Multiple sequence alignment - TraesCS5D01G408300

Loading Multiple Alignment...

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 TraesCS5D01G408300 chr5D 100.000 2697 0 0 1 2697 472991511 472994207 0.000000e+00 4981
1 TraesCS5D01G408300 chr5D 100.000 1776 0 0 2968 4743 472994478 472996253 0.000000e+00 3280
2 TraesCS5D01G408300 chr5A 89.242 1134 66 20 674 1785 592617661 592618760 0.000000e+00 1367
3 TraesCS5D01G408300 chr5A 93.622 878 39 8 2968 3828 592619776 592620653 0.000000e+00 1295
4 TraesCS5D01G408300 chr5A 93.445 595 35 3 1870 2460 592619055 592619649 0.000000e+00 880
5 TraesCS5D01G408300 chr5A 89.170 277 24 4 4235 4508 592621444 592621717 1.630000e-89 340
6 TraesCS5D01G408300 chr5A 87.500 192 7 8 4553 4743 592621713 592621888 6.220000e-49 206
7 TraesCS5D01G408300 chr5A 89.247 93 9 1 4146 4237 592621320 592621412 1.080000e-21 115
8 TraesCS5D01G408300 chr5B 94.499 709 27 3 2970 3666 580286076 580286784 0.000000e+00 1083
9 TraesCS5D01G408300 chr5B 93.916 526 21 3 819 1338 580279439 580279959 0.000000e+00 784
10 TraesCS5D01G408300 chr5B 94.077 439 17 4 1333 1771 580284447 580284876 0.000000e+00 658
11 TraesCS5D01G408300 chr5B 95.599 409 18 0 66 474 580276889 580277297 0.000000e+00 656
12 TraesCS5D01G408300 chr5B 92.675 314 20 2 1870 2181 580285273 580285585 2.600000e-122 449
13 TraesCS5D01G408300 chr5B 84.765 361 37 10 3883 4237 580287817 580288165 3.510000e-91 346
14 TraesCS5D01G408300 chr5B 88.321 274 10 10 548 821 580277748 580277999 4.610000e-80 309
15 TraesCS5D01G408300 chr5B 85.906 298 24 11 4235 4528 580288200 580288483 7.710000e-78 302
16 TraesCS5D01G408300 chr5B 83.986 281 18 2 2180 2457 580285679 580285935 1.320000e-60 244
17 TraesCS5D01G408300 chr5B 90.805 174 13 1 3658 3828 580286963 580287136 3.690000e-56 230
18 TraesCS5D01G408300 chr5B 92.405 158 11 1 4587 4743 580288510 580288667 1.720000e-54 224
19 TraesCS5D01G408300 chr5B 97.143 70 2 0 1 70 580274580 580274649 8.340000e-23 119
20 TraesCS5D01G408300 chr7D 80.934 792 141 8 2974 3758 448845688 448846476 6.740000e-173 617
21 TraesCS5D01G408300 chr7D 76.606 996 124 64 788 1713 448843526 448844482 9.360000e-122 448
22 TraesCS5D01G408300 chr7D 87.281 228 19 4 2227 2444 448845166 448845393 7.880000e-63 252
23 TraesCS5D01G408300 chr7A 80.591 778 145 5 2986 3758 547119581 547118805 3.160000e-166 595
24 TraesCS5D01G408300 chr7A 81.370 467 69 15 1044 1501 547121215 547120758 9.700000e-97 364
25 TraesCS5D01G408300 chr7B 80.101 789 148 7 2974 3758 466664450 466665233 3.180000e-161 579
26 TraesCS5D01G408300 chr7B 78.213 817 163 12 2974 3783 466282017 466282825 4.230000e-140 508
27 TraesCS5D01G408300 chr7B 79.665 477 63 24 1144 1612 466661121 466661571 3.560000e-81 313


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 TraesCS5D01G408300 chr5D 472991511 472996253 4742 False 4130.5 4981 100.00000 1 4743 2 chr5D.!!$F1 4742
1 TraesCS5D01G408300 chr5A 592617661 592621888 4227 False 700.5 1367 90.37100 674 4743 6 chr5A.!!$F1 4069
2 TraesCS5D01G408300 chr5B 580274580 580279959 5379 False 467.0 784 93.74475 1 1338 4 chr5B.!!$F1 1337
3 TraesCS5D01G408300 chr5B 580284447 580288667 4220 False 442.0 1083 89.88975 1333 4743 8 chr5B.!!$F2 3410
4 TraesCS5D01G408300 chr7D 448843526 448846476 2950 False 439.0 617 81.60700 788 3758 3 chr7D.!!$F1 2970
5 TraesCS5D01G408300 chr7A 547118805 547121215 2410 True 479.5 595 80.98050 1044 3758 2 chr7A.!!$R1 2714
6 TraesCS5D01G408300 chr7B 466282017 466282825 808 False 508.0 508 78.21300 2974 3783 1 chr7B.!!$F1 809
7 TraesCS5D01G408300 chr7B 466661121 466665233 4112 False 446.0 579 79.88300 1144 3758 2 chr7B.!!$F2 2614

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
107 2352 1.202405 CGAAGCCAAACCTTGCAGTTT 60.202 47.619 0.00 0.0 40.57 2.66 F
1308 5453 0.824595 ATGCAGCTGACCAAGTGCAA 60.825 50.000 20.43 0.0 42.33 4.08 F
1579 5725 0.473755 AGACAACTGACATGGCCACA 59.526 50.000 8.16 0.0 0.00 4.17 F
2683 9306 0.035317 ACGTCTGATCTGCAAGCCAA 59.965 50.000 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1326 5471 0.249741 ACCCGTCTCCGAACACAAAG 60.250 55.0 0.00 0.00 35.63 2.77 R
2664 9287 0.035317 TTGGCTTGCAGATCAGACGT 59.965 50.0 0.00 0.00 0.00 4.34 R
3323 9952 0.669318 GATGCCGTCGTTGAACTCCA 60.669 55.0 0.00 0.00 0.00 3.86 R
4393 11945 0.175760 TTGGGAGTGCAGTCGATAGC 59.824 55.0 15.26 5.23 0.00 2.97 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
57 58 6.539826 CCTTGCATAGATTCAGTAACATCACA 59.460 38.462 0.00 0.00 0.00 3.58
58 59 6.908870 TGCATAGATTCAGTAACATCACAC 57.091 37.500 0.00 0.00 0.00 3.82
107 2352 1.202405 CGAAGCCAAACCTTGCAGTTT 60.202 47.619 0.00 0.00 40.57 2.66
114 2359 2.256117 AACCTTGCAGTTTAGAGCGT 57.744 45.000 0.00 0.00 0.00 5.07
176 2421 5.772672 TCACAAGTGTTGGCACCTAATTAAT 59.227 36.000 0.00 0.00 46.35 1.40
179 2424 5.914898 AGTGTTGGCACCTAATTAATTCC 57.085 39.130 3.39 0.00 46.35 3.01
192 2437 5.836821 AATTAATTCCGAGGCTCTTTTCC 57.163 39.130 13.50 0.00 0.00 3.13
207 2452 5.505173 TCTTTTCCTGAAAGAGCTTTGTG 57.495 39.130 0.00 0.00 46.69 3.33
231 2476 4.755123 ACTTACTCTTTGGGAATGTTGTCG 59.245 41.667 0.00 0.00 0.00 4.35
293 2538 7.548097 AGTAGTCTGTATATGGTCTGTTTGTG 58.452 38.462 0.00 0.00 0.00 3.33
302 2547 2.162608 TGGTCTGTTTGTGTCGGTTTTG 59.837 45.455 0.00 0.00 0.00 2.44
313 2558 1.300311 CGGTTTTGGCCCGGTTTTC 60.300 57.895 0.00 0.00 41.78 2.29
325 2570 4.202080 GGCCCGGTTTTCTATTCATTAACC 60.202 45.833 0.00 0.00 35.91 2.85
355 2600 8.438513 CAATTATATTCTGTAACGATGAGGCTG 58.561 37.037 0.00 0.00 0.00 4.85
359 2604 2.362397 TCTGTAACGATGAGGCTGATCC 59.638 50.000 8.41 0.00 0.00 3.36
460 2705 5.924356 TGACTAGTCCAGAAAACAATGTCA 58.076 37.500 20.11 0.00 0.00 3.58
461 2706 6.353323 TGACTAGTCCAGAAAACAATGTCAA 58.647 36.000 20.11 0.00 0.00 3.18
494 3001 3.618351 AGGATGCAGGTTGAGATTTGAG 58.382 45.455 0.00 0.00 0.00 3.02
528 3035 6.879458 AGTCATGCTTAGGTTTTAAGATTCGT 59.121 34.615 0.00 0.00 0.00 3.85
544 3051 4.391216 AGATTCGTGATGCTGACTTTTGAG 59.609 41.667 0.00 0.00 0.00 3.02
569 3191 1.644786 GGTGACAACGCATACAGGGC 61.645 60.000 0.00 0.00 0.00 5.19
574 3196 1.892474 ACAACGCATACAGGGCAAATT 59.108 42.857 0.00 0.00 0.00 1.82
615 3237 8.827677 GTTTATATTAGATGACGACTTTTGGCT 58.172 33.333 0.00 0.00 0.00 4.75
641 3263 7.639113 TTATATCCGTTTTTCAGCCTGAATT 57.361 32.000 8.18 0.00 36.11 2.17
649 3271 7.148755 CCGTTTTTCAGCCTGAATTTAAATGAG 60.149 37.037 17.75 8.78 36.11 2.90
655 3277 8.816640 TCAGCCTGAATTTAAATGAGAAAAAC 57.183 30.769 0.39 0.00 0.00 2.43
656 3278 7.872483 TCAGCCTGAATTTAAATGAGAAAAACC 59.128 33.333 0.39 0.00 0.00 3.27
657 3279 7.118245 CAGCCTGAATTTAAATGAGAAAAACCC 59.882 37.037 0.39 0.00 0.00 4.11
658 3280 6.934083 GCCTGAATTTAAATGAGAAAAACCCA 59.066 34.615 0.39 0.00 0.00 4.51
659 3281 7.443879 GCCTGAATTTAAATGAGAAAAACCCAA 59.556 33.333 0.39 0.00 0.00 4.12
660 3282 9.506018 CCTGAATTTAAATGAGAAAAACCCAAT 57.494 29.630 0.39 0.00 0.00 3.16
662 3284 8.782144 TGAATTTAAATGAGAAAAACCCAATGC 58.218 29.630 0.39 0.00 0.00 3.56
710 3332 1.933247 AAAATGTTGCACGTGGTTGG 58.067 45.000 18.88 0.00 0.00 3.77
738 3360 6.764085 TCCATTGACTTTTCACTTCGAAGTTA 59.236 34.615 27.79 18.02 37.08 2.24
739 3361 6.851330 CCATTGACTTTTCACTTCGAAGTTAC 59.149 38.462 27.79 13.60 37.08 2.50
740 3362 7.254795 CCATTGACTTTTCACTTCGAAGTTACT 60.255 37.037 27.79 3.94 37.08 2.24
741 3363 8.761497 CATTGACTTTTCACTTCGAAGTTACTA 58.239 33.333 27.79 12.83 37.08 1.82
742 3364 7.925703 TGACTTTTCACTTCGAAGTTACTAG 57.074 36.000 27.79 22.05 37.08 2.57
743 3365 7.486647 TGACTTTTCACTTCGAAGTTACTAGT 58.513 34.615 27.79 24.64 37.08 2.57
744 3366 8.623903 TGACTTTTCACTTCGAAGTTACTAGTA 58.376 33.333 27.79 7.85 37.08 1.82
745 3367 8.794308 ACTTTTCACTTCGAAGTTACTAGTAC 57.206 34.615 27.79 0.00 37.08 2.73
746 3368 8.628280 ACTTTTCACTTCGAAGTTACTAGTACT 58.372 33.333 27.79 0.00 37.08 2.73
747 3369 9.116054 CTTTTCACTTCGAAGTTACTAGTACTC 57.884 37.037 27.79 0.00 37.08 2.59
748 3370 7.976135 TTCACTTCGAAGTTACTAGTACTCT 57.024 36.000 27.79 1.65 37.08 3.24
749 3371 7.361889 TCACTTCGAAGTTACTAGTACTCTG 57.638 40.000 27.79 12.00 37.08 3.35
750 3372 6.022821 CACTTCGAAGTTACTAGTACTCTGC 58.977 44.000 27.79 2.47 37.08 4.26
810 3433 4.403453 CTGGTTTAACTTGATGCTTACGC 58.597 43.478 0.00 0.00 0.00 4.42
1086 5208 3.616721 ACCGCTGACGAGCAAGGT 61.617 61.111 0.00 0.00 46.62 3.50
1221 5349 4.818546 ACATATTGCCGTACGTACTCTACT 59.181 41.667 22.55 7.93 0.00 2.57
1308 5453 0.824595 ATGCAGCTGACCAAGTGCAA 60.825 50.000 20.43 0.00 42.33 4.08
1579 5725 0.473755 AGACAACTGACATGGCCACA 59.526 50.000 8.16 0.00 0.00 4.17
1731 7534 9.877178 TTTACTTTCCTGCAAAAGAAATTGTTA 57.123 25.926 16.01 1.04 38.30 2.41
1747 7550 8.395633 AGAAATTGTTATACTTTACCGACATGC 58.604 33.333 0.00 0.00 0.00 4.06
1748 7551 7.618502 AATTGTTATACTTTACCGACATGCA 57.381 32.000 0.00 0.00 0.00 3.96
1749 7552 7.801716 ATTGTTATACTTTACCGACATGCAT 57.198 32.000 0.00 0.00 0.00 3.96
1750 7553 6.597262 TGTTATACTTTACCGACATGCATG 57.403 37.500 25.09 25.09 0.00 4.06
1773 7576 2.034558 TGGCTAGCAGTTGAAAAACAGC 59.965 45.455 18.24 0.00 35.71 4.40
1972 8352 7.485913 GTGCATGTGAATTTATCGATGTTTCTT 59.514 33.333 8.54 0.00 0.00 2.52
1993 8373 5.710567 TCTTCTTGTTCACTCGAATCCTAGA 59.289 40.000 0.00 0.00 32.61 2.43
2049 8437 7.766283 AGCATGGCTAGTTTCTATTTTCTTTC 58.234 34.615 0.00 0.00 36.99 2.62
2087 8476 4.390297 GCATTTTTAAGTTTTATGCCGGCA 59.610 37.500 34.80 34.80 36.48 5.69
2260 8745 4.589216 TGATTAATATGCAGCAAAGGCC 57.411 40.909 0.00 0.00 42.56 5.19
2285 8770 2.093537 ATTCGAGATGAGCCCTCCGC 62.094 60.000 0.00 0.00 37.98 5.54
2356 8841 0.530744 TCAACTATGCTTCGGCGACT 59.469 50.000 10.16 0.00 45.37 4.18
2398 8889 2.612972 CGTAAGTGGACACCTTCATGCT 60.613 50.000 0.00 0.00 0.00 3.79
2426 8918 6.410243 TGTGTATTTGAATTTGCATGCATG 57.590 33.333 23.37 22.70 0.00 4.06
2430 8925 7.269511 GTGTATTTGAATTTGCATGCATGTTTG 59.730 33.333 26.79 4.46 0.00 2.93
2435 8931 3.316071 TTTGCATGCATGTTTGTAGGG 57.684 42.857 26.79 0.00 0.00 3.53
2446 8942 1.134946 GTTTGTAGGGATGCATGTGCC 59.865 52.381 2.46 0.00 41.18 5.01
2477 9100 7.119116 TCGTCAACAACATCATAAGCTTTGTAT 59.881 33.333 3.20 0.00 30.28 2.29
2527 9150 5.359194 TGAAGGATTAAACTCCTAGCCTG 57.641 43.478 0.00 0.00 45.15 4.85
2531 9154 6.487299 AGGATTAAACTCCTAGCCTGTTAG 57.513 41.667 0.00 0.00 44.04 2.34
2535 9158 2.239681 ACTCCTAGCCTGTTAGTGCT 57.760 50.000 0.00 0.00 41.57 4.40
2536 9159 2.541466 ACTCCTAGCCTGTTAGTGCTT 58.459 47.619 0.00 0.00 39.00 3.91
2538 9161 4.094476 ACTCCTAGCCTGTTAGTGCTTAA 58.906 43.478 0.00 0.00 39.00 1.85
2539 9162 4.717280 ACTCCTAGCCTGTTAGTGCTTAAT 59.283 41.667 0.00 0.00 39.00 1.40
2540 9163 5.163395 ACTCCTAGCCTGTTAGTGCTTAATC 60.163 44.000 0.00 0.00 39.00 1.75
2541 9164 4.714802 TCCTAGCCTGTTAGTGCTTAATCA 59.285 41.667 0.00 0.00 39.00 2.57
2542 9165 5.188948 TCCTAGCCTGTTAGTGCTTAATCAA 59.811 40.000 0.00 0.00 39.00 2.57
2543 9166 5.880332 CCTAGCCTGTTAGTGCTTAATCAAA 59.120 40.000 0.00 0.00 39.00 2.69
2544 9167 5.629079 AGCCTGTTAGTGCTTAATCAAAC 57.371 39.130 0.00 0.00 32.94 2.93
2545 9168 5.070001 AGCCTGTTAGTGCTTAATCAAACA 58.930 37.500 0.00 0.00 32.94 2.83
2546 9169 5.534654 AGCCTGTTAGTGCTTAATCAAACAA 59.465 36.000 0.00 0.00 32.94 2.83
2547 9170 6.040391 AGCCTGTTAGTGCTTAATCAAACAAA 59.960 34.615 0.00 0.00 32.94 2.83
2548 9171 6.143919 GCCTGTTAGTGCTTAATCAAACAAAC 59.856 38.462 0.00 0.00 0.00 2.93
2550 9173 7.920682 CCTGTTAGTGCTTAATCAAACAAACTT 59.079 33.333 0.00 0.00 0.00 2.66
2551 9174 9.301153 CTGTTAGTGCTTAATCAAACAAACTTT 57.699 29.630 0.00 0.00 0.00 2.66
2553 9176 6.588348 AGTGCTTAATCAAACAAACTTTGC 57.412 33.333 1.14 0.00 0.00 3.68
2554 9177 6.340522 AGTGCTTAATCAAACAAACTTTGCT 58.659 32.000 1.14 0.00 0.00 3.91
2555 9178 6.818142 AGTGCTTAATCAAACAAACTTTGCTT 59.182 30.769 1.14 0.00 0.00 3.91
2557 9180 6.019961 TGCTTAATCAAACAAACTTTGCTTCG 60.020 34.615 1.14 0.00 0.00 3.79
2558 9181 6.562086 GCTTAATCAAACAAACTTTGCTTCGG 60.562 38.462 1.14 0.00 0.00 4.30
2561 9184 4.915704 TCAAACAAACTTTGCTTCGGTAG 58.084 39.130 1.14 0.00 0.00 3.18
2574 9197 8.836268 TTTGCTTCGGTAGAAAAGTTTATAGA 57.164 30.769 0.00 0.00 35.71 1.98
2575 9198 9.444600 TTTGCTTCGGTAGAAAAGTTTATAGAT 57.555 29.630 0.00 0.00 35.71 1.98
2576 9199 9.444600 TTGCTTCGGTAGAAAAGTTTATAGATT 57.555 29.630 0.00 0.00 35.71 2.40
2578 9201 9.917872 GCTTCGGTAGAAAAGTTTATAGATTTC 57.082 33.333 0.00 0.00 35.71 2.17
2596 9219 7.330900 AGATTTCACTGCAGATTAAAGATGG 57.669 36.000 23.35 0.00 0.00 3.51
2598 9221 6.748333 TTTCACTGCAGATTAAAGATGGAG 57.252 37.500 23.35 5.33 38.26 3.86
2600 9223 6.244552 TCACTGCAGATTAAAGATGGAGAT 57.755 37.500 23.35 0.00 36.08 2.75
2602 9225 7.795047 TCACTGCAGATTAAAGATGGAGATTA 58.205 34.615 23.35 0.00 36.08 1.75
2603 9226 7.930325 TCACTGCAGATTAAAGATGGAGATTAG 59.070 37.037 23.35 0.00 36.08 1.73
2605 9228 8.489489 ACTGCAGATTAAAGATGGAGATTAGAA 58.511 33.333 23.35 0.00 36.08 2.10
2606 9229 9.334947 CTGCAGATTAAAGATGGAGATTAGAAA 57.665 33.333 8.42 0.00 34.65 2.52
2608 9231 9.336171 GCAGATTAAAGATGGAGATTAGAAAGT 57.664 33.333 0.00 0.00 0.00 2.66
2613 9236 9.886132 TTAAAGATGGAGATTAGAAAGTACACC 57.114 33.333 0.00 0.00 0.00 4.16
2617 9240 6.928348 TGGAGATTAGAAAGTACACCTTCA 57.072 37.500 0.00 0.00 31.27 3.02
2619 9242 7.918076 TGGAGATTAGAAAGTACACCTTCAAT 58.082 34.615 0.00 0.00 31.27 2.57
2620 9243 9.042450 TGGAGATTAGAAAGTACACCTTCAATA 57.958 33.333 0.00 0.00 31.27 1.90
2621 9244 9.886132 GGAGATTAGAAAGTACACCTTCAATAA 57.114 33.333 0.00 0.00 31.27 1.40
2663 9286 9.224267 TCTTTTGGATCTAAATCTATATGCAGC 57.776 33.333 4.96 0.00 32.12 5.25
2664 9287 8.922931 TTTTGGATCTAAATCTATATGCAGCA 57.077 30.769 4.96 0.00 32.12 4.41
2665 9288 7.912056 TTGGATCTAAATCTATATGCAGCAC 57.088 36.000 0.00 0.00 32.12 4.40
2666 9289 6.101997 TGGATCTAAATCTATATGCAGCACG 58.898 40.000 0.00 0.00 32.12 5.34
2667 9290 6.102663 GGATCTAAATCTATATGCAGCACGT 58.897 40.000 0.00 0.00 32.12 4.49
2668 9291 6.254589 GGATCTAAATCTATATGCAGCACGTC 59.745 42.308 0.00 0.00 32.12 4.34
2669 9292 6.332735 TCTAAATCTATATGCAGCACGTCT 57.667 37.500 0.00 0.00 0.00 4.18
2670 9293 6.152379 TCTAAATCTATATGCAGCACGTCTG 58.848 40.000 0.00 9.73 45.62 3.51
2671 9294 4.590850 AATCTATATGCAGCACGTCTGA 57.409 40.909 16.09 0.00 45.72 3.27
2672 9295 4.797800 ATCTATATGCAGCACGTCTGAT 57.202 40.909 16.09 10.21 45.72 2.90
2673 9296 4.166187 TCTATATGCAGCACGTCTGATC 57.834 45.455 16.09 0.00 45.72 2.92
2674 9297 3.823304 TCTATATGCAGCACGTCTGATCT 59.177 43.478 16.09 5.09 45.72 2.75
2675 9298 2.214387 TATGCAGCACGTCTGATCTG 57.786 50.000 16.09 6.57 45.72 2.90
2676 9299 3.088044 GCAGCACGTCTGATCTGC 58.912 61.111 16.09 11.61 45.72 4.26
2677 9300 4.584688 CAGCACGTCTGATCTGCA 57.415 55.556 8.72 0.00 45.72 4.41
2678 9301 2.831597 CAGCACGTCTGATCTGCAA 58.168 52.632 8.72 0.00 45.72 4.08
2679 9302 0.720027 CAGCACGTCTGATCTGCAAG 59.280 55.000 8.72 0.00 45.72 4.01
2680 9303 1.018226 AGCACGTCTGATCTGCAAGC 61.018 55.000 6.65 3.21 33.06 4.01
2681 9304 1.975363 GCACGTCTGATCTGCAAGCC 61.975 60.000 0.00 0.00 0.00 4.35
2682 9305 0.671472 CACGTCTGATCTGCAAGCCA 60.671 55.000 0.00 0.00 0.00 4.75
2683 9306 0.035317 ACGTCTGATCTGCAAGCCAA 59.965 50.000 0.00 0.00 0.00 4.52
2684 9307 1.339438 ACGTCTGATCTGCAAGCCAAT 60.339 47.619 0.00 0.00 0.00 3.16
2685 9308 2.093500 ACGTCTGATCTGCAAGCCAATA 60.093 45.455 0.00 0.00 0.00 1.90
2686 9309 3.136763 CGTCTGATCTGCAAGCCAATAT 58.863 45.455 0.00 0.00 0.00 1.28
2687 9310 3.059120 CGTCTGATCTGCAAGCCAATATG 60.059 47.826 0.00 0.00 0.00 1.78
2688 9311 4.132336 GTCTGATCTGCAAGCCAATATGA 58.868 43.478 0.00 0.00 0.00 2.15
2689 9312 4.024218 GTCTGATCTGCAAGCCAATATGAC 60.024 45.833 0.00 0.00 0.00 3.06
2690 9313 2.874086 TGATCTGCAAGCCAATATGACG 59.126 45.455 0.00 0.00 0.00 4.35
2691 9314 2.689553 TCTGCAAGCCAATATGACGA 57.310 45.000 0.00 0.00 0.00 4.20
2692 9315 3.198409 TCTGCAAGCCAATATGACGAT 57.802 42.857 0.00 0.00 0.00 3.73
2693 9316 4.335400 TCTGCAAGCCAATATGACGATA 57.665 40.909 0.00 0.00 0.00 2.92
2694 9317 4.309933 TCTGCAAGCCAATATGACGATAG 58.690 43.478 0.00 0.00 46.19 2.08
2695 9318 2.807967 TGCAAGCCAATATGACGATAGC 59.192 45.455 0.00 0.00 42.67 2.97
2696 9319 2.160417 GCAAGCCAATATGACGATAGCC 59.840 50.000 0.00 0.00 42.67 3.93
3048 9677 2.136791 CACGATAGGGCAGATGGGT 58.863 57.895 0.00 0.00 43.77 4.51
3103 9732 1.555075 TGTCCAATTCCCTCTTCCTCG 59.445 52.381 0.00 0.00 0.00 4.63
3167 9796 0.251341 AACAATGGGGGCTCAGACAC 60.251 55.000 0.00 0.00 0.00 3.67
3168 9797 1.136329 ACAATGGGGGCTCAGACACT 61.136 55.000 0.00 0.00 0.00 3.55
3175 9804 1.073284 GGGGCTCAGACACTAAAACCA 59.927 52.381 0.00 0.00 0.00 3.67
3261 9890 3.930848 GGAAGTTCGGTATCATCAACGTT 59.069 43.478 0.00 0.00 0.00 3.99
3323 9952 2.186903 CATTACCAGCCTCCGCGT 59.813 61.111 4.92 0.00 41.18 6.01
3723 10561 4.214119 CACAACACCGATGAACTTCAAGAT 59.786 41.667 0.00 0.00 0.00 2.40
3784 10626 6.976925 CGACTTACCGTATCCAGAAATAAAGT 59.023 38.462 0.00 0.00 0.00 2.66
3790 10632 5.459107 CCGTATCCAGAAATAAAGTGAGTCG 59.541 44.000 0.00 0.00 0.00 4.18
3794 10636 6.829229 TCCAGAAATAAAGTGAGTCGTCTA 57.171 37.500 0.00 0.00 0.00 2.59
3820 10662 5.067674 GTGAGACTTATATTGCCATTTGCCA 59.932 40.000 0.00 0.00 40.16 4.92
3828 11119 0.527113 TGCCATTTGCCATGAGTTCG 59.473 50.000 0.00 0.00 40.16 3.95
3850 11141 5.803461 TCGTAGGTCATCAATTTGACTAACG 59.197 40.000 20.08 20.08 45.37 3.18
3935 11418 7.684670 TGATATGCTTTTGATCGTTAGTCAAC 58.315 34.615 0.00 0.00 35.47 3.18
3937 11420 5.940192 TGCTTTTGATCGTTAGTCAACAT 57.060 34.783 0.00 0.00 35.47 2.71
3938 11421 6.312399 TGCTTTTGATCGTTAGTCAACATT 57.688 33.333 0.00 0.00 35.47 2.71
3939 11422 6.734137 TGCTTTTGATCGTTAGTCAACATTT 58.266 32.000 0.00 0.00 35.47 2.32
3940 11423 7.199766 TGCTTTTGATCGTTAGTCAACATTTT 58.800 30.769 0.00 0.00 35.47 1.82
3941 11424 7.704472 TGCTTTTGATCGTTAGTCAACATTTTT 59.296 29.630 0.00 0.00 35.47 1.94
3961 11444 3.612472 TTTTCTTTTGCGGGTAGTTCG 57.388 42.857 0.00 0.00 0.00 3.95
3982 11465 8.784043 AGTTCGCAAATTGAGTATCTAAAAACT 58.216 29.630 0.00 0.00 34.92 2.66
3999 11482 4.678538 AAACTAGAGGGAGTACTGGAGT 57.321 45.455 0.00 0.00 0.00 3.85
4050 11542 1.891919 GCTCAAGTGTGTGCCGGAA 60.892 57.895 5.05 0.00 38.13 4.30
4051 11543 1.237285 GCTCAAGTGTGTGCCGGAAT 61.237 55.000 5.05 0.00 38.13 3.01
4094 11586 6.113411 GGTGCCTGTGTCTATTTGTACTATT 58.887 40.000 0.00 0.00 0.00 1.73
4095 11587 7.093245 TGGTGCCTGTGTCTATTTGTACTATTA 60.093 37.037 0.00 0.00 0.00 0.98
4096 11588 7.931948 GGTGCCTGTGTCTATTTGTACTATTAT 59.068 37.037 0.00 0.00 0.00 1.28
4230 11741 5.193663 TGTAGTGAGATCATTCTAGCTGC 57.806 43.478 0.00 0.00 30.30 5.25
4290 11838 5.703130 ACTGATCGAGGGAAAAAGAAGAAAG 59.297 40.000 0.00 0.00 0.00 2.62
4292 11840 4.699925 TCGAGGGAAAAAGAAGAAAGGA 57.300 40.909 0.00 0.00 0.00 3.36
4304 11852 2.529389 AAAGGACCGGCAGAGGGT 60.529 61.111 0.00 0.00 41.48 4.34
4305 11853 2.804828 GAAAGGACCGGCAGAGGGTG 62.805 65.000 0.00 0.00 38.07 4.61
4328 11879 0.679960 GCTGGCCCGGAATTAACAGT 60.680 55.000 0.73 0.00 0.00 3.55
4334 11885 3.760151 GGCCCGGAATTAACAGTAAACTT 59.240 43.478 0.73 0.00 0.00 2.66
4336 11887 4.456566 GCCCGGAATTAACAGTAAACTTGA 59.543 41.667 0.73 0.00 0.00 3.02
4372 11924 3.059325 CAGAGCAAAGAGAAAACTGACCG 60.059 47.826 0.00 0.00 0.00 4.79
4386 11938 2.900546 ACTGACCGGAGTTGAAGAAGAT 59.099 45.455 9.46 0.00 0.00 2.40
4393 11945 0.035056 AGTTGAAGAAGATGGCCCGG 60.035 55.000 0.00 0.00 0.00 5.73
4439 11991 1.671845 GTCTACCCTCAGACGTAGCTG 59.328 57.143 0.00 0.00 35.92 4.24
4469 12021 4.146058 CACTGCAGTGTGCCTTCA 57.854 55.556 34.04 0.00 44.23 3.02
4530 12088 2.104859 CAGCTCGGCAGACCATGTG 61.105 63.158 0.00 0.00 34.57 3.21
4540 12098 3.662117 GACCATGTGGGAAGGGGGC 62.662 68.421 3.77 0.00 41.15 5.80
4542 12100 2.043652 CATGTGGGAAGGGGGCAG 60.044 66.667 0.00 0.00 0.00 4.85
4547 12105 4.760220 GGGAAGGGGGCAGGAGGA 62.760 72.222 0.00 0.00 0.00 3.71
4548 12106 3.093172 GGAAGGGGGCAGGAGGAG 61.093 72.222 0.00 0.00 0.00 3.69
4549 12107 3.093172 GAAGGGGGCAGGAGGAGG 61.093 72.222 0.00 0.00 0.00 4.30
4550 12108 4.767892 AAGGGGGCAGGAGGAGGG 62.768 72.222 0.00 0.00 0.00 4.30
4557 12115 4.101077 CAGGAGGAGGGGGAGGCT 62.101 72.222 0.00 0.00 0.00 4.58
4619 12194 0.537143 AATGAAACACGGCTGAGGCA 60.537 50.000 6.86 0.00 40.87 4.75
4620 12195 1.237285 ATGAAACACGGCTGAGGCAC 61.237 55.000 6.86 0.00 40.87 5.01
4621 12196 2.594592 AAACACGGCTGAGGCACC 60.595 61.111 6.86 0.00 40.87 5.01
4627 12202 2.743928 GGCTGAGGCACCGAACAG 60.744 66.667 0.00 0.00 40.87 3.16
4628 12203 3.426568 GCTGAGGCACCGAACAGC 61.427 66.667 16.07 16.07 46.25 4.40
4629 12204 3.114616 CTGAGGCACCGAACAGCG 61.115 66.667 0.00 0.00 40.47 5.18
4630 12205 3.573772 CTGAGGCACCGAACAGCGA 62.574 63.158 0.00 0.00 44.57 4.93
4631 12206 2.357034 GAGGCACCGAACAGCGAA 60.357 61.111 0.00 0.00 44.57 4.70
4632 12207 2.665185 AGGCACCGAACAGCGAAC 60.665 61.111 0.00 0.00 44.57 3.95
4633 12208 4.072088 GGCACCGAACAGCGAACG 62.072 66.667 0.00 0.00 44.57 3.95
4634 12209 4.719616 GCACCGAACAGCGAACGC 62.720 66.667 11.31 11.31 44.57 4.84
4635 12210 3.334751 CACCGAACAGCGAACGCA 61.335 61.111 20.66 0.00 44.57 5.24
4717 12293 0.606401 CAGTCACGAATGGGGCAGTT 60.606 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 2.203907 AGGTGCTCCAGCCTCTGT 60.204 61.111 7.70 0.00 41.18 3.41
58 59 2.583520 GAGGTGCTCCAGCCTCTG 59.416 66.667 7.70 0.00 45.78 3.35
176 2421 1.348064 TCAGGAAAAGAGCCTCGGAA 58.652 50.000 0.00 0.00 32.12 4.30
179 2424 3.045601 TCTTTCAGGAAAAGAGCCTCG 57.954 47.619 0.00 0.00 46.64 4.63
192 2437 5.988561 AGAGTAAGTCACAAAGCTCTTTCAG 59.011 40.000 0.00 0.00 30.12 3.02
207 2452 5.107065 CGACAACATTCCCAAAGAGTAAGTC 60.107 44.000 0.00 0.00 0.00 3.01
271 2516 6.360370 ACACAAACAGACCATATACAGACT 57.640 37.500 0.00 0.00 0.00 3.24
302 2547 4.202080 GGTTAATGAATAGAAAACCGGGCC 60.202 45.833 6.32 0.00 31.09 5.80
355 2600 4.520492 TCTTTTCAAAACAGAGGCAGGATC 59.480 41.667 0.00 0.00 0.00 3.36
359 2604 5.291858 GGTTTTCTTTTCAAAACAGAGGCAG 59.708 40.000 10.17 0.00 44.73 4.85
415 2660 0.948623 CACTCATCCCGCGTGAAACA 60.949 55.000 4.92 0.00 35.74 2.83
422 2667 2.100631 GTCAACCACTCATCCCGCG 61.101 63.158 0.00 0.00 0.00 6.46
460 2705 8.494433 TCAACCTGCATCCTAAGTATCTATTTT 58.506 33.333 0.00 0.00 0.00 1.82
461 2706 8.034313 TCAACCTGCATCCTAAGTATCTATTT 57.966 34.615 0.00 0.00 0.00 1.40
494 3001 7.617041 AAACCTAAGCATGACTGAGATTAAC 57.383 36.000 0.00 0.00 0.00 2.01
513 3020 5.122396 GTCAGCATCACGAATCTTAAAACCT 59.878 40.000 0.00 0.00 0.00 3.50
528 3035 4.756642 CCTACAACTCAAAAGTCAGCATCA 59.243 41.667 0.00 0.00 33.48 3.07
559 3181 3.524541 CTCCAAAATTTGCCCTGTATGC 58.475 45.455 0.00 0.00 0.00 3.14
569 3191 3.986277 ACAGAAGCTGCTCCAAAATTTG 58.014 40.909 1.00 0.00 34.37 2.32
574 3196 8.046708 TCTAATATAAACAGAAGCTGCTCCAAA 58.953 33.333 1.00 0.00 34.37 3.28
615 3237 7.455641 TTCAGGCTGAAAAACGGATATAAAA 57.544 32.000 26.78 0.00 32.71 1.52
641 3263 7.554118 TGTTTGCATTGGGTTTTTCTCATTTAA 59.446 29.630 0.00 0.00 0.00 1.52
649 3271 3.540617 ACCTGTTTGCATTGGGTTTTTC 58.459 40.909 0.00 0.00 0.00 2.29
655 3277 1.549203 AGCTACCTGTTTGCATTGGG 58.451 50.000 0.00 0.00 0.00 4.12
656 3278 4.158394 ACATAAGCTACCTGTTTGCATTGG 59.842 41.667 0.00 0.00 0.00 3.16
657 3279 5.314923 ACATAAGCTACCTGTTTGCATTG 57.685 39.130 0.00 0.00 0.00 2.82
658 3280 6.414732 TCTACATAAGCTACCTGTTTGCATT 58.585 36.000 0.00 0.00 0.00 3.56
659 3281 5.989477 TCTACATAAGCTACCTGTTTGCAT 58.011 37.500 0.00 0.00 0.00 3.96
660 3282 5.186992 TCTCTACATAAGCTACCTGTTTGCA 59.813 40.000 0.00 0.00 0.00 4.08
661 3283 5.661458 TCTCTACATAAGCTACCTGTTTGC 58.339 41.667 0.00 0.00 0.00 3.68
662 3284 7.101652 TCTCTCTACATAAGCTACCTGTTTG 57.898 40.000 0.00 0.00 0.00 2.93
697 3319 3.578272 GACGCCAACCACGTGCAA 61.578 61.111 10.91 0.00 45.24 4.08
710 3332 7.474772 TTCGAAGTGAAAAGTCAATGGACGC 62.475 44.000 0.00 0.00 40.43 5.19
810 3433 7.869429 AGTTGGATTTTTCTTATCAGCAAAGTG 59.131 33.333 0.00 0.00 0.00 3.16
1074 5196 0.391228 TGTTGCTACCTTGCTCGTCA 59.609 50.000 0.00 0.00 0.00 4.35
1079 5201 1.242076 CTTGCTGTTGCTACCTTGCT 58.758 50.000 0.00 0.00 40.48 3.91
1081 5203 2.618241 TGAACTTGCTGTTGCTACCTTG 59.382 45.455 0.00 0.00 39.30 3.61
1086 5208 1.597195 CACGTGAACTTGCTGTTGCTA 59.403 47.619 10.90 0.00 39.30 3.49
1221 5349 2.026729 TCATGAAAGTAATGGCGGGTGA 60.027 45.455 0.00 0.00 0.00 4.02
1324 5469 1.419374 CCGTCTCCGAACACAAAGAG 58.581 55.000 0.00 0.00 35.63 2.85
1326 5471 0.249741 ACCCGTCTCCGAACACAAAG 60.250 55.000 0.00 0.00 35.63 2.77
1731 7534 3.876914 CACCATGCATGTCGGTAAAGTAT 59.123 43.478 24.58 0.00 0.00 2.12
1747 7550 1.825090 TTCAACTGCTAGCCACCATG 58.175 50.000 13.29 4.60 0.00 3.66
1748 7551 2.584835 TTTCAACTGCTAGCCACCAT 57.415 45.000 13.29 0.00 0.00 3.55
1749 7552 2.356665 TTTTCAACTGCTAGCCACCA 57.643 45.000 13.29 0.00 0.00 4.17
1750 7553 2.360801 TGTTTTTCAACTGCTAGCCACC 59.639 45.455 13.29 0.00 33.58 4.61
1820 7893 2.704572 AGTTACATCTTGGCTGCTGAC 58.295 47.619 0.00 0.00 0.00 3.51
1972 8352 5.977489 TTCTAGGATTCGAGTGAACAAGA 57.023 39.130 0.00 0.00 36.81 3.02
2049 8437 8.829612 ACTTAAAAATGCTGATGAAACCAAAAG 58.170 29.630 0.00 0.00 0.00 2.27
2062 8450 5.445806 GCCGGCATAAAACTTAAAAATGCTG 60.446 40.000 24.80 7.32 45.36 4.41
2087 8476 6.039717 AGTTCAGACTGTAATGCATGTTTTGT 59.960 34.615 0.00 0.00 33.99 2.83
2196 8680 7.218204 CGGTTGATCAATATTCTTTCGAAAACC 59.782 37.037 12.12 10.23 31.91 3.27
2260 8745 1.610102 GGGCTCATCTCGAATCCCATG 60.610 57.143 0.00 0.00 36.78 3.66
2285 8770 7.287927 TGTGGGACTATTAAGAGACAGATAAGG 59.712 40.741 3.65 0.00 0.00 2.69
2356 8841 3.118629 CGATGTCTCTCCAAATCCCAGAA 60.119 47.826 0.00 0.00 0.00 3.02
2398 8889 6.832804 CATGCAAATTCAAATACACATGCAA 58.167 32.000 0.97 0.00 44.58 4.08
2426 8918 1.134946 GGCACATGCATCCCTACAAAC 59.865 52.381 6.15 0.00 44.36 2.93
2430 8925 1.312815 GAAGGCACATGCATCCCTAC 58.687 55.000 6.15 0.00 44.36 3.18
2435 8931 1.003116 GACGATGAAGGCACATGCATC 60.003 52.381 6.15 4.23 44.36 3.91
2446 8942 5.961843 GCTTATGATGTTGTTGACGATGAAG 59.038 40.000 0.00 0.00 0.00 3.02
2490 9113 3.897239 TCCTTCAAACACACTGGATTGT 58.103 40.909 0.00 0.00 0.00 2.71
2509 9132 6.049790 CACTAACAGGCTAGGAGTTTAATCC 58.950 44.000 0.00 0.00 39.89 3.01
2527 9150 8.055986 GCAAAGTTTGTTTGATTAAGCACTAAC 58.944 33.333 16.70 0.00 0.00 2.34
2531 9154 6.588348 AGCAAAGTTTGTTTGATTAAGCAC 57.412 33.333 16.70 0.00 0.00 4.40
2535 9158 6.334202 ACCGAAGCAAAGTTTGTTTGATTAA 58.666 32.000 20.63 0.00 38.02 1.40
2536 9159 5.897050 ACCGAAGCAAAGTTTGTTTGATTA 58.103 33.333 20.63 0.00 38.02 1.75
2538 9161 4.385358 ACCGAAGCAAAGTTTGTTTGAT 57.615 36.364 20.63 4.86 34.10 2.57
2539 9162 3.859411 ACCGAAGCAAAGTTTGTTTGA 57.141 38.095 20.63 0.00 34.10 2.69
2540 9163 4.915704 TCTACCGAAGCAAAGTTTGTTTG 58.084 39.130 20.63 14.08 34.10 2.93
2541 9164 5.570234 TTCTACCGAAGCAAAGTTTGTTT 57.430 34.783 16.44 16.44 36.77 2.83
2542 9165 5.570234 TTTCTACCGAAGCAAAGTTTGTT 57.430 34.783 16.70 8.33 0.00 2.83
2543 9166 5.124936 ACTTTTCTACCGAAGCAAAGTTTGT 59.875 36.000 16.70 0.00 45.66 2.83
2544 9167 5.578776 ACTTTTCTACCGAAGCAAAGTTTG 58.421 37.500 11.41 11.41 45.66 2.93
2545 9168 5.830000 ACTTTTCTACCGAAGCAAAGTTT 57.170 34.783 8.79 0.00 45.66 2.66
2546 9169 5.830000 AACTTTTCTACCGAAGCAAAGTT 57.170 34.783 16.46 16.46 46.69 2.66
2548 9171 8.932791 TCTATAAACTTTTCTACCGAAGCAAAG 58.067 33.333 7.82 7.82 42.23 2.77
2550 9173 9.444600 AATCTATAAACTTTTCTACCGAAGCAA 57.555 29.630 0.00 0.00 0.00 3.91
2551 9174 9.444600 AAATCTATAAACTTTTCTACCGAAGCA 57.555 29.630 0.00 0.00 0.00 3.91
2557 9180 9.989869 GCAGTGAAATCTATAAACTTTTCTACC 57.010 33.333 0.00 0.00 0.00 3.18
2570 9193 9.064706 CCATCTTTAATCTGCAGTGAAATCTAT 57.935 33.333 14.67 0.00 0.00 1.98
2571 9194 8.267183 TCCATCTTTAATCTGCAGTGAAATCTA 58.733 33.333 14.67 0.00 0.00 1.98
2572 9195 7.114754 TCCATCTTTAATCTGCAGTGAAATCT 58.885 34.615 14.67 1.13 0.00 2.40
2573 9196 7.281774 TCTCCATCTTTAATCTGCAGTGAAATC 59.718 37.037 14.67 0.00 0.00 2.17
2574 9197 7.114754 TCTCCATCTTTAATCTGCAGTGAAAT 58.885 34.615 14.67 0.00 0.00 2.17
2575 9198 6.475504 TCTCCATCTTTAATCTGCAGTGAAA 58.524 36.000 14.67 11.21 0.00 2.69
2576 9199 6.053632 TCTCCATCTTTAATCTGCAGTGAA 57.946 37.500 14.67 3.62 0.00 3.18
2578 9201 6.939132 AATCTCCATCTTTAATCTGCAGTG 57.061 37.500 14.67 1.38 0.00 3.66
2580 9203 8.899427 TTCTAATCTCCATCTTTAATCTGCAG 57.101 34.615 7.63 7.63 0.00 4.41
2582 9205 9.336171 ACTTTCTAATCTCCATCTTTAATCTGC 57.664 33.333 0.00 0.00 0.00 4.26
2587 9210 9.886132 GGTGTACTTTCTAATCTCCATCTTTAA 57.114 33.333 0.00 0.00 0.00 1.52
2588 9211 9.268282 AGGTGTACTTTCTAATCTCCATCTTTA 57.732 33.333 0.00 0.00 0.00 1.85
2589 9212 8.152023 AGGTGTACTTTCTAATCTCCATCTTT 57.848 34.615 0.00 0.00 0.00 2.52
2591 9214 7.400339 TGAAGGTGTACTTTCTAATCTCCATCT 59.600 37.037 8.11 0.00 40.21 2.90
2594 9217 6.928348 TGAAGGTGTACTTTCTAATCTCCA 57.072 37.500 8.11 0.00 40.21 3.86
2595 9218 9.886132 TTATTGAAGGTGTACTTTCTAATCTCC 57.114 33.333 8.11 0.00 40.21 3.71
2637 9260 9.224267 GCTGCATATAGATTTAGATCCAAAAGA 57.776 33.333 0.00 0.00 32.44 2.52
2638 9261 9.006839 TGCTGCATATAGATTTAGATCCAAAAG 57.993 33.333 0.00 0.00 32.44 2.27
2639 9262 8.786898 GTGCTGCATATAGATTTAGATCCAAAA 58.213 33.333 5.27 0.00 32.44 2.44
2640 9263 7.118245 CGTGCTGCATATAGATTTAGATCCAAA 59.882 37.037 5.27 0.00 32.44 3.28
2641 9264 6.591448 CGTGCTGCATATAGATTTAGATCCAA 59.409 38.462 5.27 0.00 32.44 3.53
2642 9265 6.101997 CGTGCTGCATATAGATTTAGATCCA 58.898 40.000 5.27 0.00 32.44 3.41
2643 9266 6.102663 ACGTGCTGCATATAGATTTAGATCC 58.897 40.000 5.27 0.00 32.44 3.36
2644 9267 7.009083 CAGACGTGCTGCATATAGATTTAGATC 59.991 40.741 5.27 0.00 37.90 2.75
2645 9268 6.810676 CAGACGTGCTGCATATAGATTTAGAT 59.189 38.462 5.27 0.00 37.90 1.98
2646 9269 6.016276 TCAGACGTGCTGCATATAGATTTAGA 60.016 38.462 5.27 0.00 44.52 2.10
2647 9270 6.152379 TCAGACGTGCTGCATATAGATTTAG 58.848 40.000 5.27 0.00 44.52 1.85
2648 9271 6.084326 TCAGACGTGCTGCATATAGATTTA 57.916 37.500 5.27 0.00 44.52 1.40
2649 9272 4.948847 TCAGACGTGCTGCATATAGATTT 58.051 39.130 5.27 0.00 44.52 2.17
2650 9273 4.590850 TCAGACGTGCTGCATATAGATT 57.409 40.909 5.27 0.00 44.52 2.40
2651 9274 4.462132 AGATCAGACGTGCTGCATATAGAT 59.538 41.667 5.27 6.45 44.52 1.98
2652 9275 3.823304 AGATCAGACGTGCTGCATATAGA 59.177 43.478 5.27 1.38 44.52 1.98
2653 9276 3.919197 CAGATCAGACGTGCTGCATATAG 59.081 47.826 5.27 0.62 44.52 1.31
2654 9277 3.905784 CAGATCAGACGTGCTGCATATA 58.094 45.455 5.27 0.00 44.52 0.86
2655 9278 2.752121 CAGATCAGACGTGCTGCATAT 58.248 47.619 5.27 0.00 44.52 1.78
2656 9279 2.214387 CAGATCAGACGTGCTGCATA 57.786 50.000 5.27 0.00 44.52 3.14
2657 9280 3.061093 CAGATCAGACGTGCTGCAT 57.939 52.632 5.27 0.00 44.52 3.96
2658 9281 4.584688 CAGATCAGACGTGCTGCA 57.415 55.556 0.00 0.00 44.52 4.41
2659 9282 3.088044 GCAGATCAGACGTGCTGC 58.912 61.111 0.00 0.00 45.64 5.25
2660 9283 0.720027 CTTGCAGATCAGACGTGCTG 59.280 55.000 0.00 0.00 46.31 4.41
2661 9284 1.018226 GCTTGCAGATCAGACGTGCT 61.018 55.000 0.00 0.00 38.09 4.40
2662 9285 1.423056 GCTTGCAGATCAGACGTGC 59.577 57.895 0.00 0.00 37.73 5.34
2663 9286 0.671472 TGGCTTGCAGATCAGACGTG 60.671 55.000 0.00 0.00 0.00 4.49
2664 9287 0.035317 TTGGCTTGCAGATCAGACGT 59.965 50.000 0.00 0.00 0.00 4.34
2665 9288 1.376543 ATTGGCTTGCAGATCAGACG 58.623 50.000 0.00 0.00 0.00 4.18
2666 9289 4.024218 GTCATATTGGCTTGCAGATCAGAC 60.024 45.833 0.00 0.00 0.00 3.51
2667 9290 4.132336 GTCATATTGGCTTGCAGATCAGA 58.868 43.478 0.00 0.00 0.00 3.27
2668 9291 3.059120 CGTCATATTGGCTTGCAGATCAG 60.059 47.826 0.00 0.00 0.00 2.90
2669 9292 2.874086 CGTCATATTGGCTTGCAGATCA 59.126 45.455 0.00 0.00 0.00 2.92
2670 9293 3.133691 TCGTCATATTGGCTTGCAGATC 58.866 45.455 0.00 0.00 0.00 2.75
2671 9294 3.198409 TCGTCATATTGGCTTGCAGAT 57.802 42.857 0.00 0.00 0.00 2.90
2672 9295 2.689553 TCGTCATATTGGCTTGCAGA 57.310 45.000 0.00 0.00 0.00 4.26
2673 9296 3.120408 GCTATCGTCATATTGGCTTGCAG 60.120 47.826 0.00 0.00 0.00 4.41
2674 9297 2.807967 GCTATCGTCATATTGGCTTGCA 59.192 45.455 0.00 0.00 0.00 4.08
2675 9298 2.160417 GGCTATCGTCATATTGGCTTGC 59.840 50.000 0.00 0.00 0.00 4.01
3048 9677 3.483788 TTGCTGGCTACGGTTGGCA 62.484 57.895 16.82 16.82 38.31 4.92
3103 9732 4.626081 AGTGGTGCCGGTGCTGAC 62.626 66.667 1.90 0.00 38.71 3.51
3167 9796 3.496331 AGGTGTGGGACATTGGTTTTAG 58.504 45.455 0.00 0.00 44.52 1.85
3168 9797 3.117474 TGAGGTGTGGGACATTGGTTTTA 60.117 43.478 0.00 0.00 44.52 1.52
3175 9804 1.561542 GGAGATGAGGTGTGGGACATT 59.438 52.381 0.00 0.00 44.52 2.71
3261 9890 4.980805 GCCGTGCACAAGGTCGGA 62.981 66.667 18.64 0.00 44.86 4.55
3323 9952 0.669318 GATGCCGTCGTTGAACTCCA 60.669 55.000 0.00 0.00 0.00 3.86
3723 10561 8.859090 AGAAATATCACTTTTGGTTGATCAACA 58.141 29.630 33.42 19.93 42.85 3.33
3765 10607 6.295719 ACTCACTTTATTTCTGGATACGGT 57.704 37.500 0.00 0.00 45.94 4.83
3794 10636 6.742109 GCAAATGGCAATATAAGTCTCACAT 58.258 36.000 0.00 0.00 43.97 3.21
3820 10662 6.313905 GTCAAATTGATGACCTACGAACTCAT 59.686 38.462 0.00 0.00 43.11 2.90
3881 11332 8.842358 TTTCTCACAAAACCGAAAGTATATCT 57.158 30.769 0.00 0.00 0.00 1.98
3910 11393 7.333174 TGTTGACTAACGATCAAAAGCATATCA 59.667 33.333 0.00 0.00 37.80 2.15
3940 11423 3.954999 CGAACTACCCGCAAAAGAAAAA 58.045 40.909 0.00 0.00 0.00 1.94
3941 11424 3.612472 CGAACTACCCGCAAAAGAAAA 57.388 42.857 0.00 0.00 0.00 2.29
3951 11434 2.073816 ACTCAATTTGCGAACTACCCG 58.926 47.619 0.00 0.00 0.00 5.28
3952 11435 5.116882 AGATACTCAATTTGCGAACTACCC 58.883 41.667 0.00 0.00 0.00 3.69
3953 11436 7.766219 TTAGATACTCAATTTGCGAACTACC 57.234 36.000 0.00 0.00 0.00 3.18
3956 11439 8.784043 AGTTTTTAGATACTCAATTTGCGAACT 58.216 29.630 0.00 0.00 0.00 3.01
3957 11440 8.950403 AGTTTTTAGATACTCAATTTGCGAAC 57.050 30.769 0.00 0.00 0.00 3.95
3960 11443 9.907576 CTCTAGTTTTTAGATACTCAATTTGCG 57.092 33.333 0.00 0.00 0.00 4.85
3982 11465 4.976442 AGATACACTCCAGTACTCCCTCTA 59.024 45.833 0.00 0.00 0.00 2.43
3999 11482 6.887626 TTGCGTAGTCCATATACAGATACA 57.112 37.500 0.00 0.00 0.00 2.29
4155 11665 6.849085 AATGTGGACACAAGGCATTATTTA 57.151 33.333 9.42 0.00 45.41 1.40
4156 11666 5.743636 AATGTGGACACAAGGCATTATTT 57.256 34.783 9.42 0.00 45.41 1.40
4199 11709 5.919272 ATGATCTCACTACATGCGATTTG 57.081 39.130 0.00 0.00 32.75 2.32
4264 11812 5.238583 TCTTCTTTTTCCCTCGATCAGTTC 58.761 41.667 0.00 0.00 0.00 3.01
4307 11855 2.826738 TTAATTCCGGGCCAGCGC 60.827 61.111 4.39 0.00 0.00 5.92
4308 11856 1.714899 CTGTTAATTCCGGGCCAGCG 61.715 60.000 4.39 0.00 0.00 5.18
4309 11857 0.679960 ACTGTTAATTCCGGGCCAGC 60.680 55.000 4.39 0.00 0.00 4.85
4310 11858 2.702592 TACTGTTAATTCCGGGCCAG 57.297 50.000 4.39 0.00 0.00 4.85
4312 11860 3.349927 AGTTTACTGTTAATTCCGGGCC 58.650 45.455 0.00 0.00 0.00 5.80
4314 11862 5.390145 CGTCAAGTTTACTGTTAATTCCGGG 60.390 44.000 0.00 0.00 0.00 5.73
4316 11864 5.077424 GCGTCAAGTTTACTGTTAATTCCG 58.923 41.667 0.00 0.00 0.00 4.30
4328 11879 0.451957 CAATGCGCGCGTCAAGTTTA 60.452 50.000 32.35 5.14 0.00 2.01
4334 11885 2.801624 CTGATCAATGCGCGCGTCA 61.802 57.895 32.35 27.93 0.00 4.35
4336 11887 2.509111 TCTGATCAATGCGCGCGT 60.509 55.556 32.35 25.30 0.00 6.01
4372 11924 1.756430 GGGCCATCTTCTTCAACTCC 58.244 55.000 4.39 0.00 0.00 3.85
4386 11938 3.536917 CAGTCGATAGCCGGGCCA 61.537 66.667 17.02 1.09 39.14 5.36
4393 11945 0.175760 TTGGGAGTGCAGTCGATAGC 59.824 55.000 15.26 5.23 0.00 2.97
4432 11984 4.017092 TGCGATGCATCAGCTACG 57.983 55.556 29.85 17.93 42.74 3.51
4469 12021 1.282157 GGATGCTCTGGTAGTTGGGTT 59.718 52.381 0.00 0.00 0.00 4.11
4521 12073 1.930656 CCCCCTTCCCACATGGTCT 60.931 63.158 0.00 0.00 34.77 3.85
4530 12088 4.760220 TCCTCCTGCCCCCTTCCC 62.760 72.222 0.00 0.00 0.00 3.97
4540 12098 4.101077 AGCCTCCCCCTCCTCCTG 62.101 72.222 0.00 0.00 0.00 3.86
4556 12114 3.138798 GCCATGGAGCTGTGCCAG 61.139 66.667 18.40 0.00 39.11 4.85
4557 12115 4.746309 GGCCATGGAGCTGTGCCA 62.746 66.667 18.40 0.00 41.76 4.92
4567 12125 0.812811 CAGAGACACGATGGCCATGG 60.813 60.000 26.56 25.49 0.00 3.66
4572 12130 2.299993 TCATTCAGAGACACGATGGC 57.700 50.000 0.00 0.00 0.00 4.40
4619 12194 2.586635 TTGCGTTCGCTGTTCGGT 60.587 55.556 17.63 0.00 39.05 4.69
4620 12195 2.170985 CTTGCGTTCGCTGTTCGG 59.829 61.111 17.63 0.00 39.05 4.30
4621 12196 2.497628 GCTTGCGTTCGCTGTTCG 60.498 61.111 17.63 3.74 40.15 3.95
4622 12197 2.497628 CGCTTGCGTTCGCTGTTC 60.498 61.111 17.63 4.48 0.00 3.18
4623 12198 4.666532 GCGCTTGCGTTCGCTGTT 62.667 61.111 17.63 0.00 46.92 3.16
4628 12203 1.408077 CAATTTGCGCTTGCGTTCG 59.592 52.632 16.38 0.00 43.34 3.95
4629 12204 0.662970 TCCAATTTGCGCTTGCGTTC 60.663 50.000 16.38 1.47 43.34 3.95
4630 12205 0.939106 GTCCAATTTGCGCTTGCGTT 60.939 50.000 16.38 0.00 43.34 4.84
4631 12206 1.371635 GTCCAATTTGCGCTTGCGT 60.372 52.632 16.38 0.00 43.34 5.24
4632 12207 0.938637 TTGTCCAATTTGCGCTTGCG 60.939 50.000 9.73 10.90 43.34 4.85
4633 12208 1.391144 GATTGTCCAATTTGCGCTTGC 59.609 47.619 9.73 0.00 39.78 4.01
4634 12209 2.919229 GAGATTGTCCAATTTGCGCTTG 59.081 45.455 9.73 4.72 0.00 4.01
4635 12210 2.821969 AGAGATTGTCCAATTTGCGCTT 59.178 40.909 9.73 0.00 0.00 4.68
4717 12293 1.635487 AGGGCTTGGAATGCAGAGTTA 59.365 47.619 0.00 0.00 39.01 2.24


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

AutoCloner maintained by Alex Coulton.