Multiple sequence alignment - TraesCS1B01G303800

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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 TraesCS1B01G303800 chr1B 100.000 3979 0 0 1 3979 526161138 526165116 0.000000e+00 7348.0
1 TraesCS1B01G303800 chr1B 89.091 605 54 11 2 599 133187271 133187870 0.000000e+00 741.0
2 TraesCS1B01G303800 chr1B 87.398 611 64 12 1 606 633860739 633860137 0.000000e+00 689.0
3 TraesCS1B01G303800 chr1B 87.113 613 65 14 1 607 416829947 416830551 0.000000e+00 682.0
4 TraesCS1B01G303800 chr1B 81.373 816 124 18 996 1807 525898577 525899368 1.210000e-179 640.0
5 TraesCS1B01G303800 chr1B 74.658 1243 235 55 1009 2223 526195465 526196655 1.000000e-130 477.0
6 TraesCS1B01G303800 chr1B 77.979 772 124 29 1040 1800 526190719 526191455 3.650000e-120 442.0
7 TraesCS1B01G303800 chr1B 76.909 563 86 25 1528 2083 526251971 526252496 3.030000e-71 279.0
8 TraesCS1B01G303800 chr1B 71.805 266 63 8 1029 1285 526251487 526251749 9.230000e-07 65.8
9 TraesCS1B01G303800 chr1D 91.368 2711 141 35 687 3375 396194990 396192351 0.000000e+00 3624.0
10 TraesCS1B01G303800 chr1D 84.307 599 48 29 3401 3979 396192286 396191714 9.720000e-151 544.0
11 TraesCS1B01G303800 chr1D 79.167 768 122 22 1040 1803 396006850 396006117 7.680000e-137 497.0
12 TraesCS1B01G303800 chr1D 77.607 585 91 31 1528 2083 395989876 395989303 6.420000e-83 318.0
13 TraesCS1B01G303800 chr1A 93.296 1984 111 12 685 2655 489263922 489265896 0.000000e+00 2907.0
14 TraesCS1B01G303800 chr1A 88.571 735 37 18 2665 3375 489265971 489266682 0.000000e+00 848.0
15 TraesCS1B01G303800 chr1A 77.140 1063 177 41 758 1804 489240031 489241043 1.250000e-154 556.0
16 TraesCS1B01G303800 chr1A 88.535 471 28 12 3518 3979 489272149 489272602 7.520000e-152 547.0
17 TraesCS1B01G303800 chr1A 79.112 766 120 24 1040 1800 489273769 489274499 3.570000e-135 492.0
18 TraesCS1B01G303800 chr1A 78.571 392 67 17 1702 2083 489282872 489283256 3.970000e-60 243.0
19 TraesCS1B01G303800 chr1A 86.429 140 19 0 1849 1988 489241130 489241269 1.910000e-33 154.0
20 TraesCS1B01G303800 chr3B 88.072 612 61 11 1 607 493160752 493160148 0.000000e+00 715.0
21 TraesCS1B01G303800 chr6B 87.889 611 57 16 3 607 57320029 57319430 0.000000e+00 702.0
22 TraesCS1B01G303800 chr6B 87.154 615 59 17 1 607 702186206 702185604 0.000000e+00 680.0
23 TraesCS1B01G303800 chr5B 87.200 625 60 15 1 617 662533212 662532600 0.000000e+00 693.0
24 TraesCS1B01G303800 chr5B 75.078 321 56 17 1495 1803 48725034 48725342 1.160000e-25 128.0
25 TraesCS1B01G303800 chr4A 87.217 618 60 16 1 607 695793697 695794306 0.000000e+00 686.0
26 TraesCS1B01G303800 chr2B 87.398 611 60 14 1 607 170798075 170798672 0.000000e+00 686.0


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 TraesCS1B01G303800 chr1B 526161138 526165116 3978 False 7348.0 7348 100.0000 1 3979 1 chr1B.!!$F4 3978
1 TraesCS1B01G303800 chr1B 133187271 133187870 599 False 741.0 741 89.0910 2 599 1 chr1B.!!$F1 597
2 TraesCS1B01G303800 chr1B 633860137 633860739 602 True 689.0 689 87.3980 1 606 1 chr1B.!!$R1 605
3 TraesCS1B01G303800 chr1B 416829947 416830551 604 False 682.0 682 87.1130 1 607 1 chr1B.!!$F2 606
4 TraesCS1B01G303800 chr1B 525898577 525899368 791 False 640.0 640 81.3730 996 1807 1 chr1B.!!$F3 811
5 TraesCS1B01G303800 chr1B 526195465 526196655 1190 False 477.0 477 74.6580 1009 2223 1 chr1B.!!$F6 1214
6 TraesCS1B01G303800 chr1B 526190719 526191455 736 False 442.0 442 77.9790 1040 1800 1 chr1B.!!$F5 760
7 TraesCS1B01G303800 chr1D 396191714 396194990 3276 True 2084.0 3624 87.8375 687 3979 2 chr1D.!!$R3 3292
8 TraesCS1B01G303800 chr1D 396006117 396006850 733 True 497.0 497 79.1670 1040 1803 1 chr1D.!!$R2 763
9 TraesCS1B01G303800 chr1D 395989303 395989876 573 True 318.0 318 77.6070 1528 2083 1 chr1D.!!$R1 555
10 TraesCS1B01G303800 chr1A 489263922 489266682 2760 False 1877.5 2907 90.9335 685 3375 2 chr1A.!!$F3 2690
11 TraesCS1B01G303800 chr1A 489272149 489274499 2350 False 519.5 547 83.8235 1040 3979 2 chr1A.!!$F4 2939
12 TraesCS1B01G303800 chr1A 489240031 489241269 1238 False 355.0 556 81.7845 758 1988 2 chr1A.!!$F2 1230
13 TraesCS1B01G303800 chr3B 493160148 493160752 604 True 715.0 715 88.0720 1 607 1 chr3B.!!$R1 606
14 TraesCS1B01G303800 chr6B 57319430 57320029 599 True 702.0 702 87.8890 3 607 1 chr6B.!!$R1 604
15 TraesCS1B01G303800 chr6B 702185604 702186206 602 True 680.0 680 87.1540 1 607 1 chr6B.!!$R2 606
16 TraesCS1B01G303800 chr5B 662532600 662533212 612 True 693.0 693 87.2000 1 617 1 chr5B.!!$R1 616
17 TraesCS1B01G303800 chr4A 695793697 695794306 609 False 686.0 686 87.2170 1 607 1 chr4A.!!$F1 606
18 TraesCS1B01G303800 chr2B 170798075 170798672 597 False 686.0 686 87.3980 1 607 1 chr2B.!!$F1 606

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
722 752 0.604243 CGGGAAAATGGTGACGTCCA 60.604 55.000 14.12 5.66 42.01 4.02 F
784 814 1.003355 AACTCGGTCCATGCACCAG 60.003 57.895 6.62 5.25 36.01 4.00 F
901 932 1.286260 GCTCCCTGGTATCTACGCG 59.714 63.158 3.53 3.53 0.00 6.01 F
1942 2593 1.581934 CTCCTTTGTGCTCGACAACA 58.418 50.000 0.00 0.00 44.53 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 2473 0.108804 CGGTACTCACGCCAAGACAT 60.109 55.0 0.00 0.0 0.00 3.06 R
2172 2829 0.321653 ACGGAGGAAGAACACATGGC 60.322 55.0 0.00 0.0 0.00 4.40 R
2272 2934 0.606401 ATGACCCACAAAGCACCTCG 60.606 55.0 0.00 0.0 0.00 4.63 R
3158 3902 0.169230 TGTGCACGACGTTTGCTTTT 59.831 45.0 20.03 0.0 40.86 2.27 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
21 22 0.827507 AGGCACGGTTTTGCTTCCAT 60.828 50.000 0.00 0.00 42.56 3.41
293 308 3.936203 ACGGGCGTGCCTCTTTCA 61.936 61.111 11.25 0.00 36.10 2.69
459 483 1.529438 TCAAGATTTGAACGCACGGTC 59.471 47.619 0.05 0.05 36.59 4.79
498 522 7.213151 CGTTTTGAATAAACGGATCTACGAAAC 59.787 37.037 13.31 0.00 46.39 2.78
502 529 8.085720 TGAATAAACGGATCTACGAAACAAAA 57.914 30.769 0.00 0.00 37.61 2.44
537 565 4.365287 CGACAAATGGCGCACATC 57.635 55.556 10.83 0.00 40.91 3.06
578 606 4.559862 ACCTAAGGAAGTTGGAGTGATG 57.440 45.455 0.00 0.00 0.00 3.07
593 622 4.367450 GAGTGATGTCTGCAAGGAGTATC 58.633 47.826 0.00 0.00 0.00 2.24
613 642 9.546909 GAGTATCCATTAATTAATGAATGCGTG 57.453 33.333 31.05 16.91 44.40 5.34
614 643 8.023128 AGTATCCATTAATTAATGAATGCGTGC 58.977 33.333 31.05 16.44 44.40 5.34
616 645 7.503521 TCCATTAATTAATGAATGCGTGCTA 57.496 32.000 31.05 7.71 44.40 3.49
617 646 8.109705 TCCATTAATTAATGAATGCGTGCTAT 57.890 30.769 31.05 0.00 44.40 2.97
618 647 8.575589 TCCATTAATTAATGAATGCGTGCTATT 58.424 29.630 31.05 0.00 44.40 1.73
619 648 9.195411 CCATTAATTAATGAATGCGTGCTATTT 57.805 29.630 31.05 0.00 44.40 1.40
622 651 5.947503 TTAATGAATGCGTGCTATTTTGC 57.052 34.783 0.00 0.00 0.00 3.68
625 654 3.911868 TGAATGCGTGCTATTTTGCTTT 58.088 36.364 0.00 0.00 0.00 3.51
626 655 3.674281 TGAATGCGTGCTATTTTGCTTTG 59.326 39.130 0.00 0.00 0.00 2.77
627 656 1.417372 TGCGTGCTATTTTGCTTTGC 58.583 45.000 0.00 0.00 0.00 3.68
628 657 1.000385 TGCGTGCTATTTTGCTTTGCT 60.000 42.857 0.00 0.00 0.00 3.91
629 658 2.227626 TGCGTGCTATTTTGCTTTGCTA 59.772 40.909 0.00 0.00 0.00 3.49
630 659 2.848302 GCGTGCTATTTTGCTTTGCTAG 59.152 45.455 0.00 0.00 0.00 3.42
631 660 3.670627 GCGTGCTATTTTGCTTTGCTAGT 60.671 43.478 0.00 0.00 0.00 2.57
634 663 5.678483 CGTGCTATTTTGCTTTGCTAGTATG 59.322 40.000 0.00 0.00 0.00 2.39
636 665 6.909357 GTGCTATTTTGCTTTGCTAGTATGAG 59.091 38.462 0.00 0.00 0.00 2.90
637 666 6.599244 TGCTATTTTGCTTTGCTAGTATGAGT 59.401 34.615 0.00 0.00 0.00 3.41
638 667 7.121168 TGCTATTTTGCTTTGCTAGTATGAGTT 59.879 33.333 0.00 0.00 0.00 3.01
639 668 8.612619 GCTATTTTGCTTTGCTAGTATGAGTTA 58.387 33.333 0.00 0.00 0.00 2.24
643 672 9.677567 TTTTGCTTTGCTAGTATGAGTTAAAAG 57.322 29.630 0.00 0.00 0.00 2.27
644 673 6.842163 TGCTTTGCTAGTATGAGTTAAAAGC 58.158 36.000 9.27 9.27 0.00 3.51
646 675 6.678164 GCTTTGCTAGTATGAGTTAAAAGCCC 60.678 42.308 5.69 0.00 0.00 5.19
647 676 5.429681 TGCTAGTATGAGTTAAAAGCCCA 57.570 39.130 0.00 0.00 0.00 5.36
648 677 5.428253 TGCTAGTATGAGTTAAAAGCCCAG 58.572 41.667 0.00 0.00 0.00 4.45
649 678 4.273724 GCTAGTATGAGTTAAAAGCCCAGC 59.726 45.833 0.00 0.00 0.00 4.85
650 679 3.621558 AGTATGAGTTAAAAGCCCAGCC 58.378 45.455 0.00 0.00 0.00 4.85
651 680 2.603075 ATGAGTTAAAAGCCCAGCCA 57.397 45.000 0.00 0.00 0.00 4.75
652 681 2.603075 TGAGTTAAAAGCCCAGCCAT 57.397 45.000 0.00 0.00 0.00 4.40
654 683 2.041620 TGAGTTAAAAGCCCAGCCATCT 59.958 45.455 0.00 0.00 0.00 2.90
655 684 2.685388 GAGTTAAAAGCCCAGCCATCTC 59.315 50.000 0.00 0.00 0.00 2.75
657 686 2.424956 GTTAAAAGCCCAGCCATCTCAG 59.575 50.000 0.00 0.00 0.00 3.35
658 687 0.700564 AAAAGCCCAGCCATCTCAGA 59.299 50.000 0.00 0.00 0.00 3.27
659 688 0.700564 AAAGCCCAGCCATCTCAGAA 59.299 50.000 0.00 0.00 0.00 3.02
660 689 0.700564 AAGCCCAGCCATCTCAGAAA 59.299 50.000 0.00 0.00 0.00 2.52
661 690 0.700564 AGCCCAGCCATCTCAGAAAA 59.299 50.000 0.00 0.00 0.00 2.29
662 691 1.287146 AGCCCAGCCATCTCAGAAAAT 59.713 47.619 0.00 0.00 0.00 1.82
663 692 2.511218 AGCCCAGCCATCTCAGAAAATA 59.489 45.455 0.00 0.00 0.00 1.40
664 693 3.053395 AGCCCAGCCATCTCAGAAAATAA 60.053 43.478 0.00 0.00 0.00 1.40
665 694 3.701040 GCCCAGCCATCTCAGAAAATAAA 59.299 43.478 0.00 0.00 0.00 1.40
666 695 4.202090 GCCCAGCCATCTCAGAAAATAAAG 60.202 45.833 0.00 0.00 0.00 1.85
669 698 6.603201 CCCAGCCATCTCAGAAAATAAAGTTA 59.397 38.462 0.00 0.00 0.00 2.24
670 699 7.415653 CCCAGCCATCTCAGAAAATAAAGTTAC 60.416 40.741 0.00 0.00 0.00 2.50
671 700 7.182761 CAGCCATCTCAGAAAATAAAGTTACG 58.817 38.462 0.00 0.00 0.00 3.18
673 702 7.278868 AGCCATCTCAGAAAATAAAGTTACGAG 59.721 37.037 0.00 0.00 0.00 4.18
674 703 7.466050 GCCATCTCAGAAAATAAAGTTACGAGG 60.466 40.741 0.00 0.00 0.00 4.63
677 706 4.939439 TCAGAAAATAAAGTTACGAGGCCC 59.061 41.667 0.00 0.00 0.00 5.80
678 707 4.698304 CAGAAAATAAAGTTACGAGGCCCA 59.302 41.667 0.00 0.00 0.00 5.36
680 709 2.327200 ATAAAGTTACGAGGCCCAGC 57.673 50.000 0.00 0.00 0.00 4.85
682 711 0.605589 AAAGTTACGAGGCCCAGCAC 60.606 55.000 0.00 0.00 0.00 4.40
683 712 2.436115 GTTACGAGGCCCAGCACC 60.436 66.667 0.00 0.00 0.00 5.01
722 752 0.604243 CGGGAAAATGGTGACGTCCA 60.604 55.000 14.12 5.66 42.01 4.02
745 775 2.177531 CAGCCAGTTGTGCGATGC 59.822 61.111 0.00 0.00 0.00 3.91
784 814 1.003355 AACTCGGTCCATGCACCAG 60.003 57.895 6.62 5.25 36.01 4.00
785 815 2.124983 CTCGGTCCATGCACCAGG 60.125 66.667 6.62 0.00 36.01 4.45
901 932 1.286260 GCTCCCTGGTATCTACGCG 59.714 63.158 3.53 3.53 0.00 6.01
1378 1963 1.597027 CAAACCGACGCCCTCAAGT 60.597 57.895 0.00 0.00 0.00 3.16
1748 2357 4.143333 CTCCGCCGACCCGTTCAT 62.143 66.667 0.00 0.00 0.00 2.57
1749 2358 3.659089 CTCCGCCGACCCGTTCATT 62.659 63.158 0.00 0.00 0.00 2.57
1942 2593 1.581934 CTCCTTTGTGCTCGACAACA 58.418 50.000 0.00 0.00 44.53 3.33
1959 2613 3.965258 AATGGCACCGGCTGGACA 61.965 61.111 21.41 14.51 40.87 4.02
1995 2649 2.438075 CTCAGCAAGCTCTGGGCC 60.438 66.667 0.00 0.00 43.05 5.80
2159 2816 4.963318 TTGGGAGCTATCTGTATGGAAG 57.037 45.455 0.00 0.00 0.00 3.46
2264 2926 8.736244 TCAGTTATACTTTCATTTTTAGGTGCC 58.264 33.333 0.00 0.00 0.00 5.01
2272 2934 3.704061 TCATTTTTAGGTGCCTAATGCCC 59.296 43.478 11.08 0.00 38.20 5.36
2394 3063 5.588958 TTGTCTCATGACCAGATGACTAG 57.411 43.478 10.71 0.00 42.28 2.57
2400 3069 7.437862 GTCTCATGACCAGATGACTAGAAATTC 59.562 40.741 0.00 0.00 37.24 2.17
2461 3132 3.006752 CCATGTGTTTGGTAGCAATTGGT 59.993 43.478 15.47 15.47 31.74 3.67
2483 3154 5.521735 GGTATTGCAAGGCTCATATAGATCG 59.478 44.000 4.94 0.00 0.00 3.69
2533 3205 2.485814 GTCATTCTTCCTGTTGTCCTGC 59.514 50.000 0.00 0.00 0.00 4.85
2550 3222 5.123820 TGTCCTGCTCATAAAGAATTTTCCG 59.876 40.000 0.00 0.00 40.09 4.30
2552 3224 5.710099 TCCTGCTCATAAAGAATTTTCCGTT 59.290 36.000 0.00 0.00 40.09 4.44
2571 3243 6.651755 CCGTTGAACATATTTACGGTAGTT 57.348 37.500 0.00 0.00 44.90 2.24
2635 3307 4.261155 GCTTGCTTTCATGTTACACTGTGA 60.261 41.667 15.86 0.00 0.00 3.58
2643 3315 5.654497 TCATGTTACACTGTGATGCTCTAG 58.346 41.667 15.86 0.00 0.00 2.43
2775 3512 5.411977 CACTGCTGAATTCTTGAGAATCTGT 59.588 40.000 7.05 2.85 43.41 3.41
2781 3518 8.174422 GCTGAATTCTTGAGAATCTGTTCTAAC 58.826 37.037 7.05 0.00 44.57 2.34
2787 3524 8.190326 TCTTGAGAATCTGTTCTAACTACCAA 57.810 34.615 0.00 0.00 44.57 3.67
2788 3525 8.647796 TCTTGAGAATCTGTTCTAACTACCAAA 58.352 33.333 0.00 0.00 44.57 3.28
2789 3526 8.833231 TTGAGAATCTGTTCTAACTACCAAAG 57.167 34.615 0.00 0.00 44.57 2.77
2985 3725 4.584325 GCTCAGACATCCAGTAGAAGAGAT 59.416 45.833 0.00 0.00 0.00 2.75
2986 3726 5.507817 GCTCAGACATCCAGTAGAAGAGATG 60.508 48.000 0.00 0.00 41.50 2.90
2987 3727 5.760131 TCAGACATCCAGTAGAAGAGATGA 58.240 41.667 5.89 0.00 38.72 2.92
2988 3728 6.190587 TCAGACATCCAGTAGAAGAGATGAA 58.809 40.000 5.89 0.00 38.72 2.57
2989 3729 6.320926 TCAGACATCCAGTAGAAGAGATGAAG 59.679 42.308 5.89 0.00 38.72 3.02
2990 3730 5.598005 AGACATCCAGTAGAAGAGATGAAGG 59.402 44.000 5.89 0.00 38.72 3.46
2991 3731 5.276440 ACATCCAGTAGAAGAGATGAAGGT 58.724 41.667 5.89 0.00 38.72 3.50
3048 3790 5.865013 TCGTCATTTCGTTTTAGCTGATACA 59.135 36.000 0.00 0.00 0.00 2.29
3049 3791 5.952064 CGTCATTTCGTTTTAGCTGATACAC 59.048 40.000 0.00 0.00 0.00 2.90
3148 3892 4.257731 TCTTACGCCATTCATGCAGTTTA 58.742 39.130 0.00 0.00 0.00 2.01
3149 3893 4.881273 TCTTACGCCATTCATGCAGTTTAT 59.119 37.500 0.00 0.00 0.00 1.40
3158 3902 7.040478 GCCATTCATGCAGTTTATTATGGACTA 60.040 37.037 12.24 0.00 34.58 2.59
3256 4000 5.162637 ACATCTGGCTATCCCTAATACCAA 58.837 41.667 0.00 0.00 0.00 3.67
3273 4017 3.268013 CCAATTTCTCGTTGGTGTGTC 57.732 47.619 0.00 0.00 40.94 3.67
3274 4018 2.616376 CCAATTTCTCGTTGGTGTGTCA 59.384 45.455 0.00 0.00 40.94 3.58
3275 4019 3.066064 CCAATTTCTCGTTGGTGTGTCAA 59.934 43.478 0.00 0.00 40.94 3.18
3277 4021 3.961477 TTTCTCGTTGGTGTGTCAATG 57.039 42.857 0.00 0.00 35.57 2.82
3278 4022 1.225855 TCTCGTTGGTGTGTCAATGC 58.774 50.000 0.00 0.00 34.58 3.56
3279 4023 0.943673 CTCGTTGGTGTGTCAATGCA 59.056 50.000 0.00 0.00 34.58 3.96
3280 4024 1.333308 CTCGTTGGTGTGTCAATGCAA 59.667 47.619 0.00 0.00 34.58 4.08
3281 4025 1.064803 TCGTTGGTGTGTCAATGCAAC 59.935 47.619 0.00 0.00 34.58 4.17
3282 4026 1.065401 CGTTGGTGTGTCAATGCAACT 59.935 47.619 0.00 0.00 0.00 3.16
3283 4027 2.289274 CGTTGGTGTGTCAATGCAACTA 59.711 45.455 0.00 0.00 0.00 2.24
3286 4030 2.877786 TGGTGTGTCAATGCAACTAGTG 59.122 45.455 0.00 0.00 0.00 2.74
3287 4031 3.138304 GGTGTGTCAATGCAACTAGTGA 58.862 45.455 0.00 0.00 0.00 3.41
3288 4032 3.753272 GGTGTGTCAATGCAACTAGTGAT 59.247 43.478 0.00 0.00 0.00 3.06
3289 4033 4.935205 GGTGTGTCAATGCAACTAGTGATA 59.065 41.667 0.00 0.00 0.00 2.15
3290 4034 5.586243 GGTGTGTCAATGCAACTAGTGATAT 59.414 40.000 0.00 0.00 0.00 1.63
3292 4036 7.362056 GGTGTGTCAATGCAACTAGTGATATTT 60.362 37.037 0.00 0.00 0.00 1.40
3293 4037 7.482743 GTGTGTCAATGCAACTAGTGATATTTG 59.517 37.037 0.00 0.00 0.00 2.32
3294 4038 6.470235 GTGTCAATGCAACTAGTGATATTTGC 59.530 38.462 7.83 7.83 43.80 3.68
3295 4039 6.375174 TGTCAATGCAACTAGTGATATTTGCT 59.625 34.615 14.31 0.54 43.86 3.91
3296 4040 6.690098 GTCAATGCAACTAGTGATATTTGCTG 59.310 38.462 14.31 7.06 43.86 4.41
3297 4041 5.762825 ATGCAACTAGTGATATTTGCTGG 57.237 39.130 14.31 0.00 43.86 4.85
3298 4042 3.378112 TGCAACTAGTGATATTTGCTGGC 59.622 43.478 14.31 0.00 43.86 4.85
3299 4043 3.378112 GCAACTAGTGATATTTGCTGGCA 59.622 43.478 7.56 0.00 40.97 4.92
3300 4044 4.142403 GCAACTAGTGATATTTGCTGGCAA 60.142 41.667 7.56 3.72 40.97 4.52
3306 4050 7.066284 ACTAGTGATATTTGCTGGCAAAACTAG 59.934 37.037 30.69 30.69 46.22 2.57
3307 4051 7.280876 CTAGTGATATTTGCTGGCAAAACTAGA 59.719 37.037 29.86 15.59 45.17 2.43
3311 4055 3.347958 TTGCTGGCAAAACTAGAAACG 57.652 42.857 5.47 0.00 32.44 3.60
3312 4056 2.294074 TGCTGGCAAAACTAGAAACGT 58.706 42.857 0.00 0.00 0.00 3.99
3317 4095 5.412526 TGGCAAAACTAGAAACGTACTTG 57.587 39.130 0.00 0.00 0.00 3.16
3375 4156 6.462552 TCTTCCATTCATTTTTGTGTGTGA 57.537 33.333 0.00 0.00 0.00 3.58
3377 4158 5.199024 TCCATTCATTTTTGTGTGTGAGG 57.801 39.130 0.00 0.00 0.00 3.86
3378 4159 4.039004 TCCATTCATTTTTGTGTGTGAGGG 59.961 41.667 0.00 0.00 0.00 4.30
3379 4160 3.451141 TTCATTTTTGTGTGTGAGGGC 57.549 42.857 0.00 0.00 0.00 5.19
3399 4204 1.973281 GCAGCAGCTTGCCAGGTTA 60.973 57.895 0.00 0.00 46.52 2.85
3409 4229 1.419381 TGCCAGGTTACTGTGTCAGA 58.581 50.000 3.70 0.00 43.36 3.27
3414 4234 4.641396 CCAGGTTACTGTGTCAGAATGAA 58.359 43.478 3.70 0.00 45.46 2.57
3441 4261 2.342659 CATCCCTCCATCCAGGTGTAT 58.657 52.381 0.00 0.00 39.02 2.29
3449 4269 5.353394 TCCATCCAGGTGTATTAGTGTTC 57.647 43.478 0.00 0.00 39.02 3.18
3456 4276 4.625742 CAGGTGTATTAGTGTTCCTGAACG 59.374 45.833 5.62 0.00 43.28 3.95
3457 4277 4.525487 AGGTGTATTAGTGTTCCTGAACGA 59.475 41.667 5.62 0.00 43.94 3.85
3458 4278 5.011329 AGGTGTATTAGTGTTCCTGAACGAA 59.989 40.000 5.62 1.03 43.94 3.85
3470 4290 3.756434 TCCTGAACGAAAAGGCATAAAGG 59.244 43.478 0.00 0.00 33.25 3.11
3495 4315 2.027625 GCCCTTGTTCGTCTGGTCG 61.028 63.158 0.00 0.00 0.00 4.79
3501 4321 1.300697 GTTCGTCTGGTCGCCACTT 60.301 57.895 0.00 0.00 0.00 3.16
3502 4322 1.006571 TTCGTCTGGTCGCCACTTC 60.007 57.895 0.00 0.00 0.00 3.01
3531 4355 5.476091 ACCTGAAGTATATCTAGCCTTGC 57.524 43.478 0.00 0.00 0.00 4.01
3540 4364 5.712084 ATATCTAGCCTTGCCATCATGAT 57.288 39.130 1.18 1.18 0.00 2.45
3541 4365 6.819947 ATATCTAGCCTTGCCATCATGATA 57.180 37.500 8.15 0.00 0.00 2.15
3542 4366 4.277515 TCTAGCCTTGCCATCATGATAC 57.722 45.455 8.15 4.41 0.00 2.24
3552 4377 4.823442 TGCCATCATGATACCATTGTCTTC 59.177 41.667 8.15 0.00 0.00 2.87
3563 4388 5.333566 ACCATTGTCTTCCCTTTTTCCTA 57.666 39.130 0.00 0.00 0.00 2.94
3582 4407 6.428083 TCCTAAAACAGTATGACCAACTGA 57.572 37.500 10.02 0.00 45.89 3.41
3668 4497 6.712998 TCAAGTCTTGGATGGAAAATAAACGA 59.287 34.615 12.66 0.00 0.00 3.85
3672 4501 7.230712 AGTCTTGGATGGAAAATAAACGAGTTT 59.769 33.333 6.46 6.46 36.63 2.66
3688 4520 4.785669 GAGTTTGGATGATAACTCGCTG 57.214 45.455 0.00 0.00 40.39 5.18
3689 4521 4.433615 GAGTTTGGATGATAACTCGCTGA 58.566 43.478 0.00 0.00 40.39 4.26
3696 4528 9.725019 TTTGGATGATAACTCGCTGATTTATAT 57.275 29.630 2.76 0.00 0.00 0.86
3697 4529 8.932945 TGGATGATAACTCGCTGATTTATATC 57.067 34.615 2.76 0.00 0.00 1.63
3698 4530 8.531146 TGGATGATAACTCGCTGATTTATATCA 58.469 33.333 0.00 0.00 38.45 2.15
3722 4560 7.449395 TCAGTTTGAGAAAGACATTGATGGATT 59.551 33.333 0.00 0.00 0.00 3.01
3724 4562 8.302438 AGTTTGAGAAAGACATTGATGGATTTC 58.698 33.333 11.87 11.87 36.98 2.17
3727 4565 8.728337 TGAGAAAGACATTGATGGATTTCTAG 57.272 34.615 17.92 0.00 42.01 2.43
3728 4566 8.324306 TGAGAAAGACATTGATGGATTTCTAGT 58.676 33.333 17.92 5.22 42.01 2.57
3729 4567 9.823647 GAGAAAGACATTGATGGATTTCTAGTA 57.176 33.333 17.92 0.00 42.01 1.82
3730 4568 9.829507 AGAAAGACATTGATGGATTTCTAGTAG 57.170 33.333 17.07 0.00 41.10 2.57
3731 4569 8.443953 AAAGACATTGATGGATTTCTAGTAGC 57.556 34.615 0.00 0.00 0.00 3.58
3732 4570 6.219473 AGACATTGATGGATTTCTAGTAGCG 58.781 40.000 0.00 0.00 0.00 4.26
3733 4571 6.040955 AGACATTGATGGATTTCTAGTAGCGA 59.959 38.462 0.00 0.00 0.00 4.93
3734 4572 5.986135 ACATTGATGGATTTCTAGTAGCGAC 59.014 40.000 0.00 0.00 0.00 5.19
3742 4580 0.926155 TCTAGTAGCGACGTAGCGTG 59.074 55.000 15.11 5.26 41.37 5.34
3749 4587 1.273455 GCGACGTAGCGTGTCTGTTT 61.273 55.000 4.51 0.00 41.37 2.83
3762 4600 5.396654 GCGTGTCTGTTTTCTGAATTTCTTC 59.603 40.000 0.00 0.00 0.00 2.87
3779 4618 9.334947 GAATTTCTTCTCCATATCACTCATTCA 57.665 33.333 0.00 0.00 0.00 2.57
3780 4619 8.905660 ATTTCTTCTCCATATCACTCATTCAG 57.094 34.615 0.00 0.00 0.00 3.02
3781 4620 7.429374 TTCTTCTCCATATCACTCATTCAGT 57.571 36.000 0.00 0.00 34.67 3.41
3782 4621 7.048629 TCTTCTCCATATCACTCATTCAGTC 57.951 40.000 0.00 0.00 30.26 3.51
3783 4622 6.608808 TCTTCTCCATATCACTCATTCAGTCA 59.391 38.462 0.00 0.00 30.26 3.41
3784 4623 6.990908 TCTCCATATCACTCATTCAGTCAT 57.009 37.500 0.00 0.00 30.26 3.06
3785 4624 7.370905 TCTCCATATCACTCATTCAGTCATT 57.629 36.000 0.00 0.00 30.26 2.57
3786 4625 7.440198 TCTCCATATCACTCATTCAGTCATTC 58.560 38.462 0.00 0.00 30.26 2.67
3787 4626 7.289549 TCTCCATATCACTCATTCAGTCATTCT 59.710 37.037 0.00 0.00 30.26 2.40
3788 4627 7.440198 TCCATATCACTCATTCAGTCATTCTC 58.560 38.462 0.00 0.00 30.26 2.87
3789 4628 7.289549 TCCATATCACTCATTCAGTCATTCTCT 59.710 37.037 0.00 0.00 30.26 3.10
3790 4629 7.932491 CCATATCACTCATTCAGTCATTCTCTT 59.068 37.037 0.00 0.00 30.26 2.85
3791 4630 8.766151 CATATCACTCATTCAGTCATTCTCTTG 58.234 37.037 0.00 0.00 30.26 3.02
3792 4631 6.350629 TCACTCATTCAGTCATTCTCTTGA 57.649 37.500 0.00 0.00 30.26 3.02
3793 4632 6.162079 TCACTCATTCAGTCATTCTCTTGAC 58.838 40.000 0.00 0.00 45.15 3.18
3811 4650 2.869801 TGACGTGTCTGTTCAAATGTCC 59.130 45.455 0.00 0.00 0.00 4.02
3842 4683 9.581099 TGTTCTAATTTTGTTTTCAGGTTTCTC 57.419 29.630 0.00 0.00 0.00 2.87
3851 4692 9.581099 TTTGTTTTCAGGTTTCTCAAATCTAAC 57.419 29.630 0.00 0.00 28.80 2.34
3860 4701 4.286297 TCTCAAATCTAACAGGTGGTGG 57.714 45.455 0.00 0.00 0.00 4.61
3865 4706 2.097110 TCTAACAGGTGGTGGTGTCT 57.903 50.000 0.00 0.00 0.00 3.41
3866 4707 1.691976 TCTAACAGGTGGTGGTGTCTG 59.308 52.381 0.00 0.00 0.00 3.51
3870 4711 0.979665 CAGGTGGTGGTGTCTGATCT 59.020 55.000 0.00 0.00 0.00 2.75
3880 4721 2.636830 GTGTCTGATCTTGATGGTGGG 58.363 52.381 0.00 0.00 0.00 4.61
3881 4722 1.561076 TGTCTGATCTTGATGGTGGGG 59.439 52.381 0.00 0.00 0.00 4.96
3882 4723 1.133976 GTCTGATCTTGATGGTGGGGG 60.134 57.143 0.00 0.00 0.00 5.40
3912 4753 3.260205 TGGGGAAAATCTGGAGAAGTCT 58.740 45.455 0.00 0.00 0.00 3.24
3921 4762 4.771114 TCTGGAGAAGTCTTGGTTTGAA 57.229 40.909 0.00 0.00 0.00 2.69
3946 4787 5.277828 GGAGTTTTGCGATCAACTTACTGTT 60.278 40.000 0.00 0.00 39.92 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 111 1.021390 ACCATGCCTCTCGCGAAAAG 61.021 55.000 11.33 10.79 42.08 2.27
104 112 0.605319 AACCATGCCTCTCGCGAAAA 60.605 50.000 11.33 0.00 42.08 2.29
215 230 0.886490 AGCGTGCCTCTCACAAAAGG 60.886 55.000 0.00 0.00 45.92 3.11
537 565 1.713937 TATGACAAATGGCGCGCTGG 61.714 55.000 32.29 17.53 0.00 4.85
578 606 8.677148 TTAATTAATGGATACTCCTTGCAGAC 57.323 34.615 0.00 0.00 37.46 3.51
593 622 8.746922 AATAGCACGCATTCATTAATTAATGG 57.253 30.769 29.22 18.83 42.46 3.16
612 641 6.599244 ACTCATACTAGCAAAGCAAAATAGCA 59.401 34.615 0.00 0.00 36.85 3.49
613 642 7.020914 ACTCATACTAGCAAAGCAAAATAGC 57.979 36.000 0.00 0.00 0.00 2.97
617 646 9.677567 CTTTTAACTCATACTAGCAAAGCAAAA 57.322 29.630 0.00 0.00 0.00 2.44
618 647 7.807907 GCTTTTAACTCATACTAGCAAAGCAAA 59.192 33.333 8.12 0.00 0.00 3.68
619 648 7.305474 GCTTTTAACTCATACTAGCAAAGCAA 58.695 34.615 8.12 0.00 0.00 3.91
620 649 6.128007 GGCTTTTAACTCATACTAGCAAAGCA 60.128 38.462 13.58 0.00 0.00 3.91
621 650 6.258899 GGCTTTTAACTCATACTAGCAAAGC 58.741 40.000 0.00 0.00 0.00 3.51
622 651 6.374333 TGGGCTTTTAACTCATACTAGCAAAG 59.626 38.462 0.00 0.00 0.00 2.77
625 654 5.428253 CTGGGCTTTTAACTCATACTAGCA 58.572 41.667 0.00 0.00 0.00 3.49
626 655 4.273724 GCTGGGCTTTTAACTCATACTAGC 59.726 45.833 0.00 0.00 0.00 3.42
627 656 4.816925 GGCTGGGCTTTTAACTCATACTAG 59.183 45.833 0.00 0.00 0.00 2.57
628 657 4.226394 TGGCTGGGCTTTTAACTCATACTA 59.774 41.667 0.00 0.00 0.00 1.82
629 658 3.010138 TGGCTGGGCTTTTAACTCATACT 59.990 43.478 0.00 0.00 0.00 2.12
630 659 3.352648 TGGCTGGGCTTTTAACTCATAC 58.647 45.455 0.00 0.00 0.00 2.39
631 660 3.730215 TGGCTGGGCTTTTAACTCATA 57.270 42.857 0.00 0.00 0.00 2.15
634 663 2.685388 GAGATGGCTGGGCTTTTAACTC 59.315 50.000 0.00 0.00 0.00 3.01
636 665 2.424956 CTGAGATGGCTGGGCTTTTAAC 59.575 50.000 0.00 0.00 0.00 2.01
637 666 2.308570 TCTGAGATGGCTGGGCTTTTAA 59.691 45.455 0.00 0.00 0.00 1.52
638 667 1.915489 TCTGAGATGGCTGGGCTTTTA 59.085 47.619 0.00 0.00 0.00 1.52
639 668 0.700564 TCTGAGATGGCTGGGCTTTT 59.299 50.000 0.00 0.00 0.00 2.27
640 669 0.700564 TTCTGAGATGGCTGGGCTTT 59.299 50.000 0.00 0.00 0.00 3.51
641 670 0.700564 TTTCTGAGATGGCTGGGCTT 59.299 50.000 0.00 0.00 0.00 4.35
643 672 1.772836 ATTTTCTGAGATGGCTGGGC 58.227 50.000 0.00 0.00 0.00 5.36
644 673 4.952335 ACTTTATTTTCTGAGATGGCTGGG 59.048 41.667 0.00 0.00 0.00 4.45
646 675 7.064609 TCGTAACTTTATTTTCTGAGATGGCTG 59.935 37.037 0.00 0.00 0.00 4.85
647 676 7.103641 TCGTAACTTTATTTTCTGAGATGGCT 58.896 34.615 0.00 0.00 0.00 4.75
648 677 7.303634 TCGTAACTTTATTTTCTGAGATGGC 57.696 36.000 0.00 0.00 0.00 4.40
649 678 7.466050 GCCTCGTAACTTTATTTTCTGAGATGG 60.466 40.741 0.00 0.00 0.00 3.51
650 679 7.402640 GCCTCGTAACTTTATTTTCTGAGATG 58.597 38.462 0.00 0.00 0.00 2.90
651 680 6.539103 GGCCTCGTAACTTTATTTTCTGAGAT 59.461 38.462 0.00 0.00 0.00 2.75
652 681 5.873164 GGCCTCGTAACTTTATTTTCTGAGA 59.127 40.000 0.00 0.00 0.00 3.27
654 683 4.939439 GGGCCTCGTAACTTTATTTTCTGA 59.061 41.667 0.84 0.00 0.00 3.27
655 684 4.698304 TGGGCCTCGTAACTTTATTTTCTG 59.302 41.667 4.53 0.00 0.00 3.02
657 686 4.438336 GCTGGGCCTCGTAACTTTATTTTC 60.438 45.833 4.53 0.00 0.00 2.29
658 687 3.442625 GCTGGGCCTCGTAACTTTATTTT 59.557 43.478 4.53 0.00 0.00 1.82
659 688 3.014623 GCTGGGCCTCGTAACTTTATTT 58.985 45.455 4.53 0.00 0.00 1.40
660 689 2.026636 TGCTGGGCCTCGTAACTTTATT 60.027 45.455 4.53 0.00 0.00 1.40
661 690 1.557832 TGCTGGGCCTCGTAACTTTAT 59.442 47.619 4.53 0.00 0.00 1.40
662 691 0.978151 TGCTGGGCCTCGTAACTTTA 59.022 50.000 4.53 0.00 0.00 1.85
663 692 0.605589 GTGCTGGGCCTCGTAACTTT 60.606 55.000 4.53 0.00 0.00 2.66
664 693 1.003718 GTGCTGGGCCTCGTAACTT 60.004 57.895 4.53 0.00 0.00 2.66
665 694 2.663196 GTGCTGGGCCTCGTAACT 59.337 61.111 4.53 0.00 0.00 2.24
666 695 2.436115 GGTGCTGGGCCTCGTAAC 60.436 66.667 4.53 0.00 0.00 2.50
671 700 4.416738 GACCTGGTGCTGGGCCTC 62.417 72.222 2.82 0.00 0.00 4.70
682 711 0.951558 CAAAAGTTCACCGGACCTGG 59.048 55.000 9.46 0.00 0.00 4.45
683 712 0.951558 CCAAAAGTTCACCGGACCTG 59.048 55.000 9.46 0.00 0.00 4.00
695 724 1.069978 CACCATTTTCCCGCCAAAAGT 59.930 47.619 0.00 0.00 0.00 2.66
696 725 1.342819 TCACCATTTTCCCGCCAAAAG 59.657 47.619 0.00 0.00 0.00 2.27
722 752 1.529244 GCACAACTGGCTGGACCTT 60.529 57.895 0.00 0.00 40.22 3.50
745 775 1.588404 CTGCGTTATCAACAGCCGTAG 59.412 52.381 0.00 0.00 32.57 3.51
784 814 4.051922 CGTCAGTTAGATACATTGAGGCC 58.948 47.826 0.00 0.00 0.00 5.19
785 815 3.491267 GCGTCAGTTAGATACATTGAGGC 59.509 47.826 2.38 2.38 40.79 4.70
901 932 4.722700 ATGGAGTGGGTGCACGCC 62.723 66.667 28.67 21.60 43.88 5.68
1219 1804 2.586635 TTGCACGAAGTCGCCGTT 60.587 55.556 0.00 0.00 41.61 4.44
1461 2046 1.340248 GAGACCTCGAACTTGGTGACA 59.660 52.381 0.00 0.00 36.59 3.58
1748 2357 2.759973 AGAGCTCCGGCCGATCAA 60.760 61.111 30.73 8.10 39.73 2.57
1749 2358 3.219928 GAGAGCTCCGGCCGATCA 61.220 66.667 30.73 9.20 39.73 2.92
1834 2473 0.108804 CGGTACTCACGCCAAGACAT 60.109 55.000 0.00 0.00 0.00 3.06
1942 2593 3.965258 TGTCCAGCCGGTGCCATT 61.965 61.111 1.90 0.00 38.69 3.16
1995 2649 2.203252 CATGGGTGGCCTCCATCG 60.203 66.667 24.81 16.25 42.63 3.84
2159 2816 1.450312 CATGGCACCGAGAAGTCCC 60.450 63.158 0.00 0.00 0.00 4.46
2169 2826 1.168714 GAGGAAGAACACATGGCACC 58.831 55.000 0.00 0.00 0.00 5.01
2172 2829 0.321653 ACGGAGGAAGAACACATGGC 60.322 55.000 0.00 0.00 0.00 4.40
2253 2915 2.096248 CGGGCATTAGGCACCTAAAAA 58.904 47.619 12.97 0.00 45.76 1.94
2264 2926 0.734889 CAAAGCACCTCGGGCATTAG 59.265 55.000 0.00 0.00 0.00 1.73
2272 2934 0.606401 ATGACCCACAAAGCACCTCG 60.606 55.000 0.00 0.00 0.00 4.63
2439 3108 3.006752 ACCAATTGCTACCAAACACATGG 59.993 43.478 0.00 0.00 46.38 3.66
2461 3132 6.286240 ACGATCTATATGAGCCTTGCAATA 57.714 37.500 0.00 0.00 0.00 1.90
2469 3140 4.035278 GTGCCTACGATCTATATGAGCC 57.965 50.000 0.00 0.00 0.00 4.70
2483 3154 3.625764 TGCAAAGATTTATCCGTGCCTAC 59.374 43.478 10.84 0.00 36.68 3.18
2494 3165 8.114331 AGAATGACAACAGATGCAAAGATTTA 57.886 30.769 0.00 0.00 0.00 1.40
2533 3205 8.970691 ATGTTCAACGGAAAATTCTTTATGAG 57.029 30.769 0.00 0.00 34.13 2.90
2613 3285 5.422666 TCACAGTGTAACATGAAAGCAAG 57.577 39.130 0.00 0.00 41.43 4.01
2621 3293 5.654497 TCTAGAGCATCACAGTGTAACATG 58.346 41.667 0.00 0.00 36.92 3.21
2672 3409 9.892130 AGAGGAGTTATTAAAAGGATACAACAG 57.108 33.333 0.00 0.00 41.41 3.16
2797 3534 8.087136 TGAATTGCATACAAGAATTAAACAGCA 58.913 29.630 0.00 0.00 39.69 4.41
2798 3535 8.375465 GTGAATTGCATACAAGAATTAAACAGC 58.625 33.333 0.00 0.00 39.69 4.40
2799 3536 9.409312 TGTGAATTGCATACAAGAATTAAACAG 57.591 29.630 0.00 0.00 39.69 3.16
2800 3537 9.409312 CTGTGAATTGCATACAAGAATTAAACA 57.591 29.630 0.00 0.00 39.69 2.83
2801 3538 9.624697 TCTGTGAATTGCATACAAGAATTAAAC 57.375 29.630 0.00 0.00 39.69 2.01
2843 3580 7.067008 ACACTAGCACAACAGAATTACAAGTTT 59.933 33.333 0.00 0.00 0.00 2.66
2844 3581 6.542370 ACACTAGCACAACAGAATTACAAGTT 59.458 34.615 0.00 0.00 0.00 2.66
2845 3582 6.055588 ACACTAGCACAACAGAATTACAAGT 58.944 36.000 0.00 0.00 0.00 3.16
2846 3583 6.545504 ACACTAGCACAACAGAATTACAAG 57.454 37.500 0.00 0.00 0.00 3.16
2847 3584 6.724263 CAACACTAGCACAACAGAATTACAA 58.276 36.000 0.00 0.00 0.00 2.41
2848 3585 5.277779 GCAACACTAGCACAACAGAATTACA 60.278 40.000 0.00 0.00 0.00 2.41
2849 3586 5.049405 AGCAACACTAGCACAACAGAATTAC 60.049 40.000 0.00 0.00 0.00 1.89
2850 3587 5.049474 CAGCAACACTAGCACAACAGAATTA 60.049 40.000 0.00 0.00 0.00 1.40
2985 3725 4.360951 AAATTGGTACCTTCGACCTTCA 57.639 40.909 14.36 0.00 37.88 3.02
2986 3726 4.633126 GGTAAATTGGTACCTTCGACCTTC 59.367 45.833 14.36 0.00 40.48 3.46
2987 3727 4.041938 TGGTAAATTGGTACCTTCGACCTT 59.958 41.667 14.36 0.00 43.52 3.50
2988 3728 3.583966 TGGTAAATTGGTACCTTCGACCT 59.416 43.478 14.36 0.00 43.52 3.85
2989 3729 3.937079 CTGGTAAATTGGTACCTTCGACC 59.063 47.826 14.36 13.81 43.52 4.79
2990 3730 3.373130 GCTGGTAAATTGGTACCTTCGAC 59.627 47.826 14.36 4.85 43.52 4.20
2991 3731 3.262405 AGCTGGTAAATTGGTACCTTCGA 59.738 43.478 14.36 0.00 43.52 3.71
3048 3790 8.526147 CCAAGAACAATGGATCAATAAAGAAGT 58.474 33.333 0.00 0.00 40.56 3.01
3049 3791 8.526147 ACCAAGAACAATGGATCAATAAAGAAG 58.474 33.333 0.00 0.00 40.56 2.85
3119 3863 5.010617 TGCATGAATGGCGTAAGAGATACTA 59.989 40.000 0.00 0.00 43.02 1.82
3148 3892 5.410439 ACGACGTTTGCTTTTAGTCCATAAT 59.590 36.000 0.00 0.00 0.00 1.28
3149 3893 4.751098 ACGACGTTTGCTTTTAGTCCATAA 59.249 37.500 0.00 0.00 0.00 1.90
3158 3902 0.169230 TGTGCACGACGTTTGCTTTT 59.831 45.000 20.03 0.00 40.86 2.27
3256 4000 3.304659 GCATTGACACACCAACGAGAAAT 60.305 43.478 0.00 0.00 0.00 2.17
3269 4013 7.959718 CAAATATCACTAGTTGCATTGACAC 57.040 36.000 0.00 0.00 0.00 3.67
3278 4022 5.565592 TTGCCAGCAAATATCACTAGTTG 57.434 39.130 1.81 0.00 36.31 3.16
3279 4023 6.209391 AGTTTTGCCAGCAAATATCACTAGTT 59.791 34.615 17.80 0.00 44.14 2.24
3280 4024 5.711976 AGTTTTGCCAGCAAATATCACTAGT 59.288 36.000 17.80 2.45 44.14 2.57
3281 4025 6.199937 AGTTTTGCCAGCAAATATCACTAG 57.800 37.500 17.80 0.00 44.14 2.57
3282 4026 7.109501 TCTAGTTTTGCCAGCAAATATCACTA 58.890 34.615 17.80 18.49 44.14 2.74
3283 4027 5.945784 TCTAGTTTTGCCAGCAAATATCACT 59.054 36.000 17.80 18.38 44.14 3.41
3286 4030 6.251376 CGTTTCTAGTTTTGCCAGCAAATATC 59.749 38.462 17.80 11.53 44.14 1.63
3287 4031 6.092748 CGTTTCTAGTTTTGCCAGCAAATAT 58.907 36.000 17.80 11.96 44.14 1.28
3288 4032 5.009210 ACGTTTCTAGTTTTGCCAGCAAATA 59.991 36.000 17.80 8.17 44.14 1.40
3289 4033 4.202111 ACGTTTCTAGTTTTGCCAGCAAAT 60.202 37.500 17.80 7.45 44.14 2.32
3290 4034 3.129638 ACGTTTCTAGTTTTGCCAGCAAA 59.870 39.130 13.57 13.57 43.23 3.68
3292 4036 2.294074 ACGTTTCTAGTTTTGCCAGCA 58.706 42.857 0.00 0.00 0.00 4.41
3293 4037 3.497262 AGTACGTTTCTAGTTTTGCCAGC 59.503 43.478 0.00 0.00 0.00 4.85
3294 4038 5.440685 CAAGTACGTTTCTAGTTTTGCCAG 58.559 41.667 0.00 0.00 0.00 4.85
3295 4039 4.260866 GCAAGTACGTTTCTAGTTTTGCCA 60.261 41.667 0.00 0.00 36.18 4.92
3296 4040 4.024302 AGCAAGTACGTTTCTAGTTTTGCC 60.024 41.667 0.00 0.00 39.54 4.52
3297 4041 5.091910 AGCAAGTACGTTTCTAGTTTTGC 57.908 39.130 0.00 0.00 39.27 3.68
3298 4042 5.235616 TGGAGCAAGTACGTTTCTAGTTTTG 59.764 40.000 0.00 0.00 0.00 2.44
3299 4043 5.362263 TGGAGCAAGTACGTTTCTAGTTTT 58.638 37.500 0.00 0.00 0.00 2.43
3300 4044 4.952460 TGGAGCAAGTACGTTTCTAGTTT 58.048 39.130 0.00 0.00 0.00 2.66
3301 4045 4.595762 TGGAGCAAGTACGTTTCTAGTT 57.404 40.909 0.00 0.00 0.00 2.24
3302 4046 4.803098 ATGGAGCAAGTACGTTTCTAGT 57.197 40.909 0.00 0.00 0.00 2.57
3303 4047 6.132791 TCTATGGAGCAAGTACGTTTCTAG 57.867 41.667 0.00 0.00 0.00 2.43
3304 4048 6.519679 TTCTATGGAGCAAGTACGTTTCTA 57.480 37.500 0.00 0.00 0.00 2.10
3305 4049 5.401531 TTCTATGGAGCAAGTACGTTTCT 57.598 39.130 0.00 0.00 0.00 2.52
3306 4050 6.037423 CATTCTATGGAGCAAGTACGTTTC 57.963 41.667 0.00 0.00 0.00 2.78
3341 4119 8.477419 AAAATGAATGGAAGAAGTTCAGGTAA 57.523 30.769 5.50 0.00 35.56 2.85
3387 4192 0.875059 GACACAGTAACCTGGCAAGC 59.125 55.000 0.00 0.00 43.36 4.01
3399 4204 7.766278 GGATGTATAAGTTCATTCTGACACAGT 59.234 37.037 0.00 0.00 32.61 3.55
3409 4229 6.332635 TGGATGGAGGGATGTATAAGTTCATT 59.667 38.462 0.00 0.00 0.00 2.57
3414 4234 4.171234 CCTGGATGGAGGGATGTATAAGT 58.829 47.826 0.00 0.00 38.35 2.24
3441 4261 3.562557 GCCTTTTCGTTCAGGAACACTAA 59.437 43.478 12.22 1.27 41.20 2.24
3449 4269 3.756434 TCCTTTATGCCTTTTCGTTCAGG 59.244 43.478 0.00 0.00 0.00 3.86
3470 4290 1.648467 GACGAACAAGGGCAGGCATC 61.648 60.000 0.00 0.00 0.00 3.91
3477 4297 2.027625 CGACCAGACGAACAAGGGC 61.028 63.158 0.00 0.00 35.09 5.19
3478 4298 2.027625 GCGACCAGACGAACAAGGG 61.028 63.158 0.00 0.00 35.09 3.95
3495 4315 4.954092 CTTCAGGTTCTAATGAAGTGGC 57.046 45.455 6.75 0.00 44.75 5.01
3501 4321 9.026121 GGCTAGATATACTTCAGGTTCTAATGA 57.974 37.037 0.00 0.00 0.00 2.57
3502 4322 9.030452 AGGCTAGATATACTTCAGGTTCTAATG 57.970 37.037 0.00 0.00 0.00 1.90
3531 4355 4.763793 GGGAAGACAATGGTATCATGATGG 59.236 45.833 18.72 3.57 33.18 3.51
3540 4364 5.333566 AGGAAAAAGGGAAGACAATGGTA 57.666 39.130 0.00 0.00 0.00 3.25
3541 4365 4.199002 AGGAAAAAGGGAAGACAATGGT 57.801 40.909 0.00 0.00 0.00 3.55
3542 4366 6.664428 TTTAGGAAAAAGGGAAGACAATGG 57.336 37.500 0.00 0.00 0.00 3.16
3552 4377 6.492087 TGGTCATACTGTTTTAGGAAAAAGGG 59.508 38.462 0.00 0.00 34.89 3.95
3582 4407 7.765695 TCAAGCTTCAGTTTCAGGATTTAAT 57.234 32.000 0.00 0.00 0.00 1.40
3588 4413 4.630644 AGATCAAGCTTCAGTTTCAGGA 57.369 40.909 0.00 0.00 0.00 3.86
3616 4441 6.605594 TGGAGAGAAAAGTACACCACAAATTT 59.394 34.615 0.00 0.00 0.00 1.82
3619 4444 5.105567 TGGAGAGAAAAGTACACCACAAA 57.894 39.130 0.00 0.00 0.00 2.83
3656 4485 9.285770 GTTATCATCCAAACTCGTTTATTTTCC 57.714 33.333 0.00 0.00 0.00 3.13
3668 4497 4.471904 TCAGCGAGTTATCATCCAAACT 57.528 40.909 0.00 0.00 38.62 2.66
3672 4501 8.531146 TGATATAAATCAGCGAGTTATCATCCA 58.469 33.333 12.22 6.46 37.20 3.41
3696 4528 6.298361 TCCATCAATGTCTTTCTCAAACTGA 58.702 36.000 0.00 0.00 0.00 3.41
3697 4529 6.564709 TCCATCAATGTCTTTCTCAAACTG 57.435 37.500 0.00 0.00 0.00 3.16
3698 4530 7.771927 AATCCATCAATGTCTTTCTCAAACT 57.228 32.000 0.00 0.00 0.00 2.66
3699 4531 8.302438 AGAAATCCATCAATGTCTTTCTCAAAC 58.698 33.333 9.49 0.00 34.38 2.93
3702 4540 8.324306 ACTAGAAATCCATCAATGTCTTTCTCA 58.676 33.333 14.97 6.77 37.57 3.27
3703 4541 8.729805 ACTAGAAATCCATCAATGTCTTTCTC 57.270 34.615 14.97 0.00 37.57 2.87
3705 4543 8.555361 GCTACTAGAAATCCATCAATGTCTTTC 58.445 37.037 0.00 6.48 31.68 2.62
3707 4545 6.703607 CGCTACTAGAAATCCATCAATGTCTT 59.296 38.462 0.00 0.00 0.00 3.01
3712 4550 5.221263 ACGTCGCTACTAGAAATCCATCAAT 60.221 40.000 0.00 0.00 0.00 2.57
3714 4552 3.630769 ACGTCGCTACTAGAAATCCATCA 59.369 43.478 0.00 0.00 0.00 3.07
3722 4560 1.325640 CACGCTACGTCGCTACTAGAA 59.674 52.381 10.57 0.00 38.32 2.10
3724 4562 0.649475 ACACGCTACGTCGCTACTAG 59.351 55.000 10.57 0.00 38.32 2.57
3727 4565 0.856490 CAGACACGCTACGTCGCTAC 60.856 60.000 10.57 0.00 38.32 3.58
3728 4566 1.293963 ACAGACACGCTACGTCGCTA 61.294 55.000 10.57 0.00 38.32 4.26
3729 4567 2.126417 AACAGACACGCTACGTCGCT 62.126 55.000 10.57 0.00 38.32 4.93
3730 4568 1.273455 AAACAGACACGCTACGTCGC 61.273 55.000 1.21 1.21 38.32 5.19
3731 4569 1.121967 GAAAACAGACACGCTACGTCG 59.878 52.381 0.00 0.00 38.32 5.12
3732 4570 2.153247 CAGAAAACAGACACGCTACGTC 59.847 50.000 0.00 0.00 38.32 4.34
3733 4571 2.124903 CAGAAAACAGACACGCTACGT 58.875 47.619 0.00 0.00 42.36 3.57
3734 4572 2.390938 TCAGAAAACAGACACGCTACG 58.609 47.619 0.00 0.00 0.00 3.51
3742 4580 7.264373 TGGAGAAGAAATTCAGAAAACAGAC 57.736 36.000 0.00 0.00 0.00 3.51
3749 4587 8.542926 TGAGTGATATGGAGAAGAAATTCAGAA 58.457 33.333 0.00 0.00 0.00 3.02
3762 4600 7.443477 AGAATGACTGAATGAGTGATATGGAG 58.557 38.462 0.00 0.00 33.83 3.86
3779 4618 3.319405 ACAGACACGTCAAGAGAATGACT 59.681 43.478 5.96 0.00 45.98 3.41
3780 4619 3.643763 ACAGACACGTCAAGAGAATGAC 58.356 45.455 0.00 0.00 44.96 3.06
3781 4620 4.202111 TGAACAGACACGTCAAGAGAATGA 60.202 41.667 0.00 0.00 0.00 2.57
3782 4621 4.051237 TGAACAGACACGTCAAGAGAATG 58.949 43.478 0.00 0.00 0.00 2.67
3783 4622 4.322080 TGAACAGACACGTCAAGAGAAT 57.678 40.909 0.00 0.00 0.00 2.40
3784 4623 3.793797 TGAACAGACACGTCAAGAGAA 57.206 42.857 0.00 0.00 0.00 2.87
3785 4624 3.793797 TTGAACAGACACGTCAAGAGA 57.206 42.857 0.00 0.00 0.00 3.10
3786 4625 4.271049 ACATTTGAACAGACACGTCAAGAG 59.729 41.667 0.00 0.00 0.00 2.85
3787 4626 4.188462 ACATTTGAACAGACACGTCAAGA 58.812 39.130 0.00 0.00 0.00 3.02
3788 4627 4.518217 GACATTTGAACAGACACGTCAAG 58.482 43.478 0.00 0.00 0.00 3.02
3789 4628 3.311322 GGACATTTGAACAGACACGTCAA 59.689 43.478 0.00 0.00 0.00 3.18
3790 4629 2.869801 GGACATTTGAACAGACACGTCA 59.130 45.455 0.00 0.00 0.00 4.35
3791 4630 2.223377 GGGACATTTGAACAGACACGTC 59.777 50.000 0.00 0.00 0.00 4.34
3792 4631 2.158813 AGGGACATTTGAACAGACACGT 60.159 45.455 0.00 0.00 0.00 4.49
3793 4632 2.494059 AGGGACATTTGAACAGACACG 58.506 47.619 0.00 0.00 0.00 4.49
3794 4633 5.473504 ACATTAGGGACATTTGAACAGACAC 59.526 40.000 0.00 0.00 0.00 3.67
3795 4634 5.630121 ACATTAGGGACATTTGAACAGACA 58.370 37.500 0.00 0.00 0.00 3.41
3796 4635 6.431234 AGAACATTAGGGACATTTGAACAGAC 59.569 38.462 0.00 0.00 0.00 3.51
3811 4650 9.981114 ACCTGAAAACAAAATTAGAACATTAGG 57.019 29.630 0.00 0.00 0.00 2.69
3842 4683 3.486383 ACACCACCACCTGTTAGATTTG 58.514 45.455 0.00 0.00 0.00 2.32
3846 4687 1.691976 CAGACACCACCACCTGTTAGA 59.308 52.381 0.00 0.00 0.00 2.10
3851 4692 0.979665 AGATCAGACACCACCACCTG 59.020 55.000 0.00 0.00 0.00 4.00
3860 4701 2.636830 CCCACCATCAAGATCAGACAC 58.363 52.381 0.00 0.00 0.00 3.67
3865 4706 0.918983 GACCCCCACCATCAAGATCA 59.081 55.000 0.00 0.00 0.00 2.92
3866 4707 1.141858 GAGACCCCCACCATCAAGATC 59.858 57.143 0.00 0.00 0.00 2.75
3870 4711 1.381867 AATGAGACCCCCACCATCAA 58.618 50.000 0.00 0.00 0.00 2.57
3880 4721 4.081476 CAGATTTTCCCCAAAATGAGACCC 60.081 45.833 0.00 0.00 41.47 4.46
3881 4722 4.081476 CCAGATTTTCCCCAAAATGAGACC 60.081 45.833 0.00 0.00 41.47 3.85
3882 4723 4.772100 TCCAGATTTTCCCCAAAATGAGAC 59.228 41.667 0.00 0.00 41.47 3.36
3912 4753 2.755655 TCGCAAAACTCCTTCAAACCAA 59.244 40.909 0.00 0.00 0.00 3.67
3921 4762 4.452455 CAGTAAGTTGATCGCAAAACTCCT 59.548 41.667 0.00 0.00 35.60 3.69


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

AutoCloner maintained by Alex Coulton.