Multiple sequence alignment - TraesCS6B01G414900

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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 TraesCS6B01G414900 chr6B 100.000 4429 0 0 1 4429 687730774 687735202 0.000000e+00 8179.0
1 TraesCS6B01G414900 chr6B 85.100 1255 173 8 2183 3428 688033490 688032241 0.000000e+00 1269.0
2 TraesCS6B01G414900 chr6B 83.439 1262 203 4 2172 3432 688064585 688063329 0.000000e+00 1168.0
3 TraesCS6B01G414900 chr6B 83.531 1263 174 17 2173 3432 688125227 688123996 0.000000e+00 1149.0
4 TraesCS6B01G414900 chr6B 84.122 951 148 3 2182 3130 687876236 687877185 0.000000e+00 917.0
5 TraesCS6B01G414900 chr6B 73.285 831 189 25 1012 1821 687135221 687134403 1.570000e-69 274.0
6 TraesCS6B01G414900 chr6B 79.365 315 49 8 3120 3433 687878516 687878815 1.610000e-49 207.0
7 TraesCS6B01G414900 chr6D 95.969 1811 73 0 1850 3660 452841056 452842866 0.000000e+00 2940.0
8 TraesCS6B01G414900 chr6D 95.352 839 37 2 1008 1845 452839741 452840578 0.000000e+00 1332.0
9 TraesCS6B01G414900 chr6D 84.579 1258 184 7 2180 3432 452907500 452908752 0.000000e+00 1240.0
10 TraesCS6B01G414900 chr6D 84.382 1255 177 9 2181 3432 452931169 452929931 0.000000e+00 1214.0
11 TraesCS6B01G414900 chr6D 76.229 1119 193 45 1009 2085 452906343 452907430 3.920000e-145 525.0
12 TraesCS6B01G414900 chr6D 77.712 839 154 26 1265 2085 452848794 452849617 2.400000e-132 483.0
13 TraesCS6B01G414900 chr6D 77.616 822 145 29 1013 1822 452485770 452484976 3.120000e-126 462.0
14 TraesCS6B01G414900 chr6D 88.131 396 33 10 1 385 452829069 452829461 4.040000e-125 459.0
15 TraesCS6B01G414900 chr6D 92.398 171 10 1 3660 3827 452843306 452843476 1.590000e-59 241.0
16 TraesCS6B01G414900 chr6D 81.313 198 11 14 844 1016 452839456 452839652 2.150000e-28 137.0
17 TraesCS6B01G414900 chr6D 81.034 174 18 4 535 695 452829690 452829861 1.670000e-24 124.0
18 TraesCS6B01G414900 chr6D 93.182 44 2 1 3660 3703 307887061 307887103 3.700000e-06 63.9
19 TraesCS6B01G414900 chr6A 95.583 1811 80 0 1850 3660 598790605 598792415 0.000000e+00 2902.0
20 TraesCS6B01G414900 chr6A 78.549 2191 376 57 1271 3429 598810406 598812534 0.000000e+00 1356.0
21 TraesCS6B01G414900 chr6A 94.222 848 46 3 1009 1855 598789723 598790568 0.000000e+00 1291.0
22 TraesCS6B01G414900 chr6A 83.984 1255 190 8 2182 3430 598860595 598861844 0.000000e+00 1194.0
23 TraesCS6B01G414900 chr6A 83.767 1269 184 10 2172 3432 598925569 598924315 0.000000e+00 1182.0
24 TraesCS6B01G414900 chr6A 77.901 1086 194 34 1012 2085 598926682 598925631 6.250000e-178 634.0
25 TraesCS6B01G414900 chr6A 77.482 826 139 34 1013 1822 598157615 598156821 6.760000e-123 451.0
26 TraesCS6B01G414900 chr6A 87.563 394 37 8 1 385 598768208 598768598 3.140000e-121 446.0
27 TraesCS6B01G414900 chr6A 88.889 252 16 8 677 921 598789250 598789496 2.590000e-77 300.0
28 TraesCS6B01G414900 chr6A 73.416 805 179 28 1009 1791 598189262 598190053 7.300000e-68 268.0
29 TraesCS6B01G414900 chr6A 89.116 147 13 3 380 526 598768645 598768788 3.520000e-41 180.0
30 TraesCS6B01G414900 chr7B 85.974 606 73 10 3827 4429 115567391 115566795 4.830000e-179 638.0
31 TraesCS6B01G414900 chr7B 83.417 597 82 11 3824 4414 36851456 36852041 5.040000e-149 538.0
32 TraesCS6B01G414900 chr5D 85.554 623 74 6 3822 4429 127883173 127883794 4.830000e-179 638.0
33 TraesCS6B01G414900 chr2B 85.486 627 72 12 3821 4429 427569599 427570224 1.740000e-178 636.0
34 TraesCS6B01G414900 chr2B 84.072 609 80 9 3827 4429 88204811 88204214 4.970000e-159 571.0
35 TraesCS6B01G414900 chr2B 86.154 65 9 0 606 670 140851457 140851521 2.210000e-08 71.3
36 TraesCS6B01G414900 chr4B 86.144 599 69 10 3822 4414 645293269 645293859 6.250000e-178 634.0
37 TraesCS6B01G414900 chr4B 91.489 47 3 1 3660 3706 29497378 29497333 3.700000e-06 63.9
38 TraesCS6B01G414900 chr4B 91.489 47 3 1 3660 3706 29516740 29516695 3.700000e-06 63.9
39 TraesCS6B01G414900 chr4B 93.182 44 2 1 3660 3703 333479181 333479139 3.700000e-06 63.9
40 TraesCS6B01G414900 chr2D 85.427 597 74 9 3824 4414 641574713 641575302 3.790000e-170 608.0
41 TraesCS6B01G414900 chr1D 84.667 600 81 9 3834 4429 411380278 411379686 4.930000e-164 588.0
42 TraesCS6B01G414900 chr3B 87.550 498 55 4 3937 4429 720237008 720237503 1.790000e-158 569.0
43 TraesCS6B01G414900 chr3B 83.793 617 80 10 3827 4427 687574199 687573587 6.430000e-158 568.0
44 TraesCS6B01G414900 chr5B 84.902 563 72 9 3827 4383 611700622 611700067 1.390000e-154 556.0
45 TraesCS6B01G414900 chr5B 97.222 36 1 0 211 246 489198580 489198615 1.330000e-05 62.1
46 TraesCS6B01G414900 chr5A 82.406 557 84 8 3874 4429 168235547 168235004 1.440000e-129 473.0
47 TraesCS6B01G414900 chr1A 81.481 135 20 2 455 588 34176397 34176267 6.060000e-19 106.0
48 TraesCS6B01G414900 chr1A 93.182 44 2 1 3660 3703 252443547 252443505 3.700000e-06 63.9
49 TraesCS6B01G414900 chr7A 95.349 43 2 0 3661 3703 333999642 333999600 7.950000e-08 69.4
50 TraesCS6B01G414900 chr4A 93.182 44 2 1 3660 3703 91639405 91639447 3.700000e-06 63.9
51 TraesCS6B01G414900 chr3A 93.182 44 2 1 3660 3703 599338850 599338808 3.700000e-06 63.9


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 TraesCS6B01G414900 chr6B 687730774 687735202 4428 False 8179.000000 8179 100.0000 1 4429 1 chr6B.!!$F1 4428
1 TraesCS6B01G414900 chr6B 688032241 688033490 1249 True 1269.000000 1269 85.1000 2183 3428 1 chr6B.!!$R2 1245
2 TraesCS6B01G414900 chr6B 688063329 688064585 1256 True 1168.000000 1168 83.4390 2172 3432 1 chr6B.!!$R3 1260
3 TraesCS6B01G414900 chr6B 688123996 688125227 1231 True 1149.000000 1149 83.5310 2173 3432 1 chr6B.!!$R4 1259
4 TraesCS6B01G414900 chr6B 687876236 687878815 2579 False 562.000000 917 81.7435 2182 3433 2 chr6B.!!$F2 1251
5 TraesCS6B01G414900 chr6B 687134403 687135221 818 True 274.000000 274 73.2850 1012 1821 1 chr6B.!!$R1 809
6 TraesCS6B01G414900 chr6D 452929931 452931169 1238 True 1214.000000 1214 84.3820 2181 3432 1 chr6D.!!$R2 1251
7 TraesCS6B01G414900 chr6D 452839456 452843476 4020 False 1162.500000 2940 91.2580 844 3827 4 chr6D.!!$F4 2983
8 TraesCS6B01G414900 chr6D 452906343 452908752 2409 False 882.500000 1240 80.4040 1009 3432 2 chr6D.!!$F5 2423
9 TraesCS6B01G414900 chr6D 452848794 452849617 823 False 483.000000 483 77.7120 1265 2085 1 chr6D.!!$F2 820
10 TraesCS6B01G414900 chr6D 452484976 452485770 794 True 462.000000 462 77.6160 1013 1822 1 chr6D.!!$R1 809
11 TraesCS6B01G414900 chr6D 452829069 452829861 792 False 291.500000 459 84.5825 1 695 2 chr6D.!!$F3 694
12 TraesCS6B01G414900 chr6A 598789250 598792415 3165 False 1497.666667 2902 92.8980 677 3660 3 chr6A.!!$F5 2983
13 TraesCS6B01G414900 chr6A 598810406 598812534 2128 False 1356.000000 1356 78.5490 1271 3429 1 chr6A.!!$F2 2158
14 TraesCS6B01G414900 chr6A 598860595 598861844 1249 False 1194.000000 1194 83.9840 2182 3430 1 chr6A.!!$F3 1248
15 TraesCS6B01G414900 chr6A 598924315 598926682 2367 True 908.000000 1182 80.8340 1012 3432 2 chr6A.!!$R2 2420
16 TraesCS6B01G414900 chr6A 598156821 598157615 794 True 451.000000 451 77.4820 1013 1822 1 chr6A.!!$R1 809
17 TraesCS6B01G414900 chr6A 598768208 598768788 580 False 313.000000 446 88.3395 1 526 2 chr6A.!!$F4 525
18 TraesCS6B01G414900 chr6A 598189262 598190053 791 False 268.000000 268 73.4160 1009 1791 1 chr6A.!!$F1 782
19 TraesCS6B01G414900 chr7B 115566795 115567391 596 True 638.000000 638 85.9740 3827 4429 1 chr7B.!!$R1 602
20 TraesCS6B01G414900 chr7B 36851456 36852041 585 False 538.000000 538 83.4170 3824 4414 1 chr7B.!!$F1 590
21 TraesCS6B01G414900 chr5D 127883173 127883794 621 False 638.000000 638 85.5540 3822 4429 1 chr5D.!!$F1 607
22 TraesCS6B01G414900 chr2B 427569599 427570224 625 False 636.000000 636 85.4860 3821 4429 1 chr2B.!!$F2 608
23 TraesCS6B01G414900 chr2B 88204214 88204811 597 True 571.000000 571 84.0720 3827 4429 1 chr2B.!!$R1 602
24 TraesCS6B01G414900 chr4B 645293269 645293859 590 False 634.000000 634 86.1440 3822 4414 1 chr4B.!!$F1 592
25 TraesCS6B01G414900 chr2D 641574713 641575302 589 False 608.000000 608 85.4270 3824 4414 1 chr2D.!!$F1 590
26 TraesCS6B01G414900 chr1D 411379686 411380278 592 True 588.000000 588 84.6670 3834 4429 1 chr1D.!!$R1 595
27 TraesCS6B01G414900 chr3B 687573587 687574199 612 True 568.000000 568 83.7930 3827 4427 1 chr3B.!!$R1 600
28 TraesCS6B01G414900 chr5B 611700067 611700622 555 True 556.000000 556 84.9020 3827 4383 1 chr5B.!!$R1 556
29 TraesCS6B01G414900 chr5A 168235004 168235547 543 True 473.000000 473 82.4060 3874 4429 1 chr5A.!!$R1 555

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
653 755 0.394216 AGAGTGCTTTGTGCCACACA 60.394 50.0 0.0 0.0 43.02 3.72 F
988 1139 1.207791 ATCGGAGGAGAGCAACCAAT 58.792 50.0 0.0 0.0 0.00 3.16 F
2250 3007 0.320421 CGTCGGGGTGTTCTTGTCAT 60.320 55.0 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 1847 0.534203 TTGACGAAACTGTGGGAGGC 60.534 55.0 0.00 0.00 0.00 4.70 R
2742 3511 0.464916 TCTGCCGCTATCCGTAGACA 60.465 55.0 0.00 0.00 34.38 3.41 R
3943 6528 0.468214 TGGGACGCAAATTTGGACCA 60.468 50.0 19.47 17.23 0.00 4.02 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
156 160 9.794653 TTTAAAGCAAAAACGTTAAAGAAACAC 57.205 25.926 0.00 0.00 38.03 3.32
173 178 1.342174 ACACGAGAAAAACGAGGGCTA 59.658 47.619 0.00 0.00 34.70 3.93
179 184 1.401905 GAAAAACGAGGGCTATGGCTG 59.598 52.381 0.00 0.00 38.73 4.85
239 245 9.838975 CTACATCTTGCTATAAGTGAGACATAG 57.161 37.037 0.00 0.00 0.00 2.23
268 274 0.820891 GTGTGCATGGGCCTATCCTG 60.821 60.000 4.53 0.00 40.13 3.86
283 289 4.082300 CCTATCCTGGATGAGATCAGAACG 60.082 50.000 19.42 0.00 33.11 3.95
289 295 3.181496 TGGATGAGATCAGAACGACTTCG 60.181 47.826 0.00 0.00 46.33 3.79
319 325 5.517054 GCTGTAACCTGTATCTTTCTTCTCG 59.483 44.000 0.00 0.00 0.00 4.04
326 332 5.298276 CCTGTATCTTTCTTCTCGTAGCTCT 59.702 44.000 0.00 0.00 0.00 4.09
352 361 5.491982 ACTCCTCCAGATTGTGTAATCAAC 58.508 41.667 0.00 0.00 44.14 3.18
385 394 3.133542 TGATCCGCTGTGAGATGAATCTT 59.866 43.478 0.00 0.00 37.25 2.40
387 396 4.736126 TCCGCTGTGAGATGAATCTTTA 57.264 40.909 0.00 0.00 37.25 1.85
413 473 6.844097 TTTTTAGGCAAATTACGGGAATCT 57.156 33.333 0.00 0.00 0.00 2.40
453 513 8.801715 AATTGATACACACAACAATCAAAGAC 57.198 30.769 1.19 0.00 40.60 3.01
463 523 4.494091 ACAATCAAAGACGGATCCTGAT 57.506 40.909 10.75 8.85 32.00 2.90
467 527 4.672587 TCAAAGACGGATCCTGATAAGG 57.327 45.455 10.75 0.00 0.00 2.69
472 532 2.900546 GACGGATCCTGATAAGGGTCAT 59.099 50.000 11.84 0.00 40.80 3.06
483 543 2.128771 AAGGGTCATATGTGTGGCAC 57.871 50.000 11.55 11.55 34.56 5.01
497 557 2.429971 TGTGGCACAAACACATGACAAT 59.570 40.909 19.74 0.00 44.16 2.71
499 559 3.870419 GTGGCACAAACACATGACAATTT 59.130 39.130 13.86 0.00 44.16 1.82
500 560 4.025813 GTGGCACAAACACATGACAATTTC 60.026 41.667 13.86 0.00 44.16 2.17
501 561 4.118410 GGCACAAACACATGACAATTTCA 58.882 39.130 0.00 0.00 39.11 2.69
504 564 5.958949 GCACAAACACATGACAATTTCAAAC 59.041 36.000 0.00 0.00 37.92 2.93
506 566 5.866633 ACAAACACATGACAATTTCAAACGT 59.133 32.000 0.00 0.00 37.92 3.99
538 628 9.725019 ATGACAAGTTTAGTAACATGAAGATGA 57.275 29.630 0.00 0.00 36.67 2.92
574 664 6.690957 TGTTAAGCATGACAACTTCTTTTTCG 59.309 34.615 0.00 0.00 0.00 3.46
592 682 8.463607 TCTTTTTCGGATAACAAGTTTCAGTTT 58.536 29.630 0.00 0.00 0.00 2.66
615 717 6.453926 TTTTTCCGGCTAACAACTTTAGTT 57.546 33.333 0.00 0.00 39.12 2.24
616 718 7.565323 TTTTTCCGGCTAACAACTTTAGTTA 57.435 32.000 0.00 0.00 36.32 2.24
617 719 7.748691 TTTTCCGGCTAACAACTTTAGTTAT 57.251 32.000 0.00 0.00 36.32 1.89
618 720 6.730960 TTCCGGCTAACAACTTTAGTTATG 57.269 37.500 0.00 0.00 36.32 1.90
634 736 4.415596 AGTTATGAAAAATGTCAGGGCCA 58.584 39.130 6.18 0.00 0.00 5.36
640 742 0.610232 AAATGTCAGGGCCAGAGTGC 60.610 55.000 6.18 0.00 0.00 4.40
644 746 1.073722 TCAGGGCCAGAGTGCTTTG 59.926 57.895 6.18 0.00 0.00 2.77
648 750 2.647297 GCCAGAGTGCTTTGTGCC 59.353 61.111 0.00 0.00 42.00 5.01
653 755 0.394216 AGAGTGCTTTGTGCCACACA 60.394 50.000 0.00 0.00 43.02 3.72
699 801 3.460857 AGATGGAGATGTTCTTACCGC 57.539 47.619 0.00 0.00 0.00 5.68
719 821 4.142513 CCGCTCCTAACCTACGTAATATCC 60.143 50.000 0.00 0.00 0.00 2.59
739 842 4.637276 TCCGATTTTAGAAGCACAACAGA 58.363 39.130 0.00 0.00 0.00 3.41
742 845 5.163913 CCGATTTTAGAAGCACAACAGAGAG 60.164 44.000 0.00 0.00 0.00 3.20
757 860 6.071560 ACAACAGAGAGGACGTCACATTTATA 60.072 38.462 18.91 0.00 0.00 0.98
812 915 4.065088 GCAATTGAGTATGGATCCGCTTA 58.935 43.478 10.34 0.00 0.00 3.09
813 916 4.515191 GCAATTGAGTATGGATCCGCTTAA 59.485 41.667 10.34 8.61 0.00 1.85
836 939 7.671495 AACAACAGGCAATTGAAAAATATCC 57.329 32.000 10.34 0.00 0.00 2.59
837 940 5.868801 ACAACAGGCAATTGAAAAATATCCG 59.131 36.000 10.34 0.00 0.00 4.18
841 944 4.709397 AGGCAATTGAAAAATATCCGTCCA 59.291 37.500 10.34 0.00 0.00 4.02
886 989 2.352960 GGAGAACGAGCATGGTCAAATC 59.647 50.000 23.68 16.93 0.00 2.17
887 990 2.352960 GAGAACGAGCATGGTCAAATCC 59.647 50.000 23.68 8.34 0.00 3.01
888 991 2.026822 AGAACGAGCATGGTCAAATCCT 60.027 45.455 23.68 10.28 0.00 3.24
915 1058 3.621682 TTCTCCTCCCCTTCCTCTATC 57.378 52.381 0.00 0.00 0.00 2.08
916 1059 1.790157 TCTCCTCCCCTTCCTCTATCC 59.210 57.143 0.00 0.00 0.00 2.59
949 1100 2.625823 CGCATTCACACCCACCCAC 61.626 63.158 0.00 0.00 0.00 4.61
951 1102 1.971167 CATTCACACCCACCCACCG 60.971 63.158 0.00 0.00 0.00 4.94
961 1112 1.518572 CACCCACCGTATCAGCGTC 60.519 63.158 0.00 0.00 0.00 5.19
976 1127 3.939592 TCAGCGTCTGTATATATCGGAGG 59.060 47.826 6.72 0.00 32.61 4.30
988 1139 1.207791 ATCGGAGGAGAGCAACCAAT 58.792 50.000 0.00 0.00 0.00 3.16
1010 1257 2.230508 CAGTGGAAAGCATGTCAAGCAT 59.769 45.455 2.46 0.00 38.60 3.79
1363 1622 1.890894 GACGGCAGAGGCTTCTACA 59.109 57.895 0.00 0.00 40.87 2.74
1585 1847 0.859232 CAAGTGGTTCGACGGTCAAG 59.141 55.000 9.10 0.00 0.00 3.02
1701 1969 4.295119 AACGCCACCGACTTCGCT 62.295 61.111 0.00 0.00 38.18 4.93
1782 2052 3.691342 CCGAGTGGGCACGAAGGA 61.691 66.667 0.00 0.00 36.20 3.36
1785 2055 0.673644 CGAGTGGGCACGAAGGAAAT 60.674 55.000 0.00 0.00 36.20 2.17
1798 2077 1.790818 AGGAAATCCCTACCTCGACC 58.209 55.000 0.00 0.00 45.48 4.79
1830 2112 2.774234 AGGTACACATCCTGATTCCTGG 59.226 50.000 0.00 0.00 33.62 4.45
1861 2617 5.447683 CGAGTCACCAACATATTTGTGATGG 60.448 44.000 5.70 5.70 41.19 3.51
1881 2637 5.720371 TGGTAATTTGTCTGACCAAATGG 57.280 39.130 5.17 0.00 42.63 3.16
1895 2651 4.735662 CCAAATGGTGTTGAAATTGCTG 57.264 40.909 0.00 0.00 0.00 4.41
1959 2715 1.006220 TGTGCTACGGTGAGTGCAG 60.006 57.895 0.00 0.00 37.48 4.41
2090 2846 3.119884 CGTTACAGGTACACACACGGATA 60.120 47.826 0.00 0.00 0.00 2.59
2104 2860 2.104967 ACGGATATTGGGTCGTCTTGA 58.895 47.619 0.00 0.00 0.00 3.02
2250 3007 0.320421 CGTCGGGGTGTTCTTGTCAT 60.320 55.000 0.00 0.00 0.00 3.06
2597 3366 6.360618 GGAGATGTTCATACTTTCCCAGATT 58.639 40.000 0.00 0.00 0.00 2.40
2729 3498 0.765510 AGGGCCTCGAATCCAATACC 59.234 55.000 0.00 0.00 0.00 2.73
2735 3504 2.550978 CTCGAATCCAATACCGCACTT 58.449 47.619 0.00 0.00 0.00 3.16
2742 3511 1.610624 CCAATACCGCACTTGACACCT 60.611 52.381 0.00 0.00 0.00 4.00
2873 3643 2.664851 CTCACCGCCAAAGTCGCA 60.665 61.111 0.00 0.00 0.00 5.10
3052 3823 5.333581 TCTGACAGGAAAGAAGGTGATCTA 58.666 41.667 1.81 0.00 0.00 1.98
3145 5257 2.111251 GGTCCTTGATAGCCGGGC 59.889 66.667 12.11 12.11 0.00 6.13
3224 5336 1.267574 TGAGCATGAGTGGGGAGGAC 61.268 60.000 0.00 0.00 0.00 3.85
3232 5344 3.923645 TGGGGAGGACCGACCAGT 61.924 66.667 11.73 0.00 41.60 4.00
3459 5589 2.438411 TGTTGTTCGTGACCCTTTTGT 58.562 42.857 0.00 0.00 0.00 2.83
3484 5614 5.422666 TGTGTGACTCAAATGTGTGATTC 57.577 39.130 0.00 0.00 0.00 2.52
3517 5647 4.387598 GCTAGCTGGATCATTTGACTGAT 58.612 43.478 7.70 0.00 38.57 2.90
3528 5658 6.381481 TCATTTGACTGATGTGCATATTCC 57.619 37.500 0.00 0.00 0.00 3.01
3592 5722 5.348451 GGATATGGTGTGTTTGTTTGAATGC 59.652 40.000 0.00 0.00 0.00 3.56
3598 5728 5.794448 GGTGTGTTTGTTTGAATGCTTTTTG 59.206 36.000 0.00 0.00 0.00 2.44
3612 5742 4.881920 TGCTTTTTGCTCTAAATTCCCAC 58.118 39.130 0.00 0.00 43.37 4.61
3646 5776 3.057736 GTGCTTCACTTGCAGATGTTGAT 60.058 43.478 0.00 0.00 41.41 2.57
3660 5790 6.314648 GCAGATGTTGATGAGTGTCTTGATAA 59.685 38.462 0.00 0.00 0.00 1.75
3662 5792 8.173775 CAGATGTTGATGAGTGTCTTGATAAAC 58.826 37.037 0.00 0.00 0.00 2.01
3703 6273 9.706691 GCATGAAGAATATTGGATGAATTGATT 57.293 29.630 0.00 0.00 0.00 2.57
3758 6331 7.818930 GCAAGATTTGATGGATTTGGACTAAAA 59.181 33.333 0.00 0.00 0.00 1.52
3776 6349 6.597562 ACTAAAAACAATGAGTAGACCCACA 58.402 36.000 0.00 0.00 0.00 4.17
3783 6356 1.045407 GAGTAGACCCACACACCACA 58.955 55.000 0.00 0.00 0.00 4.17
3803 6376 2.125106 GACGAAGCGCCCCATCTT 60.125 61.111 2.29 0.00 0.00 2.40
3809 6382 2.439156 GCGCCCCATCTTCAGCTT 60.439 61.111 0.00 0.00 0.00 3.74
3839 6412 0.035739 GTAAGGGCAACTCCAACGGA 59.964 55.000 0.00 0.00 36.21 4.69
3890 6464 3.039588 TCGGCGCGGACAAAAGAC 61.040 61.111 14.27 0.00 0.00 3.01
4155 6745 0.107214 GGCCGTCCTCATCCAAATCA 60.107 55.000 0.00 0.00 0.00 2.57
4176 6772 2.158842 ACCATCCACATCTAGCAAGCTC 60.159 50.000 0.00 0.00 0.00 4.09
4270 6891 1.159713 CCGACAGCAGCAACAAGTCA 61.160 55.000 0.00 0.00 0.00 3.41
4304 6925 2.259204 CCGTCGCTTTACCCACGA 59.741 61.111 0.00 0.00 34.06 4.35
4414 7036 2.033602 GTGCCTTTGCCGTACCCT 59.966 61.111 0.00 0.00 36.33 4.34
4417 7039 1.077716 GCCTTTGCCGTACCCTGAT 60.078 57.895 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 136 7.536622 TCGTGTTTCTTTAACGTTTTTGCTTTA 59.463 29.630 5.91 0.00 39.72 1.85
156 160 1.933853 CCATAGCCCTCGTTTTTCTCG 59.066 52.381 0.00 0.00 0.00 4.04
209 214 6.265649 TCTCACTTATAGCAAGATGTAGGGAC 59.734 42.308 0.00 0.00 0.00 4.46
268 274 3.367607 CGAAGTCGTTCTGATCTCATCC 58.632 50.000 0.00 0.00 34.11 3.51
283 289 0.645868 GTTACAGCCATCGCGAAGTC 59.354 55.000 15.24 0.00 41.18 3.01
289 295 2.135933 GATACAGGTTACAGCCATCGC 58.864 52.381 0.00 0.00 0.00 4.58
319 325 2.729194 TCTGGAGGAGTTCAGAGCTAC 58.271 52.381 0.00 0.00 35.37 3.58
326 332 5.248248 TGATTACACAATCTGGAGGAGTTCA 59.752 40.000 0.00 0.00 41.09 3.18
352 361 1.519455 GCGGATCACTCACCCGAAG 60.519 63.158 0.00 0.00 45.58 3.79
453 513 4.467795 ACATATGACCCTTATCAGGATCCG 59.532 45.833 10.38 1.36 44.19 4.18
463 523 2.573915 TGTGCCACACATATGACCCTTA 59.426 45.455 10.38 0.00 39.62 2.69
467 527 2.556189 TGTTTGTGCCACACATATGACC 59.444 45.455 10.38 0.00 44.16 4.02
483 543 6.329838 ACGTTTGAAATTGTCATGTGTTTG 57.670 33.333 0.00 0.00 35.70 2.93
568 658 8.989653 AAAACTGAAACTTGTTATCCGAAAAA 57.010 26.923 0.00 0.00 0.00 1.94
569 659 8.989653 AAAAACTGAAACTTGTTATCCGAAAA 57.010 26.923 0.00 0.00 0.00 2.29
592 682 6.453926 AACTAAAGTTGTTAGCCGGAAAAA 57.546 33.333 5.05 0.00 36.80 1.94
597 687 6.730960 TTCATAACTAAAGTTGTTAGCCGG 57.269 37.500 0.00 0.00 38.90 6.13
615 717 4.263905 ACTCTGGCCCTGACATTTTTCATA 60.264 41.667 0.00 0.00 0.00 2.15
616 718 3.094572 CTCTGGCCCTGACATTTTTCAT 58.905 45.455 0.00 0.00 0.00 2.57
617 719 2.158475 ACTCTGGCCCTGACATTTTTCA 60.158 45.455 0.00 0.00 0.00 2.69
618 720 2.229784 CACTCTGGCCCTGACATTTTTC 59.770 50.000 0.00 0.00 0.00 2.29
628 730 1.228367 CACAAAGCACTCTGGCCCT 60.228 57.895 0.00 0.00 0.00 5.19
683 785 1.757699 AGGAGCGGTAAGAACATCTCC 59.242 52.381 0.00 0.00 41.92 3.71
690 792 2.684881 CGTAGGTTAGGAGCGGTAAGAA 59.315 50.000 0.00 0.00 0.00 2.52
699 801 6.998968 ATCGGATATTACGTAGGTTAGGAG 57.001 41.667 0.00 0.00 0.00 3.69
719 821 5.163913 CCTCTCTGTTGTGCTTCTAAAATCG 60.164 44.000 0.00 0.00 0.00 3.34
728 830 0.753262 ACGTCCTCTCTGTTGTGCTT 59.247 50.000 0.00 0.00 0.00 3.91
739 842 8.786826 TTTCAAATATAAATGTGACGTCCTCT 57.213 30.769 14.12 0.00 28.54 3.69
742 845 7.167468 GCCATTTCAAATATAAATGTGACGTCC 59.833 37.037 14.12 5.06 40.93 4.79
757 860 7.416664 GCCCATATATATGACGCCATTTCAAAT 60.417 37.037 21.97 0.00 35.75 2.32
776 879 1.764134 CAATTGCACTTGGGCCCATAT 59.236 47.619 29.23 14.75 0.00 1.78
777 880 1.193323 CAATTGCACTTGGGCCCATA 58.807 50.000 29.23 15.84 0.00 2.74
778 881 0.544833 TCAATTGCACTTGGGCCCAT 60.545 50.000 29.23 9.26 0.00 4.00
779 882 1.152376 TCAATTGCACTTGGGCCCA 60.152 52.632 24.45 24.45 0.00 5.36
780 883 1.187567 ACTCAATTGCACTTGGGCCC 61.188 55.000 17.59 17.59 29.17 5.80
781 884 1.544724 TACTCAATTGCACTTGGGCC 58.455 50.000 16.01 0.00 29.17 5.80
812 915 6.368516 CGGATATTTTTCAATTGCCTGTTGTT 59.631 34.615 0.00 0.00 0.00 2.83
813 916 5.868801 CGGATATTTTTCAATTGCCTGTTGT 59.131 36.000 0.00 0.00 0.00 3.32
841 944 1.775385 CCCAACCCAACTTGTCAAGT 58.225 50.000 12.62 12.62 45.46 3.16
886 989 1.219393 GGGAGGAGAAAGCACGAGG 59.781 63.158 0.00 0.00 0.00 4.63
887 990 1.219393 GGGGAGGAGAAAGCACGAG 59.781 63.158 0.00 0.00 0.00 4.18
888 991 0.836400 AAGGGGAGGAGAAAGCACGA 60.836 55.000 0.00 0.00 0.00 4.35
915 1058 6.038161 TGTGAATGCGATAATTGTTTAGGAGG 59.962 38.462 0.00 0.00 0.00 4.30
916 1059 6.907212 GTGTGAATGCGATAATTGTTTAGGAG 59.093 38.462 0.00 0.00 0.00 3.69
949 1100 5.433005 CGATATATACAGACGCTGATACGG 58.567 45.833 12.77 0.00 37.37 4.02
951 1102 6.292973 CCTCCGATATATACAGACGCTGATAC 60.293 46.154 12.77 0.00 35.18 2.24
961 1112 5.163602 GGTTGCTCTCCTCCGATATATACAG 60.164 48.000 0.00 0.00 0.00 2.74
976 1127 2.479566 TCCACTGATTGGTTGCTCTC 57.520 50.000 0.00 0.00 46.97 3.20
988 1139 1.881973 GCTTGACATGCTTTCCACTGA 59.118 47.619 6.09 0.00 0.00 3.41
1182 1435 2.042843 CTGAGGTAGGTCCGGGCT 60.043 66.667 5.77 0.00 41.99 5.19
1237 1490 4.090761 TGTACTCCGTAACCCTATCGAT 57.909 45.455 2.16 2.16 0.00 3.59
1512 1774 1.474498 GGGTTGGTGTTGAAGACGACT 60.474 52.381 0.00 0.00 0.00 4.18
1585 1847 0.534203 TTGACGAAACTGTGGGAGGC 60.534 55.000 0.00 0.00 0.00 4.70
1651 1919 2.665185 GCAGTTGCCGACGTTCCT 60.665 61.111 0.00 0.00 34.31 3.36
1767 2037 1.087501 GATTTCCTTCGTGCCCACTC 58.912 55.000 0.00 0.00 0.00 3.51
1770 2040 1.001393 GGGATTTCCTTCGTGCCCA 60.001 57.895 0.00 0.00 35.63 5.36
1774 2044 2.481449 CGAGGTAGGGATTTCCTTCGTG 60.481 54.545 0.00 0.00 45.47 4.35
1782 2052 0.822164 CACGGTCGAGGTAGGGATTT 59.178 55.000 0.00 0.00 0.00 2.17
1785 2055 1.929860 ATCCACGGTCGAGGTAGGGA 61.930 60.000 6.72 0.00 0.00 4.20
1798 2077 2.595124 TGTGTACCTATGCATCCACG 57.405 50.000 0.19 0.00 0.00 4.94
1830 2112 2.028484 TTGGTGACTCGACCGTGC 59.972 61.111 0.00 0.00 39.07 5.34
1895 2651 2.410262 CGTCGATGTCTTCAGTTTGCAC 60.410 50.000 0.00 0.00 0.00 4.57
1959 2715 1.445871 ATAGTTTCCCGGCGTGTTTC 58.554 50.000 6.01 0.00 0.00 2.78
2090 2846 6.882140 TGTAATATGTTTCAAGACGACCCAAT 59.118 34.615 0.00 0.00 0.00 3.16
2250 3007 4.574674 AGACCCAGAAGCATGTGAATAA 57.425 40.909 0.00 0.00 0.00 1.40
2387 3155 5.128827 TGAGTATATCTTGAACCCACCACTC 59.871 44.000 0.00 0.00 0.00 3.51
2742 3511 0.464916 TCTGCCGCTATCCGTAGACA 60.465 55.000 0.00 0.00 34.38 3.41
2873 3643 0.883370 GTTTCGACGCCCCAAAGTCT 60.883 55.000 0.00 0.00 35.38 3.24
3052 3823 2.249413 CTGCTCTGGCCCATCGAAGT 62.249 60.000 0.00 0.00 37.74 3.01
3145 5257 2.812619 GGGCCCATCTCCTTCCTCG 61.813 68.421 19.95 0.00 0.00 4.63
3224 5336 3.611766 ACTTCCTTCATTACTGGTCGG 57.388 47.619 0.00 0.00 0.00 4.79
3232 5344 3.369471 CCTCTCGGCAACTTCCTTCATTA 60.369 47.826 0.00 0.00 0.00 1.90
3351 5472 9.524106 CGGTATAAACTTATAAGTCACATCACA 57.476 33.333 18.28 0.00 38.57 3.58
3394 5524 3.449018 AGTGTATGTACTGCCCTCTTCAG 59.551 47.826 0.00 0.00 37.56 3.02
3459 5589 7.228308 TGAATCACACATTTGAGTCACACATTA 59.772 33.333 0.00 0.00 43.68 1.90
3484 5614 1.377725 CAGCTAGCCACCCCAACTG 60.378 63.158 12.13 0.00 0.00 3.16
3517 5647 1.212688 CTGGGGTGAGGAATATGCACA 59.787 52.381 0.00 0.00 34.33 4.57
3528 5658 5.630415 TGTTATTAAGGATCTGGGGTGAG 57.370 43.478 0.00 0.00 0.00 3.51
3592 5722 5.728637 AGGTGGGAATTTAGAGCAAAAAG 57.271 39.130 0.00 0.00 0.00 2.27
3598 5728 6.603599 ACTTTGATAAGGTGGGAATTTAGAGC 59.396 38.462 0.00 0.00 35.61 4.09
3646 5776 8.655970 CATATGAAACGTTTATCAAGACACTCA 58.344 33.333 14.65 3.36 0.00 3.41
3703 6273 8.341903 CACTTTACACACACATTGATGACTTAA 58.658 33.333 0.00 0.00 0.00 1.85
3704 6274 7.497579 ACACTTTACACACACATTGATGACTTA 59.502 33.333 0.00 0.00 0.00 2.24
3710 6280 5.163571 TGCAACACTTTACACACACATTGAT 60.164 36.000 0.00 0.00 0.00 2.57
3758 6331 3.496160 GGTGTGTGGGTCTACTCATTGTT 60.496 47.826 0.00 0.00 0.00 2.83
3776 6349 1.591594 CGCTTCGTCTGTGTGGTGT 60.592 57.895 0.00 0.00 0.00 4.16
3783 6356 3.665675 GATGGGGCGCTTCGTCTGT 62.666 63.158 7.64 0.00 0.00 3.41
3809 6382 0.901114 TGCCCTTACGGTGAGCTACA 60.901 55.000 0.00 0.00 0.00 2.74
3839 6412 1.883084 GCGGACGAAATGGATCGCT 60.883 57.895 0.00 0.00 46.51 4.93
3943 6528 0.468214 TGGGACGCAAATTTGGACCA 60.468 50.000 19.47 17.23 0.00 4.02
3946 6531 2.869636 GCATTTGGGACGCAAATTTGGA 60.870 45.455 23.54 1.54 30.66 3.53
4026 6611 1.300697 AGTTGAACGACCGTCAGGC 60.301 57.895 0.00 0.00 42.76 4.85
4039 6624 4.329545 GAGGTGGCGGGCAGTTGA 62.330 66.667 3.75 0.00 0.00 3.18
4133 6718 4.731853 TGGATGAGGACGGCCCCA 62.732 66.667 1.76 0.00 34.66 4.96
4155 6745 1.842562 AGCTTGCTAGATGTGGATGGT 59.157 47.619 0.00 0.00 0.00 3.55
4200 6796 1.568118 GGGTGGCTAGGGTTGGCTAA 61.568 60.000 0.00 0.00 0.00 3.09
4292 6913 2.418976 GGATGAACTTCGTGGGTAAAGC 59.581 50.000 0.00 0.00 0.00 3.51
4297 6918 1.295423 CGGGATGAACTTCGTGGGT 59.705 57.895 0.00 0.00 0.00 4.51
4304 6925 2.584608 CGGAGGCGGGATGAACTT 59.415 61.111 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.