Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006492.1 Kokia drynarioides strain JFW-HI SEQ_121076, 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: 186520
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:386 original size:16 final size:16
Alignment explanation
Indices: 365--396 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
355 GACTATTAAG
365 ACTATTCCTTAACTGT
1 ACTATTCCTTAACTGT
381 ACTATTCCTTAACTGT
1 ACTATTCCTTAACTGT
397 TCCTCTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (16 bp):
ACTATTCCTTAACTGT
Found at i:2723 original size:20 final size:20
Alignment explanation
Indices: 2698--2749 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2688 AGTCTTCAAG
*
2698 GTATCGGTAGAACTGTAGTT
1 GTATCGGTAGAACTGGAGTT
*
2718 GTATCGGTAGAAGTGGAGTT
1 GTATCGGTAGAACTGGAGTT
* *
2738 ATACCGGTAGAA
1 GTATCGGTAGAA
2750 GTCTCACTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (20 bp):
GTATCGGTAGAACTGGAGTT
Found at i:14228 original size:18 final size:18
Alignment explanation
Indices: 14207--14241 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14197 ATCTGAACTT
*
14207 CTAATAGTATCGAAGCTG
1 CTAATAATATCGAAGCTG
*
14225 CTAATAATATCTAAGCT
1 CTAATAATATCGAAGCT
14242 ATTATAAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (18 bp):
CTAATAATATCGAAGCTG
Found at i:15364 original size:29 final size:29
Alignment explanation
Indices: 15322--15380 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
15312 TCTCTCGGTA
*
15322 GAACGCCTTGTGATCTCCCCAAACTATTT
1 GAACGCCTTGTGATATCCCCAAACTATTT
15351 GAACGCCTTGTGATATCCCCAAACTATTT
1 GAACGCCTTGTGATATCCCCAAACTATTT
15380 G
1 G
15381 GGATTCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (29 bp):
GAACGCCTTGTGATATCCCCAAACTATTT
Found at i:16959 original size:24 final size:24
Alignment explanation
Indices: 16927--16975 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
16917 TGATGAGTTG
16927 CATCCGCTTTTAGGCTCAGAAGCA
1 CATCCGCTTTTAGGCTCAGAAGCA
16951 CATCCGCTTTTAGGCTCAGAAGCA
1 CATCCGCTTTTAGGCTCAGAAGCA
16975 C
1 C
16976 CACAGCCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (24 bp):
CATCCGCTTTTAGGCTCAGAAGCA
Found at i:19110 original size:12 final size:12
Alignment explanation
Indices: 19093--19117 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19083 TGAACATGAT
19093 AAGATCAAGGTA
1 AAGATCAAGGTA
19105 AAGATCAAGGTA
1 AAGATCAAGGTA
19117 A
1 A
19118 GTTTTGCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (12 bp):
AAGATCAAGGTA
Found at i:19304 original size:6 final size:6
Alignment explanation
Indices: 19293--19323 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
19283 GATAATCTAT
*
19293 CCTCCC CCTCCC CCTCCC CCTCCC TCTCCC C
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC C
19324 GTTATTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.81, G:0.00, T:0.19
Consensus pattern (6 bp):
CCTCCC
Found at i:20339 original size:282 final size:282
Alignment explanation
Indices: 19846--21692 Score: 3145
Period size: 282 Copynumber: 6.6 Consensus size: 282
19836 GACTAACGCA
* * *
19846 GTGCTGCCAGTTCTTAAAGCAAGGTCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
1 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
19911 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
66 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
*
19976 ACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATGAAGCTGTTCGACAA
131 ACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAAGCTGTTCGACAA
** *
20041 CTTCTAGAATCTAATCCAGCTGAGCCGCCACATTCTGCAGGCTCAATGAATGAATCATCAAAAGA
196 CTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTGCAGGCTCAAGGAATGAATCATCAAAAGA
*
20106 TACAAAAACTGAGACTAATGTG
261 TACGAAAACTGAGACTAATGTG
20128 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
1 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
20193 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
66 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
*
20258 ACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAAGTTGTTCGACAA
131 ACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAAGCTGTTCGACAA
* *
20323 CTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTGCAGTCTTAAGGAATGAATCATCAAAAGA
196 CTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTGCAGGCTCAAGGAATGAATCATCAAAAGA
20388 TACGAAAACTGAGACTAATGTG
261 TACGAAAACTGAGACTAATGTG
20410 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
1 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
*
20475 AGGAGTCAACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
66 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
* *
20540 ACAAATCAAAATTACCAATTGTCGAGGCAAGATCTCTGGAGGATTTACATAAAGCTGTTCGACAA
131 ACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAAGCTGTTCGACAA
*
20605 CTTCCAGAATCTAATCCAGCTGAGCCGCCACATTCTGCAGGCTCAAGGAATGAATCATCAAAAGA
196 CTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTGCAGGCTCAAGGAATGAATCATCAAAAGA
20670 TACGAAAACTGAGACTAATGTG
261 TACGAAAACTGAGACTAATGTG
20692 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
1 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
20757 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
66 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
*
20822 ACAAATCCAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAAGCTGTTCGACAA
131 ACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAAGCTGTTCGACAA
* * * *
20887 CTTCTGGAATCTAATCTATCTCAGCCGCCACATTCTGCAGGCTCAAGGAATGAATCATCAAAAGA
196 CTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTGCAGGCTCAAGGAATGAATCATCAAAAGA
20952 TACGAAAACTGAGACTAATGTG
261 TACGAAAACTGAGACTAATGTG
*
20974 GTGCTGCCTGTTCTTGAAGCAAGACCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
1 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
21039 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
66 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
*
21104 ACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGGTATACATAAAGCTGTTCGACAA
131 ACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAAGCTGTTCGACAA
*
21169 CTTCCGGAATCTAATCCAGCTGAGCCGCTACATTCTGCAGGCTCAAGGAATGAATCATCAAAAGA
196 CTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTGCAGGCTCAAGGAATGAATCATCAAAAGA
*
21234 TATGAAAACTGAGACTAATGTG
261 TACGAAAACTGAGACTAATGTG
**
21256 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGAGGTGGCTTTTAAGCAACTTCATGA
1 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
* * *
21321 AGGAGTCGACGTTGAGGAAGTAATTGTTCCAAGTATGATTGAGAAACAGCCAGATCTTGGAGATA
66 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
* * * * * *** * *
21386 AAAAATCAAAATTACCTGTTGTTGAGGCAAGATCTCTGCAGGACATAGGCAAAGCTATTCAACAA
131 ACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAAGCTGTTCGACAA
** * * *
21451 CTTGTGAAACCTAAT-C--C--A---G-CACATTCTTCAGGCTCAAGGAATGAATCATCAAAAGA
196 CTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTGCAGGCTCAAGGAATGAATCATCAAAAGA
* * * *
21507 TTCGAAGACCGAGACTAATGCG
261 TACGAAAACTGAGACTAATGTG
*
21529 GTGCTGCCAGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
1 GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
* * * *
21594 AGGAGTTGACAATGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGACCATGGAGATA
66 AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
*
21659 ACAAATCAAAATTACCTGTTGTCGAGGCAAGATC
131 ACAAATCAAAATTACCTATTGTCGAGGCAAGATC
21693 AGCAGAAGAT
Statistics
Matches: 1489, Mismatches: 76, Indels: 9
0.95 0.05 0.01
Matches are distributed among these distances:
273 204 0.14
274 1 0.00
277 1 0.00
279 1 0.00
281 1 0.00
282 1281 0.86
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (282 bp):
GTGCTGCCTGTTCTTGAAGCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGA
AGGAGTCGACATTGAGGAAGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGATCTTGGAGATA
ACAAATCAAAATTACCTATTGTCGAGGCAAGATCTCTGGAGGATATACATAAAGCTGTTCGACAA
CTTCCGGAATCTAATCCAGCTGAGCCGCCACATTCTGCAGGCTCAAGGAATGAATCATCAAAAGA
TACGAAAACTGAGACTAATGTG
Found at i:21795 original size:138 final size:138
Alignment explanation
Indices: 21547--21830 Score: 460
Period size: 138 Copynumber: 2.1 Consensus size: 138
21537 AGTTCTTGAA
* * * *
21547 GCAAGATCAGCCGAAGATATTGATTTGGCTTTTAAGCAACTTCATGAAGGAGTTGACAATGAGGA
1 GCAAGATCAGCAGAAGATATTGATTTGGCTTTCAAGCAACTGCATGAAGGAGCTGACAATGAGGA
*
21612 AGTAATTGTTCCGAGTATGATTGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTG
66 AGTAATTGTTCCAAGTATGATTGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTG
21677 TTGTCGAG
131 TTGTCGAG
***
21685 GCAAGATCAGCAGAAGATATTGATTTGGCTTTCAAGCAACTGCATGAAGGAGCTGATGTTGAGGA
1 GCAAGATCAGCAGAAGATATTGATTTGGCTTTCAAGCAACTGCATGAAGGAGCTGACAATGAGGA
* * *
21750 AGTAATTGTTCCAAGTATGATTGAGAAACTGCCAGATCTTGGAGATAACAAATCACAATTACCTG
66 AGTAATTGTTCCAAGTATGATTGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTG
*
21815 TTGTGGAG
131 TTGTCGAG
21823 GCAAGATC
1 GCAAGATC
21831 TCTGAAGGAA
Statistics
Matches: 134, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
138 134 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (138 bp):
GCAAGATCAGCAGAAGATATTGATTTGGCTTTCAAGCAACTGCATGAAGGAGCTGACAATGAGGA
AGTAATTGTTCCAAGTATGATTGAGAAACTGCCAGACCATGGAGATAACAAATCAAAATTACCTG
TTGTCGAG
Found at i:24424 original size:41 final size:41
Alignment explanation
Indices: 24378--24459 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
24368 GTGATGCAGG
24378 AGCTTAATTTTGAAATATTTTATTTTATTTTATAATATTTA
1 AGCTTAATTTTGAAATATTTTATTTTATTTTATAATATTTA
24419 AGCTTAATTTTGAAATATTTTATTTTATTTTATAATATTTA
1 AGCTTAATTTTGAAATATTTTATTTTATTTTATAATATTTA
24460 GTTTAAAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (41 bp):
AGCTTAATTTTGAAATATTTTATTTTATTTTATAATATTTA
Found at i:24435 original size:21 final size:21
Alignment explanation
Indices: 24378--24438 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
24368 GTGATGCAGG
*
24378 AGCTTAATTTTGAAATATTTT
1 AGCTTAATTTTGAAATATTTA
* *
24399 A-TTTTATTTT-ATAATATTTA
1 AGCTTAATTTTGA-AATATTTA
24419 AGCTTAATTTTGAAATATTT
1 AGCTTAATTTTGAAATATTT
24439 TATTTTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.47
21 15 0.47
22 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (21 bp):
AGCTTAATTTTGAAATATTTA
Found at i:28768 original size:31 final size:31
Alignment explanation
Indices: 28717--28798 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 31
28707 ATTAACAACC
* *
28717 AAGTGACTTCAAT-AAAACTTTTGAATAGTT
1 AAGTGACTTAAATGAAAACTTTCGAATAGTT
28747 AAGTGACTTAAATGAAAACTTTCGAATAGTT
1 AAGTGACTTAAATGAAAACTTTCGAATAGTT
* * **
28778 CACTGACCAAAATGAAAACTT
1 AAGTGACTTAAATGAAAACTT
28799 AACCATAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 12 0.27
31 33 0.73
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (31 bp):
AAGTGACTTAAATGAAAACTTTCGAATAGTT
Found at i:34062 original size:21 final size:21
Alignment explanation
Indices: 34038--34088 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
34028 AAGATAATAT
34038 TACCGATACAAGT-ATGACTTC
1 TACCGATACAAGTCATG-CTTC
* *
34059 TACCGAAACATGTCATGCTTC
1 TACCGATACAAGTCATGCTTC
*
34080 TACCAATAC
1 TACCGATAC
34089 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (21 bp):
TACCGATACAAGTCATGCTTC
Found at i:45173 original size:20 final size:20
Alignment explanation
Indices: 45137--45180 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
45127 CCCGAAAATA
*
45137 AAAAATCGAGACTGAGAACC
1 AAAAATCAAGACTGAGAACC
*
45157 AAAAATCAAGA-TCGAGACCC
1 AAAAATCAAGACT-GAGAACC
45177 AAAA
1 AAAA
45181 CTGATCGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.55, C:0.20, G:0.16, T:0.09
Consensus pattern (20 bp):
AAAAATCAAGACTGAGAACC
Found at i:45572 original size:17 final size:19
Alignment explanation
Indices: 45527--45574 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
45517 AGTATTTTAT
45527 TAATTT-ATATTAAAGTGA
1 TAATTTAATATTAAAGTGA
*
45545 TTATCTTAATATTAAA-T-A
1 TAAT-TTAATATTAAAGTGA
45563 TAATTTAATATT
1 TAATTTAATATT
45575 TATCTCGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 8 0.31
18 7 0.27
19 3 0.12
20 8 0.31
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (19 bp):
TAATTTAATATTAAAGTGA
Found at i:46068 original size:29 final size:30
Alignment explanation
Indices: 46015--46071 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
46005 GAATTGGATC
*
46015 AAATCAAAATTTCATGTATAAAATTGCAAA
1 AAATCAAAATTTCATATATAAAATTGCAAA
*
46045 AAATCAAAA-TTCATATATACAATTGCA
1 AAATCAAAATTTCATATATAAAATTGCA
46072 CATTAAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTGCAAA
Found at i:53788 original size:10 final size:10
Alignment explanation
Indices: 53766--53824 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
53756 AATAAAATAT
*
53766 TTTAA-ATAT
1 TTTAATATAA
53775 TTTAATATAA
1 TTTAATATAA
53785 TTTAATATAAA
1 TTTAATAT-AA
** **
53796 ACTAAT-TTT
1 TTTAATATAA
53805 TTTAATATAA
1 TTTAATATAA
53815 TTTAATATAA
1 TTTAATATAA
53825 AAATAATTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
9 9 0.24
10 23 0.61
11 6 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTAATATAA
Found at i:53794 original size:40 final size:40
Alignment explanation
Indices: 53748--53824 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
53738 TGAACTCAAA
*
53748 AATATAAAAATAAAATATTTTAA-ATATTTTAATATAATTT
1 AATATAAAAAT-AAATATTTTAATATAATTTAATATAATTT
* * *
53788 AATATAAAACTAATTTTTTTAATATAATTTAATATAA
1 AATATAAAAATAAATATTTTAATATAATTTAATATAA
53825 AAATAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 9 0.28
40 23 0.72
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (40 bp):
AATATAAAAATAAATATTTTAATATAATTTAATATAATTT
Found at i:53808 original size:30 final size:30
Alignment explanation
Indices: 53774--53832 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
53764 ATTTTAAATA
*
53774 TTTTAATATAATTTAATATAAAACTAATTT
1 TTTTAATATAATTTAATATAAAAATAATTT
53804 TTTTAATATAATTTAATATAAAAATAATT
1 TTTTAATATAATTTAATATAAAAATAATT
53833 ATATTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
TTTTAATATAATTTAATATAAAAATAATTT
Found at i:54202 original size:13 final size:13
Alignment explanation
Indices: 54184--54218 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
54174 TTTTTTTGCC
54184 GTTAACT-TTAATA
1 GTTAACTATTAA-A
54197 GTTAACTATTAAA
1 GTTAACTATTAAA
54210 GTTAACTAT
1 GTTAACTAT
54219 CTTTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (13 bp):
GTTAACTATTAAA
Found at i:54325 original size:19 final size:20
Alignment explanation
Indices: 54291--54336 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
54281 AACTATAAAA
54291 AATAAAAATAAATAAAATTT
1 AATAAAAATAAATAAAATTT
* * *
54311 -ATAAAAATTATTAAAGTTT
1 AATAAAAATAAATAAAATTT
54330 AATAAAA
1 AATAAAA
54337 TGTATAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAAAAATAAATAAAATTT
Found at i:54395 original size:20 final size:20
Alignment explanation
Indices: 54367--54436 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 20
54357 TTAGGATTTT
*
54367 TTATGAAAATCGTAAAAAAA
1 TTATAAAAATCGTAAAAAAA
* **
54387 TTATAAAAAAACGT-AAAATT
1 TTAT-AAAAATCGTAAAAAAA
* *
54407 TTATAAAAATTATGAAAAAAAA
1 TTATAAAAA-T-CGTAAAAAAA
54429 TTATAAAA
1 TTATAAAA
54437 TGCATAAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 5 0.14
20 12 0.32
21 8 0.22
22 12 0.32
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (20 bp):
TTATAAAAATCGTAAAAAAA
Found at i:54641 original size:19 final size:18
Alignment explanation
Indices: 54619--54689 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 18
54609 GTACGATAAT
54619 TTTTATAATATTTTACGAA
1 TTTTATAATATTTTACG-A
*
54638 TTTTAT-ATTTATTTAC-A
1 TTTTATAATAT-TTTACGA
*
54655 TTTCTATAATTTTCTTACGA
1 TTT-TATAATATT-TTACGA
*
54675 TTTTATAAAATTTTA
1 TTTTATAATATTTTA
54690 TAATTTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
17 4 0.09
18 10 0.23
19 26 0.59
20 4 0.09
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTATAATATTTTACGA
Found at i:54760 original size:30 final size:30
Alignment explanation
Indices: 54705--54762 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
54695 TTTTTTCTAA
*
54705 TTTTTAATAAAATTTAAATATTTTTATAGT
1 TTTTTAATAAAATTTAAATAATTTTATAGT
54735 TTTTTAATGAAAATTT-AATAATTTTATA
1 TTTTTAAT-AAAATTTAAATAATTTTATA
54763 ACTTTTATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTTTAATAAAATTTAAATAATTTTATAGT
Found at i:56980 original size:3 final size:3
Alignment explanation
Indices: 56972--56999 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
56962 CACATTTTCT
56972 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
57000 CTACACGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:57841 original size:41 final size:41
Alignment explanation
Indices: 57700--57945 Score: 280
Period size: 41 Copynumber: 5.9 Consensus size: 41
57690 GGTGTATAAA
* * * * *
57700 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGA-AATTGTAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTA-TGAAT
* * *
57741 AAATGGAATACTCATGTCTCGAAATGAGAATGAGATT-TTAATTT
1 -AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAA--T
*
57785 AAGGAAAACTCATGTCTCGAGATGAGAATGAGATTATGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
57826 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* * * * *
57867 AAGGAAGACTCAAGTATCGAAATGAGAATGAGATTTTGATT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* * *
57908 AAGGATGACTCATGTCTTGAGATGAGAATGAGAATATG
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATG
57946 GTTAAAGGAA
Statistics
Matches: 175, Mismatches: 24, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
41 108 0.62
42 35 0.20
43 31 0.18
44 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.27
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
Found at i:57934 original size:123 final size:126
Alignment explanation
Indices: 57700--57945 Score: 338
Period size: 123 Copynumber: 2.0 Consensus size: 126
57690 GGTGTATAAA
* * * * * * *
57700 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATGGAATACTCATGTCTCGAAA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGAATAAATGGAAGACTCAAGTATCGAAA
*
57765 TGAGAATGAGATTTTAATTTAAGGAAAACTCATGTCTCGAGATGAGAATGAGATTATGAAT
66 TGAGAATGAGATTTTAATTTAAGGAAAACTCATGTCTCGAGATGAGAATGAGAATATGAAT
*
57826 AAGGAAGACTCATGTCTCGAGATGAGAATGAG-ATTATGAAT-AA-GGAAGACTCAAGTATCGAA
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGAAAT-TGAATAAATGGAAGACTCAAGTATCGAA
* ** *
57888 ATGAGAATGAGATTTTGA-TTAAGGATGACTCATGTCTTGAGATGAGAATGAGAATATG
65 ATGAGAATGAGATTTTAATTTAAGGAAAACTCATGTCTCGAGATGAGAATGAGAATATG
57946 GTTAAAGGAA
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
123 36 0.34
124 33 0.31
125 4 0.04
126 33 0.31
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.27
Consensus pattern (126 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGAATAAATGGAAGACTCAAGTATCGAAA
TGAGAATGAGATTTTAATTTAAGGAAAACTCATGTCTCGAGATGAGAATGAGAATATGAAT
Found at i:57955 original size:124 final size:127
Alignment explanation
Indices: 57699--57958 Score: 341
Period size: 124 Copynumber: 2.1 Consensus size: 127
57689 TGGTGTATAA
* * * * * * *
57699 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATGGAATACTCATGTCTCGAA
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGAATAAATGGAAGACTCAAGTATCGAA
*
57764 ATGAGAATGAGATTTTAATTTAAGGAAAACTCATGTCTCGAGATGAGAATGAGATTATGAAT
66 ATGAGAATGAGATTTTAATTTAAGGAAAACTCATGTCTCGAGATGAGAATGAGAATATGAAT
*
57826 -AAGGAAGACTCATGTCTCGAGATGAGAATGAG-ATTATGAAT-AA-GGAAGACTCAAGTATCGA
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAAAT-TGAATAAATGGAAGACTCAAGTATCGA
* ** * **
57887 AATGAGAATGAGATTTTGA-TTAAGGATGACTCATGTCTTGAGATGAGAATGAGAATATGGTT
65 AATGAGAATGAGATTTTAATTTAAGGAAAACTCATGTCTCGAGATGAGAATGAGAATATGAAT
57949 AAAGGAAGAC
1 AAAGGAAGAC
57959 ATATGACTCG
Statistics
Matches: 116, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
123 37 0.32
124 42 0.36
125 4 0.03
126 33 0.28
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (127 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGAATAAATGGAAGACTCAAGTATCGAA
ATGAGAATGAGATTTTAATTTAAGGAAAACTCATGTCTCGAGATGAGAATGAGAATATGAAT
Found at i:60075 original size:39 final size:39
Alignment explanation
Indices: 60030--60117 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 39
60020 ACAATGTCTG
* *
60030 GATTTCAAAGC-AAGAGTAAGCCGATGGAGCTTATTTCGA
1 GATTTCAAAGCGAACAG-AAGACGATGGAGCTTATTTCGA
* * **
60069 GATTTCAAAATCGACCAGCGGACGATGGAGCTTATTTCGA
1 GATTTC-AAAGCGAACAGAAGACGATGGAGCTTATTTCGA
60109 GATTTCAAA
1 GATTTCAAA
60118 ATCGACCAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
39 9 0.22
40 29 0.71
41 3 0.07
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (39 bp):
GATTTCAAAGCGAACAGAAGACGATGGAGCTTATTTCGA
Found at i:60099 original size:40 final size:40
Alignment explanation
Indices: 60051--60131 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
60041 AAGAGTAAGC
60051 CGATGGAGCTTATTTCGAGATTTCAAAATCGACCAGCGGA
1 CGATGGAGCTTATTTCGAGATTTCAAAATCGACCAGCGGA
60091 CGATGGAGCTTATTTCGAGATTTCAAAATCGACCAGCGGA
1 CGATGGAGCTTATTTCGAGATTTCAAAATCGACCAGCGGA
60131 C
1 C
60132 AGTGTTGCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (40 bp):
CGATGGAGCTTATTTCGAGATTTCAAAATCGACCAGCGGA
Found at i:64320 original size:214 final size:214
Alignment explanation
Indices: 63951--64378 Score: 829
Period size: 214 Copynumber: 2.0 Consensus size: 214
63941 AAGGAAAAAG
*
63951 GTGCAAATGAGAATTGATTAATTAGAAGGACCAAGTGAGTAAATTGACCTAAAGGATTGCTAGTG
1 GTGCAAAGGAGAATTGATTAATTAGAAGGACCAAGTGAGTAAATTGACCTAAAGGATTGCTAGTG
64016 GGTGGATTTTCATGACAAATATTGATTAATAATAGGATAAGTTAAGGTTAAAAAGATGATTAGTT
66 GGTGGATTTTCATGACAAATATTGATTAATAATAGGATAAGTTAAGGTTAAAAAGATGATTAGTT
*
64081 AAGTTAATTATGAAAGTCTAAGAAATTACAAAAATGTCATTGTATATATATTAAATTAAAGAAAG
131 AAGTTAATTATGAAAGTATAAGAAATTACAAAAATGTCATTGTATATATATTAAATTAAAGAAAG
64146 AAAGATGATAATTTCACAT
196 AAAGATGATAATTTCACAT
*
64165 GTGCAAAGGTGAATTGATTAATTAGAAGGACCAAGTGAGTAAATTGACCTAAAGGATTGCTAGTG
1 GTGCAAAGGAGAATTGATTAATTAGAAGGACCAAGTGAGTAAATTGACCTAAAGGATTGCTAGTG
64230 GGTGGATTTTCATGACAAATATTGATTAATAATAGGATAAGTTAAGGTTAAAAAGATGATTAGTT
66 GGTGGATTTTCATGACAAATATTGATTAATAATAGGATAAGTTAAGGTTAAAAAGATGATTAGTT
64295 AAGTTAATTATGAAAGTATAAGAAATTACAAAAATGTCATTGTATATATATTAAATTAAAGAAAG
131 AAGTTAATTATGAAAGTATAAGAAATTACAAAAATGTCATTGTATATATATTAAATTAAAGAAAG
64360 AAAGATGATAATTTCACAT
196 AAAGATGATAATTTCACAT
64379 TTTCTTTCTT
Statistics
Matches: 211, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
214 211 1.00
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.31
Consensus pattern (214 bp):
GTGCAAAGGAGAATTGATTAATTAGAAGGACCAAGTGAGTAAATTGACCTAAAGGATTGCTAGTG
GGTGGATTTTCATGACAAATATTGATTAATAATAGGATAAGTTAAGGTTAAAAAGATGATTAGTT
AAGTTAATTATGAAAGTATAAGAAATTACAAAAATGTCATTGTATATATATTAAATTAAAGAAAG
AAAGATGATAATTTCACAT
Found at i:64410 original size:3 final size:3
Alignment explanation
Indices: 64396--64432 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
64386 CTTTCTTTCT
*
64396 TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
64433 CTACACGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:65272 original size:41 final size:41
Alignment explanation
Indices: 65131--65398 Score: 282
Period size: 41 Copynumber: 6.6 Consensus size: 41
65121 GGTGTATATA
* * * ** *
65131 AAGGAAGATTCATGTCTCGAGTTGAGCATGA-AAAATTGTAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTA-TGAAT
* * * *
65172 AAATGGAAGATTCATGTCTCGAAATGAGAATGAGATTTTGATTT
1 -AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGA-AT
*
65216 AAGGAAGACTCATGTCTTGAGATGAGAATGAGATTATGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
65257 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* *
65298 AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTG-AT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* * *
65338 GAAGGATGACTCTTGTCTCGAGAT---AA-GA-ATGA-GAAT
1 -AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
*
65374 AAGGAAGACTCTTGTCTCGAGATGA
1 AAGGAAGACTCATGTCTCGAGATGA
65399 CTCTAAGACA
Statistics
Matches: 197, Mismatches: 22, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
35 23 0.12
36 4 0.02
37 2 0.01
38 2 0.01
40 2 0.01
41 97 0.49
42 35 0.18
43 30 0.15
44 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.28
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
Found at i:75185 original size:55 final size:55
Alignment explanation
Indices: 75114--75224 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
75104 CCTAGAAAAA
*
75114 CAAGCTTATTAGTACAAAAGGAACACTTCTTAATATTTGCAAATAAAGTCTCCTT
1 CAAGCTTATTAGTACAAAAGGAACACTTCTTAAAATTTGCAAATAAAGTCTCCTT
75169 CAAGCTTATTAGTACAAAAGGAACACTTCTTAAAATTTGCAAATAAAGTCTCCTT
1 CAAGCTTATTAGTACAAAAGGAACACTTCTTAAAATTTGCAAATAAAGTCTCCTT
75224 C
1 C
75225 CTTAGTACCT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (55 bp):
CAAGCTTATTAGTACAAAAGGAACACTTCTTAAAATTTGCAAATAAAGTCTCCTT
Found at i:77587 original size:10 final size:10
Alignment explanation
Indices: 77572--77601 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
77562 TTCTTTCTTT
77572 TTTTTTTTGA
1 TTTTTTTTGA
77582 TTTTTTTTGA
1 TTTTTTTTGA
77592 TTTTTTTTGA
1 TTTTTTTTGA
77602 ATGCTAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:84330 original size:21 final size:21
Alignment explanation
Indices: 84306--84351 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
84296 TAAAATGCCT
84306 AAACCCAAACCCTTTTAAACC
1 AAACCCAAACCCTTTTAAACC
* *
84327 AAACCCAAACCCTTTTGATCC
1 AAACCCAAACCCTTTTAAACC
84348 AAAC
1 AAAC
84352 TAAGCCTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (21 bp):
AAACCCAAACCCTTTTAAACC
Found at i:86269 original size:14 final size:13
Alignment explanation
Indices: 86254--86278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
86244 AAAAAGAGGA
86254 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
86267 AAAAAAAAGAAA
1 AAAAAAAAGAAA
86279 TAGAAATAGA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:87253 original size:18 final size:18
Alignment explanation
Indices: 87215--87256 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
87205 TCCAAAAAAA
* *
87215 AAAAGAGAAGAGAGAGAG
1 AAAAGAGAAGAAAAAGAG
*
87233 AAAAGAGAAGAAAAAGGG
1 AAAAGAGAAGAAAAAGAG
87251 AAAAGA
1 AAAAGA
87257 AAAAAGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AAAAGAGAAGAAAAAGAG
Found at i:87276 original size:23 final size:23
Alignment explanation
Indices: 87208--87290 Score: 64
Period size: 23 Copynumber: 3.5 Consensus size: 23
87198 CATTGTATCC
*
87208 AAAAAA-AAAAAGAGAAGAGAGAGAG
1 AAAAAAGAAAAAAAGAAGA-A-A-AG
* *
87233 AAAAGAGAAGAAAAAG-GGAAAAG
1 AAAAAAGAA-AAAAAGAAGAAAAG
87256 AAAAAAGAAAAAAAGAAGAAAA-
1 AAAAAAGAAAAAAAGAAGAAAAG
*
87278 ATAAAAATAAAAA
1 A-AAAAAGAAAAA
87291 GGAGAGGTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
22 7 0.15
23 25 0.52
24 1 0.02
25 6 0.12
26 4 0.08
27 5 0.10
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (23 bp):
AAAAAAGAAAAAAAGAAGAAAAG
Found at i:88302 original size:49 final size:49
Alignment explanation
Indices: 88143--88423 Score: 185
Period size: 49 Copynumber: 5.7 Consensus size: 49
88133 AAGACGAGAT
** * ** *
88143 GGGAAAGATTGAAGCCACAACGGTGAATCTTGCACCATA-AGAATGTGAA
1 GGGAAAGATTGAAGCCACAACGGCAAACCTTATACCTTAGAG-ATGTGAA
* * *
88192 -GGAAGAGATTAAAGCCACAATGGCAAATCTTATACCTTAGAGATGT-AA
1 GGGAA-AGATTGAAGCCACAACGGCAAACCTTATACCTTAGAGATGTGAA
* * * *
88240 TGGGAAAGGTTGAAGCCGCAACGGTAAACCTTATACCTTAGTGATGTGAA
1 -GGGAAAGATTGAAGCCACAACGGCAAACCTTATACCTTAGAGATGTGAA
* **** ** * * * *
88290 GGGAAAAATTGAAGTTGTAACGGTGAATCTTATACCCTAAAGATG-AAGA
1 GGGAAAGATTGAAGCCACAACGGCAAACCTTATACCTTAGAGATGTGA-A
* ** * * *
88339 GGGAAAGGTAAAAGCCACAACGGCGAACCTTATACCCTAGAGACGTGAA
1 GGGAAAGATTGAAGCCACAACGGCAAACCTTATACCTTAGAGATGTGAA
* * *
88388 GGGAAAGATTGGAGCCTCAACGAC-AACTCTTATACC
1 GGGAAAGATTGAAGCCACAACGGCAAAC-CTTATACC
88424 CTGAAGATGT
Statistics
Matches: 180, Mismatches: 44, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
48 10 0.06
49 161 0.89
50 9 0.05
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (49 bp):
GGGAAAGATTGAAGCCACAACGGCAAACCTTATACCTTAGAGATGTGAA
Found at i:88319 original size:98 final size:98
Alignment explanation
Indices: 88217--88398 Score: 240
Period size: 98 Copynumber: 1.9 Consensus size: 98
88207 CACAATGGCA
* * * ** * * *
88217 AATCTTATACCTTAGAGATGTAA-TGGGAAAGGTTGAAGCCGCAACGGTAAACCTTATACCTTAG
1 AATCTTATACCCTAAAGATG-AAGAGGGAAAGGTAAAAGCCACAACGGCAAACCTTATACCCTAG
* *
88281 TGATGTGAAGGGAAAAATTGAAGTTGTAACGGTG
65 AGACGTGAAGGGAAAAATTGAAGTTGTAACGGTG
*
88315 AATCTTATACCCTAAAGATGAAGAGGGAAAGGTAAAAGCCACAACGGCGAACCTTATACCCTAGA
1 AATCTTATACCCTAAAGATGAAGAGGGAAAGGTAAAAGCCACAACGGCAAACCTTATACCCTAGA
*
88380 GACGTGAAGGGAAAGATTG
66 GACGTGAAGGGAAAAATTG
88399 GAGCCTCAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 2 0.03
98 69 0.97
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (98 bp):
AATCTTATACCCTAAAGATGAAGAGGGAAAGGTAAAAGCCACAACGGCAAACCTTATACCCTAGA
GACGTGAAGGGAAAAATTGAAGTTGTAACGGTG
Found at i:88930 original size:131 final size:133
Alignment explanation
Indices: 88713--89274 Score: 539
Period size: 131 Copynumber: 4.2 Consensus size: 133
88703 ACCATCGGGT
* * * * * * *
88713 AGATTGAAGGCATCTTCCAATCTTTTACCCTTAATTAAGATAGGCAAATTGAAGTCACATTCGAA
1 AGATTGAA-GCATCGTCCAATCTTTTACCCCTAGTCAAG--GGGCAGATTGAAGTCACATTCCAA
* * *
88778 TCTTTTACCCCTAGTCAAAAGGGGCAGATTGAAGCCACATTCCTATCTTTTACCCCT-AATCCAA
63 TCTTTTACCCCTAATCCAAAGGGGCAGATTGAAGCCACATTCCAATCTTTTACCCCTAAAT-CAA
*
88842 -AGGGGT
127 GAGGGGC
88848 AGATTGAAGC-T-GTCCAATCTTTTACCCCTAGTCAATGGGGCAGATTGAAGTCACCA-TCCAAT
1 AGATTGAAGCATCGTCCAATCTTTTACCCCTAGTCAA-GGGGCAGATTGAAGTCA-CATTCCAAT
* * * * * *
88910 CTTTTACCCCTAATCCAAAGGGGTAGGTTGAAGCCATATTCCTATCTTTTA-CCTTGAATCTAA-
64 CTTTTACCCCTAATCCAAAGGGGCAGATTGAAGCCACATTCCAATCTTTTACCCCTAAATC-AAG
88973 AGGGGC
128 AGGGGC
* * **
88979 AGATTAAAG--TCGTCCAATCTTTTACCCCTAGTTAAGAGGGGCAGATTGAAGTCACCGTCCAAT
1 AGATTGAAGCATCGTCCAATCTTTTACCCCTAG-TCA-AGGGGCAGATTGAAGTCACATTCCAAT
* * *
89042 CTTTTACCCC-GA-CCATA-GGGTAGATTGAAG-C-C-TTCCAATCTTTTACCCCT-AATCAAGA
64 CTTTTACCCCTAATCCAAAGGGGCAGATTGAAGCCACATTCCAATCTTTTACCCCTAAATCAAGA
89100 GGGGC
129 GGGGC
* * * * **
89105 AGATTGAAGCTATCTTCCAATCTTTTACCTCTAATCAAGAGGGACAGATTGAAGCCACATTATAA
1 AGATTGAAGC-ATCGTCCAATCTTTTACCCCTAGTCAAG-GGG-CAGATTGAAGTCACATTCCAA
* *
89170 TATTTTACCCCTAGT-CAAGATGGGGCAGATTGAAGCCATCA-TCCAATCTTTTACCCCTAAATC
63 TCTTTTACCCCTAATCCAA-A-GGGGCAGATTGAAGCCA-CATTCCAATCTTTTACCCCTAAATC
* *
89233 AAGAGAGGT
125 AAGAGGGGC
*
89242 AGATTGAAGCTATCATCCAATCTTTTACCCCTA
1 AGATTGAAGC-ATCGTCCAATCTTTTACCCCTA
89275 AGTTAAGAGG
Statistics
Matches: 360, Mismatches: 42, Indels: 48
0.80 0.09 0.11
Matches are distributed among these distances:
125 2 0.01
126 30 0.08
127 5 0.01
128 6 0.02
129 57 0.16
130 11 0.03
131 106 0.29
132 57 0.16
133 15 0.04
134 3 0.01
135 8 0.02
136 18 0.05
137 42 0.12
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (133 bp):
AGATTGAAGCATCGTCCAATCTTTTACCCCTAGTCAAGGGGCAGATTGAAGTCACATTCCAATCT
TTTACCCCTAATCCAAAGGGGCAGATTGAAGCCACATTCCAATCTTTTACCCCTAAATCAAGAGG
GGC
Found at i:89283 original size:46 final size:45
Alignment explanation
Indices: 88713--89300 Score: 443
Period size: 45 Copynumber: 13.3 Consensus size: 45
88703 ACCATCGGGT
* * * **
88713 AGATTGAAGGC-ATCTTCCAATCTTTTACCCTTAATTAAGATAGGC
1 AGATTGAA-GCTATCATCCAATCTTTTACCCCTAATCAAGAGGGGC
* * * *
88758 AAATTGAAG-TCA-CATTCGAATCTTTTACCCCTAGTCAAAAGGGGC
1 AGATTGAAGCT-ATCA-TCCAATCTTTTACCCCTAATCAAGAGGGGC
* * *
88803 AGATTGAAGCCA-CATTCCTATCTTTTACCCCTAATCCAA-AGGGGT
1 AGATTGAAGCTATCA-TCCAATCTTTTACCCCTAAT-CAAGAGGGGC
* * *
88848 AGATTGAAGC--T-GTCCAATCTTTTACCCCTAGTCAA-TGGGGC
1 AGATTGAAGCTATCATCCAATCTTTTACCCCTAATCAAGAGGGGC
* *
88889 AGATTGAAG-TCACCATCCAATCTTTTACCCCTAATCCAA-AGGGGT
1 AGATTGAAGCT-ATCATCCAATCTTTTACCCCTAAT-CAAGAGGGGC
* * * *
88934 AGGTTGAAGCCAT-ATTCCTATCTTTTA-CCTTGAATCTAA-AGGGGC
1 AGATTGAAGCTATCA-TCCAATCTTTTACCCCT-AATC-AAGAGGGGC
* * * *
88979 AGATTAAAG---TCGTCCAATCTTTTACCCCTAGTTAAGAGGGGC
1 AGATTGAAGCTATCATCCAATCTTTTACCCCTAATCAAGAGGGGC
* * * * * *
89021 AGATTGAAG-TCACCGTCCAATCTTTTACCCC-GA-CCATA-GGGT
1 AGATTGAAGCT-ATCATCCAATCTTTTACCCCTAATCAAGAGGGGC
*
89063 AGATTGAAGC---CTTCCAATCTTTTACCCCTAATCAAGAGGGGC
1 AGATTGAAGCTATCATCCAATCTTTTACCCCTAATCAAGAGGGGC
* * *
89105 AGATTGAAGCTATCTTCCAATCTTTTACCTCTAATCAAGAGGGAC
1 AGATTGAAGCTATCATCCAATCTTTTACCCCTAATCAAGAGGGGC
* ** * *
89150 AGATTGAAGCCA-CATTATAATATTTTACCCCTAGTCAAGATGGGGC
1 AGATTGAAGCTATCA-TCCAATCTTTTACCCCTAATCAAGA-GGGGC
* * *
89196 AGATTGAAGCCATCATCCAATCTTTTACCCCTAAATCAAGAGAGGT
1 AGATTGAAGCTATCATCCAATCTTTTACCCCT-AATCAAGAGGGGC
* *
89242 AGATTGAAGCTATCATCCAATCTTTTACCCCTAAGTTAAGAGGGTC
1 AGATTGAAGCTATCATCCAATCTTTTACCCCTAA-TCAAGAGGGGC
* *
89288 ATATTGAAACTAT
1 AGATTGAAGCTAT
89301 TATCTCACTC
Statistics
Matches: 436, Mismatches: 74, Indels: 65
0.76 0.13 0.11
Matches are distributed among these distances:
39 17 0.04
40 1 0.00
41 21 0.05
42 71 0.16
43 5 0.01
44 27 0.06
45 200 0.46
46 85 0.19
47 9 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (45 bp):
AGATTGAAGCTATCATCCAATCTTTTACCCCTAATCAAGAGGGGC
Found at i:89754 original size:48 final size:49
Alignment explanation
Indices: 89672--89768 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 49
89662 TCAAACCCCA
* **
89672 ATCTTCCTGATGAGATACAAAGAAGTGGATCAAAATGATGAAGC-AAAC
1 ATCTTCCTGATGAGATACAAAGAAGTGGACCAAAACAATGAAGCGAAAC
* * * *
89720 ATCTTCTTGATGAGATATAGAGAAGTGTACCAAAACAATGAAGCGAAAC
1 ATCTTCCTGATGAGATACAAAGAAGTGGACCAAAACAATGAAGCGAAAC
89769 TCAATGTGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
48 37 0.90
49 4 0.10
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (49 bp):
ATCTTCCTGATGAGATACAAAGAAGTGGACCAAAACAATGAAGCGAAAC
Found at i:89885 original size:48 final size:48
Alignment explanation
Indices: 89795--89886 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
89785 TTCAAACCCC
** * **
89795 CATCTTCCTAATGAGATATAGGGAAGTGAATCAAAATGATGAAGTGGT
1 CATCTTCCTAATGAGATATAGAAAAGTGAACCAAAACAATGAAGTGGT
* *
89843 CATCTTCCTTATGAGATATAGAAAAGTGGACCAAAACAATGAAG
1 CATCTTCCTAATGAGATATAGAAAAGTGAACCAAAACAATGAAG
89887 CGAAGCTCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (48 bp):
CATCTTCCTAATGAGATATAGAAAAGTGAACCAAAACAATGAAGTGGT
Found at i:89935 original size:76 final size:76
Alignment explanation
Indices: 89843--90041 Score: 317
Period size: 76 Copynumber: 2.6 Consensus size: 76
89833 ATGAAGTGGT
* *
89843 CATCTTCCTTATGAGATATAGAAAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAA
1 CATCTTCCTTATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAA
89908 CTTTAAACCCC
66 CTTTAAACCCC
* *
89919 CATCTTCTTTATGAGATACAGAGAAGTGGACCAAAACAATGAATCGAAGCTCAATGTGAGTGAAA
1 CATCTTCCTTATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAA
*
89984 CTTTAAACTCC
66 CTTTAAACCCC
* * * *
89995 CATCTTCCTGATAAGATACAGAGAAGTGAATCAAAACAATGAAGCGA
1 CATCTTCCTTATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGA
90042 TGATCTTCTT
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 112 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (76 bp):
CATCTTCCTTATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAA
CTTTAAACCCC
Found at i:89961 original size:124 final size:124
Alignment explanation
Indices: 89622--89954 Score: 479
Period size: 124 Copynumber: 2.7 Consensus size: 124
89612 ACGATGGAGC
* * * *
89622 GGACCAAAAAAATGAAGCGAAGCTCAATGTGAGTCAAACTTCAAACCCCAATCTTCCTGATGAGA
1 GGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCCATCTTCCTAATGAGA
* *
89687 TACAAAGAAGTGGATCAAAATGATGAAGCAAACATCTTCTTGATGAGATATAGAGAAGT
66 TACAGAGAAGTGGATCAAAATGATGAAGCAAACATCTTCTTGATGAGATATAGAAAAGT
* *
89746 GTACCAAAACAATGAAGCGAAACTCAATGTGAGTGAAACTTCAAACCCCCATCTTCCTAATGAGA
1 GGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCCATCTTCCTAATGAGA
* * * ****
89811 TATAGGGAAGTGAATCAAAATGATGAAGTGGTCATCTTCCTT-ATGAGATATAGAAAAGT
66 TACAGAGAAGTGGATCAAAATGATGAAGCAAACATCTT-CTTGATGAGATATAGAAAAGT
* * *
89870 GGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTTAAACCCCCATCTTCTTTATGAGA
1 GGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCCATCTTCCTAATGAGA
*
89935 TACAGAGAAGTGGACCAAAA
66 TACAGAGAAGTGGATCAAAA
89955 CAATGAATCG
Statistics
Matches: 184, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
124 181 0.98
125 3 0.02
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (124 bp):
GGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCCATCTTCCTAATGAGA
TACAGAGAAGTGGATCAAAATGATGAAGCAAACATCTTCTTGATGAGATATAGAAAAGT
Found at i:90072 original size:200 final size:200
Alignment explanation
Indices: 89719--90153 Score: 613
Period size: 200 Copynumber: 2.2 Consensus size: 200
89709 ATGAAGCAAA
* *
89719 CATCTTCTTGATGAGATATAGAGAAGTGTACCAAAACAATGAAGCGAAACTCAATGTGAGTGAAA
1 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAACTCAATGTGAGTGAAA
* * * ** * *
89784 CTTCAAACCCCCATCTTCCTAATGAGATATAGGGAAGTGAATCAAAATGATGAAGTGGTCATCTT
66 CTTCAAACCCCCATCTTCCTAATAAGATACAGAGAAGTGAATCAAAACAATGAAGCGATCATCTT
* * *
89849 CCTTATGAGATATAGAAAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAACTTTAA
131 CCTTATGAGATACAGAAAAGTGGACCAAAACAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAA
89914 ACCCC
196 ACCCC
* * *
89919 CATCTTCTTTATGAGATACAGAGAAGTGGACCAAAACAATGAATCGAAGCTCAATGTGAGTGAAA
1 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAACTCAATGTGAGTGAAA
* * * *
89984 CTTTAAACTCCCATCTTCCTGATAAGATACAGAGAAGTGAATCAAAACAATGAAGCGATGATCTT
66 CTTCAAACCCCCATCTTCCTAATAAGATACAGAGAAGTGAATCAAAACAATGAAGCGATCATCTT
* * *
90049 -CTTAATGAGATACAGAGAAGTGGACTAAAACAATGAAGCAAAGCTCAATGTGTGTGAAACTTCA
131 CCTT-ATGAGATACAGAAAAGTGGACCAAAACAATGAAGCAAAGCTCAATGTGAGTGAAACTTCA
*
90113 AACCCT
195 AACCCC
* * *
90119 CATTTTCCTGATGAGATACAGA-AAGTGGATCAAAA
1 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAAA
90154 TGATGAAGTA
Statistics
Matches: 207, Mismatches: 27, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
199 15 0.07
200 192 0.93
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (200 bp):
CATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAACTCAATGTGAGTGAAA
CTTCAAACCCCCATCTTCCTAATAAGATACAGAGAAGTGAATCAAAACAATGAAGCGATCATCTT
CCTTATGAGATACAGAAAAGTGGACCAAAACAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAA
ACCCC
Found at i:90214 original size:123 final size:122
Alignment explanation
Indices: 89919--90510 Score: 715
Period size: 122 Copynumber: 4.8 Consensus size: 122
89909 TTTAAACCCC
* *
89919 CATCTTCTTTATGAGATACAGAGAAGTGGACCAAAACAATGAATCGAAGCTCAATGTGAGTGAAA
1 CATCTTCTTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAA
* * *
89984 CTTTAAACTCCCATCTTCCTGATAAGATACAGAGAAGTGAATCAAAACAATGAAGCGAT
66 CTTCAAAC-CCCATCTTCCTGATGAGATACAGAGAAGTGGATC-AAACAATGAAGCGAT
* * * *
90043 GATCTTCTTAATGAGATACAGAGAAGTGGACTAAAACAATGAAGCAAAGCTCAATGTGTGTGAAA
1 CATCTTCTTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAA
* **
90108 CTTCAAACCCTCATTTTCCTGATGAGATACAGA-AAGTGGATCAAA-ATGATGAAGTAAT
66 CTTCAAACCC-CATCTTCCTGATGAGATACAGAGAAGTGGATCAAACA--ATGAAGCGAT
* * * * * * *
90166 CATCTTCTTGATAAGATACAGAGAAGTGGACCAAAATAGTGAATCAAAGCTCAATATGAGTGAAA
1 CATCTTCTTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAA
* * ** *
90231 CTTCAAACCCCATCTTCCTGATGAGATATAAAGAAGTGGATCAAACAACAAAGCGTT
66 CTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAACAATGAAGCGAT
* * * * * * * *
90288 CATATTCTTGATGAGATATAAAGAAGTGAACCAAAACAGTGAAGCGAAGCTCAGTATGAGTGAAA
1 CATCTTCTTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAA
* * *
90353 CTTCAAACCCCATCTTCTTGATGAGATATAGAGAAGTGGATCAAACAATGAAGGGGA-
66 CTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAACAATGAA-GCGAT
* * * *
90410 CATATTCTTAATGAGATACAGAGAAGTGGACCAAAACAATGAAACGGAGCTCAATAG-GAGTCAA
1 CATCTTCTTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAAT-GTGAGTGAA
* * *
90474 ACTCCAAACCCCATCTTCCTAATGAAATACAGAGAAG
65 ACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
90511 AGGACCAAGA
Statistics
Matches: 402, Mismatches: 59, Indels: 16
0.84 0.12 0.03
Matches are distributed among these distances:
121 1 0.00
122 216 0.54
123 98 0.24
124 87 0.22
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.23
Consensus pattern (122 bp):
CATCTTCTTAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAAA
CTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAACAATGAAGCGAT
Found at i:92283 original size:30 final size:29
Alignment explanation
Indices: 92257--92398 Score: 114
Period size: 30 Copynumber: 4.8 Consensus size: 29
92247 AGAAATTGTT
92257 TTTTGGCCCTCAAACTATCCAAAAATTATG
1 TTTTGGCCCTCAAACT-TCCAAAAATTATG
* *
92287 TTTTGACTCC-CAAACTTCCAAAATTTCAT-
1 TTTTGGC-CCTCAAACTTCCAAAAATT-ATG
* ** *
92316 ATTTGATCCTCGAACTTCCCAAAAATT-TAG
1 TTTTGGCCCTCAAACTT-CCAAAAATTAT-G
*
92346 ATTTGG-CCTCCAAACTTTCCAAAAATTATG
1 TTTTGGCCCT-CAAAC-TTCCAAAAATTATG
92376 TTTTGGCCCT-AAACTTTCCAAAA
1 TTTTGGCCCTCAAAC-TTCCAAAA
92399 TTTCATTTTT
Statistics
Matches: 93, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
28 3 0.03
29 36 0.39
30 46 0.49
31 8 0.09
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (29 bp):
TTTTGGCCCTCAAACTTCCAAAAATTATG
Found at i:92414 original size:29 final size:28
Alignment explanation
Indices: 92256--92415 Score: 106
Period size: 29 Copynumber: 5.4 Consensus size: 28
92246 TAGAAATTGT
* * *
92256 TTTTTGGCCCTCAAACTATCCAAAAATTA
1 TTTTTGACCCT-AAACTTTCCAAAATTTA
*
92285 TGTTTTGACTCCCAAAC-TTCCAAAATTTCA
1 T-TTTTGAC-CCTAAACTTTCCAAAATTT-A
* * * *
92315 TATTTGATCCTCGAACTTCCCAAAAATTTA
1 TTTTTGACCCT-AAACTTTCC-AAAATTTA
** * * *
92345 GATTTGGCCTCCAAACTTTCCAAAAATTA
1 TTTTTGACC-CTAAACTTTCCAAAATTTA
*
92374 TGTTTTGGCCCTAAACTTTCCAAAATTTCA
1 T-TTTTGACCCTAAACTTTCCAAAATTT-A
92404 TTTTTGACCCTA
1 TTTTTGACCCTA
92416 TTTTTTTCCC
Statistics
Matches: 101, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
28 2 0.02
29 51 0.50
30 38 0.38
31 10 0.10
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (28 bp):
TTTTTGACCCTAAACTTTCCAAAATTTA
Found at i:92462 original size:21 final size:20
Alignment explanation
Indices: 92415--92462 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
92405 TTTTGACCCT
**
92415 ATTTTTTTCCCCTTATTTTC
1 ATTTTTTTCCCCAAATTTTC
*
92435 ACATTTTTTCCCCAAAATTTTC
1 A-TTTTTTTCCCC-AAATTTTC
92457 ATTTTT
1 ATTTTT
92463 GTTTTAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 14 0.64
22 7 0.32
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTTTCCCCAAATTTTC
Found at i:93782 original size:79 final size:79
Alignment explanation
Indices: 93689--93849 Score: 322
Period size: 79 Copynumber: 2.0 Consensus size: 79
93679 TTTTAAAGTC
93689 AGATTGTATTACCTATTTATTTAAAACCTATAAAACCAATATTATAAAATTTAAAATACAAGTTT
1 AGATTGTATTACCTATTTATTTAAAACCTATAAAACCAATATTATAAAATTTAAAATACAAGTTT
93754 ATTTTCTCGACTTT
66 ATTTTCTCGACTTT
93768 AGATTGTATTACCTATTTATTTAAAACCTATAAAACCAATATTATAAAATTTAAAATACAAGTTT
1 AGATTGTATTACCTATTTATTTAAAACCTATAAAACCAATATTATAAAATTTAAAATACAAGTTT
93833 ATTTTCTCGACTTT
66 ATTTTCTCGACTTT
93847 AGA
1 AGA
93850 CTCTAAAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (79 bp):
AGATTGTATTACCTATTTATTTAAAACCTATAAAACCAATATTATAAAATTTAAAATACAAGTTT
ATTTTCTCGACTTT
Found at i:99042 original size:18 final size:17
Alignment explanation
Indices: 99017--99050 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
99007 TATTTCTTTT
99017 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
99034 CTAATCTTTTATTGATT
1 CTAA-CTTTTATTGATT
99051 TTCTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:104624 original size:13 final size:12
Alignment explanation
Indices: 104606--104658 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
104596 GTCATTGCAA
104606 TTTTTCTGTTAAT
1 TTTTTCT-TTAAT
*
104619 TTTTTCTTTTA-
1 TTTTTCTTTAAT
*
104630 TTTTACTTTAAT
1 TTTTTCTTTAAT
*
104642 TTGTTTCTTTAGT
1 TT-TTTCTTTAAT
104655 TTTT
1 TTTT
104659 GCAGGAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
11 9 0.27
12 7 0.21
13 17 0.52
ACGTcount: A:0.13, C:0.08, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTAAT
Found at i:104640 original size:23 final size:25
Alignment explanation
Indices: 104605--104651 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
104595 TGTCATTGCA
*
104605 ATTTTTCTGTTAATTT-TTTCTTTT
1 ATTTTACTGTTAATTTGTTTCTTTT
104629 ATTTTACT-TTAATTTGTTTCTTT
1 ATTTTACTGTTAATTTGTTTCTTT
104652 AGTTTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (25 bp):
ATTTTACTGTTAATTTGTTTCTTTT
Found at i:106446 original size:14 final size:15
Alignment explanation
Indices: 106422--106473 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
106412 ATTGAAACAG
106422 AAGAAGAGAAAAGAA
1 AAGAAGAGAAAAGAA
106437 AAGAAG-GAAAAGAA
1 AAGAAGAGAAAAGAA
** *
106451 GGGAAGAAAAAAGAAA
1 AAGAAGAGAAAAG-AA
106467 AAGAAGA
1 AAGAAGA
106474 AGAAGTTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 12 0.40
15 11 0.37
16 7 0.23
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
AAGAAGAGAAAAGAA
Found at i:106468 original size:21 final size:22
Alignment explanation
Indices: 106432--106472 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
106422 AAGAAGAGAA
*
106432 AAGAAAAGAAGGAAAAGAAGGG
1 AAGAAAAGAAGAAAAAGAAGGG
106454 AAGAAAA-AAGAAAAAGAAG
1 AAGAAAAGAAGAAAAAGAAG
106473 AAGAAGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
AAGAAAAGAAGAAAAAGAAGGG
Found at i:106473 original size:24 final size:24
Alignment explanation
Indices: 106415--106476 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
106405 TATGGGTATT
*
106415 GAAACAGAAGAAGAGAAAAGAAAA
1 GAAAAAGAAGAAGAGAAAAGAAAA
* *
106439 GAAGGAA-AAGAAGGGAAGAA-AAAA
1 GAA-AAAGAAGAAGAGAA-AAGAAAA
106463 GAAAAAGAAGAAGA
1 GAAAAAGAAGAAGA
106477 AGTTGTTCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
23 2 0.07
24 25 0.83
25 3 0.10
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (24 bp):
GAAAAAGAAGAAGAGAAAAGAAAA
Found at i:115179 original size:16 final size:16
Alignment explanation
Indices: 115158--115190 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
115148 GAAATTTGTA
*
115158 TGTTAAAGGACTAAAT
1 TGTTAAAGGAATAAAT
115174 TGTTAAAGGAATAAAT
1 TGTTAAAGGAATAAAT
115190 T
1 T
115191 TATAAGGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.33
Consensus pattern (16 bp):
TGTTAAAGGAATAAAT
Found at i:116876 original size:22 final size:22
Alignment explanation
Indices: 116850--116896 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
116840 GATAAACAAA
116850 GTAAGAATGATGAATTATAAAT
1 GTAAGAATGATGAATTATAAAT
116872 GTAAGAATGATGAATTATAAAT
1 GTAAGAATGATGAATTATAAAT
116894 GTA
1 GTA
116897 TATATTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (22 bp):
GTAAGAATGATGAATTATAAAT
Found at i:117561 original size:16 final size:16
Alignment explanation
Indices: 117536--117566 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
117526 CTCCATTTAA
117536 CATCAAACATACCAAC
1 CATCAAACATACCAAC
*
117552 CATCACACATACCAA
1 CATCAAACATACCAA
117567 TGAAATATTG
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:0.48, C:0.39, G:0.00, T:0.13
Consensus pattern (16 bp):
CATCAAACATACCAAC
Found at i:118007 original size:34 final size:34
Alignment explanation
Indices: 117959--118077 Score: 139
Period size: 34 Copynumber: 3.5 Consensus size: 34
117949 ACACGGGTAA
* * *
117959 CCATTCAACACACCAAATGCTCATAAAAGCTAGT
1 CCATCCAACACACCAAATGCTCGTAAGAGCTAGT
* * * *
117993 CCAACCAACACACCATATGCCCGTAAGAGCTAAT
1 CCATCCAACACACCAAATGCTCGTAAGAGCTAGT
* * * *
118027 CCCTCCAACACACCAAATGTTTGTAAGAGGTAGT
1 CCATCCAACACACCAAATGCTCGTAAGAGCTAGT
118061 CCATCCAACACACCAAA
1 CCATCCAACACACCAAA
118078 ACACTGTAAC
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.39, C:0.33, G:0.11, T:0.18
Consensus pattern (34 bp):
CCATCCAACACACCAAATGCTCGTAAGAGCTAGT
Found at i:133297 original size:46 final size:46
Alignment explanation
Indices: 133238--133333 Score: 165
Period size: 46 Copynumber: 2.1 Consensus size: 46
133228 AAATTACTAG
* * *
133238 TACACCACATGATAACTACAATATTTTCTAAGTGCATAACTAGTAT
1 TACACCACATGATAACTACAATATTGTCCAAATGCATAACTAGTAT
133284 TACACCACATGATAACTACAATATTGTCCAAATGCATAACTAGTAT
1 TACACCACATGATAACTACAATATTGTCCAAATGCATAACTAGTAT
133330 TACA
1 TACA
133334 AATTAGTAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (46 bp):
TACACCACATGATAACTACAATATTGTCCAAATGCATAACTAGTAT
Found at i:133370 original size:59 final size:59
Alignment explanation
Indices: 133278--133392 Score: 212
Period size: 59 Copynumber: 1.9 Consensus size: 59
133268 AGTGCATAAC
*
133278 TAGTATTACACCACATGATAACTACAATATTGTCCAAATGCATAACTAGTATTACAAAT
1 TAGTAGTACACCACATGATAACTACAATATTGTCCAAATGCATAACTAGTATTACAAAT
*
133337 TAGTAGTACACCACATGATAACTACAATATTGTCCAAGTGCATAACTAGTATTACA
1 TAGTAGTACACCACATGATAACTACAATATTGTCCAAATGCATAACTAGTATTACA
133393 CCATATAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (59 bp):
TAGTAGTACACCACATGATAACTACAATATTGTCCAAATGCATAACTAGTATTACAAAT
Found at i:133405 original size:19 final size:19
Alignment explanation
Indices: 133378--133414 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
133368 GTCCAAGTGC
*
133378 ATAACTAGTATTACACCAT
1 ATAACTAGTACTACACCAT
*
133397 ATAATTAGTACTACACCA
1 ATAACTAGTACTACACCA
133415 CATTAAAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (19 bp):
ATAACTAGTACTACACCAT
Found at i:153876 original size:7 final size:7
Alignment explanation
Indices: 153864--153896 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
153854 CATTCAACAA
153864 TTTTTTC
1 TTTTTTC
153871 TTTTTT-
1 TTTTTTC
153877 TCTTTTTC
1 T-TTTTTC
153885 TTTTTTC
1 TTTTTTC
153892 TTTTT
1 TTTTT
153897 CCCATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 22 0.92
8 1 0.04
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:153888 original size:13 final size:14
Alignment explanation
Indices: 153865--153897 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
153855 ATTCAACAAT
153865 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
153879 TTTTTC-TTTTTTC
1 TTTTTCTTTTTTTC
153892 TTTTTC
1 TTTTTC
153898 CCATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:153904 original size:21 final size:21
Alignment explanation
Indices: 153864--153904 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
153854 CATTCAACAA
** *
153864 TTTTTTCTTTTTTTCTTTTTC
1 TTTTTTCTTTTTCCCATTTTC
153885 TTTTTTCTTTTTCCCATTTT
1 TTTTTTCTTTTTCCCATTTT
153905 TATAAATGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTCTTTTTCCCATTTTC
Found at i:160980 original size:30 final size:30
Alignment explanation
Indices: 160923--161280 Score: 212
Period size: 29 Copynumber: 12.3 Consensus size: 30
160913 CCAAAATCTT
* * *
160923 ATTTTAACCCTTAAACTTTTC-AAAATTAT
1 ATTTTAACCCCTAAACTTCTCTAAAATTAC
160952 ATTTTAACCCCTAAACTTCTCTAAAATTAC
1 ATTTTAACCCCTAAACTTCTCTAAAATTAC
* *
160982 ATTTTAACTACC-AAACTT-TCCTAAAATCAC
1 ATTTTAAC-CCCTAAACTTCT-CTAAAATTAC
* *
161012 ATTTTAACCCCTAAACTTC-CCAAAATCAC
1 ATTTTAACCCCTAAACTTCTCTAAAATTAC
* * * * *
161041 ATTTTGACACC-AAAATTTTCCAAAAATTAC
1 ATTTTAACCCCTAAACTTCT-CTAAAATTAC
** * * * *
161071 ATTTTTGCCCTTGAACTTC-CAAAAATCAC
1 ATTTTAACCCCTAAACTTCTCTAAAATTAC
* * *
161100 ATTTT--TCCCTCGAAC-T-TCAAAAATTCAC
1 ATTTTAACCCCT-AAACTTCTCTAAAATT-AC
* *
161128 ATTTT-ACCCATAAACTTCT-AAAAATTAC
1 ATTTTAACCCCTAAACTTCTCTAAAATTAC
** *
161156 ATTTTTGCCCCTAAACTTC-CAAAAATTAC
1 ATTTTAACCCCTAAACTTCTCTAAAATTAC
** * * *
161185 ATTTTTGCCTC-GAACTTCT-TAAAAATCAC
1 ATTTTAACCCCTAAACTTCTCT-AAAATTAC
* * *
161214 ATTTTTA-GCCTAAGCTT-TCTCAAAATTAC
1 ATTTTAACCCCTAAACTTCTCT-AAAATTAC
*
161243 ATTTTTACCCCTAAACTT-TCTAAAATTAC
1 ATTTTAACCCCTAAACTTCTCTAAAATTAC
161272 ATTTTAACC
1 ATTTTAACC
161281 TTGAACTCTC
Statistics
Matches: 265, Mismatches: 43, Indels: 42
0.76 0.12 0.12
Matches are distributed among these distances:
27 11 0.04
28 34 0.13
29 143 0.54
30 71 0.27
31 6 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
ATTTTAACCCCTAAACTTCTCTAAAATTAC
Found at i:161268 original size:58 final size:58
Alignment explanation
Indices: 160934--161276 Score: 235
Period size: 59 Copynumber: 5.9 Consensus size: 58
160924 TTTTAACCCT
* * * *
160934 TAAACTTTTC-AAAATTATATTTTAACCCCTAAACTTCTCTAAAATTACATTTTAACTA-CC
1 TAAACTTTCCAAAAATTACATTTTTACCCCTAAACTT-TCTAAAATCACATTTT---TAGCC
* * * * * * *
160994 -AAACTTTCCTAAAATCACATTTTAACCCCTAAACTTCCCAAAATCACATTTTGACACC
1 TAAACTTTCCAAAAATTACATTTTTACCCCTAAACTTTCTAAAATCACATTTTTA-GCC
* * * * * * * *
161052 AAAATTTTCCAAAAATTACATTTTTGCCCTTGAACTTCCAAAAATCACATTTTT-CCC
1 TAAACTTTCCAAAAATTACATTTTTACCCCTAAACTTTCTAAAATCACATTTTTAGCC
* * *
161109 TCGAAC-TT-CAAAAATTCACA-TTTTACCCATAAAC-TTCTAAAAATTACATTTTT-GCCCC
1 T-AAACTTTCCAAAAATT-ACATTTTTACCCCTAAACTTTCT-AAAATCACATTTTTAG--CC
* * *
161167 TAAAC-TTCCAAAAATTACATTTTTGCCTC-GAAC-TTCTTAAAAATCACATTTTTAGCC
1 TAAACTTTCCAAAAATTACATTTTTACCCCTAAACTTTC-T-AAAATCACATTTTTAGCC
* *
161224 TAAGCTTTCTC-AAAATTACATTTTTACCCCTAAACTTTCTAAAATTACATTTT
1 TAAACTTTC-CAAAAATTACATTTTTACCCCTAAACTTTCTAAAATCACATTTT
161277 AACCTTGAAC
Statistics
Matches: 228, Mismatches: 38, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
55 2 0.01
56 33 0.14
57 27 0.12
58 68 0.30
59 71 0.31
60 27 0.12
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (58 bp):
TAAACTTTCCAAAAATTACATTTTTACCCCTAAACTTTCTAAAATCACATTTTTAGCC
Found at i:161287 original size:87 final size:86
Alignment explanation
Indices: 160961--161287 Score: 290
Period size: 87 Copynumber: 3.8 Consensus size: 86
160951 TATTTTAACC
* * * * *
160961 CCTAAAC-TTCTCTAAAATTACATTTTAACTACC-AAACTTTCCTAAAATCACATTTTAACCCCT
1 CCTAAACTTTCTCAAAAATTACATTTTTAC-CCCTAAAC-TTCCAAAAATCACATTTTAACCTC-
* * *
161024 AAACTTCCCAAAATCACATTTTGACA
63 GAACTT-CAAAAATCACATTTTTA-A
* * * * * **
161050 CCAAAATTTTC-CAAAAATTACATTTTTGCCCTTGAACTTCCAAAAATCACATTTTTCCCTCGAA
1 CCTAAACTTTCTCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTAACCTCGAA
*
161114 CTTCAAAAATTCACA-TTTTAC
66 CTTCAAAAA-TCACATTTTTAA
* * **
161135 CCATAAAC-TTCT-AAAAATTACATTTTTGCCCCTAAACTTCCAAAAATTACATTTTTGCCTCGA
1 CC-TAAACTTTCTCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTAACCTCGA
*
161198 ACTTCTTAAAAATCACATTTTTAG
65 ACTTC--AAAAATCACATTTTTAA
* * * * *
161222 CCTAAGCTTTCTC-AAAATTACATTTTTACCCCTAAACTTTCTAAAATTACATTTTAACCTTGAA
1 CCTAAACTTTCTCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTAACCTCGAA
161286 CT
66 CT
161288 CTCTGAAACT
Statistics
Matches: 198, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
85 57 0.29
86 21 0.11
87 73 0.37
88 21 0.11
89 23 0.12
90 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (86 bp):
CCTAAACTTTCTCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTAACCTCGAA
CTTCAAAAATCACATTTTTAA
Found at i:162009 original size:23 final size:23
Alignment explanation
Indices: 161983--162037 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
161973 TCGAAGACCA
161983 AAATGTTTTTTAAAACGGACTTT
1 AAATGTTTTTTAAAACGGACTTT
162006 AAATGTTTTTTAAAACGGACTTT
1 AAATGTTTTTTAAAACGGACTTT
162029 AAATGTTTT
1 AAATGTTTT
162038 ATGGTGATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (23 bp):
AAATGTTTTTTAAAACGGACTTT
Found at i:163371 original size:150 final size:149
Alignment explanation
Indices: 163036--163689 Score: 767
Period size: 150 Copynumber: 4.4 Consensus size: 149
163026 TGATTAAAAC
* * ** * *
163036 AAAATCTCTACTTTACTTCAAAATAAAAACTTTTATTTCAAAATAGTT-AAAAAATCAAAAATTT
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
** * * * **
163100 GTTTAAAAATTTAAACACTTTCTTTAAAATCACTGAAAAACAGT-TTTTTAATTTTTAGAAACCT
66 GTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACA-TATTTTT-ATTTTTAAAAATAT
*
163164 AAACTTTCTTTATTTTTTAATA
129 AAACTTT-TTTTTTTTTTAATA
* *
163186 AAAAT-ATTACTTTACTTAAAAATCCAAAATTTTATTTCGAAATAGTTAAAAAAA-CAAAA-TTT
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
163248 AGTTTAAAAATTTAAATTTTTTTTCTTTAAAATCACT-AAAAACATATTTTTATTTTTTAAAAAT
66 -GTTTAAAAATTTAAA--CTTTTTCTTTAAAATAACTAAAAAACATATTTTTA-TTTTTAAAAAT
*
163312 CTAAACTTTTTTTTTTTTTAATA
127 ATAAACTTTTTTTTTTTTTAATA
* * *
163335 AAAATCACTAATTTACTTAAAAATCCAAATTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTT
163400 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAACATATTTTTATTTTTAAAAATATA
65 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATATA
* *
163464 AA--TTTTCTCTTTTTAA-A
130 AACTTTTTTTTTTTTTAATA
* ** *
163481 GAAAATCACTATTTTACTTAAAAAAT--AATTTTTTTGTTTCGAAATAGTTAAAAAAATCAAAAC
1 -AAAATCACTACTTTACTT-AAAAATCCAA-ACTTTTATTTCGAAATAGTTAAAAAAATCAAAAC
*
163544 TTTGTTTAAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAACATA-TTTTATTTTTAAAAATA
63 TTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATA
**
163608 TAAACTTTGTTTCTTTTTTTTTTTTA
128 TAAAC--T-TTT-TTTTTTTTTAATA
* * *
163634 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATTGTTTAAAAAAA
1 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAG-TTAAAAAAA
163690 AACCAAAACT
Statistics
Matches: 445, Mismatches: 35, Indels: 45
0.85 0.07 0.09
Matches are distributed among these distances:
146 74 0.17
147 55 0.12
148 9 0.02
149 90 0.20
150 111 0.25
151 32 0.07
152 59 0.13
153 15 0.03
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (149 bp):
AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATATAA
ACTTTTTTTTTTTTTAATA
Found at i:163612 original size:50 final size:50
Alignment explanation
Indices: 163402--163615 Score: 144
Period size: 50 Copynumber: 4.4 Consensus size: 50
163392 CAAAACTTTG
*
163402 TTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAACATATTTTTATT
1 TTTAAAAATATAAACTTTTTCTTTAAAATAACTAAAAAACATA-TTTTATT
* *
163452 TTTAAAAATATAAA-TTTTCTCTTT---TTAA--AGAAAATCACTATTTTA--
1 TTTAAAAATATAAACTTTT-TCTTTAAAATAACTA-AAAAACA-TATTTTATT
* ** * * ** * ** *
163497 CTTAAAAA-ATAATTTTTTTGTTTCGAAATAGTTAAAAAAATCAAAACTT-TG
1 TTTAAAAATATAAACTTTTTCTTT-AAAATAACT-AAAAAA-CATATTTTATT
* *
163548 TTTAAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTATT
1 TTTAAAAATATAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTATT
163598 TTTAAAAATATAAACTTT
1 TTTAAAAATATAAACTTT
163616 GTTTCTTTTT
Statistics
Matches: 120, Mismatches: 27, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
44 8 0.07
45 11 0.09
47 14 0.12
48 4 0.03
49 9 0.08
50 48 0.40
51 15 0.12
52 11 0.09
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (50 bp):
TTTAAAAATATAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTATT
Found at i:163670 original size:299 final size:299
Alignment explanation
Indices: 163036--163701 Score: 793
Period size: 299 Copynumber: 2.2 Consensus size: 299
163026 TGATTAAAAC
* * * * * * *
163036 AAAATCTCTACTTTACTTCAAAATAAAAACTTTTATTTCAAAATAGTT--AAAAAATCAAAAATT
1 AAAATCACTAATTTACTTAAAAATACAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
* * *
163099 TGTTTAAAAATTTAAACACTTTCTTTAAAATCACTGAAAAACAGTTTTTTAATTTTTAGAAACCT
66 TGTTTAAAAATTTAAACACTTTCTTTAAAATAACTGAAAAACAGTTTTTTAATTTTTAAAAACAT
* * *
163164 AAACTTTCTTTATTTTTTAATAAAAATATTACTTTACTTAAAAATCCAAAATTTTATTTCGAAAT
131 AAACTTTCTCTACTTTTTAATAAAAATACTACTTTACTTAAAAAT-CAAAATTTTATTTCGAAAT
* *
163229 AGTTAAAAAAACAAAATTTAGTTTAAAAATTTAAATTTTTTTTCTTTAAAATCACTAAAAACATA
195 AGTTAAAAAAACAAAATTTAGTTTAAAAATTTAAA-TCTTTTTCTTTAAAATAACTAAAAACATA
*
163294 TTTTTATTTTTTAAAAATCTAAACTTTTTTTTTTTTTAATA
259 TTTTTATTTTTTAAAAATATAAACTTTTTTTTTTTTTAATA
* *
163335 AAAATCACTAATTTACTTAAAAATCCAAATTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
1 AAAATCACTAATTTACTTAAAAATACAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
** *
163400 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAACA-TATTTTT-ATTTTTAAAAATA
66 TGTTTAAAAATTTAAACACTTTCTTTAAAATAACTGAAAAACAGT-TTTTTAATTTTTAAAAACA
* ** *
163462 TAAA-TTT-TCT-CTTTTTAA-AGAAAATCACTATTTTACTTAAAAAAT-AATTTTTTTGTTTCG
130 TAAACTTTCTCTACTTTTTAATA-AAAAT-ACTACTTTACTT-AAAAATCAA-AATTTTATTTCG
*
163522 AAATAGTTAAAAAAATCAAAACTTT-GTTTAAAATTTTAAA-CTTTTTCTTTAAAATAACTAAAA
191 AAATAGTTAAAAAAA-CAAAA-TTTAGTTTAAAAATTTAAATCTTTTTCTTTAAAATAACT-AAA
**
163585 AACATA-TTTTA-TTTTTAAAAATATAAACTTTGTTTCTTTTTTTTTTTTA
253 AACATATTTTTATTTTTTAAAAATATAAAC--T-TTT-TTTTTTTTTAATA
* * ** *
163634 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATTGTTTAAAAAAAAACCAAAAC
1 AAAATCACTAATTTACTTAAAAATACAAACTTTTATTTCGAAA-TAATT-AAAAAAAATCAAAAC
163699 TTT
64 TTT
163702 TCCCCAAATC
Statistics
Matches: 317, Mismatches: 34, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
295 17 0.05
296 36 0.11
297 46 0.15
298 31 0.10
299 109 0.34
300 15 0.05
301 63 0.20
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (299 bp):
AAAATCACTAATTTACTTAAAAATACAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
TGTTTAAAAATTTAAACACTTTCTTTAAAATAACTGAAAAACAGTTTTTTAATTTTTAAAAACAT
AAACTTTCTCTACTTTTTAATAAAAATACTACTTTACTTAAAAATCAAAATTTTATTTCGAAATA
GTTAAAAAAACAAAATTTAGTTTAAAAATTTAAATCTTTTTCTTTAAAATAACTAAAAACATATT
TTTATTTTTTAAAAATATAAACTTTTTTTTTTTTTAATA
Found at i:164143 original size:3 final size:3
Alignment explanation
Indices: 164137--164174 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
164127 AATAATAATA
*
164137 ATG ATG ATG ATG ATG ATG ATG ATG ATG GTG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
164175 AATTTGGGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:164233 original size:11 final size:11
Alignment explanation
Indices: 164197--164232 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
164187 TGACTAGCCT
164197 AAAAA-GAAAG
1 AAAAAGGAAAG
164207 AAAAAGGAAAG
1 AAAAAGGAAAG
164218 AAAAAGGAAA-
1 AAAAAGGAAAG
164228 AAAAA
1 AAAAA
164233 ACCTCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAGGAAAG
Found at i:164541 original size:12 final size:13
Alignment explanation
Indices: 164519--164550 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
164509 GTATACAATG
164519 AAATGAAATAAAT
1 AAATGAAATAAAT
164532 AAAT-AAATAAAT
1 AAATGAAATAAAT
164544 AAATGAA
1 AAATGAA
164551 CCTTTATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (13 bp):
AAATGAAATAAAT
Found at i:164613 original size:42 final size:42
Alignment explanation
Indices: 164563--164873 Score: 424
Period size: 42 Copynumber: 7.4 Consensus size: 42
164553 TTTATGCTTA
* *
164563 GGCCTCTAATTGCAATGAAAAGTAAATGGACCTCCACACCTA
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* * * * * *
164605 AGCTTCTAAATGCAACGAAAAGTAAATGGACCTTCACACTTA
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* *
164647 GGTCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
*
164689 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
*
164731 GGCCTCTAAATGCAATGAAAATTAAATGGACCTCCACACCTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* * * * *
164773 GGCCTCTGAATGCGATGAAAAGTAAATGGGCCTCCTCACTTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* * *
164815 GGCCTCTGAATGCGATGAAAAGTAAATGGACCTCCACACTTG
1 GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
* *
164857 GACCTTTAAATGCAATG
1 GGCCTCTAAATGCAATG
164874 GATGCTTTCC
Statistics
Matches: 238, Mismatches: 31, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 238 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (42 bp):
GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTG
Found at i:170686 original size:21 final size:21
Alignment explanation
Indices: 170662--170716 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
170652 TAGAGGTAAG
*
170662 ACTTGTATCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
* *
170683 ACTTGTATTGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
*
170704 ACTTATATCGGTA
1 ACTTGTATCGGTA
170717 CAAATCTGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:175998 original size:20 final size:20
Alignment explanation
Indices: 175973--176016 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
175963 ATGATTTGTG
*
175973 TTAAGAGTAAATAGA-CTTAA
1 TTAAGAGTAAA-AGAGATTAA
*
175993 TTAAGATTAAAAGAGATTAA
1 TTAAGAGTAAAAGAGATTAA
176013 TTAA
1 TTAA
176017 AGCTTAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (20 bp):
TTAAGAGTAAAAGAGATTAA
Found at i:177869 original size:21 final size:21
Alignment explanation
Indices: 177845--177902 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
177835 TAGAGGTGAG
177845 ACTTGTATCGGTAGAA-GAGTC
1 ACTTGTATCGGTAGAACGA-TC
* * *
177866 ACTTGTTTCGGTAAAACTATC
1 ACTTGTATCGGTAGAACGATC
177887 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
177903 ATCTGAACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACGATC
Done.