Multiple sequence alignment - TraesCS7B01G368600

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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 TraesCS7B01G368600 chr7B 100.000 2935 0 0 1 2935 632801429 632798495 0.000000e+00 5421.0
1 TraesCS7B01G368600 chr7B 92.273 2239 73 45 745 2935 633000999 633003185 0.000000e+00 3085.0
2 TraesCS7B01G368600 chr7B 83.451 1420 123 60 747 2127 591566041 591567387 0.000000e+00 1218.0
3 TraesCS7B01G368600 chr7B 83.589 1237 110 36 760 1967 591684290 591685462 0.000000e+00 1074.0
4 TraesCS7B01G368600 chr7B 81.123 1478 157 73 840 2278 569439782 569438388 0.000000e+00 1072.0
5 TraesCS7B01G368600 chr7B 82.286 1225 108 58 840 2011 569481658 569480490 0.000000e+00 959.0
6 TraesCS7B01G368600 chr7B 86.364 506 36 13 1 489 632999801 633000290 3.350000e-144 521.0
7 TraesCS7B01G368600 chr7B 86.592 358 26 13 2594 2935 569479344 569478993 2.760000e-100 375.0
8 TraesCS7B01G368600 chr7B 87.316 339 25 9 2610 2935 569436449 569436116 3.570000e-99 372.0
9 TraesCS7B01G368600 chr7B 85.329 334 32 8 2610 2928 591054590 591054259 2.180000e-86 329.0
10 TraesCS7B01G368600 chr7B 79.630 324 42 14 1896 2215 591600786 591601089 8.240000e-51 211.0
11 TraesCS7B01G368600 chr7B 84.513 226 20 9 2398 2610 569437106 569436883 2.960000e-50 209.0
12 TraesCS7B01G368600 chr7B 86.154 195 22 3 2150 2343 569480374 569480184 3.830000e-49 206.0
13 TraesCS7B01G368600 chr7B 92.908 141 6 1 544 680 633000863 633001003 4.960000e-48 202.0
14 TraesCS7B01G368600 chr7B 85.792 183 22 2 2150 2331 348751317 348751138 1.070000e-44 191.0
15 TraesCS7B01G368600 chr7D 89.646 1130 48 18 741 1830 573969068 573970168 0.000000e+00 1375.0
16 TraesCS7B01G368600 chr7D 84.491 1109 87 42 956 2013 548066756 548065682 0.000000e+00 1016.0
17 TraesCS7B01G368600 chr7D 79.695 1576 165 71 840 2356 530361639 530360160 0.000000e+00 994.0
18 TraesCS7B01G368600 chr7D 84.361 1087 92 52 840 1886 530430732 530429684 0.000000e+00 994.0
19 TraesCS7B01G368600 chr7D 80.845 1420 141 61 780 2135 548324919 548326271 0.000000e+00 994.0
20 TraesCS7B01G368600 chr7D 84.007 1088 85 29 752 1795 548560700 548561742 0.000000e+00 963.0
21 TraesCS7B01G368600 chr7D 88.259 494 39 8 1933 2412 573970209 573970697 9.120000e-160 573.0
22 TraesCS7B01G368600 chr7D 88.131 337 28 2 2610 2935 548327202 548327537 9.860000e-105 390.0
23 TraesCS7B01G368600 chr7D 87.353 340 24 10 2610 2935 530428613 530428279 3.570000e-99 372.0
24 TraesCS7B01G368600 chr7D 86.510 341 28 8 2610 2935 548064578 548064241 2.780000e-95 359.0
25 TraesCS7B01G368600 chr7D 79.015 548 55 33 1852 2376 548561771 548562281 1.310000e-83 320.0
26 TraesCS7B01G368600 chr7D 86.900 229 15 8 2395 2610 573970713 573970939 2.920000e-60 243.0
27 TraesCS7B01G368600 chr7D 86.900 229 15 8 2395 2610 574248341 574248567 2.920000e-60 243.0
28 TraesCS7B01G368600 chr7D 86.047 215 25 3 2398 2608 530429278 530429065 2.940000e-55 226.0
29 TraesCS7B01G368600 chr7D 92.199 141 10 1 2272 2412 574248186 574248325 6.420000e-47 198.0
30 TraesCS7B01G368600 chr7D 85.870 184 22 2 2150 2332 548326351 548326531 2.990000e-45 193.0
31 TraesCS7B01G368600 chr7D 93.878 98 3 1 1 95 574068401 574068498 8.480000e-31 145.0
32 TraesCS7B01G368600 chr7D 100.000 47 0 0 1853 1899 573970166 573970212 1.450000e-13 87.9
33 TraesCS7B01G368600 chrUn 84.722 1368 120 37 921 2253 337590753 337589440 0.000000e+00 1286.0
34 TraesCS7B01G368600 chrUn 84.912 1193 102 42 747 1909 355335377 355334233 0.000000e+00 1134.0
35 TraesCS7B01G368600 chr7A 82.718 1545 153 61 752 2253 632265736 632267209 0.000000e+00 1269.0
36 TraesCS7B01G368600 chr7A 82.470 1312 115 47 956 2229 617551813 617550579 0.000000e+00 1042.0
37 TraesCS7B01G368600 chr7A 83.698 1098 81 29 752 1793 632187997 632189052 0.000000e+00 946.0
38 TraesCS7B01G368600 chr7A 87.565 772 60 21 804 1556 663750871 663750117 0.000000e+00 861.0
39 TraesCS7B01G368600 chr7A 83.171 820 70 21 824 1596 631872521 631871723 0.000000e+00 688.0
40 TraesCS7B01G368600 chr7A 90.269 483 27 5 1592 2058 663750116 663749638 5.380000e-172 614.0
41 TraesCS7B01G368600 chr7A 89.021 337 26 1 2610 2935 630673955 630674291 9.790000e-110 407.0
42 TraesCS7B01G368600 chr7A 85.799 169 16 5 537 701 663574417 663574581 3.890000e-39 172.0
43 TraesCS7B01G368600 chr7A 79.681 251 27 10 1925 2165 632190123 632190359 3.030000e-35 159.0
44 TraesCS7B01G368600 chr7A 90.000 110 6 1 752 861 617551978 617551874 1.420000e-28 137.0
45 TraesCS7B01G368600 chr7A 84.536 97 15 0 2616 2712 630440342 630440438 2.410000e-16 97.1
46 TraesCS7B01G368600 chr7A 87.931 58 5 2 233 288 663751147 663751090 1.890000e-07 67.6
47 TraesCS7B01G368600 chr4A 85.623 1099 91 30 745 1822 141908875 141907823 0.000000e+00 1092.0
48 TraesCS7B01G368600 chr2B 86.339 183 21 2 2150 2331 49036099 49036278 2.310000e-46 196.0
49 TraesCS7B01G368600 chr4B 84.021 194 25 4 2150 2340 158048899 158048709 6.460000e-42 182.0
50 TraesCS7B01G368600 chr5D 80.288 208 17 11 560 744 227704454 227704248 5.100000e-28 135.0
51 TraesCS7B01G368600 chr5B 80.193 207 19 9 560 744 251251070 251250864 5.100000e-28 135.0
52 TraesCS7B01G368600 chr5A 80.288 208 17 10 560 744 305556234 305556028 5.100000e-28 135.0


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 TraesCS7B01G368600 chr7B 632798495 632801429 2934 True 5421.000000 5421 100.000000 1 2935 1 chr7B.!!$R3 2934
1 TraesCS7B01G368600 chr7B 632999801 633003185 3384 False 1269.333333 3085 90.515000 1 2935 3 chr7B.!!$F4 2934
2 TraesCS7B01G368600 chr7B 591566041 591567387 1346 False 1218.000000 1218 83.451000 747 2127 1 chr7B.!!$F1 1380
3 TraesCS7B01G368600 chr7B 591684290 591685462 1172 False 1074.000000 1074 83.589000 760 1967 1 chr7B.!!$F3 1207
4 TraesCS7B01G368600 chr7B 569436116 569439782 3666 True 551.000000 1072 84.317333 840 2935 3 chr7B.!!$R4 2095
5 TraesCS7B01G368600 chr7B 569478993 569481658 2665 True 513.333333 959 85.010667 840 2935 3 chr7B.!!$R5 2095
6 TraesCS7B01G368600 chr7D 530360160 530361639 1479 True 994.000000 994 79.695000 840 2356 1 chr7D.!!$R1 1516
7 TraesCS7B01G368600 chr7D 548064241 548066756 2515 True 687.500000 1016 85.500500 956 2935 2 chr7D.!!$R3 1979
8 TraesCS7B01G368600 chr7D 548560700 548562281 1581 False 641.500000 963 81.511000 752 2376 2 chr7D.!!$F3 1624
9 TraesCS7B01G368600 chr7D 573969068 573970939 1871 False 569.725000 1375 91.201250 741 2610 4 chr7D.!!$F4 1869
10 TraesCS7B01G368600 chr7D 530428279 530430732 2453 True 530.666667 994 85.920333 840 2935 3 chr7D.!!$R2 2095
11 TraesCS7B01G368600 chr7D 548324919 548327537 2618 False 525.666667 994 84.948667 780 2935 3 chr7D.!!$F2 2155
12 TraesCS7B01G368600 chrUn 337589440 337590753 1313 True 1286.000000 1286 84.722000 921 2253 1 chrUn.!!$R1 1332
13 TraesCS7B01G368600 chrUn 355334233 355335377 1144 True 1134.000000 1134 84.912000 747 1909 1 chrUn.!!$R2 1162
14 TraesCS7B01G368600 chr7A 632265736 632267209 1473 False 1269.000000 1269 82.718000 752 2253 1 chr7A.!!$F3 1501
15 TraesCS7B01G368600 chr7A 631871723 631872521 798 True 688.000000 688 83.171000 824 1596 1 chr7A.!!$R1 772
16 TraesCS7B01G368600 chr7A 617550579 617551978 1399 True 589.500000 1042 86.235000 752 2229 2 chr7A.!!$R2 1477
17 TraesCS7B01G368600 chr7A 632187997 632190359 2362 False 552.500000 946 81.689500 752 2165 2 chr7A.!!$F5 1413
18 TraesCS7B01G368600 chr7A 663749638 663751147 1509 True 514.200000 861 88.588333 233 2058 3 chr7A.!!$R3 1825
19 TraesCS7B01G368600 chr4A 141907823 141908875 1052 True 1092.000000 1092 85.623000 745 1822 1 chr4A.!!$R1 1077

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
249 267 0.034670 AATGCAGAGGAACAGAGGGC 60.035 55.0 0.0 0.0 0.00 5.19 F
713 1324 0.252742 ACCACCTACCCCTTGAGGAG 60.253 60.0 0.0 0.0 38.24 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 2809 1.466167 CGAGCTACAAGCAACTGCATT 59.534 47.619 4.22 0.0 45.56 3.56 R
2037 3856 2.832643 TGCATCTTCCCCAACATGAT 57.167 45.000 0.00 0.0 0.00 2.45 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 5.427378 TCTGCAATATGATGGTTTCGAAGA 58.573 37.500 0.00 0.00 0.00 2.87
31 32 4.034048 GCAATATGATGGTTTCGAAGACGT 59.966 41.667 0.00 0.00 40.69 4.34
38 39 3.992643 TGGTTTCGAAGACGTGGATTTA 58.007 40.909 0.00 0.00 40.69 1.40
95 99 3.664888 TGCTGCCCCTGCCATCTT 61.665 61.111 0.00 0.00 36.33 2.40
97 101 2.515523 CTGCCCCTGCCATCTTCG 60.516 66.667 0.00 0.00 36.33 3.79
98 102 3.329889 TGCCCCTGCCATCTTCGT 61.330 61.111 0.00 0.00 36.33 3.85
146 164 0.036577 AGCCACAGATGCAGTCAGTC 60.037 55.000 0.00 0.00 0.00 3.51
149 167 1.675116 CCACAGATGCAGTCAGTCAGG 60.675 57.143 0.00 0.00 0.00 3.86
152 170 0.036577 AGATGCAGTCAGTCAGGCAC 60.037 55.000 0.00 0.00 39.34 5.01
177 195 4.867047 GCCTGCTACATATACATAGCACAG 59.133 45.833 13.36 10.07 46.82 3.66
178 196 4.867047 CCTGCTACATATACATAGCACAGC 59.133 45.833 13.36 0.00 46.82 4.40
249 267 0.034670 AATGCAGAGGAACAGAGGGC 60.035 55.000 0.00 0.00 0.00 5.19
280 300 7.975866 GAACAAGTTCCATTGCATATAACTG 57.024 36.000 1.51 3.80 33.28 3.16
314 334 5.371115 TCAACTGCCTTGTTAATTAGTGC 57.629 39.130 0.00 0.00 0.00 4.40
315 335 4.824537 TCAACTGCCTTGTTAATTAGTGCA 59.175 37.500 0.00 0.00 0.00 4.57
327 347 7.641760 TGTTAATTAGTGCATGCATATCACTG 58.358 34.615 29.37 10.39 40.80 3.66
337 357 5.758924 CATGCATATCACTGGTTTCAGATG 58.241 41.667 0.00 0.00 43.49 2.90
355 375 5.878669 TCAGATGATCCACAACATTCTTCAG 59.121 40.000 0.00 0.00 0.00 3.02
380 400 2.038863 TAAGCCCTCAACTCCCAGAA 57.961 50.000 0.00 0.00 0.00 3.02
389 409 5.398353 CCCTCAACTCCCAGAAATATCACAT 60.398 44.000 0.00 0.00 0.00 3.21
396 416 7.456725 ACTCCCAGAAATATCACATCCATTAG 58.543 38.462 0.00 0.00 0.00 1.73
397 417 7.293299 ACTCCCAGAAATATCACATCCATTAGA 59.707 37.037 0.00 0.00 0.00 2.10
398 418 7.453393 TCCCAGAAATATCACATCCATTAGAC 58.547 38.462 0.00 0.00 0.00 2.59
399 419 6.656693 CCCAGAAATATCACATCCATTAGACC 59.343 42.308 0.00 0.00 0.00 3.85
400 420 7.226441 CCAGAAATATCACATCCATTAGACCA 58.774 38.462 0.00 0.00 0.00 4.02
401 421 7.886970 CCAGAAATATCACATCCATTAGACCAT 59.113 37.037 0.00 0.00 0.00 3.55
409 429 9.950496 ATCACATCCATTAGACCATTACTAATC 57.050 33.333 0.00 0.00 38.13 1.75
410 430 9.159254 TCACATCCATTAGACCATTACTAATCT 57.841 33.333 0.00 0.00 38.13 2.40
442 462 2.977405 AGCAAAATCGAGCTGACAAC 57.023 45.000 0.00 0.00 40.13 3.32
447 467 4.093408 GCAAAATCGAGCTGACAACTGATA 59.907 41.667 0.00 0.00 0.00 2.15
471 491 5.068198 ACTCCACAGTTTCTTCACGTTAGTA 59.932 40.000 0.00 0.00 0.00 1.82
472 492 5.526115 TCCACAGTTTCTTCACGTTAGTAG 58.474 41.667 0.00 0.00 0.00 2.57
480 500 7.861872 AGTTTCTTCACGTTAGTAGAGAGAAAC 59.138 37.037 19.13 19.13 0.00 2.78
483 503 5.027206 TCACGTTAGTAGAGAGAAACACG 57.973 43.478 0.00 0.00 0.00 4.49
489 509 6.248839 CGTTAGTAGAGAGAAACACGACATTC 59.751 42.308 0.00 0.00 0.00 2.67
491 511 6.274157 AGTAGAGAGAAACACGACATTCAT 57.726 37.500 0.00 0.00 0.00 2.57
492 512 6.692486 AGTAGAGAGAAACACGACATTCATT 58.308 36.000 0.00 0.00 0.00 2.57
495 515 6.226787 AGAGAGAAACACGACATTCATTCTT 58.773 36.000 0.00 0.00 0.00 2.52
497 517 5.991606 AGAGAAACACGACATTCATTCTTCA 59.008 36.000 0.00 0.00 0.00 3.02
498 518 6.146837 AGAGAAACACGACATTCATTCTTCAG 59.853 38.462 0.00 0.00 0.00 3.02
500 520 6.260936 AGAAACACGACATTCATTCTTCAGTT 59.739 34.615 0.00 0.00 0.00 3.16
501 521 7.441157 AGAAACACGACATTCATTCTTCAGTTA 59.559 33.333 0.00 0.00 0.00 2.24
502 522 6.467723 ACACGACATTCATTCTTCAGTTAC 57.532 37.500 0.00 0.00 0.00 2.50
517 960 7.119387 TCTTCAGTTACCTCTGATCATCTACA 58.881 38.462 0.00 0.00 42.84 2.74
523 966 8.200792 AGTTACCTCTGATCATCTACAACATTC 58.799 37.037 0.00 0.00 0.00 2.67
538 981 1.209747 ACATTCCTCGGGCCTCTAAAC 59.790 52.381 0.84 0.00 0.00 2.01
539 982 1.209504 CATTCCTCGGGCCTCTAAACA 59.790 52.381 0.84 0.00 0.00 2.83
540 983 1.580059 TTCCTCGGGCCTCTAAACAT 58.420 50.000 0.84 0.00 0.00 2.71
542 985 1.209504 TCCTCGGGCCTCTAAACATTG 59.790 52.381 0.84 0.00 0.00 2.82
583 1121 0.674269 ACTGACCTCTCGAGTCGACC 60.674 60.000 12.09 2.76 0.00 4.79
584 1122 1.697772 CTGACCTCTCGAGTCGACCG 61.698 65.000 12.09 15.45 0.00 4.79
589 1127 0.516001 CTCTCGAGTCGACCGTGAAA 59.484 55.000 22.21 8.24 0.00 2.69
700 1311 3.644606 CCAGCAGGCTCACCACCT 61.645 66.667 0.00 0.00 39.06 4.00
701 1312 2.293318 CCAGCAGGCTCACCACCTA 61.293 63.158 0.00 0.00 39.06 3.08
703 1314 2.269241 GCAGGCTCACCACCTACC 59.731 66.667 0.00 0.00 39.06 3.18
704 1315 2.990479 CAGGCTCACCACCTACCC 59.010 66.667 0.00 0.00 39.06 3.69
705 1316 2.285442 AGGCTCACCACCTACCCC 60.285 66.667 0.00 0.00 39.06 4.95
706 1317 2.285442 GGCTCACCACCTACCCCT 60.285 66.667 0.00 0.00 35.26 4.79
707 1318 1.923909 GGCTCACCACCTACCCCTT 60.924 63.158 0.00 0.00 35.26 3.95
708 1319 1.299976 GCTCACCACCTACCCCTTG 59.700 63.158 0.00 0.00 0.00 3.61
709 1320 1.198759 GCTCACCACCTACCCCTTGA 61.199 60.000 0.00 0.00 0.00 3.02
710 1321 0.905357 CTCACCACCTACCCCTTGAG 59.095 60.000 0.00 0.00 0.00 3.02
711 1322 0.546747 TCACCACCTACCCCTTGAGG 60.547 60.000 0.00 0.00 38.92 3.86
712 1323 0.546747 CACCACCTACCCCTTGAGGA 60.547 60.000 0.00 0.00 38.24 3.71
713 1324 0.252742 ACCACCTACCCCTTGAGGAG 60.253 60.000 0.00 0.00 38.24 3.69
714 1325 0.983378 CCACCTACCCCTTGAGGAGG 60.983 65.000 0.00 0.21 45.86 4.30
723 1334 3.056628 CTTGAGGAGGATCGTGTGC 57.943 57.895 0.00 0.00 34.37 4.57
724 1335 0.460987 CTTGAGGAGGATCGTGTGCC 60.461 60.000 0.00 0.00 34.37 5.01
725 1336 0.904865 TTGAGGAGGATCGTGTGCCT 60.905 55.000 0.00 0.00 37.18 4.75
728 1339 2.501610 GAGGATCGTGTGCCTCCC 59.498 66.667 0.00 0.00 43.91 4.30
729 1340 3.432051 GAGGATCGTGTGCCTCCCG 62.432 68.421 0.00 0.00 43.91 5.14
730 1341 4.530857 GGATCGTGTGCCTCCCGG 62.531 72.222 0.00 0.00 0.00 5.73
731 1342 3.771160 GATCGTGTGCCTCCCGGT 61.771 66.667 0.00 0.00 0.00 5.28
732 1343 4.082523 ATCGTGTGCCTCCCGGTG 62.083 66.667 0.00 0.00 0.00 4.94
734 1345 3.687102 CGTGTGCCTCCCGGTGTA 61.687 66.667 0.00 0.00 0.00 2.90
735 1346 2.047560 GTGTGCCTCCCGGTGTAC 60.048 66.667 0.00 0.00 0.00 2.90
736 1347 3.315949 TGTGCCTCCCGGTGTACC 61.316 66.667 0.00 0.00 0.00 3.34
806 1419 1.081509 TTTGCCGCTGTTCAATCGC 60.082 52.632 0.00 0.00 0.00 4.58
921 1552 0.818296 CCTCGCCGGGAGATATAAGG 59.182 60.000 18.35 0.00 46.23 2.69
922 1553 0.818296 CTCGCCGGGAGATATAAGGG 59.182 60.000 13.05 0.00 46.23 3.95
924 1555 1.258445 CGCCGGGAGATATAAGGGCT 61.258 60.000 2.18 0.00 38.39 5.19
930 1576 1.066787 GGAGATATAAGGGCTCGTGGC 60.067 57.143 1.89 1.89 40.90 5.01
950 1596 4.522971 GCGATCGCCTTCTTCCTT 57.477 55.556 29.48 0.00 34.56 3.36
951 1597 2.009888 GCGATCGCCTTCTTCCTTG 58.990 57.895 29.48 0.00 34.56 3.61
952 1598 2.009888 CGATCGCCTTCTTCCTTGC 58.990 57.895 0.26 0.00 0.00 4.01
953 1599 1.432270 CGATCGCCTTCTTCCTTGCC 61.432 60.000 0.26 0.00 0.00 4.52
978 1628 4.227982 CCCAATTTCCCCATCAAATCCTTT 59.772 41.667 0.00 0.00 0.00 3.11
1426 2096 2.401766 GCGCCAAGGTCATCACAGG 61.402 63.158 0.00 0.00 0.00 4.00
1432 2108 1.064906 CAAGGTCATCACAGGAGCCAT 60.065 52.381 0.00 0.00 33.37 4.40
1433 2109 0.545171 AGGTCATCACAGGAGCCATG 59.455 55.000 0.00 0.00 33.37 3.66
1434 2110 0.465097 GGTCATCACAGGAGCCATGG 60.465 60.000 7.63 7.63 0.00 3.66
1502 2229 1.372499 CCCTGACGCGAAGACGAAA 60.372 57.895 15.93 0.00 42.66 3.46
1919 2809 7.598869 CAGTTGTAACTAGAACTACTGCAATGA 59.401 37.037 21.13 0.00 41.41 2.57
1946 3738 2.602257 TGCTTGTAGCTCGTATGCAT 57.398 45.000 3.79 3.79 42.97 3.96
1947 3739 2.204237 TGCTTGTAGCTCGTATGCATG 58.796 47.619 10.16 0.00 42.97 4.06
1948 3740 2.205074 GCTTGTAGCTCGTATGCATGT 58.795 47.619 10.16 0.00 38.45 3.21
1949 3741 2.609459 GCTTGTAGCTCGTATGCATGTT 59.391 45.455 10.16 0.00 38.45 2.71
2037 3856 6.423776 AAGGATTTGGAAAGAAATTGCTCA 57.576 33.333 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.598589 CCGTAAATCCACGTCTTCGAA 58.401 47.619 0.00 0.00 40.31 3.71
28 29 2.048033 TGCGCCGTAAATCCACGT 60.048 55.556 4.18 0.00 40.31 4.49
31 32 1.807981 CGACTGCGCCGTAAATCCA 60.808 57.895 3.84 0.00 0.00 3.41
89 93 2.365617 AGCTGGTATACCACGAAGATGG 59.634 50.000 21.05 9.60 46.10 3.51
95 99 0.459899 CAGCAGCTGGTATACCACGA 59.540 55.000 21.05 0.00 42.01 4.35
97 101 2.103094 TGATCAGCAGCTGGTATACCAC 59.897 50.000 21.05 16.59 42.01 4.16
98 102 2.397597 TGATCAGCAGCTGGTATACCA 58.602 47.619 23.23 23.23 45.30 3.25
110 128 2.437002 TGCAGCGCATGATCAGCA 60.437 55.556 11.47 8.93 31.71 4.41
152 170 3.119137 TGCTATGTATATGTAGCAGGCCG 60.119 47.826 14.49 0.00 45.97 6.13
280 300 6.342282 CAAGGCAGTTGATGGTCTGAAACC 62.342 50.000 0.00 0.00 42.92 3.27
295 315 4.380867 GCATGCACTAATTAACAAGGCAGT 60.381 41.667 14.21 0.00 32.84 4.40
314 334 5.529800 TCATCTGAAACCAGTGATATGCATG 59.470 40.000 10.16 0.00 33.49 4.06
315 335 5.687780 TCATCTGAAACCAGTGATATGCAT 58.312 37.500 3.79 3.79 33.49 3.96
327 347 5.416952 AGAATGTTGTGGATCATCTGAAACC 59.583 40.000 0.00 0.00 0.00 3.27
337 357 7.396540 AATTACCTGAAGAATGTTGTGGATC 57.603 36.000 0.00 0.00 0.00 3.36
355 375 3.053917 TGGGAGTTGAGGGCTTAATTACC 60.054 47.826 0.00 0.00 0.00 2.85
403 423 9.681062 TTTTGCTGGCTTAGTTTATAGATTAGT 57.319 29.630 0.00 0.00 0.00 2.24
406 426 8.345565 CGATTTTGCTGGCTTAGTTTATAGATT 58.654 33.333 0.00 0.00 0.00 2.40
407 427 7.715249 TCGATTTTGCTGGCTTAGTTTATAGAT 59.285 33.333 0.00 0.00 0.00 1.98
408 428 7.045416 TCGATTTTGCTGGCTTAGTTTATAGA 58.955 34.615 0.00 0.00 0.00 1.98
409 429 7.246674 TCGATTTTGCTGGCTTAGTTTATAG 57.753 36.000 0.00 0.00 0.00 1.31
410 430 6.238374 GCTCGATTTTGCTGGCTTAGTTTATA 60.238 38.462 0.00 0.00 0.00 0.98
411 431 5.449177 GCTCGATTTTGCTGGCTTAGTTTAT 60.449 40.000 0.00 0.00 0.00 1.40
416 436 2.012673 AGCTCGATTTTGCTGGCTTAG 58.987 47.619 0.00 0.00 38.21 2.18
442 462 4.623167 CGTGAAGAAACTGTGGAGTATCAG 59.377 45.833 0.00 0.00 36.25 2.90
447 467 2.981859 ACGTGAAGAAACTGTGGAGT 57.018 45.000 0.00 0.00 0.00 3.85
460 480 5.237127 TCGTGTTTCTCTCTACTAACGTGAA 59.763 40.000 0.00 0.00 0.00 3.18
461 481 4.751600 TCGTGTTTCTCTCTACTAACGTGA 59.248 41.667 0.00 0.00 0.00 4.35
471 491 5.788450 AGAATGAATGTCGTGTTTCTCTCT 58.212 37.500 0.00 0.00 0.00 3.10
472 492 6.146184 TGAAGAATGAATGTCGTGTTTCTCTC 59.854 38.462 0.00 0.00 0.00 3.20
480 500 5.858475 GGTAACTGAAGAATGAATGTCGTG 58.142 41.667 0.00 0.00 0.00 4.35
498 518 7.439655 GGAATGTTGTAGATGATCAGAGGTAAC 59.560 40.741 0.09 4.95 0.00 2.50
500 520 6.841229 AGGAATGTTGTAGATGATCAGAGGTA 59.159 38.462 0.09 0.00 0.00 3.08
501 521 5.664908 AGGAATGTTGTAGATGATCAGAGGT 59.335 40.000 0.09 0.00 0.00 3.85
502 522 6.172136 AGGAATGTTGTAGATGATCAGAGG 57.828 41.667 0.09 0.00 0.00 3.69
517 960 1.580059 TTAGAGGCCCGAGGAATGTT 58.420 50.000 0.00 0.00 0.00 2.71
523 966 1.668419 CAATGTTTAGAGGCCCGAGG 58.332 55.000 0.00 0.00 0.00 4.63
555 1093 5.254901 ACTCGAGAGGTCAGTGTACTAATT 58.745 41.667 21.68 0.00 0.00 1.40
562 1100 0.035036 TCGACTCGAGAGGTCAGTGT 59.965 55.000 21.68 0.00 32.92 3.55
584 1122 1.069227 GCTGGACGTGGTGATTTTCAC 60.069 52.381 0.00 0.00 46.23 3.18
589 1127 2.047274 CCGCTGGACGTGGTGATT 60.047 61.111 0.00 0.00 41.42 2.57
683 1294 2.293318 TAGGTGGTGAGCCTGCTGG 61.293 63.158 5.03 5.03 37.54 4.85
684 1295 1.078848 GTAGGTGGTGAGCCTGCTG 60.079 63.158 0.00 0.00 37.54 4.41
685 1296 2.294078 GGTAGGTGGTGAGCCTGCT 61.294 63.158 0.00 0.00 38.53 4.24
686 1297 2.269241 GGTAGGTGGTGAGCCTGC 59.731 66.667 0.00 0.00 37.54 4.85
689 1300 1.923909 AAGGGGTAGGTGGTGAGCC 60.924 63.158 0.00 0.00 0.00 4.70
691 1302 0.905357 CTCAAGGGGTAGGTGGTGAG 59.095 60.000 0.00 0.00 0.00 3.51
692 1303 0.546747 CCTCAAGGGGTAGGTGGTGA 60.547 60.000 0.00 0.00 0.00 4.02
693 1304 0.546747 TCCTCAAGGGGTAGGTGGTG 60.547 60.000 0.00 0.00 34.30 4.17
694 1305 0.252742 CTCCTCAAGGGGTAGGTGGT 60.253 60.000 0.00 0.00 34.30 4.16
695 1306 0.983378 CCTCCTCAAGGGGTAGGTGG 60.983 65.000 0.00 0.00 42.03 4.61
697 1308 1.027815 ATCCTCCTCAAGGGGTAGGT 58.972 55.000 0.00 0.00 46.23 3.08
698 1309 1.723288 GATCCTCCTCAAGGGGTAGG 58.277 60.000 0.00 0.00 46.23 3.18
700 1311 0.635009 ACGATCCTCCTCAAGGGGTA 59.365 55.000 0.00 0.00 46.23 3.69
701 1312 0.978146 CACGATCCTCCTCAAGGGGT 60.978 60.000 0.00 0.00 46.23 4.95
703 1314 0.176680 CACACGATCCTCCTCAAGGG 59.823 60.000 0.00 0.00 46.23 3.95
705 1316 0.460987 GGCACACGATCCTCCTCAAG 60.461 60.000 0.00 0.00 0.00 3.02
706 1317 0.904865 AGGCACACGATCCTCCTCAA 60.905 55.000 0.00 0.00 0.00 3.02
707 1318 1.305297 AGGCACACGATCCTCCTCA 60.305 57.895 0.00 0.00 0.00 3.86
708 1319 1.439644 GAGGCACACGATCCTCCTC 59.560 63.158 0.00 0.00 42.30 3.71
709 1320 3.622514 GAGGCACACGATCCTCCT 58.377 61.111 0.00 0.00 42.30 3.69
711 1322 2.501610 GGGAGGCACACGATCCTC 59.498 66.667 0.00 0.00 46.25 3.71
737 1348 2.061740 AACTTGTTCTCCGTCGCTAC 57.938 50.000 0.00 0.00 0.00 3.58
738 1349 2.608752 GGAAACTTGTTCTCCGTCGCTA 60.609 50.000 0.00 0.00 0.00 4.26
739 1350 1.499049 GAAACTTGTTCTCCGTCGCT 58.501 50.000 0.00 0.00 0.00 4.93
740 1351 0.511653 GGAAACTTGTTCTCCGTCGC 59.488 55.000 0.00 0.00 0.00 5.19
741 1352 0.782384 CGGAAACTTGTTCTCCGTCG 59.218 55.000 19.16 0.00 45.62 5.12
750 1361 3.645975 CGCGCCACGGAAACTTGT 61.646 61.111 0.00 0.00 38.44 3.16
864 1484 2.202663 GACGCGAGCAGAGCATGA 60.203 61.111 15.93 0.00 34.19 3.07
865 1485 3.260483 GGACGCGAGCAGAGCATG 61.260 66.667 15.93 0.00 34.19 4.06
866 1486 4.862092 CGGACGCGAGCAGAGCAT 62.862 66.667 15.93 0.00 34.19 3.79
869 1489 3.805307 AGTCGGACGCGAGCAGAG 61.805 66.667 15.93 0.00 0.00 3.35
953 1599 1.963985 TTTGATGGGGAAATTGGGGG 58.036 50.000 0.00 0.00 0.00 5.40
970 1620 3.010696 GGAGAAGTGGGGAGAAAGGATTT 59.989 47.826 0.00 0.00 43.98 2.17
978 1628 0.417437 TGGATGGAGAAGTGGGGAGA 59.583 55.000 0.00 0.00 0.00 3.71
1419 2089 2.191375 CGCCATGGCTCCTGTGAT 59.809 61.111 33.07 0.00 39.32 3.06
1426 2096 4.916293 TCATCGGCGCCATGGCTC 62.916 66.667 33.07 26.32 42.02 4.70
1432 2108 2.819595 GCTTCTTCATCGGCGCCA 60.820 61.111 28.98 14.46 0.00 5.69
1433 2109 2.512515 AGCTTCTTCATCGGCGCC 60.513 61.111 19.07 19.07 0.00 6.53
1434 2110 2.705826 CAGCTTCTTCATCGGCGC 59.294 61.111 0.00 0.00 0.00 6.53
1581 2314 2.050714 GTCACCGTCGACGAAGCA 60.051 61.111 37.65 16.23 43.02 3.91
1719 2452 1.880675 CCTGATTGGCTGCATCATCTC 59.119 52.381 0.50 0.00 30.15 2.75
1919 2809 1.466167 CGAGCTACAAGCAACTGCATT 59.534 47.619 4.22 0.00 45.56 3.56
1946 3738 8.541133 TCTTTCGATCACATACATAACAAACA 57.459 30.769 0.00 0.00 0.00 2.83
1947 3739 9.478019 CTTCTTTCGATCACATACATAACAAAC 57.522 33.333 0.00 0.00 0.00 2.93
1948 3740 9.214957 ACTTCTTTCGATCACATACATAACAAA 57.785 29.630 0.00 0.00 0.00 2.83
1949 3741 8.771920 ACTTCTTTCGATCACATACATAACAA 57.228 30.769 0.00 0.00 0.00 2.83
2006 3816 7.537596 TTTCTTTCCAAATCCTTTGCAGATA 57.462 32.000 0.00 0.00 39.31 1.98
2037 3856 2.832643 TGCATCTTCCCCAACATGAT 57.167 45.000 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.