Multiple sequence alignment - TraesCS3A01G091900

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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 TraesCS3A01G091900 chr3A 100.000 3680 0 0 1 3680 57897684 57894005 0.000000e+00 6796
1 TraesCS3A01G091900 chr3D 93.570 2815 103 28 934 3680 46476920 46474116 0.000000e+00 4124
2 TraesCS3A01G091900 chr3D 88.592 561 40 8 2 556 46478333 46477791 0.000000e+00 660
3 TraesCS3A01G091900 chr3B 92.976 2819 108 23 934 3680 72488658 72485858 0.000000e+00 4026
4 TraesCS3A01G091900 chr3B 92.217 424 22 4 133 556 72708319 72707907 1.140000e-164 590
5 TraesCS3A01G091900 chr2B 93.108 711 36 2 1040 1738 5489073 5488364 0.000000e+00 1029
6 TraesCS3A01G091900 chr5B 91.586 725 48 9 1026 1738 562419021 562419744 0.000000e+00 989
7 TraesCS3A01G091900 chr1B 88.997 718 66 8 1033 1738 493683691 493682975 0.000000e+00 876
8 TraesCS3A01G091900 chr1B 93.515 293 19 0 1446 1738 8393671 8393379 1.570000e-118 436
9 TraesCS3A01G091900 chr1A 88.187 728 70 2 1026 1753 541158536 541157825 0.000000e+00 854
10 TraesCS3A01G091900 chr4A 88.049 728 74 1 1026 1753 640150234 640149520 0.000000e+00 850
11 TraesCS3A01G091900 chr7B 88.912 487 54 0 1252 1738 432764249 432763763 5.260000e-168 601
12 TraesCS3A01G091900 chr7B 96.250 80 3 0 1041 1120 432764325 432764246 8.290000e-27 132


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 TraesCS3A01G091900 chr3A 57894005 57897684 3679 True 6796.0 6796 100.000 1 3680 1 chr3A.!!$R1 3679
1 TraesCS3A01G091900 chr3D 46474116 46478333 4217 True 2392.0 4124 91.081 2 3680 2 chr3D.!!$R1 3678
2 TraesCS3A01G091900 chr3B 72485858 72488658 2800 True 4026.0 4026 92.976 934 3680 1 chr3B.!!$R1 2746
3 TraesCS3A01G091900 chr2B 5488364 5489073 709 True 1029.0 1029 93.108 1040 1738 1 chr2B.!!$R1 698
4 TraesCS3A01G091900 chr5B 562419021 562419744 723 False 989.0 989 91.586 1026 1738 1 chr5B.!!$F1 712
5 TraesCS3A01G091900 chr1B 493682975 493683691 716 True 876.0 876 88.997 1033 1738 1 chr1B.!!$R2 705
6 TraesCS3A01G091900 chr1A 541157825 541158536 711 True 854.0 854 88.187 1026 1753 1 chr1A.!!$R1 727
7 TraesCS3A01G091900 chr4A 640149520 640150234 714 True 850.0 850 88.049 1026 1753 1 chr4A.!!$R1 727
8 TraesCS3A01G091900 chr7B 432763763 432764325 562 True 366.5 601 92.581 1041 1738 2 chr7B.!!$R1 697

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
606 613 0.037303 ACCCTGCTCCTGTGATTGTG 59.963 55.0 0.00 0.0 0.00 3.33 F
671 679 0.097674 GCGTGCACCTTAGCTTGATG 59.902 55.0 12.15 0.0 34.99 3.07 F
2093 2693 0.038744 CTGTCCATGGGGTTGAAGCT 59.961 55.0 13.02 0.0 34.93 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 2231 0.039180 TAGCTCGAACACCTCCCAGA 59.961 55.0 0.0 0.0 0.0 3.86 R
2342 2942 0.109532 TTCCGCATCACCAACCTTGA 59.890 50.0 0.0 0.0 0.0 3.02 R
2951 3576 0.997363 TTCCTCCCCTCACTCGTAGA 59.003 55.0 0.0 0.0 0.0 2.59 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
66 67 9.265901 TCAAGTTCTATCTATATTTGCTTCTGC 57.734 33.333 0.00 0.00 40.20 4.26
93 94 6.984474 AGTTTCGAACTGATGAACAAACTCTA 59.016 34.615 0.00 0.00 41.01 2.43
94 95 7.657761 AGTTTCGAACTGATGAACAAACTCTAT 59.342 33.333 0.00 0.00 41.01 1.98
96 97 8.462143 TTCGAACTGATGAACAAACTCTATAC 57.538 34.615 0.00 0.00 0.00 1.47
99 100 7.061905 CGAACTGATGAACAAACTCTATACGTT 59.938 37.037 0.00 0.00 0.00 3.99
100 101 7.582435 ACTGATGAACAAACTCTATACGTTG 57.418 36.000 0.00 0.00 0.00 4.10
110 111 3.128242 ACTCTATACGTTGGTGTTCTCCG 59.872 47.826 0.00 0.00 0.00 4.63
120 121 2.289195 TGGTGTTCTCCGTTGTGGTATC 60.289 50.000 0.00 0.00 39.52 2.24
121 122 2.289195 GGTGTTCTCCGTTGTGGTATCA 60.289 50.000 0.00 0.00 39.52 2.15
122 123 3.395639 GTGTTCTCCGTTGTGGTATCAA 58.604 45.455 0.00 0.00 39.52 2.57
123 124 4.000988 GTGTTCTCCGTTGTGGTATCAAT 58.999 43.478 0.00 0.00 39.52 2.57
124 125 4.454504 GTGTTCTCCGTTGTGGTATCAATT 59.545 41.667 0.00 0.00 39.52 2.32
125 126 5.640357 GTGTTCTCCGTTGTGGTATCAATTA 59.360 40.000 0.00 0.00 39.52 1.40
126 127 6.315393 GTGTTCTCCGTTGTGGTATCAATTAT 59.685 38.462 0.00 0.00 39.52 1.28
127 128 6.537301 TGTTCTCCGTTGTGGTATCAATTATC 59.463 38.462 0.00 0.00 39.52 1.75
155 157 3.262405 ACCATGCTTCTGAAATGGCAATT 59.738 39.130 17.16 0.00 43.96 2.32
196 198 2.421751 TCCCTCTGGTAGAGTTCTCG 57.578 55.000 5.24 0.00 40.72 4.04
223 225 1.732259 CATGTCACCAAGAAGTACGGC 59.268 52.381 0.00 0.00 0.00 5.68
228 230 0.320697 ACCAAGAAGTACGGCCTGTC 59.679 55.000 0.00 0.00 0.00 3.51
229 231 0.320374 CCAAGAAGTACGGCCTGTCA 59.680 55.000 0.00 0.00 0.00 3.58
244 246 1.080705 GTCACCGGACAAGGAGACG 60.081 63.158 9.46 0.00 43.73 4.18
319 326 2.156098 TCCACCCGCAGAATTTTGTAC 58.844 47.619 0.00 0.00 0.00 2.90
320 327 1.201414 CCACCCGCAGAATTTTGTACC 59.799 52.381 0.00 0.00 0.00 3.34
321 328 1.883275 CACCCGCAGAATTTTGTACCA 59.117 47.619 0.00 0.00 0.00 3.25
322 329 2.095263 CACCCGCAGAATTTTGTACCAG 60.095 50.000 0.00 0.00 0.00 4.00
324 331 3.244630 ACCCGCAGAATTTTGTACCAGTA 60.245 43.478 0.00 0.00 0.00 2.74
326 333 4.398044 CCCGCAGAATTTTGTACCAGTAAT 59.602 41.667 0.00 0.00 0.00 1.89
327 334 5.448632 CCCGCAGAATTTTGTACCAGTAATC 60.449 44.000 0.00 0.00 0.00 1.75
328 335 5.123186 CCGCAGAATTTTGTACCAGTAATCA 59.877 40.000 0.00 0.00 0.00 2.57
329 336 6.183360 CCGCAGAATTTTGTACCAGTAATCAT 60.183 38.462 0.00 0.00 0.00 2.45
330 337 7.011950 CCGCAGAATTTTGTACCAGTAATCATA 59.988 37.037 0.00 0.00 0.00 2.15
355 362 4.774124 TCCTGATCAAATTCCTGTGCTAG 58.226 43.478 0.00 0.00 0.00 3.42
360 367 7.333921 CCTGATCAAATTCCTGTGCTAGATATC 59.666 40.741 0.00 0.00 0.00 1.63
361 368 7.738847 TGATCAAATTCCTGTGCTAGATATCA 58.261 34.615 5.32 0.00 0.00 2.15
362 369 8.380867 TGATCAAATTCCTGTGCTAGATATCAT 58.619 33.333 5.32 0.00 0.00 2.45
370 377 5.474578 TGTGCTAGATATCATTCCTGTCC 57.525 43.478 5.32 0.00 0.00 4.02
371 378 4.021981 TGTGCTAGATATCATTCCTGTCCG 60.022 45.833 5.32 0.00 0.00 4.79
372 379 3.056536 TGCTAGATATCATTCCTGTCCGC 60.057 47.826 5.32 0.00 0.00 5.54
373 380 3.194542 GCTAGATATCATTCCTGTCCGCT 59.805 47.826 5.32 0.00 0.00 5.52
374 381 3.674528 AGATATCATTCCTGTCCGCTG 57.325 47.619 5.32 0.00 0.00 5.18
375 382 3.234353 AGATATCATTCCTGTCCGCTGA 58.766 45.455 5.32 0.00 0.00 4.26
376 383 3.837146 AGATATCATTCCTGTCCGCTGAT 59.163 43.478 5.32 0.00 0.00 2.90
380 387 0.254178 ATTCCTGTCCGCTGATTGCT 59.746 50.000 0.00 0.00 40.11 3.91
383 390 0.463295 CCTGTCCGCTGATTGCTGAT 60.463 55.000 0.00 0.00 37.26 2.90
385 392 1.063616 CTGTCCGCTGATTGCTGATTG 59.936 52.381 0.00 0.00 37.26 2.67
392 399 3.727079 CGCTGATTGCTGATTGTCTTGTC 60.727 47.826 0.00 0.00 40.11 3.18
394 401 3.402110 TGATTGCTGATTGTCTTGTCGT 58.598 40.909 0.00 0.00 0.00 4.34
397 404 1.000717 TGCTGATTGTCTTGTCGTCGA 60.001 47.619 0.00 0.00 0.00 4.20
410 417 3.228749 TGTCGTCGAAACTACGTGATTC 58.771 45.455 0.00 0.00 41.08 2.52
423 430 1.079503 GTGATTCGCAGGTTGAGGTC 58.920 55.000 0.00 0.00 0.00 3.85
425 432 1.347707 TGATTCGCAGGTTGAGGTCTT 59.652 47.619 0.00 0.00 0.00 3.01
436 443 4.019231 AGGTTGAGGTCTTTGGGAAGATAC 60.019 45.833 0.00 0.00 43.41 2.24
516 523 1.522580 GGTCATCGGAAGCAGAGGC 60.523 63.158 0.00 0.00 41.61 4.70
563 570 3.417069 CCCACAGGTTCAGTTGTATGA 57.583 47.619 0.00 0.00 0.00 2.15
564 571 3.955471 CCCACAGGTTCAGTTGTATGAT 58.045 45.455 0.00 0.00 0.00 2.45
565 572 4.335416 CCCACAGGTTCAGTTGTATGATT 58.665 43.478 0.00 0.00 0.00 2.57
566 573 4.396166 CCCACAGGTTCAGTTGTATGATTC 59.604 45.833 0.00 0.00 0.00 2.52
567 574 5.248640 CCACAGGTTCAGTTGTATGATTCT 58.751 41.667 0.00 0.00 0.00 2.40
568 575 5.707298 CCACAGGTTCAGTTGTATGATTCTT 59.293 40.000 0.00 0.00 0.00 2.52
569 576 6.878923 CCACAGGTTCAGTTGTATGATTCTTA 59.121 38.462 0.00 0.00 0.00 2.10
570 577 7.390440 CCACAGGTTCAGTTGTATGATTCTTAA 59.610 37.037 0.00 0.00 0.00 1.85
571 578 8.950210 CACAGGTTCAGTTGTATGATTCTTAAT 58.050 33.333 0.00 0.00 0.00 1.40
595 602 9.542462 AATAAAAGTTAAAGAAAAACCCTGCTC 57.458 29.630 0.00 0.00 0.00 4.26
596 603 5.531122 AAGTTAAAGAAAAACCCTGCTCC 57.469 39.130 0.00 0.00 0.00 4.70
597 604 4.804597 AGTTAAAGAAAAACCCTGCTCCT 58.195 39.130 0.00 0.00 0.00 3.69
598 605 4.584743 AGTTAAAGAAAAACCCTGCTCCTG 59.415 41.667 0.00 0.00 0.00 3.86
599 606 2.755952 AAGAAAAACCCTGCTCCTGT 57.244 45.000 0.00 0.00 0.00 4.00
600 607 1.986882 AGAAAAACCCTGCTCCTGTG 58.013 50.000 0.00 0.00 0.00 3.66
601 608 1.494721 AGAAAAACCCTGCTCCTGTGA 59.505 47.619 0.00 0.00 0.00 3.58
602 609 2.108952 AGAAAAACCCTGCTCCTGTGAT 59.891 45.455 0.00 0.00 0.00 3.06
603 610 2.683211 AAAACCCTGCTCCTGTGATT 57.317 45.000 0.00 0.00 0.00 2.57
604 611 1.915141 AAACCCTGCTCCTGTGATTG 58.085 50.000 0.00 0.00 0.00 2.67
605 612 0.773644 AACCCTGCTCCTGTGATTGT 59.226 50.000 0.00 0.00 0.00 2.71
606 613 0.037303 ACCCTGCTCCTGTGATTGTG 59.963 55.000 0.00 0.00 0.00 3.33
607 614 0.679002 CCCTGCTCCTGTGATTGTGG 60.679 60.000 0.00 0.00 0.00 4.17
610 617 0.890542 TGCTCCTGTGATTGTGGCAC 60.891 55.000 11.55 11.55 36.81 5.01
613 620 0.602638 TCCTGTGATTGTGGCACGTC 60.603 55.000 13.77 13.84 39.07 4.34
618 625 1.964373 GATTGTGGCACGTCCGGTT 60.964 57.895 13.77 0.00 37.80 4.44
620 627 2.668185 ATTGTGGCACGTCCGGTTCA 62.668 55.000 13.77 0.00 37.80 3.18
622 629 1.079681 GTGGCACGTCCGGTTCATA 60.080 57.895 0.00 0.00 37.80 2.15
636 643 3.602483 GGTTCATAGCCGAACTTTACCA 58.398 45.455 10.14 0.00 43.92 3.25
637 644 4.196971 GGTTCATAGCCGAACTTTACCAT 58.803 43.478 10.14 0.00 43.92 3.55
638 645 4.035208 GGTTCATAGCCGAACTTTACCATG 59.965 45.833 10.14 0.00 43.92 3.66
650 658 3.370978 ACTTTACCATGATTTGTCGAGCG 59.629 43.478 0.00 0.00 0.00 5.03
655 663 1.014044 ATGATTTGTCGAGCGTGCGT 61.014 50.000 0.00 0.00 0.00 5.24
656 664 1.225475 GATTTGTCGAGCGTGCGTG 60.225 57.895 0.00 0.00 0.00 5.34
663 671 2.736995 GAGCGTGCGTGCACCTTA 60.737 61.111 18.51 0.00 43.49 2.69
665 673 4.445545 GCGTGCGTGCACCTTAGC 62.446 66.667 18.51 12.29 43.49 3.09
666 674 2.738521 CGTGCGTGCACCTTAGCT 60.739 61.111 18.51 0.00 43.49 3.32
667 675 2.317609 CGTGCGTGCACCTTAGCTT 61.318 57.895 18.51 0.00 43.49 3.74
668 676 1.207593 GTGCGTGCACCTTAGCTTG 59.792 57.895 13.90 0.00 40.79 4.01
669 677 1.070615 TGCGTGCACCTTAGCTTGA 59.929 52.632 12.15 0.00 34.99 3.02
670 678 0.321564 TGCGTGCACCTTAGCTTGAT 60.322 50.000 12.15 0.00 34.99 2.57
671 679 0.097674 GCGTGCACCTTAGCTTGATG 59.902 55.000 12.15 0.00 34.99 3.07
673 681 1.675714 CGTGCACCTTAGCTTGATGGA 60.676 52.381 12.15 0.00 34.99 3.41
674 682 1.740025 GTGCACCTTAGCTTGATGGAC 59.260 52.381 5.22 0.00 34.99 4.02
676 684 2.040278 TGCACCTTAGCTTGATGGACTT 59.960 45.455 0.00 0.00 34.99 3.01
677 685 2.421424 GCACCTTAGCTTGATGGACTTG 59.579 50.000 0.00 0.00 0.00 3.16
678 686 3.869912 GCACCTTAGCTTGATGGACTTGA 60.870 47.826 0.00 0.00 0.00 3.02
679 687 4.326826 CACCTTAGCTTGATGGACTTGAA 58.673 43.478 0.00 0.00 0.00 2.69
680 688 4.154918 CACCTTAGCTTGATGGACTTGAAC 59.845 45.833 0.00 0.00 0.00 3.18
681 689 3.691609 CCTTAGCTTGATGGACTTGAACC 59.308 47.826 0.00 0.00 0.00 3.62
682 690 4.566488 CCTTAGCTTGATGGACTTGAACCT 60.566 45.833 0.00 0.00 0.00 3.50
683 691 2.787994 AGCTTGATGGACTTGAACCTG 58.212 47.619 0.00 0.00 0.00 4.00
685 693 3.327757 AGCTTGATGGACTTGAACCTGTA 59.672 43.478 0.00 0.00 0.00 2.74
686 694 3.437049 GCTTGATGGACTTGAACCTGTAC 59.563 47.826 0.00 0.00 0.00 2.90
687 695 4.641396 CTTGATGGACTTGAACCTGTACA 58.359 43.478 0.00 0.00 0.00 2.90
688 696 4.908601 TGATGGACTTGAACCTGTACAT 57.091 40.909 0.00 0.00 40.13 2.29
689 697 4.578871 TGATGGACTTGAACCTGTACATG 58.421 43.478 0.00 0.00 37.81 3.21
690 698 4.285775 TGATGGACTTGAACCTGTACATGA 59.714 41.667 0.00 0.00 37.81 3.07
692 700 3.244422 TGGACTTGAACCTGTACATGACC 60.244 47.826 0.00 0.00 0.00 4.02
693 701 3.244422 GGACTTGAACCTGTACATGACCA 60.244 47.826 0.00 0.00 0.00 4.02
695 703 4.326826 ACTTGAACCTGTACATGACCATG 58.673 43.478 0.00 8.34 44.15 3.66
696 704 3.348647 TGAACCTGTACATGACCATGG 57.651 47.619 11.19 11.19 42.91 3.66
697 705 2.642311 TGAACCTGTACATGACCATGGT 59.358 45.455 19.89 19.89 42.91 3.55
698 706 2.787473 ACCTGTACATGACCATGGTG 57.213 50.000 25.52 11.08 42.91 4.17
699 707 1.340017 ACCTGTACATGACCATGGTGC 60.340 52.381 25.52 14.46 42.91 5.01
700 708 1.382522 CTGTACATGACCATGGTGCC 58.617 55.000 25.52 9.69 42.91 5.01
701 709 0.991146 TGTACATGACCATGGTGCCT 59.009 50.000 25.52 3.00 42.91 4.75
707 741 1.047002 TGACCATGGTGCCTTTTTGG 58.953 50.000 25.52 0.00 39.35 3.28
727 761 4.729918 CTTGGCGGCAGGGCTCTT 62.730 66.667 13.71 0.00 42.84 2.85
732 766 4.335647 CGGCAGGGCTCTTGGTGT 62.336 66.667 0.00 0.00 0.00 4.16
734 768 2.113986 GCAGGGCTCTTGGTGTGT 59.886 61.111 0.00 0.00 0.00 3.72
735 769 1.529244 GCAGGGCTCTTGGTGTGTT 60.529 57.895 0.00 0.00 0.00 3.32
738 772 2.617274 GGGCTCTTGGTGTGTTCGC 61.617 63.158 0.00 0.00 0.00 4.70
739 773 2.617274 GGCTCTTGGTGTGTTCGCC 61.617 63.158 0.00 0.00 43.87 5.54
740 774 2.617274 GCTCTTGGTGTGTTCGCCC 61.617 63.158 0.00 0.00 43.03 6.13
754 788 2.740826 GCCCGCGTCTGCTTTGTA 60.741 61.111 4.92 0.00 39.65 2.41
755 789 2.106683 GCCCGCGTCTGCTTTGTAT 61.107 57.895 4.92 0.00 39.65 2.29
756 790 1.644786 GCCCGCGTCTGCTTTGTATT 61.645 55.000 4.92 0.00 39.65 1.89
758 792 1.359848 CCGCGTCTGCTTTGTATTCT 58.640 50.000 4.92 0.00 39.65 2.40
759 793 1.324736 CCGCGTCTGCTTTGTATTCTC 59.675 52.381 4.92 0.00 39.65 2.87
760 794 1.992667 CGCGTCTGCTTTGTATTCTCA 59.007 47.619 0.00 0.00 39.65 3.27
761 795 2.222596 CGCGTCTGCTTTGTATTCTCAC 60.223 50.000 0.00 0.00 39.65 3.51
762 796 2.736721 GCGTCTGCTTTGTATTCTCACA 59.263 45.455 0.00 0.00 38.39 3.58
764 798 4.237724 CGTCTGCTTTGTATTCTCACAGA 58.762 43.478 0.00 0.00 0.00 3.41
765 799 4.867047 CGTCTGCTTTGTATTCTCACAGAT 59.133 41.667 0.00 0.00 35.37 2.90
766 800 6.036470 CGTCTGCTTTGTATTCTCACAGATA 58.964 40.000 0.00 0.00 35.37 1.98
767 801 6.020281 CGTCTGCTTTGTATTCTCACAGATAC 60.020 42.308 0.00 0.00 35.37 2.24
768 802 7.038659 GTCTGCTTTGTATTCTCACAGATACT 58.961 38.462 0.00 0.00 35.37 2.12
786 1032 9.712305 ACAGATACTATATTTCATAGCAACACC 57.288 33.333 0.00 0.00 0.00 4.16
787 1033 9.710900 CAGATACTATATTTCATAGCAACACCA 57.289 33.333 0.00 0.00 0.00 4.17
791 1037 8.383318 ACTATATTTCATAGCAACACCATGAC 57.617 34.615 0.00 0.00 0.00 3.06
796 1042 4.334552 TCATAGCAACACCATGACATTGT 58.665 39.130 0.00 0.00 0.00 2.71
801 1047 3.119849 GCAACACCATGACATTGTACTCC 60.120 47.826 0.00 0.00 0.00 3.85
805 1051 4.000325 CACCATGACATTGTACTCCGAAA 59.000 43.478 0.00 0.00 0.00 3.46
806 1052 4.635765 CACCATGACATTGTACTCCGAAAT 59.364 41.667 0.00 0.00 0.00 2.17
808 1054 5.710099 ACCATGACATTGTACTCCGAAATTT 59.290 36.000 0.00 0.00 0.00 1.82
809 1055 6.882140 ACCATGACATTGTACTCCGAAATTTA 59.118 34.615 0.00 0.00 0.00 1.40
810 1056 7.148306 ACCATGACATTGTACTCCGAAATTTAC 60.148 37.037 0.00 0.00 0.00 2.01
811 1057 7.065803 CCATGACATTGTACTCCGAAATTTACT 59.934 37.037 0.00 0.00 0.00 2.24
812 1058 7.972832 TGACATTGTACTCCGAAATTTACTT 57.027 32.000 0.00 0.00 0.00 2.24
813 1059 7.802738 TGACATTGTACTCCGAAATTTACTTG 58.197 34.615 0.00 0.00 0.00 3.16
814 1060 7.094975 TGACATTGTACTCCGAAATTTACTTGG 60.095 37.037 0.00 0.00 0.00 3.61
815 1061 6.938030 ACATTGTACTCCGAAATTTACTTGGA 59.062 34.615 0.00 0.00 0.00 3.53
816 1062 7.446013 ACATTGTACTCCGAAATTTACTTGGAA 59.554 33.333 0.00 0.00 0.00 3.53
817 1063 7.429636 TTGTACTCCGAAATTTACTTGGAAG 57.570 36.000 0.00 0.00 0.00 3.46
818 1064 5.410439 TGTACTCCGAAATTTACTTGGAAGC 59.590 40.000 0.00 0.00 0.00 3.86
819 1065 4.652822 ACTCCGAAATTTACTTGGAAGCT 58.347 39.130 0.00 0.00 0.00 3.74
820 1066 5.801380 ACTCCGAAATTTACTTGGAAGCTA 58.199 37.500 0.00 0.00 0.00 3.32
821 1067 6.415573 ACTCCGAAATTTACTTGGAAGCTAT 58.584 36.000 0.00 0.00 0.00 2.97
822 1068 6.316390 ACTCCGAAATTTACTTGGAAGCTATG 59.684 38.462 0.00 0.00 0.00 2.23
823 1069 6.411376 TCCGAAATTTACTTGGAAGCTATGA 58.589 36.000 0.00 0.00 0.00 2.15
824 1070 7.054124 TCCGAAATTTACTTGGAAGCTATGAT 58.946 34.615 0.00 0.00 0.00 2.45
825 1071 7.012327 TCCGAAATTTACTTGGAAGCTATGATG 59.988 37.037 0.00 0.00 0.00 3.07
833 1079 9.679661 TTACTTGGAAGCTATGATGAAATTACA 57.320 29.630 0.00 0.00 0.00 2.41
834 1080 8.579850 ACTTGGAAGCTATGATGAAATTACAA 57.420 30.769 0.00 0.00 0.00 2.41
871 1409 4.832248 TGGAATGTGGAGTGTAGTTCATC 58.168 43.478 0.00 0.00 0.00 2.92
872 1410 4.285775 TGGAATGTGGAGTGTAGTTCATCA 59.714 41.667 0.00 0.00 0.00 3.07
873 1411 5.045651 TGGAATGTGGAGTGTAGTTCATCAT 60.046 40.000 0.00 0.00 0.00 2.45
875 1413 6.703607 GGAATGTGGAGTGTAGTTCATCATAG 59.296 42.308 0.00 0.00 0.00 2.23
876 1414 5.011090 TGTGGAGTGTAGTTCATCATAGC 57.989 43.478 0.00 0.00 0.00 2.97
877 1415 4.466015 TGTGGAGTGTAGTTCATCATAGCA 59.534 41.667 0.00 0.00 0.00 3.49
878 1416 5.046663 TGTGGAGTGTAGTTCATCATAGCAA 60.047 40.000 0.00 0.00 0.00 3.91
879 1417 5.874810 GTGGAGTGTAGTTCATCATAGCAAA 59.125 40.000 0.00 0.00 0.00 3.68
880 1418 5.874810 TGGAGTGTAGTTCATCATAGCAAAC 59.125 40.000 0.00 0.00 0.00 2.93
881 1419 5.874810 GGAGTGTAGTTCATCATAGCAAACA 59.125 40.000 0.00 0.00 0.00 2.83
882 1420 6.183360 GGAGTGTAGTTCATCATAGCAAACAC 60.183 42.308 0.00 0.00 35.97 3.32
883 1421 6.467677 AGTGTAGTTCATCATAGCAAACACT 58.532 36.000 0.00 0.00 39.97 3.55
885 1423 5.643348 TGTAGTTCATCATAGCAAACACTGG 59.357 40.000 0.00 0.00 0.00 4.00
886 1424 4.012374 AGTTCATCATAGCAAACACTGGG 58.988 43.478 0.00 0.00 0.00 4.45
888 1426 4.032960 TCATCATAGCAAACACTGGGTT 57.967 40.909 0.00 0.00 42.98 4.11
896 1434 3.758715 AACACTGGGTTTTTGCAGC 57.241 47.368 0.00 0.00 35.82 5.25
901 1439 0.881600 CTGGGTTTTTGCAGCTTGCC 60.882 55.000 5.82 0.00 44.23 4.52
907 1445 1.427592 TTTTGCAGCTTGCCGTTTGC 61.428 50.000 5.82 0.00 44.23 3.68
915 1453 1.067915 GCTTGCCGTTTGCCATCTTAA 60.068 47.619 0.00 0.00 40.16 1.85
925 1463 5.007234 CGTTTGCCATCTTAATCGTCCATTA 59.993 40.000 0.00 0.00 0.00 1.90
926 1464 6.199393 GTTTGCCATCTTAATCGTCCATTAC 58.801 40.000 0.00 0.00 0.00 1.89
927 1465 5.290493 TGCCATCTTAATCGTCCATTACT 57.710 39.130 0.00 0.00 0.00 2.24
929 1467 5.527214 TGCCATCTTAATCGTCCATTACTTG 59.473 40.000 0.00 0.00 0.00 3.16
930 1468 5.758296 GCCATCTTAATCGTCCATTACTTGA 59.242 40.000 0.00 0.00 0.00 3.02
931 1469 6.428159 GCCATCTTAATCGTCCATTACTTGAT 59.572 38.462 0.00 0.00 0.00 2.57
932 1470 7.360438 GCCATCTTAATCGTCCATTACTTGATC 60.360 40.741 0.00 0.00 0.00 2.92
944 1517 1.741401 CTTGATCGGTGCCGCTTCA 60.741 57.895 5.64 8.60 39.59 3.02
1003 1576 1.391577 TTCATTCGATGGCCACATGG 58.608 50.000 8.16 0.00 37.47 3.66
1917 2517 1.818363 CTCGCTGATGGTGCATGCT 60.818 57.895 20.33 0.00 0.00 3.79
1918 2518 1.374343 CTCGCTGATGGTGCATGCTT 61.374 55.000 20.33 0.66 0.00 3.91
1964 2564 3.991051 ACGTGAGCAGTGGGACGG 61.991 66.667 0.00 0.00 36.14 4.79
2034 2634 0.172578 TCGGAGTACATTGCCGTGAG 59.827 55.000 13.57 0.00 45.02 3.51
2064 2664 1.228644 TGAGGCCATGCAGTTGCTT 60.229 52.632 5.01 0.00 42.66 3.91
2081 2681 3.159472 TGCTTCAAGAAATGCTGTCCAT 58.841 40.909 0.00 0.00 35.06 3.41
2093 2693 0.038744 CTGTCCATGGGGTTGAAGCT 59.961 55.000 13.02 0.00 34.93 3.74
2169 2769 1.338655 GATGAGGGCTCGGAGTACTTC 59.661 57.143 6.90 6.90 0.00 3.01
2298 2898 3.699067 GGCAATGATCGACAAAGGAATG 58.301 45.455 0.00 0.00 0.00 2.67
2342 2942 2.632377 CAAGCTCATTGATGGGTACGT 58.368 47.619 0.00 0.00 41.83 3.57
2637 3237 2.367567 GTTAATCCCCTCTGCGGATACA 59.632 50.000 0.00 0.00 39.28 2.29
2721 3321 3.304659 CGCAGTTAGATGGTTTGTGCTTT 60.305 43.478 0.00 0.00 0.00 3.51
2728 3328 4.415596 AGATGGTTTGTGCTTTATGGGAA 58.584 39.130 0.00 0.00 0.00 3.97
2768 3368 4.099573 TGAAGGATAGGCGAAGGTAAAGAG 59.900 45.833 0.00 0.00 0.00 2.85
2828 3453 9.542462 TCTACATATTGCACTTATTGTACCTTC 57.458 33.333 0.00 0.00 0.00 3.46
2935 3560 2.365237 GGCCTCCCTAACTCCCGT 60.365 66.667 0.00 0.00 0.00 5.28
2951 3576 1.238439 CCGTGAACATGAAACCTGCT 58.762 50.000 0.00 0.00 0.00 4.24
2986 3611 5.340027 GGGGAGGAATTACAAGAGAATCCAA 60.340 44.000 0.00 0.00 33.66 3.53
3035 3660 7.413877 GCAAACAATCTGAGATTCTAGTTGGAG 60.414 40.741 12.77 7.28 0.00 3.86
3089 3714 1.090052 GGCCAACCTACGATGCAGAC 61.090 60.000 0.00 0.00 0.00 3.51
3118 3760 4.225942 TGGAGTCCAGACAAGATTATTGCT 59.774 41.667 8.12 0.00 0.00 3.91
3221 3865 7.794041 TGTTACTGTAAGGGTTTGTTCTTCTA 58.206 34.615 0.00 0.00 39.30 2.10
3433 4078 6.310224 TGTTCAGTGCTTTTAAGTTTTCTTGC 59.690 34.615 0.00 0.00 40.70 4.01
3493 4139 5.728351 TTTCAGTCAACAGTTAACTTCCG 57.272 39.130 5.07 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.116806 CACTCGCTATACCTATCCTACAGAT 58.883 44.000 0.00 0.00 39.15 2.90
57 58 1.333619 GTTCGAAACTGGCAGAAGCAA 59.666 47.619 23.66 4.10 44.61 3.91
81 82 5.603596 ACACCAACGTATAGAGTTTGTTCA 58.396 37.500 0.00 0.00 0.00 3.18
89 90 3.128242 ACGGAGAACACCAACGTATAGAG 59.872 47.826 0.00 0.00 35.85 2.43
93 94 2.224113 ACAACGGAGAACACCAACGTAT 60.224 45.455 0.00 0.00 36.69 3.06
94 95 1.136695 ACAACGGAGAACACCAACGTA 59.863 47.619 0.00 0.00 36.69 3.57
96 97 0.303493 CACAACGGAGAACACCAACG 59.697 55.000 0.00 0.00 0.00 4.10
99 100 1.121378 TACCACAACGGAGAACACCA 58.879 50.000 0.00 0.00 38.63 4.17
100 101 2.289195 TGATACCACAACGGAGAACACC 60.289 50.000 0.00 0.00 38.63 4.16
120 121 9.806203 TTCAGAAGCATGGTAATTTGATAATTG 57.194 29.630 0.00 0.00 35.61 2.32
123 124 9.806203 CATTTCAGAAGCATGGTAATTTGATAA 57.194 29.630 0.00 0.00 0.00 1.75
124 125 8.415553 CCATTTCAGAAGCATGGTAATTTGATA 58.584 33.333 0.00 0.00 33.90 2.15
125 126 7.270047 CCATTTCAGAAGCATGGTAATTTGAT 58.730 34.615 0.00 0.00 33.90 2.57
126 127 6.632909 CCATTTCAGAAGCATGGTAATTTGA 58.367 36.000 0.00 0.00 33.90 2.69
127 128 5.292589 GCCATTTCAGAAGCATGGTAATTTG 59.707 40.000 13.36 0.00 39.88 2.32
155 157 1.806542 GAGCGCTGAAATCCACAAGAA 59.193 47.619 18.48 0.00 0.00 2.52
196 198 1.000896 CTTGGTGACATGGGGGTCC 60.001 63.158 0.00 0.00 42.32 4.46
228 230 2.432628 GCGTCTCCTTGTCCGGTG 60.433 66.667 0.00 0.00 0.00 4.94
229 231 2.600769 AGCGTCTCCTTGTCCGGT 60.601 61.111 0.00 0.00 0.00 5.28
244 246 2.621517 CTTGGGCCAGGATCTCCAGC 62.622 65.000 10.68 1.06 38.89 4.85
303 310 2.159382 ACTGGTACAAAATTCTGCGGG 58.841 47.619 0.00 0.00 38.70 6.13
306 313 9.503427 GTTATGATTACTGGTACAAAATTCTGC 57.497 33.333 0.00 0.00 38.70 4.26
319 326 8.915057 ATTTGATCAGGAGTTATGATTACTGG 57.085 34.615 0.00 0.00 37.52 4.00
321 328 9.566432 GGAATTTGATCAGGAGTTATGATTACT 57.434 33.333 0.00 0.00 37.52 2.24
322 329 9.566432 AGGAATTTGATCAGGAGTTATGATTAC 57.434 33.333 0.00 0.00 37.52 1.89
324 331 8.057623 ACAGGAATTTGATCAGGAGTTATGATT 58.942 33.333 0.00 0.00 37.52 2.57
326 333 6.825213 CACAGGAATTTGATCAGGAGTTATGA 59.175 38.462 0.00 0.00 0.00 2.15
327 334 6.459298 GCACAGGAATTTGATCAGGAGTTATG 60.459 42.308 0.00 0.00 0.00 1.90
328 335 5.591877 GCACAGGAATTTGATCAGGAGTTAT 59.408 40.000 0.00 0.00 0.00 1.89
329 336 4.943705 GCACAGGAATTTGATCAGGAGTTA 59.056 41.667 0.00 0.00 0.00 2.24
330 337 3.760684 GCACAGGAATTTGATCAGGAGTT 59.239 43.478 0.00 0.00 0.00 3.01
346 353 5.477510 GACAGGAATGATATCTAGCACAGG 58.522 45.833 3.98 0.00 0.00 4.00
355 362 3.667497 TCAGCGGACAGGAATGATATC 57.333 47.619 0.00 0.00 0.00 1.63
360 367 0.379669 GCAATCAGCGGACAGGAATG 59.620 55.000 0.00 0.00 0.00 2.67
361 368 2.785868 GCAATCAGCGGACAGGAAT 58.214 52.632 0.00 0.00 0.00 3.01
362 369 4.301505 GCAATCAGCGGACAGGAA 57.698 55.556 0.00 0.00 0.00 3.36
371 378 3.727079 CGACAAGACAATCAGCAATCAGC 60.727 47.826 0.00 0.00 46.19 4.26
372 379 3.434641 ACGACAAGACAATCAGCAATCAG 59.565 43.478 0.00 0.00 0.00 2.90
373 380 3.402110 ACGACAAGACAATCAGCAATCA 58.598 40.909 0.00 0.00 0.00 2.57
374 381 3.482598 CGACGACAAGACAATCAGCAATC 60.483 47.826 0.00 0.00 0.00 2.67
375 382 2.413112 CGACGACAAGACAATCAGCAAT 59.587 45.455 0.00 0.00 0.00 3.56
376 383 1.792367 CGACGACAAGACAATCAGCAA 59.208 47.619 0.00 0.00 0.00 3.91
380 387 3.713288 AGTTTCGACGACAAGACAATCA 58.287 40.909 0.00 0.00 0.00 2.57
383 390 3.038017 CGTAGTTTCGACGACAAGACAA 58.962 45.455 0.00 0.00 42.98 3.18
385 392 2.399754 CACGTAGTTTCGACGACAAGAC 59.600 50.000 0.00 0.00 41.61 3.01
392 399 1.008745 GCGAATCACGTAGTTTCGACG 60.009 52.381 22.85 8.11 46.98 5.12
394 401 2.247637 CTGCGAATCACGTAGTTTCGA 58.752 47.619 22.85 11.73 46.98 3.71
410 417 1.237285 CCCAAAGACCTCAACCTGCG 61.237 60.000 0.00 0.00 0.00 5.18
436 443 3.885521 GGTCGGGTCGCCGTAGAG 61.886 72.222 1.33 0.00 34.52 2.43
465 472 1.816863 GAACCAGGTCGACTGCCTCA 61.817 60.000 16.46 0.00 46.14 3.86
544 551 5.248640 AGAATCATACAACTGAACCTGTGG 58.751 41.667 0.00 0.00 0.00 4.17
569 576 9.542462 GAGCAGGGTTTTTCTTTAACTTTTATT 57.458 29.630 0.00 0.00 0.00 1.40
570 577 8.148351 GGAGCAGGGTTTTTCTTTAACTTTTAT 58.852 33.333 0.00 0.00 0.00 1.40
571 578 7.343574 AGGAGCAGGGTTTTTCTTTAACTTTTA 59.656 33.333 0.00 0.00 0.00 1.52
572 579 6.156256 AGGAGCAGGGTTTTTCTTTAACTTTT 59.844 34.615 0.00 0.00 0.00 2.27
573 580 5.661312 AGGAGCAGGGTTTTTCTTTAACTTT 59.339 36.000 0.00 0.00 0.00 2.66
574 581 5.069119 CAGGAGCAGGGTTTTTCTTTAACTT 59.931 40.000 0.00 0.00 0.00 2.66
575 582 4.584743 CAGGAGCAGGGTTTTTCTTTAACT 59.415 41.667 0.00 0.00 0.00 2.24
576 583 4.341235 ACAGGAGCAGGGTTTTTCTTTAAC 59.659 41.667 0.00 0.00 0.00 2.01
577 584 4.340950 CACAGGAGCAGGGTTTTTCTTTAA 59.659 41.667 0.00 0.00 0.00 1.52
578 585 3.888930 CACAGGAGCAGGGTTTTTCTTTA 59.111 43.478 0.00 0.00 0.00 1.85
579 586 2.695147 CACAGGAGCAGGGTTTTTCTTT 59.305 45.455 0.00 0.00 0.00 2.52
580 587 2.091885 TCACAGGAGCAGGGTTTTTCTT 60.092 45.455 0.00 0.00 0.00 2.52
581 588 1.494721 TCACAGGAGCAGGGTTTTTCT 59.505 47.619 0.00 0.00 0.00 2.52
582 589 1.981256 TCACAGGAGCAGGGTTTTTC 58.019 50.000 0.00 0.00 0.00 2.29
583 590 2.629617 CAATCACAGGAGCAGGGTTTTT 59.370 45.455 0.00 0.00 0.00 1.94
584 591 2.242043 CAATCACAGGAGCAGGGTTTT 58.758 47.619 0.00 0.00 0.00 2.43
585 592 1.145738 ACAATCACAGGAGCAGGGTTT 59.854 47.619 0.00 0.00 0.00 3.27
586 593 0.773644 ACAATCACAGGAGCAGGGTT 59.226 50.000 0.00 0.00 0.00 4.11
587 594 0.037303 CACAATCACAGGAGCAGGGT 59.963 55.000 0.00 0.00 0.00 4.34
588 595 0.679002 CCACAATCACAGGAGCAGGG 60.679 60.000 0.00 0.00 0.00 4.45
589 596 1.310933 GCCACAATCACAGGAGCAGG 61.311 60.000 0.00 0.00 0.00 4.85
590 597 0.607217 TGCCACAATCACAGGAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
591 598 0.890542 GTGCCACAATCACAGGAGCA 60.891 55.000 0.00 0.00 34.73 4.26
592 599 1.878775 GTGCCACAATCACAGGAGC 59.121 57.895 0.00 0.00 34.73 4.70
593 600 0.603707 ACGTGCCACAATCACAGGAG 60.604 55.000 0.00 0.00 34.27 3.69
594 601 0.602638 GACGTGCCACAATCACAGGA 60.603 55.000 0.00 0.00 34.27 3.86
595 602 1.577328 GGACGTGCCACAATCACAGG 61.577 60.000 0.00 0.00 36.34 4.00
596 603 1.868997 GGACGTGCCACAATCACAG 59.131 57.895 0.00 0.00 36.34 3.66
597 604 1.958715 CGGACGTGCCACAATCACA 60.959 57.895 0.00 0.00 35.94 3.58
598 605 2.677003 CCGGACGTGCCACAATCAC 61.677 63.158 0.00 0.00 35.94 3.06
599 606 2.358125 CCGGACGTGCCACAATCA 60.358 61.111 0.00 0.00 35.94 2.57
600 607 1.908066 GAACCGGACGTGCCACAATC 61.908 60.000 9.46 0.00 35.94 2.67
601 608 1.964373 GAACCGGACGTGCCACAAT 60.964 57.895 9.46 0.00 35.94 2.71
602 609 2.589442 GAACCGGACGTGCCACAA 60.589 61.111 9.46 0.00 35.94 3.33
603 610 1.817911 TATGAACCGGACGTGCCACA 61.818 55.000 9.46 0.00 35.94 4.17
604 611 1.079681 TATGAACCGGACGTGCCAC 60.080 57.895 9.46 0.00 35.94 5.01
605 612 1.216977 CTATGAACCGGACGTGCCA 59.783 57.895 9.46 0.00 35.94 4.92
606 613 2.171725 GCTATGAACCGGACGTGCC 61.172 63.158 9.46 0.00 0.00 5.01
607 614 2.171725 GGCTATGAACCGGACGTGC 61.172 63.158 9.46 0.00 0.00 5.34
618 625 4.746535 TCATGGTAAAGTTCGGCTATGA 57.253 40.909 0.00 0.00 0.00 2.15
620 627 5.885912 ACAAATCATGGTAAAGTTCGGCTAT 59.114 36.000 0.00 0.00 0.00 2.97
622 629 4.079253 ACAAATCATGGTAAAGTTCGGCT 58.921 39.130 0.00 0.00 0.00 5.52
636 643 1.014044 ACGCACGCTCGACAAATCAT 61.014 50.000 3.88 0.00 0.00 2.45
637 644 1.663388 ACGCACGCTCGACAAATCA 60.663 52.632 3.88 0.00 0.00 2.57
638 645 1.225475 CACGCACGCTCGACAAATC 60.225 57.895 3.88 0.00 0.00 2.17
650 658 1.207593 CAAGCTAAGGTGCACGCAC 59.792 57.895 13.78 13.78 45.49 5.34
655 663 1.630369 AGTCCATCAAGCTAAGGTGCA 59.370 47.619 0.00 0.00 34.99 4.57
656 664 2.409948 AGTCCATCAAGCTAAGGTGC 57.590 50.000 0.00 0.00 0.00 5.01
658 666 4.327680 GTTCAAGTCCATCAAGCTAAGGT 58.672 43.478 0.00 0.00 0.00 3.50
659 667 3.691609 GGTTCAAGTCCATCAAGCTAAGG 59.308 47.826 0.00 0.00 0.00 2.69
660 668 4.394300 CAGGTTCAAGTCCATCAAGCTAAG 59.606 45.833 0.00 0.00 0.00 2.18
661 669 4.202461 ACAGGTTCAAGTCCATCAAGCTAA 60.202 41.667 0.00 0.00 0.00 3.09
662 670 3.327757 ACAGGTTCAAGTCCATCAAGCTA 59.672 43.478 0.00 0.00 0.00 3.32
663 671 2.107204 ACAGGTTCAAGTCCATCAAGCT 59.893 45.455 0.00 0.00 0.00 3.74
665 673 4.641396 TGTACAGGTTCAAGTCCATCAAG 58.359 43.478 0.00 0.00 0.00 3.02
666 674 4.698201 TGTACAGGTTCAAGTCCATCAA 57.302 40.909 0.00 0.00 0.00 2.57
667 675 4.285775 TCATGTACAGGTTCAAGTCCATCA 59.714 41.667 7.49 0.00 0.00 3.07
668 676 4.631813 GTCATGTACAGGTTCAAGTCCATC 59.368 45.833 7.49 0.00 0.00 3.51
669 677 4.565652 GGTCATGTACAGGTTCAAGTCCAT 60.566 45.833 7.49 0.00 0.00 3.41
670 678 3.244422 GGTCATGTACAGGTTCAAGTCCA 60.244 47.826 7.49 0.00 0.00 4.02
671 679 3.244422 TGGTCATGTACAGGTTCAAGTCC 60.244 47.826 7.49 1.75 0.00 3.85
673 681 4.326826 CATGGTCATGTACAGGTTCAAGT 58.673 43.478 7.49 0.00 34.23 3.16
674 682 3.691118 CCATGGTCATGTACAGGTTCAAG 59.309 47.826 7.49 4.63 37.11 3.02
676 684 2.642311 ACCATGGTCATGTACAGGTTCA 59.358 45.455 13.00 7.59 37.11 3.18
677 685 3.009723 CACCATGGTCATGTACAGGTTC 58.990 50.000 16.53 2.52 37.11 3.62
678 686 2.879756 GCACCATGGTCATGTACAGGTT 60.880 50.000 16.53 0.00 37.11 3.50
679 687 1.340017 GCACCATGGTCATGTACAGGT 60.340 52.381 16.53 0.96 37.11 4.00
680 688 1.382522 GCACCATGGTCATGTACAGG 58.617 55.000 16.53 0.00 37.11 4.00
681 689 1.065199 AGGCACCATGGTCATGTACAG 60.065 52.381 16.53 1.82 37.11 2.74
682 690 0.991146 AGGCACCATGGTCATGTACA 59.009 50.000 16.53 0.00 37.11 2.90
683 691 2.128771 AAGGCACCATGGTCATGTAC 57.871 50.000 16.53 1.61 37.11 2.90
685 693 2.014010 AAAAGGCACCATGGTCATGT 57.986 45.000 16.53 0.00 37.11 3.21
686 694 2.613474 CCAAAAAGGCACCATGGTCATG 60.613 50.000 16.53 5.29 38.51 3.07
687 695 1.624813 CCAAAAAGGCACCATGGTCAT 59.375 47.619 16.53 4.97 0.00 3.06
688 696 1.047002 CCAAAAAGGCACCATGGTCA 58.953 50.000 16.53 0.00 0.00 4.02
689 697 1.047801 ACCAAAAAGGCACCATGGTC 58.952 50.000 16.53 10.07 40.23 4.02
690 698 1.416030 GAACCAAAAAGGCACCATGGT 59.584 47.619 13.00 13.00 45.97 3.55
692 700 3.132925 CAAGAACCAAAAAGGCACCATG 58.867 45.455 0.00 0.00 43.14 3.66
693 701 2.104622 CCAAGAACCAAAAAGGCACCAT 59.895 45.455 0.00 0.00 43.14 3.55
695 703 1.810031 GCCAAGAACCAAAAAGGCACC 60.810 52.381 0.00 0.00 43.14 5.01
696 704 1.581934 GCCAAGAACCAAAAAGGCAC 58.418 50.000 0.00 0.00 43.14 5.01
697 705 0.103937 CGCCAAGAACCAAAAAGGCA 59.896 50.000 0.00 0.00 42.10 4.75
698 706 0.599991 CCGCCAAGAACCAAAAAGGC 60.600 55.000 0.00 0.00 43.14 4.35
699 707 0.599991 GCCGCCAAGAACCAAAAAGG 60.600 55.000 0.00 0.00 45.67 3.11
700 708 0.103937 TGCCGCCAAGAACCAAAAAG 59.896 50.000 0.00 0.00 0.00 2.27
701 709 0.103937 CTGCCGCCAAGAACCAAAAA 59.896 50.000 0.00 0.00 0.00 1.94
734 768 4.980805 AAAGCAGACGCGGGCGAA 62.981 61.111 20.98 0.00 45.49 4.70
738 772 0.373716 GAATACAAAGCAGACGCGGG 59.626 55.000 12.47 0.00 45.49 6.13
739 773 1.324736 GAGAATACAAAGCAGACGCGG 59.675 52.381 12.47 0.00 45.49 6.46
740 774 1.992667 TGAGAATACAAAGCAGACGCG 59.007 47.619 3.53 3.53 45.49 6.01
743 777 7.038659 AGTATCTGTGAGAATACAAAGCAGAC 58.961 38.462 0.00 0.00 34.87 3.51
744 778 7.175347 AGTATCTGTGAGAATACAAAGCAGA 57.825 36.000 0.00 0.00 36.21 4.26
760 794 9.712305 GGTGTTGCTATGAAATATAGTATCTGT 57.288 33.333 0.00 0.00 0.00 3.41
761 795 9.710900 TGGTGTTGCTATGAAATATAGTATCTG 57.289 33.333 0.00 0.00 0.00 2.90
765 799 9.489084 GTCATGGTGTTGCTATGAAATATAGTA 57.511 33.333 0.00 0.00 44.80 1.82
766 800 7.992608 TGTCATGGTGTTGCTATGAAATATAGT 59.007 33.333 0.00 0.00 44.80 2.12
767 801 8.382030 TGTCATGGTGTTGCTATGAAATATAG 57.618 34.615 0.00 0.00 44.80 1.31
768 802 8.922931 ATGTCATGGTGTTGCTATGAAATATA 57.077 30.769 0.00 0.00 44.80 0.86
772 1018 5.243507 ACAATGTCATGGTGTTGCTATGAAA 59.756 36.000 0.00 0.00 44.80 2.69
777 1023 4.905429 AGTACAATGTCATGGTGTTGCTA 58.095 39.130 2.83 0.00 0.00 3.49
779 1025 3.119849 GGAGTACAATGTCATGGTGTTGC 60.120 47.826 2.83 0.00 0.00 4.17
783 1029 3.245518 TCGGAGTACAATGTCATGGTG 57.754 47.619 2.83 0.00 0.00 4.17
786 1032 7.974675 AGTAAATTTCGGAGTACAATGTCATG 58.025 34.615 0.00 0.00 0.00 3.07
787 1033 8.450964 CAAGTAAATTTCGGAGTACAATGTCAT 58.549 33.333 0.00 0.00 0.00 3.06
789 1035 7.118680 TCCAAGTAAATTTCGGAGTACAATGTC 59.881 37.037 0.00 0.00 0.00 3.06
790 1036 6.938030 TCCAAGTAAATTTCGGAGTACAATGT 59.062 34.615 0.00 0.00 0.00 2.71
791 1037 7.372451 TCCAAGTAAATTTCGGAGTACAATG 57.628 36.000 0.00 0.00 0.00 2.82
796 1042 5.801380 AGCTTCCAAGTAAATTTCGGAGTA 58.199 37.500 0.00 0.00 0.00 2.59
801 1047 7.919690 TCATCATAGCTTCCAAGTAAATTTCG 58.080 34.615 0.00 0.00 0.00 3.46
808 1054 9.679661 TTGTAATTTCATCATAGCTTCCAAGTA 57.320 29.630 0.00 0.00 0.00 2.24
809 1055 8.579850 TTGTAATTTCATCATAGCTTCCAAGT 57.420 30.769 0.00 0.00 0.00 3.16
810 1056 8.896744 TCTTGTAATTTCATCATAGCTTCCAAG 58.103 33.333 0.00 0.00 0.00 3.61
811 1057 8.806429 TCTTGTAATTTCATCATAGCTTCCAA 57.194 30.769 0.00 0.00 0.00 3.53
812 1058 8.806429 TTCTTGTAATTTCATCATAGCTTCCA 57.194 30.769 0.00 0.00 0.00 3.53
833 1079 7.888021 TCCACATTCCATGTACAGTATTTTCTT 59.112 33.333 0.33 0.00 42.70 2.52
834 1080 7.402054 TCCACATTCCATGTACAGTATTTTCT 58.598 34.615 0.33 0.00 42.70 2.52
839 1085 5.189736 ACACTCCACATTCCATGTACAGTAT 59.810 40.000 0.33 0.00 42.70 2.12
843 1089 4.530553 ACTACACTCCACATTCCATGTACA 59.469 41.667 0.00 0.00 42.70 2.90
844 1090 5.086104 ACTACACTCCACATTCCATGTAC 57.914 43.478 0.00 0.00 42.70 2.90
845 1091 5.247337 TGAACTACACTCCACATTCCATGTA 59.753 40.000 0.00 0.00 42.70 2.29
847 1093 4.578871 TGAACTACACTCCACATTCCATG 58.421 43.478 0.00 0.00 0.00 3.66
849 1095 4.285775 TGATGAACTACACTCCACATTCCA 59.714 41.667 0.00 0.00 0.00 3.53
850 1096 4.832248 TGATGAACTACACTCCACATTCC 58.168 43.478 0.00 0.00 0.00 3.01
852 1098 6.051717 GCTATGATGAACTACACTCCACATT 58.948 40.000 0.00 0.00 0.00 2.71
853 1099 5.129320 TGCTATGATGAACTACACTCCACAT 59.871 40.000 0.00 0.00 0.00 3.21
860 1398 6.402550 CCAGTGTTTGCTATGATGAACTACAC 60.403 42.308 0.00 0.00 34.98 2.90
862 1400 5.065218 CCCAGTGTTTGCTATGATGAACTAC 59.935 44.000 0.00 0.00 0.00 2.73
863 1401 5.185454 CCCAGTGTTTGCTATGATGAACTA 58.815 41.667 0.00 0.00 0.00 2.24
876 1414 1.665169 GCTGCAAAAACCCAGTGTTTG 59.335 47.619 6.09 6.09 46.39 2.93
878 1416 1.194218 AGCTGCAAAAACCCAGTGTT 58.806 45.000 1.02 0.00 39.43 3.32
879 1417 1.134729 CAAGCTGCAAAAACCCAGTGT 60.135 47.619 1.02 0.00 0.00 3.55
880 1418 1.574134 CAAGCTGCAAAAACCCAGTG 58.426 50.000 1.02 0.00 0.00 3.66
881 1419 0.179076 GCAAGCTGCAAAAACCCAGT 60.179 50.000 1.02 0.00 44.26 4.00
882 1420 2.608640 GCAAGCTGCAAAAACCCAG 58.391 52.632 1.02 0.00 44.26 4.45
883 1421 4.852962 GCAAGCTGCAAAAACCCA 57.147 50.000 1.02 0.00 44.26 4.51
893 1431 1.870055 AGATGGCAAACGGCAAGCTG 61.870 55.000 0.00 0.00 41.71 4.24
894 1432 1.181098 AAGATGGCAAACGGCAAGCT 61.181 50.000 0.00 0.00 46.43 3.74
901 1439 2.675844 TGGACGATTAAGATGGCAAACG 59.324 45.455 0.00 0.00 0.00 3.60
907 1445 7.148738 CGATCAAGTAATGGACGATTAAGATGG 60.149 40.741 0.00 3.07 32.72 3.51
915 1453 3.717707 CACCGATCAAGTAATGGACGAT 58.282 45.455 0.00 0.00 32.72 3.73
925 1463 1.741770 GAAGCGGCACCGATCAAGT 60.742 57.895 14.43 0.00 42.83 3.16
926 1464 1.091771 ATGAAGCGGCACCGATCAAG 61.092 55.000 14.43 0.00 42.83 3.02
927 1465 1.078497 ATGAAGCGGCACCGATCAA 60.078 52.632 14.43 0.00 42.83 2.57
929 1467 1.521457 TGATGAAGCGGCACCGATC 60.521 57.895 14.43 10.57 42.83 3.69
930 1468 1.815421 GTGATGAAGCGGCACCGAT 60.815 57.895 14.43 2.72 42.83 4.18
931 1469 2.434185 GTGATGAAGCGGCACCGA 60.434 61.111 14.43 0.00 42.83 4.69
932 1470 3.499737 GGTGATGAAGCGGCACCG 61.500 66.667 4.30 4.30 42.20 4.94
967 1540 3.637926 AAACGCCGCCGAGGTAGAC 62.638 63.158 0.00 0.00 43.70 2.59
968 1541 3.346631 GAAACGCCGCCGAGGTAGA 62.347 63.158 0.00 0.00 43.70 2.59
969 1542 2.884207 GAAACGCCGCCGAGGTAG 60.884 66.667 0.00 0.00 43.70 3.18
970 1543 2.510064 AATGAAACGCCGCCGAGGTA 62.510 55.000 0.00 0.00 43.70 3.08
971 1544 3.894547 AATGAAACGCCGCCGAGGT 62.895 57.895 0.00 0.00 43.70 3.85
972 1545 3.095898 GAATGAAACGCCGCCGAGG 62.096 63.158 0.00 0.00 44.97 4.63
1410 2010 2.811317 GCGTCCAGGAAGTGCGAG 60.811 66.667 4.13 0.00 0.00 5.03
1631 2231 0.039180 TAGCTCGAACACCTCCCAGA 59.961 55.000 0.00 0.00 0.00 3.86
1887 2487 0.728129 TCAGCGAGTAAGCAACGTCG 60.728 55.000 0.00 0.00 40.15 5.12
1917 2517 4.707934 TCCAGATCACCAATACGACAGTAA 59.292 41.667 0.00 0.00 36.29 2.24
1918 2518 4.274978 TCCAGATCACCAATACGACAGTA 58.725 43.478 0.00 0.00 37.24 2.74
1950 2550 3.321648 ATGCCGTCCCACTGCTCA 61.322 61.111 0.00 0.00 0.00 4.26
1964 2564 4.148825 AGCCTCGTCGGACCATGC 62.149 66.667 1.91 0.00 33.16 4.06
1995 2595 4.034048 CCGATGAGGCAAGTATACACAAAC 59.966 45.833 5.50 0.00 0.00 2.93
2034 2634 0.183492 TGGCCTCACTGATATTGCCC 59.817 55.000 3.32 0.00 38.10 5.36
2041 2641 0.330604 AACTGCATGGCCTCACTGAT 59.669 50.000 3.32 0.00 0.00 2.90
2064 2664 2.449464 CCCATGGACAGCATTTCTTGA 58.551 47.619 15.22 0.00 0.00 3.02
2081 2681 2.945440 GCATCATACAGCTTCAACCCCA 60.945 50.000 0.00 0.00 0.00 4.96
2169 2769 1.938577 CCTTCATGGAGCATCTTGTCG 59.061 52.381 0.00 0.00 38.35 4.35
2322 2922 2.609459 GACGTACCCATCAATGAGCTTG 59.391 50.000 0.00 0.00 36.09 4.01
2342 2942 0.109532 TTCCGCATCACCAACCTTGA 59.890 50.000 0.00 0.00 0.00 3.02
2457 3057 4.734266 ACTTCTCAGCTTCCTTTGGATTT 58.266 39.130 0.00 0.00 0.00 2.17
2637 3237 7.397221 TGACTCTTCTCACCAACATCATAAAT 58.603 34.615 0.00 0.00 0.00 1.40
2728 3328 2.694616 TCAGCCCCCTTTAGCTTTTT 57.305 45.000 0.00 0.00 37.18 1.94
2800 3400 7.931948 AGGTACAATAAGTGCAATATGTAGACC 59.068 37.037 7.38 8.65 34.11 3.85
2828 3453 7.700656 CCTACTATTTTTACCATTTCCTTTGCG 59.299 37.037 0.00 0.00 0.00 4.85
2836 3461 7.351166 TGGCTAGCCTACTATTTTTACCATTT 58.649 34.615 33.07 0.00 36.94 2.32
2867 3492 4.102113 GCAGCCTCATGGTGGTTT 57.898 55.556 7.35 0.00 42.81 3.27
2935 3560 3.006430 TCGTAGAGCAGGTTTCATGTTCA 59.994 43.478 0.00 0.00 31.02 3.18
2951 3576 0.997363 TTCCTCCCCTCACTCGTAGA 59.003 55.000 0.00 0.00 0.00 2.59
2986 3611 6.013842 CCTTACAAGGCGAGAAAAGAAAAT 57.986 37.500 0.00 0.00 39.76 1.82
3011 3636 7.821846 GTCTCCAACTAGAATCTCAGATTGTTT 59.178 37.037 4.06 0.00 0.00 2.83
3035 3660 5.117592 GCACACAAGCAGAAAATAACATGTC 59.882 40.000 0.00 0.00 0.00 3.06
3249 3893 6.071616 GCACTGGAAAAAGATTACCATTACCA 60.072 38.462 0.00 0.00 0.00 3.25
3250 3894 6.152831 AGCACTGGAAAAAGATTACCATTACC 59.847 38.462 0.00 0.00 0.00 2.85
3313 3958 8.344831 ACATGTGAATGACATTATAATGGTTCG 58.655 33.333 25.45 15.58 43.20 3.95
3388 4033 7.435305 TGAACATCAGCAAGATTTGAATCAAA 58.565 30.769 11.10 11.10 37.89 2.69
3493 4139 7.659390 AGCTATAATTAGGTCAAGCAGAATGTC 59.341 37.037 0.00 0.00 32.06 3.06


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

AutoCloner maintained by Alex Coulton.