Multiple sequence alignment - TraesCS4D01G082500

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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 TraesCS4D01G082500 chr4D 100.000 3499 0 0 1 3499 55966159 55962661 0.000000e+00 6462.0
1 TraesCS4D01G082500 chr4D 95.455 44 1 1 2469 2512 55963655 55963613 6.270000e-08 69.4
2 TraesCS4D01G082500 chr4D 95.455 44 1 1 2505 2547 55963691 55963648 6.270000e-08 69.4
3 TraesCS4D01G082500 chr4D 100.000 35 0 0 2585 2619 59065839 59065805 8.110000e-07 65.8
4 TraesCS4D01G082500 chr4B 94.920 1496 57 4 1020 2512 82935267 82933788 0.000000e+00 2324.0
5 TraesCS4D01G082500 chr4B 89.522 544 54 3 4 546 97535255 97535796 0.000000e+00 686.0
6 TraesCS4D01G082500 chr4B 90.775 271 21 3 550 819 515411665 515411398 3.320000e-95 359.0
7 TraesCS4D01G082500 chr4A 92.898 1563 83 12 865 2411 540957547 540959097 0.000000e+00 2246.0
8 TraesCS4D01G082500 chr4A 92.248 387 29 1 1307 1693 540846762 540847147 6.600000e-152 547.0
9 TraesCS4D01G082500 chr4A 84.277 477 67 5 2038 2512 540902334 540902804 3.180000e-125 459.0
10 TraesCS4D01G082500 chr4A 88.218 348 40 1 1692 2039 540878576 540878922 6.990000e-112 414.0
11 TraesCS4D01G082500 chr4A 80.331 544 94 10 2750 3282 720948445 720948986 1.960000e-107 399.0
12 TraesCS4D01G082500 chr4A 87.988 333 37 1 980 1309 540710361 540710693 1.180000e-104 390.0
13 TraesCS4D01G082500 chr4A 80.682 88 13 3 3388 3473 25038805 25038720 8.110000e-07 65.8
14 TraesCS4D01G082500 chr4A 81.707 82 9 5 3368 3446 715950300 715950222 2.920000e-06 63.9
15 TraesCS4D01G082500 chr5D 82.419 893 134 18 2623 3499 564447956 564447071 0.000000e+00 758.0
16 TraesCS4D01G082500 chr5D 89.011 546 59 1 1 546 458697202 458697746 0.000000e+00 675.0
17 TraesCS4D01G082500 chr5D 79.493 868 136 32 2620 3462 176089025 176089875 2.340000e-161 579.0
18 TraesCS4D01G082500 chr5D 80.183 767 114 23 2631 3374 436204136 436203385 1.100000e-149 540.0
19 TraesCS4D01G082500 chr5D 78.251 915 142 38 2620 3493 36482888 36483786 5.140000e-148 534.0
20 TraesCS4D01G082500 chr5D 80.331 483 65 17 2631 3087 548531546 548532024 4.330000e-89 339.0
21 TraesCS4D01G082500 chr5D 100.000 35 0 0 2585 2619 375662474 375662440 8.110000e-07 65.8
22 TraesCS4D01G082500 chr3D 80.865 925 109 25 2620 3494 531688349 531687443 0.000000e+00 665.0
23 TraesCS4D01G082500 chr3D 81.571 700 83 29 2620 3299 596698243 596697570 1.430000e-148 536.0
24 TraesCS4D01G082500 chr3D 93.258 267 14 3 554 819 306028957 306029220 1.180000e-104 390.0
25 TraesCS4D01G082500 chr3D 83.465 254 38 4 2667 2917 171124027 171123775 2.100000e-57 233.0
26 TraesCS4D01G082500 chr3D 97.500 40 1 0 2580 2619 596698310 596698271 6.270000e-08 69.4
27 TraesCS4D01G082500 chr3D 96.875 32 1 0 2551 2582 596698409 596698378 2.000000e-03 54.7
28 TraesCS4D01G082500 chr7D 88.029 543 65 0 1 543 548148825 548149367 0.000000e+00 643.0
29 TraesCS4D01G082500 chr7D 81.375 800 107 27 2620 3381 141353890 141353095 6.420000e-172 614.0
30 TraesCS4D01G082500 chr1A 87.569 547 67 1 1 546 82966953 82967499 1.770000e-177 632.0
31 TraesCS4D01G082500 chr6B 87.500 544 68 0 4 547 707143677 707143134 2.290000e-176 628.0
32 TraesCS4D01G082500 chr6B 87.417 151 18 1 1841 1991 69955874 69956023 4.640000e-39 172.0
33 TraesCS4D01G082500 chr5A 79.845 903 149 22 2620 3499 436907951 436907059 2.290000e-176 628.0
34 TraesCS4D01G082500 chr5A 84.507 71 9 2 3385 3453 527900056 527900126 6.270000e-08 69.4
35 TraesCS4D01G082500 chr1D 81.343 804 114 22 2715 3499 445206852 445206066 3.840000e-174 621.0
36 TraesCS4D01G082500 chr1D 80.284 705 113 15 2621 3303 469051661 469052361 3.120000e-140 508.0
37 TraesCS4D01G082500 chr1D 91.985 262 19 2 558 818 365804560 365804820 1.980000e-97 366.0
38 TraesCS4D01G082500 chr1D 100.000 29 0 0 2551 2579 109280466 109280494 2.000000e-03 54.7
39 TraesCS4D01G082500 chr1B 79.843 893 144 26 2620 3493 543078157 543079032 1.380000e-173 619.0
40 TraesCS4D01G082500 chr2D 79.601 902 133 28 2620 3476 151990512 151989617 1.800000e-167 599.0
41 TraesCS4D01G082500 chr2D 79.672 792 146 11 2691 3476 423561137 423560355 1.100000e-154 556.0
42 TraesCS4D01G082500 chr2D 93.985 266 14 2 558 822 644999394 644999130 5.440000e-108 401.0
43 TraesCS4D01G082500 chr2D 78.879 535 101 12 2967 3493 453763522 453762992 5.560000e-93 351.0
44 TraesCS4D01G082500 chr2D 82.043 323 42 12 2631 2941 351048196 351047878 9.630000e-66 261.0
45 TraesCS4D01G082500 chr7A 85.952 541 73 3 7 546 730340990 730340452 3.030000e-160 575.0
46 TraesCS4D01G082500 chr7A 85.582 541 75 3 7 546 730388269 730387731 6.560000e-157 564.0
47 TraesCS4D01G082500 chr7A 79.741 696 94 31 2620 3281 6842057 6841375 8.850000e-126 460.0
48 TraesCS4D01G082500 chr3A 85.662 544 76 2 7 549 7977890 7977348 3.920000e-159 571.0
49 TraesCS4D01G082500 chr3A 76.862 376 47 19 2634 2970 21322164 21321790 3.590000e-40 176.0
50 TraesCS4D01G082500 chr2B 78.831 907 143 33 2620 3484 759544529 759545428 1.820000e-157 566.0
51 TraesCS4D01G082500 chr2B 84.249 546 82 4 4 547 513463844 513464387 2.390000e-146 529.0
52 TraesCS4D01G082500 chr2B 91.144 271 19 5 558 825 603430010 603430278 2.570000e-96 363.0
53 TraesCS4D01G082500 chr7B 79.650 801 141 18 2691 3484 68830559 68829774 1.100000e-154 556.0
54 TraesCS4D01G082500 chr7B 92.620 271 17 3 550 819 149805434 149805702 1.520000e-103 387.0
55 TraesCS4D01G082500 chr7B 91.667 264 20 2 556 818 598296145 598296407 7.140000e-97 364.0
56 TraesCS4D01G082500 chr7B 85.714 91 12 1 3409 3499 243868959 243869048 1.030000e-15 95.3
57 TraesCS4D01G082500 chr2A 77.510 956 164 29 2585 3493 179991515 179990564 8.600000e-146 527.0
58 TraesCS4D01G082500 chr6A 77.130 857 132 47 2620 3435 597845711 597844878 4.150000e-119 438.0
59 TraesCS4D01G082500 chr3B 76.941 837 134 34 2620 3414 40541621 40540802 4.180000e-114 422.0
60 TraesCS4D01G082500 chr3B 92.135 267 18 3 553 818 598188100 598188364 1.190000e-99 374.0
61 TraesCS4D01G082500 chr3B 91.760 267 18 3 556 819 427264691 427264426 5.520000e-98 368.0
62 TraesCS4D01G082500 chr6D 93.333 135 9 0 1840 1974 33243274 33243408 2.130000e-47 200.0


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 TraesCS4D01G082500 chr4D 55962661 55966159 3498 True 2200.266667 6462 96.970 1 3499 3 chr4D.!!$R2 3498
1 TraesCS4D01G082500 chr4B 82933788 82935267 1479 True 2324.000000 2324 94.920 1020 2512 1 chr4B.!!$R1 1492
2 TraesCS4D01G082500 chr4B 97535255 97535796 541 False 686.000000 686 89.522 4 546 1 chr4B.!!$F1 542
3 TraesCS4D01G082500 chr4A 540957547 540959097 1550 False 2246.000000 2246 92.898 865 2411 1 chr4A.!!$F5 1546
4 TraesCS4D01G082500 chr4A 720948445 720948986 541 False 399.000000 399 80.331 2750 3282 1 chr4A.!!$F6 532
5 TraesCS4D01G082500 chr5D 564447071 564447956 885 True 758.000000 758 82.419 2623 3499 1 chr5D.!!$R3 876
6 TraesCS4D01G082500 chr5D 458697202 458697746 544 False 675.000000 675 89.011 1 546 1 chr5D.!!$F3 545
7 TraesCS4D01G082500 chr5D 176089025 176089875 850 False 579.000000 579 79.493 2620 3462 1 chr5D.!!$F2 842
8 TraesCS4D01G082500 chr5D 436203385 436204136 751 True 540.000000 540 80.183 2631 3374 1 chr5D.!!$R2 743
9 TraesCS4D01G082500 chr5D 36482888 36483786 898 False 534.000000 534 78.251 2620 3493 1 chr5D.!!$F1 873
10 TraesCS4D01G082500 chr3D 531687443 531688349 906 True 665.000000 665 80.865 2620 3494 1 chr3D.!!$R2 874
11 TraesCS4D01G082500 chr3D 596697570 596698409 839 True 220.033333 536 91.982 2551 3299 3 chr3D.!!$R3 748
12 TraesCS4D01G082500 chr7D 548148825 548149367 542 False 643.000000 643 88.029 1 543 1 chr7D.!!$F1 542
13 TraesCS4D01G082500 chr7D 141353095 141353890 795 True 614.000000 614 81.375 2620 3381 1 chr7D.!!$R1 761
14 TraesCS4D01G082500 chr1A 82966953 82967499 546 False 632.000000 632 87.569 1 546 1 chr1A.!!$F1 545
15 TraesCS4D01G082500 chr6B 707143134 707143677 543 True 628.000000 628 87.500 4 547 1 chr6B.!!$R1 543
16 TraesCS4D01G082500 chr5A 436907059 436907951 892 True 628.000000 628 79.845 2620 3499 1 chr5A.!!$R1 879
17 TraesCS4D01G082500 chr1D 445206066 445206852 786 True 621.000000 621 81.343 2715 3499 1 chr1D.!!$R1 784
18 TraesCS4D01G082500 chr1D 469051661 469052361 700 False 508.000000 508 80.284 2621 3303 1 chr1D.!!$F3 682
19 TraesCS4D01G082500 chr1B 543078157 543079032 875 False 619.000000 619 79.843 2620 3493 1 chr1B.!!$F1 873
20 TraesCS4D01G082500 chr2D 151989617 151990512 895 True 599.000000 599 79.601 2620 3476 1 chr2D.!!$R1 856
21 TraesCS4D01G082500 chr2D 423560355 423561137 782 True 556.000000 556 79.672 2691 3476 1 chr2D.!!$R3 785
22 TraesCS4D01G082500 chr2D 453762992 453763522 530 True 351.000000 351 78.879 2967 3493 1 chr2D.!!$R4 526
23 TraesCS4D01G082500 chr7A 730340452 730340990 538 True 575.000000 575 85.952 7 546 1 chr7A.!!$R2 539
24 TraesCS4D01G082500 chr7A 730387731 730388269 538 True 564.000000 564 85.582 7 546 1 chr7A.!!$R3 539
25 TraesCS4D01G082500 chr7A 6841375 6842057 682 True 460.000000 460 79.741 2620 3281 1 chr7A.!!$R1 661
26 TraesCS4D01G082500 chr3A 7977348 7977890 542 True 571.000000 571 85.662 7 549 1 chr3A.!!$R1 542
27 TraesCS4D01G082500 chr2B 759544529 759545428 899 False 566.000000 566 78.831 2620 3484 1 chr2B.!!$F3 864
28 TraesCS4D01G082500 chr2B 513463844 513464387 543 False 529.000000 529 84.249 4 547 1 chr2B.!!$F1 543
29 TraesCS4D01G082500 chr7B 68829774 68830559 785 True 556.000000 556 79.650 2691 3484 1 chr7B.!!$R1 793
30 TraesCS4D01G082500 chr2A 179990564 179991515 951 True 527.000000 527 77.510 2585 3493 1 chr2A.!!$R1 908
31 TraesCS4D01G082500 chr6A 597844878 597845711 833 True 438.000000 438 77.130 2620 3435 1 chr6A.!!$R1 815
32 TraesCS4D01G082500 chr3B 40540802 40541621 819 True 422.000000 422 76.941 2620 3414 1 chr3B.!!$R1 794

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
182 183 0.181114 CAGATCCCCTCATTGCCGAA 59.819 55.0 0.00 0.00 0.00 4.30 F
895 896 0.249155 CAAATGCCGCCATGGTGATC 60.249 55.0 27.12 17.21 41.21 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1059 1076 1.002366 CACTACGCATTGGAGAGTGC 58.998 55.0 0.0 0.0 37.97 4.40 R
2704 2841 0.263172 TAGAGGAAGAGGAGGCTGGG 59.737 60.0 0.0 0.0 0.00 4.45 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
123 124 1.475930 GGATAGCCCTTTCTCACCTGC 60.476 57.143 0.00 0.00 0.00 4.85
128 129 0.537371 CCCTTTCTCACCTGCCGTTT 60.537 55.000 0.00 0.00 0.00 3.60
154 155 3.497942 GGAGCTTGGAGTAAACCTTTCCA 60.498 47.826 0.00 0.00 39.16 3.53
155 156 4.142038 GAGCTTGGAGTAAACCTTTCCAA 58.858 43.478 5.21 5.21 45.95 3.53
179 180 0.548031 TGACAGATCCCCTCATTGCC 59.452 55.000 0.00 0.00 0.00 4.52
182 183 0.181114 CAGATCCCCTCATTGCCGAA 59.819 55.000 0.00 0.00 0.00 4.30
221 222 1.678627 GGAGTCATCTTCGCTCAGCTA 59.321 52.381 0.00 0.00 0.00 3.32
222 223 2.295909 GGAGTCATCTTCGCTCAGCTAT 59.704 50.000 0.00 0.00 0.00 2.97
227 228 0.461548 TCTTCGCTCAGCTATGTGGG 59.538 55.000 0.00 0.00 35.01 4.61
286 287 2.197605 TCAACCTCTGGTCGTCGCA 61.198 57.895 0.00 0.00 33.12 5.10
287 288 2.022129 CAACCTCTGGTCGTCGCAC 61.022 63.158 0.00 0.00 33.12 5.34
504 505 6.438186 TGAGGGCAGATTGTAATCATATGA 57.562 37.500 8.10 8.10 37.89 2.15
508 509 7.236529 AGGGCAGATTGTAATCATATGACAAT 58.763 34.615 16.87 16.87 44.43 2.71
568 569 9.636789 AAAAGGTAAAAACAGTACTTCCTATGT 57.363 29.630 0.00 0.00 0.00 2.29
569 570 9.636789 AAAGGTAAAAACAGTACTTCCTATGTT 57.363 29.630 0.00 0.00 37.47 2.71
570 571 9.636789 AAGGTAAAAACAGTACTTCCTATGTTT 57.363 29.630 0.00 0.00 45.21 2.83
571 572 9.281371 AGGTAAAAACAGTACTTCCTATGTTTC 57.719 33.333 8.55 0.00 43.17 2.78
572 573 9.281371 GGTAAAAACAGTACTTCCTATGTTTCT 57.719 33.333 8.55 0.00 43.17 2.52
584 585 9.077885 ACTTCCTATGTTTCTTTTTAATCTGCA 57.922 29.630 0.00 0.00 0.00 4.41
603 604 8.757982 ATCTGCATATAAGATTTGGTCAAAGT 57.242 30.769 2.55 0.00 29.94 2.66
604 605 8.579850 TCTGCATATAAGATTTGGTCAAAGTT 57.420 30.769 2.55 1.84 33.32 2.66
605 606 9.679661 TCTGCATATAAGATTTGGTCAAAGTTA 57.320 29.630 2.55 3.72 33.32 2.24
612 613 9.981114 ATAAGATTTGGTCAAAGTTAAACCTTG 57.019 29.630 7.80 0.00 34.05 3.61
613 614 7.418337 AGATTTGGTCAAAGTTAAACCTTGT 57.582 32.000 7.80 0.00 34.05 3.16
614 615 7.847096 AGATTTGGTCAAAGTTAAACCTTGTT 58.153 30.769 7.80 0.00 34.05 2.83
615 616 8.973182 AGATTTGGTCAAAGTTAAACCTTGTTA 58.027 29.630 7.80 0.00 34.05 2.41
616 617 9.589111 GATTTGGTCAAAGTTAAACCTTGTTAA 57.411 29.630 7.80 0.00 34.05 2.01
617 618 8.760103 TTTGGTCAAAGTTAAACCTTGTTAAC 57.240 30.769 0.00 0.00 42.05 2.01
718 719 9.632638 AATTTTGATACCATATAGCTTCAGTGT 57.367 29.630 0.00 0.00 0.00 3.55
719 720 9.632638 ATTTTGATACCATATAGCTTCAGTGTT 57.367 29.630 0.00 0.00 0.00 3.32
720 721 9.461312 TTTTGATACCATATAGCTTCAGTGTTT 57.539 29.630 0.00 0.00 0.00 2.83
721 722 9.461312 TTTGATACCATATAGCTTCAGTGTTTT 57.539 29.630 0.00 0.00 0.00 2.43
723 724 9.764363 TGATACCATATAGCTTCAGTGTTTTAG 57.236 33.333 0.00 0.00 0.00 1.85
724 725 9.982651 GATACCATATAGCTTCAGTGTTTTAGA 57.017 33.333 0.00 0.00 0.00 2.10
726 727 8.668510 ACCATATAGCTTCAGTGTTTTAGATG 57.331 34.615 0.00 0.00 0.00 2.90
727 728 8.267894 ACCATATAGCTTCAGTGTTTTAGATGT 58.732 33.333 0.00 0.00 0.00 3.06
728 729 9.113838 CCATATAGCTTCAGTGTTTTAGATGTT 57.886 33.333 0.00 0.00 0.00 2.71
729 730 9.926751 CATATAGCTTCAGTGTTTTAGATGTTG 57.073 33.333 0.00 0.00 0.00 3.33
730 731 9.890629 ATATAGCTTCAGTGTTTTAGATGTTGA 57.109 29.630 0.00 0.00 0.00 3.18
731 732 8.798859 ATAGCTTCAGTGTTTTAGATGTTGAT 57.201 30.769 0.00 0.00 0.00 2.57
732 733 9.890629 ATAGCTTCAGTGTTTTAGATGTTGATA 57.109 29.630 0.00 0.00 0.00 2.15
733 734 8.798859 AGCTTCAGTGTTTTAGATGTTGATAT 57.201 30.769 0.00 0.00 0.00 1.63
734 735 9.236006 AGCTTCAGTGTTTTAGATGTTGATATT 57.764 29.630 0.00 0.00 0.00 1.28
735 736 9.846248 GCTTCAGTGTTTTAGATGTTGATATTT 57.154 29.630 0.00 0.00 0.00 1.40
814 815 5.843019 ACAGACTAAAAGAAATGGAGGGA 57.157 39.130 0.00 0.00 0.00 4.20
815 816 5.810095 ACAGACTAAAAGAAATGGAGGGAG 58.190 41.667 0.00 0.00 0.00 4.30
816 817 5.310857 ACAGACTAAAAGAAATGGAGGGAGT 59.689 40.000 0.00 0.00 0.00 3.85
817 818 6.500751 ACAGACTAAAAGAAATGGAGGGAGTA 59.499 38.462 0.00 0.00 0.00 2.59
818 819 6.819146 CAGACTAAAAGAAATGGAGGGAGTAC 59.181 42.308 0.00 0.00 0.00 2.73
819 820 6.500751 AGACTAAAAGAAATGGAGGGAGTACA 59.499 38.462 0.00 0.00 0.00 2.90
820 821 7.017254 AGACTAAAAGAAATGGAGGGAGTACAA 59.983 37.037 0.00 0.00 0.00 2.41
821 822 7.699878 ACTAAAAGAAATGGAGGGAGTACAAT 58.300 34.615 0.00 0.00 0.00 2.71
822 823 8.832735 ACTAAAAGAAATGGAGGGAGTACAATA 58.167 33.333 0.00 0.00 0.00 1.90
823 824 9.331282 CTAAAAGAAATGGAGGGAGTACAATAG 57.669 37.037 0.00 0.00 0.00 1.73
824 825 7.510675 AAAGAAATGGAGGGAGTACAATAGA 57.489 36.000 0.00 0.00 0.00 1.98
825 826 7.698163 AAGAAATGGAGGGAGTACAATAGAT 57.302 36.000 0.00 0.00 0.00 1.98
826 827 7.309770 AGAAATGGAGGGAGTACAATAGATC 57.690 40.000 0.00 0.00 0.00 2.75
827 828 5.730296 AATGGAGGGAGTACAATAGATCG 57.270 43.478 0.00 0.00 0.00 3.69
828 829 3.497332 TGGAGGGAGTACAATAGATCGG 58.503 50.000 0.00 0.00 0.00 4.18
829 830 3.117246 TGGAGGGAGTACAATAGATCGGT 60.117 47.826 0.00 0.00 0.00 4.69
830 831 3.506844 GGAGGGAGTACAATAGATCGGTC 59.493 52.174 0.00 0.00 0.00 4.79
831 832 4.400120 GAGGGAGTACAATAGATCGGTCT 58.600 47.826 2.49 2.49 38.52 3.85
832 833 5.514484 GGAGGGAGTACAATAGATCGGTCTA 60.514 48.000 8.09 8.09 41.03 2.59
833 834 5.315348 AGGGAGTACAATAGATCGGTCTAC 58.685 45.833 7.76 0.00 39.66 2.59
834 835 5.068636 GGGAGTACAATAGATCGGTCTACA 58.931 45.833 7.76 0.00 39.66 2.74
835 836 5.048852 GGGAGTACAATAGATCGGTCTACAC 60.049 48.000 7.76 4.22 39.66 2.90
836 837 5.530171 GGAGTACAATAGATCGGTCTACACA 59.470 44.000 7.76 0.00 39.66 3.72
837 838 6.207025 GGAGTACAATAGATCGGTCTACACAT 59.793 42.308 7.76 0.00 39.66 3.21
838 839 6.971602 AGTACAATAGATCGGTCTACACATG 58.028 40.000 7.76 7.69 39.66 3.21
839 840 4.621991 ACAATAGATCGGTCTACACATGC 58.378 43.478 7.76 0.00 39.66 4.06
840 841 3.944055 ATAGATCGGTCTACACATGCC 57.056 47.619 7.76 0.00 39.66 4.40
841 842 1.781786 AGATCGGTCTACACATGCCT 58.218 50.000 0.00 0.00 31.36 4.75
842 843 1.410517 AGATCGGTCTACACATGCCTG 59.589 52.381 0.00 0.00 31.36 4.85
843 844 0.465705 ATCGGTCTACACATGCCTGG 59.534 55.000 0.00 0.00 0.00 4.45
844 845 1.815421 CGGTCTACACATGCCTGGC 60.815 63.158 12.87 12.87 0.00 4.85
845 846 1.299648 GGTCTACACATGCCTGGCA 59.700 57.895 25.65 25.65 44.86 4.92
846 847 0.322456 GGTCTACACATGCCTGGCAA 60.322 55.000 27.24 7.73 43.62 4.52
847 848 1.533625 GTCTACACATGCCTGGCAAA 58.466 50.000 27.24 2.61 43.62 3.68
848 849 1.470098 GTCTACACATGCCTGGCAAAG 59.530 52.381 27.24 22.49 43.62 2.77
849 850 1.350684 TCTACACATGCCTGGCAAAGA 59.649 47.619 27.24 18.73 43.62 2.52
850 851 2.161855 CTACACATGCCTGGCAAAGAA 58.838 47.619 27.24 9.50 43.62 2.52
851 852 0.675633 ACACATGCCTGGCAAAGAAC 59.324 50.000 27.24 0.00 43.62 3.01
852 853 0.675083 CACATGCCTGGCAAAGAACA 59.325 50.000 27.24 0.00 43.62 3.18
853 854 1.274167 CACATGCCTGGCAAAGAACAT 59.726 47.619 27.24 3.81 43.62 2.71
854 855 1.547372 ACATGCCTGGCAAAGAACATC 59.453 47.619 27.24 0.00 43.62 3.06
855 856 1.822990 CATGCCTGGCAAAGAACATCT 59.177 47.619 27.24 2.08 43.62 2.90
856 857 1.999648 TGCCTGGCAAAGAACATCTT 58.000 45.000 21.08 0.00 38.59 2.40
857 858 2.318908 TGCCTGGCAAAGAACATCTTT 58.681 42.857 21.08 0.00 46.75 2.52
858 859 3.495331 TGCCTGGCAAAGAACATCTTTA 58.505 40.909 21.08 0.00 44.23 1.85
859 860 3.894427 TGCCTGGCAAAGAACATCTTTAA 59.106 39.130 21.08 0.00 44.23 1.52
860 861 4.022068 TGCCTGGCAAAGAACATCTTTAAG 60.022 41.667 21.08 4.42 44.23 1.85
861 862 4.488879 CCTGGCAAAGAACATCTTTAAGC 58.511 43.478 5.12 5.97 44.23 3.09
862 863 4.219288 CCTGGCAAAGAACATCTTTAAGCT 59.781 41.667 5.12 0.00 44.23 3.74
863 864 5.125100 TGGCAAAGAACATCTTTAAGCTG 57.875 39.130 5.12 0.00 44.23 4.24
883 884 2.546368 TGTTGTACTGACGTCAAATGCC 59.454 45.455 20.49 6.76 0.00 4.40
891 892 2.699768 CGTCAAATGCCGCCATGGT 61.700 57.895 14.67 0.00 41.21 3.55
892 893 1.153784 GTCAAATGCCGCCATGGTG 60.154 57.895 18.88 18.88 41.21 4.17
893 894 1.303970 TCAAATGCCGCCATGGTGA 60.304 52.632 27.12 10.85 41.21 4.02
894 895 0.683828 TCAAATGCCGCCATGGTGAT 60.684 50.000 27.12 10.30 41.21 3.06
895 896 0.249155 CAAATGCCGCCATGGTGATC 60.249 55.000 27.12 17.21 41.21 2.92
922 935 3.632604 CCGTATCTCCAACTCTAGCTTCA 59.367 47.826 0.00 0.00 0.00 3.02
938 951 7.010771 TCTAGCTTCAGTGGCCTAAAGATATA 58.989 38.462 3.32 0.00 0.00 0.86
939 952 5.859495 AGCTTCAGTGGCCTAAAGATATAC 58.141 41.667 3.32 0.00 0.00 1.47
940 953 5.366768 AGCTTCAGTGGCCTAAAGATATACA 59.633 40.000 3.32 0.00 0.00 2.29
941 954 5.698545 GCTTCAGTGGCCTAAAGATATACAG 59.301 44.000 3.32 0.00 0.00 2.74
942 955 6.686632 GCTTCAGTGGCCTAAAGATATACAGT 60.687 42.308 3.32 0.00 0.00 3.55
943 956 7.471539 GCTTCAGTGGCCTAAAGATATACAGTA 60.472 40.741 3.32 0.00 0.00 2.74
948 961 8.204836 AGTGGCCTAAAGATATACAGTACAAAG 58.795 37.037 3.32 0.00 0.00 2.77
956 969 9.862371 AAAGATATACAGTACAAAGTCAGAGTG 57.138 33.333 0.00 0.00 0.00 3.51
975 988 9.397280 TCAGAGTGGTAGATGTGCTATATATAC 57.603 37.037 0.00 0.00 0.00 1.47
1018 1032 1.893544 TCCGAGGTAGAATAGAGCGG 58.106 55.000 0.00 0.00 38.68 5.52
1024 1038 1.138266 GGTAGAATAGAGCGGCCACAA 59.862 52.381 2.24 0.00 0.00 3.33
1059 1076 0.536687 ATGGCCATGGCGATCAAGAG 60.537 55.000 29.90 0.00 43.06 2.85
1075 1092 1.186200 AGAGCACTCTCCAATGCGTA 58.814 50.000 0.00 0.00 46.74 4.42
1147 1164 3.615709 GCGGGCAGCCCAAAAGTT 61.616 61.111 30.86 0.00 45.83 2.66
1231 1248 2.126031 GACGACGGCTTCCTCCAC 60.126 66.667 0.00 0.00 0.00 4.02
1726 1743 1.532238 GGGTAAGATGCCCACCTCC 59.468 63.158 0.00 0.00 45.40 4.30
1816 1833 1.678970 GCATGGCTTCCTCCGGTTT 60.679 57.895 0.00 0.00 0.00 3.27
1936 1953 1.439644 CCTGGACGCTAAGAGGCTC 59.560 63.158 6.34 6.34 0.00 4.70
1940 1957 1.874466 GACGCTAAGAGGCTCACGC 60.874 63.158 18.26 14.11 0.00 5.34
2053 2070 3.434319 TACCGCGTCGTGGAGGAC 61.434 66.667 30.66 0.00 36.58 3.85
2080 2097 3.665675 GAGTGACCTGCGGCGGAAT 62.666 63.158 11.13 0.00 0.00 3.01
2095 2112 2.029844 GAATAGGGCCGAGCGCATC 61.030 63.158 11.47 3.18 44.06 3.91
2231 2248 4.308458 TGTTCACGGCGGTGGAGG 62.308 66.667 22.51 0.00 44.50 4.30
2341 2358 2.666619 CGTGTACGACCTAAAAGACGCT 60.667 50.000 0.00 0.00 43.02 5.07
2344 2361 4.917415 GTGTACGACCTAAAAGACGCTAAA 59.083 41.667 0.00 0.00 0.00 1.85
2368 2385 4.595538 TTTGCGTCGGAGCCGTGT 62.596 61.111 8.96 0.00 40.74 4.49
2411 2428 3.507233 GGATTGAACTGAATGAACCAGCA 59.493 43.478 0.00 0.00 35.14 4.41
2413 2430 2.507484 TGAACTGAATGAACCAGCAGG 58.493 47.619 0.00 0.00 42.21 4.85
2416 2433 0.524862 CTGAATGAACCAGCAGGCAC 59.475 55.000 0.00 0.00 39.06 5.01
2418 2435 1.926511 GAATGAACCAGCAGGCACCG 61.927 60.000 0.00 0.00 39.06 4.94
2433 2450 2.438434 CCGGTGCTTCCCATGGAC 60.438 66.667 15.22 2.06 0.00 4.02
2446 2463 2.042686 CATGGACATTCGACATGGGT 57.957 50.000 0.00 0.00 38.58 4.51
2447 2464 3.192541 CATGGACATTCGACATGGGTA 57.807 47.619 0.00 0.00 38.58 3.69
2448 2465 2.684001 TGGACATTCGACATGGGTAC 57.316 50.000 0.00 0.00 0.00 3.34
2475 2492 3.658757 GCCAGTTGCTTGTAAATTCCA 57.341 42.857 0.00 0.00 36.87 3.53
2476 2493 4.192429 GCCAGTTGCTTGTAAATTCCAT 57.808 40.909 0.00 0.00 36.87 3.41
2477 2494 4.568956 GCCAGTTGCTTGTAAATTCCATT 58.431 39.130 0.00 0.00 36.87 3.16
2478 2495 4.389687 GCCAGTTGCTTGTAAATTCCATTG 59.610 41.667 0.00 0.00 36.87 2.82
2479 2496 5.782047 CCAGTTGCTTGTAAATTCCATTGA 58.218 37.500 0.00 0.00 0.00 2.57
2480 2497 6.222389 CCAGTTGCTTGTAAATTCCATTGAA 58.778 36.000 0.00 0.00 34.33 2.69
2481 2498 6.875195 CCAGTTGCTTGTAAATTCCATTGAAT 59.125 34.615 0.00 0.00 43.08 2.57
2482 2499 8.034215 CCAGTTGCTTGTAAATTCCATTGAATA 58.966 33.333 0.00 0.00 40.34 1.75
2483 2500 9.421806 CAGTTGCTTGTAAATTCCATTGAATAA 57.578 29.630 0.00 0.00 40.34 1.40
2484 2501 9.995003 AGTTGCTTGTAAATTCCATTGAATAAA 57.005 25.926 0.00 0.00 40.34 1.40
2486 2503 9.434420 TTGCTTGTAAATTCCATTGAATAAAGG 57.566 29.630 0.00 0.00 40.34 3.11
2487 2504 8.040132 TGCTTGTAAATTCCATTGAATAAAGGG 58.960 33.333 0.00 0.00 40.34 3.95
2488 2505 8.257306 GCTTGTAAATTCCATTGAATAAAGGGA 58.743 33.333 0.00 0.00 46.85 4.20
2493 2510 4.712122 TCCATTGAATAAAGGGAAACGC 57.288 40.909 0.00 0.00 45.57 4.84
2494 2511 4.340617 TCCATTGAATAAAGGGAAACGCT 58.659 39.130 0.00 0.00 45.57 5.07
2495 2512 4.398044 TCCATTGAATAAAGGGAAACGCTC 59.602 41.667 0.00 0.00 45.57 5.03
2496 2513 4.157656 CCATTGAATAAAGGGAAACGCTCA 59.842 41.667 0.00 0.00 42.62 4.26
2497 2514 4.759516 TTGAATAAAGGGAAACGCTCAC 57.240 40.909 0.00 0.00 0.00 3.51
2498 2515 3.745799 TGAATAAAGGGAAACGCTCACA 58.254 40.909 0.00 0.00 0.00 3.58
2499 2516 4.138290 TGAATAAAGGGAAACGCTCACAA 58.862 39.130 0.00 0.00 0.00 3.33
2500 2517 4.764823 TGAATAAAGGGAAACGCTCACAAT 59.235 37.500 0.00 0.00 0.00 2.71
2501 2518 4.965119 ATAAAGGGAAACGCTCACAATC 57.035 40.909 0.00 0.00 0.00 2.67
2502 2519 1.534729 AAGGGAAACGCTCACAATCC 58.465 50.000 0.00 0.00 0.00 3.01
2503 2520 0.400213 AGGGAAACGCTCACAATCCA 59.600 50.000 0.00 0.00 31.63 3.41
2504 2521 1.202879 AGGGAAACGCTCACAATCCAA 60.203 47.619 0.00 0.00 31.63 3.53
2505 2522 1.611491 GGGAAACGCTCACAATCCAAA 59.389 47.619 0.00 0.00 31.63 3.28
2506 2523 2.035321 GGGAAACGCTCACAATCCAAAA 59.965 45.455 0.00 0.00 31.63 2.44
2507 2524 3.306019 GGGAAACGCTCACAATCCAAAAT 60.306 43.478 0.00 0.00 31.63 1.82
2522 2539 9.452287 ACAATCCAAAATTCCATTGAATAAAGG 57.548 29.630 0.00 0.00 40.34 3.11
2547 2564 1.667724 CGCTCACAATCCAGAATCCAC 59.332 52.381 0.00 0.00 0.00 4.02
2548 2565 2.019984 GCTCACAATCCAGAATCCACC 58.980 52.381 0.00 0.00 0.00 4.61
2549 2566 2.283298 CTCACAATCCAGAATCCACCG 58.717 52.381 0.00 0.00 0.00 4.94
2582 2669 6.411376 TCTACAACCGGATATGTCAAACATT 58.589 36.000 9.46 0.00 39.88 2.71
2728 2870 1.616374 GCCTCCTCTTCCTCTATTCCG 59.384 57.143 0.00 0.00 0.00 4.30
2963 3206 1.456705 CTCTCCCTCCTCTTCCCCG 60.457 68.421 0.00 0.00 0.00 5.73
2978 3239 1.305381 CCCGAACTCCTCCTCCAGT 60.305 63.158 0.00 0.00 0.00 4.00
3053 3329 2.060383 CACCCGGATCTCCTGCTGA 61.060 63.158 0.73 0.00 0.00 4.26
3072 3348 0.824759 AATCTCGTACTGGTGCTCCC 59.175 55.000 1.59 0.00 0.00 4.30
3168 3502 0.336737 AGAGAGGGACGAGGTGGATT 59.663 55.000 0.00 0.00 0.00 3.01
3173 3507 1.299976 GGACGAGGTGGATTGGCTT 59.700 57.895 0.00 0.00 0.00 4.35
3177 3511 0.322456 CGAGGTGGATTGGCTTGGAA 60.322 55.000 0.00 0.00 0.00 3.53
3289 3630 4.354212 CAGCGCCACGTGACGTTG 62.354 66.667 24.20 24.20 38.32 4.10
3292 3633 4.042060 CGCCACGTGACGTTGACG 62.042 66.667 19.30 16.74 38.32 4.35
3349 3691 4.039357 CCGAGCGAGTCCACGTGT 62.039 66.667 15.65 0.00 35.59 4.49
3350 3692 2.050351 CGAGCGAGTCCACGTGTT 60.050 61.111 15.65 0.00 35.59 3.32
3494 3866 5.406163 AGGGACCTTCTGGATTGAAAAATT 58.594 37.500 0.00 0.00 37.04 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 4.964241 GCTATCCCGGCCCCTCCT 62.964 72.222 0.00 0.00 0.00 3.69
110 111 2.178912 TAAACGGCAGGTGAGAAAGG 57.821 50.000 0.00 0.00 0.00 3.11
112 113 2.343101 CGATAAACGGCAGGTGAGAAA 58.657 47.619 0.00 0.00 38.46 2.52
113 114 2.004583 CGATAAACGGCAGGTGAGAA 57.995 50.000 0.00 0.00 38.46 2.87
128 129 3.371965 AGGTTTACTCCAAGCTCCGATA 58.628 45.455 0.00 0.00 27.87 2.92
249 250 6.619801 GTTGACAACCTCTAAACAATCAGT 57.380 37.500 7.10 0.00 0.00 3.41
286 287 3.541632 ACAATTGACCTCAAACTGTCGT 58.458 40.909 13.59 0.00 39.55 4.34
287 288 4.282068 CAACAATTGACCTCAAACTGTCG 58.718 43.478 13.59 0.00 39.55 4.35
375 376 3.811810 GCCATAGCATTAGCATCCCTTGA 60.812 47.826 0.00 0.00 45.49 3.02
504 505 4.961730 TGGGGAGCTTTATTGCATAATTGT 59.038 37.500 0.00 0.00 34.99 2.71
508 509 4.609301 ACTTGGGGAGCTTTATTGCATAA 58.391 39.130 0.00 0.00 34.99 1.90
558 559 9.077885 TGCAGATTAAAAAGAAACATAGGAAGT 57.922 29.630 0.00 0.00 0.00 3.01
577 578 9.193806 ACTTTGACCAAATCTTATATGCAGATT 57.806 29.630 0.00 0.00 41.84 2.40
578 579 8.757982 ACTTTGACCAAATCTTATATGCAGAT 57.242 30.769 0.00 0.00 31.94 2.90
579 580 8.579850 AACTTTGACCAAATCTTATATGCAGA 57.420 30.769 0.00 0.00 0.00 4.26
586 587 9.981114 CAAGGTTTAACTTTGACCAAATCTTAT 57.019 29.630 13.60 0.00 37.36 1.73
587 588 8.973182 ACAAGGTTTAACTTTGACCAAATCTTA 58.027 29.630 23.32 0.00 37.36 2.10
588 589 7.847096 ACAAGGTTTAACTTTGACCAAATCTT 58.153 30.769 23.32 0.00 37.36 2.40
589 590 7.418337 ACAAGGTTTAACTTTGACCAAATCT 57.582 32.000 23.32 0.00 37.36 2.40
590 591 9.589111 TTAACAAGGTTTAACTTTGACCAAATC 57.411 29.630 23.32 0.00 37.36 2.17
591 592 9.373603 GTTAACAAGGTTTAACTTTGACCAAAT 57.626 29.630 23.32 0.54 37.36 2.32
592 593 8.586744 AGTTAACAAGGTTTAACTTTGACCAAA 58.413 29.630 23.32 10.45 45.85 3.28
593 594 8.124808 AGTTAACAAGGTTTAACTTTGACCAA 57.875 30.769 23.32 12.15 45.85 3.67
594 595 7.706100 AGTTAACAAGGTTTAACTTTGACCA 57.294 32.000 23.32 7.60 45.85 4.02
692 693 9.632638 ACACTGAAGCTATATGGTATCAAAATT 57.367 29.630 0.00 0.00 0.00 1.82
693 694 9.632638 AACACTGAAGCTATATGGTATCAAAAT 57.367 29.630 0.00 0.00 0.00 1.82
694 695 9.461312 AAACACTGAAGCTATATGGTATCAAAA 57.539 29.630 0.00 0.00 0.00 2.44
695 696 9.461312 AAAACACTGAAGCTATATGGTATCAAA 57.539 29.630 0.00 0.00 0.00 2.69
697 698 9.764363 CTAAAACACTGAAGCTATATGGTATCA 57.236 33.333 0.00 0.00 0.00 2.15
698 699 9.982651 TCTAAAACACTGAAGCTATATGGTATC 57.017 33.333 0.00 0.00 0.00 2.24
700 701 9.764363 CATCTAAAACACTGAAGCTATATGGTA 57.236 33.333 0.00 0.00 0.00 3.25
701 702 8.267894 ACATCTAAAACACTGAAGCTATATGGT 58.732 33.333 0.00 0.00 0.00 3.55
702 703 8.668510 ACATCTAAAACACTGAAGCTATATGG 57.331 34.615 0.00 0.00 0.00 2.74
703 704 9.926751 CAACATCTAAAACACTGAAGCTATATG 57.073 33.333 0.00 0.00 0.00 1.78
704 705 9.890629 TCAACATCTAAAACACTGAAGCTATAT 57.109 29.630 0.00 0.00 0.00 0.86
705 706 9.890629 ATCAACATCTAAAACACTGAAGCTATA 57.109 29.630 0.00 0.00 0.00 1.31
706 707 8.798859 ATCAACATCTAAAACACTGAAGCTAT 57.201 30.769 0.00 0.00 0.00 2.97
707 708 9.890629 ATATCAACATCTAAAACACTGAAGCTA 57.109 29.630 0.00 0.00 0.00 3.32
708 709 8.798859 ATATCAACATCTAAAACACTGAAGCT 57.201 30.769 0.00 0.00 0.00 3.74
709 710 9.846248 AAATATCAACATCTAAAACACTGAAGC 57.154 29.630 0.00 0.00 0.00 3.86
788 789 9.225682 TCCCTCCATTTCTTTTAGTCTGTATAT 57.774 33.333 0.00 0.00 0.00 0.86
789 790 8.618240 TCCCTCCATTTCTTTTAGTCTGTATA 57.382 34.615 0.00 0.00 0.00 1.47
790 791 7.182930 ACTCCCTCCATTTCTTTTAGTCTGTAT 59.817 37.037 0.00 0.00 0.00 2.29
791 792 6.500751 ACTCCCTCCATTTCTTTTAGTCTGTA 59.499 38.462 0.00 0.00 0.00 2.74
792 793 5.310857 ACTCCCTCCATTTCTTTTAGTCTGT 59.689 40.000 0.00 0.00 0.00 3.41
793 794 5.810095 ACTCCCTCCATTTCTTTTAGTCTG 58.190 41.667 0.00 0.00 0.00 3.51
794 795 6.500751 TGTACTCCCTCCATTTCTTTTAGTCT 59.499 38.462 0.00 0.00 0.00 3.24
795 796 6.708285 TGTACTCCCTCCATTTCTTTTAGTC 58.292 40.000 0.00 0.00 0.00 2.59
796 797 6.697641 TGTACTCCCTCCATTTCTTTTAGT 57.302 37.500 0.00 0.00 0.00 2.24
797 798 9.331282 CTATTGTACTCCCTCCATTTCTTTTAG 57.669 37.037 0.00 0.00 0.00 1.85
798 799 9.053472 TCTATTGTACTCCCTCCATTTCTTTTA 57.947 33.333 0.00 0.00 0.00 1.52
799 800 7.928873 TCTATTGTACTCCCTCCATTTCTTTT 58.071 34.615 0.00 0.00 0.00 2.27
800 801 7.510675 TCTATTGTACTCCCTCCATTTCTTT 57.489 36.000 0.00 0.00 0.00 2.52
801 802 7.472100 CGATCTATTGTACTCCCTCCATTTCTT 60.472 40.741 0.00 0.00 0.00 2.52
802 803 6.015010 CGATCTATTGTACTCCCTCCATTTCT 60.015 42.308 0.00 0.00 0.00 2.52
803 804 6.159988 CGATCTATTGTACTCCCTCCATTTC 58.840 44.000 0.00 0.00 0.00 2.17
804 805 5.012148 CCGATCTATTGTACTCCCTCCATTT 59.988 44.000 0.00 0.00 0.00 2.32
805 806 4.528596 CCGATCTATTGTACTCCCTCCATT 59.471 45.833 0.00 0.00 0.00 3.16
806 807 4.090090 CCGATCTATTGTACTCCCTCCAT 58.910 47.826 0.00 0.00 0.00 3.41
807 808 3.117246 ACCGATCTATTGTACTCCCTCCA 60.117 47.826 0.00 0.00 0.00 3.86
808 809 3.498334 ACCGATCTATTGTACTCCCTCC 58.502 50.000 0.00 0.00 0.00 4.30
809 810 4.400120 AGACCGATCTATTGTACTCCCTC 58.600 47.826 0.00 0.00 31.46 4.30
810 811 4.456662 AGACCGATCTATTGTACTCCCT 57.543 45.455 0.00 0.00 31.46 4.20
811 812 5.048852 GTGTAGACCGATCTATTGTACTCCC 60.049 48.000 0.00 0.00 39.66 4.30
812 813 5.530171 TGTGTAGACCGATCTATTGTACTCC 59.470 44.000 0.00 0.00 39.66 3.85
813 814 6.615264 TGTGTAGACCGATCTATTGTACTC 57.385 41.667 0.00 0.00 39.66 2.59
814 815 6.515200 GCATGTGTAGACCGATCTATTGTACT 60.515 42.308 0.00 0.00 39.66 2.73
815 816 5.629849 GCATGTGTAGACCGATCTATTGTAC 59.370 44.000 0.00 0.00 39.66 2.90
816 817 5.278808 GGCATGTGTAGACCGATCTATTGTA 60.279 44.000 0.00 0.00 39.66 2.41
817 818 4.501571 GGCATGTGTAGACCGATCTATTGT 60.502 45.833 0.00 0.00 39.66 2.71
818 819 3.990469 GGCATGTGTAGACCGATCTATTG 59.010 47.826 0.00 0.00 39.66 1.90
819 820 3.898123 AGGCATGTGTAGACCGATCTATT 59.102 43.478 0.00 0.00 39.66 1.73
820 821 3.256879 CAGGCATGTGTAGACCGATCTAT 59.743 47.826 0.00 0.00 39.66 1.98
821 822 2.623416 CAGGCATGTGTAGACCGATCTA 59.377 50.000 0.00 0.00 36.29 1.98
822 823 1.410517 CAGGCATGTGTAGACCGATCT 59.589 52.381 0.00 0.00 39.15 2.75
823 824 1.539065 CCAGGCATGTGTAGACCGATC 60.539 57.143 0.00 0.00 0.00 3.69
824 825 0.465705 CCAGGCATGTGTAGACCGAT 59.534 55.000 0.00 0.00 0.00 4.18
825 826 1.897423 CCAGGCATGTGTAGACCGA 59.103 57.895 0.00 0.00 0.00 4.69
826 827 1.815421 GCCAGGCATGTGTAGACCG 60.815 63.158 6.55 0.00 0.00 4.79
827 828 0.322456 TTGCCAGGCATGTGTAGACC 60.322 55.000 17.09 0.00 38.76 3.85
828 829 1.470098 CTTTGCCAGGCATGTGTAGAC 59.530 52.381 17.09 0.00 38.76 2.59
829 830 1.350684 TCTTTGCCAGGCATGTGTAGA 59.649 47.619 17.09 10.40 38.76 2.59
830 831 1.825090 TCTTTGCCAGGCATGTGTAG 58.175 50.000 17.09 8.20 38.76 2.74
831 832 1.885887 GTTCTTTGCCAGGCATGTGTA 59.114 47.619 17.09 0.00 38.76 2.90
832 833 0.675633 GTTCTTTGCCAGGCATGTGT 59.324 50.000 17.09 0.00 38.76 3.72
833 834 0.675083 TGTTCTTTGCCAGGCATGTG 59.325 50.000 17.09 8.72 38.76 3.21
834 835 1.547372 GATGTTCTTTGCCAGGCATGT 59.453 47.619 17.09 0.00 38.76 3.21
835 836 1.822990 AGATGTTCTTTGCCAGGCATG 59.177 47.619 17.09 11.82 38.76 4.06
836 837 2.226962 AGATGTTCTTTGCCAGGCAT 57.773 45.000 17.09 0.00 38.76 4.40
837 838 1.999648 AAGATGTTCTTTGCCAGGCA 58.000 45.000 11.22 11.22 31.57 4.75
838 839 4.488879 CTTAAAGATGTTCTTTGCCAGGC 58.511 43.478 3.66 3.66 45.45 4.85
839 840 4.219288 AGCTTAAAGATGTTCTTTGCCAGG 59.781 41.667 11.73 0.00 45.45 4.45
840 841 5.159209 CAGCTTAAAGATGTTCTTTGCCAG 58.841 41.667 11.73 6.91 45.45 4.85
841 842 4.584325 ACAGCTTAAAGATGTTCTTTGCCA 59.416 37.500 11.73 0.00 43.03 4.92
842 843 5.126396 ACAGCTTAAAGATGTTCTTTGCC 57.874 39.130 11.73 2.00 43.03 4.52
851 852 5.405571 ACGTCAGTACAACAGCTTAAAGATG 59.594 40.000 0.00 0.00 37.69 2.90
852 853 5.539048 ACGTCAGTACAACAGCTTAAAGAT 58.461 37.500 0.00 0.00 0.00 2.40
853 854 4.940463 ACGTCAGTACAACAGCTTAAAGA 58.060 39.130 0.00 0.00 0.00 2.52
854 855 4.743151 TGACGTCAGTACAACAGCTTAAAG 59.257 41.667 15.76 0.00 0.00 1.85
855 856 4.684877 TGACGTCAGTACAACAGCTTAAA 58.315 39.130 15.76 0.00 0.00 1.52
856 857 4.310357 TGACGTCAGTACAACAGCTTAA 57.690 40.909 15.76 0.00 0.00 1.85
857 858 3.994204 TGACGTCAGTACAACAGCTTA 57.006 42.857 15.76 0.00 0.00 3.09
858 859 2.882927 TGACGTCAGTACAACAGCTT 57.117 45.000 15.76 0.00 0.00 3.74
859 860 2.882927 TTGACGTCAGTACAACAGCT 57.117 45.000 19.11 0.00 0.00 4.24
860 861 3.799035 CATTTGACGTCAGTACAACAGC 58.201 45.455 19.11 0.00 0.00 4.40
861 862 3.363970 GGCATTTGACGTCAGTACAACAG 60.364 47.826 19.11 7.79 0.00 3.16
862 863 2.546368 GGCATTTGACGTCAGTACAACA 59.454 45.455 19.11 0.00 0.00 3.33
863 864 2.411031 CGGCATTTGACGTCAGTACAAC 60.411 50.000 19.11 8.07 42.66 3.32
883 884 2.475466 GGCAGTGATCACCATGGCG 61.475 63.158 22.21 1.26 0.00 5.69
891 892 1.775385 TGGAGATACGGCAGTGATCA 58.225 50.000 0.00 0.00 0.00 2.92
892 893 2.101582 AGTTGGAGATACGGCAGTGATC 59.898 50.000 0.00 0.00 0.00 2.92
893 894 2.101582 GAGTTGGAGATACGGCAGTGAT 59.898 50.000 0.00 0.00 0.00 3.06
894 895 1.476891 GAGTTGGAGATACGGCAGTGA 59.523 52.381 0.00 0.00 0.00 3.41
895 896 1.478510 AGAGTTGGAGATACGGCAGTG 59.521 52.381 0.00 0.00 0.00 3.66
922 935 7.670605 TTGTACTGTATATCTTTAGGCCACT 57.329 36.000 5.01 0.00 0.00 4.00
938 951 5.138276 TCTACCACTCTGACTTTGTACTGT 58.862 41.667 0.00 0.00 0.00 3.55
939 952 5.707242 TCTACCACTCTGACTTTGTACTG 57.293 43.478 0.00 0.00 0.00 2.74
940 953 5.775701 ACATCTACCACTCTGACTTTGTACT 59.224 40.000 0.00 0.00 0.00 2.73
941 954 5.864474 CACATCTACCACTCTGACTTTGTAC 59.136 44.000 0.00 0.00 0.00 2.90
942 955 5.566826 GCACATCTACCACTCTGACTTTGTA 60.567 44.000 0.00 0.00 0.00 2.41
943 956 4.800914 GCACATCTACCACTCTGACTTTGT 60.801 45.833 0.00 0.00 0.00 2.83
948 961 4.927978 ATAGCACATCTACCACTCTGAC 57.072 45.455 0.00 0.00 0.00 3.51
975 988 8.690884 GGATGGAGGGATATATGATATATCACG 58.309 40.741 25.61 0.00 38.94 4.35
1009 1023 1.077716 GGGTTGTGGCCGCTCTATT 60.078 57.895 18.96 0.00 0.00 1.73
1018 1032 2.084546 GATCTAAGTGTGGGTTGTGGC 58.915 52.381 0.00 0.00 0.00 5.01
1024 1038 1.139058 GCCATCGATCTAAGTGTGGGT 59.861 52.381 0.00 0.00 0.00 4.51
1059 1076 1.002366 CACTACGCATTGGAGAGTGC 58.998 55.000 0.00 0.00 37.97 4.40
1075 1092 1.078848 GAGCGCCATCAGGAACACT 60.079 57.895 2.29 0.00 36.89 3.55
1098 1115 2.106332 GCGGTATCAGGTGGGTCG 59.894 66.667 0.00 0.00 0.00 4.79
1147 1164 3.865383 CCCGAGCTAGCCATGGCA 61.865 66.667 37.18 21.91 44.88 4.92
1306 1323 1.337260 ACGCTGAAGGCCATATCGATC 60.337 52.381 5.01 0.00 37.74 3.69
1726 1743 2.821366 GCCACCTGCATGACGAGG 60.821 66.667 0.00 0.01 40.77 4.63
1750 1767 4.373116 GAGAACCGCGTCTGCCCA 62.373 66.667 4.92 0.00 38.08 5.36
1761 1778 1.819903 AGAAGAGGCAGTACGAGAACC 59.180 52.381 0.00 0.00 0.00 3.62
2053 2070 3.374402 AGGTCACTCCAGACGGCG 61.374 66.667 4.80 4.80 39.42 6.46
2210 2227 3.414700 CACCGCCGTGAACAGCTC 61.415 66.667 0.00 0.00 43.14 4.09
2332 2349 4.497507 GCAAAGGACAGTTTAGCGTCTTTT 60.498 41.667 0.00 0.00 40.73 2.27
2341 2358 1.068895 TCCGACGCAAAGGACAGTTTA 59.931 47.619 0.00 0.00 0.00 2.01
2344 2361 1.006102 CTCCGACGCAAAGGACAGT 60.006 57.895 0.00 0.00 32.33 3.55
2368 2385 3.691342 CCGGCGGTGTCCTGAGAA 61.691 66.667 19.97 0.00 0.00 2.87
2416 2433 2.438434 GTCCATGGGAAGCACCGG 60.438 66.667 13.02 0.00 40.11 5.28
2418 2435 1.106285 GAATGTCCATGGGAAGCACC 58.894 55.000 13.02 0.00 31.38 5.01
2445 2462 1.814169 GCAACTGGCTAGCGGGTAC 60.814 63.158 9.00 2.77 40.25 3.34
2446 2463 2.582436 GCAACTGGCTAGCGGGTA 59.418 61.111 9.00 0.00 40.25 3.69
2451 2468 9.660694 AATGGAATTTACAAGCAACTGGCTAGC 62.661 40.741 6.04 6.04 44.35 3.42
2452 2469 6.350445 AATGGAATTTACAAGCAACTGGCTAG 60.350 38.462 0.00 0.00 44.35 3.42
2453 2470 5.480073 AATGGAATTTACAAGCAACTGGCTA 59.520 36.000 0.00 0.00 44.35 3.93
2454 2471 4.284234 AATGGAATTTACAAGCAACTGGCT 59.716 37.500 0.00 0.00 46.73 4.75
2455 2472 3.658757 TGGAATTTACAAGCAACTGGC 57.341 42.857 0.00 0.00 45.30 4.85
2456 2473 5.782047 TCAATGGAATTTACAAGCAACTGG 58.218 37.500 0.00 0.00 31.22 4.00
2457 2474 7.894376 ATTCAATGGAATTTACAAGCAACTG 57.106 32.000 0.00 0.00 40.87 3.16
2458 2475 9.995003 TTTATTCAATGGAATTTACAAGCAACT 57.005 25.926 0.00 0.00 40.87 3.16
2471 2488 4.770010 AGCGTTTCCCTTTATTCAATGGAA 59.230 37.500 0.00 0.00 37.45 3.53
2472 2489 4.340617 AGCGTTTCCCTTTATTCAATGGA 58.659 39.130 0.00 0.00 31.94 3.41
2473 2490 4.157656 TGAGCGTTTCCCTTTATTCAATGG 59.842 41.667 0.00 0.00 0.00 3.16
2474 2491 5.095490 GTGAGCGTTTCCCTTTATTCAATG 58.905 41.667 0.00 0.00 0.00 2.82
2475 2492 4.764823 TGTGAGCGTTTCCCTTTATTCAAT 59.235 37.500 0.00 0.00 0.00 2.57
2476 2493 4.138290 TGTGAGCGTTTCCCTTTATTCAA 58.862 39.130 0.00 0.00 0.00 2.69
2477 2494 3.745799 TGTGAGCGTTTCCCTTTATTCA 58.254 40.909 0.00 0.00 0.00 2.57
2478 2495 4.759516 TTGTGAGCGTTTCCCTTTATTC 57.240 40.909 0.00 0.00 0.00 1.75
2479 2496 4.157840 GGATTGTGAGCGTTTCCCTTTATT 59.842 41.667 0.00 0.00 0.00 1.40
2480 2497 3.694566 GGATTGTGAGCGTTTCCCTTTAT 59.305 43.478 0.00 0.00 0.00 1.40
2481 2498 3.078837 GGATTGTGAGCGTTTCCCTTTA 58.921 45.455 0.00 0.00 0.00 1.85
2482 2499 1.886542 GGATTGTGAGCGTTTCCCTTT 59.113 47.619 0.00 0.00 0.00 3.11
2483 2500 1.202879 TGGATTGTGAGCGTTTCCCTT 60.203 47.619 0.00 0.00 0.00 3.95
2484 2501 0.400213 TGGATTGTGAGCGTTTCCCT 59.600 50.000 0.00 0.00 0.00 4.20
2485 2502 1.243902 TTGGATTGTGAGCGTTTCCC 58.756 50.000 0.00 0.00 0.00 3.97
2486 2503 3.363341 TTTTGGATTGTGAGCGTTTCC 57.637 42.857 0.00 0.00 0.00 3.13
2487 2504 4.385748 GGAATTTTGGATTGTGAGCGTTTC 59.614 41.667 0.00 0.00 0.00 2.78
2488 2505 4.202202 TGGAATTTTGGATTGTGAGCGTTT 60.202 37.500 0.00 0.00 0.00 3.60
2489 2506 3.320541 TGGAATTTTGGATTGTGAGCGTT 59.679 39.130 0.00 0.00 0.00 4.84
2490 2507 2.890311 TGGAATTTTGGATTGTGAGCGT 59.110 40.909 0.00 0.00 0.00 5.07
2491 2508 3.574284 TGGAATTTTGGATTGTGAGCG 57.426 42.857 0.00 0.00 0.00 5.03
2492 2509 5.481105 TCAATGGAATTTTGGATTGTGAGC 58.519 37.500 0.00 0.00 31.22 4.26
2493 2510 9.656040 TTATTCAATGGAATTTTGGATTGTGAG 57.344 29.630 0.00 0.00 40.87 3.51
2496 2513 9.452287 CCTTTATTCAATGGAATTTTGGATTGT 57.548 29.630 0.00 0.00 40.87 2.71
2497 2514 8.895737 CCCTTTATTCAATGGAATTTTGGATTG 58.104 33.333 0.00 0.00 40.87 2.67
2498 2515 8.834733 TCCCTTTATTCAATGGAATTTTGGATT 58.165 29.630 0.00 0.00 40.87 3.01
2499 2516 8.391305 TCCCTTTATTCAATGGAATTTTGGAT 57.609 30.769 0.00 0.00 40.87 3.41
2500 2517 7.805083 TCCCTTTATTCAATGGAATTTTGGA 57.195 32.000 0.00 0.44 40.87 3.53
2501 2518 8.729756 GTTTCCCTTTATTCAATGGAATTTTGG 58.270 33.333 0.00 1.30 40.87 3.28
2502 2519 8.442384 CGTTTCCCTTTATTCAATGGAATTTTG 58.558 33.333 0.00 0.00 40.87 2.44
2503 2520 7.119116 GCGTTTCCCTTTATTCAATGGAATTTT 59.881 33.333 0.00 0.00 40.87 1.82
2504 2521 6.593770 GCGTTTCCCTTTATTCAATGGAATTT 59.406 34.615 0.00 0.00 40.87 1.82
2505 2522 6.070824 AGCGTTTCCCTTTATTCAATGGAATT 60.071 34.615 0.00 0.00 40.87 2.17
2506 2523 5.422012 AGCGTTTCCCTTTATTCAATGGAAT 59.578 36.000 0.00 0.00 45.50 3.01
2507 2524 4.770010 AGCGTTTCCCTTTATTCAATGGAA 59.230 37.500 0.00 0.00 37.45 3.53
2522 2539 1.808411 TCTGGATTGTGAGCGTTTCC 58.192 50.000 0.00 0.00 0.00 3.13
2547 2564 2.460918 CGGTTGTAGATGCTCTAACGG 58.539 52.381 0.00 0.00 29.58 4.44
2548 2565 2.098607 TCCGGTTGTAGATGCTCTAACG 59.901 50.000 0.00 0.00 29.58 3.18
2549 2566 3.795623 TCCGGTTGTAGATGCTCTAAC 57.204 47.619 0.00 0.00 29.58 2.34
2701 2838 2.690510 GAAGAGGAGGCTGGGGCT 60.691 66.667 0.00 0.00 42.48 5.19
2704 2841 0.263172 TAGAGGAAGAGGAGGCTGGG 59.737 60.000 0.00 0.00 0.00 4.45
2978 3239 3.068691 CCTCCGGACTCGCCAGAA 61.069 66.667 0.00 0.00 35.94 3.02
3022 3289 4.681978 GGGTGAGACAAGCCGCGT 62.682 66.667 4.92 0.00 0.00 6.01
3053 3329 0.824759 GGGAGCACCAGTACGAGATT 59.175 55.000 1.58 0.00 39.85 2.40
3082 3359 2.688958 AGGAAGATCACCTACTACGCAC 59.311 50.000 9.29 0.00 35.84 5.34
3138 3472 2.438614 CCTCTCTCACTCCGGCGA 60.439 66.667 9.30 0.00 0.00 5.54
3149 3483 0.336737 AATCCACCTCGTCCCTCTCT 59.663 55.000 0.00 0.00 0.00 3.10
3168 3502 2.929903 GCGTTGCCATTCCAAGCCA 61.930 57.895 0.00 0.00 0.00 4.75
3173 3507 1.298157 CTCTTCGCGTTGCCATTCCA 61.298 55.000 5.77 0.00 0.00 3.53
3177 3511 2.436646 CCCTCTTCGCGTTGCCAT 60.437 61.111 5.77 0.00 0.00 4.40
3289 3630 3.103911 CTTCGTCACCGTGGCGTC 61.104 66.667 23.77 0.51 46.84 5.19
3292 3633 2.432628 CTCCTTCGTCACCGTGGC 60.433 66.667 0.00 0.00 35.01 5.01
3349 3691 4.960469 CACATAGGACTGACTAAGGGGTAA 59.040 45.833 0.00 0.00 0.00 2.85
3350 3692 4.543689 CACATAGGACTGACTAAGGGGTA 58.456 47.826 0.00 0.00 0.00 3.69
3454 3826 3.507622 GTCCCTTCAAATGGGTCTCAAAG 59.492 47.826 0.00 0.00 44.84 2.77


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

AutoCloner maintained by Alex Coulton.