Multiple sequence alignment - TraesCS5D01G524200

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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 TraesCS5D01G524200 chr5D 100.000 3812 0 0 1 3812 543504730 543500919 0.000000e+00 7040.0
1 TraesCS5D01G524200 chr5D 86.002 1043 100 24 1572 2607 551058227 551059230 0.000000e+00 1075.0
2 TraesCS5D01G524200 chr5D 89.641 753 47 15 2606 3348 551059299 551060030 0.000000e+00 929.0
3 TraesCS5D01G524200 chr5D 87.003 654 60 13 995 1627 551057597 551058246 0.000000e+00 713.0
4 TraesCS5D01G524200 chr5D 76.622 1202 204 48 1015 2160 552422797 552421617 3.280000e-165 592.0
5 TraesCS5D01G524200 chr5D 75.662 1208 208 54 998 2141 552051662 552050477 1.210000e-144 523.0
6 TraesCS5D01G524200 chr5D 73.906 1211 239 40 983 2149 552458418 552457241 7.620000e-112 414.0
7 TraesCS5D01G524200 chr5D 78.860 544 95 18 1609 2142 551612067 551612600 2.180000e-92 350.0
8 TraesCS5D01G524200 chr5D 82.772 267 23 6 3392 3655 551060121 551060367 2.310000e-52 217.0
9 TraesCS5D01G524200 chr5D 80.851 141 23 3 983 1120 552444195 552444056 1.450000e-19 108.0
10 TraesCS5D01G524200 chr5D 90.385 52 5 0 1359 1410 543536421 543536370 6.830000e-08 69.4
11 TraesCS5D01G524200 chr5B 87.330 1760 148 32 907 2607 685323200 685321457 0.000000e+00 1945.0
12 TraesCS5D01G524200 chr5B 86.472 1508 139 33 907 2358 685503643 685505141 0.000000e+00 1594.0
13 TraesCS5D01G524200 chr5B 93.333 525 16 5 351 859 685323719 685323198 0.000000e+00 758.0
14 TraesCS5D01G524200 chr5B 90.424 543 46 3 2606 3142 685321388 685320846 0.000000e+00 710.0
15 TraesCS5D01G524200 chr5B 84.783 552 74 10 1 547 451190265 451189719 2.590000e-151 545.0
16 TraesCS5D01G524200 chr5B 95.821 335 13 1 3193 3526 685320842 685320508 1.200000e-149 540.0
17 TraesCS5D01G524200 chr5B 94.627 335 17 1 3193 3526 685505762 685506096 5.640000e-143 518.0
18 TraesCS5D01G524200 chr5B 74.794 1214 228 35 992 2149 698256529 698257720 3.450000e-130 475.0
19 TraesCS5D01G524200 chr5B 74.424 1216 224 51 993 2142 703529332 703530526 3.490000e-120 442.0
20 TraesCS5D01G524200 chr5B 75.632 870 158 38 1306 2142 699998183 699999031 2.150000e-102 383.0
21 TraesCS5D01G524200 chr5B 72.873 1246 262 50 985 2186 700229664 700228451 3.620000e-95 359.0
22 TraesCS5D01G524200 chr5B 91.406 256 18 3 3559 3812 685320511 685320258 7.840000e-92 348.0
23 TraesCS5D01G524200 chr5B 91.406 256 18 3 3559 3812 685506093 685506346 7.840000e-92 348.0
24 TraesCS5D01G524200 chr5B 93.805 226 13 1 2382 2607 685505138 685505362 4.720000e-89 339.0
25 TraesCS5D01G524200 chr5B 94.975 199 4 3 2950 3142 685505560 685505758 1.330000e-79 307.0
26 TraesCS5D01G524200 chr5B 84.308 325 20 5 548 859 685503339 685503645 4.820000e-74 289.0
27 TraesCS5D01G524200 chr5B 96.154 104 4 0 2606 2709 685505431 685505534 1.820000e-38 171.0
28 TraesCS5D01G524200 chr5B 78.212 179 33 5 2330 2503 703530710 703530887 4.030000e-20 110.0
29 TraesCS5D01G524200 chr5B 92.424 66 5 0 2829 2894 693009576 693009511 1.130000e-15 95.3
30 TraesCS5D01G524200 chr5B 93.617 47 3 0 1364 1410 703539868 703539914 1.900000e-08 71.3
31 TraesCS5D01G524200 chr1A 91.985 549 41 3 1 548 278788395 278788941 0.000000e+00 767.0
32 TraesCS5D01G524200 chr1A 71.113 952 199 39 993 1888 569698599 569699530 8.470000e-37 165.0
33 TraesCS5D01G524200 chr1A 70.842 950 196 49 993 1888 569656820 569657742 1.100000e-30 145.0
34 TraesCS5D01G524200 chr1A 75.451 277 54 11 2330 2594 569702551 569702825 5.170000e-24 122.0
35 TraesCS5D01G524200 chr1A 79.330 179 31 5 2330 2503 569742489 569742666 1.860000e-23 121.0
36 TraesCS5D01G524200 chr1A 78.212 179 33 5 2330 2503 569660741 569660918 4.030000e-20 110.0
37 TraesCS5D01G524200 chr1A 79.545 132 23 3 987 1115 295466106 295466236 1.460000e-14 91.6
38 TraesCS5D01G524200 chr4A 87.709 659 62 9 987 1627 616897548 616896891 0.000000e+00 750.0
39 TraesCS5D01G524200 chr4A 90.071 564 54 2 1583 2145 616896899 616896337 0.000000e+00 730.0
40 TraesCS5D01G524200 chr4A 75.084 1184 209 60 1020 2142 616618706 616617548 1.240000e-129 473.0
41 TraesCS5D01G524200 chr4A 89.790 333 23 6 2606 2937 616895833 616895511 2.120000e-112 416.0
42 TraesCS5D01G524200 chr4A 88.542 288 32 1 3525 3811 616895493 616895206 7.840000e-92 348.0
43 TraesCS5D01G524200 chr4A 77.818 550 109 11 1645 2186 616229899 616229355 1.020000e-85 327.0
44 TraesCS5D01G524200 chr4A 79.888 179 30 5 2330 2503 624482078 624481901 4.000000e-25 126.0
45 TraesCS5D01G524200 chr4A 79.330 179 31 5 2330 2503 624451301 624451124 1.860000e-23 121.0
46 TraesCS5D01G524200 chr4A 82.609 115 19 1 990 1103 616754889 616754775 2.420000e-17 100.0
47 TraesCS5D01G524200 chr2B 87.184 554 56 12 1 548 280486368 280485824 1.950000e-172 616.0
48 TraesCS5D01G524200 chr3B 86.607 560 64 11 1 555 578284987 578285540 3.260000e-170 608.0
49 TraesCS5D01G524200 chr5A 85.118 551 74 6 1 547 88639771 88639225 1.200000e-154 556.0
50 TraesCS5D01G524200 chr5A 83.424 549 76 12 1 544 639100435 639099897 2.640000e-136 496.0
51 TraesCS5D01G524200 chr6D 83.574 554 74 14 1 548 273913351 273913893 1.580000e-138 503.0
52 TraesCS5D01G524200 chr6B 82.342 555 79 13 1 547 72392289 72391746 7.460000e-127 464.0
53 TraesCS5D01G524200 chr2A 80.893 560 79 22 1 547 655520284 655520828 2.120000e-112 416.0
54 TraesCS5D01G524200 chr7D 89.399 283 26 4 267 547 75808904 75808624 1.680000e-93 353.0
55 TraesCS5D01G524200 chr1D 77.883 529 99 15 1711 2229 227868168 227868688 2.860000e-81 313.0
56 TraesCS5D01G524200 chr1D 78.519 135 25 3 987 1118 208239262 208239129 6.780000e-13 86.1
57 TraesCS5D01G524200 chr1D 78.195 133 23 5 987 1115 227867360 227867490 3.160000e-11 80.5
58 TraesCS5D01G524200 chr1B 76.335 562 86 23 1001 1525 39517728 39517177 1.360000e-64 257.0
59 TraesCS5D01G524200 chr1B 73.936 564 93 30 983 1497 115748947 115749505 1.090000e-40 178.0
60 TraesCS5D01G524200 chr1B 79.545 132 23 3 987 1115 327487326 327487456 1.460000e-14 91.6
61 TraesCS5D01G524200 chr3A 87.054 224 24 4 1 222 466483201 466482981 8.180000e-62 248.0


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 TraesCS5D01G524200 chr5D 543500919 543504730 3811 True 7040.000000 7040 100.000000 1 3812 1 chr5D.!!$R1 3811
1 TraesCS5D01G524200 chr5D 551057597 551060367 2770 False 733.500000 1075 86.354500 995 3655 4 chr5D.!!$F2 2660
2 TraesCS5D01G524200 chr5D 552421617 552422797 1180 True 592.000000 592 76.622000 1015 2160 1 chr5D.!!$R4 1145
3 TraesCS5D01G524200 chr5D 552050477 552051662 1185 True 523.000000 523 75.662000 998 2141 1 chr5D.!!$R3 1143
4 TraesCS5D01G524200 chr5D 552457241 552458418 1177 True 414.000000 414 73.906000 983 2149 1 chr5D.!!$R6 1166
5 TraesCS5D01G524200 chr5D 551612067 551612600 533 False 350.000000 350 78.860000 1609 2142 1 chr5D.!!$F1 533
6 TraesCS5D01G524200 chr5B 685320258 685323719 3461 True 860.200000 1945 91.662800 351 3812 5 chr5B.!!$R4 3461
7 TraesCS5D01G524200 chr5B 451189719 451190265 546 True 545.000000 545 84.783000 1 547 1 chr5B.!!$R1 546
8 TraesCS5D01G524200 chr5B 685503339 685506346 3007 False 509.428571 1594 91.678143 548 3812 7 chr5B.!!$F4 3264
9 TraesCS5D01G524200 chr5B 698256529 698257720 1191 False 475.000000 475 74.794000 992 2149 1 chr5B.!!$F1 1157
10 TraesCS5D01G524200 chr5B 699998183 699999031 848 False 383.000000 383 75.632000 1306 2142 1 chr5B.!!$F2 836
11 TraesCS5D01G524200 chr5B 700228451 700229664 1213 True 359.000000 359 72.873000 985 2186 1 chr5B.!!$R3 1201
12 TraesCS5D01G524200 chr5B 703529332 703530887 1555 False 276.000000 442 76.318000 993 2503 2 chr5B.!!$F5 1510
13 TraesCS5D01G524200 chr1A 278788395 278788941 546 False 767.000000 767 91.985000 1 548 1 chr1A.!!$F1 547
14 TraesCS5D01G524200 chr4A 616895206 616897548 2342 True 561.000000 750 89.028000 987 3811 4 chr4A.!!$R6 2824
15 TraesCS5D01G524200 chr4A 616617548 616618706 1158 True 473.000000 473 75.084000 1020 2142 1 chr4A.!!$R2 1122
16 TraesCS5D01G524200 chr4A 616229355 616229899 544 True 327.000000 327 77.818000 1645 2186 1 chr4A.!!$R1 541
17 TraesCS5D01G524200 chr2B 280485824 280486368 544 True 616.000000 616 87.184000 1 548 1 chr2B.!!$R1 547
18 TraesCS5D01G524200 chr3B 578284987 578285540 553 False 608.000000 608 86.607000 1 555 1 chr3B.!!$F1 554
19 TraesCS5D01G524200 chr5A 88639225 88639771 546 True 556.000000 556 85.118000 1 547 1 chr5A.!!$R1 546
20 TraesCS5D01G524200 chr5A 639099897 639100435 538 True 496.000000 496 83.424000 1 544 1 chr5A.!!$R2 543
21 TraesCS5D01G524200 chr6D 273913351 273913893 542 False 503.000000 503 83.574000 1 548 1 chr6D.!!$F1 547
22 TraesCS5D01G524200 chr6B 72391746 72392289 543 True 464.000000 464 82.342000 1 547 1 chr6B.!!$R1 546
23 TraesCS5D01G524200 chr2A 655520284 655520828 544 False 416.000000 416 80.893000 1 547 1 chr2A.!!$F1 546
24 TraesCS5D01G524200 chr1B 39517177 39517728 551 True 257.000000 257 76.335000 1001 1525 1 chr1B.!!$R1 524

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
882 923 0.033366 TTGCTGCTTGCTCAGTACGA 59.967 50.0 0.0 0.0 43.37 3.43 F
914 955 0.105760 TCTGAAAGCCCAAAGCCCAA 60.106 50.0 0.0 0.0 45.47 4.12 F
924 965 0.250424 CAAAGCCCAAAGCCCAAAGG 60.250 55.0 0.0 0.0 45.47 3.11 F
960 1001 0.378257 AAACTGAGCAGCACACAACG 59.622 50.0 0.0 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 1884 0.040958 GCCTGAAGTGAAGTGCGTTG 60.041 55.00 0.00 0.00 0.00 4.10 R
1800 2005 0.764369 ATGAGGATAGCGGGCCAGAA 60.764 55.00 7.23 0.00 0.00 3.02 R
2761 3101 0.815734 GTGAGCCAGCATGCAGAAAT 59.184 50.00 21.98 0.79 31.97 2.17 R
2900 3241 5.220710 ACATGCTACACTCTTCACTCTTT 57.779 39.13 0.00 0.00 0.00 2.52 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
28 29 2.081462 ACGAAATCGGGCTACTTTTGG 58.919 47.619 7.81 0.00 44.95 3.28
107 109 5.277828 GCTTTACTGGACAGGTTTACAACAG 60.278 44.000 4.14 0.00 0.00 3.16
134 136 1.226491 CGCCAGGGAGTTACGTACG 60.226 63.158 15.01 15.01 0.00 3.67
140 142 1.435105 GGAGTTACGTACGGGAGCC 59.565 63.158 21.06 10.17 0.00 4.70
187 189 3.939592 CAGCTGATGAAGATGTGTGATGT 59.060 43.478 8.42 0.00 37.53 3.06
237 243 3.263503 TTCGTGACGCTCTCGGTGG 62.264 63.158 0.00 0.00 40.69 4.61
248 256 1.457643 CTCGGTGGGGAGATGGCTA 60.458 63.158 0.00 0.00 36.08 3.93
256 264 0.689623 GGGAGATGGCTACCATGGAG 59.310 60.000 21.47 12.61 45.26 3.86
344 363 9.645059 TGTGTTTGTTCTAGATTGATCTTCTAG 57.355 33.333 19.32 19.32 42.63 2.43
366 385 9.122779 TCTAGAAAGTGTAATAGGCTAGACTTC 57.877 37.037 1.68 0.00 35.08 3.01
409 434 1.365699 CCCCATAACACTCGTTTCGG 58.634 55.000 0.00 0.00 36.52 4.30
529 557 4.532834 TCTATGCAATGGAAAGGGGTAAC 58.467 43.478 0.00 0.00 27.55 2.50
630 658 9.442047 AACACAAAACATGATTTTGAAAACCTA 57.558 25.926 26.24 0.00 40.73 3.08
851 892 2.890945 TCTGAAAGCCCAAAGCCTAAAC 59.109 45.455 0.00 0.00 45.47 2.01
859 900 4.163268 AGCCCAAAGCCTAAACAAAGAAAA 59.837 37.500 0.00 0.00 45.47 2.29
860 901 4.878971 GCCCAAAGCCTAAACAAAGAAAAA 59.121 37.500 0.00 0.00 34.35 1.94
861 902 5.530915 GCCCAAAGCCTAAACAAAGAAAAAT 59.469 36.000 0.00 0.00 34.35 1.82
862 903 6.513230 GCCCAAAGCCTAAACAAAGAAAAATG 60.513 38.462 0.00 0.00 34.35 2.32
863 904 6.542005 CCCAAAGCCTAAACAAAGAAAAATGT 59.458 34.615 0.00 0.00 0.00 2.71
864 905 7.066887 CCCAAAGCCTAAACAAAGAAAAATGTT 59.933 33.333 0.00 0.00 41.31 2.71
865 906 7.909641 CCAAAGCCTAAACAAAGAAAAATGTTG 59.090 33.333 0.00 0.00 39.57 3.33
866 907 6.603237 AGCCTAAACAAAGAAAAATGTTGC 57.397 33.333 0.00 0.00 39.57 4.17
867 908 6.348498 AGCCTAAACAAAGAAAAATGTTGCT 58.652 32.000 0.00 0.00 39.57 3.91
868 909 6.258507 AGCCTAAACAAAGAAAAATGTTGCTG 59.741 34.615 0.00 0.00 39.57 4.41
869 910 6.421405 CCTAAACAAAGAAAAATGTTGCTGC 58.579 36.000 0.00 0.00 39.57 5.25
870 911 6.258507 CCTAAACAAAGAAAAATGTTGCTGCT 59.741 34.615 0.00 0.00 39.57 4.24
871 912 6.499234 AAACAAAGAAAAATGTTGCTGCTT 57.501 29.167 0.00 0.00 39.57 3.91
872 913 5.473796 ACAAAGAAAAATGTTGCTGCTTG 57.526 34.783 0.00 0.00 0.00 4.01
873 914 4.201841 ACAAAGAAAAATGTTGCTGCTTGC 60.202 37.500 0.00 0.00 43.25 4.01
874 915 3.464111 AGAAAAATGTTGCTGCTTGCT 57.536 38.095 0.00 0.00 43.37 3.91
875 916 3.387397 AGAAAAATGTTGCTGCTTGCTC 58.613 40.909 0.00 0.00 43.37 4.26
876 917 2.894763 AAAATGTTGCTGCTTGCTCA 57.105 40.000 0.00 4.26 43.37 4.26
877 918 2.433868 AAATGTTGCTGCTTGCTCAG 57.566 45.000 0.00 0.00 43.37 3.35
878 919 1.325355 AATGTTGCTGCTTGCTCAGT 58.675 45.000 0.00 1.18 43.37 3.41
879 920 2.189594 ATGTTGCTGCTTGCTCAGTA 57.810 45.000 0.00 0.00 43.37 2.74
880 921 1.229428 TGTTGCTGCTTGCTCAGTAC 58.771 50.000 0.00 0.00 43.37 2.73
881 922 0.164647 GTTGCTGCTTGCTCAGTACG 59.835 55.000 0.00 0.00 43.37 3.67
882 923 0.033366 TTGCTGCTTGCTCAGTACGA 59.967 50.000 0.00 0.00 43.37 3.43
883 924 0.667487 TGCTGCTTGCTCAGTACGAC 60.667 55.000 0.00 0.00 43.37 4.34
884 925 1.678269 GCTGCTTGCTCAGTACGACG 61.678 60.000 0.00 0.00 38.95 5.12
885 926 0.387367 CTGCTTGCTCAGTACGACGT 60.387 55.000 5.52 5.52 0.00 4.34
886 927 0.876399 TGCTTGCTCAGTACGACGTA 59.124 50.000 2.97 2.97 0.00 3.57
887 928 1.471287 TGCTTGCTCAGTACGACGTAT 59.529 47.619 11.46 0.00 0.00 3.06
888 929 1.846782 GCTTGCTCAGTACGACGTATG 59.153 52.381 11.46 10.37 0.00 2.39
889 930 2.731341 GCTTGCTCAGTACGACGTATGT 60.731 50.000 11.46 0.00 0.00 2.29
890 931 3.499048 CTTGCTCAGTACGACGTATGTT 58.501 45.455 11.46 0.00 0.00 2.71
891 932 2.858839 TGCTCAGTACGACGTATGTTG 58.141 47.619 11.46 10.26 35.45 3.33
892 933 2.485038 TGCTCAGTACGACGTATGTTGA 59.515 45.455 11.46 13.58 33.40 3.18
893 934 3.058085 TGCTCAGTACGACGTATGTTGAA 60.058 43.478 11.46 0.33 33.40 2.69
894 935 3.916172 GCTCAGTACGACGTATGTTGAAA 59.084 43.478 11.46 0.00 33.40 2.69
895 936 4.561606 GCTCAGTACGACGTATGTTGAAAT 59.438 41.667 11.46 0.00 33.40 2.17
896 937 5.275788 GCTCAGTACGACGTATGTTGAAATC 60.276 44.000 11.46 5.03 33.40 2.17
897 938 5.946298 TCAGTACGACGTATGTTGAAATCT 58.054 37.500 11.46 0.00 33.40 2.40
898 939 5.798434 TCAGTACGACGTATGTTGAAATCTG 59.202 40.000 11.46 10.03 33.40 2.90
899 940 5.798434 CAGTACGACGTATGTTGAAATCTGA 59.202 40.000 11.46 0.00 33.40 3.27
900 941 6.307077 CAGTACGACGTATGTTGAAATCTGAA 59.693 38.462 11.46 0.00 33.40 3.02
901 942 6.864685 AGTACGACGTATGTTGAAATCTGAAA 59.135 34.615 11.46 0.00 33.40 2.69
914 955 0.105760 TCTGAAAGCCCAAAGCCCAA 60.106 50.000 0.00 0.00 45.47 4.12
915 956 0.758123 CTGAAAGCCCAAAGCCCAAA 59.242 50.000 0.00 0.00 45.47 3.28
916 957 0.758123 TGAAAGCCCAAAGCCCAAAG 59.242 50.000 0.00 0.00 45.47 2.77
917 958 0.603707 GAAAGCCCAAAGCCCAAAGC 60.604 55.000 0.00 0.00 45.47 3.51
918 959 2.055689 AAAGCCCAAAGCCCAAAGCC 62.056 55.000 0.00 0.00 45.47 4.35
919 960 4.020617 GCCCAAAGCCCAAAGCCC 62.021 66.667 0.00 0.00 45.47 5.19
924 965 0.250424 CAAAGCCCAAAGCCCAAAGG 60.250 55.000 0.00 0.00 45.47 3.11
936 977 1.227380 CCAAAGGAGAGGCCGATCG 60.227 63.158 8.51 8.51 43.43 3.69
960 1001 0.378257 AAACTGAGCAGCACACAACG 59.622 50.000 0.00 0.00 0.00 4.10
1103 1180 4.803426 GACGAGCCCGAGCACCTG 62.803 72.222 0.00 0.00 43.56 4.00
1178 1273 3.089874 TTCCATGGAGCTCCCCCG 61.090 66.667 29.95 17.20 34.29 5.73
1210 1308 4.706842 TCCTCTACAACTGGCTCTTTTT 57.293 40.909 0.00 0.00 0.00 1.94
1501 1655 0.393448 TTCCGGGTTGTCGTCATCAA 59.607 50.000 0.00 0.00 0.00 2.57
1568 1767 2.029964 TCTTCGCCGGTGACCAAC 59.970 61.111 19.40 0.00 0.00 3.77
1642 1841 4.874966 GTGCTCTGCTCTTCATCTTGTTAT 59.125 41.667 0.00 0.00 0.00 1.89
1644 1843 5.114780 GCTCTGCTCTTCATCTTGTTATGA 58.885 41.667 0.00 0.00 34.07 2.15
1658 1857 6.356556 TCTTGTTATGACCGATCCATTCATT 58.643 36.000 4.23 0.00 32.24 2.57
1685 1884 0.615331 TGCCTCCTGTCCTCATTGAC 59.385 55.000 0.00 0.00 35.77 3.18
1800 2005 1.451387 CTTACGAGGCCGGCCATTT 60.451 57.895 45.13 29.86 40.78 2.32
1858 2063 2.917227 GGGGTTGGCACACTTGGG 60.917 66.667 0.00 0.00 39.29 4.12
1936 2141 2.186076 GACTCGGCGTAAAGTCATCAG 58.814 52.381 18.77 3.26 41.26 2.90
2240 2463 3.615496 GCATTGAATGTTTGGTCAGATGC 59.385 43.478 7.05 0.00 34.40 3.91
2242 2465 2.777094 TGAATGTTTGGTCAGATGCGA 58.223 42.857 0.00 0.00 0.00 5.10
2253 2476 5.698832 TGGTCAGATGCGAAGTTATTTTTG 58.301 37.500 0.00 0.00 0.00 2.44
2256 2479 6.688813 GGTCAGATGCGAAGTTATTTTTGATC 59.311 38.462 0.00 0.00 0.00 2.92
2260 2483 9.378597 CAGATGCGAAGTTATTTTTGATCTATG 57.621 33.333 0.00 0.00 0.00 2.23
2277 2542 6.646653 TGATCTATGATTTTCGTGGTGCTATC 59.353 38.462 0.00 0.00 0.00 2.08
2359 2624 8.910351 ATAGTACCATATCTTCTCCTTTTTGC 57.090 34.615 0.00 0.00 0.00 3.68
2364 2629 6.183360 ACCATATCTTCTCCTTTTTGCAATCG 60.183 38.462 0.00 0.00 0.00 3.34
2391 2656 7.762615 CACTGATAAATCCATGTTTGCAGAAAT 59.237 33.333 14.67 0.00 33.19 2.17
2525 2795 2.928116 GGTGTCAGTATTCGGTAACTGC 59.072 50.000 6.97 4.32 42.31 4.40
2588 2858 1.718396 TGTCAGCAAGCTCGAGATTG 58.282 50.000 33.27 33.27 43.64 2.67
2761 3101 2.028203 TGTTGCCAAGAGATGACGATGA 60.028 45.455 0.00 0.00 0.00 2.92
2870 3211 9.726438 AAGAGTAAAGAGTATAACATGCAGTTT 57.274 29.630 6.82 0.00 41.64 2.66
2900 3241 8.972458 TTTATATCCAGCAAGCAATGTTACTA 57.028 30.769 0.00 0.00 0.00 1.82
2914 3255 7.386299 AGCAATGTTACTAAAGAGTGAAGAGTG 59.614 37.037 0.00 0.00 36.28 3.51
3150 3499 3.118992 TCTGCTAGGCTACAGTGTTCATG 60.119 47.826 17.67 0.00 35.37 3.07
3152 3501 2.555199 CTAGGCTACAGTGTTCATGGC 58.445 52.381 0.00 2.50 0.00 4.40
3153 3502 0.035056 AGGCTACAGTGTTCATGGCC 60.035 55.000 0.00 8.28 38.50 5.36
3155 3504 1.683011 GGCTACAGTGTTCATGGCCAT 60.683 52.381 14.09 14.09 38.16 4.40
3187 3536 9.802039 TGGTTTATTATATTCCATACTGGGTTC 57.198 33.333 0.00 0.00 38.32 3.62
3188 3537 9.802039 GGTTTATTATATTCCATACTGGGTTCA 57.198 33.333 0.00 0.00 38.32 3.18
3274 3624 8.725148 GTGCATTCTTGACCTATATTTATGGAG 58.275 37.037 0.00 0.00 0.00 3.86
3302 3652 0.529378 GCTCTGTTCCAAATGCCTGG 59.471 55.000 0.00 0.00 37.87 4.45
3388 3797 6.723298 ATTTTCTTCATGTGTGGGTGTTTA 57.277 33.333 0.00 0.00 0.00 2.01
3416 3825 7.013846 TGGTTGGTAATCTGTTTTCTTTACAGG 59.986 37.037 0.00 0.00 42.53 4.00
3542 3953 4.523168 TTCATGGTGATGATTGATCCCA 57.477 40.909 0.00 0.00 38.43 4.37
3589 4000 1.615392 GGGCATTGTTCTTCTGCAGTT 59.385 47.619 14.67 0.00 37.64 3.16
3623 4034 6.042666 TCCATATCAAATTGTGGGACTCGATA 59.957 38.462 1.96 0.00 32.58 2.92
3624 4035 6.147821 CCATATCAAATTGTGGGACTCGATAC 59.852 42.308 0.00 0.00 0.00 2.24
3645 4056 4.435425 ACGATACGTGCTTTTAGGCAATA 58.565 39.130 0.00 0.00 44.18 1.90
3700 4111 1.644509 ACCACTATGTGCTGGACTCA 58.355 50.000 0.00 0.00 31.34 3.41
3705 4116 2.899900 ACTATGTGCTGGACTCAACTCA 59.100 45.455 0.00 0.00 0.00 3.41
3716 4127 3.118738 GGACTCAACTCAACGGGATACAT 60.119 47.826 0.00 0.00 39.74 2.29
3806 4220 8.018537 TCACATAGTAGCTTCCTATGCTTTTA 57.981 34.615 23.09 9.40 43.58 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.403734 TCTTTCCAAAAGTAGCCCGATTT 58.596 39.130 0.00 0.00 0.00 2.17
28 29 8.811378 CAAAAGGAGTCTTGATTTGTTTCTTTC 58.189 33.333 0.00 0.00 32.75 2.62
134 136 2.801631 CCTGACCATCTCGGCTCCC 61.802 68.421 0.00 0.00 39.03 4.30
140 142 2.544686 CGTACTAGTCCTGACCATCTCG 59.455 54.545 0.00 0.00 0.00 4.04
187 189 0.825425 TTGGATCGGTTGCTTGGCAA 60.825 50.000 0.00 0.00 46.80 4.52
237 243 0.689623 CTCCATGGTAGCCATCTCCC 59.310 60.000 12.58 0.00 43.15 4.30
248 256 0.546267 AGCAGACACCTCTCCATGGT 60.546 55.000 12.58 0.00 38.53 3.55
256 264 2.620585 AGCAAAAGAAAGCAGACACCTC 59.379 45.455 0.00 0.00 0.00 3.85
344 363 8.950208 AATGAAGTCTAGCCTATTACACTTTC 57.050 34.615 0.00 0.00 0.00 2.62
366 385 4.911610 CGAAAACCTGAGTAGCACAAAATG 59.088 41.667 0.00 0.00 0.00 2.32
409 434 4.664677 ACCACACTCGCTCGCCAC 62.665 66.667 0.00 0.00 0.00 5.01
574 602 6.466812 AGATTTTGTTATTTTGCTTCAGGGG 58.533 36.000 0.00 0.00 0.00 4.79
575 603 7.761249 CCTAGATTTTGTTATTTTGCTTCAGGG 59.239 37.037 0.00 0.00 0.00 4.45
724 765 3.398920 CGAGTAGCAACATGGGCG 58.601 61.111 0.00 0.00 36.08 6.13
851 892 4.276460 GCAAGCAGCAACATTTTTCTTTG 58.724 39.130 0.00 0.00 44.79 2.77
865 906 1.678269 CGTCGTACTGAGCAAGCAGC 61.678 60.000 0.00 0.00 46.19 5.25
866 907 0.387367 ACGTCGTACTGAGCAAGCAG 60.387 55.000 0.00 0.00 41.63 4.24
867 908 0.876399 TACGTCGTACTGAGCAAGCA 59.124 50.000 0.00 0.00 0.00 3.91
868 909 1.846782 CATACGTCGTACTGAGCAAGC 59.153 52.381 7.36 0.00 0.00 4.01
869 910 3.132629 ACATACGTCGTACTGAGCAAG 57.867 47.619 7.36 0.00 0.00 4.01
870 911 3.058085 TCAACATACGTCGTACTGAGCAA 60.058 43.478 7.36 0.00 0.00 3.91
871 912 2.485038 TCAACATACGTCGTACTGAGCA 59.515 45.455 7.36 0.00 0.00 4.26
872 913 3.127081 TCAACATACGTCGTACTGAGC 57.873 47.619 7.36 0.00 0.00 4.26
873 914 6.021390 CAGATTTCAACATACGTCGTACTGAG 60.021 42.308 7.36 1.16 0.00 3.35
874 915 5.798434 CAGATTTCAACATACGTCGTACTGA 59.202 40.000 7.36 8.22 0.00 3.41
875 916 5.798434 TCAGATTTCAACATACGTCGTACTG 59.202 40.000 7.36 9.73 0.00 2.74
876 917 5.946298 TCAGATTTCAACATACGTCGTACT 58.054 37.500 7.36 0.00 0.00 2.73
877 918 6.621737 TTCAGATTTCAACATACGTCGTAC 57.378 37.500 7.36 0.00 0.00 3.67
878 919 6.183360 GCTTTCAGATTTCAACATACGTCGTA 60.183 38.462 7.69 7.69 0.00 3.43
879 920 5.389516 GCTTTCAGATTTCAACATACGTCGT 60.390 40.000 2.21 2.21 0.00 4.34
880 921 5.015733 GCTTTCAGATTTCAACATACGTCG 58.984 41.667 0.00 0.00 0.00 5.12
881 922 5.324697 GGCTTTCAGATTTCAACATACGTC 58.675 41.667 0.00 0.00 0.00 4.34
882 923 4.156008 GGGCTTTCAGATTTCAACATACGT 59.844 41.667 0.00 0.00 0.00 3.57
883 924 4.155826 TGGGCTTTCAGATTTCAACATACG 59.844 41.667 0.00 0.00 0.00 3.06
884 925 5.643379 TGGGCTTTCAGATTTCAACATAC 57.357 39.130 0.00 0.00 0.00 2.39
885 926 6.662865 TTTGGGCTTTCAGATTTCAACATA 57.337 33.333 0.00 0.00 0.00 2.29
886 927 5.544650 CTTTGGGCTTTCAGATTTCAACAT 58.455 37.500 0.00 0.00 0.00 2.71
887 928 4.740334 GCTTTGGGCTTTCAGATTTCAACA 60.740 41.667 0.00 0.00 38.06 3.33
888 929 3.742882 GCTTTGGGCTTTCAGATTTCAAC 59.257 43.478 0.00 0.00 38.06 3.18
889 930 3.244181 GGCTTTGGGCTTTCAGATTTCAA 60.244 43.478 0.00 0.00 41.46 2.69
890 931 2.299867 GGCTTTGGGCTTTCAGATTTCA 59.700 45.455 0.00 0.00 41.46 2.69
891 932 2.354103 GGGCTTTGGGCTTTCAGATTTC 60.354 50.000 0.00 0.00 41.46 2.17
892 933 1.625315 GGGCTTTGGGCTTTCAGATTT 59.375 47.619 0.00 0.00 41.46 2.17
893 934 1.269958 GGGCTTTGGGCTTTCAGATT 58.730 50.000 0.00 0.00 41.46 2.40
894 935 0.114954 TGGGCTTTGGGCTTTCAGAT 59.885 50.000 0.00 0.00 41.46 2.90
895 936 0.105760 TTGGGCTTTGGGCTTTCAGA 60.106 50.000 0.00 0.00 41.46 3.27
896 937 0.758123 TTTGGGCTTTGGGCTTTCAG 59.242 50.000 0.00 0.00 41.46 3.02
897 938 0.758123 CTTTGGGCTTTGGGCTTTCA 59.242 50.000 0.00 0.00 41.46 2.69
898 939 0.603707 GCTTTGGGCTTTGGGCTTTC 60.604 55.000 0.00 0.00 41.46 2.62
899 940 1.451504 GCTTTGGGCTTTGGGCTTT 59.548 52.632 0.00 0.00 41.46 3.51
900 941 2.519622 GGCTTTGGGCTTTGGGCTT 61.520 57.895 0.00 0.00 41.46 4.35
901 942 2.924635 GGCTTTGGGCTTTGGGCT 60.925 61.111 0.00 0.00 41.46 5.19
914 955 2.766660 GGCCTCTCCTTTGGGCTT 59.233 61.111 0.00 0.00 44.70 4.35
915 956 3.721706 CGGCCTCTCCTTTGGGCT 61.722 66.667 0.00 0.00 45.35 5.19
916 957 2.949705 GATCGGCCTCTCCTTTGGGC 62.950 65.000 0.00 0.00 44.59 5.36
917 958 1.147153 GATCGGCCTCTCCTTTGGG 59.853 63.158 0.00 0.00 0.00 4.12
918 959 1.227380 CGATCGGCCTCTCCTTTGG 60.227 63.158 7.38 0.00 0.00 3.28
919 960 1.227380 CCGATCGGCCTCTCCTTTG 60.227 63.158 23.37 0.00 0.00 2.77
924 965 0.460311 TTTTCTCCGATCGGCCTCTC 59.540 55.000 29.62 0.00 34.68 3.20
932 973 1.663135 GCTGCTCAGTTTTCTCCGATC 59.337 52.381 0.00 0.00 0.00 3.69
936 977 1.265365 GTGTGCTGCTCAGTTTTCTCC 59.735 52.381 4.41 0.00 0.00 3.71
968 1022 3.430790 GGTGGAGAATATTTTTGGGCTGC 60.431 47.826 0.00 0.00 0.00 5.25
980 1034 1.835531 GAGGGTTTCGGGTGGAGAATA 59.164 52.381 0.00 0.00 0.00 1.75
981 1035 0.618981 GAGGGTTTCGGGTGGAGAAT 59.381 55.000 0.00 0.00 0.00 2.40
1178 1273 3.135530 AGTTGTAGAGGAATCCCAGCATC 59.864 47.826 0.00 0.00 33.88 3.91
1501 1655 3.117745 TCATCCTCATTCATGTCCAGGT 58.882 45.455 0.00 0.00 0.00 4.00
1553 1716 1.890041 CTTGTTGGTCACCGGCGAA 60.890 57.895 9.30 0.00 0.00 4.70
1568 1767 3.114616 CACGGCTCGCTCCACTTG 61.115 66.667 0.00 0.00 0.00 3.16
1642 1841 4.576053 GTGAATCAATGAATGGATCGGTCA 59.424 41.667 0.00 0.00 0.00 4.02
1644 1843 4.577693 CAGTGAATCAATGAATGGATCGGT 59.422 41.667 4.50 0.00 30.53 4.69
1658 1857 0.615331 GGACAGGAGGCAGTGAATCA 59.385 55.000 0.00 0.00 0.00 2.57
1685 1884 0.040958 GCCTGAAGTGAAGTGCGTTG 60.041 55.000 0.00 0.00 0.00 4.10
1800 2005 0.764369 ATGAGGATAGCGGGCCAGAA 60.764 55.000 7.23 0.00 0.00 3.02
1912 2117 2.093890 TGACTTTACGCCGAGTCCATA 58.906 47.619 9.33 0.00 41.19 2.74
1936 2141 1.978580 TGGGGAGAAGTTCCTTGAGAC 59.021 52.381 0.00 0.00 45.98 3.36
2208 2431 9.949174 GACCAAACATTCAATGCTTTAAATTTT 57.051 25.926 0.00 0.00 0.00 1.82
2214 2437 6.647334 TCTGACCAAACATTCAATGCTTTA 57.353 33.333 0.00 0.00 0.00 1.85
2219 2442 3.855379 CGCATCTGACCAAACATTCAATG 59.145 43.478 0.00 0.00 0.00 2.82
2220 2443 3.758023 TCGCATCTGACCAAACATTCAAT 59.242 39.130 0.00 0.00 0.00 2.57
2231 2454 5.938322 TCAAAAATAACTTCGCATCTGACC 58.062 37.500 0.00 0.00 0.00 4.02
2253 2476 6.870965 AGATAGCACCACGAAAATCATAGATC 59.129 38.462 0.00 0.00 0.00 2.75
2256 2479 6.923508 TGTAGATAGCACCACGAAAATCATAG 59.076 38.462 0.00 0.00 0.00 2.23
2260 2483 5.109903 AGTGTAGATAGCACCACGAAAATC 58.890 41.667 0.00 0.00 37.56 2.17
2268 2491 5.339008 AAATTCGAGTGTAGATAGCACCA 57.661 39.130 0.00 0.00 37.56 4.17
2308 2573 2.753055 TTGCACTCATAGGTACGCAA 57.247 45.000 0.00 0.00 37.05 4.85
2359 2624 5.428496 ACATGGATTTATCAGTGCGATTG 57.572 39.130 0.00 0.00 35.39 2.67
2364 2629 4.746729 TGCAAACATGGATTTATCAGTGC 58.253 39.130 0.00 0.00 0.00 4.40
2391 2656 3.970410 CCTTGCAGGGCCTCACCA 61.970 66.667 0.95 0.00 42.05 4.17
2525 2795 3.648339 ACAAGCACCACTGCATTAAAG 57.352 42.857 0.00 0.00 46.97 1.85
2588 2858 0.956902 AACACCATTAACGCGGGGAC 60.957 55.000 12.47 0.00 0.00 4.46
2616 2956 2.812011 GTCCGTGGTACATTTTCAAGCT 59.188 45.455 0.00 0.00 44.52 3.74
2761 3101 0.815734 GTGAGCCAGCATGCAGAAAT 59.184 50.000 21.98 0.79 31.97 2.17
2900 3241 5.220710 ACATGCTACACTCTTCACTCTTT 57.779 39.130 0.00 0.00 0.00 2.52
2914 3255 8.616076 AGCTCAATATTTCAGTTTACATGCTAC 58.384 33.333 0.00 0.00 0.00 3.58
2968 3309 3.986996 TCTTCATGCAACTCAGATCCA 57.013 42.857 0.00 0.00 0.00 3.41
3123 3472 6.549736 TGAACACTGTAGCCTAGCAGAATATA 59.450 38.462 7.89 0.00 36.62 0.86
3125 3474 4.709886 TGAACACTGTAGCCTAGCAGAATA 59.290 41.667 7.89 0.00 36.62 1.75
3150 3499 9.051679 GGAATATAATAAACCAAAACAATGGCC 57.948 33.333 0.00 0.00 44.75 5.36
3178 3527 6.697641 AATAAGGAAACTCTGAACCCAGTA 57.302 37.500 0.00 0.00 42.68 2.74
3184 3533 9.490379 TGTCTAAGAAATAAGGAAACTCTGAAC 57.510 33.333 0.00 0.00 42.68 3.18
3186 3535 9.712305 CTTGTCTAAGAAATAAGGAAACTCTGA 57.288 33.333 0.00 0.00 36.22 3.27
3187 3536 9.712305 TCTTGTCTAAGAAATAAGGAAACTCTG 57.288 33.333 0.00 0.00 38.96 3.35
3274 3624 0.250901 TGGAACAGAGCCTTGCTTCC 60.251 55.000 10.07 10.07 39.88 3.46
3277 3627 1.891150 CATTTGGAACAGAGCCTTGCT 59.109 47.619 0.00 0.00 42.39 3.91
3388 3797 7.558444 TGTAAAGAAAACAGATTACCAACCACT 59.442 33.333 0.00 0.00 0.00 4.00
3522 3933 3.435457 GGTGGGATCAATCATCACCATGA 60.435 47.826 20.41 0.00 44.60 3.07
3523 3934 2.889045 GGTGGGATCAATCATCACCATG 59.111 50.000 20.41 0.00 44.60 3.66
3542 3953 1.434513 ATGTGTCACCATGGTGGGGT 61.435 55.000 38.12 20.34 42.97 4.95
3589 4000 7.877097 CCCACAATTTGATATGGAGAACAAAAA 59.123 33.333 2.79 0.00 36.19 1.94
3623 4034 2.373540 TGCCTAAAAGCACGTATCGT 57.626 45.000 0.00 0.00 42.36 3.73
3624 4035 3.944422 ATTGCCTAAAAGCACGTATCG 57.056 42.857 0.00 0.00 43.97 2.92
3645 4056 4.325030 CCACACCCCTAATGAACCATTACT 60.325 45.833 0.00 0.00 35.54 2.24
3684 4095 2.899900 TGAGTTGAGTCCAGCACATAGT 59.100 45.455 0.00 0.00 0.00 2.12
3700 4111 4.819105 TCAGAATGTATCCCGTTGAGTT 57.181 40.909 0.00 0.00 37.40 3.01
3705 4116 3.914426 AGCTTCAGAATGTATCCCGTT 57.086 42.857 0.00 0.00 37.40 4.44
3716 4127 7.168219 ACAGATTACCATGTTAAGCTTCAGAA 58.832 34.615 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.