Multiple sequence alignment - TraesCS4D01G294400

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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 TraesCS4D01G294400 chr4D 100.000 2875 0 0 1 2875 464797255 464794381 0.000000e+00 5310.0
1 TraesCS4D01G294400 chr1D 90.109 1830 99 24 1 1766 88243698 88241887 0.000000e+00 2302.0
2 TraesCS4D01G294400 chr1D 88.750 720 46 17 1 711 88281850 88281157 0.000000e+00 848.0
3 TraesCS4D01G294400 chr1D 89.262 447 28 9 1 440 87904394 87904827 2.520000e-150 542.0
4 TraesCS4D01G294400 chr1D 89.262 447 28 9 1 440 88215177 88215610 2.520000e-150 542.0
5 TraesCS4D01G294400 chr1D 84.932 438 46 6 2177 2595 88226532 88226096 2.650000e-115 425.0
6 TraesCS4D01G294400 chr1D 87.336 229 17 9 485 711 88215804 88216022 4.760000e-63 252.0
7 TraesCS4D01G294400 chr1D 88.095 168 7 5 1762 1921 88241861 88241699 1.360000e-43 187.0
8 TraesCS4D01G294400 chr1D 94.545 55 2 1 658 711 87905145 87905199 1.840000e-12 84.2
9 TraesCS4D01G294400 chr1D 93.617 47 3 0 1000 1046 88216304 88216350 1.430000e-08 71.3
10 TraesCS4D01G294400 chr1A 87.894 1842 101 41 1 1766 84795962 84794167 0.000000e+00 2054.0
11 TraesCS4D01G294400 chr1A 85.426 693 40 23 1 684 85005846 85005206 0.000000e+00 664.0
12 TraesCS4D01G294400 chr1A 88.367 447 32 10 1 440 84621679 84622112 1.180000e-143 520.0
13 TraesCS4D01G294400 chr1A 88.143 447 33 10 1 440 84484482 84484915 5.490000e-142 514.0
14 TraesCS4D01G294400 chr1A 84.486 477 49 9 2050 2525 84793776 84793324 5.650000e-122 448.0
15 TraesCS4D01G294400 chr1B 87.794 1147 54 21 704 1766 142133063 142131919 0.000000e+00 1264.0
16 TraesCS4D01G294400 chr1B 84.648 951 100 25 1941 2875 142131641 142130721 0.000000e+00 905.0
17 TraesCS4D01G294400 chr1B 91.103 517 36 6 43 549 142133748 142133232 0.000000e+00 691.0
18 TraesCS4D01G294400 chr1B 84.175 733 44 26 1 707 141845720 141846406 0.000000e+00 645.0
19 TraesCS4D01G294400 chr1B 87.033 455 29 15 1 438 142038229 142038670 1.200000e-133 486.0
20 TraesCS4D01G294400 chr1B 91.354 347 22 3 1 342 142094489 142094832 4.340000e-128 468.0
21 TraesCS4D01G294400 chr1B 83.404 235 21 13 485 710 142102864 142103089 4.860000e-48 202.0
22 TraesCS4D01G294400 chr1B 96.875 64 1 1 649 711 142133176 142133113 3.920000e-19 106.0
23 TraesCS4D01G294400 chr1B 93.750 48 3 0 999 1046 142103366 142103413 3.970000e-09 73.1
24 TraesCS4D01G294400 chr3B 92.727 55 3 1 658 711 535704137 535704083 8.540000e-11 78.7


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 TraesCS4D01G294400 chr4D 464794381 464797255 2874 True 5310.000000 5310 100.000000 1 2875 1 chr4D.!!$R1 2874
1 TraesCS4D01G294400 chr1D 88241699 88243698 1999 True 1244.500000 2302 89.102000 1 1921 2 chr1D.!!$R3 1920
2 TraesCS4D01G294400 chr1D 88281157 88281850 693 True 848.000000 848 88.750000 1 711 1 chr1D.!!$R2 710
3 TraesCS4D01G294400 chr1D 87904394 87905199 805 False 313.100000 542 91.903500 1 711 2 chr1D.!!$F1 710
4 TraesCS4D01G294400 chr1D 88215177 88216350 1173 False 288.433333 542 90.071667 1 1046 3 chr1D.!!$F2 1045
5 TraesCS4D01G294400 chr1A 84793324 84795962 2638 True 1251.000000 2054 86.190000 1 2525 2 chr1A.!!$R2 2524
6 TraesCS4D01G294400 chr1A 85005206 85005846 640 True 664.000000 664 85.426000 1 684 1 chr1A.!!$R1 683
7 TraesCS4D01G294400 chr1B 142130721 142133748 3027 True 741.500000 1264 90.105000 43 2875 4 chr1B.!!$R1 2832
8 TraesCS4D01G294400 chr1B 141845720 141846406 686 False 645.000000 645 84.175000 1 707 1 chr1B.!!$F1 706

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
533 778 0.179094 GTGACCGGTCCGAATATGCA 60.179 55.0 31.19 7.48 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2638 0.32121 AATCCCACGAACGACATGCA 60.321 50.0 0.14 0.0 0.0 3.96 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
102 103 1.002087 TCTTGGAGGAGCTTTCGGAAC 59.998 52.381 0.00 0.00 0.00 3.62
244 245 5.720202 TGTGTCGCTGATGAGTTAATTAGT 58.280 37.500 0.00 0.00 0.00 2.24
288 289 5.257262 TGCAGTGCCACTGGTTAATTATTA 58.743 37.500 25.24 0.00 46.01 0.98
289 290 5.356751 TGCAGTGCCACTGGTTAATTATTAG 59.643 40.000 25.24 0.00 46.01 1.73
290 291 5.357032 GCAGTGCCACTGGTTAATTATTAGT 59.643 40.000 25.24 0.00 46.01 2.24
291 292 6.540914 GCAGTGCCACTGGTTAATTATTAGTA 59.459 38.462 25.24 0.00 46.01 1.82
318 325 3.601443 AGTGCCACTGACTTAGCTTAG 57.399 47.619 0.00 0.00 0.00 2.18
343 358 9.798994 AGCTACTGTGTTATTATGTACTGTAAC 57.201 33.333 0.00 0.00 30.61 2.50
379 394 5.778241 CCCAAACTTAGTTTATGGGTTCCTT 59.222 40.000 21.05 0.00 35.38 3.36
398 418 2.715749 TGCCATGTAATCCTGTGAGG 57.284 50.000 0.00 0.00 36.46 3.86
483 555 6.204688 ACGAACAATGTCTGAATCTGCTAAAA 59.795 34.615 0.00 0.00 0.00 1.52
503 748 2.800250 AGCCAAGTTTCTGAATCTGGG 58.200 47.619 14.95 14.95 0.00 4.45
514 759 3.008330 CTGAATCTGGGTGAGCTTTCTG 58.992 50.000 0.00 0.00 0.00 3.02
524 769 0.670854 GAGCTTTCTGTGACCGGTCC 60.671 60.000 31.19 21.86 0.00 4.46
529 774 1.548081 TTCTGTGACCGGTCCGAATA 58.452 50.000 31.19 10.01 0.00 1.75
533 778 0.179094 GTGACCGGTCCGAATATGCA 60.179 55.000 31.19 7.48 0.00 3.96
594 839 7.112122 TGCATGGACTAAATAGATGTGAAGTT 58.888 34.615 0.00 0.00 0.00 2.66
626 871 7.267128 AGAAAAACAAATGCTGAATGTCTCAA 58.733 30.769 0.00 0.00 32.17 3.02
750 1071 5.125356 TGGCACTAACAGATGATACAATGG 58.875 41.667 0.00 0.00 0.00 3.16
840 1174 3.698040 CCTCAGCTTTACTTCCATTGCAT 59.302 43.478 0.00 0.00 0.00 3.96
908 1242 2.887783 GCTCGATCAATCCTCACCTCTA 59.112 50.000 0.00 0.00 0.00 2.43
941 1282 3.786635 CAAGTCTATGTAAAGCTCGGCT 58.213 45.455 0.00 0.00 42.56 5.52
942 1283 3.719173 AGTCTATGTAAAGCTCGGCTC 57.281 47.619 0.00 0.00 38.25 4.70
943 1284 3.024547 AGTCTATGTAAAGCTCGGCTCA 58.975 45.455 0.00 0.00 38.25 4.26
944 1285 3.447586 AGTCTATGTAAAGCTCGGCTCAA 59.552 43.478 0.00 0.00 38.25 3.02
945 1286 3.552294 GTCTATGTAAAGCTCGGCTCAAC 59.448 47.826 0.00 2.28 38.25 3.18
946 1287 2.472695 ATGTAAAGCTCGGCTCAACA 57.527 45.000 12.34 12.34 38.25 3.33
947 1288 1.508632 TGTAAAGCTCGGCTCAACAC 58.491 50.000 0.00 0.00 38.25 3.32
948 1289 1.202592 TGTAAAGCTCGGCTCAACACA 60.203 47.619 0.00 0.05 38.25 3.72
949 1290 1.871039 GTAAAGCTCGGCTCAACACAA 59.129 47.619 0.00 0.00 38.25 3.33
989 1333 3.259374 GGTCTCCTCAACTCAACAGATCA 59.741 47.826 0.00 0.00 0.00 2.92
1060 1404 2.533435 TGGCTCTCCCAGGTGACT 59.467 61.111 0.00 0.00 39.18 3.41
1061 1405 1.610673 TGGCTCTCCCAGGTGACTC 60.611 63.158 0.00 0.00 39.18 3.36
1062 1406 2.363172 GGCTCTCCCAGGTGACTCC 61.363 68.421 0.00 0.00 40.21 3.85
1099 1459 3.499338 TGTGAAATGTGATGAAGGCCTT 58.501 40.909 20.65 20.65 0.00 4.35
1102 1462 0.813184 AATGTGATGAAGGCCTTGCG 59.187 50.000 26.25 0.00 0.00 4.85
1105 1484 0.598065 GTGATGAAGGCCTTGCGTTT 59.402 50.000 26.25 0.00 36.76 3.60
1108 1487 1.269448 GATGAAGGCCTTGCGTTTGAA 59.731 47.619 26.25 0.00 36.76 2.69
1109 1488 0.667993 TGAAGGCCTTGCGTTTGAAG 59.332 50.000 26.25 0.00 36.76 3.02
1113 1492 0.383949 GGCCTTGCGTTTGAAGTTGA 59.616 50.000 0.00 0.00 0.00 3.18
1125 1504 6.482835 CGTTTGAAGTTGAACTGAACATGTA 58.517 36.000 0.00 0.00 0.00 2.29
1127 1506 5.651172 TGAAGTTGAACTGAACATGTACG 57.349 39.130 0.00 0.00 0.00 3.67
1128 1507 5.113383 TGAAGTTGAACTGAACATGTACGT 58.887 37.500 0.00 0.00 0.00 3.57
1167 1546 3.361158 CGGCGGTGTTGATGGCAA 61.361 61.111 0.00 0.00 0.00 4.52
1202 1581 0.107116 ACGTAACCAACAAGTGCCCA 60.107 50.000 0.00 0.00 0.00 5.36
1350 1729 4.043200 GCACCGGCTGCAACTTCC 62.043 66.667 19.85 0.00 46.29 3.46
1352 1731 3.884774 ACCGGCTGCAACTTCCCA 61.885 61.111 0.00 0.00 0.00 4.37
1385 1779 4.003788 ACCGGCGACTGTGAAGGG 62.004 66.667 9.30 0.00 0.00 3.95
1391 1785 2.743928 GACTGTGAAGGGCGCCTG 60.744 66.667 28.56 10.18 32.13 4.85
1508 1902 1.611556 GGACGGGTACAACCTCCCT 60.612 63.158 0.00 0.00 41.40 4.20
1610 2004 3.699894 CCGGAGCTGCAGGTCACT 61.700 66.667 38.37 18.53 43.82 3.41
1760 2194 1.099879 CCGGCCTACTACAGCTACGT 61.100 60.000 0.00 0.00 0.00 3.57
1785 2249 1.663739 GCAGGAGTACGTGGTCACA 59.336 57.895 0.00 0.00 33.23 3.58
1832 2298 2.924105 GCCCAGGTTTGAGCAGTGC 61.924 63.158 7.13 7.13 0.00 4.40
1833 2299 2.620112 CCCAGGTTTGAGCAGTGCG 61.620 63.158 10.00 0.00 0.00 5.34
1834 2300 1.893808 CCAGGTTTGAGCAGTGCGT 60.894 57.895 10.00 0.00 0.00 5.24
1835 2301 1.280746 CAGGTTTGAGCAGTGCGTG 59.719 57.895 10.00 0.00 0.00 5.34
1921 2396 4.619336 GCGGTGTGTAATATTTTGTGTTGG 59.381 41.667 0.00 0.00 0.00 3.77
1922 2397 5.563085 GCGGTGTGTAATATTTTGTGTTGGA 60.563 40.000 0.00 0.00 0.00 3.53
1923 2398 6.083630 CGGTGTGTAATATTTTGTGTTGGAG 58.916 40.000 0.00 0.00 0.00 3.86
1924 2399 6.072948 CGGTGTGTAATATTTTGTGTTGGAGA 60.073 38.462 0.00 0.00 0.00 3.71
1925 2400 7.081976 GGTGTGTAATATTTTGTGTTGGAGAC 58.918 38.462 0.00 0.00 0.00 3.36
2005 2606 5.659525 TGTACTATTTAGAGGCTAAGGTGCA 59.340 40.000 0.00 0.00 34.04 4.57
2009 2610 3.611766 TTAGAGGCTAAGGTGCACTTC 57.388 47.619 17.98 0.06 40.64 3.01
2017 2618 2.870372 GGTGCACTTCGCCATGTC 59.130 61.111 17.98 0.00 44.77 3.06
2025 2626 2.032030 CACTTCGCCATGTCGTTCTTTT 60.032 45.455 0.00 0.00 0.00 2.27
2026 2627 2.223377 ACTTCGCCATGTCGTTCTTTTC 59.777 45.455 0.00 0.00 0.00 2.29
2027 2628 2.163818 TCGCCATGTCGTTCTTTTCT 57.836 45.000 0.00 0.00 0.00 2.52
2028 2629 2.489971 TCGCCATGTCGTTCTTTTCTT 58.510 42.857 0.00 0.00 0.00 2.52
2029 2630 2.875933 TCGCCATGTCGTTCTTTTCTTT 59.124 40.909 0.00 0.00 0.00 2.52
2030 2631 3.314080 TCGCCATGTCGTTCTTTTCTTTT 59.686 39.130 0.00 0.00 0.00 2.27
2031 2632 4.041723 CGCCATGTCGTTCTTTTCTTTTT 58.958 39.130 0.00 0.00 0.00 1.94
2032 2633 4.085619 CGCCATGTCGTTCTTTTCTTTTTG 60.086 41.667 0.00 0.00 0.00 2.44
2033 2634 4.318050 GCCATGTCGTTCTTTTCTTTTTGC 60.318 41.667 0.00 0.00 0.00 3.68
2034 2635 4.085619 CCATGTCGTTCTTTTCTTTTTGCG 60.086 41.667 0.00 0.00 0.00 4.85
2035 2636 4.343811 TGTCGTTCTTTTCTTTTTGCGA 57.656 36.364 0.00 0.00 0.00 5.10
2036 2637 4.092816 TGTCGTTCTTTTCTTTTTGCGAC 58.907 39.130 0.00 0.00 44.92 5.19
2037 2638 4.142773 TGTCGTTCTTTTCTTTTTGCGACT 60.143 37.500 13.44 0.00 44.94 4.18
2038 2639 4.202358 GTCGTTCTTTTCTTTTTGCGACTG 59.798 41.667 0.00 0.00 42.50 3.51
2039 2640 3.061863 CGTTCTTTTCTTTTTGCGACTGC 60.062 43.478 0.00 0.00 43.20 4.40
2077 2678 8.360390 GGGATTAACTCTTGTTTTCTTTGACAT 58.640 33.333 0.00 0.00 37.59 3.06
2083 2684 7.378181 ACTCTTGTTTTCTTTGACATGTTGTT 58.622 30.769 0.00 0.00 0.00 2.83
2119 2721 9.153721 GATGATTTTGGTTTGATTTTATCTGCA 57.846 29.630 0.00 0.00 0.00 4.41
2134 2737 1.888512 TCTGCATTGCCTTGAGTTTCC 59.111 47.619 6.12 0.00 0.00 3.13
2145 2748 4.789802 GCCTTGAGTTTCCTTTTTGACGAG 60.790 45.833 0.00 0.00 0.00 4.18
2159 2762 1.618837 TGACGAGAAAACAGCTAGGCT 59.381 47.619 0.00 0.00 40.77 4.58
2176 2779 5.530171 GCTAGGCTCTGATTTTCATTGATGA 59.470 40.000 0.00 0.00 34.44 2.92
2202 2805 9.495572 AAAAAGGTAGAAATCAAACAAACACAA 57.504 25.926 0.00 0.00 0.00 3.33
2211 2814 2.113910 AACAAACACAAACGCGATCC 57.886 45.000 15.93 0.00 0.00 3.36
2212 2815 1.018148 ACAAACACAAACGCGATCCA 58.982 45.000 15.93 0.00 0.00 3.41
2213 2816 1.402259 ACAAACACAAACGCGATCCAA 59.598 42.857 15.93 0.00 0.00 3.53
2266 2869 3.198068 CGCCTGAGTACATAGCATGTTT 58.802 45.455 7.02 0.00 41.63 2.83
2292 2895 8.316946 TCTCACATGTTCAAGATGAATCTAAGT 58.683 33.333 0.60 0.00 38.79 2.24
2293 2896 8.260270 TCACATGTTCAAGATGAATCTAAGTG 57.740 34.615 0.60 0.00 38.79 3.16
2295 2898 6.094603 ACATGTTCAAGATGAATCTAAGTGGC 59.905 38.462 0.60 0.00 38.79 5.01
2298 2901 5.946942 TCAAGATGAATCTAAGTGGCTCT 57.053 39.130 0.00 0.00 35.76 4.09
2303 2906 4.412796 TGAATCTAAGTGGCTCTGATGG 57.587 45.455 0.00 0.00 0.00 3.51
2307 2910 2.497675 TCTAAGTGGCTCTGATGGTGTC 59.502 50.000 0.00 0.00 0.00 3.67
2344 2947 3.351740 TGTGTTGTGATGTTGTTGGAGT 58.648 40.909 0.00 0.00 0.00 3.85
2371 2974 1.216710 GTTCCGAGAGCAGAGTGGG 59.783 63.158 0.00 0.00 0.00 4.61
2389 2992 7.764901 CAGAGTGGGGTTCTAACTAATCTAAAC 59.235 40.741 0.00 0.00 0.00 2.01
2409 3012 3.023832 ACCTTGACTTGACCAAACCAAG 58.976 45.455 12.70 12.70 44.75 3.61
2444 3047 8.696175 CGGTTAAACAAGTTCCATTCATTTTAC 58.304 33.333 0.00 0.00 0.00 2.01
2448 3051 8.647143 AAACAAGTTCCATTCATTTTACTGTG 57.353 30.769 0.00 0.00 0.00 3.66
2499 3102 4.019771 TGCCATAATGTGTACAACTCCAGA 60.020 41.667 0.00 0.00 0.00 3.86
2521 3124 6.201806 CAGACTACTGCCAGCAAATAGTATTC 59.798 42.308 13.45 7.32 37.33 1.75
2522 3125 5.050490 ACTACTGCCAGCAAATAGTATTCG 58.950 41.667 12.33 0.00 30.68 3.34
2525 3128 4.941263 ACTGCCAGCAAATAGTATTCGAAA 59.059 37.500 0.00 0.00 0.00 3.46
2527 3130 5.636837 TGCCAGCAAATAGTATTCGAAAAC 58.363 37.500 0.00 0.00 0.00 2.43
2528 3131 5.034797 GCCAGCAAATAGTATTCGAAAACC 58.965 41.667 0.00 0.00 0.00 3.27
2529 3132 5.578776 CCAGCAAATAGTATTCGAAAACCC 58.421 41.667 0.00 0.00 0.00 4.11
2530 3133 5.263185 CAGCAAATAGTATTCGAAAACCCG 58.737 41.667 0.00 0.00 0.00 5.28
2531 3134 4.033019 GCAAATAGTATTCGAAAACCCGC 58.967 43.478 0.00 0.00 0.00 6.13
2532 3135 4.437659 GCAAATAGTATTCGAAAACCCGCA 60.438 41.667 0.00 0.00 0.00 5.69
2533 3136 5.732247 GCAAATAGTATTCGAAAACCCGCAT 60.732 40.000 0.00 0.00 0.00 4.73
2534 3137 5.668558 AATAGTATTCGAAAACCCGCATC 57.331 39.130 0.00 0.00 0.00 3.91
2535 3138 2.285977 AGTATTCGAAAACCCGCATCC 58.714 47.619 0.00 0.00 0.00 3.51
2536 3139 2.093128 AGTATTCGAAAACCCGCATCCT 60.093 45.455 0.00 0.00 0.00 3.24
2537 3140 1.834188 ATTCGAAAACCCGCATCCTT 58.166 45.000 0.00 0.00 0.00 3.36
2538 3141 0.878416 TTCGAAAACCCGCATCCTTG 59.122 50.000 0.00 0.00 0.00 3.61
2539 3142 0.958382 TCGAAAACCCGCATCCTTGG 60.958 55.000 0.00 0.00 0.00 3.61
2542 3145 2.650322 GAAAACCCGCATCCTTGGATA 58.350 47.619 1.37 0.00 0.00 2.59
2556 3169 7.577426 GCATCCTTGGATAATGAAACTGAAACA 60.577 37.037 1.37 0.00 0.00 2.83
2564 3177 9.076596 GGATAATGAAACTGAAACAATAGCAAC 57.923 33.333 0.00 0.00 0.00 4.17
2605 3218 2.607187 CGTAAGAATCTCTTGGTGCGT 58.393 47.619 0.00 0.00 37.29 5.24
2611 3224 4.074970 AGAATCTCTTGGTGCGTCAATTT 58.925 39.130 0.00 0.00 0.00 1.82
2616 3229 0.958091 TTGGTGCGTCAATTTCCTGG 59.042 50.000 0.00 0.00 0.00 4.45
2623 3236 2.614057 GCGTCAATTTCCTGGGACTATG 59.386 50.000 0.00 0.00 0.00 2.23
2635 3248 1.405121 GGGACTATGACCACAACGGAC 60.405 57.143 0.00 0.00 38.63 4.79
2643 3256 2.034066 CACAACGGACAGGGGCAT 59.966 61.111 0.00 0.00 0.00 4.40
2644 3257 2.040544 CACAACGGACAGGGGCATC 61.041 63.158 0.00 0.00 0.00 3.91
2654 3267 3.118992 GGACAGGGGCATCAAAAGAAATC 60.119 47.826 0.00 0.00 0.00 2.17
2658 3271 1.471501 GGGCATCAAAAGAAATCCCGC 60.472 52.381 0.00 0.00 0.00 6.13
2666 3279 1.767759 AAGAAATCCCGCCATTCCAG 58.232 50.000 0.00 0.00 0.00 3.86
2668 3281 1.005924 AGAAATCCCGCCATTCCAGTT 59.994 47.619 0.00 0.00 0.00 3.16
2680 3293 4.084537 GCCATTCCAGTTGATATCGTAACG 60.085 45.833 0.00 0.00 32.24 3.18
2681 3294 5.286438 CCATTCCAGTTGATATCGTAACGA 58.714 41.667 0.00 0.00 41.13 3.85
2683 3296 6.423905 CCATTCCAGTTGATATCGTAACGATT 59.576 38.462 0.00 0.00 44.59 3.34
2684 3297 7.042051 CCATTCCAGTTGATATCGTAACGATTT 60.042 37.037 0.00 0.00 44.59 2.17
2689 3302 7.846107 CCAGTTGATATCGTAACGATTTTGAAG 59.154 37.037 0.00 0.00 44.59 3.02
2694 3307 2.158841 TCGTAACGATTTTGAAGCCTGC 59.841 45.455 0.00 0.00 0.00 4.85
2695 3308 2.727916 CGTAACGATTTTGAAGCCTGCC 60.728 50.000 0.00 0.00 0.00 4.85
2750 3363 9.297586 TGATGATAGATAAAACACTTACGTCAC 57.702 33.333 0.00 0.00 0.00 3.67
2762 3375 3.243771 ACTTACGTCACACTTCCTTGAGG 60.244 47.826 0.00 0.00 34.49 3.86
2769 3383 0.679505 CACTTCCTTGAGGACGGTGA 59.320 55.000 19.32 0.00 45.39 4.02
2773 3387 0.898789 TCCTTGAGGACGGTGAGGAC 60.899 60.000 0.00 0.00 39.78 3.85
2779 3393 0.900647 AGGACGGTGAGGACAGAAGG 60.901 60.000 0.00 0.00 0.00 3.46
2780 3394 1.592223 GACGGTGAGGACAGAAGGG 59.408 63.158 0.00 0.00 0.00 3.95
2782 3396 0.900647 ACGGTGAGGACAGAAGGGAG 60.901 60.000 0.00 0.00 0.00 4.30
2784 3398 1.872773 GGTGAGGACAGAAGGGAGAT 58.127 55.000 0.00 0.00 0.00 2.75
2791 3405 5.966935 TGAGGACAGAAGGGAGATAGAATTT 59.033 40.000 0.00 0.00 0.00 1.82
2801 3415 7.519032 AGGGAGATAGAATTTCTACTCTTCG 57.481 40.000 21.83 0.00 30.79 3.79
2802 3416 6.492087 AGGGAGATAGAATTTCTACTCTTCGG 59.508 42.308 21.83 0.00 30.79 4.30
2810 3424 7.893658 AGAATTTCTACTCTTCGGAAACTACA 58.106 34.615 0.00 0.00 32.84 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 181 2.116125 GGGCTTGCTGAACCACCT 59.884 61.111 0.00 0.00 0.00 4.00
288 289 1.072173 TCAGTGGCACTGCAATGTACT 59.928 47.619 36.65 2.65 45.54 2.73
289 290 1.197721 GTCAGTGGCACTGCAATGTAC 59.802 52.381 36.65 25.85 45.54 2.90
290 291 1.072173 AGTCAGTGGCACTGCAATGTA 59.928 47.619 36.65 19.74 45.54 2.29
291 292 0.179009 AGTCAGTGGCACTGCAATGT 60.179 50.000 36.65 18.80 45.54 2.71
318 325 9.798994 AGTTACAGTACATAATAACACAGTAGC 57.201 33.333 0.00 0.00 31.29 3.58
343 358 0.251341 AGTTTGGGCCCTGCAACTAG 60.251 55.000 25.70 0.00 0.00 2.57
379 394 2.195727 TCCTCACAGGATTACATGGCA 58.804 47.619 0.00 0.00 40.06 4.92
398 418 8.768955 CCATGCTACTAACTGAGTAATTGATTC 58.231 37.037 0.00 0.00 40.23 2.52
406 426 8.755028 TGTAATTTCCATGCTACTAACTGAGTA 58.245 33.333 0.00 0.00 39.81 2.59
408 446 8.554528 CATGTAATTTCCATGCTACTAACTGAG 58.445 37.037 5.24 0.00 33.90 3.35
483 555 2.108952 ACCCAGATTCAGAAACTTGGCT 59.891 45.455 9.77 0.00 0.00 4.75
503 748 0.249911 ACCGGTCACAGAAAGCTCAC 60.250 55.000 0.00 0.00 0.00 3.51
514 759 0.179094 TGCATATTCGGACCGGTCAC 60.179 55.000 34.40 22.34 0.00 3.67
524 769 5.907945 CAGATTCAGAAGCTTTGCATATTCG 59.092 40.000 0.00 0.00 0.00 3.34
529 774 3.428532 ACCAGATTCAGAAGCTTTGCAT 58.571 40.909 0.00 0.00 0.00 3.96
533 778 6.469782 TTTTCAACCAGATTCAGAAGCTTT 57.530 33.333 0.00 0.00 0.00 3.51
559 804 5.823209 TTTAGTCCATGCATCAACATCAG 57.177 39.130 0.00 0.00 0.00 2.90
594 839 5.645624 TCAGCATTTGTTTTTCTTCGTTGA 58.354 33.333 0.00 0.00 0.00 3.18
741 1061 5.221048 CGGATGTTCCCTTTTCCATTGTATC 60.221 44.000 0.00 0.00 31.13 2.24
750 1071 4.712122 TTTATGCGGATGTTCCCTTTTC 57.288 40.909 0.00 0.00 31.13 2.29
799 1121 0.938637 GCATGATGAGAGCCGAGACG 60.939 60.000 0.00 0.00 0.00 4.18
840 1174 3.650070 TTGTGTTTGTGTGACTTGCAA 57.350 38.095 0.00 0.00 0.00 4.08
929 1263 1.508632 TGTGTTGAGCCGAGCTTTAC 58.491 50.000 0.00 3.08 39.88 2.01
941 1282 7.770201 TGAAATGAAGATGAACTTTGTGTTGA 58.230 30.769 0.00 0.00 39.30 3.18
942 1283 7.168637 CCTGAAATGAAGATGAACTTTGTGTTG 59.831 37.037 0.00 0.00 39.30 3.33
943 1284 7.147846 ACCTGAAATGAAGATGAACTTTGTGTT 60.148 33.333 0.00 0.00 42.38 3.32
944 1285 6.322201 ACCTGAAATGAAGATGAACTTTGTGT 59.678 34.615 0.00 0.00 39.13 3.72
945 1286 6.742109 ACCTGAAATGAAGATGAACTTTGTG 58.258 36.000 0.00 0.00 39.13 3.33
946 1287 6.774656 AGACCTGAAATGAAGATGAACTTTGT 59.225 34.615 0.00 0.00 39.13 2.83
947 1288 7.211966 AGACCTGAAATGAAGATGAACTTTG 57.788 36.000 0.00 0.00 39.13 2.77
948 1289 6.432472 GGAGACCTGAAATGAAGATGAACTTT 59.568 38.462 0.00 0.00 39.13 2.66
949 1290 5.942826 GGAGACCTGAAATGAAGATGAACTT 59.057 40.000 0.00 0.00 42.03 2.66
1099 1459 3.189495 TGTTCAGTTCAACTTCAAACGCA 59.811 39.130 0.00 0.00 0.00 5.24
1102 1462 6.410914 CGTACATGTTCAGTTCAACTTCAAAC 59.589 38.462 2.30 0.00 0.00 2.93
1105 1484 5.113383 ACGTACATGTTCAGTTCAACTTCA 58.887 37.500 2.30 0.00 0.00 3.02
1108 1487 3.734231 CGACGTACATGTTCAGTTCAACT 59.266 43.478 2.30 0.00 0.00 3.16
1109 1488 3.488310 ACGACGTACATGTTCAGTTCAAC 59.512 43.478 2.30 0.00 0.00 3.18
1113 1492 4.114073 TGAAACGACGTACATGTTCAGTT 58.886 39.130 2.30 3.02 0.00 3.16
1125 1504 1.064803 TGCAGCAAAATGAAACGACGT 59.935 42.857 0.00 0.00 0.00 4.34
1127 1506 2.053627 CCTGCAGCAAAATGAAACGAC 58.946 47.619 8.66 0.00 0.00 4.34
1128 1507 1.000385 CCCTGCAGCAAAATGAAACGA 60.000 47.619 8.66 0.00 0.00 3.85
1167 1546 4.309950 GTGGAACGTGACGCCCCT 62.310 66.667 4.25 0.00 0.00 4.79
1438 1832 2.047179 GGTCCTCGTGCAGGTTCC 60.047 66.667 6.26 1.88 43.95 3.62
1508 1902 4.248842 CTGGTCCACACGGCCACA 62.249 66.667 2.24 0.00 35.44 4.17
1610 2004 3.950794 CTTCTTGCCCGTGCCGCTA 62.951 63.158 0.00 0.00 36.33 4.26
1617 2017 2.978010 CGTTGCCTTCTTGCCCGT 60.978 61.111 0.00 0.00 0.00 5.28
1760 2194 1.742880 ACGTACTCCTGCGCGTAGA 60.743 57.895 26.43 10.16 35.71 2.59
1785 2249 1.528824 CCATCTGGACGGGCAGAAT 59.471 57.895 0.00 0.00 37.39 2.40
1833 2299 4.341783 AGTCCTGGGCTGCTGCAC 62.342 66.667 17.89 14.87 44.33 4.57
1834 2300 4.340246 CAGTCCTGGGCTGCTGCA 62.340 66.667 16.43 0.88 41.91 4.41
1835 2301 4.341783 ACAGTCCTGGGCTGCTGC 62.342 66.667 27.44 7.10 37.47 5.25
1836 2302 2.359602 CACAGTCCTGGGCTGCTG 60.360 66.667 27.44 19.56 37.47 4.41
2005 2606 1.878953 AAAGAACGACATGGCGAAGT 58.121 45.000 31.27 12.54 34.83 3.01
2009 2610 2.969443 AAGAAAAGAACGACATGGCG 57.031 45.000 21.98 21.98 37.29 5.69
2013 2614 4.733405 GTCGCAAAAAGAAAAGAACGACAT 59.267 37.500 7.27 0.00 45.73 3.06
2014 2615 4.092816 GTCGCAAAAAGAAAAGAACGACA 58.907 39.130 7.27 0.00 45.73 4.35
2016 2617 4.339429 CAGTCGCAAAAAGAAAAGAACGA 58.661 39.130 0.00 0.00 0.00 3.85
2017 2618 3.061863 GCAGTCGCAAAAAGAAAAGAACG 60.062 43.478 0.00 0.00 38.36 3.95
2034 2635 1.626654 CCCACGAACGACATGCAGTC 61.627 60.000 0.14 0.00 44.02 3.51
2035 2636 1.667830 CCCACGAACGACATGCAGT 60.668 57.895 0.14 0.00 0.00 4.40
2036 2637 0.740868 ATCCCACGAACGACATGCAG 60.741 55.000 0.14 0.00 0.00 4.41
2037 2638 0.321210 AATCCCACGAACGACATGCA 60.321 50.000 0.14 0.00 0.00 3.96
2038 2639 1.647346 TAATCCCACGAACGACATGC 58.353 50.000 0.14 0.00 0.00 4.06
2039 2640 3.259064 AGTTAATCCCACGAACGACATG 58.741 45.455 0.14 0.00 0.00 3.21
2040 2641 3.194968 AGAGTTAATCCCACGAACGACAT 59.805 43.478 0.14 0.00 0.00 3.06
2041 2642 2.559668 AGAGTTAATCCCACGAACGACA 59.440 45.455 0.14 0.00 0.00 4.35
2042 2643 3.227810 AGAGTTAATCCCACGAACGAC 57.772 47.619 0.14 0.00 0.00 4.34
2043 2644 3.006110 ACAAGAGTTAATCCCACGAACGA 59.994 43.478 0.14 0.00 0.00 3.85
2044 2645 3.323243 ACAAGAGTTAATCCCACGAACG 58.677 45.455 0.00 0.00 0.00 3.95
2045 2646 5.684550 AAACAAGAGTTAATCCCACGAAC 57.315 39.130 0.00 0.00 36.84 3.95
2048 2649 5.941948 AGAAAACAAGAGTTAATCCCACG 57.058 39.130 0.00 0.00 36.84 4.94
2077 2678 7.171167 CCAAAATCATCAACTGCAATAACAACA 59.829 33.333 0.00 0.00 0.00 3.33
2083 2684 7.440198 TCAAACCAAAATCATCAACTGCAATA 58.560 30.769 0.00 0.00 0.00 1.90
2119 2721 5.359756 GTCAAAAAGGAAACTCAAGGCAAT 58.640 37.500 0.00 0.00 42.68 3.56
2134 2737 5.444122 CCTAGCTGTTTTCTCGTCAAAAAG 58.556 41.667 0.00 0.00 0.00 2.27
2145 2748 5.182001 TGAAAATCAGAGCCTAGCTGTTTTC 59.818 40.000 17.49 17.49 39.88 2.29
2176 2779 9.495572 TTGTGTTTGTTTGATTTCTACCTTTTT 57.504 25.926 0.00 0.00 0.00 1.94
2213 2816 2.296792 GCCATGCCACCTTTTGTTTTT 58.703 42.857 0.00 0.00 0.00 1.94
2218 2821 2.432972 GCGCCATGCCACCTTTTG 60.433 61.111 0.00 0.00 37.76 2.44
2245 2848 2.515926 ACATGCTATGTACTCAGGCG 57.484 50.000 0.00 0.00 42.78 5.52
2266 2869 8.316946 ACTTAGATTCATCTTGAACATGTGAGA 58.683 33.333 0.00 4.14 39.45 3.27
2274 2877 6.036953 CAGAGCCACTTAGATTCATCTTGAAC 59.963 42.308 0.00 0.00 39.45 3.18
2292 2895 2.106338 TGAAAAGACACCATCAGAGCCA 59.894 45.455 0.00 0.00 0.00 4.75
2293 2896 2.783135 TGAAAAGACACCATCAGAGCC 58.217 47.619 0.00 0.00 0.00 4.70
2295 2898 6.754702 ATGAATGAAAAGACACCATCAGAG 57.245 37.500 0.00 0.00 0.00 3.35
2323 2926 3.351740 ACTCCAACAACATCACAACACA 58.648 40.909 0.00 0.00 0.00 3.72
2344 2947 5.084818 TCTGCTCTCGGAACAAATATCAA 57.915 39.130 0.00 0.00 0.00 2.57
2371 2974 9.722184 AAGTCAAGGTTTAGATTAGTTAGAACC 57.278 33.333 0.00 0.00 37.41 3.62
2389 2992 2.362077 CCTTGGTTTGGTCAAGTCAAGG 59.638 50.000 20.99 20.99 41.30 3.61
2409 3012 5.335426 GGAACTTGTTTAACCGAATCCTTCC 60.335 44.000 0.00 0.00 0.00 3.46
2419 3022 9.758651 AGTAAAATGAATGGAACTTGTTTAACC 57.241 29.630 0.00 0.00 0.00 2.85
2444 3047 4.877823 TGAGCATAACTTGAATAGGCACAG 59.122 41.667 0.00 0.00 32.77 3.66
2448 3051 6.382869 ACATTGAGCATAACTTGAATAGGC 57.617 37.500 0.00 0.00 0.00 3.93
2499 3102 5.050490 CGAATACTATTTGCTGGCAGTAGT 58.950 41.667 17.16 16.86 35.21 2.73
2521 3124 0.958382 TCCAAGGATGCGGGTTTTCG 60.958 55.000 0.00 0.00 0.00 3.46
2522 3125 1.474330 ATCCAAGGATGCGGGTTTTC 58.526 50.000 0.00 0.00 32.98 2.29
2525 3128 2.174639 TCATTATCCAAGGATGCGGGTT 59.825 45.455 11.82 0.00 36.17 4.11
2527 3130 2.566833 TCATTATCCAAGGATGCGGG 57.433 50.000 11.82 0.00 36.17 6.13
2528 3131 3.885297 AGTTTCATTATCCAAGGATGCGG 59.115 43.478 11.82 1.31 36.17 5.69
2529 3132 4.576053 TCAGTTTCATTATCCAAGGATGCG 59.424 41.667 11.82 0.57 36.17 4.73
2530 3133 6.455360 TTCAGTTTCATTATCCAAGGATGC 57.545 37.500 11.82 0.00 36.17 3.91
2531 3134 7.829725 TGTTTCAGTTTCATTATCCAAGGATG 58.170 34.615 11.82 0.00 36.17 3.51
2532 3135 8.421249 TTGTTTCAGTTTCATTATCCAAGGAT 57.579 30.769 6.84 6.84 38.54 3.24
2533 3136 7.831691 TTGTTTCAGTTTCATTATCCAAGGA 57.168 32.000 0.00 0.00 0.00 3.36
2534 3137 9.793252 CTATTGTTTCAGTTTCATTATCCAAGG 57.207 33.333 0.00 0.00 0.00 3.61
2535 3138 9.294030 GCTATTGTTTCAGTTTCATTATCCAAG 57.706 33.333 0.00 0.00 0.00 3.61
2536 3139 8.801299 TGCTATTGTTTCAGTTTCATTATCCAA 58.199 29.630 0.00 0.00 0.00 3.53
2537 3140 8.347004 TGCTATTGTTTCAGTTTCATTATCCA 57.653 30.769 0.00 0.00 0.00 3.41
2538 3141 9.076596 GTTGCTATTGTTTCAGTTTCATTATCC 57.923 33.333 0.00 0.00 0.00 2.59
2539 3142 9.846248 AGTTGCTATTGTTTCAGTTTCATTATC 57.154 29.630 0.00 0.00 0.00 1.75
2542 3145 7.491682 ACAGTTGCTATTGTTTCAGTTTCATT 58.508 30.769 0.00 0.00 0.00 2.57
2586 3199 3.585862 TGACGCACCAAGAGATTCTTAC 58.414 45.455 0.00 0.00 33.78 2.34
2599 3212 0.608035 TCCCAGGAAATTGACGCACC 60.608 55.000 0.00 0.00 0.00 5.01
2605 3218 3.849574 TGGTCATAGTCCCAGGAAATTGA 59.150 43.478 0.00 0.00 0.00 2.57
2611 3224 1.906574 GTTGTGGTCATAGTCCCAGGA 59.093 52.381 0.00 0.00 0.00 3.86
2616 3229 1.274167 TGTCCGTTGTGGTCATAGTCC 59.726 52.381 0.00 0.00 39.52 3.85
2623 3236 2.032071 CCCCTGTCCGTTGTGGTC 59.968 66.667 0.00 0.00 39.52 4.02
2635 3248 2.169144 GGGATTTCTTTTGATGCCCCTG 59.831 50.000 0.00 0.00 31.33 4.45
2643 3256 2.495669 GGAATGGCGGGATTTCTTTTGA 59.504 45.455 0.00 0.00 0.00 2.69
2644 3257 2.233431 TGGAATGGCGGGATTTCTTTTG 59.767 45.455 0.00 0.00 0.00 2.44
2654 3267 2.154462 GATATCAACTGGAATGGCGGG 58.846 52.381 0.00 0.00 0.00 6.13
2658 3271 5.286438 TCGTTACGATATCAACTGGAATGG 58.714 41.667 2.33 0.00 0.00 3.16
2666 3279 6.627671 GGCTTCAAAATCGTTACGATATCAAC 59.372 38.462 20.80 7.47 46.30 3.18
2668 3281 6.019075 CAGGCTTCAAAATCGTTACGATATCA 60.019 38.462 20.80 2.85 46.30 2.15
2680 3293 2.560105 AGTTCTGGCAGGCTTCAAAATC 59.440 45.455 15.73 0.00 0.00 2.17
2681 3294 2.601905 AGTTCTGGCAGGCTTCAAAAT 58.398 42.857 15.73 0.00 0.00 1.82
2682 3295 2.071778 AGTTCTGGCAGGCTTCAAAA 57.928 45.000 15.73 0.00 0.00 2.44
2683 3296 2.071778 AAGTTCTGGCAGGCTTCAAA 57.928 45.000 15.73 0.00 0.00 2.69
2684 3297 2.949177 TAAGTTCTGGCAGGCTTCAA 57.051 45.000 21.93 5.21 0.00 2.69
2689 3302 7.602265 TCAAAAATTATTTAAGTTCTGGCAGGC 59.398 33.333 15.73 8.24 0.00 4.85
2762 3375 0.898789 TCCCTTCTGTCCTCACCGTC 60.899 60.000 0.00 0.00 0.00 4.79
2769 3383 6.209026 AGAAATTCTATCTCCCTTCTGTCCT 58.791 40.000 0.00 0.00 0.00 3.85
2773 3387 8.477419 AGAGTAGAAATTCTATCTCCCTTCTG 57.523 38.462 19.38 0.00 32.51 3.02
2779 3393 7.513371 TCCGAAGAGTAGAAATTCTATCTCC 57.487 40.000 19.38 8.00 32.51 3.71
2780 3394 9.240159 GTTTCCGAAGAGTAGAAATTCTATCTC 57.760 37.037 17.20 17.20 32.54 2.75
2784 3398 9.017509 TGTAGTTTCCGAAGAGTAGAAATTCTA 57.982 33.333 0.00 0.00 32.54 2.10
2838 3452 6.018262 TGTTGGTCGTTGTTGATTCTAGAAAG 60.018 38.462 9.71 0.00 0.00 2.62
2849 3464 1.746220 TCCCTTTGTTGGTCGTTGTTG 59.254 47.619 0.00 0.00 0.00 3.33
2850 3465 2.131776 TCCCTTTGTTGGTCGTTGTT 57.868 45.000 0.00 0.00 0.00 2.83
2854 3469 1.064825 AGGATCCCTTTGTTGGTCGT 58.935 50.000 8.55 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.