Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013737.1 Kokia drynarioides strain JFW-HI SEQ_128765, 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: 19903
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:2348 original size:19 final size:19
Alignment explanation
Indices: 2326--2363 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2316 TTACTAATGT
2326 AACTA-ATATATATTTCAAA
1 AACTACATATAT-TTTCAAA
*
2345 AACTACATTTATTTTCAAA
1 AACTACATATATTTTCAAA
2364 TATTACATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (19 bp):
AACTACATATATTTTCAAA
Found at i:2787 original size:17 final size:17
Alignment explanation
Indices: 2755--2799 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
2745 TTAAAATTAT
*
2755 TTTTTTAAA-TATAAAA
1 TTTTTTAAATTACAAAA
2771 TTTTTTAAATTACAAAA
1 TTTTTTAAATTACAAAA
* *
2788 TTATTAAAATTA
1 TTTTTTAAATTA
2800 TTTTTTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTTTAAATTACAAAA
Found at i:2826 original size:47 final size:46
Alignment explanation
Indices: 2738--2827 Score: 146
Period size: 46 Copynumber: 1.9 Consensus size: 46
2728 AAATGATTTT
*
2738 AAAATTATTAAAATTATTTTTTTAAATATAAAATTTTTTAAATTAC
1 AAAATTATTAAAATTATTTTTTTAAATATAAAATTTATTAAATTAC
2784 AAAATTATTAAAATTATTTTTTTGAAATAATAAAA-TTATTAAAT
1 AAAATTATTAAAATTATTTTTTT-AAAT-ATAAAATTTATTAAAT
2828 AATTTTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
46 23 0.56
47 12 0.29
48 6 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (46 bp):
AAAATTATTAAAATTATTTTTTTAAATATAAAATTTATTAAATTAC
Found at i:2833 original size:30 final size:30
Alignment explanation
Indices: 2771--2833 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2761 AAATATAAAA
* *
2771 TTTTTTAAATTACAAAATTATTAAAATTAT
1 TTTTTTAAATAACAAAATTATTAAAATAAT
*
2801 TTTTTTGAAATAATAAAATTATT-AAATAAT
1 TTTTTT-AAATAACAAAATTATTAAAATAAT
2831 TTT
1 TTT
2834 AATTTCCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (30 bp):
TTTTTTAAATAACAAAATTATTAAAATAAT
Found at i:5002 original size:17 final size:17
Alignment explanation
Indices: 4980--5012 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4970 TGTTAGTAAG
*
4980 CATTGTCGTTGCATTTT
1 CATTGTCATTGCATTTT
4997 CATTGTCATTGCATTT
1 CATTGTCATTGCATTT
5013 AAATGTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.52
Consensus pattern (17 bp):
CATTGTCATTGCATTTT
Found at i:8027 original size:350 final size:351
Alignment explanation
Indices: 7384--8086 Score: 1318
Period size: 350 Copynumber: 2.0 Consensus size: 351
7374 GCAGTCACAA
*
7384 TTAAGGATTTACATTATGGACACCAATTTAAAGTGAATGGCCAGCGACTGAAACATTATTTTGGG
1 TTAAGGATTTACATGATGGACACCAATTTAAAGTGAATGGCCAGCGACTGAAACATTATTTTGGG
7449 AACATTGATCAAAAGCAGGAAGAGACCATTAAATTGGTCGATTTTTTTTTTAATTTTTCTTGAAA
66 AACATTGATCAAAAGCAGGAAGAGACCATTAAATTGGTCGA-TTTTTTTTTAATTTTTCTTGAAA
* * * *
7514 TTTTTATTATGCAATTTTTTTTTCTTTTATTTTTGTTTTTATTCAAGTTTGTTTCACTTCGTGTT
130 TTTTTATTATGCAATTTTATTTTATTTTAATTTTGTTTTTATTCAAGTTTGTTTCACTGCGTGTT
* *
7579 TTTTGCAGAATAAACAGGAAACATTATCGATGCATTTGAACTTCTTTGTCAACGTAATTCGTATA
195 TTTTGCAAAATAAACAGGAAACATTATCGATGCATTTGAACTTCATTGTCAACGTAATTCGTATA
7644 GTTGTAGTGCAACTACAGTTCGTGAACCAGAATCTTCTAAGCCAAAGGAGAAAAAGGAGCCAGTG
260 GTTGTAGTGCAACTACAGTTCGTGAACCAGAATCTTCTAAGCCAAAGGAGAAAAAGGAGCCAGTG
*
7709 TTATTTTTAATGAAAGCGGCCAAAGAT
325 ATATTTTTAATGAAAGCGGCCAAAGAT
7736 TTAAGGATTTACATGATGGACACCAATTTAAAGTGAATGGCCAGCGACTGAAACATTATTTTGGG
1 TTAAGGATTTACATGATGGACACCAATTTAAAGTGAATGGCCAGCGACTGAAACATTATTTTGGG
7801 AACATTGATCAAAAGCAGGAAGAGACCATTAAATTGGTCGA-TTTTTTTTAATTTTTCTTGAAAT
66 AACATTGATCAAAAGCAGGAAGAGACCATTAAATTGGTCGATTTTTTTTTAATTTTTCTTGAAAT
7865 TTTTATTATGCAATTTTATTTTATTTTAATTTTGTTTTTATTCAAGTTTGTTTCACTGCGTGTTT
131 TTTTATTATGCAATTTTATTTTATTTTAATTTTGTTTTTATTCAAGTTTGTTTCACTGCGTGTTT
7930 TTTGCAAAATAAACAGGAAACATTATCGATGCATTTGAACTTCATTGTCAACGTAATTCGTATAG
196 TTTGCAAAATAAACAGGAAACATTATCGATGCATTTGAACTTCATTGTCAACGTAATTCGTATAG
7995 TTGTAGTGCAACTACAGTTCGTGAACCAGAATCTTCTAAGCCAAAGGAGAAAAAGGAGCCAGTGA
261 TTGTAGTGCAACTACAGTTCGTGAACCAGAATCTTCTAAGCCAAAGGAGAAAAAGGAGCCAGTGA
8060 TATTTTTAATGAAAGCGGCCAAAGAT
326 TATTTTTAATGAAAGCGGCCAAAGAT
8086 T
1 T
8087 GATTTCAAGA
Statistics
Matches: 343, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
350 238 0.69
352 105 0.31
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (351 bp):
TTAAGGATTTACATGATGGACACCAATTTAAAGTGAATGGCCAGCGACTGAAACATTATTTTGGG
AACATTGATCAAAAGCAGGAAGAGACCATTAAATTGGTCGATTTTTTTTTAATTTTTCTTGAAAT
TTTTATTATGCAATTTTATTTTATTTTAATTTTGTTTTTATTCAAGTTTGTTTCACTGCGTGTTT
TTTGCAAAATAAACAGGAAACATTATCGATGCATTTGAACTTCATTGTCAACGTAATTCGTATAG
TTGTAGTGCAACTACAGTTCGTGAACCAGAATCTTCTAAGCCAAAGGAGAAAAAGGAGCCAGTGA
TATTTTTAATGAAAGCGGCCAAAGAT
Found at i:9248 original size:11 final size:11
Alignment explanation
Indices: 9229--9284 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
9219 GGTTGGGCCC
*
9229 TTTTTAATTTA
1 TTTTAAATTTA
9240 TTTTAAATTTGA
1 TTTTAAATTT-A
9252 -TTTAAATTTAA
1 TTTTAAATTT-A
* *
9263 ATTTAAATTAA
1 TTTTAAATTTA
*
9274 TCTTAAATTTA
1 TTTTAAATTTA
9285 AATTTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:9262 original size:6 final size:6
Alignment explanation
Indices: 9241--9302 Score: 78
Period size: 6 Copynumber: 10.8 Consensus size: 6
9231 TTTAATTTAT
*
9241 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
9287 TTT-AA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
9303 TTACAAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
4 2 0.04
5 11 0.22
6 33 0.67
7 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:9263 original size:17 final size:16
Alignment explanation
Indices: 9231--9304 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 16
9221 TTGGGCCCTT
*
9231 TTTAATTTATTTTAAA
1 TTTAATTTAATTTAAA
*
9247 TTTGATTTAAATTTAAA
1 TTTAATTT-AATTTAAA
*
9264 TTTAAATTAATCTTAAA
1 TTTAATTTAAT-TTAAA
9281 TTTAAATTTAATTTAAA
1 TTT-AATTTAATTTAAA
9298 TTTAATT
1 TTTAATT
9305 ACAAAATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
16 14 0.28
17 29 0.58
18 7 0.14
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (16 bp):
TTTAATTTAATTTAAA
Found at i:9269 original size:23 final size:23
Alignment explanation
Indices: 9253--9296 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
9243 TAAATTTGAT
9253 TTAAATTTAAATTTAAATTAATC
1 TTAAATTTAAATTTAAATTAATC
*
9276 TTAAATTTAAATTTAATTTAA
1 TTAAATTTAAATTTAAATTAA
9297 ATTTAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTAATC
Found at i:9304 original size:11 final size:12
Alignment explanation
Indices: 9241--9302 Score: 78
Period size: 11 Copynumber: 5.4 Consensus size: 12
9231 TTTAATTTAT
*
9241 TTTAAATTT-GA
1 TTTAAATTTAAA
9252 TTTAAATTTAAA
1 TTTAAATTTAAA
9264 TTTAAA-TT-AA
1 TTTAAATTTAAA
9274 TCTTAAATTTAAA
1 T-TTAAATTTAAA
9287 TTT-AATTTAAA
1 TTTAAATTTAAA
9298 TTTAA
1 TTTAA
9303 TTACAAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
10 3 0.07
11 27 0.60
12 12 0.27
13 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:9391 original size:16 final size:16
Alignment explanation
Indices: 9360--9397 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9350 CCCAATGGGG
9360 CCCAAA-TTAAAAAAA
1 CCCAAACTTAAAAAAA
*
9375 CCCAAACTTAAATAAA
1 CCCAAACTTAAAAAAA
*
9391 CCAAAAC
1 CCCAAAC
9398 GGCCTAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (16 bp):
CCCAAACTTAAAAAAA
Found at i:10031 original size:12 final size:12
Alignment explanation
Indices: 10014--10052 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10004 AATATCGCTA
10014 ACATCAATAATG
1 ACATCAATAATG
*
10026 ACATCAATAATA
1 ACATCAATAATG
*
10038 ACATTTAATAATG
1 ACA-TCAATAATG
10051 AC
1 AC
10053 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (12 bp):
ACATCAATAATG
Found at i:11153 original size:29 final size:28
Alignment explanation
Indices: 11111--11543 Score: 263
Period size: 30 Copynumber: 14.6 Consensus size: 28
11101 AAACTATTCT
* * *
11111 AAAATTACCATTTTACCCTCTAACTTCT
1 AAAAATACCATTTTACCCTCAAACTTCC
*
11139 AAAAATCCCATTTTTTACCC-CAAAACTTCC
1 AAAAATACCA--TTTTACCCTC-AAACTTCC
*
11169 AAAAAATTACCA-TTTACCCCCCAAACTTCC
1 -AAAAA-TACCATTTTA-CCCTCAAACTTCC
* * *
11199 AAAATTCCCATTTTTGACCC-CAAAACTTCT
1 AAAAATACCA-TTTT-ACCCTC-AAACTTCC
* *
11229 AAAAATTACCATTTTAACCTTAAACTTCC
1 AAAAA-TACCATTTTACCCTCAAACTTCC
* *
11258 AAAAATTACCATTTTACCCCCCCGAACTTCC
1 AAAAA-TACCATTTTA--CCCTCAAACTTCC
* * *
11289 AAAAATCCCATTTTTAACCTTGAAACTTCC
1 AAAAATACCA-TTTT-ACCCTCAAACTTCC
**
11319 AAAAATTACCATTTTACCAACAAACTTCC
1 AAAAA-TACCATTTTACCCTCAAACTTCC
* * *
11348 AAAAATTATCATTTTACCCCCGAA-TTCCC
1 AAAAA-TACCATTTTACCCTCAAACTT-CC
* * *
11377 AAAAATCCCATTTTTGACTCC-GAAAGCTT-T
1 AAAAATACCA-TTTT-AC-CCTCAAA-CTTCC
11407 AAAAATTACCATTTTACCCTCAAACTTCC
1 AAAAA-TACCATTTTACCCTCAAACTTCC
* * *
11436 AAAAGTCCCATTTTTGA-CCTAGAAACTTCC
1 AAAAATACCA-TTTT-ACCCT-CAAACTTCC
*
11466 AAAAATTACCATTTTACCCTCGAA-TTCCC
1 AAAAA-TACCATTTTACCCTCAAACTT-CC
*
11495 AAAAATCCCATTTTTTACCC-CAAAACTTCC
1 AAAAATACCA--TTTTACCCTC-AAACTTCC
11525 AAAAATCACCATTTTACCC
1 AAAAAT-ACCATTTTACCC
11544 NNNNNNNNNN
Statistics
Matches: 319, Mismatches: 48, Indels: 75
0.72 0.11 0.17
Matches are distributed among these distances:
28 32 0.10
29 113 0.35
30 119 0.37
31 48 0.15
32 7 0.02
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAAATACCATTTTACCCTCAAACTTCC
Found at i:11233 original size:59 final size:59
Alignment explanation
Indices: 11111--11543 Score: 434
Period size: 59 Copynumber: 7.3 Consensus size: 59
11101 AAACTATTCT
* * *
11111 AAAATTACCATTTTACCCTCTAACTTCTAAAAATCCCATTTTTTACCCCAAAACTTCCAA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC-A
* * *
11171 AAAATTACCA-TTTACCCCCCAAACTTCCAAAATTCCCATTTTTGACCCCAAAACTTCTA
1 AAAATTACCATTTTA-CCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
* * * *** **
11230 AAAATTACCATTTTAACCTTAAACTTCCAAAAATTACCATTTTACCCCCCCGAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAA-TCCCATTTTTGACCCCAAAACTTCCA
* * * * *
11290 AAAA-TCCCATTTTTAACCTTGAAACTTCCAAAAATTACCA-TTTT-A-CCAACAAACTTCCA
1 AAAATTACCA-TTTT-ACCCTCAAACTTCCAAAAA-TCCCATTTTTGACCCCA-AAACTTCCA
* * * * * *
11349 AAAATTATCATTTTACCCCCGAA-TTCCCAAAAATCCCATTTTTGACTCCGAAAGCTT-TA
1 AAAATTACCATTTTACCCTCAAACTT-CCAAAAATCCCATTTTTGAC-CCCAAAACTTCCA
* *
11408 AAAATTACCATTTTACCCTCAAACTTCCAAAAGTCCCATTTTTGA-CCTAGAAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA-AAACTTCCA
* *
11467 AAAATTACCATTTTACCCTCGAA-TTCCCAAAAATCCCATTTTTTACCCCAAAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTT-CCAAAAATCCCATTTTTGACCCCAAAACTTCCA
*
11526 AAAATCACCATTTTACCC
1 AAAATTACCATTTTACCC
11544 NNNNNNNNNN
Statistics
Matches: 308, Mismatches: 48, Indels: 35
0.79 0.12 0.09
Matches are distributed among these distances:
57 9 0.03
58 25 0.08
59 155 0.50
60 94 0.31
61 25 0.08
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
Found at i:11292 original size:90 final size:89
Alignment explanation
Indices: 11132--11439 Score: 367
Period size: 90 Copynumber: 3.4 Consensus size: 89
11122 TTTACCCTCT
* * * *
11132 AACTTCTAAAAA-TCCCATTTTTTACCCCAAAACTTCCAAAAAATTACCA-TTTACCCCCCAAAC
1 AACTTCTAAAAATTACCA-TTTTAACCTC-AAACTTCC-AAAAATTACCATTTTACCCCCCGAAC
*
11195 TTCCAAAATTCCCATTTTTGACCCCAA
63 TTCCAAAAATCCCATTTTTGACCCCAA
*
11222 AACTTCTAAAAATTACCATTTTAACCTTAAACTTCCAAAAATTACCATTTTACCCCCCCGAACTT
1 AACTTCTAAAAATTACCATTTTAACCTCAAACTTCCAAAAATTACCATTTTA-CCCCCCGAACTT
* ***
11287 CCAAAAATCCCATTTTTAACCTTGA
65 CCAAAAATCCCATTTTTGACCCCAA
* * *
11312 AACTTCCAAAAATTACCATTTT-ACCAACAAACTTCCAAAAATTATCATTTTA-CCCCCGAA-TT
1 AACTTCTAAAAATTACCATTTTAACC-TCAAACTTCCAAAAATTACCATTTTACCCCCCGAACTT
*
11374 CCCAAAAATCCCATTTTTGACTCCGAA
65 -CCAAAAATCCCATTTTTGAC-CCCAA
* *
11401 AGCTT-TAAAAATTACCATTTTACCCTCAAACTTCCAAAA
1 AACTTCTAAAAATTACCATTTTAACCTCAAACTTCCAAAA
11440 GTCCCATTTT
Statistics
Matches: 189, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
87 2 0.01
88 66 0.35
89 23 0.12
90 94 0.50
91 4 0.02
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30
Consensus pattern (89 bp):
AACTTCTAAAAATTACCATTTTAACCTCAAACTTCCAAAAATTACCATTTTACCCCCCGAACTTC
CAAAAATCCCATTTTTGACCCCAA
Found at i:12828 original size:11 final size:11
Alignment explanation
Indices: 12809--12864 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
12799 GGTTGGGCCC
*
12809 TTTTTAATTTA
1 TTTTAAATTTA
12820 TTTTAAATTTGA
1 TTTTAAATTT-A
12832 -TTTAAATTTAA
1 TTTTAAATTT-A
* *
12843 ATTTAAATTAA
1 TTTTAAATTTA
*
12854 TCTTAAATTTA
1 TTTTAAATTTA
12865 AATTTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:12842 original size:6 final size:6
Alignment explanation
Indices: 12821--12882 Score: 78
Period size: 6 Copynumber: 10.8 Consensus size: 6
12811 TTTAATTTAT
*
12821 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
12867 TTT-AA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
12883 TTACAAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
4 2 0.04
5 11 0.22
6 33 0.67
7 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:12843 original size:17 final size:16
Alignment explanation
Indices: 12811--12884 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 16
12801 TTGGGCCCTT
*
12811 TTTAATTTATTTTAAA
1 TTTAATTTAATTTAAA
*
12827 TTTGATTTAAATTTAAA
1 TTTAATTT-AATTTAAA
*
12844 TTTAAATTAATCTTAAA
1 TTTAATTTAAT-TTAAA
12861 TTTAAATTTAATTTAAA
1 TTT-AATTTAATTTAAA
12878 TTTAATT
1 TTTAATT
12885 ACAAAATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
16 14 0.28
17 29 0.58
18 7 0.14
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (16 bp):
TTTAATTTAATTTAAA
Found at i:12849 original size:23 final size:23
Alignment explanation
Indices: 12833--12876 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
12823 TAAATTTGAT
12833 TTAAATTTAAATTTAAATTAATC
1 TTAAATTTAAATTTAAATTAATC
*
12856 TTAAATTTAAATTTAATTTAA
1 TTAAATTTAAATTTAAATTAA
12877 ATTTAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTAATC
Found at i:12884 original size:11 final size:12
Alignment explanation
Indices: 12821--12882 Score: 78
Period size: 11 Copynumber: 5.4 Consensus size: 12
12811 TTTAATTTAT
*
12821 TTTAAATTT-GA
1 TTTAAATTTAAA
12832 TTTAAATTTAAA
1 TTTAAATTTAAA
12844 TTTAAA-TT-AA
1 TTTAAATTTAAA
12854 TCTTAAATTTAAA
1 T-TTAAATTTAAA
12867 TTT-AATTTAAA
1 TTTAAATTTAAA
12878 TTTAA
1 TTTAA
12883 TTACAAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
10 3 0.07
11 27 0.60
12 12 0.27
13 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:12971 original size:16 final size:16
Alignment explanation
Indices: 12940--12977 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12930 CCCAATGGGG
12940 CCCAAA-TTAAAAAAA
1 CCCAAACTTAAAAAAA
*
12955 CCCAAACTTAAATAAA
1 CCCAAACTTAAAAAAA
*
12971 CCAAAAC
1 CCCAAAC
12978 GGCCTAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (16 bp):
CCCAAACTTAAAAAAA
Found at i:13611 original size:12 final size:12
Alignment explanation
Indices: 13594--13632 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
13584 AATATCGCTA
13594 ACATCAATAATG
1 ACATCAATAATG
*
13606 ACATCAATAATA
1 ACATCAATAATG
*
13618 ACATTTAATAATG
1 ACA-TCAATAATG
13631 AC
1 AC
13633 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (12 bp):
ACATCAATAATG
Found at i:14733 original size:29 final size:28
Alignment explanation
Indices: 14691--15123 Score: 263
Period size: 30 Copynumber: 14.6 Consensus size: 28
14681 AAACTATTCT
* * *
14691 AAAATTACCATTTTACCCTCTAACTTCT
1 AAAAATACCATTTTACCCTCAAACTTCC
*
14719 AAAAATCCCATTTTTTACCC-CAAAACTTCC
1 AAAAATACCA--TTTTACCCTC-AAACTTCC
*
14749 AAAAAATTACCA-TTTACCCCCCAAACTTCC
1 -AAAAA-TACCATTTTA-CCCTCAAACTTCC
* * *
14779 AAAATTCCCATTTTTGACCC-CAAAACTTCT
1 AAAAATACCA-TTTT-ACCCTC-AAACTTCC
* *
14809 AAAAATTACCATTTTAACCTTAAACTTCC
1 AAAAA-TACCATTTTACCCTCAAACTTCC
* *
14838 AAAAATTACCATTTTACCCCCCCGAACTTCC
1 AAAAA-TACCATTTTA--CCCTCAAACTTCC
* * *
14869 AAAAATCCCATTTTTAACCTTGAAACTTCC
1 AAAAATACCA-TTTT-ACCCTCAAACTTCC
**
14899 AAAAATTACCATTTTACCAACAAACTTCC
1 AAAAA-TACCATTTTACCCTCAAACTTCC
* * *
14928 AAAAATTATCATTTTACCCCCGAA-TTCCC
1 AAAAA-TACCATTTTACCCTCAAACTT-CC
* * *
14957 AAAAATCCCATTTTTGACTCC-GAAAGCTT-T
1 AAAAATACCA-TTTT-AC-CCTCAAA-CTTCC
14987 AAAAATTACCATTTTACCCTCAAACTTCC
1 AAAAA-TACCATTTTACCCTCAAACTTCC
* * *
15016 AAAAGTCCCATTTTTGA-CCTAGAAACTTCC
1 AAAAATACCA-TTTT-ACCCT-CAAACTTCC
*
15046 AAAAATTACCATTTTACCCTCGAA-TTCCC
1 AAAAA-TACCATTTTACCCTCAAACTT-CC
*
15075 AAAAATCCCATTTTTTACCC-CAAAACTTCC
1 AAAAATACCA--TTTTACCCTC-AAACTTCC
15105 AAAAATCACCATTTTACCC
1 AAAAAT-ACCATTTTACCC
15124 NNNNNNNNNN
Statistics
Matches: 319, Mismatches: 48, Indels: 75
0.72 0.11 0.17
Matches are distributed among these distances:
28 32 0.10
29 113 0.35
30 119 0.37
31 48 0.15
32 7 0.02
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAAATACCATTTTACCCTCAAACTTCC
Found at i:14813 original size:59 final size:59
Alignment explanation
Indices: 14691--15123 Score: 434
Period size: 59 Copynumber: 7.3 Consensus size: 59
14681 AAACTATTCT
* * *
14691 AAAATTACCATTTTACCCTCTAACTTCTAAAAATCCCATTTTTTACCCCAAAACTTCCAA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC-A
* * *
14751 AAAATTACCA-TTTACCCCCCAAACTTCCAAAATTCCCATTTTTGACCCCAAAACTTCTA
1 AAAATTACCATTTTA-CCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
* * * *** **
14810 AAAATTACCATTTTAACCTTAAACTTCCAAAAATTACCATTTTACCCCCCCGAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAA-TCCCATTTTTGACCCCAAAACTTCCA
* * * * *
14870 AAAA-TCCCATTTTTAACCTTGAAACTTCCAAAAATTACCA-TTTT-A-CCAACAAACTTCCA
1 AAAATTACCA-TTTT-ACCCTCAAACTTCCAAAAA-TCCCATTTTTGACCCCA-AAACTTCCA
* * * * * *
14929 AAAATTATCATTTTACCCCCGAA-TTCCCAAAAATCCCATTTTTGACTCCGAAAGCTT-TA
1 AAAATTACCATTTTACCCTCAAACTT-CCAAAAATCCCATTTTTGAC-CCCAAAACTTCCA
* *
14988 AAAATTACCATTTTACCCTCAAACTTCCAAAAGTCCCATTTTTGA-CCTAGAAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA-AAACTTCCA
* *
15047 AAAATTACCATTTTACCCTCGAA-TTCCCAAAAATCCCATTTTTTACCCCAAAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTT-CCAAAAATCCCATTTTTGACCCCAAAACTTCCA
*
15106 AAAATCACCATTTTACCC
1 AAAATTACCATTTTACCC
15124 NNNNNNNNNN
Statistics
Matches: 308, Mismatches: 48, Indels: 35
0.79 0.12 0.09
Matches are distributed among these distances:
57 9 0.03
58 25 0.08
59 155 0.50
60 94 0.31
61 25 0.08
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
Found at i:14872 original size:90 final size:89
Alignment explanation
Indices: 14712--15019 Score: 367
Period size: 90 Copynumber: 3.4 Consensus size: 89
14702 TTTACCCTCT
* * * *
14712 AACTTCTAAAAA-TCCCATTTTTTACCCCAAAACTTCCAAAAAATTACCA-TTTACCCCCCAAAC
1 AACTTCTAAAAATTACCA-TTTTAACCTC-AAACTTCC-AAAAATTACCATTTTACCCCCCGAAC
*
14775 TTCCAAAATTCCCATTTTTGACCCCAA
63 TTCCAAAAATCCCATTTTTGACCCCAA
*
14802 AACTTCTAAAAATTACCATTTTAACCTTAAACTTCCAAAAATTACCATTTTACCCCCCCGAACTT
1 AACTTCTAAAAATTACCATTTTAACCTCAAACTTCCAAAAATTACCATTTTA-CCCCCCGAACTT
* ***
14867 CCAAAAATCCCATTTTTAACCTTGA
65 CCAAAAATCCCATTTTTGACCCCAA
* * *
14892 AACTTCCAAAAATTACCATTTT-ACCAACAAACTTCCAAAAATTATCATTTTA-CCCCCGAA-TT
1 AACTTCTAAAAATTACCATTTTAACC-TCAAACTTCCAAAAATTACCATTTTACCCCCCGAACTT
*
14954 CCCAAAAATCCCATTTTTGACTCCGAA
65 -CCAAAAATCCCATTTTTGAC-CCCAA
* *
14981 AGCTT-TAAAAATTACCATTTTACCCTCAAACTTCCAAAA
1 AACTTCTAAAAATTACCATTTTAACCTCAAACTTCCAAAA
15020 GTCCCATTTT
Statistics
Matches: 189, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
87 2 0.01
88 66 0.35
89 23 0.12
90 94 0.50
91 4 0.02
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30
Consensus pattern (89 bp):
AACTTCTAAAAATTACCATTTTAACCTCAAACTTCCAAAAATTACCATTTTACCCCCCGAACTTC
CAAAAATCCCATTTTTGACCCCAA
Found at i:16408 original size:11 final size:11
Alignment explanation
Indices: 16389--16444 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
16379 GGTTGGGCCC
*
16389 TTTTTAATTTA
1 TTTTAAATTTA
16400 TTTTAAATTTGA
1 TTTTAAATTT-A
16412 -TTTAAATTTAA
1 TTTTAAATTT-A
* *
16423 ATTTAAATTAA
1 TTTTAAATTTA
*
16434 TCTTAAATTTA
1 TTTTAAATTTA
16445 AATTTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:16422 original size:6 final size:6
Alignment explanation
Indices: 16401--16462 Score: 78
Period size: 6 Copynumber: 10.8 Consensus size: 6
16391 TTTAATTTAT
*
16401 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
16447 TTT-AA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
16463 TTACAAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
4 2 0.04
5 11 0.22
6 33 0.67
7 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:16423 original size:17 final size:16
Alignment explanation
Indices: 16391--16464 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 16
16381 TTGGGCCCTT
*
16391 TTTAATTTATTTTAAA
1 TTTAATTTAATTTAAA
*
16407 TTTGATTTAAATTTAAA
1 TTTAATTT-AATTTAAA
*
16424 TTTAAATTAATCTTAAA
1 TTTAATTTAAT-TTAAA
16441 TTTAAATTTAATTTAAA
1 TTT-AATTTAATTTAAA
16458 TTTAATT
1 TTTAATT
16465 ACAAAATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
16 14 0.28
17 29 0.58
18 7 0.14
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (16 bp):
TTTAATTTAATTTAAA
Found at i:16429 original size:23 final size:23
Alignment explanation
Indices: 16413--16456 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
16403 TAAATTTGAT
16413 TTAAATTTAAATTTAAATTAATC
1 TTAAATTTAAATTTAAATTAATC
*
16436 TTAAATTTAAATTTAATTTAA
1 TTAAATTTAAATTTAAATTAA
16457 ATTTAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTAATC
Found at i:16464 original size:11 final size:12
Alignment explanation
Indices: 16401--16462 Score: 78
Period size: 11 Copynumber: 5.4 Consensus size: 12
16391 TTTAATTTAT
*
16401 TTTAAATTT-GA
1 TTTAAATTTAAA
16412 TTTAAATTTAAA
1 TTTAAATTTAAA
16424 TTTAAA-TT-AA
1 TTTAAATTTAAA
16434 TCTTAAATTTAAA
1 T-TTAAATTTAAA
16447 TTT-AATTTAAA
1 TTTAAATTTAAA
16458 TTTAA
1 TTTAA
16463 TTACAAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
10 3 0.07
11 27 0.60
12 12 0.27
13 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:16551 original size:16 final size:16
Alignment explanation
Indices: 16520--16557 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16510 CCCAATGGGG
16520 CCCAAA-TTAAAAAAA
1 CCCAAACTTAAAAAAA
*
16535 CCCAAACTTAAATAAA
1 CCCAAACTTAAAAAAA
*
16551 CCAAAAC
1 CCCAAAC
16558 GGCCTAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (16 bp):
CCCAAACTTAAAAAAA
Found at i:17191 original size:12 final size:12
Alignment explanation
Indices: 17174--17212 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17164 AATATCGCTA
17174 ACATCAATAATG
1 ACATCAATAATG
*
17186 ACATCAATAATA
1 ACATCAATAATG
*
17198 ACATTTAATAATG
1 ACA-TCAATAATG
17211 AC
1 AC
17213 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.28
Consensus pattern (12 bp):
ACATCAATAATG
Found at i:18313 original size:29 final size:28
Alignment explanation
Indices: 18278--18786 Score: 309
Period size: 29 Copynumber: 17.2 Consensus size: 28
18268 TCTAAAATTA
* *
18278 CCATTTTACCCTCTAACTTCTAAAAATC
1 CCATTTTACCCTCAAACTTCCAAAAATC
*
18306 CCATTTTTTACCC-CAAAACTTCCAAAAAATTA
1 CCA--TTTTACCCTC-AAACTTCC-AAAAA-TC
* *
18338 CCA-TTTACCCCCCAAACTTCCAAAATTC
1 CCATTTTA-CCCTCAAACTTCCAAAAATC
* *
18366 CCATTTTTGACCC-CAAAACTTCTAAAAATTA
1 CCA-TTTT-ACCCTC-AAACTTCCAAAAA-TC
* * *
18397 CCATTTTAACCTTAAACTTCCAAAAATTA
1 CCATTTTACCCTCAAACTTCCAAAAA-TC
* *
18426 CCATTTTACCCCCCCGAACTTCCAAAAATC
1 CCATTTTA--CCCTCAAACTTCCAAAAATC
* * *
18456 CCATTTTTAACCTTGAAACTTCCAAAAATTA
1 CCA-TTTT-ACCCTCAAACTTCCAAAAA-TC
** *
18487 CCATTTTACCAACAAACTTCCAAAAATTA
1 CCATTTTACCCTCAAACTTCCAAAAA-TC
* * *
18516 TCATTTTACCCCCGAA-TTCCCAAAAATC
1 CCATTTTACCCTCAAACTT-CCAAAAATC
* * *
18544 CCATTTTTGACTCC-GAAAGCTT-TAAAAATTA
1 CCA-TTTT-AC-CCTCAAA-CTTCCAAAAA-TC
*
18575 CCATTTTACCCTCAAACTTCCAAAAGTC
1 CCATTTTACCCTCAAACTTCCAAAAATC
* *
18603 CCATTTTTGA-CCTAGAAACTTCCAAAAATTA
1 CCA-TTTT-ACCCT-CAAACTTCCAAAAA-TC
*
18634 CCATTTTACCCTCGAA-TTCCCAAAAATC
1 CCATTTTACCCTCAAACTT-CCAAAAATC
18662 CCATTTTTTACCC-CAAAACTTCCAAAAATC
1 CCA--TTTTACCCTC-AAACTTCCAAAAATC
* *
18692 ACCATTTTACCCTCGAACTTCCAAAAGTC
1 -CCATTTTACCCTCAAACTTCCAAAAATC
* * *
18721 CTATTTTTTACCTTGAAACTTCCAAAAATTAC
1 CCA--TTTTACCCTCAAACTTCCAAAAA-T-C
* *
18753 CC-TTTTACCCCCAAACTTCCAAAAGTC
1 CCATTTTACCCTCAAACTTCCAAAAATC
18780 CCATTTT
1 CCATTTT
18787 TAACCCCAAA
Statistics
Matches: 380, Mismatches: 57, Indels: 88
0.72 0.11 0.17
Matches are distributed among these distances:
27 3 0.01
28 34 0.09
29 145 0.38
30 140 0.37
31 49 0.13
32 9 0.02
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (28 bp):
CCATTTTACCCTCAAACTTCCAAAAATC
Found at i:18393 original size:59 final size:59
Alignment explanation
Indices: 18271--18796 Score: 521
Period size: 59 Copynumber: 8.9 Consensus size: 59
18261 AAACTATTCT
* * *
18271 AAAATTACCATTTTACCCTCTAACTTCTAAAAATCCCATTTTTTACCCCAAAACTTCCAA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC-A
* * *
18331 AAAATTACCA-TTTACCCCCCAAACTTCCAAAATTCCCATTTTTGACCCCAAAACTTCTA
1 AAAATTACCATTTTA-CCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
* * * *** **
18390 AAAATTACCATTTTAACCTTAAACTTCCAAAAATTACCATTTTACCCCCCCGAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAA-TCCCATTTTTGACCCCAAAACTTCCA
* * * * *
18450 AAAA-TCCCATTTTTAACCTTGAAACTTCCAAAAATTACCA-TTTT-A-CCAACAAACTTCCA
1 AAAATTACCA-TTTT-ACCCTCAAACTTCCAAAAA-TCCCATTTTTGACCCCA-AAACTTCCA
* * * * * *
18509 AAAATTATCATTTTACCCCCGAA-TTCCCAAAAATCCCATTTTTGACTCCGAAAGCTT-TA
1 AAAATTACCATTTTACCCTCAAACTT-CCAAAAATCCCATTTTTGAC-CCCAAAACTTCCA
* *
18568 AAAATTACCATTTTACCCTCAAACTTCCAAAAGTCCCATTTTTGA-CCTAGAAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCA-AAACTTCCA
* *
18627 AAAATTACCATTTTACCCTCGAA-TTCCCAAAAATCCCATTTTTTACCCCAAAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTT-CCAAAAATCCCATTTTTGACCCCAAAACTTCCA
* * * * * ***
18686 AAAATCACCATTTTACCCTCGAACTTCCAAAAGTCCTATTTTTTACCTTGAAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
* * * *
18745 AAAATTACCCTTTTACCCCCAAACTTCCAAAAGTCCCATTTTTAACCCCAAA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAA
18797 TTTTCTCGAA
Statistics
Matches: 386, Mismatches: 62, Indels: 37
0.80 0.13 0.08
Matches are distributed among these distances:
57 9 0.02
58 25 0.06
59 231 0.60
60 96 0.25
61 25 0.06
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
Found at i:18452 original size:90 final size:89
Alignment explanation
Indices: 18292--18776 Score: 393
Period size: 90 Copynumber: 5.4 Consensus size: 89
18282 TTTACCCTCT
* * * *
18292 AACTTCTAAAAA-TCCCATTTTTTACCCCAAAACTTCCAAAAAATTACCA-TTTACCCCCCAAAC
1 AACTTCTAAAAATTACCA-TTTTAACCTC-AAACTTCC-AAAAATTACCATTTTACCCCCCGAAC
*
18355 TTCCAAAATTCCCATTTTTGACCCCAA
63 TTCCAAAAATCCCATTTTTGACCCCAA
*
18382 AACTTCTAAAAATTACCATTTTAACCTTAAACTTCCAAAAATTACCATTTTACCCCCCCGAACTT
1 AACTTCTAAAAATTACCATTTTAACCTCAAACTTCCAAAAATTACCATTTTA-CCCCCCGAACTT
* ***
18447 CCAAAAATCCCATTTTTAACCTTGA
65 CCAAAAATCCCATTTTTGACCCCAA
* * *
18472 AACTTCCAAAAATTACCATTTT-ACCAACAAACTTCCAAAAATTATCATTTTA-CCCCCGAA-TT
1 AACTTCTAAAAATTACCATTTTAACC-TCAAACTTCCAAAAATTACCATTTTACCCCCCGAACTT
*
18534 CCCAAAAATCCCATTTTTGACTCCGAA
65 -CCAAAAATCCCATTTTTGAC-CCCAA
* * * * *** **
18561 AGCTT-TAAAAATTACCATTTTACCCTCAAACTTCC-AAAAGTCCCATTTTTGACCTAGAAACTT
1 AACTTCTAAAAATTACCATTTTAACCTCAAACTTCCAAAAATTACCATTTTACCCCCCG-AACTT
* *
18624 CCAAAAATTACCA-TTTT-ACCCTC-G
65 CCAAAAA-TCCCATTTTTGACCC-CAA
* * * * * *
18648 AA-TTCCCAAAAA-TCCCATTTTTTACCCCAAAACTTCCAAAAATCACCATTTTA-CCCTCGAAC
1 AACTT-CTAAAAATTACCA-TTTTAACCTC-AAACTTCCAAAAATTACCATTTTACCCCCCGAAC
* * * ***
18710 TTCCAAAAGTCCTATTTTTTACCTTGA
63 TTCCAAAAATCCCATTTTTGACCCCAA
* * * *
18737 AACTTCCAAAAATTACCCTTTTACCCCCAAACTTCCAAAA
1 AACTTCTAAAAATTACCATTTTAACCTCAAACTTCCAAAA
18777 GTCCCATTTT
Statistics
Matches: 319, Mismatches: 54, Indels: 46
0.76 0.13 0.11
Matches are distributed among these distances:
86 2 0.01
87 23 0.07
88 106 0.33
89 68 0.21
90 116 0.36
91 4 0.01
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (89 bp):
AACTTCTAAAAATTACCATTTTAACCTCAAACTTCCAAAAATTACCATTTTACCCCCCGAACTTC
CAAAAATCCCATTTTTGACCCCAA
Done.