Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 14 of 18
Found at i:2332753 original size:27 final size:27
Alignment explanation
Indices: 2332714--2332779 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
2332704 CCACCATGTG
*
2332714 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
2332741 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
2332768 TTTGTCAAAAAT
1 TTTGTCAAAAAT
2332780 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:2332809 original size:24 final size:24
Alignment explanation
Indices: 2332741--2332810 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
2332731 TTACTTTGTA
* *
2332741 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG---CTTGTTG
*
2332768 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
2332792 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
2332811 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 17 0.46
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:2335618 original size:5 final size:5
Alignment explanation
Indices: 2335599--2335637 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
2335589 TACCAAAAGA
* * *
2335599 AAAAA AAAAT AAAAC AAAAC AAAGC AAAAC AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
2335638 GCAGTAAGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.03
Consensus pattern (5 bp):
AAAAC
Found at i:2336475 original size:2 final size:2
Alignment explanation
Indices: 2336468--2336498 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2336458 TCTAACTATG
*
2336468 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2336499 GAATATTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2337132 original size:37 final size:37
Alignment explanation
Indices: 2337080--2337163 Score: 150
Period size: 37 Copynumber: 2.3 Consensus size: 37
2337070 TTTATTTTTC
* *
2337080 GTGGATTGGCGCTGCCACCCAAATTCTAACAATCATA
1 GTGGATTGGCACTGCCACCCAAATACTAACAATCATA
2337117 GTGGATTGGCACTGCCACCCAAATACTAACAATCATA
1 GTGGATTGGCACTGCCACCCAAATACTAACAATCATA
2337154 GTGGATTGGC
1 GTGGATTGGC
2337164 CAAGCCACCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (37 bp):
GTGGATTGGCACTGCCACCCAAATACTAACAATCATA
Found at i:2337171 original size:37 final size:37
Alignment explanation
Indices: 2337080--2337178 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 37
2337070 TTTATTTTTC
*
2337080 GTGGATTGGCGC-TGCCACCCAAATTCTAACAATCATA
1 GTGGATTGGC-CATGCCACCCAAATACTAACAATCATA
2337117 GTGGATTGG-CACTGCCACCCAAATACTAACAATCATA
1 GTGGATTGGCCA-TGCCACCCAAATACTAACAATCATA
* *
2337154 GTGGATTGGCCAAGCCACCTAAATA
1 GTGGATTGGCCATGCCACCCAAATA
2337179 TTACTTGTCG
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
35 1 0.02
37 53 0.95
38 2 0.04
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (37 bp):
GTGGATTGGCCATGCCACCCAAATACTAACAATCATA
Found at i:2341881 original size:37 final size:37
Alignment explanation
Indices: 2341829--2341912 Score: 141
Period size: 37 Copynumber: 2.3 Consensus size: 37
2341819 TTTATTTTTC
* *
2341829 GTGGATTGGCGCTGCCACCCAAATTCTAACAATCATA
1 GTGGATTGGCACTGCCACCCAAATACTAACAATCATA
*
2341866 GTGGATTGGCACTGCCACCTAAATACTAACAATCATA
1 GTGGATTGGCACTGCCACCCAAATACTAACAATCATA
2341903 GTGGATTGGC
1 GTGGATTGGC
2341913 CAAGACACCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (37 bp):
GTGGATTGGCACTGCCACCCAAATACTAACAATCATA
Found at i:2341927 original size:37 final size:37
Alignment explanation
Indices: 2341829--2341927 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 37
2341819 TTTATTTTTC
* * * *
2341829 GTGGATTGGCGCTGCCACCCAAATTCTAACAATCATA
1 GTGGATTGGCACAGACACCCAAATACTAACAATCATA
* * *
2341866 GTGGATTGGCACTGCCACCTAAATACTAACAATCATA
1 GTGGATTGGCACAGACACCCAAATACTAACAATCATA
2341903 GTGGATTGGC-CAAGACACCCAAATA
1 GTGGATTGGCAC-AGACACCCAAATA
2341928 TTACTTGTCG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 1 0.02
37 54 0.98
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (37 bp):
GTGGATTGGCACAGACACCCAAATACTAACAATCATA
Found at i:2342088 original size:30 final size:30
Alignment explanation
Indices: 2342027--2342124 Score: 107
Period size: 26 Copynumber: 3.4 Consensus size: 30
2342017 TTATTTTTTT
* * **
2342027 AATAAGTTTTTATATTTTTA-TTATATTTA
1 AATAAGTTTTTATCTTTTAATTTATACCTA
2342056 AATAAGTTTTTATCTTTTAATTTATACCT-
1 AATAAGTTTTTATCTTTTAATTTATACCTA
2342085 -A-AA-TTTTTATCTTTTAATTTATACCTA
1 AATAAGTTTTTATCTTTTAATTTATACCTA
* *
2342112 ATTAAGCTTTTAT
1 AATAAGTTTTTAT
2342125 TTTAGGTGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
26 23 0.40
27 2 0.03
28 1 0.02
29 20 0.34
30 12 0.21
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (30 bp):
AATAAGTTTTTATCTTTTAATTTATACCTA
Found at i:2342717 original size:23 final size:23
Alignment explanation
Indices: 2342690--2342734 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2342680 ATCTATTTAT
2342690 TAAGA-CAAACAACTTTGTATTGC
1 TAAGACCAAACAACTTT-TATTGC
*
2342713 TAAGACCAAGCAACTTTTATTG
1 TAAGACCAAACAACTTTTATTG
2342735 TGCTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
TAAGACCAAACAACTTTTATTGC
Found at i:2343022 original size:21 final size:21
Alignment explanation
Indices: 2342989--2343041 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
2342979 ATTTTAAATT
2342989 TTAATGTTATAATTTAGAATTT-A
1 TTAAT-TT-TAATTT-GAATTTGA
*
2343012 TTAATTTTAATTTTAATTTGA
1 TTAATTTTAATTTGAATTTGA
*
2343033 TTATTTTTA
1 TTAATTTTA
2343042 TTATCTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 15 0.56
22 2 0.07
23 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (21 bp):
TTAATTTTAATTTGAATTTGA
Found at i:2343061 original size:190 final size:190
Alignment explanation
Indices: 2342736--2343104 Score: 564
Period size: 190 Copynumber: 1.9 Consensus size: 190
2342726 CTTTTATTGT
* * *
2342736 GCTTTATTAGTAAGACAAACTAAATTTGAAAGTGTGATCTAATTTTATGAGTTATTTTGAATTTT
1 GCTTTATTAGTAAGACAAACTAAATTTGAAAGTGTGATCTAAATTTACGAGTTATTTTAAATTTT
* * *
2342801 AATGTTATGATTGAGAATTATCAATTTTACATTTTAATCCGGCTATTTTTATTATCTTACAATGA
66 AATGTTATAATTGAGAATTATCAATTTTACATTTTAATCCGACTATTTTTATTATCTTAAAATGA
* *
2342866 AAAACAAAAATAAAGTTAAGTTTTGCCTCATTCAATAGCTTAAATACTCTTTGTTGTTGA
131 AAAACAAAAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTCTTTGTTGTTGA
*
2342926 GCTTTATTAGTAAGATAAACTAAATTTGCAAA-TGTGATCTAAATTTACGAGTTATTTTAAATTT
1 GCTTTATTAGTAAGACAAACTAAATTTG-AAAGTGTGATCTAAATTTACGAGTTATTTTAAATTT
* * ** *
2342990 TAATGTTATAATTTAGAATTTATTAATTTTA-ATTTTAATTTGATTATTTTTATTATCTTATAAA
65 TAATGTTATAATTGAGAA-TTATCAATTTTACATTTTAATCCGACTATTTTTATTATCTTA-AAA
2343054 T-AAAAACAAAAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTC
128 TGAAAAACAAAAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTC
2343105 CTTGGCTTAA
Statistics
Matches: 162, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
190 145 0.90
191 17 0.10
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (190 bp):
GCTTTATTAGTAAGACAAACTAAATTTGAAAGTGTGATCTAAATTTACGAGTTATTTTAAATTTT
AATGTTATAATTGAGAATTATCAATTTTACATTTTAATCCGACTATTTTTATTATCTTAAAATGA
AAAACAAAAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTCTTTGTTGTTGA
Found at i:2344473 original size:55 final size:53
Alignment explanation
Indices: 2344367--2344564 Score: 229
Period size: 55 Copynumber: 3.7 Consensus size: 53
2344357 GGGGGCAATT
* * * *
2344367 AGGGATTAGGGTTTTTGAGTTAAGGTTTACAATTTTTGAGAAATTAAAATGGAG
1 AGGGATTAGGGATTTTGAGTTAAGGTTTATAA-TTTTAAGAAATTAGAATGGAG
* * *
2344421 AGGGTTTAGGGATTTTGAGTTTAGGGTTTATAATATTTAAGAAATTAGAATGGAA
1 AGGGATTAGGGATTTTGAG-TTAAGGTTTATAAT-TTTAAGAAATTAGAATGGAG
* * * *
2344476 AGGGATTAGGGATTTTGAATTAAGATTTGGT--TTTGGAAGAAATTAGAATGGAG
1 AGGGATTAGGGATTTTGAGTTAAGGTTT-ATAATTT-TAAGAAATTAGAATGGAG
*
2344529 AGAGATTAGGGATTTTGAGTTAAGGTTTATAATTTT
1 AGGGATTAGGGATTTTGAGTTAAGGTTTATAATTTT
2344565 TTTTGTTTTA
Statistics
Matches: 119, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
52 3 0.03
53 42 0.35
54 28 0.24
55 46 0.39
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (53 bp):
AGGGATTAGGGATTTTGAGTTAAGGTTTATAATTTTAAGAAATTAGAATGGAG
Found at i:2349262 original size:5 final size:5
Alignment explanation
Indices: 2349243--2349281 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
2349233 TACCAAAAGA
* *
2349243 AAAAA AAAAC AAAAC AAAAC AAAGC AAAAC AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
2349282 GCAGTAAGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:2350776 original size:37 final size:37
Alignment explanation
Indices: 2350731--2350817 Score: 131
Period size: 37 Copynumber: 2.4 Consensus size: 37
2350721 GAATTGGCGC
*
2350731 TGCCACCCAAATTCTAACAATCATAGTGGATTAG-CA
1 TGCCACCCAAATACTAACAATCATAGTGGATTAGCCA
*
2350767 TTGCCACCCAAATACTAACAATCATAGTGGATTGGCCA
1 -TGCCACCCAAATACTAACAATCATAGTGGATTAGCCA
*
2350805 AGCCACCCAAATA
1 TGCCACCCAAATA
2350818 TTACTTGTCG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 44 0.96
38 2 0.04
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.22
Consensus pattern (37 bp):
TGCCACCCAAATACTAACAATCATAGTGGATTAGCCA
Found at i:2355521 original size:37 final size:37
Alignment explanation
Indices: 2355469--2355552 Score: 141
Period size: 37 Copynumber: 2.3 Consensus size: 37
2355459 TTTATTTTTC
* *
2355469 GTGGATTGGCGCTGCCACCCAAATTCTAACAATCATA
1 GTGGATTGGCACTGCCACCCAAATACTAACAATCATA
*
2355506 GTGGATTGGCACTGCCACCTAAATACTAACAATCATA
1 GTGGATTGGCACTGCCACCCAAATACTAACAATCATA
2355543 GTGGATTGGC
1 GTGGATTGGC
2355553 CAAGACACCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (37 bp):
GTGGATTGGCACTGCCACCCAAATACTAACAATCATA
Found at i:2355567 original size:37 final size:37
Alignment explanation
Indices: 2355469--2355567 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 37
2355459 TTTATTTTTC
* * * *
2355469 GTGGATTGGCGCTGCCACCCAAATTCTAACAATCATA
1 GTGGATTGGCACAGACACCCAAATACTAACAATCATA
* * *
2355506 GTGGATTGGCACTGCCACCTAAATACTAACAATCATA
1 GTGGATTGGCACAGACACCCAAATACTAACAATCATA
2355543 GTGGATTGGC-CAAGACACCCAAATA
1 GTGGATTGGCAC-AGACACCCAAATA
2355568 TTACTTGTCG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 1 0.02
37 54 0.98
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (37 bp):
GTGGATTGGCACAGACACCCAAATACTAACAATCATA
Found at i:2355728 original size:30 final size:30
Alignment explanation
Indices: 2355667--2355764 Score: 107
Period size: 26 Copynumber: 3.4 Consensus size: 30
2355657 TTATTTTTTT
* * **
2355667 AATAAGTTTTTATATTTTTA-TTATATTTA
1 AATAAGTTTTTATCTTTTAATTTATACCTA
2355696 AATAAGTTTTTATCTTTTAATTTATACCT-
1 AATAAGTTTTTATCTTTTAATTTATACCTA
2355725 -A-AA-TTTTTATCTTTTAATTTATACCTA
1 AATAAGTTTTTATCTTTTAATTTATACCTA
* *
2355752 ATTAAGCTTTTAT
1 AATAAGTTTTTAT
2355765 TTTAGGTGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
26 23 0.40
27 2 0.03
28 1 0.02
29 20 0.34
30 12 0.21
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (30 bp):
AATAAGTTTTTATCTTTTAATTTATACCTA
Found at i:2356357 original size:23 final size:23
Alignment explanation
Indices: 2356330--2356374 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2356320 ATCTATTTAT
2356330 TAAGA-CAAACAACTTTGTATTGC
1 TAAGACCAAACAACTTT-TATTGC
*
2356353 TAAGACCAAGCAACTTTTATTG
1 TAAGACCAAACAACTTTTATTG
2356375 TGCTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
TAAGACCAAACAACTTTTATTGC
Found at i:2356662 original size:21 final size:21
Alignment explanation
Indices: 2356629--2356681 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
2356619 ATTTTAAATT
2356629 TTAATGTTATAATTTAAAATTT-A
1 TTAAT-TT-TAATTT-AAATTTGA
*
2356652 TTAATTTTAATTTTAATTTGA
1 TTAATTTTAATTTAAATTTGA
*
2356673 TTATTTTTA
1 TTAATTTTA
2356682 TTATCTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 15 0.56
22 2 0.07
23 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TTAATTTTAATTTAAATTTGA
Found at i:2356701 original size:190 final size:190
Alignment explanation
Indices: 2356376--2356744 Score: 555
Period size: 190 Copynumber: 1.9 Consensus size: 190
2356366 CTTTTATTGT
* * *
2356376 GCTTTATTAGTAAGACAAACTAAATTTGAAAGTGTGATCTAATTTTATGAGTTATTTTGAATTTT
1 GCTTTATTAGTAAGACAAACTAAATTTGAAAGTGTGATCTAAATTTACGAGTTATTTTAAATTTT
* * * *
2356441 AATGTTATGATTGAGAATTATCAATTTTACATTTTAATCCGGCTATTTTTATTATCTTACAATGA
66 AATGTTATAATTGAAAATTATCAATTTTACATTTTAATCCGACTATTTTTATTATCTTAAAATGA
* *
2356506 AAAACAAAAATAAAGTTAAGTTTTGCCTCATTCAATAGCTTAAATACTCTTTGTTGTTGA
131 AAAACAAAAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTCTTTGTTGTTGA
*
2356566 GCTTTATTAGTAAGATAAACTAAATTTGCAAA-TGTGATCTAAATTTACGAGTTATTTTAAATTT
1 GCTTTATTAGTAAGACAAACTAAATTTG-AAAGTGTGATCTAAATTTACGAGTTATTTTAAATTT
* * ** *
2356630 TAATGTTATAATTTAAAATTTATTAATTTTA-ATTTTAATTTGATTATTTTTATTATCTTATAAA
65 TAATGTTATAATTGAAAA-TTATCAATTTTACATTTTAATCCGACTATTTTTATTATCTTA-AAA
2356694 T-AAAAACAAAAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTC
128 TGAAAAACAAAAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTC
2356745 CTTGGCTTAA
Statistics
Matches: 161, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
190 144 0.89
191 17 0.11
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.44
Consensus pattern (190 bp):
GCTTTATTAGTAAGACAAACTAAATTTGAAAGTGTGATCTAAATTTACGAGTTATTTTAAATTTT
AATGTTATAATTGAAAATTATCAATTTTACATTTTAATCCGACTATTTTTATTATCTTAAAATGA
AAAACAAAAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTCTTTGTTGTTGA
Found at i:2358113 original size:55 final size:53
Alignment explanation
Indices: 2358007--2358204 Score: 229
Period size: 55 Copynumber: 3.7 Consensus size: 53
2357997 GGGGGCAATT
* * * *
2358007 AGGGATTAGGGTTTTTGAGTTAAGGTTTACAATTTTTGAGAAATTAAAATGGAG
1 AGGGATTAGGGATTTTGAGTTAAGGTTTATAA-TTTTAAGAAATTAGAATGGAG
* * *
2358061 AGGGTTTAGGGATTTTGAGTTTAGGGTTTATAATATTTAAGAAATTAGAATGGAA
1 AGGGATTAGGGATTTTGAG-TTAAGGTTTATAAT-TTTAAGAAATTAGAATGGAG
* * * *
2358116 AGGGATTAGGGATTTTGAATTAAGATTTGGT--TTTGGAAGAAATTAGAATGGAG
1 AGGGATTAGGGATTTTGAGTTAAGGTTT-ATAATTT-TAAGAAATTAGAATGGAG
*
2358169 AGAGATTAGGGATTTTGAGTTAAGGTTTATAATTTT
1 AGGGATTAGGGATTTTGAGTTAAGGTTTATAATTTT
2358205 TTTTGTTTTA
Statistics
Matches: 119, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
52 3 0.03
53 42 0.35
54 28 0.24
55 46 0.39
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (53 bp):
AGGGATTAGGGATTTTGAGTTAAGGTTTATAATTTTAAGAAATTAGAATGGAG
Found at i:2362887 original size:5 final size:5
Alignment explanation
Indices: 2362873--2362917 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
2362863 TATAAAATAC
* * *
2362873 CAAAA GAAAA AAAAA CAAAA CAAAA CAAAG CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
2362918 GCAGTAAGCG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.80, C:0.16, G:0.04, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:2364410 original size:37 final size:37
Alignment explanation
Indices: 2364365--2364451 Score: 131
Period size: 37 Copynumber: 2.4 Consensus size: 37
2364355 GAATTGGCGC
*
2364365 TGCCACCCAAATTCTAACAATCATAGTGGATTAG-CA
1 TGCCACCCAAATACTAACAATCATAGTGGATTAGCCA
*
2364401 TTGCCACCCAAATACTAACAATCATAGTGGATTGGCCA
1 -TGCCACCCAAATACTAACAATCATAGTGGATTAGCCA
*
2364439 AGCCACCCAAATA
1 TGCCACCCAAATA
2364452 TTACTTGTCG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 44 0.96
38 2 0.04
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.22
Consensus pattern (37 bp):
TGCCACCCAAATACTAACAATCATAGTGGATTAGCCA
Found at i:2369178 original size:37 final size:37
Alignment explanation
Indices: 2369108--2369178 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
2369098 TGGATTAGCG
* * * *
2369108 CTGCCATCCAAATTCTAACAATCATAGTGGATTGGCA
1 CTGCCACCCAAATACTAACAATCATAATAGATTGGCA
*
2369145 CTGCCACCCAAATACTAACAATTATAATAGATTG
1 CTGCCACCCAAATACTAACAATCATAATAGATTG
2369179 ACCAAGCCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (37 bp):
CTGCCACCCAAATACTAACAATCATAATAGATTGGCA
Found at i:2369193 original size:37 final size:37
Alignment explanation
Indices: 2369110--2369195 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
2369100 GATTAGCGCT
* * * * *
2369110 GCCATCCAAATTCTAACAATCATAGTGGATTGGCACT
1 GCCATCCAAATACTAACAATCATAATAGATTGCCACA
* *
2369147 GCCACCCAAATACTAACAATTATAATAGATTGACCA-A
1 GCCATCCAAATACTAACAATCATAATAGATTG-CCACA
2369184 GCCATCCAAATA
1 GCCATCCAAATA
2369196 TTACTTATCA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
37 38 0.95
38 2 0.05
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.23
Consensus pattern (37 bp):
GCCATCCAAATACTAACAATCATAATAGATTGCCACA
Found at i:2369330 original size:29 final size:27
Alignment explanation
Indices: 2369284--2369348 Score: 94
Period size: 29 Copynumber: 2.3 Consensus size: 27
2369274 CTCTGAATTA
2369284 TTTATTTATTTAATAAGTTTTTATATT
1 TTTATTTATTTAATAAGTTTTTATATT
*
2369311 TTTATTATATTTAAATAAGTTTTTATCTT
1 TTTATT-TATTT-AATAAGTTTTTATATT
*
2369340 TTAATTTAT
1 TTTATTTAT
2369349 ACCTAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 6 0.18
28 8 0.24
29 20 0.59
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTATTTATTTAATAAGTTTTTATATT
Found at i:2369414 original size:16 final size:17
Alignment explanation
Indices: 2369376--2369414 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2369366 TTTTAGGTGA
*
2369376 AATA-TTTATTTATGTT
1 AATAGTTTATTTATGTC
2369392 AATAGTTTATTTATGTC
1 AATAGTTTATTTATGTC
2369409 AA-AGTT
1 AATAGTT
2369415 AAAGGTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (17 bp):
AATAGTTTATTTATGTC
Found at i:2369510 original size:31 final size:31
Alignment explanation
Indices: 2369450--2369518 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
2369440 AAATTAAAAG
*
2369450 TTTATTTAAATATAAATTAAAATGTTAAGGA
1 TTTATTTAAATATAAATTAAAATGGTAAGGA
*
2369481 TTTATTTAAATATAAATTAAAA-GAGTAAGGG
1 TTTATTTAAATATAAATTAAAATG-GTAAGGA
2369512 TTTATTT
1 TTTATTT
2369519 GGGTGTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (31 bp):
TTTATTTAAATATAAATTAAAATGGTAAGGA
Found at i:2369940 original size:23 final size:23
Alignment explanation
Indices: 2369914--2369958 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2369904 ATCTATTTAT
2369914 TAAGA-CAAACAACTTTGTATTGC
1 TAAGACCAAACAACTTT-TATTGC
*
2369937 TAAGACCAAGCAACTTTTATTG
1 TAAGACCAAACAACTTTTATTG
2369959 TGCTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
TAAGACCAAACAACTTTTATTGC
Found at i:2370180 original size:180 final size:183
Alignment explanation
Indices: 2369960--2370323 Score: 511
Period size: 191 Copynumber: 2.0 Consensus size: 183
2369950 CTTTTATTGT
* *
2369960 GCTTTATTAGTAAGACAAACTAAATTTGAAAGTGTGATCTAATTTTAC-G-AATTTTAATGTTAT
1 GCTTTATTAGTAAGACAAACTAAATTTGAAAGTATGATCTAAATTTACAGTAATTTTAATGTTAT
*
2370023 AATTGAG-AGTTATCAATTTTACATTTTAATCCGATTATTTTTATTATCTTACAATTAAAAACAA
66 AATTGAGAAGTTATCAATTTTACATTTTAATCCGATTATTTTTATTATCTTACAAATAAAAACAA
* *
2370087 AAATAAAGTTAAGTTTTGCCTCATTCAATAGCTTAAATACTCCTTGTTGTTGA
131 AAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTCCTTGTTGTTGA
*
2370140 GCTTTATTAGTAAGATAAACTAAATTTGCAAA-TATGATCTAAATTTACGAGTTATTTTAAATTT
1 GCTTTATTAGTAAGACAAACTAAATTTG-AAAGTATGATCTAAATTTAC-AG------T-AATTT
* * * * * *
2370204 TAATGTTATAATTTAGAATTTATTAATTTTATATTTTAATTCGATTATTTTTATTATCTTATAAA
57 TAATGTTATAATTGAGAAGTTATCAATTTTACATTTTAATCCGATTATTTTTATTATCTTACAAA
2370269 TAAAAACAAAAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTCCTTG
122 TAAAAACAAAAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTCCTTG
2370324 GCTTAAAAGA
Statistics
Matches: 160, Mismatches: 12, Indels: 13
0.86 0.06 0.07
Matches are distributed among these distances:
180 41 0.26
181 3 0.02
182 1 0.01
190 20 0.12
191 95 0.59
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (183 bp):
GCTTTATTAGTAAGACAAACTAAATTTGAAAGTATGATCTAAATTTACAGTAATTTTAATGTTAT
AATTGAGAAGTTATCAATTTTACATTTTAATCCGATTATTTTTATTATCTTACAAATAAAAACAA
AAATAAAGTTAAATTTTGACTCATTCAATAGCTTAAATACTCCTTGTTGTTGA
Found at i:2373430 original size:5 final size:5
Alignment explanation
Indices: 2373408--2373476 Score: 54
Period size: 5 Copynumber: 13.6 Consensus size: 5
2373398 AAATAAATAA
* * *
2373408 ATTTT ATGTTT AAATTT AATTT ATTTT ATTTT ATTTT A-TTT -TTTT ATTTAA
1 ATTTT AT-TTT -ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T
2373459 ATTATT A-TTT ATTTT ATT
1 ATT-TT ATTTT ATTTT ATT
2373477 AAAAAATTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
4 9 0.17
5 32 0.60
6 10 0.19
7 2 0.04
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (5 bp):
ATTTT
Found at i:2373468 original size:20 final size:20
Alignment explanation
Indices: 2373416--2373476 Score: 81
Period size: 19 Copynumber: 3.1 Consensus size: 20
2373406 AAATTTTATG
*
2373416 TTTAAATTTAATTTATTTTA
1 TTTAAATTTTATTTATTTTA
*
2373436 TTT-TATTTTATTT-TTTTA
1 TTTAAATTTTATTTATTTTA
2373454 TTTAAATTATTATTTATTTTA
1 TTTAAATT-TTATTTATTTTA
2373475 TT
1 TT
2373477 AAAAAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 8 0.23
19 11 0.31
20 9 0.26
21 7 0.20
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTAAATTTTATTTATTTTA
Found at i:2373475 original size:12 final size:12
Alignment explanation
Indices: 2373432--2373477 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
2373422 TTTAATTTAT
2373432 TTTATTTTA-T-
1 TTTATTTTATTA
*
2373442 TTTATTTTTTTA
1 TTTATTTTATTA
**
2373454 TTTAAATTATTA
1 TTTATTTTATTA
2373466 TTTATTTTATTA
1 TTTATTTTATTA
2373478 AAAAATTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
10 8 0.29
11 1 0.04
12 19 0.68
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:2373485 original size:20 final size:20
Alignment explanation
Indices: 2373443--2373490 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2373433 TTATTTTATT
**
2373443 TTATTTTTTTATTTAAATTA
1 TTATTTTTTTATTTAAAAAA
2373463 TTATTTATTTTA-TTAAAAAA
1 TTATTT-TTTTATTTAAAAAA
2373483 TTATTTTT
1 TTATTTTT
2373491 ATTAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 18 0.72
21 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTTTTATTTAAAAAA
Found at i:2375214 original size:2 final size:2
Alignment explanation
Indices: 2375207--2375237 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2375197 AAATTAATTT
2375207 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2375238 TAACGTACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2376840 original size:2 final size:2
Alignment explanation
Indices: 2376833--2376860 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2376823 CTCCGTGTGC
2376833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2376861 TTGACACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2379822 original size:22 final size:23
Alignment explanation
Indices: 2379783--2379825 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2379773 AGTATTTCAT
2379783 TTGTAATTTATGCTATTATAAAC
1 TTGTAATTTATGCTATTATAAAC
2379806 TTGTAA-TTAT-CTGATTATAA
1 TTGTAATTTATGCT-ATTATAA
2379826 TAATGAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.11
22 11 0.58
23 6 0.32
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (23 bp):
TTGTAATTTATGCTATTATAAAC
Found at i:2380960 original size:102 final size:102
Alignment explanation
Indices: 2380809--2381005 Score: 286
Period size: 102 Copynumber: 1.9 Consensus size: 102
2380799 AATAGTGACG
* * * * * *
2380809 TGGTAGTTTACCATTGTTGATTAAATTGGTGATTTGGTGGTTTATCATTGTTGATTAAATGAGAG
1 TGGTAGCTTACCATTGTTGATTAAATGGGTGATTTAGTGGCTTACCATTGTTGACTAAATGAGAG
2380874 ATTTGGTAGCTTACCATTATTGATTAAATGAGAAATT
66 ATTTGGTAGCTTACCATTATTGATTAAATGAGAAATT
* *
2380911 TGGTAGCTTACTATTGTTGATTAAATGGGTGATTTAGTGGCTTACCATTGTTGACTAAATGGGAG
1 TGGTAGCTTACCATTGTTGATTAAATGGGTGATTTAGTGGCTTACCATTGTTGACTAAATGAGAG
* ** *
2380976 ATTTGGTAGGTTGTCATTGTTGATTAAATG
66 ATTTGGTAGCTTACCATTATTGATTAAATG
2381006 GTAGTTTTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 83 1.00
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (102 bp):
TGGTAGCTTACCATTGTTGATTAAATGGGTGATTTAGTGGCTTACCATTGTTGACTAAATGAGAG
ATTTGGTAGCTTACCATTATTGATTAAATGAGAAATT
Found at i:2381005 original size:34 final size:34
Alignment explanation
Indices: 2380809--2381006 Score: 220
Period size: 34 Copynumber: 5.8 Consensus size: 34
2380799 AATAGTGACG
* * *
2380809 TGGTAGTTTACCATTGTTGATTAAATTGGTGATT
1 TGGTAGGTTACCATTGTTGATTAAATGGGAGATT
* *
2380843 TGGT-GGTTTATCATTGTTGATTAAATGAGAGATT
1 TGGTAGG-TTACCATTGTTGATTAAATGGGAGATT
* * * *
2380877 TGGTAGCTTACCATTATTGATTAAATGAGAAATT
1 TGGTAGGTTACCATTGTTGATTAAATGGGAGATT
* * *
2380911 TGGTAGCTTACTATTGTTGATTAAATGGGTGATT
1 TGGTAGGTTACCATTGTTGATTAAATGGGAGATT
* *
2380945 TAGT-GGCTTACCATTGTTGACTAAATGGGAGATT
1 TGGTAGG-TTACCATTGTTGATTAAATGGGAGATT
**
2380979 TGGTAGGTTGTCATTGTTGATTAAATGG
1 TGGTAGGTTACCATTGTTGATTAAATGG
2381007 TAGTTTTTAC
Statistics
Matches: 137, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
33 2 0.01
34 132 0.96
35 3 0.02
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (34 bp):
TGGTAGGTTACCATTGTTGATTAAATGGGAGATT
Found at i:2385490 original size:34 final size:34
Alignment explanation
Indices: 2385420--2385638 Score: 262
Period size: 34 Copynumber: 6.5 Consensus size: 34
2385410 AAGTGGGAGA
* *
2385420 ATTGTTGATTAAAT-GGTGATTTGATAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * **
2385453 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGTC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
*
2385487 ATTGTTGACTAAATGGGAT-ATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGG-TGATTTGGTAGCTTACC
* ** *
2385521 ATTGTTGATTAAATGAGAAATTTAGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
*
2385555 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * **
2385589 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGTC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
2385623 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2385639 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
33 14 0.09
34 143 0.91
35 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.42
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2385569 original size:102 final size:101
Alignment explanation
Indices: 2385420--2385638 Score: 323
Period size: 102 Copynumber: 2.2 Consensus size: 101
2385410 AAGTGGGAGA
** * * *
2385420 ATTGTTGATTAAATGGTGATTTGATAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGATAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
* *
2385485 TCATTGTTGACTAAATGGGATATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
2385521 ATTGTTGATTAAATGAGAAATTT-AGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCT
1 ATTGTTGATTAAATG-GAAATTTGA-TAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCT
* **
2385585 TACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGTC
64 TACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
2385623 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2385639 TGGTTTTTAC
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
101 17 0.16
102 89 0.84
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.42
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGATAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:2385848 original size:17 final size:18
Alignment explanation
Indices: 2385826--2385864 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2385816 CACGTAATTT
*
2385826 TTTTAT-ATTTTTTTTTA
1 TTTTATGATTATTTTTTA
*
2385843 TTTTATGCTTATTTTTTA
1 TTTTATGATTATTTTTTA
2385861 TTTT
1 TTTT
2385865 TCTTCTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTATGATTATTTTTTA
Found at i:2388980 original size:24 final size:25
Alignment explanation
Indices: 2388952--2389078 Score: 114
Period size: 27 Copynumber: 4.9 Consensus size: 25
2388942 AATAAAAATT
2388952 AGCCACCAATTTTGACAAAC-AACA
1 AGCCACCAATTTTGACAAACAAACA
2388976 AGCCACCAATTTTGACAAACAAACA
1 AGCCACCAATTTTGACAAACAAACA
** *
2389001 AGCCTTC-ATATTTGACAAATACAAAGGA
1 AGCCACCAAT-TTTGAC-AA-ACAAA-CA
* * *
2389029 AACCACCATTTTTGACAAACACAAAA
1 AGCCACCAATTTTGACAAACA-AACA
* *
2389055 TAACCACCATTTTTGACAAACAAA
1 -AGCCACCAATTTTGACAAACAAA
2389079 TGGGTGGCTT
Statistics
Matches: 87, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
24 22 0.25
25 15 0.17
26 8 0.09
27 30 0.34
28 11 0.13
29 1 0.01
ACGTcount: A:0.46, C:0.25, G:0.08, T:0.20
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAACAAACA
Found at i:2389019 original size:25 final size:24
Alignment explanation
Indices: 2388952--2389004 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2388942 AATAAAAATT
2388952 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
2388976 AGCCACCAATTTTGACAAACAAACA
1 AGCCACCAATTTTGACAAAC-AACA
2389001 AGCC
1 AGCC
2389005 TTCATATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.45, C:0.30, G:0.09, T:0.15
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:2389079 original size:24 final size:24
Alignment explanation
Indices: 2388954--2389079 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
2388944 TAAAAATTAG
* *
2388954 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* *
2388978 CCACCAATTTTGACAAACAAACAA
1 CCACCATTTTTGACAAACAAATAA
** * *
2389002 GCCTTCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
2389031 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
2389058 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
2389080 GGGTGGCTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 25 0.30
25 12 0.14
26 4 0.05
27 21 0.25
28 16 0.19
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:2390982 original size:21 final size:22
Alignment explanation
Indices: 2390956--2391001 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2390946 ATCTGTTGAA
* *
2390956 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
2390977 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
2390999 ACT
1 ACT
2391002 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:2393573 original size:24 final size:25
Alignment explanation
Indices: 2393546--2393615 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
2393536 AATAAAAATT
*
2393546 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
2393570 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
**
2393595 AGCCTTC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
2393616 CAAAGGAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:2393639 original size:28 final size:27
Alignment explanation
Indices: 2393600--2393670 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
2393590 AAACAAGCCT
* *
2393600 TCATATTTGACAAATACAAAGGA-AACCA
1 TCATTTTTGACAAACACAAA--ATAACCA
2393628 TCATTTTTGACAAACACAAAATAACCA
1 TCATTTTTGACAAACACAAAATAACCA
*
2393655 CCATTTTTGACAAACA
1 TCATTTTTGACAAACA
2393671 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.25
Consensus pattern (27 bp):
TCATTTTTGACAAACACAAAATAACCA
Found at i:2404727 original size:16 final size:18
Alignment explanation
Indices: 2404702--2404739 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2404692 AATATACGTA
2404702 ATATTAAAAAAT-T-AAT
1 ATATTAAAAAATATAAAT
*
2404718 ATATTTAAAAATATAAAT
1 ATATTAAAAAATATAAAT
2404736 ATAT
1 ATAT
2404740 AAACTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 1 0.05
18 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTAAAAAATATAAAT
Found at i:2404736 original size:18 final size:17
Alignment explanation
Indices: 2404705--2404739 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2404695 ATACGTAATA
*
2404705 TTAAAAAATTAATATAT
1 TTAAAAAATAAATATAT
2404722 TTAAAAATATAAATATAT
1 TTAAAAA-ATAAATATAT
2404740 AAACTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAAATAAATATAT
Found at i:2405752 original size:25 final size:25
Alignment explanation
Indices: 2405705--2405752 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2405695 AAACTATACA
*
2405705 TTAATATGGTAAATTTTTAATTATT
1 TTAATATGGTAAATTTTGAATTATT
*
2405730 TTAATAT-TTAAATTTTGATATTA
1 TTAATATGGTAAATTTTGA-ATTA
2405753 ATATAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (25 bp):
TTAATATGGTAAATTTTGAATTATT
Found at i:2406687 original size:2 final size:2
Alignment explanation
Indices: 2406680--2406709 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2406670 TTTCCTAGCA
2406680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2406710 CTTCAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2407560 original size:21 final size:20
Alignment explanation
Indices: 2407516--2407561 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2407506 TGATTTTTTT
*
2407516 AATTAATATTATTAAATATT
1 AATTAATATTATTAAATATA
* *
2407536 AATTAATATTTTTCATATATA
1 AATTAATATTATT-AAATATA
2407557 AATTA
1 AATTA
2407562 TCATGTGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTAATATTATTAAATATA
Found at i:2407600 original size:38 final size:39
Alignment explanation
Indices: 2407556--2407636 Score: 155
Period size: 38 Copynumber: 2.1 Consensus size: 39
2407546 TTTCATATAT
2407556 AAATTATCATGTGGGTCATGACACTTTTTCAAAA-GAAA
1 AAATTATCATGTGGGTCATGACACTTTTTCAAAAGGAAA
2407594 AAATTATCATGTGGGTCATGACACTTTTTCAAAAGGAAA
1 AAATTATCATGTGGGTCATGACACTTTTTCAAAAGGAAA
2407633 AAAT
1 AAAT
2407637 GAACTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 34 0.81
39 8 0.19
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (39 bp):
AAATTATCATGTGGGTCATGACACTTTTTCAAAAGGAAA
Found at i:2408243 original size:23 final size:22
Alignment explanation
Indices: 2408188--2408243 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
2408178 GCATGATTAA
2408188 AAAATAA-ATAGTTTAAATAAT
1 AAAATAATATAGTTTAAATAAT
*
2408209 AAAATATTTATA-TTTAAATATAT
1 AAAATA-ATATAGTTTAAATA-AT
2408232 AAATATAATATA
1 AAA-ATAATATA
2408244 AAAATAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 6 0.21
22 8 0.28
23 12 0.41
24 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATAATATAGTTTAAATAAT
Found at i:2409459 original size:14 final size:14
Alignment explanation
Indices: 2409437--2409467 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2409427 TATTAGAAAC
2409437 ATTAAATAATTTTT
1 ATTAAATAATTTTT
*
2409451 ATTATATAATTTTT
1 ATTAAATAATTTTT
2409465 ATT
1 ATT
2409468 TTTAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTAAATAATTTTT
Found at i:2409533 original size:42 final size:35
Alignment explanation
Indices: 2409451--2409533 Score: 85
Period size: 42 Copynumber: 2.2 Consensus size: 35
2409441 AATAATTTTT
2409451 ATTATATAATTTTTATTTTTAATAAATTTATTATA
1 ATTATATAATTTTTATTTTTAATAAATTTATTATA
* *
2409486 TTTATATTATATTTTATGTTTTATATAAAAATATTAATTATA
1 ATTATATAAT-TTTTAT-TTTTA-AT--AAAT-TT-ATTATA
2409528 ATTATA
1 ATTATA
2409534 AGTAAAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
35 8 0.21
36 6 0.16
37 5 0.13
38 2 0.05
40 4 0.11
41 2 0.05
42 11 0.29
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
ATTATATAATTTTTATTTTTAATAAATTTATTATA
Found at i:2409568 original size:22 final size:22
Alignment explanation
Indices: 2409542--2409589 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
2409532 TAAGTAAAAC
*
2409542 AATTTAATTCATAAATATTTTT
1 AATTTAATTCATAAAAATTTTT
* *
2409564 AATTTTATTTATAAAAATTTTT
1 AATTTAATTCATAAAAATTTTT
2409586 AATT
1 AATT
2409590 AATAAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTAATTCATAAAAATTTTT
Found at i:2409773 original size:44 final size:44
Alignment explanation
Indices: 2409725--2409815 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 44
2409715 AATTTAAAAA
* *
2409725 ATTTACTTGATTTAATTTTTAAAA-TAATTTTAAAAATGTTTT-TT
1 ATTTACTTGATAT-A-TTTAAAAATTAATTTTAAAAATGTTTTATT
* * *
2409769 ATTTATTTGATATATTTAAAAATTAATTTTTAAAATTTTTTATT
1 ATTTACTTGATATATTTAAAAATTAATTTTAAAAATGTTTTATT
2409813 ATT
1 ATT
2409816 CATAATAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 7 0.17
43 17 0.43
44 16 0.40
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (44 bp):
ATTTACTTGATATATTTAAAAATTAATTTTAAAAATGTTTTATT
Found at i:2416722 original size:10 final size:10
Alignment explanation
Indices: 2416695--2416740 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
2416685 TTTAAAATAT
*
2416695 TATAGATTTA
1 TATATATTTA
2416705 TATAATATTTA
1 TAT-ATATTTA
*
2416716 TATATATTTT
1 TATATATTTA
*
2416726 TATATATTTT
1 TATATATTTA
2416736 TATAT
1 TATAT
2416741 TCGTATCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
TATATATTTA
Found at i:2416729 original size:12 final size:12
Alignment explanation
Indices: 2416701--2416740 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
2416691 ATATTATAGA
*
2416701 TTTATATA-ATA
1 TTTATATATATT
2416712 TTTATATATA-T
1 TTTATATATATT
2416723 TTT-TATATATT
1 TTTATATATATT
2416734 TTTATAT
1 TTTATAT
2416741 TCGTATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 6 0.24
11 15 0.60
12 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTATATATATT
Found at i:2417700 original size:17 final size:17
Alignment explanation
Indices: 2417659--2417701 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2417649 TTAACTTTAA
* *
2417659 ATTTAATTACATAAAAT
1 ATTTAAATACAAAAAAT
2417676 -TTTAAAATACAAAAAAT
1 ATTT-AAATACAAAAAAT
2417693 ATTTAAATA
1 ATTTAAATA
2417702 AATAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.14
17 16 0.73
18 3 0.14
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTAAATACAAAAAAT
Found at i:2420833 original size:181 final size:181
Alignment explanation
Indices: 2420529--2420891 Score: 708
Period size: 181 Copynumber: 2.0 Consensus size: 181
2420519 TGGCCAAGGA
2420529 TGGCTTTCACAGGAGATGCCCTATTGATAAGGGGCTGTGGGAGGACAGATTTTCAGGTATAATGC
1 TGGCTTTCACAGGAGATGCCCTATTGATAAGGGGCTGTGGGAGGACAGATTTTCAGGTATAATGC
2420594 CTTGAAAAATGATATTGCAGCTAGATGCAAAAATGAATTTGACTCAGTAATGTTTTTAATATCAA
66 CTTGAAAAATGATATTGCAGCTAGATGCAAAAATGAATTTGACTCAGTAATGTTTTTAATATCAA
2420659 ACAATGAGAGTCATAGCTTCTAAAATATTAATTATGTCAACCAACCTTGGC
131 ACAATGAGAGTCATAGCTTCTAAAATATTAATTATGTCAACCAACCTTGGC
*
2420710 TGGCTTTCGCAGGAGATGCCCTATTGATAAGGGGCTGTGGGAGGACAGATTTTCAGGTATAATGC
1 TGGCTTTCACAGGAGATGCCCTATTGATAAGGGGCTGTGGGAGGACAGATTTTCAGGTATAATGC
2420775 CTTGAAAAATGATATTGCAGCTAGATGCAAAAATGAATTTGACTCAGTAATGTTTTTAATATCAA
66 CTTGAAAAATGATATTGCAGCTAGATGCAAAAATGAATTTGACTCAGTAATGTTTTTAATATCAA
*
2420840 ACAATGAGAGTCATAGCTTCTAAAATATTAATTATGTCAACCCACCTTGGC
131 ACAATGAGAGTCATAGCTTCTAAAATATTAATTATGTCAACCAACCTTGGC
2420891 T
1 T
2420892 TTCTTATGCA
Statistics
Matches: 180, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 180 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (181 bp):
TGGCTTTCACAGGAGATGCCCTATTGATAAGGGGCTGTGGGAGGACAGATTTTCAGGTATAATGC
CTTGAAAAATGATATTGCAGCTAGATGCAAAAATGAATTTGACTCAGTAATGTTTTTAATATCAA
ACAATGAGAGTCATAGCTTCTAAAATATTAATTATGTCAACCAACCTTGGC
Found at i:2422365 original size:2 final size:2
Alignment explanation
Indices: 2422358--2422382 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2422348 ATAAATAAAC
2422358 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2422383 GATTATGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2422825 original size:2 final size:2
Alignment explanation
Indices: 2422820--2422853 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2422810 AAAAAATCTG
*
2422820 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2422854 TCTCCAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2423090 original size:5 final size:5
Alignment explanation
Indices: 2423082--2423231 Score: 51
Period size: 5 Copynumber: 29.8 Consensus size: 5
2423072 ATAAAATTAA
* * * * * *
2423082 ATAAT ATAAAT ATAAT ATAAA ATAAA ATAAA ATTAT -TATAT AAAAA ATAAT
1 ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT
* * * * * *
2423133 ATAAAT ATAAC A-AAA AT-AT ATAAT -TATT TTAAA ATTTAT ATAAAT
1 AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT AT-AAT
* * * *
2423178 ATAAA ATATAT AAAAT ATAATT ATAAT ATAAT AAAAT A-AAT A-AAT ACAAT
1 ATAAT ATA-AT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
2423228 ATAA
1 ATAA
2423232 ATTATCAAAT
Statistics
Matches: 109, Mismatches: 24, Indels: 24
0.69 0.15 0.15
Matches are distributed among these distances:
4 18 0.17
5 65 0.60
6 26 0.24
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:2423096 original size:21 final size:21
Alignment explanation
Indices: 2423080--2423150 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 21
2423070 AGATAAAATT
*
2423080 AAATAATAT-AAATATAATATA
1 AAATAAAATAAAATA-AATATA
* *
2423101 AAATAAAATAAAATTATTATA
1 AAATAAAATAAAATAAATATA
* *
2423122 TAA-AAAATAATATAAATATA
1 AAATAAAATAAAATAAATATA
*
2423142 ACA-AAAATA
1 AAATAAAATA
2423151 TATAATTATT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 21 0.52
21 15 0.38
22 4 0.10
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATAAAATAAAATAAATATA
Found at i:2423098 original size:11 final size:11
Alignment explanation
Indices: 2423082--2423233 Score: 84
Period size: 11 Copynumber: 14.0 Consensus size: 11
2423072 ATAAAATTAA
2423082 ATAATATAAAT
1 ATAATATAAAT
2423093 ATAATATAAA-
1 ATAATATAAAT
*
2423103 ATAAAATAAAATT
1 ATAATAT-AAA-T
* *
2423116 ATTATATAAAAA
1 ATAATAT-AAAT
2423128 ATAATATAAAT
1 ATAATATAAAT
*
2423139 ATAACA-AAA-
1 ATAATATAAAT
*
2423148 AT-ATATAATT
1 ATAATATAAAT
**
2423158 ATTTTA-AAAT
1 ATAATATAAAT
*
2423168 -TTATATAAAT
1 ATAATATAAAT
* *
2423178 ATAAAATATAT
1 ATAATATAAAT
* *
2423189 AAAATATAATT
1 ATAATATAAAT
2423200 ATAATAT-AAT
1 ATAATATAAAT
*
2423210 AAAATAAATAAAT
1 ATAAT--ATAAAT
*
2423223 ACAATATAAAT
1 ATAATATAAAT
2423234 TATCAAATTA
Statistics
Matches: 107, Mismatches: 23, Indels: 22
0.70 0.15 0.14
Matches are distributed among these distances:
8 2 0.02
9 8 0.07
10 24 0.22
11 49 0.46
12 8 0.07
13 16 0.15
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:2423122 original size:23 final size:21
Alignment explanation
Indices: 2423080--2423232 Score: 75
Period size: 21 Copynumber: 7.1 Consensus size: 21
2423070 AGATAAAATT
*
2423080 AAATAATATAAATATAATATA
1 AAATAAAATAAATATAATATA
*
2423101 AAATAAAATAAA-ATTATTATA
1 AAATAAAATAAATA-TAATATA
*
2423122 TAA-AAAAT-AATATAAATATA
1 AAATAAAATAAATAT-AATATA
* *
2423142 ACAA-AAATATATAAT-TATTTTA
1 A-AATAAA-ATA-AATATAATATA
* * *
2423164 AAATTTATATAAATATAAAAT-
1 AAA-TAAAATAAATATAATATA
*
2423185 ATATAAAATATAATTATAATATA
1 AAATAAAATA-AA-TATAATATA
* *
2423208 ATAAAATAAATAAATACAATATA
1 A-AATA-AAATAAATATAATATA
2423231 AA
1 AA
2423233 TTATCAAATT
Statistics
Matches: 98, Mismatches: 19, Indels: 29
0.67 0.13 0.20
Matches are distributed among these distances:
19 3 0.03
20 17 0.17
21 33 0.34
22 21 0.21
23 12 0.12
24 7 0.07
25 5 0.05
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATAAAATAAATATAATATA
Found at i:2423217 original size:35 final size:34
Alignment explanation
Indices: 2423072--2423236 Score: 110
Period size: 35 Copynumber: 4.8 Consensus size: 34
2423062 ATTAAACAAG
* *
2423072 ATAAAATTAAATA-ATATAAATATAATATAAAATAAA
1 ATAAAA-TAAATATATA-AAATATAAT-TATAATATA
* * *
2423108 ATAAAATTATTATATAAAAAATAA-TATAA-AT-
1 ATAAAATAAATATATAAAATATAATTATAATATA
* * * *
2423139 ATAACAA-AAATATAT-AATTAT-TTTAAAATTTA
1 ATAA-AATAAATATATAAAATATAATTATAATATA
2423171 TATAAATATAAAATATATAAAATATAATTATAATATA
1 -ATAAA-AT-AAATATATAAAATATAATTATAATATA
* *
2423208 ATAAAATAAATAAATACAATATAAATTAT
1 ATAAAATAAATATATAAAATAT-AATTAT
2423237 CAAATTAGTT
Statistics
Matches: 99, Mismatches: 18, Indels: 25
0.70 0.13 0.18
Matches are distributed among these distances:
30 8 0.08
31 11 0.11
32 4 0.04
33 9 0.09
34 13 0.13
35 27 0.27
36 19 0.19
37 8 0.08
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (34 bp):
ATAAAATAAATATATAAAATATAATTATAATATA
Found at i:2423250 original size:85 final size:85
Alignment explanation
Indices: 2423085--2423250 Score: 212
Period size: 84 Copynumber: 2.0 Consensus size: 85
2423075 AAATTAAATA
* * *
2423085 ATATAAATATAATATAAAATAAAATAAAATTATTATATAAAAAATAATATAAATATAACAAAAAT
1 ATATAAATATAAAATAAAATAAAATAAAATTATAATATAAAAAATAATATAAATACAACAAAAAT
*
2423150 ATATAATTATTTTAAAATTT
66 ATATAATTAGTTTAAAATTT
* * * *
2423170 ATATAAATATAAAAT-ATATAAAATATAATTATAATATAATAAAATAA-ATAAATACAATATAAA
1 ATATAAATATAAAATAAAATAAAATAAAATTATAATATAA-AAAATAATATAAATACAACAAAAA
2423233 T-TATCAAATTAGTTTAAA
65 TATAT--AATTAGTTTAAA
2423251 TATATCTAGG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
83 3 0.04
84 35 0.50
85 32 0.46
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.36
Consensus pattern (85 bp):
ATATAAATATAAAATAAAATAAAATAAAATTATAATATAAAAAATAATATAAATACAACAAAAAT
ATATAATTAGTTTAAAATTT
Found at i:2424278 original size:12 final size:12
Alignment explanation
Indices: 2424261--2424303 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2424251 TTTAATAATA
2424261 AAAATAAAAAAT
1 AAAATAAAAAAT
2424273 AAAAT---AAAT
1 AAAATAAAAAAT
2424282 AAAATAAAAAAT
1 AAAATAAAAAAT
*
2424294 TAAATAAAAA
1 AAAATAAAAA
2424304 GGTTGAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 9 0.33
12 18 0.67
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:2424281 original size:9 final size:9
Alignment explanation
Indices: 2424269--2424302 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2424259 TAAAAATAAA
2424269 AAATAAAAT
1 AAATAAAAT
2424278 AAATAAAAT
1 AAATAAAAT
*
2424287 AAA-AAATT
1 AAATAAAAT
2424295 AAATAAAA
1 AAATAAAA
2424303 AGGTTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2424285 original size:21 final size:21
Alignment explanation
Indices: 2424261--2424301 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2424251 TTTAATAATA
2424261 AAAATAAAAAATAAAATAAAT
1 AAAATAAAAAATAAAATAAAT
*
2424282 AAAATAAAAAATTAAATAAA
1 AAAATAAAAAATAAAATAAA
2424302 AAGGTTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAATAAAAAATAAAATAAAT
Found at i:2429602 original size:16 final size:17
Alignment explanation
Indices: 2429571--2429604 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2429561 ATTAAGTTTA
*
2429571 TTTAATGAATAAATATT
1 TTTAATGAAAAAATATT
2429588 TTTAAT-AAAAAATATT
1 TTTAATGAAAAAATATT
2429604 T
1 T
2429605 AGTGAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAATGAAAAAATATT
Found at i:2432314 original size:2 final size:2
Alignment explanation
Indices: 2432309--2432333 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2432299 TATATATATA
2432309 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2432334 TTCAAAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2434983 original size:18 final size:20
Alignment explanation
Indices: 2434947--2434989 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2434937 TTTTTTTAAT
*
2434947 TATAACTTTTAATATATAAA
1 TATAAATTTTAATATATAAA
2434967 -ATAAATTTTAA-ATATAAA
1 TATAAATTTTAATATATAAA
2434985 TATAA
1 TATAA
2434990 TATATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAAATTTTAATATATAAA
Found at i:2435520 original size:6 final size:7
Alignment explanation
Indices: 2435497--2435528 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
2435487 AACATTTTTA
2435497 TATATAT
1 TATATAT
2435504 TATATAT
1 TATATAT
2435511 TATA-AT
1 TATATAT
2435517 TATAT-T
1 TATATAT
2435523 TATATA
1 TATATA
2435529 ATATTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 12 0.52
7 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:2439838 original size:31 final size:31
Alignment explanation
Indices: 2439742--2439844 Score: 95
Period size: 31 Copynumber: 3.3 Consensus size: 31
2439732 TTAAAAATTA
*
2439742 ATATTTAATAAA-TTTAAGTATTAAATTTTCAT
1 ATATTTAATAAATTTTAAAT-TTAAA-TTTCAT
* * * *
2439774 ATATATAAT--TTTTTAAATTATAACTTTTAAT
1 ATATTTAATAAATTTTAAATT-TAA-ATTTCAT
*
2439805 ATATTTAATAAATTTTAAATTTAAATATCAT
1 ATATTTAATAAATTTTAAATTTAAATTTCAT
2439836 ATATTTAAT
1 ATATTTAAT
2439845 TTATATTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
30 1 0.02
31 35 0.62
32 11 0.20
33 9 0.16
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (31 bp):
ATATTTAATAAATTTTAAATTTAAATTTCAT
Found at i:2440169 original size:20 final size:22
Alignment explanation
Indices: 2440144--2440190 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
2440134 TTAATTATAA
2440144 AATATT-TA-AATATAAAAAAT
1 AATATTATATAATATAAAAAAT
*
2440164 AATATTATATTAATATAATAAAT
1 AATATTATA-TAATATAAAAAAT
2440187 AATA
1 AATA
2440191 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 2 0.09
23 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATATTATATAATATAAAAAAT
Found at i:2440374 original size:13 final size:13
Alignment explanation
Indices: 2440364--2440389 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2440354 TTATATATAT
2440364 AATCTAAATATTA
1 AATCTAAATATTA
2440377 AATCTAAATATTA
1 AATCTAAATATTA
2440390 TATTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
AATCTAAATATTA
Found at i:2442674 original size:14 final size:14
Alignment explanation
Indices: 2442649--2442688 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2442639 ATATATCAAA
2442649 ATTTTATTAAATATC
1 ATTTT-TTAAATATC
*
2442664 ATTTTTTAAATATG
1 ATTTTTTAAATATC
*
2442678 ATTATTTAAAT
1 ATTTTTTAAAT
2442689 TAATTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (14 bp):
ATTTTTTAAATATC
Found at i:2442790 original size:12 final size:12
Alignment explanation
Indices: 2442773--2442798 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2442763 TTGATTTTTT
2442773 TTTTTCAATTTA
1 TTTTTCAATTTA
2442785 TTTTTCAATTTA
1 TTTTTCAATTTA
2442797 TT
1 TT
2442799 AAGTCTCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTCAATTTA
Found at i:2446801 original size:20 final size:20
Alignment explanation
Indices: 2446776--2446816 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2446766 GTGTATAAGG
2446776 CTTAGATATTATAAATCATA
1 CTTAGATATTATAAATCATA
2446796 CTTAGATATTATAAATCATA
1 CTTAGATATTATAAATCATA
2446816 C
1 C
2446817 CTAGCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (20 bp):
CTTAGATATTATAAATCATA
Found at i:2450933 original size:2 final size:2
Alignment explanation
Indices: 2450928--2450956 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2450918 TTTATATATA
2450928 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2450957 ATCTGTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2456411 original size:15 final size:15
Alignment explanation
Indices: 2456388--2456437 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
2456378 TTAAGATACG
* *
2456388 AAATTAAAATTAAAA
1 AAATAAAAAATAAAA
2456403 AAATAAAAAATAATAA
1 AAATAAAAAATAA-AA
2456419 CAAATAAAATAATAAAA
1 -AAATAAAA-AATAAAA
2456436 AA
1 AA
2456438 TTCTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 11 0.37
16 4 0.13
17 10 0.33
18 5 0.17
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAAAAAATAAAA
Found at i:2458997 original size:13 final size:13
Alignment explanation
Indices: 2458979--2459004 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2458969 TACACAAAGT
2458979 ATGTATCGATACA
1 ATGTATCGATACA
2458992 ATGTATCGATACA
1 ATGTATCGATACA
2459005 CAAAAACATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2459002 original size:32 final size:33
Alignment explanation
Indices: 2458961--2459024 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
2458951 TAGCCAAACT
**
2458961 TGTATCGATACAC-AAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAACATGTATCGATACAA
2458993 TGTATCGATACACAAAAACATGTATCGATACA
1 TGTATCGATACACAAAAACATGTATCGATACA
2459025 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACAAAAACATGTATCGATACAA
Found at i:2468630 original size:169 final size:169
Alignment explanation
Indices: 2468329--2468690 Score: 399
Period size: 169 Copynumber: 2.1 Consensus size: 169
2468319 CGTAGTCTAT
* ** * *
2468329 CTGTCGGCTTTGACCCTGGAGACTACCCCATCTAAAGTCTGTCTGTCAGCTTTGACCCTAGAGAT
1 CTGTCAGCTTTGACCCTGGAGACTACCCCATCTAAAGTCTACCTGTCAGCTTCGACCCTAGAGAC
* ** * * *
2468394 TGCCTCATTTTAAGTCTGCATGTCGGCTTCATCCCTGGAGACGTTTCTATCCCTTAGTCTGCCTG
66 TGCCTCATTTAAAGTCTGCATGTCAACTTCATCCCTAGAGACGTTTCTATCCCTTAGTATACCTG
*
2468459 TCGATTTTAACCCTAGAAACTTTCTTTTTCTTAGTCTGC
131 TCGACTTTAACCCTAGAAACTTTCTTTTTCTTAGTCTGC
* * * * * *
2468498 CTGTCAGCTTTGACCTTGGAGACTACCTCATTTAAAGTCTACCTGTCGGCTTCGTCCCTGGAGAC
1 CTGTCAGCTTTGACCCTGGAGACTACCCCATCTAAAGTCTACCTGTCAGCTTCGACCCTAGAGAC
* * *
2468563 TGCCTCATTTAAAGTCTGCCTGTCAATTTCGTCCCTAGAGAC-TTTCCTA-CCCTTCAGTATACC
66 TGCCTCATTTAAAGTCTGCATGTCAACTTCATCCCTAGAGACGTTT-CTATCCCTT-AGTATACC
* * * * *
2468626 TGTCGACTTTGACCCTGGAGA-TTGTC-TTATCTAAAGTCTGC
129 TGTCGACTTTAACCCTAGAAACTT-TCTTTTTCT-TAGTCTGC
* * *
2468667 CTTTCGGCTTTGACCCTGAAGACT
1 CTGTCAGCTTTGACCCTGGAGACT
2468691 TTCTACCCTT
Statistics
Matches: 159, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
168 15 0.09
169 144 0.91
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (169 bp):
CTGTCAGCTTTGACCCTGGAGACTACCCCATCTAAAGTCTACCTGTCAGCTTCGACCCTAGAGAC
TGCCTCATTTAAAGTCTGCATGTCAACTTCATCCCTAGAGACGTTTCTATCCCTTAGTATACCTG
TCGACTTTAACCCTAGAAACTTTCTTTTTCTTAGTCTGC
Found at i:2468779 original size:169 final size:167
Alignment explanation
Indices: 2468575--2469662 Score: 975
Period size: 169 Copynumber: 6.4 Consensus size: 167
2468565 CCTCATTTAA
* * * * * *
2468575 AGTCTGCCTGTCAATTTCGTCCCTAGAGACTTTCCTACCCTTCAGTATACCTGTCGACTTTGACC
1 AGTCTGCCTGTCGATTTTGACCCTGGAGACTTTCCTACCC-TCAGTCTACCTGTCGGCTTTGACC
* *
2468640 CTGGAGA-TTGT-CTTATCTAAAGTCTGCCTTTCGGCTTTGACCCTGAAGACTTTC-TA-CCCTT
65 CTGGAGACTT-TCCTT-CCT-AAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTCTTATCCCTT
* *
2468701 AGTCTGACTGTCAGCTTTGATCCTGAAAACTTTTCTATCTCTT
127 AGTCTGACTGTCAGCTTTGA-CCTGAAGACTTTTC-ATCCCTT
* * * * * *
2468744 AGTCTGCCTGTCTG-CTTTGACCCGGGAAACTTTCCTATCCCTTAGTATGCCTGTCGGCTTTGAC
1 AGTCTGCCTGTC-GATTTTGACCCTGGAGACTTTCCTA-CCCTCAGTCTACCTGTCGGCTTTGAC
* * * * * * * *
2468808 CCTGAAGACTTTTCTATCCCTAAGTCTGCCTATCGGCTTTGACCTTGGAGATTTTTCCTATCCTT
64 CCTGGAGACTTTCCT-T-CCTAAGTCTGCCTGTCGGCTTTGACCCTGAAGA-CTTTCTTATCCCT
* *
2468873 TAGTCTAACTGTCGGCTTTGACCCTGGAA-ACTTTTCATCCCTT
126 TAGTCTGACTGTCAGCTTTGA-CCT-GAAGACTTTTCATCCCTT
* * * * * * * *
2468916 AGTCTGCCTGTCGATTTTAACCCTGGAGACTTTTCAACCCTTAGTCTGCCTATCGACTTTGACCT
1 AGTCTGCCTGTCGATTTTGACCCTGGAGACTTTCCTACCCTCAGTCTACCTGTCGGCTTTGACCC
*
2468981 TGGAGACTTTCCTTCCCTCAA-TCTGCCTGTCAGCTTTGACCCT-AGAGACTTT-TCT-TCCCTT
66 TGGAGACTTTCCTT-CCT-AAGTCTGCCTGTCGGCTTTGACCCTGA-AGACTTTCT-TATCCCTT
* *
2469042 AGTCTGCCTATCAGCTTTGACCTTGAAGACTTTTCATCCCTT
127 AGTCTGACTGTCAGCTTTGACC-TGAAGACTTTTCATCCCTT
* * *
2469084 AGTCTACCTGTCGATTTTGACCCTGGAGACTTTTCAACCCTCAGTCTACCTGTCGGCTTTGACCC
1 AGTCTGCCTGTCGATTTTGACCCTGGAGACTTTCCTACCCTCAGTCTACCTGTCGGCTTTGACCC
* * * * *
2469149 TAGAGACTCTCCTTCCTTTAGTCTGCCTGTAGGCTTTGACCCTGGAGACTTTTCTT-TCCCTTAG
66 TGGAGACTTTCCTTCC-TAAGTCTGCCTGTCGGCTTTGACCCTGAAGAC-TTTCTTATCCCTTAG
* * * ***
2469213 T-TTACCTGTCGGCTTTGACACTGAAGACCTTTCATTTATT
129 TCTGA-CTGTCAGCTTTGAC-CTGAAGACTTTTCATCCCTT
* * * * *
2469253 AGTCTGCTTG-CTGGTTTTGACCTTGGAGACTTTTC-AACCTCAGTCTACCTTGTCGGCTTTGAC
1 AGTCTGCCTGTC-GATTTTGACCCTGGAGACTTTCCTACCCTCAGTCTACC-TGTCGGCTTTGAC
* * * * * * *
2469316 CTTAGAGACTTTCCTTCCTTCAGTCTGTCTGTCGGCTTTGACCTTGGAGACTTTCTTATCCCCTA
64 CCTGGAGACTTTCCTTCC-TAAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTCTTATCCCTTA
* * * *
2469381 GTCTGCCTATCGGCTTTGACCCTGAAGACTTTTC-TACCCTC
128 GTCTGACTGTCAGCTTTGA-CCTGAAGACTTTTCAT-CCCTT
* * * *
2469422 AGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTCCCTCAGTCTGCCTGTCGGCTTTGACCT
1 AGTCTGCCTGTCGATTTTGACCCTGGAGACTTTCCTACCCTCAGTCTACCTGTCGGCTTTGACCC
* * * * *
2469487 TGGAGACTTTCTTTCCCTAAGTTTGCCTGTCGGCTTTGACCCT-AGAGGCTTTCATATCCCTAAG
66 TGGAGACTTTCCTT-CCTAAGTCTGCCTGTCGGCTTTGACCCTGA-AGACTTTCTTATCCCTTAG
* * * * *
2469551 TTTGCCTGTTAGCTTTGACCTTGGAGACTTTCTTATCCCTT
129 TCTGACTGTCAGCTTTGACC-TGAAGACTTT-TCATCCCTT
* * * * * * * *
2469592 AGTCTGCCTGTCGGTTTTGACCTTGGAGACTTTCTTTCCCTAAGTCTGCCCGTTGGCTTTGACCC
1 AGTCTGCCTGTCGATTTTGACCCTGGAGACTTTCCTACCCTCAGTCTACCTGTCGGCTTTGACCC
*
2469657 GGGAGA
66 TGGAGA
2469663 ATTTTTTTTT
Statistics
Matches: 763, Mismatches: 121, Indels: 69
0.80 0.13 0.07
Matches are distributed among these distances:
167 8 0.01
168 155 0.20
169 336 0.44
170 146 0.19
171 46 0.06
172 37 0.05
173 32 0.04
174 3 0.00
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (167 bp):
AGTCTGCCTGTCGATTTTGACCCTGGAGACTTTCCTACCCTCAGTCTACCTGTCGGCTTTGACCC
TGGAGACTTTCCTTCCTAAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTCTTATCCCTTAGTC
TGACTGTCAGCTTTGACCTGAAGACTTTTCATCCCTT
Found at i:2468939 original size:42 final size:42
Alignment explanation
Indices: 2468406--2469667 Score: 899
Period size: 42 Copynumber: 29.8 Consensus size: 42
2468396 CCTCATTTTA
* * *
2468406 AGTCTGCATGTCGGC-TTCATCCCTGGAGACGTTTCTATCCCTT
1 AGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTTC-ATCCCTT
** * * * * **
2468449 AGTCTGCCTGTCGATTTTAACCCTAGAAAC-TTTCTTTTTCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTT
* * **
2468491 AGTCTGCCTGTCAGCTTTGACCTTGGAGACTACCTCAT---TT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTTCATCCCTT
* * * **
2468531 AAAGTCTACCTGTCGGCTTCGTCCCTGGAGACTGCCTCAT---TT
1 --AGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTTCATCCCTT
** * * *
2468573 AAAGTCTGCCTGTC-AATTTCGTCCCTAGAGAC-TTTCCTACCCTT
1 --AGTCTGCCTGTCGGCTTT-GACCCTGGAGACTTTTCAT-CCCTT
* * * * * ** *
2468617 CAGTATACCTGTCGACTTTGACCCTGGAGA-TTGTCTTATCTAA
1 -AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCT-T
* *
2468660 AGTCTGCCTTTCGGCTTTGACCCTGAAGAC-TTTC-TACCCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAT-CCCTT
* * * * * *
2468701 AGTCTGACTGTCAGCTTTGATCCTGAAAACTTTTCTATCTCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTT
* * * *
2468744 AGTCTGCCTGTCTGCTTTGACCCGGGAAACTTTCCTATCCCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTT
* * *
2468787 AGTATGCCTGTCGGCTTTGACCCTGAAGACTTTTCTATCCCTA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTT
* * * *
2468830 AGTCTGCCTATCGGCTTTGACCTTGGAGATTTTTCCTATCCTTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTT-C-ATCCCTT
** *
2468874 AGTCTAACTGTCGGCTTTGACCCTGGAAACTTTTCATCCCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
** * *
2468916 AGTCTGCCTGTCGATTTTAACCCTGGAGACTTTTCAACCCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
* * * * * *
2468958 AGTCTGCCTATCGACTTTGACCTTGGAGACTTTCCTTCCCTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
* * * *
2469000 AATCTGCCTGTCAGCTTTGACCCTAGAGACTTTTCTTCCCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
* * * *
2469042 AGTCTGCCTATCAGCTTTGACCTTGAAGACTTTTCATCCCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
* ** * *
2469084 AGTCTACCTGTCGATTTTGACCCTGGAGACTTTTCAACCCTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
* * * * * *
2469126 AGTCTACCTGTCGGCTTTGACCCTAGAGACTCTCCTTCCTTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
* *
2469168 AGTCTGCCTGTAGGCTTTGACCCTGGAGACTTTTCTTTCCCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTT
* * * * * ***
2469211 AGTTTACCTGTCGGCTTTGACACTGAAGACCTTTCATTTATT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
* * * * *
2469253 AGTCTGCTTG-CTGGTTTTGACCTTGGAGACTTTTCA-ACCTC
1 AGTCTGCCTGTC-GGCTTTGACCCTGGAGACTTTTCATCCCTT
* * * * *
2469294 AGTCTACCTTGTCGGCTTTGACCTTAGAGAC-TTTCCTTCCTT
1 AGTCTGCC-TGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
* * * *
2469336 CAGTCTGTCTGTCGGCTTTGACCTTGGAGACTTTCTTATCCCCT
1 -AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-TCATCCCTT
* * *
2469380 AGTCTGCCTATCGGCTTTGACCCTGAAGACTTTTC-TACCCTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAT-CCCTT
* * * *
2469422 AGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTCCCTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
* * *
2469464 AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TTTCTTTCCCTA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTT
* * * *
2469506 AGTTTGCCTGTCGGCTTTGACCCTAGAGGC-TTTCATATCCCTA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC--ATCCCTT
* ** * *
2469549 AGTTTGCCTGTTAGCTTTGACCTTGGAGACTTTCTTATCCCTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-TCATCCCTT
* * * *
2469592 AGTCTGCCTGTCGGTTTTGACCTTGGAGAC-TTTCTTTCCCTA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTT
* * * *
2469634 AGTCTGCCCGTTGGCTTTGACCCGGGAGAATTTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTT
2469668 TTTTTTTTTT
Statistics
Matches: 968, Mismatches: 216, Indels: 70
0.77 0.17 0.06
Matches are distributed among these distances:
40 5 0.01
41 45 0.05
42 572 0.59
43 291 0.30
44 54 0.06
45 1 0.00
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.37
Consensus pattern (42 bp):
AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTT
Found at i:2469311 original size:127 final size:124
Alignment explanation
Indices: 2468660--2469627 Score: 586
Period size: 127 Copynumber: 7.6 Consensus size: 124
2468650 TCTTATCTAA
* * * * * *
2468660 AGTCTGCCTTTCGGCTTTGACCCTGAAGACTTT-CTACCCTTAGTCTGACTGTCAGCTTTGATCC
1 AGTCTACCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGA-CC
* * * * * * * *
2468724 -TGAAAACTTTTCTATCTCTTAGTCTGCCTGTCTGCTTTGACCCGGGAA-ACTTTCCTATCCCTT
65 TTGAAGAC-TTTCT-TATC-TAGTCTGCCTATCGGCTTTGACCC-TGAAGACTTTTCTA-ACCTC
* * * * * *
2468787 AGTATGCCTGTCGGCTTTGACCCTGAAGACTTTTCTATCCCTAAGTCTGCCTATCGGCTTTGACC
1 AGTCTACCTGTCGGCTTTGACCCTGGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * ** * *
2468852 TTGGAGATTTTTCCTATCCTTTAGTCTAACTGTCGGCTTTGACCCTGGAA-ACTTTTC-ATCCCT
65 TTGAAGA-CTTTCTTAT-C--TAGTCTGCCTATCGGCTTTGACCCT-GAAGACTTTTCTA-ACCT
*
2468915 T
124 C
* ** * * ** * *
2468916 AGTCTGCCTGTCGATTTTAACCCTGGAGACTTTTCAACCCTTAGTCTGCCTATCGACTTTGACCT
1 AGTCTACCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* ** * * * ** *
2468981 TGGAGACTTTCCTTCCCTCAATCTGCCTGTCAGCTTTGACCCT-AGAGACTTTTCTTCCCTT
66 TGAAGACTTT-CTTATCT-AGTCTGCCTATCGGCTTTGACCCTGA-AGACTTTTCTAACCTC
* * * * * * * * ** *
2469042 AGTCTGCCTATCAGCTTTGACCTTGAAGACTTTTCATCCCTTAGTCTACCTGTCGATTTTGACCC
1 AGTCTACCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * * * * * * * *
2469107 TGGAGACTTT-TCAACCCTCAGTCTACCTGTCGGCTTTGACCCT-AGAGACTCTCCT-TCCTTT
66 TGAAGACTTTCT-TA-TCT-AGTCTGCCTATCGGCTTTGACCCTGA-AGACTTTTCTAACC-TC
* * * * *
2469168 AGTCTGCCTGTAGGCTTTGACCCTGGAGACTTTTCTTTCCCTTAGTTTACCTGTCGGCTTTGACA
1 AGTCTACCTGTCGGCTTTGACCCTGGAGAC-TTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGAC-
* * *
2469233 C-TGAAGACCTTTCATTTAT-TAGTCTG-CT-TGCTGGTTTTGACCTTGGAGACTTTTC-AACCT
64 CTTGAAGA-CTTTC--TTATCTAGTCTGCCTAT-C-GGCTTTGACCCTGAAGACTTTTCTAACCT
2469293 C
124 C
* * *
2469294 AGTCTACCTTGTCGGCTTTGACCTTAGAGACTTTCCTT-CCTTCAGTCTGTCTGTCGGCTTTGAC
1 AGTCTACC-TGTCGGCTTTGACCCTGGAGACTTTCCTTCCCTT-AGTCTGCCTGTCGGCTTTGAC
* *
2469358 CTTGGAGACTTTCTTATCCCCTAGTCTGCCTATCGGCTTTGACCCTGAAGACTTTTCTACCCTC
64 CTTGAAGACTTTCTTAT---CTAGTCTGCCTATCGGCTTTGACCCTGAAGACTTTTCTAACCTC
* * *
2469422 AGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTCCCTCAGTCTGCCTGTCGGCTTTGACCT
1 AGTCTACCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * * * * *
2469487 TGGAGACTTTCTT-TCCCTAAGTTTGCCTGTCGGCTTTGACCCT-AGAGGC-TTTCATATCCCTA
66 TGAAGACTTTCTTAT--CT-AGTCTGCCTATCGGCTTTGACCCTGA-AGACTTTTC-TA-ACCTC
* * ** * * *
2469549 AGTTTGCCTGTTAGCTTTGACCTTGGAGACTTTCTTATCCCTTAGTCTGCCTGTCGGTTTTGACC
1 AGTCTACCTGTCGGCTTTGACCCTGGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACC
*
2469614 TTGGAGACTTTCTT
65 TTGAAGACTTTCTT
2469628 TCCCTAAGTC
Statistics
Matches: 692, Mismatches: 108, Indels: 81
0.79 0.12 0.09
Matches are distributed among these distances:
123 4 0.01
124 2 0.00
125 24 0.03
126 225 0.33
127 232 0.34
128 104 0.15
129 68 0.10
130 32 0.05
131 1 0.00
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.38
Consensus pattern (124 bp):
AGTCTACCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
TGAAGACTTTCTTATCTAGTCTGCCTATCGGCTTTGACCCTGAAGACTTTTCTAACCTC
Found at i:2470121 original size:21 final size:20
Alignment explanation
Indices: 2470093--2470136 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2470083 TAAAGTTTAT
* * *
2470093 AAAAAAATTATTAAACATAA
1 AAAAAAATAAATAAAAATAA
2470113 AAAATAAATAAATAAAAATAA
1 AAAA-AAATAAATAAAAATAA
2470134 AAA
1 AAA
2470137 CTTTGGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAAAATAAATAAAAATAA
Found at i:2470776 original size:16 final size:15
Alignment explanation
Indices: 2470757--2470787 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2470747 AAAAAAATAA
2470757 AAAATAATAACAAAAT
1 AAAATAATAA-AAAAT
2470773 AAAATAATAAAAAAT
1 AAAATAATAAAAAAT
2470788 TCTCTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:2474042 original size:28 final size:28
Alignment explanation
Indices: 2474011--2474075 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
2474001 TAAAGGGGTT
2474011 AATTAAAATTTTACAT-ATGATAAAATTC-
1 AATTAAAATTTTA-ATCATG-TAAAATTCA
* *
2474039 AATTAAAACTTTAATCATGTAAAGTTCA
1 AATTAAAATTTTAATCATGTAAAATTCA
2474067 AATTAAAAT
1 AATTAAAAT
2474076 ACTATGAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.37
Consensus pattern (28 bp):
AATTAAAATTTTAATCATGTAAAATTCA
Found at i:2482600 original size:29 final size:30
Alignment explanation
Indices: 2482554--2482627 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
2482544 ACCTTTTAAC
*
2482554 AATAAATTTGTATATTTTT-A-TTATATTGA
1 AATAAATTTATAT-TTTTTAATTTATATTGA
* *
2482583 AATAAATTTTTATTTTTTAATTTATATTTA
1 AATAAATTTATATTTTTTAATTTATATTGA
2482613 AATAAATTTATATTT
1 AATAAATTTATATTT
2482628 CAAATGAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.12
29 13 0.32
30 22 0.55
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
AATAAATTTATATTTTTTAATTTATATTGA
Found at i:2482622 original size:16 final size:16
Alignment explanation
Indices: 2482574--2482632 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
2482564 TATATTTTTA
*
2482574 TTATATTGAAATAAAT
1 TTATATTTAAATAAAT
* * *
2482590 TTTTATTT--TTTAAT
1 TTATATTTAAATAAAT
2482604 TTATATTTAAATAAAT
1 TTATATTTAAATAAAT
2482620 TTATATTTCAAAT
1 TTATATTT-AAAT
2482633 GAAAGATTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
14 11 0.33
16 18 0.55
17 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
TTATATTTAAATAAAT
Found at i:2483028 original size:116 final size:115
Alignment explanation
Indices: 2482874--2483095 Score: 309
Period size: 116 Copynumber: 1.9 Consensus size: 115
2482864 ATCCACGAGC
* * *
2482874 ATTTTTATTTATATTAAAAATATATTTATGTTTAAATTAATTAGAGTTTTTCTATATAATTTAAA
1 ATTTCTATTTATATTAAAAATATATCTATGTTTAAATTAATTAGAGTTTTTCTATACAATTTAAA
** * * *
2482939 AATTAAAAATTTATTTGGCACAGATTAAAGGTTAAAAATTTACCATAGAT
66 AATTAAAAATTTATTTGAAAAAAATTAAAGATTAAAAATTTACCATAGAT
* * *
2482989 ATTTCTATTTATGTTAAAAAGTATATCTATTTTTAAATTAATTAGAGTTTTTTTATACAATTTAA
1 ATTTCTATTTATATTAAAAA-TATATCTATGTTTAAATTAATTAGAGTTTTTCTATACAATTTAA
** *
2483054 AGGTTAAATATTTATTTGAAAAAAATTAAAGATTAAAAATTT
65 AAATTAAAAATTTATTTGAAAAAAATTAAAGATTAAAAATTT
2483096 GTTTAATTAT
Statistics
Matches: 92, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
115 18 0.20
116 74 0.80
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (115 bp):
ATTTCTATTTATATTAAAAATATATCTATGTTTAAATTAATTAGAGTTTTTCTATACAATTTAAA
AATTAAAAATTTATTTGAAAAAAATTAAAGATTAAAAATTTACCATAGAT
Found at i:2487991 original size:24 final size:24
Alignment explanation
Indices: 2487959--2488005 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2487949 CGTCTTAGTG
*
2487959 CCCAATTCTCAAGTGGCTTTTATA
1 CCCAATTCTCAAGTGACTTTTATA
2487983 CCCAATTCTCAAGTGACTTTTAT
1 CCCAATTCTCAAGTGACTTTTAT
2488006 CAAAGCATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.38
Consensus pattern (24 bp):
CCCAATTCTCAAGTGACTTTTATA
Found at i:2488378 original size:3 final size:3
Alignment explanation
Indices: 2488370--2488402 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2488360 TCTAATTACA
2488370 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2488403 TCCTACTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2489532 original size:23 final size:21
Alignment explanation
Indices: 2489498--2489543 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
2489488 TATAAGTATA
*
2489498 TTTTAAATAATAAAATAATTT
1 TTTTAAATAATAAAATAAATT
*
2489519 TTTTAAATTAAATAAGATAAATT
1 TTTTAAA-T-AATAAAATAAATT
2489542 TT
1 TT
2489544 GGATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTTAAATAATAAAATAAATT
Found at i:2489625 original size:28 final size:30
Alignment explanation
Indices: 2489594--2489664 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 30
2489584 TTTATAAAAA
*
2489594 AAATTATAATTTAAATT-TA-AAATTTATT
1 AAATTATAATTTAAATTATATAAATTAATT
2489622 AAA-TATTAA-TT-AATTATATAAATTAATT
1 AAATTA-TAATTTAAATTATATAAATTAATT
*
2489650 AAATTATATTTTAAA
1 AAATTATAATTTAAA
2489665 CTTCGACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
26 4 0.11
27 6 0.17
28 19 0.54
29 4 0.11
30 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
AAATTATAATTTAAATTATATAAATTAATT
Found at i:2490246 original size:19 final size:19
Alignment explanation
Indices: 2490214--2490257 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2490204 AATATTGATC
2490214 ATATA-AAAAGTAATTAAA
1 ATATATAAAAGTAATTAAA
* *
2490232 ATATATAAAATTAATTTAA
1 ATATATAAAAGTAATTAAA
*
2490251 ATTTATA
1 ATATATA
2490258 TCAAAATAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
ATATATAAAAGTAATTAAA
Found at i:2490502 original size:25 final size:24
Alignment explanation
Indices: 2490474--2490529 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
2490464 TTATTTTTAT
2490474 ATTTTTATAATTAAATTTAAATAA-A
1 ATTTTTATAA-TAAA-TTAAATAATA
* *
2490499 ATTTTT-TTATCAATTAAATAATA
1 ATTTTTATAATAAATTAAATAATA
2490522 ATTTTTAT
1 ATTTTTAT
2490530 TAAACTAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 8 0.30
23 10 0.37
24 3 0.11
25 6 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTTTATAATAAATTAAATAATA
Found at i:2490852 original size:13 final size:14
Alignment explanation
Indices: 2490836--2490867 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2490826 GTATATTTAT
2490836 AAAATTTATTG-AA
1 AAAATTTATTGTAA
2490849 AAAATTTATTGTAA
1 AAAATTTATTGTAA
2490863 AAAAT
1 AAAAT
2490868 AAAGATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (14 bp):
AAAATTTATTGTAA
Found at i:2491451 original size:16 final size:14
Alignment explanation
Indices: 2491415--2491443 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2491405 AAAAATTATA
2491415 TAATAATATATTTT
1 TAATAATATATTTT
2491429 TAATAATATATTTT
1 TAATAATATATTTT
2491443 T
1 T
2491444 TAATTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATAATATATTTT
Found at i:2494266 original size:39 final size:41
Alignment explanation
Indices: 2494223--2494301 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
2494213 TTAATTCAAA
* *
2494223 TTAATATAATTTAATT-T-TAAATTTATTAATAAAAATATT
1 TTAATATAATTTAATTATATAAATATATAAATAAAAATATT
* *
2494262 TTAATTTAATTTAATTATATAAATATATAAATAATAATAT
1 TTAATATAATTTAATTATATAAATATATAAATAAAAATAT
2494302 AAAAATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 15 0.44
40 1 0.03
41 18 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
TTAATATAATTTAATTATATAAATATATAAATAAAAATATT
Found at i:2494285 original size:27 final size:29
Alignment explanation
Indices: 2494232--2494289 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
2494222 ATTAATATAA
2494232 TTTAATTTTAAATTTATTAATAAAAATAT
1 TTTAATTTTAAATTTATTAATAAAAATAT
*
2494261 TTTAA-TTT-AATTTAATTATATAAATATAT
1 TTTAATTTTAAATTT-ATTA-ATAAAAATAT
2494290 AAATAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 5 0.19
28 7 0.27
29 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTAATTTTAAATTTATTAATAAAAATAT
Found at i:2494771 original size:26 final size:25
Alignment explanation
Indices: 2494733--2494781 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
2494723 TTTTTATATG
*
2494733 AAATAAAACTTATCTGAATATAAAA
1 AAATAAAACTTATCTAAATATAAAA
* *
2494758 AAATAAAAATTTATTTAAATATAA
1 AAAT-AAAACTTATCTAAATATAA
2494782 TTAAAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATAAAACTTATCTAAATATAAAA
Found at i:2495176 original size:2 final size:2
Alignment explanation
Indices: 2495171--2495207 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2495161 TGTATTTTAC
2495171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2495208 AGAATATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2495885 original size:15 final size:15
Alignment explanation
Indices: 2495859--2495898 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2495849 TTTTTATTCA
2495859 TAAA-TTAA-ATATT
1 TAAATTTAATATATT
2495872 TAAATTTAATATATT
1 TAAATTTAATATATT
2495887 TAAATTCTAATA
1 TAAATT-TAATA
2495899 ATTAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 11 0.46
16 5 0.21
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATTTAATATATT
Found at i:2499371 original size:22 final size:21
Alignment explanation
Indices: 2499337--2499377 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2499327 AATTGATTGA
2499337 TTTTTTTAAATTTAAAAAACT
1 TTTTTTTAAATTTAAAAAACT
*
2499358 TTTTTATTATATTTAAAAAA
1 TTTTT-TTAAATTTAAAAAA
2499378 TAAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTTTTAAATTTAAAAAACT
Found at i:2499513 original size:11 final size:12
Alignment explanation
Indices: 2499502--2499542 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
2499492 TAATATCAAA
2499502 TTAAATAAAAA-
1 TTAAATAAAAAT
2499513 TTAAATAAAAAT
1 TTAAATAAAAAT
2499525 TTAAATAAAAAT
1 TTAAATAAAAAT
2499537 TTAAAT
1 TTAAAT
2499543 TTATTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAATAAAAAT
Found at i:2504349 original size:22 final size:22
Alignment explanation
Indices: 2504321--2504397 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
2504311 TTTCACGTAA
2504321 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
*
2504343 CATTTCATGCTTGTCACGTAA----
1 CATTTCATGCATG-CA--TAATTTT
2504364 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
2504386 CATTTCATGCAT
1 CATTTCATGCAT
2504398 TTCAAAAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
18 3 0.07
20 2 0.04
21 12 0.26
22 24 0.52
23 2 0.04
25 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (22 bp):
CATTTCATGCATGCATAATTTT
Found at i:2504369 original size:21 final size:21
Alignment explanation
Indices: 2504300--2504373 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
2504290 CATGCATTTT
* *
2504300 CATTTCATGTTTTTCACGTAA
1 CATTTCATGCTTGTCACGTAA
*
2504321 CATTTCATGCATG-CA--TAA
1 CATTTCATGCTTGTCACGTAA
2504339 TTTTCATTTCATGCTTGTCACGTAA
1 ----CATTTCATGCTTGTCACGTAA
2504364 CATTTCATGC
1 CATTTCATGC
2504374 ATGCATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
18 3 0.07
20 2 0.05
21 20 0.48
22 12 0.29
23 2 0.05
25 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (21 bp):
CATTTCATGCTTGTCACGTAA
Found at i:2504418 original size:43 final size:43
Alignment explanation
Indices: 2504295--2504447 Score: 186
Period size: 43 Copynumber: 3.5 Consensus size: 43
2504285 CATTGCATGC
**
2504295 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCATTTCACGTAACATTTCATGCATGCATA
2504338 ATTTTCATTTCATGC-TTGTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCATT-TCACGTAACATTTCATGCATGCATA
** *
2504381 ATTTTCATTTCATGCATTTCA-AAAACATTTCATTGCATTGCACTTC
1 ATTTTCATTTCATGCATTTCACGTAACATTTCA-TGCA-TGCA--TA
2504427 A-TTTCATTTCATTGCATTTCA
1 ATTTTCATTTCA-TGCATTTCA
2504448 TTGCATTGCA
Statistics
Matches: 99, Mismatches: 4, Indels: 11
0.87 0.04 0.10
Matches are distributed among these distances:
42 11 0.11
43 61 0.62
44 6 0.06
45 10 0.10
46 11 0.11
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.45
Consensus pattern (43 bp):
ATTTTCATTTCATGCATTTCACGTAACATTTCATGCATGCATA
Found at i:2504419 original size:5 final size:5
Alignment explanation
Indices: 2504406--2504479 Score: 85
Period size: 5 Copynumber: 14.8 Consensus size: 5
2504396 ATTTCAAAAA
* * * * * *
2504406 CATTT CATTG CATTG CACTT CATTT CATTT CATTG CATTT CATTG CATTG
1 CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT
*
2504456 CATTT CATTT CATTT CATTA CATT
1 CATTT CATTT CATTT CATTT CATT
2504480 GCTTTCATGC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 60 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.50
Consensus pattern (5 bp):
CATTT
Found at i:2504429 original size:10 final size:10
Alignment explanation
Indices: 2504406--2504491 Score: 86
Period size: 10 Copynumber: 8.8 Consensus size: 10
2504396 ATTTCAAAAA
* *
2504406 CATTTCATTG
1 CATTGCATTT
*
2504416 CATTGCACTT
1 CATTGCATTT
*
2504426 CATTTCATTT
1 CATTGCATTT
2504436 CATTGCATTT
1 CATTGCATTT
*
2504446 CATTGCATTG
1 CATTGCATTT
*
2504456 CATTTCATTT
1 CATTGCATTT
* *
2504466 CATTTCATTA
1 CATTGCATTT
2504476 CATTGC-TTT
1 CATTGCATTT
2504485 CA-TGCAT
1 CATTGCAT
2504492 GAAATGGTCG
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
8 3 0.05
9 5 0.08
10 55 0.87
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.49
Consensus pattern (10 bp):
CATTGCATTT
Found at i:2504429 original size:15 final size:14
Alignment explanation
Indices: 2504409--2504487 Score: 77
Period size: 15 Copynumber: 5.4 Consensus size: 14
2504399 TCAAAAACAT
*
2504409 TTCATTGCATTGCA
1 TTCATTTCATTGCA
*
2504423 CTTCATTTCATTTCA
1 -TTCATTTCATTGCA
2504438 TTGCATTTCATTGCA
1 TT-CATTTCATTGCA
*
2504453 TTGCATTTCATTTCA
1 TT-CATTTCATTGCA
* *
2504468 TTTCATTACATTGCT
1 -TTCATTTCATTGCA
2504483 TTCAT
1 TTCAT
2504488 GCATGAAATG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
14 7 0.13
15 46 0.84
16 2 0.04
ACGTcount: A:0.20, C:0.22, G:0.08, T:0.51
Consensus pattern (14 bp):
TTCATTTCATTGCA
Done.