Multiple sequence alignment - TraesCS1A01G315100

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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 TraesCS1A01G315100 chr1A 100.000 3056 0 0 1 3056 506540050 506543105 0.000000e+00 5644.0
1 TraesCS1A01G315100 chr1A 95.749 541 12 2 1 541 506524822 506525351 0.000000e+00 861.0
2 TraesCS1A01G315100 chr1A 85.792 183 21 2 565 743 506491208 506491389 4.020000e-44 189.0
3 TraesCS1A01G315100 chr1A 88.387 155 14 4 2815 2968 506542051 506542202 1.870000e-42 183.0
4 TraesCS1A01G315100 chr1A 88.387 155 14 4 2002 2153 506542864 506543017 1.870000e-42 183.0
5 TraesCS1A01G315100 chr1A 91.250 80 7 0 2668 2747 506541973 506542052 3.220000e-20 110.0
6 TraesCS1A01G315100 chr1A 95.349 43 2 0 2747 2789 506542751 506542793 5.470000e-08 69.4
7 TraesCS1A01G315100 chr1A 95.349 43 2 0 2702 2744 506542796 506542838 5.470000e-08 69.4
8 TraesCS1A01G315100 chr1D 92.242 1998 114 23 745 2721 410495224 410497201 0.000000e+00 2793.0
9 TraesCS1A01G315100 chr1D 84.439 1221 162 19 975 2174 459818712 459817499 0.000000e+00 1177.0
10 TraesCS1A01G315100 chr1D 84.791 1098 144 13 1128 2209 462359136 462358046 0.000000e+00 1081.0
11 TraesCS1A01G315100 chr1D 88.934 741 71 6 1460 2192 410497201 410497938 0.000000e+00 904.0
12 TraesCS1A01G315100 chr1D 85.662 544 66 7 1672 2209 462312977 462312440 2.060000e-156 562.0
13 TraesCS1A01G315100 chr1D 91.558 154 10 3 2815 2968 410497749 410497899 3.090000e-50 209.0
14 TraesCS1A01G315100 chr1D 86.885 183 21 2 565 745 410493061 410493242 5.170000e-48 202.0
15 TraesCS1A01G315100 chr1D 90.141 71 7 0 2669 2739 459817759 459817689 3.240000e-15 93.5
16 TraesCS1A01G315100 chr1D 87.342 79 10 0 2669 2747 462312724 462312646 1.170000e-14 91.6
17 TraesCS1A01G315100 chr1D 87.342 79 10 0 2669 2747 462358342 462358264 1.170000e-14 91.6
18 TraesCS1A01G315100 chr1B 91.790 1559 81 18 745 2260 553138128 553139682 0.000000e+00 2126.0
19 TraesCS1A01G315100 chr1B 86.528 1054 132 6 1146 2192 637388658 637387608 0.000000e+00 1151.0
20 TraesCS1A01G315100 chr1B 84.806 1132 149 16 1031 2145 631824807 631825932 0.000000e+00 1116.0
21 TraesCS1A01G315100 chr1B 86.929 941 113 8 1276 2209 637478371 637477434 0.000000e+00 1048.0
22 TraesCS1A01G315100 chr1B 91.667 552 34 7 1 542 603285936 603285387 0.000000e+00 754.0
23 TraesCS1A01G315100 chr1B 91.486 552 34 7 1 541 603292359 603291810 0.000000e+00 747.0
24 TraesCS1A01G315100 chr1B 84.768 453 20 14 2292 2740 553141935 553142342 2.840000e-110 409.0
25 TraesCS1A01G315100 chr1B 82.721 272 20 15 2808 3056 553142342 553142609 1.850000e-52 217.0
26 TraesCS1A01G315100 chr1B 94.776 134 7 0 610 743 553137922 553138055 3.090000e-50 209.0
27 TraesCS1A01G315100 chr1B 87.342 79 10 0 2669 2747 631825704 631825782 1.170000e-14 91.6
28 TraesCS1A01G315100 chr4D 93.028 545 32 6 1 541 504048386 504048928 0.000000e+00 791.0
29 TraesCS1A01G315100 chr3B 91.971 548 32 11 1 541 14539105 14538563 0.000000e+00 758.0
30 TraesCS1A01G315100 chr3B 91.956 547 33 10 1 541 14532777 14532236 0.000000e+00 756.0
31 TraesCS1A01G315100 chr3B 91.621 549 34 11 1 541 761428487 761427943 0.000000e+00 749.0
32 TraesCS1A01G315100 chr2B 91.636 550 35 7 1 541 632372012 632372559 0.000000e+00 750.0
33 TraesCS1A01G315100 chr6B 91.336 554 37 9 1 544 704559131 704559683 0.000000e+00 747.0
34 TraesCS1A01G315100 chr6A 94.286 35 2 0 1515 1549 454648458 454648492 2.000000e-03 54.7


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 TraesCS1A01G315100 chr1A 506540050 506543105 3055 False 1043.133333 5644 93.120333 1 3056 6 chr1A.!!$F3 3055
1 TraesCS1A01G315100 chr1A 506524822 506525351 529 False 861.000000 861 95.749000 1 541 1 chr1A.!!$F2 540
2 TraesCS1A01G315100 chr1D 410493061 410497938 4877 False 1027.000000 2793 89.904750 565 2968 4 chr1D.!!$F1 2403
3 TraesCS1A01G315100 chr1D 459817499 459818712 1213 True 635.250000 1177 87.290000 975 2739 2 chr1D.!!$R1 1764
4 TraesCS1A01G315100 chr1D 462358046 462359136 1090 True 586.300000 1081 86.066500 1128 2747 2 chr1D.!!$R3 1619
5 TraesCS1A01G315100 chr1D 462312440 462312977 537 True 326.800000 562 86.502000 1672 2747 2 chr1D.!!$R2 1075
6 TraesCS1A01G315100 chr1B 637387608 637388658 1050 True 1151.000000 1151 86.528000 1146 2192 1 chr1B.!!$R3 1046
7 TraesCS1A01G315100 chr1B 637477434 637478371 937 True 1048.000000 1048 86.929000 1276 2209 1 chr1B.!!$R4 933
8 TraesCS1A01G315100 chr1B 603285387 603285936 549 True 754.000000 754 91.667000 1 542 1 chr1B.!!$R1 541
9 TraesCS1A01G315100 chr1B 603291810 603292359 549 True 747.000000 747 91.486000 1 541 1 chr1B.!!$R2 540
10 TraesCS1A01G315100 chr1B 553137922 553142609 4687 False 740.250000 2126 88.513750 610 3056 4 chr1B.!!$F1 2446
11 TraesCS1A01G315100 chr1B 631824807 631825932 1125 False 603.800000 1116 86.074000 1031 2747 2 chr1B.!!$F2 1716
12 TraesCS1A01G315100 chr4D 504048386 504048928 542 False 791.000000 791 93.028000 1 541 1 chr4D.!!$F1 540
13 TraesCS1A01G315100 chr3B 14538563 14539105 542 True 758.000000 758 91.971000 1 541 1 chr3B.!!$R2 540
14 TraesCS1A01G315100 chr3B 14532236 14532777 541 True 756.000000 756 91.956000 1 541 1 chr3B.!!$R1 540
15 TraesCS1A01G315100 chr3B 761427943 761428487 544 True 749.000000 749 91.621000 1 541 1 chr3B.!!$R3 540
16 TraesCS1A01G315100 chr2B 632372012 632372559 547 False 750.000000 750 91.636000 1 541 1 chr2B.!!$F1 540
17 TraesCS1A01G315100 chr6B 704559131 704559683 552 False 747.000000 747 91.336000 1 544 1 chr6B.!!$F1 543

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
569 585 0.036732 AAGCCAAAGCGTCTCCATGA 59.963 50.000 0.00 0.0 46.67 3.07 F
947 2969 0.459585 GCAAAGCTGATCGTCCGGTA 60.460 55.000 0.00 0.0 0.00 4.02 F
1917 3966 1.212935 GCTGAGGCCAGGATAAAAGGA 59.787 52.381 5.01 0.0 40.72 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 3672 0.030501 ATCCCCGTGTCCCAATAGGA 60.031 55.0 0.0 0.0 44.91 2.94 R
1967 4764 0.035056 CCTCTTCTCCGGGTTGCATT 60.035 55.0 0.0 0.0 0.00 3.56 R
2734 8300 0.108138 AGAAGACCTTGATTCGCCGG 60.108 55.0 0.0 0.0 0.00 6.13 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
110 112 0.674581 ACGTCACGGGAGTCGACATA 60.675 55.000 19.50 0.00 44.67 2.29
171 173 2.492484 GTCGAAGCAGAGGTTCTCCTTA 59.508 50.000 7.27 0.00 45.24 2.69
177 179 2.029290 GCAGAGGTTCTCCTTAACGTCA 60.029 50.000 10.82 0.00 45.24 4.35
438 444 1.550327 AGTTCTGATCGAGGCTCACA 58.450 50.000 15.95 10.17 0.00 3.58
466 472 0.682852 TACGTGGACCCCTTCACTTG 59.317 55.000 0.00 0.00 0.00 3.16
544 560 4.216257 CCGTCAGATCAAAACCAACAGAAT 59.784 41.667 0.00 0.00 0.00 2.40
545 561 5.278463 CCGTCAGATCAAAACCAACAGAATT 60.278 40.000 0.00 0.00 0.00 2.17
546 562 6.072728 CCGTCAGATCAAAACCAACAGAATTA 60.073 38.462 0.00 0.00 0.00 1.40
547 563 7.359595 CGTCAGATCAAAACCAACAGAATTAA 58.640 34.615 0.00 0.00 0.00 1.40
548 564 7.535258 CGTCAGATCAAAACCAACAGAATTAAG 59.465 37.037 0.00 0.00 0.00 1.85
549 565 8.567948 GTCAGATCAAAACCAACAGAATTAAGA 58.432 33.333 0.00 0.00 0.00 2.10
550 566 9.130661 TCAGATCAAAACCAACAGAATTAAGAA 57.869 29.630 0.00 0.00 0.00 2.52
551 567 9.748708 CAGATCAAAACCAACAGAATTAAGAAA 57.251 29.630 0.00 0.00 0.00 2.52
552 568 9.971922 AGATCAAAACCAACAGAATTAAGAAAG 57.028 29.630 0.00 0.00 0.00 2.62
553 569 8.593492 ATCAAAACCAACAGAATTAAGAAAGC 57.407 30.769 0.00 0.00 0.00 3.51
554 570 6.983890 TCAAAACCAACAGAATTAAGAAAGCC 59.016 34.615 0.00 0.00 0.00 4.35
555 571 6.478512 AAACCAACAGAATTAAGAAAGCCA 57.521 33.333 0.00 0.00 0.00 4.75
556 572 6.478512 AACCAACAGAATTAAGAAAGCCAA 57.521 33.333 0.00 0.00 0.00 4.52
557 573 6.478512 ACCAACAGAATTAAGAAAGCCAAA 57.521 33.333 0.00 0.00 0.00 3.28
558 574 6.515832 ACCAACAGAATTAAGAAAGCCAAAG 58.484 36.000 0.00 0.00 0.00 2.77
559 575 5.406477 CCAACAGAATTAAGAAAGCCAAAGC 59.594 40.000 0.00 0.00 40.32 3.51
560 576 4.798574 ACAGAATTAAGAAAGCCAAAGCG 58.201 39.130 0.00 0.00 46.67 4.68
561 577 4.278419 ACAGAATTAAGAAAGCCAAAGCGT 59.722 37.500 0.00 0.00 46.67 5.07
562 578 4.853743 CAGAATTAAGAAAGCCAAAGCGTC 59.146 41.667 0.00 0.00 46.67 5.19
563 579 4.762251 AGAATTAAGAAAGCCAAAGCGTCT 59.238 37.500 0.00 0.00 46.67 4.18
564 580 4.686839 ATTAAGAAAGCCAAAGCGTCTC 57.313 40.909 0.00 0.00 46.67 3.36
565 581 1.239347 AAGAAAGCCAAAGCGTCTCC 58.761 50.000 0.00 0.00 46.67 3.71
566 582 0.108585 AGAAAGCCAAAGCGTCTCCA 59.891 50.000 0.00 0.00 46.67 3.86
567 583 1.168714 GAAAGCCAAAGCGTCTCCAT 58.831 50.000 0.00 0.00 46.67 3.41
568 584 0.883833 AAAGCCAAAGCGTCTCCATG 59.116 50.000 0.00 0.00 46.67 3.66
569 585 0.036732 AAGCCAAAGCGTCTCCATGA 59.963 50.000 0.00 0.00 46.67 3.07
570 586 0.674895 AGCCAAAGCGTCTCCATGAC 60.675 55.000 0.00 0.00 46.67 3.06
571 587 0.674895 GCCAAAGCGTCTCCATGACT 60.675 55.000 0.00 0.00 43.25 3.41
572 588 1.363744 CCAAAGCGTCTCCATGACTC 58.636 55.000 0.00 0.00 43.25 3.36
573 589 1.363744 CAAAGCGTCTCCATGACTCC 58.636 55.000 0.00 0.00 43.25 3.85
574 590 0.976641 AAAGCGTCTCCATGACTCCA 59.023 50.000 0.00 0.00 43.25 3.86
575 591 1.198713 AAGCGTCTCCATGACTCCAT 58.801 50.000 0.00 0.00 43.25 3.41
576 592 2.073252 AGCGTCTCCATGACTCCATA 57.927 50.000 0.00 0.00 43.25 2.74
577 593 1.683917 AGCGTCTCCATGACTCCATAC 59.316 52.381 0.00 0.00 43.25 2.39
578 594 1.269831 GCGTCTCCATGACTCCATACC 60.270 57.143 0.00 0.00 43.25 2.73
579 595 2.031870 CGTCTCCATGACTCCATACCA 58.968 52.381 0.00 0.00 43.25 3.25
592 608 7.398829 TGACTCCATACCATGTTTAGCTAAAA 58.601 34.615 20.22 11.18 0.00 1.52
608 624 3.181512 GCTAAAACATGTGCTGCTCTCTC 60.182 47.826 0.00 0.00 0.00 3.20
706 722 0.951525 TAACGGTGCACCAATGACGG 60.952 55.000 34.16 18.73 35.14 4.79
735 751 2.605837 TTGCGTAATTAGGCCGATCA 57.394 45.000 23.42 5.53 36.33 2.92
739 755 2.221055 GCGTAATTAGGCCGATCAACTG 59.779 50.000 17.40 0.00 0.00 3.16
756 2758 3.631145 ACTGAGTAACGCGTAGAAACA 57.369 42.857 14.46 8.96 0.00 2.83
840 2851 5.043903 GGCCGTCTATATATACAGCACATG 58.956 45.833 8.29 0.00 0.00 3.21
902 2913 3.839432 GCTCCGGCCGTCTAGCTT 61.839 66.667 27.56 0.00 32.18 3.74
939 2961 2.935201 AGTCGATCAAGCAAAGCTGATC 59.065 45.455 15.29 15.29 39.62 2.92
947 2969 0.459585 GCAAAGCTGATCGTCCGGTA 60.460 55.000 0.00 0.00 0.00 4.02
1274 3322 2.181021 CGCCGAACGCTACCTCTT 59.819 61.111 0.00 0.00 34.21 2.85
1310 3358 1.376812 TCAGTGCTCTCGAGGCGTA 60.377 57.895 13.56 0.74 0.00 4.42
1343 3391 3.853330 CATCGTTCAGCCGCGTGG 61.853 66.667 11.67 11.67 38.77 4.94
1527 3575 2.124983 CTCATGCACCGGGACCTG 60.125 66.667 6.32 0.10 0.00 4.00
1548 3596 2.954753 GCCGGAGAACGTGCTTGTG 61.955 63.158 5.05 0.00 42.24 3.33
1623 3672 2.207924 CGGGCCGCCCTACTCTAAT 61.208 63.158 26.29 0.00 42.67 1.73
1710 3759 2.418910 CGACTCATGGGCTCTCGGT 61.419 63.158 0.00 0.00 0.00 4.69
1911 3960 2.844362 CCCGCTGAGGCCAGGATA 60.844 66.667 5.01 0.00 40.72 2.59
1917 3966 1.212935 GCTGAGGCCAGGATAAAAGGA 59.787 52.381 5.01 0.00 40.72 3.36
1967 4764 1.544691 GGTCTTGAGCGGTCTTCTACA 59.455 52.381 16.64 0.00 0.00 2.74
2046 5366 1.328430 ACGCCAACCCTAGAGCTACC 61.328 60.000 0.00 0.00 0.00 3.18
2072 5392 7.225538 CAGGAGTTGATCGATTAGCATACTTTT 59.774 37.037 0.00 0.00 0.00 2.27
2201 5542 3.425625 CCACCACACACATATTGTAACGC 60.426 47.826 0.00 0.00 35.67 4.84
2203 5544 3.006940 CCACACACATATTGTAACGCCT 58.993 45.455 0.00 0.00 35.67 5.52
2227 5568 4.405116 TTGCAATTTGGTTTCTTGCTCT 57.595 36.364 0.00 0.00 44.29 4.09
2273 5638 2.099921 TGTTTGTTTGCTTGCCGTGTAT 59.900 40.909 0.00 0.00 0.00 2.29
2277 5642 1.265635 GTTTGCTTGCCGTGTATGACA 59.734 47.619 0.00 0.00 0.00 3.58
2289 5654 6.202762 TGCCGTGTATGACAGATCAAATATTC 59.797 38.462 0.00 0.00 38.69 1.75
2290 5655 6.202762 GCCGTGTATGACAGATCAAATATTCA 59.797 38.462 0.00 0.00 38.69 2.57
2324 7887 5.639082 TGTAGATGTGCAGTTTAGATGTGTG 59.361 40.000 0.00 0.00 0.00 3.82
2333 7896 8.830580 GTGCAGTTTAGATGTGTGATACAATAT 58.169 33.333 0.00 0.00 43.77 1.28
2335 7898 9.869844 GCAGTTTAGATGTGTGATACAATATTC 57.130 33.333 0.00 0.00 43.77 1.75
2357 7923 5.724328 TCGGAATCATGCCTATCTATTCAC 58.276 41.667 0.00 0.00 0.00 3.18
2389 7955 7.268199 TGTGTTATCCTCGATAAGAATACGT 57.732 36.000 0.00 0.00 35.54 3.57
2401 7967 7.066163 TCGATAAGAATACGTCTTTCTACACCA 59.934 37.037 12.53 0.44 44.64 4.17
2515 8081 7.477144 TTGTAAGTGATAGTTGTGTGACTTG 57.523 36.000 0.00 0.00 0.00 3.16
2524 8090 8.773645 TGATAGTTGTGTGACTTGATGTAAAAG 58.226 33.333 0.00 0.00 0.00 2.27
2526 8092 6.785191 AGTTGTGTGACTTGATGTAAAAGTG 58.215 36.000 0.00 0.00 37.98 3.16
2527 8093 6.597672 AGTTGTGTGACTTGATGTAAAAGTGA 59.402 34.615 0.00 0.00 37.98 3.41
2528 8094 7.283127 AGTTGTGTGACTTGATGTAAAAGTGAT 59.717 33.333 0.00 0.00 37.98 3.06
2529 8095 8.556194 GTTGTGTGACTTGATGTAAAAGTGATA 58.444 33.333 0.00 0.00 37.98 2.15
2530 8096 8.669946 TGTGTGACTTGATGTAAAAGTGATAA 57.330 30.769 0.00 0.00 37.98 1.75
2531 8097 9.283768 TGTGTGACTTGATGTAAAAGTGATAAT 57.716 29.630 0.00 0.00 37.98 1.28
2563 8129 2.668250 TGACGACGACAATTAGTGTGG 58.332 47.619 0.00 0.00 41.96 4.17
2594 8160 2.338809 TCCTCTCTTCCAACACCATGT 58.661 47.619 0.00 0.00 0.00 3.21
2595 8161 2.711009 TCCTCTCTTCCAACACCATGTT 59.289 45.455 0.00 0.00 42.08 2.71
2705 8271 0.894184 TTCGAGGTCTTGAGCGGTCT 60.894 55.000 16.64 0.00 0.00 3.85
2706 8272 0.894184 TCGAGGTCTTGAGCGGTCTT 60.894 55.000 16.64 0.00 0.00 3.01
2707 8273 0.456995 CGAGGTCTTGAGCGGTCTTC 60.457 60.000 16.64 3.60 0.00 2.87
2708 8274 0.892063 GAGGTCTTGAGCGGTCTTCT 59.108 55.000 16.64 5.90 0.00 2.85
2709 8275 0.605589 AGGTCTTGAGCGGTCTTCTG 59.394 55.000 16.64 3.56 0.00 3.02
2710 8276 1.016653 GGTCTTGAGCGGTCTTCTGC 61.017 60.000 16.64 2.56 45.49 4.26
2716 8282 3.343972 GCGGTCTTCTGCAAAGCA 58.656 55.556 0.00 0.00 44.61 3.91
2717 8283 1.654220 GCGGTCTTCTGCAAAGCAA 59.346 52.632 0.00 0.00 44.61 3.91
2718 8284 0.661483 GCGGTCTTCTGCAAAGCAAC 60.661 55.000 0.00 0.00 44.61 4.17
2719 8285 0.040067 CGGTCTTCTGCAAAGCAACC 60.040 55.000 1.47 1.47 38.41 3.77
2720 8286 0.315251 GGTCTTCTGCAAAGCAACCC 59.685 55.000 0.00 0.00 38.41 4.11
2721 8287 0.040067 GTCTTCTGCAAAGCAACCCG 60.040 55.000 0.00 0.00 38.41 5.28
2722 8288 1.172180 TCTTCTGCAAAGCAACCCGG 61.172 55.000 0.00 0.00 38.41 5.73
2723 8289 1.152860 TTCTGCAAAGCAACCCGGA 60.153 52.632 0.73 0.00 38.41 5.14
2724 8290 1.172180 TTCTGCAAAGCAACCCGGAG 61.172 55.000 0.73 0.00 38.41 4.63
2725 8291 1.600636 CTGCAAAGCAACCCGGAGA 60.601 57.895 0.73 0.00 38.41 3.71
2726 8292 1.152860 TGCAAAGCAACCCGGAGAA 60.153 52.632 0.73 0.00 34.76 2.87
2727 8293 1.172180 TGCAAAGCAACCCGGAGAAG 61.172 55.000 0.73 0.00 34.76 2.85
2728 8294 0.889186 GCAAAGCAACCCGGAGAAGA 60.889 55.000 0.73 0.00 0.00 2.87
2729 8295 1.160137 CAAAGCAACCCGGAGAAGAG 58.840 55.000 0.73 0.00 0.00 2.85
2730 8296 1.056660 AAAGCAACCCGGAGAAGAGA 58.943 50.000 0.73 0.00 0.00 3.10
2731 8297 0.321996 AAGCAACCCGGAGAAGAGAC 59.678 55.000 0.73 0.00 0.00 3.36
2732 8298 0.543174 AGCAACCCGGAGAAGAGACT 60.543 55.000 0.73 0.00 0.00 3.24
2733 8299 0.108567 GCAACCCGGAGAAGAGACTC 60.109 60.000 0.73 0.00 36.31 3.36
2739 8305 2.802106 GAGAAGAGACTCCCGGCG 59.198 66.667 0.00 0.00 0.00 6.46
2740 8306 1.749638 GAGAAGAGACTCCCGGCGA 60.750 63.158 9.30 0.00 0.00 5.54
2741 8307 1.304217 AGAAGAGACTCCCGGCGAA 60.304 57.895 9.30 0.00 0.00 4.70
2742 8308 0.684805 AGAAGAGACTCCCGGCGAAT 60.685 55.000 9.30 0.00 0.00 3.34
2743 8309 0.249114 GAAGAGACTCCCGGCGAATC 60.249 60.000 9.30 0.00 0.00 2.52
2744 8310 0.970937 AAGAGACTCCCGGCGAATCA 60.971 55.000 9.30 0.00 0.00 2.57
2745 8311 0.970937 AGAGACTCCCGGCGAATCAA 60.971 55.000 9.30 0.00 0.00 2.57
2746 8312 0.528684 GAGACTCCCGGCGAATCAAG 60.529 60.000 9.30 0.12 0.00 3.02
2747 8313 1.521681 GACTCCCGGCGAATCAAGG 60.522 63.158 9.30 0.00 0.00 3.61
2748 8314 2.240162 GACTCCCGGCGAATCAAGGT 62.240 60.000 9.30 0.00 0.00 3.50
2749 8315 1.521681 CTCCCGGCGAATCAAGGTC 60.522 63.158 9.30 0.00 0.00 3.85
2756 8322 2.416836 CGGCGAATCAAGGTCTTCTACA 60.417 50.000 0.00 0.00 0.00 2.74
2766 8332 1.804748 GGTCTTCTACAAAGCAACCCG 59.195 52.381 0.00 0.00 0.00 5.28
2785 8351 3.267908 GAGAAGAGACTCCCGGTGA 57.732 57.895 0.00 0.00 0.00 4.02
2787 8353 2.104170 GAGAAGAGACTCCCGGTGAAT 58.896 52.381 0.00 0.00 0.00 2.57
2788 8354 2.100087 GAGAAGAGACTCCCGGTGAATC 59.900 54.545 0.00 0.00 0.00 2.52
2789 8355 0.818296 AAGAGACTCCCGGTGAATCG 59.182 55.000 0.00 0.00 0.00 3.34
2790 8356 0.034380 AGAGACTCCCGGTGAATCGA 60.034 55.000 0.00 0.00 0.00 3.59
2791 8357 0.382515 GAGACTCCCGGTGAATCGAG 59.617 60.000 0.00 0.48 0.00 4.04
2792 8358 1.227002 GACTCCCGGTGAATCGAGC 60.227 63.158 0.00 0.00 0.00 5.03
2793 8359 2.278857 CTCCCGGTGAATCGAGCG 60.279 66.667 0.00 0.00 36.60 5.03
2794 8360 4.508128 TCCCGGTGAATCGAGCGC 62.508 66.667 0.00 0.00 35.52 5.92
2795 8361 4.514577 CCCGGTGAATCGAGCGCT 62.515 66.667 11.27 11.27 35.52 5.92
2796 8362 2.956964 CCGGTGAATCGAGCGCTC 60.957 66.667 27.64 27.64 35.52 5.03
2797 8363 2.202610 CGGTGAATCGAGCGCTCA 60.203 61.111 34.69 22.54 0.00 4.26
2798 8364 1.805539 CGGTGAATCGAGCGCTCAA 60.806 57.895 34.69 20.63 0.00 3.02
2799 8365 1.746727 CGGTGAATCGAGCGCTCAAG 61.747 60.000 34.69 20.77 0.00 3.02
2800 8366 1.346538 GTGAATCGAGCGCTCAAGC 59.653 57.895 34.69 20.96 37.78 4.01
2801 8367 1.079888 TGAATCGAGCGCTCAAGCA 60.080 52.632 34.69 23.11 42.21 3.91
2802 8368 0.460811 TGAATCGAGCGCTCAAGCAT 60.461 50.000 34.69 18.33 42.21 3.79
2803 8369 0.231790 GAATCGAGCGCTCAAGCATC 59.768 55.000 34.69 20.73 42.21 3.91
2804 8370 0.460811 AATCGAGCGCTCAAGCATCA 60.461 50.000 34.69 10.95 42.21 3.07
2805 8371 0.875040 ATCGAGCGCTCAAGCATCAG 60.875 55.000 34.69 17.15 42.21 2.90
2806 8372 1.808799 CGAGCGCTCAAGCATCAGT 60.809 57.895 34.69 0.00 42.21 3.41
2807 8373 1.714414 GAGCGCTCAAGCATCAGTG 59.286 57.895 31.91 0.00 42.21 3.66
2808 8374 1.703438 GAGCGCTCAAGCATCAGTGG 61.703 60.000 31.91 0.00 42.21 4.00
2809 8375 1.742880 GCGCTCAAGCATCAGTGGA 60.743 57.895 0.00 0.00 42.21 4.02
2810 8376 1.300971 GCGCTCAAGCATCAGTGGAA 61.301 55.000 0.00 0.00 42.21 3.53
2811 8377 1.376543 CGCTCAAGCATCAGTGGAAT 58.623 50.000 2.50 0.00 42.21 3.01
2841 8407 2.191128 AGCATCAGTGGTTCAAGGAC 57.809 50.000 0.00 0.00 30.39 3.85
2862 8428 1.831736 GCCAACCCTAGAGCTACAAGA 59.168 52.381 0.00 0.00 0.00 3.02
2871 8437 5.277825 CCTAGAGCTACAAGAAGTTGATCG 58.722 45.833 0.00 0.00 42.03 3.69
2896 8462 8.610035 CGATTAGCATGCATAATCACATCTAAT 58.390 33.333 29.08 18.28 38.85 1.73
2940 8506 8.859156 ACAAACATTGTACATGAATTTAATCGC 58.141 29.630 0.00 0.00 43.27 4.58
2941 8507 8.858186 CAAACATTGTACATGAATTTAATCGCA 58.142 29.630 0.00 0.00 0.00 5.10
2942 8508 9.585099 AAACATTGTACATGAATTTAATCGCAT 57.415 25.926 0.00 0.00 0.00 4.73
2943 8509 8.564648 ACATTGTACATGAATTTAATCGCATG 57.435 30.769 14.79 14.79 42.75 4.06
2944 8510 8.404765 ACATTGTACATGAATTTAATCGCATGA 58.595 29.630 20.06 7.64 40.29 3.07
2945 8511 8.898792 CATTGTACATGAATTTAATCGCATGAG 58.101 33.333 20.06 0.00 40.29 2.90
2946 8512 7.552458 TGTACATGAATTTAATCGCATGAGT 57.448 32.000 20.06 7.78 40.29 3.41
2947 8513 8.655651 TGTACATGAATTTAATCGCATGAGTA 57.344 30.769 20.06 7.09 40.29 2.59
2948 8514 9.271828 TGTACATGAATTTAATCGCATGAGTAT 57.728 29.630 20.06 7.04 40.29 2.12
2949 8515 9.533983 GTACATGAATTTAATCGCATGAGTATG 57.466 33.333 20.06 0.00 40.29 2.39
2950 8516 8.382030 ACATGAATTTAATCGCATGAGTATGA 57.618 30.769 20.06 0.00 40.29 2.15
2951 8517 8.839343 ACATGAATTTAATCGCATGAGTATGAA 58.161 29.630 20.06 0.00 40.29 2.57
2952 8518 9.326339 CATGAATTTAATCGCATGAGTATGAAG 57.674 33.333 12.42 0.00 40.29 3.02
2969 8535 5.883685 ATGAAGGAGATGTGAGATAAGCA 57.116 39.130 0.00 0.00 0.00 3.91
3021 8627 1.347243 ACCCCACGTTAACACCACCT 61.347 55.000 6.39 0.00 0.00 4.00
3027 8633 3.495753 CCACGTTAACACCACCTTAACTC 59.504 47.826 6.39 0.00 33.60 3.01
3028 8634 4.121317 CACGTTAACACCACCTTAACTCA 58.879 43.478 6.39 0.00 33.60 3.41
3037 8643 5.830991 ACACCACCTTAACTCAAATTAAGCA 59.169 36.000 0.64 0.00 39.74 3.91
3041 8647 6.349363 CCACCTTAACTCAAATTAAGCAGGTC 60.349 42.308 0.64 0.00 39.74 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 173 3.485463 TCCTGAAGGAAACATGACGTT 57.515 42.857 0.00 0.00 42.18 3.99
496 509 7.437267 GGCTTAACACGCAGTTAGATCTATTAA 59.563 37.037 2.58 2.57 41.61 1.40
513 529 4.464112 GTTTTGATCTGACGGCTTAACAC 58.536 43.478 0.00 0.00 0.00 3.32
544 560 2.812011 GGAGACGCTTTGGCTTTCTTAA 59.188 45.455 0.00 0.00 36.09 1.85
545 561 2.224426 TGGAGACGCTTTGGCTTTCTTA 60.224 45.455 0.00 0.00 36.09 2.10
546 562 1.239347 GGAGACGCTTTGGCTTTCTT 58.761 50.000 0.00 0.00 36.09 2.52
547 563 0.108585 TGGAGACGCTTTGGCTTTCT 59.891 50.000 0.00 0.00 36.09 2.52
548 564 1.135575 CATGGAGACGCTTTGGCTTTC 60.136 52.381 0.00 0.00 36.09 2.62
549 565 0.883833 CATGGAGACGCTTTGGCTTT 59.116 50.000 0.00 0.00 36.09 3.51
550 566 0.036732 TCATGGAGACGCTTTGGCTT 59.963 50.000 0.00 0.00 36.09 4.35
551 567 0.674895 GTCATGGAGACGCTTTGGCT 60.675 55.000 0.00 0.00 37.53 4.75
552 568 1.796796 GTCATGGAGACGCTTTGGC 59.203 57.895 0.00 0.00 37.53 4.52
559 575 6.009010 ACATGGTATGGAGTCATGGAGACG 62.009 50.000 0.00 0.00 42.77 4.18
560 576 3.389329 ACATGGTATGGAGTCATGGAGAC 59.611 47.826 0.00 0.00 41.64 3.36
561 577 3.657610 ACATGGTATGGAGTCATGGAGA 58.342 45.455 0.00 0.00 41.64 3.71
562 578 4.428294 AACATGGTATGGAGTCATGGAG 57.572 45.455 0.00 0.00 41.64 3.86
563 579 4.860802 AAACATGGTATGGAGTCATGGA 57.139 40.909 0.00 0.00 41.64 3.41
564 580 4.516698 GCTAAACATGGTATGGAGTCATGG 59.483 45.833 0.00 0.00 41.64 3.66
565 581 5.371526 AGCTAAACATGGTATGGAGTCATG 58.628 41.667 0.00 0.00 42.65 3.07
566 582 5.636903 AGCTAAACATGGTATGGAGTCAT 57.363 39.130 0.00 0.00 37.40 3.06
567 583 6.553953 TTAGCTAAACATGGTATGGAGTCA 57.446 37.500 2.97 0.00 33.60 3.41
568 584 7.694886 GTTTTAGCTAAACATGGTATGGAGTC 58.305 38.462 18.45 0.00 44.49 3.36
569 585 7.625828 GTTTTAGCTAAACATGGTATGGAGT 57.374 36.000 18.45 0.00 44.49 3.85
592 608 3.836762 CTGAGAGAGCAGCACATGT 57.163 52.632 0.00 0.00 0.00 3.21
608 624 2.132740 GCATCGTCTTAGAGAGGCTG 57.867 55.000 0.00 3.39 40.51 4.85
706 722 4.554723 GCCTAATTACGCAATGTCCATGTC 60.555 45.833 2.04 0.00 0.00 3.06
735 751 3.968649 TGTTTCTACGCGTTACTCAGTT 58.031 40.909 20.78 0.00 0.00 3.16
739 755 3.303406 ACACTGTTTCTACGCGTTACTC 58.697 45.455 20.78 5.61 0.00 2.59
756 2758 0.595095 GTTCGGACACGGACTACACT 59.405 55.000 0.00 0.00 45.23 3.55
807 2810 2.076622 ATAGACGGCCAGCACGCTAG 62.077 60.000 2.24 0.00 34.00 3.42
902 2913 1.296056 GACTGCTCGGCGGCTAAAAA 61.296 55.000 18.47 0.78 38.71 1.94
947 2969 0.034767 TGAGGGTACACGATCGACCT 60.035 55.000 24.34 18.92 33.48 3.85
1077 3113 3.261643 TGGCTGCTGTTCTCTGATTCTTA 59.738 43.478 0.00 0.00 0.00 2.10
1343 3391 2.281484 TGTCAAGTTGGCCGGAGC 60.281 61.111 5.05 0.00 38.76 4.70
1527 3575 1.668151 AAGCACGTTCTCCGGCTTC 60.668 57.895 0.00 0.00 44.35 3.86
1548 3596 3.607370 GAGGTTCCCGTGGCTGTCC 62.607 68.421 0.00 0.00 0.00 4.02
1608 3657 1.920610 TAGGATTAGAGTAGGGCGGC 58.079 55.000 0.00 0.00 0.00 6.53
1623 3672 0.030501 ATCCCCGTGTCCCAATAGGA 60.031 55.000 0.00 0.00 44.91 2.94
1710 3759 1.144716 GAGCTCGGCCATCATGACA 59.855 57.895 2.24 0.00 0.00 3.58
1848 3897 1.558167 TTCCTGGTTGGCATCCGCTA 61.558 55.000 9.91 0.00 38.60 4.26
1911 3960 0.395173 ACAGTGTTGGCGGTCCTTTT 60.395 50.000 0.00 0.00 0.00 2.27
1967 4764 0.035056 CCTCTTCTCCGGGTTGCATT 60.035 55.000 0.00 0.00 0.00 3.56
2046 5366 5.777802 AGTATGCTAATCGATCAACTCCTG 58.222 41.667 0.00 0.00 0.00 3.86
2201 5542 4.083696 GCAAGAAACCAAATTGCAATCAGG 60.084 41.667 21.99 21.99 46.64 3.86
2289 5654 8.746922 AACTGCACATCTACAACAAATTTATG 57.253 30.769 0.00 0.00 0.00 1.90
2324 7887 6.992063 AGGCATGATTCCGAATATTGTATC 57.008 37.500 0.00 0.00 0.00 2.24
2333 7896 6.166279 GTGAATAGATAGGCATGATTCCGAA 58.834 40.000 0.00 0.00 0.00 4.30
2335 7898 5.482006 TGTGAATAGATAGGCATGATTCCG 58.518 41.667 0.00 0.00 0.00 4.30
2357 7923 9.045223 TCTTATCGAGGATAACACATCAAATTG 57.955 33.333 0.00 0.00 32.10 2.32
2389 7955 5.984725 TCACTCACTTTTGGTGTAGAAAGA 58.015 37.500 3.14 0.00 45.50 2.52
2445 8011 8.358148 CGACCGGCCTAATGTAATCTTATATAT 58.642 37.037 0.00 0.00 0.00 0.86
2452 8018 2.037144 ACGACCGGCCTAATGTAATCT 58.963 47.619 0.00 0.00 0.00 2.40
2463 8029 0.600255 CAAGATATCCACGACCGGCC 60.600 60.000 0.00 0.00 0.00 6.13
2533 8099 9.217278 ACTAATTGTCGTCGTCATACTCTATAT 57.783 33.333 0.00 0.00 0.00 0.86
2534 8100 8.493547 CACTAATTGTCGTCGTCATACTCTATA 58.506 37.037 0.00 0.00 0.00 1.31
2535 8101 7.012138 ACACTAATTGTCGTCGTCATACTCTAT 59.988 37.037 0.00 0.00 29.79 1.98
2536 8102 6.314648 ACACTAATTGTCGTCGTCATACTCTA 59.685 38.462 0.00 0.00 29.79 2.43
2537 8103 5.123502 ACACTAATTGTCGTCGTCATACTCT 59.876 40.000 0.00 0.00 29.79 3.24
2538 8104 5.227391 CACACTAATTGTCGTCGTCATACTC 59.773 44.000 0.00 0.00 35.67 2.59
2539 8105 5.093457 CACACTAATTGTCGTCGTCATACT 58.907 41.667 0.00 0.00 35.67 2.12
2540 8106 4.264614 CCACACTAATTGTCGTCGTCATAC 59.735 45.833 0.00 0.00 35.67 2.39
2541 8107 4.082625 ACCACACTAATTGTCGTCGTCATA 60.083 41.667 0.00 0.00 35.67 2.15
2542 8108 3.250744 CCACACTAATTGTCGTCGTCAT 58.749 45.455 0.00 0.00 35.67 3.06
2543 8109 2.034939 ACCACACTAATTGTCGTCGTCA 59.965 45.455 0.00 0.00 35.67 4.35
2544 8110 2.407361 CACCACACTAATTGTCGTCGTC 59.593 50.000 0.00 0.00 35.67 4.20
2545 8111 2.223876 ACACCACACTAATTGTCGTCGT 60.224 45.455 0.00 0.00 35.67 4.34
2546 8112 2.400399 ACACCACACTAATTGTCGTCG 58.600 47.619 0.00 0.00 35.67 5.12
2547 8113 2.735134 GGACACCACACTAATTGTCGTC 59.265 50.000 0.00 0.00 39.46 4.20
2548 8114 2.367567 AGGACACCACACTAATTGTCGT 59.632 45.455 0.00 0.00 39.46 4.34
2549 8115 3.040147 AGGACACCACACTAATTGTCG 57.960 47.619 0.00 0.00 39.46 4.35
2550 8116 6.870971 TTAAAGGACACCACACTAATTGTC 57.129 37.500 0.00 0.00 35.67 3.18
2551 8117 6.433093 GGATTAAAGGACACCACACTAATTGT 59.567 38.462 0.00 0.00 39.97 2.71
2552 8118 6.659242 AGGATTAAAGGACACCACACTAATTG 59.341 38.462 0.00 0.00 0.00 2.32
2553 8119 6.790319 AGGATTAAAGGACACCACACTAATT 58.210 36.000 0.00 0.00 0.00 1.40
2554 8120 6.215636 AGAGGATTAAAGGACACCACACTAAT 59.784 38.462 0.00 0.00 0.00 1.73
2555 8121 5.546499 AGAGGATTAAAGGACACCACACTAA 59.454 40.000 0.00 0.00 0.00 2.24
2556 8122 5.091552 AGAGGATTAAAGGACACCACACTA 58.908 41.667 0.00 0.00 0.00 2.74
2563 8129 5.422214 TGGAAGAGAGGATTAAAGGACAC 57.578 43.478 0.00 0.00 0.00 3.67
2594 8160 5.630121 AGAATCTGAATACCAACACACCAA 58.370 37.500 0.00 0.00 0.00 3.67
2595 8161 5.241403 AGAATCTGAATACCAACACACCA 57.759 39.130 0.00 0.00 0.00 4.17
2596 8162 6.575162 AAAGAATCTGAATACCAACACACC 57.425 37.500 0.00 0.00 0.00 4.16
2597 8163 9.559958 CAATAAAGAATCTGAATACCAACACAC 57.440 33.333 0.00 0.00 0.00 3.82
2598 8164 9.295825 ACAATAAAGAATCTGAATACCAACACA 57.704 29.630 0.00 0.00 0.00 3.72
2599 8165 9.559958 CACAATAAAGAATCTGAATACCAACAC 57.440 33.333 0.00 0.00 0.00 3.32
2600 8166 9.295825 ACACAATAAAGAATCTGAATACCAACA 57.704 29.630 0.00 0.00 0.00 3.33
2653 8219 7.672240 TCCAACAGTGTTTTCTTTACCTTTTT 58.328 30.769 5.57 0.00 0.00 1.94
2654 8220 7.234661 TCCAACAGTGTTTTCTTTACCTTTT 57.765 32.000 5.57 0.00 0.00 2.27
2658 8224 4.499188 GCCTCCAACAGTGTTTTCTTTACC 60.499 45.833 5.57 0.00 0.00 2.85
2659 8225 4.338400 AGCCTCCAACAGTGTTTTCTTTAC 59.662 41.667 5.57 0.00 0.00 2.01
2660 8226 4.338118 CAGCCTCCAACAGTGTTTTCTTTA 59.662 41.667 5.57 0.00 0.00 1.85
2661 8227 3.131046 CAGCCTCCAACAGTGTTTTCTTT 59.869 43.478 5.57 0.00 0.00 2.52
2662 8228 2.689983 CAGCCTCCAACAGTGTTTTCTT 59.310 45.455 5.57 0.00 0.00 2.52
2663 8229 2.301346 CAGCCTCCAACAGTGTTTTCT 58.699 47.619 5.57 0.00 0.00 2.52
2664 8230 1.338020 CCAGCCTCCAACAGTGTTTTC 59.662 52.381 5.57 0.00 0.00 2.29
2705 8271 1.152860 TCCGGGTTGCTTTGCAGAA 60.153 52.632 0.00 0.00 40.61 3.02
2706 8272 1.600636 CTCCGGGTTGCTTTGCAGA 60.601 57.895 0.00 0.00 40.61 4.26
2707 8273 1.172180 TTCTCCGGGTTGCTTTGCAG 61.172 55.000 0.00 0.00 40.61 4.41
2708 8274 1.152860 TTCTCCGGGTTGCTTTGCA 60.153 52.632 0.00 0.00 36.47 4.08
2709 8275 0.889186 TCTTCTCCGGGTTGCTTTGC 60.889 55.000 0.00 0.00 0.00 3.68
2710 8276 1.160137 CTCTTCTCCGGGTTGCTTTG 58.840 55.000 0.00 0.00 0.00 2.77
2711 8277 1.056660 TCTCTTCTCCGGGTTGCTTT 58.943 50.000 0.00 0.00 0.00 3.51
2712 8278 0.321996 GTCTCTTCTCCGGGTTGCTT 59.678 55.000 0.00 0.00 0.00 3.91
2713 8279 0.543174 AGTCTCTTCTCCGGGTTGCT 60.543 55.000 0.00 0.00 0.00 3.91
2714 8280 0.108567 GAGTCTCTTCTCCGGGTTGC 60.109 60.000 0.00 0.00 0.00 4.17
2715 8281 0.533032 GGAGTCTCTTCTCCGGGTTG 59.467 60.000 0.00 0.00 43.42 3.77
2716 8282 2.979058 GGAGTCTCTTCTCCGGGTT 58.021 57.895 0.00 0.00 43.42 4.11
2717 8283 4.768404 GGAGTCTCTTCTCCGGGT 57.232 61.111 0.00 0.00 43.42 5.28
2722 8288 1.313812 TTCGCCGGGAGTCTCTTCTC 61.314 60.000 2.18 0.00 0.00 2.87
2723 8289 0.684805 ATTCGCCGGGAGTCTCTTCT 60.685 55.000 2.18 0.00 0.00 2.85
2724 8290 0.249114 GATTCGCCGGGAGTCTCTTC 60.249 60.000 2.18 0.00 0.00 2.87
2725 8291 0.970937 TGATTCGCCGGGAGTCTCTT 60.971 55.000 2.18 0.00 32.89 2.85
2726 8292 0.970937 TTGATTCGCCGGGAGTCTCT 60.971 55.000 2.18 0.00 32.89 3.10
2727 8293 0.528684 CTTGATTCGCCGGGAGTCTC 60.529 60.000 2.18 0.00 32.89 3.36
2728 8294 1.517832 CTTGATTCGCCGGGAGTCT 59.482 57.895 2.18 0.00 32.89 3.24
2729 8295 1.521681 CCTTGATTCGCCGGGAGTC 60.522 63.158 2.18 6.04 32.35 3.36
2730 8296 2.240162 GACCTTGATTCGCCGGGAGT 62.240 60.000 2.18 0.00 0.00 3.85
2731 8297 1.521681 GACCTTGATTCGCCGGGAG 60.522 63.158 2.18 0.00 0.00 4.30
2732 8298 1.550130 AAGACCTTGATTCGCCGGGA 61.550 55.000 2.18 0.00 0.00 5.14
2733 8299 1.078426 AAGACCTTGATTCGCCGGG 60.078 57.895 2.18 0.00 0.00 5.73
2734 8300 0.108138 AGAAGACCTTGATTCGCCGG 60.108 55.000 0.00 0.00 0.00 6.13
2735 8301 2.194271 GTAGAAGACCTTGATTCGCCG 58.806 52.381 0.00 0.00 0.00 6.46
2736 8302 3.247006 TGTAGAAGACCTTGATTCGCC 57.753 47.619 0.00 0.00 0.00 5.54
2737 8303 4.436183 GCTTTGTAGAAGACCTTGATTCGC 60.436 45.833 0.00 0.00 0.00 4.70
2738 8304 4.690748 TGCTTTGTAGAAGACCTTGATTCG 59.309 41.667 0.00 0.00 0.00 3.34
2739 8305 6.374578 GTTGCTTTGTAGAAGACCTTGATTC 58.625 40.000 0.00 0.00 0.00 2.52
2740 8306 5.241728 GGTTGCTTTGTAGAAGACCTTGATT 59.758 40.000 0.00 0.00 0.00 2.57
2741 8307 4.762251 GGTTGCTTTGTAGAAGACCTTGAT 59.238 41.667 0.00 0.00 0.00 2.57
2742 8308 4.134563 GGTTGCTTTGTAGAAGACCTTGA 58.865 43.478 0.00 0.00 0.00 3.02
2743 8309 3.253432 GGGTTGCTTTGTAGAAGACCTTG 59.747 47.826 0.00 0.00 0.00 3.61
2744 8310 3.487372 GGGTTGCTTTGTAGAAGACCTT 58.513 45.455 0.00 0.00 0.00 3.50
2745 8311 2.550208 CGGGTTGCTTTGTAGAAGACCT 60.550 50.000 0.00 0.00 0.00 3.85
2746 8312 1.804748 CGGGTTGCTTTGTAGAAGACC 59.195 52.381 0.00 0.00 0.00 3.85
2747 8313 1.804748 CCGGGTTGCTTTGTAGAAGAC 59.195 52.381 0.00 0.00 0.00 3.01
2748 8314 1.695242 TCCGGGTTGCTTTGTAGAAGA 59.305 47.619 0.00 0.00 0.00 2.87
2749 8315 2.076863 CTCCGGGTTGCTTTGTAGAAG 58.923 52.381 0.00 0.00 0.00 2.85
2756 8322 1.056660 TCTCTTCTCCGGGTTGCTTT 58.943 50.000 0.00 0.00 0.00 3.51
2779 8345 2.956964 GAGCGCTCGATTCACCGG 60.957 66.667 23.61 0.00 0.00 5.28
2783 8349 0.460811 ATGCTTGAGCGCTCGATTCA 60.461 50.000 30.75 26.59 45.83 2.57
2785 8351 0.460811 TGATGCTTGAGCGCTCGATT 60.461 50.000 30.75 17.14 45.83 3.34
2787 8353 1.517913 CTGATGCTTGAGCGCTCGA 60.518 57.895 30.75 28.15 45.83 4.04
2788 8354 1.808799 ACTGATGCTTGAGCGCTCG 60.809 57.895 30.75 19.30 45.83 5.03
2789 8355 1.703438 CCACTGATGCTTGAGCGCTC 61.703 60.000 30.42 30.42 45.83 5.03
2790 8356 1.744368 CCACTGATGCTTGAGCGCT 60.744 57.895 11.27 11.27 45.83 5.92
2791 8357 1.300971 TTCCACTGATGCTTGAGCGC 61.301 55.000 0.00 0.00 45.83 5.92
2792 8358 1.329906 GATTCCACTGATGCTTGAGCG 59.670 52.381 0.00 0.00 45.83 5.03
2793 8359 1.329906 CGATTCCACTGATGCTTGAGC 59.670 52.381 0.00 0.00 42.50 4.26
2794 8360 2.864946 CTCGATTCCACTGATGCTTGAG 59.135 50.000 0.00 0.00 0.00 3.02
2795 8361 2.897436 CTCGATTCCACTGATGCTTGA 58.103 47.619 0.00 0.00 0.00 3.02
2796 8362 1.329906 GCTCGATTCCACTGATGCTTG 59.670 52.381 0.00 0.00 0.00 4.01
2797 8363 1.661341 GCTCGATTCCACTGATGCTT 58.339 50.000 0.00 0.00 0.00 3.91
2798 8364 0.529337 CGCTCGATTCCACTGATGCT 60.529 55.000 0.00 0.00 0.00 3.79
2799 8365 1.930100 CGCTCGATTCCACTGATGC 59.070 57.895 0.00 0.00 0.00 3.91
2800 8366 0.529337 AGCGCTCGATTCCACTGATG 60.529 55.000 2.64 0.00 0.00 3.07
2801 8367 0.249238 GAGCGCTCGATTCCACTGAT 60.249 55.000 23.61 0.00 0.00 2.90
2802 8368 1.139734 GAGCGCTCGATTCCACTGA 59.860 57.895 23.61 0.00 0.00 3.41
2803 8369 0.737367 TTGAGCGCTCGATTCCACTG 60.737 55.000 30.75 0.00 0.00 3.66
2804 8370 0.459237 CTTGAGCGCTCGATTCCACT 60.459 55.000 30.75 0.00 0.00 4.00
2805 8371 2.002127 CTTGAGCGCTCGATTCCAC 58.998 57.895 30.75 7.24 0.00 4.02
2806 8372 1.811266 GCTTGAGCGCTCGATTCCA 60.811 57.895 30.75 11.62 0.00 3.53
2807 8373 1.156645 ATGCTTGAGCGCTCGATTCC 61.157 55.000 30.75 19.73 45.83 3.01
2808 8374 0.231790 GATGCTTGAGCGCTCGATTC 59.768 55.000 30.75 22.47 45.83 2.52
2809 8375 0.460811 TGATGCTTGAGCGCTCGATT 60.461 50.000 30.75 17.14 45.83 3.34
2810 8376 0.875040 CTGATGCTTGAGCGCTCGAT 60.875 55.000 30.75 19.58 45.83 3.59
2811 8377 1.517913 CTGATGCTTGAGCGCTCGA 60.518 57.895 30.75 28.15 45.83 4.04
2841 8407 0.535335 TTGTAGCTCTAGGGTTGGCG 59.465 55.000 0.00 0.00 0.00 5.69
2862 8428 6.866010 TTATGCATGCTAATCGATCAACTT 57.134 33.333 20.33 0.00 0.00 2.66
2919 8485 8.785468 TCATGCGATTAAATTCATGTACAATG 57.215 30.769 0.00 0.00 37.95 2.82
2932 8498 6.816136 TCTCCTTCATACTCATGCGATTAAA 58.184 36.000 0.00 0.00 31.73 1.52
2933 8499 6.405278 TCTCCTTCATACTCATGCGATTAA 57.595 37.500 0.00 0.00 31.73 1.40
2934 8500 6.015095 ACATCTCCTTCATACTCATGCGATTA 60.015 38.462 0.00 0.00 31.73 1.75
2935 8501 4.944619 TCTCCTTCATACTCATGCGATT 57.055 40.909 0.00 0.00 31.73 3.34
2936 8502 4.282957 ACATCTCCTTCATACTCATGCGAT 59.717 41.667 0.00 0.00 31.73 4.58
2937 8503 3.638627 ACATCTCCTTCATACTCATGCGA 59.361 43.478 0.00 0.00 31.73 5.10
2938 8504 3.739810 CACATCTCCTTCATACTCATGCG 59.260 47.826 0.00 0.00 31.73 4.73
2939 8505 4.953667 TCACATCTCCTTCATACTCATGC 58.046 43.478 0.00 0.00 31.73 4.06
2940 8506 6.402456 TCTCACATCTCCTTCATACTCATG 57.598 41.667 0.00 0.00 0.00 3.07
2941 8507 8.718158 TTATCTCACATCTCCTTCATACTCAT 57.282 34.615 0.00 0.00 0.00 2.90
2942 8508 7.255766 GCTTATCTCACATCTCCTTCATACTCA 60.256 40.741 0.00 0.00 0.00 3.41
2943 8509 7.090173 GCTTATCTCACATCTCCTTCATACTC 58.910 42.308 0.00 0.00 0.00 2.59
2944 8510 6.552725 TGCTTATCTCACATCTCCTTCATACT 59.447 38.462 0.00 0.00 0.00 2.12
2945 8511 6.753180 TGCTTATCTCACATCTCCTTCATAC 58.247 40.000 0.00 0.00 0.00 2.39
2946 8512 6.552725 ACTGCTTATCTCACATCTCCTTCATA 59.447 38.462 0.00 0.00 0.00 2.15
2947 8513 5.366186 ACTGCTTATCTCACATCTCCTTCAT 59.634 40.000 0.00 0.00 0.00 2.57
2948 8514 4.713814 ACTGCTTATCTCACATCTCCTTCA 59.286 41.667 0.00 0.00 0.00 3.02
2949 8515 5.275067 ACTGCTTATCTCACATCTCCTTC 57.725 43.478 0.00 0.00 0.00 3.46
2950 8516 6.183360 CCTTACTGCTTATCTCACATCTCCTT 60.183 42.308 0.00 0.00 0.00 3.36
2951 8517 5.304101 CCTTACTGCTTATCTCACATCTCCT 59.696 44.000 0.00 0.00 0.00 3.69
2952 8518 5.537188 CCTTACTGCTTATCTCACATCTCC 58.463 45.833 0.00 0.00 0.00 3.71
3000 8606 0.946528 GTGGTGTTAACGTGGGGTTC 59.053 55.000 0.26 0.00 40.09 3.62
3004 8610 2.547299 TAAGGTGGTGTTAACGTGGG 57.453 50.000 0.26 0.00 0.00 4.61
3021 8627 8.402798 TGAATGACCTGCTTAATTTGAGTTAA 57.597 30.769 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.