Multiple sequence alignment - TraesCS1A01G078000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G078000 chr1A 100.000 2477 0 0 1 2477 60807187 60809663 0.000000e+00 4575
1 TraesCS1A01G078000 chr1A 100.000 359 0 0 2810 3168 60809996 60810354 0.000000e+00 664
2 TraesCS1A01G078000 chr1D 87.793 1917 136 53 568 2462 62767252 62769092 0.000000e+00 2154
3 TraesCS1A01G078000 chr1D 82.862 566 45 22 1 528 62766692 62767243 8.010000e-126 460
4 TraesCS1A01G078000 chr1B 87.591 1781 145 44 548 2294 100036628 100038366 0.000000e+00 1995
5 TraesCS1A01G078000 chr5B 76.014 838 176 18 1336 2165 45242000 45242820 8.180000e-111 411
6 TraesCS1A01G078000 chr5A 75.534 842 180 18 1332 2165 36020931 36021754 1.070000e-104 390
7 TraesCS1A01G078000 chr5A 75.060 838 184 20 1336 2165 36166423 36167243 1.800000e-97 366
8 TraesCS1A01G078000 chr5A 74.940 838 185 20 1336 2165 36076082 36076902 8.350000e-96 361
9 TraesCS1A01G078000 chr5A 74.702 838 187 20 1336 2165 36049309 36050129 1.810000e-92 350
10 TraesCS1A01G078000 chr5A 74.762 840 183 23 1336 2165 36195456 36196276 1.810000e-92 350
11 TraesCS1A01G078000 chr5A 77.778 378 82 2 1336 1712 36104243 36104619 6.830000e-57 231
12 TraesCS1A01G078000 chr5A 77.570 321 70 2 1336 1655 36132772 36133091 3.220000e-45 193
13 TraesCS1A01G078000 chr5A 76.735 245 44 12 1926 2165 36104644 36104880 1.190000e-24 124
14 TraesCS1A01G078000 chr5A 81.513 119 22 0 1336 1454 36034890 36035008 7.230000e-17 99


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G078000 chr1A 60807187 60810354 3167 False 2619.5 4575 100.0000 1 3168 2 chr1A.!!$F1 3167
1 TraesCS1A01G078000 chr1D 62766692 62769092 2400 False 1307.0 2154 85.3275 1 2462 2 chr1D.!!$F1 2461
2 TraesCS1A01G078000 chr1B 100036628 100038366 1738 False 1995.0 1995 87.5910 548 2294 1 chr1B.!!$F1 1746
3 TraesCS1A01G078000 chr5B 45242000 45242820 820 False 411.0 411 76.0140 1336 2165 1 chr5B.!!$F1 829
4 TraesCS1A01G078000 chr5A 36020931 36021754 823 False 390.0 390 75.5340 1332 2165 1 chr5A.!!$F1 833
5 TraesCS1A01G078000 chr5A 36166423 36167243 820 False 366.0 366 75.0600 1336 2165 1 chr5A.!!$F6 829
6 TraesCS1A01G078000 chr5A 36076082 36076902 820 False 361.0 361 74.9400 1336 2165 1 chr5A.!!$F4 829
7 TraesCS1A01G078000 chr5A 36049309 36050129 820 False 350.0 350 74.7020 1336 2165 1 chr5A.!!$F3 829
8 TraesCS1A01G078000 chr5A 36195456 36196276 820 False 350.0 350 74.7620 1336 2165 1 chr5A.!!$F7 829

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
489 530 0.732571 TTGAGAATCGGCAAATCGGC 59.267 50.0 0.0 0.0 38.61 5.54 F
1819 1921 0.034670 ACATTGAGGAGCAGAAGGGC 60.035 55.0 0.0 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1951 0.179192 CCATGTCGCGGATGTTGTTG 60.179 55.000 6.13 0.0 0.0 3.33 R
3124 3242 2.682856 TGCTGACTTTTGACCAGTTGAC 59.317 45.455 0.00 0.0 0.0 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 132 7.784633 AAAATGTTCATTTGTTGGAATTCGT 57.215 28.000 10.84 0.00 0.00 3.85
118 138 7.331934 TGTTCATTTGTTGGAATTCGTGAAAAA 59.668 29.630 0.00 0.00 0.00 1.94
119 139 7.227992 TCATTTGTTGGAATTCGTGAAAAAC 57.772 32.000 0.00 0.00 0.00 2.43
121 141 7.493971 TCATTTGTTGGAATTCGTGAAAAACAT 59.506 29.630 0.00 0.00 0.00 2.71
152 172 8.836268 ATTCATGAACATTTGTTTGCATTAGT 57.164 26.923 11.07 0.00 38.56 2.24
154 174 7.432059 TCATGAACATTTGTTTGCATTAGTGA 58.568 30.769 0.00 0.00 38.56 3.41
260 280 8.722480 AAAAGAAATGAAAAGAAACAAGGGAG 57.278 30.769 0.00 0.00 0.00 4.30
261 281 5.847304 AGAAATGAAAAGAAACAAGGGAGC 58.153 37.500 0.00 0.00 0.00 4.70
262 282 4.607293 AATGAAAAGAAACAAGGGAGCC 57.393 40.909 0.00 0.00 0.00 4.70
263 283 2.316108 TGAAAAGAAACAAGGGAGCCC 58.684 47.619 0.00 0.00 0.00 5.19
264 284 1.618837 GAAAAGAAACAAGGGAGCCCC 59.381 52.381 0.91 2.16 45.90 5.80
322 363 1.962144 CACCTTTCCCAGCAAGCAG 59.038 57.895 0.00 0.00 0.00 4.24
346 387 2.744377 GAATAGGAGCTCCCCCGC 59.256 66.667 29.54 13.02 36.42 6.13
348 389 3.751049 AATAGGAGCTCCCCCGCGA 62.751 63.158 29.54 8.27 36.42 5.87
358 399 2.668212 CCCCGCGAGTGCTCAAAA 60.668 61.111 8.23 0.00 39.65 2.44
389 430 2.880890 ACGACTGCAAGAAAGCTTTGAT 59.119 40.909 18.30 1.58 37.43 2.57
421 462 2.141535 TTTTTCGGACGGCATTTTGG 57.858 45.000 0.00 0.00 0.00 3.28
425 466 1.211709 CGGACGGCATTTTGGAACC 59.788 57.895 0.00 0.00 0.00 3.62
434 475 3.243602 GGCATTTTGGAACCAGTAACGTT 60.244 43.478 5.88 5.88 0.00 3.99
447 488 7.972832 ACCAGTAACGTTCAATTCAGATTAA 57.027 32.000 2.82 0.00 0.00 1.40
462 503 9.790344 AATTCAGATTAATAAGATGTGAGGGAG 57.210 33.333 0.00 0.00 29.87 4.30
463 504 8.553085 TTCAGATTAATAAGATGTGAGGGAGA 57.447 34.615 0.00 0.00 29.87 3.71
470 511 6.838401 ATAAGATGTGAGGGAGAGGAAAAT 57.162 37.500 0.00 0.00 0.00 1.82
472 513 4.853007 AGATGTGAGGGAGAGGAAAATTG 58.147 43.478 0.00 0.00 0.00 2.32
473 514 4.537688 AGATGTGAGGGAGAGGAAAATTGA 59.462 41.667 0.00 0.00 0.00 2.57
477 518 5.014544 TGTGAGGGAGAGGAAAATTGAGAAT 59.985 40.000 0.00 0.00 0.00 2.40
479 520 4.775236 AGGGAGAGGAAAATTGAGAATCG 58.225 43.478 0.00 0.00 38.61 3.34
487 528 4.500477 GGAAAATTGAGAATCGGCAAATCG 59.500 41.667 0.00 0.00 38.61 3.34
489 530 0.732571 TTGAGAATCGGCAAATCGGC 59.267 50.000 0.00 0.00 38.61 5.54
516 558 5.704217 TTTTGATTACAAAACGGTGCAAC 57.296 34.783 0.00 0.00 46.60 4.17
531 573 4.133856 GTGCAACCGTGATCTATTATGC 57.866 45.455 0.00 0.47 0.00 3.14
532 574 3.559655 GTGCAACCGTGATCTATTATGCA 59.440 43.478 10.55 10.55 39.95 3.96
533 575 3.809279 TGCAACCGTGATCTATTATGCAG 59.191 43.478 10.55 0.00 37.61 4.41
534 576 3.187227 GCAACCGTGATCTATTATGCAGG 59.813 47.826 0.00 0.00 33.00 4.85
536 578 2.368548 ACCGTGATCTATTATGCAGGCA 59.631 45.455 0.00 0.00 0.00 4.75
537 579 2.738846 CCGTGATCTATTATGCAGGCAC 59.261 50.000 0.00 0.00 0.00 5.01
538 580 3.392882 CGTGATCTATTATGCAGGCACA 58.607 45.455 0.00 0.00 0.00 4.57
539 581 3.809279 CGTGATCTATTATGCAGGCACAA 59.191 43.478 0.00 0.00 0.00 3.33
540 582 4.084171 CGTGATCTATTATGCAGGCACAAG 60.084 45.833 0.00 0.00 0.00 3.16
541 583 4.214971 GTGATCTATTATGCAGGCACAAGG 59.785 45.833 0.00 0.00 0.00 3.61
542 584 4.102996 TGATCTATTATGCAGGCACAAGGA 59.897 41.667 0.00 0.00 0.00 3.36
543 585 4.502105 TCTATTATGCAGGCACAAGGAA 57.498 40.909 0.00 0.00 0.00 3.36
544 586 4.854173 TCTATTATGCAGGCACAAGGAAA 58.146 39.130 0.00 0.00 0.00 3.13
545 587 5.448654 TCTATTATGCAGGCACAAGGAAAT 58.551 37.500 0.00 0.00 0.00 2.17
546 588 4.660789 ATTATGCAGGCACAAGGAAATC 57.339 40.909 0.00 0.00 0.00 2.17
588 632 6.796552 CGCGTACGTTGACCAATAGTATATTA 59.203 38.462 17.90 0.00 33.53 0.98
589 633 7.482743 CGCGTACGTTGACCAATAGTATATTAT 59.517 37.037 17.90 0.00 33.53 1.28
590 634 9.773328 GCGTACGTTGACCAATAGTATATTATA 57.227 33.333 17.90 0.00 0.00 0.98
661 709 6.381420 AGAGATTAAGCTAAGCTAGTTGTGGA 59.619 38.462 0.00 0.00 38.25 4.02
672 720 1.725625 GTTGTGGATGTGTTGCGCG 60.726 57.895 0.00 0.00 0.00 6.86
723 771 2.101415 TCTGGCATCGACTGTATCCAAG 59.899 50.000 0.00 0.00 0.00 3.61
729 777 2.959516 TCGACTGTATCCAAGCAGTTG 58.040 47.619 5.77 5.77 44.89 3.16
783 831 1.303799 CGACAAGCAGCAGCAGGATT 61.304 55.000 3.17 0.00 45.49 3.01
798 846 2.086869 AGGATTGACAATTGCGTCAGG 58.913 47.619 5.05 0.00 46.14 3.86
799 847 1.812571 GGATTGACAATTGCGTCAGGT 59.187 47.619 5.05 0.00 46.14 4.00
800 848 2.414559 GGATTGACAATTGCGTCAGGTG 60.415 50.000 5.05 0.00 46.14 4.00
801 849 1.674359 TTGACAATTGCGTCAGGTGT 58.326 45.000 5.05 0.00 46.14 4.16
830 878 2.663188 GCTATCGAAGCCCAGCGG 60.663 66.667 7.98 0.00 46.25 5.52
898 946 1.321743 GTGATCAACGTCGTGATGAGC 59.678 52.381 7.45 10.62 38.38 4.26
902 956 0.987715 CAACGTCGTGATGAGCTGAG 59.012 55.000 0.00 0.00 0.00 3.35
919 973 4.578516 AGCTGAGCTCTATATATACCGCTG 59.421 45.833 16.19 4.59 30.62 5.18
935 990 1.751351 CGCTGGATCTCAACCTCACTA 59.249 52.381 0.00 0.00 0.00 2.74
941 996 3.181495 GGATCTCAACCTCACTAGACACG 60.181 52.174 0.00 0.00 0.00 4.49
946 1001 1.037493 ACCTCACTAGACACGCACAA 58.963 50.000 0.00 0.00 0.00 3.33
971 1050 5.009010 ACACACAACAATCCATCTTCAGTTC 59.991 40.000 0.00 0.00 0.00 3.01
1064 1143 3.546397 GTCGCTCGCCTTCTTCGC 61.546 66.667 0.00 0.00 0.00 4.70
1150 1232 3.421844 GTTAAGAAGGAAGTGGCCATGT 58.578 45.455 9.72 0.00 0.00 3.21
1155 1237 0.257039 AGGAAGTGGCCATGTCCATC 59.743 55.000 29.63 12.67 38.57 3.51
1200 1282 1.446272 CCTCGTCCGGTTGCTCTTC 60.446 63.158 0.00 0.00 0.00 2.87
1227 1309 0.526954 GCTGGGTCCACGTACGTATG 60.527 60.000 22.34 15.26 0.00 2.39
1228 1310 0.526954 CTGGGTCCACGTACGTATGC 60.527 60.000 22.34 13.04 0.00 3.14
1229 1311 1.249469 TGGGTCCACGTACGTATGCA 61.249 55.000 22.34 6.24 0.00 3.96
1230 1312 0.103572 GGGTCCACGTACGTATGCAT 59.896 55.000 22.34 3.79 0.00 3.96
1231 1313 1.337703 GGGTCCACGTACGTATGCATA 59.662 52.381 22.34 1.16 0.00 3.14
1232 1314 2.223782 GGGTCCACGTACGTATGCATAA 60.224 50.000 22.34 0.00 0.00 1.90
1233 1315 3.047796 GGTCCACGTACGTATGCATAAG 58.952 50.000 22.34 16.80 0.00 1.73
1234 1316 2.470257 GTCCACGTACGTATGCATAAGC 59.530 50.000 22.34 2.14 42.57 3.09
1303 1402 4.270325 CAGATGTATCTATCCATGCATGCG 59.730 45.833 21.69 14.24 34.85 4.73
1313 1412 1.483316 CATGCATGCGCTTGGTATTG 58.517 50.000 22.96 2.62 39.12 1.90
1318 1417 2.536803 GCATGCGCTTGGTATTGATTTG 59.463 45.455 22.96 0.00 34.30 2.32
1319 1418 2.276472 TGCGCTTGGTATTGATTTGC 57.724 45.000 9.73 0.00 0.00 3.68
1320 1419 1.818060 TGCGCTTGGTATTGATTTGCT 59.182 42.857 9.73 0.00 0.00 3.91
1322 1421 2.187707 CGCTTGGTATTGATTTGCTGC 58.812 47.619 0.00 0.00 0.00 5.25
1323 1422 2.187707 GCTTGGTATTGATTTGCTGCG 58.812 47.619 0.00 0.00 0.00 5.18
1324 1423 2.415893 GCTTGGTATTGATTTGCTGCGT 60.416 45.455 0.00 0.00 0.00 5.24
1325 1424 3.181501 GCTTGGTATTGATTTGCTGCGTA 60.182 43.478 0.00 0.00 0.00 4.42
1373 1475 2.482142 GGATCGGTGCTCTTAGACAAGG 60.482 54.545 0.00 0.00 32.22 3.61
1407 1509 2.504244 CACGGAGAAGGACGCGAC 60.504 66.667 15.93 6.56 0.00 5.19
1423 1525 2.079049 GACGAACAACATCGGCCTC 58.921 57.895 0.00 0.00 45.14 4.70
1501 1603 2.579787 GACATCGTCGTCCTGGCG 60.580 66.667 4.48 4.48 0.00 5.69
1633 1735 2.162681 CCATCCACCTTCAACTTCACC 58.837 52.381 0.00 0.00 0.00 4.02
1697 1799 4.710167 TCGTCGTCCTCTCCGGCA 62.710 66.667 0.00 0.00 0.00 5.69
1699 1801 4.131088 GTCGTCCTCTCCGGCACC 62.131 72.222 0.00 0.00 0.00 5.01
1785 1887 1.680522 ATCAGCGCCAGGTACCAGAG 61.681 60.000 15.94 8.01 0.00 3.35
1789 1891 2.904131 GCCAGGTACCAGAGAGCC 59.096 66.667 15.94 0.00 0.00 4.70
1794 1896 2.787567 GGTACCAGAGAGCCCTCGC 61.788 68.421 7.15 0.00 44.08 5.03
1817 1919 1.093159 GCACATTGAGGAGCAGAAGG 58.907 55.000 0.00 0.00 0.00 3.46
1818 1920 1.747709 CACATTGAGGAGCAGAAGGG 58.252 55.000 0.00 0.00 0.00 3.95
1819 1921 0.034670 ACATTGAGGAGCAGAAGGGC 60.035 55.000 0.00 0.00 0.00 5.19
1821 1923 1.557269 ATTGAGGAGCAGAAGGGCGT 61.557 55.000 0.00 0.00 39.27 5.68
1827 1929 3.741476 GCAGAAGGGCGTGCAAGG 61.741 66.667 0.79 0.00 39.62 3.61
1828 1930 3.058160 CAGAAGGGCGTGCAAGGG 61.058 66.667 0.79 0.00 0.00 3.95
2180 2285 0.042188 CAACTGAAACTGCCACGACG 60.042 55.000 0.00 0.00 0.00 5.12
2184 2289 0.102663 TGAAACTGCCACGACGTACA 59.897 50.000 0.00 1.00 0.00 2.90
2185 2290 0.505655 GAAACTGCCACGACGTACAC 59.494 55.000 0.00 0.00 0.00 2.90
2233 2338 7.850982 CAGCGTATAGTAATGGTTTGAATTCAC 59.149 37.037 7.89 0.00 0.00 3.18
2319 2427 7.719633 TGATTTATAAAAGGATGTGGCTAGGTC 59.280 37.037 1.21 0.00 0.00 3.85
2320 2428 6.824958 TTATAAAAGGATGTGGCTAGGTCT 57.175 37.500 0.00 0.00 0.00 3.85
2321 2429 3.636153 AAAAGGATGTGGCTAGGTCTC 57.364 47.619 0.00 0.00 0.00 3.36
2322 2430 1.115467 AAGGATGTGGCTAGGTCTCG 58.885 55.000 0.00 0.00 0.00 4.04
2323 2431 0.757188 AGGATGTGGCTAGGTCTCGG 60.757 60.000 0.00 0.00 0.00 4.63
2324 2432 1.043673 GGATGTGGCTAGGTCTCGGT 61.044 60.000 0.00 0.00 0.00 4.69
2325 2433 0.386113 GATGTGGCTAGGTCTCGGTC 59.614 60.000 0.00 0.00 0.00 4.79
2326 2434 0.033011 ATGTGGCTAGGTCTCGGTCT 60.033 55.000 0.00 0.00 0.00 3.85
2327 2435 0.622136 TGTGGCTAGGTCTCGGTCTA 59.378 55.000 0.00 0.00 0.00 2.59
2328 2436 1.023502 GTGGCTAGGTCTCGGTCTAC 58.976 60.000 0.00 0.00 0.00 2.59
2329 2437 0.917533 TGGCTAGGTCTCGGTCTACT 59.082 55.000 0.00 0.00 0.00 2.57
2330 2438 1.310904 GGCTAGGTCTCGGTCTACTG 58.689 60.000 0.00 0.00 0.00 2.74
2331 2439 1.134159 GGCTAGGTCTCGGTCTACTGA 60.134 57.143 0.00 0.00 0.00 3.41
2332 2440 2.641305 GCTAGGTCTCGGTCTACTGAA 58.359 52.381 0.00 0.00 0.00 3.02
2333 2441 3.015327 GCTAGGTCTCGGTCTACTGAAA 58.985 50.000 0.00 0.00 0.00 2.69
2334 2442 3.181498 GCTAGGTCTCGGTCTACTGAAAC 60.181 52.174 0.00 0.00 0.00 2.78
2335 2443 2.872732 AGGTCTCGGTCTACTGAAACA 58.127 47.619 0.00 0.00 0.00 2.83
2336 2444 3.432378 AGGTCTCGGTCTACTGAAACAT 58.568 45.455 0.00 0.00 0.00 2.71
2337 2445 4.597004 AGGTCTCGGTCTACTGAAACATA 58.403 43.478 0.00 0.00 0.00 2.29
2338 2446 5.014858 AGGTCTCGGTCTACTGAAACATAA 58.985 41.667 0.00 0.00 0.00 1.90
2339 2447 5.100943 GGTCTCGGTCTACTGAAACATAAC 58.899 45.833 0.00 0.00 0.00 1.89
2340 2448 5.100943 GTCTCGGTCTACTGAAACATAACC 58.899 45.833 0.00 0.00 0.00 2.85
2341 2449 4.768448 TCTCGGTCTACTGAAACATAACCA 59.232 41.667 0.00 0.00 0.00 3.67
2342 2450 5.244402 TCTCGGTCTACTGAAACATAACCAA 59.756 40.000 0.00 0.00 0.00 3.67
2343 2451 5.856156 TCGGTCTACTGAAACATAACCAAA 58.144 37.500 0.00 0.00 0.00 3.28
2345 2453 6.370442 TCGGTCTACTGAAACATAACCAAATG 59.630 38.462 0.00 0.00 0.00 2.32
2349 2457 8.230486 GTCTACTGAAACATAACCAAATGTCAG 58.770 37.037 0.00 0.00 39.16 3.51
2354 2462 7.199766 TGAAACATAACCAAATGTCAGTCAAC 58.800 34.615 0.00 0.00 39.16 3.18
2453 2571 2.299013 TGAGCCATAACGAAGTGTCAGT 59.701 45.455 0.00 0.00 45.00 3.41
2458 2576 4.091509 GCCATAACGAAGTGTCAGTAACTG 59.908 45.833 0.00 0.00 45.00 3.16
2468 2586 5.122512 GTGTCAGTAACTGAGACTTAGCA 57.877 43.478 0.00 0.00 46.70 3.49
2469 2587 5.529791 GTGTCAGTAACTGAGACTTAGCAA 58.470 41.667 0.00 0.00 46.70 3.91
2470 2588 5.983720 GTGTCAGTAACTGAGACTTAGCAAA 59.016 40.000 0.00 0.00 46.70 3.68
2471 2589 6.479001 GTGTCAGTAACTGAGACTTAGCAAAA 59.521 38.462 0.00 0.00 46.70 2.44
2472 2590 6.479001 TGTCAGTAACTGAGACTTAGCAAAAC 59.521 38.462 0.00 0.00 41.46 2.43
2473 2591 6.702282 GTCAGTAACTGAGACTTAGCAAAACT 59.298 38.462 0.00 0.00 41.46 2.66
2474 2592 6.701841 TCAGTAACTGAGACTTAGCAAAACTG 59.298 38.462 10.27 10.27 35.39 3.16
2475 2593 6.480320 CAGTAACTGAGACTTAGCAAAACTGT 59.520 38.462 0.00 0.00 32.44 3.55
2476 2594 7.011482 CAGTAACTGAGACTTAGCAAAACTGTT 59.989 37.037 0.00 0.00 32.44 3.16
2842 2960 7.900782 TCTATTTGTTTCTCTCCGTTTTAGG 57.099 36.000 0.00 0.00 0.00 2.69
2843 2961 7.447594 TCTATTTGTTTCTCTCCGTTTTAGGT 58.552 34.615 0.00 0.00 0.00 3.08
2844 2962 8.587608 TCTATTTGTTTCTCTCCGTTTTAGGTA 58.412 33.333 0.00 0.00 0.00 3.08
2845 2963 7.668525 ATTTGTTTCTCTCCGTTTTAGGTAG 57.331 36.000 0.00 0.00 0.00 3.18
2846 2964 5.143376 TGTTTCTCTCCGTTTTAGGTAGG 57.857 43.478 0.00 0.00 0.00 3.18
2847 2965 4.590222 TGTTTCTCTCCGTTTTAGGTAGGT 59.410 41.667 0.00 0.00 0.00 3.08
2848 2966 5.070847 TGTTTCTCTCCGTTTTAGGTAGGTT 59.929 40.000 0.00 0.00 0.00 3.50
2849 2967 5.813513 TTCTCTCCGTTTTAGGTAGGTTT 57.186 39.130 0.00 0.00 0.00 3.27
2850 2968 5.813513 TCTCTCCGTTTTAGGTAGGTTTT 57.186 39.130 0.00 0.00 0.00 2.43
2851 2969 5.544650 TCTCTCCGTTTTAGGTAGGTTTTG 58.455 41.667 0.00 0.00 0.00 2.44
2852 2970 4.644498 TCTCCGTTTTAGGTAGGTTTTGG 58.356 43.478 0.00 0.00 0.00 3.28
2853 2971 4.102996 TCTCCGTTTTAGGTAGGTTTTGGT 59.897 41.667 0.00 0.00 0.00 3.67
2854 2972 4.388485 TCCGTTTTAGGTAGGTTTTGGTC 58.612 43.478 0.00 0.00 0.00 4.02
2855 2973 4.102996 TCCGTTTTAGGTAGGTTTTGGTCT 59.897 41.667 0.00 0.00 0.00 3.85
2856 2974 5.306678 TCCGTTTTAGGTAGGTTTTGGTCTA 59.693 40.000 0.00 0.00 0.00 2.59
2857 2975 6.013466 TCCGTTTTAGGTAGGTTTTGGTCTAT 60.013 38.462 0.00 0.00 0.00 1.98
2858 2976 6.656270 CCGTTTTAGGTAGGTTTTGGTCTATT 59.344 38.462 0.00 0.00 0.00 1.73
2859 2977 7.148356 CCGTTTTAGGTAGGTTTTGGTCTATTC 60.148 40.741 0.00 0.00 0.00 1.75
2860 2978 7.148356 CGTTTTAGGTAGGTTTTGGTCTATTCC 60.148 40.741 0.00 0.00 0.00 3.01
2861 2979 4.482952 AGGTAGGTTTTGGTCTATTCCG 57.517 45.455 0.00 0.00 0.00 4.30
2862 2980 3.842436 AGGTAGGTTTTGGTCTATTCCGT 59.158 43.478 0.00 0.00 0.00 4.69
2863 2981 4.287845 AGGTAGGTTTTGGTCTATTCCGTT 59.712 41.667 0.00 0.00 0.00 4.44
2864 2982 5.005740 GGTAGGTTTTGGTCTATTCCGTTT 58.994 41.667 0.00 0.00 0.00 3.60
2865 2983 5.474532 GGTAGGTTTTGGTCTATTCCGTTTT 59.525 40.000 0.00 0.00 0.00 2.43
2866 2984 5.700722 AGGTTTTGGTCTATTCCGTTTTC 57.299 39.130 0.00 0.00 0.00 2.29
2867 2985 5.382616 AGGTTTTGGTCTATTCCGTTTTCT 58.617 37.500 0.00 0.00 0.00 2.52
2868 2986 5.831525 AGGTTTTGGTCTATTCCGTTTTCTT 59.168 36.000 0.00 0.00 0.00 2.52
2869 2987 6.322969 AGGTTTTGGTCTATTCCGTTTTCTTT 59.677 34.615 0.00 0.00 0.00 2.52
2870 2988 6.982141 GGTTTTGGTCTATTCCGTTTTCTTTT 59.018 34.615 0.00 0.00 0.00 2.27
2871 2989 7.493320 GGTTTTGGTCTATTCCGTTTTCTTTTT 59.507 33.333 0.00 0.00 0.00 1.94
2872 2990 9.518906 GTTTTGGTCTATTCCGTTTTCTTTTTA 57.481 29.630 0.00 0.00 0.00 1.52
2873 2991 9.518906 TTTTGGTCTATTCCGTTTTCTTTTTAC 57.481 29.630 0.00 0.00 0.00 2.01
2874 2992 8.454570 TTGGTCTATTCCGTTTTCTTTTTACT 57.545 30.769 0.00 0.00 0.00 2.24
2875 2993 8.454570 TGGTCTATTCCGTTTTCTTTTTACTT 57.545 30.769 0.00 0.00 0.00 2.24
2876 2994 8.905850 TGGTCTATTCCGTTTTCTTTTTACTTT 58.094 29.630 0.00 0.00 0.00 2.66
2877 2995 9.740239 GGTCTATTCCGTTTTCTTTTTACTTTT 57.260 29.630 0.00 0.00 0.00 2.27
2879 2997 9.955208 TCTATTCCGTTTTCTTTTTACTTTTCC 57.045 29.630 0.00 0.00 0.00 3.13
2880 2998 9.961265 CTATTCCGTTTTCTTTTTACTTTTCCT 57.039 29.630 0.00 0.00 0.00 3.36
2882 3000 9.661563 ATTCCGTTTTCTTTTTACTTTTCCTTT 57.338 25.926 0.00 0.00 0.00 3.11
2883 3001 9.491675 TTCCGTTTTCTTTTTACTTTTCCTTTT 57.508 25.926 0.00 0.00 0.00 2.27
2884 3002 9.142515 TCCGTTTTCTTTTTACTTTTCCTTTTC 57.857 29.630 0.00 0.00 0.00 2.29
2885 3003 9.146984 CCGTTTTCTTTTTACTTTTCCTTTTCT 57.853 29.630 0.00 0.00 0.00 2.52
2948 3066 5.826866 CGTCAAACACGTGAACTTTTTAG 57.173 39.130 25.01 7.04 44.07 1.85
2949 3067 5.552807 CGTCAAACACGTGAACTTTTTAGA 58.447 37.500 25.01 9.07 44.07 2.10
2950 3068 6.016718 CGTCAAACACGTGAACTTTTTAGAA 58.983 36.000 25.01 0.00 44.07 2.10
2951 3069 6.685403 CGTCAAACACGTGAACTTTTTAGAAT 59.315 34.615 25.01 0.00 44.07 2.40
2952 3070 7.217447 CGTCAAACACGTGAACTTTTTAGAATT 59.783 33.333 25.01 0.00 44.07 2.17
2953 3071 8.521059 GTCAAACACGTGAACTTTTTAGAATTC 58.479 33.333 25.01 0.00 0.00 2.17
2954 3072 8.237949 TCAAACACGTGAACTTTTTAGAATTCA 58.762 29.630 25.01 0.00 0.00 2.57
2955 3073 8.855279 CAAACACGTGAACTTTTTAGAATTCAA 58.145 29.630 25.01 0.00 33.09 2.69
2956 3074 9.581099 AAACACGTGAACTTTTTAGAATTCAAT 57.419 25.926 25.01 0.00 33.09 2.57
2957 3075 9.581099 AACACGTGAACTTTTTAGAATTCAATT 57.419 25.926 25.01 0.00 33.09 2.32
3037 3155 9.903682 ATGACTTTTATTCAAACTCATGAACTG 57.096 29.630 0.00 0.00 41.78 3.16
3038 3156 8.902806 TGACTTTTATTCAAACTCATGAACTGT 58.097 29.630 0.00 0.00 41.78 3.55
3039 3157 9.736023 GACTTTTATTCAAACTCATGAACTGTT 57.264 29.630 0.00 0.00 41.78 3.16
3046 3164 9.603921 ATTCAAACTCATGAACTGTTTTCAAAT 57.396 25.926 8.42 6.90 41.78 2.32
3047 3165 9.434420 TTCAAACTCATGAACTGTTTTCAAATT 57.566 25.926 8.42 0.00 34.50 1.82
3048 3166 9.086336 TCAAACTCATGAACTGTTTTCAAATTC 57.914 29.630 8.42 0.00 32.42 2.17
3049 3167 8.871862 CAAACTCATGAACTGTTTTCAAATTCA 58.128 29.630 8.42 0.00 38.49 2.57
3050 3168 9.603921 AAACTCATGAACTGTTTTCAAATTCAT 57.396 25.926 5.89 0.00 41.92 2.57
3051 3169 9.603921 AACTCATGAACTGTTTTCAAATTCATT 57.396 25.926 0.00 0.00 40.57 2.57
3090 3208 8.611654 AATCTTGACAATTTCCAAATTCAAGG 57.388 30.769 18.18 3.75 40.39 3.61
3091 3209 7.358770 TCTTGACAATTTCCAAATTCAAGGA 57.641 32.000 18.18 8.86 40.39 3.36
3092 3210 7.209475 TCTTGACAATTTCCAAATTCAAGGAC 58.791 34.615 18.18 2.93 40.39 3.85
3093 3211 5.852827 TGACAATTTCCAAATTCAAGGACC 58.147 37.500 0.00 0.00 36.52 4.46
3094 3212 5.365025 TGACAATTTCCAAATTCAAGGACCA 59.635 36.000 0.00 0.00 36.52 4.02
3095 3213 6.043012 TGACAATTTCCAAATTCAAGGACCAT 59.957 34.615 0.00 0.00 36.52 3.55
3096 3214 6.840527 ACAATTTCCAAATTCAAGGACCATT 58.159 32.000 0.00 0.00 36.52 3.16
3097 3215 7.289310 ACAATTTCCAAATTCAAGGACCATTT 58.711 30.769 0.00 0.00 36.52 2.32
3098 3216 7.779326 ACAATTTCCAAATTCAAGGACCATTTT 59.221 29.630 0.00 0.00 36.52 1.82
3099 3217 8.631797 CAATTTCCAAATTCAAGGACCATTTTT 58.368 29.630 0.00 0.00 36.52 1.94
3118 3236 5.394224 TTTTTCAGAACCCGTGAACTTTT 57.606 34.783 0.00 0.00 33.63 2.27
3119 3237 5.394224 TTTTCAGAACCCGTGAACTTTTT 57.606 34.783 0.00 0.00 33.63 1.94
3140 3258 7.696992 TTTTTAGAGTCAACTGGTCAAAAGT 57.303 32.000 0.00 0.00 0.00 2.66
3141 3259 6.920569 TTTAGAGTCAACTGGTCAAAAGTC 57.079 37.500 0.00 0.00 0.00 3.01
3142 3260 4.487714 AGAGTCAACTGGTCAAAAGTCA 57.512 40.909 0.00 0.00 0.00 3.41
3143 3261 4.446371 AGAGTCAACTGGTCAAAAGTCAG 58.554 43.478 0.00 0.00 34.91 3.51
3144 3262 2.945668 AGTCAACTGGTCAAAAGTCAGC 59.054 45.455 0.00 0.00 32.19 4.26
3145 3263 2.682856 GTCAACTGGTCAAAAGTCAGCA 59.317 45.455 0.00 0.00 32.19 4.41
3146 3264 2.945008 TCAACTGGTCAAAAGTCAGCAG 59.055 45.455 0.00 0.00 42.67 4.24
3147 3265 2.717639 ACTGGTCAAAAGTCAGCAGT 57.282 45.000 0.00 0.00 44.59 4.40
3148 3266 3.004752 ACTGGTCAAAAGTCAGCAGTT 57.995 42.857 0.00 0.00 46.68 3.16
3149 3267 4.150897 ACTGGTCAAAAGTCAGCAGTTA 57.849 40.909 0.00 0.00 46.68 2.24
3150 3268 4.130118 ACTGGTCAAAAGTCAGCAGTTAG 58.870 43.478 0.00 0.00 46.68 2.34
3151 3269 4.130118 CTGGTCAAAAGTCAGCAGTTAGT 58.870 43.478 0.00 0.00 34.13 2.24
3152 3270 3.876914 TGGTCAAAAGTCAGCAGTTAGTG 59.123 43.478 0.00 0.00 0.00 2.74
3153 3271 3.251004 GGTCAAAAGTCAGCAGTTAGTGG 59.749 47.826 0.00 0.00 0.00 4.00
3154 3272 3.877508 GTCAAAAGTCAGCAGTTAGTGGT 59.122 43.478 0.00 0.00 37.36 4.16
3155 3273 4.024809 GTCAAAAGTCAGCAGTTAGTGGTC 60.025 45.833 0.00 0.00 33.38 4.02
3156 3274 3.838244 AAAGTCAGCAGTTAGTGGTCA 57.162 42.857 0.00 0.00 33.38 4.02
3157 3275 3.838244 AAGTCAGCAGTTAGTGGTCAA 57.162 42.857 0.00 0.00 33.38 3.18
3158 3276 3.113260 AGTCAGCAGTTAGTGGTCAAC 57.887 47.619 0.00 0.00 33.38 3.18
3159 3277 2.700897 AGTCAGCAGTTAGTGGTCAACT 59.299 45.455 0.00 0.00 43.40 3.16
3166 3284 3.326747 AGTTAGTGGTCAACTGATTCGC 58.673 45.455 0.00 0.00 40.26 4.70
3167 3285 3.006967 AGTTAGTGGTCAACTGATTCGCT 59.993 43.478 0.00 5.06 40.26 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 121 6.695278 TCAGAATGTTTTTCACGAATTCCAAC 59.305 34.615 0.00 0.00 37.40 3.77
110 130 7.856492 TCATGAATTCAGAATGTTTTTCACG 57.144 32.000 14.54 0.00 34.28 4.35
112 132 9.767228 ATGTTCATGAATTCAGAATGTTTTTCA 57.233 25.926 12.12 9.65 37.40 2.69
118 138 9.550406 AAACAAATGTTCATGAATTCAGAATGT 57.450 25.926 12.12 13.67 37.25 2.71
119 139 9.805966 CAAACAAATGTTCATGAATTCAGAATG 57.194 29.630 12.12 7.70 37.25 2.67
121 141 7.494952 TGCAAACAAATGTTCATGAATTCAGAA 59.505 29.630 12.12 13.70 37.25 3.02
239 259 4.991056 GGCTCCCTTGTTTCTTTTCATTTC 59.009 41.667 0.00 0.00 0.00 2.17
317 358 3.264897 CTATTCCGCGCGCTGCTT 61.265 61.111 30.48 15.16 43.27 3.91
322 363 4.951963 AGCTCCTATTCCGCGCGC 62.952 66.667 27.36 23.91 0.00 6.86
358 399 4.712122 TCTTGCAGTCGTTTTTCCTTTT 57.288 36.364 0.00 0.00 0.00 2.27
370 411 7.698836 TTTTAATCAAAGCTTTCTTGCAGTC 57.301 32.000 9.23 0.00 34.99 3.51
389 430 7.813148 TGCCGTCCGAAAAATATTCAATTTTAA 59.187 29.630 0.00 0.00 31.67 1.52
411 452 2.667171 CGTTACTGGTTCCAAAATGCCG 60.667 50.000 0.00 0.00 0.00 5.69
421 462 5.917541 TCTGAATTGAACGTTACTGGTTC 57.082 39.130 0.00 2.84 43.13 3.62
434 475 9.565090 CCCTCACATCTTATTAATCTGAATTGA 57.435 33.333 0.00 0.00 0.00 2.57
447 488 6.838401 ATTTTCCTCTCCCTCACATCTTAT 57.162 37.500 0.00 0.00 0.00 1.73
454 495 4.559862 TCTCAATTTTCCTCTCCCTCAC 57.440 45.455 0.00 0.00 0.00 3.51
462 503 4.701956 TTGCCGATTCTCAATTTTCCTC 57.298 40.909 0.00 0.00 0.00 3.71
463 504 5.654497 GATTTGCCGATTCTCAATTTTCCT 58.346 37.500 0.00 0.00 0.00 3.36
470 511 0.732571 GCCGATTTGCCGATTCTCAA 59.267 50.000 0.00 0.00 0.00 3.02
472 513 1.151777 TCGCCGATTTGCCGATTCTC 61.152 55.000 0.00 0.00 0.00 2.87
473 514 1.153449 TCGCCGATTTGCCGATTCT 60.153 52.632 0.00 0.00 0.00 2.40
477 518 1.153449 AATCTCGCCGATTTGCCGA 60.153 52.632 0.00 0.00 39.28 5.54
510 552 3.559655 TGCATAATAGATCACGGTTGCAC 59.440 43.478 8.11 0.00 34.24 4.57
516 558 2.738846 GTGCCTGCATAATAGATCACGG 59.261 50.000 0.00 0.00 0.00 4.94
518 560 4.214971 CCTTGTGCCTGCATAATAGATCAC 59.785 45.833 1.70 0.00 0.00 3.06
528 570 1.188863 GGATTTCCTTGTGCCTGCAT 58.811 50.000 0.00 0.00 0.00 3.96
531 573 0.523072 CACGGATTTCCTTGTGCCTG 59.477 55.000 0.00 0.00 31.32 4.85
532 574 0.609131 CCACGGATTTCCTTGTGCCT 60.609 55.000 2.81 0.00 33.82 4.75
533 575 1.883021 CCACGGATTTCCTTGTGCC 59.117 57.895 2.81 0.00 33.82 5.01
534 576 1.212751 GCCACGGATTTCCTTGTGC 59.787 57.895 2.81 2.62 33.82 4.57
536 578 0.958822 GTTGCCACGGATTTCCTTGT 59.041 50.000 2.81 0.00 33.82 3.16
537 579 1.247567 AGTTGCCACGGATTTCCTTG 58.752 50.000 0.00 0.00 35.27 3.61
538 580 1.613437 CAAGTTGCCACGGATTTCCTT 59.387 47.619 0.00 0.00 0.00 3.36
539 581 1.247567 CAAGTTGCCACGGATTTCCT 58.752 50.000 0.00 0.00 0.00 3.36
540 582 0.388520 GCAAGTTGCCACGGATTTCC 60.389 55.000 17.36 0.00 37.42 3.13
541 583 0.313672 TGCAAGTTGCCACGGATTTC 59.686 50.000 24.59 0.00 44.23 2.17
542 584 0.968405 ATGCAAGTTGCCACGGATTT 59.032 45.000 24.59 0.00 44.23 2.17
543 585 0.244450 CATGCAAGTTGCCACGGATT 59.756 50.000 24.59 0.00 44.23 3.01
544 586 1.885157 CATGCAAGTTGCCACGGAT 59.115 52.632 24.59 8.53 44.23 4.18
545 587 2.918345 GCATGCAAGTTGCCACGGA 61.918 57.895 24.59 6.33 44.23 4.69
546 588 2.431260 GCATGCAAGTTGCCACGG 60.431 61.111 24.59 12.20 44.23 4.94
561 603 0.388263 TATTGGTCAACGTACGCGCA 60.388 50.000 16.72 0.00 42.83 6.09
593 637 1.063764 GTGTCGTTACGCCACCAAAAA 59.936 47.619 7.75 0.00 0.00 1.94
661 709 0.799152 CATCATTGCGCGCAACACAT 60.799 50.000 44.93 31.98 38.88 3.21
723 771 4.849383 ACGCGTGTTTAATTAATCAACTGC 59.151 37.500 12.93 12.28 0.00 4.40
729 777 5.500831 GCGTAACGCGTGTTTAATTAATC 57.499 39.130 20.86 0.00 44.55 1.75
761 809 0.950555 CCTGCTGCTGCTTGTCGTTA 60.951 55.000 17.00 0.00 40.48 3.18
783 831 2.224185 ACTACACCTGACGCAATTGTCA 60.224 45.455 7.40 2.97 46.15 3.58
798 846 2.033407 CGATAGCTTGCATGCACTACAC 60.033 50.000 22.58 14.90 34.99 2.90
799 847 2.159114 TCGATAGCTTGCATGCACTACA 60.159 45.455 22.58 4.47 34.99 2.74
800 848 2.473816 TCGATAGCTTGCATGCACTAC 58.526 47.619 22.58 12.81 34.99 2.73
801 849 2.888834 TCGATAGCTTGCATGCACTA 57.111 45.000 22.58 19.49 34.99 2.74
896 944 4.578516 CAGCGGTATATATAGAGCTCAGCT 59.421 45.833 17.77 0.00 43.88 4.24
897 945 4.261405 CCAGCGGTATATATAGAGCTCAGC 60.261 50.000 17.77 1.58 32.05 4.26
898 946 5.126779 TCCAGCGGTATATATAGAGCTCAG 58.873 45.833 17.77 11.48 32.05 3.35
902 956 5.765677 TGAGATCCAGCGGTATATATAGAGC 59.234 44.000 10.01 10.01 0.00 4.09
919 973 3.181495 CGTGTCTAGTGAGGTTGAGATCC 60.181 52.174 0.00 0.00 0.00 3.36
935 990 1.135803 GTTGTGTGTTTGTGCGTGTCT 60.136 47.619 0.00 0.00 0.00 3.41
941 996 2.886081 TGGATTGTTGTGTGTTTGTGC 58.114 42.857 0.00 0.00 0.00 4.57
946 1001 4.889409 ACTGAAGATGGATTGTTGTGTGTT 59.111 37.500 0.00 0.00 0.00 3.32
971 1050 3.119352 TCGATCTGGAGATGGATATTGCG 60.119 47.826 0.00 0.00 34.95 4.85
1101 1180 0.453282 CAACATCGTGCTTCTTGCCG 60.453 55.000 0.00 0.00 42.00 5.69
1150 1232 0.878416 CGCGGGTTTTTCTTGATGGA 59.122 50.000 0.00 0.00 0.00 3.41
1155 1237 1.065031 CGATGCGCGGGTTTTTCTTG 61.065 55.000 8.83 0.00 36.03 3.02
1200 1282 3.625897 TGGACCCAGCAGTCGTGG 61.626 66.667 0.00 0.00 37.66 4.94
1227 1309 2.606308 CGGATCATGGCTTTGCTTATGC 60.606 50.000 0.00 0.00 40.20 3.14
1228 1310 2.880268 TCGGATCATGGCTTTGCTTATG 59.120 45.455 0.00 0.00 0.00 1.90
1229 1311 2.880890 GTCGGATCATGGCTTTGCTTAT 59.119 45.455 0.00 0.00 0.00 1.73
1230 1312 2.288666 GTCGGATCATGGCTTTGCTTA 58.711 47.619 0.00 0.00 0.00 3.09
1231 1313 1.098050 GTCGGATCATGGCTTTGCTT 58.902 50.000 0.00 0.00 0.00 3.91
1232 1314 0.035152 TGTCGGATCATGGCTTTGCT 60.035 50.000 0.00 0.00 0.00 3.91
1233 1315 0.810648 TTGTCGGATCATGGCTTTGC 59.189 50.000 0.00 0.00 0.00 3.68
1234 1316 3.788333 ATTTGTCGGATCATGGCTTTG 57.212 42.857 0.00 0.00 0.00 2.77
1235 1317 4.497300 CAAATTTGTCGGATCATGGCTTT 58.503 39.130 10.15 0.00 0.00 3.51
1303 1402 2.187707 CGCAGCAAATCAATACCAAGC 58.812 47.619 0.00 0.00 0.00 4.01
1313 1412 5.169561 CGTACATCATTTTACGCAGCAAATC 59.830 40.000 0.00 0.00 35.13 2.17
1318 1417 3.342269 CACGTACATCATTTTACGCAGC 58.658 45.455 1.25 0.00 43.94 5.25
1319 1418 3.181525 TGCACGTACATCATTTTACGCAG 60.182 43.478 1.25 0.00 43.94 5.18
1320 1419 2.737252 TGCACGTACATCATTTTACGCA 59.263 40.909 1.25 0.00 43.94 5.24
1322 1421 3.242284 CCCTGCACGTACATCATTTTACG 60.242 47.826 0.00 0.00 45.27 3.18
1323 1422 3.486875 GCCCTGCACGTACATCATTTTAC 60.487 47.826 0.00 0.00 0.00 2.01
1324 1423 2.680841 GCCCTGCACGTACATCATTTTA 59.319 45.455 0.00 0.00 0.00 1.52
1325 1424 1.472480 GCCCTGCACGTACATCATTTT 59.528 47.619 0.00 0.00 0.00 1.82
1407 1509 1.413767 CTCGAGGCCGATGTTGTTCG 61.414 60.000 3.91 0.00 44.62 3.95
1633 1735 1.580845 CGAAGTTGGCCTTGAGCTGG 61.581 60.000 3.32 0.00 43.05 4.85
1656 1758 0.951040 CGTCTGGGTGAAGTTCCTGC 60.951 60.000 0.00 0.00 0.00 4.85
1773 1875 1.002274 AGGGCTCTCTGGTACCTGG 59.998 63.158 17.82 8.78 0.00 4.45
1794 1896 1.078918 TGCTCCTCAATGTGCTCCG 60.079 57.895 0.00 0.00 0.00 4.63
1810 1912 3.741476 CCTTGCACGCCCTTCTGC 61.741 66.667 0.00 0.00 0.00 4.26
1847 1949 1.305219 ATGTCGCGGATGTTGTTGGG 61.305 55.000 6.13 0.00 0.00 4.12
1849 1951 0.179192 CCATGTCGCGGATGTTGTTG 60.179 55.000 6.13 0.00 0.00 3.33
1906 2008 4.415332 CTCGACGTGTCCACCCCG 62.415 72.222 0.00 0.00 0.00 5.73
2042 2144 1.138247 CGTCGTCCCTAAACTCCCG 59.862 63.158 0.00 0.00 0.00 5.14
2147 2252 0.664761 CAGTTGGTGGTTCTGCAGTG 59.335 55.000 14.67 0.00 0.00 3.66
2180 2285 0.877071 TCGAGTTCAGGACGGTGTAC 59.123 55.000 0.00 0.00 0.00 2.90
2184 2289 1.135139 CATGATCGAGTTCAGGACGGT 59.865 52.381 0.00 0.00 29.04 4.83
2185 2290 1.135139 ACATGATCGAGTTCAGGACGG 59.865 52.381 7.61 0.00 32.03 4.79
2191 2296 1.362768 GCTGCACATGATCGAGTTCA 58.637 50.000 0.00 0.00 0.00 3.18
2192 2297 0.299895 CGCTGCACATGATCGAGTTC 59.700 55.000 0.00 0.00 0.00 3.01
2233 2338 6.787085 CAAGTTAGGTAGAGGACAAACTTG 57.213 41.667 14.87 14.87 46.23 3.16
2313 2421 4.008330 TGTTTCAGTAGACCGAGACCTAG 58.992 47.826 0.00 0.00 0.00 3.02
2319 2427 5.068234 TGGTTATGTTTCAGTAGACCGAG 57.932 43.478 0.00 0.00 0.00 4.63
2320 2428 5.471556 TTGGTTATGTTTCAGTAGACCGA 57.528 39.130 0.00 0.00 0.00 4.69
2321 2429 6.148811 ACATTTGGTTATGTTTCAGTAGACCG 59.851 38.462 0.00 0.00 35.24 4.79
2322 2430 7.174253 TGACATTTGGTTATGTTTCAGTAGACC 59.826 37.037 0.00 0.00 38.80 3.85
2323 2431 8.094798 TGACATTTGGTTATGTTTCAGTAGAC 57.905 34.615 0.00 0.00 38.80 2.59
2324 2432 7.936847 ACTGACATTTGGTTATGTTTCAGTAGA 59.063 33.333 8.47 0.00 39.67 2.59
2325 2433 8.099364 ACTGACATTTGGTTATGTTTCAGTAG 57.901 34.615 8.47 0.00 39.67 2.57
2326 2434 7.717436 TGACTGACATTTGGTTATGTTTCAGTA 59.283 33.333 9.62 0.87 40.64 2.74
2327 2435 6.545666 TGACTGACATTTGGTTATGTTTCAGT 59.454 34.615 9.48 9.48 41.99 3.41
2328 2436 6.969366 TGACTGACATTTGGTTATGTTTCAG 58.031 36.000 0.00 0.00 38.80 3.02
2329 2437 6.951062 TGACTGACATTTGGTTATGTTTCA 57.049 33.333 0.00 0.00 38.80 2.69
2330 2438 7.379529 CAGTTGACTGACATTTGGTTATGTTTC 59.620 37.037 5.19 0.00 46.59 2.78
2331 2439 7.202526 CAGTTGACTGACATTTGGTTATGTTT 58.797 34.615 5.19 0.00 46.59 2.83
2332 2440 6.738114 CAGTTGACTGACATTTGGTTATGTT 58.262 36.000 5.19 0.00 46.59 2.71
2333 2441 6.317789 CAGTTGACTGACATTTGGTTATGT 57.682 37.500 5.19 0.00 46.59 2.29
2424 2542 4.943705 ACTTCGTTATGGCTCAATTGATGT 59.056 37.500 8.96 0.00 0.00 3.06
2431 2549 3.244078 ACTGACACTTCGTTATGGCTCAA 60.244 43.478 0.00 0.00 0.00 3.02
2432 2550 2.299013 ACTGACACTTCGTTATGGCTCA 59.701 45.455 0.00 0.00 0.00 4.26
2436 2554 5.466819 TCAGTTACTGACACTTCGTTATGG 58.533 41.667 11.42 0.00 35.39 2.74
2816 2934 8.780249 CCTAAAACGGAGAGAAACAAATAGAAA 58.220 33.333 0.00 0.00 0.00 2.52
2817 2935 7.935210 ACCTAAAACGGAGAGAAACAAATAGAA 59.065 33.333 0.00 0.00 0.00 2.10
2818 2936 7.447594 ACCTAAAACGGAGAGAAACAAATAGA 58.552 34.615 0.00 0.00 0.00 1.98
2819 2937 7.668525 ACCTAAAACGGAGAGAAACAAATAG 57.331 36.000 0.00 0.00 0.00 1.73
2820 2938 7.820872 CCTACCTAAAACGGAGAGAAACAAATA 59.179 37.037 0.00 0.00 0.00 1.40
2821 2939 6.653740 CCTACCTAAAACGGAGAGAAACAAAT 59.346 38.462 0.00 0.00 0.00 2.32
2822 2940 5.993441 CCTACCTAAAACGGAGAGAAACAAA 59.007 40.000 0.00 0.00 0.00 2.83
2823 2941 5.070847 ACCTACCTAAAACGGAGAGAAACAA 59.929 40.000 0.00 0.00 0.00 2.83
2824 2942 4.590222 ACCTACCTAAAACGGAGAGAAACA 59.410 41.667 0.00 0.00 0.00 2.83
2825 2943 5.144692 ACCTACCTAAAACGGAGAGAAAC 57.855 43.478 0.00 0.00 0.00 2.78
2826 2944 5.813513 AACCTACCTAAAACGGAGAGAAA 57.186 39.130 0.00 0.00 0.00 2.52
2827 2945 5.813513 AAACCTACCTAAAACGGAGAGAA 57.186 39.130 0.00 0.00 0.00 2.87
2828 2946 5.511888 CCAAAACCTACCTAAAACGGAGAGA 60.512 44.000 0.00 0.00 0.00 3.10
2829 2947 4.694037 CCAAAACCTACCTAAAACGGAGAG 59.306 45.833 0.00 0.00 0.00 3.20
2830 2948 4.102996 ACCAAAACCTACCTAAAACGGAGA 59.897 41.667 0.00 0.00 0.00 3.71
2831 2949 4.392047 ACCAAAACCTACCTAAAACGGAG 58.608 43.478 0.00 0.00 0.00 4.63
2832 2950 4.102996 AGACCAAAACCTACCTAAAACGGA 59.897 41.667 0.00 0.00 0.00 4.69
2833 2951 4.392047 AGACCAAAACCTACCTAAAACGG 58.608 43.478 0.00 0.00 0.00 4.44
2834 2952 7.148356 GGAATAGACCAAAACCTACCTAAAACG 60.148 40.741 0.00 0.00 0.00 3.60
2835 2953 7.148356 CGGAATAGACCAAAACCTACCTAAAAC 60.148 40.741 0.00 0.00 0.00 2.43
2836 2954 6.880529 CGGAATAGACCAAAACCTACCTAAAA 59.119 38.462 0.00 0.00 0.00 1.52
2837 2955 6.013466 ACGGAATAGACCAAAACCTACCTAAA 60.013 38.462 0.00 0.00 0.00 1.85
2838 2956 5.484998 ACGGAATAGACCAAAACCTACCTAA 59.515 40.000 0.00 0.00 0.00 2.69
2839 2957 5.025453 ACGGAATAGACCAAAACCTACCTA 58.975 41.667 0.00 0.00 0.00 3.08
2840 2958 3.842436 ACGGAATAGACCAAAACCTACCT 59.158 43.478 0.00 0.00 0.00 3.08
2841 2959 4.212143 ACGGAATAGACCAAAACCTACC 57.788 45.455 0.00 0.00 0.00 3.18
2842 2960 6.429078 AGAAAACGGAATAGACCAAAACCTAC 59.571 38.462 0.00 0.00 0.00 3.18
2843 2961 6.536447 AGAAAACGGAATAGACCAAAACCTA 58.464 36.000 0.00 0.00 0.00 3.08
2844 2962 5.382616 AGAAAACGGAATAGACCAAAACCT 58.617 37.500 0.00 0.00 0.00 3.50
2845 2963 5.700722 AGAAAACGGAATAGACCAAAACC 57.299 39.130 0.00 0.00 0.00 3.27
2846 2964 7.997107 AAAAGAAAACGGAATAGACCAAAAC 57.003 32.000 0.00 0.00 0.00 2.43
2847 2965 9.518906 GTAAAAAGAAAACGGAATAGACCAAAA 57.481 29.630 0.00 0.00 0.00 2.44
2848 2966 8.905850 AGTAAAAAGAAAACGGAATAGACCAAA 58.094 29.630 0.00 0.00 0.00 3.28
2849 2967 8.454570 AGTAAAAAGAAAACGGAATAGACCAA 57.545 30.769 0.00 0.00 0.00 3.67
2850 2968 8.454570 AAGTAAAAAGAAAACGGAATAGACCA 57.545 30.769 0.00 0.00 0.00 4.02
2851 2969 9.740239 AAAAGTAAAAAGAAAACGGAATAGACC 57.260 29.630 0.00 0.00 0.00 3.85
2853 2971 9.955208 GGAAAAGTAAAAAGAAAACGGAATAGA 57.045 29.630 0.00 0.00 0.00 1.98
2854 2972 9.961265 AGGAAAAGTAAAAAGAAAACGGAATAG 57.039 29.630 0.00 0.00 0.00 1.73
2856 2974 9.661563 AAAGGAAAAGTAAAAAGAAAACGGAAT 57.338 25.926 0.00 0.00 0.00 3.01
2857 2975 9.491675 AAAAGGAAAAGTAAAAAGAAAACGGAA 57.508 25.926 0.00 0.00 0.00 4.30
2858 2976 9.142515 GAAAAGGAAAAGTAAAAAGAAAACGGA 57.857 29.630 0.00 0.00 0.00 4.69
2859 2977 9.146984 AGAAAAGGAAAAGTAAAAAGAAAACGG 57.853 29.630 0.00 0.00 0.00 4.44
2927 3045 7.964545 ATTCTAAAAAGTTCACGTGTTTGAC 57.035 32.000 16.51 10.25 0.00 3.18
2928 3046 8.237949 TGAATTCTAAAAAGTTCACGTGTTTGA 58.762 29.630 16.51 4.99 0.00 2.69
2929 3047 8.388319 TGAATTCTAAAAAGTTCACGTGTTTG 57.612 30.769 16.51 2.56 0.00 2.93
2930 3048 8.973835 TTGAATTCTAAAAAGTTCACGTGTTT 57.026 26.923 16.51 10.65 30.96 2.83
2931 3049 9.581099 AATTGAATTCTAAAAAGTTCACGTGTT 57.419 25.926 16.51 3.65 30.96 3.32
3013 3131 9.736023 AACAGTTCATGAGTTTGAATAAAAGTC 57.264 29.630 9.35 0.00 45.09 3.01
3020 3138 9.603921 ATTTGAAAACAGTTCATGAGTTTGAAT 57.396 25.926 11.13 9.46 37.88 2.57
3021 3139 9.434420 AATTTGAAAACAGTTCATGAGTTTGAA 57.566 25.926 11.13 8.06 35.79 2.69
3022 3140 9.086336 GAATTTGAAAACAGTTCATGAGTTTGA 57.914 29.630 11.13 1.34 35.79 2.69
3023 3141 8.871862 TGAATTTGAAAACAGTTCATGAGTTTG 58.128 29.630 11.13 6.90 35.79 2.93
3024 3142 9.603921 ATGAATTTGAAAACAGTTCATGAGTTT 57.396 25.926 5.89 5.89 37.91 2.66
3025 3143 9.603921 AATGAATTTGAAAACAGTTCATGAGTT 57.396 25.926 5.53 0.00 38.93 3.01
3064 3182 9.059260 CCTTGAATTTGGAAATTGTCAAGATTT 57.941 29.630 19.29 0.00 41.41 2.17
3065 3183 8.431222 TCCTTGAATTTGGAAATTGTCAAGATT 58.569 29.630 19.29 0.00 41.41 2.40
3066 3184 7.874528 GTCCTTGAATTTGGAAATTGTCAAGAT 59.125 33.333 19.29 0.00 41.41 2.40
3067 3185 7.209475 GTCCTTGAATTTGGAAATTGTCAAGA 58.791 34.615 19.29 9.32 41.41 3.02
3068 3186 6.424812 GGTCCTTGAATTTGGAAATTGTCAAG 59.575 38.462 14.40 14.40 40.05 3.02
3069 3187 6.126940 TGGTCCTTGAATTTGGAAATTGTCAA 60.127 34.615 2.06 1.61 38.64 3.18
3070 3188 5.365025 TGGTCCTTGAATTTGGAAATTGTCA 59.635 36.000 2.06 0.00 38.64 3.58
3071 3189 5.852827 TGGTCCTTGAATTTGGAAATTGTC 58.147 37.500 2.06 0.00 38.64 3.18
3072 3190 5.885449 TGGTCCTTGAATTTGGAAATTGT 57.115 34.783 2.06 0.00 38.64 2.71
3073 3191 7.748691 AAATGGTCCTTGAATTTGGAAATTG 57.251 32.000 2.06 0.00 38.64 2.32
3074 3192 8.765488 AAAAATGGTCCTTGAATTTGGAAATT 57.235 26.923 0.00 0.00 41.06 1.82
3096 3214 5.394224 AAAAGTTCACGGGTTCTGAAAAA 57.606 34.783 0.00 0.00 29.44 1.94
3097 3215 5.394224 AAAAAGTTCACGGGTTCTGAAAA 57.606 34.783 0.00 0.00 29.44 2.29
3116 3234 7.392113 TGACTTTTGACCAGTTGACTCTAAAAA 59.608 33.333 0.00 0.00 0.00 1.94
3117 3235 6.882140 TGACTTTTGACCAGTTGACTCTAAAA 59.118 34.615 0.00 0.00 0.00 1.52
3118 3236 6.411376 TGACTTTTGACCAGTTGACTCTAAA 58.589 36.000 0.00 0.00 0.00 1.85
3119 3237 5.984725 TGACTTTTGACCAGTTGACTCTAA 58.015 37.500 0.00 0.00 0.00 2.10
3120 3238 5.601662 CTGACTTTTGACCAGTTGACTCTA 58.398 41.667 0.00 0.00 0.00 2.43
3121 3239 4.446371 CTGACTTTTGACCAGTTGACTCT 58.554 43.478 0.00 0.00 0.00 3.24
3122 3240 3.002759 GCTGACTTTTGACCAGTTGACTC 59.997 47.826 0.00 0.00 0.00 3.36
3123 3241 2.945668 GCTGACTTTTGACCAGTTGACT 59.054 45.455 0.00 0.00 0.00 3.41
3124 3242 2.682856 TGCTGACTTTTGACCAGTTGAC 59.317 45.455 0.00 0.00 0.00 3.18
3125 3243 2.945008 CTGCTGACTTTTGACCAGTTGA 59.055 45.455 0.00 0.00 0.00 3.18
3126 3244 2.684881 ACTGCTGACTTTTGACCAGTTG 59.315 45.455 0.00 0.00 30.01 3.16
3127 3245 3.004752 ACTGCTGACTTTTGACCAGTT 57.995 42.857 0.00 0.00 30.01 3.16
3128 3246 2.717639 ACTGCTGACTTTTGACCAGT 57.282 45.000 0.00 0.00 0.00 4.00
3129 3247 4.024556 CACTAACTGCTGACTTTTGACCAG 60.025 45.833 0.00 0.00 0.00 4.00
3130 3248 3.876914 CACTAACTGCTGACTTTTGACCA 59.123 43.478 0.00 0.00 0.00 4.02
3131 3249 3.251004 CCACTAACTGCTGACTTTTGACC 59.749 47.826 0.00 0.00 0.00 4.02
3132 3250 3.877508 ACCACTAACTGCTGACTTTTGAC 59.122 43.478 0.00 0.00 0.00 3.18
3133 3251 4.127171 GACCACTAACTGCTGACTTTTGA 58.873 43.478 0.00 0.00 0.00 2.69
3134 3252 3.876914 TGACCACTAACTGCTGACTTTTG 59.123 43.478 0.00 0.00 0.00 2.44
3135 3253 4.150897 TGACCACTAACTGCTGACTTTT 57.849 40.909 0.00 0.00 0.00 2.27
3136 3254 3.838244 TGACCACTAACTGCTGACTTT 57.162 42.857 0.00 0.00 0.00 2.66
3137 3255 3.134804 AGTTGACCACTAACTGCTGACTT 59.865 43.478 0.00 0.00 37.03 3.01
3138 3256 2.700897 AGTTGACCACTAACTGCTGACT 59.299 45.455 0.00 0.00 37.03 3.41
3139 3257 2.802816 CAGTTGACCACTAACTGCTGAC 59.197 50.000 5.11 0.00 45.70 3.51
3140 3258 3.111853 CAGTTGACCACTAACTGCTGA 57.888 47.619 5.11 0.00 45.70 4.26
3145 3263 3.006967 AGCGAATCAGTTGACCACTAACT 59.993 43.478 0.00 0.00 38.84 2.24
3146 3264 3.326747 AGCGAATCAGTTGACCACTAAC 58.673 45.455 0.00 0.00 32.76 2.34
3147 3265 3.678056 AGCGAATCAGTTGACCACTAA 57.322 42.857 0.00 0.00 32.76 2.24


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.