Multiple sequence alignment - TraesCS2D01G113000

Loading Multiple Alignment...

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 TraesCS2D01G113000 chr2D 100.000 2900 0 0 1 2900 62560853 62557954 0.000000e+00 5356.0
1 TraesCS2D01G113000 chr2D 84.052 696 82 17 1545 2223 62564670 62563987 0.000000e+00 643.0
2 TraesCS2D01G113000 chr2D 84.369 531 63 10 2381 2898 62563625 62563102 1.200000e-138 503.0
3 TraesCS2D01G113000 chr2D 85.956 413 36 11 1032 1432 62565143 62564741 3.460000e-114 422.0
4 TraesCS2D01G113000 chr2D 74.018 866 127 67 636 1432 62553774 62552938 2.220000e-66 263.0
5 TraesCS2D01G113000 chr2D 78.348 448 47 34 599 1042 62565663 62565262 8.030000e-61 244.0
6 TraesCS2D01G113000 chr2D 79.448 326 47 15 1596 1911 62552853 62552538 2.260000e-51 213.0
7 TraesCS2D01G113000 chr2D 79.180 317 40 17 1591 1904 62289436 62289143 2.280000e-46 196.0
8 TraesCS2D01G113000 chr2D 78.571 266 50 5 46 306 209130573 209130310 4.970000e-38 169.0
9 TraesCS2D01G113000 chr2D 82.011 189 28 4 1042 1230 253618391 253618573 3.870000e-34 156.0
10 TraesCS2D01G113000 chr2D 96.875 32 1 0 2398 2429 62558368 62558337 1.000000e-03 54.7
11 TraesCS2D01G113000 chr2D 96.875 32 1 0 2486 2517 62558456 62558425 1.000000e-03 54.7
12 TraesCS2D01G113000 chr2A 89.880 1502 85 29 1 1459 63608332 63606855 0.000000e+00 1869.0
13 TraesCS2D01G113000 chr2A 83.200 875 93 25 1544 2383 63606823 63605968 0.000000e+00 752.0
14 TraesCS2D01G113000 chr2A 85.463 454 43 11 2381 2819 63609755 63609310 4.410000e-123 451.0
15 TraesCS2D01G113000 chr2A 85.584 437 40 11 1009 1432 63611232 63610806 1.230000e-118 436.0
16 TraesCS2D01G113000 chr2A 81.280 422 41 25 636 1046 63611756 63611362 1.010000e-79 307.0
17 TraesCS2D01G113000 chr2A 78.841 397 61 19 1057 1446 63588998 63588618 2.230000e-61 246.0
18 TraesCS2D01G113000 chr2A 80.952 315 44 13 1595 1903 63588551 63588247 4.830000e-58 235.0
19 TraesCS2D01G113000 chr2A 79.573 328 45 15 1580 1904 63137792 63137484 6.290000e-52 215.0
20 TraesCS2D01G113000 chr2A 96.875 32 0 1 2398 2429 63609647 63609617 5.000000e-03 52.8
21 TraesCS2D01G113000 chr2B 88.089 1125 68 23 340 1445 98265379 98264302 0.000000e+00 1275.0
22 TraesCS2D01G113000 chr2B 88.790 562 46 9 1551 2105 98264273 98263722 0.000000e+00 673.0
23 TraesCS2D01G113000 chr2B 80.626 831 99 37 1575 2357 98286320 98285504 1.160000e-163 586.0
24 TraesCS2D01G113000 chr2B 86.520 408 33 10 1037 1432 98286802 98286405 2.060000e-116 429.0
25 TraesCS2D01G113000 chr2B 82.697 393 36 12 1092 1484 402001377 402001017 1.300000e-83 320.0
26 TraesCS2D01G113000 chr2B 87.591 274 29 5 2381 2652 98285308 98285038 2.170000e-81 313.0
27 TraesCS2D01G113000 chr2B 78.194 454 50 31 599 1042 98287337 98286923 8.030000e-61 244.0
28 TraesCS2D01G113000 chr2B 82.178 303 28 15 950 1234 98257173 98256879 1.340000e-58 237.0
29 TraesCS2D01G113000 chr2B 77.551 441 57 32 1004 1434 97933921 97933513 8.080000e-56 228.0
30 TraesCS2D01G113000 chr2B 91.262 103 9 0 1809 1911 98256323 98256221 1.080000e-29 141.0
31 TraesCS2D01G113000 chr2B 85.039 127 7 2 2784 2898 98262293 98262167 5.080000e-23 119.0
32 TraesCS2D01G113000 chr2B 75.926 216 36 12 2043 2248 784725408 784725617 2.380000e-16 97.1
33 TraesCS2D01G113000 chr1A 83.232 328 23 13 1157 1484 560195251 560194956 3.680000e-69 272.0
34 TraesCS2D01G113000 chr7A 90.385 156 15 0 1320 1475 288241014 288240859 3.790000e-49 206.0
35 TraesCS2D01G113000 chr7D 77.181 298 54 11 14 301 483478246 483477953 8.320000e-36 161.0
36 TraesCS2D01G113000 chr7D 77.103 214 35 10 2043 2247 136944524 136944316 8.490000e-21 111.0
37 TraesCS2D01G113000 chr7D 76.699 206 35 7 2053 2247 613635585 613635382 5.110000e-18 102.0
38 TraesCS2D01G113000 chr4D 78.302 212 35 6 2043 2247 482161680 482161473 3.030000e-25 126.0
39 TraesCS2D01G113000 chr6D 83.465 127 16 3 2129 2251 408691634 408691759 2.360000e-21 113.0
40 TraesCS2D01G113000 chrUn 77.249 189 33 6 2067 2247 45773909 45773723 5.110000e-18 102.0
41 TraesCS2D01G113000 chr3D 77.249 189 33 6 2067 2247 592869390 592869204 5.110000e-18 102.0
42 TraesCS2D01G113000 chr6B 81.102 127 20 2 2125 2248 50480657 50480782 6.610000e-17 99.0


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 TraesCS2D01G113000 chr2D 62557954 62560853 2899 True 1821.800000 5356 97.916667 1 2900 3 chr2D.!!$R4 2899
1 TraesCS2D01G113000 chr2D 62563102 62565663 2561 True 453.000000 643 83.181250 599 2898 4 chr2D.!!$R5 2299
2 TraesCS2D01G113000 chr2D 62552538 62553774 1236 True 238.000000 263 76.733000 636 1911 2 chr2D.!!$R3 1275
3 TraesCS2D01G113000 chr2A 63605968 63611756 5788 True 644.633333 1869 87.047000 1 2819 6 chr2A.!!$R3 2818
4 TraesCS2D01G113000 chr2A 63588247 63588998 751 True 240.500000 246 79.896500 1057 1903 2 chr2A.!!$R2 846
5 TraesCS2D01G113000 chr2B 98262167 98265379 3212 True 689.000000 1275 87.306000 340 2898 3 chr2B.!!$R4 2558
6 TraesCS2D01G113000 chr2B 98285038 98287337 2299 True 393.000000 586 83.232750 599 2652 4 chr2B.!!$R5 2053

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
108 3539 0.041224 GCTGAGACATCATGCATGCG 60.041 55.0 22.25 16.87 35.65 4.73 F
1469 5213 0.171455 GTCGCTCGTTGTGATCTCCT 59.829 55.0 0.00 0.00 37.53 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 5334 0.043310 GCGGTTTCGTATAAGCAGCG 60.043 55.0 5.39 5.39 38.89 5.18 R
2646 6969 0.678684 CGGTATTTTTGCCCGTCCCT 60.679 55.0 0.00 0.00 37.00 4.20 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
69 3500 2.054799 ACACACACAAGATACCCCACT 58.945 47.619 0.00 0.00 0.00 4.00
75 3506 1.628846 ACAAGATACCCCACTCACACC 59.371 52.381 0.00 0.00 0.00 4.16
76 3507 1.628340 CAAGATACCCCACTCACACCA 59.372 52.381 0.00 0.00 0.00 4.17
77 3508 1.276622 AGATACCCCACTCACACCAC 58.723 55.000 0.00 0.00 0.00 4.16
78 3509 1.203313 AGATACCCCACTCACACCACT 60.203 52.381 0.00 0.00 0.00 4.00
79 3510 2.043939 AGATACCCCACTCACACCACTA 59.956 50.000 0.00 0.00 0.00 2.74
80 3511 2.634639 TACCCCACTCACACCACTAT 57.365 50.000 0.00 0.00 0.00 2.12
81 3512 2.634639 ACCCCACTCACACCACTATA 57.365 50.000 0.00 0.00 0.00 1.31
86 3517 2.420129 CCACTCACACCACTATAAGGCC 60.420 54.545 0.00 0.00 0.00 5.19
89 3520 1.754803 TCACACCACTATAAGGCCTCG 59.245 52.381 5.23 0.00 0.00 4.63
90 3521 0.464452 ACACCACTATAAGGCCTCGC 59.536 55.000 5.23 0.00 0.00 5.03
93 3524 1.040646 CCACTATAAGGCCTCGCTGA 58.959 55.000 5.23 0.00 0.00 4.26
98 3529 1.418334 ATAAGGCCTCGCTGAGACAT 58.582 50.000 5.23 0.00 0.00 3.06
105 3536 1.540580 CCTCGCTGAGACATCATGCAT 60.541 52.381 0.00 0.00 34.12 3.96
108 3539 0.041224 GCTGAGACATCATGCATGCG 60.041 55.000 22.25 16.87 35.65 4.73
120 3551 1.200103 GCATGCGTCATCGTCATCG 59.800 57.895 0.00 0.00 39.49 3.84
129 3560 2.203771 ATCGTCATCGCTCCTCCCC 61.204 63.158 0.00 0.00 36.96 4.81
139 3570 1.270358 CGCTCCTCCCCTATAAAGCAC 60.270 57.143 0.00 0.00 0.00 4.40
143 3574 3.395941 CTCCTCCCCTATAAAGCACCATT 59.604 47.826 0.00 0.00 0.00 3.16
156 3587 2.497273 AGCACCATTGGCATCCTTAAAC 59.503 45.455 1.54 0.00 0.00 2.01
160 3591 3.270960 ACCATTGGCATCCTTAAACCCTA 59.729 43.478 1.54 0.00 0.00 3.53
162 3593 4.099419 CCATTGGCATCCTTAAACCCTAAC 59.901 45.833 0.00 0.00 0.00 2.34
175 3606 1.770061 ACCCTAACCAAACGACTCCAA 59.230 47.619 0.00 0.00 0.00 3.53
183 3614 1.219522 AAACGACTCCAACTTCGCCG 61.220 55.000 0.00 0.00 38.88 6.46
206 3637 1.066430 GGCGATAGTCAAGTCAACCCA 60.066 52.381 0.00 0.00 43.13 4.51
240 3671 4.754114 GCCATCTGAAGTGGTATGAAGATC 59.246 45.833 0.00 0.00 39.01 2.75
246 3677 2.111384 AGTGGTATGAAGATCCGCACT 58.889 47.619 0.00 0.00 34.61 4.40
308 3739 4.404640 TCTGAAGGAGAACTACGAAGGAA 58.595 43.478 0.00 0.00 0.00 3.36
310 3741 5.047943 TCTGAAGGAGAACTACGAAGGAAAG 60.048 44.000 0.00 0.00 0.00 2.62
316 3747 3.258622 AGAACTACGAAGGAAAGACCAGG 59.741 47.826 0.00 0.00 42.04 4.45
318 3749 1.275291 CTACGAAGGAAAGACCAGGCA 59.725 52.381 0.00 0.00 42.04 4.75
324 3755 1.743252 GAAAGACCAGGCAGGCTCG 60.743 63.158 0.00 0.00 43.14 5.03
574 4017 3.227614 ACCCGCCAAAACAAAATACTCT 58.772 40.909 0.00 0.00 0.00 3.24
668 4111 3.445096 TCTCGAGTGCATCAGAAATCAGA 59.555 43.478 13.13 0.00 0.00 3.27
815 4288 1.683707 TCTGCCGTCATCAGCTCCT 60.684 57.895 0.00 0.00 0.00 3.69
821 4294 4.166888 TCATCAGCTCCTGCCGGC 62.167 66.667 22.73 22.73 40.80 6.13
866 4339 2.312436 GGTTTCGCCAGCGTACGTT 61.312 57.895 17.90 8.23 40.74 3.99
886 4374 2.146724 CACTCTCACACCCCCACCA 61.147 63.158 0.00 0.00 0.00 4.17
892 4380 1.228245 CACACCCCCACCAACTGAG 60.228 63.158 0.00 0.00 0.00 3.35
946 4451 2.945668 GGCCTTGAGCTATAACCACTTG 59.054 50.000 0.00 0.00 43.05 3.16
957 4482 6.206829 AGCTATAACCACTTGAACCAAGAAAC 59.793 38.462 13.00 0.00 43.42 2.78
966 4491 6.542370 CACTTGAACCAAGAAACCTTCTCTAA 59.458 38.462 13.00 0.00 43.42 2.10
976 4501 7.971183 AGAAACCTTCTCTAATCAGTTTCAC 57.029 36.000 13.89 0.00 43.36 3.18
997 4522 1.140407 CCTCGCGTCCTTCGATTGTC 61.140 60.000 5.77 0.00 42.86 3.18
1294 5013 1.299773 CCGGAATCTGAGCGAGCTC 60.300 63.158 17.42 17.42 43.01 4.09
1295 5014 1.732917 CGGAATCTGAGCGAGCTCT 59.267 57.895 23.39 5.53 43.12 4.09
1307 5029 1.016627 CGAGCTCTCCTCTGACTGAG 58.983 60.000 12.85 2.46 42.30 3.35
1376 5114 3.353836 GCGGACCTGCGCAAGAAA 61.354 61.111 14.09 0.00 43.02 2.52
1451 5195 2.572284 GCTACCAACTCCGCTCGT 59.428 61.111 0.00 0.00 0.00 4.18
1452 5196 1.516603 GCTACCAACTCCGCTCGTC 60.517 63.158 0.00 0.00 0.00 4.20
1459 5203 4.462417 CTCCGCTCGTCGCTCGTT 62.462 66.667 5.51 0.00 40.80 3.85
1462 5206 3.816920 CGCTCGTCGCTCGTTGTG 61.817 66.667 0.00 0.00 40.80 3.33
1463 5207 2.428569 GCTCGTCGCTCGTTGTGA 60.429 61.111 0.00 0.00 40.80 3.58
1464 5208 1.801913 GCTCGTCGCTCGTTGTGAT 60.802 57.895 0.00 0.00 40.80 3.06
1465 5209 1.734359 GCTCGTCGCTCGTTGTGATC 61.734 60.000 0.00 0.00 40.80 2.92
1466 5210 0.179187 CTCGTCGCTCGTTGTGATCT 60.179 55.000 0.00 0.00 40.80 2.75
1467 5211 0.179197 TCGTCGCTCGTTGTGATCTC 60.179 55.000 0.00 0.00 40.80 2.75
1468 5212 1.134530 CGTCGCTCGTTGTGATCTCC 61.135 60.000 0.00 0.00 37.53 3.71
1469 5213 0.171455 GTCGCTCGTTGTGATCTCCT 59.829 55.000 0.00 0.00 37.53 3.69
1470 5214 0.888619 TCGCTCGTTGTGATCTCCTT 59.111 50.000 0.00 0.00 0.00 3.36
1471 5215 1.272490 TCGCTCGTTGTGATCTCCTTT 59.728 47.619 0.00 0.00 0.00 3.11
1472 5216 1.656095 CGCTCGTTGTGATCTCCTTTC 59.344 52.381 0.00 0.00 0.00 2.62
1473 5217 2.672478 CGCTCGTTGTGATCTCCTTTCT 60.672 50.000 0.00 0.00 0.00 2.52
1474 5218 3.427638 CGCTCGTTGTGATCTCCTTTCTA 60.428 47.826 0.00 0.00 0.00 2.10
1475 5219 3.860536 GCTCGTTGTGATCTCCTTTCTAC 59.139 47.826 0.00 0.00 0.00 2.59
1476 5220 4.381079 GCTCGTTGTGATCTCCTTTCTACT 60.381 45.833 0.00 0.00 0.00 2.57
1477 5221 5.163642 GCTCGTTGTGATCTCCTTTCTACTA 60.164 44.000 0.00 0.00 0.00 1.82
1478 5222 6.460399 GCTCGTTGTGATCTCCTTTCTACTAT 60.460 42.308 0.00 0.00 0.00 2.12
1479 5223 7.028926 TCGTTGTGATCTCCTTTCTACTATC 57.971 40.000 0.00 0.00 0.00 2.08
1480 5224 6.829298 TCGTTGTGATCTCCTTTCTACTATCT 59.171 38.462 0.00 0.00 0.00 1.98
1481 5225 7.991460 TCGTTGTGATCTCCTTTCTACTATCTA 59.009 37.037 0.00 0.00 0.00 1.98
1482 5226 8.788806 CGTTGTGATCTCCTTTCTACTATCTAT 58.211 37.037 0.00 0.00 0.00 1.98
1485 5229 9.513906 TGTGATCTCCTTTCTACTATCTATCTG 57.486 37.037 0.00 0.00 0.00 2.90
1486 5230 9.515226 GTGATCTCCTTTCTACTATCTATCTGT 57.485 37.037 0.00 0.00 0.00 3.41
1487 5231 9.733556 TGATCTCCTTTCTACTATCTATCTGTC 57.266 37.037 0.00 0.00 0.00 3.51
1488 5232 9.174166 GATCTCCTTTCTACTATCTATCTGTCC 57.826 40.741 0.00 0.00 0.00 4.02
1489 5233 8.046867 TCTCCTTTCTACTATCTATCTGTCCA 57.953 38.462 0.00 0.00 0.00 4.02
1490 5234 8.674173 TCTCCTTTCTACTATCTATCTGTCCAT 58.326 37.037 0.00 0.00 0.00 3.41
1491 5235 8.642935 TCCTTTCTACTATCTATCTGTCCATG 57.357 38.462 0.00 0.00 0.00 3.66
1494 5238 9.253832 CTTTCTACTATCTATCTGTCCATGGAT 57.746 37.037 19.62 3.97 0.00 3.41
1499 5243 8.140112 ACTATCTATCTGTCCATGGATAAACC 57.860 38.462 19.62 4.90 39.54 3.27
1510 5254 3.604875 TGGATAAACCAACTCGTCTCC 57.395 47.619 0.00 0.00 46.75 3.71
1511 5255 2.235402 TGGATAAACCAACTCGTCTCCC 59.765 50.000 0.00 0.00 46.75 4.30
1518 5262 0.318441 CAACTCGTCTCCCTTGCTGA 59.682 55.000 0.00 0.00 0.00 4.26
1519 5263 1.066573 CAACTCGTCTCCCTTGCTGAT 60.067 52.381 0.00 0.00 0.00 2.90
1520 5264 2.145397 ACTCGTCTCCCTTGCTGATA 57.855 50.000 0.00 0.00 0.00 2.15
1521 5265 2.672098 ACTCGTCTCCCTTGCTGATAT 58.328 47.619 0.00 0.00 0.00 1.63
1524 5268 3.300388 TCGTCTCCCTTGCTGATATCTT 58.700 45.455 3.98 0.00 0.00 2.40
1526 5270 4.162320 TCGTCTCCCTTGCTGATATCTTTT 59.838 41.667 3.98 0.00 0.00 2.27
1531 5275 7.602265 GTCTCCCTTGCTGATATCTTTTCTATC 59.398 40.741 3.98 0.00 0.00 2.08
1532 5276 7.512058 TCTCCCTTGCTGATATCTTTTCTATCT 59.488 37.037 3.98 0.00 0.00 1.98
1534 5278 9.331466 TCCCTTGCTGATATCTTTTCTATCTAT 57.669 33.333 3.98 0.00 0.00 1.98
1535 5279 9.598517 CCCTTGCTGATATCTTTTCTATCTATC 57.401 37.037 3.98 0.00 0.00 2.08
1540 5284 9.801873 GCTGATATCTTTTCTATCTATCTGTCC 57.198 37.037 3.98 0.00 0.00 4.02
1570 5324 4.271776 ACGATCACACATTGCATATCTGTG 59.728 41.667 14.16 14.16 44.51 3.66
1577 5334 4.034858 CACATTGCATATCTGTGACCTGTC 59.965 45.833 11.61 0.00 42.20 3.51
1628 5385 2.987547 GTGGAGGTGGTCGACGGA 60.988 66.667 9.92 0.00 0.00 4.69
1720 5477 0.535335 TACGGTGCCATCAAGAGGTC 59.465 55.000 0.00 0.00 0.00 3.85
1721 5478 1.296392 CGGTGCCATCAAGAGGTCA 59.704 57.895 0.00 0.00 0.00 4.02
1722 5479 0.742281 CGGTGCCATCAAGAGGTCAG 60.742 60.000 0.00 0.00 0.00 3.51
1723 5480 0.393537 GGTGCCATCAAGAGGTCAGG 60.394 60.000 0.00 0.00 0.00 3.86
1724 5481 0.326264 GTGCCATCAAGAGGTCAGGT 59.674 55.000 0.00 0.00 0.00 4.00
1737 5499 5.094387 AGAGGTCAGGTCCTTGATTTTCTA 58.906 41.667 0.00 0.00 38.02 2.10
1745 5507 5.248477 AGGTCCTTGATTTTCTACTGCAGTA 59.752 40.000 24.63 24.63 0.00 2.74
1750 5512 6.757010 CCTTGATTTTCTACTGCAGTATACGT 59.243 38.462 26.22 11.96 0.00 3.57
1754 5516 5.648178 TTTCTACTGCAGTATACGTTCCA 57.352 39.130 26.22 3.44 0.00 3.53
1756 5518 6.947644 TTCTACTGCAGTATACGTTCCATA 57.052 37.500 26.22 2.12 0.00 2.74
1913 5683 0.251916 AACTGATCGCCATTTCCGGA 59.748 50.000 0.00 0.00 0.00 5.14
1922 5696 2.483013 CGCCATTTCCGGAGTTAGATCA 60.483 50.000 3.34 0.00 0.00 2.92
1985 5759 5.303589 GTGCCTACACAATGTATCCCTACTA 59.696 44.000 0.00 0.00 46.61 1.82
2062 5839 6.305693 AGCAGTCAATCTGTGTAAACTTTC 57.694 37.500 0.00 0.00 45.23 2.62
2238 6053 7.979444 ACAACAAAGCTAAGCAGAGTAAATA 57.021 32.000 0.00 0.00 0.00 1.40
2239 6054 8.391075 ACAACAAAGCTAAGCAGAGTAAATAA 57.609 30.769 0.00 0.00 0.00 1.40
2244 6059 9.677567 CAAAGCTAAGCAGAGTAAATAAAAACA 57.322 29.630 0.00 0.00 0.00 2.83
2252 6072 9.952188 AGCAGAGTAAATAAAAACAGAAAGAAC 57.048 29.630 0.00 0.00 0.00 3.01
2304 6126 8.316946 GGGTGTTCATCTTCTGATATCATCATA 58.683 37.037 5.72 0.00 38.85 2.15
2335 6157 4.151335 CGTTCTTCAAGAGACTCACCATTG 59.849 45.833 5.02 0.61 33.02 2.82
2349 6171 4.042884 TCACCATTGAATGATCCCTCTCT 58.957 43.478 6.76 0.00 0.00 3.10
2354 6176 5.889853 CCATTGAATGATCCCTCTCTTTTGA 59.110 40.000 6.76 0.00 0.00 2.69
2357 6179 6.317663 TGAATGATCCCTCTCTTTTGATGA 57.682 37.500 0.00 0.00 0.00 2.92
2359 6181 6.600822 TGAATGATCCCTCTCTTTTGATGAAC 59.399 38.462 0.00 0.00 0.00 3.18
2364 6186 7.506938 TGATCCCTCTCTTTTGATGAACTTTTT 59.493 33.333 0.00 0.00 0.00 1.94
2365 6187 8.940397 ATCCCTCTCTTTTGATGAACTTTTTA 57.060 30.769 0.00 0.00 0.00 1.52
2366 6188 8.166422 TCCCTCTCTTTTGATGAACTTTTTAC 57.834 34.615 0.00 0.00 0.00 2.01
2367 6189 7.041372 TCCCTCTCTTTTGATGAACTTTTTACG 60.041 37.037 0.00 0.00 0.00 3.18
2369 6191 7.798982 CCTCTCTTTTGATGAACTTTTTACGTC 59.201 37.037 0.00 0.00 0.00 4.34
2370 6192 8.203937 TCTCTTTTGATGAACTTTTTACGTCA 57.796 30.769 0.00 0.00 0.00 4.35
2429 6554 6.959361 AGTGTTTACTTGCATAAGACAACTG 58.041 36.000 0.00 0.00 37.36 3.16
2527 6839 9.294030 CTTGCATAAGACAACTAAAAATGGATC 57.706 33.333 0.00 0.00 35.92 3.36
2539 6851 8.252964 ACTAAAAATGGATCGTTGTAGACTTC 57.747 34.615 6.62 0.00 0.00 3.01
2544 6856 4.556233 TGGATCGTTGTAGACTTCACAAG 58.444 43.478 0.00 0.00 36.61 3.16
2548 6860 6.369065 GGATCGTTGTAGACTTCACAAGAATT 59.631 38.462 0.00 0.00 36.61 2.17
2646 6969 4.216902 CACATTCCAACAATGCAAGAGAGA 59.783 41.667 0.00 0.00 0.00 3.10
2649 6972 2.089980 CCAACAATGCAAGAGAGAGGG 58.910 52.381 0.00 0.00 0.00 4.30
2650 6973 2.290514 CCAACAATGCAAGAGAGAGGGA 60.291 50.000 0.00 0.00 0.00 4.20
2654 6977 1.333636 ATGCAAGAGAGAGGGACGGG 61.334 60.000 0.00 0.00 0.00 5.28
2675 6998 3.054166 GCAAAAATACCGTCAACCCAAC 58.946 45.455 0.00 0.00 0.00 3.77
2684 7007 3.386402 ACCGTCAACCCAACATGAAAATT 59.614 39.130 0.00 0.00 0.00 1.82
2696 7019 7.334171 CCCAACATGAAAATTTAGTTGATTCCC 59.666 37.037 19.04 0.00 41.41 3.97
2712 7035 5.764131 TGATTCCCGAAAAATTGTACACAC 58.236 37.500 0.00 0.00 0.00 3.82
2715 7038 4.200874 TCCCGAAAAATTGTACACACTGT 58.799 39.130 0.00 0.00 0.00 3.55
2717 7040 5.821470 TCCCGAAAAATTGTACACACTGTTA 59.179 36.000 0.00 0.00 0.00 2.41
2787 7119 7.504403 TGCAATCAAGAAAAAGGTTAATTCCA 58.496 30.769 0.00 0.00 0.00 3.53
2796 7426 8.807118 AGAAAAAGGTTAATTCCAAGGAATCTC 58.193 33.333 14.33 8.12 43.26 2.75
2812 7442 1.295792 TCTCGCTGAAACCAACACAC 58.704 50.000 0.00 0.00 0.00 3.82
2898 7543 7.606456 TGAACCATCTTCTACTCGCTTTAATTT 59.394 33.333 0.00 0.00 0.00 1.82
2899 7544 7.923414 ACCATCTTCTACTCGCTTTAATTTT 57.077 32.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.892609 GGTTTTCCATAATAAACTGGACAGTT 58.107 34.615 11.69 11.69 45.54 3.16
4 5 7.461182 TGGTTTTCCATAATAAACTGGACAG 57.539 36.000 0.00 0.00 46.22 3.51
21 3446 3.572255 TGTGATGGTTTAGCCTGGTTTTC 59.428 43.478 0.00 0.00 38.35 2.29
69 3500 1.754803 CGAGGCCTTATAGTGGTGTGA 59.245 52.381 6.77 0.00 0.00 3.58
75 3506 1.957177 TCTCAGCGAGGCCTTATAGTG 59.043 52.381 6.77 0.50 0.00 2.74
76 3507 1.957877 GTCTCAGCGAGGCCTTATAGT 59.042 52.381 6.77 0.00 0.00 2.12
77 3508 1.957177 TGTCTCAGCGAGGCCTTATAG 59.043 52.381 6.77 0.57 32.68 1.31
78 3509 2.067365 TGTCTCAGCGAGGCCTTATA 57.933 50.000 6.77 0.00 32.68 0.98
79 3510 1.342819 GATGTCTCAGCGAGGCCTTAT 59.657 52.381 6.77 0.00 32.68 1.73
80 3511 0.747255 GATGTCTCAGCGAGGCCTTA 59.253 55.000 6.77 0.00 32.68 2.69
81 3512 1.260538 TGATGTCTCAGCGAGGCCTT 61.261 55.000 6.77 0.00 32.68 4.35
86 3517 1.527311 CATGCATGATGTCTCAGCGAG 59.473 52.381 22.59 0.00 34.12 5.03
89 3520 0.041224 CGCATGCATGATGTCTCAGC 60.041 55.000 30.64 10.26 34.12 4.26
90 3521 1.260825 GACGCATGCATGATGTCTCAG 59.739 52.381 30.09 15.19 34.12 3.35
93 3524 1.871676 GATGACGCATGCATGATGTCT 59.128 47.619 33.53 25.03 36.38 3.41
98 3529 0.459934 TGACGATGACGCATGCATGA 60.460 50.000 30.64 9.71 43.96 3.07
108 3539 0.318275 GGAGGAGCGATGACGATGAC 60.318 60.000 0.00 0.00 42.66 3.06
120 3551 1.072489 GGTGCTTTATAGGGGAGGAGC 59.928 57.143 0.00 0.00 0.00 4.70
129 3560 4.147321 AGGATGCCAATGGTGCTTTATAG 58.853 43.478 0.00 0.00 0.00 1.31
139 3570 2.750814 AGGGTTTAAGGATGCCAATGG 58.249 47.619 0.00 0.00 0.00 3.16
143 3574 2.650322 TGGTTAGGGTTTAAGGATGCCA 59.350 45.455 0.00 0.00 0.00 4.92
156 3587 2.148768 GTTGGAGTCGTTTGGTTAGGG 58.851 52.381 0.00 0.00 0.00 3.53
160 3591 1.937899 CGAAGTTGGAGTCGTTTGGTT 59.062 47.619 0.00 0.00 32.61 3.67
162 3593 0.234884 GCGAAGTTGGAGTCGTTTGG 59.765 55.000 0.00 0.00 39.46 3.28
183 3614 3.445857 GGTTGACTTGACTATCGCCTAC 58.554 50.000 0.00 0.00 0.00 3.18
198 3629 1.608283 GCCTCTACAGTGTGGGTTGAC 60.608 57.143 5.88 0.00 0.00 3.18
206 3637 2.238084 TCAGATGGCCTCTACAGTGT 57.762 50.000 3.32 0.00 31.13 3.55
240 3671 2.949451 ATGACTGAGTTCTAGTGCGG 57.051 50.000 0.00 0.00 0.00 5.69
246 3677 4.713553 TGGTTGCAAATGACTGAGTTCTA 58.286 39.130 0.00 0.00 0.00 2.10
287 3718 4.785511 TTCCTTCGTAGTTCTCCTTCAG 57.214 45.455 0.00 0.00 0.00 3.02
298 3729 1.275291 TGCCTGGTCTTTCCTTCGTAG 59.725 52.381 0.00 0.00 37.07 3.51
308 3739 2.456287 GAACGAGCCTGCCTGGTCTT 62.456 60.000 0.00 0.00 38.35 3.01
310 3741 2.435059 GAACGAGCCTGCCTGGTC 60.435 66.667 0.00 0.00 38.35 4.02
316 3747 3.254024 TTCCAGGGAACGAGCCTGC 62.254 63.158 0.00 0.00 0.00 4.85
318 3749 0.618968 ATCTTCCAGGGAACGAGCCT 60.619 55.000 0.00 0.00 0.00 4.58
324 3755 3.759086 GAGAAACCAATCTTCCAGGGAAC 59.241 47.826 0.00 0.00 0.00 3.62
387 3818 6.515043 AAGAACAACTTCATCAAAAATGCG 57.485 33.333 0.00 0.00 32.91 4.73
523 3966 9.936759 GAAGATATTTGGTTTTGTTAAATCCCA 57.063 29.630 0.00 0.00 0.00 4.37
604 4047 2.027745 AGAAGAGAATTTGAGAGCGGCA 60.028 45.455 1.45 0.00 0.00 5.69
668 4111 0.810823 TTCTTTTCCGTCGGTGCGTT 60.811 50.000 11.88 0.00 0.00 4.84
866 4339 1.841556 GTGGGGGTGTGAGAGTGGA 60.842 63.158 0.00 0.00 0.00 4.02
892 4380 6.993902 AGGCCTATATATAGCTTACTCGTCTC 59.006 42.308 1.29 0.00 0.00 3.36
946 4451 6.937465 ACTGATTAGAGAAGGTTTCTTGGTTC 59.063 38.462 0.00 0.00 40.87 3.62
976 4501 0.867753 CAATCGAAGGACGCGAGGAG 60.868 60.000 15.93 0.00 41.49 3.69
997 4522 2.420642 CTTGGTCTCCGCCATCATATG 58.579 52.381 0.00 0.00 38.48 1.78
1052 4755 2.031163 GCACCACCGTCTTGCTCT 59.969 61.111 0.00 0.00 33.26 4.09
1307 5029 1.128692 CCTGAAACGAATCCGCAGAAC 59.871 52.381 0.00 0.00 39.95 3.01
1451 5195 0.888619 AAGGAGATCACAACGAGCGA 59.111 50.000 0.00 0.00 34.30 4.93
1452 5196 1.656095 GAAAGGAGATCACAACGAGCG 59.344 52.381 0.00 0.00 34.30 5.03
1459 5203 9.513906 CAGATAGATAGTAGAAAGGAGATCACA 57.486 37.037 0.00 0.00 0.00 3.58
1461 5205 9.733556 GACAGATAGATAGTAGAAAGGAGATCA 57.266 37.037 0.00 0.00 0.00 2.92
1462 5206 9.174166 GGACAGATAGATAGTAGAAAGGAGATC 57.826 40.741 0.00 0.00 0.00 2.75
1463 5207 8.674173 TGGACAGATAGATAGTAGAAAGGAGAT 58.326 37.037 0.00 0.00 0.00 2.75
1464 5208 8.046867 TGGACAGATAGATAGTAGAAAGGAGA 57.953 38.462 0.00 0.00 0.00 3.71
1465 5209 8.739039 CATGGACAGATAGATAGTAGAAAGGAG 58.261 40.741 0.00 0.00 0.00 3.69
1466 5210 7.671819 CCATGGACAGATAGATAGTAGAAAGGA 59.328 40.741 5.56 0.00 0.00 3.36
1467 5211 7.671819 TCCATGGACAGATAGATAGTAGAAAGG 59.328 40.741 11.44 0.00 0.00 3.11
1468 5212 8.642935 TCCATGGACAGATAGATAGTAGAAAG 57.357 38.462 11.44 0.00 0.00 2.62
1473 5217 9.256228 GGTTTATCCATGGACAGATAGATAGTA 57.744 37.037 18.99 0.00 35.97 1.82
1474 5218 7.734865 TGGTTTATCCATGGACAGATAGATAGT 59.265 37.037 18.99 0.00 41.93 2.12
1475 5219 8.138928 TGGTTTATCCATGGACAGATAGATAG 57.861 38.462 18.99 0.00 41.93 2.08
1476 5220 8.375506 GTTGGTTTATCCATGGACAGATAGATA 58.624 37.037 18.99 0.00 46.60 1.98
1477 5221 7.072961 AGTTGGTTTATCCATGGACAGATAGAT 59.927 37.037 18.99 0.21 46.60 1.98
1478 5222 6.386927 AGTTGGTTTATCCATGGACAGATAGA 59.613 38.462 18.99 0.00 46.60 1.98
1479 5223 6.595682 AGTTGGTTTATCCATGGACAGATAG 58.404 40.000 18.99 0.00 46.60 2.08
1480 5224 6.575244 AGTTGGTTTATCCATGGACAGATA 57.425 37.500 18.99 2.06 46.60 1.98
1481 5225 5.440610 GAGTTGGTTTATCCATGGACAGAT 58.559 41.667 18.99 3.24 46.60 2.90
1482 5226 4.622933 CGAGTTGGTTTATCCATGGACAGA 60.623 45.833 18.99 0.00 46.60 3.41
1483 5227 3.623060 CGAGTTGGTTTATCCATGGACAG 59.377 47.826 18.99 0.00 46.60 3.51
1484 5228 3.008594 ACGAGTTGGTTTATCCATGGACA 59.991 43.478 18.99 0.87 46.60 4.02
1485 5229 3.606687 ACGAGTTGGTTTATCCATGGAC 58.393 45.455 18.99 4.42 46.60 4.02
1486 5230 3.517901 AGACGAGTTGGTTTATCCATGGA 59.482 43.478 18.88 18.88 46.60 3.41
1487 5231 3.871594 GAGACGAGTTGGTTTATCCATGG 59.128 47.826 4.97 4.97 46.60 3.66
1488 5232 3.871594 GGAGACGAGTTGGTTTATCCATG 59.128 47.826 0.00 0.00 46.60 3.66
1489 5233 3.118371 GGGAGACGAGTTGGTTTATCCAT 60.118 47.826 0.00 0.00 46.60 3.41
1490 5234 2.235402 GGGAGACGAGTTGGTTTATCCA 59.765 50.000 0.00 0.00 45.60 3.41
1491 5235 2.500504 AGGGAGACGAGTTGGTTTATCC 59.499 50.000 0.00 0.00 0.00 2.59
1494 5238 2.549349 GCAAGGGAGACGAGTTGGTTTA 60.549 50.000 0.00 0.00 0.00 2.01
1495 5239 1.814248 GCAAGGGAGACGAGTTGGTTT 60.814 52.381 0.00 0.00 0.00 3.27
1499 5243 0.318441 TCAGCAAGGGAGACGAGTTG 59.682 55.000 0.00 0.00 0.00 3.16
1501 5245 2.145397 TATCAGCAAGGGAGACGAGT 57.855 50.000 0.00 0.00 0.00 4.18
1502 5246 2.890311 AGATATCAGCAAGGGAGACGAG 59.110 50.000 5.32 0.00 0.00 4.18
1505 5249 5.679601 AGAAAAGATATCAGCAAGGGAGAC 58.320 41.667 5.32 0.00 0.00 3.36
1506 5250 5.965033 AGAAAAGATATCAGCAAGGGAGA 57.035 39.130 5.32 0.00 0.00 3.71
1507 5251 7.678837 AGATAGAAAAGATATCAGCAAGGGAG 58.321 38.462 5.32 0.00 32.98 4.30
1508 5252 7.623999 AGATAGAAAAGATATCAGCAAGGGA 57.376 36.000 5.32 0.00 32.98 4.20
1518 5262 8.744652 CCGTGGACAGATAGATAGAAAAGATAT 58.255 37.037 0.00 0.00 0.00 1.63
1519 5263 7.942894 TCCGTGGACAGATAGATAGAAAAGATA 59.057 37.037 0.00 0.00 0.00 1.98
1520 5264 6.778069 TCCGTGGACAGATAGATAGAAAAGAT 59.222 38.462 0.00 0.00 0.00 2.40
1521 5265 6.127101 TCCGTGGACAGATAGATAGAAAAGA 58.873 40.000 0.00 0.00 0.00 2.52
1524 5268 5.531659 GTCTCCGTGGACAGATAGATAGAAA 59.468 44.000 0.99 0.00 36.35 2.52
1526 5270 4.643463 GTCTCCGTGGACAGATAGATAGA 58.357 47.826 0.99 0.00 36.35 1.98
1531 5275 1.664873 TCGTCTCCGTGGACAGATAG 58.335 55.000 5.98 0.00 36.12 2.08
1532 5276 2.219458 GATCGTCTCCGTGGACAGATA 58.781 52.381 5.98 0.00 36.12 1.98
1534 5278 0.322187 TGATCGTCTCCGTGGACAGA 60.322 55.000 5.98 4.69 36.12 3.41
1535 5279 0.179161 GTGATCGTCTCCGTGGACAG 60.179 60.000 5.98 0.37 36.12 3.51
1536 5280 0.891904 TGTGATCGTCTCCGTGGACA 60.892 55.000 5.98 0.00 36.12 4.02
1538 5282 0.891904 TGTGTGATCGTCTCCGTGGA 60.892 55.000 0.00 0.00 35.01 4.02
1539 5283 0.173481 ATGTGTGATCGTCTCCGTGG 59.827 55.000 0.00 0.00 35.01 4.94
1540 5284 1.655597 CAATGTGTGATCGTCTCCGTG 59.344 52.381 0.00 0.00 35.01 4.94
1570 5324 1.065102 TCGTATAAGCAGCGACAGGTC 59.935 52.381 0.00 0.00 0.00 3.85
1577 5334 0.043310 GCGGTTTCGTATAAGCAGCG 60.043 55.000 5.39 5.39 38.89 5.18
1673 5430 2.791927 CCGACGACGAGCAGATCA 59.208 61.111 9.28 0.00 42.66 2.92
1706 5463 0.615331 GACCTGACCTCTTGATGGCA 59.385 55.000 0.00 0.00 0.00 4.92
1720 5477 4.326826 TGCAGTAGAAAATCAAGGACCTG 58.673 43.478 0.00 0.00 0.00 4.00
1721 5478 4.042187 ACTGCAGTAGAAAATCAAGGACCT 59.958 41.667 20.16 0.00 0.00 3.85
1722 5479 4.327680 ACTGCAGTAGAAAATCAAGGACC 58.672 43.478 20.16 0.00 0.00 4.46
1723 5480 7.043325 CGTATACTGCAGTAGAAAATCAAGGAC 60.043 40.741 29.05 9.89 33.52 3.85
1724 5481 6.978659 CGTATACTGCAGTAGAAAATCAAGGA 59.021 38.462 29.05 6.16 33.52 3.36
1737 5499 3.550233 CGCTATGGAACGTATACTGCAGT 60.550 47.826 25.12 25.12 0.00 4.40
1745 5507 3.211865 TCAGTCTCGCTATGGAACGTAT 58.788 45.455 0.00 0.00 0.00 3.06
1750 5512 5.654603 TTAGTTTCAGTCTCGCTATGGAA 57.345 39.130 0.00 0.00 0.00 3.53
1754 5516 5.127194 TCACCATTAGTTTCAGTCTCGCTAT 59.873 40.000 0.00 0.00 0.00 2.97
1756 5518 3.258372 TCACCATTAGTTTCAGTCTCGCT 59.742 43.478 0.00 0.00 0.00 4.93
1860 5625 4.186926 GCTGCTTGACTATCATCACAGAA 58.813 43.478 0.00 0.00 0.00 3.02
1913 5683 2.501723 ACTGGGCACGATTGATCTAACT 59.498 45.455 0.00 0.00 0.00 2.24
1922 5696 0.606401 CACTGGAACTGGGCACGATT 60.606 55.000 0.00 0.00 0.00 3.34
2205 6017 7.013274 TCTGCTTAGCTTTGTTGTAAGTCAAAT 59.987 33.333 5.60 0.00 37.81 2.32
2220 6032 9.284968 TCTGTTTTTATTTACTCTGCTTAGCTT 57.715 29.630 5.60 0.00 0.00 3.74
2258 6078 3.442167 GCATCATGCGTGGCACCA 61.442 61.111 12.86 11.50 43.04 4.17
2267 6087 0.889994 TGAACACCCAAGCATCATGC 59.110 50.000 0.00 0.00 45.46 4.06
2304 6126 7.910683 GTGAGTCTCTTGAAGAACGAAAAATTT 59.089 33.333 0.65 0.00 35.21 1.82
2310 6132 3.383505 TGGTGAGTCTCTTGAAGAACGAA 59.616 43.478 0.65 0.00 35.21 3.85
2311 6133 2.956333 TGGTGAGTCTCTTGAAGAACGA 59.044 45.455 0.65 0.00 35.21 3.85
2313 6135 5.300752 TCAATGGTGAGTCTCTTGAAGAAC 58.699 41.667 0.65 0.00 35.21 3.01
2320 6142 5.435291 GGATCATTCAATGGTGAGTCTCTT 58.565 41.667 0.00 0.00 34.49 2.85
2328 6150 4.434545 AGAGAGGGATCATTCAATGGTG 57.565 45.455 0.00 0.00 0.00 4.17
2335 6157 6.827762 AGTTCATCAAAAGAGAGGGATCATTC 59.172 38.462 0.00 0.00 0.00 2.67
2475 6787 9.162764 GTAAACACTAATAGAAAGATCAAGCCA 57.837 33.333 0.00 0.00 0.00 4.75
2476 6788 9.384764 AGTAAACACTAATAGAAAGATCAAGCC 57.615 33.333 0.00 0.00 0.00 4.35
2522 6834 4.279922 TCTTGTGAAGTCTACAACGATCCA 59.720 41.667 0.00 0.00 34.58 3.41
2523 6835 4.806330 TCTTGTGAAGTCTACAACGATCC 58.194 43.478 0.00 0.00 34.58 3.36
2527 6839 5.140177 GCAATTCTTGTGAAGTCTACAACG 58.860 41.667 0.00 0.00 35.44 4.10
2548 6860 7.829211 AGTAGATTTTTAGGCTAAGTGAATGCA 59.171 33.333 7.09 0.00 0.00 3.96
2576 6894 7.889469 ACTACTGTAATTTTTCCGACTGAGTA 58.111 34.615 0.00 0.00 0.00 2.59
2581 6899 8.529476 ACTGATACTACTGTAATTTTTCCGACT 58.471 33.333 0.00 0.00 31.80 4.18
2646 6969 0.678684 CGGTATTTTTGCCCGTCCCT 60.679 55.000 0.00 0.00 37.00 4.20
2654 6977 3.054166 GTTGGGTTGACGGTATTTTTGC 58.946 45.455 0.00 0.00 0.00 3.68
2667 6990 8.606040 ATCAACTAAATTTTCATGTTGGGTTG 57.394 30.769 17.58 0.00 38.64 3.77
2675 6998 8.755696 TTTCGGGAATCAACTAAATTTTCATG 57.244 30.769 0.00 0.00 0.00 3.07
2684 7007 8.077386 GTGTACAATTTTTCGGGAATCAACTAA 58.923 33.333 0.00 0.00 0.00 2.24
2696 7019 9.872757 AACTATAACAGTGTGTACAATTTTTCG 57.127 29.630 0.00 0.00 37.63 3.46
2762 7094 7.504403 TGGAATTAACCTTTTTCTTGATTGCA 58.496 30.769 0.00 0.00 0.00 4.08
2787 7119 2.814336 GTTGGTTTCAGCGAGATTCCTT 59.186 45.455 0.00 0.00 0.00 3.36
2796 7426 0.732571 ACAGTGTGTTGGTTTCAGCG 59.267 50.000 0.00 0.00 0.00 5.18
2812 7442 4.927425 CCAATTTGGAATCTGCTTTCACAG 59.073 41.667 10.03 0.00 40.96 3.66


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

AutoCloner maintained by Alex Coulton.