Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016326.1 Corchorus olitorius cultivar O-4 contig16359, 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: 163870
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1079 original size:333 final size:342
Alignment explanation
Indices: 55--1258 Score: 1263
Period size: 333 Copynumber: 3.6 Consensus size: 342
45 GTGACCAAAT
**
55 CTCAGCAACATTGGATTTAATCA-TTTGTTTTTAAGAGCATCAGAAACCGGTTTCGATTTAATCA
1 CTCAGCAACATTGGATTTAAGAATTTTG-TTTTAAGAGCATCAGAAACCGGTTTCGATTTAATCA
* * * *
119 GAAATTAAT-TC-GAAA-AAATA-GG-TAAAT-CGATATA-ATA-AG-GGTCAAAAGTCCTTCAA
65 GAAATTAATATCAGAAATAAATATGGATAAATACGAAAAACATACAGACGTCAAAAGCCCTTCAA
*
175 TCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTGGGGCCAAAAATTGAGG-AAAAATTT
130 TCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAAATTT
*
239 TTCGGGTCATTTTTTGTAAAATTTTAGCCAAAATCGTGTACTAACCATCATAGTTTTTGGCTAAA
195 TTCGGGTCATTTTTTGTAAAAATTTAGCCAAAATCGTGTACTAACCATCATAGTTTTTGGCTAAA
* *
304 AACGCGTTCCGGGGTCCTGGCTTAGTTTTGCATGATTTTTGGCGCTGAGACTCCTTGAAATATTT
260 AACGCGTTTCGGGGTCCTGGCTTAGTTTTGCATGATTTTTGGCGCTGAGACTCCTTGAAATATCT
*
369 ATACTCATCTAATAAGAG
325 ATACTCATCTAATAAAAG
* * *
387 CTCAGCCAA-ATTGGATTTAAGAATTTTGTTTTAACAGCATC-TAAACCATGTTTCGATTTAATC
1 CTCAG-CAACATTGGATTTAAGAATTTTGTTTTAAGAGCATCAGAAACC-GGTTTCGATTTAATC
* * * *
450 A-AAATTTAATATCAGAAATTAATATGGAATAAATAGGAAAAACGATACTAGAAACGTGAAATGC
64 AGAAA-TTAATATCAGAAATAAATATGG-ATAAATACGAAAAAC-ATAC-AG--ACGTCAAAAGC
* * * * * * * * * **
514 CCTTCAACCTATTAGGTGCTGAATTATATAT-TTTTTATTAGTATTTTAGCTAAAAATTGA--TT
123 CCTTCAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTGTGGCCAAAAATTGAGGAA
* * ** * ** * * **
576 AAAA-GTCTCGGGTCAACTTTTG-CAAAATTGTAGCCGTAATTGTGTACTAACCGTCACGGGTTT
188 AAAATTTTTCGGGTCATTTTTTGTAAAAATT-TAGCCAAAATCGTGTACTAACCATCA-TAGTTT
* * * * ** *
639 TTGGCTAAAAACGCGGTAT-AGGG-CCTCGGCTCAGTTTTGCAAGATTTTTTACG-TCAGGACTC
251 TTGGCTAAAAACGC-GTTTCGGGGTCCT-GGCTTAGTTTTGCATGATTTTTGGCGCTGA-GACTC
* * * * * ** *
701 ATTGAAACATCTATATTTATCTGACCAAAT
313 CTTGAAATATCTATACTCATCTAATAAAAG
** **
731 CTTTGCAACATTGGATTTAATCA-TTTGTTTTTAAGAGCATCAGAAACCGGTTTCGATTTAATCA
1 CTCAGCAACATTGGATTTAAGAATTTTG-TTTTAAGAGCATCAGAAACCGGTTTCGATTTAATCA
* * * *
795 GAAATTAAT-TC-GAAA-AAATA-GG-TAAAT-CGATATA-ATA-AG-GGTCAAAAGTCCTTCAA
65 GAAATTAATATCAGAAATAAATATGGATAAATACGAAAAACATACAGACGTCAAAAGCCCTTCAA
851 TCTTTTTGGCGTTGAATTATATATATTTTT-TGAGTATTGTGGCCAAAAATTGAGGAAAAAATTT
130 TCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAAATTT
915 TTCGGGTCATTTTTTTGTAAAAATTTAGCCAAAATCGTGTACTAACCATCATAGTTTTTGGCTAA
195 TTCGGGTCA-TTTTTTGTAAAAATTTAGCCAAAATCGTGTACTAACCATCATAGTTTTTGGCTAA
980 AAACGCGTTTCGGGGTCCTGGCTTAGTTTTGCATGATTTTTGGCGCTGAGACTCCTTGAAATATC
259 AAACGCGTTTCGGGGTCCTGGCTTAGTTTTGCATGATTTTTGGCGCTGAGACTCCTTGAAATATC
1045 TATACTCATCTAATAAAAG
324 TATACTCATCTAATAAAAG
* * ** *
1064 CTCAGCCAA-ATTGGATTTAAGAATTTTGTTTTAATAGCATCTA-AATCATGTTTTGATTTAATC
1 CTCAG-CAACATTGGATTTAAGAATTTTGTTTTAAGAGCATC-AGAAACCGGTTTCGATTTAATC
* * * * *
1127 AAAAATTAATATCAGAAATTAATATGGAATAAATAGGAAAAACGATACTAGAAACGTGAAATGCC
64 AGAAATTAATATCAGAAATAAATATGG-ATAAATACGAAAAAC-ATAC-AG--ACGTCAAAAGCC
* * * *
1192 CTTCACTCTTTTTGACGTTGAATTTTATATATTTTTATGAGTATTGTGGCGAAAAATTGAGGAAA
124 CTTCAATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAA
1257 AA
189 AA
1259 TCTTTCAGGT
Statistics
Matches: 689, Mismatches: 128, Indels: 94
0.76 0.14 0.10
Matches are distributed among these distances:
330 51 0.07
331 13 0.02
332 56 0.08
333 142 0.21
334 46 0.07
335 17 0.02
336 6 0.01
337 6 0.01
338 10 0.01
339 9 0.01
340 6 0.01
341 7 0.01
342 12 0.02
343 52 0.08
344 121 0.18
345 34 0.05
346 32 0.05
347 40 0.06
348 29 0.04
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (342 bp):
CTCAGCAACATTGGATTTAAGAATTTTGTTTTAAGAGCATCAGAAACCGGTTTCGATTTAATCAG
AAATTAATATCAGAAATAAATATGGATAAATACGAAAAACATACAGACGTCAAAAGCCCTTCAAT
CTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAAAAATTTT
TCGGGTCATTTTTTGTAAAAATTTAGCCAAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAA
ACGCGTTTCGGGGTCCTGGCTTAGTTTTGCATGATTTTTGGCGCTGAGACTCCTTGAAATATCTA
TACTCATCTAATAAAAG
Found at i:1691 original size:331 final size:330
Alignment explanation
Indices: 5--4527 Score: 3301
Period size: 331 Copynumber: 13.7 Consensus size: 330
1 GCAA
* * * * * * * * *
5 GATTTTTGACGTCAAGACTCATTGAAACATCTATATTTATGTGACCAAATCTCAGCAACATTGGA
1 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
** * * ** *
70 TTTAATCATTTGTTTTTAAGAGCATC-AGAAACCGGTTTCGATTTAATCAGAAATTAATTCGAAA
66 TTTAAGGATTTGTTTTTACGAGCATCTA-AATCATGTTTCGATTTAATCAGAAATTAATTCAAAA
* * * * * * * *
134 AAATAGGTAAATCGATATAATAAGGGTCAAAAGTCCTTCAATCTTTTT-GGCGTTGAATTATATA
130 AAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGGCATTGAATTATATA
** * *
198 TATTTTTATGAGTATTGGGGCCAAAAATTGAGGAAAAAT-TTTTCGGGTCATTTTTTGTAAAATT
195 T-TTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTT-GGGTCAATTTTTGCAAAATT
* ** * * * *
262 TTAGCCAAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAACGCGTTCCGGGGTCCTGGCTT
258 TTAGCCGAAATCGTGTACTAACCATCACGGTTTTT-GCTAAAAACGCGTT-CTGGGCCCCGGCTC
327 AGTTTTGCAT
321 AGTTTTGCAT
* * * * * *
337 GATTTTTGGCGCTGAGACTCCTTGAAATATTTATACTCATCTAA-TAAGAGCTCAGCCAAATTGG
1 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAA-ATCTCAGCCACATTGG
* * *
401 ATTTAAGAATTTTGTTTTAAC-AGCATCTAAACCATGTTTCGATTTAATCA-AAATTTAATATCA
65 ATTTAAGGA-TTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAA-TTAAT-TC-
* * * * * *
464 GAAATTAATATGGAATAAATAGGAAAAACGATACTAGAAACGTGAAATGCCCTTCAACCTATTAG
126 -------A-A---AA-AAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
* * * ** * * *
529 GTGC--TGAATTATATATTTTTTATTAGTATTTTAGCTAAAAATTGA-TTAAAA-GTCTCGGGTC
179 G-GCATTGAATTATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTTGGGTC
* * * * * *
590 AACTTTTGCAAAATTGTAGCCGTAATTGTGTACTAACCGTCACGGGTTTTTGGCTAAAAACGCGG
243 AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GGTTTTT-GCTAAAAACGCGT
* * *
655 TATAGGGCCTCGGCTCAGTTTTGCAA
306 TCT-GGGCCCCGGCTCAGTTTTGCAT
** * * * * * ** *
681 GATTTTTTACGTC-AGGACTCATTGAAACATCTATATTTATCTGACCAAATCTTTGCAACATTGG
1 GATTTTTGGCGCCGA-GACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGG
** * * ** *
745 ATTTAATCATTTGTTTTTAAGAGCATC-AGAAACCGGTTTCGATTTAATCAGAAATTAATTCGAA
65 ATTTAAGGATTTGTTTTTACGAGCATCTA-AATCATGTTTCGATTTAATCAGAAATTAATTCAAA
* * * * * * * *
809 AAAATAGGTAAATCGATATAATAAGGGTCAAAAGTCCTTCAATCTTTTT-GGCGTTGAATTATAT
129 AAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGGCATTGAATTATAT
* * *
873 ATATTTTT-TGAGTATTGTGGCCAAAAATTGAGGAAAAA-ATTTTTCGGGTCATTTTTTTGTAAA
194 AT-TTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATA-TTTT-GGGTCA-ATTTTTGCAAA
* * ** * * *
936 AATTTAGCCAAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCTGG
255 ATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT-GCTAAAAACGCG-TTCTGGGCCCCGG
*
1001 CTTAGTTTTGCAT
318 CTCAGTTTTGCAT
* * ** * *
1014 GATTTTTGGCGCTGAGACTCCTTGAAATATCTATACTCATCTAATAAAAGCTCAGCCAAATTGGA
1 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
* ** * *
1079 TTTAAGAATTT-TGTTTTAATAGCATCTAAATCATGTTTTGATTTAATCAAAAATTAATATCAGA
66 TTTAAGGATTTGT-TTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAAT-TC---
* * * * *
1143 AATTAATATGGAATAAATAGGAAAAACGATACTAGAAACGTGAAATGCCCTTCACTCTTTTT-GA
126 -----A-A---AA-AAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGG
* * * * * ** *
1207 CGTTGAATTTTATATATTTTTATGAGTATTGTGGCGAAAAATTGAGGAAAAATCTTTCAGGTAAA
181 CATTGAATTATATAT-TTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTTGGGTCAA
* * *
1272 TTTATGCAAAATTTT---C---A-CG-G---------T-----TTTTGGCTAAAAACCCGTTCTA
245 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGCTAAAAACGCGTTCT-
* **
1315 GTGCCCCTACTCAGTTTTGCAT
309 GGGCCCCGGCTCAGTTTTGCAT
* * * * *
1337 GATTTTTTGCGCCGAGACTCCTTGAAATATATATATTCATCTAATCAAATCTCTGTCACATTGGA
1 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
* * * * *
1402 TTTAAGGATTTGTTTTTACGTGTATGTAAATCATGATTCGATTGAAT-ATGAAATTAATTCTAAA
66 TTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCA-GAAATTAATTC-AAA
* * * * * * *
1466 AAAATAGG-AAAACGATATTAGACGCATGAAAAGGCTTTCTATATTTTTGGGCATTAAATTATAT
129 AAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGGCATTGAATTATAT
* * * * *
1530 A-TTTTTAAGAGTATTTTGGCTAAAAATTGAGGAAAAAAATTTTGGGTCAAATTTTGCAAATTTT
194 ATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAATTT
* ** * *
1594 TAACCGAAGCCGTGTACTAACCATCACGGTTTTTGCCTAAAAACTCGTTCTAAGGCCCCGGCTCA
259 TAGCCGAAATCGTGTACTAACCATCACGGTTTTTG-CTAAAAACGCGTTCT-GGGCCCCGGCTCA
*
1659 GATTTGCAT
322 GTTTTGCAT
* * * * *
1668 GATTTTCT-GCGCCGAGTCTCCTTGAAATATGTATATTCATCTAATCAAATCTTAGCCACATTGT
1 GATTTT-TGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGG
* * * ** **
1732 ATTTAAGAATTTGTTTTTACGAGCATTTGAAA-AATGTTTCGATTTAATTTGAAATTAATTC-GG
65 ATTTAAGGATTTGTTTTTACGAGCATCT-AAATCATGTTTCGATTTAATCAGAAATTAATTCAAA
* ** *
1795 AAAATCAGGAAAAACGATATTTGAAGCACGAAAAGCCCTTTAATCTTTTT-GG-AGTTGAATTAT
129 AAAAT-AGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGGCA-TTGAATTAT
* * * * *
1858 ATATTTTTTCTGAGTGTTTTGGCCAAAAATTGAGGCAAAATATTTTGGATCATTTTTTTGCAAAA
192 ATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTTGGGTCA-ATTTTTGCAAAA
* * * *
1923 TTTTAGCCGAAATC--GTA-T-ACCATTACGGTTTTTTGCTAAAAACGCGTT-TCGCGACCCTGT
256 TTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTGCTAAAAACGCGTTCT-G-GGCCCCGG
1983 CTCAGTTTTGCAT
318 CTCAGTTTTGCAT
* * * * *
1996 TATTTCTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAAACTCAGCCAAATTGTA
1 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
*
2061 TTTAAGGATTTG-TTTTACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATT-ATGTCAAAA
66 TTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAAT-TC-AAA
* *
2124 AAGAATAGGAAAAACGATATTAGAAGCGTGAAAA-CTCCTTCAACCTTCTTGGTGC--TG-ATTA
129 AA-AATAGGAAAAACGATATTAGAAGCGTGAAAAGC-CCTTCAATCTTTTTGG-GCATTGAATT-
* * * ** * * * *
2185 ATATATTTTTTATTAGTATTTTAGCTAAAAATTGA-TTAAAA-GTCTCGGGTCAACTTTTGCAAA
190 ATATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAA
* * * * * * *
2248 ATTGTAGCCGTAATTGTGTACTAACCATCACGGGTTTTTGGCTAAAAACGCGGTATGGGGCCTCT
255 ATTTTAGCCGAAATCGTGTACTAACCATCAC-GGTTTTT-GCTAAAAACGCGTTCT-GGGCCCCG
*
2313 GCTCAGTTTTGCAA
317 GCTCAGTTTTGCAT
* * * * * * * *
2327 GATTTTTGACGTCAAGACTCATTGAAACATCTATATTTATCTGACCAAATCTCAGCAACATTGGA
1 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
** * * * *
2392 TTTAATCATTTGTTTTTAAGAGCATC-AGAAAC-CGATTTCGATTTAATCAGAAATTAATTCGAA
66 TTTAAGGATTTGTTTTTACGAGCATCTA-AATCATG-TTTCGATTTAATCAGAAATTAATTCAAA
* * * * * * * *
2455 AAAATAGGTAAATCGATATAATAAGGGTCAAAAGTCCTTCAATCTTTTT-GGCGTTGAATTATAT
129 AAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGGCATTGAATTATAT
* * * * * *
2519 ATTTTTTATGAGTATTGTGGCCAAAAATTGGGGAAAACTTTTTTGGGTCATTTTTTGTAAAATTT
194 ATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAATTT
* ** * * * *
2584 TAGCCAAAATCGTGTACTAACCATCATAGTTTTTGGCT-AAAA-GCGTTCCGGGGTCCTGGCTTA
259 TAGCCGAAATCGTGTACTAACCATCACGGTTTTT-GCTAAAAACGCGTT-CTGGGCCCCGGCTCA
2647 GTTTTGCAT
322 GTTTTGCAT
* * * * * * *
2656 TATTTTTGGCGCTGAGACTCCTTGAAATATCAATACTCATCTAA-TAACAGCTCAGCCAAATTGG
1 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAA-ATCTCAGCCACATTGG
* * * * * *
2720 ATTTGAA-AATTTTGATTTAAC-AACATCTAAATCATGTTTCGATTTAATCAAAAATTAATATTG
65 ATTT-AAGGA-TTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATT-A-ATTC
* * * * * * * * * * *
2783 GAATAAATAGGAAAAACGAAACTAGAAACGTGAAATGCTCTTCACTCTTTTT-GACGTTGAATTT
126 AAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGGCATTGAATTA
* * * * ** *
2847 TATATATTTTTATGAGTATTGTGGCGAAAAATTGGGGAAAAATCTTTCAGGTAAATTTTTGC---
191 TATAT-TTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAA
* * * **
2909 -----A----AAA---T-T--T-----TCACGGTTTTTGACTAAAAACTCATTCTAGTGCCCCAT
255 ATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG-CTAAAAACGCGTTCT-GGGCCCCGG
*
2954 CTCAGATTTGCAT
318 CTCAGTTTTGCAT
* * * **
2967 GATTTTCT-GCGCCGAGTCTCCTTGAAATATGTATATTCATCTAATCAAATCTCAGCCACATTTT
1 GATTTT-TGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGG
* * * ** **
3031 ATTTAAGAATTTGTTCTTACGAGCATCTGAAA-AATGTTTCGATTTAATTTGAAATTAATTCGGA
65 ATTTAAGGATTTGTTTTTACGAGCATCT-AAATCATGTTTCGATTTAATCAGAAATTAATTCAAA
* * *
3095 AAATTAGGAAAAACGATATTAGAAGCGCGAAAAGCCCTTTAATCTTTTT-GG-AGTTGAATTATA
129 AAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGGCA-TTGAATTATA
* * *
3158 TATTTTTTCA-GAGTGTTTTGGCCAAAAATTGAGGCAAAATATTTTGGGTCATTTTTTTGCAAAA
193 TATTTTTT-ATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTTGGGTCA-ATTTTTGCAAAA
* * * * *
3222 TTTTAGCCGAAATCGTATACTAACCATTACGGTTTTTTGCTAAAAACGCGTT-TCGCGACCCTGT
256 TTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTGCTAAAAACGCGTTCT-G-GGCCCCGG
3286 CTCAGTTTTGCAT
318 CTCAGTTTTGCAT
* * * * * * *
3299 TATTTCTGGCGCCGAGACTTCTTGAAAAATCTATATTCATCTAACCAAAACTCAGCCAAATTGTA
1 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
* *
3364 TTTAAGGATTTG-TTTTACGAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAAGTCAGAAA
66 TTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCA-AAA
* * * *
3428 AGAAAAGGAAAAACGATATTAGAAGCGTGAAAA-CACCTTCAACCTTCTTGGTG--TTGATTTAT
130 A-AATAGGAAAAACGATATTAGAAGCGTGAAAAGC-CCTTCAATCTTTTTGG-GCATTGAATTAT
* ** * ** * * *
3490 ATATTTTTTATTAGTATTTTAACTTAAAAA-TGA-TTAAAA-CTCTCGGGTCAATTTTTGCAAAA
192 ATATTTTTTATGAGTATTTTGGC-CAAAAATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAA
* * * * *
3552 TTGTAGCC-ATAATTGTGTACTAACCATCACGGGTTTTTGGCTAAAAACGCGGTATGGGGCCTCG
256 TTTTAGCCGA-AATCGTGTACTAACCATCAC-GGTTTTT-GCTAAAAACGCGTTCT-GGGCCCCG
*
3616 GCTCAGTTTTGCAA
317 GCTCAGTTTTGCAT
* * * * * * * * * * *
3630 AACTTTTGACGTCAAGACTCATTGAAACATCTATATTTATCTGACCAATTCTCAGCAACATTGGA
1 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
** ** * * *
3695 TTTAATCATTTGTTTTTACGAGTTTCTAAGTCTTGTTTCGATTTAATCAGAAATTAATTTGGAAA
66 TTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAA-TT-CAAA
* * * *
3760 TAAAATAGGAAAAACGATATTAGAAGCGCGAAAAAGACTTTCAATTTTTTTGGTG--TTGAATTA
129 -AAAATAGGAAAAACGATATTAGAAGCGTG-AAAAGCCCTTCAATCTTTTTGG-GCATTGAATTA
* * * *** * * * * *
3823 TCTATTTTTTATGATTATTTTCGCTTGAAA-TAAAGAAAAATCTTTCGGGTCAATTTTTACAAAA
191 TATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAA
* * * * **
3887 TTTTAGCCGAAATCTTATACTAACCATCACGGTTTTCAGCTAAAAACGCGTTCCGCGG-CCTAGC
256 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT-TGCTAAAAACGCGTTCTG-GGCCCCGGC
*
3951 TCAGTTTGGCAT
319 TCAGTTTTGCAT
* * * * * * * *
3963 GATTTTTGGTGTCAAAACTCCTTGAAATATTTATATTCATCTAACCAAATCTCAGACGCATTAGA
1 GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
* * * * *
4028 TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTCTCAATTTAATTAGAAATTAATTCGGGAA
66 TTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTC---AA
* *
4093 AAAAA-A-GAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATGGC---GAATTA
128 AAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG--GGCATTGAATTA
* * **
4153 TATATTTTTTATGAGTATTCTAGCCAAAAATTGA-G-AAAATATCTTTCGACTCAATTTTTGCAA
191 TATATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATAT-TTT-GGGTCAATTTTTGCAA
* * * * *
4216 AATTGTAGCCGAAATCGTGTACTAAACACCACGGTTTTTTTGCTAAAAACGCGTTTCAGGGCCAC
254 AATTTTAGCCGAAATCGTGTACTAACCATCACGG--TTTTTGCTAAAAACGCG-TTCTGGGCCCC
*
4281 GGCTCTGTTTTGCAT
316 GGCTCAGTTTTGCAT
* * * *
4296 GATTTTTGGCGCCGAGACTCCTT-AAATTATCTTTATTCATCTAATCAAATCTCAGCTACATTGT
1 GATTTTTGGCGCCGAGACTCCTTGAAA-TATCTATATTCATCTAACCAAATCTCAGCCACATTGG
* * *** * * * *
4360 ATTGAAGGATTTATTTTTATTTGCATCTGAATCTTGTTTCGATTTAATTACAAATTAATTCAGAA
65 ATTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCA-AA
** * * * * * * *
4425 AAAATATTAAAAGCGATATTAAAAGTGTGAAAAG-TCTTCCAAT-TTTTTTGGCGTTGAAGTATA
129 AAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTT-CAATCTTTTTGGGCATTGAATTATA
* * *
4488 TATATTTTATGAGTATTTTTGCCAAAAAATGAGGAAAAAT
193 TATTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAAT
4528 CTTTCGGATT
Statistics
Matches: 3282, Mismatches: 696, Indels: 423
0.75 0.16 0.10
Matches are distributed among these distances:
308 91 0.03
309 106 0.03
310 35 0.01
311 101 0.03
312 6 0.00
314 2 0.00
315 3 0.00
316 2 0.00
317 2 0.00
320 3 0.00
321 3 0.00
322 6 0.00
323 127 0.04
324 7 0.00
325 2 0.00
326 25 0.01
327 46 0.01
328 121 0.04
329 192 0.06
330 288 0.09
331 604 0.18
332 414 0.13
333 554 0.17
334 120 0.04
335 51 0.02
336 1 0.00
338 1 0.00
339 2 0.00
340 1 0.00
342 1 0.00
343 54 0.02
344 122 0.04
345 31 0.01
346 61 0.02
347 63 0.02
348 34 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (330 bp):
GATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
TTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCAAAAA
AATAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGGCATTGAATTATATAT
TTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAATTTTA
GCCGAAATCGTGTACTAACCATCACGGTTTTTGCTAAAAACGCGTTCTGGGCCCCGGCTCAGTTT
TGCAT
Found at i:3776 original size:333 final size:328
Alignment explanation
Indices: 2987--4544 Score: 1467
Period size: 333 Copynumber: 4.7 Consensus size: 328
2977 GCCGAGTCTC
* * * * ** * *
2987 CTTGAAATATGTATATTCATCTAATCAAATCTCAGCCACATTTTATTTAAGAATTTGTTCTTACG
1 CTTGAAAAATCTATATTCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACG
*** ** **
3052 AGCATCTGAAAAATGTTTCGATTTAATTTGAAATTAATTCGG-AAAATTAGGAAAAACGATATTA
66 AGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTA
* * * *
3116 GAAGCGCGAAAAGCCCTTTAATCTTTTTGGAGTTGAATTATATATTTTTTCA-GAGTGTTTTGGC
131 GAAGCGCGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTATATATTTTTT-ATGAGTATTTTAGC
* * * *
3180 CAAAAATTGAGGCAAAATATTTTGGGTCATTTTTTTGCAAAATTTTAGCCGAAATCGTATACTAA
195 CAAAAATTGA-G-AAAATCTTTCGGGTCA-ATTTTTGCAAAATTGTAGCCGAAATCGTATACTAA
* * * *
3245 CCATTACGGTTTTTTGCTAAAAACGCGTTTCGCGACC-CTGTCTCAGTTTTGCATTATTTCTGGC
257 CCATCACGGTTTTTTGCTAAAAACGCGTTTCGCGGCCTC-GGCTCAGTTTTGCATAATTT-TGGC
* *
3309 GCCGAGACTT
320 GTCAAGAC-T
* *
3319 CTTGAAAAATCTATATTCATCTAACCAAAACTCAGCCAA-ATTGTATTTAAGGATTTG-TTTTAC
1 CTTGAAAAATCTATATTCATCTAACCAAATCTCAG-CAACATTGGATTTAAGGATTTGTTTTTAC
* * *
3382 GAGCATCTGAATCATGTTTCGATTTAATCAGAAATTAAGTCAGAAAAGAAAAGGAAAAACGATAT
65 GAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAATTCGGAAAA-AAAAGGAAAAACGATAT
* * * * *
3447 TAGAAGCGTGAAAA-CACCTTCAACCTTCTTGGTGTTGATTTATATATTTTTTATTAGTATTTTA
129 TAGAAGCGCGAAAAGC-CCTTCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTTTA
* * * * * *
3511 ACTTAAAAA-TGATTAAAA-CTCTCGGGTCAATTTTTGCAAAATTGTAGCC-ATAATTGTGTACT
193 GC-CAAAAATTGA-GAAAATCTTTCGGGTCAATTTTTGCAAAATTGTAGCCGA-AATCGTATACT
* * * *
3573 AACCATCACGGGTTTTTGGCTAAAAACGCGGTAT-GGGGCCTCGGCTCAGTTTTGCAAAACTTTT
255 AACCATCAC-GGTTTTTTGCTAAAAACGC-GTTTCGCGGCCTCGGCTCAGTTTTGCATAA-TTTT
*
3637 GACGTCAAGACT
317 GGCGTCAAGACT
* * * * **
3649 CATTGAAACATCTATATTTATCTGACCAATTCTCAGCAACATTGGATTTAATCATTTGTTTTTAC
1 C-TTGAAAAATCTATATTCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTAC
** *
3714 GAGTTTCT-AAGTCTTGTTTCGATTTAATCAGAAATTAATTTGGAAATAAAATAGGAAAAACGAT
65 GAGCATCTGAA-TCTTGTTTCGATTTAATCAGAAATTAATTCGGAAA-AAAA-AGGAAAAACGAT
* * * * *
3778 ATTAGAAGCGCGAAAAAGACTTTCAATTTTTTTGGTGTTGAATTATCTATTTTTTATGATTATTT
127 ATTAGAAGCGCG-AAAAGCCCTTCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTT
* *** ** * * *
3843 TCGCTTGAAATAAAGAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCTTATACT
191 TAGCCAAAAATTGAG-AAAATCTTTCGGGTCAATTTTTGCAAAATTGTAGCCGAAATCGTATACT
** * * * *
3908 AACCATCACGGTTTTCAGCTAAAAACGCGTTCCGCGGCCT-AGCTCAGTTTGGCATGATTTTTGG
255 AACCATCACGGTTTTTTGCTAAAAACGCGTTTCGCGGCCTCGGCTCAGTTTTGCAT-AATTTTGG
* *
3972 TGTCAAAACT
319 CGTCAAGACT
* * * *
3982 CCTTGAAATATTTATATTCATCTAACCAAATCTCAG-ACGCATTAGATTTAAGGATTTGTTTTTA
1 -CTTGAAAAATCTATATTCATCTAACCAAATCTCAGCA-ACATTGGATTTAAGGATTTGTTTTTA
* * * *
4046 CGAGCATCTGAATCTTGTCTCAATTTAATTAGAAATTAATTCGGGAAAAAAAA-GAAAAACAATA
64 CGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAATTC-GGAAAAAAAAGGAAAAACGATA
** * ** *
4110 TTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATGGCGAATTATATATTTTTTATGAGTATTCTA
128 TTAGAAGCGCGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTTTA
** *
4175 GCCAAAAATTGAGAAAATATCTTTCGACTCAATTTTTGCAAAATTGTAGCCGAAATCGTGTACTA
193 GCCAAAAATTGAG-AAA-ATCTTTCGGGTCAATTTTTGCAAAATTGTAGCCGAAATCGTATACTA
* * * * *
4240 AACACCACGGTTTTTTTGCTAAAAACGCGTTTCAG-GGCCACGGCTCTGTTTTGCATGATTTTTG
256 ACCATCACGG-TTTTTTGCTAAAAACGCGTTTC-GCGGCCTCGGCTCAGTTTTGCAT-AATTTTG
* *
4304 GCGCCGAGACT
318 GCGTCAAGACT
* * * * * * *
4315 CCTT-AAATTATCTTTATTCATCTAATCAAATCTCAGCTACATTGTATTGAAGGATTTATTTTTA
1 -CTTGAAA-AATCTATATTCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTA
*** * * * * ** *
4379 TTTGCATCTGAATCTTGTTTCGATTTAATTACAAATTAATTCAGAAAAAATATTAAAAGCGATAT
64 CGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAAAGGAAAAACGATAT
* * * * * * * * *
4444 TAAAAGTGTGAAAAG-TCTTCCAATTTTTTTGGCGTTGAAGTATATATATTTTATGAGTATTTTT
129 TAGAAGCGCGAAAAGCCCTT-CAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTTTA
* * *
4508 GCCAAAAAATGAGGAAAAATCTTTCGGATTAATTTTT
193 GCCAAAAATTGA-G-AAAATCTTTCGGGTCAATTTTT
4545 ACCATCATGT
Statistics
Matches: 1003, Mismatches: 185, Indels: 75
0.79 0.15 0.06
Matches are distributed among these distances:
329 1 0.00
330 96 0.10
331 209 0.21
332 148 0.15
333 412 0.41
334 91 0.09
335 45 0.04
336 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (328 bp):
CTTGAAAAATCTATATTCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTA
GAAGCGCGAAAAGCCCTTCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTTTAGCC
AAAAATTGAGAAAATCTTTCGGGTCAATTTTTGCAAAATTGTAGCCGAAATCGTATACTAACCAT
CACGGTTTTTTGCTAAAAACGCGTTTCGCGGCCTCGGCTCAGTTTTGCATAATTTTGGCGTCAAG
ACT
Found at i:4848 original size:20 final size:20
Alignment explanation
Indices: 4823--4860 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4813 GCGTAATATG
*
4823 TAACTTAAGATATGTTTTGA
1 TAACTTAAAATATGTTTTGA
4843 TAACTTAAAATATGTTTT
1 TAACTTAAAATATGTTTT
4861 AATCAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (20 bp):
TAACTTAAAATATGTTTTGA
Found at i:6840 original size:30 final size:31
Alignment explanation
Indices: 6804--6864 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
6794 TGGTGGTTAG
6804 CAAGTGCCAAAATGGACAAACTTT-AATGTT
1 CAAGTGCCAAAATGGACAAACTTTGAATGTT
*
6834 CAAGTGCCAAAATGGACAAATTTTGAATGTT
1 CAAGTGCCAAAATGGACAAACTTTGAATGTT
6865 GTTAACAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (31 bp):
CAAGTGCCAAAATGGACAAACTTTGAATGTT
Found at i:9963 original size:1 final size:1
Alignment explanation
Indices: 9957--9985 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
9947 GTAAATATAT
9957 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9986 CATAAAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26258 original size:16 final size:16
Alignment explanation
Indices: 26237--26273 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
26227 GGGTCTATTC
26237 TGGATTAGTAAATCTA
1 TGGATTAGTAAATCTA
26253 TGGATTAGTAAATCTA
1 TGGATTAGTAAATCTA
26269 TGGAT
1 TGGAT
26274 ACCGGATGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (16 bp):
TGGATTAGTAAATCTA
Found at i:26313 original size:13 final size:13
Alignment explanation
Indices: 26295--26337 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
26285 TACCAAAAAA
26295 AATTATCATTAAC
1 AATTATCATTAAC
*
26308 AATTATCATTAAA
1 AATTATCATTAAC
26321 AATTATCATTAAC
1 AATTATCATTAAC
26334 AATT
1 AATT
26338 TCTATAGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTATCATTAAC
Found at i:30862 original size:26 final size:29
Alignment explanation
Indices: 30808--30862 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
30798 TGAGAGAAAA
*
30808 CAAATATATATTATTATATATTTGGAATTC
1 CAAATATATATTATGATATATTT-GAATTC
30838 CAAATA-ATATT-TGATATATTT-AATT
1 CAAATATATATTATGATATATTTGAATT
30863 ATAATTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
28 9 0.38
29 5 0.21
30 6 0.25
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (29 bp):
CAAATATATATTATGATATATTTGAATTC
Found at i:39938 original size:2 final size:2
Alignment explanation
Indices: 39931--39959 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39921 ATGACAACAA
39931 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 A
39960 ATGAGTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53573 original size:84 final size:84
Alignment explanation
Indices: 53469--53636 Score: 282
Period size: 84 Copynumber: 2.0 Consensus size: 84
53459 CATGCTCTAG
*
53469 AGTCACTTGGTTGCTTTGCTTATCTACCTGATCATTCTCCACCTTCTTCTCAGCTTCTTCAGTCA
1 AGTCACTTGGGTGCTTTGCTTATCTACCTGATCATTCTCCACCTTCTTCTCAGCTTCTTCAGTCA
*
53534 CAGAATGAATATCTCGAAC
66 CAGAATGAATATCGCGAAC
* * *
53553 AGTCACTTGGGTGCTTTGCTTATCTACCTGATCTTTCTCCACTTTCTTCTCAGGTTCTTCAGTCA
1 AGTCACTTGGGTGCTTTGCTTATCTACCTGATCATTCTCCACCTTCTTCTCAGCTTCTTCAGTCA
*
53618 CAGGATGAATATCGCGAAC
66 CAGAATGAATATCGCGAAC
53637 TGTATCCACC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.37
Consensus pattern (84 bp):
AGTCACTTGGGTGCTTTGCTTATCTACCTGATCATTCTCCACCTTCTTCTCAGCTTCTTCAGTCA
CAGAATGAATATCGCGAAC
Found at i:54309 original size:156 final size:156
Alignment explanation
Indices: 54024--54338 Score: 576
Period size: 156 Copynumber: 2.0 Consensus size: 156
54014 CATTAGCTGC
54024 CTTGTCATTCAATGCTTCAACTTCATCTTCTTGAAGCCTGGCAGTCACACCAGAAGAAGTATCAG
1 CTTGTCATTCAATGCTTCAACTTCATCTTCTTGAAGCCTGGCAGTCACACCAGAAGAAGTATCAG
54089 CAGACTCCTCAACCTTTTTGTCCTGATAATCAGCAGCTAGTGCATTTTCCCTTAATTCCCCACCA
66 CAGACTCCTCAACCTTTTTGTCCTGATAATCAGCAGCTAGTGCATTTTCCCTTAATTCCCCACCA
54154 TTAACCTCTTGAGGCAAAACCTCCAA
131 TTAACCTCTTGAGGCAAAACCTCCAA
* *
54180 CTTGTCATTCAATGTTTCGACTTCATCTTCTTGAAGCCTGGCAGTCACACCAGAAGAAGTATCAG
1 CTTGTCATTCAATGCTTCAACTTCATCTTCTTGAAGCCTGGCAGTCACACCAGAAGAAGTATCAG
* *
54245 CAGACTCCTCAACCTTTTTGTCTTGATAATCAGCAGCTAGTGCATTTTCCCTTAATTCCTCACCA
66 CAGACTCCTCAACCTTTTTGTCCTGATAATCAGCAGCTAGTGCATTTTCCCTTAATTCCCCACCA
* *
54310 TTAATCTCTTGAGGCAAAATCTCCAA
131 TTAACCTCTTGAGGCAAAACCTCCAA
54336 CTT
1 CTT
54339 AGATTCCATT
Statistics
Matches: 153, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
156 153 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (156 bp):
CTTGTCATTCAATGCTTCAACTTCATCTTCTTGAAGCCTGGCAGTCACACCAGAAGAAGTATCAG
CAGACTCCTCAACCTTTTTGTCCTGATAATCAGCAGCTAGTGCATTTTCCCTTAATTCCCCACCA
TTAACCTCTTGAGGCAAAACCTCCAA
Found at i:62272 original size:7 final size:7
Alignment explanation
Indices: 62260--62290 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
62250 CTTTTCTTTC
62260 CCTTTTT
1 CCTTTTT
62267 CCTTTTT
1 CCTTTTT
62274 CC-TTTT
1 CCTTTTT
62280 CCTTTTT
1 CCTTTTT
62287 CCTT
1 CCTT
62291 CTTGCCCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (7 bp):
CCTTTTT
Found at i:62283 original size:20 final size:19
Alignment explanation
Indices: 62251--62290 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
62241 TACATTGTAC
62251 TTTTCTTTCCCTTTTTCCT
1 TTTTCTTTCCCTTTTTCCT
*
62270 TTTTCCTTTTCCTTTTTCCT
1 TTTT-CTTTCCCTTTTTCCT
62290 T
1 T
62291 CTTGCCCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTCTTTCCCTTTTTCCT
Found at i:67971 original size:15 final size:15
Alignment explanation
Indices: 67951--67981 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
67941 ACAATACATT
67951 AACTATCAAATAGAA
1 AACTATCAAATAGAA
67966 AACTATCAAATAGAA
1 AACTATCAAATAGAA
67981 A
1 A
67982 CAGGTTAATC
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:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:76180 original size:36 final size:36
Alignment explanation
Indices: 76133--76201 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
76123 TTGAGATTAC
76133 AAACGCACAGGAACACCGCACACCGCTACATAACCG
1 AAACGCACAGGAACACCGCACACCGCTACATAACCG
* * *
76169 AAACGCACAGGAAGACTGTACACCGCTACATAA
1 AAACGCACAGGAACACCGCACACCGCTACATAA
76202 TTAACTACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.33, G:0.17, T:0.09
Consensus pattern (36 bp):
AAACGCACAGGAACACCGCACACCGCTACATAACCG
Found at i:76255 original size:13 final size:13
Alignment explanation
Indices: 76237--76266 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
76227 CTATGAGCCA
76237 ACAAACCCCTTCT
1 ACAAACCCCTTCT
76250 ACAAACCCCTTCT
1 ACAAACCCCTTCT
76263 ACAA
1 ACAA
76267 CAAATACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (13 bp):
ACAAACCCCTTCT
Found at i:85019 original size:21 final size:21
Alignment explanation
Indices: 84994--85062 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
84984 TGGTTATGGA
*
84994 GGCGGCTACGGAGGTGGCGGT
1 GGCGGCTACGGAGGAGGCGGT
*
85015 GGCGG-T--GGAAGGCGAGGTGGT
1 GGCGGCTACGG-A-G-GAGGCGGT
85036 GGCGGCTACGGAGGAGGCGGT
1 GGCGGCTACGGAGGAGGCGGT
85057 GGCGGC
1 GGCGGC
85063 GGAAGCGGCG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
18 2 0.05
19 1 0.03
20 2 0.05
21 29 0.74
22 2 0.05
23 1 0.03
24 2 0.05
ACGTcount: A:0.12, C:0.17, G:0.59, T:0.12
Consensus pattern (21 bp):
GGCGGCTACGGAGGAGGCGGT
Found at i:85040 original size:42 final size:42
Alignment explanation
Indices: 84994--85080 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
84984 TGGTTATGGA
* *
84994 GGCGGCTACGGAGGTGGCGGTGGCGGTGGAAG-GCGAGGTGGT
1 GGCGGCTACGGAGGAGGCGGTGGCGGCGGAAGCG-GAGGTGGT
*
85036 GGCGGCTACGGAGGAGGCGGTGGCGGCGGAAGCGGCGGTGGT
1 GGCGGCTACGGAGGAGGCGGTGGCGGCGGAAGCGGAGGTGGT
85078 GGC
1 GGC
85081 TGTTTCAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.60, T:0.11
Consensus pattern (42 bp):
GGCGGCTACGGAGGAGGCGGTGGCGGCGGAAGCGGAGGTGGT
Found at i:85065 original size:18 final size:18
Alignment explanation
Indices: 85002--85076 Score: 51
Period size: 21 Copynumber: 3.8 Consensus size: 18
84992 GAGGCGGCTA
*
85002 CGGAGGTGGCGGTGGCGG
1 CGGAGGAGGCGGTGGCGG
* *
85020 TGGAAGGCGAGGTGGTGGCGG
1 CGG-A-G-GAGGCGGTGGCGG
85041 CTACGGAGGAGGCGGTGGCGG
1 ---CGGAGGAGGCGGTGGCGG
* *
85062 CGGAAGCGGCGGTGG
1 CGGAGGAGGCGGTGG
85077 TGGCTGTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
18 15 0.34
19 1 0.02
20 1 0.02
21 23 0.52
22 1 0.02
23 1 0.02
24 2 0.05
ACGTcount: A:0.12, C:0.16, G:0.61, T:0.11
Consensus pattern (18 bp):
CGGAGGAGGCGGTGGCGG
Found at i:127860 original size:19 final size:20
Alignment explanation
Indices: 127830--127867 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
127820 AAGTTCAAAA
127830 TAAATAAAAACTACCCATTT
1 TAAATAAAAACTACCCATTT
*
127850 TAAAT-AAAACTACTCATT
1 TAAATAAAAACTACCCATT
127868 AGAGGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAATAAAAACTACCCATTT
Found at i:132353 original size:16 final size:15
Alignment explanation
Indices: 132317--132353 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
132307 AATAATTTTT
132317 TTTTTTCAAAAAACA
1 TTTTTTCAAAAAACA
*
132332 TATTTTCAAAAAATCA
1 TTTTTTCAAAAAA-CA
132348 TTTTTT
1 TTTTTT
132354 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTTTCAAAAAACA
Found at i:135382 original size:104 final size:104
Alignment explanation
Indices: 135248--135456 Score: 382
Period size: 104 Copynumber: 2.0 Consensus size: 104
135238 CGATAGTTAC
* *
135248 ATTGAACTTCAATTAATCCGGAGGTGAGCTTTGTCGGGACTCGGGCCTCAAACCGAGTGAACTGA
1 ATTGAACTTCAATTAATCCGGAGATGAGCTTTATCGGGACTCGGGCCTCAAACCGAGTGAACTGA
*
135313 AAGTCTCTTAGTGCCTATAAATTCTTAGAATTGGCTCAT
66 AAGTCTCTTAGTGCCTATAAATTCTTAGAACTGGCTCAT
135352 ATTGAACTTCAATTAATCCGGAGATGAGCTTTATCGGGACTCGGGCCTCAAACCGAGTGAACTGA
1 ATTGAACTTCAATTAATCCGGAGATGAGCTTTATCGGGACTCGGGCCTCAAACCGAGTGAACTGA
*
135417 AAGTCTCTTAGTGTCTATAAATTCTTAGAACTGGCTCAT
66 AAGTCTCTTAGTGCCTATAAATTCTTAGAACTGGCTCAT
135456 A
1 A
135457 AAAGAATCCG
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (104 bp):
ATTGAACTTCAATTAATCCGGAGATGAGCTTTATCGGGACTCGGGCCTCAAACCGAGTGAACTGA
AAGTCTCTTAGTGCCTATAAATTCTTAGAACTGGCTCAT
Found at i:139166 original size:24 final size:25
Alignment explanation
Indices: 139134--139181 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
139124 GCCTTGGATA
139134 CCGGGTGTGATAAAAAAAA-AAAAC
1 CCGGGTGTGATAAAAAAAAGAAAAC
139158 CCGGGTGTGATAAAAAAAAGAAAA
1 CCGGGTGTGATAAAAAAAAGAAAA
139182 AAGAATGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.54, C:0.10, G:0.23, T:0.12
Consensus pattern (25 bp):
CCGGGTGTGATAAAAAAAAGAAAAC
Found at i:156737 original size:2 final size:2
Alignment explanation
Indices: 156730--156754 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
156720 TTTCACAAAA
156730 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 A
156755 AGAGCATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:159658 original size:323 final size:320
Alignment explanation
Indices: 159028--159982 Score: 1100
Period size: 321 Copynumber: 3.0 Consensus size: 320
159018 TGGTAAAAAT
* * * * *
159028 GACCAAAAAGATTTT-TCCTCAATTTTTGGCAAAAACACTCATAAAAATATATATAATTCAACGC
1 GACCCAAAA-ATTTTAT-CTCAATTTTTTGCCACAATACTCATAAAAA-ATATATAATTCAACGC
** * * * * * *
159092 TGAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGAATTAATCT
63 CAAAAAGATT-AAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTTCCGAATTAATTT
* * *
159157 CTAATTAAATCGAAATAAGATTCT-GATGCACGTAAAAACAAATCATTAAATCCAATGTGGCCT-
127 CTAATTAAATCGAAATAAGATT-TAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGG-CTG
* * * *** * * **
159220 AGATTTGATTAGACT-AATAAAGATATTTCAAGGAGTCTCCACACCAAAAACCATGCAAAACAGA
190 AGATTTGGTTCGA-TGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGA
* * * * * * * *
159284 ACCGTGACCCCGGAAGGCGTTTTTAGTCAAAATCTGTGATGGTTAGTACACGATTTCGGCTGAAA
254 GCCGGGACTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-GTTAGTACACGATTTCGGCTAAAA
*
159349 ACT
318 ACC
* * * * * *
159352 GACCCGAAAA-TTTCTCTCAATTTTTTGTCACATTACTCAGAAAAAATATATAATTCAACTCCAA
1 GACCCAAAAATTTTATCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAA
159416 AAAGATTAACGGGCTTTTCACGCTTCTAATATCGTTTTTTTCATTTTTTTTTCCGAATTAATTTC
66 AAAGATTAA-GGGCTTTTCACGCTTCTAATATCG--TTTTTCATTTTTTTTTCCGAATTAATTTC
* * * *
159481 TAATTAAATCGAAATAAGATTTAGAGGCTCGTAAAAACAAATCCTCATATACAATGTGGCTGACA
128 TAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGA
* ** **
159546 ATTGGTTCGATGAATATAGATAAATCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTTG
193 TTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCG
* * * *
159611 GGGCTCCGAAACACGTTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTTGGCTAAAAACC
258 GGACTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-GTTAGTACACGATTTCGGCTAAAAACC
159675 GACCCAAAAATTTTTATCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCA
1 GACCCAAAAA-TTTTATCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCA
* * *
159740 AAAAGATTAATGGGCTTTTCACGCTTCTAATATCATTTATC-CTTTTTTTT-CGAATTAATTTCT
65 AAAAGATTAA-GGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTTCCGAATTAATTTCT
* * * * * *
159803 AATTAAGTCGAAACAAGATTGAGATGCTCGAAAAAATAAATCCTTATATCCAATATGGCTGAGAT
129 AATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGAT
* *
159868 TTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGCCGG
194 TTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGG
* * * *
159933 GTCTCCGGAACGCGTTTTTAGCCATAAGCCGTGATG--AGTAAACGATTTCG
259 GACTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGTTAGTACACGATTTCG
159983 AATAAAATTT
Statistics
Matches: 534, Mismatches: 88, Indels: 24
0.83 0.14 0.04
Matches are distributed among these distances:
318 12 0.02
320 2 0.00
321 201 0.38
322 38 0.07
323 193 0.36
324 7 0.01
325 81 0.15
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (320 bp):
GACCCAAAAATTTTATCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAA
AAAGATTAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTTCCGAATTAATTTCTAA
TTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTT
GGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGA
CTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGTTAGTACACGATTTCGGCTAAAAACC
Found at i:161220 original size:332 final size:327
Alignment explanation
Indices: 160354--161435 Score: 1107
Period size: 332 Copynumber: 3.3 Consensus size: 327
160344 CCAAACGAAC
* * * ** *
160354 ACGATTTTCGGCTAAAAATTGAGACGCA-TTTTTTTTCTCAATTTTTTGTGACAAT-TGTCATAA
1 ACGATTTTCGGCTAAAAACTGA-CCGAATTTTTTTTTCTCAATTTTTTGCCACAATAT-TCAGAA
* * * * *
160417 AAAATATATAATTTAACGCCAAAAAAATTGAAGGATTTTTCACACTTCTAATATCGTTTTTCAAT
64 AAAATATATAATTCAACACCAAAAAAATTG-AGG-TTTTTCACGCTTTTAATATCATTTTTCAA-
* * * *
160482 TTTTTTTTCCGAATTAATTTCTAATTAAAACGAAACAAGATTCAGATTCTCGTAAATATAAATCG
126 -TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA-AAAAATCC
* * * *
160547 TTAAATCGAATTTGGCTGGGA-TTT--GA----TTCGATTAATATAGATATTTCAAGGAGTCTTT
189 TTAAATCTAATGTGGCTGGGAGTTTGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT
* ** * * * * * *
160605 ACACC-AAAATCATGCAAAACTGAGCCGGGGTCCGGGAACGTGGTTTTAG-CAAAAAACCGTGAT
254 ATACCAAAAATCATGCAAAACTGAGCCGGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCATGAT
160668 GGTTAGTAT
319 GGTTAGTAT
* * * * *** * * * *
160677 AGGATTTCAGCGAAAGTTTTGAAAAAACTGACCTAAAAAATTTTTCCTCATTTTTTTCCCATAAT
1 ACGATTT--TCG---G--CT--AAAAACTGACC-GAATTTTTTTTTCTCAATTTTTTGCCACAAT
* * * ** * *
160742 AGTCAGAAAAAATACACAATTCAACACACAAAAAAATTGAAATATTTTCTCGCTTTAAATATCAT
56 ATTCAGAAAAAATATATAATTCAACAC-CAAAAAAATTGAGGT-TTTTCACGCTTTTAATATCAT
* * * *
160807 TTTTCTATTTTTTTCCGAATCT-ATTTCGAATTAAATCGAAACAATATTCAG-TGTTCGTAAAAA
119 TTTTCAATTTTTTTCCGAAT-TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAA
160870 AAAATCCTTAAATCTAATGTGGCTGGGAGTTTGAGATTGGTTAGATGAATATAGATATTTCAAGG
182 AAAATCCTTAAATCTAATGTGGCTGGGAGTTTGAGATTGGTTAGATGAATATAGATATTTCAAGG
* *
160935 AGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCCAAAACGCGTTTTTAGCCCAAAA
247 AGTCTTTATACCAAAAATCATGCAAAACTGAGCCG-GGCCCCCGAAACGCGTTTTTAGCCCAAAA
161000 ACCATGATGGTTAGTAT
311 ACCATGATGGTTAGTAT
* * *
161017 ACGATTTTCGGCTAAAAACTGACTCGATTTTTTTTTTCTGAATTTTTTGCCACAATATTCATAAA
1 ACGATTTTCGGCTAAAAACTGAC-CGAATTTTTTTTTCTCAATTTTTTGCCACAATATTCAGAAA
* * * * *
161082 ATATATAAAATTCAACACCAAAAAGATTGATGGTCTTTCCACGCTTTTAATATAATTTTTCCAAT
65 AAATATATAATTCAACACCAAAAAAATTGA-GGT-TTTTCACGCTTTTAATATCATTTTT-CAAT
* *
161147 TTTTTTCCAAATTAATTT-TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATCCTT
127 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA-AAAATCCTT
* ** * *
161211 AAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATATTTCAAGTAGTCTTTCT
191 AAATCTAATGTGGCTGGGAGTTTGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTAT
* * *
161276 ACCAAAAATCATGCAAAACTGAGCCGGGGCCCTCGAAACGCGTTTTTATCCCAAAAACCATGATT
256 ACCAAAAATCATGCAAAACTGAGCC-GGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCATGATG
*
161341 G-T-GTAC
320 GTTAGTAT
* * * *
161347 ACGATTTTCGGCTAAAAACTGACCCGAATTTTTTTTTCTGAACTTTTTGCTACAATACTCAGAAA
1 ACGATTTTCGGCTAAAAACTGA-CCGAATTTTTTTTTCTCAATTTTTTGCCACAATATTCAGAAA
*
161412 AAATATATAATACAACACCAAAAA
65 AAATATATAATTCAACACCAAAAA
161436 TTCAAATCCT
Statistics
Matches: 623, Mismatches: 102, Indels: 61
0.79 0.13 0.08
Matches are distributed among these distances:
323 6 0.01
325 2 0.00
328 1 0.00
330 124 0.20
331 150 0.24
332 163 0.26
333 66 0.11
334 11 0.02
335 1 0.00
337 33 0.05
338 24 0.04
339 15 0.02
340 27 0.04
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (327 bp):
ACGATTTTCGGCTAAAAACTGACCGAATTTTTTTTTCTCAATTTTTTGCCACAATATTCAGAAAA
AATATATAATTCAACACCAAAAAAATTGAGGTTTTTCACGCTTTTAATATCATTTTTCAATTTTT
TTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCCTTAAATC
TAATGTGGCTGGGAGTTTGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATACCAA
AAATCATGCAAAACTGAGCCGGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCATGATGGTTAGT
AT
Found at i:161696 original size:283 final size:287
Alignment explanation
Indices: 161157--161720 Score: 732
Period size: 284 Copynumber: 2.0 Consensus size: 287
161147 TTTTTTCCAA
*
161157 ATTAATTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATCCTTAAATCTAATGT
1 ATTAATTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATCCTTAAATCCAATGT
*
161222 GGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATATTTCAAGTAGTCTTTCTACCAAAAATCA
66 GGCT-AGA-CC-GAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTACCAAAAATCA
* *
161287 TGCAAAACTGAGCCGGGGCCCTCGAAACGCGTTTTTATCCCAAAAACCATGATTGTGTACACGAT
128 TGCAAAACTGAGCCGGGG-CCTCGAAACGCGTTTTTATCCCAAAAACCATGATGGTATACACGAT
*** * *
161352 TTTCGGCTAAAAACTGACCCGAATTTTTTTTTCTGAACTTTTTGCTACAATACTCAG-AAAAAAT
192 TTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAACTTTTTGCCACAATACTCAGAAAAAAAT
161416 ATATAATACAACACCAAAAATTCAAATCCTT
257 ATATAATACAACACCAAAAATTCAAATCCTT
* * *
161447 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAATCAAATCCTTATATCCAATG
1 ATTAATTT-TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATCCTTAAATCCAATG
* * *
161512 TGGCT-GA-C-A-TTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGC-GCCAAAAATCAT
65 TGGCTAGACCGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTACCAAAAATCAT
* * ** * * * *
161572 GCAAAATTGAGTCTTGG-CTCGGGAACGTGTTTTTA-GCCAAAAACCGTGATGGTTAATACACGA
129 GCAAAACTGAGCCGGGGCCTC-GAAACGCGTTTTTATCCCAAAAACCATGATGG-T-ATACACGA
* * *
161635 -TTTCGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAAA
191 TTTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAACTTTTTGCCACAATACTCAGAAAAAAA
* *
161699 TATATAATTCAACGCCAAAAAT
256 TATATAATACAACACCAAAAAT
161721 ATTGACGAGC
Statistics
Matches: 240, Mismatches: 28, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
282 17 0.07
283 62 0.26
284 91 0.38
285 2 0.01
287 1 0.00
289 2 0.01
290 8 0.03
291 57 0.24
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (287 bp):
ATTAATTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATCCTTAAATCCAATGT
GGCTAGACCGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGC
AAAACTGAGCCGGGGCCTCGAAACGCGTTTTTATCCCAAAAACCATGATGGTATACACGATTTTC
GGCTAAAAACTGACCCGAAAAGTTTTTTCTCAACTTTTTGCCACAATACTCAGAAAAAAATATAT
AATACAACACCAAAAATTCAAATCCTT
Found at i:163127 original size:333 final size:331
Alignment explanation
Indices: 162501--163870 Score: 2287
Period size: 333 Copynumber: 4.1 Consensus size: 331
162491 AATCCATGAT
*
162501 AAAACTGACCCGAAAAATTTTTCTTTTATTTTTGGCCACAATACTTGTAAAAAATATATAATTCA
1 AAAACTGACCCGAAAAATTTTTCTTTTATTATTGGCCACAATACTTGTAAAAAATATATAATTCA
* * * *
162566 ATGACAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTATCATATTTTTTCCGAATTAA
66 ATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTCGAATTAA
*
162631 TTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGGTTGTGACT
131 TTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGGTTGTGGCT
* *
162696 GAGAATTGGTTAGATGAATATAGATATTTCAAGGAGACTTGGCGCAAAAAATCATGCAAAACTGA
196 GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGA
* *
162761 GCCGGGGTCCCGGATTGCGTTTTTCGCCAAAAACTGTGATGGTTTGTACACGATTTCTGCTAAAA
261 GCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAAAA
*
162826 TTTAGC
326 TTTTGC
** * * *
162832 AAAACTGACCCGAAATTTTTTATCTTTTATTATTGGCCACAATACTTGTAAAAATTATATATTTT
1 AAAACTGACCCGAAAAATTTT-TCTTTTATTATTGGCCACAATACTTGTAAAAAATATATAATTC
*
162897 AAT-CCTAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTACTTTTTTCGGAAT
65 AATGCC-AAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTC-GAAT
* * * *
162961 TAATTTATAATAAAATCGAATCAAGATTCTGATACTCGTAAAAACAAATCCTTAAATCGGTTGTT
128 TAATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGGTTGTG
* *
163026 GCTCAGATTTGGATAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAAC
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAAC
** * *
163091 TGAGCCATGGTCTCGGAATGCGTTTTTCACCAAAAACTGTGATGGTTAGTACACGATTTCTGCTA
258 TGAGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTA
163156 AAATTTTGC
323 AAATTTTGC
* **
163165 AAAACTGACCCGAAAAATTTTTCTTTTAATCATTGGCCACAGCACTTGTAAAAAATATATAATTC
1 AAAACTGACCCGAAAAATTTTTCTTTT-ATTATTGGCCACAATACTTGTAAAAAATATATAATTC
*
163230 AATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTGTCCTATTTTTTTCGAATTA
65 AATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTCGAATTA
* *
163295 ATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACATATCCTTAAATCGATTGTGGC
130 ATTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGGTTGTGGC
* *
163360 TGATATTTGGTTAGATGAATATAGATATTTCAAGCAGTCTTGGCGCAAAAAATCATGCAAAACTG
195 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTG
163425 AGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGG--AGTACACGATTTCTGCTAAA
260 AGCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAAA
163488 ATTTTGC
325 ATTTTGC
*
163495 AAAACTGACCCGAAAAATTTTTCTTTTATTATTGGCCACAACACTTGTAAAAAATATATAATTCA
1 AAAACTGACCCGAAAAATTTTTCTTTTATTATTGGCCACAATACTTGTAAAAAATATATAATTCA
163560 ATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTCGAATTAA
66 ATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTCGAATTAA
* *
163625 TTTATAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAGTCGGTTGTGGCT
131 TTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGGTTGTGGCT
*
163690 GAGATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGA
196 GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGA
*
163755 GCCGGGGTCCCGGAATGTGTTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAAA
261 GCCGGGGTCCCGGAATGCG-TTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCT-AA
163820 AATTTTGC
324 AATTTTGC
* *
163828 AAAACTGACCCGAAAAAATTTTCTTTTATTTTTGGCCACAATA
1 AAAACTGACCCGAAAAATTTTTCTTTTATTATTGGCCACAATA
Statistics
Matches: 965, Mismatches: 65, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
329 241 0.25
330 77 0.08
331 20 0.02
332 279 0.29
333 346 0.36
334 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (331 bp):
AAAACTGACCCGAAAAATTTTTCTTTTATTATTGGCCACAATACTTGTAAAAAATATATAATTCA
ATGCCAAAAATATTAAAGGGCATTTCACGCTTCGAATATCGTTTTTCCTATTTTTTTCGAATTAA
TTTATAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCGGTTGTGGCT
GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGA
GCCGGGGTCCCGGAATGCGTTTTTCGCCAAAAACTGTGATGGTTAGTACACGATTTCTGCTAAAA
TTTTGC
Done.