Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397294.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_477.0, 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: 347590
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 9656 characters in sequence are not A, C, G, or T
Found at i:584 original size:14 final size:14
Alignment explanation
Indices: 550--584 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
540 CTTTTTCTTC
550 CTTTCTCTGTATTT
1 CTTTCTCTGTATTT
*
564 C-TTCTCTTTATTT
1 CTTTCTCTGTATTT
577 CTTTCTCT
1 CTTTCTCT
585 CGTGTGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.06, C:0.26, G:0.03, T:0.66
Consensus pattern (14 bp):
CTTTCTCTGTATTT
Found at i:3671 original size:25 final size:25
Alignment explanation
Indices: 3618--3677 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
3608 GTGGTCATAA
* * *
3618 CCACCTATATCAACTCGTGGCCTAG
1 CCACGTATAACAACCCGTGGCCTAG
**
3643 CCACGTATAACAACCCGTGGCCTTT
1 CCACGTATAACAACCCGTGGCCTAG
3668 CCACGTATAA
1 CCACGTATAA
3678 TCACAAACCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (25 bp):
CCACGTATAACAACCCGTGGCCTAG
Found at i:6430 original size:25 final size:26
Alignment explanation
Indices: 6365--6435 Score: 63
Period size: 29 Copynumber: 2.7 Consensus size: 26
6355 NNTGCCTTAG
* *
6365 TACCTTTTGAACTTTGTTAGGTGCCT
1 TACCTTTTGAACTTTGTGAGATGCCT
* *
6391 TAACACCTATGGAACTTTGTGAGATGCC-
1 T---ACCTTTTGAACTTTGTGAGATGCCT
*
6419 TACCTTTTGAACATTGT
1 TACCTTTTGAACTTTGT
6436 TAGGTATCGT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
25 13 0.37
26 1 0.03
28 1 0.03
29 20 0.57
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (26 bp):
TACCTTTTGAACTTTGTGAGATGCCT
Found at i:7668 original size:18 final size:19
Alignment explanation
Indices: 7645--7688 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
7635 GGGCTGAAAG
7645 AATATTTTTA-AATAAAAT
1 AATATTTTTACAATAAAAT
7663 AATATTTTTACGAATAAAAT
1 AATATTTTTAC-AATAAAAT
7683 AATATT
1 AATATT
7689 AAAATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.42
20 14 0.58
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AATATTTTTACAATAAAAT
Found at i:25025 original size:18 final size:19
Alignment explanation
Indices: 25004--25041 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
24994 GATGAAAAGA
25004 TAAA-TATTCATTTGCTAT
1 TAAATTATTCATTTGCTAT
* *
25022 TAAATTCTTCATTTGTTAT
1 TAAATTATTCATTTGCTAT
25041 T
1 T
25042 TTATTTTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (19 bp):
TAAATTATTCATTTGCTAT
Found at i:33714 original size:76 final size:75
Alignment explanation
Indices: 33587--33748 Score: 215
Period size: 76 Copynumber: 2.1 Consensus size: 75
33577 AAATACCATC
33587 TATTTTAATTTTAGGTAATCTATAAAATAGGAAATTGTTTTCTACTTTAAAA-ACAATTCCTAAA
1 TATTTTAATTTTAGGTAATCTATAAAATAGGAAATTGTTTTCTACTTTAAAAGA-AATTCCTAAA
33651 ATTAAGGATAG
65 ATTAAGGATAG
* * * *
33662 -ATTTTTAATTTTGGGTGAT-TCATAAAAATAGGAAATTG-TTTCTTATTTTAAAAGAAATTTCT
1 TA-TTTTAATTTTAGGTAATCT-AT-AAAATAGGAAATTGTTTTC-TACTTTAAAAGAAATTCCT
33724 AAAATTAAGGATAG
62 AAAATTAAGGATAG
33738 TATTTTAATTT
1 TATTTTAATTT
33749 GGAAATTTGA
Statistics
Matches: 77, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
74 2 0.03
75 21 0.27
76 52 0.68
77 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.43
Consensus pattern (75 bp):
TATTTTAATTTTAGGTAATCTATAAAATAGGAAATTGTTTTCTACTTTAAAAGAAATTCCTAAAA
TTAAGGATAG
Found at i:35842 original size:74 final size:74
Alignment explanation
Indices: 35692--35904 Score: 277
Period size: 74 Copynumber: 2.9 Consensus size: 74
35682 GTAGATTGTG
* ** * * *
35692 AGACAGAGAAGACTTAGTCAACTAAGAAGCATGGTT-GTCAACTAAGAGCTCACTGCCAGAGACT
1 AGACAGAGAAGACTTAATCAACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTATCAAAAAAT
35756 TCAATTACA
66 TCAATTACA
35765 AGACAGA-AAGCACTTAATCAACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTATCAAAAAA
1 AGACAGAGAAG-ACTTAATCAACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTATCAAAAAA
*
35829 TTCAATTTCA
65 TTCAATTACA
* * ** * * *
35839 AGACAAAGAAGACTTAATCGACTAAGAAATATGGTTAGTCAACTAAGAGCACTCTATCTAAAAAT
1 AGACAGAGAAGACTTAATCAACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTATCAAAAAAT
35904 T
66 T
35905 TGAATTTAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
72 3 0.02
73 31 0.25
74 86 0.70
75 3 0.02
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (74 bp):
AGACAGAGAAGACTTAATCAACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTATCAAAAAAT
TCAATTACA
Found at i:43196 original size:15 final size:16
Alignment explanation
Indices: 43178--43212 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
43168 TATTCTTGTT
43178 TTTAGTTTT-AGTTGC
1 TTTAGTTTTCAGTTGC
*
43193 TTTAGTTTTCAGTTGT
1 TTTAGTTTTCAGTTGC
43209 TTTA
1 TTTA
43213 AAAATTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.63
Consensus pattern (16 bp):
TTTAGTTTTCAGTTGC
Found at i:46224 original size:13 final size:13
Alignment explanation
Indices: 46206--46231 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46196 AGAACAAAAA
46206 TCAAATAAATCTT
1 TCAAATAAATCTT
46219 TCAAATAAATCTT
1 TCAAATAAATCTT
46232 AGAGTCCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TCAAATAAATCTT
Found at i:50522 original size:73 final size:72
Alignment explanation
Indices: 50444--50632 Score: 256
Period size: 72 Copynumber: 2.6 Consensus size: 72
50434 TCTGAGAATT
* * *
50444 AATCTCTTTTCTTTAAAAGATTGATTCTTC-TCAACACAGAATGCTTCCTTTTCACTTTTTGAAG
1 AATCTCTTTTCTTCAAAAGATTGATTCTTCAT-AACACAGAATGCTTCCTTTT-ACTTCTGGAAG
50508 TTGAGAACC
64 TTGAGAACC
* * * *
50517 AATCTCTTCTCTTCAAGAGATTGATTCTTCATAACACAAAATGCTTCCTTTTGCTTCTGGAAGTT
1 AATCTCTTTTCTTCAAAAGATTGATTCTTCATAACACAGAATGCTTCCTTTTACTTCTGGAAGTT
*
50582 GAGAATC
66 GAGAACC
*
50589 AATCT-TTTGTCTTCAAAAGATTGATTTTTCATAACACAGAATGC
1 AATCTCTTT-TCTTCAAAAGATTGATTCTTCATAACACAGAATGC
50633 CTTTTTTTTT
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
71 2 0.02
72 53 0.52
73 46 0.45
74 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (72 bp):
AATCTCTTTTCTTCAAAAGATTGATTCTTCATAACACAGAATGCTTCCTTTTACTTCTGGAAGTT
GAGAACC
Found at i:65716 original size:36 final size:37
Alignment explanation
Indices: 65656--65826 Score: 124
Period size: 36 Copynumber: 4.8 Consensus size: 37
65646 TAAGTGCAGA
* * *
65656 AGGGCTAGATGTGGGGCGTTATACCACATGAAT-ACT
1 AGGGCCAGATGTGGGGCATCATACCACATGAATGACT
* * *
65692 TGGGCCAGATGTGGGGCATCATACCACA--CATGACG
1 AGGGCCAGATGTGGGGCATCATACCACATGAATGACT
* * *
65727 AGGGCCAAATGTGGGGCATCATA-TACATG--TGACA
1 AGGGCCAGATGTGGGGCATCATACCACATGAATGACT
* ** * * *
65761 AGGGCTAGACATGAGGCGTTATACCACATGAAT-ACTT
1 AGGGCCAGATGTGGGGCATCATACCACATGAATGAC-T
* *
65798 A-GGCCAAATGTAGGGCATCATACCACATG
1 AGGGCCAGATGTGGGGCATCATACCACATG
65827 TGATAAGGGC
Statistics
Matches: 101, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
34 25 0.25
35 28 0.28
36 46 0.46
37 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.21
Consensus pattern (37 bp):
AGGGCCAGATGTGGGGCATCATACCACATGAATGACT
Found at i:65854 original size:105 final size:105
Alignment explanation
Indices: 65655--65847 Score: 260
Period size: 105 Copynumber: 1.8 Consensus size: 105
65645 TTAAGTGCAG
** * * * *
65655 AAGGGCTAGATGTGGGGCGTTATACCACATGAATACTTGGGCCAGATGTGGGGCATCATACCACA
1 AAGGGCTAGACATGAGGCGTTATACCACATGAATACTTAGGCCAAATGTAGGGCATCATACCACA
* **
65720 CATGACGAGGGCCAAATGTGGGGCATCATATACATGTGAC
66 CATGACAAGGGCCAAATGTGGAACATCATATACATGTGAC
65760 AAGGGCTAGACATGAGGCGTTATACCACATGAATACTTAGGCCAAATGTAGGGCATCATACCACA
1 AAGGGCTAGACATGAGGCGTTATACCACATGAATACTTAGGCCAAATGTAGGGCATCATACCACA
** * * *
65825 TGTGATAAGGGCTAGATGTGGAA
66 CATGACAAGGGCCAAATGTGGAA
65848 TGTCATACCA
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
105 74 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (105 bp):
AAGGGCTAGACATGAGGCGTTATACCACATGAATACTTAGGCCAAATGTAGGGCATCATACCACA
CATGACAAGGGCCAAATGTGGAACATCATATACATGTGAC
Found at i:68187 original size:505 final size:505
Alignment explanation
Indices: 67208--68214 Score: 1355
Period size: 505 Copynumber: 2.0 Consensus size: 505
67198 CTTATACTTT
* * * *
67208 TCTTGTACTTACTAGATAGACTTGAGTTGTTAACATAAAGTTCTAATTTATTTATAAGTCTTCGT
1 TCTTGTACTTACTAGATAGACTAGAGTTGTTAACATAAAGTTCTAATTTACTTATAAGTCTCCAT
* * * **
67273 AGAGTTTCTTATAACAATATCAATCTTAACGAATTTACTCTATGTTTATGCAAATTGAAATTAAG
66 AGAATTTCTTATAAAAATATCAATCTTAACGAATTTACTATATGCCTATGCAAATTGAAATTAAG
* * * *
67338 AAAGACTGATTAAGTTTAGACTCTAATCTTGGCAACATATGACATGTAAGTGTGTGTCTACCATA
131 AAAGACTCATTAAGTTTAGACTCTAATCTTAGCAACATATGACATGTAAATGTATGTCTACCATA
* * *
67403 CACGGAAATCAAATCAATCAGCTTATGTAATTGATATTAAACATATGCTATTTCATTCAAGGCTT
196 CACGCAAATCAAATCAATCAGCTCATGTAATTGATATTAAACATATGCTATTTCATCCAAGGCTT
* * * * *
67468 ACTCTGAACTCCTTTTCTCGATTTTGTTTAGGTTCCAAATCAATCTAATTGGTGACCAAGCAATC
261 ACTCTAAACTCCTTCTCTAGATTTGGTTTAGGTTCCAAATCAATCTAATTAGTGACCAAGCAATC
* * * * * *
67533 AGACGCATTAAGAACAGAATTGAAATAAACAACTCAAACCCTATCCATCATAAGCTAGAAAGAAT
326 AAACGCATTAAGAACAGAATAGAAATAAACAACTCAAACACTATCAATCATAAACAAGAAAGAAT
* * ** * * *
67598 ATTAAAAACTCAAACTGCACATTAGGTTTAATTCTAATTTTAGATTAAAAAATTAGATTCCCATT
391 ACTAAAAACTCAAACTACACATTAGGTGCAATTCTAATTTGAGATTAAAAAATTAGATCCCCATA
* * *
67663 GGTGCTAAAAACGTCATCCAAAAAAGTATAAACATTAAAGCTAAACATCA
456 AGTGCTAAAAACATCATCCAAAAAAGTATAAACATTAAAACTAAACATCA
* * * *
67713 TCTTTTACTTACTAGATAGGCTAGAGTTGTTAACCTAGAGTTCTAATTTACTTATAAGTCTCCAT
1 TCTTGTACTTACTAGATAGACTAGAGTTGTTAACATAAAGTTCTAATTTACTTATAAGTCTCCAT
* *
67778 CGAATTTCTTATAAAAATAAT-TATCTTAATC-AATTTACTATATGCCTATGCAAATTGAAATTA
66 AGAATTTCTTATAAAAAT-ATCAATCTTAA-CGAATTTACTATATGCCTATGCAAATTGAAATTA
* *
67841 AGAAAGGCTCATTAAGTTTAGACTCTAATCTTAGCTACATATGACATGTAAATGTATGTCTACCC
129 AGAAAGACTCATTAAGTTTAGACTCTAATCTTAGCAACATATGACATGTAAATGTATGTCTA-CC
* * ** *
67906 TTA-ACGCAAATCAAATCAATCATCTCATGTAATTGATATTGCACATATGCTTTTTCATCCAAGG
193 ATACACGCAAATCAAATCAATCAGCTCATGTAATTGATATTAAACATATGCTATTTCATCCAAGG
* * *
67970 CTTACTCTAAACTCC-TCTCTTAG-TTTGGTTTAGGTTTTCAAATCAATCTAATTAGTGGCTAAG
258 CTTACTCTAAACTCCTTCTC-TAGATTTGGTTTAGG-TTCCAAATCAATCTAATTAGTGACCAAG
* * *
68033 CAATCAAATGCATTAATAACA-AGATAGAAATAAACAACTCAAACATTATCAATCATAAACAAGA
321 CAATCAAACGCATTAAGAACAGA-ATAGAAATAAACAACTCAAACACTATCAATCATAAACAAGA
* * *
68097 AAGAATACTAAAAACTCATACTACACATTGGGTGCAATTGCT-ATTTGAGATTAAAAAATTAGCT
385 AAGAATACTAAAAACTCAAACTACACATTAGGTGCAATT-CTAATTTGAGATTAAAAAATTAGAT
68161 CCCCATAAGTGGC-AAAAACATCATCCAAAAAAGTATAAACATTAAAACTAAACA
449 CCCCATAAGT-GCTAAAAACATCATCCAAAAAAGTATAAACATTAAAACTAAACA
68215 AGAAAGTATA
Statistics
Matches: 435, Mismatches: 59, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
504 14 0.03
505 410 0.94
506 11 0.03
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (505 bp):
TCTTGTACTTACTAGATAGACTAGAGTTGTTAACATAAAGTTCTAATTTACTTATAAGTCTCCAT
AGAATTTCTTATAAAAATATCAATCTTAACGAATTTACTATATGCCTATGCAAATTGAAATTAAG
AAAGACTCATTAAGTTTAGACTCTAATCTTAGCAACATATGACATGTAAATGTATGTCTACCATA
CACGCAAATCAAATCAATCAGCTCATGTAATTGATATTAAACATATGCTATTTCATCCAAGGCTT
ACTCTAAACTCCTTCTCTAGATTTGGTTTAGGTTCCAAATCAATCTAATTAGTGACCAAGCAATC
AAACGCATTAAGAACAGAATAGAAATAAACAACTCAAACACTATCAATCATAAACAAGAAAGAAT
ACTAAAAACTCAAACTACACATTAGGTGCAATTCTAATTTGAGATTAAAAAATTAGATCCCCATA
AGTGCTAAAAACATCATCCAAAAAAGTATAAACATTAAAACTAAACATCA
Found at i:69365 original size:29 final size:29
Alignment explanation
Indices: 69328--69462 Score: 148
Period size: 29 Copynumber: 4.6 Consensus size: 29
69318 TCTTATCTTT
*
69328 AATTAAGACAAAACATGTTATCTTGTTTA
1 AATTAAGACAAAACATGTTTTCTTGTTTA
* *
69357 AATTGAGAC-AAACATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTTTA
** ** *
69385 GTTTAAGACAAAACAAAATTTTCTTATCTTA
1 AATTAAGACAAAAC-ATGTTTTCTTGT-TTA
*
69416 AATTAAGAC-ATACATGTTTTTCTTGTTTA
1 AATTAAGACAAAACATG-TTTTCTTGTTTA
69445 AATTAAGACAAAACATGT
1 AATTAAGACAAAACATGT
69463 AAAAGCTGCT
Statistics
Matches: 84, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
28 23 0.27
29 26 0.31
30 26 0.31
31 9 0.11
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
AATTAAGACAAAACATGTTTTCTTGTTTA
Found at i:81929 original size:62 final size:61
Alignment explanation
Indices: 81858--81973 Score: 137
Period size: 62 Copynumber: 1.9 Consensus size: 61
81848 TGTTTTGAAT
* * * * *
81858 TTTGGCTTTCAGTATTGATATT-GTTTCCACTTTGG-GCATTGGATTTGGTATTTGTTTAGCC
1 TTTGGCTTTCAAT-TTGACATTGGTTTCCACCTTGGTGC-TTGAATTTCGTATTTGTTTAGCC
*
81919 TTTGGTCTTTCAATTTGACATTGGTTTCGACCTTGGTGCTTGAATTTCGTATTTG
1 TTTGG-CTTTCAATTTGACATTGGTTTCCACCTTGGTGCTTGAATTTCGTATTTG
81974 GTTGATGTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
61 12 0.26
62 32 0.70
63 2 0.04
ACGTcount: A:0.15, C:0.14, G:0.22, T:0.49
Consensus pattern (61 bp):
TTTGGCTTTCAATTTGACATTGGTTTCCACCTTGGTGCTTGAATTTCGTATTTGTTTAGCC
Found at i:107666 original size:16 final size:16
Alignment explanation
Indices: 107645--107681 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
107635 CCTATCTTAC
107645 TTTCTTTATTTCTCCT
1 TTTCTTTATTTCTCCT
*
107661 TTTCTTTCTTTCTCCT
1 TTTCTTTATTTCTCCT
107677 TTTCT
1 TTTCT
107682 CTTCTCACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTCTTTATTTCTCCT
Found at i:107881 original size:11 final size:11
Alignment explanation
Indices: 107854--107884 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
107844 GGGTGTGCAT
107854 GGGTCGGTTTC
1 GGGTCGGTTTC
107865 -GGTCGGTTTC
1 GGGTCGGTTTC
107875 GGGTCGGTTT
1 GGGTCGGTTT
107885 TTCGTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.00, C:0.16, G:0.45, T:0.39
Consensus pattern (11 bp):
GGGTCGGTTTC
Found at i:108140 original size:32 final size:32
Alignment explanation
Indices: 108104--108167 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
108094 AGGCCGGCGC
*
108104 GGCAGGGGGGAATCGAGACTCGTGGGAGGGGG
1 GGCAGGGGGGAATCGAGACTCGTGGAAGGGGG
*
108136 GGCAGGGGGGAATCGGGACTCGTGGAAGGGGG
1 GGCAGGGGGGAATCGAGACTCGTGGAAGGGGG
108168 CCGGGGGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.12, G:0.59, T:0.09
Consensus pattern (32 bp):
GGCAGGGGGGAATCGAGACTCGTGGAAGGGGG
Found at i:108197 original size:30 final size:28
Alignment explanation
Indices: 108125--108208 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 28
108115 ATCGAGACTC
*
108125 GTGGGAGGGGGGGCAGGGGGGAATCGGGA
1 GTGGGAGGGGGGGC-CGGGGGAATCGGGA
* *
108154 CTCGTGGA-AGGGGGCCGGGGGAATCGTAGGA
1 GT-G-GGAGGGGGGGCCGGGGGAATCG--GGA
108185 GTGGGAGGGGGGGCCGGGGGAATC
1 GTGGGAGGGGGGGCCGGGGGAATC
108209 AAGTCGAGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
29 14 0.31
30 24 0.53
31 7 0.16
ACGTcount: A:0.17, C:0.12, G:0.62, T:0.10
Consensus pattern (28 bp):
GTGGGAGGGGGGGCCGGGGGAATCGGGA
Found at i:108361 original size:22 final size:22
Alignment explanation
Indices: 108336--108377 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
108326 TAGTAGGGGG
*
108336 CGGGCACGGTAGCCGGGGTAGT
1 CGGGCACGGTAGCCGAGGTAGT
*
108358 CGGGCAGGGTAGCCGAGGTA
1 CGGGCACGGTAGCCGAGGTA
108378 ACCGGGGGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.21, G:0.50, T:0.12
Consensus pattern (22 bp):
CGGGCACGGTAGCCGAGGTAGT
Found at i:108383 original size:22 final size:22
Alignment explanation
Indices: 108336--108383 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
108326 TAGTAGGGGG
* **
108336 CGGGCACGGTAGCCGGGGTAGT
1 CGGGCACGGTAGCCGAGGTAAC
*
108358 CGGGCAGGGTAGCCGAGGTAAC
1 CGGGCACGGTAGCCGAGGTAAC
108380 CGGG
1 CGGG
108384 GGCTCGGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.23, G:0.50, T:0.10
Consensus pattern (22 bp):
CGGGCACGGTAGCCGAGGTAAC
Found at i:113562 original size:33 final size:34
Alignment explanation
Indices: 113484--113563 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 34
113474 AAAGTTAGTG
*
113484 TGAGTTGTGCTTGCTCCCATGAAAAAGTAAATTA
1 TGAGTTGTGCTTGCTCCCATGAAAAAGGAAATTA
* * * * *
113518 TGGGTTATGCTTGCTCCTAT-AAAAAGGCAATTG
1 TGAGTTGTGCTTGCTCCCATGAAAAAGGAAATTA
*
113551 TTAGTTGTGCTTG
1 TGAGTTGTGCTTG
113564 AGCTCAAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
33 20 0.54
34 17 0.46
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (34 bp):
TGAGTTGTGCTTGCTCCCATGAAAAAGGAAATTA
Found at i:120043 original size:17 final size:17
Alignment explanation
Indices: 120021--120060 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
120011 TAAAATAAAA
120021 AGCACCCAAGA-AAGGGG
1 AGCACCCAA-ACAAGGGG
*
120038 AGCACCCAAACGAGGGG
1 AGCACCCAAACAAGGGG
120055 AGCACC
1 AGCACC
120061 AGAGCTATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.38, C:0.30, G:0.33, T:0.00
Consensus pattern (17 bp):
AGCACCCAAACAAGGGG
Found at i:136563 original size:33 final size:33
Alignment explanation
Indices: 136526--136592 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
136516 TGGAATTAGA
136526 TCCATAATTGTGCTGATTTTTGAAACATTTAAT
1 TCCATAATTGTGCTGATTTTTGAAACATTTAAT
136559 TCCATAATTGTGCTGATTTTTGAAACATTTAAT
1 TCCATAATTGTGCTGATTTTTGAAACATTTAAT
136592 T
1 T
136593 TAAGGAATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (33 bp):
TCCATAATTGTGCTGATTTTTGAAACATTTAAT
Found at i:137074 original size:17 final size:19
Alignment explanation
Indices: 137041--137075 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
137031 AAAATTGTTT
137041 AAATTTGTAATTTATAATA
1 AAATTTGTAATTTATAATA
137060 AAATTT-TAA-TTATAAT
1 AAATTTGTAATTTATAAT
137076 CCTAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AAATTTGTAATTTATAATA
Found at i:152295 original size:14 final size:14
Alignment explanation
Indices: 152276--152306 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
152266 TGTGTAGACG
*
152276 TGTGTGTTTGTGTC
1 TGTGTGTGTGTGTC
152290 TGTGTGTGTGTGTC
1 TGTGTGTGTGTGTC
152304 TGT
1 TGT
152307 ATCAAATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.39, T:0.55
Consensus pattern (14 bp):
TGTGTGTGTGTGTC
Found at i:157818 original size:60 final size:60
Alignment explanation
Indices: 157752--157884 Score: 194
Period size: 60 Copynumber: 2.2 Consensus size: 60
157742 AGATTTGTGT
* * * * *
157752 CGTGACACGCTGTGTGGTGGTAGATATGGCATGACACGTTGTGTGCTAACAGATATATGG
1 CGTGACACGCTGAGTGGTGGCAGATATGGCATGACACGCTGAGTGCTAACAGATATAAGG
* *
157812 CGTGACACGCTGAGTGGTGGCAGATATGGCATGACACGCTGAGTGCTATCAGATTTAAGG
1 CGTGACACGCTGAGTGGTGGCAGATATGGCATGACACGCTGAGTGCTAACAGATATAAGG
*
157872 CATGACACGCTGA
1 CGTGACACGCTGA
157885 CTGAAAGTAG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (60 bp):
CGTGACACGCTGAGTGGTGGCAGATATGGCATGACACGCTGAGTGCTAACAGATATAAGG
Found at i:157836 original size:31 final size:31
Alignment explanation
Indices: 157689--158450 Score: 193
Period size: 31 Copynumber: 25.0 Consensus size: 31
157679 CAGATTTAAA
** *
157689 GCGTGACACGCTGAGTGAAAGCAGATTTATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * ** * * * *
157720 GGGTCACACATTGAGTGG-CGATAGATTTGTG
1 GCGTGACACGCTGAGTGGTAG-CAGATATATG
* * * *
157751 TCGTGACACGCTGTGTGGTGGTAG--ATATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * * * *
157780 GCATGACACGTTGTGTGCTAACAGATATATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
*
157811 GCGTGACACGCTGAGTGGTGGCAG--ATATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * * * *
157840 GCATGACACGCTGAGTGCTATCAGATTTAAG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * ** * *
157871 GCATGACACGCTGACTGAAAGTAGATTTATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * * * *
157902 GGGTCACACACTG-GCTGTTGGCA-A-ATATG
1 GCGTGACACGCTGAG-TGGTAGCAGATATATG
* ********** *
157931 GTGTGACACNNNNNNNNNNAGCAAATATATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * ** *
157962 GCGAGACACACTGAGTTATGGCAGAT-T-TG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * *
157991 TGCTGTGACACGTTGAGTGCTAGTAG--ATATG
1 -GC-GTGACACGCTGAGTGGTAGCAGATATATG
* *
158022 GCGTGACATGCTGAGTGCTA-CTAGATATATG
1 GCGTGACACGCTGAGTGGTAGC-AGATATATG
* * * * * * *
158053 GAGTGACATGTTAAGTGTTAACAGATTTATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * ** *
158084 GGGTCACACATTGAGTGGTGGCAGAT-T-TG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * * * *
158113 TGCTGTGACATGTTAAGTGCTAGTAGATATATG
1 -GC-GTGACACGCTGAGTGGTAGCAGATATATG
* * *
158146 GTGTGACACACTGAGTGGTGGCAGAT-T-TG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * *
158175 TGCTGTGACACGCTGAGTGGTGGCAGATTTGTG
1 -GC-GTGACACGCTGAGTGGTAGCAGATATATG
* * * *
158208 CCGTGACACACTGAGTGGTGGTAG--ATATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * * * * *
158237 GCATGACATGCTGAGTGTTACCAGATTTAGG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * * *
158268 GCGTGACATGCTGAGTGCTAGCAAATTTATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * * * *
158299 G-GTCACACGCTGAGTGGTGGTAGATTTGTG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * * * *
158329 CCATGACATGATGAGTGGTGGCAGATATGAT-
1 GCGTGACACGCTGAGTGGTAGCAGATAT-ATG
* * *
158360 --GTGACAGGCTGAGTGCTACCAGATATATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* ** * *
158389 GAGTGACACATTGAGTGCTAGCAGATTTATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
* * * * * *
158420 GGGTTACACGTTGGGTGGTGGCAGATTTATG
1 GCGTGACACGCTGAGTGGTAGCAGATATATG
158451 CCATAACATG
Statistics
Matches: 527, Mismatches: 171, Indels: 66
0.69 0.22 0.09
Matches are distributed among these distances:
28 2 0.00
29 122 0.23
30 35 0.07
31 357 0.68
32 7 0.01
33 4 0.01
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.28
Consensus pattern (31 bp):
GCGTGACACGCTGAGTGGTAGCAGATATATG
Found at i:157853 original size:29 final size:29
Alignment explanation
Indices: 157754--157884 Score: 118
Period size: 29 Copynumber: 4.4 Consensus size: 29
157744 ATTTGTGTCG
* * * *
157754 TGACACGCTGTGTGGTGGTAGATATGGCA
1 TGACACGCTGAGTGCTAGCAGATATGGCA
* * * *
157783 TGACACGTTGTGTGCTAACAGATATATGGCG
1 TGACACGCTGAGTGCTAGCAG--ATATGGCA
* *
157814 TGACACGCTGAGTGGTGGCAGATATGGCA
1 TGACACGCTGAGTGCTAGCAGATATGGCA
* *
157843 TGACACGCTGAGTGCTATCAGATTTAAGGCA
1 TGACACGCTGAGTGCTAGCAGA--TATGGCA
157874 TGACACGCTGA
1 TGACACGCTGA
157885 CTGAAAGTAG
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
29 42 0.51
31 40 0.49
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (29 bp):
TGACACGCTGAGTGCTAGCAGATATGGCA
Found at i:158214 original size:62 final size:62
Alignment explanation
Indices: 157966--158452 Score: 247
Period size: 62 Copynumber: 8.0 Consensus size: 62
157956 TATATGGCGA
** * * * * *
157966 GACACACTGAGTTATGGCAGATTTGTGCTGTGACACGTTGAGTGCTAGTAGA--TATGGCGT
1 GACACACTGAGTGGTGGCAGATTTATGCTGTGACACGCTGAGTGGTAGCAGATTTATGCCGT
** * * * ** * * * * * **
158026 GACATGCTGAGTGCT-ACTAGATATATGGAGTGACATGTTAAGTGTTAACAGATTTATGGGGT
1 GACACACTGAGTGGTGGC-AGATTTATGCTGTGACACGCTGAGTGGTAGCAGATTTATGCCGT
* * * * * * * * * **
158088 CACACATTGAGTGGTGGCAGATTTGTGCTGTGACATGTTAAGTGCTAGTAGATATATGGTGT
1 GACACACTGAGTGGTGGCAGATTTATGCTGTGACACGCTGAGTGGTAGCAGATTTATGCCGT
* * *
158150 GACACACTGAGTGGTGGCAGATTTGTGCTGTGACACGCTGAGTGGTGGCAGATTTGTGCCGT
1 GACACACTGAGTGGTGGCAGATTTATGCTGTGACACGCTGAGTGGTAGCAGATTTATGCCGT
* * * * * * *
158212 GACACACTGAGTGGTGGTAGA--TATGGC-ATGACATGCTGAGTGTTACCAGATTTAGGGCGT
1 GACACACTGAGTGGTGGCAGATTTAT-GCTGTGACACGCTGAGTGGTAGCAGATTTATGCCGT
** * * * * * * * * *
158272 GACATGCTGAGTGCTAGCAAATTTATG-GGTCACACGCTGAGTGGTGGTAGATTTGTGCCAT
1 GACACACTGAGTGGTGGCAGATTTATGCTGTGACACGCTGAGTGGTAGCAGATTTATGCCGT
* * * * * * **
158333 GACATGA-TGAGTGGTGGCAGA--TATGATGTGACAGGCTGAGTGCTACCAGATATATGGAGT
1 GACA-CACTGAGTGGTGGCAGATTTATGCTGTGACACGCTGAGTGGTAGCAGATTTATGCCGT
* * * ** * * * *
158393 GACACATTGAGTGCTAGCAGATTTATGGGGTTACACGTTGGGTGGTGGCAGATTTATGCC
1 GACACACTGAGTGGTGGCAGATTTATGCTGTGACACGCTGAGTGGTAGCAGATTTATGCC
158453 ATAACATGTT
Statistics
Matches: 313, Mismatches: 101, Indels: 24
0.71 0.23 0.05
Matches are distributed among these distances:
59 6 0.02
60 116 0.37
61 40 0.13
62 150 0.48
63 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (62 bp):
GACACACTGAGTGGTGGCAGATTTATGCTGTGACACGCTGAGTGGTAGCAGATTTATGCCGT
Found at i:158232 original size:93 final size:93
Alignment explanation
Indices: 157955--158235 Score: 278
Period size: 93 Copynumber: 3.0 Consensus size: 93
157945 NNNNNAGCAA
* * * * * * *
157955 ATATATGGCGAGACACACTGAGTTATGGCAGATTTGTGCTGTGACACGTTGAGTGCTAGTAGATA
1 ATATATGGAGTGACACACTGAGTGATGGCAGATTTGTGCTGTGACACGTTGAGTGGTGGCAGATT
*
158020 TG-G-CGTGACATGCTGAGTGCTACTAG
66 TGTGCCGTGACATGCTGAGTGCTAGTAG
*** * * ** * ** * *
158046 ATATATGGAGTGACATGTTAAGTGTTAACAGATTTATGGGGTCACACATTGAGTGGTGGCAGATT
1 ATATATGGAGTGACACACTGAGTGATGGCAGATTTGTGCTGTGACACGTTGAGTGGTGGCAGATT
* * *
158111 TGTGCTGTGACATGTTAAGTGCTAGTAG
66 TGTGCCGTGACATGCTGAGTGCTAGTAG
* * *
158139 ATATATGGTGTGACACACTGAGTGGTGGCAGATTTGTGCTGTGACACGCTGAGTGGTGGCAGATT
1 ATATATGGAGTGACACACTGAGTGATGGCAGATTTGTGCTGTGACACGTTGAGTGGTGGCAGATT
** * *
158204 TGTGCCGTGACACACTGAGTGGTGGTAG
66 TGTGCCGTGACATGCTGAGTGCTAGTAG
158232 ATAT
1 ATAT
158236 GGCATGACAT
Statistics
Matches: 144, Mismatches: 44, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
91 48 0.33
92 1 0.01
93 95 0.66
ACGTcount: A:0.25, C:0.13, G:0.32, T:0.30
Consensus pattern (93 bp):
ATATATGGAGTGACACACTGAGTGATGGCAGATTTGTGCTGTGACACGTTGAGTGGTGGCAGATT
TGTGCCGTGACATGCTGAGTGCTAGTAG
Found at i:158328 original size:121 final size:122
Alignment explanation
Indices: 158128--158459 Score: 353
Period size: 121 Copynumber: 2.7 Consensus size: 122
158118 TGACATGTTA
** * * * * * * ** *
158128 AGTGCTAGTAGATATATGGTGTGACACACTGAGTGGTGGCAGATTTGTGCTGTGACACGCTGAGT
1 AGTGCTACCAGATATAGGGAGTGACACACTGAGTGCTAGCAAATTTATGGGGTCACACGCTGAGT
* * * *
158193 GGTGGCAGATTTGTGCCGTGACA-CACTGAGTGGTGGTAGATATGGCATGACATGCTG
66 GGTGGCAGATTTGTGCCATGACATCA-TGAGTGGTGGCAGATATGACATGACAGGCTG
* * * **
158250 AGTGTTACCAGATTTAGGGCGTGACATGCTGAGTGCTAGCAAATTTAT-GGGTCACACGCTGAGT
1 AGTGCTACCAGATATAGGGAGTGACACACTGAGTGCTAGCAAATTTATGGGGTCACACGCTGAGT
* * **
158314 GGTGGTAGATTTGTGCCATGACATGATGAGTGGTGGCAGATATGATGTGACAGGCTG
66 GGTGGCAGATTTGTGCCATGACATCATGAGTGGTGGCAGATATGACATGACAGGCTG
* * * * * *
158371 AGTGCTACCAGATATATGGAGTGACACATTGAGTGCTAGCAGATTTATGGGGTTACACGTTGGGT
1 AGTGCTACCAGATATAGGGAGTGACACACTGAGTGCTAGCAAATTTATGGGGTCACACGCTGAGT
* *
158436 GGTGGCAGATTTATGCCATAACAT
66 GGTGGCAGATTTGTGCCATGACAT
158460 GTTGAGTGCT
Statistics
Matches: 171, Mismatches: 37, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
121 100 0.58
122 71 0.42
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.28
Consensus pattern (122 bp):
AGTGCTACCAGATATAGGGAGTGACACACTGAGTGCTAGCAAATTTATGGGGTCACACGCTGAGT
GGTGGCAGATTTGTGCCATGACATCATGAGTGGTGGCAGATATGACATGACAGGCTG
Found at i:158389 original size:90 final size:89
Alignment explanation
Indices: 158213--158405 Score: 208
Period size: 90 Copynumber: 2.1 Consensus size: 89
158203 TTGTGCCGTG
* * * *
158213 ACACACTGAGTGGTGGTAGATATGGCATGACATGCTGAGTGTTACCAGATTTAGGGCGTGACATG
1 ACACACTGAGTGGTGGTAGATATGGCATGACATGATGAGTGGTACCAGA-TTAGGACGTGACAGG
* *
158278 CTGAGTGCTAGCAAATTTATGGGTC
65 CTGAGTGCTACCAAATATATGGGTC
* * ** * *
158303 ACACGCTGAGTGGTGGTAGATTTGTGCCATGACATGATGAGTGGTGGCAGA-TATGATGTGACAG
1 ACACACTGAGTGGTGGTAGATATG-G-CATGACATGATGAGTGGTACCAGATTAGGACGTGACAG
* *
158367 GCTGAGTGCTACCAGATATATGGAGTG
64 GCTGAGTGCTACCAAATATATGG-GTC
*
158394 ACACATTGAGTG
1 ACACACTGAGTG
158406 CTAGCAGATT
Statistics
Matches: 84, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
90 51 0.61
91 13 0.15
92 20 0.24
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.27
Consensus pattern (89 bp):
ACACACTGAGTGGTGGTAGATATGGCATGACATGATGAGTGGTACCAGATTAGGACGTGACAGGC
TGAGTGCTACCAAATATATGGGTC
Found at i:162356 original size:31 final size:31
Alignment explanation
Indices: 162321--162864 Score: 606
Period size: 31 Copynumber: 17.3 Consensus size: 31
162311 AGAAACAAAT
* *
162321 AAATGTTGTTACATGCCATGCATATA-AAGTA
1 AAATGTTGTTACACGCCATGCATA-ACAAGTC
* * *
162352 AAATGTTGTTATACGCCATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* * * *
162383 AAACGTTGTCACAAGCAATGCATAACAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
*
162414 AAATGTTGTTACACACCATGCATAACAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* * *
162445 AAATGTTGTTACACGTCATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* ** *
162476 AAATATTGTTACACGTAATACATAACAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
** *
162507 AAATGTTGTTACACGTAATGCATAATAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
** *
162538 AAATGTTGTTACACGTTATGCATAACATGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* *
162569 AAATGTTGTTACATGCCATACGCCATGCATATCAAGTA
1 AAATGTTGTT--A---C--ACGCCATGCATAACAAGTC
*
162607 AAATGTTGTTACACGCAATGCATAACAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* * *
162638 AAACGTTGTTACACGTCATGCATAACATGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* * *
162669 AAATGTTGTTACATGCCATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* *
162700 AAATGTTGTTACACGCAATGCATGACAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* *
162731 AAATATTGTTACACGCCATGCATATCAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* *
162762 AAATGTTGTTGCACGCCAAGCATATA-AAGTC
1 AAATGTTGTTACACGCCATGCATA-ACAAGTC
*
162793 AAATGTTGTTACACGCAATGCATAACAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
** * *
162824 AAATGTTGTTACACGCCACACATATCAAGTA
1 AAATGTTGTTACACGCCATGCATAACAAGTC
162855 AAATGTTGTT
1 AAATGTTGTT
162865 GCACACCAAC
Statistics
Matches: 434, Mismatches: 69, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
30 1 0.00
31 405 0.93
33 2 0.00
36 2 0.00
38 24 0.06
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (31 bp):
AAATGTTGTTACACGCCATGCATAACAAGTC
Found at i:163593 original size:47 final size:47
Alignment explanation
Indices: 163520--163904 Score: 361
Period size: 47 Copynumber: 8.3 Consensus size: 47
163510 CGTCTGACAC
* * * * *
163520 ACTCTAAACCCTAGCGTGCCACAGATTCTCACCATGGCGTCTCACAA
1 ACTCTGAACCCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACAA
* * * * *
163567 ACTCTGAACGCTAGCATGTCAAAGATTTCCTCCATGGTGTGT--CAA
1 ACTCTGAACCCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACAA
* * * * *
163612 ACTCTAAACGC-AGGCATGTTACAGCTTCCCTCCATGGCGTGTCACAA
1 ACTCTGAACCCTA-GCGTGTCACAGATTCCCTCCATGGCGTGTCACAA
* ** * * *
163659 AC-CTTGAATCCTAATGTGTCATAGATTTCCTCCATGGGGTGTCACAA
1 ACTC-TGAACCCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACAA
* * *
163706 AC-CTTGAACCCTGGTGTGTCACAGATTCCCTCCATGGCATGT--CAA
1 ACTC-TGAACCCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACAA
* * *
163751 ACTCTGAACTCTAGTGTGTCACAGATTCCCTCCATGGTGTGTCACAA
1 ACTCTGAACCCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACAA
* ** * * *
163798 ACTCTAAACCCTTCCTTGTCATAAATTCCCTCCATGGCGTGTCACAA
1 ACTCTGAACCCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACAA
** *
163845 ACTCTGAACCCTCCCTTGTCACAGATTCCCTCCATGGCGTGTCACAA
1 ACTCTGAACCCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACAA
*
163892 ATTCTGAACCCTA
1 ACTCTGAACCCTA
163905 CCCTATGATA
Statistics
Matches: 277, Mismatches: 53, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
44 1 0.00
45 76 0.27
46 2 0.01
47 197 0.71
48 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (47 bp):
ACTCTGAACCCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACAA
Found at i:163657 original size:92 final size:92
Alignment explanation
Indices: 163520--163903 Score: 346
Period size: 92 Copynumber: 4.1 Consensus size: 92
163510 CGTCTGACAC
* * * * * * *
163520 ACTCTAAACCCTAGCGTGCCACAGATTCTCACCATGGCGTCTCACAAACTCTGAACGCTAGCATG
1 ACTCTAAACCCTGGCATGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAAC-CTAGCGTG
* *
163585 TCAAAGATTTCCTCCATGGTGTGT-CAA
65 TCACAGATTCCCTCCATGGTGTGTACAA
* * * * **
163612 ACTCTAAACGCAGGCATGTTACAGCTTCCCTCCATGGCGTGTCACAAAC-CTTGAATCCTAATGT
1 ACTCTAAACCCTGGCATGTCACAGATTCCCTCCATGGCGTGTCACAAACTC-TGAA-CCTAGCGT
* * *
163676 GTCATAGATTTCCTCCATGGGGTGTCACAA
64 GTCACAGATTCCCTCCATGGTGTGT-ACAA
* ** * *
163706 AC-CTTGAACCCTGGTGTGTCACAGATTCCCTCCATGGCATGT--CAAACTCTGAACTCTAGTGT
1 ACTC-TAAACCCTGGCATGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAAC-CTAGCGT
163768 GTCACAGATTCCCTCCATGGTGTGTCACAA
64 GTCACAGATTCCCTCCATGGTGTGT-ACAA
** * * * ** *
163798 ACTCTAAACCCTTCCTTGTCATAAATTCCCTCCATGGCGTGTCACAAACTCTGAACCCTCCCTTG
1 ACTCTAAACCCTGGCATGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAA-CCTAGCGTG
*
163863 TCACAGATTCCCTCCATGGCGTGTCACAA
65 TCACAGATTCCCTCCATGGTGTGT-ACAA
* *
163892 ATTCTGAACCCT
1 ACTCTAAACCCT
163904 ACCCTATGAT
Statistics
Matches: 239, Mismatches: 42, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
91 2 0.01
92 144 0.60
93 4 0.02
94 88 0.37
95 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (92 bp):
ACTCTAAACCCTGGCATGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACCTAGCGTGT
CACAGATTCCCTCCATGGTGTGTACAA
Found at i:163732 original size:139 final size:139
Alignment explanation
Indices: 163551--163888 Score: 373
Period size: 139 Copynumber: 2.4 Consensus size: 139
163541 CAGATTCTCA
* * ** * * * *
163551 CCATGGCGTCTCACAAACTCTGAACGCTAGCATGTCAAAGATTTCCTCCATGGTGTGTCAAACTC
1 CCATGGCGTGTCACAAACTCTGAACCCTCCCTTGTCACAGATTCCCTCCATGGCGTGTCAAACTC
* * * *
163616 TAAACGC-AG-GCATGTTACAGCTTCCCTCCATGGCGTGTCACAAAC-CTTGAATCC-TAATGTG
66 TAAACGCTAGTG--TGTCACAGATTCCCTCCATGGCGTGTCACAAACTC-TAAACCCTTAAT-TG
* *
163677 TCATAGATTTCCT
127 TCATAAATTCCCT
* ** *
163690 CCATGGGGTGTCACAAAC-CTTGAACCCT-GGTGTGTCACAGATTCCCTCCATGGCATGTCAAAC
1 CCATGGCGTGTCACAAACTC-TGAACCCTCCCT-TGTCACAGATTCCCTCCATGGCGTGTCAAAC
* * * **
163753 TCTGAACTCTAGTGTGTCACAGATTCCCTCCATGGTGTGTCACAAACTCTAAACCCTTCCTTGTC
64 TCTAAACGCTAGTGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTAAACCCTTAATTGTC
163818 ATAAATTCCCT
129 ATAAATTCCCT
163829 CCATGGCGTGTCACAAACTCTGAACCCTCCCTTGTCACAGATTCCCTCCATGGCGTGTCA
1 CCATGGCGTGTCACAAACTCTGAACCCTCCCTTGTCACAGATTCCCTCCATGGCGTGTCA
163889 CAAATTCTGA
Statistics
Matches: 167, Mismatches: 24, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
138 2 0.01
139 157 0.94
140 7 0.04
141 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (139 bp):
CCATGGCGTGTCACAAACTCTGAACCCTCCCTTGTCACAGATTCCCTCCATGGCGTGTCAAACTC
TAAACGCTAGTGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTAAACCCTTAATTGTCAT
AAATTCCCT
Found at i:165788 original size:30 final size:30
Alignment explanation
Indices: 165752--165810 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
165742 GAAAAGACAA
** *
165752 TTATAAAACCAAAGTTGGTAAGGATAAAAT
1 TTATAAAACCAAAGCAGATAAGGATAAAAT
*
165782 TTATAAAACCATAGCAGATAAGGATAAAA
1 TTATAAAACCAAAGCAGATAAGGATAAAA
165811 CTAAGAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.24
Consensus pattern (30 bp):
TTATAAAACCAAAGCAGATAAGGATAAAAT
Found at i:168675 original size:2 final size:2
Alignment explanation
Indices: 168668--168719 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
168658 CAAGTACTCA
168668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
168710 AT AT AT AT AT
1 AT AT AT AT AT
168720 TTCTTAGTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:169220 original size:18 final size:17
Alignment explanation
Indices: 169197--169230 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
169187 TTTTTTTTGG
169197 TTTAAAAAATAATTTAAT
1 TTTAAAAAAT-ATTTAAT
*
169215 TTTAAAATATATTTAA
1 TTTAAAAAATATTTAA
169231 AACATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAAAAATATTTAAT
Found at i:169273 original size:26 final size:24
Alignment explanation
Indices: 169235--169307 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 24
169225 ATTTAAAACA
* *
169235 TTAAAAAAATTAAATATTAATATATT
1 TTAAATAATTTAAA-ATTAA-ATATT
*
169261 TTAAATAATTTAAAATGTTAATATT
1 TTAAATAATTTAAAAT-TAAATATT
169286 TTAGAATATATTTAAAATTAAA
1 TTA-AATA-ATTTAAAATTAAA
169308 CTCAAATCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 10 0.25
26 21 0.52
27 9 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (24 bp):
TTAAATAATTTAAAATTAAATATT
Found at i:169276 original size:27 final size:27
Alignment explanation
Indices: 169246--169303 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
169236 TAAAAAAATT
169246 AAATATTAATATATTTTA-AATA-ATTTA
1 AAATATT-A-ATATTTTAGAATATATTTA
*
169273 AAATGTTAATATTTTAGAATATATTTA
1 AAATATTAATATTTTAGAATATATTTA
169300 AAAT
1 AAAT
169304 TAAACTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 8 0.29
26 5 0.18
27 15 0.54
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
AAATATTAATATTTTAGAATATATTTA
Found at i:169306 original size:25 final size:24
Alignment explanation
Indices: 169256--169306 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 24
169246 AAATATTAAT
169256 ATATTTTAAATAATTTAAAATGTTA
1 ATATTTTAAATAATTTAAAA-GTTA
169281 ATATTTTAGAATATATTTAAAA-TTA
1 ATATTTTA-AATA-ATTTAAAAGTTA
169306 A
1 A
169307 ACTCAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 12 0.50
26 4 0.17
27 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
ATATTTTAAATAATTTAAAAGTTA
Found at i:170161 original size:11 final size:11
Alignment explanation
Indices: 170094--170164 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
170084 ATAAAAAATC
*
170094 AATAATCAAAA
1 AATAATAAAAA
170105 AATAAATAAAAA
1 AAT-AATAAAAA
*
170117 TAA-AATAAAAC
1 -AATAATAAAAA
* *
170128 AA-AATCACAA
1 AATAATAAAAA
**
170138 AATACGAAAAA
1 AATAATAAAAA
170149 AATAATAAAAA
1 AATAATAAAAA
170160 AATAA
1 AATAA
170165 CATCCGAGCA
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 9 0.20
11 28 0.61
12 7 0.15
13 2 0.04
ACGTcount: A:0.76, C:0.07, G:0.01, T:0.15
Consensus pattern (11 bp):
AATAATAAAAA
Found at i:171086 original size:15 final size:16
Alignment explanation
Indices: 171054--171087 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
171044 ATTATATAAA
171054 TTATAATTTTTTATTT
1 TTATAATTTTTTATTT
* *
171070 TTATATTTTTTTCTTT
1 TTATAATTTTTTATTT
171086 TT
1 TT
171088 CAAATAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATAATTTTTTATTT
Found at i:171634 original size:29 final size:29
Alignment explanation
Indices: 171598--171653 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
171588 GTGTATTAGA
171598 ACCCTTTAAGCATTTATATAAAAAATGAC
1 ACCCTTTAAGCATTTATATAAAAAATGAC
*
171627 ACCCTTTAAGCATTTATATGAAAAATG
1 ACCCTTTAAGCATTTATATAAAAAATG
171654 GCCAAGTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (29 bp):
ACCCTTTAAGCATTTATATAAAAAATGAC
Found at i:185111 original size:19 final size:23
Alignment explanation
Indices: 185051--185103 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
185041 TATACAAACT
*
185051 ATGAATGATAACATAAAACCCCA
1 ATGAATGATAATATAAAACCCCA
*
185074 ATGAATGATAATATAAAACCTCA
1 ATGAATGATAATATAAAACCCCA
185097 ATGAATG
1 ATGAATG
185104 TAAAAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (23 bp):
ATGAATGATAATATAAAACCCCA
Found at i:185115 original size:23 final size:23
Alignment explanation
Indices: 185051--185115 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
185041 TATACAAACT
* *
185051 ATGAATGATAACATAAAACCCCA
1 ATGAATGATAAAAAAAAACCCCA
* * *
185074 ATGAATGATAATATAAAACCTCA
1 ATGAATGATAAAAAAAAACCCCA
185097 ATGAATG-TAAAAAACAAAC
1 ATGAATGATAAAAAA-AAAC
185116 TTAGAAAGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.14
23 32 0.86
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.20
Consensus pattern (23 bp):
ATGAATGATAAAAAAAAACCCCA
Found at i:191477 original size:21 final size:21
Alignment explanation
Indices: 191453--191500 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
191443 CAGTTGATCT
*
191453 TCTATCAATAGATCAATGATG
1 TCTATCAATAGATAAATGATG
*
191474 TCTATCGATAGATAAATGATG
1 TCTATCAATAGATAAATGATG
191495 TGCTAT
1 T-CTAT
191501 GCTACTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
TCTATCAATAGATAAATGATG
Found at i:191729 original size:112 final size:111
Alignment explanation
Indices: 191517--191729 Score: 241
Period size: 112 Copynumber: 1.9 Consensus size: 111
191507 CTCTGCTAAC
* *
191517 CTATCAATAGATGTTGACATCTATCGATAGCTACCTTCTTGTCTTGCTCCCAAGTGAGAAACTAT
1 CTATCAATAGATGTTGACATCTATCGATAGCTACCTGCCTGTCTTGCTCCCAAGTGAGAAACTAT
** * *
191582 TGACAGATATATGCATCTATCGATATTTTCACAAAAGCTCTCTGAAA
66 CAACAGATAGATGCATCTATCGATAGTTT-ACAAAAGCTCTCTGAAA
* * ** *
191629 CTATCAATAGATGTTGGCATCTATTGATAGCTACCTGGCCTGTCTTGCT-TTAGGGTGAGAAACT
1 CTATCAATAGATGTTGACATCTATCGATAGCTACCT-GCCTGTCTTGCTCCCA-AGTGAGAAACT
* * * *
191693 ATCAATAGATAGCTTCATCTACTTGATAGTTT-CAAAA
64 ATCAACAGATAGATGCATCTA-TCGATAGTTTACAAAA
191730 ACGTTATTTA
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
112 40 0.48
113 35 0.42
114 8 0.10
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (111 bp):
CTATCAATAGATGTTGACATCTATCGATAGCTACCTGCCTGTCTTGCTCCCAAGTGAGAAACTAT
CAACAGATAGATGCATCTATCGATAGTTTACAAAAGCTCTCTGAAA
Found at i:191889 original size:63 final size:63
Alignment explanation
Indices: 191752--191970 Score: 275
Period size: 62 Copynumber: 3.5 Consensus size: 63
191742 ATCTCTTTGC
*
191752 AACTATCGATAGATGTTGGCATCTATCGATAGCTACCGAGCTTGTCTTGCTC-CCAGGTGAAA
1 AACTATCGATAGATGTTGGCATCTATCGATAGCTACCAAGCTTGTCTTGCTCTCCAGGTGAAA
** * *
191814 AACTATTAATAGATGTTGGCATCCATCGATAGCTATCAAGGCTTGTCTTGCTCTCC-GGTGAAA
1 AACTATCGATAGATGTTGGCATCTATCGATAGCTACCAA-GCTTGTCTTGCTCTCCAGGTGAAA
* * * * * *
191877 ATCTATCGATAGATGTTGTCATTTATCGATAGTTACCAAGCATGTCTTG-T-TCCTGGGTGAAA
1 AACTATCGATAGATGTTGGCATCTATCGATAGCTACCAAGCTTGTCTTGCTCTCC-AGGTGAAA
* *
191939 AACTATAGATAGATGTTGTCATCTATCGATAG
1 AACTATCGATAGATGTTGGCATCTATCGATAG
191971 ATGAATGAGG
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
60 3 0.02
61 1 0.01
62 79 0.58
63 51 0.38
64 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (63 bp):
AACTATCGATAGATGTTGGCATCTATCGATAGCTACCAAGCTTGTCTTGCTCTCCAGGTGAAA
Found at i:200524 original size:283 final size:282
Alignment explanation
Indices: 200017--200582 Score: 830
Period size: 283 Copynumber: 2.0 Consensus size: 282
200007 AACCAACACC
* *
200017 ATAAGTCTAGGTATACTTTTTAGCAACAAGATGGGCTTTAAGATGAGCCACTAATCCATCACGAT
1 ATAAGTCTAGGTATACCTTTTAGCAACAAGATGAGCTTTAAGATGAGCCACTAATCCATCACGAT
* ** * * * *
200082 TTACCTTTGCAGCAAATACCCATTTACACCCAATAGCTTTTTTCCTAGTTGGCAAATCAACCAAA
66 TTACCTTTACAAAAAATACCCATTTACACCCAATAGCTTTCTTCCTAATAGCCAAATCAACCAAA
* * *
200147 TCCCAAGTACCATTAGCACCTAAGGCCACCATCTCCTCTACCATAATAGCATGATAGCCAGGATG
131 TCCCAAGTACCATTAGCACCTAAGGCCACCATCTCCTCTACCATAATAGCATCACAGCCAAGATG
* * * * * *
200212 AGGCAGGGCTTCATAAATAGTTTTAGGAATTGAAACAGCATTTAAGGATGCTACAAATGAACTAG
196 AGGCAGGGCTTCATAAACAATTTTAGGAATTGAAACAGAATCTAAGAATGCTACAAACGAACTAG
200277 AAAAAAGAATACAAGTGATCATA
261 AAAAAA-AATACAAGTGATCATA
* * *
200300 ATAAGTCTAGGTATACCTTTTAGCAATAAGACT-AGTTTTAAGATGAGCCACTGATCCATCACGA
1 ATAAGTCTAGGTATACCTTTTAGCAACAAGA-TGAGCTTTAAGATGAGCCACTAATCCATCACGA
* *
200364 TTTACCTTTACAAAAAATACCCATTTGCGCCCAATAGCTTTCTTCCTAATAGCCAAATCAACCAA
65 TTTACCTTTACAAAAAATACCCATTTACACCCAATAGCTTTCTTCCTAATAGCCAAATCAACCAA
* *
200429 ATCCCAAGTACCATTAGCATCTAAGGCCACTATCTCCTCTACCATAATAGCA-CACCAGCCAAGA
130 ATCCCAAGTACCATTAGCACCTAAGGCCACCATCTCCTCTACCATAATAGCATCA-CAGCCAAGA
* * *
200493 TGAGGCAGGGTTTCATGAACAATTTTAGGAATTGAAACAGAATCTGAGAATGCTACAAACGAACT
194 TGAGGCAGGGCTTCATAAACAATTTTAGGAATTGAAACAGAATCTAAGAATGCTACAAACGAACT
*
200558 AGAAAAAAAATACAGGTGATCATA
259 AGAAAAAAAATACAAGTGATCATA
200582 A
1 A
200583 GAAATAAAGG
Statistics
Matches: 252, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
282 17 0.07
283 234 0.93
284 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (282 bp):
ATAAGTCTAGGTATACCTTTTAGCAACAAGATGAGCTTTAAGATGAGCCACTAATCCATCACGAT
TTACCTTTACAAAAAATACCCATTTACACCCAATAGCTTTCTTCCTAATAGCCAAATCAACCAAA
TCCCAAGTACCATTAGCACCTAAGGCCACCATCTCCTCTACCATAATAGCATCACAGCCAAGATG
AGGCAGGGCTTCATAAACAATTTTAGGAATTGAAACAGAATCTAAGAATGCTACAAACGAACTAG
AAAAAAAATACAAGTGATCATA
Found at i:207004 original size:25 final size:25
Alignment explanation
Indices: 206976--207032 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
206966 AAATAAAATC
206976 CCTATAATTATAGTGATTCCTAATT
1 CCTATAATTATAGTGATTCCTAATT
* *
207001 CCTATGATTATGGTGATTCCTAATT
1 CCTATAATTATAGTGATTCCTAATT
*
207026 CCCATAA
1 CCTATAA
207033 GGATGTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (25 bp):
CCTATAATTATAGTGATTCCTAATT
Found at i:209562 original size:21 final size:21
Alignment explanation
Indices: 209538--209617 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
209528 AGGTACATAT
209538 GTTGTCTTAATTAAGATAAGA
1 GTTGTCTTAATTAAGATAAGA
* * *
209559 GTTGTTTTAATTTAGATCAGA
1 GTTGTCTTAATTAAGATAAGA
* * *
209580 GTATATGTGTTAATTTAAGACACGA
1 G--T-TGTCTTAA-TTAAGATAAGA
*
209605 GATGTCTTAATTA
1 GTTGTCTTAATTA
209618 TATTATTTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
21 22 0.49
22 7 0.16
23 1 0.02
24 7 0.16
25 8 0.18
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (21 bp):
GTTGTCTTAATTAAGATAAGA
Found at i:216937 original size:21 final size:20
Alignment explanation
Indices: 216909--216948 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
216899 ACATTTTTGT
*
216909 TTCAAATATATTGATACATG
1 TTCAAATATATCGATACATG
216929 TTCACAATATATCGATACAT
1 TTCA-AATATATCGATACAT
216949 ATGATCATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (20 bp):
TTCAAATATATCGATACATG
Found at i:227081 original size:21 final size:21
Alignment explanation
Indices: 227041--227081 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
227031 AAATGTGTTC
* **
227041 ATACATGTTTATAATGTATCG
1 ATACATGTTCATAACATATCG
227062 ATACATGTTCATAACATATC
1 ATACATGTTCATAACATATC
227082 AAAACAATTT
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:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACATGTTCATAACATATCG
Found at i:228313 original size:80 final size:78
Alignment explanation
Indices: 228229--228391 Score: 188
Period size: 80 Copynumber: 2.1 Consensus size: 78
228219 ACATCATCGA
*
228229 TTCCCCTTATATATATTGGCTCTAATCCC-A-GTTAGGGACTAAAAATACCATAGGGTTAAACTT
1 TTCCCCTTATATATATTGGCTCTAATCCCAATGTAAGGG--TAAAAATACCATAGGGTT-AACTT
*
228292 GGTCAGT-GTGCCATCTT
63 GGGCA-TCGTGCCA-CTT
* * * * * *
228309 TTCCCCTTTTATATGTTGGCTTTAGTCCCAATGTAAGGGTAAGAATACCATAGGGTTAATTTGGG
1 TTCCCCTTATATATATTGGCTCTAATCCCAATGTAAGGGTAAAAATACCATAGGGTTAACTTGGG
228374 CATCGTGCCACTT
66 CATCGTGCCACTT
228387 TTCCC
1 TTCCC
228392 TTTCTTCATT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 9 0.12
79 14 0.19
80 42 0.58
81 1 0.01
82 6 0.08
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (78 bp):
TTCCCCTTATATATATTGGCTCTAATCCCAATGTAAGGGTAAAAATACCATAGGGTTAACTTGGG
CATCGTGCCACTT
Found at i:228659 original size:313 final size:313
Alignment explanation
Indices: 228087--228706 Score: 863
Period size: 313 Copynumber: 2.0 Consensus size: 313
228077 CTTTTTGTTG
* **
228087 ATTCATGTGTTTGACATGATTTGTTATTAATGCTTGATCTTAGTATGATCTTTTATGAAATTTCA
1 ATTCATGTGTTTGACATGATTTGTTATTAATGCTTAATCTTAGTATGATCTTCCATGAAATTTCA
**
228152 ATTGTGTTGTGATTGGCTCGAGTCCTAGTGTAGGGGTAAAAATACCATAAGGATAAGATTGATGA
66 ATTGTGTTGTGATTGGCTCGAGTCCTAGTGTAGGGGTAAAAATACCATAAGGATAAGATTGACAA
* * * *
228217 GCACATCATCGATTCCCCTTATATATATTGGCTCTAATCCCAGTTAGGGACTAAAAATACCATAG
131 ACACATCATCCATTCCCCATATATATATTGGCTCTAATCCCAGTTAGGGACTAAAAATACCATAA
* *
228282 GGTTAAACTTGGTCAGTGTGCCATCTTTTCCCCTTTTATATGTTGGCTTTAGTCCCAATGTAAGG
196 GGTTAAACTTGGCCAATGTGCCATCTTTTCCCCTTTTATATGTTGGCTTTAGTCCCAATGTAAGG
**
228347 GTAAGAATACCATAGGGTTAATTTGGGCATCGTGCCAC-TTTTCCCTTTCTTC
261 GTAAGAATACCATAGGGTTAATTTGGGCATCGCACCACTTTTTCCCTTTCTTC
* *
228399 ATTCAATGTGTTTGACATGATTTGTTATTGATGCTTAATCTTGGTATGATCTTCCATGAAATTTC
1 ATTC-ATGTGTTTGACATGATTTGTTATTAATGCTTAATCTTAGTATGATCTTCCATGAAATTTC
* ** * * * * *
228464 AATTTTGTTGTGATTGGCTTTAGTCCTAGTGTGGGGGTAAGAATATCAT-AGAGATGAGATTGGC
65 AATTGTGTTGTGATTGGCTCGAGTCCTAGTGTAGGGGTAAAAATACCATAAG-GATAAGATTGAC
** * * * * *
228528 AAATGCATCATCCATTCCCCATATATATATTGGCTCTAGTCCTAGTGT-GGGGCTAAGAATATCA
129 AAACACATCATCCATTCCCCATATATATATTGGCTCTAATCCCAGT-TAGGGACTAAAAATACCA
* *
228592 TAAGGTTAAGCTTGGCCAATGTGCCA-CTTTTTCCCTGTTTATATGTTGG-TTCTAGTCCCAATG
193 TAAGGTTAAACTTGGCCAATGTGCCATCTTTTCCCCT-TTTATATGTTGGCTT-TAGTCCCAATG
*
228655 TAAGGGTAAGAATACCATTGGGTTAATTTGGGCATCGCACCACTTTTTCCCT
256 TAAGGGTAAGAATACCATAGGGTTAATTTGGGCATCGCACCACTTTTTCCCT
228707 CTTTGTGAGT
Statistics
Matches: 269, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
312 17 0.06
313 243 0.90
314 9 0.03
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (313 bp):
ATTCATGTGTTTGACATGATTTGTTATTAATGCTTAATCTTAGTATGATCTTCCATGAAATTTCA
ATTGTGTTGTGATTGGCTCGAGTCCTAGTGTAGGGGTAAAAATACCATAAGGATAAGATTGACAA
ACACATCATCCATTCCCCATATATATATTGGCTCTAATCCCAGTTAGGGACTAAAAATACCATAA
GGTTAAACTTGGCCAATGTGCCATCTTTTCCCCTTTTATATGTTGGCTTTAGTCCCAATGTAAGG
GTAAGAATACCATAGGGTTAATTTGGGCATCGCACCACTTTTTCCCTTTCTTC
Found at i:228760 original size:69 final size:69
Alignment explanation
Indices: 228645--228809 Score: 217
Period size: 69 Copynumber: 2.4 Consensus size: 69
228635 TGTTGGTTCT
* ** * *
228645 AGTCCCAATGTA-AGGGTAAGAATACCATTGGGTTAATTTGGGCATCGCACCACTTTTTCCCTCT
1 AGTCCTAATGTAGA-GGTAAGAATACCATAAGGTTAAGTTGGGCATCGCACCACTTTTTCCCTCA
*
228709 TTGTG
65 TTATG
* *
228714 AGTCCTAATGTAGAGGTAAGAATACCATAAGGTTAAGTTGGTCATCGTACCACTTTTTCCCTCAT
1 AGTCCTAATGTAGAGGTAAGAATACCATAAGGTTAAGTTGGGCATCGCACCACTTTTTCCCTCAT
228779 TATG
66 TATG
*
228783 AGTCCTAGTGT-GAGGATAAGAATACCA
1 AGTCCTAATGTAGAGG-TAAGAATACCA
228810 CTAGGATGAG
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
68 4 0.05
69 80 0.94
70 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (69 bp):
AGTCCTAATGTAGAGGTAAGAATACCATAAGGTTAAGTTGGGCATCGCACCACTTTTTCCCTCAT
TATG
Found at i:232190 original size:28 final size:29
Alignment explanation
Indices: 232116--232246 Score: 131
Period size: 29 Copynumber: 4.5 Consensus size: 29
232106 GCATGCTTGT
232116 TTAATTTAGACAAGAAAACATGTTTGATC
1 TTAATTTAGACAAGAAAACATGTTTGATC
* *
232145 TTAATTTAGACAAGAAAATATGTTT-CTC
1 TTAATTTAGACAAGAAAACATGTTTGATC
* * * *
232173 TTAATTTAAGACAAAAAAATTATTTTTTATC
1 TTAATTT-AGACAAGAAAA-CATGTTTGATC
* * *
232204 GTAATCTAGACAAGAAAACATATTTG-TC
1 TTAATTTAGACAAGAAAACATGTTTGATC
* *
232232 TCAATTTAGATAAGA
1 TTAATTTAGACAAGA
232247 TAAAATATTT
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
28 22 0.26
29 39 0.46
30 16 0.19
31 7 0.08
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.37
Consensus pattern (29 bp):
TTAATTTAGACAAGAAAACATGTTTGATC
Found at i:232217 original size:59 final size:58
Alignment explanation
Indices: 232116--232239 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 58
232106 GCATGCTTGT
* * * * *
232116 TTAATTT-AGACAAGAAAACATGTTTGATCTTAATTTAGACAAGAAAATATGTTTCTC
1 TTAATTTAAGACAAAAAAACATGTTTGATCGTAATCTAGACAAGAAAACATATTTCTC
* * * *
232173 TTAATTTAAGACAAAAAAATTATTTTTTATCGTAATCTAGACAAGAAAACATATTTGTC
1 TTAATTTAAGACAAAAAAA-CATGTTTGATCGTAATCTAGACAAGAAAACATATTTCTC
*
232232 TCAATTTA
1 TTAATTTA
232240 GATAAGATAA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 7 0.13
58 10 0.18
59 38 0.69
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (58 bp):
TTAATTTAAGACAAAAAAACATGTTTGATCGTAATCTAGACAAGAAAACATATTTCTC
Found at i:233597 original size:35 final size:35
Alignment explanation
Indices: 233524--233597 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
233514 TATGATTATT
* * * *
233524 AATTTTTTTAAGAAAAATGAGTTTTTCTTGCATCA
1 AATTGTTTTAAGAAAAATGAGTTTTTCCTACATAA
233559 AATTGTTTTAAGAAAAA-GAGTTTTTCCTACATTAA
1 AATTGTTTTAAGAAAAATGAGTTTTTCCTACA-TAA
233594 AATT
1 AATT
233598 CTATTATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 12 0.35
35 22 0.65
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (35 bp):
AATTGTTTTAAGAAAAATGAGTTTTTCCTACATAA
Found at i:234068 original size:6 final size:6
Alignment explanation
Indices: 234057--234083 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
234047 TCAAATTGGG
234057 TTAAAA TTAAAA TTAAAA TTAAAA TTA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTA
234084 TAGATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TTAAAA
Found at i:238868 original size:66 final size:67
Alignment explanation
Indices: 238752--238899 Score: 165
Period size: 66 Copynumber: 2.2 Consensus size: 67
238742 TATAAGATTG
* * * **
238752 TATATATGATGTAAATTCTATATACCATATGAGATGATTGAGTATTCATGATAAATGCCATGAGA
1 TATATATGATGTATATTCTATATACCA-ATGAAATGATTGAGAAAGCATGATAAATGCCATGAGA
238817 TAA
65 TAA
* * * *
238820 TGTATATGATGTATGTTCTATACTA-C-ATGAAATGATTGAGAAAGCATGATGAATGCCGTGAGA
1 TATATATGATGTATATTCTATA-TACCAATGAAATGATTGAGAAAGCATGATAAATGCCATGAGA
*
238883 TTA
65 TAA
*
238886 TATATATGACGTAT
1 TATATATGATGTAT
238900 TTTTCAAATA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
66 45 0.67
68 20 0.30
69 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (67 bp):
TATATATGATGTATATTCTATATACCAATGAAATGATTGAGAAAGCATGATAAATGCCATGAGAT
AA
Found at i:239229 original size:16 final size:16
Alignment explanation
Indices: 239208--239241 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
239198 TTGTACTCTA
239208 TGTTGACATGAAAATG
1 TGTTGACATGAAAATG
239224 TGTTGACATGAAAATG
1 TGTTGACATGAAAATG
239240 TG
1 TG
239242 CTTAGTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (16 bp):
TGTTGACATGAAAATG
Found at i:244599 original size:20 final size:20
Alignment explanation
Indices: 244551--244600 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
244541 TGCAAATTTG
244551 ACGTGTTGCACACTCAAACA
1 ACGTGTTGCACACTCAAACA
* *
244571 ACATTTTGCACACTCAAACA
1 ACGTGTTGCACACTCAAACA
*
244591 ATGTGTTGCA
1 ACGTGTTGCA
244601 ATTCCCAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (20 bp):
ACGTGTTGCACACTCAAACA
Found at i:249590 original size:2 final size:2
Alignment explanation
Indices: 249583--249607 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
249573 GGCTTATGGC
249583 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
249608 ATGTTACGAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:271726 original size:28 final size:28
Alignment explanation
Indices: 271677--271730 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
271667 TTTTGAAAAA
*
271677 TATATTTTCTCTATAGAGTAATTCATAG
1 TATATTTTCTCTATAGACTAATTCATAG
271705 TATATTTTCTCTATA-ACCTAATTCAT
1 TATATTTTCTCTATAGA-CTAATTCAT
271731 CATAATTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (28 bp):
TATATTTTCTCTATAGACTAATTCATAG
Found at i:272028 original size:21 final size:21
Alignment explanation
Indices: 271982--272029 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
271972 ATATGGATTT
271982 TTTAGATTAAAATAAAATAATA
1 TTTA-ATTAAAATAAAATAATA
272004 --TAATTAAAAATAAAA-AATA
1 TTTAATT-AAAATAAAATAATA
272023 TTTAATT
1 TTTAATT
272030 TATTTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 7 0.30
20 11 0.48
21 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTAATTAAAATAAAATAATA
Found at i:274862 original size:2 final size:2
Alignment explanation
Indices: 274855--274879 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
274845 TTGTTTTGCA
274855 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 T
274880 GTGCATGCAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:277190 original size:265 final size:265
Alignment explanation
Indices: 276699--277206 Score: 741
Period size: 265 Copynumber: 1.9 Consensus size: 265
276689 TTAAAACTGT
* *
276699 TCTCTCACCATTCAAATATGTTGGAGTGCCCTTTTTATAGCTTGAAATGATTTTGATTTGGAGCC
1 TCTCTAACCATTCAAATATGTTGGAGTGCCCTTTTTATAGCTTGAAATGATTTGGATTTGGAGCC
* * *
276764 ATTCTAGAACTTTGAAGCAGAGAAATAGACATTGTGAGAGCAAAATTTGACCATTGGTTGCTAAA
66 ATTCTAGAACTCTGAAGCAGACAAATAGACAGTGTGAGAGCAAAATTTGACCATTGGTTGCTAAA
* * * * * * *
276829 AACAACTTAGAGGATCCATCCCTTGAAGAAAAATTTGTTTTAGGGAGCTTTTGTCCATGTAGGGA
131 AACAACATAGAGGATCCATCCCTTGAACAAAAAATTGCTTCAGGGAGATTTTGTCCATGCAGGGA
276894 TTGATCCCTTCTTCCAAAATTTCATATCTTGCACTTTTAAATCTTGAAAATGTTGTTTCTTTGTT
196 TTGATCCCTTCTTCCAAAATTTCATATCTTGCACTTTTAAATCTTGAAAATGTTGTTTCTTTGTT
276959 TCGAA
261 TCGAA
* *
276964 TCTCTAACCA-TCTAAATGTGTTGGAGTGCCCTTTTTATATCTTGAAATGATTTGGATTTGGAGC
1 TCTCTAACCATTC-AAATATGTTGGAGTGCCCTTTTTATAGCTTGAAATGATTTGGATTTGGAGC
** * * * * *
277028 TGTTGTAGAACTCTGAAGTAGACAACTAGACAGTGTGAGAGCCAAATTTGACCATTTGTTGCTAA
65 CATTCTAGAACTCTGAAGCAGACAAATAGACAGTGTGAGAGCAAAATTTGACCATTGGTTGCTAA
* * * *
277093 AATCAACATAGAGTATCGATCCCTTGAACAAAAAATTGCTTCAGGGTGATATTTGT-CATGCAGG
130 AAACAACATAGAGGATCCATCCCTTGAACAAAAAATTGCTTCAGGGAGAT-TTTGTCCATGCAGG
**
277157 GATTGATTTCTTCTTCCAAAATTTCATATCTTGCACTTTTAAATCTTGAA
194 GATTGATCCCTTCTTCCAAAATTTCATATCTTGCACTTTTAAATCTTGAA
277207 GGTTTTGTTT
Statistics
Matches: 214, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
264 2 0.01
265 207 0.97
266 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (265 bp):
TCTCTAACCATTCAAATATGTTGGAGTGCCCTTTTTATAGCTTGAAATGATTTGGATTTGGAGCC
ATTCTAGAACTCTGAAGCAGACAAATAGACAGTGTGAGAGCAAAATTTGACCATTGGTTGCTAAA
AACAACATAGAGGATCCATCCCTTGAACAAAAAATTGCTTCAGGGAGATTTTGTCCATGCAGGGA
TTGATCCCTTCTTCCAAAATTTCATATCTTGCACTTTTAAATCTTGAAAATGTTGTTTCTTTGTT
TCGAA
Found at i:290594 original size:21 final size:21
Alignment explanation
Indices: 290570--290609 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
290560 TCTTCTTTCC
290570 TTTTCTCTCTTTCTTTCTTAT
1 TTTTCTCTCTTTCTTTCTTAT
* *
290591 TTTTTTTTCTTTCTTTCTT
1 TTTTCTCTCTTTCTTTCTT
290610 CAAAACCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCTCTCTTTCTTTCTTAT
Found at i:290737 original size:9 final size:9
Alignment explanation
Indices: 290723--290761 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
290713 AGTTTTGAAG
290723 AAAAAAAGA
1 AAAAAAAGA
290732 AAAAAAAGA
1 AAAAAAAGA
290741 GAAAAAAAGA
1 -AAAAAAAGA
* *
290751 AGAAATAGA
1 AAAAAAAGA
290760 AA
1 AA
290762 CAAGCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:301694 original size:6 final size:6
Alignment explanation
Indices: 301683--301730 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
301673 AATTATATTA
* * *
301683 AAAAAT AAAAAT AAAATAT ATAAGAT TATAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAA-AT A-AAAAT AAAAAT AAAAAT AAAAAT AAAA
301731 TATATGACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 27 0.79
7 5 0.15
8 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:301703 original size:33 final size:32
Alignment explanation
Indices: 301664--301735 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
301654 TATAATGTAT
*
301664 AATATATAAAATTATATTAAAAAATAAAAATAA
1 AATATATAAAATTATAAT-AAAAATAAAAATAA
*
301697 AATATATAAGATTATAATAAAAATAAAAATAA
1 AATATATAAAATTATAATAAAAATAAAAATAA
301729 AATATAT
1 AATATAT
301736 GACATTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
32 21 0.57
33 16 0.43
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (32 bp):
AATATATAAAATTATAATAAAAATAAAAATAA
Found at i:302498 original size:34 final size:34
Alignment explanation
Indices: 302460--302527 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
302450 ATTAGGACCC
*
302460 ACATGGGTATGGCCCACTAAACCTTAGTAAGCCT
1 ACATGGGTATGGCCCACTAAACCCTAGTAAGCCT
*
302494 ACATGGGTATGGCCCACTAGACCCTAGTAAGCCT
1 ACATGGGTATGGCCCACTAAACCCTAGTAAGCCT
302528 CTCAACATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (34 bp):
ACATGGGTATGGCCCACTAAACCCTAGTAAGCCT
Found at i:304035 original size:223 final size:225
Alignment explanation
Indices: 303613--304057 Score: 504
Period size: 223 Copynumber: 2.0 Consensus size: 225
303603 TTTGGACATC
** * *
303613 TCTTAGCAATGGTTAAGCCCCCATTGCTCTTGGACATTCATGATGCATCATAGAAGTGGAATCAC
1 TCTTAGCAATGGTTAAGCCCCCATCACTCTTAGACATTCATGATGCATAATAGAAGTGGAATCAC
* ** * *
303678 AGCCTCGTTCTGAGAATGGAATTTATACCTCACTTTAATATAGGGGTAATGATAAAACCCCCAAA
66 AACCTCACTCTGAGAATGAAATTTATACCTCACTCTAATATAGGGGTAATGATAAAACCCCCAAA
* * ** *
303743 ACCTTTGGATTAACAATCAAACATTTCACATTGTATATTATCATATCCTCATAATCATAATGTAT
131 ACCTTTGGATTAACAAACAAACATATCACATTGTATAACATCATATCCTCATAATCATAAAGTAT
* **
303808 GGTATGTAGAATTTACATCACATACTTAGT
196 GGTATATAGAAACTACATCACATACTTAGT
* * * * *
303838 TCTTAGTAATGGTTCAGCTCCCATCACTCTTAGACATTCATGATGCA-AATGGAAGTGG-ATCAG
1 TCTTAGCAATGGTTAAGCCCCCATCACTCTTAGACATTCATGATGCATAATAGAAGTGGAATCAC
* * * *** **
303901 AACCTCACTCTGAGAGTGAAATTTATACCTCACTCTAATATAGTGGTAATGGTAAAACCTTTATC
66 AACCTCACTCTGAGAATGAAATTTATACCTCACTCTAATATAGGGGTAATGATAAAACCCCCAAA
* * * * * *
303966 A-CTTTTGAGTTAACAAACAAACATATCATATCT-TATAACCTCATGTCCTTATACTCATAACAG
131 ACCTTTGGA-TTAACAAACAAACATATCACAT-TGTATAACATCATATCCTCATAATCATAA-AG
304029 -ATGGTATATAGAAACTACATCACATACTT
193 TATGGTATATAGAAACTACATCACATACTT
304058 GACAGCACAA
Statistics
Matches: 181, Mismatches: 36, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
222 6 0.03
223 123 0.68
224 11 0.06
225 41 0.23
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (225 bp):
TCTTAGCAATGGTTAAGCCCCCATCACTCTTAGACATTCATGATGCATAATAGAAGTGGAATCAC
AACCTCACTCTGAGAATGAAATTTATACCTCACTCTAATATAGGGGTAATGATAAAACCCCCAAA
ACCTTTGGATTAACAAACAAACATATCACATTGTATAACATCATATCCTCATAATCATAAAGTAT
GGTATATAGAAACTACATCACATACTTAGT
Found at i:304169 original size:67 final size:67
Alignment explanation
Indices: 304087--304300 Score: 277
Period size: 67 Copynumber: 3.2 Consensus size: 67
304077 AGTACTCAAT
* *
304087 ATCATCTCATATGGTATGTGGAATCTACCTCACATACTAGCATCTTATCATTCATCATGTATTCT
1 ATCATCTCATATGGTATGTGGAATCTACCTCACATACTAGCATCATATCATTCATCATGTACTCT
304152 TC
66 TC
* * * *
304154 ATCATCTCATATGGTATGTGGAATCTACCTCACATACTATCATCACATCATTCCTCATGTGCTCT
1 ATCATCTCATATGGTATGTGGAATCTACCTCACATACTAGCATCATATCATTCATCATGTACTCT
304219 TC
66 TC
* * ** ** * *
304221 ATCATCTTATATGGTATGTGGAAACTATATCATGTACCTAGCATCGTATCATTTATCATGTACT-
1 ATCATCTCATATGGTATGTGGAATCTACCTCACATA-CTAGCATCATATCATTCATCATGTACTC
304285 TTC
65 TTC
304288 TATCATCTCATAT
1 -ATCATCTCATAT
304301 TCTTCCTAGC
Statistics
Matches: 126, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
67 94 0.75
68 32 0.25
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (67 bp):
ATCATCTCATATGGTATGTGGAATCTACCTCACATACTAGCATCATATCATTCATCATGTACTCT
TC
Found at i:311807 original size:77 final size:77
Alignment explanation
Indices: 311697--311860 Score: 238
Period size: 77 Copynumber: 2.1 Consensus size: 77
311687 AATGCTATCT
* * * * * *
311697 ATTTTAATATTGGGTGATTCATAGAGAATAGGAAATTTTTTCCTCCTCCAAAAGAAATTCTTAAA
1 ATTTTAATTTTGGGTGACTCATAAAGAATAGGAAATTGTTTCCTACTCCAAAAGAAATTCCTAAA
311762 ATTAAGGATAGA
66 ATTAAGGATAGA
* **
311774 ATTTTAATTTTGGGTGACTCATAAAGAATAGGAAATTGTTTCTTACTTTAAAAGAAATTCCTAAA
1 ATTTTAATTTTGGGTGACTCATAAAGAATAGGAAATTGTTTCCTACTCCAAAAGAAATTCCTAAA
*
311839 ATTAAGGATAGC
66 ATTAAGGATAGA
311851 ATTTTAATTT
1 ATTTTAATTT
311861 GAGAAATTCA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (77 bp):
ATTTTAATTTTGGGTGACTCATAAAGAATAGGAAATTGTTTCCTACTCCAAAAGAAATTCCTAAA
ATTAAGGATAGA
Found at i:312125 original size:17 final size:15
Alignment explanation
Indices: 312098--312131 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
312088 AGGTTTCCAA
312098 AATTAAAAAAGGTTTT
1 AATTAAAAAA-GTTTT
312114 AATTATAAAAAGTTTT
1 AATTA-AAAAAGTTTT
312130 AA
1 AA
312132 AATGGAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (15 bp):
AATTAAAAAAGTTTT
Found at i:315771 original size:20 final size:20
Alignment explanation
Indices: 315746--315785 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
315736 AGAAAAAAGA
315746 TAGAAAAACTCAAGAATTGT
1 TAGAAAAACTCAAGAATTGT
315766 TAGAAAAACTCAAGAATTGT
1 TAGAAAAACTCAAGAATTGT
315786 ACTCTTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (20 bp):
TAGAAAAACTCAAGAATTGT
Found at i:318695 original size:18 final size:19
Alignment explanation
Indices: 318668--318703 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
318658 ATTATTTATT
318668 TCCTAAC-TTTCAAAAATG
1 TCCTAACTTTTCAAAAATG
*
318686 TCCTAGCTTTTCAAAAAT
1 TCCTAACTTTTCAAAAAT
318704 ACCCAAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (19 bp):
TCCTAACTTTTCAAAAATG
Found at i:319089 original size:20 final size:20
Alignment explanation
Indices: 319064--319117 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
319054 TTCCTCTTTG
319064 ATGTATCGATACATTTGGC-A
1 ATGTATCGATACATTT-GCTA
*
319084 ATGTATCGATACATTTTCTA
1 ATGTATCGATACATTTGCTA
*
319104 ATGTATCCATACAT
1 ATGTATCGATACAT
319118 CTAGCTCGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTGCTA
Found at i:323100 original size:35 final size:35
Alignment explanation
Indices: 323054--323194 Score: 140
Period size: 35 Copynumber: 4.0 Consensus size: 35
323044 TTTAAGAAGC
** *
323054 CCAATTAACTTAATTGTTTAATTTAATCACTTAGGT
1 CCAA-TAACTTAATTAATTAATTTAATCAATTAGGT
* * * *
323090 CTAATAACTTAATTAAATAATTTAATTAATTAAGT
1 CCAATAACTTAATTAATTAATTTAATCAATTAGGT
* *
323125 CCAATAACTTGATTAAATAAATTTAATCAATTAGG-
1 CCAATAACTTAATT-AATTAATTTAATCAATTAGGT
** *
323160 CCGAATAACTTAATTAAACAATTTAATGAATTAGG
1 CC-AATAACTTAATTAATTAATTTAATCAATTAGG
323195 CTCAACTTAA
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
35 56 0.65
36 30 0.35
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (35 bp):
CCAATAACTTAATTAATTAATTTAATCAATTAGGT
Found at i:323195 original size:35 final size:34
Alignment explanation
Indices: 323073--323222 Score: 153
Period size: 35 Copynumber: 4.3 Consensus size: 34
323063 TTAATTGTTT
* * *
323073 AATTTAATCACTTAGGTCTAATAACTTAATTAAAT
1 AATTTAATCAATTAGG-CCAATAACTTAATTAAAC
* * * *
323108 AATTTAATTAATTAAGTCCAATAACTTGATTAAATA
1 AATTTAATCAATT-AGGCCAATAACTTAATTAAA-C
323144 AATTTAATCAATTAGGCCGAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCC-AATAACTTAATTAAAC
*
323179 AATTTAATGAATTAGG-C--TCAACTTAATTAAAC
1 AATTTAATCAATTAGGCCAAT-AACTTAATTAAAC
323211 AATTTTAATCAA
1 AA-TTTAATCAA
323223 GTGCTTGAGA
Statistics
Matches: 98, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
31 1 0.01
32 15 0.15
33 8 0.08
34 1 0.01
35 45 0.46
36 28 0.29
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (34 bp):
AATTTAATCAATTAGGCCAATAACTTAATTAAAC
Found at i:324125 original size:16 final size:17
Alignment explanation
Indices: 324099--324133 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
324089 TGTACCAGTC
324099 TCTAGGCATCATTGATG
1 TCTAGGCATCATTGATG
324116 TCTA-GCATCATTGATG
1 TCTAGGCATCATTGATG
324132 TC
1 TC
324134 CAGTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (17 bp):
TCTAGGCATCATTGATG
Found at i:327931 original size:25 final size:25
Alignment explanation
Indices: 327894--327948 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
327884 TGGTCATAAC
*
327894 CACGTATATCAACTCCTGGCCTTGA
1 CACGTATAACAACTCCTGGCCTTGA
** *
327919 CACGTATAACAACTTGTGGCCTTGC
1 CACGTATAACAACTCCTGGCCTTGA
327944 CACGT
1 CACGT
327949 GTAATCACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (25 bp):
CACGTATAACAACTCCTGGCCTTGA
Found at i:331505 original size:7 final size:7
Alignment explanation
Indices: 331495--331519 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
331485 AGAGTAAATT
331495 GTTTAGG
1 GTTTAGG
331502 GTTTAGG
1 GTTTAGG
331509 GTTTAGG
1 GTTTAGG
331516 GTTT
1 GTTT
331520 GTCCTAGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:344348 original size:23 final size:23
Alignment explanation
Indices: 344321--344369 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
344311 TAAACAATAT
344321 TCATGCAATA-ACCTATAAACCAG
1 TCATGCAA-AGACCTATAAACCAG
* *
344344 TCATGCAAAGACCTATCAATCAG
1 TCATGCAAAGACCTATAAACCAG
344367 TCA
1 TCA
344370 GGTAATGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (23 bp):
TCATGCAAAGACCTATAAACCAG
Done.