Multiple sequence alignment - TraesCS5A01G243100

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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 TraesCS5A01G243100 chr5A 100.000 2975 0 0 1 2975 457892981 457895955 0.000000e+00 5494.0
1 TraesCS5A01G243100 chr5A 78.348 351 68 5 1225 1568 619454571 619454920 1.390000e-53 220.0
2 TraesCS5A01G243100 chr5A 73.077 364 80 16 1064 1418 667323625 667323979 2.420000e-21 113.0
3 TraesCS5A01G243100 chr5A 71.930 399 92 14 1225 1619 631858944 631858562 6.790000e-17 99.0
4 TraesCS5A01G243100 chr5A 82.609 69 8 4 456 520 655362740 655362672 1.150000e-04 58.4
5 TraesCS5A01G243100 chr5A 92.308 39 3 0 1048 1086 54653199 54653237 4.140000e-04 56.5
6 TraesCS5A01G243100 chr5B 95.115 1433 60 4 937 2369 421178402 421179824 0.000000e+00 2250.0
7 TraesCS5A01G243100 chr5B 97.857 560 10 2 2418 2975 421179822 421180381 0.000000e+00 966.0
8 TraesCS5A01G243100 chr5B 87.956 274 31 2 86 358 421177336 421177608 3.700000e-84 322.0
9 TraesCS5A01G243100 chr5B 92.857 168 6 4 731 894 421178228 421178393 3.830000e-59 239.0
10 TraesCS5A01G243100 chr5B 77.311 357 64 12 1225 1565 611953122 611953477 8.410000e-46 195.0
11 TraesCS5A01G243100 chr5B 84.127 63 6 3 459 520 63680061 63680002 1.150000e-04 58.4
12 TraesCS5A01G243100 chr5D 94.975 1413 60 6 687 2089 356197197 356198608 0.000000e+00 2206.0
13 TraesCS5A01G243100 chr5D 85.179 560 41 10 2418 2975 356198983 356199502 1.210000e-148 536.0
14 TraesCS5A01G243100 chr5D 90.270 185 9 4 2194 2369 356198801 356198985 1.780000e-57 233.0
15 TraesCS5A01G243100 chr5D 77.591 357 66 10 1225 1568 495308797 495309152 1.400000e-48 204.0
16 TraesCS5A01G243100 chr5D 80.734 109 18 3 422 528 339983148 339983041 6.830000e-12 82.4
17 TraesCS5A01G243100 chr5D 89.130 46 5 0 1048 1093 64292430 64292385 1.150000e-04 58.4
18 TraesCS5A01G243100 chr4B 73.352 364 79 16 1064 1418 621752158 621752512 5.210000e-23 119.0
19 TraesCS5A01G243100 chr4D 87.654 81 8 2 1339 1418 486937243 486937322 3.160000e-15 93.5
20 TraesCS5A01G243100 chr7B 96.364 55 1 1 2366 2420 4907411 4907358 4.080000e-14 89.8
21 TraesCS5A01G243100 chr7B 96.364 55 1 1 2364 2418 562993166 562993113 4.080000e-14 89.8
22 TraesCS5A01G243100 chr7B 83.158 95 15 1 429 522 650644412 650644506 5.280000e-13 86.1
23 TraesCS5A01G243100 chr6B 96.364 55 0 2 2366 2420 57286908 57286856 4.080000e-14 89.8
24 TraesCS5A01G243100 chr6B 88.889 72 4 3 2350 2418 617617746 617617816 5.280000e-13 86.1
25 TraesCS5A01G243100 chr6B 84.091 88 9 3 2335 2418 234689170 234689256 2.460000e-11 80.5
26 TraesCS5A01G243100 chr1A 96.364 55 1 1 2364 2418 516778098 516778151 4.080000e-14 89.8
27 TraesCS5A01G243100 chr1A 82.609 69 9 3 455 520 351648218 351648286 1.150000e-04 58.4
28 TraesCS5A01G243100 chr3B 92.063 63 4 1 2356 2418 487221484 487221423 1.470000e-13 87.9
29 TraesCS5A01G243100 chr3B 93.220 59 2 2 2360 2418 228751815 228751759 5.280000e-13 86.1
30 TraesCS5A01G243100 chr3B 84.286 70 8 3 454 520 323019366 323019297 6.880000e-07 65.8
31 TraesCS5A01G243100 chr6A 93.333 60 1 3 2360 2418 16618134 16618077 5.280000e-13 86.1
32 TraesCS5A01G243100 chr6A 83.824 68 8 3 456 520 488016377 488016310 8.900000e-06 62.1
33 TraesCS5A01G243100 chr2A 81.553 103 19 0 549 651 16797648 16797546 5.280000e-13 86.1
34 TraesCS5A01G243100 chr2A 94.872 39 2 0 1491 1529 88281374 88281412 8.900000e-06 62.1
35 TraesCS5A01G243100 chrUn 83.824 68 8 3 456 520 129509548 129509481 8.900000e-06 62.1
36 TraesCS5A01G243100 chr2D 94.872 39 2 0 1491 1529 87806688 87806726 8.900000e-06 62.1
37 TraesCS5A01G243100 chr2D 94.286 35 1 1 1059 1093 462790432 462790399 5.000000e-03 52.8
38 TraesCS5A01G243100 chr3D 85.000 60 8 1 470 528 162696534 162696593 3.200000e-05 60.2
39 TraesCS5A01G243100 chr3A 91.892 37 3 0 612 648 719073490 719073526 5.000000e-03 52.8


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 TraesCS5A01G243100 chr5A 457892981 457895955 2974 False 5494.000000 5494 100.000000 1 2975 1 chr5A.!!$F2 2974
1 TraesCS5A01G243100 chr5B 421177336 421180381 3045 False 944.250000 2250 93.446250 86 2975 4 chr5B.!!$F2 2889
2 TraesCS5A01G243100 chr5D 356197197 356199502 2305 False 991.666667 2206 90.141333 687 2975 3 chr5D.!!$F2 2288

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
241 243 0.034059 ACTCTTGTGGGACGAGCTTG 59.966 55.0 0.0 0.0 29.55 4.01 F
914 1422 0.465460 TGAACCAGGCAGACACAACC 60.465 55.0 0.0 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1655 1.566231 GGGAGGATGGTGATGTCCTTT 59.434 52.381 0.0 0.0 44.7 3.11 R
2370 3012 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.0 0.0 0.0 4.20 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
32 33 9.961264 ATCTTCTAGAATACATCATGCATGAAT 57.039 29.630 31.79 24.03 40.69 2.57
33 34 9.788889 TCTTCTAGAATACATCATGCATGAATT 57.211 29.630 31.79 25.23 40.69 2.17
44 45 8.916062 ACATCATGCATGAATTATTAACCTTGA 58.084 29.630 31.79 5.70 40.69 3.02
45 46 9.188588 CATCATGCATGAATTATTAACCTTGAC 57.811 33.333 31.79 0.00 40.69 3.18
46 47 8.291191 TCATGCATGAATTATTAACCTTGACA 57.709 30.769 26.87 0.00 33.08 3.58
47 48 8.747471 TCATGCATGAATTATTAACCTTGACAA 58.253 29.630 26.87 0.00 33.08 3.18
48 49 9.027129 CATGCATGAATTATTAACCTTGACAAG 57.973 33.333 22.59 8.31 0.00 3.16
49 50 8.121305 TGCATGAATTATTAACCTTGACAAGT 57.879 30.769 14.03 0.00 0.00 3.16
50 51 8.584157 TGCATGAATTATTAACCTTGACAAGTT 58.416 29.630 14.03 10.40 0.00 2.66
51 52 9.076596 GCATGAATTATTAACCTTGACAAGTTC 57.923 33.333 14.03 8.73 0.00 3.01
63 64 4.746535 TGACAAGTTCAAGGTCTACACA 57.253 40.909 0.00 0.00 32.84 3.72
64 65 5.092554 TGACAAGTTCAAGGTCTACACAA 57.907 39.130 0.00 0.00 32.84 3.33
65 66 4.873827 TGACAAGTTCAAGGTCTACACAAC 59.126 41.667 0.00 0.00 32.84 3.32
66 67 4.839121 ACAAGTTCAAGGTCTACACAACA 58.161 39.130 0.00 0.00 0.00 3.33
67 68 5.250200 ACAAGTTCAAGGTCTACACAACAA 58.750 37.500 0.00 0.00 0.00 2.83
68 69 5.708230 ACAAGTTCAAGGTCTACACAACAAA 59.292 36.000 0.00 0.00 0.00 2.83
69 70 6.207810 ACAAGTTCAAGGTCTACACAACAAAA 59.792 34.615 0.00 0.00 0.00 2.44
70 71 6.827586 AGTTCAAGGTCTACACAACAAAAA 57.172 33.333 0.00 0.00 0.00 1.94
111 112 1.460255 TCCTTGTGGGAAGGCTTGG 59.540 57.895 3.46 0.00 41.91 3.61
112 113 2.278330 CCTTGTGGGAAGGCTTGGC 61.278 63.158 3.46 0.00 37.23 4.52
135 136 3.695816 GCTCCATCAAGCGGATTAAAAC 58.304 45.455 0.00 0.00 32.57 2.43
171 172 5.886715 CAAATTCAAATTTGTGCGTCTCA 57.113 34.783 17.47 0.00 46.27 3.27
193 194 6.871844 TCACCATCTTTGAAAATGTGTTTGA 58.128 32.000 0.00 0.00 0.00 2.69
203 205 8.422973 TTGAAAATGTGTTTGATCTTTTGGAG 57.577 30.769 0.00 0.00 0.00 3.86
222 224 6.928348 TGGAGGTTGTTCTAGAAATGAGTA 57.072 37.500 6.78 0.00 0.00 2.59
224 226 6.497259 TGGAGGTTGTTCTAGAAATGAGTACT 59.503 38.462 6.78 0.00 0.00 2.73
234 236 5.153950 AGAAATGAGTACTCTTGTGGGAC 57.846 43.478 23.01 7.24 0.00 4.46
241 243 0.034059 ACTCTTGTGGGACGAGCTTG 59.966 55.000 0.00 0.00 29.55 4.01
246 248 2.045561 TGTGGGACGAGCTTGAAAAA 57.954 45.000 8.31 0.00 0.00 1.94
263 265 2.054140 AAAACGTGCGTGCCGTTCAT 62.054 50.000 17.09 9.71 46.85 2.57
268 270 2.030401 TGCGTGCCGTTCATGTACC 61.030 57.895 0.00 0.00 34.19 3.34
269 271 2.030401 GCGTGCCGTTCATGTACCA 61.030 57.895 0.00 0.00 34.19 3.25
311 313 2.741145 AGCTCTAGAGTTCCCGTTCAT 58.259 47.619 20.75 0.00 0.00 2.57
339 341 7.330262 TGAGAATTTTCCTAATCCATTTTGCC 58.670 34.615 0.00 0.00 0.00 4.52
344 346 1.956477 CCTAATCCATTTTGCCCCGAG 59.044 52.381 0.00 0.00 0.00 4.63
352 354 1.459450 TTTTGCCCCGAGACTAATGC 58.541 50.000 0.00 0.00 0.00 3.56
376 783 7.715686 TGCCCATGTGTTTATATGTTTATACGA 59.284 33.333 0.00 0.00 0.00 3.43
391 798 8.725405 TGTTTATACGATCCAAATAAAGCTCA 57.275 30.769 0.00 0.00 0.00 4.26
392 799 9.168451 TGTTTATACGATCCAAATAAAGCTCAA 57.832 29.630 0.00 0.00 0.00 3.02
396 803 5.894807 ACGATCCAAATAAAGCTCAAATGG 58.105 37.500 0.00 0.00 0.00 3.16
398 805 6.071391 ACGATCCAAATAAAGCTCAAATGGTT 60.071 34.615 0.00 0.00 0.00 3.67
399 806 7.122055 ACGATCCAAATAAAGCTCAAATGGTTA 59.878 33.333 0.00 0.00 0.00 2.85
400 807 7.645340 CGATCCAAATAAAGCTCAAATGGTTAG 59.355 37.037 0.00 0.00 0.00 2.34
401 808 7.169158 TCCAAATAAAGCTCAAATGGTTAGG 57.831 36.000 0.00 0.00 0.00 2.69
402 809 6.723977 TCCAAATAAAGCTCAAATGGTTAGGT 59.276 34.615 0.00 0.00 0.00 3.08
403 810 7.234577 TCCAAATAAAGCTCAAATGGTTAGGTT 59.765 33.333 0.00 0.00 32.63 3.50
404 811 7.877612 CCAAATAAAGCTCAAATGGTTAGGTTT 59.122 33.333 0.00 0.00 42.02 3.27
405 812 9.271828 CAAATAAAGCTCAAATGGTTAGGTTTT 57.728 29.630 0.00 0.00 40.37 2.43
406 813 9.845740 AAATAAAGCTCAAATGGTTAGGTTTTT 57.154 25.926 0.00 0.00 40.37 1.94
441 848 8.859236 AACCAACCTATTAGAGTTTAAGTTCC 57.141 34.615 0.00 0.00 0.00 3.62
442 849 7.981142 ACCAACCTATTAGAGTTTAAGTTCCA 58.019 34.615 0.00 0.00 0.00 3.53
443 850 8.101419 ACCAACCTATTAGAGTTTAAGTTCCAG 58.899 37.037 0.00 0.00 0.00 3.86
444 851 8.319146 CCAACCTATTAGAGTTTAAGTTCCAGA 58.681 37.037 0.00 0.00 0.00 3.86
445 852 9.152595 CAACCTATTAGAGTTTAAGTTCCAGAC 57.847 37.037 0.00 0.00 0.00 3.51
446 853 8.667592 ACCTATTAGAGTTTAAGTTCCAGACT 57.332 34.615 0.00 0.00 41.47 3.24
456 863 4.373156 AAGTTCCAGACTTGGCATTAGT 57.627 40.909 0.00 0.00 46.66 2.24
457 864 3.679389 AGTTCCAGACTTGGCATTAGTG 58.321 45.455 0.00 0.00 44.63 2.74
458 865 3.327757 AGTTCCAGACTTGGCATTAGTGA 59.672 43.478 0.00 0.00 44.63 3.41
459 866 4.018960 AGTTCCAGACTTGGCATTAGTGAT 60.019 41.667 0.00 0.00 44.63 3.06
460 867 4.574674 TCCAGACTTGGCATTAGTGATT 57.425 40.909 0.00 0.00 44.63 2.57
461 868 4.264253 TCCAGACTTGGCATTAGTGATTG 58.736 43.478 0.00 0.00 44.63 2.67
462 869 4.012374 CCAGACTTGGCATTAGTGATTGT 58.988 43.478 0.00 0.00 37.73 2.71
463 870 5.045942 TCCAGACTTGGCATTAGTGATTGTA 60.046 40.000 0.00 0.00 44.63 2.41
464 871 5.824624 CCAGACTTGGCATTAGTGATTGTAT 59.175 40.000 0.00 0.00 37.73 2.29
465 872 6.319658 CCAGACTTGGCATTAGTGATTGTATT 59.680 38.462 0.00 0.00 37.73 1.89
466 873 7.148018 CCAGACTTGGCATTAGTGATTGTATTT 60.148 37.037 0.00 0.00 37.73 1.40
467 874 8.246180 CAGACTTGGCATTAGTGATTGTATTTT 58.754 33.333 0.00 0.00 0.00 1.82
468 875 8.806146 AGACTTGGCATTAGTGATTGTATTTTT 58.194 29.630 0.00 0.00 0.00 1.94
491 898 9.810545 TTTTTGAATTTATTTCAGACCTTTCGT 57.189 25.926 0.00 0.00 44.90 3.85
492 899 9.458374 TTTTGAATTTATTTCAGACCTTTCGTC 57.542 29.630 0.00 0.00 44.90 4.20
493 900 6.827641 TGAATTTATTTCAGACCTTTCGTCG 58.172 36.000 0.00 0.00 39.44 5.12
494 901 6.647481 TGAATTTATTTCAGACCTTTCGTCGA 59.353 34.615 0.00 0.00 39.44 4.20
495 902 7.333423 TGAATTTATTTCAGACCTTTCGTCGAT 59.667 33.333 0.00 0.00 39.44 3.59
496 903 6.403333 TTTATTTCAGACCTTTCGTCGATG 57.597 37.500 0.00 0.00 46.92 3.84
497 904 3.380479 TTTCAGACCTTTCGTCGATGT 57.620 42.857 4.21 0.00 46.92 3.06
498 905 4.508461 TTTCAGACCTTTCGTCGATGTA 57.492 40.909 4.21 0.00 46.92 2.29
499 906 3.482722 TCAGACCTTTCGTCGATGTAC 57.517 47.619 4.21 0.00 46.92 2.90
500 907 2.159612 TCAGACCTTTCGTCGATGTACG 60.160 50.000 4.21 0.00 46.92 3.67
501 908 1.808945 AGACCTTTCGTCGATGTACGT 59.191 47.619 4.21 0.00 46.92 3.57
502 909 2.227388 AGACCTTTCGTCGATGTACGTT 59.773 45.455 4.21 0.00 46.92 3.99
503 910 2.589014 ACCTTTCGTCGATGTACGTTC 58.411 47.619 4.21 0.00 43.31 3.95
504 911 2.030893 ACCTTTCGTCGATGTACGTTCA 60.031 45.455 4.21 0.00 43.31 3.18
505 912 2.592897 CCTTTCGTCGATGTACGTTCAG 59.407 50.000 4.21 0.00 43.31 3.02
506 913 2.975410 TTCGTCGATGTACGTTCAGT 57.025 45.000 4.21 0.00 43.31 3.41
507 914 2.236741 TCGTCGATGTACGTTCAGTG 57.763 50.000 4.21 0.00 43.31 3.66
508 915 1.135888 TCGTCGATGTACGTTCAGTGG 60.136 52.381 4.21 0.00 43.31 4.00
509 916 1.625616 GTCGATGTACGTTCAGTGGG 58.374 55.000 0.00 0.00 43.13 4.61
510 917 1.200716 GTCGATGTACGTTCAGTGGGA 59.799 52.381 0.00 0.00 43.13 4.37
511 918 1.471287 TCGATGTACGTTCAGTGGGAG 59.529 52.381 0.00 0.00 43.13 4.30
512 919 1.469251 CGATGTACGTTCAGTGGGAGG 60.469 57.143 0.00 0.00 37.22 4.30
513 920 1.822990 GATGTACGTTCAGTGGGAGGA 59.177 52.381 0.00 0.00 0.00 3.71
514 921 1.254026 TGTACGTTCAGTGGGAGGAG 58.746 55.000 0.00 0.00 0.00 3.69
515 922 1.202964 TGTACGTTCAGTGGGAGGAGA 60.203 52.381 0.00 0.00 0.00 3.71
516 923 1.201880 GTACGTTCAGTGGGAGGAGAC 59.798 57.143 0.00 0.00 0.00 3.36
517 924 1.213013 CGTTCAGTGGGAGGAGACG 59.787 63.158 0.00 0.00 0.00 4.18
518 925 1.524863 CGTTCAGTGGGAGGAGACGT 61.525 60.000 0.00 0.00 0.00 4.34
519 926 0.680061 GTTCAGTGGGAGGAGACGTT 59.320 55.000 0.00 0.00 0.00 3.99
520 927 1.070289 GTTCAGTGGGAGGAGACGTTT 59.930 52.381 0.00 0.00 0.00 3.60
521 928 0.966920 TCAGTGGGAGGAGACGTTTC 59.033 55.000 0.00 0.00 0.00 2.78
522 929 0.969894 CAGTGGGAGGAGACGTTTCT 59.030 55.000 6.02 0.00 33.37 2.52
523 930 2.168496 CAGTGGGAGGAGACGTTTCTA 58.832 52.381 6.02 0.00 29.47 2.10
524 931 2.761208 CAGTGGGAGGAGACGTTTCTAT 59.239 50.000 6.02 0.00 29.47 1.98
525 932 3.025262 AGTGGGAGGAGACGTTTCTATC 58.975 50.000 6.02 4.91 29.47 2.08
526 933 2.022195 TGGGAGGAGACGTTTCTATCG 58.978 52.381 6.02 0.00 29.47 2.92
527 934 2.295885 GGGAGGAGACGTTTCTATCGA 58.704 52.381 6.02 0.00 29.47 3.59
528 935 2.291190 GGGAGGAGACGTTTCTATCGAG 59.709 54.545 6.02 0.00 29.47 4.04
529 936 3.204526 GGAGGAGACGTTTCTATCGAGA 58.795 50.000 6.02 0.00 29.47 4.04
530 937 3.249080 GGAGGAGACGTTTCTATCGAGAG 59.751 52.174 6.02 0.00 31.77 3.20
531 938 2.614983 AGGAGACGTTTCTATCGAGAGC 59.385 50.000 1.12 0.00 31.77 4.09
532 939 2.287129 GGAGACGTTTCTATCGAGAGCC 60.287 54.545 1.12 0.00 31.77 4.70
533 940 2.614983 GAGACGTTTCTATCGAGAGCCT 59.385 50.000 1.12 0.00 31.77 4.58
534 941 2.356382 AGACGTTTCTATCGAGAGCCTG 59.644 50.000 1.12 0.00 31.77 4.85
535 942 2.093106 ACGTTTCTATCGAGAGCCTGT 58.907 47.619 1.12 0.00 31.77 4.00
536 943 2.159366 ACGTTTCTATCGAGAGCCTGTG 60.159 50.000 1.12 0.00 31.77 3.66
537 944 2.097629 CGTTTCTATCGAGAGCCTGTGA 59.902 50.000 1.12 0.00 31.77 3.58
538 945 3.243234 CGTTTCTATCGAGAGCCTGTGAT 60.243 47.826 1.12 0.00 31.77 3.06
539 946 3.998099 TTCTATCGAGAGCCTGTGATG 57.002 47.619 1.12 0.00 31.77 3.07
540 947 2.937519 TCTATCGAGAGCCTGTGATGT 58.062 47.619 1.12 0.00 0.00 3.06
541 948 4.086706 TCTATCGAGAGCCTGTGATGTA 57.913 45.455 1.12 0.00 0.00 2.29
542 949 4.657013 TCTATCGAGAGCCTGTGATGTAT 58.343 43.478 1.12 0.00 0.00 2.29
543 950 5.073428 TCTATCGAGAGCCTGTGATGTATT 58.927 41.667 1.12 0.00 0.00 1.89
544 951 4.679373 ATCGAGAGCCTGTGATGTATTT 57.321 40.909 0.00 0.00 0.00 1.40
545 952 5.791336 ATCGAGAGCCTGTGATGTATTTA 57.209 39.130 0.00 0.00 0.00 1.40
546 953 5.791336 TCGAGAGCCTGTGATGTATTTAT 57.209 39.130 0.00 0.00 0.00 1.40
547 954 5.773575 TCGAGAGCCTGTGATGTATTTATC 58.226 41.667 0.00 0.00 0.00 1.75
548 955 5.536538 TCGAGAGCCTGTGATGTATTTATCT 59.463 40.000 0.00 0.00 0.00 1.98
549 956 5.861251 CGAGAGCCTGTGATGTATTTATCTC 59.139 44.000 0.00 0.00 0.00 2.75
550 957 6.515696 CGAGAGCCTGTGATGTATTTATCTCA 60.516 42.308 0.00 0.00 31.87 3.27
551 958 7.129457 AGAGCCTGTGATGTATTTATCTCAA 57.871 36.000 0.00 0.00 32.21 3.02
552 959 7.215789 AGAGCCTGTGATGTATTTATCTCAAG 58.784 38.462 0.00 0.00 32.21 3.02
553 960 7.070447 AGAGCCTGTGATGTATTTATCTCAAGA 59.930 37.037 0.00 0.00 32.21 3.02
554 961 7.743749 AGCCTGTGATGTATTTATCTCAAGAT 58.256 34.615 0.00 0.00 38.51 2.40
555 962 7.660617 AGCCTGTGATGTATTTATCTCAAGATG 59.339 37.037 2.72 0.00 36.05 2.90
556 963 7.658982 GCCTGTGATGTATTTATCTCAAGATGA 59.341 37.037 2.72 0.00 36.05 2.92
557 964 9.722184 CCTGTGATGTATTTATCTCAAGATGAT 57.278 33.333 2.72 0.55 36.05 2.45
564 971 9.889128 TGTATTTATCTCAAGATGATGTGACAA 57.111 29.630 2.72 0.00 36.05 3.18
568 975 9.942850 TTTATCTCAAGATGATGTGACAACTAA 57.057 29.630 2.72 0.00 36.05 2.24
569 976 9.591792 TTATCTCAAGATGATGTGACAACTAAG 57.408 33.333 2.72 0.00 36.05 2.18
570 977 6.997655 TCTCAAGATGATGTGACAACTAAGT 58.002 36.000 0.00 0.00 0.00 2.24
571 978 7.093354 TCTCAAGATGATGTGACAACTAAGTC 58.907 38.462 0.00 0.00 38.99 3.01
572 979 6.997655 TCAAGATGATGTGACAACTAAGTCT 58.002 36.000 0.00 0.00 39.27 3.24
573 980 7.445121 TCAAGATGATGTGACAACTAAGTCTT 58.555 34.615 0.00 0.00 39.27 3.01
574 981 7.933577 TCAAGATGATGTGACAACTAAGTCTTT 59.066 33.333 0.00 0.00 39.27 2.52
575 982 7.897575 AGATGATGTGACAACTAAGTCTTTC 57.102 36.000 0.00 0.00 39.27 2.62
576 983 7.445121 AGATGATGTGACAACTAAGTCTTTCA 58.555 34.615 0.00 0.00 39.27 2.69
577 984 7.933577 AGATGATGTGACAACTAAGTCTTTCAA 59.066 33.333 0.00 0.00 39.27 2.69
578 985 7.857734 TGATGTGACAACTAAGTCTTTCAAA 57.142 32.000 0.00 0.00 39.27 2.69
579 986 8.275015 TGATGTGACAACTAAGTCTTTCAAAA 57.725 30.769 0.00 0.00 39.27 2.44
580 987 8.181573 TGATGTGACAACTAAGTCTTTCAAAAC 58.818 33.333 0.00 0.00 39.27 2.43
581 988 7.681939 TGTGACAACTAAGTCTTTCAAAACT 57.318 32.000 0.00 0.00 39.27 2.66
582 989 7.526608 TGTGACAACTAAGTCTTTCAAAACTG 58.473 34.615 0.00 0.00 39.27 3.16
583 990 7.174253 TGTGACAACTAAGTCTTTCAAAACTGT 59.826 33.333 0.00 0.00 39.27 3.55
584 991 8.021396 GTGACAACTAAGTCTTTCAAAACTGTT 58.979 33.333 0.00 0.00 39.27 3.16
585 992 8.573035 TGACAACTAAGTCTTTCAAAACTGTTT 58.427 29.630 0.00 0.00 39.27 2.83
630 1037 9.938280 TGTATTTATAGGGATTAGTGTATGTGC 57.062 33.333 0.00 0.00 0.00 4.57
631 1038 9.938280 GTATTTATAGGGATTAGTGTATGTGCA 57.062 33.333 0.00 0.00 0.00 4.57
636 1043 6.439636 AGGGATTAGTGTATGTGCATATGT 57.560 37.500 6.16 0.00 0.00 2.29
637 1044 7.553504 AGGGATTAGTGTATGTGCATATGTA 57.446 36.000 6.16 0.00 0.00 2.29
638 1045 8.150827 AGGGATTAGTGTATGTGCATATGTAT 57.849 34.615 6.16 0.05 0.00 2.29
639 1046 8.043113 AGGGATTAGTGTATGTGCATATGTATG 58.957 37.037 6.16 0.00 36.78 2.39
640 1047 8.040727 GGGATTAGTGTATGTGCATATGTATGA 58.959 37.037 6.16 0.00 35.75 2.15
641 1048 9.091784 GGATTAGTGTATGTGCATATGTATGAG 57.908 37.037 6.16 0.00 35.75 2.90
642 1049 9.645059 GATTAGTGTATGTGCATATGTATGAGT 57.355 33.333 6.16 0.00 35.75 3.41
643 1050 8.816640 TTAGTGTATGTGCATATGTATGAGTG 57.183 34.615 6.16 0.00 35.75 3.51
644 1051 6.820335 AGTGTATGTGCATATGTATGAGTGT 58.180 36.000 6.16 0.00 35.75 3.55
645 1052 7.275183 AGTGTATGTGCATATGTATGAGTGTT 58.725 34.615 6.16 0.00 35.75 3.32
646 1053 7.770433 AGTGTATGTGCATATGTATGAGTGTTT 59.230 33.333 6.16 0.00 35.75 2.83
647 1054 7.852454 GTGTATGTGCATATGTATGAGTGTTTG 59.148 37.037 6.16 0.00 35.75 2.93
648 1055 5.233957 TGTGCATATGTATGAGTGTTTGC 57.766 39.130 4.29 0.00 35.75 3.68
649 1056 4.699257 TGTGCATATGTATGAGTGTTTGCA 59.301 37.500 4.29 0.00 35.75 4.08
650 1057 5.357596 TGTGCATATGTATGAGTGTTTGCAT 59.642 36.000 4.29 0.00 40.52 3.96
651 1058 6.541641 TGTGCATATGTATGAGTGTTTGCATA 59.458 34.615 4.29 0.00 40.52 3.14
652 1059 7.066766 TGTGCATATGTATGAGTGTTTGCATAA 59.933 33.333 4.29 0.00 40.52 1.90
653 1060 7.914871 GTGCATATGTATGAGTGTTTGCATAAA 59.085 33.333 4.29 0.00 40.52 1.40
674 1081 6.949578 AAAAACAAATATGTGATTCCGCAG 57.050 33.333 0.00 0.00 40.46 5.18
715 1204 3.886505 TGAAGTTGTAGCCGGTGATTTTT 59.113 39.130 1.90 0.00 0.00 1.94
873 1378 1.692519 GCCCCACGGTCAGATAATAGT 59.307 52.381 0.00 0.00 0.00 2.12
874 1379 2.895404 GCCCCACGGTCAGATAATAGTA 59.105 50.000 0.00 0.00 0.00 1.82
875 1380 3.056749 GCCCCACGGTCAGATAATAGTAG 60.057 52.174 0.00 0.00 0.00 2.57
877 1382 5.017490 CCCCACGGTCAGATAATAGTAGAT 58.983 45.833 0.00 0.00 0.00 1.98
878 1383 5.125739 CCCCACGGTCAGATAATAGTAGATC 59.874 48.000 0.00 0.00 0.00 2.75
914 1422 0.465460 TGAACCAGGCAGACACAACC 60.465 55.000 0.00 0.00 0.00 3.77
922 1430 0.668535 GCAGACACAACCAAAGGACC 59.331 55.000 0.00 0.00 0.00 4.46
944 1452 2.233186 CCAGCAGTTCACTGATCTCTCA 59.767 50.000 11.29 0.00 46.59 3.27
945 1453 3.252400 CAGCAGTTCACTGATCTCTCAC 58.748 50.000 11.29 0.00 46.59 3.51
958 1466 1.564818 TCTCTCACCTACTCCGTGGAT 59.435 52.381 0.00 0.00 0.00 3.41
1826 2339 1.608154 GAAGGGGAAGGCTGTACCC 59.392 63.158 12.19 12.19 43.69 3.69
1884 2397 2.631012 AAATCTGGGAGGCGGATGGC 62.631 60.000 0.00 0.00 42.51 4.40
1902 2415 2.358737 CAGGGTCACGGCTTCCAC 60.359 66.667 0.00 0.00 0.00 4.02
1969 2482 2.342650 GCTGAATTTCTGGGCCGCA 61.343 57.895 0.00 0.00 0.00 5.69
2056 2570 7.784037 TGTTGTACACTAGGAAGTTTGAGTTA 58.216 34.615 0.00 0.00 31.97 2.24
2064 2578 8.999431 CACTAGGAAGTTTGAGTTATGCTTAAA 58.001 33.333 0.00 0.00 31.97 1.52
2070 2584 7.873739 AGTTTGAGTTATGCTTAAAACATGC 57.126 32.000 0.00 0.00 36.93 4.06
2089 2603 3.133691 TGCTTGTAGCTGTTCTTCAGTG 58.866 45.455 0.00 0.00 45.23 3.66
2097 2611 5.948992 AGCTGTTCTTCAGTGGTTTTATC 57.051 39.130 0.00 0.00 45.23 1.75
2179 2693 2.432146 CCAGCTAGTCTGCCATTCTGTA 59.568 50.000 8.23 0.00 41.50 2.74
2180 2694 3.118629 CCAGCTAGTCTGCCATTCTGTAA 60.119 47.826 8.23 0.00 41.50 2.41
2369 3011 5.005740 TCAGATTGGGATGCTGCATAATAC 58.994 41.667 16.23 2.64 0.00 1.89
2370 3012 5.008331 CAGATTGGGATGCTGCATAATACT 58.992 41.667 16.23 7.74 0.00 2.12
2371 3013 5.123502 CAGATTGGGATGCTGCATAATACTC 59.876 44.000 16.23 9.99 0.00 2.59
2372 3014 3.423539 TGGGATGCTGCATAATACTCC 57.576 47.619 16.23 11.99 0.00 3.85
2373 3015 2.040278 TGGGATGCTGCATAATACTCCC 59.960 50.000 23.56 23.56 41.07 4.30
2375 3017 3.604582 GGATGCTGCATAATACTCCCTC 58.395 50.000 16.23 0.00 0.00 4.30
2376 3018 3.604582 GATGCTGCATAATACTCCCTCC 58.395 50.000 16.23 0.00 0.00 4.30
2377 3019 1.344438 TGCTGCATAATACTCCCTCCG 59.656 52.381 0.00 0.00 0.00 4.63
2378 3020 1.344763 GCTGCATAATACTCCCTCCGT 59.655 52.381 0.00 0.00 0.00 4.69
2379 3021 2.610727 GCTGCATAATACTCCCTCCGTC 60.611 54.545 0.00 0.00 0.00 4.79
2380 3022 1.968493 TGCATAATACTCCCTCCGTCC 59.032 52.381 0.00 0.00 0.00 4.79
2381 3023 1.275573 GCATAATACTCCCTCCGTCCC 59.724 57.143 0.00 0.00 0.00 4.46
2382 3024 2.605257 CATAATACTCCCTCCGTCCCA 58.395 52.381 0.00 0.00 0.00 4.37
2383 3025 2.852714 TAATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2384 3026 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2385 3027 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2386 3028 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2387 3029 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2388 3030 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2389 3031 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2390 3032 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2391 3033 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2392 3034 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2393 3035 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2394 3036 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2395 3037 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
2396 3038 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
2397 3039 3.684788 CCGTCCCAAAATAAGTGTCTCAG 59.315 47.826 0.00 0.00 0.00 3.35
2398 3040 3.125316 CGTCCCAAAATAAGTGTCTCAGC 59.875 47.826 0.00 0.00 0.00 4.26
2399 3041 4.327680 GTCCCAAAATAAGTGTCTCAGCT 58.672 43.478 0.00 0.00 0.00 4.24
2400 3042 4.762251 GTCCCAAAATAAGTGTCTCAGCTT 59.238 41.667 0.00 0.00 0.00 3.74
2401 3043 5.241728 GTCCCAAAATAAGTGTCTCAGCTTT 59.758 40.000 0.00 0.00 0.00 3.51
2402 3044 5.241506 TCCCAAAATAAGTGTCTCAGCTTTG 59.758 40.000 0.00 0.00 0.00 2.77
2403 3045 5.010012 CCCAAAATAAGTGTCTCAGCTTTGT 59.990 40.000 0.00 0.00 0.00 2.83
2404 3046 6.206634 CCCAAAATAAGTGTCTCAGCTTTGTA 59.793 38.462 0.00 0.00 0.00 2.41
2405 3047 7.078228 CCAAAATAAGTGTCTCAGCTTTGTAC 58.922 38.462 0.00 0.00 0.00 2.90
2406 3048 7.041098 CCAAAATAAGTGTCTCAGCTTTGTACT 60.041 37.037 0.00 0.00 0.00 2.73
2407 3049 8.988934 CAAAATAAGTGTCTCAGCTTTGTACTA 58.011 33.333 0.00 0.00 0.00 1.82
2408 3050 9.555727 AAAATAAGTGTCTCAGCTTTGTACTAA 57.444 29.630 0.00 0.00 0.00 2.24
2409 3051 8.535690 AATAAGTGTCTCAGCTTTGTACTAAC 57.464 34.615 0.00 0.00 0.00 2.34
2410 3052 5.793030 AGTGTCTCAGCTTTGTACTAACT 57.207 39.130 0.00 0.00 0.00 2.24
2411 3053 5.774630 AGTGTCTCAGCTTTGTACTAACTC 58.225 41.667 0.00 0.00 0.00 3.01
2412 3054 5.536916 AGTGTCTCAGCTTTGTACTAACTCT 59.463 40.000 0.00 0.00 0.00 3.24
2413 3055 5.631512 GTGTCTCAGCTTTGTACTAACTCTG 59.368 44.000 0.00 1.84 0.00 3.35
2414 3056 5.535030 TGTCTCAGCTTTGTACTAACTCTGA 59.465 40.000 12.93 12.93 0.00 3.27
2415 3057 6.090129 GTCTCAGCTTTGTACTAACTCTGAG 58.910 44.000 23.41 23.41 44.27 3.35
2416 3058 5.770663 TCTCAGCTTTGTACTAACTCTGAGT 59.229 40.000 25.60 4.06 43.70 3.41
2417 3059 6.940867 TCTCAGCTTTGTACTAACTCTGAGTA 59.059 38.462 25.60 17.50 43.70 2.59
2418 3060 7.612244 TCTCAGCTTTGTACTAACTCTGAGTAT 59.388 37.037 25.60 4.44 43.70 2.12
2419 3061 8.803397 TCAGCTTTGTACTAACTCTGAGTATA 57.197 34.615 11.30 5.34 32.21 1.47
2420 3062 9.409918 TCAGCTTTGTACTAACTCTGAGTATAT 57.590 33.333 11.30 0.00 32.21 0.86
2423 3065 9.804758 GCTTTGTACTAACTCTGAGTATATTGT 57.195 33.333 11.30 5.62 32.21 2.71
2449 3091 2.945008 CCATTTCGGCTAGCAATTCAGA 59.055 45.455 18.24 2.77 0.00 3.27
2544 3186 4.017808 GGCAGACTAAGAGAGGTACTGAA 58.982 47.826 0.00 0.00 41.55 3.02
2616 3258 5.340403 CAGTTGTGAAAATGTTGCTGATACG 59.660 40.000 0.00 0.00 0.00 3.06
2893 3536 0.517316 GTTGCCGAGTCATTGACCAC 59.483 55.000 13.14 7.25 32.18 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.961264 ATTCATGCATGATGTATTCTAGAAGAT 57.039 29.630 29.13 11.94 36.56 2.40
7 8 9.788889 AATTCATGCATGATGTATTCTAGAAGA 57.211 29.630 29.13 10.10 36.56 2.87
18 19 8.916062 TCAAGGTTAATAATTCATGCATGATGT 58.084 29.630 29.13 21.09 36.56 3.06
19 20 9.188588 GTCAAGGTTAATAATTCATGCATGATG 57.811 33.333 29.13 18.76 36.56 3.07
20 21 8.916062 TGTCAAGGTTAATAATTCATGCATGAT 58.084 29.630 29.13 18.10 36.56 2.45
21 22 8.291191 TGTCAAGGTTAATAATTCATGCATGA 57.709 30.769 25.42 25.42 34.44 3.07
22 23 8.929827 TTGTCAAGGTTAATAATTCATGCATG 57.070 30.769 21.07 21.07 0.00 4.06
23 24 8.752187 ACTTGTCAAGGTTAATAATTCATGCAT 58.248 29.630 16.85 0.00 0.00 3.96
24 25 8.121305 ACTTGTCAAGGTTAATAATTCATGCA 57.879 30.769 16.85 0.00 0.00 3.96
25 26 8.986477 AACTTGTCAAGGTTAATAATTCATGC 57.014 30.769 16.85 0.00 0.00 4.06
41 42 5.092554 TGTGTAGACCTTGAACTTGTCAA 57.907 39.130 0.00 0.00 44.20 3.18
42 43 4.746535 TGTGTAGACCTTGAACTTGTCA 57.253 40.909 0.00 0.00 0.00 3.58
43 44 4.873827 TGTTGTGTAGACCTTGAACTTGTC 59.126 41.667 0.00 0.00 0.00 3.18
44 45 4.839121 TGTTGTGTAGACCTTGAACTTGT 58.161 39.130 0.00 0.00 0.00 3.16
45 46 5.811399 TTGTTGTGTAGACCTTGAACTTG 57.189 39.130 0.00 0.00 0.00 3.16
46 47 6.827586 TTTTGTTGTGTAGACCTTGAACTT 57.172 33.333 0.00 0.00 0.00 2.66
47 48 6.827586 TTTTTGTTGTGTAGACCTTGAACT 57.172 33.333 0.00 0.00 0.00 3.01
92 93 0.040204 CCAAGCCTTCCCACAAGGAT 59.960 55.000 4.49 0.00 46.94 3.24
115 116 3.621268 TCGTTTTAATCCGCTTGATGGAG 59.379 43.478 0.00 0.00 39.30 3.86
120 121 4.389687 GGTACTTCGTTTTAATCCGCTTGA 59.610 41.667 0.00 0.00 0.00 3.02
165 166 5.149273 CACATTTTCAAAGATGGTGAGACG 58.851 41.667 0.00 0.00 0.00 4.18
171 172 7.729116 AGATCAAACACATTTTCAAAGATGGT 58.271 30.769 0.00 0.00 0.00 3.55
193 194 7.944554 TCATTTCTAGAACAACCTCCAAAAGAT 59.055 33.333 4.18 0.00 0.00 2.40
203 205 7.873505 ACAAGAGTACTCATTTCTAGAACAACC 59.126 37.037 24.44 0.00 0.00 3.77
222 224 0.034059 CAAGCTCGTCCCACAAGAGT 59.966 55.000 0.00 0.00 34.69 3.24
224 226 0.756294 TTCAAGCTCGTCCCACAAGA 59.244 50.000 0.00 0.00 0.00 3.02
280 282 8.908903 CGGGAACTCTAGAGCTTATATGAATAT 58.091 37.037 19.97 0.00 0.00 1.28
291 293 2.217510 TGAACGGGAACTCTAGAGCT 57.782 50.000 19.97 7.64 0.00 4.09
292 294 3.528597 AATGAACGGGAACTCTAGAGC 57.471 47.619 19.97 4.23 0.00 4.09
304 306 8.986477 ATTAGGAAAATTCTCAAAATGAACGG 57.014 30.769 0.00 0.00 0.00 4.44
339 341 0.469917 ACATGGGCATTAGTCTCGGG 59.530 55.000 0.00 0.00 0.00 5.14
344 346 7.510549 ACATATAAACACATGGGCATTAGTC 57.489 36.000 0.00 0.00 0.00 2.59
374 781 5.894807 ACCATTTGAGCTTTATTTGGATCG 58.105 37.500 9.71 0.00 0.00 3.69
376 783 7.400052 ACCTAACCATTTGAGCTTTATTTGGAT 59.600 33.333 9.71 2.44 0.00 3.41
415 822 9.293404 GGAACTTAAACTCTAATAGGTTGGTTT 57.707 33.333 0.00 0.00 35.32 3.27
416 823 8.442374 TGGAACTTAAACTCTAATAGGTTGGTT 58.558 33.333 0.00 0.00 35.32 3.67
417 824 7.981142 TGGAACTTAAACTCTAATAGGTTGGT 58.019 34.615 0.00 0.00 35.32 3.67
418 825 8.319146 TCTGGAACTTAAACTCTAATAGGTTGG 58.681 37.037 0.00 0.00 35.32 3.77
419 826 9.152595 GTCTGGAACTTAAACTCTAATAGGTTG 57.847 37.037 0.00 0.00 35.32 3.77
420 827 9.102453 AGTCTGGAACTTAAACTCTAATAGGTT 57.898 33.333 0.00 0.00 39.05 3.50
421 828 8.667592 AGTCTGGAACTTAAACTCTAATAGGT 57.332 34.615 0.00 0.00 33.03 3.08
422 829 9.372369 CAAGTCTGGAACTTAAACTCTAATAGG 57.628 37.037 0.00 0.00 46.69 2.57
423 830 9.372369 CCAAGTCTGGAACTTAAACTCTAATAG 57.628 37.037 0.00 0.00 46.69 1.73
424 831 7.822822 GCCAAGTCTGGAACTTAAACTCTAATA 59.177 37.037 0.00 0.00 46.69 0.98
425 832 6.655425 GCCAAGTCTGGAACTTAAACTCTAAT 59.345 38.462 0.00 0.00 46.69 1.73
426 833 5.995897 GCCAAGTCTGGAACTTAAACTCTAA 59.004 40.000 0.00 0.00 46.69 2.10
427 834 5.071250 TGCCAAGTCTGGAACTTAAACTCTA 59.929 40.000 0.00 0.00 46.69 2.43
428 835 4.141482 TGCCAAGTCTGGAACTTAAACTCT 60.141 41.667 0.00 0.00 46.69 3.24
429 836 4.134563 TGCCAAGTCTGGAACTTAAACTC 58.865 43.478 0.00 0.00 46.69 3.01
430 837 4.164843 TGCCAAGTCTGGAACTTAAACT 57.835 40.909 0.00 0.00 46.69 2.66
431 838 5.453567 AATGCCAAGTCTGGAACTTAAAC 57.546 39.130 0.00 0.00 46.69 2.01
432 839 6.206634 CACTAATGCCAAGTCTGGAACTTAAA 59.793 38.462 0.00 0.00 46.69 1.52
433 840 5.705441 CACTAATGCCAAGTCTGGAACTTAA 59.295 40.000 0.00 0.00 46.69 1.85
434 841 5.012664 TCACTAATGCCAAGTCTGGAACTTA 59.987 40.000 0.00 0.00 46.69 2.24
436 843 3.327757 TCACTAATGCCAAGTCTGGAACT 59.672 43.478 0.00 0.00 46.92 3.01
437 844 3.674997 TCACTAATGCCAAGTCTGGAAC 58.325 45.455 0.00 0.00 46.92 3.62
438 845 4.574674 ATCACTAATGCCAAGTCTGGAA 57.425 40.909 0.00 0.00 46.92 3.53
439 846 4.263462 ACAATCACTAATGCCAAGTCTGGA 60.263 41.667 0.00 0.00 46.92 3.86
440 847 4.012374 ACAATCACTAATGCCAAGTCTGG 58.988 43.478 0.00 0.00 46.65 3.86
441 848 6.932356 ATACAATCACTAATGCCAAGTCTG 57.068 37.500 0.00 0.00 0.00 3.51
442 849 7.944729 AAATACAATCACTAATGCCAAGTCT 57.055 32.000 0.00 0.00 0.00 3.24
443 850 8.986477 AAAAATACAATCACTAATGCCAAGTC 57.014 30.769 0.00 0.00 0.00 3.01
469 876 6.647481 TCGACGAAAGGTCTGAAATAAATTCA 59.353 34.615 0.00 0.00 45.23 2.57
470 877 7.057149 TCGACGAAAGGTCTGAAATAAATTC 57.943 36.000 0.00 0.00 43.79 2.17
471 878 7.119262 ACATCGACGAAAGGTCTGAAATAAATT 59.881 33.333 0.00 0.00 43.79 1.82
472 879 6.594159 ACATCGACGAAAGGTCTGAAATAAAT 59.406 34.615 0.00 0.00 43.79 1.40
473 880 5.929992 ACATCGACGAAAGGTCTGAAATAAA 59.070 36.000 0.00 0.00 43.79 1.40
474 881 5.475719 ACATCGACGAAAGGTCTGAAATAA 58.524 37.500 0.00 0.00 43.79 1.40
475 882 5.068234 ACATCGACGAAAGGTCTGAAATA 57.932 39.130 0.00 0.00 43.79 1.40
476 883 3.926616 ACATCGACGAAAGGTCTGAAAT 58.073 40.909 0.00 0.00 43.79 2.17
477 884 3.380479 ACATCGACGAAAGGTCTGAAA 57.620 42.857 0.00 0.00 43.79 2.69
478 885 3.668757 CGTACATCGACGAAAGGTCTGAA 60.669 47.826 0.00 0.00 45.82 3.02
479 886 2.159612 CGTACATCGACGAAAGGTCTGA 60.160 50.000 0.00 0.00 45.82 3.27
480 887 2.174764 CGTACATCGACGAAAGGTCTG 58.825 52.381 0.00 0.00 45.82 3.51
481 888 1.808945 ACGTACATCGACGAAAGGTCT 59.191 47.619 0.00 0.00 45.82 3.85
482 889 2.253392 ACGTACATCGACGAAAGGTC 57.747 50.000 0.00 0.00 45.82 3.85
483 890 2.030893 TGAACGTACATCGACGAAAGGT 60.031 45.455 0.00 3.49 45.82 3.50
484 891 2.587956 TGAACGTACATCGACGAAAGG 58.412 47.619 0.00 0.00 45.82 3.11
485 892 3.057739 CACTGAACGTACATCGACGAAAG 59.942 47.826 0.00 0.00 45.82 2.62
486 893 2.975193 CACTGAACGTACATCGACGAAA 59.025 45.455 0.00 0.00 45.82 3.46
487 894 2.577450 CACTGAACGTACATCGACGAA 58.423 47.619 0.00 0.00 45.82 3.85
488 895 1.135888 CCACTGAACGTACATCGACGA 60.136 52.381 0.00 0.00 45.82 4.20
490 897 1.200716 TCCCACTGAACGTACATCGAC 59.799 52.381 0.00 0.00 42.86 4.20
491 898 1.471287 CTCCCACTGAACGTACATCGA 59.529 52.381 0.00 0.00 42.86 3.59
492 899 1.469251 CCTCCCACTGAACGTACATCG 60.469 57.143 0.00 0.00 46.00 3.84
493 900 1.822990 TCCTCCCACTGAACGTACATC 59.177 52.381 0.00 0.00 0.00 3.06
494 901 1.825474 CTCCTCCCACTGAACGTACAT 59.175 52.381 0.00 0.00 0.00 2.29
495 902 1.202964 TCTCCTCCCACTGAACGTACA 60.203 52.381 0.00 0.00 0.00 2.90
496 903 1.201880 GTCTCCTCCCACTGAACGTAC 59.798 57.143 0.00 0.00 0.00 3.67
497 904 1.542492 GTCTCCTCCCACTGAACGTA 58.458 55.000 0.00 0.00 0.00 3.57
498 905 1.524863 CGTCTCCTCCCACTGAACGT 61.525 60.000 0.00 0.00 0.00 3.99
499 906 1.213013 CGTCTCCTCCCACTGAACG 59.787 63.158 0.00 0.00 0.00 3.95
500 907 0.680061 AACGTCTCCTCCCACTGAAC 59.320 55.000 0.00 0.00 0.00 3.18
501 908 1.343465 GAAACGTCTCCTCCCACTGAA 59.657 52.381 0.00 0.00 0.00 3.02
502 909 0.966920 GAAACGTCTCCTCCCACTGA 59.033 55.000 0.00 0.00 0.00 3.41
503 910 0.969894 AGAAACGTCTCCTCCCACTG 59.030 55.000 0.00 0.00 0.00 3.66
504 911 2.599408 TAGAAACGTCTCCTCCCACT 57.401 50.000 0.00 0.00 35.12 4.00
505 912 2.223525 CGATAGAAACGTCTCCTCCCAC 60.224 54.545 0.00 0.00 35.12 4.61
506 913 2.022195 CGATAGAAACGTCTCCTCCCA 58.978 52.381 0.00 0.00 35.12 4.37
507 914 2.295885 TCGATAGAAACGTCTCCTCCC 58.704 52.381 0.00 0.00 46.15 4.30
521 928 5.384063 AATACATCACAGGCTCTCGATAG 57.616 43.478 0.00 0.00 0.00 2.08
522 929 5.791336 AAATACATCACAGGCTCTCGATA 57.209 39.130 0.00 0.00 0.00 2.92
523 930 4.679373 AAATACATCACAGGCTCTCGAT 57.321 40.909 0.00 0.00 0.00 3.59
524 931 5.536538 AGATAAATACATCACAGGCTCTCGA 59.463 40.000 0.00 0.00 0.00 4.04
525 932 5.777802 AGATAAATACATCACAGGCTCTCG 58.222 41.667 0.00 0.00 0.00 4.04
526 933 6.753180 TGAGATAAATACATCACAGGCTCTC 58.247 40.000 0.00 0.00 0.00 3.20
527 934 6.737720 TGAGATAAATACATCACAGGCTCT 57.262 37.500 0.00 0.00 0.00 4.09
528 935 7.212976 TCTTGAGATAAATACATCACAGGCTC 58.787 38.462 0.00 0.00 29.13 4.70
529 936 7.129457 TCTTGAGATAAATACATCACAGGCT 57.871 36.000 0.00 0.00 29.13 4.58
530 937 7.658982 TCATCTTGAGATAAATACATCACAGGC 59.341 37.037 0.00 0.00 32.63 4.85
531 938 9.722184 ATCATCTTGAGATAAATACATCACAGG 57.278 33.333 0.00 0.00 32.63 4.00
538 945 9.889128 TTGTCACATCATCTTGAGATAAATACA 57.111 29.630 0.00 0.00 32.63 2.29
542 949 9.942850 TTAGTTGTCACATCATCTTGAGATAAA 57.057 29.630 0.00 0.00 32.63 1.40
543 950 9.591792 CTTAGTTGTCACATCATCTTGAGATAA 57.408 33.333 0.00 0.00 32.63 1.75
544 951 8.753133 ACTTAGTTGTCACATCATCTTGAGATA 58.247 33.333 0.00 0.00 32.63 1.98
545 952 7.619050 ACTTAGTTGTCACATCATCTTGAGAT 58.381 34.615 0.00 0.00 34.56 2.75
546 953 6.997655 ACTTAGTTGTCACATCATCTTGAGA 58.002 36.000 0.00 0.00 0.00 3.27
547 954 7.095910 AGACTTAGTTGTCACATCATCTTGAG 58.904 38.462 0.00 0.00 39.27 3.02
548 955 6.997655 AGACTTAGTTGTCACATCATCTTGA 58.002 36.000 0.00 0.00 39.27 3.02
549 956 7.664082 AAGACTTAGTTGTCACATCATCTTG 57.336 36.000 0.00 0.00 39.27 3.02
550 957 7.933577 TGAAAGACTTAGTTGTCACATCATCTT 59.066 33.333 0.00 0.00 39.27 2.40
551 958 7.445121 TGAAAGACTTAGTTGTCACATCATCT 58.555 34.615 0.00 0.00 39.27 2.90
552 959 7.658179 TGAAAGACTTAGTTGTCACATCATC 57.342 36.000 0.00 0.00 39.27 2.92
553 960 8.450578 TTTGAAAGACTTAGTTGTCACATCAT 57.549 30.769 0.00 0.00 39.27 2.45
554 961 7.857734 TTTGAAAGACTTAGTTGTCACATCA 57.142 32.000 0.00 0.00 39.27 3.07
555 962 8.398665 AGTTTTGAAAGACTTAGTTGTCACATC 58.601 33.333 0.00 0.00 39.27 3.06
556 963 8.184192 CAGTTTTGAAAGACTTAGTTGTCACAT 58.816 33.333 0.00 0.00 39.27 3.21
557 964 7.174253 ACAGTTTTGAAAGACTTAGTTGTCACA 59.826 33.333 0.00 0.00 39.27 3.58
558 965 7.527457 ACAGTTTTGAAAGACTTAGTTGTCAC 58.473 34.615 0.00 0.00 39.27 3.67
559 966 7.681939 ACAGTTTTGAAAGACTTAGTTGTCA 57.318 32.000 0.00 0.00 39.27 3.58
560 967 8.965986 AAACAGTTTTGAAAGACTTAGTTGTC 57.034 30.769 0.00 0.00 37.23 3.18
604 1011 9.938280 GCACATACACTAATCCCTATAAATACA 57.062 33.333 0.00 0.00 0.00 2.29
605 1012 9.938280 TGCACATACACTAATCCCTATAAATAC 57.062 33.333 0.00 0.00 0.00 1.89
610 1017 9.267071 ACATATGCACATACACTAATCCCTATA 57.733 33.333 1.58 0.00 0.00 1.31
611 1018 8.150827 ACATATGCACATACACTAATCCCTAT 57.849 34.615 1.58 0.00 0.00 2.57
612 1019 7.553504 ACATATGCACATACACTAATCCCTA 57.446 36.000 1.58 0.00 0.00 3.53
613 1020 6.439636 ACATATGCACATACACTAATCCCT 57.560 37.500 1.58 0.00 0.00 4.20
614 1021 8.040727 TCATACATATGCACATACACTAATCCC 58.959 37.037 1.58 0.00 33.76 3.85
615 1022 9.091784 CTCATACATATGCACATACACTAATCC 57.908 37.037 1.58 0.00 33.76 3.01
616 1023 9.645059 ACTCATACATATGCACATACACTAATC 57.355 33.333 1.58 0.00 33.76 1.75
617 1024 9.428097 CACTCATACATATGCACATACACTAAT 57.572 33.333 1.58 0.00 33.76 1.73
618 1025 8.421002 ACACTCATACATATGCACATACACTAA 58.579 33.333 1.58 0.00 33.76 2.24
619 1026 7.951591 ACACTCATACATATGCACATACACTA 58.048 34.615 1.58 0.00 33.76 2.74
620 1027 6.820335 ACACTCATACATATGCACATACACT 58.180 36.000 1.58 0.00 33.76 3.55
621 1028 7.482654 AACACTCATACATATGCACATACAC 57.517 36.000 1.58 0.00 33.76 2.90
622 1029 7.467131 GCAAACACTCATACATATGCACATACA 60.467 37.037 1.58 0.00 33.76 2.29
623 1030 6.852853 GCAAACACTCATACATATGCACATAC 59.147 38.462 1.58 0.00 33.76 2.39
624 1031 6.541641 TGCAAACACTCATACATATGCACATA 59.458 34.615 1.58 0.00 37.61 2.29
625 1032 5.357596 TGCAAACACTCATACATATGCACAT 59.642 36.000 1.58 0.00 37.61 3.21
626 1033 4.699257 TGCAAACACTCATACATATGCACA 59.301 37.500 1.58 0.00 37.61 4.57
627 1034 5.233957 TGCAAACACTCATACATATGCAC 57.766 39.130 1.58 0.00 37.61 4.57
628 1035 7.565323 TTATGCAAACACTCATACATATGCA 57.435 32.000 1.58 0.00 45.36 3.96
629 1036 8.854979 TTTTATGCAAACACTCATACATATGC 57.145 30.769 1.58 0.00 33.76 3.14
633 1040 9.539825 TTTGTTTTTATGCAAACACTCATACAT 57.460 25.926 1.19 0.00 44.51 2.29
634 1041 8.932945 TTTGTTTTTATGCAAACACTCATACA 57.067 26.923 1.19 0.00 44.51 2.29
638 1045 9.539825 ACATATTTGTTTTTATGCAAACACTCA 57.460 25.926 1.19 0.00 44.51 3.41
639 1046 9.796062 CACATATTTGTTTTTATGCAAACACTC 57.204 29.630 1.19 0.00 44.51 3.51
640 1047 9.539825 TCACATATTTGTTTTTATGCAAACACT 57.460 25.926 1.19 0.00 44.51 3.55
645 1052 8.867935 CGGAATCACATATTTGTTTTTATGCAA 58.132 29.630 0.00 0.00 32.34 4.08
646 1053 7.009999 GCGGAATCACATATTTGTTTTTATGCA 59.990 33.333 0.00 0.00 32.34 3.96
647 1054 7.009999 TGCGGAATCACATATTTGTTTTTATGC 59.990 33.333 0.00 0.00 32.34 3.14
648 1055 8.404889 TGCGGAATCACATATTTGTTTTTATG 57.595 30.769 0.00 0.00 32.34 1.90
649 1056 7.706179 CCTGCGGAATCACATATTTGTTTTTAT 59.294 33.333 0.00 0.00 32.34 1.40
650 1057 7.032580 CCTGCGGAATCACATATTTGTTTTTA 58.967 34.615 0.00 0.00 32.34 1.52
651 1058 5.868801 CCTGCGGAATCACATATTTGTTTTT 59.131 36.000 0.00 0.00 32.34 1.94
652 1059 5.184864 TCCTGCGGAATCACATATTTGTTTT 59.815 36.000 0.00 0.00 32.34 2.43
653 1060 4.704540 TCCTGCGGAATCACATATTTGTTT 59.295 37.500 0.00 0.00 32.34 2.83
656 1063 4.898829 TTCCTGCGGAATCACATATTTG 57.101 40.909 6.01 0.00 36.71 2.32
674 1081 9.722056 CAACTTCAAATAGTAACTATGCATTCC 57.278 33.333 3.54 0.00 0.00 3.01
689 1096 4.274602 TCACCGGCTACAACTTCAAATA 57.725 40.909 0.00 0.00 0.00 1.40
690 1097 3.134574 TCACCGGCTACAACTTCAAAT 57.865 42.857 0.00 0.00 0.00 2.32
691 1098 2.623878 TCACCGGCTACAACTTCAAA 57.376 45.000 0.00 0.00 0.00 2.69
715 1204 9.965824 CAGTGGAAAATAGCTTTTAGAAAGAAA 57.034 29.630 0.00 0.00 34.73 2.52
716 1205 8.576442 CCAGTGGAAAATAGCTTTTAGAAAGAA 58.424 33.333 1.68 0.00 34.73 2.52
717 1206 7.942341 TCCAGTGGAAAATAGCTTTTAGAAAGA 59.058 33.333 10.20 0.00 34.73 2.52
718 1207 8.110860 TCCAGTGGAAAATAGCTTTTAGAAAG 57.889 34.615 10.20 0.00 34.73 2.62
727 1218 3.806949 TGGTTCCAGTGGAAAATAGCT 57.193 42.857 26.19 0.00 43.86 3.32
878 1383 0.841961 TCAGGCCATGGATCTGGAAG 59.158 55.000 25.52 9.00 38.69 3.46
914 1422 0.178992 TGAACTGCTGGGGTCCTTTG 60.179 55.000 0.00 0.00 0.00 2.77
922 1430 1.554160 AGAGATCAGTGAACTGCTGGG 59.446 52.381 7.76 0.00 43.46 4.45
944 1452 1.422781 TCGGATATCCACGGAGTAGGT 59.577 52.381 21.70 0.00 41.61 3.08
945 1453 2.195741 TCGGATATCCACGGAGTAGG 57.804 55.000 21.70 2.06 41.61 3.18
958 1466 1.772453 GGGGGTGAAGGAATTCGGATA 59.228 52.381 0.00 0.00 0.00 2.59
1141 1653 2.019984 GAGGATGGTGATGTCCTTTGC 58.980 52.381 0.00 0.00 44.70 3.68
1143 1655 1.566231 GGGAGGATGGTGATGTCCTTT 59.434 52.381 0.00 0.00 44.70 3.11
1186 1698 3.851128 GGCAGGCGGGAGGTAGAC 61.851 72.222 0.00 0.00 0.00 2.59
1570 2083 2.202544 CACGAGCGAGCTCACCTC 60.203 66.667 22.81 16.53 42.86 3.85
1826 2339 3.698040 CCCACTCCCAATCAATTTCTCAG 59.302 47.826 0.00 0.00 0.00 3.35
1884 2397 3.636231 TGGAAGCCGTGACCCTGG 61.636 66.667 0.00 0.00 0.00 4.45
1902 2415 2.202932 CATGTCGGCCGGAAGAGG 60.203 66.667 27.83 2.70 0.00 3.69
1969 2482 3.221771 CGGAGAACAGGAGATCTCATCT 58.778 50.000 23.85 18.93 43.34 2.90
2056 2570 5.047802 ACAGCTACAAGCATGTTTTAAGCAT 60.048 36.000 20.68 10.49 45.56 3.79
2064 2578 4.136796 TGAAGAACAGCTACAAGCATGTT 58.863 39.130 0.00 13.06 45.56 2.71
2112 2626 9.251440 TGACAGTAGTAACAATATACTCCTTGT 57.749 33.333 0.00 0.00 37.34 3.16
2135 2649 7.601856 TGGTTTGAATTTGAACTCCATATGAC 58.398 34.615 3.65 0.00 0.00 3.06
2348 2990 5.251764 GAGTATTATGCAGCATCCCAATCT 58.748 41.667 12.38 6.18 0.00 2.40
2369 3011 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2370 3012 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2371 3013 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2372 3014 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2373 3015 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
2375 3017 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
2376 3018 3.125316 GCTGAGACACTTATTTTGGGACG 59.875 47.826 0.00 0.00 0.00 4.79
2377 3019 4.327680 AGCTGAGACACTTATTTTGGGAC 58.672 43.478 0.00 0.00 0.00 4.46
2378 3020 4.640771 AGCTGAGACACTTATTTTGGGA 57.359 40.909 0.00 0.00 0.00 4.37
2379 3021 5.010012 ACAAAGCTGAGACACTTATTTTGGG 59.990 40.000 0.00 0.00 0.00 4.12
2380 3022 6.076981 ACAAAGCTGAGACACTTATTTTGG 57.923 37.500 0.00 0.00 0.00 3.28
2381 3023 7.865707 AGTACAAAGCTGAGACACTTATTTTG 58.134 34.615 0.00 0.00 0.00 2.44
2382 3024 9.555727 TTAGTACAAAGCTGAGACACTTATTTT 57.444 29.630 0.00 0.00 0.00 1.82
2383 3025 8.989980 GTTAGTACAAAGCTGAGACACTTATTT 58.010 33.333 0.00 0.00 0.00 1.40
2384 3026 8.368668 AGTTAGTACAAAGCTGAGACACTTATT 58.631 33.333 0.00 0.00 0.00 1.40
2385 3027 7.897864 AGTTAGTACAAAGCTGAGACACTTAT 58.102 34.615 0.00 0.00 0.00 1.73
2386 3028 7.230913 AGAGTTAGTACAAAGCTGAGACACTTA 59.769 37.037 0.00 0.00 0.00 2.24
2387 3029 6.041069 AGAGTTAGTACAAAGCTGAGACACTT 59.959 38.462 0.00 0.00 0.00 3.16
2388 3030 5.536916 AGAGTTAGTACAAAGCTGAGACACT 59.463 40.000 0.00 0.00 0.00 3.55
2389 3031 5.631512 CAGAGTTAGTACAAAGCTGAGACAC 59.368 44.000 0.00 0.00 0.00 3.67
2390 3032 5.535030 TCAGAGTTAGTACAAAGCTGAGACA 59.465 40.000 0.00 0.00 0.00 3.41
2391 3033 6.015027 TCAGAGTTAGTACAAAGCTGAGAC 57.985 41.667 0.00 0.00 0.00 3.36
2392 3034 5.770663 ACTCAGAGTTAGTACAAAGCTGAGA 59.229 40.000 25.73 9.57 46.52 3.27
2394 3036 7.704578 ATACTCAGAGTTAGTACAAAGCTGA 57.295 36.000 8.80 0.00 32.47 4.26
2397 3039 9.804758 ACAATATACTCAGAGTTAGTACAAAGC 57.195 33.333 8.80 0.00 32.47 3.51
2404 3046 8.812972 TGGAAACACAATATACTCAGAGTTAGT 58.187 33.333 8.80 0.00 33.40 2.24
2424 3066 3.782889 ATTGCTAGCCGAAATGGAAAC 57.217 42.857 13.29 0.00 42.00 2.78
2544 3186 9.649316 AGAGAAGCCTTACTAAGAGTATATTGT 57.351 33.333 0.00 0.00 29.64 2.71
2742 3385 7.178274 TGAACAAGGATATTTGTAGCCATTTGT 59.822 33.333 0.00 0.00 40.24 2.83


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

AutoCloner maintained by Alex Coulton.