Multiple sequence alignment - TraesCS5D01G370400

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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 TraesCS5D01G370400 chr5D 100.000 6202 0 0 1 6202 445310523 445316724 0.000000e+00 11454.0
1 TraesCS5D01G370400 chr5D 98.649 74 1 0 5050 5123 445315503 445315576 1.400000e-26 132.0
2 TraesCS5D01G370400 chr5D 98.649 74 1 0 4981 5054 445315572 445315645 1.400000e-26 132.0
3 TraesCS5D01G370400 chr5D 88.889 108 11 1 5962 6068 445489317 445489424 1.400000e-26 132.0
4 TraesCS5D01G370400 chr5B 95.929 4225 98 16 868 5054 542945285 542949473 0.000000e+00 6782.0
5 TraesCS5D01G370400 chr5B 91.041 1172 62 17 5050 6202 542949400 542950547 0.000000e+00 1543.0
6 TraesCS5D01G370400 chr5B 86.260 131 14 2 5962 6091 543297105 543297232 8.380000e-29 139.0
7 TraesCS5D01G370400 chr5A 95.323 3528 107 21 1 3509 562860274 562863762 0.000000e+00 5548.0
8 TraesCS5D01G370400 chr5A 95.377 1579 35 7 3492 5054 562863871 562865427 0.000000e+00 2477.0
9 TraesCS5D01G370400 chr5A 92.910 677 33 4 5050 5712 562865354 562866029 0.000000e+00 970.0
10 TraesCS5D01G370400 chr5A 90.393 458 24 11 5708 6152 562889087 562889537 8.960000e-163 584.0
11 TraesCS5D01G370400 chr5A 100.000 32 0 0 6171 6202 562890158 562890189 6.710000e-05 60.2
12 TraesCS5D01G370400 chr6B 91.924 1102 51 11 3486 4565 48694378 48695463 0.000000e+00 1507.0
13 TraesCS5D01G370400 chrUn 94.895 764 37 2 3486 4248 205758458 205759220 0.000000e+00 1194.0
14 TraesCS5D01G370400 chrUn 90.741 324 14 8 4243 4565 205760079 205760387 9.620000e-113 418.0
15 TraesCS5D01G370400 chr4D 87.410 278 32 3 2326 2602 1690455 1690180 3.610000e-82 316.0
16 TraesCS5D01G370400 chr4D 79.130 230 29 9 5962 6187 1690149 1689935 2.330000e-29 141.0
17 TraesCS5D01G370400 chr4D 100.000 33 0 0 5981 6013 1639022 1638990 1.870000e-05 62.1


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 TraesCS5D01G370400 chr5D 445310523 445316724 6201 False 3906.000000 11454 99.099333 1 6202 3 chr5D.!!$F2 6201
1 TraesCS5D01G370400 chr5B 542945285 542950547 5262 False 4162.500000 6782 93.485000 868 6202 2 chr5B.!!$F2 5334
2 TraesCS5D01G370400 chr5A 562860274 562866029 5755 False 2998.333333 5548 94.536667 1 5712 3 chr5A.!!$F1 5711
3 TraesCS5D01G370400 chr5A 562889087 562890189 1102 False 322.100000 584 95.196500 5708 6202 2 chr5A.!!$F2 494
4 TraesCS5D01G370400 chr6B 48694378 48695463 1085 False 1507.000000 1507 91.924000 3486 4565 1 chr6B.!!$F1 1079
5 TraesCS5D01G370400 chrUn 205758458 205760387 1929 False 806.000000 1194 92.818000 3486 4565 2 chrUn.!!$F1 1079
6 TraesCS5D01G370400 chr4D 1689935 1690455 520 True 228.500000 316 83.270000 2326 6187 2 chr4D.!!$R2 3861

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
617 619 0.754472 TAGTTAGCCGGGCATGTACC 59.246 55.000 23.09 0.00 0.0 3.34 F
1362 1388 0.456653 GCGCGATTGATTGGTTGCTT 60.457 50.000 12.10 0.00 0.0 3.91 F
1860 1889 1.824230 TGCAATTTAGTGGTCCCATGC 59.176 47.619 1.33 1.33 0.0 4.06 F
2633 2665 0.940126 GCCATGGTTAGCTGACATCG 59.060 55.000 14.67 0.00 0.0 3.84 F
3033 3065 3.001736 GCAATCACTAGCCTGAATTCGAC 59.998 47.826 0.04 0.00 0.0 4.20 F
4734 5765 0.107831 TAGTGGTGCAGGCGAAAAGT 59.892 50.000 0.00 0.00 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 1495 1.214589 CCTGGGGTACACGACGAAG 59.785 63.158 0.00 0.00 0.00 3.79 R
2215 2246 1.550065 CATGAGTCTTACGGCACTCG 58.450 55.000 0.00 0.00 41.81 4.18 R
2883 2915 2.819595 CACCTCGCGGGGAACATG 60.820 66.667 36.26 16.65 34.80 3.21 R
4615 5646 2.939103 CGCATCTAACTTTTCCTCAGGG 59.061 50.000 0.00 0.00 0.00 4.45 R
5024 6069 0.035881 TCTGCTGCTGGTTCTGAAGG 59.964 55.000 6.69 0.00 0.00 3.46 R
5917 6992 1.382914 AACCTGCCAAACTCCCCTAT 58.617 50.000 0.00 0.00 0.00 2.57 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
34 35 7.417496 AGTTTAGTTAGTTTAAGAAGGTGCG 57.583 36.000 0.00 0.00 0.00 5.34
81 82 5.823209 TGGTTTGTCGATCTTACGATCTA 57.177 39.130 7.54 0.00 43.14 1.98
90 91 7.811236 TGTCGATCTTACGATCTAAAGTTTGTT 59.189 33.333 7.54 0.00 43.14 2.83
106 107 8.664211 AAAGTTTGTTGTAGAGGAAAGTAGAG 57.336 34.615 0.00 0.00 0.00 2.43
107 108 7.362802 AGTTTGTTGTAGAGGAAAGTAGAGT 57.637 36.000 0.00 0.00 0.00 3.24
142 143 2.290896 TGAAGGGATCTTGTTGGCGATT 60.291 45.455 0.00 0.00 32.52 3.34
161 162 5.524284 CGATTAAGGTGAGAGGTGACATAG 58.476 45.833 0.00 0.00 0.00 2.23
193 195 4.655186 CCCATCATTAATGATTTGGGGTGT 59.345 41.667 32.54 11.42 46.38 4.16
243 245 2.483188 GGAAGACAAAGAGGACGTGTGT 60.483 50.000 0.00 0.00 0.00 3.72
247 249 2.540101 GACAAAGAGGACGTGTGTGAAG 59.460 50.000 0.00 0.00 0.00 3.02
297 299 2.355010 AGGATAGGGCATGAGTTTGC 57.645 50.000 0.00 0.00 42.01 3.68
311 313 3.248446 TTTGCGCCCTAGCCTCGTT 62.248 57.895 4.18 0.00 36.02 3.85
315 317 3.459063 GCCCTAGCCTCGTTCGGT 61.459 66.667 0.00 0.00 0.00 4.69
340 342 6.429692 TGAATAAGTGAAATGACGATGTTGGT 59.570 34.615 0.00 0.00 0.00 3.67
384 386 5.131809 AGAAGTGGAGGAGAATGATTTAGGG 59.868 44.000 0.00 0.00 0.00 3.53
406 408 5.067954 GGTAAAGTAAGAAAGAAGGGCACA 58.932 41.667 0.00 0.00 0.00 4.57
413 415 4.388577 AGAAAGAAGGGCACATTTACCT 57.611 40.909 0.00 0.00 35.78 3.08
433 435 3.624861 CCTCCAGTGTGAAGAACATATGC 59.375 47.826 1.58 0.00 41.97 3.14
442 444 5.357878 TGTGAAGAACATATGCCTTTGGATC 59.642 40.000 1.58 0.00 32.36 3.36
451 453 2.449464 TGCCTTTGGATCCAATGTGAG 58.551 47.619 27.53 20.31 35.70 3.51
485 487 3.009723 CAACCGAACAAGGATGCTACAT 58.990 45.455 0.00 0.00 34.73 2.29
486 488 3.350219 ACCGAACAAGGATGCTACATT 57.650 42.857 0.00 0.00 34.73 2.71
494 496 7.060633 CGAACAAGGATGCTACATTAACAAAAC 59.939 37.037 0.00 0.00 0.00 2.43
497 499 8.082242 ACAAGGATGCTACATTAACAAAACTTC 58.918 33.333 0.00 0.00 0.00 3.01
516 518 1.740296 CACCCGCTAGTCCAAACCG 60.740 63.158 0.00 0.00 0.00 4.44
541 543 3.322541 TGACGGAGATTGGTACTTGTGAA 59.677 43.478 0.00 0.00 0.00 3.18
542 544 4.020573 TGACGGAGATTGGTACTTGTGAAT 60.021 41.667 0.00 0.00 0.00 2.57
543 545 4.906618 ACGGAGATTGGTACTTGTGAATT 58.093 39.130 0.00 0.00 0.00 2.17
544 546 4.695455 ACGGAGATTGGTACTTGTGAATTG 59.305 41.667 0.00 0.00 0.00 2.32
545 547 4.695455 CGGAGATTGGTACTTGTGAATTGT 59.305 41.667 0.00 0.00 0.00 2.71
546 548 5.390885 CGGAGATTGGTACTTGTGAATTGTG 60.391 44.000 0.00 0.00 0.00 3.33
547 549 5.705441 GGAGATTGGTACTTGTGAATTGTGA 59.295 40.000 0.00 0.00 0.00 3.58
548 550 6.375455 GGAGATTGGTACTTGTGAATTGTGAT 59.625 38.462 0.00 0.00 0.00 3.06
549 551 7.149569 AGATTGGTACTTGTGAATTGTGATG 57.850 36.000 0.00 0.00 0.00 3.07
550 552 6.942005 AGATTGGTACTTGTGAATTGTGATGA 59.058 34.615 0.00 0.00 0.00 2.92
551 553 5.940192 TGGTACTTGTGAATTGTGATGAC 57.060 39.130 0.00 0.00 0.00 3.06
552 554 4.759693 TGGTACTTGTGAATTGTGATGACC 59.240 41.667 0.00 0.00 0.00 4.02
553 555 4.156008 GGTACTTGTGAATTGTGATGACCC 59.844 45.833 0.00 0.00 0.00 4.46
554 556 3.831323 ACTTGTGAATTGTGATGACCCA 58.169 40.909 0.00 0.00 0.00 4.51
575 577 5.356751 CCCAACGACATAAAATCCTTCATGA 59.643 40.000 0.00 0.00 0.00 3.07
577 579 6.316140 CCAACGACATAAAATCCTTCATGAGA 59.684 38.462 0.00 0.00 0.00 3.27
617 619 0.754472 TAGTTAGCCGGGCATGTACC 59.246 55.000 23.09 0.00 0.00 3.34
736 739 9.893305 ACTAATTTCAGTACAAAGTTATGCAAC 57.107 29.630 0.00 0.00 34.67 4.17
737 740 7.851822 AATTTCAGTACAAAGTTATGCAACG 57.148 32.000 0.00 0.00 39.78 4.10
738 741 5.994887 TTCAGTACAAAGTTATGCAACGT 57.005 34.783 0.00 0.00 39.78 3.99
746 749 5.163703 ACAAAGTTATGCAACGTTTGAGACA 60.164 36.000 16.54 0.00 39.78 3.41
757 760 7.489435 TGCAACGTTTGAGACATTTATTTTGAA 59.511 29.630 0.00 0.00 0.00 2.69
781 784 7.855784 AACTGAGGGAGTATTTTGGAATTTT 57.144 32.000 0.00 0.00 33.09 1.82
797 800 9.519191 TTTGGAATTTTAGTTCATCTCATCTCA 57.481 29.630 0.00 0.00 0.00 3.27
798 801 9.690913 TTGGAATTTTAGTTCATCTCATCTCAT 57.309 29.630 0.00 0.00 0.00 2.90
799 802 9.334947 TGGAATTTTAGTTCATCTCATCTCATC 57.665 33.333 0.00 0.00 0.00 2.92
800 803 9.558396 GGAATTTTAGTTCATCTCATCTCATCT 57.442 33.333 0.00 0.00 0.00 2.90
803 806 9.767228 ATTTTAGTTCATCTCATCTCATCTCAG 57.233 33.333 0.00 0.00 0.00 3.35
813 816 7.674120 TCTCATCTCATCTCAGAGTTCAAAAA 58.326 34.615 0.00 0.00 36.97 1.94
905 910 0.820482 TGAGTGTTCGAGTGGACCGA 60.820 55.000 0.00 0.00 0.00 4.69
967 972 4.024984 CCTCCCCTCACCCCTCCA 62.025 72.222 0.00 0.00 0.00 3.86
1311 1336 0.468648 CTAGGGTTTCGGTGGATCCC 59.531 60.000 9.90 0.00 37.12 3.85
1334 1359 2.287970 CGGCCTGTGTGCGATAGTTATA 60.288 50.000 0.00 0.00 39.35 0.98
1335 1360 3.318017 GGCCTGTGTGCGATAGTTATAG 58.682 50.000 0.00 0.00 39.35 1.31
1362 1388 0.456653 GCGCGATTGATTGGTTGCTT 60.457 50.000 12.10 0.00 0.00 3.91
1469 1495 1.981256 TCAAGAAGGTGAACAAGGGC 58.019 50.000 0.00 0.00 0.00 5.19
1537 1563 5.934625 GTGAGTGAGCTCCTCTGAATTTTTA 59.065 40.000 23.96 6.45 40.95 1.52
1635 1664 2.825532 TGATAGCCTATGAGCACGCATA 59.174 45.455 0.00 0.00 34.23 3.14
1667 1696 6.039047 CGGTTGAATGGATTCAGAGATTTCAT 59.961 38.462 2.46 0.00 46.34 2.57
1748 1777 5.594317 AGACAGGTGTTGCTGTTCTAATTTT 59.406 36.000 0.00 0.00 33.50 1.82
1777 1806 6.046762 TCAGGGATAGATAAGTGTGATAGGGA 59.953 42.308 0.00 0.00 0.00 4.20
1825 1854 4.836825 TGCTGTTTCAGGATTTCTCTAGG 58.163 43.478 0.00 0.00 31.21 3.02
1860 1889 1.824230 TGCAATTTAGTGGTCCCATGC 59.176 47.619 1.33 1.33 0.00 4.06
1904 1933 7.220300 ACGATTATTCTTCGTTTGCTACTAGTG 59.780 37.037 5.39 0.00 46.96 2.74
2076 2105 8.012957 TCAAATGGAAAAGTTAAAGGTGCTTA 57.987 30.769 0.00 0.00 0.00 3.09
2113 2142 6.611381 CAAACCTGTATCACACTGTTATTGG 58.389 40.000 0.00 0.00 0.00 3.16
2133 2162 2.030805 GGTTGATCTGTTGGTTGTCTGC 60.031 50.000 0.00 0.00 0.00 4.26
2215 2246 1.407258 ACTGCTGAGAGAGTAATCGCC 59.593 52.381 0.00 0.00 0.00 5.54
2275 2306 4.532834 GGGCAAATCTTGGTCCTATGTTA 58.467 43.478 0.00 0.00 0.00 2.41
2605 2637 6.319658 CCACATTTTGTCATGCTCTATTAGGT 59.680 38.462 0.00 0.00 0.00 3.08
2633 2665 0.940126 GCCATGGTTAGCTGACATCG 59.060 55.000 14.67 0.00 0.00 3.84
2984 3016 5.112129 AGTGTTGGTTTGAGTACCTTCTT 57.888 39.130 0.00 0.00 39.04 2.52
3031 3063 3.201290 AGCAATCACTAGCCTGAATTCG 58.799 45.455 0.04 0.00 0.00 3.34
3033 3065 3.001736 GCAATCACTAGCCTGAATTCGAC 59.998 47.826 0.04 0.00 0.00 4.20
4419 5450 4.459337 CCGTTCATCCTCTTTTAGGCTTTT 59.541 41.667 0.00 0.00 46.10 2.27
4553 5584 8.988934 GTCACAGTTCAGAAGAAAACATACATA 58.011 33.333 0.00 0.00 35.08 2.29
4554 5585 8.988934 TCACAGTTCAGAAGAAAACATACATAC 58.011 33.333 0.00 0.00 35.08 2.39
4615 5646 5.404066 AGCATGTATTTACAAAAACGGTTGC 59.596 36.000 0.00 0.00 39.99 4.17
4734 5765 0.107831 TAGTGGTGCAGGCGAAAAGT 59.892 50.000 0.00 0.00 0.00 2.66
4740 5771 3.068873 TGGTGCAGGCGAAAAGTTTTTAT 59.931 39.130 1.64 0.00 0.00 1.40
4771 5804 2.616376 TCATAACTGTGCGCTTTGTGTT 59.384 40.909 9.73 9.25 0.00 3.32
4814 5847 2.420687 GCGATGAAATCCTCCTTGACCT 60.421 50.000 0.00 0.00 41.39 3.85
4889 5922 1.961277 GCTTGCTGCAGTGTACGGT 60.961 57.895 16.64 0.00 42.31 4.83
4898 5931 1.481871 CAGTGTACGGTATGGGAGGT 58.518 55.000 0.00 0.00 0.00 3.85
4990 6035 4.517663 TGGGAACATGCAAGGTGG 57.482 55.556 0.00 0.00 33.40 4.61
4991 6036 1.907807 TGGGAACATGCAAGGTGGC 60.908 57.895 0.00 0.00 33.40 5.01
4992 6037 2.568090 GGAACATGCAAGGTGGCG 59.432 61.111 0.00 0.00 36.28 5.69
4993 6038 2.568090 GAACATGCAAGGTGGCGG 59.432 61.111 0.00 0.00 36.28 6.13
4994 6039 2.203480 AACATGCAAGGTGGCGGT 60.203 55.556 0.00 0.00 36.28 5.68
4995 6040 2.200170 GAACATGCAAGGTGGCGGTC 62.200 60.000 0.00 0.00 36.28 4.79
4996 6041 2.672651 CATGCAAGGTGGCGGTCA 60.673 61.111 0.00 0.00 36.28 4.02
4997 6042 2.360350 ATGCAAGGTGGCGGTCAG 60.360 61.111 0.00 0.00 36.28 3.51
4998 6043 2.894257 ATGCAAGGTGGCGGTCAGA 61.894 57.895 0.00 0.00 36.28 3.27
4999 6044 2.743928 GCAAGGTGGCGGTCAGAG 60.744 66.667 0.00 0.00 0.00 3.35
5000 6045 2.743928 CAAGGTGGCGGTCAGAGC 60.744 66.667 0.00 0.00 0.00 4.09
5001 6046 2.925170 AAGGTGGCGGTCAGAGCT 60.925 61.111 0.00 0.00 34.52 4.09
5002 6047 2.520536 AAGGTGGCGGTCAGAGCTT 61.521 57.895 0.00 0.00 34.52 3.74
5003 6048 2.738213 AAGGTGGCGGTCAGAGCTTG 62.738 60.000 0.00 0.00 34.52 4.01
5004 6049 3.426568 GTGGCGGTCAGAGCTTGC 61.427 66.667 0.00 0.00 34.52 4.01
5005 6050 3.939939 TGGCGGTCAGAGCTTGCA 61.940 61.111 0.00 0.00 34.52 4.08
5006 6051 3.123620 GGCGGTCAGAGCTTGCAG 61.124 66.667 0.00 0.00 34.52 4.41
5007 6052 3.797546 GCGGTCAGAGCTTGCAGC 61.798 66.667 0.00 0.47 42.84 5.25
5008 6053 2.357881 CGGTCAGAGCTTGCAGCA 60.358 61.111 10.16 0.00 45.56 4.41
5009 6054 2.389020 CGGTCAGAGCTTGCAGCAG 61.389 63.158 10.16 0.00 45.56 4.24
5010 6055 2.688794 GGTCAGAGCTTGCAGCAGC 61.689 63.158 1.95 1.95 45.56 5.25
5031 6076 2.356278 GCATGGTGGGCCTTCAGA 59.644 61.111 4.53 0.00 35.27 3.27
5032 6077 1.304381 GCATGGTGGGCCTTCAGAA 60.304 57.895 4.53 0.00 35.27 3.02
5033 6078 1.598701 GCATGGTGGGCCTTCAGAAC 61.599 60.000 4.53 0.00 35.27 3.01
5034 6079 0.967380 CATGGTGGGCCTTCAGAACC 60.967 60.000 4.53 2.83 35.27 3.62
5035 6080 1.434513 ATGGTGGGCCTTCAGAACCA 61.435 55.000 12.95 12.95 44.59 3.67
5036 6081 1.303643 GGTGGGCCTTCAGAACCAG 60.304 63.158 4.53 0.00 32.84 4.00
5037 6082 1.973812 GTGGGCCTTCAGAACCAGC 60.974 63.158 4.53 0.00 32.84 4.85
5038 6083 2.436109 GGGCCTTCAGAACCAGCA 59.564 61.111 0.84 0.00 0.00 4.41
5039 6084 1.676967 GGGCCTTCAGAACCAGCAG 60.677 63.158 0.84 0.00 0.00 4.24
5040 6085 2.338785 GGCCTTCAGAACCAGCAGC 61.339 63.158 0.00 0.00 0.00 5.25
5041 6086 1.601759 GCCTTCAGAACCAGCAGCA 60.602 57.895 0.00 0.00 0.00 4.41
5042 6087 1.584380 GCCTTCAGAACCAGCAGCAG 61.584 60.000 0.00 0.00 0.00 4.24
5043 6088 0.035881 CCTTCAGAACCAGCAGCAGA 59.964 55.000 0.00 0.00 0.00 4.26
5044 6089 1.544093 CCTTCAGAACCAGCAGCAGAA 60.544 52.381 0.00 0.00 0.00 3.02
5045 6090 1.534595 CTTCAGAACCAGCAGCAGAAC 59.465 52.381 0.00 0.00 0.00 3.01
5046 6091 0.250467 TCAGAACCAGCAGCAGAACC 60.250 55.000 0.00 0.00 0.00 3.62
5047 6092 0.535780 CAGAACCAGCAGCAGAACCA 60.536 55.000 0.00 0.00 0.00 3.67
5048 6093 0.183492 AGAACCAGCAGCAGAACCAA 59.817 50.000 0.00 0.00 0.00 3.67
5049 6094 1.032014 GAACCAGCAGCAGAACCAAA 58.968 50.000 0.00 0.00 0.00 3.28
5050 6095 1.615392 GAACCAGCAGCAGAACCAAAT 59.385 47.619 0.00 0.00 0.00 2.32
5051 6096 0.963962 ACCAGCAGCAGAACCAAATG 59.036 50.000 0.00 0.00 0.00 2.32
5052 6097 0.389426 CCAGCAGCAGAACCAAATGC 60.389 55.000 0.00 0.00 42.87 3.56
5053 6098 0.315886 CAGCAGCAGAACCAAATGCA 59.684 50.000 0.00 0.00 45.01 3.96
5054 6099 1.042229 AGCAGCAGAACCAAATGCAA 58.958 45.000 0.00 0.00 45.01 4.08
5055 6100 1.000506 AGCAGCAGAACCAAATGCAAG 59.999 47.619 0.00 0.00 45.01 4.01
5056 6101 1.938016 GCAGCAGAACCAAATGCAAGG 60.938 52.381 0.00 0.00 45.01 3.61
5142 6199 2.886523 CAGAACCAGATGCAAAACCAGA 59.113 45.455 0.00 0.00 0.00 3.86
5221 6278 0.960364 TTCATTCAAGCGGGCTGACC 60.960 55.000 0.00 0.00 0.00 4.02
5269 6327 1.076727 TTCCTGGCCAGAGTCGAGA 59.923 57.895 34.91 18.36 0.00 4.04
5373 6431 3.244976 CGATTCACCATTGGTTTTGCTC 58.755 45.455 5.34 0.00 31.02 4.26
5417 6475 4.152402 GTGCAAGTAGTCATGATTGTTCGT 59.848 41.667 0.00 0.00 0.00 3.85
5513 6571 3.172050 GCTCGGATATGTATGTACTGCG 58.828 50.000 0.00 0.00 0.00 5.18
5535 6593 1.811965 TGCAACTTATGATGCGTGCTT 59.188 42.857 6.41 0.00 43.66 3.91
5548 6606 1.650912 GTGCTTGGATAGGCGCATG 59.349 57.895 10.83 0.00 38.62 4.06
5553 6611 1.159713 TTGGATAGGCGCATGCTTCG 61.160 55.000 17.13 0.81 42.25 3.79
5570 6634 7.571428 GCATGCTTCGGTCTAAAATATAACCTC 60.571 40.741 11.37 0.00 0.00 3.85
5591 6655 3.259374 TCAAGTCCTGAACTCTGATCCAC 59.741 47.826 0.00 0.00 37.17 4.02
5604 6668 4.245660 TCTGATCCACGACAATTCTTGAC 58.754 43.478 0.00 0.00 0.00 3.18
5632 6696 5.355071 CAGATGGTTGCTGTTAAATAGCTGA 59.645 40.000 12.56 1.71 41.66 4.26
5636 6700 6.649155 TGGTTGCTGTTAAATAGCTGAGATA 58.351 36.000 12.56 0.00 41.66 1.98
5681 6747 2.954318 AGCTGGTGATATGTTGATTGGC 59.046 45.455 0.00 0.00 0.00 4.52
5756 6824 4.458989 TCACATCCCATGTAGAAAAACAGC 59.541 41.667 0.00 0.00 42.70 4.40
5758 6826 3.410631 TCCCATGTAGAAAAACAGCGA 57.589 42.857 0.00 0.00 31.70 4.93
5789 6857 6.299805 AGAGATGAACCAACAGCTGTTATA 57.700 37.500 30.67 15.54 36.64 0.98
5791 6859 6.765036 AGAGATGAACCAACAGCTGTTATATG 59.235 38.462 30.67 19.34 36.64 1.78
5793 6861 7.564793 AGATGAACCAACAGCTGTTATATGTA 58.435 34.615 30.67 16.05 35.16 2.29
5794 6862 8.213679 AGATGAACCAACAGCTGTTATATGTAT 58.786 33.333 30.67 19.55 35.16 2.29
5795 6863 7.786178 TGAACCAACAGCTGTTATATGTATC 57.214 36.000 30.67 20.06 36.32 2.24
5796 6864 6.765989 TGAACCAACAGCTGTTATATGTATCC 59.234 38.462 30.67 16.51 36.32 2.59
5797 6865 6.247229 ACCAACAGCTGTTATATGTATCCA 57.753 37.500 30.67 0.00 36.32 3.41
5803 6871 7.735917 ACAGCTGTTATATGTATCCAAAGCTA 58.264 34.615 15.25 0.00 36.38 3.32
5804 6872 8.378565 ACAGCTGTTATATGTATCCAAAGCTAT 58.621 33.333 15.25 0.00 36.38 2.97
5833 6901 2.227191 GCAGCAGCAGATGAGATCG 58.773 57.895 0.00 0.00 41.58 3.69
5914 6989 8.773645 GCAATAGTTTTGCTGGTTATTCTTTTT 58.226 29.630 10.64 0.00 41.87 1.94
6019 7102 5.437060 TCAAACTGGACTAGTGCTTTTCTT 58.563 37.500 15.92 0.00 40.26 2.52
6024 7110 7.719871 ACTGGACTAGTGCTTTTCTTAGATA 57.280 36.000 15.92 0.00 38.49 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.212274 TCGCACCTTCTTAAACTAACTAAACT 58.788 34.615 0.00 0.00 0.00 2.66
34 35 2.111384 TCATTGGCAGTACCCTCTCTC 58.889 52.381 0.00 0.00 37.83 3.20
81 82 8.265764 ACTCTACTTTCCTCTACAACAAACTTT 58.734 33.333 0.00 0.00 0.00 2.66
90 91 4.017808 GCCTCACTCTACTTTCCTCTACA 58.982 47.826 0.00 0.00 0.00 2.74
142 143 4.023980 CCACTATGTCACCTCTCACCTTA 58.976 47.826 0.00 0.00 0.00 2.69
161 162 6.966534 ATCATTAATGATGGGAGAAACCAC 57.033 37.500 26.47 0.00 45.27 4.16
193 195 1.546029 CACCGACATCTTCTCCTCACA 59.454 52.381 0.00 0.00 0.00 3.58
243 245 6.161855 TCTTCTCAAGCTAAGTGAACTTCA 57.838 37.500 0.00 0.00 37.40 3.02
247 249 5.178438 CACCTTCTTCTCAAGCTAAGTGAAC 59.822 44.000 0.00 0.00 0.00 3.18
297 299 4.570663 CCGAACGAGGCTAGGGCG 62.571 72.222 0.00 2.20 39.81 6.13
311 313 4.811908 TCGTCATTTCACTTATTCACCGA 58.188 39.130 0.00 0.00 0.00 4.69
315 317 6.429692 ACCAACATCGTCATTTCACTTATTCA 59.570 34.615 0.00 0.00 0.00 2.57
340 342 0.320374 CTAGAGGTTTCACGCCACCA 59.680 55.000 0.00 0.00 35.25 4.17
384 386 6.819397 ATGTGCCCTTCTTTCTTACTTTAC 57.181 37.500 0.00 0.00 0.00 2.01
406 408 5.304686 TGTTCTTCACACTGGAGGTAAAT 57.695 39.130 0.00 0.00 0.00 1.40
413 415 3.264193 AGGCATATGTTCTTCACACTGGA 59.736 43.478 4.29 0.00 38.61 3.86
433 435 3.285484 CCTCTCACATTGGATCCAAAGG 58.715 50.000 30.28 24.99 39.55 3.11
442 444 0.898320 ACTCGTCCCTCTCACATTGG 59.102 55.000 0.00 0.00 0.00 3.16
451 453 0.962356 TCGGTTGGTACTCGTCCCTC 60.962 60.000 0.00 0.00 0.00 4.30
485 487 2.657143 AGCGGGTGGAAGTTTTGTTAA 58.343 42.857 0.00 0.00 0.00 2.01
486 488 2.351706 AGCGGGTGGAAGTTTTGTTA 57.648 45.000 0.00 0.00 0.00 2.41
494 496 0.323629 TTTGGACTAGCGGGTGGAAG 59.676 55.000 0.00 0.00 0.00 3.46
497 499 1.376812 GGTTTGGACTAGCGGGTGG 60.377 63.158 0.00 0.00 0.00 4.61
516 518 4.330074 CACAAGTACCAATCTCCGTCATTC 59.670 45.833 0.00 0.00 0.00 2.67
533 535 3.831323 TGGGTCATCACAATTCACAAGT 58.169 40.909 0.00 0.00 0.00 3.16
541 543 2.559698 TGTCGTTGGGTCATCACAAT 57.440 45.000 0.00 0.00 39.28 2.71
542 544 2.559698 ATGTCGTTGGGTCATCACAA 57.440 45.000 0.00 0.00 34.28 3.33
543 545 3.686916 TTATGTCGTTGGGTCATCACA 57.313 42.857 0.00 0.00 0.00 3.58
544 546 5.448632 GGATTTTATGTCGTTGGGTCATCAC 60.449 44.000 0.00 0.00 0.00 3.06
545 547 4.638421 GGATTTTATGTCGTTGGGTCATCA 59.362 41.667 0.00 0.00 0.00 3.07
546 548 4.881850 AGGATTTTATGTCGTTGGGTCATC 59.118 41.667 0.00 0.00 0.00 2.92
547 549 4.855340 AGGATTTTATGTCGTTGGGTCAT 58.145 39.130 0.00 0.00 0.00 3.06
548 550 4.295141 AGGATTTTATGTCGTTGGGTCA 57.705 40.909 0.00 0.00 0.00 4.02
549 551 4.698304 TGAAGGATTTTATGTCGTTGGGTC 59.302 41.667 0.00 0.00 0.00 4.46
550 552 4.658063 TGAAGGATTTTATGTCGTTGGGT 58.342 39.130 0.00 0.00 0.00 4.51
551 553 5.356751 TCATGAAGGATTTTATGTCGTTGGG 59.643 40.000 0.00 0.00 33.37 4.12
552 554 6.316140 TCTCATGAAGGATTTTATGTCGTTGG 59.684 38.462 0.00 0.00 33.37 3.77
553 555 7.307493 TCTCATGAAGGATTTTATGTCGTTG 57.693 36.000 0.00 0.00 33.37 4.10
554 556 6.540189 CCTCTCATGAAGGATTTTATGTCGTT 59.460 38.462 15.10 0.00 33.37 3.85
577 579 3.859414 GCGCCCTCAGAGCATCCT 61.859 66.667 0.00 0.00 33.66 3.24
726 729 5.689383 AATGTCTCAAACGTTGCATAACT 57.311 34.783 0.00 0.00 35.73 2.24
736 739 9.232082 TCAGTTTCAAAATAAATGTCTCAAACG 57.768 29.630 0.00 0.00 0.00 3.60
738 741 9.748708 CCTCAGTTTCAAAATAAATGTCTCAAA 57.251 29.630 0.00 0.00 0.00 2.69
757 760 7.855784 AAAATTCCAAAATACTCCCTCAGTT 57.144 32.000 0.00 0.00 36.43 3.16
781 784 7.289310 ACTCTGAGATGAGATGAGATGAACTA 58.711 38.462 12.44 0.00 37.50 2.24
791 794 7.148440 GGAGTTTTTGAACTCTGAGATGAGATG 60.148 40.741 12.44 0.00 46.32 2.90
797 800 8.601546 AGATAAGGAGTTTTTGAACTCTGAGAT 58.398 33.333 12.44 0.00 46.32 2.75
798 801 7.967908 AGATAAGGAGTTTTTGAACTCTGAGA 58.032 34.615 12.44 3.79 46.32 3.27
799 802 8.614469 AAGATAAGGAGTTTTTGAACTCTGAG 57.386 34.615 16.23 2.45 46.32 3.35
905 910 2.426023 GCGTCTGACAAGTGGGGT 59.574 61.111 8.73 0.00 0.00 4.95
988 1004 4.899239 GTCCATCGCCGGAGCTGG 62.899 72.222 20.71 20.71 35.10 4.85
1209 1228 2.612493 CCCGAACCACTTGGGGGAT 61.612 63.158 2.59 0.00 40.91 3.85
1311 1336 4.155733 TATCGCACACAGGCCGGG 62.156 66.667 8.08 0.95 0.00 5.73
1362 1388 0.682852 GCCGCCATACCATACCAGTA 59.317 55.000 0.00 0.00 0.00 2.74
1469 1495 1.214589 CCTGGGGTACACGACGAAG 59.785 63.158 0.00 0.00 0.00 3.79
1618 1647 2.224378 ACATTATGCGTGCTCATAGGCT 60.224 45.455 0.00 0.00 31.33 4.58
1635 1664 5.476599 TCTGAATCCATTCAACCGAAACATT 59.523 36.000 3.64 0.00 45.26 2.71
1673 1702 7.235079 TCAGATGGGTTATTTTCACACCTAAA 58.765 34.615 0.00 0.00 0.00 1.85
1777 1806 7.759489 TTTGGTAGTTGATTTGCTACTGATT 57.241 32.000 0.00 0.00 38.06 2.57
1825 1854 2.206815 TTGCAGCACATCACAACAAC 57.793 45.000 0.00 0.00 0.00 3.32
1860 1889 4.082274 TCGTATGCATTGACAAAAGCAG 57.918 40.909 19.26 9.72 42.72 4.24
1904 1933 3.503363 TCAAGCAGGAAACATGATGTGAC 59.497 43.478 0.00 0.00 0.00 3.67
2076 2105 2.224257 ACAGGTTTGCATTTTCCGCATT 60.224 40.909 0.00 0.00 39.58 3.56
2113 2142 2.880890 AGCAGACAACCAACAGATCAAC 59.119 45.455 0.00 0.00 0.00 3.18
2133 2162 8.496707 AAGGCAGCAAATCCAATTTTATTTAG 57.503 30.769 0.00 0.00 0.00 1.85
2215 2246 1.550065 CATGAGTCTTACGGCACTCG 58.450 55.000 0.00 0.00 41.81 4.18
2633 2665 3.119849 ACGCAAAAGGTTATGATGCACTC 60.120 43.478 0.00 0.00 36.84 3.51
2883 2915 2.819595 CACCTCGCGGGGAACATG 60.820 66.667 36.26 16.65 34.80 3.21
3031 3063 6.828672 AGATAAAAGGATCAAACGTTTCGTC 58.171 36.000 11.37 11.62 39.99 4.20
3033 3065 8.440833 ACTAAGATAAAAGGATCAAACGTTTCG 58.559 33.333 11.37 7.31 0.00 3.46
4615 5646 2.939103 CGCATCTAACTTTTCCTCAGGG 59.061 50.000 0.00 0.00 0.00 4.45
4740 5771 4.437255 GCGCACAGTTATGAATCATGTGAA 60.437 41.667 16.23 0.00 43.02 3.18
4771 5804 5.741510 CGCAAACTAAAATGACACAGAAACA 59.258 36.000 0.00 0.00 0.00 2.83
4814 5847 6.821031 TTAAAATTAAACTGCGCTAGGGAA 57.179 33.333 11.61 0.00 0.00 3.97
4889 5922 2.420827 CGTGGTATTTGCACCTCCCATA 60.421 50.000 0.00 0.00 39.50 2.74
4898 5931 2.106477 TCATGCTCGTGGTATTTGCA 57.894 45.000 0.00 0.00 38.05 4.08
4988 6033 3.889134 CTGCAAGCTCTGACCGCCA 62.889 63.158 0.00 0.00 0.00 5.69
4989 6034 3.123620 CTGCAAGCTCTGACCGCC 61.124 66.667 0.00 0.00 0.00 6.13
5004 6049 3.449227 CACCATGCCCTGCTGCTG 61.449 66.667 0.00 0.00 0.00 4.41
5005 6050 4.753662 CCACCATGCCCTGCTGCT 62.754 66.667 0.00 0.00 0.00 4.24
5014 6059 1.304381 TTCTGAAGGCCCACCATGC 60.304 57.895 0.00 0.00 39.06 4.06
5015 6060 0.967380 GGTTCTGAAGGCCCACCATG 60.967 60.000 0.00 0.00 39.06 3.66
5016 6061 1.384191 GGTTCTGAAGGCCCACCAT 59.616 57.895 0.00 0.00 39.06 3.55
5017 6062 2.067932 CTGGTTCTGAAGGCCCACCA 62.068 60.000 0.00 1.52 39.06 4.17
5018 6063 1.303643 CTGGTTCTGAAGGCCCACC 60.304 63.158 0.00 0.00 0.00 4.61
5019 6064 1.973812 GCTGGTTCTGAAGGCCCAC 60.974 63.158 0.00 0.00 0.00 4.61
5020 6065 2.416107 CTGCTGGTTCTGAAGGCCCA 62.416 60.000 0.00 0.00 0.00 5.36
5021 6066 1.676967 CTGCTGGTTCTGAAGGCCC 60.677 63.158 0.00 0.00 0.00 5.80
5022 6067 2.338785 GCTGCTGGTTCTGAAGGCC 61.339 63.158 0.00 0.00 0.00 5.19
5023 6068 1.584380 CTGCTGCTGGTTCTGAAGGC 61.584 60.000 0.00 0.00 0.00 4.35
5024 6069 0.035881 TCTGCTGCTGGTTCTGAAGG 59.964 55.000 6.69 0.00 0.00 3.46
5025 6070 1.534595 GTTCTGCTGCTGGTTCTGAAG 59.465 52.381 6.69 0.00 0.00 3.02
5026 6071 1.597742 GTTCTGCTGCTGGTTCTGAA 58.402 50.000 6.69 0.00 0.00 3.02
5027 6072 0.250467 GGTTCTGCTGCTGGTTCTGA 60.250 55.000 6.69 0.00 0.00 3.27
5028 6073 0.535780 TGGTTCTGCTGCTGGTTCTG 60.536 55.000 6.69 0.00 0.00 3.02
5029 6074 0.183492 TTGGTTCTGCTGCTGGTTCT 59.817 50.000 6.69 0.00 0.00 3.01
5030 6075 1.032014 TTTGGTTCTGCTGCTGGTTC 58.968 50.000 6.69 0.00 0.00 3.62
5031 6076 1.342174 CATTTGGTTCTGCTGCTGGTT 59.658 47.619 6.69 0.00 0.00 3.67
5032 6077 0.963962 CATTTGGTTCTGCTGCTGGT 59.036 50.000 6.69 0.00 0.00 4.00
5033 6078 0.389426 GCATTTGGTTCTGCTGCTGG 60.389 55.000 6.69 0.00 35.49 4.85
5034 6079 0.315886 TGCATTTGGTTCTGCTGCTG 59.684 50.000 0.00 0.00 39.16 4.41
5035 6080 1.000506 CTTGCATTTGGTTCTGCTGCT 59.999 47.619 0.00 0.00 39.16 4.24
5036 6081 1.425412 CTTGCATTTGGTTCTGCTGC 58.575 50.000 0.00 0.00 39.16 5.25
5037 6082 1.614903 TCCTTGCATTTGGTTCTGCTG 59.385 47.619 0.00 0.00 39.16 4.41
5038 6083 1.891150 CTCCTTGCATTTGGTTCTGCT 59.109 47.619 0.00 0.00 39.16 4.24
5039 6084 1.067354 CCTCCTTGCATTTGGTTCTGC 60.067 52.381 0.00 0.00 38.87 4.26
5040 6085 1.067354 GCCTCCTTGCATTTGGTTCTG 60.067 52.381 0.00 0.00 0.00 3.02
5041 6086 1.260544 GCCTCCTTGCATTTGGTTCT 58.739 50.000 0.00 0.00 0.00 3.01
5042 6087 0.109132 CGCCTCCTTGCATTTGGTTC 60.109 55.000 0.00 0.00 0.00 3.62
5043 6088 1.535204 CCGCCTCCTTGCATTTGGTT 61.535 55.000 0.00 0.00 0.00 3.67
5044 6089 1.978617 CCGCCTCCTTGCATTTGGT 60.979 57.895 0.00 0.00 0.00 3.67
5045 6090 1.937546 GACCGCCTCCTTGCATTTGG 61.938 60.000 0.00 0.00 0.00 3.28
5046 6091 1.243342 TGACCGCCTCCTTGCATTTG 61.243 55.000 0.00 0.00 0.00 2.32
5047 6092 0.962356 CTGACCGCCTCCTTGCATTT 60.962 55.000 0.00 0.00 0.00 2.32
5048 6093 1.377725 CTGACCGCCTCCTTGCATT 60.378 57.895 0.00 0.00 0.00 3.56
5049 6094 2.249413 CTCTGACCGCCTCCTTGCAT 62.249 60.000 0.00 0.00 0.00 3.96
5050 6095 2.922503 TCTGACCGCCTCCTTGCA 60.923 61.111 0.00 0.00 0.00 4.08
5051 6096 2.125350 CTCTGACCGCCTCCTTGC 60.125 66.667 0.00 0.00 0.00 4.01
5052 6097 2.125350 GCTCTGACCGCCTCCTTG 60.125 66.667 0.00 0.00 0.00 3.61
5053 6098 1.915769 AAGCTCTGACCGCCTCCTT 60.916 57.895 0.00 0.00 0.00 3.36
5054 6099 2.284258 AAGCTCTGACCGCCTCCT 60.284 61.111 0.00 0.00 0.00 3.69
5055 6100 2.125350 CAAGCTCTGACCGCCTCC 60.125 66.667 0.00 0.00 0.00 4.30
5056 6101 2.817396 GCAAGCTCTGACCGCCTC 60.817 66.667 0.00 0.00 0.00 4.70
5142 6199 1.945394 GTTCGGCATCTGATTCTGCAT 59.055 47.619 4.34 0.00 40.18 3.96
5247 6304 3.316573 GACTCTGGCCAGGAACCCG 62.317 68.421 32.23 15.43 0.00 5.28
5269 6327 1.274167 TCGTCCAGCCGAAAATACTGT 59.726 47.619 0.00 0.00 33.15 3.55
5315 6373 2.113774 CTGCACACAGGGAAGGCA 59.886 61.111 0.00 0.00 40.48 4.75
5402 6460 3.849911 ACGATGACGAACAATCATGACT 58.150 40.909 0.00 0.00 42.66 3.41
5417 6475 5.630061 TCTAACGTCGATTTACAACGATGA 58.370 37.500 14.07 0.00 44.79 2.92
5513 6571 1.818850 CACGCATCATAAGTTGCAGC 58.181 50.000 0.00 0.00 39.81 5.25
5535 6593 1.595109 CGAAGCATGCGCCTATCCA 60.595 57.895 13.01 0.00 39.83 3.41
5548 6606 7.494952 ACTTGAGGTTATATTTTAGACCGAAGC 59.505 37.037 0.00 0.00 37.26 3.86
5553 6611 8.483758 TCAGGACTTGAGGTTATATTTTAGACC 58.516 37.037 0.00 0.00 0.00 3.85
5570 6634 3.594134 GTGGATCAGAGTTCAGGACTTG 58.406 50.000 0.00 0.00 39.19 3.16
5604 6668 6.749118 GCTATTTAACAGCAACCATCTGAAAG 59.251 38.462 0.00 0.00 38.93 2.62
5636 6700 7.649306 GCTCTTGTGTGATTACAAAGAAAACAT 59.351 33.333 12.69 0.00 39.81 2.71
5681 6747 5.185454 TGCCAAGAAGTCATTAGGTGTATG 58.815 41.667 0.00 0.00 0.00 2.39
5756 6824 2.685388 TGGTTCATCTCTACAGCTCTCG 59.315 50.000 0.00 0.00 0.00 4.04
5758 6826 3.834813 TGTTGGTTCATCTCTACAGCTCT 59.165 43.478 0.00 0.00 0.00 4.09
5789 6857 8.623903 CACAATTGTGTATAGCTTTGGATACAT 58.376 33.333 27.08 0.00 43.61 2.29
5827 6895 3.125146 CGACTCTGATCTGATCCGATCTC 59.875 52.174 22.77 13.53 40.32 2.75
5833 6901 2.287308 CCGTTCGACTCTGATCTGATCC 60.287 54.545 14.71 0.00 0.00 3.36
5914 6989 2.923629 ACCTGCCAAACTCCCCTATAAA 59.076 45.455 0.00 0.00 0.00 1.40
5917 6992 1.382914 AACCTGCCAAACTCCCCTAT 58.617 50.000 0.00 0.00 0.00 2.57
5919 6994 1.382914 ATAACCTGCCAAACTCCCCT 58.617 50.000 0.00 0.00 0.00 4.79
6124 7213 4.990543 TGTGAATTTGTGATCTGTCGTC 57.009 40.909 0.00 0.00 0.00 4.20
6125 7214 6.166279 ACTATGTGAATTTGTGATCTGTCGT 58.834 36.000 0.00 0.00 0.00 4.34
6158 7247 1.611673 CGCTGTTCCAAGTTGGGAGAT 60.612 52.381 21.85 0.00 38.32 2.75


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

AutoCloner maintained by Alex Coulton.