Multiple sequence alignment - TraesCS1B01G324200

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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 TraesCS1B01G324200 chr1B 100.000 4703 0 0 1 4703 549781044 549785746 0.000000e+00 8685
1 TraesCS1B01G324200 chr1A 94.722 4244 205 7 1 4238 504577910 504582140 0.000000e+00 6578
2 TraesCS1B01G324200 chr1A 92.558 215 16 0 4354 4568 504585739 504585953 4.570000e-80 309
3 TraesCS1B01G324200 chr1A 95.161 124 6 0 4233 4356 504585577 504585700 3.710000e-46 196
4 TraesCS1B01G324200 chr1D 94.389 4010 204 11 361 4356 408511089 408515091 0.000000e+00 6139
5 TraesCS1B01G324200 chr1D 92.097 329 24 2 1 328 408510439 408510766 3.320000e-126 462
6 TraesCS1B01G324200 chr1D 96.154 104 4 0 4600 4703 38280701 38280804 2.250000e-38 171
7 TraesCS1B01G324200 chr2D 94.595 111 5 1 4594 4703 440182770 440182660 2.250000e-38 171
8 TraesCS1B01G324200 chr2D 94.444 108 5 1 4596 4703 42524858 42524752 1.050000e-36 165
9 TraesCS1B01G324200 chr7A 96.117 103 4 0 4601 4703 35356380 35356482 8.090000e-38 169
10 TraesCS1B01G324200 chr5B 96.117 103 4 0 4601 4703 334971471 334971369 8.090000e-38 169
11 TraesCS1B01G324200 chr5B 96.117 103 4 0 4601 4703 664099889 664099787 8.090000e-38 169
12 TraesCS1B01G324200 chr7D 96.040 101 4 0 4603 4703 424919266 424919166 1.050000e-36 165
13 TraesCS1B01G324200 chr4A 92.793 111 7 1 4593 4703 179762604 179762713 4.870000e-35 159
14 TraesCS1B01G324200 chr2B 90.833 120 9 2 4585 4703 582686685 582686803 4.870000e-35 159


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 TraesCS1B01G324200 chr1B 549781044 549785746 4702 False 8685.0 8685 100.000 1 4703 1 chr1B.!!$F1 4702
1 TraesCS1B01G324200 chr1A 504577910 504585953 8043 False 2361.0 6578 94.147 1 4568 3 chr1A.!!$F1 4567
2 TraesCS1B01G324200 chr1D 408510439 408515091 4652 False 3300.5 6139 93.243 1 4356 2 chr1D.!!$F2 4355

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
913 1223 0.537188 CCCAGGAATAGCGTGTGACT 59.463 55.0 0.00 0.0 0.00 3.41 F
1774 2085 0.039618 CACCACCTACAATTGCCCCT 59.960 55.0 5.05 0.0 0.00 4.79 F
1926 2238 0.671796 ACTCCGATGACGTGACAACA 59.328 50.0 0.00 0.0 37.88 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2642 2954 0.881118 TTTCGGTAAGCCTCGTACGT 59.119 50.000 16.05 0.0 0.00 3.57 R
3093 3406 0.850100 TCAGGTTGGCCTTCTTCCAA 59.150 50.000 3.32 0.0 44.18 3.53 R
3796 4109 1.897615 CGGGGTCCTAGCTCCTACG 60.898 68.421 0.00 0.0 0.00 3.51 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
56 58 7.499321 TTTGTATTTACCTGTGTAGTTGGTG 57.501 36.000 0.00 0.00 35.48 4.17
120 122 5.064579 TGGTCGCATACAAACTAACATCATG 59.935 40.000 0.00 0.00 0.00 3.07
290 295 4.280174 ACCTACGAGTTCAAGTGCTTTCTA 59.720 41.667 0.00 0.00 0.00 2.10
328 333 3.464907 CTCGAAGATGATCCTGCATTGT 58.535 45.455 0.00 0.00 33.89 2.71
335 340 5.888901 AGATGATCCTGCATTGTCCATTAT 58.111 37.500 0.00 0.00 0.00 1.28
336 341 5.710567 AGATGATCCTGCATTGTCCATTATG 59.289 40.000 0.00 0.00 0.00 1.90
407 702 2.813754 CCCACACCCGATGCTATTTATG 59.186 50.000 0.00 0.00 0.00 1.90
421 716 7.574021 TGCTATTTATGGAGGATAGTTGGAT 57.426 36.000 0.00 0.00 0.00 3.41
521 830 7.690454 TCATGGAAATATAGAAGAGTTGGGA 57.310 36.000 0.00 0.00 0.00 4.37
522 831 8.101309 TCATGGAAATATAGAAGAGTTGGGAA 57.899 34.615 0.00 0.00 0.00 3.97
523 832 8.727149 TCATGGAAATATAGAAGAGTTGGGAAT 58.273 33.333 0.00 0.00 0.00 3.01
526 835 9.225682 TGGAAATATAGAAGAGTTGGGAATAGT 57.774 33.333 0.00 0.00 0.00 2.12
537 846 7.245292 AGAGTTGGGAATAGTGCTCTAGATAT 58.755 38.462 1.55 0.00 32.32 1.63
561 870 3.118775 TCGTGAAGGACCATAGATTGTGG 60.119 47.826 0.00 0.00 42.55 4.17
690 999 1.259507 GCGTGCTTCAACTGTAAACGA 59.740 47.619 0.00 0.00 0.00 3.85
693 1002 4.523813 CGTGCTTCAACTGTAAACGAATT 58.476 39.130 0.00 0.00 0.00 2.17
905 1215 2.839836 GGGAGCCCCAGGAATAGC 59.160 66.667 5.45 0.00 44.65 2.97
913 1223 0.537188 CCCAGGAATAGCGTGTGACT 59.463 55.000 0.00 0.00 0.00 3.41
965 1275 8.485578 TTTTGGGAAGAATATTAAAGGTGTGT 57.514 30.769 0.00 0.00 0.00 3.72
1092 1403 4.194640 CGGTCATTGTCAAGATGGAGAAT 58.805 43.478 0.00 0.00 31.60 2.40
1120 1431 4.466370 ACTGGTCTATTTCGGAGATCAACA 59.534 41.667 0.00 0.00 33.69 3.33
1121 1432 5.129485 ACTGGTCTATTTCGGAGATCAACAT 59.871 40.000 0.00 0.00 33.69 2.71
1124 1435 6.049149 GGTCTATTTCGGAGATCAACATTGA 58.951 40.000 0.00 0.00 42.14 2.57
1127 1438 3.586100 TTCGGAGATCAACATTGACGA 57.414 42.857 0.00 0.00 40.49 4.20
1135 1446 4.996758 AGATCAACATTGACGATGACAACA 59.003 37.500 9.78 0.00 40.49 3.33
1339 1650 0.179048 CGCTACTGATGGGGAATGCA 60.179 55.000 0.00 0.00 0.00 3.96
1350 1661 1.619432 GGGGAATGCAAGGATGTGGAA 60.619 52.381 0.00 0.00 0.00 3.53
1354 1665 3.703052 GGAATGCAAGGATGTGGAAGAAT 59.297 43.478 0.00 0.00 0.00 2.40
1415 1726 2.005095 AGGCCTGCCTCATGATGTT 58.995 52.632 3.11 0.00 44.43 2.71
1421 1732 1.931841 CTGCCTCATGATGTTCGTCTG 59.068 52.381 0.00 0.00 0.00 3.51
1429 1740 4.705023 TCATGATGTTCGTCTGTCTCCTTA 59.295 41.667 0.00 0.00 0.00 2.69
1458 1769 4.832608 GCCGCCTACTCCAACGGG 62.833 72.222 2.17 0.00 45.72 5.28
1482 1793 1.534729 GGAACCTTGCCGTCTTCATT 58.465 50.000 0.00 0.00 0.00 2.57
1500 1811 8.067784 GTCTTCATTAATTCTTTCAACACGTCA 58.932 33.333 0.00 0.00 0.00 4.35
1525 1836 2.740826 GCTTTCGTGCCGCCTACA 60.741 61.111 0.00 0.00 0.00 2.74
1655 1966 1.213926 CATCAAGCCTAAGCCCCTCTT 59.786 52.381 0.00 0.00 41.25 2.85
1658 1969 1.283321 CAAGCCTAAGCCCCTCTTTCT 59.717 52.381 0.00 0.00 41.25 2.52
1774 2085 0.039618 CACCACCTACAATTGCCCCT 59.960 55.000 5.05 0.00 0.00 4.79
1782 2093 4.086457 CCTACAATTGCCCCTACAGTTTT 58.914 43.478 5.05 0.00 0.00 2.43
1784 2095 5.357032 CCTACAATTGCCCCTACAGTTTTAG 59.643 44.000 5.05 0.00 0.00 1.85
1921 2233 1.642037 GGACGACTCCGATGACGTGA 61.642 60.000 0.00 0.00 38.28 4.35
1926 2238 0.671796 ACTCCGATGACGTGACAACA 59.328 50.000 0.00 0.00 37.88 3.33
2217 2529 3.230976 GAACTCTTTCATTGGGTGGGTT 58.769 45.455 0.00 0.00 0.00 4.11
2265 2577 2.564062 CCAAGCCAGATGGTCATTTGTT 59.436 45.455 0.00 0.00 37.57 2.83
2289 2601 4.759782 ACAAGGATGAGAACCTATTGACG 58.240 43.478 0.00 0.00 36.67 4.35
2642 2954 2.288666 GCCAATGCGAATTACCAGAGA 58.711 47.619 0.00 0.00 0.00 3.10
2760 3072 1.339291 GCAAGTGCTCTTTTCCTGCTT 59.661 47.619 0.00 0.00 38.21 3.91
2775 3087 9.617975 CTTTTCCTGCTTTAAAATCTAGTTCAG 57.382 33.333 0.00 0.00 0.00 3.02
2865 3177 9.817365 CTTGTGACATTTGTAGATACTTCTTTG 57.183 33.333 0.00 0.00 33.17 2.77
3093 3406 9.643693 CTAATTTTGTTATGGCAGATTGTCTTT 57.356 29.630 0.00 0.00 0.00 2.52
3243 3556 1.192428 GGGTCGTCTGTTACATCCCT 58.808 55.000 0.00 0.00 37.55 4.20
3291 3604 0.953471 CTGCACCGAAATCGTTCCCA 60.953 55.000 1.79 0.00 37.74 4.37
3315 3628 5.912149 TTATCATCCCATACCTGCTCTTT 57.088 39.130 0.00 0.00 0.00 2.52
3357 3670 3.067742 CCAAGTTCAATGCCATGATCTCC 59.932 47.826 0.00 0.00 30.85 3.71
3492 3805 1.035932 GCTCAGTGCCAGCCATCAAT 61.036 55.000 0.00 0.00 35.15 2.57
3508 3821 5.128205 CCATCAATGTAGCAATCAAGGAGA 58.872 41.667 0.00 0.00 0.00 3.71
3512 3825 7.707624 TCAATGTAGCAATCAAGGAGAAATT 57.292 32.000 0.00 0.00 0.00 1.82
3567 3880 6.014156 ACCGAATATATAAGAAGGAGCTTGCT 60.014 38.462 0.00 0.00 0.00 3.91
3639 3952 6.158695 AGCAAGGGATTCACTTCTATTTCCTA 59.841 38.462 0.00 0.00 0.00 2.94
3789 4102 2.740447 GTTGTTGTACCTTCCATCGTCC 59.260 50.000 0.00 0.00 0.00 4.79
3796 4109 3.447025 CTTCCATCGTCCGAGGGGC 62.447 68.421 18.93 0.00 45.20 5.80
3826 4139 1.375523 GACCCCGAAGCGAACATGT 60.376 57.895 0.00 0.00 0.00 3.21
3857 4170 5.948992 AGTCAAAGGATTCTTACAACAGC 57.051 39.130 0.00 0.00 32.01 4.40
3951 4272 7.202016 TCTGGTCAATCACATTCTTTTGTAC 57.798 36.000 0.00 0.00 0.00 2.90
3973 4294 8.536175 TGTACCATGTTGTTCTAGATGATGTTA 58.464 33.333 0.00 0.00 0.00 2.41
3978 4299 8.607459 CATGTTGTTCTAGATGATGTTAAGGTC 58.393 37.037 0.00 0.00 0.00 3.85
4065 4386 3.728076 TCGATGCATCTGTTAGTACCC 57.272 47.619 23.73 0.00 0.00 3.69
4070 4391 2.438021 TGCATCTGTTAGTACCCATCCC 59.562 50.000 0.00 0.00 0.00 3.85
4080 4401 1.276989 GTACCCATCCCGTTTGACTCA 59.723 52.381 0.00 0.00 0.00 3.41
4189 4510 7.323656 GTCTCATACAATTTGAAGTTTTGACCG 59.676 37.037 2.79 0.00 0.00 4.79
4260 8023 5.259627 TGATACCATATACACCCGACCTA 57.740 43.478 0.00 0.00 0.00 3.08
4336 8099 2.338620 GGCCGACAAAACCAAGGC 59.661 61.111 0.00 0.00 46.51 4.35
4356 8119 2.733026 GCCTTGCAACATAAAAGCAGTG 59.267 45.455 0.00 0.00 39.72 3.66
4357 8120 2.733026 CCTTGCAACATAAAAGCAGTGC 59.267 45.455 7.13 7.13 39.72 4.40
4358 8121 2.049077 TGCAACATAAAAGCAGTGCG 57.951 45.000 10.00 0.00 33.75 5.34
4360 8123 1.068610 GCAACATAAAAGCAGTGCGGA 60.069 47.619 10.00 0.00 0.00 5.54
4362 8125 2.185004 ACATAAAAGCAGTGCGGACT 57.815 45.000 10.00 2.68 0.00 3.85
4363 8126 3.328382 ACATAAAAGCAGTGCGGACTA 57.672 42.857 10.03 0.00 0.00 2.59
4364 8127 3.262420 ACATAAAAGCAGTGCGGACTAG 58.738 45.455 10.03 5.70 0.00 2.57
4365 8128 2.380084 TAAAAGCAGTGCGGACTAGG 57.620 50.000 10.03 0.00 0.00 3.02
4375 8179 1.833787 GCGGACTAGGGACCAAACCA 61.834 60.000 0.00 0.00 0.00 3.67
4408 8212 6.071784 ACCCGTCCTTGTGTTTATATTTTTCC 60.072 38.462 0.00 0.00 0.00 3.13
4472 8276 3.512516 GCAAGCTGTCGGCCCATC 61.513 66.667 0.00 0.00 43.05 3.51
4487 8291 1.365633 CATCCTCGGCCAGCTCTAC 59.634 63.158 2.24 0.00 0.00 2.59
4499 8303 3.805108 GCCAGCTCTACGATTTCCATCAT 60.805 47.826 0.00 0.00 0.00 2.45
4503 8307 5.985530 CAGCTCTACGATTTCCATCATGTTA 59.014 40.000 0.00 0.00 0.00 2.41
4515 8319 1.832883 TCATGTTATGCCACCGCTTT 58.167 45.000 0.00 0.00 35.36 3.51
4522 8326 2.671619 GCCACCGCTTTAGTGCCA 60.672 61.111 0.00 0.00 33.75 4.92
4536 8340 7.201609 CGCTTTAGTGCCACTATTATTTCTCAA 60.202 37.037 5.21 0.00 29.64 3.02
4576 8380 2.806945 TGAGGGATTCAACCACCATC 57.193 50.000 0.00 0.00 35.46 3.51
4577 8381 1.065491 TGAGGGATTCAACCACCATCG 60.065 52.381 0.00 0.00 37.31 3.84
4578 8382 0.255890 AGGGATTCAACCACCATCGG 59.744 55.000 0.00 0.00 0.00 4.18
4579 8383 0.751643 GGGATTCAACCACCATCGGG 60.752 60.000 0.00 0.00 41.29 5.14
4591 8395 2.751166 CCATCGGGTATGCTCTTAGG 57.249 55.000 0.00 0.00 33.92 2.69
4592 8396 2.248248 CCATCGGGTATGCTCTTAGGA 58.752 52.381 0.00 0.00 33.92 2.94
4593 8397 2.028930 CCATCGGGTATGCTCTTAGGAC 60.029 54.545 0.00 0.00 33.92 3.85
4594 8398 2.447408 TCGGGTATGCTCTTAGGACA 57.553 50.000 0.00 0.00 0.00 4.02
4595 8399 2.742348 TCGGGTATGCTCTTAGGACAA 58.258 47.619 0.00 0.00 0.00 3.18
4596 8400 3.101437 TCGGGTATGCTCTTAGGACAAA 58.899 45.455 0.00 0.00 0.00 2.83
4597 8401 3.516300 TCGGGTATGCTCTTAGGACAAAA 59.484 43.478 0.00 0.00 0.00 2.44
4598 8402 3.871594 CGGGTATGCTCTTAGGACAAAAG 59.128 47.826 0.00 0.00 0.00 2.27
4599 8403 4.382685 CGGGTATGCTCTTAGGACAAAAGA 60.383 45.833 0.00 0.00 0.00 2.52
4600 8404 5.685075 CGGGTATGCTCTTAGGACAAAAGAT 60.685 44.000 0.00 0.00 32.72 2.40
4601 8405 6.462487 CGGGTATGCTCTTAGGACAAAAGATA 60.462 42.308 0.00 0.00 32.72 1.98
4602 8406 7.280356 GGGTATGCTCTTAGGACAAAAGATAA 58.720 38.462 0.00 0.00 32.72 1.75
4603 8407 7.442666 GGGTATGCTCTTAGGACAAAAGATAAG 59.557 40.741 0.00 0.00 32.72 1.73
4604 8408 7.442666 GGTATGCTCTTAGGACAAAAGATAAGG 59.557 40.741 0.00 0.00 32.72 2.69
4605 8409 5.745227 TGCTCTTAGGACAAAAGATAAGGG 58.255 41.667 0.00 0.00 32.72 3.95
4606 8410 5.250774 TGCTCTTAGGACAAAAGATAAGGGT 59.749 40.000 0.00 0.00 32.72 4.34
4607 8411 5.818336 GCTCTTAGGACAAAAGATAAGGGTC 59.182 44.000 0.00 0.00 32.72 4.46
4608 8412 6.352308 GCTCTTAGGACAAAAGATAAGGGTCT 60.352 42.308 0.00 0.00 32.72 3.85
4609 8413 6.947464 TCTTAGGACAAAAGATAAGGGTCTG 58.053 40.000 0.00 0.00 0.00 3.51
4610 8414 6.500751 TCTTAGGACAAAAGATAAGGGTCTGT 59.499 38.462 0.00 0.00 0.00 3.41
4611 8415 5.584551 AGGACAAAAGATAAGGGTCTGTT 57.415 39.130 0.00 0.00 0.00 3.16
4612 8416 5.953571 AGGACAAAAGATAAGGGTCTGTTT 58.046 37.500 0.00 0.00 0.00 2.83
4613 8417 5.770162 AGGACAAAAGATAAGGGTCTGTTTG 59.230 40.000 0.00 0.00 35.18 2.93
4614 8418 5.048013 GGACAAAAGATAAGGGTCTGTTTGG 60.048 44.000 0.00 0.00 34.38 3.28
4615 8419 5.454966 ACAAAAGATAAGGGTCTGTTTGGT 58.545 37.500 0.00 0.00 34.38 3.67
4616 8420 5.897250 ACAAAAGATAAGGGTCTGTTTGGTT 59.103 36.000 0.00 0.00 34.38 3.67
4617 8421 6.040504 ACAAAAGATAAGGGTCTGTTTGGTTC 59.959 38.462 0.00 0.00 34.38 3.62
4618 8422 4.302559 AGATAAGGGTCTGTTTGGTTCC 57.697 45.455 0.00 0.00 0.00 3.62
4619 8423 3.655777 AGATAAGGGTCTGTTTGGTTCCA 59.344 43.478 0.00 0.00 0.00 3.53
4620 8424 2.838637 AAGGGTCTGTTTGGTTCCAA 57.161 45.000 0.00 0.00 0.00 3.53
4621 8425 2.838637 AGGGTCTGTTTGGTTCCAAA 57.161 45.000 12.29 12.29 34.09 3.28
4622 8426 3.328535 AGGGTCTGTTTGGTTCCAAAT 57.671 42.857 18.11 0.31 38.07 2.32
4623 8427 4.463050 AGGGTCTGTTTGGTTCCAAATA 57.537 40.909 18.11 14.87 38.07 1.40
4624 8428 4.810345 AGGGTCTGTTTGGTTCCAAATAA 58.190 39.130 18.11 10.23 38.07 1.40
4625 8429 4.832823 AGGGTCTGTTTGGTTCCAAATAAG 59.167 41.667 18.11 17.33 38.07 1.73
4626 8430 4.587262 GGGTCTGTTTGGTTCCAAATAAGT 59.413 41.667 18.11 0.00 38.07 2.24
4627 8431 5.278808 GGGTCTGTTTGGTTCCAAATAAGTC 60.279 44.000 18.11 15.15 38.07 3.01
4628 8432 5.300792 GGTCTGTTTGGTTCCAAATAAGTCA 59.699 40.000 18.11 10.94 38.07 3.41
4629 8433 6.206498 GTCTGTTTGGTTCCAAATAAGTCAC 58.794 40.000 18.11 10.99 38.07 3.67
4630 8434 5.300792 TCTGTTTGGTTCCAAATAAGTCACC 59.699 40.000 18.11 5.59 38.07 4.02
4631 8435 4.956700 TGTTTGGTTCCAAATAAGTCACCA 59.043 37.500 18.11 7.77 38.07 4.17
4632 8436 5.422331 TGTTTGGTTCCAAATAAGTCACCAA 59.578 36.000 18.11 0.00 41.48 3.67
4633 8437 5.523438 TTGGTTCCAAATAAGTCACCAAC 57.477 39.130 1.42 0.00 38.97 3.77
4634 8438 4.798882 TGGTTCCAAATAAGTCACCAACT 58.201 39.130 0.00 0.00 41.10 3.16
4635 8439 6.155393 TTTGGTTCCAAATAAGTCACCAACTT 59.845 34.615 12.29 0.00 42.59 2.66
4676 8480 7.856145 AAAAAGTGACATATTTTGCCAAACA 57.144 28.000 0.00 0.00 0.00 2.83
4677 8481 7.481275 AAAAGTGACATATTTTGCCAAACAG 57.519 32.000 0.00 0.00 0.00 3.16
4678 8482 5.138125 AGTGACATATTTTGCCAAACAGG 57.862 39.130 0.00 0.00 41.84 4.00
4691 8495 4.718940 CCAAACAGGCCCAACTTATAAG 57.281 45.455 11.05 11.05 0.00 1.73
4692 8496 4.086457 CCAAACAGGCCCAACTTATAAGT 58.914 43.478 12.50 12.50 42.04 2.24
4693 8497 4.157840 CCAAACAGGCCCAACTTATAAGTC 59.842 45.833 18.28 6.09 38.57 3.01
4694 8498 4.650972 AACAGGCCCAACTTATAAGTCA 57.349 40.909 18.28 0.00 38.57 3.41
4695 8499 3.951663 ACAGGCCCAACTTATAAGTCAC 58.048 45.455 18.28 8.25 38.57 3.67
4696 8500 3.279434 CAGGCCCAACTTATAAGTCACC 58.721 50.000 18.28 15.72 38.57 4.02
4697 8501 2.241430 AGGCCCAACTTATAAGTCACCC 59.759 50.000 18.28 15.00 38.57 4.61
4698 8502 2.651455 GCCCAACTTATAAGTCACCCC 58.349 52.381 18.28 3.57 38.57 4.95
4699 8503 2.025699 GCCCAACTTATAAGTCACCCCA 60.026 50.000 18.28 0.00 38.57 4.96
4700 8504 3.562609 GCCCAACTTATAAGTCACCCCAA 60.563 47.826 18.28 0.00 38.57 4.12
4701 8505 4.014406 CCCAACTTATAAGTCACCCCAAC 58.986 47.826 18.28 0.00 38.57 3.77
4702 8506 4.263771 CCCAACTTATAAGTCACCCCAACT 60.264 45.833 18.28 0.00 38.57 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 7.748847 TGTCGAATTTAATAAGTGCCTTCTTC 58.251 34.615 0.00 0.00 0.00 2.87
71 73 0.464735 CGGGCCCCATGTCGAATTTA 60.465 55.000 18.66 0.00 0.00 1.40
99 101 4.633565 TGCATGATGTTAGTTTGTATGCGA 59.366 37.500 0.00 0.00 41.55 5.10
120 122 6.002704 AGATCAAATCCAGTGGATATCTTGC 58.997 40.000 25.09 13.08 42.27 4.01
290 295 2.076863 CGAGGAGTGCGAAAGGAAAAT 58.923 47.619 0.00 0.00 0.00 1.82
328 333 3.563390 CACACACACACACACATAATGGA 59.437 43.478 0.00 0.00 0.00 3.41
335 340 1.276705 ACTACCACACACACACACACA 59.723 47.619 0.00 0.00 0.00 3.72
336 341 1.663643 CACTACCACACACACACACAC 59.336 52.381 0.00 0.00 0.00 3.82
407 702 2.225467 GCTTGCATCCAACTATCCTCC 58.775 52.381 0.00 0.00 0.00 4.30
517 826 7.283354 CACGATATATCTAGAGCACTATTCCCA 59.717 40.741 10.93 0.00 0.00 4.37
518 827 7.499563 TCACGATATATCTAGAGCACTATTCCC 59.500 40.741 10.93 0.00 0.00 3.97
519 828 8.439993 TCACGATATATCTAGAGCACTATTCC 57.560 38.462 10.93 0.00 0.00 3.01
520 829 9.929722 CTTCACGATATATCTAGAGCACTATTC 57.070 37.037 10.93 0.00 0.00 1.75
521 830 8.898761 CCTTCACGATATATCTAGAGCACTATT 58.101 37.037 10.93 0.00 0.00 1.73
522 831 8.268605 TCCTTCACGATATATCTAGAGCACTAT 58.731 37.037 10.93 0.00 0.00 2.12
523 832 7.549842 GTCCTTCACGATATATCTAGAGCACTA 59.450 40.741 10.93 0.00 0.00 2.74
524 833 6.373216 GTCCTTCACGATATATCTAGAGCACT 59.627 42.308 10.93 0.00 0.00 4.40
525 834 6.403855 GGTCCTTCACGATATATCTAGAGCAC 60.404 46.154 10.93 6.16 0.00 4.40
526 835 5.648526 GGTCCTTCACGATATATCTAGAGCA 59.351 44.000 10.93 0.00 0.00 4.26
537 846 5.221441 CCACAATCTATGGTCCTTCACGATA 60.221 44.000 0.00 0.00 32.08 2.92
561 870 1.065636 GTACCCCTGGTGCTCCTTTAC 60.066 57.143 6.34 0.00 36.19 2.01
568 877 1.562672 GGTCATGTACCCCTGGTGCT 61.563 60.000 3.07 0.00 43.16 4.40
597 906 2.034221 GCACTTGGTGGGGAGTCC 59.966 66.667 0.00 0.00 33.64 3.85
690 999 7.004086 TGGATTCTAGAAGTGGTGAAACAATT 58.996 34.615 11.53 0.00 39.98 2.32
693 1002 5.163248 TGTGGATTCTAGAAGTGGTGAAACA 60.163 40.000 11.53 4.34 39.98 2.83
905 1215 3.995048 TCTCTGTACTCACTAGTCACACG 59.005 47.826 0.00 0.00 37.15 4.49
913 1223 4.511786 ATCCTGCTCTCTGTACTCACTA 57.488 45.455 0.00 0.00 0.00 2.74
1092 1403 2.500098 CTCCGAAATAGACCAGTTGGGA 59.500 50.000 2.79 0.00 36.85 4.37
1120 1431 1.995484 CTCGCTGTTGTCATCGTCAAT 59.005 47.619 0.00 0.00 35.19 2.57
1121 1432 1.418373 CTCGCTGTTGTCATCGTCAA 58.582 50.000 0.00 0.00 35.19 3.18
1124 1435 0.388649 GTCCTCGCTGTTGTCATCGT 60.389 55.000 0.00 0.00 35.19 3.73
1127 1438 1.620819 AGAAGTCCTCGCTGTTGTCAT 59.379 47.619 0.00 0.00 0.00 3.06
1135 1446 2.665603 GGCCAAGAAGTCCTCGCT 59.334 61.111 0.00 0.00 0.00 4.93
1188 1499 2.592102 ACACCCATGTGATCTGCTTT 57.408 45.000 0.00 0.00 45.76 3.51
1318 1629 1.747206 GCATTCCCCATCAGTAGCGTT 60.747 52.381 0.00 0.00 0.00 4.84
1339 1650 1.342374 GGCCCATTCTTCCACATCCTT 60.342 52.381 0.00 0.00 0.00 3.36
1350 1661 2.685999 GAAGCAGGGGCCCATTCT 59.314 61.111 27.72 15.05 42.56 2.40
1415 1726 3.340928 TCGACAATAAGGAGACAGACGA 58.659 45.455 0.00 0.00 0.00 4.20
1421 1732 2.722071 CGAGCTCGACAATAAGGAGAC 58.278 52.381 32.06 0.00 43.02 3.36
1470 1781 6.016693 TGTTGAAAGAATTAATGAAGACGGCA 60.017 34.615 0.00 0.00 0.00 5.69
1473 1784 7.069569 ACGTGTTGAAAGAATTAATGAAGACG 58.930 34.615 0.00 0.00 35.48 4.18
1482 1793 7.201487 CGTATCCATGACGTGTTGAAAGAATTA 60.201 37.037 0.00 0.00 35.58 1.40
1525 1836 4.431131 CTGGAGCGGTGGGGCAAT 62.431 66.667 0.00 0.00 34.64 3.56
1594 1905 0.390472 CAACCGAGGCTCTGGAAGAC 60.390 60.000 25.17 0.00 38.67 3.01
1921 2233 3.890756 TCTTTGATCAATGCCTGTGTTGT 59.109 39.130 9.40 0.00 0.00 3.32
1926 2238 3.952323 CCTCATCTTTGATCAATGCCTGT 59.048 43.478 9.40 0.00 0.00 4.00
2217 2529 1.186200 CCAGATCCTCGTTGTCCTGA 58.814 55.000 0.00 0.00 0.00 3.86
2265 2577 6.338146 CGTCAATAGGTTCTCATCCTTGTTA 58.662 40.000 0.00 0.00 36.60 2.41
2289 2601 1.539827 AGGTTAATGTTCTGCAACCGC 59.460 47.619 0.00 0.00 44.20 5.68
2642 2954 0.881118 TTTCGGTAAGCCTCGTACGT 59.119 50.000 16.05 0.00 0.00 3.57
2792 3104 7.045416 TGGTAGCATTTCTAATCACAACGTAT 58.955 34.615 0.00 0.00 0.00 3.06
2796 3108 6.908825 TGTTGGTAGCATTTCTAATCACAAC 58.091 36.000 0.00 0.00 34.31 3.32
2941 3253 9.743581 AGCATATACAATGACATGAATTCCATA 57.256 29.630 0.00 0.20 33.31 2.74
2942 3254 8.520351 CAGCATATACAATGACATGAATTCCAT 58.480 33.333 0.00 0.00 35.44 3.41
3093 3406 0.850100 TCAGGTTGGCCTTCTTCCAA 59.150 50.000 3.32 0.00 44.18 3.53
3243 3556 4.650734 TGTTTAGGAATGACATCAGCACA 58.349 39.130 0.00 0.00 0.00 4.57
3291 3604 6.460103 AAGAGCAGGTATGGGATGATAAAT 57.540 37.500 0.00 0.00 0.00 1.40
3315 3628 3.389656 TGGTAACAGACATGGTGTTCTCA 59.610 43.478 16.49 13.41 46.17 3.27
3492 3805 6.151648 CCTTCAATTTCTCCTTGATTGCTACA 59.848 38.462 0.00 0.00 32.94 2.74
3508 3821 5.163109 TGGATTCCTTTTTGGCCTTCAATTT 60.163 36.000 3.32 0.00 34.98 1.82
3512 3825 2.969628 TGGATTCCTTTTTGGCCTTCA 58.030 42.857 3.32 0.00 35.26 3.02
3567 3880 3.684697 CGGACAGGAGGAGTAGTGACATA 60.685 52.174 0.00 0.00 0.00 2.29
3595 3908 4.191544 TGCTTTGATAGTAAGCTGCGAAT 58.808 39.130 8.78 0.00 46.30 3.34
3596 3909 3.595173 TGCTTTGATAGTAAGCTGCGAA 58.405 40.909 8.78 0.00 46.30 4.70
3789 4102 2.203308 TAGCTCCTACGCCCCTCG 60.203 66.667 0.00 0.00 45.38 4.63
3796 4109 1.897615 CGGGGTCCTAGCTCCTACG 60.898 68.421 0.00 0.00 0.00 3.51
3826 4139 3.266772 AGAATCCTTTGACTACCATGCCA 59.733 43.478 0.00 0.00 0.00 4.92
3951 4272 7.554118 ACCTTAACATCATCTAGAACAACATGG 59.446 37.037 0.00 0.00 0.00 3.66
4080 4401 5.166398 GCAGAAATGTAGCAAGCTTTTGAT 58.834 37.500 0.00 0.00 0.00 2.57
4165 4486 6.582295 CCGGTCAAAACTTCAAATTGTATGAG 59.418 38.462 0.00 0.00 0.00 2.90
4204 4525 8.691661 TTAATATATTTCCCCTTGCTGACTTC 57.308 34.615 2.68 0.00 0.00 3.01
4260 8023 4.879545 GGTCGTAATATTGTGTTGTCCCAT 59.120 41.667 0.00 0.00 0.00 4.00
4336 8099 2.733026 GCACTGCTTTTATGTTGCAAGG 59.267 45.455 0.00 0.00 36.22 3.61
4356 8119 1.078637 GGTTTGGTCCCTAGTCCGC 60.079 63.158 0.00 0.00 0.00 5.54
4357 8120 0.249398 CTGGTTTGGTCCCTAGTCCG 59.751 60.000 0.00 0.00 0.00 4.79
4358 8121 0.618981 CCTGGTTTGGTCCCTAGTCC 59.381 60.000 0.00 0.00 0.00 3.85
4360 8123 1.498176 GGCCTGGTTTGGTCCCTAGT 61.498 60.000 0.00 0.00 0.00 2.57
4362 8125 1.464395 TGGCCTGGTTTGGTCCCTA 60.464 57.895 3.32 0.00 0.00 3.53
4363 8126 2.780924 TGGCCTGGTTTGGTCCCT 60.781 61.111 3.32 0.00 0.00 4.20
4364 8127 2.600470 GTGGCCTGGTTTGGTCCC 60.600 66.667 3.32 0.00 0.00 4.46
4365 8128 2.983592 CGTGGCCTGGTTTGGTCC 60.984 66.667 3.32 0.00 0.00 4.46
4408 8212 3.947834 AGCCAAATTCGGACCAATTCTAG 59.052 43.478 0.00 0.00 0.00 2.43
4449 8253 2.833533 GCCGACAGCTTGCACAACA 61.834 57.895 0.00 0.00 38.99 3.33
4472 8276 1.739338 AATCGTAGAGCTGGCCGAGG 61.739 60.000 0.00 0.00 43.63 4.63
4480 8284 4.679373 ACATGATGGAAATCGTAGAGCT 57.321 40.909 0.00 0.00 43.63 4.09
4487 8291 4.539870 GTGGCATAACATGATGGAAATCG 58.460 43.478 0.00 0.00 0.00 3.34
4499 8303 2.080693 CACTAAAGCGGTGGCATAACA 58.919 47.619 0.00 0.00 43.41 2.41
4503 8307 3.590824 GCACTAAAGCGGTGGCAT 58.409 55.556 0.00 0.00 43.41 4.40
4550 8354 1.604278 GGTTGAATCCCTCAATAGCGC 59.396 52.381 0.00 0.00 45.74 5.92
4552 8356 2.952310 GGTGGTTGAATCCCTCAATAGC 59.048 50.000 0.00 0.00 45.74 2.97
4568 8372 0.691078 AGAGCATACCCGATGGTGGT 60.691 55.000 0.00 0.00 46.35 4.16
4569 8373 0.469917 AAGAGCATACCCGATGGTGG 59.530 55.000 0.00 0.00 46.35 4.61
4570 8374 2.289072 CCTAAGAGCATACCCGATGGTG 60.289 54.545 0.00 0.00 46.35 4.17
4572 8376 2.028930 GTCCTAAGAGCATACCCGATGG 60.029 54.545 0.00 0.00 35.91 3.51
4573 8377 2.628178 TGTCCTAAGAGCATACCCGATG 59.372 50.000 0.00 0.00 38.73 3.84
4574 8378 2.958818 TGTCCTAAGAGCATACCCGAT 58.041 47.619 0.00 0.00 0.00 4.18
4575 8379 2.447408 TGTCCTAAGAGCATACCCGA 57.553 50.000 0.00 0.00 0.00 5.14
4576 8380 3.536956 TTTGTCCTAAGAGCATACCCG 57.463 47.619 0.00 0.00 0.00 5.28
4577 8381 5.099042 TCTTTTGTCCTAAGAGCATACCC 57.901 43.478 0.00 0.00 0.00 3.69
4578 8382 7.442666 CCTTATCTTTTGTCCTAAGAGCATACC 59.557 40.741 0.00 0.00 35.28 2.73
4579 8383 7.442666 CCCTTATCTTTTGTCCTAAGAGCATAC 59.557 40.741 0.00 0.00 35.28 2.39
4580 8384 7.127339 ACCCTTATCTTTTGTCCTAAGAGCATA 59.873 37.037 0.00 0.00 35.28 3.14
4581 8385 6.069381 ACCCTTATCTTTTGTCCTAAGAGCAT 60.069 38.462 0.00 0.00 35.28 3.79
4582 8386 5.250774 ACCCTTATCTTTTGTCCTAAGAGCA 59.749 40.000 0.00 0.00 35.28 4.26
4583 8387 5.746284 ACCCTTATCTTTTGTCCTAAGAGC 58.254 41.667 0.00 0.00 35.28 4.09
4584 8388 7.044798 CAGACCCTTATCTTTTGTCCTAAGAG 58.955 42.308 0.00 0.00 35.28 2.85
4585 8389 6.500751 ACAGACCCTTATCTTTTGTCCTAAGA 59.499 38.462 0.00 0.00 36.18 2.10
4586 8390 6.712276 ACAGACCCTTATCTTTTGTCCTAAG 58.288 40.000 0.00 0.00 0.00 2.18
4587 8391 6.697641 ACAGACCCTTATCTTTTGTCCTAA 57.302 37.500 0.00 0.00 0.00 2.69
4588 8392 6.697641 AACAGACCCTTATCTTTTGTCCTA 57.302 37.500 0.00 0.00 0.00 2.94
4589 8393 5.584551 AACAGACCCTTATCTTTTGTCCT 57.415 39.130 0.00 0.00 0.00 3.85
4590 8394 5.048013 CCAAACAGACCCTTATCTTTTGTCC 60.048 44.000 0.00 0.00 31.67 4.02
4591 8395 5.535030 ACCAAACAGACCCTTATCTTTTGTC 59.465 40.000 0.00 0.00 31.67 3.18
4592 8396 5.454966 ACCAAACAGACCCTTATCTTTTGT 58.545 37.500 0.00 0.00 31.67 2.83
4593 8397 6.405278 AACCAAACAGACCCTTATCTTTTG 57.595 37.500 0.00 0.00 32.45 2.44
4594 8398 5.538813 GGAACCAAACAGACCCTTATCTTTT 59.461 40.000 0.00 0.00 0.00 2.27
4595 8399 5.077564 GGAACCAAACAGACCCTTATCTTT 58.922 41.667 0.00 0.00 0.00 2.52
4596 8400 4.105697 TGGAACCAAACAGACCCTTATCTT 59.894 41.667 0.00 0.00 0.00 2.40
4597 8401 3.655777 TGGAACCAAACAGACCCTTATCT 59.344 43.478 0.00 0.00 0.00 1.98
4598 8402 4.028993 TGGAACCAAACAGACCCTTATC 57.971 45.455 0.00 0.00 0.00 1.75
4599 8403 4.463050 TTGGAACCAAACAGACCCTTAT 57.537 40.909 3.62 0.00 32.44 1.73
4600 8404 3.955524 TTGGAACCAAACAGACCCTTA 57.044 42.857 3.62 0.00 32.44 2.69
4601 8405 2.838637 TTGGAACCAAACAGACCCTT 57.161 45.000 3.62 0.00 32.44 3.95
4602 8406 2.838637 TTTGGAACCAAACAGACCCT 57.161 45.000 14.02 0.00 40.51 4.34
4603 8407 4.587262 ACTTATTTGGAACCAAACAGACCC 59.413 41.667 23.08 0.00 46.80 4.46
4604 8408 5.300792 TGACTTATTTGGAACCAAACAGACC 59.699 40.000 23.08 17.02 46.80 3.85
4605 8409 6.206498 GTGACTTATTTGGAACCAAACAGAC 58.794 40.000 23.08 19.25 46.80 3.51
4606 8410 5.300792 GGTGACTTATTTGGAACCAAACAGA 59.699 40.000 23.08 11.42 46.80 3.41
4607 8411 5.068460 TGGTGACTTATTTGGAACCAAACAG 59.932 40.000 19.23 18.64 46.80 3.16
4608 8412 4.956700 TGGTGACTTATTTGGAACCAAACA 59.043 37.500 19.23 7.15 46.80 2.83
4609 8413 5.523438 TGGTGACTTATTTGGAACCAAAC 57.477 39.130 19.23 8.57 46.80 2.93
4610 8414 5.659079 AGTTGGTGACTTATTTGGAACCAAA 59.341 36.000 19.15 19.15 46.21 3.28
4611 8415 5.205056 AGTTGGTGACTTATTTGGAACCAA 58.795 37.500 1.83 1.83 43.50 3.67
4612 8416 4.798882 AGTTGGTGACTTATTTGGAACCA 58.201 39.130 0.00 0.00 33.92 3.67
4613 8417 5.784578 AAGTTGGTGACTTATTTGGAACC 57.215 39.130 0.00 0.00 46.61 3.62
4652 8456 7.012232 CCTGTTTGGCAAAATATGTCACTTTTT 59.988 33.333 15.29 0.00 45.06 1.94
4653 8457 6.482973 CCTGTTTGGCAAAATATGTCACTTTT 59.517 34.615 15.29 0.00 45.06 2.27
4654 8458 5.990996 CCTGTTTGGCAAAATATGTCACTTT 59.009 36.000 15.29 0.00 45.06 2.66
4655 8459 5.540911 CCTGTTTGGCAAAATATGTCACTT 58.459 37.500 15.29 0.00 45.06 3.16
4656 8460 5.138125 CCTGTTTGGCAAAATATGTCACT 57.862 39.130 15.29 0.00 45.06 3.41
4670 8474 4.086457 ACTTATAAGTTGGGCCTGTTTGG 58.914 43.478 12.50 0.00 35.21 3.28
4671 8475 4.764823 TGACTTATAAGTTGGGCCTGTTTG 59.235 41.667 18.96 0.00 39.88 2.93
4672 8476 4.765339 GTGACTTATAAGTTGGGCCTGTTT 59.235 41.667 18.96 0.00 39.88 2.83
4673 8477 4.332828 GTGACTTATAAGTTGGGCCTGTT 58.667 43.478 18.96 0.00 39.88 3.16
4674 8478 3.308188 GGTGACTTATAAGTTGGGCCTGT 60.308 47.826 18.96 0.00 39.88 4.00
4675 8479 3.279434 GGTGACTTATAAGTTGGGCCTG 58.721 50.000 18.96 0.00 39.88 4.85
4676 8480 2.241430 GGGTGACTTATAAGTTGGGCCT 59.759 50.000 18.96 0.00 39.88 5.19
4677 8481 2.651455 GGGTGACTTATAAGTTGGGCC 58.349 52.381 18.96 16.42 39.88 5.80
4678 8482 2.025699 TGGGGTGACTTATAAGTTGGGC 60.026 50.000 18.96 7.26 39.88 5.36
4679 8483 4.014406 GTTGGGGTGACTTATAAGTTGGG 58.986 47.826 18.96 0.00 39.88 4.12
4680 8484 4.918588 AGTTGGGGTGACTTATAAGTTGG 58.081 43.478 18.96 0.00 39.88 3.77


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

AutoCloner maintained by Alex Coulton.