Multiple sequence alignment - TraesCS4D01G272200

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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 TraesCS4D01G272200 chr4D 100.000 5839 0 0 1 5839 442548434 442554272 0.000000e+00 10783
1 TraesCS4D01G272200 chr4D 95.300 617 24 3 2 618 47729318 47728707 0.000000e+00 974
2 TraesCS4D01G272200 chr4B 94.413 3723 135 35 1547 5221 551048707 551052404 0.000000e+00 5655
3 TraesCS4D01G272200 chr4B 88.101 790 56 21 5083 5839 551052486 551053270 0.000000e+00 904
4 TraesCS4D01G272200 chr4B 89.307 664 26 15 693 1333 551047867 551048508 0.000000e+00 791
5 TraesCS4D01G272200 chr4A 95.071 1623 64 10 1665 3277 24861941 24860325 0.000000e+00 2540
6 TraesCS4D01G272200 chr4A 93.425 1597 72 20 3259 4848 24860295 24858725 0.000000e+00 2337
7 TraesCS4D01G272200 chr4A 93.767 722 36 6 4294 5012 24858624 24857909 0.000000e+00 1075
8 TraesCS4D01G272200 chr4A 82.948 909 57 51 701 1584 24862777 24861942 0.000000e+00 730
9 TraesCS4D01G272200 chrUn 93.629 722 37 6 4294 5012 339715842 339716557 0.000000e+00 1070
10 TraesCS4D01G272200 chrUn 93.629 722 37 6 4294 5012 397315816 397316531 0.000000e+00 1070
11 TraesCS4D01G272200 chrUn 94.669 619 29 2 2 619 83929024 83928409 0.000000e+00 957
12 TraesCS4D01G272200 chr1D 95.447 615 23 2 2 614 406828810 406828199 0.000000e+00 976
13 TraesCS4D01G272200 chr1D 94.146 615 29 5 2 614 415984396 415985005 0.000000e+00 929
14 TraesCS4D01G272200 chr2D 95.122 615 24 3 2 614 598269731 598269121 0.000000e+00 965
15 TraesCS4D01G272200 chr2D 94.634 615 26 3 2 614 47490704 47490095 0.000000e+00 946
16 TraesCS4D01G272200 chr6D 94.839 620 24 5 2 618 464465389 464466003 0.000000e+00 961
17 TraesCS4D01G272200 chr6D 95.041 605 27 1 2 606 14615555 14616156 0.000000e+00 948
18 TraesCS4D01G272200 chr5B 94.137 614 32 2 2 614 10581071 10581681 0.000000e+00 931
19 TraesCS4D01G272200 chr2A 88.221 399 42 4 4182 4578 780535433 780535038 6.850000e-129 472
20 TraesCS4D01G272200 chr1B 81.219 607 76 20 5083 5654 641205537 641206140 6.900000e-124 455
21 TraesCS4D01G272200 chr3A 86.047 430 51 7 4182 4608 126067178 126066755 2.480000e-123 453
22 TraesCS4D01G272200 chr3A 85.912 433 49 8 4182 4608 588385247 588385673 8.920000e-123 451
23 TraesCS4D01G272200 chr3B 85.227 440 56 7 4172 4608 314587842 314588275 1.490000e-120 444


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 TraesCS4D01G272200 chr4D 442548434 442554272 5838 False 10783.0 10783 100.00000 1 5839 1 chr4D.!!$F1 5838
1 TraesCS4D01G272200 chr4D 47728707 47729318 611 True 974.0 974 95.30000 2 618 1 chr4D.!!$R1 616
2 TraesCS4D01G272200 chr4B 551047867 551053270 5403 False 2450.0 5655 90.60700 693 5839 3 chr4B.!!$F1 5146
3 TraesCS4D01G272200 chr4A 24857909 24862777 4868 True 1670.5 2540 91.30275 701 5012 4 chr4A.!!$R1 4311
4 TraesCS4D01G272200 chrUn 339715842 339716557 715 False 1070.0 1070 93.62900 4294 5012 1 chrUn.!!$F1 718
5 TraesCS4D01G272200 chrUn 397315816 397316531 715 False 1070.0 1070 93.62900 4294 5012 1 chrUn.!!$F2 718
6 TraesCS4D01G272200 chrUn 83928409 83929024 615 True 957.0 957 94.66900 2 619 1 chrUn.!!$R1 617
7 TraesCS4D01G272200 chr1D 406828199 406828810 611 True 976.0 976 95.44700 2 614 1 chr1D.!!$R1 612
8 TraesCS4D01G272200 chr1D 415984396 415985005 609 False 929.0 929 94.14600 2 614 1 chr1D.!!$F1 612
9 TraesCS4D01G272200 chr2D 598269121 598269731 610 True 965.0 965 95.12200 2 614 1 chr2D.!!$R2 612
10 TraesCS4D01G272200 chr2D 47490095 47490704 609 True 946.0 946 94.63400 2 614 1 chr2D.!!$R1 612
11 TraesCS4D01G272200 chr6D 464465389 464466003 614 False 961.0 961 94.83900 2 618 1 chr6D.!!$F2 616
12 TraesCS4D01G272200 chr6D 14615555 14616156 601 False 948.0 948 95.04100 2 606 1 chr6D.!!$F1 604
13 TraesCS4D01G272200 chr5B 10581071 10581681 610 False 931.0 931 94.13700 2 614 1 chr5B.!!$F1 612
14 TraesCS4D01G272200 chr1B 641205537 641206140 603 False 455.0 455 81.21900 5083 5654 1 chr1B.!!$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
684 686 0.032130 TCGTGTGCTCCTGTCTTGTC 59.968 55.000 0.0 0.0 0.00 3.18 F
812 816 0.041535 AAAGCAGGCATGGAATGGGA 59.958 50.000 0.0 0.0 46.86 4.37 F
1313 1358 0.099436 CGTTGATGCAAAGCCCTAGC 59.901 55.000 0.0 0.0 40.32 3.42 F
1706 1790 0.179111 TCATCGGATTCAGACACGGC 60.179 55.000 0.0 0.0 0.00 5.68 F
3364 3516 1.349026 CCTCTGCTTCTGGAGTTTCCA 59.651 52.381 0.0 0.0 45.98 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 2381 0.110056 GTCGTGTCTTTGGCATGCAG 60.110 55.0 21.36 8.71 0.00 4.41 R
2482 2572 0.674895 GGAGCCTGTTAGCTGTGGTG 60.675 60.0 0.00 0.00 45.15 4.17 R
2621 2715 1.380524 TCGAACAAAAAGGGCACGAA 58.619 45.0 0.00 0.00 0.00 3.85 R
3517 3669 0.462581 TTAGCATCTCCCTTGCAGCG 60.463 55.0 0.00 0.00 42.62 5.18 R
5067 5898 0.105709 GAGGGAGGGGGAGAAGAGAG 60.106 65.0 0.00 0.00 0.00 3.20 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
144 145 8.528044 TTTTCTGTCTTGTTAGGGTTTATGTT 57.472 30.769 0.00 0.00 0.00 2.71
201 202 3.747852 AGATGGAATAAAGGTCTCCCCA 58.252 45.455 0.00 0.00 34.66 4.96
296 297 0.617935 TGGTGGATTTGCTCGGATCA 59.382 50.000 0.00 0.00 0.00 2.92
358 359 7.124599 TGAATCCTTCCAACCTACGTTATTCTA 59.875 37.037 0.00 0.00 0.00 2.10
396 397 2.125512 CTGGTGCGCTGGTCCTAC 60.126 66.667 9.73 0.00 0.00 3.18
478 480 3.458163 GAGGGGTGATGACGGCGA 61.458 66.667 16.62 0.00 0.00 5.54
508 510 1.661112 GGCTCGCTTTAGTGCTTGTAG 59.339 52.381 0.00 0.00 0.00 2.74
509 511 2.338500 GCTCGCTTTAGTGCTTGTAGT 58.662 47.619 0.00 0.00 0.00 2.73
510 512 2.345942 GCTCGCTTTAGTGCTTGTAGTC 59.654 50.000 0.00 0.00 0.00 2.59
541 543 2.445905 AGGTGGTCTACGGATCTGGATA 59.554 50.000 6.47 0.00 0.00 2.59
596 598 9.577222 TGCCATAATTGAAGATGAATAGATTGA 57.423 29.630 0.00 0.00 0.00 2.57
631 633 5.463499 AAAAACAAACACGCCATTCTTTC 57.537 34.783 0.00 0.00 0.00 2.62
632 634 3.791973 AACAAACACGCCATTCTTTCA 57.208 38.095 0.00 0.00 0.00 2.69
633 635 3.791973 ACAAACACGCCATTCTTTCAA 57.208 38.095 0.00 0.00 0.00 2.69
634 636 3.443976 ACAAACACGCCATTCTTTCAAC 58.556 40.909 0.00 0.00 0.00 3.18
635 637 3.119316 ACAAACACGCCATTCTTTCAACA 60.119 39.130 0.00 0.00 0.00 3.33
636 638 2.774439 ACACGCCATTCTTTCAACAC 57.226 45.000 0.00 0.00 0.00 3.32
637 639 2.020720 ACACGCCATTCTTTCAACACA 58.979 42.857 0.00 0.00 0.00 3.72
638 640 2.033299 ACACGCCATTCTTTCAACACAG 59.967 45.455 0.00 0.00 0.00 3.66
639 641 1.001378 ACGCCATTCTTTCAACACAGC 60.001 47.619 0.00 0.00 0.00 4.40
640 642 1.689959 GCCATTCTTTCAACACAGCG 58.310 50.000 0.00 0.00 0.00 5.18
641 643 1.266718 GCCATTCTTTCAACACAGCGA 59.733 47.619 0.00 0.00 0.00 4.93
642 644 2.666619 GCCATTCTTTCAACACAGCGAG 60.667 50.000 0.00 0.00 0.00 5.03
643 645 2.578495 CATTCTTTCAACACAGCGAGC 58.422 47.619 0.00 0.00 0.00 5.03
644 646 1.953559 TTCTTTCAACACAGCGAGCT 58.046 45.000 0.00 0.00 0.00 4.09
645 647 1.953559 TCTTTCAACACAGCGAGCTT 58.046 45.000 0.00 0.00 0.00 3.74
646 648 2.288666 TCTTTCAACACAGCGAGCTTT 58.711 42.857 0.00 0.00 0.00 3.51
647 649 2.032054 TCTTTCAACACAGCGAGCTTTG 59.968 45.455 9.42 9.42 0.00 2.77
648 650 0.662619 TTCAACACAGCGAGCTTTGG 59.337 50.000 14.64 1.77 0.00 3.28
649 651 0.179059 TCAACACAGCGAGCTTTGGA 60.179 50.000 14.64 1.99 0.00 3.53
650 652 0.877071 CAACACAGCGAGCTTTGGAT 59.123 50.000 14.64 1.91 0.00 3.41
651 653 1.267806 CAACACAGCGAGCTTTGGATT 59.732 47.619 14.64 0.00 0.00 3.01
652 654 1.160137 ACACAGCGAGCTTTGGATTC 58.840 50.000 14.64 0.00 0.00 2.52
653 655 1.159285 CACAGCGAGCTTTGGATTCA 58.841 50.000 3.49 0.00 0.00 2.57
654 656 1.741706 CACAGCGAGCTTTGGATTCAT 59.258 47.619 3.49 0.00 0.00 2.57
655 657 2.938451 CACAGCGAGCTTTGGATTCATA 59.062 45.455 3.49 0.00 0.00 2.15
656 658 2.939103 ACAGCGAGCTTTGGATTCATAC 59.061 45.455 0.00 0.00 0.00 2.39
657 659 3.201290 CAGCGAGCTTTGGATTCATACT 58.799 45.455 0.00 0.00 0.00 2.12
658 660 3.002042 CAGCGAGCTTTGGATTCATACTG 59.998 47.826 0.00 0.00 0.00 2.74
659 661 2.289002 GCGAGCTTTGGATTCATACTGG 59.711 50.000 0.00 0.00 0.00 4.00
660 662 2.289002 CGAGCTTTGGATTCATACTGGC 59.711 50.000 0.00 0.00 0.00 4.85
661 663 2.620585 GAGCTTTGGATTCATACTGGCC 59.379 50.000 0.00 0.00 0.00 5.36
662 664 1.683385 GCTTTGGATTCATACTGGCCC 59.317 52.381 0.00 0.00 0.00 5.80
663 665 2.949963 GCTTTGGATTCATACTGGCCCA 60.950 50.000 0.00 0.00 0.00 5.36
664 666 3.569491 CTTTGGATTCATACTGGCCCAT 58.431 45.455 0.00 0.00 0.00 4.00
665 667 3.686227 TTGGATTCATACTGGCCCATT 57.314 42.857 0.00 0.00 0.00 3.16
666 668 3.228188 TGGATTCATACTGGCCCATTC 57.772 47.619 0.00 0.00 0.00 2.67
667 669 2.154462 GGATTCATACTGGCCCATTCG 58.846 52.381 0.00 0.00 0.00 3.34
668 670 2.487265 GGATTCATACTGGCCCATTCGT 60.487 50.000 0.00 0.00 0.00 3.85
669 671 2.036958 TTCATACTGGCCCATTCGTG 57.963 50.000 0.00 0.00 0.00 4.35
670 672 0.908910 TCATACTGGCCCATTCGTGT 59.091 50.000 0.00 0.00 0.00 4.49
671 673 1.016627 CATACTGGCCCATTCGTGTG 58.983 55.000 0.00 0.00 0.00 3.82
672 674 0.748005 ATACTGGCCCATTCGTGTGC 60.748 55.000 0.00 0.00 0.00 4.57
673 675 1.836999 TACTGGCCCATTCGTGTGCT 61.837 55.000 0.00 0.00 0.00 4.40
674 676 2.359850 TGGCCCATTCGTGTGCTC 60.360 61.111 0.00 0.00 0.00 4.26
675 677 3.134127 GGCCCATTCGTGTGCTCC 61.134 66.667 0.00 0.00 0.00 4.70
676 678 2.045926 GCCCATTCGTGTGCTCCT 60.046 61.111 0.00 0.00 0.00 3.69
677 679 2.401766 GCCCATTCGTGTGCTCCTG 61.402 63.158 0.00 0.00 0.00 3.86
678 680 1.003355 CCCATTCGTGTGCTCCTGT 60.003 57.895 0.00 0.00 0.00 4.00
679 681 1.021390 CCCATTCGTGTGCTCCTGTC 61.021 60.000 0.00 0.00 0.00 3.51
680 682 0.036952 CCATTCGTGTGCTCCTGTCT 60.037 55.000 0.00 0.00 0.00 3.41
681 683 1.609061 CCATTCGTGTGCTCCTGTCTT 60.609 52.381 0.00 0.00 0.00 3.01
682 684 1.462283 CATTCGTGTGCTCCTGTCTTG 59.538 52.381 0.00 0.00 0.00 3.02
683 685 0.464036 TTCGTGTGCTCCTGTCTTGT 59.536 50.000 0.00 0.00 0.00 3.16
684 686 0.032130 TCGTGTGCTCCTGTCTTGTC 59.968 55.000 0.00 0.00 0.00 3.18
685 687 0.249447 CGTGTGCTCCTGTCTTGTCA 60.249 55.000 0.00 0.00 0.00 3.58
686 688 1.806247 CGTGTGCTCCTGTCTTGTCAA 60.806 52.381 0.00 0.00 0.00 3.18
687 689 2.288666 GTGTGCTCCTGTCTTGTCAAA 58.711 47.619 0.00 0.00 0.00 2.69
688 690 2.682856 GTGTGCTCCTGTCTTGTCAAAA 59.317 45.455 0.00 0.00 0.00 2.44
689 691 2.945008 TGTGCTCCTGTCTTGTCAAAAG 59.055 45.455 0.00 0.00 0.00 2.27
690 692 3.206150 GTGCTCCTGTCTTGTCAAAAGA 58.794 45.455 0.00 0.00 0.00 2.52
691 693 3.627577 GTGCTCCTGTCTTGTCAAAAGAA 59.372 43.478 0.00 0.00 0.00 2.52
724 728 2.226200 AGAGAGCAGATGTCGATGATCG 59.774 50.000 8.83 8.83 42.10 3.69
725 729 1.952990 AGAGCAGATGTCGATGATCGT 59.047 47.619 15.06 0.00 41.35 3.73
726 730 3.142174 AGAGCAGATGTCGATGATCGTA 58.858 45.455 15.06 5.90 41.35 3.43
727 731 3.755905 AGAGCAGATGTCGATGATCGTAT 59.244 43.478 15.06 10.46 41.35 3.06
728 732 4.938226 AGAGCAGATGTCGATGATCGTATA 59.062 41.667 15.06 3.02 41.35 1.47
729 733 5.588246 AGAGCAGATGTCGATGATCGTATAT 59.412 40.000 15.06 7.70 41.35 0.86
766 770 1.071857 GATGAGATCAGCAGGCATGGA 59.928 52.381 0.00 0.00 31.58 3.41
772 776 1.751927 CAGCAGGCATGGAAGGGAC 60.752 63.158 0.00 0.00 0.00 4.46
773 777 2.825836 GCAGGCATGGAAGGGACG 60.826 66.667 0.00 0.00 0.00 4.79
774 778 2.124570 CAGGCATGGAAGGGACGG 60.125 66.667 0.00 0.00 0.00 4.79
775 779 2.285368 AGGCATGGAAGGGACGGA 60.285 61.111 0.00 0.00 0.00 4.69
776 780 1.694169 AGGCATGGAAGGGACGGAT 60.694 57.895 0.00 0.00 0.00 4.18
777 781 1.227383 GGCATGGAAGGGACGGATT 59.773 57.895 0.00 0.00 0.00 3.01
778 782 0.395724 GGCATGGAAGGGACGGATTT 60.396 55.000 0.00 0.00 0.00 2.17
779 783 1.474330 GCATGGAAGGGACGGATTTT 58.526 50.000 0.00 0.00 0.00 1.82
780 784 1.824852 GCATGGAAGGGACGGATTTTT 59.175 47.619 0.00 0.00 0.00 1.94
781 785 2.159240 GCATGGAAGGGACGGATTTTTC 60.159 50.000 0.00 0.00 0.00 2.29
782 786 3.356290 CATGGAAGGGACGGATTTTTCT 58.644 45.455 0.00 0.00 0.00 2.52
783 787 3.067684 TGGAAGGGACGGATTTTTCTC 57.932 47.619 0.00 0.00 0.00 2.87
784 788 2.007608 GGAAGGGACGGATTTTTCTCG 58.992 52.381 0.00 0.00 0.00 4.04
785 789 2.354403 GGAAGGGACGGATTTTTCTCGA 60.354 50.000 0.00 0.00 0.00 4.04
789 793 3.007614 AGGGACGGATTTTTCTCGAGAAA 59.992 43.478 31.62 31.62 41.77 2.52
811 815 0.906775 AAAAGCAGGCATGGAATGGG 59.093 50.000 0.00 0.00 46.86 4.00
812 816 0.041535 AAAGCAGGCATGGAATGGGA 59.958 50.000 0.00 0.00 46.86 4.37
813 817 0.396695 AAGCAGGCATGGAATGGGAG 60.397 55.000 0.00 0.00 46.86 4.30
814 818 2.496291 GCAGGCATGGAATGGGAGC 61.496 63.158 0.00 0.00 46.86 4.70
1168 1202 1.018840 TCCTCCTCATCTTCCTCCCA 58.981 55.000 0.00 0.00 0.00 4.37
1172 1206 4.140350 TCCTCCTCATCTTCCTCCCATATT 60.140 45.833 0.00 0.00 0.00 1.28
1177 1211 5.188751 CCTCATCTTCCTCCCATATTACCTC 59.811 48.000 0.00 0.00 0.00 3.85
1178 1212 5.094387 TCATCTTCCTCCCATATTACCTCC 58.906 45.833 0.00 0.00 0.00 4.30
1180 1214 3.116862 TCTTCCTCCCATATTACCTCCGT 60.117 47.826 0.00 0.00 0.00 4.69
1182 1216 3.236896 TCCTCCCATATTACCTCCGTTC 58.763 50.000 0.00 0.00 0.00 3.95
1183 1217 2.029290 CCTCCCATATTACCTCCGTTCG 60.029 54.545 0.00 0.00 0.00 3.95
1184 1218 2.626743 CTCCCATATTACCTCCGTTCGT 59.373 50.000 0.00 0.00 0.00 3.85
1185 1219 3.822735 CTCCCATATTACCTCCGTTCGTA 59.177 47.826 0.00 0.00 0.00 3.43
1203 1237 7.746916 CCGTTCGTAATAGATCAATCAGAGTAG 59.253 40.741 0.00 0.00 0.00 2.57
1204 1238 8.283992 CGTTCGTAATAGATCAATCAGAGTAGT 58.716 37.037 0.00 0.00 0.00 2.73
1211 1245 3.232213 TCAATCAGAGTAGTTGCGACC 57.768 47.619 0.00 0.00 0.00 4.79
1224 1258 4.514577 CGACCCGGCATCGCTCTT 62.515 66.667 12.66 0.00 31.96 2.85
1226 1260 4.514577 ACCCGGCATCGCTCTTCG 62.515 66.667 0.00 0.00 40.15 3.79
1236 1270 2.864931 CGCTCTTCGCTTGATCCGC 61.865 63.158 0.00 0.00 36.13 5.54
1269 1307 1.334869 GCTGCCGATTTATGGAACCAG 59.665 52.381 0.00 0.00 0.00 4.00
1270 1308 2.917933 CTGCCGATTTATGGAACCAGA 58.082 47.619 0.00 0.00 0.00 3.86
1272 1310 1.597663 GCCGATTTATGGAACCAGACG 59.402 52.381 0.00 0.00 0.00 4.18
1313 1358 0.099436 CGTTGATGCAAAGCCCTAGC 59.901 55.000 0.00 0.00 40.32 3.42
1348 1393 0.543277 TTCTCGGCCAGATGAAGCAT 59.457 50.000 2.24 0.00 0.00 3.79
1362 1407 3.414272 GCATGGTGCTGGTCGATC 58.586 61.111 0.00 0.00 40.96 3.69
1363 1408 1.153289 GCATGGTGCTGGTCGATCT 60.153 57.895 0.00 0.00 40.96 2.75
1365 1410 1.153289 ATGGTGCTGGTCGATCTGC 60.153 57.895 19.57 19.57 0.00 4.26
1368 1413 1.812922 GTGCTGGTCGATCTGCTGG 60.813 63.158 25.25 0.00 33.58 4.85
1369 1414 1.984026 TGCTGGTCGATCTGCTGGA 60.984 57.895 25.25 5.61 33.58 3.86
1371 1416 0.676184 GCTGGTCGATCTGCTGGATA 59.324 55.000 19.17 0.00 34.33 2.59
1372 1417 1.274728 GCTGGTCGATCTGCTGGATAT 59.725 52.381 19.17 0.00 34.33 1.63
1373 1418 2.493675 GCTGGTCGATCTGCTGGATATA 59.506 50.000 19.17 0.00 34.33 0.86
1374 1419 3.674682 GCTGGTCGATCTGCTGGATATAC 60.675 52.174 19.17 0.00 34.33 1.47
1375 1420 3.761218 CTGGTCGATCTGCTGGATATACT 59.239 47.826 0.00 0.00 34.33 2.12
1376 1421 3.759086 TGGTCGATCTGCTGGATATACTC 59.241 47.826 0.00 0.00 34.33 2.59
1377 1422 3.129638 GGTCGATCTGCTGGATATACTCC 59.870 52.174 0.00 0.00 45.19 3.85
1378 1423 4.013728 GTCGATCTGCTGGATATACTCCT 58.986 47.826 0.00 0.00 45.21 3.69
1379 1424 4.013050 TCGATCTGCTGGATATACTCCTG 58.987 47.826 0.00 0.00 45.21 3.86
1387 1432 2.555325 TGGATATACTCCTGCGTTACGG 59.445 50.000 6.94 0.00 45.21 4.02
1415 1460 7.171508 GCATATCATTTCGGTCACTCTGAATTA 59.828 37.037 0.00 0.00 40.58 1.40
1416 1461 9.045223 CATATCATTTCGGTCACTCTGAATTAA 57.955 33.333 0.00 0.00 40.58 1.40
1417 1462 9.784531 ATATCATTTCGGTCACTCTGAATTAAT 57.215 29.630 0.00 0.00 40.58 1.40
1466 1511 0.954452 CAGCGGCCTAATTGATTCCC 59.046 55.000 0.00 0.00 0.00 3.97
1538 1583 7.704789 ATTTGTAGCTTTTTCTCTGCAAAAG 57.295 32.000 8.94 3.87 44.01 2.27
1604 1688 1.815613 TGGCCATAACAAACGATGGTG 59.184 47.619 0.00 0.00 43.94 4.17
1608 1692 3.627577 GCCATAACAAACGATGGTGATCT 59.372 43.478 3.04 0.00 43.94 2.75
1609 1693 4.096382 GCCATAACAAACGATGGTGATCTT 59.904 41.667 3.04 0.00 43.94 2.40
1610 1694 5.393027 GCCATAACAAACGATGGTGATCTTT 60.393 40.000 3.04 0.00 43.94 2.52
1611 1695 6.620678 CCATAACAAACGATGGTGATCTTTT 58.379 36.000 0.00 0.00 38.26 2.27
1612 1696 7.090173 CCATAACAAACGATGGTGATCTTTTT 58.910 34.615 0.00 0.00 38.26 1.94
1644 1728 6.098982 CCTATTTGGTCAGTAGAGTCCATCTT 59.901 42.308 0.00 0.00 39.64 2.40
1692 1776 3.490800 TTTGTGCATCCATGTTCATCG 57.509 42.857 0.00 0.00 0.00 3.84
1706 1790 0.179111 TCATCGGATTCAGACACGGC 60.179 55.000 0.00 0.00 0.00 5.68
1714 1798 2.191354 TTCAGACACGGCCGTACGAG 62.191 60.000 33.70 21.51 37.61 4.18
1814 1900 9.817809 TCGATTTTGCTACACTAAATTCTCTAT 57.182 29.630 0.00 0.00 34.45 1.98
2099 2187 6.601613 GGATCAACAAATTACCATGGTCAGTA 59.398 38.462 23.76 0.00 0.00 2.74
2291 2381 3.350219 TGATGCCCCTTCTTGTAAGTC 57.650 47.619 0.00 0.00 0.00 3.01
2440 2530 4.440663 GGATCTGTATTTCCTTTGGCTTGC 60.441 45.833 0.00 0.00 0.00 4.01
2482 2572 3.894547 TTTCGAAGCCCTCACCGCC 62.895 63.158 0.00 0.00 0.00 6.13
2548 2638 5.523916 CCTGAAGGAAATGGATAAGTACGTG 59.476 44.000 0.00 0.00 37.39 4.49
2557 2647 5.456548 TGGATAAGTACGTGACAACTCAA 57.543 39.130 0.00 0.00 0.00 3.02
2558 2648 5.224888 TGGATAAGTACGTGACAACTCAAC 58.775 41.667 0.00 0.00 0.00 3.18
2566 2656 3.243434 ACGTGACAACTCAACACTCCTAG 60.243 47.826 0.00 0.00 33.13 3.02
2621 2715 7.425224 AGTAGAAATGTATCAGGCACTACTT 57.575 36.000 0.00 0.00 36.84 2.24
3114 3208 5.431765 GAGCTTTCAGATACTGGAATGGAA 58.568 41.667 0.00 0.00 27.62 3.53
3187 3281 6.311935 CGACAAAGCCATTGAATTTGAATCAT 59.688 34.615 15.88 0.00 41.85 2.45
3364 3516 1.349026 CCTCTGCTTCTGGAGTTTCCA 59.651 52.381 0.00 0.00 45.98 3.53
3740 3892 1.741706 AGATGGCAAAAGAGCATGACG 59.258 47.619 0.00 0.00 35.83 4.35
3784 3936 1.918957 CCTTTGACCTCTCTGGGGAAT 59.081 52.381 0.00 0.00 41.11 3.01
4015 4182 5.651139 AGCATTGCACTGAATATCTCTGTTT 59.349 36.000 11.91 0.00 34.22 2.83
4103 4272 0.108329 CGTGGGATAGACCGCAAGTT 60.108 55.000 0.00 0.00 41.08 2.66
4131 4300 3.375922 CGGTGTCCTTGTTGTAACTTTGT 59.624 43.478 0.00 0.00 0.00 2.83
4155 4324 9.546428 TGTTGACCATATACAAGTAAGATCATG 57.454 33.333 0.00 0.00 0.00 3.07
4197 4366 7.826744 TCACTTAACACTGGTCATATATTTGCA 59.173 33.333 0.00 0.00 0.00 4.08
4203 4372 7.282585 ACACTGGTCATATATTTGCATGTACT 58.717 34.615 0.00 0.00 0.00 2.73
4224 4393 3.824001 TGAGTTGGAAATGGAATGGGA 57.176 42.857 0.00 0.00 0.00 4.37
4242 4411 7.653311 GGAATGGGAAATATAATGTGCAAGTTC 59.347 37.037 0.00 0.00 0.00 3.01
4247 4416 7.147976 GGAAATATAATGTGCAAGTTCCATCC 58.852 38.462 7.89 0.00 34.66 3.51
4248 4417 6.655078 AATATAATGTGCAAGTTCCATCCC 57.345 37.500 0.00 0.00 0.00 3.85
4283 4453 1.078426 GGTCGGTTATGCACTGGCT 60.078 57.895 0.00 0.00 41.91 4.75
4375 5201 2.834549 AGGTGATCATCGACAAGTCCTT 59.165 45.455 0.00 0.00 0.00 3.36
4512 5338 4.564821 CCCGGTCACCAAAGGTATATATGG 60.565 50.000 0.00 0.00 38.91 2.74
4519 5345 6.385759 TCACCAAAGGTATATATGGTCACACT 59.614 38.462 3.22 0.00 44.12 3.55
4525 5351 8.638629 AAGGTATATATGGTCACACTCTAGTC 57.361 38.462 0.00 0.00 0.00 2.59
4552 5378 2.163010 CACTGATCATCCTTTGTGCACC 59.837 50.000 15.69 0.00 0.00 5.01
4557 5383 2.874014 TCATCCTTTGTGCACCATTGA 58.126 42.857 15.69 6.54 0.00 2.57
4573 5399 0.829990 TTGAGGTGCTGTCTGTCACA 59.170 50.000 0.00 0.00 35.04 3.58
4574 5400 1.051008 TGAGGTGCTGTCTGTCACAT 58.949 50.000 0.00 0.00 33.23 3.21
5044 5875 6.610075 AAAAATGATCACATGGCTTACCTT 57.390 33.333 0.00 0.00 36.79 3.50
5045 5876 5.841957 AAATGATCACATGGCTTACCTTC 57.158 39.130 0.00 0.00 36.79 3.46
5047 5878 4.142609 TGATCACATGGCTTACCTTCTC 57.857 45.455 0.00 0.00 36.63 2.87
5048 5879 3.776969 TGATCACATGGCTTACCTTCTCT 59.223 43.478 0.00 0.00 36.63 3.10
5049 5880 4.225942 TGATCACATGGCTTACCTTCTCTT 59.774 41.667 0.00 0.00 36.63 2.85
5050 5881 4.207891 TCACATGGCTTACCTTCTCTTC 57.792 45.455 0.00 0.00 36.63 2.87
5051 5882 3.055094 TCACATGGCTTACCTTCTCTTCC 60.055 47.826 0.00 0.00 36.63 3.46
5052 5883 2.239907 ACATGGCTTACCTTCTCTTCCC 59.760 50.000 0.00 0.00 36.63 3.97
5053 5884 1.286248 TGGCTTACCTTCTCTTCCCC 58.714 55.000 0.00 0.00 36.63 4.81
5054 5885 0.547075 GGCTTACCTTCTCTTCCCCC 59.453 60.000 0.00 0.00 0.00 5.40
5073 5904 3.426474 CCCCCTCTTTCCCTCTCTT 57.574 57.895 0.00 0.00 0.00 2.85
5074 5905 1.208706 CCCCCTCTTTCCCTCTCTTC 58.791 60.000 0.00 0.00 0.00 2.87
5091 5966 4.924187 CTCCCCCTCCCTCGCGAT 62.924 72.222 10.36 0.00 0.00 4.58
5114 5989 1.697754 ATCCCCGATGGCTTCCCTT 60.698 57.895 0.00 0.00 0.00 3.95
5161 6249 2.284921 CCTCCCTCCTCTGGTGCA 60.285 66.667 0.00 0.00 0.00 4.57
5264 6353 1.221021 GCGACGGGGATTCTTCCTT 59.779 57.895 0.00 0.00 42.20 3.36
5295 6384 2.729479 CGCTCCTGACCATGGCTCT 61.729 63.158 13.04 0.00 0.00 4.09
5381 6489 0.965866 TGGACGAGTCTGGCTGGTAG 60.966 60.000 0.00 0.00 36.26 3.18
5462 6570 4.789075 CTTGGTGCGCTGCCATGC 62.789 66.667 21.32 0.00 35.71 4.06
5656 6793 4.785453 CTCTGTCTTGGGCCGCCC 62.785 72.222 22.81 22.81 45.71 6.13
5683 6820 2.603473 GGTTTGTGGCCCCTTCCC 60.603 66.667 0.00 0.00 0.00 3.97
5692 6829 2.044946 CCCCTTCCCTTGCTTCGG 60.045 66.667 0.00 0.00 0.00 4.30
5693 6830 2.757077 CCCTTCCCTTGCTTCGGT 59.243 61.111 0.00 0.00 0.00 4.69
5694 6831 1.675641 CCCTTCCCTTGCTTCGGTG 60.676 63.158 0.00 0.00 0.00 4.94
5695 6832 1.073199 CCTTCCCTTGCTTCGGTGT 59.927 57.895 0.00 0.00 0.00 4.16
5696 6833 0.955919 CCTTCCCTTGCTTCGGTGTC 60.956 60.000 0.00 0.00 0.00 3.67
5697 6834 0.035458 CTTCCCTTGCTTCGGTGTCT 59.965 55.000 0.00 0.00 0.00 3.41
5698 6835 0.250295 TTCCCTTGCTTCGGTGTCTG 60.250 55.000 0.00 0.00 0.00 3.51
5699 6836 1.118965 TCCCTTGCTTCGGTGTCTGA 61.119 55.000 0.00 0.00 0.00 3.27
5700 6837 0.036010 CCCTTGCTTCGGTGTCTGAT 60.036 55.000 0.00 0.00 0.00 2.90
5717 6854 1.640670 TGATTTTCCCCCTCCCTTCTG 59.359 52.381 0.00 0.00 0.00 3.02
5722 6859 3.732849 CCCCTCCCTTCTGTGGGC 61.733 72.222 0.00 0.00 46.67 5.36
5726 6863 2.935481 TCCCTTCTGTGGGCCCTG 60.935 66.667 25.70 13.48 46.67 4.45
5822 6959 0.249489 CGCTCGGGCTATATATGGGC 60.249 60.000 13.51 13.51 36.09 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.537371 CCGGTGAAAGGCAGAAACCT 60.537 55.000 0.00 0.00 43.91 3.50
144 145 1.304464 TCTCGCCTTCCTGAGCAGA 60.304 57.895 0.00 0.00 32.20 4.26
201 202 2.687566 CTGGAACGGGGGCTAGGT 60.688 66.667 0.00 0.00 0.00 3.08
296 297 0.304705 ACGTAGACGAACAACGACGT 59.695 50.000 9.41 0.00 43.94 4.34
508 510 2.099831 CCACCTAGCGACGACGAC 59.900 66.667 12.29 2.46 42.66 4.34
509 511 2.359107 ACCACCTAGCGACGACGA 60.359 61.111 12.29 0.00 42.66 4.20
510 512 1.086067 TAGACCACCTAGCGACGACG 61.086 60.000 2.12 2.12 42.93 5.12
541 543 9.974980 ACAACGAACACCAGAAATAAAAATTAT 57.025 25.926 0.00 0.00 0.00 1.28
614 616 3.242712 GTGTTGAAAGAATGGCGTGTTTG 59.757 43.478 0.00 0.00 0.00 2.93
618 620 2.653890 CTGTGTTGAAAGAATGGCGTG 58.346 47.619 0.00 0.00 0.00 5.34
619 621 1.001378 GCTGTGTTGAAAGAATGGCGT 60.001 47.619 0.00 0.00 0.00 5.68
620 622 1.689959 GCTGTGTTGAAAGAATGGCG 58.310 50.000 0.00 0.00 0.00 5.69
621 623 1.266718 TCGCTGTGTTGAAAGAATGGC 59.733 47.619 0.00 0.00 0.00 4.40
622 624 2.666619 GCTCGCTGTGTTGAAAGAATGG 60.667 50.000 0.00 0.00 0.00 3.16
623 625 2.225019 AGCTCGCTGTGTTGAAAGAATG 59.775 45.455 0.00 0.00 0.00 2.67
624 626 2.498167 AGCTCGCTGTGTTGAAAGAAT 58.502 42.857 0.00 0.00 0.00 2.40
625 627 1.953559 AGCTCGCTGTGTTGAAAGAA 58.046 45.000 0.00 0.00 0.00 2.52
626 628 1.953559 AAGCTCGCTGTGTTGAAAGA 58.046 45.000 0.00 0.00 0.00 2.52
627 629 2.378806 CAAAGCTCGCTGTGTTGAAAG 58.621 47.619 0.84 0.00 0.00 2.62
628 630 1.065401 CCAAAGCTCGCTGTGTTGAAA 59.935 47.619 8.19 0.00 29.47 2.69
629 631 0.662619 CCAAAGCTCGCTGTGTTGAA 59.337 50.000 8.19 0.00 29.47 2.69
630 632 0.179059 TCCAAAGCTCGCTGTGTTGA 60.179 50.000 8.19 0.00 29.47 3.18
631 633 0.877071 ATCCAAAGCTCGCTGTGTTG 59.123 50.000 8.19 2.20 29.47 3.33
632 634 1.537202 GAATCCAAAGCTCGCTGTGTT 59.463 47.619 8.19 0.00 29.47 3.32
633 635 1.160137 GAATCCAAAGCTCGCTGTGT 58.840 50.000 8.19 0.00 29.47 3.72
634 636 1.159285 TGAATCCAAAGCTCGCTGTG 58.841 50.000 2.02 2.02 0.00 3.66
635 637 2.119801 ATGAATCCAAAGCTCGCTGT 57.880 45.000 0.00 0.00 0.00 4.40
636 638 3.002042 CAGTATGAATCCAAAGCTCGCTG 59.998 47.826 0.00 0.00 39.69 5.18
637 639 3.201290 CAGTATGAATCCAAAGCTCGCT 58.799 45.455 0.00 0.00 39.69 4.93
638 640 2.289002 CCAGTATGAATCCAAAGCTCGC 59.711 50.000 0.00 0.00 39.69 5.03
639 641 2.289002 GCCAGTATGAATCCAAAGCTCG 59.711 50.000 0.00 0.00 39.69 5.03
640 642 2.620585 GGCCAGTATGAATCCAAAGCTC 59.379 50.000 0.00 0.00 39.69 4.09
641 643 2.659428 GGCCAGTATGAATCCAAAGCT 58.341 47.619 0.00 0.00 39.69 3.74
642 644 1.683385 GGGCCAGTATGAATCCAAAGC 59.317 52.381 4.39 0.00 39.69 3.51
643 645 3.017048 TGGGCCAGTATGAATCCAAAG 57.983 47.619 0.00 0.00 39.69 2.77
644 646 3.686227 ATGGGCCAGTATGAATCCAAA 57.314 42.857 13.78 0.00 39.69 3.28
645 647 3.565307 GAATGGGCCAGTATGAATCCAA 58.435 45.455 13.78 0.00 39.69 3.53
646 648 2.487086 CGAATGGGCCAGTATGAATCCA 60.487 50.000 13.78 0.00 39.69 3.41
647 649 2.154462 CGAATGGGCCAGTATGAATCC 58.846 52.381 13.78 0.00 39.69 3.01
648 650 2.549754 CACGAATGGGCCAGTATGAATC 59.450 50.000 13.78 0.00 39.69 2.52
649 651 2.092429 ACACGAATGGGCCAGTATGAAT 60.092 45.455 20.75 0.00 39.69 2.57
650 652 1.280710 ACACGAATGGGCCAGTATGAA 59.719 47.619 20.75 0.00 39.69 2.57
651 653 0.908910 ACACGAATGGGCCAGTATGA 59.091 50.000 20.75 0.00 39.69 2.15
652 654 1.016627 CACACGAATGGGCCAGTATG 58.983 55.000 13.78 14.08 0.00 2.39
653 655 3.476740 CACACGAATGGGCCAGTAT 57.523 52.632 13.78 0.00 0.00 2.12
660 662 1.003355 ACAGGAGCACACGAATGGG 60.003 57.895 0.00 0.00 0.00 4.00
661 663 0.036952 AGACAGGAGCACACGAATGG 60.037 55.000 0.00 0.00 0.00 3.16
662 664 1.462283 CAAGACAGGAGCACACGAATG 59.538 52.381 0.00 0.00 0.00 2.67
663 665 1.070758 ACAAGACAGGAGCACACGAAT 59.929 47.619 0.00 0.00 0.00 3.34
664 666 0.464036 ACAAGACAGGAGCACACGAA 59.536 50.000 0.00 0.00 0.00 3.85
665 667 0.032130 GACAAGACAGGAGCACACGA 59.968 55.000 0.00 0.00 0.00 4.35
666 668 0.249447 TGACAAGACAGGAGCACACG 60.249 55.000 0.00 0.00 0.00 4.49
667 669 1.953559 TTGACAAGACAGGAGCACAC 58.046 50.000 0.00 0.00 0.00 3.82
668 670 2.708216 TTTGACAAGACAGGAGCACA 57.292 45.000 0.00 0.00 0.00 4.57
669 671 3.206150 TCTTTTGACAAGACAGGAGCAC 58.794 45.455 0.00 0.00 0.00 4.40
670 672 3.558931 TCTTTTGACAAGACAGGAGCA 57.441 42.857 0.00 0.00 0.00 4.26
671 673 4.900635 TTTCTTTTGACAAGACAGGAGC 57.099 40.909 0.00 0.00 0.00 4.70
672 674 5.734503 GCCTTTTCTTTTGACAAGACAGGAG 60.735 44.000 9.08 0.00 38.21 3.69
673 675 4.097892 GCCTTTTCTTTTGACAAGACAGGA 59.902 41.667 9.08 0.00 38.21 3.86
674 676 4.363138 GCCTTTTCTTTTGACAAGACAGG 58.637 43.478 2.67 2.67 38.21 4.00
675 677 4.363138 GGCCTTTTCTTTTGACAAGACAG 58.637 43.478 0.00 0.00 38.21 3.51
676 678 3.132111 GGGCCTTTTCTTTTGACAAGACA 59.868 43.478 0.84 0.00 38.21 3.41
677 679 3.717707 GGGCCTTTTCTTTTGACAAGAC 58.282 45.455 0.84 0.00 38.21 3.01
678 680 2.360801 CGGGCCTTTTCTTTTGACAAGA 59.639 45.455 0.84 0.00 38.21 3.02
679 681 2.100749 ACGGGCCTTTTCTTTTGACAAG 59.899 45.455 0.84 0.00 36.33 3.16
680 682 2.100087 GACGGGCCTTTTCTTTTGACAA 59.900 45.455 0.84 0.00 0.00 3.18
681 683 1.679153 GACGGGCCTTTTCTTTTGACA 59.321 47.619 0.84 0.00 0.00 3.58
682 684 1.334689 CGACGGGCCTTTTCTTTTGAC 60.335 52.381 0.84 0.00 0.00 3.18
683 685 0.948678 CGACGGGCCTTTTCTTTTGA 59.051 50.000 0.84 0.00 0.00 2.69
684 686 0.948678 TCGACGGGCCTTTTCTTTTG 59.051 50.000 0.84 0.00 0.00 2.44
685 687 1.202722 TCTCGACGGGCCTTTTCTTTT 60.203 47.619 0.84 0.00 0.00 2.27
686 688 0.395312 TCTCGACGGGCCTTTTCTTT 59.605 50.000 0.84 0.00 0.00 2.52
687 689 0.037232 CTCTCGACGGGCCTTTTCTT 60.037 55.000 0.84 0.00 0.00 2.52
688 690 0.898789 TCTCTCGACGGGCCTTTTCT 60.899 55.000 0.84 0.00 0.00 2.52
689 691 0.458716 CTCTCTCGACGGGCCTTTTC 60.459 60.000 0.84 0.00 0.00 2.29
690 692 1.592223 CTCTCTCGACGGGCCTTTT 59.408 57.895 0.84 0.00 0.00 2.27
691 693 3.007973 GCTCTCTCGACGGGCCTTT 62.008 63.158 0.84 0.00 0.00 3.11
724 728 6.222038 TCAATCTCTGCCCGGAATATATAC 57.778 41.667 0.73 0.00 0.00 1.47
725 729 6.611236 TCATCAATCTCTGCCCGGAATATATA 59.389 38.462 0.73 0.00 0.00 0.86
726 730 5.426509 TCATCAATCTCTGCCCGGAATATAT 59.573 40.000 0.73 0.00 0.00 0.86
727 731 4.777366 TCATCAATCTCTGCCCGGAATATA 59.223 41.667 0.73 0.00 0.00 0.86
728 732 3.584406 TCATCAATCTCTGCCCGGAATAT 59.416 43.478 0.73 0.00 0.00 1.28
729 733 2.972021 TCATCAATCTCTGCCCGGAATA 59.028 45.455 0.73 0.00 0.00 1.75
766 770 2.565834 TCTCGAGAAAAATCCGTCCCTT 59.434 45.455 14.01 0.00 0.00 3.95
796 800 2.496291 GCTCCCATTCCATGCCTGC 61.496 63.158 0.00 0.00 0.00 4.85
811 815 3.326210 CGCTCAATCGGCTCGCTC 61.326 66.667 0.00 0.00 0.00 5.03
812 816 3.356639 TTCGCTCAATCGGCTCGCT 62.357 57.895 0.00 0.00 0.00 4.93
813 817 2.864931 CTTCGCTCAATCGGCTCGC 61.865 63.158 0.00 0.00 0.00 5.03
814 818 1.205485 CTCTTCGCTCAATCGGCTCG 61.205 60.000 0.00 0.00 0.00 5.03
928 939 2.415843 GTGCGTGCGGCTATAGGA 59.584 61.111 0.00 0.00 44.05 2.94
1168 1202 8.571461 TGATCTATTACGAACGGAGGTAATAT 57.429 34.615 12.03 3.74 39.52 1.28
1172 1206 6.487668 TGATTGATCTATTACGAACGGAGGTA 59.512 38.462 0.00 0.00 0.00 3.08
1177 1211 6.439599 ACTCTGATTGATCTATTACGAACGG 58.560 40.000 0.00 0.00 0.00 4.44
1178 1212 8.283992 ACTACTCTGATTGATCTATTACGAACG 58.716 37.037 0.00 0.00 0.00 3.95
1180 1214 9.952188 CAACTACTCTGATTGATCTATTACGAA 57.048 33.333 0.00 0.00 0.00 3.85
1182 1216 7.060059 CGCAACTACTCTGATTGATCTATTACG 59.940 40.741 0.00 0.00 0.00 3.18
1183 1217 8.076781 TCGCAACTACTCTGATTGATCTATTAC 58.923 37.037 0.00 0.00 0.00 1.89
1184 1218 8.076781 GTCGCAACTACTCTGATTGATCTATTA 58.923 37.037 0.00 0.00 0.00 0.98
1185 1219 6.920758 GTCGCAACTACTCTGATTGATCTATT 59.079 38.462 0.00 0.00 0.00 1.73
1224 1258 0.737367 CAACAGAGCGGATCAAGCGA 60.737 55.000 6.74 0.00 40.04 4.93
1226 1260 0.674895 ACCAACAGAGCGGATCAAGC 60.675 55.000 4.46 4.46 0.00 4.01
1236 1270 1.576421 GGCAGCGAAACCAACAGAG 59.424 57.895 0.00 0.00 0.00 3.35
1269 1307 0.606604 ACACCCCACATACAGTCGTC 59.393 55.000 0.00 0.00 0.00 4.20
1270 1308 0.606604 GACACCCCACATACAGTCGT 59.393 55.000 0.00 0.00 0.00 4.34
1272 1310 2.093973 CAGAGACACCCCACATACAGTC 60.094 54.545 0.00 0.00 0.00 3.51
1348 1393 2.265739 GCAGATCGACCAGCACCA 59.734 61.111 0.00 0.00 0.00 4.17
1368 1413 2.593257 GCCGTAACGCAGGAGTATATC 58.407 52.381 0.00 0.00 0.00 1.63
1369 1414 1.068748 CGCCGTAACGCAGGAGTATAT 60.069 52.381 0.00 0.00 0.00 0.86
1371 1416 1.065273 CGCCGTAACGCAGGAGTAT 59.935 57.895 0.00 0.00 0.00 2.12
1372 1417 2.486504 CGCCGTAACGCAGGAGTA 59.513 61.111 0.00 0.00 0.00 2.59
1380 1425 2.717595 CGAAATGATATGCGCCGTAACG 60.718 50.000 4.18 0.00 0.00 3.18
1381 1426 2.411031 CCGAAATGATATGCGCCGTAAC 60.411 50.000 4.18 0.00 0.00 2.50
1382 1427 1.795872 CCGAAATGATATGCGCCGTAA 59.204 47.619 4.18 0.00 0.00 3.18
1383 1428 1.269883 ACCGAAATGATATGCGCCGTA 60.270 47.619 4.18 0.00 0.00 4.02
1387 1432 1.867233 AGTGACCGAAATGATATGCGC 59.133 47.619 0.00 0.00 0.00 6.09
1390 1435 7.488187 AATTCAGAGTGACCGAAATGATATG 57.512 36.000 0.00 0.00 0.00 1.78
1466 1511 2.820787 CCGGGCCACTTCTAGTATCTAG 59.179 54.545 4.39 0.00 0.00 2.43
1538 1583 6.759497 ACCTAAACACTTCCTTCATATTGC 57.241 37.500 0.00 0.00 0.00 3.56
1623 1707 4.593206 ACAAGATGGACTCTACTGACCAAA 59.407 41.667 0.00 0.00 35.64 3.28
1626 1710 4.116747 CACAAGATGGACTCTACTGACC 57.883 50.000 0.00 0.00 32.41 4.02
1644 1728 3.081061 GCACTGACCAAATCATACCACA 58.919 45.455 0.00 0.00 36.48 4.17
1692 1776 0.804933 GTACGGCCGTGTCTGAATCC 60.805 60.000 40.02 12.23 0.00 3.01
1706 1790 2.282290 ACGTTGTTTTGTTCTCGTACGG 59.718 45.455 16.52 6.42 32.54 4.02
1714 1798 2.222486 GCAGCAACACGTTGTTTTGTTC 60.222 45.455 11.33 0.00 38.77 3.18
1826 1912 7.121463 TGCCATGTATGTTAGTTAACCGATTTT 59.879 33.333 0.88 0.00 35.37 1.82
1833 1919 6.130298 TGCATGCCATGTATGTTAGTTAAC 57.870 37.500 16.68 0.00 36.74 2.01
2120 2210 9.403110 GAATGGAAGCATTATCATTTGTCATAC 57.597 33.333 0.00 0.00 33.95 2.39
2291 2381 0.110056 GTCGTGTCTTTGGCATGCAG 60.110 55.000 21.36 8.71 0.00 4.41
2440 2530 2.278659 ATCGCGCATTGACAACGTCG 62.279 55.000 8.75 0.00 34.95 5.12
2482 2572 0.674895 GGAGCCTGTTAGCTGTGGTG 60.675 60.000 0.00 0.00 45.15 4.17
2548 2638 2.633481 ACCCTAGGAGTGTTGAGTTGTC 59.367 50.000 11.48 0.00 0.00 3.18
2557 2647 3.697190 ATCATCTGACCCTAGGAGTGT 57.303 47.619 11.48 0.00 0.00 3.55
2558 2648 6.015918 AGAATATCATCTGACCCTAGGAGTG 58.984 44.000 11.48 0.00 0.00 3.51
2566 2656 9.434420 CTTGATAAAGAGAATATCATCTGACCC 57.566 37.037 0.00 0.00 39.00 4.46
2621 2715 1.380524 TCGAACAAAAAGGGCACGAA 58.619 45.000 0.00 0.00 0.00 3.85
2951 3045 9.970395 CATACTTCATATGTACAAATGCCAAAT 57.030 29.630 0.00 0.00 36.63 2.32
3114 3208 5.047660 TGTTGAAGCTGGTTTAACTTGTTGT 60.048 36.000 22.17 0.00 35.98 3.32
3364 3516 2.020720 CGTGTAGAGCTGGTCATCTCT 58.979 52.381 9.78 8.99 41.97 3.10
3517 3669 0.462581 TTAGCATCTCCCTTGCAGCG 60.463 55.000 0.00 0.00 42.62 5.18
3740 3892 0.396695 TCATGGGTACTCGAGTCCCC 60.397 60.000 33.40 33.40 43.82 4.81
3784 3936 8.150945 GCCTCATCTCTTACTTTATCAATGGTA 58.849 37.037 0.00 0.00 0.00 3.25
4015 4182 4.211920 CAACCCCTACAAAGAAAGGAACA 58.788 43.478 0.00 0.00 34.58 3.18
4103 4272 2.509651 AACAAGGACACCGCCGGTA 61.510 57.895 9.25 0.00 32.11 4.02
4170 4339 8.840321 GCAAATATATGACCAGTGTTAAGTGAT 58.160 33.333 0.00 0.00 0.00 3.06
4182 4351 7.992608 ACTCAAGTACATGCAAATATATGACCA 59.007 33.333 0.00 0.00 0.00 4.02
4197 4366 6.153340 CCATTCCATTTCCAACTCAAGTACAT 59.847 38.462 0.00 0.00 0.00 2.29
4203 4372 4.125124 TCCCATTCCATTTCCAACTCAA 57.875 40.909 0.00 0.00 0.00 3.02
4224 4393 6.840705 AGGGATGGAACTTGCACATTATATTT 59.159 34.615 0.00 0.00 0.00 1.40
4242 4411 1.605710 CTCGCTGCAATAAAGGGATGG 59.394 52.381 0.00 0.00 36.20 3.51
4247 4416 0.734889 CCCACTCGCTGCAATAAAGG 59.265 55.000 0.00 0.00 0.00 3.11
4248 4417 1.398390 GACCCACTCGCTGCAATAAAG 59.602 52.381 0.00 0.00 0.00 1.85
4283 4453 2.039418 ACCGCTAGTATCAAGGATGCA 58.961 47.619 0.00 0.00 0.00 3.96
4375 5201 0.526211 CTCCATCGTCGTCTTGTCCA 59.474 55.000 0.00 0.00 0.00 4.02
4455 5281 1.898472 CCATAGCCTGAGGATCACGAT 59.102 52.381 0.65 0.00 42.56 3.73
4512 5338 5.182190 TCAGTGATCAAGACTAGAGTGTGAC 59.818 44.000 0.00 0.00 0.00 3.67
4552 5378 1.802960 GTGACAGACAGCACCTCAATG 59.197 52.381 0.00 0.00 0.00 2.82
4557 5383 2.568956 ACATATGTGACAGACAGCACCT 59.431 45.455 7.78 0.00 38.23 4.00
4573 5399 5.332743 ACAGGATTGTCCAAAACCACATAT 58.667 37.500 0.00 0.00 39.61 1.78
4574 5400 4.735369 ACAGGATTGTCCAAAACCACATA 58.265 39.130 0.00 0.00 39.61 2.29
5055 5886 1.208706 GAAGAGAGGGAAAGAGGGGG 58.791 60.000 0.00 0.00 0.00 5.40
5056 5887 2.115427 GAGAAGAGAGGGAAAGAGGGG 58.885 57.143 0.00 0.00 0.00 4.79
5057 5888 2.115427 GGAGAAGAGAGGGAAAGAGGG 58.885 57.143 0.00 0.00 0.00 4.30
5058 5889 2.115427 GGGAGAAGAGAGGGAAAGAGG 58.885 57.143 0.00 0.00 0.00 3.69
5059 5890 2.115427 GGGGAGAAGAGAGGGAAAGAG 58.885 57.143 0.00 0.00 0.00 2.85
5060 5891 1.273896 GGGGGAGAAGAGAGGGAAAGA 60.274 57.143 0.00 0.00 0.00 2.52
5061 5892 1.208706 GGGGGAGAAGAGAGGGAAAG 58.791 60.000 0.00 0.00 0.00 2.62
5062 5893 0.800239 AGGGGGAGAAGAGAGGGAAA 59.200 55.000 0.00 0.00 0.00 3.13
5063 5894 0.340208 GAGGGGGAGAAGAGAGGGAA 59.660 60.000 0.00 0.00 0.00 3.97
5064 5895 1.595058 GGAGGGGGAGAAGAGAGGGA 61.595 65.000 0.00 0.00 0.00 4.20
5065 5896 1.074850 GGAGGGGGAGAAGAGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
5066 5897 1.074850 GGGAGGGGGAGAAGAGAGG 60.075 68.421 0.00 0.00 0.00 3.69
5067 5898 0.105709 GAGGGAGGGGGAGAAGAGAG 60.106 65.000 0.00 0.00 0.00 3.20
5068 5899 1.939082 CGAGGGAGGGGGAGAAGAGA 61.939 65.000 0.00 0.00 0.00 3.10
5069 5900 1.456705 CGAGGGAGGGGGAGAAGAG 60.457 68.421 0.00 0.00 0.00 2.85
5070 5901 2.690452 CGAGGGAGGGGGAGAAGA 59.310 66.667 0.00 0.00 0.00 2.87
5071 5902 3.157949 GCGAGGGAGGGGGAGAAG 61.158 72.222 0.00 0.00 0.00 2.85
5074 5905 4.924187 ATCGCGAGGGAGGGGGAG 62.924 72.222 16.66 0.00 0.00 4.30
5140 6228 2.445654 CCAGAGGAGGGAGGGAGC 60.446 72.222 0.00 0.00 0.00 4.70
5264 6353 3.134792 GAGCGGGCTCAGAGTCGA 61.135 66.667 15.45 0.00 42.31 4.20
5348 6456 2.033448 TCCACCAATGACGCCACC 59.967 61.111 0.00 0.00 0.00 4.61
5356 6464 1.021390 GCCAGACTCGTCCACCAATG 61.021 60.000 0.00 0.00 0.00 2.82
5357 6465 1.194781 AGCCAGACTCGTCCACCAAT 61.195 55.000 0.00 0.00 0.00 3.16
5359 6467 2.203640 AGCCAGACTCGTCCACCA 60.204 61.111 0.00 0.00 0.00 4.17
5437 6545 4.424711 GCGCACCAAGGATCCCCA 62.425 66.667 8.55 0.00 33.88 4.96
5511 6620 2.123077 AGATGGAGGAGGCGAGGG 60.123 66.667 0.00 0.00 0.00 4.30
5598 6733 1.987855 CCACTAGCCCCGAGGACAA 60.988 63.158 0.00 0.00 33.47 3.18
5656 6793 3.439540 CACAAACCGCCCATCCCG 61.440 66.667 0.00 0.00 0.00 5.14
5657 6794 3.068064 CCACAAACCGCCCATCCC 61.068 66.667 0.00 0.00 0.00 3.85
5670 6807 4.299796 GCAAGGGAAGGGGCCACA 62.300 66.667 8.31 0.00 0.00 4.17
5676 6813 1.675641 CACCGAAGCAAGGGAAGGG 60.676 63.158 0.00 0.00 0.00 3.95
5677 6814 0.955919 GACACCGAAGCAAGGGAAGG 60.956 60.000 0.00 0.00 0.00 3.46
5683 6820 3.365364 GGAAAATCAGACACCGAAGCAAG 60.365 47.826 0.00 0.00 0.00 4.01
5692 6829 1.341089 GGGAGGGGGAAAATCAGACAC 60.341 57.143 0.00 0.00 0.00 3.67
5693 6830 0.999712 GGGAGGGGGAAAATCAGACA 59.000 55.000 0.00 0.00 0.00 3.41
5694 6831 1.299939 AGGGAGGGGGAAAATCAGAC 58.700 55.000 0.00 0.00 0.00 3.51
5695 6832 1.923148 GAAGGGAGGGGGAAAATCAGA 59.077 52.381 0.00 0.00 0.00 3.27
5696 6833 1.925959 AGAAGGGAGGGGGAAAATCAG 59.074 52.381 0.00 0.00 0.00 2.90
5697 6834 1.640670 CAGAAGGGAGGGGGAAAATCA 59.359 52.381 0.00 0.00 0.00 2.57
5698 6835 1.641192 ACAGAAGGGAGGGGGAAAATC 59.359 52.381 0.00 0.00 0.00 2.17
5699 6836 1.359130 CACAGAAGGGAGGGGGAAAAT 59.641 52.381 0.00 0.00 0.00 1.82
5700 6837 0.777446 CACAGAAGGGAGGGGGAAAA 59.223 55.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.