Multiple sequence alignment - TraesCS4B01G289800

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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 TraesCS4B01G289800 chr4B 100.000 2859 0 0 1 2859 574531446 574528588 0.000000e+00 5280.0
1 TraesCS4B01G289800 chr4D 92.134 1373 77 13 930 2284 459589632 459588273 0.000000e+00 1908.0
2 TraesCS4B01G289800 chr4A 94.409 1091 42 5 530 1613 8581989 8583067 0.000000e+00 1659.0
3 TraesCS4B01G289800 chr4A 93.520 679 29 8 1611 2281 8583148 8583819 0.000000e+00 996.0
4 TraesCS4B01G289800 chr4A 92.667 300 18 4 2562 2858 8584392 8584690 2.040000e-116 429.0
5 TraesCS4B01G289800 chr4A 90.234 256 9 6 247 498 8581751 8581994 1.280000e-83 320.0
6 TraesCS4B01G289800 chr4A 92.661 218 15 1 2352 2569 8583826 8584042 2.140000e-81 313.0
7 TraesCS4B01G289800 chr4A 87.149 249 30 2 1 248 8581247 8581494 6.030000e-72 281.0
8 TraesCS4B01G289800 chr6A 92.537 67 3 2 2271 2336 565317055 565317120 8.430000e-16 95.3
9 TraesCS4B01G289800 chr3D 98.148 54 1 0 2283 2336 11592260 11592207 8.430000e-16 95.3
10 TraesCS4B01G289800 chr3D 98.148 54 1 0 2283 2336 610359389 610359336 8.430000e-16 95.3
11 TraesCS4B01G289800 chr2B 98.148 54 1 0 2283 2336 121512049 121512102 8.430000e-16 95.3
12 TraesCS4B01G289800 chr1D 98.148 54 1 0 2283 2336 285371888 285371835 8.430000e-16 95.3
13 TraesCS4B01G289800 chr1A 98.148 54 1 0 2283 2336 493207984 493208037 8.430000e-16 95.3
14 TraesCS4B01G289800 chr7B 96.491 57 1 1 2277 2333 733361483 733361538 3.030000e-15 93.5
15 TraesCS4B01G289800 chr5B 98.113 53 1 0 2282 2334 544518988 544519040 3.030000e-15 93.5
16 TraesCS4B01G289800 chr6B 89.552 67 5 2 2278 2342 52217884 52217818 1.830000e-12 84.2


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 TraesCS4B01G289800 chr4B 574528588 574531446 2858 True 5280.000000 5280 100.000000 1 2859 1 chr4B.!!$R1 2858
1 TraesCS4B01G289800 chr4D 459588273 459589632 1359 True 1908.000000 1908 92.134000 930 2284 1 chr4D.!!$R1 1354
2 TraesCS4B01G289800 chr4A 8581247 8584690 3443 False 666.333333 1659 91.773333 1 2858 6 chr4A.!!$F1 2857

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
465 729 0.105778 TTTTGCTTTTGCCCCTTCCG 59.894 50.0 0.0 0.0 46.87 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2704 0.683412 GGTGTACTCCCTCCGTTTGT 59.317 55.0 2.33 0.0 0.0 2.83 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
29 30 1.068250 CAGGGCGCTAGTCTTAGGC 59.932 63.158 7.64 0.00 0.00 3.93
32 33 1.589196 GGCGCTAGTCTTAGGCACG 60.589 63.158 7.64 0.00 0.00 5.34
36 37 1.140407 GCTAGTCTTAGGCACGCGTG 61.140 60.000 34.01 34.01 0.00 5.34
46 47 2.356313 CACGCGTGCAGGAAGACT 60.356 61.111 28.16 0.00 0.00 3.24
59 61 2.779506 GGAAGACTTCCCGTTGTCATT 58.220 47.619 21.88 0.00 44.30 2.57
96 98 3.016997 TCGATAGAGGAACGGCGAT 57.983 52.632 16.62 0.00 42.67 4.58
100 102 2.582687 GATAGAGGAACGGCGATAACG 58.417 52.381 16.62 0.00 42.93 3.18
133 135 2.661566 CGTTCTGACGGCAGCAGTG 61.662 63.158 15.33 0.00 45.32 3.66
147 149 1.782028 GCAGTGGTCGTTTGGTGGTC 61.782 60.000 0.00 0.00 0.00 4.02
149 151 0.179056 AGTGGTCGTTTGGTGGTCTG 60.179 55.000 0.00 0.00 0.00 3.51
158 160 5.411669 GTCGTTTGGTGGTCTGAGAATTAAT 59.588 40.000 0.00 0.00 0.00 1.40
265 525 4.065088 GCCCATTCTTTCCTTGGTTTTTC 58.935 43.478 0.00 0.00 0.00 2.29
269 529 4.400529 TTCTTTCCTTGGTTTTTCCTGC 57.599 40.909 0.00 0.00 37.07 4.85
345 608 3.322828 GGCCTTAGTTACCGGTGATATGA 59.677 47.826 19.93 0.00 0.00 2.15
354 617 2.028839 ACCGGTGATATGAACGAACACA 60.029 45.455 6.12 0.00 33.82 3.72
414 678 4.285863 CTGCAATTCCCATTTTACCCCTA 58.714 43.478 0.00 0.00 0.00 3.53
428 692 2.231529 ACCCCTAGACAGAATCGATCG 58.768 52.381 9.36 9.36 0.00 3.69
429 693 2.158652 ACCCCTAGACAGAATCGATCGA 60.159 50.000 21.86 21.86 0.00 3.59
462 726 3.402186 GCTTTTGCTTTTGCCCCTT 57.598 47.368 0.00 0.00 46.87 3.95
463 727 1.229428 GCTTTTGCTTTTGCCCCTTC 58.771 50.000 0.00 0.00 46.87 3.46
464 728 1.882912 CTTTTGCTTTTGCCCCTTCC 58.117 50.000 0.00 0.00 46.87 3.46
465 729 0.105778 TTTTGCTTTTGCCCCTTCCG 59.894 50.000 0.00 0.00 46.87 4.30
466 730 1.045911 TTTGCTTTTGCCCCTTCCGT 61.046 50.000 0.00 0.00 46.87 4.69
467 731 1.045911 TTGCTTTTGCCCCTTCCGTT 61.046 50.000 0.00 0.00 46.87 4.44
468 732 1.289066 GCTTTTGCCCCTTCCGTTC 59.711 57.895 0.00 0.00 40.15 3.95
469 733 1.964448 CTTTTGCCCCTTCCGTTCC 59.036 57.895 0.00 0.00 0.00 3.62
470 734 1.862602 CTTTTGCCCCTTCCGTTCCG 61.863 60.000 0.00 0.00 0.00 4.30
471 735 2.627839 TTTTGCCCCTTCCGTTCCGT 62.628 55.000 0.00 0.00 0.00 4.69
500 764 4.910585 GTGCGATACCCCGGCAGG 62.911 72.222 0.00 0.00 37.36 4.85
504 768 3.857038 GATACCCCGGCAGGCGAA 61.857 66.667 19.71 0.25 35.76 4.70
505 769 3.809374 GATACCCCGGCAGGCGAAG 62.809 68.421 19.71 10.99 35.76 3.79
523 787 4.404098 CCCCAGCGCCCGTAAACT 62.404 66.667 2.29 0.00 0.00 2.66
524 788 2.818274 CCCAGCGCCCGTAAACTC 60.818 66.667 2.29 0.00 0.00 3.01
525 789 2.264794 CCAGCGCCCGTAAACTCT 59.735 61.111 2.29 0.00 0.00 3.24
526 790 1.810030 CCAGCGCCCGTAAACTCTC 60.810 63.158 2.29 0.00 0.00 3.20
527 791 2.158959 CAGCGCCCGTAAACTCTCG 61.159 63.158 2.29 0.00 0.00 4.04
528 792 2.884207 GCGCCCGTAAACTCTCGG 60.884 66.667 0.00 0.00 45.42 4.63
529 793 2.884207 CGCCCGTAAACTCTCGGC 60.884 66.667 0.00 0.00 44.63 5.54
530 794 2.510918 GCCCGTAAACTCTCGGCC 60.511 66.667 0.00 0.00 44.63 6.13
531 795 2.186125 CCCGTAAACTCTCGGCCC 59.814 66.667 0.00 0.00 44.63 5.80
532 796 2.356780 CCCGTAAACTCTCGGCCCT 61.357 63.158 0.00 0.00 44.63 5.19
533 797 1.153628 CCGTAAACTCTCGGCCCTG 60.154 63.158 0.00 0.00 40.28 4.45
534 798 1.810030 CGTAAACTCTCGGCCCTGC 60.810 63.158 0.00 0.00 0.00 4.85
636 900 1.228306 CTATCTCCCGCCTCTCCGT 60.228 63.158 0.00 0.00 0.00 4.69
637 901 1.228184 TATCTCCCGCCTCTCCGTC 60.228 63.158 0.00 0.00 0.00 4.79
638 902 1.706995 TATCTCCCGCCTCTCCGTCT 61.707 60.000 0.00 0.00 0.00 4.18
639 903 3.522731 CTCCCGCCTCTCCGTCTG 61.523 72.222 0.00 0.00 0.00 3.51
645 909 3.465403 CCTCTCCGTCTGCCCCTG 61.465 72.222 0.00 0.00 0.00 4.45
646 910 4.154347 CTCTCCGTCTGCCCCTGC 62.154 72.222 0.00 0.00 38.26 4.85
715 982 0.980423 GGTGAGCAGGTTCTTCTCCT 59.020 55.000 0.00 0.00 35.45 3.69
718 985 0.539518 GAGCAGGTTCTTCTCCTCCC 59.460 60.000 0.00 0.00 32.37 4.30
719 986 0.118144 AGCAGGTTCTTCTCCTCCCT 59.882 55.000 0.00 0.00 32.37 4.20
726 993 3.319689 GGTTCTTCTCCTCCCTTCTATCG 59.680 52.174 0.00 0.00 0.00 2.92
827 1094 1.069906 GCGCGCGATCTAATCCAAAAT 60.070 47.619 37.18 0.00 0.00 1.82
828 1095 2.602217 GCGCGCGATCTAATCCAAAATT 60.602 45.455 37.18 0.00 0.00 1.82
843 1110 0.322187 AAATTAGCCCCGTTCGCTGT 60.322 50.000 0.00 0.00 37.12 4.40
874 1141 5.738208 GCTTGCTAGGCGGTAGATTAGTTTA 60.738 44.000 0.00 0.00 0.00 2.01
901 1170 2.253610 ACTCCACGGGACAACTGAATA 58.746 47.619 0.00 0.00 0.00 1.75
904 1173 1.737793 CCACGGGACAACTGAATAAGC 59.262 52.381 0.00 0.00 0.00 3.09
912 1181 2.038557 ACAACTGAATAAGCCCGTCACT 59.961 45.455 0.00 0.00 0.00 3.41
913 1182 2.386661 ACTGAATAAGCCCGTCACTG 57.613 50.000 0.00 0.00 0.00 3.66
915 1184 0.981183 TGAATAAGCCCGTCACTGGT 59.019 50.000 0.00 0.00 0.00 4.00
916 1185 2.167693 CTGAATAAGCCCGTCACTGGTA 59.832 50.000 0.00 0.00 0.00 3.25
1026 1300 1.138266 TCCCGTACAAAGCTATCTGGC 59.862 52.381 0.00 0.00 0.00 4.85
1302 1576 4.950205 AAAAGGTCTAACGTTCTCTCCA 57.050 40.909 2.82 0.00 0.00 3.86
1366 1641 5.546526 TGAAAACATAGGATTTGCCCAAAC 58.453 37.500 0.00 0.00 37.37 2.93
1558 1834 4.130118 GTGTATTCCGAGATCCAATGCTT 58.870 43.478 0.00 0.00 0.00 3.91
1889 2260 2.562738 AGCTTGCTTTTAATGGTGTCCC 59.437 45.455 0.00 0.00 0.00 4.46
2016 2387 4.345257 GCCCTCTGGATATTAGAAGTGTGA 59.655 45.833 0.00 0.00 0.00 3.58
2109 2480 4.579340 TGGAGCTCTATACTGTCTAAACGG 59.421 45.833 14.64 0.00 37.81 4.44
2120 2491 4.250464 CTGTCTAAACGGCTAAACCATGA 58.750 43.478 0.00 0.00 39.03 3.07
2178 2549 6.925165 GCAATGTAATTCACCCCTATCATTTG 59.075 38.462 0.00 0.00 31.22 2.32
2180 2551 7.587037 ATGTAATTCACCCCTATCATTTGTG 57.413 36.000 0.00 0.00 0.00 3.33
2205 2577 7.661437 TGTAGACTTATGTGCTCAATTGAGTTT 59.339 33.333 30.88 17.87 43.85 2.66
2207 2579 8.034058 AGACTTATGTGCTCAATTGAGTTTAC 57.966 34.615 30.88 25.80 43.85 2.01
2211 2583 3.745975 TGTGCTCAATTGAGTTTACCTCG 59.254 43.478 30.88 8.91 43.64 4.63
2284 2656 7.088589 ACTGAATTGTATTGCTCAATGGTAC 57.911 36.000 5.43 0.00 35.95 3.34
2285 2657 6.886459 ACTGAATTGTATTGCTCAATGGTACT 59.114 34.615 5.43 0.00 35.95 2.73
2286 2658 7.066284 ACTGAATTGTATTGCTCAATGGTACTC 59.934 37.037 5.43 0.00 35.95 2.59
2287 2659 6.318648 TGAATTGTATTGCTCAATGGTACTCC 59.681 38.462 5.43 0.00 35.95 3.85
2288 2660 4.150897 TGTATTGCTCAATGGTACTCCC 57.849 45.455 5.43 0.00 32.50 4.30
2289 2661 3.780294 TGTATTGCTCAATGGTACTCCCT 59.220 43.478 5.43 0.00 32.50 4.20
2290 2662 3.567478 ATTGCTCAATGGTACTCCCTC 57.433 47.619 0.00 0.00 0.00 4.30
2291 2663 1.204146 TGCTCAATGGTACTCCCTCC 58.796 55.000 0.00 0.00 0.00 4.30
2292 2664 0.105039 GCTCAATGGTACTCCCTCCG 59.895 60.000 0.00 0.00 0.00 4.63
2293 2665 1.486211 CTCAATGGTACTCCCTCCGT 58.514 55.000 0.00 0.00 0.00 4.69
2294 2666 1.831736 CTCAATGGTACTCCCTCCGTT 59.168 52.381 0.00 0.00 33.79 4.44
2295 2667 1.829222 TCAATGGTACTCCCTCCGTTC 59.171 52.381 0.00 0.00 31.49 3.95
2296 2668 1.134491 CAATGGTACTCCCTCCGTTCC 60.134 57.143 0.00 0.00 31.49 3.62
2297 2669 0.338814 ATGGTACTCCCTCCGTTCCT 59.661 55.000 0.00 0.00 0.00 3.36
2298 2670 1.002069 TGGTACTCCCTCCGTTCCTA 58.998 55.000 0.00 0.00 0.00 2.94
2299 2671 1.358787 TGGTACTCCCTCCGTTCCTAA 59.641 52.381 0.00 0.00 0.00 2.69
2300 2672 2.225343 TGGTACTCCCTCCGTTCCTAAA 60.225 50.000 0.00 0.00 0.00 1.85
2301 2673 3.036819 GGTACTCCCTCCGTTCCTAAAT 58.963 50.000 0.00 0.00 0.00 1.40
2302 2674 4.218312 GGTACTCCCTCCGTTCCTAAATA 58.782 47.826 0.00 0.00 0.00 1.40
2303 2675 4.837298 GGTACTCCCTCCGTTCCTAAATAT 59.163 45.833 0.00 0.00 0.00 1.28
2304 2676 6.012745 GGTACTCCCTCCGTTCCTAAATATA 58.987 44.000 0.00 0.00 0.00 0.86
2305 2677 6.152492 GGTACTCCCTCCGTTCCTAAATATAG 59.848 46.154 0.00 0.00 0.00 1.31
2328 2700 6.466812 AGGTCTTTTTAGGCATTTCAAATGG 58.533 36.000 12.14 0.00 0.00 3.16
2329 2701 6.269769 AGGTCTTTTTAGGCATTTCAAATGGA 59.730 34.615 12.14 0.00 0.00 3.41
2330 2702 6.368791 GGTCTTTTTAGGCATTTCAAATGGAC 59.631 38.462 12.14 7.59 0.00 4.02
2331 2703 7.154656 GTCTTTTTAGGCATTTCAAATGGACT 58.845 34.615 12.14 3.08 0.00 3.85
2332 2704 8.303876 GTCTTTTTAGGCATTTCAAATGGACTA 58.696 33.333 12.14 2.16 0.00 2.59
2333 2705 8.303876 TCTTTTTAGGCATTTCAAATGGACTAC 58.696 33.333 12.14 0.00 0.00 2.73
2334 2706 7.531857 TTTTAGGCATTTCAAATGGACTACA 57.468 32.000 12.14 0.00 0.00 2.74
2335 2707 7.531857 TTTAGGCATTTCAAATGGACTACAA 57.468 32.000 12.14 1.11 0.00 2.41
2336 2708 7.531857 TTAGGCATTTCAAATGGACTACAAA 57.468 32.000 12.14 0.00 0.00 2.83
2337 2709 5.783111 AGGCATTTCAAATGGACTACAAAC 58.217 37.500 12.14 0.00 0.00 2.93
2338 2710 4.621034 GGCATTTCAAATGGACTACAAACG 59.379 41.667 12.14 0.00 0.00 3.60
2339 2711 4.621034 GCATTTCAAATGGACTACAAACGG 59.379 41.667 12.14 0.00 0.00 4.44
2340 2712 5.563867 GCATTTCAAATGGACTACAAACGGA 60.564 40.000 12.14 0.00 0.00 4.69
2341 2713 5.682943 TTTCAAATGGACTACAAACGGAG 57.317 39.130 0.00 0.00 0.00 4.63
2342 2714 3.670625 TCAAATGGACTACAAACGGAGG 58.329 45.455 0.00 0.00 0.00 4.30
2343 2715 2.747446 CAAATGGACTACAAACGGAGGG 59.253 50.000 0.00 0.00 0.00 4.30
2344 2716 1.946984 ATGGACTACAAACGGAGGGA 58.053 50.000 0.00 0.00 0.00 4.20
2345 2717 1.263356 TGGACTACAAACGGAGGGAG 58.737 55.000 0.00 0.00 0.00 4.30
2346 2718 1.264295 GGACTACAAACGGAGGGAGT 58.736 55.000 0.00 0.00 0.00 3.85
2347 2719 2.225091 TGGACTACAAACGGAGGGAGTA 60.225 50.000 0.00 0.00 0.00 2.59
2348 2720 2.165234 GGACTACAAACGGAGGGAGTAC 59.835 54.545 0.00 0.00 0.00 2.73
2349 2721 2.821969 GACTACAAACGGAGGGAGTACA 59.178 50.000 0.00 0.00 0.00 2.90
2350 2722 2.560105 ACTACAAACGGAGGGAGTACAC 59.440 50.000 0.00 0.00 0.00 2.90
2370 2742 4.002982 CACCTTAGTGCATGCTTTCACTA 58.997 43.478 20.33 14.81 42.81 2.74
2381 2753 5.510671 CATGCTTTCACTAACGTTGTTCTT 58.489 37.500 11.99 0.00 0.00 2.52
2512 2884 1.188863 GGGCCAGATCAAGCAATGTT 58.811 50.000 4.39 0.00 0.00 2.71
2547 2919 5.105310 GGAAGATGGTTCTAACTGCTAGTGA 60.105 44.000 0.00 0.00 0.00 3.41
2553 2925 5.189736 TGGTTCTAACTGCTAGTGATGGAAT 59.810 40.000 0.00 0.00 0.00 3.01
2569 2941 2.108075 TGGAATCATCACCACCACAGTT 59.892 45.455 0.00 0.00 0.00 3.16
2571 2943 4.202514 TGGAATCATCACCACCACAGTTAA 60.203 41.667 0.00 0.00 0.00 2.01
2572 2944 4.949856 GGAATCATCACCACCACAGTTAAT 59.050 41.667 0.00 0.00 0.00 1.40
2573 2945 5.163622 GGAATCATCACCACCACAGTTAATG 60.164 44.000 0.00 0.00 0.00 1.90
2574 2946 4.365514 TCATCACCACCACAGTTAATGT 57.634 40.909 0.00 0.00 45.43 2.71
2575 2947 5.491323 TCATCACCACCACAGTTAATGTA 57.509 39.130 0.00 0.00 41.41 2.29
2576 2948 6.061022 TCATCACCACCACAGTTAATGTAT 57.939 37.500 0.00 0.00 41.41 2.29
2577 2949 6.112734 TCATCACCACCACAGTTAATGTATC 58.887 40.000 0.00 0.00 41.41 2.24
2578 2950 5.491323 TCACCACCACAGTTAATGTATCA 57.509 39.130 0.00 0.00 41.41 2.15
2579 2951 6.061022 TCACCACCACAGTTAATGTATCAT 57.939 37.500 0.00 0.00 41.41 2.45
2580 2952 7.189079 TCACCACCACAGTTAATGTATCATA 57.811 36.000 0.00 0.00 41.41 2.15
2581 2953 7.045416 TCACCACCACAGTTAATGTATCATAC 58.955 38.462 0.00 0.00 41.41 2.39
2582 2954 6.260050 CACCACCACAGTTAATGTATCATACC 59.740 42.308 0.00 0.00 41.41 2.73
2583 2955 5.465390 CCACCACAGTTAATGTATCATACCG 59.535 44.000 0.00 0.00 41.41 4.02
2584 2956 5.465390 CACCACAGTTAATGTATCATACCGG 59.535 44.000 0.00 0.00 41.41 5.28
2585 2957 4.451096 CCACAGTTAATGTATCATACCGGC 59.549 45.833 0.00 0.00 41.41 6.13
2586 2958 5.297547 CACAGTTAATGTATCATACCGGCT 58.702 41.667 0.00 0.00 41.41 5.52
2587 2959 5.405571 CACAGTTAATGTATCATACCGGCTC 59.594 44.000 0.00 0.00 41.41 4.70
2588 2960 5.069914 ACAGTTAATGTATCATACCGGCTCA 59.930 40.000 0.00 0.00 41.60 4.26
2589 2961 5.405571 CAGTTAATGTATCATACCGGCTCAC 59.594 44.000 0.00 0.00 0.00 3.51
2590 2962 5.069914 AGTTAATGTATCATACCGGCTCACA 59.930 40.000 0.00 0.00 0.00 3.58
2591 2963 2.882927 TGTATCATACCGGCTCACAC 57.117 50.000 0.00 0.00 0.00 3.82
2659 3390 3.191539 GCGCTGCTGCTGAGGTAC 61.192 66.667 14.03 0.00 36.97 3.34
2668 3399 4.023980 TGCTGCTGAGGTACTTATGTACT 58.976 43.478 16.06 5.18 46.04 2.73
2669 3400 4.142160 TGCTGCTGAGGTACTTATGTACTG 60.142 45.833 16.06 7.65 46.04 2.74
2671 3402 5.394224 GCTGCTGAGGTACTTATGTACTGAA 60.394 44.000 16.06 4.24 46.04 3.02
2673 3404 7.182817 TGCTGAGGTACTTATGTACTGAATT 57.817 36.000 16.06 0.00 46.04 2.17
2674 3405 8.301252 TGCTGAGGTACTTATGTACTGAATTA 57.699 34.615 16.06 1.07 46.04 1.40
2675 3406 8.755028 TGCTGAGGTACTTATGTACTGAATTAA 58.245 33.333 16.06 0.00 46.04 1.40
2719 3450 6.385759 TCATCCTTGACTTTACCTATAGCCAA 59.614 38.462 0.00 0.00 0.00 4.52
2722 3453 6.013206 TCCTTGACTTTACCTATAGCCAACAA 60.013 38.462 0.00 0.00 0.00 2.83
2766 3497 8.267894 ACTGTAGTCATGGTTTATGAGCTTAAT 58.732 33.333 0.00 0.00 46.09 1.40
2792 3523 6.395629 TCTTTTAGACCTTTCAGTGTATCCG 58.604 40.000 0.00 0.00 0.00 4.18
2793 3524 5.733620 TTTAGACCTTTCAGTGTATCCGT 57.266 39.130 0.00 0.00 0.00 4.69
2803 3534 1.555075 AGTGTATCCGTGCCTGTCAAT 59.445 47.619 0.00 0.00 0.00 2.57
2858 3590 7.614124 AATCCAAAAATGTGCATTATTGACC 57.386 32.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.755698 TAAGACTAGCGCCCTGGAGG 60.756 60.000 2.29 0.00 39.47 4.30
18 19 2.945315 CACGCGTGCCTAAGACTAG 58.055 57.895 28.16 0.00 0.00 2.57
29 30 1.891060 GAAGTCTTCCTGCACGCGTG 61.891 60.000 34.01 34.01 0.00 5.34
32 33 3.567473 GGAAGTCTTCCTGCACGC 58.433 61.111 22.42 0.00 46.57 5.34
46 47 2.226330 CCTTGTCAATGACAACGGGAA 58.774 47.619 23.28 3.96 45.88 3.97
59 61 2.557317 GAAACCGACTTGACCTTGTCA 58.443 47.619 0.00 0.00 41.09 3.58
76 78 1.097232 TCGCCGTTCCTCTATCGAAA 58.903 50.000 0.00 0.00 0.00 3.46
103 105 2.813908 AGAACGATCCGCCAACGC 60.814 61.111 0.00 0.00 38.22 4.84
116 118 2.320587 CCACTGCTGCCGTCAGAAC 61.321 63.158 0.00 0.00 42.95 3.01
128 130 1.782028 GACCACCAAACGACCACTGC 61.782 60.000 0.00 0.00 0.00 4.40
129 131 0.179056 AGACCACCAAACGACCACTG 60.179 55.000 0.00 0.00 0.00 3.66
133 135 0.391597 TCTCAGACCACCAAACGACC 59.608 55.000 0.00 0.00 0.00 4.79
168 170 8.472007 AAGTTCATGTACAAACCCTATCAAAA 57.528 30.769 0.00 0.00 0.00 2.44
208 210 4.927978 TTTCTTTTGCGAAAGGGATCAA 57.072 36.364 23.38 9.47 42.05 2.57
209 211 4.927978 TTTTCTTTTGCGAAAGGGATCA 57.072 36.364 23.38 3.87 42.05 2.92
219 221 3.487574 TGCACGGTTATTTTTCTTTTGCG 59.512 39.130 0.00 0.00 0.00 4.85
265 525 3.042887 GCACGTTAAGAAAACTTGCAGG 58.957 45.455 12.68 0.00 42.63 4.85
345 608 1.027792 AAAGTGCCCGTGTGTTCGTT 61.028 50.000 0.00 0.00 0.00 3.85
414 678 4.338400 TGGTGTATTCGATCGATTCTGTCT 59.662 41.667 20.18 0.96 0.00 3.41
428 692 1.826385 AAGCTGCTGGTGGTGTATTC 58.174 50.000 1.35 0.00 0.00 1.75
429 693 2.292828 AAAGCTGCTGGTGGTGTATT 57.707 45.000 1.35 0.00 0.00 1.89
452 716 4.184439 GGAACGGAAGGGGCAAAA 57.816 55.556 0.00 0.00 0.00 2.44
465 729 1.154073 CGGGAGAGACGAACGGAAC 60.154 63.158 0.00 0.00 0.00 3.62
466 730 1.601759 ACGGGAGAGACGAACGGAA 60.602 57.895 0.00 0.00 34.93 4.30
467 731 2.033141 ACGGGAGAGACGAACGGA 59.967 61.111 0.00 0.00 34.93 4.69
468 732 2.178521 CACGGGAGAGACGAACGG 59.821 66.667 0.00 0.00 34.93 4.44
469 733 2.504244 GCACGGGAGAGACGAACG 60.504 66.667 0.00 0.00 34.93 3.95
470 734 2.267681 ATCGCACGGGAGAGACGAAC 62.268 60.000 0.00 0.00 34.41 3.95
471 735 0.745486 TATCGCACGGGAGAGACGAA 60.745 55.000 0.00 0.00 34.41 3.85
506 770 4.404098 AGTTTACGGGCGCTGGGG 62.404 66.667 7.64 0.00 0.00 4.96
507 771 2.818274 GAGTTTACGGGCGCTGGG 60.818 66.667 7.64 0.00 0.00 4.45
508 772 1.810030 GAGAGTTTACGGGCGCTGG 60.810 63.158 7.64 1.29 0.00 4.85
509 773 2.158959 CGAGAGTTTACGGGCGCTG 61.159 63.158 7.64 2.40 0.00 5.18
510 774 2.181021 CGAGAGTTTACGGGCGCT 59.819 61.111 7.64 0.00 0.00 5.92
511 775 2.884207 CCGAGAGTTTACGGGCGC 60.884 66.667 0.00 0.00 44.59 6.53
516 780 1.810030 GCAGGGCCGAGAGTTTACG 60.810 63.158 0.00 0.00 0.00 3.18
517 781 1.449778 GGCAGGGCCGAGAGTTTAC 60.450 63.158 0.00 0.00 39.62 2.01
518 782 2.987125 GGCAGGGCCGAGAGTTTA 59.013 61.111 0.00 0.00 39.62 2.01
621 885 3.729489 AGACGGAGAGGCGGGAGA 61.729 66.667 0.00 0.00 0.00 3.71
715 982 2.792947 GCCGGTGCGATAGAAGGGA 61.793 63.158 1.90 0.00 39.76 4.20
718 985 2.230940 CGTGCCGGTGCGATAGAAG 61.231 63.158 13.19 0.00 41.78 2.85
719 986 2.202690 CGTGCCGGTGCGATAGAA 60.203 61.111 13.19 0.00 41.78 2.10
827 1094 2.047655 CACAGCGAACGGGGCTAA 60.048 61.111 0.00 0.00 39.08 3.09
828 1095 4.077184 CCACAGCGAACGGGGCTA 62.077 66.667 0.00 0.00 39.08 3.93
843 1110 1.031571 CCGCCTAGCAAGCAAATCCA 61.032 55.000 0.00 0.00 0.00 3.41
874 1141 3.143728 GTTGTCCCGTGGAGTACAAAAT 58.856 45.455 0.00 0.00 33.92 1.82
901 1170 2.351706 TTTTTACCAGTGACGGGCTT 57.648 45.000 0.46 0.00 0.00 4.35
904 1173 3.692101 TGCATATTTTTACCAGTGACGGG 59.308 43.478 0.00 0.00 0.00 5.28
912 1181 5.065859 CGTGGTGATCTGCATATTTTTACCA 59.934 40.000 0.00 0.00 33.65 3.25
913 1182 5.295787 TCGTGGTGATCTGCATATTTTTACC 59.704 40.000 0.00 0.00 0.00 2.85
915 1184 6.257849 GTCTCGTGGTGATCTGCATATTTTTA 59.742 38.462 0.00 0.00 0.00 1.52
916 1185 5.065218 GTCTCGTGGTGATCTGCATATTTTT 59.935 40.000 0.00 0.00 0.00 1.94
969 1239 2.548178 ACGCAGTCATCAAAGCCTG 58.452 52.632 0.00 0.00 29.74 4.85
1107 1381 0.600557 CTGCTGAGACAACGGACTCT 59.399 55.000 0.00 0.00 36.86 3.24
1209 1483 1.904537 TCAGGATTCTTGAGCTGCTCA 59.095 47.619 27.35 27.35 38.87 4.26
1212 1486 4.451774 GTGATATCAGGATTCTTGAGCTGC 59.548 45.833 5.42 0.00 0.00 5.25
1287 1561 7.609146 TCAGTATTAGTTGGAGAGAACGTTAGA 59.391 37.037 0.00 0.00 0.00 2.10
1292 1566 8.568794 TGATATCAGTATTAGTTGGAGAGAACG 58.431 37.037 0.00 0.00 0.00 3.95
1320 1594 6.539826 TCATGCAACATCCTTACTCAATGTAG 59.460 38.462 0.00 0.00 33.42 2.74
1392 1667 8.532977 AAACAACTATTCATATGCAAACAACC 57.467 30.769 0.00 0.00 0.00 3.77
1558 1834 9.150348 CTGTAACTGTGATGTGTAAATGATACA 57.850 33.333 0.00 0.00 33.18 2.29
1863 2234 4.021981 ACACCATTAAAAGCAAGCTCTTCC 60.022 41.667 0.00 0.00 0.00 3.46
2120 2491 5.806654 ACACCATTGCTGAATTTAAACCT 57.193 34.783 0.00 0.00 0.00 3.50
2178 2549 6.591834 ACTCAATTGAGCACATAAGTCTACAC 59.408 38.462 30.95 0.00 45.79 2.90
2180 2551 7.602517 AACTCAATTGAGCACATAAGTCTAC 57.397 36.000 30.95 0.00 45.79 2.59
2302 2674 8.260114 CCATTTGAAATGCCTAAAAAGACCTAT 58.740 33.333 12.26 0.00 0.00 2.57
2303 2675 7.453126 TCCATTTGAAATGCCTAAAAAGACCTA 59.547 33.333 12.26 0.00 0.00 3.08
2304 2676 6.269769 TCCATTTGAAATGCCTAAAAAGACCT 59.730 34.615 12.26 0.00 0.00 3.85
2305 2677 6.368791 GTCCATTTGAAATGCCTAAAAAGACC 59.631 38.462 12.26 0.00 0.00 3.85
2306 2678 7.154656 AGTCCATTTGAAATGCCTAAAAAGAC 58.845 34.615 12.26 10.86 0.00 3.01
2307 2679 7.301868 AGTCCATTTGAAATGCCTAAAAAGA 57.698 32.000 12.26 0.00 0.00 2.52
2308 2680 8.087750 TGTAGTCCATTTGAAATGCCTAAAAAG 58.912 33.333 12.26 0.00 0.00 2.27
2309 2681 7.957002 TGTAGTCCATTTGAAATGCCTAAAAA 58.043 30.769 12.26 2.62 0.00 1.94
2310 2682 7.531857 TGTAGTCCATTTGAAATGCCTAAAA 57.468 32.000 12.26 4.58 0.00 1.52
2311 2683 7.531857 TTGTAGTCCATTTGAAATGCCTAAA 57.468 32.000 12.26 6.93 0.00 1.85
2312 2684 7.375053 GTTTGTAGTCCATTTGAAATGCCTAA 58.625 34.615 12.26 1.00 0.00 2.69
2313 2685 6.348950 CGTTTGTAGTCCATTTGAAATGCCTA 60.349 38.462 12.26 10.85 0.00 3.93
2314 2686 5.564651 CGTTTGTAGTCCATTTGAAATGCCT 60.565 40.000 12.26 11.73 0.00 4.75
2315 2687 4.621034 CGTTTGTAGTCCATTTGAAATGCC 59.379 41.667 12.26 5.23 0.00 4.40
2316 2688 4.621034 CCGTTTGTAGTCCATTTGAAATGC 59.379 41.667 12.26 0.23 0.00 3.56
2317 2689 6.007936 TCCGTTTGTAGTCCATTTGAAATG 57.992 37.500 10.84 10.84 0.00 2.32
2318 2690 5.183140 CCTCCGTTTGTAGTCCATTTGAAAT 59.817 40.000 0.00 0.00 0.00 2.17
2319 2691 4.517453 CCTCCGTTTGTAGTCCATTTGAAA 59.483 41.667 0.00 0.00 0.00 2.69
2320 2692 4.069304 CCTCCGTTTGTAGTCCATTTGAA 58.931 43.478 0.00 0.00 0.00 2.69
2321 2693 3.558321 CCCTCCGTTTGTAGTCCATTTGA 60.558 47.826 0.00 0.00 0.00 2.69
2322 2694 2.747446 CCCTCCGTTTGTAGTCCATTTG 59.253 50.000 0.00 0.00 0.00 2.32
2323 2695 2.640826 TCCCTCCGTTTGTAGTCCATTT 59.359 45.455 0.00 0.00 0.00 2.32
2324 2696 2.236395 CTCCCTCCGTTTGTAGTCCATT 59.764 50.000 0.00 0.00 0.00 3.16
2325 2697 1.831736 CTCCCTCCGTTTGTAGTCCAT 59.168 52.381 0.00 0.00 0.00 3.41
2326 2698 1.263356 CTCCCTCCGTTTGTAGTCCA 58.737 55.000 0.00 0.00 0.00 4.02
2327 2699 1.264295 ACTCCCTCCGTTTGTAGTCC 58.736 55.000 0.00 0.00 0.00 3.85
2328 2700 2.821969 TGTACTCCCTCCGTTTGTAGTC 59.178 50.000 0.00 0.00 0.00 2.59
2329 2701 2.560105 GTGTACTCCCTCCGTTTGTAGT 59.440 50.000 0.00 0.00 0.00 2.73
2330 2702 2.094338 GGTGTACTCCCTCCGTTTGTAG 60.094 54.545 2.33 0.00 0.00 2.74
2331 2703 1.895131 GGTGTACTCCCTCCGTTTGTA 59.105 52.381 2.33 0.00 0.00 2.41
2332 2704 0.683412 GGTGTACTCCCTCCGTTTGT 59.317 55.000 2.33 0.00 0.00 2.83
2333 2705 0.974383 AGGTGTACTCCCTCCGTTTG 59.026 55.000 10.36 0.00 0.00 2.93
2334 2706 1.725803 AAGGTGTACTCCCTCCGTTT 58.274 50.000 10.36 0.00 0.00 3.60
2335 2707 2.225217 ACTAAGGTGTACTCCCTCCGTT 60.225 50.000 10.36 1.03 0.00 4.44
2336 2708 1.357079 ACTAAGGTGTACTCCCTCCGT 59.643 52.381 10.36 5.66 0.00 4.69
2337 2709 1.749634 CACTAAGGTGTACTCCCTCCG 59.250 57.143 10.36 5.12 38.54 4.63
2338 2710 1.481363 GCACTAAGGTGTACTCCCTCC 59.519 57.143 10.36 0.00 44.65 4.30
2339 2711 2.176889 TGCACTAAGGTGTACTCCCTC 58.823 52.381 10.36 0.00 44.65 4.30
2340 2712 2.320681 TGCACTAAGGTGTACTCCCT 57.679 50.000 10.36 4.67 44.65 4.20
2341 2713 2.906354 CATGCACTAAGGTGTACTCCC 58.094 52.381 10.36 2.27 44.65 4.30
2342 2714 2.093447 AGCATGCACTAAGGTGTACTCC 60.093 50.000 21.98 5.81 44.65 3.85
2343 2715 3.252974 AGCATGCACTAAGGTGTACTC 57.747 47.619 21.98 0.00 44.65 2.59
2344 2716 3.703001 AAGCATGCACTAAGGTGTACT 57.297 42.857 21.98 0.00 44.65 2.73
2345 2717 3.751175 TGAAAGCATGCACTAAGGTGTAC 59.249 43.478 21.98 0.00 44.65 2.90
2346 2718 3.751175 GTGAAAGCATGCACTAAGGTGTA 59.249 43.478 21.98 0.00 44.65 2.90
2347 2719 2.554032 GTGAAAGCATGCACTAAGGTGT 59.446 45.455 21.98 0.00 44.65 4.16
2348 2720 2.816087 AGTGAAAGCATGCACTAAGGTG 59.184 45.455 21.98 0.00 43.10 4.00
2349 2721 3.146104 AGTGAAAGCATGCACTAAGGT 57.854 42.857 21.98 0.00 43.10 3.50
2362 2734 5.064198 TGGTGAAGAACAACGTTAGTGAAAG 59.936 40.000 0.00 0.00 39.39 2.62
2370 2742 1.670811 CTGCTGGTGAAGAACAACGTT 59.329 47.619 0.00 0.00 39.39 3.99
2371 2743 1.299541 CTGCTGGTGAAGAACAACGT 58.700 50.000 0.00 0.00 39.39 3.99
2427 2799 9.248291 GATAAACTCATTGCTTTTTCAAACAGA 57.752 29.630 0.00 0.00 0.00 3.41
2431 2803 8.134895 AGACGATAAACTCATTGCTTTTTCAAA 58.865 29.630 0.00 0.00 0.00 2.69
2491 2863 1.342674 ACATTGCTTGATCTGGCCCAT 60.343 47.619 0.00 0.00 0.00 4.00
2512 2884 3.370840 ACCATCTTCCATAGCTTTGCA 57.629 42.857 0.00 0.00 0.00 4.08
2520 2892 5.957771 AGCAGTTAGAACCATCTTCCATA 57.042 39.130 0.00 0.00 37.10 2.74
2547 2919 2.309755 ACTGTGGTGGTGATGATTCCAT 59.690 45.455 0.00 0.00 36.09 3.41
2553 2925 4.365514 ACATTAACTGTGGTGGTGATGA 57.634 40.909 0.00 0.00 36.48 2.92
2559 2931 5.465390 CGGTATGATACATTAACTGTGGTGG 59.535 44.000 4.83 0.00 38.92 4.61
2569 2941 4.557895 CGTGTGAGCCGGTATGATACATTA 60.558 45.833 1.90 0.00 0.00 1.90
2571 2943 2.288213 CGTGTGAGCCGGTATGATACAT 60.288 50.000 1.90 0.00 0.00 2.29
2572 2944 1.066454 CGTGTGAGCCGGTATGATACA 59.934 52.381 1.90 0.00 0.00 2.29
2573 2945 1.767289 CGTGTGAGCCGGTATGATAC 58.233 55.000 1.90 0.00 0.00 2.24
2574 2946 0.031585 GCGTGTGAGCCGGTATGATA 59.968 55.000 1.90 0.00 0.00 2.15
2575 2947 1.227263 GCGTGTGAGCCGGTATGAT 60.227 57.895 1.90 0.00 0.00 2.45
2576 2948 1.033202 TAGCGTGTGAGCCGGTATGA 61.033 55.000 1.90 0.00 37.26 2.15
2577 2949 0.595053 CTAGCGTGTGAGCCGGTATG 60.595 60.000 1.90 0.00 37.61 2.39
2578 2950 0.750546 TCTAGCGTGTGAGCCGGTAT 60.751 55.000 1.90 0.00 37.61 2.73
2579 2951 0.961857 TTCTAGCGTGTGAGCCGGTA 60.962 55.000 1.90 0.00 37.26 4.02
2580 2952 2.273179 TTCTAGCGTGTGAGCCGGT 61.273 57.895 1.90 0.00 39.62 5.28
2581 2953 1.805945 GTTCTAGCGTGTGAGCCGG 60.806 63.158 0.00 0.00 38.01 6.13
2582 2954 0.388649 AAGTTCTAGCGTGTGAGCCG 60.389 55.000 0.00 0.00 38.01 5.52
2583 2955 1.351153 GAAGTTCTAGCGTGTGAGCC 58.649 55.000 0.00 0.00 38.01 4.70
2584 2956 1.067495 AGGAAGTTCTAGCGTGTGAGC 60.067 52.381 2.25 0.00 37.41 4.26
2585 2957 2.229062 TCAGGAAGTTCTAGCGTGTGAG 59.771 50.000 2.25 0.00 0.00 3.51
2586 2958 2.235891 TCAGGAAGTTCTAGCGTGTGA 58.764 47.619 2.25 0.00 0.00 3.58
2587 2959 2.724977 TCAGGAAGTTCTAGCGTGTG 57.275 50.000 2.25 0.00 0.00 3.82
2588 2960 3.746045 TTTCAGGAAGTTCTAGCGTGT 57.254 42.857 2.25 0.00 0.00 4.49
2589 2961 4.142816 CCATTTTCAGGAAGTTCTAGCGTG 60.143 45.833 2.25 0.00 0.00 5.34
2590 2962 4.003648 CCATTTTCAGGAAGTTCTAGCGT 58.996 43.478 2.25 0.00 0.00 5.07
2591 2963 4.003648 ACCATTTTCAGGAAGTTCTAGCG 58.996 43.478 2.25 0.00 0.00 4.26
2668 3399 6.631016 ACGCTGTAGATCTGAAGTTAATTCA 58.369 36.000 5.18 0.00 45.79 2.57
2669 3400 8.804688 ATACGCTGTAGATCTGAAGTTAATTC 57.195 34.615 5.18 0.00 38.50 2.17
2671 3402 7.941919 TGATACGCTGTAGATCTGAAGTTAAT 58.058 34.615 5.18 0.00 0.00 1.40
2673 3404 6.937436 TGATACGCTGTAGATCTGAAGTTA 57.063 37.500 5.18 0.00 0.00 2.24
2674 3405 5.836821 TGATACGCTGTAGATCTGAAGTT 57.163 39.130 5.18 0.00 0.00 2.66
2675 3406 5.048364 GGATGATACGCTGTAGATCTGAAGT 60.048 44.000 5.18 1.23 0.00 3.01
2677 3408 5.073428 AGGATGATACGCTGTAGATCTGAA 58.927 41.667 5.18 0.00 0.00 3.02
2683 3414 4.207955 AGTCAAGGATGATACGCTGTAGA 58.792 43.478 0.00 0.00 38.01 2.59
2766 3497 8.195436 CGGATACACTGAAAGGTCTAAAAGATA 58.805 37.037 0.00 0.00 39.30 1.98
2769 3500 6.090898 CACGGATACACTGAAAGGTCTAAAAG 59.909 42.308 0.00 0.00 39.30 2.27
2792 3523 2.356135 ACACGGATTATTGACAGGCAC 58.644 47.619 0.00 0.00 0.00 5.01
2793 3524 2.779755 ACACGGATTATTGACAGGCA 57.220 45.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.