Multiple sequence alignment - TraesCS4A01G437000

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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 TraesCS4A01G437000 chr4A 100.000 6155 0 0 1 6155 706839859 706833705 0.000000e+00 11367.0
1 TraesCS4A01G437000 chr4A 94.553 2203 94 6 989 3181 706706649 706708835 0.000000e+00 3380.0
2 TraesCS4A01G437000 chr7A 93.899 4901 213 30 843 5686 23385953 23390824 0.000000e+00 7315.0
3 TraesCS4A01G437000 chr7A 94.483 2574 123 11 1050 3614 23523459 23520896 0.000000e+00 3949.0
4 TraesCS4A01G437000 chr7A 84.731 2266 299 30 1175 3415 23354751 23356994 0.000000e+00 2224.0
5 TraesCS4A01G437000 chr7A 82.746 284 22 13 780 1040 23523773 23523494 1.730000e-55 228.0
6 TraesCS4A01G437000 chr7A 86.087 115 7 4 594 708 23525645 23525540 1.400000e-21 115.0
7 TraesCS4A01G437000 chr7A 81.061 132 21 4 5361 5491 168877553 168877425 1.090000e-17 102.0
8 TraesCS4A01G437000 chr7A 100.000 30 0 0 3612 3641 23357128 23357157 8.620000e-04 56.5
9 TraesCS4A01G437000 chr7D 93.298 3059 154 25 843 3865 22943664 22946707 0.000000e+00 4466.0
10 TraesCS4A01G437000 chr7D 94.964 2800 123 11 1075 3863 22974896 22972104 0.000000e+00 4373.0
11 TraesCS4A01G437000 chr7D 95.236 2057 61 7 4130 6155 22946715 22948765 0.000000e+00 3221.0
12 TraesCS4A01G437000 chr7D 94.412 2058 76 8 4130 6155 22972094 22970044 0.000000e+00 3127.0
13 TraesCS4A01G437000 chr7D 84.835 2242 289 33 1187 3408 22904421 22906631 0.000000e+00 2209.0
14 TraesCS4A01G437000 chr7D 89.447 199 6 6 843 1040 22975080 22974896 2.870000e-58 237.0
15 TraesCS4A01G437000 chr7D 79.688 256 47 5 5238 5491 542887533 542887281 4.900000e-41 180.0
16 TraesCS4A01G437000 chr7D 77.743 319 46 17 4829 5128 542887996 542887684 8.200000e-39 172.0
17 TraesCS4A01G437000 chr7D 95.000 60 3 0 649 708 22979507 22979448 1.830000e-15 95.3
18 TraesCS4A01G437000 chr7D 97.917 48 1 0 841 888 22978218 22978171 3.950000e-12 84.2
19 TraesCS4A01G437000 chrUn 92.696 2615 137 22 1075 3654 89917648 89915053 0.000000e+00 3722.0
20 TraesCS4A01G437000 chrUn 92.696 2615 137 22 1075 3654 89979660 89982255 0.000000e+00 3722.0
21 TraesCS4A01G437000 chrUn 89.447 199 6 6 843 1040 89917832 89917648 2.870000e-58 237.0
22 TraesCS4A01G437000 chrUn 89.447 199 6 6 843 1040 89979476 89979660 2.870000e-58 237.0
23 TraesCS4A01G437000 chrUn 95.000 60 3 0 649 708 89925735 89925676 1.830000e-15 95.3
24 TraesCS4A01G437000 chr5A 85.867 2250 290 20 1175 3415 41953840 41956070 0.000000e+00 2368.0
25 TraesCS4A01G437000 chr5D 92.359 1649 105 11 1055 2689 361184116 361182475 0.000000e+00 2327.0
26 TraesCS4A01G437000 chr7B 97.512 603 10 5 1 598 249766473 249765871 0.000000e+00 1026.0
27 TraesCS4A01G437000 chr7B 97.479 595 11 4 1 591 592231984 592231390 0.000000e+00 1013.0
28 TraesCS4A01G437000 chr7B 78.599 257 47 7 5238 5491 585946387 585946136 4.940000e-36 163.0
29 TraesCS4A01G437000 chr6B 97.647 595 10 4 1 591 398364277 398364871 0.000000e+00 1018.0
30 TraesCS4A01G437000 chr4B 97.647 595 10 4 1 591 164291756 164291162 0.000000e+00 1018.0
31 TraesCS4A01G437000 chr4B 97.157 598 13 4 1 594 332902226 332901629 0.000000e+00 1007.0
32 TraesCS4A01G437000 chr3B 97.647 595 10 4 1 591 786985017 786985611 0.000000e+00 1018.0
33 TraesCS4A01G437000 chr3B 96.700 606 16 4 1 602 661720010 661720615 0.000000e+00 1005.0
34 TraesCS4A01G437000 chr3B 80.451 266 44 5 5228 5491 675558157 675558416 4.870000e-46 196.0
35 TraesCS4A01G437000 chr5B 97.479 595 11 4 1 591 25638855 25639449 0.000000e+00 1013.0
36 TraesCS4A01G437000 chr5B 97.157 598 13 4 1 594 484746129 484745532 0.000000e+00 1007.0
37 TraesCS4A01G437000 chr5B 78.082 219 19 12 4826 5034 663110785 663110586 1.810000e-20 111.0
38 TraesCS4A01G437000 chr3A 77.869 366 75 5 5134 5494 693154017 693153653 8.030000e-54 222.0
39 TraesCS4A01G437000 chr3D 78.840 293 58 4 5198 5488 579276200 579275910 1.750000e-45 195.0
40 TraesCS4A01G437000 chr2B 80.660 212 24 7 4825 5030 691040744 691040944 1.380000e-31 148.0
41 TraesCS4A01G437000 chr1D 87.778 90 8 2 4915 5002 216532386 216532474 1.090000e-17 102.0
42 TraesCS4A01G437000 chr1B 76.705 176 25 13 4909 5074 46172081 46171912 3.950000e-12 84.2
43 TraesCS4A01G437000 chr2A 75.796 157 28 9 5262 5414 14402607 14402457 3.080000e-08 71.3


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 TraesCS4A01G437000 chr4A 706833705 706839859 6154 True 11367.000000 11367 100.0000 1 6155 1 chr4A.!!$R1 6154
1 TraesCS4A01G437000 chr4A 706706649 706708835 2186 False 3380.000000 3380 94.5530 989 3181 1 chr4A.!!$F1 2192
2 TraesCS4A01G437000 chr7A 23385953 23390824 4871 False 7315.000000 7315 93.8990 843 5686 1 chr7A.!!$F1 4843
3 TraesCS4A01G437000 chr7A 23520896 23525645 4749 True 1430.666667 3949 87.7720 594 3614 3 chr7A.!!$R2 3020
4 TraesCS4A01G437000 chr7A 23354751 23357157 2406 False 1140.250000 2224 92.3655 1175 3641 2 chr7A.!!$F2 2466
5 TraesCS4A01G437000 chr7D 22943664 22948765 5101 False 3843.500000 4466 94.2670 843 6155 2 chr7D.!!$F2 5312
6 TraesCS4A01G437000 chr7D 22904421 22906631 2210 False 2209.000000 2209 84.8350 1187 3408 1 chr7D.!!$F1 2221
7 TraesCS4A01G437000 chr7D 22970044 22979507 9463 True 1583.300000 4373 94.3480 649 6155 5 chr7D.!!$R1 5506
8 TraesCS4A01G437000 chrUn 89915053 89917832 2779 True 1979.500000 3722 91.0715 843 3654 2 chrUn.!!$R2 2811
9 TraesCS4A01G437000 chrUn 89979476 89982255 2779 False 1979.500000 3722 91.0715 843 3654 2 chrUn.!!$F1 2811
10 TraesCS4A01G437000 chr5A 41953840 41956070 2230 False 2368.000000 2368 85.8670 1175 3415 1 chr5A.!!$F1 2240
11 TraesCS4A01G437000 chr5D 361182475 361184116 1641 True 2327.000000 2327 92.3590 1055 2689 1 chr5D.!!$R1 1634
12 TraesCS4A01G437000 chr7B 249765871 249766473 602 True 1026.000000 1026 97.5120 1 598 1 chr7B.!!$R1 597
13 TraesCS4A01G437000 chr7B 592231390 592231984 594 True 1013.000000 1013 97.4790 1 591 1 chr7B.!!$R3 590
14 TraesCS4A01G437000 chr6B 398364277 398364871 594 False 1018.000000 1018 97.6470 1 591 1 chr6B.!!$F1 590
15 TraesCS4A01G437000 chr4B 164291162 164291756 594 True 1018.000000 1018 97.6470 1 591 1 chr4B.!!$R1 590
16 TraesCS4A01G437000 chr4B 332901629 332902226 597 True 1007.000000 1007 97.1570 1 594 1 chr4B.!!$R2 593
17 TraesCS4A01G437000 chr3B 786985017 786985611 594 False 1018.000000 1018 97.6470 1 591 1 chr3B.!!$F3 590
18 TraesCS4A01G437000 chr3B 661720010 661720615 605 False 1005.000000 1005 96.7000 1 602 1 chr3B.!!$F1 601
19 TraesCS4A01G437000 chr5B 25638855 25639449 594 False 1013.000000 1013 97.4790 1 591 1 chr5B.!!$F1 590
20 TraesCS4A01G437000 chr5B 484745532 484746129 597 True 1007.000000 1007 97.1570 1 594 1 chr5B.!!$R1 593

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
965 6205 0.319383 CAGCTGCGCTAGATAGGTGG 60.319 60.0 9.73 0.0 36.40 4.61 F
1167 6489 0.234106 CTCTTGTCGCAACAGCACAG 59.766 55.0 0.00 0.0 36.57 3.66 F
1833 7162 0.961019 TCGCCGGCCGTTATATTACT 59.039 50.0 26.12 0.0 38.35 2.24 F
3740 9163 0.452987 CACGCATGCAGGCAAGTATT 59.547 50.0 24.53 0.0 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2714 8077 0.801872 TTCCATCAATCAACACGCCG 59.198 50.000 0.00 0.00 0.00 6.46 R
2799 8162 1.675310 CGGCCATTCCAGCTGACAA 60.675 57.895 17.39 7.98 39.03 3.18 R
3787 9210 0.319083 TCGACCACTTTACACGGCAT 59.681 50.000 0.00 0.00 0.00 4.40 R
5337 10791 0.541863 GGTTGTCAGGATGGGATCGT 59.458 55.000 0.00 0.00 36.16 3.73 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
528 532 2.574399 GTGTCCCTCGTCTCCTGC 59.426 66.667 0.00 0.00 0.00 4.85
591 596 1.234615 CCGCTGGTTTTGACACCGAT 61.235 55.000 0.00 0.00 40.09 4.18
618 623 4.929808 GCCCATACTCCAAATACAGATACG 59.070 45.833 0.00 0.00 0.00 3.06
619 624 5.510861 GCCCATACTCCAAATACAGATACGT 60.511 44.000 0.00 0.00 0.00 3.57
620 625 5.926542 CCCATACTCCAAATACAGATACGTG 59.073 44.000 0.00 0.00 0.00 4.49
624 629 4.036567 TCCAAATACAGATACGTGGTCG 57.963 45.455 0.00 0.00 43.34 4.79
625 630 2.538449 CCAAATACAGATACGTGGTCGC 59.462 50.000 0.00 0.00 41.18 5.19
626 631 2.503920 AATACAGATACGTGGTCGCC 57.496 50.000 0.00 0.00 41.18 5.54
627 632 1.395635 ATACAGATACGTGGTCGCCA 58.604 50.000 0.00 0.00 41.18 5.69
628 633 0.736636 TACAGATACGTGGTCGCCAG 59.263 55.000 0.00 0.00 41.18 4.85
629 634 1.878522 CAGATACGTGGTCGCCAGC 60.879 63.158 0.00 0.00 41.18 4.85
630 635 2.183300 GATACGTGGTCGCCAGCA 59.817 61.111 0.00 0.00 41.18 4.41
631 636 2.125673 ATACGTGGTCGCCAGCAC 60.126 61.111 3.34 3.34 45.94 4.40
696 701 2.740826 GTCGCCAGCACGCCTTTA 60.741 61.111 0.00 0.00 0.00 1.85
712 717 3.458189 CCTTTAAGAGGCAGGTGTATCG 58.542 50.000 0.00 0.00 39.09 2.92
715 720 1.853963 AAGAGGCAGGTGTATCGTCT 58.146 50.000 0.00 0.00 0.00 4.18
716 721 1.394618 AGAGGCAGGTGTATCGTCTC 58.605 55.000 0.00 0.00 0.00 3.36
718 723 2.172930 AGAGGCAGGTGTATCGTCTCTA 59.827 50.000 0.00 0.00 0.00 2.43
719 724 2.550606 GAGGCAGGTGTATCGTCTCTAG 59.449 54.545 0.00 0.00 0.00 2.43
720 725 1.001158 GGCAGGTGTATCGTCTCTAGC 60.001 57.143 0.00 0.00 0.00 3.42
722 727 1.609555 CAGGTGTATCGTCTCTAGCCC 59.390 57.143 0.00 0.00 0.00 5.19
723 728 0.960286 GGTGTATCGTCTCTAGCCCC 59.040 60.000 0.00 0.00 0.00 5.80
724 729 1.688772 GTGTATCGTCTCTAGCCCCA 58.311 55.000 0.00 0.00 0.00 4.96
725 730 2.240279 GTGTATCGTCTCTAGCCCCAT 58.760 52.381 0.00 0.00 0.00 4.00
727 732 3.069729 GTGTATCGTCTCTAGCCCCATTT 59.930 47.826 0.00 0.00 0.00 2.32
728 733 4.280174 GTGTATCGTCTCTAGCCCCATTTA 59.720 45.833 0.00 0.00 0.00 1.40
730 735 5.542635 TGTATCGTCTCTAGCCCCATTTAAT 59.457 40.000 0.00 0.00 0.00 1.40
731 736 5.568620 ATCGTCTCTAGCCCCATTTAATT 57.431 39.130 0.00 0.00 0.00 1.40
732 737 5.367945 TCGTCTCTAGCCCCATTTAATTT 57.632 39.130 0.00 0.00 0.00 1.82
734 739 6.285990 TCGTCTCTAGCCCCATTTAATTTAC 58.714 40.000 0.00 0.00 0.00 2.01
735 740 6.053005 CGTCTCTAGCCCCATTTAATTTACA 58.947 40.000 0.00 0.00 0.00 2.41
736 741 6.540914 CGTCTCTAGCCCCATTTAATTTACAA 59.459 38.462 0.00 0.00 0.00 2.41
737 742 7.228706 CGTCTCTAGCCCCATTTAATTTACAAT 59.771 37.037 0.00 0.00 0.00 2.71
739 744 7.724061 TCTCTAGCCCCATTTAATTTACAATCC 59.276 37.037 0.00 0.00 0.00 3.01
740 745 7.591821 TCTAGCCCCATTTAATTTACAATCCT 58.408 34.615 0.00 0.00 0.00 3.24
741 746 6.731292 AGCCCCATTTAATTTACAATCCTC 57.269 37.500 0.00 0.00 0.00 3.71
742 747 5.301805 AGCCCCATTTAATTTACAATCCTCG 59.698 40.000 0.00 0.00 0.00 4.63
746 1768 7.309194 CCCCATTTAATTTACAATCCTCGGATC 60.309 40.741 0.00 0.00 33.08 3.36
756 1778 6.627087 ACAATCCTCGGATCCATATGTATT 57.373 37.500 13.41 0.64 33.08 1.89
763 1785 7.619698 TCCTCGGATCCATATGTATTTAGACAT 59.380 37.037 13.41 0.00 42.68 3.06
764 1786 8.260818 CCTCGGATCCATATGTATTTAGACATT 58.739 37.037 13.41 0.00 40.54 2.71
800 2818 0.961753 GCAAAAGACCTGACTTGGGG 59.038 55.000 0.00 0.00 0.00 4.96
846 2950 1.588932 CGCTGGCGTCGTATGTGAT 60.589 57.895 6.83 0.00 34.35 3.06
894 2998 3.889520 GGAGGTGTCCGAGTAAGATTT 57.110 47.619 0.00 0.00 31.37 2.17
937 6177 2.746362 CCGAGTCGTGGTTTACTACTCT 59.254 50.000 12.31 0.00 45.22 3.24
938 6178 3.935203 CCGAGTCGTGGTTTACTACTCTA 59.065 47.826 12.31 0.00 45.22 2.43
965 6205 0.319383 CAGCTGCGCTAGATAGGTGG 60.319 60.000 9.73 0.00 36.40 4.61
974 6214 7.337184 GCTGCGCTAGATAGGTGGATATATATA 59.663 40.741 9.73 0.00 0.00 0.86
1043 6313 5.947503 CGTAGCAGAGAAATCAGAAAGAG 57.052 43.478 0.00 0.00 0.00 2.85
1044 6314 5.645624 CGTAGCAGAGAAATCAGAAAGAGA 58.354 41.667 0.00 0.00 0.00 3.10
1045 6315 6.096036 CGTAGCAGAGAAATCAGAAAGAGAA 58.904 40.000 0.00 0.00 0.00 2.87
1046 6316 6.253298 CGTAGCAGAGAAATCAGAAAGAGAAG 59.747 42.308 0.00 0.00 0.00 2.85
1047 6317 6.357579 AGCAGAGAAATCAGAAAGAGAAGA 57.642 37.500 0.00 0.00 0.00 2.87
1048 6318 6.400568 AGCAGAGAAATCAGAAAGAGAAGAG 58.599 40.000 0.00 0.00 0.00 2.85
1164 6486 2.253758 GCCTCTTGTCGCAACAGCA 61.254 57.895 0.00 0.00 36.57 4.41
1167 6489 0.234106 CTCTTGTCGCAACAGCACAG 59.766 55.000 0.00 0.00 36.57 3.66
1833 7162 0.961019 TCGCCGGCCGTTATATTACT 59.039 50.000 26.12 0.00 38.35 2.24
2101 7449 8.537728 AATTCACATTTCCTGGCTAATAATCA 57.462 30.769 0.00 0.00 0.00 2.57
2105 7453 9.639563 TCACATTTCCTGGCTAATAATCAAATA 57.360 29.630 0.00 0.00 0.00 1.40
2294 7651 2.362397 TGAAGCGGTTAATTTGGTTGCA 59.638 40.909 0.00 0.00 0.00 4.08
2319 7676 1.185618 AGTGCTGCGTTCTAGGGTCA 61.186 55.000 0.00 0.00 0.00 4.02
2427 7784 1.939934 CCGAGAAGCTGTTTGACAACA 59.060 47.619 0.00 0.00 40.82 3.33
2439 7796 5.860641 TGTTTGACAACAAGAAGACGTTAC 58.139 37.500 0.00 0.00 40.10 2.50
2461 7818 3.411446 TCCGCTTTGACATGTCTGAATT 58.589 40.909 25.55 0.00 0.00 2.17
2550 7911 4.759693 TGCACACGTATTTCTTTCCTGAAT 59.240 37.500 0.00 0.00 0.00 2.57
2564 7925 4.581309 TCCTGAATTTCCTTCTCATGCT 57.419 40.909 0.00 0.00 34.75 3.79
2646 8009 2.969950 AGGAGCCAACCATATAGCGTTA 59.030 45.455 0.00 0.00 0.00 3.18
2714 8077 4.377839 TCTCATTCAACTCCTCGATGAC 57.622 45.455 0.00 0.00 0.00 3.06
2799 8162 5.596836 CTCAAATCTAGGAGCAGAGAACT 57.403 43.478 0.00 0.00 0.00 3.01
2934 8299 5.912892 TCGACATATTTACCTGATCTTGCA 58.087 37.500 0.00 0.00 0.00 4.08
3433 8824 1.593750 CAGTCGAGGCCAGCTATGC 60.594 63.158 5.01 0.00 0.00 3.14
3508 8899 2.813754 TGATTAGTCACCAAGCACTTGC 59.186 45.455 4.82 0.00 39.16 4.01
3522 8913 2.155155 GCACTTGCTGTTCGTACTGTAC 59.845 50.000 7.90 7.90 38.21 2.90
3526 8925 5.631929 CACTTGCTGTTCGTACTGTACATTA 59.368 40.000 17.35 0.00 0.00 1.90
3714 9137 1.567357 ATTAAACCCCGCTGCCAAAT 58.433 45.000 0.00 0.00 0.00 2.32
3740 9163 0.452987 CACGCATGCAGGCAAGTATT 59.547 50.000 24.53 0.00 0.00 1.89
3787 9210 1.354031 TCCATTTTGGCCAGCTCAGTA 59.646 47.619 5.11 0.00 37.47 2.74
3814 9237 5.349270 CCGTGTAAAGTGGTCGAATTTCATA 59.651 40.000 0.00 0.00 0.00 2.15
3866 9289 7.812648 TGTCCCGAAATATAAGAGTGTTTTTG 58.187 34.615 0.00 0.00 0.00 2.44
3900 9323 6.787225 ACAAAACTTGTCACGCTACAAAATA 58.213 32.000 4.90 0.00 40.56 1.40
3974 9397 0.817654 ATTCCACTCTCGTCATCGCA 59.182 50.000 0.00 0.00 36.96 5.10
4042 9465 3.011708 TCCCTCCATCTATCCATCGATCA 59.988 47.826 0.00 0.00 0.00 2.92
4053 9476 2.296190 TCCATCGATCAATCTACACCGG 59.704 50.000 0.00 0.00 0.00 5.28
4057 9480 2.756207 TCGATCAATCTACACCGGTGAA 59.244 45.455 40.21 24.11 0.00 3.18
4070 9493 1.212455 CGGTGAAAAGGCAAAACGGC 61.212 55.000 0.00 0.00 41.61 5.68
4071 9494 0.179097 GGTGAAAAGGCAAAACGGCA 60.179 50.000 0.00 0.00 44.47 5.69
4078 9501 2.256461 GCAAAACGGCAGCTCTGG 59.744 61.111 0.00 0.00 0.00 3.86
4095 9518 2.039216 TCTGGCCGGAGTAAACATTTCA 59.961 45.455 11.27 0.00 0.00 2.69
4136 9559 5.245301 GGTTTTGGATAAAGGGCACTACTTT 59.755 40.000 0.00 0.00 40.87 2.66
4172 9595 5.427481 AGGCCCACTAGTGCTAAATTTAGTA 59.573 40.000 22.94 17.61 33.32 1.82
4373 9796 7.097192 TGTTATGTACTCCAGAATGTTCAGTC 58.903 38.462 0.00 0.00 0.00 3.51
4682 10108 3.411446 CTCTTTAGTGTGGTGAATGCCA 58.589 45.455 0.00 0.00 35.93 4.92
4766 10213 5.760253 AGTAGAAGCATATTGGTGTGCATAC 59.240 40.000 4.79 4.79 44.06 2.39
4813 10260 5.938710 TGAGTACTTGTCTGTCTAGTGTAGG 59.061 44.000 0.00 0.00 34.37 3.18
4949 10402 2.324541 AGTTGAGCAGAGTTGAGACCT 58.675 47.619 0.00 0.00 0.00 3.85
5002 10456 3.088532 GAGAGCTTGAGAAGAGGAGTGA 58.911 50.000 0.00 0.00 0.00 3.41
5196 10650 0.392998 GGACCATGGACTGTTCGCAT 60.393 55.000 21.47 0.00 0.00 4.73
5282 10736 0.250038 GCAGCCAAGACACTCACTCA 60.250 55.000 0.00 0.00 0.00 3.41
5286 10740 1.069204 GCCAAGACACTCACTCACTCA 59.931 52.381 0.00 0.00 0.00 3.41
5303 10757 1.750399 CATTGCGCAACCCTAGCCT 60.750 57.895 27.64 3.42 0.00 4.58
5337 10791 1.004560 CTCACTTTGCTGCCTCCGA 60.005 57.895 0.00 0.00 0.00 4.55
5434 10888 4.399618 CCTTCTCGAGAGAAAGGTGATACA 59.600 45.833 19.51 0.00 45.75 2.29
5537 10993 4.354387 TGGGTGGGTTTTTAGATAGTTGGA 59.646 41.667 0.00 0.00 0.00 3.53
5722 11178 1.689243 GCTGGCCAATGGGGAAATCC 61.689 60.000 7.01 0.00 40.01 3.01
5811 11267 7.606456 GGAAGTTATCACACTGATCAACCTTTA 59.394 37.037 0.00 0.00 38.26 1.85
5829 11285 8.304596 CAACCTTTAAAACCCTAAATCCTTCTC 58.695 37.037 0.00 0.00 0.00 2.87
5846 11302 3.383698 TCTCTCGGGGAAGTTATCACT 57.616 47.619 0.00 0.00 33.11 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
528 532 1.286260 GCGTCTAGGCGGATGGTAG 59.714 63.158 19.86 0.00 0.00 3.18
591 596 4.966168 TCTGTATTTGGAGTATGGGCACTA 59.034 41.667 0.00 0.00 0.00 2.74
624 629 3.741476 CCAGAAAGGCGTGCTGGC 61.741 66.667 14.86 0.00 42.30 4.85
626 631 1.597854 TGACCAGAAAGGCGTGCTG 60.598 57.895 0.81 0.81 43.14 4.41
627 632 1.598130 GTGACCAGAAAGGCGTGCT 60.598 57.895 0.00 0.00 43.14 4.40
628 633 1.166531 AAGTGACCAGAAAGGCGTGC 61.167 55.000 0.00 0.00 43.14 5.34
629 634 0.868406 GAAGTGACCAGAAAGGCGTG 59.132 55.000 0.00 0.00 43.14 5.34
630 635 0.250338 GGAAGTGACCAGAAAGGCGT 60.250 55.000 0.00 0.00 43.14 5.68
631 636 0.955919 GGGAAGTGACCAGAAAGGCG 60.956 60.000 0.00 0.00 43.14 5.52
632 637 0.402121 AGGGAAGTGACCAGAAAGGC 59.598 55.000 0.00 0.00 43.14 4.35
633 638 2.373502 AGAAGGGAAGTGACCAGAAAGG 59.626 50.000 0.00 0.00 45.67 3.11
634 639 3.778954 AGAAGGGAAGTGACCAGAAAG 57.221 47.619 0.00 0.00 0.00 2.62
693 698 3.767673 AGACGATACACCTGCCTCTTAAA 59.232 43.478 0.00 0.00 0.00 1.52
696 701 1.751924 GAGACGATACACCTGCCTCTT 59.248 52.381 0.00 0.00 0.00 2.85
708 713 6.681729 AATTAAATGGGGCTAGAGACGATA 57.318 37.500 0.00 0.00 0.00 2.92
709 714 5.568620 AATTAAATGGGGCTAGAGACGAT 57.431 39.130 0.00 0.00 0.00 3.73
710 715 5.367945 AAATTAAATGGGGCTAGAGACGA 57.632 39.130 0.00 0.00 0.00 4.20
711 716 6.053005 TGTAAATTAAATGGGGCTAGAGACG 58.947 40.000 0.00 0.00 0.00 4.18
712 717 7.875327 TTGTAAATTAAATGGGGCTAGAGAC 57.125 36.000 0.00 0.00 0.00 3.36
715 720 7.591821 AGGATTGTAAATTAAATGGGGCTAGA 58.408 34.615 0.00 0.00 0.00 2.43
716 721 7.308589 CGAGGATTGTAAATTAAATGGGGCTAG 60.309 40.741 0.00 0.00 0.00 3.42
718 723 5.301805 CGAGGATTGTAAATTAAATGGGGCT 59.698 40.000 0.00 0.00 0.00 5.19
719 724 5.508994 CCGAGGATTGTAAATTAAATGGGGC 60.509 44.000 0.00 0.00 0.00 5.80
720 725 5.830991 TCCGAGGATTGTAAATTAAATGGGG 59.169 40.000 0.00 0.00 0.00 4.96
722 727 7.230510 TGGATCCGAGGATTGTAAATTAAATGG 59.769 37.037 7.39 0.00 34.60 3.16
723 728 8.165239 TGGATCCGAGGATTGTAAATTAAATG 57.835 34.615 7.39 0.00 34.60 2.32
724 729 8.940397 ATGGATCCGAGGATTGTAAATTAAAT 57.060 30.769 7.39 0.00 34.60 1.40
727 732 8.602424 ACATATGGATCCGAGGATTGTAAATTA 58.398 33.333 7.39 0.00 34.60 1.40
728 733 7.461749 ACATATGGATCCGAGGATTGTAAATT 58.538 34.615 7.39 0.00 34.60 1.82
730 735 6.433847 ACATATGGATCCGAGGATTGTAAA 57.566 37.500 7.39 0.00 34.60 2.01
731 736 7.733773 ATACATATGGATCCGAGGATTGTAA 57.266 36.000 7.39 1.03 34.60 2.41
732 737 7.733773 AATACATATGGATCCGAGGATTGTA 57.266 36.000 7.39 13.04 34.60 2.41
734 739 8.478066 TCTAAATACATATGGATCCGAGGATTG 58.522 37.037 7.39 2.94 34.60 2.67
735 740 8.478877 GTCTAAATACATATGGATCCGAGGATT 58.521 37.037 7.39 2.37 34.60 3.01
736 741 7.619698 TGTCTAAATACATATGGATCCGAGGAT 59.380 37.037 7.39 3.97 37.59 3.24
737 742 6.951778 TGTCTAAATACATATGGATCCGAGGA 59.048 38.462 7.39 0.00 0.00 3.71
769 1791 1.126846 GTCTTTTGCCAGACGATCACG 59.873 52.381 0.00 0.00 45.75 4.35
773 1795 1.347707 TCAGGTCTTTTGCCAGACGAT 59.652 47.619 0.00 0.00 43.78 3.73
774 1796 0.756294 TCAGGTCTTTTGCCAGACGA 59.244 50.000 0.00 0.00 43.78 4.20
776 1798 2.262423 AGTCAGGTCTTTTGCCAGAC 57.738 50.000 0.00 0.00 42.34 3.51
777 1799 2.575532 CAAGTCAGGTCTTTTGCCAGA 58.424 47.619 0.00 0.00 0.00 3.86
800 2818 2.743928 CAGACGAACCAGCCCAGC 60.744 66.667 0.00 0.00 0.00 4.85
846 2950 1.101635 CGTCCGATCTGGGCTCACTA 61.102 60.000 6.63 0.00 41.63 2.74
888 2992 4.699257 GGACTCAGATCAAGCACAAATCTT 59.301 41.667 0.00 0.00 0.00 2.40
889 2993 4.260170 GGACTCAGATCAAGCACAAATCT 58.740 43.478 0.00 0.00 0.00 2.40
891 2995 4.025040 TGGACTCAGATCAAGCACAAAT 57.975 40.909 0.00 0.00 0.00 2.32
894 2998 2.568509 TGATGGACTCAGATCAAGCACA 59.431 45.455 0.00 0.00 0.00 4.57
965 6205 7.834881 TCAAGGGGACGTGGATATATATATC 57.165 40.000 20.32 20.32 40.50 1.63
974 6214 0.322546 GCTTTCAAGGGGACGTGGAT 60.323 55.000 0.00 0.00 40.50 3.41
1040 6310 7.020827 TCTCTTCTCTTCTCTTCTCTTCTCT 57.979 40.000 0.00 0.00 0.00 3.10
1041 6311 7.607991 TCTTCTCTTCTCTTCTCTTCTCTTCTC 59.392 40.741 0.00 0.00 0.00 2.87
1042 6312 7.461749 TCTTCTCTTCTCTTCTCTTCTCTTCT 58.538 38.462 0.00 0.00 0.00 2.85
1043 6313 7.607991 TCTCTTCTCTTCTCTTCTCTTCTCTTC 59.392 40.741 0.00 0.00 0.00 2.87
1044 6314 7.461749 TCTCTTCTCTTCTCTTCTCTTCTCTT 58.538 38.462 0.00 0.00 0.00 2.85
1045 6315 7.020827 TCTCTTCTCTTCTCTTCTCTTCTCT 57.979 40.000 0.00 0.00 0.00 3.10
1046 6316 7.106239 TCTCTCTTCTCTTCTCTTCTCTTCTC 58.894 42.308 0.00 0.00 0.00 2.87
1047 6317 7.020827 TCTCTCTTCTCTTCTCTTCTCTTCT 57.979 40.000 0.00 0.00 0.00 2.85
1048 6318 7.607991 TCTTCTCTCTTCTCTTCTCTTCTCTTC 59.392 40.741 0.00 0.00 0.00 2.87
1164 6486 4.021925 GCGTGGAGAAGGGCCTGT 62.022 66.667 6.92 0.00 0.00 4.00
1210 6538 4.880426 ATGACGGGATCGGGGGCT 62.880 66.667 0.00 0.00 41.39 5.19
1241 6569 1.575244 CAGATGATGCGGTCGATGTT 58.425 50.000 0.00 0.00 0.00 2.71
1833 7162 6.183360 GCACAAATCTTATCATGAACGTACCA 60.183 38.462 0.00 0.00 0.00 3.25
2009 7357 6.437928 TGCATTTACAGTGCTAGTTTTCTTG 58.562 36.000 0.00 0.00 42.92 3.02
2105 7453 8.321353 TGAAACAAATGGACACTACTCATAGAT 58.679 33.333 0.00 0.00 32.23 1.98
2107 7455 7.905604 TGAAACAAATGGACACTACTCATAG 57.094 36.000 0.00 0.00 34.25 2.23
2294 7651 2.408050 CTAGAACGCAGCACTTCTTGT 58.592 47.619 7.49 0.00 0.00 3.16
2319 7676 3.950395 GGTTGGCTAGATTGATCAAAGCT 59.050 43.478 23.24 19.52 37.85 3.74
2375 7732 1.151668 CAAGCTCTGTCTTCCCAACG 58.848 55.000 0.00 0.00 0.00 4.10
2427 7784 3.057734 CAAAGCGGAGTAACGTCTTCTT 58.942 45.455 0.00 0.00 35.98 2.52
2439 7796 2.084610 TCAGACATGTCAAAGCGGAG 57.915 50.000 27.02 6.87 0.00 4.63
2550 7911 5.047802 GGAAATGTGAAGCATGAGAAGGAAA 60.048 40.000 0.00 0.00 37.96 3.13
2564 7925 7.345422 TCAGAAAGTCAAATGGAAATGTGAA 57.655 32.000 0.00 0.00 0.00 3.18
2646 8009 2.178912 TCCGCCTCGTCAAAAAGAAT 57.821 45.000 0.00 0.00 0.00 2.40
2714 8077 0.801872 TTCCATCAATCAACACGCCG 59.198 50.000 0.00 0.00 0.00 6.46
2799 8162 1.675310 CGGCCATTCCAGCTGACAA 60.675 57.895 17.39 7.98 39.03 3.18
2934 8299 2.702592 TGAACCGTTTCTCAACCTGT 57.297 45.000 0.00 0.00 32.36 4.00
3306 8688 2.089980 GCATGCTTCTCCACTGACAAT 58.910 47.619 11.37 0.00 0.00 2.71
3313 8695 1.941999 GCCTTGGCATGCTTCTCCAC 61.942 60.000 18.92 0.00 0.00 4.02
3440 8831 4.228097 CTATGCAGCGCACACGGC 62.228 66.667 11.47 5.57 43.04 5.68
3441 8832 3.566853 CCTATGCAGCGCACACGG 61.567 66.667 11.47 8.13 43.04 4.94
3549 8948 3.565482 TCTCACAAACCTGCAAGCTTTAG 59.435 43.478 0.00 0.00 0.00 1.85
3714 9137 1.517361 CCTGCATGCGTGGTCTCTA 59.483 57.895 14.09 0.00 0.00 2.43
3740 9163 3.304726 GCGGTGTCTATCTGAATCATCGA 60.305 47.826 10.00 0.00 35.10 3.59
3787 9210 0.319083 TCGACCACTTTACACGGCAT 59.681 50.000 0.00 0.00 0.00 4.40
3814 9237 3.343617 AGTACTTTACAATGGCGTGCAT 58.656 40.909 0.00 0.00 0.00 3.96
3866 9289 4.917415 GTGACAAGTTTTGTACATGGATGC 59.083 41.667 0.00 0.00 45.52 3.91
3900 9323 3.812609 GGGCATTTTTGGAAACGAACAAT 59.187 39.130 0.00 0.00 31.96 2.71
3974 9397 4.107072 TGGAGAGATGGAGTGAAGGAAAT 58.893 43.478 0.00 0.00 0.00 2.17
4042 9465 2.224670 TGCCTTTTCACCGGTGTAGATT 60.225 45.455 32.74 0.00 0.00 2.40
4053 9476 1.208259 CTGCCGTTTTGCCTTTTCAC 58.792 50.000 0.00 0.00 0.00 3.18
4057 9480 1.109323 AGAGCTGCCGTTTTGCCTTT 61.109 50.000 0.00 0.00 0.00 3.11
4070 9493 0.741221 GTTTACTCCGGCCAGAGCTG 60.741 60.000 16.28 0.00 45.69 4.24
4071 9494 1.192146 TGTTTACTCCGGCCAGAGCT 61.192 55.000 16.28 6.14 37.39 4.09
4078 9501 3.335579 ACTCTGAAATGTTTACTCCGGC 58.664 45.455 0.00 0.00 0.00 6.13
4095 9518 4.423625 AAACCAAACTGCAGTCTACTCT 57.576 40.909 21.95 0.00 0.00 3.24
4136 9559 2.481441 AGTGGGCCTATGATCACAAGA 58.519 47.619 4.53 0.00 33.01 3.02
4172 9595 2.105134 TCCTACCATCACAAACCACGTT 59.895 45.455 0.00 0.00 0.00 3.99
4252 9675 4.496895 CGTTGCAGAAAGTTCAGAAAACAG 59.503 41.667 0.00 0.00 0.00 3.16
4481 9904 8.877779 CCTGAATTGACTACTCTGAACATTTAG 58.122 37.037 0.00 0.00 0.00 1.85
4531 9957 7.567458 TCCAATCACATGAATCATCTCTACAA 58.433 34.615 0.00 0.00 0.00 2.41
4682 10108 7.615365 TCCACTAAATGTTCATTTGGATTAGCT 59.385 33.333 21.92 0.00 0.00 3.32
4813 10260 8.038944 TCTATAATTCAACACTCACAACCTACC 58.961 37.037 0.00 0.00 0.00 3.18
4949 10402 4.032310 TGGTAGAACCGCCCTTATAAAGA 58.968 43.478 0.00 0.00 42.58 2.52
4962 10416 4.832248 TCTCAATGACATGTGGTAGAACC 58.168 43.478 1.15 0.00 39.22 3.62
4964 10418 4.223700 AGCTCTCAATGACATGTGGTAGAA 59.776 41.667 1.15 0.00 0.00 2.10
5002 10456 2.491022 GGAGGAGGAGCGCGTGTAT 61.491 63.158 8.43 0.00 0.00 2.29
5048 10502 1.909986 TCATTCCCATAACCCGTGACA 59.090 47.619 0.00 0.00 0.00 3.58
5130 10584 9.515226 TTCTGTTAGCAACTCATTAATTAACCT 57.485 29.630 0.00 0.00 0.00 3.50
5196 10650 1.410004 CTTAGGCCCATGACCGAGTA 58.590 55.000 0.00 0.00 0.00 2.59
5282 10736 1.026718 GCTAGGGTTGCGCAATGAGT 61.027 55.000 27.79 13.70 0.00 3.41
5286 10740 1.452108 GAGGCTAGGGTTGCGCAAT 60.452 57.895 27.79 13.36 0.00 3.56
5303 10757 4.271807 AGTGAGAGGAATAGTGGATGGA 57.728 45.455 0.00 0.00 0.00 3.41
5337 10791 0.541863 GGTTGTCAGGATGGGATCGT 59.458 55.000 0.00 0.00 36.16 3.73
5425 10879 3.814316 GCTCCCCAAAAACTGTATCACCT 60.814 47.826 0.00 0.00 0.00 4.00
5434 10888 2.800250 CTGAGATGCTCCCCAAAAACT 58.200 47.619 0.00 0.00 0.00 2.66
5521 10977 7.939784 ATCCAAGGTCCAACTATCTAAAAAC 57.060 36.000 0.00 0.00 0.00 2.43
5537 10993 4.902448 GTCCTCTGGTCTTATATCCAAGGT 59.098 45.833 0.00 0.00 35.53 3.50
5722 11178 2.486203 CGAGACTTCCTCATCCCGATAG 59.514 54.545 0.00 0.00 42.06 2.08
5811 11267 4.324331 CCCGAGAGAAGGATTTAGGGTTTT 60.324 45.833 0.00 0.00 33.22 2.43
5829 11285 3.024547 TCAGAGTGATAACTTCCCCGAG 58.975 50.000 0.00 0.00 0.00 4.63
5879 11335 3.057548 CTTGCCTGCGGTGCATCA 61.058 61.111 9.15 0.00 38.13 3.07
6046 11502 5.775195 TCGATCTGGTCCATCATAGTTATGT 59.225 40.000 0.00 0.00 35.26 2.29


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

AutoCloner maintained by Alex Coulton.