Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002663.1 Hibiscus syriacus cultivar Beakdansim tig00005465_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: 975815
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 4
Found at i:249009 original size:63 final size:63
Alignment explanation
Indices: 248941--249064 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
248931 CGTGGTGAGT
* *
248941 CGGGTCCATGAAATAATTTTTCATTAATTCATTTCACAATTACTAGATTAATCAGAAATAACA
1 CGGGTCCATAAAATAATTTCTCATTAATTCATTTCACAATTACTAGATTAATCAGAAATAACA
* **
249004 CGGGTCTATAAAATAATTTCTCATTAATTTGTTTCACAATTACTAGATTAATCAGAAATAA
1 CGGGTCCATAAAATAATTTCTCATTAATTCATTTCACAATTACTAGATTAATCAGAAATAA
249065 TAACGTAGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.36
Consensus pattern (63 bp):
CGGGTCCATAAAATAATTTCTCATTAATTCATTTCACAATTACTAGATTAATCAGAAATAACA
Found at i:268864 original size:29 final size:31
Alignment explanation
Indices: 268789--268864 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 31
268779 CGTCATTAAC
268789 AATTTAAT-GATATAATTGAAACAAAAAATCAA
1 AATTTAATAG-TATAATT-AAACAAAAAATCAA
* * *
268821 AATCTAGTA-TCATAATT-AAC-AAAAATGAA
1 AATTTAATAGT-ATAATTAAACAAAAAATCAA
268850 AATTTAATAGTATAA
1 AATTTAATAGTATAA
268865 ACTATACAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
29 19 0.53
30 4 0.11
31 1 0.03
32 12 0.33
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (31 bp):
AATTTAATAGTATAATTAAACAAAAAATCAA
Found at i:271998 original size:7 final size:7
Alignment explanation
Indices: 271987--272022 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
271977 CCCCCACCCC
271987 CTCCCTT
1 CTCCCTT
*
271994 TTCCCTT
1 CTCCCTT
272001 CTCCCTT
1 CTCCCTT
272008 CTCCCTT
1 CTCCCTT
272015 CTCCCTT
1 CTCCCTT
272022 C
1 C
272023 CCCAACACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (7 bp):
CTCCCTT
Found at i:272442 original size:23 final size:22
Alignment explanation
Indices: 272415--272459 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
272405 ATTTATAAAA
272415 GATAAACAAATAAAAAATATAAT
1 GATAAACAAAT-AAAAATATAAT
**
272438 GATAAACATCTAAAAATATAAT
1 GATAAACAAATAAAAATATAAT
272460 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.24
Consensus pattern (22 bp):
GATAAACAAATAAAAATATAAT
Found at i:275482 original size:220 final size:220
Alignment explanation
Indices: 275100--275541 Score: 875
Period size: 220 Copynumber: 2.0 Consensus size: 220
275090 CAGTCGTATA
275100 CAAAAGTTAACATGCTCGATATCAACATACACTACTGATTATTTCAAGCTATATTACTACATCAG
1 CAAAAGTTAACATGCTCGATATCAACATACACTACTGATTATTTCAAGCTATATTACTACATCAG
*
275165 GCCAGGAAGCCAAAGAAGGAAAAACCATCCCACAAGGCCATGAATTCGGTTTTCACAGATCGAAA
66 GCCAGGAAGCCAAAGAAGGAAAAACCATCCCACAAGGCCATGAACTCGGTTTTCACAGATCGAAA
275230 ATTAGTTTGCAATCAAGGAAATAACCAAGAACACTCACGATCGGTGGAAAAACCATCCCACAAGG
131 ATTAGTTTGCAATCAAGGAAATAACCAAGAACACTCACGATCGGTGGAAAAACCATCCCACAAGG
275295 TCATGAACTCAGTTTTCATAATAGC
196 TCATGAACTCAGTTTTCATAATAGC
275320 CAAAAGTTAACATGCTCGATATCAACATACACTACTGATTATTTCAAGCTATATTACTACATCAG
1 CAAAAGTTAACATGCTCGATATCAACATACACTACTGATTATTTCAAGCTATATTACTACATCAG
275385 GCCAGGAAGCCAAAGAAGGAAAAACCATCCCACAAGGCCATGAACTCGGTTTTCACAGATCGAAA
66 GCCAGGAAGCCAAAGAAGGAAAAACCATCCCACAAGGCCATGAACTCGGTTTTCACAGATCGAAA
275450 ATTAGTTTGCAATCAAGGAAATAACCAAGAACACTCACGATCGGTGGAAAAACCATCCCACAAGG
131 ATTAGTTTGCAATCAAGGAAATAACCAAGAACACTCACGATCGGTGGAAAAACCATCCCACAAGG
275515 TCATGAACTCAGTTTTCATAATAGC
196 TCATGAACTCAGTTTTCATAATAGC
275540 CA
1 CA
275542 TTGTATCCTG
Statistics
Matches: 221, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 221 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (220 bp):
CAAAAGTTAACATGCTCGATATCAACATACACTACTGATTATTTCAAGCTATATTACTACATCAG
GCCAGGAAGCCAAAGAAGGAAAAACCATCCCACAAGGCCATGAACTCGGTTTTCACAGATCGAAA
ATTAGTTTGCAATCAAGGAAATAACCAAGAACACTCACGATCGGTGGAAAAACCATCCCACAAGG
TCATGAACTCAGTTTTCATAATAGC
Found at i:282197 original size:127 final size:127
Alignment explanation
Indices: 281971--282225 Score: 492
Period size: 127 Copynumber: 2.0 Consensus size: 127
281961 ATTAATTTAA
*
281971 TAAATTTAATCATTCGTATTTAAAAATTCTATCAATTTAGTACTTTTTCCTCTCTTAAATGGCAT
1 TAAATTTAATCATTCGTATTTAAAAATTCTATCAATTTAGTACTTTTTCCTCTCTTAAATGACAT
282036 ATTCTTCATTGTTCATCATCATCATCCATACTTGGTACTCTTATTAATCACTAGTTAAATTT
66 ATTCTTCATTGTTCATCATCATCATCCATACTTGGTACTCTTATTAATCACTAGTTAAATTT
282098 TAAATTTAATCATTCGTATTTAAAAATTCTATCAATTTAGTACTTTTTCCTCTCTTAAATGACAT
1 TAAATTTAATCATTCGTATTTAAAAATTCTATCAATTTAGTACTTTTTCCTCTCTTAAATGACAT
*
282163 ATTCTTCATTGTTCATCATCATCATCCATACTTGGTACTCTTATTAATCACTAGTTAACTTT
66 ATTCTTCATTGTTCATCATCATCATCCATACTTGGTACTCTTATTAATCACTAGTTAAATTT
282225 T
1 T
282226 TAATGTTAGA
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.46
Consensus pattern (127 bp):
TAAATTTAATCATTCGTATTTAAAAATTCTATCAATTTAGTACTTTTTCCTCTCTTAAATGACAT
ATTCTTCATTGTTCATCATCATCATCCATACTTGGTACTCTTATTAATCACTAGTTAAATTT
Found at i:282542 original size:20 final size:20
Alignment explanation
Indices: 282517--282567 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
282507 ACTTAATACT
282517 CAACTCAAAAAGTTCACGAG
1 CAACTCAAAAAGTTCACGAG
* *
282537 CAACTCGAAAAGTTCTCGAG
1 CAACTCAAAAAGTTCACGAG
*
282557 TAACTCGAAAA
1 CAACTC-AAAA
282568 TATAATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (20 bp):
CAACTCAAAAAGTTCACGAG
Found at i:291467 original size:20 final size:21
Alignment explanation
Indices: 291444--291541 Score: 93
Period size: 20 Copynumber: 4.9 Consensus size: 21
291434 TTTCAATTTT
291444 GCAACGCGAATATGT-AAA-TC
1 GCAACGCGAATA-GTCAAATTC
*
291464 GCAACGCGAATTTGT-AAA-TC
1 GCAACGCGAA-TAGTCAAATTC
* *
291484 ACAACGCGGA-AGTCAAATTC
1 GCAACGCGAATAGTCAAATTC
291504 GCAACGC-AATAGTCAAATTC
1 GCAACGCGAATAGTCAAATTC
*
291524 GCAACGCCAA-AGTCAAAT
1 GCAACGCGAATAGTCAAAT
291542 GTTTTTATGT
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 58 0.87
21 3 0.04
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.18
Consensus pattern (21 bp):
GCAACGCGAATAGTCAAATTC
Found at i:293638 original size:45 final size:45
Alignment explanation
Indices: 293584--293692 Score: 200
Period size: 45 Copynumber: 2.4 Consensus size: 45
293574 CCATCACCTG
293584 ATCGAGCCTCTTCTCCACCTCCACCATCACCTATTCCATCACAGC
1 ATCGAGCCTCTTCTCCACCTCCACCATCACCTATTCCATCACAGC
* *
293629 ATCGAGCCTCTTCTCCACCTCTACCATCACCTATTCCATCACATC
1 ATCGAGCCTCTTCTCCACCTCCACCATCACCTATTCCATCACAGC
293674 ATCGAGCCTCTTCTCCACC
1 ATCGAGCCTCTTCTCCACC
293693 ATCACCTCAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.21, C:0.46, G:0.06, T:0.27
Consensus pattern (45 bp):
ATCGAGCCTCTTCTCCACCTCCACCATCACCTATTCCATCACAGC
Found at i:294311 original size:21 final size:21
Alignment explanation
Indices: 294282--294329 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
294272 TTCATCATCG
*
294282 AAGAAGCCCCTCTCA-CTGTTC
1 AAGAGGCCCCTCTCATC-GTTC
*
294303 AAGAGGCCCCTGTCATCGTTC
1 AAGAGGCCCCTCTCATCGTTC
294324 AAGAGG
1 AAGAGG
294330 TCTCGTCCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (21 bp):
AAGAGGCCCCTCTCATCGTTC
Found at i:295801 original size:61 final size:62
Alignment explanation
Indices: 295699--295838 Score: 185
Period size: 66 Copynumber: 2.2 Consensus size: 62
295689 TTTTACATTG
*
295699 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
* * * *
295759 AAAGTTGATTTGTTTAATTTGATGTGTAAATAATAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAATTGATTTGT
295824 A
62 A
295825 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
295839 GTTTCTAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
60 17 0.25
61 17 0.25
64 4 0.06
66 31 0.45
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:295944 original size:20 final size:20
Alignment explanation
Indices: 295921--296017 Score: 98
Period size: 20 Copynumber: 5.2 Consensus size: 20
295911 GATTTTCGGT
295921 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
* *
295941 TTGCGAATTTGTCTATCGC-
1 TTGCGAATTTGACTTTCGCG
** *
295960 -AACG--CTT-A-TTTCGCG
1 TTGCGAATTTGACTTTCGCG
295975 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
295995 TTGCGAATTTAACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
296015 TTG
1 TTG
296018 ATCGCAACAT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
14 5 0.08
16 4 0.07
18 4 0.07
19 1 0.02
20 46 0.77
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:296221 original size:20 final size:20
Alignment explanation
Indices: 296196--296262 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
296186 AGTTGTAGAT
*
296196 TTTGACTATCGCATTGCGAA
1 TTTGACTATCGCGTTGCGAA
*
296216 TTTGACTATCGTGTTGCGAA
1 TTTGACTATCGCGTTGCGAA
* *
296236 TTTGAGTATCGCGTTTCGAA
1 TTTGACTATCGCGTTGCGAA
296256 TTTGACT
1 TTTGACT
296263 TATGTGTTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (20 bp):
TTTGACTATCGCGTTGCGAA
Found at i:296256 original size:40 final size:40
Alignment explanation
Indices: 296196--296274 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
296186 AGTTGTAGAT
296196 TTTGACTATCGCATTGCGAATTTGAC-TATCGTGTTGCGAA
1 TTTGACTATCGCATTGCGAATTTGACTTAT-GTGTTGCGAA
* * *
296236 TTTGAGTATCGCGTTTCGAATTTGACTTATGTGTTGCGA
1 TTTGACTATCGCATTGCGAATTTGACTTATGTGTTGCGA
296275 TTTACAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 32 0.91
41 3 0.09
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (40 bp):
TTTGACTATCGCATTGCGAATTTGACTTATGTGTTGCGAA
Found at i:296760 original size:35 final size:34
Alignment explanation
Indices: 296679--296766 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
296669 AATTAACGTT
* **
296679 TAGCCCAATTCACGTTTTATGTGCATTTTAACCA
1 TAGCCCAATTCACGTTTTATGTGCACTGAAACCA
**
296713 TAGCCCAATTCACGTTTTATGTGCACTGAAA-TT
1 TAGCCCAATTCACGTTTTATGTGCACTGAAACCA
296746 TGAAGCCCAATTCACGTTTTA
1 T--AGCCCAATTCACGTTTTA
296767 ATTTGATGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
33 1 0.02
34 28 0.60
35 18 0.38
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (34 bp):
TAGCCCAATTCACGTTTTATGTGCACTGAAACCA
Found at i:298407 original size:35 final size:35
Alignment explanation
Indices: 298227--298415 Score: 142
Period size: 36 Copynumber: 5.4 Consensus size: 35
298217 AATATTCTAA
* *
298227 ATTAAAAGATATTTATTATCTCTTTACATTTAAAT
1 ATTAAAAGATATTTATTATCTTTTTAAATTTAAAT
* * *
298262 ATTAATAGGATAATTA-TATCCTTTTAAATATCTTAAA-
1 ATTAA-AAGATATTTATTAT-CTTTTTAA-AT-TTAAAT
* *
298299 A-TAAAA-ATATTTATTATATTTTT-AATTATGAAT
1 ATTAAAAGATATTTATTATCTTTTTAAATT-TAAAT
* * *
298332 ATTAAAAGGATA-TTAATATCTTTTCGAATATTTTAA-
1 ATTAAAA-GATATTTATTATCTTTT-TAA-ATTTAAAT
*
298368 ATTAAAATATATTTATTATCTTTTTAAATTTAAAT
1 ATTAAAAGATATTTATTATCTTTTTAAATTTAAAT
298403 ATTAATAA-ATATT
1 ATTAA-AAGATATT
298416 AAAAATATAT
Statistics
Matches: 120, Mismatches: 18, Indels: 32
0.71 0.11 0.19
Matches are distributed among these distances:
31 1 0.01
32 5 0.04
33 2 0.02
34 21 0.17
35 37 0.31
36 39 0.32
37 7 0.06
38 8 0.07
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (35 bp):
ATTAAAAGATATTTATTATCTTTTTAAATTTAAAT
Found at i:298407 original size:71 final size:70
Alignment explanation
Indices: 298216--298407 Score: 237
Period size: 70 Copynumber: 2.7 Consensus size: 70
298206 TTCATTGATG
* * * *
298216 GAATATTCTAAATTAAAAGATATTTATTATCTCTTTACATTTAAATATTAATAGGATAATTATAT
1 GAATATTTTAAATTAAAA-ATATTTATTATCTTTTTAAATTTAAATATTAAAAGGATAATTATAT
298281 CCTTTT
65 CCTTTT
* * * * *
298287 AAATATCTTAAAATAAAAATATTTATTATATTTTT-AATTATGAATATTAAAAGGAT-ATTAATA
1 GAATATTTTAAATTAAAAATATTTATTATCTTTTTAAATT-TAAATATTAAAAGGATAATT-ATA
298350 T-CTTTT
64 TCCTTTT
298356 CGAATATTTTAAATTAAAATATATTTATTATCTTTTTAAATTTAAATATTAA
1 -GAATATTTTAAATTAAAA-ATATTTATTATCTTTTTAAATTTAAATATTAA
298408 TAAATATTAA
Statistics
Matches: 102, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
69 11 0.11
70 48 0.47
71 39 0.38
72 4 0.04
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (70 bp):
GAATATTTTAAATTAAAAATATTTATTATCTTTTTAAATTTAAATATTAAAAGGATAATTATATC
CTTTT
Found at i:303829 original size:34 final size:33
Alignment explanation
Indices: 303753--303859 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
303743 GTGGTAAGAA
* *
303753 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
303787 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
303822 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
303856 ATTT
1 ATTT
303860 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:303841 original size:36 final size:34
Alignment explanation
Indices: 303786--303864 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
303776 TTTAAATAGT
*
303786 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
303818 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
303852 TATTATTTATTTA
1 TATTATTTTTTTA
303865 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:304026 original size:17 final size:17
Alignment explanation
Indices: 303984--304032 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
303974 TGGTAATATT
*
303984 TTTTATAATTTATGTTAA
1 TTTTA-AATTTATTTTAA
*
304002 TATTTAAATTTATTTTTA
1 T-TTTAAATTTATTTTAA
*
304020 TTTTAAAGTTATT
1 TTTTAAATTTATT
304033 ATGAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 11 0.41
18 12 0.44
19 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTTAAATTTATTTTAA
Found at i:305671 original size:21 final size:21
Alignment explanation
Indices: 305643--305736 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
305633 TATGCCATCT
*
305643 CCGCAGGGTTACATTTCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
305664 CTGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
305685 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
305706 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
305727 CCGCAGGGTT
1 CCGCAGGGTT
305737 TTATACCATA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 2 0.03
21 62 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:309992 original size:21 final size:21
Alignment explanation
Indices: 309959--310029 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
309949 CGCGAATATG
*
309959 TAAA-TCGCATTGCGATTTTC
1 TAAATTCGCGTTGCGATTTTC
309979 TAAATTCGCGTTGCGATTTTC
1 TAAATTCGCGTTGCGATTTTC
*
310000 TAAATTCGCGTTACGATTTTC
1 TAAATTCGCGTTGCGATTTTC
310021 TAAATTCGC
1 TAAATTCGC
310030 AACGCGATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 4 0.08
21 44 0.92
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (21 bp):
TAAATTCGCGTTGCGATTTTC
Found at i:310037 original size:21 final size:21
Alignment explanation
Indices: 309919--310037 Score: 80
Period size: 21 Copynumber: 5.8 Consensus size: 21
309909 AATGGCCAAC
* * *
309919 AAATTCACAACGCGA-ATTCC
1 AAATTCGCAACGCGATTTTCT
* * * *
309939 AATTTCGCAACGCGAATATGT
1 AAATTCGCAACGCGATTTTCT
**
309960 AAA-TCGCATTGCGATTTTCT
1 AAATTCGCAACGCGATTTTCT
***
309980 AAATTCGCGTTGCGATTTTCT
1 AAATTCGCAACGCGATTTTCT
****
310001 AAATTCGCGTTACGATTTTCT
1 AAATTCGCAACGCGATTTTCT
310022 AAATTCGCAACGCGAT
1 AAATTCGCAACGCGAT
310038 AGTCAAATTC
Statistics
Matches: 79, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
20 28 0.35
21 51 0.65
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (21 bp):
AAATTCGCAACGCGATTTTCT
Found at i:310037 original size:42 final size:41
Alignment explanation
Indices: 309942--310037 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 41
309932 GAATTCCAAT
* * *
309942 TTCGCAACGCGAATATGTAAATCGCATTGCGATTTTCTAAA
1 TTCGCAACGCGATTATCTAAATCGCATTACGATTTTCTAAA
*** * *
309983 TTCGCGTTGCGATTTTCTAAATTCGCGTTACGATTTTCTAAA
1 TTCGCAACGCGATTATCTAAA-TCGCATTACGATTTTCTAAA
310025 TTCGCAACGCGAT
1 TTCGCAACGCGAT
310038 AGTCAAATTC
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
41 15 0.35
42 28 0.65
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (41 bp):
TTCGCAACGCGATTATCTAAATCGCATTACGATTTTCTAAA
Found at i:310047 original size:20 final size:20
Alignment explanation
Indices: 310022--310072 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
310012 ACGATTTTCT
*
310022 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACGCGAAAGTC
* *
310042 AAATTCTCAATGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
310062 AAATTCGCAAC
1 AAATTCGCAAC
310073 TGAATTTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.22
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:310084 original size:19 final size:19
Alignment explanation
Indices: 310060--310110 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
310050 AATGCGAAAG
310060 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
310079 TCAAATTCACAACTGAATT
1 TCAAATTCGCAACTGAATT
310098 TCAAATTCGCAAC
1 TCAAATTCGCAAC
310111 AGGTTTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:310875 original size:12 final size:12
Alignment explanation
Indices: 310854--310887 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
310844 ACCACATTTC
*
310854 CAATACCAAACA
1 CAATATCAAACA
310866 CAATATCAAACA
1 CAATATCAAACA
*
310878 CAATCTCAAA
1 CAATATCAAA
310888 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:313673 original size:20 final size:20
Alignment explanation
Indices: 313645--313706 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
313635 CGCGAAATAA
313645 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
* *
313665 GCGTAGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATC
313685 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
313705 GC
1 GC
313707 AACGCTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:313835 original size:25 final size:25
Alignment explanation
Indices: 313797--313846 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
313787 AAATCAATTA
*
313797 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
313822 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
313847 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:314275 original size:24 final size:24
Alignment explanation
Indices: 314224--314275 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
314214 TTTCATATGT
* *
314224 AATTGGAGTTTGAATTTAAATTTC
1 AATTGGAGTTTGAATTTAAATATA
*
314248 AATTGGAGTTTGAATTTCAATATA
1 AATTGGAGTTTGAATTTAAATATA
314272 AATT
1 AATT
314276 TTGACTCCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (24 bp):
AATTGGAGTTTGAATTTAAATATA
Found at i:316419 original size:21 final size:21
Alignment explanation
Indices: 316395--316490 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
316385 GGCGGGACCA
*
316395 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * *
316416 CTTGAACGGTGAGAGGAGCTT
1 CTTGAACGATGAGAGGGGCCT
* *
316437 CTTCG-ATGATGATAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
*
316458 CTTGAACGAT-AGGAGGCGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
316479 CTTGAATGATGA
1 CTTGAACGATGA
316491 TAGGTGCATC
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 2 0.03
21 54 0.93
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:316488 original size:42 final size:42
Alignment explanation
Indices: 316395--316494 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
316385 GGCGGGACCA
* * * *
316395 CTTGAACGATGACAGGGGCCTCTTGAACGGTGAGAGGAGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACGATGAGAGGAGCCT
*
316437 CTTCG-ATGATGATAGGGGCCTCTTGAACGAT-AGGAGGCGCCT
1 CTT-GAATGATGATAGGGGCCTCTTGAACGATGA-GAGGAGCCT
316479 CTTGAATGATGATAGG
1 CTTGAATGATGATAGG
316495 TGCATCGGGC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
41 2 0.04
42 47 0.94
43 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACGATGAGAGGAGCCT
Found at i:328479 original size:95 final size:93
Alignment explanation
Indices: 328305--328480 Score: 255
Period size: 95 Copynumber: 1.8 Consensus size: 93
328295 CCAAGAAAAA
*
328305 TATTATTTTTAAATAATTTGTAATATTAATTAAAAAATTTAAATTAAAAAAATGATGGAATTCGT
1 TATTATTTTTAAATAATTTGTAATATTAATTAAAAAA--TAAATTAAAAAAATGATAGAATTCGT
* *
328370 CTCTTCGAGATGACGACTCGCTTAAGAAAT
64 CTCCTCAAGATGACGACTCGCTTAAGAAAT
*
328400 TATTATTTTTAAATAATTTGTAATATTAATTTAAAAA-AAATTAAAAAAAAGGTGATAGAATTCG
1 TATTATTTTTAAATAATTTGTAATATTAATTAAAAAATAAATT-AAAAAAA--TGATAGAATTCG
*
328464 TCTCCTCAAGGTGACGA
63 TCTCCTCAAGATGACGA
328481 GTCCCGCCTG
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
92 5 0.07
93 7 0.10
95 61 0.84
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (93 bp):
TATTATTTTTAAATAATTTGTAATATTAATTAAAAAATAAATTAAAAAAATGATAGAATTCGTCT
CCTCAAGATGACGACTCGCTTAAGAAAT
Found at i:328639 original size:18 final size:17
Alignment explanation
Indices: 328606--328641 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
328596 GGATTCAATT
*
328606 TTAAAAAAATATATTAA
1 TTAAAAAAATAAATTAA
328623 TTAAAAAAGATAAATTAA
1 TTAAAAAA-ATAAATTAA
328641 T
1 T
328642 AATTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAAAAAAATAAATTAA
Found at i:335894 original size:24 final size:24
Alignment explanation
Indices: 335864--335945 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 24
335854 GTATAAATTA
335864 CACCGAAGTGTCACGTAGAATTTG
1 CACCGAAGTGTCACGTAGAATTTG
* * *
335888 TC-TCGAAG-GATCGCATAGAAATTTG
1 -CACCGAAGTG-TCACGTAG-AATTTG
*
335913 CACCGAAGTGCCACGTAGAA-TTG
1 CACCGAAGTGTCACGTAGAATTTG
*
335936 CACCGTAGTG
1 CACCGAAGTG
335946 CCATAGAAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
23 13 0.29
24 14 0.31
25 17 0.38
26 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (24 bp):
CACCGAAGTGTCACGTAGAATTTG
Found at i:335958 original size:23 final size:22
Alignment explanation
Indices: 335901--335958 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
335891 CGAAGGATCG
335901 CATAGAAATTTGCACCGAAGTGC
1 CATAGAAA-TTGCACCGAAGTGC
*
335924 CACGTAG-AATTGCACCGTAGTGC
1 CA--TAGAAATTGCACCGAAGTGC
335947 CATAGAAGATTG
1 CATAGAA-ATTG
335959 TCCATAAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 3 0.10
22 1 0.03
23 21 0.70
24 2 0.07
25 3 0.10
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (22 bp):
CATAGAAATTGCACCGAAGTGC
Found at i:336223 original size:30 final size:31
Alignment explanation
Indices: 336180--336252 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
336170 TTCACATAGT
* *
336180 TTTATCGCGTAGACATATCA-TTTCCATACC
1 TTTATCACATAGACATATCATTTTCCATACC
336210 TTTATCACATAGACATATCATTTTCCATACC
1 TTTATCACATAGACATATCATTTTCCATACC
*
336241 TTTATTACATAG
1 TTTATCACATAG
336253 CTCATATAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 18 0.46
31 21 0.54
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (31 bp):
TTTATCACATAGACATATCATTTTCCATACC
Found at i:337325 original size:8 final size:8
Alignment explanation
Indices: 337312--337337 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
337302 TTGCTCAATG
337312 ACCCTTTT
1 ACCCTTTT
337320 ACCCTTTT
1 ACCCTTTT
337328 ACCCTTTT
1 ACCCTTTT
337336 AC
1 AC
337338 TTCTCCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (8 bp):
ACCCTTTT
Found at i:339639 original size:30 final size:31
Alignment explanation
Indices: 339605--339668 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
339595 TTATATCGCG
339605 TAGACATATCA-TTTCCATACCTTTATCACA
1 TAGACATATCATTTTCCATACCTTTATCACA
*
339635 TAGACATATCATTTTCTATACCTTTATCACA
1 TAGACATATCATTTTCCATACCTTTATCACA
339666 TAG
1 TAG
339669 CTCATATAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (31 bp):
TAGACATATCATTTTCCATACCTTTATCACA
Found at i:348931 original size:46 final size:46
Alignment explanation
Indices: 348864--348961 Score: 196
Period size: 46 Copynumber: 2.1 Consensus size: 46
348854 AATGATTAAT
348864 AAAGATTCTGAATGGATATTATCTTTTAATTATCTTAAATTATTTA
1 AAAGATTCTGAATGGATATTATCTTTTAATTATCTTAAATTATTTA
348910 AAAGATTCTGAATGGATATTATCTTTTAATTATCTTAAATTATTTA
1 AAAGATTCTGAATGGATATTATCTTTTAATTATCTTAAATTATTTA
348956 AAAGAT
1 AAAGAT
348962 ATTTAATTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (46 bp):
AAAGATTCTGAATGGATATTATCTTTTAATTATCTTAAATTATTTA
Found at i:361083 original size:2 final size:2
Alignment explanation
Indices: 361078--361110 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
361068 TTTTAACATA
*
361078 AT AT AT AT AT AT AT AT GT 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 A
361111 AATGAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:361169 original size:22 final size:24
Alignment explanation
Indices: 361123--361172 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
361113 TGAAAATGAA
*
361123 AATAAAATATTTTTCAATTAAGTT
1 AATAAAATATATTTCAATTAAGTT
361147 AATAAAATATATTT-AA-TAAGTT
1 AATAAAATATATTTCAATTAAGTT
361169 AATA
1 AATA
361173 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.40
23 2 0.08
24 13 0.52
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
AATAAAATATATTTCAATTAAGTT
Found at i:361175 original size:24 final size:23
Alignment explanation
Indices: 361124--361198 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 23
361114 GAAAATGAAA
*
361124 ATAAAATATTTTTCAATTAAGTTA-
1 ATAAAATATATTT-AA-TAAGTTAT
361148 ATAAAATATATTTAATAAGTTAAT
1 ATAAAATATATTTAATAAGTT-AT
* **
361172 ATAAAAAATATTTTTTAAGTTCAT
1 ATAAAATATATTTAATAAGTT-AT
361196 ATA
1 ATA
361199 TATAAAAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 6 0.14
23 3 0.07
24 35 0.80
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (23 bp):
ATAAAATATATTTAATAAGTTAT
Found at i:361205 original size:26 final size:25
Alignment explanation
Indices: 361124--361205 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 25
361114 GAAAATGAAA
*
361124 ATAAAATATTTTTCAA-TTA-AGT-T
1 ATAAAATATTTTTTAAGTTATA-TAT
*
361147 AATAAAATATATTTAATAAGTTA-ATAT
1 -ATAAAATAT-TTT-TTAAGTTATATAT
*
361174 AAAAAATATTTTTTAAGTTCATATAT
1 ATAAAATATTTTTTAAGTT-ATATAT
361200 ATAAAA
1 ATAAAA
361206 AAGTATGGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
24 15 0.32
25 7 0.15
26 20 0.43
27 5 0.11
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (25 bp):
ATAAAATATTTTTTAAGTTATATAT
Found at i:365706 original size:3 final size:3
Alignment explanation
Indices: 365698--365722 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
365688 AATAAGGGTC
365698 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
365723 GGATTCTAAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:366569 original size:22 final size:22
Alignment explanation
Indices: 366528--366595 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
366518 CTCGTATAAA
366528 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
366551 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
366573 TACACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
366595 T
1 T
366596 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 32 0.73
23 12 0.27
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:367367 original size:2 final size:2
Alignment explanation
Indices: 367355--367388 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
367345 ATTTCATTTC
*
367355 AT AT CT 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
367389 CCTCAAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:367645 original size:18 final size:18
Alignment explanation
Indices: 367624--367658 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
367614 TCCCATCTAG
367624 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
367642 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
367659 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:368244 original size:21 final size:21
Alignment explanation
Indices: 368220--368264 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
368210 TCTTGTTCGT
* *
368220 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
368241 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
368262 TTG
1 TTG
368265 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:371440 original size:22 final size:22
Alignment explanation
Indices: 371399--371466 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
371389 CTCGTATAAA
371399 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
371422 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
371444 TACACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
371466 T
1 T
371467 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 32 0.73
23 12 0.27
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:372228 original size:2 final size:2
Alignment explanation
Indices: 372221--372245 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
372211 TTCATTCATT
372221 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
372246 CCTCAAGATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:372503 original size:18 final size:18
Alignment explanation
Indices: 372482--372516 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
372472 TCCCATCTAG
372482 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
372500 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
372517 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:373102 original size:21 final size:21
Alignment explanation
Indices: 373078--373122 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
373068 TCTTGTTCGT
* *
373078 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
373099 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
373120 TTG
1 TTG
373123 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:374164 original size:39 final size:39
Alignment explanation
Indices: 374104--374304 Score: 208
Period size: 39 Copynumber: 5.2 Consensus size: 39
374094 TCTATGACTT
* * *
374104 GTAAGATCTTA-CTGCAGGCTCCTCTGTTTTGTGCTCAGG
1 GTAAGTTCTTATC-GCAAGCTCCTCTGCTTTGTGCTCAGG
* *
374143 GTAAGTTCTTATCGTAAGCTCCTATGCTTTGTGCTCAGG
1 GTAAGTTCTTATCGCAAGCTCCTCTGCTTTGTGCTCAGG
* * * *
374182 GTAAGTTCTTATCGTAGGCTCTTCTACTTTGTGCTCAGG
1 GTAAGTTCTTATCGCAAGCTCCTCTGCTTTGTGCTCAGG
* * * * *
374221 GTAAGTCCTTATCGCAGGTTCCTCTACTTTGTGTTCAGG
1 GTAAGTTCTTATCGCAAGCTCCTCTGCTTTGTGCTCAGG
* * * *
374260 GTATG-TCTTTACCGCAAGCTTCTCTGCTTTGTGCACAGG
1 GTAAGTTC-TTATCGCAAGCTCCTCTGCTTTGTGCTCAGG
374299 GTAAGT
1 GTAAGT
374305 CATTACCGCA
Statistics
Matches: 135, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
38 1 0.01
39 133 0.99
40 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (39 bp):
GTAAGTTCTTATCGCAAGCTCCTCTGCTTTGTGCTCAGG
Found at i:376172 original size:17 final size:18
Alignment explanation
Indices: 376133--376177 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
376123 ATGTTCTATG
376133 TTTAAGTTATTAATCAAC
1 TTTAAGTTATTAATCAAC
* *
376151 TTTAAATTATTAAT-ATC
1 TTTAAGTTATTAATCAAC
376168 TTTAAGTTAT
1 TTTAAGTTAT
376178 CCTTGAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (18 bp):
TTTAAGTTATTAATCAAC
Found at i:380910 original size:10 final size:10
Alignment explanation
Indices: 380895--380968 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
380885 CATTTAATAA
380895 ATAAACGAAC
1 ATAAACGAAC
380905 ATAAACGAAC
1 ATAAACGAAC
*
380915 ----ACAAAC
1 ATAAACGAAC
380921 ATAAACGAAC
1 ATAAACGAAC
** *
380931 ACGAAC-ATAA
1 ATAAACGA-AC
380941 ATGAACACGAAC
1 AT-AA-ACGAAC
380953 ATAAACGAAC
1 ATAAACGAAC
380963 ATAAAC
1 ATAAAC
380969 ATTGGACCCT
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 33 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.22, G:0.09, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:380923 original size:16 final size:16
Alignment explanation
Indices: 380902--380970 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
380892 TAAATAAACG
380902 AACATAAACGAACACA
1 AACATAAACGAACACA
*
380918 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
380934 AACATAAATGAACACG
1 AACATAAACGAACACA
*
380950 AACATAAACGAACATA
1 AACATAAACGAACACA
380966 AACAT
1 AACAT
380971 TGGACCCTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.59, C:0.22, G:0.09, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:381661 original size:38 final size:38
Alignment explanation
Indices: 381619--381693 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
381609 TAAATGAATG
381619 AACATAAACGAACATAACCGAACAAACATAACCGAACA
1 AACATAAACGAACATAACCGAACAAACATAACCGAACA
* * *
381657 AACATAAACGAACATAACTGAACGAACATAACTGAAC
1 AACATAAACGAACATAACCGAACAAACATAACCGAAC
381694 GTTCACGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.56, C:0.24, G:0.09, T:0.11
Consensus pattern (38 bp):
AACATAAACGAACATAACCGAACAAACATAACCGAACA
Found at i:381680 original size:14 final size:14
Alignment explanation
Indices: 381625--381694 Score: 76
Period size: 14 Copynumber: 5.3 Consensus size: 14
381615 AATGAACATA
381625 AACGAACATAACCG
1 AACGAACATAACCG
*
381639 AACAAACATAACCG
1 AACGAACATAACCG
*
381653 AACAAACAT-A---
1 AACGAACATAACCG
*
381663 AACGAACATAACTG
1 AACGAACATAACCG
*
381677 AACGAACATAACTG
1 AACGAACATAACCG
381691 AACG
1 AACG
381695 TTCACGAACG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
10 8 0.16
11 1 0.02
13 1 0.02
14 40 0.80
ACGTcount: A:0.54, C:0.24, G:0.11, T:0.10
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:382691 original size:2 final size:2
Alignment explanation
Indices: 382684--382724 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
382674 CGGGTAAGAG
382684 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
382725 ATTTTGCGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:382936 original size:3 final size:3
Alignment explanation
Indices: 382928--382954 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
382918 ATGACCACCG
382928 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
382955 ATCATCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:387285 original size:35 final size:34
Alignment explanation
Indices: 387234--387326 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 34
387224 TGAAATTATT
*
387234 AAAATGTTTTTC-AAGTTTGGTAA-CCAACTTTG
1 AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG
** *
387266 AAAAAATGGTTTTCAAAGTTTGGTAAATGTATCTTTG
1 --AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTG
*
387303 AAAATGGTTTTCAAAATTTGGTAA
1 AAAATGGTTTTCAAAGTTTGGTAA
387327 ATGTTTCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
34 13 0.25
35 30 0.59
36 2 0.04
37 6 0.12
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG
Found at i:387327 original size:35 final size:35
Alignment explanation
Indices: 387268--387341 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
387258 CAACTTTGAA
*
387268 AAAATGGTTTTCAAAGTTTGGTAAATGTATCTTTG
1 AAAATGGTTTTCAAAATTTGGTAAATGTATCTTTG
*
387303 AAAATGGTTTTCAAAATTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAATTTGGTAAATGTATCTTTG
387338 AAAA
1 AAAA
387342 ATAGTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (35 bp):
AAAATGGTTTTCAAAATTTGGTAAATGTATCTTTG
Found at i:387981 original size:7 final size:7
Alignment explanation
Indices: 387969--387999 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
387959 TCGATGGTGC
387969 GGATTTT
1 GGATTTT
387976 GGATTTT
1 GGATTTT
387983 GGATTTT
1 GGATTTT
387990 GGATTTT
1 GGATTTT
387997 GGA
1 GGA
388000 AGATGCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (7 bp):
GGATTTT
Found at i:394936 original size:15 final size:15
Alignment explanation
Indices: 394916--394997 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
394906 TTCCAGAAAA
394916 TGAATTACTGGAATT
1 TGAATTACTGGAATT
394931 TGAATTACTGGAATT
1 TGAATTACTGGAATT
* **
394946 TGAATTACTAGAAAA
1 TGAATTACTGGAATT
394961 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
394976 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
394990 TGAATTAC
1 TGAATTAC
394998 ATTTCTGTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:394950 original size:30 final size:30
Alignment explanation
Indices: 394916--394997 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
394906 TTCCAGAAAA
**
394916 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
*
394946 TGAATTACTAGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
394976 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
394998 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:394974 original size:45 final size:44
Alignment explanation
Indices: 394910--394997 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 44
394900 TTGGTTTTCC
**
394910 AGAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACT
1 AGAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACT
394955 AGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 AGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
394998 ATTTCTGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.34
45 27 0.66
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (44 bp):
AGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACT
Found at i:395003 original size:20 final size:20
Alignment explanation
Indices: 394980--395049 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
394970 GGAATTTGAA
394980 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
395000 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
395020 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
395040 TTCTGGAAAA
1 TTCTGGAAAA
395050 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:395266 original size:24 final size:24
Alignment explanation
Indices: 395210--395277 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
395200 CTTTACTAAA
*
395210 ATAT-TATTGAAATATATAAATAATT
1 ATATATATT-AAATATA-AAAAAATT
395235 AT-TCATATTAAATATAAAAAAATT
1 ATAT-ATATTAAATATAAAAAAATT
395259 ATATATATTAAA-ATAAAAA
1 ATATATATTAAATATAAAAA
395278 TATAATATCT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
23 7 0.18
24 18 0.46
25 10 0.26
26 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (24 bp):
ATATATATTAAATATAAAAAAATT
Found at i:395285 original size:23 final size:24
Alignment explanation
Indices: 395209--395285 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
395199 TCTTTACTAA
*
395209 AATAT-TATTGAAATATATAAATAAT
1 AATATATATT-AAATATA-AAAAAAT
*
395234 TAT-TCATATTAAATATAAAAAAAT
1 AATAT-ATATTAAATATAAAAAAAT
* *
395258 TATATATATTAAA-ATAAAAATAT
1 AATATATATTAAATATAAAAAAAT
395281 AATAT
1 AATAT
395286 CTTTATTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
23 13 0.29
24 18 0.40
25 10 0.22
26 4 0.09
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (24 bp):
AATATATATTAAATATAAAAAAAT
Found at i:395310 original size:50 final size:50
Alignment explanation
Indices: 395256--395350 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 50
395246 ATATAAAAAA
* *
395256 ATTATATATATTAAA-A-TAAAAATATAATATCT-TTATTATATATATAATTG
1 ATTAT-TATA-TAAATATTAAAAATA-AATATATATTATTATAAATATAATTG
*
395306 ATTATTTTATAAATATTAAAAATAAATATATATTATTATAAATAT
1 ATTATTATATAAATATTAAAAATAAATATATATTATTATAAATAT
395351 TAATAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
48 4 0.10
49 10 0.26
50 25 0.64
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (50 bp):
ATTATTATATAAATATTAAAAATAAATATATATTATTATAAATATAATTG
Found at i:395355 original size:26 final size:26
Alignment explanation
Indices: 395308--395360 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 26
395298 TATAATTGAT
395308 TATTTTATAAATATTAAAAATAAATATA
1 TATTTTATAAATATT--AAATAAATATA
395336 TATTATTATAAATATT-AATAAATAT
1 TATT-TTATAAATATTAAATAAATAT
395361 TTTAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 9 0.38
28 4 0.17
29 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TATTTTATAAATATTAAATAAATATA
Found at i:395374 original size:9 final size:9
Alignment explanation
Indices: 395312--395370 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
395302 ATTGATTATT
395312 TTATAAATA
1 TTATAAATA
*
395321 TTAAAAATAA
1 TTATAAAT-A
* *
395331 ATATATATTA
1 TTATA-AATA
395341 TTATAAATA
1 TTATAAATA
395350 TTAATAAATA
1 TT-ATAAATA
*
395360 TTTTAAATA
1 TTATAAATA
395369 TT
1 TT
395371 TTAATAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
9 20 0.50
10 18 0.45
11 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TTATAAATA
Found at i:395642 original size:41 final size:40
Alignment explanation
Indices: 395557--395673 Score: 173
Period size: 41 Copynumber: 2.9 Consensus size: 40
395547 ATGAATTACA
* *
395557 TTCCGGAAAACGAATTACGT-AAAACAAAACGGGAAATATT
1 TTCCGGAAAACGAATTACGTGAAAA-AACACGGGAAACATT
*
395597 TTCCGGAAAACGAAATACGTGAACAAAACACGGGAAACATT
1 TTCCGGAAAACGAATTACGTGAA-AAAACACGGGAAACATT
395638 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAA-AAACACGGGAA
395674 TTCGGGGAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
40 20 0.29
41 48 0.69
42 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (40 bp):
TTCCGGAAAACGAATTACGTGAAAAAACACGGGAAACATT
Found at i:402433 original size:19 final size:19
Alignment explanation
Indices: 402409--402446 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
402399 AGCTGCTATC
402409 GACCAATTTCTTTTGTAGT
1 GACCAATTTCTTTTGTAGT
402428 GACCAATTTCTTTTGTAGT
1 GACCAATTTCTTTTGTAGT
402447 TTAATGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (19 bp):
GACCAATTTCTTTTGTAGT
Found at i:411516 original size:30 final size:29
Alignment explanation
Indices: 411445--411529 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 29
411435 TTAAAAGTAT
411445 GTCC-CTAATAATAAATATTGAAAAATTG
1 GTCCACTAATAATAAATATTGAAAAATTG
* *
411473 GTCCACTAGTAATAAGTATTGAAAAAATTG
1 GTCCACTAATAATAAATATTG-AAAAATTG
** *
411503 AG-CCTTTAATAATAAATGTTAGAAAAA
1 -GTCCACTAATAATAAATATT-GAAAAA
411530 AATATTGGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 4 0.09
29 14 0.30
30 26 0.57
31 2 0.04
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (29 bp):
GTCCACTAATAATAAATATTGAAAAATTG
Found at i:411644 original size:32 final size:29
Alignment explanation
Indices: 411576--411659 Score: 107
Period size: 29 Copynumber: 2.8 Consensus size: 29
411566 AAAAAAATAA
* *
411576 ATTATAAAAATAAGCTCATAATAATAAAT
1 ATTAAAAAAATAAACTCATAATAATAAAT
*
411605 ATTAAAAAAATAAACTCATGATAATAAAT
1 ATTAAAAAAATAAACTCATAATAATAAAT
411634 ATTAGAAAAAATTAAAAC-CATAATAA
1 ATTA-AAAAAA-T-AAACTCATAATAA
411660 CAAGAATTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 30 0.62
30 6 0.12
31 8 0.17
32 4 0.08
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (29 bp):
ATTAAAAAAATAAACTCATAATAATAAAT
Found at i:415552 original size:25 final size:24
Alignment explanation
Indices: 415532--415604 Score: 112
Period size: 25 Copynumber: 3.0 Consensus size: 24
415522 AATATATTTT
*
415532 ATAAATAAGATTTTTTTTATAACA
1 ATAAATAAGATTTTTTTTATAATA
415556 ATAAATAAGATATTTTTTTATAATA
1 ATAAATAAGAT-TTTTTTTATAATA
*
415581 ATAAATAAGA-TATTTTTATAATA
1 ATAAATAAGATTTTTTTTATAATA
415604 A
1 A
415605 AAACCATTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
23 13 0.28
24 11 0.24
25 22 0.48
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (24 bp):
ATAAATAAGATTTTTTTTATAATA
Found at i:423953 original size:22 final size:24
Alignment explanation
Indices: 423913--423956 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
423903 ACTCGATTAG
423913 AAATTGAATTTTTTCGAGTCGAAA
1 AAATTGAATTTTTTCGAGTCGAAA
423937 AAATTG-ATTTTTT-GAGTCGA
1 AAATTGAATTTTTTCGAGTCGA
423957 GTTTTGCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 7 0.35
24 6 0.30
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (24 bp):
AAATTGAATTTTTTCGAGTCGAAA
Found at i:426822 original size:23 final size:23
Alignment explanation
Indices: 426792--426843 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
426782 AACATATTTT
*
426792 TTTAAATGCAATGGATTTATGTA
1 TTTAAATGCAATAGATTTATGTA
426815 TTTAAATGCAATAGATTTATGTA
1 TTTAAATGCAATAGATTTATGTA
*
426838 CTTAAA
1 TTTAAA
426844 GTTTTTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.42
Consensus pattern (23 bp):
TTTAAATGCAATAGATTTATGTA
Found at i:434454 original size:23 final size:23
Alignment explanation
Indices: 434362--434451 Score: 126
Period size: 23 Copynumber: 3.9 Consensus size: 23
434352 CACCACAGCT
*
434362 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
434385 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
434408 CGTAGAATTGCACCGTAGTGCTA
1 CGTAGAATTGCACCGAAGTGCCA
* *
434431 TGTAGAATTGCACCGTAGTGC
1 CGTAGAATTGCACCGAAGTGC
434452 TATATAAGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:440915 original size:270 final size:269
Alignment explanation
Indices: 440379--441415 Score: 1140
Period size: 268 Copynumber: 3.9 Consensus size: 269
440369 GATTTGTCAG
* * ** * * * *
440379 CAATATCCCTGCTGCCATC-AGACTTGAGCAACTTGTTCTCTTTTTCCGACTCATCAGAACTAGA
1 CAATATCCCCGCTGCCATCAAG-CTTGAGTAACTCATCCTCTTTCTCTGACTCATCAGAGCTAGA
* * * *
440443 AGTTTGTCCTGTAGTTTCAGCTTCAGCT-ACCTGCA-TCAAA-GAGTTGAAAGATATTG------
65 AGTTTGGCCTGTAGCTTCAGCTTCTG-TGACCTGCATTCAAATCA-TTGAAAGATATTGTTCACT
* * *
440499 -TT---ATGTACTTCAGTATATACTAATATTATAGTTTGACCTTTGCCAAAACAAAATGAAAGGT
128 TTTGAAATGTACTTCAGTACATACTAATATTATACTTTGACCTTTGCCAAAACAAAAAG-AAGGT
* * * *
440560 ACACGGTAAACACAGTGCTAATAATTAGCTATTCCTAGTTAATCAACCTTCTGCCTTGGTTTTGT
192 ACAAGGTAAACACAGTGCTAA-AATTAACTTTTCCTAGTTAATCTACCTTCTGCCTTGGTTTTGT
*
440625 GCTAGATTCATCAA
256 ACTAGATTCATCAA
* * ** **
440639 CAATATCCCCACTGCCATCAAACTTGAGTAACTCATCGACTTTCTCCAACTCATCAGAGCTAGAA
1 CAATATCCCCGCTGCCATCAAGCTTGAGTAACTCATCCTCTTTCTCTGACTCATCAGAGCTAGAA
* * *
440704 GTTTGGCCTGTAGCTCCAACCTCTGTGACCTGCATTCAAATCATTGAAAGATATTGTTCACTTTA
66 GTTTGGCCTGTAGCTTCAGCTTCTGTGACCTGCATTCAAATCATTGAAAGATATTGTTCACTTT-
440769 AT-AAATGTA-TTACAGTACATACTAATATTATAC-TTGACCTTTGCCAAAACAAAACAGAAGGT
130 -TGAAATGTACTT-CAGTACATACTAATATTATACTTTGACCTTTGCCAAAACAAAA-AGAAGGT
* * * * * *
440831 ATAAGGTAAACACAATGCTCAAATCATCTTTTCCTAGTTAATCTACCTTCTGCCTTGGTTTTGAA
192 ACAAGGTAAACACAGTGCTAAAATTAACTTTTCCTAGTTAATCTACCTTCTGCCTTGGTTTTGTA
440896 CTAGATTCATCAA
257 CTAGATTCATCAA
* *
440909 CAATATCCCCGCTGCCATCAAGCTTGAGTAACTCATCTTCTTTCTCTGACTCATAAGAGCTAGAA
1 CAATATCCCCGCTGCCATCAAGCTTGAGTAACTCATCCTCTTTCTCTGACTCATCAGAGCTAGAA
* *
440974 GTTTGGCAC-ATAGCTTCAGCTTCTGTGACCTGCATTCAAATCATTGAAAGATATAGTTCACTTT
66 GTTTGGC-CTGTAGCTTCAGCTTCTGTGACCTGCATTCAAATCATTGAAAGATATTGTTCAC-TT
* * * *
441038 TTGAAATATAC-TCA--AGCATGCTAATATTATACTTTGACCTCTGCCAAAACAAAATGGAAGGT
129 TTGAAATGTACTTCAGTA-CATACTAATATTATACTTTGACCTTTGCCAAAACAAAA-AGAAGGT
* ** * * * *
441100 ACAA--TAAATACAGCACTAAAAATTAACTTCTCCTAGTTAATCTACCTCCAGACTTGGTTTTGT
192 ACAAGGTAAACACAGTGCT-AAAATTAACTTTTCCTAGTTAATCTACCTTCTGCCTTGGTTTTGT
*
441163 ACTAGATTCATCAG
256 ACTAGATTCATCAA
441177 CAATATCCCCGCTGCCATCAAGCTTGAGTAACTCATCCTCTTTCTCTGACTCATCAGAGCTAGAA
1 CAATATCCCCGCTGCCATCAAGCTTGAGTAACTCATCCTCTTTCTCTGACTCATCAGAGCTAGAA
** * * * *
441242 GTCAGTG-CTGTAGCTTCAGCTTCTGTGATCTGCATTCAAAGCATTGAGAGATATTGTTCAAATT
66 GTTTG-GCCTGTAGCTTCAGCTTCTGTGACCTGCATTCAAATCATTGAAAGATATTGTTC-ACTT
** *
441306 TTGAAATGTACTTCAGT--ATACTAATATTATACTTTGACCTTTTTCAAAATAAAAAGTAAGGTA
129 TTGAAATGTACTTCAGTACATACTAATATTATACTTTGACCTTTGCCAAAACAAAAAG-AAGGTA
* * *
441369 C--GATAAACACAGTGCTAAAAATTAAATTTTTCCTAGTTACTCTACCT
193 CAAGGTAAACACAGTGCT-AAAATT-AACTTTTCCTAGTTAATCTACCT
441416 CAGTTAGAGA
Statistics
Matches: 657, Mismatches: 86, Indels: 59
0.82 0.11 0.07
Matches are distributed among these distances:
259 1 0.00
260 77 0.12
261 19 0.03
262 1 0.00
267 12 0.02
268 245 0.37
269 57 0.09
270 171 0.26
271 49 0.07
272 25 0.04
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (269 bp):
CAATATCCCCGCTGCCATCAAGCTTGAGTAACTCATCCTCTTTCTCTGACTCATCAGAGCTAGAA
GTTTGGCCTGTAGCTTCAGCTTCTGTGACCTGCATTCAAATCATTGAAAGATATTGTTCACTTTT
GAAATGTACTTCAGTACATACTAATATTATACTTTGACCTTTGCCAAAACAAAAAGAAGGTACAA
GGTAAACACAGTGCTAAAATTAACTTTTCCTAGTTAATCTACCTTCTGCCTTGGTTTTGTACTAG
ATTCATCAA
Found at i:443743 original size:2 final size:2
Alignment explanation
Indices: 443736--443762 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
443726 TCTTCTAAAC
443736 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
443763 TTGTTACAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:449239 original size:14 final size:14
Alignment explanation
Indices: 449194--449240 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
449184 CCTCGCATAG
* *
449194 CTCGCTCGGATAGC
1 CTCGGTCGGATGGC
* *
449208 CTCAGTCGGATGCC
1 CTCGGTCGGATGGC
449222 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
449236 CTCGG
1 CTCGG
449241 ATGCCCAGCG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.11, C:0.34, G:0.34, T:0.21
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:452315 original size:21 final size:21
Alignment explanation
Indices: 452289--452336 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
452279 CGAAGAATGG
452289 CAAGTTTAGATCGTTCATTTC
1 CAAGTTTAGATCGTTCATTTC
452310 CAAGTTTAGATCGTTCATTTC
1 CAAGTTTAGATCGTTCATTTC
452331 CAAGTT
1 CAAGTT
452337 GATTAACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (21 bp):
CAAGTTTAGATCGTTCATTTC
Found at i:461599 original size:15 final size:17
Alignment explanation
Indices: 461569--461601 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
461559 TTAACGAGCT
461569 AAAATATATAATTTTTA
1 AAAATATATAATTTTTA
*
461586 AAAAT-TATATTTTTTA
1 AAAATATATAATTTTTA
461602 TCCCTGGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAAATATATAATTTTTA
Found at i:461890 original size:15 final size:15
Alignment explanation
Indices: 461872--461919 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
461862 GGCTGAGTGC
461872 TTTGGCATAGGTTGG
1 TTTGGCATAGGTTGG
*
461887 TTTGGCAT--GCT--
1 TTTGGCATAGGTTGG
461898 TTT-GCATAGGTTGG
1 TTTGGCATAGGTTGG
461912 TTTGGCAT
1 TTTGGCAT
461920 GCTTTCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
10 4 0.15
11 3 0.12
12 2 0.08
13 2 0.08
14 3 0.12
15 12 0.46
ACGTcount: A:0.12, C:0.10, G:0.33, T:0.44
Consensus pattern (15 bp):
TTTGGCATAGGTTGG
Found at i:461897 original size:25 final size:25
Alignment explanation
Indices: 461869--461924 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
461859 TTAGGCTGAG
461869 TGCTTTGGCATAGGTTGGTTTGGCA
1 TGCTTTGGCATAGGTTGGTTTGGCA
*
461894 TGCTTTTGCATAGGTTGGTTTGGCA
1 TGCTTTGGCATAGGTTGGTTTGGCA
461919 TGCTTT
1 TGCTTT
461925 CCATATACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.11, C:0.12, G:0.32, T:0.45
Consensus pattern (25 bp):
TGCTTTGGCATAGGTTGGTTTGGCA
Found at i:465017 original size:157 final size:157
Alignment explanation
Indices: 464731--465045 Score: 630
Period size: 157 Copynumber: 2.0 Consensus size: 157
464721 AACTGTCTTG
464731 ATCAAAACTCAAGACTACATAACAATTTTCAGTGGCAATATTGCCATTTATTCAGCAAATATTTG
1 ATCAAAACTCAAGACTACATAACAATTTTCAGTGGCAATATTGCCATTTATTCAGCAAATATTTG
464796 AAGTGGAAGCCGACCACGCAAGATCAATGGGGGTCATGATACGTTTAGTGTATTACAGGGAGTTC
66 AAGTGGAAGCCGACCACGCAAGATCAATGGGGGTCATGATACGTTTAGTGTATTACAGGGAGTTC
464861 TCGATGTCGATGACAAAGCGGTACTTA
131 TCGATGTCGATGACAAAGCGGTACTTA
464888 ATCAAAACTCAAGACTACATAACAATTTTCAGTGGCAATATTGCCATTTATTCAGCAAATATTTG
1 ATCAAAACTCAAGACTACATAACAATTTTCAGTGGCAATATTGCCATTTATTCAGCAAATATTTG
464953 AAGTGGAAGCCGACCACGCAAGATCAATGGGGGTCATGATACGTTTAGTGTATTACAGGGAGTTC
66 AAGTGGAAGCCGACCACGCAAGATCAATGGGGGTCATGATACGTTTAGTGTATTACAGGGAGTTC
465018 TCGATGTCGATGACAAAGCGGTACTTA
131 TCGATGTCGATGACAAAGCGGTACTTA
465045 A
1 A
465046 CATCCCTCTT
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (157 bp):
ATCAAAACTCAAGACTACATAACAATTTTCAGTGGCAATATTGCCATTTATTCAGCAAATATTTG
AAGTGGAAGCCGACCACGCAAGATCAATGGGGGTCATGATACGTTTAGTGTATTACAGGGAGTTC
TCGATGTCGATGACAAAGCGGTACTTA
Found at i:474755 original size:2 final size:2
Alignment explanation
Indices: 474748--474803 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
474738 GAAAAAGATA
474748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
474789 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
474804 ACGAAATTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:474812 original size:23 final size:23
Alignment explanation
Indices: 474748--474813 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
474738 GAAAAAGATA
* *
474748 ATATATATATATATATA-TATAT
1 ATATATATATATAGAAATTATAT
* *
474770 ATATATATATATATATATTATAT
1 ATATATATATATAGAAATTATAT
474793 ATATATATATA-ACGAAATTAT
1 ATATATATATATA-GAAATTAT
474814 TTAAATTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
22 18 0.45
23 22 0.55
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATATATATATAGAAATTATAT
Found at i:477608 original size:57 final size:57
Alignment explanation
Indices: 477523--477642 Score: 177
Period size: 57 Copynumber: 2.1 Consensus size: 57
477513 CTGAAGTTGA
* * *
477523 TGCTGCTCGTGTTGAATGTGCAATGCATGTGACGGTGGTTGTTGTTGTTGTTGCTGC
1 TGCTGCTCGTGTTGAATGTGCAATGCATGTGAAGGTGGCTGTTGTTGTTGTGGCTGC
* * * *
477580 TGCTGCTGGTGTTGGATGTGTAATGCATGTGAAGGTTGCTGTTGTTGTTGTGGCTGC
1 TGCTGCTCGTGTTGAATGTGCAATGCATGTGAAGGTGGCTGTTGTTGTTGTGGCTGC
477637 TGCTGC
1 TGCTGC
477643 GGTAATGACG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.10, C:0.13, G:0.37, T:0.40
Consensus pattern (57 bp):
TGCTGCTCGTGTTGAATGTGCAATGCATGTGAAGGTGGCTGTTGTTGTTGTGGCTGC
Found at i:478952 original size:2 final size:2
Alignment explanation
Indices: 478945--478974 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
478935 CGTTCAGATT
478945 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
478975 AGGAACAAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:483440 original size:13 final size:14
Alignment explanation
Indices: 483419--483468 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
483409 TCAGAAGATG
*
483419 ATAACATAG-TAAA
1 ATAAAATAGTTAAA
483432 ATAAAATAGTTAAA
1 ATAAAATAGTTAAA
483446 A-AAAATGAGTTAAA
1 ATAAAAT-AGTTAAA
483460 AT-AAATAGT
1 ATAAAATAGT
483469 ATTCTACTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 16 0.48
14 17 0.52
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (14 bp):
ATAAAATAGTTAAA
Found at i:490876 original size:27 final size:27
Alignment explanation
Indices: 490822--490877 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
490812 CCGCCATCAC
* *
490822 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCACAACAT
*
490849 CACTTTGAACTTGAAAGTCCACAACAT
1 CACTTTGAACTTGAAACTCCACAACAT
490876 CA
1 CA
490878 ATATCTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.27
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAACAT
Found at i:493721 original size:35 final size:35
Alignment explanation
Indices: 493675--493781 Score: 162
Period size: 34 Copynumber: 3.1 Consensus size: 35
493665 GATTACTAAA
*
493675 CCCGTCCCCGTTTAACATAAACGGTTTTTCTCCAT
1 CCCGTCCCCGTTTAGCATAAACGGTTTTTCTCCAT
* *
493710 CCCGTCCCCGTTTAGCATAAGCGG-TTTTCCCCAT
1 CCCGTCCCCGTTTAGCATAAACGGTTTTTCTCCAT
* *
493744 CCCGTCCCCGTTTAGCATAAACGGTTTTTTTTCAT
1 CCCGTCCCCGTTTAGCATAAACGGTTTTTCTCCAT
493779 CCC
1 CCC
493782 CGTTTAATTC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
34 32 0.50
35 32 0.50
ACGTcount: A:0.17, C:0.36, G:0.14, T:0.34
Consensus pattern (35 bp):
CCCGTCCCCGTTTAGCATAAACGGTTTTTCTCCAT
Found at i:494521 original size:21 final size:20
Alignment explanation
Indices: 494497--494567 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 20
494487 GGGTTATTTC
*
494497 AAAATGTTAATATTTTTCTTT
1 AAAATATTAATATTTTT-TTT
*
494518 AAAAATATATAATTTTATTTTTTT
1 -AAAATAT-TAA-TAT-TTTTTTT
* *
494542 AAAATTTTAAATAATTTTTTT
1 AAAATATT-AATATTTTTTTT
494563 AAAAT
1 AAAAT
494568 CACCAATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
21 12 0.30
22 8 0.20
23 11 0.28
24 5 0.12
25 4 0.10
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (20 bp):
AAAATATTAATATTTTTTTT
Found at i:501411 original size:25 final size:24
Alignment explanation
Indices: 501366--501412 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
501356 AAAAATATAA
* *
501366 AAATAAATATTATTATAATTTTTT
1 AAATAAATAGTATAATAATTTTTT
*
501390 AAATATAATAGTATAATTATTTT
1 AAATA-AATAGTATAATAATTTT
501413 GAGTCGACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
AAATAAATAGTATAATAATTTTTT
Found at i:508026 original size:60 final size:60
Alignment explanation
Indices: 507920--508058 Score: 183
Period size: 60 Copynumber: 2.3 Consensus size: 60
507910 ATGATTTGGG
* *
507920 AAAAG-TACACAAATGGTCATCCTACTATAAGATATTACTTTATTAAGTCTCTCAACTATT
1 AAAAGTTACA-AAATGGTCATCCAACTATAAGATATTACTTTATTAAGTCCCTCAACTATT
* * * * *
507980 AAAAGTTACAAAATGGTCATTCAACTAT-AGAATGTTGCTTTGTTAAGTCCCTCGACTATT
1 AAAAGTTACAAAATGGTCATCCAACTATAAG-ATATTACTTTATTAAGTCCCTCAACTATT
508040 AAAAGTTACAAAATGGTCA
1 AAAAGTTACAAAATGGTCA
508059 CTTGACTATT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 2 0.03
60 64 0.91
61 4 0.06
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (60 bp):
AAAAGTTACAAAATGGTCATCCAACTATAAGATATTACTTTATTAAGTCCCTCAACTATT
Found at i:524822 original size:3 final size:3
Alignment explanation
Indices: 524814--524865 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
524804 CTTGAAGAGA
* * ** * *
524814 AAG AAG AAG ATG AAG ATG AAG AAG AAG AAG GTG AAG ATG ATG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
524862 AAG A
1 AAG A
524866 GTAAGGGCTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.35, T:0.10
Consensus pattern (3 bp):
AAG
Found at i:524840 original size:21 final size:21
Alignment explanation
Indices: 524814--524865 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
524804 CTTGAAGAGA
524814 AAGAAGAAGATGAAGATGAAG
1 AAGAAGAAGATGAAGATGAAG
* *
524835 AAGAAGAAGGTGAAGATGATG
1 AAGAAGAAGATGAAGATGAAG
524856 AAGAAGAAGA
1 AAGAAGAAGA
524866 GTAAGGGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.35, T:0.10
Consensus pattern (21 bp):
AAGAAGAAGATGAAGATGAAG
Found at i:526508 original size:143 final size:146
Alignment explanation
Indices: 526350--526641 Score: 482
Period size: 149 Copynumber: 2.0 Consensus size: 146
526340 AAACATAAAA
526350 TAAATTTGAAATTTATTTTCAAATGTTGAACACTTATTTTTTATGAAG-T-AAAATAAAAATAAA
1 TAAATTTGAAATTTATTTTCAAATGTTGAACACTTATTTTTTATGAAGATAAAAATAAAAATAAA
*
526413 ATAAAACGTTAAATAATTATTTTAATAAAAAATAAAACAAAAATATAATATAAATACATATTTAA
66 ATAAAACGTTAAATAATTATTTTAATAAAAAATAAAACAAAAATATAACATAAATACATATTTAA
*
526478 TAAT-AAGTTTTCTCT
131 TAATAAAATTTTCTCT
526493 TAAATTTGAAATTTATTTTCAAATGTTGAACACTTATTTTTTATGAAGTAAAATAAAAATAAAAA
1 TAAATTTGAAATTTATTTTCAAATGTTGAACACTTATTTTTTATGAAG----ATAAAAATAAAAA
* * *
526558 TAAAATAAAACGTTAGATAATTATTTTAATAAAAAATAAAGCAAAAATATAACATAAATACGTAT
62 TAAAATAAAACGTTAAATAATTATTTTAATAAAAAATAAAACAAAAATATAACATAAATACATAT
526623 TTAATAATAAAATTTTCTC
127 TTAATAATAAAATTTTCTC
526642 CGTTCCATAC
Statistics
Matches: 137, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
143 48 0.35
148 1 0.01
149 79 0.58
150 9 0.07
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.37
Consensus pattern (146 bp):
TAAATTTGAAATTTATTTTCAAATGTTGAACACTTATTTTTTATGAAGATAAAAATAAAAATAAA
ATAAAACGTTAAATAATTATTTTAATAAAAAATAAAACAAAAATATAACATAAATACATATTTAA
TAATAAAATTTTCTCT
Found at i:531280 original size:20 final size:20
Alignment explanation
Indices: 531257--531298 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
531247 CAATTACTTT
*
531257 CAATTTTCTGCAAAAGCTTC
1 CAATTTTCTACAAAAGCTTC
531277 CAATTTTCTACAAAAGCTTC
1 CAATTTTCTACAAAAGCTTC
531297 CA
1 CA
531299 CCAAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (20 bp):
CAATTTTCTACAAAAGCTTC
Found at i:536016 original size:23 final size:21
Alignment explanation
Indices: 535964--536025 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
535954 TTTTGGTGCA
*
535964 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
535984 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
536005 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
536026 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:536046 original size:20 final size:21
Alignment explanation
Indices: 536007--536046 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
535997 CCCCCTTTGA
*
536007 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
536028 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
536047 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:540454 original size:12 final size:12
Alignment explanation
Indices: 540437--540468 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
540427 CTATCGTAAA
540437 TTCGCGTTGCAT
1 TTCGCGTTGCAT
540449 TTCGCGTTGCAT
1 TTCGCGTTGCAT
540461 TTCGCGTT
1 TTCGCGTT
540469 TCGCGTTGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.25, G:0.25, T:0.44
Consensus pattern (12 bp):
TTCGCGTTGCAT
Found at i:540516 original size:42 final size:42
Alignment explanation
Indices: 540467--540606 Score: 212
Period size: 42 Copynumber: 3.3 Consensus size: 42
540457 GCATTTCGCG
* *
540467 TTTCGCGTTGCGATAGT-TGAAAATCCG-CGTTGCGATTTTCCA
1 TTTCGCGTTGCGATAGTCT-ACAGT-CGTCGTTGCGATTTTCCA
*
540509 TTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 TTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCA
*
540551 TTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 TTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCA
540593 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
540607 TTTCCATTTC
Statistics
Matches: 93, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
41 1 0.01
42 91 0.98
43 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.39
Consensus pattern (42 bp):
TTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCA
Found at i:540604 original size:62 final size:62
Alignment explanation
Indices: 540536--540668 Score: 266
Period size: 62 Copynumber: 2.1 Consensus size: 62
540526 CTACAGTTGT
540536 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCG
540598 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCG
540660 CGTTGCGAT
1 CGTTGCGAT
540669 AGTTGAAAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.41
Consensus pattern (62 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCG
Found at i:540608 original size:104 final size:106
Alignment explanation
Indices: 540492--540765 Score: 412
Period size: 104 Copynumber: 2.6 Consensus size: 106
540482 GTTGAAAATC
540492 CGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCGC
1 CGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCGC
* * * *
540557 GTTGCGATAGTCT-ACAGTTGTCGTTGCGAT-TT-TC-CATTT
66 GTTGCGATAGT-TGAAAATCG-CGTTGCGATATTATCGCATTG
540596 CGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCGC
1 CGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCGC
*
540661 GTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTG
66 GTTGCGATAGTTGAAAATCGCGTTGCGATA-TT----ATCGCATTG
540707 CGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 CGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
540766 AATTCGTTGT
Statistics
Matches: 156, Mismatches: 5, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
103 10 0.06
104 80 0.51
105 2 0.01
110 2 0.01
111 62 0.40
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (106 bp):
CGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCGC
GTTGCGATAGTTGAAAATCGCGTTGCGATATTATCGCATTG
Found at i:540683 original size:21 final size:21
Alignment explanation
Indices: 540657--540708 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
540647 ATTTTCCATT
540657 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
540678 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
540699 TCGCGTTGCG
1 TCGCGTTGCG
540709 CGTTGCGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:540706 original size:62 final size:65
Alignment explanation
Indices: 540553--540740 Score: 174
Period size: 62 Copynumber: 2.9 Consensus size: 65
540543 ATTTTCCATT
* * * * * **
540553 TCGCGTTGCGATAGTCT-ACAGT-TGTCGTTGCGATTTTCCATTTCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTCTAAAACTGCGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAAAA
* * * *
540615 TCGCGTTGCGATAGTCT-ACAGT-TGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTCTAAAACTGCGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAAAA
540678 TCGCGTTGCGATAGT-TGAAAA-TCGCGTTGCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 TCGCGTTGCGATAGTCT-AAAACT-GCG-T---CGTTGCGATTTTCCATTTCGCGTTGCGATAGT
540741 CTACAGTTGT
Statistics
Matches: 110, Mismatches: 7, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
62 55 0.50
63 19 0.17
64 2 0.02
65 1 0.01
66 1 0.01
69 32 0.29
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.38
Consensus pattern (65 bp):
TCGCGTTGCGATAGTCTAAAACTGCGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAAAA
Found at i:541411 original size:6 final size:6
Alignment explanation
Indices: 541395--541438 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
541385 TCTCATCTCG
541395 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
541439 AATACGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:541574 original size:20 final size:21
Alignment explanation
Indices: 541549--541588 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
541539 AACTGTAGAC
541549 TATCGCAA-CGAATTTGCGCG
1 TATCGCAACCGAATTTGCGCG
541569 TATCGCAACGCGAATTTGCG
1 TATCGCAAC-CGAATTTGCG
541589 ATAGTGGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
TATCGCAACCGAATTTGCGCG
Found at i:541629 original size:20 final size:21
Alignment explanation
Indices: 541609--541735 Score: 89
Period size: 20 Copynumber: 6.1 Consensus size: 21
541599 TCGCGTTGCG
541609 ATTTCAACTATCGCAACGCGA
1 ATTTCAACTATCGCAACGCGA
* ** *
541630 AATGGAA-AATCGCAACGCGCA
1 ATTTCAACTATCGCAACGCG-A
*
541651 TTTTCAACTATCGCAACGCGA
1 ATTTCAACTATCGCAACGCGA
* ** *
541672 AATGGAA-AATCGCAACGCGA
1 ATTTCAACTATCGCAACGCGA
* *
541692 TTTTTAACTATCGCAACGCGA
1 ATTTCAACTATCGCAACGCGA
* ** *
541713 AATGGAA-AATCGCAACGCGA
1 ATTTCAACTATCGCAACGCGA
541733 ATT
1 ATT
541736 AGGGATCGCA
Statistics
Matches: 78, Mismatches: 25, Indels: 7
0.71 0.23 0.06
Matches are distributed among these distances:
20 40 0.51
21 27 0.35
22 11 0.14
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (21 bp):
ATTTCAACTATCGCAACGCGA
Found at i:541707 original size:41 final size:41
Alignment explanation
Indices: 541606--541732 Score: 229
Period size: 41 Copynumber: 3.1 Consensus size: 41
541596 AGATCGCGTT
541606 GCGA-TTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
1 GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
541646 GCGCATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
1 GCG-ATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
*
541688 GCGATTTTTAACTATCGCAACGCGAAATGGAAAATCGCAAC
1 GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
541729 GCGA
1 GCGA
541733 ATTAGGGATC
Statistics
Matches: 84, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
40 3 0.04
41 42 0.50
42 39 0.46
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
GCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAC
Found at i:544387 original size:3 final size:3
Alignment explanation
Indices: 544379--544423 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
544369 TATTTTCAAA
* * *
544379 TAT TAT TAT TAT TAT TGT TGT TGT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
544424 CTTGTAGTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:549960 original size:33 final size:33
Alignment explanation
Indices: 549919--550003 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
549909 GAAACCTACC
*
549919 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
*
549952 CTCGCTCGGTTGCCCTCGGATGCTCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * *
549985 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
550004 TCGGATAGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 44 0.96
ACGTcount: A:0.08, C:0.38, G:0.27, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:550097 original size:29 final size:29
Alignment explanation
Indices: 550060--550117 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
550050 GCAATCTCTT
550060 GTAGCTCGCCAGGAAGACATGGCGACCTA
1 GTAGCTCGCCAGGAAGACATGGCGACCTA
* * *
550089 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCAGGAAGACATGGCGACCTA
550118 CGACCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCAGGAAGACATGGCGACCTA
Found at i:554601 original size:35 final size:35
Alignment explanation
Indices: 554553--554633 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
554543 TCTAAACCTT
* * *
554553 AAATTGAAGTATTTTAGAATTTGGGATTTAAAATT
1 AAATTGAATTATTTTAGAATTTAGGATTTAAAATG
* * *
554588 TAATTGAATTATTTTTGAATTTAGGATTTAGAATG
1 AAATTGAATTATTTTAGAATTTAGGATTTAAAATG
554623 AAATTGAATTA
1 AAATTGAATTA
554634 CTTCGGAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTAGGATTTAAAATG
Found at i:556623 original size:125 final size:124
Alignment explanation
Indices: 556404--556636 Score: 295
Period size: 125 Copynumber: 1.9 Consensus size: 124
556394 AAGTGTGGTG
*
556404 GTTTTCATGAAATTTGACCATTTAATTAAAGCAAAAGTATGGGAGTGGGTAGTGTAATTTAGCCA
1 GTTTTCATGAAATTTGACCATTTAATTAAAACAAAAGTATGGGAGTGGGTAGTGTAATTTAGCCA
* * * * *
556469 TGTATTTTAAAACATAAACATACGATTGTCTAAAATATAAATGGAAGAAACTATGTGGC
66 TGCATATCAAAACACAAACATACGATTGTCCAAAATATAAATGGAAGAAACTATGTGGC
* * * * *
556528 GTTTTTATGAAATTTGATCATTTAAATTAAAATACAAGTATGGGGGTGGGTAGTGTAATTTAGCC
1 GTTTTCATGAAATTTGACCATTT-AATTAAAACAAAAGTATGGGAGTGGGTAGTGTAATTTAGCC
* ** * ** *
556593 ATGCCTATCAAAACACGCACATGCTTTTGTCCAAAATTTAAATG
65 ATGCATATCAAAACACAAACATACGATTGTCCAAAATATAAATG
556637 TGAGAATTTA
Statistics
Matches: 90, Mismatches: 18, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
124 21 0.23
125 69 0.77
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (124 bp):
GTTTTCATGAAATTTGACCATTTAATTAAAACAAAAGTATGGGAGTGGGTAGTGTAATTTAGCCA
TGCATATCAAAACACAAACATACGATTGTCCAAAATATAAATGGAAGAAACTATGTGGC
Done.