Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019687.1 Corchorus olitorius cultivar O-4 contig19720, 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: 6163
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Found at i:1846 original size:321 final size:320
Alignment explanation
Indices: 286--6004 Score: 4695
Period size: 321 Copynumber: 17.4 Consensus size: 320
276 CTAAATCGTG
* ** *
286 TTGTTTCTATTTAATTAGAAATTAATTCAGAAAATAAATGGAAAATTGATATTATAAGCGTG-AA
1 TTGTTTCGATTTAATTAGAAATTAATTC-GAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAA
* * * * *
350 AAGCCTTCAATATTTTTGACGTTGAATTATATATTTTTTTTCTAAGTATTTGTGGCAAAAAACTG
64 AACCCTTCAATCTTTTTGGCGTTGAATTATATA--TTTTTTCTGAGTA-TTGTGGCAAAAAATTG
* * * * * *
415 AGTAAAAATTTTTC-GTGTCAGTTTTTAGCTGAAATCGTGGACTAACCATCACTGTTTTTGGCTA
126 AG-AAAAACTTTTCAG-GTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGCTA
* * *
479 AAAACGCGTTTCGGGGGACTCGACTCAGTTTTGCATGGTTTTTGGCATACAA-ACTCCTTGAAAT
189 AAAACGCGTTTC-GGGGCCTCGTCTCAGTTTTGCATGATTTTTGGCATA-AAGACTCCTTGAAAT
* * * * * *
543 ATATATACTCATATAACCAAAACTCAGCCACATTTGATTTAAGAATTTGTTTTTACGAGCATCTG
252 ATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
608 AATC
317 AATC
* * *
612 TTGTTTCGATTTTATTAGAAA-TAGATTCGAAAAAAAAAT-GAAAAACGATATTGGAAGCATGAA
1 TTGTTTCGATTTAATTAGAAATTA-ATTCG--AAAAAAATGGAAAAACGATATTAGAAGCGTGAA
* * *
675 AGACCCTTCAAT-TTTTTAGGCGTTGAATTATATA-CTTTTCTGAGTATTGTGGC-AAAAATTAA
63 AAACCCTTCAATCTTTTT-GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA
* * *** *
737 GGAAAACTTTTCGATTCTGTTTCTTGCAAAAATTTAGGCCGAAATCGTGTATTAA-CTATCACGG
127 GAAAAACTTTTC-A----G------GTAAGTTTTTA-GCCGAAATCGTGTACTAATC-ATCACGG
* * * * * * * * * * **
801 TTTTTGGCTAATAATGCGTTCCGGAGCCAT-GGCTCAATTTTGCCTAATTTTTGCCGTAATTACT
179 TTTTTGGCTAAAAACGCGTTTCGGGGCC-TCGTCTCAGTTTTGCATGATTTTTGGCATAAAGACT
* * * * * *
865 CATTGAAATATCTATATTCATCGAATCATATCTCAGCCACATTGGATTTAAGGATTTGTCTTTAC
243 CCTTGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
*
930 GAGCATTTGAATC
308 GAGCATCTGAATC
* ** * *
943 TTGTTTCGATTTAATTAGAAATAAATTCGGTAAAAATGGAAAAATGATATTAGAAGCGTGAAAAC
1 TTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAA
* * * * *
1008 CCCTTCAATATTTTTGGCTTTGAATTATATATTTATTCTGAGCATTGTGGCAAAGAATTGAGGAA
66 CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAA
* * * * * * *
1073 AAAATTTTCGGGTATTATTTTGCAAAATTATAACCAAAATCGTTTACT--T-ATTACGGTTTTTG
130 AAACTTTTCAGGTA--A-GTT------TT-TAGCCGAAATCGTGTACTAATCATCACGGTTTTTG
* * * * *
1135 GCTAAAAACAC-ATTCTGGGGCCCTGGT-TTAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTG
185 GCTAAAAACGCGTTTC-GGGG-CCTCGTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTG
* * * * *
1198 AAATATCTATATGTTCATCGAACCAAATC-CAAGTCACATTGGATTTAACGATTTGTTTTTACAA
248 AAATAT-T-TATATTCATCTAACCAAATCTC-AGCCACATTGGATTTAAGGATTTGTTTTTACGA
*
1262 GCATTTGAATC
310 GCATCTGAATC
* * * *
1273 TTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAAAGGAAAAATGATATTGGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * * * * * *
1338 ATCGTTCATTTTTTTTTGCATTGAATTATATAATTTTTCTGAATATTTTGGCAAAAAATTGAGGA
65 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GA
** * * * * * *
1403 AAAACTTTTTGGGTAAGTTTTTA--CAAAAT--TTTAGCCGAAATCGTGTCACGGTTTTTGTCTC
129 AAAACTTTTCAGGTAAGTTTTTAGCCGAAATCGTGTA--C-TAATC--ATCACGGTTTTTGGCTA
* * * * * * * *
1464 AAAACGCGTTTCGGAGTCC-CAG-GTAAATTTTGCAAGATTTTTGTCACAAAAACT-C--GAAAT
189 AAAACGCGTTTCGG-GGCCTC-GTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAAT
* * * *
1524 ATTTTATATTCAT-TGAACCAAATCTCAGGCACATTAGATATAAGGATTTATTTTTACGAGCATC
252 A-TTTATATTCATCT-AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* *
1588 TAAATA
315 TGAATC
* *
1594 TTGTTTCGATTTAATTGGAAATTAATTAGAAAAAATATGGAAAAACGATATTAGAAGCGTG-AAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGAAAAAA-ATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * * ** *
1658 GCCCGTCAATCTTTTTGGCTTTGAATTATATATTTTTTCTAAATATT-TTTCAAACAGATTGAGA
65 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAA-AAATTGAGA
*
1722 AAAACTTTTCAGGTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTAGCTAAAAAC
129 AAAACTTTTCAGGTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAAC
* * * * *
1787 GCGTTTTGGGGCATCGTCTCAGTTTTGTATGGTTTTTGGCATAAAGACTCCTTGAAATATCTATA
194 GCGTTTCGGGGCCTCGTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATTTATA
* * * * * * *
1852 TTCATCTAACCAAATCTCGGTCACATTGGTTTTAAGGATTTATTTTTGCAAGCATCTAAATC
259 TTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
* ** * *
1914 TTGTTTCGATTTAATTAGAAATAAATTCGGTAAAAATGGAAAAACGATATTAAAACCGTGAAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAA
* * *
1979 ACCTTCAAT-TTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTGTGACAAAAAATTGAGAAA
66 CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG--A
* * *
2043 AAAACTTTTCGGGTCAA-TTTTTAGCCGAAAATCGTGTACTAA-CTATCACGATTTTTAGCT-AA
129 AAAACTTTTCAGGT-AAGTTTTTAGCCG-AAATCGTGTACTAATC-ATCACGGTTTTTGGCTAAA
* * * * * **
2105 AACGAGTTTCGCGGCCTCGTCTCAGTTTTCCTTGGTTTTTCACATAAAGACTCCTTGAAATATCT
191 AACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATAT-T
* * * *
2170 T-TATTCATCTATCCAAATCTCAGCCACATTGAATTTAAGGATTAGTTTTTAC-ATGCATCAGAA
255 TATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA-GCATCTGAA
2233 TC
319 TC
* *
2235 TTGTTACGATTTAATTAGAAATTAATTCAGAAAAAATAT-GAAAAACGGTATTAGAAGCGTGAAA
1 TTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAA-ATGGAAAAACGATATTAGAAGCGTGAAA
* * * * * * *
2299 AGCCTTTTAATTTTTTTGTCATTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGG
64 AACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-G
* ** *
2364 AAAAAGTTTTCGGGTCAGTTGTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTT
128 AAAAA-CTTT----TCA---G--GTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTT
* * * * * ** *
2428 TGGCTAAAAACGCGTTCCGGAG-TTCCATCTCAATTTT-CAATGATTTTTTGGCGCAAAGGCTCC
183 TGGCTAAAAACGCGTTTCGGGGCCT-CGTCTCAGTTTTGC-ATGA-TTTTTGGCATAAAGACTCC
* * * * * *
2491 TGGAAATATTTATATTCATCGAATCAAATCTCAGCCACATTGGATATAAGAACTTGTTTTTACGA
245 TTGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA
*
2556 GCATCCGAATC
310 GCATCTGAATC
* * * *
2567 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGTAAAAAATGATATTGGAAGCGTG-AAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATG-GAAAAACGATATTAGAAGCGTGAAAA
* * * *
2631 AGCCTGTCAAT-TTTTTGGCATTGAATTATATATTTTTTCTGAATATT-TTGCGAAAAAA-TGAG
65 ACCCT-TCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGAG
* * * *
2693 AAAAAAACTCTTC-GAGTCAGTTTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAA
128 --AAAAACTTTTCAG-GTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAA
* * * *
2757 AAACGCGTTACGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCTTTGAAATATT
190 AAACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATT
* * * * * *
2822 AATATTCATCTAACCAAATATCAGCCACAATGGACTAAAGGATTTGTTTTTACAAGCATCTGAAT
255 TATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
2887 -
320 C
* * * *
2887 TATGTTTCAATATAATTAGAAATAAATTCGGAAAAAAA-GGAAAAACGATATTAGAGGCGTGAAA
1 T-TGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* *
2951 AACCCTTCAATCTTTTTGGCGTTGAATTATATATTTGTTCTGAGTATTGTGGCAAAGAATTGAGG
64 AACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-G
* * ** ** * * *
3016 AAAAATTTTTCGGGTTTGTTTTT-GCAAAATTTTAGTCGAAATTGT-TTACTCATCACTGTTTTT
128 AAAAACTTTTCAGGTAAGTTTTTAGCCGAA----A-TCG----TGTACTAATCATCACGGTTTTT
* ** * ** * * * * * *
3079 GGCTAAAAATGCG-TTCTAAGGCCCCAACTCAGTTTTGAATGATATTTGTCGTAAAGATTGCTTG
184 GGCTAAAAACGCGTTTC-GGGGCCTCGTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTG
* * * * * * *
3143 GAATATCTATATTCATCGAACTAAATCTCAGCCACACTGGATTTAACGATTTGTTTTTACGAGAA
248 AAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
3208 TCTGAATC
313 TCTGAATC
* * *
3216 TTGTTTCGATTTATTTAGAAATTAATTCGGAAAAAAATAGATAAACGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* ** * *
3281 ACCCTTCAATCTTTTTGGCATTGAATTATGCA-TTTTTATGAGTATTGTGGCAAAAAAATGAGAA
65 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG--
* * * ** * * * * *
3345 AAAAAATTTTCTGATCGGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTCGCTAAAGA
128 AAAAACTTTTCAGGTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAA
* * *
3410 TGTGTTTCGGGGCCTCGTCTTAGTTTTGCAT-AGTTTTTGGCATAAAGACTCCTTGAAATATTTA
193 CGCGTTTCGGGGCCTCGTCTCAGTTTTGCATGA-TTTTTGGCATAAAGACTCCTTGAAATATTTA
* * *
3474 TATTCATCTAACCAAATCTCAGCCATATTGGATTTAAGGATTTGCTTTTACGAGTATCTGAATC
257 TATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
**
3538 TTGTTTCGATTTAATTAGAAA-TATATTCG-GGAAAATGGAAAAACGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTA-ATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * *
3601 ACCCTTCAATTTTTTTGGCGTTGAATTATATATATTTTTATGAATA-AGTTGCAAACAAATTGAG
65 ACCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTTCTGAGTATTGTGGCAAA-AAATTGAG
* * * **
3665 AAAAAACTTTTCAGGTCAGTTTTTAGACGAAATCGTGTACTAATCAATCACTGTTTTTTTTCCCT
128 -AAAAACTTTTCAGGTAAGTTTTTAGCCGAAATCGTGTACTAATC-ATCAC-G--GTTTTTGGCT
* *
3730 AAAAACGCGTTTCGGGGCCTCGTCTCAGTTTTGTATGGTTTTTGGCATAAAGACTCCTTGAAATA
188 AAAAACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATA
* **
3795 TCTATATTCATCTAAGAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-A
253 TTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
*
3859 AGTA
318 A-TC
* * * *
3863 TTGTTTTGATTTAATT-GAAAACTAATTCGAAGAAAAACGG-AAAACGATATTAGAAGCATGAAA
1 TTGTTTCGATTTAATTAG-AAATTAATTCGAA-AAAAATGGAAAAACGATATTAGAAGCGTGAAA
3926 AACCCTTCAAAT-TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG
64 AACCCTTC-AATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-
* ** * * * * *
3990 GAAAAACCTTTCGGGTCAGTTTTTGCAAAATTTTAGCTGAAATAGTGTATTAACCATCAAGGTTT
127 GAAAAA-CTTT----TCAG-----GTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTT
* * * * * * ** * *
4055 TTGGCTAAAAACCCGGTAT-GGAG-TTCCGACTCAATTTT-CAATGATTTTTGGCGCAAAGAATA
182 TTGGCTAAAAACGC-GTTTCGGGGCCT-CGTCTCAGTTTTGC-ATGATTTTTGGCATAAAGACTC
* * * * *
4117 C-TGAATATATATATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGAATTTGTTTTTAC
244 CTTGAA-ATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
*
4181 GAGCATCCGAATC
308 GAGCATCTGAATC
* ** * *
4194 TTGATTAAATTTAATTATAAATTAATTCGAAAAAAATGGAAAAAACGATATTGGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATGG-AAAAACGATATTAGAAGCGTGAAAA
* * * * *
4259 GCCATTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAATATT-TTGCGAAAAAATTGAGA
65 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGAG-
* * * * * *
4323 AAAAACTCTTC-GAGTCAGTTTTTAGTCGAAATCATATACTAATCAATCACGGTTTTTGACTAAA
128 AAAAACTTTTCAG-GTAAGTTTTTAGCCGAAATCGTGTACTAATC-ATCACGGTTTTTGGCTAAA
* * * * *
4387 AACGCGTTACGGGGCCTCGTCTTAGTCTTGTATGATTTTTGGCATAAAGACTCTTTGAAATATTT
191 AACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATTT
* * * * *
4452 ATATTCATCTAACCAAATCTCAGCCACAATGGACTAAAGGAGTTGTTTTTACAAGCATCTGAATC
256 ATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
* * * * * * * *
4517 ATGTTTCGATATAATTAGAAATAAATTCG-GAAAATTAGGAACAAGGATATTAGAGGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAT-GGAAAAACGATATTAGAAGCGTGAAAA
* ** *
4581 ACCCTTCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAATGAACTGAGGA
65 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GA
* * * * * * *
4646 AAAATTTTTCGGGTTGGTTAATGCAAAATTTTAGTCGAAAT--TGT-TTACTCATCACTGTTTTT
129 AAAACTTTTC----AGG-TAA-G----TTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTT
* ** * * * * * *
4708 GGCTAAAAATGCG-TTCTAAGGCCCCAG-CTCAGTTTTGAATGATATTTGTCGTAAAGACTGCTT
184 GGCTAAAAACGCGTTTC-GGGGCCTC-GTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTT
* * * * * * *
4771 GGAATATCTATATTCATCGAACCAAATCTCAGGCACACTGGATTTAACGATTTGTTTTTACGAGA
247 GAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
4836 ATCTGAATC
312 ATCTGAATC
* * *
4845 TTGTTTCGATTTATTTAGAAATTAATTCGGAAAAAAATAGATAAACGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* ** * *
4910 ACCCTTCAATCTTTTTGGCATTGAATTATGCA-TTTTTATGAGTATTGTGGCAAAAAAATGAGAA
65 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG--
* * * ** * * * *
4974 AAAAAATTTTCTGATCGGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTCGCTAAAAA
128 AAAAACTTTTCAGGTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAA
* * *
5039 TGTGTTTCGGGGCCTCGTCTAAGTTTTGCAT-AGTTTTTGGCATAAAGACTCCTTGAAATATTTA
193 CGCGTTTCGGGGCCTCGTCTCAGTTTTGCATGA-TTTTTGGCATAAAGACTCCTTGAAATATTTA
* * *
5103 TATTCATCTAACCAAATCTCAGCCATATTGGATTTAAGGATTTGCTTTTACGAGTATCTGAATC
257 TATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
* * * * *
5167 ATGTTTCGATATAATTAGAAATAAATTCGGGAAAAAA-GGAAAAACGATATTAGAGGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
*
5231 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAGAATTGAGGA
65 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GA
* * ** * * **
5296 AAAATTTTTCGGGTTTGTTTTTACAAAATATTAGCCGAAAT--TGT-TTACTCATCACTATTTTT
129 AAAACTTTTCAGGTAAG---TT------T-TTAGCCGAAATCGTGTACTAATCATCACGGTTTTT
* ** * * * * * * * *
5358 GGCTAAAAATGCG-TTCTAAGGCCCCAG-CTCAATTTTGAATGATATTTGTCGTAAAGATTGCTT
184 GGCTAAAAACGCGTTTC-GGGGCCTC-GTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTT
* * * * * *
5421 GGAATATCTATATTCATCGAACCAAATCTCAGCCACACTGGATTTAACGATTTGTTTTTACGAGA
247 GAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
*
5486 ATCTAAATC
312 ATCTGAATC
* * * *
5495 TTGTTTCGATTTATTTAGAAATTAATTAGGAAAAAAAATAGATAAACGATATTAGAAGCGTGAAA
1 TTGTTTCGATTTAATTAGAAATTAATT-CG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
*
5560 AACCCTTCAATCTTTTTGGCATTGTGAAAAACCCTTCAATCTTTTTGGCATTGAATTATGCGTTT
64 AACCCTTCAATCTTTTTGGC-----G--------TTGAA-----TT---A-T--A-TAT---TTT
* * * * ** * *
5625 TTATGAGTATTGTGGCAAAAAA-TGAGAAAACAATTTTCTGATCGGATTTTAGCTGAAATCGTGT
101 TTCTGAGTATTGTGGCAAAAAATTGAGAAAA-ACTTTTCAGGTAAGTTTTTAGCCGAAATCGTGT
* * * * * *
5689 ACTAACCATCACGGTTTTTCGCTAAAAATGTGTTTCGGGGCCTCATCTAAGTTTTGCAT-AGTTT
165 ACTAATCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATGA-TTT
*
5753 TTGACATAAAGACTCCTTGAAATATATTCGAGAAAATGGAATATTTATATTCATCTAACCAAATC
229 TTGGCATAAAGACTCC----------TT---G---A---AATATTTATATTCATCTAACCAAATC
* * * * *
5818 TCAGCCACAATGGACTAAAGGATTTGTTTTTACAAGTATCTGAATC
275 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
* * * *
5864 ATGTTTCGATATAATTAGAAATAAATTCGGGAAAAAAA-GGAAAAACGATATTAGAGGCGTGAAA
1 TTGTTTCGATTTAATTAGAAATTAATTC--GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * * *
5928 TACCCTTCAATCTTTTTGGCCTTGATTTATATATTTTTTTCTGAGTATTGTGGCAAAGAATTGAG
64 AACCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGA-
5993 GAAAAACTTTTC
127 GAAAAACTTTTC
6005 GGGTTTGTTT
Statistics
Matches: 4339, Mismatches: 771, Indels: 550
0.77 0.14 0.10
Matches are distributed among these distances:
317 7 0.00
318 50 0.01
319 110 0.03
320 255 0.06
321 601 0.14
322 597 0.14
323 214 0.05
324 14 0.00
325 249 0.06
326 129 0.03
327 31 0.01
328 553 0.13
329 163 0.04
330 223 0.05
331 512 0.12
332 281 0.06
333 12 0.00
334 4 0.00
335 23 0.01
341 23 0.01
342 9 0.00
343 11 0.00
344 2 0.00
346 1 0.00
347 11 0.00
348 3 0.00
349 4 0.00
350 55 0.01
351 4 0.00
352 1 0.00
354 2 0.00
355 6 0.00
356 5 0.00
357 12 0.00
358 23 0.01
360 2 0.00
363 1 0.00
368 42 0.01
369 93 0.02
370 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (320 bp):
TTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAA
CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAA
AACTTTTCAGGTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAACGC
GTTTCGGGGCCTCGTCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATTTATATT
CATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
Found at i:3437 original size:650 final size:645
Alignment explanation
Indices: 286--5583 Score: 4428
Period size: 650 Copynumber: 8.1 Consensus size: 645
276 CTAAATCGTG
* * ** *
286 TTGTTTCTATTTAATTAGAAATTAATTCAGAAAATAAATGGAAAATTGATATTATAAGCGTG-AA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AAA-GGAAAAACGATATTAGAAGCGTGAAA
* * * * * *
350 AAGCCTTCAATATTTTTGACGTTGAATTATATATTTTTTTTCTAAGTATTTGTGGCAAAAAACTG
64 AACCCTTCAATCTTTTTGGCATTGAATTATATA--TTTTTTCTGAGTA-TTGTGGCAAAAAATTG
* * * * * * * *
415 AGTAAAAATTTTTCGTGTCAGTTTTTAGCTGAAA---TCGT-G-GA-C--TAAC-CATCACTGTT
126 AGGAAAAACTTTTCGGGT-AGTTTTT-GC-AAAATTTTAGTCGAAATCGTTTACTCATCACGGTT
* * * * *
471 TTTGGCTAAAAACGCGTTTCGGGGGACTCGACTCAGTTTTGCATGGTTTTTGGCATACAA-ACTC
188 TTTGGCTAAAAACGCG-TTCTGGGGCCTCGTCTCAGTTTTGTATGATTTTTGGCATA-AAGACTC
* * * * * *
535 CTTGAAATATATATACTCATATAACCAAAACTCAGCCACATTTGATTTAAGAATTTGTTTTTACG
251 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* * *
600 AGCATCTGAATCTTGTTTCGATTTTATTAGAAATAGATTC-GAAAAAAAAATGAAAAACGATATT
316 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATA-GAAAAACGATATT
* * * * *
664 GGAAGCATGAAAGACCCTTCAATTTTTTAGGCGTTGAATTATATA-CTTTTCTGAGTATTGTGGC
380 AGAAGCGTGAAAAACCCTTCAATTTTTT-GGCATTGAATTATATATTTTTTCTGAGTATTGTGGC
* * * * * *
728 -AAAAATTAAG-GAAAACTTTTCGATTCTGTTTCTTGCAAAAATTTAGGCCGAAATCGTGTATTA
444 AAAAAATTGAGAAAAAAC--TT---TTCTG----AT-C-AGATTTTA-GCCGAAATCGTGTACTA
* * * * * * * * *
791 ACTATCACGGTTTTTGGCTAATAATGCGTTCCGGAGCCATGGCTCAATTTTGCCTAATTTTTGCC
497 ACCATCACGGTTTTTGGCTAA-AACGCGTTTCGGGGCC-TCGCTCAGTTTTGCATGATTTTTGGC
* ** * * *
856 GTAATTACTCATTGAAATATCTATATTCATCGAATCATATCTCAGCCACATTGGATTTAAGGATT
560 ATAAAGACTC-TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATT
* *
921 TGTCTTTACGAGCATTTGAATC
624 TGTTTTTACGAGCATCTGAATC
* * * * *
943 TTGTTTCGATTTAATTAGAAATAAATTCGGTAAAAATGGAAAAATGATATTAGAAGCGTGAAAAC
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAA
* * * * *
1008 CCCTTCAATATTTTTGGCTTTGAATTATATATTTATTCTGAGCATTGTGGCAAAGAATTGAGGAA
66 CCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAA
* * * ** * * *
1073 AAAATTTTCGGGTATTATTTTGCAAAATTATAACCAAAATCGTTTACTTATTACGGTTTTTGGCT
131 AAACTTTTCGGGTAGT-TTTTGCAAAATTTTAGTCGAAATCGTTTACTCATCACGGTTTTTGGCT
* * * * * *
1138 AAAAACACATTCTGGGGCCCTGGT-TTAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAAT
195 AAAAACGCGTTCTGGGG-CCTCGTCTCAGTTTTGTATGATTTTTGGCATAAAGACTCCTTGAAAT
* * * *
1202 ATCTATATGTTCATCGAACCAAATC-CAAGTCACATTGGATTTAACGATTTGTTTTTACAAGCAT
259 ATCTATA--TTCATCTAACCAAATCTC-AGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * *
1266 TTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAA-AGGAAAAATGATATTGGAAG
321 CTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATA-GAAAAACGATATTAGAAG
* * * * * * *
1330 CGTGAAAAATCGTTCATTTTTTTTTGCATTGAATTATATAATTTTTCTGAATATTTTGGCAAAAA
385 CGTGAAAAACCCTTCA-ATTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAA
* * * * * * * **
1395 ATTGAGGAAAAACTTTT-TGGGTAAGTTTTTA--CAAAAT--TTTAGCCGAAATCGTGTCACGGT
449 ATTGAGAAAAAACTTTTCT-GATCAGATTTTAGCCGAAATCGTGTA--C-TAA-C-CATCACGGT
* * * * * * * * *
1455 TTTTGTCTCAAAACGCGTTTCGGAGTCC-CAGGTAAATTTTGCAAGATTTTTGTCACAAAAACTC
508 TTTTGGCT-AAAACGCGTTTCGG-GGCCTC-GCTCAGTTTTGCATGATTTTTGGCATAAAGACTC
* * * * *
1519 --GAAATATTTTATATTCAT-TGAACCAAATCTCAGGCACATTAGATATAAGGATTTATTTTTAC
570 TTGAAATA-TCTATATTCATCT-AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
* *
1581 GAGCATCTAAATA
633 GAGCATCTGAATC
* *
1594 TTGTTTCGATTTAATTGGAAATTAATT-AGAAAAAATATGGAAAAACGATATTAGAAGCGTG-AA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA-A-GGAAAAACGATATTAGAAGCGTGAAA
* * * * * ** *
1657 AGCCCGTCAATCTTTTTGGCTTTGAATTATATATTTTTTCTAAATATT-TTTCAAACAGATTGA-
64 AACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAA-AAATTGAG
* * *
1720 GAAAAACTTTTCAGGTAAG----T------TTTTAGCCGAAATCGTGTACTAATCATCACGGTTT
128 GAAAAACTTTTCGGGT-AGTTTTTGCAAAATTTTAGTCGAAATCGT-T--TACTCATCACGGTTT
* * * *
1775 TTAGCTAAAAACGCGTTTTGGGGCATCGTCTCAGTTTTGTATGGTTTTTGGCATAAAGACTCCTT
189 TTGGCTAAAAACGCGTTCTGGGGCCTCGTCTCAGTTTTGTATGATTTTTGGCATAAAGACTCCTT
* * * * * *
1840 GAAATATCTATATTCATCTAACCAAATCTCGGTCACATTGGTTTTAAGGATTTATTTTTGCAAGC
254 GAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
* * * *
1905 ATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGG-TAAAAATGGAAAAACGATATTAAAA
319 ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATAGAAAAACGATATTAGAA
* * * * *
1969 CCGTGAAAAAACCTTCAATTTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTGTGACAAAAA
384 GCGTGAAAAACCCTTCAATTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAA
* * * *
2034 ATTGAGAAAAAAACTTTTCGGGTCA-ATTTTTAGCCGAAAATCGTGTACTAACTATCACGATTTT
449 ATTGAG-AAAAAACTTTTCTGATCAGA-TTTTAGCCG-AAATCGTGTACTAACCATCACGGTTTT
* * * * * * **
2098 TAGCTAAAACGAGTTTCGCGGCCTCGTCTCAGTTTTCCTTGGTTTTTCACATAAAGACTCCTTGA
511 TGGCTAAAACGCGTTTCGGGGCCTCG-CTCAGTTTTGCATGATTTTTGGCATAAAGACT-CTTGA
* * * *
2163 AATATCTTTATTCATCTATCCAAATCTCAGCCACATTGAATTTAAGGATTAGTTTTTAC-ATGCA
574 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA-GCA
*
2227 TCAGAATC
638 TCTGAATC
* * * *
2235 TTGTTACGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGGTATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA-AGGAAAAACGATATTAGAAGCGTGAAAA
* * * * * *
2300 GCCTTTTAATTTTTTTGTCATTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGGA
65 ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA
* * * * *
2365 AAAAGTTTTCGGGTCAGTTGTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTT
130 AAAACTTTTCGGGT-AGTTTTTGCAAAATTTTAGTCGAAATCGTTTACT---CATCACGGTTTTT
* * * * * ** ** * *
2429 GGCTAAAAACGCGTTCCGGAG-TTCCATCTCAATTTTCAATGATTTTTTGGCGCAAAGGCTCCTG
191 GGCTAAAAACGCGTTCTGGGGCCT-CGTCTCAGTTTTGTATGA-TTTTTGGCATAAAGACTCCTT
* * * * * *
2493 GAAATATTTATATTCATCGAATCAAATCTCAGCCACATTGGATATAAGAACTTGTTTTTACGAGC
254 GAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
* * * * *
2558 ATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATGTA-AAAAATGATATTGGA
319 ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAA-ATAGAAAAACGATATTAGA
* * *
2622 AGCGTG-AAAAGCCTGTCAATTTTTTGGCATTGAATTATATATTTTTTCTGAATATT-TTGCGAA
383 AGCGTGAAAAACCCT-TCAATTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGC-AA
* * *
2685 AAAA-TGAGAAAAAAACTCTTC-GAGTCAGTTTTTAGCCGAAATCATGTACTAACCATCACGGTT
446 AAAATTGAG-AAAAAACTTTTCTGA-TCAGATTTTAGCCGAAATCGTGTACTAACCATCACGGTT
* *
2748 TTTGGCTAAAAACGCGTTACGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCTT
509 TTTGGCT-AAAACGCGTTTCGGGGCCTCG-CTCAGTTTTGCATGATTTTTGGCATAAAGACTC-T
* * * * *
2813 TGAAATAT-TAATATTCATCTAACCAAATATCAGCCACAATGGACTAAAGGATTTGTTTTTACAA
571 TGAAATATCT-ATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA
2877 GCATCTGAAT-
635 GCATCTGAATC
* * * *
2887 TATGTTTCAATATAATTAGAAATAAATTCGGAAAAAAAGGAAAAACGATATTAGAGGCGTGAAAA
1 T-TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAA
* * *
2952 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTGTTCTGAGTATTGTGGCAAAGAATTGAGGA
65 ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA
* * * *
3017 AAAATTTTTCGGGTTTGTTTTTGCAAAATTTTAGTCGAAATTGTTTACTCATCACTGTTTTTGGC
130 AAAACTTTTCGGG-TAGTTTTTGCAAAATTTTAGTCGAAATCGTTTACTCATCACGGTTTTTGGC
* ** * ** * * * * * * *
3082 TAAAAATGCGTTCTAAGGCCCCAACTCAGTTTTGAATGATATTTGTCGTAAAGATTGCTTGGAAT
194 TAAAAACGCGTTCTGGGGCCTCGTCTCAGTTTTGTATGATTTTTGGCATAAAGACTCCTTGAAAT
* * * * *
3147 ATCTATATTCATCGAACTAAATCTCAGCCACACTGGATTTAACGATTTGTTTTTACGAGAATCTG
259 ATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
* * *
3212 AATCTTGTTTCGATTTATTTAGAAATTAATTCGGAAAAAAATAGATAAACGATATTAGAAGCGTG
324 AATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATAGAAAAACGATATTAGAAGCGTG
** * *
3277 AAAAACCCTTCAATCTTTTTGGCATTGAATTATGCA-TTTTTATGAGTATTGTGGCAAAAAAATG
389 AAAAACCCTTCAAT-TTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG
* * * *
3341 AGAAAAAAAATTTTCTGATCGGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTCGCTA
453 AG-AAAAAACTTTTCTGATCAGATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTA
* * *
3406 AAGATGTGTTTCGGGGCCTCGTCTTAGTTTTGCAT-AGTTTTTGGCATAAAGACTCCTTGAAATA
517 AA-ACGCGTTTCGGGGCCTCG-CTCAGTTTTGCATGA-TTTTTGGCATAAAGACT-CTTGAAATA
* * * *
3470 TTTATATTCATCTAACCAAATCTCAGCCATATTGGATTTAAGGATTTGCTTTTACGAGTATCTGA
578 TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
3535 ATC
643 ATC
* *
3538 TTGTTTCGATTTAATTAGAAA-TATATTCGG-GAAAATGGAAAAACGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTA-ATTCGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAA
* * * * * *
3601 ACCCTTCAATTTTTTTGGCGTTGAATTATATATATTTTTATGAATA-AGTTGCAAACAAATTGAG
65 ACCCTTCAATCTTTTTGGCATTGAATTATATAT-TTTTTCTGAGTATTGTGGCAAA-AAATTGAG
* * * ** * ** * * **
3665 AAAAAACTTTTCAGGTCAGTTTTTAGACGAAATCGT-GTAC-TAATCAATCACT-GT---TTTTT
128 GAAAAACTTTTCGGGT-AGTTTTT-G-CAAAATTTTAGT-CGAAATCGTTTACTCATCACGGTTT
** *
3724 TTCCCTAAAAACGCGTT-TCGGGGCCTCGTCTCAGTTTTGTATGGTTTTTGGCATAAAGACTCCT
189 TTGGCTAAAAACGCGTTCT-GGGGCCTCGTCTCAGTTTTGTATGATTTTTGGCATAAAGACTCCT
**
3788 TGAAATATCTATATTCATCTAAGAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
253 TGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* * * *
3853 CATCT-AAGTATTGTTTTGATTTAATT-GAAA-ACTAATTC-GAAGAAAAA-CGGAAAACGATAT
318 CATCTGAA-TCTTGTTTCGATTTAATTAGAAATA--AATTCGGAA-AAAAATAGAAAAACGATAT
* *
3913 TAGAAGCATGAAAAACCCTTCAAATTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGG
379 TAGAAGCGTGAAAAACCCTTC-AATTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGG
* ** * * * *
3978 CAAAAAATTGAGGAAAAACCTTTCGGGTCAGTTTTTGCAAAATTTTAGCTGAAATAGTGTATTAA
443 CAAAAAATTGA-GAAAAAACTTT----TC---TGAT-C-AGATTTTAGCCGAAATCGTGTACTAA
* * * * * *
4043 CCATCAAGGTTTTTGGCTAAAAACCCGGTAT-GGAG-TTCCGACTCAATTTT-CAATGATTTTTG
498 CCATCACGGTTTTTGGCT-AAAACGC-GTTTCGGGGCCT-CG-CTCAGTTTTGC-ATGATTTTTG
** * * * * * *
4105 GCGCAAAGAATAC-TGAATATATATATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGA
558 GCATAAAGACT-CTTGAA-ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGG
*
4169 ATTTGTTTTTACGAGCATCCGAATC
621 ATTTGTTTTTACGAGCATCTGAATC
* ** * *
4194 TTGATTAAATTTAATTATAAATTAATTC-GAAAAAAATGGAAAAAACGATATTGGAAGCGTGAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAA-GG-AAAAACGATATTAGAAGCGTGAAA
* * * *
4258 AGCCATTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAATATT-TTGCGAAAAAATTGAG
64 AACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGAG
* * ** * *
4322 AAAAAACTCTTC--G-AG----T-C-AGTTTTTAGTCGAAATCATATACTAATCAATCACGGTTT
128 GAAAAACTTTTCGGGTAGTTTTTGCAAAATTTTAGTCGAAATCGT-T--TACTC-ATCACGGTTT
* * * *
4378 TTGACTAAAAACGCGTTAC-GGGGCCTCGTCTTAGTCTTGTATGATTTTTGGCATAAAGACTCTT
189 TTGGCTAAAAACGCGTT-CTGGGGCCTCGTCTCAGTTTTGTATGATTTTTGGCATAAAGACTCCT
* * * * * *
4442 TGAAATATTTATATTCATCTAACCAAATCTCAGCCACAATGGACTAAAGGAGTTGTTTTTACAAG
253 TGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* * * * *
4507 CATCTGAATCATGTTTCGATATAATTAGAAATAAATTCGG--AAAATTAGGAACAAGGATATTAG
318 CATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATA-GAAAAACGATATTAG
*
4570 AGGCGTGAAAAACCCTTCAATCTTTTTGG-AGTTGAATTATATATTTTTTCTGAGTATTGTGGCA
382 AAGCGTGAAAAACCCTTCAAT-TTTTTGGCA-TTGAATTATATATTTTTTCTGAGTATTGTGGCA
** * * * * * * *
4634 ATGAACTGAGGAAAAATTTTTCGGGTTGGTTAATGCAAAATTTTAGTCGAAATTGTTTACT---C
445 AAAAATTGAGAAAAAACTTTTC----T-G---AT-C-AGATTTTAGCCGAAATCGTGTACTAACC
* * ** * * * * *
4696 ATCACTGTTTTTGGCTAAAAATGCG-TTCTAAGGCCCCAGCTCAGTTTTGAATGATATTTGTCGT
500 ATCACGGTTTTTGGCT-AAAACGCGTTTC-GGGGCCTC-GCTCAGTTTTGCATGATTTTTGGCAT
* * * * *
4760 AAAGACTGCTTGGAATATCTATATTCATCGAACCAAATCTCAGGCACACTGGATTTAACGATTTG
562 AAAGACT-CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG
*
4825 TTTTTACGAGAATCTGAATC
626 TTTTTACGAGCATCTGAATC
* * *
4845 TTGTTTCGATTTATTTAGAAATTAATTCGGAAAAAAATAGATAAACGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAA
** * * *
4910 ACCCTTCAATCTTTTTGGCATTGAATTATGCA-TTTTTATGAGTATTGTGGCAAAAAAATGAGAA
65 ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-G
* * ** *
4974 AAAAAATTTTC---T-G---AT-C-GGATTTTAG-CTGAAATCGTGTACTAACCATCACGGTTTT
129 AAAAACTTTTCGGGTAGTTTTTGCAAAATTTTAGTC-GAAATCGTTTACT---CATCACGGTTTT
* * * * *
5029 TCGCTAAAAATGTGTT-TCGGGGCCTCGTCTAAGTTTTGCAT-AGTTTTTGGCATAAAGACTCCT
190 TGGCTAAAAACGCGTTCT-GGGGCCTCGTCTCAGTTTTGTATGA-TTTTTGGCATAAAGACTCCT
* * *
5092 TGAAATATTTATATTCATCTAACCAAATCTCAGCCATATTGGATTTAAGGATTTGCTTTTACGAG
253 TGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* * * * *
5157 TATCTGAATCATGTTTCGATATAATTAGAAATAAATTCGGGAAAAAA-GGAAAAACGATATTAGA
318 CATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATAGAAAAACGATATTAGA
* *
5221 GGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAA
383 AGCGTGAAAAACCCTTCAAT-TTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAA
* * * * * * * *
5286 GAATTGAGGAAAAATTTTTCGGGTTTGTTTTTACAAAATATTAGCCGAAATTGTTTACT---CAT
447 AAATTGAGAAAAAACTTTTC-----TG---AT-C-AGATTTTAGCCGAAATCGTGTACTAACCAT
** * ** * * * * * *
5348 CACTATTTTTGGCTAAAAATGCG-TTCTAAGGCCCCAGCTCAATTTTGAATGATATTTGTCGTAA
502 CACGGTTTTTGGCT-AAAACGCGTTTC-GGGGCCTC-GCTCAGTTTTGCATGATTTTTGGCATAA
* * * * *
5412 AGATTGCTTGGAATATCTATATTCATCGAACCAAATCTCAGCCACACTGGATTTAACGATTTGTT
564 AGACT-CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
* *
5477 TTTACGAGAATCTAAATC
628 TTTACGAGCATCTGAATC
* * * *
5495 TTGTTTCGATTTATTTAGAAATTAATTAGGAAAAAAAATAGATAAACGATATTAGAAGCGTGAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAA-GGAAAAACGATATTAGAAGCGTGAAA
5560 AACCCTTCAATCTTTTTGGCATTG
64 AACCCTTCAATCTTTTTGGCATTG
5584 TGAAAAACCC
Statistics
Matches: 3837, Mismatches: 619, Indels: 376
0.79 0.13 0.08
Matches are distributed among these distances:
638 4 0.00
639 80 0.02
640 80 0.02
641 181 0.05
642 73 0.02
643 100 0.03
645 7 0.00
646 67 0.02
647 179 0.05
648 9 0.00
649 242 0.06
650 810 0.21
651 430 0.11
652 243 0.06
653 404 0.11
654 320 0.08
655 39 0.01
656 190 0.05
657 76 0.02
658 59 0.02
659 53 0.01
660 25 0.01
661 120 0.03
662 32 0.01
663 9 0.00
664 5 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (645 bp):
TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAA
CCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAA
AAACTTTTCGGGTAGTTTTTGCAAAATTTTAGTCGAAATCGTTTACTCATCACGGTTTTTGGCTA
AAAACGCGTTCTGGGGCCTCGTCTCAGTTTTGTATGATTTTTGGCATAAAGACTCCTTGAAATAT
CTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
TCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATAGAAAAACGATATTAGAAGCGTGAA
AAACCCTTCAATTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
AAAAACTTTTCTGATCAGATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAC
GCGTTTCGGGGCCTCGCTCAGTTTTGCATGATTTTTGGCATAAAGACTCTTGAAATATCTATATT
CATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
Found at i:3535 original size:322 final size:322
Alignment explanation
Indices: 286--6004 Score: 4719
Period size: 322 Copynumber: 17.4 Consensus size: 322
276 CTAAATCGTG
* * ** *
286 TTGTTTCTATTTAATTAGAAATTAATTCAGAAAATAAATGGAAAATTGATATTATAAGCGTG-AA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAA
* * * * * *
350 AAGCCTTCAATATTTTTGACGTTGAATTATATATTTTTTTTCTAAGTATTTGTGGCAAAAAACTG
65 AACCCTTCAATCTTTTTGGCATTGAATTATATA--TTTTTTCTGAGTA-TTGTGGCAAAAAATTG
* * * * *
415 AGTAAAAATTTTTCGTG-TCAGTTTTTAGCTGAAATCGTGGACTAACCATCACTGTTTTTGGCTA
127 AGAAAAAACTTTTC-TGATCAGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCTA
* * *
479 AAAACGCGTTTCGGGGGACTCGACTCAGTTTTGCATGGTTTTTGGCATACAA-ACTCCTTGAAAT
191 AAAACGCGTTTC-GGGGCCTCGTCTCAGTTTTGCATAGTTTTTGGCATA-AAGACTCCTTGAAAT
* * * * * *
543 ATATATACTCATATAACCAAAACTCAGCCACATTTGATTTAAGAATTTGTTTTTACGAGCATCTG
254 ATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
608 AATC
319 AATC
* * * *
612 TTGTTTCGATTTTATTAGAAA-TAGATTCGAAAAAAAAAT-GAAAAACGATATTGGAAGCATGAA
1 TTGTTTCGATTTAATTAGAAATTA-ATTCG-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAA
* * * *
675 AGACCCTTCAAT-TTTTTAGGCGTTGAATTATATA-CTTTTCTGAGTATTGTGGC-AAAAATTAA
64 AAACCCTTCAATCTTTTT-GGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA
* * * * * * *
737 G-GAAAACTTTTCGATTCTGTTTCTTGCAAAAATTTAGGCCGAAATCGTGTATTAACTATCACGG
128 GAAAAAAC--TT---TTCTG----AT-C-AGATTTTA-GCTGAAATCGTGTACTAACCATCACGG
* * * * * * * * * * **
801 TTTTTGGCTAATAATGCGTTCCGGAGCCAT-GGCTCAATTTTGCCTAATTTTTGCCGTAATTACT
181 TTTTTGGCTAAAAACGCGTTTCGGGGCC-TCGTCTCAGTTTTGCATAGTTTTTGGCATAAAGACT
* * * * * *
865 CATTGAAATATCTATATTCATCGAATCATATCTCAGCCACATTGGATTTAAGGATTTGTCTTTAC
245 CCTTGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
*
930 GAGCATTTGAATC
310 GAGCATCTGAATC
* * *
943 TTGTTTCGATTTAATTAGAAATAAATTCGG-TAAAAATGGAAAAATGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * * *
1007 CCCCTTCAATATTTTTGGCTTTGAATTATATATTTATTCTGAGCATTGTGGCAAAGAATTGAGGA
66 ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GA
* * * * ** * * *
1072 AAAAA-TTTTCGGGTATTATTTTGCAAAATTATAACCAAAATCGTTTACT---TATTACGGTTTT
130 AAAAACTTTTC-----TGA---T-C-AGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTT
* * * * *
1133 TGGCTAAAAACAC-ATTCTGGGGCCCTGGT-TTAGTTTTGCAT-GATTTTTGGCGTAAAGACTCC
185 TGGCTAAAAACGCGTTTC-GGGG-CCTCGTCTCAGTTTTGCATAG-TTTTTGGCATAAAGACTCC
* * * *
1195 TTGAAATATCTATATGTTCATCGAACCAAATC-CAAGTCACATTGGATTTAACGATTTGTTTTTA
247 TTGAAATAT-T-TATATTCATCTAACCAAATCTC-AGCCACATTGGATTTAAGGATTTGTTTTTA
* *
1259 CAAGCATTTGAATC
309 CGAGCATCTGAATC
* * * * *
1273 TTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAAAGGAAAAATGATATTGGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * * * * * *
1338 ATCGTTCATTTTTTTTTGCATTGAATTATATAATTTTTCTGAATATTTTGGCAAAAAATTGAGGA
66 ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAA
* * * * * * ** *
1403 AAAACTTTT-TGGGTAAGTTTTTA-C-AAAAT--TTTAGCCGAAATCGTGTCACGGTTTTTGTCT
131 AAAACTTTTCT-GATCAGATTTTAGCTGAAATCGTGTA--C-TAA-C-CATCACGGTTTTTGGCT
* * * * * * * *
1463 CAAAACGCGTTTCGGAGTCC-CAG-GTAAATTTTGCA-AGATTTTTGTCACAAAAACT-C--GAA
190 AAAAACGCGTTTCGG-GGCCTC-GTCTCAGTTTTGCATAG-TTTTTGGCATAAAGACTCCTTGAA
* * * *
1522 ATATTTTATATTCAT-TGAACCAAATCTCAGGCACATTAGATATAAGGATTTATTTTTACGAGCA
252 ATA-TTTATATTCATCT-AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* *
1586 TCTAAATA
315 TCTGAATC
* *
1594 TTGTTTCGATTTAATTGGAAATTAATT-AGAAAAAATATGGAAAAACGATATTAGAAGCGTG-AA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA-ATGGAAAAACGATATTAGAAGCGTGAAA
* * * * * ** *
1657 AGCCCGTCAATCTTTTTGGCTTTGAATTATATATTTTTTCTAAATATT-TTTCAAACAGATTGAG
65 AACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAA-AAATTGAG
* * * * * * *
1721 -AAAAACTTTTCAGGTAAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTAGCTAAAA
129 AAAAAACTTTTCTGATCAGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
* * * * *
1785 ACGCGTTTTGGGGCATCGTCTCAGTTTTGTATGGTTTTTGGCATAAAGACTCCTTGAAATATCTA
194 ACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATAGTTTTTGGCATAAAGACTCCTTGAAATATTTA
* * * * * * *
1850 TATTCATCTAACCAAATCTCGGTCACATTGGTTTTAAGGATTTATTTTTGCAAGCATCTAAATC
259 TATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
* * * *
1914 TTGTTTCGATTTAATTAGAAATAAATTCGG-TAAAAATGGAAAAACGATATTAAAACCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * *
1978 AACCTTCAAT-TTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTGTGACAAAAAATTGAGAA
66 ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-A
* * * * * *
2042 AAAAACTTTTCGGGTCA-ATTTTTAGCCGAAAATCGTGTACTAACTATCACGATTTTTAGCT-AA
130 AAAAACTTTTCTGATCAGA-TTTTAGCTG-AAATCGTGTACTAACCATCACGGTTTTTGGCTAAA
* * * * * **
2105 AACGAGTTTCGCGGCCTCGTCTCAGTTTTCCTTGGTTTTTCACATAAAGACTCCTTGAAATATCT
193 AACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATAGTTTTTGGCATAAAGACTCCTTGAAATAT-T
* * * *
2170 T-TATTCATCTATCCAAATCTCAGCCACATTGAATTTAAGGATTAGTTTTTAC-ATGCATCAGAA
257 TATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA-GCATCTGAA
2233 TC
321 TC
* * *
2235 TTGTTACGATTTAATTAGAAATTAATTCAGAAAAAATAT-GAAAAACGGTATTAGAAGCGTGAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA-ATGGAAAAACGATATTAGAAGCGTGAAA
* * * * * * *
2299 AGCCTTTTAATTTTTTTGTCATTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGG
65 AACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
* * * *
2364 AAAAAGTTTTCGGGTCAGTTGTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTT
130 AAAAACTTTTCTGATCA------G----ATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTT
* * * * * * ** *
2428 TGGCTAAAAACGCGTTCCGGAG-TTCCATCTCAATTTT-CAATGATTTTTTGGCGCAAAGGCTCC
185 TGGCTAAAAACGCGTTTCGGGGCCT-CGTCTCAGTTTTGC-AT-AGTTTTTGGCATAAAGACTCC
* * * * * *
2491 TGGAAATATTTATATTCATCGAATCAAATCTCAGCCACATTGGATATAAGAACTTGTTTTTACGA
247 TTGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA
*
2556 GCATCCGAATC
312 GCATCTGAATC
* * *
2567 TTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAATGTAAAAAATGATATTGGAAGCGTG-AA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATG-GAAAAACGATATTAGAAGCGTGAAA
* * *
2630 AAGCCTGTCAAT-TTTTTGGCATTGAATTATATATTTTTTCTGAATATT-TTGCGAAAAAA-TGA
65 AACCCT-TCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGA
* * * *
2692 GAAAAAAACTCTTC-GAGTCAGTTTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTA
128 G-AAAAAACTTTTCTGA-TCAGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCTA
* * * *
2756 AAAACGCGTTACGGGGCCCCGACTCAGTTTTGCAT-GATTTTTGGCATAAAGACTCTTTGAAATA
191 AAAACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATAG-TTTTTGGCATAAAGACTCCTTGAAATA
* * * * * *
2820 TTAATATTCATCTAACCAAATATCAGCCACAATGGACTAAAGGATTTGTTTTTACAAGCATCTGA
255 TTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
2885 AT-
320 ATC
* * * *
2887 TATGTTTCAATATAATTAGAAATAAATTCGGAAAAAAA-GGAAAAACGATATTAGAGGCGTGAAA
1 T-TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * * *
2951 AACCCTTCAATCTTTTTGGCGTTGAATTATATATTTGTTCTGAGTATTGTGGCAAAGAATTGAGG
65 AACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
* * * * * *
3016 AAAAATTTTTCGGGTTTGTTTTTGCAAAATTTTAG-TCGAAATTGTTTACT---CATCACTGTTT
130 AAAAACTTTTC-----TG---AT-C-AGATTTTAGCT-GAAATCGTGTACTAACCATCACGGTTT
* ** * ** * * * * * *
3077 TTGGCTAAAAATGCG-TTCTAAGGCCCCAACTCAGTTTTGAAT-GATATTTGTCGTAAAGATTGC
184 TTGGCTAAAAACGCGTTTC-GGGGCCTCGTCTCAGTTTTGCATAG-TTTTTGGCATAAAGACTCC
* * * * * *
3140 TTGGAATATCTATATTCATCGAACTAAATCTCAGCCACACTGGATTTAACGATTTGTTTTTACGA
247 TTGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA
*
3205 GAATCTGAATC
312 GCATCTGAATC
* * *
3216 TTGTTTCGATTTATTTAGAAATTAATTCGGAAAAAAATAGATAAACGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
** * *
3281 ACCCTTCAATCTTTTTGGCATTGAATTATGCA-TTTTTATGAGTATTGTGGCAAAAAAATGAGAA
66 ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-A
* * * *
3345 AAAAAATTTTCTGATCGGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTCGCTAAAGA
130 AAAAACTTTTCTGATCAGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
* * *
3410 TGTGTTTCGGGGCCTCGTCTTAGTTTTGCATAGTTTTTGGCATAAAGACTCCTTGAAATATTTAT
195 CGCGTTTCGGGGCCTCGTCTCAGTTTTGCATAGTTTTTGGCATAAAGACTCCTTGAAATATTTAT
* * *
3475 ATTCATCTAACCAAATCTCAGCCATATTGGATTTAAGGATTTGCTTTTACGAGTATCTGAATC
260 ATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
*
3538 TTGTTTCGATTTAATTAGAAA-TATATTCGG--GAAAATGGAAAAACGATATTAGAAGCGTGAAA
1 TTGTTTCGATTTAATTAGAAATTA-ATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * * * * *
3600 AACCCTTCAATTTTTTTGGCGTTGAATTATATATATTTTTATGAATA-AGTTGCAAACAAATTGA
65 AACCCTTCAATCTTTTTGGCATTGAATTATATAT-TTTTTCTGAGTATTGTGGCAAA-AAATTGA
* * * * * **
3664 GAAAAAACTTTTCAGGTCAGTTTTTAGAC-GAAATCGTGTACTAATCAATCACTGTTTTTTTTCC
128 GAAAAAACTTTTCTGATCAGATTTTAG-CTGAAATCGTGTACTAA-CCATCAC-G--GTTTTTGG
* *
3728 CTAAAAACGCGTTTCGGGGCCTCGTCTCAGTTTTGTATGGTTTTTGGCATAAAGACTCCTTGAAA
188 CTAAAAACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATAGTTTTTGGCATAAAGACTCCTTGAAA
* **
3793 TATCTATATTCATCTAAGAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
253 TATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
*
3858 -AAGTA
318 GAA-TC
* * * *
3863 TTGTTTTGATTTAATT-GAAAACTAATTC-GAAGAAAAACGG-AAAACGATATTAGAAGCATGAA
1 TTGTTTCGATTTAATTAG-AAATTAATTCGGAA-AAAAATGGAAAAACGATATTAGAAGCGTGAA
*
3925 AAACCCTTCAAAT-TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA
64 AAACCCTTC-AATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA
* ** * * * *
3989 GGAAAAACCTTTCGGGTCAGTTTTTGCAAAATTTTAGCTGAAATAGTGTATTAACCATCAAGGTT
128 -GAAAAAACTTT----TC---TGAT-C-AGATTTTAGCTGAAATCGTGTACTAACCATCACGGTT
* * * * * * ** *
4054 TTTGGCTAAAAACCCGGTAT-GGAG-TTCCGACTCAATTTT-CA-ATGATTTTTGGCGCAAAGAA
183 TTTGGCTAAAAACGC-GTTTCGGGGCCT-CGTCTCAGTTTTGCATA-G-TTTTTGGCATAAAGAC
* * * * * *
4115 TAC-TGAATATATATATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGAATTTGTTTTT
244 TCCTTGAA-ATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
*
4179 ACGAGCATCCGAATC
308 ACGAGCATCTGAATC
* ** * *
4194 TTGATTAAATTTAATTATAAATTAATTC-GAAAAAAATGGAAAAAACGATATTGGAAGCGTGAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGG-AAAAACGATATTAGAAGCGTGAAA
* * * *
4258 AGCCATTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAATATT-TTGCGAAAAAATTGAG
65 AACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGAG
* * * * * *
4322 AAAAAACTCTTC-GAGTCAGTTTTTAG-TCGAAATCATATACTAATCAATCACGGTTTTTGACTA
129 AAAAAACTTTTCTGA-TCAGATTTTAGCT-GAAATCGTGTACTAA-CCATCACGGTTTTTGGCTA
* * * * *
4385 AAAACGCGTTACGGGGCCTCGTCTTAGTCTTGTAT-GATTTTTGGCATAAAGACTCTTTGAAATA
191 AAAACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATAG-TTTTTGGCATAAAGACTCCTTGAAATA
* * * * *
4449 TTTATATTCATCTAACCAAATCTCAGCCACAATGGACTAAAGGAGTTGTTTTTACAAGCATCTGA
255 TTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
4514 ATC
320 ATC
* * * ** * * *
4517 ATGTTTCGATATAATTAGAAATAAATTCGGAAAATTA-GGAACAAGGATATTAGAGGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
** * *
4581 ACCCTTCAATCTTTTTGG-AGTTGAATTATATATTTTTTCTGAGTATTGTGGCAATGAACTGAGG
66 ACCCTTCAATCTTTTTGGCA-TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
* * * * *
4645 AAAAATTTTTCGGGTTGGTTAATGCAAAATTTTAG-TCGAAATTGTTTACT---CATCACTGTTT
130 AAAAACTTTTC----T-G---AT-C-AGATTTTAGCT-GAAATCGTGTACTAACCATCACGGTTT
* ** * * * * * *
4706 TTGGCTAAAAATGCG-TTCTAAGGCCCCAG-CTCAGTTTTGAAT-GATATTTGTCGTAAAGACTG
184 TTGGCTAAAAACGCGTTTC-GGGGCCTC-GTCTCAGTTTTGCATAG-TTTTTGGCATAAAGACTC
* * * * * *
4768 CTTGGAATATCTATATTCATCGAACCAAATCTCAGGCACACTGGATTTAACGATTTGTTTTTACG
246 CTTGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
*
4833 AGAATCTGAATC
311 AGCATCTGAATC
* * *
4845 TTGTTTCGATTTATTTAGAAATTAATTCGGAAAAAAATAGATAAACGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
** * *
4910 ACCCTTCAATCTTTTTGGCATTGAATTATGCA-TTTTTATGAGTATTGTGGCAAAAAAATGAGAA
66 ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-A
* * *
4974 AAAAAATTTTCTGATCGGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTCGCTAAAAA
130 AAAAACTTTTCTGATCAGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
* * *
5039 TGTGTTTCGGGGCCTCGTCTAAGTTTTGCATAGTTTTTGGCATAAAGACTCCTTGAAATATTTAT
195 CGCGTTTCGGGGCCTCGTCTCAGTTTTGCATAGTTTTTGGCATAAAGACTCCTTGAAATATTTAT
* * *
5104 ATTCATCTAACCAAATCTCAGCCATATTGGATTTAAGGATTTGCTTTTACGAGTATCTGAATC
260 ATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
* * * * *
5167 ATGTTTCGATATAATTAGAAATAAATTCGGGAAAAAA-GGAAAAACGATATTAGAGGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * *
5231 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAGAATTGAGGA
66 ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAA
* * * * * * * **
5296 AAAATTTTTCGGGTTTGTTTTTACAAAATATTAGCCGAAATTGTTTACT---CATCACTATTTTT
131 AAAACTTTTC-----TG---AT-C-AGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTT
* ** * * * * * * * *
5358 GGCTAAAAATGCG-TTCTAAGGCCCCAG-CTCAATTTTGAAT-GATATTTGTCGTAAAGATTGCT
186 GGCTAAAAACGCGTTTC-GGGGCCTC-GTCTCAGTTTTGCATAG-TTTTTGGCATAAAGACTCCT
* * * * *
5420 TGGAATATCTATATTCATCGAACCAAATCTCAGCCACACTGGATTTAACGATTTGTTTTTACGAG
248 TGAAATATTTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* *
5485 AATCTAAATC
313 CATCTGAATC
* * * *
5495 TTGTTTCGATTTATTTAGAAATTAATTAGGAAAAAAAATAGATAAACGATATTAGAAGCGTGAAA
1 TTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
5560 AACCCTTCAATCTTTTTGGCATTGTGAAAAACCCTTCAATCTTTTTGGCATTGAATTATGCGTTT
65 AACCCTTCAATCTTTTTGGCA-T-TG-----------AA-----TT---A-T--A-TAT---TTT
* *
5625 TTATGAGTATTGTGGCAAAAAA-TGAGAAAACAA-TTTTCTGATCGGATTTTAGCTGAAATCGTG
102 TTCTGAGTATTGTGGCAAAAAATTGAGAAAA-AACTTTTCTGATCAGATTTTAGCTGAAATCGTG
* * * * *
5688 TACTAACCATCACGGTTTTTCGCTAAAAATGTGTTTCGGGGCCTCATCTAAGTTTTGCATAGTTT
166 TACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGTCTCAGTTTTGCATAGTTT
*
5753 TTGACATAAAGACTCCTTGAAATATATTCGAGAAAATGGAATATTTATATTCATCTAACCAAATC
231 TTGGCATAAAGACTCC----------TT---G---A---AATATTTATATTCATCTAACCAAATC
* * * * *
5818 TCAGCCACAATGGACTAAAGGATTTGTTTTTACAAGTATCTGAATC
277 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
* * * *
5864 ATGTTTCGATATAATTAGAAATAAATTCGGGAAAAAAA-GGAAAAACGATATTAGAGGCGTGAAA
1 TTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * * *
5928 TACCCTTCAATCTTTTTGGCCTTGATTTATATATTTTTTTCTGAGTATTGTGGCAAAGAATTGAG
65 AACCCTTCAATCTTTTTGGCATTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGAG
*
5993 GAAAAACTTTTC
129 AAAAAACTTTTC
6005 GGGTTTGTTT
Statistics
Matches: 4349, Mismatches: 756, Indels: 560
0.77 0.13 0.10
Matches are distributed among these distances:
317 7 0.00
318 49 0.01
319 133 0.03
320 251 0.06
321 587 0.13
322 593 0.14
323 210 0.05
324 23 0.01
325 243 0.06
326 130 0.03
327 26 0.01
328 559 0.13
329 145 0.03
330 222 0.05
331 530 0.12
332 291 0.07
333 6 0.00
334 11 0.00
335 20 0.00
341 25 0.01
342 12 0.00
343 4 0.00
344 2 0.00
346 1 0.00
347 19 0.00
348 3 0.00
349 1 0.00
350 53 0.01
351 5 0.00
352 3 0.00
354 1 0.00
355 4 0.00
357 12 0.00
358 25 0.01
360 2 0.00
363 1 0.00
366 2 0.00
367 1 0.00
368 42 0.01
369 93 0.02
370 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (322 bp):
TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAA
AAAACTTTTCTGATCAGATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
GCGTTTCGGGGCCTCGTCTCAGTTTTGCATAGTTTTTGGCATAAAGACTCCTTGAAATATTTATA
TTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
Found at i:5586 original size:29 final size:29
Alignment explanation
Indices: 5554--5612 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5544 TATTAGAAGC
5554 GTGAAAAACCCTTCAATCTTTTTGGCATT
1 GTGAAAAACCCTTCAATCTTTTTGGCATT
5583 GTGAAAAACCCTTCAATCTTTTTGGCATT
1 GTGAAAAACCCTTCAATCTTTTTGGCATT
5612 G
1 G
5613 AATTATGCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (29 bp):
GTGAAAAACCCTTCAATCTTTTTGGCATT
Done.