Multiple sequence alignment - TraesCS4B01G005700

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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 TraesCS4B01G005700 chr4B 100.000 4253 0 0 1 4253 3830896 3835148 0.000000e+00 7854.0
1 TraesCS4B01G005700 chr4B 82.682 358 55 3 15 368 3821169 3820815 1.150000e-80 311.0
2 TraesCS4B01G005700 chr4D 92.719 3310 172 33 965 4253 3251294 3254555 0.000000e+00 4713.0
3 TraesCS4B01G005700 chr4D 96.154 390 11 1 1 390 3250392 3250777 6.000000e-178 634.0
4 TraesCS4B01G005700 chr4D 92.141 369 16 6 421 777 3250763 3251130 3.790000e-140 508.0
5 TraesCS4B01G005700 chr4D 84.887 311 47 0 9 319 3241959 3241649 8.880000e-82 315.0
6 TraesCS4B01G005700 chr4D 94.690 113 5 1 785 896 3251169 3251281 1.570000e-39 174.0
7 TraesCS4B01G005700 chr4A 90.780 3525 172 51 783 4247 602272237 602268806 0.000000e+00 4567.0
8 TraesCS4B01G005700 chr4A 92.809 445 22 5 1691 2135 735504453 735504019 1.670000e-178 636.0
9 TraesCS4B01G005700 chr4A 94.949 396 16 1 1 396 602273014 602272623 6.040000e-173 617.0
10 TraesCS4B01G005700 chr4A 90.164 366 20 7 424 774 602272640 602272276 3.000000e-126 462.0
11 TraesCS4B01G005700 chr4A 85.032 314 47 0 6 319 602307571 602307884 1.910000e-83 320.0
12 TraesCS4B01G005700 chr3A 80.079 1516 229 38 1784 3248 426652880 426654373 0.000000e+00 1059.0
13 TraesCS4B01G005700 chr3B 79.921 1514 233 40 1784 3248 413992271 413993762 0.000000e+00 1046.0
14 TraesCS4B01G005700 chr3D 82.976 840 117 15 2426 3254 307568070 307567246 0.000000e+00 736.0
15 TraesCS4B01G005700 chr5B 78.185 1091 194 28 1749 2822 636895494 636896557 0.000000e+00 656.0
16 TraesCS4B01G005700 chr5B 83.040 454 69 6 2819 3270 636898075 636898522 5.120000e-109 405.0
17 TraesCS4B01G005700 chr5B 92.857 42 1 2 4213 4253 166363991 166364031 4.590000e-05 60.2
18 TraesCS4B01G005700 chr5D 78.376 1059 194 25 1780 2822 506158367 506159406 0.000000e+00 654.0
19 TraesCS4B01G005700 chr1D 80.882 816 134 12 2438 3239 2119970 2119163 1.300000e-174 623.0
20 TraesCS4B01G005700 chr1D 80.000 565 86 18 1783 2322 2120537 2119975 3.990000e-105 392.0
21 TraesCS4B01G005700 chr2B 94.586 314 11 4 1822 2135 146777767 146777460 8.270000e-132 481.0
22 TraesCS4B01G005700 chr7B 80.328 122 20 3 3059 3178 605909337 605909456 5.860000e-14 89.8
23 TraesCS4B01G005700 chr7B 90.909 44 2 2 4211 4253 658500410 658500368 1.650000e-04 58.4
24 TraesCS4B01G005700 chr7B 90.909 44 2 2 4211 4253 658628054 658628012 1.650000e-04 58.4
25 TraesCS4B01G005700 chr7B 90.909 44 2 2 4211 4253 658738410 658738368 1.650000e-04 58.4
26 TraesCS4B01G005700 chrUn 90.909 44 2 2 4211 4253 462444187 462444145 1.650000e-04 58.4
27 TraesCS4B01G005700 chr1B 96.970 33 1 0 4221 4253 595784175 595784207 5.940000e-04 56.5
28 TraesCS4B01G005700 chr2A 100.000 29 0 0 4225 4253 40247439 40247411 2.000000e-03 54.7


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 TraesCS4B01G005700 chr4B 3830896 3835148 4252 False 7854.00 7854 100.000000 1 4253 1 chr4B.!!$F1 4252
1 TraesCS4B01G005700 chr4D 3250392 3254555 4163 False 1507.25 4713 93.926000 1 4253 4 chr4D.!!$F1 4252
2 TraesCS4B01G005700 chr4A 602268806 602273014 4208 True 1882.00 4567 91.964333 1 4247 3 chr4A.!!$R2 4246
3 TraesCS4B01G005700 chr3A 426652880 426654373 1493 False 1059.00 1059 80.079000 1784 3248 1 chr3A.!!$F1 1464
4 TraesCS4B01G005700 chr3B 413992271 413993762 1491 False 1046.00 1046 79.921000 1784 3248 1 chr3B.!!$F1 1464
5 TraesCS4B01G005700 chr3D 307567246 307568070 824 True 736.00 736 82.976000 2426 3254 1 chr3D.!!$R1 828
6 TraesCS4B01G005700 chr5B 636895494 636898522 3028 False 530.50 656 80.612500 1749 3270 2 chr5B.!!$F2 1521
7 TraesCS4B01G005700 chr5D 506158367 506159406 1039 False 654.00 654 78.376000 1780 2822 1 chr5D.!!$F1 1042
8 TraesCS4B01G005700 chr1D 2119163 2120537 1374 True 507.50 623 80.441000 1783 3239 2 chr1D.!!$R1 1456

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
397 398 0.038892 GTACCAACGGTGCGAGAAGA 60.039 55.0 0.00 0.0 36.19 2.87 F
694 709 0.039888 GCGGGTTGCACGTGTAATTT 60.040 50.0 21.92 0.0 45.45 1.82 F
2253 2417 0.038744 ACCATGAAGGCAGGAAGGTG 59.961 55.0 0.00 0.0 43.14 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 1456 0.244450 CTTACGGTGTGGCGAAGGTA 59.756 55.0 0.0 0.0 0.0 3.08 R
2653 2842 0.036765 ATGCCGGCGAAGTAGAACAA 60.037 50.0 23.9 0.0 0.0 2.83 R
4079 5795 0.955919 GGAGCGGGAGAAACTGTTGG 60.956 60.0 0.0 0.0 0.0 3.77 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
89 90 2.094182 AGGACATTGTCGCTATTGTCGT 60.094 45.455 10.56 0.00 39.45 4.34
315 316 1.226746 GGGACGAGAACAAAGTGTGG 58.773 55.000 0.00 0.00 0.00 4.17
365 366 3.361158 CGGGCGCCATTGTTGACA 61.361 61.111 30.85 0.00 0.00 3.58
370 371 1.405105 GGCGCCATTGTTGACATGTAT 59.595 47.619 24.80 0.00 0.00 2.29
371 372 2.453080 GCGCCATTGTTGACATGTATG 58.547 47.619 0.00 0.00 0.00 2.39
372 373 2.453080 CGCCATTGTTGACATGTATGC 58.547 47.619 0.00 0.00 0.00 3.14
373 374 2.453080 GCCATTGTTGACATGTATGCG 58.547 47.619 0.00 0.00 0.00 4.73
393 394 2.807895 CGGTACCAACGGTGCGAG 60.808 66.667 13.54 0.00 39.20 5.03
394 395 2.652530 GGTACCAACGGTGCGAGA 59.347 61.111 7.15 0.00 39.20 4.04
395 396 1.005867 GGTACCAACGGTGCGAGAA 60.006 57.895 7.15 0.00 39.20 2.87
396 397 1.012486 GGTACCAACGGTGCGAGAAG 61.012 60.000 7.15 0.00 39.20 2.85
397 398 0.038892 GTACCAACGGTGCGAGAAGA 60.039 55.000 0.00 0.00 36.19 2.87
398 399 0.675083 TACCAACGGTGCGAGAAGAA 59.325 50.000 0.00 0.00 36.19 2.52
399 400 0.600255 ACCAACGGTGCGAGAAGAAG 60.600 55.000 0.00 0.00 32.98 2.85
400 401 0.319555 CCAACGGTGCGAGAAGAAGA 60.320 55.000 0.00 0.00 0.00 2.87
401 402 1.497991 CAACGGTGCGAGAAGAAGAA 58.502 50.000 0.00 0.00 0.00 2.52
402 403 2.069273 CAACGGTGCGAGAAGAAGAAT 58.931 47.619 0.00 0.00 0.00 2.40
403 404 1.997669 ACGGTGCGAGAAGAAGAATC 58.002 50.000 0.00 0.00 0.00 2.52
404 405 0.917259 CGGTGCGAGAAGAAGAATCG 59.083 55.000 0.00 0.00 39.40 3.34
405 406 1.467543 CGGTGCGAGAAGAAGAATCGA 60.468 52.381 0.00 0.00 38.72 3.59
406 407 2.796383 CGGTGCGAGAAGAAGAATCGAT 60.796 50.000 0.00 0.00 38.72 3.59
407 408 2.792116 GGTGCGAGAAGAAGAATCGATC 59.208 50.000 0.00 0.00 38.72 3.69
408 409 2.465839 GTGCGAGAAGAAGAATCGATCG 59.534 50.000 9.36 9.36 38.72 3.69
409 410 2.354821 TGCGAGAAGAAGAATCGATCGA 59.645 45.455 21.86 21.86 38.72 3.59
410 411 2.970609 GCGAGAAGAAGAATCGATCGAG 59.029 50.000 23.84 6.11 38.72 4.04
411 412 2.970609 CGAGAAGAAGAATCGATCGAGC 59.029 50.000 23.84 17.11 38.72 5.03
412 413 3.303725 CGAGAAGAAGAATCGATCGAGCT 60.304 47.826 23.84 19.04 38.72 4.09
413 414 4.084276 CGAGAAGAAGAATCGATCGAGCTA 60.084 45.833 23.84 0.00 38.72 3.32
414 415 5.103290 AGAAGAAGAATCGATCGAGCTAC 57.897 43.478 23.84 13.48 0.00 3.58
415 416 4.576873 AGAAGAAGAATCGATCGAGCTACA 59.423 41.667 23.84 0.00 0.00 2.74
416 417 4.902443 AGAAGAATCGATCGAGCTACAA 57.098 40.909 23.84 0.00 0.00 2.41
417 418 5.250235 AGAAGAATCGATCGAGCTACAAA 57.750 39.130 23.84 0.00 0.00 2.83
418 419 5.651530 AGAAGAATCGATCGAGCTACAAAA 58.348 37.500 23.84 0.00 0.00 2.44
419 420 6.100004 AGAAGAATCGATCGAGCTACAAAAA 58.900 36.000 23.84 0.00 0.00 1.94
420 421 5.957910 AGAATCGATCGAGCTACAAAAAG 57.042 39.130 23.84 0.00 0.00 2.27
421 422 4.268884 AGAATCGATCGAGCTACAAAAAGC 59.731 41.667 23.84 0.00 43.11 3.51
432 433 4.485163 GCTACAAAAAGCTGTACCAATGG 58.515 43.478 0.00 0.00 39.50 3.16
433 434 4.022329 GCTACAAAAAGCTGTACCAATGGT 60.022 41.667 10.81 10.81 39.50 3.55
434 435 4.320608 ACAAAAAGCTGTACCAATGGTG 57.679 40.909 16.41 0.00 36.19 4.17
480 481 1.188863 GTAGTCCCCAACGCCTCTAA 58.811 55.000 0.00 0.00 0.00 2.10
481 482 1.551883 GTAGTCCCCAACGCCTCTAAA 59.448 52.381 0.00 0.00 0.00 1.85
484 485 0.393808 TCCCCAACGCCTCTAAATGC 60.394 55.000 0.00 0.00 0.00 3.56
485 486 1.384222 CCCCAACGCCTCTAAATGCC 61.384 60.000 0.00 0.00 0.00 4.40
529 530 1.534163 GAAAAGGGAACACGTACAGCC 59.466 52.381 0.00 0.00 0.00 4.85
623 630 1.423721 CTCCCATGCATGTCGTGTCG 61.424 60.000 24.58 7.82 0.00 4.35
627 634 1.805539 ATGCATGTCGTGTCGTCCG 60.806 57.895 0.00 0.00 0.00 4.79
694 709 0.039888 GCGGGTTGCACGTGTAATTT 60.040 50.000 21.92 0.00 45.45 1.82
752 767 1.414919 TGGTTTCTAACGTGAGCACCT 59.585 47.619 17.68 0.00 0.00 4.00
767 782 6.566942 CGTGAGCACCTGAGTAGATTATACTC 60.567 46.154 10.82 10.82 43.06 2.59
768 783 5.770663 TGAGCACCTGAGTAGATTATACTCC 59.229 44.000 14.25 1.06 42.32 3.85
770 785 5.081032 GCACCTGAGTAGATTATACTCCCT 58.919 45.833 14.25 0.00 42.32 4.20
771 786 5.184287 GCACCTGAGTAGATTATACTCCCTC 59.816 48.000 14.25 2.24 42.32 4.30
772 787 6.548321 CACCTGAGTAGATTATACTCCCTCT 58.452 44.000 14.25 0.00 42.32 3.69
773 788 6.432783 CACCTGAGTAGATTATACTCCCTCTG 59.567 46.154 14.25 3.23 42.32 3.35
777 792 7.990055 TGAGTAGATTATACTCCCTCTGATCA 58.010 38.462 14.25 0.00 42.32 2.92
778 793 8.106462 TGAGTAGATTATACTCCCTCTGATCAG 58.894 40.741 17.07 17.07 42.32 2.90
779 794 8.225863 AGTAGATTATACTCCCTCTGATCAGA 57.774 38.462 23.75 23.75 35.85 3.27
780 795 8.845793 AGTAGATTATACTCCCTCTGATCAGAT 58.154 37.037 25.30 12.95 36.76 2.90
781 796 9.120538 GTAGATTATACTCCCTCTGATCAGATC 57.879 40.741 25.30 15.20 36.76 2.75
863 910 9.367444 GTAGCAATAGAACAAACACAGTACTAT 57.633 33.333 0.00 0.00 0.00 2.12
899 946 4.687215 TGAGCAGCCACCACTCGC 62.687 66.667 0.00 0.00 32.98 5.03
903 950 2.591429 CAGCCACCACTCGCACAA 60.591 61.111 0.00 0.00 0.00 3.33
917 964 1.603802 CGCACAACCACTTGATCAACT 59.396 47.619 3.38 0.00 0.00 3.16
918 965 2.349817 CGCACAACCACTTGATCAACTC 60.350 50.000 3.38 0.00 0.00 3.01
919 966 2.349817 GCACAACCACTTGATCAACTCG 60.350 50.000 3.38 0.00 0.00 4.18
920 967 3.130633 CACAACCACTTGATCAACTCGA 58.869 45.455 3.38 0.00 0.00 4.04
935 982 4.024048 TCAACTCGATCAGCAAAGGAAAAC 60.024 41.667 0.00 0.00 0.00 2.43
966 1013 1.907240 TTCCCCTTGGGCTAGCTATT 58.093 50.000 15.72 0.00 43.94 1.73
967 1014 1.435256 TCCCCTTGGGCTAGCTATTC 58.565 55.000 15.72 0.00 43.94 1.75
968 1015 0.402121 CCCCTTGGGCTAGCTATTCC 59.598 60.000 15.72 7.77 35.35 3.01
970 1017 0.402121 CCTTGGGCTAGCTATTCCCC 59.598 60.000 21.88 18.21 39.30 4.81
972 1019 2.854253 TGGGCTAGCTATTCCCCAG 58.146 57.895 21.88 1.44 42.41 4.45
983 1030 0.114364 ATTCCCCAGTCCCCACAAAC 59.886 55.000 0.00 0.00 0.00 2.93
984 1031 2.014033 TTCCCCAGTCCCCACAAACC 62.014 60.000 0.00 0.00 0.00 3.27
987 1034 1.112916 CCCAGTCCCCACAAACCAAC 61.113 60.000 0.00 0.00 0.00 3.77
989 1036 1.826487 AGTCCCCACAAACCAACGC 60.826 57.895 0.00 0.00 0.00 4.84
990 1037 2.519780 TCCCCACAAACCAACGCC 60.520 61.111 0.00 0.00 0.00 5.68
993 1040 4.639171 CCACAAACCAACGCCGGC 62.639 66.667 19.07 19.07 0.00 6.13
1042 1092 0.112995 TTTTCCATGGGAGCAGCAGT 59.887 50.000 13.02 0.00 31.21 4.40
1186 1236 3.066814 GGGCGTACCACTCCGTCT 61.067 66.667 0.00 0.00 39.85 4.18
1380 1433 9.699703 TTTCTTTTTAGCCGCATTATTAGTTTT 57.300 25.926 0.00 0.00 0.00 2.43
1381 1434 8.905103 TCTTTTTAGCCGCATTATTAGTTTTC 57.095 30.769 0.00 0.00 0.00 2.29
1382 1435 7.971722 TCTTTTTAGCCGCATTATTAGTTTTCC 59.028 33.333 0.00 0.00 0.00 3.13
1383 1436 5.761165 TTAGCCGCATTATTAGTTTTCCC 57.239 39.130 0.00 0.00 0.00 3.97
1384 1437 3.898482 AGCCGCATTATTAGTTTTCCCT 58.102 40.909 0.00 0.00 0.00 4.20
1385 1438 4.278310 AGCCGCATTATTAGTTTTCCCTT 58.722 39.130 0.00 0.00 0.00 3.95
1386 1439 4.709886 AGCCGCATTATTAGTTTTCCCTTT 59.290 37.500 0.00 0.00 0.00 3.11
1387 1440 5.889289 AGCCGCATTATTAGTTTTCCCTTTA 59.111 36.000 0.00 0.00 0.00 1.85
1388 1441 6.039382 AGCCGCATTATTAGTTTTCCCTTTAG 59.961 38.462 0.00 0.00 0.00 1.85
1389 1442 6.206498 CCGCATTATTAGTTTTCCCTTTAGC 58.794 40.000 0.00 0.00 0.00 3.09
1390 1443 6.206498 CGCATTATTAGTTTTCCCTTTAGCC 58.794 40.000 0.00 0.00 0.00 3.93
1391 1444 6.206498 GCATTATTAGTTTTCCCTTTAGCCG 58.794 40.000 0.00 0.00 0.00 5.52
1392 1445 5.823209 TTATTAGTTTTCCCTTTAGCCGC 57.177 39.130 0.00 0.00 0.00 6.53
1393 1446 2.863132 TAGTTTTCCCTTTAGCCGCA 57.137 45.000 0.00 0.00 0.00 5.69
1394 1447 2.215942 AGTTTTCCCTTTAGCCGCAT 57.784 45.000 0.00 0.00 0.00 4.73
1395 1448 2.525368 AGTTTTCCCTTTAGCCGCATT 58.475 42.857 0.00 0.00 0.00 3.56
1396 1449 3.692690 AGTTTTCCCTTTAGCCGCATTA 58.307 40.909 0.00 0.00 0.00 1.90
1397 1450 4.278310 AGTTTTCCCTTTAGCCGCATTAT 58.722 39.130 0.00 0.00 0.00 1.28
1398 1451 4.709886 AGTTTTCCCTTTAGCCGCATTATT 59.290 37.500 0.00 0.00 0.00 1.40
1399 1452 5.889289 AGTTTTCCCTTTAGCCGCATTATTA 59.111 36.000 0.00 0.00 0.00 0.98
1400 1453 6.039382 AGTTTTCCCTTTAGCCGCATTATTAG 59.961 38.462 0.00 0.00 0.00 1.73
1401 1454 4.699925 TCCCTTTAGCCGCATTATTAGT 57.300 40.909 0.00 0.00 0.00 2.24
1402 1455 5.043737 TCCCTTTAGCCGCATTATTAGTT 57.956 39.130 0.00 0.00 0.00 2.24
1403 1456 5.442391 TCCCTTTAGCCGCATTATTAGTTT 58.558 37.500 0.00 0.00 0.00 2.66
1422 1475 0.244450 TACCTTCGCCACACCGTAAG 59.756 55.000 0.00 0.00 0.00 2.34
1424 1477 0.244450 CCTTCGCCACACCGTAAGTA 59.756 55.000 0.00 0.00 0.00 2.24
1425 1478 1.343506 CTTCGCCACACCGTAAGTAC 58.656 55.000 0.00 0.00 0.00 2.73
1463 1516 3.382546 CCAAATGTGTCCATGGAAGGATC 59.617 47.826 18.20 3.91 40.42 3.36
1466 1519 5.715439 AATGTGTCCATGGAAGGATCTAA 57.285 39.130 18.20 0.00 40.42 2.10
1504 1557 7.275888 TGGTTTTAATGGCTCTATAATGCAG 57.724 36.000 0.00 0.00 0.00 4.41
1533 1586 9.092876 CGGAAATGCCTTTATTAATTTAAAGCA 57.907 29.630 0.00 1.38 37.69 3.91
1550 1603 8.723942 TTTAAAGCAGGCAAAAATGTCTTTTA 57.276 26.923 0.00 0.00 33.44 1.52
1616 1677 3.298619 CATCCTAATTTGGTGGCATGGA 58.701 45.455 5.81 0.00 0.00 3.41
1623 1684 2.133281 TTGGTGGCATGGAATCTCAG 57.867 50.000 0.00 0.00 0.00 3.35
1625 1686 1.634973 TGGTGGCATGGAATCTCAGAA 59.365 47.619 0.00 0.00 0.00 3.02
1841 1946 2.662596 GTGACCATCACCGAGCCA 59.337 61.111 0.00 0.00 41.37 4.75
1859 1964 1.143305 CAGAACTGGTGCGAGAAGTG 58.857 55.000 0.00 0.00 0.00 3.16
1860 1965 0.753262 AGAACTGGTGCGAGAAGTGT 59.247 50.000 0.00 0.00 0.00 3.55
1985 2090 0.548031 GGAAGATCATCACCCCTGCA 59.452 55.000 0.00 0.00 0.00 4.41
1994 2099 1.002069 TCACCCCTGCATTCCATCTT 58.998 50.000 0.00 0.00 0.00 2.40
2253 2417 0.038744 ACCATGAAGGCAGGAAGGTG 59.961 55.000 0.00 0.00 43.14 4.00
2345 2521 4.392940 CTGTGAGTTCATTCTCCTTTGGT 58.607 43.478 0.00 0.00 33.93 3.67
2352 2528 6.365520 AGTTCATTCTCCTTTGGTGTTTACT 58.634 36.000 0.00 0.00 0.00 2.24
2355 2531 7.921786 TCATTCTCCTTTGGTGTTTACTATG 57.078 36.000 0.00 0.00 0.00 2.23
2370 2546 2.362736 ACTATGCATGGTTCAGCACAG 58.637 47.619 10.30 0.00 44.49 3.66
2382 2558 6.356556 TGGTTCAGCACAGCAATATTACTAT 58.643 36.000 0.00 0.00 0.00 2.12
2538 2715 1.984424 AGAGAGAAGGCCTTGAAAGCT 59.016 47.619 26.25 13.63 0.00 3.74
2577 2754 2.033793 CGATCTTCTCGGGCTGCTA 58.966 57.895 0.00 0.00 43.82 3.49
2653 2842 1.556911 ACCTGATCGGAGAATGCAAGT 59.443 47.619 2.08 0.00 43.58 3.16
2794 2983 4.178861 GCACGACGCCAGATTACA 57.821 55.556 0.00 0.00 32.94 2.41
2805 2994 2.745281 GCCAGATTACAACGGCTTAACA 59.255 45.455 0.00 0.00 41.50 2.41
2806 2995 3.377172 GCCAGATTACAACGGCTTAACAT 59.623 43.478 0.00 0.00 41.50 2.71
3183 4893 0.963856 TCTCGCCGTCCTACACACAT 60.964 55.000 0.00 0.00 0.00 3.21
3189 4899 1.375396 GTCCTACACACATGCGCCA 60.375 57.895 4.18 0.00 0.00 5.69
3201 4911 4.875713 GCGCCATTCCCCATCGGT 62.876 66.667 0.00 0.00 0.00 4.69
3204 4916 1.754380 CGCCATTCCCCATCGGTCTA 61.754 60.000 0.00 0.00 0.00 2.59
3207 4919 2.605257 CCATTCCCCATCGGTCTACTA 58.395 52.381 0.00 0.00 0.00 1.82
3314 5026 0.107831 TCGAATAAATGGGCTCGGGG 59.892 55.000 0.00 0.00 32.25 5.73
3454 5166 1.117150 GGCAAGTATACCGGACAGGA 58.883 55.000 9.46 0.00 45.00 3.86
3483 5195 3.953775 CCGGTGCTCCCAGTTGGT 61.954 66.667 0.00 0.00 34.77 3.67
3701 5414 2.231964 GGAACTTGCATGCCTCAATGAA 59.768 45.455 16.68 0.00 0.00 2.57
3705 5418 0.322366 TGCATGCCTCAATGAACGGA 60.322 50.000 16.68 0.00 0.00 4.69
3891 5607 1.682854 CCAATGTTGTTCAGGTGCTGT 59.317 47.619 0.00 0.00 32.61 4.40
3908 5624 2.549754 GCTGTTCTTGCTTGCTTGTAGA 59.450 45.455 0.00 0.00 0.00 2.59
3964 5680 4.346418 CAGAGGAAGAAGTATACAGGCCAT 59.654 45.833 5.01 0.00 0.00 4.40
3983 5699 2.731571 GCTGTGTCATCCCGGCCTA 61.732 63.158 0.00 0.00 0.00 3.93
3985 5701 1.305802 TGTGTCATCCCGGCCTACT 60.306 57.895 0.00 0.00 0.00 2.57
4084 5800 4.927782 ACTTGCTCGCCGCCAACA 62.928 61.111 0.00 0.00 38.05 3.33
4086 5802 4.927782 TTGCTCGCCGCCAACAGT 62.928 61.111 0.00 0.00 38.05 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 4.161295 CGAGCTCCCATTCCCGCA 62.161 66.667 8.47 0.00 0.00 5.69
315 316 5.501156 AGAAATCCATTACTCTTCCACCAC 58.499 41.667 0.00 0.00 0.00 4.16
365 366 2.660552 GGTACCGCGCGCATACAT 60.661 61.111 31.61 16.73 0.00 2.29
390 391 2.970609 GCTCGATCGATTCTTCTTCTCG 59.029 50.000 19.78 3.18 0.00 4.04
391 392 4.223320 AGCTCGATCGATTCTTCTTCTC 57.777 45.455 19.78 0.00 0.00 2.87
392 393 4.576873 TGTAGCTCGATCGATTCTTCTTCT 59.423 41.667 19.78 8.08 0.00 2.85
393 394 4.849883 TGTAGCTCGATCGATTCTTCTTC 58.150 43.478 19.78 9.10 0.00 2.87
394 395 4.902443 TGTAGCTCGATCGATTCTTCTT 57.098 40.909 19.78 2.23 0.00 2.52
395 396 4.902443 TTGTAGCTCGATCGATTCTTCT 57.098 40.909 19.78 12.56 0.00 2.85
396 397 5.950965 TTTTGTAGCTCGATCGATTCTTC 57.049 39.130 19.78 15.75 0.00 2.87
397 398 5.220491 GCTTTTTGTAGCTCGATCGATTCTT 60.220 40.000 19.78 7.12 38.15 2.52
398 399 4.268884 GCTTTTTGTAGCTCGATCGATTCT 59.731 41.667 19.78 19.57 38.15 2.40
399 400 4.509891 GCTTTTTGTAGCTCGATCGATTC 58.490 43.478 19.78 13.40 38.15 2.52
400 401 4.522297 GCTTTTTGTAGCTCGATCGATT 57.478 40.909 19.78 12.55 38.15 3.34
408 409 7.959066 ACCATTGGTACAGCTTTTTGTAGCTC 61.959 42.308 6.54 0.00 46.75 4.09
409 410 6.214220 ACCATTGGTACAGCTTTTTGTAGCT 61.214 40.000 6.54 0.00 46.75 3.32
410 411 4.022329 ACCATTGGTACAGCTTTTTGTAGC 60.022 41.667 6.54 8.07 46.79 3.58
411 412 5.009610 ACACCATTGGTACAGCTTTTTGTAG 59.990 40.000 8.31 0.00 42.39 2.74
412 413 4.890581 ACACCATTGGTACAGCTTTTTGTA 59.109 37.500 8.31 0.00 42.39 2.41
413 414 3.704061 ACACCATTGGTACAGCTTTTTGT 59.296 39.130 8.31 0.00 42.39 2.83
414 415 4.050553 CACACCATTGGTACAGCTTTTTG 58.949 43.478 8.31 0.00 42.39 2.44
415 416 3.957497 TCACACCATTGGTACAGCTTTTT 59.043 39.130 8.31 0.00 42.39 1.94
416 417 3.561143 TCACACCATTGGTACAGCTTTT 58.439 40.909 8.31 0.00 42.39 2.27
417 418 3.222173 TCACACCATTGGTACAGCTTT 57.778 42.857 8.31 0.00 42.39 3.51
418 419 2.949177 TCACACCATTGGTACAGCTT 57.051 45.000 8.31 0.00 42.39 3.74
419 420 2.949177 TTCACACCATTGGTACAGCT 57.051 45.000 8.31 0.00 42.39 4.24
420 421 4.236935 CATTTTCACACCATTGGTACAGC 58.763 43.478 8.31 0.00 42.39 4.40
421 422 5.221880 CACATTTTCACACCATTGGTACAG 58.778 41.667 8.31 0.00 42.39 2.74
422 423 4.500545 GCACATTTTCACACCATTGGTACA 60.501 41.667 8.31 0.00 32.11 2.90
423 424 3.987220 GCACATTTTCACACCATTGGTAC 59.013 43.478 8.31 0.00 32.11 3.34
424 425 3.006323 GGCACATTTTCACACCATTGGTA 59.994 43.478 8.31 0.00 32.11 3.25
425 426 2.224257 GGCACATTTTCACACCATTGGT 60.224 45.455 1.37 1.37 35.62 3.67
426 427 2.037511 AGGCACATTTTCACACCATTGG 59.962 45.455 0.00 0.00 0.00 3.16
427 428 3.006110 AGAGGCACATTTTCACACCATTG 59.994 43.478 0.00 0.00 0.00 2.82
428 429 3.233507 AGAGGCACATTTTCACACCATT 58.766 40.909 0.00 0.00 0.00 3.16
429 430 2.880443 AGAGGCACATTTTCACACCAT 58.120 42.857 0.00 0.00 0.00 3.55
430 431 2.363306 AGAGGCACATTTTCACACCA 57.637 45.000 0.00 0.00 0.00 4.17
431 432 4.265073 AGATAGAGGCACATTTTCACACC 58.735 43.478 0.00 0.00 0.00 4.16
432 433 6.985188 TTAGATAGAGGCACATTTTCACAC 57.015 37.500 0.00 0.00 0.00 3.82
433 434 7.933577 CCTATTAGATAGAGGCACATTTTCACA 59.066 37.037 0.00 0.00 34.77 3.58
434 435 8.150945 TCCTATTAGATAGAGGCACATTTTCAC 58.849 37.037 0.00 0.00 34.77 3.18
480 481 1.745087 CTTAAGCACATGGACGGCATT 59.255 47.619 0.00 0.00 0.00 3.56
481 482 1.382522 CTTAAGCACATGGACGGCAT 58.617 50.000 0.00 0.00 0.00 4.40
484 485 2.107950 TTCCTTAAGCACATGGACGG 57.892 50.000 0.00 0.00 0.00 4.79
485 486 3.535561 AGATTCCTTAAGCACATGGACG 58.464 45.455 0.00 0.00 0.00 4.79
529 530 6.158175 TGTGTTTTGTTTTGTTGAATTCCG 57.842 33.333 2.27 0.00 0.00 4.30
627 634 0.388520 GTCTTTTGGCCCGTTGCATC 60.389 55.000 0.00 0.00 43.89 3.91
694 709 5.421056 AGGAAAATGTCTGTAGGATCACGTA 59.579 40.000 0.00 0.00 0.00 3.57
703 718 5.063944 CGGACATCAAGGAAAATGTCTGTAG 59.936 44.000 13.60 2.90 46.85 2.74
752 767 7.990055 TGATCAGAGGGAGTATAATCTACTCA 58.010 38.462 19.71 7.55 44.18 3.41
825 872 2.390225 ATTGCTACTCCCTCCGATCT 57.610 50.000 0.00 0.00 0.00 2.75
863 910 4.368315 CTCACCGTTGCACTGCTATATAA 58.632 43.478 1.98 0.00 0.00 0.98
899 946 3.130633 TCGAGTTGATCAAGTGGTTGTG 58.869 45.455 20.46 3.75 34.98 3.33
917 964 2.857483 TGGTTTTCCTTTGCTGATCGA 58.143 42.857 0.00 0.00 41.38 3.59
918 965 3.191162 TGATGGTTTTCCTTTGCTGATCG 59.809 43.478 0.00 0.00 41.38 3.69
919 966 4.789012 TGATGGTTTTCCTTTGCTGATC 57.211 40.909 0.00 0.00 41.38 2.92
920 967 5.337813 GGAATGATGGTTTTCCTTTGCTGAT 60.338 40.000 0.00 0.00 38.68 2.90
935 982 2.322658 CAAGGGGAATGGGAATGATGG 58.677 52.381 0.00 0.00 0.00 3.51
961 1008 1.279025 TGTGGGGACTGGGGAATAGC 61.279 60.000 0.00 0.00 0.00 2.97
966 1013 2.466186 GGTTTGTGGGGACTGGGGA 61.466 63.158 0.00 0.00 0.00 4.81
967 1014 2.117423 GGTTTGTGGGGACTGGGG 59.883 66.667 0.00 0.00 0.00 4.96
968 1015 1.112916 GTTGGTTTGTGGGGACTGGG 61.113 60.000 0.00 0.00 0.00 4.45
970 1017 2.029743 CGTTGGTTTGTGGGGACTG 58.970 57.895 0.00 0.00 0.00 3.51
972 1019 2.725641 GCGTTGGTTTGTGGGGAC 59.274 61.111 0.00 0.00 0.00 4.46
984 1031 4.101790 ATGCTTTCGCCGGCGTTG 62.102 61.111 44.16 33.35 40.74 4.10
989 1036 3.746889 TTGCCATGCTTTCGCCGG 61.747 61.111 0.00 0.00 34.43 6.13
990 1037 2.504681 GTTGCCATGCTTTCGCCG 60.505 61.111 0.00 0.00 34.43 6.46
993 1040 1.512734 GCTCGTTGCCATGCTTTCG 60.513 57.895 0.00 0.00 35.15 3.46
1005 1052 3.821421 AAAGATTCTATCCCGCTCGTT 57.179 42.857 0.00 0.00 0.00 3.85
1013 1060 4.764308 GCTCCCATGGAAAAGATTCTATCC 59.236 45.833 15.22 10.21 34.84 2.59
1042 1092 0.390603 GCGTACACATACACCAGCCA 60.391 55.000 0.00 0.00 0.00 4.75
1093 1143 1.002134 CCCACTTCAACGCCCTCAT 60.002 57.895 0.00 0.00 0.00 2.90
1102 1152 2.203280 CCACCACGCCCACTTCAA 60.203 61.111 0.00 0.00 0.00 2.69
1105 1155 3.953775 CCTCCACCACGCCCACTT 61.954 66.667 0.00 0.00 0.00 3.16
1191 1241 1.807981 CTCCATAAACGGCGCGTCA 60.808 57.895 12.89 0.00 39.99 4.35
1197 1247 2.298593 GAGACGCTCCATAAACGGC 58.701 57.895 0.00 0.00 34.19 5.68
1245 1295 3.958147 AACGTCATGGCTGCCGAGG 62.958 63.158 14.98 13.60 0.00 4.63
1248 1298 3.049674 ACAACGTCATGGCTGCCG 61.050 61.111 14.98 3.82 0.00 5.69
1340 1390 7.332678 GGCTAAAAAGAAACATTACGGTAGAGA 59.667 37.037 0.00 0.00 0.00 3.10
1341 1391 7.461918 GGCTAAAAAGAAACATTACGGTAGAG 58.538 38.462 0.00 0.00 0.00 2.43
1343 1393 6.245724 CGGCTAAAAAGAAACATTACGGTAG 58.754 40.000 0.00 0.00 0.00 3.18
1344 1394 5.390779 GCGGCTAAAAAGAAACATTACGGTA 60.391 40.000 0.00 0.00 0.00 4.02
1380 1433 4.699925 ACTAATAATGCGGCTAAAGGGA 57.300 40.909 0.00 0.00 0.00 4.20
1381 1434 5.767816 AAACTAATAATGCGGCTAAAGGG 57.232 39.130 0.00 0.00 0.00 3.95
1382 1435 6.485648 AGGTAAACTAATAATGCGGCTAAAGG 59.514 38.462 0.00 0.00 0.00 3.11
1383 1436 7.492352 AGGTAAACTAATAATGCGGCTAAAG 57.508 36.000 0.00 0.00 0.00 1.85
1384 1437 7.254522 CGAAGGTAAACTAATAATGCGGCTAAA 60.255 37.037 0.00 0.00 0.00 1.85
1385 1438 6.201425 CGAAGGTAAACTAATAATGCGGCTAA 59.799 38.462 0.00 0.00 0.00 3.09
1386 1439 5.693104 CGAAGGTAAACTAATAATGCGGCTA 59.307 40.000 0.00 0.00 0.00 3.93
1387 1440 4.510340 CGAAGGTAAACTAATAATGCGGCT 59.490 41.667 0.00 0.00 0.00 5.52
1388 1441 4.769215 CGAAGGTAAACTAATAATGCGGC 58.231 43.478 0.00 0.00 0.00 6.53
1389 1442 4.319261 GGCGAAGGTAAACTAATAATGCGG 60.319 45.833 0.00 0.00 0.00 5.69
1390 1443 4.271533 TGGCGAAGGTAAACTAATAATGCG 59.728 41.667 0.00 0.00 0.00 4.73
1391 1444 5.065474 TGTGGCGAAGGTAAACTAATAATGC 59.935 40.000 0.00 0.00 0.00 3.56
1392 1445 6.457799 GGTGTGGCGAAGGTAAACTAATAATG 60.458 42.308 0.00 0.00 0.00 1.90
1393 1446 5.587443 GGTGTGGCGAAGGTAAACTAATAAT 59.413 40.000 0.00 0.00 0.00 1.28
1394 1447 4.937015 GGTGTGGCGAAGGTAAACTAATAA 59.063 41.667 0.00 0.00 0.00 1.40
1395 1448 4.506758 GGTGTGGCGAAGGTAAACTAATA 58.493 43.478 0.00 0.00 0.00 0.98
1396 1449 3.340928 GGTGTGGCGAAGGTAAACTAAT 58.659 45.455 0.00 0.00 0.00 1.73
1397 1450 2.769893 GGTGTGGCGAAGGTAAACTAA 58.230 47.619 0.00 0.00 0.00 2.24
1398 1451 1.337074 CGGTGTGGCGAAGGTAAACTA 60.337 52.381 0.00 0.00 0.00 2.24
1399 1452 0.601841 CGGTGTGGCGAAGGTAAACT 60.602 55.000 0.00 0.00 0.00 2.66
1400 1453 0.881600 ACGGTGTGGCGAAGGTAAAC 60.882 55.000 0.00 0.00 0.00 2.01
1401 1454 0.678395 TACGGTGTGGCGAAGGTAAA 59.322 50.000 0.00 0.00 0.00 2.01
1402 1455 0.678395 TTACGGTGTGGCGAAGGTAA 59.322 50.000 0.00 0.00 0.00 2.85
1403 1456 0.244450 CTTACGGTGTGGCGAAGGTA 59.756 55.000 0.00 0.00 0.00 3.08
1422 1475 2.859538 TGGTTGTTTTCAGACGACGTAC 59.140 45.455 0.00 0.00 35.23 3.67
1424 1477 2.012937 TGGTTGTTTTCAGACGACGT 57.987 45.000 0.00 0.00 35.23 4.34
1425 1478 3.392769 TTTGGTTGTTTTCAGACGACG 57.607 42.857 0.00 0.00 35.23 5.12
1466 1519 8.499967 GCCATTAAAACCAAACATAACGAAAAT 58.500 29.630 0.00 0.00 0.00 1.82
1504 1557 9.589111 TTTAAATTAATAAAGGCATTTCCGACC 57.411 29.630 0.00 0.00 40.77 4.79
1563 1621 8.047310 AGACCACTAGATTTCATACCGAAAAAT 58.953 33.333 0.00 0.00 46.48 1.82
1569 1627 5.301045 TGGTAGACCACTAGATTTCATACCG 59.699 44.000 0.00 0.00 42.01 4.02
1599 1660 4.646040 TGAGATTCCATGCCACCAAATTAG 59.354 41.667 0.00 0.00 0.00 1.73
1616 1677 4.098654 CGTGTGGGAGACTATTCTGAGATT 59.901 45.833 0.00 0.00 29.47 2.40
1623 1684 2.000447 GTTGCGTGTGGGAGACTATTC 59.000 52.381 0.00 0.00 0.00 1.75
1625 1686 0.973632 TGTTGCGTGTGGGAGACTAT 59.026 50.000 0.00 0.00 0.00 2.12
1699 1786 8.599774 ACACGGTTAAAATTTCATTTTCTGTTG 58.400 29.630 0.00 0.00 41.26 3.33
1720 1807 8.193250 AGCAGTTTAATTACATAGTTACACGG 57.807 34.615 0.00 0.00 0.00 4.94
1730 1817 9.449719 AGCTTGTTACTAGCAGTTTAATTACAT 57.550 29.630 19.49 0.00 41.11 2.29
1731 1818 8.842358 AGCTTGTTACTAGCAGTTTAATTACA 57.158 30.769 19.49 0.00 41.11 2.41
1732 1819 9.756461 GAAGCTTGTTACTAGCAGTTTAATTAC 57.244 33.333 19.49 0.00 41.11 1.89
1733 1820 8.653338 CGAAGCTTGTTACTAGCAGTTTAATTA 58.347 33.333 19.49 0.00 41.11 1.40
1735 1822 6.872020 TCGAAGCTTGTTACTAGCAGTTTAAT 59.128 34.615 19.49 0.00 41.11 1.40
1736 1823 6.218019 TCGAAGCTTGTTACTAGCAGTTTAA 58.782 36.000 19.49 0.00 41.11 1.52
1841 1946 0.753262 ACACTTCTCGCACCAGTTCT 59.247 50.000 0.00 0.00 0.00 3.01
1859 1964 2.096248 TGACCCAACTTGTTGGACAAC 58.904 47.619 28.19 17.42 44.82 3.32
1860 1965 2.096248 GTGACCCAACTTGTTGGACAA 58.904 47.619 28.19 13.34 44.82 3.18
2253 2417 0.957888 GCTCACCCTGAAGCTGGAAC 60.958 60.000 0.00 0.00 0.00 3.62
2286 2450 1.604308 CTTGTCCATGGCCTGCACA 60.604 57.895 6.96 2.51 0.00 4.57
2345 2521 4.155826 GTGCTGAACCATGCATAGTAAACA 59.844 41.667 0.00 0.00 41.45 2.83
2352 2528 1.097232 GCTGTGCTGAACCATGCATA 58.903 50.000 0.00 0.00 41.45 3.14
2355 2531 0.245539 ATTGCTGTGCTGAACCATGC 59.754 50.000 0.00 0.00 0.00 4.06
2382 2558 2.033299 GCCGCAGCAGAGCAATTAAATA 59.967 45.455 0.00 0.00 39.53 1.40
2386 2562 1.078214 AGCCGCAGCAGAGCAATTA 60.078 52.632 0.00 0.00 43.56 1.40
2398 2574 1.020861 CATTAGCACAGTCAGCCGCA 61.021 55.000 0.00 0.00 0.00 5.69
2400 2576 1.717937 GCATTAGCACAGTCAGCCG 59.282 57.895 0.00 0.00 41.58 5.52
2538 2715 2.273179 ACCACTCGTAGCTTCGCCA 61.273 57.895 8.00 0.00 0.00 5.69
2577 2754 0.250901 GTGCCATGTTGGACTCCAGT 60.251 55.000 0.00 0.00 40.96 4.00
2653 2842 0.036765 ATGCCGGCGAAGTAGAACAA 60.037 50.000 23.90 0.00 0.00 2.83
2805 2994 4.953579 ACCATGGTTACGATTTTTAGGCAT 59.046 37.500 13.00 0.00 0.00 4.40
2806 2995 4.156922 CACCATGGTTACGATTTTTAGGCA 59.843 41.667 16.84 0.00 0.00 4.75
2988 4698 0.539669 TCTCTGGCCTGAACTCGTCA 60.540 55.000 13.89 0.00 34.17 4.35
3183 4893 4.873810 CCGATGGGGAATGGCGCA 62.874 66.667 10.83 0.00 38.47 6.09
3189 4899 2.963782 GTGTAGTAGACCGATGGGGAAT 59.036 50.000 0.00 0.00 39.97 3.01
3201 4911 1.460504 CGTGCTCTGGGTGTAGTAGA 58.539 55.000 0.00 0.00 0.00 2.59
3204 4916 1.533273 ACCGTGCTCTGGGTGTAGT 60.533 57.895 0.00 0.00 34.58 2.73
3470 5182 4.112634 AGATAAAAACCAACTGGGAGCA 57.887 40.909 0.00 0.00 41.15 4.26
3562 5275 7.668469 AGATCTAGGGTTTTGTTTAAATTCCGT 59.332 33.333 0.00 0.00 31.37 4.69
3575 5288 2.483889 GCGCTGCTAGATCTAGGGTTTT 60.484 50.000 27.21 0.00 33.87 2.43
3701 5414 2.445085 TCCACCACCACTGTCCGT 60.445 61.111 0.00 0.00 0.00 4.69
3705 5418 1.531748 CCAACTCCACCACCACTGT 59.468 57.895 0.00 0.00 0.00 3.55
3891 5607 5.420725 TCCTATCTACAAGCAAGCAAGAA 57.579 39.130 0.00 0.00 0.00 2.52
3964 5680 4.408821 GGCCGGGATGACACAGCA 62.409 66.667 2.18 0.00 0.00 4.41
3983 5699 1.251251 GTGCAAATCAAGCTCCCAGT 58.749 50.000 0.00 0.00 0.00 4.00
3985 5701 1.820519 GATGTGCAAATCAAGCTCCCA 59.179 47.619 12.24 0.00 0.00 4.37
4079 5795 0.955919 GGAGCGGGAGAAACTGTTGG 60.956 60.000 0.00 0.00 0.00 3.77
4081 5797 1.375326 GGGAGCGGGAGAAACTGTT 59.625 57.895 0.00 0.00 0.00 3.16
4084 5800 2.960688 GCTGGGAGCGGGAGAAACT 61.961 63.158 0.00 0.00 0.00 2.66
4086 5802 3.717294 GGCTGGGAGCGGGAGAAA 61.717 66.667 0.00 0.00 43.62 2.52


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

AutoCloner maintained by Alex Coulton.