Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016457.1 Corchorus olitorius cultivar O-4 contig16490, 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: 21824
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Found at i:41 original size:31 final size:31
Alignment explanation
Indices: 5--101 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
1 AATC
5 AATTGACAGATTTTGTTAAGTAGAGGGACTC-
1 AATTGACAGATTTTGTTAAGTAGAGGGAC-CA
* ** *
36 AATTGACACCAAATTG-TAAGTAGAAGGACCA
1 AATTGACA-GATTTTGTTAAGTAGAGGGACCA
67 AATTGACAG-TTTT-TATAA-TAGAGGGACCA
1 AATTGACAGATTTTGT-TAAGTAGAGGGACCA
96 AATTGA
1 AATTGA
102 TCCTTTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
29 18 0.33
30 4 0.07
31 28 0.52
32 4 0.07
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (31 bp):
AATTGACAGATTTTGTTAAGTAGAGGGACCA
Found at i:93 original size:29 final size:31
Alignment explanation
Indices: 56--125 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
46 AAATTGTAAG
*
56 TAGAAGGACCAAATTGA-CAGTTTTTAT-AA
1 TAGAGGGACCAAATTGATCAGTTTTTATAAA
**
85 TAGAGGGACCAAATTGATCCTTTTTTATAAA
1 TAGAGGGACCAAATTGATCAGTTTTTATAAA
116 TAGAGGGACC
1 TAGAGGGACC
126 TGTACGGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 16 0.44
30 8 0.22
31 12 0.33
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (31 bp):
TAGAGGGACCAAATTGATCAGTTTTTATAAA
Found at i:2068 original size:27 final size:28
Alignment explanation
Indices: 2015--2068 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2005 TAAAGTAAGT
*
2015 GAAAAAATAGACTAATATTAAGTTAAAGC
1 GAAAAAATAGACTAATATT-AGATAAAGC
*
2044 GAAAACATAGACTAATATT-GATAAA
1 GAAAAAATAGACTAATATTAGATAAA
2069 AATATAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
29 18 0.78
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (28 bp):
GAAAAAATAGACTAATATTAGATAAAGC
Found at i:8514 original size:55 final size:56
Alignment explanation
Indices: 8412--8522 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 56
8402 CCTTTCTCGG
* *
8412 TCAGGCTAAAATCATTAAATCAGAAAGAGGAATCAAGCACATATTGATGAAAGCTA
1 TCAGGCTAAAATCATCAAATCAGAAAGAGGAATCAAGCAAATATTGATGAAAGCTA
** *
8468 TCAGGCTAAAATCATCCGATCAG-AAGAGGAATGAAGCAAATATTGATGAAAGCTA
1 TCAGGCTAAAATCATCAAATCAGAAAGAGGAATCAAGCAAATATTGATGAAAGCTA
8523 ATTGTGAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 30 0.60
56 20 0.40
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (56 bp):
TCAGGCTAAAATCATCAAATCAGAAAGAGGAATCAAGCAAATATTGATGAAAGCTA
Found at i:9419 original size:14 final size:15
Alignment explanation
Indices: 9381--9411 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9371 CCAAATTGGA
9381 GTACCAATAAAGGGG
1 GTACCAATAAAGGGG
9396 GTACCAATAAAGGGG
1 GTACCAATAAAGGGG
9411 G
1 G
9412 ACTTATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.35, T:0.13
Consensus pattern (15 bp):
GTACCAATAAAGGGG
Found at i:12582 original size:22 final size:22
Alignment explanation
Indices: 12554--12606 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
12544 GGTCATTTGT
12554 TGTTTATCTTTTATGATACTTA
1 TGTTTATCTTTTATGATACTTA
12576 TGTTTATCTTTTATGATACTTA
1 TGTTTATCTTTTATGATACTTA
*
12598 TGTATATCT
1 TGTTTATCT
12607 CCCAAGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58
Consensus pattern (22 bp):
TGTTTATCTTTTATGATACTTA
Found at i:15240 original size:26 final size:26
Alignment explanation
Indices: 15205--15261 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
15195 CGTGTCTTTG
*
15205 TGTGTTTGTCTT-TTCGTGTACCTTCA
1 TGTGTCTGTCTTCTT-GTGTACCTTCA
*
15231 TGTGTCTGTCTTCTTGTGTACCTTCG
1 TGTGTCTGTCTTCTTGTGTACCTTCA
15257 TGTGT
1 TGTGT
15262 GTCGTGTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.05, C:0.19, G:0.23, T:0.53
Consensus pattern (26 bp):
TGTGTCTGTCTTCTTGTGTACCTTCA
Found at i:15271 original size:26 final size:26
Alignment explanation
Indices: 15206--15276 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
15196 GTGTCTTTGT
*
15206 GTGTTTGTCTT-TTCGTGTACCTTCA
1 GTGTCTGTCTTCTTCGTGTACCTTCA
15231 TGTGTCTGTCTTCTT-GTGTACCTTC-
1 -GTGTCTGTCTTCTTCGTGTACCTTCA
*
15256 GTGTGTGTCGTGTCTTCGTGT
1 GTGTCTGTC-T-TCTTCGTGT
15277 GTTTGTCTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 8 0.21
25 1 0.03
26 24 0.62
27 6 0.15
ACGTcount: A:0.04, C:0.20, G:0.25, T:0.51
Consensus pattern (26 bp):
GTGTCTGTCTTCTTCGTGTACCTTCA
Found at i:15279 original size:69 final size:69
Alignment explanation
Indices: 15168--15330 Score: 290
Period size: 69 Copynumber: 2.4 Consensus size: 69
15158 AGCCCCACCG
* * *
15168 TGTCTTCTCGTGTACCTTCGTGTGTGTCGTGTCTTTGTGTGTTTGTCTTTTCGTGTACCTTCATG
1 TGTCTTCTTGTGTACCTTCGTGTGTGTCGTGTCTTCGTGTGTTTGTCTTCTCGTGTACCTTCATG
15233 TGTC
66 TGTC
*
15237 TGTCTTCTTGTGTACCTTCGTGTGTGTCGTGTCTTCGTGTGTTTGTCTTCTCGTGTACCTTCGTG
1 TGTCTTCTTGTGTACCTTCGTGTGTGTCGTGTCTTCGTGTGTTTGTCTTCTCGTGTACCTTCATG
15302 TGTC
66 TGTC
15306 TGTCTTCTTGTGTACCTTCGTGTGT
1 TGTCTTCTTGTGTACCTTCGTGTGT
15331 CTGTCTTCTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 90 1.00
ACGTcount: A:0.04, C:0.21, G:0.25, T:0.50
Consensus pattern (69 bp):
TGTCTTCTTGTGTACCTTCGTGTGTGTCGTGTCTTCGTGTGTTTGTCTTCTCGTGTACCTTCATG
TGTC
Found at i:15304 original size:26 final size:26
Alignment explanation
Indices: 15269--15357 Score: 146
Period size: 26 Copynumber: 3.5 Consensus size: 26
15259 TGTGTCGTGT
*
15269 CTTCGTGTGTTTGTCTTCTCGTGTAC
1 CTTCGTGTGTCTGTCTTCTCGTGTAC
*
15295 CTTCGTGTGTCTGTCTTCTTGTGTAC
1 CTTCGTGTGTCTGTCTTCTCGTGTAC
15321 CTTCGTGTGTCTGTCTTCTCGTGTAC
1 CTTCGTGTGTCTGTCTTCTCGTGTAC
15347 CTT--TGTGTCTG
1 CTTCGTGTGTCTG
15358 CTGGCCTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
24 8 0.13
26 52 0.87
ACGTcount: A:0.03, C:0.24, G:0.24, T:0.49
Consensus pattern (26 bp):
CTTCGTGTGTCTGTCTTCTCGTGTAC
Found at i:15403 original size:54 final size:55
Alignment explanation
Indices: 15334--15628 Score: 329
Period size: 54 Copynumber: 5.4 Consensus size: 55
15324 CGTGTGTCTG
*
15334 TCTTCTCG-TGTACCTTTGTGTCTGCTGGCCTTGCCTCACTGCGGAGAGCCTCCA
1 TCTTCTCGTTGTACCTTTGTGTCTGCTGGCCTCGCCTCACTGCGGAGAGCCTCCA
* * * * *
15388 TCTTGT-TTTGTACCTTCGTGTCTGCTGGCCTCGCCTCATTGCGG-GTCGCCT-CA
1 TCTTCTCGTTGTACCTTTGTGTCTGCTGGCCTCGCCTCACTGCGGAG-AGCCTCCA
* *
15441 GTCTTCTCGTTG-ACCTTTGTGTCTGCTGGCCTCACCTCACTGCGGAGAGCCTCCG
1 -TCTTCTCGTTGTACCTTTGTGTCTGCTGGCCTCGCCTCACTGCGGAGAGCCTCCA
* * * *
15496 TCTTCTCG-TGTACCTTCGTGTCTGCTGGCATCGCCTCACTACGGAGAGCCTCCG
1 TCTTCTCGTTGTACCTTTGTGTCTGCTGGCCTCGCCTCACTGCGGAGAGCCTCCA
* * **
15550 TCTTCTCGTT-TACCTTCGTGTTGTC-GCTGGCCTTGCCTCACTGCGGAGTGCCTCTG
1 TCTTCTCGTTGTACCTT--TG-TGTCTGCTGGCCTCGCCTCACTGCGGAGAGCCTCCA
*
15606 TCTTCTCG-TGTACCTTCGTGTCT
1 TCTTCTCGTTGTACCTTTGTGTCT
15629 TCTTGTGTAC
Statistics
Matches: 204, Mismatches: 24, Indels: 26
0.80 0.09 0.10
Matches are distributed among these distances:
53 9 0.04
54 143 0.70
55 7 0.03
56 41 0.20
57 4 0.02
ACGTcount: A:0.08, C:0.33, G:0.24, T:0.35
Consensus pattern (55 bp):
TCTTCTCGTTGTACCTTTGTGTCTGCTGGCCTCGCCTCACTGCGGAGAGCCTCCA
Found at i:15479 original size:108 final size:108
Alignment explanation
Indices: 15333--15628 Score: 400
Period size: 108 Copynumber: 2.7 Consensus size: 108
15323 TCGTGTGTCT
* * **
15333 GTCTTCTCG-TGTACCTTTGTGTCTGCTGGCCTTGCCTCACTGCGGAGAGCCTCCATCTTGTTTT
1 GTCTTCTCGTTG-ACCTTTGTGTCTGCTGGCCTTGCCTCACTGCGGAGAGCCTCCGTCTTCTCGT
* * * *
15397 GTACCTTCGTGTCTGCTGGCCTCGCCTCATTGCGG-GTCGCCTCA
65 GTACCTTCGTGTCTGCTGGCATCGCCTCACTACGGAG-AGCCTCA
**
15441 GTCTTCTCGTTGACCTTTGTGTCTGCTGGCCTCACCTCACTGCGGAGAGCCTCCGTCTTCTCGTG
1 GTCTTCTCGTTGACCTTTGTGTCTGCTGGCCTTGCCTCACTGCGGAGAGCCTCCGTCTTCTCGTG
*
15506 TACCTTCGTGTCTGCTGGCATCGCCTCACTACGGAGAGCCTCC
66 TACCTTCGTGTCTGCTGGCATCGCCTCACTACGGAGAGCCTCA
* * *
15549 GTCTTCTCGTTTACCTTCGTGTTGTC-GCTGGCCTTGCCTCACTGCGGAGTGCCTCTGTCTTCTC
1 GTCTTCTCGTTGACCTT--TG-TGTCTGCTGGCCTTGCCTCACTGCGGAGAGCCTCCGTCTTCTC
15613 GTGTACCTTCGTGTCT
63 GTGTACCTTCGTGTCT
15629 TCTTGTGTAC
Statistics
Matches: 167, Mismatches: 16, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
108 108 0.65
109 3 0.02
110 52 0.31
111 4 0.02
ACGTcount: A:0.08, C:0.33, G:0.24, T:0.35
Consensus pattern (108 bp):
GTCTTCTCGTTGACCTTTGTGTCTGCTGGCCTTGCCTCACTGCGGAGAGCCTCCGTCTTCTCGTG
TACCTTCGTGTCTGCTGGCATCGCCTCACTACGGAGAGCCTCA
Found at i:15629 original size:20 final size:20
Alignment explanation
Indices: 15604--15650 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
15594 GGAGTGCCTC
15604 TGTCTTCTCGTGTACCTTCG
1 TGTCTTCTCGTGTACCTTCG
* *
15624 TGTCTTCTTGTGTACCTTTG
1 TGTCTTCTCGTGTACCTTCG
15644 TGTCTTC
1 TGTCTTC
15651 ACTATTGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.04, C:0.26, G:0.19, T:0.51
Consensus pattern (20 bp):
TGTCTTCTCGTGTACCTTCG
Found at i:15953 original size:16 final size:16
Alignment explanation
Indices: 15932--15963 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15922 GGCCTAATCC
*
15932 CCACTCATTCTCTTAG
1 CCACTCACTCTCTTAG
15948 CCACTCACTCTCTTAG
1 CCACTCACTCTCTTAG
15964 AAGATTGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.41, G:0.06, T:0.34
Consensus pattern (16 bp):
CCACTCACTCTCTTAG
Found at i:19267 original size:332 final size:333
Alignment explanation
Indices: 16682--20450 Score: 4960
Period size: 332 Copynumber: 11.4 Consensus size: 333
16672 GGTGCCCTGA
* * * * **
16682 CTCAGTGTTGCATGA-TTTTGGTAGCCAAGACTCCTTGTAATATCTATATTCATCTATTCAAATC
1 CTCAGTTTTGTATGATTTTTGG-CGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATC
* * ** * *
16746 TCAACCACATAAGATTTAAAGATTTGTTTTTATAAGCATCAGAATCCAGTTTCTATATT-ATAGG
65 TCAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGAT-TTAATTGG
* * ** *
16810 AAATTAATTTGGAAAAGCATAGGAAAAACGATATTCGAAGCGTGGAAAACCCTTCAATTTTTTTG
129 AAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTG
* * * ** * * * *
16875 GCGATGATTTATATATTTTTTCTGAGTATTTTGGGTAAAAATTGATGAAATATAATTCGGGTCAA
194 GCGATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAA
** * * * * * *
16940 TTTTTGCAAAATCTTGATCGAAATCATGTG----CTATCACAATTTTCAGCTAGAAACGCATTCC
259 TTTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTTCC
* *
17001 AGGGCTCCGG
324 GGGGCCCCGG
* * * ** *
17011 TTCAGTTTTGTATGATTTTTGACGCCAAGACTCCTTGAAATATCTATATTCATCTATTCAAATTT
1 CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
* * * * *
17076 CAGCTACATATGATTTAAAAATTTGTTTTTATGAGCATCAGAATCCAGTTTCAACTTAATTGGAA
66 CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATTGGAA
** * *
17141 ATTAATTCGGAAAAATATAAGAAAAACGAAATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGC
131 ATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGC
* * *
17206 GATGATTTATATGCTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCTGGTCATTT
196 GATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATT
* * * *
17271 TTTGCAAAATCTTAGACGAAATCGTATGCTAACTATCACAG-TTCCGGCTAAAAATGCGTTCCGG
261 TTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTTCCGG
**
17335 GGTTCCGG
326 GGCCCCGG
* * *
17343 CTCAGTTTTGAATGATTTTTGGCGCCAAGACTCCGTGGAAAATCTATATTCATCTACCCAAATCT
1 CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
* * * * * * *
17408 TAGGCACATAAGATTTAAAGATTT-ATTTTACGAGCATCAGAATCTAGTTTCGATTTAATAGGAG
66 CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATTGGAA
* * * * * * *
17472 ATTAATTCGGAAAAGCATTGAAAAAACAATATTCGAAGC-GTAAAAAACCTTCAATTTTTTTGAC
131 ATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGC
* * *
17536 GATAATTTATATATTTTTTATGAGTATTTTGGCCGAAAA-TTGAGGAAAAATCATTCGGGTCAAT
196 GATGATTTATATACTTTTTATTAGTATTTTGGCC-AAAATTTGAGGAAAAATCATTCGGGTCAAT
* * * * * * *
17600 TTTTGCAAAATCTTGACCGAAATCGTGTGCCAACTATCAAAATTTTCGACTAAAAACGCGTTCCA
260 TTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTTCCG
* * *
17665 GTGCCCTGT
325 GGGCCCCGG
* *** *
17674 TTCAGTTTTGTATGATTTTTGGCTTTAAGACTCATTGGAATATCTATATTCATCTACCCAAATCT
1 CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
*
17739 CAGCCAC--ATGATTTAAAGATTTATTTTTACGAGCATCAGAATCCA-TTTCGATTTAATTGGAA
66 CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATTGGAA
** * * * *
17801 ATTAATTCGGAAAAATATAGGTAAAACGATATTCTAGGCTTTAAAAACACTTCAATCTTTTTGGC
131 ATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGC
* * * * *
17866 TATGATTTATATATTTTTTATGATTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGATCAATT
196 GATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATT
* * *
17931 TTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAGATGCGTTCCGG
261 TTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTTCCGG
*
17996 GGCCCCGA
326 GGCCCCGG
** * *
18004 CTCAGTTTTGTATGA-TTTTGAAGCCAAGACTCCTTTGAATATCTATATTCATCTGCCCAAATCT
1 CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
* * * * *
18068 CAGACACATATGGTTTAAAGAATTGTTTTTACGAGAATCAGAATCCAATTTCGATTTAATTGGAA
66 CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATTGGAA
** *
18133 ATTAATTCTAAAAAGCATAAGAAAAACGATATTCGAAGCTTTAAAAA-CCTTCAATCTTTTTGGC
131 ATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGC
* * *
18197 GATGATTTATATACTTTTTATTTGTTTTTTGGCCAAAATTTGATGAAAAATCATTCGGGTCAATT
196 GATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATT
* * *
18262 TTTGCAAAATCTTGACCGAAATCGTGTGCGT---TA-CA-A-TTTTCGCCTAAAAATGCGTTCCA
261 TTTGCAAAATCTTGGCCGAAATCGTGTGC-TAACTATCACAGTTTTCGGCTAAAAATGCGTTCCG
*
18321 GGGCCCCGA
325 GGGCCCCGG
* * * * * * * *
18330 CTCAGTATTGTATGATTTTTGGTGGCAAGACTCATTTGAATATCTATATTTATCTGCCAAAATCT
1 CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
* * * * *
18395 CAGACACATATGGTTTAAAGAATTGTTTTTACGAACATCAGAATCCAATTTCGATTTAATTGGAA
66 CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATTGGAA
18460 ATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAA-CCTTCAATCTTTTTGGC
131 ATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGC
* *
18524 GATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATTATTCGGGTCAATA
196 GATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATT
* *
18589 TTTGCAAAATCTTGGCCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAATGCGTTTCGG
261 TTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTTCCGG
*
18654 GGCCCCAG
326 GGCCCCGG
* * * *
18662 CTCAGTTTTGAATGATATTTT-GCGCTACGACTCCTTGGAATATTTATATTCATCTACCCAAATC
1 CTCAGTTTTGTATGAT-TTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATC
* * *
18726 TCATCCACATATGATTTAAAGATTTGTTTTTATGAGCATC-GAAATCCAGTTAT-GATTTATTTG
65 TCAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAG-AATCCAGTT-TCGATTTAATTG
* * * *
18789 GAAATTAATTCGGAAAAGCATAGGAACAATGATATTCGAAGCTTTAAAAACCATTCAATATTTTT
128 GAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTT
* *
18854 GGCGATGATTTATATACTTTTTACGT-GTATTTTGGCCAAAAATTGAGGAAAAATCATTCGGGTC
193 GGCGATGATTTATATACTTTTTA-TTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTC
* * * *
18918 AATTTTTGCAAAATCTTGGCCGAAATCATGTGCTAACTATCATAATTTTCGGCTAAAAACGCGTT
257 AATTTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTT
**
18983 CTAGGGCCCCGG
322 CCGGGGCCCCGG
* * * * * * *
18995 CCCAGTTTTGTATGTTTTTTGGCGCCAAGAATCCTTAGAATATCAATATTTATCTACCAAAATCT
1 CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
* * * *
19060 CATCCACATATGATTTAAAAATTTGTTTTTACGAGCATCAGAATCTAATTTCGATTTAATT-GAA
66 CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATTGGAA
** *
19124 ATTAATTCGGAAAAGCATAGGAAAAATTATATTCGAAGCTTTAAAAACACTTCAATCTTTTTGGC
131 ATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGC
* * * * *
19189 -ATTGATTTATATACTTTTTGTTAGTATTTTGGCCAAAATTTGAGGAAATATCATTCAGGTGAAA
196 GA-TGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAAT
* * *
19253 TTTTGTAAAATCTTGGCCGAAATCGTGTGCTAACCATCATAGTTTTCGGCTAAAAATGCGTTCCG
260 TTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTTCCG
19318 GGGCCCCGG
325 GGGCCCCGG
* * * *
19327 TTCAGTTTTGTATGATTTTTGGCACCACGACTCCTTGGAATAACTATATTCATCTACCCAAATCT
1 CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
* * * *
19392 CAGCCACATAAGATTTATAGATTTGTTTTTACGAGCATCGGAATCCAGTTACGATTTAATAT-GA
66 CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAAT-TGGA
**
19456 AATTAATTCCTAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGG
130 AATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGG
*
19521 CGATGATTTATATACTTTTTATTAGTATTTTGGGCAAAATTTGAGGAAAAATCATTCGGGTCAAT
195 CGATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAAT
* *
19586 TTTTGCAAAATCTTGGCCGAAAT--TGTG-----T-GCACAGTTTTCGGCTAAAAATGCGTTTC-
260 TTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTTCCG
*
19642 GGGCCCCAG
325 GGGCCCCGG
* * * *
19651 CTCAGTTTTGAATGATTTTTTGCGCCACGACTCCTTGGAATATTTATATTCATCTACCCAAATCT
1 CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
* * * **
19716 CATCCACATATGATTTAAAGATTTGTTTTTATGAGCATC-GAAATCCAGTTTTGATTTGTTTGGA
66 CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAG-AATCCAGTTTCGATTTAATTGGA
*
19780 AATTAATTCGGAAAAGCATAGGAAAAATGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGG
130 AATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGG
* * *
19845 CGATGATTTATATAATTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGATCAGT
195 CGATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAAT
* *
19910 TTTTGAAAAATCTTGGCCGAAATCGTGTGCT--CCATCACAGTTTTCGGCTAAAAATGCGTTCCG
260 TTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTTCCG
19973 GGGCCCCGG
325 GGGCCCCGG
* * * *
19982 TTCAGTTTTGTATGATTTTTGGCACCAAGATTCCTTGGAATAACTATATTCATCTACCCAAATCT
1 CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
* * * * *
20047 TAGCCACATAAGATTTATAGATTTGTTTTTACGAGTATCGGAATCCAGTTTCGATTTAATAT-GA
66 CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAAT-TGGA
*
20111 AATTAATTCAGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGG
130 AATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGG
20176 CGATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAAT
195 CGATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAAT
*
20241 TTTTGCAAAATCTTGGCCGAAATCGTGTGCTTAC-ATCACAGTTTTCGGCTAAAAATGCGTTCCG
260 TTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTTCCG
* *
20305 GTGCCCCGA
325 GGGCCCCGG
* * * * *
20314 CTCAGTTTTGAATGATTTTTGGCGCCAAGACACCTTGAAATATCTATATTCATCCAACCAAATCT
1 CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
* * * * *
20379 CAGGCACATAAGATTTAATGATTTGTTTTTACGAGCATTAGAATCCAGTTTCGATTTAATAGGAA
66 CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATTGGAA
20444 ATTAATT
131 ATTAATT
20451 TTGGCAAAAT
Statistics
Matches: 3011, Mismatches: 381, Indels: 93
0.86 0.11 0.03
Matches are distributed among these distances:
323 2 0.00
324 264 0.09
325 25 0.01
326 48 0.02
327 256 0.09
328 4 0.00
329 351 0.12
330 314 0.10
331 568 0.19
332 781 0.26
333 395 0.13
334 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (333 bp):
CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCT
CAGCCACATATGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATTGGAA
ATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGC
GATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATT
TTTGCAAAATCTTGGCCGAAATCGTGTGCTAACTATCACAGTTTTCGGCTAAAAATGCGTTCCGG
GGCCCCGG
Found at i:19825 original size:989 final size:985
Alignment explanation
Indices: 16705--20450 Score: 4940
Period size: 989 Copynumber: 3.8 Consensus size: 985
16695 GATTTTGGTA
* ** * *
16705 GCCAAGACTCCTTGTAATATCTATATTCATCTATTCAAATCTCAACCACATAAGATTTAAAGATT
1 GCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCTCATCCACATATGATTTAAAGATT
* * *
16770 TGTTTTTATAAGCATCAGAATCCAGTTTCT-ATATT-ATAGGAAATTAATTTGGAAAAGCATAGG
66 TGTTTTTATGAGCATCAGAATCCAGTTT-TGAT-TTAATTGGAAATTAATTCGGAAAAGCATAGG
* ** * * *
16833 AAAAACGATATTCGAAGCGTGGAAAACCCTTCAATTTTTTTGGCGATGATTTATATATTTTTTCT
129 AAAAACGATATTCGAAGCTTTAAAAACCATTCAATCTTTTTGGCGATGATTTATATATTTTTAC-
* ** * * * * *
16898 GAGTATTTTGGGTAAAAATTGATGAAATATAATTCGGGTCAATTTTTGCAAAATCTTGATCGAAA
193 GTGTATTTTGGCCAAAAATTGAGGAAAAATCATTCGGATCAATTTTTGCAAAATCTTGACCGAAA
* * * * *
16963 TCATGTGCT--ATCACAATTTTCAGCTAGAAACGCATTCCAGGGCTCCGGTTCAGTTTTGTATGA
258 TCATGTGCTCCATCACAATTTTCGGCTAAAAACGCGTTCCAGGGCCCCGGCTCAGTTTTGTATGA
** * *
17026 TTTTTGACGCCAAGACTCCTTGAAATATCTATATTCATCTATTCAAATTTCAGCTACATATGATT
323 TTTTTGACGCCAAGACTCCTTG-AATATCTATATTCATCTACCCAAATCTCAGCCACATATGATT
* * * * *
17091 TAAAAATTTGTTTTTATGAGCATCAGAATCCAGTTTCAACTTAATTGGAAATTAATTCGGAAAAA
387 TAAAAATTTGTTTTTACGAGCATCAGAATCCAATTTCGATTTAATTGGAAATTAATTCGGAAAAG
* * *
17156 TATAAGAAAAACGAAATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGCGATGATTTATATGCT
452 CATAAGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGCGATGATTTATATACT
* * *
17221 TTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCTGGTCATTTTTTGCAAAATCTTAG
517 TTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTTGG
* * * ** *
17286 ACGAAATCGTATGCTAACTATCACAG-TTCCGGCTAAAAATGCGTTCCGGGGTTCCGGCTCAGTT
582 CCGAAATCGTGTGCTAAC-ATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCCCCGACTCAGTT
* *
17350 TTGAATGATTTTTGGCGCCAAGACTCCGTGGAA-AATCTATATTCATCTACCCAAATCTTAGGCA
646 TTGAATGATTTTTGGCGCCAAGACTCCTTGGAATAA-CTATATTCATCTACCCAAATCTCAGGCA
* * *
17414 CATAAGATTTAAAGATTT-ATTTTACGAGCATCAGAATCTAGTTTCGATTTAATAGGAGATTAAT
710 CATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATAGGAAATTAAT
* * * * * * * *
17478 TCGGAAAAGCATTGAAAAAACAATATTCGAAGCGTAAAAAACCTTCAATTTTTTTGACGATAATT
775 TCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCTTCAATCTTTTTGGCGATGATT
* *
17543 TATATATTTTTTATGAGTATTTTGGCCGAAAA-TTGAGGAAAAATCATTCGGGTCAATTTTTGCA
840 TATATACTTTTTATTAGTATTTTGGCC-AAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCA
* * * * * * *
17607 AAATCTTGACCGAAATCGTGTGCCAACTATCAAAATTTTCGACTAAAAACGCGTTCCAGTG-CCC
904 AAATCTTGGCCGAAATTGTGTG----C-A-C--AGTTTTCGGCTAAAAATGCGTTTCAGGGCCCC
* * * *
17671 TGTTTCAGTTTTGTATGATTTTTGGC
961 AG-CTCAGTTTTGAATGATTTTTTGC
*** * *
17697 TTTAAGACTCATTGGAATATCTATATTCATCTACCCAAATCTCAGCCAC--ATGATTTAAAGATT
1 GCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCTCATCCACATATGATTTAAAGATT
* * * ** *
17760 TATTTTTACGAGCATCAGAATCCA-TTTCGATTTAATTGGAAATTAATTCGGAAAAATATAGGTA
66 TGTTTTTATGAGCATCAGAATCCAGTTTTGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAA
* * * *
17824 AAACGATATTCTAGGCTTTAAAAA-CACTTCAATCTTTTTGGCTATGATTTATATATTTTTTATG
131 AAACGATATTCGAAGCTTTAAAAACCA-TTCAATCTTTTTGGCGATGATTTATATA-TTTTTACG
*
17888 AT-TATTTTGGCCAAAATTTGAGGAAAAATCATTCGGATCAATTTTTGCAAAATCTTGACCGAAA
194 -TGTATTTTGGCCAAAAATTGAGGAAAAATCATTCGGATCAATTTTTGCAAAATCTTGACCGAAA
* * * * * *
17952 TCGTGTGCTAACCATCACAGTTTTCGGCTAAAGATGCGTTCCGGGGCCCCGACTCAGTTTTGTAT
258 TCATGTGCT--CCATCACAATTTTCGGCTAAAAACGCGTTCCAGGGCCCCGGCTCAGTTTTGTAT
* * * *
18017 GA-TTTTGAAGCCAAGACTCCTTTGAATATCTATATTCATCTGCCCAAATCTCAGACACATATGG
321 GATTTTTGACGCCAAGACTCC-TTGAATATCTATATTCATCTACCCAAATCTCAGCCACATATGA
* **
18081 TTTAAAGAA-TTGTTTTTACGAGAATCAGAATCCAATTTCGATTTAATTGGAAATTAATTCTAAA
385 TTTAAA-AATTTGTTTTTACGAGCATCAGAATCCAATTTCGATTTAATTGGAAATTAATTCGGAA
18145 AAGCATAAGAAAAACGATATTCGAAGCTTTAAAAA-CCTTCAATCTTTTTGGCGATGATTTATAT
449 AAGCATAAGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGCGATGATTTATAT
* * *
18209 ACTTTTTATTTGTTTTTTGGCCAAAATTTGATGAAAAATCATTCGGGTCAATTTTTGCAAAATCT
514 ACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCT
* * * *
18274 TGACCGAAATCGTGTGCGT----T-ACAATTTTCGCCTAAAAATGCGTTCCAGGGCCCCGACTCA
579 TGGCCGAAATCGTGTGC-TAACATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCCCCGACTCA
* * * * * * * * * * *
18334 GTATTGTATGATTTTTGGTGGCAAGACTCATTTGAATATCTATATTTATCTGCCAAAATCTCAGA
643 GTTTTGAATGATTTTTGGCGCCAAGACTCCTTGGAATAACTATATTCATCTACCCAAATCTCAGG
* * * * * *
18399 CACATATGGTTTAAAGAATTGTTTTTACGAACATCAGAATCCAATTTCGATTTAATTGGAAATTA
708 CACATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATAGGAAATTA
18464 ATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCTTCAATCTTTTTGGCGATGA
773 ATTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCTTCAATCTTTTTGGCGATGA
* *
18529 TTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATTATTCGGGTCAATATTTGC
838 TTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGC
* *
18594 AAAATCTTGGCCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAATGCGTTTCGGGGCCC
903 AAAATCTTGGCCGAAAT--TGTG-T-----GCACAGTTTTCGGCTAAAAATGCGTTTCAGGGCCC
*
18659 CAGCTCAGTTTTGAATGATATTTTGC
960 CAGCTCAGTTTTGAATGATTTTTTGC
* * *
18685 GCTACGACTCCTTGGAATATTTATATTCATCTACCCAAATCTCATCCACATATGATTTAAAGATT
1 GCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCTCATCCACATATGATTTAAAGATT
* *
18750 TGTTTTTATGAGCATC-GAAATCCAGTTATGATTTATTTGGAAATTAATTCGGAAAAGCATAGGA
66 TGTTTTTATGAGCATCAG-AATCCAGTTTTGATTTAATTGGAAATTAATTCGGAAAAGCATAGGA
* * *
18814 ACAATGATATTCGAAGCTTTAAAAACCATTCAATATTTTTGGCGATGATTTATATACTTTTTACG
130 AAAACGATATTCGAAGCTTTAAAAACCATTCAATCTTTTTGGCGATGATTTATATA-TTTTTACG
* *
18879 TGTATTTTGGCCAAAAATTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTTGGCCGAAAT
194 TGTATTTTGGCCAAAAATTGAGGAAAAATCATTCGGATCAATTTTTGCAAAATCTTGACCGAAAT
* * * *
18944 CATGTGCTAACTATCATAATTTTCGGCTAAAAACGCGTTCTAGGGCCCCGGCCCAGTTTTGTATG
259 CATGTGCT--CCATCACAATTTTCGGCTAAAAACGCGTTCCAGGGCCCCGGCTCAGTTTTGTATG
* * * * * * *
19009 TTTTTTGGCGCCAAGAATCCTTAGAATATCAATATTTATCTACCAAAATCTCATCCACATATGAT
322 ATTTTTGACGCCAAGACTCCTT-GAATATCTATATTCATCTACCCAAATCTCAGCCACATATGAT
*
19074 TTAAAAATTTGTTTTTACGAGCATCAGAATCTAATTTCGATTTAATT-GAAATTAATTCGGAAAA
386 TTAAAAATTTGTTTTTACGAGCATCAGAATCCAATTTCGATTTAATTGGAAATTAATTCGGAAAA
* ** *
19138 GCATAGGAAAAATTATATTCGAAGCTTTAAAAACACTTCAATCTTTTTGGC-ATTGATTTATATA
451 GCATAAGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGCGA-TGATTTATATA
* * * * * *
19202 CTTTTTGTTAGTATTTTGGCCAAAATTTGAGGAAATATCATTCAGGTGAAATTTTGTAAAATCTT
515 CTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTT
* **
19267 GGCCGAAATCGTGTGCTAACCATCATAGTTTTCGGCTAAAAATGCGTTCCGGGGCCCCGGTTCAG
580 GGCCGAAATCGTGTGCTAA-CATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCCCCGACTCAG
* * * *
19332 TTTTGTATGATTTTTGGCACCACGACTCCTTGGAATAACTATATTCATCTACCCAAATCTCAGCC
644 TTTTGAATGATTTTTGGCGCCAAGACTCCTTGGAATAACTATATTCATCTACCCAAATCTCAGGC
* * * *
19397 ACATAAGATTTATAGATTTGTTTTTACGAGCATCGGAATCCAGTTACGATTTAATATGAAATTAA
709 ACATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATAGGAAATTAA
**
19462 TTCCTAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGCGATGA
774 TTCGGAAAAGCATAGGAAAAACGATATTCGAAGCTTTAAAAA-CCTTCAATCTTTTTGGCGATGA
*
19527 TTTATATACTTTTTATTAGTATTTTGGGCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGC
838 TTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGC
19592 AAAATCTTGGCCGAAATTGTGTGCACAGTTTTCGGCTAAAAATGCGTTTC-GGGCCCCAGCTCAG
903 AAAATCTTGGCCGAAATTGTGTGCACAGTTTTCGGCTAAAAATGCGTTTCAGGGCCCCAGCTCAG
19656 TTTTGAATGATTTTTTGC
968 TTTTGAATGATTTTTTGC
* *
19674 GCCACGACTCCTTGGAATATTTATATTCATCTACCCAAATCTCATCCACATATGATTTAAAGATT
1 GCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCTCATCCACATATGATTTAAAGATT
**
19739 TGTTTTTATGAGCATC-GAAATCCAGTTTTGATTTGTTTGGAAATTAATTCGGAAAAGCATAGGA
66 TGTTTTTATGAGCATCAG-AATCCAGTTTTGATTTAATTGGAAATTAATTCGGAAAAGCATAGGA
* * *
19803 AAAATGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGCGATGATTTATATAATTTTTA-T
130 AAAACGATATTCGAAGCTTTAAAAACCATTCAATCTTTTTGGCGATGATTTATAT-ATTTTTACG
* * * *
19867 TAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGATCAGTTTTTGAAAAATCTTGGCCGAAA
194 T-GTATTTTGGCCAAAAATTGAGGAAAAATCATTCGGATCAATTTTTGCAAAATCTTGACCGAAA
* * * * *
19932 TCGTGTGCTCCATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCCCCGGTTCAGTTTTGTATGA
258 TCATGTGCTCCATCACAATTTTCGGCTAAAAACGCGTTCCAGGGCCCCGGCTCAGTTTTGTATGA
* * * * * *
19997 TTTTTGGCACCAAGATTCCTTGGAATAACTATATTCATCTACCCAAATCTTAGCCACATAAGATT
323 TTTTTGACGCCAAGACTCCTT-GAATATCTATATTCATCTACCCAAATCTCAGCCACATATGATT
* * * * * *
20062 TATAGATTTGTTTTTACGAGTATCGGAATCCAGTTTCGATTTAATAT-GAAATTAATTCAGAAAA
387 TAAAAATTTGTTTTTACGAGCATCAGAATCCAATTTCGATTTAAT-TGGAAATTAATTCGGAAAA
*
20126 GCATAGGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGCGATGATTTATATAC
451 GCATAAGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGCGATGATTTATATAC
20191 TTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTTG
516 TTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTTG
* *
20256 GCCGAAATCGTGTGCTTACATCACAGTTTTCGGCTAAAAATGCGTTCCGGTGCCCCGACTCAGTT
581 GCCGAAATCGTGTGCTAACATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCCCCGACTCAGTT
* * * * *
20321 TTGAATGATTTTTGGCGCCAAGACACCTTGAAATATCTATATTCATCCAACCAAATCTCAGGCAC
646 TTGAATGATTTTTGGCGCCAAGACTCCTTGGAATAACTATATTCATCTACCCAAATCTCAGGCAC
* *
20386 ATAAGATTTAATGATTTGTTTTTACGAGCATTAGAATCCAGTTTCGATTTAATAGGAAATTAATT
711 ATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATAGGAAATTAATT
20451 TTGGCAAAAT
Statistics
Matches: 2410, Mismatches: 297, Indels: 99
0.86 0.11 0.04
Matches are distributed among these distances:
986 3 0.00
987 400 0.17
988 409 0.17
989 426 0.18
990 106 0.04
991 356 0.15
992 371 0.15
993 49 0.02
995 1 0.00
996 5 0.00
997 183 0.08
998 101 0.04
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (985 bp):
GCCAAGACTCCTTGGAATATCTATATTCATCTACCCAAATCTCATCCACATATGATTTAAAGATT
TGTTTTTATGAGCATCAGAATCCAGTTTTGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAA
AAACGATATTCGAAGCTTTAAAAACCATTCAATCTTTTTGGCGATGATTTATATATTTTTACGTG
TATTTTGGCCAAAAATTGAGGAAAAATCATTCGGATCAATTTTTGCAAAATCTTGACCGAAATCA
TGTGCTCCATCACAATTTTCGGCTAAAAACGCGTTCCAGGGCCCCGGCTCAGTTTTGTATGATTT
TTGACGCCAAGACTCCTTGAATATCTATATTCATCTACCCAAATCTCAGCCACATATGATTTAAA
AATTTGTTTTTACGAGCATCAGAATCCAATTTCGATTTAATTGGAAATTAATTCGGAAAAGCATA
AGAAAAACGATATTCGAAGCTTTAAAAACCCTTCAATCTTTTTGGCGATGATTTATATACTTTTT
ATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTTGGCCGA
AATCGTGTGCTAACATCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCCCCGACTCAGTTTTGAA
TGATTTTTGGCGCCAAGACTCCTTGGAATAACTATATTCATCTACCCAAATCTCAGGCACATAAG
ATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATTTAATAGGAAATTAATTCGGAA
AAGCATAGGAAAAACGATATTCGAAGCTTTAAAAACCTTCAATCTTTTTGGCGATGATTTATATA
CTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATCTT
GGCCGAAATTGTGTGCACAGTTTTCGGCTAAAAATGCGTTTCAGGGCCCCAGCTCAGTTTTGAAT
GATTTTTTGC
Found at i:20614 original size:210 final size:210
Alignment explanation
Indices: 20238--20661 Score: 654
Period size: 210 Copynumber: 2.0 Consensus size: 210
20228 CATTCGGGTC
* * * *
20238 AATTTTTGCAAAATCTTGGCCGAAATCGTGTGCTTACATCACAGTTTTCGGCTAAAAATGCGTTC
1 AATTTTGGCAAAATCTTGGCCGAAATCGTATGCTAACATCACAGTTTTCGGCTAAAAATGCGTTA
* * * * *
20303 CGGTGCCCCGACTCAGTTTTGAATGATTTTTGGCGCCAAGACACCTTGAAATATCTATATTCATC
66 CGGGGCCCCGACTCAGTTTTGAATGAGTTTTGGCACCAAGACACCTTAAAATAACTATATTCATC
* *
20368 CAACCAAATCTCAGGCACATAAGATTTAATGATTTGTTTTTACGAGCATTAGAATCCAGTTTCGA
131 CAACCAAATCTCAGCCACATAAGATTTAATGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGA
20433 TTTAATA-GGAAATT
196 TTTAATATGGAAATT
20447 AATTTTGGCAAAATCTTGGCCGAAATCGTATGCTAACCATCACAGTTTTCGGCTAAAAATGCGTT
1 AATTTTGGCAAAATCTTGGCCGAAATCGTATGCTAA-CATCACAGTTTTCGGCTAAAAATGCGTT
** * *
20512 ACGGGGCCCCGGTTCAGTTTTGTATGAGTTTTGGCACCAAGACTCCTTAAAATAACTATATTCAT
65 ACGGGGCCCCGACTCAGTTTTGAATGAGTTTTGGCACCAAGACACCTTAAAATAACTATATTCAT
* * *
20577 CTACCCAAATCTCAGCCACATAAGATTT-ATAGATTTGTTTTTACGAGCGTCAGAATCCAGTTTC
130 CCAACCAAATCTCAGCCACATAAGATTTAAT-GATTTGTTTTTACGAGCATCAGAATCCAGTTTC
20641 GATTTAATATGGAAATT
194 GATTTAATATGGAAATT
20658 AATT
1 AATT
20662 CGGAAAAGCA
Statistics
Matches: 194, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
209 35 0.18
210 148 0.76
211 11 0.06
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (210 bp):
AATTTTGGCAAAATCTTGGCCGAAATCGTATGCTAACATCACAGTTTTCGGCTAAAAATGCGTTA
CGGGGCCCCGACTCAGTTTTGAATGAGTTTTGGCACCAAGACACCTTAAAATAACTATATTCATC
CAACCAAATCTCAGCCACATAAGATTTAATGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGA
TTTAATATGGAAATT
Found at i:21119 original size:333 final size:334
Alignment explanation
Indices: 20447--21824 Score: 2074
Period size: 333 Copynumber: 4.1 Consensus size: 334
20437 ATAGGAAATT
* *
20447 AATTTTGGCAAAATCTTGGCCGAAATCGTATGCTAACCATCACAGTTTTCGGCTAAAAATGCGTT
1 AATTTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAATGCGTT
* **
20512 ACGGGGCCCCGGTTCAGTTTTGTATGAGTTTTGGCACCAAGACTCCTTAAAATAACTATATTCAT
66 CCGGGGCCCCGGTTCAGTTTTGTATGAGTTTTGGCACCAAGACTCCTTGGAATAACTATATTCAT
* *
20577 CTACCCAAATCTCAGCCACATAAGATTTATAGATTTGTTTTTACGAGCGTCAGAATCCAGTTTCG
131 CTACCCAAATCTCAGCCACATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCG
* *
20642 ATTTAATATGGAAATTAATTCGGAAAAGCATAGGAAAAATGATTTTCGAAGCTTTAAAAACCCTT
196 ATTTAATATGGAAATTAATTCGGAAAAGCATAGGAAAAATTATATTCGAAGCTTTAAAAACCCTT
* *
20707 CAATCTTTTTGGCGATGATTTATATACTTTTTACGT-GTATTTTGGCCAAAAATTGAGGAAAAAT
261 CAATCTTTTTGGCGATGATTTATATACTTTTTA-TTAGTATTTTGGCCAAAATTTGAGGAAAAAT
20771 CATTCGGGTC
325 CATTCGGGTC
* * * * * *
20781 AATTTTTGCAAAATCTTGGCCGAAATCATGTGTTAACTATCATAATTTTCGGCTAAAAACGCGTT
1 AATTTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAATGCGTT
** * * * * * *
20846 CTAGGGCCCCGGTTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTTGAATATCAATATTTAT
66 CCGGGGCCCCGGTTCAGTTTTGTATGAGTTTTGGCACCAAGACTCCTTGGAATAACTATATTCAT
* * ** * * *
20911 CTACCAAAATCTCATCCACATTTGATTTAAAAATTTGTTTTTACGACCATCAGAATCCAATTTCG
131 CTACCCAAATCTCAGCCACATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCG
20976 ATTTAAT-TGGAAATTAATTCGGAAAAGCATAGGAAAAATTATATTCGAAGCTTTAAAAACCCTT
196 ATTTAATATGGAAATTAATTCGGAAAAGCATAGGAAAAATTATATTCGAAGCTTTAAAAACCCTT
*
21040 CAATCTTTTTGGCGTTGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATC
261 CAATCTTTTTGGCGATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATC
21105 ATTCGGGTC
326 ATTCGGGTC
*
21114 AATTTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACCATCATAGTTTTCGGCTAAAAATGCGTT
1 AATTTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAATGCGTT
* *
21179 CCGGGGCCCCGGTTCACTTTTGTATGATTTTTGGCACCAAGACTCCTTGGAATAACTATATTCAT
66 CCGGGGCCCCGGTTCAGTTTTGTATGAGTTTTGGCACCAAGACTCCTTGGAATAACTATATTCAT
* *
21244 CTACCCAAATCTCAGCCACATAAGATTTATAGATTTGTTTTTACGAGCATCGGAATCCAGTTTCG
131 CTACCCAAATCTCAGCCACATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCG
* *
21309 ATTTAATAT-GAAATTAATTCGGAAAAGCATAGGAAAAACGT-CATTCGAAGCTTTAAAAACCCT
196 ATTTAATATGGAAATTAATTCGGAAAAGCATAGGAAAAA-TTATATTCGAAGCTTTAAAAACCCT
* *
21372 TCAATATTTTTGGCGTTGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAAT
260 TCAATCTTTTTGGCGATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAAT
*
21437 CATTCCGGTC
325 CATTCGGGTC
* *
21447 AATTTTTGCAAAATCTTCGCCGAAATCGTTTGCTAACCATCACAGTTTTCGGCTAAAAATGCGTT
1 AATTTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAATGCGTT
* * * * * *
21512 CCCGGGCCCCGGCTCAGTTTTGAATGAGTTTTGGCGCCAAGAATCCTTGGAATATCTATATTCAT
66 CCGGGGCCCCGGTTCAGTTTTGTATGAGTTTTGGCACCAAGACTCCTTGGAATAACTATATTCAT
* * * *
21577 CTACCCAAATCTCATCCACATATGATTTAAAGATTTGGTTTAACGAGCATCAGAATCCAGTTTCG
131 CTACCCAAATCTCAGCCACATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCG
* * ** * *
21642 ATTTAATA-GGAAATTAATTCGGAAAAGCTTTGGAAAAACAATATTCGAAGC-GTAAAAA-GCTT
196 ATTTAATATGGAAATTAATTCGGAAAAGCATAGGAAAAATTATATTCGAAGCTTTAAAAACCCTT
* * *
21704 CAATTTTTTTGGCGATGATTTATATA-TTGTTTATGAGTATTTTGGCCGAAAA-TTGAGTAAAAA
261 CAATCTTTTTGGCGATGATTTATATACTT-TTTATTAGTATTTTGGCC-AAAATTTGAGGAAAAA
21767 TCATTCGGGTC
324 TCATTCGGGTC
21778 AATTTTTGCAAAATCTTGGCCGAAATCG-GTGCTAACCATCACAGTTT
1 AATTTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACCATCACAGTTT
Statistics
Matches: 948, Mismatches: 89, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
330 20 0.02
331 91 0.10
332 11 0.01
333 649 0.68
334 177 0.19
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (334 bp):
AATTTTTGCAAAATCTTGGCCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAATGCGTT
CCGGGGCCCCGGTTCAGTTTTGTATGAGTTTTGGCACCAAGACTCCTTGGAATAACTATATTCAT
CTACCCAAATCTCAGCCACATAAGATTTAAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCG
ATTTAATATGGAAATTAATTCGGAAAAGCATAGGAAAAATTATATTCGAAGCTTTAAAAACCCTT
CAATCTTTTTGGCGATGATTTATATACTTTTTATTAGTATTTTGGCCAAAATTTGAGGAAAAATC
ATTCGGGTC
Done.