Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015209.1 Corchorus olitorius cultivar O-4 contig15242, 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: 177355
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3264 original size:21 final size:21
Alignment explanation
Indices: 3214--3264 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
3204 CTTCAACGTA
*
3214 GAAATATTGATAACCACGTTAT
1 GAAAT-TTGATAACCACATTAT
* *
3236 GAAAATTTGTTAACCTCATTAT
1 G-AAATTTGATAACCACATTAT
3258 GAAATTT
1 GAAATTT
3265 TCATGATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 15 0.60
23 4 0.16
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (21 bp):
GAAATTTGATAACCACATTAT
Found at i:3541 original size:22 final size:22
Alignment explanation
Indices: 3507--3583 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
3497 TTTTCTATGT
*
3507 AATTTTGACAACCTCTCCATAA
1 AATTTTGATAACCTCTCCATAA
* * *
3529 AATTTTCATAACCTCTCTATGA
1 AATTTTGATAACCTCTCCATAA
*
3551 AATTTTGTTAACCTC-CC-TAGGA
1 AATTTTGATAACCTCTCCATA--A
3573 AATTTTGATAA
1 AATTTTGATAA
3584 GCACAAATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 42 0.95
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTCTCCATAA
Found at i:3576 original size:44 final size:43
Alignment explanation
Indices: 3499--3795 Score: 171
Period size: 44 Copynumber: 6.8 Consensus size: 43
3489 GTAATATCTT
* ** * *
3499 TTCTATGTAATTTTGACAACCTCTCC-ATAAAATTTTCATAACC
1 TTCTATGAAATTTTGTTAACCTC-CCTATGAAATTTTGATAACC
*
3542 TCTCTATGAAATTTTGTTAACCTCCCTAGGAAATTTTGATAA--
1 T-TCTATGAAATTTTGTTAACCTCCCTATGAAATTTTGATAACC
* * *
3584 -GC-A-CAAATTTTGGTT-ACCTCCCTCCTTATGAAATTTTGTTAACC
1 TTCTATGAAATTTT-GTTAACCT--C-CC-TATGAAATTTTGATAACC
* ** * * *
3628 TTTTTATGAAATTTTAATAA-CTACACTATAAAATTTCGATAACC
1 -TTCTATGAAATTTTGTTAACCT-CCCTATGAAATTTTGATAACC
** *
3672 TTCATATGAAATTTCATTAACCTCCCTAAGAAATTTTGATAACC
1 TTC-TATGAAATTTTGTTAACCTCCCTATGAAATTTTGATAACC
* * ** *
3716 TTTTTATGAAATTTTGGTAACCTCTATATGAAATTATGATAA-C
1 -TTCTATGAAATTTTGTTAACCTCCCTATGAAATTTTGATAACC
* * * *
3759 TACACTATGAAGTTTTGATAACCTCCATATGAAATTT
1 T--TCTATGAAATTTTGTTAACCTCCCTATGAAATTT
3796 CGGTAACCGC
Statistics
Matches: 194, Mismatches: 41, Indels: 37
0.71 0.15 0.14
Matches are distributed among these distances:
38 11 0.06
39 4 0.02
40 2 0.01
41 2 0.01
42 15 0.08
43 6 0.03
44 136 0.70
45 5 0.03
46 1 0.01
47 4 0.02
48 8 0.04
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.40
Consensus pattern (43 bp):
TTCTATGAAATTTTGTTAACCTCCCTATGAAATTTTGATAACC
Found at i:3634 original size:22 final size:22
Alignment explanation
Indices: 3604--3826 Score: 139
Period size: 22 Copynumber: 10.1 Consensus size: 22
3594 TGGTTACCTC
* *
3604 CCTCCTTATGAAATTTTGTTAA
1 CCTCTTTATGAAATTTTGATAA
* *
3626 CCTTTTTATGAAATTTTAATAA
1 CCTCTTTATGAAATTTTGATAA
** * *
3648 -CTACACTATAAAATTTCGATAA
1 CCT-CTTTATGAAATTTTGATAA
* *
3670 CCT-TCATATGAAA-TTTCATTAA
1 CCTCT-TTATGAAATTTTGA-TAA
** *
3692 CCTCCCTAAGAAATTTTGATAA
1 CCTCTTTATGAAATTTTGATAA
* *
3714 CCTTTTTATGAAATTTTGGTAA
1 CCTCTTTATGAAATTTTGATAA
* *
3736 CCTCTATATGAAATTATGATAA
1 CCTCTTTATGAAATTTTGATAA
** *
3758 -CTACACTATGAAGTTTTGATAA
1 CCT-CTTTATGAAATTTTGATAA
** * *
3780 CCTCCATATGAAATTTCGGTAA
1 CCTCTTTATGAAATTTTGATAA
* * *
3802 CCGCATTATGAAATTTTTATAA
1 CCTCTTTATGAAATTTTGATAA
3824 CCT
1 CCT
3827 TCCTATATAA
Statistics
Matches: 149, Mismatches: 44, Indels: 16
0.71 0.21 0.08
Matches are distributed among these distances:
21 7 0.05
22 134 0.90
23 8 0.05
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
CCTCTTTATGAAATTTTGATAA
Found at i:3841 original size:66 final size:66
Alignment explanation
Indices: 3604--3841 Score: 193
Period size: 66 Copynumber: 3.6 Consensus size: 66
3594 TGGTTACCTC
* ** * * *
3604 CCTCCTTATGAAATTTTGT-TAACCTTTTTATGAAATTTTAATAA-CTACACTATAAAATTTCGA
1 CCTCATTATGAAATTTT-TATAACCTTCCTATGAAATTTTGATAACCTACA-TATGAAATTTCGG
3667 TAA
64 TAA
* * * *** *
3670 CCTTCA-TATGAAA-TTTCATTAACCTCCCTAAGAAATTTTGATAACCTTTTTATGAAATTTTGG
1 CC-TCATTATGAAATTTTTA-TAACCTTCCTATGAAATTTTGATAACCTACATATGAAATTTCGG
3733 TAA
64 TAA
* * * * *
3736 CCTC-TATATGAAATTATGATAA-CTACACTATGAAGTTTTGATAACCTCCATATGAAATTTCGG
1 CCTCAT-TATGAAATTTTTATAACCTTC-CTATGAAATTTTGATAACCTACATATGAAATTTCGG
3799 TAA
64 TAA
*
3802 CCGCATTATGAAATTTTTATAACCTTCCTAT-ATAATTTTG
1 CCTCATTATGAAATTTTTATAACCTTCCTATGA-AATTTTG
3842 GTTTGATTGT
Statistics
Matches: 134, Mismatches: 27, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
65 9 0.07
66 114 0.85
67 11 0.08
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.40
Consensus pattern (66 bp):
CCTCATTATGAAATTTTTATAACCTTCCTATGAAATTTTGATAACCTACATATGAAATTTCGGTA
A
Found at i:4144 original size:29 final size:29
Alignment explanation
Indices: 4073--4144 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
4063 TAAAAGGCTA
*
4073 TGCTTTCTAACTTTGATTCTTGGCTTATT
1 TGCTTTCTAATTTTGATTCTTGGCTTATT
* * *
4102 TGTTTTCTAGTTTTGATTTTTGGCTTATT
1 TGCTTTCTAATTTTGATTCTTGGCTTATT
4131 TGCTTTCTAATTTT
1 TGCTTTCTAATTTT
4145 ACTTGTATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.61
Consensus pattern (29 bp):
TGCTTTCTAATTTTGATTCTTGGCTTATT
Found at i:8860 original size:31 final size:29
Alignment explanation
Indices: 8822--8893 Score: 110
Period size: 28 Copynumber: 2.4 Consensus size: 29
8812 ACGTCTGTTA
*
8822 TTGTCCTAAATTCTAAGAGTTCAGGGGGCAT
1 TTGTCCTAAATT-T-AGAGTTCAAGGGGCAT
8853 TTGTCCTAAA-TTAGAGTTCAAGGGGCAT
1 TTGTCCTAAATTTAGAGTTCAAGGGGCAT
8881 TTGTCCTAAATTT
1 TTGTCCTAAATTT
8894 GTTTTGCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 25 0.64
29 3 0.08
30 1 0.03
31 10 0.26
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (29 bp):
TTGTCCTAAATTTAGAGTTCAAGGGGCAT
Found at i:12451 original size:37 final size:37
Alignment explanation
Indices: 12410--12480 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
12400 ACATAATTAT
* * *
12410 TCATAAAGTTATGTCTATTTGGATAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
12447 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
12481 ATGTTGATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:15632 original size:2 final size:2
Alignment explanation
Indices: 15625--15652 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15615 AATCCTCTTA
15625 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
15653 TGAGATATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17648 original size:33 final size:33
Alignment explanation
Indices: 17606--17676 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
17596 AAGCAGCTGA
* *
17606 TCAGCAAAAGGTCAGTGAGCTGATTAATCCAAG
1 TCAGCAAAAGGTCAGTGAGATGATCAATCCAAG
17639 TCAGCAAAAGGTCAGTGAGATGATCAATCCAAG
1 TCAGCAAAAGGTCAGTGAGATGATCAATCCAAG
*
17672 CCAGC
1 TCAGC
17677 TGAAGGAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (33 bp):
TCAGCAAAAGGTCAGTGAGATGATCAATCCAAG
Found at i:24035 original size:57 final size:56
Alignment explanation
Indices: 23958--24073 Score: 196
Period size: 57 Copynumber: 2.1 Consensus size: 56
23948 AACTACTTAC
*
23958 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACA
1 AAAGCTCGCTAAATTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAG-ACA
* *
24015 AAAGTTCGCTAAATTTAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGACA
1 AAAGCTCGCTAAATTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGACA
24071 AAA
1 AAA
24074 AAAAACCAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 6 0.11
57 50 0.89
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19
Consensus pattern (56 bp):
AAAGCTCGCTAAATTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGACA
Found at i:25113 original size:38 final size:38
Alignment explanation
Indices: 25060--25323 Score: 368
Period size: 38 Copynumber: 6.9 Consensus size: 38
25050 AAATTTATTA
* * *
25060 GTCTTTGTCCTAAGCGAATAATGAAATTGATCGTTTAG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTAG
* *
25098 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGTTTGG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTAG
* *
25136 GTCTTGATCCCAAGCGAATGATGAAATTGATCGCTTAG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTAG
*
25174 GTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTAG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTAG
* *
25212 GTATTGGTCCTAAGCGAATAATGAAATTGATCGCTTAG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTAG
* *
25250 GTCTTGGTCCCAAGCGAATGATGAAATTGATCGCTTGG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTAG
* ** *
25288 GTCTTGATCAAAATCGAATAAT-AAATTTGATCGCTT
1 GTCTTGGTCCCAAGCGAATAATGAAA-TTGATCGCTT
25324 TGTTGAAAGT
Statistics
Matches: 205, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
37 3 0.01
38 202 0.99
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (38 bp):
GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTAG
Found at i:29474 original size:35 final size:36
Alignment explanation
Indices: 29412--29489 Score: 131
Period size: 35 Copynumber: 2.1 Consensus size: 36
29402 ATCACTAAAT
29412 AATTATTTGTGCTAAAAAAAAACAGCATGATCAAGTTC
1 AATTATTTGTGCT--AAAAAAACAGCATGATCAAGTTC
29450 AATTATTTGTGCT-AAAAAACAGCATGATCAAGTTC
1 AATTATTTGTGCTAAAAAAACAGCATGATCAAGTTC
29485 AATTA
1 AATTA
29490 GTACCATCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
35 27 0.68
38 13 0.32
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (36 bp):
AATTATTTGTGCTAAAAAAACAGCATGATCAAGTTC
Found at i:38887 original size:13 final size:13
Alignment explanation
Indices: 38869--38893 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38859 TTATAATTCC
38869 AAATAATATTTAT
1 AAATAATATTTAT
38882 AAATAATATTTA
1 AAATAATATTTA
38894 AAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:39129 original size:24 final size:24
Alignment explanation
Indices: 39103--39161 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
39093 TCTAGTATAT
39103 AAATTATTATAAAACATTAAAACTAA
1 AAATTATTATAAAA-ATTAAAACT-A
*
39129 AAACTTA-TATATAAATTAAAACTA
1 AAA-TTATTATAAAAATTAAAACTA
39153 AAATTATTA
1 AAATTATTA
39162 ATTTTTAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.10
24 6 0.20
25 9 0.30
26 9 0.30
27 3 0.10
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (24 bp):
AAATTATTATAAAAATTAAAACTA
Found at i:46375 original size:1 final size:1
Alignment explanation
Indices: 46369--46438 Score: 59
Period size: 1 Copynumber: 70.0 Consensus size: 1
46359 ATAATTTCTG
* * * * * * * * *
46369 AAAAAAAAAAAACAAAAAAACAAAAAAAACAAAAAAACAAAAACAAAAACAAAACAAAACAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
46434 AAAAA
1 AAAAA
46439 CAGAATTGTG
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:46395 original size:17 final size:17
Alignment explanation
Indices: 46369--46438 Score: 99
Period size: 17 Copynumber: 4.1 Consensus size: 17
46359 ATAATTTCTG
46369 AAAA-AAAAAAAACAAA
1 AAAACAAAAAAAACAAA
46385 AAAACAAAAAAAACAAA
1 AAAACAAAAAAAACAAA
*
46402 AAAACAAAAACAAA-AAC
1 AAAACAAAAA-AAACAAA
46419 AAAACAAAACAAAACAAA
1 AAAACAAAA-AAAACAAA
46437 AA
1 AA
46439 CAGAATTGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.08
17 36 0.75
18 8 0.17
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAACAAAAAAAACAAA
Found at i:46439 original size:6 final size:6
Alignment explanation
Indices: 46370--46440 Score: 71
Period size: 6 Copynumber: 12.2 Consensus size: 6
46360 TAATTTCTGA
*
46370 AAAAAA AAAAAC AAAAA- AACAAA- AAAAAC AAAAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AA-AAAC AAAAAC --AAAAAC AAAAAC AAAAAC
46419 -AAAAC -AAAAC -AAAAC AAAAAC A
1 AAAAAC AAAAAC AAAAAC AAAAAC A
46441 GAATTGTGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
5 20 0.34
6 33 0.56
8 6 0.10
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:50414 original size:218 final size:218
Alignment explanation
Indices: 50036--50469 Score: 715
Period size: 218 Copynumber: 2.0 Consensus size: 218
50026 CAATAATAAA
* * *
50036 GGCAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTACACAAGCGGGTCTTGAAGGGTGA
1 GGCAAATTATACAATACACCGGCAGTGGAGTTTAGCAGACTACACAAGCGGGTCCTAAAGGGTGA
* * * *
50101 CATGTATCATCTAGGGACTAGTTTGAAATATTTAAAACTTAATTAATTCAAAAATTGGACATGTG
66 CATGTATCATCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGAACATGTG
* * *
50166 TCAACTTCACAACCCGCTTATGGAGTCCAAATTTTACACTGCCGGTGTATCAAATAATTACCCAT
131 TCAACTCCACAACCCGCTTATGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATTACCCAT
50231 AATAAAATTTGATAATTATTTAT
196 AATAAAATTTGATAATTATTTAT
* *
50254 GGCAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTATACAAGCGGGTCCTAAAGGGTGA
1 GGCAAATTATACAATACACCGGCAGTGGAGTTTAGCAGACTACACAAGCGGGTCCTAAAGGGTGA
* * *
50319 CATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTGATTAAAAAAATGAACATGTG
66 CATGTATCATCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGAACATGTG
* *
50384 TCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGTCGGTGTATCAAATAATTACCCAT
131 TCAACTCCACAACCCGCTTATGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATTACCCAT
50449 AATAAAATTTGATAATTATTT
196 AATAAAATTTGATAATTATTT
50470 TTTGGGTTTT
Statistics
Matches: 199, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
218 199 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (218 bp):
GGCAAATTATACAATACACCGGCAGTGGAGTTTAGCAGACTACACAAGCGGGTCCTAAAGGGTGA
CATGTATCATCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGAACATGTG
TCAACTCCACAACCCGCTTATGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATTACCCAT
AATAAAATTTGATAATTATTTAT
Found at i:50696 original size:2 final size:2
Alignment explanation
Indices: 50689--50716 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
50679 ATAAACTGTC
50689 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
50717 TGCATTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:56864 original size:16 final size:16
Alignment explanation
Indices: 56843--56876 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
56833 ATGTTGATTA
56843 ATATATGTAAGTACTT
1 ATATATGTAAGTACTT
56859 ATATATGTAAGTACTT
1 ATATATGTAAGTACTT
56875 AT
1 AT
56877 CATCAATACC
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:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
ATATATGTAAGTACTT
Found at i:57616 original size:21 final size:21
Alignment explanation
Indices: 57587--57627 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57577 CGGTCATATA
*
57587 TACTCTACAGATTAGATTATG
1 TACTCTACAGATGAGATTATG
*
57608 TACTGTACAGATGAGATTAT
1 TACTCTACAGATGAGATTAT
57628 TAGAGCAGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (21 bp):
TACTCTACAGATGAGATTATG
Found at i:63365 original size:2 final size:2
Alignment explanation
Indices: 63360--63394 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
63350 GTTTCACTAC
63360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63395 GGTTAAACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63784 original size:15 final size:15
Alignment explanation
Indices: 63766--63794 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
63756 ACCACGAAAT
63766 CCACCACCTCCACGA
1 CCACCACCTCCACGA
63781 CCACCACCTCCACG
1 CCACCACCTCCACG
63795 GCCAAAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.62, G:0.07, T:0.07
Consensus pattern (15 bp):
CCACCACCTCCACGA
Found at i:68434 original size:29 final size:30
Alignment explanation
Indices: 68397--68460 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
68387 TGTAGCGTTC
* *
68397 GGATGTTTTGCCCCCTAAACT-TTAATTTT
1 GGATATTTTGCCCCCTAAACTCTCAATTTT
68426 GGATATTTTGCCCCCTAAACTCTCAATTTT
1 GGATATTTTGCCCCCTAAACTCTCAATTTT
68456 GGATA
1 GGATA
68461 CTTAGGCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (30 bp):
GGATATTTTGCCCCCTAAACTCTCAATTTT
Found at i:69025 original size:10 final size:10
Alignment explanation
Indices: 69010--69041 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
69000 GTATGTTATC
69010 CAGGGGACAA
1 CAGGGGACAA
69020 CAGGGGACAA
1 CAGGGGACAA
*
69030 CAGAGGACAA
1 CAGGGGACAA
69040 CA
1 CA
69042 AAAATTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.22, G:0.34, T:0.00
Consensus pattern (10 bp):
CAGGGGACAA
Found at i:72488 original size:18 final size:19
Alignment explanation
Indices: 72465--72504 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
72455 AATGGTCATA
72465 ATTG-AATGGGAGCATCAC
1 ATTGAAATGGGAGCATCAC
72483 ATTGAAAAATGGGAGCATCAC
1 ATTG--AAATGGGAGCATCAC
72504 A
1 A
72505 ACGGGAGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (19 bp):
ATTGAAATGGGAGCATCAC
Found at i:79132 original size:147 final size:147
Alignment explanation
Indices: 78865--79604 Score: 704
Period size: 147 Copynumber: 5.0 Consensus size: 147
78855 AAGACTAAGA
** ** * * * **
78865 TCAAGGAATTCTAGATTCCTTAGGTGAAACAACTGCAAAGGAATTGAACCATTGAAG-TAATTAT
1 TCAAGGAATTCTAGATTCCTTAAATGAAACAACTGCGGAGGAATAGAACCACTAAAGCT-ATTGC
* * *
78929 CCCTCATGTTAAGATGCACCAGTTTGGTCAAGTTGCAGAACCCTGTCCCTGGAATTTCACCTCGG
65 CCCTCATGTTAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTCGG
* **
78994 ATTGCATTGTTGGAAATG
130 ATTGAATTGAAGGAAATG
* * *
79012 TCAAGGAATTGTAGATTCCTTGAATAAAACAACTGCGGAGGAATAGAACCAAC-AAAGCTATTGC
1 TCAAGGAATTCTAGATTCCTTAAATGAAACAACTGCGGAGGAATAGAACC-ACTAAAGCTATTGC
* * * * * *
79076 CCCACATGTTGAGATGCACCAGCTCAGTCAAGTTGCTGAACCCTGTCCCTGGAATTTCACCGCGG
65 CCCTCATGTTAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTCGG
*
79141 AATGAATT-ACCA-GAAATG
130 ATTGAATTGA--AGGAAATG
* * * * * * *
79159 TCAAGAAATTGTAGATTTCTTAAATGAAACAACTGCAGAGGAATAGAACCTCTGAAATGATTTTG
1 TCAAGGAATTCTAGATTCCTTAAATGAAACAACTGCGGAGGAATAGAACCACT-AAA-GCTATTG
* * ** * * * *
79224 --GCTCATGTCAAGATGCAGAAGTTTAGTCATATTGCTGAACCCTGCCCCTGGAGTTTCACCTTG
64 CCCCTCATGTTAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTCG
** * **
79287 GATTCTATTAAAGGAAACA
129 GATTGAATTGAAGGAAATG
* * * * * *
79306 TCAAGGAATTCTAGATTACTTAAATGAAACAACTGTGGAGGAATAGGACCACTGAA-TTCATT-T
1 TCAAGGAATTCTAGATTCCTTAAATGAAACAACTGCGGAGGAATAGAACCACTAAAGCT-ATTGC
* * * * *
79369 CCCTCCATGTCAAGATGCACTAGTTTCGTCAAATTGCTGAACCCTGTCCCCGGAATTTCACCTTG
65 CCCT-CATGTTAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTCG
79434 GATTGAATTGAAGGAAATG
129 GATTGAATTGAAGGAAATG
* * * * * * * **
79453 TCAAGGAATTCTAGATTCCTTAGATGGAACAACTCCGGAGGAATAGAACCATTGAATCCATTATC
1 TCAAGGAATTCTAGATTCCTTAAATGAAACAACTGCGGAGGAATAGAACCACTAAAGCTATTGCC
* * * *
79518 CCTCATGTTAAGATGCACCAATTTTGTCAAATTGCTCAACCCTGTCCCTGGAATTTCACCTGGGA
66 CCTCATGTTAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTCGGA
** *
79583 TAAAATTGATGGAAATG
131 TTGAATTGAAGGAAATG
79600 TCAAG
1 TCAAG
79605 AAACGTCAGG
Statistics
Matches: 486, Mismatches: 92, Indels: 30
0.80 0.15 0.05
Matches are distributed among these distances:
144 1 0.00
145 2 0.00
146 6 0.01
147 461 0.95
148 11 0.02
149 5 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (147 bp):
TCAAGGAATTCTAGATTCCTTAAATGAAACAACTGCGGAGGAATAGAACCACTAAAGCTATTGCC
CCTCATGTTAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTCGGA
TTGAATTGAAGGAAATG
Found at i:79418 original size:294 final size:293
Alignment explanation
Indices: 78865--79583 Score: 801
Period size: 294 Copynumber: 2.4 Consensus size: 293
78855 AAGACTAAGA
* * * *
78865 TCAAGGAATTCTAGATTCCTTAGGTGAAACAACTGCAAAGGAATTGAACCATTGAAGTAATTATC
1 TCAAGGAATTCTAGATTCCTTAGATGAAACAACTGCAGAGGAATAGAACCATTGAAATAATTATC
* * *
78930 CCTCATGTTAAGATGCACCAGTTTGGTCAAGTTGCAGAACCCTGTCCCTGGAATTTCACCTCGGA
66 CCTCATGTTAAGATGCACAAGTTTAGTCAA-TTGCTGAACCCTGTCCCTGGAATTTCACCTCGGA
*** ** * * *
78995 TTGCATTGTTGGAAATGTCAAGGAATTGTAGATTCCTTGAATAAAACAACTGCGGAGGAATAGAA
130 TTGCATTAAAGGAAACATCAAGGAATTCTAGATTACTTAAATAAAACAACTGCGGAGGAATAGAA
** *
79060 CCAACAAAGCTATTGCCCCACATGTTGAGATGCACCAGCTCAGTCAAGTTGCTGAACCCTGTCCC
195 CCAACAAAGCTATTGCCCCACATGTCAAGATGCACCAGCTCAGTCAAATTGCTGAACCCTGTCCC
*
79125 TGGAATTTCACCGCGGAATGAATT-ACCA-GAAATG
260 CGGAATTTCACCGCGGAATGAATTGA--AGGAAATG
* * * * * *
79159 TCAAGAAATTGTAGATTTCTTAAATGAAACAACTGCAGAGGAATAGAACC-TCTGAAATGATTTT
1 TCAAGGAATTCTAGATTCCTTAGATGAAACAACTGCAGAGGAATAGAACCAT-TGAAATAATTAT
** * * * * *
79223 GGCTCATGTCAAGATGCAGAAGTTTAGTCATATTGCTGAACCCTGCCCCTGGAGTTTCACCTTGG
65 CCCTCATGTTAAGATGCACAAGTTTAGTCA-ATTGCTGAACCCTGTCCCTGGAATTTCACCTCGG
* *
79288 ATT-CTATTAAAGGAAACATCAAGGAATTCTAGATTACTTAAATGAAACAACTGTGGAGGAATAG
129 ATTGC-ATTAAAGGAAACATCAAGGAATTCTAGATTACTTAAATAAAACAACTGCGGAGGAATAG
* * * * * *
79352 GACC-ACTGAA-TTCATTTCCCTC-CATGTCAAGATGCACTAGTTTC-GTCAAATTGCTGAACCC
193 AACCAAC-AAAGCT-ATTGCCC-CACATGTCAAGATGCACCAG-CTCAGTCAAATTGCTGAACCC
** *
79413 TGTCCCCGGAATTTCACCTTGGATTGAATTGAAGGAAATG
254 TGTCCCCGGAATTTCACCGCGGAATGAATTGAAGGAAATG
* * * *
79453 TCAAGGAATTCTAGATTCCTTAGATGGAACAACTCCGGAGGAATAGAACCATTG-AATCCATTAT
1 TCAAGGAATTCTAGATTCCTTAGATGAAACAACTGCAGAGGAATAGAACCATTGAAAT-AATTAT
* * *
79517 CCCTCATGTTAAGATGCACCAA-TTTTGTCAAATTGCTCAACCCTGTCCCTGGAATTTCACCTGG
65 CCCTCATGTTAAGATGCA-CAAGTTTAGTC-AATTGCTGAACCCTGTCCCTGGAATTTCACCTCG
79581 GAT
128 GAT
79584 AAAATTGATG
Statistics
Matches: 351, Mismatches: 61, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
293 9 0.03
294 333 0.95
295 9 0.03
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (293 bp):
TCAAGGAATTCTAGATTCCTTAGATGAAACAACTGCAGAGGAATAGAACCATTGAAATAATTATC
CCTCATGTTAAGATGCACAAGTTTAGTCAATTGCTGAACCCTGTCCCTGGAATTTCACCTCGGAT
TGCATTAAAGGAAACATCAAGGAATTCTAGATTACTTAAATAAAACAACTGCGGAGGAATAGAAC
CAACAAAGCTATTGCCCCACATGTCAAGATGCACCAGCTCAGTCAAATTGCTGAACCCTGTCCCC
GGAATTTCACCGCGGAATGAATTGAAGGAAATG
Found at i:83574 original size:147 final size:146
Alignment explanation
Indices: 83355--84241 Score: 904
Period size: 147 Copynumber: 6.0 Consensus size: 146
83345 AACACTAAGA
** * * * *
83355 TCAAGGAATTCTAGATTCCTTAAACAAAACAATTCCGGAGGAATAGTACCTTTGAACATATTTCT
1 TCAAGGAATT-TAGATTCCTTAAATGAAACAACTCCGGAGGAATAGAACCATTGAACACATTTCT
* *
83420 CCCCATGTCAAGATGCACTAATTTTGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGGA
65 CCCCATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGGA
* * *
83485 TTGAATTGTCGGAGATG
130 TTAAATTGTAGGAAATG
*
83502 TCGAGGAATTTGAGATTCCTTAAATGAAACAACTCCGGAGGAATAGAACCATTGAACACATTTCT
1 TCAAGGAATTT-AGATTCCTTAAATGAAACAACTCCGGAGGAATAGAACCATTGAACACATTTCT
* *
83567 CCACATGTAAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGT-CCTAGGAATTTCACCTTGG
65 CCCCATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCCT-GGAATTTCACCTTGG
* *
83631 AGTAAATTGTGGGAAATG
129 ATTAAATTGTAGGAAATG
* * * * * * * *
83649 TCAAGTAATTCTAGATTTCTTAAATGAAACAATTCCGGAGGAATAGTACCACTGAAGA-AATTCC
1 TCAAGGAATT-TAGATTCCTTAAATGAAACAACTCCGGAGGAATAGAACCATTGAACACATTTCT
* * * * * * * * ***
83713 CCCCAATGTCAAGTTCCACTAGTTCAATCAAATTGTTTAACTCTGTCCCAGGAATTTCACCGCCG
65 CCCC-ATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGG
*
83778 ATTGAATTGTAGGAAATG
129 ATTAAATTGTAGGAAATG
* ** * * ** *
83796 TCAAGGAATTTTAGATTCCTTAAGTGAAACAGGTGCGGAAGAATAGATTCATTGAAC-CAATTGC
1 TCAAGGAA-TTTAGATTCCTTAAATGAAACAACTCCGGAGGAATAGAACCATTGAACAC-ATTTC
* * * * * *
83860 TCCCCATGTCAAGGTGCACTAGTTCAGCCAAATTGCTGAACCCTGT-CCTGGGGATTGCACTTTG
64 TCCCCATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCCT-GGAATTTCACCTTG
83924 GATTAAATTGTAGGAAATG
128 GATTAAATTGTAGGAAATG
* ** * * *
83943 TCAAGGAATTTCAGATTCCTTAAATGAAACAACTGCTCAGGAAAAAAACCATTGAAC-CTGTTTC
1 TCAAGGAATTT-AGATTCCTTAAATGAAACAACTCCGGAGGAATAGAACCATTGAACAC-ATTTC
* * * * *
84007 GCCCCATGCCAAGATACACTAGTTTCGTCAAATTGCTGAACCCTGTCTCTGGAATTTCACCTTGG
64 TCCCCATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGG
*** *
84072 AGCGAATTGTAAGAAATG
129 ATTAAATTGTAGGAAATG
* * * * ** * **
84090 TCAAGGAATTCGAGATTCCTTAGATGAAACAGCTGCATAGGAATAGAACCATT-AAAATCATTGA
1 TCAAGGAATT-TAGATTCCTTAAATGAAACAACTCCGGAGGAATAGAACCATTGAACA-CATTTC
** * * * *
84154 AACTCATGTCAAGATGCACCAGTTTGGTCAAATTGCTGAACCCTGTCCTTGGAATTTCACCTTGG
64 TCCCCATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGG
84219 ATTAAATTGTAGGAAATG
129 ATTAAATTGTAGGAAATG
84237 TCAAG
1 TCAAG
84242 CGACATCAGG
Statistics
Matches: 604, Mismatches: 122, Indels: 28
0.80 0.16 0.04
Matches are distributed among these distances:
146 18 0.03
147 571 0.95
148 15 0.02
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (146 bp):
TCAAGGAATTTAGATTCCTTAAATGAAACAACTCCGGAGGAATAGAACCATTGAACACATTTCTC
CCCATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGGAT
TAAATTGTAGGAAATG
Found at i:83894 original size:294 final size:291
Alignment explanation
Indices: 83355--84241 Score: 1006
Period size: 294 Copynumber: 3.0 Consensus size: 291
83345 AACACTAAGA
** * *
83355 TCAAGGAATTCTAGATTCCTTAAACAAAACAATTCCGGAGGAATAGTACCTTTGAACATATTTCT
1 TCAAGGAATTCTAGATTCCTTAAATGAAACAATTCCGGAGGAATAGTACCATTGAACA-ATTTCC
* * *
83420 CCCCATGTCAAGATGCACTAATTTTGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGGA
65 CCCCATGTCAAGATACACT-AGTTCGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGGA
* * * * * *
83485 TTGAATTGTCGGAGATGTCGAGGAATTTGAGATTCCTTAAATGAAACAACTCCGGAGGAATAGAA
129 TTGAATTGTAGGAAATGTCAAGGAATTTGAGATTCCTTAAGTGAAACAGCTGCGGAGGAATAGAA
* *
83550 CCATTGAACACATTTCTCCACATGTAAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCT
194 CCATTGAACA-ATTGCTCCACATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCT
* *
83615 AGGAATTTCACCTTGGAGTAAATTGTGGGAAATG
258 AGGAATTTCACCTTGGATTAAATTGTAGGAAATG
* * * * *
83649 TCAAGTAATTCTAGATTTCTTAAATGAAACAATTCCGGAGGAATAGTACCACTGAAGAAATTCCC
1 TCAAGGAATTCTAGATTCCTTAAATGAAACAATTCCGGAGGAATAGTACCATTGAACAATTTCCC
* * * * * * * ***
83714 CCCAATGTCAAGTTCCACTAGTTCAATCAAATTGTTTAACTCTGTCCCAGGAATTTCACCGCCGA
66 CCC-ATGTCAAGATACACTAGTTC-GTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGGA
* * * *
83779 TTGAATTGTAGGAAATGTCAAGGAATTTTAGATTCCTTAAGTGAAACAGGTGCGGAAGAATAGAT
129 TTGAATTGTAGGAAATGTCAAGGAATTTGAGATTCCTTAAGTGAAACAGCTGCGGAGGAATAGAA
* * * * *
83844 TCATTGAACCAATTGCTCCCCATGTCAAGGTGCACTAGTTCAGCCAAATTGCTGAACCCTGTCCT
194 CCATTGAA-CAATTGCTCCACATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCT
* * * *
83909 GGGGATTGCACTTTGGATTAAATTGTAGGAAATG
258 AGGAATTTCACCTTGGATTAAATTGTAGGAAATG
* * ** * ** **
83943 TCAAGGAATT-TCAGATTCCTTAAATGAAACAACTGCTCAGGAAAAAAACCATTGAACCTGTTTC
1 TCAAGGAATTCT-AGATTCCTTAAATGAAACAATTCCGGAGGAATAGTACCATTGAA-CAATTTC
* * *
84007 GCCCCATGCCAAGATACACTAGTTTCGTCAAATTGCTGAACCCTGTCTCTGGAATTTCACCTTGG
64 CCCCCATGTCAAGATACACTAG-TTCGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGG
** * * **
84072 AGCGAATTGTAAGAAATGTCAAGGAATTCGAGATTCCTT-AGATGAAACAGCTGCATAGGAATAG
128 ATTGAATTGTAGGAAATGTCAAGGAATTTGAGATTCCTTAAG-TGAAACAGCTGCGGAGGAATAG
* *** * * *
84136 AACCATT-AAAATCATTGAAACTCATGTCAAGATGCACCAGTTTGGTCAAATTGCTGAACCCTGT
192 AACCATTGAACA--ATTGCTCCACATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGT
*
84200 CCTTGGAATTTCACCTTGGATTAAATTGTAGGAAATG
255 CCTAGGAATTTCACCTTGGATTAAATTGTAGGAAATG
84237 TCAAG
1 TCAAG
84242 CGACATCAGG
Statistics
Matches: 488, Mismatches: 96, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
292 1 0.00
293 16 0.03
294 459 0.94
295 12 0.02
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (291 bp):
TCAAGGAATTCTAGATTCCTTAAATGAAACAATTCCGGAGGAATAGTACCATTGAACAATTTCCC
CCCATGTCAAGATACACTAGTTCGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTGGATT
GAATTGTAGGAAATGTCAAGGAATTTGAGATTCCTTAAGTGAAACAGCTGCGGAGGAATAGAACC
ATTGAACAATTGCTCCACATGTCAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCTAGG
AATTTCACCTTGGATTAAATTGTAGGAAATG
Found at i:84187 original size:441 final size:441
Alignment explanation
Indices: 83418--84241 Score: 1021
Period size: 441 Copynumber: 1.9 Consensus size: 441
83408 GAACATATTT
** * *
83418 CTCCCCATGTCAAGATGCACTAATTTTGTCAAATTGCTGAACCCTGTCCCTGGAATTTCACCTTG
1 CTCCCCATGTCAAGATGCACTAATTCAGCCAAATTGCTGAACCCTGTCCCTGGAATTGCACCTTG
* * * * * * * *
83483 GATTGAATTGTCGGAGATGTCGAGGAATTTGAGATTCCTTAAATGAAACAACTCCGGAGGAATAG
66 GATTAAATTGTAGGAAATGTCAAGGAATTTCAGATTCCTTAAATGAAACAACTCCGCAGGAAAAA
* * *
83548 AACCATTGAACACATTTCTCCACATGTAAAGATGCACTAGTTTAGTCAAATTGCTGAACCCTGTC
131 AACCATTGAACACATTTCGCCACATGCAAAGATACACTAGTTTAGTCAAATTGCTGAACCCTGTC
* ** * * *
83613 CTAGGAATTTCACCTTGGAGTAAATTGTGGGAAATGTCAAGTAATTCTAGATTTCTTAAATGAAA
196 CTAGGAATTTCACCTTGGAGCAAATTGTAAGAAATGTCAAGGAATTCGAGATTCCTTAAATGAAA
* * * *** * *
83678 CAATTCCGGAGGAATAGTACCACTGAAGAAATTCCCCCCAATGTCAAGTTCCACTAGTTCAATCA
261 CAACTCCAGAGGAATAGAACCACTGAAGAAATTAAACCCAATGTCAAGATCCACCAGTTCAATCA
* * * *
83743 AATTGTTTAACTCTGTCCCAGGAATTTCACCGCCGATTGAATTGTAGGAAATGTCAAGGAATTTT
326 AATTGCTGAACCCTGTCCCAGGAATTTCACCGCCGATTAAATTGTAGGAAATGTCAAGGAATTTT
83808 AGATTCCTTAAGTGAAACAGGTGCGGAAGAATAGATTCATTGAACCAATTG
391 AGATTCCTTAAGTGAAACAGGTGCGGAAGAATAGATTCATTGAACCAATTG
* * * *
83859 CTCCCCATGTCAAGGTGCACTAGTTCAGCCAAATTGCTGAACCCTGT-CCTGGGGATTGCACTTT
1 CTCCCCATGTCAAGATGCACTAATTCAGCCAAATTGCTGAACCCTGTCCCT-GGAATTGCACCTT
* *
83923 GGATTAAATTGTAGGAAATGTCAAGGAATTTCAGATTCCTTAAATGAAACAACTGCTCAGGAAAA
65 GGATTAAATTGTAGGAAATGTCAAGGAATTTCAGATTCCTTAAATGAAACAACTCCGCAGGAAAA
* * * *
83988 AAACCATTGAAC-CTGTTTCGCCCCATGCCAAGATACACTAGTTTCGTCAAATTGCTGAACCCTG
130 AAACCATTGAACAC-ATTTCGCCACATGCAAAGATACACTAGTTTAGTCAAATTGCTGAACCCTG
* *
84052 TCTCT-GGAATTTCACCTTGGAGCGAATTGTAAGAAATGTCAAGGAATTCGAGATTCCTTAGATG
194 TC-CTAGGAATTTCACCTTGGAGCAAATTGTAAGAAATGTCAAGGAATTCGAGATTCCTTAAATG
* * * * * *
84116 AAACAGCTGCATAGGAATAGAACCA-TTAA-AATCATTGAAACTC-ATGTCAAGATGCACCAGTT
258 AAACAACTCCAGAGGAATAGAACCACTGAAGAA--ATT-AAACCCAATGTCAAGATCCACCAGTT
*** ** ***
84178 TGGTCAAATTGCTGAACCCTGTCCTTGGAATTTCACCTTGGATTAAATTGTAGGAAATGTCAAG
320 CAATCAAATTGCTGAACCCTGTCCCAGGAATTTCACCGCCGATTAAATTGTAGGAAATGTCAAG
84242 CGACATCAGG
Statistics
Matches: 318, Mismatches: 59, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
439 2 0.01
440 7 0.02
441 305 0.96
442 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (441 bp):
CTCCCCATGTCAAGATGCACTAATTCAGCCAAATTGCTGAACCCTGTCCCTGGAATTGCACCTTG
GATTAAATTGTAGGAAATGTCAAGGAATTTCAGATTCCTTAAATGAAACAACTCCGCAGGAAAAA
AACCATTGAACACATTTCGCCACATGCAAAGATACACTAGTTTAGTCAAATTGCTGAACCCTGTC
CTAGGAATTTCACCTTGGAGCAAATTGTAAGAAATGTCAAGGAATTCGAGATTCCTTAAATGAAA
CAACTCCAGAGGAATAGAACCACTGAAGAAATTAAACCCAATGTCAAGATCCACCAGTTCAATCA
AATTGCTGAACCCTGTCCCAGGAATTTCACCGCCGATTAAATTGTAGGAAATGTCAAGGAATTTT
AGATTCCTTAAGTGAAACAGGTGCGGAAGAATAGATTCATTGAACCAATTG
Found at i:93128 original size:21 final size:21
Alignment explanation
Indices: 93090--93129 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
93080 CGCTGTTCTA
* *
93090 ATAATCTCATCTGTACAGTAC
1 ATAATCTAATCTGCACAGTAC
*
93111 ATAATCTAATTTGCACAGT
1 ATAATCTAATCTGCACAGT
93130 GTAATTTCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (21 bp):
ATAATCTAATCTGCACAGTAC
Found at i:106659 original size:13 final size:13
Alignment explanation
Indices: 106641--106666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
106631 GCATCTTGCT
106641 TTGGCTAAATAAA
1 TTGGCTAAATAAA
106654 TTGGCTAAATAAA
1 TTGGCTAAATAAA
106667 ATTAATAAGG
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:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
TTGGCTAAATAAA
Found at i:132323 original size:31 final size:32
Alignment explanation
Indices: 132288--132359 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
132278 GGTATTACTG
* *
132288 ACGTGACAATGTCATGTC-AGA-TAAAAATGAC
1 ACGTGACAATGTCACGTCGA-ACCAAAAATGAC
*
132319 ACGTGACAATGTCACGTCGAACCAAAAATGTC
1 ACGTGACAATGTCACGTCGAACCAAAAATGAC
132351 ACGTGACAA
1 ACGTGACAA
132360 AACCACGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 18 0.50
32 18 0.50
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (32 bp):
ACGTGACAATGTCACGTCGAACCAAAAATGAC
Found at i:136163 original size:21 final size:22
Alignment explanation
Indices: 136137--136183 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
136127 GGTGTGCTTG
*
136137 TTTGATGTCATGGCATTTTC-T
1 TTTGATGTCATGACATTTTCGT
136158 TTTGATGTCATGACATTTTCGT
1 TTTGATGTCATGACATTTTCGT
136180 TTTG
1 TTTG
136184 GGGCCAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.15, C:0.13, G:0.19, T:0.53
Consensus pattern (22 bp):
TTTGATGTCATGACATTTTCGT
Found at i:151384 original size:38 final size:38
Alignment explanation
Indices: 151342--151417 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
151332 TAAACTGCTT
151342 CCTGCTATGGTTAGAATCAAGCAAAGAACAGAAAAAAA
1 CCTGCTATGGTTAGAATCAAGCAAAGAACAGAAAAAAA
151380 CCTGCTATGGTTAGAATCAAGCAAAGAACAGAAAAAAA
1 CCTGCTATGGTTAGAATCAAGCAAAGAACAGAAAAAAA
151418 AACCTAGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.16
Consensus pattern (38 bp):
CCTGCTATGGTTAGAATCAAGCAAAGAACAGAAAAAAA
Found at i:153957 original size:4 final size:4
Alignment explanation
Indices: 153950--153976 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
153940 AACATCTTCA
153950 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
153977 CTACACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:161993 original size:33 final size:33
Alignment explanation
Indices: 161947--162011 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
161937 ACTGGTAGGT
* *
161947 CTAGGGCGGCATGCCATGGTTGGTGCCGCCCTC
1 CTAGGGCGACATGCCATGGTTAGTGCCGCCCTC
161980 CTAGGGCGACATGCCATGGTTAGTGCCGCCCT
1 CTAGGGCGACATGCCATGGTTAGTGCCGCCCT
162012 AGGAGGAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.12, C:0.32, G:0.34, T:0.22
Consensus pattern (33 bp):
CTAGGGCGACATGCCATGGTTAGTGCCGCCCTC
Found at i:162068 original size:10 final size:10
Alignment explanation
Indices: 162055--162129 Score: 59
Period size: 10 Copynumber: 7.5 Consensus size: 10
162045 TTTTTTAATT
162055 ATTAATTATA
1 ATTAATTATA
*
162065 ATTAATAATA
1 ATTAATTATA
162075 A-TAATT-TAA
1 ATTAATTAT-A
*
162084 ATTAATAATA
1 ATTAATTATA
162094 ATTAA-TATTA
1 ATTAATTA-TA
162104 A-TAATTAAATA
1 ATTAATT--ATA
*
162115 ATTAATAATA
1 ATTAATTATA
162125 ATTAA
1 ATTAA
162130 AAAAATAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
8 1 0.02
9 10 0.19
10 32 0.62
11 4 0.08
12 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATTAATTATA
Found at i:162088 original size:29 final size:28
Alignment explanation
Indices: 162055--162123 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
162045 TTTTTTAATT
162055 ATTAATTATAATTAATAATAATAATTTAA
1 ATTAATTATAATTAATAATAATAA-TTAA
* *
162084 ATTAATAATAATTAATATTAATAATTAA
1 ATTAATTATAATTAATAATAATAATTAA
162112 A-TAATTAATAAT
1 ATTAATT-ATAAT
162124 AATTAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.11
28 10 0.28
29 22 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTAATTATAATTAATAATAATAATTAA
Found at i:162089 original size:16 final size:15
Alignment explanation
Indices: 162055--162130 Score: 86
Period size: 16 Copynumber: 5.1 Consensus size: 15
162045 TTTTTTAATT
*
162055 ATTAATTATAATT-A
1 ATTAATAATAATTAA
162069 A-TAATAATAATTTAA
1 ATTAATAATAA-TTAA
162084 ATTAATAATAATTAA
1 ATTAATAATAATTAA
*
162099 TATTAATAATTAAAT-A
1 -ATTAATAA-TAATTAA
162115 ATTAATAATAATTAA
1 ATTAATAATAATTAA
162130 A
1 A
162131 AAAATAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
13 8 0.15
14 7 0.13
15 16 0.30
16 18 0.34
17 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAATAATAATTAA
Found at i:162105 original size:13 final size:14
Alignment explanation
Indices: 162057--162123 Score: 75
Period size: 13 Copynumber: 4.7 Consensus size: 14
162047 TTTTAATTAT
*
162057 TAATTATAATT-AA
1 TAATAATAATTAAA
162070 TAATAATAATTTAAA
1 TAATAATAA-TTAAA
162085 TTAATAATAATT-AA
1 -TAATAATAATTAAA
*
162099 TATTAATAATTAAA
1 TAATAATAATTAAA
162113 TAATTAATAAT
1 TAA-TAATAAT
162124 AATTAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
13 18 0.39
14 8 0.17
15 11 0.24
16 9 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATAATAATTAAA
Found at i:165336 original size:327 final size:328
Alignment explanation
Indices: 164517--165668 Score: 1265
Period size: 332 Copynumber: 3.5 Consensus size: 328
164507 AATTACGCGA
* * ** *
164517 AATATTTTT-CTCA-ATTATTAGACACAATACTCATAAAAAATATATAATTCAACGGCAAAAAGA
1 AATATTTTTCCTCATATTTTTAGCCACAATACTCAT-AGGAATATATAATTCAACGCCAAAAAGA
* * * * * * *
164580 TTGAACGGCTTCTCACGCTTCTAATATCGTTTTCCCTATTTTTTTTTCAAATTAATTTTTAATTA
65 TTGAAAGGCTTTTCACGCTTCCAATATCGTTTTTCCTA-TATTTTCT-GAATTAATTTTTAATTA
** * *
164645 AATCGAAACATGATTCAAATGTTCGTAAAAA-ACAATCCTTAAATCCAATGTGGTGGCTAAGATT
128 AATCGAAACAAAATTCAAATGCTCGTAAAAACA-AATCCTTAAATCC-AT-T-GTGGCTGAGATT
* * * * * * * * **
164709 TGGTTAGATGAATAAAGATATTTCAATGAGTTTTGCCACAAAAAATCATGCAAAACTGACCCATG
189 TGGTTAGATAAATATAGATATTTCAAAGAGTATTGGCGCCAAAAATCATGCAAAACTGAGCCGGG
* * * * *
164774 GCACC-AGAACGCATTTTTAGCCAAAAAACCGTGATTGGAACACGTTTTCGGCTAAAATTTTACA
254 GCACCGA-AACGC-GTTTTAGCC-AAAAACCGTGATTAGTACACGATTTCGGCTAAAATTTTGCA
* *
164838 AAAATTGACTCGA
316 AAAATTGACCCGT
** *
164851 AATATTTTTCCTCA-A-TTTTAGCTGCAATACTCATA--AATTATATACACTTCAATGCCAAAAA
1 AATATTTTTCCTCATATTTTTAGCCACAATACTCATAGGAA-TATATA-A-TTCAACGCCAAAAA
* ** * *
164912 GATTG-GAGGACTTTTCACGCTTTTAATATAGTTTTT-C-ATATTTATCTGAATTAATTTCTAAT
63 GATTGAAAGG-CTTTTCACGCTTCCAATATCGTTTTTCCTATATTT-TCTGAATTAATTTTTAAT
* * * * * * *
164974 TAAATCAAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATTCATTGCGGCTGAGATTTT
126 TAAATCGAAACAAAATTCAAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * * * *
165039 ATTAGATAAATGTAGATATTTCAAAGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGC
191 GTTAGATAAATATAGATATTTCAAAGAGTATTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGC
* * * *
165104 TCCGAAATGCGTTTATAGCCAAAAACCGTGA-T-GTACAAGATTTCAGCTAAAATTTTGCAAAAA
256 ACCGAAACGCGTTT-TAGCCAAAAACCGTGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
165167 TTGACCCGT
320 TTGACCCGT
* * *
165176 AAGATTTTTCCTCATATTTTTA-CCACAATAGTCATATGGAATATATAATTCAATGCCAAAAAGA
1 AATATTTTTCCTCATATTTTTAGCCACAATACTCATA-GGAATATATAATTCAACGCCAAAAAGA
* *
165240 TTGAAAGGTTTTTCACGCTTCCAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATA
65 TTGAAAGGCTTTTCACGCTTCCAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTAAA
* * * * *
165305 TCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTA
130 TCGAAACAAAATTCAAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTA
* * * *
165370 GATTAATATAGATATTTCAAGGATTATTGGCG-CAAAAGATCATGCAAAACTGAGCCGGGGCCCC
195 GATAAATATAGATATTTCAAAGAGTATTGGCGCCAAAA-ATCATGCAAAACTGAGCCGGGGCACC
* * *
165434 GGAACGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCGAAAATTTTGCAAAAA
259 GAAACGCGTTTT-AGCCAAAAACCGTGA---TTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
*
165499 TTGACCTGT
320 TTGACCCGT
*
165508 AATATTTTTCCTCAT-TTTTTAGCCACAATACTCATAAGGAATATATAATTCAACACCAAAAAGA
1 AATATTTTTCCTCATATTTTTAGCCACAATACTCAT-AGGAATATATAATTCAACGCCAAAAAGA
* *
165572 TTGAAAGGCTTTTCACGCTTCCAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTCATTATA
65 TTGAAAGGCTTTTCACGCTTCCAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTAAA
* *
165637 TCGAAAGAAAATTTAAATGCTCGTAAAAACAA
130 TCGAAACAAAATTCAAATGCTCGTAAAAACAA
165669 TAGTCATATG
Statistics
Matches: 698, Mismatches: 94, Indels: 54
0.83 0.11 0.06
Matches are distributed among these distances:
325 46 0.07
326 60 0.09
327 169 0.24
328 85 0.12
329 4 0.01
330 2 0.00
331 66 0.09
332 192 0.28
333 6 0.01
334 63 0.09
335 5 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (328 bp):
AATATTTTTCCTCATATTTTTAGCCACAATACTCATAGGAATATATAATTCAACGCCAAAAAGAT
TGAAAGGCTTTTCACGCTTCCAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTAAAT
CGAAACAAAATTCAAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAG
ATAAATATAGATATTTCAAAGAGTATTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCACCGA
AACGCGTTTTAGCCAAAAACCGTGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC
CGT
Found at i:165770 original size:133 final size:133
Alignment explanation
Indices: 165532--165801 Score: 461
Period size: 133 Copynumber: 2.0 Consensus size: 133
165522 TTTTTTAGCC
*
165532 ACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCTTTTCACGCTTCCAAT
1 ACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCGTTTCACGCTTCCAAT
*
165597 ATCGTTTTTCCTATATTTTCTGAATTAATTTTTCATTATATCGAAAGAAAATTTAAATGCTCGTA
66 ATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
165662 AAA
131 AAA
* * * * *
165665 ACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTG-AAGAGCGTTTCACGCTTCTAA
1 ACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAG-GCGTTTCACGCTTCCAA
165729 TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
65 TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
165794 AAAA
130 AAAA
165798 ACAA
1 ACAA
165802 ATCCTCAAGT
Statistics
Matches: 129, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
132 3 0.02
133 126 0.98
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (133 bp):
ACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCGTTTCACGCTTCCAAT
ATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
AAA
Found at i:166103 original size:465 final size:464
Alignment explanation
Indices: 165200--166133 Score: 1563
Period size: 465 Copynumber: 2.0 Consensus size: 464
165190 TATTTTTACC
*
165200 ACAATAGTCATATGGAATATATAATTCAATGCCAAAAAGATTGAAAGGTTTTTCACGCTTCCAAT
1 ACAATAGTCATATGGAATATATAATTCAACGCCAAAAAGATTGAAAGG-TTTTCACGCTTCCAAT
165265 ATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
65 ATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
165330 AAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATT
130 AAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATT
***
165395 ATTGGCGCAAAAGATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGT
195 ATTAAAGCAAAAGATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGT
* * *
165460 GATGGTTAGTACACGATTTCGGCGAAAATTTTGCAAAAATTGACCTGTAATATTTTTCCTCATTT
260 GATGGCTAGTACACGATTTCGGCGAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTT
* *
165525 TTTAGCCACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCTTTTCACGC
325 TTTAACCACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCGTTTCACGC
*
165590 TTCCAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTCATTATATCGAAAGAAAATTTAAAT
390 TTCCAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAAT
165655 GCTCGTAAAA
455 GCTCGTAAAA
* *
165665 ACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTGAAGAGCG-TTTCACGCTTCTAA
1 ACAATAGTCATATGGAATATATAATTCAACGCCAAAAAGATTGAA-AG-GTTTTCACGCTTCCAA
165729 TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
64 TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
165794 AAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAT
129 AAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAT
* ** *
165859 TATTAAAGCAAACA-ATCGTGCAAAACTGAGTTGGGGCCCCGTAACGCGATTTT-AGCCAAAAAC
194 TATTAAAGCAAA-AGATCATGCAAAACTGAGCCGGGGCCCCGGAACGCG-TTTTCAGCCAAAAAC
*
165922 TGTGATGGCTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCA
257 TGTGATGGCTAGTACACGATTTCGGCGAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCA
* * * **
165987 TTTTTTAACCACAATAGTCATATGGAATATATAATTCGATGCCAAAAAGATT-AAAGAGCGTTTC
322 TTTTTTAACCACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAG-GCGTTTC
*
166051 ACGCTTCTAATATCG-TTTTCCTATATTTTCTGAATTAATTTTTAATTTATATCGAAAGAAAATT
386 ACGCTTCCAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAA-TTATATCGAAAGAAAATT
166115 TAAATGCTCGTAAAA
450 TAAATGCTCGTAAAA
166130 ACAA
1 ACAA
166134 ATCCTCAACT
Statistics
Matches: 440, Mismatches: 23, Indels: 12
0.93 0.05 0.03
Matches are distributed among these distances:
464 33 0.08
465 399 0.91
466 7 0.02
467 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (464 bp):
ACAATAGTCATATGGAATATATAATTCAACGCCAAAAAGATTGAAAGGTTTTCACGCTTCCAATA
TCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAA
AAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTA
TTAAAGCAAAAGATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGTG
ATGGCTAGTACACGATTTCGGCGAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTTT
TTAACCACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCGTTTCACGCT
TCCAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATG
CTCGTAAAA
Found at i:166772 original size:324 final size:324
Alignment explanation
Indices: 165665--166898 Score: 1871
Period size: 332 Copynumber: 3.8 Consensus size: 324
165655 GCTCGTAAAA
*
165665 ACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTGAAGAGCGTTTCACGCTTCTAAT
1 ACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTGAAGAGCATTTCACGCTTCTAAT
165730 ATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
66 ATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
*
165795 AAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATT
131 AAAACAAATCCTCAACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGA-A-TT--A-GATT
** * * ** * *
165860 ATTAAAGCAAACAATCGTGCAAAACTGAGTTGGGGCCCCGTAACGCGATTTTAGCCAAAAACTGT
191 ATTAGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGT
*
165925 GATGGCTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTT
256 GAT-G-TTGT-CACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTT
165990 TTTAACC
318 TTTAACC
* * *
165997 ACAATAGTCATATGGAATATATAATTCGATGCCAAAAAGATTAAAGAGCGTTTCACGCTTCTAAT
1 ACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTGAAGAGCATTTCACGCTTCTAAT
166062 ATCG-TTTTCCTATATTTTCTGAATTAATTTTTAATTTATATCGAAAGAAAATTTAAATGCTCGT
66 ATCGTTTTTCCTATATTTTCTGAATTAATTTTTAA-TTATATCGAAAGAAAATTTAAATGCTCGT
*
166126 AAAAACAAATCCTCAACTCCATTGTGATTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAT
130 AAAAACAAATCCTCAACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGA-A-TT--A-GAT
* *
166191 TATTAGCGCAAAAAATCATGCAAATCTGAGCCAGGGCCCCGGAACGCGTTTTTAGCCAAAAACTG
190 TATTAGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTG
*
166256 TGA---TG--ACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGTAAGATTTTTCCTCA-TTTT
255 TGATGTTGTCACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTTTT
*
166315 T-ATC
320 TAACC
*
166319 ACAATAGTCATATGGAATATATAATTTGACGCCAAAAAGATTGAAGAGCATTTCACGCTTCTAAT
1 ACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTGAAGAGCATTTCACGCTTCTAAT
* * * *
166384 GTTGTTTTTCCTTTATTTTCGGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
66 ATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
* *
166449 AAAACAAATCCTCAACTCCATTGTTGTTGAGATTTTGTTAGATTAATATAG-A-T-GATTATTAG
131 AAAACAAATCCTCAACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGAATTAGATTATTAG
166511 CGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGT
196 CGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATG-
*
166576 TTTGTTCACGATTTCGGCTAAAATTTTGCAAATATTGACCCGTAAGATTTTTCCTCATTTTTTAA
260 -TTG-TCACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTTTTTAA
166641 CC
323 CC
166643 ACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTGAAGAGCATTTCACGCTTCTAAT
1 ACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTGAAGAGCATTTCACGCTTCTAAT
*
166708 ATTGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
66 ATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
* * *
166773 AAAACAAATCCTCAAGTCCATTGAGGTTGAGATTTGGTTAGAATAATATAGATATTTCAAGGATT
131 AAAACAAATCCTCAACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGA-A-TT--A-GATT
* * *
166838 ATTGGCGCAAAAAAATCATGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTCAG-CAAAAA
191 ATTAGCGC-AAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAA
166899 TTGACCTGTA
Statistics
Matches: 836, Mismatches: 45, Indels: 42
0.91 0.05 0.05
Matches are distributed among these distances:
314 69 0.08
318 1 0.00
319 2 0.00
320 1 0.00
322 191 0.23
323 38 0.05
324 223 0.27
326 1 0.00
327 1 0.00
328 1 0.00
331 30 0.04
332 234 0.28
333 44 0.05
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (324 bp):
ACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTGAAGAGCATTTCACGCTTCTAAT
ATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTA
AAAACAAATCCTCAACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGAATTAGATTATTAG
CGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGT
TGTCACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTTTTTAACC
Found at i:167169 original size:133 final size:133
Alignment explanation
Indices: 166931--167201 Score: 454
Period size: 133 Copynumber: 2.0 Consensus size: 133
166921 ATTTTTTAGC
* * *
166931 AACAATACTTATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCTTTTCACGCTTCCAT
1 AACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCGTTTCACGCTTCCAA
166996 TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
66 TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
167061 AAA
131 AAA
* * * * *
167064 AACAATAGTCATATGGAATATATAATTCAACCCCAATAAGATTG-AAGAGCGTTTCACGCTTCTA
1 AACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAG-GCGTTTCACGCTTCCA
167128 ATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCG
65 ATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCG
167193 TAAA
130 TAAA
167197 AACAA
1 AACAA
167202 ATCCTCAAGT
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
132 3 0.02
133 126 0.98
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (133 bp):
AACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCGTTTCACGCTTCCAA
TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
AAA
Found at i:167823 original size:333 final size:333
Alignment explanation
Indices: 167064--167984 Score: 1490
Period size: 332 Copynumber: 2.8 Consensus size: 333
167054 TGCTCGTAAA
* * * * *
167064 AACAATAGTCATATGGAATATATAATTCAACCCCAATAAGATTGAAGAGCGTTTCACGCTTCTAA
1 AACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAGAGCGTTTCACGCTTCCAA
167129 TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
66 TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
* *
167194 AAAAACAAATCCTCAAGTCCATTGTAGTTGAGATTTGGTTAGATTCATATAGATATTTCAAGGAT
131 AAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAT
* * * ** * * *
167259 TATTGGCGCAAAAAATCGTGCAAAACTGAGTCGAGGCCCCATAACACGATTTTAGCC-AAAAATT
196 TATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAAAT
* * *
167323 GTGATGGTTAGTACACGGTTTCGGCTAAAATTTTGCAAAAATTGACATGTAAGATTTTTCCTCAT
261 GAGATGGTTAGTACACGATTTCGGCGAAAATTTTGCAAAAATTGACATGTAAGATTTTTCCTCAT
167388 TTTTTAGC
326 TTTTTAGC
* * * *
167396 CACAATACTCATAAGGAATATATAATTCAACGCCCAAAAGATTGAA-AGGGCTTTCACGCTTCCA
1 AACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAGAGCG-TTTCACGCTTCCA
* * * *
167460 ATATCGTTTTTCCCAGATTTTCTGAATTAATTATTAATTATATCGAAAGAAAATTTAAGTGCTCG
65 ATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCG
167525 TAAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGA
130 TAAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGA
* *
167590 TTATTAGCGCAAAAAACCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAAA
195 TTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAAA
* *
167655 TGAGATGGTTAGTACACGATTTCGGCGAAAATTTTGCAAAAATTGACCTGTAATATTTTTCCTCA
260 TGAGATGGTTAGTACACGATTTCGGCGAAAATTTTGCAAAAATTGACATGTAAGATTTTTCCTCA
167720 TTTTTTAGC
325 TTTTTTAGC
* *
167729 AACAATACTTATAAGGAATATATAATTCAACACCAAAAAGATTGAAGAGCGTTTCACGCTTCCAT
1 AACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAGAGCGTTTCACGCTTCCAA
167794 TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
66 TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
167859 AAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAT
131 AAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAT
* * *
167924 TATTGGCG-AAAAAATCATGCAAAACTAAGCCGGTGCCCCGGAACGCGTTTTCAG-CAAAAAA
196 TATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAA
167985 TAGATATCTC
Statistics
Matches: 542, Mismatches: 44, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
331 10 0.02
332 267 0.49
333 262 0.48
334 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (333 bp):
AACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAGAGCGTTTCACGCTTCCAA
TATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGT
AAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAT
TATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAAAAT
GAGATGGTTAGTACACGATTTCGGCGAAAATTTTGCAAAAATTGACATGTAAGATTTTTCCTCAT
TTTTTAGC
Found at i:168801 original size:7 final size:7
Alignment explanation
Indices: 168791--168816 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
168781 AAGAAGCAAG
168791 GATTGAA
1 GATTGAA
168798 GATTGAA
1 GATTGAA
168805 GATTGAA
1 GATTGAA
168812 GATTG
1 GATTG
168817 GAGCTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (7 bp):
GATTGAA
Found at i:170113 original size:22 final size:22
Alignment explanation
Indices: 170075--170123 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
170065 CAGCAAGTCA
170075 TAAACAGAACTC-AAAAACAGT
1 TAAACAGAACTCAAAAAACAGT
170096 TAAACAGGAACTCCAAAAAACAGT
1 TAAACA-GAACT-CAAAAAACAGT
170120 TAAA
1 TAAA
170124 GAAACAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 6 0.24
22 5 0.20
23 1 0.04
24 13 0.52
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (22 bp):
TAAACAGAACTCAAAAAACAGT
Found at i:170212 original size:14 final size:14
Alignment explanation
Indices: 170193--170236 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
170183 ACACTAAGTA
*
170193 AGGAACTAAAAAAC
1 AGGAACTCAAAAAC
* *
170207 AGGAACTCACAAAT
1 AGGAACTCAAAAAC
*
170221 AGGAAATCAAAAAC
1 AGGAACTCAAAAAC
170235 AG
1 AG
170237 CAAATCAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.09
Consensus pattern (14 bp):
AGGAACTCAAAAAC
Found at i:170241 original size:14 final size:14
Alignment explanation
Indices: 170201--170244 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
170191 TAAGGAACTA
*
170201 AAAAACAGGAACTC
1 AAAAACAGGAAATC
* *
170215 ACAAATAGGAAATC
1 AAAAACAGGAAATC
*
170229 AAAAACAGCAAATC
1 AAAAACAGGAAATC
170243 AA
1 AA
170245 TGACTCAAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.61, C:0.18, G:0.11, T:0.09
Consensus pattern (14 bp):
AAAAACAGGAAATC
Found at i:173021 original size:13 final size:13
Alignment explanation
Indices: 173003--173027 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
172993 TAACATATAT
173003 ATACAATATCAGC
1 ATACAATATCAGC
173016 ATACAATATCAG
1 ATACAATATCAG
173028 AGATAGAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
ATACAATATCAGC
Found at i:174587 original size:15 final size:15
Alignment explanation
Indices: 174550--174593 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
174540 AGAAACCGAC
174550 TATATTATTTTATAAA
1 TATATTA-TTTATAAA
* *
174566 AAAATTATTTATAAA
1 TATATTATTTATAAA
*
174581 TATATTATATATA
1 TATATTATTTATA
174594 TTATATATGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATTATTTATAAA
Found at i:175984 original size:154 final size:154
Alignment explanation
Indices: 175760--176066 Score: 501
Period size: 154 Copynumber: 2.0 Consensus size: 154
175750 ATATAGATAT
* * * *
175760 TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAATGCGTTTTTAGC
1 TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGACGGGGCCCCAGAACGCGATTTTAGC
*
175825 CAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTT
66 CAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTT
*
175890 TTCCTCATATTTTTA-TCACAATAG
131 TTCCTCAT-TTTTTAGCCACAATAG
*
175914 TTCAAGGATTATTGGCGCAAAAAATCATG-AGAAACTGAGACGGGTCCCCAGAACGCGATTTTAG
1 TTCAAGGATTATTGGCGCAAAAAATCATGCA-AAACTGAGACGGGGCCCCAGAACGCGATTTTAG
* *
175978 CCAAAAACAGTGATGGTTAGTACACGATTTCGGCTGAAATTTTGCAAAAATTGACCTGTAAGATT
65 CCAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATT
176043 TTTCCTCATTTTTTAGCCACAATA
130 TTTCCTCATTTTTTAGCCACAATA
176067 CTCATAAGAA
Statistics
Matches: 142, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
153 7 0.05
154 135 0.95
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (154 bp):
TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGACGGGGCCCCAGAACGCGATTTTAGC
CAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTT
TTCCTCATTTTTTAGCCACAATAG
Found at i:176746 original size:331 final size:330
Alignment explanation
Indices: 175914--177353 Score: 2116
Period size: 331 Copynumber: 4.4 Consensus size: 330
175904 ATCACAATAG
* * *
175914 TTCAAGGATTATTGGCGCAAAAAATCATG-AGAAACTGAGACGGGTCCCCAGAACGCGATTTTAG
1 TTCAAGGATTATTGGCGCAAAAAATCATGCA-AAACTGAGCCGGGGCCCCGGAACGCGATTTTAG
* *
175978 CCAAAAACAGTGATGGTTAGTACACGATTTCGGCTGAAATTTTGCAAAAATTGACCTGTAAGATT
65 CCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGTAAGATT
* *
176043 TTTCCTCATTTTTTAGCCACAATACTCATAAGAAATATATAATTCAACGCCAAAAAGATTGAAAG
130 TTTCCTCA-TTTTTAACCACAATACTCATAAGGAATATATAATTCAACGCCAAAAAGATTGAAAG
* * * *
176108 GGCTTTCACGCTTCCAATA-AAGTTTCTCC-ATATTTCCTGAATTAATTATTAATTATATCGAAA
194 GGCTTTCACGCTTCCAATATCA-TTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAA
* * *
176171 GAAAATTTTAATGCACGTAAAAAAAAATACCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTA
258 GAAAATTTAAATGCTCGTAAAAATAAAT-CCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTA
*
176236 ATATGAAAT
322 ATATGATAT
* *
176245 TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCACCGGAATGCG-TTTT---
1 TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGATTTTAGC
* *
176306 -----A---TGATGGTTAGTAAACGATTTCGGCTAAAATTTTGTAAAAATTGATCC-GTAAGATT
66 CAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCTGTAAGATT
* * * *
176362 TTTCCTCATATTTTTACCGCAATAGTCATATGGAATATATAATTCAACGCCAAAAAGATTGAAA-
130 TTTCCTCAT-TTTTAACCACAATACTCATAAGGAATATATAATTCAACGCCAAAAAGATTGAAAG
176426 GGCTTTTCACGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAA
194 GGC-TTTCACGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAA
* * *
176491 GAAAATTTAAATGCTCGT-AAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAA
258 GAAAATTTAAATGCTCGTAAAAATAAATCCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTAA
176555 TATAGATAT
323 TAT-GATAT
* *
176564 TTCAAGGATTATTAGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGC
1 TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGATTTTAGC
* *
176629 CAAAAACTGTGATGGCTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTT
66 CAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGTAAGATTT
* * *
176694 TTCCTCAGTTTTTAACCACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTG-AAGG
131 TTCCTCA-TTTTTAACCACAATACTCATAAGGAATATATAATTCAACGCCAAAAAGATTGAAAGG
* *
176758 GCGTTTCACGCTTCTAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAG
195 GC-TTTCACGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAG
*
176823 AAAATTTAAATGCTCGTAAAAGTAAATCCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTAAT
259 AAAATTTAAATGCTCGTAAAAATAAATCCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTAAT
*
176888 ATGACAT
324 ATGATAT
* * *
176895 TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGTCGAGGCCCCGTAACGCGATTTTAGC
1 TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGATTTTAGC
*
176960 CAAAAACTGTGATGATTAGTACACGATTTCGGCT-AAATTTTGC-AAAATTGACCTGTAAGATTT
66 CAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGTAAGATTT
** *
177023 TTCCTCATTTTTAGTCACAATACTCATAAGGAATATATAATTCAACACC-AAAAGATTGAAAGGG
131 TTCCTCATTTTTAACCACAATACTCATAAGGAATATATAATTCAACGCCAAAAAGATTGAAAGGG
*
177087 CTTTCACGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCCAAAGAA
196 CTTTCACGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAA
* * * *
177152 AATTTAAATGCTCGTAAAAATAAATTCTCAAGTCCATTGTGGTTGAGATTTGGTGAGATTAATAT
261 AATTTAAATGCTCGTAAAAATAAATCCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTAATAT
177217 AGATAT
326 -GATAT
* * * *
177223 TTCAAGGACTATTGGCGCCAAAAATCGTGCAAAACTGAGCCGGGGCCCCGTAACGCGATTTTAGC
1 TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGATTTTAGC
* *
177288 CAAATACTGTGATGGTTAGTACACGATTTCGG-TGAAAATTTTGCAGAAATTGACCTGTAAGATT
66 CAAAAACTGTGATGGTTAGTACACGATTTCGGCT-AAAATTTTGCAAAAATTGACCTGTAAGATT
177352 TT
130 TT
177354 AG
Statistics
Matches: 1009, Mismatches: 72, Indels: 57
0.89 0.06 0.05
Matches are distributed among these distances:
318 42 0.04
319 193 0.19
320 55 0.05
322 1 0.00
327 131 0.13
328 137 0.14
329 35 0.03
330 37 0.04
331 331 0.33
332 47 0.05
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (330 bp):
TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGATTTTAGC
CAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGTAAGATTT
TTCCTCATTTTTAACCACAATACTCATAAGGAATATATAATTCAACGCCAAAAAGATTGAAAGGG
CTTTCACGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAA
AATTTAAATGCTCGTAAAAATAAATCCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTAATAT
GATAT
Found at i:177340 original size:659 final size:649
Alignment explanation
Indices: 175914--177353 Score: 2175
Period size: 650 Copynumber: 2.2 Consensus size: 649
175904 ATCACAATAG
* *
175914 TTCAAGGATTATTGGCGCAAAAAATCATG-AGAAACTGAGACGGGTCCCCAGAACGCGATTTTAG
1 TTCAAGGATTATTGGCGCAAAAAATCATGCA-AAACTGAGCCGGGGCCCC-GAACGCGATTTTAG
*
175978 CCAAAAACAGTGATGGTTAGTACACGATTTCGGCTG-AAATTTTGCAAAAATTGACCTGTAAGAT
64 CCAAAAACTGTGATGGTTAGTACACGATTTCGGCTGAAAATTTTGCAAAAATTGACCTGTAAGAT
* *
176042 TTTTCCTCATTTTTTAGCCACAATACTCATAAGAAATATATAATTCAACGCCAAAAAGATTGAAA
129 TTTTCCTCAGTTTTTAACCACAATACTCATAAGAAATATATAATTCAACGCCAAAAAGATTGAAA
176107 GGGCTTTCACGCTTCCAATAAAGTTTCTCCATATTTCCTGAATTAATTATTAATTATATCGAAAG
194 GGGCTTTCACGCTTCCAATAAAGTTTCTCCATATTTCCTGAATTAATTATTAATTATATCGAAAG
*
176172 AAAATTTTAATGCACGTAAAAAAAAATACCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTAA
259 AAAATTTAAATGCACGTAAAAAAAAATACCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTAA
* *
176237 TATGAAATTTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCACCGGAATGCG
324 TATGAAATTTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGAGGCACCGGAACGCG
*
176302 TTTTATGATGGTTAGTAAACGATTTCGGCTAAAATTTTGTAAAAATTGATCCGTAAGATTTTTCC
389 TTTTATGATGATTAGTAAACGATTTCGGCTAAAATTTTGTAAAAATTGATCCGTAAGATTTTTCC
* * * *
176367 TCATATTTTTACCGCAATAGTCATATGGAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTT
454 TCA-ATTTTTACCACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCTTT
*
176432 TCACGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAAT
518 TCACGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCCAAAGAAAAT
*
176497 TTAAATGCTCGTAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGAT
583 TTAAATGCTCGTAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTGAGATTAATATAGAT
176562 AT
648 AT
* *
176564 TTCAAGGATTATTAGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGC
1 TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCC-GAACGCGATTTTAGC
* *
176629 CAAAAACTGTGATGGCTAGTACACGATTTCGGCT-AAAATTTTGCAAAAATTGACCCGTAAGATT
65 CAAAAACTGTGATGGTTAGTACACGATTTCGGCTGAAAATTTTGCAAAAATTGACCTGTAAGATT
* * * *
176693 TTTCCTCAGTTTTTAACCACAATAGTCATATGGAATATATAATTCGACGCCAAAAAGATTG-AAG
130 TTTCCTCAGTTTTTAACCACAATACTCATAAGAAATATATAATTCAACGCCAAAAAGATTGAAAG
* ** * * *
176757 GGCGTTTCACGCTTCTAATATCGTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAA
195 GGC-TTTCACGCTTCCAATAAAGTTTCTCC-ATATTTCCTGAATTAATTATTAATTATATCGAAA
* **
176822 GAAAATTTAAATGCTCGTAAAAGTAAAT-CCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTA
258 GAAAATTTAAATGCACGTAAAAAAAAATACCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTA
* * * *
176886 ATATGACATTTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGTCGAGGCCCCGTAACGC
323 ATATGAAATTTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGAGGCACCGGAACGC
* *
176951 GATTTTAGCCAAAAACTGTGATGATTAGTACACGATTTCGGCT-AAATTTTG-CAAAATTGA-CC
388 G-TTTT--------A---TGATGATTAGTAAACGATTTCGGCTAAAATTTTGTAAAAATTGATCC
*
177013 TGTAAGATTTTTCCTC-ATTTTTAGTCACAATACTCATAAGGAATATATAATTCAACACC-AAAA
441 -GTAAGATTTTTCCTCAATTTTTA-CCACAATACTCATAAGGAATATATAATTCAACACCAAAAA
177076 GATTGAAAGGGC-TTTCACGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATT
504 GATTGAAA-GGCTTTTCACGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATT
* *
177140 ATATCCAAAGAAAATTTAAATGCTCGTAAAAATAAATTCTCAAGTCCATTGTGGTTGAGATTTGG
568 ATATCCAAAGAAAATTTAAATGCTCGT-AAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGG
177205 TGAGATTAATATAGATAT
632 TGAGATTAATATAGATAT
* * *
177223 TTCAAGGACTATTGGCGCCAAAAATCGTGCAAAACTGAGCCGGGGCCCCGTAACGCGATTTTAGC
1 TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCG-AACGCGATTTTAGC
* *
177288 CAAATACTGTGATGGTTAGTACACGATTTCGG-TGAAAATTTTGCAGAAATTGACCTGTAAGATT
65 CAAAAACTGTGATGGTTAGTACACGATTTCGGCTGAAAATTTTGCAAAAATTGACCTGTAAGATT
177352 TT
130 TT
177354 AG
Statistics
Matches: 717, Mismatches: 51, Indels: 35
0.89 0.06 0.04
Matches are distributed among these distances:
649 6 0.01
650 291 0.41
651 61 0.09
658 99 0.14
659 206 0.29
660 23 0.03
661 8 0.01
662 23 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (649 bp):
TTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGAACGCGATTTTAGCC
AAAAACTGTGATGGTTAGTACACGATTTCGGCTGAAAATTTTGCAAAAATTGACCTGTAAGATTT
TTCCTCAGTTTTTAACCACAATACTCATAAGAAATATATAATTCAACGCCAAAAAGATTGAAAGG
GCTTTCACGCTTCCAATAAAGTTTCTCCATATTTCCTGAATTAATTATTAATTATATCGAAAGAA
AATTTAAATGCACGTAAAAAAAAATACCTCAAGTCCATTGTGGTTAAAATTTGGTTAGATTAATA
TGAAATTTCAAGGATTATTGGCGCAAAAAATCATGCAAAACTGAGCCGAGGCACCGGAACGCGTT
TTATGATGATTAGTAAACGATTTCGGCTAAAATTTTGTAAAAATTGATCCGTAAGATTTTTCCTC
AATTTTTACCACAATACTCATAAGGAATATATAATTCAACACCAAAAAGATTGAAAGGCTTTTCA
CGCTTCCAATATCATTTTTCCTATATTTTCTGAATTAATTTTTAATTATATCCAAAGAAAATTTA
AATGCTCGTAAAACAAATCCTCAAGTCCATTGTGGTTGAGATTTGGTGAGATTAATATAGATAT
Done.