Multiple sequence alignment - TraesCS5B01G399800

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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 TraesCS5B01G399800 chr5B 100.000 3443 0 0 1 3443 577226238 577229680 0.000000e+00 6359
1 TraesCS5B01G399800 chr5B 85.143 175 18 3 489 663 78209925 78210091 4.570000e-39 172
2 TraesCS5B01G399800 chr5B 85.143 175 18 3 489 663 406551285 406551451 4.570000e-39 172
3 TraesCS5B01G399800 chr5D 91.123 2895 123 49 1 2798 469500773 469503630 0.000000e+00 3799
4 TraesCS5B01G399800 chr5D 79.061 277 22 18 2841 3089 469503633 469503901 1.280000e-34 158
5 TraesCS5B01G399800 chr5A 91.133 2842 155 41 1 2801 590539049 590541834 0.000000e+00 3762
6 TraesCS5B01G399800 chr5A 82.006 628 45 31 2839 3442 590541834 590542417 4.020000e-129 472
7 TraesCS5B01G399800 chr4D 90.849 1508 129 7 942 2447 26479953 26481453 0.000000e+00 2012
8 TraesCS5B01G399800 chr4D 83.391 1457 223 17 994 2441 50070786 50072232 0.000000e+00 1332
9 TraesCS5B01G399800 chr4B 90.782 1508 130 7 942 2447 39014799 39016299 0.000000e+00 2006
10 TraesCS5B01G399800 chr4B 83.162 1455 230 13 997 2444 73609979 73608533 0.000000e+00 1315
11 TraesCS5B01G399800 chr4A 90.782 1508 130 7 942 2447 576932020 576930520 0.000000e+00 2006
12 TraesCS5B01G399800 chr4A 83.001 1453 233 13 997 2441 547046170 547044724 0.000000e+00 1303
13 TraesCS5B01G399800 chr4A 81.224 1454 267 5 993 2443 486126022 486124572 0.000000e+00 1168
14 TraesCS5B01G399800 chr4A 85.465 172 17 3 489 660 740036344 740036507 4.570000e-39 172
15 TraesCS5B01G399800 chr6B 89.219 1076 107 8 650 1719 691828827 691827755 0.000000e+00 1336
16 TraesCS5B01G399800 chr6B 87.719 114 10 3 489 602 14230868 14230759 2.790000e-26 130
17 TraesCS5B01G399800 chr3B 89.126 1076 108 8 650 1719 8696090 8695018 0.000000e+00 1330
18 TraesCS5B01G399800 chr3B 86.656 622 75 7 647 1263 606328969 606329587 0.000000e+00 682
19 TraesCS5B01G399800 chr3B 84.571 175 19 4 489 663 815340959 815341125 2.130000e-37 167
20 TraesCS5B01G399800 chr2A 88.879 1079 111 8 647 1719 635594430 635595505 0.000000e+00 1319
21 TraesCS5B01G399800 chr7A 84.571 175 19 3 489 663 497657884 497657718 2.130000e-37 167
22 TraesCS5B01G399800 chr3A 84.571 175 19 3 489 663 82906803 82906969 2.130000e-37 167


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 TraesCS5B01G399800 chr5B 577226238 577229680 3442 False 6359.0 6359 100.0000 1 3443 1 chr5B.!!$F3 3442
1 TraesCS5B01G399800 chr5D 469500773 469503901 3128 False 1978.5 3799 85.0920 1 3089 2 chr5D.!!$F1 3088
2 TraesCS5B01G399800 chr5A 590539049 590542417 3368 False 2117.0 3762 86.5695 1 3442 2 chr5A.!!$F1 3441
3 TraesCS5B01G399800 chr4D 26479953 26481453 1500 False 2012.0 2012 90.8490 942 2447 1 chr4D.!!$F1 1505
4 TraesCS5B01G399800 chr4D 50070786 50072232 1446 False 1332.0 1332 83.3910 994 2441 1 chr4D.!!$F2 1447
5 TraesCS5B01G399800 chr4B 39014799 39016299 1500 False 2006.0 2006 90.7820 942 2447 1 chr4B.!!$F1 1505
6 TraesCS5B01G399800 chr4B 73608533 73609979 1446 True 1315.0 1315 83.1620 997 2444 1 chr4B.!!$R1 1447
7 TraesCS5B01G399800 chr4A 576930520 576932020 1500 True 2006.0 2006 90.7820 942 2447 1 chr4A.!!$R3 1505
8 TraesCS5B01G399800 chr4A 547044724 547046170 1446 True 1303.0 1303 83.0010 997 2441 1 chr4A.!!$R2 1444
9 TraesCS5B01G399800 chr4A 486124572 486126022 1450 True 1168.0 1168 81.2240 993 2443 1 chr4A.!!$R1 1450
10 TraesCS5B01G399800 chr6B 691827755 691828827 1072 True 1336.0 1336 89.2190 650 1719 1 chr6B.!!$R2 1069
11 TraesCS5B01G399800 chr3B 8695018 8696090 1072 True 1330.0 1330 89.1260 650 1719 1 chr3B.!!$R1 1069
12 TraesCS5B01G399800 chr3B 606328969 606329587 618 False 682.0 682 86.6560 647 1263 1 chr3B.!!$F1 616
13 TraesCS5B01G399800 chr2A 635594430 635595505 1075 False 1319.0 1319 88.8790 647 1719 1 chr2A.!!$F1 1072

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
547 573 0.033011 AGATCTGGCCGAGTAGTGGT 60.033 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2608 2728 1.043673 AGATCTACAGACGGGGTGGC 61.044 60.0 0.0 0.0 0.0 5.01 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
45 46 0.321996 GAGTGAGGAGGTTGGTGGTC 59.678 60.000 0.00 0.00 0.00 4.02
75 76 6.467677 TGGACTCATCTGAAACCTTTTCTAG 58.532 40.000 0.68 0.00 0.00 2.43
135 151 1.455383 GCAAGACCAACCCACACCTG 61.455 60.000 0.00 0.00 0.00 4.00
152 168 1.002468 CCTGCTCAATTTATTCCGGCG 60.002 52.381 0.00 0.00 0.00 6.46
194 210 4.069304 TCACACGGTTAATTTTCCAGAGG 58.931 43.478 0.00 0.00 0.00 3.69
195 211 2.817844 ACACGGTTAATTTTCCAGAGGC 59.182 45.455 0.00 0.00 0.00 4.70
196 212 2.081462 ACGGTTAATTTTCCAGAGGCG 58.919 47.619 0.00 0.00 0.00 5.52
197 213 1.400494 CGGTTAATTTTCCAGAGGCGG 59.600 52.381 0.00 0.00 0.00 6.13
198 214 1.749063 GGTTAATTTTCCAGAGGCGGG 59.251 52.381 0.00 0.00 0.00 6.13
199 215 1.749063 GTTAATTTTCCAGAGGCGGGG 59.251 52.381 0.00 0.00 0.00 5.73
200 216 1.291109 TAATTTTCCAGAGGCGGGGA 58.709 50.000 0.00 0.00 0.00 4.81
223 239 0.178918 GAGGGGAGGGGTAGATCCAG 60.179 65.000 0.00 0.00 37.33 3.86
228 244 1.763546 GAGGGGTAGATCCAGCCTGC 61.764 65.000 9.29 0.00 38.11 4.85
289 305 0.744414 CTCTGCATACAACCCGTGGG 60.744 60.000 2.58 2.58 42.03 4.61
290 306 2.360600 TGCATACAACCCGTGGGC 60.361 61.111 4.41 0.00 39.32 5.36
291 307 2.360600 GCATACAACCCGTGGGCA 60.361 61.111 4.41 0.00 39.32 5.36
403 423 3.464720 TCCTGAGATCTGGTGAGAGTT 57.535 47.619 0.00 0.00 36.48 3.01
404 424 3.360867 TCCTGAGATCTGGTGAGAGTTC 58.639 50.000 0.00 0.00 36.48 3.01
405 425 2.430332 CCTGAGATCTGGTGAGAGTTCC 59.570 54.545 0.00 0.00 0.00 3.62
409 429 1.484240 GATCTGGTGAGAGTTCCCCTG 59.516 57.143 0.00 0.00 0.00 4.45
410 430 0.487325 TCTGGTGAGAGTTCCCCTGA 59.513 55.000 0.00 0.00 0.00 3.86
411 431 1.079490 TCTGGTGAGAGTTCCCCTGAT 59.921 52.381 0.00 0.00 0.00 2.90
412 432 1.484240 CTGGTGAGAGTTCCCCTGATC 59.516 57.143 0.00 0.00 0.00 2.92
413 433 1.079490 TGGTGAGAGTTCCCCTGATCT 59.921 52.381 0.00 0.00 0.00 2.75
414 434 1.484240 GGTGAGAGTTCCCCTGATCTG 59.516 57.143 0.00 0.00 0.00 2.90
415 435 1.484240 GTGAGAGTTCCCCTGATCTGG 59.516 57.143 11.58 11.58 0.00 3.86
416 436 1.079490 TGAGAGTTCCCCTGATCTGGT 59.921 52.381 16.63 0.00 0.00 4.00
417 437 2.192263 GAGAGTTCCCCTGATCTGGTT 58.808 52.381 16.63 0.00 0.00 3.67
418 438 3.245984 TGAGAGTTCCCCTGATCTGGTTA 60.246 47.826 16.63 2.39 0.00 2.85
419 439 3.108376 AGAGTTCCCCTGATCTGGTTAC 58.892 50.000 16.63 11.10 0.00 2.50
420 440 2.170817 GAGTTCCCCTGATCTGGTTACC 59.829 54.545 16.63 0.00 0.00 2.85
429 449 4.202305 CCTGATCTGGTTACCATCTCCTTC 60.202 50.000 3.88 0.00 30.82 3.46
435 455 3.839490 TGGTTACCATCTCCTTCGGTTTA 59.161 43.478 0.00 0.00 34.12 2.01
440 460 3.447944 ACCATCTCCTTCGGTTTAGTCTC 59.552 47.826 0.00 0.00 0.00 3.36
460 482 3.937706 CTCTAGTTTGGTGCCTGATCTTG 59.062 47.826 0.00 0.00 0.00 3.02
461 483 1.251251 AGTTTGGTGCCTGATCTTGC 58.749 50.000 0.00 0.00 0.00 4.01
462 484 0.961019 GTTTGGTGCCTGATCTTGCA 59.039 50.000 5.74 5.74 34.54 4.08
463 485 1.340889 GTTTGGTGCCTGATCTTGCAA 59.659 47.619 10.64 0.00 39.57 4.08
464 486 1.250328 TTGGTGCCTGATCTTGCAAG 58.750 50.000 20.81 20.81 39.57 4.01
465 487 0.401356 TGGTGCCTGATCTTGCAAGA 59.599 50.000 30.23 30.23 39.57 3.02
467 489 1.093159 GTGCCTGATCTTGCAAGAGG 58.907 55.000 31.14 26.61 39.57 3.69
468 490 0.679002 TGCCTGATCTTGCAAGAGGC 60.679 55.000 34.73 34.73 41.64 4.70
477 499 3.432186 GCAAGAGGCGTGGTTTGT 58.568 55.556 0.00 0.00 0.00 2.83
478 500 1.733526 GCAAGAGGCGTGGTTTGTT 59.266 52.632 0.00 0.00 0.00 2.83
484 510 0.968393 AGGCGTGGTTTGTTTGTGGT 60.968 50.000 0.00 0.00 0.00 4.16
485 511 0.739561 GGCGTGGTTTGTTTGTGGTA 59.260 50.000 0.00 0.00 0.00 3.25
495 521 4.893424 TTGTTTGTGGTAGCTGTTCTTC 57.107 40.909 0.00 0.00 0.00 2.87
502 528 1.819903 GGTAGCTGTTCTTCTCTCGGT 59.180 52.381 0.00 0.00 0.00 4.69
504 530 2.734276 AGCTGTTCTTCTCTCGGTTC 57.266 50.000 0.00 0.00 0.00 3.62
541 567 0.820871 GTCTTCAGATCTGGCCGAGT 59.179 55.000 22.42 0.00 0.00 4.18
542 568 2.025155 GTCTTCAGATCTGGCCGAGTA 58.975 52.381 22.42 0.00 0.00 2.59
543 569 2.034053 GTCTTCAGATCTGGCCGAGTAG 59.966 54.545 22.42 8.73 0.00 2.57
546 572 0.387202 CAGATCTGGCCGAGTAGTGG 59.613 60.000 15.38 0.00 0.00 4.00
547 573 0.033011 AGATCTGGCCGAGTAGTGGT 60.033 55.000 0.00 0.00 0.00 4.16
548 574 0.386113 GATCTGGCCGAGTAGTGGTC 59.614 60.000 0.00 0.00 0.00 4.02
595 621 9.886132 ATTTAGTTAGTGGTTTGGATAGTAGTG 57.114 33.333 0.00 0.00 0.00 2.74
596 622 6.930068 AGTTAGTGGTTTGGATAGTAGTGT 57.070 37.500 0.00 0.00 0.00 3.55
597 623 7.312415 AGTTAGTGGTTTGGATAGTAGTGTT 57.688 36.000 0.00 0.00 0.00 3.32
599 625 7.234988 AGTTAGTGGTTTGGATAGTAGTGTTCT 59.765 37.037 0.00 0.00 0.00 3.01
600 626 8.526147 GTTAGTGGTTTGGATAGTAGTGTTCTA 58.474 37.037 0.00 0.00 0.00 2.10
615 642 6.882610 AGTGTTCTATGCTGTGAATTTTCA 57.117 33.333 0.00 0.00 34.20 2.69
618 645 8.025445 AGTGTTCTATGCTGTGAATTTTCATTC 58.975 33.333 0.00 0.00 39.73 2.67
622 649 1.913403 GCTGTGAATTTTCATTCGGCG 59.087 47.619 0.00 0.00 41.77 6.46
623 650 2.414029 GCTGTGAATTTTCATTCGGCGA 60.414 45.455 4.99 4.99 41.77 5.54
720 748 0.036577 CTGCAGAAGTAGGCACAGCT 60.037 55.000 8.42 0.00 35.86 4.24
725 753 3.610349 GCAGAAGTAGGCACAGCTTTTTC 60.610 47.826 0.00 0.00 0.00 2.29
726 754 3.565482 CAGAAGTAGGCACAGCTTTTTCA 59.435 43.478 0.00 0.00 0.00 2.69
733 764 2.544486 GGCACAGCTTTTTCACCTCAAG 60.544 50.000 0.00 0.00 0.00 3.02
768 799 1.065701 GAAGCTGCCAGCATCTGATTG 59.934 52.381 20.53 0.00 45.56 2.67
769 800 0.034380 AGCTGCCAGCATCTGATTGT 60.034 50.000 20.53 0.00 45.56 2.71
771 802 1.202268 GCTGCCAGCATCTGATTGTTC 60.202 52.381 12.82 0.00 41.89 3.18
788 819 2.560981 TGTTCAGATCTGGTCGTGCTTA 59.439 45.455 22.42 0.00 0.00 3.09
794 825 1.448985 TCTGGTCGTGCTTATTTGCC 58.551 50.000 0.00 0.00 0.00 4.52
805 836 5.741510 CGTGCTTATTTGCCGAATTAATTGA 59.258 36.000 5.17 0.00 0.00 2.57
862 897 4.256920 ACTCTGCATTTCTGTCACATACC 58.743 43.478 0.00 0.00 0.00 2.73
891 955 2.611225 AGATCTGAATCTCGGTTGCC 57.389 50.000 0.00 0.00 37.75 4.52
903 967 1.001633 TCGGTTGCCTCTGTTTACTCC 59.998 52.381 0.00 0.00 0.00 3.85
928 999 4.157656 AGTCTCTGAGATGTGCAGTAAGAC 59.842 45.833 11.07 0.00 37.43 3.01
1188 1265 4.748144 GTCAAGGCCTGCAGGGGG 62.748 72.222 33.46 10.79 35.18 5.40
2607 2727 6.375377 TGTTAAGTTTCCGATACATGTTTGC 58.625 36.000 2.30 0.00 0.00 3.68
2608 2728 3.740044 AGTTTCCGATACATGTTTGCG 57.260 42.857 2.30 5.68 0.00 4.85
2609 2729 2.159572 AGTTTCCGATACATGTTTGCGC 60.160 45.455 2.30 0.00 0.00 6.09
2610 2730 0.730265 TTCCGATACATGTTTGCGCC 59.270 50.000 2.30 0.00 0.00 6.53
2611 2731 0.391793 TCCGATACATGTTTGCGCCA 60.392 50.000 2.30 0.00 0.00 5.69
2612 2732 0.248054 CCGATACATGTTTGCGCCAC 60.248 55.000 2.30 1.63 0.00 5.01
2613 2733 0.248054 CGATACATGTTTGCGCCACC 60.248 55.000 2.30 0.00 0.00 4.61
2614 2734 0.100503 GATACATGTTTGCGCCACCC 59.899 55.000 2.30 0.00 0.00 4.61
2675 2800 0.185901 TGCTGCCTGAGGAGGTTTTT 59.814 50.000 0.65 0.00 42.15 1.94
2732 2857 8.746922 TGTTTTGCTGAAATCATTACAGAATC 57.253 30.769 0.00 0.00 34.07 2.52
2770 2905 4.973168 TCAAGTTTGTAGTTGCTCCTCAT 58.027 39.130 0.00 0.00 35.15 2.90
2771 2906 5.376625 TCAAGTTTGTAGTTGCTCCTCATT 58.623 37.500 0.00 0.00 35.15 2.57
2772 2907 5.827797 TCAAGTTTGTAGTTGCTCCTCATTT 59.172 36.000 0.00 0.00 35.15 2.32
2801 2936 3.802139 CGTGTGTTTTGCTTCACTCTAGA 59.198 43.478 0.00 0.00 35.82 2.43
2802 2937 4.270084 CGTGTGTTTTGCTTCACTCTAGAA 59.730 41.667 0.00 0.00 35.82 2.10
2803 2938 5.050091 CGTGTGTTTTGCTTCACTCTAGAAT 60.050 40.000 0.00 0.00 35.82 2.40
2804 2939 6.511767 CGTGTGTTTTGCTTCACTCTAGAATT 60.512 38.462 0.00 0.00 35.82 2.17
2805 2940 6.634436 GTGTGTTTTGCTTCACTCTAGAATTG 59.366 38.462 0.00 0.00 35.82 2.32
2806 2941 6.318648 TGTGTTTTGCTTCACTCTAGAATTGT 59.681 34.615 0.00 0.00 35.82 2.71
2807 2942 7.497579 TGTGTTTTGCTTCACTCTAGAATTGTA 59.502 33.333 0.00 0.00 35.82 2.41
2808 2943 8.012241 GTGTTTTGCTTCACTCTAGAATTGTAG 58.988 37.037 3.22 3.22 0.00 2.74
2809 2944 6.727824 TTTGCTTCACTCTAGAATTGTAGC 57.272 37.500 18.55 18.55 35.04 3.58
2810 2945 5.667539 TGCTTCACTCTAGAATTGTAGCT 57.332 39.130 22.60 0.00 35.39 3.32
2811 2946 6.042638 TGCTTCACTCTAGAATTGTAGCTT 57.957 37.500 22.60 0.00 35.39 3.74
2812 2947 5.871524 TGCTTCACTCTAGAATTGTAGCTTG 59.128 40.000 22.60 4.74 35.39 4.01
2813 2948 5.872070 GCTTCACTCTAGAATTGTAGCTTGT 59.128 40.000 18.28 1.81 32.58 3.16
2814 2949 6.370166 GCTTCACTCTAGAATTGTAGCTTGTT 59.630 38.462 18.28 0.00 32.58 2.83
2815 2950 7.095017 GCTTCACTCTAGAATTGTAGCTTGTTT 60.095 37.037 18.28 0.00 32.58 2.83
2816 2951 8.677148 TTCACTCTAGAATTGTAGCTTGTTTT 57.323 30.769 4.75 0.00 0.00 2.43
2817 2952 8.677148 TCACTCTAGAATTGTAGCTTGTTTTT 57.323 30.769 4.75 0.00 0.00 1.94
2863 3005 2.018542 TGTTGGCCAGTAGCGTAATC 57.981 50.000 5.11 0.00 45.17 1.75
2865 3007 0.818938 TTGGCCAGTAGCGTAATCGA 59.181 50.000 5.11 0.00 45.17 3.59
2866 3008 0.101759 TGGCCAGTAGCGTAATCGAC 59.898 55.000 0.00 0.00 45.17 4.20
2881 3023 4.592485 AATCGACTAGTCACATGATCCC 57.408 45.455 22.37 0.00 0.00 3.85
2932 3075 1.738099 CAGTTTCCTCTGTCGCGGG 60.738 63.158 6.13 0.00 0.00 6.13
2983 3144 3.986006 GGGCCGGTATCGATGCGA 61.986 66.667 8.54 0.00 41.13 5.10
2985 3146 3.097728 GCCGGTATCGATGCGACG 61.098 66.667 8.54 6.67 39.18 5.12
3017 3186 4.124943 CCTGCAGCAGGCCCATCT 62.125 66.667 28.85 0.00 45.13 2.90
3018 3187 2.516460 CTGCAGCAGGCCCATCTC 60.516 66.667 15.35 0.00 43.89 2.75
3026 3195 3.934962 GGCCCATCTCTCTCGCCC 61.935 72.222 0.00 0.00 33.30 6.13
3089 3258 1.556911 TCAGTTCCAGCTTCCATCCTC 59.443 52.381 0.00 0.00 0.00 3.71
3091 3260 0.620556 GTTCCAGCTTCCATCCTCCA 59.379 55.000 0.00 0.00 0.00 3.86
3092 3261 0.620556 TTCCAGCTTCCATCCTCCAC 59.379 55.000 0.00 0.00 0.00 4.02
3093 3262 0.252881 TCCAGCTTCCATCCTCCACT 60.253 55.000 0.00 0.00 0.00 4.00
3116 3287 1.375326 GGATGCTATTCCCCGTCCC 59.625 63.158 0.00 0.00 32.20 4.46
3117 3288 1.415672 GGATGCTATTCCCCGTCCCA 61.416 60.000 0.00 0.00 32.20 4.37
3118 3289 0.250338 GATGCTATTCCCCGTCCCAC 60.250 60.000 0.00 0.00 0.00 4.61
3119 3290 0.694444 ATGCTATTCCCCGTCCCACT 60.694 55.000 0.00 0.00 0.00 4.00
3120 3291 1.335132 TGCTATTCCCCGTCCCACTC 61.335 60.000 0.00 0.00 0.00 3.51
3121 3292 2.041206 GCTATTCCCCGTCCCACTCC 62.041 65.000 0.00 0.00 0.00 3.85
3122 3293 0.689745 CTATTCCCCGTCCCACTCCA 60.690 60.000 0.00 0.00 0.00 3.86
3123 3294 0.979187 TATTCCCCGTCCCACTCCAC 60.979 60.000 0.00 0.00 0.00 4.02
3124 3295 3.661072 TATTCCCCGTCCCACTCCACA 62.661 57.143 0.00 0.00 0.00 4.17
3125 3296 4.016706 CCCCGTCCCACTCCACAC 62.017 72.222 0.00 0.00 0.00 3.82
3126 3297 4.016706 CCCGTCCCACTCCACACC 62.017 72.222 0.00 0.00 0.00 4.16
3127 3298 4.373116 CCGTCCCACTCCACACCG 62.373 72.222 0.00 0.00 0.00 4.94
3128 3299 4.373116 CGTCCCACTCCACACCGG 62.373 72.222 0.00 0.00 0.00 5.28
3129 3300 4.699522 GTCCCACTCCACACCGGC 62.700 72.222 0.00 0.00 33.14 6.13
3190 3361 0.546122 TGAACAACAGGTGGAGTGCT 59.454 50.000 0.00 0.00 0.00 4.40
3191 3362 1.765904 TGAACAACAGGTGGAGTGCTA 59.234 47.619 0.00 0.00 0.00 3.49
3201 3372 0.970427 TGGAGTGCTAGCGTGGATGA 60.970 55.000 10.77 0.00 0.00 2.92
3228 3399 2.740714 GGTGATCGCGCCAGACAAC 61.741 63.158 0.00 0.00 44.29 3.32
3244 3415 5.583854 CCAGACAACTTTGATGATCGAATCT 59.416 40.000 0.00 0.00 0.00 2.40
3247 3418 4.201753 ACAACTTTGATGATCGAATCTGCG 60.202 41.667 0.00 0.00 0.00 5.18
3252 3423 2.027605 GATCGAATCTGCGGCGGA 59.972 61.111 14.84 14.84 0.00 5.54
3253 3424 1.591594 GATCGAATCTGCGGCGGAA 60.592 57.895 16.55 0.00 0.00 4.30
3254 3425 1.151777 GATCGAATCTGCGGCGGAAA 61.152 55.000 16.55 0.00 0.00 3.13
3255 3426 1.429148 ATCGAATCTGCGGCGGAAAC 61.429 55.000 16.55 11.45 0.00 2.78
3256 3427 2.791927 GAATCTGCGGCGGAAACC 59.208 61.111 16.55 4.26 0.00 3.27
3365 3539 3.986006 TGTGCCAGTCGACGACCC 61.986 66.667 23.76 13.17 32.18 4.46
3366 3540 3.986006 GTGCCAGTCGACGACCCA 61.986 66.667 23.76 15.49 32.18 4.51
3367 3541 3.680786 TGCCAGTCGACGACCCAG 61.681 66.667 23.76 13.80 32.18 4.45
3368 3542 3.371063 GCCAGTCGACGACCCAGA 61.371 66.667 23.76 0.00 32.18 3.86
3369 3543 2.567049 CCAGTCGACGACCCAGAC 59.433 66.667 23.76 0.00 32.18 3.51
3370 3544 2.567049 CAGTCGACGACCCAGACC 59.433 66.667 23.76 0.00 35.65 3.85
3371 3545 1.972223 CAGTCGACGACCCAGACCT 60.972 63.158 23.76 0.86 35.65 3.85
3372 3546 1.674980 AGTCGACGACCCAGACCTC 60.675 63.158 23.76 0.00 35.65 3.85
3396 3570 3.259425 GACCGCGTCGTGTAGGTGT 62.259 63.158 4.92 0.00 37.07 4.16
3402 3576 0.242825 CGTCGTGTAGGTGTGTGGAT 59.757 55.000 0.00 0.00 0.00 3.41
3430 3604 4.323477 CCCGCTTTCCCACCGACA 62.323 66.667 0.00 0.00 0.00 4.35
3442 3616 2.429571 CCGACACCCACGTACGTG 60.430 66.667 35.57 35.57 45.02 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.937706 GGTTTCAGATGAGTCCATGACAG 59.062 47.826 0.00 0.00 34.60 3.51
75 76 1.591327 CCCACCAAACTTGCGTTGC 60.591 57.895 0.00 0.00 32.65 4.17
135 151 1.940613 AGACGCCGGAATAAATTGAGC 59.059 47.619 5.05 0.00 0.00 4.26
152 168 3.254892 GAAGACCGGTCAGAATTCAGAC 58.745 50.000 35.00 19.67 0.00 3.51
199 215 3.040814 TACCCCTCCCCTCCCCTC 61.041 72.222 0.00 0.00 0.00 4.30
200 216 2.941118 ATCTACCCCTCCCCTCCCCT 62.941 65.000 0.00 0.00 0.00 4.79
228 244 4.778143 CCCGTTCCCCGAAGCCAG 62.778 72.222 0.00 0.00 39.56 4.85
239 255 4.202284 TGCAACTCCTTATATACCCCGTTC 60.202 45.833 0.00 0.00 0.00 3.95
403 423 2.022035 AGATGGTAACCAGATCAGGGGA 60.022 50.000 9.23 0.00 36.75 4.81
404 424 2.370189 GAGATGGTAACCAGATCAGGGG 59.630 54.545 9.23 2.86 36.75 4.79
405 425 2.370189 GGAGATGGTAACCAGATCAGGG 59.630 54.545 9.23 5.50 36.75 4.45
409 429 3.983741 CGAAGGAGATGGTAACCAGATC 58.016 50.000 0.00 0.00 36.75 2.75
429 449 3.678548 GCACCAAACTAGAGACTAAACCG 59.321 47.826 0.00 0.00 0.00 4.44
435 455 2.609747 TCAGGCACCAAACTAGAGACT 58.390 47.619 0.00 0.00 0.00 3.24
440 460 2.421424 GCAAGATCAGGCACCAAACTAG 59.579 50.000 0.00 0.00 0.00 2.57
460 482 0.102300 AAACAAACCACGCCTCTTGC 59.898 50.000 0.00 0.00 0.00 4.01
461 483 1.134175 ACAAACAAACCACGCCTCTTG 59.866 47.619 0.00 0.00 0.00 3.02
462 484 1.134175 CACAAACAAACCACGCCTCTT 59.866 47.619 0.00 0.00 0.00 2.85
463 485 0.738389 CACAAACAAACCACGCCTCT 59.262 50.000 0.00 0.00 0.00 3.69
464 486 0.248866 CCACAAACAAACCACGCCTC 60.249 55.000 0.00 0.00 0.00 4.70
465 487 0.968393 ACCACAAACAAACCACGCCT 60.968 50.000 0.00 0.00 0.00 5.52
467 489 1.862411 GCTACCACAAACAAACCACGC 60.862 52.381 0.00 0.00 0.00 5.34
468 490 1.673920 AGCTACCACAAACAAACCACG 59.326 47.619 0.00 0.00 0.00 4.94
469 491 2.425668 ACAGCTACCACAAACAAACCAC 59.574 45.455 0.00 0.00 0.00 4.16
470 492 2.729194 ACAGCTACCACAAACAAACCA 58.271 42.857 0.00 0.00 0.00 3.67
471 493 3.380320 AGAACAGCTACCACAAACAAACC 59.620 43.478 0.00 0.00 0.00 3.27
473 495 4.947388 AGAAGAACAGCTACCACAAACAAA 59.053 37.500 0.00 0.00 0.00 2.83
476 498 4.381411 AGAGAAGAACAGCTACCACAAAC 58.619 43.478 0.00 0.00 0.00 2.93
477 499 4.632153 GAGAGAAGAACAGCTACCACAAA 58.368 43.478 0.00 0.00 0.00 2.83
478 500 3.305403 CGAGAGAAGAACAGCTACCACAA 60.305 47.826 0.00 0.00 0.00 3.33
484 510 2.492484 GGAACCGAGAGAAGAACAGCTA 59.508 50.000 0.00 0.00 0.00 3.32
485 511 1.273886 GGAACCGAGAGAAGAACAGCT 59.726 52.381 0.00 0.00 0.00 4.24
495 521 2.481104 GCATCTTCAGAGGAACCGAGAG 60.481 54.545 0.00 0.00 0.00 3.20
502 528 2.039480 ACAGCAAGCATCTTCAGAGGAA 59.961 45.455 0.00 0.00 0.00 3.36
504 530 2.008329 GACAGCAAGCATCTTCAGAGG 58.992 52.381 0.00 0.00 0.00 3.69
541 567 4.462834 ACAATGAATCTCAGACGACCACTA 59.537 41.667 0.00 0.00 0.00 2.74
542 568 3.259374 ACAATGAATCTCAGACGACCACT 59.741 43.478 0.00 0.00 0.00 4.00
543 569 3.589988 ACAATGAATCTCAGACGACCAC 58.410 45.455 0.00 0.00 0.00 4.16
546 572 5.164233 TCAAGACAATGAATCTCAGACGAC 58.836 41.667 0.00 0.00 0.00 4.34
547 573 5.391312 TCAAGACAATGAATCTCAGACGA 57.609 39.130 0.00 0.00 0.00 4.20
548 574 6.659361 AATCAAGACAATGAATCTCAGACG 57.341 37.500 0.00 0.00 32.06 4.18
594 620 7.022979 CGAATGAAAATTCACAGCATAGAACA 58.977 34.615 0.00 0.00 40.49 3.18
595 621 6.470235 CCGAATGAAAATTCACAGCATAGAAC 59.530 38.462 0.00 0.00 40.49 3.01
596 622 6.554419 CCGAATGAAAATTCACAGCATAGAA 58.446 36.000 0.00 0.00 40.49 2.10
597 623 5.449041 GCCGAATGAAAATTCACAGCATAGA 60.449 40.000 0.00 0.00 40.49 1.98
599 625 4.671377 GCCGAATGAAAATTCACAGCATA 58.329 39.130 0.00 0.00 40.49 3.14
600 626 3.514645 GCCGAATGAAAATTCACAGCAT 58.485 40.909 0.00 0.00 40.49 3.79
615 642 2.510238 GCAGACAGCTCGCCGAAT 60.510 61.111 0.00 0.00 41.15 3.34
639 666 2.026641 CAATCATCCAATTCACCGGCT 58.973 47.619 0.00 0.00 0.00 5.52
647 674 4.891756 GGAGATCACACCAATCATCCAATT 59.108 41.667 0.00 0.00 0.00 2.32
720 748 6.716628 AGCATGATCTAACTTGAGGTGAAAAA 59.283 34.615 0.00 0.00 0.00 1.94
725 753 4.331992 CACAGCATGATCTAACTTGAGGTG 59.668 45.833 0.00 0.00 39.69 4.00
726 754 4.223700 TCACAGCATGATCTAACTTGAGGT 59.776 41.667 0.00 0.00 39.69 3.85
768 799 2.086054 AAGCACGACCAGATCTGAAC 57.914 50.000 24.62 15.22 0.00 3.18
769 800 4.471904 AATAAGCACGACCAGATCTGAA 57.528 40.909 24.62 0.00 0.00 3.02
771 802 3.242543 GCAAATAAGCACGACCAGATCTG 60.243 47.826 16.24 16.24 0.00 2.90
775 806 1.448985 GGCAAATAAGCACGACCAGA 58.551 50.000 0.00 0.00 35.83 3.86
776 807 0.096976 CGGCAAATAAGCACGACCAG 59.903 55.000 0.00 0.00 35.83 4.00
779 810 2.825086 ATTCGGCAAATAAGCACGAC 57.175 45.000 0.00 0.00 37.09 4.34
782 813 6.751888 ACTCAATTAATTCGGCAAATAAGCAC 59.248 34.615 0.00 0.00 35.83 4.40
788 819 8.506168 TCTTCTACTCAATTAATTCGGCAAAT 57.494 30.769 0.00 0.00 0.00 2.32
862 897 6.531948 ACCGAGATTCAGATCTTAAAAAGACG 59.468 38.462 0.00 0.00 42.66 4.18
891 955 4.004314 TCAGAGACTCGGAGTAAACAGAG 58.996 47.826 11.27 0.00 37.90 3.35
903 967 1.472082 ACTGCACATCTCAGAGACTCG 59.528 52.381 0.91 0.00 35.61 4.18
928 999 2.886523 TGAAAAACAGAGCATCCACTGG 59.113 45.455 0.00 0.00 38.30 4.00
2607 2727 2.351336 GATCTACAGACGGGGTGGCG 62.351 65.000 0.00 0.00 0.00 5.69
2608 2728 1.043673 AGATCTACAGACGGGGTGGC 61.044 60.000 0.00 0.00 0.00 5.01
2609 2729 1.486211 AAGATCTACAGACGGGGTGG 58.514 55.000 0.00 0.00 0.00 4.61
2610 2730 3.288964 AGTAAGATCTACAGACGGGGTG 58.711 50.000 0.00 0.00 0.00 4.61
2611 2731 3.666345 AGTAAGATCTACAGACGGGGT 57.334 47.619 0.00 0.00 0.00 4.95
2612 2732 7.756395 TTATAAGTAAGATCTACAGACGGGG 57.244 40.000 0.00 0.00 0.00 5.73
2613 2733 9.011095 TGATTATAAGTAAGATCTACAGACGGG 57.989 37.037 0.00 0.00 0.00 5.28
2675 2800 1.826096 TCGTTCATGGGATACAACGGA 59.174 47.619 13.17 1.12 41.51 4.69
2747 2872 4.973168 TGAGGAGCAACTACAAACTTGAT 58.027 39.130 0.00 0.00 0.00 2.57
2748 2873 4.415881 TGAGGAGCAACTACAAACTTGA 57.584 40.909 0.00 0.00 0.00 3.02
2771 2906 2.953020 AGCAAAACACACGAGCAAAAA 58.047 38.095 0.00 0.00 0.00 1.94
2772 2907 2.645730 AGCAAAACACACGAGCAAAA 57.354 40.000 0.00 0.00 0.00 2.44
2821 2956 7.781056 ACAAGCTACAATTCTCCTTTCAAAAA 58.219 30.769 0.00 0.00 0.00 1.94
2822 2957 7.346751 ACAAGCTACAATTCTCCTTTCAAAA 57.653 32.000 0.00 0.00 0.00 2.44
2823 2958 6.959639 ACAAGCTACAATTCTCCTTTCAAA 57.040 33.333 0.00 0.00 0.00 2.69
2824 2959 6.239008 CCAACAAGCTACAATTCTCCTTTCAA 60.239 38.462 0.00 0.00 0.00 2.69
2825 2960 5.241506 CCAACAAGCTACAATTCTCCTTTCA 59.758 40.000 0.00 0.00 0.00 2.69
2826 2961 5.703876 CCAACAAGCTACAATTCTCCTTTC 58.296 41.667 0.00 0.00 0.00 2.62
2827 2962 4.021981 GCCAACAAGCTACAATTCTCCTTT 60.022 41.667 0.00 0.00 0.00 3.11
2828 2963 3.507622 GCCAACAAGCTACAATTCTCCTT 59.492 43.478 0.00 0.00 0.00 3.36
2829 2964 3.084786 GCCAACAAGCTACAATTCTCCT 58.915 45.455 0.00 0.00 0.00 3.69
2830 2965 2.164422 GGCCAACAAGCTACAATTCTCC 59.836 50.000 0.00 0.00 0.00 3.71
2831 2966 2.819608 TGGCCAACAAGCTACAATTCTC 59.180 45.455 0.61 0.00 0.00 2.87
2832 2967 2.821969 CTGGCCAACAAGCTACAATTCT 59.178 45.455 7.01 0.00 0.00 2.40
2833 2968 2.558359 ACTGGCCAACAAGCTACAATTC 59.442 45.455 7.01 0.00 0.00 2.17
2834 2969 2.597455 ACTGGCCAACAAGCTACAATT 58.403 42.857 7.01 0.00 0.00 2.32
2835 2970 2.292828 ACTGGCCAACAAGCTACAAT 57.707 45.000 7.01 0.00 0.00 2.71
2836 2971 2.778299 CTACTGGCCAACAAGCTACAA 58.222 47.619 7.01 0.00 0.00 2.41
2837 2972 1.610624 GCTACTGGCCAACAAGCTACA 60.611 52.381 20.84 0.00 31.63 2.74
2838 2973 1.087501 GCTACTGGCCAACAAGCTAC 58.912 55.000 20.84 0.00 31.63 3.58
2863 3005 2.031870 TGGGGATCATGTGACTAGTCG 58.968 52.381 17.85 3.88 0.00 4.18
2865 3007 2.768527 CAGTGGGGATCATGTGACTAGT 59.231 50.000 0.00 0.00 0.00 2.57
2866 3008 3.033909 TCAGTGGGGATCATGTGACTAG 58.966 50.000 0.00 0.00 0.00 2.57
2881 3023 0.036875 GGGTCCTTCTGGTTCAGTGG 59.963 60.000 0.00 0.00 32.61 4.00
2968 3111 3.097728 CGTCGCATCGATACCGGC 61.098 66.667 0.00 13.05 38.42 6.13
3141 3312 2.022129 CGACGACTTTGCCTTCGCT 61.022 57.895 0.00 0.00 38.88 4.93
3144 3315 0.640768 CGATCGACGACTTTGCCTTC 59.359 55.000 10.26 0.00 45.77 3.46
3190 3361 2.421314 CCGGCATCATCCACGCTA 59.579 61.111 0.00 0.00 0.00 4.26
3212 3383 0.602638 AAAGTTGTCTGGCGCGATCA 60.603 50.000 12.10 6.32 0.00 2.92
3220 3391 5.583854 AGATTCGATCATCAAAGTTGTCTGG 59.416 40.000 0.21 0.00 0.00 3.86
3228 3399 2.349249 GCCGCAGATTCGATCATCAAAG 60.349 50.000 0.21 0.00 0.00 2.77
3269 3443 0.460987 GATCGACCTTGACCTGCAGG 60.461 60.000 31.60 31.60 42.17 4.85
3332 3506 4.388080 CACACACATGCACGCCCG 62.388 66.667 0.00 0.00 0.00 6.13
3333 3507 3.286751 ACACACACATGCACGCCC 61.287 61.111 0.00 0.00 0.00 6.13
3334 3508 2.051076 CACACACACATGCACGCC 60.051 61.111 0.00 0.00 0.00 5.68
3335 3509 2.726912 GCACACACACATGCACGC 60.727 61.111 0.00 0.00 41.65 5.34
3336 3510 2.051076 GGCACACACACATGCACG 60.051 61.111 0.00 0.00 43.93 5.34
3337 3511 1.008194 CTGGCACACACACATGCAC 60.008 57.895 0.00 0.00 43.93 4.57
3338 3512 1.446516 GACTGGCACACACACATGCA 61.447 55.000 0.00 0.00 43.93 3.96
3339 3513 1.283793 GACTGGCACACACACATGC 59.716 57.895 0.00 0.00 41.29 4.06
3340 3514 0.879839 TCGACTGGCACACACACATG 60.880 55.000 0.00 0.00 0.00 3.21
3341 3515 0.880278 GTCGACTGGCACACACACAT 60.880 55.000 8.70 0.00 0.00 3.21
3342 3516 1.520564 GTCGACTGGCACACACACA 60.521 57.895 8.70 0.00 0.00 3.72
3343 3517 2.585869 CGTCGACTGGCACACACAC 61.586 63.158 14.70 0.00 0.00 3.82
3344 3518 2.279186 CGTCGACTGGCACACACA 60.279 61.111 14.70 0.00 0.00 3.72
3345 3519 2.027024 TCGTCGACTGGCACACAC 59.973 61.111 14.70 0.00 0.00 3.82
3365 3539 2.973899 CGGTCCAGGTGAGGTCTG 59.026 66.667 0.00 0.00 0.00 3.51
3366 3540 2.997897 GCGGTCCAGGTGAGGTCT 60.998 66.667 0.00 0.00 0.00 3.85
3367 3541 4.436998 CGCGGTCCAGGTGAGGTC 62.437 72.222 0.00 0.00 0.00 3.85
3369 3543 4.436998 GACGCGGTCCAGGTGAGG 62.437 72.222 12.47 0.00 0.00 3.86
3370 3544 4.778415 CGACGCGGTCCAGGTGAG 62.778 72.222 12.47 0.00 0.00 3.51
3388 3562 1.594833 GCCGATCCACACACCTACA 59.405 57.895 0.00 0.00 0.00 2.74
3389 3563 1.518572 CGCCGATCCACACACCTAC 60.519 63.158 0.00 0.00 0.00 3.18
3396 3570 2.126228 GACGAACGCCGATCCACA 60.126 61.111 4.79 0.00 41.76 4.17
3416 3590 2.671963 GGGTGTCGGTGGGAAAGC 60.672 66.667 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.