Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011317.1 Kokia drynarioides strain JFW-HI SEQ_126297, 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: 169063
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:4291 original size:11 final size:9
Alignment explanation
Indices: 4267--4300 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
4257 CCAATAAAAC
4267 AAATTTTTA
1 AAATTTTTA
4276 AAATTTTATGA
1 AAATTTT-T-A
4287 AAATTTTTA
1 AAATTTTTA
4296 AAATT
1 AAATT
4301 GTTTGAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 13 0.57
10 2 0.09
11 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (9 bp):
AAATTTTTA
Found at i:4460 original size:20 final size:20
Alignment explanation
Indices: 4437--4479 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
4427 CTTTTTATAT
*
4437 TTTTATGAT-TTTTTTAAACA
1 TTTTATGATATTTTCTAAA-A
*
4457 TTTTTTGATATTTTCTAAAA
1 TTTTATGATATTTTCTAAAA
4477 TTT
1 TTT
4480 CTAAGTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTATGATATTTTCTAAAA
Found at i:10390 original size:21 final size:21
Alignment explanation
Indices: 10366--10413 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
10356 CAAGTGACAG
*
10366 TTCTACAGAAATAACTCTTAC
1 TTCTACAGAAACAACTCTTAC
* * *
10387 TTCTACCGATACAAGTCTTAC
1 TTCTACAGAAACAACTCTTAC
10408 TTCTAC
1 TTCTAC
10414 CAATACCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.35
Consensus pattern (21 bp):
TTCTACAGAAACAACTCTTAC
Found at i:12631 original size:5 final size:5
Alignment explanation
Indices: 12621--12649 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12611 TTTATATAAA
12621 TATTT TATTT TATTT TATTT TATTT TATT
1 TATTT TATTT TATTT TATTT TATTT TATT
12650 ATGTGATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:23232 original size:213 final size:205
Alignment explanation
Indices: 23005--23384 Score: 559
Period size: 206 Copynumber: 1.8 Consensus size: 205
22995 AAAGAATCAA
* *
23005 AAATAATTTTATTTAAGTTATTTTTATTATAGT-AGTAACATT-TTTATTTATTTAAAACCA-AT
1 AAATAATTTTATTTAAGTTATTTTTATTATA-TCAGTAAC-TTCTCTATTTATCTAAAACCATA-
23067 TTTTAATTTAATATTTTAGTAATTAATTTACATGTTTTTATTGTGAAAAATAAGTATCATATGCA
63 TTTTAATTT-A-A--TTA-T-A-TAATTTACATGTTTTTATTGTGAAAAATAAGTATCATATGCA
* **
23132 TTTTGATATTTTCATTTCCATTTAACAAACATGGTTTTTTTTTATTTTTAAATTTAAAGAATCAA
121 TTTTGATATTTTCATTTCCAGTTAACAAACATAATTTTTTTTT-TTTTTAAATTTAAAGAATCAA
23197 AATTATTTTAAAAATAAAAAT
185 AATTATTTTAAAAATAAAAAT
*
23218 AAATAATTTTATTTAAGTTATTTTTATTATATCAGTAACTTCTCTATTTATCTAAAATCATATTT
1 AAATAATTTTATTTAAGTTATTTTTATTATATCAGTAACTTCTCTATTTATCTAAAACCATATTT
* *
23283 TAATTTAATTATATATTTTGCATGTTTTTATTGTGAAAAATAAGTATCATATGCATTTTGATATT
66 TAATTTAATTATATAATTTACATGTTTTTATTGTGAAAAATAAGTATCATATGCATTTTGATATT
*
23348 TTCATTTTCAGTTAACAAACATAATTTTTTTTTTTTT
131 TTCATTTCCAGTTAACAAACATAATTTTTTTTTTTTT
23385 GAAAAACATA
Statistics
Matches: 155, Mismatches: 9, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
205 4 0.03
206 79 0.51
207 1 0.01
208 1 0.01
209 3 0.02
211 1 0.01
212 4 0.03
213 61 0.39
214 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (205 bp):
AAATAATTTTATTTAAGTTATTTTTATTATATCAGTAACTTCTCTATTTATCTAAAACCATATTT
TAATTTAATTATATAATTTACATGTTTTTATTGTGAAAAATAAGTATCATATGCATTTTGATATT
TTCATTTCCAGTTAACAAACATAATTTTTTTTTTTTTTAAATTTAAAGAATCAAAATTATTTTAA
AAATAAAAAT
Found at i:29395 original size:26 final size:25
Alignment explanation
Indices: 29355--29429 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 25
29345 ACATTAAATA
29355 TAATA-ATAAATTATATTTAAATAATT
1 TAATATATAAA-TATA-TTAAATAATT
*
29381 TAATATATAAATATA-TAAA-ATTT
1 TAATATATAAATATATTAAATAATT
*
29404 TAAATATATATATATATATAATATAA
1 T-AATATATAAATATAT-TAA-ATAA
29430 AATTAATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 4 0.10
24 17 0.43
26 12 0.30
27 6 0.15
28 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATATATAAATATATTAAATAATT
Found at i:29399 original size:24 final size:25
Alignment explanation
Indices: 29367--29426 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
29357 ATAATAAATT
*
29367 ATATTTAAATAATTT-AATATATAA
1 ATATATAAATAATTTAAATATATAA
* *
29391 ATATATAAA-ATTTTAAATATATAT
1 ATATATAAATAATTTAAATATATAA
29415 ATATATATAATA
1 ATATATA-AATA
29427 TAAAATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 23 0.77
25 2 0.07
26 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATAAATAATTTAAATATATAA
Found at i:46445 original size:41 final size:41
Alignment explanation
Indices: 46399--46739 Score: 352
Period size: 41 Copynumber: 8.4 Consensus size: 41
46389 AAAGGTAAAA
* * * *
46399 CATTAGAGGTGCTTATAGGAAAGCGTCACTAAAGGTCAGGG
1 CATTAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGGG
*
46440 CATTAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAGGG
1 CATTAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGGG
* * * * **
46481 CATTAACGGCGCTTATAGAAAAGCACCGCTAAAGGTTAAAG
1 CATTAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGGG
* * * * *
46522 CATTAGCGGTGCTTATGGGTAAGCGCCGCTAAAAGTCAGGT
1 CATTAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGGG
* * * *
46563 CATTAGCGGCGC-GACA--TAAGCGCCGCTAAAGGT-TGAGG
1 CATTAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAG-GG
* *
46601 CATTAGTGGCGCTTAT-GGAAAAGCGCCGCTAAAGGTCGGGG
1 CATTAGCGGCGCTTATAGG-AAAGCGCCGCTAAAGGTCAGGG
*
46642 CATTAGCGGCGCTTAT-GGAGAAGCGCCGCTAAAGGTCAAGG
1 CATTAGCGGCGCTTATAGGA-AAGCGCCGCTAAAGGTCAGGG
* ** *
46683 CATTAGCGACGCTTATAAAAAAGCGCCGCTAAAGGTCAGAG
1 CATTAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGGG
* *
46724 CATTAGTGACGCTTAT
1 CATTAGCGGCGCTTAT
46740 GGAGAAGTGC
Statistics
Matches: 250, Mismatches: 42, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
37 1 0.00
38 28 0.11
39 1 0.00
40 2 0.01
41 216 0.86
42 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (41 bp):
CATTAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTCAGGG
Found at i:46709 original size:161 final size:161
Alignment explanation
Indices: 46438--46729 Score: 424
Period size: 161 Copynumber: 1.8 Consensus size: 161
46428 TAAAGGTCAG
46438 GGCATTAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAGGGCATTAACGGCGCTTATAGAAAA
1 GGCATTAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAGGGCATTAACGGCGCTTATAGAAAA
* ** ****
46503 GCACCGCTAAAGGTTAAAGCATTAGCGGTGCTTATGGGTAAGCGCCGCTAAAAGTCAG-GTCATT
66 GCACCGCTAAAGGTCAAAGCATTAGCGACGCTTATAAAAAAGCGCCGCTAAAAGTCAGAG-CATT
46567 AGCGGCGCGACATAAGCGCCGCTAAAGGTTGA
130 AGCGGCGCGACATAAGCGCCGCTAAAGGTTGA
* * * * * *
46599 GGCATTAGTGGCGCTTATGGAAAAGCGCCGCTAAAGGTCGGGGCATTAGCGGCGCTTATGGAGAA
1 GGCATTAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAGGGCATTAACGGCGCTTATAGAAAA
* * *
46664 GCGCCGCTAAAGGTCAAGGCATTAGCGACGCTTATAAAAAAGCGCCGCTAAAGGTCAGAGCATTA
66 GCACCGCTAAAGGTCAAAGCATTAGCGACGCTTATAAAAAAGCGCCGCTAAAAGTCAGAGCATTA
46729 G
131 G
46730 TGACGCTTAT
Statistics
Matches: 114, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
161 113 0.99
162 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.31, T:0.19
Consensus pattern (161 bp):
GGCATTAGCGGCGCTTATAGAAAAGCGCCGCTAAAGGTCAGGGCATTAACGGCGCTTATAGAAAA
GCACCGCTAAAGGTCAAAGCATTAGCGACGCTTATAAAAAAGCGCCGCTAAAAGTCAGAGCATTA
GCGGCGCGACATAAGCGCCGCTAAAGGTTGA
Found at i:46740 original size:82 final size:82
Alignment explanation
Indices: 46399--46746 Score: 389
Period size: 82 Copynumber: 4.3 Consensus size: 82
46389 AAAGGTAAAA
* * * * *
46399 CATTAGAGGTGCTTATAGGA-AAGCGTCACTAAAGGTCAGGGCATTAGCGGCGCTTATAGAAAAG
1 CATTAGCGGCGCTTAT-GGAGAAGCGCCGCTAAAGGTCAAGGCATTAGCGGCGCTTATAGAAAAG
46463 CGCCGCTAAAGGTCAGGG
65 CGCCGCTAAAGGTCAGGG
* * * * * * * * **
46481 CATTAACGGCGCTTATAGAAAAGCACCGCTAAAGGTTAAAGCATTAGCGGTGCTTATGGGTAAGC
1 CATTAGCGGCGCTTATGGAGAAGCGCCGCTAAAGGTCAAGGCATTAGCGGCGCTTATAGAAAAGC
* *
46546 GCCGCTAAAAGTCAGGT
66 GCCGCTAAAGGTCAGGG
* * * ** * *
46563 CATTAGCGGCGC-GA--CATAAGCGCCGCTAAAGGTTGAGGCATTAGTGGCGCTTATGGAAAAGC
1 CATTAGCGGCGCTTATGGAGAAGCGCCGCTAAAGGTCAAGGCATTAGCGGCGCTTATAGAAAAGC
*
46625 GCCGCTAAAGGTCGGGG
66 GCCGCTAAAGGTCAGGG
* *
46642 CATTAGCGGCGCTTATGGAGAAGCGCCGCTAAAGGTCAAGGCATTAGCGACGCTTATAAAAAAGC
1 CATTAGCGGCGCTTATGGAGAAGCGCCGCTAAAGGTCAAGGCATTAGCGGCGCTTATAGAAAAGC
*
46707 GCCGCTAAAGGTCAGAG
66 GCCGCTAAAGGTCAGGG
* *
46724 CATTAGTGACGCTTATGGAGAAG
1 CATTAGCGGCGCTTATGGAGAAG
46747 TGCTGCTAGA
Statistics
Matches: 219, Mismatches: 43, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
79 65 0.30
80 1 0.00
81 3 0.01
82 150 0.68
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.20
Consensus pattern (82 bp):
CATTAGCGGCGCTTATGGAGAAGCGCCGCTAAAGGTCAAGGCATTAGCGGCGCTTATAGAAAAGC
GCCGCTAAAGGTCAGGG
Found at i:48504 original size:59 final size:59
Alignment explanation
Indices: 48431--48678 Score: 238
Period size: 59 Copynumber: 4.2 Consensus size: 59
48421 ATTCGAGGAC
* * *
48431 AAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAAATGGAAAGTTTAGAGGTTT-GAGGGTA
1 AAAATGG-AATTTTTGAAAGTTTTGGGGTTAAAAATGGAAATTTTGGAAGTTTAG-GGGTA
** * ** * * *
48491 AAAAT-GAATTTTTTGGGAGTTTTAGGGTCGAAAATGGAATTTTTGAAAGTTCAGGGGT-
1 AAAATGGAA-TTTTTGAAAGTTTTGGGGTTAAAAATGGAAATTTTGGAAGTTTAGGGGTA
** * ** *
48549 AAAATGGAATTTTTGAAAGTTCAGGGG-T-AAAATGGAATTTTTGGAAGTTTTTGGGTT
1 AAAATGGAATTTTTGAAAGTTTTGGGGTTAAAAATGGAAATTTTGGAAGTTTAGGGGTA
* * *
48606 AAAATGGAATTTTTGGAAGTTTCGAGGTTAAAAAT-GAAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGAAAGTTTTGGGGTTAAAAATGGAAA-TTTTGGAAGTTTAGGGGTA
48665 AAAATGGAATTTTT
1 AAAATGGAATTTTT
48679 TGACAGATTA
Statistics
Matches: 152, Mismatches: 29, Indels: 15
0.78 0.15 0.08
Matches are distributed among these distances:
56 24 0.16
57 23 0.15
58 24 0.16
59 75 0.49
60 6 0.04
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.37
Consensus pattern (59 bp):
AAAATGGAATTTTTGAAAGTTTTGGGGTTAAAAATGGAAATTTTGGAAGTTTAGGGGTA
Found at i:48512 original size:29 final size:29
Alignment explanation
Indices: 48431--48678 Score: 220
Period size: 29 Copynumber: 8.5 Consensus size: 29
48421 ATTCGAGGAC
* **
48431 AAAATGGTAATTTTTGAAAGTTTTGGGGTTA
1 AAAATGG-AATTTTTGGAAGTTTCAGGG-TA
** * * *
48462 AAAATGGAAAGTTTAGAGGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCAGGGTA
* * *
48491 AAAAT-GAATTTTTTGGGAGTTTTAGGGTCG
1 AAAATGGAA-TTTTTGGAAGTTTCAGGGT-A
*
48521 AAAATGGAATTTTTGAAAG-TTCAGGGGT-
1 AAAATGGAATTTTTGGAAGTTTCA-GGGTA
*
48549 AAAATGGAATTTTTGAAAG-TTCAGGGGT-
1 AAAATGGAATTTTTGGAAGTTTCA-GGGTA
** *
48577 AAAATGGAATTTTTGGAAGTTTTTGGGTT
1 AAAATGGAATTTTTGGAAGTTTCAGGGTA
*
48606 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTC-AGGGTA
*
48636 AAAATGAAATTTTTGGAAGTTT-AGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCA-GGGTA
48665 AAAATGGAATTTTT
1 AAAATGGAATTTTT
48679 TGACAGATTA
Statistics
Matches: 182, Mismatches: 27, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
28 54 0.30
29 64 0.35
30 54 0.30
31 10 0.05
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCAGGGTA
Found at i:50597 original size:17 final size:17
Alignment explanation
Indices: 50579--50686 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
50569 AATGGGACTT
*
50579 TTTAAATTTAAAAT-AT
1 TTTAAATTTAAAATAAA
*
50595 TTTAATTTTAAAAGTAAA
1 TTTAAATTTAAAA-TAAA
* **
50613 TTTAAACTTAATTTAAA
1 TTTAAATTTAAAATAAA
*
50630 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
50647 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
50664 -TTAAATCTTATAATAAA
1 TTTAAAT-TTAAAATAAA
50681 TTTAAA
1 TTTAAA
50687 AAGGAATTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
16 18 0.24
17 43 0.57
18 15 0.20
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:50618 original size:6 final size:6
Alignment explanation
Indices: 50595--50686 Score: 61
Period size: 6 Copynumber: 16.0 Consensus size: 6
50585 TTTAAAATAT
* ** *
50595 TTTAAT TTTAAA AGTAAA TTTAAA CTT-AA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
50642 -ACAAA TTTAAA TTTAAA -ATAAA -TTAAA TCTTATAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTA-AA TTTAAA TTTAAA
50687 AAGGAATTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
4 2 0.03
5 17 0.26
6 42 0.64
7 3 0.05
8 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:50627 original size:11 final size:12
Alignment explanation
Indices: 50609--50686 Score: 53
Period size: 11 Copynumber: 6.8 Consensus size: 12
50599 ATTTTAAAAG
50609 TAAATTTAAACT
1 TAAATTTAAACT
*
50621 T-AATTTAAATT
1 TAAATTTAAACT
50632 TAAATTTAAAAC-
1 TAAATTT-AAACT
*
50644 -AAATTTAAATT
1 TAAATTTAAACT
*
50655 TAAA-ATAAA-T
1 TAAATTTAAACT
50665 TAAATCTTATAA--
1 TAAAT-TTA-AACT
50677 TAAATTTAAA
1 TAAATTTAAA
50687 AAGGAATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
10 10 0.19
11 23 0.43
12 16 0.30
13 5 0.09
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATTTAAACT
Found at i:50628 original size:29 final size:28
Alignment explanation
Indices: 50581--50635 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
50571 TGGGACTTTT
* *
50581 TAAATTTAAAATATTTTAATTTTAAAAG
1 TAAATTTAAAATAATTTAAATTTAAAAG
*
50609 TAAATTTAAACTTAATTTAAATTTAAA
1 TAAATTTAAA-ATAATTTAAATTTAAA
50636 TTTAAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
TAAATTTAAAATAATTTAAATTTAAAAG
Found at i:50635 original size:23 final size:23
Alignment explanation
Indices: 50609--50658 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
50599 ATTTTAAAAG
*
50609 TAAATTT-AAACTTAATTTAAATT
1 TAAATTTAAAAC-AAATTTAAATT
50632 TAAATTTAAAACAAATTTAAATT
1 TAAATTTAAAACAAATTTAAATT
50655 TAAA
1 TAAA
50659 ATAAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATTTAAAACAAATTTAAATT
Found at i:53548 original size:43 final size:42
Alignment explanation
Indices: 53473--53606 Score: 144
Period size: 43 Copynumber: 3.0 Consensus size: 42
53463 ATCTGTTAAT
* *
53473 TTTAACAGCGTTTGTGGGAAAAGCGCCACTAAAGACCATGTTC
1 TTTAAC-GCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTC
*
53516 TTTAACGGCGTTTGTGGAAAAAACGCCGCTAAACTAAAGACCATGTTC
1 TTTAAC-GCGTTTGTGGAAAAAGCGCCG-----CTAAAGACCATGTTC
* *
53564 TTTAGCGCGTTTGT-GAGAAAAGCGCCGCTAAAGACCCTGTTC
1 TTTAACGCGTTTGTGGA-AAAAGCGCCGCTAAAGACCATGTTC
53606 T
1 T
53607 ATAGCGGCAT
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
42 15 0.19
43 24 0.31
46 2 0.03
47 17 0.22
48 20 0.26
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (42 bp):
TTTAACGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTC
Found at i:53592 original size:47 final size:48
Alignment explanation
Indices: 53500--53595 Score: 151
Period size: 47 Copynumber: 2.0 Consensus size: 48
53490 GAAAAGCGCC
53500 ACTAAAGACCATGTTCTTTAACGGCGTTTGTGGAAAAAACGCCGCTAA
1 ACTAAAGACCATGTTCTTTAACGGCGTTTGTGGAAAAAACGCCGCTAA
* *
53548 ACTAAAGACCATGTTCTTTAGC-GCGTTTGT-GAGAAAAGCGCCGCTAA
1 ACTAAAGACCATGTTCTTTAACGGCGTTTGTGGA-AAAAACGCCGCTAA
53595 A
1 A
53596 GACCCTGTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 2 0.04
47 22 0.49
48 21 0.47
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (48 bp):
ACTAAAGACCATGTTCTTTAACGGCGTTTGTGGAAAAAACGCCGCTAA
Found at i:53612 original size:42 final size:41
Alignment explanation
Indices: 53480--53612 Score: 140
Period size: 42 Copynumber: 3.0 Consensus size: 41
53470 AATTTTAACA
* *
53480 GCGTTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTTTAAC
1 GCGTTTGT-GGAAAAGCGCCGCTAAAGACCATGTTCTTTAGC
*
53522 GGCGTTTGTGGAAAAAACGCCGCTAAACTAAAGACCATGTTCTTTAGC
1 -GCGTTTGTGG-AAAAGCGCCG-----CTAAAGACCATGTTCTTTAGC
* *
53570 GCGTTTGTGAGAAAAGCGCCGCTAAAGACCCTGTTCTATAGC
1 GCGTTTGTG-GAAAAGCGCCGCTAAAGACCATGTTCTTTAGC
53612 G
1 G
53613 GCATTTTTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
42 22 0.29
43 16 0.21
47 18 0.23
48 21 0.27
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (41 bp):
GCGTTTGTGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGC
Found at i:56219 original size:31 final size:33
Alignment explanation
Indices: 56184--56244 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
56174 TAATAATCAT
*
56184 AATTTAA-AAAATTAAT-TTTATAA-TAAATTTG
1 AATTTAACAAAA-TAATATTAATAATTAAATTTG
56215 AATTTAACAAAATAATATTAATAATTAAAT
1 AATTTAACAAAATAATATTAATAATTAAAT
56245 CTTTAAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 11 0.42
32 10 0.38
33 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (33 bp):
AATTTAACAAAATAATATTAATAATTAAATTTG
Found at i:58781 original size:41 final size:39
Alignment explanation
Indices: 58704--58782 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
58694 ACACAATGTG
* *
58704 TCATTGTGATTTAGTTACAAAAACATTTATAATCCCTTT
1 TCATGGTGATTTAGTTACAAAAAAATTTATAATCCCTTT
* *
58743 TCATGGTGTTTTAGTTACAAGAACAAATTTATATTCCCTT
1 TCATGGTGATTTAGTTACAA-AA-AAATTTATAATCCCTT
58783 CTTCTCAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 18 0.53
40 2 0.06
41 14 0.41
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (39 bp):
TCATGGTGATTTAGTTACAAAAAAATTTATAATCCCTTT
Found at i:68501 original size:12 final size:13
Alignment explanation
Indices: 68479--68507 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
68469 AGGGTATAAT
68479 AAAATATTTTAAA
1 AAAATATTTTAAA
68492 AAAATA-TTTAAA
1 AAAATATTTTAAA
68504 AAAA
1 AAAA
68508 AACATATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATATTTTAAA
Found at i:68508 original size:13 final size:13
Alignment explanation
Indices: 68479--68508 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
68469 AGGGTATAAT
*
68479 AAAATATTTTAAA
1 AAAATATTTAAAA
68492 AAAATATTTAAAA
1 AAAATATTTAAAA
68505 AAAA
1 AAAA
68509 ACATATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATATTTAAAA
Found at i:69832 original size:4 final size:4
Alignment explanation
Indices: 69825--69851 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
69815 GTTTCTTTCT
69825 TTCC TTCC TTCC TTCC TTCC TTCC TTC
1 TTCC TTCC TTCC TTCC TTCC TTCC TTC
69852 TATAATCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (4 bp):
TTCC
Found at i:75009 original size:29 final size:30
Alignment explanation
Indices: 74976--75374 Score: 195
Period size: 30 Copynumber: 13.4 Consensus size: 30
74966 GGTTAAAATG
74976 AAATTTT-GGAAAGTTTGAGGGCT-AAATTT
1 AAATTTTAGG-AAGTTTGAGGGCTCAAATTT
* *
75005 GAATTTTAAGGAAGTTT-AGGGGTCAAATTT
1 AAATTTT-AGGAAGTTTGAGGGCTCAAATTT
* * **
75035 AAATTTTTAGGAAGTTTGA-GG-TTAGATCC
1 AAA-TTTTAGGAAGTTTGAGGGCTCAAATTT
* * * **
75064 AAATTTTTGGAAAATTTG-GGGGTCAAATAC
1 AAATTTTAGG-AAGTTTGAGGGCTCAAATTT
* * **
75094 AAATTTTTGGAAAGTTTG-GGGGTCAAATCC
1 AAATTTTAGG-AAGTTTGAGGGCTCAAATTT
* * *
75124 AAATTTTTTAGGGAATTTTGAGGG-TTAAATCT
1 AAA--TTTTA-GGAAGTTTGAGGGCTCAAATTT
*
75156 AAATTTTTAGGAAGTTT-AGGGGTCAAATTT
1 AAA-TTTTAGGAAGTTTGAGGGCTCAAATTT
**
75186 AAATTTTTAGGAAGTTTGA-GG-TCAAATCC
1 AAA-TTTTAGGAAGTTTGAGGGCTCAAATTT
*
75215 AAATTTTTAGGAAGTTTG-GGGGTCAAATTT
1 AAA-TTTTAGGAAGTTTGAGGGCTCAAATTT
* * **
75245 GAATTTTTGGAAAGTTTG-GGG-TCAAATCC
1 AAATTTTAGG-AAGTTTGAGGGCTCAAATTT
* * * *
75274 AAATTTTTTGTAAGTTT-AGGGATAAAATTT
1 AAA-TTTTAGGAAGTTTGAGGGCTCAAATTT
* * * *
75304 GAATTTTAGGGAAG-TTCA-GGATCAAATCT
1 AAATTTTA-GGAAGTTTGAGGGCTCAAATTT
* * * *
75333 AAATTTTTAGGAAGTTCGAGGGTTAAAATAT
1 AAA-TTTTAGGAAGTTTGAGGGCTCAAATTT
75364 AAATTTT-GGAA
1 AAATTTTAGGAA
75375 AGTTCAGGGA
Statistics
Matches: 300, Mismatches: 45, Indels: 50
0.76 0.11 0.13
Matches are distributed among these distances:
28 6 0.02
29 105 0.35
30 140 0.47
31 25 0.08
32 19 0.06
33 5 0.02
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (30 bp):
AAATTTTAGGAAGTTTGAGGGCTCAAATTT
Found at i:75033 original size:30 final size:30
Alignment explanation
Indices: 75006--75348 Score: 301
Period size: 30 Copynumber: 11.5 Consensus size: 30
74996 GCTAAATTTG
* *
75006 AATTTTAAGGAAGTTTAGGGGTCAAATTTA
1 AATTTTTAGGAAGTTTAGGGGTCAAATCTA
* * * *
75036 AATTTTTAGGAAGTTT-GAGGTTAGATCCA
1 AATTTTTAGGAAGTTTAGGGGTCAAATCTA
* *
75065 AATTTTT-GGAAAATTTGGGGGTCAAATAC-A
1 AATTTTTAGG-AAGTTTAGGGGTCAAAT-CTA
* *
75095 AATTTTT-GGAAAGTTTGGGGGTCAAATCCA
1 AATTTTTAGG-AAGTTTAGGGGTCAAATCTA
* *
75125 AATTTTTTAGGGAA-TTTTGAGGGTTAAATCTA
1 AA-TTTTTA-GGAAGTTTAG-GGGTCAAATCTA
*
75157 AATTTTTAGGAAGTTTAGGGGTCAAATTTA
1 AATTTTTAGGAAGTTTAGGGGTCAAATCTA
* *
75187 AATTTTTAGGAAGTTT-GAGGTCAAATCCA
1 AATTTTTAGGAAGTTTAGGGGTCAAATCTA
* * *
75216 AATTTTTAGGAAGTTTGGGGGTCAAATTTG
1 AATTTTTAGGAAGTTTAGGGGTCAAATCTA
*
75246 AATTTTT-GGAAAGTTT-GGGGTCAAATCCA
1 AATTTTTAGG-AAGTTTAGGGGTCAAATCTA
* * * * * *
75275 AATTTTTTGTAAGTTTAGGGATAAAATTTG
1 AATTTTTAGGAAGTTTAGGGGTCAAATCTA
* *
75305 AA-TTTTAGGGAAGTTCA-GGATCAAATCTA
1 AATTTTTA-GGAAGTTTAGGGGTCAAATCTA
75334 AATTTTTAGGAAGTT
1 AATTTTTAGGAAGTT
75349 CGAGGGTTAA
Statistics
Matches: 259, Mismatches: 39, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 94 0.36
30 127 0.49
31 20 0.08
32 14 0.05
33 2 0.01
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (30 bp):
AATTTTTAGGAAGTTTAGGGGTCAAATCTA
Found at i:75169 original size:121 final size:121
Alignment explanation
Indices: 75024--75348 Score: 308
Period size: 121 Copynumber: 2.7 Consensus size: 121
75014 GGAAGTTTAG
* * * *
75024 GGGTCAAATTTAAATTTTTAGGAAGTTT-GAGGTTAGATCCAAATTTTT-GGAAAATTTGGGGGT
1 GGGTCAAATCTAAATTTTTAGGAAGTTTAGAGGTCAAATCCAAATTTTTAGG-AAATTT-GAGGT
75087 CAAATACAAATTTTT-GGAAAGTTTGGGGGTCAAATCCAAATTTTTTAGGGAATTTTGA
64 CAAATACAAATTTTTAGG-AAGTTTGGGGGTCAAATCCAAATTTTTTAGGGAATTTTGA
* * ** *
75145 GGGTTAAATCTAAATTTTTAGGAAGTTTAGGGGTCAAATTTAAATTTTTAGGAAGTTTGAGGTCA
1 GGGTCAAATCTAAATTTTTAGGAAGTTTAGAGGTCAAATCCAAATTTTTAGGAAATTTGAGGTCA
* *** * *
75210 AATCCAAATTTTTAGGAAGTTTGGGGGTCAAATTTGAA-TTTTT-GGAAAGTTTG-
66 AATACAAATTTTTAGGAAGTTTGGGGGTCAAATCCAAATTTTTTAGGGAATTTTGA
* * * * *** * * *
75263 GGGTCAAATCCAAATTTTTTGTAAGTTTAG-GGATAAAATTTGAA-TTTTAGGGAAGTTCAGGAT
1 GGGTCAAATCTAAATTTTTAGGAAGTTTAGAGG-TCAAATCCAAATTTTTAGGAAATTTGAGG-T
75326 CAAAT-CTAAATTTTTAGGAAGTT
64 CAAATAC-AAATTTTTAGGAAGTT
75349 CGAGGGTTAA
Statistics
Matches: 173, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
117 16 0.09
118 57 0.33
119 8 0.05
120 5 0.03
121 63 0.36
122 22 0.13
123 2 0.01
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (121 bp):
GGGTCAAATCTAAATTTTTAGGAAGTTTAGAGGTCAAATCCAAATTTTTAGGAAATTTGAGGTCA
AATACAAATTTTTAGGAAGTTTGGGGGTCAAATCCAAATTTTTTAGGGAATTTTGA
Found at i:75237 original size:59 final size:59
Alignment explanation
Indices: 74986--75348 Score: 308
Period size: 59 Copynumber: 6.1 Consensus size: 59
74976 AAATTTTGGA
* * * * **
74986 AAGTTTGAGGG-CTAAATTTGAATTTTAAGGAAGTTTAGGGGTCAAATTTAAATTTTTAGG
1 AAGTTTGGGGGTC-AAATTTAAATTTTTAGGAAGTTT-GAGGTCAAATCCAAATTTTTAGG
* * * ** * * *
75046 AAGTTT-GAGGTTAGATCCAAATTTTT-GGAAAATTTGGGGGTCAAATACAAATTTTT-GG
1 AAGTTTGGGGGTCAAATTTAAATTTTTAGG-AAGTTT-GAGGTCAAATCCAAATTTTTAGG
** * * *
75104 AAAGTTTGGGGGTCAAATCCAAATTTTTTAGGGAATTTTGAGGGTTAAATCTAAATTTTTAGG
1 -AAGTTTGGGGGTCAAATTTAAA-TTTTTA-GGAAGTTTGA-GGTCAAATCCAAATTTTTAGG
*
75167 AAGTTTAGGGGTCAAATTTAAATTTTTAGGAAGTTTGAGGTCAAATCCAAATTTTTAGG
1 AAGTTTGGGGGTCAAATTTAAATTTTTAGGAAGTTTGAGGTCAAATCCAAATTTTTAGG
* * * *
75226 AAGTTTGGGGGTCAAATTTGAATTTTT-GGAAAGTTTGGGGTCAAATCCAAATTTTTTGT
1 AAGTTTGGGGGTCAAATTTAAATTTTTAGG-AAGTTTGAGGTCAAATCCAAATTTTTAGG
* * * * * *
75285 AAGTTTAGGGATAAAATTTGAA-TTTTAGGGAAG-TTCAGGATCAAATCTAAATTTTTAGG
1 AAGTTTGGGGGTCAAATTTAAATTTTTA-GGAAGTTTGAGG-TCAAATCCAAATTTTTAGG
75344 AAGTT
1 AAGTT
75349 CGAGGGTTAA
Statistics
Matches: 251, Mismatches: 39, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
58 14 0.06
59 153 0.61
60 29 0.12
61 12 0.05
62 39 0.16
63 4 0.02
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.38
Consensus pattern (59 bp):
AAGTTTGGGGGTCAAATTTAAATTTTTAGGAAGTTTGAGGTCAAATCCAAATTTTTAGG
Found at i:75378 original size:59 final size:58
Alignment explanation
Indices: 75150--75382 Score: 229
Period size: 59 Copynumber: 4.0 Consensus size: 58
75140 TTTGAGGGTT
* * * *
75150 AAATCTAAATTTTTAGGAAGTTTAGGGGTCAAATTTAAATTTTTAGG-AAGTTTGAGGTC
1 AAATCCAAATTTTTAGGAAGTTGAGGGGTAAAATTTAAA-TTTTAGGAAAG-TTCAGGTC
* * * **
75209 AAATCCAAATTTTTAGGAAGTTTG-GGGGTCAAATTTGAATTTTTGGAAAGTTTGGGGTC
1 AAATCCAAATTTTTAGGAAG-TTGAGGGGTAAAATTTAAATTTTAGGAAAG-TTCAGGTC
* * * * * *
75268 AAATCCAAATTTTTTGTAAGTTTAGGGATAAAATTTGAATTTTAGGGAAGTTCAGGATC
1 AAATCCAAATTTTTAGGAAGTTGAGGGGTAAAATTTAAATTTTAGGAAAGTTCAGG-TC
* * *
75327 AAATCTAAATTTTTAGGAAGTTCGAGGGTTAAAATATAAATTTT-GGAAAGTTCAGG
1 AAATCCAAATTTTTAGGAAGTT-GAGGGGTAAAATTTAAATTTTAGGAAAGTTCAGG
75383 GAAAAATGTA
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
58 12 0.08
59 116 0.79
60 19 0.13
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (58 bp):
AAATCCAAATTTTTAGGAAGTTGAGGGGTAAAATTTAAATTTTAGGAAAGTTCAGGTC
Found at i:84290 original size:12 final size:12
Alignment explanation
Indices: 84259--84287 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
84249 ATGTTTACAA
84259 ATTTTTAATAAT
1 ATTTTTAATAAT
84271 ATTTTTAA-AAT
1 ATTTTTAATAAT
84282 ATTTTT
1 ATTTTT
84288 TAATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTTAATAAT
Found at i:85107 original size:16 final size:17
Alignment explanation
Indices: 85086--85126 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
85076 TTATTATTTC
85086 AAAATATAATTTAA-AT
1 AAAATATAATTTAATAT
85102 AAAATAT--TTTAATAT
1 AAAATATAATTTAATAT
85117 AAAA-ATAATT
1 AAAATATAATT
85127 AATTAAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 7 0.32
15 6 0.27
16 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATAATTTAATAT
Found at i:85216 original size:12 final size:12
Alignment explanation
Indices: 85199--85226 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
85189 TATTAAAATT
85199 TAATAACAACAA
1 TAATAACAACAA
85211 TAATAACAACAA
1 TAATAACAACAA
85223 TAAT
1 TAAT
85227 CATCTATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (12 bp):
TAATAACAACAA
Found at i:85409 original size:16 final size:16
Alignment explanation
Indices: 85390--85440 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
85380 ACTTTATTTC
* *
85390 ATTACAATTCTATTCT
1 ATTATAATTCTATTCA
85406 ATTATAA-TCTTATTCA
1 ATTATAATTC-TATTCA
*
85422 ATTATAATTTTATTCA
1 ATTATAATTCTATTCA
85438 ATT
1 ATT
85441 TCAATAAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 2 0.07
16 27 0.90
17 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATAATTCTATTCA
Found at i:100573 original size:29 final size:29
Alignment explanation
Indices: 100535--100630 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 29
100525 AATAATACAA
* * *
100535 ATACAATTACATATACAATCATGTCACAG
1 ATACAGTTACAAATACAGTCATGTCACAG
*
100564 ATACAGTTACAGATACAGTCATGTCACAG
1 ATACAGTTACAAATACAGTCATGTCACAG
** * *
100593 ATGTAGTTACAAATGCAGTAATGTCACAG
1 ATACAGTTACAAATACAGTCATGTCACAG
*
100622 ATATAGTTA
1 ATACAGTTA
100631 TGGATGCAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (29 bp):
ATACAGTTACAAATACAGTCATGTCACAG
Found at i:100637 original size:29 final size:29
Alignment explanation
Indices: 100555--100639 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
100545 ATATACAATC
* * *
100555 ATGTCACAGATACAGTTACAGATACAGTC
1 ATGTCACAGATATAGTTACAGATGCAGTA
* *
100584 ATGTCACAGATGTAGTTACAAATGCAGTA
1 ATGTCACAGATATAGTTACAGATGCAGTA
**
100613 ATGTCACAGATATAGTTATGGATGCAG
1 ATGTCACAGATATAGTTACAGATGCAG
100640 GCATGATACA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (29 bp):
ATGTCACAGATATAGTTACAGATGCAGTA
Found at i:100659 original size:58 final size:58
Alignment explanation
Indices: 100529--100665 Score: 141
Period size: 58 Copynumber: 2.4 Consensus size: 58
100519 TATAGAAATA
* * * * *
100529 ATACAAATACAATTACATATACAATCATGTCACAGATACAGTTACAGATACAGTCATG
1 ATACAAATACAGTTACAAATGCAATAATGTCACAGATACAGTTACAGATACAGGCATG
* ** * * ** *
100587 -TCACAGATGTAGTTACAAATGCAGTAATGTCACAGATATAGTTATGGATGCAGGCATG
1 AT-ACAAATACAGTTACAAATGCAATAATGTCACAGATACAGTTACAGATACAGGCATG
100645 ATACAAATACAGTTACAAATG
1 ATACAAATACAGTTACAAATG
100666 TAAACGTGAT
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
57 1 0.02
58 59 0.97
59 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (58 bp):
ATACAAATACAGTTACAAATGCAATAATGTCACAGATACAGTTACAGATACAGGCATG
Found at i:100824 original size:40 final size:40
Alignment explanation
Indices: 100737--100845 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
100727 TCGGTGTGAC
* * * *
100737 ACATTGCAGTGTTTACAGTGTCACTGTCAGTTTAGTGGTA
1 ACATTGTAGTGTTTACAGTGTCACTGCCAGTTCAGTGATA
* * * *
100777 ACCTTGTAGTATTTACAGTGTCACTGCCGGTTCAGTTATA
1 ACATTGTAGTGTTTACAGTGTCACTGCCAGTTCAGTGATA
* *
100817 ATATTGTAGTGTTTACAATGTCACTGCCA
1 ACATTGTAGTGTTTACAGTGTCACTGCCA
100846 ACTCAGTAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (40 bp):
ACATTGTAGTGTTTACAGTGTCACTGCCAGTTCAGTGATA
Found at i:100852 original size:40 final size:38
Alignment explanation
Indices: 100780--100859 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 38
100770 AGTGGTAACC
* ***
100780 TTGTAGTATTTACAGTGTCACTGCCGGTTCAGTTATAATA
1 TTGTAGTATTTACAATGTCACTGCCAACTCAG-TA-AATA
*
100820 TTGTAGTGTTTACAATGTCACTGCCAACTCAGTAAATA
1 TTGTAGTATTTACAATGTCACTGCCAACTCAGTAAATA
100858 TT
1 TT
100860 CTCAAGTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 6 0.17
39 2 0.06
40 27 0.77
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (38 bp):
TTGTAGTATTTACAATGTCACTGCCAACTCAGTAAATA
Found at i:101510 original size:56 final size:56
Alignment explanation
Indices: 101400--101579 Score: 219
Period size: 56 Copynumber: 3.3 Consensus size: 56
101390 GATCCATGCT
*
101400 CGTGTTCCTC-CAAACAGTATAGACACACACCCTGGAC-ACCCCCATGTGCCAGCC
1 CGTGTACCTCTCAAACAGTATAGACACACACCCTGGACAACCCCCATGTGCCAGCC
* * * *
101454 CGTG-A-GTCTTCAAACAGTATAGACACACACCCTGAACATATCCCCGTGTGCCAGCC
1 CGTGTACCTC-TCAAACAGTATAGACACACACCCTGGACA-ACCCCCATGTGCCAGCC
*
101510 CGTGTACCTCTC-AACAGTATAGACACACACTCTGGACACACCCCCATGTGCCAGCC
1 CGTGTACCTCTCAAACAGTATAGACACACACCCTGGACA-ACCCCCATGTGCCAGCC
* *
101566 CATGTGCCT-TCAAA
1 CGTGTACCTCTCAAA
101580 AAACACTATT
Statistics
Matches: 106, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
52 2 0.02
54 30 0.28
55 2 0.02
56 67 0.63
57 3 0.03
58 2 0.02
ACGTcount: A:0.27, C:0.37, G:0.17, T:0.19
Consensus pattern (56 bp):
CGTGTACCTCTCAAACAGTATAGACACACACCCTGGACAACCCCCATGTGCCAGCC
Found at i:103048 original size:7 final size:8
Alignment explanation
Indices: 103028--103058 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
103018 TTATGTGTTC
103028 ATTTTTCT
1 ATTTTTCT
103036 ATTTTTCT
1 ATTTTTCT
103044 ATTTTTCT
1 ATTTTTCT
103052 ATTTTTC
1 ATTTTTC
103059 ATATAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTCT
Found at i:104201 original size:18 final size:19
Alignment explanation
Indices: 104180--104221 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
104170 TTTATGATGA
*
104180 AAATA-ATATTTAATATTT
1 AAATAGATATTTAATATTC
*
104198 AAATATGATATTTGATATTC
1 AAATA-GATATTTAATATTC
104218 AAAT
1 AAAT
104222 TTATTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
20 15 0.75
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
AAATAGATATTTAATATTC
Found at i:105571 original size:13 final size:13
Alignment explanation
Indices: 105553--105579 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
105543 TATATCATGA
105553 TTAGTATTAATGG
1 TTAGTATTAATGG
105566 TTAGTATTAATGG
1 TTAGTATTAATGG
105579 T
1 T
105580 AAATAGGTTG
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:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TTAGTATTAATGG
Found at i:106704 original size:103 final size:103
Alignment explanation
Indices: 106516--106749 Score: 396
Period size: 103 Copynumber: 2.3 Consensus size: 103
106506 GTGTTGCGAG
106516 TCCTCGACAGCTCGTGTGAGCAGCATCGTGATTCAAAAAAAGAGAAATGGATCCTATATGGATTA
1 TCCT-GACAGCTCGTGTGAGCAGCATCGTGATTCAAAAAAAGAGAAATGGATCCTATATGGATTA
* *
106581 CAAGTCCTGTAATGGTTGGGACTTATGCTTTATGCATAC
65 CAAGTCCTATAATGGCTGGGACTTATGCTTTATGCATAC
* * *
106620 TTCTGACAGCTCGTGTGAGCAGCATCGTGATTCAAAAAAAGAGATATGGATCTTATATGGATTAC
1 TCCTGACAGCTCGTGTGAGCAGCATCGTGATTCAAAAAAAGAGAAATGGATCCTATATGGATTAC
* *
106685 AGGTCCTATGATGGCTGGGACTTATGCTTTATGCATAC
66 AAGTCCTATAATGGCTGGGACTTATGCTTTATGCATAC
106723 TCCTGACAGCTCGTGTGAGCAGCATCG
1 TCCTGACAGCTCGTGTGAGCAGCATCG
106750 ATAGGAAATA
Statistics
Matches: 122, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 119 0.98
104 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (103 bp):
TCCTGACAGCTCGTGTGAGCAGCATCGTGATTCAAAAAAAGAGAAATGGATCCTATATGGATTAC
AAGTCCTATAATGGCTGGGACTTATGCTTTATGCATAC
Found at i:109726 original size:34 final size:34
Alignment explanation
Indices: 109683--109753 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
109673 ACACTTTAGT
109683 ATTAAATTAAGAACATTTGGTAATGATGAAACCC
1 ATTAAATTAAGAACATTTGGTAATGATGAAACCC
109717 ATTAAATTAAGAACATTTGGTAATGATGAAACCC
1 ATTAAATTAAGAACATTTGGTAATGATGAAACCC
109751 ATT
1 ATT
109754 TAAAACATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (34 bp):
ATTAAATTAAGAACATTTGGTAATGATGAAACCC
Found at i:110767 original size:38 final size:38
Alignment explanation
Indices: 110716--110801 Score: 163
Period size: 38 Copynumber: 2.3 Consensus size: 38
110706 ATTCCTATAT
110716 CATATACAAATTATTCTAGCATGTGTATGATCTTAAAA
1 CATATACAAATTATTCTAGCATGTGTATGATCTTAAAA
110754 CATATACAAATTATTCTAGCATGTGTATGATCTTAAAA
1 CATATACAAATTATTCTAGCATGTGTATGATCTTAAAA
*
110792 CATGTACAAA
1 CATATACAAA
110802 CAATCAAACA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (38 bp):
CATATACAAATTATTCTAGCATGTGTATGATCTTAAAA
Found at i:114287 original size:23 final size:23
Alignment explanation
Indices: 114231--114289 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 23
114221 TGTATCGTCT
114231 TTTTTATTGTCCCTATAATTTGAA
1 TTTTT-TTGTCCCTATAATTTGAA
* *
114255 -TTTTTGGTCCTTATAATTTGAA
1 TTTTTTTGTCCCTATAATTTGAA
114277 TTTTTTTGTCCCT
1 TTTTTTTGTCCCT
114290 GTGGTTCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.58
Consensus pattern (23 bp):
TTTTTTTGTCCCTATAATTTGAA
Found at i:114337 original size:23 final size:23
Alignment explanation
Indices: 114307--114372 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
114297 ATTTTTTCCC
114307 TCCCTGTAATTCAAATTTTTTTA
1 TCCCTGTAATTCAAATTTTTTTA
** * * *
114330 TCTTTGTAAATCGAA-TTTTTTG
1 TCCCTGTAATTCAAATTTTTTTA
*
114352 TCCCTATAATTCAAATTTTTT
1 TCCCTGTAATTCAAATTTTTT
114373 AGTTTATGTA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
22 16 0.50
23 16 0.50
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (23 bp):
TCCCTGTAATTCAAATTTTTTTA
Found at i:114368 original size:22 final size:22
Alignment explanation
Indices: 114232--114372 Score: 70
Period size: 22 Copynumber: 6.3 Consensus size: 22
114222 GTATCGTCTT
**
114232 TTTTATTGTCCCTATAATTTGAA
1 TTTT-TTGTCCCTATAATTCAAA
* * * *
114255 TTTTTGGTCCTTATAATTTGAAT
1 TTTTTTGTCCCTATAA-TTCAAA
* **
114278 TTTTTTGTCCCTGTGGTTC--A
1 TTTTTTGTCCCTATAATTCAAA
* *
114298 TTTTTTCCCTCCCTGTAATTCAAA
1 TTTTTT--GTCCCTATAATTCAAA
* ** * * *
114322 TTTTTTTATCTTTGTAAATCGAA
1 -TTTTTTGTCCCTATAATTCAAA
114345 TTTTTTGTCCCTATAATTCAAA
1 TTTTTTGTCCCTATAATTCAAA
114367 TTTTTT
1 TTTTTT
114373 AGTTTATGTA
Statistics
Matches: 86, Mismatches: 26, Indels: 13
0.69 0.21 0.10
Matches are distributed among these distances:
20 6 0.07
22 44 0.51
23 29 0.34
24 1 0.01
25 6 0.07
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.55
Consensus pattern (22 bp):
TTTTTTGTCCCTATAATTCAAA
Found at i:124387 original size:1 final size:1
Alignment explanation
Indices: 124381--124405 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
124371 CTCCTTTTAC
124381 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
124406 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:129224 original size:17 final size:17
Alignment explanation
Indices: 129194--129257 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
129184 CTTTTTTTTT
**
129194 AATTTATTGCAAATTTA
1 AATTTATTTTAAATTTA
*
129211 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
129228 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
129245 AATTTAATTTTAA
1 AATTT-ATTTTAA
129258 GATTAAAAGT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
17 32 0.84
18 6 0.16
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:129227 original size:6 final size:6
Alignment explanation
Indices: 129204--129257 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
129194 AATTTATTGC
* *
129204 AAATTT AGATTT -ATTTT AAATTT AAA-TT -AATCTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT-TT AAATTT AAATTT
*
129250 AATTTT AA
1 AAATTT AA
129258 GATTAAAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
4 2 0.05
5 5 0.13
6 29 0.74
7 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:129233 original size:11 final size:12
Alignment explanation
Indices: 129204--129257 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
129194 AATTTATTGC
*
129204 AAATTTAGATTT
1 AAATTTAAATTT
*
129216 -ATTTTAAATTT
1 AAATTTAAATTT
129227 AAA-TT-AATCTT
1 AAATTTAAAT-TT
129238 AAATTTAAATTT
1 AAATTTAAATTT
*
129250 AATTTTAA
1 AAATTTAA
129258 GATTAAAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 3 0.09
11 16 0.47
12 12 0.35
13 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
AAATTTAAATTT
Found at i:130286 original size:29 final size:30
Alignment explanation
Indices: 130213--130559 Score: 291
Period size: 29 Copynumber: 11.8 Consensus size: 30
130203 ATAGGTCCCG
***
130213 AAACTTCTAAATAA-TCCATTTTTGACCTTG
1 AAACTTCTAAA-AATTCCATTTTTGACCCCC
* * *
130243 AAACTTCCAAAAATTCTAGTTTT-ACCCCC
1 AAACTTCTAAAAATTCCATTTTTGACCCCC
* * **
130272 GAACTTCTAAAAATTCCATTTTTGAACCTG
1 AAACTTCTAAAAATTCCATTTTTGACCCCC
* **
130302 AAACTTCTAAAAATTCCA-TTTTAACCCTT
1 AAACTTCTAAAAATTCCATTTTTGACCCCC
* * *
130331 AAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCTAAAAATTCCATTTTTGACCCCC
* *
130361 AAACTTCCAAAAATTCCATTTTT-ACCCTC
1 AAACTTCTAAAAATTCCATTTTTGACCCCC
* * *
130390 GAACTAAC-AAAAATTCCATTTTTGACCCCA
1 AAACT-TCTAAAAATTCCATTTTTGACCCCC
* * *
130420 AAACTTTTAAAAATTCTATTTTT-ACCCTC
1 AAACTTCTAAAAATTCCATTTTTGACCCCC
* * *
130449 AAACTTCCAAAAATTCTA-TTTTGACCCCA
1 AAACTTCTAAAAATTCCATTTTTGACCCCC
* *
130478 AAACTT-TCAAAAATTTCGTTTTTGA-CCCC
1 AAACTTCT-AAAAATTCCATTTTTGACCCCC
* * *
130507 GAACTT-TCAAAAATTCCATTTTTGACCTCA
1 AAACTTCT-AAAAATTCCATTTTTGACCCCC
*
130537 AAACTTCTAAAAATTTCATTTTT
1 AAACTTCTAAAAATTCCATTTTT
130560 AACCTCAAAT
Statistics
Matches: 255, Mismatches: 51, Indels: 22
0.78 0.16 0.07
Matches are distributed among these distances:
28 4 0.02
29 133 0.52
30 117 0.46
31 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (30 bp):
AAACTTCTAAAAATTCCATTTTTGACCCCC
Found at i:130552 original size:59 final size:59
Alignment explanation
Indices: 130214--130589 Score: 379
Period size: 59 Copynumber: 6.4 Consensus size: 59
130204 TAGGTCCCGA
* ** * * *
130214 AACTTCTAAATAA-TCCATTTTTGACCTTGAAACTTCCAAAAA-TTCTAGTTTTACCCCCG
1 AACTTCCAAA-AATTCCATTTTTGACCTCAAAACTTCTAAAAATTTC-ATTTTTACCCTCG
* * * * **
130273 AACTTCTAAAAATTCCATTTTTGAACCT-GAAACTTCTAAAAATTCCATTTTAACCCTTA
1 AACTTCCAAAAATTCCATTTTTG-ACCTCAAAACTTCTAAAAATTTCATTTTTACCCTCG
* * *
130332 AACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCTAAAAATTTCATTTTTACCCTCG
** * * *
130391 AACTAACAAAAATTCCATTTTTGACCCCAAAACTTTTAAAAA-TTCTATTTTTACCCTCA
1 AACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCTAAAAATTTC-ATTTTTACCCTCG
* * *
130450 AACTTCCAAAAATTCTA-TTTTGACCCCAAAACTT-TCAAAAATTTCGTTTTTGACCC-CG
1 AACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCT-AAAAATTTCATTTTT-ACCCTCG
* * *
130508 AACTTTCAAAAATTCCATTTTTGACCTCAAAACTTCTAAAAATTTCATTTTTAACCTCA
1 AACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCTAAAAATTTCATTTTTACCCTCG
* *
130567 AATTTTCCTAAAATTACCATTTT
1 AA-CTTCCAAAAATT-CCATTTT
130590 ACCCTTTGAG
Statistics
Matches: 270, Mismatches: 34, Indels: 24
0.82 0.10 0.07
Matches are distributed among these distances:
57 1 0.00
58 54 0.20
59 192 0.71
60 16 0.06
61 7 0.03
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (59 bp):
AACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCTAAAAATTTCATTTTTACCCTCG
Found at i:130565 original size:30 final size:30
Alignment explanation
Indices: 130213--130568 Score: 290
Period size: 30 Copynumber: 12.1 Consensus size: 30
130203 ATAGGTCCCG
**
130213 AAACTTCTAAATAA-TCCATTTTTGACCTTG
1 AAACTTCTAAA-AATTCCATTTTTGACCTCA
* * * * *
130243 AAACTTCCAAAAATTCTAGTTTT-ACCCCC
1 AAACTTCTAAAAATTCCATTTTTGACCTCA
* *
130272 GAACTTCTAAAAATTCCATTTTTGAACCT-G
1 AAACTTCTAAAAATTCCATTTTTG-ACCTCA
* *
130302 AAACTTCTAAAAATTCCA-TTTTAACC-CTT
1 AAACTTCTAAAAATTCCATTTTTGACCTC-A
* *
130331 AAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCTAAAAATTCCATTTTTGACCTCA
*
130361 AAACTTCCAAAAATTCCATTTTT-ACCCTC-
1 AAACTTCTAAAAATTCCATTTTTGA-CCTCA
* * *
130390 GAACTAAC-AAAAATTCCATTTTTGACCCCA
1 AAACT-TCTAAAAATTCCATTTTTGACCTCA
* *
130420 AAACTTTTAAAAATTCTATTTTT-ACCCTC-
1 AAACTTCTAAAAATTCCATTTTTGA-CCTCA
* * *
130449 AAACTTCCAAAAATTCTA-TTTTGACCCCA
1 AAACTTCTAAAAATTCCATTTTTGACCTCA
* * *
130478 AAACTT-TCAAAAATTTCGTTTTTGACC-CC
1 AAACTTCT-AAAAATTCCATTTTTGACCTCA
*
130507 GAACTT-TCAAAAATTCCATTTTTGACCTCA
1 AAACTTCT-AAAAATTCCATTTTTGACCTCA
* *
130537 AAACTTCTAAAAATTTCATTTTTAACCTCA
1 AAACTTCTAAAAATTCCATTTTTGACCTCA
130567 AA
1 AA
130569 TTTTCCTAAA
Statistics
Matches: 266, Mismatches: 41, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
28 10 0.04
29 124 0.47
30 127 0.48
31 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (30 bp):
AAACTTCTAAAAATTCCATTTTTGACCTCA
Found at i:135666 original size:13 final size:13
Alignment explanation
Indices: 135648--135674 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
135638 CAAGATACTT
135648 TGAATGCTCACTG
1 TGAATGCTCACTG
135661 TGAATGCTCACTG
1 TGAATGCTCACTG
135674 T
1 T
135675 ACAAGACCGT
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:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TGAATGCTCACTG
Found at i:142700 original size:208 final size:205
Alignment explanation
Indices: 142342--142867 Score: 786
Period size: 208 Copynumber: 2.5 Consensus size: 205
142332 TACCAACTCA
* * * *
142342 AGGCTCAAAGCGAGCAAATTTTCGAACCCCAACTTTCTGATGAGATACTAAGAAGCAGAGCGAAG
1 AGGCTCAAAGCGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAG
142407 CAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGT
66 CAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGT
* *
142472 ACAGAGAAGCGGATTAAAACAAACGACA-CGGTCATCTTCTTGATGAGATACTGAGAAGAAGGCC
131 ACAGAGAAGCGGATTAAAACAAACGA-AGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACC
*
142536 AAATCCATGAAACG
195 AAAT-CA--AAACC
*
142550 AGGCTCAAAGCGAGCAAATCTTCGAACCTCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAG
1 AGGCTCAAAGCGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAG
*
142615 CAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGGT
66 CAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGT
*
142680 ACAGAGAAGCGGATTAAAACAAACGAAGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
131 ACAGAGAAGCGGATTAAAACAAACGAAGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
*
142745 AATCAAACCC
196 AATCAAAACC
* * * * *
142755 ACGCTCGATA-TGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATATTGAGAAGCAGGTCGAA
1 AGGCTC-AAAGCGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAA
* *** **
142819 GTAATAAAACGGTCCTCTTCCTGATGAGATACTGAGAAGAAGACCAAAT
65 GCAATAAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAAT
142868 CAAGCCCACG
Statistics
Matches: 292, Mismatches: 23, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
205 66 0.23
206 36 0.12
207 3 0.01
208 187 0.64
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (205 bp):
AGGCTCAAAGCGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAG
CAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGT
ACAGAGAAGCGGATTAAAACAAACGAAGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
AATCAAAACC
Found at i:142943 original size:118 final size:119
Alignment explanation
Indices: 142709--142984 Score: 437
Period size: 118 Copynumber: 2.3 Consensus size: 119
142699 CAAACGAAGT
142709 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAAT
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATA-GAGCAAAT
* *
142774 CTTCGAACCCCAACTTCCTGATGAGATATTGAGAAGCAGGTCGAAGTAATAAAAC
65 CTTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGTAATAAAAC
* *
142829 GGTCCTCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAGCCCACGCTCGATA-AGCAAATC
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATAGAGCAAATC
* *
142893 TTCGAACCCCAGCTTCCTGATGTGATACTAAGAAGCAGGTCGAAGTAATAAAAC
66 TTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGTAATAAAAC
* * * * *
142947 GGTTAGCTTCCTGATGAAATACGGAGAAGTAGACCAAA
1 GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
142985 ATCATCTTCC
Statistics
Matches: 144, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
118 90 0.62
120 54 0.38
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (119 bp):
GGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATAGAGCAAATC
TTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGTAATAAAAC
Found at i:143398 original size:17 final size:16
Alignment explanation
Indices: 143372--143429 Score: 80
Period size: 17 Copynumber: 3.5 Consensus size: 16
143362 GGGCCCGTTT
143372 TTTAATTTATTTTAAA
1 TTTAATTTATTTTAAA
143388 TTTAGATTTATTTTAAA
1 TTTA-ATTTATTTTAAA
* *
143405 TTTAAATTAATCTTAAA
1 TTT-AATTTATTTTAAA
143422 TTTAATTT
1 TTTAATTT
143430 CAAGATTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 8 0.22
17 28 0.76
18 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
TTTAATTTATTTTAAA
Found at i:144153 original size:3 final size:3
Alignment explanation
Indices: 144145--144198 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
144135 CTGATAGCAT
* * * * *
144145 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAT TAA TGA CAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
144193 TAA TAA
1 TAA TAA
144199 ACGGTGGTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:144482 original size:17 final size:17
Alignment explanation
Indices: 144443--144485 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
144433 CAACATCGAT
144443 TTCTAAAGAGTTTTTCAG
1 TTCTAAA-AGTTTTTCAG
*
144461 ATCTAAAAG-TTTTCATG
1 TTCTAAAAGTTTTTCA-G
144478 TTCTAAAA
1 TTCTAAAA
144486 ACAAGTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 10 0.45
18 6 0.27
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (17 bp):
TTCTAAAAGTTTTTCAG
Found at i:145420 original size:30 final size:30
Alignment explanation
Indices: 145298--145423 Score: 157
Period size: 30 Copynumber: 4.2 Consensus size: 30
145288 CCCAGGAGGT
145298 CCCAAAACTTCCAAAAATTCCATTTTTGAC
1 CCCAAAACTTCCAAAAATTCCATTTTTGAC
*** *
145328 CTTGAAACTTCCAAAAATTCCATATTT-AC
1 CCCAAAACTTCCAAAAATTCCATTTTTGAC
* *
145357 CCTC-GAACTTCCAAAAATTACATTTTTTGAC
1 CC-CAAAACTTCCAAAAATTCCA-TTTTTGAC
*
145388 CCCAAAACTTCCAAAAATTCCATTTTTAAC
1 CCCAAAACTTCCAAAAATTCCATTTTTGAC
145418 CCCAAA
1 CCCAAA
145424 TTTTATCGAA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
29 19 0.24
30 41 0.51
31 20 0.25
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (30 bp):
CCCAAAACTTCCAAAAATTCCATTTTTGAC
Found at i:146728 original size:9 final size:9
Alignment explanation
Indices: 146716--146776 Score: 61
Period size: 10 Copynumber: 6.6 Consensus size: 9
146706 TTTTTAAATT
*
146716 TTTTATAAG
1 TTTTATAAA
*
146725 TTTTAT-AG
1 TTTTATAAA
*
146733 TTTTCATAAC
1 TTTT-ATAAA
146743 TTTTAATAAA
1 TTTT-ATAAA
146753 TTTTATAAA
1 TTTTATAAA
146762 TTTATATAAA
1 TTT-TATAAA
146772 TTTTA
1 TTTTA
146777 ATTAAGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
8 6 0.13
9 18 0.39
10 22 0.48
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (9 bp):
TTTTATAAA
Found at i:146728 original size:10 final size:10
Alignment explanation
Indices: 146703--146775 Score: 53
Period size: 10 Copynumber: 7.5 Consensus size: 10
146693 GAAAAAAAAC
*
146703 ATTTTTTTAA
1 ATTTTTATAA
146713 ATTTTT-TATA
1 ATTTTTATA-A
*
146723 AGTTTTAT-A
1 ATTTTTATAA
* *
146732 GTTTTCATAA
1 ATTTTTATAA
* *
146742 CTTTTAATAA
1 ATTTTTATAA
146752 A-TTTTATAA
1 ATTTTTATAA
*
146761 ATTTATATAA
1 ATTTTTATAA
146771 ATTTT
1 ATTTT
146776 AATTAAGAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
9 16 0.33
10 32 0.65
11 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:147604 original size:13 final size:13
Alignment explanation
Indices: 147586--147619 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
147576 ATTATTTATA
*
147586 TTTAATTTGGTAT
1 TTTAATTTGATAT
147599 TTTAATTTGATAT
1 TTTAATTTGATAT
147612 TTTAATTT
1 TTTAATTT
147620 TTGAGGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (13 bp):
TTTAATTTGATAT
Found at i:157527 original size:20 final size:20
Alignment explanation
Indices: 157504--157550 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
157494 AAAAATTGTA
*
157504 ATAATTTGTCACAATCTTTT
1 ATAATTTGTCACAATATTTT
* *
157524 ATAATTTTTTACAATATTTT
1 ATAATTTGTCACAATATTTT
*
157544 AAAATTT
1 ATAATTT
157551 CTAATAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAATTTGTCACAATATTTT
Found at i:159588 original size:30 final size:30
Alignment explanation
Indices: 159520--159590 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
159510 TCCAATGTGA
*
159520 TACTCAAACTTGACAACTTTTTCTAATATG
1 TACTTAAACTTGACAACTTTTTCTAATATG
* *
159550 TACCTAAACTTGA-AACTTTTTTTAAGT-TGG
1 TACTTAAACTTGACAACTTTTTCTAA-TAT-G
159580 TACTTAAACTT
1 TACTTAAACTT
159591 TTTGGGGTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.42
Consensus pattern (30 bp):
TACTTAAACTTGACAACTTTTTCTAATATG
Found at i:159612 original size:58 final size:57
Alignment explanation
Indices: 159541--159652 Score: 129
Period size: 59 Copynumber: 1.9 Consensus size: 57
159531 GACAACTTTT
*
159541 TCTAATATGTACCTAAACTTGAAACT-TTTTT-TAAGTTGGTACTTAAACTTTTTGGGG
1 TCTAATATGTACCTAAACTT--AACTCTTTTTCTAAGTTGGTACCTAAACTTTTTGGGG
* * * *
159598 TCTAATTTGGTACCTGAACTTAACTCTTTTTCCTAATTTGGTACCTAATCTTTTT
1 TCTAATAT-GTACCTAAACTTAACTCTTTTT-CTAAGTTGGTACCTAAACTTTTT
159653 TTTTAATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
56 4 0.09
57 12 0.26
58 11 0.24
59 19 0.41
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.46
Consensus pattern (57 bp):
TCTAATATGTACCTAAACTTAACTCTTTTTCTAAGTTGGTACCTAAACTTTTTGGGG
Found at i:164346 original size:20 final size:20
Alignment explanation
Indices: 164323--164365 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
164313 TATTTTTTAA
164323 ATTTTAAAAATTCAAAAATT
1 ATTTTAAAAATTCAAAAATT
* * *
164343 ATTTTTAAATTTTAAAAATT
1 ATTTTAAAAATTCAAAAATT
164363 ATT
1 ATT
164366 AAAACTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTAAAAATTCAAAAATT
Found at i:164379 original size:28 final size:28
Alignment explanation
Indices: 164316--164376 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 28
164306 ATTTAAATAT
*
164316 TTTTTAAATTTTAAAAATTCAAAAATTA
1 TTTTTAAATTTTAAAAATTCAAAAACTA
164344 TTTTTAAATTTTAAAAATT-ATTAAAACTA
1 TTTTTAAATTTTAAAAATTCA--AAAACTA
164373 TTTT
1 TTTT
164377 AAAAGGTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 1 0.03
28 19 0.63
29 10 0.33
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTTAAATTTTAAAAATTCAAAAACTA
Found at i:168054 original size:58 final size:58
Alignment explanation
Indices: 167985--168104 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 58
167975 AAAAAGAATT
*
167985 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTT-GAGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGGA-TTTAAAAATATTTGGGTTTA
*
168043 GTTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGATTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
168101 GTTT
1 GTTT
168105 CTTGATGGGT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
57 3 0.05
58 53 0.91
59 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (58 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
Done.