Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 57 of 218
Found at i:17471231 original size:17 final size:16
Alignment explanation
Indices: 17471206--17471255 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 16
17471196 TTAGTTATGA
17471206 TATATAAAATATCTAT
1 TATATAAAATATCTAT
*
17471222 TATGATAAAACATCT-T
1 TAT-ATAAAATATCTAT
*
17471238 TATA-AAAATTTCTAT
1 TATATAAAATATCTAT
17471253 TAT
1 TAT
17471256 TTAGGAAGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 7 0.24
15 5 0.17
16 7 0.24
17 10 0.34
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (16 bp):
TATATAAAATATCTAT
Found at i:17485425 original size:43 final size:43
Alignment explanation
Indices: 17485331--17485418 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
17485321 TTACTAAAAG
17485331 AATGATTTTGTGGAAAATTGCTTAAATTCTTGAACTTGGGATT
1 AATGATTTTGTGGAAAATTGCTTAAATTCTTGAACTTGGGATT
17485374 AATGATTTTGTGGAAAATTGCTTAAATTCTTGAACTTGGGATT
1 AATGATTTTGTGGAAAATTGCTTAAATTCTTGAACTTGGGATT
17485417 AA
1 AA
17485419 GCATTTTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (43 bp):
AATGATTTTGTGGAAAATTGCTTAAATTCTTGAACTTGGGATT
Found at i:17492491 original size:11 final size:11
Alignment explanation
Indices: 17492471--17492527 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
17492461 TAAAAAATAA
17492471 AAAAAGTATTTT
1 AAAAA-TATTTT
17492483 AAAAATATTTT
1 AAAAATATTTT
*
17492494 -AAAATA---A
1 AAAAATATTTT
17492501 AAAAAGTATTTT
1 AAAAA-TATTTT
17492513 AAAAATATTTT
1 AAAAATATTTT
17492524 AAAA
1 AAAA
17492528 TTAAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
8 4 0.11
9 2 0.05
10 6 0.16
11 16 0.42
12 10 0.26
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:17492533 original size:31 final size:30
Alignment explanation
Indices: 17492464--17492535 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
17492454 TTAAAAATAA
17492464 AAAATAAAAAAAGTATTTTAAAAATATTTT
1 AAAATAAAAAAAGTATTTTAAAAATATTTT
17492494 AAAATAAAAAAAGTATTTTAAAAATATTTT
1 AAAATAAAAAAAGTATTTTAAAAATATTTT
*
17492524 AAAATTAAAAAA
1 AAAATAAAAAAA
17492536 TAATATATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAATAAAAAAAGTATTTTAAAAATATTTT
Found at i:17493404 original size:25 final size:25
Alignment explanation
Indices: 17493354--17493400 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
17493344 AATTCTGGGC
17493354 TTTGGTTTTTTATATTTTTTTTGTA
1 TTTGGTTTTTTATATTTTTTTTGTA
*
17493379 TTTGGTTTATT-T-TTTTTTTTGT
1 TTTGGTTTTTTATATTTTTTTTGT
17493401 GTATGCGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 1 0.05
25 10 0.48
ACGTcount: A:0.09, C:0.00, G:0.13, T:0.79
Consensus pattern (25 bp):
TTTGGTTTTTTATATTTTTTTTGTA
Found at i:17493716 original size:44 final size:44
Alignment explanation
Indices: 17493645--17494193 Score: 230
Period size: 44 Copynumber: 12.6 Consensus size: 44
17493635 TTCTTCTGTT
* *
17493645 TACTCCACTGCAACTTCAGCGG-TATAAGATCTGCTTGCTTAGTC
1 TACTCCACTGCAACTTCAG-GGAGATAAGATCTGCTTGCTTAATC
* * *
17493689 TACTCCGCTGCAACTTCAGGGAGATAAGA-CTAG-ATGC--GATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCT-GCTTGCTTAATC
* * *
17493730 TACT-CTCTGTAACTTCAGAGAGATAAGATCTGTCATT--TTAATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTG-C-TTGCTTAATC
* ** * * * *
17493773 CACTCGGCTACAACTTTAGGGAGATAGGAT-T-ATTGACTTTAATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTGCTTG-C-TTAATC
* * * *
17493817 TGCTCCACTACAACTTTAGGGAGATAAGAT-TCGTCAT-CTTCAATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCT-G-CTTGCTT-AATC
* * * * *
17493862 TGCCCCACTACAACTTCAGGGGGATAAGATCTGCTTGCTTAGTC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTGCTTGCTTAATC
* * * *
17493906 TGCTCCGCTGCAACTTTAGGGAGATAAGA-CTAG-ATGC--AATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCT-GCTTGCTTAATC
* ** **
17493947 TGCT-CTTTGCAACTTCAGACAGATAAGATCTGTCATT--TTAATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTG-C-TTGCTTAATC
* * * * *
17493990 TGCTCCACTACAACTTCAGAGAGATAGGAT-T-ATTGGCTTTAATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTGCTT-GC-TTAATC
* * *
17494034 TGCTCCACTGCAACTTCAGAGAGATAAGATTTGCTAT-CTTCAATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTGCT-TGCTT-AATC
** * * * * *
17494079 CGCTCCACTACAACTTCAGGGATATAGGATTTACTAT-CTTCAATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTGCT-TGCTT-AATC
** * * * *
17494124 CGCTCCATTGCAACTTTAGGGAGATAGGATTTG-TAT-CTTCAATC
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTGCT-TGCTT-AATC
** *
17494168 CGCTCTACTGCAACTTCAGGGAGATA
1 TACTCCACTGCAACTTCAGGGAGATA
17494194 GGATTTGTAT
Statistics
Matches: 403, Mismatches: 67, Indels: 70
0.75 0.12 0.13
Matches are distributed among these distances:
40 46 0.11
41 17 0.04
43 30 0.07
44 197 0.49
45 109 0.27
46 2 0.00
47 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
TACTCCACTGCAACTTCAGGGAGATAAGATCTGCTTGCTTAATC
Found at i:17494032 original size:217 final size:217
Alignment explanation
Indices: 17493649--17494099 Score: 679
Period size: 217 Copynumber: 2.1 Consensus size: 217
17493639 TCTGTTTACT
* * *
17493649 CCACTGCAACTTCAGCGGTATAAGATCTGCTTGCTTAGTCTACTCCGCTGCAACTTCAGGGAGAT
1 CCACTACAACTTCAGGGGGATAAGATCTGCTTGCTTAGTCTACTCCGCTGCAACTTCAGGGAGAT
* * * *
17493714 AAGACTAGATGCGATCTACTCTCTGTAACTTCAGAGAGATAAGATCTGTCATTTTAATCCACTCG
66 AAGACTAGATGCAATCTACTCTCTGCAACTTCAGACAGATAAGATCTGTCATTTTAATCCACTCC
* * * * *
17493779 GCTACAACTTTAGGGAGATAGGATTATTGACTTTAATCTGCTCCACTACAACTTTAGGGAGATAA
131 ACTACAACTTCAGAGAGATAGGATTATTGACTTTAATCTGCTCCACTACAACTTCAGAGAGATAA
*
17493844 GATTCG-TCATCTTCAATCTGCC
196 GATTCGCT-ATCTTCAATCCGCC
* *
17493866 CCACTACAACTTCAGGGGGATAAGATCTGCTTGCTTAGTCTGCTCCGCTGCAACTTTAGGGAGAT
1 CCACTACAACTTCAGGGGGATAAGATCTGCTTGCTTAGTCTACTCCGCTGCAACTTCAGGGAGAT
* * **
17493931 AAGACTAGATGCAATCTGCTCTTTGCAACTTCAGACAGATAAGATCTGTCATTTTAATCTGCTCC
66 AAGACTAGATGCAATCTACTCTCTGCAACTTCAGACAGATAAGATCTGTCATTTTAATCCACTCC
* *
17493996 ACTACAACTTCAGAGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAA
131 ACTACAACTTCAGAGAGATAGGATTATTGACTTTAATCTGCTCCACTACAACTTCAGAGAGATAA
* *
17494061 GATTTGCTATCTTCAATCCGCT
196 GATTCGCTATCTTCAATCCGCC
17494083 CCACTACAACTTCAGGG
1 CCACTACAACTTCAGGG
17494100 ATATAGGATT
Statistics
Matches: 210, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
217 209 1.00
218 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (217 bp):
CCACTACAACTTCAGGGGGATAAGATCTGCTTGCTTAGTCTACTCCGCTGCAACTTCAGGGAGAT
AAGACTAGATGCAATCTACTCTCTGCAACTTCAGACAGATAAGATCTGTCATTTTAATCCACTCC
ACTACAACTTCAGAGAGATAGGATTATTGACTTTAATCTGCTCCACTACAACTTCAGAGAGATAA
GATTCGCTATCTTCAATCCGCC
Found at i:17494106 original size:89 final size:88
Alignment explanation
Indices: 17493813--17494245 Score: 353
Period size: 89 Copynumber: 4.9 Consensus size: 88
17493803 TATTGACTTT
* * * * * * * *
17493813 AATCTGCTCCACTACAACTTTAGGGAGATAAGATTCGTCATCTTCAATCTGCCCCACTACAACTT
1 AATCCGCTCCACTACAACTTCAGGGAGATAGGATT-ATTATCTTCAATCCGCTCCACTGCAACTT
* * *
17493878 CAGGGGGATAAGATCTGCT-TGCTT-
65 CAGAGAGATAAGATTTG-TAT-CTTC
* * * * * * * * * * **
17493902 AGTCTGCTCCGCTGCAACTTTAGGGAGATAAGACTA-GA--TGCAATCTGCT-CTTTGCAACTTC
1 AATCCGCTCCACTACAACTTCAGGGAGATAGGATTATTATCTTCAATCCGCTCCACTGCAACTTC
* * *
17493963 AGACAGATAAGATCTGTCAT-TTT
66 AGAGAGATAAGATTTGT-ATCTTC
* * ** * *
17493986 AATCTGCTCCACTACAACTTCAGAGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTC
1 AATCCGCTCCACTACAACTTCAGGGAGATAGGATTATTATCTTCAATCCGCTCCACTGCAACTTC
17494051 AGAGAGATAAGATTTGCTATCTTC
66 AGAGAGATAAGATTTG-TATCTTC
* * *
17494075 AATCCGCTCCACTACAACTTCAGGGATATAGGATTTACTATCTTCAATCCGCTCCATTGCAACTT
1 AATCCGCTCCACTACAACTTCAGGGAGATAGGA-TTATTATCTTCAATCCGCTCCACTGCAACTT
* * *
17494140 TAGGGAGATAGGATTTGTATCTTC
65 CAGAGAGATAAGATTTGTATCTTC
* * *
17494164 AATCCGCTCTACTGCAACTTCAGGGAGATAGGATT-TGTATCTTCAATCCGCTCCACTGTAACTT
1 AATCCGCTCCACTACAACTTCAGGGAGATAGGATTAT-TATCTTCAATCCGCTCCACTGCAACTT
*
17494228 CA-AGAAGATAGGATTTGT
65 CAGAG-AGATAAGATTTGT
17494246 GGTTTCACCG
Statistics
Matches: 282, Mismatches: 50, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
83 3 0.01
84 51 0.18
85 10 0.04
87 11 0.04
88 67 0.24
89 101 0.36
90 39 0.14
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (88 bp):
AATCCGCTCCACTACAACTTCAGGGAGATAGGATTATTATCTTCAATCCGCTCCACTGCAACTTC
AGAGAGATAAGATTTGTATCTTC
Found at i:17494194 original size:44 final size:44
Alignment explanation
Indices: 17493783--17494245 Score: 370
Period size: 44 Copynumber: 10.5 Consensus size: 44
17493773 CACTCGGCTA
* * *
17493783 CAACTTTAGGGAGATAGGATTAT-TGA-CTTTAATCTGCTCCACTA
1 CAACTTCAGGGAGATAGGATT-TGT-ATCTTCAATCTGCTCCACTG
* * * * *
17493827 CAACTTTAGGGAGATAAGATTCGTCATCTTCAATCTGCCCCACTA
1 CAACTTCAGGGAGATAGGATTTGT-ATCTTCAATCTGCTCCACTG
* * * * *
17493872 CAACTTCAGGGGGATAAGATCTGCT-TGCTT-AGTCTGCTCCGCTG
1 CAACTTCAGGGAGATAGGATTTG-TAT-CTTCAATCTGCTCCACTG
* * * * * **
17493916 CAACTTTAGGGAGATAAGACTAG-A--TGCAATCTGCT-CTTTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCTGCTCCACTG
** * * * *
17493956 CAACTTCAGACAGATAAGATCTGTCAT-TTTAATCTGCTCCACTA
1 CAACTTCAGGGAGATAGGATTTGT-ATCTTCAATCTGCTCCACTG
* ** *
17494000 CAACTTCAGAGAGATAGGATTAT-TGGCTTTAATCTGCTCCACTG
1 CAACTTCAGGGAGATAGGATT-TGTATCTTCAATCTGCTCCACTG
* * * *
17494044 CAACTTCAGAGAGATAAGATTTGCTATCTTCAATCCGCTCCACTA
1 CAACTTCAGGGAGATAGGATTTG-TATCTTCAATCTGCTCCACTG
* * * *
17494089 CAACTTCAGGGATATAGGATTTACTATCTTCAATCCGCTCCATTG
1 CAACTTCAGGGAGATAGGATTT-GTATCTTCAATCTGCTCCACTG
* * *
17494134 CAACTTTAGGGAGATAGGATTTGTATCTTCAATCCGCTCTACTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCTGCTCCACTG
*
17494178 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCTGCTCCACTG
* * *
17494222 TAACTTCAAGAAGATAGGATTTGT
1 CAACTTCAGGGAGATAGGATTTGT
17494246 GGTTTCACCG
Statistics
Matches: 343, Mismatches: 61, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
40 21 0.06
41 7 0.02
42 1 0.00
43 10 0.03
44 190 0.55
45 113 0.33
46 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
CAACTTCAGGGAGATAGGATTTGTATCTTCAATCTGCTCCACTG
Found at i:17502925 original size:82 final size:82
Alignment explanation
Indices: 17502788--17502947 Score: 302
Period size: 82 Copynumber: 2.0 Consensus size: 82
17502778 AAAATAAATT
*
17502788 TCTTTACATAAAATGAACTACAAATAAGGCTTTGCCTTAATACTCAAGACCTTAATCCTCCTAAG
1 TCTTTACATAAAATGAACTACAAATAAGGCTTTGCCCTAATACTCAAGACCTTAATCCTCCTAAG
*
17502853 TAACGAGGTCAACAGAA
66 TAACGAGGCCAACAGAA
17502870 TCTTTACATAAAATGAACTACAAATAAGGCTTTGCCCTAATACTCAAGACCTTAATCCTCCTAAG
1 TCTTTACATAAAATGAACTACAAATAAGGCTTTGCCCTAATACTCAAGACCTTAATCCTCCTAAG
17502935 TAACGAGGCCAAC
66 TAACGAGGCCAAC
17502948 TTCTGTCCCC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (82 bp):
TCTTTACATAAAATGAACTACAAATAAGGCTTTGCCCTAATACTCAAGACCTTAATCCTCCTAAG
TAACGAGGCCAACAGAA
Found at i:17506547 original size:25 final size:27
Alignment explanation
Indices: 17506511--17506560 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
17506501 AATTTGGCAT
17506511 AAAACATAT-AAATAAATAA-AATAAAG
1 AAAACATATAAAAT-AATAATAATAAAG
17506537 AAAAC-TATAAAATAATAATAATAA
1 AAAACATATAAAATAATAATAATAA
17506561 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (27 bp):
AAAACATATAAAATAATAATAATAAAG
Found at i:17506555 original size:3 final size:3
Alignment explanation
Indices: 17506543--17506574 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
17506533 AAAGAAAACT
17506543 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17506575 GTAACGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:17506871 original size:23 final size:24
Alignment explanation
Indices: 17506822--17506873 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
17506812 GACTATATTG
*
17506822 AAATCAGAATAAAATTTGAGAAAA
1 AAATCAGAATAAAATTTGAAAAAA
*
17506846 AAATCATAAT-AAATTT-AAAAATA
1 AAATCAGAATAAAATTTGAAAAA-A
17506869 AAATC
1 AAATC
17506874 GAAATAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.16
23 12 0.48
24 9 0.36
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (24 bp):
AAATCAGAATAAAATTTGAAAAAA
Found at i:17507888 original size:23 final size:23
Alignment explanation
Indices: 17507862--17507906 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17507852 AATTCTGGGC
*
17507862 TTTGGTTTTTTATATTT-TTTGTA
1 TTTGGTTTATTAT-TTTCTTTGTA
17507885 TTTGGTTTATTATTTTCTTTGT
1 TTTGGTTTATTATTTTCTTTGT
17507907 GTATGTGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.11, C:0.02, G:0.13, T:0.73
Consensus pattern (23 bp):
TTTGGTTTATTATTTTCTTTGTA
Found at i:17517008 original size:6 final size:6
Alignment explanation
Indices: 17516997--17517024 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
17516987 AAGTAACTTT
17516997 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
17517025 TATGTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:17522227 original size:16 final size:18
Alignment explanation
Indices: 17522191--17522228 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
17522181 TTTTTTTTGT
*
17522191 TTTTCATTCTTTAATAAG
1 TTTTCATTCTTTAAGAAG
17522209 TTTTCATT-TTT-AGAAG
1 TTTTCATTCTTTAAGAAG
17522225 TTTT
1 TTTT
17522229 GTATGCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 8 0.42
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.61
Consensus pattern (18 bp):
TTTTCATTCTTTAAGAAG
Found at i:17522740 original size:21 final size:21
Alignment explanation
Indices: 17522716--17522757 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17522706 ATTTCCATAC
*
17522716 ATTATCTTTAAATTTACATTT
1 ATTATCTTCAAATTTACATTT
*
17522737 ATTATCTTCAAATTTTCATTT
1 ATTATCTTCAAATTTACATTT
17522758 TCATGCATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATCTTCAAATTTACATTT
Found at i:17525042 original size:16 final size:16
Alignment explanation
Indices: 17524973--17525040 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
17524963 TTTGGTTCGC
17524973 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
17524989 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
17525005 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
17525021 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
17525037 TGTA
1 TGTA
17525041 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:17525075 original size:45 final size:44
Alignment explanation
Indices: 17525021--17525115 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
17525011 GGATTAGAGG
* *
17525021 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
17525066 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
17525110 TGTAAT
1 TGTAAT
17525116 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:17525426 original size:124 final size:127
Alignment explanation
Indices: 17525196--17525426 Score: 396
Period size: 124 Copynumber: 1.8 Consensus size: 127
17525186 ATGATTATTG
17525196 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
* *
17525261 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTAGCAGAAATTTGTTTTGGTAAA
64 ACATAATTACTATTAAATATATTTTAATTAAAATATATAATTAGCAGAAATTTGTTTTGGTAAA
*
17525325 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
17525387 ATAATTACTATTAAATATATTTTAATTAAAATATATAATT
66 ATAATTACTATTAAATATATTTTAATTAAAATATATAATT
17525427 TAATAAAATT
Statistics
Matches: 99, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
124 70 0.71
125 1 0.01
128 23 0.23
129 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (127 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTACTATTAAATATATTTTAATTAAAATATATAATTAGCAGAAATTTGTTTTGGTAAA
Found at i:17525428 original size:18 final size:17
Alignment explanation
Indices: 17525401--17525435 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17525391 TTACTATTAA
*
17525401 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
17525419 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
17525436 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17525465 original size:124 final size:125
Alignment explanation
Indices: 17525209--17525594 Score: 390
Period size: 124 Copynumber: 3.0 Consensus size: 125
17525199 TTGTTATTTA
*
17525209 AATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAAACATAATTATTAT
1 AATTTTAATAAGATTA---ATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTAT
* ** ** ** * *
17525274 TTAATATATTTTAATTAAAATATATAA-TTAGCAGAAATT-TGTTTTGGTAAATTATT-TTATTT
63 TAAATATATTTTAATTAAAATATATAATTTAATA-AAATTCT-TAATAATTAA-TATTCTTATAT
*
17525336 A
125 G
*
17525337 AATTTTAATAAGATTAA-TATCAATAATAAATAATTTAATCATATTTAAACATAATTACTATTAA
1 AATTTTAATAAGATTAATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAA
17525401 ATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATG
66 ATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATG
* * * * * * * * **
17525461 AA-TTTACTCAA-ACCATAATTATTATTAAATATGATACTGTAA-AATATAAAATAACATAATTA
1 AATTTTAAT-AAGA--TTAATTATCAAT-AATA-AATAATTTAATCATAT-TTA-AACATAATTA
* *
17525523 TTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA
59 TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA
17525588 TG
124 TG
17525590 AATTT
1 AATTT
17525595 ACTCAAATCA
Statistics
Matches: 221, Mismatches: 25, Indels: 22
0.82 0.09 0.08
Matches are distributed among these distances:
123 10 0.05
124 87 0.39
125 9 0.04
126 5 0.02
127 8 0.04
128 24 0.11
129 76 0.34
130 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (125 bp):
AATTTTAATAAGATTAATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAA
ATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATG
Found at i:17525551 original size:18 final size:17
Alignment explanation
Indices: 17525530--17525564 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17525520 TTATTATTAA
17525530 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
17525548 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
17525565 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:17525627 original size:17 final size:16
Alignment explanation
Indices: 17525605--17525651 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
17525595 ACTCAAATCA
17525605 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
17525622 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
17525636 TAAATATATGATTTAA
1 T-AATATATGATTTAA
17525652 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:17525652 original size:17 final size:17
Alignment explanation
Indices: 17525624--17525657 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17525614 ATTATAACTA
*
17525624 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
17525641 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
17525658 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:17525800 original size:93 final size:91
Alignment explanation
Indices: 17525690--17525883 Score: 284
Period size: 92 Copynumber: 2.1 Consensus size: 91
17525680 GATTATAGTT
* *
17525690 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTA-ATATAATTAT-ATAATAATATATAATTTC
* *
17525753 ATAAAATTCTTGATAATAAAAATTTTCTTA
63 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
17525783 TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAGTGATATATAATTTCATA
1 TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAATAATATATAATTTCATA
17525848 AAATTCTTAATAATAAAATGTTCTTA
66 AAATTCTTAATAATAAAATGTTCTTA
17525874 TATGAATTTA
1 TATGAATTTA
17525884 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
91 21 0.23
92 40 0.43
93 29 0.31
94 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (91 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAATATAATTATATAATAATATATAATTTCATA
AAATTCTTAATAATAAAATGTTCTTA
Found at i:17527294 original size:11 final size:11
Alignment explanation
Indices: 17527280--17527306 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
17527270 AAAAATCAAT
17527280 ACAAAAGTTTC
1 ACAAAAGTTTC
17527291 ACAAAAGTTTC
1 ACAAAAGTTTC
17527302 ACAAA
1 ACAAA
17527307 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:17537484 original size:11 final size:11
Alignment explanation
Indices: 17537468--17537494 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
17537458 TAGAAATTAG
17537468 TTTGTGAAACT
1 TTTGTGAAACT
17537479 TTTGTGAAACT
1 TTTGTGAAACT
17537490 TTTGT
1 TTTGT
17537495 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:17539014 original size:91 final size:92
Alignment explanation
Indices: 17538891--17539083 Score: 286
Period size: 91 Copynumber: 2.1 Consensus size: 92
17538881 TTGATTTTAG
*
17538891 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAACATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
*
17538955 TAT-TAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
17538982 TAAATTCATATAAGAA-ATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAACA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
17539046 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
17539074 CAAATTCATA
1 TAAATTCATA
17539084 AACTATAATC
Statistics
Matches: 93, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
90 1 0.01
91 59 0.63
92 30 0.32
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAACATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:17539131 original size:48 final size:52
Alignment explanation
Indices: 17539061--17539159 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
17539051 AATAATTATT
17539061 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
17539109 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
17539160 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:17539141 original size:17 final size:17
Alignment explanation
Indices: 17539116--17539149 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17539106 ATAATTTTAA
*
17539116 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
17539133 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
17539150 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:17539166 original size:17 final size:16
Alignment explanation
Indices: 17539121--17539168 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
17539111 TTTAAATTTT
17539121 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
17539138 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
17539152 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
17539169 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:17539307 original size:127 final size:129
Alignment explanation
Indices: 17539156--17539387 Score: 405
Period size: 127 Copynumber: 1.8 Consensus size: 129
17539146 ATATTAGTTA
*
17539156 TAATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
*
17539221 TATATATTTTAATT-ATTATATTTAATAATAATTATGTTATTTTATATTTTACAGTATCATATT
66 TATATATTTTAATTAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGTATCATATT
*
17539284 TAATAATA-ATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
*
17539348 TATATATTTTAATTAAAATATATTTAATAGTAATTATGTT
66 TATATATTTTAATT-AAATATATTTAATAATAATTATGTT
17539388 TAAATATGAT
Statistics
Matches: 98, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
127 69 0.70
128 7 0.07
129 22 0.22
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (129 bp):
TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
TATATATTTTAATTAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGTATCATATT
Found at i:17539364 original size:18 final size:17
Alignment explanation
Indices: 17539336--17539370 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17539326 ATTATTAAGA
*
17539336 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17539353 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17539371 TTAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17539489 original size:124 final size:127
Alignment explanation
Indices: 17539345--17539575 Score: 396
Period size: 124 Copynumber: 1.8 Consensus size: 127
17539335 AATTTTATTA
* *
17539345 AATTATATATTTTAATTAAAATATATTTAATAGTAATTATGTTTAAATATGATTAAATTATTTAT
1 AATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAATATGATTAAATTATTTAT
17539410 TATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTACCAAAACAAATTTCTGCT
66 TATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTACCAAAACAAATTTCTGCT
17539469 AATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAATATGATTAAATTATTTAT
1 AATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAATATGATTAAATTATTTAT
*
17539534 TTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 TATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
17539576 CAATAATCAT
Statistics
Matches: 99, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
124 69 0.70
125 2 0.02
128 23 0.23
129 5 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (127 bp):
AATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTTAAATATGATTAAATTATTTAT
TATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTACCAAAACAAATTTCTGCT
Found at i:17539705 original size:44 final size:45
Alignment explanation
Indices: 17539656--17539750 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
17539646 TTACACCTCT
* *
17539656 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
17539700 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
17539745 ATTACA
1 ATTACA
17539751 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:17539750 original size:16 final size:16
Alignment explanation
Indices: 17539731--17539798 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
17539721 GATTTGCTAT
* *
17539731 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
17539747 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17539763 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17539779 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17539795 TACA
1 TACA
17539799 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:17540392 original size:5 final size:5
Alignment explanation
Indices: 17540382--17540408 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
17540372 ACAATTTAAA
17540382 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
17540409 CGTAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:17542146 original size:229 final size:226
Alignment explanation
Indices: 17541681--17542515 Score: 1052
Period size: 227 Copynumber: 3.6 Consensus size: 226
17541671 AAAAAACAAA
* *
17541681 TTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACCAAAAAAAAAATTTATATTTTT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTA-C-----AAAAATTTTTATTTTT
* * * * * **
17541746 TTTTGTGTCTGAGTCAGATTTAAAAATACGAAAAAAAAATAATAAAAATTTTTTTTGGGTAATGG
60 TTTCGTGTCAGAATCAGA-TAAAAAATACGAAAAAAAAATAATAAAAA--ATTTTTGGGTGCTGG
* * *
17541811 CCTGTCAATGGCCGACACCCAGTACACAGTACGAAGAAAAA--ATTTT-TTTTTTTTTCGTGTCA
122 CCTGTCAATGGCCGACACCCAGTATACAGTACCAA-AAAAATTTTTTTGTTTTTTTTTCGTGTCA
*
17541873 GAATCAGATAAAAAATACG-AAAAAAATAAAAATAAAAATTT
186 GAATCAGATAAAAAATACGAAAAAAAATAAAAA-AAAATTTT
* *
17541914 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACCAAATTTTTTATTTTATTTTCG
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACAAAAATTTTTATTTT-TTTTCG
17541979 TGTCAGAATCAGATAAAAAAATACGAAAAAAAAATAATAATAAAATTTTTGGGTGCTGGCCTGTC
65 TGTCAGAATCAGAT-AAAAAATACGAAAAAAAAATAATAA-AAAATTTTTGGGTGCTGGCCTGTC
* * *
17542044 AATGGTCGGCACCCAGTGTACAGTACCAAAAAAATTTTTTTGTTTTTTTTTCGTGTCAGAATCAG
128 AATGGCCGACACCCAGTATACAGTACCAAAAAAATTTTTTTGTTTTTTTTTCGTGTCAGAATCAG
*
17542109 ATAAAAAATACGAAAAAAAATAAAAAAAAGTTTT
193 ATAAAAAATACGAAAAAAAATAAAAAAAAATTTT
17542143 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACAAAAAAAAATTTTTATTTTTTT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTAC----AAAAATTTTTA--TTTTT
*
17542208 TTTCGTGTCAGAATCAGATAAAAAATACG-AAAAAAAATAAAAAAAAAATTTTT-GGTGCTGGCC
60 TTTCGTGTCAGAATCAGATAAAAAATACGAAAAAAAAAT-AATAAAAAATTTTTGGGTGCTGGCC
* * *
17542271 AGTCAATGGCCGACACCCAGTCTACAGTACCAAAAAAAATTTTTTTGTTTTTTTTT-GTATCAGA
124 TGTCAATGGCCGACACCCAGTATACAGTACC-AAAAAAATTTTTTTGTTTTTTTTTCGTGTCAGA
* *
17542335 ATCAGATAAAAAAATACGAAAAAAAAGAATAATAAAATTTTTT
188 ATCAGAT-AAAAAATACGAAAAAAAATAA-AA-AAAA-ATTTT
* *
17542378 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCA--GTAC-G-AAAAAAATATTTTTTTATTTTTTC
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACAAAAAT-TTTTATT-TTTTTTC
17542439 GTGTCAGAATCAGATAAAAAATACGAAAAAAATAA-AA-AAAAAA--TTTGGGTGCTGGCCTGTC
64 GTGTCAGAATCAGATAAAAAATACGAAAAAAA-AATAATAAAAAATTTTTGGGTGCTGGCCTGTC
*
17542500 AATGGCCGGCACCCAG
128 AATGGCCGACACCCAG
17542516 AACAAATTAT
Statistics
Matches: 545, Mismatches: 33, Indels: 56
0.86 0.05 0.09
Matches are distributed among these distances:
224 3 0.01
225 28 0.05
226 13 0.02
227 95 0.17
228 54 0.10
229 89 0.16
230 13 0.02
231 52 0.10
232 64 0.12
233 70 0.13
234 24 0.04
235 40 0.07
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (226 bp):
TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACAAAAATTTTTATTTTTTTTCGT
GTCAGAATCAGATAAAAAATACGAAAAAAAAATAATAAAAAATTTTTGGGTGCTGGCCTGTCAAT
GGCCGACACCCAGTATACAGTACCAAAAAAATTTTTTTGTTTTTTTTTCGTGTCAGAATCAGATA
AAAAATACGAAAAAAAATAAAAAAAAATTTT
Found at i:17542161 original size:116 final size:114
Alignment explanation
Indices: 17541681--17542515 Score: 1035
Period size: 116 Copynumber: 7.3 Consensus size: 114
17541671 AAAAAACAAA
* * * *
17541681 TTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACCAAAAAAAAAATTTATATTTTT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACC--AAAAAAATTTTTTTTTTTT
* * * *
17541746 TTTT-GTGTCTGAGTCAGATTTAAAAATACGAAAAAAAAATAATAAAAATTTTTT
64 TTTTCGTGTCAGAATCAGA-TAAAAAATACG-AAAAAAAATAA-AAAAA-ATTTT
** * ** * *
17541800 TTGGGTAATGGCCTGTCAATGGCCGACACCCAGTACACAGTACGAAGAAAAA--ATTTTTTTTTT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACCAA-AAAAATTTTTTTTTTTTT
*
17541863 TTTCGTGTCAGAATCAGATAAAAAATACG-AAAAAAATAAAAATAAAAATTT
65 TTTCGTGTCAGAATCAGATAAAAAATACGAAAAAAAAT-AAAA-AAAATTTT
* *
17541914 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACC----AAATTTTTTATTTTATT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACCAAAAAAATTTTTTTTTTTTTT
17541975 TTCGTGTCAGAATCAGATAAAAAAATACGAAAAAAAAATAATAATAAAA-TTT
66 TTCGTGTCAGAATCAGAT-AAAAAATACG-AAAAAAAATAA-AA-AAAATTTT
*
17542027 TTGGGTGCTGGCCTGTCAATGGTCGGCACCCAGTGTACAGTACCAAAAAAATTTTTTTGTTTTTT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACCAAAAAAATTTTTTT-TTTTTT
17542092 TTTCGTGTCAGAATCAGATAAAAAATACGAAAAAAAATAAAAAAAAGTTTT
65 TTTCGTGTCAGAATCAGATAAAAAATACGAAAAAAAATAAAAAAAA-TTTT
* *
17542143 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACAAAAAAAAATTTTTATTTTTTT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTAC-CAAAAAAATTTTTTTTTTTTT
*
17542208 TTTCGTGTCAGAATCAGATAAAAAATACGAAAAAAAATAAAAAAAAAATTT
65 TTTCGTGTCAGAATCAGATAAAAAATACGAAAAAAAAT-AAAAAAAATTTT
* * *
17542259 TT-GGTGCTGGCCAGTCAATGGCCGACACCCAGTCTACAGTACCAAAAAAAATTTTTTTGTTTTT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACC-AAAAAAATTTTTTT-TTTTT
* *
17542323 TTTT-GTATCAGAATCAGATAAAAAAATACGAAAAAAAAGAATAATAAAATTTTTT
64 TTTTCGTGTCAGAATCAGAT-AAAAAATACGAAAAAAAATAA-AA-AAAA--TTTT
* *
17542378 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCA--GTAC-G----AAAAAAATATTTTTTTATTTT
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACCAAAAAAATTTTTTTTTTTTTT
**
17542436 TTCGTGTCAGAATCAGATAAAAAATACG-AAAAAAATAAAAAAAA-AAT
66 TTCGTGTCAGAATCAGATAAAAAATACGAAAAAAAATAAAAAAAATTTT
17542483 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAG
1 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAG
17542516 AACAAATTAT
Statistics
Matches: 640, Mismatches: 47, Indels: 71
0.84 0.06 0.09
Matches are distributed among these distances:
105 33 0.05
108 4 0.01
109 5 0.01
110 9 0.01
111 45 0.07
112 37 0.06
113 48 0.08
114 70 0.11
115 73 0.11
116 155 0.24
117 59 0.09
118 32 0.05
119 43 0.07
120 27 0.04
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (114 bp):
TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTGTACAGTACCAAAAAAATTTTTTTTTTTTTT
TTCGTGTCAGAATCAGATAAAAAATACGAAAAAAAATAAAAAAAATTTT
Found at i:17544715 original size:119 final size:114
Alignment explanation
Indices: 17544461--17545674 Score: 1070
Period size: 119 Copynumber: 10.5 Consensus size: 114
17544451 ATGATTCTTT
*
17544461 TGGGTGCCGGCCATTGACAGGCCAGCACC-CAAAA--TTTTTTTTTTA-TTTTTTTCGTATTTTT
1 TGGGTGCCGGCCATTGACAGGCCAGCACCAAAAAATTTTTTTTTTTTATTTTTTTTCGTATTTTT
*
17544522 TATCTAATTCTGACACGAAAAAAAAGTAAAATTTTTTTCTTTCGTACTGTGTAC
66 TATCTGATTCTGACACGAAAAAAAA-T--AA-TTTTTT-TTTCGTACTGTGTAC
17544576 TGGGTGCCGGCCATTGACAGGCCAGCACCAAAAAATTTTGTTTTTTTTTATTATTTTTTTTCGTA
1 TGGGTGCCGGCCATTGACAGGCCAGCACCAAAAAA---T-TTTTTTTTT-TTATTTTTTTTCGTA
17544641 TTTTTTATCTGATTCTGACACGAAAAAAAATAATTTTTTTTTCGTACTGTGTAC
61 TTTTTTATCTGATTCTGACACGAAAAAAAATAATTTTTTTTTCGTACTGTGTAC
* *
17544695 TAGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTGTTTTTTTTTTATTTATTTATTTTCG
1 TGGGTGCCGGCCATTGACAGGCCAGCA-CCAAAAA-ATT-TTTTTTTTTTA--T-TTT-TTTTCG
*
17544760 TATTTTTTATCTGATTCTAACAC-AAAAAAAATAAAAATTTTTTTTTTTCGTACTGTGTAC
59 TATTTTTTATCTGATTCTGACACGAAAAAAAAT---AA--TTTTTTTTTCGTACTGTGTAC
* * *
17544820 TGGGTGCCGGCCATTGACAGGTCAGCACCCAAAAA---TTTTTTTTTATTTTTTTTCTTATTTTT
1 TGGGTGCCGGCCATTGACAGGCCAGCACCAAAAAATTTTTTTTTTTTATTTTTTTTCGTATTTTT
*
17544882 TATCTGATTCTGACACG----AAAAT--TTTTTTTTCCGTACTGTGTAC
66 TATCTGATTCTGACACGAAAAAAAATAATTTTTTTTTCGTACTGTGTAC
* * **
17544925 TGAGTGCCGGCCATTGACAGGCCAACACTCAAAAAA-------AATTTA-TTTTTTTCGTATTTT
1 TGGGTGCCGGCCATTGACAGGCCAGCAC-CAAAAAATTTTTTTTTTTTATTTTTTTTCGTATTTT
* * * *** *
17544982 TTATCTAATTTTGACACGAAAAAAAACAAAAAAAAAAAATTTTTTGGTACTGTAG-AC
65 TTATCTGATTCTGACACG------AA-AAAAAATAATTTTTTTTTCGTACTGT-GTAC
* *
17545039 TGGGTGCCGGCCATTGACAGGCCAGCAGCGAAAAAA---TTTTTTTTAATTTTTTTTCGTATTTT
1 TGGGTGCCGGCCATTGACAGGCCAGCA-CCAAAAAATTTTTTTTTTTTATTTTTTTTCGTA-TTT
* ***** * ** *
17545101 TTTATCTGATTCTGACAC-AAAAAAATAAAAAAAAATTTTGGTACTGTACAT
64 TTTATCTGATTCTGACACGAAAAAAA-ATAATTTTTTTTTCGTACTGTGTAC
*
17545152 TGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAA-TTTTTTTATTTATTTTTTTTTCGTATTT
1 TGGGTGCCGGCCATTGACAGGCCAGCA-CCAAAAAATTTTTTTTTTTTA-TTTTTTTTCGTA-TT
* * ** * **
17545216 TTTTATTTGATTCTGACACGAAAAAAAAAACAAAAAAAAATTTTTTTAGTACTGTACAC
63 TTTTATCTGATTCTGACACG------AAAA-AAAATAATTTTTTTTTCGTACTGTGTAC
* *
17545275 TGTGTGCCGGCCATTGACAGGCCAGCACC-CAAAATTTTTTTTTTTTATTTTTTTTCGTATTTTT
1 TGGGTGCCGGCCATTGACAGGCCAGCACCAAAAAATTTTTTTTTTTTATTTTTTTTCGTATTTTT
* **
17545339 TATCTGATTCTGACACGAAAAAAAAATAAAATTTTTTTTTGGTACTGTACAC
66 TATCTGATTCTGACACG-AAAAAAAAT--AATTTTTTTTTCGTACTGTGTAC
* ** *
17545391 TGGGTGCCGGCCATTGACAGGCCGGCATCCCCAAAA-TTTTTTTTTTAATTTTTTTTCGTATTTT
1 TGGGTGCCGGCCATTGACAGGCCAGCA-CCAAAAAATTTTTTTTTTTTATTTTTTTTCGTA-TTT
17545455 TTTATCTGATTCTGACACGAAAAAAAATAAAAATTTTTTTTTCTTCGTACTGTGTAC
64 TTTATCTGATTCTGACACGAAAAAAAAT---AA--TTTTTTT-TTCGTACTGTGTAC
* * **
17545512 TGGGTGCCGGCGATTGACAGGCCAACACCCAAAAAA---AATTTTTTTATTTTTTTTCGTATTTT
1 TGGGTGCCGGCCATTGACAGGCCAGCA-CCAAAAAATTTTTTTTTTTTATTTTTTTTCGTATTTT
* * * **
17545574 TAAATCTGACTCTGACAC------AAA-AATTTTTTTTTAGTACTGTACAC
65 T-TATCTGATTCTGACACGAAAAAAAATAATTTTTTTTTCGTACTGTGTAC
* * *
17545618 TGGGTGCTGGCCATTGACAGGCCAGCACC-CAAAATTTTTTTTTTTGTTTTTTTTTTC
1 TGGGTGCCGGCCATTGACAGGCCAGCACCAAAAAATTTTTTTTTTT-TATTTTTTTTC
17545675 TTTCGTATAT
Statistics
Matches: 943, Mismatches: 84, Indels: 151
0.80 0.07 0.13
Matches are distributed among these distances:
101 30 0.03
102 4 0.00
104 4 0.00
105 47 0.05
106 41 0.04
107 13 0.01
108 10 0.01
109 2 0.00
112 14 0.01
113 59 0.06
114 49 0.05
115 71 0.08
116 85 0.09
117 39 0.04
118 48 0.05
119 96 0.10
120 72 0.08
121 87 0.09
122 21 0.02
123 56 0.06
124 49 0.05
125 46 0.05
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.41
Consensus pattern (114 bp):
TGGGTGCCGGCCATTGACAGGCCAGCACCAAAAAATTTTTTTTTTTTATTTTTTTTCGTATTTTT
TATCTGATTCTGACACGAAAAAAAATAATTTTTTTTTCGTACTGTGTAC
Found at i:17545234 original size:116 final size:114
Alignment explanation
Indices: 17544963--17545671 Score: 713
Period size: 116 Copynumber: 6.1 Consensus size: 114
17544953 TCAAAAAAAA
* * *
17544963 TTTA-TTTTTTTCGTA-TTTTTTATCTAATTTTGACACGAAAAAAAACAAAAAAAAAAAATTTTT
1 TTTATTTTTTTTCGTATTTTTTTATCTGATTCTGACAC---AAAAAA-AATAAAAAAAAA--TTT
* * * *
17545026 TGGTACTGTAGACTGGGTGCCGGCCATTGACAGGCCAGCAGCGAAAAAATTTTTT
60 TGGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTT
*
17545081 TTAATTTTTTTTCGTATTTTTTTATCTGATTCTGACAC-AAAAAAATAAAAAAAAATTTTGGTAC
1 TTTATTTTTTTTCGTATTTTTTTATCTGATTCTGACACAAAAAAAATAAAAAAAAATTTTGGTAC
*
17545145 TGTACATTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTT
66 TGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAAAATTTTTTT
* *
17545195 ATTTATTTTTTTTTCGTATTTTTTTATTTGATTCTGACACGAAAAAAAAAACAAAAAAAAATTTT
1 -TTTA-TTTTTTTTCGTATTTTTTTATCTGATTCTGACAC---AAAAAAAATAAAAAAAAA---T
* * *
17545260 TTTAGTACTGTACACTGTGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
58 TTTGGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA-ATTTTTTT
*****
17545318 TTTATTTTTTTTCGTA-TTTTTTATCTGATTCTGACACGAAAAAAAAATAAAATTTTTTTTTGGT
1 TTTATTTTTTTTCGTATTTTTTTATCTGATTCTGACAC--AAAAAAAATAAAAAAAAATTTTGGT
* *
17545382 ACTGTACACTGGGTGCCGGCCATTGACAGGCCGGCATCCCCAAAATTTTTTT
64 ACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCA-CCCAAAAATTTTTTT
****
17545434 TTTAATTTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAATAAAAATTTTTTTTTCT
1 TTT-ATTTTTTTTCGTATTTTTTTATCTGATTCTGACAC-AAAAAAAATAAAAA---AAAATT-T
* ** * * ***
17545499 TCGTACTGTGTACTGGGTGCCGGCGATTGACAGGCCAACACCCAAAAAAAATTTT
60 TGGTACTGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTT
** * **** *
17545554 TTTATTTTTTTTCGTATTTTTAAATCTGACTCTGACAC---AAAAAT-----TTTTTTTTAGTAC
1 TTTATTTTTTTTCGTATTTTTTTATCTGATTCTGACACAAAAAAAATAAAAAAAAATTTTGGTAC
* *
17545611 TGTACACTGGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTT
66 TGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTT
*
17545660 TTTGTTTTTTTT
1 TTTATTTTTTTT
17545672 TTCTTTCGTA
Statistics
Matches: 516, Mismatches: 55, Indels: 52
0.83 0.09 0.08
Matches are distributed among these distances:
106 57 0.11
107 6 0.01
113 42 0.08
114 11 0.02
115 20 0.04
116 88 0.17
117 32 0.06
118 24 0.05
119 56 0.11
120 75 0.15
121 47 0.09
122 8 0.02
123 50 0.10
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (114 bp):
TTTATTTTTTTTCGTATTTTTTTATCTGATTCTGACACAAAAAAAATAAAAAAAAATTTTGGTAC
TGTACACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTT
Found at i:17547843 original size:21 final size:21
Alignment explanation
Indices: 17547796--17547847 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
17547786 GCGGTGACGG
* **
17547796 TGAGATTAGTTACTGTAGCGG
1 TGAGATTAGATACTGTAGCAA
*
17547817 TAAGATTAGATACTGTAGCAA
1 TGAGATTAGATACTGTAGCAA
17547838 TGAGATTAGA
1 TGAGATTAGA
17547848 AACAATGGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (21 bp):
TGAGATTAGATACTGTAGCAA
Found at i:17549603 original size:22 final size:22
Alignment explanation
Indices: 17549575--17549629 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
17549565 CAAAACAGCA
17549575 GTTTCTCCCCTCGTTCCTACTG
1 GTTTCTCCCCTCGTTCCTACTG
* *
17549597 GTTTCT-CCCTTGTTCTTACTG
1 GTTTCTCCCCTCGTTCCTACTG
17549618 GTTTCTCCCCTC
1 GTTTCTCCCCTC
17549630 TTTTTTGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.04, C:0.38, G:0.13, T:0.45
Consensus pattern (22 bp):
GTTTCTCCCCTCGTTCCTACTG
Found at i:17551703 original size:13 final size:13
Alignment explanation
Indices: 17551685--17551807 Score: 70
Period size: 13 Copynumber: 8.6 Consensus size: 13
17551675 AAGCAACCGT
17551685 AAATGGGAATGGG
1 AAATGGGAATGGG
17551698 AAATGGGAATGGG
1 AAATGGGAATGGG
17551711 AAATGGGAGGA-GGG
1 AAATGGGA--ATGGG
* *
17551725 GAATCGATGGAAGAGGG
1 AAAT-G--GGAA-TGGG
17551742 AAAATGGGAAATGGG
1 -AAATGGG-AATGGG
17551757 AAATGGGAGGA-GGG
1 AAATGGGA--ATGGG
* **
17551771 CACGGTGGAATAGGG
1 AAATG-GGAAT-GGG
17551786 AAAATGGGAATGGG
1 -AAATGGGAATGGG
17551800 AAATGGGA
1 AAATGGGA
17551808 GGAGGGCACA
Statistics
Matches: 86, Mismatches: 9, Indels: 30
0.69 0.07 0.24
Matches are distributed among these distances:
13 31 0.36
14 21 0.24
15 20 0.23
16 4 0.05
17 7 0.08
18 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.47, T:0.12
Consensus pattern (13 bp):
AAATGGGAATGGG
Found at i:17551704 original size:7 final size:7
Alignment explanation
Indices: 17551685--17551764 Score: 60
Period size: 7 Copynumber: 11.1 Consensus size: 7
17551675 AAGCAACCGT
17551685 AAATGGG
1 AAATGGG
17551692 -AATGGG
1 AAATGGG
17551698 AAATGGG
1 AAATGGG
17551705 -AATGGG
1 AAATGGG
17551711 AAATGGG
1 AAATGGG
*
17551718 AGGA-GGG
1 A-AATGGG
*
17551725 GAATCGATGG
1 AAAT-G--GG
17551735 AAGA-GGG
1 AA-ATGGG
17551742 AAAATGGG
1 -AAATGGG
17551750 AAATGGG
1 AAATGGG
17551757 AAATGGG
1 AAATGGG
17551764 A
1 A
17551765 GGAGGGCACG
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
6 13 0.22
7 34 0.58
8 7 0.12
9 1 0.02
10 3 0.05
11 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.46, T:0.12
Consensus pattern (7 bp):
AAATGGG
Found at i:17551799 original size:43 final size:43
Alignment explanation
Indices: 17551690--17551823 Score: 191
Period size: 43 Copynumber: 3.1 Consensus size: 43
17551680 ACCGTAAATG
* *
17551690 GGAAT-GGG-AAATGGGAATGGGAAATGGGAGGAGGGGAATCGAT
1 GGAATAGGGAAAATGGGAATGGGAAATGGGAGGA-GGGCA-CGGT
*
17551733 GGAAGAGGGAAAATGGGAAATGGGAAATGGGAGGAGGGCACGGT
1 GGAATAGGGAAAATGGG-AATGGGAAATGGGAGGAGGGCACGGT
*
17551777 GGAATAGGGAAAATGGGAATGGGAAATGGGAGGAGGGCACAGT
1 GGAATAGGGAAAATGGGAATGGGAAATGGGAGGAGGGCACGGT
17551820 GGAA
1 GGAA
17551824 GGGGGAATCG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
43 33 0.40
44 22 0.27
45 11 0.13
46 17 0.20
ACGTcount: A:0.37, C:0.04, G:0.49, T:0.11
Consensus pattern (43 bp):
GGAATAGGGAAAATGGGAATGGGAAATGGGAGGAGGGCACGGT
Found at i:17552007 original size:29 final size:29
Alignment explanation
Indices: 17551876--17552333 Score: 774
Period size: 30 Copynumber: 15.5 Consensus size: 29
17551866 CATTGTATTT
17551876 GTGTATTTTAAAAATAAAAATATATATGTA
1 GTGTATTTTAAAAATAAAAA-ATATATGTA
*
17551906 ATGTATTTTAAAAATAAAGAAATATATGTA
1 GTGTATTTTAAAAATAAA-AAATATATGTA
17551936 GTGTATTTTAAAAATAAAAAAATATATGTA
1 GTGTATTTTAAAAAT-AAAAAATATATGTA
17551966 GTGTATTTTAAAAAT-AAAAATATATGTA
1 GTGTATTTTAAAAATAAAAAATATATGTA
*
17551994 GTGTATTTTAAAAATAAAAAATATATATA
1 GTGTATTTTAAAAATAAAAAATATATGTA
17552023 GTGTATTTTAAAAATAAAGAAATATATGTA
1 GTGTATTTTAAAAATAAA-AAATATATGTA
17552053 GTGTATTTTAAAAATAAAAAATATATGTA
1 GTGTATTTTAAAAATAAAAAATATATGTA
*
17552082 GTGTATTTTAAAAATAAAAAATATATGTG
1 GTGTATTTTAAAAATAAAAAATATATGTA
* *
17552111 GTGTATTTAAAAAATAAAAAAAATATGTA
1 GTGTATTTTAAAAATAAAAAATATATGTA
17552140 GTGTATTTTAAAAATAAAAAAATATATGTA
1 GTGTATTTTAAAAAT-AAAAAATATATGTA
17552170 GTGTATTTTAAAAATAAAAAAATATATGTA
1 GTGTATTTTAAAAAT-AAAAAATATATGTA
17552200 GTGTATTTTAAAAATAAAAAATATATATGTA
1 GTGTATTTTAAAAAT-AAAAA-ATATATGTA
17552231 GTGTATTTTAAAAATAAAAAATATATGTA
1 GTGTATTTTAAAAATAAAAAATATATGTA
17552260 GTGTATTTTAAAAATAAAAAAATATATGTA
1 GTGTATTTTAAAAAT-AAAAAATATATGTA
17552290 GTGTATTTTAAAAATAAAAAAATATATGTA
1 GTGTATTTTAAAAAT-AAAAAATATATGTA
17552320 GTGTATTTTAAAAA
1 GTGTATTTTAAAAA
17552334 CAAATCGATT
Statistics
Matches: 411, Mismatches: 10, Indels: 14
0.94 0.02 0.03
Matches are distributed among these distances:
28 28 0.07
29 133 0.32
30 221 0.54
31 29 0.07
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.37
Consensus pattern (29 bp):
GTGTATTTTAAAAATAAAAAATATATGTA
Found at i:17555918 original size:21 final size:21
Alignment explanation
Indices: 17555894--17555942 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
17555884 CATTGTTTCT
*
17555894 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
17555915 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
17555936 AATCTCA
1 AATCTCA
17555943 TTGCCACCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.35, G:0.08, T:0.24
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:17560030 original size:10 final size:10
Alignment explanation
Indices: 17560015--17560077 Score: 60
Period size: 10 Copynumber: 6.3 Consensus size: 10
17560005 AATCACGTTC
17560015 AAAATTA-TA
1 AAAATTATTA
17560024 GAAAATTATTA
1 -AAAATTATTA
17560035 AAATATTATTA
1 AAA-ATTATTA
17560046 AAAATTA-TA
1 AAAATTATTA
17560055 AAAATATATT-
1 AAAAT-TATTA
**
17560065 GGAATTATTA
1 AAAATTATTA
17560075 AAA
1 AAA
17560078 CCGTCCATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
9 11 0.25
10 20 0.45
11 13 0.30
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (10 bp):
AAAATTATTA
Found at i:17560044 original size:11 final size:11
Alignment explanation
Indices: 17560028--17560061 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
17560018 ATTATAGAAA
17560028 ATTATTAAAAT
1 ATTATTAAAAT
17560039 ATTATTAAAA-
1 ATTATTAAAAT
*
17560049 ATTATAAAAAT
1 ATTATTAAAAT
17560060 AT
1 AT
17560062 ATTGGAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTATTAAAAT
Found at i:17560049 original size:21 final size:19
Alignment explanation
Indices: 17560025--17560077 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 19
17560015 AAAATTATAG
17560025 AAAATTATTAAAATATTATT
1 AAAATTATTAAAATA-TATT
*
17560045 AAAAATTATAAAAATATATT
1 -AAAATTATTAAAATATATT
**
17560065 GGAATTATTAAAA
1 AAAATTATTAAAA
17560078 CCGTCCATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 10 0.36
20 4 0.14
21 14 0.50
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAATTATTAAAATATATT
Found at i:17561186 original size:16 final size:16
Alignment explanation
Indices: 17561165--17561201 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
17561155 GGGCCTTAAG
*
17561165 GTTTGTTTAGGGTTTT
1 GTTTGTTTAAGGTTTT
17561181 GTTTGTTTAAGGTTTT
1 GTTTGTTTAAGGTTTT
*
17561197 ATTTG
1 GTTTG
17561202 AGGGTTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.27, T:0.62
Consensus pattern (16 bp):
GTTTGTTTAAGGTTTT
Found at i:17565284 original size:4 final size:4
Alignment explanation
Indices: 17565277--17565301 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17565267 TATTTGAACG
17565277 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
17565302 GTTAATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:17566788 original size:15 final size:15
Alignment explanation
Indices: 17566750--17566790 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
17566740 TTGACCTGAA
*
17566750 TCGAACCGACCGCAG
1 TCGAACCGGCCGCAG
17566765 TCGAACCGGCCGCAG
1 TCGAACCGGCCGCAG
17566780 TCGAACCGGCC
1 TCGAACCGGCC
17566791 TGGGGTACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.22, C:0.41, G:0.29, T:0.07
Consensus pattern (15 bp):
TCGAACCGGCCGCAG
Found at i:17572411 original size:18 final size:18
Alignment explanation
Indices: 17572388--17572422 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17572378 GTATTACAAG
*
17572388 TTTCCATTTTCATTTTTA
1 TTTCCATTTCCATTTTTA
17572406 TTTCCATTTCCATTTTT
1 TTTCCATTTCCATTTTT
17572423 GGAAACCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCCATTTCCATTTTTA
Found at i:17573465 original size:15 final size:13
Alignment explanation
Indices: 17573401--17573489 Score: 67
Period size: 13 Copynumber: 6.9 Consensus size: 13
17573391 TTTAATTAAA
*
17573401 ACATAAAAATAAT
1 ACATAAATATAAT
*
17573414 A-ATACATGATAAT
1 ACATAAAT-ATAAT
* * **
17573427 TCATGAATGCAAT
1 ACATAAATATAAT
17573440 ACATAAATATAAT
1 ACATAAATATAAT
17573453 ACAT-AATA-ATAT
1 ACATAAATATA-AT
* *
17573465 ATATAAATGTAAT
1 ACATAAATATAAT
17573478 ACATAAATATAA
1 ACATAAATATAA
17573490 CAAGGATAAG
Statistics
Matches: 56, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
11 1 0.02
12 13 0.23
13 37 0.66
14 5 0.09
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.30
Consensus pattern (13 bp):
ACATAAATATAAT
Found at i:17573488 original size:38 final size:36
Alignment explanation
Indices: 17573407--17573489 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 36
17573397 TAAAACATAA
* *
17573407 AAATAATAATACATGATAATTCATGAATGCAATACAT
1 AAAT-ATAATACATAATAATTCATAAATGCAATACAT
* *
17573444 AAATATAATACATAATAATATATATAAATGTAATACAT
1 AAATATAATACATAATAAT-T-CATAAATGCAATACAT
17573482 AAATATAA
1 AAATATAA
17573490 CAAGGATAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 14 0.35
37 5 0.12
38 21 0.52
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (36 bp):
AAATATAATACATAATAATTCATAAATGCAATACAT
Found at i:17575319 original size:102 final size:102
Alignment explanation
Indices: 17575140--17575329 Score: 292
Period size: 102 Copynumber: 1.9 Consensus size: 102
17575130 CTGTAACATC
*
17575140 AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTGCAATTTCAGGAAGATAAGAGTCGCCATA
1 AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGAGTCGCCATA
17575205 ATTTGTACCTTTAATCTGTTCCATCCGCTACAACTTT
66 ATTTGTACCTTTAATCTGTTCCATCCGCTACAACTTT
* * * *
17575242 AGGGAGATAAGGCTGGTGGCTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAG-GTTCGTCAT
1 AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGAG-TCGCCAT
* * *
17575306 AATTTTTAGCTTTAATCTTTTCCA
65 AATTTGTACCTTTAATCTGTTCCA
17575330 CTGCAATGCT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 1 0.01
102 78 0.99
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (102 bp):
AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGAGTCGCCATA
ATTTGTACCTTTAATCTGTTCCATCCGCTACAACTTT
Found at i:17575398 original size:143 final size:143
Alignment explanation
Indices: 17575228--17575578 Score: 472
Period size: 143 Copynumber: 2.5 Consensus size: 143
17575218 ATCTGTTCCA
* *
17575228 TCCGCTACAACTTTAGGGAGATAAGGCTGGTGGCTTCAGTCTGCTCCACTGCAACTTCAGGAAGA
1 TCCGCTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGA
* * * * * * * ** *
17575293 TAAGGTTCGTCATAATTTTTAGCTTTAATCTTTTCCACTGCAATGCTAGGGAAATAAGATTCGCT
66 TAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATAAGATTCGAT
17575358 GTCTTTAGTCTGC
131 GTCTTTAGTCTGC
* * * **
17575371 TCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACTACTTTTGGAAGA
1 TCCGCTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGA
*
17575436 TAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGTAACGCCAAAGAAATAAGATTCGAT
66 TAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATAAGATTCGAT
17575501 GTCTTTAGTCTGC
131 GTCTTTAGTCTGC
* * ** * *
17575514 TCCACTACAACTTCAGGGAGATAAGACT--TCACTTCAATCCGCTCCACTGCAACTTCAGGGAGA
1 TCCGCTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGA
17575577 TA
66 TA
17575579 GGATTATTGG
Statistics
Matches: 179, Mismatches: 29, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
141 29 0.16
143 150 0.84
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (143 bp):
TCCGCTACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGA
TAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATAAGATTCGAT
GTCTTTAGTCTGC
Found at i:17575436 original size:245 final size:245
Alignment explanation
Indices: 17574990--17575472 Score: 711
Period size: 245 Copynumber: 2.0 Consensus size: 245
17574980 TGCTCCACTG
17574990 CAACTTCAGGGAGATAAGGCTAGTGGCTTCGATATGCTCCACTGCAACTTCAGGAAGATAAGATC
1 CAACTTCAGGGAGATAAGGCTAGTGGCTTCGATATGCTCCACTGCAACTTCAGGAAGATAAGATC
* *
17575055 CGCCATAACTTGTGGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGCTTTCTTCA
66 CGCCATAACTTGTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGCTGTCTTCA
* * *
17575120 ATCTGCTTCGCTGTAACATCAGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTGCAATTTCA
131 ATCTGCTCCGCTGCAACATCAGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAATTTCA
17575185 GGAAGATAAGAGT-CGCCATAATTTGTACCTTTAATCTGTTCCATCCGCTA
196 GGAAGATAAGA-TCCGCCATAATTTGTACCTTTAATCTGTTCCATCCGCTA
* * * *
17575235 CAACTTTAGGGAGATAAGGCTGGTGGCTTC-AGTCTGCTCCACTGCAACTTCAGGAAGATAAGGT
1 CAACTTCAGGGAGATAAGGCTAGTGGCTTCGA-TATGCTCCACTGCAACTTCAGGAAGATAAGAT
* * * * * * *
17575299 TCGTCATAATTTTTAGCTTTAATCTTTTCCACTGCAATGCTAGGGAAATAAGATTCGCTGTCTTT
65 CCGCCATAACTTGTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGCTGTCTTC
* * * * *
17575364 AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACTACTTT
130 AATCTGCTCCGCTGCAACATCAGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTAC-AATTT
* *
17575429 -TGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCA
194 CAGGAAGATAAGATCCGCCATAATTTGTACCTTTAATCTGTTCCA
17575473 CTGTAACGCC
Statistics
Matches: 212, Mismatches: 23, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
244 2 0.01
245 206 0.97
246 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (245 bp):
CAACTTCAGGGAGATAAGGCTAGTGGCTTCGATATGCTCCACTGCAACTTCAGGAAGATAAGATC
CGCCATAACTTGTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGCTGTCTTCA
ATCTGCTCCGCTGCAACATCAGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAATTTCA
GGAAGATAAGATCCGCCATAATTTGTACCTTTAATCTGTTCCATCCGCTA
Found at i:17575567 original size:42 final size:43
Alignment explanation
Indices: 17575512--17575626 Score: 133
Period size: 44 Copynumber: 2.7 Consensus size: 43
17575502 TCTTTAGTCT
* *
17575512 GCTCCACTACAACTTCAGGGAGATAAGA-CTTCACTTCAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATATTCACTTCAATCC
* ** * *
17575554 GCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TATTCACTTCAATCC
* *
17575598 ACTCGACTGCAACTTCAGGGAGATAAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGAT
17575627 TTGGCATAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 26 0.43
43 1 0.02
44 34 0.56
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATATTCACTTCAATCC
Found at i:17585649 original size:13 final size:13
Alignment explanation
Indices: 17585592--17585680 Score: 58
Period size: 13 Copynumber: 6.9 Consensus size: 13
17585582 TTTAATAAAA
*
17585592 ACATAAAAATAAT
1 ACATAAATATAAT
*
17585605 A-ATACATGATAAT
1 ACATAAAT-ATAAT
* * **
17585618 GCATGAATGCAAT
1 ACATAAATATAAT
*
17585631 AGATAAATATAAT
1 ACATAAATATAAT
17585644 ACAT-AATA-ATAT
1 ACATAAATATA-AT
* *
17585656 ATATAAATGTAAT
1 ACATAAATATAAT
17585669 ACATAAATATAA
1 ACATAAATATAA
17585681 CAAGGATAAT
Statistics
Matches: 54, Mismatches: 17, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
11 1 0.02
12 13 0.24
13 35 0.65
14 5 0.09
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
ACATAAATATAAT
Found at i:17586944 original size:13 final size:14
Alignment explanation
Indices: 17586926--17586954 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17586916 ACTGTTAATG
17586926 TTTGTTTT-TTTAT
1 TTTGTTTTGTTTAT
17586939 TTTGTTTTGTTTAT
1 TTTGTTTTGTTTAT
17586953 TT
1 TT
17586955 AATCTGCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (14 bp):
TTTGTTTTGTTTAT
Found at i:17593061 original size:14 final size:14
Alignment explanation
Indices: 17593042--17593072 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
17593032 TTCGTTGACG
17593042 ATGCAACTTGGGTT
1 ATGCAACTTGGGTT
17593056 ATGCAACTTGGGTT
1 ATGCAACTTGGGTT
17593070 ATG
1 ATG
17593073 AGTTGACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.29, T:0.35
Consensus pattern (14 bp):
ATGCAACTTGGGTT
Found at i:17597652 original size:13 final size:13
Alignment explanation
Indices: 17597634--17597684 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
17597624 ATTTAAAAAT
17597634 AATAATTTTTAAA
1 AATAATTTTTAAA
17597647 AATAATTTTT-AA
1 AATAATTTTTAAA
17597659 AAT--TTTTTAAAA
1 AATAATTTTT-AAA
*
17597671 AATAATATTTAAA
1 AATAATTTTTAAA
17597684 A
1 A
17597685 TATTTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 5 0.15
12 10 0.30
13 14 0.42
14 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATAATTTTTAAA
Found at i:17597666 original size:24 final size:24
Alignment explanation
Indices: 17597639--17597725 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 24
17597629 AAAATAATAA
*
17597639 TTTTT-AAAAATAATTTTTAAAAT
1 TTTTTAAAAAATAATATTTAAAAT
17597662 TTTTTAAAAAATAATATTTAAAA-
1 TTTTTAAAAAATAATATTTAAAAT
* * *
17597685 TATTTAAAATAT-ACATTTAAAAT
1 TTTTTAAAAAATAATATTTAAAAT
* *
17597708 ATTATAAACCAAATAATA
1 TTTTTAAA--AAATAATA
17597726 AATTTGAAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
22 9 0.18
23 20 0.40
24 16 0.32
25 3 0.06
26 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTTAAAAAATAATATTTAAAAT
Found at i:17597669 original size:23 final size:22
Alignment explanation
Indices: 17597637--17597702 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 22
17597627 TAAAAATAAT
17597637 AATTTTTAAAAATAATTTTTAA
1 AATTTTTAAAAATAATTTTTAA
*
17597659 AATTTTTTAAAAAATAATATTTAA
1 AA-TTTTT-AAAAATAATTTTTAA
*
17597683 AATATTTAAAATATACATTT
1 AATTTTTAAAA-ATA-ATTT
17597703 AAAATATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 6 0.16
23 12 0.32
24 19 0.51
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTTTTAAAAATAATTTTTAA
Found at i:17597715 original size:23 final size:23
Alignment explanation
Indices: 17597644--17597715 Score: 74
Period size: 24 Copynumber: 3.1 Consensus size: 23
17597634 AATAATTTTT
** *
17597644 AAAAATAATTTTTAAAATTTTTTA
1 AAAAATAACATTTAAAA-TATTTA
*
17597668 AAAAATAATATTTAAAATATTTA
1 AAAAATAACATTTAAAATATTTA
*
17597691 AAATAT-ACATTTAAAATATTATA
1 AAAAATAACATTTAAAATATT-TA
17597714 AA
1 AA
17597716 CCAAATAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
22 13 0.30
23 14 0.33
24 16 0.37
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAAATAACATTTAAAATATTTA
Found at i:17597803 original size:22 final size:23
Alignment explanation
Indices: 17597769--17597829 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
17597759 TTTTAAATGT
* *
17597769 TTTATAATATTAAAAAAAT-ATA
1 TTTAAAATTTTAAAAAAATAATA
17597791 TTTAAAATTTT-AAAAAATAATA
1 TTTAAAATTTTAAAAAAATAATA
*
17597813 TTATAAAACATTTAAAA
1 TT-TAAAA-TTTTAAAA
17597830 TATTATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 7 0.22
22 14 0.44
23 5 0.16
24 3 0.09
25 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTAAAATTTTAAAAAAATAATA
Found at i:17597826 original size:24 final size:21
Alignment explanation
Indices: 17597781--17597829 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
17597771 TATAATATTA
*
17597781 AAAAAATATATTTAAAATTTT
1 AAAAAATATATTTAAAAATTT
17597802 AAAAAATAATATTATAAAACATTT
1 AAAAAAT-ATATT-TAAAA-ATTT
17597826 AAAA
1 AAAA
17597830 TATTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 5 0.21
23 5 0.21
24 7 0.29
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAATATATTTAAAAATTT
Found at i:17597862 original size:24 final size:24
Alignment explanation
Indices: 17597834--17597887 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
17597824 TTAAAATATT
*
17597834 ATAAAACCAACAATA-AACAAATAA
1 ATAAAACAAACAA-AGAACAAATAA
* *
17597858 ATAAAACAAATAAAGGACAAATAA
1 ATAAAACAAACAAAGAACAAATAA
17597882 ATAAAA
1 ATAAAA
17597888 AAAGTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.72, C:0.11, G:0.04, T:0.13
Consensus pattern (24 bp):
ATAAAACAAACAAAGAACAAATAA
Found at i:17597866 original size:13 final size:12
Alignment explanation
Indices: 17597848--17597911 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 12
17597838 AACCAACAAT
17597848 AAACAAATAAATA
1 AAACAAATAAA-A
17597861 AAACAAAT-AAA
1 AAACAAATAAAA
**
17597872 GGACAAATAAATA
1 AAACAAATAAA-A
17597885 AAA-AAAGT-AAA
1 AAACAAA-TAAAA
17597896 AAACAAAATAAAA
1 AAAC-AAATAAAA
17597909 AAA
1 AAA
17597912 TGAAAAAGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
11 11 0.27
12 10 0.24
13 20 0.49
ACGTcount: A:0.78, C:0.06, G:0.05, T:0.11
Consensus pattern (12 bp):
AAACAAATAAAA
Found at i:17597895 original size:24 final size:24
Alignment explanation
Indices: 17597850--17597939 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
17597840 CCAACAATAA
17597850 ACAAATAAATAAAACAAA-TAAAGG
1 ACAAATAAATAAAA-AAAGTAAAGG
17597874 ACAAATAAATAAAAAAAGTAAA--
1 ACAAATAAATAAAAAAAGTAAAGG
*
17597896 A-AACA-AAATAAAAAAATGAAAAAGG
1 ACAA-ATAAATAAAAAAA-G-TAAAGG
*
17597921 ACAAAGAAATGAAAAAAAG
1 ACAAATAAAT-AAAAAAAG
17597940 AATCAGAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
21 13 0.23
22 3 0.05
23 6 0.11
24 18 0.32
25 2 0.04
26 7 0.12
27 7 0.12
ACGTcount: A:0.74, C:0.06, G:0.10, T:0.10
Consensus pattern (24 bp):
ACAAATAAATAAAAAAAGTAAAGG
Found at i:17597937 original size:29 final size:31
Alignment explanation
Indices: 17597900--17597970 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
17597890 AGTAAAAAAC
*
17597900 AAAATAAAAA-AAT-GAAAAAGG-ACAAA-G
1 AAAAAAAAAAGAATAGAAAAAGGAACAAATG
17597927 AAATGAAAAAAAGAATCAGAAAAAGGAACAAATG
1 AAA--AAAAAAAGAAT-AGAAAAAGGAACAAATG
17597961 AAAAAAAAAA
1 AAAAAAAAAA
17597971 TTCAGACTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
27 3 0.08
29 6 0.17
30 3 0.08
32 15 0.42
33 5 0.14
34 4 0.11
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (31 bp):
AAAAAAAAAAGAATAGAAAAAGGAACAAATG
Found at i:17602207 original size:22 final size:23
Alignment explanation
Indices: 17602182--17602225 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
17602172 ATTATACACT
17602182 TTAAAATTT-TCAAATATTTTAA
1 TTAAAATTTCTCAAATATTTTAA
** *
17602204 TTAAGCTTTCTCAAATTTTTTA
1 TTAAAATTTCTCAAATATTTTA
17602226 TAAATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAAAATTTCTCAAATATTTTAA
Found at i:17618396 original size:25 final size:28
Alignment explanation
Indices: 17618354--17618405 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
17618344 AGAACACCTA
*
17618354 TATATTATATAAAGAAAT-ATGTATATG
1 TATACTATATAAAGAAATCATGTATATG
17618381 TATACTATAT-AA-AAATGCATGTATA
1 TATACTATATAAAGAAAT-CATGTATA
17618406 AGTTTAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 4 0.18
26 2 0.09
27 16 0.73
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (28 bp):
TATACTATATAAAGAAATCATGTATATG
Found at i:17620019 original size:50 final size:49
Alignment explanation
Indices: 17619944--17620434 Score: 260
Period size: 50 Copynumber: 9.8 Consensus size: 49
17619934 TCTGCTCCAC
* * * * *
17619944 TGCAATGTCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
1 TGCAATGTAAGGAAACT-AGATCCGCCGTCGTAGCTTCAATCTTTTTAAT
* * **
17619994 TGCAATGTTAGGAAAACTAGATCCGCCGTCGTAGCTTCAATCTATTCCAT
1 TGCAATGTAAGG-AAACTAGATCCGCCGTCGTAGCTTCAATCTTTTTAAT
* * ** *
17620044 TGCACTGCTAAGG-AAGTAAGATCCGCCGTTTTGGCTTCAATCTTTTTAAT
1 TGCAATG-TAAGGAAACT-AGATCCGCCGTCGTAGCTTCAATCTTTTTAAT
* * * * *
17620094 TGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCT-AC
1 TGCAAT-GTAAGGAAACTAGATCCGCCGTCGTAGCTTCAATCT-TTTTAAT
* * * * * *
17620144 TGCATTGCTAAGG-AAGTAAGATCCGCCGTTGT-GACTTTAATCCTTTTGAT
1 TGCAATG-TAAGGAAACT-AGATCCGCCGTCGTAG-CTTCAATCTTTTTAAT
* * * * * ** *
17620194 TGCAATATCAGGGAAACCAGATCTGCCGTCATAGCTTCAAT-TTGTTCCAC
1 TGCAATGT-AAGGAAACTAGATCCGCCGTCGTAGCTTCAATCTT-TTTAAT
* * * * *
17620244 TGCACTGCTAAGG-AAGTAAGATCCGCCGTTGT-GACTTCAATATTTTTGAT
1 TGCAATG-TAAGGAAACT-AGATCCGCCGTCGTAG-CTTCAATCTTTTTAAT
* * * * * ** *
17620294 TGCAATATCAGGGAAACCAGATCCGTCGTCGTAGCTTCAATCTGTTCCAC
1 TGCAATGT-AAGGAAACTAGATCCGCCGTCGTAGCTTCAATCTTTTTAAT
* * * * * *
17620344 TGCACTGCTAAGG-AAGTAAGATCCGCTGTTGTGGCTTTAATCTTTTTAAT
1 TGCAATG-TAAGGAAACT-AGATCCGCCGTCGTAGCTTCAATCTTTTTAAT
* * * *
17620394 TGCAATATTAGGGAAACCAGATCCGTCGTCGTAGCTTCAAT
1 TGCAAT-GTAAGGAAACTAGATCCGCCGTCGTAGCTTCAAT
17620435 TTGTTCTACT
Statistics
Matches: 319, Mismatches: 97, Indels: 50
0.68 0.21 0.11
Matches are distributed among these distances:
49 17 0.05
50 278 0.87
51 24 0.08
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (49 bp):
TGCAATGTAAGGAAACTAGATCCGCCGTCGTAGCTTCAATCTTTTTAAT
Found at i:17620128 original size:100 final size:100
Alignment explanation
Indices: 17619928--17620461 Score: 782
Period size: 100 Copynumber: 5.3 Consensus size: 100
17619918 GGATTAGTTA
* * * *
17619928 CTTCTATCTGCTCCACTGCAATG-TCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTA
1 CTTCAATCTGTTCCACTGCACTGCT-AAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTA
* * *
17619992 ATTGCAATGTTAGGAAAACTAGATCCGCCGTCGTAG
65 ATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAG
* * *
17620028 CTTCAATCTATTCCATTGCACTGCTAAGGAAGTAAGATCCGCCGTTTTGGCTTCAATCTTTTTAA
1 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
17620093 TTGCAATATTAGGGAAACCAGATCCGCCGTCGTAG
66 TTGCAATATTAGGGAAACCAGATCCGCCGTCGTAG
* * * * * *
17620128 CTTCAATCTGTTCTACTGCATTGCTAAGGAAGTAAGATCCGCCGTTGTGACTTTAATCCTTTTGA
1 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* * *
17620193 TTGCAATATCAGGGAAACCAGATCTGCCGTCATAG
66 TTGCAATATTAGGGAAACCAGATCCGCCGTCGTAG
* * * *
17620228 CTTCAATTTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGACTTCAATATTTTTGA
1 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* *
17620293 TTGCAATATCAGGGAAACCAGATCCGTCGTCGTAG
66 TTGCAATATTAGGGAAACCAGATCCGCCGTCGTAG
* *
17620328 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCTGTTGTGGCTTTAATCTTTTTAA
1 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
*
17620393 TTGCAATATTAGGGAAACCAGATCCGTCGTCGTAG
66 TTGCAATATTAGGGAAACCAGATCCGCCGTCGTAG
* *
17620428 CTTCAATTTGTTCTACTGCACTGCTAAGGAAGTA
1 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
17620462 GAATTACTGC
Statistics
Matches: 393, Mismatches: 40, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
100 392 1.00
101 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.32
Consensus pattern (100 bp):
CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
TTGCAATATTAGGGAAACCAGATCCGCCGTCGTAG
Found at i:17620893 original size:262 final size:262
Alignment explanation
Indices: 17620455--17621612 Score: 1856
Period size: 262 Copynumber: 4.4 Consensus size: 262
17620445 GCACTGCTAA
* **
17620455 GGAAGTAGAATTACT-GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCTGCCATCTT
*
17620519 CGATCTGCTCCACTACTGCTTAGGGAAATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
* *
17620584 AGTGAGATAGAACTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATA
131 AGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATA
* *
17620649 TTTGATCTACTCTTCTACTGCTTAGGGAGATAAGATCTGTTCTTCAATCTATTCCGCTGCTGCCC
196 TTTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTGTTCTTCAATCTATTCCGCTGCTGCCC
17620714 AG
261 AG
*
17620716 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCTGCCATCTT
17620781 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
*
17620846 AGTGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATA
131 AGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATA
* *
17620911 TTTGATCTGCTCTTCTACTGCTTAGGGAGATAAGATCTGTTCTTTAATCTATTCCGCTGCTGCCC
196 TTTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTGTTCTTCAATCTATTCCGCTGCTGCCC
17620976 AG
261 AG
17620978 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAAT-TCGCCATCT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCT-GCCATCT
17621042 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCC
65 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCC
*
17621107 CAGGGAGATAAAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCAT
130 CAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCAT
17621172 ATTTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTGTTCTTCAATCTATTCCGCTGCTGCC
195 ATTTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTGTTCTTCAATCTATTCCGCTGCTGCC
17621237 CAG
260 CAG
*
17621240 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCTGCCATATT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCTGCCATCTT
** *** * **
17621305 CGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTAAAATCTTCAATCTATTCTGCTGCTGCCC
66 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
** * * **
17621370 AGGGA-AGTAGAATTACCGGCTTCAATGTACTCCACGGTAACCACAGGGAGGTAAAATCTGCCAT
131 AGGGAGA-TAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCAT
* * * ** *
17621434 CTTTGACCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTG
195 ATTTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTG--TTCTTCAATCTATTCCGCTGCTG
*
17621499 CCTAG
258 CCCAG
* * * * *
17621504 GGAAGTAGAATTACCGGCTTCAATATACTCCACGGCAA-TCACAGGAAGGTAAAATCTGCCATCT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACT-TCAGGGAGGTAAAATCTGCCATCT
* * *
17621568 TTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGCTATCTT
65 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTT
17621613 CAACCTGCTC
Statistics
Matches: 843, Mismatches: 47, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
261 16 0.02
262 703 0.83
263 2 0.00
264 122 0.14
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (262 bp):
GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCTGCCATCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
AGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATA
TTTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTGTTCTTCAATCTATTCCGCTGCTGCCC
AG
Found at i:17621638 original size:132 final size:131
Alignment explanation
Indices: 17620455--17621615 Score: 1600
Period size: 132 Copynumber: 8.8 Consensus size: 131
17620445 GCACTGCTAA
*
17620455 GGAAGTAGAATTACT-GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTT
* * * *
17620519 CGATCTGCTCCACTACTGCTTAGGGAAATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG-TATCTTCAATCTATTCCGCTGCTGCCC
17620584 AG
130 AG
* * * ** *
17620586 TG-AGATAGAACTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATAT
1 GGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCT
* **
17620650 TTGATCTACTCTTCTACTGCTTAGGGAGATAAGATCTGT-TCTTCAATCTATTCCGCTGCTGCCC
65 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATCTTCAATCTATTCCGCTGCTGCCC
17620714 AG
130 AG
* * *
17620716 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTT
* * *
17620781 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG-TATCTTCAATCTATTCCGCTGCTGCCC
17620846 AG
130 AG
* * ** *
17620848 TG-AGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATAT
1 GGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCT
** *
17620912 TTGATCTGCTCTTCTACTGCTTAGGGAGATAAGATCTGT-TCTTTAATCTATTCCGCTGCTGCCC
65 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATCTTCAATCTATTCCGCTGCTGCCC
17620976 AG
130 AG
* *
17620978 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAAT-TCGCCATCT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCT-GCCATCT
* * *
17621042 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCC
65 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG-TATCTTCAATCTATTCCGCTGCTGCC
17621107 CAG
129 CAG
* * ** *
17621110 GG-AGATAAAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATAT
1 GGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCT
*
17621174 TTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTGT-TCTTCAATCTATTCCGCTGCTGCCC
65 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATCTTCAATCTATTCCGCTGCTGCCC
17621238 AG
130 AG
* * *
17621240 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCTGCCATATT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTT
* ** ** *
17621305 CGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTAAAATCTTCAATCTATTCTGCTGCTGCCC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GTATCTTCAATCTATTCCGCTGCTGCCC
17621370 AG
130 AG
* * *
17621372 GGAAGTAGAATTACCGGCTTCAATGTACTCCACGGTAACCACAGGGAGGTAAAATCTGCCATCTT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTT
* ** * *
17621437 TGACCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCT
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG-TATCTTCAATCTATTCCGCTGCTGCCC
17621502 AG
130 AG
* * * * * * *
17621504 GGAAGTAGAATTACCGGCTTCAATATACTCCACGGCAATCACAGGAAGGTAAAATCTGCCATCTT
1 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTT
*
17621569 TGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGCTATCTTCAA
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG-TATCTTCAA
17621616 CCTGCTCCCC
Statistics
Matches: 923, Mismatches: 91, Indels: 31
0.88 0.09 0.03
Matches are distributed among these distances:
130 342 0.37
131 24 0.03
132 557 0.60
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (131 bp):
GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTT
TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTATCTTCAATCTATTCCGCTGCTGCCCA
G
Found at i:17622946 original size:7 final size:7
Alignment explanation
Indices: 17622932--17622964 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
17622922 TCCATTTTAT
17622932 TTTTTCA
1 TTTTTCA
*
17622939 TTTCTCA
1 TTTTTCA
17622946 TTTTTCA
1 TTTTTCA
17622953 TTTTTCA
1 TTTTTCA
17622960 TTTTT
1 TTTTT
17622965 TCACATCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:17622950 original size:15 final size:15
Alignment explanation
Indices: 17622930--17622967 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
17622920 TCTCCATTTT
17622930 ATTTTTTCATTTCTC
1 ATTTTTTCATTTCTC
*
17622945 A-TTTTTCATTTTTC
1 ATTTTTTCATTTCTC
17622959 ATTTTTTCA
1 ATTTTTTCA
17622968 CATCACTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTTCATTTCTC
Found at i:17628276 original size:25 final size:28
Alignment explanation
Indices: 17628234--17628285 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
17628224 AGAACACCTA
*
17628234 TATATTATATAAAGAAAT-ATGTATATG
1 TATACTATATAAAGAAATCATGTATATG
17628261 TATACTATAT-AA-AAATGCATGTATA
1 TATACTATATAAAGAAAT-CATGTATA
17628286 AGTTTAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 4 0.18
26 2 0.09
27 16 0.73
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (28 bp):
TATACTATATAAAGAAATCATGTATATG
Found at i:17633543 original size:19 final size:19
Alignment explanation
Indices: 17633506--17633544 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17633496 ATTGCGTGTC
* * *
17633506 TGAATAGAAAAGAACGAAA
1 TGAATAAAAAAAAAAGAAA
17633525 TGAATAAAAAAAAAAGAAA
1 TGAATAAAAAAAAAAGAAA
17633544 T
1 T
17633545 AGGAAACATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.15, T:0.13
Consensus pattern (19 bp):
TGAATAAAAAAAAAAGAAA
Found at i:17633827 original size:26 final size:26
Alignment explanation
Indices: 17633793--17633865 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
17633783 AATTTTCTCC
17633793 AAATTTTATCGAGGGTAAAATCATCA
1 AAATTTTATCGAGGGTAAAATCATCA
* * *
17633819 AAATTTTATTGAAGGCAAAATCATCA
1 AAATTTTATCGAGGGTAAAATCATCA
*
17633845 AAATTTTA-CTGGGGGTAAAAT
1 AAATTTTATC-GAGGGTAAAAT
17633866 TGCCAAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (26 bp):
AAATTTTATCGAGGGTAAAATCATCA
Found at i:17634397 original size:43 final size:43
Alignment explanation
Indices: 17634331--17634496 Score: 215
Period size: 43 Copynumber: 3.9 Consensus size: 43
17634321 AACACATAGT
* * *
17634331 TCGCCCATTGGTGAATACAATACACAAGCAGACTTCATACAAC
1 TCGCCCATTGGTGAATACTATACACAAGCAAACTTTATACAAC
** *
17634374 TCGCCCATTGACGAATATTATACACAAGCAAACTTTATACAAC
1 TCGCCCATTGGTGAATACTATACACAAGCAAACTTTATACAAC
* * **
17634417 TTGCCTATTGGTGAATACTATACACAATTAAACTTTATACAAC
1 TCGCCCATTGGTGAATACTATACACAAGCAAACTTTATACAAC
* * *
17634460 TCTCCCATTGGTAAATATTATACACAAGCAAACTTTA
1 TCGCCCATTGGTGAATACTATACACAAGCAAACTTTA
17634497 CAGCAGACTT
Statistics
Matches: 103, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 103 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.28
Consensus pattern (43 bp):
TCGCCCATTGGTGAATACTATACACAAGCAAACTTTATACAAC
Found at i:17634440 original size:86 final size:86
Alignment explanation
Indices: 17634337--17634496 Score: 239
Period size: 86 Copynumber: 1.9 Consensus size: 86
17634327 TAGTTCGCCC
* *
17634337 ATTGGTGAATACAATACACAAGCAGACTTCATACAACTCGCCCATTGACGAATATTATACACAAG
1 ATTGGTGAATACAATACACAAGCAAACTTCATACAACTCGCCCATTGACAAATATTATACACAAG
17634402 CAAACTTTATACAACTTGCCT
66 CAAACTTTATACAACTTGCCT
* ** * * **
17634423 ATTGGTGAATACTATACACAATTAAACTTTATACAACTCTCCCATTGGTAAATATTATACACAAG
1 ATTGGTGAATACAATACACAAGCAAACTTCATACAACTCGCCCATTGACAAATATTATACACAAG
17634488 CAAACTTTA
66 CAAACTTTA
17634497 CAGCAGACTT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 65 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (86 bp):
ATTGGTGAATACAATACACAAGCAAACTTCATACAACTCGCCCATTGACAAATATTATACACAAG
CAAACTTTATACAACTTGCCT
Found at i:17637767 original size:21 final size:21
Alignment explanation
Indices: 17637726--17637767 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17637716 TTAGAAATGC
* *
17637726 TTTTGTCCTAAAAGTAATTTT
1 TTTTGTCCCAAAACTAATTTT
*
17637747 TTTTGTCCCAAAACTACTTTT
1 TTTTGTCCCAAAACTAATTTT
17637768 GAGAAGCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTTGTCCCAAAACTAATTTT
Found at i:17644699 original size:47 final size:46
Alignment explanation
Indices: 17644613--17644705 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 46
17644603 ATCCAATGAT
* * * *
17644613 AAATGGATGTCCATACCCCCAAATTTATCCTATTGTAACCCTTAAA
1 AAATGAATGTCCATACCCCCAAATTTATCATATTATAACCCCTAAA
* * *
17644659 AAATGAATGTCCATAACCCCTAAATTTATTATTTTATAACCCCTAAA
1 AAATGAATGTCCAT-ACCCCCAAATTTATCATATTATAACCCCTAAA
17644706 TTACTTATAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 13 0.33
47 26 0.67
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (46 bp):
AAATGAATGTCCATACCCCCAAATTTATCATATTATAACCCCTAAA
Found at i:17659640 original size:35 final size:36
Alignment explanation
Indices: 17659576--17659646 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
17659566 TTTAATTATA
17659576 TTATTGTTAACAAATTTAACTTATATAAACAAAATT
1 TTATTGTTAACAAATTTAACTTATATAAACAAAATT
*
17659612 TTATTGTTAA-AAATTTAA-TTAATTTAAACAAAATT
1 TTATTGTTAACAAATTTAACTT-ATATAAACAAAATT
17659647 GAAATATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 2 0.06
35 21 0.64
36 10 0.30
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (36 bp):
TTATTGTTAACAAATTTAACTTATATAAACAAAATT
Found at i:17662978 original size:18 final size:17
Alignment explanation
Indices: 17662955--17663004 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
17662945 TAAGCCTAAA
17662955 GCTTTCTCTTGCTCTTTC
1 GCTTTCTCTT-CTCTTTC
* *
17662973 GCTTTCACTT-TCCTTTT
1 GCTTTCTCTTCT-CTTTC
17662990 GCTTT-TCTTCTCTTT
1 GCTTTCTCTTCTCTTT
17663005 TCTTAACAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 8 0.30
17 10 0.37
18 9 0.33
ACGTcount: A:0.02, C:0.30, G:0.08, T:0.60
Consensus pattern (17 bp):
GCTTTCTCTTCTCTTTC
Found at i:17665711 original size:25 final size:25
Alignment explanation
Indices: 17665679--17665736 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
17665669 TTCAAGGATC
* * *
17665679 AAAA-TGAATTTAGTTGTCAAATTT
1 AAAAGTGAATCTAATTGCCAAATTT
17665703 AAAAGTGAATCTAATTGCCAAATTT
1 AAAAGTGAATCTAATTGCCAAATTT
17665728 AAAAGTGAA
1 AAAAGTGAA
17665737 AAAAAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (25 bp):
AAAAGTGAATCTAATTGCCAAATTT
Found at i:17674105 original size:18 final size:18
Alignment explanation
Indices: 17674068--17674106 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17674058 TGTATTTGTC
*
17674068 AAACTGTGCTTATTCGTT
1 AAACTGTGCTTATTCCTT
17674086 AAACTGTGCTCT-TTCCTT
1 AAACTGTGCT-TATTCCTT
17674104 AAA
1 AAA
17674107 TCCTTACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41
Consensus pattern (18 bp):
AAACTGTGCTTATTCCTT
Found at i:17685154 original size:31 final size:31
Alignment explanation
Indices: 17685116--17685204 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 31
17685106 TTGAGCCCTC
*
17685116 AAAATTTTTGAAAATTTTAATTAGACCCTTT-
1 AAAATTTTTGAAAATTTTAATTA-AACCTTTG
*
17685147 AAAATTTTTTGAAAATTATT-ATTAAACTTTTG
1 AAAA-TTTTTGAAAATT-TTAATTAAACCTTTG
*
17685179 AAAAATTTT-AAAATTTTCAATTAAAC
1 AAAATTTTTGAAAATTTT-AATTAAAC
17685205 TCTTGACTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
29 2 0.04
30 6 0.12
31 20 0.40
32 20 0.40
33 2 0.04
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (31 bp):
AAAATTTTTGAAAATTTTAATTAAACCTTTG
Found at i:17688086 original size:27 final size:27
Alignment explanation
Indices: 17688055--17688113 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
17688045 CACATAGTGT
17688055 TAGTGACAATTCAGTGCAATTAAATGA
1 TAGTGACAATTCAGTGCAATTAAATGA
* ** * * *
17688082 TAGTGGCGCTTCGGTGCAATTTAGTGA
1 TAGTGACAATTCAGTGCAATTAAATGA
17688109 TAGTG
1 TAGTG
17688114 GCTCATTGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (27 bp):
TAGTGACAATTCAGTGCAATTAAATGA
Found at i:17691436 original size:16 final size:17
Alignment explanation
Indices: 17691415--17691446 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17691405 AAATATGCAA
17691415 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
17691431 TCACATAACTTCATAT
1 TCACATAACTTCATAT
17691447 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:17691669 original size:43 final size:43
Alignment explanation
Indices: 17691599--17691769 Score: 161
Period size: 43 Copynumber: 4.0 Consensus size: 43
17691589 GACTCGTACA
* * *
17691599 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGAAAACACATATCG
* * * * * *
17691642 ATGCTAATATCCCAGACAG-GGTCTTACA-CAAATCAAATAT-A
1 ATGCCAATGTCCCAGAC-GTGGTCTTACATGAAAACACATATCG
* * * *
17691683 ATGCCAATGTCCTAGACATGGTCTTACACGTAAACACA-AGTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGAAAACACATA-TCG
* *
17691726 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACGTATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGAAAACACATATCG
17691769 A
1 A
17691770 AATCCTATGT
Statistics
Matches: 100, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
41 24 0.24
42 15 0.15
43 59 0.59
44 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGAAAACACATATCG
Found at i:17691739 original size:84 final size:84
Alignment explanation
Indices: 17691598--17691753 Score: 208
Period size: 84 Copynumber: 1.9 Consensus size: 84
17691588 AGACTCGTAC
* * * * *
17691598 AATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCTAATATCCCAGACAG-G
1 AATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCAACATCCCAGAC-GTG
17691662 GTCTTACACAAATCAAATAT
65 GTCTTACACAAATCAAATAT
* * *
17691682 AATGCCAATGTCCTAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAACGTCCCAGACGTG
1 AATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCGATGCCAACATCCCAGACGTG
17691746 GTCTTACA
65 GTCTTACA
17691754 TGAAAACACG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 2 0.03
84 60 0.97
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (84 bp):
AATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCAACATCCCAGACGTGG
TCTTACACAAATCAAATAT
Found at i:17711139 original size:2 final size:2
Alignment explanation
Indices: 17711132--17711185 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
17711122 ATTTTTATTT
* **
17711132 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CG TG CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
17711174 CA CA CA CA CA CA
1 CA CA CA CA CA CA
17711186 AACCTTGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.46, C:0.48, G:0.04, T:0.02
Consensus pattern (2 bp):
CA
Found at i:17711588 original size:16 final size:16
Alignment explanation
Indices: 17711569--17711599 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17711559 TTAGGGACTT
*
17711569 CAATACCCTTTTTACA
1 CAATAACCTTTTTACA
17711585 CAATAACCTTTTTAC
1 CAATAACCTTTTTAC
17711600 CGCACTAAAC
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:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (16 bp):
CAATAACCTTTTTACA
Found at i:17720072 original size:105 final size:101
Alignment explanation
Indices: 17719891--17720107 Score: 274
Period size: 105 Copynumber: 2.1 Consensus size: 101
17719881 AATTGGTAGA
* * * *
17719891 TAAGATCATGGTTGGACCATGGCAGTGTTTAAATGTAAGACCATAGCTGAGCTATGGAATTTTAA
1 TAAGACCATGGTTGGACCATGACAGTATTTAAATGTAAGACCATAGCTGAGCTATGGAATTCTAA
* **
17719956 TGAAAATACCATAACTGGGTTATGGCACCT-TGAACG
66 TGAAAAGACCATAACTGGGTTATGGCA-CTACAAACG
* * *
17719992 TAAGACCATGGTTGGACCATGACAGTATATATACATGTGTAAGACCATAGCTGGGCTATGGCATT
1 TAAGACCATGGTTGGACCATGACAGTAT-T-TA-A-ATGTAAGACCATAGCTGAGCTATGGAATT
* *
17720057 CTGATGATAAGACCATAACTGGGTTATGGCACTACAAACG
62 CTAATGAAAAGACCATAACTGGGTTATGGCACTACAAACG
17720097 TAAGACCATGG
1 TAAGACCATGG
17720108 CAGACTCATG
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
101 25 0.25
102 1 0.01
103 2 0.02
104 3 0.03
105 68 0.69
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGACAGTATTTAAATGTAAGACCATAGCTGAGCTATGGAATTCTAA
TGAAAAGACCATAACTGGGTTATGGCACTACAAACG
Found at i:17721203 original size:23 final size:21
Alignment explanation
Indices: 17721176--17721231 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 21
17721166 TTTATATCAG
17721176 TTTTAATATTTTTAATAATTTT
1 TTTTAATATTTTT-ATAATTTT
* * *
17721198 TATTTAAAAATTTTATGATTTT
1 T-TTTAATATTTTTATAATTTT
*
17721220 TTATAATATTTT
1 TTTTAATATTTT
17721232 AAGCATTCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 8 0.30
22 9 0.33
23 10 0.37
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTAATATTTTTATAATTTT
Found at i:17721270 original size:20 final size:21
Alignment explanation
Indices: 17721247--17721296 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
17721237 TTCTTATATG
17721247 TTTTTATAAAATTT-CAAATT
1 TTTTTATAAAATTTACAAATT
* * *
17721267 TTTTTATTAATTTTATAAATT
1 TTTTTATAAAATTTACAAATT
*
17721288 TTGTTATAA
1 TTTTTATAA
17721297 TTTATTAGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTTATAAAATTTACAAATT
Found at i:17742867 original size:3 final size:3
Alignment explanation
Indices: 17742859--17742894 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
17742849 ACCAGCCATC
*
17742859 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17742895 CATCTCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17751094 original size:37 final size:37
Alignment explanation
Indices: 17751020--17751100 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
17751010 ATGGAGAAAT
* *
17751020 ATGAAA-CATTTGGAAATGATTAAGGTTTTATTAAAA
1 ATGAAATCATTTGGAAATGAATAAGGTTTTATCAAAA
** * *
17751056 ATGAAATCATTTGGAAATGAATGTGGTTTTCTCCAAA
1 ATGAAATCATTTGGAAATGAATAAGGTTTTATCAAAA
17751093 ATGGAAAT
1 AT-GAAAT
17751101 GAAAATGAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
36 6 0.16
37 26 0.70
38 5 0.14
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.35
Consensus pattern (37 bp):
ATGAAATCATTTGGAAATGAATAAGGTTTTATCAAAA
Found at i:17751115 original size:7 final size:7
Alignment explanation
Indices: 17751091--17751129 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
17751081 GTTTTCTCCA
17751091 AAATG-G
1 AAATGAG
17751097 AAATGA-
1 AAATGAG
17751103 AAATGAG
1 AAATGAG
17751110 AAATGAG
1 AAATGAG
17751117 AAATGAG
1 AAATGAG
17751124 AAATGA
1 AAATGA
17751130 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (7 bp):
AAATGAG
Found at i:17758294 original size:22 final size:23
Alignment explanation
Indices: 17758240--17758295 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
17758230 TACACCACAC
*
17758240 CAGTAGGCACCGAAGTACTTATA
1 CAGTAGGCACCGAAATACTTATA
* *
17758263 CAGTAAGCACCGAAAT-GTTGA-A
1 CAGTAGGCACCGAAATACTT-ATA
17758285 CAGTAGGCACC
1 CAGTAGGCACC
17758296 ATAGTGCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (23 bp):
CAGTAGGCACCGAAATACTTATA
Found at i:17758310 original size:22 final size:22
Alignment explanation
Indices: 17758285--17758329 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
17758275 AAATGTTGAA
*
17758285 CAGTAGGCACCATAGTGCAAAT
1 CAGTAGGCACCATAGTGAAAAT
17758307 CAGTAGGCACCATAGTGAAAAT
1 CAGTAGGCACCATAGTGAAAAT
17758329 C
1 C
17758330 CTGTACAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (22 bp):
CAGTAGGCACCATAGTGAAAAT
Found at i:17760151 original size:320 final size:320
Alignment explanation
Indices: 17759569--17760211 Score: 1286
Period size: 320 Copynumber: 2.0 Consensus size: 320
17759559 GTTACCTATT
17759569 ACAAAGTTTCCAACCAAACTCATCAATTTTATACTAATTACTAACTTCATTTGAATCAAAACACT
1 ACAAAGTTTCCAACCAAACTCATCAATTTTATACTAATTACTAACTTCATTTGAATCAAAACACT
17759634 TCAAGAACATATCAATCAAGTTCAAATAACCACATTTAACTTCTTAACAACCTTCATTACCTATT
66 TCAAGAACATATCAATCAAGTTCAAATAACCACATTTAACTTCTTAACAACCTTCATTACCTATT
17759699 CAACCATTAGATTTAGCATTCCATTGCCATGACATACATATCAATCAAATTATCCAAATACTAAG
131 CAACCATTAGATTTAGCATTCCATTGCCATGACATACATATCAATCAAATTATCCAAATACTAAG
17759764 CCTTTATATATACCAAACTATCTTGAAACATGTCAATTTATATGCCAAACATATTCCAAGTATAT
196 CCTTTATATATACCAAACTATCTTGAAACATGTCAATTTATATGCCAAACATATTCCAAGTATAT
17759829 AAATCAAAATATACCAATTCACCTAGGCATCACCAATGCCAATTCATGCATTTCTAAATC
261 AAATCAAAATATACCAATTCACCTAGGCATCACCAATGCCAATTCATGCATTTCTAAATC
17759889 ACAAAGTTTCCAACCAAACTCATCAATTTTATACTAATTACTAACTTCATTTGAATCAAAACACT
1 ACAAAGTTTCCAACCAAACTCATCAATTTTATACTAATTACTAACTTCATTTGAATCAAAACACT
17759954 TCAAGAACATATCAATCAAGTTCAAATAACCACATTTAACTTCTTAACAACCTTCATTACCTATT
66 TCAAGAACATATCAATCAAGTTCAAATAACCACATTTAACTTCTTAACAACCTTCATTACCTATT
17760019 CAACCATTAGATTTAGCATTCCATTGCCATGACATACATATCAATCAAATTATCCAAATACTAAG
131 CAACCATTAGATTTAGCATTCCATTGCCATGACATACATATCAATCAAATTATCCAAATACTAAG
17760084 CCTTTATATATACCAAACTATCTTGAAACATGTCAATTTATATGCCAAACATATTCCAAGTATAT
196 CCTTTATATATACCAAACTATCTTGAAACATGTCAATTTATATGCCAAACATATTCCAAGTATAT
17760149 AAATCAAAATATACCAATTCACCTAGGCATCACCAATGCCAATTCATGCATTTCTAAATC
261 AAATCAAAATATACCAATTCACCTAGGCATCACCAATGCCAATTCATGCATTTCTAAATC
17760209 ACA
1 ACA
17760212 TACCAAGACC
Statistics
Matches: 323, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
320 323 1.00
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.31
Consensus pattern (320 bp):
ACAAAGTTTCCAACCAAACTCATCAATTTTATACTAATTACTAACTTCATTTGAATCAAAACACT
TCAAGAACATATCAATCAAGTTCAAATAACCACATTTAACTTCTTAACAACCTTCATTACCTATT
CAACCATTAGATTTAGCATTCCATTGCCATGACATACATATCAATCAAATTATCCAAATACTAAG
CCTTTATATATACCAAACTATCTTGAAACATGTCAATTTATATGCCAAACATATTCCAAGTATAT
AAATCAAAATATACCAATTCACCTAGGCATCACCAATGCCAATTCATGCATTTCTAAATC
Found at i:17774669 original size:21 final size:21
Alignment explanation
Indices: 17774644--17774685 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
17774634 AAAAGAAAGG
17774644 AAAACTAAAACTGAAATTATA
1 AAAACTAAAACTGAAATTATA
17774665 AAAACTAAAACTGAAATTATA
1 AAAACTAAAACTGAAATTATA
17774686 TAGAAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAACTAAAACTGAAATTATA
Found at i:17782706 original size:13 final size:13
Alignment explanation
Indices: 17782688--17782721 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17782678 AGAGGAGGAG
*
17782688 AGCCACCATGAGA
1 AGCCACAATGAGA
*
17782701 AGCCACAATGAGC
1 AGCCACAATGAGA
17782714 AGCCACAA
1 AGCCACAA
17782722 ATAACCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.32, G:0.21, T:0.06
Consensus pattern (13 bp):
AGCCACAATGAGA
Found at i:17785960 original size:20 final size:19
Alignment explanation
Indices: 17785937--17786006 Score: 90
Period size: 20 Copynumber: 3.7 Consensus size: 19
17785927 AATTACAAAA
17785937 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
17785956 CAAAAATTCAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
* *
17785976 TAAAATTCAAAA-AA-TAT
1 AAAAATTCAAAATAATTTT
17785993 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
17786007 TTATTTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.18
18 7 0.16
19 11 0.24
20 19 0.42
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:17785981 original size:39 final size:38
Alignment explanation
Indices: 17785938--17786021 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
17785928 ATTACAAAAA
*
17785938 AAAATTCAAAATAATTTTCAAAAATT-CAAAA-TAATTTTT
1 AAAATTCAAAA-AA-TAT-AAAAATTCCAAAATTAATTTTT
*
17785977 AAAATTCAAAAAATATAAAAATTCCAAAATTTATTTTTT
1 AAAATTCAAAAAATATAAAAATTCCAAAA-TTAATTTTT
17786016 AAAATT
1 AAAATT
17786022 ATAAGAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
36 7 0.17
37 7 0.17
38 2 0.05
39 24 0.60
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (38 bp):
AAAATTCAAAAAATATAAAAATTCCAAAATTAATTTTT
Found at i:17794195 original size:5 final size:6
Alignment explanation
Indices: 17794162--17794217 Score: 52
Period size: 5 Copynumber: 10.3 Consensus size: 6
17794152 ACATACAGAG
* *
17794162 AGAGAA AGAGAG AG-GAG AGA-AA AGAGAA AG-GAA AGAGAA A-AG-A
1 AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA
17794205 AGAG-A AGAGAA AG
1 AGAGAA AGAGAA AG
17794218 GGGTTTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
4 2 0.05
5 23 0.53
6 18 0.42
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (6 bp):
AGAGAA
Found at i:17802440 original size:31 final size:31
Alignment explanation
Indices: 17802398--17802458 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
17802388 ATTCAACATC
* *
17802398 GGTACATAGTACCTGATATAATATAAACACT
1 GGTACAAAGTACCTGATATAACATAAACACT
* *
17802429 GGTACAAAGTACTTGCTATAACATAAACAC
1 GGTACAAAGTACCTGATATAACATAAACAC
17802459 CGATACATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (31 bp):
GGTACAAAGTACCTGATATAACATAAACACT
Found at i:17817477 original size:69 final size:69
Alignment explanation
Indices: 17817366--17817504 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
17817356 ACCCTAAGTG
17817366 TAAAACCTCTATTAGCAATATATTAAATAGTTTTTAATATATTATTCATAACTTTATTTATGGAA
1 TAAAACCTCTATTAGCAATATATTAAATAGTTTTTAATATATTATTCATAACTTTATTTATGGAA
17817431 TTTT
66 TTTT
*
17817435 TAAAACCTCTATTAGTAATATATTAAATAGTTTTTAATATATTATTCATAACTTTATTTATGGAA
1 TAAAACCTCTATTAGCAATATATTAAATAGTTTTTAATATATTATTCATAACTTTATTTATGGAA
17817500 TTTT
66 TTTT
17817504 T
1 T
17817505 CGGCATAATA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (69 bp):
TAAAACCTCTATTAGCAATATATTAAATAGTTTTTAATATATTATTCATAACTTTATTTATGGAA
TTTT
Found at i:17825329 original size:3 final size:3
Alignment explanation
Indices: 17825321--17825360 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
17825311 GTAATAGATT
*
17825321 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
17825361 TTGATAAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17832883 original size:25 final size:24
Alignment explanation
Indices: 17832848--17832942 Score: 91
Period size: 25 Copynumber: 3.8 Consensus size: 24
17832838 AAGGCTTTTT
* * *
17832848 CAGAGATTTCGCCACAATAACTTTA
1 CAGAGAGTTCACCACAA-AGCTTTA
** * *
17832873 CAGAGAGTTCGTCATAAGGGCTTTA
1 CAGAGAGTTCACCACAA-AGCTTTA
*
17832898 CAGAGAGTTCACCATAAAGGCTTTA
1 CAGAGAGTTCACCACAAA-GCTTTA
17832923 CAGAGAGTTCACCACAAAGC
1 CAGAGAGTTCACCACAAAGC
17832943 CTTGGTTTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
24 2 0.03
25 57 0.97
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (24 bp):
CAGAGAGTTCACCACAAAGCTTTA
Found at i:17837511 original size:23 final size:22
Alignment explanation
Indices: 17837468--17837525 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
17837458 AAAAGGTATC
* *
17837468 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
17837489 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
17837512 TGCATATCATATCT
1 TACAAATCATATCT
17837526 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Done.