Multiple sequence alignment - TraesCS3D01G495500

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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 TraesCS3D01G495500 chr3D 100.000 3161 0 0 1 3161 587607218 587610378 0.000000e+00 5838.0
1 TraesCS3D01G495500 chr3A 93.120 1497 76 13 1097 2570 716988120 716989612 0.000000e+00 2169.0
2 TraesCS3D01G495500 chr3A 88.046 527 29 6 1 509 716981437 716981947 7.550000e-166 593.0
3 TraesCS3D01G495500 chr3A 93.798 258 16 0 2575 2832 716990275 716990532 3.820000e-104 388.0
4 TraesCS3D01G495500 chr3A 95.299 234 10 1 2929 3161 716991369 716991602 1.380000e-98 370.0
5 TraesCS3D01G495500 chr3A 90.123 162 4 5 729 882 716987965 716988122 1.920000e-47 200.0
6 TraesCS3D01G495500 chr3B 92.826 1143 62 5 1446 2576 784926604 784927738 0.000000e+00 1639.0
7 TraesCS3D01G495500 chr3B 94.374 551 23 5 914 1456 784925589 784926139 0.000000e+00 839.0
8 TraesCS3D01G495500 chr3B 92.509 267 10 3 1 262 784924228 784924489 1.070000e-99 374.0
9 TraesCS3D01G495500 chr3B 90.545 275 11 5 671 934 784925047 784925317 1.800000e-92 350.0
10 TraesCS3D01G495500 chr3B 92.019 213 14 3 2575 2787 784949860 784950069 2.380000e-76 296.0
11 TraesCS3D01G495500 chr3B 91.244 217 14 2 312 524 784924831 784925046 1.110000e-74 291.0
12 TraesCS3D01G495500 chr3B 91.549 213 15 3 2575 2787 784942463 784942672 1.110000e-74 291.0
13 TraesCS3D01G495500 chr3B 90.610 213 17 3 2575 2787 784935522 784935731 2.400000e-71 279.0
14 TraesCS3D01G495500 chr3B 90.610 213 17 3 2575 2787 784946157 784946366 2.400000e-71 279.0
15 TraesCS3D01G495500 chr3B 92.593 81 5 1 2900 2979 784942674 784942754 7.160000e-22 115.0
16 TraesCS3D01G495500 chr3B 91.358 81 6 1 2900 2979 784935733 784935813 3.330000e-20 110.0
17 TraesCS3D01G495500 chr3B 91.358 81 6 1 2900 2979 784939107 784939187 3.330000e-20 110.0
18 TraesCS3D01G495500 chr3B 91.358 81 6 1 2900 2979 784946368 784946448 3.330000e-20 110.0
19 TraesCS3D01G495500 chr3B 91.358 81 6 1 2900 2979 784950071 784950151 3.330000e-20 110.0
20 TraesCS3D01G495500 chr5B 80.452 1371 169 49 898 2209 426995124 426993794 0.000000e+00 955.0
21 TraesCS3D01G495500 chr5B 93.694 111 6 1 2331 2441 34150918 34151027 7.010000e-37 165.0
22 TraesCS3D01G495500 chr5D 80.119 1343 159 51 898 2183 361405056 361403765 0.000000e+00 902.0
23 TraesCS3D01G495500 chr5D 93.694 111 6 1 2331 2441 378046638 378046529 7.010000e-37 165.0
24 TraesCS3D01G495500 chr5A 79.646 1356 163 56 898 2185 461939145 461937835 0.000000e+00 870.0
25 TraesCS3D01G495500 chr6B 88.511 235 27 0 1301 1535 152108732 152108498 5.160000e-73 285.0
26 TraesCS3D01G495500 chr6B 93.694 111 6 1 2331 2441 297460733 297460624 7.010000e-37 165.0
27 TraesCS3D01G495500 chr6D 88.085 235 28 0 1301 1535 79820438 79820204 2.400000e-71 279.0
28 TraesCS3D01G495500 chr6A 86.809 235 31 0 1301 1535 96452612 96452378 2.420000e-66 263.0
29 TraesCS3D01G495500 chrUn 93.694 111 6 1 2331 2441 206786267 206786158 7.010000e-37 165.0
30 TraesCS3D01G495500 chr4D 93.694 111 6 1 2331 2441 123323091 123322982 7.010000e-37 165.0
31 TraesCS3D01G495500 chr4A 93.694 111 6 1 2331 2441 246670323 246670432 7.010000e-37 165.0
32 TraesCS3D01G495500 chr4A 79.851 134 12 11 2065 2187 2701375 2701504 2.020000e-12 84.2
33 TraesCS3D01G495500 chr1B 93.694 111 6 1 2331 2441 672566513 672566622 7.010000e-37 165.0
34 TraesCS3D01G495500 chr2A 80.741 135 15 11 2065 2190 614570544 614570676 9.330000e-16 95.3


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 TraesCS3D01G495500 chr3D 587607218 587610378 3160 False 5838.00 5838 100.0000 1 3161 1 chr3D.!!$F1 3160
1 TraesCS3D01G495500 chr3A 716987965 716991602 3637 False 781.75 2169 93.0850 729 3161 4 chr3A.!!$F2 2432
2 TraesCS3D01G495500 chr3A 716981437 716981947 510 False 593.00 593 88.0460 1 509 1 chr3A.!!$F1 508
3 TraesCS3D01G495500 chr3B 784924228 784927738 3510 False 698.60 1639 92.2996 1 2576 5 chr3B.!!$F1 2575
4 TraesCS3D01G495500 chr5B 426993794 426995124 1330 True 955.00 955 80.4520 898 2209 1 chr5B.!!$R1 1311
5 TraesCS3D01G495500 chr5D 361403765 361405056 1291 True 902.00 902 80.1190 898 2183 1 chr5D.!!$R1 1285
6 TraesCS3D01G495500 chr5A 461937835 461939145 1310 True 870.00 870 79.6460 898 2185 1 chr5A.!!$R1 1287

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
667 969 0.181587 TTGAGGAAACTTGGTGGCGA 59.818 50.0 0.0 0.0 44.43 5.54 F
1179 1805 0.173481 TCATCCTCGTCGCCTTCTTG 59.827 55.0 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 2680 0.244994 ATGGACACTCGACAGCTCAC 59.755 55.0 0.0 0.00 0.00 3.51 R
2457 3624 0.897863 TGCTAATGGGCAGCCGTTTT 60.898 50.0 5.0 1.22 38.29 2.43 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
53 54 1.377333 GAACGGAAAGAGCTGGGGG 60.377 63.158 0.00 0.00 0.00 5.40
78 79 2.762327 TGTTAGGTAGTTAAGGAGGCCG 59.238 50.000 0.00 0.00 0.00 6.13
108 109 9.185192 GGAGCACAATTAATGCACTAAATAATC 57.815 33.333 14.45 2.44 45.92 1.75
154 155 1.516603 GCCACGTTCTCTCGCCTAC 60.517 63.158 0.00 0.00 0.00 3.18
155 156 1.935327 GCCACGTTCTCTCGCCTACT 61.935 60.000 0.00 0.00 0.00 2.57
156 157 1.376543 CCACGTTCTCTCGCCTACTA 58.623 55.000 0.00 0.00 0.00 1.82
157 158 1.331138 CCACGTTCTCTCGCCTACTAG 59.669 57.143 0.00 0.00 0.00 2.57
213 219 2.695666 ACCATGAACCTGTCTATCTCCG 59.304 50.000 0.00 0.00 0.00 4.63
289 399 4.331968 TGTTTAACACCAGGATCCACATC 58.668 43.478 15.82 0.00 0.00 3.06
301 411 7.557719 ACCAGGATCCACATCTAACATAAAAAG 59.442 37.037 15.82 0.00 0.00 2.27
302 412 7.557719 CCAGGATCCACATCTAACATAAAAAGT 59.442 37.037 15.82 0.00 0.00 2.66
383 685 7.357532 CGTTATCTCACTGTTTTTGTTTCATGC 60.358 37.037 0.00 0.00 0.00 4.06
470 772 3.941483 ACATGCTTTTATGGAGAAGTCGG 59.059 43.478 0.00 0.00 32.32 4.79
474 776 3.600388 CTTTTATGGAGAAGTCGGCACT 58.400 45.455 0.00 0.00 0.00 4.40
533 835 9.970395 AATATATAAACAATCATGTGGCTTGTG 57.030 29.630 0.00 0.00 40.46 3.33
534 836 3.389925 AAACAATCATGTGGCTTGTGG 57.610 42.857 0.00 0.00 40.46 4.17
535 837 1.999648 ACAATCATGTGGCTTGTGGT 58.000 45.000 0.00 0.00 38.69 4.16
536 838 3.153369 ACAATCATGTGGCTTGTGGTA 57.847 42.857 0.00 0.00 38.69 3.25
537 839 3.084039 ACAATCATGTGGCTTGTGGTAG 58.916 45.455 0.00 0.00 38.69 3.18
538 840 1.755179 ATCATGTGGCTTGTGGTAGC 58.245 50.000 0.00 0.00 40.48 3.58
551 853 4.819082 GTAGCCACGCGACCATAA 57.181 55.556 15.93 0.00 0.00 1.90
552 854 3.053662 GTAGCCACGCGACCATAAA 57.946 52.632 15.93 0.00 0.00 1.40
553 855 0.648958 GTAGCCACGCGACCATAAAC 59.351 55.000 15.93 0.00 0.00 2.01
554 856 0.460635 TAGCCACGCGACCATAAACC 60.461 55.000 15.93 0.00 0.00 3.27
555 857 1.743995 GCCACGCGACCATAAACCT 60.744 57.895 15.93 0.00 0.00 3.50
556 858 0.460635 GCCACGCGACCATAAACCTA 60.461 55.000 15.93 0.00 0.00 3.08
557 859 1.567504 CCACGCGACCATAAACCTAG 58.432 55.000 15.93 0.00 0.00 3.02
558 860 0.928229 CACGCGACCATAAACCTAGC 59.072 55.000 15.93 0.00 0.00 3.42
559 861 0.822164 ACGCGACCATAAACCTAGCT 59.178 50.000 15.93 0.00 0.00 3.32
560 862 1.206371 ACGCGACCATAAACCTAGCTT 59.794 47.619 15.93 0.00 0.00 3.74
561 863 1.593006 CGCGACCATAAACCTAGCTTG 59.407 52.381 0.00 0.00 0.00 4.01
562 864 1.940613 GCGACCATAAACCTAGCTTGG 59.059 52.381 13.05 13.05 0.00 3.61
563 865 2.561569 CGACCATAAACCTAGCTTGGG 58.438 52.381 18.75 11.16 0.00 4.12
564 866 2.745152 CGACCATAAACCTAGCTTGGGG 60.745 54.545 18.75 11.44 0.00 4.96
565 867 1.063942 ACCATAAACCTAGCTTGGGGC 60.064 52.381 18.75 0.00 42.19 5.80
566 868 1.064017 CCATAAACCTAGCTTGGGGCA 60.064 52.381 18.75 2.94 44.79 5.36
567 869 2.424812 CCATAAACCTAGCTTGGGGCAT 60.425 50.000 18.75 5.17 44.79 4.40
568 870 3.299503 CATAAACCTAGCTTGGGGCATT 58.700 45.455 18.75 9.88 44.79 3.56
569 871 1.560505 AAACCTAGCTTGGGGCATTG 58.439 50.000 18.75 0.00 44.79 2.82
570 872 0.972471 AACCTAGCTTGGGGCATTGC 60.972 55.000 18.75 0.00 44.79 3.56
571 873 1.076485 CCTAGCTTGGGGCATTGCT 60.076 57.895 8.82 0.00 44.79 3.91
572 874 0.685458 CCTAGCTTGGGGCATTGCTT 60.685 55.000 8.82 0.00 44.79 3.91
573 875 0.458669 CTAGCTTGGGGCATTGCTTG 59.541 55.000 8.82 0.00 44.79 4.01
574 876 0.251742 TAGCTTGGGGCATTGCTTGT 60.252 50.000 8.82 0.00 44.79 3.16
575 877 1.375013 GCTTGGGGCATTGCTTGTG 60.375 57.895 8.82 0.00 41.35 3.33
576 878 1.375013 CTTGGGGCATTGCTTGTGC 60.375 57.895 8.82 0.76 41.78 4.57
618 920 4.929808 ACTTATGCAAGTACTCGAGTTTGG 59.070 41.667 25.44 11.37 43.33 3.28
619 921 3.678056 ATGCAAGTACTCGAGTTTGGA 57.322 42.857 25.44 23.09 0.00 3.53
620 922 3.462483 TGCAAGTACTCGAGTTTGGAA 57.538 42.857 25.44 1.28 0.00 3.53
621 923 3.390135 TGCAAGTACTCGAGTTTGGAAG 58.610 45.455 25.44 10.35 0.00 3.46
622 924 3.181469 TGCAAGTACTCGAGTTTGGAAGT 60.181 43.478 25.44 4.97 0.00 3.01
623 925 3.808174 GCAAGTACTCGAGTTTGGAAGTT 59.192 43.478 25.44 11.37 0.00 2.66
624 926 4.272748 GCAAGTACTCGAGTTTGGAAGTTT 59.727 41.667 25.44 4.33 0.00 2.66
625 927 5.558463 GCAAGTACTCGAGTTTGGAAGTTTC 60.558 44.000 25.44 5.10 0.00 2.78
626 928 5.272283 AGTACTCGAGTTTGGAAGTTTCA 57.728 39.130 25.44 0.00 0.00 2.69
627 929 5.855045 AGTACTCGAGTTTGGAAGTTTCAT 58.145 37.500 25.44 0.00 0.00 2.57
628 930 6.989659 AGTACTCGAGTTTGGAAGTTTCATA 58.010 36.000 25.44 0.00 0.00 2.15
629 931 7.439381 AGTACTCGAGTTTGGAAGTTTCATAA 58.561 34.615 25.44 0.00 0.00 1.90
630 932 7.929785 AGTACTCGAGTTTGGAAGTTTCATAAA 59.070 33.333 25.44 0.00 0.00 1.40
631 933 7.562454 ACTCGAGTTTGGAAGTTTCATAAAA 57.438 32.000 13.58 0.00 0.00 1.52
632 934 8.166422 ACTCGAGTTTGGAAGTTTCATAAAAT 57.834 30.769 13.58 0.00 0.00 1.82
633 935 9.280174 ACTCGAGTTTGGAAGTTTCATAAAATA 57.720 29.630 13.58 0.00 0.00 1.40
634 936 9.760660 CTCGAGTTTGGAAGTTTCATAAAATAG 57.239 33.333 3.62 0.00 0.00 1.73
635 937 9.496873 TCGAGTTTGGAAGTTTCATAAAATAGA 57.503 29.630 0.00 0.00 0.00 1.98
654 956 9.807921 AAAATAGAAATGGTCTTTACTTGAGGA 57.192 29.630 0.00 0.00 37.84 3.71
655 957 9.807921 AAATAGAAATGGTCTTTACTTGAGGAA 57.192 29.630 0.00 0.00 37.84 3.36
656 958 9.807921 AATAGAAATGGTCTTTACTTGAGGAAA 57.192 29.630 0.00 0.00 37.84 3.13
657 959 7.511959 AGAAATGGTCTTTACTTGAGGAAAC 57.488 36.000 0.00 0.00 29.66 2.78
658 960 7.290813 AGAAATGGTCTTTACTTGAGGAAACT 58.709 34.615 0.00 0.00 36.75 2.66
659 961 7.780271 AGAAATGGTCTTTACTTGAGGAAACTT 59.220 33.333 0.00 0.00 34.23 2.66
660 962 6.884280 ATGGTCTTTACTTGAGGAAACTTG 57.116 37.500 0.00 0.00 44.43 3.16
661 963 5.130350 TGGTCTTTACTTGAGGAAACTTGG 58.870 41.667 0.00 0.00 44.43 3.61
662 964 5.131067 GGTCTTTACTTGAGGAAACTTGGT 58.869 41.667 0.00 0.00 44.43 3.67
663 965 5.008712 GGTCTTTACTTGAGGAAACTTGGTG 59.991 44.000 0.00 0.00 44.43 4.17
664 966 5.008712 GTCTTTACTTGAGGAAACTTGGTGG 59.991 44.000 0.00 0.00 44.43 4.61
665 967 1.692411 ACTTGAGGAAACTTGGTGGC 58.308 50.000 0.00 0.00 44.43 5.01
666 968 0.593128 CTTGAGGAAACTTGGTGGCG 59.407 55.000 0.00 0.00 44.43 5.69
667 969 0.181587 TTGAGGAAACTTGGTGGCGA 59.818 50.000 0.00 0.00 44.43 5.54
668 970 0.534203 TGAGGAAACTTGGTGGCGAC 60.534 55.000 0.00 0.00 44.43 5.19
669 971 0.534203 GAGGAAACTTGGTGGCGACA 60.534 55.000 0.00 0.00 44.43 4.35
694 996 1.486439 CCGCGTGCAATTCAAAAAGT 58.514 45.000 4.92 0.00 0.00 2.66
695 997 1.857837 CCGCGTGCAATTCAAAAAGTT 59.142 42.857 4.92 0.00 0.00 2.66
696 998 2.283884 CCGCGTGCAATTCAAAAAGTTT 59.716 40.909 4.92 0.00 0.00 2.66
697 999 3.242252 CCGCGTGCAATTCAAAAAGTTTT 60.242 39.130 4.92 0.00 0.00 2.43
758 1062 6.840780 AAAAGTATGAAGCTGCCACTATTT 57.159 33.333 0.00 0.00 0.00 1.40
759 1063 6.442513 AAAGTATGAAGCTGCCACTATTTC 57.557 37.500 0.00 0.00 0.00 2.17
761 1065 5.500234 AGTATGAAGCTGCCACTATTTCAA 58.500 37.500 0.00 0.00 32.21 2.69
762 1066 4.708726 ATGAAGCTGCCACTATTTCAAC 57.291 40.909 0.00 0.00 32.21 3.18
763 1067 3.485394 TGAAGCTGCCACTATTTCAACA 58.515 40.909 0.00 0.00 0.00 3.33
764 1068 4.081406 TGAAGCTGCCACTATTTCAACAT 58.919 39.130 0.00 0.00 0.00 2.71
765 1069 4.082625 TGAAGCTGCCACTATTTCAACATG 60.083 41.667 0.00 0.00 0.00 3.21
766 1070 3.424703 AGCTGCCACTATTTCAACATGT 58.575 40.909 0.00 0.00 0.00 3.21
767 1071 4.588899 AGCTGCCACTATTTCAACATGTA 58.411 39.130 0.00 0.00 0.00 2.29
953 1557 7.012894 TCCATTTGTCCCATAATAAAGCGTTAG 59.987 37.037 0.00 0.00 0.00 2.34
968 1572 4.541648 TAGGCTCCCCTCCGCTCC 62.542 72.222 0.00 0.00 41.75 4.70
1168 1794 1.871676 TCGTCCTAATCGTCATCCTCG 59.128 52.381 0.00 0.00 0.00 4.63
1179 1805 0.173481 TCATCCTCGTCGCCTTCTTG 59.827 55.000 0.00 0.00 0.00 3.02
1219 1845 1.699083 TCTTCTTGGTCTGCATCCACA 59.301 47.619 9.80 0.00 34.45 4.17
1225 1851 1.589716 GGTCTGCATCCACAACTGCC 61.590 60.000 0.00 0.00 37.59 4.85
1500 2615 1.303561 GCTTGCCTCCCACATCACA 60.304 57.895 0.00 0.00 0.00 3.58
1665 2795 2.124653 ATCGACGCGGAGGAGAGT 60.125 61.111 12.47 0.00 0.00 3.24
1692 2822 2.534990 GAGAGGATCATCCGGGAAGAT 58.465 52.381 14.22 14.22 42.75 2.40
1860 2990 3.642778 GAGGTTCACGCTGCGGCTA 62.643 63.158 26.95 8.08 36.09 3.93
1907 3052 3.934684 GCGCATGAAGAGCCTCGC 61.935 66.667 0.30 0.00 37.02 5.03
1910 3055 2.185350 CATGAAGAGCCTCGCCGT 59.815 61.111 0.00 0.00 0.00 5.68
2373 3540 7.951591 TGCTTGAGCTTTAATTTAGGAGTTTT 58.048 30.769 4.44 0.00 42.66 2.43
2416 3583 1.846007 TGGGTTGTTGGCATATGTCC 58.154 50.000 4.54 7.02 0.00 4.02
2433 3600 3.028130 TGTCCGGCTACATACTGAATGA 58.972 45.455 0.00 0.00 39.07 2.57
2476 3643 0.897863 AAAACGGCTGCCCATTAGCA 60.898 50.000 14.12 0.00 42.88 3.49
2517 3684 7.460296 CAATTTTACGAAACTTGTTTGCCTTT 58.540 30.769 3.27 0.00 0.00 3.11
2523 3690 7.266922 ACGAAACTTGTTTGCCTTTCTAATA 57.733 32.000 3.27 0.00 0.00 0.98
2549 3717 4.713792 ATGTTCTTTCACCTGGTCTCTT 57.286 40.909 0.00 0.00 0.00 2.85
2580 4406 5.581874 GGATGTTTTAAGGGCATCACATTTG 59.418 40.000 13.93 0.00 40.35 2.32
2655 4481 8.810990 ATTTATGAACATTCCCTAAAACCGTA 57.189 30.769 0.00 0.00 0.00 4.02
2707 4533 9.801714 GCATAATTGTCATATTTTTAAGCATGC 57.198 29.630 10.51 10.51 0.00 4.06
2824 4650 6.783708 TTAGAATGTGTGGTGAAGGTTTTT 57.216 33.333 0.00 0.00 0.00 1.94
2832 4658 6.647067 TGTGTGGTGAAGGTTTTTAAAACTTG 59.353 34.615 18.31 0.00 45.40 3.16
2835 4661 6.874664 GTGGTGAAGGTTTTTAAAACTTGGAA 59.125 34.615 18.31 0.50 45.40 3.53
2836 4662 7.064134 GTGGTGAAGGTTTTTAAAACTTGGAAG 59.936 37.037 18.31 0.00 45.40 3.46
2837 4663 7.101054 GGTGAAGGTTTTTAAAACTTGGAAGT 58.899 34.615 18.31 0.00 45.40 3.01
2838 4664 8.252417 GGTGAAGGTTTTTAAAACTTGGAAGTA 58.748 33.333 18.31 0.00 45.40 2.24
2839 4665 9.642327 GTGAAGGTTTTTAAAACTTGGAAGTAA 57.358 29.630 18.31 0.00 45.40 2.24
2840 4666 9.642327 TGAAGGTTTTTAAAACTTGGAAGTAAC 57.358 29.630 18.31 0.41 45.40 2.50
2841 4667 8.692110 AAGGTTTTTAAAACTTGGAAGTAACG 57.308 30.769 18.31 0.00 43.85 3.18
2842 4668 7.829725 AGGTTTTTAAAACTTGGAAGTAACGT 58.170 30.769 18.31 0.00 38.57 3.99
2843 4669 8.955388 AGGTTTTTAAAACTTGGAAGTAACGTA 58.045 29.630 18.31 0.00 38.57 3.57
2844 4670 9.566530 GGTTTTTAAAACTTGGAAGTAACGTAA 57.433 29.630 18.31 0.00 38.57 3.18
2851 4677 9.857957 AAAACTTGGAAGTAACGTAATTTTTGA 57.142 25.926 0.00 0.00 38.57 2.69
2852 4678 9.857957 AAACTTGGAAGTAACGTAATTTTTGAA 57.142 25.926 0.00 0.00 38.57 2.69
2959 5572 5.223449 ACAAGGGAACTAATGAAGAACGA 57.777 39.130 0.00 0.00 42.68 3.85
2972 5585 4.188462 TGAAGAACGAACAAAGAGAAGCA 58.812 39.130 0.00 0.00 0.00 3.91
3023 5636 1.266466 GCGAGGCGTACTTCTGTAAC 58.734 55.000 0.00 0.00 0.00 2.50
3027 5640 1.616865 AGGCGTACTTCTGTAACTGCA 59.383 47.619 0.00 0.00 0.00 4.41
3028 5641 1.993370 GGCGTACTTCTGTAACTGCAG 59.007 52.381 13.48 13.48 37.81 4.41
3102 5716 0.249031 CGCACAGGTCGATGCATAGA 60.249 55.000 5.29 5.29 42.17 1.98
3116 5730 0.647410 CATAGAGACCAAACGCGCAG 59.353 55.000 5.73 2.42 0.00 5.18
3142 5756 4.036852 CACATCTACCTCATGCTCGTAGAA 59.963 45.833 15.73 5.18 41.22 2.10
3155 5769 2.891580 CTCGTAGAAGCCCAGCCTATTA 59.108 50.000 0.00 0.00 34.09 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 4.676459 GCCTCCTTAACTACCTAACACGAC 60.676 50.000 0.00 0.00 0.00 4.34
78 79 5.064441 AGTGCATTAATTGTGCTCCTTTC 57.936 39.130 15.70 3.84 42.92 2.62
154 155 4.676723 GCGCAGGGAATAGAATCTAGCTAG 60.677 50.000 15.01 15.01 0.00 3.42
155 156 3.193691 GCGCAGGGAATAGAATCTAGCTA 59.806 47.826 0.30 0.00 0.00 3.32
156 157 2.028567 GCGCAGGGAATAGAATCTAGCT 60.029 50.000 0.30 0.00 0.00 3.32
157 158 2.342179 GCGCAGGGAATAGAATCTAGC 58.658 52.381 0.30 0.00 0.00 3.42
335 633 3.371285 GTGAATAGACCCGCTCAAACTTC 59.629 47.826 0.00 0.00 0.00 3.01
347 645 5.892568 ACAGTGAGATAACGTGAATAGACC 58.107 41.667 0.00 0.00 0.00 3.85
383 685 6.700960 CCAGCAGAGATAAGAGATTACAAGTG 59.299 42.308 0.00 0.00 0.00 3.16
531 833 4.367023 TGGTCGCGTGGCTACCAC 62.367 66.667 12.15 6.69 46.82 4.16
533 835 0.460635 TTTATGGTCGCGTGGCTACC 60.461 55.000 5.77 6.47 43.46 3.18
534 836 0.648958 GTTTATGGTCGCGTGGCTAC 59.351 55.000 5.77 0.00 0.00 3.58
535 837 0.460635 GGTTTATGGTCGCGTGGCTA 60.461 55.000 5.77 0.00 0.00 3.93
536 838 1.743995 GGTTTATGGTCGCGTGGCT 60.744 57.895 5.77 0.00 0.00 4.75
537 839 0.460635 TAGGTTTATGGTCGCGTGGC 60.461 55.000 5.77 0.00 0.00 5.01
538 840 1.567504 CTAGGTTTATGGTCGCGTGG 58.432 55.000 5.77 0.00 0.00 4.94
539 841 0.928229 GCTAGGTTTATGGTCGCGTG 59.072 55.000 5.77 0.00 0.00 5.34
540 842 0.822164 AGCTAGGTTTATGGTCGCGT 59.178 50.000 5.77 0.00 0.00 6.01
541 843 1.593006 CAAGCTAGGTTTATGGTCGCG 59.407 52.381 3.96 0.00 0.00 5.87
542 844 1.940613 CCAAGCTAGGTTTATGGTCGC 59.059 52.381 3.96 0.00 0.00 5.19
543 845 2.561569 CCCAAGCTAGGTTTATGGTCG 58.438 52.381 3.96 0.00 0.00 4.79
544 846 2.932261 CCCCAAGCTAGGTTTATGGTC 58.068 52.381 3.96 0.00 0.00 4.02
545 847 1.063942 GCCCCAAGCTAGGTTTATGGT 60.064 52.381 3.96 0.00 38.99 3.55
546 848 1.064017 TGCCCCAAGCTAGGTTTATGG 60.064 52.381 3.96 4.24 44.23 2.74
547 849 2.435372 TGCCCCAAGCTAGGTTTATG 57.565 50.000 3.96 0.00 44.23 1.90
548 850 3.299503 CAATGCCCCAAGCTAGGTTTAT 58.700 45.455 3.96 0.00 44.23 1.40
549 851 2.733956 CAATGCCCCAAGCTAGGTTTA 58.266 47.619 3.96 0.00 44.23 2.01
550 852 1.560505 CAATGCCCCAAGCTAGGTTT 58.439 50.000 3.96 0.00 44.23 3.27
551 853 0.972471 GCAATGCCCCAAGCTAGGTT 60.972 55.000 0.12 0.12 44.23 3.50
552 854 1.380380 GCAATGCCCCAAGCTAGGT 60.380 57.895 0.00 0.00 44.23 3.08
553 855 0.685458 AAGCAATGCCCCAAGCTAGG 60.685 55.000 0.00 0.00 44.23 3.02
554 856 0.458669 CAAGCAATGCCCCAAGCTAG 59.541 55.000 0.00 0.00 44.23 3.42
555 857 0.251742 ACAAGCAATGCCCCAAGCTA 60.252 50.000 0.00 0.00 44.23 3.32
556 858 1.534717 ACAAGCAATGCCCCAAGCT 60.535 52.632 0.00 0.00 44.23 3.74
557 859 1.375013 CACAAGCAATGCCCCAAGC 60.375 57.895 0.00 0.00 44.14 4.01
558 860 1.375013 GCACAAGCAATGCCCCAAG 60.375 57.895 0.00 0.00 41.58 3.61
559 861 2.742403 GCACAAGCAATGCCCCAA 59.258 55.556 0.00 0.00 41.58 4.12
594 896 6.071784 TCCAAACTCGAGTACTTGCATAAGTA 60.072 38.462 20.39 0.00 45.07 2.24
596 898 5.168569 TCCAAACTCGAGTACTTGCATAAG 58.831 41.667 20.39 7.55 39.86 1.73
597 899 5.142061 TCCAAACTCGAGTACTTGCATAA 57.858 39.130 20.39 3.93 0.00 1.90
598 900 4.794278 TCCAAACTCGAGTACTTGCATA 57.206 40.909 20.39 6.22 0.00 3.14
599 901 3.678056 TCCAAACTCGAGTACTTGCAT 57.322 42.857 20.39 0.00 0.00 3.96
600 902 3.181469 ACTTCCAAACTCGAGTACTTGCA 60.181 43.478 20.39 3.76 0.00 4.08
601 903 3.391049 ACTTCCAAACTCGAGTACTTGC 58.609 45.455 20.39 0.00 0.00 4.01
602 904 5.522460 TGAAACTTCCAAACTCGAGTACTTG 59.478 40.000 20.39 19.48 0.00 3.16
603 905 5.667466 TGAAACTTCCAAACTCGAGTACTT 58.333 37.500 20.39 7.68 0.00 2.24
604 906 5.272283 TGAAACTTCCAAACTCGAGTACT 57.728 39.130 20.39 6.37 0.00 2.73
605 907 7.647907 TTATGAAACTTCCAAACTCGAGTAC 57.352 36.000 20.39 1.66 0.00 2.73
606 908 8.665643 TTTTATGAAACTTCCAAACTCGAGTA 57.334 30.769 20.39 0.00 0.00 2.59
607 909 7.562454 TTTTATGAAACTTCCAAACTCGAGT 57.438 32.000 13.58 13.58 0.00 4.18
608 910 9.760660 CTATTTTATGAAACTTCCAAACTCGAG 57.239 33.333 11.84 11.84 0.00 4.04
609 911 9.496873 TCTATTTTATGAAACTTCCAAACTCGA 57.503 29.630 0.00 0.00 0.00 4.04
628 930 9.807921 TCCTCAAGTAAAGACCATTTCTATTTT 57.192 29.630 0.00 0.00 32.51 1.82
629 931 9.807921 TTCCTCAAGTAAAGACCATTTCTATTT 57.192 29.630 0.00 0.00 32.51 1.40
630 932 9.807921 TTTCCTCAAGTAAAGACCATTTCTATT 57.192 29.630 0.00 0.00 32.51 1.73
631 933 9.232473 GTTTCCTCAAGTAAAGACCATTTCTAT 57.768 33.333 0.00 0.00 32.51 1.98
632 934 8.437575 AGTTTCCTCAAGTAAAGACCATTTCTA 58.562 33.333 0.00 0.00 32.51 2.10
633 935 7.290813 AGTTTCCTCAAGTAAAGACCATTTCT 58.709 34.615 0.00 0.00 35.32 2.52
634 936 7.511959 AGTTTCCTCAAGTAAAGACCATTTC 57.488 36.000 0.00 0.00 0.00 2.17
635 937 7.201911 CCAAGTTTCCTCAAGTAAAGACCATTT 60.202 37.037 0.00 0.00 0.00 2.32
636 938 6.265422 CCAAGTTTCCTCAAGTAAAGACCATT 59.735 38.462 0.00 0.00 0.00 3.16
637 939 5.770162 CCAAGTTTCCTCAAGTAAAGACCAT 59.230 40.000 0.00 0.00 0.00 3.55
638 940 5.130350 CCAAGTTTCCTCAAGTAAAGACCA 58.870 41.667 0.00 0.00 0.00 4.02
639 941 5.008712 CACCAAGTTTCCTCAAGTAAAGACC 59.991 44.000 0.00 0.00 0.00 3.85
640 942 5.008712 CCACCAAGTTTCCTCAAGTAAAGAC 59.991 44.000 0.00 0.00 0.00 3.01
641 943 5.130350 CCACCAAGTTTCCTCAAGTAAAGA 58.870 41.667 0.00 0.00 0.00 2.52
642 944 4.261614 GCCACCAAGTTTCCTCAAGTAAAG 60.262 45.833 0.00 0.00 0.00 1.85
643 945 3.634910 GCCACCAAGTTTCCTCAAGTAAA 59.365 43.478 0.00 0.00 0.00 2.01
644 946 3.219281 GCCACCAAGTTTCCTCAAGTAA 58.781 45.455 0.00 0.00 0.00 2.24
645 947 2.808933 CGCCACCAAGTTTCCTCAAGTA 60.809 50.000 0.00 0.00 0.00 2.24
646 948 1.692411 GCCACCAAGTTTCCTCAAGT 58.308 50.000 0.00 0.00 0.00 3.16
647 949 0.593128 CGCCACCAAGTTTCCTCAAG 59.407 55.000 0.00 0.00 0.00 3.02
648 950 0.181587 TCGCCACCAAGTTTCCTCAA 59.818 50.000 0.00 0.00 0.00 3.02
649 951 0.534203 GTCGCCACCAAGTTTCCTCA 60.534 55.000 0.00 0.00 0.00 3.86
650 952 0.534203 TGTCGCCACCAAGTTTCCTC 60.534 55.000 0.00 0.00 0.00 3.71
651 953 0.818040 GTGTCGCCACCAAGTTTCCT 60.818 55.000 0.00 0.00 35.44 3.36
652 954 0.818040 AGTGTCGCCACCAAGTTTCC 60.818 55.000 0.00 0.00 42.88 3.13
653 955 0.586802 GAGTGTCGCCACCAAGTTTC 59.413 55.000 0.00 0.00 42.88 2.78
654 956 0.180406 AGAGTGTCGCCACCAAGTTT 59.820 50.000 0.00 0.00 42.88 2.66
655 957 0.532862 CAGAGTGTCGCCACCAAGTT 60.533 55.000 0.00 0.00 42.88 2.66
656 958 1.069765 CAGAGTGTCGCCACCAAGT 59.930 57.895 0.00 0.00 42.88 3.16
657 959 2.320587 GCAGAGTGTCGCCACCAAG 61.321 63.158 0.00 0.00 42.88 3.61
658 960 2.280797 GCAGAGTGTCGCCACCAA 60.281 61.111 0.00 0.00 42.88 3.67
705 1009 6.040842 GGGAGCCATATGTCAAATAACACAAT 59.959 38.462 1.24 0.00 30.55 2.71
873 1186 3.917329 ATATACGTGAGGTGGATGACG 57.083 47.619 0.00 0.00 37.82 4.35
968 1572 8.001881 ACCTCTGTTGAGTAGTACTAATGATG 57.998 38.462 7.74 0.00 38.61 3.07
1114 1740 1.372087 CTGGATGGGCTGAACTTCGC 61.372 60.000 0.00 0.00 0.00 4.70
1168 1794 2.872858 AGAACAAGAACAAGAAGGCGAC 59.127 45.455 0.00 0.00 0.00 5.19
1179 1805 3.070748 GAGGCAGAGGAAGAACAAGAAC 58.929 50.000 0.00 0.00 0.00 3.01
1219 1845 2.672996 GGTGTCGCCATGGCAGTT 60.673 61.111 34.93 0.00 42.06 3.16
1225 1851 0.103208 GAGTAGGAGGTGTCGCCATG 59.897 60.000 4.97 0.00 40.61 3.66
1559 2680 0.244994 ATGGACACTCGACAGCTCAC 59.755 55.000 0.00 0.00 0.00 3.51
1602 2732 3.050275 GAAGCTGACGGTGGCACC 61.050 66.667 26.95 26.95 34.05 5.01
1612 2742 1.004560 CCTCCGTTGCAGAAGCTGA 60.005 57.895 0.00 0.00 42.74 4.26
1635 2765 2.360225 TCGATGACGACGGTGGGA 60.360 61.111 0.00 0.00 43.81 4.37
1692 2822 4.764336 CGCGCCAGTTCGTCCGTA 62.764 66.667 0.00 0.00 0.00 4.02
2069 3223 2.651361 CGTCCAACTCGGCACTCT 59.349 61.111 0.00 0.00 33.14 3.24
2329 3496 9.683069 CTCAAGCAACAAAACTACTTATTTGAT 57.317 29.630 5.35 0.00 38.50 2.57
2416 3583 5.527214 TGGAAAATCATTCAGTATGTAGCCG 59.473 40.000 0.00 0.00 37.40 5.52
2433 3600 2.482721 CCGCTAAACGTGTCTGGAAAAT 59.517 45.455 0.00 0.00 41.42 1.82
2457 3624 0.897863 TGCTAATGGGCAGCCGTTTT 60.898 50.000 5.00 1.22 38.29 2.43
2493 3660 7.547722 AGAAAGGCAAACAAGTTTCGTAAAATT 59.452 29.630 0.00 0.00 34.69 1.82
2500 3667 7.326063 CCTTATTAGAAAGGCAAACAAGTTTCG 59.674 37.037 0.00 0.00 39.69 3.46
2517 3684 7.829211 CCAGGTGAAAGAACATTCCTTATTAGA 59.171 37.037 0.00 0.00 0.00 2.10
2523 3690 4.141158 AGACCAGGTGAAAGAACATTCCTT 60.141 41.667 0.00 0.00 0.00 3.36
2549 3717 4.735369 TGCCCTTAAAACATCCTGAGAAA 58.265 39.130 0.00 0.00 0.00 2.52
2682 4508 9.998381 CGCATGCTTAAAAATATGACAATTATG 57.002 29.630 17.13 0.00 0.00 1.90
2737 4563 8.489990 TTCTTCAAAATGCTTGTTTCATCAAA 57.510 26.923 0.00 0.00 0.00 2.69
2774 4600 9.840427 AAACATTCTTGTACTGTATAACAATGC 57.160 29.630 18.23 0.00 35.21 3.56
2921 5534 9.636789 AGTTCCCTTGTTTAGTTATAGTTTGTT 57.363 29.630 0.00 0.00 0.00 2.83
2931 5544 8.847196 GTTCTTCATTAGTTCCCTTGTTTAGTT 58.153 33.333 0.00 0.00 0.00 2.24
2959 5572 6.469782 TTCATTCCTTTGCTTCTCTTTGTT 57.530 33.333 0.00 0.00 0.00 2.83
2972 5585 5.183904 GTGGTTCAGTAGCATTCATTCCTTT 59.816 40.000 0.00 0.00 36.50 3.11
3102 5716 2.665185 GACCTGCGCGTTTGGTCT 60.665 61.111 27.35 8.04 44.84 3.85
3116 5730 2.544694 CGAGCATGAGGTAGATGTGACC 60.545 54.545 0.00 0.00 37.22 4.02
3142 5756 3.780624 CGTGTTAATAGGCTGGGCT 57.219 52.632 0.00 1.68 0.00 5.19


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

AutoCloner maintained by Alex Coulton.