Multiple sequence alignment - TraesCS7D01G058800

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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 TraesCS7D01G058800 chr7D 100.000 4499 0 0 1 4499 31948530 31944032 0.000000e+00 8309
1 TraesCS7D01G058800 chr7D 92.574 1010 64 8 2194 3198 536650895 536649892 0.000000e+00 1439
2 TraesCS7D01G058800 chr7D 90.963 1018 58 9 2194 3197 10631059 10632056 0.000000e+00 1339
3 TraesCS7D01G058800 chr7D 96.897 419 13 0 1090 1508 109949814 109950232 0.000000e+00 702
4 TraesCS7D01G058800 chr5D 91.241 2626 176 25 1884 4496 404854326 404856910 0.000000e+00 3526
5 TraesCS7D01G058800 chr4A 88.218 2979 239 43 465 3361 696006026 696008974 0.000000e+00 3454
6 TraesCS7D01G058800 chr4A 91.582 594 33 9 3907 4496 696009527 696010107 0.000000e+00 804
7 TraesCS7D01G058800 chr4A 88.462 468 48 3 3 465 696005589 696006055 1.090000e-155 560
8 TraesCS7D01G058800 chr2A 88.547 2017 163 31 1884 3890 736006408 736008366 0.000000e+00 2383
9 TraesCS7D01G058800 chr2A 92.084 619 37 9 3882 4496 736008422 736009032 0.000000e+00 861
10 TraesCS7D01G058800 chr2D 91.995 1524 111 8 1884 3402 604077657 604079174 0.000000e+00 2128
11 TraesCS7D01G058800 chr2D 92.329 1108 67 10 3394 4496 604128930 604130024 0.000000e+00 1559
12 TraesCS7D01G058800 chr2D 98.734 790 10 0 1090 1879 477990845 477991634 0.000000e+00 1404
13 TraesCS7D01G058800 chr2D 95.431 197 8 1 1090 1286 477991882 477991687 3.380000e-81 313
14 TraesCS7D01G058800 chr2D 95.604 182 8 0 1090 1271 73454832 73455013 4.400000e-75 292
15 TraesCS7D01G058800 chr2D 93.717 191 8 4 1091 1279 73456213 73456025 2.650000e-72 283
16 TraesCS7D01G058800 chr6D 92.391 1012 68 6 2194 3198 425082208 425081199 0.000000e+00 1434
17 TraesCS7D01G058800 chr6D 91.454 1018 57 8 2194 3197 17969890 17968889 0.000000e+00 1371
18 TraesCS7D01G058800 chr6D 96.984 431 13 0 1090 1520 276587900 276588330 0.000000e+00 725
19 TraesCS7D01G058800 chr6D 96.316 190 7 0 1090 1279 415403231 415403042 3.380000e-81 313
20 TraesCS7D01G058800 chr6D 81.006 179 30 2 73 251 298139551 298139725 6.070000e-29 139
21 TraesCS7D01G058800 chr7A 89.243 1097 97 11 1785 2875 32012867 32011786 0.000000e+00 1352
22 TraesCS7D01G058800 chr7A 86.577 1043 98 27 3 1023 32025537 32024515 0.000000e+00 1112
23 TraesCS7D01G058800 chr7A 88.971 680 63 9 3831 4499 32011097 32010419 0.000000e+00 830
24 TraesCS7D01G058800 chr7A 80.946 698 73 32 910 1568 32013910 32013234 8.690000e-137 497
25 TraesCS7D01G058800 chr7A 92.135 178 12 2 2034 2210 32023444 32023268 2.690000e-62 250
26 TraesCS7D01G058800 chr4B 90.981 1009 69 7 2194 3196 535342860 535341868 0.000000e+00 1339
27 TraesCS7D01G058800 chr4B 78.615 491 66 23 1265 1733 116356010 116355537 5.690000e-74 289
28 TraesCS7D01G058800 chr4B 94.475 181 10 0 1891 2071 116355310 116355130 3.430000e-71 279
29 TraesCS7D01G058800 chr2B 91.086 875 58 6 2194 3062 359317981 359317121 0.000000e+00 1166
30 TraesCS7D01G058800 chr2B 90.971 875 59 6 2194 3062 373106628 373107488 0.000000e+00 1160
31 TraesCS7D01G058800 chr2B 81.564 179 25 3 73 251 13184341 13184171 1.690000e-29 141
32 TraesCS7D01G058800 chr6B 94.000 650 34 4 2552 3198 92353615 92354262 0.000000e+00 979
33 TraesCS7D01G058800 chr6B 83.333 324 29 15 1265 1568 180390933 180391251 4.430000e-70 276
34 TraesCS7D01G058800 chrUn 100.000 415 0 0 1465 1879 477296179 477296593 0.000000e+00 767
35 TraesCS7D01G058800 chr7B 92.026 464 33 3 1894 2353 630109326 630108863 0.000000e+00 649
36 TraesCS7D01G058800 chr7B 84.286 350 36 10 1245 1578 630110011 630109665 1.560000e-84 324
37 TraesCS7D01G058800 chr5B 80.000 490 61 22 1265 1733 460195982 460195509 1.210000e-85 327
38 TraesCS7D01G058800 chr5B 95.580 181 8 0 1891 2071 460195282 460195102 1.580000e-74 291
39 TraesCS7D01G058800 chr1B 84.706 340 33 9 1245 1568 144274774 144274438 5.610000e-84 322
40 TraesCS7D01G058800 chr1B 78.776 490 67 22 1265 1733 637313531 637313058 1.220000e-75 294
41 TraesCS7D01G058800 chr1B 78.411 491 68 20 1265 1733 27091643 27092117 7.370000e-73 285
42 TraesCS7D01G058800 chr1B 95.506 178 8 0 1891 2068 27092344 27092521 7.370000e-73 285
43 TraesCS7D01G058800 chr1B 94.475 181 10 0 1891 2071 637312831 637312651 3.430000e-71 279
44 TraesCS7D01G058800 chr1B 81.006 179 30 2 73 251 253825118 253825292 6.070000e-29 139


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 TraesCS7D01G058800 chr7D 31944032 31948530 4498 True 8309.0 8309 100.000000 1 4499 1 chr7D.!!$R1 4498
1 TraesCS7D01G058800 chr7D 536649892 536650895 1003 True 1439.0 1439 92.574000 2194 3198 1 chr7D.!!$R2 1004
2 TraesCS7D01G058800 chr7D 10631059 10632056 997 False 1339.0 1339 90.963000 2194 3197 1 chr7D.!!$F1 1003
3 TraesCS7D01G058800 chr5D 404854326 404856910 2584 False 3526.0 3526 91.241000 1884 4496 1 chr5D.!!$F1 2612
4 TraesCS7D01G058800 chr4A 696005589 696010107 4518 False 1606.0 3454 89.420667 3 4496 3 chr4A.!!$F1 4493
5 TraesCS7D01G058800 chr2A 736006408 736009032 2624 False 1622.0 2383 90.315500 1884 4496 2 chr2A.!!$F1 2612
6 TraesCS7D01G058800 chr2D 604077657 604079174 1517 False 2128.0 2128 91.995000 1884 3402 1 chr2D.!!$F3 1518
7 TraesCS7D01G058800 chr2D 604128930 604130024 1094 False 1559.0 1559 92.329000 3394 4496 1 chr2D.!!$F4 1102
8 TraesCS7D01G058800 chr2D 477990845 477991634 789 False 1404.0 1404 98.734000 1090 1879 1 chr2D.!!$F2 789
9 TraesCS7D01G058800 chr6D 425081199 425082208 1009 True 1434.0 1434 92.391000 2194 3198 1 chr6D.!!$R3 1004
10 TraesCS7D01G058800 chr6D 17968889 17969890 1001 True 1371.0 1371 91.454000 2194 3197 1 chr6D.!!$R1 1003
11 TraesCS7D01G058800 chr7A 32010419 32013910 3491 True 893.0 1352 86.386667 910 4499 3 chr7A.!!$R1 3589
12 TraesCS7D01G058800 chr7A 32023268 32025537 2269 True 681.0 1112 89.356000 3 2210 2 chr7A.!!$R2 2207
13 TraesCS7D01G058800 chr4B 535341868 535342860 992 True 1339.0 1339 90.981000 2194 3196 1 chr4B.!!$R1 1002
14 TraesCS7D01G058800 chr4B 116355130 116356010 880 True 284.0 289 86.545000 1265 2071 2 chr4B.!!$R2 806
15 TraesCS7D01G058800 chr2B 359317121 359317981 860 True 1166.0 1166 91.086000 2194 3062 1 chr2B.!!$R2 868
16 TraesCS7D01G058800 chr2B 373106628 373107488 860 False 1160.0 1160 90.971000 2194 3062 1 chr2B.!!$F1 868
17 TraesCS7D01G058800 chr6B 92353615 92354262 647 False 979.0 979 94.000000 2552 3198 1 chr6B.!!$F1 646
18 TraesCS7D01G058800 chr7B 630108863 630110011 1148 True 486.5 649 88.156000 1245 2353 2 chr7B.!!$R1 1108
19 TraesCS7D01G058800 chr5B 460195102 460195982 880 True 309.0 327 87.790000 1265 2071 2 chr5B.!!$R1 806
20 TraesCS7D01G058800 chr1B 637312651 637313531 880 True 286.5 294 86.625500 1265 2071 2 chr1B.!!$R2 806
21 TraesCS7D01G058800 chr1B 27091643 27092521 878 False 285.0 285 86.958500 1265 2068 2 chr1B.!!$F2 803

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
488 528 0.110056 CGCAAGTTGCATCCTGTGTC 60.110 55.0 26.56 0.0 45.36 3.67 F
978 1037 0.250945 TGTTGGCACGATGGGCTTTA 60.251 50.0 0.00 0.0 0.00 1.85 F
2542 3426 0.107410 CCGGTAAGTGGCCTGCATTA 60.107 55.0 3.32 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 3204 0.983467 TGGCAGTGGCAGTGAGATTA 59.017 50.000 25.96 3.68 43.71 1.75 R
2606 3500 1.577328 CCCAGTGCACGTAAGCCAAG 61.577 60.000 12.01 0.00 45.62 3.61 R
3970 5347 1.227002 GGCTCGAAGCTCCGTTAGG 60.227 63.158 0.00 0.00 41.99 2.69 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
24 25 2.100989 AGCAGGTGCCTACTACACTAC 58.899 52.381 0.00 0.00 43.38 2.73
41 42 6.354794 ACACTACAGCATTTGTCCTAGTTA 57.645 37.500 0.00 0.00 41.29 2.24
127 132 5.990996 CACCAGGCAACATAGAAACAAAATT 59.009 36.000 0.00 0.00 41.41 1.82
129 134 5.409214 CCAGGCAACATAGAAACAAAATTGG 59.591 40.000 0.00 0.00 41.41 3.16
131 136 7.151308 CAGGCAACATAGAAACAAAATTGGTA 58.849 34.615 0.00 0.00 41.41 3.25
158 163 0.530744 AAAGCTACACGATCCGAGCA 59.469 50.000 0.00 0.00 37.40 4.26
172 177 0.239347 CGAGCAAAGCAAACCAGGAG 59.761 55.000 0.00 0.00 0.00 3.69
173 178 1.322442 GAGCAAAGCAAACCAGGAGT 58.678 50.000 0.00 0.00 0.00 3.85
217 222 5.529060 TCACTTCTTCCTTTTCTGCTTCTTC 59.471 40.000 0.00 0.00 0.00 2.87
268 273 1.558233 AACGGAGATCCTCGACCTTT 58.442 50.000 11.50 0.00 0.00 3.11
273 278 0.340208 AGATCCTCGACCTTTCCCCT 59.660 55.000 0.00 0.00 0.00 4.79
283 288 2.645297 GACCTTTCCCCTCTTCCTCTTT 59.355 50.000 0.00 0.00 0.00 2.52
289 294 6.467339 CCTTTCCCCTCTTCCTCTTTTTCTTA 60.467 42.308 0.00 0.00 0.00 2.10
301 306 2.570415 TTTTCTTACCACCATCGGCA 57.430 45.000 0.00 0.00 0.00 5.69
302 307 1.816074 TTTCTTACCACCATCGGCAC 58.184 50.000 0.00 0.00 0.00 5.01
307 312 4.758251 CCACCATCGGCACTCGCA 62.758 66.667 0.00 0.00 41.24 5.10
308 313 3.490759 CACCATCGGCACTCGCAC 61.491 66.667 0.00 0.00 41.24 5.34
316 321 2.505118 GCACTCGCACTCTCGTCC 60.505 66.667 0.00 0.00 38.36 4.79
318 323 3.432588 ACTCGCACTCTCGTCCGG 61.433 66.667 0.00 0.00 0.00 5.14
336 341 3.252284 CCCTGGTGCACCCTCTGT 61.252 66.667 32.62 0.00 34.29 3.41
338 343 1.488705 CCCTGGTGCACCCTCTGTTA 61.489 60.000 32.62 11.58 34.29 2.41
368 373 2.348998 CGGCAGCCTCCAAGTTCT 59.651 61.111 10.54 0.00 0.00 3.01
376 381 2.639839 AGCCTCCAAGTTCTGCTTCTTA 59.360 45.455 0.00 0.00 34.69 2.10
409 414 6.676456 GCACAATCATTCACCAGCTACTAAAG 60.676 42.308 0.00 0.00 0.00 1.85
410 415 6.595326 CACAATCATTCACCAGCTACTAAAGA 59.405 38.462 0.00 0.00 0.00 2.52
417 422 4.695455 TCACCAGCTACTAAAGAACAATGC 59.305 41.667 0.00 0.00 0.00 3.56
474 514 4.613570 GTGTTAAGCACAATTTCGCAAG 57.386 40.909 0.00 0.00 46.91 4.01
475 515 4.041723 GTGTTAAGCACAATTTCGCAAGT 58.958 39.130 0.00 0.00 46.91 3.16
476 516 4.502645 GTGTTAAGCACAATTTCGCAAGTT 59.497 37.500 0.00 0.00 46.91 2.66
477 517 4.502282 TGTTAAGCACAATTTCGCAAGTTG 59.498 37.500 0.00 0.00 32.44 3.16
478 518 1.490621 AGCACAATTTCGCAAGTTGC 58.509 45.000 18.18 18.18 40.69 4.17
479 519 1.202394 AGCACAATTTCGCAAGTTGCA 60.202 42.857 26.56 11.72 45.36 4.08
480 520 1.794116 GCACAATTTCGCAAGTTGCAT 59.206 42.857 26.56 10.75 45.36 3.96
481 521 2.159934 GCACAATTTCGCAAGTTGCATC 60.160 45.455 26.56 0.00 45.36 3.91
482 522 2.409378 CACAATTTCGCAAGTTGCATCC 59.591 45.455 26.56 0.00 45.36 3.51
483 523 2.297033 ACAATTTCGCAAGTTGCATCCT 59.703 40.909 26.56 6.42 45.36 3.24
484 524 2.642139 ATTTCGCAAGTTGCATCCTG 57.358 45.000 26.56 10.68 45.36 3.86
485 525 1.317613 TTTCGCAAGTTGCATCCTGT 58.682 45.000 26.56 0.00 45.36 4.00
486 526 0.592637 TTCGCAAGTTGCATCCTGTG 59.407 50.000 26.56 9.26 45.36 3.66
487 527 0.534877 TCGCAAGTTGCATCCTGTGT 60.535 50.000 26.56 0.00 45.36 3.72
488 528 0.110056 CGCAAGTTGCATCCTGTGTC 60.110 55.000 26.56 0.00 45.36 3.67
489 529 1.242076 GCAAGTTGCATCCTGTGTCT 58.758 50.000 22.90 0.00 44.26 3.41
490 530 2.426522 GCAAGTTGCATCCTGTGTCTA 58.573 47.619 22.90 0.00 44.26 2.59
491 531 2.417933 GCAAGTTGCATCCTGTGTCTAG 59.582 50.000 22.90 0.00 44.26 2.43
492 532 3.005554 CAAGTTGCATCCTGTGTCTAGG 58.994 50.000 0.00 0.00 39.29 3.02
493 533 6.899155 GCAAGTTGCATCCTGTGTCTAGGA 62.899 50.000 22.90 0.00 44.26 2.94
538 578 2.363795 TCCTTCCCCGTCGCATCT 60.364 61.111 0.00 0.00 0.00 2.90
553 593 3.052909 ATCTGCGCCATGCTTCCCT 62.053 57.895 4.18 0.00 46.63 4.20
652 693 0.392595 GGGGTAAGGAAAGCTCACCG 60.393 60.000 0.00 0.00 0.00 4.94
845 889 1.382695 TTCCCCGTCATCTCCTCCC 60.383 63.158 0.00 0.00 0.00 4.30
921 979 0.385751 CGCGGATTAGAGCAGAGGAA 59.614 55.000 0.00 0.00 0.00 3.36
968 1027 2.358125 TGGACCGATGTTGGCACG 60.358 61.111 0.00 0.00 0.00 5.34
969 1028 2.047655 GGACCGATGTTGGCACGA 60.048 61.111 0.00 0.00 0.00 4.35
977 1036 0.899717 ATGTTGGCACGATGGGCTTT 60.900 50.000 0.00 0.00 0.00 3.51
978 1037 0.250945 TGTTGGCACGATGGGCTTTA 60.251 50.000 0.00 0.00 0.00 1.85
1037 1103 4.778143 GTGCCCGGCGAGGATTGT 62.778 66.667 9.30 0.00 45.00 2.71
1038 1104 4.776322 TGCCCGGCGAGGATTGTG 62.776 66.667 9.30 0.00 45.00 3.33
1888 2636 9.522804 CTAGACAGTTCCTACATAATCAAAGTC 57.477 37.037 0.00 0.00 0.00 3.01
2299 3180 3.072476 TCACACTAGCCCTGTTTTAGCTT 59.928 43.478 0.00 0.00 38.06 3.74
2321 3202 6.529125 GCTTGATTTGGTTCACAAGACATATG 59.471 38.462 0.00 0.00 41.16 1.78
2323 3204 5.711506 TGATTTGGTTCACAAGACATATGCT 59.288 36.000 1.58 0.00 40.82 3.79
2330 3211 6.763135 GGTTCACAAGACATATGCTAATCTCA 59.237 38.462 1.58 0.00 0.00 3.27
2362 3243 4.273724 GCCAGGAATCCGACTTAATTTCTC 59.726 45.833 0.00 0.00 0.00 2.87
2469 3350 9.000486 GTATAAAGTTAAATCTAGGGGACATGC 58.000 37.037 0.00 0.00 0.00 4.06
2486 3367 5.586243 GGACATGCTTGATCTTACTGCTTTA 59.414 40.000 6.60 0.00 0.00 1.85
2542 3426 0.107410 CCGGTAAGTGGCCTGCATTA 60.107 55.000 3.32 0.00 0.00 1.90
2543 3427 1.680555 CCGGTAAGTGGCCTGCATTAA 60.681 52.381 3.32 0.00 0.00 1.40
2563 3456 7.542130 GCATTAACTTCAGTTCACAATTAAGGG 59.458 37.037 0.00 0.00 39.31 3.95
2606 3500 9.899226 AAAAAGAATAACATAACTTGACTCAGC 57.101 29.630 0.00 0.00 0.00 4.26
2646 3549 3.567164 GGCAGACCTGATGATAACATTGG 59.433 47.826 0.47 5.01 36.82 3.16
2742 3655 2.503356 AGAAGACAGCCGGATGAATTCT 59.497 45.455 29.47 27.87 0.00 2.40
2835 3787 2.100252 GCATAGCAATTCCAGCATGTGT 59.900 45.455 0.00 0.00 0.00 3.72
2862 3814 8.225603 TCAGCAAAACTTCTATAAATGGGATC 57.774 34.615 0.00 0.00 0.00 3.36
2969 3932 0.249120 CCTGGTCGTGCAATACCTCA 59.751 55.000 17.21 0.66 36.67 3.86
3289 4256 1.002250 CGTGCGCGTTCTTCTGTACT 61.002 55.000 12.43 0.00 0.00 2.73
3321 4288 1.127951 GAACATTGGCGGTCAAGTACG 59.872 52.381 0.14 0.00 38.95 3.67
3332 4299 2.475852 GGTCAAGTACGCTGTAGTCTCG 60.476 54.545 0.00 0.00 0.00 4.04
3368 4335 3.004734 TGAAAGGTAAAAAGAGCTGCAGC 59.995 43.478 31.53 31.53 42.49 5.25
3384 4351 0.378257 CAGCGCGCAAATAGTTCCAT 59.622 50.000 35.10 4.19 0.00 3.41
3388 4355 2.223157 GCGCGCAAATAGTTCCATGTAA 60.223 45.455 29.10 0.00 0.00 2.41
3389 4356 3.548014 GCGCGCAAATAGTTCCATGTAAT 60.548 43.478 29.10 0.00 0.00 1.89
3684 4653 7.860373 TCATTTCCTCATGAAACTTTAAACACG 59.140 33.333 0.00 0.00 45.38 4.49
3694 4663 6.757947 TGAAACTTTAAACACGTGTAGCTACT 59.242 34.615 23.69 1.22 0.00 2.57
3711 4682 5.256474 AGCTACTCTATGTTGGTTGCAAAT 58.744 37.500 0.00 0.00 35.04 2.32
3712 4683 5.124457 AGCTACTCTATGTTGGTTGCAAATG 59.876 40.000 0.00 0.00 35.04 2.32
3719 4690 4.734398 TGTTGGTTGCAAATGAGTTTCT 57.266 36.364 0.00 0.00 0.00 2.52
3792 4772 5.600484 ACCCTTGTTCACCATTGTATTTTCA 59.400 36.000 0.00 0.00 0.00 2.69
3798 4778 7.881142 TGTTCACCATTGTATTTTCAAGGTAG 58.119 34.615 0.00 0.00 32.23 3.18
3852 4864 7.601886 AGCCGAATCTTCATAATTCTATCACAG 59.398 37.037 0.00 0.00 32.15 3.66
3953 5329 5.888724 TGAGTTCAACCAAAGGTCAAACATA 59.111 36.000 12.99 3.01 33.12 2.29
3969 5346 8.499162 GGTCAAACATATATTTTCATCTCCGAG 58.501 37.037 0.00 0.00 0.00 4.63
3970 5347 8.012241 GTCAAACATATATTTTCATCTCCGAGC 58.988 37.037 0.00 0.00 0.00 5.03
4020 5399 1.935873 CATTGGGTGATGTGCTAGTCG 59.064 52.381 0.00 0.00 0.00 4.18
4027 5406 2.594119 GATGTGCTAGTCGCGGTCGT 62.594 60.000 6.13 0.00 43.27 4.34
4029 5408 3.051479 TGCTAGTCGCGGTCGTCA 61.051 61.111 6.13 0.00 43.27 4.35
4117 5496 4.156008 ACCGAGATAAAAGTGTGATTTGGC 59.844 41.667 0.00 0.00 0.00 4.52
4129 5508 2.831526 GTGATTTGGCTGGTTAACCCAT 59.168 45.455 21.97 4.46 44.15 4.00
4159 5538 8.620116 TGTTTGACAACTCATCTATTGATTGA 57.380 30.769 0.00 0.00 32.72 2.57
4160 5539 9.234827 TGTTTGACAACTCATCTATTGATTGAT 57.765 29.630 0.00 0.00 32.72 2.57
4185 5565 5.708736 ACCTGTTGGTGATGTTATGGATA 57.291 39.130 0.00 0.00 46.51 2.59
4186 5566 5.684704 ACCTGTTGGTGATGTTATGGATAG 58.315 41.667 0.00 0.00 46.51 2.08
4303 5688 4.455533 GCTCCTCAAATGACACATGTTACA 59.544 41.667 0.00 0.00 0.00 2.41
4323 5708 5.841957 ACATTTCTAATCCTGTTGATGCC 57.158 39.130 0.00 0.00 32.68 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.108168 TGTAGTAGGCACCTGCTTAGG 58.892 52.381 12.75 0.00 39.61 2.69
1 2 2.761208 AGTGTAGTAGGCACCTGCTTAG 59.239 50.000 12.75 0.00 39.61 2.18
61 62 6.047870 AGTATCTTGCTTCAAGTGATGCTAG 58.952 40.000 18.17 18.17 43.69 3.42
127 132 3.435327 CGTGTAGCTTTTTGCATCTACCA 59.565 43.478 0.00 0.00 45.94 3.25
129 134 4.921470 TCGTGTAGCTTTTTGCATCTAC 57.079 40.909 0.00 0.00 45.94 2.59
131 136 3.375299 GGATCGTGTAGCTTTTTGCATCT 59.625 43.478 0.00 0.00 45.94 2.90
158 163 1.115326 GGCCACTCCTGGTTTGCTTT 61.115 55.000 0.00 0.00 40.17 3.51
172 177 2.890945 AGTTGTCTAACCATTTGGCCAC 59.109 45.455 3.88 0.00 37.52 5.01
173 178 3.153919 GAGTTGTCTAACCATTTGGCCA 58.846 45.455 0.00 0.00 37.52 5.36
175 180 3.821033 AGTGAGTTGTCTAACCATTTGGC 59.179 43.478 0.00 0.00 37.52 4.52
176 181 5.765182 AGAAGTGAGTTGTCTAACCATTTGG 59.235 40.000 0.00 0.00 37.52 3.28
268 273 4.288887 GGTAAGAAAAAGAGGAAGAGGGGA 59.711 45.833 0.00 0.00 0.00 4.81
273 278 5.640158 TGGTGGTAAGAAAAAGAGGAAGA 57.360 39.130 0.00 0.00 0.00 2.87
283 288 1.349688 AGTGCCGATGGTGGTAAGAAA 59.650 47.619 0.00 0.00 0.00 2.52
289 294 4.760047 GCGAGTGCCGATGGTGGT 62.760 66.667 0.00 0.00 41.76 4.16
318 323 4.729918 CAGAGGGTGCACCAGGGC 62.730 72.222 35.78 19.27 43.89 5.19
320 325 0.321653 GTAACAGAGGGTGCACCAGG 60.322 60.000 35.78 22.87 43.89 4.45
322 327 0.766674 AGGTAACAGAGGGTGCACCA 60.767 55.000 35.78 12.18 40.53 4.17
336 341 2.124901 CCGCGGATGCCAAGGTAA 60.125 61.111 24.07 0.00 38.08 2.85
365 370 4.881273 TGTGCAGAAAACTAAGAAGCAGAA 59.119 37.500 0.00 0.00 0.00 3.02
368 373 5.299028 TGATTGTGCAGAAAACTAAGAAGCA 59.701 36.000 0.00 0.00 0.00 3.91
376 381 4.341806 TGGTGAATGATTGTGCAGAAAACT 59.658 37.500 0.00 0.00 0.00 2.66
409 414 1.267806 CTGTGGTCTGTGGCATTGTTC 59.732 52.381 0.00 0.00 0.00 3.18
410 415 1.133823 TCTGTGGTCTGTGGCATTGTT 60.134 47.619 0.00 0.00 0.00 2.83
417 422 2.839486 TTAGCTTCTGTGGTCTGTGG 57.161 50.000 0.00 0.00 0.00 4.17
470 510 1.242076 AGACACAGGATGCAACTTGC 58.758 50.000 5.98 6.82 42.53 4.01
471 511 3.005554 CCTAGACACAGGATGCAACTTG 58.994 50.000 4.47 4.47 42.53 3.16
472 512 2.906389 TCCTAGACACAGGATGCAACTT 59.094 45.455 0.00 0.00 42.53 2.66
473 513 2.234908 GTCCTAGACACAGGATGCAACT 59.765 50.000 0.00 0.00 46.34 3.16
474 514 2.028112 TGTCCTAGACACAGGATGCAAC 60.028 50.000 0.00 0.00 46.34 4.17
475 515 2.256306 TGTCCTAGACACAGGATGCAA 58.744 47.619 0.00 0.00 46.34 4.08
476 516 1.937191 TGTCCTAGACACAGGATGCA 58.063 50.000 0.00 0.00 46.34 3.96
485 525 5.044328 AGGATAAGGTAGTGTGTCCTAGACA 60.044 44.000 0.00 0.00 40.50 3.41
486 526 5.447757 AGGATAAGGTAGTGTGTCCTAGAC 58.552 45.833 0.00 0.00 34.48 2.59
487 527 5.728937 AGGATAAGGTAGTGTGTCCTAGA 57.271 43.478 0.00 0.00 34.48 2.43
488 528 5.302313 GGAAGGATAAGGTAGTGTGTCCTAG 59.698 48.000 0.00 0.00 35.14 3.02
489 529 5.206587 GGAAGGATAAGGTAGTGTGTCCTA 58.793 45.833 0.00 0.00 35.14 2.94
490 530 4.031611 GGAAGGATAAGGTAGTGTGTCCT 58.968 47.826 0.00 0.00 37.68 3.85
491 531 3.134262 GGGAAGGATAAGGTAGTGTGTCC 59.866 52.174 0.00 0.00 0.00 4.02
492 532 3.134262 GGGGAAGGATAAGGTAGTGTGTC 59.866 52.174 0.00 0.00 0.00 3.67
493 533 3.113043 GGGGAAGGATAAGGTAGTGTGT 58.887 50.000 0.00 0.00 0.00 3.72
494 534 2.102588 CGGGGAAGGATAAGGTAGTGTG 59.897 54.545 0.00 0.00 0.00 3.82
495 535 2.395619 CGGGGAAGGATAAGGTAGTGT 58.604 52.381 0.00 0.00 0.00 3.55
496 536 1.070289 GCGGGGAAGGATAAGGTAGTG 59.930 57.143 0.00 0.00 0.00 2.74
497 537 1.421480 GCGGGGAAGGATAAGGTAGT 58.579 55.000 0.00 0.00 0.00 2.73
498 538 0.685660 GGCGGGGAAGGATAAGGTAG 59.314 60.000 0.00 0.00 0.00 3.18
569 609 4.742201 TCTCGCTCGTTGCCCAGC 62.742 66.667 0.00 0.00 38.78 4.85
628 668 4.325109 GGTGAGCTTTCCTTACCCCTTTAT 60.325 45.833 0.00 0.00 42.79 1.40
629 669 3.009805 GGTGAGCTTTCCTTACCCCTTTA 59.990 47.826 0.00 0.00 42.79 1.85
630 670 2.225041 GGTGAGCTTTCCTTACCCCTTT 60.225 50.000 0.00 0.00 42.79 3.11
631 671 1.354705 GGTGAGCTTTCCTTACCCCTT 59.645 52.381 0.00 0.00 42.79 3.95
632 672 0.992695 GGTGAGCTTTCCTTACCCCT 59.007 55.000 0.00 0.00 42.79 4.79
652 693 4.083862 AAGGCCGACGCTTCCTCC 62.084 66.667 0.00 0.00 34.44 4.30
864 920 0.821711 CGGAAGCAAACCAACCAGGA 60.822 55.000 0.00 0.00 41.22 3.86
900 957 0.952280 CCTCTGCTCTAATCCGCGTA 59.048 55.000 4.92 0.00 0.00 4.42
921 979 4.452733 GGCGGCTGTAACCTCGCT 62.453 66.667 0.00 0.00 46.31 4.93
950 1008 2.390599 CGTGCCAACATCGGTCCAG 61.391 63.158 0.00 0.00 0.00 3.86
954 1012 1.745115 CCATCGTGCCAACATCGGT 60.745 57.895 0.00 0.00 0.00 4.69
959 1018 0.250945 TAAAGCCCATCGTGCCAACA 60.251 50.000 0.00 0.00 0.00 3.33
960 1019 1.065551 GATAAAGCCCATCGTGCCAAC 59.934 52.381 0.00 0.00 0.00 3.77
968 1027 4.081050 GGCCGGATAAAGCCCATC 57.919 61.111 5.05 0.00 43.76 3.51
1033 1099 0.248289 GCCATTTCTGCTGCCACAAT 59.752 50.000 0.00 0.00 0.00 2.71
1036 1102 2.575461 GGCCATTTCTGCTGCCAC 59.425 61.111 0.00 0.00 43.46 5.01
1037 1103 3.063704 CGGCCATTTCTGCTGCCA 61.064 61.111 2.24 0.00 44.22 4.92
1263 1346 1.219393 CTTCCTGAAGTCCGCCTCC 59.781 63.158 0.00 0.00 33.87 4.30
1888 2636 4.671880 TGAACGAAAATCCACAATACGG 57.328 40.909 0.00 0.00 0.00 4.02
2243 3124 2.995466 TAGCATGCAAACTTCAGTGC 57.005 45.000 21.98 0.00 41.29 4.40
2299 3180 5.711506 AGCATATGTCTTGTGAACCAAATCA 59.288 36.000 4.29 0.00 31.20 2.57
2321 3202 1.012841 GCAGTGGCAGTGAGATTAGC 58.987 55.000 25.96 4.62 40.72 3.09
2323 3204 0.983467 TGGCAGTGGCAGTGAGATTA 59.017 50.000 25.96 3.68 43.71 1.75
2469 3350 5.582665 GGTCCAGTAAAGCAGTAAGATCAAG 59.417 44.000 0.00 0.00 0.00 3.02
2486 3367 1.613630 CCCAGTAGCAGGGTCCAGT 60.614 63.158 0.00 0.00 41.61 4.00
2542 3426 8.793592 GTTATCCCTTAATTGTGAACTGAAGTT 58.206 33.333 0.00 0.00 41.64 2.66
2543 3427 8.164070 AGTTATCCCTTAATTGTGAACTGAAGT 58.836 33.333 0.00 0.00 0.00 3.01
2606 3500 1.577328 CCCAGTGCACGTAAGCCAAG 61.577 60.000 12.01 0.00 45.62 3.61
2646 3549 4.198028 AGGAACCCAAACTACGTATGTC 57.802 45.455 0.00 0.00 0.00 3.06
2835 3787 8.415950 TCCCATTTATAGAAGTTTTGCTGAAA 57.584 30.769 0.00 0.00 0.00 2.69
2862 3814 6.294899 CCATTCCAGGTATATGCCAAATGAAG 60.295 42.308 22.57 11.15 32.12 3.02
2969 3932 6.831868 TGGTAAAAAGAGGAAGCTGTTTAGTT 59.168 34.615 0.00 0.00 30.35 2.24
3136 4100 4.702081 GACGTCGTGCGCCAGAGT 62.702 66.667 4.18 4.61 46.11 3.24
3321 4288 1.281899 GCATTGACCGAGACTACAGC 58.718 55.000 0.00 0.00 0.00 4.40
3332 4299 0.890683 CTTTCAGGTGGGCATTGACC 59.109 55.000 0.00 0.00 0.00 4.02
3368 4335 3.666883 TTACATGGAACTATTTGCGCG 57.333 42.857 0.00 0.00 0.00 6.86
3496 4463 7.598278 ACAATAGACCATGTTTGCGATAAAAA 58.402 30.769 0.00 0.00 0.00 1.94
3537 4505 3.430895 TGAAGTCATTTAGTCGCGAAACC 59.569 43.478 12.06 0.00 0.00 3.27
3679 4648 5.399858 CAACATAGAGTAGCTACACGTGTT 58.600 41.667 28.55 26.29 34.13 3.32
3684 4653 4.567159 GCAACCAACATAGAGTAGCTACAC 59.433 45.833 25.28 19.11 0.00 2.90
3694 4663 6.265196 AGAAACTCATTTGCAACCAACATAGA 59.735 34.615 0.00 0.00 0.00 1.98
3792 4772 5.309806 ACCACCAATACTTGACTTCTACCTT 59.690 40.000 0.00 0.00 0.00 3.50
3798 4778 4.819630 TGTTCACCACCAATACTTGACTTC 59.180 41.667 0.00 0.00 0.00 3.01
3816 4796 4.071423 TGAAGATTCGGCTGATTTGTTCA 58.929 39.130 12.06 12.06 0.00 3.18
3895 4976 3.503363 ACACGTGCAATGATCTGTTGAAT 59.497 39.130 17.22 0.00 0.00 2.57
3920 5296 3.421919 TGGTTGAACTCATCAGCATCA 57.578 42.857 0.00 0.00 40.74 3.07
3953 5329 5.230942 CGTTAGGCTCGGAGATGAAAATAT 58.769 41.667 9.69 0.00 33.89 1.28
3969 5346 1.878975 GCTCGAAGCTCCGTTAGGC 60.879 63.158 0.00 0.00 38.45 3.93
3970 5347 1.227002 GGCTCGAAGCTCCGTTAGG 60.227 63.158 0.00 0.00 41.99 2.69
4020 5399 2.240230 TCAATGGTTTGACGACCGC 58.760 52.632 0.00 0.00 42.83 5.68
4027 5406 4.447138 AGGTGGTTAGTCAATGGTTTGA 57.553 40.909 0.00 0.00 39.54 2.69
4029 5408 5.046159 TCGATAGGTGGTTAGTCAATGGTTT 60.046 40.000 0.00 0.00 0.00 3.27
4086 5465 6.934645 TCACACTTTTATCTCGGTTTCAATCT 59.065 34.615 0.00 0.00 0.00 2.40
4091 5470 6.801862 CCAAATCACACTTTTATCTCGGTTTC 59.198 38.462 0.00 0.00 0.00 2.78
4117 5496 7.040062 TTGTCAAACAAGATATGGGTTAACCAG 60.040 37.037 25.71 7.35 42.53 4.00
4129 5508 9.942850 TCAATAGATGAGTTGTCAAACAAGATA 57.057 29.630 0.00 0.00 38.88 1.98
4159 5538 5.045213 TCCATAACATCACCAACAGGTACAT 60.045 40.000 0.00 0.00 33.30 2.29
4160 5539 4.287326 TCCATAACATCACCAACAGGTACA 59.713 41.667 0.00 0.00 33.30 2.90
4173 5553 6.349300 ACACCTTCACACTATCCATAACATC 58.651 40.000 0.00 0.00 0.00 3.06
4185 5565 3.576078 TCAAATGGACACCTTCACACT 57.424 42.857 0.00 0.00 0.00 3.55
4186 5566 4.647424 TTTCAAATGGACACCTTCACAC 57.353 40.909 0.00 0.00 0.00 3.82
4225 5607 9.014297 GGAATAGGGAAAACCATTGATATGTAG 57.986 37.037 0.00 0.00 43.89 2.74
4226 5608 8.506921 TGGAATAGGGAAAACCATTGATATGTA 58.493 33.333 0.00 0.00 43.89 2.29
4227 5609 7.361438 TGGAATAGGGAAAACCATTGATATGT 58.639 34.615 0.00 0.00 43.89 2.29
4303 5688 5.513233 AGTGGCATCAACAGGATTAGAAAT 58.487 37.500 0.00 0.00 32.57 2.17


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

AutoCloner maintained by Alex Coulton.