Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015226.1 Kokia drynarioides strain JFW-HI SEQ_130270, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 713267
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:381674 original size:41 final size:41
Alignment explanation
Indices: 381559--381680 Score: 156
Period size: 41 Copynumber: 3.0 Consensus size: 41
381549 GGATGGTAGT
* **
381559 TTCAATCTGTCCCTCTTAATTAAGGGTAAAAGACAAGATGC
1 TTCAATCTGTCCCTCTTAACTAAGGGTAAAAGATTAGATGC
* * *
381600 TTCAATCTGCCCCTCTTGACTAAGGGTAAAAGATTGGAAT-C
1 TTCAATCTGTCCCTCTTAACTAAGGGTAAAAGATTAG-ATGC
* *
381641 TTCAATTTGTCCCTCTTAACTAGGGGTAAAAGATTAGATG
1 TTCAATCTGTCCCTCTTAACTAAGGGTAAAAGATTAGATG
381681 ATGGCTACAA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 2 0.03
41 64 0.94
42 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (41 bp):
TTCAATCTGTCCCTCTTAACTAAGGGTAAAAGATTAGATGC
Found at i:381733 original size:39 final size:39
Alignment explanation
Indices: 381688--382694 Score: 589
Period size: 39 Copynumber: 25.8 Consensus size: 39
381678 ATGATGGCTA
381688 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
** * ** *
381727 CAATCTGCCCCATGATTAGCGTAAGAGATTGGATGCCTA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
** *
381766 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATAACTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-GGTTT
* *** *
381806 -GATCTGCCCCATGATCGGGGTAAGAGATCAAATGGTTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
* * * * *
381844 CAATCTGCCCCATTATCAGGGTAAAAGCTT-GACTGATTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGA-TGGTT-T
* * * * * ** * *
381884 -GAT-TTCCCTTATTATTGGGGTAAGAGATCAGATAGTTG
1 CAATCTGCCC-CATGATCGGGGTAAGAGATTGGATGGTTT
* * * * * *
381922 CAGTCTGCCTCATGATCGAGGTAAGAGATTGGCTGACTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATG-GTTT
* * * *
381962 -GATCTGCCCCATGATCGGGGTAAGAGATCGGATGATTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
* ** * *
382000 CAATCTGCCTCATGATCAAGGTAAGAGATT-GACTGACTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGA-TG-GTTT
* * * * * *
382040 -GATCTACCCCATGATCAGGGTAAGAGATTTGAATTGTTG
1 CAATCTGCCCCATGATCGGGGTAAGAGA-TTGGATGGTTT
* * *
382079 CAATCTGCCTCATGATAGGGGTAAGAGATT-GATTGATTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGA-TGGTT-T
* * ** *
382119 -GATCTGTCCCATGATCGGGGTAAGAGATCAGATGGTTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
* * *
382157 CAATCTGCCCCATTATCGGGGTAAGAGA--GAGACTGACTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTG-GA-TG-GTTT
* * * *
382197 -GACCTGCCCCATGATCAGGGTAAGAGATCGGATGGTTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTT-T
** *
382236 -AATCTGCCCCATGATCGGGGTAAGAGATT-GACTAACTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGA-T-GGTTT
* * ** * * *
382275 -GATCTACCTAATGATCGAGGTAAGAGATCGGATGGTTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
* * *
382313 CAATCAGCCCCATGATTGGGGTAAGAGATT-GACTGATTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGA-TGGTT-T
* * * * *
382353 -GATCTACCCCATGATCGGGGTAGGAGATCGGATGGTTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
* * *
382391 CAATCTACCCCATGATCGAGGTAAGAGATT-GACTGACTTT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGA-TG-GTTT
* * ** * *
382431 -GATCTGCCTCATGATCGGGGTAAGAGATCAGTTGGTTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
* *** * *
382469 CAATCTGCCCTATGATCGGGGTAAGAGACCAGCTGGTTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
* * * *
382508 CAATCTGCCCTATGATCGAGGTAAGAGATTGGATGACTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATG-GTTT
* * ** * * *
382548 -GATCTGCCCTATGATCTAGGTAAGAGATTTGATGGCTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
* * * * * *
382586 CATTCTGCCTCATGATCGAGGTAAGATATTGGATGACTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATG-GTTT
* ** *
382626 -GATCTGCCCCATGATCAAGGTAAGAGATCGGATGGTTT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
* *
382664 CAATCTGCCCCATGATCGAGGTAAAAGATTG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTG
382695 ACTGACTATG
Statistics
Matches: 724, Mismatches: 203, Indels: 82
0.72 0.20 0.08
Matches are distributed among these distances:
38 24 0.03
39 651 0.90
40 47 0.06
41 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (39 bp):
CAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTT
Found at i:382363 original size:117 final size:115
Alignment explanation
Indices: 381690--382695 Score: 704
Period size: 117 Copynumber: 8.6 Consensus size: 115
381680 GATGGCTACA
* * * *
381690 ATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTTCAATCTGCCCCATGATTAGCGTAAGAGA
1 ATCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTGCAATCTGCCCCATGATCAGGGTAAGAGA
** **
381755 TTGGATGCCTACAATCTGCCCCATGATCGGGGTAAGAGATTGGATAACTGTG
66 TT-GATGATTGTAATCTGCCCCATGATCGGGGTAAGAGATT-GATAACTGTG
* *** * * *
381807 ATCTGCCCCATGATCGGGGTAAGAGATCAAATGGTTGCAATCTGCCCCATTATCAGGGTAAAAGC
1 ATCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTGCAATCTGCCCCATGATCAGGGTAAGAGA
* * * * * * *
381872 TTGACTGATTGTGAT-TTCCCTTATTATTGGGGTAAGAGATCAGAT-AGT-TG
66 TTGA-TGATTGTAATCTGCCC-CATGATCGGGGTAAGAGAT-TGATAACTGTG
* * ** ** *
381922 CAGTCTGCCTCATGATCGAGGTAAGAGATTGGCTGACTGTGATCTGCCCCATGATCGGGGTAAGA
1 -A-TCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTGCAATCTGCCCCATGATCAGGGTAAGA
* * * ** *
381987 GATCGGATGATTGCAATCTGCCTCATGATCAAGGTAAGAGATTGACTGACTGTG
64 GAT-TGATGATTGTAATCTGCCCCATGATCGGGGTAAGAGATTGA-TAACTGTG
* * * *
382041 ATCTACCCCATGATC-AGGGTAAGAGATTTGAATTGTTGCAATCTGCCTCATGAT-AGGGGTAAG
1 ATCTGCCCCATGATCGA-GGTAAGAGA-TTGGATGGTTGCAATCTGCCCCATGATCA-GGGTAAG
* * * *** **
382104 AGATTGATTGATTGTGATCTGTCCCATGATCGGGGTAAGAGATCAGATGGTTGCA
63 AGATTGA-TGATTGTAATCTGCCCCATGATCGGGGTAAGAGAT-TGATAACTGTG
* * ** ** *
382159 ATCTGCCCCATTATCGGGGTAAGAGA--GAGACTGACTGTGACCTGCCCCATGATCAGGGTAAGA
1 ATCTGCCCCATGATCGAGGTAAGAGATTG-GA-TGGTTGCAATCTGCCCCATGATCAGGGTAAGA
* *
382222 GATCGGATGGTTGTAATCTGCCCCATGATCGGGGTAAGAGATTGACTAACTGTG
64 GAT-TGATGATTGTAATCTGCCCCATGATCGGGGTAAGAGATTGA-TAACTGTG
* ** * * **
382276 ATCTACCTAATGATCGAGGTAAGAGATCGGATGGTTGCAATCAGCCCCATGATTGGGGTAAGAGA
1 ATCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTGCAATCTGCCCCATGATCAGGGTAAGAGA
* * * * *** **
382341 TTGACTGATTGTGATCTACCCCATGATCGGGGTAGGAGATCGGATGGTTGCA
66 TTGA-TGATTGTAATCTGCCCCATGATCGGGGTAAGAGAT-TGATAACTGTG
* * * *
382393 ATCTACCCCATGATCGAGGTAAGAGATT-GACTGACTTTG--ATCTGCCTCATGATCGGGGTAAG
1 ATCTGCCCCATGATCGAGGTAAGAGATTGGA-TG--GTTGCAATCTGCCCCATGATCAGGGTAAG
* * * * * ** * *** **
382455 AGATCAGTTGGTTGCAATCTGCCCTATGATCGGGGTAAGAGACCAGCTGGTTGCA
63 AGAT-TGATGATTGTAATCTGCCCCATGATCGGGGTAAGAGA-TTGATAACTGTG
* ** ** *
382510 ATCTGCCCTATGATCGAGGTAAGAGATTGGATGACTGTGATCTGCCCTATGATCTA-GGTAAGAG
1 ATCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTGCAATCTGCCCCATGATC-AGGGTAAGAG
** * * * * * *
382574 ATTTGATGGCTGCATTCTGCCTCATGATCGAGGTAAGATATTGGATGACTGTG
65 A-TTGATGATTGTAATCTGCCCCATGATCGGGGTAAGAGATT-GATAACTGTG
* * * *
382627 ATCTGCCCCATGATCAAGGTAAGAGATCGGATGGTTTCAATCTGCCCCATGATC-GAGGTAAAAG
1 ATCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTGCAATCTGCCCCATGATCAG-GGTAAGAG
382691 ATTGA
65 ATTGA
382696 CTGACTATGA
Statistics
Matches: 687, Mismatches: 164, Indels: 77
0.74 0.18 0.08
Matches are distributed among these distances:
115 5 0.01
116 23 0.03
117 547 0.80
118 104 0.15
119 8 0.01
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (115 bp):
ATCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTGCAATCTGCCCCATGATCAGGGTAAGAGA
TTGATGATTGTAATCTGCCCCATGATCGGGGTAAGAGATTGATAACTGTG
Found at i:382514 original size:78 final size:78
Alignment explanation
Indices: 381688--382692 Score: 952
Period size: 78 Copynumber: 12.9 Consensus size: 78
381678 ATGATGGCTA
* * ** *
381688 CAATCTGCCCCATGATCGGGGTAAGAGATTGGA-TGGTT-TCAATCTGCCCCATGATTAGCGTAA
1 CAATCTGCCCCATGATCGGGGTAAGAGATT-GACTGATTGT-GATCTGCCCCATGATCGGGGTAA
* ** *
381751 GAGATTGGATGCCTA
64 GAGATCGGATGGTTG
* *
381766 CAATCTGCCCCATGATCGGGGTAAGAGATTGGA-TAACTGTGATCTGCCCCATGATCGGGGTAAG
1 CAATCTGCCCCATGATCGGGGTAAGAGATT-GACTGATTGTGATCTGCCCCATGATCGGGGTAAG
**
381830 AGATCAAATGGTTG
65 AGATCGGATGGTTG
* * * * * * * *
381844 CAATCTGCCCCATTATCAGGGTAAAAGCTTGACTGATTGTGAT-TTCCCTTATTATTGGGGTAAG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATTGTGATCTGCCC-CATGATCGGGGTAAG
* *
381908 AGATCAGATAGTTG
65 AGATCGGATGGTTG
* * * * *
381922 CAGTCTGCCTCATGATCGAGGTAAGAGATTGGCTGACTGTGATCTGCCCCATGATCGGGGTAAGA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATTGTGATCTGCCCCATGATCGGGGTAAGA
*
381987 GATCGGATGATTG
66 GATCGGATGGTTG
* ** * * *
382000 CAATCTGCCTCATGATCAAGGTAAGAGATTGACTGACTGTGATCTACCCCATGATCAGGGTAAGA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATTGTGATCTGCCCCATGATCGGGGTAAGA
* * *
382065 GATTTGAATTGTTG
66 GA-TCGGATGGTTG
* * * *
382079 CAATCTGCCTCATGATAGGGGTAAGAGATTGATTGATTGTGATCTGTCCCATGATCGGGGTAAGA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATTGTGATCTGCCCCATGATCGGGGTAAGA
*
382144 GATCAGATGGTTG
66 GATCGGATGGTTG
* ** * * *
382157 CAATCTGCCCCATTATCGGGGTAAGAGAGAGACTGACTGTGACCTGCCCCATGATCAGGGTAAGA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATTGTGATCTGCCCCATGATCGGGGTAAGA
382222 GATCGGATGGTTG
66 GATCGGATGGTTG
* * * * ** *
382235 TAATCTGCCCCATGATCGGGGTAAGAGATTGACTAACTGTGATCTACCTAATGATCGAGGTAAGA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATTGTGATCTGCCCCATGATCGGGGTAAGA
382300 GATCGGATGGTTG
66 GATCGGATGGTTG
* * * *
382313 CAATCAGCCCCATGATTGGGGTAAGAGATTGACTGATTGTGATCTACCCCATGATCGGGGTAGGA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATTGTGATCTGCCCCATGATCGGGGTAAGA
382378 GATCGGATGGTTG
66 GATCGGATGGTTG
* * *
382391 CAATCTACCCCATGATCGAGGTAAGAGATTGACTGACTT-TGATCTGCCTCATGATCGGGGTAAG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGA-TTGTGATCTGCCCCATGATCGGGGTAAG
* *
382455 AGATCAGTTGGTTG
65 AGATCGGATGGTTG
* ** * ** * *
382469 CAATCTGCCCTATGATCGGGGTAAGAGA-CCAGCTGGTTGCAATCTGCCCTATGATCGAGGTAAG
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGA-CTGATTGTGATCTGCCCCATGATCGGGGTAAG
* **
382533 AGATTGGATGACTG
65 AGATCGGATGGTTG
** * ** * * *
382547 TGATCTGCCCTATGATCTAGGTAAGAGATT---TGATGGCTGCATTCTGCCTCATGATCGAGGTA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATTG-TG-A-TCTGCCCCATGATCGGGGTA
* * **
382609 AGATATTGGATGACTG
63 AGAGATCGGATGGTTG
** ** * * * *
382625 TGATCTGCCCCATGATCAAGGTAAGAGATCGGA-TGGTT-TCAATCTGCCCCATGATCGAGGTAA
1 CAATCTGCCCCATGATCGGGGTAAGAGAT-TGACTGATTGT-GATCTGCCCCATGATCGGGGTAA
*
382688 AAGAT
64 GAGAT
382693 TGACTGACTA
Statistics
Matches: 772, Mismatches: 139, Indels: 32
0.82 0.15 0.03
Matches are distributed among these distances:
75 4 0.01
77 10 0.01
78 680 0.88
79 75 0.10
81 3 0.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (78 bp):
CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATTGTGATCTGCCCCATGATCGGGGTAAGA
GATCGGATGGTTG
Found at i:383934 original size:9 final size:9
Alignment explanation
Indices: 383899--383948 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
383889 CTCCTTTTTC
383899 TTTTTC-TT
1 TTTTTCTTT
*
383907 TTCTTCTTT
1 TTTTTCTTT
*
383916 CTTCTTCTTT
1 -TTTTTCTTT
383926 TTTTTCTTT
1 TTTTTCTTT
383935 TTTTTCTTT
1 TTTTTCTTT
383944 TTTTT
1 TTTTT
383949 TTGGTGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 5 0.13
9 24 0.63
10 9 0.24
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:383945 original size:18 final size:19
Alignment explanation
Indices: 383895--383948 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
383885 ATCTCTCCTT
*
383895 TTTCTTTTTC-TTTTCTTC
1 TTTCTTTTTCTTTTTTTTC
*
383913 TTTCTTCTTCTTTTTTTTC
1 TTTCTTTTTCTTTTTTTTC
383932 TTT-TTTTTCTTTTTTTT
1 TTTCTTTTTCTTTTTTTT
383949 TTGGTGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 22 0.69
19 10 0.31
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTCTTTTTCTTTTTTTTC
Found at i:384787 original size:9 final size:9
Alignment explanation
Indices: 384770--384819 Score: 50
Period size: 8 Copynumber: 5.6 Consensus size: 9
384760 TTCATTTTGA
*
384770 CTTTCCTTT
1 CTTTTCTTT
384779 CTTTTCTTT
1 CTTTTCTTT
384788 CTTTTTCTTT
1 C-TTTTCTTT
384798 -TTTTCTTT
1 CTTTTCTTT
*
384806 -TTTTTTCTT
1 CTTTTCT-TT
384815 CTTTT
1 CTTTT
384820 TTTGGAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
8 13 0.36
9 11 0.31
10 12 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
CTTTTCTTT
Found at i:384793 original size:10 final size:10
Alignment explanation
Indices: 384775--384820 Score: 55
Period size: 9 Copynumber: 5.0 Consensus size: 10
384765 TTTGACTTTC
384775 CTTTC-TTTT
1 CTTTCTTTTT
384784 CTTTCTTTTT
1 CTTTCTTTTT
384794 C-TT-TTTTT
1 CTTTCTTTTT
*
384802 CTTTTTTTTT
1 CTTTCTTTTT
384812 C-TTCTTTTT
1 CTTTCTTTTT
384821 TTGGAGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.18
9 16 0.48
10 11 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:384801 original size:18 final size:18
Alignment explanation
Indices: 384775--384820 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 18
384765 TTTGACTTTC
384775 CTTTCTTTTCTTTCTTTTT
1 CTTT-TTTTCTTTCTTTTT
*
384794 CTTTTTTTCTTTTTTTTT
1 CTTTTTTTCTTTCTTTTT
384812 CTTCTTTTT
1 CTT-TTTTT
384821 TTGGAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
CTTTTTTTCTTTCTTTTT
Found at i:384821 original size:14 final size:14
Alignment explanation
Indices: 384780--384822 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
384770 CTTTCCTTTC
384780 TTTTCTTTCTTTTTCT
1 TTTTC-TTCTTTTT-T
384796 TTTT-TTC-TTTTT
1 TTTTCTTCTTTTTT
384808 TTTTCTTCTTTTTT
1 TTTTCTTCTTTTTT
384822 T
1 T
384823 GGAGTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.20
13 7 0.28
14 9 0.36
16 4 0.16
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTCTTTTTT
Found at i:389129 original size:28 final size:29
Alignment explanation
Indices: 389096--389166 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 29
389086 TTTTTTAGAC
*
389096 TTTTAGGGGTAAAAAGTAACTTTGAAAAA
1 TTTTAGGGTTAAAAAGTAACTTTGAAAAA
* *
389125 -TTTAGGGTTAAAATGTAATTTTGAAAAA
1 TTTTAGGGTTAAAAAGTAACTTTGAAAAA
389153 TTTTAGGGTTAAAA
1 TTTTAGGGTTAAAA
389167 CTATGATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 25 0.66
29 13 0.34
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.37
Consensus pattern (29 bp):
TTTTAGGGTTAAAAAGTAACTTTGAAAAA
Found at i:389188 original size:30 final size:29
Alignment explanation
Indices: 389097--389368 Score: 212
Period size: 30 Copynumber: 9.2 Consensus size: 29
389087 TTTTTAGACT
* * * *
389097 TTTAGGGGTAAAAAGTAACTTT-GAAAAA
1 TTTAGGGTTAAAATGTAATTTTAGAAAAG
*
389125 TTTAGGGTTAAAATGTAATTTT-GAAAAAT
1 TTTAGGGTTAAAATGTAATTTTAG-AAAAG
* *
389154 TTTAGGGTTAAAACTATGATTTTAGAAAAG
1 TTTAGGGTTAAAA-TGTAATTTTAGAAAAG
* *
389184 TTTAGGGTT-AAATGTAATTTTGGAAAAC
1 TTTAGGGTTAAAATGTAATTTTAGAAAAG
* *
389212 TTTATGGATTAAAATGTAATTTTATG-ATAG
1 TTTA-GGGTTAAAATGTAATTTTA-GAAAAG
* * *
389242 TTTGGGGTTAAAATGTGATTTTTAAAAAAG
1 TTTAGGGTTAAAATGT-AATTTTAGAAAAG
*
389272 TTTAGGGGTTAAAATGTAATTTTAGGAAAG
1 TTTA-GGGTTAAAATGTAATTTTAGAAAAG
* * * * *
389302 TTTGGAGGTAAAAATGTAACTTTGGAGAAG
1 TTTAG-GGTTAAAATGTAATTTTAGAAAAG
* * * *
389332 -TTCGGGTGTCAAAATATTATTTTTGAAAAG
1 TTTAGGGT-T-AAAATGTAATTTTAGAAAAG
389362 TTTAGGG
1 TTTAGGG
389369 ACCTCCTGGG
Statistics
Matches: 193, Mismatches: 38, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
28 39 0.20
29 39 0.20
30 96 0.50
31 19 0.10
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (29 bp):
TTTAGGGTTAAAATGTAATTTTAGAAAAG
Found at i:389210 original size:59 final size:60
Alignment explanation
Indices: 389097--389327 Score: 224
Period size: 58 Copynumber: 3.9 Consensus size: 60
389087 TTTTTAGACT
* * * *
389097 TTTAGGGG-TAAAAAGTAACTTT-GAAAAATTTAGGGTTAAAATGTAATTTT-GAAAAAT
1 TTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAAC
* *
389154 TTTA-GGGTTAAAACTATGATTTTAGAAAAGTTTAGGGTT-AAATGTAATTTTGG-AAAAC
1 TTTAGGGGTTAAAA-TGTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAAC
* * * * * ** *
389212 TTTATGGATTAAAATGTAATTTTATG-ATAGTTTGGGGTTAAAATGTGATTTTTAAAAAAG
1 TTTAGGGGTTAAAATGTAATTTTA-GAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAAC
* * * *
389272 TTTAGGGGTTAAAATGTAATTTTAGGAAAGTTTGGAGGTAAAAATGTAACTTTGGA
1 TTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAG-GGTTAAAATGTAATTTTGGA
389328 GAAGTTCGGG
Statistics
Matches: 141, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
56 3 0.02
57 9 0.06
58 44 0.31
59 36 0.26
60 34 0.24
61 15 0.11
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.38
Consensus pattern (60 bp):
TTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAAAC
Found at i:397168 original size:17 final size:17
Alignment explanation
Indices: 397119--397197 Score: 61
Period size: 17 Copynumber: 4.6 Consensus size: 17
397109 ATCACATTCC
* *
397119 CATTGTCATTACATTTT
1 CATTGTCATTGCATTTG
* * *
397136 AATTGTCACTGTATTTG
1 CATTGTCATTGCATTTG
*
397153 CATTGTCATTGCATTTC
1 CATTGTCATTGCATTTG
*
397170 CATTTGTTATTGTCA-TTG
1 CA-TTGTCATTG-CATTTG
*
397188 CATTTTCATT
1 CATTGTCATT
397198 TGTTATTGTA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
17 33 0.70
18 12 0.26
19 2 0.04
ACGTcount: A:0.20, C:0.16, G:0.11, T:0.52
Consensus pattern (17 bp):
CATTGTCATTGCATTTG
Found at i:397186 original size:24 final size:24
Alignment explanation
Indices: 397154--397206 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
397144 CTGTATTTGC
397154 ATTGTCATTGCATTTCCATTTGTT
1 ATTGTCATTGCATTTCCATTTGTT
*
397178 ATTGTCATTGCATTTTCATTTGTT
1 ATTGTCATTGCATTTCCATTTGTT
397202 ATTGT
1 ATTGT
397207 AATTTAGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (24 bp):
ATTGTCATTGCATTTCCATTTGTT
Found at i:397791 original size:12 final size:11
Alignment explanation
Indices: 397774--397799 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
397764 CCTCAATCAC
397774 AAAAAAAAAGG
1 AAAAAAAAAGG
397785 AAAAAAAAAGG
1 AAAAAAAAAGG
397796 AAAA
1 AAAA
397800 GAAGAAAAAA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:398297 original size:26 final size:26
Alignment explanation
Indices: 398261--398356 Score: 77
Period size: 26 Copynumber: 3.7 Consensus size: 26
398251 ATGTCGTTGT
* *
398261 ATGAGCATGTCCAGAATTGTCACTTC
1 ATGAACATGTCCAGAATTGTCACTAC
* * * *
398287 A-GAAACTTGTCTAGAATTATCGCTAC
1 ATG-AACATGTCCAGAATTGTCACTAC
* **
398313 ATGAACATGTCCAGAGTTGTCACTGT
1 ATGAACATGTCCAGAATTGTCACTAC
* *
398339 ATGAGCGTGTCCAGAATT
1 ATGAACATGTCCAGAATT
398357 ATGCCCAGAA
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
25 1 0.02
26 50 0.96
27 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (26 bp):
ATGAACATGTCCAGAATTGTCACTAC
Found at i:407084 original size:27 final size:27
Alignment explanation
Indices: 407034--407119 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 27
407024 AAAACACCAA
*
407034 TTTTCATAAATGTGAG-CTTTTGTGGTTG
1 TTTTTATAAAT-TGAGTC-TTTGTGGTTG
407062 TTTTTATAAATTGAGTCTTTGTGGTTG
1 TTTTTATAAATTGAGTCTTTGTGGTTG
* * * *
407089 TCTTTGTAAAGTGAGTCTTTGTTGTTG
1 TTTTTATAAATTGAGTCTTTGTGGTTG
407116 TTTT
1 TTTT
407120 CGTTTAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
27 40 0.78
28 11 0.22
ACGTcount: A:0.16, C:0.06, G:0.23, T:0.55
Consensus pattern (27 bp):
TTTTTATAAATTGAGTCTTTGTGGTTG
Found at i:407254 original size:28 final size:28
Alignment explanation
Indices: 407213--407358 Score: 143
Period size: 28 Copynumber: 5.2 Consensus size: 28
407203 AAGGGAACTA
** *
407213 CCTTTGTGACTGATTTTGTTAAAGGAAG
1 CCTTTGTGGTTGATTCTGTTAAAGGAAG
* *
407241 CCTTTTTGGTTGATTCTATTAAAGGAAG
1 CCTTTGTGGTTGATTCTGTTAAAGGAAG
* * *
407269 CATTTGTGGTTGATAT-TGTTAAATGAAA
1 CCTTTGTGGTTGAT-TCTGTTAAAGGAAG
*
407297 TCTTTGTGGTTGATTCTGTTAAAGGAAG
1 CCTTTGTGGTTGATTCTGTTAAAGGAAG
* * * *
407325 CCTTCGTGGCTGATCCTTTTAAAAGG-AG
1 CCTTTGTGGTTGATTCTGTT-AAAGGAAG
407353 CCTTTG
1 CCTTTG
407359 CGGATATCTC
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
27 1 0.01
28 88 0.93
29 6 0.06
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (28 bp):
CCTTTGTGGTTGATTCTGTTAAAGGAAG
Found at i:410608 original size:16 final size:17
Alignment explanation
Indices: 410582--410616 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
410572 AAAATTTGGA
410582 ATAAGTATTTATAATTT
1 ATAAGTATTTATAATTT
*
410599 ATAA-TATTTATATTTT
1 ATAAGTATTTATAATTT
410615 AT
1 AT
410617 CATTCAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATAAGTATTTATAATTT
Found at i:410781 original size:2 final size:2
Alignment explanation
Indices: 410763--410796 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
410753 GATAAAATTT
* *
410763 TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
410797 ATGATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:410980 original size:32 final size:30
Alignment explanation
Indices: 410938--411005 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 30
410928 TGAATGACTT
* *
410938 AATTAATTTTTTTAATATTAAAAAATCATCAG
1 AATT-ATTTTTTTAAAATT-AAAAATCATCAA
*
410970 AATTA-TTTTTTAAAATTAAAAATCATTAA
1 AATTATTTTTTTAAAATTAAAAATCATCAA
410999 AATTATT
1 AATTATT
411006 AAAAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 15 0.47
30 12 0.38
31 1 0.03
32 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (30 bp):
AATTATTTTTTTAAAATTAAAAATCATCAA
Found at i:410990 original size:29 final size:30
Alignment explanation
Indices: 410945--411005 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
410935 CTTAATTAAT
* *
410945 TTTTTTAATATTAAAAAATCATCAGAATTA
1 TTTTTTAAAATTAAAAAATCATCAAAATTA
*
410975 TTTTTTAAAATT-AAAAATCATTAAAATTA
1 TTTTTTAAAATTAAAAAATCATCAAAATTA
411004 TT
1 TT
411006 AAAAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (30 bp):
TTTTTTAAAATTAAAAAATCATCAAAATTA
Found at i:411006 original size:9 final size:9
Alignment explanation
Indices: 410979--411024 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
410969 GAATTATTTT
410979 TTAAAATTA
1 TTAAAATTA
*
410988 --AAAATCA
1 TTAAAATTA
410995 TTAAAATTA
1 TTAAAATTA
*
411004 TTAAAAATA
1 TTAAAATTA
411013 TATAAAATTA
1 T-TAAAATTA
411023 TT
1 TT
411025 CGTAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
7 6 0.20
9 16 0.53
10 8 0.27
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (9 bp):
TTAAAATTA
Found at i:411008 original size:19 final size:19
Alignment explanation
Indices: 410984--411024 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
410974 ATTTTTTAAA
410984 ATTAAAAATCAT-TAAAATT
1 ATTAAAAAT-ATATAAAATT
411003 ATTAAAAATATATAAAATT
1 ATTAAAAATATATAAAATT
411022 ATT
1 ATT
411025 CGTAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTAAAAATATATAAAATT
Found at i:411186 original size:21 final size:23
Alignment explanation
Indices: 411145--411193 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
411135 GATGATTTGA
*
411145 TAAAAAAATATAAATCTAATAAC
1 TAAAAAAATATAAATCAAATAAC
*
411168 TAAAAAAAT-TAAAT-AAATATC
1 TAAAAAAATATAAATCAAATAAC
411189 TAAAA
1 TAAAA
411194 TGACTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 5 0.21
23 9 0.38
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAAAAATATAAATCAAATAAC
Found at i:411667 original size:35 final size:35
Alignment explanation
Indices: 411597--411672 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
411587 ATTTATAAAA
* *
411597 TTTTAAATTAATAATAATAAAATTATATTTTAATT
1 TTTTAAAATAATAATAATAAAATTATATTTAAATT
* *
411632 TTTTAAAATAATAA-AATATTAATT-TATTTAAAAT
1 TTTTAAAATAATAATAATA-AAATTATATTTAAATT
*
411666 TTATAAA
1 TTTTAAA
411673 GATATAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 18 0.51
35 17 0.49
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
TTTTAAAATAATAATAATAAAATTATATTTAAATT
Found at i:414036 original size:30 final size:29
Alignment explanation
Indices: 413990--414064 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
413980 AAATTTTAAA
*
413990 TTAATAATAATAAAATTATATTTTAA-CCTT
1 TTAA-AATAATAAAATT-TAATTTAATCCTT
414020 TTAAAATAATATAAATTTAATTTAATCCTT
1 TTAAAATAATA-AAATTTAATTTAATCCTT
* *
414050 TAAAAATTATAAAAT
1 TTAAAATAATAAAAT
414065 ATAAAATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 18 0.45
30 22 0.55
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (29 bp):
TTAAAATAATAAAATTTAATTTAATCCTT
Found at i:415610 original size:22 final size:22
Alignment explanation
Indices: 415580--415621 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
415570 CAAAATTAAA
*
415580 TCAATATAAAGAATA-ATCTGAC
1 TCAAAATAAA-AATAGATCTGAC
415602 TCAAAATAAAAATAGATCTG
1 TCAAAATAAAAATAGATCTG
415622 GATAGGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (22 bp):
TCAAAATAAAAATAGATCTGAC
Found at i:417290 original size:24 final size:25
Alignment explanation
Indices: 417263--417318 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 25
417253 AAATATGTTA
417263 ATTATATTATAT-TTAA-ACCAAATT
1 ATTATATTATATATTAACACC-AATT
*
417287 ATTA-A-TAAATATTAACACCAATT
1 ATTATATTATATATTAACACCAATT
417310 -TTATATTAT
1 ATTATATTAT
417319 TAATAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
22 7 0.27
23 10 0.38
24 9 0.35
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTATATTATATATTAACACCAATT
Found at i:417296 original size:40 final size:43
Alignment explanation
Indices: 417216--417298 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 43
417206 ATCAACATTA
*
417216 TTAATATATTATATTTAATACCCAATTATTAATTATTAAATATG
1 TTAATATATTATATTTAATACCCAA-TATTAATTAATAAATATG
417260 TTAATTATATTATATTTAA-A-CCAA-ATT-ATTAATAAATAT
1 TTAA-TATATTATATTTAATACCCAATATTAATTAATAAATAT
417299 TAACACCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
40 11 0.30
41 3 0.08
43 4 0.11
44 5 0.14
45 14 0.38
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (43 bp):
TTAATATATTATATTTAATACCCAATATTAATTAATAAATATG
Found at i:417581 original size:16 final size:18
Alignment explanation
Indices: 417552--417594 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
417542 GTAATTTGAA
417552 AAATAATATATTTATTAC
1 AAATAATATATTTATTAC
*
417570 AAATAA-AT-TTTATTTC
1 AAATAATATATTTATTAC
*
417586 AAATTATAT
1 AAATAATAT
417595 TTGCTTCGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 12 0.55
17 4 0.18
18 6 0.27
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAATATATTTATTAC
Found at i:418988 original size:29 final size:30
Alignment explanation
Indices: 418934--418994 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
418924 TAGTGACATC
*
418934 ATTTTCGTATTTAATTAAAAAAATAAA-TT
1 ATTTTCGTAATTAATTAAAAAAATAAAGTT
**
418963 ATTTTCGTAATTAATTAAAATTATAAAGTT
1 ATTTTCGTAATTAATTAAAAAAATAAAGTT
418993 AT
1 AT
418995 CTATATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (30 bp):
ATTTTCGTAATTAATTAAAAAAATAAAGTT
Found at i:422383 original size:15 final size:15
Alignment explanation
Indices: 422351--422388 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
422341 TTAGTATAAT
422351 ATTTGATA--TTTGA
1 ATTTGATATTTTTGA
*
422364 ATTTGATATTTTTTA
1 ATTTGATATTTTTGA
422379 ATTTGATATT
1 ATTTGATATT
422389 AAAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
15 14 0.64
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
ATTTGATATTTTTGA
Found at i:422759 original size:25 final size:25
Alignment explanation
Indices: 422672--422760 Score: 81
Period size: 25 Copynumber: 3.4 Consensus size: 25
422662 AATTGAATCC
* *
422672 AAAAAAAA-AATTAAGTACCAAATT
1 AAAAAAAATAATTAAATATCAAATT
422696 AAAAAAAAATATTAATTTCAAATATCAAATT
1 --AAAAAAA-A-TAA-TT-AAATATCAAATT
* *
422727 AGATAAAATAATTAAATATCAAATT
1 AAAAAAAATAATTAAATATCAAATT
422752 AAAAAAAAT
1 AAAAAAAAT
422761 CAAATTTAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
25 19 0.37
26 9 0.17
27 4 0.08
28 1 0.02
29 7 0.13
30 2 0.04
31 10 0.19
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAAAAAATAATTAAATATCAAATT
Found at i:423242 original size:30 final size:29
Alignment explanation
Indices: 423200--423290 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 29
423190 TTTTTTAAAA
423200 TTAATAAA-AATAAAATTATATTTTAACTCT
1 TTAA-AAATAATAAAATTATATTTTAA-TCT
* *
423230 TTAAAAATAATAAAATTTTAATTTAATCAT
1 TTAAAAATAATAAAATTATATTTTAATC-T
* *
423260 TTAAAAATTAT-AATTTA-ATTTTAATCT
1 TTAAAAATAATAAAATTATATTTTAATCT
423287 TTAA
1 TTAA
423291 TTTTTTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.09
28 8 0.15
29 9 0.17
30 31 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAAAAATAATAAAATTATATTTTAATCT
Found at i:433651 original size:21 final size:20
Alignment explanation
Indices: 433606--433658 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
433596 TTGTGCTAGC
*
433606 TCTACCGATACAAGTATGATT
1 TCTACCGATACAAATATGA-T
433627 TCTACCGATACAAATCATGCA-
1 TCTACCGATACAAAT-ATG-AT
433648 TCTACCGATAC
1 TCTACCGATAC
433659 CAAAAACTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 25 0.86
22 3 0.10
23 1 0.03
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (20 bp):
TCTACCGATACAAATATGAT
Found at i:440810 original size:21 final size:23
Alignment explanation
Indices: 440784--440826 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
440774 GTACTAGCTC
440784 TACCAATACAAGT-ATG-ATTTT
1 TACCAATACAAGTCATGCATTTT
440805 TACCAATACAAGTCATGCATTT
1 TACCAATACAAGTCATGCATTT
440827 ACCGATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.65
22 3 0.15
23 4 0.20
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (23 bp):
TACCAATACAAGTCATGCATTTT
Found at i:447347 original size:52 final size:52
Alignment explanation
Indices: 447259--447497 Score: 343
Period size: 52 Copynumber: 4.6 Consensus size: 52
447249 TAAATGAAAA
*
447259 AGGTCCAATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
* * * * * * *
447311 AGGTTCGATGACTATGTGGCATCGTGAATATTTGAATCCCTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
* * **
447363 AGGTTCGATGACTATATGTCATTGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
* * *
447415 AGGTCCAATGACTATGTATCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
447467 AGGTCCGATGACTATGTGTCATCATGAGTAT
1 AGGTCCGATGACTATGTGTCATCATGAGTAT
447498 TAAATGAGAA
Statistics
Matches: 163, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 163 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
Found at i:447538 original size:62 final size:62
Alignment explanation
Indices: 447446--447619 Score: 217
Period size: 62 Copynumber: 2.8 Consensus size: 62
447436 TCATGAGTAT
* * * * *
447446 ATGAATCCT-TTACGGATTATGAGGTCCGATGACTATGTGTCATCATGAGTATTAAATGAGAA
1 ATGAATCCTATTACAGATTA-AAGGTTCGATGACTATGTGTCATCGTGAGTATTAAAAGAGAA
* * *
447508 ATGGATCCTATTATAGATTAAAGGTTCGATGACTTTGTGTCATCGTGAGTATTAAAAGAGAA
1 ATGAATCCTATTACAGATTAAAGGTTCGATGACTATGTGTCATCGTGAGTATTAAAAGAGAA
* * *
447570 ATGAATCCTATTACGGATTTAAGG-TCTGATGACTCTGTGTCATCGTGAGT
1 ATGAATCCTATTACAGATTAAAGGTTC-GATGACTATGTGTCATCGTGAGT
447620 TATCAGATGC
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
61 2 0.02
62 87 0.90
63 8 0.08
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (62 bp):
ATGAATCCTATTACAGATTAAAGGTTCGATGACTATGTGTCATCGTGAGTATTAAAAGAGAA
Found at i:455241 original size:20 final size:21
Alignment explanation
Indices: 455216--455254 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
455206 GTAAGGAATT
455216 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
455236 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
455255 TAACAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:471649 original size:19 final size:19
Alignment explanation
Indices: 471589--471651 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
471579 TATATTGAAT
*
471589 TGGCTCATAAGAGCAATAC
1 TGGCTCGTAAGAGCAATAC
* * * *
471608 TAGCTTGTAAGAGTAACAC
1 TGGCTCGTAAGAGCAATAC
*
471627 TGGCTCGTAAGAGCAATAT
1 TGGCTCGTAAGAGCAATAC
471646 TGGCTC
1 TGGCTC
471652 ACAAGAGCGT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (19 bp):
TGGCTCGTAAGAGCAATAC
Found at i:471872 original size:35 final size:36
Alignment explanation
Indices: 471762--471882 Score: 131
Period size: 36 Copynumber: 3.4 Consensus size: 36
471752 ATTATTATTG
* * * *
471762 GGAATCTTGAAGAACTAGTATGAG-TTAAATTTACT-
1 GGAAACTTGAAGAGCTCGTATGAGCTGAAA-TTACTA
* *
471797 GAGAATCTTGAAGAGCTCGTATGAGTTGAAATTACTA
1 G-GAAACTTGAAGAGCTCGTATGAGCTGAAATTACTA
* *
471834 GGAAACTTGAAGGGCTCGTATGAGCTG-AATTATTA
1 GGAAACTTGAAGAGCTCGTATGAGCTGAAATTACTA
471869 GGAAACTTGAAGAG
1 GGAAACTTGAAGAG
471883 ATCATTGAGA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 21 0.28
36 49 0.65
37 5 0.07
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (36 bp):
GGAAACTTGAAGAGCTCGTATGAGCTGAAATTACTA
Found at i:482894 original size:40 final size:40
Alignment explanation
Indices: 482834--483019 Score: 214
Period size: 40 Copynumber: 4.7 Consensus size: 40
482824 TATAAACATG
* * * *
482834 CGGCTTAGCAAGCTTGGAGCCAGTGATGTAATTTAAGCTA
1 CGGCTTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTA
482874 CGGCTTAGCAGGCTTTGAGCC-GTTGATGTGATTCAAGCTA
1 CGGCTTAGCAGGCTTTGAGCCAG-TGATGTGATTCAAGCTA
* *
482914 CGACTTAGCAGGCTTTGAGCCATTGATGTGATTCAAGCTA
1 CGGCTTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTA
* * *
482954 TGGCTTAGTAGGCTTTGA-CCTGGTGATGTGATTCAAGCTA
1 CGGCTTAGCAGGCTTTGAGCC-AGTGATGTGATTCAAGCTA
* * * * *
482994 CGACTTAACAAGCTTTAAGCCGGTGA
1 CGGCTTAGCAGGCTTTGAGCCAGTGA
483020 GAAGATTTAG
Statistics
Matches: 125, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
39 3 0.02
40 120 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (40 bp):
CGGCTTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTA
Found at i:482970 original size:80 final size:80
Alignment explanation
Indices: 482837--483019 Score: 251
Period size: 80 Copynumber: 2.3 Consensus size: 80
482827 AAACATGCGG
* * *
482837 CTTAGCAAGCTTGGAGCCAGTGATGTAATTTAAGCTACGGCTTAGCAGGCTTTGAGCC-GTTGAT
1 CTTAGCAAGCTTTGAGCCAGTGATGTAATTCAAGCTACGGCTTAGCAGGCTTTGA-CCTGGTGAT
482901 GTGATTCAAGCTACGA
65 GTGATTCAAGCTACGA
* * * * *
482917 CTTAGCAGGCTTTGAGCCATTGATGTGATTCAAGCTATGGCTTAGTAGGCTTTGACCTGGTGATG
1 CTTAGCAAGCTTTGAGCCAGTGATGTAATTCAAGCTACGGCTTAGCAGGCTTTGACCTGGTGATG
482982 TGATTCAAGCTACGA
66 TGATTCAAGCTACGA
* * *
482997 CTTAACAAGCTTTAAGCCGGTGA
1 CTTAGCAAGCTTTGAGCCAGTGA
483020 GAAGATTTAG
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 2 0.02
80 87 0.98
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (80 bp):
CTTAGCAAGCTTTGAGCCAGTGATGTAATTCAAGCTACGGCTTAGCAGGCTTTGACCTGGTGATG
TGATTCAAGCTACGA
Found at i:483045 original size:80 final size:80
Alignment explanation
Indices: 482837--483057 Score: 189
Period size: 80 Copynumber: 2.8 Consensus size: 80
482827 AAACATGCGG
* ** * * * * * *
482837 CTTAGCAAGCTTGGAGCCAGTGATGTA-ATTTAAGCTACGGCTTAGCAGGCTTTGAGCCGTTGAT
1 CTTAACAAGCTTTAAGCCAGTGATG-AGATTCAAGCTATGACCTAGTAGGCTTTGAGCCGGTGAT
482901 GTGATTCAAGCTACGA
65 GTGATTCAAGCTACGA
* * * * * * *
482917 CTTAGCAGGCTTTGAGCCATTGATGTGATTCAAGCTATGGCTTAGTAGGCTTTGA-CCTGGTGAT
1 CTTAACAAGCTTTAAGCCAGTGATGAGATTCAAGCTATGACCTAGTAGGCTTTGAGCC-GGTGAT
482981 GTGATTCAAGCTACGA
65 GTGATTCAAGCTACGA
* * * * * *
482997 CTTAACAAGCTTTAAGCCGGTGA-GAAGATTTAGGTTATGACCTGGTAGGCATT-AGCCGGTG
1 CTTAACAAGCTTTAAGCCAGTGATG-AGATTCAAGCTATGACCTAGTAGGCTTTGAGCCGGTG
483058 TAATTGTATT
Statistics
Matches: 116, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
79 8 0.07
80 108 0.93
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (80 bp):
CTTAACAAGCTTTAAGCCAGTGATGAGATTCAAGCTATGACCTAGTAGGCTTTGAGCCGGTGATG
TGATTCAAGCTACGA
Found at i:486372 original size:16 final size:16
Alignment explanation
Indices: 486355--486384 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
486345 CCATACTTTA
486355 AAAT-TTTATTTATTT
1 AAATGTTTATTTATTT
486370 AAATGTTTATTTATT
1 AAATGTTTATTTATT
486385 GTTGCTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
AAATGTTTATTTATTT
Found at i:489156 original size:40 final size:40
Alignment explanation
Indices: 489093--489264 Score: 238
Period size: 40 Copynumber: 4.3 Consensus size: 40
489083 CTTACGCGGT
* * * * *
489093 TTAGCAGGTTTTCAGCCGGTGATGTAATTCAAGCTACGAT
1 TTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGAC
*
489133 TTAGCAGGCTTTGAGCCATTGATGTGATTCAAGCTACGAC
1 TTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGAC
*
489173 TTAGCAGGCTTTGAGCCAGTGATATGATTCAAGCTAC-AGC
1 TTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGA-C
* * *
489213 TTAGCAAGCTTTGAGCCAGTGATGTGATTCAAGCTATGGC
1 TTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGAC
489253 TTAGCAGGCTTT
1 TTAGCAGGCTTT
489265 AAGTCGGTAA
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.01
40 116 0.99
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (40 bp):
TTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGAC
Found at i:489282 original size:40 final size:40
Alignment explanation
Indices: 489119--489283 Score: 163
Period size: 40 Copynumber: 4.1 Consensus size: 40
489109 CGGTGATGTA
** * *
489119 ATTCAAGCTACGATTTAGCAGGCTTTGAGCCATTGATG-TG
1 ATTCAAGCTACGGCTTAGCAGGCTTTGAGCCAGT-AAGATG
* * *
489159 ATTCAAGCTACGACTTAGCAGGCTTTGAGCCAGTGATATG
1 ATTCAAGCTACGGCTTAGCAGGCTTTGAGCCAGTAAGATG
* * *
489199 ATTCAAGCTACAGCTTAGCAAGCTTTGAGCCAGTGATG-TG
1 ATTCAAGCTACGGCTTAGCAGGCTTTGAGCCAGT-AAGATG
* * * * *
489239 ATTCAAGCTATGGCTTAGCAGGCTTTAAGTCGGTAAGAAG
1 ATTCAAGCTACGGCTTAGCAGGCTTTGAGCCAGTAAGATG
489279 ATTCA
1 ATTCA
489284 GGTTATGACT
Statistics
Matches: 103, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 2 0.02
40 101 0.98
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (40 bp):
ATTCAAGCTACGGCTTAGCAGGCTTTGAGCCAGTAAGATG
Found at i:489304 original size:80 final size:80
Alignment explanation
Indices: 489119--489283 Score: 215
Period size: 80 Copynumber: 2.1 Consensus size: 80
489109 CGGTGATGTA
* *
489119 ATTCAAGCTAC-GATTTAGCAGGCTTTGAGCCATTGATGTGATTCAAGCTACGACTTAGCAGGCT
1 ATTCAAGCTACAG-CTTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGACTTAGCAGGCT
* * * *
489183 TTGAGCCAGTGATATG
65 TTAAGCCAGTAAGAAG
* * *
489199 ATTCAAGCTACAGCTTAGCAAGCTTTGAGCCAGTGATGTGATTCAAGCTATGGCTTAGCAGGCTT
1 ATTCAAGCTACAGCTTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGACTTAGCAGGCTT
* *
489264 TAAGTCGGTAAGAAG
66 TAAGCCAGTAAGAAG
489279 ATTCA
1 ATTCA
489284 GGTTATGACT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 72 0.99
81 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (80 bp):
ATTCAAGCTACAGCTTAGCAGGCTTTGAGCCAGTGATGTGATTCAAGCTACGACTTAGCAGGCTT
TAAGCCAGTAAGAAG
Found at i:497040 original size:27 final size:26
Alignment explanation
Indices: 496986--497162 Score: 159
Period size: 25 Copynumber: 6.8 Consensus size: 26
496976 TAAGGAGTAA
496986 TCTGATTCTGGCTCG-AAGAAGC-ATTAT
1 TCTGA-TCTGGCTCGTAAG-AGCGA-TAT
497013 TCTGATACTGGCTCGTAAGAGCGATAT
1 TCTGAT-CTGGCTCGTAAGAGCGATAT
* *
497040 TTTGATTCTGACTCGTAAGAGCGATAT
1 TCTGA-TCTGGCTCGTAAGAGCGATAT
* *
497067 TCTGA-CTGTCTCGTAAGAGTGATAT
1 TCTGATCTGGCTCGTAAGAGCGATAT
* * *
497092 TCT-ATTTGGCTCATAAGAGCAATAT
1 TCTGATCTGGCTCGTAAGAGCGATAT
* * *
497117 TCTG-TCTAGCTCGTAAAATCGATAT
1 TCTGATCTGGCTCGTAAGAGCGATAT
*
497142 TCTG-TCTGGGCTCGTATGAGC
1 TCTGATCT-GGCTCGTAAGAGC
497163 TAAATTTCTA
Statistics
Matches: 123, Mismatches: 20, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
24 1 0.01
25 61 0.50
26 10 0.08
27 46 0.37
28 5 0.04
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (26 bp):
TCTGATCTGGCTCGTAAGAGCGATAT
Found at i:498534 original size:35 final size:35
Alignment explanation
Indices: 498493--498594 Score: 96
Period size: 40 Copynumber: 2.8 Consensus size: 35
498483 TATTGGTCGA
498493 TTTATCCGACTAGAGCTGGGCGCAAACATCATTGG
1 TTTATCCGACTAGAGCTGGGCGCAAACATCATTGG
* * * * *
498528 TTTATCCTACTAGAGTTGGGCTCACATTTAATATCGTTGG
1 TTTATCCGACTAGAGCTGGG--CGCA---AACATCATTGG
* *
498568 TTTAACCGACTAGCGCTGGGCGCAAAC
1 TTTATCCGACTAGAGCTGGGCGCAAAC
498595 TCTTTCGCGG
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
35 20 0.39
37 3 0.06
38 3 0.06
40 25 0.49
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.29
Consensus pattern (35 bp):
TTTATCCGACTAGAGCTGGGCGCAAACATCATTGG
Found at i:501134 original size:25 final size:25
Alignment explanation
Indices: 501106--501174 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 25
501096 GGCTTTTCGG
* *
501106 ATAATTCACCACAAGGGCTTTACAA
1 ATAACTCACCACAAAGGCTTTACAA
* *
501131 ATAACTCGCCACAAAGGCTTTACAT
1 ATAACTCACCACAAAGGCTTTACAA
* *
501156 AGAACTCGCCACAAAGGCT
1 ATAACTCACCACAAAGGCT
501175 CCAATTGGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (25 bp):
ATAACTCACCACAAAGGCTTTACAA
Found at i:501449 original size:45 final size:45
Alignment explanation
Indices: 501399--501486 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
501389 TGGTGGACTA
* * **
501399 CATTTTCGCCATATTGACCTTCGAGTTTACTATTTCAACGAATTG
1 CATTTTCACCATATTGACCTTCAAGTTTACTATCCCAACGAATTG
* *
501444 CATTTTCACCATATTTACCTTCAAGTTTATTATCCCAACGAAT
1 CATTTTCACCATATTGACCTTCAAGTTTACTATCCCAACGAAT
501487 GTCATCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (45 bp):
CATTTTCACCATATTGACCTTCAAGTTTACTATCCCAACGAATTG
Found at i:501833 original size:14 final size:16
Alignment explanation
Indices: 501803--501834 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
501793 CTACAGGGAC
501803 ATCAACCATACAAATA
1 ATCAACCATACAAATA
501819 ATCAA-CATA-AAATA
1 ATCAACCATACAAATA
501833 AT
1 AT
501835 AGTCAAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (16 bp):
ATCAACCATACAAATA
Found at i:510040 original size:7 final size:7
Alignment explanation
Indices: 510028--510053 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
510018 ATTTCACCCA
510028 TTGACTG
1 TTGACTG
510035 TTGACTG
1 TTGACTG
510042 TTGACTG
1 TTGACTG
510049 TTGAC
1 TTGAC
510054 CATTGACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (7 bp):
TTGACTG
Found at i:510059 original size:14 final size:14
Alignment explanation
Indices: 510025--510060 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
510015 TGAATTTCAC
510025 CCATTGACTGTTGA
1 CCATTGACTGTTGA
**
510039 CTGTTGACTGTTGA
1 CCATTGACTGTTGA
510053 CCATTGAC
1 CCATTGAC
510061 CATTGACTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (14 bp):
CCATTGACTGTTGA
Found at i:510092 original size:20 final size:20
Alignment explanation
Indices: 510055--510091 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
510045 ACTGTTGACC
510055 ATTGACCATTGACTTTTTCT
1 ATTGACCATTGACTTTTTCT
510075 ATTGACCATTGA-TTTTT
1 ATTGACCATTGACTTTTT
510092 TTTTGGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (20 bp):
ATTGACCATTGACTTTTTCT
Found at i:512564 original size:22 final size:22
Alignment explanation
Indices: 512533--512579 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
512523 GCTCAAGATA
512533 GGGAGCGAGGTAGGAAGCAACC
1 GGGAGCGAGGTAGGAAGCAACC
*
512555 GGGAGTGAGGTAGGAAGCAACC
1 GGGAGCGAGGTAGGAAGCAACC
512577 GGG
1 GGG
512580 CTCAATAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.49, T:0.06
Consensus pattern (22 bp):
GGGAGCGAGGTAGGAAGCAACC
Found at i:513962 original size:22 final size:22
Alignment explanation
Indices: 513937--513982 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
513927 GCCCAACTTT
513937 AACCCTTAACCCAATCTAACCC
1 AACCCTTAACCCAATCTAACCC
*
513959 AACCCTTGACCCAATCTAACCC
1 AACCCTTAACCCAATCTAACCC
513981 AA
1 AA
513983 TTCGACTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.43, G:0.02, T:0.17
Consensus pattern (22 bp):
AACCCTTAACCCAATCTAACCC
Found at i:514039 original size:27 final size:26
Alignment explanation
Indices: 514009--514101 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 26
513999 CTGATTTAAT
*
514009 CATTGACTTTGACTCGTTGACACGACC
1 CATTGACTTTGACTCATTGAC-CGACC
*
514036 CATTCACTTTGAACT-ATTGACCTGACC
1 CATTGACTTTG-ACTCATTGACC-GACC
* * *
514063 CGTTGACTTTGACCCATTGACTCGACT
1 CATTGACTTTGACTCATTGAC-CGACC
514090 CATTGACTTTGA
1 CATTGACTTTGA
514102 TCTCGACCTG
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
26 3 0.05
27 48 0.87
28 4 0.07
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (26 bp):
CATTGACTTTGACTCATTGACCGACC
Found at i:514077 original size:14 final size:14
Alignment explanation
Indices: 514009--514101 Score: 66
Period size: 13 Copynumber: 6.9 Consensus size: 14
513999 CTGATTTAAT
*
514009 CATTGACTTTGACT
1 CATTGACTTTGACC
* **
514023 CGTTGAC-ACGACC
1 CATTGACTTTGACC
* *
514036 CATTCACTTTGAAC
1 CATTGACTTTGACC
* *
514050 TATTGAC-CTGACC
1 CATTGACTTTGACC
*
514063 CGTTGACTTTGACC
1 CATTGACTTTGACC
* *
514077 CATTGAC-TCGACT
1 CATTGACTTTGACC
514090 CATTGACTTTGA
1 CATTGACTTTGA
514102 TCTCGACCTG
Statistics
Matches: 56, Mismatches: 20, Indels: 6
0.68 0.24 0.07
Matches are distributed among these distances:
13 28 0.50
14 28 0.50
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (14 bp):
CATTGACTTTGACC
Found at i:514134 original size:20 final size:20
Alignment explanation
Indices: 514111--514148 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
514101 ATCTCGACCT
514111 GTTGACCGTCGACTTTTTCC
1 GTTGACCGTCGACTTTTTCC
* *
514131 GTTGATCGTTGACTTTTT
1 GTTGACCGTCGACTTTTT
514149 TCGGGAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (20 bp):
GTTGACCGTCGACTTTTTCC
Found at i:516606 original size:15 final size:16
Alignment explanation
Indices: 516569--516606 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
516559 ATATGAATAC
*
516569 AATTTAGTCTTAGTTT
1 AATTTAGTCTTAATTT
*
516585 AACTTAGT-TTAATTT
1 AATTTAGTCTTAATTT
516600 AATTTAG
1 AATTTAG
516607 ATACTTTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (16 bp):
AATTTAGTCTTAATTT
Found at i:517287 original size:17 final size:18
Alignment explanation
Indices: 517250--517290 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
517240 GTGGGAAATG
*
517250 AATTTTTTTACGATGATTA
1 AATTTATTTACGA-GATTA
517269 AATTTATTTACGA-ATTA
1 AATTTATTTACGAGATTA
517286 AATTT
1 AATTT
517291 TATATCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
19 12 0.57
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (18 bp):
AATTTATTTACGAGATTA
Found at i:518118 original size:24 final size:23
Alignment explanation
Indices: 518091--518160 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
518081 CCATTAACAT
518091 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* * *
518115 TGTTCATAAACATGTTCATTTAA
1 TGTTCGTGAACATGTTCAATTAA
* *
518138 TGTTCGTGAACATATTCGATTAA
1 TGTTCGTGAACATGTTCAATTAA
518161 ATTAAATGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:518187 original size:23 final size:23
Alignment explanation
Indices: 518144--518189 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
518134 TTAATGTTCG
*
518144 TGAACATATTCGATTAAATTAAA
1 TGAACATATTCGATGAAATTAAA
*
518167 TGAACATGTTCG-TGAACATTAAA
1 TGAACATATTCGATGAA-ATTAAA
518190 CAAACAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (23 bp):
TGAACATATTCGATGAAATTAAA
Found at i:520758 original size:27 final size:27
Alignment explanation
Indices: 520723--520847 Score: 105
Period size: 27 Copynumber: 4.7 Consensus size: 27
520713 GTTTGATTGT
* *
520723 GCCATAAAGGCGTTCCTTTATAGATTA
1 GCCAAAAAGGCTTTCCTTTATAGATTA
*
520750 GCCAAAAAGGCTTTCCTTTA-ATA-TA
1 GCCAAAAAGGCTTTCCTTTATAGATTA
* * ** *
520775 TGCCACAAA-GATGACCTTTTATAGAAT-
1 -GCCAAAAAGGCTTTCC-TTTATAGATTA
* *
520802 GCCACAAAGGTTTTCCTTTATAGATTA
1 GCCAAAAAGGCTTTCCTTTATAGATTA
*
520829 GCCAAAAAAGCTTTCCTTT
1 GCCAAAAAGGCTTTCCTTT
520848 CATATATGCC
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
25 6 0.08
26 30 0.39
27 40 0.52
28 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (27 bp):
GCCAAAAAGGCTTTCCTTTATAGATTA
Found at i:520821 original size:26 final size:26
Alignment explanation
Indices: 520722--520863 Score: 101
Period size: 27 Copynumber: 5.4 Consensus size: 26
520712 CGTTTGATTG
* * *
520722 TGCCATAAAGGCGTTCCTTTATAGAT
1 TGCCACAAAGGCTTTCCTTTATAGAA
* *
520748 TAGCCAAAAAGGCTTTCCTTTAATA-TA
1 T-GCCACAAAGGCTTTCCTTT-ATAGAA
* **
520775 TGCCACAAA-GATGACCTTTTATAGAA
1 TGCCACAAAGGCTTTCC-TTTATAGAA
* *
520801 TGCCACAAAGGTTTTCCTTTATAGAT
1 TGCCACAAAGGCTTTCCTTTATAGAA
* * *
520827 TAGCCAAAAAAGCTTTCCTTTCATA-TA
1 T-GCCACAAAGGCTTTCCTTT-ATAGAA
520854 TGCCACAAAG
1 TGCCACAAAG
520864 ACGACCTTTT
Statistics
Matches: 89, Mismatches: 20, Indels: 14
0.72 0.16 0.11
Matches are distributed among these distances:
25 7 0.08
26 37 0.42
27 39 0.44
28 6 0.07
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (26 bp):
TGCCACAAAGGCTTTCCTTTATAGAA
Found at i:520891 original size:79 final size:79
Alignment explanation
Indices: 520735--520897 Score: 281
Period size: 79 Copynumber: 2.1 Consensus size: 79
520725 CATAAAGGCG
* * * *
520735 TTCCTTTATAGATTAGCCAAAAAGGCTTTCCTTTAATATATGCCACAAAGATGACCTTTTATAGA
1 TTCCTTTATAGATTAGCCAAAAAAGCTTTCCTTTAATATATGCCACAAAGACGACCTTTTACAAA
520800 ATGCCACAAAGGTT
66 ATGCCACAAAGGTT
*
520814 TTCCTTTATAGATTAGCCAAAAAAGCTTTCCTTTCATATATGCCACAAAGACGACCTTTTACAAA
1 TTCCTTTATAGATTAGCCAAAAAAGCTTTCCTTTAATATATGCCACAAAGACGACCTTTTACAAA
520879 ATGCCACAAAGGTT
66 ATGCCACAAAGGTT
520893 TTCCT
1 TTCCT
520898 ATTAAGAGTT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (79 bp):
TTCCTTTATAGATTAGCCAAAAAAGCTTTCCTTTAATATATGCCACAAAGACGACCTTTTACAAA
ATGCCACAAAGGTT
Found at i:529406 original size:21 final size:21
Alignment explanation
Indices: 529380--529421 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
529370 TAAACAATGA
529380 CAAAAAGTATCAATACCTTTT
1 CAAAAAGTATCAATACCTTTT
*
529401 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTATCAATACCTTTT
529422 ATTAAATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (21 bp):
CAAAAAGTATCAATACCTTTT
Found at i:531727 original size:22 final size:22
Alignment explanation
Indices: 531699--531741 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
531689 TATTATTTGC
*
531699 ATTATTTAATTT-TTATTTATTA
1 ATTATTT-ATTTGTGATTTATTA
531721 ATTATTTATTTGTGATTTATT
1 ATTATTTATTTGTGATTTATT
531742 TTTTTACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
ATTATTTATTTGTGATTTATTA
Found at i:539016 original size:21 final size:21
Alignment explanation
Indices: 538977--539016 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
538967 CATGAAGGTT
* *
538977 TTGAGAAAGTTGTTCTTGAGA
1 TTGAGAAAGTTCTACTTGAGA
*
538998 TTGAGAAAGTTCTAGTTGA
1 TTGAGAAAGTTCTACTTGA
539017 ATTTCAACCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.38
Consensus pattern (21 bp):
TTGAGAAAGTTCTACTTGAGA
Found at i:542846 original size:49 final size:49
Alignment explanation
Indices: 542653--543545 Score: 288
Period size: 49 Copynumber: 18.2 Consensus size: 49
542643 ATCCTAAAGT
* * * * * *
542653 TGAAGAGGGATAGGTTGAAGTTGCAACGATGGACCTAACACCCTAAAAC
1 TGAAGAGGGATAAGTTGAAGTCGTAACGGTAGACTTAACACCCTAAAAC
** * * *
542702 CAAAGAGGGGTAAATTGAAG-CTGTAATGGTAGA-TCTAACACCCTAAAAC
1 TGAAGAGGGATAAGTTGAAGTC-GTAACGGTAGACT-TAACACCCTAAAAC
* * * * * * * *
542751 TGAAGAAGGA-AAATTAAAGCCGCAATGGTGGATCTT-ACACCTTAAAAC
1 TGAAGAGGGATAAGTTGAAGTCGTAACGGTAGA-CTTAACACCCTAAAAC
*
542799 TGAAGAGGGATAAGTTAAAGTCGTAACGGTAGACTTAACACCCTAAAA-
1 TGAAGAGGGATAAGTTGAAGTCGTAACGGTAGACTTAACACCCTAAAAC
* * * * * **
542847 TAAATGAGGGA-AAGTTTGAAGTCGCAA-TGTTGACTTTTACACTTTAAAA-
1 TGAA-GAGGGATAAG-TTGAAGTCGTAACGGTAGAC-TTAACACCCTAAAAC
* * *
542896 TCGAAGAGGGATAGGTTGAAGTTGCAGTAGC-G-A-ACTTAACACCATAAAA-
1 T-GAAGAGGGATAAGTTGAAG-T-C-GTAACGGTAGACTTAACACCCTAAAAC
* * **
542945 TCGAAGAGGGAT-AGATTGAAGCCATAACGGT-GGGTCTAACACCCTAAAAC
1 T-GAAGAGGGATAAG-TTGAAGTCGTAACGGTAGACT-TAACACCCTAAAAC
** * * * * *
542995 CAAAAAGGGA-AAGATTAAAGTCATAACGATAGATCTT-ACACCTTAAAAC
1 TGAAGAGGGATAAG-TTGAAGTCGTAACGGTAGA-CTTAACACCCTAAAAC
* * * * * *
543044 TGAAGAGGGAT-AGTTAAAGCCGTAATGGTAGACCTAACACCTTTAAA-
1 TGAAGAGGGATAAGTTGAAGTCGTAACGGTAGACTTAACACCCTAAAAC
* * * *
543091 TCGAAGAGGGAT-AGATTAAAGTCATAATGGCAGA-TCTAACACCCTAAAAC
1 T-GAAGAGGGATAAG-TTGAAGTCGTAACGGTAGACT-TAACACCCTAAAAC
* * * * **
543141 TGAAGAGGGA-AAGATTGAAGTCGTAACGATAAATTTTACACTTTAAAA-
1 TGAAGAGGGATAAG-TTGAAGTCGTAACGGTAGACTTAACACCCTAAAAC
* * *** * *
543189 TCGAAGAGGGATAGGTTGAAGTCGTAATGACGGACCTAATACCCTAAAA-
1 T-GAAGAGGGATAAGTTGAAGTCGTAACGGTAGACTTAACACCCTAAAAC
* * * ** ***
543238 TCAAATAGGGAT-AGATTGAAGCCACAACGACGGA-TCTAACACCCCT-AAAC
1 T-GAAGAGGGATAAG-TTGAAGTCGTAACGGTAGACT-TAACA-CCCTAAAAC
** * * * * * * *
543288 CAAATAGGGAAAATATTGAAGTCGCAATGGTGGATCTT-ACACCTTAAAAC
1 TGAAGAGGGATAA-GTTGAAGTCGTAACGGTAGA-CTTAACACCCTAAAAC
* * * * *
543338 TGAAGAGGGATAGGTTGAAGCCGTAACGGTGGACCTAACACTCTAAAA-
1 TGAAGAGGGATAAGTTGAAGTCGTAACGGTAGACTTAACACCCTAAAAC
* * * * * *
543386 TCGAAGACGGATATGTTAAAGTCATAACGATAGA-TCTAATACCCTAAAAC
1 T-GAAGAGGGATAAGTTGAAGTCGTAACGGTAGACT-TAACACCCTAAAAC
** * * * * *
543436 CAAAGAGGAAAAAATTGAAG-CTGCAACGGT-GAATCTT-ACACCTTAAAA-
1 TGAAGAGGGATAAGTTGAAGTC-GTAACGGTAG-A-CTTAACACCCTAAAAC
* * * * * *
543484 TCGAAGAGGGATAGGTGGAAGTCGCAACGGT-GAACATAACAACTTAAAAC
1 T-GAAGAGGGATAAGTTGAAGTCGTAACGGTAG-ACTTAACACCCTAAAAC
**
543534 CAAAGAGGGATA
1 TGAAGAGGGATA
543546 GATTGTAGCC
Statistics
Matches: 631, Mismatches: 157, Indels: 112
0.70 0.17 0.12
Matches are distributed among these distances:
46 3 0.00
47 5 0.01
48 99 0.16
49 466 0.74
50 50 0.08
51 4 0.01
52 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.21
Consensus pattern (49 bp):
TGAAGAGGGATAAGTTGAAGTCGTAACGGTAGACTTAACACCCTAAAAC
Found at i:542986 original size:147 final size:145
Alignment explanation
Indices: 542787--543603 Score: 677
Period size: 147 Copynumber: 5.6 Consensus size: 145
542777 GGTGGATCTT
* * * * *
542787 ACACCTTAAAA-CTGAAGAGGGATA-AGTTAAAGTCGTAACGGTAGA-CTTAACACCCTAAAA-T
1 ACACCTTAAAATC-GAAGAGGGATAGA-TTGAAGCCATAACGGTGGATC-TAACACCCTAAAACC
* * * *
542848 AAATGAGGGAAAGTTTGAAGTCGCAATGTTGACTTTTACACTTTAAAATCGAAGAGGGATAGGTT
63 AAA-GAGGGAAAGATTGAAGTCGCAACGTTGA-TCTTACACCTTAAAATCGAAGAGGGATAGGTT
* * * *
542913 GAAGTTGCAGTAGCGAACTTA
126 GAAGTCGTAAT-GCGAACCTA
* *
542934 ACACCATAAAATCGAAGAGGGATAGATTGAAGCCATAACGGTGGGTCTAACACCCTAAAACCAAA
1 ACACCTTAAAATCGAAGAGGGATAGATTGAAGCCATAACGGTGGATCTAACACCCTAAAACCAAA
* * ** * *
542999 AAGGGAAAGATTAAAGTCATAACGATAGATCTTACACCTTAAAA-CTGAAGAGGGATA-GTTAAA
66 GAGGGAAAGATTGAAGTCGCAACG-TTGATCTTACACCTTAAAATC-GAAGAGGGATAGGTTGAA
*
543062 GCCGTAATG-GTAGACCTA
129 GTCGTAATGCG-A-ACCTA
* * * * ** **
543080 ACACCTTTAAATCGAAGAGGGATAGATTAAAGTCATAATGGCAGATCTAACACCCTAAAACTGAA
1 ACACCTTAAAATCGAAGAGGGATAGATTGAAGCCATAACGGTGGATCTAACACCCTAAAACCAAA
* ** * *
543145 GAGGGAAAGATTGAAGTCGTAACGATAAATTTTACACTTTAAAATCGAAGAGGGATAGGTTGAAG
66 GAGGGAAAGATTGAAGTCGCAACG-TTGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAG
*
543210 TCGTAATGACGGACCTA
130 TCGTAATG-CGAACCTA
* * * * * **
543227 ATACCCTAAAATCAAATAGGGATAGATTGAAGCCACAACGACGGATCTAACACCCCT-AAACCAA
1 ACACCTTAAAATCGAAGAGGGATAGATTGAAGCCATAACGGTGGATCTAACA-CCCTAAAACCAA
* * * *
543291 ATAGGGAAAATATTGAAGTCGCAATGGTGGATCTTACACCTTAAAA-CTGAAGAGGGATAGGTTG
65 AGAGGG-AAAGATTGAAGTCGCAA-CGTTGATCTTACACCTTAAAATC-GAAGAGGGATAGGTTG
* * * *
543355 AAGCCGTAACGGTGGACCTA
127 AAGTCGTAA-TGCGAACCTA
* * * * * *
543375 ACA-CTCTAAAATCGAAGACGGATATG-TTAAAGTCATAACGATAGATCTAATACCCTAAAACCA
1 ACACCT-TAAAATCGAAGAGGGATA-GATTGAAGCCATAACGGTGGATCTAACACCCTAAAACCA
* * * *
543438 AAGAGGAAAAAATTGAAG-CTGCAACGGTGAATCTTACACCTTAAAATCGAAGAGGGATAGGTGG
64 AAGAGGGAAAGATTGAAGTC-GCAACGTTG-ATCTTACACCTTAAAATCGAAGAGGGATAGGTTG
* * * *
543502 AAGTCGCAACGGTGAACATA
127 AAGTCGTAA-TGCGAACCTA
* * * * * * **
543522 ACAACTTAAAACCAAAGAGGGATAGATTGTAGCCACAACAGTGGATCTAACACCCTAAAATTAAA
1 ACACCTTAAAATCGAAGAGGGATAGATTGAAGCCATAACGGTGGATCTAACACCCTAAAACCAAA
*
543587 GAGGGAACATATTGAAG
66 GAGGGAA-AGATTGAAG
543604 CCGCTATGGC
Statistics
Matches: 542, Mismatches: 102, Indels: 51
0.78 0.15 0.07
Matches are distributed among these distances:
144 1 0.00
145 2 0.00
146 122 0.23
147 280 0.52
148 133 0.25
149 4 0.01
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (145 bp):
ACACCTTAAAATCGAAGAGGGATAGATTGAAGCCATAACGGTGGATCTAACACCCTAAAACCAAA
GAGGGAAAGATTGAAGTCGCAACGTTGATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGT
CGTAATGCGAACCTA
Found at i:543148 original size:244 final size:241
Alignment explanation
Indices: 542653--543161 Score: 542
Period size: 244 Copynumber: 2.1 Consensus size: 241
542643 ATCCTAAAGT
* *
542653 TGAAGAGGGATAGGTTGAAGTTGCAACGATGGACCTAACACCCTAAAACCAAAGAGGGGTAAATT
1 TGAAGAGGGATAGGTTGAAGTTGCAACGA--GACCTAACACCATAAAACCAAAGAGGGATAAATT
** * * * * * * *
542718 GAAGCTGTAATGGTAGATCTAACACCCTAAAACTGAAGAAGGAAAATTAAAGCCGCAATGGTGGA
64 GAAGCCATAACGGTAGATCTAACACCCTAAAACTCAAAAAGGAAAATTAAAGCCACAACGATAGA
* *
542783 TCTTACACCTTAAAACTGAAGAGGGATAAGTTAAAGTCGTAACGGTAGACTTAACACCCTAAAAT
129 TCTTACACCTTAAAACTGAAGAGGGATAAGTTAAAGCCGTAACGGTAGACCTAACACCCTAAAAT
* * * ** * * **
542848 AAATGAGGGAAAGTTTGAAGTCGCAATGTTGACTTTTACACTTTAAAA
194 AAATGAGGGAAAGATTAAAGTCACAATGCAGACTCTAACACCCTAAAA
* * * *
542896 TCGAAGAGGGATAGGTTGAAGTTGCAGTAGCGA-ACTTAACACCATAAAATCGAAGAGGGATAGA
1 T-GAAGAGGGATAGGTTGAAGTTGCA--A-CGAGACCTAACACCATAAAACCAAAGAGGGATAAA
* * * *
542960 TTGAAGCCATAACGGTGGGTCTAACACCCTAAAAC-CAAAAAGGGAAAGATTAAAGTCATAACGA
62 TTGAAGCCATAACGGTAGATCTAACACCCTAAAACTCAAAAA-GGAAA-ATTAAAGCCACAACGA
* * *
543024 TAGATCTTACACCTTAAAACTGAAGAGGGAT-AGTTAAAGCCGTAATGGTAGACCTAACACCTTT
125 TAGATCTTACACCTTAAAACTGAAGAGGGATAAGTTAAAGCCGTAACGGTAGACCTAACACCCTA
* * *
543088 AAATCGAA-GAGGGATAGATTAAAGTCATAATGGCAGA-TCTAACACCCTAAAA
190 AAAT-AAATGAGGGAAAGATTAAAGTCACAAT-GCAGACTCTAACACCCTAAAA
* *
543140 CTGAAGAGGGAAAGATTGAAGT
1 -TGAAGAGGGATAGGTTGAAGT
543162 CGTAACGATA
Statistics
Matches: 219, Mismatches: 38, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
243 5 0.02
244 163 0.74
245 47 0.21
246 1 0.00
247 3 0.01
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (241 bp):
TGAAGAGGGATAGGTTGAAGTTGCAACGAGACCTAACACCATAAAACCAAAGAGGGATAAATTGA
AGCCATAACGGTAGATCTAACACCCTAAAACTCAAAAAGGAAAATTAAAGCCACAACGATAGATC
TTACACCTTAAAACTGAAGAGGGATAAGTTAAAGCCGTAACGGTAGACCTAACACCCTAAAATAA
ATGAGGGAAAGATTAAAGTCACAATGCAGACTCTAACACCCTAAAA
Found at i:543575 original size:98 final size:98
Alignment explanation
Indices: 542655--543592 Score: 444
Period size: 98 Copynumber: 9.6 Consensus size: 98
542645 CCTAAAGTTG
* *** * * * * * * **
542655 AAGAGGGATAGGTTGAAGTTGCAACGATGGACCTAACACCCTAAAACCAAAGAGGGGTAAATTGA
1 AAGAGGGATAGATTGAAGCCACAACGGTGGATCTAACACCTTAAAATCGAAGAGGGATAGGTTGA
* * * * **
542720 AG-CTGTAATGGTAGATCTAACACCCTAAAACTG
66 AGTC-GCAACGATAGAACTAACACCCTAAAACCA
* * * * * * * *
542753 AAGAAGGA-AAATTAAAGCCGCAATGGTGGATCTTACACCTTAAAA-CTGAAGAGGGATAAGTTA
1 AAGAGGGATAGATTGAAGCCACAACGGTGGATCTAACACCTTAAAATC-GAAGAGGGATAGGTTG
* * *
542816 AAGTCGTAACGGTAG-ACTTAACACCCTAAAA-TA
65 AAGTCGCAACGATAGAAC-TAACACCCTAAAACCA
* * * * * * * * *
542849 AATGAGGGAAAGTTTGAAGTCGCAA-TGTTGACTTTTACACTTTAAAATCGAAGAGGGATAGGTT
1 AA-GAGGGATAGATTGAAGCCACAACGGTGGA-TCTAACACCTTAAAATCGAAGAGGGATAGGTT
* * * *
542913 GAAGTTGC-A-G-TAGCGAACTTAACACCATAAAATCG
64 GAAGTCGCAACGATA--GAAC-TAACACCCTAAAACCA
* * * * * * * * *
542948 AAGAGGGATAGATTGAAGCCATAACGGTGGGTCTAACACCCTAAAACCAAAAAGGGAAAGATTAA
1 AAGAGGGATAGATTGAAGCCACAACGGTGGATCTAACACCTTAAAATCGAAGAGGGATAGGTTGA
** * * * **
543013 AGTCATAACGATAGATCTTACACCTTAAAACTG
66 AGTCGCAACGATAGAACTAACACCCTAAAACCA
* ** * * * * * *
543046 AAGAGGGATAG-TTAAAGCCGTAATGGTAGACCTAACACCTTTAAATCGAAGAGGGATAGATTAA
1 AAGAGGGATAGATTGAAGCCACAACGGTGGATCTAACACCTTAAAATCGAAGAGGGATAGGTTGA
** * ** * **
543110 AGTCATAATGGCAGATCTAACACCCTAAAACTG
66 AGTCGCAACGATAGAACTAACACCCTAAAACCA
* * ** * ** * * *
543143 AAGAGGGAAAGATTGAAGTCGTAACGATAAATTTTACACTTTAAAATCGAAGAGGGATAGGTTGA
1 AAGAGGGATAGATTGAAGCCACAACGGTGGATCTAACACCTTAAAATCGAAGAGGGATAGGTTGA
* * ** * * *
543208 AGTCGTAATGACGGACCTAATACCCTAAAATCA
66 AGTCGCAACGATAGAACTAACACCCTAAAACCA
* ** * * * * * **
543241 AATAGGGATAGATTGAAGCCACAACGACGGATCTAACACCCCT-AAACCAAATAGGGAAAATATT
1 AAGAGGGATAGATTGAAGCCACAACGGTGGATCTAACA-CCTTAAAATCGAAGAGGG-ATAGGTT
* * * * * * **
543305 GAAGTCGCAATGGTGGATCTTACACCTTAAAACTG
64 GAAGTCGCAACGATAGAACTAACACCCTAAAACCA
* ** * * * *
543340 AAGAGGGATAGGTTGAAGCCGTAACGGTGGACCTAACA-CTCTAAAATCGAAGACGGATATGTTA
1 AAGAGGGATAGATTGAAGCCACAACGGTGGATCTAACACCT-TAAAATCGAAGAGGGATAGGTTG
** * *
543404 AAGTCATAACGATAGATCTAATACCCTAAAACCA
65 AAGTCGCAACGATAGAACTAACACCCTAAAACCA
* * * ** * * *
543438 AAGAGGAAAAAATTGAAGCTGCAACGGTGAATCTTACACCTTAAAATCGAAGAGGGATAGGTGGA
1 AAGAGGGATAGATTGAAGCCACAACGGTGGATCTAACACCTTAAAATCGAAGAGGGATAGGTTGA
* * *
543503 AGTCGCAACGGT-GAACATAACAACTTAAAACCA
66 AGTCGCAACGATAGAAC-TAACACCCTAAAACCA
* * * **
543536 AAGAGGGATAGATTGTAGCCACAACAGTGGATCTAACACCCTAAAATTAAAGAGGGA
1 AAGAGGGATAGATTGAAGCCACAACGGTGGATCTAACACCTTAAAATCGAAGAGGGA
543593 ACATATTGAA
Statistics
Matches: 635, Mismatches: 183, Indels: 44
0.74 0.21 0.05
Matches are distributed among these distances:
95 2 0.00
96 6 0.01
97 158 0.25
98 383 0.60
99 83 0.13
100 1 0.00
101 2 0.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (98 bp):
AAGAGGGATAGATTGAAGCCACAACGGTGGATCTAACACCTTAAAATCGAAGAGGGATAGGTTGA
AGTCGCAACGATAGAACTAACACCCTAAAACCA
Found at i:552579 original size:15 final size:15
Alignment explanation
Indices: 552555--552605 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
552545 ATTTATTGGG
*
552555 TCATCTTTCTTCTCT
1 TCATCCTTCTTCTCT
552570 TCATCCTTCTTCTCT
1 TCATCCTTCTTCTCT
552585 TC-T--TTCTTCTCT
1 TCATCCTTCTTCTCT
*
552597 TCTTCCTTC
1 TCATCCTTC
552606 CCTTCCTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 11 0.34
13 1 0.03
14 1 0.03
15 19 0.59
ACGTcount: A:0.04, C:0.37, G:0.00, T:0.59
Consensus pattern (15 bp):
TCATCCTTCTTCTCT
Found at i:552591 original size:12 final size:12
Alignment explanation
Indices: 552558--552610 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
552548 TATTGGGTCA
552558 TCTTTCTTCTCT
1 TCTTTCTTCTCT
552570 TCATCCTTCTTCTCT
1 TC-T--TTCTTCTCT
552585 TCTTTCTTCTCT
1 TCTTTCTTCTCT
* *
552597 TCTTCCTTCCCT
1 TCTTTCTTCTCT
552609 TC
1 TC
552611 CTCACTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
12 23 0.64
13 1 0.03
14 1 0.03
15 11 0.31
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTTTCTTCTCT
Found at i:559826 original size:23 final size:22
Alignment explanation
Indices: 559796--559839 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
559786 TAAAAAATAA
*
559796 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
559818 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
559840 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:561888 original size:26 final size:26
Alignment explanation
Indices: 561852--561904 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
561842 ATGCAATGAT
561852 GAAATTAATTGTCAGAGTAATTGTAA
1 GAAATTAATTGTCAGAGTAATTGTAA
*
561878 GAAATTAATTGTCGGAGTAATTGTAA
1 GAAATTAATTGTCAGAGTAATTGTAA
561904 G
1 G
561905 TCAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.34
Consensus pattern (26 bp):
GAAATTAATTGTCAGAGTAATTGTAA
Found at i:565097 original size:2 final size:2
Alignment explanation
Indices: 565090--565122 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
565080 ACAGGCCTAC
565090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
565123 GTGTGTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:569370 original size:27 final size:28
Alignment explanation
Indices: 569315--569375 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
569305 AAAATAAAAT
* * *
569315 TTTTGGATACTCAGGGGTAAAATGGTAA
1 TTTTGGACACTCAGGGGGAAAATGATAA
*
569343 TTTTGGACACTC-GGGGGCAAATGATAA
1 TTTTGGACACTCAGGGGGAAAATGATAA
569370 TTTTGG
1 TTTTGG
569376 GAAAGTTCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.33
Consensus pattern (28 bp):
TTTTGGACACTCAGGGGGAAAATGATAA
Found at i:569431 original size:59 final size:57
Alignment explanation
Indices: 569367--569511 Score: 139
Period size: 59 Copynumber: 2.5 Consensus size: 57
569357 GGGCAAATGA
*
569367 TAATTTTGGGAAAGTTCGGGGTCAAAAATAAAATTTTTAAACATTCGAGG-GTAAAATAG
1 TAATTTT-GGAAAATTCGGGGT-AAAAATAAAATTTTTAAACA-TCGAGGTGTAAAATAG
* * * ** * * *
569426 TAATTTTTGAAAATTTTGGGGTTTAAAATGGAATTTTTATACATCTAGGTGTAAAATGG
1 TAATTTTGGAAAA-TTCGGGG-TAAAAATAAAATTTTTAAACATCGAGGTGTAAAATAG
* *
569485 TAATCTTGGAAAAATCGGGGTAAAAAT
1 TAATTTTGGAAAATTCGGGGTAAAAAT
569512 GTAATATTAG
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
57 6 0.09
58 14 0.20
59 48 0.70
60 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (57 bp):
TAATTTTGGAAAATTCGGGGTAAAAATAAAATTTTTAAACATCGAGGTGTAAAATAG
Found at i:569507 original size:28 final size:28
Alignment explanation
Indices: 569471--569554 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 28
569461 TTTATACATC
* *
569471 TAGGTGTAAAATGGTAATCTTGGAAAAA
1 TAGGGGTAAAATGGTAATATTGGAAAAA
* **
569499 TCGGGGTAAAAAT-GTAATATTAGG-AAGT
1 TAGGGGT-AAAATGGTAATATT-GGAAAAA
*
569527 TAGGGGTAAAATGGTAACTTTTGGAAAA
1 TAGGGGTAAAATGGTAA-TATTGGAAAA
569555 CTCGAGATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
27 5 0.12
28 26 0.60
29 12 0.28
ACGTcount: A:0.40, C:0.04, G:0.27, T:0.29
Consensus pattern (28 bp):
TAGGGGTAAAATGGTAATATTGGAAAAA
Found at i:569596 original size:88 final size:86
Alignment explanation
Indices: 569502--569783 Score: 295
Period size: 88 Copynumber: 3.2 Consensus size: 86
569492 GGAAAAATCG
* * * *
569502 GGGTAAAAATGTAA-TATTAGGAAGTTAGGGGTAAAATGGTAACTTTTGGAAAACTCGAGATCAA
1 GGGT-AAAATGTAATTTTTA-GAAGTTAGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAA
*
569566 AAATGGAATTTTTGGGGAGTTCGA
64 AAATGGAATTTTT-GGAAGTTCGA
* * *
569590 GGGTAAAATGGTAATTTTTTAG-AGTTTGGGGTAAAATGGT-ATTTTTGGAAATAT-TAGGGTCA
1 GGGTAAAAT-GTAA-TTTTTAGAAGTTAGGGGTAAAATGGTAATTTTTGGAAAAATCGA-GGTC-
*
569652 AAAAATGGAATTTTTTGAAGTTCGA
62 AAAAATGGAATTTTTGGAAGTTCGA
* * * * *
569677 GGGTAAAGTGATAATTTTTAGAAGTTCGAGGGTAAAATAGTAATTTTTGAAAAAATC-AGGGTTA
1 GGGTAAAATG-TAATTTTTAGAAGTTAG-GGGTAAAATGGTAATTTTTGGAAAAATCGA-GGTCA
*
569741 AAAATAGAATTTTTGGAAGTTCGA
63 AAAATGGAATTTTTGGAAGTTCGA
569765 GGGTAAAAATGTAATTTTT
1 GGGT-AAAATGTAATTTTT
569784 GGAAAAATCA
Statistics
Matches: 165, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
86 9 0.05
87 43 0.26
88 86 0.52
89 23 0.14
90 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.34
Consensus pattern (86 bp):
GGGTAAAATGTAATTTTTAGAAGTTAGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAA
ATGGAATTTTTGGAAGTTCGA
Found at i:569598 original size:29 final size:28
Alignment explanation
Indices: 569565--569787 Score: 157
Period size: 29 Copynumber: 7.6 Consensus size: 28
569555 CTCGAGATCA
*
569565 AAAATGGAATTTTTGGGGAGTTCGAGGGT
1 AAAATGGAATTTTT-GGAAGTTCGAGGGT
* *
569594 AAAATGGTAATTTTT-TAGAGTTTG-GGGT
1 AAAATGG-AATTTTTGGA-AGTTCGAGGGT
* * *
569622 AAAATGGTATTTTTGGAAATAT-TAGGGT
1 AAAATGGAATTTTTGGAAGT-TCGAGGGT
*
569650 CAAAAAATGGAATTTTTTGAAGTTCGAGGGT
1 ---AAAATGGAATTTTTGGAAGTTCGAGGGT
* * *
569681 AAAGTGATAATTTTTAGAAGTTCGAGGGT
1 AAAATG-GAATTTTTGGAAGTTCGAGGGT
* * **
569710 AAAATAGTAATTTTTGAAAAAATC-AGGGTT
1 AAAAT-GGAATTTTTG-GAAGTTCGAGGG-T
*
569740 AAAAATAGAATTTTTGGAAGTTCGAGGGT
1 -AAAATGGAATTTTTGGAAGTTCGAGGGT
*
569769 AAAAATGTAATTTTTGGAA
1 -AAAATGGAATTTTTGGAA
569788 AAATCAAGGT
Statistics
Matches: 153, Mismatches: 26, Indels: 30
0.73 0.12 0.14
Matches are distributed among these distances:
27 8 0.05
28 22 0.14
29 70 0.46
30 26 0.17
31 27 0.18
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGT
Found at i:569802 original size:29 final size:30
Alignment explanation
Indices: 569705--569817 Score: 112
Period size: 29 Copynumber: 3.9 Consensus size: 30
569695 TAGAAGTTCG
*
569705 AGGGT-AAAATAGTAATTTTTGAAAAAATC
1 AGGGTAAAAATAGTAATTTTTGGAAAAATC
**
569734 AGGGTTAAAAATAG-AATTTTTGG-AAGTTC
1 AGGG-TAAAAATAGTAATTTTTGGAAAAATC
569763 GAGGGTAAAAAT-GTAATTTTTGGAAAAATC
1 -AGGGTAAAAATAGTAATTTTTGGAAAAATC
* * *
569793 AAGGTCAAAAT-GGAA-TTTTGGAAAA
1 AGGGTAAAAATAGTAATTTTTGGAAAA
569818 GTTTAAGGGT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
28 11 0.15
29 36 0.51
30 17 0.24
31 7 0.10
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (30 bp):
AGGGTAAAAATAGTAATTTTTGGAAAAATC
Found at i:569810 original size:88 final size:88
Alignment explanation
Indices: 569564--569817 Score: 230
Period size: 88 Copynumber: 2.9 Consensus size: 88
569554 ACTCGAGATC
* * * ** * *
569564 AAAAATGGAATTTTTGGGGAGTTCGAGGGTAAAATGGTAATTTTTTAG-AGTTTG-GGGTAAAAT
1 AAAAATAGAATTTTT-GGAAGTTCGAGGGTAAAATGATAA-TTTTTAGAAAATCGAAGGTAAAAT
* * * *
569627 GGTATTTTTGGAAATATTAGGGTCA
64 GGAATTTTTGAAAAAATCAGGGTCA
* * * ** *
569652 AAAAATGGAATTTTTTGAAGTTCGAGGGTAAAGTGATAATTTTTAGAAGTTCGAGGGTAAAATAG
1 AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTAGAAAATCGAAGGTAAAAT-G
* *
569717 TAATTTTTGAAAAAATCAGGGT-T
65 GAATTTTTGAAAAAATCAGGGTCA
*
569740 AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATG-TAATTTTTGGAAAAATC-AAGGTCAAAA
1 AAAAATAGAATTTTTGGAAGTTCGAGGGT-AAAATGATAATTTTTAG-AAAATCGAAGGT-AAAA
*
569803 TGGAATTTTGGAAAA
63 TGGAATTTTTGAAAA
569818 GTTTAAGGGT
Statistics
Matches: 140, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
86 7 0.05
87 25 0.18
88 76 0.54
89 32 0.23
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.33
Consensus pattern (88 bp):
AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTAGAAAATCGAAGGTAAAATGG
AATTTTTGAAAAAATCAGGGTCA
Found at i:569820 original size:59 final size:58
Alignment explanation
Indices: 569689--569815 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 58
569679 GTAAAGTGAT
* *
569689 AATTTTTAGAAGTTCGAGGGTAAAATAGTAATTTTTGAAAAAATCAGGGTTAAAAATAG
1 AATTTTTGGAAGTTCGAGGGTAAAAT-GTAATTTTTGAAAAAATCAAGGTTAAAAATAG
* * *
569748 AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATCAAGG-TCAAAATGG
1 AATTTTTGGAAGTTCGAGGGT-AAAATGTAATTTTTGAAAAAATCAAGGTTAAAAATAG
569806 AA-TTTTGGAA
1 AATTTTTGGAA
569816 AAGTTTAAGG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
57 8 0.13
58 9 0.15
59 40 0.65
60 5 0.08
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (58 bp):
AATTTTTGGAAGTTCGAGGGTAAAATGTAATTTTTGAAAAAATCAAGGTTAAAAATAG
Found at i:569827 original size:59 final size:58
Alignment explanation
Indices: 569689--569834 Score: 161
Period size: 59 Copynumber: 2.5 Consensus size: 58
569679 GTAAAGTGAT
* * *
569689 AATTTTTAGAAGTTCGAGGGTAAAATAGTAATTTTTGAAAAAATCAGGGTTAAAAATAG
1 AATTTTTGGAAGTTCAAGGGTAAAAT-GTAATTTTTGAAAAAATCAAGGTTAAAAATAG
* * * *
569748 AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATCAAGG-TCAAAATGG
1 AATTTTTGGAAGTTCAAGGGT-AAAATGTAATTTTTGAAAAAATCAAGGTTAAAAATAG
*
569806 AA-TTTTGGAAAAGTTTAAGGGTCAAAATG
1 AATTTTTGG--AAGTTCAAGGGT-AAAATG
569835 CGATTTTTAG
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
57 6 0.08
58 9 0.12
59 56 0.74
60 5 0.07
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.32
Consensus pattern (58 bp):
AATTTTTGGAAGTTCAAGGGTAAAATGTAATTTTTGAAAAAATCAAGGTTAAAAATAG
Found at i:569831 original size:30 final size:30
Alignment explanation
Indices: 569705--569842 Score: 99
Period size: 29 Copynumber: 4.7 Consensus size: 30
569695 TAGAAGTTCG
* *
569705 AGGGT-AAAATAGTAATTTTTGAAAAAATC-
1 AGGGTCAAAAT-GGAATTTTTGGAAAAATCA
* * ** *
569734 AGGGTTAAAAATAGAATTTTTGG-AAGTTCG
1 AGGG-TCAAAATGGAATTTTTGGAAAAATCA
* *
569764 AGGGTAAAAATGTAATTTTTGGAAAAATCA
1 AGGGTCAAAATGGAATTTTTGGAAAAATCA
* *
569794 A-GGTCAAAATGGAA-TTTTGGAAAAGTTTA
1 AGGGTCAAAATGGAATTTTTGGAAAA-ATCA
569823 AGGGTCAAAATGCG-ATTTTT
1 AGGGTCAAAATG-GAATTTTT
569843 AGACACTTTA
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
28 10 0.11
29 38 0.44
30 29 0.33
31 10 0.11
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.32
Consensus pattern (30 bp):
AGGGTCAAAATGGAATTTTTGGAAAAATCA
Found at i:570958 original size:12 final size:12
Alignment explanation
Indices: 570943--570995 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
570933 TCGTTTTACT
570943 TTTTTTTATTAA
1 TTTTTTTATTAA
*
570955 TTTTGTTATT-A
1 TTTTTTTATTAA
570966 TTATTTTTATTAA
1 TT-TTTTTATTAA
570979 TATTATTGTTATTAA
1 T-TT-TT-TTATTAA
570994 TT
1 TT
570996 AATGTTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 3 0.09
12 16 0.47
13 3 0.09
14 4 0.12
15 8 0.24
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (12 bp):
TTTTTTTATTAA
Found at i:570966 original size:3 final size:3
Alignment explanation
Indices: 570960--571044 Score: 82
Period size: 3 Copynumber: 28.0 Consensus size: 3
570950 ATTAATTTTG
* * * * *
570960 TTA TTA TTA TTT TTA TTA ATA TTA TTG TTA TTAA TTA ATG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* *
571006 GTA TTA -TA TTTA TTA TTA TTA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
571045 ATGTTATTAA
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
2 2 0.03
3 58 0.89
4 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:570966 original size:15 final size:15
Alignment explanation
Indices: 570948--571041 Score: 88
Period size: 15 Copynumber: 6.4 Consensus size: 15
570938 TTACTTTTTT
*
570948 TTATTAATTTTGTTA
1 TTATTAATTTTATTA
*
570963 TTATTATTTTTATTA
1 TTATTAATTTTATTA
*
570978 ATATT-ATTGTTATTA
1 TTATTAATT-TTATTA
*
570993 --ATTAATGTTATTA
1 TTATTAATTTTATTA
*
571006 GTATT-ATATTTATTA
1 TTATTAAT-TTTATTA
*
571021 TTATTAATATTATTA
1 TTATTAATTTTATTA
571036 TTATTA
1 TTATTA
571042 TTAATGTTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
13 9 0.14
14 6 0.09
15 48 0.74
16 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
TTATTAATTTTATTA
Found at i:571807 original size:17 final size:17
Alignment explanation
Indices: 571787--571826 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
571777 CCAAATGGAT
*
571787 TTAAATTTAATATAAAC
1 TTAAATTTAAAATAAAC
*
571804 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAC
571821 TTAAAT
1 TTAAAT
571827 CTGTTGGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAAATAAAC
Found at i:572430 original size:321 final size:321
Alignment explanation
Indices: 571848--572491 Score: 1216
Period size: 321 Copynumber: 2.0 Consensus size: 321
571838 GAACAAATTG
571848 GGCTTCAACAACTGCCCCTCTTTGCTCGTTGCTGTGTAACAGGAATGGAGCAAAGACTAAAAAGA
1 GGCTTCAACAACTGCCCCTCTTTGCTCGTTGCTGTGTAACAGGAATGGAGCAAAGACTAAAAAGA
571913 AGACCAATTTTGTCCAATCCTATTGAATCCTAGCTCAACTATCGACTACTTCAAAATGACAGCAC
66 AGACCAATTTTGTCCAATCCTATTGAATCCTAGCTCAACTATCGACTACTTCAAAATGACAGCAC
* * *
571978 TTGACTTGTAGTTCCATTCCACTCCACTACGACTGCGGGGAGAATGAGATCTGTTATCCAACTTT
131 TTGACTTGTAGTTCCATTCCACTCCACTACGACTACAGGGAGAATGAGATCCGTTATCCAACTTT
*
572043 GTTGCATGCTCGAATAGGATTGGATGTCGAGGCTTCATCTTACTCTTACTACAACTTCAGAGAGA
196 GCTGCATGCTCGAATAGGATTGGATGTCGAGGCTTCATCTTACTCTTACTACAACTTCAGAGAGA
572108 TAAAAATTCGCTATTTTGACCCGATTTACTGCAACTTCGATGTAGAAGCTTCATAAGTTAC
261 TAAAAATTCGCTATTTTGACCCGATTTACTGCAACTTCGATGTAGAAGCTTCATAAGTTAC
*
572169 GGCTTCAACAACTGCCCCTCTTTGCTCGTTGCTGTGTAACAGGAATGGAGTAAAGACTAAAAAGA
1 GGCTTCAACAACTGCCCCTCTTTGCTCGTTGCTGTGTAACAGGAATGGAGCAAAGACTAAAAAGA
*
572234 AGACCAATTTTGTCCAATCCTGTTGAATCCTAGCTCAACTATCGACTACTTCAAAATGACAGCAC
66 AGACCAATTTTGTCCAATCCTATTGAATCCTAGCTCAACTATCGACTACTTCAAAATGACAGCAC
*
572299 TTGACTTGTAGTTTCATTCCACTCCACTACGACTACAGGGAGAATGAGATCCGTTATCCAACTTT
131 TTGACTTGTAGTTCCATTCCACTCCACTACGACTACAGGGAGAATGAGATCCGTTATCCAACTTT
572364 GCTGCATGCTCGAATAGGATTGGATGTCGAGGCTTCATCTTACTCTTACTACAACTTCAGAGAGA
196 GCTGCATGCTCGAATAGGATTGGATGTCGAGGCTTCATCTTACTCTTACTACAACTTCAGAGAGA
*
572429 TAAAAATTCGCTATTTTGACCTGATTTACTGCAACTTCGATGTAGAAGCTTCATAAGTTAC
261 TAAAAATTCGCTATTTTGACCCGATTTACTGCAACTTCGATGTAGAAGCTTCATAAGTTAC
572490 GG
1 GG
572492 ATTTAATCTG
Statistics
Matches: 315, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
321 315 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (321 bp):
GGCTTCAACAACTGCCCCTCTTTGCTCGTTGCTGTGTAACAGGAATGGAGCAAAGACTAAAAAGA
AGACCAATTTTGTCCAATCCTATTGAATCCTAGCTCAACTATCGACTACTTCAAAATGACAGCAC
TTGACTTGTAGTTCCATTCCACTCCACTACGACTACAGGGAGAATGAGATCCGTTATCCAACTTT
GCTGCATGCTCGAATAGGATTGGATGTCGAGGCTTCATCTTACTCTTACTACAACTTCAGAGAGA
TAAAAATTCGCTATTTTGACCCGATTTACTGCAACTTCGATGTAGAAGCTTCATAAGTTAC
Found at i:572721 original size:49 final size:49
Alignment explanation
Indices: 572653--573031 Score: 329
Period size: 49 Copynumber: 7.7 Consensus size: 49
572643 AGGTATTAGG
* * *
572653 TTCGCCATTGCGACTTAAATCTTTCCCTTCGTATCTTTGTGGTACTGGA
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGA
* * * *
572702 TTCGCTATTGCGGCTTAAATCTTTCCCTT-TTGTGTTTTCGTGGTACTAGA
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGT-CTTT-GTGGTACTGGA
* * ** * *
572752 TTCGCCGTTGTGGCTTAAATCTTTTACTTCATG-CTTCTGAGGTACAAGG-
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCTT-TGTGGTAC-TGGA
* * * * * * *
572801 CTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGA
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGA
* * * ** *
572850 TTCGCCGTTGCGGCTTAAGTCTTTCCCTTTATGTCCCTGAGGTACTAGG-
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACT-GGA
* * *
572899 TTCGCCATTGCGACTTAAA-CATTTCCCTT-GTGTCTTCGTGGTACTGGA
1 TTCGCCATTGCGGCTTAAATC-TTTCCCTTCATGTCTTTGTGGTACTGGA
* * *
572947 TTCGCCATTACAGCTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGA
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGA
* * * **
572996 TTCACCGTTGCGGCTTAAATTTTTTGCTTCATGTCT
1 TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCT
573032 CTAAGGTATA
Statistics
Matches: 261, Mismatches: 57, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
47 2 0.01
48 40 0.15
49 176 0.67
50 41 0.16
51 2 0.01
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.40
Consensus pattern (49 bp):
TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCTTTGTGGTACTGGA
Found at i:572873 original size:98 final size:97
Alignment explanation
Indices: 572538--572984 Score: 332
Period size: 98 Copynumber: 4.6 Consensus size: 97
572528 TGCTGCTTTA
* ** * * * *
572538 ATCTTCATGGTACTAAATTCGTCGTTGCGGATTAAAT-TTTCCTTTCATGCTTCTGAGGTATAAG
1 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAG
* * ** **
572602 GCTCGTCATTGCGACTTAAACCTTTCTTTTTT
66 GCTCGCCATTGCGACTTAAACATTTCCCTCAT
* * * * * * *
572634 GTGTCTCTGAGGTATTAGG-TTCGCCATTGCGACTTAAATCTTTCCCTTCGTAT-CTT-TGTGGT
1 ATCT-TC-GTGGTACT-GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTC--ATGCTTCTGAGGT
* * * * **
572696 AC-TGGATTCGCTATTGCGGCTTAAATC-TTTCCCTTTTGT
61 ACAAGG-CTCGCCATTGCGACTTAAA-CATTTCCC--TCAT
* * * * **
572735 GTTTTCGTGGTACTAGATTCGCCGTTGTGGCTTAAATCTTTTACTTCATGCTTCTGAGGTACAAG
1 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAG
* *
572800 GCTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
66 GCTCGCCATTGCGACTTAAACATTTCCCT-CAT
* * * *
572833 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAGTCTTTCCCTTTATG-TCCCTGAGGTACTA
1 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTACAA
* **
572897 GGTTCGCCATTGCGACTTAAACATTTCCCTTGT
65 GGCTCGCCATTGCGACTTAAACATTTCCCTCAT
* * * *
572930 GTCTTCGTGGTACTGGATTCGCCATTACAGCTTAAATCTTTCCCTTCATGTCTTC
1 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTC
572985 GTGGTACTGG
Statistics
Matches: 271, Mismatches: 61, Indels: 36
0.74 0.17 0.10
Matches are distributed among these distances:
96 2 0.01
97 51 0.19
98 109 0.40
99 93 0.34
100 8 0.03
101 8 0.03
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (97 bp):
ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAG
GCTCGCCATTGCGACTTAAACATTTCCCTCAT
Found at i:572993 original size:146 final size:146
Alignment explanation
Indices: 572538--573072 Score: 462
Period size: 146 Copynumber: 3.6 Consensus size: 146
572528 TGCTGCTTTA
* ** * *
572538 ATCTTCATGGTACTAAATTCGTCGTTGCGGATTAAAT-TTT-CCTTTCATG-CTTCTGAGGTA-T
1 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTT-ATGTC-TCTGAGGTACT
* * * ** * **
572599 AAGGCTCGTCATTGCGACTTAAACCTTT-CTTTTTTGTGTCTCTGAGGTATTAGGTTCGCCATTG
64 -AGGTTCGCCATTGCGACTTAAA-CTTTCCCTTCATG-CT-TCTGAGGTACAAGGTTCGCCATTG
*
572663 CGACTTAAATCTTTCCCTTCGT
125 CGACTTAAATCTTTCCCTTCAT
* ** * * *
572685 ATCTTTGTGGTACTGGATTCGCTATTGCGGCTTAAATCTTTCCCTTT-TGTGTTTTCGTGGTACT
1 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTTATGT-CTCT-GAGGTACT
* * * * ** * *
572749 AGATTCGCCGTTGTGGCTTAAATCTTTTACTTCATGCTTCTGAGGTACAAGGCTCGCCGTTGCGA
64 AGGTTCGCCATTGCGACTTAAA-CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGA
* *
572814 CTTAAACCTTTCCCTCCAT
128 CTTAAATCTTTCCCTTCAT
* *
572833 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAGTCTTTCCCTTTATGTCCCTGAGGTACTAG
1 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTTATGTCTCTGAGGTACTAG
* * * *
572898 GTTCGCCATTGCGACTTAAACATTTCCCTT-GTGTCTTC-GTGGTAC-TGGATTCGCCATTAC-A
66 GTTCGCCATTGCGACTTAAAC-TTTCCCTTCATG-CTTCTGAGGTACAAGG-TTCGCCATTGCGA
572959 GCTTAAATCTTTCCCTTCAT
128 -CTTAAATCTTTCCCTTCAT
* * * ** * *
572979 GTCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATTTTTTGCTTCATGTCTCTAAGGTA-TAA
1 ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTTATGTCTCTGAGGTACT-A
*
573043 GGTTTGCCATTGCGACTTAAACCTTTCCCT
65 GGTTCGCCATTGCGACTTAAA-CTTTCCCT
573073 CTATGTTTCG
Statistics
Matches: 312, Mismatches: 62, Indels: 29
0.77 0.15 0.07
Matches are distributed among these distances:
145 4 0.01
146 114 0.37
147 67 0.21
148 88 0.28
149 34 0.11
150 5 0.02
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (146 bp):
ATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTTATGTCTCTGAGGTACTAG
GTTCGCCATTGCGACTTAAACTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTT
AAATCTTTCCCTTCAT
Found at i:583908 original size:30 final size:30
Alignment explanation
Indices: 583872--583943 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
583862 CCTTTAAATA
583872 ATAAAAAATTAATATAATATTTTAAAACTT
1 ATAAAAAATTAATATAATATTTTAAAACTT
583902 ATAAAAAATTAATATAATATTTTAAAACTT
1 ATAAAAAATTAATATAATATTTTAAAACTT
583932 ATAAAAAATTAA
1 ATAAAAAATTAA
583944 GCTATTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (30 bp):
ATAAAAAATTAATATAATATTTTAAAACTT
Found at i:588133 original size:4 final size:4
Alignment explanation
Indices: 588124--588151 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
588114 TAGCGAATAA
588124 AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT
588152 GTTTGACTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:590827 original size:16 final size:18
Alignment explanation
Indices: 590802--590836 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
590792 ATTATTTTCT
590802 TAAAATAGATTT-TTTTA
1 TAAAATAGATTTCTTTTA
590819 TAAAA-AGATTTCTTTTA
1 TAAAATAGATTTCTTTTA
590836 T
1 T
590837 TCTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (18 bp):
TAAAATAGATTTCTTTTA
Found at i:591143 original size:44 final size:44
Alignment explanation
Indices: 591095--591206 Score: 102
Period size: 44 Copynumber: 2.5 Consensus size: 44
591085 TTAATATGAT
*
591095 TTAATATAAAAATA-ATTATATTAAGAATGT-TATTAAATTATATA
1 TTAATATAAAAATATATT-TAATAAGAAT-TATATTAAATTATATA
* * *
591139 TTAATATTAAATTATATTTAATAATAATTATATTAAATTATTTATA
1 TTAATATAAAAATATATTTAATAAGAATTATATTAAATTA--TATA
** * *
591185 TTTTTATTAAATTATATTTAAT
1 TTAATATAAAAATATATTTAAT
591207 TATAATCTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
43 1 0.02
44 30 0.52
45 3 0.05
46 24 0.41
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (44 bp):
TTAATATAAAAATATATTTAATAAGAATTATATTAAATTATATA
Found at i:591156 original size:16 final size:16
Alignment explanation
Indices: 591125--591202 Score: 72
Period size: 16 Copynumber: 4.9 Consensus size: 16
591115 TTAAGAATGT
591125 TATTAAATTATATATTAA
1 TATTAAA-T-TATATTAA
591143 TATTAAATTATATTTAA
1 TATTAAATTATA-TTAA
*
591160 TAAT-AATTATATTAA
1 TATTAAATTATATTAA
* **
591175 -ATT-ATTTATATTTT
1 TATTAAATTATATTAA
591189 TATTAAATTATATT
1 TATTAAATTATATT
591203 TAATTATAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
14 10 0.20
15 7 0.14
16 19 0.37
17 8 0.16
18 7 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAAATTATATTAA
Found at i:591179 original size:10 final size:10
Alignment explanation
Indices: 591125--591210 Score: 62
Period size: 10 Copynumber: 9.2 Consensus size: 10
591115 TTAAGAATGT
591125 TATTAAATTA
1 TATTAAATTA
591135 TA-T--ATTAA
1 TATTAAATT-A
591143 TATTAAATTA
1 TATTAAATTA
*
591153 TATTTAA-TA
1 TATTAAATTA
591162 -A-T-AATTA
1 TATTAAATTA
591169 TATTAAATTA
1 TATTAAATTA
* *
591179 T-TTATATTTT
1 TATTA-AATTA
591189 TATTAAATTA
1 TATTAAATTA
*
591199 TATTTAATTA
1 TATTAAATTA
591209 TA
1 TA
591211 ATCTTATTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
6 2 0.03
7 6 0.10
8 5 0.08
9 8 0.13
10 33 0.55
11 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TATTAAATTA
Found at i:591186 original size:30 final size:30
Alignment explanation
Indices: 591135--591209 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
591125 TATTAAATTA
*
591135 TATATTAATATTAAATTATATTTAATAAT-AAT
1 TATATTAA-ATT-ATTTATATTT-ATAATAAAT
* *
591167 TATATTAAATTATTTATATTTTTATTAAAT
1 TATATTAAATTATTTATATTTATAATAAAT
*
591197 TATATTTAATTAT
1 TATATTAAATTAT
591210 AATCTTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 3 0.08
30 24 0.63
31 3 0.08
32 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TATATTAAATTATTTATATTTATAATAAAT
Found at i:591193 original size:46 final size:44
Alignment explanation
Indices: 591125--591212 Score: 131
Period size: 46 Copynumber: 2.0 Consensus size: 44
591115 TTAAGAATGT
591125 TATTAAATTATATATTAATATTAAATTATATTTAATAATAATTA
1 TATTAAATTATATATTAATATTAAATTATATTTAATAATAATTA
** *
591169 TATTAAATTATTTATATTTTTATTAAATTATATTTAATTATAAT
1 TATTAAATTA--TATATTAATATTAAATTATATTTAATAATAAT
591213 CTTATTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 10 0.26
46 29 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (44 bp):
TATTAAATTATATATTAATATTAAATTATATTTAATAATAATTA
Found at i:591217 original size:26 final size:25
Alignment explanation
Indices: 591125--591219 Score: 83
Period size: 26 Copynumber: 3.8 Consensus size: 25
591115 TTAAGAATGT
*
591125 TATTAAATTATATATTAATATTAAATTA
1 TATTTAATTATA-ATT--TATTAAATTA
*
591153 TATTTAATAATAATTATATTAAA-T-
1 TATTTAATTATAATT-TATTAAATTA
*
591177 TATTT-A-TAT-TTTTATTAAATTA
1 TATTTAATTATAATTTATTAAATTA
591199 TATTTAATTATAATCTTATTA
1 TATTTAATTATAAT-TTATTA
591220 TATTTAATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
20 7 0.12
21 3 0.05
22 7 0.12
23 2 0.04
24 8 0.14
25 2 0.04
26 14 0.25
27 3 0.05
28 10 0.18
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTTAATTATAATTTATTAAATTA
Found at i:593107 original size:21 final size:20
Alignment explanation
Indices: 593073--593114 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
593063 TTTAAATTAA
593073 TAAAAGTAAAATTACATTTT
1 TAAAAGTAAAATTACATTTT
*
593093 TAAATAGTGAAATTACATTTT
1 TAAA-AGTAAAATTACATTTT
593114 T
1 T
593115 TTATTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (20 bp):
TAAAAGTAAAATTACATTTT
Found at i:595382 original size:22 final size:23
Alignment explanation
Indices: 595342--595388 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
595332 CCCACTGTTT
595342 TTGCTACCATTTCACTATT-ATG
1 TTGCTACCATTTCACTATTAATG
* * *
595364 TTGCTACTATTTTATTATTAATG
1 TTGCTACCATTTCACTATTAATG
595387 TT
1 TT
595389 TAAATATTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.23, C:0.15, G:0.09, T:0.53
Consensus pattern (23 bp):
TTGCTACCATTTCACTATTAATG
Found at i:599787 original size:17 final size:18
Alignment explanation
Indices: 599762--599799 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
599752 ATTAAATTTT
*
599762 AATAAAAAAAA-ATTAAA
1 AATAAAAAAAATATAAAA
*
599779 AATAGAAAAAATATAAAA
1 AATAAAAAAAATATAAAA
599797 AAT
1 AAT
599800 TGTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (18 bp):
AATAAAAAAAATATAAAA
Found at i:599796 original size:8 final size:8
Alignment explanation
Indices: 599769--599860 Score: 51
Period size: 9 Copynumber: 10.5 Consensus size: 8
599759 TTTAATAAAA
599769 AAAAAT-T
1 AAAAATAT
*
599776 AAAAATAGA
1 AAAAATA-T
599785 AAAAATAT
1 AAAAATAT
*
599793 AAAAAATTGT
1 -AAAAA-TAT
*
599803 AAAATTTTAT
1 AAAA--ATAT
*
599813 AAAAATTGT
1 AAAAA-TAT
599822 AAAAAATTAT
1 -AAAAA-TAT
599832 AAAATATAT
1 AAAA-ATAT
*
599841 AGAAATAT
1 AAAAATAT
599849 AAAAATAT
1 AAAAATAT
599857 AAAA
1 AAAA
599861 TTTTATAAAG
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
7 6 0.09
8 15 0.23
9 28 0.42
10 17 0.26
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (8 bp):
AAAAATAT
Found at i:599806 original size:19 final size:19
Alignment explanation
Indices: 599766--599835 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 19
599756 AATTTTAATA
* * *
599766 AAAAAAAATTAAAAATAG-
1 AAAAAATATAAAAAATTGT
599784 AAAAAATATAAAAAATTGT
1 AAAAAATATAAAAAATTGT
* *
599803 -AAAATTTTATAAAAATTGT
1 AAAAAATATA-AAAAATTGT
599822 AAAAAATTATAAAA
1 AAAAAA-TATAAAA
599836 TATATAGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 22 0.54
19 9 0.22
20 7 0.17
21 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAAAATATAAAAAATTGT
Found at i:599808 original size:49 final size:49
Alignment explanation
Indices: 599712--599817 Score: 119
Period size: 49 Copynumber: 2.2 Consensus size: 49
599702 TTTTATTAAA
* * * *
599712 AATATAAAAAAAATTAAAATCAATAAAATTTATAAATATTATTAAATTTT
1 AATA-AAAAAAAATTAAAATCAAAAAAATATATAAAAATTATAAAATTTT
*
599762 AATAAAAAAAAATTAAAAAT-AGAAAAAATATA-AAAAATTGTAAAATTTT
1 AATAAAAAAAAATT-AAAATCA-AAAAAATATATAAAAATTATAAAATTTT
599811 -ATAAAAA
1 AATAAAAA
599818 TTGTAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
48 7 0.14
49 25 0.51
50 17 0.35
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (49 bp):
AATAAAAAAAAATTAAAATCAAAAAAATATATAAAAATTATAAAATTTT
Found at i:599835 original size:9 final size:9
Alignment explanation
Indices: 599775--599860 Score: 54
Period size: 10 Copynumber: 9.6 Consensus size: 9
599765 AAAAAAAAAT
599775 TAAAAA-TA
1 TAAAAATTA
* *
599783 GAAAAAATA
1 TAAAAATTA
*
599792 TAAAAAATTG
1 T-AAAAATTA
*
599802 TAAAATTTTA
1 TAAAA-ATTA
*
599812 TAAAAATTG
1 TAAAAATTA
599821 TAAAAAATTA
1 T-AAAAATTA
599831 T-AAAATATA
1 TAAAAAT-TA
*
599840 TAGAAA-TA
1 TAAAAATTA
599848 TAAAAA-TA
1 TAAAAATTA
599856 TAAAA
1 TAAAA
599861 TTTTATAAAG
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
8 24 0.39
9 12 0.20
10 25 0.41
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:599862 original size:54 final size:53
Alignment explanation
Indices: 599768--599908 Score: 160
Period size: 54 Copynumber: 2.6 Consensus size: 53
599758 TTTTAATAAA
* * * *
599768 AAAAAATTA-AAAATAGAAAAAATATAAAAAATTGTAAAATTTTATAAAAATTGT
1 AAAAAATTATAAAATATAAGAAATAT-AAAAATTATAAAATTTTAT-AAAATCGT
*
599822 AAAAAATTATAAAATATATAGAAATATAAAAA-TATAAAATTTTATAAAGTCGT
1 AAAAAATTATAAAATATA-AGAAATATAAAAATTATAAAATTTTATAAAATCGT
599875 AAGAAAATTATACAAAATATAAAGAAATATAAAA
1 AA-AAAATTAT--AAAATAT-AAGAAATATAAAA
599909 TTCGTAAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
53 8 0.11
54 29 0.38
55 12 0.16
56 26 0.34
57 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (53 bp):
AAAAAATTATAAAATATAAGAAATATAAAAATTATAAAATTTTATAAAATCGT
Found at i:601432 original size:20 final size:20
Alignment explanation
Indices: 601399--601446 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
601389 AATTAATAAT
*
601399 TTAA-TTAAAATAAGGTTTA
1 TTAAGTTAAAATAAGGTTAA
*
601418 TTAAGTTAAAGTAAGGTTAA
1 TTAAGTTAAAATAAGGTTAA
*
601438 TTATGTTAA
1 TTAAGTTAA
601447 TTAACCACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (20 bp):
TTAAGTTAAAATAAGGTTAA
Found at i:602762 original size:19 final size:20
Alignment explanation
Indices: 602725--602766 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
602715 TTGTTGTTGT
602725 TTTCCCACTTTTTACCACTA
1 TTTCCCACTTTTTACCACTA
**
602745 TTTCCCA-TTTTTTGCACTA
1 TTTCCCACTTTTTACCACTA
602764 TTT
1 TTT
602767 TGCTATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.17, C:0.29, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTCCCACTTTTTACCACTA
Found at i:619682 original size:3 final size:3
Alignment explanation
Indices: 619674--619700 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
619664 GTAAGAAAAC
619674 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
619701 TGAAAAGGAC
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.