Multiple sequence alignment - TraesCS4B01G155000

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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 TraesCS4B01G155000 chr4B 100.000 4113 0 0 1 4113 275996564 276000676 0.000000e+00 7596.0
1 TraesCS4B01G155000 chr4B 90.000 380 24 6 209 575 626511705 626511327 2.880000e-131 479.0
2 TraesCS4B01G155000 chr4B 84.247 146 21 2 2040 2184 34729958 34729814 1.540000e-29 141.0
3 TraesCS4B01G155000 chr4D 93.289 1490 41 14 2625 4074 294004475 294005945 0.000000e+00 2143.0
4 TraesCS4B01G155000 chr4D 93.862 1401 37 10 639 2008 294002497 294003879 0.000000e+00 2065.0
5 TraesCS4B01G155000 chr4D 93.682 459 20 5 2050 2502 294004022 294004477 0.000000e+00 678.0
6 TraesCS4B01G155000 chr4D 100.000 67 0 0 4047 4113 294005940 294006006 1.550000e-24 124.0
7 TraesCS4B01G155000 chr4A 92.300 1039 34 16 603 1616 324705566 324706583 0.000000e+00 1434.0
8 TraesCS4B01G155000 chr4A 87.865 890 75 16 2969 3830 324708014 324708898 0.000000e+00 1014.0
9 TraesCS4B01G155000 chr4A 87.262 526 22 10 1610 2121 324706879 324707373 3.590000e-155 558.0
10 TraesCS4B01G155000 chr4A 91.379 232 11 2 2625 2856 324707659 324707881 3.990000e-80 309.0
11 TraesCS4B01G155000 chr4A 90.547 201 17 1 2304 2502 324707461 324707661 8.770000e-67 265.0
12 TraesCS4B01G155000 chr4A 94.286 140 6 2 2500 2637 1910498 1910359 3.220000e-51 213.0
13 TraesCS4B01G155000 chr4A 80.000 225 42 3 363 585 513319462 513319685 3.290000e-36 163.0
14 TraesCS4B01G155000 chr4A 89.076 119 4 2 3829 3938 324712928 324713046 5.540000e-29 139.0
15 TraesCS4B01G155000 chr7A 85.149 606 65 16 1 588 2372660 2372062 7.610000e-167 597.0
16 TraesCS4B01G155000 chr1B 91.053 380 20 5 209 575 89518910 89519288 6.140000e-138 501.0
17 TraesCS4B01G155000 chr1B 91.057 369 20 2 220 575 89516708 89517076 1.720000e-133 486.0
18 TraesCS4B01G155000 chrUn 88.011 367 22 6 222 575 443345865 443345508 8.230000e-112 414.0
19 TraesCS4B01G155000 chrUn 86.634 202 26 1 375 575 348938252 348938453 5.350000e-54 222.0
20 TraesCS4B01G155000 chrUn 86.634 202 26 1 375 575 348984552 348984753 5.350000e-54 222.0
21 TraesCS4B01G155000 chrUn 86.634 202 26 1 375 575 407785126 407784925 5.350000e-54 222.0
22 TraesCS4B01G155000 chrUn 93.525 139 8 1 2489 2627 74542272 74542135 5.390000e-49 206.0
23 TraesCS4B01G155000 chrUn 80.628 191 33 4 333 521 310629348 310629160 1.190000e-30 145.0
24 TraesCS4B01G155000 chr5B 93.213 221 13 2 1 220 506798102 506798321 1.430000e-84 324.0
25 TraesCS4B01G155000 chr2B 93.220 177 12 0 1 177 728409762 728409938 1.130000e-65 261.0
26 TraesCS4B01G155000 chr2B 97.656 128 3 0 2500 2627 518742387 518742260 1.920000e-53 220.0
27 TraesCS4B01G155000 chr2B 77.236 123 24 2 2153 2272 371159933 371160054 7.380000e-08 69.4
28 TraesCS4B01G155000 chr6B 91.975 162 12 1 1 162 653312135 653311975 4.140000e-55 226.0
29 TraesCS4B01G155000 chr3D 96.183 131 5 0 2496 2626 443434369 443434239 8.950000e-52 215.0
30 TraesCS4B01G155000 chr7D 96.124 129 5 0 2499 2627 490590800 490590928 1.160000e-50 211.0
31 TraesCS4B01G155000 chr6D 94.776 134 7 0 2500 2633 81770383 81770250 4.170000e-50 209.0
32 TraesCS4B01G155000 chr2D 95.420 131 6 0 2497 2627 536091156 536091026 4.170000e-50 209.0
33 TraesCS4B01G155000 chr2D 94.161 137 7 1 2490 2626 561025757 561025622 1.500000e-49 207.0
34 TraesCS4B01G155000 chr3B 91.781 146 11 1 2500 2645 749091019 749090875 6.970000e-48 202.0
35 TraesCS4B01G155000 chr3A 79.151 259 45 9 330 583 158003190 158003444 1.970000e-38 171.0


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 TraesCS4B01G155000 chr4B 275996564 276000676 4112 False 7596.0 7596 100.00000 1 4113 1 chr4B.!!$F1 4112
1 TraesCS4B01G155000 chr4D 294002497 294006006 3509 False 1252.5 2143 95.20825 639 4113 4 chr4D.!!$F1 3474
2 TraesCS4B01G155000 chr4A 324705566 324708898 3332 False 716.0 1434 89.87060 603 3830 5 chr4A.!!$F3 3227
3 TraesCS4B01G155000 chr7A 2372062 2372660 598 True 597.0 597 85.14900 1 588 1 chr7A.!!$R1 587
4 TraesCS4B01G155000 chr1B 89516708 89519288 2580 False 493.5 501 91.05500 209 575 2 chr1B.!!$F1 366

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
636 2643 0.035056 GGGCACAGGCTTGTCATACT 60.035 55.0 0.00 0.0 40.87 2.12 F
1018 3033 0.325296 TATGGGCCTCCTCGACAAGT 60.325 55.0 4.53 0.0 0.00 3.16 F
1263 3278 0.594028 CGACGGTGATCCCACATACG 60.594 60.0 0.00 0.0 44.93 3.06 F
2622 5114 0.035820 CGAATTTTGGGACGGAGGGA 60.036 55.0 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 5095 0.035820 TCCCTCCGTCCCAAAATTCG 60.036 55.000 0.00 0.00 0.00 3.34 R
2612 5104 0.679321 AACTCGTACTCCCTCCGTCC 60.679 60.000 0.00 0.00 0.00 4.79 R
3043 5598 0.179026 TAGCCCTCTCGTACGCATCT 60.179 55.000 11.24 4.21 0.00 2.90 R
3725 6339 2.108976 CAGCCACTGACACGGTGT 59.891 61.111 14.66 14.66 38.92 4.16 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
111 112 4.680237 CGGCCTGACGGTGAGCAA 62.680 66.667 0.00 0.00 0.00 3.91
386 2392 3.138128 GTCGAAAATGCCCCCGGG 61.138 66.667 15.80 15.80 38.57 5.73
458 2465 2.429933 ATAGTGCCCATCCCAGATCT 57.570 50.000 0.00 0.00 0.00 2.75
523 2530 1.404391 CATCAAGCAGCCAGATCCAAC 59.596 52.381 0.00 0.00 0.00 3.77
524 2531 0.674581 TCAAGCAGCCAGATCCAACG 60.675 55.000 0.00 0.00 0.00 4.10
525 2532 1.377725 AAGCAGCCAGATCCAACGG 60.378 57.895 0.00 0.00 0.00 4.44
526 2533 3.512516 GCAGCCAGATCCAACGGC 61.513 66.667 5.19 5.19 46.62 5.68
529 2536 4.424711 GCCAGATCCAACGGCCCA 62.425 66.667 0.00 0.00 40.07 5.36
530 2537 2.354729 CCAGATCCAACGGCCCAA 59.645 61.111 0.00 0.00 0.00 4.12
531 2538 1.304052 CCAGATCCAACGGCCCAAA 60.304 57.895 0.00 0.00 0.00 3.28
532 2539 0.897863 CCAGATCCAACGGCCCAAAA 60.898 55.000 0.00 0.00 0.00 2.44
533 2540 1.185315 CAGATCCAACGGCCCAAAAT 58.815 50.000 0.00 0.00 0.00 1.82
534 2541 1.134946 CAGATCCAACGGCCCAAAATC 59.865 52.381 0.00 0.00 0.00 2.17
535 2542 0.459899 GATCCAACGGCCCAAAATCC 59.540 55.000 0.00 0.00 0.00 3.01
536 2543 0.252012 ATCCAACGGCCCAAAATCCA 60.252 50.000 0.00 0.00 0.00 3.41
537 2544 0.470080 TCCAACGGCCCAAAATCCAA 60.470 50.000 0.00 0.00 0.00 3.53
538 2545 0.394565 CCAACGGCCCAAAATCCAAA 59.605 50.000 0.00 0.00 0.00 3.28
539 2546 1.003003 CCAACGGCCCAAAATCCAAAT 59.997 47.619 0.00 0.00 0.00 2.32
540 2547 2.551938 CCAACGGCCCAAAATCCAAATT 60.552 45.455 0.00 0.00 0.00 1.82
541 2548 2.470983 ACGGCCCAAAATCCAAATTG 57.529 45.000 0.00 0.00 0.00 2.32
542 2549 1.085893 CGGCCCAAAATCCAAATTGC 58.914 50.000 0.00 0.00 0.00 3.56
543 2550 1.338960 CGGCCCAAAATCCAAATTGCT 60.339 47.619 0.00 0.00 0.00 3.91
544 2551 2.086094 GGCCCAAAATCCAAATTGCTG 58.914 47.619 0.00 0.00 0.00 4.41
545 2552 2.552809 GGCCCAAAATCCAAATTGCTGT 60.553 45.455 0.00 0.00 0.00 4.40
546 2553 2.485038 GCCCAAAATCCAAATTGCTGTG 59.515 45.455 0.00 0.00 0.00 3.66
547 2554 3.806507 GCCCAAAATCCAAATTGCTGTGA 60.807 43.478 0.00 0.00 0.00 3.58
548 2555 4.387598 CCCAAAATCCAAATTGCTGTGAA 58.612 39.130 0.00 0.00 0.00 3.18
549 2556 4.820716 CCCAAAATCCAAATTGCTGTGAAA 59.179 37.500 0.00 0.00 0.00 2.69
550 2557 5.049267 CCCAAAATCCAAATTGCTGTGAAAG 60.049 40.000 0.00 0.00 0.00 2.62
564 2571 5.288543 CTGTGAAAGCTTGTAGGAACATC 57.711 43.478 0.00 0.00 34.97 3.06
565 2572 4.072131 TGTGAAAGCTTGTAGGAACATCC 58.928 43.478 0.00 0.00 34.97 3.51
567 2574 4.762251 GTGAAAGCTTGTAGGAACATCCTT 59.238 41.667 0.00 0.00 46.91 3.36
568 2575 5.003804 TGAAAGCTTGTAGGAACATCCTTC 58.996 41.667 0.00 0.00 46.91 3.46
569 2576 4.917906 AAGCTTGTAGGAACATCCTTCT 57.082 40.909 3.90 0.00 46.91 2.85
570 2577 4.479786 AGCTTGTAGGAACATCCTTCTC 57.520 45.455 3.90 0.00 46.91 2.87
571 2578 4.100373 AGCTTGTAGGAACATCCTTCTCT 58.900 43.478 3.90 0.00 46.91 3.10
572 2579 4.534103 AGCTTGTAGGAACATCCTTCTCTT 59.466 41.667 3.90 0.00 46.91 2.85
573 2580 5.721960 AGCTTGTAGGAACATCCTTCTCTTA 59.278 40.000 3.90 0.00 46.91 2.10
574 2581 6.385467 AGCTTGTAGGAACATCCTTCTCTTAT 59.615 38.462 3.90 0.00 46.91 1.73
575 2582 6.704050 GCTTGTAGGAACATCCTTCTCTTATC 59.296 42.308 3.90 0.00 46.91 1.75
576 2583 7.418483 GCTTGTAGGAACATCCTTCTCTTATCT 60.418 40.741 3.90 0.00 46.91 1.98
577 2584 7.589958 TGTAGGAACATCCTTCTCTTATCTC 57.410 40.000 3.90 0.00 46.91 2.75
578 2585 7.358263 TGTAGGAACATCCTTCTCTTATCTCT 58.642 38.462 3.90 0.00 46.91 3.10
579 2586 7.841729 TGTAGGAACATCCTTCTCTTATCTCTT 59.158 37.037 3.90 0.00 46.91 2.85
580 2587 7.123355 AGGAACATCCTTCTCTTATCTCTTG 57.877 40.000 0.00 0.00 46.91 3.02
581 2588 6.900186 AGGAACATCCTTCTCTTATCTCTTGA 59.100 38.462 0.00 0.00 46.91 3.02
582 2589 7.568366 AGGAACATCCTTCTCTTATCTCTTGAT 59.432 37.037 0.00 0.00 46.91 2.57
583 2590 7.656948 GGAACATCCTTCTCTTATCTCTTGATG 59.343 40.741 0.00 0.00 32.19 3.07
584 2591 7.065120 ACATCCTTCTCTTATCTCTTGATGG 57.935 40.000 0.00 0.00 33.23 3.51
585 2592 5.543507 TCCTTCTCTTATCTCTTGATGGC 57.456 43.478 0.00 0.00 34.32 4.40
586 2593 4.346418 TCCTTCTCTTATCTCTTGATGGCC 59.654 45.833 0.00 0.00 34.32 5.36
587 2594 4.347583 CCTTCTCTTATCTCTTGATGGCCT 59.652 45.833 3.32 0.00 34.32 5.19
588 2595 5.541868 CCTTCTCTTATCTCTTGATGGCCTA 59.458 44.000 3.32 0.00 34.32 3.93
589 2596 6.042552 CCTTCTCTTATCTCTTGATGGCCTAA 59.957 42.308 3.32 0.00 34.32 2.69
590 2597 7.256619 CCTTCTCTTATCTCTTGATGGCCTAAT 60.257 40.741 3.32 0.00 34.32 1.73
591 2598 8.727100 TTCTCTTATCTCTTGATGGCCTAATA 57.273 34.615 3.32 0.00 34.32 0.98
592 2599 8.907829 TCTCTTATCTCTTGATGGCCTAATAT 57.092 34.615 3.32 0.00 34.32 1.28
593 2600 8.756927 TCTCTTATCTCTTGATGGCCTAATATG 58.243 37.037 3.32 0.00 34.32 1.78
594 2601 7.855375 TCTTATCTCTTGATGGCCTAATATGG 58.145 38.462 3.32 0.00 34.32 2.74
595 2602 7.459125 TCTTATCTCTTGATGGCCTAATATGGT 59.541 37.037 3.32 0.00 34.32 3.55
596 2603 5.912149 TCTCTTGATGGCCTAATATGGTT 57.088 39.130 3.32 0.00 0.00 3.67
597 2604 5.624159 TCTCTTGATGGCCTAATATGGTTG 58.376 41.667 3.32 0.00 0.00 3.77
598 2605 4.728772 TCTTGATGGCCTAATATGGTTGG 58.271 43.478 3.32 0.00 0.00 3.77
599 2606 2.875296 TGATGGCCTAATATGGTTGGC 58.125 47.619 3.32 0.00 44.22 4.52
600 2607 1.812571 GATGGCCTAATATGGTTGGCG 59.187 52.381 3.32 0.00 45.75 5.69
601 2608 0.840617 TGGCCTAATATGGTTGGCGA 59.159 50.000 3.32 0.00 45.75 5.54
605 2612 2.767505 CCTAATATGGTTGGCGAGTCC 58.232 52.381 0.00 0.00 0.00 3.85
611 2618 0.907704 TGGTTGGCGAGTCCCTACAT 60.908 55.000 11.94 0.00 33.12 2.29
613 2620 0.527817 GTTGGCGAGTCCCTACATCG 60.528 60.000 7.15 0.00 39.40 3.84
633 2640 1.604593 GTGGGCACAGGCTTGTCAT 60.605 57.895 0.00 0.00 40.87 3.06
634 2641 0.322456 GTGGGCACAGGCTTGTCATA 60.322 55.000 0.00 0.00 40.87 2.15
635 2642 0.322456 TGGGCACAGGCTTGTCATAC 60.322 55.000 0.00 0.00 40.87 2.39
636 2643 0.035056 GGGCACAGGCTTGTCATACT 60.035 55.000 0.00 0.00 40.87 2.12
795 2810 2.092212 AGACATTTCAGTATGGGCCCAG 60.092 50.000 31.97 17.02 36.16 4.45
844 2859 1.837051 TTCACGGGGCACAGTCTCT 60.837 57.895 0.00 0.00 0.00 3.10
845 2860 1.407656 TTCACGGGGCACAGTCTCTT 61.408 55.000 0.00 0.00 0.00 2.85
921 2936 0.927029 TCCCCTTCTCTCAGATCCGA 59.073 55.000 0.00 0.00 0.00 4.55
927 2942 4.429108 CCTTCTCTCAGATCCGAAAACTC 58.571 47.826 0.00 0.00 0.00 3.01
1018 3033 0.325296 TATGGGCCTCCTCGACAAGT 60.325 55.000 4.53 0.00 0.00 3.16
1132 3147 3.035576 GACCGCTGCCCGCTAAAAC 62.036 63.158 0.00 0.00 36.13 2.43
1151 3166 6.505044 AAAACTCGACATATTGTTAACCCC 57.495 37.500 2.48 0.00 0.00 4.95
1182 3197 5.875224 TCTTTGTACCATCAATCTGACCAA 58.125 37.500 0.00 0.00 0.00 3.67
1195 3210 3.006940 TCTGACCAACTGTTGTGTTGTC 58.993 45.455 18.38 17.02 44.01 3.18
1216 3231 2.783228 TTTTTGTCGCGTTGGGTCT 58.217 47.368 5.77 0.00 0.00 3.85
1217 3232 0.658897 TTTTTGTCGCGTTGGGTCTC 59.341 50.000 5.77 0.00 0.00 3.36
1218 3233 1.161563 TTTTGTCGCGTTGGGTCTCC 61.162 55.000 5.77 0.00 0.00 3.71
1259 3274 4.429212 CGCGACGGTGATCCCACA 62.429 66.667 0.00 0.00 44.93 4.17
1263 3278 0.594028 CGACGGTGATCCCACATACG 60.594 60.000 0.00 0.00 44.93 3.06
1302 3317 0.673333 ATGCGCCGATGAAAGTCACA 60.673 50.000 4.18 0.00 0.00 3.58
1413 3428 4.891727 CCCATCTCCCCGTTCGCG 62.892 72.222 0.00 0.00 40.93 5.87
1460 3475 5.991606 CCTCATCCAACTTCTCGCATTAATA 59.008 40.000 0.00 0.00 0.00 0.98
1543 3577 1.586028 CCCGGATGTGGCTTTTGTG 59.414 57.895 0.73 0.00 0.00 3.33
1618 3652 0.723981 GGCAAGTGCTTTAGCTCTCG 59.276 55.000 6.76 0.00 43.19 4.04
1640 3974 2.555199 GTCTCTTTCGTGGGATCATGG 58.445 52.381 0.00 0.00 0.00 3.66
2048 4522 3.014623 CCCCTCCGTTCCAAAATACTTC 58.985 50.000 0.00 0.00 0.00 3.01
2071 4545 4.620184 CGAACTTCTACGTTTGTCCTAAGG 59.380 45.833 0.00 0.00 0.00 2.69
2081 4555 4.917415 CGTTTGTCCTAAGGCAAATTTCTG 59.083 41.667 8.22 0.00 37.02 3.02
2279 4769 5.644977 ACTAAGTATTTTGGAGCAAAGGC 57.355 39.130 0.00 0.00 34.72 4.35
2280 4770 5.076873 ACTAAGTATTTTGGAGCAAAGGCA 58.923 37.500 0.00 0.00 44.61 4.75
2281 4771 4.525912 AAGTATTTTGGAGCAAAGGCAG 57.474 40.909 0.00 0.00 44.61 4.85
2282 4772 3.500343 AGTATTTTGGAGCAAAGGCAGT 58.500 40.909 0.00 0.00 44.61 4.40
2283 4773 4.662278 AGTATTTTGGAGCAAAGGCAGTA 58.338 39.130 0.00 0.00 44.61 2.74
2284 4774 5.264395 AGTATTTTGGAGCAAAGGCAGTAT 58.736 37.500 0.00 0.00 44.61 2.12
2285 4775 5.716703 AGTATTTTGGAGCAAAGGCAGTATT 59.283 36.000 0.00 0.00 44.61 1.89
2286 4776 6.889722 AGTATTTTGGAGCAAAGGCAGTATTA 59.110 34.615 0.00 0.00 44.61 0.98
2345 4835 4.142902 CGTGGGTGCAGTTAATTGACTTAG 60.143 45.833 0.00 0.00 0.00 2.18
2346 4836 4.760204 GTGGGTGCAGTTAATTGACTTAGT 59.240 41.667 0.00 0.00 0.00 2.24
2375 4865 4.632688 GCTTTGGTTATACCTTCGCTTACA 59.367 41.667 0.00 0.00 39.58 2.41
2506 4998 9.684702 TCTATCTTGGGTAAAATATTACTCCCT 57.315 33.333 17.09 5.50 41.08 4.20
2507 4999 9.945904 CTATCTTGGGTAAAATATTACTCCCTC 57.054 37.037 17.09 0.00 41.08 4.30
2508 5000 7.145474 TCTTGGGTAAAATATTACTCCCTCC 57.855 40.000 17.09 3.91 41.08 4.30
2509 5001 5.556006 TGGGTAAAATATTACTCCCTCCG 57.444 43.478 17.09 0.00 41.08 4.63
2510 5002 4.970640 TGGGTAAAATATTACTCCCTCCGT 59.029 41.667 17.09 0.00 41.08 4.69
2511 5003 5.070847 TGGGTAAAATATTACTCCCTCCGTC 59.929 44.000 17.09 0.00 41.08 4.79
2512 5004 5.512060 GGGTAAAATATTACTCCCTCCGTCC 60.512 48.000 11.95 0.00 41.01 4.79
2513 5005 4.701651 AAAATATTACTCCCTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
2514 5006 3.339713 AATATTACTCCCTCCGTCCCA 57.660 47.619 0.00 0.00 0.00 4.37
2515 5007 2.852714 TATTACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2516 5008 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2517 5009 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
2518 5010 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2519 5011 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2520 5012 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2521 5013 1.004277 CTCCCTCCGTCCCAAAATTCA 59.996 52.381 0.00 0.00 0.00 2.57
2522 5014 1.638589 TCCCTCCGTCCCAAAATTCAT 59.361 47.619 0.00 0.00 0.00 2.57
2523 5015 1.750778 CCCTCCGTCCCAAAATTCATG 59.249 52.381 0.00 0.00 0.00 3.07
2524 5016 2.446435 CCTCCGTCCCAAAATTCATGT 58.554 47.619 0.00 0.00 0.00 3.21
2525 5017 2.423538 CCTCCGTCCCAAAATTCATGTC 59.576 50.000 0.00 0.00 0.00 3.06
2526 5018 3.347216 CTCCGTCCCAAAATTCATGTCT 58.653 45.455 0.00 0.00 0.00 3.41
2527 5019 3.758554 CTCCGTCCCAAAATTCATGTCTT 59.241 43.478 0.00 0.00 0.00 3.01
2528 5020 4.912586 TCCGTCCCAAAATTCATGTCTTA 58.087 39.130 0.00 0.00 0.00 2.10
2529 5021 4.941263 TCCGTCCCAAAATTCATGTCTTAG 59.059 41.667 0.00 0.00 0.00 2.18
2530 5022 4.941263 CCGTCCCAAAATTCATGTCTTAGA 59.059 41.667 0.00 0.00 0.00 2.10
2531 5023 5.590259 CCGTCCCAAAATTCATGTCTTAGAT 59.410 40.000 0.00 0.00 0.00 1.98
2532 5024 6.095440 CCGTCCCAAAATTCATGTCTTAGATT 59.905 38.462 0.00 0.00 0.00 2.40
2533 5025 7.362920 CCGTCCCAAAATTCATGTCTTAGATTT 60.363 37.037 0.00 0.00 0.00 2.17
2534 5026 7.485913 CGTCCCAAAATTCATGTCTTAGATTTG 59.514 37.037 0.00 0.00 0.00 2.32
2535 5027 8.306761 GTCCCAAAATTCATGTCTTAGATTTGT 58.693 33.333 0.00 0.00 0.00 2.83
2536 5028 8.522830 TCCCAAAATTCATGTCTTAGATTTGTC 58.477 33.333 0.00 0.00 0.00 3.18
2537 5029 8.526147 CCCAAAATTCATGTCTTAGATTTGTCT 58.474 33.333 0.00 0.00 0.00 3.41
2544 5036 9.952188 TTCATGTCTTAGATTTGTCTAGATACG 57.048 33.333 0.00 0.00 0.00 3.06
2545 5037 8.568794 TCATGTCTTAGATTTGTCTAGATACGG 58.431 37.037 0.00 0.00 0.00 4.02
2546 5038 8.568794 CATGTCTTAGATTTGTCTAGATACGGA 58.431 37.037 0.00 0.00 0.00 4.69
2547 5039 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
2548 5040 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
2549 5041 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
2550 5042 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
2568 5060 9.516546 ACGGATGTATCTAATACTAAGACATGA 57.483 33.333 0.00 0.00 36.70 3.07
2569 5061 9.776158 CGGATGTATCTAATACTAAGACATGAC 57.224 37.037 0.00 0.00 36.70 3.06
2580 5072 9.988815 AATACTAAGACATGACTTGATACATCC 57.011 33.333 18.80 0.00 0.00 3.51
2581 5073 7.423844 ACTAAGACATGACTTGATACATCCA 57.576 36.000 18.80 0.00 0.00 3.41
2582 5074 8.027524 ACTAAGACATGACTTGATACATCCAT 57.972 34.615 18.80 0.00 0.00 3.41
2583 5075 9.147732 ACTAAGACATGACTTGATACATCCATA 57.852 33.333 18.80 0.00 0.00 2.74
2586 5078 9.857656 AAGACATGACTTGATACATCCATATTT 57.142 29.630 9.67 0.00 0.00 1.40
2604 5096 9.093970 TCCATATTTAGACAAATGTAAGACACG 57.906 33.333 0.00 0.00 35.88 4.49
2605 5097 9.093970 CCATATTTAGACAAATGTAAGACACGA 57.906 33.333 0.00 0.00 35.88 4.35
2611 5103 9.658475 TTAGACAAATGTAAGACACGAATTTTG 57.342 29.630 0.00 0.00 0.00 2.44
2612 5104 7.138736 AGACAAATGTAAGACACGAATTTTGG 58.861 34.615 0.00 0.00 0.00 3.28
2613 5105 6.212955 ACAAATGTAAGACACGAATTTTGGG 58.787 36.000 0.00 0.00 0.00 4.12
2614 5106 6.039941 ACAAATGTAAGACACGAATTTTGGGA 59.960 34.615 0.00 0.00 0.00 4.37
2615 5107 5.622770 ATGTAAGACACGAATTTTGGGAC 57.377 39.130 0.00 0.00 0.00 4.46
2616 5108 3.495377 TGTAAGACACGAATTTTGGGACG 59.505 43.478 0.00 0.00 0.00 4.79
2617 5109 1.519408 AGACACGAATTTTGGGACGG 58.481 50.000 0.00 0.00 0.00 4.79
2618 5110 1.071071 AGACACGAATTTTGGGACGGA 59.929 47.619 0.00 0.00 0.00 4.69
2619 5111 1.463444 GACACGAATTTTGGGACGGAG 59.537 52.381 0.00 0.00 0.00 4.63
2620 5112 0.802494 CACGAATTTTGGGACGGAGG 59.198 55.000 0.00 0.00 0.00 4.30
2621 5113 0.322187 ACGAATTTTGGGACGGAGGG 60.322 55.000 0.00 0.00 0.00 4.30
2622 5114 0.035820 CGAATTTTGGGACGGAGGGA 60.036 55.000 0.00 0.00 0.00 4.20
2623 5115 1.751437 GAATTTTGGGACGGAGGGAG 58.249 55.000 0.00 0.00 0.00 4.30
2624 5116 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2625 5117 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2626 5118 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
2643 5135 4.634883 GGAGTACGAGTTAGACAGTGATGA 59.365 45.833 0.00 0.00 0.00 2.92
2709 5201 2.607631 TCGTTCCGTTTTCCAAGTCT 57.392 45.000 0.00 0.00 0.00 3.24
2717 5209 5.187687 TCCGTTTTCCAAGTCTACAACTTT 58.812 37.500 0.00 0.00 46.26 2.66
2732 5224 7.432252 GTCTACAACTTTGTTTGATTTGTCAGG 59.568 37.037 0.00 0.00 42.35 3.86
2792 5284 4.584743 TGCTGTCTTTGTCTACTCTCTTGA 59.415 41.667 0.00 0.00 0.00 3.02
2796 5288 6.382608 TGTCTTTGTCTACTCTCTTGAATCG 58.617 40.000 0.00 0.00 0.00 3.34
2799 5291 4.966965 TGTCTACTCTCTTGAATCGGTC 57.033 45.455 0.00 0.00 0.00 4.79
2838 5330 8.590204 TGAGTTTGTAAGAATCACATGGTAGTA 58.410 33.333 0.00 0.00 0.00 1.82
2868 5366 8.867097 GGGAAAACATGGATCTAGTAGTACATA 58.133 37.037 2.52 0.00 0.00 2.29
2914 5412 1.202394 GCATGCGGCATGGAAATGTTA 60.202 47.619 35.98 0.00 41.64 2.41
2996 5551 6.723131 ATTGTTCTTCTTACCTAAACTCGC 57.277 37.500 0.00 0.00 0.00 5.03
3040 5595 3.935203 GTCGCTTCAGAAGGAAATCATCA 59.065 43.478 12.30 0.00 34.44 3.07
3043 5598 4.573607 CGCTTCAGAAGGAAATCATCATCA 59.426 41.667 12.30 0.00 34.44 3.07
3111 5666 2.637872 CTCCTCCACCCTTTGAAGTGTA 59.362 50.000 0.00 0.00 31.88 2.90
3147 5702 1.808945 CATGCTCGTTTTTGCTCCTCT 59.191 47.619 0.00 0.00 0.00 3.69
3487 6092 4.368067 AGCTGTAATGTTAAGTAGGGGGA 58.632 43.478 0.00 0.00 0.00 4.81
3613 6219 5.869888 GCCATGATAATCCCTAGTACTTTCG 59.130 44.000 0.00 0.00 0.00 3.46
3631 6237 2.505405 TCGTCTGCACAGTTACTCTCT 58.495 47.619 0.00 0.00 0.00 3.10
3641 6247 2.029828 CAGTTACTCTCTGGACGCTGTT 60.030 50.000 0.00 0.00 0.00 3.16
3656 6262 7.302524 TGGACGCTGTTTGTTCTAAATAAATC 58.697 34.615 0.00 0.00 0.00 2.17
3725 6339 5.121811 GCTCTCAATGAAGATTGCTCCTAA 58.878 41.667 0.00 0.00 39.16 2.69
3762 6376 5.883673 GGCTGGTATTCCTATGTAAAACACA 59.116 40.000 0.00 0.00 36.69 3.72
3800 6414 4.000988 GGCATCGAAAGGTTTGAACTAGA 58.999 43.478 0.00 0.00 0.00 2.43
3830 6444 0.229753 CGTTCGTAGGATCGCATTGC 59.770 55.000 0.00 0.00 0.00 3.56
3884 6498 3.051081 CTGTAGGCAGCTTCTCAACTT 57.949 47.619 0.00 0.00 35.77 2.66
3899 6513 0.240945 AACTTTGCACATACCGCAGC 59.759 50.000 0.00 0.00 41.18 5.25
3940 6554 8.533657 AGAGATGGAGATAGAGAAATAGCAATG 58.466 37.037 0.00 0.00 0.00 2.82
3941 6555 7.104939 AGATGGAGATAGAGAAATAGCAATGC 58.895 38.462 0.00 0.00 0.00 3.56
3942 6556 6.430962 TGGAGATAGAGAAATAGCAATGCT 57.569 37.500 13.92 13.92 43.41 3.79
3943 6557 6.462500 TGGAGATAGAGAAATAGCAATGCTC 58.538 40.000 12.53 0.00 40.44 4.26
3944 6558 6.042437 TGGAGATAGAGAAATAGCAATGCTCA 59.958 38.462 12.53 0.00 40.44 4.26
3945 6559 7.104939 GGAGATAGAGAAATAGCAATGCTCAT 58.895 38.462 12.53 0.00 40.44 2.90
3946 6560 7.607223 GGAGATAGAGAAATAGCAATGCTCATT 59.393 37.037 12.53 8.17 40.44 2.57
3947 6561 8.921353 AGATAGAGAAATAGCAATGCTCATTT 57.079 30.769 12.53 15.30 40.44 2.32
3948 6562 9.352191 AGATAGAGAAATAGCAATGCTCATTTT 57.648 29.630 12.53 10.58 40.44 1.82
3951 6565 7.424001 AGAGAAATAGCAATGCTCATTTTAGC 58.576 34.615 12.53 9.35 40.44 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 1.379146 GGCCGTTTCCTCTTTCCCT 59.621 57.895 0.00 0.00 0.00 4.20
98 99 2.671177 CGCCTTTGCTCACCGTCAG 61.671 63.158 0.00 0.00 34.43 3.51
99 100 2.664851 CGCCTTTGCTCACCGTCA 60.665 61.111 0.00 0.00 34.43 4.35
102 103 3.121030 CTCCGCCTTTGCTCACCG 61.121 66.667 0.00 0.00 34.43 4.94
227 2221 4.785453 CCCTCAGTCCTTGCCGCC 62.785 72.222 0.00 0.00 0.00 6.13
233 2227 0.338120 CTCTCCCTCCCTCAGTCCTT 59.662 60.000 0.00 0.00 0.00 3.36
386 2392 1.731098 CGCACGTAATTTTTCTGCCCC 60.731 52.381 0.00 0.00 0.00 5.80
393 2400 0.669077 TGCCACCGCACGTAATTTTT 59.331 45.000 0.00 0.00 41.12 1.94
458 2465 0.673956 CTGGAGAGTCTCGTCCGTCA 60.674 60.000 13.97 4.42 35.37 4.35
523 2530 1.085893 GCAATTTGGATTTTGGGCCG 58.914 50.000 0.00 0.00 0.00 6.13
524 2531 2.086094 CAGCAATTTGGATTTTGGGCC 58.914 47.619 0.00 0.00 0.00 5.80
525 2532 2.485038 CACAGCAATTTGGATTTTGGGC 59.515 45.455 0.00 0.00 0.00 5.36
526 2533 4.005487 TCACAGCAATTTGGATTTTGGG 57.995 40.909 0.00 0.00 0.00 4.12
527 2534 5.992729 CTTTCACAGCAATTTGGATTTTGG 58.007 37.500 0.00 0.00 0.00 3.28
537 2544 9.088566 ATGTTCCTACAAGCTTTCACAGCAATT 62.089 37.037 0.00 0.00 43.07 2.32
538 2545 7.694695 ATGTTCCTACAAGCTTTCACAGCAAT 61.695 38.462 0.00 0.00 43.07 3.56
539 2546 6.440052 ATGTTCCTACAAGCTTTCACAGCAA 61.440 40.000 0.00 0.00 43.07 3.91
540 2547 4.987926 ATGTTCCTACAAGCTTTCACAGCA 60.988 41.667 0.00 0.00 43.07 4.41
541 2548 3.503748 ATGTTCCTACAAGCTTTCACAGC 59.496 43.478 0.00 0.00 41.83 4.40
542 2549 4.154918 GGATGTTCCTACAAGCTTTCACAG 59.845 45.833 0.00 0.00 37.91 3.66
543 2550 4.072131 GGATGTTCCTACAAGCTTTCACA 58.928 43.478 0.00 0.00 37.91 3.58
544 2551 4.686839 GGATGTTCCTACAAGCTTTCAC 57.313 45.455 0.00 0.00 37.91 3.18
556 2563 7.568366 ATCAAGAGATAAGAGAAGGATGTTCCT 59.432 37.037 0.00 0.00 39.95 3.36
557 2564 7.118496 TCAAGAGATAAGAGAAGGATGTTCC 57.882 40.000 0.00 0.00 36.58 3.62
558 2565 7.656948 CCATCAAGAGATAAGAGAAGGATGTTC 59.343 40.741 0.00 0.00 31.88 3.18
559 2566 7.507829 CCATCAAGAGATAAGAGAAGGATGTT 58.492 38.462 0.00 0.00 31.88 2.71
560 2567 6.464180 GCCATCAAGAGATAAGAGAAGGATGT 60.464 42.308 0.00 0.00 31.88 3.06
561 2568 5.933463 GCCATCAAGAGATAAGAGAAGGATG 59.067 44.000 0.00 0.00 31.88 3.51
562 2569 5.012975 GGCCATCAAGAGATAAGAGAAGGAT 59.987 44.000 0.00 0.00 31.88 3.24
563 2570 4.346418 GGCCATCAAGAGATAAGAGAAGGA 59.654 45.833 0.00 0.00 31.88 3.36
564 2571 4.347583 AGGCCATCAAGAGATAAGAGAAGG 59.652 45.833 5.01 0.00 31.88 3.46
565 2572 5.549742 AGGCCATCAAGAGATAAGAGAAG 57.450 43.478 5.01 0.00 31.88 2.85
566 2573 7.623999 ATTAGGCCATCAAGAGATAAGAGAA 57.376 36.000 5.01 0.00 31.88 2.87
567 2574 8.756927 CATATTAGGCCATCAAGAGATAAGAGA 58.243 37.037 5.01 0.00 31.88 3.10
568 2575 7.986320 CCATATTAGGCCATCAAGAGATAAGAG 59.014 40.741 5.01 0.00 31.88 2.85
569 2576 7.459125 ACCATATTAGGCCATCAAGAGATAAGA 59.541 37.037 5.01 0.00 31.88 2.10
570 2577 7.628234 ACCATATTAGGCCATCAAGAGATAAG 58.372 38.462 5.01 0.00 31.88 1.73
571 2578 7.574021 ACCATATTAGGCCATCAAGAGATAA 57.426 36.000 5.01 0.00 31.88 1.75
572 2579 7.397221 CAACCATATTAGGCCATCAAGAGATA 58.603 38.462 5.01 0.00 31.88 1.98
573 2580 6.243900 CAACCATATTAGGCCATCAAGAGAT 58.756 40.000 5.01 0.00 33.87 2.75
574 2581 5.456619 CCAACCATATTAGGCCATCAAGAGA 60.457 44.000 5.01 0.00 0.00 3.10
575 2582 4.763793 CCAACCATATTAGGCCATCAAGAG 59.236 45.833 5.01 0.00 0.00 2.85
576 2583 4.728772 CCAACCATATTAGGCCATCAAGA 58.271 43.478 5.01 0.00 0.00 3.02
577 2584 3.256631 GCCAACCATATTAGGCCATCAAG 59.743 47.826 5.01 0.00 41.25 3.02
578 2585 3.230134 GCCAACCATATTAGGCCATCAA 58.770 45.455 5.01 0.00 41.25 2.57
579 2586 2.813726 CGCCAACCATATTAGGCCATCA 60.814 50.000 5.01 0.00 44.18 3.07
580 2587 1.812571 CGCCAACCATATTAGGCCATC 59.187 52.381 5.01 0.00 44.18 3.51
581 2588 1.423541 TCGCCAACCATATTAGGCCAT 59.576 47.619 5.01 0.00 44.18 4.40
582 2589 0.840617 TCGCCAACCATATTAGGCCA 59.159 50.000 5.01 0.00 44.18 5.36
583 2590 1.202770 ACTCGCCAACCATATTAGGCC 60.203 52.381 0.00 0.00 44.18 5.19
584 2591 2.143925 GACTCGCCAACCATATTAGGC 58.856 52.381 0.00 0.00 43.61 3.93
585 2592 2.550208 GGGACTCGCCAACCATATTAGG 60.550 54.545 0.00 0.00 38.95 2.69
586 2593 2.368875 AGGGACTCGCCAACCATATTAG 59.631 50.000 0.00 0.00 38.95 1.73
587 2594 2.404559 AGGGACTCGCCAACCATATTA 58.595 47.619 0.00 0.00 38.95 0.98
588 2595 1.213296 AGGGACTCGCCAACCATATT 58.787 50.000 0.00 0.00 38.95 1.28
589 2596 1.692519 GTAGGGACTCGCCAACCATAT 59.307 52.381 0.00 0.00 41.75 1.78
590 2597 1.117150 GTAGGGACTCGCCAACCATA 58.883 55.000 0.00 0.00 41.75 2.74
591 2598 0.907704 TGTAGGGACTCGCCAACCAT 60.908 55.000 0.00 0.00 41.75 3.55
592 2599 0.907704 ATGTAGGGACTCGCCAACCA 60.908 55.000 0.00 0.00 41.75 3.67
593 2600 0.179081 GATGTAGGGACTCGCCAACC 60.179 60.000 0.00 0.00 41.75 3.77
594 2601 0.527817 CGATGTAGGGACTCGCCAAC 60.528 60.000 0.00 0.00 41.75 3.77
595 2602 1.672854 CCGATGTAGGGACTCGCCAA 61.673 60.000 0.00 0.00 41.75 4.52
596 2603 2.125326 CCGATGTAGGGACTCGCCA 61.125 63.158 0.00 0.00 41.75 5.69
597 2604 2.728817 CCGATGTAGGGACTCGCC 59.271 66.667 0.00 0.00 41.75 5.54
605 2612 2.189521 GTGCCCACCCGATGTAGG 59.810 66.667 0.00 0.00 0.00 3.18
613 2620 4.603535 ACAAGCCTGTGCCCACCC 62.604 66.667 0.00 0.00 38.69 4.61
633 2640 2.788640 GCCATACCGGGCGTGAGTA 61.789 63.158 6.32 0.00 45.40 2.59
634 2641 4.157120 GCCATACCGGGCGTGAGT 62.157 66.667 6.32 0.00 45.40 3.41
671 2685 2.917227 TCGTGCTGGCCTCTCACA 60.917 61.111 18.02 2.42 0.00 3.58
786 2801 2.443390 GAATGCAGCTGGGCCCAT 60.443 61.111 28.82 9.02 0.00 4.00
844 2859 1.228862 GGCTTGGCCTTTCCCTCAA 60.229 57.895 3.32 0.00 46.69 3.02
845 2860 2.440599 GGCTTGGCCTTTCCCTCA 59.559 61.111 3.32 0.00 46.69 3.86
921 2936 1.900486 CTACCAGTCTCCCCGAGTTTT 59.100 52.381 0.00 0.00 0.00 2.43
927 2942 1.898154 CCAACTACCAGTCTCCCCG 59.102 63.158 0.00 0.00 0.00 5.73
1132 3147 3.128349 CGGGGGTTAACAATATGTCGAG 58.872 50.000 8.10 0.00 0.00 4.04
1151 3166 3.853104 TGGTACAAAGATCTGGCGG 57.147 52.632 0.00 0.00 31.92 6.13
1215 3230 0.460987 GAGCCACATCTGAACGGGAG 60.461 60.000 0.00 0.00 0.00 4.30
1216 3231 1.596934 GAGCCACATCTGAACGGGA 59.403 57.895 0.00 0.00 0.00 5.14
1217 3232 1.450312 GGAGCCACATCTGAACGGG 60.450 63.158 0.00 0.00 0.00 5.28
1218 3233 1.811266 CGGAGCCACATCTGAACGG 60.811 63.158 0.00 0.00 0.00 4.44
1302 3317 1.262417 CGCTTAATCATGATGCTGCGT 59.738 47.619 26.84 9.87 37.80 5.24
1527 3544 0.387622 CAGCACAAAAGCCACATCCG 60.388 55.000 0.00 0.00 34.23 4.18
1543 3577 1.079057 GACCCTTCCGAACTCCAGC 60.079 63.158 0.00 0.00 0.00 4.85
1618 3652 0.902531 TGATCCCACGAAAGAGACCC 59.097 55.000 0.00 0.00 0.00 4.46
1640 3974 3.013276 TCGAACACGATGATATCCAGC 57.987 47.619 0.00 0.00 0.00 4.85
1829 4172 3.119459 ACGCACACAAGGAGTACTAGATG 60.119 47.826 0.00 0.00 0.00 2.90
2027 4501 2.801077 AGTATTTTGGAACGGAGGGG 57.199 50.000 0.00 0.00 0.00 4.79
2048 4522 4.620184 CCTTAGGACAAACGTAGAAGTTCG 59.380 45.833 0.00 0.00 32.43 3.95
2071 4545 7.713764 ATTGGTCAAACTTACAGAAATTTGC 57.286 32.000 0.00 0.00 33.09 3.68
2302 4792 3.375610 ACGGCGCACAAATTCACAATATA 59.624 39.130 10.83 0.00 0.00 0.86
2345 4835 6.565999 GCGAAGGTATAACCAAAGCATATGAC 60.566 42.308 6.97 0.00 41.95 3.06
2346 4836 5.468746 GCGAAGGTATAACCAAAGCATATGA 59.531 40.000 6.97 0.00 41.95 2.15
2375 4865 8.164070 ACAGAAATACATACAAAGAGGTTCCTT 58.836 33.333 0.00 0.00 0.00 3.36
2443 4935 4.812626 CCTCAAGCAAAGAACTGCAAAATT 59.187 37.500 0.00 0.00 45.18 1.82
2502 4994 1.068948 TGAATTTTGGGACGGAGGGA 58.931 50.000 0.00 0.00 0.00 4.20
2503 4995 1.750778 CATGAATTTTGGGACGGAGGG 59.249 52.381 0.00 0.00 0.00 4.30
2504 4996 2.423538 GACATGAATTTTGGGACGGAGG 59.576 50.000 0.00 0.00 0.00 4.30
2505 4997 3.347216 AGACATGAATTTTGGGACGGAG 58.653 45.455 0.00 0.00 0.00 4.63
2506 4998 3.433306 AGACATGAATTTTGGGACGGA 57.567 42.857 0.00 0.00 0.00 4.69
2507 4999 4.941263 TCTAAGACATGAATTTTGGGACGG 59.059 41.667 0.00 0.00 0.00 4.79
2508 5000 6.683974 ATCTAAGACATGAATTTTGGGACG 57.316 37.500 0.00 0.00 0.00 4.79
2509 5001 8.306761 ACAAATCTAAGACATGAATTTTGGGAC 58.693 33.333 0.00 0.00 0.00 4.46
2510 5002 8.421249 ACAAATCTAAGACATGAATTTTGGGA 57.579 30.769 0.00 0.00 0.00 4.37
2511 5003 8.526147 AGACAAATCTAAGACATGAATTTTGGG 58.474 33.333 0.00 0.00 31.46 4.12
2518 5010 9.952188 CGTATCTAGACAAATCTAAGACATGAA 57.048 33.333 0.00 0.00 36.98 2.57
2519 5011 8.568794 CCGTATCTAGACAAATCTAAGACATGA 58.431 37.037 0.00 0.00 36.98 3.07
2520 5012 8.568794 TCCGTATCTAGACAAATCTAAGACATG 58.431 37.037 0.00 0.00 36.98 3.21
2521 5013 8.693120 TCCGTATCTAGACAAATCTAAGACAT 57.307 34.615 0.00 0.00 36.98 3.06
2522 5014 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
2523 5015 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
2524 5016 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
2542 5034 9.516546 TCATGTCTTAGTATTAGATACATCCGT 57.483 33.333 0.00 0.00 38.21 4.69
2543 5035 9.776158 GTCATGTCTTAGTATTAGATACATCCG 57.224 37.037 0.00 0.00 38.21 4.18
2554 5046 9.988815 GGATGTATCAAGTCATGTCTTAGTATT 57.011 33.333 4.85 0.00 0.00 1.89
2555 5047 9.147732 TGGATGTATCAAGTCATGTCTTAGTAT 57.852 33.333 4.85 3.09 0.00 2.12
2556 5048 8.533569 TGGATGTATCAAGTCATGTCTTAGTA 57.466 34.615 4.85 0.00 0.00 1.82
2557 5049 7.423844 TGGATGTATCAAGTCATGTCTTAGT 57.576 36.000 4.85 0.52 0.00 2.24
2560 5052 9.857656 AAATATGGATGTATCAAGTCATGTCTT 57.142 29.630 0.00 0.00 0.00 3.01
2578 5070 9.093970 CGTGTCTTACATTTGTCTAAATATGGA 57.906 33.333 0.00 0.00 34.81 3.41
2579 5071 9.093970 TCGTGTCTTACATTTGTCTAAATATGG 57.906 33.333 0.00 0.00 34.81 2.74
2585 5077 9.658475 CAAAATTCGTGTCTTACATTTGTCTAA 57.342 29.630 0.00 0.00 0.00 2.10
2586 5078 8.286800 CCAAAATTCGTGTCTTACATTTGTCTA 58.713 33.333 0.00 0.00 0.00 2.59
2587 5079 7.138736 CCAAAATTCGTGTCTTACATTTGTCT 58.861 34.615 0.00 0.00 0.00 3.41
2588 5080 6.362283 CCCAAAATTCGTGTCTTACATTTGTC 59.638 38.462 0.00 0.00 0.00 3.18
2589 5081 6.039941 TCCCAAAATTCGTGTCTTACATTTGT 59.960 34.615 0.00 0.00 0.00 2.83
2590 5082 6.362283 GTCCCAAAATTCGTGTCTTACATTTG 59.638 38.462 0.00 0.00 0.00 2.32
2591 5083 6.443792 GTCCCAAAATTCGTGTCTTACATTT 58.556 36.000 0.00 0.00 0.00 2.32
2592 5084 5.334569 CGTCCCAAAATTCGTGTCTTACATT 60.335 40.000 0.00 0.00 0.00 2.71
2593 5085 4.153475 CGTCCCAAAATTCGTGTCTTACAT 59.847 41.667 0.00 0.00 0.00 2.29
2594 5086 3.495377 CGTCCCAAAATTCGTGTCTTACA 59.505 43.478 0.00 0.00 0.00 2.41
2595 5087 3.120442 CCGTCCCAAAATTCGTGTCTTAC 60.120 47.826 0.00 0.00 0.00 2.34
2596 5088 3.068560 CCGTCCCAAAATTCGTGTCTTA 58.931 45.455 0.00 0.00 0.00 2.10
2597 5089 1.877443 CCGTCCCAAAATTCGTGTCTT 59.123 47.619 0.00 0.00 0.00 3.01
2598 5090 1.071071 TCCGTCCCAAAATTCGTGTCT 59.929 47.619 0.00 0.00 0.00 3.41
2599 5091 1.463444 CTCCGTCCCAAAATTCGTGTC 59.537 52.381 0.00 0.00 0.00 3.67
2600 5092 1.519408 CTCCGTCCCAAAATTCGTGT 58.481 50.000 0.00 0.00 0.00 4.49
2601 5093 0.802494 CCTCCGTCCCAAAATTCGTG 59.198 55.000 0.00 0.00 0.00 4.35
2602 5094 0.322187 CCCTCCGTCCCAAAATTCGT 60.322 55.000 0.00 0.00 0.00 3.85
2603 5095 0.035820 TCCCTCCGTCCCAAAATTCG 60.036 55.000 0.00 0.00 0.00 3.34
2604 5096 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2605 5097 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2606 5098 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2607 5099 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2608 5100 1.252904 CGTACTCCCTCCGTCCCAAA 61.253 60.000 0.00 0.00 0.00 3.28
2609 5101 1.679977 CGTACTCCCTCCGTCCCAA 60.680 63.158 0.00 0.00 0.00 4.12
2610 5102 2.044650 CGTACTCCCTCCGTCCCA 60.045 66.667 0.00 0.00 0.00 4.37
2611 5103 1.823041 CTCGTACTCCCTCCGTCCC 60.823 68.421 0.00 0.00 0.00 4.46
2612 5104 0.679321 AACTCGTACTCCCTCCGTCC 60.679 60.000 0.00 0.00 0.00 4.79
2613 5105 1.939255 CTAACTCGTACTCCCTCCGTC 59.061 57.143 0.00 0.00 0.00 4.79
2614 5106 1.556911 TCTAACTCGTACTCCCTCCGT 59.443 52.381 0.00 0.00 0.00 4.69
2615 5107 1.939255 GTCTAACTCGTACTCCCTCCG 59.061 57.143 0.00 0.00 0.00 4.63
2616 5108 2.944349 CTGTCTAACTCGTACTCCCTCC 59.056 54.545 0.00 0.00 0.00 4.30
2617 5109 3.374678 CACTGTCTAACTCGTACTCCCTC 59.625 52.174 0.00 0.00 0.00 4.30
2618 5110 3.008813 TCACTGTCTAACTCGTACTCCCT 59.991 47.826 0.00 0.00 0.00 4.20
2619 5111 3.341823 TCACTGTCTAACTCGTACTCCC 58.658 50.000 0.00 0.00 0.00 4.30
2620 5112 4.634883 TCATCACTGTCTAACTCGTACTCC 59.365 45.833 0.00 0.00 0.00 3.85
2621 5113 5.220700 CCTCATCACTGTCTAACTCGTACTC 60.221 48.000 0.00 0.00 0.00 2.59
2622 5114 4.636648 CCTCATCACTGTCTAACTCGTACT 59.363 45.833 0.00 0.00 0.00 2.73
2623 5115 4.395542 ACCTCATCACTGTCTAACTCGTAC 59.604 45.833 0.00 0.00 0.00 3.67
2624 5116 4.586884 ACCTCATCACTGTCTAACTCGTA 58.413 43.478 0.00 0.00 0.00 3.43
2625 5117 3.422796 ACCTCATCACTGTCTAACTCGT 58.577 45.455 0.00 0.00 0.00 4.18
2626 5118 4.169508 CAACCTCATCACTGTCTAACTCG 58.830 47.826 0.00 0.00 0.00 4.18
2643 5135 7.175641 CCTGTTTCTTGAAATCATCTACAACCT 59.824 37.037 0.00 0.00 0.00 3.50
2709 5201 7.164230 ACCTGACAAATCAAACAAAGTTGTA 57.836 32.000 0.00 0.00 41.31 2.41
2717 5209 4.277476 ACAGGAACCTGACAAATCAAACA 58.723 39.130 25.03 0.00 46.30 2.83
2792 5284 4.956085 TCATCGATAATTGGTGACCGATT 58.044 39.130 20.25 20.25 40.42 3.34
2796 5288 5.354234 ACAAACTCATCGATAATTGGTGACC 59.646 40.000 0.00 0.00 0.00 4.02
2799 5291 8.196802 TCTTACAAACTCATCGATAATTGGTG 57.803 34.615 0.00 0.00 0.00 4.17
2838 5330 5.456921 ACTAGATCCATGTTTTCCCACAT 57.543 39.130 0.00 0.00 37.93 3.21
2868 5366 4.999310 TCATATAGTGAGGGGAATCGTCT 58.001 43.478 0.00 0.00 31.80 4.18
2996 5551 2.099263 CACCTGGTAGACATAGTCCGTG 59.901 54.545 0.00 0.00 32.18 4.94
3040 5595 0.955178 CCCTCTCGTACGCATCTGAT 59.045 55.000 11.24 0.00 0.00 2.90
3043 5598 0.179026 TAGCCCTCTCGTACGCATCT 60.179 55.000 11.24 4.21 0.00 2.90
3147 5702 2.741878 GCTTGCATTAAGTAGAGCGGGA 60.742 50.000 0.00 0.00 38.70 5.14
3292 5858 4.399934 TCTCTACACATAACCATACACGCA 59.600 41.667 0.00 0.00 0.00 5.24
3506 6112 7.839907 ACACCATCAAGCAAAATTACACATAT 58.160 30.769 0.00 0.00 0.00 1.78
3509 6115 5.528043 ACACCATCAAGCAAAATTACACA 57.472 34.783 0.00 0.00 0.00 3.72
3613 6219 2.558795 TCCAGAGAGTAACTGTGCAGAC 59.441 50.000 6.17 0.00 38.38 3.51
3631 6237 6.621316 TTTATTTAGAACAAACAGCGTCCA 57.379 33.333 0.00 0.00 0.00 4.02
3656 6262 5.872617 TCAGATGTTACGGACCATTTACAAG 59.127 40.000 0.00 0.00 0.00 3.16
3725 6339 2.108976 CAGCCACTGACACGGTGT 59.891 61.111 14.66 14.66 38.92 4.16
3762 6376 7.595819 TTCGATGCCCCAATTTAAATCTTAT 57.404 32.000 0.10 0.00 0.00 1.73
3763 6377 7.411486 TTTCGATGCCCCAATTTAAATCTTA 57.589 32.000 0.10 0.00 0.00 2.10
3830 6444 2.432628 GCCGGGTGAGTCAACTCG 60.433 66.667 8.36 9.87 45.72 4.18
3884 6498 4.071459 TTGCTGCGGTATGTGCAA 57.929 50.000 0.00 0.00 42.70 4.08
3899 6513 4.216902 TCCATCTCTGAACTGTTTGCATTG 59.783 41.667 0.00 0.00 0.00 2.82
3940 6554 5.644644 ACACTAAGCATTGCTAAAATGAGC 58.355 37.500 12.39 0.00 38.25 4.26
3941 6555 7.412853 CCTACACTAAGCATTGCTAAAATGAG 58.587 38.462 12.39 6.12 38.25 2.90
3942 6556 6.318648 CCCTACACTAAGCATTGCTAAAATGA 59.681 38.462 12.39 0.00 38.25 2.57
3943 6557 6.318648 TCCCTACACTAAGCATTGCTAAAATG 59.681 38.462 12.39 10.51 38.25 2.32
3944 6558 6.423182 TCCCTACACTAAGCATTGCTAAAAT 58.577 36.000 12.39 0.00 38.25 1.82
3945 6559 5.811190 TCCCTACACTAAGCATTGCTAAAA 58.189 37.500 12.39 0.00 38.25 1.52
3946 6560 5.429681 TCCCTACACTAAGCATTGCTAAA 57.570 39.130 12.39 2.49 38.25 1.85
3947 6561 5.429681 TTCCCTACACTAAGCATTGCTAA 57.570 39.130 12.39 0.00 38.25 3.09
3948 6562 5.188948 TCTTTCCCTACACTAAGCATTGCTA 59.811 40.000 12.39 0.00 38.25 3.49
3949 6563 4.019321 TCTTTCCCTACACTAAGCATTGCT 60.019 41.667 5.03 5.03 42.56 3.91
3950 6564 4.261801 TCTTTCCCTACACTAAGCATTGC 58.738 43.478 0.00 0.00 0.00 3.56
3951 6565 6.817765 TTTCTTTCCCTACACTAAGCATTG 57.182 37.500 0.00 0.00 0.00 2.82
3952 6566 6.948309 ACATTTCTTTCCCTACACTAAGCATT 59.052 34.615 0.00 0.00 0.00 3.56
3953 6567 6.485171 ACATTTCTTTCCCTACACTAAGCAT 58.515 36.000 0.00 0.00 0.00 3.79
3954 6568 5.876357 ACATTTCTTTCCCTACACTAAGCA 58.124 37.500 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.