Multiple sequence alignment - TraesCS6A01G276500

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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 TraesCS6A01G276500 chr6A 100.000 3269 0 0 1 3269 503601596 503604864 0.000000e+00 6037.0
1 TraesCS6A01G276500 chr6A 91.515 1426 93 14 916 2324 503498796 503500210 0.000000e+00 1938.0
2 TraesCS6A01G276500 chr6A 97.669 901 19 1 2342 3242 503525213 503526111 0.000000e+00 1546.0
3 TraesCS6A01G276500 chr6A 95.596 545 23 1 1 545 61739433 61738890 0.000000e+00 872.0
4 TraesCS6A01G276500 chr6A 85.813 578 82 0 2505 3082 503487894 503488471 5.990000e-172 614.0
5 TraesCS6A01G276500 chr6A 94.737 57 3 0 780 836 503498674 503498730 4.490000e-14 89.8
6 TraesCS6A01G276500 chr6B 91.412 1537 95 8 783 2304 544642864 544644378 0.000000e+00 2073.0
7 TraesCS6A01G276500 chr6B 90.299 134 13 0 637 770 680698769 680698636 3.350000e-40 176.0
8 TraesCS6A01G276500 chr6D 91.602 1024 68 7 916 1924 363015196 363016216 0.000000e+00 1399.0
9 TraesCS6A01G276500 chr6D 94.118 476 22 4 1921 2396 363020688 363021157 0.000000e+00 719.0
10 TraesCS6A01G276500 chr6D 80.938 682 110 11 2510 3179 437621644 437620971 3.740000e-144 521.0
11 TraesCS6A01G276500 chr6D 86.385 213 23 3 3027 3238 363006305 363006512 9.120000e-56 228.0
12 TraesCS6A01G276500 chr6D 98.387 62 1 0 778 839 363015037 363015098 3.450000e-20 110.0
13 TraesCS6A01G276500 chr5D 95.963 545 21 1 1 544 311368586 311369130 0.000000e+00 883.0
14 TraesCS6A01G276500 chr5D 81.590 239 42 2 16 253 287308622 287308385 2.570000e-46 196.0
15 TraesCS6A01G276500 chr7D 93.956 546 30 3 1 544 579082191 579082735 0.000000e+00 822.0
16 TraesCS6A01G276500 chr7D 78.947 665 122 12 2517 3172 119741249 119741904 1.390000e-118 436.0
17 TraesCS6A01G276500 chr7B 85.818 550 71 6 1 545 7067344 7066797 7.870000e-161 577.0
18 TraesCS6A01G276500 chr7B 87.970 133 15 1 637 769 685410774 685410905 4.370000e-34 156.0
19 TraesCS6A01G276500 chr7B 88.889 54 5 1 2446 2498 679675015 679675068 7.570000e-07 65.8
20 TraesCS6A01G276500 chr2D 84.699 549 81 3 2512 3059 547154500 547155046 2.220000e-151 545.0
21 TraesCS6A01G276500 chr2D 82.711 509 82 5 2533 3040 284574214 284574717 6.430000e-122 448.0
22 TraesCS6A01G276500 chr2D 81.273 534 94 6 2510 3040 431928531 431929061 8.380000e-116 427.0
23 TraesCS6A01G276500 chr2D 73.452 840 188 24 1455 2272 560327374 560328200 1.920000e-72 283.0
24 TraesCS6A01G276500 chr2D 87.500 136 13 4 637 771 538275471 538275603 1.570000e-33 154.0
25 TraesCS6A01G276500 chr7A 81.850 573 94 8 2515 3086 124366853 124367416 1.060000e-129 473.0
26 TraesCS6A01G276500 chr4D 84.532 459 67 3 2604 3059 16671668 16672125 4.970000e-123 451.0
27 TraesCS6A01G276500 chr2B 82.546 487 80 4 2554 3040 777387056 777387537 1.080000e-114 424.0
28 TraesCS6A01G276500 chr3B 83.566 286 37 6 2803 3086 578758286 578758009 3.240000e-65 259.0
29 TraesCS6A01G276500 chr5A 78.756 386 60 16 1003 1377 69039601 69039227 4.220000e-59 239.0
30 TraesCS6A01G276500 chr5B 92.308 104 7 1 637 740 635603643 635603541 2.630000e-31 147.0
31 TraesCS6A01G276500 chr1B 90.164 61 2 3 2434 2494 558290910 558290854 3.500000e-10 76.8


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 TraesCS6A01G276500 chr6A 503601596 503604864 3268 False 6037.0 6037 100.0000 1 3269 1 chr6A.!!$F3 3268
1 TraesCS6A01G276500 chr6A 503525213 503526111 898 False 1546.0 1546 97.6690 2342 3242 1 chr6A.!!$F2 900
2 TraesCS6A01G276500 chr6A 503498674 503500210 1536 False 1013.9 1938 93.1260 780 2324 2 chr6A.!!$F4 1544
3 TraesCS6A01G276500 chr6A 61738890 61739433 543 True 872.0 872 95.5960 1 545 1 chr6A.!!$R1 544
4 TraesCS6A01G276500 chr6A 503487894 503488471 577 False 614.0 614 85.8130 2505 3082 1 chr6A.!!$F1 577
5 TraesCS6A01G276500 chr6B 544642864 544644378 1514 False 2073.0 2073 91.4120 783 2304 1 chr6B.!!$F1 1521
6 TraesCS6A01G276500 chr6D 363015037 363016216 1179 False 754.5 1399 94.9945 778 1924 2 chr6D.!!$F3 1146
7 TraesCS6A01G276500 chr6D 437620971 437621644 673 True 521.0 521 80.9380 2510 3179 1 chr6D.!!$R1 669
8 TraesCS6A01G276500 chr5D 311368586 311369130 544 False 883.0 883 95.9630 1 544 1 chr5D.!!$F1 543
9 TraesCS6A01G276500 chr7D 579082191 579082735 544 False 822.0 822 93.9560 1 544 1 chr7D.!!$F2 543
10 TraesCS6A01G276500 chr7D 119741249 119741904 655 False 436.0 436 78.9470 2517 3172 1 chr7D.!!$F1 655
11 TraesCS6A01G276500 chr7B 7066797 7067344 547 True 577.0 577 85.8180 1 545 1 chr7B.!!$R1 544
12 TraesCS6A01G276500 chr2D 547154500 547155046 546 False 545.0 545 84.6990 2512 3059 1 chr2D.!!$F4 547
13 TraesCS6A01G276500 chr2D 284574214 284574717 503 False 448.0 448 82.7110 2533 3040 1 chr2D.!!$F1 507
14 TraesCS6A01G276500 chr2D 431928531 431929061 530 False 427.0 427 81.2730 2510 3040 1 chr2D.!!$F2 530
15 TraesCS6A01G276500 chr2D 560327374 560328200 826 False 283.0 283 73.4520 1455 2272 1 chr2D.!!$F5 817
16 TraesCS6A01G276500 chr7A 124366853 124367416 563 False 473.0 473 81.8500 2515 3086 1 chr7A.!!$F1 571

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
937 1033 0.036388 GATCAGGTCGTGCTTTCCCA 60.036 55.0 0.0 0.0 0.00 4.37 F
1678 1784 0.107945 GCAGGACATCGCCTTCTTCT 60.108 55.0 0.0 0.0 35.66 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2055 0.459411 GAGAGAGAACTCGGGCTTGC 60.459 60.0 0.0 0.0 46.64 4.01 R
3192 3328 0.251354 AGCTCCATCGCTGATGTTGT 59.749 50.0 14.5 0.0 38.28 3.32 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
119 120 4.213270 CAGGCTGACTTCATGTTACGAAAA 59.787 41.667 9.42 0.00 0.00 2.29
175 176 1.152673 GGGCCAAGATCATCCACCC 60.153 63.158 4.39 0.00 0.00 4.61
299 300 1.300233 GCTTCCATCCGTAGCCGAG 60.300 63.158 0.00 0.00 35.63 4.63
324 325 1.376424 CTCTGCGGCATTGGTGAGT 60.376 57.895 1.75 0.00 0.00 3.41
394 397 3.615536 AACCCTAACGTCGCGTCCG 62.616 63.158 16.86 16.86 39.99 4.79
555 560 9.999009 CCTAACGAGAGGGAAATTTTTATTAAC 57.001 33.333 0.00 0.00 32.39 2.01
558 563 9.516546 AACGAGAGGGAAATTTTTATTAACTCT 57.483 29.630 0.00 0.00 35.67 3.24
559 564 9.163899 ACGAGAGGGAAATTTTTATTAACTCTC 57.836 33.333 0.00 0.00 42.88 3.20
561 566 8.507524 AGAGGGAAATTTTTATTAACTCTCGG 57.492 34.615 0.00 0.00 0.00 4.63
562 567 7.556635 AGAGGGAAATTTTTATTAACTCTCGGG 59.443 37.037 0.00 0.00 0.00 5.14
563 568 7.179966 AGGGAAATTTTTATTAACTCTCGGGT 58.820 34.615 0.00 0.00 0.00 5.28
564 569 8.330993 AGGGAAATTTTTATTAACTCTCGGGTA 58.669 33.333 0.00 0.00 0.00 3.69
565 570 8.959548 GGGAAATTTTTATTAACTCTCGGGTAA 58.040 33.333 0.00 0.00 0.00 2.85
566 571 9.778993 GGAAATTTTTATTAACTCTCGGGTAAC 57.221 33.333 0.00 0.00 28.95 2.50
578 583 7.951347 ACTCTCGGGTAACTTTTATTAGAGA 57.049 36.000 0.00 0.00 33.74 3.10
580 585 7.951347 TCTCGGGTAACTTTTATTAGAGAGT 57.049 36.000 0.00 0.00 0.00 3.24
581 586 8.358582 TCTCGGGTAACTTTTATTAGAGAGTT 57.641 34.615 0.00 0.00 36.42 3.01
582 587 8.810041 TCTCGGGTAACTTTTATTAGAGAGTTT 58.190 33.333 0.00 0.00 34.46 2.66
583 588 9.433153 CTCGGGTAACTTTTATTAGAGAGTTTT 57.567 33.333 0.00 0.00 34.46 2.43
584 589 9.783081 TCGGGTAACTTTTATTAGAGAGTTTTT 57.217 29.630 0.00 0.00 34.46 1.94
597 602 6.351327 AGAGAGTTTTTCTTTTGTCACTCG 57.649 37.500 0.00 0.00 35.87 4.18
598 603 5.875359 AGAGAGTTTTTCTTTTGTCACTCGT 59.125 36.000 0.00 0.00 35.87 4.18
599 604 5.869350 AGAGTTTTTCTTTTGTCACTCGTG 58.131 37.500 0.00 0.00 36.56 4.35
600 605 4.412207 AGTTTTTCTTTTGTCACTCGTGC 58.588 39.130 0.00 0.00 0.00 5.34
601 606 4.083003 AGTTTTTCTTTTGTCACTCGTGCA 60.083 37.500 0.00 0.00 0.00 4.57
602 607 4.427096 TTTTCTTTTGTCACTCGTGCAA 57.573 36.364 0.00 0.00 0.00 4.08
603 608 3.673746 TTCTTTTGTCACTCGTGCAAG 57.326 42.857 0.00 0.00 31.82 4.01
604 609 2.899976 TCTTTTGTCACTCGTGCAAGA 58.100 42.857 1.47 1.47 31.82 3.02
605 610 2.866156 TCTTTTGTCACTCGTGCAAGAG 59.134 45.455 25.45 25.45 43.56 2.85
606 611 1.581934 TTTGTCACTCGTGCAAGAGG 58.418 50.000 29.26 19.33 42.31 3.69
607 612 0.880278 TTGTCACTCGTGCAAGAGGC 60.880 55.000 29.26 19.77 42.31 4.70
608 613 2.029844 GTCACTCGTGCAAGAGGCC 61.030 63.158 29.26 14.99 43.89 5.19
609 614 2.743928 CACTCGTGCAAGAGGCCC 60.744 66.667 29.26 0.00 43.89 5.80
610 615 3.241530 ACTCGTGCAAGAGGCCCA 61.242 61.111 29.26 0.00 43.89 5.36
611 616 2.743928 CTCGTGCAAGAGGCCCAC 60.744 66.667 20.50 0.00 43.89 4.61
630 635 1.935933 CGCTGGCGTCTTTATTAGGT 58.064 50.000 6.83 0.00 34.35 3.08
631 636 2.277084 CGCTGGCGTCTTTATTAGGTT 58.723 47.619 6.83 0.00 34.35 3.50
632 637 2.676342 CGCTGGCGTCTTTATTAGGTTT 59.324 45.455 6.83 0.00 34.35 3.27
633 638 3.126343 CGCTGGCGTCTTTATTAGGTTTT 59.874 43.478 6.83 0.00 34.35 2.43
634 639 4.379082 CGCTGGCGTCTTTATTAGGTTTTT 60.379 41.667 6.83 0.00 34.35 1.94
653 658 4.364415 TTTTGTTTCTGGAAGTGTTCGG 57.636 40.909 0.00 0.00 33.76 4.30
654 659 1.961793 TGTTTCTGGAAGTGTTCGGG 58.038 50.000 0.00 0.00 33.76 5.14
655 660 0.591659 GTTTCTGGAAGTGTTCGGGC 59.408 55.000 0.00 0.00 33.76 6.13
656 661 0.472471 TTTCTGGAAGTGTTCGGGCT 59.528 50.000 0.00 0.00 33.76 5.19
657 662 0.250295 TTCTGGAAGTGTTCGGGCTG 60.250 55.000 0.00 0.00 33.76 4.85
658 663 1.118965 TCTGGAAGTGTTCGGGCTGA 61.119 55.000 0.00 0.00 33.76 4.26
659 664 0.671781 CTGGAAGTGTTCGGGCTGAG 60.672 60.000 0.00 0.00 0.00 3.35
660 665 1.118965 TGGAAGTGTTCGGGCTGAGA 61.119 55.000 0.00 0.00 0.00 3.27
661 666 0.390472 GGAAGTGTTCGGGCTGAGAG 60.390 60.000 0.00 0.00 0.00 3.20
662 667 0.603569 GAAGTGTTCGGGCTGAGAGA 59.396 55.000 0.00 0.00 0.00 3.10
663 668 0.605589 AAGTGTTCGGGCTGAGAGAG 59.394 55.000 0.00 0.00 0.00 3.20
667 672 2.055042 TTCGGGCTGAGAGAGCTCC 61.055 63.158 10.93 1.70 46.85 4.70
668 673 2.441901 CGGGCTGAGAGAGCTCCT 60.442 66.667 10.93 7.30 46.85 3.69
669 674 2.784356 CGGGCTGAGAGAGCTCCTG 61.784 68.421 10.93 0.39 46.85 3.86
671 676 2.500646 GCTGAGAGAGCTCCTGGC 59.499 66.667 10.93 9.86 45.21 4.85
672 677 3.092780 GCTGAGAGAGCTCCTGGCC 62.093 68.421 10.93 0.00 45.21 5.36
673 678 2.364842 TGAGAGAGCTCCTGGCCC 60.365 66.667 10.93 0.00 43.05 5.80
674 679 3.535962 GAGAGAGCTCCTGGCCCG 61.536 72.222 10.93 0.00 43.05 6.13
675 680 4.067512 AGAGAGCTCCTGGCCCGA 62.068 66.667 10.93 0.00 43.05 5.14
676 681 3.077556 GAGAGCTCCTGGCCCGAA 61.078 66.667 10.93 0.00 43.05 4.30
677 682 3.378399 GAGAGCTCCTGGCCCGAAC 62.378 68.421 10.93 0.00 43.05 3.95
678 683 4.821589 GAGCTCCTGGCCCGAACG 62.822 72.222 0.87 0.00 43.05 3.95
680 685 4.388499 GCTCCTGGCCCGAACGAA 62.388 66.667 0.00 0.00 34.27 3.85
681 686 2.345991 CTCCTGGCCCGAACGAAA 59.654 61.111 0.00 0.00 0.00 3.46
682 687 1.078426 CTCCTGGCCCGAACGAAAT 60.078 57.895 0.00 0.00 0.00 2.17
683 688 1.078708 TCCTGGCCCGAACGAAATC 60.079 57.895 0.00 0.00 0.00 2.17
684 689 2.461110 CCTGGCCCGAACGAAATCG 61.461 63.158 0.00 0.48 46.33 3.34
685 690 1.447140 CTGGCCCGAACGAAATCGA 60.447 57.895 10.16 0.00 45.48 3.59
686 691 0.810031 CTGGCCCGAACGAAATCGAT 60.810 55.000 10.16 0.00 45.48 3.59
687 692 0.808453 TGGCCCGAACGAAATCGATC 60.808 55.000 10.16 6.42 45.48 3.69
694 699 3.708195 ACGAAATCGATCGGTCGTT 57.292 47.368 25.88 6.95 43.78 3.85
695 700 1.542544 ACGAAATCGATCGGTCGTTC 58.457 50.000 25.88 14.12 43.78 3.95
696 701 1.796617 ACGAAATCGATCGGTCGTTCC 60.797 52.381 25.88 4.85 43.78 3.62
697 702 4.952564 ACGAAATCGATCGGTCGTTCCC 62.953 54.545 25.88 5.67 43.78 3.97
700 705 3.145551 CGATCGGTCGTTCCCCCT 61.146 66.667 10.62 0.00 42.78 4.79
701 706 2.499685 GATCGGTCGTTCCCCCTG 59.500 66.667 0.00 0.00 0.00 4.45
702 707 2.284405 ATCGGTCGTTCCCCCTGT 60.284 61.111 0.00 0.00 0.00 4.00
703 708 2.294132 GATCGGTCGTTCCCCCTGTC 62.294 65.000 0.00 0.00 0.00 3.51
704 709 4.078516 CGGTCGTTCCCCCTGTCC 62.079 72.222 0.00 0.00 0.00 4.02
705 710 2.926242 GGTCGTTCCCCCTGTCCA 60.926 66.667 0.00 0.00 0.00 4.02
706 711 2.663196 GTCGTTCCCCCTGTCCAG 59.337 66.667 0.00 0.00 0.00 3.86
707 712 3.319198 TCGTTCCCCCTGTCCAGC 61.319 66.667 0.00 0.00 0.00 4.85
708 713 4.760047 CGTTCCCCCTGTCCAGCG 62.760 72.222 0.00 0.00 0.00 5.18
715 720 4.717629 CCTGTCCAGCGCGAACGA 62.718 66.667 12.10 0.00 43.93 3.85
716 721 2.507102 CTGTCCAGCGCGAACGAT 60.507 61.111 12.10 0.00 43.93 3.73
717 722 2.048597 TGTCCAGCGCGAACGATT 60.049 55.556 12.10 0.00 43.93 3.34
718 723 2.283780 CTGTCCAGCGCGAACGATTG 62.284 60.000 12.10 0.00 43.93 2.67
719 724 2.813474 TCCAGCGCGAACGATTGG 60.813 61.111 12.10 7.08 43.93 3.16
720 725 3.118454 CCAGCGCGAACGATTGGT 61.118 61.111 12.10 0.00 43.93 3.67
721 726 2.677003 CCAGCGCGAACGATTGGTT 61.677 57.895 12.10 0.00 43.93 3.67
730 735 3.192922 CGATTGGTTCGGGGCGAC 61.193 66.667 0.00 0.00 44.28 5.19
731 736 2.267961 GATTGGTTCGGGGCGACT 59.732 61.111 0.00 0.00 34.89 4.18
732 737 1.814169 GATTGGTTCGGGGCGACTC 60.814 63.158 0.00 0.00 34.89 3.36
733 738 3.325201 ATTGGTTCGGGGCGACTCC 62.325 63.158 0.00 0.00 34.89 3.85
735 740 4.144703 GGTTCGGGGCGACTCCTC 62.145 72.222 0.00 0.00 34.89 3.71
736 741 4.144703 GTTCGGGGCGACTCCTCC 62.145 72.222 0.00 0.00 34.89 4.30
747 752 4.821589 CTCCTCCCCAGCGCGAAC 62.822 72.222 12.10 0.00 0.00 3.95
765 770 3.613702 GTCGGCGCGTTATCGGTG 61.614 66.667 8.43 0.00 37.56 4.94
766 771 4.118995 TCGGCGCGTTATCGGTGT 62.119 61.111 8.43 0.00 37.56 4.16
767 772 3.613702 CGGCGCGTTATCGGTGTC 61.614 66.667 8.43 0.00 37.56 3.67
768 773 3.259751 GGCGCGTTATCGGTGTCC 61.260 66.667 8.43 0.00 37.56 4.02
769 774 2.507547 GCGCGTTATCGGTGTCCA 60.508 61.111 8.43 0.00 37.56 4.02
770 775 2.095847 GCGCGTTATCGGTGTCCAA 61.096 57.895 8.43 0.00 37.56 3.53
771 776 1.426041 GCGCGTTATCGGTGTCCAAT 61.426 55.000 8.43 0.00 37.56 3.16
772 777 1.842720 CGCGTTATCGGTGTCCAATA 58.157 50.000 0.00 0.00 37.56 1.90
773 778 2.195096 CGCGTTATCGGTGTCCAATAA 58.805 47.619 0.00 0.00 37.56 1.40
774 779 2.604011 CGCGTTATCGGTGTCCAATAAA 59.396 45.455 0.00 0.00 37.56 1.40
775 780 3.062369 CGCGTTATCGGTGTCCAATAAAA 59.938 43.478 0.00 0.00 37.56 1.52
776 781 4.435784 CGCGTTATCGGTGTCCAATAAAAA 60.436 41.667 0.00 0.00 37.56 1.94
848 942 3.804036 AGTCATGTACTCGAGAGGAGAG 58.196 50.000 21.68 4.37 46.23 3.20
849 943 3.452990 AGTCATGTACTCGAGAGGAGAGA 59.547 47.826 21.68 6.78 46.23 3.10
850 944 4.080807 AGTCATGTACTCGAGAGGAGAGAA 60.081 45.833 21.68 0.00 46.23 2.87
851 945 4.272504 GTCATGTACTCGAGAGGAGAGAAG 59.727 50.000 21.68 0.00 46.23 2.85
852 946 3.269538 TGTACTCGAGAGGAGAGAAGG 57.730 52.381 21.68 0.00 46.23 3.46
853 947 2.092861 TGTACTCGAGAGGAGAGAAGGG 60.093 54.545 21.68 0.00 46.23 3.95
854 948 0.257616 ACTCGAGAGGAGAGAAGGGG 59.742 60.000 21.68 0.00 46.23 4.79
855 949 0.467290 CTCGAGAGGAGAGAAGGGGG 60.467 65.000 6.58 0.00 46.23 5.40
856 950 2.131067 CGAGAGGAGAGAAGGGGGC 61.131 68.421 0.00 0.00 0.00 5.80
857 951 1.002274 GAGAGGAGAGAAGGGGGCA 59.998 63.158 0.00 0.00 0.00 5.36
858 952 1.002792 AGAGGAGAGAAGGGGGCAG 59.997 63.158 0.00 0.00 0.00 4.85
859 953 2.690510 AGGAGAGAAGGGGGCAGC 60.691 66.667 0.00 0.00 0.00 5.25
860 954 3.803162 GGAGAGAAGGGGGCAGCC 61.803 72.222 1.26 1.26 0.00 4.85
861 955 2.690510 GAGAGAAGGGGGCAGCCT 60.691 66.667 12.43 0.00 0.00 4.58
862 956 2.690510 AGAGAAGGGGGCAGCCTC 60.691 66.667 12.43 7.24 0.00 4.70
863 957 4.168291 GAGAAGGGGGCAGCCTCG 62.168 72.222 12.43 0.00 0.00 4.63
864 958 4.722535 AGAAGGGGGCAGCCTCGA 62.723 66.667 12.43 0.00 0.00 4.04
865 959 4.168291 GAAGGGGGCAGCCTCGAG 62.168 72.222 12.43 5.13 0.00 4.04
866 960 4.722535 AAGGGGGCAGCCTCGAGA 62.723 66.667 15.71 0.00 0.00 4.04
937 1033 0.036388 GATCAGGTCGTGCTTTCCCA 60.036 55.000 0.00 0.00 0.00 4.37
958 1054 3.980646 TTGTTTCTGGTTCCATCGTTG 57.019 42.857 0.00 0.00 0.00 4.10
994 1094 1.066114 CGACTCTTCGTTGCTCGGAC 61.066 60.000 2.56 0.00 40.61 4.79
995 1095 1.066114 GACTCTTCGTTGCTCGGACG 61.066 60.000 2.56 0.00 41.62 4.79
997 1097 2.430921 CTTCGTTGCTCGGACGCT 60.431 61.111 2.56 0.00 40.16 5.07
1214 1314 2.584418 CGTCGCCTGCATCCTGAG 60.584 66.667 0.00 0.00 0.00 3.35
1378 1478 4.794439 CGCTGCCCGACATCGACA 62.794 66.667 2.09 0.00 40.29 4.35
1385 1485 3.116463 CGACATCGACATCGGGGA 58.884 61.111 11.38 0.00 43.02 4.81
1386 1486 1.299165 CGACATCGACATCGGGGAC 60.299 63.158 11.38 0.00 43.02 4.46
1387 1487 2.679132 CGACATCGACATCGGGGACC 62.679 65.000 11.38 0.00 44.66 4.46
1405 1505 0.389166 CCTCTCGATTAGATGCCGCC 60.389 60.000 0.00 0.00 32.41 6.13
1406 1506 0.730834 CTCTCGATTAGATGCCGCCG 60.731 60.000 0.00 0.00 32.41 6.46
1444 1544 3.914117 TCGTCCGGTCGCACCAAA 61.914 61.111 16.54 0.00 38.47 3.28
1449 1549 1.301874 CCGGTCGCACCAAAGGTTA 60.302 57.895 0.00 0.00 38.47 2.85
1451 1551 0.446222 CGGTCGCACCAAAGGTTATG 59.554 55.000 6.21 0.00 38.47 1.90
1482 1582 0.668706 CTCGCCATCCCGTCATGATC 60.669 60.000 0.00 0.00 0.00 2.92
1628 1731 2.507944 GATCGCCATCCAGCCACT 59.492 61.111 0.00 0.00 0.00 4.00
1639 1742 1.140589 CAGCCACTAGAGGTCTGCG 59.859 63.158 14.23 0.00 0.00 5.18
1643 1746 3.141488 ACTAGAGGTCTGCGCCGG 61.141 66.667 4.18 0.00 0.00 6.13
1644 1747 4.577246 CTAGAGGTCTGCGCCGGC 62.577 72.222 19.07 19.07 40.52 6.13
1678 1784 0.107945 GCAGGACATCGCCTTCTTCT 60.108 55.000 0.00 0.00 35.66 2.85
1695 1801 1.026182 TCTACGGCCGCTTCTTCGTA 61.026 55.000 28.58 6.34 37.10 3.43
1731 1837 0.178941 ACCTCCGGGTCTACACTGTT 60.179 55.000 0.00 0.00 43.38 3.16
1738 1844 1.201880 GGGTCTACACTGTTCTCGACC 59.798 57.143 0.00 0.00 40.04 4.79
1743 1849 0.828022 ACACTGTTCTCGACCAACCA 59.172 50.000 1.01 0.00 0.00 3.67
1748 1866 2.035961 CTGTTCTCGACCAACCAGAAGA 59.964 50.000 1.01 0.00 0.00 2.87
1765 1883 1.880340 GAGGATCTTGGCACTCGCG 60.880 63.158 0.00 0.00 39.92 5.87
1782 1900 1.653115 CGGCGCCGTCTTCTACTAT 59.347 57.895 39.71 0.00 34.35 2.12
1950 2068 3.423154 CACCGCAAGCCCGAGTTC 61.423 66.667 0.00 0.00 0.00 3.01
2324 2442 2.675658 TCTTTGGACAAAAGGGGAGG 57.324 50.000 2.41 0.00 44.69 4.30
2325 2443 1.856920 TCTTTGGACAAAAGGGGAGGT 59.143 47.619 2.41 0.00 44.69 3.85
2326 2444 2.246327 TCTTTGGACAAAAGGGGAGGTT 59.754 45.455 2.41 0.00 44.69 3.50
2327 2445 3.464080 TCTTTGGACAAAAGGGGAGGTTA 59.536 43.478 2.41 0.00 44.69 2.85
2328 2446 4.107311 TCTTTGGACAAAAGGGGAGGTTAT 59.893 41.667 2.41 0.00 44.69 1.89
2329 2447 5.313772 TCTTTGGACAAAAGGGGAGGTTATA 59.686 40.000 2.41 0.00 44.69 0.98
2330 2448 5.806955 TTGGACAAAAGGGGAGGTTATAT 57.193 39.130 0.00 0.00 0.00 0.86
2331 2449 6.911993 TTGGACAAAAGGGGAGGTTATATA 57.088 37.500 0.00 0.00 0.00 0.86
2332 2450 7.474474 TTGGACAAAAGGGGAGGTTATATAT 57.526 36.000 0.00 0.00 0.00 0.86
2333 2451 7.474474 TGGACAAAAGGGGAGGTTATATATT 57.526 36.000 0.00 0.00 0.00 1.28
2334 2452 7.889178 TGGACAAAAGGGGAGGTTATATATTT 58.111 34.615 0.00 0.00 0.00 1.40
2335 2453 9.016243 TGGACAAAAGGGGAGGTTATATATTTA 57.984 33.333 0.00 0.00 0.00 1.40
2513 2631 6.242396 AGCCATCAGATAGACTACGAACTAT 58.758 40.000 0.00 0.00 32.87 2.12
3192 3328 3.345737 GGTGACGAGATTGATGCGA 57.654 52.632 0.00 0.00 0.00 5.10
3242 3378 4.430765 CGTAGCGGTCGGCAACCT 62.431 66.667 5.08 0.00 46.87 3.50
3243 3379 2.047560 GTAGCGGTCGGCAACCTT 60.048 61.111 5.08 0.00 46.87 3.50
3244 3380 2.047655 TAGCGGTCGGCAACCTTG 60.048 61.111 5.08 0.00 46.87 3.61
3258 3394 4.100707 CAACCTTGCATCAGTAATGGTG 57.899 45.455 0.00 0.00 35.77 4.17
3259 3395 2.094675 ACCTTGCATCAGTAATGGTGC 58.905 47.619 21.06 21.06 35.77 5.01
3260 3396 2.093890 CCTTGCATCAGTAATGGTGCA 58.906 47.619 26.02 26.02 44.97 4.57
3261 3397 2.691526 CCTTGCATCAGTAATGGTGCAT 59.308 45.455 29.51 0.00 45.80 3.96
3262 3398 3.243301 CCTTGCATCAGTAATGGTGCATC 60.243 47.826 29.51 2.29 45.80 3.91
3263 3399 2.300433 TGCATCAGTAATGGTGCATCC 58.700 47.619 26.02 0.00 42.13 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 6.040842 ACAAGTCTTTCAGCACATATTGGTTT 59.959 34.615 0.00 0.00 31.87 3.27
175 176 0.320697 ACCTCCGGAAGAAAACCTCG 59.679 55.000 7.17 0.00 0.00 4.63
273 274 1.299648 CGGATGGAAGCAAGGGTGA 59.700 57.895 0.00 0.00 0.00 4.02
299 300 4.615815 ATGCCGCAGAGATCGGGC 62.616 66.667 0.00 7.53 46.51 6.13
324 325 3.677148 GCAACAAGATCGATCTGTGAGGA 60.677 47.826 27.93 0.00 37.19 3.71
394 397 4.366684 CCTTGGTGGGGGCCTGAC 62.367 72.222 0.84 0.00 0.00 3.51
552 557 9.466497 TCTCTAATAAAAGTTACCCGAGAGTTA 57.534 33.333 0.00 0.00 0.00 2.24
553 558 8.358582 TCTCTAATAAAAGTTACCCGAGAGTT 57.641 34.615 0.00 0.00 0.00 3.01
554 559 7.614974 ACTCTCTAATAAAAGTTACCCGAGAGT 59.385 37.037 11.15 11.15 45.95 3.24
555 560 7.998580 ACTCTCTAATAAAAGTTACCCGAGAG 58.001 38.462 0.00 0.00 44.46 3.20
556 561 7.951347 ACTCTCTAATAAAAGTTACCCGAGA 57.049 36.000 0.00 0.00 0.00 4.04
557 562 8.999220 AAACTCTCTAATAAAAGTTACCCGAG 57.001 34.615 0.00 0.00 31.94 4.63
558 563 9.783081 AAAAACTCTCTAATAAAAGTTACCCGA 57.217 29.630 0.00 0.00 31.94 5.14
571 576 8.552034 CGAGTGACAAAAGAAAAACTCTCTAAT 58.448 33.333 0.00 0.00 33.49 1.73
572 577 7.548075 ACGAGTGACAAAAGAAAAACTCTCTAA 59.452 33.333 0.00 0.00 33.49 2.10
573 578 7.010183 CACGAGTGACAAAAGAAAAACTCTCTA 59.990 37.037 0.00 0.00 33.49 2.43
574 579 5.875359 ACGAGTGACAAAAGAAAAACTCTCT 59.125 36.000 0.00 0.00 33.49 3.10
575 580 5.960105 CACGAGTGACAAAAGAAAAACTCTC 59.040 40.000 0.00 0.00 33.49 3.20
576 581 5.673818 GCACGAGTGACAAAAGAAAAACTCT 60.674 40.000 7.50 0.00 33.49 3.24
577 582 4.495828 GCACGAGTGACAAAAGAAAAACTC 59.504 41.667 7.50 0.00 0.00 3.01
578 583 4.083003 TGCACGAGTGACAAAAGAAAAACT 60.083 37.500 7.50 0.00 0.00 2.66
579 584 4.162812 TGCACGAGTGACAAAAGAAAAAC 58.837 39.130 7.50 0.00 0.00 2.43
580 585 4.427096 TGCACGAGTGACAAAAGAAAAA 57.573 36.364 7.50 0.00 0.00 1.94
581 586 4.155099 TCTTGCACGAGTGACAAAAGAAAA 59.845 37.500 7.50 0.00 0.00 2.29
582 587 3.687212 TCTTGCACGAGTGACAAAAGAAA 59.313 39.130 7.50 0.00 0.00 2.52
583 588 3.266636 TCTTGCACGAGTGACAAAAGAA 58.733 40.909 7.50 0.00 0.00 2.52
584 589 2.866156 CTCTTGCACGAGTGACAAAAGA 59.134 45.455 11.91 8.61 0.00 2.52
585 590 2.032549 CCTCTTGCACGAGTGACAAAAG 60.033 50.000 17.96 6.99 0.00 2.27
586 591 1.939934 CCTCTTGCACGAGTGACAAAA 59.060 47.619 17.96 0.00 0.00 2.44
587 592 1.581934 CCTCTTGCACGAGTGACAAA 58.418 50.000 17.96 0.00 0.00 2.83
588 593 0.880278 GCCTCTTGCACGAGTGACAA 60.880 55.000 17.96 9.54 40.77 3.18
589 594 1.300931 GCCTCTTGCACGAGTGACA 60.301 57.895 17.96 2.11 40.77 3.58
590 595 2.029844 GGCCTCTTGCACGAGTGAC 61.030 63.158 17.96 8.78 43.89 3.67
591 596 2.343758 GGCCTCTTGCACGAGTGA 59.656 61.111 17.96 0.00 43.89 3.41
592 597 2.743928 GGGCCTCTTGCACGAGTG 60.744 66.667 17.96 10.92 43.89 3.51
611 616 1.935933 ACCTAATAAAGACGCCAGCG 58.064 50.000 11.05 11.05 46.03 5.18
612 617 4.696899 AAAACCTAATAAAGACGCCAGC 57.303 40.909 0.00 0.00 0.00 4.85
631 636 4.381079 CCCGAACACTTCCAGAAACAAAAA 60.381 41.667 0.00 0.00 0.00 1.94
632 637 3.129638 CCCGAACACTTCCAGAAACAAAA 59.870 43.478 0.00 0.00 0.00 2.44
633 638 2.685897 CCCGAACACTTCCAGAAACAAA 59.314 45.455 0.00 0.00 0.00 2.83
634 639 2.294074 CCCGAACACTTCCAGAAACAA 58.706 47.619 0.00 0.00 0.00 2.83
635 640 1.961793 CCCGAACACTTCCAGAAACA 58.038 50.000 0.00 0.00 0.00 2.83
636 641 0.591659 GCCCGAACACTTCCAGAAAC 59.408 55.000 0.00 0.00 0.00 2.78
637 642 0.472471 AGCCCGAACACTTCCAGAAA 59.528 50.000 0.00 0.00 0.00 2.52
638 643 0.250295 CAGCCCGAACACTTCCAGAA 60.250 55.000 0.00 0.00 0.00 3.02
639 644 1.118965 TCAGCCCGAACACTTCCAGA 61.119 55.000 0.00 0.00 0.00 3.86
640 645 0.671781 CTCAGCCCGAACACTTCCAG 60.672 60.000 0.00 0.00 0.00 3.86
641 646 1.118965 TCTCAGCCCGAACACTTCCA 61.119 55.000 0.00 0.00 0.00 3.53
642 647 0.390472 CTCTCAGCCCGAACACTTCC 60.390 60.000 0.00 0.00 0.00 3.46
643 648 0.603569 TCTCTCAGCCCGAACACTTC 59.396 55.000 0.00 0.00 0.00 3.01
644 649 0.605589 CTCTCTCAGCCCGAACACTT 59.394 55.000 0.00 0.00 0.00 3.16
645 650 1.882989 GCTCTCTCAGCCCGAACACT 61.883 60.000 0.00 0.00 43.17 3.55
646 651 1.446966 GCTCTCTCAGCCCGAACAC 60.447 63.158 0.00 0.00 43.17 3.32
647 652 2.973899 GCTCTCTCAGCCCGAACA 59.026 61.111 0.00 0.00 43.17 3.18
655 660 2.433994 GGGCCAGGAGCTCTCTCAG 61.434 68.421 14.64 4.37 39.74 3.35
656 661 2.364842 GGGCCAGGAGCTCTCTCA 60.365 66.667 14.64 0.00 39.74 3.27
657 662 3.535962 CGGGCCAGGAGCTCTCTC 61.536 72.222 14.64 0.00 41.26 3.20
658 663 3.608759 TTCGGGCCAGGAGCTCTCT 62.609 63.158 14.64 6.28 41.26 3.10
659 664 3.077556 TTCGGGCCAGGAGCTCTC 61.078 66.667 14.64 3.76 41.26 3.20
660 665 3.394836 GTTCGGGCCAGGAGCTCT 61.395 66.667 14.64 0.00 41.26 4.09
661 666 4.821589 CGTTCGGGCCAGGAGCTC 62.822 72.222 4.39 4.71 43.05 4.09
663 668 3.894547 TTTCGTTCGGGCCAGGAGC 62.895 63.158 4.39 2.01 42.60 4.70
664 669 1.078426 ATTTCGTTCGGGCCAGGAG 60.078 57.895 4.39 0.00 0.00 3.69
665 670 1.078708 GATTTCGTTCGGGCCAGGA 60.079 57.895 4.39 0.00 0.00 3.86
666 671 2.461110 CGATTTCGTTCGGGCCAGG 61.461 63.158 4.39 0.00 35.50 4.45
667 672 0.810031 ATCGATTTCGTTCGGGCCAG 60.810 55.000 4.39 0.00 39.56 4.85
668 673 0.808453 GATCGATTTCGTTCGGGCCA 60.808 55.000 4.39 0.00 39.56 5.36
669 674 1.932277 GATCGATTTCGTTCGGGCC 59.068 57.895 0.00 0.00 39.56 5.80
684 689 2.294132 GACAGGGGGAACGACCGATC 62.294 65.000 0.00 0.00 40.11 3.69
685 690 2.284405 ACAGGGGGAACGACCGAT 60.284 61.111 0.00 0.00 40.11 4.18
686 691 2.993264 GACAGGGGGAACGACCGA 60.993 66.667 0.00 0.00 40.11 4.69
687 692 4.078516 GGACAGGGGGAACGACCG 62.079 72.222 0.00 0.00 40.11 4.79
688 693 2.926242 TGGACAGGGGGAACGACC 60.926 66.667 0.00 0.00 38.08 4.79
689 694 2.663196 CTGGACAGGGGGAACGAC 59.337 66.667 0.00 0.00 0.00 4.34
690 695 3.319198 GCTGGACAGGGGGAACGA 61.319 66.667 1.01 0.00 0.00 3.85
691 696 4.760047 CGCTGGACAGGGGGAACG 62.760 72.222 8.36 0.00 37.68 3.95
698 703 3.989698 ATCGTTCGCGCTGGACAGG 62.990 63.158 5.56 0.00 41.05 4.00
699 704 2.094659 AATCGTTCGCGCTGGACAG 61.095 57.895 5.56 0.00 41.05 3.51
700 705 2.048597 AATCGTTCGCGCTGGACA 60.049 55.556 5.56 0.00 41.05 4.02
701 706 2.395690 CAATCGTTCGCGCTGGAC 59.604 61.111 5.56 2.94 41.05 4.02
702 707 2.813474 CCAATCGTTCGCGCTGGA 60.813 61.111 5.56 0.00 42.27 3.86
703 708 2.563086 GAACCAATCGTTCGCGCTGG 62.563 60.000 5.56 6.98 41.51 4.85
704 709 1.225745 GAACCAATCGTTCGCGCTG 60.226 57.895 5.56 0.00 41.51 5.18
705 710 3.165498 GAACCAATCGTTCGCGCT 58.835 55.556 5.56 0.00 41.51 5.92
714 719 1.814169 GAGTCGCCCCGAACCAATC 60.814 63.158 0.00 0.00 37.72 2.67
715 720 2.267961 GAGTCGCCCCGAACCAAT 59.732 61.111 0.00 0.00 37.72 3.16
716 721 4.011517 GGAGTCGCCCCGAACCAA 62.012 66.667 7.05 0.00 37.72 3.67
718 723 4.144703 GAGGAGTCGCCCCGAACC 62.145 72.222 0.00 4.67 37.72 3.62
719 724 4.144703 GGAGGAGTCGCCCCGAAC 62.145 72.222 0.00 0.00 37.72 3.95
730 735 4.821589 GTTCGCGCTGGGGAGGAG 62.822 72.222 5.56 0.00 36.39 3.69
748 753 3.613702 CACCGATAACGCGCCGAC 61.614 66.667 5.73 0.00 38.29 4.79
749 754 4.118995 ACACCGATAACGCGCCGA 62.119 61.111 5.73 0.00 38.29 5.54
750 755 3.613702 GACACCGATAACGCGCCG 61.614 66.667 5.73 4.78 38.29 6.46
751 756 3.259751 GGACACCGATAACGCGCC 61.260 66.667 5.73 0.00 38.29 6.53
752 757 1.426041 ATTGGACACCGATAACGCGC 61.426 55.000 5.73 0.00 38.29 6.86
753 758 1.842720 TATTGGACACCGATAACGCG 58.157 50.000 3.53 3.53 38.29 6.01
754 759 4.603231 TTTTATTGGACACCGATAACGC 57.397 40.909 9.26 0.00 38.99 4.84
755 760 5.791480 GTGTTTTTATTGGACACCGATAACG 59.209 40.000 9.26 0.00 38.99 3.18
756 761 5.791480 CGTGTTTTTATTGGACACCGATAAC 59.209 40.000 9.26 3.61 38.99 1.89
757 762 5.469421 ACGTGTTTTTATTGGACACCGATAA 59.531 36.000 6.42 6.42 40.31 1.75
758 763 4.996122 ACGTGTTTTTATTGGACACCGATA 59.004 37.500 0.00 0.00 40.31 2.92
759 764 3.816523 ACGTGTTTTTATTGGACACCGAT 59.183 39.130 0.00 0.00 40.31 4.18
760 765 3.204526 ACGTGTTTTTATTGGACACCGA 58.795 40.909 0.00 0.00 40.31 4.69
761 766 3.612472 ACGTGTTTTTATTGGACACCG 57.388 42.857 0.00 0.00 40.31 4.94
762 767 4.922719 TGAACGTGTTTTTATTGGACACC 58.077 39.130 0.00 0.00 40.31 4.16
763 768 5.575019 ACTGAACGTGTTTTTATTGGACAC 58.425 37.500 0.00 0.00 40.09 3.67
764 769 5.821516 ACTGAACGTGTTTTTATTGGACA 57.178 34.783 0.00 0.00 0.00 4.02
765 770 6.528774 ACAAACTGAACGTGTTTTTATTGGAC 59.471 34.615 0.13 0.00 35.71 4.02
766 771 6.528423 CACAAACTGAACGTGTTTTTATTGGA 59.472 34.615 0.13 0.00 35.71 3.53
767 772 6.691442 CACAAACTGAACGTGTTTTTATTGG 58.309 36.000 0.13 0.00 35.71 3.16
768 773 6.175087 GCACAAACTGAACGTGTTTTTATTG 58.825 36.000 0.13 0.00 35.71 1.90
769 774 5.289917 GGCACAAACTGAACGTGTTTTTATT 59.710 36.000 0.13 0.00 35.71 1.40
770 775 4.801516 GGCACAAACTGAACGTGTTTTTAT 59.198 37.500 0.13 0.00 35.71 1.40
771 776 4.167268 GGCACAAACTGAACGTGTTTTTA 58.833 39.130 0.13 0.00 35.71 1.52
772 777 2.990514 GGCACAAACTGAACGTGTTTTT 59.009 40.909 0.13 0.00 35.71 1.94
773 778 2.601804 GGCACAAACTGAACGTGTTTT 58.398 42.857 0.13 0.00 35.71 2.43
774 779 1.135228 GGGCACAAACTGAACGTGTTT 60.135 47.619 0.00 0.00 38.04 2.83
775 780 0.454196 GGGCACAAACTGAACGTGTT 59.546 50.000 0.00 0.00 33.13 3.32
776 781 1.711060 CGGGCACAAACTGAACGTGT 61.711 55.000 0.00 0.00 33.13 4.49
848 942 4.168291 CTCGAGGCTGCCCCCTTC 62.168 72.222 16.57 5.24 34.69 3.46
849 943 4.722535 TCTCGAGGCTGCCCCCTT 62.723 66.667 16.57 0.00 34.69 3.95
850 944 4.722535 TTCTCGAGGCTGCCCCCT 62.723 66.667 16.57 0.00 38.12 4.79
851 945 4.475135 GTTCTCGAGGCTGCCCCC 62.475 72.222 16.57 6.84 0.00 5.40
852 946 4.821589 CGTTCTCGAGGCTGCCCC 62.822 72.222 16.57 1.39 39.71 5.80
853 947 3.760035 TCGTTCTCGAGGCTGCCC 61.760 66.667 16.57 6.06 41.35 5.36
880 974 2.432874 ACCGGAAACAAAGGGAAAAAGG 59.567 45.455 9.46 0.00 0.00 3.11
924 1018 2.293399 AGAAACAATGGGAAAGCACGAC 59.707 45.455 0.00 0.00 0.00 4.34
928 1022 2.676748 ACCAGAAACAATGGGAAAGCA 58.323 42.857 0.00 0.00 42.48 3.91
937 1033 4.503741 CAACGATGGAACCAGAAACAAT 57.496 40.909 0.00 0.00 0.00 2.71
958 1054 0.387929 TCGACGATGTAGGATTGGCC 59.612 55.000 0.00 0.00 0.00 5.36
1309 1409 3.376918 GTGCCCCTCTTTGCTGCC 61.377 66.667 0.00 0.00 0.00 4.85
1378 1478 1.424302 TCTAATCGAGAGGTCCCCGAT 59.576 52.381 5.81 5.81 43.81 4.18
1384 1484 1.667467 GCGGCATCTAATCGAGAGGTC 60.667 57.143 0.00 0.00 38.28 3.85
1385 1485 0.315568 GCGGCATCTAATCGAGAGGT 59.684 55.000 0.00 0.00 38.28 3.85
1386 1486 0.389166 GGCGGCATCTAATCGAGAGG 60.389 60.000 3.07 0.00 37.70 3.69
1387 1487 0.730834 CGGCGGCATCTAATCGAGAG 60.731 60.000 10.53 0.00 37.70 3.20
1394 1494 3.857038 GGACCCGGCGGCATCTAA 61.857 66.667 23.20 0.00 0.00 2.10
1433 1533 1.530323 ACATAACCTTTGGTGCGACC 58.470 50.000 0.00 0.00 35.34 4.79
1438 1538 2.230266 CCCGGAAACATAACCTTTGGTG 59.770 50.000 0.73 0.00 35.34 4.17
1442 1542 1.552578 GCCCCGGAAACATAACCTTT 58.447 50.000 0.73 0.00 0.00 3.11
1444 1544 1.305287 GGCCCCGGAAACATAACCT 59.695 57.895 0.73 0.00 0.00 3.50
1449 1549 4.109675 CGAGGGCCCCGGAAACAT 62.110 66.667 21.43 0.00 0.00 2.71
1580 1683 1.213013 CGCCAGAAGCAGACGTAGT 59.787 57.895 0.00 0.00 45.17 2.73
1673 1779 0.172803 GAAGAAGCGGCCGTAGAAGA 59.827 55.000 28.70 0.00 0.00 2.87
1678 1784 1.137404 GTACGAAGAAGCGGCCGTA 59.863 57.895 28.70 5.24 36.58 4.02
1695 1801 1.371558 GTTCTCGCCCTTGGTCAGT 59.628 57.895 0.00 0.00 0.00 3.41
1721 1827 2.295349 GGTTGGTCGAGAACAGTGTAGA 59.705 50.000 0.00 0.00 0.00 2.59
1731 1837 1.203013 TCCTCTTCTGGTTGGTCGAGA 60.203 52.381 0.00 0.00 0.00 4.04
1738 1844 2.290514 TGCCAAGATCCTCTTCTGGTTG 60.291 50.000 0.00 0.00 33.78 3.77
1743 1849 1.480137 CGAGTGCCAAGATCCTCTTCT 59.520 52.381 0.00 0.00 33.78 2.85
1748 1866 2.185350 CGCGAGTGCCAAGATCCT 59.815 61.111 0.00 0.00 38.08 3.24
1765 1883 1.878734 AGTATAGTAGAAGACGGCGCC 59.121 52.381 19.07 19.07 0.00 6.53
1770 1888 2.350580 GCGGCCAGTATAGTAGAAGACG 60.351 54.545 2.24 0.00 0.00 4.18
1771 1889 2.350580 CGCGGCCAGTATAGTAGAAGAC 60.351 54.545 2.24 0.00 0.00 3.01
1772 1890 1.878088 CGCGGCCAGTATAGTAGAAGA 59.122 52.381 2.24 0.00 0.00 2.87
1801 1919 2.183555 GGGTTCTGCGTAGTCCCG 59.816 66.667 16.65 0.00 32.78 5.14
1802 1920 2.582978 GGGGTTCTGCGTAGTCCC 59.417 66.667 20.82 20.82 37.94 4.46
1937 2055 0.459411 GAGAGAGAACTCGGGCTTGC 60.459 60.000 0.00 0.00 46.64 4.01
1950 2068 4.492955 GCAGTCCAAGCGAGAGAG 57.507 61.111 0.00 0.00 0.00 3.20
2339 2457 7.879677 GCCACCCGGTAGTTATTACTAATAAAT 59.120 37.037 0.00 6.71 38.55 1.40
2340 2458 7.147585 TGCCACCCGGTAGTTATTACTAATAAA 60.148 37.037 0.00 0.00 38.55 1.40
2454 2572 5.774690 AGTTGGGCATATGTCTTTTCTCAAA 59.225 36.000 7.36 0.00 0.00 2.69
2455 2573 5.324409 AGTTGGGCATATGTCTTTTCTCAA 58.676 37.500 7.36 0.00 0.00 3.02
2456 2574 4.922206 AGTTGGGCATATGTCTTTTCTCA 58.078 39.130 7.36 0.00 0.00 3.27
2590 2708 3.612472 TTCGGTTTGCGAACTTTTAGG 57.388 42.857 16.37 0.60 36.03 2.69
2600 2718 6.624710 TGAATTTGAATAATTCGGTTTGCG 57.375 33.333 0.00 0.00 38.99 4.85
3192 3328 0.251354 AGCTCCATCGCTGATGTTGT 59.749 50.000 14.50 0.00 38.28 3.32
3238 3374 2.493278 GCACCATTACTGATGCAAGGTT 59.507 45.455 0.00 0.00 38.00 3.50
3244 3380 2.300433 TGGATGCACCATTACTGATGC 58.700 47.619 4.16 0.00 44.64 3.91


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

AutoCloner maintained by Alex Coulton.