Multiple sequence alignment - TraesCS3D01G361800

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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 TraesCS3D01G361800 chr3D 100.000 3404 0 0 1 3404 475883408 475880005 0.000000e+00 6287.0
1 TraesCS3D01G361800 chr3D 85.714 581 70 7 2828 3404 137882708 137883279 4.860000e-168 601.0
2 TraesCS3D01G361800 chr3D 85.880 517 63 3 2897 3404 3623762 3623247 2.990000e-150 542.0
3 TraesCS3D01G361800 chr3D 84.360 211 19 8 119 327 475890869 475890671 9.640000e-46 195.0
4 TraesCS3D01G361800 chr3B 91.098 2786 100 42 14 2702 633377664 633374930 0.000000e+00 3635.0
5 TraesCS3D01G361800 chr3B 82.789 337 33 15 119 445 633380173 633379852 9.300000e-71 278.0
6 TraesCS3D01G361800 chr3A 91.676 2631 101 44 140 2697 619100621 619098036 0.000000e+00 3537.0
7 TraesCS3D01G361800 chr3A 89.655 116 12 0 1010 1125 364949762 364949647 7.610000e-32 148.0
8 TraesCS3D01G361800 chr5D 87.931 580 63 5 2828 3402 101767360 101766783 0.000000e+00 676.0
9 TraesCS3D01G361800 chr5D 81.461 178 29 4 2823 2999 464406773 464406599 3.540000e-30 143.0
10 TraesCS3D01G361800 chr4D 84.007 569 73 11 2828 3386 315903860 315903300 6.470000e-147 531.0
11 TraesCS3D01G361800 chr4D 94.068 118 6 1 1271 1387 450198271 450198388 9.710000e-41 178.0
12 TraesCS3D01G361800 chr6B 88.079 302 36 0 1968 2269 41915269 41915570 3.230000e-95 359.0
13 TraesCS3D01G361800 chr6B 92.473 186 14 0 2117 2302 715617871 715617686 2.010000e-67 267.0
14 TraesCS3D01G361800 chr7D 77.446 603 95 29 2819 3404 495314794 495315372 4.240000e-84 322.0
15 TraesCS3D01G361800 chr7D 84.393 173 25 2 2827 2999 221000971 221000801 5.840000e-38 169.0
16 TraesCS3D01G361800 chr2A 83.106 367 47 8 2828 3183 707076606 707076244 1.520000e-83 320.0
17 TraesCS3D01G361800 chr2A 81.865 193 29 6 2828 3016 65393971 65393781 1.260000e-34 158.0
18 TraesCS3D01G361800 chr2A 100.000 29 0 0 40 68 632389182 632389210 2.000000e-03 54.7
19 TraesCS3D01G361800 chr1D 76.871 441 69 21 2883 3309 428621027 428620606 5.720000e-53 219.0
20 TraesCS3D01G361800 chr1D 80.000 205 31 9 2826 3023 467128913 467129114 3.540000e-30 143.0
21 TraesCS3D01G361800 chr2B 93.220 118 6 2 1271 1387 380510570 380510454 4.520000e-39 172.0
22 TraesCS3D01G361800 chr2B 77.444 133 24 4 2828 2955 557337134 557337003 1.310000e-09 75.0
23 TraesCS3D01G361800 chr1B 77.143 175 32 6 2846 3015 189320331 189320502 1.010000e-15 95.3


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 TraesCS3D01G361800 chr3D 475880005 475883408 3403 True 6287.0 6287 100.0000 1 3404 1 chr3D.!!$R2 3403
1 TraesCS3D01G361800 chr3D 137882708 137883279 571 False 601.0 601 85.7140 2828 3404 1 chr3D.!!$F1 576
2 TraesCS3D01G361800 chr3D 3623247 3623762 515 True 542.0 542 85.8800 2897 3404 1 chr3D.!!$R1 507
3 TraesCS3D01G361800 chr3B 633374930 633380173 5243 True 1956.5 3635 86.9435 14 2702 2 chr3B.!!$R1 2688
4 TraesCS3D01G361800 chr3A 619098036 619100621 2585 True 3537.0 3537 91.6760 140 2697 1 chr3A.!!$R2 2557
5 TraesCS3D01G361800 chr5D 101766783 101767360 577 True 676.0 676 87.9310 2828 3402 1 chr5D.!!$R1 574
6 TraesCS3D01G361800 chr4D 315903300 315903860 560 True 531.0 531 84.0070 2828 3386 1 chr4D.!!$R1 558
7 TraesCS3D01G361800 chr7D 495314794 495315372 578 False 322.0 322 77.4460 2819 3404 1 chr7D.!!$F1 585

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
706 3250 0.035915 GAGCGCCTTTTCTTCCTCCT 60.036 55.0 2.29 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 5041 0.722848 CAAAATTACGGGTCGTCGGG 59.277 55.0 0.0 0.0 41.54 5.14 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
76 2574 2.174360 GGGAGTACTACCCACTTCGTT 58.826 52.381 13.90 0.00 46.05 3.85
77 2575 3.356290 GGGAGTACTACCCACTTCGTTA 58.644 50.000 13.90 0.00 46.05 3.18
89 2587 3.418094 CACTTCGTTAGAGCAGTCTACG 58.582 50.000 0.00 0.00 34.84 3.51
90 2588 2.419324 ACTTCGTTAGAGCAGTCTACGG 59.581 50.000 0.00 0.00 34.84 4.02
94 2592 2.477525 CGTTAGAGCAGTCTACGGTTCC 60.478 54.545 0.00 0.00 34.84 3.62
113 2611 1.068083 GCGGGCGAGATCATCTTCA 59.932 57.895 0.00 0.00 0.00 3.02
131 2653 6.349973 TCTTCATGCTATGCGACTAAAAAG 57.650 37.500 0.00 0.00 0.00 2.27
133 2655 3.938334 TCATGCTATGCGACTAAAAAGCA 59.062 39.130 0.00 0.00 45.46 3.91
145 2667 6.087687 GCGACTAAAAAGCATTAGAAAACCAC 59.912 38.462 9.94 0.00 36.57 4.16
186 2708 8.635765 AATAGTGCTCAATAACCAAAGAAAGA 57.364 30.769 0.00 0.00 0.00 2.52
187 2709 6.959639 AGTGCTCAATAACCAAAGAAAGAA 57.040 33.333 0.00 0.00 0.00 2.52
188 2710 6.739112 AGTGCTCAATAACCAAAGAAAGAAC 58.261 36.000 0.00 0.00 0.00 3.01
346 2869 6.801367 TCACAAACTATATTAACGTCGCTC 57.199 37.500 0.00 0.00 0.00 5.03
347 2870 6.558009 TCACAAACTATATTAACGTCGCTCT 58.442 36.000 0.00 0.00 0.00 4.09
348 2871 6.690098 TCACAAACTATATTAACGTCGCTCTC 59.310 38.462 0.00 0.00 0.00 3.20
349 2872 5.975939 ACAAACTATATTAACGTCGCTCTCC 59.024 40.000 0.00 0.00 0.00 3.71
350 2873 4.401525 ACTATATTAACGTCGCTCTCCG 57.598 45.455 0.00 0.00 38.61 4.63
351 2874 2.047679 ATATTAACGTCGCTCTCCGC 57.952 50.000 0.00 0.00 36.73 5.54
352 2875 1.019673 TATTAACGTCGCTCTCCGCT 58.980 50.000 0.00 0.00 36.73 5.52
375 2898 6.404844 GCTTGCTAGGGAAAAATTAGTCTTCC 60.405 42.308 0.00 0.00 38.33 3.46
393 2918 5.010820 GTCTTCCGCCTACAGAATTACCTAT 59.989 44.000 0.00 0.00 0.00 2.57
442 2967 8.570068 AGTTTTCCCACTAAATTAAGCGATAA 57.430 30.769 0.00 0.00 0.00 1.75
443 2968 9.185680 AGTTTTCCCACTAAATTAAGCGATAAT 57.814 29.630 0.00 0.00 35.69 1.28
448 2973 9.444600 TCCCACTAAATTAAGCGATAATAATCC 57.555 33.333 0.00 0.00 32.96 3.01
573 3099 0.601558 GGTACAAGGACGTGCTCTGA 59.398 55.000 10.99 0.00 0.00 3.27
619 3145 0.167470 GATTCACGACGACTCGGACA 59.833 55.000 0.00 0.00 44.80 4.02
706 3250 0.035915 GAGCGCCTTTTCTTCCTCCT 60.036 55.000 2.29 0.00 0.00 3.69
765 3315 2.342279 CCCGCGGTTTGAGAGACA 59.658 61.111 26.12 0.00 0.00 3.41
786 3336 0.390860 CATTTTCAAACCACCCCGCA 59.609 50.000 0.00 0.00 0.00 5.69
833 3393 4.293634 AGCTCAGCTCCTCCCTATCTATAA 59.706 45.833 0.00 0.00 30.62 0.98
835 3395 5.574740 GCTCAGCTCCTCCCTATCTATAAGA 60.575 48.000 0.00 0.00 0.00 2.10
838 3398 4.608473 AGCTCCTCCCTATCTATAAGACCA 59.392 45.833 0.00 0.00 0.00 4.02
839 3399 5.257577 AGCTCCTCCCTATCTATAAGACCAT 59.742 44.000 0.00 0.00 0.00 3.55
840 3400 6.452000 AGCTCCTCCCTATCTATAAGACCATA 59.548 42.308 0.00 0.00 0.00 2.74
841 3401 6.548251 GCTCCTCCCTATCTATAAGACCATAC 59.452 46.154 0.00 0.00 0.00 2.39
842 3402 6.660800 TCCTCCCTATCTATAAGACCATACG 58.339 44.000 0.00 0.00 0.00 3.06
843 3403 5.828859 CCTCCCTATCTATAAGACCATACGG 59.171 48.000 0.00 0.00 38.77 4.02
844 3404 5.763355 TCCCTATCTATAAGACCATACGGG 58.237 45.833 0.00 0.00 44.81 5.28
845 3405 4.341520 CCCTATCTATAAGACCATACGGGC 59.658 50.000 0.00 0.00 43.02 6.13
846 3406 4.954202 CCTATCTATAAGACCATACGGGCA 59.046 45.833 0.00 0.00 46.60 5.36
847 3407 4.803098 ATCTATAAGACCATACGGGCAC 57.197 45.455 0.00 0.00 46.60 5.01
848 3408 2.555325 TCTATAAGACCATACGGGCACG 59.445 50.000 6.92 6.92 46.60 5.34
895 3455 2.088104 TCTAATCCTCGAGGCCACAT 57.912 50.000 27.39 12.18 34.44 3.21
917 3477 1.803366 GACCCGAGACCAGAACACGT 61.803 60.000 0.00 0.00 0.00 4.49
937 3525 0.246635 GCGAGCAAGGAGTGGTAGAA 59.753 55.000 0.00 0.00 38.34 2.10
996 3584 1.003597 AGCTGGAGCAGTGCTGAAG 60.004 57.895 25.35 19.69 45.16 3.02
1471 4059 3.911698 TGTGTCACGCCAGCGAGT 61.912 61.111 20.32 0.00 42.83 4.18
2377 4965 4.349503 TTCAGCACATGGCCGCCT 62.350 61.111 11.61 0.00 46.50 5.52
2416 5004 1.758783 CAGCTGAAAGTTTGGAACGC 58.241 50.000 8.42 0.00 35.30 4.84
2417 5005 0.307760 AGCTGAAAGTTTGGAACGCG 59.692 50.000 3.53 3.53 35.30 6.01
2418 5006 0.660300 GCTGAAAGTTTGGAACGCGG 60.660 55.000 12.47 0.00 35.30 6.46
2419 5007 0.660300 CTGAAAGTTTGGAACGCGGC 60.660 55.000 12.47 0.92 36.23 6.53
2420 5008 1.371267 GAAAGTTTGGAACGCGGCC 60.371 57.895 12.47 12.61 36.23 6.13
2422 5010 2.070654 AAAGTTTGGAACGCGGCCAG 62.071 55.000 19.88 0.00 36.64 4.85
2424 5012 2.033448 TTTGGAACGCGGCCAGAT 59.967 55.556 19.88 0.00 36.64 2.90
2425 5013 2.331893 TTTGGAACGCGGCCAGATG 61.332 57.895 19.88 0.00 36.64 2.90
2439 5041 3.070576 GATGCCCCACTTGCCACC 61.071 66.667 0.00 0.00 0.00 4.61
2560 5175 7.898014 ACTCCTACATGTATCTGTTGTGATA 57.102 36.000 5.91 0.00 0.00 2.15
2577 5192 6.605471 TGTGATACCATCTGTTCTAGTGTT 57.395 37.500 0.00 0.00 0.00 3.32
2578 5193 7.712204 TGTGATACCATCTGTTCTAGTGTTA 57.288 36.000 0.00 0.00 0.00 2.41
2579 5194 7.544622 TGTGATACCATCTGTTCTAGTGTTAC 58.455 38.462 0.00 0.00 0.00 2.50
2623 5246 5.994054 TCAATTAGATCAAGTAGCCTGATGC 59.006 40.000 0.00 0.00 41.71 3.91
2702 5325 7.062605 GGTCGATGAAGAAAACAGTTCGTTATA 59.937 37.037 0.00 0.00 36.59 0.98
2703 5326 8.102716 GTCGATGAAGAAAACAGTTCGTTATAG 58.897 37.037 0.00 0.00 36.59 1.31
2704 5327 7.811236 TCGATGAAGAAAACAGTTCGTTATAGT 59.189 33.333 0.00 0.00 36.59 2.12
2705 5328 7.893236 CGATGAAGAAAACAGTTCGTTATAGTG 59.107 37.037 0.00 0.00 36.59 2.74
2706 5329 6.884187 TGAAGAAAACAGTTCGTTATAGTGC 58.116 36.000 0.00 0.00 36.59 4.40
2707 5330 6.480651 TGAAGAAAACAGTTCGTTATAGTGCA 59.519 34.615 0.00 0.00 36.59 4.57
2708 5331 6.224420 AGAAAACAGTTCGTTATAGTGCAC 57.776 37.500 9.40 9.40 36.59 4.57
2709 5332 5.178809 AGAAAACAGTTCGTTATAGTGCACC 59.821 40.000 14.63 0.00 36.59 5.01
2710 5333 2.602878 ACAGTTCGTTATAGTGCACCG 58.397 47.619 14.63 9.78 0.00 4.94
2711 5334 2.029649 ACAGTTCGTTATAGTGCACCGT 60.030 45.455 14.63 4.89 0.00 4.83
2712 5335 2.597305 CAGTTCGTTATAGTGCACCGTC 59.403 50.000 14.63 7.57 0.00 4.79
2713 5336 1.922545 GTTCGTTATAGTGCACCGTCC 59.077 52.381 14.63 1.28 0.00 4.79
2714 5337 0.457035 TCGTTATAGTGCACCGTCCC 59.543 55.000 14.63 0.00 0.00 4.46
2715 5338 0.868602 CGTTATAGTGCACCGTCCCG 60.869 60.000 14.63 7.33 0.00 5.14
2716 5339 0.457035 GTTATAGTGCACCGTCCCGA 59.543 55.000 14.63 0.00 0.00 5.14
2717 5340 0.742505 TTATAGTGCACCGTCCCGAG 59.257 55.000 14.63 0.00 0.00 4.63
2718 5341 1.731433 TATAGTGCACCGTCCCGAGC 61.731 60.000 14.63 0.00 0.00 5.03
2722 5345 4.814294 GCACCGTCCCGAGCGAAT 62.814 66.667 0.00 0.00 0.00 3.34
2723 5346 2.885644 CACCGTCCCGAGCGAATG 60.886 66.667 0.00 0.00 0.00 2.67
2724 5347 3.066190 ACCGTCCCGAGCGAATGA 61.066 61.111 0.00 0.00 0.00 2.57
2725 5348 2.417516 CCGTCCCGAGCGAATGAT 59.582 61.111 0.00 0.00 0.00 2.45
2726 5349 1.105167 ACCGTCCCGAGCGAATGATA 61.105 55.000 0.00 0.00 0.00 2.15
2727 5350 0.663568 CCGTCCCGAGCGAATGATAC 60.664 60.000 0.00 0.00 0.00 2.24
2728 5351 0.030235 CGTCCCGAGCGAATGATACA 59.970 55.000 0.00 0.00 0.00 2.29
2729 5352 1.535226 CGTCCCGAGCGAATGATACAA 60.535 52.381 0.00 0.00 0.00 2.41
2730 5353 2.128035 GTCCCGAGCGAATGATACAAG 58.872 52.381 0.00 0.00 0.00 3.16
2731 5354 1.068588 TCCCGAGCGAATGATACAAGG 59.931 52.381 0.00 0.00 0.00 3.61
2732 5355 0.861837 CCGAGCGAATGATACAAGGC 59.138 55.000 0.00 0.00 0.00 4.35
2733 5356 1.570813 CGAGCGAATGATACAAGGCA 58.429 50.000 0.00 0.00 0.00 4.75
2734 5357 1.258982 CGAGCGAATGATACAAGGCAC 59.741 52.381 0.00 0.00 0.00 5.01
2736 5359 2.541762 GAGCGAATGATACAAGGCACTC 59.458 50.000 0.00 0.00 38.49 3.51
2737 5360 2.169352 AGCGAATGATACAAGGCACTCT 59.831 45.455 0.00 0.00 38.49 3.24
2738 5361 2.541762 GCGAATGATACAAGGCACTCTC 59.458 50.000 0.00 0.00 38.49 3.20
2739 5362 3.739519 GCGAATGATACAAGGCACTCTCT 60.740 47.826 0.00 0.00 38.49 3.10
2740 5363 4.499865 GCGAATGATACAAGGCACTCTCTA 60.500 45.833 0.00 0.00 38.49 2.43
2741 5364 5.777802 CGAATGATACAAGGCACTCTCTAT 58.222 41.667 0.00 0.00 38.49 1.98
2742 5365 5.632764 CGAATGATACAAGGCACTCTCTATG 59.367 44.000 0.00 0.00 38.49 2.23
2743 5366 6.515696 CGAATGATACAAGGCACTCTCTATGA 60.516 42.308 0.00 0.00 38.49 2.15
2744 5367 6.931790 ATGATACAAGGCACTCTCTATGAT 57.068 37.500 0.00 0.00 38.49 2.45
2745 5368 6.094193 TGATACAAGGCACTCTCTATGATG 57.906 41.667 0.00 0.00 38.49 3.07
2746 5369 3.834489 ACAAGGCACTCTCTATGATGG 57.166 47.619 0.00 0.00 38.49 3.51
2747 5370 3.378512 ACAAGGCACTCTCTATGATGGA 58.621 45.455 0.00 0.00 38.49 3.41
2748 5371 3.387374 ACAAGGCACTCTCTATGATGGAG 59.613 47.826 0.00 0.00 38.49 3.86
2749 5372 1.969923 AGGCACTCTCTATGATGGAGC 59.030 52.381 0.36 0.00 0.00 4.70
2750 5373 1.690893 GGCACTCTCTATGATGGAGCA 59.309 52.381 0.36 0.00 0.00 4.26
2751 5374 2.302445 GGCACTCTCTATGATGGAGCAT 59.698 50.000 0.36 0.00 0.00 3.79
2752 5375 3.327626 GCACTCTCTATGATGGAGCATG 58.672 50.000 0.36 3.29 0.00 4.06
2753 5376 3.244146 GCACTCTCTATGATGGAGCATGT 60.244 47.826 0.36 0.00 0.00 3.21
2754 5377 4.558178 CACTCTCTATGATGGAGCATGTC 58.442 47.826 0.36 0.00 0.00 3.06
2755 5378 4.038883 CACTCTCTATGATGGAGCATGTCA 59.961 45.833 0.36 0.00 0.00 3.58
2756 5379 4.652881 ACTCTCTATGATGGAGCATGTCAA 59.347 41.667 0.36 0.00 0.00 3.18
2757 5380 5.307456 ACTCTCTATGATGGAGCATGTCAAT 59.693 40.000 0.36 0.00 0.00 2.57
2758 5381 6.183361 ACTCTCTATGATGGAGCATGTCAATT 60.183 38.462 0.36 0.00 0.00 2.32
2759 5382 7.015974 ACTCTCTATGATGGAGCATGTCAATTA 59.984 37.037 0.36 0.00 0.00 1.40
2760 5383 7.738847 TCTCTATGATGGAGCATGTCAATTAA 58.261 34.615 0.36 0.00 0.00 1.40
2761 5384 8.380867 TCTCTATGATGGAGCATGTCAATTAAT 58.619 33.333 0.36 0.00 0.00 1.40
2762 5385 8.331730 TCTATGATGGAGCATGTCAATTAATG 57.668 34.615 0.00 0.00 0.00 1.90
2763 5386 8.158789 TCTATGATGGAGCATGTCAATTAATGA 58.841 33.333 0.00 0.00 35.05 2.57
2764 5387 7.591421 ATGATGGAGCATGTCAATTAATGAA 57.409 32.000 0.00 0.00 40.50 2.57
2765 5388 7.407393 TGATGGAGCATGTCAATTAATGAAA 57.593 32.000 0.00 0.00 40.50 2.69
2766 5389 8.014070 TGATGGAGCATGTCAATTAATGAAAT 57.986 30.769 0.00 0.00 40.50 2.17
2767 5390 8.479689 TGATGGAGCATGTCAATTAATGAAATT 58.520 29.630 0.00 0.00 40.50 1.82
2768 5391 9.970395 GATGGAGCATGTCAATTAATGAAATTA 57.030 29.630 0.00 0.00 40.50 1.40
2769 5392 9.754382 ATGGAGCATGTCAATTAATGAAATTAC 57.246 29.630 0.00 0.00 38.79 1.89
2770 5393 7.914871 TGGAGCATGTCAATTAATGAAATTACG 59.085 33.333 0.00 0.00 38.79 3.18
2771 5394 7.379529 GGAGCATGTCAATTAATGAAATTACGG 59.620 37.037 0.00 0.00 38.79 4.02
2772 5395 7.771183 AGCATGTCAATTAATGAAATTACGGT 58.229 30.769 0.00 0.00 38.79 4.83
2773 5396 8.898761 AGCATGTCAATTAATGAAATTACGGTA 58.101 29.630 0.00 0.00 38.79 4.02
2774 5397 9.509855 GCATGTCAATTAATGAAATTACGGTAA 57.490 29.630 2.62 2.62 38.79 2.85
2783 5406 7.611213 AATGAAATTACGGTAACTTCTCTGG 57.389 36.000 19.14 0.00 32.46 3.86
2784 5407 6.349243 TGAAATTACGGTAACTTCTCTGGA 57.651 37.500 19.14 0.66 0.00 3.86
2785 5408 6.942976 TGAAATTACGGTAACTTCTCTGGAT 58.057 36.000 19.14 0.00 0.00 3.41
2786 5409 8.070034 TGAAATTACGGTAACTTCTCTGGATA 57.930 34.615 19.14 0.00 0.00 2.59
2787 5410 8.195436 TGAAATTACGGTAACTTCTCTGGATAG 58.805 37.037 19.14 0.00 0.00 2.08
2788 5411 5.511234 TTACGGTAACTTCTCTGGATAGC 57.489 43.478 0.00 0.00 0.00 2.97
2789 5412 3.362706 ACGGTAACTTCTCTGGATAGCA 58.637 45.455 0.00 0.00 0.00 3.49
2790 5413 3.961408 ACGGTAACTTCTCTGGATAGCAT 59.039 43.478 0.00 0.00 0.00 3.79
2791 5414 4.202161 ACGGTAACTTCTCTGGATAGCATG 60.202 45.833 0.00 0.00 0.00 4.06
2792 5415 4.038042 CGGTAACTTCTCTGGATAGCATGA 59.962 45.833 0.00 0.00 0.00 3.07
2793 5416 5.293560 GGTAACTTCTCTGGATAGCATGAC 58.706 45.833 0.00 0.00 0.00 3.06
2794 5417 5.163405 GGTAACTTCTCTGGATAGCATGACA 60.163 44.000 0.00 0.00 0.00 3.58
2795 5418 4.399004 ACTTCTCTGGATAGCATGACAC 57.601 45.455 0.00 0.00 0.00 3.67
2796 5419 3.771479 ACTTCTCTGGATAGCATGACACA 59.229 43.478 0.00 0.00 0.00 3.72
2797 5420 4.223700 ACTTCTCTGGATAGCATGACACAA 59.776 41.667 0.00 0.00 0.00 3.33
2798 5421 5.104610 ACTTCTCTGGATAGCATGACACAAT 60.105 40.000 0.00 0.00 0.00 2.71
2799 5422 5.363562 TCTCTGGATAGCATGACACAATT 57.636 39.130 0.00 0.00 0.00 2.32
2800 5423 5.121105 TCTCTGGATAGCATGACACAATTG 58.879 41.667 3.24 3.24 0.00 2.32
2801 5424 3.628942 TCTGGATAGCATGACACAATTGC 59.371 43.478 5.05 0.00 36.63 3.56
2803 5426 3.379057 TGGATAGCATGACACAATTGCTG 59.621 43.478 10.81 5.95 45.76 4.41
2804 5427 3.243301 GGATAGCATGACACAATTGCTGG 60.243 47.826 10.81 0.00 45.76 4.85
2805 5428 1.913778 AGCATGACACAATTGCTGGA 58.086 45.000 5.05 0.00 44.63 3.86
2806 5429 1.542915 AGCATGACACAATTGCTGGAC 59.457 47.619 5.05 3.64 44.63 4.02
2807 5430 1.270274 GCATGACACAATTGCTGGACA 59.730 47.619 5.05 8.47 33.61 4.02
2808 5431 2.094390 GCATGACACAATTGCTGGACAT 60.094 45.455 5.05 10.08 33.61 3.06
2809 5432 3.507786 CATGACACAATTGCTGGACATG 58.492 45.455 20.48 20.48 32.27 3.21
2810 5433 1.887854 TGACACAATTGCTGGACATGG 59.112 47.619 5.05 0.00 0.00 3.66
2811 5434 1.203052 GACACAATTGCTGGACATGGG 59.797 52.381 5.05 0.00 0.00 4.00
2812 5435 0.108520 CACAATTGCTGGACATGGGC 60.109 55.000 5.05 0.00 0.00 5.36
2813 5436 0.542467 ACAATTGCTGGACATGGGCA 60.542 50.000 5.05 0.00 0.00 5.36
2815 5438 0.609662 AATTGCTGGACATGGGCAAC 59.390 50.000 15.79 0.00 46.39 4.17
2816 5439 0.251922 ATTGCTGGACATGGGCAACT 60.252 50.000 15.79 6.82 46.39 3.16
2817 5440 0.469705 TTGCTGGACATGGGCAACTT 60.470 50.000 11.56 0.00 40.38 2.66
2818 5441 0.469705 TGCTGGACATGGGCAACTTT 60.470 50.000 0.00 0.00 32.79 2.66
2819 5442 0.681175 GCTGGACATGGGCAACTTTT 59.319 50.000 0.00 0.00 0.00 2.27
2820 5443 1.337167 GCTGGACATGGGCAACTTTTC 60.337 52.381 0.00 0.00 0.00 2.29
2821 5444 1.962807 CTGGACATGGGCAACTTTTCA 59.037 47.619 0.00 0.00 0.00 2.69
2822 5445 2.564062 CTGGACATGGGCAACTTTTCAT 59.436 45.455 0.00 0.00 0.00 2.57
2823 5446 2.971330 TGGACATGGGCAACTTTTCATT 59.029 40.909 0.00 0.00 0.00 2.57
2824 5447 3.390639 TGGACATGGGCAACTTTTCATTT 59.609 39.130 0.00 0.00 0.00 2.32
2825 5448 4.141528 TGGACATGGGCAACTTTTCATTTT 60.142 37.500 0.00 0.00 0.00 1.82
2826 5449 4.452114 GGACATGGGCAACTTTTCATTTTC 59.548 41.667 0.00 0.00 0.00 2.29
2853 5476 7.938563 TTTCGACAAAAGGTGGATTTTATTG 57.061 32.000 0.00 0.00 34.00 1.90
2862 5485 6.715347 AGGTGGATTTTATTGGCTCAATAC 57.285 37.500 7.02 0.00 36.26 1.89
2863 5486 6.194235 AGGTGGATTTTATTGGCTCAATACA 58.806 36.000 7.02 0.16 36.26 2.29
2886 5509 5.359009 CAGAGCATCAAAGGGATACAAACAT 59.641 40.000 0.00 0.00 37.82 2.71
2895 5518 7.615365 TCAAAGGGATACAAACATAAAGAGCAT 59.385 33.333 0.00 0.00 39.74 3.79
2901 5524 7.499232 GGATACAAACATAAAGAGCATACACCT 59.501 37.037 0.00 0.00 0.00 4.00
2941 5564 2.289565 TGCACACAATTAACACGGACA 58.710 42.857 0.00 0.00 0.00 4.02
3010 5633 3.211045 GAAACTATGCCAAGGCGGATAA 58.789 45.455 6.60 0.00 45.51 1.75
3195 5839 1.060713 CGACGTTGGAGTGACATCAC 58.939 55.000 3.72 3.72 46.77 3.06
3208 5852 2.291465 TGACATCACTTGCAGCTCAAAC 59.709 45.455 0.00 0.00 33.65 2.93
3242 5886 0.803380 GTGCCGCCAAAATCTCATGC 60.803 55.000 0.00 0.00 0.00 4.06
3247 5891 1.741706 CGCCAAAATCTCATGCAGACT 59.258 47.619 0.00 0.00 32.26 3.24
3268 5912 1.002069 TTTGGTGATCCCATGCCTCT 58.998 50.000 4.04 0.00 44.74 3.69
3315 5959 3.443045 GGCATGAACACTGGCCCG 61.443 66.667 0.00 0.00 40.55 6.13
3332 5976 2.679639 GCCCGAGACAATACACCATGAA 60.680 50.000 0.00 0.00 0.00 2.57
3339 5983 6.313519 AGACAATACACCATGAACCTACAT 57.686 37.500 0.00 0.00 0.00 2.29
3364 6008 1.368579 GCCATGGTTGCAACAAGCT 59.631 52.632 29.55 9.03 45.94 3.74
3388 6033 7.011482 GCTATCAATATCATCGAACATTACCCC 59.989 40.741 0.00 0.00 0.00 4.95
3395 6040 1.444119 CGAACATTACCCCGGCCATG 61.444 60.000 2.24 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 2545 7.176909 AGTGGGTAGTACTCCCTCTATAAAT 57.823 40.000 22.78 6.70 44.13 1.40
59 2557 3.693578 GCTCTAACGAAGTGGGTAGTACT 59.306 47.826 0.00 0.00 45.00 2.73
70 2568 2.419324 ACCGTAGACTGCTCTAACGAAG 59.581 50.000 0.00 0.00 30.37 3.79
74 2572 2.477525 CGGAACCGTAGACTGCTCTAAC 60.478 54.545 4.99 0.00 30.37 2.34
76 2574 1.376543 CGGAACCGTAGACTGCTCTA 58.623 55.000 4.99 0.00 34.35 2.43
77 2575 1.935327 GCGGAACCGTAGACTGCTCT 61.935 60.000 14.63 0.00 42.09 4.09
90 2588 3.792053 ATGATCTCGCCCGCGGAAC 62.792 63.158 30.73 17.92 40.25 3.62
94 2592 2.018866 GAAGATGATCTCGCCCGCG 61.019 63.158 0.00 0.00 41.35 6.46
100 2598 3.303760 CGCATAGCATGAAGATGATCTCG 59.696 47.826 0.00 0.00 28.93 4.04
104 2602 4.268797 AGTCGCATAGCATGAAGATGAT 57.731 40.909 0.00 0.00 31.62 2.45
131 2653 5.453567 AAGGTCAAGTGGTTTTCTAATGC 57.546 39.130 0.00 0.00 0.00 3.56
133 2655 6.133356 TCCAAAGGTCAAGTGGTTTTCTAAT 58.867 36.000 0.00 0.00 33.88 1.73
134 2656 5.511363 TCCAAAGGTCAAGTGGTTTTCTAA 58.489 37.500 0.00 0.00 33.88 2.10
135 2657 5.118729 TCCAAAGGTCAAGTGGTTTTCTA 57.881 39.130 0.00 0.00 33.88 2.10
136 2658 3.976015 TCCAAAGGTCAAGTGGTTTTCT 58.024 40.909 0.00 0.00 33.88 2.52
137 2659 4.937201 ATCCAAAGGTCAAGTGGTTTTC 57.063 40.909 0.00 0.00 33.88 2.29
138 2660 8.664669 ATTATATCCAAAGGTCAAGTGGTTTT 57.335 30.769 0.00 0.00 33.88 2.43
145 2667 7.933577 TGAGCACTATTATATCCAAAGGTCAAG 59.066 37.037 0.00 0.00 0.00 3.02
183 2705 7.214467 TGACTTTTGTGACTTTCTTGTTCTT 57.786 32.000 0.00 0.00 0.00 2.52
184 2706 6.817765 TGACTTTTGTGACTTTCTTGTTCT 57.182 33.333 0.00 0.00 0.00 3.01
185 2707 7.061094 CAGTTGACTTTTGTGACTTTCTTGTTC 59.939 37.037 0.00 0.00 0.00 3.18
186 2708 6.863126 CAGTTGACTTTTGTGACTTTCTTGTT 59.137 34.615 0.00 0.00 0.00 2.83
187 2709 6.381801 CAGTTGACTTTTGTGACTTTCTTGT 58.618 36.000 0.00 0.00 0.00 3.16
188 2710 5.287035 GCAGTTGACTTTTGTGACTTTCTTG 59.713 40.000 0.00 0.00 0.00 3.02
346 2869 1.821216 TTTTTCCCTAGCAAGCGGAG 58.179 50.000 0.00 0.00 0.00 4.63
347 2870 2.507407 ATTTTTCCCTAGCAAGCGGA 57.493 45.000 0.00 0.00 0.00 5.54
348 2871 3.694566 ACTAATTTTTCCCTAGCAAGCGG 59.305 43.478 0.00 0.00 0.00 5.52
349 2872 4.636206 AGACTAATTTTTCCCTAGCAAGCG 59.364 41.667 0.00 0.00 0.00 4.68
350 2873 6.404844 GGAAGACTAATTTTTCCCTAGCAAGC 60.405 42.308 0.00 0.00 35.43 4.01
351 2874 6.183360 CGGAAGACTAATTTTTCCCTAGCAAG 60.183 42.308 0.00 0.00 37.64 4.01
352 2875 5.646360 CGGAAGACTAATTTTTCCCTAGCAA 59.354 40.000 0.00 0.00 37.64 3.91
375 2898 3.990092 TGCATAGGTAATTCTGTAGGCG 58.010 45.455 0.00 0.00 0.00 5.52
393 2918 2.596346 TCCATTTCTCCTTTGCTTGCA 58.404 42.857 0.00 0.00 0.00 4.08
455 2980 6.598753 CGTAAAAGACGTTGGGATTATCAT 57.401 37.500 0.00 0.00 46.86 2.45
498 3024 1.078115 CCCATCCATCCATCCATCCA 58.922 55.000 0.00 0.00 0.00 3.41
573 3099 3.825160 TTCTTGCGTTCGGGCAGCT 62.825 57.895 0.00 0.00 44.94 4.24
619 3145 1.865788 ATGCGATGCGGTTTTGTGCT 61.866 50.000 0.00 0.00 0.00 4.40
706 3250 4.014847 CGAAAGCCATTGAAATTAGCGA 57.985 40.909 0.00 0.00 0.00 4.93
765 3315 1.275010 GCGGGGTGGTTTGAAAATGAT 59.725 47.619 0.00 0.00 0.00 2.45
833 3393 2.890371 GTCGTGCCCGTATGGTCT 59.110 61.111 0.00 0.00 36.04 3.85
835 3395 3.060020 CTCGTCGTGCCCGTATGGT 62.060 63.158 0.00 0.00 36.04 3.55
838 3398 3.411418 CTGCTCGTCGTGCCCGTAT 62.411 63.158 15.98 0.00 35.01 3.06
839 3399 4.111016 CTGCTCGTCGTGCCCGTA 62.111 66.667 15.98 0.00 35.01 4.02
841 3401 2.055310 TATACTGCTCGTCGTGCCCG 62.055 60.000 15.98 9.83 0.00 6.13
842 3402 0.314302 ATATACTGCTCGTCGTGCCC 59.686 55.000 15.98 0.00 0.00 5.36
843 3403 2.983402 TATATACTGCTCGTCGTGCC 57.017 50.000 15.98 0.05 0.00 5.01
844 3404 2.657372 GCTTATATACTGCTCGTCGTGC 59.343 50.000 12.19 12.19 0.00 5.34
845 3405 3.885358 TGCTTATATACTGCTCGTCGTG 58.115 45.455 7.99 0.00 0.00 4.35
846 3406 3.609644 GCTGCTTATATACTGCTCGTCGT 60.610 47.826 7.99 0.00 0.00 4.34
847 3407 2.911723 GCTGCTTATATACTGCTCGTCG 59.088 50.000 7.99 0.00 0.00 5.12
848 3408 3.057174 AGGCTGCTTATATACTGCTCGTC 60.057 47.826 0.00 2.65 0.00 4.20
895 3455 1.975407 GTTCTGGTCTCGGGTCGGA 60.975 63.158 0.00 0.00 0.00 4.55
917 3477 0.898326 TCTACCACTCCTTGCTCGCA 60.898 55.000 0.00 0.00 0.00 5.10
937 3525 6.937436 ACTAACAACCTCTCGTTTGAAATT 57.063 33.333 0.00 0.00 29.93 1.82
996 3584 1.794222 CTTGGTCGTCGCCATTTCC 59.206 57.895 8.83 0.00 38.48 3.13
1449 4037 2.972505 CTGGCGTGACACACCACC 60.973 66.667 11.34 4.31 33.67 4.61
1467 4055 4.154347 GGGAGCAGGCTGGACTCG 62.154 72.222 17.64 0.00 0.00 4.18
2043 4631 2.272146 CCATTGGGGTCCACCTCG 59.728 66.667 0.00 0.00 40.19 4.63
2377 4965 2.283529 GCCCTGACGGAACAGAGGA 61.284 63.158 7.83 0.00 39.94 3.71
2418 5006 3.455469 GCAAGTGGGGCATCTGGC 61.455 66.667 0.00 0.00 43.74 4.85
2419 5007 2.757099 GGCAAGTGGGGCATCTGG 60.757 66.667 0.00 0.00 0.00 3.86
2420 5008 2.036098 TGGCAAGTGGGGCATCTG 59.964 61.111 0.00 0.00 38.55 2.90
2422 5010 3.070576 GGTGGCAAGTGGGGCATC 61.071 66.667 0.00 0.00 45.62 3.91
2439 5041 0.722848 CAAAATTACGGGTCGTCGGG 59.277 55.000 0.00 0.00 41.54 5.14
2452 5054 5.644977 GGTAACTTCTAGCCTGCAAAATT 57.355 39.130 0.00 0.00 0.00 1.82
2548 5156 6.305272 AGAACAGATGGTATCACAACAGAT 57.695 37.500 0.00 0.00 0.00 2.90
2550 5158 6.533012 CACTAGAACAGATGGTATCACAACAG 59.467 42.308 0.00 0.00 0.00 3.16
2560 5175 6.770746 ATACGTAACACTAGAACAGATGGT 57.229 37.500 0.00 0.00 0.00 3.55
2578 5193 9.436957 AATTGAATGTCTCTCAGTTAAATACGT 57.563 29.630 0.00 0.00 0.00 3.57
2623 5246 7.854916 ACATTAAACAAACCGCAAATGAAATTG 59.145 29.630 0.00 0.00 36.10 2.32
2655 5278 6.072397 CGACCAACCATAATCTAACCAAAACA 60.072 38.462 0.00 0.00 0.00 2.83
2656 5279 6.149807 TCGACCAACCATAATCTAACCAAAAC 59.850 38.462 0.00 0.00 0.00 2.43
2661 5284 5.607477 TCATCGACCAACCATAATCTAACC 58.393 41.667 0.00 0.00 0.00 2.85
2662 5285 6.984474 TCTTCATCGACCAACCATAATCTAAC 59.016 38.462 0.00 0.00 0.00 2.34
2663 5286 7.119709 TCTTCATCGACCAACCATAATCTAA 57.880 36.000 0.00 0.00 0.00 2.10
2665 5288 5.614324 TCTTCATCGACCAACCATAATCT 57.386 39.130 0.00 0.00 0.00 2.40
2666 5289 6.677781 TTTCTTCATCGACCAACCATAATC 57.322 37.500 0.00 0.00 0.00 1.75
2667 5290 6.432783 TGTTTTCTTCATCGACCAACCATAAT 59.567 34.615 0.00 0.00 0.00 1.28
2668 5291 5.765677 TGTTTTCTTCATCGACCAACCATAA 59.234 36.000 0.00 0.00 0.00 1.90
2710 5333 2.128035 CTTGTATCATTCGCTCGGGAC 58.872 52.381 0.00 0.00 0.00 4.46
2711 5334 1.068588 CCTTGTATCATTCGCTCGGGA 59.931 52.381 0.00 0.00 0.00 5.14
2712 5335 1.502231 CCTTGTATCATTCGCTCGGG 58.498 55.000 0.00 0.00 0.00 5.14
2713 5336 0.861837 GCCTTGTATCATTCGCTCGG 59.138 55.000 0.00 0.00 0.00 4.63
2714 5337 1.258982 GTGCCTTGTATCATTCGCTCG 59.741 52.381 0.00 0.00 0.00 5.03
2715 5338 2.541762 GAGTGCCTTGTATCATTCGCTC 59.458 50.000 0.00 0.00 0.00 5.03
2716 5339 2.169352 AGAGTGCCTTGTATCATTCGCT 59.831 45.455 0.00 0.00 0.00 4.93
2717 5340 2.541762 GAGAGTGCCTTGTATCATTCGC 59.458 50.000 0.00 0.00 0.00 4.70
2718 5341 4.052159 AGAGAGTGCCTTGTATCATTCG 57.948 45.455 0.00 0.00 0.00 3.34
2719 5342 6.753180 TCATAGAGAGTGCCTTGTATCATTC 58.247 40.000 0.00 0.00 0.00 2.67
2720 5343 6.737720 TCATAGAGAGTGCCTTGTATCATT 57.262 37.500 0.00 0.00 0.00 2.57
2721 5344 6.295745 CCATCATAGAGAGTGCCTTGTATCAT 60.296 42.308 0.00 0.00 0.00 2.45
2722 5345 5.011431 CCATCATAGAGAGTGCCTTGTATCA 59.989 44.000 0.00 0.00 0.00 2.15
2723 5346 5.244851 TCCATCATAGAGAGTGCCTTGTATC 59.755 44.000 0.00 0.00 0.00 2.24
2724 5347 5.150715 TCCATCATAGAGAGTGCCTTGTAT 58.849 41.667 0.00 0.00 0.00 2.29
2725 5348 4.546674 TCCATCATAGAGAGTGCCTTGTA 58.453 43.478 0.00 0.00 0.00 2.41
2726 5349 3.378512 TCCATCATAGAGAGTGCCTTGT 58.621 45.455 0.00 0.00 0.00 3.16
2727 5350 3.803021 GCTCCATCATAGAGAGTGCCTTG 60.803 52.174 0.00 0.00 32.86 3.61
2728 5351 2.368221 GCTCCATCATAGAGAGTGCCTT 59.632 50.000 0.00 0.00 32.86 4.35
2729 5352 1.969923 GCTCCATCATAGAGAGTGCCT 59.030 52.381 0.00 0.00 32.86 4.75
2730 5353 1.690893 TGCTCCATCATAGAGAGTGCC 59.309 52.381 0.00 0.00 32.86 5.01
2731 5354 3.244146 ACATGCTCCATCATAGAGAGTGC 60.244 47.826 0.00 0.00 32.86 4.40
2732 5355 4.038883 TGACATGCTCCATCATAGAGAGTG 59.961 45.833 0.00 0.00 32.86 3.51
2733 5356 4.221530 TGACATGCTCCATCATAGAGAGT 58.778 43.478 0.00 0.00 32.86 3.24
2734 5357 4.868314 TGACATGCTCCATCATAGAGAG 57.132 45.455 0.00 0.00 32.86 3.20
2735 5358 5.820404 ATTGACATGCTCCATCATAGAGA 57.180 39.130 0.00 0.00 32.86 3.10
2736 5359 7.974482 TTAATTGACATGCTCCATCATAGAG 57.026 36.000 0.00 0.00 0.00 2.43
2737 5360 8.158789 TCATTAATTGACATGCTCCATCATAGA 58.841 33.333 0.00 0.00 0.00 1.98
2738 5361 8.331730 TCATTAATTGACATGCTCCATCATAG 57.668 34.615 0.00 0.00 0.00 2.23
2739 5362 8.694581 TTCATTAATTGACATGCTCCATCATA 57.305 30.769 0.00 0.00 32.84 2.15
2740 5363 7.591421 TTCATTAATTGACATGCTCCATCAT 57.409 32.000 0.00 0.00 32.84 2.45
2741 5364 7.407393 TTTCATTAATTGACATGCTCCATCA 57.593 32.000 0.00 0.00 32.84 3.07
2742 5365 8.882415 AATTTCATTAATTGACATGCTCCATC 57.118 30.769 0.00 0.00 35.15 3.51
2743 5366 9.754382 GTAATTTCATTAATTGACATGCTCCAT 57.246 29.630 0.00 0.00 37.07 3.41
2744 5367 7.914871 CGTAATTTCATTAATTGACATGCTCCA 59.085 33.333 0.00 0.00 37.07 3.86
2745 5368 7.379529 CCGTAATTTCATTAATTGACATGCTCC 59.620 37.037 0.00 0.00 37.07 4.70
2746 5369 7.915397 ACCGTAATTTCATTAATTGACATGCTC 59.085 33.333 0.00 0.00 37.07 4.26
2747 5370 7.771183 ACCGTAATTTCATTAATTGACATGCT 58.229 30.769 0.00 0.00 37.07 3.79
2748 5371 7.985634 ACCGTAATTTCATTAATTGACATGC 57.014 32.000 0.00 0.00 37.07 4.06
2757 5380 9.158233 CCAGAGAAGTTACCGTAATTTCATTAA 57.842 33.333 21.77 0.00 37.00 1.40
2758 5381 8.533657 TCCAGAGAAGTTACCGTAATTTCATTA 58.466 33.333 21.77 6.30 37.00 1.90
2759 5382 7.391620 TCCAGAGAAGTTACCGTAATTTCATT 58.608 34.615 21.77 10.99 37.00 2.57
2760 5383 6.942976 TCCAGAGAAGTTACCGTAATTTCAT 58.057 36.000 21.77 11.53 37.00 2.57
2761 5384 6.349243 TCCAGAGAAGTTACCGTAATTTCA 57.651 37.500 21.77 4.97 37.00 2.69
2762 5385 7.169476 GCTATCCAGAGAAGTTACCGTAATTTC 59.831 40.741 15.32 15.32 35.41 2.17
2763 5386 6.985059 GCTATCCAGAGAAGTTACCGTAATTT 59.015 38.462 0.00 0.00 0.00 1.82
2764 5387 6.097839 TGCTATCCAGAGAAGTTACCGTAATT 59.902 38.462 0.00 0.00 0.00 1.40
2765 5388 5.597182 TGCTATCCAGAGAAGTTACCGTAAT 59.403 40.000 0.00 0.00 0.00 1.89
2766 5389 4.951715 TGCTATCCAGAGAAGTTACCGTAA 59.048 41.667 0.00 0.00 0.00 3.18
2767 5390 4.529897 TGCTATCCAGAGAAGTTACCGTA 58.470 43.478 0.00 0.00 0.00 4.02
2768 5391 3.362706 TGCTATCCAGAGAAGTTACCGT 58.637 45.455 0.00 0.00 0.00 4.83
2769 5392 4.038042 TCATGCTATCCAGAGAAGTTACCG 59.962 45.833 0.00 0.00 0.00 4.02
2770 5393 5.163405 TGTCATGCTATCCAGAGAAGTTACC 60.163 44.000 0.00 0.00 0.00 2.85
2771 5394 5.751028 GTGTCATGCTATCCAGAGAAGTTAC 59.249 44.000 0.00 0.00 0.00 2.50
2772 5395 5.422012 TGTGTCATGCTATCCAGAGAAGTTA 59.578 40.000 0.00 0.00 0.00 2.24
2773 5396 4.223700 TGTGTCATGCTATCCAGAGAAGTT 59.776 41.667 0.00 0.00 0.00 2.66
2774 5397 3.771479 TGTGTCATGCTATCCAGAGAAGT 59.229 43.478 0.00 0.00 0.00 3.01
2775 5398 4.397481 TGTGTCATGCTATCCAGAGAAG 57.603 45.455 0.00 0.00 0.00 2.85
2776 5399 4.824479 TTGTGTCATGCTATCCAGAGAA 57.176 40.909 0.00 0.00 0.00 2.87
2777 5400 5.121105 CAATTGTGTCATGCTATCCAGAGA 58.879 41.667 0.00 0.00 0.00 3.10
2778 5401 4.261072 GCAATTGTGTCATGCTATCCAGAG 60.261 45.833 7.40 0.00 37.12 3.35
2779 5402 3.628942 GCAATTGTGTCATGCTATCCAGA 59.371 43.478 7.40 0.00 37.12 3.86
2780 5403 3.961182 GCAATTGTGTCATGCTATCCAG 58.039 45.455 7.40 0.00 37.12 3.86
2787 5410 1.270274 TGTCCAGCAATTGTGTCATGC 59.730 47.619 7.40 0.00 40.34 4.06
2788 5411 3.507786 CATGTCCAGCAATTGTGTCATG 58.492 45.455 7.40 14.40 0.00 3.07
2789 5412 2.494471 CCATGTCCAGCAATTGTGTCAT 59.506 45.455 7.40 8.16 0.00 3.06
2790 5413 1.887854 CCATGTCCAGCAATTGTGTCA 59.112 47.619 7.40 6.49 0.00 3.58
2791 5414 1.203052 CCCATGTCCAGCAATTGTGTC 59.797 52.381 7.40 0.00 0.00 3.67
2792 5415 1.259609 CCCATGTCCAGCAATTGTGT 58.740 50.000 7.40 0.00 0.00 3.72
2793 5416 0.108520 GCCCATGTCCAGCAATTGTG 60.109 55.000 7.40 4.35 0.00 3.33
2794 5417 0.542467 TGCCCATGTCCAGCAATTGT 60.542 50.000 7.40 0.00 32.56 2.71
2795 5418 0.609151 TTGCCCATGTCCAGCAATTG 59.391 50.000 0.00 0.00 41.35 2.32
2796 5419 3.070115 TTGCCCATGTCCAGCAATT 57.930 47.368 5.81 0.00 41.35 2.32
2797 5420 4.870069 TTGCCCATGTCCAGCAAT 57.130 50.000 5.81 0.00 41.35 3.56
2798 5421 0.469705 AAGTTGCCCATGTCCAGCAA 60.470 50.000 5.81 5.81 43.83 3.91
2799 5422 0.469705 AAAGTTGCCCATGTCCAGCA 60.470 50.000 0.00 0.00 33.97 4.41
2800 5423 0.681175 AAAAGTTGCCCATGTCCAGC 59.319 50.000 0.00 0.00 0.00 4.85
2801 5424 1.962807 TGAAAAGTTGCCCATGTCCAG 59.037 47.619 0.00 0.00 0.00 3.86
2802 5425 2.079170 TGAAAAGTTGCCCATGTCCA 57.921 45.000 0.00 0.00 0.00 4.02
2803 5426 3.683365 AATGAAAAGTTGCCCATGTCC 57.317 42.857 0.00 0.00 0.00 4.02
2804 5427 5.299949 AGAAAATGAAAAGTTGCCCATGTC 58.700 37.500 0.00 0.00 0.00 3.06
2805 5428 5.294734 AGAAAATGAAAAGTTGCCCATGT 57.705 34.783 0.00 0.00 0.00 3.21
2806 5429 6.622833 AAAGAAAATGAAAAGTTGCCCATG 57.377 33.333 0.00 0.00 0.00 3.66
2807 5430 7.467131 CGAAAAAGAAAATGAAAAGTTGCCCAT 60.467 33.333 0.00 0.00 0.00 4.00
2808 5431 6.183360 CGAAAAAGAAAATGAAAAGTTGCCCA 60.183 34.615 0.00 0.00 0.00 5.36
2809 5432 6.036626 TCGAAAAAGAAAATGAAAAGTTGCCC 59.963 34.615 0.00 0.00 0.00 5.36
2810 5433 6.899771 GTCGAAAAAGAAAATGAAAAGTTGCC 59.100 34.615 0.00 0.00 0.00 4.52
2811 5434 7.452231 TGTCGAAAAAGAAAATGAAAAGTTGC 58.548 30.769 0.00 0.00 0.00 4.17
2812 5435 9.804547 TTTGTCGAAAAAGAAAATGAAAAGTTG 57.195 25.926 0.00 0.00 0.00 3.16
2815 5438 9.476761 CCTTTTGTCGAAAAAGAAAATGAAAAG 57.523 29.630 22.98 7.76 39.04 2.27
2816 5439 8.994170 ACCTTTTGTCGAAAAAGAAAATGAAAA 58.006 25.926 22.98 0.00 39.04 2.29
2817 5440 8.439286 CACCTTTTGTCGAAAAAGAAAATGAAA 58.561 29.630 22.98 0.54 39.04 2.69
2818 5441 7.064016 CCACCTTTTGTCGAAAAAGAAAATGAA 59.936 33.333 22.98 1.12 39.04 2.57
2819 5442 6.533367 CCACCTTTTGTCGAAAAAGAAAATGA 59.467 34.615 22.98 1.71 39.04 2.57
2820 5443 6.533367 TCCACCTTTTGTCGAAAAAGAAAATG 59.467 34.615 22.98 17.15 39.04 2.32
2821 5444 6.635755 TCCACCTTTTGTCGAAAAAGAAAAT 58.364 32.000 22.98 10.69 39.04 1.82
2822 5445 6.026947 TCCACCTTTTGTCGAAAAAGAAAA 57.973 33.333 22.98 9.42 39.04 2.29
2823 5446 5.646577 TCCACCTTTTGTCGAAAAAGAAA 57.353 34.783 22.98 3.46 39.04 2.52
2824 5447 5.845391 ATCCACCTTTTGTCGAAAAAGAA 57.155 34.783 22.98 4.05 39.04 2.52
2825 5448 5.845391 AATCCACCTTTTGTCGAAAAAGA 57.155 34.783 22.98 10.43 39.04 2.52
2826 5449 6.902224 AAAATCCACCTTTTGTCGAAAAAG 57.098 33.333 18.17 18.17 37.08 2.27
2839 5462 6.194235 TGTATTGAGCCAATAAAATCCACCT 58.806 36.000 8.60 0.00 37.94 4.00
2862 5485 4.701651 TGTTTGTATCCCTTTGATGCTCTG 59.298 41.667 0.00 0.00 37.04 3.35
2863 5486 4.922206 TGTTTGTATCCCTTTGATGCTCT 58.078 39.130 0.00 0.00 37.04 4.09
2873 5496 7.499232 GTGTATGCTCTTTATGTTTGTATCCCT 59.501 37.037 0.00 0.00 0.00 4.20
2886 5509 3.455910 AGATGCCAGGTGTATGCTCTTTA 59.544 43.478 0.00 0.00 0.00 1.85
2895 5518 2.118679 ACTATGCAGATGCCAGGTGTA 58.881 47.619 1.72 0.00 41.18 2.90
2901 5524 4.011966 CATCCTAACTATGCAGATGCCA 57.988 45.455 1.72 0.00 41.18 4.92
2931 5554 1.141234 TGTGCGTGTGTCCGTGTTA 59.859 52.632 0.00 0.00 0.00 2.41
2941 5564 2.525055 GTGTGATTTTTGTGTGCGTGT 58.475 42.857 0.00 0.00 0.00 4.49
2984 5607 1.948611 GCCTTGGCATAGTTTCGGTCA 60.949 52.381 6.79 0.00 0.00 4.02
2992 5615 3.290948 TTTTATCCGCCTTGGCATAGT 57.709 42.857 12.45 0.00 37.80 2.12
3044 5667 3.058160 AACACCTGCTCGGCATGC 61.058 61.111 9.90 9.90 38.13 4.06
3091 5722 1.872234 CGTGTCCACATACGGAGCG 60.872 63.158 0.00 0.00 35.10 5.03
3110 5741 0.388134 TCGCGTTTAGTCTGAGTGGC 60.388 55.000 5.77 0.00 0.00 5.01
3195 5839 2.143122 TCTTACCGTTTGAGCTGCAAG 58.857 47.619 1.02 0.00 37.87 4.01
3197 5841 2.143122 CTTCTTACCGTTTGAGCTGCA 58.857 47.619 1.02 0.00 0.00 4.41
3208 5852 1.802880 CGGCACCATCTCTTCTTACCG 60.803 57.143 0.00 0.00 0.00 4.02
3268 5912 1.333308 CATCGACAAACACTTGCACCA 59.667 47.619 0.00 0.00 35.84 4.17
3315 5959 5.730550 TGTAGGTTCATGGTGTATTGTCTC 58.269 41.667 0.00 0.00 0.00 3.36
3332 5976 3.697439 ATGGCGGCGCAATGTAGGT 62.697 57.895 34.36 2.34 0.00 3.08
3364 6008 7.039270 CGGGGTAATGTTCGATGATATTGATA 58.961 38.462 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.