Multiple sequence alignment - TraesCS6D01G211900

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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 TraesCS6D01G211900 chr6D 100.000 2991 0 0 1 2991 299167274 299170264 0.000000e+00 5524.0
1 TraesCS6D01G211900 chr6D 91.818 110 9 0 561 670 63722284 63722393 1.440000e-33 154.0
2 TraesCS6D01G211900 chr6B 95.112 1698 58 17 696 2380 462148212 462149897 0.000000e+00 2652.0
3 TraesCS6D01G211900 chr6B 86.632 576 52 15 1 556 462147628 462148198 5.480000e-172 614.0
4 TraesCS6D01G211900 chr6B 86.513 304 33 4 2643 2942 462150207 462150506 7.990000e-86 327.0
5 TraesCS6D01G211900 chr6B 90.948 232 10 4 2413 2643 462149898 462150119 4.850000e-78 302.0
6 TraesCS6D01G211900 chr6A 93.599 1656 73 10 791 2423 420366225 420364580 0.000000e+00 2440.0
7 TraesCS6D01G211900 chr6A 97.170 212 5 1 1 212 420380692 420380482 1.020000e-94 357.0
8 TraesCS6D01G211900 chr6A 84.810 237 20 7 325 558 420366523 420366300 1.080000e-54 224.0
9 TraesCS6D01G211900 chr6A 88.649 185 16 3 2643 2827 420102318 420102139 1.400000e-53 220.0
10 TraesCS6D01G211900 chr6A 90.840 131 9 3 2414 2543 420364557 420364429 3.960000e-39 172.0
11 TraesCS6D01G211900 chr6A 91.270 126 8 2 203 328 420380330 420380208 5.130000e-38 169.0
12 TraesCS6D01G211900 chr6A 89.916 119 11 1 555 672 542255960 542256078 5.160000e-33 152.0
13 TraesCS6D01G211900 chr6A 88.608 79 7 2 666 742 420366296 420366218 8.830000e-16 95.3
14 TraesCS6D01G211900 chr2D 82.861 811 130 8 1022 1829 482418557 482417753 0.000000e+00 719.0
15 TraesCS6D01G211900 chr2B 82.550 808 129 10 1022 1823 566454204 566453403 0.000000e+00 701.0
16 TraesCS6D01G211900 chr2A 82.367 811 131 9 1022 1829 625008490 625007689 0.000000e+00 695.0
17 TraesCS6D01G211900 chr2A 91.150 113 9 1 561 672 565185300 565185188 5.160000e-33 152.0
18 TraesCS6D01G211900 chr5A 91.525 118 8 2 561 676 653853668 653853551 8.580000e-36 161.0
19 TraesCS6D01G211900 chr5A 92.593 108 7 1 562 668 368761217 368761324 1.440000e-33 154.0
20 TraesCS6D01G211900 chr5D 89.344 122 11 2 548 667 382294580 382294701 5.160000e-33 152.0
21 TraesCS6D01G211900 chr4D 91.743 109 9 0 562 670 39211020 39210912 5.160000e-33 152.0
22 TraesCS6D01G211900 chr7D 91.071 112 9 1 561 671 617094258 617094147 1.860000e-32 150.0
23 TraesCS6D01G211900 chr3A 90.435 115 10 1 555 668 608386697 608386811 1.860000e-32 150.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G211900 chr6D 299167274 299170264 2990 False 5524.000 5524 100.00000 1 2991 1 chr6D.!!$F2 2990
1 TraesCS6D01G211900 chr6B 462147628 462150506 2878 False 973.750 2652 89.80125 1 2942 4 chr6B.!!$F1 2941
2 TraesCS6D01G211900 chr6A 420364429 420366523 2094 True 732.825 2440 89.46425 325 2543 4 chr6A.!!$R2 2218
3 TraesCS6D01G211900 chr2D 482417753 482418557 804 True 719.000 719 82.86100 1022 1829 1 chr2D.!!$R1 807
4 TraesCS6D01G211900 chr2B 566453403 566454204 801 True 701.000 701 82.55000 1022 1823 1 chr2B.!!$R1 801
5 TraesCS6D01G211900 chr2A 625007689 625008490 801 True 695.000 695 82.36700 1022 1829 1 chr2A.!!$R2 807

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
147 148 0.165944 GTTGAGGGCGATGTTTGACG 59.834 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2181 0.029567 CGCGGCCTTGTGTACAAAAA 59.97 50.0 0.0 0.0 35.15 1.94 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
25 26 2.005370 ATTAGGGCTGCATCATTGGG 57.995 50.000 0.50 0.00 0.00 4.12
58 59 1.937899 GTTGCCACTCAAACACGTACT 59.062 47.619 0.00 0.00 36.26 2.73
83 84 1.905215 ACCTGTAGAAGCATCAGCACT 59.095 47.619 0.00 0.00 45.49 4.40
147 148 0.165944 GTTGAGGGCGATGTTTGACG 59.834 55.000 0.00 0.00 0.00 4.35
175 176 5.193527 TCCATAATCCATGTCCTCTTTTCCA 59.806 40.000 0.00 0.00 32.21 3.53
205 208 5.965033 TCTCTCCAAGAAAATCCTGCTAT 57.035 39.130 0.00 0.00 0.00 2.97
219 222 3.073062 TCCTGCTATAAGGAATCCTTGCC 59.927 47.826 23.89 9.81 44.44 4.52
224 227 1.204146 TAAGGAATCCTTGCCTCGCT 58.796 50.000 23.89 0.00 44.44 4.93
235 238 3.056313 GCCTCGCTCCAACCAATGC 62.056 63.158 0.00 0.00 0.00 3.56
240 243 0.664761 CGCTCCAACCAATGCCTATG 59.335 55.000 0.00 0.00 0.00 2.23
266 269 1.674322 GTATTGCACGCACCCCAGT 60.674 57.895 0.00 0.00 0.00 4.00
286 289 2.726760 GTGCACACTCTACGAACTTGAG 59.273 50.000 13.17 0.00 0.00 3.02
310 313 0.328450 ATCCCTGCCCCCAGTTCATA 60.328 55.000 0.00 0.00 37.38 2.15
323 326 6.062095 CCCCAGTTCATAAGGAATATTCGTT 58.938 40.000 22.84 22.84 37.93 3.85
347 350 6.377912 TCTCTTATTTTTCCAGAAAACCCCA 58.622 36.000 5.08 0.00 39.70 4.96
356 359 3.072476 TCCAGAAAACCCCACAGTAGAAG 59.928 47.826 0.00 0.00 0.00 2.85
385 388 7.592885 AAATAAAATGAGCAGCATCCTGTAT 57.407 32.000 0.00 0.00 41.26 2.29
415 423 7.696992 TTTGTCCTTGGCTTATAACTTTAGG 57.303 36.000 0.00 0.00 0.00 2.69
416 424 6.382919 TGTCCTTGGCTTATAACTTTAGGT 57.617 37.500 0.00 0.00 0.00 3.08
417 425 6.786122 TGTCCTTGGCTTATAACTTTAGGTT 58.214 36.000 0.00 0.00 41.54 3.50
419 427 7.392393 TGTCCTTGGCTTATAACTTTAGGTTTC 59.608 37.037 0.00 0.00 39.17 2.78
486 507 4.933330 TCTTAACGACTATCCACTGCATC 58.067 43.478 0.00 0.00 0.00 3.91
560 583 9.036671 AGGTTGATGTTGGTAAAAATTAAAACG 57.963 29.630 0.00 0.00 0.00 3.60
605 628 9.970395 TTATAAGACGTTTTAGACTTTCAGACA 57.030 29.630 4.75 0.00 0.00 3.41
606 629 6.585389 AAGACGTTTTAGACTTTCAGACAC 57.415 37.500 0.00 0.00 0.00 3.67
607 630 5.903810 AGACGTTTTAGACTTTCAGACACT 58.096 37.500 0.00 0.00 0.00 3.55
608 631 5.749109 AGACGTTTTAGACTTTCAGACACTG 59.251 40.000 0.00 0.00 0.00 3.66
609 632 5.416947 ACGTTTTAGACTTTCAGACACTGT 58.583 37.500 0.00 0.00 32.61 3.55
610 633 5.873164 ACGTTTTAGACTTTCAGACACTGTT 59.127 36.000 0.00 0.00 32.61 3.16
611 634 6.035758 ACGTTTTAGACTTTCAGACACTGTTC 59.964 38.462 0.00 0.00 32.61 3.18
612 635 6.035650 CGTTTTAGACTTTCAGACACTGTTCA 59.964 38.462 0.00 0.00 32.61 3.18
613 636 7.412563 CGTTTTAGACTTTCAGACACTGTTCAA 60.413 37.037 0.00 0.00 32.61 2.69
614 637 7.915293 TTTAGACTTTCAGACACTGTTCAAA 57.085 32.000 0.00 0.00 32.61 2.69
615 638 7.915293 TTAGACTTTCAGACACTGTTCAAAA 57.085 32.000 0.00 0.00 32.61 2.44
616 639 6.183309 AGACTTTCAGACACTGTTCAAAAC 57.817 37.500 0.00 0.00 32.61 2.43
617 640 5.705441 AGACTTTCAGACACTGTTCAAAACA 59.295 36.000 0.00 0.00 39.52 2.83
618 641 6.206634 AGACTTTCAGACACTGTTCAAAACAA 59.793 34.615 0.00 0.00 41.61 2.83
619 642 6.924111 ACTTTCAGACACTGTTCAAAACAAT 58.076 32.000 0.00 0.00 41.61 2.71
620 643 8.050778 ACTTTCAGACACTGTTCAAAACAATA 57.949 30.769 0.00 0.00 41.61 1.90
621 644 7.968405 ACTTTCAGACACTGTTCAAAACAATAC 59.032 33.333 0.00 0.00 41.61 1.89
622 645 6.993786 TCAGACACTGTTCAAAACAATACA 57.006 33.333 0.00 0.00 41.61 2.29
623 646 7.384439 TCAGACACTGTTCAAAACAATACAA 57.616 32.000 0.00 0.00 41.61 2.41
624 647 7.821652 TCAGACACTGTTCAAAACAATACAAA 58.178 30.769 0.00 0.00 41.61 2.83
625 648 8.465999 TCAGACACTGTTCAAAACAATACAAAT 58.534 29.630 0.00 0.00 41.61 2.32
626 649 8.745837 CAGACACTGTTCAAAACAATACAAATC 58.254 33.333 0.00 0.00 41.61 2.17
627 650 8.465999 AGACACTGTTCAAAACAATACAAATCA 58.534 29.630 0.00 0.00 41.61 2.57
628 651 8.994429 ACACTGTTCAAAACAATACAAATCAA 57.006 26.923 0.00 0.00 41.61 2.57
629 652 9.429359 ACACTGTTCAAAACAATACAAATCAAA 57.571 25.926 0.00 0.00 41.61 2.69
630 653 9.687717 CACTGTTCAAAACAATACAAATCAAAC 57.312 29.630 0.00 0.00 41.61 2.93
631 654 9.651913 ACTGTTCAAAACAATACAAATCAAACT 57.348 25.926 0.00 0.00 41.61 2.66
632 655 9.904647 CTGTTCAAAACAATACAAATCAAACTG 57.095 29.630 0.00 0.00 41.61 3.16
633 656 9.429359 TGTTCAAAACAATACAAATCAAACTGT 57.571 25.926 0.00 0.00 38.72 3.55
634 657 9.900264 GTTCAAAACAATACAAATCAAACTGTC 57.100 29.630 0.00 0.00 0.00 3.51
635 658 9.868277 TTCAAAACAATACAAATCAAACTGTCT 57.132 25.926 0.00 0.00 0.00 3.41
636 659 9.299963 TCAAAACAATACAAATCAAACTGTCTG 57.700 29.630 0.00 0.00 0.00 3.51
637 660 9.299963 CAAAACAATACAAATCAAACTGTCTGA 57.700 29.630 0.00 0.00 0.00 3.27
638 661 9.868277 AAAACAATACAAATCAAACTGTCTGAA 57.132 25.926 0.00 0.00 0.00 3.02
640 663 9.467258 AACAATACAAATCAAACTGTCTGAATG 57.533 29.630 0.00 0.00 0.00 2.67
641 664 8.632679 ACAATACAAATCAAACTGTCTGAATGT 58.367 29.630 9.78 9.78 33.82 2.71
642 665 9.121517 CAATACAAATCAAACTGTCTGAATGTC 57.878 33.333 8.58 0.00 32.46 3.06
643 666 6.949352 ACAAATCAAACTGTCTGAATGTCT 57.051 33.333 1.46 0.00 0.00 3.41
644 667 7.338800 ACAAATCAAACTGTCTGAATGTCTT 57.661 32.000 1.46 0.00 0.00 3.01
645 668 8.450578 ACAAATCAAACTGTCTGAATGTCTTA 57.549 30.769 1.46 0.00 0.00 2.10
646 669 9.071276 ACAAATCAAACTGTCTGAATGTCTTAT 57.929 29.630 1.46 0.00 0.00 1.73
657 680 9.658475 TGTCTGAATGTCTTATAAAAACAAACG 57.342 29.630 4.87 0.00 0.00 3.60
658 681 9.113876 GTCTGAATGTCTTATAAAAACAAACGG 57.886 33.333 4.87 6.98 0.00 4.44
659 682 9.058174 TCTGAATGTCTTATAAAAACAAACGGA 57.942 29.630 4.87 8.54 0.00 4.69
660 683 9.329913 CTGAATGTCTTATAAAAACAAACGGAG 57.670 33.333 4.87 0.00 0.00 4.63
661 684 8.293867 TGAATGTCTTATAAAAACAAACGGAGG 58.706 33.333 4.87 0.00 0.00 4.30
662 685 6.563222 TGTCTTATAAAAACAAACGGAGGG 57.437 37.500 0.00 0.00 0.00 4.30
663 686 6.297582 TGTCTTATAAAAACAAACGGAGGGA 58.702 36.000 0.00 0.00 0.00 4.20
664 687 6.428771 TGTCTTATAAAAACAAACGGAGGGAG 59.571 38.462 0.00 0.00 0.00 4.30
665 688 6.429078 GTCTTATAAAAACAAACGGAGGGAGT 59.571 38.462 0.00 0.00 0.00 3.85
666 689 7.603784 GTCTTATAAAAACAAACGGAGGGAGTA 59.396 37.037 0.00 0.00 0.00 2.59
667 690 8.323567 TCTTATAAAAACAAACGGAGGGAGTAT 58.676 33.333 0.00 0.00 0.00 2.12
668 691 8.866970 TTATAAAAACAAACGGAGGGAGTATT 57.133 30.769 0.00 0.00 0.00 1.89
679 702 7.008021 ACGGAGGGAGTATTTAACTTTACAA 57.992 36.000 0.00 0.00 39.07 2.41
683 706 7.336176 GGAGGGAGTATTTAACTTTACAACTGG 59.664 40.741 0.00 0.00 39.07 4.00
731 755 4.038282 TGCTTTCACTGATTCATTGTTGCT 59.962 37.500 4.19 0.00 0.00 3.91
737 761 9.791820 TTTCACTGATTCATTGTTGCTTATATG 57.208 29.630 4.19 0.00 0.00 1.78
745 769 4.963276 TTGTTGCTTATATGCTCCACAC 57.037 40.909 11.48 2.64 0.00 3.82
756 780 1.559682 TGCTCCACACCTAATTCTCCC 59.440 52.381 0.00 0.00 0.00 4.30
761 785 4.918588 TCCACACCTAATTCTCCCTTTTC 58.081 43.478 0.00 0.00 0.00 2.29
816 845 9.612066 TTGCATCCTAAAAGAAATTCTTGTTTT 57.388 25.926 9.21 2.93 40.19 2.43
1018 1047 4.473477 ACTATGAGTGCAGACCTAAACC 57.527 45.455 0.00 0.00 0.00 3.27
1126 1155 4.351938 TCAAGTCCGTGGACCGCG 62.352 66.667 20.61 20.61 45.59 6.46
1716 1748 2.437895 GGCAGCGTTAGGTTCCCC 60.438 66.667 0.00 0.00 0.00 4.81
1877 1929 2.024414 CCGGAAAAATCATGTCCTCCC 58.976 52.381 0.00 0.00 0.00 4.30
1889 1941 1.354368 TGTCCTCCCCAGTTTTCATCC 59.646 52.381 0.00 0.00 0.00 3.51
1920 1972 5.590259 AGATCCAGGAATTAACATTTGGTCG 59.410 40.000 0.00 0.00 0.00 4.79
1993 2050 1.228245 GGAGCAGCCAACCTGAACA 60.228 57.895 0.00 0.00 44.64 3.18
2080 2137 0.818296 GGCTCCGCAGAGAAGTAGAA 59.182 55.000 0.00 0.00 43.39 2.10
2124 2181 1.153901 CCGACGCTGTCAATACGGT 60.154 57.895 8.91 0.00 36.38 4.83
2193 2251 2.025155 ACGGCAGTAGATCGAGTGAAT 58.975 47.619 14.17 0.00 0.00 2.57
2232 2290 0.689623 CAGCTCCTCTTGGACCTGTT 59.310 55.000 0.00 0.00 39.86 3.16
2406 2469 5.106948 GCTTTGCTTCCCTTTTAATTCAAGC 60.107 40.000 0.00 0.00 37.38 4.01
2410 2473 4.389992 GCTTCCCTTTTAATTCAAGCTTGC 59.610 41.667 21.99 0.00 34.64 4.01
2411 2474 5.540911 CTTCCCTTTTAATTCAAGCTTGCA 58.459 37.500 21.99 11.97 0.00 4.08
2420 2515 0.599558 TCAAGCTTGCAATGTGCCTC 59.400 50.000 21.99 0.00 44.23 4.70
2480 2576 2.211250 TAGGTAACACTCCACTCGCT 57.789 50.000 0.00 0.00 41.41 4.93
2520 2616 5.105063 CGAAATCTTCAGTCAGCTGTCATA 58.895 41.667 14.67 0.00 43.05 2.15
2536 2632 7.335422 CAGCTGTCATACAAGTTTCTCCTTATT 59.665 37.037 5.25 0.00 0.00 1.40
2546 2642 9.454859 ACAAGTTTCTCCTTATTCAAATAGGAG 57.545 33.333 10.43 10.43 45.44 3.69
2547 2643 9.454859 CAAGTTTCTCCTTATTCAAATAGGAGT 57.545 33.333 14.99 0.00 44.64 3.85
2612 2708 3.449737 TGGTTATGTACTCCCTCCTTTCG 59.550 47.826 0.00 0.00 0.00 3.46
2621 2717 8.716674 TGTACTCCCTCCTTTCGTAAATATAT 57.283 34.615 0.00 0.00 0.00 0.86
2622 2718 9.812347 TGTACTCCCTCCTTTCGTAAATATATA 57.188 33.333 0.00 0.00 0.00 0.86
2648 2744 8.522178 AGTCTTTCTAGAGATTTTAACGTGTG 57.478 34.615 0.00 0.00 0.00 3.82
2649 2745 8.358148 AGTCTTTCTAGAGATTTTAACGTGTGA 58.642 33.333 0.00 0.00 0.00 3.58
2650 2746 8.640291 GTCTTTCTAGAGATTTTAACGTGTGAG 58.360 37.037 0.00 0.00 0.00 3.51
2651 2747 8.358148 TCTTTCTAGAGATTTTAACGTGTGAGT 58.642 33.333 0.00 0.00 0.00 3.41
2652 2748 9.622004 CTTTCTAGAGATTTTAACGTGTGAGTA 57.378 33.333 0.00 0.00 0.00 2.59
2654 2750 9.569167 TTCTAGAGATTTTAACGTGTGAGTATG 57.431 33.333 0.00 0.00 0.00 2.39
2677 2863 2.187946 GCTCGGGGAGGACACATG 59.812 66.667 0.00 0.00 0.00 3.21
2683 2869 1.202533 CGGGGAGGACACATGATGTAC 60.203 57.143 0.00 0.72 43.56 2.90
2694 2880 5.141182 ACACATGATGTACTAGGGTAGGAG 58.859 45.833 0.00 0.00 40.88 3.69
2702 2888 3.759815 ACTAGGGTAGGAGCAGAGAAA 57.240 47.619 0.00 0.00 0.00 2.52
2722 2908 9.178758 AGAGAAAGACCATGGAAATTGTATAAC 57.821 33.333 21.47 0.00 0.00 1.89
2761 2947 3.748048 TCAAACTCTTTGGATCAAGCTCG 59.252 43.478 0.00 0.00 40.98 5.03
2773 2959 4.742659 GGATCAAGCTCGAGTGTCTATTTC 59.257 45.833 15.13 1.78 0.00 2.17
2779 2965 3.190874 CTCGAGTGTCTATTTCCCAAGC 58.809 50.000 3.62 0.00 0.00 4.01
2781 2967 3.007506 TCGAGTGTCTATTTCCCAAGCAA 59.992 43.478 0.00 0.00 0.00 3.91
2786 2972 6.245408 AGTGTCTATTTCCCAAGCAACAATA 58.755 36.000 0.00 0.00 0.00 1.90
2821 3007 4.250116 CAGTACAACTGCAACTCTCTCT 57.750 45.455 0.00 0.00 39.62 3.10
2828 3014 4.464069 ACTGCAACTCTCTCTTGTATCC 57.536 45.455 0.00 0.00 0.00 2.59
2843 3029 2.291346 TGTATCCAGACCAGACCTTCGA 60.291 50.000 0.00 0.00 0.00 3.71
2848 3034 3.644399 GACCAGACCTTCGACGGCC 62.644 68.421 8.05 0.00 0.00 6.13
2871 3057 1.062587 GCGAAAATGACCTGACATCCG 59.937 52.381 0.00 0.00 0.00 4.18
2873 3059 2.348666 CGAAAATGACCTGACATCCGAC 59.651 50.000 0.00 0.00 0.00 4.79
2876 3062 1.852633 ATGACCTGACATCCGACTGA 58.147 50.000 0.00 0.00 0.00 3.41
2877 3063 1.852633 TGACCTGACATCCGACTGAT 58.147 50.000 0.00 0.00 0.00 2.90
2895 3082 3.091545 TGATGAGAAACCATCCTTTGCC 58.908 45.455 0.00 0.00 41.60 4.52
2899 3086 0.247460 GAAACCATCCTTTGCCCTGC 59.753 55.000 0.00 0.00 0.00 4.85
2922 3109 1.325355 TTCTTCCGTTCCACGACTCT 58.675 50.000 0.00 0.00 46.05 3.24
2927 3115 1.507174 CGTTCCACGACTCTCCCTC 59.493 63.158 0.00 0.00 46.05 4.30
2930 3118 0.677098 TTCCACGACTCTCCCTCTCG 60.677 60.000 0.00 0.00 0.00 4.04
2942 3130 2.161486 CCTCTCGCTGCAAGTACGC 61.161 63.158 0.00 0.00 35.30 4.42
2944 3132 4.196826 CTCGCTGCAAGTACGCGC 62.197 66.667 5.73 0.00 45.87 6.86
2945 3133 4.717629 TCGCTGCAAGTACGCGCT 62.718 61.111 5.73 0.00 45.87 5.92
2946 3134 4.489795 CGCTGCAAGTACGCGCTG 62.490 66.667 5.73 10.50 40.42 5.18
2947 3135 3.414700 GCTGCAAGTACGCGCTGT 61.415 61.111 5.73 8.05 35.30 4.40
2948 3136 2.092291 GCTGCAAGTACGCGCTGTA 61.092 57.895 5.73 6.93 35.30 2.74
2955 3143 3.469136 TACGCGCTGTACGTACGA 58.531 55.556 24.41 9.08 44.55 3.43
2956 3144 1.344837 TACGCGCTGTACGTACGAG 59.655 57.895 24.41 17.87 44.55 4.18
2957 3145 1.351430 TACGCGCTGTACGTACGAGT 61.351 55.000 24.41 17.49 44.55 4.18
2958 3146 2.206487 CGCGCTGTACGTACGAGTG 61.206 63.158 24.41 21.91 46.11 3.51
2959 3147 1.866496 GCGCTGTACGTACGAGTGG 60.866 63.158 24.41 18.22 46.11 4.00
2960 3148 1.499056 CGCTGTACGTACGAGTGGT 59.501 57.895 24.41 0.61 36.87 4.16
2961 3149 0.721154 CGCTGTACGTACGAGTGGTA 59.279 55.000 24.41 0.00 36.87 3.25
2962 3150 1.527793 CGCTGTACGTACGAGTGGTAC 60.528 57.143 24.41 13.73 46.54 3.34
2969 3157 2.686558 GTACGAGTGGTACAACGTCA 57.313 50.000 10.27 0.00 46.48 4.35
2970 3158 2.578495 GTACGAGTGGTACAACGTCAG 58.422 52.381 10.27 0.00 46.48 3.51
2971 3159 0.313043 ACGAGTGGTACAACGTCAGG 59.687 55.000 0.00 0.00 46.48 3.86
2972 3160 0.594602 CGAGTGGTACAACGTCAGGA 59.405 55.000 0.00 0.00 44.16 3.86
2973 3161 1.401148 CGAGTGGTACAACGTCAGGAG 60.401 57.143 0.00 0.00 44.16 3.69
2974 3162 1.612463 GAGTGGTACAACGTCAGGAGT 59.388 52.381 0.00 0.00 44.16 3.85
2975 3163 1.340248 AGTGGTACAACGTCAGGAGTG 59.660 52.381 0.00 0.00 44.16 3.51
2976 3164 0.677288 TGGTACAACGTCAGGAGTGG 59.323 55.000 0.00 0.00 31.92 4.00
2977 3165 0.037605 GGTACAACGTCAGGAGTGGG 60.038 60.000 0.00 0.00 0.00 4.61
2978 3166 0.037605 GTACAACGTCAGGAGTGGGG 60.038 60.000 0.00 0.00 0.00 4.96
2979 3167 0.470456 TACAACGTCAGGAGTGGGGT 60.470 55.000 0.00 0.00 0.00 4.95
2980 3168 0.470456 ACAACGTCAGGAGTGGGGTA 60.470 55.000 0.00 0.00 0.00 3.69
2981 3169 0.902531 CAACGTCAGGAGTGGGGTAT 59.097 55.000 0.00 0.00 0.00 2.73
2982 3170 0.902531 AACGTCAGGAGTGGGGTATG 59.097 55.000 0.00 0.00 0.00 2.39
2983 3171 1.144057 CGTCAGGAGTGGGGTATGC 59.856 63.158 0.00 0.00 0.00 3.14
2984 3172 1.527370 GTCAGGAGTGGGGTATGCC 59.473 63.158 0.00 0.00 0.00 4.40
2985 3173 2.063979 TCAGGAGTGGGGTATGCCG 61.064 63.158 0.00 0.00 34.97 5.69
2986 3174 2.063979 CAGGAGTGGGGTATGCCGA 61.064 63.158 0.00 0.00 34.97 5.54
2987 3175 2.064581 AGGAGTGGGGTATGCCGAC 61.065 63.158 0.00 0.00 34.97 4.79
2988 3176 2.504519 GAGTGGGGTATGCCGACC 59.495 66.667 0.00 0.00 38.93 4.79
2989 3177 2.040606 AGTGGGGTATGCCGACCT 59.959 61.111 4.28 0.00 39.66 3.85
2990 3178 2.189521 GTGGGGTATGCCGACCTG 59.810 66.667 4.28 0.00 39.66 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.048603 GGCAACTGGAGCCCATCAC 61.049 63.158 1.64 0.00 46.50 3.06
34 35 1.388547 GTGTTTGAGTGGCAACTGGA 58.611 50.000 0.00 0.00 36.52 3.86
58 59 3.368427 GCTGATGCTTCTACAGGTGTACA 60.368 47.826 0.00 0.00 36.03 2.90
132 133 0.539986 ATACCGTCAAACATCGCCCT 59.460 50.000 0.00 0.00 0.00 5.19
147 148 6.380079 AAGAGGACATGGATTATGGATACC 57.620 41.667 0.00 0.00 41.25 2.73
187 190 6.575244 TCCTTATAGCAGGATTTTCTTGGA 57.425 37.500 0.00 0.00 38.11 3.53
188 191 7.040132 GGATTCCTTATAGCAGGATTTTCTTGG 60.040 40.741 0.00 0.00 42.89 3.61
189 192 7.723172 AGGATTCCTTATAGCAGGATTTTCTTG 59.277 37.037 0.00 0.00 42.89 3.02
205 208 1.139058 GAGCGAGGCAAGGATTCCTTA 59.861 52.381 17.54 0.00 42.67 2.69
219 222 0.107703 TAGGCATTGGTTGGAGCGAG 60.108 55.000 0.00 0.00 0.00 5.03
235 238 3.403038 GTGCAATACTGGTAGCCATAGG 58.597 50.000 0.00 0.00 30.82 2.57
240 243 0.742990 TGCGTGCAATACTGGTAGCC 60.743 55.000 0.00 0.00 0.00 3.93
247 250 1.377202 CTGGGGTGCGTGCAATACT 60.377 57.895 0.00 0.00 0.00 2.12
248 251 1.674322 ACTGGGGTGCGTGCAATAC 60.674 57.895 0.00 0.00 0.00 1.89
266 269 2.361119 ACTCAAGTTCGTAGAGTGTGCA 59.639 45.455 0.00 0.00 40.83 4.57
286 289 3.346734 TGGGGGCAGGGATGGAAC 61.347 66.667 0.00 0.00 0.00 3.62
323 326 6.266786 GTGGGGTTTTCTGGAAAAATAAGAGA 59.733 38.462 9.65 0.00 41.37 3.10
333 336 3.050089 TCTACTGTGGGGTTTTCTGGAA 58.950 45.455 0.00 0.00 0.00 3.53
340 343 2.054799 TCAGCTTCTACTGTGGGGTTT 58.945 47.619 0.00 0.00 38.84 3.27
342 345 1.729586 TTCAGCTTCTACTGTGGGGT 58.270 50.000 0.00 0.00 38.84 4.95
347 350 8.239998 GCTCATTTTATTTTCAGCTTCTACTGT 58.760 33.333 0.00 0.00 38.84 3.55
356 359 5.233689 GGATGCTGCTCATTTTATTTTCAGC 59.766 40.000 0.00 0.00 43.90 4.26
475 496 4.197750 CTGAGCTAAAAGATGCAGTGGAT 58.802 43.478 0.00 0.00 0.00 3.41
486 507 9.846248 AATTATTTTAGTGCACTGAGCTAAAAG 57.154 29.630 29.57 0.00 43.43 2.27
579 602 9.970395 TGTCTGAAAGTCTAAAACGTCTTATAA 57.030 29.630 0.00 0.00 33.76 0.98
580 603 9.403110 GTGTCTGAAAGTCTAAAACGTCTTATA 57.597 33.333 0.00 0.00 33.76 0.98
581 604 8.142551 AGTGTCTGAAAGTCTAAAACGTCTTAT 58.857 33.333 0.00 0.00 33.76 1.73
582 605 7.434307 CAGTGTCTGAAAGTCTAAAACGTCTTA 59.566 37.037 0.00 0.00 32.44 2.10
583 606 6.255887 CAGTGTCTGAAAGTCTAAAACGTCTT 59.744 38.462 0.00 0.00 32.44 3.01
584 607 5.749109 CAGTGTCTGAAAGTCTAAAACGTCT 59.251 40.000 0.00 0.00 32.44 4.18
585 608 5.519206 ACAGTGTCTGAAAGTCTAAAACGTC 59.481 40.000 3.70 0.00 35.18 4.34
586 609 5.416947 ACAGTGTCTGAAAGTCTAAAACGT 58.583 37.500 3.70 0.00 35.18 3.99
587 610 5.968387 ACAGTGTCTGAAAGTCTAAAACG 57.032 39.130 3.70 0.00 35.18 3.60
588 611 7.303634 TGAACAGTGTCTGAAAGTCTAAAAC 57.696 36.000 0.00 0.00 35.18 2.43
589 612 7.915293 TTGAACAGTGTCTGAAAGTCTAAAA 57.085 32.000 0.00 0.00 35.18 1.52
590 613 7.915293 TTTGAACAGTGTCTGAAAGTCTAAA 57.085 32.000 0.00 0.00 35.18 1.85
591 614 7.389330 TGTTTTGAACAGTGTCTGAAAGTCTAA 59.611 33.333 0.00 0.00 36.25 2.10
592 615 6.876789 TGTTTTGAACAGTGTCTGAAAGTCTA 59.123 34.615 0.00 0.00 36.25 2.59
593 616 5.705441 TGTTTTGAACAGTGTCTGAAAGTCT 59.295 36.000 0.00 0.00 36.25 3.24
594 617 5.938322 TGTTTTGAACAGTGTCTGAAAGTC 58.062 37.500 0.00 0.00 36.25 3.01
595 618 5.957842 TGTTTTGAACAGTGTCTGAAAGT 57.042 34.783 0.00 0.00 36.25 2.66
596 619 7.967854 TGTATTGTTTTGAACAGTGTCTGAAAG 59.032 33.333 0.00 0.00 43.27 2.62
597 620 7.821652 TGTATTGTTTTGAACAGTGTCTGAAA 58.178 30.769 0.00 0.00 43.27 2.69
598 621 7.384439 TGTATTGTTTTGAACAGTGTCTGAA 57.616 32.000 0.00 0.00 43.27 3.02
599 622 6.993786 TGTATTGTTTTGAACAGTGTCTGA 57.006 33.333 0.00 0.00 43.27 3.27
600 623 8.633075 ATTTGTATTGTTTTGAACAGTGTCTG 57.367 30.769 0.00 0.00 43.27 3.51
601 624 8.465999 TGATTTGTATTGTTTTGAACAGTGTCT 58.534 29.630 0.00 0.00 43.27 3.41
602 625 8.627487 TGATTTGTATTGTTTTGAACAGTGTC 57.373 30.769 0.00 0.00 43.27 3.67
603 626 8.994429 TTGATTTGTATTGTTTTGAACAGTGT 57.006 26.923 0.00 0.00 43.27 3.55
604 627 9.687717 GTTTGATTTGTATTGTTTTGAACAGTG 57.312 29.630 0.00 0.00 43.27 3.66
605 628 9.651913 AGTTTGATTTGTATTGTTTTGAACAGT 57.348 25.926 0.00 0.00 43.27 3.55
606 629 9.904647 CAGTTTGATTTGTATTGTTTTGAACAG 57.095 29.630 0.00 0.00 43.27 3.16
607 630 9.429359 ACAGTTTGATTTGTATTGTTTTGAACA 57.571 25.926 0.00 0.00 40.21 3.18
608 631 9.900264 GACAGTTTGATTTGTATTGTTTTGAAC 57.100 29.630 0.00 0.00 0.00 3.18
609 632 9.868277 AGACAGTTTGATTTGTATTGTTTTGAA 57.132 25.926 0.00 0.00 0.00 2.69
610 633 9.299963 CAGACAGTTTGATTTGTATTGTTTTGA 57.700 29.630 0.00 0.00 0.00 2.69
611 634 9.299963 TCAGACAGTTTGATTTGTATTGTTTTG 57.700 29.630 0.00 0.00 0.00 2.44
612 635 9.868277 TTCAGACAGTTTGATTTGTATTGTTTT 57.132 25.926 0.00 0.00 0.00 2.43
614 637 9.467258 CATTCAGACAGTTTGATTTGTATTGTT 57.533 29.630 0.00 0.00 0.00 2.83
615 638 8.632679 ACATTCAGACAGTTTGATTTGTATTGT 58.367 29.630 7.89 0.00 0.00 2.71
616 639 9.121517 GACATTCAGACAGTTTGATTTGTATTG 57.878 33.333 9.10 0.00 0.00 1.90
617 640 9.071276 AGACATTCAGACAGTTTGATTTGTATT 57.929 29.630 9.10 1.77 0.00 1.89
618 641 8.627208 AGACATTCAGACAGTTTGATTTGTAT 57.373 30.769 9.10 5.18 0.00 2.29
619 642 8.450578 AAGACATTCAGACAGTTTGATTTGTA 57.549 30.769 9.10 0.00 0.00 2.41
620 643 6.949352 AGACATTCAGACAGTTTGATTTGT 57.051 33.333 8.95 8.95 0.00 2.83
631 654 9.658475 CGTTTGTTTTTATAAGACATTCAGACA 57.342 29.630 5.05 0.00 0.00 3.41
632 655 9.113876 CCGTTTGTTTTTATAAGACATTCAGAC 57.886 33.333 5.05 0.00 0.00 3.51
633 656 9.058174 TCCGTTTGTTTTTATAAGACATTCAGA 57.942 29.630 5.05 0.43 0.00 3.27
634 657 9.329913 CTCCGTTTGTTTTTATAAGACATTCAG 57.670 33.333 5.05 0.24 0.00 3.02
635 658 8.293867 CCTCCGTTTGTTTTTATAAGACATTCA 58.706 33.333 5.05 0.00 0.00 2.57
636 659 7.753580 CCCTCCGTTTGTTTTTATAAGACATTC 59.246 37.037 5.05 2.42 0.00 2.67
637 660 7.449086 TCCCTCCGTTTGTTTTTATAAGACATT 59.551 33.333 5.05 0.00 0.00 2.71
638 661 6.943718 TCCCTCCGTTTGTTTTTATAAGACAT 59.056 34.615 5.05 0.00 0.00 3.06
639 662 6.297582 TCCCTCCGTTTGTTTTTATAAGACA 58.702 36.000 1.00 1.00 0.00 3.41
640 663 6.429078 ACTCCCTCCGTTTGTTTTTATAAGAC 59.571 38.462 0.00 0.00 0.00 3.01
641 664 6.536447 ACTCCCTCCGTTTGTTTTTATAAGA 58.464 36.000 0.00 0.00 0.00 2.10
642 665 6.812879 ACTCCCTCCGTTTGTTTTTATAAG 57.187 37.500 0.00 0.00 0.00 1.73
643 666 8.866970 AATACTCCCTCCGTTTGTTTTTATAA 57.133 30.769 0.00 0.00 0.00 0.98
644 667 8.866970 AAATACTCCCTCCGTTTGTTTTTATA 57.133 30.769 0.00 0.00 0.00 0.98
645 668 7.770366 AAATACTCCCTCCGTTTGTTTTTAT 57.230 32.000 0.00 0.00 0.00 1.40
646 669 8.567104 GTTAAATACTCCCTCCGTTTGTTTTTA 58.433 33.333 0.00 0.00 0.00 1.52
647 670 7.286087 AGTTAAATACTCCCTCCGTTTGTTTTT 59.714 33.333 0.00 0.00 28.23 1.94
648 671 6.774170 AGTTAAATACTCCCTCCGTTTGTTTT 59.226 34.615 0.00 0.00 28.23 2.43
649 672 6.301486 AGTTAAATACTCCCTCCGTTTGTTT 58.699 36.000 0.00 0.00 28.23 2.83
650 673 5.872963 AGTTAAATACTCCCTCCGTTTGTT 58.127 37.500 0.00 0.00 28.23 2.83
651 674 5.494390 AGTTAAATACTCCCTCCGTTTGT 57.506 39.130 0.00 0.00 28.23 2.83
652 675 6.812879 AAAGTTAAATACTCCCTCCGTTTG 57.187 37.500 0.00 0.00 35.54 2.93
653 676 7.452562 TGTAAAGTTAAATACTCCCTCCGTTT 58.547 34.615 0.00 0.00 35.54 3.60
654 677 7.008021 TGTAAAGTTAAATACTCCCTCCGTT 57.992 36.000 0.00 0.00 35.54 4.44
655 678 6.610075 TGTAAAGTTAAATACTCCCTCCGT 57.390 37.500 0.00 0.00 35.54 4.69
656 679 7.064253 CAGTTGTAAAGTTAAATACTCCCTCCG 59.936 40.741 0.00 0.00 35.54 4.63
657 680 7.336176 CCAGTTGTAAAGTTAAATACTCCCTCC 59.664 40.741 0.00 0.00 35.54 4.30
658 681 7.881751 ACCAGTTGTAAAGTTAAATACTCCCTC 59.118 37.037 0.00 0.00 35.54 4.30
659 682 7.752638 ACCAGTTGTAAAGTTAAATACTCCCT 58.247 34.615 0.00 0.00 35.54 4.20
660 683 7.881751 AGACCAGTTGTAAAGTTAAATACTCCC 59.118 37.037 0.00 0.00 35.54 4.30
661 684 8.843885 AGACCAGTTGTAAAGTTAAATACTCC 57.156 34.615 0.00 0.00 35.54 3.85
662 685 9.485206 TGAGACCAGTTGTAAAGTTAAATACTC 57.515 33.333 0.00 0.00 35.54 2.59
668 691 9.787435 ACATAATGAGACCAGTTGTAAAGTTAA 57.213 29.630 0.00 0.00 0.00 2.01
731 755 6.239887 GGGAGAATTAGGTGTGGAGCATATAA 60.240 42.308 0.00 0.00 0.00 0.98
737 761 1.840635 AGGGAGAATTAGGTGTGGAGC 59.159 52.381 0.00 0.00 0.00 4.70
745 769 5.193679 ACATTCCGAAAAGGGAGAATTAGG 58.806 41.667 0.00 0.00 41.52 2.69
756 780 6.039616 TCCTCAAAACAAACATTCCGAAAAG 58.960 36.000 0.00 0.00 0.00 2.27
761 785 6.039616 TCTTTTCCTCAAAACAAACATTCCG 58.960 36.000 0.00 0.00 0.00 4.30
816 845 1.073548 AGGGCGTTCGGGCTAAAAA 59.926 52.632 0.00 0.00 41.87 1.94
827 856 4.335647 CCAGGTCAGCAGGGCGTT 62.336 66.667 0.00 0.00 0.00 4.84
831 860 1.333636 CCTCTACCAGGTCAGCAGGG 61.334 65.000 0.00 0.00 37.53 4.45
857 886 0.678048 GCATTTGCTCCTCTTCCCGT 60.678 55.000 0.00 0.00 38.21 5.28
1018 1047 0.656259 TCGCCAATCTCGTAGTCTCG 59.344 55.000 0.00 0.00 0.00 4.04
1410 1439 1.282930 GGACGACGTTGTCAGGCTTC 61.283 60.000 31.70 13.68 40.72 3.86
1579 1611 2.579787 CGCCTTCTCGCCGTAGTG 60.580 66.667 0.00 0.00 0.00 2.74
1611 1643 2.098233 CACGTACATCACCACGCCC 61.098 63.158 0.00 0.00 41.80 6.13
1716 1748 4.148825 CCGGAGAACAGCCTCGGG 62.149 72.222 0.00 0.00 43.88 5.14
1877 1929 5.698545 GGATCTAATCTCGGATGAAAACTGG 59.301 44.000 0.00 0.00 0.00 4.00
1889 1941 8.839310 AATGTTAATTCCTGGATCTAATCTCG 57.161 34.615 0.00 0.00 0.00 4.04
1916 1968 1.401018 GCCTGCATTACAAACACGACC 60.401 52.381 0.00 0.00 0.00 4.79
1920 1972 1.336795 GGTGGCCTGCATTACAAACAC 60.337 52.381 3.32 0.00 0.00 3.32
1993 2050 3.148279 GTCTCGGATCCGGTGGCT 61.148 66.667 32.79 0.00 40.25 4.75
2080 2137 0.235144 CGTCTCGATCGCCGACTATT 59.765 55.000 24.65 0.00 43.23 1.73
2112 2169 6.050454 TGTGTACAAAAACCGTATTGACAG 57.950 37.500 0.00 0.00 0.00 3.51
2124 2181 0.029567 CGCGGCCTTGTGTACAAAAA 59.970 50.000 0.00 0.00 35.15 1.94
2193 2251 4.142271 GCTGCTACTGCTCTTCTTCTAAGA 60.142 45.833 0.00 0.00 40.48 2.10
2232 2290 6.127196 ACAACAAAGGATAAAGCTGGACAAAA 60.127 34.615 0.00 0.00 0.00 2.44
2380 2443 5.296748 TGAATTAAAAGGGAAGCAAAGCAC 58.703 37.500 0.00 0.00 0.00 4.40
2480 2576 5.758296 AGATTTCGTTGCAACTTGAGACTTA 59.242 36.000 26.09 5.84 0.00 2.24
2520 2616 9.454859 CTCCTATTTGAATAAGGAGAAACTTGT 57.545 33.333 14.84 0.00 46.61 3.16
2543 2639 8.175716 CGATTGTTTCTCCTTGTTTATTACTCC 58.824 37.037 0.00 0.00 0.00 3.85
2544 2640 8.932791 TCGATTGTTTCTCCTTGTTTATTACTC 58.067 33.333 0.00 0.00 0.00 2.59
2545 2641 8.842358 TCGATTGTTTCTCCTTGTTTATTACT 57.158 30.769 0.00 0.00 0.00 2.24
2546 2642 9.543018 CTTCGATTGTTTCTCCTTGTTTATTAC 57.457 33.333 0.00 0.00 0.00 1.89
2547 2643 9.496873 TCTTCGATTGTTTCTCCTTGTTTATTA 57.503 29.630 0.00 0.00 0.00 0.98
2548 2644 8.391075 TCTTCGATTGTTTCTCCTTGTTTATT 57.609 30.769 0.00 0.00 0.00 1.40
2589 2685 4.441634 CGAAAGGAGGGAGTACATAACCAG 60.442 50.000 0.00 0.00 0.00 4.00
2590 2686 3.449737 CGAAAGGAGGGAGTACATAACCA 59.550 47.826 0.00 0.00 0.00 3.67
2591 2687 3.450096 ACGAAAGGAGGGAGTACATAACC 59.550 47.826 0.00 0.00 0.00 2.85
2622 2718 8.979574 CACACGTTAAAATCTCTAGAAAGACTT 58.020 33.333 0.00 0.00 0.00 3.01
2633 2729 7.576750 TGTCATACTCACACGTTAAAATCTC 57.423 36.000 0.00 0.00 0.00 2.75
2643 2739 2.196749 GAGCCATGTCATACTCACACG 58.803 52.381 9.23 0.00 0.00 4.49
2644 2740 2.196749 CGAGCCATGTCATACTCACAC 58.803 52.381 12.95 0.00 0.00 3.82
2647 2743 0.752658 CCCGAGCCATGTCATACTCA 59.247 55.000 12.95 0.00 0.00 3.41
2648 2744 0.034059 CCCCGAGCCATGTCATACTC 59.966 60.000 5.36 5.36 0.00 2.59
2649 2745 0.398522 TCCCCGAGCCATGTCATACT 60.399 55.000 0.00 0.00 0.00 2.12
2650 2746 0.034059 CTCCCCGAGCCATGTCATAC 59.966 60.000 0.00 0.00 0.00 2.39
2651 2747 1.121407 CCTCCCCGAGCCATGTCATA 61.121 60.000 0.00 0.00 0.00 2.15
2652 2748 2.446848 CCTCCCCGAGCCATGTCAT 61.447 63.158 0.00 0.00 0.00 3.06
2653 2749 3.083349 CCTCCCCGAGCCATGTCA 61.083 66.667 0.00 0.00 0.00 3.58
2654 2750 2.764128 TCCTCCCCGAGCCATGTC 60.764 66.667 0.00 0.00 0.00 3.06
2677 2863 4.076394 CTCTGCTCCTACCCTAGTACATC 58.924 52.174 0.00 0.00 0.00 3.06
2683 2869 3.634910 GTCTTTCTCTGCTCCTACCCTAG 59.365 52.174 0.00 0.00 0.00 3.02
2684 2870 3.627747 GGTCTTTCTCTGCTCCTACCCTA 60.628 52.174 0.00 0.00 0.00 3.53
2685 2871 2.462723 GTCTTTCTCTGCTCCTACCCT 58.537 52.381 0.00 0.00 0.00 4.34
2686 2872 1.483004 GGTCTTTCTCTGCTCCTACCC 59.517 57.143 0.00 0.00 0.00 3.69
2694 2880 4.219288 ACAATTTCCATGGTCTTTCTCTGC 59.781 41.667 12.58 0.00 0.00 4.26
2702 2888 5.130350 CGGGTTATACAATTTCCATGGTCT 58.870 41.667 12.58 0.00 0.00 3.85
2761 2947 4.072131 TGTTGCTTGGGAAATAGACACTC 58.928 43.478 0.00 0.00 0.00 3.51
2773 2959 5.466393 CCTTTTGAGTTTATTGTTGCTTGGG 59.534 40.000 0.00 0.00 0.00 4.12
2779 2965 6.507023 ACTGCTCCTTTTGAGTTTATTGTTG 58.493 36.000 0.00 0.00 43.48 3.33
2781 2967 6.770785 TGTACTGCTCCTTTTGAGTTTATTGT 59.229 34.615 0.00 0.00 43.48 2.71
2786 2972 5.066505 CAGTTGTACTGCTCCTTTTGAGTTT 59.933 40.000 0.00 0.00 43.48 2.66
2807 2993 4.464069 GGATACAAGAGAGAGTTGCAGT 57.536 45.455 0.00 0.00 0.00 4.40
2828 3014 1.213013 CCGTCGAAGGTCTGGTCTG 59.787 63.158 9.48 0.00 0.00 3.51
2843 3029 4.708386 TCATTTTCGCCGGGCCGT 62.708 61.111 26.32 0.03 0.00 5.68
2848 3034 0.953471 TGTCAGGTCATTTTCGCCGG 60.953 55.000 0.00 0.00 0.00 6.13
2851 3037 1.062587 CGGATGTCAGGTCATTTTCGC 59.937 52.381 0.00 0.00 0.00 4.70
2871 3057 4.142513 GCAAAGGATGGTTTCTCATCAGTC 60.143 45.833 7.08 0.00 43.82 3.51
2873 3059 3.129988 GGCAAAGGATGGTTTCTCATCAG 59.870 47.826 7.08 0.00 43.82 2.90
2876 3062 2.043526 AGGGCAAAGGATGGTTTCTCAT 59.956 45.455 0.00 0.00 0.00 2.90
2877 3063 1.428912 AGGGCAAAGGATGGTTTCTCA 59.571 47.619 0.00 0.00 0.00 3.27
2879 3065 1.928868 CAGGGCAAAGGATGGTTTCT 58.071 50.000 0.00 0.00 0.00 2.52
2880 3066 0.247460 GCAGGGCAAAGGATGGTTTC 59.753 55.000 0.00 0.00 0.00 2.78
2881 3067 1.194121 GGCAGGGCAAAGGATGGTTT 61.194 55.000 0.00 0.00 0.00 3.27
2882 3068 1.610379 GGCAGGGCAAAGGATGGTT 60.610 57.895 0.00 0.00 0.00 3.67
2883 3069 2.037847 GGCAGGGCAAAGGATGGT 59.962 61.111 0.00 0.00 0.00 3.55
2886 3072 1.203225 AGAAAAGGCAGGGCAAAGGAT 60.203 47.619 0.00 0.00 0.00 3.24
2887 3073 0.188342 AGAAAAGGCAGGGCAAAGGA 59.812 50.000 0.00 0.00 0.00 3.36
2895 3082 0.881796 GGAACGGAAGAAAAGGCAGG 59.118 55.000 0.00 0.00 0.00 4.85
2922 3109 1.890894 GTACTTGCAGCGAGAGGGA 59.109 57.895 17.30 0.00 0.00 4.20
2930 3118 2.092291 TACAGCGCGTACTTGCAGC 61.092 57.895 8.43 5.53 35.58 5.25
2943 3131 2.165282 GTACCACTCGTACGTACAGC 57.835 55.000 24.50 0.00 38.17 4.40
2950 3138 2.578495 CTGACGTTGTACCACTCGTAC 58.422 52.381 0.00 0.00 46.53 3.67
2951 3139 1.536766 CCTGACGTTGTACCACTCGTA 59.463 52.381 0.00 0.00 36.67 3.43
2952 3140 0.313043 CCTGACGTTGTACCACTCGT 59.687 55.000 0.00 0.00 39.21 4.18
2953 3141 0.594602 TCCTGACGTTGTACCACTCG 59.405 55.000 0.00 0.00 0.00 4.18
2954 3142 1.612463 ACTCCTGACGTTGTACCACTC 59.388 52.381 0.00 0.00 0.00 3.51
2955 3143 1.340248 CACTCCTGACGTTGTACCACT 59.660 52.381 0.00 0.00 0.00 4.00
2956 3144 1.604693 CCACTCCTGACGTTGTACCAC 60.605 57.143 0.00 0.00 0.00 4.16
2957 3145 0.677288 CCACTCCTGACGTTGTACCA 59.323 55.000 0.00 0.00 0.00 3.25
2958 3146 0.037605 CCCACTCCTGACGTTGTACC 60.038 60.000 0.00 0.00 0.00 3.34
2959 3147 0.037605 CCCCACTCCTGACGTTGTAC 60.038 60.000 0.00 0.00 0.00 2.90
2960 3148 0.470456 ACCCCACTCCTGACGTTGTA 60.470 55.000 0.00 0.00 0.00 2.41
2961 3149 0.470456 TACCCCACTCCTGACGTTGT 60.470 55.000 0.00 0.00 0.00 3.32
2962 3150 0.902531 ATACCCCACTCCTGACGTTG 59.097 55.000 0.00 0.00 0.00 4.10
2963 3151 0.902531 CATACCCCACTCCTGACGTT 59.097 55.000 0.00 0.00 0.00 3.99
2964 3152 1.614241 GCATACCCCACTCCTGACGT 61.614 60.000 0.00 0.00 0.00 4.34
2965 3153 1.144057 GCATACCCCACTCCTGACG 59.856 63.158 0.00 0.00 0.00 4.35
2966 3154 1.527370 GGCATACCCCACTCCTGAC 59.473 63.158 0.00 0.00 0.00 3.51
2967 3155 2.063979 CGGCATACCCCACTCCTGA 61.064 63.158 0.00 0.00 0.00 3.86
2968 3156 2.063979 TCGGCATACCCCACTCCTG 61.064 63.158 0.00 0.00 0.00 3.86
2969 3157 2.064581 GTCGGCATACCCCACTCCT 61.065 63.158 0.00 0.00 0.00 3.69
2970 3158 2.504519 GTCGGCATACCCCACTCC 59.495 66.667 0.00 0.00 0.00 3.85
2971 3159 2.064581 AGGTCGGCATACCCCACTC 61.065 63.158 3.22 0.00 40.71 3.51
2972 3160 2.040606 AGGTCGGCATACCCCACT 59.959 61.111 3.22 0.00 40.71 4.00
2973 3161 2.189521 CAGGTCGGCATACCCCAC 59.810 66.667 3.22 0.00 40.71 4.61


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

AutoCloner maintained by Alex Coulton.