Multiple sequence alignment - TraesCS6B01G040500

Loading Multiple Alignment...

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 TraesCS6B01G040500 chr6B 100.000 5718 0 0 1 5718 25242172 25247889 0.000000e+00 10560.0
1 TraesCS6B01G040500 chr6B 80.000 325 43 18 131 444 63388407 63388094 2.680000e-53 220.0
2 TraesCS6B01G040500 chrUn 94.257 3796 174 24 1332 5105 71319051 71315278 0.000000e+00 5762.0
3 TraesCS6B01G040500 chrUn 94.162 531 23 5 5138 5664 71314920 71314394 0.000000e+00 802.0
4 TraesCS6B01G040500 chrUn 85.211 710 66 12 146 852 31644436 31643763 0.000000e+00 693.0
5 TraesCS6B01G040500 chrUn 90.583 446 28 3 868 1310 71319551 71319117 3.840000e-161 579.0
6 TraesCS6B01G040500 chr6D 93.436 2529 115 22 2589 5086 13589393 13591901 0.000000e+00 3703.0
7 TraesCS6B01G040500 chr6D 94.859 1206 52 7 1330 2532 13587742 13588940 0.000000e+00 1875.0
8 TraesCS6B01G040500 chr6D 96.627 504 13 3 5165 5664 13592169 13592672 0.000000e+00 833.0
9 TraesCS6B01G040500 chr6D 91.337 404 28 3 907 1310 13587289 13587685 3.900000e-151 545.0
10 TraesCS6B01G040500 chr6D 92.000 200 15 1 1330 1529 225837564 225837366 4.360000e-71 279.0
11 TraesCS6B01G040500 chr6D 92.308 169 12 1 1087 1255 225837843 225837676 7.400000e-59 239.0
12 TraesCS6B01G040500 chr6D 95.312 64 3 0 2469 2532 13588941 13589004 1.010000e-17 102.0
13 TraesCS6B01G040500 chr5B 91.166 1913 110 25 2589 4470 492582791 492584675 0.000000e+00 2542.0
14 TraesCS6B01G040500 chr5B 88.915 1272 111 18 1330 2589 492581447 492582700 0.000000e+00 1541.0
15 TraesCS6B01G040500 chr5B 87.957 1204 128 11 1332 2526 492612419 492613614 0.000000e+00 1404.0
16 TraesCS6B01G040500 chr5B 82.260 699 106 12 1333 2025 618490945 618490259 6.380000e-164 588.0
17 TraesCS6B01G040500 chr5B 92.879 323 20 3 4465 4784 492584921 492585243 3.120000e-127 466.0
18 TraesCS6B01G040500 chr5B 90.083 363 27 6 946 1308 492581035 492581388 4.040000e-126 462.0
19 TraesCS6B01G040500 chr5B 88.136 236 20 6 4783 5015 492585326 492585556 2.030000e-69 274.0
20 TraesCS6B01G040500 chr5B 87.671 146 10 6 5189 5333 492585576 492585714 4.580000e-36 163.0
21 TraesCS6B01G040500 chr5B 82.439 205 14 10 5451 5655 492586123 492586305 5.930000e-35 159.0
22 TraesCS6B01G040500 chr4B 92.175 869 57 7 7 871 561619126 561619987 0.000000e+00 1218.0
23 TraesCS6B01G040500 chr4B 74.619 788 119 46 132 874 289050787 289050036 7.300000e-69 272.0
24 TraesCS6B01G040500 chr4B 94.203 69 1 3 5650 5718 668064920 668064855 1.010000e-17 102.0
25 TraesCS6B01G040500 chr4B 89.610 77 6 1 5644 5718 144074309 144074385 4.720000e-16 97.1
26 TraesCS6B01G040500 chr7B 93.590 780 43 7 97 874 555577914 555578688 0.000000e+00 1157.0
27 TraesCS6B01G040500 chr3D 86.798 659 76 11 218 874 40232082 40231433 0.000000e+00 725.0
28 TraesCS6B01G040500 chr3D 81.190 521 79 16 1500 2012 73652662 73652153 8.920000e-108 401.0
29 TraesCS6B01G040500 chr4D 83.499 703 100 10 1330 2025 68095435 68094742 4.830000e-180 641.0
30 TraesCS6B01G040500 chr4D 76.382 796 117 38 132 871 368874429 368875209 4.210000e-96 363.0
31 TraesCS6B01G040500 chr4D 78.261 414 60 23 45 446 12970446 12970841 7.400000e-59 239.0
32 TraesCS6B01G040500 chr4D 92.857 70 3 2 5649 5717 42134183 42134115 3.650000e-17 100.0
33 TraesCS6B01G040500 chr4D 86.364 88 6 6 5636 5718 344588171 344588257 2.190000e-14 91.6
34 TraesCS6B01G040500 chr5A 76.543 810 115 35 126 871 575168783 575169581 1.950000e-99 374.0
35 TraesCS6B01G040500 chr4A 81.365 381 41 13 10 364 722013731 722013355 3.370000e-72 283.0
36 TraesCS6B01G040500 chr4A 78.692 413 62 19 263 657 722013601 722013197 9.510000e-63 252.0
37 TraesCS6B01G040500 chr2A 92.500 200 12 3 1330 1529 379360986 379360790 3.370000e-72 283.0
38 TraesCS6B01G040500 chr6A 79.679 374 54 18 78 444 143010662 143011020 3.420000e-62 250.0
39 TraesCS6B01G040500 chr6A 92.727 165 11 1 1519 1683 564002961 564003124 2.660000e-58 237.0
40 TraesCS6B01G040500 chr6A 85.567 97 6 8 5629 5718 328167627 328167532 1.700000e-15 95.3
41 TraesCS6B01G040500 chr3A 93.333 165 10 1 1519 1683 23810643 23810806 5.720000e-60 243.0
42 TraesCS6B01G040500 chr1A 92.727 165 11 1 1519 1683 491735048 491735211 2.660000e-58 237.0
43 TraesCS6B01G040500 chr1A 91.176 68 4 2 5652 5718 134384892 134384826 2.190000e-14 91.6
44 TraesCS6B01G040500 chr7A 84.337 249 28 6 1049 1287 680718110 680718357 3.440000e-57 233.0
45 TraesCS6B01G040500 chr7D 94.030 67 4 0 5652 5718 459386793 459386859 1.010000e-17 102.0
46 TraesCS6B01G040500 chr7D 88.750 80 5 3 5643 5718 518793724 518793803 1.700000e-15 95.3
47 TraesCS6B01G040500 chr2B 94.030 67 4 0 5652 5718 770679808 770679742 1.010000e-17 102.0


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 TraesCS6B01G040500 chr6B 25242172 25247889 5717 False 10560.0 10560 100.000000 1 5718 1 chr6B.!!$F1 5717
1 TraesCS6B01G040500 chrUn 71314394 71319551 5157 True 2381.0 5762 93.000667 868 5664 3 chrUn.!!$R2 4796
2 TraesCS6B01G040500 chrUn 31643763 31644436 673 True 693.0 693 85.211000 146 852 1 chrUn.!!$R1 706
3 TraesCS6B01G040500 chr6D 13587289 13592672 5383 False 1411.6 3703 94.314200 907 5664 5 chr6D.!!$F1 4757
4 TraesCS6B01G040500 chr5B 492612419 492613614 1195 False 1404.0 1404 87.957000 1332 2526 1 chr5B.!!$F1 1194
5 TraesCS6B01G040500 chr5B 492581035 492586305 5270 False 801.0 2542 88.755571 946 5655 7 chr5B.!!$F2 4709
6 TraesCS6B01G040500 chr5B 618490259 618490945 686 True 588.0 588 82.260000 1333 2025 1 chr5B.!!$R1 692
7 TraesCS6B01G040500 chr4B 561619126 561619987 861 False 1218.0 1218 92.175000 7 871 1 chr4B.!!$F2 864
8 TraesCS6B01G040500 chr4B 289050036 289050787 751 True 272.0 272 74.619000 132 874 1 chr4B.!!$R1 742
9 TraesCS6B01G040500 chr7B 555577914 555578688 774 False 1157.0 1157 93.590000 97 874 1 chr7B.!!$F1 777
10 TraesCS6B01G040500 chr3D 40231433 40232082 649 True 725.0 725 86.798000 218 874 1 chr3D.!!$R1 656
11 TraesCS6B01G040500 chr3D 73652153 73652662 509 True 401.0 401 81.190000 1500 2012 1 chr3D.!!$R2 512
12 TraesCS6B01G040500 chr4D 68094742 68095435 693 True 641.0 641 83.499000 1330 2025 1 chr4D.!!$R2 695
13 TraesCS6B01G040500 chr4D 368874429 368875209 780 False 363.0 363 76.382000 132 871 1 chr4D.!!$F3 739
14 TraesCS6B01G040500 chr5A 575168783 575169581 798 False 374.0 374 76.543000 126 871 1 chr5A.!!$F1 745
15 TraesCS6B01G040500 chr4A 722013197 722013731 534 True 267.5 283 80.028500 10 657 2 chr4A.!!$R1 647

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
745 986 0.389948 GGCGGTGTGAGTTCGAATCT 60.390 55.000 0.00 0.00 0.00 2.40 F
1385 1678 0.248215 CTGCCGCGTTGGATGATTTC 60.248 55.000 4.92 0.00 42.00 2.17 F
1702 2002 0.532573 TGAGAGCGATGTCCAGGAAC 59.467 55.000 0.00 0.00 0.00 3.62 F
1707 2007 1.134580 AGCGATGTCCAGGAACATGAG 60.135 52.381 0.00 5.14 39.93 2.90 F
3691 4409 0.948678 TGCGCTTTTTGGACTGTACC 59.051 50.000 9.73 0.00 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2371 0.179000 GGATACTGTCCACTGGGCAG 59.821 60.000 25.53 25.53 46.96 4.85 R
2332 2636 0.919710 GGGGACTTTGGTAGCTGGAT 59.080 55.000 0.00 0.00 0.00 3.41 R
3691 4409 0.322546 GTTAAGACAGCCACCTGGGG 60.323 60.000 0.00 0.00 43.53 4.96 R
3701 4419 9.834628 CTACTTGACTAGAAAGAGTTAAGACAG 57.165 37.037 13.18 7.27 42.68 3.51 R
5135 6235 1.155889 CACTTATGCTGCCGACAACA 58.844 50.000 0.00 0.00 0.00 3.33 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
179 218 8.828644 TGTCAAATTTGATGAACCATTTTCAAG 58.171 29.630 23.05 0.00 39.73 3.02
666 899 9.887406 CCACACTTGTTCTTATAAAATAAACGT 57.113 29.630 0.00 0.00 0.00 3.99
710 943 3.472283 TTGGTGTAGTGGTTAGCGAAA 57.528 42.857 0.00 0.00 0.00 3.46
712 945 1.723003 GGTGTAGTGGTTAGCGAAACG 59.277 52.381 0.00 0.00 39.13 3.60
745 986 0.389948 GGCGGTGTGAGTTCGAATCT 60.390 55.000 0.00 0.00 0.00 2.40
847 1090 1.666553 CGTGTGCGCCAGAAACCTA 60.667 57.895 4.18 0.00 0.00 3.08
891 1134 0.396974 GGCCAATCCAACAGCCCATA 60.397 55.000 0.00 0.00 39.60 2.74
892 1135 0.746659 GCCAATCCAACAGCCCATAC 59.253 55.000 0.00 0.00 0.00 2.39
893 1136 1.959508 GCCAATCCAACAGCCCATACA 60.960 52.381 0.00 0.00 0.00 2.29
894 1137 2.455557 CCAATCCAACAGCCCATACAA 58.544 47.619 0.00 0.00 0.00 2.41
895 1138 2.166254 CCAATCCAACAGCCCATACAAC 59.834 50.000 0.00 0.00 0.00 3.32
896 1139 1.750193 ATCCAACAGCCCATACAACG 58.250 50.000 0.00 0.00 0.00 4.10
897 1140 0.398696 TCCAACAGCCCATACAACGT 59.601 50.000 0.00 0.00 0.00 3.99
902 1145 2.744709 GCCCATACAACGTGCGGT 60.745 61.111 0.00 0.00 0.00 5.68
904 1147 0.812412 GCCCATACAACGTGCGGTAT 60.812 55.000 0.00 0.00 0.00 2.73
918 1161 2.167693 TGCGGTATCATCCTTCGTTTCT 59.832 45.455 0.00 0.00 0.00 2.52
931 1174 1.071814 GTTTCTGTACCGGCCCACA 59.928 57.895 0.00 2.13 0.00 4.17
934 1177 1.697082 TTCTGTACCGGCCCACACAA 61.697 55.000 0.00 0.00 0.00 3.33
935 1178 1.002624 CTGTACCGGCCCACACAAT 60.003 57.895 0.00 0.00 0.00 2.71
936 1179 0.608035 CTGTACCGGCCCACACAATT 60.608 55.000 0.00 0.00 0.00 2.32
941 1184 2.658422 GGCCCACACAATTGCCTG 59.342 61.111 5.05 0.00 40.77 4.85
956 1202 1.918253 CCTGACCAATCCCCTCCTG 59.082 63.158 0.00 0.00 0.00 3.86
1053 1299 2.764547 CCTCCTCCCCCGGAAGAC 60.765 72.222 0.73 0.00 31.44 3.01
1066 1312 3.733295 CGGAAGACGGAGGAGGAGACT 62.733 61.905 0.00 0.00 41.37 3.24
1067 1313 1.212441 GGAAGACGGAGGAGGAGACTA 59.788 57.143 0.00 0.00 44.43 2.59
1310 1556 2.597805 CCGGATCGGGATCGGACT 60.598 66.667 13.96 0.00 44.15 3.85
1364 1654 5.734720 TCCTGAAGTTTCGATGCTAGATTT 58.265 37.500 0.00 0.00 0.00 2.17
1385 1678 0.248215 CTGCCGCGTTGGATGATTTC 60.248 55.000 4.92 0.00 42.00 2.17
1489 1782 1.539827 CGCCCTTTACAAGTTTCTGGG 59.460 52.381 0.00 0.00 36.41 4.45
1541 1834 5.317733 TGGTAATTACTCCGGCATTTTTG 57.682 39.130 15.05 0.00 0.00 2.44
1690 1990 0.584396 CTAGCGGTAGAGTGAGAGCG 59.416 60.000 16.62 0.00 39.48 5.03
1702 2002 0.532573 TGAGAGCGATGTCCAGGAAC 59.467 55.000 0.00 0.00 0.00 3.62
1707 2007 1.134580 AGCGATGTCCAGGAACATGAG 60.135 52.381 0.00 5.14 39.93 2.90
1804 2105 1.667724 CGTCCAGAACATCCAGAATGC 59.332 52.381 0.00 0.00 39.12 3.56
1917 2221 2.100916 TCTCCATCGTAACTTAGCAGGC 59.899 50.000 0.00 0.00 0.00 4.85
2067 2371 5.164061 CCAAACTTATTTTCAATGAGCACGC 60.164 40.000 0.00 0.00 0.00 5.34
2350 2654 2.019156 GCATCCAGCTACCAAAGTCCC 61.019 57.143 0.00 0.00 41.15 4.46
2470 2774 9.619316 TTCATTTATATAAAATCGAAATGCCGG 57.381 29.630 11.80 0.00 37.40 6.13
2745 3445 6.459161 GCGTCTTTCTTCTTTTGGTTCCTTTA 60.459 38.462 0.00 0.00 0.00 1.85
2746 3446 7.649057 CGTCTTTCTTCTTTTGGTTCCTTTAT 58.351 34.615 0.00 0.00 0.00 1.40
3098 3799 5.163248 TGGACACAAAGAGTTCAGGTATTCA 60.163 40.000 0.00 0.00 0.00 2.57
3099 3800 5.409826 GGACACAAAGAGTTCAGGTATTCAG 59.590 44.000 0.00 0.00 0.00 3.02
3105 3806 5.753721 AGAGTTCAGGTATTCAGCTCTTT 57.246 39.130 0.00 0.00 0.00 2.52
3282 3987 5.750352 AAAATCTGCATGGGAAAAGACAT 57.250 34.783 0.00 0.00 0.00 3.06
3300 4005 5.111293 AGACATTTTTCAAGGTTGCAACTG 58.889 37.500 27.64 19.26 0.00 3.16
3382 4087 5.048846 TCAAGTAAGCCCTTCTCTTTGTT 57.951 39.130 0.00 0.00 0.00 2.83
3431 4138 7.815549 TCTGCTGTTCATCGTATTACTTTGTAA 59.184 33.333 0.00 0.00 0.00 2.41
3530 4239 9.155975 CACCTGTTGATATGTTCTTATATAGCC 57.844 37.037 0.00 0.00 0.00 3.93
3661 4379 7.723172 ACGCCTTATTACTCTACCTTACATAGT 59.277 37.037 0.00 0.00 0.00 2.12
3691 4409 0.948678 TGCGCTTTTTGGACTGTACC 59.051 50.000 9.73 0.00 0.00 3.34
3708 4426 1.923395 CCCCCAGGTGGCTGTCTTA 60.923 63.158 0.00 0.00 0.00 2.10
3834 4555 1.694048 GGGACCCTGGATGAGTCAGAT 60.694 57.143 2.09 0.00 34.36 2.90
3874 4595 2.570415 TGATTTTGTGGGCGAGGTTA 57.430 45.000 0.00 0.00 0.00 2.85
3875 4596 2.156098 TGATTTTGTGGGCGAGGTTAC 58.844 47.619 0.00 0.00 0.00 2.50
3876 4597 1.471287 GATTTTGTGGGCGAGGTTACC 59.529 52.381 0.00 0.00 0.00 2.85
3918 4639 7.592938 TCAGTCACATTGTGTTATTTGAATCC 58.407 34.615 16.06 0.00 34.79 3.01
3930 4651 7.534239 GTGTTATTTGAATCCGAAGAAAGACAC 59.466 37.037 0.00 0.00 0.00 3.67
3931 4652 7.227711 TGTTATTTGAATCCGAAGAAAGACACA 59.772 33.333 0.00 0.00 0.00 3.72
3963 4684 2.159599 GCTTCTGCACGATTCCTTTCAG 60.160 50.000 0.00 0.00 39.41 3.02
3986 4707 4.762251 GGAGGTAATATGCCATTTCACCTC 59.238 45.833 16.87 16.87 46.39 3.85
3990 4711 5.009010 GGTAATATGCCATTTCACCTCAGTG 59.991 44.000 0.00 0.00 46.00 3.66
4091 4817 5.445964 AGTAAAACTTGAAAGGAAGGCAGA 58.554 37.500 0.00 0.00 0.00 4.26
4105 4831 1.414919 AGGCAGACAAAGAACCGTACA 59.585 47.619 0.00 0.00 0.00 2.90
4115 4848 8.092687 AGACAAAGAACCGTACAATATACTTGT 58.907 33.333 0.00 6.03 36.49 3.16
4219 4954 8.816894 TCTATTGTCAAAGAGAGGTCATACTTT 58.183 33.333 0.00 0.00 30.26 2.66
4393 5136 4.551702 TGCTTCTAAGTGGTGAGCATTA 57.448 40.909 0.00 0.00 0.00 1.90
4415 5158 1.801178 CTTCGCCAAAGAGAACAGTCC 59.199 52.381 0.00 0.00 37.12 3.85
4426 5185 5.476091 AGAGAACAGTCCTAGTTTCCAAG 57.524 43.478 0.00 0.00 0.00 3.61
4514 5524 9.114952 TCACAATTACTGTTACATCACTTTCAA 57.885 29.630 0.00 0.00 35.47 2.69
4529 5539 5.713389 TCACTTTCAATGAAATGGATGAGCT 59.287 36.000 9.02 0.00 30.85 4.09
4537 5547 4.682787 TGAAATGGATGAGCTGTACTACG 58.317 43.478 0.00 0.00 0.00 3.51
4565 5575 9.013229 TGCATGATCAGTTTCAGTTTTATACTT 57.987 29.630 0.09 0.00 33.85 2.24
4847 5944 4.666512 AGAACTTGGCAATCTGTTATGGT 58.333 39.130 0.00 0.00 0.00 3.55
4889 5986 4.083003 TGTTGTGCCGATCCTTTTTGTATC 60.083 41.667 0.00 0.00 0.00 2.24
4904 6001 5.811399 TTTGTATCGGCCAGATTTTGTAG 57.189 39.130 13.95 0.00 40.66 2.74
4950 6050 5.710567 AGTCTCCATATCCATGATGCATTTG 59.289 40.000 0.00 1.86 33.67 2.32
4963 6063 5.698832 TGATGCATTTGTAAGACGAAAAGG 58.301 37.500 0.00 0.00 0.00 3.11
4989 6089 2.584835 TGGCAGTATTTCCTTGCAGT 57.415 45.000 0.00 0.00 39.54 4.40
5031 6131 0.523072 GTGCGTGGCTTGTTCATCAT 59.477 50.000 0.00 0.00 0.00 2.45
5069 6169 5.163713 GCACAAAGAGATCATTACCCAGTTC 60.164 44.000 0.00 0.00 0.00 3.01
5110 6210 8.940768 AAATTACATGCCATGTACAAATTACC 57.059 30.769 16.87 0.00 44.79 2.85
5111 6211 6.458232 TTACATGCCATGTACAAATTACCC 57.542 37.500 16.87 0.00 44.79 3.69
5112 6212 4.348486 ACATGCCATGTACAAATTACCCA 58.652 39.130 8.96 0.00 42.78 4.51
5113 6213 4.159506 ACATGCCATGTACAAATTACCCAC 59.840 41.667 8.96 0.00 42.78 4.61
5114 6214 3.093057 TGCCATGTACAAATTACCCACC 58.907 45.455 0.00 0.00 0.00 4.61
5115 6215 2.429250 GCCATGTACAAATTACCCACCC 59.571 50.000 0.00 0.00 0.00 4.61
5116 6216 3.028130 CCATGTACAAATTACCCACCCC 58.972 50.000 0.00 0.00 0.00 4.95
5117 6217 2.903375 TGTACAAATTACCCACCCCC 57.097 50.000 0.00 0.00 0.00 5.40
5181 6606 3.067180 AGGCGCACAATCTTATCCATTTG 59.933 43.478 10.83 0.00 0.00 2.32
5256 6682 8.523915 AGGTTCAATACATCATCTTAATGCAA 57.476 30.769 0.00 0.00 32.58 4.08
5443 6869 0.036875 GCCTACAAGTTCCTGCACCT 59.963 55.000 0.00 0.00 0.00 4.00
5551 7269 7.835822 TCCATGATGTAAAGTAAAATTGGTGG 58.164 34.615 0.00 0.00 0.00 4.61
5674 7393 4.706842 AAATACATAATGCTCCCTCCGT 57.293 40.909 0.00 0.00 0.00 4.69
5675 7394 4.706842 AATACATAATGCTCCCTCCGTT 57.293 40.909 0.00 0.00 0.00 4.44
5676 7395 2.622064 ACATAATGCTCCCTCCGTTC 57.378 50.000 0.00 0.00 0.00 3.95
5677 7396 1.141053 ACATAATGCTCCCTCCGTTCC 59.859 52.381 0.00 0.00 0.00 3.62
5678 7397 1.417890 CATAATGCTCCCTCCGTTCCT 59.582 52.381 0.00 0.00 0.00 3.36
5679 7398 2.464796 TAATGCTCCCTCCGTTCCTA 57.535 50.000 0.00 0.00 0.00 2.94
5680 7399 1.580059 AATGCTCCCTCCGTTCCTAA 58.420 50.000 0.00 0.00 0.00 2.69
5681 7400 1.580059 ATGCTCCCTCCGTTCCTAAA 58.420 50.000 0.00 0.00 0.00 1.85
5682 7401 1.580059 TGCTCCCTCCGTTCCTAAAT 58.420 50.000 0.00 0.00 0.00 1.40
5683 7402 2.754465 TGCTCCCTCCGTTCCTAAATA 58.246 47.619 0.00 0.00 0.00 1.40
5684 7403 3.314693 TGCTCCCTCCGTTCCTAAATAT 58.685 45.455 0.00 0.00 0.00 1.28
5685 7404 4.485875 TGCTCCCTCCGTTCCTAAATATA 58.514 43.478 0.00 0.00 0.00 0.86
5686 7405 4.903049 TGCTCCCTCCGTTCCTAAATATAA 59.097 41.667 0.00 0.00 0.00 0.98
5687 7406 5.011738 TGCTCCCTCCGTTCCTAAATATAAG 59.988 44.000 0.00 0.00 0.00 1.73
5688 7407 5.011840 GCTCCCTCCGTTCCTAAATATAAGT 59.988 44.000 0.00 0.00 0.00 2.24
5689 7408 6.661304 TCCCTCCGTTCCTAAATATAAGTC 57.339 41.667 0.00 0.00 0.00 3.01
5690 7409 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
5691 7410 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
5692 7411 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
5693 7412 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
5694 7413 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
5711 7430 9.750125 AAGTCTTTTTAGACATTTCAAATGGAC 57.250 29.630 14.70 8.92 41.02 4.02
5712 7431 9.136323 AGTCTTTTTAGACATTTCAAATGGACT 57.864 29.630 14.70 14.18 41.02 3.85
5717 7436 9.959749 TTTTAGACATTTCAAATGGACTACAAC 57.040 29.630 14.70 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.889832 AGATAAGAAAAGAAGCATGCCG 57.110 40.909 15.66 0.00 0.00 5.69
3 4 6.448207 AGAAGATAAGAAAAGAAGCATGCC 57.552 37.500 15.66 0.00 0.00 4.40
4 5 7.760437 AGAAGAAGATAAGAAAAGAAGCATGC 58.240 34.615 10.51 10.51 0.00 4.06
46 63 6.626302 ACAAGTTTCACGAATTTGGAAAAGA 58.374 32.000 9.57 0.00 38.77 2.52
47 64 6.885735 ACAAGTTTCACGAATTTGGAAAAG 57.114 33.333 9.57 6.95 38.77 2.27
48 65 7.659652 AAACAAGTTTCACGAATTTGGAAAA 57.340 28.000 9.57 2.21 38.77 2.29
49 66 7.600752 AGAAAACAAGTTTCACGAATTTGGAAA 59.399 29.630 0.00 2.05 46.98 3.13
202 241 9.467258 TCATCAAATTTGAAAGAAGTTCATCAC 57.533 29.630 23.91 0.00 45.71 3.06
324 484 7.268586 TGGATTTGGAAAAAGTTCATCGAAAA 58.731 30.769 0.00 0.00 35.25 2.29
663 896 5.978934 ACAGTTCTGTTCGAAAATAACGT 57.021 34.783 10.05 8.72 32.41 3.99
691 924 2.758009 GTTTCGCTAACCACTACACCA 58.242 47.619 0.00 0.00 0.00 4.17
710 943 1.474879 CCGCCACAAATTTAATCCCGT 59.525 47.619 0.00 0.00 0.00 5.28
712 945 2.232696 ACACCGCCACAAATTTAATCCC 59.767 45.455 0.00 0.00 0.00 3.85
758 999 4.787381 AATTCCGGAAAAACGCAAAAAG 57.213 36.364 23.08 0.00 0.00 2.27
880 1123 0.109781 GCACGTTGTATGGGCTGTTG 60.110 55.000 0.00 0.00 0.00 3.33
891 1134 0.535335 AGGATGATACCGCACGTTGT 59.465 50.000 0.00 0.00 34.73 3.32
892 1135 1.593006 GAAGGATGATACCGCACGTTG 59.407 52.381 0.00 0.00 34.73 4.10
893 1136 1.801395 CGAAGGATGATACCGCACGTT 60.801 52.381 0.00 0.00 34.73 3.99
894 1137 0.248907 CGAAGGATGATACCGCACGT 60.249 55.000 0.00 0.00 34.73 4.49
895 1138 0.248907 ACGAAGGATGATACCGCACG 60.249 55.000 0.00 0.00 34.73 5.34
896 1139 1.935933 AACGAAGGATGATACCGCAC 58.064 50.000 0.00 0.00 34.73 5.34
897 1140 2.167693 AGAAACGAAGGATGATACCGCA 59.832 45.455 0.00 0.00 34.73 5.69
902 1145 4.202080 CCGGTACAGAAACGAAGGATGATA 60.202 45.833 0.00 0.00 0.00 2.15
904 1147 2.094390 CCGGTACAGAAACGAAGGATGA 60.094 50.000 0.00 0.00 0.00 2.92
918 1161 0.891449 CAATTGTGTGGGCCGGTACA 60.891 55.000 1.90 3.55 0.00 2.90
931 1174 1.560505 GGGATTGGTCAGGCAATTGT 58.439 50.000 7.40 0.00 0.00 2.71
934 1177 0.259938 GAGGGGATTGGTCAGGCAAT 59.740 55.000 0.00 0.00 0.00 3.56
935 1178 1.691219 GAGGGGATTGGTCAGGCAA 59.309 57.895 0.00 0.00 0.00 4.52
936 1179 2.308722 GGAGGGGATTGGTCAGGCA 61.309 63.158 0.00 0.00 0.00 4.75
941 1184 1.077429 GCACAGGAGGGGATTGGTC 60.077 63.158 0.00 0.00 0.00 4.02
1053 1299 2.249844 GAGAGTAGTCTCCTCCTCCG 57.750 60.000 15.67 0.00 43.26 4.63
1066 1312 3.506096 CGGCGACTGCGGAGAGTA 61.506 66.667 12.26 0.00 43.58 2.59
1264 1510 2.955751 CTAGCTAGCACCCGCGGAAC 62.956 65.000 30.73 15.71 45.49 3.62
1310 1556 3.506096 CGGGACTGTCTCGCGCTA 61.506 66.667 17.99 0.00 46.89 4.26
1364 1654 3.974835 ATCATCCAACGCGGCAGCA 62.975 57.895 12.47 0.00 45.49 4.41
1395 1688 2.332654 GGTGGCCGTACCTGCAAAG 61.333 63.158 4.97 0.00 40.22 2.77
1489 1782 1.138464 GGGTATCGAGGTGGAGAAACC 59.862 57.143 0.00 0.00 40.85 3.27
1541 1834 3.143728 ACACTGTACCGGTTTCATTTCC 58.856 45.455 15.04 0.00 0.00 3.13
1557 1850 9.264719 TCAAACATATATCTAGCATTGACACTG 57.735 33.333 0.00 0.00 0.00 3.66
1590 1883 1.815003 CATTTCTGCCCTCCAAGTGAC 59.185 52.381 0.00 0.00 0.00 3.67
1690 1990 2.911484 GTCCTCATGTTCCTGGACATC 58.089 52.381 0.00 0.00 45.87 3.06
1702 2002 5.121811 CCTATTCAAACTGAGGTCCTCATG 58.878 45.833 22.10 16.98 39.92 3.07
1707 2007 3.636153 AGCCTATTCAAACTGAGGTCC 57.364 47.619 0.00 0.00 0.00 4.46
1917 2221 6.431234 GCTCCCTATATGTGGAAAATGGTAAG 59.569 42.308 0.00 0.00 0.00 2.34
2067 2371 0.179000 GGATACTGTCCACTGGGCAG 59.821 60.000 25.53 25.53 46.96 4.85
2097 2401 9.986833 CATCAAACTGAAATTATATCGACACAA 57.013 29.630 0.00 0.00 0.00 3.33
2332 2636 0.919710 GGGGACTTTGGTAGCTGGAT 59.080 55.000 0.00 0.00 0.00 3.41
2350 2654 4.520492 AGTAGTGCCACTTTTCTTGAATGG 59.480 41.667 1.02 0.00 0.00 3.16
2470 2774 6.828502 GGAATGACCTCAAGAAACAAAAAC 57.171 37.500 0.00 0.00 35.41 2.43
2722 3422 9.817809 AAATAAAGGAACCAAAAGAAGAAAGAC 57.182 29.630 0.00 0.00 0.00 3.01
3282 3987 4.021544 ACAGACAGTTGCAACCTTGAAAAA 60.022 37.500 25.62 0.00 0.00 1.94
3300 4005 8.948631 TGGTTATGATGAGAAGAATAACAGAC 57.051 34.615 0.00 0.00 37.27 3.51
3382 4087 5.528043 AACAAGGCAATGTTGACACATAA 57.472 34.783 7.74 0.00 43.34 1.90
3431 4138 9.588096 AAAGTATTCCATAGAACAAGTTTTCCT 57.412 29.630 0.00 0.00 33.97 3.36
3530 4239 2.575532 TCCTCTCTGCCACAACAAAAG 58.424 47.619 0.00 0.00 0.00 2.27
3661 4379 3.202906 CAAAAAGCGCATAGGTAGGCTA 58.797 45.455 11.47 0.00 34.82 3.93
3691 4409 0.322546 GTTAAGACAGCCACCTGGGG 60.323 60.000 0.00 0.00 43.53 4.96
3701 4419 9.834628 CTACTTGACTAGAAAGAGTTAAGACAG 57.165 37.037 13.18 7.27 42.68 3.51
3762 4482 3.584848 GTCAGGGGATATTGACTATGCCT 59.415 47.826 0.74 0.00 45.31 4.75
3775 4495 7.184862 AGAACATGAAAATTAAGTCAGGGGAT 58.815 34.615 0.00 0.00 29.97 3.85
3834 4555 1.697432 AGTGGGTTCATGAGGAAACGA 59.303 47.619 0.00 0.00 44.51 3.85
3867 4588 4.850347 AGATAGATTTCCGGTAACCTCG 57.150 45.455 0.00 0.00 0.00 4.63
3874 4595 4.717280 ACTGAAGGAAGATAGATTTCCGGT 59.283 41.667 0.00 0.00 46.93 5.28
3875 4596 5.163405 TGACTGAAGGAAGATAGATTTCCGG 60.163 44.000 0.00 0.00 46.93 5.14
3876 4597 5.751028 GTGACTGAAGGAAGATAGATTTCCG 59.249 44.000 0.00 0.00 46.93 4.30
3918 4639 6.521133 GCAACTGAATAATGTGTCTTTCTTCG 59.479 38.462 0.00 0.00 0.00 3.79
3963 4684 4.729868 AGGTGAAATGGCATATTACCTCC 58.270 43.478 18.33 9.30 31.83 4.30
3986 4707 2.292267 AGAAAAGGCACACTGTCACTG 58.708 47.619 0.00 0.00 0.00 3.66
3990 4711 4.743493 TCAAAAAGAAAAGGCACACTGTC 58.257 39.130 0.00 0.00 0.00 3.51
3994 4715 4.268644 GCTTCTCAAAAAGAAAAGGCACAC 59.731 41.667 0.00 0.00 43.39 3.82
3998 4720 5.220662 GGTTTGCTTCTCAAAAAGAAAAGGC 60.221 40.000 0.00 0.00 45.35 4.35
4072 4798 3.631250 TGTCTGCCTTCCTTTCAAGTTT 58.369 40.909 0.00 0.00 0.00 2.66
4091 4817 8.611654 AACAAGTATATTGTACGGTTCTTTGT 57.388 30.769 0.00 0.00 31.50 2.83
4115 4848 8.474025 GGGTGGTCAATATCATATTTGTTGAAA 58.526 33.333 0.00 0.00 31.38 2.69
4219 4954 6.605594 ACCTCACAAGAAAAGGACAAACATTA 59.394 34.615 0.00 0.00 34.16 1.90
4393 5136 3.330267 GACTGTTCTCTTTGGCGAAGAT 58.670 45.455 17.32 1.69 43.23 2.40
4507 5517 5.479375 ACAGCTCATCCATTTCATTGAAAGT 59.521 36.000 16.34 3.42 34.92 2.66
4514 5524 5.163405 ACGTAGTACAGCTCATCCATTTCAT 60.163 40.000 0.38 0.00 41.94 2.57
4529 5539 4.450082 ACTGATCATGCAACGTAGTACA 57.550 40.909 0.00 0.00 45.00 2.90
4537 5547 9.065871 GTATAAAACTGAAACTGATCATGCAAC 57.934 33.333 0.00 0.00 0.00 4.17
4889 5986 3.181497 CCATGTTCTACAAAATCTGGCCG 60.181 47.826 0.00 0.00 0.00 6.13
4892 5989 6.573664 TGTTCCATGTTCTACAAAATCTGG 57.426 37.500 0.00 0.00 0.00 3.86
4904 6001 6.624423 ACTTTCTTATGCATGTTCCATGTTC 58.376 36.000 10.16 0.00 0.00 3.18
4950 6050 5.410439 TGCCATTTCTACCTTTTCGTCTTAC 59.590 40.000 0.00 0.00 0.00 2.34
4963 6063 5.125417 TGCAAGGAAATACTGCCATTTCTAC 59.875 40.000 12.52 1.85 42.22 2.59
4989 6089 7.323420 CACCTCACTCTTGTTATCAGTCATTA 58.677 38.462 0.00 0.00 0.00 1.90
5088 6188 5.952347 TGGGTAATTTGTACATGGCATGTAA 59.048 36.000 34.87 24.75 46.36 2.41
5130 6230 2.818130 ATGCTGCCGACAACATTTTT 57.182 40.000 0.00 0.00 27.97 1.94
5131 6231 3.255642 ACTTATGCTGCCGACAACATTTT 59.744 39.130 0.00 0.00 34.49 1.82
5132 6232 2.819608 ACTTATGCTGCCGACAACATTT 59.180 40.909 0.00 0.00 34.49 2.32
5133 6233 2.162208 CACTTATGCTGCCGACAACATT 59.838 45.455 0.00 0.00 34.49 2.71
5134 6234 1.739466 CACTTATGCTGCCGACAACAT 59.261 47.619 0.00 0.00 36.57 2.71
5135 6235 1.155889 CACTTATGCTGCCGACAACA 58.844 50.000 0.00 0.00 0.00 3.33
5181 6606 5.415701 TGGAGAAACCAATAAATCAGAGCAC 59.584 40.000 0.00 0.00 46.75 4.40
5216 6641 8.664798 TGTATTGAACCTTTCAGATAAATGACG 58.335 33.333 0.00 0.00 41.38 4.35
5443 6869 1.629043 AACCTCAGAGCAGTACGGAA 58.371 50.000 0.00 0.00 0.00 4.30
5551 7269 5.844004 TCTTCAACACCTTCTACTCTTCAC 58.156 41.667 0.00 0.00 0.00 3.18
5656 7375 2.367567 GGAACGGAGGGAGCATTATGTA 59.632 50.000 0.00 0.00 0.00 2.29
5658 7377 1.417890 AGGAACGGAGGGAGCATTATG 59.582 52.381 0.00 0.00 0.00 1.90
5659 7378 1.807814 AGGAACGGAGGGAGCATTAT 58.192 50.000 0.00 0.00 0.00 1.28
5660 7379 2.464796 TAGGAACGGAGGGAGCATTA 57.535 50.000 0.00 0.00 0.00 1.90
5661 7380 1.580059 TTAGGAACGGAGGGAGCATT 58.420 50.000 0.00 0.00 0.00 3.56
5664 7383 5.011840 ACTTATATTTAGGAACGGAGGGAGC 59.988 44.000 0.00 0.00 0.00 4.70
5665 7384 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
5667 7386 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
5668 7387 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
5685 7404 9.750125 GTCCATTTGAAATGTCTAAAAAGACTT 57.250 29.630 15.93 0.00 39.41 3.01
5686 7405 9.136323 AGTCCATTTGAAATGTCTAAAAAGACT 57.864 29.630 15.93 14.21 39.41 3.24
5691 7410 9.959749 GTTGTAGTCCATTTGAAATGTCTAAAA 57.040 29.630 15.93 14.59 0.00 1.52


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

AutoCloner maintained by Alex Coulton.