Multiple sequence alignment - TraesCS7B01G227700

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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 TraesCS7B01G227700 chr7B 100.000 4643 0 0 1 4643 427887202 427882560 0.000000e+00 8575.0
1 TraesCS7B01G227700 chr7B 90.558 3103 146 70 1621 4643 405970930 405967895 0.000000e+00 3971.0
2 TraesCS7B01G227700 chr7B 93.246 533 34 2 3 534 406019900 406019369 0.000000e+00 784.0
3 TraesCS7B01G227700 chr7B 93.246 533 34 2 3 534 406044483 406043952 0.000000e+00 784.0
4 TraesCS7B01G227700 chr7B 95.132 493 16 1 975 1459 405971518 405971026 0.000000e+00 771.0
5 TraesCS7B01G227700 chr7B 89.313 131 14 0 548 678 406019382 406019252 1.030000e-36 165.0
6 TraesCS7B01G227700 chr7B 89.313 131 13 1 548 678 406043965 406043836 3.720000e-36 163.0
7 TraesCS7B01G227700 chr7B 86.400 125 5 7 872 984 405972497 405972373 4.880000e-25 126.0
8 TraesCS7B01G227700 chr7B 85.124 121 13 2 675 794 406006259 406006143 8.160000e-23 119.0
9 TraesCS7B01G227700 chr7B 92.857 56 4 0 1500 1555 405971027 405970972 1.070000e-11 82.4
10 TraesCS7B01G227700 chr7B 88.060 67 6 2 2102 2166 382279243 382279309 1.390000e-10 78.7
11 TraesCS7B01G227700 chr7A 90.976 2161 131 28 1500 3624 475207629 475205497 0.000000e+00 2852.0
12 TraesCS7B01G227700 chr7A 88.669 556 21 8 944 1459 475208181 475207628 1.410000e-179 640.0
13 TraesCS7B01G227700 chr7A 95.380 303 6 5 4345 4643 475204859 475204561 4.200000e-130 475.0
14 TraesCS7B01G227700 chr7A 79.710 207 18 13 3813 4008 475205386 475205193 1.360000e-25 128.0
15 TraesCS7B01G227700 chr7A 88.372 86 2 1 4081 4166 475204986 475204909 3.820000e-16 97.1
16 TraesCS7B01G227700 chr7D 93.647 1511 59 12 2157 3641 413545576 413544077 0.000000e+00 2224.0
17 TraesCS7B01G227700 chr7D 83.666 1053 87 28 3 1019 413547854 413546851 0.000000e+00 913.0
18 TraesCS7B01G227700 chr7D 88.619 659 51 14 1500 2157 413546278 413545643 0.000000e+00 780.0
19 TraesCS7B01G227700 chr7D 90.973 565 25 6 921 1459 413546841 413546277 0.000000e+00 737.0
20 TraesCS7B01G227700 chr7D 95.561 383 10 2 4264 4643 413535619 413535241 1.430000e-169 606.0
21 TraesCS7B01G227700 chr7D 82.035 462 45 26 3813 4253 413543984 413543540 4.420000e-95 359.0
22 TraesCS7B01G227700 chr7D 94.737 38 0 2 4242 4279 413540452 413540417 1.800000e-04 58.4
23 TraesCS7B01G227700 chr3D 84.143 782 90 20 3 779 298582407 298583159 0.000000e+00 726.0
24 TraesCS7B01G227700 chr3D 89.888 534 51 3 3 534 362870705 362870173 0.000000e+00 684.0
25 TraesCS7B01G227700 chr1B 83.739 781 90 22 3 779 651552424 651551677 0.000000e+00 704.0
26 TraesCS7B01G227700 chr1B 90.909 66 4 1 2110 2175 118121150 118121087 2.300000e-13 87.9
27 TraesCS7B01G227700 chr1B 90.909 66 4 2 2110 2175 118132216 118132279 2.300000e-13 87.9
28 TraesCS7B01G227700 chr5D 90.056 533 51 2 3 534 324384947 324384416 0.000000e+00 689.0
29 TraesCS7B01G227700 chr5D 90.000 530 51 2 3 531 555477496 555478024 0.000000e+00 684.0
30 TraesCS7B01G227700 chr1A 90.000 530 51 2 3 531 362047547 362048075 0.000000e+00 684.0
31 TraesCS7B01G227700 chr1A 92.308 65 3 1 2110 2174 74435810 74435748 1.780000e-14 91.6
32 TraesCS7B01G227700 chr1D 92.424 66 3 2 2110 2175 74277676 74277739 4.950000e-15 93.5
33 TraesCS7B01G227700 chrUn 96.226 53 1 1 2107 2159 65440854 65440905 8.280000e-13 86.1


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 TraesCS7B01G227700 chr7B 427882560 427887202 4642 True 8575.000000 8575 100.000000 1 4643 1 chr7B.!!$R2 4642
1 TraesCS7B01G227700 chr7B 405967895 405972497 4602 True 1237.600000 3971 91.236750 872 4643 4 chr7B.!!$R3 3771
2 TraesCS7B01G227700 chr7B 406019252 406019900 648 True 474.500000 784 91.279500 3 678 2 chr7B.!!$R4 675
3 TraesCS7B01G227700 chr7B 406043836 406044483 647 True 473.500000 784 91.279500 3 678 2 chr7B.!!$R5 675
4 TraesCS7B01G227700 chr7A 475204561 475208181 3620 True 838.420000 2852 88.621400 944 4643 5 chr7A.!!$R1 3699
5 TraesCS7B01G227700 chr7D 413540417 413547854 7437 True 845.233333 2224 88.946167 3 4279 6 chr7D.!!$R2 4276
6 TraesCS7B01G227700 chr3D 298582407 298583159 752 False 726.000000 726 84.143000 3 779 1 chr3D.!!$F1 776
7 TraesCS7B01G227700 chr3D 362870173 362870705 532 True 684.000000 684 89.888000 3 534 1 chr3D.!!$R1 531
8 TraesCS7B01G227700 chr1B 651551677 651552424 747 True 704.000000 704 83.739000 3 779 1 chr1B.!!$R2 776
9 TraesCS7B01G227700 chr5D 324384416 324384947 531 True 689.000000 689 90.056000 3 534 1 chr5D.!!$R1 531
10 TraesCS7B01G227700 chr5D 555477496 555478024 528 False 684.000000 684 90.000000 3 531 1 chr5D.!!$F1 528
11 TraesCS7B01G227700 chr1A 362047547 362048075 528 False 684.000000 684 90.000000 3 531 1 chr1A.!!$F1 528

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
846 874 0.096628 TTCTTAGCGTCGCGTCTCTC 59.903 55.000 12.30 0.00 0.00 3.20 F
1491 2556 0.166814 GGCTAAGCGCTCAGTGTTTG 59.833 55.000 12.06 0.00 39.13 2.93 F
1660 2726 0.391661 GCTGTGGCTGAGGAAATCGA 60.392 55.000 0.00 0.00 35.22 3.59 F
2633 3792 1.342496 TCGATGATGAGGAGCCACATC 59.658 52.381 16.83 16.83 41.94 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2960 0.322277 CACCCACAAGATGAGCAGCT 60.322 55.0 0.00 0.00 0.00 4.24 R
3232 4403 0.967380 AAAGCCAATTCCTCAGCCCG 60.967 55.0 0.00 0.00 0.00 6.13 R
3333 4504 1.382692 GCCCATCTCTTTCAGCTGGC 61.383 60.0 15.13 0.56 37.11 4.85 R
3881 5060 0.388134 TACAGCTCGACCTGCGTTTC 60.388 55.0 7.66 0.00 41.80 2.78 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
102 104 4.708576 TTGTGTTCCTACATGGTGGTAA 57.291 40.909 0.00 0.00 36.50 2.85
160 162 3.953612 TGGCAACATCTACCAATCATTCC 59.046 43.478 0.00 0.00 46.17 3.01
231 233 5.827797 ACAGAATGACAAACCACATACAACT 59.172 36.000 0.00 0.00 39.69 3.16
427 430 9.435688 AAGTTAAATCATGTAAAAATCTTGCCC 57.564 29.630 0.00 0.00 0.00 5.36
439 442 9.660180 GTAAAAATCTTGCCCATTTATTTACCA 57.340 29.630 0.00 0.00 0.00 3.25
519 522 0.179048 CAGGACTTGCAGGTGTCACA 60.179 55.000 6.05 0.00 35.11 3.58
520 523 0.107456 AGGACTTGCAGGTGTCACAG 59.893 55.000 6.05 0.00 35.11 3.66
521 524 0.886490 GGACTTGCAGGTGTCACAGG 60.886 60.000 6.05 0.00 35.11 4.00
522 525 0.886490 GACTTGCAGGTGTCACAGGG 60.886 60.000 6.05 0.00 33.75 4.45
523 526 1.344953 ACTTGCAGGTGTCACAGGGA 61.345 55.000 0.00 0.00 0.00 4.20
524 527 0.604780 CTTGCAGGTGTCACAGGGAG 60.605 60.000 5.12 0.00 0.00 4.30
525 528 1.344953 TTGCAGGTGTCACAGGGAGT 61.345 55.000 5.12 0.00 0.00 3.85
526 529 1.004440 GCAGGTGTCACAGGGAGTC 60.004 63.158 5.12 0.00 0.00 3.36
527 530 1.476007 GCAGGTGTCACAGGGAGTCT 61.476 60.000 5.12 0.00 0.00 3.24
528 531 0.605589 CAGGTGTCACAGGGAGTCTC 59.394 60.000 5.12 0.00 0.00 3.36
529 532 0.485099 AGGTGTCACAGGGAGTCTCT 59.515 55.000 5.12 0.00 0.00 3.10
530 533 1.133009 AGGTGTCACAGGGAGTCTCTT 60.133 52.381 5.12 0.00 0.00 2.85
531 534 1.694696 GGTGTCACAGGGAGTCTCTTT 59.305 52.381 5.12 0.00 0.00 2.52
532 535 2.104963 GGTGTCACAGGGAGTCTCTTTT 59.895 50.000 5.12 0.00 0.00 2.27
533 536 3.433740 GGTGTCACAGGGAGTCTCTTTTT 60.434 47.826 5.12 0.00 0.00 1.94
603 608 9.323985 AGACATCACATTAAGCTATTTCTCTTC 57.676 33.333 0.00 0.00 0.00 2.87
612 617 8.603242 TTAAGCTATTTCTCTTCGTGAGTTTT 57.397 30.769 0.00 0.00 43.13 2.43
624 629 7.535139 TCTTCGTGAGTTTTTGTTTCAGATTT 58.465 30.769 0.00 0.00 0.00 2.17
628 633 7.272515 TCGTGAGTTTTTGTTTCAGATTTTCAC 59.727 33.333 0.00 0.00 0.00 3.18
672 678 4.822026 TCGGAGGAGAATCTTTTTGAGAC 58.178 43.478 0.00 0.00 37.17 3.36
689 695 3.253432 TGAGACGATAGCGCTACATGAAT 59.747 43.478 21.49 2.92 42.48 2.57
717 724 8.956533 TCATGAAACGATTCTATATGGTCAAA 57.043 30.769 6.98 0.00 36.48 2.69
788 802 6.288294 TGAAAATCTCCTCTTTCTCAAACGA 58.712 36.000 0.00 0.00 33.55 3.85
800 828 0.241213 TCAAACGACGCCTCTCTCTG 59.759 55.000 0.00 0.00 0.00 3.35
801 829 0.734253 CAAACGACGCCTCTCTCTGG 60.734 60.000 0.00 0.00 0.00 3.86
808 836 0.107214 CGCCTCTCTCTGGTCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
810 838 1.212935 GCCTCTCTCTGGTCTCTCTCT 59.787 57.143 0.00 0.00 0.00 3.10
816 844 1.742831 CTCTGGTCTCTCTCTGGAACG 59.257 57.143 0.00 0.00 0.00 3.95
820 848 0.812549 GTCTCTCTCTGGAACGGACC 59.187 60.000 0.00 0.00 39.80 4.46
824 852 0.176680 CTCTCTGGAACGGACCCATG 59.823 60.000 0.00 0.00 39.80 3.66
833 861 2.403252 ACGGACCCATGCTTTCTTAG 57.597 50.000 0.00 0.00 0.00 2.18
846 874 0.096628 TTCTTAGCGTCGCGTCTCTC 59.903 55.000 12.30 0.00 0.00 3.20
865 893 7.853524 GTCTCTCCGGACGATATATATTGTAG 58.146 42.308 14.49 11.64 30.59 2.74
866 894 6.990939 TCTCTCCGGACGATATATATTGTAGG 59.009 42.308 20.83 20.83 33.07 3.18
867 895 6.892485 TCTCCGGACGATATATATTGTAGGA 58.108 40.000 24.45 24.45 35.96 2.94
868 896 6.990939 TCTCCGGACGATATATATTGTAGGAG 59.009 42.308 32.71 32.71 45.20 3.69
869 897 6.656902 TCCGGACGATATATATTGTAGGAGT 58.343 40.000 23.32 7.67 34.64 3.85
870 898 7.795047 TCCGGACGATATATATTGTAGGAGTA 58.205 38.462 23.32 11.23 34.64 2.59
893 921 6.575162 AATTTGCAACTCCGAATTAAGAGT 57.425 33.333 0.00 4.40 45.18 3.24
901 929 5.648572 ACTCCGAATTAAGAGTAGTTTCCG 58.351 41.667 7.85 0.00 41.51 4.30
915 943 6.656003 AGTAGTTTCCGTTCGATTCAAAAAG 58.344 36.000 0.00 0.00 0.00 2.27
916 944 5.494632 AGTTTCCGTTCGATTCAAAAAGT 57.505 34.783 0.00 0.00 0.00 2.66
917 945 6.607735 AGTTTCCGTTCGATTCAAAAAGTA 57.392 33.333 0.00 0.00 0.00 2.24
918 946 7.198306 AGTTTCCGTTCGATTCAAAAAGTAT 57.802 32.000 0.00 0.00 0.00 2.12
919 947 7.295930 AGTTTCCGTTCGATTCAAAAAGTATC 58.704 34.615 0.00 0.00 0.00 2.24
1283 2346 4.099170 CTGCGTTGCTGCTGCTCC 62.099 66.667 17.00 6.11 40.48 4.70
1336 2399 3.736126 GCAAGGTGATTTCCTATGCTTGC 60.736 47.826 0.00 0.00 37.95 4.01
1341 2404 4.823989 GGTGATTTCCTATGCTTGCATACT 59.176 41.667 10.84 0.00 0.00 2.12
1397 2461 6.487689 AGACGAAGAGTTCAAATTCAATCC 57.512 37.500 0.00 0.00 0.00 3.01
1473 2538 3.769536 CTTTTGCCAAAGGTATAAGCGG 58.230 45.455 2.32 0.00 36.48 5.52
1474 2539 1.099689 TTGCCAAAGGTATAAGCGGC 58.900 50.000 0.00 0.00 40.02 6.53
1475 2540 0.254747 TGCCAAAGGTATAAGCGGCT 59.745 50.000 0.00 0.00 40.27 5.52
1476 2541 1.487142 TGCCAAAGGTATAAGCGGCTA 59.513 47.619 1.35 0.00 40.27 3.93
1477 2542 2.092861 TGCCAAAGGTATAAGCGGCTAA 60.093 45.455 1.35 0.00 40.27 3.09
1478 2543 2.548480 GCCAAAGGTATAAGCGGCTAAG 59.452 50.000 1.35 0.00 36.58 2.18
1479 2544 2.548480 CCAAAGGTATAAGCGGCTAAGC 59.452 50.000 1.35 1.82 37.41 3.09
1480 2545 2.150397 AAGGTATAAGCGGCTAAGCG 57.850 50.000 1.35 0.00 43.00 4.68
1481 2546 0.319641 AGGTATAAGCGGCTAAGCGC 60.320 55.000 1.35 0.00 43.00 5.92
1482 2547 0.319641 GGTATAAGCGGCTAAGCGCT 60.320 55.000 2.64 2.64 43.00 5.92
1483 2548 1.061485 GTATAAGCGGCTAAGCGCTC 58.939 55.000 12.06 0.00 43.00 5.03
1484 2549 0.671796 TATAAGCGGCTAAGCGCTCA 59.328 50.000 12.06 0.00 43.00 4.26
1485 2550 0.598680 ATAAGCGGCTAAGCGCTCAG 60.599 55.000 12.06 6.86 43.00 3.35
1486 2551 1.945354 TAAGCGGCTAAGCGCTCAGT 61.945 55.000 12.06 0.00 43.00 3.41
1487 2552 3.558411 GCGGCTAAGCGCTCAGTG 61.558 66.667 12.06 3.64 39.13 3.66
1488 2553 2.125912 CGGCTAAGCGCTCAGTGT 60.126 61.111 12.06 0.00 39.13 3.55
1489 2554 1.738099 CGGCTAAGCGCTCAGTGTT 60.738 57.895 12.06 0.00 39.13 3.32
1490 2555 1.291877 CGGCTAAGCGCTCAGTGTTT 61.292 55.000 12.06 0.00 39.13 2.83
1491 2556 0.166814 GGCTAAGCGCTCAGTGTTTG 59.833 55.000 12.06 0.00 39.13 2.93
1492 2557 0.166814 GCTAAGCGCTCAGTGTTTGG 59.833 55.000 12.06 0.00 35.14 3.28
1493 2558 1.512926 CTAAGCGCTCAGTGTTTGGT 58.487 50.000 12.06 0.00 0.00 3.67
1494 2559 1.461127 CTAAGCGCTCAGTGTTTGGTC 59.539 52.381 12.06 0.00 0.00 4.02
1495 2560 1.166531 AAGCGCTCAGTGTTTGGTCC 61.167 55.000 12.06 0.00 0.00 4.46
1496 2561 2.617274 GCGCTCAGTGTTTGGTCCC 61.617 63.158 0.00 0.00 0.00 4.46
1497 2562 2.317609 CGCTCAGTGTTTGGTCCCG 61.318 63.158 0.00 0.00 0.00 5.14
1498 2563 1.966451 GCTCAGTGTTTGGTCCCGG 60.966 63.158 0.00 0.00 0.00 5.73
1513 2578 2.830370 CGGGCTTGCTCCAATCCC 60.830 66.667 6.77 6.77 43.89 3.85
1547 2612 1.668793 CACACGATCTGCTGTGCCA 60.669 57.895 0.00 0.00 39.71 4.92
1567 2632 4.296265 GGCGACGGGACAAAAGAT 57.704 55.556 0.00 0.00 0.00 2.40
1592 2657 1.197721 CGGCGAGCAGATTGTTTTCTT 59.802 47.619 0.00 0.00 0.00 2.52
1594 2659 3.642705 GGCGAGCAGATTGTTTTCTTTT 58.357 40.909 0.00 0.00 0.00 2.27
1600 2665 7.113027 CGAGCAGATTGTTTTCTTTTTGTTTC 58.887 34.615 0.00 0.00 0.00 2.78
1602 2667 8.189709 AGCAGATTGTTTTCTTTTTGTTTCTC 57.810 30.769 0.00 0.00 0.00 2.87
1603 2668 8.037166 AGCAGATTGTTTTCTTTTTGTTTCTCT 58.963 29.630 0.00 0.00 0.00 3.10
1605 2670 8.598075 CAGATTGTTTTCTTTTTGTTTCTCTGG 58.402 33.333 0.00 0.00 0.00 3.86
1606 2671 6.720012 TTGTTTTCTTTTTGTTTCTCTGGC 57.280 33.333 0.00 0.00 0.00 4.85
1607 2672 6.036577 TGTTTTCTTTTTGTTTCTCTGGCT 57.963 33.333 0.00 0.00 0.00 4.75
1608 2673 6.463360 TGTTTTCTTTTTGTTTCTCTGGCTT 58.537 32.000 0.00 0.00 0.00 4.35
1610 2675 5.659440 TTCTTTTTGTTTCTCTGGCTTGT 57.341 34.783 0.00 0.00 0.00 3.16
1611 2676 5.659440 TCTTTTTGTTTCTCTGGCTTGTT 57.341 34.783 0.00 0.00 0.00 2.83
1612 2677 6.036577 TCTTTTTGTTTCTCTGGCTTGTTT 57.963 33.333 0.00 0.00 0.00 2.83
1613 2678 5.868801 TCTTTTTGTTTCTCTGGCTTGTTTG 59.131 36.000 0.00 0.00 0.00 2.93
1614 2679 3.799281 TTGTTTCTCTGGCTTGTTTGG 57.201 42.857 0.00 0.00 0.00 3.28
1615 2680 3.011566 TGTTTCTCTGGCTTGTTTGGA 57.988 42.857 0.00 0.00 0.00 3.53
1616 2681 3.565307 TGTTTCTCTGGCTTGTTTGGAT 58.435 40.909 0.00 0.00 0.00 3.41
1617 2682 3.960102 TGTTTCTCTGGCTTGTTTGGATT 59.040 39.130 0.00 0.00 0.00 3.01
1618 2683 4.202141 TGTTTCTCTGGCTTGTTTGGATTG 60.202 41.667 0.00 0.00 0.00 2.67
1619 2684 3.507162 TCTCTGGCTTGTTTGGATTGA 57.493 42.857 0.00 0.00 0.00 2.57
1636 2701 8.615360 TTGGATTGATTGTTTGGGGATTATTA 57.385 30.769 0.00 0.00 0.00 0.98
1659 2725 0.674581 TGCTGTGGCTGAGGAAATCG 60.675 55.000 0.00 0.00 39.59 3.34
1660 2726 0.391661 GCTGTGGCTGAGGAAATCGA 60.392 55.000 0.00 0.00 35.22 3.59
1661 2727 1.745141 GCTGTGGCTGAGGAAATCGAT 60.745 52.381 0.00 0.00 35.22 3.59
1698 2765 3.808728 ACTAGAGCAAGCAAACAACAGA 58.191 40.909 0.00 0.00 0.00 3.41
1700 2767 3.637998 AGAGCAAGCAAACAACAGATG 57.362 42.857 0.00 0.00 0.00 2.90
1703 2770 4.280174 AGAGCAAGCAAACAACAGATGAAT 59.720 37.500 0.00 0.00 0.00 2.57
1704 2771 5.474532 AGAGCAAGCAAACAACAGATGAATA 59.525 36.000 0.00 0.00 0.00 1.75
1705 2772 6.016024 AGAGCAAGCAAACAACAGATGAATAA 60.016 34.615 0.00 0.00 0.00 1.40
1706 2773 6.694447 AGCAAGCAAACAACAGATGAATAAT 58.306 32.000 0.00 0.00 0.00 1.28
1707 2774 7.829725 AGCAAGCAAACAACAGATGAATAATA 58.170 30.769 0.00 0.00 0.00 0.98
1708 2775 7.972277 AGCAAGCAAACAACAGATGAATAATAG 59.028 33.333 0.00 0.00 0.00 1.73
1734 2801 5.441718 AAGACAGGAATTTCATCTAGGCA 57.558 39.130 0.00 0.00 0.00 4.75
1748 2815 2.009774 CTAGGCAATCGTTGACCAAGG 58.990 52.381 0.71 0.00 40.48 3.61
1766 2833 4.262121 CCAAGGAAGAAATGAATGCACACA 60.262 41.667 0.00 0.00 0.00 3.72
1775 2842 6.643770 AGAAATGAATGCACACAAGTTTGATC 59.356 34.615 0.00 0.00 0.00 2.92
1783 2850 4.035558 GCACACAAGTTTGATCTGAGTTGA 59.964 41.667 17.65 0.00 32.05 3.18
1795 2862 2.022035 TCTGAGTTGACCCCCATAGGAT 60.022 50.000 0.00 0.00 38.24 3.24
1864 2931 4.547671 TGTGGTTTTAACTGAATTCCCCA 58.452 39.130 2.27 0.00 0.00 4.96
1866 2933 5.011533 TGTGGTTTTAACTGAATTCCCCATG 59.988 40.000 2.27 0.00 0.00 3.66
1877 2944 1.498264 TTCCCCATGCCCATCATTTG 58.502 50.000 0.00 0.00 31.79 2.32
1883 2950 1.394266 ATGCCCATCATTTGGTCGGC 61.394 55.000 0.00 0.00 44.83 5.54
1900 2967 3.123620 CGCCTGTCCAAGCTGCTC 61.124 66.667 1.00 0.00 0.00 4.26
1916 2983 2.744202 CTGCTCATCTTGTGGGTGTTAC 59.256 50.000 0.00 0.00 0.00 2.50
1925 2992 5.245531 TCTTGTGGGTGTTACTGATTCATC 58.754 41.667 0.00 0.00 0.00 2.92
1926 2993 4.632327 TGTGGGTGTTACTGATTCATCA 57.368 40.909 0.00 0.00 35.16 3.07
1944 3011 6.187727 TCATCAATTCCCCTTCATAGTACC 57.812 41.667 0.00 0.00 0.00 3.34
1946 3013 4.035112 TCAATTCCCCTTCATAGTACCGT 58.965 43.478 0.00 0.00 0.00 4.83
1967 3034 4.026310 CGTTACACGATAATACCAGTTGCC 60.026 45.833 0.00 0.00 46.05 4.52
1971 3038 4.574828 ACACGATAATACCAGTTGCCAATC 59.425 41.667 0.00 0.00 0.00 2.67
2121 3200 5.249780 TGCAAAATTAAGTACTCCCTCCA 57.750 39.130 0.00 0.00 0.00 3.86
2205 3351 5.764686 TCTTTTAAGCTGCAGAAACTGATCA 59.235 36.000 20.43 0.00 32.44 2.92
2206 3352 6.262944 TCTTTTAAGCTGCAGAAACTGATCAA 59.737 34.615 20.43 0.00 32.44 2.57
2248 3394 6.699688 TGGATACCCTCTCCCTCTTATTTTA 58.300 40.000 0.00 0.00 31.32 1.52
2633 3792 1.342496 TCGATGATGAGGAGCCACATC 59.658 52.381 16.83 16.83 41.94 3.06
3110 4281 2.408333 GGATTGTCCCATCAAGCCG 58.592 57.895 0.00 0.00 42.53 5.52
3310 4481 5.099042 ACAGTGAAGGTATTGGGATGTAC 57.901 43.478 0.00 0.00 0.00 2.90
3333 4504 4.444022 CCAGATGGTCTCCCTTACAATGAG 60.444 50.000 0.00 0.00 0.00 2.90
3382 4553 2.640184 GTAGGACCCCGGAGAAAATTG 58.360 52.381 0.73 0.00 0.00 2.32
3401 4572 8.523915 AAAATTGATCCATGCTATTGACAGTA 57.476 30.769 0.00 0.00 0.00 2.74
3421 4592 2.281484 TGCAAGCCCGGTCAGTTC 60.281 61.111 0.00 0.00 0.00 3.01
3456 4627 3.807622 TGATCTCAAGTGTGTTTCGGTTC 59.192 43.478 0.00 0.00 0.00 3.62
3457 4628 2.198406 TCTCAAGTGTGTTTCGGTTCG 58.802 47.619 0.00 0.00 0.00 3.95
3458 4629 1.931172 CTCAAGTGTGTTTCGGTTCGT 59.069 47.619 0.00 0.00 0.00 3.85
3459 4630 2.348660 TCAAGTGTGTTTCGGTTCGTT 58.651 42.857 0.00 0.00 0.00 3.85
3624 4795 4.205996 CGTTCGATCTGCTCTGTGAAATAG 59.794 45.833 0.00 0.00 0.00 1.73
3625 4796 4.991153 TCGATCTGCTCTGTGAAATAGT 57.009 40.909 0.00 0.00 0.00 2.12
3709 4880 2.017783 GGTAAACGTCGACGCTGCA 61.018 57.895 35.92 17.03 44.43 4.41
3710 4881 1.411089 GTAAACGTCGACGCTGCAG 59.589 57.895 35.92 10.11 44.43 4.41
3847 5018 3.840666 AGTGAAGGTGTATGGATGTGAGT 59.159 43.478 0.00 0.00 0.00 3.41
3878 5057 1.067212 GAGTCGAGTGAGGTGTGTGTT 59.933 52.381 0.00 0.00 0.00 3.32
3880 5059 2.691526 AGTCGAGTGAGGTGTGTGTTTA 59.308 45.455 0.00 0.00 0.00 2.01
3881 5060 3.050619 GTCGAGTGAGGTGTGTGTTTAG 58.949 50.000 0.00 0.00 0.00 1.85
4029 5211 1.993653 CCTGTCTGCTCATCCCCAA 59.006 57.895 0.00 0.00 0.00 4.12
4033 5215 1.064463 TGTCTGCTCATCCCCAATTCC 60.064 52.381 0.00 0.00 0.00 3.01
4034 5216 1.213926 GTCTGCTCATCCCCAATTCCT 59.786 52.381 0.00 0.00 0.00 3.36
4035 5217 1.492176 TCTGCTCATCCCCAATTCCTC 59.508 52.381 0.00 0.00 0.00 3.71
4150 5472 7.372396 CGGTAATATTTCGTGCAAAATCACTAC 59.628 37.037 0.00 2.08 34.92 2.73
4169 5491 1.710809 ACCTAGGTTGGCTGGATTTGT 59.289 47.619 9.21 0.00 0.00 2.83
4205 5539 0.036765 ACCGTCTAAGCGCCAATTGA 60.037 50.000 7.12 0.00 0.00 2.57
4207 5541 1.261619 CCGTCTAAGCGCCAATTGATC 59.738 52.381 7.12 0.00 0.00 2.92
4287 8720 3.746108 GCACGACGAATTTGAGCAA 57.254 47.368 0.00 0.00 0.00 3.91
4288 8721 1.595609 GCACGACGAATTTGAGCAAG 58.404 50.000 0.00 0.00 0.00 4.01
4289 8722 1.595609 CACGACGAATTTGAGCAAGC 58.404 50.000 0.00 0.00 0.00 4.01
4290 8723 1.069973 CACGACGAATTTGAGCAAGCA 60.070 47.619 0.00 0.00 0.00 3.91
4291 8724 1.601903 ACGACGAATTTGAGCAAGCAA 59.398 42.857 0.00 0.00 0.00 3.91
4292 8725 2.032799 ACGACGAATTTGAGCAAGCAAA 59.967 40.909 0.00 0.00 41.49 3.68
4300 8733 4.799419 TTTGAGCAAGCAAATTTGAAGC 57.201 36.364 22.31 19.19 33.16 3.86
4301 8734 2.758009 TGAGCAAGCAAATTTGAAGCC 58.242 42.857 22.31 14.03 0.00 4.35
4302 8735 2.102757 TGAGCAAGCAAATTTGAAGCCA 59.897 40.909 22.31 15.95 0.00 4.75
4303 8736 2.477754 GAGCAAGCAAATTTGAAGCCAC 59.522 45.455 22.31 13.27 0.00 5.01
4304 8737 1.192980 GCAAGCAAATTTGAAGCCACG 59.807 47.619 22.31 3.53 0.00 4.94
4305 8738 1.192980 CAAGCAAATTTGAAGCCACGC 59.807 47.619 22.31 3.58 0.00 5.34
4306 8739 0.388659 AGCAAATTTGAAGCCACGCA 59.611 45.000 22.31 0.00 0.00 5.24
4307 8740 0.785979 GCAAATTTGAAGCCACGCAG 59.214 50.000 22.31 0.00 0.00 5.18
4308 8741 1.421382 CAAATTTGAAGCCACGCAGG 58.579 50.000 13.08 0.00 41.84 4.85
4309 8742 1.000385 CAAATTTGAAGCCACGCAGGA 60.000 47.619 13.08 0.00 41.22 3.86
4310 8743 1.549203 AATTTGAAGCCACGCAGGAT 58.451 45.000 0.00 0.00 41.22 3.24
4311 8744 1.098050 ATTTGAAGCCACGCAGGATC 58.902 50.000 0.00 0.00 41.22 3.36
4312 8745 1.298157 TTTGAAGCCACGCAGGATCG 61.298 55.000 0.00 0.00 41.22 3.69
4313 8746 2.892425 GAAGCCACGCAGGATCGG 60.892 66.667 0.00 0.00 41.22 4.18
4314 8747 4.473520 AAGCCACGCAGGATCGGG 62.474 66.667 0.00 0.00 41.22 5.14
4336 8769 4.112341 GGCAAGCTGAGCGCCTTG 62.112 66.667 14.91 16.77 42.78 3.61
4337 8770 3.360340 GCAAGCTGAGCGCCTTGT 61.360 61.111 20.40 0.00 40.39 3.16
4338 8771 2.866028 CAAGCTGAGCGCCTTGTC 59.134 61.111 2.29 0.00 40.39 3.18
4339 8772 2.359230 AAGCTGAGCGCCTTGTCC 60.359 61.111 2.29 0.00 40.39 4.02
4340 8773 3.909086 AAGCTGAGCGCCTTGTCCC 62.909 63.158 2.29 0.00 40.39 4.46
4342 8775 4.785453 CTGAGCGCCTTGTCCCCC 62.785 72.222 2.29 0.00 0.00 5.40
4368 8801 4.197498 GCAATGAATGCGGCGGCT 62.197 61.111 17.76 0.00 46.87 5.52
4524 9118 4.662961 CGTGGGCTGCGTCACTCA 62.663 66.667 17.93 0.00 0.00 3.41
4525 9119 3.044305 GTGGGCTGCGTCACTCAC 61.044 66.667 14.60 4.14 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 104 8.768955 GTTTCGAAGACTTTCATGATATAGCAT 58.231 33.333 0.00 0.00 34.32 3.79
231 233 9.623000 ATTCTATCAGATCAATTTCACATGACA 57.377 29.630 0.00 0.00 0.00 3.58
345 347 8.073735 AGATTATGGGGAAAAACCATTTAGGAT 58.926 33.333 1.91 0.00 46.25 3.24
426 429 8.801882 TGGTAGAGACTTTGGTAAATAAATGG 57.198 34.615 0.00 0.00 0.00 3.16
439 442 8.383175 TGGAATGTAGAATTTGGTAGAGACTTT 58.617 33.333 0.00 0.00 0.00 2.66
533 536 0.930726 ACTCCCTGTCCCCACAAAAA 59.069 50.000 0.00 0.00 29.82 1.94
534 537 0.476771 GACTCCCTGTCCCCACAAAA 59.523 55.000 0.00 0.00 39.69 2.44
535 538 0.401395 AGACTCCCTGTCCCCACAAA 60.401 55.000 0.00 0.00 46.46 2.83
536 539 0.836400 GAGACTCCCTGTCCCCACAA 60.836 60.000 0.00 0.00 46.46 3.33
537 540 1.229209 GAGACTCCCTGTCCCCACA 60.229 63.158 0.00 0.00 46.46 4.17
538 541 0.545548 AAGAGACTCCCTGTCCCCAC 60.546 60.000 0.00 0.00 46.46 4.61
539 542 0.252284 GAAGAGACTCCCTGTCCCCA 60.252 60.000 0.00 0.00 46.46 4.96
540 543 0.041982 AGAAGAGACTCCCTGTCCCC 59.958 60.000 0.00 0.00 46.46 4.81
541 544 1.552792 CAAGAAGAGACTCCCTGTCCC 59.447 57.143 0.00 0.00 46.46 4.46
542 545 2.530701 TCAAGAAGAGACTCCCTGTCC 58.469 52.381 0.00 0.00 46.46 4.02
543 546 7.093945 GGATATATCAAGAAGAGACTCCCTGTC 60.094 44.444 14.60 0.00 45.67 3.51
544 547 6.723977 GGATATATCAAGAAGAGACTCCCTGT 59.276 42.308 14.60 0.00 0.00 4.00
545 548 6.953520 AGGATATATCAAGAAGAGACTCCCTG 59.046 42.308 14.60 0.00 0.00 4.45
546 549 7.114849 AGGATATATCAAGAAGAGACTCCCT 57.885 40.000 14.60 0.00 0.00 4.20
603 608 7.383361 GTGAAAATCTGAAACAAAAACTCACG 58.617 34.615 0.00 0.00 0.00 4.35
651 657 3.614616 CGTCTCAAAAAGATTCTCCTCCG 59.385 47.826 0.00 0.00 36.11 4.63
672 678 4.168760 TGATCATTCATGTAGCGCTATCG 58.831 43.478 21.96 12.06 39.07 2.92
689 695 8.367156 TGACCATATAGAATCGTTTCATGATCA 58.633 33.333 8.83 0.00 34.08 2.92
763 777 6.936900 TCGTTTGAGAAAGAGGAGATTTTCAT 59.063 34.615 0.56 0.00 36.11 2.57
764 778 6.202954 GTCGTTTGAGAAAGAGGAGATTTTCA 59.797 38.462 0.56 0.00 36.11 2.69
781 795 0.241213 CAGAGAGAGGCGTCGTTTGA 59.759 55.000 0.00 0.00 0.00 2.69
788 802 0.393808 GAGAGACCAGAGAGAGGCGT 60.394 60.000 0.00 0.00 0.00 5.68
800 828 0.812549 GTCCGTTCCAGAGAGAGACC 59.187 60.000 0.00 0.00 0.00 3.85
801 829 0.812549 GGTCCGTTCCAGAGAGAGAC 59.187 60.000 0.00 0.00 0.00 3.36
808 836 1.488705 AAGCATGGGTCCGTTCCAGA 61.489 55.000 0.00 0.00 37.75 3.86
810 838 0.608035 GAAAGCATGGGTCCGTTCCA 60.608 55.000 0.00 0.00 38.82 3.53
846 874 6.939132 ACTCCTACAATATATATCGTCCGG 57.061 41.667 0.00 0.00 0.00 5.14
865 893 4.965119 ATTCGGAGTTGCAAATTACTCC 57.035 40.909 20.88 20.88 43.83 3.85
866 894 7.748847 TCTTAATTCGGAGTTGCAAATTACTC 58.251 34.615 0.00 3.92 0.00 2.59
867 895 7.390718 ACTCTTAATTCGGAGTTGCAAATTACT 59.609 33.333 0.00 0.00 39.44 2.24
868 896 7.527457 ACTCTTAATTCGGAGTTGCAAATTAC 58.473 34.615 0.00 0.00 39.44 1.89
869 897 7.681939 ACTCTTAATTCGGAGTTGCAAATTA 57.318 32.000 0.00 0.00 39.44 1.40
870 898 6.575162 ACTCTTAATTCGGAGTTGCAAATT 57.425 33.333 0.00 0.00 39.44 1.82
883 911 7.752557 ATCGAACGGAAACTACTCTTAATTC 57.247 36.000 0.00 0.00 0.00 2.17
893 921 6.607735 ACTTTTTGAATCGAACGGAAACTA 57.392 33.333 0.00 0.00 0.00 2.24
901 929 6.128282 TGGAGCAGATACTTTTTGAATCGAAC 60.128 38.462 0.00 0.00 0.00 3.95
915 943 3.728076 TCCGTTGTATGGAGCAGATAC 57.272 47.619 0.00 0.00 0.00 2.24
916 944 3.006859 CCATCCGTTGTATGGAGCAGATA 59.993 47.826 0.00 0.00 45.77 1.98
917 945 2.224378 CCATCCGTTGTATGGAGCAGAT 60.224 50.000 0.00 0.00 45.77 2.90
918 946 1.138859 CCATCCGTTGTATGGAGCAGA 59.861 52.381 0.00 0.00 45.77 4.26
919 947 1.586422 CCATCCGTTGTATGGAGCAG 58.414 55.000 0.00 0.00 45.77 4.24
1271 2334 1.601759 GAACTGGGAGCAGCAGCAA 60.602 57.895 3.17 0.00 45.49 3.91
1283 2346 3.965539 CTGGAGCAGCCGGAACTGG 62.966 68.421 5.05 0.00 46.81 4.00
1397 2461 6.183360 TGGCTCAATTGCAGAATTATAAGGTG 60.183 38.462 0.00 0.00 30.20 4.00
1439 2504 0.872388 GCAAAAGGTACCCGTGACAG 59.128 55.000 8.74 0.00 0.00 3.51
1457 2522 2.249844 TAGCCGCTTATACCTTTGGC 57.750 50.000 0.00 0.00 42.76 4.52
1458 2523 2.548480 GCTTAGCCGCTTATACCTTTGG 59.452 50.000 0.00 0.00 0.00 3.28
1459 2524 2.221055 CGCTTAGCCGCTTATACCTTTG 59.779 50.000 0.00 0.00 0.00 2.77
1460 2525 2.480845 CGCTTAGCCGCTTATACCTTT 58.519 47.619 0.00 0.00 0.00 3.11
1461 2526 2.150397 CGCTTAGCCGCTTATACCTT 57.850 50.000 0.00 0.00 0.00 3.50
1462 2527 3.888093 CGCTTAGCCGCTTATACCT 57.112 52.632 0.00 0.00 0.00 3.08
1474 2539 1.461127 GACCAAACACTGAGCGCTTAG 59.539 52.381 26.01 26.01 0.00 2.18
1475 2540 1.508632 GACCAAACACTGAGCGCTTA 58.491 50.000 13.26 6.52 0.00 3.09
1476 2541 1.166531 GGACCAAACACTGAGCGCTT 61.167 55.000 13.26 0.00 0.00 4.68
1477 2542 1.598130 GGACCAAACACTGAGCGCT 60.598 57.895 11.27 11.27 0.00 5.92
1478 2543 2.617274 GGGACCAAACACTGAGCGC 61.617 63.158 0.00 0.00 0.00 5.92
1479 2544 2.317609 CGGGACCAAACACTGAGCG 61.318 63.158 0.00 0.00 0.00 5.03
1480 2545 1.966451 CCGGGACCAAACACTGAGC 60.966 63.158 0.00 0.00 0.00 4.26
1481 2546 1.302511 CCCGGGACCAAACACTGAG 60.303 63.158 18.48 0.00 0.00 3.35
1482 2547 2.833227 CCCGGGACCAAACACTGA 59.167 61.111 18.48 0.00 0.00 3.41
1483 2548 2.976494 AAGCCCGGGACCAAACACTG 62.976 60.000 29.31 0.00 0.00 3.66
1484 2549 2.763645 AAGCCCGGGACCAAACACT 61.764 57.895 29.31 5.79 0.00 3.55
1485 2550 2.203437 AAGCCCGGGACCAAACAC 60.203 61.111 29.31 2.84 0.00 3.32
1486 2551 2.203422 CAAGCCCGGGACCAAACA 60.203 61.111 29.31 0.00 0.00 2.83
1487 2552 3.680786 GCAAGCCCGGGACCAAAC 61.681 66.667 29.31 4.69 0.00 2.93
1488 2553 3.860930 GAGCAAGCCCGGGACCAAA 62.861 63.158 29.31 0.00 0.00 3.28
1489 2554 4.344865 GAGCAAGCCCGGGACCAA 62.345 66.667 29.31 0.00 0.00 3.67
1492 2557 3.645268 ATTGGAGCAAGCCCGGGAC 62.645 63.158 29.31 16.50 0.00 4.46
1493 2558 3.338250 ATTGGAGCAAGCCCGGGA 61.338 61.111 29.31 0.00 0.00 5.14
1494 2559 2.830370 GATTGGAGCAAGCCCGGG 60.830 66.667 19.09 19.09 0.00 5.73
1495 2560 2.830370 GGATTGGAGCAAGCCCGG 60.830 66.667 0.00 0.00 43.25 5.73
1547 2612 2.203042 TTTTGTCCCGTCGCCGTT 60.203 55.556 0.00 0.00 0.00 4.44
1567 2632 4.393155 AATCTGCTCGCCGTGGCA 62.393 61.111 12.06 7.20 42.06 4.92
1592 2657 4.221703 TCCAAACAAGCCAGAGAAACAAAA 59.778 37.500 0.00 0.00 0.00 2.44
1594 2659 3.360867 TCCAAACAAGCCAGAGAAACAA 58.639 40.909 0.00 0.00 0.00 2.83
1600 2665 4.021719 ACAATCAATCCAAACAAGCCAGAG 60.022 41.667 0.00 0.00 0.00 3.35
1602 2667 4.261578 ACAATCAATCCAAACAAGCCAG 57.738 40.909 0.00 0.00 0.00 4.85
1603 2668 4.686191 AACAATCAATCCAAACAAGCCA 57.314 36.364 0.00 0.00 0.00 4.75
1605 2670 4.213906 CCCAAACAATCAATCCAAACAAGC 59.786 41.667 0.00 0.00 0.00 4.01
1606 2671 4.756135 CCCCAAACAATCAATCCAAACAAG 59.244 41.667 0.00 0.00 0.00 3.16
1607 2672 4.410228 TCCCCAAACAATCAATCCAAACAA 59.590 37.500 0.00 0.00 0.00 2.83
1608 2673 3.969976 TCCCCAAACAATCAATCCAAACA 59.030 39.130 0.00 0.00 0.00 2.83
1610 2675 5.839517 AATCCCCAAACAATCAATCCAAA 57.160 34.783 0.00 0.00 0.00 3.28
1611 2676 7.507797 AATAATCCCCAAACAATCAATCCAA 57.492 32.000 0.00 0.00 0.00 3.53
1612 2677 7.843760 AGTAATAATCCCCAAACAATCAATCCA 59.156 33.333 0.00 0.00 0.00 3.41
1613 2678 8.143835 CAGTAATAATCCCCAAACAATCAATCC 58.856 37.037 0.00 0.00 0.00 3.01
1614 2679 8.695456 ACAGTAATAATCCCCAAACAATCAATC 58.305 33.333 0.00 0.00 0.00 2.67
1615 2680 8.477256 CACAGTAATAATCCCCAAACAATCAAT 58.523 33.333 0.00 0.00 0.00 2.57
1616 2681 7.578571 GCACAGTAATAATCCCCAAACAATCAA 60.579 37.037 0.00 0.00 0.00 2.57
1617 2682 6.127479 GCACAGTAATAATCCCCAAACAATCA 60.127 38.462 0.00 0.00 0.00 2.57
1618 2683 6.096846 AGCACAGTAATAATCCCCAAACAATC 59.903 38.462 0.00 0.00 0.00 2.67
1619 2684 5.957774 AGCACAGTAATAATCCCCAAACAAT 59.042 36.000 0.00 0.00 0.00 2.71
1636 2701 1.699054 TTCCTCAGCCACAGCACAGT 61.699 55.000 0.00 0.00 43.56 3.55
1659 2725 6.251801 GCTCTAGTTCGTAGTCTTTGTGAATC 59.748 42.308 0.00 0.00 0.00 2.52
1660 2726 6.094061 GCTCTAGTTCGTAGTCTTTGTGAAT 58.906 40.000 0.00 0.00 0.00 2.57
1661 2727 5.009310 TGCTCTAGTTCGTAGTCTTTGTGAA 59.991 40.000 0.00 0.00 0.00 3.18
1707 2774 7.554476 GCCTAGATGAAATTCCTGTCTTTTACT 59.446 37.037 0.00 0.00 0.00 2.24
1708 2775 7.336931 TGCCTAGATGAAATTCCTGTCTTTTAC 59.663 37.037 0.00 0.00 0.00 2.01
1718 2785 5.296780 TCAACGATTGCCTAGATGAAATTCC 59.703 40.000 0.00 0.00 0.00 3.01
1722 2789 3.938963 GGTCAACGATTGCCTAGATGAAA 59.061 43.478 0.00 0.00 0.00 2.69
1734 2801 5.070001 TCATTTCTTCCTTGGTCAACGATT 58.930 37.500 0.00 0.00 0.00 3.34
1748 2815 6.476380 TCAAACTTGTGTGCATTCATTTCTTC 59.524 34.615 0.00 0.00 0.00 2.87
1766 2833 3.498661 GGGGGTCAACTCAGATCAAACTT 60.499 47.826 0.00 0.00 0.00 2.66
1775 2842 1.879575 TCCTATGGGGGTCAACTCAG 58.120 55.000 0.00 0.00 35.33 3.35
1805 2872 9.670442 AGAAGTTAATCTCTAATATACCACCCA 57.330 33.333 0.00 0.00 0.00 4.51
1883 2950 3.123620 GAGCAGCTTGGACAGGCG 61.124 66.667 0.00 0.00 38.56 5.52
1893 2960 0.322277 CACCCACAAGATGAGCAGCT 60.322 55.000 0.00 0.00 0.00 4.24
1897 2964 2.744202 CAGTAACACCCACAAGATGAGC 59.256 50.000 0.00 0.00 0.00 4.26
1900 2967 5.003160 TGAATCAGTAACACCCACAAGATG 58.997 41.667 0.00 0.00 0.00 2.90
1916 2983 7.002879 ACTATGAAGGGGAATTGATGAATCAG 58.997 38.462 0.00 0.00 38.19 2.90
1925 2992 4.417426 ACGGTACTATGAAGGGGAATTG 57.583 45.455 0.00 0.00 0.00 2.32
1926 2993 5.426185 TGTAACGGTACTATGAAGGGGAATT 59.574 40.000 12.67 0.00 0.00 2.17
1946 3013 5.087391 TGGCAACTGGTATTATCGTGTAA 57.913 39.130 0.00 0.00 37.61 2.41
1967 3034 3.504863 CAAGGTCAAATTGGAGCGATTG 58.495 45.455 6.38 3.42 40.14 2.67
2007 3081 4.188462 TGTGGCCGAACTATAATTCAGTG 58.812 43.478 0.00 0.00 0.00 3.66
2107 3186 3.788116 TTGGGATGGAGGGAGTACTTA 57.212 47.619 0.00 0.00 0.00 2.24
2121 3200 3.950397 TCAGCGACACTTATTTTGGGAT 58.050 40.909 0.00 0.00 0.00 3.85
2205 3351 9.705290 GGTATCCATCACAAAAACAAAATACTT 57.295 29.630 0.00 0.00 0.00 2.24
2206 3352 8.311109 GGGTATCCATCACAAAAACAAAATACT 58.689 33.333 0.00 0.00 0.00 2.12
2248 3394 8.497745 AGTCACCTACAATTTCATCCAGATTAT 58.502 33.333 0.00 0.00 0.00 1.28
2433 3591 6.966435 AATACATGCAATTACAAAAGGTGC 57.034 33.333 0.00 0.00 35.75 5.01
2740 3902 2.882927 TAACCCAATCATCGTCCTCG 57.117 50.000 0.00 0.00 38.55 4.63
3010 4172 2.910199 TCTCCCTTCATCTTTGCATCG 58.090 47.619 0.00 0.00 0.00 3.84
3053 4215 3.437049 GTCCATTCAGACCTTACAACAGC 59.563 47.826 0.00 0.00 0.00 4.40
3110 4281 1.949525 TGGACTTGTTGCTTTCTCTGC 59.050 47.619 0.00 0.00 0.00 4.26
3232 4403 0.967380 AAAGCCAATTCCTCAGCCCG 60.967 55.000 0.00 0.00 0.00 6.13
3333 4504 1.382692 GCCCATCTCTTTCAGCTGGC 61.383 60.000 15.13 0.56 37.11 4.85
3382 4553 5.350914 GCAGATACTGTCAATAGCATGGATC 59.649 44.000 0.00 0.00 33.43 3.36
3401 4572 2.129555 AACTGACCGGGCTTGCAGAT 62.130 55.000 9.82 0.00 32.86 2.90
3456 4627 7.298122 ACTAGCATCAAAACATCTAACAAACG 58.702 34.615 0.00 0.00 0.00 3.60
3457 4628 7.478667 CGACTAGCATCAAAACATCTAACAAAC 59.521 37.037 0.00 0.00 0.00 2.93
3458 4629 7.360861 CCGACTAGCATCAAAACATCTAACAAA 60.361 37.037 0.00 0.00 0.00 2.83
3459 4630 6.092122 CCGACTAGCATCAAAACATCTAACAA 59.908 38.462 0.00 0.00 0.00 2.83
3624 4795 7.359598 GCGAGATGTTCTTACAATGGATCATAC 60.360 40.741 0.00 0.00 37.91 2.39
3625 4796 6.646653 GCGAGATGTTCTTACAATGGATCATA 59.353 38.462 0.00 0.00 37.91 2.15
3878 5057 0.601558 AGCTCGACCTGCGTTTCTAA 59.398 50.000 0.00 0.00 41.80 2.10
3880 5059 1.373497 CAGCTCGACCTGCGTTTCT 60.373 57.895 0.00 0.00 41.80 2.52
3881 5060 0.388134 TACAGCTCGACCTGCGTTTC 60.388 55.000 7.66 0.00 41.80 2.78
4011 5193 0.549950 ATTGGGGATGAGCAGACAGG 59.450 55.000 0.00 0.00 0.00 4.00
4014 5196 1.213926 AGGAATTGGGGATGAGCAGAC 59.786 52.381 0.00 0.00 0.00 3.51
4029 5211 2.107950 TTTGCGAATCGTGGAGGAAT 57.892 45.000 4.07 0.00 0.00 3.01
4033 5215 1.656652 AGGATTTGCGAATCGTGGAG 58.343 50.000 18.80 0.00 42.12 3.86
4034 5216 2.546778 GTAGGATTTGCGAATCGTGGA 58.453 47.619 25.43 9.30 42.12 4.02
4035 5217 1.597663 GGTAGGATTTGCGAATCGTGG 59.402 52.381 25.43 0.00 42.12 4.94
4150 5472 2.514458 ACAAATCCAGCCAACCTAGG 57.486 50.000 7.41 7.41 0.00 3.02
4169 5491 2.691996 TGCCATGCAGCCCTCCTA 60.692 61.111 0.00 0.00 33.32 2.94
4272 8705 2.314561 TTGCTTGCTCAAATTCGTCG 57.685 45.000 0.00 0.00 0.00 5.12
4278 8711 4.214758 GGCTTCAAATTTGCTTGCTCAAAT 59.785 37.500 13.54 6.41 45.54 2.32
4279 8712 3.560896 GGCTTCAAATTTGCTTGCTCAAA 59.439 39.130 13.54 0.00 39.87 2.69
4280 8713 3.132925 GGCTTCAAATTTGCTTGCTCAA 58.867 40.909 13.54 0.04 0.00 3.02
4281 8714 2.102757 TGGCTTCAAATTTGCTTGCTCA 59.897 40.909 13.54 12.62 0.00 4.26
4282 8715 2.477754 GTGGCTTCAAATTTGCTTGCTC 59.522 45.455 13.54 10.70 0.00 4.26
4283 8716 2.486918 GTGGCTTCAAATTTGCTTGCT 58.513 42.857 13.54 0.00 0.00 3.91
4284 8717 1.192980 CGTGGCTTCAAATTTGCTTGC 59.807 47.619 13.54 15.16 0.00 4.01
4285 8718 1.192980 GCGTGGCTTCAAATTTGCTTG 59.807 47.619 13.54 6.88 0.00 4.01
4286 8719 1.202510 TGCGTGGCTTCAAATTTGCTT 60.203 42.857 13.54 0.00 0.00 3.91
4287 8720 0.388659 TGCGTGGCTTCAAATTTGCT 59.611 45.000 13.54 0.00 0.00 3.91
4288 8721 0.785979 CTGCGTGGCTTCAAATTTGC 59.214 50.000 13.54 1.77 0.00 3.68
4289 8722 1.000385 TCCTGCGTGGCTTCAAATTTG 60.000 47.619 12.15 12.15 35.26 2.32
4290 8723 1.327303 TCCTGCGTGGCTTCAAATTT 58.673 45.000 0.00 0.00 35.26 1.82
4291 8724 1.474077 GATCCTGCGTGGCTTCAAATT 59.526 47.619 0.00 0.00 35.26 1.82
4292 8725 1.098050 GATCCTGCGTGGCTTCAAAT 58.902 50.000 0.00 0.00 35.26 2.32
4293 8726 1.298157 CGATCCTGCGTGGCTTCAAA 61.298 55.000 0.00 0.00 35.26 2.69
4294 8727 1.741401 CGATCCTGCGTGGCTTCAA 60.741 57.895 0.00 0.00 35.26 2.69
4295 8728 2.125552 CGATCCTGCGTGGCTTCA 60.126 61.111 0.00 0.00 35.26 3.02
4296 8729 2.892425 CCGATCCTGCGTGGCTTC 60.892 66.667 0.00 0.00 35.26 3.86
4297 8730 4.473520 CCCGATCCTGCGTGGCTT 62.474 66.667 0.00 0.00 35.26 4.35
4300 8733 4.838152 CACCCCGATCCTGCGTGG 62.838 72.222 0.00 0.00 34.84 4.94
4325 8758 4.785453 GGGGGACAAGGCGCTCAG 62.785 72.222 7.64 0.00 0.00 3.35
4343 8776 2.102749 CATTCATTGCCGTGCCCG 59.897 61.111 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.