Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011650.1 Corchorus capsularis cultivar CVL-1 contig11671, 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: 89246
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:561 original size:25 final size:25
Alignment explanation
Indices: 533--648 Score: 124
Period size: 25 Copynumber: 4.6 Consensus size: 25
523 CAGCCTATGT
*
533 GTTTTCTAAACGCAAGCACAGACTC
1 GTTTGCTAAACGCAAGCACAGACTC
*
558 GTTTGCTAAACGTAAGCACAGACTC
1 GTTTGCTAAACGCAAGCACAGACTC
* * *
583 GTTTGATAAACGCAAGCATAGGCTC
1 GTTTGCTAAACGCAAGCACAGACTC
* * ** *
608 GTTTGCTCAACACAAGCGGAGGCTC
1 GTTTGCTAAACGCAAGCACAGACTC
* *
633 ATTTGCCAAACGCAAG
1 GTTTGCTAAACGCAAG
649 AACATGAGCG
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 76 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (25 bp):
GTTTGCTAAACGCAAGCACAGACTC
Found at i:2988 original size:22 final size:22
Alignment explanation
Indices: 2958--3007 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
2948 AAGAAAAGAT
*
2958 TCACCTCCACATTATGATATAA
1 TCACATCCACATTATGATATAA
2980 TCACATCCACATTATGATATAA
1 TCACATCCACATTATGATATAA
3002 TCACAT
1 TCACAT
3008 GTGAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (22 bp):
TCACATCCACATTATGATATAA
Found at i:3887 original size:22 final size:22
Alignment explanation
Indices: 3862--3972 Score: 116
Period size: 22 Copynumber: 5.0 Consensus size: 22
3852 TCATCAAAAA
*
3862 GTTATCAAAATTTCTTAGGGAG
1 GTTATCAAAATTTCATAGGGAG
* * *
3884 GTTAACAAAATTTCATACGAAG
1 GTTATCAAAATTTCATAGGGAG
* * * *
3906 GTTATCGAAATTTTATAGTGTG
1 GTTATCAAAATTTCATAGGGAG
* *
3928 GTTATCAAAATTTCATAAGAAG
1 GTTATCAAAATTTCATAGGGAG
3950 GTTAAT-AAAATTTCATAGGGAG
1 GTT-ATCAAAATTTCATAGGGAG
3972 G
1 G
3973 GATATTATCA
Statistics
Matches: 69, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
22 67 0.97
23 2 0.03
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAG
Found at i:3895 original size:44 final size:43
Alignment explanation
Indices: 3847--3972 Score: 130
Period size: 44 Copynumber: 2.9 Consensus size: 43
3837 TAAGTTACTG
*
3847 AAATTTCATCAAAAAGTTATCAAAATTTCTTAGGGAGGTTAACA
1 AAATTTCAT-AAAAGGTTATCAAAATTTCTTAGGGAGGTTAACA
* * * * *
3891 AAATTTCATACGAAGGTTATCGAAATTT-TATAGTGTGGTTATCA
1 AAATTTCATA-AAAGGTTATCAAAATTTCT-TAGGGAGGTTAACA
*
3935 AAATTTCATAAGAAGGTTAAT-AAAATTTCATAGGGAGG
1 AAATTTCATAA-AAGGTT-ATCAAAATTTCTTAGGGAGG
3973 GATATTATCA
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
43 2 0.03
44 62 0.94
45 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.33
Consensus pattern (43 bp):
AAATTTCATAAAAGGTTATCAAAATTTCTTAGGGAGGTTAACA
Found at i:4234 original size:43 final size:44
Alignment explanation
Indices: 4150--4246 Score: 119
Period size: 43 Copynumber: 2.2 Consensus size: 44
4140 TAGGTAATTG
* *
4150 AATTTCATAGTGTGGTTATCAAGATTTTATGAGGAGGTTATCAA
1 AATTTCATAGTGCGGTTATCAAGATTTTATGAGGAGATTATCAA
* *
4194 AATTTTCATAGTGCGGTTA-CCA-ATTTTAT-AGTGTGATTATCAA
1 AA-TTTCATAGTGCGGTTATCAAGATTTTATGAG-GAGATTATCAA
4237 AATTTCATAG
1 AATTTCATAG
4247 GAAGATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
42 10 0.21
43 18 0.38
44 4 0.09
45 15 0.32
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (44 bp):
AATTTCATAGTGCGGTTATCAAGATTTTATGAGGAGATTATCAA
Found at i:4246 original size:22 final size:22
Alignment explanation
Indices: 4150--4419 Score: 134
Period size: 22 Copynumber: 12.3 Consensus size: 22
4140 TAGGTAATTG
4150 AATTTCATAGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * *
4172 GATTTTATGAG-GAGGTTATCAA
1 AATTTCAT-AGTGTGGTTATCAA
* *
4194 AATTTTCATAGTGCGGTTA-C-C
1 AA-TTTCATAGTGTGGTTATCAA
* *
4215 AATTTTATAGTGTGATTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * *
4237 AATTTCATAG-GAAGATTATTAA
1 AATTTCATAGTG-TGGTTATCAA
* ****
4259 AATTTTATACCAAGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
* ** *
4281 AATTTTCATAGTATGACTATTAA
1 AA-TTTCATAGTGTGGTTATCAA
* * *
4304 AATTTTAAAGTGTGATTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * *
4326 AATTTCACAATATGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * * **
4348 AATTTCGTAGGGAGGTTATTGA
1 AATTTCATAGTGTGGTTATCAA
* * * *
4370 AATTTTATAATGAGATTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * *
4392 ATTTTTACAGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
*
4414 TATTTC
1 AATTTC
4420 TATGCTGGAG
Statistics
Matches: 181, Mismatches: 59, Indels: 16
0.71 0.23 0.06
Matches are distributed among these distances:
20 13 0.07
21 4 0.02
22 136 0.75
23 28 0.15
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTATCAA
Found at i:4323 original size:45 final size:45
Alignment explanation
Indices: 4215--4330 Score: 144
Period size: 45 Copynumber: 2.6 Consensus size: 45
4205 TGCGGTTACC
*
4215 AATTTTATAGTGTGATTATCAAAA-TTTCATAGGAAGATTATTAA
1 AATTTTATAGTGTGATTATCAAAATTTTCATAGGAAGACTATTAA
**** * * *
4259 AATTTTATACCAAGGTTATCAAAATTTTCATAGTATGACTATTAA
1 AATTTTATAGTGTGATTATCAAAATTTTCATAGGAAGACTATTAA
*
4304 AATTTTAAAGTGTGATTATCAAAATTT
1 AATTTTATAGTGTGATTATCAAAATTT
4331 CACAATATGG
Statistics
Matches: 57, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
44 19 0.33
45 38 0.67
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (45 bp):
AATTTTATAGTGTGATTATCAAAATTTTCATAGGAAGACTATTAA
Found at i:4352 original size:44 final size:44
Alignment explanation
Indices: 4215--4352 Score: 150
Period size: 44 Copynumber: 3.1 Consensus size: 44
4205 TGCGGTTACC
* *
4215 AATTTTATAGTGTGATTATCAAAATTTCATAGGAAGATTATTAA
1 AATTTTATAGTGTGATTATCAAAATTTCATAGTATGATTATTAA
**** * *
4259 AATTTTATACCAAGGTTATCAAAATTTTCATAGTATGACTATTAA
1 AATTTTATAGTGTGATTATCAAAA-TTTCATAGTATGATTATTAA
* * * * *
4304 AATTTTAAAGTGTGATTATCAAAATTTCACAATATGGTTATCAA
1 AATTTTATAGTGTGATTATCAAAATTTCATAGTATGATTATTAA
4348 AATTT
1 AATTT
4353 CGTAGGGAGG
Statistics
Matches: 74, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
44 39 0.53
45 35 0.47
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (44 bp):
AATTTTATAGTGTGATTATCAAAATTTCATAGTATGATTATTAA
Found at i:5593 original size:32 final size:32
Alignment explanation
Indices: 5552--5615 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
5542 TAACTTGAAA
5552 TCAATTTCCACCAAACTTCAATCTCACATGTG
1 TCAATTTCCACCAAACTTCAATCTCACATGTG
* *
5584 TCAATTTCCACCAAACTTTAATCTCACGTGTG
1 TCAATTTCCACCAAACTTCAATCTCACATGTG
5616 AAACACATGG
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:0.30, C:0.30, G:0.08, T:0.33
Consensus pattern (32 bp):
TCAATTTCCACCAAACTTCAATCTCACATGTG
Found at i:6023 original size:27 final size:26
Alignment explanation
Indices: 5961--6031 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
5951 AAGGAATCAC
* * *
5961 CAGGAGTATTTTTGTCATTTTCGCCT
1 CAGGGGTATTTTCGTCATTTTCGACT
* * *
5987 CAGGGATATTTTGGTCATTTTCATACT
1 CAGGGGTATTTTCGTCATTTTC-GACT
6014 CAGGGGTATTTTCGTCAT
1 CAGGGGTATTTTCGTCAT
6032 CTTTACACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 19 0.51
27 18 0.49
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (26 bp):
CAGGGGTATTTTCGTCATTTTCGACT
Found at i:9696 original size:82 final size:82
Alignment explanation
Indices: 9559--9827 Score: 441
Period size: 82 Copynumber: 3.3 Consensus size: 82
9549 TAATCCATTG
* *
9559 TAATTTGGAAAAATTAAGAAAGTCAAACACAGTTAAAGACTTAATTCAAGGTAATTAAGGAAAGC
1 TAATTTGGGATAATTAAGAAAGTCAAACACAGTTAAAGACTTAATTCAAGGTAATTAAGGAAAGC
9624 AAGCAAAGTTAGGGTCT
66 AAGCAAAGTTAGGGTCT
9641 TAATTTGGGATAATTAAGAAAGTCAAACACAGTTAAAGACTTAATTCAAGGTAATTAAGGAAAGC
1 TAATTTGGGATAATTAAGAAAGTCAAACACAGTTAAAGACTTAATTCAAGGTAATTAAGGAAAGC
*
9706 AAGCACAGTTAGGGTCT
66 AAGCAAAGTTAGGGTCT
* * *
9723 TAATTTAGGATAATTCAGAAAGTCAAACACAGTTAAAGACTTAATTCAGGGTAATTAAGGAAAGC
1 TAATTTGGGATAATTAAGAAAGTCAAACACAGTTAAAGACTTAATTCAAGGTAATTAAGGAAAGC
* *
9788 AAACACAA-TTAGAGTCT
66 AAGCA-AAGTTAGGGTCT
*
9805 TAGTTTGGGATAATTAAGAAAGT
1 TAATTTGGGATAATTAAGAAAGT
9828 TAAGCACAAA
Statistics
Matches: 174, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
82 173 0.99
83 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (82 bp):
TAATTTGGGATAATTAAGAAAGTCAAACACAGTTAAAGACTTAATTCAAGGTAATTAAGGAAAGC
AAGCAAAGTTAGGGTCT
Found at i:9819 original size:41 final size:40
Alignment explanation
Indices: 9559--9910 Score: 259
Period size: 41 Copynumber: 8.7 Consensus size: 40
9549 TAATCCATTG
* * * *
9559 TAATTTGGAAAAATTAAGAAAGTCAAACACAGTTAAAGACT
1 TAATTTGGGATAATTAAGAAAG-CAAACACAGTTAGAGTCT
** * * *
9600 TAATTCAAGG-TAATTAAGGAAAGCAAGCAAAGTTAGGGTCT
1 TAATT-TGGGATAATTAA-GAAAGCAAACACAGTTAGAGTCT
* *
9641 TAATTTGGGATAATTAAGAAAGTCAAACACAGTTAAAGACT
1 TAATTTGGGATAATTAAGAAAG-CAAACACAGTTAGAGTCT
** * *
9682 TAATTCAAGG-TAATTAAGGAAAGCAAGCACAGTTAGGGTCT
1 TAATT-TGGGATAATTAA-GAAAGCAAACACAGTTAGAGTCT
* * * *
9723 TAATTTAGGATAATTCAGAAAGTCAAACACAGTTAAAGACT
1 TAATTTGGGATAATTAAGAAAG-CAAACACAGTTAGAGTCT
* *
9764 TAATTCAGGG-TAATTAAGGAAAGCAAACACAATTAGAGTCT
1 TAATT-TGGGATAATTAA-GAAAGCAAACACAGTTAGAGTCT
* * * ***
9805 TAGTTTGGGATAATTAAGAAAGTTAAGCACAAACA-AGGTCT
1 TAATTTGGGATAATTAAGAAAG-CAAACACAGTTAGA-GTCT
* * * *
9846 TAATTCGGGATAATTAA-ATAAGTAAACACAGTCAAAGTCT
1 TAATTTGGGATAATTAAGA-AAGCAAACACAGTTAGAGTCT
9886 TAATTT-GG-TAATTAAGAATAGCAAA
1 TAATTTGGGATAATTAAGAA-AGCAAA
9911 GTCTTAATTC
Statistics
Matches: 247, Mismatches: 47, Indels: 36
0.75 0.14 0.11
Matches are distributed among these distances:
38 8 0.03
39 8 0.03
40 43 0.17
41 168 0.68
42 20 0.08
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.26
Consensus pattern (40 bp):
TAATTTGGGATAATTAAGAAAGCAAACACAGTTAGAGTCT
Found at i:9848 original size:82 final size:81
Alignment explanation
Indices: 9559--9973 Score: 412
Period size: 82 Copynumber: 5.2 Consensus size: 81
9549 TAATCCATTG
* * *
9559 TAATTTGGAAAAATTAAGAAAGTCAAACACAGTTAAAGACTTAATTCAAGGTAATTAAGGAAAGC
1 TAATTTGG-ATAATTAAGAAAGTCAAACACAGATAAAGACTTAATTCAGGGTAATTAAGGAAAGC
* * *
9624 AAGCAAAGTTAGGGTCT
65 AAACACAGTTAGAGTCT
* *
9641 TAATTTGGGATAATTAAGAAAGTCAAACACAGTTAAAGACTTAATTCAAGGTAATTAAGGAAAGC
1 TAATTT-GGATAATTAAGAAAGTCAAACACAGATAAAGACTTAATTCAGGGTAATTAAGGAAAGC
* *
9706 AAGCACAGTTAGGGTCT
65 AAACACAGTTAGAGTCT
* *
9723 TAATTTAGGATAATTCAGAAAGTCAAACACAGTTAAAGACTTAATTCAGGGTAATTAAGGAAAGC
1 TAATTT-GGATAATTAAGAAAGTCAAACACAGATAAAGACTTAATTCAGGGTAATTAAGGAAAGC
*
9788 AAACACAATTAGAGTCT
65 AAACACAGTTAGAGTCT
* * * * * * *
9805 TAGTTTGGGATAATTAAGAAAGTTAAGCACAAACAAGGTCTTAATTC-GGGATAATTAA--ATAA
1 TAATTT-GGATAATTAAGAAAGTCAAACACAGATAAAGACTTAATTCAGGG-TAATTAAGGA-AA
* * *
9867 GTAAACACAGTCAAAGTCT
63 GCAAACACAGTTAGAGTCT
* *
9886 TAATTTGG-TAATTAAGAATAG-C--A-A-AG-T-----CTTAATTCAGGGTAATTAAGAAAAGT
1 TAATTTGGATAATTAAGAA-AGTCAAACACAGATAAAGACTTAATTCAGGGTAATTAAGGAAAGC
* *
9939 AAACACAGTCAAAGTCT
65 AAACACAGTTAGAGTCT
9956 TAATTTGG-TAATTAAGAA
1 TAATTTGGATAATTAAGAA
9974 GAGCAAAGTC
Statistics
Matches: 299, Mismatches: 27, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
69 15 0.05
70 42 0.14
71 1 0.00
75 1 0.00
76 1 0.00
79 10 0.03
80 5 0.02
81 25 0.08
82 197 0.66
83 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (81 bp):
TAATTTGGATAATTAAGAAAGTCAAACACAGATAAAGACTTAATTCAGGGTAATTAAGGAAAGCA
AACACAGTTAGAGTCT
Found at i:9946 original size:70 final size:70
Alignment explanation
Indices: 9842--10318 Score: 636
Period size: 70 Copynumber: 6.9 Consensus size: 70
9832 CACAAACAAG
* * * *
9842 GTCTTAATTC-GGGATAATTAA-ATAAGTAAACACAGTCAAAGTCTTAATTTGGTAATTAAGAAT
1 GTCTTAATTCAGGG-TAATTAAGAAAAGTAAGCATAGTCAAAGTCTTAATTTGGTAATTAAGAAA
9905 AGCAAA
65 AGCAAA
* * *
9911 GTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAAAGTCTTAATTTGGTAATTAAGAAGA
1 GTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAAGTCTTAATTTGGTAATTAAGAAAA
9976 GCAAA
66 GCAAA
* *
9981 GTC-----T-----TAATTAAGAAAAGTAAACACAGTCAAAGTCTTAATTTGGTAATTAAGAAAA
1 GTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAAGTCTTAATTTGGTAATTAAGAAAA
*
10036 GCAAG
66 GCAAA
* * *
10041 GTCTTAATTTAGGGTAATTAAAAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAA
1 GTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAAGTCTTAATTTGGTAATTAAGAAAA
*
10106 GCAAG
66 GCAAA
* *
10111 GTCTTAATTCAGGATAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAA
1 GTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAAGTCTTAATTTGGTAATTAAGAAAA
*
10176 GTAAA
66 GCAAA
*
10181 GTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAACGTCTTAATTTGGTAATTAAGAAAA
1 GTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAAGTCTTAATTTGGTAATTAAGAAAA
*
10246 ACAAA
66 GCAAA
* * * *
10251 GTCTTAATTCAGGGTAATTAAGAAAAGTGAGCATAGTCAAGGTCTTAATTCAGTTTAATTAAGAA
1 GTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAAGTCTTAATT-TG-GTAATTAAGAA
10316 AAG
64 AAG
10319 TAAACACAGT
Statistics
Matches: 372, Mismatches: 22, Indels: 25
0.89 0.05 0.06
Matches are distributed among these distances:
60 57 0.15
65 2 0.01
69 17 0.05
70 283 0.76
71 1 0.00
72 12 0.03
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (70 bp):
GTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGTCAAAGTCTTAATTTGGTAATTAAGAAAA
GCAAA
Found at i:9981 original size:29 final size:29
Alignment explanation
Indices: 9948--10067 Score: 116
Period size: 31 Copynumber: 4.0 Consensus size: 29
9938 TAAACACAGT
*
9948 CAAAGTCTTAATTTGGTAATTAAGAAGAG
1 CAAAGTCTTAATTTGGTAATTAAGAAAAG
* ** * *
9977 CAAAGTCTTAATTAAGAAAAGTAA-ACACAG
1 CAAAGTCTTAATT-TGGTAATTAAGA-AAAG
10007 TCAAAGTCTTAATTTGGTAATTAAGAAAAG
1 -CAAAGTCTTAATTTGGTAATTAAGAAAAG
* *
10037 CAAGGTCTTAATTTAGGGTAATTAAAAAAAG
1 CAAAGTCTTAATTT--GGTAATTAAGAAAAG
10068 TAAGCATAGT
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
29 27 0.37
30 18 0.25
31 28 0.38
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.28
Consensus pattern (29 bp):
CAAAGTCTTAATTTGGTAATTAAGAAAAG
Found at i:10082 original size:41 final size:39
Alignment explanation
Indices: 10037--10364 Score: 214
Period size: 41 Copynumber: 8.9 Consensus size: 39
10027 TTAAGAAAAG
*
10037 CAAGGTCTTAATTTAGGGTAATTAAAAAAAGTAAGCATAGT
1 CAAGGTCTTAATTT--GGTAATTAAGAAAAGTAAGCATAGT
10078 CAAGGTCTTAATTTGGTAATT-----AAG-AA--A-AG-
1 CAAGGTCTTAATTTGGTAATTAAGAAAAGTAAGCATAGT
*
10107 CAAGGTCTTAATTCAGGATAATTAAGAAAAGTAAGCATAGT
1 CAAGGTCTTAATT-TGG-TAATTAAGAAAAGTAAGCATAGT
10148 CAAGGTCTTAATTTGGTAATTAAG--AA--AAG--TA--
1 CAAGGTCTTAATTTGGTAATTAAGAAAAGTAAGCATAGT
*
10179 -AA-GTCTTAATTCAGGGTAATTAAGAAAAGTAAGCATAGT
1 CAAGGTCTTAATT--TGGTAATTAAGAAAAGTAAGCATAGT
*
10218 CAACGTCTTAATTTGGTAATTAAG-AAA--AA-C--A--
1 CAAGGTCTTAATTTGGTAATTAAGAAAAGTAAGCATAGT
* *
10249 -AA-GTCTTAATTCAGGGTAATTAAGAAAAGTGAGCATAGT
1 CAAGGTCTTAATT--TGGTAATTAAGAAAAGTAAGCATAGT
* * * *
10288 CAAGGTCTTAATTCAGTTTAATTAAGAAAAGTAAACACAGT
1 CAAGGTCTTAATT-TG-GTAATTAAGAAAAGTAAGCATAGT
* * *
10329 -AAAGTCTTAATTCAAGGTAATTAAGAAAAGCAAGCA
1 CAAGGTCTTAATT--TGGTAATTAAGAAAAGTAAGCA
10365 GTTAAAGGAC
Statistics
Matches: 232, Mismatches: 17, Indels: 77
0.71 0.05 0.24
Matches are distributed among these distances:
29 31 0.13
30 8 0.03
31 26 0.11
32 3 0.01
33 7 0.03
34 4 0.02
35 8 0.03
36 5 0.02
37 7 0.03
38 3 0.01
39 26 0.11
40 37 0.16
41 67 0.29
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (39 bp):
CAAGGTCTTAATTTGGTAATTAAGAAAAGTAAGCATAGT
Found at i:10111 original size:29 final size:31
Alignment explanation
Indices: 10078--10277 Score: 97
Period size: 29 Copynumber: 6.0 Consensus size: 31
10068 TAAGCATAGT
*
10078 CAAGGTCTTAATT-TGG-TAATTAAGAAAAG
1 CAAGGTCTTAATTCAGGATAATTAAGAAAAG
10107 CAAGGTCTTAATTCAGGATAATTAAGAAAAGTAAGCATAG
1 CAAGGTCTTAATTCAGGATAATT-----AAG-AA--A-AG
*
10147 TCAAGGTCTTAATT-TGG-TAATTAAGAAAAG
1 -CAAGGTCTTAATTCAGGATAATTAAGAAAAG
* * *
10177 TAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAG
1 CAAGGTCTTAATTCAGGATAATTAAG--AA--AAG
* *
10212 CATAGTCAACGTCTTAATT-TGG-TAATTAAGAAAAA
1 CA-AG-----GTCTTAATTCAGGATAATTAAGAAAAG
* *
10247 CAAAGTCTTAATTCAGGGTAATTAAGAAAAG
1 CAAGGTCTTAATTCAGGATAATTAAGAAAAG
10278 TGAGCATAGT
Statistics
Matches: 133, Mismatches: 12, Indels: 50
0.68 0.06 0.26
Matches are distributed among these distances:
29 33 0.25
30 8 0.06
31 26 0.20
33 4 0.03
34 4 0.03
35 8 0.06
36 4 0.03
37 4 0.03
39 14 0.11
40 6 0.05
41 22 0.17
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (31 bp):
CAAGGTCTTAATTCAGGATAATTAAGAAAAG
Found at i:10410 original size:37 final size:36
Alignment explanation
Indices: 10316--10588 Score: 289
Period size: 37 Copynumber: 7.2 Consensus size: 36
10306 TAATTAAGAA
* * *
10316 AAGTAAACA-CAGTAAA-GTCTTAATTCAAGGTAATT
1 AAGTAAA-AGCAGTAAAGGACTTAATTCATGGAAATT
* *
10351 AAGAAAAGCAAGCAGTTAAAGGACTTAATTCAGGGAAATT
1 AAG-TAA--AAGCAG-TAAAGGACTTAATTCATGGAAATT
*
10391 AAGTAAAAGCAGCTAAAGGACTTAATTCATGGTAATT
1 AAGTAAAAGCAG-TAAAGGACTTAATTCATGGAAATT
* * *
10428 AAGTAAAAGCAGTAAAACGACTTAATTTAGGGAAATT
1 AAGTAAAAGCAGT-AAAGGACTTAATTCATGGAAATT
* * *
10465 AAGTAAAAGCAGTAAAATGATTTAATTCATGGTAATT
1 AAGTAAAAGCAGT-AAAGGACTTAATTCATGGAAATT
*
10502 AAGTAAAAGCAGTTAAAGGACTTAATTCATGGTAATT
1 AAGTAAAAGCAG-TAAAGGACTTAATTCATGGAAATT
10539 AAGTAAAAGCAGCAGTTAAAGGACTTAATTCATGGAAATT
1 AAGT-AAA--AGCAG-TAAAGGACTTAATTCATGGAAATT
10579 AAGTTAAAAG
1 AAG-TAAAAG
10589 ACTTAATTCA
Statistics
Matches: 206, Mismatches: 20, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
35 3 0.01
36 3 0.01
37 129 0.63
38 10 0.05
39 6 0.03
40 54 0.26
41 1 0.00
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (36 bp):
AAGTAAAAGCAGTAAAGGACTTAATTCATGGAAATT
Found at i:10460 original size:74 final size:75
Alignment explanation
Indices: 10334--10588 Score: 336
Period size: 74 Copynumber: 3.4 Consensus size: 75
10324 ACAGTAAAGT
* *
10334 CTTAATTCAAGGTAATTAAGAAAAGCAAGCAGTTAAAGGACTTAATTCAGGGAAATTAAGTAAAA
1 CTTAATTCATGGTAATTAAGATAA--AAGCAGTTAAAGGACTTAATTCAGGGAAATTAAGTAAAA
10399 GCAGCTAAAGGA
64 GCAGCTAAAGGA
* * *
10411 CTTAATTCATGGTAATTAAG-TAAAAGCAGTAAAACGACTTAATTTAGGGAAATTAAGTAAAAGC
1 CTTAATTCATGGTAATTAAGATAAAAGCAGTTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGC
*
10475 AG-TAAAATGA
66 AGCT-AAAGGA
* * *
10485 TTTAATTCATGGTAATTAAG-TAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAAGTAAAAGC
1 CTTAATTCATGGTAATTAAGATAAAAGCAGTTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGC
10549 AGCAGTTAAAGGA
66 AGC---TAAAGGA
* *
10562 CTTAATTCATGGAAATTAAGTTAAAAG
1 CTTAATTCATGGTAATTAAGATAAAAG
10589 ACTTAATTCA
Statistics
Matches: 157, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
73 1 0.01
74 105 0.67
76 2 0.01
77 42 0.27
78 7 0.04
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (75 bp):
CTTAATTCATGGTAATTAAGATAAAAGCAGTTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGC
AGCTAAAGGA
Found at i:10490 original size:111 final size:114
Alignment explanation
Indices: 10360--10588 Score: 338
Period size: 111 Copynumber: 2.0 Consensus size: 114
10350 TAAGAAAAGC
*
10360 AAGCAGTTAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGCTAAAGGACTTAATTCATGGTA
1 AAGCAGTAAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGCTAAAGGACTTAATTCATGGTA
*
10425 ATTAAGT-AAA-AGCAGTAAAACGACTTAATTTAGGGAAATTAAG-TAA
66 ATTAAGTAAAACAGCAGTAAAACGACTTAATTCAGGGAAATTAAGTTAA
* * * * *
10471 AAGCAGTAAAATGATTTAATTCATGGTAATTAAGTAAAAGCAGTTAAAGGACTTAATTCATGGTA
1 AAGCAGTAAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGCTAAAGGACTTAATTCATGGTA
* * *
10536 ATTAAGTAAAAGCAGCAGTTAAAGGACTTAATTCATGGAAATTAAGTTAA
66 ATTAAGTAAAA-CAGCAGTAAAACGACTTAATTCAGGGAAATTAAGTTAA
10586 AAG
1 AAG
10589 ACTTAATTCA
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
111 66 0.63
112 3 0.03
114 29 0.28
115 6 0.06
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.27
Consensus pattern (114 bp):
AAGCAGTAAAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGCTAAAGGACTTAATTCATGGTA
ATTAAGTAAAACAGCAGTAAAACGACTTAATTCAGGGAAATTAAGTTAA
Found at i:10584 original size:28 final size:28
Alignment explanation
Indices: 10552--10615 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
10542 TAAAAGCAGC
*
10552 AGTTAAAGGACTTAATTCATGGAAATTA
1 AGTTAAAAGACTTAATTCATGGAAATTA
10580 AGTTAAAAGACTTAATTCATGGAAATTA
1 AGTTAAAAGACTTAATTCATGGAAATTA
*
10608 AGTAAAAA
1 AGTTAAAA
10616 CAGACAAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (28 bp):
AGTTAAAAGACTTAATTCATGGAAATTA
Found at i:10675 original size:41 final size:41
Alignment explanation
Indices: 10621--10980 Score: 514
Period size: 41 Copynumber: 8.8 Consensus size: 41
10611 AAAAACAGAC
*
10621 AAGCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-T
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
*
10661 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGATAAAG-T
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
* * *
10702 AAGGCACATACATAATTTCAAGGAAGGAAATTAAGTAAAG-T
1 AA-GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
* *
10743 AAGGCACATACTTAATTTCAAGGAAGGAAATTAAGTAAAGAT
1 AA-GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
10785 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA-AGT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGA-T
*
10826 AAGCACAGACTTAATTTCAAGGACGGAAATTAGGTAAAGAT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
* *
10867 AAGCACAGACTTATTTTCAAGGAAGGGAATTAGGTAAAGAT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
*
10908 AAGCACAGACTTAATTTCAAGGAATGAAATTAGGTAAAGACT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGA-T
* * *
10950 -AGCACATACTTAATTTTAGGGAAGGAAATTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTA
10981 AGTAGAGTCA
Statistics
Matches: 294, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
40 3 0.01
41 286 0.97
42 5 0.02
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.24
Consensus pattern (41 bp):
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
Found at i:11035 original size:32 final size:32
Alignment explanation
Indices: 10990--11151 Score: 236
Period size: 32 Copynumber: 4.9 Consensus size: 32
10980 AAGTAGAGTC
**
10990 AATAAAGGGCTTAATTCAGGGTAATTAAGTAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
11022 AATAAAGAACTTAATTCAGGGTAATTAAGTGGAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGT--AG
*
11056 TCAATAAA-AGAGTTAATTCAGGGTAATTAAGTAG
1 --AATAAAGA-ACTTAATTCAGGGTAATTAAGTAG
11090 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
*
11122 AATAAAGAACTTAATTCAGGATAATTAAGT
1 AATAAAGAACTTAATTCAGGGTAATTAAGT
11152 GGAGTCAATA
Statistics
Matches: 119, Mismatches: 5, Indels: 12
0.88 0.04 0.09
Matches are distributed among these distances:
32 86 0.72
33 1 0.01
34 4 0.03
35 1 0.01
36 27 0.23
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.28
Consensus pattern (32 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTAG
Found at i:11057 original size:68 final size:67
Alignment explanation
Indices: 10976--11151 Score: 270
Period size: 68 Copynumber: 2.6 Consensus size: 67
10966 TAGGGAAGGA
*
10976 AATTAAGTAGAGTCAATAAAGGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
1 AATTAAGT-GAGTCAATAAAGAGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
11041 GGT
65 GGT
11044 AATTAAGTGGAGTCAATAAAAGAG-TTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCA
1 AATTAAGT-GAGTCAAT-AAAGAGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCA
11108 GGGT
64 GGGT
* *
11112 AATTAAGT-AG--AATAAAGAACTTAATTCAGGATAATTAAGT
1 AATTAAGTGAGTCAATAAAGAGCTTAATTCAGGGTAATTAAGT
11152 GGAGTCAATA
Statistics
Matches: 102, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
63 5 0.05
64 22 0.22
66 2 0.02
68 68 0.67
69 5 0.05
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.28
Consensus pattern (67 bp):
AATTAAGTGAGTCAATAAAGAGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAGG
GT
Found at i:11185 original size:100 final size:100
Alignment explanation
Indices: 10990--11188 Score: 285
Period size: 100 Copynumber: 2.0 Consensus size: 100
10980 AAGTAGAGTC
** *
10990 AATAAAGGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAGGGTAATTAAGTGGA
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAGGATAATTAAGTGGA
* * ***
11055 GTCAATAAAAGAGTTAATTCAGGGTAATTAAGTAG
66 GTCAATAAAAGACTCAATTCAGAAAAATTAAGTAG
11090 AATAAAGAACTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAGGATAATTAAGTGGA
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAGGATAATTAAGTGGA
*
11155 GTCAAT-AAAGAACTCAA-TCTGAAAAGATTAAGTA
66 GTCAATAAAAG-ACTCAATTCAGAAAA-ATTAAGTA
11189 AAACAATAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
99 8 0.09
100 80 0.91
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (100 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAGGATAATTAAGTGGA
GTCAATAAAAGACTCAATTCAGAAAAATTAAGTAG
Found at i:19456 original size:22 final size:21
Alignment explanation
Indices: 19406--19480 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
19396 TAAAGAGCTT
*
19406 TTATCAAAATTTT-AAATGATGG
1 TTATC-AAATTTTCAAA-GATGC
*
19428 TTTTCAAATTTTCAAAGACTGC
1 TTATCAAATTTTCAAAGA-TGC
*
19450 TTATCAAACTTTTCATAAGATGA
1 TTATCAAA-TTTTCA-AAGATGC
*
19473 TTGTCAAA
1 TTATCAAA
19481 ATTTAATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.20
22 16 0.36
23 15 0.34
24 4 0.09
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (21 bp):
TTATCAAATTTTCAAAGATGC
Found at i:20011 original size:76 final size:76
Alignment explanation
Indices: 19885--20059 Score: 314
Period size: 76 Copynumber: 2.3 Consensus size: 76
19875 TGCACTAAGC
* *
19885 CACTAGCCATTCTTAAAAGGCCAGTTCATAATAGCAATATAAACTTCCATGAAAACGGACCTACT
1 CACTAGCCGTTCTTAAGAGGCCAGTTCATAATAGCAATATAAACTTCCATGAAAACGGACCTACT
19950 AATTCAGACTG
66 AATTCAGACTG
* *
19961 CACTAGCCGTTCTTAAGGGGCCAGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACT
1 CACTAGCCGTTCTTAAGAGGCCAGTTCATAATAGCAATATAAACTTCCATGAAAACGGACCTACT
20026 AATTCAGACTG
66 AATTCAGACTG
20037 CACTAGCCGTTCTTAAGAGGCCA
1 CACTAGCCGTTCTTAAGAGGCCA
20060 ATTAATATAA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 94 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (76 bp):
CACTAGCCGTTCTTAAGAGGCCAGTTCATAATAGCAATATAAACTTCCATGAAAACGGACCTACT
AATTCAGACTG
Found at i:21411 original size:20 final size:20
Alignment explanation
Indices: 21386--21423 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
21376 TTTAGTTTTA
21386 GGTTGATTTGGTCTCTGCTG
1 GGTTGATTTGGTCTCTGCTG
21406 GGTTGATTTGGTCTCTGC
1 GGTTGATTTGGTCTCTGC
21424 GTTTTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.34, T:0.45
Consensus pattern (20 bp):
GGTTGATTTGGTCTCTGCTG
Found at i:24948 original size:76 final size:76
Alignment explanation
Indices: 24822--25201 Score: 733
Period size: 76 Copynumber: 5.0 Consensus size: 76
24812 GGCACGCACT
24822 AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
1 AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
*
24887 ATTAAGGGGCC
66 CTTAAGGGGCC
24898 AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
1 AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
24963 CTTAAGGGGCC
66 CTTAAGGGGCC
24974 AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
1 AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
*
25039 ATTAAGGGGCC
66 CTTAAGGGGCC
25050 AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
1 AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
25115 CTTAAGGGGCC
66 CTTAAGGGGCC
25126 AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
1 AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
*
25191 CTTAAGAGGCC
66 CTTAAGGGGCC
25202 GATTAATATA
Statistics
Matches: 300, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 300 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (76 bp):
AGTTCATAATAGCAATATAAACTTCCATGAAAATGGACCTACTAATTCAGACTGCACTAGCCGTT
CTTAAGGGGCC
Found at i:32694 original size:25 final size:27
Alignment explanation
Indices: 32639--32695 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
32629 GGGAGATATT
*
32639 AAAGATGGAGTAGAATTTTTCAAAAAA
1 AAAGATGGAGTAGAATTCTTCAAAAAA
32666 AAAGATGGAGTAGAA-TCTT-AAAAAA
1 AAAGATGGAGTAGAATTCTTCAAAAAA
32691 AAAGA
1 AAAGA
32696 ACAAGTTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 11 0.38
26 3 0.10
27 15 0.52
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.21
Consensus pattern (27 bp):
AAAGATGGAGTAGAATTCTTCAAAAAA
Found at i:33872 original size:167 final size:167
Alignment explanation
Indices: 33594--33927 Score: 641
Period size: 167 Copynumber: 2.0 Consensus size: 167
33584 TTAGGACTTT
33594 ATTGATTTATTCTTCCTTTTCACTACTAGAAATCTATGTCTTCAGCGACTTACGACAATTGCGAC
1 ATTGATTTATTCTTCCTTTTCACTACTAGAAATCTATGTCTTCAGCGACTTACGACAATTGCGAC
*
33659 ATTCAAATCCGTCGCATTAAGTGCTTTCTGCGACGAATTGTGTGACTTACTTGCGACAAACATAA
66 ATTCAAATCCGTCGCATTAAGTGCTTTCTGCGACGAATTATGTGACTTACTTGCGACAAACATAA
*
33724 GAATTCGGATATCCCGTGCAACTTTTGGCAACCGCGA
131 GAATCCGGATATCCCGTGCAACTTTTGGCAACCGCGA
33761 ATTGATTTATTCTTCCTTTTCACTACTAGAAATCTATGTCTTCAGCGACTTACGACAATTGCGAC
1 ATTGATTTATTCTTCCTTTTCACTACTAGAAATCTATGTCTTCAGCGACTTACGACAATTGCGAC
33826 ATTCAAATCCGTCGCATTAAGTGCTTTCTGCGACGAATTATGTGACTTACTTGCGACAAACATAA
66 ATTCAAATCCGTCGCATTAAGTGCTTTCTGCGACGAATTATGTGACTTACTTGCGACAAACATAA
*
33891 GAATCCGGATATCCTGTGCAACTTTTGGCAACCGCGA
131 GAATCCGGATATCCCGTGCAACTTTTGGCAACCGCGA
33928 TAACACAAGC
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 164 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (167 bp):
ATTGATTTATTCTTCCTTTTCACTACTAGAAATCTATGTCTTCAGCGACTTACGACAATTGCGAC
ATTCAAATCCGTCGCATTAAGTGCTTTCTGCGACGAATTATGTGACTTACTTGCGACAAACATAA
GAATCCGGATATCCCGTGCAACTTTTGGCAACCGCGA
Found at i:34118 original size:6 final size:6
Alignment explanation
Indices: 34103--34142 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
34093 AAAAAGTTAT
*
34103 AAAAAA AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
34143 GAAACAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:39411 original size:27 final size:26
Alignment explanation
Indices: 39381--39441 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
39371 GTATCTTTTT
39381 TAAAATATATTTCTAAATTA-CCATTAC
1 TAAAATATATTT-T-AATTATCCATTAC
*
39408 T-AAATAATATTTTAATTATTCCATTAT
1 TAAAAT-ATATTTTAATTA-TCCATTAC
39435 TAAAATA
1 TAAAATA
39442 ATGGAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
25 5 0.17
26 5 0.17
27 15 0.52
28 4 0.14
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAAATATATTTTAATTATCCATTAC
Found at i:41932 original size:43 final size:41
Alignment explanation
Indices: 41892--41974 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 41
41882 ATTTCATACT
*
41892 ATAATATCAAAAAATTATAGGGAGATTAACAAAATCTCATAGAG
1 ATAATATC-AAAAATTATAGGAAGATT-ACAAAAT-TCATAGAG
* *
41936 ATATTATCAAAAATTATAGGAAGGTTACAAAATTCATAG
1 ATAATATCAAAAATTATAGGAAGATTACAAAATTCATAG
41975 GCAAGTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 6 0.17
42 7 0.19
43 16 0.44
44 7 0.19
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (41 bp):
ATAATATCAAAAATTATAGGAAGATTACAAAATTCATAGAG
Found at i:41933 original size:22 final size:21
Alignment explanation
Indices: 41902--41975 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 21
41892 ATAATATCAA
41902 AAAATT-ATAGGGAGATTAAC
1 AAAATTCATAGGGAGATTAAC
* * *
41922 AAAATCTCATAGAGATATTATC
1 AAAAT-TCATAGGGAGATTAAC
* *
41944 AAAAATT-ATAGGAAGGTT-AC
1 -AAAATTCATAGGGAGATTAAC
41964 AAAATTCATAGG
1 AAAATTCATAGG
41976 CAAGTTTATT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 6 0.14
20 11 0.26
21 8 0.19
22 12 0.29
23 5 0.12
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (21 bp):
AAAATTCATAGGGAGATTAAC
Found at i:42074 original size:22 final size:21
Alignment explanation
Indices: 42025--42100 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
42015 TCTATGGAGT
*
42025 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTTATAGGTAA
**
42046 TTATCAAAATTTTATACGGTGG
1 TTATCAAAATTTTATA-GGTAA
* * *
42068 TTATCAAAATTTAATAGATAG
1 TTATCAAAATTTTATAGGTAA
*
42089 TTATAAAAATTT
1 TTATCAAAATTT
42101 CATAAAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 29 0.62
22 18 0.38
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.42
Consensus pattern (21 bp):
TTATCAAAATTTTATAGGTAA
Found at i:48382 original size:15 final size:15
Alignment explanation
Indices: 48362--48481 Score: 96
Period size: 15 Copynumber: 8.4 Consensus size: 15
48352 AAGAGCCTCG
48362 ACCTCCTCCACCCCA
1 ACCTCCTCCACCCCA
*
48377 ACCTCCACCACCCCA
1 ACCTCCTCCACCCCA
48392 ACCTCCAT-CACCCCA
1 ACCTCC-TCCACCCCA
48407 A--T-CT--A-CCCA
1 ACCTCCTCCACCCCA
*
48416 ACCTCCGCCACCCCA
1 ACCTCCTCCACCCCA
*
48431 ACCTCC-GCATCCCCA
1 ACCTCCTCCA-CCCCA
48446 ACCTCCAT-CACCCCA
1 ACCTCC-TCCACCCCA
* *
48461 ATCTCCACCACCCCA
1 ACCTCCTCCACCCCA
*
48476 ATCTCC
1 ACCTCC
48482 CCAACCTCCC
Statistics
Matches: 88, Mismatches: 6, Indels: 22
0.76 0.05 0.19
Matches are distributed among these distances:
9 5 0.06
10 1 0.01
11 2 0.02
12 2 0.02
13 1 0.01
14 3 0.03
15 72 0.82
16 2 0.02
ACGTcount: A:0.24, C:0.61, G:0.02, T:0.13
Consensus pattern (15 bp):
ACCTCCTCCACCCCA
Found at i:48404 original size:30 final size:29
Alignment explanation
Indices: 48362--48481 Score: 108
Period size: 30 Copynumber: 4.2 Consensus size: 29
48352 AAGAGCCTCG
48362 ACCTCC-TCCACCCCAACCTCCACCACCCCA
1 ACCTCCAT-CACCCCAACCTCC-CCACCCCA
*
48392 ACCTCCATCACCCCAA--T--CTA-CCCA
1 ACCTCCATCACCCCAACCTCCCCACCCCA
** *
48416 ACCTCCGCCACCCCAACCTCCGCATCCCCA
1 ACCTCCATCACCCCAACCTCCCCA-CCCCA
*
48446 ACCTCCATCACCCCAATCTCCACCACCCCA
1 ACCTCCATCACCCCAACCTCC-CCACCCCA
*
48476 ATCTCC
1 ACCTCC
48482 CCAACCTCCC
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
24 18 0.25
25 2 0.03
26 1 0.01
28 2 0.03
30 46 0.64
31 3 0.04
ACGTcount: A:0.24, C:0.61, G:0.02, T:0.13
Consensus pattern (29 bp):
ACCTCCATCACCCCAACCTCCCCACCCCA
Found at i:48445 original size:54 final size:54
Alignment explanation
Indices: 48362--48464 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
48352 AAGAGCCTCG
*
48362 ACCTCCTCCACCCCAACCTCCACCACCCCAACCTCCATCACCCCAATCTACCCA
1 ACCTCCGCCACCCCAACCTCCACCACCCCAACCTCCATCACCCCAATCTACCCA
*
48416 ACCTCCGCCACCCCAACCTCC-GCATCCCCAACCTCCATCACCCCAATCT
1 ACCTCCGCCACCCCAACCTCCACCA-CCCCAACCTCCATCACCCCAATCT
48465 CCACCACCCC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 2 0.04
54 44 0.96
ACGTcount: A:0.24, C:0.60, G:0.02, T:0.14
Consensus pattern (54 bp):
ACCTCCGCCACCCCAACCTCCACCACCCCAACCTCCATCACCCCAATCTACCCA
Found at i:48490 original size:24 final size:24
Alignment explanation
Indices: 48387--48492 Score: 81
Period size: 24 Copynumber: 4.2 Consensus size: 24
48377 ACCTCCACCA
48387 CCCCAACCTCCATCACCCCAATCT
1 CCCCAACCTCCATCACCCCAATCT
* **
48411 ACCCAACCTCCGCCACCCCAACCTCCGCAT
1 CCCCAACCTCCATCACCCCAA--T---C-T
48441 CCCCAACCTCCATCACCCCAATCT
1 CCCCAACCTCCATCACCCCAATCT
* *
48465 CCACC-ACC-CCAATCTCCCCAACCT
1 CC-CCAACCTCC-ATCACCCCAATCT
48489 CCCC
1 CCCC
48493 TTCTATAGGA
Statistics
Matches: 66, Mismatches: 8, Indels: 17
0.73 0.09 0.19
Matches are distributed among these distances:
23 4 0.06
24 37 0.56
25 3 0.05
26 1 0.02
28 1 0.02
29 1 0.02
30 19 0.29
ACGTcount: A:0.24, C:0.61, G:0.02, T:0.13
Consensus pattern (24 bp):
CCCCAACCTCCATCACCCCAATCT
Found at i:56009 original size:20 final size:21
Alignment explanation
Indices: 55974--56019 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
55964 AAATATTATA
55974 TTTATCCTATAATGGGTAGTT
1 TTTATCCTATAATGGGTAGTT
*
55995 TTTATCTTA-AATGGGTAGTT
1 TTTATCCTATAATGGGTAGTT
56015 TTTAT
1 TTTAT
56020 TTTATTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (21 bp):
TTTATCCTATAATGGGTAGTT
Found at i:70013 original size:256 final size:256
Alignment explanation
Indices: 69558--70031 Score: 939
Period size: 256 Copynumber: 1.9 Consensus size: 256
69548 AATTTATAGC
69558 ACTCAAAGCTTCTAGAAATGGCCCGATGATCCCAAGCTTATGCTATGCTGATGACTGTTATTTAT
1 ACTCAAAGCTTCTAGAAATGGCCCGATGATCCCAAGCTTATGCTATGCTGATGACTGTTATTTAT
69623 TTTCCAAAATTGAACCACTAAGCTTAACAACTCTAAAGGACAAATTAATGCAGTTTTGCCAAGCC
66 TTTCCAAAATTGAACCACTAAGCTTAACAACTCTAAAGGACAAATTAATGCAGTTTTGCCAAGCC
69688 TCGGGCCAATCGATAAATCTAAAAAAATGTTCTATGATATTTTCACAAAATACCAGTCTAGAACT
131 TCGGGCCAATCGATAAATCTAAAAAAATGTTCTATGATATTTTCACAAAATACCAGTCTAGAACT
69753 TAAAATTGATGTCTCACTCTTTTAGAAATGGCTTCTAGAAACTCAAAGCTTTGAGTCTAGA
196 TAAAATTGATGTCTCACTCTTTTAGAAATGGCTTCTAGAAACTCAAAGCTTTGAGTCTAGA
69814 ACTCAAAGCTTCTAGAAATGGCCCGATGATCCCAAGCTTATGCTATGCTGATGACTGTTATTTAT
1 ACTCAAAGCTTCTAGAAATGGCCCGATGATCCCAAGCTTATGCTATGCTGATGACTGTTATTTAT
69879 TTTCCAAAATTGAACCACTAAGCTTAACAACTCTAAAGGACAAATTAATGCAGTTTTGCCAAGCC
66 TTTCCAAAATTGAACCACTAAGCTTAACAACTCTAAAGGACAAATTAATGCAGTTTTGCCAAGCC
*
69944 TCGGGCCAATCGATAAATCTAAAAAATTGTTCTATGATATTTTCACAAAATACCAGTCTAGAACT
131 TCGGGCCAATCGATAAATCTAAAAAAATGTTCTATGATATTTTCACAAAATACCAGTCTAGAACT
70009 TAAAATTGATGTCTCACTCTTTT
196 TAAAATTGATGTCTCACTCTTTT
70032 TTAATATTCC
Statistics
Matches: 217, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
256 217 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (256 bp):
ACTCAAAGCTTCTAGAAATGGCCCGATGATCCCAAGCTTATGCTATGCTGATGACTGTTATTTAT
TTTCCAAAATTGAACCACTAAGCTTAACAACTCTAAAGGACAAATTAATGCAGTTTTGCCAAGCC
TCGGGCCAATCGATAAATCTAAAAAAATGTTCTATGATATTTTCACAAAATACCAGTCTAGAACT
TAAAATTGATGTCTCACTCTTTTAGAAATGGCTTCTAGAAACTCAAAGCTTTGAGTCTAGA
Found at i:73896 original size:2 final size:2
Alignment explanation
Indices: 73891--73931 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
73881 TTTTTTTTAC
*
73891 TA TA TA TA TA TA TA T- TA T- TT TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73931 T
1 T
73932 TAAAAGTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:73919 original size:22 final size:24
Alignment explanation
Indices: 73885--73932 Score: 82
Period size: 22 Copynumber: 2.1 Consensus size: 24
73875 TTTTCTTTTT
73885 TTTTACTATATATATATATAT-TA
1 TTTTACTATATATATATATATATA
73908 TTTTA-TATATATATATATATATA
1 TTTTACTATATATATATATATATA
73931 TT
1 TT
73933 AAAAGTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTACTATATATATATATATATA
Found at i:78525 original size:29 final size:28
Alignment explanation
Indices: 78493--78554 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
78483 GGCATTTATT
*
78493 TCATTTTCACATCTATGGGGGCATTTTGG
1 TCATTTTCACATCTA-GAGGGCATTTTGG
** * *
78522 TCATTTTTGCATTTAGAGGGTATTTTGG
1 TCATTTTCACATCTAGAGGGCATTTTGG
78550 TCATT
1 TCATT
78555 CTTAATCTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.47
Consensus pattern (28 bp):
TCATTTTCACATCTAGAGGGCATTTTGG
Found at i:79563 original size:28 final size:28
Alignment explanation
Indices: 79527--79584 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
79517 TAACATACTC
*
79527 CAGTCACCTCATAGATGGCATTTTCATA
1 CAGTCACCTCATACATGGCATTTTCATA
79555 CAGTCACCTCATACATGGCATTTTCATA
1 CAGTCACCTCATACATGGCATTTTCATA
79583 CA
1 CA
79585 AGGCATTGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
CAGTCACCTCATACATGGCATTTTCATA
Found at i:79583 original size:15 final size:15
Alignment explanation
Indices: 79535--79591 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
79525 TCCAGTCACC
*
79535 TCATAGATGGCATTT
1 TCATACATGGCATTT
* **
79550 TCATACA-GTCA-CC
1 TCATACATGGCATTT
79563 TCATACATGGCATTT
1 TCATACATGGCATTT
*
79578 TCATACAAGGCATT
1 TCATACATGGCATT
79592 GGCATCATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
13 7 0.22
14 6 0.19
15 19 0.59
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (15 bp):
TCATACATGGCATTT
Found at i:81826 original size:54 final size:55
Alignment explanation
Indices: 81670--81829 Score: 252
Period size: 55 Copynumber: 2.9 Consensus size: 55
81660 ATCGGTAATT
* *
81670 AAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGCAATTAAGTGGA
1 AAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTGAA
* *
81725 AATAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAACCAGTAATTAAGT-AA
1 AAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTGAA
*
81779 AAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATC-GATAATTAAG
1 AAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAG-TAATTAAG
81830 AGTTAAAATG
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
53 1 0.01
54 47 0.48
55 49 0.51
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (55 bp):
AAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTGAA
Found at i:82088 original size:22 final size:21
Alignment explanation
Indices: 82063--82290 Score: 112
Period size: 22 Copynumber: 10.6 Consensus size: 21
82053 TGGTAATTAG
82063 TAATCAGTAAAAAGTAAGAAGA
1 TAATCAGTAAAAAGTAA-AAGA
* *
82085 TAATCA--ACAAGAGTAAAATAA
1 TAATCAGTA-AAAAGTAAAA-GA
* *
82106 TAGTCGGTAAAAAGTGAAATAG-
1 TAATCAGTAAAAAGT-AAA-AGA
*
82128 TAATCAGTAAGAA-TAAGAA-A
1 TAATCAGTAAAAAGTAA-AAGA
* *
82148 GTAATAAGTAAGAAGTAAAAGGA
1 -TAATCAGTAAAAAGTAAAA-GA
* * *
82171 -AATCCGT-AAGAGTAAAAAGG
1 TAATCAGTAAAAAGT-AAAAGA
*** * *
82191 TGGCCAGTAAAGAGTAAAAAGC
1 TAATCAGTAAAAAGT-AAAAGA
*
82213 TAATCAGTAAGAAA-TAAAAAGG
1 TAATCAGTAA-AAAGT-AAAAGA
* *
82235 TAATCAGTAAAAAGAAAAAGG
1 TAATCAGTAAAAAGTAAAAGA
*
82256 CAATCAGTAAAAAGTAAAAGA
1 TAATCAGTAAAAAGTAAAAGA
82277 GTAATCAGTAAAAA
1 -TAATCAGTAAAAA
82291 AGGAGCAGAA
Statistics
Matches: 158, Mismatches: 30, Indels: 36
0.71 0.13 0.16
Matches are distributed among these distances:
20 11 0.07
21 67 0.42
22 72 0.46
23 7 0.04
24 1 0.01
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.18
Consensus pattern (21 bp):
TAATCAGTAAAAAGTAAAAGA
Found at i:82253 original size:43 final size:42
Alignment explanation
Indices: 82062--82290 Score: 144
Period size: 43 Copynumber: 5.3 Consensus size: 42
82052 ATGGTAATTA
* * ** *
82062 GTAATCAGTAAAAAGTAAGAAGATAATCAACAAGAGTAAAATA-
1 GTAATCAGTAAAAAG-AAAAAGCTAATCAGTAAGAATAAAA-AG
* * * *
82105 ATAGTCGGTAAAAAGTGAAATAG-TAATCAGTAAGAATAAGAAA-
1 GTAATCAGTAAAAA--GAAAAAGCTAATCAGTAAGAATAA-AAAG
* * * ** * *
82148 GTAATAAGTAAGAAGTAAAAGGAAATCCGTAAGAGTAAAAAG
1 GTAATCAGTAAAAAGAAAAAGCTAATCAGTAAGAATAAAAAG
*** *
82190 GTGGCCAGTAAAGAGTAAAAAGCTAATCAGTAAGAAATAAAAAG
1 GTAATCAGTAAAAAG-AAAAAGCTAATCAGTAAG-AATAAAAAG
*
82234 GTAATCAGTAAAAAGAAAAAGGC-AATCAGTAAAAAGT-AAAAG
1 GTAATCAGTAAAAAGAAAAA-GCTAATCAGTAAGAA-TAAAAAG
82276 AGTAATCAGTAAAAA
1 -GTAATCAGTAAAAA
82291 AGGAGCAGAA
Statistics
Matches: 142, Mismatches: 34, Indels: 20
0.72 0.17 0.10
Matches are distributed among these distances:
41 8 0.06
42 29 0.20
43 77 0.54
44 27 0.19
45 1 0.01
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.17
Consensus pattern (42 bp):
GTAATCAGTAAAAAGAAAAAGCTAATCAGTAAGAATAAAAAG
Found at i:82286 original size:15 final size:15
Alignment explanation
Indices: 82268--82323 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
82258 ATCAGTAAAA
82268 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
82283 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
82297 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
82311 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
82324 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:82289 original size:21 final size:20
Alignment explanation
Indices: 82061--82289 Score: 129
Period size: 21 Copynumber: 10.7 Consensus size: 20
82051 AATGGTAATT
*
82061 AGTAATCAGTAAAAAGTAAGA
1 AGTAATCAGT-AAAAGTAAAA
** *
82082 AGATAATCAACAAGAGTAAAA
1 AG-TAATCAGTAAAAGTAAAA
* * * *
82103 TAATAGTCGGTAAAAAGTGAAAT
1 -AGTAATCAGT-AAAAGT-AAAA
82126 AGTAATCAGTAAGAA-TAAGAA
1 AGTAATCAGTAA-AAGTAA-AA
*
82147 AGTAATAAGTAAGAAGTAAAA
1 AGTAATCAGTAA-AAGTAAAA
* * * *
82168 GGAAATCCGTAAGAGTAAAA
1 AGTAATCAGTAAAAGTAAAA
***
82188 AGGTGGCCAGTAAAGAGTAAAA
1 A-GTAATCAGTAAA-AGTAAAA
*
82210 AGCTAATCAGTAAGAAATAAAA
1 AG-TAATCAGTAA-AAGTAAAA
82232 AGGTAATCAGTAAAAAG-AAAA
1 A-GTAATCAGT-AAAAGTAAAA
*
82253 AGGCAATCAGTAAAAAGTAAAA
1 A-GTAATCAGT-AAAAGTAAAA
82275 GAGTAATCAGTAAAA
1 -AGTAATCAGTAAAA
82290 AAGGAGCAGA
Statistics
Matches: 158, Mismatches: 35, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
20 9 0.06
21 73 0.46
22 68 0.43
23 8 0.05
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.17
Consensus pattern (20 bp):
AGTAATCAGTAAAAGTAAAA
Found at i:82355 original size:22 final size:21
Alignment explanation
Indices: 82305--82361 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 21
82295 GCAGAAAATA
*
82305 GTAATCAGTAAAAGAGTAAAATG
1 GTAATCAGTAAAA-AATAAAA-G
82328 GTAATCAGTAAAAAATAAGAAG
1 GTAATCAGTAAAAAATAA-AAG
82350 GTAATCAGTAAA
1 GTAATCAGTAAA
82362 GAGTAAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.21
Consensus pattern (21 bp):
GTAATCAGTAAAAAATAAAAG
Found at i:82447 original size:42 final size:43
Alignment explanation
Indices: 82401--82484 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
82391 ATCAATAAAA
82401 GATAATCAGTAAGAGTAAAACAGTAACCAGT-AAGAGCAAAGT
1 GATAATCAGTAAGAGTAAAACAGTAACCAGTAAAGAGCAAAGT
* * * * *
82443 GATAATTAGTAAGAGTCAAATAGTAATCAGTAAAGAGTAAAG
1 GATAATCAGTAAGAGTAAAACAGTAACCAGTAAAGAGCAAAG
82485 GGTGATCAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 27 0.75
43 9 0.25
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.20
Consensus pattern (43 bp):
GATAATCAGTAAGAGTAAAACAGTAACCAGTAAAGAGCAAAGT
Found at i:82469 original size:21 final size:21
Alignment explanation
Indices: 82403--82480 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
82393 CAATAAAAGA
* *
82403 TAATCAGTAAGAGTAAAACAG
1 TAATCAGTAAGAGTCAAATAG
*
82424 TAACCAGTAAGAG-CAAAGT-G
1 TAATCAGTAAGAGTCAAA-TAG
*
82444 ATAATTAGTAAGAGTCAAATAG
1 -TAATCAGTAAGAGTCAAATAG
82466 TAATCAGTAAAGAGT
1 TAATCAGT-AAGAGT
82481 AAAGGGTGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 31 0.67
22 11 0.24
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.22
Consensus pattern (21 bp):
TAATCAGTAAGAGTCAAATAG
Found at i:82572 original size:13 final size:13
Alignment explanation
Indices: 82556--82604 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
82546 GGTAATAAAT
82556 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
82569 AAAAGAGAGTAATTGG
1 AAAAGAGAGTAA---G
82585 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
82598 AAAAGAG
1 AAAAGAG
82605 TAAAAATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.13
13 15 0.48
16 8 0.26
17 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Found at i:82573 original size:29 final size:30
Alignment explanation
Indices: 82547--82604 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
82537 GTAAAAAGTG
82547 GTAATAAATAAAAGAGAGTAAGAAAAGAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGAGA
***
82577 GTAATTGGTAAAA-AGAGTAAGAAAAGAG
1 GTAATAAATAAAAGAGAGTAAGAAAAGAG
82605 TAAAAATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.16
Consensus pattern (30 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGAGA
Found at i:82617 original size:29 final size:30
Alignment explanation
Indices: 82554--82619 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
82544 GTGGTAATAA
* *
82554 ATAAAAGAGAGTAAGAAAAGAGAGTAATTG
1 ATAAAAGAGAGTAAGAAAAGAGAGAAAATG
*
82584 GTAAAA-AGAGTAAGAAAAGAGTA-AAAATG
1 ATAAAAGAGAGTAAGAAAAGAG-AGAAAATG
82613 ATAAAAG
1 ATAAAAG
82620 TAGCAAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (30 bp):
ATAAAAGAGAGTAAGAAAAGAGAGAAAATG
Found at i:85342 original size:14 final size:14
Alignment explanation
Indices: 85319--85369 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
85309 ACAAGAGACA
*
85319 TTTTTC-AAAATTG
1 TTTTTCAAAAATAG
*
85332 TTTTTCAAAAAAAG
1 TTTTTCAAAAATAG
*
85346 GTTTTCAAAAATGAG
1 TTTTTCAAAAAT-AG
85361 -TTTTCAAAA
1 TTTTTCAAAA
85370 GGTTTTGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 6 0.19
14 24 0.75
15 2 0.06
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (14 bp):
TTTTTCAAAAATAG
Found at i:88444 original size:45 final size:45
Alignment explanation
Indices: 88054--88432 Score: 535
Period size: 45 Copynumber: 8.4 Consensus size: 45
88044 TTCAATAAGA
* * * * *
88054 TTATCAAAGTCGACCCCAAAATAGGTCTTTCTCAGTTTTCAGCAC
1 TTATCAAAGTTGACCTCAGAACAGGTCTTTCTCAGTTTTCAGCAG
* * * **
88099 TTATCAAAATTGACTTCAAAACAGGTCTTTCTCAGTTTTCAATAG
1 TTATCAAAGTTGACCTCAGAACAGGTCTTTCTCAGTTTTCAGCAG
* * * *
88144 TTATCAAAATTGACCTTAGAATAGATCTTTCTCAGTTTTCAGCAG
1 TTATCAAAGTTGACCTCAGAACAGGTCTTTCTCAGTTTTCAGCAG
* * * *
88189 TTATCAAAATTGACCTTAGAATAGATCTTTCTCAGTTTTCAGCAG
1 TTATCAAAGTTGACCTCAGAACAGGTCTTTCTCAGTTTTCAGCAG
*
88234 TTATCAAAGTTGACCGCAGAACAGGTCTTTCTCAGTTTTCAGCAG
1 TTATCAAAGTTGACCTCAGAACAGGTCTTTCTCAGTTTTCAGCAG
*
88279 TTATCAAAATTGACCTCAGAACAGGTCTTTCTCAGTTTTCAGCAG
1 TTATCAAAGTTGACCTCAGAACAGGTCTTTCTCAGTTTTCAGCAG
*
88324 TTATCAAAGTTGACCTCAGAACAGATCTTTCTCAGTTTTCAGCAG
1 TTATCAAAGTTGACCTCAGAACAGGTCTTTCTCAGTTTTCAGCAG
*
88369 TTATCAAAGTTGACCTCAGAACAGGTCTTTTTCAGTTTT-AGCAG
1 TTATCAAAGTTGACCTCAGAACAGGTCTTTCTCAGTTTTCAGCAG
* *
88413 TTATCAAAGTCGACCACAGA
1 TTATCAAAGTTGACCTCAGA
88433 CTACTCTCTT
Statistics
Matches: 306, Mismatches: 28, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
44 23 0.08
45 283 0.92
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (45 bp):
TTATCAAAGTTGACCTCAGAACAGGTCTTTCTCAGTTTTCAGCAG
Done.