Multiple sequence alignment - TraesCS2D01G407200

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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 TraesCS2D01G407200 chr2D 100.000 3410 0 0 1 3410 522628697 522632106 0.000000e+00 6298
1 TraesCS2D01G407200 chr2D 78.959 1402 262 30 1023 2412 577609368 577607988 0.000000e+00 924
2 TraesCS2D01G407200 chr2D 78.689 1403 264 23 1023 2412 522689388 522690768 0.000000e+00 902
3 TraesCS2D01G407200 chr2D 78.216 1345 258 29 1040 2368 522897805 522899130 0.000000e+00 828
4 TraesCS2D01G407200 chr2D 74.697 1403 300 40 1034 2410 75760789 75759416 1.060000e-159 573
5 TraesCS2D01G407200 chr2D 74.486 1411 300 53 1044 2416 75674915 75676303 1.070000e-154 556
6 TraesCS2D01G407200 chr2D 85.045 448 56 7 2957 3400 379861966 379862406 2.410000e-121 446
7 TraesCS2D01G407200 chr2A 92.090 2655 129 46 441 3077 667941656 667944247 0.000000e+00 3664
8 TraesCS2D01G407200 chr2A 79.642 1395 255 25 1028 2412 715806819 715808194 0.000000e+00 976
9 TraesCS2D01G407200 chr2A 77.833 1403 276 25 1023 2412 667959476 667960856 0.000000e+00 835
10 TraesCS2D01G407200 chr2A 74.947 1413 297 47 1034 2410 75656519 75655128 2.270000e-166 595
11 TraesCS2D01G407200 chr2A 86.638 232 16 3 207 423 667941372 667941603 3.400000e-60 243
12 TraesCS2D01G407200 chr2B 94.726 1896 75 14 989 2873 615577799 615579680 0.000000e+00 2924
13 TraesCS2D01G407200 chr2B 87.600 879 51 21 1 859 615576820 615577660 0.000000e+00 966
14 TraesCS2D01G407200 chr2B 78.571 1400 271 26 1023 2412 694944102 694945482 0.000000e+00 896
15 TraesCS2D01G407200 chr2B 77.857 1400 281 24 1023 2412 615736044 615737424 0.000000e+00 841
16 TraesCS2D01G407200 chr2B 77.061 1395 285 26 1031 2412 615788473 615789845 0.000000e+00 771
17 TraesCS2D01G407200 chr2B 72.979 940 199 42 1034 1941 116848094 116847178 9.320000e-71 278
18 TraesCS2D01G407200 chr7D 83.913 460 66 6 2943 3400 547272444 547272897 1.880000e-117 433
19 TraesCS2D01G407200 chr7D 82.468 462 72 6 2943 3400 35179096 35178640 2.470000e-106 396
20 TraesCS2D01G407200 chr5D 85.678 398 52 4 3004 3400 334047309 334046916 6.810000e-112 414
21 TraesCS2D01G407200 chr5D 85.213 399 53 4 3004 3400 334049517 334049123 4.100000e-109 405
22 TraesCS2D01G407200 chr3A 82.213 461 71 8 2942 3400 12025225 12024774 1.480000e-103 387
23 TraesCS2D01G407200 chr4B 82.057 457 69 10 2947 3400 139633358 139633804 8.930000e-101 377
24 TraesCS2D01G407200 chr5B 81.385 462 77 6 2942 3400 276665175 276664720 5.380000e-98 368
25 TraesCS2D01G407200 chr1D 83.500 400 58 5 3002 3400 420655654 420655262 1.930000e-97 366


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 TraesCS2D01G407200 chr2D 522628697 522632106 3409 False 6298.0 6298 100.0000 1 3410 1 chr2D.!!$F3 3409
1 TraesCS2D01G407200 chr2D 577607988 577609368 1380 True 924.0 924 78.9590 1023 2412 1 chr2D.!!$R2 1389
2 TraesCS2D01G407200 chr2D 522689388 522690768 1380 False 902.0 902 78.6890 1023 2412 1 chr2D.!!$F4 1389
3 TraesCS2D01G407200 chr2D 522897805 522899130 1325 False 828.0 828 78.2160 1040 2368 1 chr2D.!!$F5 1328
4 TraesCS2D01G407200 chr2D 75759416 75760789 1373 True 573.0 573 74.6970 1034 2410 1 chr2D.!!$R1 1376
5 TraesCS2D01G407200 chr2D 75674915 75676303 1388 False 556.0 556 74.4860 1044 2416 1 chr2D.!!$F1 1372
6 TraesCS2D01G407200 chr2A 667941372 667944247 2875 False 1953.5 3664 89.3640 207 3077 2 chr2A.!!$F3 2870
7 TraesCS2D01G407200 chr2A 715806819 715808194 1375 False 976.0 976 79.6420 1028 2412 1 chr2A.!!$F2 1384
8 TraesCS2D01G407200 chr2A 667959476 667960856 1380 False 835.0 835 77.8330 1023 2412 1 chr2A.!!$F1 1389
9 TraesCS2D01G407200 chr2A 75655128 75656519 1391 True 595.0 595 74.9470 1034 2410 1 chr2A.!!$R1 1376
10 TraesCS2D01G407200 chr2B 615576820 615579680 2860 False 1945.0 2924 91.1630 1 2873 2 chr2B.!!$F4 2872
11 TraesCS2D01G407200 chr2B 694944102 694945482 1380 False 896.0 896 78.5710 1023 2412 1 chr2B.!!$F3 1389
12 TraesCS2D01G407200 chr2B 615736044 615737424 1380 False 841.0 841 77.8570 1023 2412 1 chr2B.!!$F1 1389
13 TraesCS2D01G407200 chr2B 615788473 615789845 1372 False 771.0 771 77.0610 1031 2412 1 chr2B.!!$F2 1381
14 TraesCS2D01G407200 chr2B 116847178 116848094 916 True 278.0 278 72.9790 1034 1941 1 chr2B.!!$R1 907
15 TraesCS2D01G407200 chr5D 334046916 334049517 2601 True 409.5 414 85.4455 3004 3400 2 chr5D.!!$R1 396

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
112 113 0.040958 CAGTTTTGTGCTCTGACGCC 60.041 55.0 0.00 0.0 0.00 5.68 F
926 1045 0.384309 TAGCGCCGGACAATCTGTAG 59.616 55.0 5.05 0.0 0.00 2.74 F
1016 1135 0.327924 TCAATGGCGGTTGACTCCAT 59.672 50.0 1.53 0.0 42.01 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1017 1136 0.395724 AGGCCACCGATTCCAATTCC 60.396 55.000 5.01 0.0 0.00 3.01 R
1836 1997 1.002990 TGCCAGGAGAGACGACGTA 60.003 57.895 0.00 0.0 0.00 3.57 R
2991 3180 1.173913 GAGGGTCCGACCAAAAATGG 58.826 55.000 19.43 0.0 41.02 3.16 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
28 29 2.729360 GCAGCGTTATCATGCACGTATA 59.271 45.455 11.84 0.00 39.75 1.47
40 41 1.472552 GCACGTATATGGGAGCACACA 60.473 52.381 0.00 0.00 0.00 3.72
59 60 1.258982 CACGCAGTTGGATATTCGCTC 59.741 52.381 0.00 0.00 41.61 5.03
91 92 3.958147 AACAGAGCACGGCGATGGG 62.958 63.158 16.62 0.49 0.00 4.00
101 102 1.234615 CGGCGATGGGTCAGTTTTGT 61.235 55.000 0.00 0.00 0.00 2.83
112 113 0.040958 CAGTTTTGTGCTCTGACGCC 60.041 55.000 0.00 0.00 0.00 5.68
237 238 0.739813 CCGGTTCAATCACGAGACCC 60.740 60.000 0.00 0.00 0.00 4.46
316 334 2.478709 CCTGCTCAGCGACTACTACTTG 60.479 54.545 0.00 0.00 0.00 3.16
355 373 2.612972 CCGCACACCTACAAAGTCAGAT 60.613 50.000 0.00 0.00 0.00 2.90
360 378 5.056480 CACACCTACAAAGTCAGATGAACA 58.944 41.667 0.00 0.00 0.00 3.18
377 395 4.717877 TGAACATTTCTTGGAGAAGCAGA 58.282 39.130 0.00 0.00 35.37 4.26
380 398 3.817647 ACATTTCTTGGAGAAGCAGACAC 59.182 43.478 0.00 0.00 35.37 3.67
381 399 3.845781 TTTCTTGGAGAAGCAGACACT 57.154 42.857 0.00 0.00 35.37 3.55
401 419 7.672239 AGACACTAGTGTTTTCTAGAGGAAGAT 59.328 37.037 28.49 0.02 45.05 2.40
423 445 1.153939 CAGTCGCACGAGCTTAGCT 60.154 57.895 6.37 6.37 43.88 3.32
424 446 0.734253 CAGTCGCACGAGCTTAGCTT 60.734 55.000 8.58 0.00 39.88 3.74
425 447 0.809385 AGTCGCACGAGCTTAGCTTA 59.191 50.000 8.58 0.00 39.88 3.09
426 448 1.192793 GTCGCACGAGCTTAGCTTAG 58.807 55.000 8.58 8.61 39.88 2.18
427 449 0.525668 TCGCACGAGCTTAGCTTAGC 60.526 55.000 16.83 16.83 39.88 3.09
428 450 1.802300 CGCACGAGCTTAGCTTAGCG 61.802 60.000 24.98 24.98 45.82 4.26
429 451 1.920762 CACGAGCTTAGCTTAGCGC 59.079 57.895 18.29 17.69 45.82 5.92
431 453 4.711980 GAGCTTAGCTTAGCGCGA 57.288 55.556 18.29 0.00 45.82 5.87
480 537 4.742201 CCGTGTGCGTCCCTCAGG 62.742 72.222 0.00 0.00 36.15 3.86
600 657 2.119495 GACATCCCAAGGAGCCTTCTA 58.881 52.381 0.00 0.00 34.05 2.10
605 662 1.916181 CCCAAGGAGCCTTCTAGGAAA 59.084 52.381 0.00 0.00 37.67 3.13
606 663 2.308866 CCCAAGGAGCCTTCTAGGAAAA 59.691 50.000 0.00 0.00 37.67 2.29
658 717 4.435436 CTGCTCGTGCCCTGCGTA 62.435 66.667 7.05 0.00 38.71 4.42
698 780 4.518249 TGTTGGCGTCATTCCATACATAA 58.482 39.130 0.00 0.00 32.92 1.90
699 781 5.129634 TGTTGGCGTCATTCCATACATAAT 58.870 37.500 0.00 0.00 32.92 1.28
700 782 6.292150 TGTTGGCGTCATTCCATACATAATA 58.708 36.000 0.00 0.00 32.92 0.98
716 798 4.344679 ACATAATATGGTTGGTGCCAATGG 59.655 41.667 6.95 0.00 42.48 3.16
880 999 1.880675 TGTTAGCGGAGAGATCGATCC 59.119 52.381 21.66 13.02 0.00 3.36
923 1042 2.370281 ATATAGCGCCGGACAATCTG 57.630 50.000 5.05 0.00 0.00 2.90
924 1043 1.037493 TATAGCGCCGGACAATCTGT 58.963 50.000 5.05 0.00 0.00 3.41
925 1044 1.037493 ATAGCGCCGGACAATCTGTA 58.963 50.000 5.05 0.00 0.00 2.74
926 1045 0.384309 TAGCGCCGGACAATCTGTAG 59.616 55.000 5.05 0.00 0.00 2.74
927 1046 2.526120 GCGCCGGACAATCTGTAGC 61.526 63.158 5.05 0.00 0.00 3.58
928 1047 1.141881 CGCCGGACAATCTGTAGCT 59.858 57.895 5.05 0.00 0.00 3.32
930 1049 1.291132 GCCGGACAATCTGTAGCTTC 58.709 55.000 5.05 0.00 0.00 3.86
931 1050 1.560923 CCGGACAATCTGTAGCTTCG 58.439 55.000 0.00 0.00 0.00 3.79
932 1051 1.134367 CCGGACAATCTGTAGCTTCGA 59.866 52.381 0.00 0.00 0.00 3.71
933 1052 2.186076 CGGACAATCTGTAGCTTCGAC 58.814 52.381 0.00 0.00 0.00 4.20
934 1053 2.186076 GGACAATCTGTAGCTTCGACG 58.814 52.381 0.00 0.00 0.00 5.12
935 1054 1.584308 GACAATCTGTAGCTTCGACGC 59.416 52.381 5.63 5.63 0.00 5.19
936 1055 0.924090 CAATCTGTAGCTTCGACGCC 59.076 55.000 10.66 0.00 0.00 5.68
937 1056 0.525668 AATCTGTAGCTTCGACGCCG 60.526 55.000 10.66 0.00 37.07 6.46
938 1057 2.938539 ATCTGTAGCTTCGACGCCGC 62.939 60.000 10.66 4.39 35.37 6.53
940 1059 2.807895 GTAGCTTCGACGCCGCAA 60.808 61.111 10.66 0.00 35.37 4.85
941 1060 2.165301 GTAGCTTCGACGCCGCAAT 61.165 57.895 10.66 0.00 35.37 3.56
942 1061 1.447140 TAGCTTCGACGCCGCAATT 60.447 52.632 10.66 0.00 35.37 2.32
966 1085 7.457024 TCAAGCAGTTATACTACACTGTACA 57.543 36.000 0.00 0.00 42.19 2.90
969 1088 8.456471 CAAGCAGTTATACTACACTGTACAGTA 58.544 37.037 27.48 12.85 42.19 2.74
974 1093 9.512588 AGTTATACTACACTGTACAGTACACTT 57.487 33.333 27.48 13.50 40.20 3.16
984 1103 7.749570 CACTGTACAGTACACTTCTATACACAC 59.250 40.741 27.48 0.00 40.20 3.82
985 1104 6.834876 TGTACAGTACACTTCTATACACACG 58.165 40.000 9.51 0.00 32.89 4.49
986 1105 4.730657 ACAGTACACTTCTATACACACGC 58.269 43.478 0.00 0.00 0.00 5.34
987 1106 3.784468 CAGTACACTTCTATACACACGCG 59.216 47.826 3.53 3.53 0.00 6.01
1016 1135 0.327924 TCAATGGCGGTTGACTCCAT 59.672 50.000 1.53 0.00 42.01 3.41
1017 1136 0.452987 CAATGGCGGTTGACTCCATG 59.547 55.000 8.45 0.00 40.24 3.66
1018 1137 0.680921 AATGGCGGTTGACTCCATGG 60.681 55.000 4.97 4.97 40.24 3.66
1019 1138 1.561769 ATGGCGGTTGACTCCATGGA 61.562 55.000 15.27 15.27 39.01 3.41
1020 1139 1.002624 GGCGGTTGACTCCATGGAA 60.003 57.895 17.00 0.00 0.00 3.53
1021 1140 0.394352 GGCGGTTGACTCCATGGAAT 60.394 55.000 17.00 5.36 0.00 3.01
2413 2586 3.262420 GCTTACGTCACAAGGTGATCAT 58.738 45.455 0.00 0.00 44.63 2.45
2425 2598 2.695147 AGGTGATCATCGTATCTGTGCA 59.305 45.455 0.00 0.00 0.00 4.57
2450 2623 3.244215 CCATAGACAGATACGCATTGGGT 60.244 47.826 11.38 11.38 0.00 4.51
2461 2634 0.318120 GCATTGGGTGGTTTGGTCTG 59.682 55.000 0.00 0.00 0.00 3.51
2483 2659 6.039270 TCTGATCGGATGTGTTTGAAACTTTT 59.961 34.615 9.69 0.00 0.00 2.27
2488 2664 7.038659 TCGGATGTGTTTGAAACTTTTGAATT 58.961 30.769 9.69 0.00 0.00 2.17
2493 2669 7.914465 TGTGTTTGAAACTTTTGAATTATGCC 58.086 30.769 9.69 0.00 0.00 4.40
2508 2684 1.373570 ATGCCTTCTACGAAAGCTGC 58.626 50.000 0.00 0.00 0.00 5.25
2556 2735 8.869897 TCGTTTTCAATGTATTCATCTACTCAC 58.130 33.333 0.00 0.00 32.56 3.51
2576 2756 3.980775 CACTTTTAATCACACAAAGGGCG 59.019 43.478 0.00 0.00 32.68 6.13
2637 2817 8.409358 AGTATTTTCATCTAAAAGCAAGTGGT 57.591 30.769 0.00 0.00 40.32 4.16
2654 2835 9.095700 AGCAAGTGGTAAGGGAAAATAAATAAA 57.904 29.630 0.00 0.00 0.00 1.40
2655 2836 9.884636 GCAAGTGGTAAGGGAAAATAAATAAAT 57.115 29.630 0.00 0.00 0.00 1.40
2702 2883 9.390795 GTATTATGATGTTGATGAAGTGAATGC 57.609 33.333 0.00 0.00 0.00 3.56
2777 2958 2.930040 GTCTGGTCCACATGATGTAACG 59.070 50.000 0.00 0.00 0.00 3.18
2783 2964 4.378046 GGTCCACATGATGTAACGACAAAC 60.378 45.833 16.46 2.35 39.59 2.93
2806 2987 3.004752 ACAAATCAAGATTCTCCGGGG 57.995 47.619 0.00 0.00 0.00 5.73
2810 2991 3.567478 ATCAAGATTCTCCGGGGAAAG 57.433 47.619 23.21 11.62 0.00 2.62
2814 2995 4.018415 TCAAGATTCTCCGGGGAAAGAAAT 60.018 41.667 23.21 3.22 35.29 2.17
2816 2997 5.037383 AGATTCTCCGGGGAAAGAAATAC 57.963 43.478 23.21 8.85 35.29 1.89
2817 2998 3.639672 TTCTCCGGGGAAAGAAATACC 57.360 47.619 16.30 0.00 0.00 2.73
2845 3034 9.277565 CGAGTACAATTGAATGTTAGAAATTGG 57.722 33.333 13.59 0.00 41.93 3.16
2863 3052 0.671251 GGCTCAGGAGGACATAGACG 59.329 60.000 0.00 0.00 0.00 4.18
2873 3062 4.082136 GGAGGACATAGACGTCTCAACTTT 60.082 45.833 23.89 5.25 36.12 2.66
2874 3063 5.125097 GGAGGACATAGACGTCTCAACTTTA 59.875 44.000 23.89 2.26 36.12 1.85
2888 3077 7.595502 CGTCTCAACTTTAGAGTTTACATGACT 59.404 37.037 0.00 0.00 43.48 3.41
2889 3078 8.704234 GTCTCAACTTTAGAGTTTACATGACTG 58.296 37.037 0.00 0.00 43.48 3.51
2900 3089 9.561069 AGAGTTTACATGACTGAAACAGTTATT 57.439 29.630 0.00 2.61 45.44 1.40
2920 3109 1.815613 TGTTTGGCCCATAATGTCACG 59.184 47.619 0.00 0.00 0.00 4.35
2921 3110 1.134175 GTTTGGCCCATAATGTCACGG 59.866 52.381 0.00 0.00 0.00 4.94
2961 3150 2.203611 CCACACATGGGCCCAACA 60.204 61.111 32.58 5.36 43.04 3.33
2962 3151 2.573083 CCACACATGGGCCCAACAC 61.573 63.158 32.58 0.00 43.04 3.32
2963 3152 1.831726 CACACATGGGCCCAACACA 60.832 57.895 32.58 4.35 0.00 3.72
2964 3153 1.155859 ACACATGGGCCCAACACAT 59.844 52.632 32.58 9.34 0.00 3.21
2988 3177 2.764637 AATCACCCCAGAACGCACCC 62.765 60.000 0.00 0.00 0.00 4.61
2991 3180 2.359975 CCCCAGAACGCACCCTTC 60.360 66.667 0.00 0.00 0.00 3.46
3002 3192 1.336795 CGCACCCTTCCATTTTTGGTC 60.337 52.381 0.00 0.00 0.00 4.02
3059 5457 0.721718 GGACATTTCTCGTTGGAGCG 59.278 55.000 0.00 0.00 40.26 5.03
3077 5475 1.810755 GCGTCCTCCTTTAAAACCAGG 59.189 52.381 0.00 0.00 0.00 4.45
3082 5480 2.812011 CCTCCTTTAAAACCAGGTGACG 59.188 50.000 0.00 0.00 0.00 4.35
3096 5494 0.321653 GTGACGCCCACCTCATCTTT 60.322 55.000 0.00 0.00 39.86 2.52
3113 5511 2.034432 TCTTTGTCATGCGTTGCAACAT 59.966 40.909 28.01 13.13 43.62 2.71
3180 5579 8.331730 ACTAACCCATACTATTGACACAAAAC 57.668 34.615 0.00 0.00 0.00 2.43
3209 5608 8.994429 AAATAACTACAGTGATCAGTCTCAAG 57.006 34.615 0.00 0.00 0.00 3.02
3212 5611 2.614259 ACAGTGATCAGTCTCAAGGGT 58.386 47.619 0.00 0.00 0.00 4.34
3213 5612 3.779444 ACAGTGATCAGTCTCAAGGGTA 58.221 45.455 0.00 0.00 0.00 3.69
3224 5623 5.765182 CAGTCTCAAGGGTACATTCAACTTT 59.235 40.000 0.00 0.00 0.00 2.66
3226 5625 5.531287 GTCTCAAGGGTACATTCAACTTTGT 59.469 40.000 0.00 0.00 0.00 2.83
3237 5636 5.752955 ACATTCAACTTTGTAAATGCACACC 59.247 36.000 0.00 0.00 0.00 4.16
3245 5644 2.080693 GTAAATGCACACCGACATGGA 58.919 47.619 0.00 0.00 42.00 3.41
3257 5656 0.678048 GACATGGAAGGTGAGTGGCC 60.678 60.000 0.00 0.00 0.00 5.36
3259 5658 0.251297 CATGGAAGGTGAGTGGCCAA 60.251 55.000 7.24 0.00 31.53 4.52
3262 5661 0.690762 GGAAGGTGAGTGGCCAACTA 59.309 55.000 7.24 0.00 40.07 2.24
3266 5665 4.566907 GGAAGGTGAGTGGCCAACTAAATA 60.567 45.833 7.24 0.00 40.07 1.40
3280 5679 8.709646 GGCCAACTAAATATATTTCTAGTCACG 58.290 37.037 13.95 6.21 0.00 4.35
3292 5691 5.654603 TTCTAGTCACGAATAAGCTCCAA 57.345 39.130 0.00 0.00 0.00 3.53
3296 5695 3.511934 AGTCACGAATAAGCTCCAACTCT 59.488 43.478 0.00 0.00 0.00 3.24
3299 5698 4.948004 TCACGAATAAGCTCCAACTCTAGA 59.052 41.667 0.00 0.00 0.00 2.43
3329 5728 6.460103 ACCATTCATTGCTAGAAGGGATAT 57.540 37.500 18.85 0.43 46.80 1.63
3330 5729 7.574021 ACCATTCATTGCTAGAAGGGATATA 57.426 36.000 18.85 0.00 46.80 0.86
3332 5731 9.284131 ACCATTCATTGCTAGAAGGGATATATA 57.716 33.333 18.85 0.00 46.80 0.86
3336 5735 7.782049 TCATTGCTAGAAGGGATATATAACCG 58.218 38.462 3.18 0.00 0.00 4.44
3337 5736 7.399191 TCATTGCTAGAAGGGATATATAACCGT 59.601 37.037 3.18 0.98 0.00 4.83
3338 5737 6.770746 TGCTAGAAGGGATATATAACCGTC 57.229 41.667 4.88 8.99 33.71 4.79
3357 5756 2.485038 GTCGTTCTTCTCTTCCTCGTCT 59.515 50.000 0.00 0.00 0.00 4.18
3362 5761 2.488545 TCTTCTCTTCCTCGTCTTTCCG 59.511 50.000 0.00 0.00 0.00 4.30
3363 5762 1.906990 TCTCTTCCTCGTCTTTCCGT 58.093 50.000 0.00 0.00 0.00 4.69
3380 5779 7.066766 GTCTTTCCGTACATCTTCTACTCCTAA 59.933 40.741 0.00 0.00 0.00 2.69
3381 5780 6.690194 TTCCGTACATCTTCTACTCCTAAC 57.310 41.667 0.00 0.00 0.00 2.34
3386 5785 6.543100 CGTACATCTTCTACTCCTAACCTCTT 59.457 42.308 0.00 0.00 0.00 2.85
3388 5787 5.591067 ACATCTTCTACTCCTAACCTCTTCG 59.409 44.000 0.00 0.00 0.00 3.79
3396 5795 0.323629 CTAACCTCTTCGCCAACCCA 59.676 55.000 0.00 0.00 0.00 4.51
3400 5799 1.256812 CCTCTTCGCCAACCCATTTT 58.743 50.000 0.00 0.00 0.00 1.82
3401 5800 1.067635 CCTCTTCGCCAACCCATTTTG 60.068 52.381 0.00 0.00 0.00 2.44
3402 5801 0.316841 TCTTCGCCAACCCATTTTGC 59.683 50.000 0.00 0.00 0.00 3.68
3403 5802 0.318120 CTTCGCCAACCCATTTTGCT 59.682 50.000 0.00 0.00 0.00 3.91
3404 5803 1.543802 CTTCGCCAACCCATTTTGCTA 59.456 47.619 0.00 0.00 0.00 3.49
3405 5804 1.173043 TCGCCAACCCATTTTGCTAG 58.827 50.000 0.00 0.00 0.00 3.42
3406 5805 0.887933 CGCCAACCCATTTTGCTAGT 59.112 50.000 0.00 0.00 0.00 2.57
3407 5806 1.402720 CGCCAACCCATTTTGCTAGTG 60.403 52.381 0.00 0.00 0.00 2.74
3408 5807 1.672737 GCCAACCCATTTTGCTAGTGC 60.673 52.381 0.00 0.00 40.20 4.40
3409 5808 1.066929 CCAACCCATTTTGCTAGTGCC 60.067 52.381 0.00 0.00 38.71 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.359107 CTGCGTGTGTGCTCCCAT 60.359 61.111 0.00 0.00 35.36 4.00
40 41 1.137086 AGAGCGAATATCCAACTGCGT 59.863 47.619 0.00 0.00 0.00 5.24
112 113 3.661025 GAAAATGCCACCGCCGTCG 62.661 63.158 0.00 0.00 0.00 5.12
221 222 0.037605 ACCGGGTCTCGTGATTGAAC 60.038 55.000 6.32 0.00 37.11 3.18
237 238 1.826327 CAGCATCGCCATTTTTACCG 58.174 50.000 0.00 0.00 0.00 4.02
276 281 4.454504 GCAGGTAGAGGTGAAATCGAAAAA 59.545 41.667 0.00 0.00 0.00 1.94
316 334 1.563173 GACACGTCGTTGTTCCAGC 59.437 57.895 0.00 0.00 0.00 4.85
355 373 4.516698 GTCTGCTTCTCCAAGAAATGTTCA 59.483 41.667 0.00 0.00 33.19 3.18
360 378 4.363991 AGTGTCTGCTTCTCCAAGAAAT 57.636 40.909 0.00 0.00 33.19 2.17
380 398 8.307483 TGTTCATCTTCCTCTAGAAAACACTAG 58.693 37.037 0.00 0.00 40.59 2.57
381 399 8.190326 TGTTCATCTTCCTCTAGAAAACACTA 57.810 34.615 0.00 0.00 33.04 2.74
401 419 0.312729 TAAGCTCGTGCGACTGTTCA 59.687 50.000 3.48 0.00 45.42 3.18
429 451 1.337817 CCTCGTGCGTGAGTTCTTCG 61.338 60.000 4.54 0.00 34.04 3.79
430 452 0.318784 ACCTCGTGCGTGAGTTCTTC 60.319 55.000 4.54 0.00 34.04 2.87
431 453 0.956633 TACCTCGTGCGTGAGTTCTT 59.043 50.000 4.54 0.00 34.04 2.52
436 459 1.226435 GAGCTACCTCGTGCGTGAG 60.226 63.158 0.00 0.00 35.70 3.51
480 537 0.739813 AACGGAACATGCGGCTACTC 60.740 55.000 0.00 0.00 34.75 2.59
669 728 1.606668 GAATGACGCCAACAACCAAGA 59.393 47.619 0.00 0.00 0.00 3.02
740 822 7.596407 TCTTAGGATCCGGGATATGATAGAAT 58.404 38.462 10.08 0.00 0.00 2.40
741 823 6.981737 TCTTAGGATCCGGGATATGATAGAA 58.018 40.000 10.08 0.00 0.00 2.10
743 825 7.461182 GATCTTAGGATCCGGGATATGATAG 57.539 44.000 10.08 4.64 41.70 2.08
772 854 0.804364 ATTGGTGACGTCGCGTACTA 59.196 50.000 21.89 4.39 41.37 1.82
773 855 0.731514 CATTGGTGACGTCGCGTACT 60.732 55.000 21.89 6.09 41.37 2.73
923 1042 1.693083 AATTGCGGCGTCGAAGCTAC 61.693 55.000 22.38 14.86 39.00 3.58
924 1043 1.418342 GAATTGCGGCGTCGAAGCTA 61.418 55.000 22.38 7.27 39.00 3.32
925 1044 2.740714 GAATTGCGGCGTCGAAGCT 61.741 57.895 22.38 1.49 39.00 3.74
926 1045 2.276680 GAATTGCGGCGTCGAAGC 60.277 61.111 16.53 15.40 39.00 3.86
927 1046 0.519175 CTTGAATTGCGGCGTCGAAG 60.519 55.000 16.53 2.01 39.00 3.79
928 1047 1.495509 CTTGAATTGCGGCGTCGAA 59.504 52.632 16.53 0.00 39.00 3.71
930 1049 2.574212 GCTTGAATTGCGGCGTCG 60.574 61.111 4.29 4.29 39.81 5.12
931 1050 1.512734 CTGCTTGAATTGCGGCGTC 60.513 57.895 9.37 0.91 0.00 5.19
932 1051 1.795170 AACTGCTTGAATTGCGGCGT 61.795 50.000 9.37 0.00 40.21 5.68
933 1052 0.167908 TAACTGCTTGAATTGCGGCG 59.832 50.000 0.51 0.51 40.21 6.46
934 1053 2.566952 ATAACTGCTTGAATTGCGGC 57.433 45.000 0.00 0.00 40.21 6.53
935 1054 4.882671 AGTATAACTGCTTGAATTGCGG 57.117 40.909 0.00 0.00 42.11 5.69
936 1055 6.036083 AGTGTAGTATAACTGCTTGAATTGCG 59.964 38.462 0.00 0.00 31.77 4.85
937 1056 7.148407 ACAGTGTAGTATAACTGCTTGAATTGC 60.148 37.037 13.22 0.00 46.28 3.56
938 1057 8.256611 ACAGTGTAGTATAACTGCTTGAATTG 57.743 34.615 13.22 0.00 46.28 2.32
940 1059 8.528643 TGTACAGTGTAGTATAACTGCTTGAAT 58.471 33.333 2.39 0.33 46.28 2.57
941 1060 7.888424 TGTACAGTGTAGTATAACTGCTTGAA 58.112 34.615 2.39 0.00 46.28 2.69
942 1061 7.176165 ACTGTACAGTGTAGTATAACTGCTTGA 59.824 37.037 27.41 0.00 46.28 3.02
966 1085 3.730061 GCGCGTGTGTATAGAAGTGTACT 60.730 47.826 8.43 0.00 0.00 2.73
969 1088 1.625616 GCGCGTGTGTATAGAAGTGT 58.374 50.000 8.43 0.00 0.00 3.55
974 1093 2.649662 CGCGCGCGTGTGTATAGA 60.650 61.111 42.49 0.00 34.35 1.98
984 1103 4.236416 ATTGAATTCCCGCGCGCG 62.236 61.111 43.73 43.73 39.44 6.86
985 1104 2.651863 CATTGAATTCCCGCGCGC 60.652 61.111 27.36 23.91 0.00 6.86
986 1105 2.024588 CCATTGAATTCCCGCGCG 59.975 61.111 25.67 25.67 0.00 6.86
987 1106 2.278792 GCCATTGAATTCCCGCGC 60.279 61.111 0.00 0.00 0.00 6.86
1016 1135 0.682855 GGCCACCGATTCCAATTCCA 60.683 55.000 0.00 0.00 0.00 3.53
1017 1136 0.395724 AGGCCACCGATTCCAATTCC 60.396 55.000 5.01 0.00 0.00 3.01
1018 1137 1.134946 CAAGGCCACCGATTCCAATTC 59.865 52.381 5.01 0.00 0.00 2.17
1019 1138 1.185315 CAAGGCCACCGATTCCAATT 58.815 50.000 5.01 0.00 0.00 2.32
1020 1139 0.684153 CCAAGGCCACCGATTCCAAT 60.684 55.000 5.01 0.00 0.00 3.16
1021 1140 1.304052 CCAAGGCCACCGATTCCAA 60.304 57.895 5.01 0.00 0.00 3.53
1836 1997 1.002990 TGCCAGGAGAGACGACGTA 60.003 57.895 0.00 0.00 0.00 3.57
2413 2586 2.627699 TCTATGGCATGCACAGATACGA 59.372 45.455 21.36 3.92 0.00 3.43
2425 2598 3.969287 ATGCGTATCTGTCTATGGCAT 57.031 42.857 4.88 4.88 35.05 4.40
2450 2623 1.628340 ACATCCGATCAGACCAAACCA 59.372 47.619 0.00 0.00 0.00 3.67
2461 2634 6.205784 TCAAAAGTTTCAAACACATCCGATC 58.794 36.000 2.41 0.00 0.00 3.69
2483 2659 5.294306 CAGCTTTCGTAGAAGGCATAATTCA 59.706 40.000 16.95 0.00 45.90 2.57
2488 2664 2.093711 TGCAGCTTTCGTAGAAGGCATA 60.094 45.455 16.95 2.71 45.90 3.14
2493 2669 4.645956 CTGAAATGCAGCTTTCGTAGAAG 58.354 43.478 7.98 0.00 39.00 2.85
2556 2735 4.497473 TCGCCCTTTGTGTGATTAAAAG 57.503 40.909 0.00 0.00 0.00 2.27
2564 2743 1.593196 TCTTCTTCGCCCTTTGTGTG 58.407 50.000 0.00 0.00 0.00 3.82
2576 2756 7.108847 TCATCTCCTCCAAATCTTTCTTCTTC 58.891 38.462 0.00 0.00 0.00 2.87
2681 2862 4.201980 CCGCATTCACTTCATCAACATCAT 60.202 41.667 0.00 0.00 0.00 2.45
2702 2883 4.860352 TGTTTAAGTACACATCGTGATCCG 59.140 41.667 0.24 0.00 36.96 4.18
2715 2896 9.859692 GTCAAAGTTAGTGACATGTTTAAGTAC 57.140 33.333 0.00 0.00 44.00 2.73
2777 2958 7.530863 GGAGAATCTTGATTTGTAGGTTTGTC 58.469 38.462 0.00 0.00 33.73 3.18
2783 2964 4.130118 CCCGGAGAATCTTGATTTGTAGG 58.870 47.826 0.73 1.08 33.73 3.18
2806 2987 8.025243 TCAATTGTACTCGTGGTATTTCTTTC 57.975 34.615 5.13 0.00 32.56 2.62
2810 2991 7.748847 ACATTCAATTGTACTCGTGGTATTTC 58.251 34.615 5.13 0.00 32.56 2.17
2814 2995 7.604549 TCTAACATTCAATTGTACTCGTGGTA 58.395 34.615 5.13 0.00 0.00 3.25
2816 2997 6.961359 TCTAACATTCAATTGTACTCGTGG 57.039 37.500 5.13 0.00 0.00 4.94
2817 2998 9.825972 AATTTCTAACATTCAATTGTACTCGTG 57.174 29.630 5.13 0.00 0.00 4.35
2820 3001 9.076596 GCCAATTTCTAACATTCAATTGTACTC 57.923 33.333 5.13 0.00 35.64 2.59
2845 3034 1.335496 GACGTCTATGTCCTCCTGAGC 59.665 57.143 8.70 0.00 32.61 4.26
2863 3052 8.704234 CAGTCATGTAAACTCTAAAGTTGAGAC 58.296 37.037 0.00 0.00 45.07 3.36
2874 3063 9.561069 AATAACTGTTTCAGTCATGTAAACTCT 57.439 29.630 0.00 4.92 44.62 3.24
2898 3087 3.119173 CGTGACATTATGGGCCAAACAAT 60.119 43.478 11.89 7.98 0.00 2.71
2900 3089 1.815613 CGTGACATTATGGGCCAAACA 59.184 47.619 11.89 0.00 0.00 2.83
2971 3160 3.948719 GGGTGCGTTCTGGGGTGA 61.949 66.667 0.00 0.00 0.00 4.02
2979 3168 2.403259 CAAAAATGGAAGGGTGCGTTC 58.597 47.619 0.00 0.00 0.00 3.95
2988 3177 1.544246 GGGTCCGACCAAAAATGGAAG 59.456 52.381 19.43 0.00 41.02 3.46
2991 3180 1.173913 GAGGGTCCGACCAAAAATGG 58.826 55.000 19.43 0.00 41.02 3.16
3002 3192 3.148279 CGAGAAGGGGAGGGTCCG 61.148 72.222 0.00 0.00 37.43 4.79
3039 5437 1.673033 CGCTCCAACGAGAAATGTCCT 60.673 52.381 0.00 0.00 38.52 3.85
3059 5457 3.819337 GTCACCTGGTTTTAAAGGAGGAC 59.181 47.826 13.42 9.22 37.01 3.85
3077 5475 0.321653 AAAGATGAGGTGGGCGTCAC 60.322 55.000 0.00 0.00 41.51 3.67
3082 5480 1.747355 CATGACAAAGATGAGGTGGGC 59.253 52.381 0.00 0.00 0.00 5.36
3092 5490 1.403323 TGTTGCAACGCATGACAAAGA 59.597 42.857 23.79 0.00 38.76 2.52
3096 5494 2.421619 TCTATGTTGCAACGCATGACA 58.578 42.857 23.79 6.34 38.76 3.58
3150 5549 9.439500 TGTGTCAATAGTATGGGTTAGTTTAAC 57.561 33.333 0.00 0.00 37.94 2.01
3193 5592 3.511540 TGTACCCTTGAGACTGATCACTG 59.488 47.826 0.00 0.00 0.00 3.66
3196 5595 4.777366 TGAATGTACCCTTGAGACTGATCA 59.223 41.667 0.00 0.00 0.00 2.92
3209 5608 6.364976 GTGCATTTACAAAGTTGAATGTACCC 59.635 38.462 11.99 0.00 32.07 3.69
3212 5611 6.920758 GGTGTGCATTTACAAAGTTGAATGTA 59.079 34.615 0.00 0.00 31.36 2.29
3213 5612 5.752955 GGTGTGCATTTACAAAGTTGAATGT 59.247 36.000 0.00 0.00 31.36 2.71
3224 5623 1.809547 CCATGTCGGTGTGCATTTACA 59.190 47.619 0.00 0.00 0.00 2.41
3226 5625 2.481289 TCCATGTCGGTGTGCATTTA 57.519 45.000 0.00 0.00 35.57 1.40
3237 5636 1.021390 GCCACTCACCTTCCATGTCG 61.021 60.000 0.00 0.00 0.00 4.35
3245 5644 3.525800 ATTTAGTTGGCCACTCACCTT 57.474 42.857 3.88 0.00 36.88 3.50
3250 5649 9.780186 ACTAGAAATATATTTAGTTGGCCACTC 57.220 33.333 3.88 0.98 36.88 3.51
3266 5665 7.952671 TGGAGCTTATTCGTGACTAGAAATAT 58.047 34.615 0.00 0.00 0.00 1.28
3280 5679 5.361285 TCTGGTCTAGAGTTGGAGCTTATTC 59.639 44.000 0.00 0.00 33.90 1.75
3292 5691 6.463614 GCAATGAATGGTATCTGGTCTAGAGT 60.464 42.308 0.00 0.00 39.20 3.24
3296 5695 5.894298 AGCAATGAATGGTATCTGGTCTA 57.106 39.130 0.00 0.00 38.18 2.59
3299 5698 5.894298 TCTAGCAATGAATGGTATCTGGT 57.106 39.130 0.00 0.00 40.97 4.00
3329 5728 4.946157 AGGAAGAGAAGAACGACGGTTATA 59.054 41.667 0.00 0.00 36.24 0.98
3330 5729 3.762823 AGGAAGAGAAGAACGACGGTTAT 59.237 43.478 0.00 0.00 36.24 1.89
3332 5731 1.962100 AGGAAGAGAAGAACGACGGTT 59.038 47.619 0.00 0.00 39.63 4.44
3334 5733 1.466024 CGAGGAAGAGAAGAACGACGG 60.466 57.143 0.00 0.00 0.00 4.79
3335 5734 1.197264 ACGAGGAAGAGAAGAACGACG 59.803 52.381 0.00 0.00 0.00 5.12
3336 5735 2.485038 AGACGAGGAAGAGAAGAACGAC 59.515 50.000 0.00 0.00 0.00 4.34
3337 5736 2.780714 AGACGAGGAAGAGAAGAACGA 58.219 47.619 0.00 0.00 0.00 3.85
3338 5737 3.562567 AAGACGAGGAAGAGAAGAACG 57.437 47.619 0.00 0.00 0.00 3.95
3357 5756 6.096001 GGTTAGGAGTAGAAGATGTACGGAAA 59.904 42.308 0.00 0.00 0.00 3.13
3362 5761 7.254863 CGAAGAGGTTAGGAGTAGAAGATGTAC 60.255 44.444 0.00 0.00 0.00 2.90
3363 5762 6.766944 CGAAGAGGTTAGGAGTAGAAGATGTA 59.233 42.308 0.00 0.00 0.00 2.29
3380 5779 0.112412 AAATGGGTTGGCGAAGAGGT 59.888 50.000 0.00 0.00 0.00 3.85
3381 5780 1.067635 CAAAATGGGTTGGCGAAGAGG 60.068 52.381 0.00 0.00 0.00 3.69
3386 5785 1.173043 CTAGCAAAATGGGTTGGCGA 58.827 50.000 0.00 0.00 0.00 5.54
3388 5787 1.672737 GCACTAGCAAAATGGGTTGGC 60.673 52.381 0.00 0.00 41.58 4.52


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

AutoCloner maintained by Alex Coulton.