Multiple sequence alignment - TraesCS4D01G255500

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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 TraesCS4D01G255500 chr4D 100.000 4462 0 0 1 4462 424464970 424469431 0.000000e+00 8240.0
1 TraesCS4D01G255500 chr4D 82.339 436 65 8 124 548 433804159 433803725 7.050000e-98 368.0
2 TraesCS4D01G255500 chr4D 81.596 451 72 9 100 542 465750533 465750980 3.280000e-96 363.0
3 TraesCS4D01G255500 chr4A 93.002 3887 169 47 611 4462 40253536 40249718 0.000000e+00 5576.0
4 TraesCS4D01G255500 chr4B 92.539 3163 144 51 1330 4462 520396784 520399884 0.000000e+00 4449.0
5 TraesCS4D01G255500 chr4B 84.930 710 39 34 544 1247 520396079 520396726 0.000000e+00 656.0
6 TraesCS4D01G255500 chr7B 86.944 674 56 16 1328 1984 407389890 407390548 0.000000e+00 728.0
7 TraesCS4D01G255500 chr1B 89.562 479 33 11 1387 1859 516975331 516974864 3.840000e-165 592.0
8 TraesCS4D01G255500 chr1B 89.072 485 36 11 1381 1859 117304837 117305310 1.790000e-163 586.0
9 TraesCS4D01G255500 chr2D 82.617 535 72 14 22 540 19215683 19216212 1.890000e-123 453.0
10 TraesCS4D01G255500 chr2D 79.828 580 68 26 4 540 559400649 559400076 1.170000e-100 377.0
11 TraesCS4D01G255500 chr7D 82.320 543 71 18 17 542 580000533 580001067 8.800000e-122 448.0
12 TraesCS4D01G255500 chr7D 82.927 451 64 11 101 541 86891386 86890939 1.160000e-105 394.0
13 TraesCS4D01G255500 chr3A 86.772 378 37 11 1500 1866 486034911 486035286 4.150000e-110 409.0
14 TraesCS4D01G255500 chr3B 81.798 456 66 12 102 546 617959489 617959938 2.540000e-97 366.0
15 TraesCS4D01G255500 chr3B 78.909 275 43 12 1 268 561546988 561546722 5.930000e-39 172.0
16 TraesCS4D01G255500 chr1A 82.135 459 52 23 101 542 547824844 547824399 2.540000e-97 366.0
17 TraesCS4D01G255500 chr6B 78.777 556 96 15 1 542 674476077 674476624 1.970000e-93 353.0
18 TraesCS4D01G255500 chrUn 91.339 254 16 3 1612 1859 479459998 479460251 4.270000e-90 342.0
19 TraesCS4D01G255500 chr6A 78.330 503 57 29 1 462 89308214 89308705 1.220000e-70 278.0
20 TraesCS4D01G255500 chr2A 84.667 150 16 7 1 147 13091045 13090900 4.650000e-30 143.0
21 TraesCS4D01G255500 chr2A 97.619 42 1 0 45 86 623089138 623089097 6.190000e-09 73.1
22 TraesCS4D01G255500 chr2A 97.222 36 0 1 44 78 719208586 719208621 4.820000e-05 60.2


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 TraesCS4D01G255500 chr4D 424464970 424469431 4461 False 8240.0 8240 100.0000 1 4462 1 chr4D.!!$F1 4461
1 TraesCS4D01G255500 chr4A 40249718 40253536 3818 True 5576.0 5576 93.0020 611 4462 1 chr4A.!!$R1 3851
2 TraesCS4D01G255500 chr4B 520396079 520399884 3805 False 2552.5 4449 88.7345 544 4462 2 chr4B.!!$F1 3918
3 TraesCS4D01G255500 chr7B 407389890 407390548 658 False 728.0 728 86.9440 1328 1984 1 chr7B.!!$F1 656
4 TraesCS4D01G255500 chr2D 19215683 19216212 529 False 453.0 453 82.6170 22 540 1 chr2D.!!$F1 518
5 TraesCS4D01G255500 chr2D 559400076 559400649 573 True 377.0 377 79.8280 4 540 1 chr2D.!!$R1 536
6 TraesCS4D01G255500 chr7D 580000533 580001067 534 False 448.0 448 82.3200 17 542 1 chr7D.!!$F1 525
7 TraesCS4D01G255500 chr6B 674476077 674476624 547 False 353.0 353 78.7770 1 542 1 chr6B.!!$F1 541

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
46 50 0.248866 CGAGGCACGGTTTTGCTTTT 60.249 50.0 0.00 0.00 42.56 2.27 F
815 952 0.313043 CAAGGACAGCAGCCAACAAG 59.687 55.0 0.00 0.00 0.00 3.16 F
1431 1619 0.250727 GCACAAGGTAACCAGCCAGA 60.251 55.0 0.00 0.00 37.17 3.86 F
1434 1622 0.678048 CAAGGTAACCAGCCAGAGGC 60.678 60.0 0.00 0.00 44.87 4.70 F
1473 1672 0.810031 ACCGCGCGCTTAGAAATCAT 60.810 50.0 30.48 0.00 0.00 2.45 F
3147 3385 0.758123 AGCTTAGGATGGAGCTGCTC 59.242 55.0 21.17 21.17 46.82 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1396 1584 0.039708 GTGCAAGTTGAAGCTGCTCC 60.040 55.0 7.16 0.0 0.0 4.70 R
1847 2064 1.531423 CAATGAGCTGCACCTTGTCT 58.469 50.0 1.02 0.0 0.0 3.41 R
3145 3383 0.106335 AGGCGCATCTTCATCTGGAG 59.894 55.0 10.83 0.0 0.0 3.86 R
3147 3385 0.179065 TCAGGCGCATCTTCATCTGG 60.179 55.0 10.83 0.0 0.0 3.86 R
3449 3687 2.099921 AGTGCTACGTCCATGCTAAGAG 59.900 50.0 0.00 0.0 0.0 2.85 R
3949 4192 0.987294 AGCCTAGACATGTGTTGCCT 59.013 50.0 1.15 0.0 0.0 4.75 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
46 50 0.248866 CGAGGCACGGTTTTGCTTTT 60.249 50.000 0.00 0.00 42.56 2.27
47 51 1.801025 CGAGGCACGGTTTTGCTTTTT 60.801 47.619 0.00 0.00 42.56 1.94
59 63 0.955428 TGCTTTTTCGCGAGAGGCAT 60.955 50.000 21.48 0.00 43.84 4.40
74 78 2.885113 CATGACCGTGCCTCTCGA 59.115 61.111 0.00 0.00 0.00 4.04
127 157 3.695830 TCTACGAGAGGCATGGTTTTT 57.304 42.857 0.00 0.00 0.00 1.94
208 327 0.674581 TTCTTCCGCGAGAGGTACGA 60.675 55.000 8.23 0.00 0.00 3.43
210 329 0.317103 CTTCCGCGAGAGGTACGATG 60.317 60.000 8.23 0.00 0.00 3.84
218 337 3.782046 CGAGAGGTACGATGGTGATTTT 58.218 45.455 0.00 0.00 0.00 1.82
343 474 9.775854 AATATGTGATCTAGTTTGGAAGATCTG 57.224 33.333 12.19 0.00 45.52 2.90
347 478 5.721480 TGATCTAGTTTGGAAGATCTGGACA 59.279 40.000 12.19 0.00 45.52 4.02
377 508 2.415625 CCAACGGTGAAAACGGTTCAAA 60.416 45.455 0.00 0.00 32.10 2.69
399 530 1.950828 TTGGACGCACGGTTTAAGAA 58.049 45.000 0.00 0.00 0.00 2.52
457 592 1.757682 AAACTCCAGGTTGCGACAAA 58.242 45.000 6.39 0.00 38.29 2.83
462 597 1.659233 CAGGTTGCGACAAATGGCA 59.341 52.632 6.39 0.00 37.85 4.92
477 612 4.312231 GCACACAAAGAGCGCGCA 62.312 61.111 35.10 0.00 0.00 6.09
542 678 3.926616 ACTCCTCAATTCGTGATTTCGT 58.073 40.909 0.00 0.00 35.07 3.85
602 739 2.930826 ATATGGGTCTACTTTGGGCG 57.069 50.000 0.00 0.00 0.00 6.13
609 746 1.804748 GTCTACTTTGGGCGGAAACTG 59.195 52.381 0.00 0.00 0.00 3.16
735 872 2.798145 CGACACAAGCTTCCAAAAACCC 60.798 50.000 0.00 0.00 0.00 4.11
781 918 1.953686 CAAAAAGGAAGGCCGAGACAA 59.046 47.619 0.00 0.00 39.96 3.18
783 920 0.765510 AAAGGAAGGCCGAGACAAGT 59.234 50.000 0.00 0.00 39.96 3.16
793 930 3.299738 GAGACAAGTCGCGAGAGAC 57.700 57.895 10.24 0.00 43.49 3.36
804 941 0.455295 GCGAGAGACGACAAGGACAG 60.455 60.000 0.00 0.00 45.77 3.51
805 942 0.455295 CGAGAGACGACAAGGACAGC 60.455 60.000 0.00 0.00 45.77 4.40
806 943 0.598562 GAGAGACGACAAGGACAGCA 59.401 55.000 0.00 0.00 0.00 4.41
807 944 0.600557 AGAGACGACAAGGACAGCAG 59.399 55.000 0.00 0.00 0.00 4.24
809 946 2.029844 GACGACAAGGACAGCAGCC 61.030 63.158 0.00 0.00 0.00 4.85
810 947 2.031012 CGACAAGGACAGCAGCCA 59.969 61.111 0.00 0.00 0.00 4.75
811 948 1.597854 CGACAAGGACAGCAGCCAA 60.598 57.895 0.00 0.00 0.00 4.52
812 949 1.845809 CGACAAGGACAGCAGCCAAC 61.846 60.000 0.00 0.00 0.00 3.77
813 950 0.819259 GACAAGGACAGCAGCCAACA 60.819 55.000 0.00 0.00 0.00 3.33
814 951 0.395586 ACAAGGACAGCAGCCAACAA 60.396 50.000 0.00 0.00 0.00 2.83
815 952 0.313043 CAAGGACAGCAGCCAACAAG 59.687 55.000 0.00 0.00 0.00 3.16
816 953 0.825010 AAGGACAGCAGCCAACAAGG 60.825 55.000 0.00 0.00 41.84 3.61
817 954 1.228245 GGACAGCAGCCAACAAGGA 60.228 57.895 0.00 0.00 41.22 3.36
818 955 1.239968 GGACAGCAGCCAACAAGGAG 61.240 60.000 0.00 0.00 41.22 3.69
819 956 1.228367 ACAGCAGCCAACAAGGAGG 60.228 57.895 0.00 0.00 41.22 4.30
820 957 1.975407 CAGCAGCCAACAAGGAGGG 60.975 63.158 0.00 0.00 41.22 4.30
821 958 2.156098 AGCAGCCAACAAGGAGGGA 61.156 57.895 0.00 0.00 41.22 4.20
822 959 1.000396 GCAGCCAACAAGGAGGGAT 60.000 57.895 0.00 0.00 41.22 3.85
823 960 1.318158 GCAGCCAACAAGGAGGGATG 61.318 60.000 0.00 0.00 40.92 3.51
824 961 0.329261 CAGCCAACAAGGAGGGATGA 59.671 55.000 0.00 0.00 40.43 2.92
825 962 0.622665 AGCCAACAAGGAGGGATGAG 59.377 55.000 0.00 0.00 41.22 2.90
826 963 0.394899 GCCAACAAGGAGGGATGAGG 60.395 60.000 0.00 0.00 41.22 3.86
827 964 0.394899 CCAACAAGGAGGGATGAGGC 60.395 60.000 0.00 0.00 41.22 4.70
828 965 0.394899 CAACAAGGAGGGATGAGGCC 60.395 60.000 0.00 0.00 0.00 5.19
865 1017 1.134491 GTCCGTCCGATTTTCTCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
868 1020 2.205074 CGTCCGATTTTCTCCCATCTG 58.795 52.381 0.00 0.00 0.00 2.90
869 1021 2.159099 CGTCCGATTTTCTCCCATCTGA 60.159 50.000 0.00 0.00 0.00 3.27
870 1022 3.493350 CGTCCGATTTTCTCCCATCTGAT 60.493 47.826 0.00 0.00 0.00 2.90
873 1041 3.181451 CCGATTTTCTCCCATCTGATCCA 60.181 47.826 0.00 0.00 0.00 3.41
890 1058 2.776526 ACCCCTGTGTGGCTTCCA 60.777 61.111 0.00 0.00 0.00 3.53
891 1059 2.391130 ACCCCTGTGTGGCTTCCAA 61.391 57.895 0.00 0.00 34.18 3.53
892 1060 1.903404 CCCCTGTGTGGCTTCCAAC 60.903 63.158 0.00 0.00 34.18 3.77
893 1061 1.903404 CCCTGTGTGGCTTCCAACC 60.903 63.158 0.00 0.00 34.18 3.77
894 1062 2.260869 CCTGTGTGGCTTCCAACCG 61.261 63.158 0.00 0.00 34.18 4.44
895 1063 2.904866 TGTGTGGCTTCCAACCGC 60.905 61.111 0.00 0.00 34.18 5.68
896 1064 3.670377 GTGTGGCTTCCAACCGCC 61.670 66.667 0.00 0.00 46.46 6.13
911 1079 4.154347 GCCGCCACAGGAGAGGAG 62.154 72.222 0.00 0.00 0.00 3.69
912 1080 4.154347 CCGCCACAGGAGAGGAGC 62.154 72.222 0.00 0.00 0.00 4.70
913 1081 4.154347 CGCCACAGGAGAGGAGCC 62.154 72.222 0.00 0.00 0.00 4.70
914 1082 3.791586 GCCACAGGAGAGGAGCCC 61.792 72.222 0.00 0.00 0.00 5.19
915 1083 2.284921 CCACAGGAGAGGAGCCCA 60.285 66.667 0.00 0.00 0.00 5.36
916 1084 2.365586 CCACAGGAGAGGAGCCCAG 61.366 68.421 0.00 0.00 0.00 4.45
917 1085 1.611851 CACAGGAGAGGAGCCCAGT 60.612 63.158 0.00 0.00 0.00 4.00
918 1086 1.611851 ACAGGAGAGGAGCCCAGTG 60.612 63.158 0.00 0.00 0.00 3.66
919 1087 2.040278 AGGAGAGGAGCCCAGTGG 59.960 66.667 0.63 0.63 0.00 4.00
930 1098 4.436998 CCAGTGGCGGACGGACTC 62.437 72.222 0.00 0.00 0.00 3.36
961 1129 1.103398 AGTGTTGCACCTGCTTCACC 61.103 55.000 16.03 5.18 41.84 4.02
970 1142 2.125552 TGCTTCACCCGATGCTCG 60.126 61.111 0.00 0.00 41.65 5.03
989 1161 3.521796 GCTGGCTGCCCCGATTTC 61.522 66.667 17.53 0.00 35.87 2.17
990 1162 2.830370 CTGGCTGCCCCGATTTCC 60.830 66.667 17.53 0.00 35.87 3.13
991 1163 4.440829 TGGCTGCCCCGATTTCCC 62.441 66.667 17.53 0.00 35.87 3.97
992 1164 4.129148 GGCTGCCCCGATTTCCCT 62.129 66.667 7.66 0.00 0.00 4.20
993 1165 2.517166 GCTGCCCCGATTTCCCTC 60.517 66.667 0.00 0.00 0.00 4.30
1004 1176 1.896122 ATTTCCCTCCCCACGACGTC 61.896 60.000 5.18 5.18 0.00 4.34
1028 1200 3.181489 ACGTCGGGTGAGATAAAGATGAC 60.181 47.826 0.00 0.00 0.00 3.06
1064 1242 2.777692 GGGAGAAGAGAGAGGAGAGAGA 59.222 54.545 0.00 0.00 0.00 3.10
1069 1247 0.468226 GAGAGAGGAGAGAGAGCGGA 59.532 60.000 0.00 0.00 0.00 5.54
1213 1391 1.006337 TTTGGCGCCATGAAACTGC 60.006 52.632 33.25 0.00 0.00 4.40
1252 1440 4.451096 ACCGTGCAGTGACAAGTATTTTAG 59.549 41.667 0.00 0.00 0.00 1.85
1332 1520 3.370978 TGAGCTCGATCCGACAATTTTTC 59.629 43.478 9.64 0.00 0.00 2.29
1385 1573 4.553330 ATTCCCGAGCGATATTACCATT 57.447 40.909 0.00 0.00 0.00 3.16
1396 1584 4.518970 CGATATTACCATTCAAGTTGGGGG 59.481 45.833 2.34 5.04 38.64 5.40
1431 1619 0.250727 GCACAAGGTAACCAGCCAGA 60.251 55.000 0.00 0.00 37.17 3.86
1432 1620 1.813513 CACAAGGTAACCAGCCAGAG 58.186 55.000 0.00 0.00 37.17 3.35
1433 1621 0.693049 ACAAGGTAACCAGCCAGAGG 59.307 55.000 0.00 0.00 37.17 3.69
1434 1622 0.678048 CAAGGTAACCAGCCAGAGGC 60.678 60.000 0.00 0.00 44.87 4.70
1435 1623 1.133809 AAGGTAACCAGCCAGAGGCA 61.134 55.000 11.06 0.00 46.58 4.75
1436 1624 1.133809 AGGTAACCAGCCAGAGGCAA 61.134 55.000 11.06 0.00 46.58 4.52
1473 1672 0.810031 ACCGCGCGCTTAGAAATCAT 60.810 50.000 30.48 0.00 0.00 2.45
1483 1685 5.554636 CGCTTAGAAATCATATGGAATCGC 58.445 41.667 2.13 0.00 0.00 4.58
1898 2115 4.855105 GCCATAGCGACCATGACA 57.145 55.556 0.00 0.00 0.00 3.58
2117 2346 2.094854 ACTGGTAATCGAGTCGAACACC 60.095 50.000 28.83 28.83 41.20 4.16
2119 2348 2.559668 TGGTAATCGAGTCGAACACCTT 59.440 45.455 32.14 20.75 41.31 3.50
2165 2398 3.289911 GCTATAGCTAACGTCTGACACG 58.710 50.000 17.75 0.00 45.67 4.49
2437 2670 1.760086 CCTGCTCATCCCGTCCTCT 60.760 63.158 0.00 0.00 0.00 3.69
2443 2676 3.528370 ATCCCGTCCTCTTCGCCG 61.528 66.667 0.00 0.00 0.00 6.46
2476 2709 4.450122 GCCTACGACGTCGACGCA 62.450 66.667 41.52 22.07 44.43 5.24
2735 2968 1.008424 CGCGCCATCGACATCTACT 60.008 57.895 0.00 0.00 38.10 2.57
2749 2982 3.179830 CATCTACTTGAAGGTCCGTTCG 58.820 50.000 0.00 0.00 0.00 3.95
2753 2986 3.457610 ACTTGAAGGTCCGTTCGTTAA 57.542 42.857 0.00 0.00 0.00 2.01
2755 2988 3.557185 ACTTGAAGGTCCGTTCGTTAAAC 59.443 43.478 0.00 0.00 34.31 2.01
2783 3016 7.586300 CGATCTTCATTCGTTTACTTGTTGTTT 59.414 33.333 0.00 0.00 32.08 2.83
2784 3017 9.872757 GATCTTCATTCGTTTACTTGTTGTTTA 57.127 29.630 0.00 0.00 0.00 2.01
2815 3053 2.925966 ATGTGATGGATGGTTTGGGT 57.074 45.000 0.00 0.00 0.00 4.51
3132 3370 2.567049 CGGGAGAACGACGAGCTT 59.433 61.111 0.00 0.00 35.47 3.74
3147 3385 0.758123 AGCTTAGGATGGAGCTGCTC 59.242 55.000 21.17 21.17 46.82 4.26
3414 3652 6.323996 ACTCCATTTCTTGACACTATCGGATA 59.676 38.462 0.00 0.00 0.00 2.59
3449 3687 7.573968 ATGGTCACTTGAAGATAAATAAGCC 57.426 36.000 0.00 0.00 0.00 4.35
3528 3766 3.823304 AGTTCCTGCAATGAAGAAACTCC 59.177 43.478 0.00 0.00 0.00 3.85
3601 3839 0.179018 GTTCTGTTCCACTGGCCACT 60.179 55.000 0.00 0.00 0.00 4.00
3621 3863 2.354773 GATGTCGGCCGATCGGAC 60.355 66.667 37.64 34.39 43.09 4.79
3626 3868 3.214123 CGGCCGATCGGACCACTA 61.214 66.667 37.64 0.00 41.23 2.74
3627 3869 2.777972 CGGCCGATCGGACCACTAA 61.778 63.158 37.64 0.00 41.23 2.24
3637 3879 0.102663 GGACCACTAAGCGCTCTACC 59.897 60.000 12.06 4.15 0.00 3.18
3643 3885 3.181479 CCACTAAGCGCTCTACCATTACA 60.181 47.826 12.06 0.00 0.00 2.41
3644 3886 3.797256 CACTAAGCGCTCTACCATTACAC 59.203 47.826 12.06 0.00 0.00 2.90
3760 4003 1.075601 ATCCCCAGCTCAGGACAAAA 58.924 50.000 3.31 0.00 34.20 2.44
3768 4011 2.092429 AGCTCAGGACAAAAGACAACCA 60.092 45.455 0.00 0.00 0.00 3.67
3769 4012 2.291741 GCTCAGGACAAAAGACAACCAG 59.708 50.000 0.00 0.00 0.00 4.00
3770 4013 2.291741 CTCAGGACAAAAGACAACCAGC 59.708 50.000 0.00 0.00 0.00 4.85
3771 4014 2.023673 CAGGACAAAAGACAACCAGCA 58.976 47.619 0.00 0.00 0.00 4.41
3772 4015 2.024414 AGGACAAAAGACAACCAGCAC 58.976 47.619 0.00 0.00 0.00 4.40
3773 4016 1.268539 GGACAAAAGACAACCAGCACG 60.269 52.381 0.00 0.00 0.00 5.34
3774 4017 0.738389 ACAAAAGACAACCAGCACGG 59.262 50.000 0.00 0.00 42.50 4.94
3775 4018 0.594796 CAAAAGACAACCAGCACGGC 60.595 55.000 0.00 0.00 39.03 5.68
3800 4043 1.084370 CGAGACGTGGCCTGGAATTC 61.084 60.000 3.32 0.00 0.00 2.17
3851 4094 1.873591 ACGAGACAATCCTTGCAACAC 59.126 47.619 0.00 0.00 0.00 3.32
3858 4101 0.675633 ATCCTTGCAACACACCAAGC 59.324 50.000 0.00 0.00 37.66 4.01
3916 4159 7.455641 TCTCCTATCCTAAGAAAAGATAGCG 57.544 40.000 0.00 0.00 38.66 4.26
3920 4163 7.040340 TCCTATCCTAAGAAAAGATAGCGACAG 60.040 40.741 0.00 0.00 38.66 3.51
3945 4188 2.289945 GCCCCTACTCATCATGGATCAC 60.290 54.545 0.00 0.00 0.00 3.06
3946 4189 2.974794 CCCCTACTCATCATGGATCACA 59.025 50.000 0.00 0.00 0.00 3.58
3947 4190 3.007723 CCCCTACTCATCATGGATCACAG 59.992 52.174 0.00 0.00 0.00 3.66
3948 4191 3.645212 CCCTACTCATCATGGATCACAGT 59.355 47.826 0.00 0.00 0.00 3.55
3949 4192 4.835056 CCCTACTCATCATGGATCACAGTA 59.165 45.833 0.00 0.00 0.00 2.74
3950 4193 5.047448 CCCTACTCATCATGGATCACAGTAG 60.047 48.000 0.00 3.08 0.00 2.57
3951 4194 4.952071 ACTCATCATGGATCACAGTAGG 57.048 45.455 0.00 0.00 0.00 3.18
3952 4195 3.070734 ACTCATCATGGATCACAGTAGGC 59.929 47.826 0.00 0.00 0.00 3.93
3953 4196 3.040477 TCATCATGGATCACAGTAGGCA 58.960 45.455 0.00 0.00 0.00 4.75
3959 4205 2.305635 TGGATCACAGTAGGCAACACAT 59.694 45.455 0.00 0.00 41.41 3.21
3983 4229 3.769300 TCTAGGCTCTCTGTATGCACAAA 59.231 43.478 0.00 0.00 33.22 2.83
3987 4233 3.253188 GGCTCTCTGTATGCACAAAACAA 59.747 43.478 0.00 0.00 33.22 2.83
3990 4236 5.106396 GCTCTCTGTATGCACAAAACAAGAT 60.106 40.000 0.00 0.00 33.22 2.40
4037 4283 2.037902 TGGTTCAGGACATCAAGCGTTA 59.962 45.455 0.00 0.00 0.00 3.18
4125 4371 8.276252 TCAAAGACAAGCCATTAATTACCTAC 57.724 34.615 0.00 0.00 0.00 3.18
4227 4475 2.681976 GCTGTGCCACTATCCAGATGTT 60.682 50.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 50 2.184322 GGTCATGCCTCTCGCGAA 59.816 61.111 11.33 0.00 42.08 4.70
47 51 4.193334 CGGTCATGCCTCTCGCGA 62.193 66.667 9.26 9.26 42.08 5.87
59 63 0.599204 GTTTTCGAGAGGCACGGTCA 60.599 55.000 0.00 0.00 0.00 4.02
127 157 4.116328 CGTGCCTCTCGCGGAAGA 62.116 66.667 6.13 0.90 44.36 2.87
204 323 3.186909 CTCTCGCAAAATCACCATCGTA 58.813 45.455 0.00 0.00 0.00 3.43
208 327 1.098050 GCCTCTCGCAAAATCACCAT 58.902 50.000 0.00 0.00 37.47 3.55
319 450 7.565029 TCCAGATCTTCCAAACTAGATCACATA 59.435 37.037 12.93 0.00 45.90 2.29
323 454 5.721480 TGTCCAGATCTTCCAAACTAGATCA 59.279 40.000 12.93 0.00 45.90 2.92
334 465 1.475403 TCCTCGTGTCCAGATCTTCC 58.525 55.000 0.00 0.00 0.00 3.46
343 474 0.739813 CCGTTGGATTCCTCGTGTCC 60.740 60.000 15.51 0.00 0.00 4.02
347 478 0.682852 TTCACCGTTGGATTCCTCGT 59.317 50.000 15.51 1.12 0.00 4.18
377 508 2.879646 TCTTAAACCGTGCGTCCAAATT 59.120 40.909 0.00 0.00 0.00 1.82
436 571 1.305201 TGTCGCAACCTGGAGTTTTC 58.695 50.000 0.00 0.00 36.18 2.29
442 577 1.523154 GCCATTTGTCGCAACCTGGA 61.523 55.000 17.15 0.00 0.00 3.86
457 592 2.956987 GCGCTCTTTGTGTGCCAT 59.043 55.556 0.00 0.00 35.17 4.40
462 597 1.714899 AAGTTGCGCGCTCTTTGTGT 61.715 50.000 33.29 11.80 0.00 3.72
467 602 1.887242 TGACAAGTTGCGCGCTCTT 60.887 52.632 33.29 29.34 0.00 2.85
469 604 2.127609 GTGACAAGTTGCGCGCTC 60.128 61.111 33.29 23.83 0.00 5.03
477 612 2.654863 CTTCCCAGGTTGTGACAAGTT 58.345 47.619 0.00 0.00 0.00 2.66
549 685 6.054941 CCACAAGCAGTTATATGTATGGACA 58.945 40.000 0.00 0.00 40.72 4.02
590 727 1.695242 TCAGTTTCCGCCCAAAGTAGA 59.305 47.619 0.00 0.00 0.00 2.59
602 739 5.573146 CAGTCTCAGTGTTTTTCAGTTTCC 58.427 41.667 0.00 0.00 0.00 3.13
609 746 2.287248 GGCTGCAGTCTCAGTGTTTTTC 60.287 50.000 16.64 0.00 36.49 2.29
783 920 1.670083 TCCTTGTCGTCTCTCGCGA 60.670 57.895 9.26 9.26 39.67 5.87
793 930 1.597854 TTGGCTGCTGTCCTTGTCG 60.598 57.895 0.00 0.00 0.00 4.35
804 941 1.000396 ATCCCTCCTTGTTGGCTGC 60.000 57.895 0.00 0.00 35.26 5.25
805 942 0.329261 TCATCCCTCCTTGTTGGCTG 59.671 55.000 0.00 0.00 35.26 4.85
806 943 0.622665 CTCATCCCTCCTTGTTGGCT 59.377 55.000 0.00 0.00 35.26 4.75
807 944 0.394899 CCTCATCCCTCCTTGTTGGC 60.395 60.000 0.00 0.00 35.26 4.52
809 946 0.394899 GGCCTCATCCCTCCTTGTTG 60.395 60.000 0.00 0.00 0.00 3.33
810 947 0.846427 TGGCCTCATCCCTCCTTGTT 60.846 55.000 3.32 0.00 0.00 2.83
811 948 1.229951 TGGCCTCATCCCTCCTTGT 60.230 57.895 3.32 0.00 0.00 3.16
812 949 0.984961 TCTGGCCTCATCCCTCCTTG 60.985 60.000 3.32 0.00 0.00 3.61
813 950 0.693767 CTCTGGCCTCATCCCTCCTT 60.694 60.000 3.32 0.00 0.00 3.36
814 951 1.074623 CTCTGGCCTCATCCCTCCT 60.075 63.158 3.32 0.00 0.00 3.69
815 952 1.383803 ACTCTGGCCTCATCCCTCC 60.384 63.158 3.32 0.00 0.00 4.30
816 953 1.743321 CGACTCTGGCCTCATCCCTC 61.743 65.000 3.32 0.00 0.00 4.30
817 954 1.760086 CGACTCTGGCCTCATCCCT 60.760 63.158 3.32 0.00 0.00 4.20
818 955 1.758514 TCGACTCTGGCCTCATCCC 60.759 63.158 3.32 0.00 0.00 3.85
819 956 1.439644 GTCGACTCTGGCCTCATCC 59.560 63.158 8.70 0.00 0.00 3.51
820 957 1.323271 TGGTCGACTCTGGCCTCATC 61.323 60.000 16.46 0.00 0.00 2.92
821 958 1.305297 TGGTCGACTCTGGCCTCAT 60.305 57.895 16.46 0.00 0.00 2.90
822 959 1.979155 CTGGTCGACTCTGGCCTCA 60.979 63.158 16.46 0.97 0.00 3.86
823 960 1.662438 CTCTGGTCGACTCTGGCCTC 61.662 65.000 16.46 0.00 0.00 4.70
824 961 1.680651 CTCTGGTCGACTCTGGCCT 60.681 63.158 16.46 0.00 0.00 5.19
825 962 2.888863 CTCTGGTCGACTCTGGCC 59.111 66.667 16.46 0.00 0.00 5.36
826 963 2.183046 GCTCTGGTCGACTCTGGC 59.817 66.667 16.46 11.34 0.00 4.85
827 964 1.247419 ACAGCTCTGGTCGACTCTGG 61.247 60.000 16.46 5.25 34.19 3.86
828 965 0.170116 GACAGCTCTGGTCGACTCTG 59.830 60.000 16.46 15.67 34.19 3.35
873 1041 2.391130 TTGGAAGCCACACAGGGGT 61.391 57.895 0.00 0.00 41.27 4.95
894 1062 4.154347 CTCCTCTCCTGTGGCGGC 62.154 72.222 0.00 0.00 0.00 6.53
895 1063 4.154347 GCTCCTCTCCTGTGGCGG 62.154 72.222 0.00 0.00 0.00 6.13
896 1064 4.154347 GGCTCCTCTCCTGTGGCG 62.154 72.222 0.00 0.00 0.00 5.69
897 1065 3.791586 GGGCTCCTCTCCTGTGGC 61.792 72.222 0.00 0.00 0.00 5.01
898 1066 2.284921 TGGGCTCCTCTCCTGTGG 60.285 66.667 0.00 0.00 0.00 4.17
899 1067 1.611851 ACTGGGCTCCTCTCCTGTG 60.612 63.158 0.00 0.00 34.60 3.66
900 1068 1.611851 CACTGGGCTCCTCTCCTGT 60.612 63.158 0.00 0.00 35.95 4.00
901 1069 2.365586 CCACTGGGCTCCTCTCCTG 61.366 68.421 0.00 0.00 0.00 3.86
902 1070 2.040278 CCACTGGGCTCCTCTCCT 59.960 66.667 0.00 0.00 0.00 3.69
913 1081 4.436998 GAGTCCGTCCGCCACTGG 62.437 72.222 0.00 0.00 0.00 4.00
914 1082 4.436998 GGAGTCCGTCCGCCACTG 62.437 72.222 0.00 0.00 34.84 3.66
925 1093 1.066587 CTCGCGGATTGAGGAGTCC 59.933 63.158 6.13 0.00 0.00 3.85
926 1094 0.526524 CACTCGCGGATTGAGGAGTC 60.527 60.000 6.13 0.00 37.64 3.36
927 1095 1.251527 ACACTCGCGGATTGAGGAGT 61.252 55.000 6.13 0.00 40.19 3.85
928 1096 0.108615 AACACTCGCGGATTGAGGAG 60.109 55.000 6.13 0.00 37.79 3.69
929 1097 0.389817 CAACACTCGCGGATTGAGGA 60.390 55.000 6.13 0.00 37.79 3.71
930 1098 1.970917 GCAACACTCGCGGATTGAGG 61.971 60.000 6.13 0.62 37.79 3.86
990 1162 4.112341 GTCGACGTCGTGGGGAGG 62.112 72.222 34.40 7.16 40.80 4.30
991 1163 4.456253 CGTCGACGTCGTGGGGAG 62.456 72.222 34.40 17.43 40.80 4.30
1004 1176 1.399440 TCTTTATCTCACCCGACGTCG 59.601 52.381 30.33 30.33 39.44 5.12
1028 1200 4.959210 TCTTCTCCCTTCTCTATGTTCTGG 59.041 45.833 0.00 0.00 0.00 3.86
1069 1247 3.317571 AGCACCCTCGCAAGCTCT 61.318 61.111 0.00 0.00 30.05 4.09
1079 1257 2.611800 TGCATCCTGGAGCACCCT 60.612 61.111 14.24 0.00 35.51 4.34
1081 1259 1.451028 GTCTGCATCCTGGAGCACC 60.451 63.158 14.24 0.00 35.65 5.01
1213 1391 0.662374 CGGTGCTGCTTGCTTGAAAG 60.662 55.000 0.00 0.00 43.37 2.62
1230 1408 3.896648 AAAATACTTGTCACTGCACGG 57.103 42.857 0.00 0.00 0.00 4.94
1306 1494 0.665298 TGTCGGATCGAGCTCATGAG 59.335 55.000 18.84 18.84 36.23 2.90
1396 1584 0.039708 GTGCAAGTTGAAGCTGCTCC 60.040 55.000 7.16 0.00 0.00 4.70
1431 1619 0.190815 AATCAAAGGTGGGGTTGCCT 59.809 50.000 0.00 0.00 36.51 4.75
1432 1620 0.608130 GAATCAAAGGTGGGGTTGCC 59.392 55.000 0.00 0.00 0.00 4.52
1433 1621 1.632589 AGAATCAAAGGTGGGGTTGC 58.367 50.000 0.00 0.00 0.00 4.17
1434 1622 3.509967 GGTAAGAATCAAAGGTGGGGTTG 59.490 47.826 0.00 0.00 0.00 3.77
1435 1623 3.774734 GGTAAGAATCAAAGGTGGGGTT 58.225 45.455 0.00 0.00 0.00 4.11
1436 1624 2.290705 CGGTAAGAATCAAAGGTGGGGT 60.291 50.000 0.00 0.00 0.00 4.95
1473 1672 4.531854 TCAGGATTTTTGGCGATTCCATA 58.468 39.130 0.00 0.00 46.04 2.74
1483 1685 7.452880 TGTCATTAGAACTCAGGATTTTTGG 57.547 36.000 0.00 0.00 0.00 3.28
1847 2064 1.531423 CAATGAGCTGCACCTTGTCT 58.469 50.000 1.02 0.00 0.00 3.41
2117 2346 9.509956 AAGAGTATATACTGTGCTCTAGGTAAG 57.490 37.037 20.13 0.00 36.50 2.34
2119 2348 7.390996 GCAAGAGTATATACTGTGCTCTAGGTA 59.609 40.741 26.63 0.00 39.26 3.08
2165 2398 5.555818 GCAACAAGTTACAAGTCGACAGTAC 60.556 44.000 19.50 13.32 0.00 2.73
2166 2399 4.505191 GCAACAAGTTACAAGTCGACAGTA 59.495 41.667 19.50 16.57 0.00 2.74
2371 2604 3.838271 GCCATCCGCGTCTCCAGA 61.838 66.667 4.92 0.00 0.00 3.86
2476 2709 2.430610 GGCGAGGATCCTCTGCACT 61.431 63.158 36.75 12.68 41.07 4.40
2735 2968 3.795877 AGTTTAACGAACGGACCTTCAA 58.204 40.909 0.00 0.00 43.20 2.69
2749 2982 8.645487 AGTAAACGAATGAAGATCGAGTTTAAC 58.355 33.333 2.65 0.00 42.76 2.01
2753 2986 6.645415 ACAAGTAAACGAATGAAGATCGAGTT 59.355 34.615 2.65 0.00 42.76 3.01
2755 2988 6.633668 ACAAGTAAACGAATGAAGATCGAG 57.366 37.500 2.65 0.00 42.76 4.04
2783 3016 6.487668 CCATCCATCACATTTGAGCACTTATA 59.512 38.462 0.00 0.00 34.35 0.98
2784 3017 5.301045 CCATCCATCACATTTGAGCACTTAT 59.699 40.000 0.00 0.00 34.35 1.73
2785 3018 4.641541 CCATCCATCACATTTGAGCACTTA 59.358 41.667 0.00 0.00 34.35 2.24
2786 3019 3.446161 CCATCCATCACATTTGAGCACTT 59.554 43.478 0.00 0.00 34.35 3.16
3145 3383 0.106335 AGGCGCATCTTCATCTGGAG 59.894 55.000 10.83 0.00 0.00 3.86
3147 3385 0.179065 TCAGGCGCATCTTCATCTGG 60.179 55.000 10.83 0.00 0.00 3.86
3354 3592 3.119096 GGCTTCGTGCGGACCTTC 61.119 66.667 0.00 0.00 44.05 3.46
3414 3652 7.907389 TCTTCAAGTGACCATTAGATTACACT 58.093 34.615 0.00 0.00 39.70 3.55
3427 3665 7.051000 AGAGGCTTATTTATCTTCAAGTGACC 58.949 38.462 0.00 0.00 0.00 4.02
3449 3687 2.099921 AGTGCTACGTCCATGCTAAGAG 59.900 50.000 0.00 0.00 0.00 2.85
3528 3766 4.324974 CAAAAATTTGCTACAATGGCCG 57.675 40.909 0.00 0.00 0.00 6.13
3601 3839 4.923710 CGATCGGCCGACATCGCA 62.924 66.667 31.18 10.50 38.18 5.10
3621 3863 2.604046 AATGGTAGAGCGCTTAGTGG 57.396 50.000 13.26 0.00 0.00 4.00
3626 3868 1.553248 TGGTGTAATGGTAGAGCGCTT 59.447 47.619 13.26 4.13 0.00 4.68
3627 3869 1.191535 TGGTGTAATGGTAGAGCGCT 58.808 50.000 11.27 11.27 0.00 5.92
3644 3886 6.446254 GATGCTTCCATCTTCCAACGTTGG 62.446 50.000 36.52 36.52 45.15 3.77
3760 4003 2.281070 CTGCCGTGCTGGTTGTCT 60.281 61.111 0.00 0.00 41.21 3.41
3826 4069 0.036010 CAAGGATTGTCTCGTGCCCT 60.036 55.000 0.00 0.00 42.34 5.19
3851 4094 1.791103 TTCCTTTTCGCCGCTTGGTG 61.791 55.000 0.00 0.00 45.02 4.17
3858 4101 1.666189 GATCTCCTTTCCTTTTCGCCG 59.334 52.381 0.00 0.00 0.00 6.46
3916 4159 1.961180 ATGAGTAGGGGCGCACTGTC 61.961 60.000 10.74 8.86 0.00 3.51
3920 4163 0.882042 CATGATGAGTAGGGGCGCAC 60.882 60.000 10.83 4.83 0.00 5.34
3945 4188 3.525537 CCTAGACATGTGTTGCCTACTG 58.474 50.000 1.15 0.00 0.00 2.74
3946 4189 2.093447 GCCTAGACATGTGTTGCCTACT 60.093 50.000 1.15 0.00 0.00 2.57
3947 4190 2.093447 AGCCTAGACATGTGTTGCCTAC 60.093 50.000 1.15 0.00 0.00 3.18
3948 4191 2.168521 GAGCCTAGACATGTGTTGCCTA 59.831 50.000 1.15 0.00 0.00 3.93
3949 4192 0.987294 AGCCTAGACATGTGTTGCCT 59.013 50.000 1.15 0.00 0.00 4.75
3950 4193 1.065854 AGAGCCTAGACATGTGTTGCC 60.066 52.381 1.15 0.00 0.00 4.52
3951 4194 2.093764 AGAGAGCCTAGACATGTGTTGC 60.094 50.000 1.15 6.06 0.00 4.17
3952 4195 3.056250 ACAGAGAGCCTAGACATGTGTTG 60.056 47.826 1.15 0.00 0.00 3.33
3953 4196 3.169099 ACAGAGAGCCTAGACATGTGTT 58.831 45.455 1.15 0.00 0.00 3.32
3959 4205 2.690497 GTGCATACAGAGAGCCTAGACA 59.310 50.000 0.00 0.00 0.00 3.41
3983 4229 6.267471 TGAGTTTTGCCCTGAATTATCTTGTT 59.733 34.615 0.00 0.00 0.00 2.83
3987 4233 5.185828 GGTTGAGTTTTGCCCTGAATTATCT 59.814 40.000 0.00 0.00 0.00 1.98
3990 4236 4.219115 TGGTTGAGTTTTGCCCTGAATTA 58.781 39.130 0.00 0.00 0.00 1.40
4227 4475 1.525941 GCCCAAGTTACGGTTTAGCA 58.474 50.000 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.