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49642 original size:25 final size:25
Alignment explanation
Indices: 49614--49669 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
49604 TTTCAGAAAT
**
49614 TTAGCTCATACGAACCCGGACAAAA
1 TTAGCTCATACGAACCCAAACAAAA
*
49639 TTAGCTCATACGAGCCCAAACAAAA
1 TTAGCTCATACGAACCCAAACAAAA
49664 TTAGCT
1 TTAGCT
49670 TATATGAGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (25 bp):
TTAGCTCATACGAACCCAAACAAAA
Found at i:49694 original size:24 final size:24
Alignment explanation
Indices: 49636--49727 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
49626 AACCCGGACA
* * *
49636 AAATTAGCTCATACGAGCCCAAACA
1 AAATTAGCTTATACGAGCCTAAA-T
*
49661 AAATTAGCTTATATGAGCCTAAAT
1 AAATTAGCTTATACGAGCCTAAAT
* * *
49685 AGATTAGCTTTTACGAGCCTAGAT
1 AAATTAGCTTATACGAGCCTAAAT
* *
49709 AAATTAGCTCATTCGAGCC
1 AAATTAGCTTATACGAGCC
49728 CAGATAGAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
24 35 0.64
25 20 0.36
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (24 bp):
AAATTAGCTTATACGAGCCTAAAT
Found at i:54199 original size:25 final size:26
Alignment explanation
Indices: 54166--54215 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
54156 GAGTCTTTCA
*
54166 AAAATTTAGCTCATACGAGCGCAAAC
1 AAAATTTAGCTCATACGAGCCCAAAC
54192 AAAA-TTAGCTCATACGAGCCCAAA
1 AAAATTTAGCTCATACGAGCCCAAA
54216 TAGGTTAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.18
Consensus pattern (26 bp):
AAAATTTAGCTCATACGAGCCCAAAC
Found at i:54231 original size:24 final size:24
Alignment explanation
Indices: 54171--54261 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
54161 TTTCAAAAAT
* * *
54171 TTAGCTCATACGAGCGCAAACAAAA
1 TTAGCTCTTACGAGCCCAAA-TAAA
* **
54196 TTAGCTCATACGAGCCCAAATAGG
1 TTAGCTCTTACGAGCCCAAATAAA
* *
54220 TTAGCTCTTACGAACCCAGATAAA
1 TTAGCTCTTACGAGCCCAAATAAA
54244 TTAGCTCATT-CGAGCCCA
1 TTAGCTC-TTACGAGCCCA
54262 GACAGAATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 34 0.62
25 21 0.38
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.22
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAAATAAA
Found at i:54659 original size:56 final size:56
Alignment explanation
Indices: 54589--54709 Score: 217
Period size: 56 Copynumber: 2.2 Consensus size: 56
54579 CATTATCTCG
* *
54589 AATGTTTA-ACCTTCCTCGAGTTGTTGTAACAATAGTGAATGTACAAGAAACATAC
1 AATGTATATACCTTCCTCGAGTTGCTGTAACAATAGTGAATGTACAAGAAACATAC
54644 AATGTATATACCTTCCTCGAGTTGCTGTAACAATAGTGAATGTACAAGAAACATAC
1 AATGTATATACCTTCCTCGAGTTGCTGTAACAATAGTGAATGTACAAGAAACATAC
54700 AATGTATATA
1 AATGTATATA
54710 AACTAACACT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 7 0.11
56 56 0.89
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (56 bp):
AATGTATATACCTTCCTCGAGTTGCTGTAACAATAGTGAATGTACAAGAAACATAC
Found at i:58506 original size:52 final size:52
Alignment explanation
Indices: 58323--58508 Score: 243
Period size: 52 Copynumber: 3.6 Consensus size: 52
58313 TTCCCATTTA
* * * *
58323 ATACTCACGATGACACAAAGTCATCGGACCTTA-AATCTGTAATAGGA-TCCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAA-AGGATTCC-T
*
58375 ATACTCACGATGACACATAGTCATCTG-ACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATC-GAACCTCATAATCCGTAAAGGATTCCT
* * *
58427 ATACTCACGATAACACATAATCATCGAACCTCATAATCCGTAAAGAATTCCT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCCT
*
58479 ATACTCATGATGACACATAGTCATCGAACC
1 ATACTCACGATGACACATAGTCATCGAACC
58509 CCAAGGGTTC
Statistics
Matches: 119, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
51 1 0.01
52 107 0.90
53 11 0.09
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCCT
Found at i:64164 original size:26 final size:24
Alignment explanation
Indices: 64122--64171 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
64112 ACATAAATTA
*
64122 TAAATTATATATGTATTTTATTAAAT
1 TAAATTATAAATGTA--TTATTAAAT
64148 TAAATTATACAAT-TATTATTAAAT
1 TAAATTATA-AATGTATTATTAAAT
64172 CGTATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 9 0.41
26 11 0.50
27 2 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TAAATTATAAATGTATTATTAAAT
Found at i:79218 original size:21 final size:21
Alignment explanation
Indices: 79194--79233 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
79184 TGACCGGCCA
*
79194 TTGACCATTAACCTTTGACCG
1 TTGACCATTAACCGTTGACCG
* *
79215 TTGATCATTGACCGTTGAC
1 TTGACCATTAACCGTTGAC
79234 TTTGGCCGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (21 bp):
TTGACCATTAACCGTTGACCG
Found at i:79244 original size:13 final size:13
Alignment explanation
Indices: 79206--79249 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
79196 GACCATTAAC
79206 CTTTGACCGTTGA
1 CTTTGACCGTTGA
*
79219 TCATTGACCGTTGA
1 -CTTTGACCGTTGA
*
79233 CTTTGGCCGTTGA
1 CTTTGACCGTTGA
79246 CTTT
1 CTTT
79250 TTTTGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.41
Consensus pattern (13 bp):
CTTTGACCGTTGA
Found at i:80336 original size:20 final size:18
Alignment explanation
Indices: 80299--80336 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 18
80289 AAAATTTATA
80299 ATATTTTATTTTATTTTG
1 ATATTTTATTTTATTTTG
80317 ATATTATTATTTTGATTTTG
1 ATATT-TTATTTT-ATTTTG
80337 GATTTTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (18 bp):
ATATTTTATTTTATTTTG
Found at i:85565 original size:23 final size:23
Alignment explanation
Indices: 85517--85570 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
85507 ATCTCAATGG
*
85517 TTTAATTTTTTAGGAAATTAATAT
1 TTTAATTTTTTA-GAAATTAAAAT
*
85541 TTTAATTTTTT-GAATTTAAAAAT
1 TTTAATTTTTTAGAAATT-AAAAT
85564 TTTAATT
1 TTTAATT
85571 CAATTGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 5 0.19
23 11 0.41
24 11 0.41
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (23 bp):
TTTAATTTTTTAGAAATTAAAAT
Found at i:85952 original size:17 final size:18
Alignment explanation
Indices: 85919--85953 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
85909 CAATAAATAA
*
85919 TTTTAAAATTATTAAATT
1 TTTTAAAATTATAAAATT
85937 TTTTAAAA-TATAAAATT
1 TTTTAAAATTATAAAATT
85954 ATTAAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAAATTATAAAATT
Found at i:86652 original size:30 final size:30
Alignment explanation
Indices: 86617--86726 Score: 145
Period size: 29 Copynumber: 3.7 Consensus size: 30
86607 AATTGAAAAT
* *
86617 AAAAATTA-TTTAATAATTTTATTATTTTAA
1 AAAAATAATTTTAATAATTTTA-TATTTTGA
86647 AAAAATAATTTTAATAATTTTATA-TTTGA
1 AAAAATAATTTTAATAATTTTATATTTTGA
* **
86676 AAAAATAA-TTTAAAAAAATTATATTTTGA
1 AAAAATAATTTTAATAATTTTATATTTTGA
86705 AAAAATAATTTTAATAATTTTA
1 AAAAATAATTTTAATAATTTTA
86727 AAATCGTTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.17
29 25 0.36
30 19 0.28
31 13 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (30 bp):
AAAAATAATTTTAATAATTTTATATTTTGA
Found at i:119673 original size:9 final size:9
Alignment explanation
Indices: 119650--119693 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
119640 TCAGTCACTT
119650 GAAAAACAAA
1 GAAAAA-AAA
*
119660 AAAAAAAAA
1 GAAAAAAAA
*
119669 GAAAAAGAA
1 GAAAAAAAA
119678 GAAAAAAAAA
1 G-AAAAAAAA
119688 GAAAAA
1 GAAAAA
119694 GAATAAATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 16 0.55
10 13 0.45
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:119694 original size:6 final size:6
Alignment explanation
Indices: 119658--119696 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
119648 TTGAAAAACA
* *
119658 AAAAAA AAAAAG AAAAAG AAGAAAA AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG AA
119697 TAAATTGCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:119694 original size:19 final size:19
Alignment explanation
Indices: 119650--119696 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
119640 TCAGTCACTT
*
119650 GAAAAACAAAAAAAAAAAA
1 GAAAAAGAAAAAAAAAAAA
*
119669 GAAAAAGAAGAAAAAAAAA
1 GAAAAAGAAAAAAAAAAAA
119688 GAAAAAGAA
1 GAAAAAGAA
119697 TAAATTGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (19 bp):
GAAAAAGAAAAAAAAAAAA
Found at i:122262 original size:2 final size:2
Alignment explanation
Indices: 122255--122283 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
122245 TGCACATCTT
122255 TA 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 TA T
122284 TAACTCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:124140 original size:19 final size:19
Alignment explanation
Indices: 124116--124156 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
124106 GAAATATGAC
124116 CCTCCAAATACATAAAAGT
1 CCTCCAAATACATAAAAGT
124135 CCTCCAAATACATAAAAGT
1 CCTCCAAATACATAAAAGT
124154 CCT
1 CCT
124157 TAGAAAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.29, G:0.05, T:0.22
Consensus pattern (19 bp):
CCTCCAAATACATAAAAGT
Found at i:131940 original size:25 final size:23
Alignment explanation
Indices: 131895--131942 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
131885 TTTGAAATAA
* *
131895 ATTTTTTTATTTATTTTTACTAT
1 ATTTTTTTATGTATTGTTACTAT
131918 ATTTTATTTATGTAGTTGTTACTAT
1 ATTTT-TTTATGTA-TTGTTACTAT
131943 TTAGAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 7 0.33
25 9 0.43
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (23 bp):
ATTTTTTTATGTATTGTTACTAT
Found at i:133011 original size:24 final size:24
Alignment explanation
Indices: 132972--133023 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
132962 TCAAATGCAT
132972 CCTCCACCCCCAATGTATCAC-CCA
1 CCTCCACCCCCAATGTATC-CTCCA
* *
132996 CCTCCACCGCCGATGTATCCTCCA
1 CCTCCACCCCCAATGTATCCTCCA
133020 CCTC
1 CCTC
133024 AAATGTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.19, C:0.54, G:0.08, T:0.19
Consensus pattern (24 bp):
CCTCCACCCCCAATGTATCCTCCA
Found at i:139431 original size:17 final size:17
Alignment explanation
Indices: 139370--139446 Score: 50
Period size: 18 Copynumber: 4.5 Consensus size: 17
139360 AGTACAAAAC
139370 AGCTCACACCTTGA-TG
1 AGCTCACACCTTGAGTG
** * *
139386 AGCTTGCAACTAG-GTTG
1 AGCTCACACCTTGAG-TG
139403 AGCTCACAACCTTGAGTG
1 AGCTCAC-ACCTTGAGTG
* * *
139421 AGCTCGCACCTTCAAATG
1 AGCTCACACCTT-GAGTG
139439 AGCTCACA
1 AGCTCACA
139447 GATATAGAGC
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
16 9 0.20
17 12 0.27
18 22 0.50
19 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (17 bp):
AGCTCACACCTTGAGTG
Found at i:163530 original size:144 final size:144
Alignment explanation
Indices: 163268--163552 Score: 428
Period size: 144 Copynumber: 2.0 Consensus size: 144
163258 AAAACTATAG
* * * *
163268 GGTAAAACTTCTTAGATCTCTGGTGTTTGTTGTATCGGTAGTAGCCATACTTGTATCGGTAGAAC
1 GGTAAAACTTCATAGATCTCTGGAGTTTGTTATATCGGTAGAAGCCATACTTGTATCGGTAGAAC
* *
163333 CTTCCCAACTACCGGTAGGAAACTACAACTATTTTTAATTTGTTTACTAACTTGACTTCTACCGA
66 CTTCCCAACTACCGATAGGAAACTACAACTATTTTTAATTTGTTTACTAACTTGACTTCTACCAA
163398 TACTTGTCTAACAA
131 TACTTGTCTAACAA
* * **
163412 GGTAAAACTTCATAGCTCTTTGGAGTTTGTTATATCGGTAGAAGTGATGA-TTGTATCGGTAGAA
1 GGTAAAACTTCATAGATCTCTGGAGTTTGTTATATCGGTAGAAGCCAT-ACTTGTATCGGTAGAA
* * * *
163476 CCTTCCCAACTACCGATAGGAAGCTACAACTATTTTTAATTTGTTTATTGACTTGACTTCTACTA
65 CCTTCCCAACTACCGATAGGAAACTACAACTATTTTTAATTTGTTTACTAACTTGACTTCTACCA
163541 ATACTTGTCTAA
130 ATACTTGTCTAA
163553 TAGGTACCGA
Statistics
Matches: 126, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
144 125 0.99
145 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (144 bp):
GGTAAAACTTCATAGATCTCTGGAGTTTGTTATATCGGTAGAAGCCATACTTGTATCGGTAGAAC
CTTCCCAACTACCGATAGGAAACTACAACTATTTTTAATTTGTTTACTAACTTGACTTCTACCAA
TACTTGTCTAACAA
Found at i:176648 original size:19 final size:20
Alignment explanation
Indices: 176597--176648 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 20
176587 TGTCTTTAGG
176597 TCAATCAAAGAATGCAAAATT
1 TCAA-CAAAGAATGCAAAATT
176618 TCAA-AAAGAATGCAAAATT
1 TCAACAAAGAATGCAAAATT
176637 TCAACAAA-AATG
1 TCAACAAAGAATG
176649 TGATCACAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 23 0.77
20 3 0.10
21 4 0.13
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.21
Consensus pattern (20 bp):
TCAACAAAGAATGCAAAATT
Found at i:177076 original size:25 final size:25
Alignment explanation
Indices: 177042--177089 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
177032 GTCATTTATA
*
177042 AAAAAAG-AAAGAAAGAAAGAAGAGG
1 AAAAAAGAAAAG-AAGAAAAAAGAGG
*
177067 AAAAGAGAAAAGAAGAAAAAAGA
1 AAAAAAGAAAAGAAGAAAAAAGA
177090 AATATATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAAAGAAGAAAAAAGAGG
Found at i:182744 original size:5 final size:5
Alignment explanation
Indices: 182734--182763 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
182724 TTCGTGCATG
*
182734 TTATT TTATT TTATT TTATT TTATT ATATT
1 TTATT TTATT TTATT TTATT TTATT TTATT
182764 GAAATGCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:188870 original size:19 final size:19
Alignment explanation
Indices: 188828--188863 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
188818 TAACAAAACT
188828 TTAATTAAGTTAATTAATC
1 TTAATTAAGTTAATTAATC
188847 TTAATTAA-TTAATTAAT
1 TTAATTAAGTTAATTAAT
188864 GTATAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TTAATTAAGTTAATTAATC
Found at i:192526 original size:18 final size:18
Alignment explanation
Indices: 192503--192539 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
192493 TTTGTGATCA
192503 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
192521 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
192539 A
1 A
192540 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:199688 original size:21 final size:19
Alignment explanation
Indices: 199638--199690 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
199628 CTGTACTAGT
199638 TCTATCGATACAAGTATAA
1 TCTATCGATACAAGTATAA
* *
199657 TTTATACCGATACAAGTCATGCA
1 TCTAT--CGATACAAGT-AT-AA
199680 TCTATCGATAC
1 TCTATCGATAC
199691 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.15
21 16 0.59
22 2 0.07
23 5 0.19
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (19 bp):
TCTATCGATACAAGTATAA
Found at i:199802 original size:21 final size:24
Alignment explanation
Indices: 199748--199804 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 24
199738 CAAGCATGCA
199748 AACTACCGATACTTCTATACATAC
1 AACTACCGATACTTCTATACATAC
* **
199772 AACTATCGATAC-TC-ATA-ATTT
1 AACTACCGATACTTCTATACATAC
199793 AACTACCGATAC
1 AACTACCGATAC
199805 AACTCAAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 13 0.45
22 3 0.10
23 2 0.07
24 11 0.38
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (24 bp):
AACTACCGATACTTCTATACATAC
Found at i:200563 original size:100 final size:102
Alignment explanation
Indices: 200431--200668 Score: 301
Period size: 100 Copynumber: 2.4 Consensus size: 102
200421 CCGAATAGAA
* * * *
200431 ATTCATATACTCACGATGACAC-T-G--ATCGGACCTTTAATTTGTCA-TGGATTCATTTACTCA
1 ATTCATTTACCCACGATGACACTTAGTCATCGGACCTTTAATCTGT-AGAGGATTCATTTACTCA
* *
200491 CAATGACAC-TAGTCATCGGACCTTTAAT-CGTAGAGG
65 CAATGACACTTAGTCATCGGACCTTTAATCCATAAAGG
* * * *
200527 ATTCGTTTACTCACTATGACACTTAGTCATCGGACCTTTAATCTGTAGAGGGTTCATTTACTCAC
1 ATTCATTTACCCACGATGACACTTAGTCATCGGACCTTTAATCTGTAGAGGATTCATTTACTCAC
* *
200592 GATGACACTTAGTCATTGGACCTTTAATCCATAAAGG
66 AATGACACTTAGTCATCGGACCTTTAATCCATAAAGG
200629 ATTCATTTACCCACGATGACACTTAGTCATCGGACTCTTT
1 ATTCATTTACCCACGATGACACTTAGTCATCGGAC-CTTT
200669 CGTTTATAGC
Statistics
Matches: 121, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
96 19 0.16
97 1 0.01
98 1 0.01
99 1 0.01
100 39 0.32
101 18 0.15
102 38 0.31
103 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (102 bp):
ATTCATTTACCCACGATGACACTTAGTCATCGGACCTTTAATCTGTAGAGGATTCATTTACTCAC
AATGACACTTAGTCATCGGACCTTTAATCCATAAAGG
Found at i:200597 original size:51 final size:51
Alignment explanation
Indices: 200431--200668 Score: 301
Period size: 51 Copynumber: 4.8 Consensus size: 51
200421 CCGAATAGAA
* * *
200431 ATTCATATACTCACGATGACAC-T-G--ATCGGACCTTTAATTTGTCA-TGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCTGT-AGAGG
*
200478 ATTCATTTACTCACAATGACAC-TAGTCATCGGACCTTTAATC-GTAGAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCTGTAGAGG
* *
200527 ATTCGTTTACTCACTATGACACTTAGTCATCGGACCTTTAATCTGTAGAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCTGTAGAGG
* * ** *
200578 GTTCATTTACTCACGATGACACTTAGTCATTGGACCTTTAATCCATAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCTGTAGAGG
*
200629 ATTCATTTACCCACGATGACACTTAGTCATCGGACTCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATCGGAC-CTTT
200669 CGTTTATAGC
Statistics
Matches: 168, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
47 21 0.12
48 2 0.01
49 24 0.14
50 34 0.20
51 83 0.49
52 4 0.02
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCTGTAGAGG
Found at i:206810 original size:21 final size:21
Alignment explanation
Indices: 206785--206824 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
206775 TCATGAATTC
206785 TTATCGTTGCATTCATTTTGA
1 TTATCGTTGCATTCATTTTGA
206806 TTATCGTTGCATTCATTTT
1 TTATCGTTGCATTCATTTT
206825 AGTTTAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.55
Consensus pattern (21 bp):
TTATCGTTGCATTCATTTTGA
Found at i:211202 original size:3 final size:3
Alignment explanation
Indices: 211166--211191 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
211156 TCACTGCTGC
211166 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
211192 AAAGCATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:212946 original size:21 final size:21
Alignment explanation
Indices: 212908--212947 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
212898 CACTCATCCT
*
212908 GCATAAGACAGAAACTAATTA
1 GCATAAGACACAAACTAATTA
* *
212929 GCATAAGAGACAATCTAAT
1 GCATAAGACACAAACTAAT
212948 GAGGGAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (21 bp):
GCATAAGACACAAACTAATTA
Found at i:216759 original size:26 final size:27
Alignment explanation
Indices: 216713--216764 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
216703 GGTTAAAAAT
216713 ATAATTATTTTTAAATATATAATTATC
1 ATAATTATTTTTAAATATATAATTATC
216740 ATAA-TATTTATTAAAT-TATAATTAT
1 ATAATTATTT-TTAAATATATAATTAT
216765 TTTTCAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
ATAATTATTTTTAAATATATAATTATC
Found at i:217588 original size:17 final size:17
Alignment explanation
Indices: 217566--217599 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
217556 TAAAATCATA
*
217566 ATTATAATCAAAATTAT
1 ATTATAATAAAAATTAT
*
217583 ATTATATTAAAAATTAT
1 ATTATAATAAAAATTAT
217600 TAAGAATGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATAATAAAAATTAT
Found at i:218635 original size:17 final size:18
Alignment explanation
Indices: 218602--218636 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
218592 AAAGTTTATT
218602 AATAGAAAAAGTAATGAA
1 AATAGAAAAAGTAATGAA
218620 AATAGAAAAAGT-ATGAA
1 AATAGAAAAAGTAATGAA
218637 GCAATCGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (18 bp):
AATAGAAAAAGTAATGAA
Found at i:218793 original size:16 final size:16
Alignment explanation
Indices: 218772--218802 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
218762 CACAATTATG
*
218772 TAAATATTATTAAAAT
1 TAAATAATATTAAAAT
218788 TAAATAATATTAAAA
1 TAAATAATATTAAAA
218803 CTATTGAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATAATATTAAAAT
Found at i:219171 original size:22 final size:21
Alignment explanation
Indices: 219129--219188 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
219119 GATTTAAGGA
*
219129 AAAATAAAAG-AAACAGAATT
1 AAAATAAAAGAAAATAGAATT
219149 AAATATAAAAGAAAATAGAATT
1 AAA-ATAAAAGAAAATAGAATT
*
219171 AAAAGAAATAGAAAATAG
1 AAAATAAA-AGAAAATAG
219189 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 11 0.31
22 21 0.60
ACGTcount: A:0.70, C:0.02, G:0.12, T:0.17
Consensus pattern (21 bp):
AAAATAAAAGAAAATAGAATT
Found at i:219179 original size:15 final size:16
Alignment explanation
Indices: 219154--219183 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
219144 GAATTAAATA
219154 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
219170 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
219184 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:220015 original size:19 final size:19
Alignment explanation
Indices: 219991--220033 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
219981 AAACATAAAT
219991 TAAATATAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
220010 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
220029 TAAAT
1 TAAAT
220034 CTTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:220817 original size:100 final size:100
Alignment explanation
Indices: 220631--220817 Score: 243
Period size: 100 Copynumber: 1.9 Consensus size: 100
220621 ATACATTGGA
* * * * **
220631 CCTTTTGACGCGAAATAAAATGACACCCAAGCGCTCCATCCCGGTTACTCAGTCTAACATGCTCT
1 CCTTTTGACGCGAAATAAAATGACAACCAAGCACTCCACCCCGGTTACTCAATCTAACACACTCT
* * *
220696 CAATTTTTTCTTCTCTTTTTTTAGAATGTGTTAGT
66 CAATTTTTTATTCTATATTTTTAGAATGTGTTAGT
* *
220731 CCTTTTGACGCGAAGTGAAATGACAACCAAGCACTCCACCCCGGTTACTCAATCTAACACACTC-
1 CCTTTTGACGCGAAATAAAATGACAACCAAGCACTCCACCCCGGTTACTCAATCTAACACACTCT
220795 CGAATTTATTTATT-TATATTTTT
66 C-AATTT-TTTATTCTATATTTTT
220818 TTCTTTTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
99 1 0.01
100 68 0.92
101 5 0.07
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.35
Consensus pattern (100 bp):
CCTTTTGACGCGAAATAAAATGACAACCAAGCACTCCACCCCGGTTACTCAATCTAACACACTCT
CAATTTTTTATTCTATATTTTTAGAATGTGTTAGT
Found at i:221530 original size:4 final size:4
Alignment explanation
Indices: 221521--221567 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
221511 TCCTAGACAA
*
221521 AAAT AAAT AAAT AGAT AAAT AAAT AAGAT AGAA- AAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA-AT A-AAT AAAT AAAT AAAT AAA
221568 AATAATTGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 5 0.14
4 27 0.73
5 4 0.11
6 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:221557 original size:17 final size:16
Alignment explanation
Indices: 221519--221569 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
221509 TTTCCTAGAC
221519 AAAAATAAATAAATAG
1 AAAAATAAATAAATAG
*
221535 ATAAATAAATAAGATAG
1 AAAAATAAATAA-ATAG
221552 AAAAATAAA-AAATA-
1 AAAAATAAATAAATAG
221566 AAAA
1 AAAA
221570 TAATTGGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 4 0.12
15 3 0.09
16 13 0.41
17 12 0.38
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAAATAAATAAATAG
Found at i:224623 original size:12 final size:12
Alignment explanation
Indices: 224608--224633 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
224598 TTAAATAAGA
224608 ATTAAAATCATC
1 ATTAAAATCATC
224620 ATTAAAATCATC
1 ATTAAAATCATC
224632 AT
1 AT
224634 CAAACAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
ATTAAAATCATC
Found at i:226385 original size:24 final size:24
Alignment explanation
Indices: 226353--226400 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
226343 AACCTGTTAA
226353 GAAACAAACGAGAAAGATCAGCCC
1 GAAACAAACGAGAAAGATCAGCCC
226377 GAAACAAACGAGAAAGATCAGCCC
1 GAAACAAACGAGAAAGATCAGCCC
226401 AAGTTGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.21, T:0.04
Consensus pattern (24 bp):
GAAACAAACGAGAAAGATCAGCCC
Found at i:226992 original size:12 final size:12
Alignment explanation
Indices: 226977--227002 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
226967 TTAAATAAGA
226977 ATTAAAATCATC
1 ATTAAAATCATC
226989 ATTAAAATCATC
1 ATTAAAATCATC
227001 AT
1 AT
227003 CAAACAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
ATTAAAATCATC
Found at i:228754 original size:24 final size:24
Alignment explanation
Indices: 228722--228769 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
228712 AACCTGTTAA
228722 GAAACAAACGAGAAAGATCAGCCC
1 GAAACAAACGAGAAAGATCAGCCC
228746 GAAACAAACGAGAAAGATCAGCCC
1 GAAACAAACGAGAAAGATCAGCCC
228770 AAGTTGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.21, T:0.04
Consensus pattern (24 bp):
GAAACAAACGAGAAAGATCAGCCC
Found at i:229617 original size:21 final size:22
Alignment explanation
Indices: 229571--229631 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
229561 CGATCTAAGG
229571 AAAAATAAAAGAAACA-A-AATT
1 AAAAATAAAAGAAA-ATAGAATT
229592 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
229614 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
229632 GGAAGTCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 1 0.03
21 15 0.42
22 19 0.53
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:229624 original size:15 final size:16
Alignment explanation
Indices: 229597--229626 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
229587 AAATTAAAAA
229597 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
229613 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
229627 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Done.