Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008375.1 Hibiscus syriacus cultivar Beakdansim tig00111132_pilon, 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: 1210889
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:353493 original size:22 final size:22
Alignment explanation
Indices: 353458--353499 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
353448 GAAGAACGTA
*
353458 CAAAGCATGCACATACATAGTT
1 CAAAGAATGCACATACATAGTT
*
353480 CAAAGAATGTACATACATAG
1 CAAAGAATGCACATACATAG
353500 AAACTCGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAAGAATGCACATACATAGTT
Found at i:355867 original size:19 final size:19
Alignment explanation
Indices: 355843--355880 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
355833 AAATAACTAA
355843 TTTCTAATTAATGATGGAC
1 TTTCTAATTAATGATGGAC
355862 TTTCTAATTAATGATGGAC
1 TTTCTAATTAATGATGGAC
355881 AAATTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTCTAATTAATGATGGAC
Found at i:355997 original size:60 final size:59
Alignment explanation
Indices: 355933--356069 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 59
355923 TAAAGTACAT
* ** *
355933 AAATGGTCCTCTGACTATAAGGTATTATTTTATTAAGT-CTTTCGACTATTAAAAGTTATA
1 AAATGGTCATCTGACTATAAAATA-TATTTTATTAAGTCCCTT-GACTATTAAAAGTTATA
* * *
355993 AAATGGTCATTTGACTATAAAATATGTTTTGTTAAGTCCCTTGACTATTAAAAGTTATA
1 AAATGGTCATCTGACTATAAAATATATTTTATTAAGTCCCTTGACTATTAAAAGTTATA
** *
356052 ATGTCGTCATCTGACTAT
1 AAATGGTCATCTGACTAT
356070 TTATTATGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 42 0.65
60 23 0.35
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (59 bp):
AAATGGTCATCTGACTATAAAATATATTTTATTAAGTCCCTTGACTATTAAAAGTTATA
Found at i:360886 original size:33 final size:33
Alignment explanation
Indices: 360844--360906 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
360834 GGCGACATCG
*
360844 AAGGTCTGCTGCAACAGACGTGGTGGATGCTCC
1 AAGGTCTGCTGCAACAGACGCGGTGGATGCTCC
* *
360877 AAGGTCTGCTGCATCAGATGCGGTGGATGC
1 AAGGTCTGCTGCAACAGACGCGGTGGATGC
360907 ATCCTCTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (33 bp):
AAGGTCTGCTGCAACAGACGCGGTGGATGCTCC
Found at i:364614 original size:26 final size:27
Alignment explanation
Indices: 364585--364635 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
364575 GACTTATTTA
*
364585 AAACGACGTAATTTTATAAA-GACTCC
1 AAACGACGTAATTCTATAAACGACTCC
**
364611 AAACGGTGTAATTCTATAAACGACT
1 AAACGACGTAATTCTATAAACGACT
364636 TTTATTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (27 bp):
AAACGACGTAATTCTATAAACGACTCC
Found at i:367106 original size:13 final size:13
Alignment explanation
Indices: 367088--367113 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
367078 GACTTTTTGG
367088 TCAAAGTCAACGA
1 TCAAAGTCAACGA
367101 TCAAAGTCAACGA
1 TCAAAGTCAACGA
367114 GTTGACTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (13 bp):
TCAAAGTCAACGA
Found at i:367161 original size:14 final size:14
Alignment explanation
Indices: 367111--367161 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
367101 TCAAAGTCAA
*
367111 CGAGTTGACT-TAG
1 CGAGTTGACTCGAG
*
367124 ACGAGTTGACTCGATC
1 -CGAGTTGACTCGA-G
*
367140 CAAGTTGACTCGAG
1 CGAGTTGACTCGAG
367154 CGAGTTGA
1 CGAGTTGA
367162 ATCAGTTAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (14 bp):
CGAGTTGACTCGAG
Found at i:367494 original size:21 final size:21
Alignment explanation
Indices: 367462--367501 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
367452 AATTTCCCAG
*
367462 TACATAGGGTATCGGTACTTC
1 TACATAGGGTATCAGTACTTC
367483 TACAT-GGAGTATCAGTACT
1 TACATAGG-GTATCAGTACT
367502 ACCTTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
TACATAGGGTATCAGTACTTC
Found at i:371333 original size:17 final size:19
Alignment explanation
Indices: 371311--371347 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
371301 TGGTATGTGT
371311 TACATGATA-TGT-ATAAA
1 TACATGATAGTGTAATAAA
*
371328 TACATGTTAGTGTAATAAA
1 TACATGATAGTGTAATAAA
371347 T
1 T
371348 TATGCGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (19 bp):
TACATGATAGTGTAATAAA
Found at i:372189 original size:30 final size:29
Alignment explanation
Indices: 372149--372206 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
372139 TTAAGTGAGC
*
372149 ACATGTAAATGTTATATGATCATGTGATT
1 ACATGTAAATGTTATACGATCATGTGATT
*
372178 ACATGTAAAATGTTATACGATTATGTGAT
1 ACATGT-AAATGTTATACGATCATGTGAT
372207 GATTTGTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (29 bp):
ACATGTAAATGTTATACGATCATGTGATT
Found at i:372337 original size:18 final size:18
Alignment explanation
Indices: 372314--372348 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
372304 AGGGATTATC
*
372314 AGTGGTCCTTCAGGACAT
1 AGTGGTCATTCAGGACAT
372332 AGTGGTCATTCAGGACA
1 AGTGGTCATTCAGGACA
372349 AATTTCAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCAGGACAT
Found at i:374318 original size:24 final size:24
Alignment explanation
Indices: 374291--374367 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
374281 CAGCTCATAT
*
374291 AAATTGCTCCGAAATACCACGTAG
1 AAATTGCTCCGAAGTACCACGTAG
* *
374315 AAATT-ATCCCGAAGGACCACGTAG
1 AAATTGCT-CCGAAGTACCACGTAG
* * *
374339 AAA-TGCACCGAAGTGCCACATAG
1 AAATTGCTCCGAAGTACCACGTAG
374362 -AATTGC
1 AAATTGC
374368 ACTGTAGTGC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
22 2 0.05
23 18 0.43
24 22 0.52
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (24 bp):
AAATTGCTCCGAAGTACCACGTAG
Found at i:374357 original size:23 final size:23
Alignment explanation
Indices: 374323--374379 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
374313 AGAAATTATC
*
374323 CCGAAG-GACCACGTAGAAATGCA
1 CCGAAGTG-CCACATAGAAATGCA
*
374346 CCGAAGTGCCACATAGAATTGCA
1 CCGAAGTGCCACATAGAAATGCA
* *
374369 CTGTAGTGCCA
1 CCGAAGTGCCA
374380 TATAAGATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (23 bp):
CCGAAGTGCCACATAGAAATGCA
Found at i:378890 original size:17 final size:19
Alignment explanation
Indices: 378868--378908 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
378858 TGGTATGTGT
378868 TACATGATA-TGT-ATAAA
1 TACATGATAGTGTAATAAA
*
378885 TACATGTTAGTGTAATAAA
1 TACATGATAGTGTAATAAA
378904 T-CATG
1 TACATG
378909 CGAATAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 8 0.38
18 7 0.33
19 6 0.29
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (19 bp):
TACATGATAGTGTAATAAA
Found at i:379295 original size:2 final size:2
Alignment explanation
Indices: 379288--379348 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
379278 GTAGCATTGG
379288 TA TA TA TA TA TA TA TA TA TA 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 TA TA TA TA
379330 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
379349 GATAATAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:381993 original size:26 final size:26
Alignment explanation
Indices: 381960--382022 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
381950 TAAATCTAAC
381960 TATAAATATATTTTTTGATTAAATGA
1 TATAAATATATTTTTTGATTAAATGA
*
381986 TATAAATATATTTTTTGATTAGATGA
1 TATAAATATATTTTTTGATTAAATGA
382012 TATAAATATAT
1 TATAAATATAT
382023 AAATAAACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (26 bp):
TATAAATATATTTTTTGATTAAATGA
Found at i:383318 original size:21 final size:21
Alignment explanation
Indices: 383292--383333 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
383282 TGTTTTCATA
383292 TTGCTAATAATAATGCTCTTG
1 TTGCTAATAATAATGCTCTTG
*
383313 TTGCTAATAATATTGCTCTTG
1 TTGCTAATAATAATGCTCTTG
383334 ATATGTTTCA
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:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (21 bp):
TTGCTAATAATAATGCTCTTG
Found at i:385362 original size:30 final size:30
Alignment explanation
Indices: 385328--385407 Score: 142
Period size: 30 Copynumber: 2.7 Consensus size: 30
385318 ATGCTTCCCA
*
385328 TGCTTTTCGTGTCGCTTCTCATGTCTGTCG
1 TGCTTTTCCTGTCGCTTCTCATGTCTGTCG
*
385358 TGCTTTTCCCGTCGCTTCTCATGTCTGTCG
1 TGCTTTTCCTGTCGCTTCTCATGTCTGTCG
385388 TGCTTTTCCTGTCGCTTCTC
1 TGCTTTTCCTGTCGCTTCTC
385408 CTCACGCCTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.03, C:0.31, G:0.20, T:0.46
Consensus pattern (30 bp):
TGCTTTTCCTGTCGCTTCTCATGTCTGTCG
Found at i:387816 original size:30 final size:30
Alignment explanation
Indices: 387760--387865 Score: 160
Period size: 30 Copynumber: 3.6 Consensus size: 30
387750 CTTATATAAC
* *
387760 AAATAGGTACCTAAAG-TATTTTTTGGTCA
1 AAATAAGTACCTAAAGTTATCTTTTGGTCA
*
387789 AAATAAGTATCTAAAGTTATCTTTTGGTCA
1 AAATAAGTACCTAAAGTTATCTTTTGGTCA
*
387819 AAATAAGTATCTAAAGTTATCTTTTGGTCA
1 AAATAAGTACCTAAAGTTATCTTTTGGTCA
*
387849 AAATAGGTACCTAAAGT
1 AAATAAGTACCTAAAGT
387866 ATTCAATTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
29 14 0.20
30 57 0.80
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (30 bp):
AAATAAGTACCTAAAGTTATCTTTTGGTCA
Found at i:388021 original size:31 final size:28
Alignment explanation
Indices: 387952--388054 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 28
387942 GAAAAGTTTG
* * * *
387952 AATAGTTTTGGTACCTATTTTGACATAA
1 AATACTTTAGGTACATATTTTGACAAAA
387980 AATACTTTAGGTACATATTTTGACTAAAA
1 AATACTTTAGGTACATATTTTGAC-AAAA
**
388009 AGATAACTTTAGGTATTTATTTTGACCAAAAA
1 A-AT-ACTTTAGGTACATATTTTGA-C-AAAA
388041 AATACTTTAGGTAC
1 AATACTTTAGGTAC
388055 TTGAATGAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 21 0.33
29 4 0.06
30 12 0.19
31 20 0.32
32 6 0.10
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.39
Consensus pattern (28 bp):
AATACTTTAGGTACATATTTTGACAAAA
Found at i:388050 original size:30 final size:30
Alignment explanation
Indices: 387952--388054 Score: 111
Period size: 31 Copynumber: 3.5 Consensus size: 30
387942 GAAAAGTTTG
* * * *
387952 AATAGTTTTGGTACCTATTTTGA-C-ATAA
1 AATACTTTAGGTACATATTTTGACCAAAAA
*
387980 AATACTTTAGGTACATATTTTGACTAAAAA
1 AATACTTTAGGTACATATTTTGACCAAAAA
* **
388010 GATAACTTTAGGTATTTATTTTGACCAAAAA
1 AAT-ACTTTAGGTACATATTTTGACCAAAAA
388041 AATACTTTAGGTAC
1 AATACTTTAGGTAC
388055 TTGAATGAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 20 0.33
30 15 0.25
31 26 0.43
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.39
Consensus pattern (30 bp):
AATACTTTAGGTACATATTTTGACCAAAAA
Found at i:389418 original size:10 final size:10
Alignment explanation
Indices: 389386--389441 Score: 76
Period size: 10 Copynumber: 5.4 Consensus size: 10
389376 AAAATCTAGT
389386 AATTTTAAAA
1 AATTTTAAAA
*
389396 AATTTATATAA
1 AATTT-TAAAA
389407 AATTTTAAAA
1 AATTTTAAAA
*
389417 AATTTATATAA
1 AATTT-TAAAA
389428 AATTTTAAAA
1 AATTTTAAAA
389438 AATT
1 AATT
389442 AAATTATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
10 22 0.55
11 18 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AATTTTAAAA
Found at i:389456 original size:22 final size:21
Alignment explanation
Indices: 389386--389441 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
389376 AAAATCTAGT
389386 AATTTTAAAAAATTTATATAA
1 AATTTTAAAAAATTTATATAA
389407 AATTTTAAAAAATTTATATAA
1 AATTTTAAAAAATTTATATAA
389428 AATTTTAAAAAATT
1 AATTTTAAAAAATT
389442 AAATTATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTTAAAAAATTTATATAA
Found at i:389880 original size:13 final size:13
Alignment explanation
Indices: 389849--389890 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
389839 AGTTTATGGT
389849 TTTTTATAAACATAA
1 TTTTTATAAA-A-AA
389864 TTTTTCA-AAAAAA
1 TTTTT-ATAAAAAA
389877 TTTTTATAAAAAA
1 TTTTTATAAAAAA
389890 T
1 T
389891 AAATTTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 14 0.56
14 1 0.04
15 8 0.32
16 1 0.04
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTTTATAAAAAA
Found at i:392748 original size:18 final size:18
Alignment explanation
Indices: 392727--392762 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
392717 TGCCCATGCT
392727 CCACTAATTACCCACGCC
1 CCACTAATTACCCACGCC
392745 CCACTAATTACCCACGCC
1 CCACTAATTACCCACGCC
392763 ATACTACACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.50, G:0.06, T:0.17
Consensus pattern (18 bp):
CCACTAATTACCCACGCC
Found at i:392768 original size:18 final size:18
Alignment explanation
Indices: 392728--392768 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
392718 GCCCATGCTC
*
392728 CACTAATTACCCACGCCC
1 CACTAATTACCCACGCCA
392746 CACTAATTACCCACGCCA
1 CACTAATTACCCACGCCA
*
392764 TACTA
1 CACTA
392769 CACGCCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.32, C:0.44, G:0.05, T:0.20
Consensus pattern (18 bp):
CACTAATTACCCACGCCA
Found at i:393442 original size:2 final size:2
Alignment explanation
Indices: 393435--393472 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
393425 CATCTAAAGC
393435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
393473 TATTTCATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:395858 original size:18 final size:17
Alignment explanation
Indices: 395837--395892 Score: 62
Period size: 16 Copynumber: 3.3 Consensus size: 17
395827 CCTTTAATAT
*
395837 TATATAATATATTTACA
1 TATATAATTTATTTACA
395854 T-TATAATTTATATTACA
1 TATATAATTTAT-TTACA
*
395871 TTATAAAATTTA-TTACA
1 -TATATAATTTATTTACA
395888 TATAT
1 TATAT
395893 CATTCACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 13 0.39
17 11 0.33
18 1 0.03
19 8 0.24
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATAATTTATTTACA
Found at i:395871 original size:17 final size:16
Alignment explanation
Indices: 395839--395876 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
395829 TTTAATATTA
395839 TATAATATATTTACAT
1 TATAATATATTTACAT
*
395855 TATAATTTATATTACAT
1 TATAATATAT-TTACAT
395872 TATAA
1 TATAA
395877 AATTTATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
TATAATATATTTACAT
Found at i:395884 original size:17 final size:17
Alignment explanation
Indices: 395835--395888 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
395825 TCCCTTTAAT
* *
395835 ATTATATAATATATTTAC
1 ATTATAAAATTTA-TTAC
*
395853 ATTAT-AATTTATATTAC
1 ATTATAAAATT-TATTAC
395870 ATTATAAAATTTATTAC
1 ATTATAAAATTTATTAC
395887 AT
1 AT
395889 ATATCATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 19 0.63
18 11 0.37
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATAAAATTTATTAC
Found at i:396951 original size:18 final size:18
Alignment explanation
Indices: 396928--396962 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
396918 TATGTTTTGT
396928 ATTTTATTTTATTTATTA
1 ATTTTATTTTATTTATTA
396946 ATTTTATTTTATTTATT
1 ATTTTATTTTATTTATT
396963 TCCTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTATTTTATTTATTA
Found at i:397070 original size:10 final size:10
Alignment explanation
Indices: 397057--397211 Score: 56
Period size: 10 Copynumber: 16.3 Consensus size: 10
397047 ATTATATTGC
397057 TATTTATTAT
1 TATTTATTAT
397067 TA-TTATTTAT
1 TATTTA-TTAT
397077 TATTTATTAT
1 TATTTATTAT
397087 T-TTTATTA-
1 TATTTATTAT
*
397095 TATATA-TA-
1 TATTTATTAT
397103 TATTTAATTA-
1 TATTT-ATTAT
*
397113 TATTTCTTAT
1 TATTTATTAT
397123 GT-TTT-TTAT
1 -TATTTATTAT
*
397132 T-TTT-TTGT
1 TATTTATTAT
397140 T-TTCTA-T-T
1 TATT-TATTAT
397148 TATTTA-TAT
1 TATTTATTAT
* *
397157 TATATCACTAT
1 TAT-TTATTAT
*
397168 TTTTTATTAT
1 TATTTATTAT
397178 TAGTTT-TCTATT
1 TA-TTTAT-TA-T
397190 TATTT-TCTAT
1 TATTTAT-TAT
397200 TATTT-TTAT
1 TATTTATTAT
397209 TAT
1 TAT
397212 ATATATATAT
Statistics
Matches: 120, Mismatches: 9, Indels: 33
0.74 0.06 0.20
Matches are distributed among these distances:
8 22 0.18
9 35 0.29
10 39 0.32
11 21 0.17
12 3 0.03
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (10 bp):
TATTTATTAT
Found at i:397114 original size:18 final size:16
Alignment explanation
Indices: 397036--397115 Score: 74
Period size: 17 Copynumber: 4.8 Consensus size: 16
397026 TTTTGTTTTC
397036 TATTTATT-TATATTA
1 TATTTATTATATATTA
397051 TATTGCTATT-TATTATTA
1 TATT--TATTATA-TATTA
*
397069 TTATTTATTATTTATTA
1 -TATTTATTATATATTA
*
397086 TTTTTATTATATATATA
1 TATTTATTATATAT-TA
397103 TATTTAATTATAT
1 TATTT-ATTATAT
397116 TTCTTATGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
15 4 0.07
16 12 0.22
17 21 0.39
18 13 0.24
19 4 0.07
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (16 bp):
TATTTATTATATATTA
Found at i:397116 original size:108 final size:113
Alignment explanation
Indices: 396985--397221 Score: 335
Period size: 108 Copynumber: 2.1 Consensus size: 113
396975 ATCATTATTT
*
396985 TTAT-TATATATATTTAGTTATATTTCTCAT-TTTCCTTATTTTTTTGTTTTCTATTTATTTATA
1 TTATATATATATATTTAATTATATTTCTCATGTTT-CTTATTTTTTTGTTTTCTATTTATTTATA
**
397048 TTATATTGCTATTTATTATTATTA-TT-TA-TTA-TT-TATTATTTTTA
65 TTATATCACTATTTATTATTATTATTTCTATTTATTTCTATTATTTTTA
* *
397092 TTATATATATATATTTAATTATATTTCTTATGTTTTTTATTTTTTTGTTTTCTATTTATTTATAT
1 TTATATATATATATTTAATTATATTTCTCATGTTTCTTATTTTTTTGTTTTCTATTTATTTATAT
*
397157 TATATCACTATTTTTTATTATTAGTTTTCTATTTATTTTCTATTATTTTTA
66 TATATCACTATTTATTATTATTA--TTTCTATTTA-TTTCTATTATTTTTA
397208 TTATATATATATAT
1 TTATATATATATAT
397222 ATATATATAT
Statistics
Matches: 114, Mismatches: 6, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
107 4 0.04
108 73 0.64
109 3 0.03
111 2 0.02
112 2 0.02
113 3 0.03
115 2 0.02
116 25 0.22
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (113 bp):
TTATATATATATATTTAATTATATTTCTCATGTTTCTTATTTTTTTGTTTTCTATTTATTTATAT
TATATCACTATTTATTATTATTATTTCTATTTATTTCTATTATTTTTA
Found at i:397188 original size:21 final size:21
Alignment explanation
Indices: 397124--397190 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
397114 ATTTCTTATG
* *
397124 TTTTTTATTTTTTTGTTTTCTA
1 TTTTTTA-TTATTAGTTTTCTA
**
397146 TTTATTTA-TATTA-TATCACTA
1 TTT-TTTATTATTAGT-TTTCTA
397167 TTTTTTATTATTAGTTTTCTA
1 TTTTTTATTATTAGTTTTCTA
397188 TTT
1 TTT
397191 ATTTTCTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
20 5 0.14
21 22 0.63
22 4 0.11
23 4 0.11
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTTTATTATTAGTTTTCTA
Found at i:397216 original size:2 final size:2
Alignment explanation
Indices: 397209--397234 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
397199 TTATTTTTAT
397209 TA TA 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
397235 ATTATATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:397301 original size:126 final size:126
Alignment explanation
Indices: 397073--397301 Score: 327
Period size: 126 Copynumber: 1.8 Consensus size: 126
397063 TTATTATTAT
* * * ** *
397073 TTATTATTTATTATTTTTATTATATATATATATTTAATTATATTTCTTATGTTTTTTATTTTTTT
1 TTATTATTTATTATATATATTATATATATATATATAATTATATTTCTTATGTTCCTTATTTTTTC
* **
397138 GTTTTCTATTTATTTATATTATATCACTATTTTTTATTATTAGTTTTCTATTTATTTTCTA
66 GTTTTCTATTGATTTATATTATATCACTATTACTTATTATTAGTTTTCTATTTATTTTCTA
397199 TTATT-TTTATTATATATATATATATATATATATATAATTATATTTCTTATGTTCCTTATTTTTT
1 TTATTATTTATTATATATAT-TATATATATATATATAATTATATTTCTTATGTTCCTTATTTTTT
* *
397263 CCGTTTTCTATTGGTTTATATTATATTA-TATTACTTATT
65 -CGTTTTCTATTGATTTATATTATATCACTATTACTTATT
397302 TCTATATTCT
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
125 12 0.13
126 55 0.61
127 23 0.26
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (126 bp):
TTATTATTTATTATATATATTATATATATATATATAATTATATTTCTTATGTTCCTTATTTTTTC
GTTTTCTATTGATTTATATTATATCACTATTACTTATTATTAGTTTTCTATTTATTTTCTA
Found at i:397307 original size:20 final size:21
Alignment explanation
Indices: 397284--397323 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
397274 TGGTTTATAT
397284 TATATTATAT-TACTTATTTC
1 TATATTATATCTACTTATTTC
* *
397304 TATATTCTATCTATTTATTT
1 TATATTATATCTACTTATTT
397324 TTTTATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTATATCTACTTATTTC
Found at i:397339 original size:14 final size:13
Alignment explanation
Indices: 397317--397350 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
397307 ATTCTATCTA
397317 TTTATTTTTTTATAT
1 TTTA-TTTTTTAT-T
397332 TTTATTTTTTATT
1 TTTATTTTTTATT
397345 TTTATT
1 TTTATT
397351 ATCTCCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 8 0.42
15 4 0.21
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:397502 original size:22 final size:21
Alignment explanation
Indices: 397477--397566 Score: 67
Period size: 20 Copynumber: 4.2 Consensus size: 21
397467 TTATTATATA
397477 TCTTATTCTTATCTTTTTATTT
1 TCTTATTC-TATCTTTTTATTT
* *
397499 TCTTTTTCCATCTTCTTTATTTT
1 TCTTATTCTATCTT-TTTA-TTT
* * *
397522 ATTTTATTTTAT-TTTTTATTC
1 -TCTTATTCTATCTTTTTATTT
* *
397543 ACTTTTTCT-TCTTTTTATTT
1 TCTTATTCTATCTTTTTATTT
397563 TCTT
1 TCTT
397567 TGTGTTATTT
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
19 1 0.02
20 16 0.31
21 7 0.14
22 15 0.29
23 5 0.10
24 7 0.14
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.73
Consensus pattern (21 bp):
TCTTATTCTATCTTTTTATTT
Found at i:397599 original size:17 final size:16
Alignment explanation
Indices: 397555--397599 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
397545 TTTTTCTTCT
397555 TTTTATTTTCTTTGTG
1 TTTTATTTTCTTTGTG
397571 --TTA-TTTCATTTGTTG
1 TTTTATTTTC-TTTG-TG
397586 TTTTATTTTCTTTG
1 TTTTATTTTCTTTG
397600 ATTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
13 4 0.17
14 7 0.29
15 2 0.08
17 7 0.29
18 4 0.17
ACGTcount: A:0.09, C:0.07, G:0.11, T:0.73
Consensus pattern (16 bp):
TTTTATTTTCTTTGTG
Found at i:398475 original size:21 final size:20
Alignment explanation
Indices: 398451--398498 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
398441 AACTATGTTG
* *
398451 TTTTTTTTTTCCTTTCATTTA
1 TTTTTTTTTTACATTCA-TTA
*
398472 TTTTTTCTTTACATTCATTA
1 TTTTTTTTTTACATTCATTA
398492 TTTTTTT
1 TTTTTTT
398499 CCTTATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTTTTTACATTCATTA
Found at i:398477 original size:20 final size:19
Alignment explanation
Indices: 398452--398498 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
398442 ACTATGTTGT
* *
398452 TTTTTTTTTCCTTTCATTTA
1 TTTTTTTTTACATTCA-TTA
398472 TTTTTTCTTTACATTCATTA
1 TTTTTT-TTTACATTCATTA
398492 TTTTTTT
1 TTTTTTT
398499 CCTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
21 8 0.33
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTTTACATTCATTA
Found at i:407590 original size:63 final size:59
Alignment explanation
Indices: 407511--407629 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 59
407501 AATACTTCGC
* * * *
407511 TTAGGATGAAAACCCGAGATGGCATCCTAAGTTGGAAAAAAAGAGCAAAAAAGAGAAAAATAT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGG--AAAAA-AG-AAAAAAGAGAAAAATAT
*
407574 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGGAAAAAAGAAAAAAGAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGGAAAAAAGAAAAAAGAGAAAAA
407630 AGAACAAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 14 0.27
60 2 0.04
61 5 0.10
63 30 0.59
ACGTcount: A:0.52, C:0.12, G:0.23, T:0.13
Consensus pattern (59 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGGAAAAAAGAAAAAAGAGAAAAATAT
Found at i:407620 original size:7 final size:7
Alignment explanation
Indices: 407608--407657 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
407598 CCCTAAATTG
407608 GAAAAAA
1 GAAAAAA
407615 GAAAAAAGA
1 G-AAAAA-A
407624 GAAAAAA
1 GAAAAAA
407631 GAACAAAA
1 GAA-AAAA
407639 G-AAAAA
1 GAAAAAA
*
407645 GAGAAAA
1 GAAAAAA
407652 GAAAAA
1 GAAAAA
407658 TAAGGTGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 5 0.14
7 15 0.41
8 15 0.41
9 2 0.05
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:407628 original size:8 final size:8
Alignment explanation
Indices: 407610--407651 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
407600 CTAAATTGGA
407610 AAAAAGA-
1 AAAAAGAG
407617 AAAAAGAG
1 AAAAAGAG
407625 AAAAA-AG
1 AAAAAGAG
407632 AACAAA-AG
1 AA-AAAGAG
407640 AAAAAGAG
1 AAAAAGAG
407648 AAAA
1 AAAA
407652 GAAAAATAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 14 0.44
8 18 0.56
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:408666 original size:41 final size:41
Alignment explanation
Indices: 408595--408674 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
408585 ACATAGGGGC
* * *
408595 CATCCACGATTTCAACTCCATGACGGAGGATATCGTGCCCA
1 CATCCACGATTTAAACTCCACGACGAAGGATATCGTGCCCA
* * *
408636 CATCCACGATTTAAACTTCACGATGAAGGATCTCGTGCC
1 CATCCACGATTTAAACTCCACGACGAAGGATATCGTGCC
408675 AACTCTACAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (41 bp):
CATCCACGATTTAAACTCCACGACGAAGGATATCGTGCCCA
Found at i:409584 original size:17 final size:17
Alignment explanation
Indices: 409552--409602 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
409542 TTTAATATTA
*
409552 TATAATATAT-TTACAT
1 TATAATTTATATTACAT
409568 TATAATTTATATTACAT
1 TATAATTTATATTACAT
* *
409585 GATACAATT-TATTACAT
1 TATA-ATTTATATTACAT
409602 T
1 T
409603 TATCATTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 9 0.31
17 17 0.59
18 3 0.10
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (17 bp):
TATAATTTATATTACAT
Found at i:410674 original size:5 final size:5
Alignment explanation
Indices: 410664--410700 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
410654 ATACGGTTTG
410664 TATTT TATTT TA-TT TA-TT TATTT TATTT TA-TT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
410701 CCTTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 12 0.40
5 18 0.60
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:410681 original size:4 final size:4
Alignment explanation
Indices: 410667--410826 Score: 52
Period size: 4 Copynumber: 39.8 Consensus size: 4
410657 CGGTTTGTAT
*
410667 TTTA TTTTA TTTA TTTA TTTTA TTTTA TTTA TTTCC TTT- TTTA TAATTA
1 TTTA -TTTA TTTA TTTA -TTTA -TTTA TTTA TTT-A TTTA TTTA T--TTA
* * * * * * *
410716 TTT- TTTA TTTT TTTA TATA TATA -TAA TTAGA TTT- CTTA TTTTA CTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA -TTTA TTTA
* * *
410763 TTT- TTTG TTT- TCTA TTTA TTTA TATTA TATTA -CTA TTTA TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA T-TTA TTTA TTTA TTTA TTTA
410809 -TTA TTT- TTCTA TTTA TTT
1 TTTA TTTA TT-TA TTTA TTT
410827 TCTATTATTT
Statistics
Matches: 122, Mismatches: 16, Indels: 35
0.71 0.09 0.20
Matches are distributed among these distances:
3 24 0.20
4 62 0.51
5 32 0.26
6 4 0.03
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:410685 original size:18 final size:18
Alignment explanation
Indices: 410664--410827 Score: 78
Period size: 18 Copynumber: 9.3 Consensus size: 18
410654 ATACGGTTTG
410664 TATTTTATTTTATTTATT
1 TATTTTATTTTATTTATT
410682 TATTTTATTTTATTTATT
1 TATTTTATTTTATTTATT
* * *
410700 TCCTTTT-TTATAATTA-T
1 T-ATTTTATTTTATTTATT
410717 T-TTTTATTTT-TTTATAT
1 TATTTTATTTTATTTAT-T
* * ** *
410734 ATATATAATTAGATTT-CT
1 -TATTTTATTTTATTTATT
*
410752 TATTTTA-CTTATTT-TT
1 TATTTTATTTTATTTATT
* *
410768 TGTTTTCTATTTATTTA--
1 TATTTTAT-TTTATTTATT
* *
410785 TATTATATTACTATTTATT
1 TATTTTATT-TTATTTATT
*
410804 TATTATTATTTT-TCTATT
1 TATT-TTATTTTATTTATT
410822 TATTTT
1 TATTTT
410828 CTATTATTTC
Statistics
Matches: 106, Mismatches: 26, Indels: 29
0.66 0.16 0.18
Matches are distributed among these distances:
15 7 0.07
16 14 0.13
17 21 0.20
18 43 0.41
19 14 0.13
20 7 0.07
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (18 bp):
TATTTTATTTTATTTATT
Found at i:410785 original size:22 final size:21
Alignment explanation
Indices: 410755--410826 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 21
410745 GATTTCTTAT
* *
410755 TTTACTTATTTTTTGTTTTCTA
1 TTTATTTATTTTAT-TTTTCTA
* * *
410777 TTTATTTATATTATATTACTA
1 TTTATTTATTTTATTTTTCTA
410798 TTTATTTATTATTATTTTTCTA
1 TTTATTTATT-TTATTTTTCTA
410820 TTTATTT
1 TTTATTT
410827 TCTATTATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 14 0.34
22 27 0.66
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (21 bp):
TTTATTTATTTTATTTTTCTA
Found at i:410801 original size:17 final size:17
Alignment explanation
Indices: 410779--410836 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
410769 GTTTTCTATT
410779 TATTTATATTA-TATTAC
1 TATTTAT-TTATTATTAC
*
410796 TATTTATTTATTATTAT
1 TATTTATTTATTATTAC
*
410813 TTTTCTATTTATT-TT-C
1 TATT-TATTTATTATTAC
410829 TA-TTATTT
1 TATTTATTT
410837 CTATCATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 5 0.14
15 1 0.03
16 4 0.11
17 17 0.49
18 8 0.23
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTATTTATTATTAC
Found at i:410813 original size:25 final size:22
Alignment explanation
Indices: 410770--410836 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
410760 TTATTTTTTG
410770 TTTTCTATTTATTTA-TATTAT
1 TTTTCTATTTATTTATTATTAT
* *
410791 ATTACTATTTATTTATTATTAT
1 TTTTCTATTTATTTATTATTAT
410813 TTTTCTATTTATTT-TCTATTAT
1 TTTTCTATTTATTTAT-TATTAT
410835 TT
1 TT
410837 CTATCATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 14 0.35
22 26 0.65
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCTATTTATTTATTATTAT
Found at i:410827 original size:11 final size:11
Alignment explanation
Indices: 410770--410840 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
410760 TTATTTTTTG
410770 TTTTCTATTTA
1 TTTTCTATTTA
*
410781 -TTTATA-TTA
1 TTTTCTATTTA
*
410790 TATTACTATTTA
1 T-TTTCTATTTA
410802 TTTAT-TA-TTA
1 TTT-TCTATTTA
410812 TTTTTCTATTTA
1 -TTTTCTATTTA
410824 TTTTCTA-TTA
1 TTTTCTATTTA
410834 -TTTCTAT
1 TTTTCTAT
410841 CATATAGATA
Statistics
Matches: 48, Mismatches: 4, Indels: 17
0.70 0.06 0.25
Matches are distributed among these distances:
9 9 0.19
10 12 0.25
11 20 0.42
12 7 0.15
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTCTATTTA
Found at i:410922 original size:10 final size:11
Alignment explanation
Indices: 410904--410977 Score: 52
Period size: 10 Copynumber: 7.1 Consensus size: 11
410894 TATTGGTTTA
410904 TATTATATTAC
1 TATTATATTAC
*
410915 TATT-TATTAT
1 TATTATATTAC
*
410925 TATTAT-TTAT
1 TATTATATTAC
410935 TATTATTATTA-
1 TATTA-TATTAC
*
410946 T-TAATATT-C
1 TATTATATTAC
410955 TATTTATATTA-
1 TA-TTATATTAC
*
410966 AATTATATTAC
1 TATTATATTAC
410977 T
1 T
410978 TATTTCTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
9 5 0.10
10 28 0.56
11 14 0.28
12 3 0.06
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTATATTAC
Found at i:410925 original size:13 final size:13
Alignment explanation
Indices: 410909--410953 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
410899 GTTTATATTA
*
410909 TATTACTATTTAT
1 TATTATTATTTAT
410922 TATTATTATTTAT
1 TATTATTATTTAT
410935 TATTATTA-TTAT
1 TATTATTATTTAT
*
410947 TAATATT
1 TATTATT
410954 CTATTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:410926 original size:3 final size:3
Alignment explanation
Indices: 410904--410953 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
410894 TATTGGTTTA
* *
410904 TAT TA- TAT TAC TATT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
410950 TAT T
1 TAT T
410954 CTATTTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:410973 original size:118 final size:118
Alignment explanation
Indices: 410730--410974 Score: 322
Period size: 118 Copynumber: 2.1 Consensus size: 118
410720 TTATTTTTTT
* *
410730 ATATATATATAATTAGATTTCTTATTTTACTTATTTTTTGTTTTCTATTTATTTATATTATATTA
1 ATATATATTTAATTAGATTTCTTATTTTACTTATTTTTTGTTTTCTATTGATTTATATTATATTA
* * *
410795 CTATTTATTTATTATTATTTTTCTATTTATTTTCTATTATTTCTATCATATAG
66 CTATTTATTTATTATTATTTATCTATTTATTATCTATTATTTCTATCATATAA
* *
410848 ATATATATTTAATTATATTTCTTATTTTACTTATTTTTTTCGTTTT-TATTGGTTTATATTATAT
1 ATATATATTTAATTAGATTTCTTATTTTACTTA-TTTTTT-GTTTTCTATTGATTTATATTATAT
*
410912 TACTATTTA-TTATTATTATTTAT-TA-TTATTAT-TATTAATATTCTATTTATATTAA
64 TACTATTTATTTATTATTATTTATCTATTTATTATCTATT-AT-TTCTA-TCATA-TAA
410967 AT-TATATT
1 ATATATATT
410975 ACTTATTTCT
Statistics
Matches: 113, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
115 4 0.04
116 8 0.07
117 7 0.06
118 54 0.48
119 35 0.31
120 5 0.04
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (118 bp):
ATATATATTTAATTAGATTTCTTATTTTACTTATTTTTTGTTTTCTATTGATTTATATTATATTA
CTATTTATTTATTATTATTTATCTATTTATTATCTATTATTTCTATCATATAA
Found at i:411005 original size:119 final size:120
Alignment explanation
Indices: 410730--411006 Score: 281
Period size: 118 Copynumber: 2.3 Consensus size: 120
410720 TTATTTTTTT
* * * * *
410730 ATATATATATAATTAGATTTCTTATTTTAC--TTATTTTTTGTTTTCTATTTATTTATATTATAT
1 ATATATATTTAACTATATTTCTTATTCTACTTTTATTTTTTGTTTTCTATTGATTTATATTATAT
* * *
410793 TACTATTTATTTATTATTATTTTTCTATTTATTTTCTATTATTTCTATCATATAG
66 TACTATTTATTTATTATTATTTATCTATTTATTATCTATTATTTCTATCATATAA
* * * *
410848 ATATATATTTAATTATATTTCTTATTTTACTTATT-TTTTTCGTTTT-TATTGGTTTATATTATA
1 ATATATATTTAACTATATTTCTTATTCTACTT-TTATTTTTTGTTTTCTATTGATTTATATTATA
*
410911 TTACTATTTA-TTATTATTATTTAT-TA-TTATTAT-TATTAATATTCTATTTATATTAA
65 TTACTATTTATTTATTATTATTTATCTATTTATTATCTATT-AT-TTCTA-TCATA-TAA
410967 AT-TATA-TT-ACT-TATTTCTATATTCTATCTATTTATTTTTT
1 ATATATATTTAACTATATTTCT-TATTCTA-CT-TTTATTTTTT
411007 TATATTTTCT
Statistics
Matches: 136, Mismatches: 12, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
115 11 0.08
116 16 0.12
117 13 0.10
118 55 0.40
119 29 0.21
120 10 0.07
121 2 0.01
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (120 bp):
ATATATATTTAACTATATTTCTTATTCTACTTTTATTTTTTGTTTTCTATTGATTTATATTATAT
TACTATTTATTTATTATTATTTATCTATTTATTATCTATTATTTCTATCATATAA
Found at i:411216 original size:36 final size:34
Alignment explanation
Indices: 411170--411264 Score: 109
Period size: 35 Copynumber: 2.6 Consensus size: 34
411160 ATTATATATC
411170 TTATTCTTATTTTTTTTCTTTTTCCATCTTCTTTATT
1 TTATT-TTATTTTTTTTCTTTTT-CATCTT-TTTATT
* *
411207 TTATTTTATTTTTTTCACTTTTTCGTCTTTTTATT
1 TTATTTTATTTTTTT-TCTTTTTCATCTTTTTATT
* *
411242 TTCTTTGATTTCTTTTTCTTTTT
1 TTATTTTATTT-TTTTTCTTTTT
411265 TTGTTAATTC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
35 21 0.41
36 19 0.37
37 11 0.22
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.75
Consensus pattern (34 bp):
TTATTTTATTTTTTTTCTTTTTCATCTTTTTATT
Found at i:412941 original size:18 final size:18
Alignment explanation
Indices: 412914--412955 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
412904 GTTCCGACCC
*
412914 GACCCAACCCGACCGGTT
1 GACCCGACCCGACCGGTT
* *
412932 TACCCGACCCGACCTGTT
1 GACCCGACCCGACCGGTT
412950 GACCCG
1 GACCCG
412956 TTGACCGTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.19, C:0.45, G:0.21, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGACCGGTT
Found at i:418058 original size:23 final size:23
Alignment explanation
Indices: 418032--418075 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
418022 CGACTGGTTT
418032 ACCCGACCCGACCAGTTGACCCG
1 ACCCGACCCGACCAGTTGACCCG
*
418055 ACCCGACCCGACCCGTTGACC
1 ACCCGACCCGACCAGTTGACC
418076 TGTTGACCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.50, G:0.20, T:0.09
Consensus pattern (23 bp):
ACCCGACCCGACCAGTTGACCCG
Found at i:418075 original size:18 final size:18
Alignment explanation
Indices: 418013--418062 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
418003 GACCGGTTCC
* **
418013 GACCTGACCCGACTGGTT
1 GACCCGACCCGACCAGTT
*
418031 TACCCGACCCGACCAGTT
1 GACCCGACCCGACCAGTT
418049 GACCCGACCCGACC
1 GACCCGACCCGACC
418063 CGACCCGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.44, G:0.22, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGACCAGTT
Found at i:423334 original size:21 final size:21
Alignment explanation
Indices: 423305--423357 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
423295 ATTCTGACTA
423305 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
423326 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
423347 TCGCAATGCGA
1 TCGCATTGCGA
423358 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:423502 original size:20 final size:20
Alignment explanation
Indices: 423347--423494 Score: 235
Period size: 20 Copynumber: 7.4 Consensus size: 20
423337 TTTTCCTAAT
*
423347 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
423367 TGGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
423387 TGGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
423407 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
423427 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
423447 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
423467 TCGCAATGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
423487 TCGCAACG
1 TCGCAACG
423495 AGATTCTGAC
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
19 1 0.01
20 119 0.99
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:423695 original size:22 final size:22
Alignment explanation
Indices: 423670--423725 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
423660 CTCTCTCCGG
423670 CGACATCCGTTCCTATATCCAA
1 CGACATCCGTTCCTATATCCAA
*
423692 CGACATCCGTTCCTATATTCAA
1 CGACATCCGTTCCTATATCCAA
423714 CGACATCC-TTCC
1 CGACATCCGTTCC
423726 CCATCCGGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.25, C:0.38, G:0.09, T:0.29
Consensus pattern (22 bp):
CGACATCCGTTCCTATATCCAA
Found at i:424403 original size:24 final size:24
Alignment explanation
Indices: 424376--424429 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
424366 GTATTCGAAA
424376 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
424400 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
424424 TTTGAT
1 TTTGAT
424430 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:426442 original size:23 final size:24
Alignment explanation
Indices: 426396--426456 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 24
426386 ATCCATTTTT
426396 TTATTAGTATTAATATATATATATA
1 TTATTAGTATT-ATATATATATATA
426421 TGTATTA-TATTATA-ATATATATA
1 T-TATTAGTATTATATATATATATA
*
426444 TTATTATTATTAT
1 TTATTAGTATTAT
426457 TACTATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.15
23 16 0.47
24 3 0.09
25 5 0.15
26 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (24 bp):
TTATTAGTATTATATATATATATA
Found at i:426450 original size:3 final size:3
Alignment explanation
Indices: 426396--426488 Score: 73
Period size: 3 Copynumber: 30.0 Consensus size: 3
426386 ATCCATTTTT
* * *
426396 TTA TTA GTA TTA ATA -TA TATA TATA TGTA TTA -TA TTA TAA TATA TATA
1 TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA T-TA T-TA
* * *
426444 TTA TTA TTA TTA TTA CTA TTA TTA TTA ATA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
426489 ATATATGTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
2 4 0.05
3 56 0.74
4 16 0.21
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:428209 original size:33 final size:32
Alignment explanation
Indices: 428146--428219 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 32
428136 TTATTATATA
* *
428146 TTTTTATTATTTTAGTTACTTAATTTTCTATTT
1 TTTTTATTATTTTAGTTA-TTAACTATCTATTT
428179 TTTTTATTATTTTAGTCT-TTAAACTATCTATTT
1 TTTTTATTATTTTAGT-TATT-AACTATCTATTT
*
428212 TTATTATT
1 TTTTTATT
428220 TAAGTACCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 2 0.06
33 33 0.92
34 1 0.03
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (32 bp):
TTTTTATTATTTTAGTTATTAACTATCTATTT
Found at i:439878 original size:11 final size:11
Alignment explanation
Indices: 439857--439914 Score: 68
Period size: 10 Copynumber: 5.4 Consensus size: 11
439847 GTACTATGCT
439857 TGAAGAAAAAAA
1 TGAA-AAAAAAA
439869 TG-AAAAAAAA
1 TGAAAAAAAAA
439879 T-AAAAAAAAA
1 TGAAAAAAAAA
*
439889 GGAAAAAAAAA
1 TGAAAAAAAAA
439900 -GAAATAAAAAA
1 TGAAA-AAAAAA
439911 TGAA
1 TGAA
439915 GAGAAAAAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
10 20 0.49
11 16 0.39
12 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (11 bp):
TGAAAAAAAAA
Found at i:441281 original size:135 final size:135
Alignment explanation
Indices: 441039--441292 Score: 465
Period size: 135 Copynumber: 1.9 Consensus size: 135
441029 GAGGTGACTT
441039 AACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAATTCATAAT
1 AACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAATTCATAAT
441104 GAGAAGAGCTTGTTCGACCTATCACTTGATTCACAGCATTTCGAATCAGTGACGCCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTTGATTCACAGCATTTCGAATCAGTGACGCCTCGCTTGAG
441169 GGATC
131 GGATC
*
441174 AACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAAT
1 AACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAATTCATAAT
* *
441239 GAGAAGAGCTTGTTTGACCTATCACTTGGTTCAC-GACATTTCGAATCAGTGACG
66 GAGAAGAGCTTGTTCGACCTATCACTTGATTCACAG-CATTTCGAATCAGTGACG
441293 TCTTTCAATG
Statistics
Matches: 115, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
134 1 0.01
135 114 0.99
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (135 bp):
AACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAATTCATAAT
GAGAAGAGCTTGTTCGACCTATCACTTGATTCACAGCATTTCGAATCAGTGACGCCTCGCTTGAG
GGATC
Found at i:441413 original size:116 final size:115
Alignment explanation
Indices: 441179--441401 Score: 254
Period size: 116 Copynumber: 1.9 Consensus size: 115
441169 GGATCAACAT
* *
441179 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAA
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGAAAGAAGAAGTTCATAATGAGAA
* ** * ** * ** * **
441244 GAGCTTGTTTGACCTATCACTTGGTTCACGACATTTCGAATCAGTGACGTC
66 GAACTTGTTCAACCTAACAC-TGAATCAAGACATAACAAAAAAGTGACGTC
441295 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGAAAGAAGAAGTTCATAATGAGAA
1 TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGAAAGAAGAAGTTCATAATGAGAA
*
441360 GAACTTGTTCAATCC-AACAAC-GAATGAAGAC-TGAACAAAAAA
66 GAACTTGTTCAA-CCTAAC-ACTGAATCAAGACAT-AACAAAAAA
441402 TTGTTTGTCT
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
114 1 0.01
115 10 0.11
116 74 0.83
117 4 0.04
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.23
Consensus pattern (115 bp):
TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGAAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTAACACTGAATCAAGACATAACAAAAAAGTGACGTC
Found at i:441503 original size:25 final size:26
Alignment explanation
Indices: 441467--441567 Score: 96
Period size: 25 Copynumber: 4.2 Consensus size: 26
441457 ATCCATTTTT
441467 TTATTAGTATTAAT-ATATATATATA
1 TTATTAGTATTAATAATATATATATA
441492 TGTATTA-TATT-ATAATATATATATA
1 T-TATTAGTATTAATAATATATATATA
*
441517 TTATTATTATT-AT--TAT-TAT-TA
1 TTATTAGTATTAATAATATATATATA
* *
441538 CTATTATTATTAATAATAT-TAT-TA
1 TTATTAGTATTAATAATATATATATA
441562 TTATTA
1 TTATTA
441568 ATATATGTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
21 12 0.18
22 5 0.07
23 3 0.04
24 20 0.29
25 23 0.34
26 5 0.07
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (26 bp):
TTATTAGTATTAATAATATATATATA
Found at i:441508 original size:27 final size:28
Alignment explanation
Indices: 441467--441559 Score: 95
Period size: 27 Copynumber: 3.4 Consensus size: 28
441457 ATCCATTTTT
*
441467 TTATTAGTATTAATATATATATA-TATGTA
1 TTATTATTA-TAATATATATATATTAT-TA
441496 TTA-TATTATAATATATATATATTATTA
1 TTATTATTATAATATATATATATTATTA
*
441523 TTATTATTATTAT-TACTAT-TATTATTA
1 TTATTATTATAATATA-TATATATTATTA
* *
441550 ATAATATTAT
1 TTATTATTAT
441560 TATTATTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
27 36 0.63
28 18 0.32
29 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (28 bp):
TTATTATTATAATATATATATATTATTA
Found at i:441523 original size:3 final size:3
Alignment explanation
Indices: 441467--441567 Score: 82
Period size: 3 Copynumber: 33.0 Consensus size: 3
441457 ATCCATTTTT
* * *
441467 TTA TTA GTA TTA ATA -TA TATA TATA TGTA TTA -TA TTA -TA ATA TATA
1 TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA T-TA
* * *
441513 TATA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA ATA ATA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
441559 TTA TTA TTA
1 TTA TTA TTA
441568 ATATATGTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
2 6 0.07
3 61 0.73
4 17 0.20
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:443231 original size:32 final size:31
Alignment explanation
Indices: 443165--443241 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
443155 GTTTTTATTA
* *
443165 TATTTTTTTATTAGTTTAGTTACTTAATTTTC
1 TATTTTTTTATTAGTTTAGTTA-TTAACTATC
*
443197 TATTTTTTTATTATTTTAGTCT-TTAAACTATC
1 TATTTTTTTATTAGTTTAGT-TATT-AACTATC
443229 TATTTTTATTATT
1 TATTTTT-TTATT
443242 TAAGTACCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
31 2 0.05
32 31 0.79
33 6 0.15
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.66
Consensus pattern (31 bp):
TATTTTTTTATTAGTTTAGTTATTAACTATC
Found at i:444301 original size:20 final size:20
Alignment explanation
Indices: 444276--444364 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
444266 TAACGCGGAA
444276 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
444296 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* * *
444316 ATCGCAATGTGGAATTGACT
1 ATCGCAACGCGGAAATGACT
444336 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
444356 ATCGCAACG
1 ATCGCAACG
444365 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 57 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:444517 original size:14 final size:14
Alignment explanation
Indices: 444498--444534 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
444488 CATCAATTAA
444498 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
444512 ACAAATCATCTTTT
1 ACAAATCAACATTT
444526 ACAAATCAA
1 ACAAATCAA
444535 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:446502 original size:20 final size:20
Alignment explanation
Indices: 446479--446632 Score: 120
Period size: 20 Copynumber: 8.3 Consensus size: 20
446469 GAAACTTAAA
*
446479 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
446499 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
446519 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
*
446539 ATCGCAAT--G-AGA-GA--
1 ATCGCAATGCGAAAATGACT
**
446553 ATCGCAATGCG-AAATGAAA
1 ATCGCAATGCGAAAATGACT
446572 ATCGCAA--C-AACAA--A--
1 ATCGCAATGCGAA-AATGACT
*
446586 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
446606 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
446626 ATCGCAA
1 ATCGCAA
446633 CGAGAGAATC
Statistics
Matches: 111, Mismatches: 9, Indels: 28
0.75 0.06 0.19
Matches are distributed among these distances:
14 15 0.14
16 9 0.08
17 7 0.06
18 4 0.04
19 7 0.06
20 69 0.62
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:446557 original size:34 final size:33
Alignment explanation
Indices: 446519--446614 Score: 102
Period size: 34 Copynumber: 2.8 Consensus size: 33
446509 GAAAATGACT
* * *
446519 ATCGCAATGCGAATTTGACTATCGCAATGAGAGA
1 ATCGCAATGCGAA-ATGACTATCGCAATGACAAA
** **
446553 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGACTATCGCAATGACAAA
*
446586 ATCGCAACGCGAAAATGACTATCGCAATG
1 ATCGCAATGCG-AAATGACTATCGCAATG
446615 CGAATTTGAC
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
33 23 0.47
34 26 0.53
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.18
Consensus pattern (33 bp):
ATCGCAATGCGAAATGACTATCGCAATGACAAA
Found at i:446707 original size:20 final size:20
Alignment explanation
Indices: 446693--446839 Score: 186
Period size: 20 Copynumber: 7.8 Consensus size: 20
446683 AATAGTTAAA
446693 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
*
446713 TTCGCATTACGATAGTCATT
1 TTCGCATTGCGATAGTCATT
446733 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
*
446753 TTCGCATTGTGATAGTCATT
1 TTCGCATTGCGATAGTCATT
*
446773 TTCGCATTGTGAT--TC--T
1 TTCGCATTGCGATAGTCATT
*
446789 CTCG--TTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
*
446807 TTCGC---GTGATAGTCATT
1 TTCGCATTGCGATAGTCATT
446824 TTCGCATTGCGATAGT
1 TTCGCATTGCGATAGT
446840 AAACTATTCT
Statistics
Matches: 111, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.05
16 6 0.05
17 16 0.14
18 6 0.05
20 77 0.69
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCATT
Found at i:448766 original size:20 final size:20
Alignment explanation
Indices: 448718--448767 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
448708 GAAACTTTAA
*
448718 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
448738 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
448758 ATCGCAACGC
1 ATCGCAACGC
448768 AAGAATCGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:448836 original size:20 final size:20
Alignment explanation
Indices: 448811--448853 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
448801 GATTCTCTCG
448811 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
448831 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
448851 TTG
1 TTG
448854 TGATTCACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:449468 original size:20 final size:20
Alignment explanation
Indices: 449445--449497 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
449435 CGATAGTCAG
*
449445 ATTCGCATTGCGTTTTACGT
1 ATTCGCATTGCGATTTACGT
*
449465 ATTCGCATTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
*
449485 AATCGCATTGCGA
1 ATTCGCATTGCGA
449498 ATTGGAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:449509 original size:21 final size:21
Alignment explanation
Indices: 449485--449537 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
449475 CAATTTACGT
*
449485 AATCGCATTGCGAATTGGAAA
1 AATCGCAATGCGAATTGGAAA
* *
449506 AATCGCAACGCGAATTTGAAA
1 AATCGCAATGCGAATTGGAAA
449527 AATCGCAATGC
1 AATCGCAATGC
449538 AATAGTCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (21 bp):
AATCGCAATGCGAATTGGAAA
Found at i:453708 original size:13 final size:13
Alignment explanation
Indices: 453686--453723 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
453676 TGTTTTATTG
453686 AAAATATATTTTAA
1 AAAAT-TATTTTAA
453700 AAAATTATTTT-A
1 AAAATTATTTTAA
*
453712 AGAATTATTTTA
1 AAAATTATTTTA
453724 TATTGTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 6 0.27
14 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AAAATTATTTTAA
Found at i:455421 original size:30 final size:29
Alignment explanation
Indices: 455358--455463 Score: 88
Period size: 30 Copynumber: 3.6 Consensus size: 29
455348 TGAAAAATAA
* * *
455358 TTTAGGTAAAATGGATTGCCTCAAAACTT-T
1 TTTACGTAAAATGAATTGCAT-AAAA-TTGT
*
455388 TTTATGTAAAATGAATTGCATGAAAATTGT
1 TTTACGTAAAATGAATTGCAT-AAAATTGT
* * ** *
455418 TTTACATAAAATTAATTATATAAAACTGT
1 TTTACGTAAAATGAATTGCATAAAATTGT
*
455447 TCTACGTAAAATGAATT
1 TTTACGTAAAATGAATT
455464 ATATTTTCTG
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
29 23 0.37
30 39 0.63
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (29 bp):
TTTACGTAAAATGAATTGCATAAAATTGT
Found at i:455456 original size:29 final size:29
Alignment explanation
Indices: 455394--455467 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
455384 CTTTTTTATG
** * *
455394 TAAAATGAATTGCATGAAAATTGTTTTACA
1 TAAAATGAATTATAT-AAAACTGTTCTACA
* *
455424 TAAAATTAATTATATAAAACTGTTCTACG
1 TAAAATGAATTATATAAAACTGTTCTACA
455453 TAAAATGAATTATAT
1 TAAAATGAATTATAT
455468 TTTCTGAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (29 bp):
TAAAATGAATTATATAAAACTGTTCTACA
Found at i:455730 original size:19 final size:19
Alignment explanation
Indices: 455706--455757 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
455696 TATTAGTATT
455706 TTATTAATATAATACTAAA
1 TTATTAATATAATACTAAA
*
455725 TTATT-ATAGTAATAGTAAA
1 TTATTAATA-TAATACTAAA
*
455744 TGTATAAAT-TAATA
1 T-TATTAATATAATA
455758 TTACTCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 3 0.11
21 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (19 bp):
TTATTAATATAATACTAAA
Found at i:455918 original size:19 final size:18
Alignment explanation
Indices: 455894--455936 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
455884 GAGTAGATAC
455894 TAATATAATATTAAAAATA
1 TAATAT-ATATTAAAAATA
455913 TAATAT-TATTAAAAA-A
1 TAATATATATTAAAAATA
*
455929 TATTATAT
1 TAATATAT
455937 GTATATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 10 0.45
19 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATATATATTAAAAATA
Found at i:455936 original size:18 final size:17
Alignment explanation
Indices: 455897--455936 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
455887 TAGATACTAA
*
455897 TATAATATTAAAAATAT
1 TATATTATTAAAAATAT
*
455914 AATATTATTAAAAAATAT
1 TATATTATT-AAAAATAT
455932 TATAT
1 TATAT
455937 GTATATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATATTATTAAAAATAT
Found at i:456711 original size:17 final size:17
Alignment explanation
Indices: 456691--456724 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
456681 AACAAAATCA
*
456691 AATTAAACATTTTCAAC
1 AATTAAACATCTTCAAC
*
456708 AATTAGACATCTTCAAC
1 AATTAAACATCTTCAAC
456725 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (17 bp):
AATTAAACATCTTCAAC
Found at i:459695 original size:10 final size:10
Alignment explanation
Indices: 459680--459718 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
459670 GGTTCACTGG
459680 TTCAACCGGA
1 TTCAACCGGA
*
459690 TTCAACCGGG
1 TTCAACCGGA
459700 TTCAACCGCGA
1 TTCAACCG-GA
*
459711 TTGAACCG
1 TTCAACCG
459719 AATTTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.21
Consensus pattern (10 bp):
TTCAACCGGA
Found at i:459703 original size:20 final size:21
Alignment explanation
Indices: 459678--459718 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
459668 TTGGTTCACT
459678 GGTTCAACCG-GATTCAACCG
1 GGTTCAACCGCGATTCAACCG
*
459698 GGTTCAACCGCGATTGAACCG
1 GGTTCAACCGCGATTCAACCG
459719 AATTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (21 bp):
GGTTCAACCGCGATTCAACCG
Found at i:467065 original size:23 final size:24
Alignment explanation
Indices: 467015--467066 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
467005 TATACGTGAC
*
467015 CACAAGAGCAGAGAAAACGCGTGT
1 CACAAGAGCAGAGAAAACGAGTGT
* *
467039 CACAAGAGCATATAAAAC-AGTGT
1 CACAAGAGCAGAGAAAACGAGTGT
467062 CACAA
1 CACAA
467067 TGATAAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (24 bp):
CACAAGAGCAGAGAAAACGAGTGT
Found at i:467523 original size:13 final size:15
Alignment explanation
Indices: 467498--467535 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
467488 AAATGATAAT
467498 TAAATTATTTTAGA-A
1 TAAATT-TTTTAGACA
467513 T-AATTTTTTAGACA
1 TAAATTTTTTAGACA
467527 TAAATTTTT
1 TAAATTTTT
467536 CATAAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.33
14 6 0.29
15 8 0.38
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (15 bp):
TAAATTTTTTAGACA
Found at i:473652 original size:23 final size:23
Alignment explanation
Indices: 473626--473670 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
473616 TCCAAATTAT
473626 ACAAATTC-AAATTTTAACTTAAA
1 ACAAATTCAAAATTTT-ACTTAAA
*
473649 ACAAGTTCAAAATTTTACTTAA
1 ACAAATTCAAAATTTTACTTAA
473671 GGTTGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (23 bp):
ACAAATTCAAAATTTTACTTAAA
Found at i:474962 original size:29 final size:27
Alignment explanation
Indices: 474930--474983 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
474920 AATTTATTTA
474930 GATATTAAACTTTCAAAACTTATATAATG
1 GATATTAAACTTT-AAAA-TTATATAATG
*
474959 GATATTAAACTTTAAAATTTTATAA
1 GATATTAAACTTTAAAATTATATAA
474984 AATAGATGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.29
28 4 0.17
29 13 0.54
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (27 bp):
GATATTAAACTTTAAAATTATATAATG
Found at i:476777 original size:2 final size:2
Alignment explanation
Indices: 476761--476793 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
476751 CAGCTGTGGA
476761 AT AT AGT AT -T AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
476794 CTTAAGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:477626 original size:58 final size:58
Alignment explanation
Indices: 477564--477679 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
477554 GACACGTTTC
477564 ATTTAACGGAGAAAATTAATACCATTGACAGCCCAATTACCTAAAGTGATAATATTTA
1 ATTTAACGGAGAAAATTAATACCATTGACAGCCCAATTACCTAAAGTGATAATATTTA
477622 ATTTAACGGAGAAAATTAATACCATTGACAGCCCAATTACCTAAAGTGATAATATTTA
1 ATTTAACGGAGAAAATTAATACCATTGACAGCCCAATTACCTAAAGTGATAATATTTA
477680 TAATATTAGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (58 bp):
ATTTAACGGAGAAAATTAATACCATTGACAGCCCAATTACCTAAAGTGATAATATTTA
Found at i:478121 original size:33 final size:33
Alignment explanation
Indices: 478074--478144 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
478064 ACAAAGTTTA
* * * *
478074 CGAT-AATTGAAATACTTGAATACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
478106 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
478139 CGATAA
1 CGATAA
478145 TTAAAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 4 0.12
33 30 0.88
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:490851 original size:12 final size:12
Alignment explanation
Indices: 490834--490858 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
490824 TCTTATACTA
490834 TTAAAAAATAAT
1 TTAAAAAATAAT
490846 TTAAAAAATAAT
1 TTAAAAAATAAT
490858 T
1 T
490859 GATGTTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAAAAAATAAT
Found at i:496734 original size:57 final size:57
Alignment explanation
Indices: 496642--496753 Score: 197
Period size: 57 Copynumber: 2.0 Consensus size: 57
496632 GAACCACTAG
** *
496642 CACCTCTGTAGCAAAACCAAGAATCTGATCCTAGTCCAAGATCTTGTGAAGATCCAT
1 CACCTCTACAGCAAAACCAAGAATCTGATCATAGTCCAAGATCTTGTGAAGATCCAT
496699 CACCTCTACAGCAAAACCAAGAATCTGATCATAGTCCAAGATCTTGTGAAGATCC
1 CACCTCTACAGCAAAACCAAGAATCTGATCATAGTCCAAGATCTTGTGAAGATCC
496754 TTCAGGTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (57 bp):
CACCTCTACAGCAAAACCAAGAATCTGATCATAGTCCAAGATCTTGTGAAGATCCAT
Found at i:500249 original size:26 final size:26
Alignment explanation
Indices: 500201--500250 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
500191 AGAAATAAAT
*
500201 AAATAAATTAAATTAAAATGAAGAAA
1 AAATAAATTAAATTAAAAAGAAGAAA
500227 AAATAAATTAAA-TAAAAGAGAAGA
1 AAATAAATTAAATTAAAA-AGAAGA
500251 TAAAGAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (26 bp):
AAATAAATTAAATTAAAAAGAAGAAA
Found at i:500287 original size:4 final size:4
Alignment explanation
Indices: 500280--500408 Score: 54
Period size: 4 Copynumber: 31.2 Consensus size: 4
500270 ATAGTAAGTA
* * * * * *
500280 AAAT AAAT ATAAA AAAT AAAAA AAAT AAA- AAAA AGAAG AAAA AAAT ATAT
1 AAAT AAAT A-AAT AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
*
500330 AAAT AAAAC AAAT AAAT CAAAT -AAT -AAT AAA- AAAGT AAA- AATATT
1 AAAT -AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAA-T AAAT AA-A-T
*
500375 ATAT ATAAT AAAT AAAT AAAAT AAA- AAAT AAAT A
1 AAAT A-AAT AAAT AAAT -AAAT AAAT AAAT AAAT A
500409 TATATATCAA
Statistics
Matches: 97, Mismatches: 13, Indels: 30
0.69 0.09 0.21
Matches are distributed among these distances:
3 17 0.18
4 52 0.54
5 27 0.28
6 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:500302 original size:9 final size:9
Alignment explanation
Indices: 500278--500402 Score: 63
Period size: 9 Copynumber: 12.8 Consensus size: 9
500268 AAATAGTAAG
*
500278 TAAAATAAA
1 TAAAAAAAA
*
500287 TATAAAAAA
1 TAAAAAAAA
500296 TAAAAAAAA
1 TAAAAAAAA
500305 TAAAAAAAA
1 TAAAAAAAA
*
500314 GAAGAAAAAA
1 TAA-AAAAAA
* *
500324 -ATATATAAA
1 TA-AAAAAAA
*
500333 TAAAACAAA
1 TAAAAAAAA
500342 TAAATCAAATAA
1 TAAA--AAA-AA
500354 TAATAAAAAA
1 TAA-AAAAAA
500364 GTAAAAATATTATA
1 -TAAAAA-A--A-A
* *
500378 TATAATAAA
1 TAAAAAAAA
*
500387 TAAATAAAA
1 TAAAAAAAA
500396 TAAAAAA
1 TAAAAAA
500403 TAAATATATA
Statistics
Matches: 89, Mismatches: 15, Indels: 24
0.70 0.12 0.19
Matches are distributed among these distances:
9 53 0.60
10 14 0.16
11 9 0.10
12 6 0.07
13 6 0.07
14 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:500362 original size:40 final size:39
Alignment explanation
Indices: 500267--500402 Score: 100
Period size: 40 Copynumber: 3.4 Consensus size: 39
500257 AAACAAAGAT
*
500267 AAAATAGTAAGTAAAATAAATATAAAAAATAAAAAAAATAA
1 AAAATAATAA-TAAAA-AAATATAAAAAATAAAAAAAATAA
* * * *
500308 AAAA-AAGAAGAAAAAAATAT-ATAAATAAAACAAATAA
1 AAAATAATAATAAAAAAATATAAAAAATAAAAAAAATAA
* * * * *
500345 ATCAAATAATAATAAAAAAGTA-AAAATATTATATATAATAA
1 A--AAATAATAATAAAAAAATATAAAA-AATAAAAAAAATAA
500386 ATAAATAA-AATAAAAAA
1 A-AAATAATAATAAAAAA
500403 TAAATATATA
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
37 16 0.21
38 6 0.08
39 16 0.21
40 23 0.31
41 14 0.19
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (39 bp):
AAAATAATAATAAAAAAATATAAAAAATAAAAAAAATAA
Found at i:500405 original size:49 final size:50
Alignment explanation
Indices: 500280--500405 Score: 127
Period size: 49 Copynumber: 2.5 Consensus size: 50
500270 ATAGTAAGTA
500280 AAATAAATATAA-AAAATAAAAAA-AATAAAAAAAAGAAGAAAAAAATATAT
1 AAATAAATA-AATAAAATAAAAAATAAT-AAAAAAAGAAGAAAAAAATATAT
* * * * *
500330 AAATAAAACAAAT-AAATCAAATAATAAT-AAAAAAGTA-AAAATATTATAT
1 AAAT-AAATAAATAAAAT-AAAAAATAATAAAAAAAGAAGAAAAAAATATAT
500379 ATAATAAATAAATAAAATAAAAAATAA
1 A-AATAAATAAATAAAATAAAAAATAA
500406 ATATATATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
49 26 0.41
50 25 0.40
51 9 0.14
52 3 0.05
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (50 bp):
AAATAAATAAATAAAATAAAAAATAATAAAAAAAGAAGAAAAAAATATAT
Found at i:500450 original size:2 final size:2
Alignment explanation
Indices: 500443--500473 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
500433 AATAAAAATA
500443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
500474 ATCTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:500494 original size:45 final size:45
Alignment explanation
Indices: 500370--500496 Score: 117
Period size: 45 Copynumber: 2.9 Consensus size: 45
500360 AAAAGTAAAA
*
500370 ATAT-TATATATA-ATAA-ATAAATAAAATAAAAA-ATAAATATAT
1 ATATATATATATATATAATATAAA-AAAATAAAAATATATATATAT
* *
500412 ATATCA-AT-TA-ATAAAACTGATAATAAAAAT-AATATATATATATAT
1 ATAT-ATATATATATATAA-T-ATAA-AAAAATAAAAATATATATATAT
*
500457 ATATATATATATATATAATCTAAAAAAATAAAAATATATA
1 ATATATATATATATATAATATAAAAAAATAAAAATATATA
500497 CTAAAATAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 21
0.71 0.06 0.22
Matches are distributed among these distances:
41 1 0.01
42 9 0.13
43 2 0.03
44 10 0.15
45 36 0.54
46 4 0.06
47 5 0.07
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (45 bp):
ATATATATATATATATAATATAAAAAAATAAAAATATATATATAT
Found at i:504856 original size:20 final size:20
Alignment explanation
Indices: 504827--504864 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
504817 CCCCTTCAAA
*
504827 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
504847 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
504865 TGCACCAAAA
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:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:508323 original size:22 final size:21
Alignment explanation
Indices: 508281--508320 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
508271 AAGTTTATTT
*
508281 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
508302 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
508321 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:510813 original size:39 final size:35
Alignment explanation
Indices: 510766--510851 Score: 102
Period size: 35 Copynumber: 2.3 Consensus size: 35
510756 GGGTTTGGTA
*
510766 TTTCAAGAGAAAC-ATTTTCAAAGGTTTTGTGTGTTTGTG
1 TTTCAAGAGAAACAATTTT--AAGGGTTT-T-T-TTTGTG
*
510805 TTTCAAGAGAAACAATTTTGAGGGTTTTTTTTGTG
1 TTTCAAGAGAAACAATTTTAAGGGTTTTTTTTGTG
510840 TTTCAAGAGAAA
1 TTTCAAGAGAAA
510852 TTGTCTCAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
35 18 0.41
36 1 0.02
37 1 0.02
38 6 0.14
39 13 0.30
40 5 0.11
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (35 bp):
TTTCAAGAGAAACAATTTTAAGGGTTTTTTTTGTG
Found at i:510887 original size:36 final size:36
Alignment explanation
Indices: 510838--511071 Score: 211
Period size: 36 Copynumber: 6.6 Consensus size: 36
510828 GTTTTTTTTG
* *
510838 TGTTTCAAGAGAAATTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
510874 TGTTTCAAAAGAAACTGTCTCAAGATAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
510911 AG-TTCTAAAAGAAACTGTCTCAA-AGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGA-GAGACAAAATT
* * *
510947 TGTTTCAAG-GAAA-AGATATTC-A-A-AG----ATTT
1 TGTTTCAAGAGAAACTG-T-CTCAAGAGAGACAAAATT
*
510976 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
511012 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
*
511049 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
511072 AACTCGTTTT
Statistics
Matches: 166, Mismatches: 16, Indels: 31
0.78 0.08 0.15
Matches are distributed among these distances:
29 14 0.08
30 6 0.04
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.01
35 7 0.04
36 76 0.46
37 56 0.34
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:511072 original size:102 final size:102
Alignment explanation
Indices: 510872--511058 Score: 256
Period size: 102 Copynumber: 1.8 Consensus size: 102
510862 AGGGACAAAA
*
510872 TTTGTTTCAAAAGAAACTGTCTCAAGATAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAAGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAAGG
510937 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
66 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
** * **
510974 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TCAAGGGAAACTGTCTC-AAG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCT-AAAAGAAACTGTCTCAAAG
511036 AGAGAC-AAGATTTTGTTTCAAGG
65 -GAGACGAA-A-TTTGTTTCAAGG
511059 GAAACTGTCT
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
100 6 0.08
101 24 0.32
102 45 0.60
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAAGG
AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
Found at i:511187 original size:37 final size:37
Alignment explanation
Indices: 511136--511324 Score: 141
Period size: 37 Copynumber: 5.4 Consensus size: 37
511126 TTAAGGTTTA
* *
511136 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT
511173 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT
** * * * *
511209 AATTTCAAAGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGAGAGACAAAATTT
*
511237 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT
* * * * *
511275 TGTTTTAAGGGAAACTACCCCAAGCGAGATAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT
*
511311 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
511325 TGTTTTCAAT
Statistics
Matches: 116, Mismatches: 23, Indels: 27
0.70 0.14 0.16
Matches are distributed among these distances:
28 2 0.02
29 13 0.11
30 2 0.02
31 1 0.01
32 1 0.01
33 1 0.01
34 1 0.01
35 2 0.02
36 30 0.26
37 60 0.52
38 3 0.03
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT
Found at i:511237 original size:102 final size:102
Alignment explanation
Indices: 511131--511348 Score: 364
Period size: 102 Copynumber: 2.1 Consensus size: 102
511121 CATTTTTAAG
* * *
511131 GTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAA
1 GTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAA
511196 GAGAGACAAAATTAATTTCAAAGGAAATGTTTTCAAT
66 GAGAGACAAAATTAATTTCAAAGGAAATGTTTTCAAT
*
511233 GTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTTAAGGGAAACTACCCCAA
1 GTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAA
* * * *
511298 GCGAGATAAAATTTATTTCAAGGGAAATGTTTTCAAT
66 GAGAGACAAAATTAATTTCAAAGGAAATGTTTTCAAT
511335 GTTTATGTTTCAAG
1 GTTTATGTTTCAAG
511349 GGAGACAAAA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 108 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (102 bp):
GTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAA
GAGAGACAAAATTAATTTCAAAGGAAATGTTTTCAAT
Found at i:511372 original size:87 final size:87
Alignment explanation
Indices: 511257--511438 Score: 274
Period size: 87 Copynumber: 2.1 Consensus size: 87
511247 AGAAACTATC
** * * *
511257 TCAAGAGAGACAAAATTTTGTTTTAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGAGAGACAAAATTTCATATCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
511322 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * * * *
511344 TCAAGGGAGACAAAATTTCATATCAAGGGAAACTATCTCAATCTAGATAAAATTCATTTCAAGGG
1 TCAAGAGAGACAAAATTTCATATCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
511409 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
511431 TCAAGAGA
1 TCAAGAGA
511439 AACTGTCTCA
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (87 bp):
TCAAGAGAGACAAAATTTCATATCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Done.