Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000521.1 Hibiscus syriacus cultivar Beakdansim tig00000999_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: 1347562
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:334484 original size:19 final size:20
Alignment explanation
Indices: 334454--334491 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
334444 AAAATATTAA
334454 TTATTAAATATTTAAAATAT
1 TTATTAAATATTTAAAATAT
*
334474 TTATT-AATATTTATAATA
1 TTATTAAATATTTAAAATA
334492 ATATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATTAAATATTTAAAATAT
Found at i:334503 original size:22 final size:22
Alignment explanation
Indices: 334478--334572 Score: 91
Period size: 22 Copynumber: 4.2 Consensus size: 22
334468 AAATATTTAT
334478 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
* * *
334500 TAATATTTTTAATATTATAAAA
1 TAATATTTATAATAATATAATA
*
334522 TACATTATATTATAATAATATATTA
1 TA-A-TAT-TTATAATAATATAATA
* * **
334547 TATTTTTTATTTTAATATAATA
1 TAATATTTATAATAATATAATA
334569 TAAT
1 TAAT
334573 TTTTTTTATA
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
22 37 0.65
23 3 0.05
24 3 0.05
25 14 0.25
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:334546 original size:18 final size:17
Alignment explanation
Indices: 334511--334550 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
334501 AATATTTTTA
334511 ATATTATAAAATACATT
1 ATATTATAAAATACATT
*
334528 ATATTATAATAATATATT
1 ATATTATAA-AATACATT
334546 ATATT
1 ATATT
334551 TTTTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTATAAAATACATT
Found at i:334557 original size:25 final size:26
Alignment explanation
Indices: 334469--334596 Score: 77
Period size: 25 Copynumber: 5.0 Consensus size: 26
334459 AAATATTTAA
*
334469 AATATTTATTAATATTT-ATAATAATAT
1 AATATTT-TTTAT-TTTAATAATAATAT
** * * *
334496 AATATAATAT-TTTTAAT-ATTATAA
1 AATATTTTTTATTTTAATAATAATAT
** * *
334520 AATACATTATATTATAATAAT-ATAT
1 AATATTTTTTATTTTAATAATAATAT
*
334545 TATATTTTTTATTTTAAT-ATAATAT
1 AATATTTTTTATTTTAATAATAATAT
*
334570 AATTTTTTTTATATTTAATAATGAATA
1 AATATTTTTTAT-TTTAATAAT-AATA
334597 ATTTTATTTA
Statistics
Matches: 77, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
24 18 0.23
25 39 0.51
26 9 0.12
27 7 0.09
28 4 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
AATATTTTTTATTTTAATAATAATAT
Found at i:334586 original size:26 final size:26
Alignment explanation
Indices: 334526--334622 Score: 94
Period size: 26 Copynumber: 3.7 Consensus size: 26
334516 ATAAAATACA
* *
334526 TTATATTATAATA-ATATATTATATTTT
1 TTATATT-TAATATA-ATATAATTTTTT
334553 TTAT-TTTAATATAATATAATTTTTT
1 TTATATTTAATATAATATAATTTTTT
*
334578 TTATATTTAATAATGA-ATAATTTTATT
1 TTATATTTAAT-ATAATATAATTTT-TT
334605 TATATATTTAA-ATAATAT
1 T-TATATTTAATATAATAT
334623 TTTAGTAAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
25 19 0.32
26 20 0.33
27 12 0.20
28 9 0.15
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTATATTTAATATAATATAATTTTTT
Found at i:334624 original size:24 final size:25
Alignment explanation
Indices: 334527--334664 Score: 67
Period size: 27 Copynumber: 5.5 Consensus size: 25
334517 TAAAATACAT
334527 TATA-TTATAATAATATATTATATTT-
1 TATATTTA-AATAATATATT-TATTTA
* *
334552 TTTATTTTAATATAATATAATTT-TTTT
1 TATA-TTTAA-ATAATAT-ATTTATTTA
334579 TATATTT-AATAATGAATAATTTTATTTA
1 TATATTTAAATAAT--AT-A-TTTATTTA
* *
334607 TATATTTAAATAATAT-TTTAGTAA
1 TATATTTAAATAATATATTTATTTA
* * * *
334631 GATATTT-AA-AATATACTAATTAA
1 TATATTTAAATAATATATTTATTTA
334654 TAT-TTTAAATA
1 TATATTTAAATA
334665 TAATATAACA
Statistics
Matches: 90, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
22 8 0.09
23 11 0.12
24 18 0.20
25 4 0.04
26 11 0.12
27 19 0.21
28 13 0.14
29 6 0.07
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (25 bp):
TATATTTAAATAATATATTTATTTA
Found at i:334817 original size:20 final size:19
Alignment explanation
Indices: 334761--334817 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
334751 TAATGAAATT
334761 ATAAA-AATAATATTTAATA
1 ATAAATAATAATA-TTAATA
* *
334780 ATAAATAAATTATTTTAATA
1 ATAAAT-AATAATATTAATA
*
334800 TTTAAATAATAATATTAA
1 -ATAAATAATAATATTAA
334818 GTTTTATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 5 0.17
20 15 0.50
21 10 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAATAATAATATTAATA
Found at i:335053 original size:30 final size:29
Alignment explanation
Indices: 334978--335069 Score: 130
Period size: 29 Copynumber: 3.1 Consensus size: 29
334968 TCTAGAAATG
334978 TTCATTTTTCAAAATTCAAATTCCAGTAA
1 TTCATTTTTCAAAATTCAAATTCCAGTAA
* * *
335007 TTTATTTTCCAAAATTCAAATTCTAGTAA
1 TTCATTTTTCAAAATTCAAATTCCAGTAA
* *
335036 TTCATTTTTCAGTAATTCAAATTCCAATAA
1 TTCATTTTTCA-AAATTCAAATTCCAGTAA
335066 TTCA
1 TTCA
335070 AATTCCGAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
29 35 0.65
30 19 0.35
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.43
Consensus pattern (29 bp):
TTCATTTTTCAAAATTCAAATTCCAGTAA
Found at i:335075 original size:15 final size:15
Alignment explanation
Indices: 334990--335075 Score: 84
Period size: 15 Copynumber: 5.8 Consensus size: 15
334980 CATTTTTCAA
334990 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
* ** *
335005 AATTTATTTTCCA-A
1 AATTCAAATTCCAGT
*
335019 AATTCAAATTCTAGT
1 AATTCAAATTCCAGT
** *
335034 AATTCATTTTTCAGT
1 AATTCAAATTCCAGT
*
335049 AATTCAAATTCCAAT
1 AATTCAAATTCCAGT
335064 AATTCAAATTCC
1 AATTCAAATTCC
335076 GAAAAACCAA
Statistics
Matches: 53, Mismatches: 17, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
14 9 0.17
15 44 0.83
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.41
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:335353 original size:18 final size:18
Alignment explanation
Indices: 335315--335353 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
335305 TCTTCAACTA
**
335315 TTAAAAGTTATAAAATTG
1 TTAAAAGTTATAAAACGG
335333 TTAAAAGTTATAAAACGG
1 TTAAAAGTTATAAAACGG
335351 TTA
1 TTA
335354 CTGACTATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (18 bp):
TTAAAAGTTATAAAACGG
Found at i:338055 original size:23 final size:23
Alignment explanation
Indices: 338029--338080 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
338019 CCAAACGACC
*
338029 GAAAAATGTGTCA-AAAGACAGA
1 GAAAAACGTGTCATAAAGACAGA
*
338051 -AGAAAACGTGTCATACAGACAGA
1 GA-AAAACGTGTCATAAAGACAGA
338074 GAAAAAC
1 GAAAAAC
338081 ATATCATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 10 0.40
23 13 0.52
24 1 0.04
ACGTcount: A:0.54, C:0.13, G:0.21, T:0.12
Consensus pattern (23 bp):
GAAAAACGTGTCATAAAGACAGA
Found at i:338056 original size:22 final size:22
Alignment explanation
Indices: 338031--338078 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
338021 AAACGACCGA
*
338031 AAAATGTGTCA-AAAGACAGAAG
1 AAAACGTGTCATAAAGACAG-AG
*
338053 AAAACGTGTCATACAGACAGAG
1 AAAACGTGTCATAAAGACAGAG
338075 AAAA
1 AAAA
338079 ACATATCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.54, C:0.12, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAACGTGTCATAAAGACAGAG
Found at i:338087 original size:23 final size:23
Alignment explanation
Indices: 338044--338092 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
338034 ATGTGTCAAA
* *
338044 AGACAGAAGAAAACGTGTCATAC
1 AGACAGAAGAAAACATATCATAC
338067 AGACAG-AGAAAAACATATCATAC
1 AGACAGAAG-AAAACATATCATAC
338090 AGA
1 AGA
338093 AAGACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.12
Consensus pattern (23 bp):
AGACAGAAGAAAACATATCATAC
Found at i:339662 original size:139 final size:139
Alignment explanation
Indices: 339402--339679 Score: 385
Period size: 139 Copynumber: 2.0 Consensus size: 139
339392 ATATATTTTT
* *
339402 TCATTAAGTCCATATTTTACTAAATAAAAATAAAAAATTCGAGTCAAATAAAATCATATGAGATA
1 TCATTAAGTCCATATTTTACTAAATAAAAATAAAAAAATCGAGTCAAACAAAATCATATGAGATA
** * * ** * * * * *
339467 CCAAAATTCAGTTCAAGTTCTGGTGAAGGGTGCATTTCTCGAGTCGAGTTAGATCACATTAACCG
66 CCAAAATTCAAATCAACTTCAGGTGAAAAGTACATTTCTCGAGTCAAATCAAATCACATTAACCG
*
339532 GAAATTTGA
131 GAAACTTGA
* * * * *
339541 TCATTAGGTCCATATTTTACTAATTAAAAATAAAAAAATCGAGTCAAACCATATCATGTGAGATA
1 TCATTAAGTCCATATTTTACTAAATAAAAATAAAAAAATCGAGTCAAACAAAATCATATGAGATA
339606 CCAAAATTCAAATCAACTTCAGGTGAAAAGTACATTTCTCGAGTCAAATCAAATCACATTAACCG
66 CCAAAATTCAAATCAACTTCAGGTGAAAAGTACATTTCTCGAGTCAAATCAAATCACATTAACCG
339671 GAAACTTGA
131 GAAACTTGA
339680 CCTGTTATTA
Statistics
Matches: 120, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
139 120 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (139 bp):
TCATTAAGTCCATATTTTACTAAATAAAAATAAAAAAATCGAGTCAAACAAAATCATATGAGATA
CCAAAATTCAAATCAACTTCAGGTGAAAAGTACATTTCTCGAGTCAAATCAAATCACATTAACCG
GAAACTTGA
Found at i:345334 original size:32 final size:30
Alignment explanation
Indices: 345293--345373 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 30
345283 TGTCTTTCGA
*
345293 GACATATGGACAGTATACCTATGTTCTAAGG
1 GACATATGGACAGT-TACCTAGGTTCTAAGG
* **
345324 GAACATATGGATAGTTTACCTAGGTTCTTCGG
1 G-ACATATGGACAG-TTACCTAGGTTCTAAGG
*
345356 GACCTATGGACAGTTACC
1 GACATATGGACAGTTACC
345374 GGGAATCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
30 5 0.12
31 11 0.26
32 25 0.60
33 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (30 bp):
GACATATGGACAGTTACCTAGGTTCTAAGG
Found at i:345426 original size:30 final size:30
Alignment explanation
Indices: 345356--345428 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
345346 GGTTCTTCGG
* * *
345356 GACCTATGGACAGTTACCGGGAATCTTTAT
1 GACCTCTGGATAGTTACCGAGAATCTTTAT
345386 GACCTCTGGATAGTTACCGA-AGATCTTTAT
1 GACCTCTGGATAGTTACCGAGA-ATCTTTAT
345416 GACCTCTGGATAG
1 GACCTCTGGATAG
345429 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 1 0.03
30 38 0.97
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGAATCTTTAT
Found at i:350349 original size:30 final size:30
Alignment explanation
Indices: 350288--350387 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
350278 TAAGGGAACA
* * * *
350288 TATGGATAGTTTACCTAGGTTCTTCAGGACC
1 TATGGATAG-TTACCAAGGATCTTTATGACC
* *
350319 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCAAGGATCTTTATGACC
* *
350349 TCTGGATAATTACCAAGGATCTTTATGACC
1 TATGGATAGTTACCAAGGATCTTTATGACC
*
350379 TCTGGATAG
1 TATGGATAG
350388 GTCATTCGGG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
30 51 0.86
31 8 0.14
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (30 bp):
TATGGATAGTTACCAAGGATCTTTATGACC
Found at i:356579 original size:77 final size:78
Alignment explanation
Indices: 356346--356582 Score: 395
Period size: 78 Copynumber: 3.1 Consensus size: 78
356336 TTGAAATTCC
* *
356346 ATACCTCTAATTAAATCACTTAAGTTAATTACATTGTTCATTTATCAAAGTAGACCCATTGATTA
1 ATACCTCTAATTAAATCACTTAAGTTAATTACATTGCTCATTTATCAAAGTAGACCCATTAATTA
356411 GTATTGACAAAAT
66 GTATTGACAAAAT
*
356424 ATACCTCTAATTAAATCACTTAAGTTAATTACATTGCTCATTTATCAAAGTAGACCCATGAATTA
1 ATACCTCTAATTAAATCACTTAAGTTAATTACATTGCTCATTTATCAAAGTAGACCCATTAATTA
*
356489 ATATTGACAAAAT
66 GTATTGACAAAAT
* * * *
356502 ATACCTCTAACTATATTACTTAAGATAATTACATTG-TCATTTATCAAAGTAGACCCATTAATTA
1 ATACCTCTAATTAAATCACTTAAGTTAATTACATTGCTCATTTATCAAAGTAGACCCATTAATTA
356566 GTATTGACAAAAT
66 GTATTGACAAAAT
356579 ATAC
1 ATAC
356583 TTATTTTGTA
Statistics
Matches: 149, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
77 43 0.29
78 106 0.71
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (78 bp):
ATACCTCTAATTAAATCACTTAAGTTAATTACATTGCTCATTTATCAAAGTAGACCCATTAATTA
GTATTGACAAAAT
Found at i:359597 original size:2 final size:2
Alignment explanation
Indices: 359590--359628 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
359580 ATCCACGTTC
359590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
359629 GACATTCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:361160 original size:34 final size:34
Alignment explanation
Indices: 361101--361167 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
361091 TTCTTGAGAG
*
361101 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTCA
1 TTGTTTTCTCCTTTTAATC-AGAGAGAAGTTGTCA
361135 TTGTTTTCTCCTTGTTAAATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-AATCAGAGAGAAGTTGT
361168 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTAATCAGAGAGAAGTTGTCA
Found at i:362874 original size:444 final size:444
Alignment explanation
Indices: 362039--362924 Score: 1371
Period size: 444 Copynumber: 2.0 Consensus size: 444
362029 ATCGTGTGAG
* *
362039 AAGACATCCCAATTGGCACTCAGATTATGTTATAGAAGGAAATATTGCATACTGCATTTTAACAG
1 AAGACATCCCAATTGGCACTCAAATTATGTTATAGAAAGAAATATTGCATACTGCATTTTAACAG
* *
362104 AGTACGGTGAGCCATCAATATACCAGGAGGCAATAAACAGCTCAGATGCTTCACTGTGGATGATG
66 AGTACGGTGAGCCATCAACATACCAGGAGGCAATAAACAGCTCAGATGCTTCACTGTAGATGATG
* * ** *
362169 GCGATGCAAGAAGAAATTGAATTCATTCATAAAAATAATACATGAGACCTTGTGCCACTACCACA
131 GCGATACAAGAAGAAATCGAAGCCATTCATAAAAATAATACATGAGACCTTGTGCCACTACCAAA
* * * * * *
362234 AGGAAGGAAACCAATTGGTAAAAAATGGGTCTTTAAAATCAAGCGCAATGGTAACGATCAAGTTG
196 AAGAAGGAAACCAATTGATAAAAAATGAGTCTTCAAAATCAAGCGAAATGATAACGATCAAGTTG
*
362299 AGAGGTATCGTGCAAGACTGATGGTCAAAGGATATGCTCAAAAAGAAGGTATTGATTTCAATGAA
261 AAAGGTATCGTGCAAGACTGATGGTCAAAGGATATGCTCAAAAAGAAGGTATTGATTTCAATGAA
* * * *
362364 ATCTTTTCTCCTGTGGTTCGACTAATAACAGTTCGAGTAGTTTTGACAATTTGTGCTACATTGAA
326 ATCTTTTCTCATGTGGTTCGACTAACAACAGTTCGAGTAGTTTTGACAATGTGTGATACATTGAA
* *
362429 TTTAAATCTAGAGCATCTAGATGTTAAAACAGCTTTTCTTAATGAAAATCTTTA
391 TTTAAATCTAGAGCAGCTAGATGTTAAAACAACTTTTCTTAATGAAAATCTTTA
* *
362483 AAGACGTCCCAATTGGCACTCAAATTATGTTATAGAAAGAAATATTGCATACTGTC-TTTTAATA
1 AAGACATCCCAATTGGCACTCAAATTATGTTATAGAAAGAAATATTGCATACTG-CATTTTAACA
*
362547 GAGTACGGTGAGCCATCAACATACCAGGAGGCAATAAACAGTTCAGATGCTTCACTGTAGATGAT
65 GAGTACGGTGAGCCATCAACATACCAGGAGGCAATAAACAGCTCAGATGCTTCACTGTAGATGAT
* *
362612 GGCGATACAAGAAGAAATCGAAGCCCTTCATAAAAATAATACATGAGACCTTGTGCCACTACTAA
130 GGCGATACAAGAAGAAATCGAAGCCATTCATAAAAATAATACATGAGACCTTGTGCCACTACCAA
* * * *
362677 AAAGAAGGAAGCCAATTGATAACAAATGAGTCTTCAAAATCAAGCGAAATGATGATGATCAAGTT
195 AAAGAAGGAAACCAATTGATAAAAAATGAGTCTTCAAAATCAAGCGAAATGATAACGATCAAGTT
* * *
362742 GAAAGGTATCGTGCAAGACTGGTGGTCAAAGGATATGCTTAAAAAGAAGGTATTGATTTTAATGA
260 GAAAGGTATCGTGCAAGACTGATGGTCAAAGGATATGCTCAAAAAGAAGGTATTGATTTCAATGA
* * *
362807 AATCTTTTCTCATGTGGTTTGACTAACAACAGTTCGTGTA-TTCTTGGCAATGTGTGATACATTG
325 AATCTTTTCTCATGTGGTTCGACTAACAACAGTTCGAGTAGTT-TTGACAATGTGTGATACATTG
* * * *
362871 AATTTACATCTAGAGCAGCTATATGTTAAAACAATTTTTCTTCATGAAAATCTT
389 AATTTAAATCTAGAGCAGCTAGATGTTAAAACAACTTTTCTTAATGAAAATCTT
362925 GAAGAAGAGA
Statistics
Matches: 399, Mismatches: 41, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
443 2 0.01
444 396 0.99
445 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (444 bp):
AAGACATCCCAATTGGCACTCAAATTATGTTATAGAAAGAAATATTGCATACTGCATTTTAACAG
AGTACGGTGAGCCATCAACATACCAGGAGGCAATAAACAGCTCAGATGCTTCACTGTAGATGATG
GCGATACAAGAAGAAATCGAAGCCATTCATAAAAATAATACATGAGACCTTGTGCCACTACCAAA
AAGAAGGAAACCAATTGATAAAAAATGAGTCTTCAAAATCAAGCGAAATGATAACGATCAAGTTG
AAAGGTATCGTGCAAGACTGATGGTCAAAGGATATGCTCAAAAAGAAGGTATTGATTTCAATGAA
ATCTTTTCTCATGTGGTTCGACTAACAACAGTTCGAGTAGTTTTGACAATGTGTGATACATTGAA
TTTAAATCTAGAGCAGCTAGATGTTAAAACAACTTTTCTTAATGAAAATCTTTA
Found at i:380014 original size:23 final size:23
Alignment explanation
Indices: 379996--380045 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
379986 ATATTAAACG
*
379996 TATAATTATAAATTAATTAAAAA
1 TATAAATATAAATTAATTAAAAA
* *
380019 TCTAAATATAATTTAATT-AAAA
1 TATAAATATAAATTAATTAAAAA
380041 TATAA
1 TATAA
380046 TATTTACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TATAAATATAAATTAATTAAAAA
Found at i:381648 original size:22 final size:23
Alignment explanation
Indices: 381613--381660 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
381603 CATTTAAATT
381613 TTTAACTAATTTATAA-TTATACA
1 TTTAACTAATTTATAATTTA-ACA
*
381636 TTTAA-TACTTTATAATTTAACA
1 TTTAACTAATTTATAATTTAACA
381658 TTT
1 TTT
381661 TAGAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAACTAATTTATAATTTAACA
Found at i:387648 original size:13 final size:13
Alignment explanation
Indices: 387632--387657 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
387622 TTTATACTTC
387632 TAATATATATAGT
1 TAATATATATAGT
387645 TAATATATATAGT
1 TAATATATATAGT
387658 ACTCGAATCG
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:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATATATATAGT
Found at i:390411 original size:2 final size:2
Alignment explanation
Indices: 390404--390437 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
390394 TTAAATTGGT
*
390404 TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
390438 CTGGGATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:398798 original size:2 final size:2
Alignment explanation
Indices: 398793--398834 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
398783 ACTATATACA
398793 AT AT 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 AT AT
398835 TTCTTCATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:399990 original size:3 final size:3
Alignment explanation
Indices: 399982--400045 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
399972 AGCAAGTGAA
399982 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
400030 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
400046 GTTTTTCTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:402970 original size:23 final size:23
Alignment explanation
Indices: 402944--403031 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
402934 AGCTCGTATA
402944 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
402967 AATTTGTC-CCGAAG-GACCGCGTAG
1 AA-TTG-CACCGAAGTG-CCACGTAG
*
402991 AATTGCATCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
403014 AAATGCATCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
403032 TATAAGATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 1 0.02
23 34 0.62
24 19 0.35
25 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:403176 original size:23 final size:23
Alignment explanation
Indices: 403145--403188 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
403135 AATACATATA
*
403145 TGTCTCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
403168 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
403189 CCCTCGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:409452 original size:23 final size:23
Alignment explanation
Indices: 409426--409502 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
409416 AACTCGTATA
409426 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
409449 AATTTGTC-CCGAAG-GACCGCGTAG
1 AA-TTG-CACCGAAGTG-CCACGTAG
* * *
409473 AATTACACTGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
409496 AAATGCA
1 AATTGCA
409503 TCATAGTGCC
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
22 1 0.02
23 21 0.50
24 19 0.45
25 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:409667 original size:18 final size:18
Alignment explanation
Indices: 409644--409680 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
409634 AAGGACCACC
409644 TCTTTAGAAAATGTGCAA
1 TCTTTAGAAAATGTGCAA
409662 TCTTTAGAAAATGTGCAA
1 TCTTTAGAAAATGTGCAA
409680 T
1 T
409681 AATCAGTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (18 bp):
TCTTTAGAAAATGTGCAA
Found at i:428425 original size:2 final size:2
Alignment explanation
Indices: 428418--428464 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
428408 TAAATTATTA
428418 AT AT 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 AT AT
428460 AT AT A
1 AT AT A
428465 AGAGAGTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:434431 original size:51 final size:51
Alignment explanation
Indices: 434355--434456 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
434345 GCACCTGTGC
434355 AAGCTATCGTTGGAATGGCTGGCTTCAGCTTGGACAAATTTCCCGATGACG
1 AAGCTATCGTTGGAATGGCTGGCTTCAGCTTGGACAAATTTCCCGATGACG
434406 AAGCTATCGTTGGAATGGCTGGCTTCAGCTTGGACAAATTTCCCGATGACG
1 AAGCTATCGTTGGAATGGCTGGCTTCAGCTTGGACAAATTTCCCGATGACG
434457 TAAGTTTAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (51 bp):
AAGCTATCGTTGGAATGGCTGGCTTCAGCTTGGACAAATTTCCCGATGACG
Found at i:436770 original size:28 final size:28
Alignment explanation
Indices: 436738--436803 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
436728 CTCTTCATTT
*
436738 ATATTATGTCGTCGAGTCAGTACTTGAA
1 ATATTATGTCGTCGACTCAGTACTTGAA
* *
436766 ATATTATGTCGTCGACTTAGTGCTTGAA
1 ATATTATGTCGTCGACTCAGTACTTGAA
436794 ATATTATGTC
1 ATATTATGTC
436804 ATTGTGTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (28 bp):
ATATTATGTCGTCGACTCAGTACTTGAA
Found at i:442155 original size:2 final size:2
Alignment explanation
Indices: 442148--442173 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
442138 TACCATAAAA
442148 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
442174 TATGCACCTT
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):
AT
Found at i:443668 original size:21 final size:21
Alignment explanation
Indices: 443642--443686 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
443632 GATTTCTGGG
* *
443642 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
443663 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
443684 CAA
1 CAA
443687 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:445160 original size:22 final size:22
Alignment explanation
Indices: 445132--445176 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
445122 TTATGGACAT
*
445132 AATTCTATGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
445154 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
445176 A
1 A
445177 TTTATACGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:445184 original size:22 final size:22
Alignment explanation
Indices: 445140--445184 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
445130 ATAATTCTAT
*
445140 GGGCACTTCGGTGCAATTCTAC
1 GGGCACTTCGGTGCAATTATAC
*
445162 GGGCACTTCGGTGCATTTATAC
1 GGGCACTTCGGTGCAATTATAC
445184 G
1 G
445185 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (22 bp):
GGGCACTTCGGTGCAATTATAC
Found at i:445556 original size:262 final size:262
Alignment explanation
Indices: 445182--445708 Score: 922
Period size: 262 Copynumber: 2.0 Consensus size: 262
445172 GTGCATTTAT
445182 ACGAGCTGTGGTGACAGCATAGTGCACAACCTCTATAGACATCAATATCGATAGTTCTCACTATA
1 ACGAGCTGTGGTGACAGCATAGTGCACAACCTCTATAGACATCAATATCGATAGTTCTCACTATA
445247 CATGGGCTAATCCAGAGATATGAACAATATAAGTTAGTGGTATGATAAATGCTATAGAAATTATA
66 CATGGGCTAATCCAGAGATATGAACAATATAAGTTAGTGGTATGATAAATGCTATAGAAATTATA
445312 TGATGTTGTGTGTATAGTATTTGATTGAAAAAAGTATGTGA-TATATG-ATATGTGAATGATGAA
131 TGATGTTGTGTGTATAGTATTTGATTG-AAAAAGTATGTGATTATATGAATATGTGAATGATGAA
*
445375 TTATGTGTATG-A-CATTTACTGCGATTAATCTGATATGATTCTATACGATATGAAAAATGCCTG
195 TTATGTGTATGTAGAATTTACTGCGATTAATCTGATATGATTCTATACGATATGAAAAATGCCTG
445438 GAA
260 GAA
445441 ACGAGCTGTGGTGACAGCATAGTGCACAACCTCTATAGAC-TCACATATCGATAGTTCTCACATA
1 ACGAGCTGTGGTGACAGCATAGTGCACAACCTCTATAGACATCA-ATATCGATAGTTCTCAC---
445505 TATACATGGGCTAATCCAGAGATATGAACAA-ATAAAGTTAGTGGTATGATAAATGCTATAGAAA
62 TATACATGGGCTAATCCAGAGATATGAACAATAT-AAGTTAGTGGTATGATAAATGCTATAGAAA
445569 TTATATGATGTTGTGTGTATAGTATTTGATTGAAAAAGTATGTGATTATATGATAATATGTGAAT
126 TTATATGATGTTGTGTGTATAGTATTTGATTGAAAAAGTATGTGATTATATG--AATATGTGAAT
445634 GATGAATTATGTGTATGTATGAATTTACTGCGATTAATCTGATATGATTCTATACGATATGAAAA
189 GATGAATTATGTGTATGTA-GAATTTACTGCGATTAATCTGATATGATTCTATACGATATGAAAA
445699 ATGCCTGGAA
253 ATGCCTGGAA
445709 TTGCTATAAC
Statistics
Matches: 255, Mismatches: 1, Indels: 15
0.94 0.00 0.06
Matches are distributed among these distances:
258 3 0.01
259 57 0.22
261 15 0.06
262 99 0.39
265 27 0.11
266 1 0.00
268 53 0.21
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (262 bp):
ACGAGCTGTGGTGACAGCATAGTGCACAACCTCTATAGACATCAATATCGATAGTTCTCACTATA
CATGGGCTAATCCAGAGATATGAACAATATAAGTTAGTGGTATGATAAATGCTATAGAAATTATA
TGATGTTGTGTGTATAGTATTTGATTGAAAAAGTATGTGATTATATGAATATGTGAATGATGAAT
TATGTGTATGTAGAATTTACTGCGATTAATCTGATATGATTCTATACGATATGAAAAATGCCTGG
AA
Found at i:445646 original size:16 final size:17
Alignment explanation
Indices: 445625--445658 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
445615 TATATGATAA
445625 TATGTGAATG-ATGAAT
1 TATGTGAATGTATGAAT
*
445641 TATGTGTATGTATGAAT
1 TATGTGAATGTATGAAT
445658 T
1 T
445659 TACTGCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (17 bp):
TATGTGAATGTATGAAT
Found at i:447510 original size:84 final size:84
Alignment explanation
Indices: 447402--447570 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
447392 CTGGTTTTGC
447402 TTCAGAAGAATCTCCTTGTTCAAACTCTTTTTCTACATGTATCTGAGTAGTCTCTGACTTTTTAG
1 TTCAGAAGAATCTCCTTGTTCAAACTCTTTTTCTACATGTATCTGAGTAGTCTCTGACTTTTTAG
447467 TGCTATCATCATCTTCTTT
66 TGCTATCATCATCTTCTTT
447486 TTCAGAAGAATCTCCTTGTTCAAACTCTTTTTCTACATGTATCTGAGTAGTCTCTGACTTTTTAG
1 TTCAGAAGAATCTCCTTGTTCAAACTCTTTTTCTACATGTATCTGAGTAGTCTCTGACTTTTTAG
447551 TGCTATCATCATCTTCTTT
66 TGCTATCATCATCTTCTTT
447570 T
1 T
447571 CTTTGTAGTT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (84 bp):
TTCAGAAGAATCTCCTTGTTCAAACTCTTTTTCTACATGTATCTGAGTAGTCTCTGACTTTTTAG
TGCTATCATCATCTTCTTT
Found at i:449197 original size:31 final size:31
Alignment explanation
Indices: 449159--449306 Score: 202
Period size: 31 Copynumber: 5.0 Consensus size: 31
449149 CCCGAAGGAC
* *
449159 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
449190 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
449221 CAGTCCATATGTTCCGAAGAACATAGGT--A
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
449250 -A-TCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
449279 CA-TCCATAT-TTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
449307 CCCTCGACCC
Statistics
Matches: 107, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
27 25 0.23
28 1 0.01
29 21 0.20
30 8 0.07
31 51 0.48
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:450193 original size:21 final size:21
Alignment explanation
Indices: 450163--450207 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
450153 ATTCTGTCGT
* *
450163 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
450184 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
450205 TTG
1 TTG
450208 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:450511 original size:22 final size:22
Alignment explanation
Indices: 450483--450528 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
450473 ATTCCTTTCC
450483 AAAATTTCATATAAAAACTCCA
1 AAAATTTCATATAAAAACTCCA
450505 AAAATTTCATATAAAAACTCCA
1 AAAATTTCATATAAAAACTCCA
450527 AA
1 AA
450529 TCTTTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAATTTCATATAAAAACTCCA
Found at i:453252 original size:31 final size:31
Alignment explanation
Indices: 453214--453367 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
453204 CCCGAAGGAC
* *
453214 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
453245 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
453276 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
453307 CAGTCCATATGTTCCGAAAAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
453338 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
453368 CCCTCGACCC
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:454265 original size:21 final size:21
Alignment explanation
Indices: 454235--454279 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
454225 ATTCTGTCGT
* *
454235 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
454256 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
454277 TTG
1 TTG
454280 CCTAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:459663 original size:37 final size:36
Alignment explanation
Indices: 459622--459873 Score: 232
Period size: 36 Copynumber: 7.0 Consensus size: 36
459612 ATATAAATAA
*
459622 AAAAACATTTTTAAAACTATATATTATATATACTTTT
1 AAAAATATTTTTAAAACTATATATTATATATA-TTTT
*
459659 AAAAAT-TGTTTTCAAAAC-ATATAATATATATATTTT
1 AAAAATAT-TTTT-AAAACTATATATTATATATATTTT
* *
459695 CAAAAATTGTTTTTACAACTATATA--ATATATA-TTT
1 -AAAAA-TATTTTTAAAACTATATATTATATATATTTT
* *** * *
459730 AAAAAAAAAATCAAAACTATATATTATATACATTTT
1 AAAAATATTTTTAAAACTATATATTATATATATTTT
*
459766 TAAAATATTTTTAAAA--ACTATATTATATATATATTT
1 AAAAATATTTTTAAAACTA-TATATTATATATAT-TTT
* *
459802 -AAAATATTTTCAAAAACTATATATTATATATGTTTT
1 AAAAATATTTT-TAAAACTATATATTATATATATTTT
* * *
459838 CAAAATATTTTCAAAACTATATAATATATATATTTT
1 AAAAATATTTTTAAAACTATATATTATATATATTTT
459874 CGAAAACCGA
Statistics
Matches: 177, Mismatches: 23, Indels: 31
0.77 0.10 0.13
Matches are distributed among these distances:
33 11 0.06
34 6 0.03
35 32 0.18
36 57 0.32
37 54 0.31
38 16 0.09
39 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (36 bp):
AAAAATATTTTTAAAACTATATATTATATATATTTT
Found at i:459788 original size:35 final size:35
Alignment explanation
Indices: 459623--459873 Score: 165
Period size: 37 Copynumber: 7.0 Consensus size: 35
459613 TATAAATAAA
* *
459623 AAAACATTTTT-AAAACTATATATTATATATACTTTT
1 AAAATATTTTTAAAAAC--TATATTATATATATTTTT
* * *
459659 AAAA-ATTGTTTTCAAAACATATAATATATATATTTTC
1 AAAATA-T-TTTTAAAAAC-TATATTATATATATTTTT
* * *
459696 AAAA-ATTGTTTTTACAACTATA-TA-ATATATATTT
1 AAAATA-T-TTTTAAAAACTATATTATATATATTTTT
* **** * *
459730 AAAAAAAAAATCAAAACTATATATTATATACATTTTT
1 AAAATATTTTTAAAAAC--TATATTATATATATTTTT
*
459767 AAAATATTTTTAAAAACTATATTATATATATATTT
1 AAAATATTTTTAAAAACTATATTATATATATTTTT
*
459802 AAAATATTTTCAAAAACTATA-TATTATATATGTTTT
1 AAAATATTTTTAAAAACTATATTA-TATATAT-TTTT
* *
459838 CAAAATA-TTTTCAAAACTATATAATATATATATTTT
1 -AAAATATTTTTAAAAACTATATTATATATAT-TTTT
459874 CGAAAACCGA
Statistics
Matches: 174, Mismatches: 29, Indels: 24
0.77 0.13 0.11
Matches are distributed among these distances:
33 5 0.03
34 14 0.08
35 51 0.29
36 37 0.21
37 62 0.36
38 5 0.03
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (35 bp):
AAAATATTTTTAAAAACTATATTATATATATTTTT
Found at i:459822 original size:24 final size:26
Alignment explanation
Indices: 459793--459842 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
459783 CTATATTATA
459793 TATATATT-TAAAATATTTTCAAAAAC
1 TATATATTAT-AAATATTTTCAAAAAC
* *
459819 TATATATTATATATGTTTTCAAAA
1 TATATATTATAAATATTTTCAAAA
459843 TATTTTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (26 bp):
TATATATTATAAATATTTTCAAAAAC
Found at i:460180 original size:5 final size:5
Alignment explanation
Indices: 460156--460180 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
460146 CCTATTCTAT
460156 CCTAA CCTAA CCTAA CCTAA CCTAA
1 CCTAA CCTAA CCTAA CCTAA CCTAA
460181 ACTATGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
CCTAA
Found at i:460386 original size:20 final size:20
Alignment explanation
Indices: 460345--460386 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
460335 AATAAATATG
*
460345 AAATAAAACTGAACAGCTAA
1 AAATAAAACTGAACAGCCAA
*
460365 AAATAGAAATTGAA-AGCCAA
1 AAATA-AAACTGAACAGCCAA
460385 AA
1 AA
460387 CAATTTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.14
Consensus pattern (20 bp):
AAATAAAACTGAACAGCCAA
Found at i:460847 original size:14 final size:14
Alignment explanation
Indices: 460830--460871 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
460820 TTCAAGCCCT
460830 AAAAA-TTGAACTA
1 AAAAAGTTGAACTA
460843 AAAAAGTTGAACTA
1 AAAAAGTTGAACTA
460857 AAAAAGTTGAACTA
1 AAAAAGTTGAACTA
460871 A
1 A
460872 TGAGTCAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.21
Consensus pattern (14 bp):
AAAAAGTTGAACTA
Found at i:465951 original size:2 final size:2
Alignment explanation
Indices: 465944--465972 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
465934 TGGAGAGGGG
465944 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
465973 TTACAGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:466701 original size:8 final size:8
Alignment explanation
Indices: 466688--466734 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
466678 GTTAGTATTT
466688 TTTAATTA
1 TTTAATTA
466696 TTTAATTA
1 TTTAATTA
466704 TTT-ATTA
1 TTTAATTA
*
466711 TTTTATTA
1 TTTAATTA
466719 -TT--TTA
1 TTTAATTA
466724 TTTAATTA
1 TTTAATTA
466732 TTT
1 TTT
466735 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 9 0.26
8 21 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTAATTA
Found at i:466733 original size:21 final size:20
Alignment explanation
Indices: 466701--466744 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
466691 AATTATTTAA
466701 TTATTTATTATTTTATTATT
1 TTATTTATTATTTTATTATT
*
466721 TTATTTAATTATTTTATTTTT
1 TTATTT-ATTATTTTATTATT
466742 TTA
1 TTA
466745 CAGTTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TTATTTATTATTTTATTATT
Found at i:467027 original size:17 final size:17
Alignment explanation
Indices: 467005--467043 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
466995 CTATTTAGAA
* *
467005 ATTTTAAATTTTTTTAT
1 ATTTTAAATTTTATAAT
*
467022 ATTTTATATTTTATAAT
1 ATTTTAAATTTTATAAT
467039 ATTTT
1 ATTTT
467044 TTTATTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTAAATTTTATAAT
Found at i:479565 original size:11 final size:12
Alignment explanation
Indices: 479541--479569 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
479531 TTATGCCATA
479541 TAAATTTTTAAT
1 TAAATTTTTAAT
479553 TAAATTTTT-AT
1 TAAATTTTTAAT
479564 TAAATT
1 TAAATT
479570 AAATAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TAAATTTTTAAT
Found at i:501133 original size:31 final size:31
Alignment explanation
Indices: 501076--501175 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
501066 TTCATGAGTT
* * *
501076 AAATTGATATTTTATCTAAAGCTTAAGTGTC
1 AAATTAATATTTTATATAAAGTTTAAGTGTC
* *
501107 AAATTAATATTTTATTTAAATTTTAAG-GATC
1 AAATTAATATTTTATATAAAGTTTAAGTG-TC
* ** *
501138 AAGTTAGCATTTTATACAAAGTTTAA-TGT-
1 AAATTAATATTTTATATAAAGTTTAAGTGTC
501167 AAATTAATA
1 AAATTAATA
501176 CCTTCTACCA
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
29 6 0.11
30 2 0.04
31 46 0.85
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (31 bp):
AAATTAATATTTTATATAAAGTTTAAGTGTC
Found at i:502411 original size:29 final size:28
Alignment explanation
Indices: 502378--502471 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
502368 CTATGACTAT
502378 CATTCTAAATTGATCCTCAAACTTTTGAA
1 CATTCTAAATTGATCC-CAAACTTTTGAA
* * * *
502407 CATTCCAAATTCATCCCTAAAC-TATAAA
1 CATTCTAAATTGATCCC-AAACTTTTGAA
*
502435 TCCCATTCTAAATTGCTCCCCAAACTTTTGAA
1 ---CATTCTAAATTGAT-CCCAAACTTTTGAA
502467 CATTC
1 CATTC
502472 CAATAACCTT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 5 0.10
29 23 0.46
31 15 0.30
32 7 0.14
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (28 bp):
CATTCTAAATTGATCCCAAACTTTTGAA
Found at i:502420 original size:60 final size:60
Alignment explanation
Indices: 502309--502474 Score: 172
Period size: 60 Copynumber: 2.8 Consensus size: 60
502299 ATTCTCAAAT
* * * * ** ** *
502309 TATGACTTTGATTCTAAATTGATCATTAAGGTTTTGAACATTTTAATTTCAT-CATGAAAC
1 TATGACTATCATTCTAAATTGATCCTCAAACTTTTGAACATTCCAAATTCATCCAT-AAAC
*
502369 TATGACTATCATTCTAAATTGATCCTCAAACTTTTGAACATTCCAAATTCATCCCTAAAC
1 TATGACTATCATTCTAAATTGATCCTCAAACTTTTGAACATTCCAAATTCATCCATAAAC
* * ** * *
502429 TATAAATCCCATTCTAAATTGCTCCCCAAACTTTTGAACATTCCAA
1 TATGACTATCATTCTAAATTGATCCTCAAACTTTTGAACATTCCAA
502475 TAACCTTCCC
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 87 0.98
61 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.37
Consensus pattern (60 bp):
TATGACTATCATTCTAAATTGATCCTCAAACTTTTGAACATTCCAAATTCATCCATAAAC
Found at i:504144 original size:7 final size:7
Alignment explanation
Indices: 504132--504167 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
504122 GAACACCAAA
504132 CTTCAAC
1 CTTCAAC
504139 CTTCAAC
1 CTTCAAC
504146 CTTCAAC
1 CTTCAAC
504153 CTTCAAC
1 CTTCAAC
504160 CTTCAAC
1 CTTCAAC
504167 C
1 C
504168 CTGTCGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.44, G:0.00, T:0.28
Consensus pattern (7 bp):
CTTCAAC
Found at i:510375 original size:21 final size:21
Alignment explanation
Indices: 510350--510397 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
510340 CCTAATATTG
510350 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
510371 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
510392 TAATGT
1 CAATGT
510398 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:512126 original size:23 final size:23
Alignment explanation
Indices: 512095--512146 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
512085 ATTATATAAT
* *
512095 GAAACTAAAAAATCCATTATTTA
1 GAAAATAAAAAATCCACTATTTA
* *
512118 GAAAATAAAAACTCCACTATTTC
1 GAAAATAAAAAATCCACTATTTA
512141 GAAAAT
1 GAAAAT
512147 GAAGAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (23 bp):
GAAAATAAAAAATCCACTATTTA
Found at i:516491 original size:2 final size:2
Alignment explanation
Indices: 516484--516516 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
516474 CTTTTCTAAT
516484 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
516517 TTAAAAAAAA
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:524537 original size:22 final size:24
Alignment explanation
Indices: 524497--524550 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
524487 TATTTTTGAA
* *
524497 TTTTTT-TTGACTTTATATTC-TT
1 TTTTTTATTGAATTTATATTCACT
524519 TTTTTTATTGAATTT-TATTCACT
1 TTTTTTATTGAATTTATATTCACT
524542 TTTTTTATT
1 TTTTTTATT
524551 ACATTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTTTATTGAATTTATATTCACT
Found at i:524630 original size:11 final size:10
Alignment explanation
Indices: 524609--524666 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
524599 TCACCTTTTT
524609 TAAAAATCAA
1 TAAAAATCAA
524619 TAAAAATACAA
1 TAAAAAT-CAA
**
524630 TAAAAAAGAA
1 TAAAAATCAA
* *
524640 TTAAAAGTGAA
1 -TAAAAATCAA
*
524651 TAAAATTCAA
1 TAAAAATCAA
524661 TAAAAA
1 TAAAAA
524667 CGTCAACTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 22 0.56
11 17 0.44
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (10 bp):
TAAAAATCAA
Found at i:524635 original size:21 final size:20
Alignment explanation
Indices: 524609--524666 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
524599 TCACCTTTTT
524609 TAAAAATCAATAAAAATACAA
1 TAAAAATCAATAAAAAT-CAA
** * *
524630 TAAAAAAGAATTAAAAGTGAA
1 TAAAAATCAA-TAAAAATCAA
*
524651 TAAAATTCAATAAAAA
1 TAAAAATCAATAAAAA
524667 CGTCAACTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
20 5 0.18
21 17 0.61
22 6 0.21
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (20 bp):
TAAAAATCAATAAAAATCAA
Found at i:524853 original size:28 final size:29
Alignment explanation
Indices: 524821--524877 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
524811 ATTCATTTTT
524821 TTAAAA-TCAATAAAAATACAATA-AAAAA
1 TTAAAAGTCAAT-AAAATACAATACAAAAA
* *
524849 TTAAAAGTGAATAAAATTCAATACAAAAA
1 TTAAAAGTCAATAAAATACAATACAAAAA
524878 GAATATGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.23
Consensus pattern (29 bp):
TTAAAAGTCAATAAAATACAATACAAAAA
Found at i:525645 original size:36 final size:36
Alignment explanation
Indices: 525605--525781 Score: 248
Period size: 36 Copynumber: 4.9 Consensus size: 36
525595 GTGCGCTACA
* * *
525605 TCCTTCCGTTCAACTTGGATCGGAAGTGTTGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
*
525641 TCCTTCCGTTCGACTTGAATCGGAAATGTCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
*
525677 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
* * *
525713 TCATTCCGTTCTACTTGAATCGAAAGT-TCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGT-CGATGCT
* *
525749 TCCTTCCGTTCGTCTTGAATCGAAAGTGTCGAT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGAT
525782 TCTATCTTTC
Statistics
Matches: 126, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
36 125 0.99
37 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
Found at i:530880 original size:10 final size:10
Alignment explanation
Indices: 530865--530892 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
530855 GGACCGGCTG
530865 AAAACCGGAA
1 AAAACCGGAA
530875 AAAACCGGAA
1 AAAACCGGAA
530885 AAAACCGG
1 AAAACCGG
530893 GATTTTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.21, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:532669 original size:19 final size:20
Alignment explanation
Indices: 532647--532685 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
532637 TTATAACTAA
*
532647 ATTTTTTTAT-TAATATTTT
1 ATTTTTTTATAAAATATTTT
532666 ATTTTTTTATAAAATATTTT
1 ATTTTTTTATAAAATATTTT
532686 GGAGACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTTTATAAAATATTTT
Found at i:545979 original size:2 final size:2
Alignment explanation
Indices: 545972--545999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
545962 AAAAACATTC
545972 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
546000 TATTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:555765 original size:114 final size:115
Alignment explanation
Indices: 555555--555784 Score: 354
Period size: 114 Copynumber: 2.0 Consensus size: 115
555545 GTCAATAGCA
* * * *
555555 TTGCATTTTCAAGGATATATGTTCCGAGGATGGACTTTGTGGATATCCCCGCCTGCATGATCTTT
1 TTGCATTTTCAAGGATATATATTCCAAGGATGGACTTTGTGGACATCCCCACCTGCATGATCTTT
* *
555620 CGAGATAATGAGATTTCAAGTTATCCATATAGAATGCTTGTTTTCGTATG
66 CGAGAAAATGAGATTTCAAGTTATCCATATAGAATGCTTGTTTTCATATG
* *
555670 TTGCATTTTCAAGGATATATATTCCAAGTATGGACTTTGTGGACAT-CCCACTTGCATGATCTTT
1 TTGCATTTTCAAGGATATATATTCCAAGGATGGACTTTGTGGACATCCCCACCTGCATGATCTTT
* **
555734 CGAGAAAATGAGATTTCGAGTTATCTGTATAGAATGCTTGTTTTCATATG
66 CGAGAAAATGAGATTTCAAGTTATCCATATAGAATGCTTGTTTTCATATG
555784 T
1 T
555785 AGTTTTCATC
Statistics
Matches: 104, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
114 62 0.60
115 42 0.40
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (115 bp):
TTGCATTTTCAAGGATATATATTCCAAGGATGGACTTTGTGGACATCCCCACCTGCATGATCTTT
CGAGAAAATGAGATTTCAAGTTATCCATATAGAATGCTTGTTTTCATATG
Found at i:556914 original size:20 final size:21
Alignment explanation
Indices: 556889--556930 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
556879 TCAATCTAAA
*
556889 TAATATTGATATCAA-AATTT
1 TAATATTAATATCAATAATTT
*
556909 TAATATTAATATTAATAATTT
1 TAATATTAATATCAATAATTT
556930 T
1 T
556931 TTAATTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TAATATTAATATCAATAATTT
Found at i:563088 original size:18 final size:19
Alignment explanation
Indices: 563055--563098 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
563045 GTTTTAAATG
*
563055 TTAATAATTTATAATTTAA
1 TTAATAATTAATAATTTAA
563074 TTAATAA-TAATAATTTAA
1 TTAATAATTAATAATTTAA
*
563092 TTGATAA
1 TTAATAA
563099 AATTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAATAATTAATAATTTAA
Found at i:563338 original size:24 final size:23
Alignment explanation
Indices: 563303--563349 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
563293 AGTCTCAGCA
563303 CCTTCATTTCCCAT-CGTTTCCTC
1 CCTTCATTTCCC-TCCGTTTCCTC
563326 CCTTCACTTTCCCTCCGTTTCCTC
1 CCTTCA-TTTCCCTCCGTTTCCTC
563350 TCATCTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.06, C:0.47, G:0.04, T:0.43
Consensus pattern (23 bp):
CCTTCATTTCCCTCCGTTTCCTC
Found at i:570569 original size:15 final size:15
Alignment explanation
Indices: 570549--570602 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
570539 TGATTCAGAG
570549 GCTCTGTATGAATTA
1 GCTCTGTATGAATTA
*
570564 GCTCTGAATG-ATTCAGA
1 GCTCTGTATGAATT---A
570581 GGCTCTGTATGAATTA
1 -GCTCTGTATGAATTA
570597 GCTCTG
1 GCTCTG
570603 AATGTGACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 3 0.09
15 15 0.47
16 1 0.03
17 1 0.03
18 9 0.28
19 3 0.09
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (15 bp):
GCTCTGTATGAATTA
Found at i:570579 original size:33 final size:33
Alignment explanation
Indices: 570537--570606 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
570527 TTAAGCGTTA
570537 AATGATTCAGAGGCTCTGTATGAATTAGCTCTG
1 AATGATTCAGAGGCTCTGTATGAATTAGCTCTG
570570 AATGATTCAGAGGCTCTGTATGAATTAGCTCTG
1 AATGATTCAGAGGCTCTGTATGAATTAGCTCTG
570603 AATG
1 AATG
570607 TGACATGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (33 bp):
AATGATTCAGAGGCTCTGTATGAATTAGCTCTG
Found at i:570587 original size:18 final size:18
Alignment explanation
Indices: 570537--570592 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
570527 TTAAGCGTTA
570537 AATGATTCAGAGGCTCTG
1 AATGATTCAGAGGCTCTG
*
570555 TATGAATT---A-GCTCTG
1 AATG-ATTCAGAGGCTCTG
570570 AATGATTCAGAGGCTCTG
1 AATGATTCAGAGGCTCTG
*
570588 TATGA
1 AATGA
570593 ATTAGCTCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
14 3 0.10
15 9 0.30
16 1 0.03
17 1 0.03
18 13 0.43
19 3 0.10
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (18 bp):
AATGATTCAGAGGCTCTG
Found at i:576008 original size:24 final size:24
Alignment explanation
Indices: 575976--576025 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
575966 CTTTATAACA
575976 GCCTCATAGGTTATTAGATATCTT
1 GCCTCATAGGTTATTAGATATCTT
576000 GCCTCATAGGTTATTAGATATCTT
1 GCCTCATAGGTTATTAGATATCTT
576024 GC
1 GC
576026 ATAACTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (24 bp):
GCCTCATAGGTTATTAGATATCTT
Found at i:578363 original size:3 final size:3
Alignment explanation
Indices: 578355--578380 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
578345 ATGTCTTATC
578355 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
578381 AGAGCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:585556 original size:64 final size:64
Alignment explanation
Indices: 585479--585643 Score: 194
Period size: 64 Copynumber: 2.6 Consensus size: 64
585469 TTGTTTGAAT
* * **
585479 GTGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGTAATT
1 GTGCAACGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGTAA-T
585542 C-
63 CG
* * * *
585543 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGTAATCG
1 GTGCAACGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGTAATCG
585607 GTGCAACGATGCATAAGG-AGTGCATCGATGCATCCCA
1 GTGCAACGATGCAT-AGGTAGTGCATCGATGCATCCCA
585644 GCAATATTAC
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
63 2 0.02
64 79 0.90
65 7 0.08
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (64 bp):
GTGCAACGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGTAATCG
Found at i:586178 original size:31 final size:31
Alignment explanation
Indices: 586139--586298 Score: 257
Period size: 31 Copynumber: 5.2 Consensus size: 31
586129 AGAGTCGAGG
586139 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
586170 TTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
586201 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* * * *
586232 ATTTATATATGTTTAAAGGTATATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
586263 GTCTACATATGTTTAAATGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
586294 GTTTA
1 GTTTA
586299 TATTGTGACC
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 116 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:586195 original size:16 final size:16
Alignment explanation
Indices: 586174--586227 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
586164 TGAACATTTT
586174 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
**
586190 ACATATG---AACAGTTT
1 ACATATGTTTAA-AG-GC
586205 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
586221 ACATATG
1 ACATATG
586228 AACAATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 7 0.24
16 14 0.48
17 2 0.07
18 2 0.07
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (16 bp):
ACATATGTTTAAAGGC
Found at i:589441 original size:64 final size:64
Alignment explanation
Indices: 589358--589521 Score: 199
Period size: 64 Copynumber: 2.6 Consensus size: 64
589348 TGTTTTAATA
* ** ** *
589358 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAAAGCAA-TC
589421 -G
63 GG
* *
589422 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAAAGCAATCGG
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAAAGCAATCGG
*
589486 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCA
589522 GCAATATTAC
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 2 0.02
64 81 0.92
65 5 0.06
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAAAGCAATCGG
Found at i:590116 original size:16 final size:16
Alignment explanation
Indices: 590095--590179 Score: 56
Period size: 16 Copynumber: 5.4 Consensus size: 16
590085 TCGAGGGTTT
590095 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
**
590111 ACATATG---AACAGTTT
1 ACATATGTTTAA-AG-GC
590126 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
**
590142 ACATATG---AACAGTTT
1 ACATATGTTTAA-AG-GC
590157 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
590173 ACATATG
1 ACATATG
590180 AACAGTTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 14 0.27
16 21 0.41
17 4 0.08
18 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (16 bp):
ACATATGTTTAAAGGC
Found at i:590129 original size:31 final size:31
Alignment explanation
Indices: 590091--590312 Score: 390
Period size: 31 Copynumber: 7.2 Consensus size: 31
590081 ATTGTCGAGG
590091 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
590122 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
590153 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
590184 GTTTATATATGTTTAAAGGCATATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
590215 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* * *
590246 ATTTATATATGTTTAAAGGCACATATGAATA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
590277 GTCTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
590308 GTTTA
1 GTTTA
590313 TATTGTTACC
Statistics
Matches: 179, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 179 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:590302 original size:16 final size:16
Alignment explanation
Indices: 590252--590303 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
590242 AACAATTTAT
590252 ATATGTTTAAAGGCAC
1 ATATGTTTAAAGGCAC
*
590268 ATATG---AATAGTCTAC
1 ATATGTTTAA-AGGC-AC
590283 ATATGTTTAAAGGCAC
1 ATATGTTTAAAGGCAC
590299 ATATG
1 ATATG
590304 AACAGTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 7 0.24
16 12 0.41
17 3 0.10
18 2 0.07
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (16 bp):
ATATGTTTAAAGGCAC
Found at i:596007 original size:12 final size:12
Alignment explanation
Indices: 595986--596015 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
595976 TTATTGTGCT
595986 TGCTCATCGGGC
1 TGCTCATCGGGC
*
595998 TGCTCCTCGGGC
1 TGCTCATCGGGC
596010 TGCTCA
1 TGCTCA
596016 GGCTCATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.37, G:0.30, T:0.27
Consensus pattern (12 bp):
TGCTCATCGGGC
Found at i:604017 original size:20 final size:21
Alignment explanation
Indices: 603978--604019 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
603968 ATAATAATAT
*
603978 CTTTATGACATATTTTTTTCTC
1 CTTTATGACA-ATGTTTTTCTC
604000 CTTTATGAC-ATGTTTTTCTC
1 CTTTATGACAATGTTTTTCTC
604020 TACGTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.17, C:0.19, G:0.07, T:0.57
Consensus pattern (21 bp):
CTTTATGACAATGTTTTTCTC
Found at i:609294 original size:41 final size:41
Alignment explanation
Indices: 609249--609380 Score: 112
Period size: 41 Copynumber: 3.2 Consensus size: 41
609239 AGTTGGAGAA
609249 ATATTTAGAATATATGTTTTATTTAATTATCTGTTTGATAT
1 ATATTTAGAATATATGTTTTATTTAATTATCTGTTTGATAT
* * * * *
609290 ATATTTATCCAATAAATTAATTTTAATATTAAATTA--TG---GAGAA
1 ATATTTA--GAATATA-T-GTTTT-AT-TT-AATTATCTGTTTGATAT
609333 ATATTTAGAATATATGTTTTATTTAATTATCTGTTTGATAT
1 ATATTTAGAATATATGTTTTATTTAATTATCTGTTTGATAT
*
609374 ACATTTA
1 ATATTTA
609381 TCCAATAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
36 5 0.07
37 2 0.03
38 4 0.06
39 4 0.06
40 1 0.01
41 21 0.31
43 15 0.22
44 1 0.01
45 4 0.06
46 4 0.06
47 2 0.03
48 5 0.07
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (41 bp):
ATATTTAGAATATATGTTTTATTTAATTATCTGTTTGATAT
Found at i:609335 original size:84 final size:84
Alignment explanation
Indices: 609242--609410 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
609232 AATATTTAGT
*
609242 TGGAGAAATATTTAGAATATATGTTTTATTTAATTATCTGTTTGATATATATTTATCCAATAAAT
1 TGGAGAAATATTTAGAATATATGTTTTATTTAATTATCTGTTTGATATACATTTATCCAATAAAT
*
609307 TAATTTTAATATTAAATTA
66 TAATTTTAATAATAAATTA
609326 TGGAGAAATATTTAGAATATATGTTTTATTTAATTATCTGTTTGATATACATTTATCCAATAAAT
1 TGGAGAAATATTTAGAATATATGTTTTATTTAATTATCTGTTTGATATACATTTATCCAATAAAT
609391 TAATTTTAATAATAAATTA
66 TAATTTTAATAATAAATTA
609410 T
1 T
609411 AAATATTTAA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (84 bp):
TGGAGAAATATTTAGAATATATGTTTTATTTAATTATCTGTTTGATATACATTTATCCAATAAAT
TAATTTTAATAATAAATTA
Found at i:609399 original size:41 final size:41
Alignment explanation
Indices: 609270--609400 Score: 108
Period size: 41 Copynumber: 3.1 Consensus size: 41
609260 ATATGTTTTA
609270 TTTAATTATCTGTTTGATATATATTTATCCAATAAATTAAT
1 TTTAATTATCTGTTTGATATATATTTATCCAATAAATTAAT
* * * * * **
609311 TTTAA-TAT-TAAATTATGGAGAAATATTTA--GAATATATGTTTT
1 TTTAATTATCT--GTT-T-GATATATATTTATCCAATAAAT-TAAT
*
609353 ATTTAATTATCTGTTTGATATACATTTATCCAATAAATTAAT
1 -TTTAATTATCTGTTTGATATATATTTATCCAATAAATTAAT
609395 TTTAAT
1 TTTAAT
609401 AATAAATTAT
Statistics
Matches: 65, Mismatches: 15, Indels: 20
0.65 0.15 0.20
Matches are distributed among these distances:
39 1 0.02
40 3 0.05
41 28 0.43
42 6 0.09
43 23 0.35
44 3 0.05
45 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (41 bp):
TTTAATTATCTGTTTGATATATATTTATCCAATAAATTAAT
Found at i:618663 original size:5 final size:5
Alignment explanation
Indices: 618653--618689 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
618643 TAAGTAAGCC
*
618653 AAAA- AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
618690 GAGCAAGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:618869 original size:100 final size:101
Alignment explanation
Indices: 618672--618858 Score: 247
Period size: 99 Copynumber: 1.9 Consensus size: 101
618662 AAAAGAAAAG
* * *
618672 AAAAGAAAAGAAAAGAAAGAGCAAGATAAAAGACAATCACAAAGATGGAACTTACAAGAAATGAA
1 AAAAGAAAAGAAAAGAAAGAGCAAGACAAAAGACAACCACAAAGATAGAACTTACAAGAAATGAA
* **
618737 GAAACTCACTGTGCGAAAATTAAGAGAAATGAACCC
66 GAAACTCACCGTGAAAAAATTAAGAGAAATGAACCC
* *
618773 AAAA-AAAA-AAAA-AACAGAGCAAGACAAGAGACAACCGCAAAGATAGAACTTACAAAGAAATG
1 AAAAGAAAAGAAAAGAA-AGAGCAAGACAAAAGACAACCACAAAGATAGAACTTAC-AAGAAATG
618835 AAGAAACTCACCG-GAAAGAAATTA
64 AAGAAACTCACCGTGAAA-AAATTA
618859 GTATAAATGA
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
98 2 0.03
99 39 0.52
100 30 0.40
101 4 0.05
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (101 bp):
AAAAGAAAAGAAAAGAAAGAGCAAGACAAAAGACAACCACAAAGATAGAACTTACAAGAAATGAA
GAAACTCACCGTGAAAAAATTAAGAGAAATGAACCC
Found at i:621644 original size:39 final size:39
Alignment explanation
Indices: 621585--621666 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
621575 GATCAAATGA
*
621585 AGAAGACTCAACCTGCTGATTAGAAGAAAAAGGTGATGT
1 AGAACACTCAACCTGCTGATTAGAAGAAAAAGGTGATGT
* *
621624 AGAACACTCAGCCTGCTGATTAGAAGACAAAGGTGATGT
1 AGAACACTCAACCTGCTGATTAGAAGAAAAAGGTGATGT
621663 AGAA
1 AGAA
621667 GACTTGAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.20
Consensus pattern (39 bp):
AGAACACTCAACCTGCTGATTAGAAGAAAAAGGTGATGT
Found at i:626298 original size:20 final size:20
Alignment explanation
Indices: 626231--626302 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 20
626221 AACTTGTTAG
626231 AATTAAATTTATTATCTAAT
1 AATTAAATTTATTATCTAAT
* *
626251 TATTAAATTTATTTTGTCTTTTAA-
1 AATTAAATTTA--TTATC---TAAT
626275 AATTAAATTTATTATCTAAT
1 AATTAAATTTATTATCTAAT
626295 AATTAAAT
1 AATTAAAT
626303 CTTAAGCGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 3 0.07
20 18 0.43
22 8 0.19
24 10 0.24
25 3 0.07
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (20 bp):
AATTAAATTTATTATCTAAT
Found at i:630484 original size:16 final size:16
Alignment explanation
Indices: 630457--630489 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
630447 GATTACAGTT
630457 AATTATTTAAAACTATA
1 AATTATTTAAAA-TATA
630474 AATTA-TTAAAATATA
1 AATTATTTAAAATATA
630489 A
1 A
630490 CAAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTATTTAAAATATA
Found at i:645805 original size:31 final size:31
Alignment explanation
Indices: 645770--645830 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
645760 TCGTGAGCCT
* *
645770 AAAATTTTCAAGCTCGACTCGAACTCGAAAG
1 AAAATATTCAAACTCGACTCGAACTCGAAAG
* *
645801 AAAATATTGAAACTCGACTTGAACTCGAAA
1 AAAATATTCAAACTCGACTCGAACTCGAAA
645831 ATGCTCGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.23
Consensus pattern (31 bp):
AAAATATTCAAACTCGACTCGAACTCGAAAG
Found at i:645887 original size:24 final size:24
Alignment explanation
Indices: 645858--645947 Score: 153
Period size: 24 Copynumber: 3.8 Consensus size: 24
645848 AGAAATCAAA
*
645858 AGCTCGATCGAAACTCGAGACTCG
1 AGCTCGATTGAAACTCGAGACTCG
645882 AGCTCGATTGAAACTCGAGACTCG
1 AGCTCGATTGAAACTCGAGACTCG
645906 AGCTCGATTGAAACTCGAGACTCG
1 AGCTCGATTGAAACTCGAGACTCG
* *
645930 AGGTCGATTGAAGCTCGA
1 AGCTCGATTGAAACTCGA
645948 TTTTGAGCTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (24 bp):
AGCTCGATTGAAACTCGAGACTCG
Found at i:645949 original size:11 final size:11
Alignment explanation
Indices: 645933--645981 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
645923 AGACTCGAGG
*
645933 TCGATTGAAGC
1 TCGATTCAAGC
**
645944 TCGATTTTGAGC
1 TCGA-TTCAAGC
645956 TCGATTCAAGC
1 TCGATTCAAGC
*
645967 CCGATTCAAGC
1 TCGATTCAAGC
645978 TCGA
1 TCGA
645982 ACTCGATTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
11 22 0.71
12 9 0.29
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (11 bp):
TCGATTCAAGC
Found at i:645990 original size:17 final size:17
Alignment explanation
Indices: 645968--646002 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
645958 GATTCAAGCC
645968 CGATTCAAGCTCGAACT
1 CGATTCAAGCTCGAACT
645985 CGATTCAAGCTCGAACT
1 CGATTCAAGCTCGAACT
646002 C
1 C
646003 AAACTCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (17 bp):
CGATTCAAGCTCGAACT
Found at i:646029 original size:35 final size:35
Alignment explanation
Indices: 645983--646051 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
645973 CAAGCTCGAA
645983 CTCGATTCAAGCTCGAACTCAAACTCCAATTTGAG
1 CTCGATTCAAGCTCGAACTCAAACTCCAATTTGAG
* *
646018 CTCGGTTCAAGCTCGAACTCAAACTCGAATTTGA
1 CTCGATTCAAGCTCGAACTCAAACTCCAATTTGA
646052 ACCTACAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (35 bp):
CTCGATTCAAGCTCGAACTCAAACTCCAATTTGAG
Found at i:648981 original size:7 final size:7
Alignment explanation
Indices: 648969--649011 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
648959 GTATATAAAT
648969 TAAACCA
1 TAAACCA
648976 TAAACCA
1 TAAACCA
* *
648983 TGAATCA
1 TAAACCA
*
648990 TAAATCA
1 TAAACCA
*
648997 TAAATCA
1 TAAACCA
649004 TAAACCA
1 TAAACCA
649011 T
1 T
649012 CAATCCTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.53, C:0.21, G:0.02, T:0.23
Consensus pattern (7 bp):
TAAACCA
Found at i:648993 original size:14 final size:14
Alignment explanation
Indices: 648969--649021 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
648959 GTATATAAAT
*
648969 TAAACCATAAACCA
1 TAAATCATAAACCA
* *
648983 TGAATCATAAATCA
1 TAAATCATAAACCA
648997 TAAATCATAAACCA
1 TAAATCATAAACCA
* *
649011 TCAATCCTAAA
1 TAAATCATAAA
649022 TCCTAAACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.53, C:0.23, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAATCATAAACCA
Found at i:649034 original size:28 final size:28
Alignment explanation
Indices: 648969--649035 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
648959 GTATATAAAT
* *
648969 TAAACCATAAACCATGAATCATAAATCA
1 TAAACTATAAACCATCAATCATAAATCA
* *
648997 TAAA-TCATAAACCATCAATCCTAAATCC
1 TAAACT-ATAAACCATCAATCATAAATCA
649025 TAAACTATAAA
1 TAAACTATAAA
649036 TTCTAAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.52, C:0.22, G:0.01, T:0.24
Consensus pattern (28 bp):
TAAACTATAAACCATCAATCATAAATCA
Found at i:649155 original size:14 final size:14
Alignment explanation
Indices: 649109--649160 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
649099 ATAGAATTTT
*
649109 TAATATATTTTTAA
1 TAATGTATTTTTAA
649123 -AATTGTATAATTATTAA
1 TAA-TGTAT--TT-TTAA
649140 TAATGTATTTTTAA
1 TAATGTATTTTTAA
649154 TAATGTA
1 TAATGTA
649161 ATTTAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
13 2 0.06
14 15 0.47
15 2 0.06
16 2 0.06
17 9 0.28
18 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TAATGTATTTTTAA
Found at i:649605 original size:2 final size:2
Alignment explanation
Indices: 649600--649640 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
649590 ATTAATGTTT
649600 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
649641 TCTATGTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:654332 original size:192 final size:192
Alignment explanation
Indices: 653992--654500 Score: 777
Period size: 192 Copynumber: 2.7 Consensus size: 192
653982 AAAACCCCAC
* * * *** *
653992 TGCCTGTTACCGATGAAATCCAAGAAATGGTTGAAGGTTTAAAAACAGACGACAATGAAGTCCTA
1 TGCCGGTTACTGATGAAATCCAAGAAATGGTCGAAGGTTTAATGGCAGGCGACAATGAAGTCCTA
* **
654057 ATGCAACAACATGACAATTCAATTCCTCATGATCTTATGTCTGTTAATGGTAACTCCATGACGGT
66 ATGCAACAACATGACAATTCAATTCCTCATGATCTTATGTCAGGCAATGGTAACTCCATGACGGT
* * *
654122 GAGGTCATCGCTAGTGTCTTCGGATAATTATGGTAGCTCTATATGGACAATGCCACCCCCAA
131 GAGGTCATCGCTAGTGTCTTCGGATAATTATGATAGCTCTATATGGACAACGCCACCACCAA
* * * *
654184 TGCTGGTTACTGCTGAAATCAAAGAAGTGGTCGAAGGTTTAATGGCAGGCGACAATGAAGTCCTA
1 TGCCGGTTACTGATGAAATCCAAGAAATGGTCGAAGGTTTAATGGCAGGCGACAATGAAGTCCTA
654249 ATGCAACAACATGACAATTCAATTCCTCATGATCTTATGTCAGGCAATGGTAACTCCATGACGGT
66 ATGCAACAACATGACAATTCAATTCCTCATGATCTTATGTCAGGCAATGGTAACTCCATGACGGT
* * * * * *
654314 GCA-GTCGTCGTTAGTGTCTTCGGATAATTATTATCGTTTTATATGGACAACGCCACCACCAA
131 G-AGGTCATCGCTAGTGTCTTCGGATAATTATGATAGCTCTATATGGACAACGCCACCACCAA
654376 TGCCGGTTACTGATGAAATCCAAGAAATGGTCGAAGGTTTAATGGCAGGCGACAATGAAGTCCTA
1 TGCCGGTTACTGATGAAATCCAAGAAATGGTCGAAGGTTTAATGGCAGGCGACAATGAAGTCCTA
* *
654441 ATGCAACAACATGACAATTCAATCCCTCGTGATCTTATGTCAGGCAATGGTAACTCCATG
66 ATGCAACAACATGACAATTCAATTCCTCATGATCTTATGTCAGGCAATGGTAACTCCATG
654501 TAGCTCTATA
Statistics
Matches: 287, Mismatches: 29, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
192 286 1.00
193 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (192 bp):
TGCCGGTTACTGATGAAATCCAAGAAATGGTCGAAGGTTTAATGGCAGGCGACAATGAAGTCCTA
ATGCAACAACATGACAATTCAATTCCTCATGATCTTATGTCAGGCAATGGTAACTCCATGACGGT
GAGGTCATCGCTAGTGTCTTCGGATAATTATGATAGCTCTATATGGACAACGCCACCACCAA
Found at i:654633 original size:154 final size:154
Alignment explanation
Indices: 654353--654654 Score: 568
Period size: 154 Copynumber: 2.0 Consensus size: 154
654343 ATTATCGTTT
654353 TATATGGACAACGCCACCACCAATGCCGGTTACTGATGAAATCCAAGAAATGGTCGAAGGTTTAA
1 TATATGGACAACGCCACCACCAATGCCGGTTACTGATGAAATCCAAGAAATGGTCGAAGGTTTAA
*
654418 TGGCAGGCGACAATGAAGTCCTAATGCAACAACATGACAATTCAATCCCTCGTGATCTTATGTCA
66 TGGCAGGCGACAATGAAGTCCTAATGCAACAACATGACAATTCAATCCCTCATGATCTTATGTCA
654483 GGCAATGGTAACTCCATGTAGCTC
131 GGCAATGGTAACTCCATGTAGCTC
654507 TATATGGACAACGCCACCACCAATGCCGGTTACTGATGAAATCCAAGAAATGGTCGAAGGTTTAA
1 TATATGGACAACGCCACCACCAATGCCGGTTACTGATGAAATCCAAGAAATGGTCGAAGGTTTAA
*
654572 TGGCAGGCGACAATGAAGTCCTAATGCAACAACATGACAATTCAATTCCTCATGATCTTATGTCA
66 TGGCAGGCGACAATGAAGTCCTAATGCAACAACATGACAATTCAATCCCTCATGATCTTATGTCA
* *
654637 GGTAATGGTAACTTCATG
131 GGCAATGGTAACTCCATG
654655 ACGTGCAGTC
Statistics
Matches: 144, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 144 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (154 bp):
TATATGGACAACGCCACCACCAATGCCGGTTACTGATGAAATCCAAGAAATGGTCGAAGGTTTAA
TGGCAGGCGACAATGAAGTCCTAATGCAACAACATGACAATTCAATCCCTCATGATCTTATGTCA
GGCAATGGTAACTCCATGTAGCTC
Found at i:661896 original size:87 final size:87
Alignment explanation
Indices: 661750--661920 Score: 288
Period size: 87 Copynumber: 2.0 Consensus size: 87
661740 ACTGCTATCT
* * *
661750 CTTCTGTGCTAATTTTGAGAACGCTTTTTGTCATCACCCATTTTATCCATTAGGTAACACATGAT
1 CTTCTCTGCTAATTTTAAGAACACTTTTTGTCATCACCCATTTTATCCATTAGGTAACACATGAT
661815 ATTTTTATATTATATAATATAG
66 ATTTTTATATTATATAATATAG
* * *
661837 CTTCTCTGCTAATTTTAAGAACATTTTTTGTCATCACCCATTTTATCCATTTGGTAACACATGGT
1 CTTCTCTGCTAATTTTAAGAACACTTTTTGTCATCACCCATTTTATCCATTAGGTAACACATGAT
661902 ATTTTTATATTATATAATA
66 ATTTTTATATTATATAATA
661921 GTATAGTAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (87 bp):
CTTCTCTGCTAATTTTAAGAACACTTTTTGTCATCACCCATTTTATCCATTAGGTAACACATGAT
ATTTTTATATTATATAATATAG
Found at i:662053 original size:21 final size:21
Alignment explanation
Indices: 662027--662070 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
662017 ATGGTACATT
662027 GTTTTCAAAATATAGTATATA
1 GTTTTCAAAATATAGTATATA
662048 GTTTTCAAAATATAGTATATA
1 GTTTTCAAAATATAGTATATA
662069 GT
1 GT
662071 ATATGGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (21 bp):
GTTTTCAAAATATAGTATATA
Found at i:670269 original size:2 final size:2
Alignment explanation
Indices: 670262--670290 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
670252 CGTACCCCCG
670262 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 A
670291 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:673402 original size:22 final size:22
Alignment explanation
Indices: 673373--673414 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
673363 ATTTGAATTT
*
673373 AATTATTTTTAAT-TTTTAAAA
1 AATTATTTATAATATTTTAAAA
673394 AATTAATTTATAATATTTTAA
1 AATT-ATTTATAATATTTTAA
673415 TTTATCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTATTTATAATATTTTAAAA
Found at i:674849 original size:28 final size:28
Alignment explanation
Indices: 674813--674891 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 28
674803 TAAATAAAAT
674813 TTATATTATTTTTATTATAAATCTAATA
1 TTATATTATTTTTATTATAAATCTAATA
* * * *
674841 TTAT-TT-TATTTATT-TTAGT-T-ATT
1 TTATATTATTTTTATTATAAATCTAATA
*
674864 TTCTATTATTTTTATTATAAATCTAATA
1 TTATATTATTTTTATTATAAATCTAATA
674892 GTTTTATAAC
Statistics
Matches: 37, Mismatches: 9, Indels: 10
0.66 0.16 0.18
Matches are distributed among these distances:
23 5 0.14
24 3 0.08
25 10 0.27
26 10 0.27
27 3 0.08
28 6 0.16
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (28 bp):
TTATATTATTTTTATTATAAATCTAATA
Found at i:674881 original size:19 final size:17
Alignment explanation
Indices: 674839--674881 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
674829 ATAAATCTAA
674839 TATTATTTTATTTATTT
1 TATTATTTTATTTATTT
*
674856 TAGTTATTTTCTATTATTTT
1 TA-TTATTTTAT-TTA-TTT
674876 TATTAT
1 TATTAT
674882 AAATCTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 8 0.36
19 7 0.32
20 5 0.23
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TATTATTTTATTTATTT
Found at i:675182 original size:15 final size:16
Alignment explanation
Indices: 675149--675207 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 16
675139 TATGTTAAAA
675149 TTTAGTTTGAGGTTCT
1 TTTAGTTTGAGGTTCT
*
675165 TTTAGTTTG-GGTTTT
1 TTTAGTTTGAGGTTCT
* *
675180 TTTCGTTTGAGGTTAAT
1 TTTAGTTTGAGGTT-CT
*
675197 TTTGGTTTGAG
1 TTTAGTTTGAG
675208 TTGTTTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 13 0.35
16 13 0.35
17 11 0.30
ACGTcount: A:0.12, C:0.03, G:0.27, T:0.58
Consensus pattern (16 bp):
TTTAGTTTGAGGTTCT
Found at i:675190 original size:31 final size:33
Alignment explanation
Indices: 675153--675220 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
675143 TTAAAATTTA
* *
675153 GTTTGAGGTT-CTTTTAGTTTGGGTT-TTTTTC
1 GTTTGAGGTTAATTTTAGTTTGAGTTGTTTTTC
* *
675184 GTTTGAGGTTAATTTTGGTTTGAGTTGTTTTTG
1 GTTTGAGGTTAATTTTAGTTTGAGTTGTTTTTC
675217 GTTT
1 GTTT
675221 TGATTTTGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 10 0.32
32 12 0.39
33 9 0.29
ACGTcount: A:0.09, C:0.03, G:0.28, T:0.60
Consensus pattern (33 bp):
GTTTGAGGTTAATTTTAGTTTGAGTTGTTTTTC
Found at i:675217 original size:16 final size:15
Alignment explanation
Indices: 675153--675220 Score: 55
Period size: 16 Copynumber: 4.3 Consensus size: 15
675143 TTAAAATTTA
* *
675153 GTTTGAGGTTCTTTTA
1 GTTTGA-GTTTTTTTG
* *
675169 GTTTGGGTTTTTTTC
1 GTTTGAGTTTTTTTG
*
675184 GTTTGAGGTTAATTTTG
1 GTTTGA-GTT-TTTTTG
675201 GTTTGAGTTGTTTTTG
1 GTTTGAGTT-TTTTTG
675217 GTTT
1 GTTT
675221 TGATTTTGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.29
16 20 0.48
17 10 0.24
ACGTcount: A:0.09, C:0.03, G:0.28, T:0.60
Consensus pattern (15 bp):
GTTTGAGTTTTTTTG
Found at i:676714 original size:19 final size:19
Alignment explanation
Indices: 676690--676730 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
676680 GCGATATTAG
676690 AACTCTTTAAAAGAATACA
1 AACTCTTTAAAAGAATACA
676709 AACTCTTTAAAAGAATACA
1 AACTCTTTAAAAGAATACA
676728 AAC
1 AAC
676731 AAAACATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.17, G:0.05, T:0.24
Consensus pattern (19 bp):
AACTCTTTAAAAGAATACA
Done.