Multiple sequence alignment - TraesCS3D01G382800

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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 TraesCS3D01G382800 chr3D 100.000 2046 0 0 1 2046 498396724 498394679 0.000000e+00 3779
1 TraesCS3D01G382800 chr3D 87.328 1381 82 49 571 1900 498356707 498355369 0.000000e+00 1495
2 TraesCS3D01G382800 chr3D 84.727 1244 108 40 832 2038 498423830 498422632 0.000000e+00 1170
3 TraesCS3D01G382800 chr3D 82.937 1219 106 50 581 1762 498484689 498483536 0.000000e+00 1005
4 TraesCS3D01G382800 chr3D 84.578 1018 76 43 544 1507 498264967 498263977 0.000000e+00 935
5 TraesCS3D01G382800 chr3D 87.701 561 49 9 1 544 126394371 126394928 9.750000e-179 636
6 TraesCS3D01G382800 chr3D 85.133 565 54 18 1 544 238593044 238592489 3.630000e-153 551
7 TraesCS3D01G382800 chr3D 100.000 158 0 0 2341 2498 498394384 498394227 2.430000e-75 292
8 TraesCS3D01G382800 chr3D 82.587 201 26 5 560 753 498424057 498423859 4.270000e-38 169
9 TraesCS3D01G382800 chr3A 89.588 970 60 16 544 1496 638447386 638446441 0.000000e+00 1194
10 TraesCS3D01G382800 chr3A 90.079 756 50 17 775 1507 638468052 638467299 0.000000e+00 957
11 TraesCS3D01G382800 chr3A 92.320 612 33 5 969 1580 638452945 638452348 0.000000e+00 857
12 TraesCS3D01G382800 chr3A 82.566 1021 94 50 852 1838 638711570 638710600 0.000000e+00 822
13 TraesCS3D01G382800 chr3A 77.249 378 45 21 571 927 638453397 638453040 1.530000e-42 183
14 TraesCS3D01G382800 chr3A 95.652 46 2 0 782 827 638711612 638711567 9.580000e-10 75
15 TraesCS3D01G382800 chr3B 86.837 980 63 22 544 1496 659276441 659275501 0.000000e+00 1035
16 TraesCS3D01G382800 chr3B 84.696 1052 75 31 568 1581 659298490 659297487 0.000000e+00 972
17 TraesCS3D01G382800 chr3B 80.236 1270 136 62 565 1762 659305872 659304646 0.000000e+00 848
18 TraesCS3D01G382800 chr3B 87.354 514 49 8 6 505 566827909 566828420 2.150000e-160 575
19 TraesCS3D01G382800 chr3B 86.592 179 11 5 1611 1777 659297489 659297312 4.240000e-43 185
20 TraesCS3D01G382800 chr3B 86.000 150 16 3 1633 1777 659296611 659296462 3.330000e-34 156
21 TraesCS3D01G382800 chr6D 87.332 521 49 8 1 505 177796687 177797206 4.630000e-162 580
22 TraesCS3D01G382800 chr6D 84.981 526 50 17 1 505 396930197 396929680 7.970000e-140 507
23 TraesCS3D01G382800 chr7A 85.870 552 59 11 7 544 215573847 215573301 1.000000e-158 569
24 TraesCS3D01G382800 chr5B 86.898 519 48 10 6 505 668818264 668818781 4.660000e-157 564
25 TraesCS3D01G382800 chr5D 85.225 555 63 4 1 542 515860762 515861310 1.010000e-153 553
26 TraesCS3D01G382800 chr2B 86.346 520 55 8 1 505 482760765 482761283 1.010000e-153 553
27 TraesCS3D01G382800 chr2D 85.905 525 45 18 1 505 322501268 322501783 1.320000e-147 532
28 TraesCS3D01G382800 chr6B 84.659 528 50 19 1 505 651405988 651406507 4.800000e-137 497
29 TraesCS3D01G382800 chr4D 84.571 525 53 17 1 505 35488656 35489172 1.730000e-136 496
30 TraesCS3D01G382800 chr1D 84.100 522 63 12 1 505 174776255 174775737 1.040000e-133 486
31 TraesCS3D01G382800 chr1D 90.175 285 12 9 1 271 196083373 196083655 8.500000e-95 357
32 TraesCS3D01G382800 chr7D 82.394 568 71 19 1 547 156110965 156110406 3.760000e-128 468
33 TraesCS3D01G382800 chr5A 82.617 512 75 11 3 506 496568892 496569397 8.200000e-120 440
34 TraesCS3D01G382800 chrUn 87.931 348 20 12 1 331 400214363 400214021 8.380000e-105 390
35 TraesCS3D01G382800 chr6A 90.909 121 10 1 964 1084 53923219 53923100 7.150000e-36 161


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 TraesCS3D01G382800 chr3D 498394227 498396724 2497 True 2035.500000 3779 100.000000 1 2498 2 chr3D.!!$R5 2497
1 TraesCS3D01G382800 chr3D 498355369 498356707 1338 True 1495.000000 1495 87.328000 571 1900 1 chr3D.!!$R3 1329
2 TraesCS3D01G382800 chr3D 498483536 498484689 1153 True 1005.000000 1005 82.937000 581 1762 1 chr3D.!!$R4 1181
3 TraesCS3D01G382800 chr3D 498263977 498264967 990 True 935.000000 935 84.578000 544 1507 1 chr3D.!!$R2 963
4 TraesCS3D01G382800 chr3D 498422632 498424057 1425 True 669.500000 1170 83.657000 560 2038 2 chr3D.!!$R6 1478
5 TraesCS3D01G382800 chr3D 126394371 126394928 557 False 636.000000 636 87.701000 1 544 1 chr3D.!!$F1 543
6 TraesCS3D01G382800 chr3D 238592489 238593044 555 True 551.000000 551 85.133000 1 544 1 chr3D.!!$R1 543
7 TraesCS3D01G382800 chr3A 638446441 638447386 945 True 1194.000000 1194 89.588000 544 1496 1 chr3A.!!$R1 952
8 TraesCS3D01G382800 chr3A 638467299 638468052 753 True 957.000000 957 90.079000 775 1507 1 chr3A.!!$R2 732
9 TraesCS3D01G382800 chr3A 638452348 638453397 1049 True 520.000000 857 84.784500 571 1580 2 chr3A.!!$R3 1009
10 TraesCS3D01G382800 chr3A 638710600 638711612 1012 True 448.500000 822 89.109000 782 1838 2 chr3A.!!$R4 1056
11 TraesCS3D01G382800 chr3B 659275501 659276441 940 True 1035.000000 1035 86.837000 544 1496 1 chr3B.!!$R1 952
12 TraesCS3D01G382800 chr3B 659304646 659305872 1226 True 848.000000 848 80.236000 565 1762 1 chr3B.!!$R2 1197
13 TraesCS3D01G382800 chr3B 566827909 566828420 511 False 575.000000 575 87.354000 6 505 1 chr3B.!!$F1 499
14 TraesCS3D01G382800 chr3B 659296462 659298490 2028 True 437.666667 972 85.762667 568 1777 3 chr3B.!!$R3 1209
15 TraesCS3D01G382800 chr6D 177796687 177797206 519 False 580.000000 580 87.332000 1 505 1 chr6D.!!$F1 504
16 TraesCS3D01G382800 chr6D 396929680 396930197 517 True 507.000000 507 84.981000 1 505 1 chr6D.!!$R1 504
17 TraesCS3D01G382800 chr7A 215573301 215573847 546 True 569.000000 569 85.870000 7 544 1 chr7A.!!$R1 537
18 TraesCS3D01G382800 chr5B 668818264 668818781 517 False 564.000000 564 86.898000 6 505 1 chr5B.!!$F1 499
19 TraesCS3D01G382800 chr5D 515860762 515861310 548 False 553.000000 553 85.225000 1 542 1 chr5D.!!$F1 541
20 TraesCS3D01G382800 chr2B 482760765 482761283 518 False 553.000000 553 86.346000 1 505 1 chr2B.!!$F1 504
21 TraesCS3D01G382800 chr2D 322501268 322501783 515 False 532.000000 532 85.905000 1 505 1 chr2D.!!$F1 504
22 TraesCS3D01G382800 chr6B 651405988 651406507 519 False 497.000000 497 84.659000 1 505 1 chr6B.!!$F1 504
23 TraesCS3D01G382800 chr4D 35488656 35489172 516 False 496.000000 496 84.571000 1 505 1 chr4D.!!$F1 504
24 TraesCS3D01G382800 chr1D 174775737 174776255 518 True 486.000000 486 84.100000 1 505 1 chr1D.!!$R1 504
25 TraesCS3D01G382800 chr7D 156110406 156110965 559 True 468.000000 468 82.394000 1 547 1 chr7D.!!$R1 546
26 TraesCS3D01G382800 chr5A 496568892 496569397 505 False 440.000000 440 82.617000 3 506 1 chr5A.!!$F1 503

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
527 564 0.450184 CTATTTGTTTGGGTCGGCCG 59.55 55.0 22.12 22.12 34.97 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2353 3114 0.107703 CCTACGGCATTCTGGCTTCA 60.108 55.0 0.0 0.0 41.25 3.02 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
106 107 1.078708 AATACCGTGTCGCCAAGGG 60.079 57.895 2.97 0.00 43.71 3.95
164 179 2.794981 CGAGTGATTTATGACGGCGAGT 60.795 50.000 16.62 0.64 0.00 4.18
344 371 3.564027 GTATGTCGGCGCTGGCAC 61.564 66.667 28.42 13.78 42.47 5.01
463 500 5.565834 CGCACTACCAACCCAAATGTAAAAT 60.566 40.000 0.00 0.00 0.00 1.82
475 512 0.538118 TGTAAAATAGGGCGGACGCT 59.462 50.000 16.72 0.00 42.59 5.07
478 515 1.906105 AAAATAGGGCGGACGCTGGA 61.906 55.000 16.72 2.25 39.80 3.86
509 546 5.411669 GTCGACCTAAATGGACAAAATCACT 59.588 40.000 3.51 0.00 39.71 3.41
510 547 6.592607 GTCGACCTAAATGGACAAAATCACTA 59.407 38.462 3.51 0.00 39.71 2.74
512 549 7.827236 TCGACCTAAATGGACAAAATCACTATT 59.173 33.333 0.00 0.00 39.71 1.73
526 563 1.201414 CACTATTTGTTTGGGTCGGCC 59.799 52.381 0.00 0.00 0.00 6.13
527 564 0.450184 CTATTTGTTTGGGTCGGCCG 59.550 55.000 22.12 22.12 34.97 6.13
672 754 2.892425 GCCGATCCAGCCGTCTTG 60.892 66.667 0.00 0.00 0.00 3.02
673 755 2.892640 CCGATCCAGCCGTCTTGA 59.107 61.111 0.00 0.00 0.00 3.02
678 760 1.734465 GATCCAGCCGTCTTGACAAAG 59.266 52.381 1.59 0.00 34.45 2.77
780 894 0.905357 AAGCTTCGCCTAGTCACCAT 59.095 50.000 0.00 0.00 0.00 3.55
907 1081 1.630369 CCAACCATCTCTCCAACTCCA 59.370 52.381 0.00 0.00 0.00 3.86
929 1103 2.591715 GCCTCACGCACCACAACT 60.592 61.111 0.00 0.00 37.47 3.16
932 1106 1.227527 CTCACGCACCACAACTCCA 60.228 57.895 0.00 0.00 0.00 3.86
933 1107 0.603707 CTCACGCACCACAACTCCAT 60.604 55.000 0.00 0.00 0.00 3.41
946 1155 2.174210 CAACTCCATCCATCCATCCAGT 59.826 50.000 0.00 0.00 0.00 4.00
965 1174 1.458445 GTGATCATCCATCATCACGCG 59.542 52.381 3.53 3.53 43.72 6.01
966 1175 1.073964 GATCATCCATCATCACGCGG 58.926 55.000 12.47 0.00 0.00 6.46
967 1176 0.952497 ATCATCCATCATCACGCGGC 60.952 55.000 12.47 0.00 0.00 6.53
1401 1639 1.347707 CAGGACAAGGACAAGGTGCTA 59.652 52.381 0.00 0.00 31.83 3.49
1496 1734 2.686915 GCCATTCCTTCATCCAAGTCTG 59.313 50.000 0.00 0.00 0.00 3.51
1581 1824 0.498927 GCGAAGATCGATCGGTTTCG 59.501 55.000 29.42 29.42 43.74 3.46
1596 1839 4.818546 TCGGTTTCGGGTGTGTTAATTAAA 59.181 37.500 0.00 0.00 36.95 1.52
1597 1840 5.297776 TCGGTTTCGGGTGTGTTAATTAAAA 59.702 36.000 0.00 0.00 36.95 1.52
1709 1997 1.991121 AGGACACACTTCCGTACAGA 58.009 50.000 0.00 0.00 41.04 3.41
1762 2061 6.985188 TTTGTATAAGGAGACAATGACAGC 57.015 37.500 0.00 0.00 36.69 4.40
1778 2077 2.914379 AGCGACTGTGCTGTTTACC 58.086 52.632 4.36 0.00 45.28 2.85
1781 2080 1.333791 GCGACTGTGCTGTTTACCAAC 60.334 52.381 0.00 0.00 0.00 3.77
1788 2543 0.656205 GCTGTTTACCAACGTGCACG 60.656 55.000 35.99 35.99 46.33 5.34
1810 2567 2.948979 TGTGTGTGTCCATTCTTTGTCC 59.051 45.455 0.00 0.00 0.00 4.02
1854 2614 8.565896 TTCTGATGGTGCATATACATTTATCC 57.434 34.615 0.00 0.00 0.00 2.59
1882 2642 9.938280 TGTATCCTTATGATAAAATTAGGGTCG 57.062 33.333 0.00 0.00 37.69 4.79
1890 2650 2.871096 AAATTAGGGTCGCTCCAACA 57.129 45.000 0.00 0.00 38.11 3.33
1904 2664 1.066303 TCCAACACCGTGCATCAAAAC 59.934 47.619 0.00 0.00 0.00 2.43
1905 2665 1.119635 CAACACCGTGCATCAAAACG 58.880 50.000 0.00 0.00 39.48 3.60
1907 2667 1.729131 CACCGTGCATCAAAACGCC 60.729 57.895 0.00 0.00 38.46 5.68
1909 2669 2.126502 CGTGCATCAAAACGCCCC 60.127 61.111 0.00 0.00 32.40 5.80
1910 2670 2.625823 CGTGCATCAAAACGCCCCT 61.626 57.895 0.00 0.00 32.40 4.79
1911 2671 1.302383 CGTGCATCAAAACGCCCCTA 61.302 55.000 0.00 0.00 32.40 3.53
1912 2672 0.885196 GTGCATCAAAACGCCCCTAA 59.115 50.000 0.00 0.00 0.00 2.69
1914 2674 1.271102 TGCATCAAAACGCCCCTAAAC 59.729 47.619 0.00 0.00 0.00 2.01
1915 2675 1.271102 GCATCAAAACGCCCCTAAACA 59.729 47.619 0.00 0.00 0.00 2.83
1916 2676 2.094234 GCATCAAAACGCCCCTAAACAT 60.094 45.455 0.00 0.00 0.00 2.71
1917 2677 3.616317 GCATCAAAACGCCCCTAAACATT 60.616 43.478 0.00 0.00 0.00 2.71
1918 2678 3.926821 TCAAAACGCCCCTAAACATTC 57.073 42.857 0.00 0.00 0.00 2.67
1919 2679 2.226912 TCAAAACGCCCCTAAACATTCG 59.773 45.455 0.00 0.00 0.00 3.34
1920 2680 1.170442 AAACGCCCCTAAACATTCGG 58.830 50.000 0.00 0.00 0.00 4.30
1921 2681 0.325602 AACGCCCCTAAACATTCGGA 59.674 50.000 0.00 0.00 0.00 4.55
1922 2682 0.544697 ACGCCCCTAAACATTCGGAT 59.455 50.000 0.00 0.00 0.00 4.18
1923 2683 1.764134 ACGCCCCTAAACATTCGGATA 59.236 47.619 0.00 0.00 0.00 2.59
1924 2684 2.171027 ACGCCCCTAAACATTCGGATAA 59.829 45.455 0.00 0.00 0.00 1.75
1925 2685 2.546789 CGCCCCTAAACATTCGGATAAC 59.453 50.000 0.00 0.00 0.00 1.89
1926 2686 3.743269 CGCCCCTAAACATTCGGATAACT 60.743 47.826 0.00 0.00 0.00 2.24
1927 2687 4.204799 GCCCCTAAACATTCGGATAACTT 58.795 43.478 0.00 0.00 0.00 2.66
1928 2688 5.370679 GCCCCTAAACATTCGGATAACTTA 58.629 41.667 0.00 0.00 0.00 2.24
1929 2689 5.469084 GCCCCTAAACATTCGGATAACTTAG 59.531 44.000 0.00 0.00 0.00 2.18
1930 2690 6.589135 CCCCTAAACATTCGGATAACTTAGT 58.411 40.000 0.00 0.00 0.00 2.24
1931 2691 6.704937 CCCCTAAACATTCGGATAACTTAGTC 59.295 42.308 0.00 0.00 0.00 2.59
1932 2692 6.704937 CCCTAAACATTCGGATAACTTAGTCC 59.295 42.308 0.00 0.00 0.00 3.85
1946 2706 3.069729 ACTTAGTCCGAACACTCTTTGCT 59.930 43.478 0.00 0.00 0.00 3.91
1947 2707 1.871080 AGTCCGAACACTCTTTGCTG 58.129 50.000 0.00 0.00 0.00 4.41
1949 2709 1.527311 GTCCGAACACTCTTTGCTGTC 59.473 52.381 0.00 0.00 0.00 3.51
1950 2710 1.412710 TCCGAACACTCTTTGCTGTCT 59.587 47.619 0.00 0.00 0.00 3.41
1981 2742 4.379499 GGACCAGTCCGAATGTTTGAATTC 60.379 45.833 0.05 0.00 40.36 2.17
1984 2745 3.089284 AGTCCGAATGTTTGAATTCCCC 58.911 45.455 2.27 0.00 33.74 4.81
1985 2746 3.089284 GTCCGAATGTTTGAATTCCCCT 58.911 45.455 2.27 0.00 33.74 4.79
1989 2750 5.417580 TCCGAATGTTTGAATTCCCCTAAAG 59.582 40.000 2.27 0.00 33.74 1.85
2016 2777 1.725169 TTGTGGGAGGTTTGGGGGAG 61.725 60.000 0.00 0.00 0.00 4.30
2039 2800 4.344865 AGCCCGCCACGTTGGATT 62.345 61.111 8.04 0.00 40.96 3.01
2043 2804 2.433491 CGCCACGTTGGATTCCGA 60.433 61.111 8.04 0.00 40.96 4.55
2044 2805 2.736682 CGCCACGTTGGATTCCGAC 61.737 63.158 12.51 12.51 40.96 4.79
2361 3122 4.563337 CCATGATACATTGTGAAGCCAG 57.437 45.455 0.00 0.00 0.00 4.85
2362 3123 4.201657 CCATGATACATTGTGAAGCCAGA 58.798 43.478 0.00 0.00 0.00 3.86
2363 3124 4.641541 CCATGATACATTGTGAAGCCAGAA 59.358 41.667 0.00 0.00 0.00 3.02
2364 3125 5.301045 CCATGATACATTGTGAAGCCAGAAT 59.699 40.000 0.00 0.00 36.81 2.40
2367 3128 2.288961 CATTGTGAAGCCAGAATGCC 57.711 50.000 0.00 0.00 43.82 4.40
2368 3129 0.813184 ATTGTGAAGCCAGAATGCCG 59.187 50.000 0.00 0.00 35.29 5.69
2369 3130 0.537143 TTGTGAAGCCAGAATGCCGT 60.537 50.000 0.00 0.00 31.97 5.68
2370 3131 0.323302 TGTGAAGCCAGAATGCCGTA 59.677 50.000 0.00 0.00 31.97 4.02
2371 3132 1.009829 GTGAAGCCAGAATGCCGTAG 58.990 55.000 0.00 0.00 31.97 3.51
2418 3179 3.710233 CGGATATCGCAAACTTCGC 57.290 52.632 0.00 0.00 0.00 4.70
2426 3187 3.762231 GCAAACTTCGCGTCGATAG 57.238 52.632 5.77 0.00 35.23 2.08
2427 3188 0.314339 GCAAACTTCGCGTCGATAGC 60.314 55.000 5.77 5.86 35.23 2.97
2428 3189 1.269166 CAAACTTCGCGTCGATAGCT 58.731 50.000 5.77 0.00 35.23 3.32
2429 3190 2.447250 CAAACTTCGCGTCGATAGCTA 58.553 47.619 5.77 0.00 35.23 3.32
2430 3191 2.102474 AACTTCGCGTCGATAGCTAC 57.898 50.000 5.77 0.00 35.23 3.58
2431 3192 0.307146 ACTTCGCGTCGATAGCTACC 59.693 55.000 5.77 0.00 35.23 3.18
2432 3193 0.306840 CTTCGCGTCGATAGCTACCA 59.693 55.000 5.77 0.00 35.23 3.25
2433 3194 0.949397 TTCGCGTCGATAGCTACCAT 59.051 50.000 5.77 0.00 35.23 3.55
2434 3195 0.516001 TCGCGTCGATAGCTACCATC 59.484 55.000 5.77 0.00 0.00 3.51
2435 3196 0.454620 CGCGTCGATAGCTACCATCC 60.455 60.000 12.78 0.00 0.00 3.51
2436 3197 0.882474 GCGTCGATAGCTACCATCCT 59.118 55.000 0.00 0.00 0.00 3.24
2437 3198 2.082231 GCGTCGATAGCTACCATCCTA 58.918 52.381 0.00 0.00 0.00 2.94
2438 3199 2.486982 GCGTCGATAGCTACCATCCTAA 59.513 50.000 0.00 0.00 0.00 2.69
2439 3200 3.057736 GCGTCGATAGCTACCATCCTAAA 60.058 47.826 0.00 0.00 0.00 1.85
2440 3201 4.558095 GCGTCGATAGCTACCATCCTAAAA 60.558 45.833 0.00 0.00 0.00 1.52
2441 3202 5.710984 CGTCGATAGCTACCATCCTAAAAT 58.289 41.667 0.00 0.00 0.00 1.82
2442 3203 6.157211 CGTCGATAGCTACCATCCTAAAATT 58.843 40.000 0.00 0.00 0.00 1.82
2443 3204 7.310664 CGTCGATAGCTACCATCCTAAAATTA 58.689 38.462 0.00 0.00 0.00 1.40
2444 3205 7.485277 CGTCGATAGCTACCATCCTAAAATTAG 59.515 40.741 0.00 0.00 0.00 1.73
2445 3206 8.305317 GTCGATAGCTACCATCCTAAAATTAGT 58.695 37.037 0.00 0.00 0.00 2.24
2446 3207 8.521176 TCGATAGCTACCATCCTAAAATTAGTC 58.479 37.037 0.00 0.00 0.00 2.59
2447 3208 7.760340 CGATAGCTACCATCCTAAAATTAGTCC 59.240 40.741 0.00 0.00 0.00 3.85
2448 3209 6.824958 AGCTACCATCCTAAAATTAGTCCA 57.175 37.500 0.00 0.00 0.00 4.02
2449 3210 7.208064 AGCTACCATCCTAAAATTAGTCCAA 57.792 36.000 0.00 0.00 0.00 3.53
2450 3211 7.816411 AGCTACCATCCTAAAATTAGTCCAAT 58.184 34.615 0.00 0.00 0.00 3.16
2451 3212 8.945193 AGCTACCATCCTAAAATTAGTCCAATA 58.055 33.333 0.00 0.00 0.00 1.90
2452 3213 9.569122 GCTACCATCCTAAAATTAGTCCAATAA 57.431 33.333 0.00 0.00 0.00 1.40
2456 3217 9.696917 CCATCCTAAAATTAGTCCAATAAATGC 57.303 33.333 0.00 0.00 0.00 3.56
2464 3225 7.722949 ATTAGTCCAATAAATGCATATGGGG 57.277 36.000 16.27 8.72 28.67 4.96
2465 3226 3.834231 AGTCCAATAAATGCATATGGGGC 59.166 43.478 16.27 9.40 32.02 5.80
2466 3227 3.577848 GTCCAATAAATGCATATGGGGCA 59.422 43.478 16.27 0.00 46.66 5.36
2467 3228 4.040217 GTCCAATAAATGCATATGGGGCAA 59.960 41.667 16.27 0.58 45.60 4.52
2468 3229 4.657504 TCCAATAAATGCATATGGGGCAAA 59.342 37.500 16.27 0.30 45.60 3.68
2469 3230 5.131642 TCCAATAAATGCATATGGGGCAAAA 59.868 36.000 16.27 0.00 45.60 2.44
2470 3231 5.826737 CCAATAAATGCATATGGGGCAAAAA 59.173 36.000 0.00 0.00 45.60 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.133294 TCTACCCCGGTCATCATGCTA 60.133 52.381 0.00 0.00 0.00 3.49
125 139 1.465777 TCGTCGTCGAACTTGAGCATA 59.534 47.619 1.37 0.00 43.34 3.14
284 307 2.033141 ACAGTTCATGCTGGCGCT 59.967 55.556 7.64 0.00 40.59 5.92
344 371 3.451556 ATGTCTCAGGCCGGCATCG 62.452 63.158 30.85 16.29 0.00 3.84
354 381 1.593750 GCTAGCGGCCATGTCTCAG 60.594 63.158 2.24 0.00 34.27 3.35
445 482 4.224147 GCCCTATTTTACATTTGGGTTGGT 59.776 41.667 0.00 0.00 37.09 3.67
448 485 3.449377 CCGCCCTATTTTACATTTGGGTT 59.551 43.478 0.00 0.00 37.09 4.11
483 520 3.773418 TTTGTCCATTTAGGTCGACCA 57.227 42.857 35.00 18.83 38.89 4.02
509 546 1.587933 GCGGCCGACCCAAACAAATA 61.588 55.000 33.48 0.00 0.00 1.40
510 547 2.926420 GCGGCCGACCCAAACAAAT 61.926 57.895 33.48 0.00 0.00 2.32
526 563 0.669318 TTAGAGCAACTCCAACGGCG 60.669 55.000 4.80 4.80 0.00 6.46
527 564 1.464997 CTTTAGAGCAACTCCAACGGC 59.535 52.381 0.00 0.00 0.00 5.68
672 754 2.139118 GACACCTGTCTGCTCTTTGTC 58.861 52.381 0.00 0.00 41.65 3.18
673 755 1.202698 GGACACCTGTCTGCTCTTTGT 60.203 52.381 5.44 0.00 44.20 2.83
678 760 2.665603 GGGGACACCTGTCTGCTC 59.334 66.667 5.44 0.00 44.20 4.26
780 894 6.710744 GCGAAAAGGGAGAATTAAGATATGGA 59.289 38.462 0.00 0.00 0.00 3.41
849 1005 1.142748 GTGCCGAGGATGAGGACAG 59.857 63.158 0.00 0.00 0.00 3.51
907 1081 1.672356 GTGGTGCGTGAGGCTTGAT 60.672 57.895 0.00 0.00 44.05 2.57
929 1103 2.195153 TCACTGGATGGATGGATGGA 57.805 50.000 0.00 0.00 0.00 3.41
932 1106 3.266254 GGATGATCACTGGATGGATGGAT 59.734 47.826 0.00 0.00 32.67 3.41
933 1107 2.641321 GGATGATCACTGGATGGATGGA 59.359 50.000 0.00 0.00 32.67 3.41
946 1155 1.606224 CCGCGTGATGATGGATGATCA 60.606 52.381 4.92 0.00 45.43 2.92
965 1174 1.735369 CGCTCTCTCTGTTTCTCTGCC 60.735 57.143 0.00 0.00 0.00 4.85
966 1175 1.627879 CGCTCTCTCTGTTTCTCTGC 58.372 55.000 0.00 0.00 0.00 4.26
967 1176 1.627879 GCGCTCTCTCTGTTTCTCTG 58.372 55.000 0.00 0.00 0.00 3.35
1496 1734 0.744771 GGAGGATGCGTGGGTTTCTC 60.745 60.000 0.00 0.00 0.00 2.87
1581 1824 9.673454 CAGTTAAGACTTTTAATTAACACACCC 57.327 33.333 0.00 0.00 40.32 4.61
1596 1839 7.503902 AGAAAGAAAGGAATGCAGTTAAGACTT 59.496 33.333 0.00 0.00 32.54 3.01
1597 1840 7.001073 AGAAAGAAAGGAATGCAGTTAAGACT 58.999 34.615 0.00 0.00 36.25 3.24
1762 2061 1.070843 CGTTGGTAAACAGCACAGTCG 60.071 52.381 0.00 0.00 35.94 4.18
1788 2543 3.243068 GGACAAAGAATGGACACACACAC 60.243 47.826 0.00 0.00 0.00 3.82
1789 2544 2.948979 GGACAAAGAATGGACACACACA 59.051 45.455 0.00 0.00 0.00 3.72
1810 2567 3.007398 AGAAGACTGTACAAGGAGCAAGG 59.993 47.826 0.00 0.00 0.00 3.61
1870 2630 2.817844 GTGTTGGAGCGACCCTAATTTT 59.182 45.455 0.00 0.00 38.00 1.82
1882 2642 1.514678 TTGATGCACGGTGTTGGAGC 61.515 55.000 10.24 0.00 0.00 4.70
1890 2650 2.642700 GGCGTTTTGATGCACGGT 59.357 55.556 0.00 0.00 36.88 4.83
1904 2664 2.536761 TATCCGAATGTTTAGGGGCG 57.463 50.000 0.00 0.00 0.00 6.13
1905 2665 3.816994 AGTTATCCGAATGTTTAGGGGC 58.183 45.455 0.00 0.00 0.00 5.80
1907 2667 6.704937 GGACTAAGTTATCCGAATGTTTAGGG 59.295 42.308 0.00 0.00 0.00 3.53
1919 2679 5.579564 AGAGTGTTCGGACTAAGTTATCC 57.420 43.478 0.00 2.80 0.00 2.59
1920 2680 6.183360 GCAAAGAGTGTTCGGACTAAGTTATC 60.183 42.308 0.00 0.00 0.00 1.75
1921 2681 5.638234 GCAAAGAGTGTTCGGACTAAGTTAT 59.362 40.000 0.00 0.00 0.00 1.89
1922 2682 4.986659 GCAAAGAGTGTTCGGACTAAGTTA 59.013 41.667 0.00 0.00 0.00 2.24
1923 2683 3.808174 GCAAAGAGTGTTCGGACTAAGTT 59.192 43.478 0.00 0.00 0.00 2.66
1924 2684 3.069729 AGCAAAGAGTGTTCGGACTAAGT 59.930 43.478 0.00 0.00 0.00 2.24
1925 2685 3.430218 CAGCAAAGAGTGTTCGGACTAAG 59.570 47.826 0.00 0.00 0.00 2.18
1926 2686 3.181469 ACAGCAAAGAGTGTTCGGACTAA 60.181 43.478 0.00 0.00 0.00 2.24
1927 2687 2.364324 ACAGCAAAGAGTGTTCGGACTA 59.636 45.455 0.00 0.00 0.00 2.59
1928 2688 1.139058 ACAGCAAAGAGTGTTCGGACT 59.861 47.619 0.00 0.00 0.00 3.85
1929 2689 1.527311 GACAGCAAAGAGTGTTCGGAC 59.473 52.381 0.00 0.00 0.00 4.79
1930 2690 1.412710 AGACAGCAAAGAGTGTTCGGA 59.587 47.619 0.00 0.00 0.00 4.55
1931 2691 1.871080 AGACAGCAAAGAGTGTTCGG 58.129 50.000 0.00 0.00 0.00 4.30
1946 2706 1.982395 CTGGTCCACGGGCTAGACA 60.982 63.158 0.00 0.00 31.99 3.41
1947 2707 1.946475 GACTGGTCCACGGGCTAGAC 61.946 65.000 8.17 0.00 0.00 2.59
1949 2709 2.893398 GACTGGTCCACGGGCTAG 59.107 66.667 0.00 0.00 0.00 3.42
1958 2719 2.178912 TCAAACATTCGGACTGGTCC 57.821 50.000 9.55 9.55 46.18 4.46
1968 2729 5.102313 CGCTTTAGGGGAATTCAAACATTC 58.898 41.667 7.93 0.00 33.04 2.67
1969 2730 4.770010 TCGCTTTAGGGGAATTCAAACATT 59.230 37.500 7.93 0.00 33.87 2.71
1971 2732 3.757270 TCGCTTTAGGGGAATTCAAACA 58.243 40.909 7.93 0.00 33.87 2.83
1974 2735 4.830600 AGTTTTCGCTTTAGGGGAATTCAA 59.169 37.500 7.93 0.00 44.41 2.69
1976 2737 5.161358 CAAGTTTTCGCTTTAGGGGAATTC 58.839 41.667 0.00 0.00 44.41 2.17
1981 2742 2.030274 CCACAAGTTTTCGCTTTAGGGG 60.030 50.000 0.00 0.00 0.00 4.79
1984 2745 3.058224 CCTCCCACAAGTTTTCGCTTTAG 60.058 47.826 0.00 0.00 0.00 1.85
1985 2746 2.882137 CCTCCCACAAGTTTTCGCTTTA 59.118 45.455 0.00 0.00 0.00 1.85
1989 2750 1.029681 AACCTCCCACAAGTTTTCGC 58.970 50.000 0.00 0.00 0.00 4.70
2340 3101 4.201657 TCTGGCTTCACAATGTATCATGG 58.798 43.478 0.00 0.00 0.00 3.66
2341 3102 5.823209 TTCTGGCTTCACAATGTATCATG 57.177 39.130 0.00 0.00 0.00 3.07
2342 3103 5.221185 GCATTCTGGCTTCACAATGTATCAT 60.221 40.000 0.00 0.00 31.97 2.45
2343 3104 4.096833 GCATTCTGGCTTCACAATGTATCA 59.903 41.667 0.00 0.00 31.97 2.15
2344 3105 4.498682 GGCATTCTGGCTTCACAATGTATC 60.499 45.833 0.00 0.00 40.14 2.24
2345 3106 3.382546 GGCATTCTGGCTTCACAATGTAT 59.617 43.478 0.00 0.00 40.14 2.29
2346 3107 2.754552 GGCATTCTGGCTTCACAATGTA 59.245 45.455 0.00 0.00 40.14 2.29
2347 3108 1.547372 GGCATTCTGGCTTCACAATGT 59.453 47.619 0.00 0.00 40.14 2.71
2348 3109 1.468565 CGGCATTCTGGCTTCACAATG 60.469 52.381 0.00 0.00 41.25 2.82
2349 3110 0.813184 CGGCATTCTGGCTTCACAAT 59.187 50.000 0.00 0.00 41.25 2.71
2350 3111 0.537143 ACGGCATTCTGGCTTCACAA 60.537 50.000 0.00 0.00 41.25 3.33
2351 3112 0.323302 TACGGCATTCTGGCTTCACA 59.677 50.000 0.00 0.00 41.25 3.58
2352 3113 1.009829 CTACGGCATTCTGGCTTCAC 58.990 55.000 0.00 0.00 41.25 3.18
2353 3114 0.107703 CCTACGGCATTCTGGCTTCA 60.108 55.000 0.00 0.00 41.25 3.02
2354 3115 0.815615 CCCTACGGCATTCTGGCTTC 60.816 60.000 0.00 0.00 41.25 3.86
2355 3116 1.224592 CCCTACGGCATTCTGGCTT 59.775 57.895 0.00 0.00 41.25 4.35
2356 3117 2.911143 CCCTACGGCATTCTGGCT 59.089 61.111 0.00 0.00 41.25 4.75
2400 3161 3.710233 GCGAAGTTTGCGATATCCG 57.290 52.632 0.00 0.00 42.21 4.18
2408 3169 0.314339 GCTATCGACGCGAAGTTTGC 60.314 55.000 15.93 9.93 39.99 3.68
2409 3170 1.269166 AGCTATCGACGCGAAGTTTG 58.731 50.000 15.93 3.55 39.99 2.93
2410 3171 2.448219 GTAGCTATCGACGCGAAGTTT 58.552 47.619 15.93 0.00 39.99 2.66
2411 3172 1.268437 GGTAGCTATCGACGCGAAGTT 60.268 52.381 15.93 3.64 39.99 2.66
2412 3173 0.307146 GGTAGCTATCGACGCGAAGT 59.693 55.000 15.93 0.00 39.99 3.01
2413 3174 0.306840 TGGTAGCTATCGACGCGAAG 59.693 55.000 15.93 6.11 39.99 3.79
2414 3175 0.949397 ATGGTAGCTATCGACGCGAA 59.051 50.000 15.93 0.00 39.99 4.70
2415 3176 0.516001 GATGGTAGCTATCGACGCGA 59.484 55.000 15.93 4.51 41.13 5.87
2416 3177 0.454620 GGATGGTAGCTATCGACGCG 60.455 60.000 3.53 3.53 0.00 6.01
2417 3178 0.882474 AGGATGGTAGCTATCGACGC 59.118 55.000 0.00 0.48 0.00 5.19
2418 3179 4.761235 TTTAGGATGGTAGCTATCGACG 57.239 45.455 0.00 0.00 0.00 5.12
2419 3180 8.305317 ACTAATTTTAGGATGGTAGCTATCGAC 58.695 37.037 0.00 0.00 35.08 4.20
2420 3181 8.418597 ACTAATTTTAGGATGGTAGCTATCGA 57.581 34.615 0.00 0.00 35.08 3.59
2421 3182 7.760340 GGACTAATTTTAGGATGGTAGCTATCG 59.240 40.741 0.00 0.00 35.08 2.92
2422 3183 8.594550 TGGACTAATTTTAGGATGGTAGCTATC 58.405 37.037 0.00 0.00 35.08 2.08
2423 3184 8.506196 TGGACTAATTTTAGGATGGTAGCTAT 57.494 34.615 0.00 0.00 35.08 2.97
2424 3185 7.924358 TGGACTAATTTTAGGATGGTAGCTA 57.076 36.000 0.00 0.00 35.08 3.32
2425 3186 6.824958 TGGACTAATTTTAGGATGGTAGCT 57.175 37.500 0.00 0.00 35.08 3.32
2426 3187 9.569122 TTATTGGACTAATTTTAGGATGGTAGC 57.431 33.333 2.63 0.00 35.08 3.58
2430 3191 9.696917 GCATTTATTGGACTAATTTTAGGATGG 57.303 33.333 2.63 0.00 35.08 3.51
2438 3199 8.596293 CCCCATATGCATTTATTGGACTAATTT 58.404 33.333 3.54 0.00 0.00 1.82
2439 3200 7.310609 GCCCCATATGCATTTATTGGACTAATT 60.311 37.037 3.54 0.00 0.00 1.40
2440 3201 6.155049 GCCCCATATGCATTTATTGGACTAAT 59.845 38.462 3.54 0.00 0.00 1.73
2441 3202 5.480073 GCCCCATATGCATTTATTGGACTAA 59.520 40.000 3.54 0.00 0.00 2.24
2442 3203 5.016173 GCCCCATATGCATTTATTGGACTA 58.984 41.667 3.54 0.00 0.00 2.59
2443 3204 3.834231 GCCCCATATGCATTTATTGGACT 59.166 43.478 3.54 0.00 0.00 3.85
2444 3205 3.577848 TGCCCCATATGCATTTATTGGAC 59.422 43.478 3.54 4.51 32.85 4.02
2445 3206 3.854437 TGCCCCATATGCATTTATTGGA 58.146 40.909 3.54 0.00 32.85 3.53
2446 3207 4.620589 TTGCCCCATATGCATTTATTGG 57.379 40.909 3.54 7.55 38.76 3.16
2447 3208 6.939132 TTTTTGCCCCATATGCATTTATTG 57.061 33.333 3.54 0.00 38.76 1.90
2470 3231 9.525826 AGAGTTCCTCAACTAAATTCAATGATT 57.474 29.630 0.00 0.00 43.37 2.57
2471 3232 9.525826 AAGAGTTCCTCAACTAAATTCAATGAT 57.474 29.630 0.00 0.00 43.37 2.45
2472 3233 8.924511 AAGAGTTCCTCAACTAAATTCAATGA 57.075 30.769 0.00 0.00 43.37 2.57


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

AutoCloner maintained by Alex Coulton.