Multiple sequence alignment - TraesCS7D01G415000

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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 TraesCS7D01G415000 chr7D 100.000 3473 0 0 1 3473 533637140 533633668 0.000000e+00 6414.0
1 TraesCS7D01G415000 chr7A 95.562 1690 55 8 827 2504 613026228 613024547 0.000000e+00 2687.0
2 TraesCS7D01G415000 chr7A 92.464 345 22 3 2 343 613030920 613030577 1.120000e-134 490.0
3 TraesCS7D01G415000 chr7A 85.902 305 34 4 345 641 613026657 613026354 2.010000e-82 316.0
4 TraesCS7D01G415000 chr7A 84.000 175 17 5 2346 2517 613022609 613022443 1.290000e-34 158.0
5 TraesCS7D01G415000 chr7B 95.184 1682 69 3 960 2638 573792956 573791284 0.000000e+00 2647.0
6 TraesCS7D01G415000 chr7B 91.493 529 37 7 1 524 573794238 573793713 0.000000e+00 721.0
7 TraesCS7D01G415000 chr7B 84.058 483 75 2 2932 3413 707963279 707963760 6.790000e-127 464.0
8 TraesCS7D01G415000 chr7B 91.566 83 5 2 3392 3473 685025491 685025572 2.830000e-21 113.0
9 TraesCS7D01G415000 chr7B 95.455 66 1 2 3408 3473 109708010 109707947 1.710000e-18 104.0
10 TraesCS7D01G415000 chr7B 84.211 57 6 2 2723 2776 121748634 121748690 6.000000e-03 52.8
11 TraesCS7D01G415000 chr4D 84.823 481 71 2 2933 3413 487200134 487199656 1.870000e-132 483.0
12 TraesCS7D01G415000 chr4D 90.370 135 11 2 4 137 484167001 484166868 3.560000e-40 176.0
13 TraesCS7D01G415000 chr4D 93.069 101 4 2 36 133 130543916 130544016 1.000000e-30 145.0
14 TraesCS7D01G415000 chr4D 90.411 73 2 3 3404 3472 462631916 462631845 1.330000e-14 91.6
15 TraesCS7D01G415000 chr1D 85.439 467 62 4 2948 3413 479536640 479536179 6.740000e-132 481.0
16 TraesCS7D01G415000 chr5B 84.989 473 70 1 2942 3413 492107338 492107810 2.420000e-131 479.0
17 TraesCS7D01G415000 chr5B 95.385 65 1 1 3411 3473 703510823 703510887 6.130000e-18 102.0
18 TraesCS7D01G415000 chr6B 84.567 473 72 1 2942 3413 706516680 706517152 5.250000e-128 468.0
19 TraesCS7D01G415000 chr6B 98.387 62 0 1 3412 3473 221996025 221996085 1.320000e-19 108.0
20 TraesCS7D01G415000 chr6B 100.000 28 0 0 2749 2776 501897955 501897928 6.000000e-03 52.8
21 TraesCS7D01G415000 chr4B 84.265 483 72 4 2932 3413 562615342 562615821 5.250000e-128 468.0
22 TraesCS7D01G415000 chr3B 84.232 482 75 1 2932 3413 127853976 127854456 5.250000e-128 468.0
23 TraesCS7D01G415000 chr3B 89.855 138 13 1 1 138 675037865 675038001 3.560000e-40 176.0
24 TraesCS7D01G415000 chr3B 89.610 77 3 2 3402 3473 770747473 770747549 3.690000e-15 93.5
25 TraesCS7D01G415000 chr3D 84.582 467 69 3 2948 3413 451894537 451894073 8.780000e-126 460.0
26 TraesCS7D01G415000 chr3D 74.738 669 123 32 1447 2083 64420683 64420029 1.240000e-64 257.0
27 TraesCS7D01G415000 chr3D 91.667 132 11 0 4 135 550254114 550253983 2.130000e-42 183.0
28 TraesCS7D01G415000 chr3D 90.789 76 3 2 3400 3472 459317296 459317222 7.930000e-17 99.0
29 TraesCS7D01G415000 chr1B 84.322 472 73 1 2942 3413 433645198 433645668 8.780000e-126 460.0
30 TraesCS7D01G415000 chr2A 91.304 138 9 3 1 137 726420826 726420961 5.920000e-43 185.0
31 TraesCS7D01G415000 chr2A 90.667 75 3 1 3403 3473 726547920 726547994 2.850000e-16 97.1
32 TraesCS7D01G415000 chr2A 83.929 56 7 2 2723 2776 462418686 462418741 6.000000e-03 52.8
33 TraesCS7D01G415000 chr2B 90.580 138 12 1 1 137 628945450 628945587 7.660000e-42 182.0
34 TraesCS7D01G415000 chr2B 95.238 63 2 1 3412 3473 319362305 319362243 7.930000e-17 99.0


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 TraesCS7D01G415000 chr7D 533633668 533637140 3472 True 6414.00 6414 100.0000 1 3473 1 chr7D.!!$R1 3472
1 TraesCS7D01G415000 chr7A 613022443 613030920 8477 True 912.75 2687 89.4820 2 2517 4 chr7A.!!$R1 2515
2 TraesCS7D01G415000 chr7B 573791284 573794238 2954 True 1684.00 2647 93.3385 1 2638 2 chr7B.!!$R2 2637
3 TraesCS7D01G415000 chr3D 64420029 64420683 654 True 257.00 257 74.7380 1447 2083 1 chr3D.!!$R1 636

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
834 5200 0.242825 TTTGCGGGTAGTGTCTCGAG 59.757 55.0 5.93 5.93 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2596 7382 0.035915 GCGAGCTCTTTCCTTCCCTT 60.036 55.0 12.85 0.0 0.0 3.95 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
39 41 5.596772 CCTTTTAGTTTTGAGGGACAGGAAA 59.403 40.000 0.00 0.00 0.00 3.13
78 80 0.336737 ACCTCCGGACTTCCTGATCT 59.663 55.000 0.00 0.00 0.00 2.75
103 105 8.121305 TCATTTATTGTAAAGGACATGCTTGT 57.879 30.769 4.68 4.68 38.07 3.16
178 183 5.120986 TCAATAACGCGCTGATGTTTTCTTA 59.879 36.000 5.73 0.00 0.00 2.10
179 184 3.889196 AACGCGCTGATGTTTTCTTAA 57.111 38.095 5.73 0.00 0.00 1.85
278 283 4.028993 TGTTGGTAGGAATGAAGGAACC 57.971 45.455 0.00 0.00 0.00 3.62
280 285 4.010349 GTTGGTAGGAATGAAGGAACCTG 58.990 47.826 0.00 0.00 34.42 4.00
340 345 6.571605 TCAGAATTGTCATGCAAAAACAGAA 58.428 32.000 6.65 0.00 40.91 3.02
436 4361 4.764679 ATAAAATTGTCGCACTGCAGAA 57.235 36.364 23.35 2.74 0.00 3.02
442 4367 3.745332 TGTCGCACTGCAGAATAATTG 57.255 42.857 23.35 8.15 0.00 2.32
464 4389 4.037327 TGTCATGCGTTTTCAAGGATTTGA 59.963 37.500 0.00 0.00 41.44 2.69
492 4417 6.433716 TGATTGCAACATGGAGAATTGTAAGA 59.566 34.615 0.00 0.00 32.60 2.10
493 4418 6.647334 TTGCAACATGGAGAATTGTAAGAA 57.353 33.333 0.00 0.00 0.00 2.52
496 4421 7.147312 TGCAACATGGAGAATTGTAAGAAAAG 58.853 34.615 0.00 0.00 0.00 2.27
536 4466 0.972883 GCCATGGTTAGGTTTTGCCA 59.027 50.000 14.67 0.00 40.61 4.92
543 4473 2.630580 GGTTAGGTTTTGCCATGTTGGA 59.369 45.455 0.00 0.00 40.96 3.53
548 4478 3.390639 AGGTTTTGCCATGTTGGATTGAA 59.609 39.130 0.00 0.00 40.96 2.69
550 4480 4.392754 GGTTTTGCCATGTTGGATTGAATC 59.607 41.667 0.00 0.00 40.96 2.52
551 4481 3.507103 TTGCCATGTTGGATTGAATCG 57.493 42.857 0.00 0.00 40.96 3.34
553 4483 2.423185 TGCCATGTTGGATTGAATCGAC 59.577 45.455 0.00 1.69 40.96 4.20
561 4491 4.135747 TGGATTGAATCGACATGCTACA 57.864 40.909 0.00 0.00 0.00 2.74
566 4496 6.634436 GGATTGAATCGACATGCTACATTTTC 59.366 38.462 0.00 0.00 0.00 2.29
567 4497 5.484173 TGAATCGACATGCTACATTTTCC 57.516 39.130 0.00 0.00 0.00 3.13
568 4498 4.335315 TGAATCGACATGCTACATTTTCCC 59.665 41.667 0.00 0.00 0.00 3.97
594 4712 5.126061 CCAAAATGGATCCTAAGTGAACCAG 59.874 44.000 14.23 0.00 40.96 4.00
607 4726 7.699812 CCTAAGTGAACCAGTTACTATCGTTAC 59.300 40.741 0.00 0.00 0.00 2.50
620 4739 2.198827 TCGTTACCTCGTAGTTCCCA 57.801 50.000 0.00 0.00 0.00 4.37
661 4781 0.670546 AACTTCAGGATCCGTGTGCG 60.671 55.000 5.98 0.00 37.95 5.34
680 4800 1.872237 CGGGAAAAGACGTGCAAGAGA 60.872 52.381 6.65 0.00 0.00 3.10
687 4807 0.596600 GACGTGCAAGAGACCGTTCA 60.597 55.000 6.65 0.00 33.03 3.18
770 5136 6.968131 TGAATCGAAGAGAGTACCAAATTG 57.032 37.500 0.00 0.00 43.63 2.32
775 5141 7.223260 TCGAAGAGAGTACCAAATTGTTAGA 57.777 36.000 0.00 0.00 0.00 2.10
776 5142 7.313646 TCGAAGAGAGTACCAAATTGTTAGAG 58.686 38.462 0.00 0.00 0.00 2.43
785 5151 8.962679 AGTACCAAATTGTTAGAGTTTTGACAA 58.037 29.630 0.00 0.00 36.55 3.18
786 5152 9.744468 GTACCAAATTGTTAGAGTTTTGACAAT 57.256 29.630 0.00 0.00 42.66 2.71
834 5200 0.242825 TTTGCGGGTAGTGTCTCGAG 59.757 55.000 5.93 5.93 0.00 4.04
863 5229 3.009033 TGAGAATCCCCAAGTCATCGTTT 59.991 43.478 0.00 0.00 0.00 3.60
865 5231 2.879103 ATCCCCAAGTCATCGTTTGT 57.121 45.000 0.00 0.00 0.00 2.83
903 5269 3.810941 TCTACTTTGTTTGTACGGCCAAG 59.189 43.478 2.24 0.00 0.00 3.61
913 5279 0.317799 TACGGCCAAGCTTTACGTCA 59.682 50.000 19.23 7.41 38.79 4.35
930 5296 3.108881 CGTCATGAGATAACGAGTGGTG 58.891 50.000 0.00 0.00 38.65 4.17
952 5318 1.626321 TCACAGATTTACGGGAGGCAA 59.374 47.619 0.00 0.00 0.00 4.52
988 5354 2.483583 TCATTCACGTTGTTTGCACC 57.516 45.000 0.00 0.00 0.00 5.01
1354 5729 1.827399 GCTCTCCCCGTTCAACAGGA 61.827 60.000 0.00 0.00 0.00 3.86
1878 6271 1.153823 CCGATCGCTCCTCGTGTTT 60.154 57.895 10.32 0.00 39.67 2.83
2101 6503 3.399181 GTGCGGATCCCAGGGACA 61.399 66.667 11.70 0.32 32.98 4.02
2475 6880 5.578727 CAGCATCACTTTCAAGTACTAGGTC 59.421 44.000 0.00 0.00 37.08 3.85
2530 7316 7.389603 TCGTCGCAATAAATAGTCACAATAG 57.610 36.000 0.00 0.00 0.00 1.73
2592 7378 4.343811 TTTCGCGTGAAGAAAGAAACAA 57.656 36.364 11.77 0.00 35.06 2.83
2595 7381 4.278858 TCGCGTGAAGAAAGAAACAATTG 58.721 39.130 5.77 3.24 0.00 2.32
2596 7382 4.034626 TCGCGTGAAGAAAGAAACAATTGA 59.965 37.500 13.59 0.00 0.00 2.57
2616 7402 1.811679 GGGAAGGAAAGAGCTCGCG 60.812 63.158 8.37 0.00 0.00 5.87
2620 7406 1.617947 AAGGAAAGAGCTCGCGGGAT 61.618 55.000 12.03 0.87 0.00 3.85
2630 7416 2.203070 CGCGGGATGGAAGGAAGG 60.203 66.667 0.00 0.00 0.00 3.46
2638 7424 1.977293 ATGGAAGGAAGGAGCTCGCC 61.977 60.000 7.83 9.14 0.00 5.54
2639 7425 2.660064 GGAAGGAAGGAGCTCGCCA 61.660 63.158 17.73 0.00 0.00 5.69
2640 7426 1.524482 GAAGGAAGGAGCTCGCCAT 59.476 57.895 17.73 8.55 0.00 4.40
2641 7427 0.753262 GAAGGAAGGAGCTCGCCATA 59.247 55.000 17.73 0.00 0.00 2.74
2642 7428 1.346068 GAAGGAAGGAGCTCGCCATAT 59.654 52.381 17.73 6.62 0.00 1.78
2643 7429 0.972883 AGGAAGGAGCTCGCCATATC 59.027 55.000 17.73 6.20 0.00 1.63
2644 7430 0.972883 GGAAGGAGCTCGCCATATCT 59.027 55.000 7.83 0.00 0.00 1.98
2645 7431 1.346068 GGAAGGAGCTCGCCATATCTT 59.654 52.381 7.83 3.14 0.00 2.40
2646 7432 2.563179 GGAAGGAGCTCGCCATATCTTA 59.437 50.000 7.83 0.00 0.00 2.10
2647 7433 3.367910 GGAAGGAGCTCGCCATATCTTAG 60.368 52.174 7.83 0.00 0.00 2.18
2648 7434 2.175202 AGGAGCTCGCCATATCTTAGG 58.825 52.381 7.83 0.00 0.00 2.69
2649 7435 1.896465 GGAGCTCGCCATATCTTAGGT 59.104 52.381 7.83 0.00 0.00 3.08
2650 7436 2.300437 GGAGCTCGCCATATCTTAGGTT 59.700 50.000 7.83 0.00 0.00 3.50
2651 7437 3.321497 GAGCTCGCCATATCTTAGGTTG 58.679 50.000 0.00 0.00 0.00 3.77
2652 7438 2.700897 AGCTCGCCATATCTTAGGTTGT 59.299 45.455 0.00 0.00 0.00 3.32
2653 7439 2.802816 GCTCGCCATATCTTAGGTTGTG 59.197 50.000 0.00 0.00 0.00 3.33
2654 7440 3.393800 CTCGCCATATCTTAGGTTGTGG 58.606 50.000 0.00 0.00 0.00 4.17
2655 7441 2.104111 TCGCCATATCTTAGGTTGTGGG 59.896 50.000 1.71 0.00 0.00 4.61
2656 7442 2.810400 CGCCATATCTTAGGTTGTGGGG 60.810 54.545 2.37 2.37 33.03 4.96
2657 7443 2.489073 GCCATATCTTAGGTTGTGGGGG 60.489 54.545 1.71 0.00 0.00 5.40
2658 7444 2.783510 CCATATCTTAGGTTGTGGGGGT 59.216 50.000 0.00 0.00 0.00 4.95
2659 7445 3.435026 CCATATCTTAGGTTGTGGGGGTG 60.435 52.174 0.00 0.00 0.00 4.61
2660 7446 0.999712 ATCTTAGGTTGTGGGGGTGG 59.000 55.000 0.00 0.00 0.00 4.61
2661 7447 0.402272 TCTTAGGTTGTGGGGGTGGT 60.402 55.000 0.00 0.00 0.00 4.16
2662 7448 0.251165 CTTAGGTTGTGGGGGTGGTG 60.251 60.000 0.00 0.00 0.00 4.17
2663 7449 0.698198 TTAGGTTGTGGGGGTGGTGA 60.698 55.000 0.00 0.00 0.00 4.02
2664 7450 1.131303 TAGGTTGTGGGGGTGGTGAG 61.131 60.000 0.00 0.00 0.00 3.51
2665 7451 2.597510 GTTGTGGGGGTGGTGAGC 60.598 66.667 0.00 0.00 0.00 4.26
2666 7452 2.776526 TTGTGGGGGTGGTGAGCT 60.777 61.111 0.00 0.00 0.00 4.09
2667 7453 2.829384 TTGTGGGGGTGGTGAGCTC 61.829 63.158 6.82 6.82 0.00 4.09
2668 7454 4.394712 GTGGGGGTGGTGAGCTCG 62.395 72.222 9.64 0.00 0.00 5.03
2677 7463 2.496817 GTGAGCTCGCCGGAGAAT 59.503 61.111 16.69 0.10 43.27 2.40
2682 7468 1.663074 GCTCGCCGGAGAATGCTAG 60.663 63.158 9.83 0.00 43.27 3.42
2685 7471 2.825264 GCCGGAGAATGCTAGCCT 59.175 61.111 13.29 1.29 0.00 4.58
2702 7488 8.526667 TGCTAGCCTATTATCTATCTTAGTGG 57.473 38.462 13.29 0.00 0.00 4.00
2703 7489 8.116669 TGCTAGCCTATTATCTATCTTAGTGGT 58.883 37.037 13.29 0.00 0.00 4.16
2704 7490 8.410141 GCTAGCCTATTATCTATCTTAGTGGTG 58.590 40.741 2.29 0.00 0.00 4.17
2705 7491 9.469097 CTAGCCTATTATCTATCTTAGTGGTGT 57.531 37.037 0.00 0.00 0.00 4.16
2706 7492 8.128322 AGCCTATTATCTATCTTAGTGGTGTG 57.872 38.462 0.00 0.00 0.00 3.82
2707 7493 7.730784 AGCCTATTATCTATCTTAGTGGTGTGT 59.269 37.037 0.00 0.00 0.00 3.72
2710 7496 6.479972 TTATCTATCTTAGTGGTGTGTGGG 57.520 41.667 0.00 0.00 0.00 4.61
2717 7503 1.059584 AGTGGTGTGTGGGGTGATGA 61.060 55.000 0.00 0.00 0.00 2.92
2720 7506 1.063642 TGGTGTGTGGGGTGATGAAAA 60.064 47.619 0.00 0.00 0.00 2.29
2727 7513 0.100503 GGGGTGATGAAAATTCGCCG 59.899 55.000 0.00 0.00 43.33 6.46
2769 7555 3.631046 CTAGAGGGATGGCCGGGC 61.631 72.222 23.42 23.42 33.83 6.13
2795 7581 2.561956 GCATAGCGGTAGGAGGCGA 61.562 63.158 10.92 0.00 0.00 5.54
2796 7582 1.286260 CATAGCGGTAGGAGGCGAC 59.714 63.158 0.00 0.00 0.00 5.19
2797 7583 1.902432 ATAGCGGTAGGAGGCGACC 60.902 63.158 0.00 0.00 0.00 4.79
2809 7595 2.033424 GGAGGCGACCATATGAAAAAGC 59.967 50.000 3.65 2.46 0.00 3.51
2818 7604 4.159135 ACCATATGAAAAAGCAGAGCAAGG 59.841 41.667 3.65 0.00 0.00 3.61
2823 7609 2.656947 AAAAGCAGAGCAAGGGTGTA 57.343 45.000 0.00 0.00 0.00 2.90
2850 7636 3.388676 ACCCGAATATCGTTGGGAATGTA 59.611 43.478 6.71 0.00 44.88 2.29
2855 7641 6.310467 CCGAATATCGTTGGGAATGTAGTATG 59.690 42.308 0.00 0.00 38.40 2.39
2859 7645 6.726490 ATCGTTGGGAATGTAGTATGTACT 57.274 37.500 0.00 0.00 40.24 2.73
2940 7726 7.919091 GTGTATATACCGATCTGTCAAAACTGA 59.081 37.037 10.38 0.00 37.69 3.41
2943 7729 8.964476 ATATACCGATCTGTCAAAACTGAAAT 57.036 30.769 0.00 0.00 36.98 2.17
2954 7740 8.690203 TGTCAAAACTGAAATAATCCTCTGAA 57.310 30.769 0.00 0.00 0.00 3.02
2956 7742 8.567948 GTCAAAACTGAAATAATCCTCTGAACA 58.432 33.333 0.00 0.00 0.00 3.18
2959 7745 8.868522 AAACTGAAATAATCCTCTGAACATGA 57.131 30.769 0.00 0.00 0.00 3.07
2961 7747 7.397221 ACTGAAATAATCCTCTGAACATGACA 58.603 34.615 0.00 0.00 0.00 3.58
2962 7748 7.335422 ACTGAAATAATCCTCTGAACATGACAC 59.665 37.037 0.00 0.00 0.00 3.67
2963 7749 6.599244 TGAAATAATCCTCTGAACATGACACC 59.401 38.462 0.00 0.00 0.00 4.16
2964 7750 2.680312 ATCCTCTGAACATGACACCG 57.320 50.000 0.00 0.00 0.00 4.94
2965 7751 1.627864 TCCTCTGAACATGACACCGA 58.372 50.000 0.00 0.00 0.00 4.69
2966 7752 1.272490 TCCTCTGAACATGACACCGAC 59.728 52.381 0.00 0.00 0.00 4.79
2967 7753 1.673033 CCTCTGAACATGACACCGACC 60.673 57.143 0.00 0.00 0.00 4.79
2968 7754 1.273606 CTCTGAACATGACACCGACCT 59.726 52.381 0.00 0.00 0.00 3.85
2969 7755 1.691976 TCTGAACATGACACCGACCTT 59.308 47.619 0.00 0.00 0.00 3.50
2970 7756 2.069273 CTGAACATGACACCGACCTTC 58.931 52.381 0.00 0.00 0.00 3.46
2971 7757 1.068474 GAACATGACACCGACCTTCG 58.932 55.000 0.00 0.00 40.07 3.79
2972 7758 0.391597 AACATGACACCGACCTTCGT 59.608 50.000 0.00 0.00 38.40 3.85
2973 7759 0.038526 ACATGACACCGACCTTCGTC 60.039 55.000 0.00 0.00 38.40 4.20
2974 7760 0.038618 CATGACACCGACCTTCGTCA 60.039 55.000 0.00 0.00 42.19 4.35
2975 7761 0.038526 ATGACACCGACCTTCGTCAC 60.039 55.000 0.00 0.00 40.91 3.67
2976 7762 1.372623 GACACCGACCTTCGTCACC 60.373 63.158 0.00 0.00 39.11 4.02
2977 7763 2.079020 GACACCGACCTTCGTCACCA 62.079 60.000 0.00 0.00 39.11 4.17
2978 7764 1.372997 CACCGACCTTCGTCACCAG 60.373 63.158 0.00 0.00 39.11 4.00
2979 7765 2.432628 CCGACCTTCGTCACCAGC 60.433 66.667 0.00 0.00 39.11 4.85
2980 7766 2.432628 CGACCTTCGTCACCAGCC 60.433 66.667 0.00 0.00 39.11 4.85
2981 7767 2.932234 CGACCTTCGTCACCAGCCT 61.932 63.158 0.00 0.00 39.11 4.58
2982 7768 1.079750 GACCTTCGTCACCAGCCTC 60.080 63.158 0.00 0.00 38.99 4.70
2983 7769 1.534235 ACCTTCGTCACCAGCCTCT 60.534 57.895 0.00 0.00 0.00 3.69
2984 7770 1.079543 CCTTCGTCACCAGCCTCTG 60.080 63.158 0.00 0.00 0.00 3.35
2985 7771 1.536073 CCTTCGTCACCAGCCTCTGA 61.536 60.000 0.00 0.00 32.44 3.27
2986 7772 0.389166 CTTCGTCACCAGCCTCTGAC 60.389 60.000 0.00 0.00 32.44 3.51
2987 7773 1.112916 TTCGTCACCAGCCTCTGACA 61.113 55.000 6.18 0.00 37.27 3.58
2988 7774 1.373497 CGTCACCAGCCTCTGACAC 60.373 63.158 6.18 0.00 37.27 3.67
2989 7775 1.004440 GTCACCAGCCTCTGACACC 60.004 63.158 0.00 0.00 37.36 4.16
2990 7776 1.459348 TCACCAGCCTCTGACACCA 60.459 57.895 0.00 0.00 32.44 4.17
2991 7777 1.302033 CACCAGCCTCTGACACCAC 60.302 63.158 0.00 0.00 32.44 4.16
2992 7778 2.348998 CCAGCCTCTGACACCACC 59.651 66.667 0.00 0.00 32.44 4.61
2993 7779 2.519622 CCAGCCTCTGACACCACCA 61.520 63.158 0.00 0.00 32.44 4.17
2994 7780 1.302033 CAGCCTCTGACACCACCAC 60.302 63.158 0.00 0.00 32.44 4.16
2995 7781 1.766059 AGCCTCTGACACCACCACA 60.766 57.895 0.00 0.00 0.00 4.17
2996 7782 1.148273 GCCTCTGACACCACCACAA 59.852 57.895 0.00 0.00 0.00 3.33
2997 7783 0.250901 GCCTCTGACACCACCACAAT 60.251 55.000 0.00 0.00 0.00 2.71
2998 7784 1.003118 GCCTCTGACACCACCACAATA 59.997 52.381 0.00 0.00 0.00 1.90
2999 7785 2.936993 GCCTCTGACACCACCACAATAG 60.937 54.545 0.00 0.00 0.00 1.73
3000 7786 2.303022 CCTCTGACACCACCACAATAGT 59.697 50.000 0.00 0.00 0.00 2.12
3001 7787 3.589988 CTCTGACACCACCACAATAGTC 58.410 50.000 0.00 0.00 0.00 2.59
3002 7788 2.969262 TCTGACACCACCACAATAGTCA 59.031 45.455 0.00 0.00 35.07 3.41
3003 7789 3.582647 TCTGACACCACCACAATAGTCAT 59.417 43.478 0.00 0.00 35.70 3.06
3004 7790 3.935203 CTGACACCACCACAATAGTCATC 59.065 47.826 0.00 0.00 35.70 2.92
3005 7791 3.326297 TGACACCACCACAATAGTCATCA 59.674 43.478 0.00 0.00 31.72 3.07
3006 7792 3.935203 GACACCACCACAATAGTCATCAG 59.065 47.826 0.00 0.00 0.00 2.90
3007 7793 3.582647 ACACCACCACAATAGTCATCAGA 59.417 43.478 0.00 0.00 0.00 3.27
3008 7794 4.186926 CACCACCACAATAGTCATCAGAG 58.813 47.826 0.00 0.00 0.00 3.35
3009 7795 4.081476 CACCACCACAATAGTCATCAGAGA 60.081 45.833 0.00 0.00 0.00 3.10
3010 7796 4.532126 ACCACCACAATAGTCATCAGAGAA 59.468 41.667 0.00 0.00 0.00 2.87
3011 7797 5.013079 ACCACCACAATAGTCATCAGAGAAA 59.987 40.000 0.00 0.00 0.00 2.52
3012 7798 5.939883 CCACCACAATAGTCATCAGAGAAAA 59.060 40.000 0.00 0.00 0.00 2.29
3013 7799 6.430925 CCACCACAATAGTCATCAGAGAAAAA 59.569 38.462 0.00 0.00 0.00 1.94
3037 7823 1.338674 TGACGGATCACATTCACACCC 60.339 52.381 0.00 0.00 0.00 4.61
3069 7855 1.540267 GGCTCCAATGCTGATATGCAG 59.460 52.381 0.00 0.00 46.71 4.41
3079 7865 1.878088 CTGATATGCAGCTTTGCGGAT 59.122 47.619 0.00 0.00 37.90 4.18
3090 7876 3.141398 GCTTTGCGGATATCCAAGATGA 58.859 45.455 21.70 1.51 35.14 2.92
3114 7900 2.413634 CGCCAAAGACGAAACCATTACC 60.414 50.000 0.00 0.00 0.00 2.85
3121 7907 4.320870 AGACGAAACCATTACCGTTGAAT 58.679 39.130 0.00 0.00 35.22 2.57
3124 7910 4.515944 ACGAAACCATTACCGTTGAATGAA 59.484 37.500 0.00 0.00 36.57 2.57
3126 7912 5.737290 CGAAACCATTACCGTTGAATGAATC 59.263 40.000 3.48 0.00 36.57 2.52
3127 7913 6.582677 AAACCATTACCGTTGAATGAATCA 57.417 33.333 3.48 0.00 36.57 2.57
3128 7914 5.818136 ACCATTACCGTTGAATGAATCAG 57.182 39.130 3.48 0.00 39.77 2.90
3129 7915 5.496556 ACCATTACCGTTGAATGAATCAGA 58.503 37.500 3.48 0.00 39.77 3.27
3131 7917 5.220854 CCATTACCGTTGAATGAATCAGACC 60.221 44.000 3.48 0.00 39.77 3.85
3133 7919 2.289444 ACCGTTGAATGAATCAGACCGT 60.289 45.455 0.00 0.00 39.77 4.83
3150 7936 3.575247 TGGCAACACCCCGGACAT 61.575 61.111 0.73 0.00 46.17 3.06
3151 7937 3.061848 GGCAACACCCCGGACATG 61.062 66.667 0.73 0.00 0.00 3.21
3152 7938 3.747976 GCAACACCCCGGACATGC 61.748 66.667 0.73 2.07 0.00 4.06
3157 7943 3.014538 ACCCCGGACATGCCATCA 61.015 61.111 0.73 0.00 35.94 3.07
3179 7965 3.016971 CCAGATCTGGCACCCCCA 61.017 66.667 28.45 0.00 44.73 4.96
3182 7968 2.044946 GATCTGGCACCCCCACAC 60.045 66.667 0.00 0.00 39.18 3.82
3194 7980 0.109412 CCCCACACGACTAAGACGTC 60.109 60.000 7.70 7.70 42.07 4.34
3206 7992 6.126288 GACTAAGACGTCGAAGAAGAAAAC 57.874 41.667 22.04 5.53 38.59 2.43
3257 8043 2.672961 GACACGATCCACCATCTTCA 57.327 50.000 0.00 0.00 0.00 3.02
3265 8051 5.104941 ACGATCCACCATCTTCAAGATACAA 60.105 40.000 0.00 0.00 32.12 2.41
3266 8052 5.994054 CGATCCACCATCTTCAAGATACAAT 59.006 40.000 0.00 0.00 32.12 2.71
3294 8080 0.322816 ACCACAATCTGCATCCGCTT 60.323 50.000 0.00 0.00 39.64 4.68
3295 8081 0.099968 CCACAATCTGCATCCGCTTG 59.900 55.000 0.00 0.00 39.64 4.01
3307 8093 1.568504 TCCGCTTGTGGATTACCTCT 58.431 50.000 0.00 0.00 37.04 3.69
3315 8101 3.445008 TGTGGATTACCTCTCAAGCTCT 58.555 45.455 0.00 0.00 37.04 4.09
3322 8108 4.441695 TCTCAAGCTCTGCGCCGG 62.442 66.667 4.18 0.00 40.39 6.13
3339 8125 2.016165 GGCGCTTGAGCAAAAACCG 61.016 57.895 7.64 0.00 42.21 4.44
3342 8128 0.028770 CGCTTGAGCAAAAACCGTCA 59.971 50.000 3.65 0.00 42.21 4.35
3346 8132 3.705604 CTTGAGCAAAAACCGTCACAAT 58.294 40.909 0.00 0.00 0.00 2.71
3350 8136 1.804372 GCAAAAACCGTCACAATGGCA 60.804 47.619 0.00 0.00 34.61 4.92
3364 8150 2.267324 GGCAGAGCCTGAGGACAC 59.733 66.667 0.65 0.00 46.69 3.67
3384 8170 1.417890 CAGGTCCACCATGAGGATACC 59.582 57.143 9.64 8.09 37.52 2.73
3406 8192 1.429148 CGCCGCAACTCCATCCTTAC 61.429 60.000 0.00 0.00 0.00 2.34
3412 8198 3.125316 CGCAACTCCATCCTTACTTGAAC 59.875 47.826 0.00 0.00 0.00 3.18
3413 8199 4.327680 GCAACTCCATCCTTACTTGAACT 58.672 43.478 0.00 0.00 0.00 3.01
3414 8200 5.488341 GCAACTCCATCCTTACTTGAACTA 58.512 41.667 0.00 0.00 0.00 2.24
3415 8201 5.582665 GCAACTCCATCCTTACTTGAACTAG 59.417 44.000 0.00 0.00 0.00 2.57
3416 8202 6.702329 CAACTCCATCCTTACTTGAACTAGT 58.298 40.000 0.00 0.00 0.00 2.57
3417 8203 7.578955 GCAACTCCATCCTTACTTGAACTAGTA 60.579 40.741 0.00 0.00 0.00 1.82
3418 8204 7.407393 ACTCCATCCTTACTTGAACTAGTAC 57.593 40.000 0.00 0.00 30.62 2.73
3419 8205 6.952358 ACTCCATCCTTACTTGAACTAGTACA 59.048 38.462 0.00 0.00 30.62 2.90
3420 8206 7.453752 ACTCCATCCTTACTTGAACTAGTACAA 59.546 37.037 0.00 0.00 30.62 2.41
3422 8208 8.258007 TCCATCCTTACTTGAACTAGTACAATG 58.742 37.037 0.00 0.00 30.62 2.82
3423 8209 7.011482 CCATCCTTACTTGAACTAGTACAATGC 59.989 40.741 0.00 0.00 30.62 3.56
3425 8211 5.585047 CCTTACTTGAACTAGTACAATGCCC 59.415 44.000 0.00 0.00 30.62 5.36
3427 8213 3.007614 ACTTGAACTAGTACAATGCCCGT 59.992 43.478 0.00 0.00 0.00 5.28
3428 8214 2.967362 TGAACTAGTACAATGCCCGTG 58.033 47.619 0.00 0.00 0.00 4.94
3430 8216 0.459585 ACTAGTACAATGCCCGTGCG 60.460 55.000 0.00 0.00 41.78 5.34
3431 8217 0.459585 CTAGTACAATGCCCGTGCGT 60.460 55.000 0.00 0.00 41.78 5.24
3452 8238 2.465860 GCCACGGGCCTTTTAATTTT 57.534 45.000 0.84 0.00 44.06 1.82
3453 8239 2.773487 GCCACGGGCCTTTTAATTTTT 58.227 42.857 0.84 0.00 44.06 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.583073 TCCCTCAAAACTAAAAGGAGCAAC 59.417 41.667 0.00 0.00 0.00 4.17
16 17 6.709018 TTTCCTGTCCCTCAAAACTAAAAG 57.291 37.500 0.00 0.00 0.00 2.27
39 41 4.030216 GGTTTATCATTCCACACCCCATT 58.970 43.478 0.00 0.00 0.00 3.16
78 80 8.121305 ACAAGCATGTCCTTTACAATAAATGA 57.879 30.769 0.00 0.00 42.70 2.57
150 155 1.665679 CATCAGCGCGTTATTGAGGTT 59.334 47.619 8.43 0.00 0.00 3.50
178 183 9.525826 AAATAATTTGATCTGACAACCTCTCTT 57.474 29.630 0.00 0.00 0.00 2.85
179 184 9.525826 AAAATAATTTGATCTGACAACCTCTCT 57.474 29.630 0.00 0.00 0.00 3.10
304 309 7.532571 CATGACAATTCTGAAGCATTTACTGA 58.467 34.615 0.00 0.00 0.00 3.41
436 4361 6.266168 TCCTTGAAAACGCATGACAATTAT 57.734 33.333 0.00 0.00 0.00 1.28
442 4367 4.382754 GTCAAATCCTTGAAAACGCATGAC 59.617 41.667 0.00 0.00 43.18 3.06
464 4389 5.046878 ACAATTCTCCATGTTGCAATCATGT 60.047 36.000 26.16 13.95 40.43 3.21
536 4466 3.949754 AGCATGTCGATTCAATCCAACAT 59.050 39.130 7.08 7.08 34.41 2.71
543 4473 6.460123 GGGAAAATGTAGCATGTCGATTCAAT 60.460 38.462 0.00 0.00 0.00 2.57
548 4478 3.214328 GGGGAAAATGTAGCATGTCGAT 58.786 45.455 0.00 0.00 0.00 3.59
550 4480 1.676006 GGGGGAAAATGTAGCATGTCG 59.324 52.381 0.00 0.00 0.00 4.35
567 4497 3.052944 TCACTTAGGATCCATTTTGGGGG 60.053 47.826 15.82 0.00 38.32 5.40
568 4498 4.249638 TCACTTAGGATCCATTTTGGGG 57.750 45.455 15.82 0.00 38.32 4.96
607 4726 1.621814 TCCTTTGTGGGAACTACGAGG 59.378 52.381 0.00 0.00 36.20 4.63
654 4774 2.241880 ACGTCTTTTCCCGCACACG 61.242 57.895 0.00 0.00 39.67 4.49
655 4775 1.278637 CACGTCTTTTCCCGCACAC 59.721 57.895 0.00 0.00 0.00 3.82
658 4778 1.781025 CTTGCACGTCTTTTCCCGCA 61.781 55.000 0.00 0.00 0.00 5.69
659 4779 1.082104 CTTGCACGTCTTTTCCCGC 60.082 57.895 0.00 0.00 0.00 6.13
661 4781 1.531578 GTCTCTTGCACGTCTTTTCCC 59.468 52.381 0.00 0.00 0.00 3.97
734 4856 9.186323 CTCTCTTCGATTCATATTATTTGTCGT 57.814 33.333 0.00 0.00 0.00 4.34
753 5119 8.834749 AACTCTAACAATTTGGTACTCTCTTC 57.165 34.615 0.78 0.00 0.00 2.87
813 5179 1.068895 TCGAGACACTACCCGCAAAAA 59.931 47.619 0.00 0.00 0.00 1.94
814 5180 0.675083 TCGAGACACTACCCGCAAAA 59.325 50.000 0.00 0.00 0.00 2.44
815 5181 0.242825 CTCGAGACACTACCCGCAAA 59.757 55.000 6.58 0.00 0.00 3.68
816 5182 0.607217 TCTCGAGACACTACCCGCAA 60.607 55.000 12.08 0.00 0.00 4.85
817 5183 1.002990 TCTCGAGACACTACCCGCA 60.003 57.895 12.08 0.00 0.00 5.69
818 5184 1.025647 ACTCTCGAGACACTACCCGC 61.026 60.000 12.08 0.00 0.00 6.13
819 5185 1.130749 CAACTCTCGAGACACTACCCG 59.869 57.143 12.08 1.44 0.00 5.28
820 5186 2.161030 ACAACTCTCGAGACACTACCC 58.839 52.381 12.08 0.00 0.00 3.69
821 5187 3.252701 TCAACAACTCTCGAGACACTACC 59.747 47.826 12.08 0.00 0.00 3.18
822 5188 4.213694 TCTCAACAACTCTCGAGACACTAC 59.786 45.833 12.08 0.00 29.71 2.73
823 5189 4.386711 TCTCAACAACTCTCGAGACACTA 58.613 43.478 12.08 0.00 29.71 2.74
824 5190 3.215151 TCTCAACAACTCTCGAGACACT 58.785 45.455 12.08 0.00 29.71 3.55
825 5191 3.627732 TCTCAACAACTCTCGAGACAC 57.372 47.619 12.08 0.00 29.71 3.67
834 5200 3.753797 GACTTGGGGATTCTCAACAACTC 59.246 47.826 0.00 0.00 0.00 3.01
863 5229 1.816835 AGATCAGCTCGACGGTTAACA 59.183 47.619 8.10 0.00 0.00 2.41
865 5231 3.276857 AGTAGATCAGCTCGACGGTTAA 58.723 45.455 0.00 0.00 34.92 2.01
903 5269 5.035443 ACTCGTTATCTCATGACGTAAAGC 58.965 41.667 0.00 0.00 42.12 3.51
913 5279 4.021456 TGTGAACACCACTCGTTATCTCAT 60.021 41.667 2.46 0.00 45.86 2.90
930 5296 2.007608 GCCTCCCGTAAATCTGTGAAC 58.992 52.381 0.00 0.00 0.00 3.18
952 5318 2.727123 TGAATGTCAGTGTGGTGGTT 57.273 45.000 0.00 0.00 0.00 3.67
988 5354 2.093152 CGAAGTCCATTCCCGTTTTACG 59.907 50.000 0.00 0.00 35.12 3.18
1149 5515 2.202919 TCGACCATGCTGCCGATG 60.203 61.111 0.00 0.00 0.00 3.84
1179 5545 1.285641 GTGGTTGTTGATGTGCCGG 59.714 57.895 0.00 0.00 0.00 6.13
1341 5716 1.566018 GCTTCGTCCTGTTGAACGGG 61.566 60.000 17.08 17.08 46.14 5.28
2128 6530 2.657944 GAGCCGCTCGCAGATCTG 60.658 66.667 18.84 18.84 41.38 2.90
2307 6709 0.959372 AGTAGCCGTACGACTGCAGT 60.959 55.000 21.88 21.88 32.36 4.40
2530 7316 7.912383 TCTAAATACGGCAACTTACATTTAGC 58.088 34.615 0.00 0.00 36.55 3.09
2543 7329 4.590918 TGACCCAAATTCTAAATACGGCA 58.409 39.130 0.00 0.00 0.00 5.69
2592 7378 3.620966 CGAGCTCTTTCCTTCCCTTCAAT 60.621 47.826 12.85 0.00 0.00 2.57
2595 7381 2.009542 GCGAGCTCTTTCCTTCCCTTC 61.010 57.143 12.85 0.00 0.00 3.46
2596 7382 0.035915 GCGAGCTCTTTCCTTCCCTT 60.036 55.000 12.85 0.00 0.00 3.95
2616 7402 0.472044 GAGCTCCTTCCTTCCATCCC 59.528 60.000 0.87 0.00 0.00 3.85
2620 7406 2.660064 GGCGAGCTCCTTCCTTCCA 61.660 63.158 8.47 0.00 0.00 3.53
2630 7416 3.243907 ACAACCTAAGATATGGCGAGCTC 60.244 47.826 2.73 2.73 0.00 4.09
2638 7424 3.435026 CCACCCCCACAACCTAAGATATG 60.435 52.174 0.00 0.00 0.00 1.78
2639 7425 2.783510 CCACCCCCACAACCTAAGATAT 59.216 50.000 0.00 0.00 0.00 1.63
2640 7426 2.201830 CCACCCCCACAACCTAAGATA 58.798 52.381 0.00 0.00 0.00 1.98
2641 7427 0.999712 CCACCCCCACAACCTAAGAT 59.000 55.000 0.00 0.00 0.00 2.40
2642 7428 0.402272 ACCACCCCCACAACCTAAGA 60.402 55.000 0.00 0.00 0.00 2.10
2643 7429 0.251165 CACCACCCCCACAACCTAAG 60.251 60.000 0.00 0.00 0.00 2.18
2644 7430 0.698198 TCACCACCCCCACAACCTAA 60.698 55.000 0.00 0.00 0.00 2.69
2645 7431 1.073629 TCACCACCCCCACAACCTA 60.074 57.895 0.00 0.00 0.00 3.08
2646 7432 2.369015 TCACCACCCCCACAACCT 60.369 61.111 0.00 0.00 0.00 3.50
2647 7433 2.115266 CTCACCACCCCCACAACC 59.885 66.667 0.00 0.00 0.00 3.77
2648 7434 2.597510 GCTCACCACCCCCACAAC 60.598 66.667 0.00 0.00 0.00 3.32
2649 7435 2.776526 AGCTCACCACCCCCACAA 60.777 61.111 0.00 0.00 0.00 3.33
2650 7436 3.249189 GAGCTCACCACCCCCACA 61.249 66.667 9.40 0.00 0.00 4.17
2651 7437 4.394712 CGAGCTCACCACCCCCAC 62.395 72.222 15.40 0.00 0.00 4.61
2657 7443 4.803426 CTCCGGCGAGCTCACCAC 62.803 72.222 20.45 3.18 0.00 4.16
2659 7445 3.082579 ATTCTCCGGCGAGCTCACC 62.083 63.158 15.40 13.13 35.94 4.02
2660 7446 1.880340 CATTCTCCGGCGAGCTCAC 60.880 63.158 15.40 3.30 35.94 3.51
2661 7447 2.496341 CATTCTCCGGCGAGCTCA 59.504 61.111 15.40 0.00 35.94 4.26
2662 7448 2.076622 TAGCATTCTCCGGCGAGCTC 62.077 60.000 9.30 2.73 35.94 4.09
2663 7449 2.081425 CTAGCATTCTCCGGCGAGCT 62.081 60.000 9.30 12.25 35.94 4.09
2664 7450 1.663074 CTAGCATTCTCCGGCGAGC 60.663 63.158 9.30 0.00 35.94 5.03
2665 7451 1.663074 GCTAGCATTCTCCGGCGAG 60.663 63.158 9.30 4.01 37.48 5.03
2666 7452 2.417516 GCTAGCATTCTCCGGCGA 59.582 61.111 9.30 0.00 34.54 5.54
2667 7453 1.806461 TAGGCTAGCATTCTCCGGCG 61.806 60.000 18.24 0.00 34.54 6.46
2668 7454 0.610687 ATAGGCTAGCATTCTCCGGC 59.389 55.000 18.24 0.00 0.00 6.13
2669 7455 4.404073 AGATAATAGGCTAGCATTCTCCGG 59.596 45.833 18.24 0.00 0.00 5.14
2677 7463 8.116669 ACCACTAAGATAGATAATAGGCTAGCA 58.883 37.037 18.24 0.00 0.00 3.49
2682 7468 7.815068 CACACACCACTAAGATAGATAATAGGC 59.185 40.741 0.00 0.00 0.00 3.93
2685 7471 7.234782 CCCCACACACCACTAAGATAGATAATA 59.765 40.741 0.00 0.00 0.00 0.98
2700 7486 0.553333 TTTCATCACCCCACACACCA 59.447 50.000 0.00 0.00 0.00 4.17
2701 7487 1.698506 TTTTCATCACCCCACACACC 58.301 50.000 0.00 0.00 0.00 4.16
2702 7488 3.611530 CGAATTTTCATCACCCCACACAC 60.612 47.826 0.00 0.00 0.00 3.82
2703 7489 2.556189 CGAATTTTCATCACCCCACACA 59.444 45.455 0.00 0.00 0.00 3.72
2704 7490 2.671070 GCGAATTTTCATCACCCCACAC 60.671 50.000 0.00 0.00 0.00 3.82
2705 7491 1.543802 GCGAATTTTCATCACCCCACA 59.456 47.619 0.00 0.00 0.00 4.17
2706 7492 1.135112 GGCGAATTTTCATCACCCCAC 60.135 52.381 0.00 0.00 0.00 4.61
2707 7493 1.181786 GGCGAATTTTCATCACCCCA 58.818 50.000 0.00 0.00 0.00 4.96
2710 7496 1.091537 TCCGGCGAATTTTCATCACC 58.908 50.000 9.30 0.00 0.00 4.02
2735 7521 2.119495 CTAGCCCCTACAATGACCAGT 58.881 52.381 0.00 0.00 0.00 4.00
2736 7522 2.366916 CTCTAGCCCCTACAATGACCAG 59.633 54.545 0.00 0.00 0.00 4.00
2737 7523 2.398588 CTCTAGCCCCTACAATGACCA 58.601 52.381 0.00 0.00 0.00 4.02
2738 7524 1.694696 CCTCTAGCCCCTACAATGACC 59.305 57.143 0.00 0.00 0.00 4.02
2739 7525 1.694696 CCCTCTAGCCCCTACAATGAC 59.305 57.143 0.00 0.00 0.00 3.06
2740 7526 1.578703 TCCCTCTAGCCCCTACAATGA 59.421 52.381 0.00 0.00 0.00 2.57
2742 7528 2.625639 CATCCCTCTAGCCCCTACAAT 58.374 52.381 0.00 0.00 0.00 2.71
2743 7529 1.414538 CCATCCCTCTAGCCCCTACAA 60.415 57.143 0.00 0.00 0.00 2.41
2744 7530 0.191064 CCATCCCTCTAGCCCCTACA 59.809 60.000 0.00 0.00 0.00 2.74
2745 7531 1.195442 GCCATCCCTCTAGCCCCTAC 61.195 65.000 0.00 0.00 0.00 3.18
2746 7532 1.158705 GCCATCCCTCTAGCCCCTA 59.841 63.158 0.00 0.00 0.00 3.53
2747 7533 2.122189 GCCATCCCTCTAGCCCCT 60.122 66.667 0.00 0.00 0.00 4.79
2751 7537 3.631046 CCCGGCCATCCCTCTAGC 61.631 72.222 2.24 0.00 0.00 3.42
2770 7556 4.602259 TACCGCTATGCTGCCGCC 62.602 66.667 0.00 0.00 34.43 6.13
2771 7557 3.038417 CTACCGCTATGCTGCCGC 61.038 66.667 0.00 0.00 0.00 6.53
2772 7558 2.356313 CCTACCGCTATGCTGCCG 60.356 66.667 0.00 0.00 0.00 5.69
2773 7559 1.005630 CTCCTACCGCTATGCTGCC 60.006 63.158 0.00 0.00 0.00 4.85
2774 7560 1.005630 CCTCCTACCGCTATGCTGC 60.006 63.158 0.00 0.00 0.00 5.25
2775 7561 1.005630 GCCTCCTACCGCTATGCTG 60.006 63.158 0.00 0.00 0.00 4.41
2776 7562 2.565645 CGCCTCCTACCGCTATGCT 61.566 63.158 0.00 0.00 0.00 3.79
2777 7563 2.049063 CGCCTCCTACCGCTATGC 60.049 66.667 0.00 0.00 0.00 3.14
2781 7567 2.635787 TATGGTCGCCTCCTACCGCT 62.636 60.000 0.00 0.00 38.70 5.52
2785 7571 3.746045 TTTCATATGGTCGCCTCCTAC 57.254 47.619 2.13 0.00 0.00 3.18
2795 7581 4.159135 CCTTGCTCTGCTTTTTCATATGGT 59.841 41.667 2.13 0.00 0.00 3.55
2796 7582 4.441079 CCCTTGCTCTGCTTTTTCATATGG 60.441 45.833 2.13 0.00 0.00 2.74
2797 7583 4.159135 ACCCTTGCTCTGCTTTTTCATATG 59.841 41.667 0.00 0.00 0.00 1.78
2809 7595 3.270877 GGTTACATACACCCTTGCTCTG 58.729 50.000 0.00 0.00 0.00 3.35
2818 7604 4.874970 ACGATATTCGGGTTACATACACC 58.125 43.478 1.69 0.00 45.59 4.16
2823 7609 3.388676 TCCCAACGATATTCGGGTTACAT 59.611 43.478 1.69 0.00 45.59 2.29
2836 7622 6.726490 AGTACATACTACATTCCCAACGAT 57.274 37.500 0.00 0.00 34.13 3.73
2865 7651 4.708177 ACTGAGACATGTATTACCATGCC 58.292 43.478 0.00 0.00 44.88 4.40
2879 7665 9.551734 CCATGATCTTTTGATATAACTGAGACA 57.448 33.333 0.00 0.00 39.67 3.41
2915 7701 8.002984 TCAGTTTTGACAGATCGGTATATACA 57.997 34.615 14.70 0.00 0.00 2.29
2919 7705 9.878667 TTATTTCAGTTTTGACAGATCGGTATA 57.121 29.630 0.00 0.00 31.71 1.47
2925 7711 9.171877 AGAGGATTATTTCAGTTTTGACAGATC 57.828 33.333 0.00 0.00 31.71 2.75
2931 7717 8.690203 TGTTCAGAGGATTATTTCAGTTTTGA 57.310 30.769 0.00 0.00 0.00 2.69
2940 7726 5.586243 CGGTGTCATGTTCAGAGGATTATTT 59.414 40.000 0.00 0.00 0.00 1.40
2943 7729 3.767131 TCGGTGTCATGTTCAGAGGATTA 59.233 43.478 0.00 0.00 0.00 1.75
2954 7740 0.038526 GACGAAGGTCGGTGTCATGT 60.039 55.000 2.38 0.00 45.59 3.21
2956 7742 0.038526 GTGACGAAGGTCGGTGTCAT 60.039 55.000 2.38 0.00 46.49 3.06
2959 7745 2.083835 CTGGTGACGAAGGTCGGTGT 62.084 60.000 2.38 0.00 46.49 4.16
2961 7747 3.048602 CTGGTGACGAAGGTCGGT 58.951 61.111 2.38 0.00 46.49 4.69
2962 7748 2.432628 GCTGGTGACGAAGGTCGG 60.433 66.667 2.38 0.00 46.49 4.79
2963 7749 2.432628 GGCTGGTGACGAAGGTCG 60.433 66.667 0.00 0.00 46.49 4.79
2964 7750 1.079750 GAGGCTGGTGACGAAGGTC 60.080 63.158 0.00 0.00 43.71 3.85
2965 7751 1.534235 AGAGGCTGGTGACGAAGGT 60.534 57.895 0.00 0.00 0.00 3.50
2966 7752 1.079543 CAGAGGCTGGTGACGAAGG 60.080 63.158 0.00 0.00 0.00 3.46
2967 7753 0.389166 GTCAGAGGCTGGTGACGAAG 60.389 60.000 10.06 0.00 34.16 3.79
2968 7754 1.112916 TGTCAGAGGCTGGTGACGAA 61.113 55.000 17.44 3.34 45.13 3.85
2969 7755 1.530655 TGTCAGAGGCTGGTGACGA 60.531 57.895 17.44 7.82 45.13 4.20
2970 7756 1.373497 GTGTCAGAGGCTGGTGACG 60.373 63.158 17.44 0.00 45.13 4.35
2971 7757 1.004440 GGTGTCAGAGGCTGGTGAC 60.004 63.158 16.31 16.31 42.93 3.67
2972 7758 1.459348 TGGTGTCAGAGGCTGGTGA 60.459 57.895 0.00 0.00 31.51 4.02
2973 7759 1.302033 GTGGTGTCAGAGGCTGGTG 60.302 63.158 0.00 0.00 31.51 4.17
2974 7760 2.520536 GGTGGTGTCAGAGGCTGGT 61.521 63.158 0.00 0.00 31.51 4.00
2975 7761 2.348998 GGTGGTGTCAGAGGCTGG 59.651 66.667 0.00 0.00 31.51 4.85
2976 7762 1.302033 GTGGTGGTGTCAGAGGCTG 60.302 63.158 0.00 0.00 0.00 4.85
2977 7763 1.344953 TTGTGGTGGTGTCAGAGGCT 61.345 55.000 0.00 0.00 0.00 4.58
2978 7764 0.250901 ATTGTGGTGGTGTCAGAGGC 60.251 55.000 0.00 0.00 0.00 4.70
2979 7765 2.303022 ACTATTGTGGTGGTGTCAGAGG 59.697 50.000 0.00 0.00 0.00 3.69
2980 7766 3.006859 TGACTATTGTGGTGGTGTCAGAG 59.993 47.826 0.00 0.00 31.87 3.35
2981 7767 2.969262 TGACTATTGTGGTGGTGTCAGA 59.031 45.455 0.00 0.00 31.87 3.27
2982 7768 3.401033 TGACTATTGTGGTGGTGTCAG 57.599 47.619 0.00 0.00 31.87 3.51
2983 7769 3.326297 TGATGACTATTGTGGTGGTGTCA 59.674 43.478 0.00 0.00 38.52 3.58
2984 7770 3.935203 CTGATGACTATTGTGGTGGTGTC 59.065 47.826 0.00 0.00 0.00 3.67
2985 7771 3.582647 TCTGATGACTATTGTGGTGGTGT 59.417 43.478 0.00 0.00 0.00 4.16
2986 7772 4.081476 TCTCTGATGACTATTGTGGTGGTG 60.081 45.833 0.00 0.00 0.00 4.17
2987 7773 4.096681 TCTCTGATGACTATTGTGGTGGT 58.903 43.478 0.00 0.00 0.00 4.16
2988 7774 4.743057 TCTCTGATGACTATTGTGGTGG 57.257 45.455 0.00 0.00 0.00 4.61
2989 7775 7.439157 TTTTTCTCTGATGACTATTGTGGTG 57.561 36.000 0.00 0.00 0.00 4.17
3012 7798 5.460646 GTGTGAATGTGATCCGTCATTTTT 58.539 37.500 8.52 0.00 36.60 1.94
3013 7799 4.082787 GGTGTGAATGTGATCCGTCATTTT 60.083 41.667 8.52 0.00 36.60 1.82
3014 7800 3.440173 GGTGTGAATGTGATCCGTCATTT 59.560 43.478 8.52 0.00 36.60 2.32
3015 7801 3.009723 GGTGTGAATGTGATCCGTCATT 58.990 45.455 7.33 7.33 36.60 2.57
3016 7802 2.632377 GGTGTGAATGTGATCCGTCAT 58.368 47.619 0.00 0.00 36.60 3.06
3017 7803 1.338674 GGGTGTGAATGTGATCCGTCA 60.339 52.381 0.00 0.00 0.00 4.35
3018 7804 1.369625 GGGTGTGAATGTGATCCGTC 58.630 55.000 0.00 0.00 0.00 4.79
3019 7805 0.391130 CGGGTGTGAATGTGATCCGT 60.391 55.000 0.00 0.00 0.00 4.69
3020 7806 0.108377 TCGGGTGTGAATGTGATCCG 60.108 55.000 0.00 0.00 37.61 4.18
3021 7807 1.656652 CTCGGGTGTGAATGTGATCC 58.343 55.000 0.00 0.00 0.00 3.36
3022 7808 1.009829 GCTCGGGTGTGAATGTGATC 58.990 55.000 0.00 0.00 0.00 2.92
3023 7809 0.615331 AGCTCGGGTGTGAATGTGAT 59.385 50.000 0.00 0.00 0.00 3.06
3024 7810 0.037326 GAGCTCGGGTGTGAATGTGA 60.037 55.000 0.00 0.00 0.00 3.58
3025 7811 1.354337 CGAGCTCGGGTGTGAATGTG 61.354 60.000 28.40 0.00 35.37 3.21
3026 7812 1.079819 CGAGCTCGGGTGTGAATGT 60.080 57.895 28.40 0.00 35.37 2.71
3027 7813 1.078759 GTCGAGCTCGGGTGTGAATG 61.079 60.000 33.98 3.88 40.29 2.67
3028 7814 1.215647 GTCGAGCTCGGGTGTGAAT 59.784 57.895 33.98 0.00 40.29 2.57
3050 7836 2.991434 CTGCATATCAGCATTGGAGC 57.009 50.000 0.00 0.00 44.68 4.70
3069 7855 3.058639 GTCATCTTGGATATCCGCAAAGC 60.059 47.826 17.04 1.28 39.43 3.51
3079 7865 3.450817 TCTTTGGCGAGTCATCTTGGATA 59.549 43.478 0.00 0.00 0.00 2.59
3090 7876 0.179067 TGGTTTCGTCTTTGGCGAGT 60.179 50.000 0.00 0.00 39.61 4.18
3114 7900 2.094258 CCACGGTCTGATTCATTCAACG 59.906 50.000 0.00 0.00 32.78 4.10
3121 7907 0.107643 TGTTGCCACGGTCTGATTCA 59.892 50.000 0.00 0.00 0.00 2.57
3124 7910 1.302511 GGTGTTGCCACGGTCTGAT 60.303 57.895 0.00 0.00 42.80 2.90
3126 7912 2.978010 GGGTGTTGCCACGGTCTG 60.978 66.667 0.00 0.00 42.80 3.51
3127 7913 4.265056 GGGGTGTTGCCACGGTCT 62.265 66.667 0.00 0.00 42.80 3.85
3133 7919 3.575247 ATGTCCGGGGTGTTGCCA 61.575 61.111 0.00 0.00 39.65 4.92
3150 7936 2.995283 CAGATCTGGAGTTTGATGGCA 58.005 47.619 15.38 0.00 0.00 4.92
3175 7961 0.109412 GACGTCTTAGTCGTGTGGGG 60.109 60.000 9.41 0.00 41.64 4.96
3176 7962 3.396491 GACGTCTTAGTCGTGTGGG 57.604 57.895 9.41 0.00 41.64 4.61
3194 7980 4.635765 TGGCAGATATGGTTTTCTTCTTCG 59.364 41.667 0.00 0.00 0.00 3.79
3206 7992 0.686789 TCCGTGGATGGCAGATATGG 59.313 55.000 0.00 0.00 0.00 2.74
3230 8016 4.934989 GGATCGTGTCCTGGGTTC 57.065 61.111 0.00 0.00 44.16 3.62
3238 8024 2.672961 TGAAGATGGTGGATCGTGTC 57.327 50.000 0.00 0.00 36.04 3.67
3249 8035 5.467735 TGCATCGATTGTATCTTGAAGATGG 59.532 40.000 17.50 0.95 35.37 3.51
3257 8043 4.122776 GTGGTCTGCATCGATTGTATCTT 58.877 43.478 0.00 0.00 0.00 2.40
3265 8051 2.558378 CAGATTGTGGTCTGCATCGAT 58.442 47.619 0.00 0.00 39.19 3.59
3266 8052 2.014335 CAGATTGTGGTCTGCATCGA 57.986 50.000 0.00 0.00 39.19 3.59
3285 8071 0.663153 GGTAATCCACAAGCGGATGC 59.337 55.000 0.00 0.00 45.39 3.91
3294 8080 3.196469 CAGAGCTTGAGAGGTAATCCACA 59.804 47.826 0.00 0.00 32.79 4.17
3295 8081 3.791245 CAGAGCTTGAGAGGTAATCCAC 58.209 50.000 0.00 0.00 32.79 4.02
3322 8108 1.268778 GACGGTTTTTGCTCAAGCGC 61.269 55.000 0.00 0.00 46.53 5.92
3327 8113 2.223688 CCATTGTGACGGTTTTTGCTCA 60.224 45.455 0.00 0.00 0.00 4.26
3331 8117 2.126467 CTGCCATTGTGACGGTTTTTG 58.874 47.619 0.00 0.00 0.00 2.44
3350 8136 4.126908 CCTGTGTCCTCAGGCTCT 57.873 61.111 2.71 0.00 46.53 4.09
3364 8150 1.417890 GGTATCCTCATGGTGGACCTG 59.582 57.143 9.90 0.00 36.30 4.00
3396 8182 7.786046 TTGTACTAGTTCAAGTAAGGATGGA 57.214 36.000 10.55 0.00 33.85 3.41
3406 8192 3.370978 CACGGGCATTGTACTAGTTCAAG 59.629 47.826 18.21 12.05 0.00 3.02
3412 8198 0.459585 ACGCACGGGCATTGTACTAG 60.460 55.000 11.77 0.00 41.24 2.57
3413 8199 0.037139 AACGCACGGGCATTGTACTA 60.037 50.000 11.77 0.00 41.24 1.82
3414 8200 1.302192 AACGCACGGGCATTGTACT 60.302 52.632 11.77 0.00 41.24 2.73
3415 8201 1.154301 CAACGCACGGGCATTGTAC 60.154 57.895 10.90 0.00 38.34 2.90
3416 8202 2.972144 GCAACGCACGGGCATTGTA 61.972 57.895 20.63 0.00 44.58 2.41
3417 8203 4.341502 GCAACGCACGGGCATTGT 62.342 61.111 20.63 0.74 44.58 2.71


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

AutoCloner maintained by Alex Coulton.