Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 50 of 136
Found at i:16531402 original size:18 final size:18
Alignment explanation
Indices: 16531379--16531413 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16531369 GTTTTTGTTT
16531379 TTGTTCTTGTTATTATTC
1 TTGTTCTTGTTATTATTC
*
16531397 TTGTTCTTTTTATTATT
1 TTGTTCTTGTTATTATT
16531414 TTATTTTACT
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:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (18 bp):
TTGTTCTTGTTATTATTC
Found at i:16537977 original size:4 final size:4
Alignment explanation
Indices: 16537968--16537993 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
16537958 CACACCTCTA
16537968 TTTG TTTG TTTG TTTG TTTG TTTG TT
1 TTTG TTTG TTTG TTTG TTTG TTTG TT
16537994 AGACTAGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:16540771 original size:521 final size:515
Alignment explanation
Indices: 16539348--16541088 Score: 2523
Period size: 521 Copynumber: 3.4 Consensus size: 515
16539338 CGTAGATACC
* * ** *
16539348 CCCTTATGATACAAAGGCATGTTGTCCCCAATTGATCTTATAGAATTGCCTTTCTACGGGTTTGA
1 CCCTTATGATACAAGGGCATGTT-TTCCCTGTTGATCTTATGGAATTGCCTTTCTACGGGTTTGA
* * * * **
16539413 TGTTATTCTTGGTATGGACCGGTTGACTAAACACAAGGCTAAGGTAGAATTTAAGACGAAAAGAA
65 TGTTATTCTTGATATGGACTGGTTGACTGAACATAAGGCTAAGGTAGAATTTAAGACGAAACTAA
* * * *
16539478 TTACTTAGAAGAATAGTGATGTGTTGGAAATTGTTGTTGTCGTTCAAATACTGTGATTTATGTCT
130 TTACTTAGAAGAATAGTGATGGGTTGGAAATTGTTGTTGTCGTTGAAAGACTGAGATTTATGTCT
*
16539543 AATGTGGTTTCAACTATGAAGGCTGAGAAGATGATGGGAACAGGTTGTGAAG----CTTAGCCTC
195 AATGTGGTTTCAACTATGAAGGCTGAGAAGATGAT-GGAAGAGGTTGTGAAGCTTACTTAGCCTC
* * * * *
16539604 TGTGATGAATTCAGTTAGTAAGGAGCTGAGAGTTCAGGATA-TTCCAATTTTTAAGGATATTCCT
259 TGTGATGAATTCAGTTAGTAAGGAGCTGAGAGTTCAGGATATTTGC-ACTCTTAAGAATTTTCCT
** * * *
16539668 AATGTGTTTCCTAAAGAGTTTTCTGGTTTGCCACCAAAATGTGAAGTGGATTTTGGTATTGAGCT
323 AACATGTTTCCTGAAGAGTTGTCTGGTTTGCCACCAGAATGTGAAGTGGATTTTGGTATTGAGCT
* * * *
16539733 CTATCTTGGTACTGCACCAGTGTCTATAGCACCCTATCGTATGCCACCAAAAGAACTCAAAGAAT
388 CTATCCTGGTACTGCACCAGTGTCTATAG--CCCTATCGTATGGCACCAAAAGAGCTCAAAGAGT
* * *
16539798 TACAGATTTAGTTGCAAGAGTTGCTTGACAGAGGGTTCA-TCTGACTGAGTTTATCTCCGTAGGG
451 TAAAGATTTAGTTGCAAGAGTTGCTTGACAGAGGGTTCATTC-GAC-GAGTGTATCTCCGTGGGG
16539862 TG
514 TG
* * *
16539864 CCCTTATGATACAAGGGCATGTTTTACCTTTTGATCTTATGGAATTGCCTTTCTATGGGTTTGAT
1 CCCTTATGATACAAGGGCATGTTTTCCCTGTTGATCTTATGGAATTGCCTTTCTACGGGTTTGAT
** *
16539929 GTTATTCTTGGCATGGACTGGTTGACTGAACATAAGGCTAAGGTAGAATTTAAGACGAAACAAAT
66 GTTATTCTTGATATGGACTGGTTGACTGAACATAAGGCTAAGGTAGAATTTAAGACGAAACTAAT
* *
16539994 TACTTAGAGGAATAGTGATGGGTTGGAAATTGTTGTTGTCGTTGAAAGACAGAGATTTATGTCTA
131 TACTTAGAAGAATAGTGATGGGTTGGAAATTGTTGTTGTCGTTGAAAGACTGAGATTTATGTCTA
**
16540059 ATGTGGTTTTGACTATGAAGGCTGAGAAGATGATGAGAAGAGGTTGTGAAGCTTACTTAGCACT-
196 ATGTGGTTTCAACTATGAAGGCTGAGAAGATGATG-GAAGAGGTTGTGAAGCTTACTTAGC-CTC
* *
16540123 TTTGATGAATTCAGTTAGTAAGGAGCTGAGAGTTCAGGATATTTGCTCTCTTAA-AGATTTTCCT
259 TGTGATGAATTCAGTTAGTAAGGAGCTGAGAGTTCAGGATATTTGCACTCTTAAGA-ATTTTCCT
* * *
16540187 AACATGTTTCCTGAAGAGTTGTCTAGTTTGCCACCAGAATGTAAAGTGGATTTTGGCATTGAGCT
323 AACATGTTTCCTGAAGAGTTGTCTGGTTTGCCACCAGAATGTGAAGTGGATTTTGGTATTGAGCT
* * * *
16540252 TTATCCTGATACTGCACCAGTGTCTATATTGCCTTATCATATGGCACCAAAAGAGCTCAAAGAGT
388 CTATCCTGGTACTGCACCAGTGTCTATA--GCCCTATCGTATGGCACCAAAAGAGCTCAAAGAGT
* * *
16540317 TAAAGATTTAGTTGTAAGAGTTGCTTGACAAATGGATT-ATTCGATCGAGTGTATCTCCGTGGGG
451 TAAAGATTTAGTTGCAAGAGTTGCTTGACAGA-GGGTTCATTCGA-CGAGTGTATCTCCGTGGGG
16540381 TG
514 TG
*
16540383 CCCTTAAGATACAAGGGCATGTTTTCCCTGTTGATCTTATTGG-ATTGCCTTTCTACGGGTTTGA
1 CCCTTATGATACAAGGGCATGTTTTCCCTGTTGATCTTA-TGGAATTGCCTTTCTACGGGTTTGA
16540447 TGTTATTCTTGATATGGACTGGTTGACTGAACATAAGGCTAAGGTAGAATTTAAGACGAAACTAA
65 TGTTATTCTTGATATGGACTGGTTGACTGAACATAAGGCTAAGGTAGAATTTAAGACGAAACTAA
* * * * *
16540512 TTTACTTAGAGGTAATAGTGATGGGTTGGAAATTGTTGATATTGTTTAAAGACTGAGATTTATGT
130 -TTACTTAGAAG-AATAGTGATGGGTTGGAAATTGTTGTTGTCGTTGAAAGACTGAGATTTATGT
* * * *
16540577 CTAATGTGGTTTCCATTATGAAGTCTGAGAAGATGATGGTAAGAGTTTGTGAAGCTTACTTAGCC
193 CTAATGTGGTTTCAACTATGAAGGCTGAGAAGATGATGG-AAGAGGTTGTGAAGCTTACTTAGCC
* *
16540642 TCTGTGATGAATTCAGTTAGTAAGGAGCTGAGAGTTTAGGATATTTGCACTGTTAAGAATTTTCC
257 TCTGTGATGAATTCAGTTAGTAAGGAGCTGAGAGTTCAGGATATTTGCACTCTTAAGAATTTTCC
*
16540707 TAACATGTTTCCTGAAGAGTTGTCTGGTTTGCCACCAGAATGTGAAGTTGATTTTGGTATTGAGC
322 TAACATGTTTCCTGAAGAGTTGTCTGGTTTGCCACCAGAATGTGAAGTGGATTTTGGTATTGAGC
* * *
16540772 TCTATCCTGGTATTGCACTAGTGTCTATAGCATCCTATCGTATGGCACGAAAAGAGCTCAAAGAG
387 TCTATCCTGGTACTGCACCAGTGTCTATAGC--CCTATCGTATGGCACCAAAAGAGCTCAAAGAG
*
16540837 TTAAAGATTTAGTTGCAAGAGTTGCTTGACAGAGGGTTCATTCGACCTAGTGTATCTCCGTGGGG
450 TTAAAGATTTAGTTGCAAGAGTTGCTTGACAGAGGGTTCATTCGA-CGAGTGTATCTCCGTGGGG
16540902 TG
514 TG
* *
16540904 CCCTTATGATATAAGGGCATGTTTTCCCTGTTGATCTTATGGAATTGTCTTTCTACGGGTTTGAT
1 CCCTTATGATACAAGGGCATGTTTTCCCTGTTGATCTTATGGAATTGCCTTTCTACGGGTTTGAT
*
16540969 GTTATTCTTGATATGGACTGGTTGACTGAACTTAAGGCTAAGGTAGAATTTAAGACGAAA-TGAA
66 GTTATTCTTGATATGGACTGGTTGACTGAACATAAGGCTAAGGTAGAATTTAAGACGAAACT-AA
*
16541033 TTACTCAGAAGAATAGTGATGGGTTGGAAATTGTTGTTGTCGTTGAAAGACTGAGA
130 TTACTTAGAAGAATAGTGATGGGTTGGAAATTGTTGTTGTCGTTGAAAGACTGAGA
16541089 AGATGATGGG
Statistics
Matches: 1103, Mismatches: 98, Indels: 45
0.89 0.08 0.04
Matches are distributed among these distances:
514 1 0.00
515 200 0.18
516 22 0.02
519 380 0.34
520 46 0.04
521 453 0.41
522 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.34
Consensus pattern (515 bp):
CCCTTATGATACAAGGGCATGTTTTCCCTGTTGATCTTATGGAATTGCCTTTCTACGGGTTTGAT
GTTATTCTTGATATGGACTGGTTGACTGAACATAAGGCTAAGGTAGAATTTAAGACGAAACTAAT
TACTTAGAAGAATAGTGATGGGTTGGAAATTGTTGTTGTCGTTGAAAGACTGAGATTTATGTCTA
ATGTGGTTTCAACTATGAAGGCTGAGAAGATGATGGAAGAGGTTGTGAAGCTTACTTAGCCTCTG
TGATGAATTCAGTTAGTAAGGAGCTGAGAGTTCAGGATATTTGCACTCTTAAGAATTTTCCTAAC
ATGTTTCCTGAAGAGTTGTCTGGTTTGCCACCAGAATGTGAAGTGGATTTTGGTATTGAGCTCTA
TCCTGGTACTGCACCAGTGTCTATAGCCCTATCGTATGGCACCAAAAGAGCTCAAAGAGTTAAAG
ATTTAGTTGCAAGAGTTGCTTGACAGAGGGTTCATTCGACGAGTGTATCTCCGTGGGGTG
Found at i:16559035 original size:27 final size:27
Alignment explanation
Indices: 16558997--16559050 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
16558987 AATAAATATG
16558997 TACATCTCTCACTGCGTCAACTACCAC
1 TACATCTCTCACTGCGTCAACTACCAC
*
16559024 TACATCTCTCACTGCGTCAACTGCCAC
1 TACATCTCTCACTGCGTCAACTACCAC
16559051 ACTTGTCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.41, G:0.09, T:0.26
Consensus pattern (27 bp):
TACATCTCTCACTGCGTCAACTACCAC
Found at i:16561277 original size:11 final size:11
Alignment explanation
Indices: 16561261--16561286 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16561251 GATTCCTAGA
16561261 AATTTATTTGT
1 AATTTATTTGT
16561272 AATTTATTTGT
1 AATTTATTTGT
16561283 AATT
1 AATT
16561287 ATAAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (11 bp):
AATTTATTTGT
Found at i:16563036 original size:15 final size:15
Alignment explanation
Indices: 16563013--16563044 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16563003 TCATTAATGA
16563013 AATGCATTAATTTTT
1 AATGCATTAATTTTT
*
16563028 AATGTATTAATTTTT
1 AATGCATTAATTTTT
16563043 AA
1 AA
16563045 AATTTTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
AATGCATTAATTTTT
Found at i:16563281 original size:16 final size:16
Alignment explanation
Indices: 16563262--16563292 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16563252 GAAAAAAACG
16563262 TATAAACTCAAAAGTA
1 TATAAACTCAAAAGTA
*
16563278 TATATACTCAAAAGT
1 TATAAACTCAAAAGT
16563293 GTAGTTATCT
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:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (16 bp):
TATAAACTCAAAAGTA
Found at i:16565074 original size:24 final size:25
Alignment explanation
Indices: 16565016--16565074 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
16565006 GTGTTATCAT
* *
16565016 CATATAAAAGTAAAATGAATTATTA
1 CATATAAAATTAAAATGAATTATAA
* *
16565041 CAT-TCGAAATTAAAAT-ATTTATAA
1 CATAT-AAAATTAAAATGAATTATAA
16565065 CATATAAAAT
1 CATATAAAAT
16565075 GCAAAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (25 bp):
CATATAAAATTAAAATGAATTATAA
Found at i:16565521 original size:16 final size:17
Alignment explanation
Indices: 16565502--16565535 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16565492 AAACTTCTCA
16565502 CCAAAAA-AAAAAACTG
1 CCAAAAATAAAAAACTG
*
16565518 CCAAAAATAAAAAGCTG
1 CCAAAAATAAAAAACTG
16565535 C
1 C
16565536 TCACACCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.21, G:0.09, T:0.09
Consensus pattern (17 bp):
CCAAAAATAAAAAACTG
Found at i:16568632 original size:3 final size:3
Alignment explanation
Indices: 16568626--16568652 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16568616 ATAATAATAA
16568626 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
16568653 CTAAACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16569308 original size:16 final size:16
Alignment explanation
Indices: 16569287--16569318 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16569277 TCTATAAAAA
16569287 AAGTGTGGAAAATAAT
1 AAGTGTGGAAAATAAT
16569303 AAGTGTGGAAAATAAT
1 AAGTGTGGAAAATAAT
16569319 GAAGAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (16 bp):
AAGTGTGGAAAATAAT
Found at i:16570378 original size:15 final size:15
Alignment explanation
Indices: 16570355--16570412 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
16570345 AATTAAGTAC
*
16570355 TTAAATTTTCAATAA
1 TTAATTTTTCAATAA
16570370 TTAATTTTTCAA-AA
1 TTAATTTTTCAATAA
* * *
16570384 CTTATTTTTTTAATAC
1 -TTAATTTTTCAATAA
*
16570400 TTACTTTTTCAAT
1 TTAATTTTTCAAT
16570413 TTATCAAACA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 2 0.06
15 32 0.91
16 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTTTTCAATAA
Found at i:16570387 original size:30 final size:30
Alignment explanation
Indices: 16570353--16570411 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
16570343 TAAATTAAGT
16570353 ACTTAAATTTTCAATAATTAATTTTTCAAA
1 ACTTAAATTTTCAATAATTAATTTTTCAAA
** * * *
16570383 ACTTATTTTTTTAATACTTACTTTTTCAA
1 ACTTAAATTTTCAATAATTAATTTTTCAA
16570412 TTTATCAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.53
Consensus pattern (30 bp):
ACTTAAATTTTCAATAATTAATTTTTCAAA
Found at i:16571567 original size:7 final size:7
Alignment explanation
Indices: 16571544--16571687 Score: 85
Period size: 7 Copynumber: 20.3 Consensus size: 7
16571534 ATTTTAGGGT
16571544 TTTAAGG
1 TTTAAGG
16571551 TTT-AGTG
1 TTTAAG-G
*
16571558 TTTATGG
1 TTTAAGG
16571565 TTTAAGG
1 TTTAAGG
*
16571572 TAT-AGTG
1 TTTAAG-G
* *
16571579 CTTATGG
1 TTTAAGG
*
16571586 TTTAGGG
1 TTTAAGG
**
16571593 TTTATTG
1 TTTAAGG
* *
16571600 TGTATGG
1 TTTAAGG
16571607 TTTAAGG
1 TTTAAGG
*
16571614 TTTAGGG
1 TTTAAGG
16571621 TTTAAGG
1 TTTAAGG
*
16571628 TTTAAGA
1 TTTAAGG
16571635 TTTAAGG
1 TTTAAGG
*
16571642 TTTTAAAG
1 -TTTAAGG
*
16571650 TTTAGGG
1 TTTAAGG
*
16571657 TTTATGG
1 TTTAAGG
**
16571664 TTTAAAC
1 TTTAAGG
*
16571671 TTTAGGG
1 TTTAAGG
16571678 TTTTAAGG
1 -TTTAAGG
16571686 TT
1 TT
16571688 CAATTACTTT
Statistics
Matches: 102, Mismatches: 29, Indels: 12
0.71 0.20 0.08
Matches are distributed among these distances:
6 4 0.04
7 84 0.82
8 14 0.14
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.48
Consensus pattern (7 bp):
TTTAAGG
Found at i:16571570 original size:21 final size:21
Alignment explanation
Indices: 16571544--16571638 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
16571534 ATTTTAGGGT
16571544 TTTAAGGTTTAGTGTTTATGG
1 TTTAAGGTTTAGTGTTTATGG
* *
16571565 TTTAAGGTATAGTGCTTATGG
1 TTTAAGGTTTAGTGTTTATGG
* * *
16571586 TTTAGGGTTTATTGTGTATGG
1 TTTAAGGTTTAGTGTTTATGG
* *
16571607 TTTAAGGTTTAGGGTTTAAGG
1 TTTAAGGTTTAGTGTTTATGG
*
16571628 TTTAAGATTTA
1 TTTAAGGTTTA
16571639 AGGTTTTAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.48
Consensus pattern (21 bp):
TTTAAGGTTTAGTGTTTATGG
Found at i:16571654 original size:36 final size:36
Alignment explanation
Indices: 16571607--16571683 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
16571597 TTGTGTATGG
*
16571607 TTTAAGGTTTAGGGTTTAAGGTTTAAGA-TTTAAGGT
1 TTTAAAGTTTAGGGTTTAAGGTTTAA-ACTTTAAGGT
* *
16571643 TTTAAAGTTTAGGGTTTATGGTTTAAACTTTAGGGT
1 TTTAAAGTTTAGGGTTTAAGGTTTAAACTTTAAGGT
16571679 TTTAA
1 TTTAA
16571684 GGTTCAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 1 0.03
36 36 0.97
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (36 bp):
TTTAAAGTTTAGGGTTTAAGGTTTAAACTTTAAGGT
Found at i:16574128 original size:20 final size:22
Alignment explanation
Indices: 16574089--16574132 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
16574079 TATATATTAT
16574089 TTTTTAAATATTAAAACCTATA
1 TTTTTAAATATTAAAACCTATA
*
16574111 TTTTT-AATA-TATAACCTATA
1 TTTTTAAATATTAAAACCTATA
16574131 TT
1 TT
16574133 AGTATGGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 4 0.19
22 5 0.24
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTTAAATATTAAAACCTATA
Found at i:16574747 original size:9 final size:9
Alignment explanation
Indices: 16574735--16574921 Score: 120
Period size: 9 Copynumber: 20.8 Consensus size: 9
16574725 TATCATATCT
16574735 TAACTTACA
1 TAACTTACA
*
16574744 TAACTCACA
1 TAACTTACA
16574753 TAACTTACA
1 TAACTTACA
16574762 TAACTTA-A
1 TAACTTACA
*
16574770 TAACATATATA
1 TAAC-T-TACA
*
16574781 TATATCATATCA
1 TA-A-CTTA-CA
*
16574793 TAACTTTCA
1 TAACTTACA
*
16574802 TAACTCACA
1 TAACTTACA
16574811 TAACTTACA
1 TAACTTACA
16574820 TAACTTACA
1 TAACTTACA
16574829 TAA--TACA
1 TAACTTACA
* *
16574836 TAA-ATATA
1 TAACTTACA
*
16574844 TATCATATA-A
1 TAAC-T-TACA
*
16574854 TAACTTTCA
1 TAACTTACA
*
16574863 TAACTCACA
1 TAACTTACA
16574872 TAACTTACA
1 TAACTTACA
16574881 TAA--TACA
1 TAACTTACA
* *
16574888 TAA-ATATA
1 TAACTTACA
* *
16574896 TATCATATCA
1 TAACTTA-CA
16574906 TAACTTACA
1 TAACTTACA
16574915 TAACTTA
1 TAACTTA
16574922 TTTATACTTA
Statistics
Matches: 142, Mismatches: 22, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
7 14 0.10
8 16 0.11
9 85 0.60
10 14 0.10
11 8 0.06
12 4 0.03
13 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.35
Consensus pattern (9 bp):
TAACTTACA
Found at i:16574861 original size:61 final size:60
Alignment explanation
Indices: 16574720--16574919 Score: 276
Period size: 58 Copynumber: 3.5 Consensus size: 60
16574710 TCTAGAAAAT
* * *
16574720 ATATATATCATATCTTAACTTACATAACTCACATAACTTACATAACTTA-AT-AACATAT
1 ATATATATCATATCATAACTTTCATAACTCACATAACTTACATAACTTACATAAACATAA
16574778 ATATATATCATATCATAACTTTCATAACTCACATAACTTACATAACTTACATAATACATAA
1 ATATATATCATATCATAACTTTCATAACTCACATAACTTACATAACTTACATAA-ACATAA
*
16574839 ATATATATCATATAATAACTTTCATAACTCACATAACTTAC---A--TA-AT--ACATAA
1 ATATATATCATATCATAACTTTCATAACTCACATAACTTACATAACTTACATAAACATAA
*
16574891 ATATATATCATATCATAACTTACATAACT
1 ATATATATCATATCATAACTTTCATAACT
16574920 TATTTATACT
Statistics
Matches: 133, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
52 33 0.25
55 2 0.02
56 2 0.02
58 48 0.36
59 2 0.02
60 1 0.01
61 45 0.34
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.35
Consensus pattern (60 bp):
ATATATATCATATCATAACTTTCATAACTCACATAACTTACATAACTTACATAAACATAA
Found at i:16574865 original size:52 final size:52
Alignment explanation
Indices: 16574742--16574921 Score: 227
Period size: 52 Copynumber: 3.3 Consensus size: 52
16574732 TCTTAACTTA
* * *
16574742 CATAACTCACATAACTTACATAACTTA-ATAACATATATATATATCATATCATAACTTT
1 CATAACTTACATAACTTACATAACTTACAT-A-ATACATAAATAT-ATATCAT-A---T
*
16574800 CATAACTCACATAACTTACATAACTTACATAATACATAAATATATATCATAT
1 CATAACTTACATAACTTACATAACTTACATAATACATAAATATATATCATAT
* * *
16574852 AATAACTTTCATAACTCACATAACTTACATAATACATAAATATATATCATAT
1 CATAACTTACATAACTTACATAACTTACATAATACATAAATATATATCATAT
16574904 CATAACTTACATAACTTA
1 CATAACTTACATAACTTA
16574922 TTTATACTTA
Statistics
Matches: 112, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
52 64 0.57
55 1 0.01
56 7 0.06
57 10 0.09
58 28 0.25
59 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (52 bp):
CATAACTTACATAACTTACATAACTTACATAATACATAAATATATATCATAT
Found at i:16574920 original size:61 final size:60
Alignment explanation
Indices: 16574720--16574919 Score: 269
Period size: 61 Copynumber: 3.5 Consensus size: 60
16574710 TCTAGAAAAT
*
16574720 ATATATATCATATCTTAACTTACATAACTCACATAACTTACATAACTTA-AT-A-ACATA
1 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAATACATA
*
16574777 TATATATATCATATCATAACTTTCATAACTCACATAACTTACATAACTTACATAATACATAA
1 -ATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAATACAT-A
* *
16574839 ATATATATCATATAATAACTTTCATAACTCACATAACTTACATAA--TAC---AT--A-A
1 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAATACATA
16574891 ATATATATCATATCATAACTTACATAACT
1 ATATATATCATATCATAACTTACATAACT
16574920 TATTTATACT
Statistics
Matches: 133, Mismatches: 5, Indels: 14
0.88 0.03 0.09
Matches are distributed among these distances:
52 28 0.21
54 1 0.01
56 2 0.02
58 47 0.35
59 5 0.04
60 1 0.01
61 48 0.36
62 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.35
Consensus pattern (60 bp):
ATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAATACATA
Found at i:16580804 original size:43 final size:43
Alignment explanation
Indices: 16580740--16581004 Score: 311
Period size: 43 Copynumber: 6.2 Consensus size: 43
16580730 GAACGGTACT
* *
16580740 TTTAGCGGCATTTGTGAA-AAAAGCGTCGCTAAAGGTCATGTT-
1 TTTAGCGGCGTTTGT-AATAAAAGCGCCGCTAAAGGTCATGTTC
* * * *
16580782 TTTAGCGACGTTTATAATAAAAACGCCACTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGGTCATGTTC
*
16580825 TTTAGCGGCGTTTGTAACAAAAGCGCCGCTAAAGG-CATGTTC
1 TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGGTCATGTTC
* * ** **
16580867 TTTAGCGGCGTTTGTGATAAAATCGCCGCTAAAGAACATGACC
1 TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGGTCATGTTC
* *
16580910 TTTAGCGGCGTTTGTTATAAAAGCACCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGGTCATGTTC
** * * * *
16580953 TTTAGCATCGTTTGTGATAAAAGCGTCACTAAATGTCATGTTC
1 TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGGTCATGTTC
16580996 TTTAGCGGC
1 TTTAGCGGC
16581005 ATTTATGTGA
Statistics
Matches: 187, Mismatches: 33, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
41 2 0.01
42 71 0.38
43 114 0.61
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGGTCATGTTC
Found at i:16580829 original size:85 final size:86
Alignment explanation
Indices: 16580740--16581025 Score: 339
Period size: 85 Copynumber: 3.3 Consensus size: 86
16580730 GAACGGTACT
* * *
16580740 TTTAGCGGCATTTGTGAAAAAAGCGTCGCTAAAGGTCATGTT-TTTAGCGACGTTTATAATAAAA
1 TTTAGCGGCATTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTGTGATAAAA
16580804 ACGCCACTAAAGGTCATGTTC
66 ACGCCACTAAAGGTCATGTTC
* *
16580825 TTTAGCGGCGTTTGT-AACAAAAGCGCCGCTAAAGG-CATGTTCTTTAGCGGCGTTTGTGATAAA
1 TTTAGCGGCATTTGTGAA-AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTGTGATAAA
* * ** **
16580888 ATCGCCGCTAAAGAACATGACC
65 AACGCCACTAAAGGTCATGTTC
* * * *
16580910 TTTAGCGGCGTTTGTTATAAAAGCACCGCTAAAGGTCATGTTCTTTAGC-ATCGTTTGTGATAAA
1 TTTAGCGGCATTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGA-CGTTTGTGATAAA
* * *
16580974 AGCGTCACTAAATGTCATGTTC
65 AACGCCACTAAAGGTCATGTTC
16580996 TTTAGCGGCATTTATGTGAAAAAAG-GCCGC
1 TTTAGCGGCA-TT-TGTGAAAAAAGCGCCGC
16581026 CAAAATTAGC
Statistics
Matches: 168, Mismatches: 26, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
84 8 0.05
85 95 0.57
86 50 0.30
87 6 0.04
88 9 0.05
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (86 bp):
TTTAGCGGCATTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGACGTTTGTGATAAAA
ACGCCACTAAAGGTCATGTTC
Found at i:16581598 original size:20 final size:20
Alignment explanation
Indices: 16581564--16581603 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16581554 ATATTTTAAA
* * *
16581564 TTATTTTGATTTTATTTTAT
1 TTATTTTAATGTTATATTAT
16581584 TTATTTTAATGTTATATTAT
1 TTATTTTAATGTTATATTAT
16581604 CCTATTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTATTTTAATGTTATATTAT
Found at i:16589484 original size:24 final size:24
Alignment explanation
Indices: 16589430--16589484 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
16589420 TTTTTTTCTT
* *
16589430 TTTTTTTCACATTCTTTTTCATTC
1 TTTTTTTCACATTATTTTTCACTC
** **
16589454 TCATTTTCATTTTATTTTTCACTC
1 TTTTTTTCACATTATTTTTCACTC
16589478 TTTTTTT
1 TTTTTTT
16589485 TAACTTTCTT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTTTCACATTATTTTTCACTC
Found at i:16592236 original size:19 final size:20
Alignment explanation
Indices: 16592214--16592257 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
16592204 TTTAAGATTG
16592214 CCTT-CGATGTCGCGACACA
1 CCTTACGATGTCGCGACACA
* *
16592233 CCTTAATGATGTCGCGACATA
1 CCTT-ACGATGTCGCGACACA
16592254 CCTT
1 CCTT
16592258 TAGAGATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
21 17 0.81
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (20 bp):
CCTTACGATGTCGCGACACA
Found at i:16597022 original size:25 final size:24
Alignment explanation
Indices: 16596969--16597030 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
16596959 GGAATATAAG
16596969 TAAAATTAATTTTTGTGAAAGGGA
1 TAAAATTAATTTTTGTGAAAGGGA
16596993 TAAAATTAATTTTTGTGAAAGGGA
1 TAAAATTAATTTTTGTGAAAGGGA
* *
16597017 TAAAAATAGTTTTT
1 TAAAATTAATTTTT
16597031 AAAATTTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (24 bp):
TAAAATTAATTTTTGTGAAAGGGA
Found at i:16598389 original size:19 final size:19
Alignment explanation
Indices: 16598352--16598389 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
16598342 TTAATTAAGT
*
16598352 TTTAATTAGATGAATTTAG
1 TTTAATTAGATGAAATTAG
16598371 TTTAATTAAGA-GAAATTAG
1 TTTAATT-AGATGAAATTAG
16598390 GAAAAAGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTAATTAGATGAAATTAG
Found at i:16599770 original size:17 final size:19
Alignment explanation
Indices: 16599748--16599783 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
16599738 AAAGTGATCT
16599748 TGAATTG-GAAA-TGAAAG
1 TGAATTGTGAAATTGAAAG
16599765 TGAATTGTGAAATTGAAAG
1 TGAATTGTGAAATTGAAAG
16599784 CTATTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 4 0.24
19 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (19 bp):
TGAATTGTGAAATTGAAAG
Found at i:16599892 original size:23 final size:23
Alignment explanation
Indices: 16599865--16599996 Score: 148
Period size: 23 Copynumber: 6.0 Consensus size: 23
16599855 GTTTTGCCAA
*
16599865 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTCATGTGTCGTATT
* *
16599888 TCAGGCGCTTTATGTGTCGTATT
1 TCAGGCACTTCATGTGTCGTATT
* * *
16599911 TCATGCACCTCGTGTGTCGTATT
1 TCAGGCACTTCATGTGTCGTATT
*
16599934 TCAGGCACTTCGTGTGTCGTA--
1 TCAGGCACTTCATGTGTCGTATT
* *
16599955 TCAGGCACCTCGTGTGT--TATT
1 TCAGGCACTTCATGTGTCGTATT
16599976 TCAGGCACTT-ATGTGTCGTAT
1 TCAGGCACTTCATGTGTCGTAT
16599997 ACTGATTAGG
Statistics
Matches: 94, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.02
20 5 0.05
21 25 0.27
22 3 0.03
23 59 0.63
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.39
Consensus pattern (23 bp):
TCAGGCACTTCATGTGTCGTATT
Found at i:16599930 original size:46 final size:45
Alignment explanation
Indices: 16599877--16599996 Score: 167
Period size: 46 Copynumber: 2.7 Consensus size: 45
16599867 AGGCACTTTA
* *
16599877 TGTGTCGTATTTCAGGCGCTTTATGTGTCGTATTTCATGCACCTCG
1 TGTGTCGTATTTCAGGCACTTTATGTGTCGTA-TTCAGGCACCTCG
**
16599923 TGTGTCGTATTTCAGGCACTTCGTGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACTTTATGTGTCGTATTCAGGCACCTCG
16599967 TGTGT--TATTTCAGGCAC-TTATGTGTCGTAT
1 TGTGTCGTATTTCAGGCACTTTATGTGTCGTAT
16599997 ACTGATTAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
41 10 0.15
42 12 0.18
44 16 0.24
46 29 0.43
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.40
Consensus pattern (45 bp):
TGTGTCGTATTTCAGGCACTTTATGTGTCGTATTCAGGCACCTCG
Found at i:16604989 original size:27 final size:27
Alignment explanation
Indices: 16604947--16605002 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
16604937 AATGTAAAGA
* * * *
16604947 ATTAGGAGCATGATATTTACGATTAAC
1 ATTAGGACCATAATATTCACAATTAAC
16604974 ATTAGGACCATAATATTCACAATTAAC
1 ATTAGGACCATAATATTCACAATTAAC
16605001 AT
1 AT
16605003 CGAATAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (27 bp):
ATTAGGACCATAATATTCACAATTAAC
Found at i:16613343 original size:2 final size:2
Alignment explanation
Indices: 16613336--16613367 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16613326 TCGCCCCTTA
16613336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16613368 TATTTTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16613617 original size:32 final size:32
Alignment explanation
Indices: 16613576--16613639 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
16613566 GGACAAAAAG
16613576 AAAAAAAAAAAAGAAGCAATCACATAGCTTCA
1 AAAAAAAAAAAAGAAGCAATCACATAGCTTCA
16613608 AAAAAAAAAAAAGAAGCAATCACATAGCTTCA
1 AAAAAAAAAAAAGAAGCAATCACATAGCTTCA
16613640 CGTAGCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.62, C:0.16, G:0.09, T:0.12
Consensus pattern (32 bp):
AAAAAAAAAAAAGAAGCAATCACATAGCTTCA
Found at i:16613669 original size:19 final size:19
Alignment explanation
Indices: 16613645--16613681 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
16613635 CTTCACGTAG
16613645 CATTATATTG-TAAAAAATA
1 CATTAT-TTGTTAAAAAATA
16613664 CATTATTTGTTAAAAAAT
1 CATTATTTGTTAAAAAAT
16613682 TTAGAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
CATTATTTGTTAAAAAATA
Found at i:16616761 original size:13 final size:13
Alignment explanation
Indices: 16616743--16616767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16616733 TTCTTTAAAA
16616743 TTTTCTTTAATTT
1 TTTTCTTTAATTT
16616756 TTTTCTTTAATT
1 TTTTCTTTAATT
16616768 ATTAATCCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTAATTT
Found at i:16618699 original size:4 final size:4
Alignment explanation
Indices: 16618692--16618741 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
16618682 ATTTTTCTTC
* *
16618692 TTCT TTCT TT-T CTCT TT-T TTCAT CTCCT TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTC-T -TTCT TTCT TTCT TTCT TTCT TTCT
16618740 TT
1 TT
16618742 ATTCTCCATC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 5 0.13
4 29 0.76
5 2 0.05
6 2 0.05
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:16618710 original size:24 final size:25
Alignment explanation
Indices: 16618683--16618740 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
16618673 AACAAACAGA
*
16618683 TTTTTCTTCTTCTTTCTTT-TCTCT
1 TTTTTCTTCTCCTTTCTTTCTCTCT
* *
16618707 TTTTTCATCTCCTTTCTTTCTTTCT
1 TTTTTCTTCTCCTTTCTTTCTCTCT
16618732 TTCTTTCTT
1 TT-TTTCTT
16618741 TATTCTCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 17 0.61
25 6 0.21
26 5 0.18
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTTCTTCTCCTTTCTTTCTCTCT
Found at i:16625616 original size:35 final size:35
Alignment explanation
Indices: 16625549--16625744 Score: 241
Period size: 35 Copynumber: 5.6 Consensus size: 35
16625539 TATTCCCTGT
* *
16625549 TTGGTGTGTTACGATTGGATTAGCTCTTATGAGCA
1 TTGGCGTGTTACGGTTGGATTAGCTCTTATGAGCA
* * * *
16625584 TTGGTGTGTTATGGTTAGG-TTATCTCTCATGAGCA
1 TTGGCGTGTTACGGTT-GGATTAGCTCTTATGAGCA
* *
16625619 TTGGAGTGTTACGGTTGAATTAGCTCTTATGAGCA
1 TTGGCGTGTTACGGTTGGATTAGCTCTTATGAGCA
* ** *
16625654 TAGGCGTGTTACAATTGGATTAGCTCTCATGAGCA
1 TTGGCGTGTTACGGTTGGATTAGCTCTTATGAGCA
*
16625689 TTGGCGTGTTACGGTTGGACTAGCTCTTATGAGCA
1 TTGGCGTGTTACGGTTGGATTAGCTCTTATGAGCA
* *
16625724 TCGGCGTGTTATGGTTGGATT
1 TTGGCGTGTTACGGTTGGATT
16625745 GACAATATAC
Statistics
Matches: 136, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
34 1 0.01
35 133 0.98
36 2 0.01
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.38
Consensus pattern (35 bp):
TTGGCGTGTTACGGTTGGATTAGCTCTTATGAGCA
Found at i:16625641 original size:70 final size:70
Alignment explanation
Indices: 16625549--16625744 Score: 268
Period size: 70 Copynumber: 2.8 Consensus size: 70
16625539 TATTCCCTGT
* * * * *
16625549 TTGGTGTGTTACGATTGGATTAGCTCTTATGAGCATTGGTGTGTTATGGTTAGG-TTATCTCTCA
1 TTGGAGTGTTACGGTTGGATTAGCTCTTATGAGCATAGGCGTGTTATGGTT-GGATTAGCTCTCA
16625613 TGAGCA
65 TGAGCA
* ***
16625619 TTGGAGTGTTACGGTTGAATTAGCTCTTATGAGCATAGGCGTGTTACAATTGGATTAGCTCTCAT
1 TTGGAGTGTTACGGTTGGATTAGCTCTTATGAGCATAGGCGTGTTATGGTTGGATTAGCTCTCAT
16625684 GAGCA
66 GAGCA
* * *
16625689 TTGGCGTGTTACGGTTGGACTAGCTCTTATGAGCATCGGCGTGTTATGGTTGGATT
1 TTGGAGTGTTACGGTTGGATTAGCTCTTATGAGCATAGGCGTGTTATGGTTGGATT
16625745 GACAATATAC
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
69 2 0.02
70 107 0.98
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.38
Consensus pattern (70 bp):
TTGGAGTGTTACGGTTGGATTAGCTCTTATGAGCATAGGCGTGTTATGGTTGGATTAGCTCTCAT
GAGCA
Found at i:16655353 original size:55 final size:55
Alignment explanation
Indices: 16655294--16655397 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
16655284 TTCAAATACT
* * *
16655294 CCATATGATGCCATAGTCCCAGACTAGGTCTTACATGATATGGTCTTCACATGCA
1 CCATAAGATGCCATAATCCCAGACTAGGTCTTACACGATATGGTCTTCACATGCA
* *
16655349 CCATAAGATGCCATAATCCCAGATTAGGTTTTACACGATATGGTCTTCA
1 CCATAAGATGCCATAATCCCAGACTAGGTCTTACACGATATGGTCTTCA
16655398 TTTTCTATGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (55 bp):
CCATAAGATGCCATAATCCCAGACTAGGTCTTACACGATATGGTCTTCACATGCA
Found at i:16659522 original size:15 final size:15
Alignment explanation
Indices: 16659502--16659531 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16659492 GAGCCCCAAG
*
16659502 GTGCGAACCTTAAAT
1 GTGCGAACCCTAAAT
16659517 GTGCGAACCCTAAAT
1 GTGCGAACCCTAAAT
16659532 ATGAACCTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (15 bp):
GTGCGAACCCTAAAT
Found at i:16662241 original size:20 final size:24
Alignment explanation
Indices: 16662197--16662246 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 24
16662187 ATAAATAAAT
16662197 AATAAATGAAAATAAGTATAGGTA
1 AATAAATGAAAATAAGTATAGGTA
16662221 AATAAAT-AAAATAA-TA-A-GTA
1 AATAAATGAAAATAAGTATAGGTA
16662241 AATAAA
1 AATAAA
16662247 AAAGGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.35
21 1 0.04
22 2 0.08
23 7 0.27
24 7 0.27
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (24 bp):
AATAAATGAAAATAAGTATAGGTA
Found at i:16670618 original size:19 final size:18
Alignment explanation
Indices: 16670552--16670618 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
16670542 CCTTACATAT
*
16670552 ATGCGAACCTTATTATGA
1 ATGCAAACCTTATTATGA
* *
16670570 ATACATACC-TATTATGA
1 ATGCAAACCTTATTATGA
*
16670587 ATGCAAACCTTATTATGT
1 ATGCAAACCTTATTATGA
16670605 ATGCAAACCCTTAT
1 ATGCAAA-CCTTAT
16670619 ACATAAGTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
17 15 0.37
18 20 0.49
19 6 0.15
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (18 bp):
ATGCAAACCTTATTATGA
Found at i:16678124 original size:16 final size:18
Alignment explanation
Indices: 16678103--16678135 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
16678093 ATCTTTTTAA
16678103 AAATTA-TAAAA-AATAT
1 AAATTATTAAAATAATAT
16678119 AAATTATTAAAATAATA
1 AAATTATTAAAATAATA
16678136 ATATAATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTATTAAAATAATAT
Found at i:16678626 original size:18 final size:20
Alignment explanation
Indices: 16678592--16678635 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
16678582 AAAAAAAATT
*
16678592 TAAAAA-TACTAATAATTTA
1 TAAAAATTACTAATAATTAA
16678611 TAAAAATTA-TAA-AATTAA
1 TAAAAATTACTAATAATTAA
16678629 TAAAAAT
1 TAAAAAT
16678636 ACACATTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
19 9 0.39
20 2 0.09
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAATTACTAATAATTAA
Found at i:16678904 original size:17 final size:16
Alignment explanation
Indices: 16678875--16678920 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 16
16678865 ATTTAAAAAT
16678875 ATTTTTTATATTTTG-
1 ATTTTTTATATTTTGA
16678890 A-TTTTTATAATATTTGA
1 ATTTTTTAT-AT-TTTGA
16678907 ATTTTTTATATTTT
1 ATTTTTTATATTTT
16678921 AAAAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 7 0.26
15 3 0.11
16 7 0.26
17 3 0.11
18 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (16 bp):
ATTTTTTATATTTTGA
Found at i:16682816 original size:45 final size:45
Alignment explanation
Indices: 16682718--16682929 Score: 248
Period size: 45 Copynumber: 4.7 Consensus size: 45
16682708 ATCGTTGGAA
* * * * ** ***
16682718 ATATAGGTGGATGCTATGTGCTAATTCCACCCGATATTAATGAAA
1 ATATAGGTGGTTGCTATGTGCTGATTTCACCGGATACCAATGGTT
*
16682763 ATAAAGGTGGTTGCTATGTGCTGATTTCACCGGATACCAATGGTT
1 ATATAGGTGGTTGCTATGTGCTGATTTCACCGGATACCAATGGTT
* *
16682808 ATATAGGTGGTTACTATGTGCTGATTTCACCAGATACCAATGGTT
1 ATATAGGTGGTTGCTATGTGCTGATTTCACCGGATACCAATGGTT
* * *
16682853 ATATAGGTGGTTGCTATGTGCCGATTTCACC-CAGTACCATTGAG-T
1 ATATAGGTGGTTGCTATGTGCTGATTTCACCGGA-TACCAATG-GTT
*
16682898 ATAAAGGTGGTTGCTATGTGCTGATTTCACCG
1 ATATAGGTGGTTGCTATGTGCTGATTTCACCG
16682930 AGTACTATTG
Statistics
Matches: 145, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.01
45 143 0.99
46 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
ATATAGGTGGTTGCTATGTGCTGATTTCACCGGATACCAATGGTT
Found at i:16682940 original size:45 final size:45
Alignment explanation
Indices: 16682722--16682953 Score: 231
Period size: 45 Copynumber: 5.2 Consensus size: 45
16682712 TTGGAAATAT
* * * ** **
16682722 AGGTGGATGCTATGTGCTAATTCCACCCGA-TATTAATGAAAATAA
1 AGGTGGTTGCTATGTGCTGATTTCA-CCGAGTACCAATGAGTATAA
*
16682767 AGGTGGTTGCTATGTGCTGATTTCACCG-GATACCAATG-GTTATAT
1 AGGTGGTTGCTATGTGCTGATTTCACCGAG-TACCAATGAG-TATAA
* *
16682812 AGGTGGTTACTATGTGCTGATTTCACC-AGATACCAATG-GTTATAT
1 AGGTGGTTGCTATGTGCTGATTTCACCGAG-TACCAATGAG-TATAA
* * *
16682857 AGGTGGTTGCTATGTGCCGATTTCACCCAGTACCATTGAGTATAA
1 AGGTGGTTGCTATGTGCTGATTTCACCGAGTACCAATGAGTATAA
* * *
16682902 AGGTGGTTGCTATGTGCTGATTTCACCGAGTACTATTGACTATAA
1 AGGTGGTTGCTATGTGCTGATTTCACCGAGTACCAATGAGTATAA
*
16682947 GGGTGGT
1 AGGTGGT
16682954 GCTGCGTGTT
Statistics
Matches: 163, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
44 3 0.02
45 157 0.96
46 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (45 bp):
AGGTGGTTGCTATGTGCTGATTTCACCGAGTACCAATGAGTATAA
Found at i:16684266 original size:44 final size:45
Alignment explanation
Indices: 16684192--16684285 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 45
16684182 TACACTCTGC
* *
16684192 ATGAACAAGTGTTTTTTGTGAGCTCTTCATATTAGCGAGCTCTAT
1 ATGAACAAGTGTTTTTTGCGAGCTCCTCATATTAGCGAGCTCTAT
* *
16684237 ATGAACAAGTG-TTTTTGCGAGCTCCTCATATTGGTGAGCTCTAT
1 ATGAACAAGTGTTTTTTGCGAGCTCCTCATATTAGCGAGCTCTAT
16684281 ATGAA
1 ATGAA
16684286 TATTTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 34 0.76
45 11 0.24
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (45 bp):
ATGAACAAGTGTTTTTTGCGAGCTCCTCATATTAGCGAGCTCTAT
Found at i:16684296 original size:44 final size:44
Alignment explanation
Indices: 16684192--16684315 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
16684182 TACACTCTGC
* *
16684192 ATGAACAAGTGTTTTTTGTGAGCTCTTCATATTAGCGAGCTCTAT
1 ATGAACAAGT-TTTTTTGCGAGCTCCTCATATTAGCGAGCTCTAT
* * *
16684237 ATGAACAAGTGTTTTTGCGAGCTCCTCATATTGGTGAGCTCTAT
1 ATGAACAAGTTTTTTTGCGAGCTCCTCATATTAGCGAGCTCTAT
* ** * * *
16684281 ATGAATATTTTTTTTTGCAAGCTCTTTATATTAGC
1 ATGAACAAGTTTTTTTGCGAGCTCCTCATATTAGC
16684316 AAGCGATAAG
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
44 55 0.85
45 10 0.15
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (44 bp):
ATGAACAAGTTTTTTTGCGAGCTCCTCATATTAGCGAGCTCTAT
Found at i:16685201 original size:11 final size:12
Alignment explanation
Indices: 16685183--16685209 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16685173 AATATGAAAT
16685183 CAAAAAAATTAA
1 CAAAAAAATTAA
16685195 CAAAAAAATTAA
1 CAAAAAAATTAA
16685207 CAA
1 CAA
16685210 TGTAAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.15
Consensus pattern (12 bp):
CAAAAAAATTAA
Found at i:16685368 original size:15 final size:15
Alignment explanation
Indices: 16685348--16685399 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
16685338 ACTACAAAAC
16685348 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
16685363 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
16685382 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
16685397 ATT
1 ATT
16685400 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:16686229 original size:18 final size:18
Alignment explanation
Indices: 16686206--16686240 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16686196 GCGACCCTCT
* *
16686206 ATATGTTTGCTAACCATG
1 ATATGTATGCGAACCATG
16686224 ATATGTATGCGAACCAT
1 ATATGTATGCGAACCAT
16686241 TTGTAAATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (18 bp):
ATATGTATGCGAACCATG
Found at i:16686282 original size:18 final size:18
Alignment explanation
Indices: 16686259--16686312 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
16686249 AGAACCCTTA
*
16686259 TATGTTGTTATGCGAACC
1 TATGTTGTTATGCAAACC
*
16686277 TATGTTGTTATGTAAACC
1 TATGTTGTTATGCAAACC
*
16686295 TATGATGTT-TGCAAACC
1 TATGTTGTTATGCAAACC
16686312 T
1 T
16686313 TAGAAGTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 8 0.25
18 24 0.75
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (18 bp):
TATGTTGTTATGCAAACC
Found at i:16688751 original size:16 final size:16
Alignment explanation
Indices: 16688730--16688761 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16688720 TCAACACAAG
16688730 TATATTCACATACATA
1 TATATTCACATACATA
*
16688746 TATATTTACATACATA
1 TATATTCACATACATA
16688762 CCAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATTCACATACATA
Found at i:16689024 original size:50 final size:50
Alignment explanation
Indices: 16688941--16689177 Score: 303
Period size: 50 Copynumber: 4.7 Consensus size: 50
16688931 CGAATCATCA
* *
16688941 TTTGTGGACAAGCCACCACTGATTTGCAAATAAACTGCCACTAATAACAC
1 TTTGTGGACAAGCCACCACTGATTTGCAGATAAACTACCACTAATAACAC
* * * * *
16688991 TTTGTGGACAAGCCACCACTGATTTACAGATAAACTATCACTGATAAAAA
1 TTTGTGGACAAGCCACCACTGATTTGCAGATAAACTACCACTAATAACAC
* * * * *
16689041 TTTGTGGACAAGCTACCACTGATTTGCAAATAAACTATCACTGACAACAC
1 TTTGTGGACAAGCCACCACTGATTTGCAGATAAACTACCACTAATAACAC
* * * *
16689091 TTTATGGACAAGCCACCACCGGTTTGCAGATAAACTTCCACTAATAACAC
1 TTTGTGGACAAGCCACCACTGATTTGCAGATAAACTACCACTAATAACAC
* * *
16689141 TTTGTGGACTAGCCACCACTGATATGCAGATATACTA
1 TTTGTGGACAAGCCACCACTGATTTGCAGATAAACTA
16689178 ACACATACTT
Statistics
Matches: 158, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 158 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (50 bp):
TTTGTGGACAAGCCACCACTGATTTGCAGATAAACTACCACTAATAACAC
Found at i:16695498 original size:16 final size:16
Alignment explanation
Indices: 16695479--16695515 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
16695469 CACAGAATAG
16695479 AGTTTTCAAAGTCTAT
1 AGTTTTCAAAGTCTAT
*
16695495 AGTTTTCACAGTCTAT
1 AGTTTTCAAAGTCTAT
16695511 AGTTT
1 AGTTT
16695516 CGAATCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (16 bp):
AGTTTTCAAAGTCTAT
Found at i:16696247 original size:16 final size:16
Alignment explanation
Indices: 16696226--16696257 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16696216 TCAATACAAG
16696226 TATATTCACAAACATA
1 TATATTCACAAACATA
*
16696242 TATATTCACATACATA
1 TATATTCACAAACATA
16696258 CCAAAACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (16 bp):
TATATTCACAAACATA
Found at i:16696572 original size:50 final size:50
Alignment explanation
Indices: 16696426--16696574 Score: 199
Period size: 50 Copynumber: 3.0 Consensus size: 50
16696416 TAAATTGACT
* * * *
16696426 AGCCACCATCGATTTACAAATAAATTGCCACTGAAAACACTTTGTGCACA
1 AGCCACCACCAATTTACAAATAAATTGCCACTGATAACACTTTGTGGACA
** * * *
16696476 AGCCACCACTGATTTACAGATAAACTACCACTGATAACACTTTGTGGACA
1 AGCCACCACCAATTTACAAATAAATTGCCACTGATAACACTTTGTGGACA
* *
16696526 AGCTACCACCAATTTGCAAATAAATTGCCACTGATAACACTTTGTGGAC
1 AGCCACCACCAATTTACAAATAAATTGCCACTGATAACACTTTGTGGAC
16696575 TACCCACAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (50 bp):
AGCCACCACCAATTTACAAATAAATTGCCACTGATAACACTTTGTGGACA
Found at i:16696595 original size:50 final size:48
Alignment explanation
Indices: 16696442--16696597 Score: 131
Period size: 50 Copynumber: 3.1 Consensus size: 48
16696432 CATCGATTTA
* * *
16696442 CAAATAAATTGCCACTGAAAACACTTTGTGCACAAGCCACCACTGATT-TA-
1 CAAATAAATTGCCACTGATAACACTTTGTGGACAA--C-CCAC-AATTGTAG
* * *
16696492 CAGATAAACTACCACTGATAACACTTTGTGGACAAGCTACCACCAATT-T-G
1 CAAATAAATTGCCACTGATAACACTTTGTGGACAA-C--CCA-CAATTGTAG
*
16696542 CAAATAAATTGCCACTGATAACACTTTGTGGACTACCCACAATTGCTAAG
1 CAAATAAATTGCCACTGATAACACTTTGTGGACAACCCACAATTG-T-AG
16696592 CAAATA
1 CAAATA
16696598 TACTACCGCA
Statistics
Matches: 88, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
46 5 0.06
47 3 0.03
48 1 0.01
49 2 0.02
50 76 0.86
51 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (48 bp):
CAAATAAATTGCCACTGATAACACTTTGTGGACAACCCACAATTGTAG
Found at i:16701160 original size:25 final size:25
Alignment explanation
Indices: 16701094--16701163 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
16701084 ACAAACACAC
* * *
16701094 CACAACTCTTATGAGCTTACCGATT
1 CACAGCTCGTATGAGCATACCGATT
*
16701119 CACAGCTCGTGA-AAGCATACCGATT
1 CACAGCTCGT-ATGAGCATACCGATT
* *
16701144 CATAGCTTGTATGAGCATAC
1 CACAGCTCGTATGAGCATAC
16701164 ATGTACAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
24 1 0.03
25 34 0.94
26 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (25 bp):
CACAGCTCGTATGAGCATACCGATT
Found at i:16708135 original size:21 final size:21
Alignment explanation
Indices: 16708111--16708157 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
16708101 CATATACACA
16708111 AATTTGTAAT-AAAAACTATAG
1 AATTTGTAATCAAAAACT-TAG
* *
16708132 AATTTGTTATCAAACACTTAG
1 AATTTGTAATCAAAAACTTAG
16708153 AATTT
1 AATTT
16708158 ACATAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (21 bp):
AATTTGTAATCAAAAACTTAG
Found at i:16708467 original size:5 final size:5
Alignment explanation
Indices: 16708459--16708516 Score: 73
Period size: 5 Copynumber: 11.2 Consensus size: 5
16708449 GGGTTAAGGT
16708459 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTCC TTTTTC TTTT- TTGTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT-C -TTTTC TTTTC TT-TTC
*
16708506 TTTTC ATTTC T
1 TTTTC TTTTC T
16708517 AGTTTTGGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
4 2 0.04
5 37 0.79
6 4 0.09
7 4 0.09
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:16708499 original size:27 final size:27
Alignment explanation
Indices: 16708464--16708515 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
16708454 AAGGTTTTTC
*
16708464 TTTTCTTTTCTT-TTCTTTTCTTTTCCT
1 TTTTCTTTT-TTGTTCTTTTCATTTCCT
16708491 TTTTCTTTTTTGTTCTTTTCATTTC
1 TTTTCTTTTTTGTTCTTTTCATTTC
16708516 TAGTTTTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (27 bp):
TTTTCTTTTTTGTTCTTTTCATTTCCT
Found at i:16712216 original size:1 final size:1
Alignment explanation
Indices: 16712210--16712247 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
16712200 TACAAAGTAC
16712210 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16712248 CAAACAAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16717596 original size:20 final size:18
Alignment explanation
Indices: 16717562--16717598 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
16717552 ATATAATTGT
16717562 AATTTTTCTAGAAAATAG
1 AATTTTTCTAGAAAATAG
16717580 AATTTATTCTAAGAAAATA
1 AATTT-TTCT-AGAAAATA
16717599 AGTTCTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
AATTTTTCTAGAAAATAG
Found at i:16723297 original size:21 final size:22
Alignment explanation
Indices: 16723273--16723316 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
16723263 AGAACAGACG
16723273 TTAGTGTAAAAAAAA-TTAACT
1 TTAGTGTAAAAAAAATTTAACT
16723294 TTAGTGTAAAAAAAATTTAACT
1 TTAGTGTAAAAAAAATTTAACT
16723316 T
1 T
16723317 ATTTTAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (22 bp):
TTAGTGTAAAAAAAATTTAACT
Found at i:16723627 original size:13 final size:13
Alignment explanation
Indices: 16723609--16723672 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
16723599 ACACTCAAAT
16723609 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
16723622 TTTTCAAAAGTA-
1 TTTTCAAAAGCAC
* *
16723634 TTTCTCAAAAGTAT
1 TTT-TCAAAAGCAC
*
16723648 TTTTCGACAA-CAC
1 TTTTC-AAAAGCAC
16723661 TTTTCAAAAGCA
1 TTTTCAAAAGCA
16723673 TTGTCAAACT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 6 0.14
13 30 0.71
14 6 0.14
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:16723858 original size:13 final size:13
Alignment explanation
Indices: 16723840--16723887 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
16723830 CTCAAATTTT
16723840 TCAAAAGCA-TCTC
1 TCAAAAGCACT-TC
16723853 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
16723866 TCAAAAGCACTTT
1 TCAAAAGCACTTC
16723879 TCAAAAGCA
1 TCAAAAGCA
16723888 TTGCCAAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 32 0.97
14 1 0.03
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:16724295 original size:7 final size:7
Alignment explanation
Indices: 16724286--16724362 Score: 68
Period size: 7 Copynumber: 11.0 Consensus size: 7
16724276 TTCTTTTTAA
*
16724286 CTCAATA
1 CTCAATT
16724293 CTCAA-T
1 CTCAATT
16724299 CGTCAA-T
1 C-TCAATT
*
16724306 CTTAAATT
1 CTCAA-TT
16724314 CTCAATT
1 CTCAATT
*
16724321 CTCAATC
1 CTCAATT
*
16724328 CTCAATC
1 CTCAATT
16724335 CTCAATT
1 CTCAATT
*
16724342 CTCAAAT
1 CTCAATT
*
16724349 CCCAATT
1 CTCAATT
16724356 CTCAATT
1 CTCAATT
16724363 ATTATTTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
6 4 0.07
7 49 0.84
8 5 0.09
ACGTcount: A:0.32, C:0.31, G:0.01, T:0.35
Consensus pattern (7 bp):
CTCAATT
Found at i:16726469 original size:21 final size:21
Alignment explanation
Indices: 16726443--16726482 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
16726433 CATTCGAAAT
16726443 TGATTGCAAGAGTGATAAGGA
1 TGATTGCAAGAGTGATAAGGA
16726464 TGATTGCAAGAGTGATAAG
1 TGATTGCAAGAGTGATAAG
16726483 CTTGATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.25
Consensus pattern (21 bp):
TGATTGCAAGAGTGATAAGGA
Found at i:16726488 original size:21 final size:21
Alignment explanation
Indices: 16726442--16726489 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
16726432 ACATTCGAAA
*
16726442 TTGATTGCAAGAGTGATAAGG
1 TTGATTGCAAGAGTGATAAGC
*
16726463 ATGATTGCAAGAGTGATAAGC
1 TTGATTGCAAGAGTGATAAGC
16726484 TTGATT
1 TTGATT
16726490 ATGTAACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGATTGCAAGAGTGATAAGC
Found at i:16732553 original size:18 final size:18
Alignment explanation
Indices: 16732532--16732567 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
16732522 GAATTTGAAA
16732532 TTCTTAAAATATTTTTAG
1 TTCTTAAAATATTTTTAG
16732550 TTCTTAAAATATTTTTAG
1 TTCTTAAAATATTTTTAG
16732568 ATTTAACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (18 bp):
TTCTTAAAATATTTTTAG
Found at i:16732573 original size:17 final size:18
Alignment explanation
Indices: 16732533--16732573 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
16732523 AATTTGAAAT
*
16732533 TCTTAAAATATTTTTAGT
1 TCTTAAAATATTTTTAGA
16732551 TCTTAAAATATTTTTAGA
1 TCTTAAAATATTTTTAGA
16732569 T-TTAA
1 TCTTAA
16732574 CAACTCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
TCTTAAAATATTTTTAGA
Found at i:16740505 original size:24 final size:24
Alignment explanation
Indices: 16740484--16740539 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
16740474 AAGATTTAGT
16740484 ATTTATTAGCATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
*
16740508 ATTTATTAGCATAATATATTTGAC
1 ATTTATTAGCATAATATATTTAAC
*
16740532 ATTGATTA
1 ATTTATTA
16740540 ATTAGGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:16748011 original size:24 final size:24
Alignment explanation
Indices: 16747983--16748034 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
16747973 TTTCTAGAAA
* *
16747983 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
16748007 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
16748031 ATTT
1 ATTT
16748035 GACGTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:16748391 original size:5 final size:5
Alignment explanation
Indices: 16748383--16748420 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
16748373 AATATATCAT
*
16748383 ATATG ATATG ATATG ATATT ATATG ATATG ATATG ATA
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATA
16748421 GCATAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (5 bp):
ATATG
Found at i:16748407 original size:20 final size:20
Alignment explanation
Indices: 16748382--16748420 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
16748372 TAATATATCA
16748382 TATATGATATGATATGATAT
1 TATATGATATGATATGATAT
16748402 TATATGATATGATATGATA
1 TATATGATATGATATGATA
16748421 GCATAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TATATGATATGATATGATAT
Found at i:16749748 original size:25 final size:25
Alignment explanation
Indices: 16749720--16749786 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 25
16749710 TTACATACAA
16749720 TAAGCTAGTGTTAGCAACAT-CAAAT
1 TAAGCTAGTGTTAGCAA-ATCCAAAT
*
16749745 TAAGCTAGTGTTAGC-AATCCTAAT
1 TAAGCTAGTGTTAGCAAATCCAAAT
16749769 TCAAAGCTAGTGTTAGCA
1 T--AAGCTAGTGTTAGCA
16749787 GCCCAATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 2 0.05
24 6 0.16
25 15 0.41
26 14 0.38
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (25 bp):
TAAGCTAGTGTTAGCAAATCCAAAT
Found at i:16754204 original size:16 final size:16
Alignment explanation
Indices: 16754183--16754218 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
16754173 GGGCTGAACG
16754183 GGGCGCACGAGCGTGT
1 GGGCGCACGAGCGTGT
16754199 GGGCGCACGAGCGTGT
1 GGGCGCACGAGCGTGT
16754215 GGGC
1 GGGC
16754219 CCACTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.25, G:0.53, T:0.11
Consensus pattern (16 bp):
GGGCGCACGAGCGTGT
Found at i:16754373 original size:27 final size:27
Alignment explanation
Indices: 16754342--16754460 Score: 134
Period size: 27 Copynumber: 4.4 Consensus size: 27
16754332 ACCCTAAAAT
*
16754342 AGGTAAAATGACCAAAATACCCTCATA
1 AGGTAAAATGACCGAAATACCCTCATA
* *
16754369 AGGTAAAATGACTGAAATACCCCCATA
1 AGGTAAAATGACCGAAATACCCTCATA
* * *
16754396 GGGTAAAATGACCGCAATACCCTTATA
1 AGGTAAAATGACCGAAATACCCTCATA
**
16754423 AGGTAAAATGATTGAAATACCC-C-TA
1 AGGTAAAATGACCGAAATACCCTCATA
16754448 CAGGGTAAAATGA
1 -A-GGTAAAATGA
16754461 TTGTTATACC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
25 2 0.03
26 1 0.01
27 74 0.96
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (27 bp):
AGGTAAAATGACCGAAATACCCTCATA
Found at i:16754471 original size:54 final size:54
Alignment explanation
Indices: 16754343--16754460 Score: 182
Period size: 54 Copynumber: 2.2 Consensus size: 54
16754333 CCCTAAAATA
** *
16754343 GGTAAAATGACCAAAATACCCTCATAAGGTAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACCGCAATACCCTCATAAGGTAAAATGACTGAAATACCCCCACAG
* * *
16754397 GGTAAAATGACCGCAATACCCTTATAAGGTAAAATGATTGAAATACCCCTACAG
1 GGTAAAATGACCGCAATACCCTCATAAGGTAAAATGACTGAAATACCCCCACAG
16754451 GGTAAAATGA
1 GGTAAAATGA
16754461 TTGTTATACC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.20
Consensus pattern (54 bp):
GGTAAAATGACCGCAATACCCTCATAAGGTAAAATGACTGAAATACCCCCACAG
Found at i:16754486 original size:54 final size:54
Alignment explanation
Indices: 16754343--16754490 Score: 136
Period size: 54 Copynumber: 2.7 Consensus size: 54
16754333 CCCTAAAATA
** * * *
16754343 GGTAAAATGACCAAAATACCC-TCATAAGGTAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACCGCAATACCCAT-AGAAGATAAAATGACTGAAATACCCCCACAG
* * * * *
16754397 GGTAAAATGACCGCAATACCCTTATAAGGTAAAATGATTGAAATACCCCTACAG
1 GGTAAAATGACCGCAATACCCATAGAAGATAAAATGACTGAAATACCCCCACAG
** ** * *
16754451 GGTAAAATGATTGTTATACCCATAGGAGATGAAATGACTG
1 GGTAAAATGACCGCAATACCCATAGAAGATAAAATGACTG
16754491 TTATGGCCTT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 77 0.99
55 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (54 bp):
GGTAAAATGACCGCAATACCCATAGAAGATAAAATGACTGAAATACCCCCACAG
Found at i:16758402 original size:15 final size:16
Alignment explanation
Indices: 16758384--16758431 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
16758374 AAAAATTTAA
16758384 AAATT-TAAAAAATAT
1 AAATTATAAAAAATAT
* *
16758399 AAATTATTAAAATTA-
1 AAATTATAAAAAATAT
16758414 AAATTATAAAAAA-AT
1 AAATTATAAAAAATAT
16758429 AAA
1 AAA
16758432 AATAAAAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 1 0.04
15 19 0.70
16 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTATAAAAAATAT
Found at i:16759220 original size:436 final size:437
Alignment explanation
Indices: 16758399--16759271 Score: 1739
Period size: 436 Copynumber: 2.0 Consensus size: 437
16758389 TAAAAAATAT
16758399 AAATTATTAAAATTAAAATTATAAAAAAATAAAAATAAAAACCTAAAATTTACTAATAAATTTTA
1 AAATTATTAAAATTAAAATTATAAAAAAATAAAAATAAAAACCTAAAATTTACTAATAAATTTTA
16758464 AAATATTAGATATTTGAACATTTTATAAATCATATTTACTAGAGCTTGAATATGATACTGTTGTC
66 AAATATTAGATATTTGAACATTTTATAAATCATATTTACTAGAGCTTGAATATGATACTGTTGTC
16758529 CTCTGGAAGGATACTAATTGTTATTTCAATTAAATAATAAAAAAATAATGTTATTTCAATTAAAT
131 CTCTGGAAGGATACTAATTGTTATTTCAATTAAATAATAAAAAAATAATGTTATTTCAATTAAAT
16758594 AATAATTTTAATTATTCCAAGTATTTTTTACTATTTCAAGACAAATTATTTGTCTATAAACTAAA
196 AATAATTTTAATTATTCCAAGTATTTTTTACTATTTCAAGACAAATTATTTGTCTATAAACTAAA
16758659 TCTTAAGCACTATTGTTAGGAGTTTGACCATTCTAAAGAACTTTGGTACAAAATAAAAAGAGCAT
261 TCTTAAGCACTATTGTTAGGAGTTTGACCATTCTAAAGAACTTTGGTACAAAATAAAAAGAGCAT
16758724 GTGCACGATGATGAATGAATAAACCTTACTCCAAACATGAAATAGGGAGTCAAGTCAAATAAAAT
326 GTGCACGATGATGAATGAATAAACCTTACTCCAAACATGAAATAGGGAGTCAAGTCAAATAAAAT
16758789 ACTGACAGTAACACTAGAAAAGTATTCAAAATTGATGTATTCTAAAA
391 ACTGACAGTAACACTAGAAAAGTATTCAAAATTGATGTATTCTAAAA
16758836 AAATTATT-AAATTAAAATTATAAAAAAATAAAAATAAAAACCTAAAATTTACTAATAAATTTTA
1 AAATTATTAAAATTAAAATTATAAAAAAATAAAAATAAAAACCTAAAATTTACTAATAAATTTTA
16758900 AAATATTAGATATTTGAACATTTTATAAATCATATTTACTAGAGCTTGAATATGATACTGTTGTC
66 AAATATTAGATATTTGAACATTTTATAAATCATATTTACTAGAGCTTGAATATGATACTGTTGTC
16758965 CTCTGGAAGGATACTAATTGTTATTTCAATTAAATAATAAAAAAATAATGTTATTTCAATTAAAT
131 CTCTGGAAGGATACTAATTGTTATTTCAATTAAATAATAAAAAAATAATGTTATTTCAATTAAAT
16759030 AATAATTTTAATTATTCCAAGTATTTTTTACTATTTCAAGACAAATTATTTGTCTATAAACTAAA
196 AATAATTTTAATTATTCCAAGTATTTTTTACTATTTCAAGACAAATTATTTGTCTATAAACTAAA
16759095 TCTTAAGCACTATTGTTAGGAGTTTGACCATTCTAAAGAACTTTGGTACAAAATAAAAAGAGCAT
261 TCTTAAGCACTATTGTTAGGAGTTTGACCATTCTAAAGAACTTTGGTACAAAATAAAAAGAGCAT
16759160 GTGCACGATGATGAATGAATAAACCTTACTCCAAACATGAAATAGGGAGTCAAGTCAAATAAAAT
326 GTGCACGATGATGAATGAATAAACCTTACTCCAAACATGAAATAGGGAGTCAAGTCAAATAAAAT
16759225 ACTGACAGTAACACTAGAAAAGTATTCAAAATTGATGTATTCTAAAA
391 ACTGACAGTAACACTAGAAAAGTATTCAAAATTGATGTATTCTAAAA
16759272 TATTAACTAT
Statistics
Matches: 436, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
436 428 0.98
437 8 0.02
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (437 bp):
AAATTATTAAAATTAAAATTATAAAAAAATAAAAATAAAAACCTAAAATTTACTAATAAATTTTA
AAATATTAGATATTTGAACATTTTATAAATCATATTTACTAGAGCTTGAATATGATACTGTTGTC
CTCTGGAAGGATACTAATTGTTATTTCAATTAAATAATAAAAAAATAATGTTATTTCAATTAAAT
AATAATTTTAATTATTCCAAGTATTTTTTACTATTTCAAGACAAATTATTTGTCTATAAACTAAA
TCTTAAGCACTATTGTTAGGAGTTTGACCATTCTAAAGAACTTTGGTACAAAATAAAAAGAGCAT
GTGCACGATGATGAATGAATAAACCTTACTCCAAACATGAAATAGGGAGTCAAGTCAAATAAAAT
ACTGACAGTAACACTAGAAAAGTATTCAAAATTGATGTATTCTAAAA
Found at i:16761495 original size:32 final size:33
Alignment explanation
Indices: 16761457--16761528 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
16761447 AAAATTTATG
*
16761457 AAATATTTT-TAGAAAATC-TGCCAAACAAC-AGA
1 AAATATTTTATACAAAATCAT-CCAAAC-ACTAGA
*
16761489 AAATATTTTATACAAATTCATCCAAACACTAGA
1 AAATATTTTATACAAAATCATCCAAACACTAGA
16761522 AAATATT
1 AAATATT
16761529 AGCTTTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 11 0.31
33 23 0.66
34 1 0.03
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (33 bp):
AAATATTTTATACAAAATCATCCAAACACTAGA
Found at i:16764750 original size:3 final size:3
Alignment explanation
Indices: 16764704--16764737 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
16764694 TTATATTAGT
*
16764704 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16764738 ACTTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16766241 original size:31 final size:31
Alignment explanation
Indices: 16766196--16766273 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
16766186 TTAATGATAC
* *
16766196 ATAAAATAT-TTTAAA-AACTTAAATCTAATA
1 ATAAATTATATTTAAATAA-TTAAATATAATA
* *
16766226 ATAAATTATATTTAAATAATTTAATATAATG
1 ATAAATTATATTTAAATAATTAAATATAATA
*
16766257 ATAAATGATATTTAAAT
1 ATAAATTATATTTAAAT
16766274 CATGGGTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 8 0.20
31 31 0.76
32 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (31 bp):
ATAAATTATATTTAAATAATTAAATATAATA
Found at i:16769461 original size:31 final size:32
Alignment explanation
Indices: 16769400--16769461 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
16769390 TCTTCATTTT
* **
16769400 TTTGAAAATTTTCATTAAACTCACTTAAAATA
1 TTTGAAAATTCTCATTAAACTCACAAAAAATA
*
16769432 TTTGAAAA-TCTCATTAATCTCACAAAAAAT
1 TTTGAAAATTCTCATTAAACTCACAAAAAAT
16769462 TAAAAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (32 bp):
TTTGAAAATTCTCATTAAACTCACAAAAAATA
Found at i:16777992 original size:23 final size:23
Alignment explanation
Indices: 16777952--16777995 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
16777942 CCTCTACACA
*
16777952 CCATCTCCATTCGACCCTACATG
1 CCATCTCCATCCGACCCTACATG
* *
16777975 CCATCTCCGTCCGGCCCTACA
1 CCATCTCCATCCGACCCTACA
16777996 CATAATCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.48, G:0.11, T:0.23
Consensus pattern (23 bp):
CCATCTCCATCCGACCCTACATG
Found at i:16779987 original size:21 final size:22
Alignment explanation
Indices: 16779940--16779984 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
16779930 AATGTTATTA
*
16779940 TAATATATGTTTTTTAAGATAT
1 TAATATATGTTTATTAAGATAT
16779962 TAATATATG-TTATTAAGAT-T
1 TAATATATGTTTATTAAGATAT
16779982 TAA
1 TAA
16779985 ATAGATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 9 0.41
22 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TAATATATGTTTATTAAGATAT
Found at i:16789178 original size:126 final size:126
Alignment explanation
Indices: 16788953--16789292 Score: 590
Period size: 126 Copynumber: 2.7 Consensus size: 126
16788943 TAATTTAAAG
16788953 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTTTTGAGAAAATAATTTCGAGTAGAGGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTTTTGAGAAAATAATTTCGAGTAGAGGTTT
16789018 CTGAGCAAACAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTGAGCAAACAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* * * * ** * *
16789079 AAGCTTCTACGTGGACGCGCTTTTGCTATAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTTTTGAGAAAATAATTTCGAGTAGAGGTTT
* *
16789144 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAG
66 CTGAGCAAACAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
16789205 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTTTTGAGAAAATAATTTCGAGTAGAGGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTTTTGAGAAAATAATTTCGAGTAGAGGTTT
16789270 CTGAGCAAACAGTGTCAAAAACA
66 CTGAGCAAACAGTGTCAAAAACA
16789293 TAGATTGCAT
Statistics
Matches: 195, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 195 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTTTTGAGAAAATAATTTCGAGTAGAGGTTT
CTGAGCAAACAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
Found at i:16795381 original size:18 final size:18
Alignment explanation
Indices: 16795355--16795397 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16795345 AACTAGAAAA
* * *
16795355 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
16795373 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
16795391 AGGATAC
1 AGGATAC
16795398 GCATCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:16797257 original size:22 final size:22
Alignment explanation
Indices: 16797232--16797320 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 22
16797222 TCTTTTAAAT
*
16797232 AGGAATTTGAGAGAAATTTGAA
1 AGGAAATTGAGAGAAATTTGAA
*
16797254 AGGAAATTGAGAGCAAATTGAGATTCAA
1 AGGAAATTGAGAG-AAA-T----TTGAA
* * *
16797282 TAGGGATTTGAGAGAAATTTGAG
1 -AGGAAATTGAGAGAAATTTGAA
16797305 AGGAAATTGAGAGAAA
1 AGGAAATTGAGAGAAA
16797321 ATTAGAGAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
22 26 0.50
23 6 0.12
24 1 0.02
27 1 0.02
28 7 0.13
29 11 0.21
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (22 bp):
AGGAAATTGAGAGAAATTTGAA
Found at i:16797291 original size:51 final size:52
Alignment explanation
Indices: 16797229--16797328 Score: 166
Period size: 51 Copynumber: 1.9 Consensus size: 52
16797219 AGCTCTTTTA
*
16797229 AATAGGAATTTGAGAGAAATTTGAAAGGAAATTGAGAGCAAATT-GAGATTC
1 AATAGGAATTTGAGAGAAATTTGAAAGGAAATTGAGAGAAAATTAGAGATTC
* *
16797280 AATAGGGATTTGAGAGAAATTTGAGAGGAAATTGAGAGAAAATTAGAGA
1 AATAGGAATTTGAGAGAAATTTGAAAGGAAATTGAGAGAAAATTAGAGA
16797329 AAGAATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 41 0.91
52 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (52 bp):
AATAGGAATTTGAGAGAAATTTGAAAGGAAATTGAGAGAAAATTAGAGATTC
Found at i:16797327 original size:10 final size:11
Alignment explanation
Indices: 16797289--16797330 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
16797279 CAATAGGGAT
*
16797289 TTGAGAGAAAT
1 TTGAGAGAAAA
*
16797300 TTGAGAGGAAA
1 TTGAGAGAAAA
16797311 TTGAGAGAAAA
1 TTGAGAGAAAA
16797322 TT-AGAGAAA
1 TTGAGAGAAA
16797331 GAATTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 7 0.25
11 21 0.75
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (11 bp):
TTGAGAGAAAA
Found at i:16801961 original size:2 final size:2
Alignment explanation
Indices: 16801956--16801984 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16801946 ATAAAAATGC
16801956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16801985 TATCTTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16808409 original size:23 final size:24
Alignment explanation
Indices: 16808360--16808410 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
16808350 TTATGTTTTT
* *
16808360 AATTTTTTTTAAGATAAGCATATA
1 AATTATTTTTAAGATAAACATATA
**
16808384 AATTATTTTTAATCTAAACATA-A
1 AATTATTTTTAAGATAAACATATA
16808407 AATT
1 AATT
16808411 GTCATTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (24 bp):
AATTATTTTTAAGATAAACATATA
Found at i:16809592 original size:1 final size:1
Alignment explanation
Indices: 16809586--16809616 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
16809576 ATTACATTGC
16809586 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16809617 CAAAGTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16809920 original size:22 final size:22
Alignment explanation
Indices: 16809892--16809933 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
16809882 TACATAATAG
16809892 ATTTATATTAAATAAAAAAAGT
1 ATTTATATTAAATAAAAAAAGT
*
16809914 ATTTATATTAAATCAAAAAA
1 ATTTATATTAAATAAAAAAA
16809934 TAAATTGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
ATTTATATTAAATAAAAAAAGT
Found at i:16818316 original size:26 final size:26
Alignment explanation
Indices: 16818286--16818338 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
16818276 TTATTAAGTC
*
16818286 AAATAAACTATGCTAATAAAAACTAA
1 AAATAAACTATACTAATAAAAACTAA
* * *
16818312 AAATATATTATACTAATAAATACTAA
1 AAATAAACTATACTAATAAAAACTAA
16818338 A
1 A
16818339 TCTTCTAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.28
Consensus pattern (26 bp):
AAATAAACTATACTAATAAAAACTAA
Found at i:16820251 original size:26 final size:26
Alignment explanation
Indices: 16820221--16820273 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
16820211 TTATTAAGTC
*
16820221 AAATAAACTATGCTAATAAAAACTAA
1 AAATAAACTATACTAATAAAAACTAA
* * *
16820247 AAATATATTATACTAATAAATACTAA
1 AAATAAACTATACTAATAAAAACTAA
16820273 A
1 A
16820274 TCTTCTAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.28
Consensus pattern (26 bp):
AAATAAACTATACTAATAAAAACTAA
Found at i:16821486 original size:38 final size:38
Alignment explanation
Indices: 16821438--16821536 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
16821428 CGAATATAAT
* * *
16821438 AATTATAATTACCATAATTATAGTAATGTT-TGACCGAA
1 AATTATAATTACAATAATTATAATAATATTCT-ACCGAA
* * *
16821476 AATTACAATTACAATAATTATAATAATATTCTATCGTA
1 AATTATAATTACAATAATTATAATAATATTCTACCGAA
16821514 AATTATAATTACAATAATTATAA
1 AATTATAATTACAATAATTATAA
16821537 CAAGGATTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
38 52 0.98
39 1 0.02
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.38
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATTCTACCGAA
Found at i:16826293 original size:22 final size:22
Alignment explanation
Indices: 16826268--16826309 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16826258 CGGATAAACA
16826268 GAGAGCACAAATGTGCTAATCG
1 GAGAGCACAAATGTGCTAATCG
**
16826290 GAGAGCACTGATGTGCTAAT
1 GAGAGCACAAATGTGCTAAT
16826310 AATCAGAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (22 bp):
GAGAGCACAAATGTGCTAATCG
Found at i:16826352 original size:27 final size:25
Alignment explanation
Indices: 16826261--16826347 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 25
16826251 GCCAAAACGG
* *
16826261 ATAAACAGAGAGCACAAATGTGC--
1 ATAATCAGAGAGCACTAATGTGCTA
* *
16826284 -TAATCGGAGAGCACTGATGTGCTA
1 ATAATCAGAGAGCACTAATGTGCTA
*
16826308 ATAATCAGAGAGCACTAATGTGGTA
1 ATAATCAGAGAGCACTAATGTGCTA
16826333 ATAATCAGAGAGCAC
1 ATAATCAGAGAGCAC
16826348 ACTAAGGTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.33
25 36 0.67
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (25 bp):
ATAATCAGAGAGCACTAATGTGCTA
Found at i:16829648 original size:224 final size:224
Alignment explanation
Indices: 16829258--16829708 Score: 866
Period size: 224 Copynumber: 2.0 Consensus size: 224
16829248 TACTTACACC
16829258 TTCGATTATTCATGGAGGTTAGTGATTCATTTAAGTTAGTTGGTGTGACTGAAGACGCACTAAGG
1 TTCGATTATTCATGGAGGTTAGTGATTCATTTAAGTTAGTTGGTGTGACTGAAGACGCACTAAGG
16829323 TTGAAACTATTTCCATACTCGTTGCGAGATCATGCACGAGCATGACTGAATTCATTGCCACCAAG
66 TTGAAACTATTTCCATACTCGTTGCGAGATCATGCACGAGCATGACTGAATTCATTGCCACCAAG
16829388 TTCAATATCTACTTGGAAAGAATTAGCAGAAAGATTTTTGGTTAAGTATTTTCCACCAAATAGGA
131 TTCAATATCTACTTGGAAAGAATTAGCAGAAAGATTTTTGGTTAAGTATTTTCCACCAAATAGGA
*
16829453 ACGTAAAGTTGTGTACTGAGATAACAACT
196 ACGTAAAGTTGTGTAATGAGATAACAACT
16829482 TTCGATTATTCATGGAGGTTAGTGATTCATTTAAGTTAGTTGGTGTGACTGAAGACGCACTAAGG
1 TTCGATTATTCATGGAGGTTAGTGATTCATTTAAGTTAGTTGGTGTGACTGAAGACGCACTAAGG
*
16829547 TTGAAACTATTTCCATACTCGTTGCGAGATCATGCACGAGCATGGCTGAATTCATTGCCACCAAG
66 TTGAAACTATTTCCATACTCGTTGCGAGATCATGCACGAGCATGACTGAATTCATTGCCACCAAG
* *
16829612 TTCAATATCTACTTGGAAAGAATTAGCAGAAAGATTTTTTGTTAAGTATTTTCCACCAAGTAGGA
131 TTCAATATCTACTTGGAAAGAATTAGCAGAAAGATTTTTGGTTAAGTATTTTCCACCAAATAGGA
16829677 ACGTAAAGTTGTGTAATGAGATAACAACT
196 ACGTAAAGTTGTGTAATGAGATAACAACT
16829706 TTC
1 TTC
16829709 CAACAATTAG
Statistics
Matches: 223, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
224 223 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (224 bp):
TTCGATTATTCATGGAGGTTAGTGATTCATTTAAGTTAGTTGGTGTGACTGAAGACGCACTAAGG
TTGAAACTATTTCCATACTCGTTGCGAGATCATGCACGAGCATGACTGAATTCATTGCCACCAAG
TTCAATATCTACTTGGAAAGAATTAGCAGAAAGATTTTTGGTTAAGTATTTTCCACCAAATAGGA
ACGTAAAGTTGTGTAATGAGATAACAACT
Found at i:16830485 original size:38 final size:37
Alignment explanation
Indices: 16830435--16830517 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 37
16830425 TTGACTGAAA
* * *
16830435 AAATTAAAATTACAATTATTATAA-TAATATTCTATCGT
1 AAATTATAATTACAATAATTATAACTAAGATT-T-TCGT
*
16830473 AAATTATAATTACAATAATTATAACTAAGATTTTGGT
1 AAATTATAATTACAATAATTATAACTAAGATTTTCGT
16830510 AAATTATA
1 AAATTATA
16830518 TTTGGTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 11 0.28
38 23 0.57
39 6 0.15
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (37 bp):
AAATTATAATTACAATAATTATAACTAAGATTTTCGT
Found at i:16831399 original size:22 final size:20
Alignment explanation
Indices: 16831357--16831403 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
16831347 ACATCCCATG
*
16831357 TTAAT-GACAACACTTTGTC
1 TTAATAGACAACACTTAGTC
*
16831376 TTTAATAGACTACACATTAGTC
1 -TTAATAGACAACAC-TTAGTC
16831398 TTAATA
1 TTAATA
16831404 CATTATTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (20 bp):
TTAATAGACAACACTTAGTC
Found at i:16835246 original size:21 final size:21
Alignment explanation
Indices: 16835220--16835275 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
16835210 AACAGTGGTG
* *
16835220 GCGGTGAGATTAGTTGCTGTA
1 GCGGTGAGATTAGATACTGTA
*
16835241 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
16835262 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
16835276 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.09, G:0.39, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:16836551 original size:27 final size:27
Alignment explanation
Indices: 16836521--16836573 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
16836511 AACTGAGAAG
16836521 TGAATAGAAAGCACAAAATATCCTATT
1 TGAATAGAAAGCACAAAATATCCTATT
* *
16836548 TGAATAGAAAGCACAGAATATGCTAT
1 TGAATAGAAAGCACAAAATATCCTAT
16836574 AGTTTCAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (27 bp):
TGAATAGAAAGCACAAAATATCCTATT
Found at i:16844832 original size:26 final size:26
Alignment explanation
Indices: 16844794--16844843 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
16844784 GTTTGACTCG
*
16844794 TAAATATTGAATAATAATATTTACGA
1 TAAATATTAAATAATAATATTTACGA
16844820 TAAATATTAAATAATAATATTTAC
1 TAAATATTAAATAATAATATTTAC
16844844 AAACTTACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (26 bp):
TAAATATTAAATAATAATATTTACGA
Found at i:16848919 original size:38 final size:38
Alignment explanation
Indices: 16848865--16848986 Score: 172
Period size: 38 Copynumber: 3.2 Consensus size: 38
16848855 AATAAGTCTG
* *
16848865 AATAACACTGGTACTAAGCCTACTAGGCACTAAGCCTA
1 AATAACACTGGCACTAAGCCTGCTAGGCACTAAGCCTA
* * * *
16848903 AATAACATTGTCACTAAGCCTGCTAGGCACTAATCCTG
1 AATAACACTGGCACTAAGCCTGCTAGGCACTAAGCCTA
* *
16848941 AATAACACTGGCACTGAGTCTGCTAGGCACTAAGCCTA
1 AATAACACTGGCACTAAGCCTGCTAGGCACTAAGCCTA
16848979 AATAACAC
1 AATAACAC
16848987 CGACAATAAG
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.22
Consensus pattern (38 bp):
AATAACACTGGCACTAAGCCTGCTAGGCACTAAGCCTA
Found at i:16850048 original size:13 final size:13
Alignment explanation
Indices: 16850030--16850055 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16850020 TAAGTATAAC
16850030 TATTATATTATTA
1 TATTATATTATTA
16850043 TATTATATTATTA
1 TATTATATTATTA
16850056 GAAAAAGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATTATTA
Found at i:16850139 original size:16 final size:16
Alignment explanation
Indices: 16850118--16850153 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16850108 AACGAAACAG
* *
16850118 AGAAGAAATGAAGGAA
1 AGAAGAAAAGAAAGAA
16850134 AGAAGAAAAGAAAGAA
1 AGAAGAAAAGAAAGAA
16850150 AGAA
1 AGAA
16850154 AAGGGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (16 bp):
AGAAGAAAAGAAAGAA
Found at i:16851232 original size:23 final size:22
Alignment explanation
Indices: 16851202--16851287 Score: 106
Period size: 21 Copynumber: 4.0 Consensus size: 22
16851192 GCTTTGCCGA
16851202 TCAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
*
16851224 CTCGGGCACTTTATGTGTCGTA-
1 -TCAGGCACTTTATGTGTCGTAT
* **
16851246 TCAGGCACCTCGTGTGTCGT-T
1 TCAGGCACTTTATGTGTCGTAT
16851267 TCAGGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
16851288 ACTGATCAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 9 0.17
21 25 0.46
23 20 0.37
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (22 bp):
TCAGGCACTTTATGTGTCGTAT
Found at i:16851252 original size:44 final size:41
Alignment explanation
Indices: 16851201--16851287 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 41
16851191 GGCTTTGCCG
* * *
16851201 ATCAGGCACTTTATGTGTCGTATCTCGGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT-T-TCAGGCAC-TTATGTGTCGT
*
16851245 ATCAGGCACCTCGTGTGTCGTTTCAGGCACTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGTTTCAGGCACTTATGTGTCGT
16851286 AT
1 AT
16851288 ACTGATCAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 13 0.33
42 7 0.18
43 1 0.03
44 18 0.46
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (41 bp):
ATCAGGCACCTCATGTGTCGTTTCAGGCACTTATGTGTCGT
Found at i:16852835 original size:3 final size:3
Alignment explanation
Indices: 16852827--16852895 Score: 129
Period size: 3 Copynumber: 22.7 Consensus size: 3
16852817 TATTGAAACA
16852827 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAGG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG
16852873 AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AA
16852896 AGTTTTGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16853924 original size:13 final size:13
Alignment explanation
Indices: 16853892--16853918 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16853882 AAGTAAGGAG
16853892 AAAGAAAGAAGAA
1 AAAGAAAGAAGAA
16853905 AAAGAAAGAAGAA
1 AAAGAAAGAAGAA
16853918 A
1 A
16853919 GTGAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAA
Found at i:16854238 original size:21 final size:21
Alignment explanation
Indices: 16854212--16854279 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
16854202 TATTTTTGAG
16854212 TACTGAATTGAATTGTGAAGT
1 TACTGAATTGAATTGTGAAGT
* *
16854233 TACTGAA-T--ATTGTTATGT
1 TACTGAATTGAATTGTGAAGT
* * *
16854251 GTACTGCATTGAACTGTGAAAT
1 -TACTGAATTGAATTGTGAAGT
16854273 TACTGAA
1 TACTGAA
16854280 GTAATGAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
20 2 0.06
21 13 0.37
22 6 0.17
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (21 bp):
TACTGAATTGAATTGTGAAGT
Done.