Multiple sequence alignment - TraesCS5A01G276000

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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 TraesCS5A01G276000 chr5A 100.000 3523 0 0 1 3523 485371333 485374855 0.000000e+00 6506.0
1 TraesCS5A01G276000 chr5D 94.890 1272 55 4 1815 3084 384469052 384470315 0.000000e+00 1980.0
2 TraesCS5A01G276000 chr5D 90.367 654 37 6 787 1438 384467189 384467818 0.000000e+00 835.0
3 TraesCS5A01G276000 chr5D 90.271 442 31 3 1 441 384425134 384425564 5.100000e-158 568.0
4 TraesCS5A01G276000 chr5D 94.286 350 17 2 1470 1816 384467818 384468167 1.860000e-147 532.0
5 TraesCS5A01G276000 chr5D 83.370 457 31 30 3083 3523 384470398 384470825 7.140000e-102 381.0
6 TraesCS5A01G276000 chr5D 94.258 209 9 2 1516 1721 384468618 384468826 2.040000e-82 316.0
7 TraesCS5A01G276000 chr5D 91.304 184 15 1 1967 2150 384468439 384468621 2.100000e-62 250.0
8 TraesCS5A01G276000 chr5D 77.447 470 70 23 1823 2258 384467855 384468322 7.550000e-62 248.0
9 TraesCS5A01G276000 chr5B 92.979 1111 68 6 1975 3083 461291223 461292325 0.000000e+00 1611.0
10 TraesCS5A01G276000 chr5B 89.843 955 72 18 737 1685 461289647 461290582 0.000000e+00 1203.0
11 TraesCS5A01G276000 chr5B 93.213 442 28 2 1 441 461288997 461289437 0.000000e+00 649.0
12 TraesCS5A01G276000 chr5B 93.003 343 21 1 1477 1816 461290584 461290926 6.790000e-137 497.0
13 TraesCS5A01G276000 chr5B 76.407 462 78 18 1823 2255 461290614 461291073 1.650000e-53 220.0
14 TraesCS5A01G276000 chr1D 80.204 884 111 35 1831 2679 448262656 448261802 3.890000e-169 604.0
15 TraesCS5A01G276000 chr1D 87.365 277 23 8 872 1145 448279958 448279691 1.230000e-79 307.0
16 TraesCS5A01G276000 chr1D 85.776 232 18 9 1259 1479 448279492 448279265 7.610000e-57 231.0
17 TraesCS5A01G276000 chr1B 78.186 926 110 53 1831 2732 613947363 613946506 1.130000e-139 507.0
18 TraesCS5A01G276000 chr1B 79.862 581 70 27 1261 1816 613947613 613947055 7.140000e-102 381.0
19 TraesCS5A01G276000 chr1B 86.207 203 20 2 946 1148 613948001 613947807 2.750000e-51 213.0
20 TraesCS5A01G276000 chr1B 89.362 47 3 2 3096 3141 613946123 613946078 1.370000e-04 58.4
21 TraesCS5A01G276000 chr6D 84.783 460 44 6 1496 1941 290071269 290071716 4.180000e-119 438.0
22 TraesCS5A01G276000 chr6D 84.683 457 44 6 1499 1941 28345216 28344772 1.940000e-117 433.0
23 TraesCS5A01G276000 chr3D 82.966 499 56 8 1459 1941 12176584 12176099 1.170000e-114 424.0
24 TraesCS5A01G276000 chr2D 83.450 429 43 8 1392 1804 644883523 644883939 1.190000e-99 374.0
25 TraesCS5A01G276000 chr2D 89.683 126 13 0 1816 1941 644884313 644884438 1.010000e-35 161.0
26 TraesCS5A01G276000 chr1A 87.179 273 25 7 878 1148 544140785 544140521 5.720000e-78 302.0
27 TraesCS5A01G276000 chr1A 94.118 119 6 1 1281 1398 544140253 544140135 2.790000e-41 180.0


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 TraesCS5A01G276000 chr5A 485371333 485374855 3522 False 6506.000000 6506 100.000000 1 3523 1 chr5A.!!$F1 3522
1 TraesCS5A01G276000 chr5D 384467189 384470825 3636 False 648.857143 1980 89.417429 787 3523 7 chr5D.!!$F2 2736
2 TraesCS5A01G276000 chr5B 461288997 461292325 3328 False 836.000000 1611 89.089000 1 3083 5 chr5B.!!$F1 3082
3 TraesCS5A01G276000 chr1D 448261802 448262656 854 True 604.000000 604 80.204000 1831 2679 1 chr1D.!!$R1 848
4 TraesCS5A01G276000 chr1D 448279265 448279958 693 True 269.000000 307 86.570500 872 1479 2 chr1D.!!$R2 607
5 TraesCS5A01G276000 chr1B 613946078 613948001 1923 True 289.850000 507 83.404250 946 3141 4 chr1B.!!$R1 2195
6 TraesCS5A01G276000 chr2D 644883523 644884438 915 False 267.500000 374 86.566500 1392 1941 2 chr2D.!!$F1 549
7 TraesCS5A01G276000 chr1A 544140135 544140785 650 True 241.000000 302 90.648500 878 1398 2 chr1A.!!$R1 520

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
359 361 0.037790 GGTGCAGAGACCAGAGTGTC 60.038 60.0 0.0 0.0 36.54 3.67 F
1125 1206 0.333993 TCCTCGGCTACTACAACCCT 59.666 55.0 0.0 0.0 0.00 4.34 F
1956 3720 0.108186 TCTAATGCTCTGTGGCGGTG 60.108 55.0 0.0 0.0 34.52 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 3690 0.745845 AGCATTAGAACAGCCAGGCG 60.746 55.000 5.55 3.56 0.0 5.52 R
2300 4071 1.530771 GGGATCTGATGGCTGTGCT 59.469 57.895 0.00 0.00 0.0 4.40 R
3163 5089 0.109735 GCCCTTTACAAACGAGCAGC 60.110 55.000 0.00 0.00 0.0 5.25 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
43 44 4.815973 TCCCCCACTCCATCCCCG 62.816 72.222 0.00 0.00 0.00 5.73
58 59 0.179020 CCCCGCTGCATTCATTCCTA 60.179 55.000 0.00 0.00 0.00 2.94
98 99 6.088016 TCATGTGTTCCTTTCATCTTTTGG 57.912 37.500 0.00 0.00 0.00 3.28
160 161 1.294659 GAGCAGTGTCCAGAAAGGCG 61.295 60.000 0.00 0.00 37.29 5.52
201 202 1.504647 TATAGGCTCCAGACGACGCG 61.505 60.000 3.53 3.53 0.00 6.01
224 225 0.960861 TCATCTCGCTCACTGGTCGT 60.961 55.000 0.00 0.00 0.00 4.34
258 260 2.287788 CCTGCATAATCGGTGATTTGGC 60.288 50.000 0.00 3.37 33.95 4.52
262 264 1.745232 TAATCGGTGATTTGGCGCTT 58.255 45.000 7.64 0.00 33.95 4.68
268 270 0.730494 GTGATTTGGCGCTTGTCTGC 60.730 55.000 7.64 0.00 0.00 4.26
279 281 0.304705 CTTGTCTGCGGTGTCACAAC 59.695 55.000 5.12 0.00 0.00 3.32
284 286 1.821241 CTGCGGTGTCACAACTGTCG 61.821 60.000 5.12 0.00 0.00 4.35
288 290 1.548973 GGTGTCACAACTGTCGAGCG 61.549 60.000 5.12 0.00 0.00 5.03
304 306 0.679505 AGCGCCTTACTGAACACTGA 59.320 50.000 2.29 0.00 0.00 3.41
344 346 5.182001 AGTTATGTTCTCAAATGTCTGGTGC 59.818 40.000 0.00 0.00 0.00 5.01
358 360 0.760567 TGGTGCAGAGACCAGAGTGT 60.761 55.000 0.00 0.00 41.30 3.55
359 361 0.037790 GGTGCAGAGACCAGAGTGTC 60.038 60.000 0.00 0.00 36.54 3.67
370 372 1.678627 CCAGAGTGTCTCCATCTACGG 59.321 57.143 0.00 0.00 0.00 4.02
390 392 2.611224 GGGCTTGCTTTTCTTCCATGTG 60.611 50.000 0.00 0.00 0.00 3.21
392 394 2.680577 CTTGCTTTTCTTCCATGTGCC 58.319 47.619 0.00 0.00 0.00 5.01
397 399 3.415212 CTTTTCTTCCATGTGCCAGAGA 58.585 45.455 0.00 0.00 0.00 3.10
399 401 3.726557 TTCTTCCATGTGCCAGAGATT 57.273 42.857 0.00 0.00 0.00 2.40
404 406 3.114606 TCCATGTGCCAGAGATTCCTTA 58.885 45.455 0.00 0.00 0.00 2.69
411 413 5.189736 TGTGCCAGAGATTCCTTATGTACTT 59.810 40.000 0.00 0.00 0.00 2.24
417 419 5.189736 AGAGATTCCTTATGTACTTGGCACA 59.810 40.000 0.00 0.00 0.00 4.57
454 527 3.350219 AGTGTGTTCTGTCACCTGTTT 57.650 42.857 0.00 0.00 37.51 2.83
455 528 3.686016 AGTGTGTTCTGTCACCTGTTTT 58.314 40.909 0.00 0.00 37.51 2.43
456 529 4.839121 AGTGTGTTCTGTCACCTGTTTTA 58.161 39.130 0.00 0.00 37.51 1.52
457 530 4.634443 AGTGTGTTCTGTCACCTGTTTTAC 59.366 41.667 0.00 0.00 37.51 2.01
460 533 4.272748 GTGTTCTGTCACCTGTTTTACCTC 59.727 45.833 0.00 0.00 32.81 3.85
463 536 3.709653 TCTGTCACCTGTTTTACCTCTGT 59.290 43.478 0.00 0.00 0.00 3.41
464 537 4.058817 CTGTCACCTGTTTTACCTCTGTC 58.941 47.826 0.00 0.00 0.00 3.51
465 538 3.452990 TGTCACCTGTTTTACCTCTGTCA 59.547 43.478 0.00 0.00 0.00 3.58
466 539 4.058817 GTCACCTGTTTTACCTCTGTCAG 58.941 47.826 0.00 0.00 0.00 3.51
467 540 3.964688 TCACCTGTTTTACCTCTGTCAGA 59.035 43.478 1.78 1.78 0.00 3.27
468 541 4.593206 TCACCTGTTTTACCTCTGTCAGAT 59.407 41.667 2.22 0.00 0.00 2.90
510 583 7.379750 TGCAGAAATGTGAATTGATCAAATGA 58.620 30.769 13.09 0.00 40.50 2.57
511 584 7.873505 TGCAGAAATGTGAATTGATCAAATGAA 59.126 29.630 13.09 0.00 40.50 2.57
512 585 8.380644 GCAGAAATGTGAATTGATCAAATGAAG 58.619 33.333 13.09 0.00 40.50 3.02
513 586 8.380644 CAGAAATGTGAATTGATCAAATGAAGC 58.619 33.333 13.09 2.13 40.50 3.86
514 587 8.311836 AGAAATGTGAATTGATCAAATGAAGCT 58.688 29.630 13.09 0.00 40.50 3.74
516 589 8.842358 AATGTGAATTGATCAAATGAAGCTTT 57.158 26.923 13.09 0.00 40.50 3.51
517 590 9.932207 AATGTGAATTGATCAAATGAAGCTTTA 57.068 25.926 13.09 0.00 40.50 1.85
531 607 6.727824 TGAAGCTTTATTTTTCGAGAGAGG 57.272 37.500 0.00 0.00 43.69 3.69
538 614 8.401709 GCTTTATTTTTCGAGAGAGGAAATGAT 58.598 33.333 0.00 0.00 43.69 2.45
545 621 6.731292 TCGAGAGAGGAAATGATAAATGGA 57.269 37.500 0.00 0.00 34.84 3.41
592 668 9.989869 GTAGTCAATCAAGCTTAAATTTACTCC 57.010 33.333 17.38 8.39 0.00 3.85
594 670 9.301897 AGTCAATCAAGCTTAAATTTACTCCTT 57.698 29.630 0.00 0.00 0.00 3.36
595 671 9.914131 GTCAATCAAGCTTAAATTTACTCCTTT 57.086 29.630 0.00 0.00 0.00 3.11
658 734 8.117813 TCAAGCTTAAATTTACTTTGTAGGGG 57.882 34.615 0.00 0.00 0.00 4.79
659 735 7.726738 TCAAGCTTAAATTTACTTTGTAGGGGT 59.273 33.333 0.00 0.00 0.00 4.95
660 736 9.016438 CAAGCTTAAATTTACTTTGTAGGGGTA 57.984 33.333 0.00 0.00 0.00 3.69
661 737 9.763837 AAGCTTAAATTTACTTTGTAGGGGTAT 57.236 29.630 0.00 0.00 0.00 2.73
662 738 9.763837 AGCTTAAATTTACTTTGTAGGGGTATT 57.236 29.630 0.00 0.00 0.00 1.89
695 771 9.797642 TTTTTAGGAAAGGGGTACTTACTTTAG 57.202 33.333 9.01 0.00 38.85 1.85
696 772 8.740616 TTTAGGAAAGGGGTACTTACTTTAGA 57.259 34.615 9.01 0.00 38.85 2.10
697 773 8.740616 TTAGGAAAGGGGTACTTACTTTAGAA 57.259 34.615 9.01 3.70 38.85 2.10
698 774 7.637548 AGGAAAGGGGTACTTACTTTAGAAA 57.362 36.000 9.01 0.00 38.85 2.52
699 775 7.687388 AGGAAAGGGGTACTTACTTTAGAAAG 58.313 38.462 9.01 0.37 38.85 2.62
700 776 6.883217 GGAAAGGGGTACTTACTTTAGAAAGG 59.117 42.308 6.94 0.00 38.85 3.11
701 777 6.384342 AAGGGGTACTTACTTTAGAAAGGG 57.616 41.667 6.94 0.09 37.74 3.95
702 778 4.786994 AGGGGTACTTACTTTAGAAAGGGG 59.213 45.833 6.94 0.00 40.31 4.79
703 779 4.080129 GGGGTACTTACTTTAGAAAGGGGG 60.080 50.000 6.94 0.00 40.31 5.40
704 780 4.537688 GGGTACTTACTTTAGAAAGGGGGT 59.462 45.833 6.94 4.69 40.31 4.95
705 781 5.726308 GGGTACTTACTTTAGAAAGGGGGTA 59.274 44.000 6.94 3.89 40.31 3.69
706 782 6.388100 GGGTACTTACTTTAGAAAGGGGGTAT 59.612 42.308 6.94 0.00 40.31 2.73
707 783 7.092264 GGGTACTTACTTTAGAAAGGGGGTATT 60.092 40.741 6.94 0.00 40.31 1.89
708 784 8.331740 GGTACTTACTTTAGAAAGGGGGTATTT 58.668 37.037 6.94 0.00 40.31 1.40
711 787 9.120658 ACTTACTTTAGAAAGGGGGTATTTACT 57.879 33.333 6.94 0.00 40.31 2.24
714 790 8.691194 ACTTTAGAAAGGGGGTATTTACTACT 57.309 34.615 6.94 0.00 40.31 2.57
715 791 9.120658 ACTTTAGAAAGGGGGTATTTACTACTT 57.879 33.333 6.94 0.00 40.31 2.24
716 792 9.970553 CTTTAGAAAGGGGGTATTTACTACTTT 57.029 33.333 0.00 0.00 32.40 2.66
744 820 9.964354 TTTTAGAAGAAAGGGGGTATTTACTAC 57.036 33.333 0.00 0.00 0.00 2.73
745 821 8.922229 TTAGAAGAAAGGGGGTATTTACTACT 57.078 34.615 0.00 0.00 0.00 2.57
747 823 8.550280 AGAAGAAAGGGGGTATTTACTACTAG 57.450 38.462 0.00 0.00 0.00 2.57
748 824 7.567994 AGAAGAAAGGGGGTATTTACTACTAGG 59.432 40.741 0.00 0.00 0.00 3.02
749 825 7.001653 AGAAAGGGGGTATTTACTACTAGGA 57.998 40.000 0.00 0.00 0.00 2.94
750 826 7.612179 AGAAAGGGGGTATTTACTACTAGGAT 58.388 38.462 0.00 0.00 0.00 3.24
751 827 7.733955 AGAAAGGGGGTATTTACTACTAGGATC 59.266 40.741 0.00 0.00 0.00 3.36
752 828 5.578073 AGGGGGTATTTACTACTAGGATCG 58.422 45.833 0.00 0.00 0.00 3.69
799 875 2.665537 CGATCAGCGATCTAATTCTGGC 59.334 50.000 13.90 0.00 44.57 4.85
805 881 5.047092 TCAGCGATCTAATTCTGGCATATCA 60.047 40.000 0.00 0.00 0.00 2.15
806 882 5.640783 CAGCGATCTAATTCTGGCATATCAA 59.359 40.000 0.00 0.00 0.00 2.57
816 892 2.635915 CTGGCATATCAATTGGCCCAAT 59.364 45.455 17.52 2.23 45.83 3.16
817 893 2.633967 TGGCATATCAATTGGCCCAATC 59.366 45.455 9.93 0.00 45.83 2.67
987 1067 1.446272 CGGCGAGGAAGACCAAGAC 60.446 63.158 0.00 0.00 38.94 3.01
994 1074 1.416401 AGGAAGACCAAGACGAAAGCA 59.584 47.619 0.00 0.00 38.94 3.91
1054 1135 2.349755 GCAACCGGCCCTTCTACA 59.650 61.111 0.00 0.00 36.11 2.74
1125 1206 0.333993 TCCTCGGCTACTACAACCCT 59.666 55.000 0.00 0.00 0.00 4.34
1195 1289 2.757077 CACCTCCAACTCCCACCC 59.243 66.667 0.00 0.00 0.00 4.61
1292 1558 3.754965 TGGTGCTGCTAACTGAAGAATT 58.245 40.909 0.00 0.00 0.00 2.17
1411 1679 3.579586 TGCCTGCTCCTGATTTTCATTTT 59.420 39.130 0.00 0.00 0.00 1.82
1419 1694 8.321353 TGCTCCTGATTTTCATTTTAGAGAGTA 58.679 33.333 0.00 0.00 0.00 2.59
1457 1736 6.089249 TCCTTTTTGGAGAAAAATCTGCTC 57.911 37.500 0.00 0.00 39.70 4.26
1605 2092 8.245195 AGTTATGCCTTTTCTTTGAAACCTAA 57.755 30.769 0.00 0.00 0.00 2.69
1622 2109 8.932791 TGAAACCTAAATAAATCGAGTCTTGTC 58.067 33.333 0.00 0.00 0.00 3.18
1623 2110 8.842358 AAACCTAAATAAATCGAGTCTTGTCA 57.158 30.769 0.00 0.00 0.00 3.58
1627 2114 9.098355 CCTAAATAAATCGAGTCTTGTCATTCA 57.902 33.333 0.00 0.00 0.00 2.57
1636 2123 3.504906 AGTCTTGTCATTCACATGCCTTG 59.495 43.478 0.00 0.00 33.90 3.61
1696 2183 6.204882 GGTAAAGCAGAAGAAAGACAAGCTAA 59.795 38.462 0.00 0.00 0.00 3.09
1712 2199 1.594862 GCTAAACTATCTGGTGCTGCG 59.405 52.381 0.00 0.00 0.00 5.18
1733 2220 6.621613 TGCGCTATCCTAGTTGATTATAGTG 58.378 40.000 9.73 0.00 35.01 2.74
1741 2228 6.998074 TCCTAGTTGATTATAGTGCCAATTGG 59.002 38.462 20.81 20.81 38.53 3.16
1771 2258 0.670546 TCACTTCTACGCTTGCTGCC 60.671 55.000 0.00 0.00 38.78 4.85
1803 2290 7.225931 CCACCGGAGAAGAAAATTATCGATTTA 59.774 37.037 9.46 0.00 36.96 1.40
1859 3623 4.823989 CCAGTAGCCTTATTCTTTGATGGG 59.176 45.833 0.00 0.00 0.00 4.00
1879 3643 3.279434 GGCGATTGGACATTTTAGAGGT 58.721 45.455 0.00 0.00 0.00 3.85
1910 3674 7.118971 GCTAAATAGATTATGCCTTCTCTGTGG 59.881 40.741 0.00 0.00 0.00 4.17
1914 3678 2.672961 TATGCCTTCTCTGTGGAACG 57.327 50.000 0.00 0.00 42.39 3.95
1924 3688 5.917541 TCTCTGTGGAACGTAAACAATTC 57.082 39.130 0.00 0.00 42.39 2.17
1926 3690 3.059461 TCTGTGGAACGTAAACAATTCGC 60.059 43.478 0.00 0.00 42.39 4.70
1941 3705 2.434185 CGCGCCTGGCTGTTCTAA 60.434 61.111 17.92 0.00 40.44 2.10
1956 3720 0.108186 TCTAATGCTCTGTGGCGGTG 60.108 55.000 0.00 0.00 34.52 4.94
2022 3786 3.243501 ACAAGCAAAACTATGTGGTGCTG 60.244 43.478 8.48 6.51 44.52 4.41
2038 3802 3.190874 GTGCTGGACTATGCTAGTTGAC 58.809 50.000 0.00 0.00 39.59 3.18
2051 3815 5.500234 TGCTAGTTGACTGGATGCTAATTT 58.500 37.500 0.00 0.00 0.00 1.82
2052 3816 5.586243 TGCTAGTTGACTGGATGCTAATTTC 59.414 40.000 0.00 0.00 0.00 2.17
2053 3817 5.586243 GCTAGTTGACTGGATGCTAATTTCA 59.414 40.000 0.00 0.00 0.00 2.69
2075 3839 7.543947 TCACAAGCATCATTCAGTTATACAG 57.456 36.000 0.00 0.00 0.00 2.74
2078 3842 6.256539 ACAAGCATCATTCAGTTATACAGTCG 59.743 38.462 0.00 0.00 0.00 4.18
2081 3845 5.920840 GCATCATTCAGTTATACAGTCGCTA 59.079 40.000 0.00 0.00 0.00 4.26
2083 3847 5.828747 TCATTCAGTTATACAGTCGCTACC 58.171 41.667 0.00 0.00 0.00 3.18
2173 3944 6.106648 TGATTGGATCCATAGCAGACTTAG 57.893 41.667 17.06 0.00 0.00 2.18
2300 4071 3.116096 AGGTACTGGCTATCTGTTGGA 57.884 47.619 0.00 0.00 37.18 3.53
2423 4194 1.212375 ACCCCATTCATCCGATGACA 58.788 50.000 10.73 3.56 39.39 3.58
2534 4307 3.197766 TGGAGGCGTGATAGATTCTGTTT 59.802 43.478 0.00 0.00 0.00 2.83
2606 4379 7.148885 GCTTCTGATAAGATTATGAGCACGTAC 60.149 40.741 0.00 0.00 0.00 3.67
2694 4474 2.577700 CAGCCGTCTCCAGTCTACTAT 58.422 52.381 0.00 0.00 0.00 2.12
2818 4622 1.970114 GCCCCATGATCATCTGCGG 60.970 63.158 4.86 3.95 0.00 5.69
2819 4623 1.756665 CCCCATGATCATCTGCGGA 59.243 57.895 4.86 0.00 0.00 5.54
2820 4624 0.321387 CCCCATGATCATCTGCGGAG 60.321 60.000 4.86 0.00 0.00 4.63
2821 4625 0.683412 CCCATGATCATCTGCGGAGA 59.317 55.000 9.76 9.76 0.00 3.71
2822 4626 1.071228 CCCATGATCATCTGCGGAGAA 59.929 52.381 11.77 0.00 0.00 2.87
2823 4627 2.141517 CCATGATCATCTGCGGAGAAC 58.858 52.381 11.77 3.91 0.00 3.01
2842 4647 6.939163 GGAGAACCAACATATGCTTGATATCT 59.061 38.462 15.37 14.19 35.97 1.98
2863 4674 9.775854 ATATCTATGTATGATTATTCCTGCTGC 57.224 33.333 0.00 0.00 0.00 5.25
2925 4752 5.916883 GGTGACATATATTGCTTGATTGTGC 59.083 40.000 0.00 0.00 0.00 4.57
3078 4915 4.081807 GCCTCCTGAAAGCATCTTCAAAAT 60.082 41.667 0.00 0.00 34.96 1.82
3107 5028 9.693739 TTATGTCATAAGCTTCCCAAAATTCTA 57.306 29.630 0.00 0.00 0.00 2.10
3108 5029 7.630242 TGTCATAAGCTTCCCAAAATTCTAG 57.370 36.000 0.00 0.00 0.00 2.43
3163 5089 4.509970 TGTGGAACATTGTACTGTTTCTCG 59.490 41.667 7.56 0.00 45.67 4.04
3166 5092 4.377431 GGAACATTGTACTGTTTCTCGCTG 60.377 45.833 2.38 0.00 39.40 5.18
3167 5093 2.480419 ACATTGTACTGTTTCTCGCTGC 59.520 45.455 0.00 0.00 0.00 5.25
3169 5095 2.065993 TGTACTGTTTCTCGCTGCTC 57.934 50.000 0.00 0.00 0.00 4.26
3241 5188 9.444600 TGAATAAAACATACTACTCCTTCAACC 57.555 33.333 0.00 0.00 0.00 3.77
3242 5189 9.668497 GAATAAAACATACTACTCCTTCAACCT 57.332 33.333 0.00 0.00 0.00 3.50
3246 5193 7.793948 AACATACTACTCCTTCAACCTTAGT 57.206 36.000 0.00 0.00 0.00 2.24
3247 5194 7.793948 ACATACTACTCCTTCAACCTTAGTT 57.206 36.000 0.00 0.00 36.33 2.24
3248 5195 7.838884 ACATACTACTCCTTCAACCTTAGTTC 58.161 38.462 0.00 0.00 32.45 3.01
3249 5196 7.453752 ACATACTACTCCTTCAACCTTAGTTCA 59.546 37.037 0.00 0.00 32.45 3.18
3250 5197 6.742559 ACTACTCCTTCAACCTTAGTTCAA 57.257 37.500 0.00 0.00 32.45 2.69
3251 5198 7.133133 ACTACTCCTTCAACCTTAGTTCAAA 57.867 36.000 0.00 0.00 32.45 2.69
3252 5199 7.571025 ACTACTCCTTCAACCTTAGTTCAAAA 58.429 34.615 0.00 0.00 32.45 2.44
3253 5200 6.694877 ACTCCTTCAACCTTAGTTCAAAAC 57.305 37.500 0.00 0.00 32.45 2.43
3254 5201 6.424032 ACTCCTTCAACCTTAGTTCAAAACT 58.576 36.000 0.00 0.00 45.40 2.66
3255 5202 6.318900 ACTCCTTCAACCTTAGTTCAAAACTG 59.681 38.462 2.65 0.00 42.84 3.16
3256 5203 5.592688 TCCTTCAACCTTAGTTCAAAACTGG 59.407 40.000 2.65 0.00 42.84 4.00
3257 5204 5.592688 CCTTCAACCTTAGTTCAAAACTGGA 59.407 40.000 2.65 0.00 42.84 3.86
3258 5205 6.445357 TTCAACCTTAGTTCAAAACTGGAC 57.555 37.500 2.65 0.00 42.84 4.02
3259 5206 4.885325 TCAACCTTAGTTCAAAACTGGACC 59.115 41.667 2.65 0.00 42.84 4.46
3260 5207 4.513406 ACCTTAGTTCAAAACTGGACCA 57.487 40.909 2.65 0.00 42.84 4.02
3261 5208 4.204799 ACCTTAGTTCAAAACTGGACCAC 58.795 43.478 2.65 0.00 42.84 4.16
3262 5209 4.079958 ACCTTAGTTCAAAACTGGACCACT 60.080 41.667 2.65 0.00 42.84 4.00
3263 5210 4.887655 CCTTAGTTCAAAACTGGACCACTT 59.112 41.667 2.65 0.00 42.84 3.16
3264 5211 5.359860 CCTTAGTTCAAAACTGGACCACTTT 59.640 40.000 2.65 0.00 42.84 2.66
3265 5212 6.127451 CCTTAGTTCAAAACTGGACCACTTTT 60.127 38.462 6.14 6.14 42.84 2.27
3266 5213 5.072040 AGTTCAAAACTGGACCACTTTTG 57.928 39.130 23.24 23.24 41.01 2.44
3267 5214 4.081697 AGTTCAAAACTGGACCACTTTTGG 60.082 41.667 26.16 12.91 44.22 3.28
3268 5215 6.276241 AGTTCAAAACTGGACCACTTTTGGA 61.276 40.000 26.16 20.40 42.48 3.53
3269 5216 8.024057 AGTTCAAAACTGGACCACTTTTGGAG 62.024 42.308 26.16 11.47 42.48 3.86
3308 5255 5.990120 AATTTGAACAAATAGCTGCTCCT 57.010 34.783 4.91 0.00 39.88 3.69
3309 5256 5.990120 ATTTGAACAAATAGCTGCTCCTT 57.010 34.783 4.91 0.00 39.08 3.36
3310 5257 7.466746 AATTTGAACAAATAGCTGCTCCTTA 57.533 32.000 4.91 0.00 39.88 2.69
3311 5258 6.500684 TTTGAACAAATAGCTGCTCCTTAG 57.499 37.500 4.91 0.00 0.00 2.18
3314 5261 2.173569 ACAAATAGCTGCTCCTTAGGGG 59.826 50.000 4.91 0.00 0.00 4.79
3315 5262 2.173569 CAAATAGCTGCTCCTTAGGGGT 59.826 50.000 4.91 0.00 36.25 4.95
3316 5263 1.723288 ATAGCTGCTCCTTAGGGGTC 58.277 55.000 4.91 0.00 36.25 4.46
3317 5264 0.398664 TAGCTGCTCCTTAGGGGTCC 60.399 60.000 4.91 0.00 36.25 4.46
3318 5265 1.690985 GCTGCTCCTTAGGGGTCCT 60.691 63.158 0.00 0.00 37.71 3.85
3319 5266 1.977293 GCTGCTCCTTAGGGGTCCTG 61.977 65.000 0.00 0.00 34.61 3.86
3323 5272 1.633945 GCTCCTTAGGGGTCCTGAAAA 59.366 52.381 0.00 0.00 34.61 2.29
3367 5320 7.227910 TCAGTAAAAGAAAGAGCCAATTTACGT 59.772 33.333 0.00 0.00 37.95 3.57
3375 5328 4.579869 AGAGCCAATTTACGTCACTGAAT 58.420 39.130 0.00 0.00 0.00 2.57
3414 5367 3.771216 ACCACAGGATTTTCATGCTCTT 58.229 40.909 0.00 0.00 30.14 2.85
3429 5382 5.129980 TCATGCTCTTATCCTGAATGACACT 59.870 40.000 0.00 0.00 0.00 3.55
3442 5395 6.294120 CCTGAATGACACTTGTGATTGCTAAA 60.294 38.462 7.83 0.00 32.15 1.85
3496 5449 0.392193 GATGTGTCCTGTCCTGCCTG 60.392 60.000 0.00 0.00 0.00 4.85
3497 5450 2.359230 GTGTCCTGTCCTGCCTGC 60.359 66.667 0.00 0.00 0.00 4.85
3498 5451 3.640407 TGTCCTGTCCTGCCTGCC 61.640 66.667 0.00 0.00 0.00 4.85
3499 5452 4.416738 GTCCTGTCCTGCCTGCCC 62.417 72.222 0.00 0.00 0.00 5.36
3500 5453 4.980592 TCCTGTCCTGCCTGCCCA 62.981 66.667 0.00 0.00 0.00 5.36
3519 5472 1.352622 ACCCACCAGCTGAAACCTGA 61.353 55.000 17.39 0.00 32.03 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.732938 GCTTTGTCTAGGAATGAATGCAGC 60.733 45.833 0.00 0.00 0.00 5.25
58 59 4.520492 CACATGAAGGGTTAAGCTTTGTCT 59.480 41.667 3.20 0.00 0.00 3.41
98 99 1.888512 TGCAGAGATGTTTTTCCTGCC 59.111 47.619 0.00 0.00 46.85 4.85
201 202 0.248990 CCAGTGAGCGAGATGAGAGC 60.249 60.000 0.00 0.00 0.00 4.09
203 204 1.098869 GACCAGTGAGCGAGATGAGA 58.901 55.000 0.00 0.00 0.00 3.27
224 225 5.408299 CGATTATGCAGGATAAATCGACCAA 59.592 40.000 18.30 0.00 33.72 3.67
262 264 0.809636 CAGTTGTGACACCGCAGACA 60.810 55.000 2.45 0.00 33.88 3.41
268 270 1.548973 GCTCGACAGTTGTGACACCG 61.549 60.000 2.45 0.00 0.00 4.94
279 281 0.109272 TTCAGTAAGGCGCTCGACAG 60.109 55.000 7.64 0.00 0.00 3.51
284 286 1.071605 CAGTGTTCAGTAAGGCGCTC 58.928 55.000 7.64 0.00 0.00 5.03
288 290 1.801178 GCACTCAGTGTTCAGTAAGGC 59.199 52.381 6.68 0.00 35.75 4.35
304 306 4.039730 ACATAACTTCTCACTCACTGCACT 59.960 41.667 0.00 0.00 0.00 4.40
332 334 1.421268 TGGTCTCTGCACCAGACATTT 59.579 47.619 18.57 0.00 41.84 2.32
335 337 4.293610 TGGTCTCTGCACCAGACA 57.706 55.556 18.57 6.35 41.84 3.41
340 342 0.037790 GACACTCTGGTCTCTGCACC 60.038 60.000 0.00 0.00 34.92 5.01
358 360 0.687757 AGCAAGCCCGTAGATGGAGA 60.688 55.000 0.00 0.00 0.00 3.71
359 361 0.179000 AAGCAAGCCCGTAGATGGAG 59.821 55.000 0.00 0.00 0.00 3.86
370 372 2.680577 CACATGGAAGAAAAGCAAGCC 58.319 47.619 0.00 0.00 0.00 4.35
390 392 5.059833 CCAAGTACATAAGGAATCTCTGGC 58.940 45.833 0.00 0.00 0.00 4.85
392 394 5.525378 GTGCCAAGTACATAAGGAATCTCTG 59.475 44.000 0.00 0.00 0.00 3.35
397 399 7.480760 AAAATGTGCCAAGTACATAAGGAAT 57.519 32.000 0.00 0.00 37.86 3.01
399 401 6.266558 ACAAAAATGTGCCAAGTACATAAGGA 59.733 34.615 0.00 0.00 37.86 3.36
404 406 6.922957 CACTAACAAAAATGTGCCAAGTACAT 59.077 34.615 0.00 0.00 40.33 2.29
411 413 5.590530 AGAACACTAACAAAAATGTGCCA 57.409 34.783 0.00 0.00 34.14 4.92
417 419 9.174166 AGAACACACTAGAACACTAACAAAAAT 57.826 29.630 0.00 0.00 0.00 1.82
480 553 8.459911 TGATCAATTCACATTTCTGCATAGAT 57.540 30.769 0.00 0.00 31.81 1.98
486 559 7.821595 TCATTTGATCAATTCACATTTCTGC 57.178 32.000 9.40 0.00 32.84 4.26
489 562 8.475331 AGCTTCATTTGATCAATTCACATTTC 57.525 30.769 9.40 0.00 32.84 2.17
510 583 7.745620 TTTCCTCTCTCGAAAAATAAAGCTT 57.254 32.000 0.00 0.00 0.00 3.74
511 584 7.607991 TCATTTCCTCTCTCGAAAAATAAAGCT 59.392 33.333 0.00 0.00 33.19 3.74
512 585 7.752695 TCATTTCCTCTCTCGAAAAATAAAGC 58.247 34.615 0.00 0.00 33.19 3.51
518 591 8.677300 CCATTTATCATTTCCTCTCTCGAAAAA 58.323 33.333 0.00 0.00 33.19 1.94
556 632 6.525629 AGCTTGATTGACTACACTACAAAGT 58.474 36.000 0.00 0.00 35.91 2.66
569 645 9.914131 AAAGGAGTAAATTTAAGCTTGATTGAC 57.086 29.630 9.86 12.10 0.00 3.18
632 708 8.749354 CCCCTACAAAGTAAATTTAAGCTTGAT 58.251 33.333 9.86 0.00 0.00 2.57
633 709 7.726738 ACCCCTACAAAGTAAATTTAAGCTTGA 59.273 33.333 9.86 0.00 0.00 3.02
634 710 7.892609 ACCCCTACAAAGTAAATTTAAGCTTG 58.107 34.615 9.86 6.56 0.00 4.01
635 711 9.763837 ATACCCCTACAAAGTAAATTTAAGCTT 57.236 29.630 3.48 3.48 0.00 3.74
636 712 9.763837 AATACCCCTACAAAGTAAATTTAAGCT 57.236 29.630 0.00 0.00 0.00 3.74
669 745 9.797642 CTAAAGTAAGTACCCCTTTCCTAAAAA 57.202 33.333 5.56 0.00 34.46 1.94
670 746 9.169721 TCTAAAGTAAGTACCCCTTTCCTAAAA 57.830 33.333 5.56 0.00 34.46 1.52
671 747 8.740616 TCTAAAGTAAGTACCCCTTTCCTAAA 57.259 34.615 5.56 0.00 34.46 1.85
672 748 8.740616 TTCTAAAGTAAGTACCCCTTTCCTAA 57.259 34.615 5.56 0.00 34.46 2.69
673 749 8.740616 TTTCTAAAGTAAGTACCCCTTTCCTA 57.259 34.615 5.56 0.00 34.46 2.94
674 750 7.256944 CCTTTCTAAAGTAAGTACCCCTTTCCT 60.257 40.741 5.56 0.00 34.20 3.36
675 751 6.883217 CCTTTCTAAAGTAAGTACCCCTTTCC 59.117 42.308 5.56 0.00 34.20 3.13
676 752 6.883217 CCCTTTCTAAAGTAAGTACCCCTTTC 59.117 42.308 5.56 0.00 34.20 2.62
677 753 6.240380 CCCCTTTCTAAAGTAAGTACCCCTTT 60.240 42.308 2.03 7.07 34.20 3.11
678 754 5.252397 CCCCTTTCTAAAGTAAGTACCCCTT 59.748 44.000 2.03 0.00 34.20 3.95
679 755 4.786994 CCCCTTTCTAAAGTAAGTACCCCT 59.213 45.833 2.03 0.00 34.20 4.79
680 756 4.080129 CCCCCTTTCTAAAGTAAGTACCCC 60.080 50.000 2.03 0.00 34.20 4.95
681 757 4.537688 ACCCCCTTTCTAAAGTAAGTACCC 59.462 45.833 2.03 0.00 34.20 3.69
682 758 5.768980 ACCCCCTTTCTAAAGTAAGTACC 57.231 43.478 2.03 0.00 34.20 3.34
685 761 9.120658 AGTAAATACCCCCTTTCTAAAGTAAGT 57.879 33.333 2.03 0.00 34.20 2.24
688 764 9.788815 AGTAGTAAATACCCCCTTTCTAAAGTA 57.211 33.333 2.03 0.00 34.67 2.24
689 765 8.691194 AGTAGTAAATACCCCCTTTCTAAAGT 57.309 34.615 2.03 0.00 34.67 2.66
690 766 9.970553 AAAGTAGTAAATACCCCCTTTCTAAAG 57.029 33.333 0.00 0.00 34.67 1.85
718 794 9.964354 GTAGTAAATACCCCCTTTCTTCTAAAA 57.036 33.333 0.00 0.00 0.00 1.52
719 795 9.342736 AGTAGTAAATACCCCCTTTCTTCTAAA 57.657 33.333 0.00 0.00 34.67 1.85
720 796 8.922229 AGTAGTAAATACCCCCTTTCTTCTAA 57.078 34.615 0.00 0.00 34.67 2.10
721 797 9.652114 CTAGTAGTAAATACCCCCTTTCTTCTA 57.348 37.037 0.00 0.00 34.67 2.10
722 798 7.567994 CCTAGTAGTAAATACCCCCTTTCTTCT 59.432 40.741 0.00 0.00 34.67 2.85
723 799 7.566509 TCCTAGTAGTAAATACCCCCTTTCTTC 59.433 40.741 0.00 0.00 34.67 2.87
724 800 7.433360 TCCTAGTAGTAAATACCCCCTTTCTT 58.567 38.462 0.00 0.00 34.67 2.52
725 801 7.001653 TCCTAGTAGTAAATACCCCCTTTCT 57.998 40.000 0.00 0.00 34.67 2.52
726 802 7.309683 CGATCCTAGTAGTAAATACCCCCTTTC 60.310 44.444 0.00 0.00 34.67 2.62
727 803 6.496218 CGATCCTAGTAGTAAATACCCCCTTT 59.504 42.308 0.00 0.00 34.67 3.11
728 804 6.015282 CGATCCTAGTAGTAAATACCCCCTT 58.985 44.000 0.00 0.00 34.67 3.95
729 805 5.314306 TCGATCCTAGTAGTAAATACCCCCT 59.686 44.000 0.00 0.00 34.67 4.79
730 806 5.574188 TCGATCCTAGTAGTAAATACCCCC 58.426 45.833 0.00 0.00 34.67 5.40
731 807 6.888632 TGATCGATCCTAGTAGTAAATACCCC 59.111 42.308 22.31 0.00 34.67 4.95
732 808 7.415429 GCTGATCGATCCTAGTAGTAAATACCC 60.415 44.444 22.31 0.00 34.67 3.69
733 809 7.474190 GCTGATCGATCCTAGTAGTAAATACC 58.526 42.308 22.31 0.00 34.67 2.73
734 810 7.064371 TCGCTGATCGATCCTAGTAGTAAATAC 59.936 40.741 22.31 0.00 43.16 1.89
735 811 7.101700 TCGCTGATCGATCCTAGTAGTAAATA 58.898 38.462 22.31 0.00 43.16 1.40
736 812 5.938710 TCGCTGATCGATCCTAGTAGTAAAT 59.061 40.000 22.31 0.00 43.16 1.40
737 813 5.303165 TCGCTGATCGATCCTAGTAGTAAA 58.697 41.667 22.31 0.00 43.16 2.01
738 814 4.891260 TCGCTGATCGATCCTAGTAGTAA 58.109 43.478 22.31 0.00 43.16 2.24
739 815 4.532314 TCGCTGATCGATCCTAGTAGTA 57.468 45.455 22.31 0.32 43.16 1.82
740 816 3.404224 TCGCTGATCGATCCTAGTAGT 57.596 47.619 22.31 0.00 43.16 2.73
770 846 7.388224 AGAATTAGATCGCTGATCGTCTACTAA 59.612 37.037 11.21 0.00 43.17 2.24
771 847 6.874664 AGAATTAGATCGCTGATCGTCTACTA 59.125 38.462 11.21 0.00 43.17 1.82
772 848 5.703592 AGAATTAGATCGCTGATCGTCTACT 59.296 40.000 11.21 8.03 43.17 2.57
773 849 5.792962 CAGAATTAGATCGCTGATCGTCTAC 59.207 44.000 11.21 6.50 43.17 2.59
775 851 4.320861 CCAGAATTAGATCGCTGATCGTCT 60.321 45.833 11.21 10.04 43.17 4.18
778 854 2.665537 GCCAGAATTAGATCGCTGATCG 59.334 50.000 11.21 0.00 43.17 3.69
779 855 3.657634 TGCCAGAATTAGATCGCTGATC 58.342 45.455 9.60 9.60 39.17 2.92
782 858 5.173664 TGATATGCCAGAATTAGATCGCTG 58.826 41.667 0.00 0.00 0.00 5.18
786 862 7.256286 GCCAATTGATATGCCAGAATTAGATC 58.744 38.462 7.12 0.00 0.00 2.75
799 875 5.337009 GGCTAAGATTGGGCCAATTGATATG 60.337 44.000 31.17 19.30 44.69 1.78
824 900 3.334583 ACGAGGCATTTCTTCTTAGCA 57.665 42.857 0.00 0.00 0.00 3.49
831 907 1.586154 CCCGCAACGAGGCATTTCTT 61.586 55.000 0.00 0.00 0.00 2.52
832 908 2.040544 CCCGCAACGAGGCATTTCT 61.041 57.895 0.00 0.00 0.00 2.52
981 1061 1.522668 TGGTGATGCTTTCGTCTTGG 58.477 50.000 0.00 0.00 0.00 3.61
982 1062 2.159476 CCATGGTGATGCTTTCGTCTTG 60.159 50.000 2.57 0.00 0.00 3.02
1261 1526 3.324930 CAGCACCAGAGCTCCCCA 61.325 66.667 10.93 0.00 44.54 4.96
1292 1558 2.618816 GGGACACATTTCCTCATCAGCA 60.619 50.000 0.00 0.00 35.76 4.41
1411 1679 8.441572 AGGAGTATAGCTGAACAATACTCTCTA 58.558 37.037 23.42 0.00 45.91 2.43
1419 1694 7.175104 TCCAAAAAGGAGTATAGCTGAACAAT 58.825 34.615 0.00 0.00 43.07 2.71
1506 1990 2.159627 GCTACTGGGATGAACAAACACG 59.840 50.000 0.00 0.00 0.00 4.49
1605 2092 7.905604 TGTGAATGACAAGACTCGATTTATT 57.094 32.000 0.00 0.00 0.00 1.40
1627 2114 1.064003 TCTACCACCACAAGGCATGT 58.936 50.000 0.00 0.00 45.34 3.21
1636 2123 4.821805 CCCAATGATACAATCTACCACCAC 59.178 45.833 0.00 0.00 0.00 4.16
1640 2127 5.372363 ACATCCCCAATGATACAATCTACCA 59.628 40.000 0.00 0.00 38.83 3.25
1712 2199 6.936279 TGGCACTATAATCAACTAGGATAGC 58.064 40.000 0.00 0.00 44.39 2.97
1741 2228 3.786818 GCGTAGAAGTGAATGATGCTTGC 60.787 47.826 0.00 0.00 0.00 4.01
1817 2304 8.696374 GCTACTGGGATGAATAAGCACTATATA 58.304 37.037 0.00 0.00 0.00 0.86
1819 2306 6.070767 GGCTACTGGGATGAATAAGCACTATA 60.071 42.308 0.00 0.00 0.00 1.31
1820 2307 5.280215 GGCTACTGGGATGAATAAGCACTAT 60.280 44.000 0.00 0.00 0.00 2.12
1822 2309 3.181450 GGCTACTGGGATGAATAAGCACT 60.181 47.826 0.00 0.00 0.00 4.40
1823 2310 3.142174 GGCTACTGGGATGAATAAGCAC 58.858 50.000 0.00 0.00 0.00 4.40
1824 2311 3.048600 AGGCTACTGGGATGAATAAGCA 58.951 45.455 0.00 0.00 0.00 3.91
1825 2312 3.778954 AGGCTACTGGGATGAATAAGC 57.221 47.619 0.00 0.00 0.00 3.09
1827 2314 7.633018 AGAATAAGGCTACTGGGATGAATAA 57.367 36.000 0.00 0.00 0.00 1.40
1828 2315 7.633018 AAGAATAAGGCTACTGGGATGAATA 57.367 36.000 0.00 0.00 0.00 1.75
1829 2316 6.521527 AAGAATAAGGCTACTGGGATGAAT 57.478 37.500 0.00 0.00 0.00 2.57
1830 2317 5.975988 AAGAATAAGGCTACTGGGATGAA 57.024 39.130 0.00 0.00 0.00 2.57
1831 2318 5.428457 TCAAAGAATAAGGCTACTGGGATGA 59.572 40.000 0.00 0.00 0.00 2.92
1859 3623 4.965119 AACCTCTAAAATGTCCAATCGC 57.035 40.909 0.00 0.00 0.00 4.58
1910 3674 1.136169 AGGCGCGAATTGTTTACGTTC 60.136 47.619 12.10 0.00 0.00 3.95
1914 3678 0.796870 GCCAGGCGCGAATTGTTTAC 60.797 55.000 12.10 0.00 0.00 2.01
1924 3688 1.815421 ATTAGAACAGCCAGGCGCG 60.815 57.895 5.55 0.00 44.76 6.86
1926 3690 0.745845 AGCATTAGAACAGCCAGGCG 60.746 55.000 5.55 3.56 0.00 5.52
1941 3705 3.633609 ATGCACCGCCACAGAGCAT 62.634 57.895 0.00 0.00 40.77 3.79
1956 3720 6.039717 ACTCAACATACCCAATGATACAATGC 59.960 38.462 0.00 0.00 39.07 3.56
2038 3802 4.707030 TGCTTGTGAAATTAGCATCCAG 57.293 40.909 0.00 0.00 39.79 3.86
2051 3815 7.105588 ACTGTATAACTGAATGATGCTTGTGA 58.894 34.615 0.00 0.00 0.00 3.58
2052 3816 7.312657 ACTGTATAACTGAATGATGCTTGTG 57.687 36.000 0.00 0.00 0.00 3.33
2053 3817 6.256539 CGACTGTATAACTGAATGATGCTTGT 59.743 38.462 0.00 0.00 0.00 3.16
2075 3839 1.871080 CAATGGATGGAGGTAGCGAC 58.129 55.000 0.00 0.00 0.00 5.19
2101 3865 7.015584 ACCCCTATTCAGCAAATCAATAATTCC 59.984 37.037 0.00 0.00 0.00 3.01
2102 3866 7.955918 ACCCCTATTCAGCAAATCAATAATTC 58.044 34.615 0.00 0.00 0.00 2.17
2109 3873 4.272489 CTGAACCCCTATTCAGCAAATCA 58.728 43.478 2.78 0.00 46.69 2.57
2173 3944 7.012327 TGGCATATTTGTAGCAAATACTCTCAC 59.988 37.037 14.18 5.57 35.24 3.51
2300 4071 1.530771 GGGATCTGATGGCTGTGCT 59.469 57.895 0.00 0.00 0.00 4.40
2423 4194 1.616628 AAGATCCAAGGGACGGCCT 60.617 57.895 7.57 0.00 32.98 5.19
2534 4307 2.093890 CAGCACCACTCAATATGCCAA 58.906 47.619 0.00 0.00 38.92 4.52
2606 4379 7.742151 TGACGAAATTGTTGAAGATCATACAG 58.258 34.615 0.00 0.00 0.00 2.74
2694 4474 3.646162 AGGAATCATATTAGGACACGGCA 59.354 43.478 0.00 0.00 0.00 5.69
2807 4611 1.936547 GTTGGTTCTCCGCAGATGATC 59.063 52.381 0.00 0.00 36.30 2.92
2818 4622 7.976135 AGATATCAAGCATATGTTGGTTCTC 57.024 36.000 5.32 5.43 44.02 2.87
2819 4623 9.445878 CATAGATATCAAGCATATGTTGGTTCT 57.554 33.333 5.32 10.80 44.02 3.01
2820 4624 9.224267 ACATAGATATCAAGCATATGTTGGTTC 57.776 33.333 5.32 5.43 44.02 3.62
2842 4647 5.639082 CACGCAGCAGGAATAATCATACATA 59.361 40.000 0.00 0.00 0.00 2.29
2863 4674 4.687948 AGATAAAGCATCGATTGGATCACG 59.312 41.667 0.00 0.00 38.81 4.35
2925 4752 6.507023 AGACAAGATGCACCTTTTTAAGTTG 58.493 36.000 0.00 0.00 0.00 3.16
2927 4754 6.507023 CAAGACAAGATGCACCTTTTTAAGT 58.493 36.000 0.00 0.00 0.00 2.24
2976 4803 7.225538 ACAAGAAAACATCAACACAAACAAACA 59.774 29.630 0.00 0.00 0.00 2.83
3107 5028 4.844349 TGCCCTTCAGCTAAATAAGTCT 57.156 40.909 0.00 0.00 0.00 3.24
3108 5029 4.884164 ACATGCCCTTCAGCTAAATAAGTC 59.116 41.667 0.00 0.00 0.00 3.01
3163 5089 0.109735 GCCCTTTACAAACGAGCAGC 60.110 55.000 0.00 0.00 0.00 5.25
3166 5092 1.607148 ACAAGCCCTTTACAAACGAGC 59.393 47.619 0.00 0.00 0.00 5.03
3167 5093 4.062991 AGTACAAGCCCTTTACAAACGAG 58.937 43.478 0.00 0.00 0.00 4.18
3169 5095 4.823790 AAGTACAAGCCCTTTACAAACG 57.176 40.909 0.00 0.00 0.00 3.60
3231 5178 6.238759 CCAGTTTTGAACTAAGGTTGAAGGAG 60.239 42.308 0.00 0.00 40.46 3.69
3233 5180 5.592688 TCCAGTTTTGAACTAAGGTTGAAGG 59.407 40.000 0.00 0.00 40.46 3.46
3234 5181 6.459710 GGTCCAGTTTTGAACTAAGGTTGAAG 60.460 42.308 0.00 0.00 40.46 3.02
3235 5182 5.358725 GGTCCAGTTTTGAACTAAGGTTGAA 59.641 40.000 0.00 0.00 40.46 2.69
3237 5184 4.642885 TGGTCCAGTTTTGAACTAAGGTTG 59.357 41.667 0.00 0.00 40.46 3.77
3238 5185 4.643334 GTGGTCCAGTTTTGAACTAAGGTT 59.357 41.667 0.00 0.00 40.46 3.50
3240 5187 4.461198 AGTGGTCCAGTTTTGAACTAAGG 58.539 43.478 0.00 0.00 40.46 2.69
3241 5188 6.451064 AAAGTGGTCCAGTTTTGAACTAAG 57.549 37.500 17.56 0.00 40.46 2.18
3242 5189 6.844097 AAAAGTGGTCCAGTTTTGAACTAA 57.156 33.333 28.95 0.00 42.88 2.24
3249 5196 3.031013 CCTCCAAAAGTGGTCCAGTTTT 58.969 45.455 25.64 25.64 44.59 2.43
3250 5197 2.243736 TCCTCCAAAAGTGGTCCAGTTT 59.756 45.455 17.56 17.56 46.11 2.66
3251 5198 1.850345 TCCTCCAAAAGTGGTCCAGTT 59.150 47.619 6.09 6.09 46.11 3.16
3252 5199 1.518367 TCCTCCAAAAGTGGTCCAGT 58.482 50.000 0.00 0.00 46.11 4.00
3253 5200 2.158608 ACTTCCTCCAAAAGTGGTCCAG 60.159 50.000 0.00 0.00 46.11 3.86
3254 5201 1.850345 ACTTCCTCCAAAAGTGGTCCA 59.150 47.619 0.00 0.00 46.11 4.02
3255 5202 2.658807 ACTTCCTCCAAAAGTGGTCC 57.341 50.000 0.00 0.00 46.11 4.46
3256 5203 4.353383 ACTACTTCCTCCAAAAGTGGTC 57.647 45.455 0.00 0.00 42.58 4.02
3257 5204 5.152934 TCTACTACTTCCTCCAAAAGTGGT 58.847 41.667 9.45 9.45 46.25 4.16
3291 5238 3.879892 CCCTAAGGAGCAGCTATTTGTTC 59.120 47.826 0.00 0.00 33.47 3.18
3298 5245 0.398664 GGACCCCTAAGGAGCAGCTA 60.399 60.000 0.00 0.00 39.89 3.32
3303 5250 1.286248 TTTCAGGACCCCTAAGGAGC 58.714 55.000 0.00 0.00 39.89 4.70
3305 5252 2.377531 GGTTTTTCAGGACCCCTAAGGA 59.622 50.000 0.00 0.00 39.89 3.36
3306 5253 2.378886 AGGTTTTTCAGGACCCCTAAGG 59.621 50.000 0.00 0.00 43.78 2.69
3308 5255 2.787035 ACAGGTTTTTCAGGACCCCTAA 59.213 45.455 0.00 0.00 36.57 2.69
3309 5256 2.424793 ACAGGTTTTTCAGGACCCCTA 58.575 47.619 0.00 0.00 36.57 3.53
3310 5257 1.231963 ACAGGTTTTTCAGGACCCCT 58.768 50.000 0.00 0.00 36.57 4.79
3311 5258 2.082140 AACAGGTTTTTCAGGACCCC 57.918 50.000 0.00 0.00 36.57 4.95
3367 5320 1.702182 TTTGGCTGCCAATTCAGTGA 58.298 45.000 32.62 14.81 43.55 3.41
3394 5347 5.009410 GGATAAGAGCATGAAAATCCTGTGG 59.991 44.000 0.00 0.00 32.00 4.17
3396 5349 6.011122 AGGATAAGAGCATGAAAATCCTGT 57.989 37.500 12.13 0.00 41.24 4.00
3400 5353 8.074972 GTCATTCAGGATAAGAGCATGAAAATC 58.925 37.037 0.00 0.00 39.15 2.17
3414 5367 5.355071 GCAATCACAAGTGTCATTCAGGATA 59.645 40.000 0.00 0.00 0.00 2.59
3442 5395 7.933577 TCCAATGCAGAAACGAAGATATTATCT 59.066 33.333 0.08 0.08 42.61 1.98
3496 5449 3.808218 TTTCAGCTGGTGGGTGGGC 62.808 63.158 15.13 0.00 43.01 5.36
3497 5450 1.903404 GTTTCAGCTGGTGGGTGGG 60.903 63.158 15.13 0.00 43.01 4.61
3498 5451 1.903404 GGTTTCAGCTGGTGGGTGG 60.903 63.158 15.13 0.00 43.01 4.61
3499 5452 1.151450 AGGTTTCAGCTGGTGGGTG 59.849 57.895 15.13 0.00 44.04 4.61
3500 5453 1.151450 CAGGTTTCAGCTGGTGGGT 59.849 57.895 15.13 0.00 39.87 4.51


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

AutoCloner maintained by Alex Coulton.