Multiple sequence alignment - TraesCS7B01G354900

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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 TraesCS7B01G354900 chr7B 100.000 3699 0 0 1778 5476 613256073 613252375 0.000000e+00 6831.0
1 TraesCS7B01G354900 chr7B 93.340 2928 174 14 2560 5476 613239388 613236471 0.000000e+00 4307.0
2 TraesCS7B01G354900 chr7B 100.000 1531 0 0 1 1531 613257850 613256320 0.000000e+00 2828.0
3 TraesCS7B01G354900 chr7B 89.630 810 57 7 1778 2562 613240472 613239665 0.000000e+00 1005.0
4 TraesCS7B01G354900 chr7B 80.996 542 85 5 3449 3972 613177354 613176813 1.100000e-111 414.0
5 TraesCS7B01G354900 chr7B 88.438 320 13 6 1232 1531 613240881 613240566 1.120000e-96 364.0
6 TraesCS7B01G354900 chr7B 79.452 438 53 19 4339 4744 613176739 613176307 5.400000e-70 276.0
7 TraesCS7B01G354900 chr7B 76.169 449 66 20 4335 4744 613151038 613150592 1.200000e-46 198.0
8 TraesCS7B01G354900 chr7D 92.169 3729 234 29 1778 5476 563665640 563661940 0.000000e+00 5216.0
9 TraesCS7B01G354900 chr7D 90.052 965 37 16 623 1531 563666695 563665734 0.000000e+00 1195.0
10 TraesCS7B01G354900 chr7D 92.076 631 36 9 1 626 563667355 563666734 0.000000e+00 876.0
11 TraesCS7B01G354900 chr7D 78.947 513 59 24 4276 4744 563526997 563526490 2.480000e-78 303.0
12 TraesCS7B01G354900 chr7D 80.357 392 62 9 3563 3939 563480029 563479638 3.230000e-72 283.0
13 TraesCS7B01G354900 chrUn 92.186 1203 86 6 2560 3759 332850979 332849782 0.000000e+00 1694.0
14 TraesCS7B01G354900 chrUn 89.630 810 57 7 1778 2562 332852063 332851256 0.000000e+00 1005.0
15 TraesCS7B01G354900 chrUn 86.115 641 33 14 623 1238 455429199 455429808 1.660000e-179 640.0
16 TraesCS7B01G354900 chrUn 88.438 320 13 6 1232 1531 332852472 332852157 1.120000e-96 364.0
17 TraesCS7B01G354900 chr7A 87.075 1176 129 15 2813 3980 649152282 649151122 0.000000e+00 1308.0
18 TraesCS7B01G354900 chr7A 86.814 857 80 19 4093 4929 649151001 649150158 0.000000e+00 926.0
19 TraesCS7B01G354900 chr7A 85.019 514 75 2 3478 3990 649185971 649185459 6.290000e-144 521.0
20 TraesCS7B01G354900 chr7A 81.722 662 58 29 836 1455 649154320 649153680 1.370000e-135 494.0
21 TraesCS7B01G354900 chr7A 80.374 535 82 11 3454 3966 649072716 649072183 8.600000e-103 385.0
22 TraesCS7B01G354900 chr7A 82.284 429 59 14 110 532 18972503 18972086 6.750000e-94 355.0
23 TraesCS7B01G354900 chr7A 78.834 463 87 5 2861 3315 649187227 649186768 8.910000e-78 302.0
24 TraesCS7B01G354900 chr7A 79.009 424 61 16 4340 4744 649072090 649071676 1.170000e-66 265.0
25 TraesCS7B01G354900 chr7A 76.803 513 68 24 4279 4744 649059723 649059215 1.970000e-59 241.0
26 TraesCS7B01G354900 chr7A 75.822 517 65 31 1016 1488 649194783 649194283 2.000000e-49 207.0
27 TraesCS7B01G354900 chr7A 89.908 109 7 3 2055 2161 112799860 112799754 2.660000e-28 137.0
28 TraesCS7B01G354900 chr7A 88.991 109 8 3 2055 2161 112776979 112776873 1.240000e-26 132.0
29 TraesCS7B01G354900 chr7A 88.393 112 9 3 2052 2161 112786244 112786353 1.240000e-26 132.0
30 TraesCS7B01G354900 chr7A 88.571 105 12 0 1914 2018 649153253 649153149 1.600000e-25 128.0
31 TraesCS7B01G354900 chr7A 84.426 122 12 4 2155 2274 649153147 649153031 4.480000e-21 113.0
32 TraesCS7B01G354900 chr7A 88.889 63 7 0 1275 1337 649074197 649074135 1.640000e-10 78.7
33 TraesCS7B01G354900 chr3D 85.036 421 47 15 110 529 548716553 548716148 1.100000e-111 414.0
34 TraesCS7B01G354900 chr3D 83.527 431 48 18 110 531 318514057 318513641 1.110000e-101 381.0
35 TraesCS7B01G354900 chr3D 83.095 420 55 13 110 525 384530740 384530333 8.670000e-98 368.0
36 TraesCS7B01G354900 chr3D 93.750 96 6 0 3664 3759 304328659 304328564 1.590000e-30 145.0
37 TraesCS7B01G354900 chr3D 90.385 104 10 0 2053 2156 108210733 108210836 2.660000e-28 137.0
38 TraesCS7B01G354900 chr4D 87.052 363 33 11 110 470 215457750 215458100 1.110000e-106 398.0
39 TraesCS7B01G354900 chr4D 81.986 433 54 17 108 532 484685177 484684761 4.060000e-91 346.0
40 TraesCS7B01G354900 chr1A 85.479 365 37 15 110 470 212016339 212016691 3.120000e-97 366.0
41 TraesCS7B01G354900 chr3A 82.448 433 53 18 110 532 408023233 408023652 1.880000e-94 357.0
42 TraesCS7B01G354900 chr3A 100.000 28 0 0 3304 3331 130587280 130587253 1.000000e-02 52.8
43 TraesCS7B01G354900 chr3B 77.015 335 42 21 3664 3972 417264818 417265143 5.680000e-35 159.0
44 TraesCS7B01G354900 chr4B 91.262 103 9 0 2060 2162 664775714 664775612 2.060000e-29 141.0
45 TraesCS7B01G354900 chr4B 75.540 139 25 9 2554 2688 352333521 352333654 5.920000e-05 60.2
46 TraesCS7B01G354900 chr1D 91.089 101 9 0 2056 2156 420554538 420554638 2.660000e-28 137.0
47 TraesCS7B01G354900 chr1D 88.288 111 10 2 2060 2167 490538212 490538102 4.450000e-26 130.0
48 TraesCS7B01G354900 chr1D 95.000 40 2 0 3294 3333 21659842 21659881 4.580000e-06 63.9
49 TraesCS7B01G354900 chr5B 89.091 110 10 2 2057 2166 551407196 551407089 9.570000e-28 135.0
50 TraesCS7B01G354900 chr1B 89.720 107 9 2 2053 2158 572529352 572529457 9.570000e-28 135.0
51 TraesCS7B01G354900 chr6D 88.696 115 6 6 2059 2172 422327410 422327518 3.440000e-27 134.0
52 TraesCS7B01G354900 chr6A 89.024 82 9 0 3250 3331 602434266 602434347 9.700000e-18 102.0
53 TraesCS7B01G354900 chr6A 75.714 140 25 8 2554 2688 255385480 255385345 1.650000e-05 62.1
54 TraesCS7B01G354900 chr6A 75.714 140 25 8 2554 2688 255445706 255445571 1.650000e-05 62.1
55 TraesCS7B01G354900 chr2B 83.333 90 9 6 3250 3335 548123678 548123765 1.640000e-10 78.7
56 TraesCS7B01G354900 chr4A 76.866 134 22 8 2560 2688 557008837 557008708 3.540000e-07 67.6
57 TraesCS7B01G354900 chr4A 76.119 134 23 8 2560 2688 565149682 565149553 1.650000e-05 62.1
58 TraesCS7B01G354900 chr4A 92.308 39 3 0 3284 3322 634423175 634423213 7.660000e-04 56.5
59 TraesCS7B01G354900 chr4A 92.308 39 3 0 3284 3322 634455444 634455482 7.660000e-04 56.5
60 TraesCS7B01G354900 chr5D 76.119 134 23 8 2560 2688 260383380 260383251 1.650000e-05 62.1


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 TraesCS7B01G354900 chr7B 613252375 613257850 5475 True 4829.5 6831 100.000000 1 5476 2 chr7B.!!$R4 5475
1 TraesCS7B01G354900 chr7B 613236471 613240881 4410 True 1892.0 4307 90.469333 1232 5476 3 chr7B.!!$R3 4244
2 TraesCS7B01G354900 chr7B 613176307 613177354 1047 True 345.0 414 80.224000 3449 4744 2 chr7B.!!$R2 1295
3 TraesCS7B01G354900 chr7D 563661940 563667355 5415 True 2429.0 5216 91.432333 1 5476 3 chr7D.!!$R3 5475
4 TraesCS7B01G354900 chr7D 563526490 563526997 507 True 303.0 303 78.947000 4276 4744 1 chr7D.!!$R2 468
5 TraesCS7B01G354900 chrUn 332849782 332852472 2690 True 1021.0 1694 90.084667 1232 3759 3 chrUn.!!$R1 2527
6 TraesCS7B01G354900 chrUn 455429199 455429808 609 False 640.0 640 86.115000 623 1238 1 chrUn.!!$F1 615
7 TraesCS7B01G354900 chr7A 649150158 649154320 4162 True 593.8 1308 85.721600 836 4929 5 chr7A.!!$R7 4093
8 TraesCS7B01G354900 chr7A 649185459 649187227 1768 True 411.5 521 81.926500 2861 3990 2 chr7A.!!$R8 1129
9 TraesCS7B01G354900 chr7A 649071676 649074197 2521 True 242.9 385 82.757333 1275 4744 3 chr7A.!!$R6 3469
10 TraesCS7B01G354900 chr7A 649059215 649059723 508 True 241.0 241 76.803000 4279 4744 1 chr7A.!!$R4 465
11 TraesCS7B01G354900 chr7A 649194283 649194783 500 True 207.0 207 75.822000 1016 1488 1 chr7A.!!$R5 472

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
737 786 0.529773 GTACTGATTGATCCGCGCCA 60.530 55.0 0.0 0.0 0.00 5.69 F
1455 1628 0.802494 GGCCACCAATAGTGTGTTCG 59.198 55.0 0.0 0.0 45.74 3.95 F
2543 2929 0.106719 CGTGCTTGGGATGGGGTAAT 60.107 55.0 0.0 0.0 0.00 1.89 F
3715 5510 0.610232 GCTGTGGTGGAATCAAGGCT 60.610 55.0 0.0 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2257 0.716108 GTACTGCACATGTGAGTCGC 59.284 55.0 29.8 13.96 0.0 5.19 R
2743 3667 0.247537 CCGTATGTTCGCCGCTTTTC 60.248 55.0 0.0 0.00 0.0 2.29 R
3850 5661 0.619255 TGGCCGAGAACCCAATCCTA 60.619 55.0 0.0 0.00 0.0 2.94 R
5389 7307 0.462789 TTTCTCTTATCCGTCCCCGC 59.537 55.0 0.0 0.00 0.0 6.13 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
43 44 9.782028 CAATACAATTTTCAATCTTCAACAACG 57.218 29.630 0.00 0.00 0.00 4.10
46 47 4.993029 TTTTCAATCTTCAACAACGGGT 57.007 36.364 0.00 0.00 0.00 5.28
49 50 2.616376 TCAATCTTCAACAACGGGTGTG 59.384 45.455 0.00 0.00 40.60 3.82
54 55 0.665835 TCAACAACGGGTGTGCAATC 59.334 50.000 0.00 0.00 40.60 2.67
127 128 2.068519 GAAAATTGCTTTTGGAGGCCG 58.931 47.619 0.00 0.00 34.73 6.13
159 160 2.001872 GGCCTCCAAATGCAAAATTCG 58.998 47.619 0.00 0.00 0.00 3.34
262 267 7.057894 AGTGTGTAAACTTTCAGGACCAAATA 58.942 34.615 0.00 0.00 0.00 1.40
267 272 5.684550 AACTTTCAGGACCAAATACGTTC 57.315 39.130 0.00 0.00 0.00 3.95
274 279 5.180492 TCAGGACCAAATACGTTCAAATGAC 59.820 40.000 0.00 0.00 0.00 3.06
275 280 4.457949 AGGACCAAATACGTTCAAATGACC 59.542 41.667 0.00 0.00 0.00 4.02
283 288 1.334599 CGTTCAAATGACCGGTTGTGG 60.335 52.381 9.42 0.00 0.00 4.17
317 322 5.234116 ACAAATTTGAGGCTTTTTAACGCAG 59.766 36.000 24.64 0.00 0.00 5.18
337 342 1.817447 GGATACTATTCGTCCTCCCGG 59.183 57.143 0.00 0.00 0.00 5.73
361 367 7.863375 CGGACCATTAATTTGTCTTTTTGTACA 59.137 33.333 12.36 0.00 0.00 2.90
365 371 9.541143 CCATTAATTTGTCTTTTTGTACAGGTT 57.459 29.630 0.00 0.00 0.00 3.50
437 443 8.349245 TCACATCCTTGTTTACTTGTACAATTG 58.651 33.333 9.13 3.24 34.10 2.32
438 444 8.134895 CACATCCTTGTTTACTTGTACAATTGT 58.865 33.333 16.68 16.68 34.10 2.71
543 549 2.362077 GCCGTACTCGACCCCTATAAAA 59.638 50.000 0.00 0.00 39.71 1.52
544 550 3.551659 GCCGTACTCGACCCCTATAAAAG 60.552 52.174 0.00 0.00 39.71 2.27
598 604 8.963725 TGAAGATTAGAAGGTACGTCTTCAATA 58.036 33.333 16.64 4.66 46.91 1.90
656 704 7.752695 AGCCTTTTTAAGTGACATTAAGATCG 58.247 34.615 0.00 0.00 0.00 3.69
658 706 7.692705 GCCTTTTTAAGTGACATTAAGATCGAC 59.307 37.037 0.00 0.00 0.00 4.20
659 707 8.717821 CCTTTTTAAGTGACATTAAGATCGACA 58.282 33.333 0.00 0.00 0.00 4.35
667 715 7.010023 GTGACATTAAGATCGACACAAACTTC 58.990 38.462 0.00 0.00 0.00 3.01
698 746 3.558418 TGTACGGAAGCAAAACTCTGTTC 59.442 43.478 0.00 0.00 0.00 3.18
737 786 0.529773 GTACTGATTGATCCGCGCCA 60.530 55.000 0.00 0.00 0.00 5.69
751 800 3.380004 TCCGCGCCAAATTATTCTTTCAT 59.620 39.130 0.00 0.00 0.00 2.57
829 878 5.659079 TCTCCTAAAAGAATCTCCACTCTCC 59.341 44.000 0.00 0.00 0.00 3.71
832 881 4.835284 AAAAGAATCTCCACTCTCCTCC 57.165 45.455 0.00 0.00 0.00 4.30
833 882 3.774842 AAGAATCTCCACTCTCCTCCT 57.225 47.619 0.00 0.00 0.00 3.69
871 944 7.062749 ACGGGCTTAGTATAATCTGATCAAA 57.937 36.000 0.00 0.00 0.00 2.69
1122 1205 1.150135 TCCTCCTCCTCTTCAACCACT 59.850 52.381 0.00 0.00 0.00 4.00
1195 1290 3.215975 ACCGAGGTCTATGAGTAAGCTC 58.784 50.000 0.00 0.00 41.97 4.09
1205 1300 4.528076 ATGAGTAAGCTCCCACTCTCTA 57.472 45.455 18.52 5.00 41.46 2.43
1213 1308 2.676748 CTCCCACTCTCTAATCCTGCT 58.323 52.381 0.00 0.00 0.00 4.24
1228 1323 2.967887 TCCTGCTGCTATGCTTGAGATA 59.032 45.455 0.00 0.00 0.00 1.98
1229 1324 3.581770 TCCTGCTGCTATGCTTGAGATAT 59.418 43.478 0.00 0.00 0.00 1.63
1339 1463 1.648504 GAACCCACGGTATGTACTGC 58.351 55.000 0.00 0.00 33.12 4.40
1364 1507 3.786450 CCCCCTACATTTCTCTTTAGGGT 59.214 47.826 10.89 0.00 46.76 4.34
1367 1510 6.354938 CCCCTACATTTCTCTTTAGGGTTAC 58.645 44.000 10.89 0.00 46.76 2.50
1441 1587 3.134127 GTCGGGAAGCATGGCCAC 61.134 66.667 8.16 0.00 0.00 5.01
1455 1628 0.802494 GGCCACCAATAGTGTGTTCG 59.198 55.000 0.00 0.00 45.74 3.95
1484 1658 7.251321 AGATTTGGTGATTCTCTCTTACTGT 57.749 36.000 0.00 0.00 0.00 3.55
1519 1693 1.144969 GCAGTACTTGCGCAGTTGTA 58.855 50.000 11.31 12.65 44.09 2.41
1821 2071 3.009723 CGACCACTTGTCCTAATTGCAT 58.990 45.455 0.00 0.00 41.18 3.96
1925 2257 5.770162 GGGTAATCTTCCATTGGATTGGTAG 59.230 44.000 6.15 0.39 38.01 3.18
2072 2411 4.660168 TCTATTATGTACTCCCTCCGTCC 58.340 47.826 0.00 0.00 0.00 4.79
2091 2430 5.183140 CCGTCCCAAAATAAGTGTCTCAATT 59.817 40.000 0.00 0.00 0.00 2.32
2223 2563 7.663827 TGTATTATGAATAGATCGAAACCCGT 58.336 34.615 0.00 0.00 39.75 5.28
2292 2632 3.243301 GGCATAACATGATTGAGCAGTGG 60.243 47.826 0.00 0.00 0.00 4.00
2332 2672 2.034066 CCCGGCCACAGTCATGTT 59.966 61.111 2.24 0.00 37.65 2.71
2371 2754 0.755686 GATCTAGACTGGGCCCACAG 59.244 60.000 24.45 16.00 44.03 3.66
2372 2755 0.339859 ATCTAGACTGGGCCCACAGA 59.660 55.000 24.45 20.50 40.97 3.41
2373 2756 0.614979 TCTAGACTGGGCCCACAGAC 60.615 60.000 24.45 13.27 40.97 3.51
2374 2757 1.612442 TAGACTGGGCCCACAGACC 60.612 63.158 24.45 10.02 40.97 3.85
2375 2758 2.395180 TAGACTGGGCCCACAGACCA 62.395 60.000 24.45 0.00 40.97 4.02
2383 2766 1.271926 GGCCCACAGACCAACATTAGT 60.272 52.381 0.00 0.00 0.00 2.24
2509 2895 1.676529 TCGTAAGCTCATCTCCGAAGG 59.323 52.381 0.00 0.00 46.03 3.46
2543 2929 0.106719 CGTGCTTGGGATGGGGTAAT 60.107 55.000 0.00 0.00 0.00 1.89
2545 2931 2.031870 GTGCTTGGGATGGGGTAATTC 58.968 52.381 0.00 0.00 0.00 2.17
2549 2935 3.691020 GCTTGGGATGGGGTAATTCATGA 60.691 47.826 0.00 0.00 0.00 3.07
2567 3232 5.853936 TCATGACGTCCTGATTTAATAGGG 58.146 41.667 18.12 0.00 34.76 3.53
2632 3299 5.344743 AAGCTCGTCTCCAATGAATCTAA 57.655 39.130 0.00 0.00 0.00 2.10
2702 3626 1.778383 AAGTGGGGCAGAAGGGGAA 60.778 57.895 0.00 0.00 0.00 3.97
2743 3667 0.806102 CATACCGTGCGAGGTGGAAG 60.806 60.000 12.54 0.00 45.54 3.46
2790 3714 1.177401 GGTTTCATCCAACAGCCCTC 58.823 55.000 0.00 0.00 0.00 4.30
2899 3973 4.641989 TGCTTTGCTTGTCTTTCTTTCTCT 59.358 37.500 0.00 0.00 0.00 3.10
2904 3978 3.248602 GCTTGTCTTTCTTTCTCTTCGCA 59.751 43.478 0.00 0.00 0.00 5.10
2916 4000 6.824196 TCTTTCTCTTCGCATCTCTACTCTTA 59.176 38.462 0.00 0.00 0.00 2.10
3027 4118 1.134694 GCAAAGCTACGCCGGAAAG 59.865 57.895 5.05 0.00 0.00 2.62
3036 4127 0.899720 ACGCCGGAAAGGTCTATTCA 59.100 50.000 5.05 0.00 43.70 2.57
3093 4185 7.814264 ATCCCTCTTTACATAGCATTTTGAG 57.186 36.000 0.00 0.00 0.00 3.02
3167 4267 1.006813 TATGGGTGCCCCTTGACAAT 58.993 50.000 11.10 0.00 45.70 2.71
3359 4740 9.361315 TGATATCAGCACATGAAAAATTTCTTG 57.639 29.630 16.00 16.00 42.53 3.02
3652 5447 3.525619 GGCCATCGAATATGCCGTA 57.474 52.632 0.00 0.00 33.59 4.02
3715 5510 0.610232 GCTGTGGTGGAATCAAGGCT 60.610 55.000 0.00 0.00 0.00 4.58
3759 5554 4.217118 GGAAGACGACTCCTTGTAAGTACA 59.783 45.833 0.00 0.00 0.00 2.90
3763 5558 6.179040 AGACGACTCCTTGTAAGTACATAGT 58.821 40.000 0.00 0.00 35.89 2.12
3774 5582 9.307121 CTTGTAAGTACATAGTTTGGATCTGAG 57.693 37.037 0.00 0.00 35.89 3.35
3850 5661 1.129058 ACTTCGTTGAGGACTGGGTT 58.871 50.000 0.00 0.00 0.00 4.11
3939 5750 1.133915 TGCCGTCTTGGAAAAGGTTCT 60.134 47.619 0.00 0.00 42.00 3.01
3998 5813 9.204570 ACTTTACTTGCTTATGTAGTGTTGTAG 57.795 33.333 0.00 0.00 0.00 2.74
4080 5928 2.349155 CGACCAAGCGTGTAGGAAAAAC 60.349 50.000 0.00 0.00 0.00 2.43
4086 5934 5.390613 CAAGCGTGTAGGAAAAACTATTGG 58.609 41.667 0.00 0.00 0.00 3.16
4088 5936 3.726782 GCGTGTAGGAAAAACTATTGGCG 60.727 47.826 0.00 0.00 0.00 5.69
4226 6089 6.861055 TCTTACATGCGAAAGAAAAATCAACC 59.139 34.615 0.00 0.00 0.00 3.77
4227 6090 5.200368 ACATGCGAAAGAAAAATCAACCT 57.800 34.783 0.00 0.00 0.00 3.50
4318 6181 6.833346 TTAACTCCCTGAGAGAGAGATCTA 57.167 41.667 0.00 0.00 46.50 1.98
4406 6280 1.077265 CAAGGAGGGTGTGGCCAAT 59.923 57.895 7.24 0.00 39.65 3.16
4421 6295 1.340991 GCCAATGGAACCCTCAAGCTA 60.341 52.381 2.05 0.00 0.00 3.32
4492 6366 4.385754 GCTGTAAATCAATCTTCCCTCCCT 60.386 45.833 0.00 0.00 0.00 4.20
4503 6377 0.250727 TCCCTCCCTTTGCTCAAACG 60.251 55.000 0.00 0.00 0.00 3.60
4596 6503 5.428253 GTTATTCTCCAGTAGTGAATGCCA 58.572 41.667 0.00 0.00 38.73 4.92
4749 6663 6.968131 TCATCAAGAGTTTACCTTTCGATG 57.032 37.500 0.00 0.00 31.08 3.84
4805 6719 0.675083 TGTTTGCACCTCCATTGCTG 59.325 50.000 0.00 0.00 40.86 4.41
4869 6783 0.605319 CGGCTTTCTGTGCTACCCAA 60.605 55.000 0.00 0.00 0.00 4.12
4964 6882 6.744175 AGATGAGGAGATTGAGCTTTATCA 57.256 37.500 10.51 0.00 0.00 2.15
5058 6976 0.108424 CTCCCGAGAGAACCAAGCAG 60.108 60.000 0.00 0.00 43.39 4.24
5224 7142 3.078594 GTGAATGCTCACCGTTGTTTT 57.921 42.857 0.00 0.00 45.41 2.43
5235 7153 2.224784 ACCGTTGTTTTCCGTTGATAGC 59.775 45.455 0.00 0.00 0.00 2.97
5245 7163 3.562182 TCCGTTGATAGCTATGGTGAGA 58.438 45.455 11.94 0.00 0.00 3.27
5273 7191 0.107703 TGCCTCCCTTGCTTCATACG 60.108 55.000 0.00 0.00 0.00 3.06
5356 7274 0.594796 CGACCACCTTTTTGCACAGC 60.595 55.000 0.00 0.00 0.00 4.40
5414 7334 4.202020 GGGGACGGATAAGAGAAATTTTGC 60.202 45.833 0.00 0.00 0.00 3.68
5442 7369 6.319911 TGCATAGCGAGCTAGATCATAACTAT 59.680 38.462 8.99 6.44 31.45 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.598493 CCCGTTGTTGAAGATTGAAAATTGTAT 59.402 33.333 0.00 0.00 0.00 2.29
34 35 1.066303 GATTGCACACCCGTTGTTGAA 59.934 47.619 0.00 0.00 35.67 2.69
35 36 0.665835 GATTGCACACCCGTTGTTGA 59.334 50.000 0.00 0.00 35.67 3.18
42 43 1.522668 TTTCTCTGATTGCACACCCG 58.477 50.000 0.00 0.00 0.00 5.28
88 89 2.400399 TCTCGTTGTACCGAAGCAAAG 58.600 47.619 0.00 0.00 36.24 2.77
127 128 2.828145 GAGGCCTCCATGGAGCTC 59.172 66.667 32.97 28.38 40.69 4.09
267 272 0.387202 TTGCCACAACCGGTCATTTG 59.613 50.000 8.04 4.67 0.00 2.32
291 296 5.901336 GCGTTAAAAAGCCTCAAATTTGTTG 59.099 36.000 17.47 10.90 0.00 3.33
292 297 5.582665 TGCGTTAAAAAGCCTCAAATTTGTT 59.417 32.000 17.47 5.74 32.21 2.83
294 299 5.333263 CCTGCGTTAAAAAGCCTCAAATTTG 60.333 40.000 12.15 12.15 32.21 2.32
295 300 4.749598 CCTGCGTTAAAAAGCCTCAAATTT 59.250 37.500 0.00 0.00 32.21 1.82
296 301 4.038642 TCCTGCGTTAAAAAGCCTCAAATT 59.961 37.500 0.00 0.00 32.21 1.82
297 302 3.572255 TCCTGCGTTAAAAAGCCTCAAAT 59.428 39.130 0.00 0.00 32.21 2.32
299 304 2.577700 TCCTGCGTTAAAAAGCCTCAA 58.422 42.857 0.00 0.00 32.21 3.02
300 305 2.264005 TCCTGCGTTAAAAAGCCTCA 57.736 45.000 0.00 0.00 32.21 3.86
301 306 3.939592 AGTATCCTGCGTTAAAAAGCCTC 59.060 43.478 0.00 0.00 32.21 4.70
334 339 6.220201 ACAAAAAGACAAATTAATGGTCCGG 58.780 36.000 13.90 0.00 31.99 5.14
336 341 9.191995 CTGTACAAAAAGACAAATTAATGGTCC 57.808 33.333 13.90 0.00 31.99 4.46
337 342 9.191995 CCTGTACAAAAAGACAAATTAATGGTC 57.808 33.333 10.91 10.91 0.00 4.02
361 367 6.266168 TGAAATACGATTGAAATGCAACCT 57.734 33.333 0.00 0.00 39.78 3.50
365 371 6.318396 TCAGGATGAAATACGATTGAAATGCA 59.682 34.615 0.00 0.00 45.97 3.96
366 372 6.728200 TCAGGATGAAATACGATTGAAATGC 58.272 36.000 0.00 0.00 45.97 3.56
397 403 4.529897 AGGATGTGACGTGTATAGGTGTA 58.470 43.478 0.00 0.00 0.00 2.90
398 404 3.362706 AGGATGTGACGTGTATAGGTGT 58.637 45.455 0.00 0.00 0.00 4.16
400 406 3.767673 ACAAGGATGTGACGTGTATAGGT 59.232 43.478 0.00 0.00 38.69 3.08
481 487 2.524306 TGGAGGCCGAATGTTTGAAAT 58.476 42.857 0.00 0.00 0.00 2.17
613 619 6.851222 AAGGCTATCATCATACAAAAGACG 57.149 37.500 0.00 0.00 0.00 4.18
656 704 3.146847 CACCCCCTTAGAAGTTTGTGTC 58.853 50.000 0.00 0.00 0.00 3.67
658 706 3.223674 ACACCCCCTTAGAAGTTTGTG 57.776 47.619 0.00 0.00 0.00 3.33
659 707 3.244318 CGTACACCCCCTTAGAAGTTTGT 60.244 47.826 0.00 0.00 0.00 2.83
667 715 0.177373 GCTTCCGTACACCCCCTTAG 59.823 60.000 0.00 0.00 0.00 2.18
726 775 2.571212 AGAATAATTTGGCGCGGATCA 58.429 42.857 8.83 0.00 0.00 2.92
727 776 3.626028 AAGAATAATTTGGCGCGGATC 57.374 42.857 8.83 0.00 0.00 3.36
728 777 3.380004 TGAAAGAATAATTTGGCGCGGAT 59.620 39.130 8.83 0.00 0.00 4.18
829 878 2.604855 CCGTCCGTCAATCGATTAGGAG 60.605 54.545 21.92 16.89 42.86 3.69
832 881 1.767289 CCCGTCCGTCAATCGATTAG 58.233 55.000 10.97 5.83 42.86 1.73
833 882 0.249155 GCCCGTCCGTCAATCGATTA 60.249 55.000 10.97 0.00 42.86 1.75
1047 1124 0.705253 TCTCGGGGAGGAAGAAGAGT 59.295 55.000 0.00 0.00 0.00 3.24
1122 1205 5.595885 CGCTCCATCTTTCTATCTTCAAGA 58.404 41.667 0.00 0.00 0.00 3.02
1195 1290 1.202627 GCAGCAGGATTAGAGAGTGGG 60.203 57.143 0.00 0.00 0.00 4.61
1205 1300 2.172082 TCTCAAGCATAGCAGCAGGATT 59.828 45.455 0.00 0.00 36.85 3.01
1347 1471 7.622479 AGCTAGGTAACCCTAAAGAGAAATGTA 59.378 37.037 0.00 0.00 42.86 2.29
1361 1485 3.132467 CAGAGTTGGTAGCTAGGTAACCC 59.868 52.174 14.25 7.95 31.97 4.11
1441 1587 4.371855 TCTAGAGCGAACACACTATTGG 57.628 45.455 0.00 0.00 0.00 3.16
1455 1628 6.160576 AGAGAGAATCACCAAATCTAGAGC 57.839 41.667 0.00 0.00 37.82 4.09
1484 1658 2.474112 ACTGCTCGGTAGGGGAAATAA 58.526 47.619 0.00 0.00 0.00 1.40
1821 2071 1.073603 CCCCCTTTTACGGTTACCACA 59.926 52.381 1.13 0.00 0.00 4.17
1925 2257 0.716108 GTACTGCACATGTGAGTCGC 59.284 55.000 29.80 13.96 0.00 5.19
2133 2472 9.862149 ATAATACTCCCTCCGTTTCAAAATAAT 57.138 29.630 0.00 0.00 0.00 1.28
2143 2482 5.078256 CCTCTGTATAATACTCCCTCCGTT 58.922 45.833 0.00 0.00 0.00 4.44
2292 2632 3.664025 GTGTTACAAAGATGCTTTCACGC 59.336 43.478 0.00 0.00 0.00 5.34
2371 2754 7.480810 AGTGAACAGAAAAACTAATGTTGGTC 58.519 34.615 0.00 0.00 36.08 4.02
2372 2755 7.404671 AGTGAACAGAAAAACTAATGTTGGT 57.595 32.000 0.00 0.00 36.08 3.67
2373 2756 8.594687 CAAAGTGAACAGAAAAACTAATGTTGG 58.405 33.333 0.00 0.00 36.08 3.77
2374 2757 9.139174 ACAAAGTGAACAGAAAAACTAATGTTG 57.861 29.630 0.00 0.00 36.08 3.33
2375 2758 9.139174 CACAAAGTGAACAGAAAAACTAATGTT 57.861 29.630 0.00 0.00 38.53 2.71
2383 2766 5.344665 CGAAAGCACAAAGTGAACAGAAAAA 59.655 36.000 0.58 0.00 35.23 1.94
2481 2867 5.292101 CGGAGATGAGCTTACGAAAAAGAAT 59.708 40.000 0.00 0.00 31.52 2.40
2509 2895 3.166489 AGCACGCTTAATCAGTAGGTC 57.834 47.619 0.00 0.00 0.00 3.85
2518 2904 1.392589 CCATCCCAAGCACGCTTAAT 58.607 50.000 3.53 0.00 34.50 1.40
2543 2929 6.099125 TCCCTATTAAATCAGGACGTCATGAA 59.901 38.462 33.36 19.36 40.22 2.57
2545 2931 5.853936 TCCCTATTAAATCAGGACGTCATG 58.146 41.667 23.54 23.54 33.42 3.07
2549 2935 6.688073 ATCATCCCTATTAAATCAGGACGT 57.312 37.500 0.00 0.00 33.42 4.34
2609 3276 4.213564 AGATTCATTGGAGACGAGCTTT 57.786 40.909 0.00 0.00 0.00 3.51
2632 3299 6.042666 ACCATAACCCAAGCACACTTAATTTT 59.957 34.615 0.00 0.00 33.74 1.82
2641 3308 5.080337 TCAAATTACCATAACCCAAGCACA 58.920 37.500 0.00 0.00 0.00 4.57
2743 3667 0.247537 CCGTATGTTCGCCGCTTTTC 60.248 55.000 0.00 0.00 0.00 2.29
2773 3697 1.075601 AGGAGGGCTGTTGGATGAAA 58.924 50.000 0.00 0.00 0.00 2.69
2849 3913 0.693049 ACAAGGTTCTTCCATCGCCT 59.307 50.000 0.00 0.00 39.02 5.52
2899 3973 5.594725 AGGAACATAAGAGTAGAGATGCGAA 59.405 40.000 0.00 0.00 0.00 4.70
2904 3978 7.397476 TGTGACAAGGAACATAAGAGTAGAGAT 59.603 37.037 0.00 0.00 0.00 2.75
2916 4000 4.734398 TTGCTTTTGTGACAAGGAACAT 57.266 36.364 0.00 0.00 27.64 2.71
3018 4109 1.664151 GTTGAATAGACCTTTCCGGCG 59.336 52.381 0.00 0.00 35.61 6.46
3022 4113 7.255277 GCAATGATAGGTTGAATAGACCTTTCC 60.255 40.741 0.59 0.00 45.06 3.13
3027 4118 6.543831 ACTTGCAATGATAGGTTGAATAGACC 59.456 38.462 0.00 0.00 37.44 3.85
3036 4127 6.772716 CCTTACCATACTTGCAATGATAGGTT 59.227 38.462 13.54 0.00 0.00 3.50
3091 4183 5.091261 TGTCTCTTTTCTTCCCATAGCTC 57.909 43.478 0.00 0.00 0.00 4.09
3093 4185 6.765915 AATTGTCTCTTTTCTTCCCATAGC 57.234 37.500 0.00 0.00 0.00 2.97
3120 4213 3.484334 GCTCTTGCATGAGAGGTTTTC 57.516 47.619 28.50 9.05 42.73 2.29
3192 4292 7.996644 ACTACCACTTTTTCAAACCTTATCTCA 59.003 33.333 0.00 0.00 0.00 3.27
3371 4752 4.906618 GCTTGGCCATATTAGTTAGCCTA 58.093 43.478 6.09 0.00 44.19 3.93
3652 5447 1.710809 ACCTTAACCTTGAGGGCACAT 59.289 47.619 1.54 0.00 38.20 3.21
3715 5510 1.397672 CATCCTTGAGCGAGAGGAGA 58.602 55.000 10.12 0.00 44.77 3.71
3763 5558 8.742777 CCAAGAAAATTATCACTCAGATCCAAA 58.257 33.333 0.00 0.00 38.19 3.28
3774 5582 8.567948 TCAGAAACAGACCAAGAAAATTATCAC 58.432 33.333 0.00 0.00 0.00 3.06
3850 5661 0.619255 TGGCCGAGAACCCAATCCTA 60.619 55.000 0.00 0.00 0.00 2.94
3992 5807 8.546244 AGTAAAAAGAAAGTAAGCGACTACAAC 58.454 33.333 0.00 0.00 37.44 3.32
3993 5808 8.652810 AGTAAAAAGAAAGTAAGCGACTACAA 57.347 30.769 0.00 0.00 37.44 2.41
3998 5813 6.072098 GCAGAGTAAAAAGAAAGTAAGCGAC 58.928 40.000 0.00 0.00 0.00 5.19
4080 5928 9.729023 TTGATTTGATAATGTTAACGCCAATAG 57.271 29.630 0.26 0.00 0.00 1.73
4226 6089 6.435904 AGCTGCTATAAATACTACTCCCTCAG 59.564 42.308 0.00 0.00 0.00 3.35
4227 6090 6.315714 AGCTGCTATAAATACTACTCCCTCA 58.684 40.000 0.00 0.00 0.00 3.86
4318 6181 7.880195 CCTCCTATGGATGAAAACGATTAAGAT 59.120 37.037 0.00 0.00 0.00 2.40
4406 6280 1.209504 CCGATTAGCTTGAGGGTTCCA 59.790 52.381 0.00 0.00 0.00 3.53
4421 6295 3.454573 TCGTAGTGGCCGCCGATT 61.455 61.111 14.07 0.00 0.00 3.34
4492 6366 8.766151 TGTATATATATTTCGCGTTTGAGCAAA 58.234 29.630 5.77 0.00 36.85 3.68
4551 6446 4.423625 GAGTAGGTACTCCATGGCATTT 57.576 45.455 6.96 0.00 45.33 2.32
4579 6483 3.464907 CATCTGGCATTCACTACTGGAG 58.535 50.000 0.00 0.00 0.00 3.86
4596 6503 4.037923 ACAAAAATTGACGTCAAGCCATCT 59.962 37.500 32.19 14.77 39.47 2.90
4749 6663 4.094294 GTCAAGGGAAAACAAAGCCAAAAC 59.906 41.667 0.00 0.00 0.00 2.43
4793 6707 2.299326 AAAAGAGCAGCAATGGAGGT 57.701 45.000 0.00 0.00 0.00 3.85
4869 6783 5.552870 AGGACATGTTGTGTAGAAAGAGT 57.447 39.130 0.00 0.00 42.36 3.24
4964 6882 8.028938 GGTATATGCAATGAGTTCACAAAAAGT 58.971 33.333 0.00 0.00 0.00 2.66
5075 6993 9.799106 CTTTCCATATAAGAGGTAAATGATGGT 57.201 33.333 0.00 0.00 35.22 3.55
5085 7003 4.649674 TGCGTCTCTTTCCATATAAGAGGT 59.350 41.667 11.95 0.00 45.52 3.85
5125 7043 3.330701 ACCACCATGAGTGTAAGATGGTT 59.669 43.478 11.73 0.00 46.30 3.67
5224 7142 3.318275 GTCTCACCATAGCTATCAACGGA 59.682 47.826 13.35 3.70 0.00 4.69
5235 7153 3.629398 GGCAAAGGAATGTCTCACCATAG 59.371 47.826 0.00 0.00 0.00 2.23
5245 7163 1.928868 CAAGGGAGGCAAAGGAATGT 58.071 50.000 0.00 0.00 0.00 2.71
5356 7274 1.361668 CTTCTTCACCATGCGTCGGG 61.362 60.000 0.00 0.00 0.00 5.14
5389 7307 0.462789 TTTCTCTTATCCGTCCCCGC 59.537 55.000 0.00 0.00 0.00 6.13
5390 7308 3.470645 AATTTCTCTTATCCGTCCCCG 57.529 47.619 0.00 0.00 0.00 5.73
5391 7309 4.202020 GCAAAATTTCTCTTATCCGTCCCC 60.202 45.833 0.00 0.00 0.00 4.81
5393 7311 5.586643 AGAGCAAAATTTCTCTTATCCGTCC 59.413 40.000 4.06 0.00 36.33 4.79
5394 7312 6.481984 CAGAGCAAAATTTCTCTTATCCGTC 58.518 40.000 6.66 0.00 37.56 4.79
5395 7313 5.163713 GCAGAGCAAAATTTCTCTTATCCGT 60.164 40.000 6.66 0.00 37.56 4.69
5396 7314 5.163723 TGCAGAGCAAAATTTCTCTTATCCG 60.164 40.000 6.66 0.00 37.56 4.18
5398 7316 7.590689 GCTATGCAGAGCAAAATTTCTCTTATC 59.409 37.037 27.68 0.00 43.62 1.75
5400 7318 6.457392 CGCTATGCAGAGCAAAATTTCTCTTA 60.457 38.462 30.81 1.51 43.62 2.10
5405 7323 4.019919 TCGCTATGCAGAGCAAAATTTC 57.980 40.909 30.81 1.29 43.62 2.17
5406 7324 3.733077 GCTCGCTATGCAGAGCAAAATTT 60.733 43.478 30.81 0.00 46.09 1.82
5409 7329 0.729116 GCTCGCTATGCAGAGCAAAA 59.271 50.000 30.81 15.59 46.09 2.44
5414 7334 2.487372 TGATCTAGCTCGCTATGCAGAG 59.513 50.000 3.34 3.34 34.33 3.35


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

AutoCloner maintained by Alex Coulton.