Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008161.1 Hibiscus syriacus cultivar Beakdansim tig00110730_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: 673301
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 4
Found at i:266538 original size:20 final size:20
Alignment explanation
Indices: 266513--266575 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 20
266503 TTTTGGTGCA
266513 GAGGGAATCGATCCCCCCTT
1 GAGGGAATCGATCCCCCCTT
* *
266533 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGA-TCCCCCCTT
266554 GAAGGGGAATCGATACCCCCCT
1 G-A-GGGAATCGAT-CCCCCCT
266576 GGGATTCTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 2 0.06
23 14 0.40
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.19
Consensus pattern (20 bp):
GAGGGAATCGATCCCCCCTT
Found at i:271603 original size:30 final size:32
Alignment explanation
Indices: 271532--271639 Score: 141
Period size: 32 Copynumber: 3.5 Consensus size: 32
271522 TAAACGACGT
*
271532 ACGTTAGCATCTCTCCTTAAGGGGCACGGTGC
1 ACGTTAGCATCTCTCCTTAAGGGGCACGGCGC
* *
271564 ACATTAGCATCTCTCCTTAAGGGGCGC-G-GC
1 ACGTTAGCATCTCTCCTTAAGGGGCACGGCGC
* *
271594 ATGTTAGCATCTCTCCTTAA-GGGCCCGGCGC
1 ACGTTAGCATCTCTCCTTAAGGGGCACGGCGC
*
271625 AGGTTAGCATCTCTC
1 ACGTTAGCATCTCTC
271640 ACCAATTCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
29 5 0.07
30 21 0.31
31 17 0.25
32 25 0.37
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.26
Consensus pattern (32 bp):
ACGTTAGCATCTCTCCTTAAGGGGCACGGCGC
Found at i:271815 original size:4 final size:4
Alignment explanation
Indices: 271806--271838 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
271796 GGCATCCCCA
*
271806 TTTC TTTC TTTC TTT- TTAC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
271839 CATCTCTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 2 0.08
4 24 0.92
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:283332 original size:2 final size:2
Alignment explanation
Indices: 283325--283382 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
283315 TATGTAATTG
283325 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
283367 AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
283383 ACAAAAATTG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:291041 original size:3 final size:3
Alignment explanation
Indices: 291033--291067 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
291023 CAAGCACTTC
291033 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
291068 AGTGCAGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (3 bp):
CCT
Found at i:292614 original size:20 final size:22
Alignment explanation
Indices: 292576--292615 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
292566 CTTAGACTTA
292576 AGGGGATGAACTAAAATTCTTG
1 AGGGGATGAACTAAAATTCTTG
292598 AGGGG-TGAACT-AAATTCT
1 AGGGGATGAACTAAAATTCT
292616 AGTGGTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.28
Consensus pattern (22 bp):
AGGGGATGAACTAAAATTCTTG
Found at i:296742 original size:19 final size:19
Alignment explanation
Indices: 296706--296745 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
296696 AATCAAAACC
*
296706 AAGAGAAAAGAAGCAAAGA
1 AAGAGAAAAGAAGAAAAGA
296725 AAGAGCAAAA-AAGAAAAGA
1 AAGAG-AAAAGAAGAAAAGA
296744 AA
1 AA
296746 ATAGATGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (19 bp):
AAGAGAAAAGAAGAAAAGA
Found at i:297798 original size:33 final size:33
Alignment explanation
Indices: 297750--297813 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
297740 AGAATCAGCG
* *
297750 TTGAAGCAATTAACATCGAATATTGAGGCATCT
1 TTGAAGAAATCAACATCGAATATTGAGGCATCT
* *
297783 TTGAAGAAATCAACATCGAATGTTGGGGCAT
1 TTGAAGAAATCAACATCGAATATTGAGGCAT
297814 GTTTAGGGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (33 bp):
TTGAAGAAATCAACATCGAATATTGAGGCATCT
Found at i:298049 original size:36 final size:36
Alignment explanation
Indices: 297972--298042 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 36
297962 TCTTTAGTTT
* *
297972 GTTTCCTTTGAAATAAAATTGTGTCTCATTTGAGAC
1 GTTTCCTTCGAAATAAAATTGTGTCTCACTTGAGAC
* * *
298008 GTTTCCTTCGAAA-CAAATTTTGTCTCGCTTGAGAC
1 GTTTCCTTCGAAATAAAATTGTGTCTCACTTGAGAC
298043 ATTTTCCCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 18 0.60
36 12 0.40
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (36 bp):
GTTTCCTTCGAAATAAAATTGTGTCTCACTTGAGAC
Found at i:298141 original size:36 final size:37
Alignment explanation
Indices: 298096--298215 Score: 122
Period size: 36 Copynumber: 3.3 Consensus size: 37
298086 ACAAAGTTGA
**
298096 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGATCAATTTCTCTAAAAACAAACTTTG
* *
298132 TCTCGCTTGAGA-CAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGATCAATTTCTCTAAAAACAAACTTTG
* * * * *
298168 TCTCTCTTAAGAT-AATTTCTCTCAAAGCAAA-TTTCA
1 TCTCACTTGAGATCAATTTCTCTAAAAACAAACTTT-G
298204 TCTCACTTGAGA
1 TCTCACTTGAGA
298216 CATTTTTTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
35 10 0.14
36 60 0.86
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (37 bp):
TCTCACTTGAGATCAATTTCTCTAAAAACAAACTTTG
Found at i:298514 original size:26 final size:26
Alignment explanation
Indices: 298468--298534 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
298458 GAGACAATTT
298468 CTTTTGAAATAAATCTTTGAGTATGTTC
1 CTTTTG-AA-AAATCTTTGAGTATGTTC
* *
298496 CTTTTGAAAAATCTTTGAGTTTGTTT
1 CTTTTGAAAAATCTTTGAGTATGTTC
* *
298522 CTCTTAAAAAATC
1 CTTTTGAAAAATC
298535 ATCTTTGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 27 0.77
27 2 0.06
28 6 0.17
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (26 bp):
CTTTTGAAAAATCTTTGAGTATGTTC
Found at i:298696 original size:30 final size:30
Alignment explanation
Indices: 298654--298726 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 30
298644 CCTTAAGGCA
*
298654 TTTCT-TTGGAAACCCAAA-ATTTTTGAGTCG
1 TTTCTCTT-GAAA-CCAAACATCTTTGAGTCG
298684 TTTCTCTTGAAA-CAAACCATCTTTGAGTCG
1 TTTCTCTTGAAACCAAA-CATCTTTGAGTCG
298714 TTT-TCCTTGAAAC
1 TTTCT-CTTGAAAC
298727 GAATTTGTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
28 4 0.11
29 1 0.03
30 30 0.81
31 2 0.05
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (30 bp):
TTTCTCTTGAAACCAAACATCTTTGAGTCG
Found at i:303690 original size:25 final size:26
Alignment explanation
Indices: 303637--303698 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
303627 TTTCTTTACA
* *
303637 ATTTACTTTTC-TTATTTTTAATTTT
1 ATTTACTTTACTTTAATTTTAATTTT
303662 -TTTACTTTACTTTAATTTT-ATTTT
1 ATTTACTTTACTTTAATTTTAATTTT
303686 ATTTACTTTACTT
1 ATTTACTTTACTT
303699 GATTATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (26 bp):
ATTTACTTTACTTTAATTTTAATTTT
Found at i:303692 original size:20 final size:19
Alignment explanation
Indices: 303653--303695 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
303643 TTTTCTTATT
303653 TTTAATTTTTTTACTTTAC
1 TTTAATTTTTTTACTTTAC
303672 TTTAATTTTATTTTA-TTTAC
1 TTTAA-TTT-TTTTACTTTAC
303692 TTTA
1 TTTA
303696 CTTGATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.23
20 12 0.55
21 5 0.23
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTAATTTTTTTACTTTAC
Found at i:316021 original size:14 final size:15
Alignment explanation
Indices: 315992--316024 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
315982 CTATTTTTAC
*
315992 TATTTACTTTATTTT
1 TATTTACTTCATTTT
316007 TATTTA-TTCATTTT
1 TATTTACTTCATTTT
316021 TATT
1 TATT
316025 GTTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTACTTCATTTT
Found at i:317407 original size:23 final size:23
Alignment explanation
Indices: 317358--317408 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
317348 TATTTTTACT
**
317358 ATTTAATTTATTTTTATTTATTC
1 ATTTAATTTATTTTTATTTATAA
*
317381 ATTTTATTGTATTTTT-TTTATAA
1 ATTTAATT-TATTTTTATTTATAA
317404 ATTTA
1 ATTTA
317409 GGTACCTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
ATTTAATTTATTTTTATTTATAA
Found at i:320890 original size:35 final size:37
Alignment explanation
Indices: 320826--320900 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 37
320816 TTCCGTCATA
320826 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
* * *
320863 CTAGGATTC-AACTC-CTAAAATATGATAGAATTTTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
320898 CTA
1 CTA
320901 TGTTTTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 21 0.60
36 5 0.14
37 9 0.26
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:321394 original size:11 final size:11
Alignment explanation
Indices: 321374--321453 Score: 60
Period size: 11 Copynumber: 7.3 Consensus size: 11
321364 TTAATTATTT
*
321374 TTATTCTAATA
1 TTATTTTAATA
321385 TTATTTTAATA
1 TTATTTTAATA
321396 TT-TTTTAA-A
1 TTATTTTAATA
*
321405 GTTATTAT-ATA
1 -TTATTTTAATA
321416 -TATTTATAACTA
1 TTATTT-TAA-TA
*
321428 TTATATTTATTA
1 TTAT-TTTAATA
*
321440 TTATTTTACTA
1 TTATTTTAATA
321451 TTA
1 TTA
321454 ACGTATATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
9 5 0.09
10 10 0.18
11 26 0.46
12 8 0.14
13 5 0.09
14 2 0.04
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:321444 original size:15 final size:15
Alignment explanation
Indices: 321406--321444 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
321396 TTTTTTAAAG
321406 TTATTATATATATTTA
1 TTATTAT-TATATTTA
* *
321422 TAACTATTATATTTA
1 TTATTATTATATTTA
321437 TTATTATT
1 TTATTATT
321445 TTACTATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTATTATATTTA
Found at i:326476 original size:16 final size:16
Alignment explanation
Indices: 326450--326498 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
326440 AGATCCAATC
326450 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
326465 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
* * *
326482 AAAAAAAAAAAAACAA
1 AAGAACAAAAAAGCAA
326498 A
1 A
326499 GAAAAAGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 5 0.17
16 18 0.62
17 6 0.21
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:326526 original size:16 final size:17
Alignment explanation
Indices: 326450--326537 Score: 50
Period size: 16 Copynumber: 5.6 Consensus size: 17
326440 AGATCCAATC
*
326450 AAGAACAAAAAAGAAAA
1 AAGAACAAAAGAGAAAA
*
326467 GAAGCAA-AAAAG-CAAAA
1 -AAG-AACAAAAGAGAAAA
*
326484 AA-AA-AAAA-A-AACA
1 AAGAACAAAAGAGAAAA
*
326497 AAG-A-AAAAGAGAAAC
1 AAGAACAAAAGAGAAAA
326512 AAGAACAAAAG-GAAAA
1 AAGAACAAAAGAGAAAA
*
326528 AAGAGCAAAA
1 AAGAACAAAA
326538 ATCAAAATGA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
13 10 0.18
14 7 0.12
15 5 0.09
16 16 0.29
17 9 0.16
18 7 0.12
19 2 0.04
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (17 bp):
AAGAACAAAAGAGAAAA
Found at i:327188 original size:22 final size:22
Alignment explanation
Indices: 327160--327210 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
327150 CCCCATCAAT
327160 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
327182 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
327204 CCTTTGA
1 CCTTTGA
327211 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:328117 original size:36 final size:36
Alignment explanation
Indices: 328070--328174 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
328060 GTGCTCACCA
328070 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
328106 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
*
328143 TTGTCTCCCTTGAGACAGTTTCTCC-TGAAACA
1 TTGTCTCTCTTGAGACAGTTTC-CCTTGAAACA
328175 TAAACATTGA
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
36 32 0.49
37 31 0.48
38 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:328155 original size:37 final size:37
Alignment explanation
Indices: 328070--328179 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
328060 GTGCTCACCA
328070 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
328106 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
328143 TTGTCTCCCTTGAGACAGTTTCTCC-TGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTC-CCTTGAAACA-AAAC
328180 ATTGAAAACA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
36 31 0.46
37 32 0.47
38 5 0.07
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:328236 original size:36 final size:36
Alignment explanation
Indices: 328189--328275 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
328179 CATTGAAAAC
** * *
328189 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
*
328225 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
328261 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
328276 CAAAACCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:328366 original size:67 final size:67
Alignment explanation
Indices: 328217--328375 Score: 223
Period size: 67 Copynumber: 2.4 Consensus size: 67
328207 TTCGTCTCTC
** *
328217 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
328282 CT
66 CT
* * *
328284 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACATAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
328349 CT
66 CT
*
328351 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
328376 ATTTCGTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 77 0.94
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
CT
Found at i:329285 original size:109 final size:104
Alignment explanation
Indices: 328940--329664 Score: 578
Period size: 109 Copynumber: 6.9 Consensus size: 104
328930 TAGCTAGAGT
* * * * *
328940 CAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAA-TAATAATTTCCTAGTTTCAGGGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC-AGTTCCAGAGCCA
* * * * *
329004 ATTTCAACTTCAC-AGCGAAGGATATTGGACCCAAGACAGCA
65 ATTTCAACTCCACGA-CGGAGGATATT-GACTCGAGACAACA
* * * ** *
329045 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAGA-AA--T----TT-CAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAA-ACAATTTCCAGTTCCAGAGCCA
* * *
329102 ATCTCAACTTCAC-A-GTGAATGATATTGGACTCGAGACAACA
65 ATTTCAACTCCACGACG-G-AGGATATT-GACTCGAGACAACA
* * * *
329143 CAAGTTCAACTTCACAGCGAAGGGACGGTTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CCAGTTCCAGAGCCA
329208 ATTTCAACTCCACGACGGAGGATATCGTG-CTACCTGAGACAACA
65 ATTTCAACTCCACGACGGAGGATAT--TGACT--C-GAGACAACA
* * * **
329252 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCA-TCCGC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCAGTTCCAGAGC-C
* * *
329316 GATTTTAACTCCACGACGGAGGATATCGTGCCACTCAAGACAACA
64 AATTTCAACTCCACGACGGAGGATAT--TG--ACTCGAGACAACA
* * * *
329361 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACA-ATTTCCAGTTCCAGAGCCA
*
329426 ATTTCAACTTCGCA-G-CGAAGGATATTGGACTCGAGACAACA
65 ATTTCAAC-TC-CACGACGGAGGATATT-GACTCGAGACAACA
* * * *
329467 CAAGTTCAACTTCACAACGAAGGGACGACTGATTGTCAAC-AA-GATTT-C-GTT-CAGAGTCAA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAGTTCCAGAGCCAA
* * * *
329527 TTTCATCTTCAC-AGCGAAGGATATTAGACTCGAGACAGCA
66 TTTCAACTCCACGA-CGGAGGATATT-GACTCGAGACAACA
* * * ** *
329567 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CCAGTTCCAGAGCCA
*
329632 ATTTCAACTTCAC-AGCGGAGGATATTGGACTCG
65 ATTTCAACTCCACGA-CGGAGGATATT-GACTCG
329665 GAACAATATT
Statistics
Matches: 513, Mismatches: 68, Indels: 77
0.78 0.10 0.12
Matches are distributed among these distances:
96 1 0.00
97 1 0.00
98 79 0.15
99 3 0.01
100 74 0.14
101 4 0.01
102 4 0.01
103 3 0.01
104 2 0.00
105 39 0.08
106 115 0.22
107 5 0.01
108 5 0.01
109 166 0.32
110 8 0.02
111 2 0.00
112 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (104 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAGTTCCAGAGCCAA
TTTCAACTCCACGACGGAGGATATTGACTCGAGACAACA
Found at i:330184 original size:35 final size:35
Alignment explanation
Indices: 330129--330224 Score: 120
Period size: 35 Copynumber: 2.6 Consensus size: 35
330119 GTCCTACTAG
*
330129 GATTCAAACTCTCAAAAATAGGATAGAATTCTGCTAT
1 GATTC-AACTC-CTAAAATAGGATAGAATTCTGCTAT
*
330166 GATTCAACTCCTAAAATAGGATAGAATTTTGCTAT
1 GATTCAACTCCTAAAATAGGATAGAATTCTGCTAT
* *
330201 GTTTTAAACTCCTAAAGATAGGAT
1 G-ATTCAACTCCTAAA-ATAGGAT
330225 CCACAAGCAC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
35 24 0.45
36 17 0.32
37 12 0.23
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (35 bp):
GATTCAACTCCTAAAATAGGATAGAATTCTGCTAT
Found at i:330685 original size:11 final size:11
Alignment explanation
Indices: 330665--330737 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
330655 ATTAATTATT
*
330665 TTATTCTAATA
1 TTATTTTAATA
330676 TTATTTTAATA
1 TTATTTTAATA
330687 TT-TTTTAA-A
1 TTATTTTAATA
*
330696 GTTATTATATATA
1 -TTATTTTA-ATA
*
330709 TT-TTATAACTA
1 TTATTTTAA-TA
*
330720 TTATATTTATTA
1 TTAT-TTTAATA
330732 TTATTT
1 TTATTT
330738 AATTATTAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
9 1 0.02
10 9 0.18
11 27 0.53
12 10 0.20
13 4 0.08
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:332494 original size:18 final size:18
Alignment explanation
Indices: 332469--332518 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
332459 AACGAAGAAA
*
332469 AAGGCAAAACCCTAAGCG
1 AAGGCAAAACCCTAAACG
* *
332487 AGGGCAAAGCCCTAAACG
1 AAGGCAAAACCCTAAACG
332505 AAGGCAAAACCCTA
1 AAGGCAAAACCCTA
332519 CTACAAATTC
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:0.44, C:0.28, G:0.22, T:0.06
Consensus pattern (18 bp):
AAGGCAAAACCCTAAACG
Found at i:338650 original size:18 final size:19
Alignment explanation
Indices: 338627--338662 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
338617 GCGGGCGGTG
338627 GTGTCTAGATCTA-GTTAA
1 GTGTCTAGATCTATGTTAA
*
338645 GTGTCTAGGTCTATGTTA
1 GTGTCTAGATCTATGTTA
338663 CATAAAGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (19 bp):
GTGTCTAGATCTATGTTAA
Found at i:339712 original size:3 final size:3
Alignment explanation
Indices: 339704--339728 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
339694 GAATAGGATT
339704 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
339729 AAGTTGGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:345865 original size:116 final size:115
Alignment explanation
Indices: 345680--345915 Score: 289
Period size: 116 Copynumber: 2.0 Consensus size: 115
345670 CCCTTTATAC
* * * * **
345680 GAGTTTTTATCATTATGAACTATTCCAATAGAAATGATGATCCAACTCCTTATGTGATGGATGAA
1 GAGTTATTCTCATTATGAACCATTCCAATAGAAATGATGATCCAACTCCTTATGTGATGAAACAA
* * *
345745 CCAAGTTCGAA-CAAGTTCTTC-CGATTAGGAACTTCTTCTCCCTCATTGGAT
66 CCAAGGTC-AATCAAGTTCTTCTC-ATTAGGAACTT-TCCCCCCTCATTGGAT
* * * *
345796 TAGTTATTCTCATTATGAACCATTCCACT-GAAAATGTTGATCCAACTCTTTATGTGATGAAACA
1 GAGTTATTCTCATTATGAACCATTCCAATAG-AAATGATGATCCAACTCCTTATGTGATGAAACA
*
345860 GCCAAGGTCAATCAAGTTCTTCTCATTAGGAACTTTCCCCCCTCATTGGAT
65 ACCAAGGTCAATCAAGTTCTTCTCATTAGGAACTTTCCCCCCTCATTGGAT
345911 GAGTT
1 GAGTT
345916 CTTCGGAATT
Statistics
Matches: 102, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
115 21 0.21
116 80 0.78
117 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (115 bp):
GAGTTATTCTCATTATGAACCATTCCAATAGAAATGATGATCCAACTCCTTATGTGATGAAACAA
CCAAGGTCAATCAAGTTCTTCTCATTAGGAACTTTCCCCCCTCATTGGAT
Found at i:346340 original size:18 final size:18
Alignment explanation
Indices: 346301--346345 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
346291 CTTTGATGAG
* * *
346301 TCTTTATCTTTTCTTGAG
1 TCTTTATCTTTGCCTGAA
346319 TCTTTATCTTTGCCTGAA
1 TCTTTATCTTTGCCTGAA
*
346337 TCTTCATCT
1 TCTTTATCT
346346 CATGAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.09, T:0.56
Consensus pattern (18 bp):
TCTTTATCTTTGCCTGAA
Found at i:351719 original size:14 final size:14
Alignment explanation
Indices: 351694--351733 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
351684 AATAAAGTTT
351694 AAATGTAAATAACAA
1 AAATG-AAATAACAA
*
351709 AAATGAAATAACAT
1 AAATGAAATAACAA
*
351723 AAATAAAATAA
1 AAATGAAATAA
351734 GATAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (14 bp):
AAATGAAATAACAA
Found at i:351738 original size:14 final size:15
Alignment explanation
Indices: 351700--351744 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
351690 GTTTAAATGT
*
351700 AAATAACA-AAAATG
1 AAATAACATAAAATA
351714 AAATAACAT-AAATA
1 AAATAACATAAAATA
*
351728 AAATAAGATAAAATA
1 AAATAACATAAAATA
351743 AA
1 AA
351745 GGGAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (15 bp):
AAATAACATAAAATA
Found at i:352234 original size:116 final size:114
Alignment explanation
Indices: 351827--352226 Score: 451
Period size: 116 Copynumber: 3.4 Consensus size: 114
351817 AAAAGCTACA
* * *
351827 AGTTCTTCTCATTATGAACACTTCCATTGAAAGTGCTT-ATCCAACTCCTTATGTGATGGATGAG
1 AGTTCTTCTCATTATGAACCCTTCAATGGAAA-TG-TTGATCCAACTCCTTATGTGATGGATGAG
* * * * ** ** * *
351891 CTAAGGTTGAACAAGCTCTTCTCATTAAGATCTGCTTCTCATTCTTTAGACG
64 CCAAGGTCGAACAAGTTCTTCTCATT-AGAACTTATTCTCCCTCATTAGATG
* * * * ** * *
351943 AGTTCTTCTTATTATGAACCCTTCCATTAGAAATGTTGATTCAACTCCTTATGTGATTCAAGATC
1 AGTTCTTCTCATTATGAACCCTT-CAATGGAAATGTTGATCCAACTCCTTATGTGATGGATGAGC
* * * * *
352008 CAAGGTCAAACAAGTTCTCCTTATTAGTAACTTATTCTTCCTCATTGGATG
65 CAAGGTCGAACAAGTTCTTCTCATTAG-AACTTATTCTCCCTCATTAGATG
*
352059 AGTTCTTCTCATTATGAACCCTTCAACTGGAAATGTTGATCCAACTCCTTGTGTGATGGATGAGC
1 AGTTCTTCTCATTATGAACCCTTCAA-TGGAAATGTTGATCCAACTCCTTATGTGATGGATGAGC
*
352124 CAAGGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATTAGATG
65 CAAGGTCGAACAAGTTCTTCTCATTA-GAACTTATTCTCCCTCATTAGATG
* *
352175 AGTTCTTCTCATTATGAACCCTTGCAATGGAAATGTAGATCTAACTCCTTAT
1 AGTTCTTCTCATTATGAACCCTT-CAATGGAAATGTTGATCCAACTCCTTAT
352227 ATAATGGAAT
Statistics
Matches: 235, Mismatches: 43, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
115 6 0.03
116 219 0.93
117 10 0.04
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (114 bp):
AGTTCTTCTCATTATGAACCCTTCAATGGAAATGTTGATCCAACTCCTTATGTGATGGATGAGCC
AAGGTCGAACAAGTTCTTCTCATTAGAACTTATTCTCCCTCATTAGATG
Found at i:353367 original size:6 final size:6
Alignment explanation
Indices: 353353--354012 Score: 1211
Period size: 6 Copynumber: 110.3 Consensus size: 6
353343 CTCAGCTTTA
*
353353 GTATAT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353401 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
* * * *
353449 GTATGT GTATGTGT GTGTGT GTGTGT GTGTGT GTATGT GTCTGT G--TGT
1 GTATGT GTA--TGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
* *
353497 GTGTGT GTCTGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353545 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353593 GTATGT GTA--T GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353639 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353687 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353735 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353783 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353831 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353879 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353927 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
353975 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GT
354013 CATTGATAAT
Statistics
Matches: 642, Mismatches: 6, Indels: 12
0.97 0.01 0.02
Matches are distributed among these distances:
4 8 0.01
6 629 0.98
8 5 0.01
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
GTATGT
Found at i:354270 original size:19 final size:18
Alignment explanation
Indices: 354246--354293 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
354236 GTTAGAATGC
*
354246 AATAAAATAAAATACAGTA
1 AATAAAATAAAATA-AATA
*
354265 AATAAATTCAAAATAAATA
1 AATAAAAT-AAAATAAATA
354284 AAT-AAATAAA
1 AATAAAATAAA
354294 CAAAAAAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 3 0.12
18 3 0.12
19 13 0.52
20 6 0.24
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (18 bp):
AATAAAATAAAATAAATA
Found at i:355437 original size:35 final size:34
Alignment explanation
Indices: 355391--355456 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
355381 TTAAACCTTT
*
355391 TTATATTTTTAATTTTGTAAA-AAATTATATTAA
1 TTATATTTTTAATTTTGTAAAGAAAATATATTAA
*
355424 TTATATTAATTTAATTTTTTAAAGAAAATATAT
1 TTATATT--TTTAATTTTGTAAAGAAAATATAT
355457 AAATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 7 0.25
35 13 0.46
36 8 0.29
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (34 bp):
TTATATTTTTAATTTTGTAAAGAAAATATATTAA
Found at i:365934 original size:14 final size:14
Alignment explanation
Indices: 365912--365950 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
365902 CTGTCTATAA
* *
365912 GCAGAGATTTTTTT
1 GCAGGGATTTATTT
365926 GCAGGGATTTATTT
1 GCAGGGATTTATTT
365940 GCAGGGATTTA
1 GCAGGGATTTA
365951 CTAACCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.41
Consensus pattern (14 bp):
GCAGGGATTTATTT
Found at i:368486 original size:19 final size:18
Alignment explanation
Indices: 368439--368486 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
368429 AGGCCAAGTA
368439 ACATGATCAGAGGAATTT
1 ACATGATCAGAGGAATTT
368457 ACATGATCAGAGGAATTT
1 ACATGATCAGAGGAATTT
*
368475 ACGTGCATCAGA
1 ACATG-ATCAGA
368487 AGCTCACATC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (18 bp):
ACATGATCAGAGGAATTT
Found at i:370596 original size:16 final size:18
Alignment explanation
Indices: 370577--370617 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
370567 CCCATATTAA
*
370577 CTTAAACCC-TTCATTC-
1 CTTAAACCCTTTCATACT
*
370593 CTTAATCCCTTTCATACT
1 CTTAAACCCTTTCATACT
370611 CTTAAAC
1 CTTAAAC
370618 TCAAATACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 8 0.40
17 6 0.30
18 6 0.30
ACGTcount: A:0.27, C:0.34, G:0.00, T:0.39
Consensus pattern (18 bp):
CTTAAACCCTTTCATACT
Found at i:376663 original size:21 final size:21
Alignment explanation
Indices: 376631--376693 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
376621 AAGTAAGATT
*
376631 TGTCCCGAAGGACCTCATGTA
1 TGTCCCGAAGGACCTCATATA
*
376652 TG-CCCTGAAGGACCTCGTATA
1 TGTCCC-GAAGGACCTCATATA
*
376673 TGTCCCGAAGAACCTCATATA
1 TGTCCCGAAGGACCTCATATA
376694 ATCCCTCGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.08
21 30 0.83
22 3 0.08
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
TGTCCCGAAGGACCTCATATA
Found at i:379775 original size:4 final size:4
Alignment explanation
Indices: 379766--379792 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
379756 TTCATATATG
379766 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
379793 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:379797 original size:2 final size:2
Alignment explanation
Indices: 379790--379825 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
379780 AAATAAATAA
379790 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
379826 TTTGCAGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:382394 original size:14 final size:14
Alignment explanation
Indices: 382371--382408 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
382361 TCTGTCTATA
*
382371 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
382384 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
382399 TGCAGGGATT
1 TGCAGGGATT
382409 ACTTCCCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:386475 original size:18 final size:18
Alignment explanation
Indices: 386434--386476 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
386424 ATATTTGACT
* *
386434 TTATTTATAATTTTTATA
1 TTATTTATAATTTTAAAA
*
386452 TATATTTGTAATTTTAAAA
1 T-TATTTATAATTTTAAAA
386471 TTATTT
1 TTATTT
386477 TATATGCCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATTTATAATTTTAAAA
Found at i:386557 original size:18 final size:18
Alignment explanation
Indices: 386534--386568 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
386524 GCCGTTTCCT
386534 GTCCCCGT-TCCCGTATCC
1 GTCCCCGTAT-CCGTATCC
386552 GTCCCCGTATCCGTATC
1 GTCCCCGTATCCGTATC
386569 AGTGCAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.09, C:0.46, G:0.17, T:0.29
Consensus pattern (18 bp):
GTCCCCGTATCCGTATCC
Found at i:393603 original size:25 final size:26
Alignment explanation
Indices: 393575--393639 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 26
393565 GGTTTTTCTA
393575 TTATTTATTTTATTATTAT-TATTAT
1 TTATTTATTTTATTATTATATATTAT
393600 TTA-TTA--TTATTATT-TATATTAT
1 TTATTTATTTTATTATTATATATTAT
*
393622 TT-TATATTATTATTATTA
1 TTATTTATT-TTATTATTA
393640 ATAATAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
21 1 0.03
22 18 0.55
24 3 0.09
25 11 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
TTATTTATTTTATTATTATATATTAT
Found at i:393604 original size:28 final size:29
Alignment explanation
Indices: 393573--393638 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 29
393563 ATGGTTTTTC
393573 TATTATTTATTT-TATTATTAT-TATTATT
1 TATTATTTATTTATATTATTATATATTA-T
*
393601 TATTATTATTATTTATATTATTTTATATTAT
1 TATTA-T-TTATTTATATTATTATATATTAT
393632 TATTATT
1 TATTATT
393639 AATAATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
28 5 0.15
29 2 0.06
30 7 0.21
31 14 0.42
32 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (29 bp):
TATTATTTATTTATATTATTATATATTAT
Found at i:393655 original size:3 final size:3
Alignment explanation
Indices: 393573--393639 Score: 79
Period size: 3 Copynumber: 22.7 Consensus size: 3
393563 ATGGTTTTTC
393573 TAT TATT TAT T-T TAT TAT TAT TAT TATT TAT TAT TAT TAT T-T ATAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT -TAT
393619 TAT T-T TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
393640 ATAATAAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
2 7 0.12
3 43 0.75
4 7 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:394097 original size:15 final size:15
Alignment explanation
Indices: 394077--394106 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
394067 CAAGGACGGG
394077 GAACCAAACAACAAC
1 GAACCAAACAACAAC
394092 GAACCAAACAACAAC
1 GAACCAAACAACAAC
394107 AAAACCACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.33, G:0.07, T:0.00
Consensus pattern (15 bp):
GAACCAAACAACAAC
Found at i:395037 original size:29 final size:28
Alignment explanation
Indices: 394969--395034 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
394959 TTTAAATTTT
* *
394969 ATATGTTTATTATTAATATATTTAAAATA
1 ATAT-TTTATTATAAATATATTAAAAATA
*
394998 TTATTATTATTATAAATATATATAATAAATA
1 ATATT-TTATTATAAATATAT-TAA-AAATA
395029 ATATTT
1 ATATTT
395035 ATTTGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.03
29 17 0.57
30 3 0.10
31 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
ATATTTTATTATAAATATATTAAAAATA
Found at i:398982 original size:8 final size:8
Alignment explanation
Indices: 398979--399027 Score: 54
Period size: 7 Copynumber: 6.6 Consensus size: 8
398969 AAAAAAAGAA
398979 AAAAAATG
1 AAAAAATG
398987 --AAA-TG
1 AAAAAATG
398992 AAAAAATG
1 AAAAAATG
399000 -AAAAATG
1 AAAAAATG
399007 -AAAAATG
1 AAAAAATG
399014 AAAAAAATG
1 -AAAAAATG
399023 AAAAA
1 AAAAA
399028 TGATGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 2 0.06
6 3 0.08
7 17 0.47
8 7 0.19
9 7 0.19
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:399002 original size:23 final size:23
Alignment explanation
Indices: 398968--399028 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
398958 TATGCTTGAA
*
398968 AAAAAAAAGAAAAA-AAATGAAATG
1 AAAAAAATGAAAAATAAA--AAATG
*
398992 -AAAAAATGAAAAATGAAAAATG
1 AAAAAAATGAAAAATAAAAAATG
399014 AAAAAAATGAAAAAT
1 AAAAAAATGAAAAAT
399029 GATGAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 5 0.15
23 26 0.79
24 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (23 bp):
AAAAAAATGAAAAATAAAAAATG
Found at i:399011 original size:16 final size:15
Alignment explanation
Indices: 398987--399030 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
398977 AAAAAAAATG
398987 AAATGAAAAAATG-AA
1 AAATG-AAAAATGAAA
399002 AAATGAAAAATGAAAA
1 AAATGAAAAATG-AAA
399018 AAATGAAAAATGA
1 AAATGAAAAATGA
399031 TGAAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 14 0.52
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AAATGAAAAATGAAA
Found at i:399026 original size:7 final size:7
Alignment explanation
Indices: 398987--399030 Score: 61
Period size: 7 Copynumber: 5.9 Consensus size: 7
398977 AAAAAAAATG
398987 AAATGAAA
1 AAATG-AA
398995 AAATGAA
1 AAATGAA
399002 AAATGAA
1 AAATGAA
399009 AAATGAAAA
1 AAATG--AA
399018 AAATGAA
1 AAATGAA
399025 AAATGA
1 AAATGA
399031 TGAAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 22 0.65
8 5 0.15
9 7 0.21
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAATGAA
Found at i:399036 original size:16 final size:16
Alignment explanation
Indices: 398987--399037 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
398977 AAAAAAAATG
398987 AAATGAAAAA--ATGAA
1 AAATGAAAAATGATG-A
**
399002 AAATGAAAAATGAAAA
1 AAATGAAAAATGATGA
399018 AAATGAAAAATGATGA
1 AAATGAAAAATGATGA
399034 AAAT
1 AAAT
399038 ATATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 10 0.33
16 19 0.63
17 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.16
Consensus pattern (16 bp):
AAATGAAAAATGATGA
Found at i:400824 original size:112 final size:114
Alignment explanation
Indices: 400631--401049 Score: 290
Period size: 122 Copynumber: 3.6 Consensus size: 114
400621 GGTAGAGTTT
* * * * *
400631 ATAATGATAGGAACTCGTCTGAAGAAGGAA-AAGAAGTTCAAAATGAGAAGAATTTGTTCAACCT
1 ATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
** *
400695 TTCGCTCGAATTCATCAC-TCGATGGATCAAC-T-TTTCCAGAGAATGTTC
65 TTCGCTCGAATTCATCACAGAGATAGATCAACATATTTCCAGA-AATGTTC
* *
400743 ATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAA-AAGCTTGTTCAACCT
1 ATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA-CTTGTTCAACCT
* * * * * *
400807 TTTGTTTG-ACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCTAGAAGTGTTC
65 TTCGCTCGAATTC-ATCAC---A-GAGATAGATCAACAT----ATTTCCAGAAATGTTC
*
400865 ATAATGAGAAGAACTCATCTGAAGAGGAAGAA-AACGTTCATAATGAGAAGAACTTGTTCAATCT
1 ATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAA-GTTCATAATGAGAAGAACTTGTTCAACCT
* * * * *
400929 TT-GCAT-GAA-TCTATCGTAGAAGGAGATAGATCAGCATTAACATGTCCATAAGGA-ATTC
65 TTCGC-TCGAATTC-ATC--A-CA-GAGATAGATCAACA-T---ATTTCCAGAA--ATGTTC
* * *
400987 ATAATGAGAAGAACTCATCT---GACGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAACTT
1 ATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
401049 T
66 T
401050 TTGCTAGATT
Statistics
Matches: 252, Mismatches: 30, Indels: 43
0.78 0.09 0.13
Matches are distributed among these distances:
111 10 0.04
112 58 0.23
117 10 0.04
118 1 0.00
119 37 0.15
120 2 0.01
121 35 0.14
122 89 0.35
123 10 0.04
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (114 bp):
ATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
TCGCTCGAATTCATCACAGAGATAGATCAACATATTTCCAGAAATGTTC
Found at i:400877 original size:122 final size:122
Alignment explanation
Indices: 400734--401050 Score: 398
Period size: 122 Copynumber: 2.6 Consensus size: 122
400724 ACTTTTCCAG
* *
400734 AGAA-TGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAA-AAGCT
1 AGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA-CT
* ** * * *
400797 TGTTCAACCTTTTGTTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCT
65 TGTTCAAACTTTTGCATGAATCTATCACAGAAGGAGATAGATCAACATCAACATGTCC
400855 AGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAA-AACGTTCATAATGAGAAGAACT
1 AGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAA-GTTCATAATGAGAAGAACT
* ** * *
400919 TGTTCAATC-TTTGCATGAATCTATCGTAGAAGGAGATAGATCAGCATTAACATGTCC
65 TGTTCAAACTTTTGCATGAATCTATCACAGAAGGAGATAGATCAACATCAACATGTCC
* * *
400976 ATAAG-GAATTCATAATGAGAAGAACTCATCT---GACGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAAGTG--TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAAC
401037 TTGTTCAAACTTTT
64 TTGTTCAAACTTTT
401051 TGCTAGATTA
Statistics
Matches: 173, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
119 34 0.20
120 6 0.03
121 49 0.28
122 82 0.47
123 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (122 bp):
AGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAAACTTTTGCATGAATCTATCACAGAAGGAGATAGATCAACATCAACATGTCC
Found at i:401300 original size:22 final size:22
Alignment explanation
Indices: 401271--401352 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
401261 TTCTATTATT
401271 TATT-TTATTATTATTATT-TAT
1 TATTATTATTATTATTATTAT-T
*
401292 TATTATTATTAATATTATTATT
1 TATTATTATTATTATTATTATT
401314 TA-TATTATT-TTA-TATTATT
1 TATTATTATTATTATTATTATT
* *
401333 AATTAATATTATTATTATTA
1 TATTATTATTATTATTATTA
401353 ATAAAATATT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
19 8 0.15
20 8 0.15
21 14 0.27
22 21 0.40
23 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTATTATTATTATTATTATT
Found at i:401365 original size:3 final size:3
Alignment explanation
Indices: 401264--401352 Score: 96
Period size: 3 Copynumber: 29.7 Consensus size: 3
401254 ATGGTTTTTC
*
401264 TAT TATT TAT T-T TAT TAT TAT TATT TAT TAT TAT TAT TAA TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
*
401310 TAT T-T ATAT TAT T-T TA- TAT TAT TAAT TAA TAT TAT TAT TAT TA
1 TAT TAT -TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TA
401353 ATAAAATATT
Statistics
Matches: 74, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
2 7 0.09
3 57 0.77
4 10 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:402917 original size:22 final size:22
Alignment explanation
Indices: 402892--402933 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
402882 TTATCCTATA
*
402892 AAATATATAATTAATTTTTAAG
1 AAATATATAATTAATATTTAAG
* *
402914 AAATATTTTATTAATATTTA
1 AAATATATAATTAATATTTA
402934 TTTTTTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AAATATATAATTAATATTTAAG
Found at i:403757 original size:13 final size:13
Alignment explanation
Indices: 403739--403765 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
403729 CATAGATTAA
403739 CAGTCTTCATATG
1 CAGTCTTCATATG
403752 CAGTCTTCATATG
1 CAGTCTTCATATG
403765 C
1 C
403766 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:408137 original size:111 final size:111
Alignment explanation
Indices: 407997--408263 Score: 525
Period size: 111 Copynumber: 2.4 Consensus size: 111
407987 TGTAAATCAT
*
407997 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
408062 TATTTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
66 TATTTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
408108 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
408173 TATTTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
66 TATTTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
408219 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAAT
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAAT
408264 GTACCTGCTC
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 155 1.00
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TATTTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
Found at i:409860 original size:267 final size:267
Alignment explanation
Indices: 409385--409904 Score: 1004
Period size: 267 Copynumber: 1.9 Consensus size: 267
409375 ATGCTCTTCA
* *
409385 CATTTAGGTCGAATAACCTACTACTTGCACGCCTTCCCCTTGAACTGTAAGGCATATCGACATTG
1 CATTTAGGTCGAAGAACCTACTACTTGCACGCCTTCCCCTTGAACTGGAAGGCATATCGACATTG
409450 AGATCGAAAAAGCTCGCAGTCGAATGCCTCCCCCTGGAGCTTGAAGCCATCGTGTCAAATGGAAA
66 AGATCGAAAAAGCTCGCAGTCGAATGCCTCCCCCTGGAGCTTGAAGCCATCGTGTCAAATGGAAA
*
409515 CTGCACAGATGGTTGCATCGATGTCATCTCCATATGGTCAAAGAAATTTGCAGATGAATGCCTTC
131 CTGCACAGATGGTTGCATCGATGTCATCTCCATATGGTCAAAGAAATTTGCAAATGAATGCCTTC
*
409580 CCCTTGAACTGGACGCGGTGTTGCCATACAGATTGTTCGTGGACCCACCTCGGTACATTGAACTG
196 CCCTTGAACTGGACGCGGTGTTGCCATACAGATTGTTCGTGGACCCACCGCGGTACATTGAACTG
409645 GTTCCTC
261 GTTCCTC
409652 CATTTAGGTCGAAGAACCTACTACTTGCACGCCTTCCCCTTGAACTGGAAGGCATATCGACATTG
1 CATTTAGGTCGAAGAACCTACTACTTGCACGCCTTCCCCTTGAACTGGAAGGCATATCGACATTG
409717 AGATCGAAAAAGCTCGCAGTCGAATGCCTCCCCCTGGAGCTTGAAGCCATCGTGTCAAATGGAAA
66 AGATCGAAAAAGCTCGCAGTCGAATGCCTCCCCCTGGAGCTTGAAGCCATCGTGTCAAATGGAAA
409782 CTGCACAGATGGTTGCATCGATGTCATCTCCATATGGTCAAAGAAATTTGCAAATGAATGCCTTC
131 CTGCACAGATGGTTGCATCGATGTCATCTCCATATGGTCAAAGAAATTTGCAAATGAATGCCTTC
409847 CCCTTGAACTGGACGCGGTGTTGCCATACAGATTGTTCGTGGACCCACCGCGGTACAT
196 CCCTTGAACTGGACGCGGTGTTGCCATACAGATTGTTCGTGGACCCACCGCGGTACAT
409905 ATCATAAGGA
Statistics
Matches: 249, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
267 249 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (267 bp):
CATTTAGGTCGAAGAACCTACTACTTGCACGCCTTCCCCTTGAACTGGAAGGCATATCGACATTG
AGATCGAAAAAGCTCGCAGTCGAATGCCTCCCCCTGGAGCTTGAAGCCATCGTGTCAAATGGAAA
CTGCACAGATGGTTGCATCGATGTCATCTCCATATGGTCAAAGAAATTTGCAAATGAATGCCTTC
CCCTTGAACTGGACGCGGTGTTGCCATACAGATTGTTCGTGGACCCACCGCGGTACATTGAACTG
GTTCCTC
Found at i:410989 original size:50 final size:50
Alignment explanation
Indices: 410927--411039 Score: 163
Period size: 50 Copynumber: 2.3 Consensus size: 50
410917 TAGCGCGGAT
* *** *
410927 CAGGGGGCGCGCTATACCCACGTGGCGCCAGATCATTGTATATCGCGGGG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAGCATATAACGCGGGG
* *
410977 CAGGGGGAGCGCTATACCCACGTGGCGCCAAATCAGCATATAACGCGGTG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAGCATATAACGCGGGG
411027 CAGGGGGCGCGCT
1 CAGGGGGCGCGCT
411040 TTCCTGTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.20, C:0.28, G:0.36, T:0.15
Consensus pattern (50 bp):
CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAGCATATAACGCGGGG
Found at i:412792 original size:19 final size:19
Alignment explanation
Indices: 412768--412804 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
412758 TCATCATTAT
412768 ATTACTAAATTTACTTTAA
1 ATTACTAAATTTACTTTAA
412787 ATTACTAAATTTACTTTA
1 ATTACTAAATTTACTTTA
412805 TATATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTACTAAATTTACTTTAA
Found at i:421866 original size:42 final size:41
Alignment explanation
Indices: 421819--421902 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 41
421809 ATTCATTTAT
*
421819 ATGCTTGCTGAAATTTATGAAAACTAATCAAAAAGTAGTAGC
1 ATGCTTGCTGAAATTCATGAAAACTAATCAAAAA-TAGTAGC
* *
421861 ATGCTTGCTGAAATTCATGAAAATTAATGAAAAATAGTAGC
1 ATGCTTGCTGAAATTCATGAAAACTAATCAAAAATAGTAGC
421902 A
1 A
421903 CCCTACAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 8 0.21
42 31 0.79
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.29
Consensus pattern (41 bp):
ATGCTTGCTGAAATTCATGAAAACTAATCAAAAATAGTAGC
Found at i:423889 original size:14 final size:13
Alignment explanation
Indices: 423876--423944 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 13
423866 GAAAACAAAT
423876 AAACAAATAAAAATA
1 AAACAAAT-AAAA-A
423891 GAAACTAAATAATAAA
1 -AAAC-AAATAA-AAA
*
423907 AAAGAAATAAAAA
1 AAACAAATAAAAA
*
423920 AGA-AAATAAAAA
1 AAACAAATAAAAA
*
423932 AACATAAATAAAA
1 AA-ACAAATAAAA
423945 CATAAATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 10 0.22
13 6 0.13
14 14 0.30
15 3 0.07
16 7 0.15
17 6 0.13
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.13
Consensus pattern (13 bp):
AAACAAATAAAAA
Found at i:423906 original size:20 final size:18
Alignment explanation
Indices: 423856--423917 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
423846 CAAAAAATAC
* * *
423856 ATAAATAACAGAAAACAA
1 ATAAATAATAAAAAAGAA
*
423874 ATAAACAAATAAAAATAGAA
1 ATAAA-TAATAAAAA-AGAA
423894 ACTAAATAATAAAAAAGAA
1 A-TAAATAATAAAAAAGAA
423913 ATAAA
1 ATAAA
423918 AAAGAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 9 0.25
19 11 0.31
20 12 0.33
21 4 0.11
ACGTcount: A:0.74, C:0.06, G:0.05, T:0.15
Consensus pattern (18 bp):
ATAAATAATAAAAAAGAA
Found at i:423915 original size:11 final size:12
Alignment explanation
Indices: 423901--423932 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
423891 GAAACTAAAT
423901 AATAAAAAAG-A
1 AATAAAAAAGAA
423912 AATAAAAAAGAA
1 AATAAAAAAGAA
423924 AATAAAAAA
1 AATAAAAAA
423933 ACATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.09
Consensus pattern (12 bp):
AATAAAAAAGAA
Found at i:423930 original size:10 final size:11
Alignment explanation
Indices: 423906--423963 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
423896 TAAATAATAA
* *
423906 AAAAGAAATAA
1 AAAAGAAACAT
423917 AAAAGAAA-AT
1 AAAAGAAACAT
423927 AAAA-AAACAT
1 AAAAGAAACAT
423937 AAATA-AAACAT
1 AAA-AGAAACAT
*
423948 AAATAAAAACAT
1 AAA-AGAAACAT
423960 AAAA
1 AAAA
423964 CAATATAAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
9 3 0.07
10 10 0.23
11 21 0.49
12 9 0.21
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.12
Consensus pattern (11 bp):
AAAAGAAACAT
Found at i:423944 original size:11 final size:11
Alignment explanation
Indices: 423925--423962 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
423915 AAAAAAGAAA
423925 ATAAA-AAAAC
1 ATAAATAAAAC
423935 ATAAATAAAAC
1 ATAAATAAAAC
423946 ATAAATAAAAAC
1 ATAAAT-AAAAC
423958 ATAAA
1 ATAAA
423963 ACAATATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 5 0.19
11 11 0.42
12 10 0.38
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
ATAAATAAAAC
Found at i:423944 original size:12 final size:12
Alignment explanation
Indices: 423929--423962 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
423919 AAGAAAATAA
423929 AAAAACATAAAT
1 AAAAACATAAAT
423941 -AAAACATAAAT
1 AAAAACATAAAT
423952 AAAAACATAAA
1 AAAAACATAAA
423963 ACAATATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAACATAAAT
Found at i:423951 original size:25 final size:24
Alignment explanation
Indices: 423872--423956 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 24
423862 AACAGAAAAC
*
423872 AAATAAACAAATAAAAATAGAAAC-T
1 AAATAAA-AAAAAAAAATA-AAACAT
* * *
423897 AAATAATAAAAAAGAAATAAAAAAGA
1 AAATAA-AAAAAAAAAATAAAACA-T
*
423923 AAATAAAAAAACATAAATAAAACAT
1 AAATAAAAAAA-AAAAATAAAACAT
423948 AAATAAAAA
1 AAATAAAAA
423957 CATAAAACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
24 3 0.06
25 29 0.59
26 17 0.35
ACGTcount: A:0.78, C:0.05, G:0.04, T:0.14
Consensus pattern (24 bp):
AAATAAAAAAAAAAAATAAAACAT
Found at i:424045 original size:32 final size:32
Alignment explanation
Indices: 423990--424067 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
423980 TAATTCAATG
*
423990 TCCTTCACATTAAC-TTAAGAATCAGCTAATA
1 TCCTTCACATTAACATTAAGAATCAACTAATA
*
424021 TCCTTTACATTAACATTAAGAATCAACTAATA
1 TCCTTCACATTAACATTAAGAATCAACTAATA
*
424053 TCCTTCACATCAACA
1 TCCTTCACATTAACA
424068 AATAAAAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 13 0.31
32 29 0.69
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (32 bp):
TCCTTCACATTAACATTAAGAATCAACTAATA
Found at i:424123 original size:31 final size:31
Alignment explanation
Indices: 424087--424149 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
424077 ATAAAACAAT
*
424087 ATAAGAATCAACTAATATCCTTCACATTAAC
1 ATAAGAATCAACTAATATACTTCACATTAAC
** *
424118 ATAAGAATCATTTAATATATTTCACATTAAC
1 ATAAGAATCAACTAATATACTTCACATTAAC
424149 A
1 A
424150 AATAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.33
Consensus pattern (31 bp):
ATAAGAATCAACTAATATACTTCACATTAAC
Found at i:424153 original size:82 final size:83
Alignment explanation
Indices: 424005--424184 Score: 263
Period size: 82 Copynumber: 2.2 Consensus size: 83
423995 CACATTAACT
* * *
424005 TAAGAATCAGCTAATATCCTTTACATTAACATTAAGAATCAACTAATATCCTTCACATCAACAAA
1 TAAGAATCAACTAATATCCTTCACATTAACATTAAGAATCAACTAATATACTTCACATCAACAAA
*
424070 TAAAAACATAAAACAATA
66 TAAAAACAGAAAACAATA
** * *
424088 TAAGAATCAACTAATATCCTTCACATTAACA-TAAGAATCATTTAATATATTTCACATTAACAAA
1 TAAGAATCAACTAATATCCTTCACATTAACATTAAGAATCAACTAATATACTTCACATCAACAAA
*
424152 TAAAAATAGAAAACAATA
66 TAAAAACAGAAAACAATA
*
424170 TAAGAATCATCTAAT
1 TAAGAATCAACTAAT
424185 TCAAAGTATT
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 58 0.67
83 29 0.33
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (83 bp):
TAAGAATCAACTAATATCCTTCACATTAACATTAAGAATCAACTAATATACTTCACATCAACAAA
TAAAAACAGAAAACAATA
Found at i:424321 original size:21 final size:21
Alignment explanation
Indices: 424275--424326 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
424265 GATTGAACTT
* * *
424275 ATAAAA-AAAGAAAATAAAAC
1 ATAAAACATAGAAAACAAAAA
*
424295 AGAAAACATAGAAAACAAAAA
1 ATAAAACATAGAAAACAAAAA
424316 ATAAAAGCATA
1 ATAAAA-CATA
424327 TAATGTATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 5 0.20
21 16 0.64
22 4 0.16
ACGTcount: A:0.75, C:0.08, G:0.08, T:0.10
Consensus pattern (21 bp):
ATAAAACATAGAAAACAAAAA
Found at i:424404 original size:33 final size:31
Alignment explanation
Indices: 424335--424412 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 31
424325 TATAATGTAT
*
424335 ACAAAAAAC-AAATAAAAACATAAAAGAAAA
1 ACAAAATACAAAATAAAAACATAAAAGAAAA
*
424365 AGAAAATACAAAATAAAAACATATAAA-ATTAAA
1 ACAAAATACAAAATAAAAACATA-AAAGA--AAA
*
424398 ACAAAATAAAAAATA
1 ACAAAATACAAAATA
424413 TATAAAAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 7 0.17
31 14 0.35
32 3 0.08
33 16 0.40
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.13
Consensus pattern (31 bp):
ACAAAATACAAAATAAAAACATAAAAGAAAA
Found at i:424576 original size:15 final size:16
Alignment explanation
Indices: 424556--424585 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
424546 TATAACCATT
424556 AAAAATAAA-AAAATA
1 AAAAATAAATAAAATA
424571 AAAAATAAATAAAAT
1 AAAAATAAATAAAAT
424586 GAATACCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAATAAATAAAATA
Found at i:424634 original size:2 final size:2
Alignment explanation
Indices: 424627--424703 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
424617 TCATTTTTAG
424627 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
424669 AT AT 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 AT AT A
424704 AATAGAAAAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:428475 original size:14 final size:14
Alignment explanation
Indices: 428456--428559 Score: 85
Period size: 14 Copynumber: 7.6 Consensus size: 14
428446 CTCTGTTCGA
428456 GTTGACTCAACGAG
1 GTTGACTCAACGAG
*
428470 GTTGACTC-A-GTAA
1 GTTGACTCAACG-AG
*
428483 GTTGACTCAACGGG
1 GTTGACTCAACGAG
*
428497 GTTGACTC-A-GTAA
1 GTTGACTCAACG-AG
*
428510 GTTGACTCAACGGG
1 GTTGACTCAACGAG
*
428524 GTTGACTC-A-GTAA
1 GTTGACTCAACG-AG
*
428537 GTTGACTCAACGGG
1 GTTGACTCAACGAG
428551 GTTGACTCA
1 GTTGACTCA
428560 TCTTAACTGG
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
12 3 0.04
13 28 0.40
14 36 0.51
15 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (14 bp):
GTTGACTCAACGAG
Found at i:428486 original size:13 final size:13
Alignment explanation
Indices: 428470--428545 Score: 66
Period size: 13 Copynumber: 5.7 Consensus size: 13
428460 ACTCAACGAG
428470 GTTGACTCAGTAA
1 GTTGACTCAGTAA
**
428483 GTTGACTCAACG-GG
1 GTTGACTC-A-GTAA
428497 GTTGACTCAGTAA
1 GTTGACTCAGTAA
**
428510 GTTGACTCAACG-GG
1 GTTGACTC-A-GTAA
428524 GTTGACTCAGTAA
1 GTTGACTCAGTAA
428537 GTTGACTCA
1 GTTGACTCA
428546 ACGGGGTTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
12 2 0.04
13 27 0.55
14 18 0.37
15 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (13 bp):
GTTGACTCAGTAA
Found at i:428489 original size:27 final size:27
Alignment explanation
Indices: 428455--428559 Score: 201
Period size: 27 Copynumber: 3.9 Consensus size: 27
428445 ACTCTGTTCG
*
428455 AGTTGACTCAACGAGGTTGACTCAGTA
1 AGTTGACTCAACGGGGTTGACTCAGTA
428482 AGTTGACTCAACGGGGTTGACTCAGTA
1 AGTTGACTCAACGGGGTTGACTCAGTA
428509 AGTTGACTCAACGGGGTTGACTCAGTA
1 AGTTGACTCAACGGGGTTGACTCAGTA
428536 AGTTGACTCAACGGGGTTGACTCA
1 AGTTGACTCAACGGGGTTGACTCA
428560 TCTTAACTGG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (27 bp):
AGTTGACTCAACGGGGTTGACTCAGTA
Found at i:435342 original size:19 final size:19
Alignment explanation
Indices: 435318--435391 Score: 103
Period size: 19 Copynumber: 3.7 Consensus size: 19
435308 GAATGCAATT
435318 AGTGCATCGATGCATGAGG
1 AGTGCATCGATGCATGAGG
* *
435337 AGTGCATCGATGCACTAATTGA
1 AGTGCATCGATGCA-TGA--GG
435359 AGTGCATCGATGCATGAGG
1 AGTGCATCGATGCATGAGG
435378 AGTGCATCGATGCA
1 AGTGCATCGATGCA
435392 CCTACTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 29 0.60
20 2 0.04
21 2 0.04
22 15 0.31
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (19 bp):
AGTGCATCGATGCATGAGG
Found at i:437552 original size:16 final size:15
Alignment explanation
Indices: 437531--437576 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 15
437521 ATTTTACTTT
437531 TTGGTCAAAGTCAAC
1 TTGGTCAAAGTCAAC
437546 GTTGGTCAAAGTCAAC
1 -TTGGTCAAAGTCAAC
437562 TCTGGTCAAAGTCAA
1 T-TGGTCAAAGTCAA
437577 TAAGTTGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 1 0.03
16 28 0.97
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (15 bp):
TTGGTCAAAGTCAAC
Found at i:438752 original size:14 final size:14
Alignment explanation
Indices: 438716--438781 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
438706 AGCAGAAAAC
* *
438716 AAAAAGAAATATAGA
1 AAAAATAAATA-ATA
438731 AAATAATAAATAATA
1 AAA-AATAAATAATA
* *
438746 GAAAATAAATGATA
1 AAAAATAAATAATA
438760 AAAAATAAA-AA-A
1 AAAAATAAATAATA
438772 AAAACATAAA
1 AAAA-ATAAA
438782 ATTTTAACAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 5 0.12
13 6 0.14
14 18 0.42
15 7 0.16
16 7 0.16
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (14 bp):
AAAAATAAATAATA
Found at i:438760 original size:17 final size:17
Alignment explanation
Indices: 438722--438753 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
438712 AAACAAAAAG
438722 AAAT-ATAGAAAATAAT
1 AAATAATAGAAAATAAT
438738 AAATAATAGAAAATAA
1 AAATAATAGAAAATAA
438754 ATGATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (17 bp):
AAATAATAGAAAATAAT
Found at i:438821 original size:24 final size:25
Alignment explanation
Indices: 438771--438830 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
438761 AAAATAAAAA
*** *
438771 AAAAACATAAAATTTTAACACATAT
1 AAAAACATAAAATAAAAACACAAAT
438796 AAAAACATAAAATAAAAAC-CAAAT
1 AAAAACATAAAATAAAAACACAAAT
438820 AAAAA-ATAAAA
1 AAAAACATAAAA
438831 CATTGTGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 6 0.19
24 9 0.29
25 16 0.52
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (25 bp):
AAAAACATAAAATAAAAACACAAAT
Found at i:438824 original size:25 final size:24
Alignment explanation
Indices: 438760--438825 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 24
438750 ATAAATGATA
* *
438760 AAAAATAAAAAAAAAACATAAAAT
1 AAAAACAAATAAAAAACATAAAAT
*** *
438784 TTTAACACATATAAAAACATAAAAT
1 AAAAACAAATA-AAAAACATAAAAT
438809 AAAAACCAAATAAAAAA
1 AAAAA-CAAATAAAAAA
438826 TAAAACATTG
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
24 5 0.17
25 20 0.67
26 5 0.17
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (24 bp):
AAAAACAAATAAAAAACATAAAAT
Found at i:439875 original size:19 final size:20
Alignment explanation
Indices: 439851--439893 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
439841 CCTAAGTATG
439851 TATACTTTATAC-CTATATA
1 TATACTTTATACACTATATA
*
439870 TATACTTTATACATTATATA
1 TATACTTTATACACTATATA
439890 TATA
1 TATA
439894 TTATACTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (20 bp):
TATACTTTATACACTATATA
Found at i:439989 original size:2 final size:2
Alignment explanation
Indices: 439971--440101 Score: 73
Period size: 2 Copynumber: 68.0 Consensus size: 2
439961 AATGTATACT
* *
439971 TA TA T- TA TA TA TG TA TA TA TA TA T- TA TA AA CT- 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
* * * * *
440011 TA TA CA TA TA TG TA TA TA CT- TA TA -A TG TA T- TG TT 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
* *
440051 CT- TA TA TA TA TA TA TA TA TT TA -A AA TA TA TA TA CT- 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
*
440092 TA TG TA TA TA
1 TA TA TA TA TA
440102 CTTATAATGT
Statistics
Matches: 99, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
1 9 0.09
2 87 0.88
3 3 0.03
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:440012 original size:14 final size:14
Alignment explanation
Indices: 439933--440094 Score: 91
Period size: 14 Copynumber: 10.9 Consensus size: 14
439923 ATGTACTTTC
439933 TACTTATATATTATA
1 TACTTATATA-TATA
439948 TACTTATAAGTATAATGTA
1 TACTTAT-A-TAT-A--TA
439967 TACTTATATTATATA
1 TACTTATA-TATATA
439982 TGTA-TATATATATTATA
1 --TACT-TATATA-TATA
*
439999 AACTTATATATATA
1 TACTTATATATATA
* *
440013 TACATATATGTATA
1 TACTTATATATATA
*
440027 TACTTATA-ATGTA
1 TACTTATATATATA
**
440040 TTGTT-TATATACT-
1 TACTTATATATA-TA
440053 TA-TATATATATATA
1 TACT-TATATATATA
* *
440067 TATTTAAAATATATA
1 TACTT-ATATATATA
440082 TACTTATATATAT
1 TACTTATATATAT
440095 GTATATACTT
Statistics
Matches: 115, Mismatches: 15, Indels: 35
0.70 0.09 0.21
Matches are distributed among these distances:
12 3 0.03
13 11 0.10
14 39 0.34
15 29 0.25
16 6 0.05
17 14 0.12
18 4 0.03
19 9 0.08
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (14 bp):
TACTTATATATATA
Found at i:440118 original size:31 final size:33
Alignment explanation
Indices: 439944--440122 Score: 111
Period size: 33 Copynumber: 5.4 Consensus size: 33
439934 ACTTATATAT
* *
439944 TATATACTTATA-AGTATAATGTATACTT-ATAT-
1 TATATACTTATATA-TAT-ATATATACTTAAAATA
* *
439976 TATATA-TGTATATATATATTATAAACTT-ATATA
1 TATATACT-TATATATATA-TATATACTTAAAATA
* * * *** *
440009 TATATACATATATGTATATACTTATAATGTATTGTT
1 TATATACTTATATATATATA--TATACT-TAAAATA
*
440045 TATATACTTATATATATATATATATTTAAAATA
1 TATATACTTATATATATATATATACTTAAAATA
* * *
440078 TATATACTTATATATATGTATATACTTATAATG
1 TATATACTTATATATATATATATACTTAAAATA
440111 TA-A-ACTTATATA
1 TATATACTTATATA
440123 CTTAAATTAT
Statistics
Matches: 118, Mismatches: 20, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
31 11 0.09
32 27 0.23
33 50 0.42
34 9 0.08
35 1 0.01
36 20 0.17
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (33 bp):
TATATACTTATATATATATATATACTTAAAATA
Found at i:440126 original size:8 final size:7
Alignment explanation
Indices: 439936--440092 Score: 63
Period size: 6 Copynumber: 23.1 Consensus size: 7
439926 TACTTTCTAC
439936 TTATATA
1 TTATATA
439943 TTATATA
1 TTATATA
439950 CTTATA-A
1 -TTATATA
*
439957 GTATA-A
1 TTATATA
*
439963 -TGTATA
1 TTATATA
*
439969 CT-TATA
1 TTATATA
439975 TTATATA
1 TTATATA
*
439982 -TGTATA
1 TTATATA
439988 -TATATA
1 TTATATA
*
439994 TTATAAA
1 TTATATA
440001 CTTATATA
1 -TTATATA
440009 -TATATA
1 TTATATA
*
440015 -CATATA
1 TTATATA
440021 TGTATATA
1 T-TATATA
440029 CTTATA-A
1 -TTATATA
*
440036 TGTAT-TGT
1 T-TATAT-A
440044 TTATATA
1 TTATATA
440051 CTTATATA
1 -TTATATA
440059 -TATATA
1 TTATATA
440065 -TATAT-
1 TTATATA
*
440070 TTA-AAA
1 TTATATA
440076 TATATATA
1 T-TATATA
440084 CTTATATA
1 -TTATATA
440092 T
1 T
440093 ATGTATATAC
Statistics
Matches: 118, Mismatches: 13, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
5 4 0.03
6 47 0.40
7 28 0.24
8 37 0.31
9 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (7 bp):
TTATATA
Found at i:440132 original size:13 final size:14
Alignment explanation
Indices: 440111--440139 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
440101 ACTTATAATG
440111 TAAACTTATATACT
1 TAAACTTATATACT
440125 TAAA-TTATATACT
1 TAAACTTATATACT
440138 TA
1 TA
440140 TAAGTATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAACTTATATACT
Found at i:440134 original size:73 final size:75
Alignment explanation
Indices: 439958--440135 Score: 210
Period size: 73 Copynumber: 2.5 Consensus size: 75
439948 TACTTATAAG
* * *
439958 TATAATGTAT-ACTTATAT--TATATATGTATATATATATTATAAACTTATATATATATACATAT
1 TATAATGTATAACTTATATACT-TAAATATATATATATATTATAAACATATATATATATACATAT
440020 ATGTATATACT
65 ATGTATATACT
*** * *
440031 TATAATGTATTGTTTATATACTTATATATATATATATATT-TAAA-ATATATATACT-TATATAT
1 TATAATGTATAACTTATATACTTAAATATATATATATATTATAAACATATATATA-TATACATAT
440093 ATGTATATACT
65 ATGTATATACT
440104 TATAATGTA-AACTTATATACTTAAAT-TATATA
1 TATAATGTATAACTTATATACTTAAATATATATA
440136 CTTATAAGTA
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
71 6 0.07
72 13 0.14
73 44 0.48
74 11 0.12
75 17 0.18
76 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (75 bp):
TATAATGTATAACTTATATACTTAAATATATATATATATTATAAACATATATATATATACATATA
TGTATATACT
Found at i:440138 original size:21 final size:23
Alignment explanation
Indices: 440088--440141 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
440078 TATATACTTA
440088 TATATA-TGTATATACTTATAATG
1 TATATACT-TATATACTTATAATG
440111 TA-A-ACTTATATACTTA-AAT-
1 TATATACTTATATACTTATAATG
440130 TATATACTTATA
1 TATATACTTATA
440142 AGTATAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.07
20 4 0.14
21 18 0.64
22 2 0.07
23 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (23 bp):
TATATACTTATATACTTATAATG
Found at i:440206 original size:93 final size:84
Alignment explanation
Indices: 440044--440214 Score: 191
Period size: 93 Copynumber: 1.9 Consensus size: 84
440034 AATGTATTGT
* *
440044 TTATATACTTATATATATATATATATTTAAAATATATATACTTATATATATGTATATACTTATAA
1 TTATATACTTATATATATATATATATTTAAAATAAATATACTTATATATATATATATACTTATAA
440109 TGTAAACTTATATACTTAAA
66 TGTAAAC-TATATACTTAAA
*
440129 TTATATACTTATA-AGTATAGTATATAGTTTATAAATAAAGTATAGTTTATATAGTTTATATATA
1 TTATATACTTATATA-TATA-TATATA-TTTA-AAATAAA-TATA-CTTATATA---TATATATA
* * *
440193 TAGTTCTTATGTAAACTATATA
57 TACTTATAATGTAAACTATATA
440215 ATATATATAG
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
84 1 0.01
85 17 0.24
86 6 0.08
87 4 0.06
88 6 0.08
89 4 0.06
90 7 0.10
92 6 0.08
93 20 0.28
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.47
Consensus pattern (84 bp):
TTATATACTTATATATATATATATATTTAAAATAAATATACTTATATATATATATATACTTATAA
TGTAAACTATATACTTAAA
Found at i:440247 original size:11 final size:11
Alignment explanation
Indices: 440216--440274 Score: 77
Period size: 11 Copynumber: 5.5 Consensus size: 11
440206 AACTATATAA
440216 TATATATAGTT
1 TATATATAGTT
440227 TATTATATAGTT
1 TA-TATATAGTT
*
440239 TACATATAG--
1 TATATATAGTT
*
440248 TATATATGGTT
1 TATATATAGTT
440259 TATATATAGTT
1 TATATATAGTT
440270 TATAT
1 TATAT
440275 TAATAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 7 0.17
11 23 0.56
12 11 0.27
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.53
Consensus pattern (11 bp):
TATATATAGTT
Found at i:440252 original size:32 final size:31
Alignment explanation
Indices: 440210--440279 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 31
440200 TATGTAAACT
440210 ATATAATATATATAGTTTATTATATAGTTTAC
1 ATATAATATATATAGTTTA-TATATAGTTTAC
* * *
440242 ATATAGTATATATGGTTTATATATAGTTTAT
1 ATATAATATATATAGTTTATATATAGTTTAC
440273 AT-TAATA
1 ATATAATA
440280 AAATATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 4 0.12
31 13 0.38
32 17 0.50
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (31 bp):
ATATAATATATATAGTTTATATATAGTTTAC
Found at i:440259 original size:20 final size:20
Alignment explanation
Indices: 440230--440274 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
440220 TATAGTTTAT
440230 TATATAGTTTACATATAGTA
1 TATATAGTTTACATATAGTA
* * *
440250 TATATGGTTTATATATAGTT
1 TATATAGTTTACATATAGTA
440270 TATAT
1 TATAT
440275 TAATAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (20 bp):
TATATAGTTTACATATAGTA
Found at i:441062 original size:21 final size:22
Alignment explanation
Indices: 441027--441068 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
441017 AATCCAAAAA
*
441027 TGCTTAGTGTTTTTAGCATTTT
1 TGCTTAATGTTTTTAGCATTTT
*
441049 TGCTTAAT-TTTTTAGGATTT
1 TGCTTAATGTTTTTAGCATTT
441069 GATAATGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.60
Consensus pattern (22 bp):
TGCTTAATGTTTTTAGCATTTT
Found at i:442756 original size:45 final size:46
Alignment explanation
Indices: 442707--442793 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 46
442697 GAACATCGAA
* * *
442707 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGAATCGATGCACAAGACCATGCATCGATGCACTTAG
442752 TGCATTTGATGAATCGATGCACAAGACCATGCATCGATGCAC
1 TGCATTTGATGAATCGATGCACAAGACCATGCATCGATGCAC
442794 AAGACCATGC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGAATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:442789 original size:20 final size:20
Alignment explanation
Indices: 442764--442809 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
442754 CATTTGATGA
442764 ATCGATGCACAAGACCATGC
1 ATCGATGCACAAGACCATGC
442784 ATCGATGCACAAGACCATGC
1 ATCGATGCACAAGACCATGC
442804 ATCGAT
1 ATCGAT
442810 ACACTCAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGATGCACAAGACCATGC
Found at i:451128 original size:45 final size:46
Alignment explanation
Indices: 451079--451166 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
451069 GAACATCGAA
* *
451079 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
451124 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
451167 CAGGCTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:452781 original size:13 final size:13
Alignment explanation
Indices: 452765--452789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
452755 AAACGAATAT
452765 AATAAATGAACAC
1 AATAAATGAACAC
452778 AATAAATGAACA
1 AATAAATGAACA
452790 ACACAAACAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.12, G:0.08, T:0.16
Consensus pattern (13 bp):
AATAAATGAACAC
Found at i:453076 original size:14 final size:14
Alignment explanation
Indices: 453054--453130 Score: 80
Period size: 14 Copynumber: 6.1 Consensus size: 14
453044 GCCCTCTGTT
*
453054 CGAAAATAAATGAA
1 CGAACATAAATGAA
453068 CGAACATAAAT---
1 CGAACATAAATGAA
453079 -GAACATAAATGAA
1 CGAACATAAATGAA
*
453092 CGTACATAAAT---
1 CGAACATAAATGAA
453103 -GAACATAAATGAA
1 CGAACATAAATGAA
453116 CGAACATAAATGAA
1 CGAACATAAATGAA
453130 C
1 C
453131 TTATAATCGA
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
10 19 0.37
14 33 0.63
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:453091 original size:24 final size:24
Alignment explanation
Indices: 453059--453130 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
453049 CTGTTCGAAA
453059 ATAAATGAACGAACATAAATGAAC
1 ATAAATGAACGAACATAAATGAAC
*
453083 ATAAATGAACGTACATAAATGAAC
1 ATAAATGAACGAACATAAATGAAC
453107 ATAAATGAACGAACATAAATGAAC
1 ATAAATGAACGAACATAAATGAAC
453131 TTATAATCGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.18
Consensus pattern (24 bp):
ATAAATGAACGAACATAAATGAAC
Found at i:453130 original size:10 final size:10
Alignment explanation
Indices: 453069--453116 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 10
453059 ATAAATGAAC
453069 GAACATAAAT
1 GAACATAAAT
453079 GAACATAAAT
1 GAACATAAAT
453089 GAACGTACATAAAT
1 G-A---ACATAAAT
453103 GAACATAAAT
1 GAACATAAAT
453113 GAAC
1 GAAC
453117 GAACATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 23 0.68
11 1 0.03
13 1 0.03
14 9 0.26
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (10 bp):
GAACATAAAT
Found at i:454644 original size:29 final size:30
Alignment explanation
Indices: 454592--454655 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
454582 ACAAGCCTTA
* * *
454592 GAAAAATTGGGGACCATTTTGTAAGTTTT-
1 GAAAAATTGGGGACCAATTCGTAAATTTTG
* *
454621 GAAAAGTTGGGGATCAATTCGTAAATTTTG
1 GAAAAATTGGGGACCAATTCGTAAATTTTG
454651 GAAAA
1 GAAAA
454656 TTGATGAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (30 bp):
GAAAAATTGGGGACCAATTCGTAAATTTTG
Found at i:462448 original size:2 final size:2
Alignment explanation
Indices: 462443--463021 Score: 166
Period size: 2 Copynumber: 289.0 Consensus size: 2
462433 TTTATAATTG
* * * *
462443 TA TA TA -A TA TA TA AA TA TA AA T- TA TA CA T- TT 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
* *
462482 GT- TCA TA TA TA -A TT TA TA -A T- TA TA CA TA GTA TA TA TA TA
1 -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
462521 GCA TA TA TA TA AA TA TA AA CTA TA TA GTT TA TA TA TA AA T- TA
1 -TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * * *
462563 TA TA TA TA AA CTA TA TA AA CTA TA TA GTT TT TA TA TA TA GTA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA
* * * * *
462607 TA TA GTT TA TA TT TA TA T- TA T- TA TA AA CTA AA TA TA AA CTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* *
462648 TA TA TA CTA TA TA TA TA AA CTA TA TA GTT TA T- TA -A TA TA -A
1 TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* *
462688 CTA TA TA TA T- TA TA TA TA AA T- TA TA TGA -A CTA TA TA TA AA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA
* * *
462728 TG TA TA GTT TA TA TT TA TA TA TA TA TA -A T- TA TA -A T- TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
462767 TA TA TGA -A CTA TA TA AA TG TA TA GTT TA CA TA TA AA CTA TA TA
1 TA TA T-A TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* *
462810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TG TG TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
462850 T- TA TA AA T- TA TA TA TA CTA TG TA TA AA T- TA CA TA GTT TA T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
462890 TA -A TA TA -A CTA -A T- TA CA TA GTT TA TA TA TA AA CTA TA TGA
1 TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA T-A
* *
462930 -A CTA TA TA TA GT- TCA TA TA TA GTT TA TA TA TA GTA TA TA AA TA
1 TA -TA TA TA TA -TA T-A TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* * *
462973 TA AA T- TG TA TA GTT 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
463015 TA T- TA TA
1 TA TA TA TA
463022 ATTGTTTCAA
Statistics
Matches: 418, Mismatches: 88, Indels: 142
0.65 0.14 0.22
Matches are distributed among these distances:
1 35 0.08
2 342 0.82
3 41 0.10
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:462491 original size:37 final size:37
Alignment explanation
Indices: 462449--462557 Score: 114
Period size: 37 Copynumber: 2.9 Consensus size: 37
462439 ATTGTATATA
*
462449 ATATATAAATATAAATTATACATTTTATATATAG-TT
1 ATATATAAATATAAATTATACATTTTATATATAGCAT
* *
462485 CATATAT-AATTTATAATTATACATAGTATATATATAGCAT
1 -ATATATAAATATA-AATTATACAT--TTTATATATAGCAT
* * *
462525 ATATATAAATATAAACTATATAGTTTATATATA
1 ATATATAAATATAAATTATACATTTTATATATA
462558 AATTATATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
36 5 0.08
37 25 0.42
39 23 0.39
40 6 0.10
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATATAAATATAAATTATACATTTTATATATAGCAT
Found at i:462521 original size:11 final size:10
Alignment explanation
Indices: 462443--463021 Score: 166
Period size: 11 Copynumber: 57.8 Consensus size: 10
462433 TTTATAATTG
462443 TATATA-ATA
1 TATATATATA
*
462452 TATAAATATA
1 TATATATATA
* *
462462 AAT-TATACA
1 TATATATATA
*
462471 T-TTTATATA
1 TATATATATA
462480 TAGT-TCATATA
1 TA-TAT-ATATA
*
462491 TA-ATTTATA
1 TATATATATA
*
462500 -AT-TATACA
1 TATATATATA
462508 TAGTATATATA
1 TA-TATATATA
*
462519 TAGCATATATA
1 TA-TATATATA
* *
462530 TAAATATAAA
1 TATATATATA
*
462540 CTATATAGTTTA
1 -TATATA-TATA
*
462552 TATATAAAT-
1 TATATATATA
462561 TATATATATA
1 TATATATATA
* *
462571 AACTATATAAA
1 TA-TATATATA
* *
462582 CTATATAGTTTT
1 -TATATA-TATA
462594 TATATATAGTA
1 TATATATA-TA
*
462605 TATATAGTTTA
1 TATATA-TATA
*
462616 TATTTATAT-
1 TATATATATA
*
462625 TAT-TATAAA
1 TATATATATA
* *
462634 CTAAATATAAA
1 -TATATATATA
462645 CTATATATACTA
1 -TATATATA-TA
*
462657 TATATATAAA
1 TATATATATA
*
462667 CTATATAGTTTA
1 -TATATA-TATA
462679 T-TA-ATATA
1 TATATATATA
462687 -ACTATATATA
1 TA-TATATATA
462697 T-TATATATA
1 TATATATATA
*
462706 AAT-TATATGA
1 TATATATAT-A
462716 -ACTATATATA
1 TA-TATATATA
* * *
462726 AATGTATAGTT
1 TATATATA-TA
*
462737 TATATTTATA
1 TATATATATA
462747 TATATATA-A
1 TATATATATA
462756 T-TATA-AT-
1 TATATATATA
462763 TATATATATGA
1 TATATATAT-A
*
462774 -ACTATATAAA
1 TA-TATATATA
* *
462784 TGTATAGTTTA
1 TATATA-TATA
* *
462795 CATATAAACTA
1 TATATATA-TA
462806 TATATATATA
1 TATATATATA
462816 TATATATATA
1 TATATATATA
462826 TATATATATA
1 TATATATATA
*
462836 TATAT-TATG
1 TATATATATA
*
462845 TGTA-AT-TA
1 TATATATATA
*
462853 TAAAT-TATA
1 TATATATATA
*
462862 TATACTATGTA
1 TATA-TATATA
* *
462873 TAAAT-TACA
1 TATATATATA
*
462882 TAGTTTAT-TA
1 TA-TATATATA
462892 -ATATA-ACTA
1 TATATATA-TA
*
462901 -AT-TACATA
1 TATATATATA
*
462909 GTTTATATATA
1 -TATATATATA
*
462920 AACTATATGA-A
1 TA-TATAT-ATA
462931 CTATATATAGT-
1 -TATATATA-TA
*
462942 TCATATATAGTT
1 T-ATATATA-TA
462954 TATATATAGTA
1 TATATATA-TA
*
462965 TATAAATATA
1 TATATATATA
* *
462975 AAT-TGTATA
1 TATATATATA
*
462984 GTTTATATATA
1 -TATATATATA
462995 TATATATATA
1 TATATATATA
463005 TATATATATA
1 TATATATATA
463015 TAT-TATA
1 TATATATA
463022 ATTGTTTCAA
Statistics
Matches: 421, Mismatches: 84, Indels: 130
0.66 0.13 0.20
Matches are distributed among these distances:
7 2 0.00
8 32 0.08
9 82 0.19
10 113 0.27
11 181 0.43
12 11 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (10 bp):
TATATATATA
Found at i:484561 original size:24 final size:24
Alignment explanation
Indices: 484529--484574 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
484519 ACAGTCTCTG
*
484529 AAACTGCCATGTATTCTGCCTCAA
1 AAACTGCCATGTATTATGCCTCAA
484553 AAACTGCCATGTATTATGCCTC
1 AAACTGCCATGTATTATGCCTC
484575 TGTAGTAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (24 bp):
AAACTGCCATGTATTATGCCTCAA
Found at i:490420 original size:85 final size:85
Alignment explanation
Indices: 490219--490406 Score: 218
Period size: 85 Copynumber: 2.2 Consensus size: 85
490209 AGGATTATAC
* * * *
490219 TAAAATAAATCGAATTTTAGGGCTCAAATTGACACTAAAGGTGAGATGCAGGAAGAAATAAAAAG
1 TAAAAAAAATAGAAATTCAGGG-TCAAATTGACACTAAAGGTGAGATGCAGGAAGAAATAAAAAG
*
490284 GTTAGGGTTAAATGAAATAAT
65 GTTAGGGTCAAATGAAATAAT
* * * * *
490305 TCAAATAAATCGAAATTCAGGGTCAAATTGACACTAAAGGTGAGTTGTAGGAAGAAATAAAAAGG
1 TAAAAAAAATAGAAATTCAGGGTCAAATTGACACTAAAGGTGAGATGCAGGAAGAAATAAAAAGG
*
490370 TTAGGGTACCAAATTGCAA-AA-
66 TTAGGGT--CAAA-TGAAATAAT
*
490391 TAAAAAAAATATAAAT
1 TAAAAAAAATAGAAAT
490407 AGGGGTTAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
85 48 0.55
86 31 0.35
87 5 0.06
88 4 0.05
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.23
Consensus pattern (85 bp):
TAAAAAAAATAGAAATTCAGGGTCAAATTGACACTAAAGGTGAGATGCAGGAAGAAATAAAAAGG
TTAGGGTCAAATGAAATAAT
Found at i:491525 original size:3 final size:3
Alignment explanation
Indices: 491511--491586 Score: 54
Period size: 3 Copynumber: 25.3 Consensus size: 3
491501 TAAACCAAAA
*
491511 AAT AAT ATT AAT AAT AAT -AT AAT AA- ATAT AA- AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT -AAT AAT
*
491555 ACT -AT AAAT AAT ATAT AAT -AT AAT AAAT AAT A
1 AAT AAT -AAT AAT A-AT AAT AAT AAT -AAT AAT A
491587 TGTACACTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
2 8 0.14
3 39 0.66
4 12 0.20
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Done.