Multiple sequence alignment - TraesCS3D01G160600

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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 TraesCS3D01G160600 chr3D 100.000 4223 0 0 1 4223 131348333 131352555 0.000000e+00 7799
1 TraesCS3D01G160600 chr3D 99.172 604 4 1 131 733 521590662 521591265 0.000000e+00 1086
2 TraesCS3D01G160600 chr3B 92.653 2627 102 43 740 3342 187800566 187803125 0.000000e+00 3698
3 TraesCS3D01G160600 chr3B 93.165 834 36 11 3406 4223 187803213 187804041 0.000000e+00 1205
4 TraesCS3D01G160600 chr3B 93.519 108 7 0 3 110 187800449 187800556 1.220000e-35 161
5 TraesCS3D01G160600 chr3A 91.593 2724 101 46 726 3403 144149387 144152028 0.000000e+00 3644
6 TraesCS3D01G160600 chr3A 89.294 850 51 20 3406 4223 144152072 144152913 0.000000e+00 1029
7 TraesCS3D01G160600 chr3A 92.647 136 7 1 1 133 144149267 144149402 4.310000e-45 193
8 TraesCS3D01G160600 chr4D 98.671 602 7 1 129 729 221285318 221284717 0.000000e+00 1066
9 TraesCS3D01G160600 chr4D 97.338 601 15 1 131 730 386936735 386936135 0.000000e+00 1020
10 TraesCS3D01G160600 chr2A 93.984 615 36 1 121 734 101841768 101842382 0.000000e+00 929
11 TraesCS3D01G160600 chr2A 94.380 605 31 3 137 739 699841234 699841837 0.000000e+00 926
12 TraesCS3D01G160600 chr7B 94.343 601 31 3 131 730 138036096 138036694 0.000000e+00 918
13 TraesCS3D01G160600 chr2B 94.176 601 30 5 131 729 131288589 131287992 0.000000e+00 911
14 TraesCS3D01G160600 chr7D 93.854 602 35 2 130 730 165112921 165113521 0.000000e+00 905
15 TraesCS3D01G160600 chr5B 93.990 599 34 2 131 728 282847114 282846517 0.000000e+00 905


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 TraesCS3D01G160600 chr3D 131348333 131352555 4222 False 7799 7799 100.000000 1 4223 1 chr3D.!!$F1 4222
1 TraesCS3D01G160600 chr3D 521590662 521591265 603 False 1086 1086 99.172000 131 733 1 chr3D.!!$F2 602
2 TraesCS3D01G160600 chr3B 187800449 187804041 3592 False 1688 3698 93.112333 3 4223 3 chr3B.!!$F1 4220
3 TraesCS3D01G160600 chr3A 144149267 144152913 3646 False 1622 3644 91.178000 1 4223 3 chr3A.!!$F1 4222
4 TraesCS3D01G160600 chr4D 221284717 221285318 601 True 1066 1066 98.671000 129 729 1 chr4D.!!$R1 600
5 TraesCS3D01G160600 chr4D 386936135 386936735 600 True 1020 1020 97.338000 131 730 1 chr4D.!!$R2 599
6 TraesCS3D01G160600 chr2A 101841768 101842382 614 False 929 929 93.984000 121 734 1 chr2A.!!$F1 613
7 TraesCS3D01G160600 chr2A 699841234 699841837 603 False 926 926 94.380000 137 739 1 chr2A.!!$F2 602
8 TraesCS3D01G160600 chr7B 138036096 138036694 598 False 918 918 94.343000 131 730 1 chr7B.!!$F1 599
9 TraesCS3D01G160600 chr2B 131287992 131288589 597 True 911 911 94.176000 131 729 1 chr2B.!!$R1 598
10 TraesCS3D01G160600 chr7D 165112921 165113521 600 False 905 905 93.854000 130 730 1 chr7D.!!$F1 600
11 TraesCS3D01G160600 chr5B 282846517 282847114 597 True 905 905 93.990000 131 728 1 chr5B.!!$R1 597

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
833 846 0.036875 CCTCTGTGTTCCCACTTCCC 59.963 60.0 0.00 0.00 42.34 3.97 F
844 857 0.106719 CCACTTCCCACCCGCATTAT 60.107 55.0 0.00 0.00 0.00 1.28 F
1768 1809 0.250901 ACACGCTCATCAAGGGCTTT 60.251 50.0 0.00 0.00 41.54 3.51 F
2302 2344 0.803117 AGCTCACGAAACTCGATCGA 59.197 50.0 18.32 18.32 43.74 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 1680 0.250234 CGAAGGAGTTGATGAGGGCA 59.750 55.0 0.0 0.0 0.00 5.36 R
2341 2383 0.460987 CCGAGAACCTGCACCTCATC 60.461 60.0 0.0 0.0 0.00 2.92 R
3135 3189 0.171231 GATTCCTGCAAAAGCCCGAC 59.829 55.0 0.0 0.0 0.00 4.79 R
3347 3410 0.173481 CTGAATCGAGTTCCTGGCGA 59.827 55.0 0.0 0.0 35.91 5.54 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
61 62 2.937959 ATCTCGCCCTCCTCCTCCAC 62.938 65.000 0.00 0.00 0.00 4.02
72 76 3.007920 CCTCCACTCTGCTGGCCT 61.008 66.667 3.32 0.00 0.00 5.19
127 131 2.359230 GTGCTCACCTCACCTGCC 60.359 66.667 0.00 0.00 0.00 4.85
784 797 4.560108 GCAGATTGTTTTGCCAAGTGAGAT 60.560 41.667 0.00 0.00 34.28 2.75
785 798 4.921515 CAGATTGTTTTGCCAAGTGAGATG 59.078 41.667 0.00 0.00 0.00 2.90
786 799 3.731652 TTGTTTTGCCAAGTGAGATGG 57.268 42.857 0.00 0.00 41.08 3.51
787 800 2.942804 TGTTTTGCCAAGTGAGATGGA 58.057 42.857 0.00 0.00 40.56 3.41
788 801 2.886523 TGTTTTGCCAAGTGAGATGGAG 59.113 45.455 0.00 0.00 40.56 3.86
816 829 3.349022 TGTGTGTTTTCCTTTCGTTCCT 58.651 40.909 0.00 0.00 0.00 3.36
817 830 3.375922 TGTGTGTTTTCCTTTCGTTCCTC 59.624 43.478 0.00 0.00 0.00 3.71
818 831 3.626217 GTGTGTTTTCCTTTCGTTCCTCT 59.374 43.478 0.00 0.00 0.00 3.69
819 832 3.625764 TGTGTTTTCCTTTCGTTCCTCTG 59.374 43.478 0.00 0.00 0.00 3.35
820 833 3.626217 GTGTTTTCCTTTCGTTCCTCTGT 59.374 43.478 0.00 0.00 0.00 3.41
821 834 3.625764 TGTTTTCCTTTCGTTCCTCTGTG 59.374 43.478 0.00 0.00 0.00 3.66
822 835 3.553828 TTTCCTTTCGTTCCTCTGTGT 57.446 42.857 0.00 0.00 0.00 3.72
823 836 3.553828 TTCCTTTCGTTCCTCTGTGTT 57.446 42.857 0.00 0.00 0.00 3.32
824 837 3.107642 TCCTTTCGTTCCTCTGTGTTC 57.892 47.619 0.00 0.00 0.00 3.18
825 838 2.143925 CCTTTCGTTCCTCTGTGTTCC 58.856 52.381 0.00 0.00 0.00 3.62
826 839 2.143925 CTTTCGTTCCTCTGTGTTCCC 58.856 52.381 0.00 0.00 0.00 3.97
827 840 1.124780 TTCGTTCCTCTGTGTTCCCA 58.875 50.000 0.00 0.00 0.00 4.37
828 841 0.391597 TCGTTCCTCTGTGTTCCCAC 59.608 55.000 0.00 0.00 42.19 4.61
829 842 0.393077 CGTTCCTCTGTGTTCCCACT 59.607 55.000 0.00 0.00 42.34 4.00
830 843 1.202651 CGTTCCTCTGTGTTCCCACTT 60.203 52.381 0.00 0.00 42.34 3.16
831 844 2.495084 GTTCCTCTGTGTTCCCACTTC 58.505 52.381 0.00 0.00 42.34 3.01
832 845 1.056660 TCCTCTGTGTTCCCACTTCC 58.943 55.000 0.00 0.00 42.34 3.46
833 846 0.036875 CCTCTGTGTTCCCACTTCCC 59.963 60.000 0.00 0.00 42.34 3.97
844 857 0.106719 CCACTTCCCACCCGCATTAT 60.107 55.000 0.00 0.00 0.00 1.28
853 866 5.882040 TCCCACCCGCATTATTTCAATATA 58.118 37.500 0.00 0.00 0.00 0.86
854 867 6.489603 TCCCACCCGCATTATTTCAATATAT 58.510 36.000 0.00 0.00 0.00 0.86
856 869 7.554835 TCCCACCCGCATTATTTCAATATATAC 59.445 37.037 0.00 0.00 0.00 1.47
857 870 7.406553 CCACCCGCATTATTTCAATATATACG 58.593 38.462 0.00 0.00 0.00 3.06
861 874 9.524106 CCCGCATTATTTCAATATATACGAGTA 57.476 33.333 0.00 0.00 0.00 2.59
885 907 6.276847 ACTATAGCAACACTGAATGTAGAGC 58.723 40.000 0.00 0.00 42.31 4.09
887 909 3.743521 AGCAACACTGAATGTAGAGCAA 58.256 40.909 0.00 0.00 42.31 3.91
903 925 3.047796 GAGCAAGTTTGTGTTCTGCATG 58.952 45.455 0.00 0.00 0.00 4.06
922 945 0.317020 GTGTGCGCTTCACTTGGTTC 60.317 55.000 22.06 1.95 45.81 3.62
943 970 8.306038 TGGTTCCAAAAGTATCATTCAGAATTG 58.694 33.333 0.00 0.00 0.00 2.32
947 974 7.451255 TCCAAAAGTATCATTCAGAATTGTGGT 59.549 33.333 2.33 0.00 31.99 4.16
964 995 3.197766 TGTGGTATCTGAATCCTGACACC 59.802 47.826 0.00 0.00 38.04 4.16
966 997 4.040047 TGGTATCTGAATCCTGACACCAT 58.960 43.478 0.55 0.00 41.11 3.55
1015 1046 1.465689 CCACAATGCTAGAAAACGGCG 60.466 52.381 4.80 4.80 0.00 6.46
1121 1152 1.740296 GCACCGGATTGCACGTACT 60.740 57.895 9.46 0.00 42.49 2.73
1123 1154 1.274596 CACCGGATTGCACGTACTAC 58.725 55.000 9.46 0.00 0.00 2.73
1125 1156 1.273048 ACCGGATTGCACGTACTACAA 59.727 47.619 9.46 0.00 0.00 2.41
1127 1158 2.737783 CCGGATTGCACGTACTACAAAA 59.262 45.455 0.00 0.00 0.00 2.44
1128 1159 3.372822 CCGGATTGCACGTACTACAAAAT 59.627 43.478 0.00 0.00 0.00 1.82
1129 1160 4.567558 CCGGATTGCACGTACTACAAAATA 59.432 41.667 0.00 0.00 0.00 1.40
1130 1161 5.276678 CCGGATTGCACGTACTACAAAATAG 60.277 44.000 0.00 0.00 0.00 1.73
1131 1162 5.290158 CGGATTGCACGTACTACAAAATAGT 59.710 40.000 0.00 0.00 0.00 2.12
1132 1163 6.473131 CGGATTGCACGTACTACAAAATAGTA 59.527 38.462 0.00 0.00 0.00 1.82
1133 1164 7.514125 CGGATTGCACGTACTACAAAATAGTAC 60.514 40.741 12.31 12.31 43.78 2.73
1134 1165 7.490402 GGATTGCACGTACTACAAAATAGTACT 59.510 37.037 17.66 0.00 44.56 2.73
1219 1253 3.977326 GGGGGAAAGATAGAGATCCTTGT 59.023 47.826 0.00 0.00 31.81 3.16
1263 1301 4.677584 TCTGTTTTCCGTGATTTTTGTGG 58.322 39.130 0.00 0.00 0.00 4.17
1278 1316 2.519063 TGGCCATATTGCGCCTGG 60.519 61.111 0.00 8.03 45.90 4.45
1342 1380 2.660064 GGAGGAGGAGAAGCGCCAA 61.660 63.158 2.29 0.00 0.00 4.52
1350 1388 2.507769 GAAGCGCCAAGGCAATGC 60.508 61.111 12.19 6.62 42.06 3.56
1639 1680 1.656652 CGGACGCCATCTTCTTCAAT 58.343 50.000 0.00 0.00 0.00 2.57
1768 1809 0.250901 ACACGCTCATCAAGGGCTTT 60.251 50.000 0.00 0.00 41.54 3.51
2300 2342 2.159503 TCAGAGCTCACGAAACTCGATC 60.160 50.000 17.77 0.00 43.74 3.69
2301 2343 1.184349 GAGCTCACGAAACTCGATCG 58.816 55.000 9.36 9.36 43.74 3.69
2302 2344 0.803117 AGCTCACGAAACTCGATCGA 59.197 50.000 18.32 18.32 43.74 3.59
2303 2345 1.402259 AGCTCACGAAACTCGATCGAT 59.598 47.619 19.78 3.36 43.74 3.59
2304 2346 2.159366 AGCTCACGAAACTCGATCGATT 60.159 45.455 19.78 10.67 43.74 3.34
2305 2347 2.214467 GCTCACGAAACTCGATCGATTC 59.786 50.000 19.78 18.46 43.74 2.52
2306 2348 2.784380 CTCACGAAACTCGATCGATTCC 59.216 50.000 19.78 7.88 43.74 3.01
2307 2349 2.162809 TCACGAAACTCGATCGATTCCA 59.837 45.455 19.78 3.65 43.74 3.53
2308 2350 3.116300 CACGAAACTCGATCGATTCCAT 58.884 45.455 19.78 7.55 43.74 3.41
2309 2351 3.060940 CACGAAACTCGATCGATTCCATG 60.061 47.826 19.78 15.00 43.74 3.66
2310 2352 2.472861 CGAAACTCGATCGATTCCATGG 59.527 50.000 19.78 4.97 43.74 3.66
2311 2353 3.458189 GAAACTCGATCGATTCCATGGT 58.542 45.455 19.78 8.21 0.00 3.55
2312 2354 3.543680 AACTCGATCGATTCCATGGTT 57.456 42.857 19.78 13.98 0.00 3.67
2313 2355 3.099267 ACTCGATCGATTCCATGGTTC 57.901 47.619 19.78 9.36 0.00 3.62
2314 2356 2.224066 ACTCGATCGATTCCATGGTTCC 60.224 50.000 19.78 0.80 0.00 3.62
2315 2357 1.760029 TCGATCGATTCCATGGTTCCA 59.240 47.619 15.15 0.00 0.00 3.53
2316 2358 2.368548 TCGATCGATTCCATGGTTCCAT 59.631 45.455 15.15 4.53 0.00 3.41
2317 2359 2.738846 CGATCGATTCCATGGTTCCATC 59.261 50.000 10.26 12.17 0.00 3.51
2318 2360 3.743521 GATCGATTCCATGGTTCCATCA 58.256 45.455 12.58 2.20 0.00 3.07
2319 2361 2.917933 TCGATTCCATGGTTCCATCAC 58.082 47.619 12.58 0.00 0.00 3.06
2320 2362 2.505407 TCGATTCCATGGTTCCATCACT 59.495 45.455 12.58 0.00 0.00 3.41
2321 2363 2.874701 CGATTCCATGGTTCCATCACTC 59.125 50.000 12.58 0.00 0.00 3.51
2322 2364 3.682436 CGATTCCATGGTTCCATCACTCA 60.682 47.826 12.58 0.00 0.00 3.41
2323 2365 4.467769 GATTCCATGGTTCCATCACTCAT 58.532 43.478 12.58 0.00 0.00 2.90
2324 2366 3.565764 TCCATGGTTCCATCACTCATC 57.434 47.619 12.58 0.00 0.00 2.92
2325 2367 2.845586 TCCATGGTTCCATCACTCATCA 59.154 45.455 12.58 0.00 0.00 3.07
2326 2368 3.266513 TCCATGGTTCCATCACTCATCAA 59.733 43.478 12.58 0.00 0.00 2.57
2327 2369 4.079615 TCCATGGTTCCATCACTCATCAAT 60.080 41.667 12.58 0.00 0.00 2.57
2338 2380 7.612633 TCCATCACTCATCAATTGATTCTTGAA 59.387 33.333 18.41 3.76 36.30 2.69
2341 2383 7.813645 TCACTCATCAATTGATTCTTGAACTG 58.186 34.615 18.41 11.46 36.30 3.16
2346 2388 8.674607 TCATCAATTGATTCTTGAACTGATGAG 58.325 33.333 18.41 1.99 41.64 2.90
2468 2510 1.159713 TGCAGCAAGGTGTTCGACAG 61.160 55.000 0.00 0.00 0.00 3.51
2520 2562 1.878522 GGTGTACAGCATCCTCGCG 60.879 63.158 19.87 0.00 36.85 5.87
2879 2921 2.051345 CAAGAACGCCAACCGCAC 60.051 61.111 0.00 0.00 41.76 5.34
3053 3107 2.355986 TGACAAGCGCGGTAGGGAT 61.356 57.895 12.91 0.00 0.00 3.85
3092 3146 4.508128 ATCATCGGCGCCGTCGTT 62.508 61.111 44.16 28.16 40.74 3.85
3102 3156 1.731613 GCCGTCGTTGTCGTCATCA 60.732 57.895 0.00 0.00 38.33 3.07
3123 3177 1.138883 GTGGCGATCGTGTCAGCTA 59.861 57.895 17.81 0.00 0.00 3.32
3169 3223 2.165998 GGAATCAAAGGCAGAAGCAGT 58.834 47.619 0.00 0.00 44.61 4.40
3188 3242 2.203195 TGGGCTGCACAGTCACAC 60.203 61.111 0.00 0.00 33.98 3.82
3236 3290 5.051891 CTCAGTTAAGAGGCCATGTTTTG 57.948 43.478 5.01 0.00 31.94 2.44
3237 3291 3.255642 TCAGTTAAGAGGCCATGTTTTGC 59.744 43.478 5.01 0.00 0.00 3.68
3342 3405 1.948834 TCTGCACACACATTGGTCTTG 59.051 47.619 0.00 0.00 0.00 3.02
3343 3406 1.677576 CTGCACACACATTGGTCTTGT 59.322 47.619 0.00 0.00 0.00 3.16
3345 3408 2.124011 CACACACATTGGTCTTGTGC 57.876 50.000 3.85 0.00 46.65 4.57
3346 3409 1.677576 CACACACATTGGTCTTGTGCT 59.322 47.619 3.85 0.00 46.65 4.40
3347 3410 2.099592 CACACACATTGGTCTTGTGCTT 59.900 45.455 3.85 0.00 46.65 3.91
3348 3411 2.358898 ACACACATTGGTCTTGTGCTTC 59.641 45.455 3.85 0.00 46.65 3.86
3349 3412 1.603802 ACACATTGGTCTTGTGCTTCG 59.396 47.619 3.85 0.00 46.65 3.79
3350 3413 0.593128 ACATTGGTCTTGTGCTTCGC 59.407 50.000 0.00 0.00 0.00 4.70
3351 3414 0.109597 CATTGGTCTTGTGCTTCGCC 60.110 55.000 0.00 0.00 0.00 5.54
3352 3415 0.537143 ATTGGTCTTGTGCTTCGCCA 60.537 50.000 0.00 0.00 0.00 5.69
3353 3416 1.165907 TTGGTCTTGTGCTTCGCCAG 61.166 55.000 0.00 0.00 0.00 4.85
3354 3417 2.328099 GGTCTTGTGCTTCGCCAGG 61.328 63.158 0.00 0.00 0.00 4.45
3355 3418 1.301716 GTCTTGTGCTTCGCCAGGA 60.302 57.895 0.00 0.00 0.00 3.86
3356 3419 0.884704 GTCTTGTGCTTCGCCAGGAA 60.885 55.000 0.00 0.00 0.00 3.36
3357 3420 0.884704 TCTTGTGCTTCGCCAGGAAC 60.885 55.000 0.00 0.00 0.00 3.62
3358 3421 0.886490 CTTGTGCTTCGCCAGGAACT 60.886 55.000 0.00 0.00 43.88 3.01
3403 3472 1.558756 CAGAGCAGACTCCCCTCAAAT 59.441 52.381 0.00 0.00 44.65 2.32
3404 3473 2.026449 CAGAGCAGACTCCCCTCAAATT 60.026 50.000 0.00 0.00 44.65 1.82
3405 3474 3.198635 CAGAGCAGACTCCCCTCAAATTA 59.801 47.826 0.00 0.00 44.65 1.40
3406 3475 4.043596 AGAGCAGACTCCCCTCAAATTAT 58.956 43.478 0.00 0.00 44.65 1.28
3407 3476 4.102367 AGAGCAGACTCCCCTCAAATTATC 59.898 45.833 0.00 0.00 44.65 1.75
3408 3477 3.782523 AGCAGACTCCCCTCAAATTATCA 59.217 43.478 0.00 0.00 0.00 2.15
3409 3478 4.228210 AGCAGACTCCCCTCAAATTATCAA 59.772 41.667 0.00 0.00 0.00 2.57
3410 3479 4.578105 GCAGACTCCCCTCAAATTATCAAG 59.422 45.833 0.00 0.00 0.00 3.02
3411 3480 5.749462 CAGACTCCCCTCAAATTATCAAGT 58.251 41.667 0.00 0.00 0.00 3.16
3412 3481 6.632672 GCAGACTCCCCTCAAATTATCAAGTA 60.633 42.308 0.00 0.00 0.00 2.24
3413 3482 6.763610 CAGACTCCCCTCAAATTATCAAGTAC 59.236 42.308 0.00 0.00 0.00 2.73
3414 3483 6.674419 AGACTCCCCTCAAATTATCAAGTACT 59.326 38.462 0.00 0.00 0.00 2.73
3415 3484 7.844779 AGACTCCCCTCAAATTATCAAGTACTA 59.155 37.037 0.00 0.00 0.00 1.82
3611 3732 0.036010 CTCACAAGAACCGGGCATCT 60.036 55.000 6.32 3.27 0.00 2.90
3684 3805 2.425592 CTCACCGCCAAGTCCACA 59.574 61.111 0.00 0.00 0.00 4.17
3687 3808 1.961277 CACCGCCAAGTCCACAGTC 60.961 63.158 0.00 0.00 0.00 3.51
3792 3913 2.357517 ACGTGCCGGCTCTTCTTG 60.358 61.111 29.70 13.20 0.00 3.02
3847 3974 2.505982 GAGGAGGCGGCATTAGCA 59.494 61.111 13.08 0.00 44.61 3.49
3876 4003 3.924918 TCTGACGGAGAAACTTCAGAG 57.075 47.619 0.00 0.00 39.62 3.35
3879 4006 2.558795 TGACGGAGAAACTTCAGAGAGG 59.441 50.000 0.00 0.00 0.00 3.69
3880 4007 2.559231 GACGGAGAAACTTCAGAGAGGT 59.441 50.000 0.00 0.00 0.00 3.85
3882 4009 2.694213 GGAGAAACTTCAGAGAGGTGC 58.306 52.381 0.00 0.00 0.00 5.01
3883 4010 2.614229 GGAGAAACTTCAGAGAGGTGCC 60.614 54.545 0.00 0.00 0.00 5.01
3884 4011 2.037772 GAGAAACTTCAGAGAGGTGCCA 59.962 50.000 0.00 0.00 0.00 4.92
3885 4012 2.439507 AGAAACTTCAGAGAGGTGCCAA 59.560 45.455 0.00 0.00 0.00 4.52
3886 4013 3.117888 AGAAACTTCAGAGAGGTGCCAAA 60.118 43.478 0.00 0.00 0.00 3.28
3887 4014 3.297134 AACTTCAGAGAGGTGCCAAAA 57.703 42.857 0.00 0.00 0.00 2.44
3888 4015 2.576615 ACTTCAGAGAGGTGCCAAAAC 58.423 47.619 0.00 0.00 0.00 2.43
3889 4016 2.092429 ACTTCAGAGAGGTGCCAAAACA 60.092 45.455 0.00 0.00 0.00 2.83
3890 4017 2.260844 TCAGAGAGGTGCCAAAACAG 57.739 50.000 0.00 0.00 0.00 3.16
3923 4074 1.963338 GCTGGCGATGGGTATCTGC 60.963 63.158 0.00 0.00 34.40 4.26
4168 4319 2.299013 TGACGGAGCAGTCAAATGTACT 59.701 45.455 7.13 0.00 46.81 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.487976 TCCATTCTTAGGCCAGCAGAG 59.512 52.381 5.01 0.00 0.00 3.35
72 76 9.083422 TGAATTTGTTGTTGGTATCCATTCTTA 57.917 29.630 0.00 0.00 31.53 2.10
127 131 1.064654 GCTTTTCTTGCAGCCCTATCG 59.935 52.381 0.00 0.00 0.00 2.92
768 775 2.887152 ACTCCATCTCACTTGGCAAAAC 59.113 45.455 0.00 0.00 34.06 2.43
784 797 6.620877 AGGAAAACACACATATCTACTCCA 57.379 37.500 0.00 0.00 0.00 3.86
785 798 7.201530 CGAAAGGAAAACACACATATCTACTCC 60.202 40.741 0.00 0.00 0.00 3.85
786 799 7.331193 ACGAAAGGAAAACACACATATCTACTC 59.669 37.037 0.00 0.00 0.00 2.59
787 800 7.159372 ACGAAAGGAAAACACACATATCTACT 58.841 34.615 0.00 0.00 0.00 2.57
788 801 7.360575 ACGAAAGGAAAACACACATATCTAC 57.639 36.000 0.00 0.00 0.00 2.59
820 833 2.824880 CGGGTGGGAAGTGGGAACA 61.825 63.158 0.00 0.00 38.70 3.18
821 834 2.033602 CGGGTGGGAAGTGGGAAC 59.966 66.667 0.00 0.00 0.00 3.62
822 835 3.961414 GCGGGTGGGAAGTGGGAA 61.961 66.667 0.00 0.00 0.00 3.97
824 837 2.204865 TAATGCGGGTGGGAAGTGGG 62.205 60.000 0.00 0.00 0.00 4.61
825 838 0.106719 ATAATGCGGGTGGGAAGTGG 60.107 55.000 0.00 0.00 0.00 4.00
826 839 1.762708 AATAATGCGGGTGGGAAGTG 58.237 50.000 0.00 0.00 0.00 3.16
827 840 2.291282 TGAAATAATGCGGGTGGGAAGT 60.291 45.455 0.00 0.00 0.00 3.01
828 841 2.374184 TGAAATAATGCGGGTGGGAAG 58.626 47.619 0.00 0.00 0.00 3.46
829 842 2.516227 TGAAATAATGCGGGTGGGAA 57.484 45.000 0.00 0.00 0.00 3.97
830 843 2.516227 TTGAAATAATGCGGGTGGGA 57.484 45.000 0.00 0.00 0.00 4.37
831 844 6.773976 ATATATTGAAATAATGCGGGTGGG 57.226 37.500 0.00 0.00 0.00 4.61
832 845 7.279090 TCGTATATATTGAAATAATGCGGGTGG 59.721 37.037 0.00 0.00 0.00 4.61
833 846 8.192068 TCGTATATATTGAAATAATGCGGGTG 57.808 34.615 0.00 0.00 0.00 4.61
853 866 7.563888 TTCAGTGTTGCTATAGTACTCGTAT 57.436 36.000 0.00 0.00 0.00 3.06
854 867 6.990341 TTCAGTGTTGCTATAGTACTCGTA 57.010 37.500 0.00 0.00 0.00 3.43
856 869 6.266323 ACATTCAGTGTTGCTATAGTACTCG 58.734 40.000 0.00 0.00 38.01 4.18
857 870 8.622157 TCTACATTCAGTGTTGCTATAGTACTC 58.378 37.037 0.00 2.05 42.29 2.59
861 874 6.127338 TGCTCTACATTCAGTGTTGCTATAGT 60.127 38.462 0.84 0.00 42.29 2.12
862 875 6.276091 TGCTCTACATTCAGTGTTGCTATAG 58.724 40.000 0.00 0.00 42.29 1.31
863 876 6.220726 TGCTCTACATTCAGTGTTGCTATA 57.779 37.500 0.00 0.00 42.29 1.31
864 877 5.089970 TGCTCTACATTCAGTGTTGCTAT 57.910 39.130 0.00 0.00 42.29 2.97
865 878 4.535526 TGCTCTACATTCAGTGTTGCTA 57.464 40.909 0.00 0.00 42.29 3.49
885 907 3.548668 CACACATGCAGAACACAAACTTG 59.451 43.478 0.00 0.00 0.00 3.16
887 909 3.425577 CACACATGCAGAACACAAACT 57.574 42.857 0.00 0.00 0.00 2.66
922 945 7.605449 ACCACAATTCTGAATGATACTTTTGG 58.395 34.615 3.22 3.63 0.00 3.28
943 970 3.197766 TGGTGTCAGGATTCAGATACCAC 59.802 47.826 10.53 0.00 46.68 4.16
947 974 4.686944 GCCAATGGTGTCAGGATTCAGATA 60.687 45.833 0.00 0.00 0.00 1.98
964 995 1.318158 GCTCCTCAACCTGGCCAATG 61.318 60.000 7.01 6.71 0.00 2.82
966 997 1.792757 ATGCTCCTCAACCTGGCCAA 61.793 55.000 7.01 0.00 0.00 4.52
1015 1046 3.116531 GGCCGGCGTCAGTTGTAC 61.117 66.667 22.54 0.00 0.00 2.90
1127 1158 8.700051 ACAGCTTGTCATTCTTATCAGTACTAT 58.300 33.333 0.00 0.00 0.00 2.12
1128 1159 7.976175 CACAGCTTGTCATTCTTATCAGTACTA 59.024 37.037 0.00 0.00 0.00 1.82
1129 1160 6.815641 CACAGCTTGTCATTCTTATCAGTACT 59.184 38.462 0.00 0.00 0.00 2.73
1130 1161 6.813649 TCACAGCTTGTCATTCTTATCAGTAC 59.186 38.462 0.00 0.00 0.00 2.73
1131 1162 6.813649 GTCACAGCTTGTCATTCTTATCAGTA 59.186 38.462 0.00 0.00 0.00 2.74
1132 1163 5.641209 GTCACAGCTTGTCATTCTTATCAGT 59.359 40.000 0.00 0.00 0.00 3.41
1133 1164 5.064452 GGTCACAGCTTGTCATTCTTATCAG 59.936 44.000 0.00 0.00 0.00 2.90
1134 1165 4.937620 GGTCACAGCTTGTCATTCTTATCA 59.062 41.667 0.00 0.00 0.00 2.15
1219 1253 5.527214 AGAAGTCGATCACACAAAATTCACA 59.473 36.000 0.00 0.00 0.00 3.58
1263 1301 1.174712 ATCACCAGGCGCAATATGGC 61.175 55.000 10.83 0.00 37.64 4.40
1278 1316 4.137543 ACCCTTGACTTGTTTGAGATCAC 58.862 43.478 0.00 0.00 0.00 3.06
1639 1680 0.250234 CGAAGGAGTTGATGAGGGCA 59.750 55.000 0.00 0.00 0.00 5.36
2047 2088 2.815211 CGCACCATCTCCACCACG 60.815 66.667 0.00 0.00 0.00 4.94
2149 2190 2.434185 TTCATCTGGCGGACGCAC 60.434 61.111 18.95 8.46 44.11 5.34
2261 2302 1.724582 GAGCTCGCTCTGAGGAGGTC 61.725 65.000 25.30 25.30 46.52 3.85
2262 2303 1.752694 GAGCTCGCTCTGAGGAGGT 60.753 63.158 20.33 20.33 45.38 3.85
2263 2304 1.727511 CTGAGCTCGCTCTGAGGAGG 61.728 65.000 18.63 4.89 45.38 4.30
2264 2305 0.747644 TCTGAGCTCGCTCTGAGGAG 60.748 60.000 20.11 14.90 45.38 3.69
2265 2306 1.301293 TCTGAGCTCGCTCTGAGGA 59.699 57.895 20.11 10.73 45.38 3.71
2266 2307 3.917058 TCTGAGCTCGCTCTGAGG 58.083 61.111 20.11 9.00 45.38 3.86
2290 2332 3.458189 ACCATGGAATCGATCGAGTTTC 58.542 45.455 23.84 20.96 0.00 2.78
2300 2342 2.874701 GAGTGATGGAACCATGGAATCG 59.125 50.000 21.47 0.00 36.70 3.34
2301 2343 3.889815 TGAGTGATGGAACCATGGAATC 58.110 45.455 21.47 15.79 36.70 2.52
2302 2344 4.079615 TGATGAGTGATGGAACCATGGAAT 60.080 41.667 21.47 6.63 36.70 3.01
2303 2345 3.266513 TGATGAGTGATGGAACCATGGAA 59.733 43.478 21.47 0.73 36.70 3.53
2304 2346 2.845586 TGATGAGTGATGGAACCATGGA 59.154 45.455 21.47 0.00 36.70 3.41
2305 2347 3.286329 TGATGAGTGATGGAACCATGG 57.714 47.619 11.19 11.19 36.70 3.66
2306 2348 5.358725 TCAATTGATGAGTGATGGAACCATG 59.641 40.000 11.27 0.00 33.40 3.66
2307 2349 5.512298 TCAATTGATGAGTGATGGAACCAT 58.488 37.500 3.38 6.00 34.85 3.55
2308 2350 4.920999 TCAATTGATGAGTGATGGAACCA 58.079 39.130 3.38 0.00 33.04 3.67
2309 2351 6.320672 AGAATCAATTGATGAGTGATGGAACC 59.679 38.462 21.39 0.00 41.88 3.62
2310 2352 7.330900 AGAATCAATTGATGAGTGATGGAAC 57.669 36.000 21.39 2.90 41.88 3.62
2311 2353 7.612633 TCAAGAATCAATTGATGAGTGATGGAA 59.387 33.333 21.39 1.78 41.88 3.53
2312 2354 7.114095 TCAAGAATCAATTGATGAGTGATGGA 58.886 34.615 21.39 8.72 41.88 3.41
2313 2355 7.329588 TCAAGAATCAATTGATGAGTGATGG 57.670 36.000 21.39 6.75 41.88 3.51
2314 2356 8.459635 AGTTCAAGAATCAATTGATGAGTGATG 58.540 33.333 21.39 13.88 41.88 3.07
2315 2357 8.459635 CAGTTCAAGAATCAATTGATGAGTGAT 58.540 33.333 21.39 4.72 44.40 3.06
2316 2358 7.662669 TCAGTTCAAGAATCAATTGATGAGTGA 59.337 33.333 21.39 19.15 42.53 3.41
2317 2359 7.813645 TCAGTTCAAGAATCAATTGATGAGTG 58.186 34.615 21.39 17.43 42.53 3.51
2318 2360 7.991084 TCAGTTCAAGAATCAATTGATGAGT 57.009 32.000 21.39 6.26 42.53 3.41
2319 2361 8.674607 TCATCAGTTCAAGAATCAATTGATGAG 58.325 33.333 21.39 11.48 42.56 2.90
2320 2362 8.570068 TCATCAGTTCAAGAATCAATTGATGA 57.430 30.769 21.39 12.96 44.16 2.92
2321 2363 7.915923 CCTCATCAGTTCAAGAATCAATTGATG 59.084 37.037 21.39 10.78 41.04 3.07
2322 2364 7.614583 ACCTCATCAGTTCAAGAATCAATTGAT 59.385 33.333 15.36 15.36 36.60 2.57
2323 2365 6.944290 ACCTCATCAGTTCAAGAATCAATTGA 59.056 34.615 11.26 11.26 34.93 2.57
2324 2366 7.027760 CACCTCATCAGTTCAAGAATCAATTG 58.972 38.462 0.00 0.00 0.00 2.32
2325 2367 6.349944 GCACCTCATCAGTTCAAGAATCAATT 60.350 38.462 0.00 0.00 0.00 2.32
2326 2368 5.125097 GCACCTCATCAGTTCAAGAATCAAT 59.875 40.000 0.00 0.00 0.00 2.57
2327 2369 4.456911 GCACCTCATCAGTTCAAGAATCAA 59.543 41.667 0.00 0.00 0.00 2.57
2338 2380 1.277557 GAGAACCTGCACCTCATCAGT 59.722 52.381 0.00 0.00 0.00 3.41
2341 2383 0.460987 CCGAGAACCTGCACCTCATC 60.461 60.000 0.00 0.00 0.00 2.92
2346 2388 4.021925 AGCCCGAGAACCTGCACC 62.022 66.667 0.00 0.00 0.00 5.01
2418 2460 4.399395 CCCAGCGAGCTGAAGGCA 62.399 66.667 24.93 0.00 46.30 4.75
2780 2822 2.815945 CCGGCCTCCTGCATCATCT 61.816 63.158 0.00 0.00 43.89 2.90
3046 3100 1.484444 CCAGCCCTGCCTATCCCTAC 61.484 65.000 0.00 0.00 0.00 3.18
3053 3107 0.547712 AAAGTCTCCAGCCCTGCCTA 60.548 55.000 0.00 0.00 0.00 3.93
3092 3146 2.048597 GCCACGGTGATGACGACA 60.049 61.111 10.28 0.00 34.93 4.35
3102 3156 3.626680 CTGACACGATCGCCACGGT 62.627 63.158 16.60 5.85 34.93 4.83
3135 3189 0.171231 GATTCCTGCAAAAGCCCGAC 59.829 55.000 0.00 0.00 0.00 4.79
3141 3195 3.006110 TCTGCCTTTGATTCCTGCAAAAG 59.994 43.478 0.24 0.24 35.09 2.27
3153 3207 1.311859 CACACTGCTTCTGCCTTTGA 58.688 50.000 0.00 0.00 38.71 2.69
3178 3232 1.270465 TGAGCTGATGGTGTGACTGTG 60.270 52.381 0.00 0.00 0.00 3.66
3345 3408 1.281899 GAATCGAGTTCCTGGCGAAG 58.718 55.000 0.00 0.00 37.60 3.79
3346 3409 0.606096 TGAATCGAGTTCCTGGCGAA 59.394 50.000 0.00 0.00 37.60 4.70
3347 3410 0.173481 CTGAATCGAGTTCCTGGCGA 59.827 55.000 0.00 0.00 35.91 5.54
3348 3411 0.173481 TCTGAATCGAGTTCCTGGCG 59.827 55.000 0.00 0.00 35.91 5.69
3349 3412 2.208431 CATCTGAATCGAGTTCCTGGC 58.792 52.381 0.00 0.00 35.91 4.85
3350 3413 3.131933 AGACATCTGAATCGAGTTCCTGG 59.868 47.826 0.00 0.00 35.91 4.45
3351 3414 4.142293 TGAGACATCTGAATCGAGTTCCTG 60.142 45.833 0.00 0.00 35.91 3.86
3352 3415 4.019858 TGAGACATCTGAATCGAGTTCCT 58.980 43.478 0.00 0.00 35.91 3.36
3353 3416 4.109050 GTGAGACATCTGAATCGAGTTCC 58.891 47.826 0.00 0.00 35.91 3.62
3354 3417 4.109050 GGTGAGACATCTGAATCGAGTTC 58.891 47.826 0.00 0.00 37.35 3.01
3355 3418 3.511540 TGGTGAGACATCTGAATCGAGTT 59.488 43.478 0.00 0.00 0.00 3.01
3356 3419 3.092301 TGGTGAGACATCTGAATCGAGT 58.908 45.455 0.00 0.00 0.00 4.18
3357 3420 3.790152 TGGTGAGACATCTGAATCGAG 57.210 47.619 0.00 0.00 0.00 4.04
3358 3421 4.442052 GGAATGGTGAGACATCTGAATCGA 60.442 45.833 0.00 0.00 0.00 3.59
3521 3642 4.019051 ACTCTTGATGTGGTGATCCATTGA 60.019 41.667 0.00 0.00 46.20 2.57
3526 3647 3.133721 AGCTACTCTTGATGTGGTGATCC 59.866 47.826 0.00 0.00 0.00 3.36
3535 3656 2.352034 CTGCTTGCAGCTACTCTTGATG 59.648 50.000 9.78 0.00 42.97 3.07
3577 3698 1.813178 TGTGAGCTCTCTTACCGACAG 59.187 52.381 16.19 0.00 0.00 3.51
3792 3913 0.690762 TGGACAAGTTCTACCAGCCC 59.309 55.000 0.00 0.00 0.00 5.19
3847 3974 0.895530 TCTCCGTCAGAATTCCGCTT 59.104 50.000 0.65 0.00 0.00 4.68
3876 4003 2.024414 AGTGTTCTGTTTTGGCACCTC 58.976 47.619 0.00 0.00 0.00 3.85
3879 4006 2.949644 AGGTAGTGTTCTGTTTTGGCAC 59.050 45.455 0.00 0.00 0.00 5.01
3880 4007 2.948979 CAGGTAGTGTTCTGTTTTGGCA 59.051 45.455 0.00 0.00 0.00 4.92
3882 4009 3.564225 GGTCAGGTAGTGTTCTGTTTTGG 59.436 47.826 0.00 0.00 33.13 3.28
3883 4010 3.247648 CGGTCAGGTAGTGTTCTGTTTTG 59.752 47.826 0.00 0.00 33.13 2.44
3884 4011 3.463944 CGGTCAGGTAGTGTTCTGTTTT 58.536 45.455 0.00 0.00 33.13 2.43
3885 4012 2.805657 GCGGTCAGGTAGTGTTCTGTTT 60.806 50.000 0.00 0.00 33.13 2.83
3886 4013 1.270147 GCGGTCAGGTAGTGTTCTGTT 60.270 52.381 0.00 0.00 33.13 3.16
3887 4014 0.317479 GCGGTCAGGTAGTGTTCTGT 59.683 55.000 0.00 0.00 33.13 3.41
3888 4015 0.603569 AGCGGTCAGGTAGTGTTCTG 59.396 55.000 0.00 0.00 0.00 3.02
3889 4016 0.603569 CAGCGGTCAGGTAGTGTTCT 59.396 55.000 0.00 0.00 0.00 3.01
3890 4017 0.389948 CCAGCGGTCAGGTAGTGTTC 60.390 60.000 0.00 0.00 0.00 3.18
3923 4074 3.192422 CCTCCATCCAGCTCTACTATTCG 59.808 52.174 0.00 0.00 0.00 3.34
4128 4279 5.424757 CGTCACCTTAAATTCAGTATCCCA 58.575 41.667 0.00 0.00 0.00 4.37
4168 4319 1.592400 CCAGCGTCCTCGTCAAGGTA 61.592 60.000 0.00 0.00 46.32 3.08


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

AutoCloner maintained by Alex Coulton.