Multiple sequence alignment - TraesCS7A01G306600

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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 TraesCS7A01G306600 chr7A 100.000 7072 0 0 1 7072 432971023 432978094 0.000000e+00 13060
1 TraesCS7A01G306600 chr7A 97.059 102 0 2 643 742 432971579 432971679 1.220000e-37 169
2 TraesCS7A01G306600 chr7A 97.059 102 0 2 557 657 432971665 432971764 1.220000e-37 169
3 TraesCS7A01G306600 chr7B 94.045 4030 159 30 643 4627 379410336 379414329 0.000000e+00 6037
4 TraesCS7A01G306600 chr7B 95.284 2396 80 17 4707 7072 379414326 379416718 0.000000e+00 3768
5 TraesCS7A01G306600 chr7B 94.483 145 3 5 514 657 379410294 379410434 1.190000e-52 219
6 TraesCS7A01G306600 chr7B 89.899 99 10 0 4616 4714 414571475 414571377 2.070000e-25 128
7 TraesCS7A01G306600 chr7D 95.059 2955 98 19 643 3571 384937951 384940883 0.000000e+00 4604
8 TraesCS7A01G306600 chr7D 93.505 2248 71 34 4707 6901 384943453 384945678 0.000000e+00 3273
9 TraesCS7A01G306600 chr7D 98.694 1072 12 2 3556 4627 384942387 384943456 0.000000e+00 1901
10 TraesCS7A01G306600 chr7D 95.139 144 4 3 514 657 384937908 384938048 2.570000e-54 224
11 TraesCS7A01G306600 chr7D 90.722 97 9 0 4617 4713 104453571 104453475 5.760000e-26 130
12 TraesCS7A01G306600 chr7D 97.101 69 1 1 6833 6901 384945692 384945759 1.610000e-21 115
13 TraesCS7A01G306600 chrUn 96.289 512 19 0 1 512 366418768 366419279 0.000000e+00 841
14 TraesCS7A01G306600 chr6A 96.094 512 20 0 1 512 172391258 172391769 0.000000e+00 835
15 TraesCS7A01G306600 chr6A 93.333 270 16 2 5 273 428685488 428685220 1.430000e-106 398
16 TraesCS7A01G306600 chr6A 96.875 96 3 0 4619 4714 569692738 569692833 2.040000e-35 161
17 TraesCS7A01G306600 chr1A 96.094 512 20 0 1 512 561730660 561730149 0.000000e+00 835
18 TraesCS7A01G306600 chr2A 92.203 513 39 1 1 512 211095862 211096374 0.000000e+00 725
19 TraesCS7A01G306600 chr2A 91.797 512 19 1 1 512 144027570 144027082 0.000000e+00 691
20 TraesCS7A01G306600 chr3D 91.423 513 39 3 1 512 105154780 105154272 0.000000e+00 699
21 TraesCS7A01G306600 chr3D 91.423 513 39 3 1 512 105186688 105186180 0.000000e+00 699
22 TraesCS7A01G306600 chr3D 91.033 513 41 3 1 512 105228348 105227840 0.000000e+00 688
23 TraesCS7A01G306600 chr4D 84.307 274 41 2 247 519 430788740 430788468 4.210000e-67 267
24 TraesCS7A01G306600 chr6B 92.553 94 7 0 4617 4710 459601732 459601639 1.240000e-27 135
25 TraesCS7A01G306600 chr6B 92.553 94 5 2 4618 4710 546656566 546656658 4.450000e-27 134
26 TraesCS7A01G306600 chr5D 93.407 91 6 0 4620 4710 383306883 383306973 1.240000e-27 135
27 TraesCS7A01G306600 chr5D 92.553 94 7 0 4619 4712 401281229 401281322 1.240000e-27 135
28 TraesCS7A01G306600 chr5D 89.524 105 8 3 4616 4718 364250214 364250317 5.760000e-26 130
29 TraesCS7A01G306600 chr5B 91.667 96 7 1 4621 4716 357414884 357414790 1.600000e-26 132


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 TraesCS7A01G306600 chr7A 432971023 432978094 7071 False 13060.000000 13060 100.0000 1 7072 1 chr7A.!!$F1 7071
1 TraesCS7A01G306600 chr7B 379410294 379416718 6424 False 3341.333333 6037 94.6040 514 7072 3 chr7B.!!$F1 6558
2 TraesCS7A01G306600 chr7D 384937908 384945759 7851 False 2023.400000 4604 95.8996 514 6901 5 chr7D.!!$F1 6387
3 TraesCS7A01G306600 chrUn 366418768 366419279 511 False 841.000000 841 96.2890 1 512 1 chrUn.!!$F1 511
4 TraesCS7A01G306600 chr6A 172391258 172391769 511 False 835.000000 835 96.0940 1 512 1 chr6A.!!$F1 511
5 TraesCS7A01G306600 chr1A 561730149 561730660 511 True 835.000000 835 96.0940 1 512 1 chr1A.!!$R1 511
6 TraesCS7A01G306600 chr2A 211095862 211096374 512 False 725.000000 725 92.2030 1 512 1 chr2A.!!$F1 511
7 TraesCS7A01G306600 chr3D 105154272 105154780 508 True 699.000000 699 91.4230 1 512 1 chr3D.!!$R1 511
8 TraesCS7A01G306600 chr3D 105186180 105186688 508 True 699.000000 699 91.4230 1 512 1 chr3D.!!$R2 511
9 TraesCS7A01G306600 chr3D 105227840 105228348 508 True 688.000000 688 91.0330 1 512 1 chr3D.!!$R3 511

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
673 675 0.181350 CCGATGGAAAGGGAGGGAAG 59.819 60.000 0.00 0.00 0.00 3.46 F
674 676 0.181350 CGATGGAAAGGGAGGGAAGG 59.819 60.000 0.00 0.00 0.00 3.46 F
731 733 0.249699 TGCCAACCACGTGTGTCTAG 60.250 55.000 15.65 0.00 0.00 2.43 F
1350 1355 0.599558 TCGTTTCGTTCGTGGATCCT 59.400 50.000 14.23 0.00 0.00 3.24 F
1353 1358 0.672401 TTTCGTTCGTGGATCCTGGC 60.672 55.000 14.23 2.42 0.00 4.85 F
1461 1466 0.976641 AACGGGATTCAGAGCTCACA 59.023 50.000 17.77 0.00 0.00 3.58 F
1770 1776 1.095600 GCCCTTGATTTCTTCGTCCC 58.904 55.000 0.00 0.00 0.00 4.46 F
2706 2734 1.202615 GCATATGCAGACTCTCAGCCA 60.203 52.381 22.84 0.00 41.59 4.75 F
3528 3579 4.389374 ACACGTCTGACAAAGGAATGAAT 58.611 39.130 8.73 0.00 0.00 2.57 F
4143 5713 2.733956 ACCAACTTTGCTGAGGACAAA 58.266 42.857 0.00 0.00 35.77 2.83 F
5414 6984 2.226437 ACGTGCTTTAACAAGATGCAGG 59.774 45.455 0.00 0.00 42.71 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 1912 1.545582 GCATTTGCCTAGCAGTCCAAA 59.454 47.619 0.00 0.0 40.61 3.28 R
2299 2322 2.303022 CAGAAAAGAGGGAGTGTGCCTA 59.697 50.000 0.00 0.0 38.79 3.93 R
2694 2722 1.257055 GCTGGTCTGGCTGAGAGTCT 61.257 60.000 0.00 0.0 0.00 3.24 R
2706 2734 1.681229 TAAATCCTTGGGGCTGGTCT 58.319 50.000 0.00 0.0 0.00 3.85 R
2992 3021 2.042686 TGGAGTACATGGCATTCAGC 57.957 50.000 0.00 0.0 44.65 4.26 R
3361 3408 3.236047 TGTGTTAGACCTAGCTCCAACA 58.764 45.455 0.00 0.0 0.00 3.33 R
3630 5200 1.496060 AGGACCATATGAACGGAGCA 58.504 50.000 3.65 0.0 0.00 4.26 R
4143 5713 3.119009 TCAATGCCATCCCTTCCAAAT 57.881 42.857 0.00 0.0 0.00 2.32 R
5349 6919 2.159254 GCAGCAACCTGACAGAACAAAA 60.159 45.455 3.32 0.0 41.77 2.44 R
5837 7408 1.117749 AGAGCCACTGTGAGCTGTGA 61.118 55.000 22.56 0.0 44.19 3.58 R
6255 7833 0.037697 TGAACGTGCCGCAGAAGTAT 60.038 50.000 0.00 0.0 0.00 2.12 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
166 167 2.886124 GGCGTCTACTTGCGAGCC 60.886 66.667 0.00 0.00 37.61 4.70
219 220 1.077716 GACTAACGCTGGCCCCAAT 60.078 57.895 0.00 0.00 0.00 3.16
512 514 4.509970 AGCTTAAATTTGTCGTTTTTGCCC 59.490 37.500 0.00 0.00 0.00 5.36
573 575 2.331805 CTAGCCGTCGGTCCGATG 59.668 66.667 24.11 24.11 41.82 3.84
584 586 1.527370 GTCCGATGGAAAGGGAGGG 59.473 63.158 0.00 0.00 31.38 4.30
627 629 3.017323 CGAGGCCGCTTTAGCATG 58.983 61.111 4.53 0.00 42.21 4.06
628 630 2.718107 GAGGCCGCTTTAGCATGC 59.282 61.111 10.51 10.51 42.21 4.06
631 633 2.884367 GCCGCTTTAGCATGCCAA 59.116 55.556 15.66 3.64 42.21 4.52
632 634 1.517039 GCCGCTTTAGCATGCCAAC 60.517 57.895 15.66 0.00 42.21 3.77
633 635 1.139520 CCGCTTTAGCATGCCAACC 59.860 57.895 15.66 0.00 42.21 3.77
634 636 1.594194 CCGCTTTAGCATGCCAACCA 61.594 55.000 15.66 0.00 42.21 3.67
635 637 0.456653 CGCTTTAGCATGCCAACCAC 60.457 55.000 15.66 0.00 42.21 4.16
636 638 0.456653 GCTTTAGCATGCCAACCACG 60.457 55.000 15.66 0.00 41.59 4.94
637 639 0.881118 CTTTAGCATGCCAACCACGT 59.119 50.000 15.66 0.00 0.00 4.49
638 640 0.595588 TTTAGCATGCCAACCACGTG 59.404 50.000 15.66 9.08 0.00 4.49
639 641 0.536233 TTAGCATGCCAACCACGTGT 60.536 50.000 15.66 0.00 0.00 4.49
640 642 1.233950 TAGCATGCCAACCACGTGTG 61.234 55.000 15.66 7.01 0.00 3.82
641 643 2.844451 GCATGCCAACCACGTGTGT 61.844 57.895 15.65 9.31 0.00 3.72
642 644 1.282570 CATGCCAACCACGTGTGTC 59.717 57.895 15.65 0.00 0.00 3.67
643 645 1.148273 ATGCCAACCACGTGTGTCT 59.852 52.632 15.65 1.27 0.00 3.41
644 646 0.394938 ATGCCAACCACGTGTGTCTA 59.605 50.000 15.65 0.00 0.00 2.59
645 647 0.249699 TGCCAACCACGTGTGTCTAG 60.250 55.000 15.65 0.00 0.00 2.43
646 648 1.566018 GCCAACCACGTGTGTCTAGC 61.566 60.000 15.65 11.32 0.00 3.42
647 649 0.949105 CCAACCACGTGTGTCTAGCC 60.949 60.000 15.65 0.00 0.00 3.93
648 650 1.006571 AACCACGTGTGTCTAGCCG 60.007 57.895 15.65 0.00 0.00 5.52
649 651 1.741327 AACCACGTGTGTCTAGCCGT 61.741 55.000 15.65 0.00 0.00 5.68
650 652 1.443872 CCACGTGTGTCTAGCCGTC 60.444 63.158 15.65 0.00 0.00 4.79
651 653 1.796355 CACGTGTGTCTAGCCGTCG 60.796 63.158 7.58 0.00 0.00 5.12
652 654 2.202440 CGTGTGTCTAGCCGTCGG 60.202 66.667 6.99 6.99 0.00 4.79
653 655 2.960170 GTGTGTCTAGCCGTCGGT 59.040 61.111 13.94 2.30 0.00 4.69
654 656 1.154073 GTGTGTCTAGCCGTCGGTC 60.154 63.158 13.94 5.34 0.00 4.79
655 657 2.338015 TGTGTCTAGCCGTCGGTCC 61.338 63.158 13.94 0.00 0.00 4.46
656 658 3.129502 TGTCTAGCCGTCGGTCCG 61.130 66.667 13.94 4.39 0.00 4.79
657 659 2.821366 GTCTAGCCGTCGGTCCGA 60.821 66.667 10.71 10.71 0.00 4.55
658 660 2.185494 GTCTAGCCGTCGGTCCGAT 61.185 63.158 18.75 3.52 38.42 4.18
659 661 2.184830 TCTAGCCGTCGGTCCGATG 61.185 63.158 24.11 24.11 41.82 3.84
664 666 4.088421 CGTCGGTCCGATGGAAAG 57.912 61.111 23.48 5.68 38.96 2.62
665 667 1.518572 CGTCGGTCCGATGGAAAGG 60.519 63.158 23.48 0.00 38.96 3.11
666 668 1.153429 GTCGGTCCGATGGAAAGGG 60.153 63.158 18.75 0.00 38.42 3.95
667 669 1.305465 TCGGTCCGATGGAAAGGGA 60.305 57.895 10.71 0.00 31.38 4.20
668 670 1.144057 CGGTCCGATGGAAAGGGAG 59.856 63.158 4.91 0.00 31.38 4.30
669 671 1.527370 GGTCCGATGGAAAGGGAGG 59.473 63.158 0.00 0.00 31.38 4.30
670 672 1.527370 GTCCGATGGAAAGGGAGGG 59.473 63.158 0.00 0.00 31.38 4.30
671 673 0.981277 GTCCGATGGAAAGGGAGGGA 60.981 60.000 0.00 0.00 31.38 4.20
672 674 0.252974 TCCGATGGAAAGGGAGGGAA 60.253 55.000 0.00 0.00 0.00 3.97
673 675 0.181350 CCGATGGAAAGGGAGGGAAG 59.819 60.000 0.00 0.00 0.00 3.46
674 676 0.181350 CGATGGAAAGGGAGGGAAGG 59.819 60.000 0.00 0.00 0.00 3.46
675 677 1.596496 GATGGAAAGGGAGGGAAGGA 58.404 55.000 0.00 0.00 0.00 3.36
676 678 1.492599 GATGGAAAGGGAGGGAAGGAG 59.507 57.143 0.00 0.00 0.00 3.69
677 679 0.550147 TGGAAAGGGAGGGAAGGAGG 60.550 60.000 0.00 0.00 0.00 4.30
678 680 1.282653 GGAAAGGGAGGGAAGGAGGG 61.283 65.000 0.00 0.00 0.00 4.30
679 681 0.253207 GAAAGGGAGGGAAGGAGGGA 60.253 60.000 0.00 0.00 0.00 4.20
680 682 0.253394 AAAGGGAGGGAAGGAGGGAG 60.253 60.000 0.00 0.00 0.00 4.30
681 683 1.162951 AAGGGAGGGAAGGAGGGAGA 61.163 60.000 0.00 0.00 0.00 3.71
682 684 1.074850 GGGAGGGAAGGAGGGAGAG 60.075 68.421 0.00 0.00 0.00 3.20
683 685 1.595058 GGGAGGGAAGGAGGGAGAGA 61.595 65.000 0.00 0.00 0.00 3.10
684 686 0.340208 GGAGGGAAGGAGGGAGAGAA 59.660 60.000 0.00 0.00 0.00 2.87
685 687 1.491668 GAGGGAAGGAGGGAGAGAAC 58.508 60.000 0.00 0.00 0.00 3.01
686 688 0.324830 AGGGAAGGAGGGAGAGAACG 60.325 60.000 0.00 0.00 0.00 3.95
687 689 1.331399 GGGAAGGAGGGAGAGAACGG 61.331 65.000 0.00 0.00 0.00 4.44
688 690 1.331399 GGAAGGAGGGAGAGAACGGG 61.331 65.000 0.00 0.00 0.00 5.28
689 691 1.962321 GAAGGAGGGAGAGAACGGGC 61.962 65.000 0.00 0.00 0.00 6.13
690 692 3.839432 GGAGGGAGAGAACGGGCG 61.839 72.222 0.00 0.00 0.00 6.13
691 693 3.069318 GAGGGAGAGAACGGGCGT 61.069 66.667 0.00 0.00 0.00 5.68
692 694 2.603776 AGGGAGAGAACGGGCGTT 60.604 61.111 0.00 0.00 41.54 4.84
693 695 2.434359 GGGAGAGAACGGGCGTTG 60.434 66.667 0.00 0.00 38.60 4.10
694 696 2.434359 GGAGAGAACGGGCGTTGG 60.434 66.667 0.00 0.00 38.60 3.77
695 697 2.434359 GAGAGAACGGGCGTTGGG 60.434 66.667 0.00 0.00 38.60 4.12
696 698 4.699522 AGAGAACGGGCGTTGGGC 62.700 66.667 0.00 0.00 38.60 5.36
731 733 0.249699 TGCCAACCACGTGTGTCTAG 60.250 55.000 15.65 0.00 0.00 2.43
745 747 1.342076 TGTCTAGCTCAGGTCCGGAAT 60.342 52.381 5.23 0.00 0.00 3.01
845 847 0.822121 ACCACGGGAGGAAAAAGTGC 60.822 55.000 0.00 0.00 0.00 4.40
856 858 1.525619 GAAAAAGTGCAGACGCGTACT 59.474 47.619 13.97 9.59 42.97 2.73
857 859 0.859232 AAAAGTGCAGACGCGTACTG 59.141 50.000 24.87 24.87 42.97 2.74
862 864 2.566529 CAGACGCGTACTGGCAGA 59.433 61.111 23.66 1.56 0.00 4.26
991 995 1.696674 TAGCGGAGGAGGGAGAGGA 60.697 63.158 0.00 0.00 0.00 3.71
1115 1119 1.340502 CCTCCTGCTTCCTTTCCCTTC 60.341 57.143 0.00 0.00 0.00 3.46
1170 1174 1.753078 GGGGCTTGGGGATTTCGAC 60.753 63.158 0.00 0.00 0.00 4.20
1186 1190 4.101448 ACCGGATCTGCTGCCACC 62.101 66.667 9.46 0.00 0.00 4.61
1254 1258 1.135546 CGCAAATGTTGGGCACGAATA 60.136 47.619 0.00 0.00 36.79 1.75
1350 1355 0.599558 TCGTTTCGTTCGTGGATCCT 59.400 50.000 14.23 0.00 0.00 3.24
1351 1356 0.713883 CGTTTCGTTCGTGGATCCTG 59.286 55.000 14.23 5.74 0.00 3.86
1352 1357 1.076332 GTTTCGTTCGTGGATCCTGG 58.924 55.000 14.23 4.73 0.00 4.45
1353 1358 0.672401 TTTCGTTCGTGGATCCTGGC 60.672 55.000 14.23 2.42 0.00 4.85
1461 1466 0.976641 AACGGGATTCAGAGCTCACA 59.023 50.000 17.77 0.00 0.00 3.58
1603 1608 9.753674 TGATGAAATGGGAAGAAAATAGTTAGT 57.246 29.630 0.00 0.00 0.00 2.24
1709 1714 1.517832 GACCTCGTATGCCTGCTGT 59.482 57.895 0.00 0.00 0.00 4.40
1770 1776 1.095600 GCCCTTGATTTCTTCGTCCC 58.904 55.000 0.00 0.00 0.00 4.46
1785 1791 3.742385 TCGTCCCGGTTTCAGTATTTTT 58.258 40.909 0.00 0.00 0.00 1.94
1786 1792 3.747529 TCGTCCCGGTTTCAGTATTTTTC 59.252 43.478 0.00 0.00 0.00 2.29
1804 1810 9.869757 GTATTTTTCTAATACCAATTGTGCCTT 57.130 29.630 4.43 0.00 0.00 4.35
1859 1865 3.575256 AGCGGGGTCGTGAATACATTATA 59.425 43.478 0.00 0.00 38.89 0.98
1906 1912 5.987347 GCTGATTGCCATTTTATATGTGCTT 59.013 36.000 0.00 0.00 35.15 3.91
2126 2149 9.449550 GATTGATACAATGCGATCACAAAATAA 57.550 29.630 1.64 0.00 31.85 1.40
2299 2322 3.435275 TGTCCTTGTCTATGCAGAGACT 58.565 45.455 34.26 2.28 45.21 3.24
2350 2373 6.319048 ACCATATTGTCCTTGTCTTGATCT 57.681 37.500 0.00 0.00 0.00 2.75
2560 2588 7.520453 GCTTCAATGTAGAACACACAAATGAGA 60.520 37.037 0.00 0.00 40.86 3.27
2694 2722 2.280119 GGCCTCGTCGCATATGCA 60.280 61.111 26.52 11.60 42.21 3.96
2706 2734 1.202615 GCATATGCAGACTCTCAGCCA 60.203 52.381 22.84 0.00 41.59 4.75
2737 2765 6.995686 GCCCCAAGGATTTAAAAAGAAGAAAA 59.004 34.615 0.00 0.00 33.47 2.29
2931 2959 6.838401 AGGATTCTGGAGAAGGTATGATTT 57.162 37.500 0.00 0.00 37.48 2.17
2948 2976 8.630037 GGTATGATTTCTTCCATAAATTTCGGT 58.370 33.333 0.00 0.00 0.00 4.69
2992 3021 9.884465 CTAGAACTTTTATTCTTTCACAACCTG 57.116 33.333 0.00 0.00 39.65 4.00
3034 3063 6.222389 CAAATACTGGAATGGCTTGTTTTCA 58.778 36.000 0.00 0.00 0.00 2.69
3115 3144 7.713750 TCCCAATAGTGAAGTTCGTTATCTAG 58.286 38.462 0.00 0.00 0.00 2.43
3116 3145 7.341256 TCCCAATAGTGAAGTTCGTTATCTAGT 59.659 37.037 0.00 0.00 0.00 2.57
3161 3206 6.859017 TGAACACTACATTCGTTCATAGCTA 58.141 36.000 0.00 0.00 42.95 3.32
3361 3408 5.068215 ACTATGACTATCTGGTGGTAGCT 57.932 43.478 0.00 0.00 0.00 3.32
3528 3579 4.389374 ACACGTCTGACAAAGGAATGAAT 58.611 39.130 8.73 0.00 0.00 2.57
3557 5127 5.527951 TCAAACCATTCAGTTATGTTGTGC 58.472 37.500 0.00 0.00 0.00 4.57
3630 5200 5.570320 TGTTTCTAAGCTTCTGCCCTTATT 58.430 37.500 0.00 0.00 40.80 1.40
4143 5713 2.733956 ACCAACTTTGCTGAGGACAAA 58.266 42.857 0.00 0.00 35.77 2.83
4502 6072 3.580895 TGACTGTGCTACCATAAACCAGA 59.419 43.478 0.00 0.00 0.00 3.86
4550 6120 5.923733 TTGTTATGTGTTCCTTTTGGTGT 57.076 34.783 0.00 0.00 41.38 4.16
4551 6121 7.406031 TTTGTTATGTGTTCCTTTTGGTGTA 57.594 32.000 0.00 0.00 41.38 2.90
4583 6153 5.674496 TCCCCTATTTTCCATGTGGATAGAA 59.326 40.000 1.98 0.00 44.98 2.10
4624 6194 5.048846 ACCCCTATGTGCCATTTAACTAG 57.951 43.478 0.00 0.00 0.00 2.57
4625 6195 4.477213 ACCCCTATGTGCCATTTAACTAGT 59.523 41.667 0.00 0.00 0.00 2.57
4626 6196 5.668535 ACCCCTATGTGCCATTTAACTAGTA 59.331 40.000 0.00 0.00 0.00 1.82
4627 6197 5.995897 CCCCTATGTGCCATTTAACTAGTAC 59.004 44.000 0.00 0.00 0.00 2.73
4628 6198 6.183361 CCCCTATGTGCCATTTAACTAGTACT 60.183 42.308 0.00 0.00 0.00 2.73
4629 6199 7.280356 CCCTATGTGCCATTTAACTAGTACTT 58.720 38.462 0.00 0.00 0.00 2.24
4630 6200 7.441458 CCCTATGTGCCATTTAACTAGTACTTC 59.559 40.741 0.00 0.00 0.00 3.01
4631 6201 7.441458 CCTATGTGCCATTTAACTAGTACTTCC 59.559 40.741 0.00 0.00 0.00 3.46
4632 6202 6.368779 TGTGCCATTTAACTAGTACTTCCT 57.631 37.500 0.00 0.00 0.00 3.36
4633 6203 6.775708 TGTGCCATTTAACTAGTACTTCCTT 58.224 36.000 0.00 0.00 0.00 3.36
4634 6204 7.228590 TGTGCCATTTAACTAGTACTTCCTTT 58.771 34.615 0.00 0.00 0.00 3.11
4635 6205 7.174253 TGTGCCATTTAACTAGTACTTCCTTTG 59.826 37.037 0.00 0.00 0.00 2.77
4636 6206 7.174426 GTGCCATTTAACTAGTACTTCCTTTGT 59.826 37.037 0.00 0.00 0.00 2.83
4637 6207 8.377034 TGCCATTTAACTAGTACTTCCTTTGTA 58.623 33.333 0.00 0.00 0.00 2.41
4638 6208 9.223099 GCCATTTAACTAGTACTTCCTTTGTAA 57.777 33.333 0.00 0.00 0.00 2.41
4654 6224 8.361592 TCCTTTGTAAACTAATATAAGAGCGC 57.638 34.615 0.00 0.00 0.00 5.92
4655 6225 8.202137 TCCTTTGTAAACTAATATAAGAGCGCT 58.798 33.333 11.27 11.27 0.00 5.92
4656 6226 8.827677 CCTTTGTAAACTAATATAAGAGCGCTT 58.172 33.333 13.26 8.09 38.15 4.68
4662 6232 8.676454 AAACTAATATAAGAGCGCTTAGATCG 57.324 34.615 13.26 12.87 37.50 3.69
4677 6247 8.676454 CGCTTAGATCGCTAAATTAGTAATCT 57.324 34.615 17.17 17.17 36.24 2.40
4678 6248 9.770503 CGCTTAGATCGCTAAATTAGTAATCTA 57.229 33.333 15.83 15.83 36.24 1.98
4686 6256 9.982651 TCGCTAAATTAGTAATCTAAATGCTCT 57.017 29.630 1.68 0.00 39.23 4.09
4704 6274 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
4705 6275 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
4706 6276 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
4851 6421 3.434309 AGCGGTTTAGACTTACCCAGTA 58.566 45.455 0.00 0.00 35.01 2.74
5300 6870 7.856145 TGGAATTTTACAATGCACAAAGTTT 57.144 28.000 0.00 0.00 0.00 2.66
5414 6984 2.226437 ACGTGCTTTAACAAGATGCAGG 59.774 45.455 0.00 0.00 42.71 4.85
5509 7080 5.572511 GTGCTTATTTTGCATCATTCGTCAA 59.427 36.000 0.00 0.00 42.69 3.18
5534 7105 8.712228 ACTCATTTCTTTTCCTAACCATTTCT 57.288 30.769 0.00 0.00 0.00 2.52
5590 7161 4.450082 TTCATGCGAAGTAACTGCTAGA 57.550 40.909 0.00 0.00 0.00 2.43
5595 7166 3.932710 TGCGAAGTAACTGCTAGAAATGG 59.067 43.478 0.00 0.00 0.00 3.16
5620 7191 7.094377 GGTTATGTTGAATCTGGAAAGCAGTTA 60.094 37.037 0.00 0.00 0.00 2.24
5672 7243 6.989759 TCGATAACAGAATAATTAAGGCTGCA 59.010 34.615 0.50 0.00 0.00 4.41
5721 7292 9.295825 TGATTGCCTTATTTTCTTTCTTGTCTA 57.704 29.630 0.00 0.00 0.00 2.59
5834 7405 2.683916 TGGTGACTGGGTCTCCATC 58.316 57.895 14.81 0.00 46.73 3.51
5837 7408 1.078528 TGACTGGGTCTCCATCGGT 59.921 57.895 0.00 0.00 43.11 4.69
5883 7454 2.887926 CCGTCTACGCAACGTAAGTGC 61.888 57.143 0.49 0.49 45.07 4.40
5959 7530 8.983702 TGTATCTAACCTAACACTTGGTTTTT 57.016 30.769 2.66 0.00 43.27 1.94
6255 7833 7.869429 CCTTTGTACCTTTTTACTCTCGAGTTA 59.131 37.037 13.13 2.31 42.54 2.24
6302 7884 7.064728 ACTCGCAGATTAATTTTGTAGTCCTTC 59.935 37.037 0.00 0.00 33.89 3.46
6303 7885 6.315393 TCGCAGATTAATTTTGTAGTCCTTCC 59.685 38.462 0.00 0.00 0.00 3.46
6316 7898 4.993705 AGTCCTTCCACCACAAAGATAA 57.006 40.909 0.00 0.00 0.00 1.75
6437 8045 3.214697 TGTGCTGTGAAACACTGTTTG 57.785 42.857 11.97 0.00 45.67 2.93
6453 8061 4.444056 ACTGTTTGCGTGAATTATGTTTGC 59.556 37.500 0.00 0.00 0.00 3.68
6454 8062 4.615949 TGTTTGCGTGAATTATGTTTGCT 58.384 34.783 0.00 0.00 0.00 3.91
6492 8100 2.787249 CTCTGCATGTTTCGGGCG 59.213 61.111 0.00 0.00 0.00 6.13
6558 8168 6.493802 TGTTGACTGGAGTAGTAGAAAGATGT 59.506 38.462 0.00 0.00 40.53 3.06
6596 8207 3.347958 TGTTTTGCAGTTGACGAATCC 57.652 42.857 0.00 0.00 0.00 3.01
6676 8288 1.017387 CGAAAACCCTGCTATCTGCC 58.983 55.000 0.00 0.00 42.00 4.85
6687 8299 2.019984 GCTATCTGCCAAGGAGGTTTG 58.980 52.381 0.00 0.00 40.61 2.93
6903 8552 1.963515 GGGTTGGCAGTCAGAAACATT 59.036 47.619 0.00 0.00 0.00 2.71
7007 8656 3.527507 TTAGTTGTATGGGGTTGGCAA 57.472 42.857 0.00 0.00 0.00 4.52
7016 8665 0.755686 GGGGTTGGCAATCACAAACA 59.244 50.000 13.32 0.00 37.27 2.83
7031 8680 8.549548 CAATCACAAACATATTGCAGTTTTTGA 58.450 29.630 15.97 15.97 43.95 2.69
7047 8696 9.301153 GCAGTTTTTGAGAAGAGAAATTTTACA 57.699 29.630 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.934781 AGATTTGGCAAATGTTTAACCCAA 58.065 33.333 28.78 0.00 0.00 4.12
166 167 7.091443 AGTTGTATCTTCTTGGACTAAAGTCG 58.909 38.462 4.13 0.00 45.65 4.18
219 220 2.831526 TGGAATGGAATCTCGTGTCTCA 59.168 45.455 0.00 0.00 0.00 3.27
419 421 2.093128 CCGGCTGACCCTTTTATGTAGT 60.093 50.000 0.00 0.00 0.00 2.73
425 427 1.281419 TCATCCGGCTGACCCTTTTA 58.719 50.000 3.28 0.00 0.00 1.52
491 493 4.084797 CCGGGCAAAAACGACAAATTTAAG 60.085 41.667 0.00 0.00 0.00 1.85
512 514 4.657824 ACACTGTCGCGAACCCCG 62.658 66.667 12.06 0.68 42.21 5.73
573 575 1.282653 CCCTCCTTCCCTCCCTTTCC 61.283 65.000 0.00 0.00 0.00 3.13
584 586 1.962321 GCCCGTTCTCTCCCTCCTTC 61.962 65.000 0.00 0.00 0.00 3.46
627 629 1.566018 GCTAGACACACGTGGTTGGC 61.566 60.000 21.57 12.45 34.19 4.52
628 630 0.949105 GGCTAGACACACGTGGTTGG 60.949 60.000 21.57 8.78 34.19 3.77
629 631 1.282248 CGGCTAGACACACGTGGTTG 61.282 60.000 21.57 12.60 34.19 3.77
630 632 1.006571 CGGCTAGACACACGTGGTT 60.007 57.895 21.57 5.58 34.19 3.67
631 633 2.138656 GACGGCTAGACACACGTGGT 62.139 60.000 21.57 14.73 39.95 4.16
632 634 1.443872 GACGGCTAGACACACGTGG 60.444 63.158 21.57 11.39 39.95 4.94
633 635 1.796355 CGACGGCTAGACACACGTG 60.796 63.158 15.48 15.48 39.95 4.49
634 636 2.559840 CGACGGCTAGACACACGT 59.440 61.111 0.00 0.00 42.88 4.49
635 637 2.202440 CCGACGGCTAGACACACG 60.202 66.667 0.00 0.00 0.00 4.49
636 638 1.154073 GACCGACGGCTAGACACAC 60.154 63.158 15.39 0.00 0.00 3.82
637 639 2.338015 GGACCGACGGCTAGACACA 61.338 63.158 15.39 0.00 0.00 3.72
638 640 2.488820 GGACCGACGGCTAGACAC 59.511 66.667 15.39 0.00 0.00 3.67
639 641 2.881539 ATCGGACCGACGGCTAGACA 62.882 60.000 21.02 0.00 39.18 3.41
640 642 2.185494 ATCGGACCGACGGCTAGAC 61.185 63.158 21.02 0.00 39.18 2.59
641 643 2.184830 CATCGGACCGACGGCTAGA 61.185 63.158 21.02 11.00 39.18 2.43
642 644 2.331805 CATCGGACCGACGGCTAG 59.668 66.667 21.02 5.20 39.18 3.42
643 645 3.214123 CCATCGGACCGACGGCTA 61.214 66.667 21.02 0.00 39.18 3.93
645 647 3.652539 TTTCCATCGGACCGACGGC 62.653 63.158 24.01 6.79 39.18 5.68
646 648 1.518572 CTTTCCATCGGACCGACGG 60.519 63.158 22.91 22.91 40.78 4.79
647 649 1.518572 CCTTTCCATCGGACCGACG 60.519 63.158 21.02 11.71 39.18 5.12
648 650 1.153429 CCCTTTCCATCGGACCGAC 60.153 63.158 21.02 0.00 39.18 4.79
649 651 1.305465 TCCCTTTCCATCGGACCGA 60.305 57.895 20.85 20.85 41.13 4.69
650 652 1.144057 CTCCCTTTCCATCGGACCG 59.856 63.158 7.84 7.84 0.00 4.79
651 653 1.527370 CCTCCCTTTCCATCGGACC 59.473 63.158 0.00 0.00 0.00 4.46
652 654 0.981277 TCCCTCCCTTTCCATCGGAC 60.981 60.000 0.00 0.00 0.00 4.79
653 655 0.252974 TTCCCTCCCTTTCCATCGGA 60.253 55.000 0.00 0.00 0.00 4.55
654 656 0.181350 CTTCCCTCCCTTTCCATCGG 59.819 60.000 0.00 0.00 0.00 4.18
655 657 0.181350 CCTTCCCTCCCTTTCCATCG 59.819 60.000 0.00 0.00 0.00 3.84
656 658 1.492599 CTCCTTCCCTCCCTTTCCATC 59.507 57.143 0.00 0.00 0.00 3.51
657 659 1.601248 CTCCTTCCCTCCCTTTCCAT 58.399 55.000 0.00 0.00 0.00 3.41
658 660 0.550147 CCTCCTTCCCTCCCTTTCCA 60.550 60.000 0.00 0.00 0.00 3.53
659 661 1.282653 CCCTCCTTCCCTCCCTTTCC 61.283 65.000 0.00 0.00 0.00 3.13
660 662 0.253207 TCCCTCCTTCCCTCCCTTTC 60.253 60.000 0.00 0.00 0.00 2.62
661 663 0.253394 CTCCCTCCTTCCCTCCCTTT 60.253 60.000 0.00 0.00 0.00 3.11
662 664 1.162951 TCTCCCTCCTTCCCTCCCTT 61.163 60.000 0.00 0.00 0.00 3.95
663 665 1.550374 TCTCCCTCCTTCCCTCCCT 60.550 63.158 0.00 0.00 0.00 4.20
664 666 1.074850 CTCTCCCTCCTTCCCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
665 667 0.340208 TTCTCTCCCTCCTTCCCTCC 59.660 60.000 0.00 0.00 0.00 4.30
666 668 1.491668 GTTCTCTCCCTCCTTCCCTC 58.508 60.000 0.00 0.00 0.00 4.30
667 669 0.324830 CGTTCTCTCCCTCCTTCCCT 60.325 60.000 0.00 0.00 0.00 4.20
668 670 1.331399 CCGTTCTCTCCCTCCTTCCC 61.331 65.000 0.00 0.00 0.00 3.97
669 671 1.331399 CCCGTTCTCTCCCTCCTTCC 61.331 65.000 0.00 0.00 0.00 3.46
670 672 1.962321 GCCCGTTCTCTCCCTCCTTC 61.962 65.000 0.00 0.00 0.00 3.46
671 673 1.990614 GCCCGTTCTCTCCCTCCTT 60.991 63.158 0.00 0.00 0.00 3.36
672 674 2.364448 GCCCGTTCTCTCCCTCCT 60.364 66.667 0.00 0.00 0.00 3.69
673 675 3.839432 CGCCCGTTCTCTCCCTCC 61.839 72.222 0.00 0.00 0.00 4.30
674 676 2.647158 AACGCCCGTTCTCTCCCTC 61.647 63.158 0.00 0.00 32.09 4.30
675 677 2.603776 AACGCCCGTTCTCTCCCT 60.604 61.111 0.00 0.00 32.09 4.20
676 678 2.434359 CAACGCCCGTTCTCTCCC 60.434 66.667 2.68 0.00 36.00 4.30
677 679 2.434359 CCAACGCCCGTTCTCTCC 60.434 66.667 2.68 0.00 36.00 3.71
678 680 2.434359 CCCAACGCCCGTTCTCTC 60.434 66.667 2.68 0.00 36.00 3.20
679 681 4.699522 GCCCAACGCCCGTTCTCT 62.700 66.667 2.68 0.00 36.00 3.10
696 698 3.017323 CATGCTAAAGCGGCCTCG 58.983 61.111 0.00 0.00 45.83 4.63
697 699 2.718107 GCATGCTAAAGCGGCCTC 59.282 61.111 11.37 0.00 45.83 4.70
700 702 1.517039 GTTGGCATGCTAAAGCGGC 60.517 57.895 18.82 1.66 45.83 6.53
701 703 1.139520 GGTTGGCATGCTAAAGCGG 59.860 57.895 18.82 0.00 45.83 5.52
702 704 0.456653 GTGGTTGGCATGCTAAAGCG 60.457 55.000 18.82 0.00 45.83 4.68
703 705 0.456653 CGTGGTTGGCATGCTAAAGC 60.457 55.000 18.82 20.36 42.50 3.51
704 706 0.881118 ACGTGGTTGGCATGCTAAAG 59.119 50.000 18.82 12.19 0.00 1.85
705 707 0.595588 CACGTGGTTGGCATGCTAAA 59.404 50.000 18.82 10.06 0.00 1.85
706 708 0.536233 ACACGTGGTTGGCATGCTAA 60.536 50.000 21.57 15.97 0.00 3.09
707 709 1.072332 ACACGTGGTTGGCATGCTA 59.928 52.632 21.57 9.16 0.00 3.49
708 710 2.203337 ACACGTGGTTGGCATGCT 60.203 55.556 21.57 0.00 0.00 3.79
709 711 2.050168 CACACGTGGTTGGCATGC 60.050 61.111 21.57 9.90 0.00 4.06
710 712 1.165907 AGACACACGTGGTTGGCATG 61.166 55.000 21.57 9.50 34.19 4.06
711 713 0.394938 TAGACACACGTGGTTGGCAT 59.605 50.000 21.57 5.04 34.19 4.40
712 714 0.249699 CTAGACACACGTGGTTGGCA 60.250 55.000 21.57 2.61 34.19 4.92
731 733 1.084370 CGTCAATTCCGGACCTGAGC 61.084 60.000 1.83 4.33 31.55 4.26
745 747 1.271163 GGAAGGAACATGGGTCGTCAA 60.271 52.381 0.00 0.00 0.00 3.18
845 847 0.458543 ATTCTGCCAGTACGCGTCTG 60.459 55.000 18.63 21.81 0.00 3.51
856 858 3.871006 CGTGAACTGCTTATATTCTGCCA 59.129 43.478 0.00 0.00 0.00 4.92
857 859 3.248602 CCGTGAACTGCTTATATTCTGCC 59.751 47.826 0.00 0.00 0.00 4.85
862 864 2.159014 TCGCCCGTGAACTGCTTATATT 60.159 45.455 0.00 0.00 0.00 1.28
991 995 2.374184 CGTCCACCTCATCTCTCTCTT 58.626 52.381 0.00 0.00 0.00 2.85
1115 1119 1.892391 GGAAATTAGCGGGCGGAGG 60.892 63.158 0.00 0.00 0.00 4.30
1186 1190 2.890474 GGCCACACGAGGTATGCG 60.890 66.667 0.00 0.00 0.00 4.73
1254 1258 2.496899 AATGACAGGACGCTCCAAAT 57.503 45.000 6.78 0.00 39.61 2.32
1309 1313 5.582269 CGATGAAGGCACCGAATATTATCAT 59.418 40.000 0.00 0.00 0.00 2.45
1350 1355 2.027561 CCGAATATTTCTATCCCGGCCA 60.028 50.000 2.24 0.00 31.32 5.36
1351 1356 2.027469 ACCGAATATTTCTATCCCGGCC 60.027 50.000 8.85 0.00 37.16 6.13
1352 1357 3.000727 CACCGAATATTTCTATCCCGGC 58.999 50.000 8.85 0.00 37.16 6.13
1353 1358 3.007614 ACCACCGAATATTTCTATCCCGG 59.992 47.826 7.68 7.68 38.44 5.73
1461 1466 9.555727 GAGAATCGATCTAGGTAGAGCTATTAT 57.444 37.037 0.00 0.65 38.96 1.28
1573 1578 9.753674 ACTATTTTCTTCCCATTTCATCAGTTA 57.246 29.630 0.00 0.00 0.00 2.24
1574 1579 8.655935 ACTATTTTCTTCCCATTTCATCAGTT 57.344 30.769 0.00 0.00 0.00 3.16
1602 1607 8.847196 ACAGGTGGAAAGAAGAATTAGTTTAAC 58.153 33.333 0.00 0.00 0.00 2.01
1603 1608 8.990163 ACAGGTGGAAAGAAGAATTAGTTTAA 57.010 30.769 0.00 0.00 0.00 1.52
1604 1609 8.990163 AACAGGTGGAAAGAAGAATTAGTTTA 57.010 30.769 0.00 0.00 0.00 2.01
1605 1610 7.898014 AACAGGTGGAAAGAAGAATTAGTTT 57.102 32.000 0.00 0.00 0.00 2.66
1610 1615 5.008712 GTCGAAACAGGTGGAAAGAAGAATT 59.991 40.000 0.00 0.00 0.00 2.17
1620 1625 2.738480 CCGGTCGAAACAGGTGGA 59.262 61.111 0.00 0.00 36.14 4.02
1709 1714 4.507157 CCACATGGACCATGGCAGAATATA 60.507 45.833 32.82 0.00 45.16 0.86
1785 1791 7.175104 AGAGAAAAGGCACAATTGGTATTAGA 58.825 34.615 10.83 0.00 0.00 2.10
1786 1792 7.396540 AGAGAAAAGGCACAATTGGTATTAG 57.603 36.000 10.83 0.00 0.00 1.73
1859 1865 1.786937 TGGCACCAACTCACCAAATT 58.213 45.000 0.00 0.00 0.00 1.82
1906 1912 1.545582 GCATTTGCCTAGCAGTCCAAA 59.454 47.619 0.00 0.00 40.61 3.28
2126 2149 5.759273 TCTTGCAGCTTTGCACAAAAATATT 59.241 32.000 0.00 0.00 45.32 1.28
2299 2322 2.303022 CAGAAAAGAGGGAGTGTGCCTA 59.697 50.000 0.00 0.00 38.79 3.93
2459 2482 9.871238 TCATTTAGGAACTCATAACACTAACTC 57.129 33.333 0.00 0.00 41.75 3.01
2521 2549 8.270137 TCTACATTGAAGCCACCCTTAATATA 57.730 34.615 0.00 0.00 32.78 0.86
2522 2550 7.149202 TCTACATTGAAGCCACCCTTAATAT 57.851 36.000 0.00 0.00 32.78 1.28
2541 2569 7.984422 AATGATCTCATTTGTGTGTTCTACA 57.016 32.000 0.00 0.00 43.48 2.74
2560 2588 9.370930 TGGAATTATTCAGGCATCTTAAATGAT 57.629 29.630 7.29 0.00 0.00 2.45
2647 2675 2.959967 TGCAAATTCGGCAGACCAT 58.040 47.368 0.96 0.00 36.11 3.55
2694 2722 1.257055 GCTGGTCTGGCTGAGAGTCT 61.257 60.000 0.00 0.00 0.00 3.24
2706 2734 1.681229 TAAATCCTTGGGGCTGGTCT 58.319 50.000 0.00 0.00 0.00 3.85
2737 2765 2.644798 AGCCAGTTCCAAGAACCACTAT 59.355 45.455 3.91 0.00 0.00 2.12
2931 2959 6.488683 ACAAGTTCACCGAAATTTATGGAAGA 59.511 34.615 14.24 9.29 27.08 2.87
2948 2976 8.506168 AGTTCTAGAATTGTTCAACAAGTTCA 57.494 30.769 19.15 6.61 41.94 3.18
2992 3021 2.042686 TGGAGTACATGGCATTCAGC 57.957 50.000 0.00 0.00 44.65 4.26
3025 3054 5.163302 TGTTGTACCATCGTGAAAACAAG 57.837 39.130 0.00 0.00 0.00 3.16
3034 3063 5.048991 GTCAGGAATTTTGTTGTACCATCGT 60.049 40.000 0.00 0.00 0.00 3.73
3149 3194 6.641169 ATCATCTGACTTAGCTATGAACGA 57.359 37.500 13.22 6.37 30.90 3.85
3161 3206 8.523915 TTGGCACATAATTAATCATCTGACTT 57.476 30.769 0.00 0.00 39.30 3.01
3197 3242 7.599245 ACCTTTCTGTCAGTATTAAGAACGAAG 59.401 37.037 0.00 0.00 0.00 3.79
3361 3408 3.236047 TGTGTTAGACCTAGCTCCAACA 58.764 45.455 0.00 0.00 0.00 3.33
3630 5200 1.496060 AGGACCATATGAACGGAGCA 58.504 50.000 3.65 0.00 0.00 4.26
4143 5713 3.119009 TCAATGCCATCCCTTCCAAAT 57.881 42.857 0.00 0.00 0.00 2.32
4550 6120 6.389869 ACATGGAAAATAGGGGAGAATCACTA 59.610 38.462 0.00 0.00 39.68 2.74
4551 6121 5.194537 ACATGGAAAATAGGGGAGAATCACT 59.805 40.000 0.00 0.00 39.68 3.41
4628 6198 8.823818 GCGCTCTTATATTAGTTTACAAAGGAA 58.176 33.333 0.00 0.00 0.00 3.36
4629 6199 8.202137 AGCGCTCTTATATTAGTTTACAAAGGA 58.798 33.333 2.64 0.00 0.00 3.36
4630 6200 8.366671 AGCGCTCTTATATTAGTTTACAAAGG 57.633 34.615 2.64 0.00 0.00 3.11
4636 6206 9.770503 CGATCTAAGCGCTCTTATATTAGTTTA 57.229 33.333 12.06 0.00 34.54 2.01
4637 6207 8.676454 CGATCTAAGCGCTCTTATATTAGTTT 57.324 34.615 12.06 0.00 34.54 2.66
4652 6222 8.676454 AGATTACTAATTTAGCGATCTAAGCG 57.324 34.615 15.28 0.00 40.04 4.68
4660 6230 9.982651 AGAGCATTTAGATTACTAATTTAGCGA 57.017 29.630 3.28 0.00 38.23 4.93
4678 6248 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
4679 6249 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
4680 6250 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
4681 6251 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
4682 6252 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4683 6253 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4684 6254 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
4685 6255 9.294614 ACTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
4688 6258 9.646522 TTTACTACTCCCTCCGTAAACTAATAT 57.353 33.333 0.00 0.00 29.71 1.28
4689 6259 9.474313 TTTTACTACTCCCTCCGTAAACTAATA 57.526 33.333 0.00 0.00 33.18 0.98
4690 6260 7.961326 TTTACTACTCCCTCCGTAAACTAAT 57.039 36.000 0.00 0.00 29.71 1.73
4691 6261 7.775053 TTTTACTACTCCCTCCGTAAACTAA 57.225 36.000 0.00 0.00 33.18 2.24
4692 6262 7.961326 ATTTTACTACTCCCTCCGTAAACTA 57.039 36.000 0.00 0.00 33.18 2.24
4693 6263 6.864151 ATTTTACTACTCCCTCCGTAAACT 57.136 37.500 0.00 0.00 33.18 2.66
4694 6264 7.326454 AGAATTTTACTACTCCCTCCGTAAAC 58.674 38.462 0.00 0.00 33.18 2.01
4695 6265 7.486407 AGAATTTTACTACTCCCTCCGTAAA 57.514 36.000 0.00 0.00 32.00 2.01
4696 6266 7.178983 TCAAGAATTTTACTACTCCCTCCGTAA 59.821 37.037 0.00 0.00 0.00 3.18
4697 6267 6.664816 TCAAGAATTTTACTACTCCCTCCGTA 59.335 38.462 0.00 0.00 0.00 4.02
4698 6268 5.482878 TCAAGAATTTTACTACTCCCTCCGT 59.517 40.000 0.00 0.00 0.00 4.69
4699 6269 5.974108 TCAAGAATTTTACTACTCCCTCCG 58.026 41.667 0.00 0.00 0.00 4.63
4700 6270 7.184067 TCTCAAGAATTTTACTACTCCCTCC 57.816 40.000 0.00 0.00 0.00 4.30
4833 6403 5.163612 CGGTAGTACTGGGTAAGTCTAAACC 60.164 48.000 5.39 0.00 40.56 3.27
4845 6415 4.643784 GGATATGGATACGGTAGTACTGGG 59.356 50.000 13.69 0.00 42.51 4.45
5270 6840 8.984891 TTGTGCATTGTAAAATTCCAATAGAG 57.015 30.769 0.00 0.00 30.41 2.43
5300 6870 5.906113 TTTAACTGAAGTGGTTGCTTTGA 57.094 34.783 0.00 0.00 0.00 2.69
5342 6912 8.806146 AGCAACCTGACAGAACAAAATATTTAT 58.194 29.630 3.32 0.00 0.00 1.40
5346 6916 5.565439 GCAGCAACCTGACAGAACAAAATAT 60.565 40.000 3.32 0.00 41.77 1.28
5349 6919 2.159254 GCAGCAACCTGACAGAACAAAA 60.159 45.455 3.32 0.00 41.77 2.44
5414 6984 3.119566 CCTTCAGGATTTTCTTCAGCAGC 60.120 47.826 0.00 0.00 37.39 5.25
5509 7080 8.579863 CAGAAATGGTTAGGAAAAGAAATGAGT 58.420 33.333 0.00 0.00 0.00 3.41
5590 7161 7.099120 GCTTTCCAGATTCAACATAACCATTT 58.901 34.615 0.00 0.00 0.00 2.32
5595 7166 6.259550 ACTGCTTTCCAGATTCAACATAAC 57.740 37.500 0.00 0.00 44.64 1.89
5664 7235 2.577059 GCACATGCATGCAGCCTT 59.423 55.556 26.69 6.06 45.39 4.35
5721 7292 4.891756 AGCAAAGCAATAGTATCAGCCAAT 59.108 37.500 4.43 0.00 0.00 3.16
5834 7405 1.665916 CCACTGTGAGCTGTGACCG 60.666 63.158 9.86 0.00 44.19 4.79
5837 7408 1.117749 AGAGCCACTGTGAGCTGTGA 61.118 55.000 22.56 0.00 44.19 3.58
5883 7454 8.876275 TTTCTCATCATCAAAAAGGAAACAAG 57.124 30.769 0.00 0.00 0.00 3.16
5884 7455 8.477256 ACTTTCTCATCATCAAAAAGGAAACAA 58.523 29.630 0.00 0.00 32.53 2.83
5959 7530 3.121929 ACTCATAGCAAAGAGGAGGGA 57.878 47.619 4.67 0.00 36.20 4.20
6255 7833 0.037697 TGAACGTGCCGCAGAAGTAT 60.038 50.000 0.00 0.00 0.00 2.12
6271 7849 8.564574 ACTACAAAATTAATCTGCGAGTTTGAA 58.435 29.630 11.56 0.00 0.00 2.69
6272 7850 8.094798 ACTACAAAATTAATCTGCGAGTTTGA 57.905 30.769 11.56 0.00 0.00 2.69
6302 7884 3.056607 CCCTTTGCTTATCTTTGTGGTGG 60.057 47.826 0.00 0.00 0.00 4.61
6303 7885 3.614870 GCCCTTTGCTTATCTTTGTGGTG 60.615 47.826 0.00 0.00 36.87 4.17
6316 7898 1.115326 GTCCAAACTGGCCCTTTGCT 61.115 55.000 14.81 0.00 40.92 3.91
6437 8045 2.867429 AGCAGCAAACATAATTCACGC 58.133 42.857 0.00 0.00 0.00 5.34
6453 8061 3.126000 GCCAGTAGAAGTTTTGCTAGCAG 59.874 47.826 18.45 2.40 0.00 4.24
6454 8062 3.074412 GCCAGTAGAAGTTTTGCTAGCA 58.926 45.455 14.93 14.93 0.00 3.49
6492 8100 0.536460 TTGGAAAAGGGCAGGTCGAC 60.536 55.000 7.13 7.13 0.00 4.20
6497 8105 1.615392 CAGAACTTGGAAAAGGGCAGG 59.385 52.381 0.00 0.00 0.00 4.85
6558 8168 8.516234 TGCAAAACAACACTCTTAACTTTTCTA 58.484 29.630 0.00 0.00 0.00 2.10
6596 8207 4.159879 ACCTTTATAGACTGGAACACTCCG 59.840 45.833 0.00 0.00 45.85 4.63
6676 8288 1.133482 AGAACCACCCAAACCTCCTTG 60.133 52.381 0.00 0.00 0.00 3.61
6687 8299 7.339466 ACAGTGAATAAATAATGAGAACCACCC 59.661 37.037 0.00 0.00 0.00 4.61
6724 8356 2.642154 ACGGTTGGTTGTGTTCCATA 57.358 45.000 0.00 0.00 34.75 2.74
6903 8552 1.832167 GTTTCTGGCTGCCAACCCA 60.832 57.895 23.51 4.10 30.80 4.51
6982 8631 5.011586 GCCAACCCCATACAACTAAACTTA 58.988 41.667 0.00 0.00 0.00 2.24
7007 8656 8.143193 TCTCAAAAACTGCAATATGTTTGTGAT 58.857 29.630 17.66 0.00 44.43 3.06


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

AutoCloner maintained by Alex Coulton.