Multiple sequence alignment - TraesCS2B01G155700

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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 TraesCS2B01G155700 chr2B 100.000 2936 0 0 1 2936 124622116 124625051 0.000000e+00 5422
1 TraesCS2B01G155700 chr2B 94.057 387 17 4 2552 2936 128309892 128309510 1.520000e-162 582
2 TraesCS2B01G155700 chr2B 89.125 377 19 10 2562 2936 123121626 123121270 1.600000e-122 449
3 TraesCS2B01G155700 chr2B 87.744 359 33 10 2549 2904 123177014 123176664 2.720000e-110 409
4 TraesCS2B01G155700 chr2B 83.916 286 15 9 2651 2936 128346714 128346460 8.130000e-61 244
5 TraesCS2B01G155700 chr5A 94.982 1375 41 9 1186 2533 439809981 439811354 0.000000e+00 2132
6 TraesCS2B01G155700 chr5A 94.626 1377 38 10 1186 2534 22978479 22977111 0.000000e+00 2100
7 TraesCS2B01G155700 chr5A 97.788 226 4 1 941 1166 390558470 390558694 3.550000e-104 388
8 TraesCS2B01G155700 chr5A 96.889 225 6 1 942 1166 22978690 22978467 2.760000e-100 375
9 TraesCS2B01G155700 chr5A 95.575 226 9 1 941 1166 439809769 439809993 7.740000e-96 361
10 TraesCS2B01G155700 chr2A 94.695 1376 37 10 1186 2533 180213164 180211797 0.000000e+00 2104
11 TraesCS2B01G155700 chr2A 91.139 395 10 9 2165 2534 758963835 758964229 2.020000e-141 512
12 TraesCS2B01G155700 chr2A 90.256 390 17 8 2552 2936 79495982 79495609 9.460000e-135 490
13 TraesCS2B01G155700 chr2A 86.041 394 34 10 2545 2936 79642402 79642028 1.270000e-108 403
14 TraesCS2B01G155700 chr2A 88.141 312 25 4 2545 2855 79503718 79503418 7.740000e-96 361
15 TraesCS2B01G155700 chr2A 95.575 226 9 1 941 1166 180213376 180213152 7.740000e-96 361
16 TraesCS2B01G155700 chr2A 90.045 221 12 3 2537 2747 79539841 79539621 8.010000e-71 278
17 TraesCS2B01G155700 chr2A 89.952 209 11 8 2557 2760 79525974 79525771 8.070000e-66 261
18 TraesCS2B01G155700 chr7A 94.622 1376 38 10 1186 2533 31809757 31811124 0.000000e+00 2098
19 TraesCS2B01G155700 chr7A 96.903 226 6 1 941 1166 31809545 31809769 7.680000e-101 377
20 TraesCS2B01G155700 chr6B 94.622 1376 38 10 1186 2533 532352969 532354336 0.000000e+00 2098
21 TraesCS2B01G155700 chr6B 96.903 226 6 1 941 1166 532352757 532352981 7.680000e-101 377
22 TraesCS2B01G155700 chr1B 94.618 1375 38 10 1186 2532 150371712 150370346 0.000000e+00 2097
23 TraesCS2B01G155700 chr1B 94.243 1129 32 9 1430 2533 150371923 150373043 0.000000e+00 1694
24 TraesCS2B01G155700 chr1B 96.889 225 6 1 942 1166 150371923 150371700 2.760000e-100 375
25 TraesCS2B01G155700 chr3A 94.473 1375 48 9 1186 2532 583078807 583080181 0.000000e+00 2093
26 TraesCS2B01G155700 chr4B 94.070 1366 59 10 1187 2532 215060773 215059410 0.000000e+00 2054
27 TraesCS2B01G155700 chr4B 95.575 226 8 2 941 1166 215060985 215060762 7.740000e-96 361
28 TraesCS2B01G155700 chr6A 94.890 1272 38 8 1184 2428 9186169 9187440 0.000000e+00 1964
29 TraesCS2B01G155700 chr6A 95.175 228 9 2 941 1168 9185958 9186183 2.780000e-95 359
30 TraesCS2B01G155700 chr3D 95.005 941 47 0 1 941 428917146 428916206 0.000000e+00 1478
31 TraesCS2B01G155700 chr3D 94.804 943 48 1 1 942 421337348 421338290 0.000000e+00 1469
32 TraesCS2B01G155700 chr3D 94.687 941 50 0 1 941 503727785 503726845 0.000000e+00 1461
33 TraesCS2B01G155700 chr5D 94.793 941 49 0 1 941 272153694 272152754 0.000000e+00 1467
34 TraesCS2B01G155700 chr5D 94.687 941 50 0 1 941 344378435 344379375 0.000000e+00 1461
35 TraesCS2B01G155700 chr5D 94.687 941 50 0 1 941 487540307 487539367 0.000000e+00 1461
36 TraesCS2B01G155700 chr1D 94.793 941 49 0 1 941 211314620 211315560 0.000000e+00 1467
37 TraesCS2B01G155700 chr7D 94.692 942 49 1 1 941 461285200 461286141 0.000000e+00 1461
38 TraesCS2B01G155700 chr4D 94.603 945 48 1 1 945 301275745 301276686 0.000000e+00 1459
39 TraesCS2B01G155700 chr2D 90.355 394 22 7 2549 2936 79258388 79258005 1.210000e-138 503
40 TraesCS2B01G155700 chr2D 88.258 264 14 7 2557 2818 79279190 79278942 1.710000e-77 300
41 TraesCS2B01G155700 chr2D 87.255 102 5 4 2835 2936 79276804 79276711 3.090000e-20 110


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 TraesCS2B01G155700 chr2B 124622116 124625051 2935 False 5422.0 5422 100.0000 1 2936 1 chr2B.!!$F1 2935
1 TraesCS2B01G155700 chr5A 439809769 439811354 1585 False 1246.5 2132 95.2785 941 2533 2 chr5A.!!$F2 1592
2 TraesCS2B01G155700 chr5A 22977111 22978690 1579 True 1237.5 2100 95.7575 942 2534 2 chr5A.!!$R1 1592
3 TraesCS2B01G155700 chr2A 180211797 180213376 1579 True 1232.5 2104 95.1350 941 2533 2 chr2A.!!$R6 1592
4 TraesCS2B01G155700 chr7A 31809545 31811124 1579 False 1237.5 2098 95.7625 941 2533 2 chr7A.!!$F1 1592
5 TraesCS2B01G155700 chr6B 532352757 532354336 1579 False 1237.5 2098 95.7625 941 2533 2 chr6B.!!$F1 1592
6 TraesCS2B01G155700 chr1B 150371923 150373043 1120 False 1694.0 1694 94.2430 1430 2533 1 chr1B.!!$F1 1103
7 TraesCS2B01G155700 chr1B 150370346 150371923 1577 True 1236.0 2097 95.7535 942 2532 2 chr1B.!!$R1 1590
8 TraesCS2B01G155700 chr3A 583078807 583080181 1374 False 2093.0 2093 94.4730 1186 2532 1 chr3A.!!$F1 1346
9 TraesCS2B01G155700 chr4B 215059410 215060985 1575 True 1207.5 2054 94.8225 941 2532 2 chr4B.!!$R1 1591
10 TraesCS2B01G155700 chr6A 9185958 9187440 1482 False 1161.5 1964 95.0325 941 2428 2 chr6A.!!$F1 1487
11 TraesCS2B01G155700 chr3D 428916206 428917146 940 True 1478.0 1478 95.0050 1 941 1 chr3D.!!$R1 940
12 TraesCS2B01G155700 chr3D 421337348 421338290 942 False 1469.0 1469 94.8040 1 942 1 chr3D.!!$F1 941
13 TraesCS2B01G155700 chr3D 503726845 503727785 940 True 1461.0 1461 94.6870 1 941 1 chr3D.!!$R2 940
14 TraesCS2B01G155700 chr5D 272152754 272153694 940 True 1467.0 1467 94.7930 1 941 1 chr5D.!!$R1 940
15 TraesCS2B01G155700 chr5D 344378435 344379375 940 False 1461.0 1461 94.6870 1 941 1 chr5D.!!$F1 940
16 TraesCS2B01G155700 chr5D 487539367 487540307 940 True 1461.0 1461 94.6870 1 941 1 chr5D.!!$R2 940
17 TraesCS2B01G155700 chr1D 211314620 211315560 940 False 1467.0 1467 94.7930 1 941 1 chr1D.!!$F1 940
18 TraesCS2B01G155700 chr7D 461285200 461286141 941 False 1461.0 1461 94.6920 1 941 1 chr7D.!!$F1 940
19 TraesCS2B01G155700 chr4D 301275745 301276686 941 False 1459.0 1459 94.6030 1 945 1 chr4D.!!$F1 944
20 TraesCS2B01G155700 chr2D 79276711 79279190 2479 True 205.0 300 87.7565 2557 2936 2 chr2D.!!$R2 379

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
23 24 0.101399 AGACTCATCGTCATGTCCGC 59.899 55.0 0.00 0.00 45.32 5.54 F
445 447 0.468400 GCCCAGAGATACCTCTCCGT 60.468 60.0 0.00 0.00 46.38 4.69 F
1013 1016 0.747644 CGTGCCATGGCCAATAGTGA 60.748 55.0 33.44 9.85 41.09 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1013 1016 1.133513 TGGTTCTGTCAAGGCCATTGT 60.134 47.619 5.01 0.0 40.05 2.71 R
1697 1718 2.297033 GCAGGTGTCATTGGTTTCACAT 59.703 45.455 0.00 0.0 33.17 3.21 R
2747 2839 0.108186 CCGGTAGTTGAGCTGATGCA 60.108 55.000 0.00 0.0 42.74 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
23 24 0.101399 AGACTCATCGTCATGTCCGC 59.899 55.000 0.00 0.00 45.32 5.54
53 54 1.486726 CGGGGCTCCAAACTATCTTCT 59.513 52.381 1.96 0.00 0.00 2.85
91 92 6.800408 ACATAAACTCATAATACCGATCGTCG 59.200 38.462 15.09 1.70 40.07 5.12
186 187 3.567478 ACCAATAGCAGAACCTGGATC 57.433 47.619 0.00 0.00 31.21 3.36
218 219 4.299978 GCTCCCACATATTCTACGAAGAC 58.700 47.826 0.00 0.00 0.00 3.01
229 230 6.949352 ATTCTACGAAGACCTTTATCGGTA 57.051 37.500 0.00 0.00 40.71 4.02
234 235 6.657836 ACGAAGACCTTTATCGGTAAAATG 57.342 37.500 1.94 0.00 40.71 2.32
242 243 6.140110 CCTTTATCGGTAAAATGGCATAACG 58.860 40.000 0.00 0.00 33.63 3.18
381 382 5.290493 TCATCCCGCAACTAACTCATTAT 57.710 39.130 0.00 0.00 0.00 1.28
391 393 8.387354 CGCAACTAACTCATTATTCACATTACA 58.613 33.333 0.00 0.00 0.00 2.41
398 400 8.284945 ACTCATTATTCACATTACATGCAAGT 57.715 30.769 0.00 0.00 0.00 3.16
445 447 0.468400 GCCCAGAGATACCTCTCCGT 60.468 60.000 0.00 0.00 46.38 4.69
449 451 3.024547 CCAGAGATACCTCTCCGTCAAA 58.975 50.000 0.00 0.00 46.38 2.69
479 481 9.521841 AGTGACAAATCCTAATCTCGATCTATA 57.478 33.333 0.00 0.00 0.00 1.31
529 531 6.384305 ACACCTGTAGAGCACCTTTATAATCT 59.616 38.462 0.00 0.00 0.00 2.40
602 604 3.681897 CGGGAGTTGCATAATCTCATAGC 59.318 47.826 0.00 0.00 0.00 2.97
674 677 3.232213 TCAAGTGCTAAGCTAACGGAG 57.768 47.619 0.00 0.00 0.00 4.63
701 704 5.065731 GGTCAAGTCAATCACATCATTCTCC 59.934 44.000 0.00 0.00 0.00 3.71
773 776 9.093458 AGGAAACTTAACCATCTTTGATTCAAT 57.907 29.630 0.00 0.00 37.44 2.57
795 798 3.382865 TGAGCTAGTCAAGTAGAGGCATG 59.617 47.826 0.00 0.00 29.64 4.06
797 800 2.804933 GCTAGTCAAGTAGAGGCATGCC 60.805 54.545 30.12 30.12 0.00 4.40
843 846 8.542497 TGTATTCACACATGTACTAAGTTTCC 57.458 34.615 0.00 0.00 0.00 3.13
844 847 6.721571 ATTCACACATGTACTAAGTTTCCG 57.278 37.500 0.00 0.00 0.00 4.30
845 848 4.562082 TCACACATGTACTAAGTTTCCGG 58.438 43.478 0.00 0.00 0.00 5.14
846 849 4.039488 TCACACATGTACTAAGTTTCCGGT 59.961 41.667 0.00 0.00 0.00 5.28
847 850 4.753107 CACACATGTACTAAGTTTCCGGTT 59.247 41.667 0.00 0.00 0.00 4.44
848 851 5.927689 CACACATGTACTAAGTTTCCGGTTA 59.072 40.000 0.00 0.00 0.00 2.85
849 852 6.424509 CACACATGTACTAAGTTTCCGGTTAA 59.575 38.462 0.00 0.00 0.00 2.01
850 853 7.118680 CACACATGTACTAAGTTTCCGGTTAAT 59.881 37.037 0.00 0.00 0.00 1.40
851 854 8.313292 ACACATGTACTAAGTTTCCGGTTAATA 58.687 33.333 0.00 0.00 0.00 0.98
852 855 8.598075 CACATGTACTAAGTTTCCGGTTAATAC 58.402 37.037 0.00 0.00 0.00 1.89
853 856 8.313292 ACATGTACTAAGTTTCCGGTTAATACA 58.687 33.333 0.00 3.81 28.60 2.29
854 857 8.814235 CATGTACTAAGTTTCCGGTTAATACAG 58.186 37.037 0.00 0.00 27.80 2.74
855 858 7.895759 TGTACTAAGTTTCCGGTTAATACAGT 58.104 34.615 0.00 0.98 0.00 3.55
856 859 8.367156 TGTACTAAGTTTCCGGTTAATACAGTT 58.633 33.333 0.00 0.00 0.00 3.16
857 860 7.895975 ACTAAGTTTCCGGTTAATACAGTTC 57.104 36.000 0.00 0.00 0.00 3.01
858 861 7.674120 ACTAAGTTTCCGGTTAATACAGTTCT 58.326 34.615 0.00 0.00 0.00 3.01
859 862 8.806146 ACTAAGTTTCCGGTTAATACAGTTCTA 58.194 33.333 0.00 0.00 0.00 2.10
860 863 9.298774 CTAAGTTTCCGGTTAATACAGTTCTAG 57.701 37.037 0.00 0.00 0.00 2.43
861 864 6.104665 AGTTTCCGGTTAATACAGTTCTAGC 58.895 40.000 0.00 0.00 0.00 3.42
862 865 5.664294 TTCCGGTTAATACAGTTCTAGCA 57.336 39.130 0.00 0.00 0.00 3.49
863 866 5.864418 TCCGGTTAATACAGTTCTAGCAT 57.136 39.130 0.00 0.00 0.00 3.79
864 867 5.839621 TCCGGTTAATACAGTTCTAGCATC 58.160 41.667 0.00 0.00 0.00 3.91
865 868 5.361571 TCCGGTTAATACAGTTCTAGCATCA 59.638 40.000 0.00 0.00 0.00 3.07
866 869 6.046593 CCGGTTAATACAGTTCTAGCATCAA 58.953 40.000 0.00 0.00 0.00 2.57
867 870 6.706270 CCGGTTAATACAGTTCTAGCATCAAT 59.294 38.462 0.00 0.00 0.00 2.57
868 871 7.870954 CCGGTTAATACAGTTCTAGCATCAATA 59.129 37.037 0.00 0.00 0.00 1.90
869 872 9.256477 CGGTTAATACAGTTCTAGCATCAATAA 57.744 33.333 0.00 0.00 0.00 1.40
926 929 6.530019 AACAACTTTATTATTGCCTCCAGG 57.470 37.500 0.00 0.00 38.53 4.45
927 930 4.956075 ACAACTTTATTATTGCCTCCAGGG 59.044 41.667 0.00 0.00 35.18 4.45
937 940 2.936823 CCTCCAGGGCATAGTTCCT 58.063 57.895 0.00 0.00 0.00 3.36
938 941 1.216990 CCTCCAGGGCATAGTTCCTT 58.783 55.000 0.00 0.00 0.00 3.36
939 942 1.141858 CCTCCAGGGCATAGTTCCTTC 59.858 57.143 0.00 0.00 0.00 3.46
952 955 2.447047 AGTTCCTTCACCCAAGTGGATT 59.553 45.455 0.00 0.00 44.64 3.01
1013 1016 0.747644 CGTGCCATGGCCAATAGTGA 60.748 55.000 33.44 9.85 41.09 3.41
1153 1156 3.963374 TGAGTGGATAGCTGCTATTGTCT 59.037 43.478 22.09 18.29 0.00 3.41
1154 1157 5.140454 TGAGTGGATAGCTGCTATTGTCTA 58.860 41.667 22.09 7.13 0.00 2.59
1155 1158 5.777223 TGAGTGGATAGCTGCTATTGTCTAT 59.223 40.000 22.09 7.91 0.00 1.98
1156 1159 6.948309 TGAGTGGATAGCTGCTATTGTCTATA 59.052 38.462 22.09 10.61 0.00 1.31
1157 1160 7.617329 TGAGTGGATAGCTGCTATTGTCTATAT 59.383 37.037 22.09 0.00 0.00 0.86
1158 1161 9.126151 GAGTGGATAGCTGCTATTGTCTATATA 57.874 37.037 22.09 0.00 0.00 0.86
1159 1162 9.653516 AGTGGATAGCTGCTATTGTCTATATAT 57.346 33.333 22.09 0.00 0.00 0.86
1305 1310 5.830991 TCTTTTTACCTTACCTTGTGTGCAT 59.169 36.000 0.00 0.00 0.00 3.96
1341 1346 8.211629 GTCAATTATCTTACCAGACCCATTAGT 58.788 37.037 0.00 0.00 0.00 2.24
1533 1541 2.230508 TGATCGTCGCAGTCCTAAAGTT 59.769 45.455 0.00 0.00 0.00 2.66
1678 1699 4.767578 ATCAAGAAGCTAGCTGAATCCA 57.232 40.909 20.16 1.25 0.00 3.41
1697 1718 3.461458 TCCATTGCATCCCCTATTGTGTA 59.539 43.478 0.00 0.00 0.00 2.90
1755 1776 1.747355 CTTTGGAAGCGGATCAATGCT 59.253 47.619 0.00 0.00 44.97 3.79
1761 1782 2.988010 AGCGGATCAATGCTCTTACA 57.012 45.000 0.00 0.00 36.53 2.41
1789 1810 7.347222 TCCCAGCTAAGGATAAACTTGAGATTA 59.653 37.037 0.43 0.00 32.02 1.75
1821 1842 8.860517 ATCTATCCAAGCCATACCAAGATATA 57.139 34.615 0.00 0.00 0.00 0.86
1826 1847 7.754624 TCCAAGCCATACCAAGATATATTTCA 58.245 34.615 0.00 0.00 0.00 2.69
2259 2301 3.626217 TGTGCGTATGTGTGTTGGTTAAA 59.374 39.130 0.00 0.00 0.00 1.52
2261 2303 5.035443 GTGCGTATGTGTGTTGGTTAAAAA 58.965 37.500 0.00 0.00 0.00 1.94
2534 2626 3.149981 GCTCAATCCAAATAGCCCCTAC 58.850 50.000 0.00 0.00 0.00 3.18
2535 2627 3.181439 GCTCAATCCAAATAGCCCCTACT 60.181 47.826 0.00 0.00 0.00 2.57
2536 2628 4.689983 GCTCAATCCAAATAGCCCCTACTT 60.690 45.833 0.00 0.00 0.00 2.24
2537 2629 5.456186 GCTCAATCCAAATAGCCCCTACTTA 60.456 44.000 0.00 0.00 0.00 2.24
2538 2630 6.584471 TCAATCCAAATAGCCCCTACTTAA 57.416 37.500 0.00 0.00 0.00 1.85
2539 2631 7.161715 TCAATCCAAATAGCCCCTACTTAAT 57.838 36.000 0.00 0.00 0.00 1.40
2540 2632 7.004086 TCAATCCAAATAGCCCCTACTTAATG 58.996 38.462 0.00 0.00 0.00 1.90
2541 2633 5.987019 TCCAAATAGCCCCTACTTAATGT 57.013 39.130 0.00 0.00 0.00 2.71
2542 2634 7.642094 ATCCAAATAGCCCCTACTTAATGTA 57.358 36.000 0.00 0.00 0.00 2.29
2543 2635 6.834107 TCCAAATAGCCCCTACTTAATGTAC 58.166 40.000 0.00 0.00 0.00 2.90
2544 2636 6.618196 TCCAAATAGCCCCTACTTAATGTACT 59.382 38.462 0.00 0.00 0.00 2.73
2545 2637 6.935208 CCAAATAGCCCCTACTTAATGTACTC 59.065 42.308 0.00 0.00 0.00 2.59
2546 2638 7.419750 CCAAATAGCCCCTACTTAATGTACTCA 60.420 40.741 0.00 0.00 0.00 3.41
2547 2639 7.873699 AATAGCCCCTACTTAATGTACTCAT 57.126 36.000 0.00 0.00 35.59 2.90
2548 2640 5.552870 AGCCCCTACTTAATGTACTCATG 57.447 43.478 0.00 0.00 34.19 3.07
2549 2641 4.969359 AGCCCCTACTTAATGTACTCATGT 59.031 41.667 0.00 0.00 34.19 3.21
2550 2642 6.141083 AGCCCCTACTTAATGTACTCATGTA 58.859 40.000 0.00 0.00 34.19 2.29
2551 2643 6.041751 AGCCCCTACTTAATGTACTCATGTAC 59.958 42.308 0.00 0.00 46.74 2.90
2601 2693 5.541101 TCGGCTGGCTTTACCTAATTAGATA 59.459 40.000 14.28 0.00 40.22 1.98
2602 2694 5.638234 CGGCTGGCTTTACCTAATTAGATAC 59.362 44.000 14.28 0.00 40.22 2.24
2609 2701 9.163899 GGCTTTACCTAATTAGATACCATTAGC 57.836 37.037 14.28 10.25 33.33 3.09
2610 2702 9.945904 GCTTTACCTAATTAGATACCATTAGCT 57.054 33.333 14.28 0.00 33.33 3.32
2624 2716 6.460103 ACCATTAGCTAGATCCAAATCCAT 57.540 37.500 0.00 0.00 31.78 3.41
2628 2720 7.094463 CCATTAGCTAGATCCAAATCCATGAAC 60.094 40.741 0.00 0.00 31.78 3.18
2631 2723 4.212214 GCTAGATCCAAATCCATGAACGAC 59.788 45.833 0.00 0.00 31.78 4.34
2645 2737 6.039047 TCCATGAACGACTATCCTAGTAACAC 59.961 42.308 0.00 0.00 39.59 3.32
2786 2878 2.270205 CCTGCTGCCCTACCACAG 59.730 66.667 0.00 0.00 36.96 3.66
2799 2891 0.036010 ACCACAGATACCTGCAGCAC 60.036 55.000 8.66 0.00 44.16 4.40
2808 2900 1.597742 ACCTGCAGCACAAGTACTTG 58.402 50.000 29.76 29.76 45.58 3.16
2845 5066 2.753452 CTGATGGTTTGCTGAGCAGATT 59.247 45.455 7.39 0.00 40.61 2.40
2861 5082 3.390135 CAGATTTGATTGATGGCCATGC 58.610 45.455 26.56 15.28 0.00 4.06
2885 5106 2.817258 CCGCTGCTTCTAGCTAGATAGT 59.183 50.000 23.81 0.00 42.97 2.12
2887 5108 4.142773 CCGCTGCTTCTAGCTAGATAGTAC 60.143 50.000 23.81 12.66 42.97 2.73
2889 5110 5.390461 CGCTGCTTCTAGCTAGATAGTACTG 60.390 48.000 23.81 14.91 42.97 2.74
2890 5111 5.472137 GCTGCTTCTAGCTAGATAGTACTGT 59.528 44.000 23.81 0.00 42.97 3.55
2891 5112 6.651643 GCTGCTTCTAGCTAGATAGTACTGTA 59.348 42.308 23.81 5.13 42.97 2.74
2892 5113 7.360607 GCTGCTTCTAGCTAGATAGTACTGTAC 60.361 44.444 23.81 9.93 42.97 2.90
2893 5114 7.737869 TGCTTCTAGCTAGATAGTACTGTACT 58.262 38.462 23.81 22.72 42.97 2.73
2894 5115 7.658167 TGCTTCTAGCTAGATAGTACTGTACTG 59.342 40.741 26.45 12.90 42.97 2.74
2895 5116 7.658575 GCTTCTAGCTAGATAGTACTGTACTGT 59.341 40.741 26.45 21.35 37.68 3.55
2897 5118 9.979578 TTCTAGCTAGATAGTACTGTACTGTAC 57.020 37.037 26.83 26.83 39.81 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.029666 GAGCCCCGGATGTGATCG 59.970 66.667 0.73 0.00 0.00 3.69
37 38 6.341316 TGATGTACAGAAGATAGTTTGGAGC 58.659 40.000 0.33 0.00 0.00 4.70
186 187 6.243900 AGAATATGTGGGAGCCAATATGAAG 58.756 40.000 0.00 0.00 34.18 3.02
218 219 6.017770 TCGTTATGCCATTTTACCGATAAAGG 60.018 38.462 0.00 0.00 31.90 3.11
242 243 6.292168 CGATGACAAAGGGAACAACGTATATC 60.292 42.308 0.00 0.00 0.00 1.63
391 393 5.430886 TGCACATCACTATAAGACTTGCAT 58.569 37.500 0.00 0.00 33.55 3.96
398 400 6.264518 TCTCGGTAATGCACATCACTATAAGA 59.735 38.462 0.00 0.00 0.00 2.10
445 447 3.485463 AGGATTTGTCACTCCGTTTGA 57.515 42.857 0.00 0.00 36.62 2.69
449 451 4.440250 CGAGATTAGGATTTGTCACTCCGT 60.440 45.833 0.00 0.00 36.62 4.69
494 496 3.099905 CTCTACAGGTGTCTCCAATGGA 58.900 50.000 0.48 0.48 39.02 3.41
529 531 3.478857 AACATCACAACGTAACTGGGA 57.521 42.857 0.00 0.00 0.00 4.37
602 604 9.212641 CTTCATGACTTATACATGTTCCTATGG 57.787 37.037 2.30 0.00 43.56 2.74
674 677 3.411446 TGATGTGATTGACTTGACCCAC 58.589 45.455 0.00 0.00 0.00 4.61
701 704 6.375945 TTGATTAACGGGATCACATCATTG 57.624 37.500 0.00 0.00 33.51 2.82
773 776 3.087370 TGCCTCTACTTGACTAGCTCA 57.913 47.619 0.00 0.00 0.00 4.26
795 798 1.599542 GACAAACAGAGTGTCACTGGC 59.400 52.381 11.04 0.00 44.00 4.85
797 800 5.292765 ACATAGACAAACAGAGTGTCACTG 58.707 41.667 11.04 0.00 46.44 3.66
838 841 5.870978 TGCTAGAACTGTATTAACCGGAAAC 59.129 40.000 9.46 0.00 0.00 2.78
839 842 6.040209 TGCTAGAACTGTATTAACCGGAAA 57.960 37.500 9.46 1.61 0.00 3.13
840 843 5.664294 TGCTAGAACTGTATTAACCGGAA 57.336 39.130 9.46 0.00 0.00 4.30
841 844 5.361571 TGATGCTAGAACTGTATTAACCGGA 59.638 40.000 9.46 0.00 0.00 5.14
842 845 5.597806 TGATGCTAGAACTGTATTAACCGG 58.402 41.667 0.00 0.00 0.00 5.28
843 846 7.715265 ATTGATGCTAGAACTGTATTAACCG 57.285 36.000 0.00 0.00 0.00 4.44
900 903 8.695456 CCTGGAGGCAATAATAAAGTTGTTATT 58.305 33.333 0.00 1.27 35.65 1.40
901 904 7.287696 CCCTGGAGGCAATAATAAAGTTGTTAT 59.712 37.037 0.00 0.00 0.00 1.89
902 905 6.605594 CCCTGGAGGCAATAATAAAGTTGTTA 59.394 38.462 0.00 0.00 0.00 2.41
903 906 5.422012 CCCTGGAGGCAATAATAAAGTTGTT 59.578 40.000 0.00 0.00 0.00 2.83
904 907 4.956075 CCCTGGAGGCAATAATAAAGTTGT 59.044 41.667 0.00 0.00 0.00 3.32
905 908 5.520376 CCCTGGAGGCAATAATAAAGTTG 57.480 43.478 0.00 0.00 0.00 3.16
919 922 1.141858 GAAGGAACTATGCCCTGGAGG 59.858 57.143 0.00 0.00 38.49 4.30
920 923 1.839994 TGAAGGAACTATGCCCTGGAG 59.160 52.381 0.00 0.00 38.49 3.86
921 924 1.559682 GTGAAGGAACTATGCCCTGGA 59.440 52.381 0.00 0.00 38.49 3.86
922 925 1.408822 GGTGAAGGAACTATGCCCTGG 60.409 57.143 0.00 0.00 38.49 4.45
923 926 1.408822 GGGTGAAGGAACTATGCCCTG 60.409 57.143 0.00 0.00 38.49 4.45
924 927 0.919710 GGGTGAAGGAACTATGCCCT 59.080 55.000 0.00 0.00 38.49 5.19
925 928 0.623723 TGGGTGAAGGAACTATGCCC 59.376 55.000 0.00 0.00 38.49 5.36
926 929 2.290960 ACTTGGGTGAAGGAACTATGCC 60.291 50.000 0.00 0.00 38.49 4.40
927 930 2.749621 CACTTGGGTGAAGGAACTATGC 59.250 50.000 0.00 0.00 45.61 3.14
928 931 3.009033 TCCACTTGGGTGAAGGAACTATG 59.991 47.826 0.00 0.00 45.61 2.23
929 932 3.256704 TCCACTTGGGTGAAGGAACTAT 58.743 45.455 0.00 0.00 45.61 2.12
930 933 2.696775 TCCACTTGGGTGAAGGAACTA 58.303 47.619 0.00 0.00 45.61 2.24
931 934 1.518367 TCCACTTGGGTGAAGGAACT 58.482 50.000 0.00 0.00 45.61 3.01
932 935 2.558359 CAATCCACTTGGGTGAAGGAAC 59.442 50.000 0.00 0.00 45.61 3.62
933 936 2.445145 TCAATCCACTTGGGTGAAGGAA 59.555 45.455 0.00 0.00 45.61 3.36
934 937 2.061848 TCAATCCACTTGGGTGAAGGA 58.938 47.619 0.00 0.00 45.61 3.36
935 938 2.162681 GTCAATCCACTTGGGTGAAGG 58.837 52.381 4.65 0.00 45.61 3.46
936 939 2.554032 GTGTCAATCCACTTGGGTGAAG 59.446 50.000 4.65 0.00 45.61 3.02
937 940 2.174639 AGTGTCAATCCACTTGGGTGAA 59.825 45.455 4.65 0.00 42.99 3.18
938 941 1.774254 AGTGTCAATCCACTTGGGTGA 59.226 47.619 0.00 0.00 42.99 4.02
939 942 2.276732 AGTGTCAATCCACTTGGGTG 57.723 50.000 0.00 0.00 42.99 4.61
1013 1016 1.133513 TGGTTCTGTCAAGGCCATTGT 60.134 47.619 5.01 0.00 40.05 2.71
1194 1199 8.209584 ACAAGAGACAGTGAATATGAAGCATAT 58.790 33.333 0.00 0.00 38.52 1.78
1241 1246 5.173774 TGAACACAAAACATGAGAGAAGC 57.826 39.130 0.00 0.00 0.00 3.86
1305 1310 8.856153 TGGTAAGATAATTGACTGCAGTTTTA 57.144 30.769 22.65 18.28 0.00 1.52
1655 1676 6.430962 TGGATTCAGCTAGCTTCTTGATAT 57.569 37.500 16.46 6.76 0.00 1.63
1678 1699 4.828939 CACATACACAATAGGGGATGCAAT 59.171 41.667 0.00 0.00 0.00 3.56
1697 1718 2.297033 GCAGGTGTCATTGGTTTCACAT 59.703 45.455 0.00 0.00 33.17 3.21
1755 1776 7.127339 AGTTTATCCTTAGCTGGGATTGTAAGA 59.873 37.037 22.32 6.42 42.77 2.10
1761 1782 6.158695 TCTCAAGTTTATCCTTAGCTGGGATT 59.841 38.462 22.32 7.61 42.77 3.01
1789 1810 4.942363 ATGGCTTGGATAGATAGGCAAT 57.058 40.909 0.00 0.00 45.76 3.56
2216 2258 6.392354 CACACAAACTATGCATTTCCAGAAT 58.608 36.000 3.54 0.00 0.00 2.40
2261 2303 9.893305 GTGTGTAAACAAGCAGTCTTATAATTT 57.107 29.630 0.00 0.00 0.00 1.82
2266 2315 6.935741 TTGTGTGTAAACAAGCAGTCTTAT 57.064 33.333 0.00 0.00 35.16 1.73
2407 2498 5.329035 AGCCATTAGTACTTGCCAATTTG 57.671 39.130 0.00 0.00 0.00 2.32
2498 2590 1.225373 TGAGCCCAATCTTGCCCTAT 58.775 50.000 0.00 0.00 0.00 2.57
2525 2617 6.141083 ACATGAGTACATTAAGTAGGGGCTA 58.859 40.000 0.00 0.00 34.15 3.93
2541 2633 4.867086 TCATCTGGACCTGTACATGAGTA 58.133 43.478 0.00 0.00 0.00 2.59
2542 2634 3.713003 TCATCTGGACCTGTACATGAGT 58.287 45.455 0.00 0.00 0.00 3.41
2543 2635 4.629092 CATCATCTGGACCTGTACATGAG 58.371 47.826 0.00 0.00 0.00 2.90
2544 2636 4.677673 CATCATCTGGACCTGTACATGA 57.322 45.455 0.00 0.00 0.00 3.07
2560 2652 2.575532 CCGACCTAATGTTGCCATCAT 58.424 47.619 0.00 0.00 0.00 2.45
2577 2669 3.707611 TCTAATTAGGTAAAGCCAGCCGA 59.292 43.478 12.54 0.00 40.61 5.54
2601 2693 5.912149 TGGATTTGGATCTAGCTAATGGT 57.088 39.130 0.00 0.00 32.66 3.55
2602 2694 6.479006 TCATGGATTTGGATCTAGCTAATGG 58.521 40.000 0.00 0.00 32.66 3.16
2609 2701 5.605534 AGTCGTTCATGGATTTGGATCTAG 58.394 41.667 0.00 0.00 32.66 2.43
2610 2702 5.614324 AGTCGTTCATGGATTTGGATCTA 57.386 39.130 0.00 0.00 32.66 1.98
2611 2703 4.494091 AGTCGTTCATGGATTTGGATCT 57.506 40.909 0.00 0.00 32.66 2.75
2612 2704 5.409826 GGATAGTCGTTCATGGATTTGGATC 59.590 44.000 0.00 0.00 0.00 3.36
2613 2705 5.072329 AGGATAGTCGTTCATGGATTTGGAT 59.928 40.000 0.00 0.00 0.00 3.41
2631 2723 6.300703 ACTCTAGCTGGTGTTACTAGGATAG 58.699 44.000 0.00 0.00 46.50 2.08
2666 2758 8.964533 AATGGTGATGATTAGTACTCCTATCT 57.035 34.615 0.00 0.00 0.00 1.98
2671 2763 9.778741 TGAATTAATGGTGATGATTAGTACTCC 57.221 33.333 0.00 0.00 0.00 3.85
2686 2778 4.261801 CCGTGACCTTCTGAATTAATGGT 58.738 43.478 0.00 0.00 0.00 3.55
2738 2830 6.172136 AGTTGAGCTGATGCATAATCTAGT 57.828 37.500 0.00 0.00 42.74 2.57
2739 2831 6.589523 GGTAGTTGAGCTGATGCATAATCTAG 59.410 42.308 0.00 0.00 42.74 2.43
2740 2832 6.459066 GGTAGTTGAGCTGATGCATAATCTA 58.541 40.000 0.00 0.00 42.74 1.98
2741 2833 5.303971 GGTAGTTGAGCTGATGCATAATCT 58.696 41.667 0.00 0.00 42.74 2.40
2742 2834 4.151335 CGGTAGTTGAGCTGATGCATAATC 59.849 45.833 0.00 0.00 42.74 1.75
2743 2835 4.060900 CGGTAGTTGAGCTGATGCATAAT 58.939 43.478 0.00 0.00 42.74 1.28
2747 2839 0.108186 CCGGTAGTTGAGCTGATGCA 60.108 55.000 0.00 0.00 42.74 3.96
2778 2870 1.482182 TGCTGCAGGTATCTGTGGTAG 59.518 52.381 17.12 0.17 42.78 3.18
2786 2878 3.252974 AGTACTTGTGCTGCAGGTATC 57.747 47.619 17.12 0.00 40.88 2.24
2799 2891 2.744202 CAGCTAAGTGCCCAAGTACTTG 59.256 50.000 25.79 25.79 46.80 3.16
2826 5047 3.192001 TCAAATCTGCTCAGCAAACCATC 59.808 43.478 0.00 0.00 38.41 3.51
2827 5048 3.159472 TCAAATCTGCTCAGCAAACCAT 58.841 40.909 0.00 0.00 38.41 3.55
2828 5049 2.585330 TCAAATCTGCTCAGCAAACCA 58.415 42.857 0.00 0.00 38.41 3.67
2829 5050 3.863142 ATCAAATCTGCTCAGCAAACC 57.137 42.857 0.00 0.00 38.41 3.27
2830 5051 4.801891 TCAATCAAATCTGCTCAGCAAAC 58.198 39.130 0.00 0.00 38.41 2.93
2831 5052 5.407502 CATCAATCAAATCTGCTCAGCAAA 58.592 37.500 0.00 0.00 38.41 3.68
2832 5053 4.142249 CCATCAATCAAATCTGCTCAGCAA 60.142 41.667 0.00 0.00 38.41 3.91
2833 5054 3.380320 CCATCAATCAAATCTGCTCAGCA 59.620 43.478 0.00 0.00 36.92 4.41
2845 5066 0.462375 GCAGCATGGCCATCAATCAA 59.538 50.000 17.61 0.00 35.86 2.57
2861 5082 0.597118 CTAGCTAGAAGCAGCGGCAG 60.597 60.000 16.15 0.00 45.56 4.85
2865 5086 4.693566 AGTACTATCTAGCTAGAAGCAGCG 59.306 45.833 26.62 13.32 45.56 5.18
2906 5127 9.247126 CTCATGACATGATCTTCTGTTAGTTAG 57.753 37.037 18.28 0.00 38.85 2.34


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

AutoCloner maintained by Alex Coulton.