Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008479.1 Hibiscus syriacus cultivar Beakdansim tig00111310_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: 457438
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 3
Found at i:211898 original size:19 final size:20
Alignment explanation
Indices: 211876--211918 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
211866 AAATCGCAAC
211876 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
211895 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
211915 GCGA
1 GCGA
211919 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:211903 original size:14 final size:14
Alignment explanation
Indices: 211904--211937 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
211894 TGCGATTTTC
211904 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
211918 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
211932 ATTTTC
1 ATTTTC
211938 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:212078 original size:14 final size:14
Alignment explanation
Indices: 212059--212095 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
212049 CATCAATTAA
212059 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
212073 ACAAATCACCTTTT
1 ACAAATCAACTTTT
212087 ACAAATCAA
1 ACAAATCAA
212096 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:213520 original size:21 final size:21
Alignment explanation
Indices: 213454--213520 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
213444 GTGAATCGAG
*
213454 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
213474 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
213496 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
213517 CTCT
1 CTCT
213521 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:213539 original size:42 final size:41
Alignment explanation
Indices: 213454--213576 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
213444 GTGAATCGAG
* * * * *
213454 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
213496 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
213538 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
213577 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:215600 original size:14 final size:14
Alignment explanation
Indices: 215581--215607 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
215571 TTTGGTTGAA
215581 ATGAAAATCGCAAT
1 ATGAAAATCGCAAT
215595 ATGAAAATCGCAA
1 ATGAAAATCGCAA
215608 CGAGATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (14 bp):
ATGAAAATCGCAAT
Found at i:215674 original size:33 final size:33
Alignment explanation
Indices: 215617--215715 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
215607 ACGAGATAAT
* *
215617 GAGAATCGCAACGCGGAAATGACTATCGTAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
215651 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
215684 GATAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
215716 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:215709 original size:19 final size:19
Alignment explanation
Indices: 215687--215776 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
215677 GCGACCAGAT
215687 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
215706 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
215726 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
215745 AATCGAAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
215764 AATCGCAATGCGA
1 AATCGCAACGCGA
215777 TTTTGGTTTC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 47 0.72
20 18 0.28
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:216341 original size:20 final size:20
Alignment explanation
Indices: 216316--216368 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
216306 GCGCTATGTA
216316 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
216336 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
216356 TATCTCGTTGCGA
1 AATCGCGTTGCGA
216369 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:216402 original size:20 final size:20
Alignment explanation
Indices: 216377--216430 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
216367 GATTTTGTAT
*
216377 TATCGCATTACGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
216397 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
216417 TATCGCATTGCGAT
1 TATCGCATTGCGAT
216431 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:216541 original size:21 final size:21
Alignment explanation
Indices: 216501--216541 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
216491 ATTGTATACC
**
216501 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
216522 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
216542 GTGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:220003 original size:3 final size:3
Alignment explanation
Indices: 219997--220041 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
219987 GGGATGGAGA
* *
219997 TTC TTC TTC TTC TTA TTC TTC TTC TTC TTA TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
220042 CACCATATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:220016 original size:15 final size:15
Alignment explanation
Indices: 219996--220040 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
219986 GGGGATGGAG
219996 ATTCTTCTTCTTCTT
1 ATTCTTCTTCTTCTT
220011 ATTCTTCTTCTTCTT
1 ATTCTTCTTCTTCTT
220026 ATTCTTCTTCTTCTT
1 ATTCTTCTTCTTCTT
220041 CCACCATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTCTTCTTCTTCTT
Found at i:221455 original size:50 final size:50
Alignment explanation
Indices: 221388--221514 Score: 150
Period size: 50 Copynumber: 2.5 Consensus size: 50
221378 TTAGCAGTAA
* **
221388 AGCGCG-CGCCCTGCACCGTGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGAC-CCCTGCACCGCGCTATACGATGAGCTGGCGCCACGT-GGGTAT
* * *
221439 AGCG-TACCCCTGCACCGCGTTATACGGTGAGCTGGCGCCACGTGGGTAT
1 AGCGCGACCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTAT
* *
221488 AGCGCGGCCCCTGCAGCGCGCTATACG
1 AGCGCGACCCCTGCACCGCGCTATACG
221515 CCACGTAGGG
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
49 10 0.16
50 49 0.77
51 5 0.08
ACGTcount: A:0.16, C:0.32, G:0.33, T:0.19
Consensus pattern (50 bp):
AGCGCGACCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTAT
Found at i:221609 original size:49 final size:47
Alignment explanation
Indices: 221551--221644 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
221541 GTACTGCGCT
221551 ATACATTTACTCCTAATAATTTTATATAGCGCAGGGAAGGTACCGCGAC
1 ATACATTTACTCC--ATAATTTTATATAGCGCAGGGAAGGTACCGCGAC
* * * *
221600 ATACCTTTACTCCATAATTTTATATAGCGCGGGGCAGGTATCGCG
1 ATACATTTACTCCATAATTTTATATAGCGCAGGGAAGGTACCGCG
221645 TTTTGTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 29 0.71
49 12 0.29
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (47 bp):
ATACATTTACTCCATAATTTTATATAGCGCAGGGAAGGTACCGCGAC
Found at i:221639 original size:47 final size:48
Alignment explanation
Indices: 221526--221644 Score: 143
Period size: 49 Copynumber: 2.5 Consensus size: 48
221516 CACGTAGGGG
** *
221526 TATAGCGCGGATCAGGTACTGCGCTATACATTTACTCCTAATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGCTATACATTTACTCC-AATAATTTTA
* * *
221575 TATAGCGCAGGGAAGGTACCGCGAC-ATACCTTTACTCC-ATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCG-CTATACATTTACTCCAATAATTTTA
*
221622 TATAGCGCGGGGCAGGTATCGCG
1 TATAGCGCGGGGCAGGTACCGCG
221645 TTTTGTATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
47 29 0.48
49 30 0.50
50 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (48 bp):
TATAGCGCGGGGCAGGTACCGCGCTATACATTTACTCCAATAATTTTA
Found at i:227478 original size:110 final size:111
Alignment explanation
Indices: 227284--227504 Score: 363
Period size: 110 Copynumber: 2.0 Consensus size: 111
227274 ATTACAAAAA
* * * *
227284 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
* *
227349 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
* *
227395 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AATTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
227459 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
227505 ATGATTTCCA
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 69 0.68
111 33 0.32
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:227642 original size:12 final size:10
Alignment explanation
Indices: 227628--227668 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
227618 ACCTTAAAAA
*
227628 GAGAGTATTT
1 GAGAGAATTT
227638 GAGAGAAATTT
1 GAGAG-AATTT
227649 -AGAGAATTT
1 GAGAGAATTT
227658 GAGAGAATTT
1 GAGAGAATTT
227668 G
1 G
227669 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:227872 original size:51 final size:51
Alignment explanation
Indices: 227779--227910 Score: 149
Period size: 51 Copynumber: 2.6 Consensus size: 51
227769 AGATATACAT
* * * * **
227779 GTATAGCGCGCTGCAGGGGCCTCGCTATA-CCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGATGCAGGGGGCACGCTATACCCCACGTGACGCCAAATCACC
*
227829 GTATAGCGCGATGCAGGGGGCACGCTATACCCCACGTGACGCCAAATCATC
1 GTATAGCGCGATGCAGGGGGCACGCTATACCCCACGTGACGCCAAATCACC
* * * * *
227880 GTATAACACGGTACAGGGGGCACGCTTTACC
1 GTATAGCGCGATGCAGGGGGCACGCTATACC
227911 GCTAACTACC
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 26 0.38
51 43 0.62
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.17
Consensus pattern (51 bp):
GTATAGCGCGATGCAGGGGGCACGCTATACCCCACGTGACGCCAAATCACC
Found at i:229563 original size:22 final size:24
Alignment explanation
Indices: 229535--229579 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
229525 GTGATATGTT
229535 AGTTCATTA-TT-TAACCAAGAGC
1 AGTTCATTATTTATAACCAAGAGC
229557 AGTTCATTATTTATAACCAAGAG
1 AGTTCATTATTTATAACCAAGAG
229580 TGGTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.43
23 2 0.10
24 10 0.48
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (24 bp):
AGTTCATTATTTATAACCAAGAGC
Found at i:242293 original size:13 final size:13
Alignment explanation
Indices: 242269--242304 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
242259 AAATTTTGGC
242269 TTTTTT-TG-CTT
1 TTTTTTGTGCCTT
242280 TTTTTTGTGCCTT
1 TTTTTTGTGCCTT
242293 TTTTTTGTGCCT
1 TTTTTTGTGCCT
242305 AAAACAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.26
12 2 0.09
13 15 0.65
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.72
Consensus pattern (13 bp):
TTTTTTGTGCCTT
Found at i:252841 original size:20 final size:20
Alignment explanation
Indices: 252806--252846 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
252796 TCTAATTAAG
*
252806 TAATTTGATTATTTTATGATT
1 TAATTTGATAATTTTAT-ATT
252827 TAATTT-ATAATTTTATATT
1 TAATTTGATAATTTTATATT
252846 T
1 T
252847 CTTCAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TAATTTGATAATTTTATATT
Found at i:253332 original size:2 final size:2
Alignment explanation
Indices: 253325--253360 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
253315 CTTATACATA
253325 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
253361 GGTTAGAAGC
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:254946 original size:20 final size:20
Alignment explanation
Indices: 254923--254967 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
254913 GGATCGGATC
254923 TGGTTTGGATCTAGTTCGAG
1 TGGTTTGGATCTAGTTCGAG
254943 TGGTTTGGATCTAGTTCGAG
1 TGGTTTGGATCTAGTTCGAG
254963 TGGTT
1 TGGTT
254968 GGTGAATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.09, G:0.36, T:0.42
Consensus pattern (20 bp):
TGGTTTGGATCTAGTTCGAG
Found at i:256630 original size:37 final size:37
Alignment explanation
Indices: 256574--256655 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
256564 GCCGTTTTCC
** *
256574 TTTGAATGATCAACCGATGGACTCTCCATCACTACTG
1 TTTGAATGAGAAACAGATGGACTCTCCATCACTACTG
* *
256611 TTTGAATGAGAAACAGATGGTCTCTCCATCACTGCTG
1 TTTGAATGAGAAACAGATGGACTCTCCATCACTACTG
*
256648 TTTAAATG
1 TTTGAATG
256656 CTAACTTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (37 bp):
TTTGAATGAGAAACAGATGGACTCTCCATCACTACTG
Found at i:258680 original size:10 final size:9
Alignment explanation
Indices: 258659--258706 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 9
258649 CTAACTAGCT
258659 AACTAA-TG
1 AACTAACTG
258667 AACTAACTTG
1 AACTAAC-TG
258677 AACTAACTG
1 AACTAACTG
*
258686 AACTGACTG
1 AACTAACTG
258695 -A-TAACT-
1 AACTAACTG
258701 AACTAA
1 AACTAA
258707 TTACAAGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
7 5 0.15
8 10 0.29
9 10 0.29
10 9 0.26
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (9 bp):
AACTAACTG
Found at i:260611 original size:33 final size:32
Alignment explanation
Indices: 260568--260635 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
260558 AATAGGATCA
260568 AAGGGAGCACCACCAGTCGAGTCAGTAGAACC
1 AAGGGAGCACCACCAGTCGAGTCAGTAGAACC
* * *
260600 AAGGGAGGCACCACTAGTCGAGTCATTAGAGCC
1 AAGGGA-GCACCACCAGTCGAGTCAGTAGAACC
260633 AAG
1 AAG
260636 AGAAGAACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.34, C:0.25, G:0.29, T:0.12
Consensus pattern (32 bp):
AAGGGAGCACCACCAGTCGAGTCAGTAGAACC
Found at i:260646 original size:33 final size:33
Alignment explanation
Indices: 260576--260648 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
260566 CAAAGGGAGC
* * *
260576 ACCACCAGTCGAGTCAGTAGAACCAAGGGAGGC
1 ACCACCAGTCGAGTCAGTAGAACCAAGAGAAGA
* * *
260609 ACCACTAGTCGAGTCATTAGAGCCAAGAGAAGA
1 ACCACCAGTCGAGTCAGTAGAACCAAGAGAAGA
260642 ACCACCA
1 ACCACCA
260649 TTTGAATCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.27, G:0.25, T:0.11
Consensus pattern (33 bp):
ACCACCAGTCGAGTCAGTAGAACCAAGAGAAGA
Found at i:263468 original size:20 final size:19
Alignment explanation
Indices: 263420--263473 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
263410 AAGGTAATTT
*
263420 GTGTATCGATGCATTGGTA
1 GTGTATCGATGCACTGGTA
*
263439 GTGCATCGATGCACT-GTA
1 GTGTATCGATGCACTGGTA
263457 GAATGTATCGATGCACT
1 G--TGTATCGATGCACT
263474 TCAAGGGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.13
19 13 0.43
20 13 0.43
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (19 bp):
GTGTATCGATGCACTGGTA
Found at i:264666 original size:2 final size:2
Alignment explanation
Indices: 264661--264690 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
264651 AAACATGTGA
264661 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
264691 GATAAGGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:265115 original size:23 final size:23
Alignment explanation
Indices: 265084--265143 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
265074 CCTTATATGT
265084 CACTTCGGTGCATTTCTACGTGG
1 CACTTCGGTGCATTTCTACGTGG
* *
265107 CACTACGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGTGG
265130 CACTTCGGTGCATT
1 CACTTCGGTGCATT
265144 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGTGG
Found at i:268474 original size:64 final size:63
Alignment explanation
Indices: 268400--268557 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 63
268390 ATTGTTCTGT
* *
268400 GTGTATCGATGCACAGGAAGTGCATCGATGCA-CCCATTAAAAATGGAAACATCGAATGCAG-TT
1 GTGTATCGATGCAAAGG-AGTGCATCGATGCACCCCATT-AAAATGAAAACATCGAA-GCAGATT
268463 A
63 A
* * *
268464 GTGTATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGCTGATTT
1 GTGTATCGATGCA-AAGGAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGCAGATTA
**
268528 GTGTATCGATGCATGGGTAGTGCATCGATG
1 GTGTATCGATGCAAAGG-AGTGCATCGATG
268558 AACATGTTAA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
63 5 0.06
64 70 0.84
65 8 0.10
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (63 bp):
GTGTATCGATGCAAAGGAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGCAGATTA
Found at i:268593 original size:20 final size:20
Alignment explanation
Indices: 268568--268605 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
268558 AACATGTTAA
268568 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
268588 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
268606 TTAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:270254 original size:23 final size:23
Alignment explanation
Indices: 270221--270288 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
270211 AACCTTATAT
270221 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
270244 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
270267 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
270289 AGCTATGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:275405 original size:15 final size:15
Alignment explanation
Indices: 275385--275414 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
275375 CTTCGTTTTG
*
275385 TTTATTTTTTTTATT
1 TTTATTTTCTTTATT
275400 TTTATTTTCTTTATT
1 TTTATTTTCTTTATT
275415 CATTGATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTATTTTCTTTATT
Found at i:276553 original size:10 final size:10
Alignment explanation
Indices: 276534--276577 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
276524 TTTCTTTCCA
276534 TTTA-TTTTT
1 TTTATTTTTT
276543 TTTATTTTTT
1 TTTATTTTTT
*
276553 TTTATTTTTA
1 TTTATTTTTT
276563 TTTATTTTTAT
1 TTTATTTTT-T
276574 TTTA
1 TTTA
276578 CTAACTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 4 0.13
10 23 0.74
11 4 0.13
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:276572 original size:16 final size:16
Alignment explanation
Indices: 276541--276576 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
276531 CCATTTATTT
*
276541 TTTTTATTTTTTTTTA
1 TTTTTATTTATTTTTA
276557 TTTTTATTTATTTTTA
1 TTTTTATTTATTTTTA
276573 TTTT
1 TTTT
276577 ACTAACTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTATTTATTTTTA
Found at i:279236 original size:19 final size:19
Alignment explanation
Indices: 279209--279250 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
279199 TTTCTTTCCA
279209 TTTATT-TTTTTA-TTATT
1 TTTATTATTTTTATTTATT
279226 TTTATTATTTTTATTTATT
1 TTTATTATTTTTATTTATT
279245 TTTATT
1 TTTATT
279251 TTACTAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 11 0.48
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTATTATTTTTATTTATT
Found at i:279237 original size:10 final size:9
Alignment explanation
Indices: 279209--279250 Score: 68
Period size: 9 Copynumber: 4.7 Consensus size: 9
279199 TTTCTTTCCA
279209 TTTATT-TT
1 TTTATTATT
279217 TTTATTATT
1 TTTATTATT
279226 TTTATTATT
1 TTTATTATT
279235 TTTATTTATT
1 TTTA-TTATT
279245 TTTATT
1 TTTATT
279251 TTACTAACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 6 0.19
9 17 0.53
10 9 0.28
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTATT
Found at i:279251 original size:10 final size:10
Alignment explanation
Indices: 279208--279251 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
279198 TTTTCTTTCC
279208 ATTTATTTTT
1 ATTTATTTTT
*
279218 TTATTATTTTT
1 AT-TTATTTTT
279229 A-TTATTTTT
1 ATTTATTTTT
279238 ATTTATTTTT
1 ATTTATTTTT
279248 ATTT
1 ATTT
279252 TACTAACTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.30
10 13 0.43
11 8 0.27
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:282736 original size:18 final size:17
Alignment explanation
Indices: 282710--282764 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 17
282700 TTCAATCAAG
282710 AAAAAAAAAGAAGCAAA
1 AAAAAAAAAGAAGCAAA
*
282727 AAAGAAAAAACAAG-AACA
1 AAA-AAAAAAGAAGCAA-A
282745 AAAAAGAAAAGAAGCAAA
1 AAAAA-AAAAGAAGCAAA
282763 AA
1 AA
282765 TCAAAAGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 7 0.22
18 23 0.72
19 2 0.06
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAGCAAA
Found at i:282736 original size:20 final size:20
Alignment explanation
Indices: 282707--282754 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
282697 AGATTCAATC
*
282707 AAGAAAAAAAAAGAAGCAAAA
1 AAGAAAAAACAAGAA-CAAAA
282728 AAGAAAAAACAAGAACAAAA
1 AAGAAAAAACAAGAACAAAA
282748 AAGAAAA
1 AAGAAAA
282755 GAAGCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (20 bp):
AAGAAAAAACAAGAACAAAA
Found at i:282770 original size:22 final size:21
Alignment explanation
Indices: 282707--282770 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
282697 AGATTCAATC
282707 AAGAAAA-AA-AAAGAAGCAAAA
1 AAGAAAAGAACAAA-AA-CAAAA
*
282728 AAGAAAA-AACAAGAACAAAA
1 AAGAAAAGAACAAAAACAAAA
282748 AAGAAAAGAAGCAAAAATCAAAA
1 AAGAAAAGAA-CAAAAA-CAAAA
282771 GGAAAAGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 12 0.32
21 13 0.35
22 7 0.19
23 5 0.14
ACGTcount: A:0.78, C:0.08, G:0.12, T:0.02
Consensus pattern (21 bp):
AAGAAAAGAACAAAAACAAAA
Found at i:283848 original size:18 final size:18
Alignment explanation
Indices: 283825--283860 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
283815 TCAACATCAA
*
283825 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
283843 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
283861 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:284665 original size:37 final size:37
Alignment explanation
Indices: 284595--284666 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
284585 TGGAACTAAG
* * *
284595 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
284632 TTTTGTCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAA
284667 CAAATATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:285426 original size:106 final size:106
Alignment explanation
Indices: 285271--285696 Score: 656
Period size: 106 Copynumber: 4.0 Consensus size: 106
285261 TCGCTCCACC
* * * *
285271 CGAGACAACACAAGTTCAACTTCACAACGGAGGGACGGCTGGTTATCAACAAATAACTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* *
285336 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
*
285377 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* ** *
285442 TTCAGAGCCAATTTCAACTTCACAGCGAAGGGCACTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* *
285483 CGAGACAGCACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCACAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* *
285548 TTCAGAACCAATTTCAACTTCACGGCAAAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
*
285589 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCC-AT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * * *
285653 TTCCAGAACCAATTTTAACTTCACGGAGGAGGATATTGGACT
66 TT-CAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
285695 CG
1 CG
285697 GAACAATACA
Statistics
Matches: 294, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
105 4 0.01
106 290 0.99
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
Found at i:287134 original size:16 final size:15
Alignment explanation
Indices: 287113--287142 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
287103 TGTATCATTA
287113 TTATTTTATTATTTAC
1 TTATTTTA-TATTTAC
287129 TTATTTTATATTTA
1 TTATTTTATATTTA
287143 TATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTTTATATTTAC
Found at i:287143 original size:11 final size:11
Alignment explanation
Indices: 287111--287177 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 11
287101 CATGTATCAT
287111 TATTAT-TTTA
1 TATTATATTTA
*
287121 TTATT-TACTTA
1 -TATTATATTTA
*
287132 TTTTATATTTA
1 TATTATATTTA
*
287143 TATTATATATA
1 TATTATATTTA
*
287154 TA-TATATATA
1 TATTATATTTA
*
287164 TA-TATATATA
1 TATTATATTTA
287174 TATT
1 TATT
287178 TACGTTATTG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
10 24 0.50
11 24 0.50
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTATATTTA
Found at i:287144 original size:6 final size:6
Alignment explanation
Indices: 287129--287179 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
287119 TATTATTTAC
* * * *
287129 TTAT-T TTATAT TTATAT TATATAT ATATAT ATATAT ATATAT ATATAT
1 TTATAT TTATAT TTATAT T-TATAT TTATAT TTATAT TTATAT TTATAT
287177 TTA
1 TTA
287180 CGTTATTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
5 4 0.10
6 33 0.79
7 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TTATAT
Found at i:287153 original size:2 final size:2
Alignment explanation
Indices: 287135--287176 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
287125 TTACTTATTT
*
287135 TA TA TT TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
287176 T
1 T
287177 TTACGTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:288883 original size:27 final size:28
Alignment explanation
Indices: 288847--288900 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
288837 TAGAAGAAAC
*
288847 ATAATTATCTTTTATCTAT-ATTATAATA
1 ATAATTATCTATTAT-TATCATTATAATA
288875 ATAA-TATCTATTATTATCATTATAAT
1 ATAATTATCTATTATTATCATTATAAT
288901 TGGATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 3 0.12
27 17 0.71
28 4 0.17
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATTATCTATTATTATCATTATAATA
Found at i:288963 original size:14 final size:15
Alignment explanation
Indices: 288922--288973 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
288912 ATATTTTTTA
**
288922 AAAAAAATAATATTT
1 AAAAAAATAATAAAT
* *
288937 AGATAAATAAT-AAT
1 AAAAAAATAATAAAT
*
288951 AAAAAAATTATAAAT
1 AAAAAAATAATAAAT
288966 AAAAAAAT
1 AAAAAAAT
288974 CATGATAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 9 0.31
15 20 0.69
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAAAAATAATAAAT
Found at i:292724 original size:32 final size:32
Alignment explanation
Indices: 292688--292757 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
292678 CCGATACTAA
292688 CAGTGTTGCATTAAGATAATACACAACAATGT
1 CAGTGTTGCATTAAGATAATACACAACAATGT
** *
292720 CAGTGTTGCATTCGGATAATGCACAACAATGT
1 CAGTGTTGCATTAAGATAATACACAACAATGT
292752 CAGTGT
1 CAGTGT
292758 CACATTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (32 bp):
CAGTGTTGCATTAAGATAATACACAACAATGT
Found at i:292771 original size:32 final size:32
Alignment explanation
Indices: 292698--292779 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
292688 CAGTGTTGCA
* **
292698 TTAAGATAATACACAACAATGTCAGTGTTGCAT
1 TTAA-ATAATGCACAACAATGTCAGTGTCACAT
***
292731 TCGGATAATGCACAACAATGTCAGTGTCACAT
1 TTAAATAATGCACAACAATGTCAGTGTCACAT
*
292763 TTAAATAATGCAAAACA
1 TTAAATAATGCACAACA
292780 GTTACAGTCA
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
32 38 0.97
33 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (32 bp):
TTAAATAATGCACAACAATGTCAGTGTCACAT
Found at i:293538 original size:29 final size:30
Alignment explanation
Indices: 293506--293564 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
293496 AAGTTAATGT
293506 GACCACCAAACT-TTCAATTGAATCAATCA
1 GACCACCAAACTATTCAATTGAATCAATCA
* * *
293535 GACCACCCAACTATTTAATTGATTCAATCA
1 GACCACCAAACTATTCAATTGAATCAATCA
293565 AATCACCGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (30 bp):
GACCACCAAACTATTCAATTGAATCAATCA
Found at i:294016 original size:17 final size:17
Alignment explanation
Indices: 293982--294017 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
293972 ATAACAAATT
*
293982 AAACAAATTATTCGTTA
1 AAACAAATTATTAGTTA
*
293999 AAACAAATTATTATTTA
1 AAACAAATTATTAGTTA
294016 AA
1 AA
294018 TTAATTGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (17 bp):
AAACAAATTATTAGTTA
Found at i:294348 original size:138 final size:141
Alignment explanation
Indices: 294179--294499 Score: 441
Period size: 138 Copynumber: 2.3 Consensus size: 141
294169 ATGGTTAAAG
* * ** * *
294179 AAAAAAATTCGGTTAATTCGGTTTGGTTAATAATTTTCAAATTAGTTCGGTTCAGTTAATAATTT
1 AAAAAAATTCGATTAATTCCGTCCGATTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTT
294244 TCAAATAAATTTTAGTTCGATTAACCGAACCAAATTAACCAAATTTTTTCTTCGATTAATTCGAT
66 TCAAATAAATTTTAGTTCGATTAACCGAACCAAATTAACCAAATTTTTTCTTCGATTAATTCGAT
294309 GAATA-ATTT-
131 GAATACATTTC
*
294318 AAAAAAA-TCGATTAATTCCGTCCGATTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTT
1 AAAAAAATTCGATTAATTCCGTCCGATTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTT
* * ** *
294382 TCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACTGAATTTTTTCTTCGATTAATTCGGT
66 TCAAATAAATTTTAGTTCGATTAACCGAACCAAATTAACCAAATTTTTTCTTCGATTAATTCGAT
* *
294447 TAATACTTTTC
131 GAATACATTTC
* * ** * *
294458 AAAAAAATTCGGTTAATTCGGTTTGGTTAATAATTTTTAAAT
1 AAAAAAATTCGATTAATTCCGTCCGATTAATAATTTTCAAAT
294500 AAAATTTGGT
Statistics
Matches: 159, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
138 114 0.72
139 10 0.06
140 7 0.04
141 28 0.18
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (141 bp):
AAAAAAATTCGATTAATTCCGTCCGATTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTT
TCAAATAAATTTTAGTTCGATTAACCGAACCAAATTAACCAAATTTTTTCTTCGATTAATTCGAT
GAATACATTTC
Found at i:294375 original size:29 final size:29
Alignment explanation
Indices: 294328--294392 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
294318 AAAAAAATCG
294328 ATTAATTCCGTCCGATTAATAATTTTCAA
1 ATTAATTCCGTCCGATTAATAATTTTCAA
* * *
294357 ATTAATTCGGTTCGGTTAATAATTTTCAA
1 ATTAATTCCGTCCGATTAATAATTTTCAA
*
294386 ATAAATT
1 ATTAATT
294393 TTGGTTCGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (29 bp):
ATTAATTCCGTCCGATTAATAATTTTCAA
Found at i:294486 original size:112 final size:113
Alignment explanation
Indices: 294357--294658 Score: 464
Period size: 112 Copynumber: 2.7 Consensus size: 113
294347 TAATTTTCAA
*
294357 ATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACT
1 ATTAATTCGGTTCGGTTAATAATTTTTAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACT
*
294422 GAATTTTTTCTTCGATTAATTCGGTTAATACTTTTCAAAAAA-ATTCG
66 GAATTTTTTCTTCGATTAATTCGGTTAATAATTTTCAAAAAAGATTCG
* * *
294469 GTTAATTCGGTTTGGTTAATAATTTTTAAATAAAATTTGGTTCGATTAACCGAACCGAATTAA-T
1 ATTAATTCGGTTCGGTTAATAATTTTTAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACT
* * *
294533 CAAATTTTTTCTTCGATTAATTCGGTTAATAATTTTCAAAAAAGTTTTG
66 -GAATTTTTTCTTCGATTAATTCGGTTAATAATTTTCAAAAAAGATTCG
* * * *
294582 ATTGATTTGGTTCGGTTAATAATTTTTAAATAAATTTTGGTTTGATTAACCGAACCGAATTAACC
1 ATTAATTCGGTTCGGTTAATAATTTTTAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACT
*
294647 GATTTTTTTCTT
66 GAATTTTTTCTT
294659 TAACCGTTAA
Statistics
Matches: 170, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
111 1 0.01
112 99 0.58
113 70 0.41
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (113 bp):
ATTAATTCGGTTCGGTTAATAATTTTTAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACT
GAATTTTTTCTTCGATTAATTCGGTTAATAATTTTCAAAAAAGATTCG
Found at i:296040 original size:32 final size:32
Alignment explanation
Indices: 296001--296074 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
295991 ATTATTTTAT
* ** *
296001 TGACATGACACATGTCATGTTATCACTTTGAG
1 TGACATGACACATATCACATTATCACATTGAG
* *
296033 TGACATGATACATATCACATTATCACATTGAT
1 TGACATGACACATATCACATTATCACATTGAG
*
296065 TGACGTGACA
1 TGACATGACA
296075 TATACTATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (32 bp):
TGACATGACACATATCACATTATCACATTGAG
Found at i:296483 original size:16 final size:16
Alignment explanation
Indices: 296464--296511 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
296454 CCGAGTCGAG
296464 CTCGAGTATTGCCGAA
1 CTCGAGTATTGCCGAA
*
296480 CTC--G-ACT--CGAA
1 CTCGAGTATTGCCGAA
296491 CTCGAGTATTGCCGAA
1 CTCGAGTATTGCCGAA
296507 CTCGA
1 CTCGA
296512 CTCGAACTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
11 7 0.28
13 3 0.12
14 3 0.12
16 12 0.48
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (16 bp):
CTCGAGTATTGCCGAA
Found at i:296497 original size:27 final size:27
Alignment explanation
Indices: 296459--296522 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
296449 ACGAGCCGAG
*
296459 TCGAGCTCGAGTATTGCCGAACTCGAC
1 TCGAACTCGAGTATTGCCGAACTCGAC
296486 TCGAACTCGAGTATTGCCGAACTCGAC
1 TCGAACTCGAGTATTGCCGAACTCGAC
296513 TCGAACTCGA
1 TCGAACTCGA
296523 AAACTCGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (27 bp):
TCGAACTCGAGTATTGCCGAACTCGAC
Found at i:296697 original size:12 final size:12
Alignment explanation
Indices: 296682--296720 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
296672 CTCGATTCAA
296682 GATTTTAAGCTC
1 GATTTTAAGCTC
*
296694 GA-TTCAAGCTC
1 GATTTTAAGCTC
*
296705 TATTTTAAGCTC
1 GATTTTAAGCTC
296717 GATT
1 GATT
296721 CAAGCTCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (12 bp):
GATTTTAAGCTC
Found at i:296713 original size:23 final size:22
Alignment explanation
Indices: 296647--296728 Score: 100
Period size: 23 Copynumber: 3.8 Consensus size: 22
296637 TCGAGACTCG
*
296647 AGCTCGATTGAAGCTCGATTTTGA
1 AGCTCGATTCAAGCTC-ATTTT-A
296671 A-CTCGATTCAAG---ATTTTA
1 AGCTCGATTCAAGCTCATTTTA
296689 AGCTCGATTCAAGCTCTATTTTA
1 AGCTCGATTCAAGCTC-ATTTTA
296712 AGCTCGATTCAAGCTCA
1 AGCTCGATTCAAGCTCA
296729 ACGGGTTAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
18 2 0.04
19 16 0.31
22 1 0.02
23 32 0.62
24 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (22 bp):
AGCTCGATTCAAGCTCATTTTA
Found at i:299126 original size:7 final size:7
Alignment explanation
Indices: 299114--299174 Score: 61
Period size: 7 Copynumber: 8.9 Consensus size: 7
299104 CATAATCGGA
299114 TTTAGGG
1 TTTAGGG
299121 TTTAGGG
1 TTTAGGG
**
299128 TTTATAG
1 TTTAGGG
*
299135 TTTAGGA
1 TTTAGGG
* *
299142 TTCATGG
1 TTTAGGG
*
299149 TTTA-TG
1 TTTAGGG
299155 TTTAGGG
1 TTTAGGG
299162 TTTAGGG
1 TTTAGGG
299169 TTTAGG
1 TTTAGG
299175 ATTAATTACA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 5 0.12
7 37 0.88
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:299300 original size:11 final size:11
Alignment explanation
Indices: 299284--299346 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
299274 GTATTATAGA
299284 ATTTTTAATAT
1 ATTTTTAATAT
299295 ATTTTTTAA-AT
1 A-TTTTTAATAT
*
299306 -TTTATAAT-T
1 ATTTTTAATAT
*** *
299315 ATCAATAATTT
1 ATTTTTAATAT
299326 ATTTTTAATAT
1 ATTTTTAATAT
299337 ATTTTTAATA
1 ATTTTTAATA
299347 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 7 0.17
10 6 0.15
11 21 0.51
12 7 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:300982 original size:23 final size:23
Alignment explanation
Indices: 300956--301024 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
300946 CACCACAGCT
*
300956 CGTAAAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
300979 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
301002 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
301025 TATAAGATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.35, C:0.26, G:0.25, T:0.14
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:301748 original size:2 final size:2
Alignment explanation
Indices: 301741--301767 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
301731 TTTTATTATC
301741 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 A
301768 CCAATGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:302246 original size:23 final size:23
Alignment explanation
Indices: 302200--302248 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
302190 TCTTATATAA
* *
302200 TCACATGAATTATTTATATCTAT
1 TCACATGAATTATTAACATCTAT
* *
302223 TCACATGATTTATTAACATGTAT
1 TCACATGAATTATTAACATCTAT
302246 TCA
1 TCA
302249 TACATATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (23 bp):
TCACATGAATTATTAACATCTAT
Found at i:305317 original size:19 final size:19
Alignment explanation
Indices: 305293--305334 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
305283 ATATCTTTTC
* *
305293 TTTCATACTCCCTTACTCT
1 TTTCATACTACCTTACACT
*
305312 TTTCATATTACCTTACACT
1 TTTCATACTACCTTACACT
305331 TTTC
1 TTTC
305335 TATCAATCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTCATACTACCTTACACT
Found at i:308026 original size:23 final size:23
Alignment explanation
Indices: 308006--308049 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
307996 ATCATATTCT
308006 TATATAATCACATGAATTATTTA
1 TATATAATCACATGAATTATTTA
* * *
308029 TATCTATTCACATGATTTATT
1 TATATAATCACATGAATTATT
308050 AACATGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (23 bp):
TATATAATCACATGAATTATTTA
Found at i:308059 original size:23 final size:23
Alignment explanation
Indices: 308013--308061 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
308003 TCTTATATAA
* *
308013 TCACATGAATTATTTATATCTAT
1 TCACATGAATTATTAACATCTAT
* *
308036 TCACATGATTTATTAACATGTAT
1 TCACATGAATTATTAACATCTAT
308059 TCA
1 TCA
308062 TACATATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (23 bp):
TCACATGAATTATTAACATCTAT
Found at i:310728 original size:17 final size:16
Alignment explanation
Indices: 310690--310721 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
310680 TATCACCGAC
*
310690 CAAATTTTACTATTCA
1 CAAAATTTACTATTCA
310706 CAAAATTTACTATTCA
1 CAAAATTTACTATTCA
310722 TGTAAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (16 bp):
CAAAATTTACTATTCA
Found at i:314576 original size:15 final size:17
Alignment explanation
Indices: 314545--314576 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
314535 ATATATTTTT
314545 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
314562 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
314577 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:314948 original size:2 final size:2
Alignment explanation
Indices: 314941--314965 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
314931 CAATTATAAA
314941 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 A
314966 ATTTCGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:321203 original size:2 final size:2
Alignment explanation
Indices: 321196--321227 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
321186 ATACATCCAA
321196 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
321228 CATACATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:321628 original size:23 final size:23
Alignment explanation
Indices: 321584--321647 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
321574 CAGCTTGTAT
*
321584 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGGGCCACGTAG
* * *
321607 AATTGCACCTAAGGGCCGCGTAG
1 AAATGCACCGAAGGGCCACGTAG
*
321630 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGGGCCA
321648 TATAAGATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.14
Consensus pattern (23 bp):
AAATGCACCGAAGGGCCACGTAG
Found at i:321930 original size:30 final size:29
Alignment explanation
Indices: 321877--321935 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
321867 TGTAAACATA
* *
321877 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
321907 TCACATATACATTTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
321936 GTAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:328169 original size:62 final size:62
Alignment explanation
Indices: 328094--328210 Score: 216
Period size: 62 Copynumber: 1.9 Consensus size: 62
328084 TCGCCAAGCA
* *
328094 CTCCTGCTCCTCGCGTGATTCCTCTTGCAGTTGCTCAGGAGACCTCATGCATGCACCTATTC
1 CTCCTCCTCCTCGCGTGATTCCTCTTGCAGCTGCTCAGGAGACCTCATGCATGCACCTATTC
328156 CTCCTCCTCCTCGCGTGATTCCTCTTGCAGCTGCTCAGGAGACCTCATGCATGCA
1 CTCCTCCTCCTCGCGTGATTCCTCTTGCAGCTGCTCAGGAGACCTCATGCATGCA
328211 GCTGTAATAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.15, C:0.37, G:0.20, T:0.29
Consensus pattern (62 bp):
CTCCTCCTCCTCGCGTGATTCCTCTTGCAGCTGCTCAGGAGACCTCATGCATGCACCTATTC
Found at i:328721 original size:21 final size:21
Alignment explanation
Indices: 328695--328735 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
328685 TTAGTTAATG
328695 AGTTTGTTAGTATAAATTATT
1 AGTTTGTTAGTATAAATTATT
* *
328716 AGTTTGTTAGTTTAAGTTAT
1 AGTTTGTTAGTATAAATTAT
328736 ATTATATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (21 bp):
AGTTTGTTAGTATAAATTATT
Found at i:329179 original size:14 final size:14
Alignment explanation
Indices: 329160--329186 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
329150 GTAATTTATT
329160 ATTTTTTGTTGTTC
1 ATTTTTTGTTGTTC
329174 ATTTTTTGTTGTT
1 ATTTTTTGTTGTT
329187 GTGTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
ATTTTTTGTTGTTC
Found at i:329314 original size:82 final size:83
Alignment explanation
Indices: 329216--329374 Score: 266
Period size: 82 Copynumber: 1.9 Consensus size: 83
329206 AGTTAGTTAG
*
329216 TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTATTCCCCTTT-AAAAAATATTGTGTTTA
1 TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTATTCCACTTTAAAAAAATATTGTGTTTA
*
329280 AAATTATTTAGTGTTTAT
66 AAAATATTTAGTGTTTAT
* * *
329298 TTTATATTAGATTATATAAAATTAATTTGTTTAATTTGTTCCAGTTTAAAAAAATATTGTGTTTA
1 TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTATTCCACTTTAAAAAAATATTGTGTTTA
329363 AAAATATTTAGT
66 AAAATATTTAGT
329375 ATTGTTTTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
82 43 0.61
83 28 0.39
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (83 bp):
TTTATATTAGAGTATATAAAATTAATTTGTTTAATTTATTCCACTTTAAAAAAATATTGTGTTTA
AAAATATTTAGTGTTTAT
Found at i:329363 original size:17 final size:17
Alignment explanation
Indices: 329341--329401 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
329331 ATTTGTTCCA
329341 GTTTAAAAAAATATTGT
1 GTTTAAAAAAATATTGT
329358 GTTTAAAAATATTTAGTATTGT
1 GTTTAAAAA-A---A-TATTGT
*
329380 -TTTAAAAAAATATTTT
1 GTTTAAAAAAATATTGT
329396 GTTTAA
1 GTTTAA
329402 TTTATTAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
16 5 0.14
17 15 0.41
18 1 0.03
20 1 0.03
21 9 0.24
22 6 0.16
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (17 bp):
GTTTAAAAAAATATTGT
Found at i:329388 original size:22 final size:23
Alignment explanation
Indices: 329352--329394 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
329342 TTTAAAAAAA
329352 TATTGTGTTT-AAAAATATTTAG
1 TATTGTGTTTAAAAAATATTTAG
329374 TATTGT-TTTAAAAAAATATTT
1 TATTGTGTTT-AAAAAATATTT
329395 TGTTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 6 0.32
23 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (23 bp):
TATTGTGTTTAAAAAATATTTAG
Found at i:329405 original size:22 final size:23
Alignment explanation
Indices: 329362--329405 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
329352 TATTGTGTTT
**
329362 AAAAATATTTAGTATTGTTTTAA
1 AAAAATATTTAGTATTAATTTAA
*
329385 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTATTAATTTA
329406 TTAGATTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTATTAATTTAA
Found at i:332587 original size:47 final size:46
Alignment explanation
Indices: 332454--332594 Score: 187
Period size: 46 Copynumber: 3.0 Consensus size: 46
332444 CATAATTATT
* * *
332454 TAGTAATGATTAGTAATAATGAA--ATTATTATTATTTAATGATTTGG
1 TAGTAATGATTAATAATAA--AATTATTATTAATATTTAATGATTTAG
*
332500 TAGTAATGATTAATAATGAAATTATTATTAATATTTAATGATTTAG
1 TAGTAATGATTAATAATAAAATTATTATTAATATTTAATGATTTAG
**
332546 TAGTAATGATTTGTAAATAAAATTATTATTAATATTTAATGATTTAG
1 TAGTAATGATTAAT-AATAAAATTATTATTAATATTTAATGATTTAG
332593 TA
1 TA
332595 ATGATTTAGT
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
44 2 0.02
46 50 0.59
47 33 0.39
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (46 bp):
TAGTAATGATTAATAATAAAATTATTATTAATATTTAATGATTTAG
Found at i:332598 original size:11 final size:11
Alignment explanation
Indices: 332582--332795 Score: 76
Period size: 11 Copynumber: 19.4 Consensus size: 11
332572 TATTAATATT
332582 TAATGATTTAG
1 TAATGATTTAG
332593 TAATGATTTAG
1 TAATGATTTAG
* *
332604 TAATTA-TTAA
1 TAATGATTTAG
* * *
332614 TATTTAAATTA-
1 TA-ATGATTTAG
332625 TAATGATTT--
1 TAATGATTTAG
*
332634 TAAT-ATTTAA
1 TAATGATTTAG
*
332644 TGATTTGATTTAG
1 T-A-ATGATTTAG
332657 TAATGATTT-G
1 TAATGATTTAG
332667 ATAAT-ATTTAG
1 -TAATGATTTAG
* *
332678 TAATAATCATTATA
1 TAATGAT--TTA-G
*
332692 TAATGA-TTAA
1 TAATGATTTAG
*
332702 TAATGATTTAATATT
1 TAATGA-TT--TA-G
332717 TAATGATTT-G
1 TAATGATTTAG
332727 --ATGATTTAG
1 TAATGATTTAG
332736 TAATGATTT-G
1 TAATGATTTAG
* *
332746 ATAATCATTATAA
1 -TAATGATT-TAG
332759 TAATGATTTAG
1 TAATGATTTAG
*
332770 TAAT-ATTATAA
1 TAATGATT-TAG
*
332781 TAATGATTTAA
1 TAATGATTTAG
332792 TAAT
1 TAAT
332796 AACGATAATA
Statistics
Matches: 158, Mismatches: 19, Indels: 52
0.69 0.08 0.23
Matches are distributed among these distances:
8 11 0.07
9 5 0.03
10 30 0.19
11 70 0.44
12 18 0.11
13 9 0.06
14 9 0.06
15 6 0.04
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (11 bp):
TAATGATTTAG
Found at i:332660 original size:16 final size:15
Alignment explanation
Indices: 332585--332668 Score: 55
Period size: 16 Copynumber: 5.3 Consensus size: 15
332575 TAATATTTAA
332585 TGATTTAGTAATGATT
1 TGATTTA-TAATGATT
*
332601 TAGTAATTATTAAT-ATT
1 T-G-ATTTA-TAATGATT
* *
332618 TAAATTATAATGATTT
1 TGATTTATAATGA-TT
*
332634 TAATATT-TAATGATT
1 TGAT-TTATAATGATT
332649 TGATTTAGTAATGATT
1 TGATTTA-TAATGATT
332665 TGAT
1 TGAT
332669 AATATTTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
14 6 0.11
15 11 0.20
16 24 0.43
17 7 0.12
18 8 0.14
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
TGATTTATAATGATT
Found at i:332676 original size:34 final size:33
Alignment explanation
Indices: 332585--332793 Score: 110
Period size: 34 Copynumber: 5.9 Consensus size: 33
332575 TAATATTTAA
332585 TGATTTAGTAATGATTT-AGTAAT-TATTAATATT
1 TGATTTAGTAATGATTTGA-TAATAT-TTAATATT
* *
332618 TAAATTA-TAATGATTT--TAATATTTAATGATT
1 TGATTTAGTAATGATTTGATAATATTTAAT-ATT
* *
332649 TGATTTAGTAATGATTTGATAATATTTAGTAATAA
1 TGATTTAGTAATGATTTGATAATATTTAAT-AT-T
*
332684 TCATTATA-TAATGATTAATAATGATTTAATATTTAATGATTT
1 TGATT-TAGTAATGA-T--T--TGA--TAATATTTAAT-A-TT
*
332726 GATGATTTAGTAATGATTTGATAATCATTATAATA-A
1 --TGATTTAGTAATGATTTGATAAT-ATT-TAATATT
*
332762 TGATTTAGTAAT-ATTATAATAATGATTTAATA
1 TGATTTAGTAATGATT-TGATAAT-ATTTAATA
332794 ATAACGATAA
Statistics
Matches: 140, Mismatches: 15, Indels: 42
0.71 0.08 0.21
Matches are distributed among these distances:
30 9 0.06
31 9 0.06
32 18 0.13
33 13 0.09
34 33 0.24
35 10 0.07
36 3 0.02
37 4 0.03
38 5 0.04
39 7 0.05
40 3 0.02
41 1 0.01
42 11 0.08
43 4 0.03
44 10 0.07
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.48
Consensus pattern (33 bp):
TGATTTAGTAATGATTTGATAATATTTAATATT
Found at i:332725 original size:8 final size:8
Alignment explanation
Indices: 332692--332734 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
332682 AATCATTATA
332692 TAATGATT
1 TAATGATT
332700 AATAATGATT
1 --TAATGATT
332710 TAAT-ATT
1 TAATGATT
332717 TAATGATT
1 TAATGATT
*
332725 TGATGATT
1 TAATGATT
332733 TA
1 TA
332735 GTAATGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 7 0.23
8 15 0.50
10 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (8 bp):
TAATGATT
Found at i:332748 original size:79 final size:76
Alignment explanation
Indices: 332624--332793 Score: 231
Period size: 79 Copynumber: 2.2 Consensus size: 76
332614 TATTTAAATT
332624 ATAATGATTTTAATATTTAATGATTTGATTTAGTAATGATTTGATAAT-ATTTAGTAATAATCAT
1 ATAATGA-TTTAATATTTAATGATTTGATTTAGTAATGATTTGATAATCA-TTA-TAATAATCAT
332688 TATA-TAATGA-T-TA
63 T-TAGTAAT-ATTATA
*
332701 ATAATGATTTAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATCATTATAATAATGAT
1 ATAATGATTTAATATTTAATGA-TT--TGATTTAGTAATGATTTGATAATCATTATAATAATCAT
332766 TTAGTAATATTATA
63 TTAGTAATATTATA
332780 ATAATGATTTAATA
1 ATAATGATTTAATA
332794 ATAACGATAA
Statistics
Matches: 85, Mismatches: 1, Indels: 12
0.87 0.01 0.12
Matches are distributed among these distances:
76 15 0.18
77 12 0.14
78 15 0.18
79 42 0.49
80 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (76 bp):
ATAATGATTTAATATTTAATGATTTGATTTAGTAATGATTTGATAATCATTATAATAATCATTTA
GTAATATTATA
Found at i:332762 original size:23 final size:23
Alignment explanation
Indices: 332678--332911 Score: 157
Period size: 23 Copynumber: 10.2 Consensus size: 23
332668 TAATATTTAG
332678 TAATAATCATTAT-ATAATGA-T
1 TAATAATCATTATAATAATGATT
* *
332699 TAATAATGATTTAATATTTAATGA-T
1 TAATAATCA-TT-ATA-ATAATGATT
* * *
332724 T--TGATGATT-TAGTAATGATT
1 TAATAATCATTATAATAATGATT
*
332744 TGATAATCATTATAATAATGATT
1 TAATAATCATTATAATAATGATT
*
332767 TAGTAAT-ATTATAATAATGATT
1 TAATAATCATTATAATAATGATT
* **
332789 TAATAATAACGATAATAAT--TT
1 TAATAATCATTATAATAATGATT
332810 AATAATAATCATTATAATAATGATT
1 --TAATAATCATTATAATAATGATT
332835 TAATATAATCATTATAATAA-GATT
1 T-A-ATAATCATTATAATAATGATT
* * *
332859 TAATAATAATGATTTAACAATGA-T
1 TAATAATCAT--TATAATAATGATT
* *
332883 TAATAATGATTTATTACTAATGATT
1 TAATAATCA-TTA-TAATAATGATT
332908 TAAT
1 TAAT
332912 TATTACTAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 38
0.74 0.10 0.17
Matches are distributed among these distances:
19 6 0.04
20 4 0.02
21 10 0.06
22 38 0.22
23 50 0.29
24 28 0.16
25 34 0.20
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (23 bp):
TAATAATCATTATAATAATGATT
Found at i:332796 original size:14 final size:14
Alignment explanation
Indices: 332777--332875 Score: 82
Period size: 14 Copynumber: 7.1 Consensus size: 14
332767 TAGTAATATT
332777 ATAATAATGATTTA
1 ATAATAATGATTTA
* *
332791 ATAATAACGATAATA
1 ATAATAATGAT-TTA
*
332806 ATTTAATAATAATCATT-
1 A--TAATAATGAT--TTA
332823 ATAATAATGATTTA
1 ATAATAATGATTTA
*
332837 AT-ATAATCA-TT-
1 ATAATAATGATTTA
332848 ATAATAA-GATTTA
1 ATAATAATGATTTA
332861 ATAATAATGATTTA
1 ATAATAATGATTTA
332875 A
1 A
332876 CAATGATTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
11 3 0.04
12 8 0.12
13 15 0.22
14 19 0.28
15 12 0.18
17 9 0.13
18 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (14 bp):
ATAATAATGATTTA
Found at i:332827 original size:20 final size:20
Alignment explanation
Indices: 332780--332817 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
332770 TAATATTATA
*
332780 ATAATGATTTAATAATAACG
1 ATAATAATTTAATAATAACG
332800 ATAATAATTTAATAATAA
1 ATAATAATTTAATAATAA
332818 TCATTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (20 bp):
ATAATAATTTAATAATAACG
Found at i:332848 original size:25 final size:26
Alignment explanation
Indices: 332746--332911 Score: 157
Period size: 25 Copynumber: 7.0 Consensus size: 26
332736 TAATGATTTG
332746 ATAATCATTATAATAATGA-TT--TA
1 ATAATCATTATAATAATGATTTAATA
*
332769 GTAAT-ATTATAATAATGATTTAATA
1 ATAATCATTATAATAATGATTTAATA
*
332794 ATAA-C--GATAAT-A--ATTTAATA
1 ATAATCATTATAATAATGATTTAATA
332814 ATAATCATTATAATAATGATTTAAT-
1 ATAATCATTATAATAATGATTTAATA
332839 ATAATCATTATAATAA-GATTTAATA
1 ATAATCATTATAATAATGATTTAATA
* *
332864 ATAATGATT-TAACAATGA-TTAATA
1 ATAATCATTATAATAATGATTTAATA
* *
332888 ATGAT--TTATTACTAATGATTTAAT
1 ATAATCATTA-TAATAATGATTTAAT
332912 TATTACTAAT
Statistics
Matches: 119, Mismatches: 9, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
20 12 0.10
21 1 0.01
22 16 0.13
23 16 0.13
24 31 0.26
25 36 0.30
26 7 0.06
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (26 bp):
ATAATCATTATAATAATGATTTAATA
Found at i:332922 original size:35 final size:34
Alignment explanation
Indices: 332755--332924 Score: 134
Period size: 35 Copynumber: 4.8 Consensus size: 34
332745 GATAATCATT
*
332755 ATAATAATGATTTAGTAATATTATAATAATGATTTA
1 ATAATAATGATTTAAT-A-ATTATAATAATGATTTA
* *
332791 ATAATAACGA--TAATAATT-TAATAATAATCATT-
1 ATAATAATGATTTAATAATTATAATAATGAT--TTA
332823 ATAATAATGATTTAATATAATCATTATAATAA-GATTTA
1 ATAATAATGATTT-A-AT-A--ATTATAATAATGATTTA
* *
332861 ATAATAATGATTTAACAATGATTAATAATGATTTA
1 ATAATAATGATTTAATAATTA-TAATAATGATTTA
* * *
332896 TTACTAATGATTTAATTATTACTAATAAT
1 ATAATAATGATTTAATAATTA-TAATAAT
332925 TAAATAATAA
Statistics
Matches: 108, Mismatches: 13, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
31 9 0.08
32 12 0.11
33 6 0.06
34 10 0.09
35 31 0.29
36 12 0.11
37 4 0.04
38 13 0.12
39 5 0.05
40 6 0.06
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (34 bp):
ATAATAATGATTTAATAATTATAATAATGATTTA
Found at i:333058 original size:17 final size:17
Alignment explanation
Indices: 333036--333069 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
333026 GATTTAGTAA
333036 TTATTATTAATAATTAT
1 TTATTATTAATAATTAT
*
333053 TTATTATTAATTATTAT
1 TTATTATTAATAATTAT
333070 AATACTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTATTAATAATTAT
Found at i:335427 original size:11 final size:11
Alignment explanation
Indices: 335413--335473 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
335403 ATAAACTATT
*
335413 CTTTAATATAG
1 CTTTAATATAA
*
335424 CTTTAACTAT-T
1 CTTTAA-TATAA
335435 CTTTAATATAA
1 CTTTAATATAA
*
335446 CTTTAACTAT-T
1 CTTTAA-TATAA
335457 CTTTAATATAA
1 CTTTAATATAA
335468 CTTTAA
1 CTTTAA
335474 CTAATAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 6 0.14
11 30 0.71
12 6 0.14
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (11 bp):
CTTTAATATAA
Found at i:335431 original size:22 final size:22
Alignment explanation
Indices: 335406--335476 Score: 133
Period size: 22 Copynumber: 3.2 Consensus size: 22
335396 ACAACTAATA
*
335406 AACTATTCTTTAATATAGCTTT
1 AACTATTCTTTAATATAACTTT
335428 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
335450 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
335472 AACTA
1 AACTA
335477 ATAAACTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.37, C:0.14, G:0.01, T:0.48
Consensus pattern (22 bp):
AACTATTCTTTAATATAACTTT
Found at i:335493 original size:15 final size:16
Alignment explanation
Indices: 335449--335497 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
335439 AATATAACTT
335449 TAACTATTCTTTAATA
1 TAACTATTCTTTAATA
***
335465 TAACT-TTAACTAATA
1 TAACTATTCTTTAATA
335480 -AACTATTCTTTAATA
1 TAACTATTCTTTAATA
335495 TAA
1 TAA
335498 TTTAGTACTA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 4 0.16
15 14 0.56
16 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (16 bp):
TAACTATTCTTTAATA
Found at i:335514 original size:31 final size:30
Alignment explanation
Indices: 335450--335515 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
335440 ATATAACTTT
*
335450 AACTATTCTTTAATATAACTTTAACTAATA
1 AACTATTCTTTAATATAACTTTAACTAAAA
335480 AACTATTCTTTAATATAA-TTTAGTACTAAAA
1 AACTATTCTTTAATATAACTTTA--ACTAAAA
335511 AACTA
1 AACTA
335516 ATTAACTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 4 0.12
30 18 0.55
31 11 0.33
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTATTCTTTAATATAACTTTAACTAAAA
Found at i:335721 original size:21 final size:21
Alignment explanation
Indices: 335697--335736 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
335687 TTTCTATATG
335697 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
335718 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
335737 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:335819 original size:18 final size:18
Alignment explanation
Indices: 335766--335820 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
335756 TTGTTTTACC
*
335766 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
335784 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
335796 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
335813 CTAATTTA
1 CTAATTTA
335821 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:336086 original size:21 final size:23
Alignment explanation
Indices: 336062--336112 Score: 81
Period size: 21 Copynumber: 2.3 Consensus size: 23
336052 TTTATGTATG
336062 ATATAACTTAAACTAAC-AA-TA
1 ATATAACTTAAACTAACTAACTA
336083 ATATAACTTAAACTAACTAACTA
1 ATATAACTTAAACTAACTAACTA
336106 AT-TAACT
1 ATATAACT
336113 AAAATTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.61
22 7 0.25
23 4 0.14
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (23 bp):
ATATAACTTAAACTAACTAACTA
Found at i:336181 original size:365 final size:361
Alignment explanation
Indices: 335453--336156 Score: 885
Period size: 365 Copynumber: 1.9 Consensus size: 361
335443 TAACTTTAAC
* * *
335453 TATTCTTTAATATAACTTTAACTAATAAACTATTCTTTAATATAATTTAGTACTAAAAAACTAAT
1 TATTCTTTAATATAACTTAAACTAATAAACTATTCTTTAATATAATTAACTACTAAAAAACTAAT
335518 TAACTAATTTTTTTTATATAATATAAATTCAACAAACAAATATAACTTAACTATTTAAATAACAC
66 TAACTAA-TTTTTTTATATAATATAAATTCAACAAACAAATATAACTTAACTATTTAAATAACAC
*
335583 AAACTAAATACATATTTTTTTTATATATAACTAACGACTAACAAACTAACTAATTATTTTTATTA
130 AAACTAAATACA-A------TTATATATAACTAAC-ACTAACAAACTAACTAATTAGTTTTATTA
* * * * *
335648 ATATGTAACTATCAAACATACTAATTAAATAATTTTTTATTTCTATATGATATAACTTAAACTAA
187 ATATATAACCATCAAACAAACTAATTAAATAATTTTATATTTATATATGATATAACTTAAACTAA
**
335713 CAATAATATAACTTAAACTAACAAACTAATTAACTAATTTTTTTTGTTTTACCCTAATTTATAAT
252 CAATAATATAACTTAAACTAACAAACTAATTAACTAA-TAATTTTGTTTTACCC--A-TTATAAT
* *
335778 AATAAACTAATTAACTAATAATTTATAACAATAAACTAATTTAAATAAT
313 AACAAACTAATTAACTAAAAATTTATAACAATAAACTAATTTAAATAAT
* * *
335827 TATTCTTTTATATAACTTAAACTAATAAACTATTTTTTATTATAATAAAACTTAAACTACTAATA
1 TATTCTTTAATATAACTTAAACTAATAAACTATTCTTTA--AT-AT--AA-TT-AACTACTAAAA
*
335892 AACTAATTAACTAA-TTTTTTATATAATATAAATTCAACAACCAAAATATAACTTAACTATTTAA
59 AACTAATTAACTAATTTTTTTATATAATATAAATTCAACAAAC-AAATATAACTTAACTATTTAA
* * * * *
335956 CTAACTACAAACTAATTAC-A-TAT-TA-GACT-A-ACTAACACACTAATTAATT-GTTTT-TTA
123 ATAAC-ACAAACTAAATACAATTATATATAACTAACACTAACAAACTAACTAATTAGTTTTATTA
*
336013 ATATATAACCATCAAACAAACTAATTAAATAATTTTATATTTATGTATGATATAACTTAAACTAA
187 ATATATAACCATCAAACAAACTAATTAAATAATTTTATATTTATATATGATATAACTTAAACTAA
*
336078 CAATAATATAACTTAAACTAACTAACTAATTAACTAA-AATTTTGTTTTA-CC-TTA-AACTAAC
252 CAATAATATAACTTAAACTAACAAACTAATTAACTAATAATTTTGTTTTACCCATTATAA-TAAC
*
336139 CAACTAATTAACTAAAAA
316 AAACTAATTAACTAAAAA
336157 AATTTTACCT
Statistics
Matches: 295, Mismatches: 25, Indels: 36
0.83 0.07 0.10
Matches are distributed among these distances:
357 2 0.01
358 22 0.07
362 2 0.01
363 10 0.03
365 98 0.33
366 4 0.01
367 17 0.06
369 1 0.00
370 3 0.01
371 2 0.01
372 3 0.01
374 36 0.12
376 2 0.01
377 2 0.01
379 30 0.10
380 27 0.09
381 34 0.12
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (361 bp):
TATTCTTTAATATAACTTAAACTAATAAACTATTCTTTAATATAATTAACTACTAAAAAACTAAT
TAACTAATTTTTTTATATAATATAAATTCAACAAACAAATATAACTTAACTATTTAAATAACACA
AACTAAATACAATTATATATAACTAACACTAACAAACTAACTAATTAGTTTTATTAATATATAAC
CATCAAACAAACTAATTAAATAATTTTATATTTATATATGATATAACTTAAACTAACAATAATAT
AACTTAAACTAACAAACTAATTAACTAATAATTTTGTTTTACCCATTATAATAACAAACTAATTA
ACTAAAAATTTATAACAATAAACTAATTTAAATAAT
Found at i:336217 original size:9 final size:9
Alignment explanation
Indices: 336188--336225 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
336178 CTAACAAACT
336188 AATAATTTAA
1 AATAA-TTAA
336198 AATAA-TAA
1 AATAATTAA
336206 AATAATTAA
1 AATAATTAA
336215 AATAATTAA
1 AATAATTAA
336224 AA
1 AA
336226 AACCTTACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.30
9 14 0.52
10 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:336438 original size:23 final size:23
Alignment explanation
Indices: 336408--336488 Score: 144
Period size: 23 Copynumber: 3.5 Consensus size: 23
336398 GCTGAAGCGC
336408 TGCAATAATGCAACAATAAGTGT
1 TGCAATAATGCAACAATAAGTGT
336431 TGCAATAATGCAACAATAAGTGT
1 TGCAATAATGCAACAATAAGTGT
* *
336454 TGTAATAATGCAACAATAAGTGA
1 TGCAATAATGCAACAATAAGTGT
336477 TGCAATAATGCA
1 TGCAATAATGCA
336489 GCTGAATTCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (23 bp):
TGCAATAATGCAACAATAAGTGT
Found at i:336606 original size:29 final size:29
Alignment explanation
Indices: 336565--336648 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 29
336555 GCAAGCATAC
* *
336565 ATGTCGCTCGGATGCCCTGGCGACTTACA
1 ATGTCGCTGGGATGCCCTGGCGACCTACA
* *
336594 ATGTCACTGGGATGCCCTGGCGACCTATA
1 ATGTCGCTGGGATGCCCTGGCGACCTACA
336623 ATGTCGCTGGGATGCCCTGGCGACCT
1 ATGTCGCTGGGATGCCCTGGCGACCT
336649 GCCCATTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.24
Consensus pattern (29 bp):
ATGTCGCTGGGATGCCCTGGCGACCTACA
Found at i:336733 original size:30 final size:30
Alignment explanation
Indices: 336699--336760 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
336689 GGCACCGAAC
*
336699 GTTGCATGAGCCATGCACAACACCACACAG
1 GTTGCACGAGCCATGCACAACACCACACAG
* *
336729 GTTGCACGAGCCATGCAGAGCACCACACAG
1 GTTGCACGAGCCATGCACAACACCACACAG
336759 GT
1 GT
336761 CGCCCGGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.32, G:0.24, T:0.13
Consensus pattern (30 bp):
GTTGCACGAGCCATGCACAACACCACACAG
Found at i:337401 original size:31 final size:31
Alignment explanation
Indices: 337353--337414 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
337343 TATACGTAAT
*
337353 AAGTTACAATAAAAATAAAATATTTTTTTAA
1 AAGTTACAATAAAAATAAAATATGTTTTTAA
*
337384 AAGTTA-AGATAAGAATAAAATATGTTTTTAA
1 AAGTTACA-ATAAAAATAAAATATGTTTTTAA
337415 GTTGATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (31 bp):
AAGTTACAATAAAAATAAAATATGTTTTTAA
Found at i:337426 original size:29 final size:26
Alignment explanation
Indices: 337366--337464 Score: 76
Period size: 26 Copynumber: 3.6 Consensus size: 26
337356 TTACAATAAA
337366 AATAAAATATTTTTTTAAAAGTTAAGATAAG
1 AATAAAATA-TTTTTT--AAGTT-AG-TAAG
337397 AATAAAATATGTTTTTAAGTTGATGTAAG
1 AATAAAATAT-TTTTTAAGTT-A-GTAAG
* *
337426 AGT-AAATA-TTTTTAAGTTAATAAG
1 AATAAAATATTTTTTAAGTTAGTAAG
* *
337450 ATTAAAATATATTTT
1 AATAAAATATTTTTT
337465 CCATTCTTGC
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
24 6 0.10
25 6 0.10
26 14 0.24
28 5 0.08
29 12 0.20
30 2 0.03
31 14 0.24
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.42
Consensus pattern (26 bp):
AATAAAATATTTTTTAAGTTAGTAAG
Found at i:338400 original size:21 final size:21
Alignment explanation
Indices: 338355--338400 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
338345 GTCGGTTCCG
*
338355 TTTTAACTATTTTTTAACTCC
1 TTTTAACTATTTTTTAACGCC
* * *
338376 TTTTAATTATTTTTTCACGCT
1 TTTTAACTATTTTTTAACGCC
338397 TTTT
1 TTTT
338401 CCCTCTCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTAACTATTTTTTAACGCC
Found at i:340893 original size:21 final size:21
Alignment explanation
Indices: 340867--340919 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
340857 GATTTTGAAA
340867 AATACTACTCCCCCTTACTTT
1 AATACTACTCCCCCTTACTTT
340888 AATACTACTCCCCCTTACTTT
1 AATACTACTCCCCCTTACTTT
*
340909 AACACTACTCC
1 AATACTACTCC
340920 TCTTAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.40, G:0.00, T:0.34
Consensus pattern (21 bp):
AATACTACTCCCCCTTACTTT
Found at i:342904 original size:19 final size:19
Alignment explanation
Indices: 342876--342912 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
342866 GAACCCCATG
*
342876 GGGGGTATCGATTCCCCTA
1 GGGGGAATCGATTCCCCTA
*
342895 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
342913 TCAACGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.27, G:0.35, T:0.24
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCTA
Found at i:342925 original size:23 final size:22
Alignment explanation
Indices: 342894--342955 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
342884 CGATTCCCCT
342894 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGGTTCCCCTTCA
* *
342916 ACGGGGGAATCGGTTCCACTTTA
1 A-GGGGGAATCGGTTCCCCTTCA
* *
342939 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
342956 TCTGCCCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTTCA
Found at i:349214 original size:20 final size:20
Alignment explanation
Indices: 349189--349231 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
349179 ATACTGAAAG
349189 TATCGATACTAGCCCAAGAC
1 TATCGATACTAGCCCAAGAC
349209 TATCGATACTAGCCCAAGAC
1 TATCGATACTAGCCCAAGAC
349229 TAT
1 TAT
349232 ACTCCAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (20 bp):
TATCGATACTAGCCCAAGAC
Found at i:350625 original size:12 final size:12
Alignment explanation
Indices: 350608--350633 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
350598 ATTGCATCAG
350608 CAATGACAACAT
1 CAATGACAACAT
350620 CAATGACAACAT
1 CAATGACAACAT
350632 CA
1 CA
350634 GTCCTAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.08, T:0.15
Consensus pattern (12 bp):
CAATGACAACAT
Found at i:371503 original size:49 final size:49
Alignment explanation
Indices: 371446--371543 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
371436 ATCTTTGGAT
*
371446 TTGGGTATAATTTTAAATTTACTTTT-TGATTTTAATTATATATTAATAA
1 TTGGGTATAATTTTAAATTTAATTTTCT-ATTTTAATTATATATTAATAA
371495 TTGGGTATAATTTTAAATTTAATTTTCTATTTTAATTATATATTAATAA
1 TTGGGTATAATTTTAAATTTAATTTTCTATTTTAATTATATATTAATAA
371544 AATAATAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 46 0.98
50 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (49 bp):
TTGGGTATAATTTTAAATTTAATTTTCTATTTTAATTATATATTAATAA
Found at i:375323 original size:18 final size:18
Alignment explanation
Indices: 375297--375334 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
375287 GTCGAATAGT
375297 CCTTCTTCTTCTCCTTTC
1 CCTTCTTCTTCTCCTTTC
* *
375315 CCTTGTTCTTCTTCTTTC
1 CCTTCTTCTTCTCCTTTC
375333 CC
1 CC
375335 GGCTCTCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.42, G:0.03, T:0.55
Consensus pattern (18 bp):
CCTTCTTCTTCTCCTTTC
Found at i:382836 original size:8 final size:8
Alignment explanation
Indices: 382798--382824 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
382788 CTTATTAAAA
382798 TTAAAATT
1 TTAAAATT
382806 TTAAAATT
1 TTAAAATT
382814 TTAAAATT
1 TTAAAATT
382822 TTA
1 TTA
382825 TTTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTAAAATT
Done.