Multiple sequence alignment - TraesCS7B01G029400

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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 TraesCS7B01G029400 chr7B 100.000 3889 0 0 1 3889 28002958 27999070 0.000000e+00 7182.0
1 TraesCS7B01G029400 chr7B 93.813 2683 116 23 561 3232 28306605 28303962 0.000000e+00 3989.0
2 TraesCS7B01G029400 chr7B 85.714 749 107 0 1546 2294 711535620 711536368 0.000000e+00 791.0
3 TraesCS7B01G029400 chr7B 83.721 301 28 13 31 311 28307265 28306966 8.290000e-67 265.0
4 TraesCS7B01G029400 chr7B 88.514 148 13 2 384 527 28306830 28306683 3.990000e-40 176.0
5 TraesCS7B01G029400 chr7D 93.030 3343 138 39 561 3889 80782575 80779314 0.000000e+00 4795.0
6 TraesCS7B01G029400 chr7D 92.199 141 9 2 50 189 80783158 80783019 8.520000e-47 198.0
7 TraesCS7B01G029400 chr7A 92.786 2523 124 32 561 3069 83534143 83531665 0.000000e+00 3598.0
8 TraesCS7B01G029400 chr7A 89.454 787 32 14 3118 3889 83530091 83529341 0.000000e+00 946.0
9 TraesCS7B01G029400 chr7A 80.000 560 99 12 2359 2909 603704549 603705104 6.050000e-108 401.0
10 TraesCS7B01G029400 chr7A 80.000 560 97 14 2359 2908 603701789 603702343 2.180000e-107 399.0
11 TraesCS7B01G029400 chr7A 79.821 560 100 12 2359 2909 603707302 603707857 2.820000e-106 396.0
12 TraesCS7B01G029400 chr7A 84.451 328 30 11 6 321 83534875 83534557 1.760000e-78 303.0
13 TraesCS7B01G029400 chr7A 83.513 279 22 15 3109 3376 83530670 83530405 5.020000e-59 239.0
14 TraesCS7B01G029400 chr1A 87.067 750 95 2 1546 2294 555689532 555690280 0.000000e+00 846.0
15 TraesCS7B01G029400 chr4A 86.853 753 97 2 1546 2297 632936289 632935538 0.000000e+00 841.0
16 TraesCS7B01G029400 chr4A 84.554 628 89 4 922 1544 668171105 668171729 1.990000e-172 616.0
17 TraesCS7B01G029400 chr4A 84.554 628 89 4 922 1544 668213644 668214268 1.990000e-172 616.0
18 TraesCS7B01G029400 chr4A 84.554 628 89 4 922 1544 668221430 668222054 1.990000e-172 616.0
19 TraesCS7B01G029400 chr4A 84.554 628 89 4 922 1544 668229312 668229936 1.990000e-172 616.0
20 TraesCS7B01G029400 chr4A 77.366 1025 163 42 2274 3255 632935471 632934473 9.500000e-151 544.0
21 TraesCS7B01G029400 chr3B 86.933 750 96 2 1546 2294 752214641 752215389 0.000000e+00 841.0
22 TraesCS7B01G029400 chr3B 77.268 1025 164 42 2274 3255 752215459 752216457 4.420000e-149 538.0
23 TraesCS7B01G029400 chr2B 86.720 753 98 2 1546 2297 245809893 245809142 0.000000e+00 835.0
24 TraesCS7B01G029400 chr2B 77.030 1010 163 43 2274 3240 245809075 245808092 2.070000e-142 516.0
25 TraesCS7B01G029400 chr1B 85.714 749 107 0 1546 2294 365016063 365016811 0.000000e+00 791.0
26 TraesCS7B01G029400 chrUn 84.554 628 89 4 922 1544 272030123 272030747 1.990000e-172 616.0
27 TraesCS7B01G029400 chrUn 84.554 628 89 4 922 1544 296574622 296575246 1.990000e-172 616.0
28 TraesCS7B01G029400 chr6D 74.254 804 123 47 2493 3255 140324885 140324125 1.070000e-65 261.0
29 TraesCS7B01G029400 chr6A 89.362 47 2 2 3482 3528 534660762 534660719 5.430000e-04 56.5


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 TraesCS7B01G029400 chr7B 27999070 28002958 3888 True 7182.000000 7182 100.000000 1 3889 1 chr7B.!!$R1 3888
1 TraesCS7B01G029400 chr7B 28303962 28307265 3303 True 1476.666667 3989 88.682667 31 3232 3 chr7B.!!$R2 3201
2 TraesCS7B01G029400 chr7B 711535620 711536368 748 False 791.000000 791 85.714000 1546 2294 1 chr7B.!!$F1 748
3 TraesCS7B01G029400 chr7D 80779314 80783158 3844 True 2496.500000 4795 92.614500 50 3889 2 chr7D.!!$R1 3839
4 TraesCS7B01G029400 chr7A 83529341 83534875 5534 True 1271.500000 3598 87.551000 6 3889 4 chr7A.!!$R1 3883
5 TraesCS7B01G029400 chr7A 603701789 603707857 6068 False 398.666667 401 79.940333 2359 2909 3 chr7A.!!$F1 550
6 TraesCS7B01G029400 chr1A 555689532 555690280 748 False 846.000000 846 87.067000 1546 2294 1 chr1A.!!$F1 748
7 TraesCS7B01G029400 chr4A 632934473 632936289 1816 True 692.500000 841 82.109500 1546 3255 2 chr4A.!!$R1 1709
8 TraesCS7B01G029400 chr4A 668171105 668171729 624 False 616.000000 616 84.554000 922 1544 1 chr4A.!!$F1 622
9 TraesCS7B01G029400 chr4A 668213644 668214268 624 False 616.000000 616 84.554000 922 1544 1 chr4A.!!$F2 622
10 TraesCS7B01G029400 chr4A 668221430 668222054 624 False 616.000000 616 84.554000 922 1544 1 chr4A.!!$F3 622
11 TraesCS7B01G029400 chr4A 668229312 668229936 624 False 616.000000 616 84.554000 922 1544 1 chr4A.!!$F4 622
12 TraesCS7B01G029400 chr3B 752214641 752216457 1816 False 689.500000 841 82.100500 1546 3255 2 chr3B.!!$F1 1709
13 TraesCS7B01G029400 chr2B 245808092 245809893 1801 True 675.500000 835 81.875000 1546 3240 2 chr2B.!!$R1 1694
14 TraesCS7B01G029400 chr1B 365016063 365016811 748 False 791.000000 791 85.714000 1546 2294 1 chr1B.!!$F1 748
15 TraesCS7B01G029400 chrUn 272030123 272030747 624 False 616.000000 616 84.554000 922 1544 1 chrUn.!!$F1 622
16 TraesCS7B01G029400 chrUn 296574622 296575246 624 False 616.000000 616 84.554000 922 1544 1 chrUn.!!$F2 622
17 TraesCS7B01G029400 chr6D 140324125 140324885 760 True 261.000000 261 74.254000 2493 3255 1 chr6D.!!$R1 762

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
361 389 0.105964 TAGTTGCAACCAGACGTGCT 59.894 50.0 25.62 6.69 0.00 4.40 F
665 921 0.243907 AGGCTGTGTGCTACGTACTG 59.756 55.0 0.00 0.00 42.39 2.74 F
2153 2438 0.110486 ACACGGGAAGATGCACCTTT 59.890 50.0 0.00 0.00 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1549 1834 0.037697 TGTGTGACACGAGGTATGGC 60.038 55.0 11.51 0.0 37.14 4.40 R
2209 2494 0.101399 CTCGGTGAAGGAGGACATCG 59.899 60.0 0.00 0.0 41.19 3.84 R
3679 8456 0.944311 GCGCAACTTCCGAACAGAGA 60.944 55.0 0.30 0.0 0.00 3.10 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
19 20 1.870055 GACGTGGCGTAGGAAGACCA 61.870 60.000 0.00 0.00 41.37 4.02
21 22 4.533318 TGGCGTAGGAAGACCACT 57.467 55.556 0.00 0.00 38.94 4.00
28 29 4.021925 GGAAGACCACTGGCCGCT 62.022 66.667 0.00 0.00 35.97 5.52
29 30 2.743928 GAAGACCACTGGCCGCTG 60.744 66.667 0.00 0.00 0.00 5.18
208 224 3.849953 GCGTTTCCTAGGTGCGCG 61.850 66.667 23.11 17.38 38.75 6.86
255 274 2.420408 CCCCGTCCCGCTTCTTATTTAA 60.420 50.000 0.00 0.00 0.00 1.52
262 281 6.471198 CGTCCCGCTTCTTATTTAATTTTTCC 59.529 38.462 0.00 0.00 0.00 3.13
265 284 8.590204 TCCCGCTTCTTATTTAATTTTTCCTTT 58.410 29.630 0.00 0.00 0.00 3.11
278 297 9.578439 TTAATTTTTCCTTTTGTGGCAATTTTG 57.422 25.926 0.00 0.00 0.00 2.44
293 314 6.928492 TGGCAATTTTGTTTTCTCCTATGAAC 59.072 34.615 0.00 0.00 0.00 3.18
306 327 7.295322 TCTCCTATGAACTTCATACCATGAG 57.705 40.000 7.31 10.23 40.94 2.90
312 333 5.255687 TGAACTTCATACCATGAGCACAAT 58.744 37.500 0.00 0.00 40.94 2.71
351 379 9.463443 AAGTGAATACAAGAAATTAGTTGCAAC 57.537 29.630 22.17 22.17 0.00 4.17
352 380 8.082242 AGTGAATACAAGAAATTAGTTGCAACC 58.918 33.333 25.62 9.45 0.00 3.77
354 382 8.081633 TGAATACAAGAAATTAGTTGCAACCAG 58.918 33.333 25.62 8.65 0.00 4.00
355 383 7.759489 ATACAAGAAATTAGTTGCAACCAGA 57.241 32.000 25.62 12.35 0.00 3.86
356 384 5.831997 ACAAGAAATTAGTTGCAACCAGAC 58.168 37.500 25.62 12.40 0.00 3.51
357 385 4.749245 AGAAATTAGTTGCAACCAGACG 57.251 40.909 25.62 0.00 0.00 4.18
358 386 4.134563 AGAAATTAGTTGCAACCAGACGT 58.865 39.130 25.62 8.93 0.00 4.34
361 389 0.105964 TAGTTGCAACCAGACGTGCT 59.894 50.000 25.62 6.69 0.00 4.40
362 390 1.160329 AGTTGCAACCAGACGTGCTC 61.160 55.000 25.62 0.00 0.00 4.26
363 391 1.153269 TTGCAACCAGACGTGCTCA 60.153 52.632 0.00 0.00 0.00 4.26
365 393 1.159713 TGCAACCAGACGTGCTCAAG 61.160 55.000 0.00 0.00 0.00 3.02
366 394 1.160329 GCAACCAGACGTGCTCAAGT 61.160 55.000 0.00 0.00 0.00 3.16
368 396 1.003545 CAACCAGACGTGCTCAAGTTG 60.004 52.381 0.00 0.00 31.56 3.16
369 397 0.464036 ACCAGACGTGCTCAAGTTGA 59.536 50.000 5.25 5.25 0.00 3.18
370 398 1.070758 ACCAGACGTGCTCAAGTTGAT 59.929 47.619 5.91 0.00 0.00 2.57
371 399 1.728971 CCAGACGTGCTCAAGTTGATC 59.271 52.381 5.91 2.52 0.00 2.92
373 401 1.079503 GACGTGCTCAAGTTGATCCC 58.920 55.000 5.91 0.00 0.00 3.85
374 402 0.687354 ACGTGCTCAAGTTGATCCCT 59.313 50.000 5.91 0.00 0.00 4.20
377 405 2.613977 CGTGCTCAAGTTGATCCCTTCT 60.614 50.000 5.91 0.00 0.00 2.85
378 406 3.006247 GTGCTCAAGTTGATCCCTTCTC 58.994 50.000 5.91 0.00 0.00 2.87
380 408 2.026822 GCTCAAGTTGATCCCTTCTCCA 60.027 50.000 5.91 0.00 0.00 3.86
381 409 3.371380 GCTCAAGTTGATCCCTTCTCCAT 60.371 47.826 5.91 0.00 0.00 3.41
382 410 4.141620 GCTCAAGTTGATCCCTTCTCCATA 60.142 45.833 5.91 0.00 0.00 2.74
432 588 1.447838 CGCCTCCTGCTTTCGCTTA 60.448 57.895 0.00 0.00 38.05 3.09
475 631 1.880027 CTACGGCAGAAAAACAGGCTT 59.120 47.619 0.00 0.00 0.00 4.35
507 666 1.666553 TGGTCGACGCCAATCACAC 60.667 57.895 9.92 0.00 35.25 3.82
542 782 3.726517 CCGAAGCAGGCCACGTTG 61.727 66.667 5.01 0.00 0.00 4.10
556 796 1.891919 CGTTGTGGGTGGACTGTGG 60.892 63.158 0.00 0.00 0.00 4.17
557 797 1.529796 GTTGTGGGTGGACTGTGGA 59.470 57.895 0.00 0.00 0.00 4.02
558 798 0.818040 GTTGTGGGTGGACTGTGGAC 60.818 60.000 0.00 0.00 0.00 4.02
571 827 2.033602 TGGACGAGCTCGAGGACA 59.966 61.111 40.58 27.32 43.02 4.02
572 828 2.333417 TGGACGAGCTCGAGGACAC 61.333 63.158 40.58 22.10 43.02 3.67
585 841 1.380112 GGACACGGAGCTAGGAGGT 60.380 63.158 0.00 0.00 0.00 3.85
593 849 1.342574 GGAGCTAGGAGGTGAGGTTCT 60.343 57.143 0.00 0.00 0.00 3.01
595 851 2.167487 GAGCTAGGAGGTGAGGTTCTTG 59.833 54.545 0.00 0.00 0.00 3.02
604 860 4.145052 AGGTGAGGTTCTTGTTCAATTCC 58.855 43.478 0.00 0.00 0.00 3.01
623 879 1.137872 CCTGCATCTTCCGTCTAGCTT 59.862 52.381 0.00 0.00 0.00 3.74
625 881 2.863137 CTGCATCTTCCGTCTAGCTTTC 59.137 50.000 0.00 0.00 0.00 2.62
626 882 2.205911 GCATCTTCCGTCTAGCTTTCC 58.794 52.381 0.00 0.00 0.00 3.13
630 886 2.233922 TCTTCCGTCTAGCTTTCCTTGG 59.766 50.000 0.00 0.00 0.00 3.61
655 911 4.333649 CAGGTCAATACAATAGGCTGTGTG 59.666 45.833 14.00 4.51 0.00 3.82
656 912 3.065371 GGTCAATACAATAGGCTGTGTGC 59.935 47.826 14.00 0.00 41.94 4.57
657 913 3.941483 GTCAATACAATAGGCTGTGTGCT 59.059 43.478 14.00 1.51 42.39 4.40
658 914 5.116180 GTCAATACAATAGGCTGTGTGCTA 58.884 41.667 14.00 0.00 42.39 3.49
659 915 5.006746 GTCAATACAATAGGCTGTGTGCTAC 59.993 44.000 14.00 5.46 42.39 3.58
660 916 2.010145 ACAATAGGCTGTGTGCTACG 57.990 50.000 0.00 0.00 42.39 3.51
661 917 1.275291 ACAATAGGCTGTGTGCTACGT 59.725 47.619 0.00 0.00 42.39 3.57
662 918 2.494471 ACAATAGGCTGTGTGCTACGTA 59.506 45.455 0.00 0.00 42.39 3.57
663 919 2.858344 CAATAGGCTGTGTGCTACGTAC 59.142 50.000 0.00 0.00 42.39 3.67
664 920 1.830279 TAGGCTGTGTGCTACGTACT 58.170 50.000 0.00 0.00 42.39 2.73
665 921 0.243907 AGGCTGTGTGCTACGTACTG 59.756 55.000 0.00 0.00 42.39 2.74
666 922 1.352156 GGCTGTGTGCTACGTACTGC 61.352 60.000 8.32 8.32 42.39 4.40
667 923 1.352156 GCTGTGTGCTACGTACTGCC 61.352 60.000 4.55 0.00 38.95 4.85
668 924 1.071019 CTGTGTGCTACGTACTGCCG 61.071 60.000 4.55 0.00 0.00 5.69
706 962 0.246086 GTCAGGTCTGGCTCTCTGTG 59.754 60.000 0.00 0.00 31.34 3.66
718 974 3.201290 GCTCTCTGTGATGTGTAATGGG 58.799 50.000 0.00 0.00 0.00 4.00
740 996 2.038952 TGTGCTCTTGAGTTGGCTGTAT 59.961 45.455 0.00 0.00 0.00 2.29
745 1001 2.371841 TCTTGAGTTGGCTGTATGTGGT 59.628 45.455 0.00 0.00 0.00 4.16
747 1003 1.271325 TGAGTTGGCTGTATGTGGTGG 60.271 52.381 0.00 0.00 0.00 4.61
778 1034 4.090761 TCTGATCAGGCAAAGTTCTTGT 57.909 40.909 22.42 0.00 0.00 3.16
795 1051 6.753744 AGTTCTTGTTCAACTTTTGCATCTTC 59.246 34.615 0.00 0.00 29.29 2.87
800 1056 4.789012 TCAACTTTTGCATCTTCCATCC 57.211 40.909 0.00 0.00 0.00 3.51
801 1057 4.410099 TCAACTTTTGCATCTTCCATCCT 58.590 39.130 0.00 0.00 0.00 3.24
842 1101 1.268133 TGCCTTTGCGTGTAAACGTTC 60.268 47.619 7.39 0.00 41.78 3.95
861 1125 3.234630 TTAGCGCAACCGGAGCACT 62.235 57.895 9.46 13.89 45.74 4.40
926 1206 5.221028 CGATTGCCAGCATTTAGGTCAATAA 60.221 40.000 0.00 0.00 34.27 1.40
936 1216 9.860650 AGCATTTAGGTCAATAATGTTACCATA 57.139 29.630 0.00 0.00 34.29 2.74
974 1259 9.455847 GTTATATTGCCTTTGAATGAGAATGAC 57.544 33.333 0.00 0.00 0.00 3.06
979 1264 7.707624 TGCCTTTGAATGAGAATGACTAATT 57.292 32.000 0.00 0.00 0.00 1.40
980 1265 8.806429 TGCCTTTGAATGAGAATGACTAATTA 57.194 30.769 0.00 0.00 0.00 1.40
1015 1300 7.587375 TTTATAGGAATGGATGATGGGATCA 57.413 36.000 0.00 0.00 44.55 2.92
1058 1343 3.384668 ACATGTCTATTTCGAGCGATGG 58.615 45.455 0.00 0.00 0.00 3.51
1123 1408 0.251474 TGGCCTTGCTGAAGCTCAAT 60.251 50.000 3.32 0.00 42.66 2.57
1126 1411 1.749634 GCCTTGCTGAAGCTCAATCAT 59.250 47.619 3.61 0.00 42.66 2.45
1239 1524 0.536687 TCGGTGTGACGAGAAGGAGT 60.537 55.000 0.00 0.00 38.06 3.85
1243 1528 2.395654 GTGTGACGAGAAGGAGTTCAC 58.604 52.381 0.00 0.00 34.82 3.18
1248 1533 2.293677 GACGAGAAGGAGTTCACACAGA 59.706 50.000 0.00 0.00 34.82 3.41
1448 1733 9.167311 GGATCATAATCATACATTAAGTCCACC 57.833 37.037 0.00 0.00 33.21 4.61
1489 1774 7.283127 TCAGATGCAACAAAAAGTTAGACTTCT 59.717 33.333 0.00 0.00 37.47 2.85
1503 1788 2.101582 AGACTTCTGTGTCAAGCGAAGT 59.898 45.455 10.66 10.66 46.15 3.01
1509 1794 2.866156 CTGTGTCAAGCGAAGTCTTGAA 59.134 45.455 7.66 0.00 46.13 2.69
1538 1823 2.159142 ACCCGGCTGAAATACGAGTAAG 60.159 50.000 0.00 0.00 0.00 2.34
1549 1834 6.586463 TGAAATACGAGTAAGCAAGAGTTCAG 59.414 38.462 0.00 0.00 0.00 3.02
1599 1884 4.005650 TCGAGAAGCAATTTCAATCAGCT 58.994 39.130 0.00 0.00 38.31 4.24
1694 1979 1.821088 AAGGAGGGGGCGATAGAAAT 58.179 50.000 0.00 0.00 39.76 2.17
1900 2185 5.160607 TCCTCCACAATACGTCTTTGATT 57.839 39.130 15.70 0.00 0.00 2.57
1970 2255 1.078848 GCGGCATGGAAGACACTCT 60.079 57.895 0.00 0.00 0.00 3.24
2153 2438 0.110486 ACACGGGAAGATGCACCTTT 59.890 50.000 0.00 0.00 0.00 3.11
2180 2465 9.447040 GAATGGAAAGACAACAAGTAAAACTAC 57.553 33.333 0.00 0.00 0.00 2.73
2209 2494 2.005451 CAATAGCTGTCAGGTGTGCTC 58.995 52.381 14.85 0.00 37.02 4.26
2233 2518 2.224209 TGTCCTCCTTCACCGAGAAAAC 60.224 50.000 0.00 0.00 35.40 2.43
2447 5589 9.987272 CAGTGGATGATATTCTAGAACAACATA 57.013 33.333 7.48 0.00 0.00 2.29
2523 5670 9.840427 TTTTCATGTATTTTCTAAGCTAACAGC 57.160 29.630 0.00 0.00 42.84 4.40
2635 5783 6.952773 TTTATTTGTAGCAAACACCTGAGT 57.047 33.333 0.00 0.00 38.00 3.41
2838 5990 0.034616 AGTGTCCAGCTCTGCAGAAC 59.965 55.000 18.85 13.95 0.00 3.01
3257 7981 5.809001 TCCATGTCAATCTTGTCTAAAGCT 58.191 37.500 0.00 0.00 0.00 3.74
3259 7983 6.149973 TCCATGTCAATCTTGTCTAAAGCTTG 59.850 38.462 0.00 0.00 0.00 4.01
3260 7984 6.149973 CCATGTCAATCTTGTCTAAAGCTTGA 59.850 38.462 0.00 0.00 32.12 3.02
3261 7985 7.148120 CCATGTCAATCTTGTCTAAAGCTTGAT 60.148 37.037 0.00 0.00 35.63 2.57
3262 7986 8.886719 CATGTCAATCTTGTCTAAAGCTTGATA 58.113 33.333 0.00 5.86 35.63 2.15
3263 7987 8.846943 TGTCAATCTTGTCTAAAGCTTGATAA 57.153 30.769 0.00 0.00 35.63 1.75
3264 7988 9.453572 TGTCAATCTTGTCTAAAGCTTGATAAT 57.546 29.630 0.00 0.00 35.63 1.28
3265 7989 9.928236 GTCAATCTTGTCTAAAGCTTGATAATC 57.072 33.333 0.00 0.00 35.63 1.75
3266 7990 9.896645 TCAATCTTGTCTAAAGCTTGATAATCT 57.103 29.630 0.00 0.00 30.32 2.40
3269 7993 9.678260 ATCTTGTCTAAAGCTTGATAATCTTGT 57.322 29.630 0.00 0.00 0.00 3.16
3270 7994 9.155975 TCTTGTCTAAAGCTTGATAATCTTGTC 57.844 33.333 0.00 0.00 0.00 3.18
3271 7995 9.160496 CTTGTCTAAAGCTTGATAATCTTGTCT 57.840 33.333 0.00 0.00 0.00 3.41
3444 8178 8.256356 ACTACATAAGGATGTTTCTAGCAGAT 57.744 34.615 0.00 0.00 44.18 2.90
3495 8229 9.146984 TGGAAAAAGTATGATCACTAAAGTACG 57.853 33.333 0.00 0.00 0.00 3.67
3496 8230 9.148104 GGAAAAAGTATGATCACTAAAGTACGT 57.852 33.333 0.00 0.00 0.00 3.57
3515 8249 5.056894 ACGTAGTGATCTAAACGCTCTTT 57.943 39.130 12.20 0.00 42.51 2.52
3516 8250 4.857588 ACGTAGTGATCTAAACGCTCTTTG 59.142 41.667 12.20 0.00 42.51 2.77
3540 8274 7.609056 TGTATTTCTTTACAGAGGGAGTACAC 58.391 38.462 0.00 0.00 0.00 2.90
3544 8278 2.119801 TACAGAGGGAGTACACGTCC 57.880 55.000 0.00 0.00 0.00 4.79
3629 8370 3.305110 GGAGTTTACAACCGCACAAATG 58.695 45.455 0.00 0.00 0.00 2.32
3679 8456 0.311790 CAGCAACCACACGAGCAATT 59.688 50.000 0.00 0.00 0.00 2.32
3680 8457 0.593128 AGCAACCACACGAGCAATTC 59.407 50.000 0.00 0.00 0.00 2.17
3737 8514 3.708403 TCCAGAGACAAGTGCATGATT 57.292 42.857 0.00 0.00 0.00 2.57
3740 8517 3.119602 CCAGAGACAAGTGCATGATTTGG 60.120 47.826 0.00 0.00 0.00 3.28
3744 8521 3.256631 AGACAAGTGCATGATTTGGAACC 59.743 43.478 0.00 0.00 0.00 3.62
3745 8522 3.233507 ACAAGTGCATGATTTGGAACCT 58.766 40.909 0.00 0.00 0.00 3.50
3746 8523 4.406456 ACAAGTGCATGATTTGGAACCTA 58.594 39.130 0.00 0.00 0.00 3.08
3762 8539 5.186198 GGAACCTACTCATGTGCTAATTGT 58.814 41.667 0.00 0.00 0.00 2.71
3829 8607 3.914312 CGGACTGCACGGAGAATATAAT 58.086 45.455 0.00 0.00 0.00 1.28
3851 8629 3.819188 GCTGGAGTGCCTGTATGC 58.181 61.111 0.00 0.00 35.68 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153881 GGTCTTCCTACGCCACGTC 60.154 63.158 0.00 0.00 41.54 4.34
2 3 1.445582 GTGGTCTTCCTACGCCACG 60.446 63.158 0.00 0.00 41.37 4.94
3 4 4.592426 GTGGTCTTCCTACGCCAC 57.408 61.111 0.00 0.00 43.52 5.01
4 5 1.541310 CCAGTGGTCTTCCTACGCCA 61.541 60.000 0.00 0.00 34.23 5.69
196 212 4.124351 CCGTTCGCGCACCTAGGA 62.124 66.667 17.98 0.00 39.70 2.94
238 254 7.544622 AGGAAAAATTAAATAAGAAGCGGGAC 58.455 34.615 0.00 0.00 0.00 4.46
255 274 7.167924 ACAAAATTGCCACAAAAGGAAAAAT 57.832 28.000 0.00 0.00 27.56 1.82
262 281 6.093909 AGGAGAAAACAAAATTGCCACAAAAG 59.906 34.615 0.00 0.00 0.00 2.27
265 284 5.096443 AGGAGAAAACAAAATTGCCACAA 57.904 34.783 0.00 0.00 0.00 3.33
267 286 6.454795 TCATAGGAGAAAACAAAATTGCCAC 58.545 36.000 0.00 0.00 0.00 5.01
277 296 7.685481 TGGTATGAAGTTCATAGGAGAAAACA 58.315 34.615 23.03 10.39 39.76 2.83
278 297 8.616076 CATGGTATGAAGTTCATAGGAGAAAAC 58.384 37.037 23.03 12.74 39.76 2.43
337 365 4.219033 CACGTCTGGTTGCAACTAATTTC 58.781 43.478 27.64 11.49 0.00 2.17
338 366 3.550030 GCACGTCTGGTTGCAACTAATTT 60.550 43.478 27.64 6.90 0.00 1.82
340 368 1.535462 GCACGTCTGGTTGCAACTAAT 59.465 47.619 27.64 6.23 0.00 1.73
343 371 1.153168 AGCACGTCTGGTTGCAACT 60.153 52.632 27.64 5.20 0.00 3.16
344 372 1.279840 GAGCACGTCTGGTTGCAAC 59.720 57.895 21.59 21.59 0.00 4.17
345 373 0.746204 TTGAGCACGTCTGGTTGCAA 60.746 50.000 0.00 0.00 0.00 4.08
346 374 1.153269 TTGAGCACGTCTGGTTGCA 60.153 52.632 0.00 0.00 0.00 4.08
347 375 1.160329 ACTTGAGCACGTCTGGTTGC 61.160 55.000 0.00 0.00 0.00 4.17
348 376 1.003545 CAACTTGAGCACGTCTGGTTG 60.004 52.381 0.00 0.00 34.54 3.77
350 378 0.464036 TCAACTTGAGCACGTCTGGT 59.536 50.000 0.00 0.00 0.00 4.00
351 379 1.728971 GATCAACTTGAGCACGTCTGG 59.271 52.381 2.05 0.00 32.15 3.86
352 380 1.728971 GGATCAACTTGAGCACGTCTG 59.271 52.381 9.19 0.00 33.81 3.51
354 382 1.079503 GGGATCAACTTGAGCACGTC 58.920 55.000 9.19 0.00 33.81 4.34
355 383 0.687354 AGGGATCAACTTGAGCACGT 59.313 50.000 9.19 0.00 41.84 4.49
356 384 1.734465 GAAGGGATCAACTTGAGCACG 59.266 52.381 9.19 0.00 41.84 5.34
357 385 3.006247 GAGAAGGGATCAACTTGAGCAC 58.994 50.000 9.19 5.26 36.22 4.40
358 386 2.026822 GGAGAAGGGATCAACTTGAGCA 60.027 50.000 9.19 0.00 33.81 4.26
361 389 4.164221 GGTATGGAGAAGGGATCAACTTGA 59.836 45.833 6.63 0.00 0.00 3.02
362 390 4.080356 TGGTATGGAGAAGGGATCAACTTG 60.080 45.833 6.63 0.00 0.00 3.16
363 391 4.111577 TGGTATGGAGAAGGGATCAACTT 58.888 43.478 1.94 1.94 0.00 2.66
365 393 3.711704 TCTGGTATGGAGAAGGGATCAAC 59.288 47.826 0.00 0.00 0.00 3.18
366 394 4.007581 TCTGGTATGGAGAAGGGATCAA 57.992 45.455 0.00 0.00 0.00 2.57
368 396 4.202409 CCTTTCTGGTATGGAGAAGGGATC 60.202 50.000 5.01 0.00 45.32 3.36
369 397 3.718956 CCTTTCTGGTATGGAGAAGGGAT 59.281 47.826 5.01 0.00 45.32 3.85
370 398 3.115390 CCTTTCTGGTATGGAGAAGGGA 58.885 50.000 5.01 0.00 45.32 4.20
371 399 2.422093 GCCTTTCTGGTATGGAGAAGGG 60.422 54.545 0.00 0.00 45.28 3.95
373 401 3.539604 CTGCCTTTCTGGTATGGAGAAG 58.460 50.000 0.00 0.00 38.35 2.85
374 402 2.356125 GCTGCCTTTCTGGTATGGAGAA 60.356 50.000 0.00 0.00 38.35 2.87
377 405 1.210478 GAGCTGCCTTTCTGGTATGGA 59.790 52.381 0.00 0.00 38.35 3.41
378 406 1.673168 GAGCTGCCTTTCTGGTATGG 58.327 55.000 0.00 0.00 38.35 2.74
380 408 0.179000 CCGAGCTGCCTTTCTGGTAT 59.821 55.000 0.00 0.00 38.35 2.73
381 409 1.192146 ACCGAGCTGCCTTTCTGGTA 61.192 55.000 0.00 0.00 38.35 3.25
382 410 2.056906 AACCGAGCTGCCTTTCTGGT 62.057 55.000 0.00 0.00 38.35 4.00
432 588 4.870021 AATCTCCTTCAGCAATTAGGGT 57.130 40.909 0.00 0.00 0.00 4.34
472 628 1.210155 CACAGCGGTTTAGGCAAGC 59.790 57.895 0.00 0.00 0.00 4.01
495 654 0.669318 CGGTGTAGTGTGATTGGCGT 60.669 55.000 0.00 0.00 0.00 5.68
500 659 2.092291 CGCGCGGTGTAGTGTGATT 61.092 57.895 24.84 0.00 34.37 2.57
536 776 1.153249 ACAGTCCACCCACAACGTG 60.153 57.895 0.00 0.00 0.00 4.49
540 780 1.529796 GTCCACAGTCCACCCACAA 59.470 57.895 0.00 0.00 0.00 3.33
541 781 2.802724 CGTCCACAGTCCACCCACA 61.803 63.158 0.00 0.00 0.00 4.17
542 782 2.030562 CGTCCACAGTCCACCCAC 59.969 66.667 0.00 0.00 0.00 4.61
547 787 2.626780 CGAGCTCGTCCACAGTCCA 61.627 63.158 27.79 0.00 34.11 4.02
549 789 1.135731 CTCGAGCTCGTCCACAGTC 59.864 63.158 33.33 0.00 40.80 3.51
550 790 2.336478 CCTCGAGCTCGTCCACAGT 61.336 63.158 33.33 0.00 40.80 3.55
551 791 2.041115 TCCTCGAGCTCGTCCACAG 61.041 63.158 33.33 22.78 40.80 3.66
552 792 2.033602 TCCTCGAGCTCGTCCACA 59.966 61.111 33.33 14.80 40.80 4.17
556 796 2.098680 CGTGTCCTCGAGCTCGTC 59.901 66.667 33.33 21.62 40.80 4.20
557 797 3.432588 CCGTGTCCTCGAGCTCGT 61.433 66.667 33.33 0.00 40.80 4.18
558 798 3.102107 CTCCGTGTCCTCGAGCTCG 62.102 68.421 30.03 30.03 41.45 5.03
571 827 1.076632 CCTCACCTCCTAGCTCCGT 60.077 63.158 0.00 0.00 0.00 4.69
572 828 0.684805 AACCTCACCTCCTAGCTCCG 60.685 60.000 0.00 0.00 0.00 4.63
585 841 3.569701 GCAGGAATTGAACAAGAACCTCA 59.430 43.478 0.00 0.00 0.00 3.86
593 849 3.191162 CGGAAGATGCAGGAATTGAACAA 59.809 43.478 0.00 0.00 0.00 2.83
595 851 2.749621 ACGGAAGATGCAGGAATTGAAC 59.250 45.455 0.00 0.00 0.00 3.18
604 860 2.593346 AAGCTAGACGGAAGATGCAG 57.407 50.000 0.00 0.00 0.00 4.41
626 882 4.576463 GCCTATTGTATTGACCTGACCAAG 59.424 45.833 0.00 0.00 0.00 3.61
630 886 4.572389 CACAGCCTATTGTATTGACCTGAC 59.428 45.833 0.00 0.00 0.00 3.51
655 911 0.668401 AAACACCGGCAGTACGTAGC 60.668 55.000 0.00 0.00 0.00 3.58
656 912 1.065358 CAAACACCGGCAGTACGTAG 58.935 55.000 0.00 0.00 0.00 3.51
657 913 0.319727 CCAAACACCGGCAGTACGTA 60.320 55.000 0.00 0.00 0.00 3.57
658 914 1.595929 CCAAACACCGGCAGTACGT 60.596 57.895 0.00 0.00 0.00 3.57
659 915 1.161563 AACCAAACACCGGCAGTACG 61.162 55.000 0.00 0.00 0.00 3.67
660 916 1.026584 AAACCAAACACCGGCAGTAC 58.973 50.000 0.00 0.00 0.00 2.73
661 917 1.025812 CAAACCAAACACCGGCAGTA 58.974 50.000 0.00 0.00 0.00 2.74
662 918 0.968393 ACAAACCAAACACCGGCAGT 60.968 50.000 0.00 0.00 0.00 4.40
663 919 0.527385 CACAAACCAAACACCGGCAG 60.527 55.000 0.00 0.00 0.00 4.85
664 920 1.513158 CACAAACCAAACACCGGCA 59.487 52.632 0.00 0.00 0.00 5.69
665 921 1.880796 GCACAAACCAAACACCGGC 60.881 57.895 0.00 0.00 0.00 6.13
666 922 1.227118 GGCACAAACCAAACACCGG 60.227 57.895 0.00 0.00 0.00 5.28
667 923 0.108615 TTGGCACAAACCAAACACCG 60.109 50.000 0.00 0.00 46.65 4.94
668 924 3.842869 TTGGCACAAACCAAACACC 57.157 47.368 0.00 0.00 46.65 4.16
706 962 2.991250 AGAGCACACCCATTACACATC 58.009 47.619 0.00 0.00 0.00 3.06
718 974 0.590195 CAGCCAACTCAAGAGCACAC 59.410 55.000 0.00 0.00 0.00 3.82
740 996 2.969262 TCAGATCAGTAACACCACCACA 59.031 45.455 0.00 0.00 0.00 4.17
778 1034 4.834496 AGGATGGAAGATGCAAAAGTTGAA 59.166 37.500 0.00 0.00 0.00 2.69
795 1051 2.490903 CTGGTCAAGAAAAGCAGGATGG 59.509 50.000 0.00 0.00 38.33 3.51
842 1101 2.434185 TGCTCCGGTTGCGCTAAG 60.434 61.111 9.73 0.00 0.00 2.18
942 1222 9.113838 CTCATTCAAAGGCAATATAACTACACT 57.886 33.333 0.00 0.00 0.00 3.55
943 1223 9.109393 TCTCATTCAAAGGCAATATAACTACAC 57.891 33.333 0.00 0.00 0.00 2.90
944 1224 9.679661 TTCTCATTCAAAGGCAATATAACTACA 57.320 29.630 0.00 0.00 0.00 2.74
1015 1300 2.549754 CACTTGATTCTTGAACGCCACT 59.450 45.455 0.00 0.00 0.00 4.00
1058 1343 1.580132 CGTTGCTTAATGCCGTCGC 60.580 57.895 0.00 0.00 42.00 5.19
1123 1408 4.971282 AGGTTCTCCAAGTGATCCATATGA 59.029 41.667 3.65 0.00 35.89 2.15
1126 1411 4.361783 TCAGGTTCTCCAAGTGATCCATA 58.638 43.478 0.00 0.00 35.89 2.74
1221 1506 0.314302 AACTCCTTCTCGTCACACCG 59.686 55.000 0.00 0.00 0.00 4.94
1239 1524 6.298441 TGTCCATTATCATCTCTGTGTGAA 57.702 37.500 0.00 0.00 0.00 3.18
1243 1528 6.343703 TCAGTTGTCCATTATCATCTCTGTG 58.656 40.000 0.00 0.00 0.00 3.66
1248 1533 7.126421 AGGTACTTCAGTTGTCCATTATCATCT 59.874 37.037 0.00 0.00 27.25 2.90
1489 1774 2.595124 TCAAGACTTCGCTTGACACA 57.405 45.000 0.00 0.00 46.73 3.72
1503 1788 1.610624 GCCGGGTCATTCAGTTCAAGA 60.611 52.381 2.18 0.00 0.00 3.02
1509 1794 0.400213 TTTCAGCCGGGTCATTCAGT 59.600 50.000 1.27 0.00 0.00 3.41
1538 1823 2.284190 GAGGTATGGCTGAACTCTTGC 58.716 52.381 0.00 0.00 0.00 4.01
1549 1834 0.037697 TGTGTGACACGAGGTATGGC 60.038 55.000 11.51 0.00 37.14 4.40
1610 1895 7.917505 GCTCTTCTTGAAATTCTTTGAACTTCA 59.082 33.333 0.90 0.90 0.00 3.02
1694 1979 4.441792 CACATCCTCGGTGATTTCATACA 58.558 43.478 0.00 0.00 38.54 2.29
1970 2255 3.812609 TCTATCAAAACGTTCTGCAGCAA 59.187 39.130 9.47 1.36 0.00 3.91
2153 2438 8.062065 AGTTTTACTTGTTGTCTTTCCATTCA 57.938 30.769 0.00 0.00 0.00 2.57
2180 2465 3.005554 CTGACAGCTATTGGACTTGGTG 58.994 50.000 0.00 0.00 0.00 4.17
2209 2494 0.101399 CTCGGTGAAGGAGGACATCG 59.899 60.000 0.00 0.00 41.19 3.84
2322 2697 9.815936 GCGAGTTTTTATAAAAAGTAGCTTACA 57.184 29.630 33.57 10.39 46.80 2.41
2523 5670 5.428496 TGACTCTGTTTCAGAATGCAAAG 57.572 39.130 0.00 0.00 40.18 2.77
2530 5677 3.118261 AGGTTGCTGACTCTGTTTCAGAA 60.118 43.478 10.98 0.04 42.81 3.02
2838 5990 4.641989 CCCTCCAATTCCATCAAAGTGTAG 59.358 45.833 0.00 0.00 0.00 2.74
3257 7981 7.011389 CGGTGATGCTTTAGACAAGATTATCAA 59.989 37.037 0.00 0.00 0.00 2.57
3259 7983 6.480320 ACGGTGATGCTTTAGACAAGATTATC 59.520 38.462 0.00 0.00 0.00 1.75
3260 7984 6.258727 CACGGTGATGCTTTAGACAAGATTAT 59.741 38.462 0.74 0.00 0.00 1.28
3261 7985 5.580691 CACGGTGATGCTTTAGACAAGATTA 59.419 40.000 0.74 0.00 0.00 1.75
3262 7986 4.393062 CACGGTGATGCTTTAGACAAGATT 59.607 41.667 0.74 0.00 0.00 2.40
3263 7987 3.935203 CACGGTGATGCTTTAGACAAGAT 59.065 43.478 0.74 0.00 0.00 2.40
3264 7988 3.325870 CACGGTGATGCTTTAGACAAGA 58.674 45.455 0.74 0.00 0.00 3.02
3265 7989 2.159653 GCACGGTGATGCTTTAGACAAG 60.160 50.000 13.29 0.00 42.62 3.16
3266 7990 1.804151 GCACGGTGATGCTTTAGACAA 59.196 47.619 13.29 0.00 42.62 3.18
3267 7991 1.438651 GCACGGTGATGCTTTAGACA 58.561 50.000 13.29 0.00 42.62 3.41
3398 8132 8.717821 TGTAGTACTCAATCTGTAACAAAATGC 58.282 33.333 0.00 0.00 0.00 3.56
3493 8227 4.698583 AAGAGCGTTTAGATCACTACGT 57.301 40.909 12.81 0.00 37.82 3.57
3494 8228 4.857588 ACAAAGAGCGTTTAGATCACTACG 59.142 41.667 8.56 8.56 37.82 3.51
3495 8229 7.988904 ATACAAAGAGCGTTTAGATCACTAC 57.011 36.000 0.00 0.00 37.82 2.73
3496 8230 8.997621 AAATACAAAGAGCGTTTAGATCACTA 57.002 30.769 0.00 0.00 37.82 2.74
3515 8249 7.576287 CGTGTACTCCCTCTGTAAAGAAATACA 60.576 40.741 0.00 0.00 34.72 2.29
3516 8250 6.750963 CGTGTACTCCCTCTGTAAAGAAATAC 59.249 42.308 0.00 0.00 0.00 1.89
3540 8274 3.535561 AGATTGTAAAGCATGAGGGACG 58.464 45.455 0.00 0.00 32.26 4.79
3544 8278 7.373493 AGTTTGAAAGATTGTAAAGCATGAGG 58.627 34.615 0.00 0.00 32.26 3.86
3629 8370 6.633634 TGTAACTTGTACTTTGCGTTAAATGC 59.366 34.615 0.00 0.00 0.00 3.56
3679 8456 0.944311 GCGCAACTTCCGAACAGAGA 60.944 55.000 0.30 0.00 0.00 3.10
3680 8457 1.221466 TGCGCAACTTCCGAACAGAG 61.221 55.000 8.16 0.00 0.00 3.35
3737 8514 4.901197 TTAGCACATGAGTAGGTTCCAA 57.099 40.909 0.00 0.00 0.00 3.53
3740 8517 6.743575 AACAATTAGCACATGAGTAGGTTC 57.256 37.500 0.00 0.00 0.00 3.62
3744 8521 7.370383 ACCAAAAACAATTAGCACATGAGTAG 58.630 34.615 0.00 0.00 0.00 2.57
3745 8522 7.230510 AGACCAAAAACAATTAGCACATGAGTA 59.769 33.333 0.00 0.00 0.00 2.59
3746 8523 6.040842 AGACCAAAAACAATTAGCACATGAGT 59.959 34.615 0.00 0.00 0.00 3.41
3762 8539 6.552445 TCCCAAATCAAAAGAGACCAAAAA 57.448 33.333 0.00 0.00 0.00 1.94
3849 8627 2.759641 CTTTGCAGGGAGAGGCAGCA 62.760 60.000 0.00 0.00 41.68 4.41
3850 8628 2.034687 TTTGCAGGGAGAGGCAGC 59.965 61.111 0.00 0.00 41.68 5.25
3851 8629 1.378250 CCTTTGCAGGGAGAGGCAG 60.378 63.158 2.05 0.00 41.68 4.85


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

AutoCloner maintained by Alex Coulton.