Multiple sequence alignment - TraesCS5B01G183100

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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 TraesCS5B01G183100 chr5B 100.000 3476 0 0 1 3476 333197581 333194106 0.000000e+00 6420.0
1 TraesCS5B01G183100 chr5B 74.463 419 88 17 1826 2233 356359719 356360129 2.780000e-36 163.0
2 TraesCS5B01G183100 chr5D 93.884 2469 125 13 542 2994 292641644 292639186 0.000000e+00 3699.0
3 TraesCS5B01G183100 chr5D 94.301 544 30 1 1 543 292642349 292641806 0.000000e+00 832.0
4 TraesCS5B01G183100 chr5D 71.820 1242 245 82 1037 2233 310496903 310498084 1.240000e-64 257.0
5 TraesCS5B01G183100 chr5A 93.206 2090 100 23 548 2600 385383878 385381794 0.000000e+00 3035.0
6 TraesCS5B01G183100 chr5A 87.956 1179 80 23 456 1589 690358557 690357396 0.000000e+00 1334.0
7 TraesCS5B01G183100 chr5A 87.543 1164 110 19 2177 3317 690356879 690355728 0.000000e+00 1314.0
8 TraesCS5B01G183100 chr5A 93.432 472 25 2 1722 2188 690357398 690356928 0.000000e+00 695.0
9 TraesCS5B01G183100 chr5A 89.094 541 56 3 2 541 385384718 385384180 0.000000e+00 669.0
10 TraesCS5B01G183100 chr5A 71.741 1235 255 74 1037 2233 404015990 404017168 9.570000e-66 261.0
11 TraesCS5B01G183100 chr5A 95.238 42 2 0 2646 2687 385381753 385381794 2.240000e-07 67.6
12 TraesCS5B01G183100 chr4B 90.767 2177 174 12 991 3148 652915646 652913478 0.000000e+00 2881.0
13 TraesCS5B01G183100 chr4B 88.686 601 57 8 145 735 652916675 652916076 0.000000e+00 723.0
14 TraesCS5B01G183100 chr4B 89.437 142 15 0 10 151 652917269 652917128 2.760000e-41 180.0
15 TraesCS5B01G183100 chr4B 86.792 159 10 5 604 751 652916033 652915875 2.150000e-37 167.0
16 TraesCS5B01G183100 chrUn 85.969 898 49 24 867 1726 127007104 127007962 0.000000e+00 889.0
17 TraesCS5B01G183100 chrUn 87.957 656 53 11 242 878 127006313 127006961 0.000000e+00 750.0
18 TraesCS5B01G183100 chrUn 88.934 244 26 1 1 244 127004185 127004427 2.030000e-77 300.0
19 TraesCS5B01G183100 chrUn 88.235 255 22 4 2452 2703 127008138 127008387 7.290000e-77 298.0
20 TraesCS5B01G183100 chrUn 86.154 195 16 1 2018 2212 127007958 127008141 2.120000e-47 200.0
21 TraesCS5B01G183100 chrUn 91.525 59 5 0 2971 3029 127008388 127008446 8.000000e-12 82.4
22 TraesCS5B01G183100 chr7D 81.065 169 27 5 4 168 2043716 2043549 2.820000e-26 130.0


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 TraesCS5B01G183100 chr5B 333194106 333197581 3475 True 6420.000000 6420 100.000000 1 3476 1 chr5B.!!$R1 3475
1 TraesCS5B01G183100 chr5D 292639186 292642349 3163 True 2265.500000 3699 94.092500 1 2994 2 chr5D.!!$R1 2993
2 TraesCS5B01G183100 chr5D 310496903 310498084 1181 False 257.000000 257 71.820000 1037 2233 1 chr5D.!!$F1 1196
3 TraesCS5B01G183100 chr5A 385381794 385384718 2924 True 1852.000000 3035 91.150000 2 2600 2 chr5A.!!$R1 2598
4 TraesCS5B01G183100 chr5A 690355728 690358557 2829 True 1114.333333 1334 89.643667 456 3317 3 chr5A.!!$R2 2861
5 TraesCS5B01G183100 chr5A 404015990 404017168 1178 False 261.000000 261 71.741000 1037 2233 1 chr5A.!!$F2 1196
6 TraesCS5B01G183100 chr4B 652913478 652917269 3791 True 987.750000 2881 88.920500 10 3148 4 chr4B.!!$R1 3138
7 TraesCS5B01G183100 chrUn 127004185 127008446 4261 False 419.900000 889 88.129000 1 3029 6 chrUn.!!$F1 3028

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
34 35 0.250901 ATGCCCCCGCTGATGATAAC 60.251 55.0 0.0 0.0 35.36 1.89 F
454 2804 1.022735 GCGACGAAGGGAGTAGATGA 58.977 55.0 0.0 0.0 0.00 2.92 F
2374 5556 0.100861 GCTAGCTGTGGAGTCCGTAC 59.899 60.0 7.7 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 5019 1.374190 CTTCAGCTGCACCTCTGGT 59.626 57.895 9.47 0.0 35.62 4.00 R
2416 5598 0.034574 TTGGGTGCACACAACTCACT 60.035 50.000 30.23 0.0 33.72 3.41 R
3374 6588 0.108945 GAGCAAGCAGATGGGCAAAC 60.109 55.000 0.00 0.0 35.83 2.93 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
34 35 0.250901 ATGCCCCCGCTGATGATAAC 60.251 55.000 0.00 0.00 35.36 1.89
275 2624 3.053291 GGATCGCAAACGCCACCA 61.053 61.111 0.00 0.00 39.84 4.17
331 2680 1.561076 CACATCTCCTTCACCATCCCA 59.439 52.381 0.00 0.00 0.00 4.37
334 2683 1.741028 TCTCCTTCACCATCCCACAA 58.259 50.000 0.00 0.00 0.00 3.33
360 2709 2.575532 CTTCAACTCCTCCACAAGCAA 58.424 47.619 0.00 0.00 0.00 3.91
454 2804 1.022735 GCGACGAAGGGAGTAGATGA 58.977 55.000 0.00 0.00 0.00 2.92
484 2834 2.265904 GGGTTTTGGTCGTCTGCCC 61.266 63.158 0.00 0.00 0.00 5.36
491 2841 4.436998 GTCGTCTGCCCGGTCCTG 62.437 72.222 0.00 0.00 0.00 3.86
576 3231 1.977854 TGGGTGATCACTACTGCACTT 59.022 47.619 24.50 0.00 0.00 3.16
769 3628 5.365314 TCTCATTTTTATTTATGGGGTGGCC 59.635 40.000 0.00 0.00 0.00 5.36
770 3629 5.032846 TCATTTTTATTTATGGGGTGGCCA 58.967 37.500 0.00 0.00 0.00 5.36
771 3630 5.669447 TCATTTTTATTTATGGGGTGGCCAT 59.331 36.000 9.72 0.00 0.00 4.40
829 3690 5.587443 TGAACAGATCATTGATGCCTTACAG 59.413 40.000 3.32 0.00 31.50 2.74
830 3691 3.881688 ACAGATCATTGATGCCTTACAGC 59.118 43.478 3.32 0.00 34.38 4.40
846 3710 5.393678 CCTTACAGCTCTCTTTACTCTCACC 60.394 48.000 0.00 0.00 0.00 4.02
981 4051 3.648545 AGAAAACCCTCTGACTAGCTTGT 59.351 43.478 0.00 0.00 0.00 3.16
1112 4192 1.770110 AGCTTGTCCACCACCTCCA 60.770 57.895 0.00 0.00 0.00 3.86
1161 4241 2.520500 ACAACCCATGGCAACGCA 60.521 55.556 6.09 0.00 42.51 5.24
1217 4297 4.194720 GGCCATCGTCGAGCTCGT 62.195 66.667 33.33 13.67 40.80 4.18
1474 4574 2.027073 GCGTTCGCACAGGTCATGA 61.027 57.895 12.33 0.00 0.00 3.07
1651 4753 1.825341 CCGATGATGGAGCTGGACA 59.175 57.895 0.00 0.00 0.00 4.02
1792 4894 2.757508 CGCTCTGCCTCTCCCAGA 60.758 66.667 0.00 0.00 37.71 3.86
2049 5164 1.203313 AGAGGCTTAGTGGTGAGGGAA 60.203 52.381 0.00 0.00 0.00 3.97
2127 5242 3.384348 GGGTGGAACTCGGTGCTA 58.616 61.111 0.00 0.00 36.74 3.49
2136 5251 1.912417 ACTCGGTGCTAGAGAGTGTT 58.088 50.000 9.89 0.00 42.87 3.32
2190 5365 3.512329 TGCATGCTGATCAACCTTTCAAT 59.488 39.130 20.33 0.00 0.00 2.57
2268 5443 4.612279 ATGCGGGGTTTGGCCACA 62.612 61.111 3.88 0.00 42.11 4.17
2270 5445 4.293648 GCGGGGTTTGGCCACAAC 62.294 66.667 3.88 13.42 42.11 3.32
2362 5544 1.005630 GGGCTATCGGTGCTAGCTG 60.006 63.158 17.23 6.07 41.11 4.24
2374 5556 0.100861 GCTAGCTGTGGAGTCCGTAC 59.899 60.000 7.70 0.00 0.00 3.67
2377 5559 0.251209 AGCTGTGGAGTCCGTACTGA 60.251 55.000 4.30 0.00 35.56 3.41
2416 5598 4.102210 GGAAATCAGTGGAGGAGATGATCA 59.898 45.833 0.00 0.00 31.31 2.92
2575 5770 3.072330 TGGTCACTGGCATTACTTCTCAA 59.928 43.478 0.00 0.00 0.00 3.02
2582 5778 5.221722 ACTGGCATTACTTCTCAAGTCTTGA 60.222 40.000 14.54 14.54 41.77 3.02
2647 5846 6.994221 TGTTTTCTCTCTTGGGAGTACTTAG 58.006 40.000 0.00 0.00 40.29 2.18
2678 5878 6.165577 CCATTTAATTCTGTTTTGGGGACTG 58.834 40.000 0.00 0.00 0.00 3.51
2679 5879 6.239572 CCATTTAATTCTGTTTTGGGGACTGT 60.240 38.462 0.00 0.00 0.00 3.55
2724 5929 1.142060 TCGAAACCAGTGAACCCATGT 59.858 47.619 0.00 0.00 0.00 3.21
2747 5954 2.365617 CCTACCTGGTAGCCTACATGTG 59.634 54.545 25.33 7.34 35.06 3.21
2769 5976 4.183865 GGCCACATAATGCTTTCTTTTCC 58.816 43.478 0.00 0.00 0.00 3.13
2784 5991 1.358152 TTTCCTCCAACCGGACATCT 58.642 50.000 9.46 0.00 35.91 2.90
2841 6048 5.378230 TTCATTCAACCAGCCATAGAGAT 57.622 39.130 0.00 0.00 0.00 2.75
2854 6061 7.148289 CCAGCCATAGAGATGCACATTAAATAG 60.148 40.741 0.00 0.00 0.00 1.73
2887 6094 3.682377 GGAAGCAAGTCTAAGAGCAGAAC 59.318 47.826 0.00 0.00 0.00 3.01
2904 6111 0.560688 AACTGGAGAAGGGGCCAAAA 59.439 50.000 4.39 0.00 32.95 2.44
2940 6147 3.610911 GGCACTAACAGAAACCTGCTAT 58.389 45.455 0.00 0.00 35.09 2.97
2976 6183 6.544928 TTGACAACTCTCATTCCTATAGCA 57.455 37.500 0.00 0.00 0.00 3.49
2977 6184 6.154203 TGACAACTCTCATTCCTATAGCAG 57.846 41.667 0.00 0.00 0.00 4.24
3047 6254 1.929806 ATGTGCTCGCATGCCTTGTG 61.930 55.000 13.15 0.24 37.17 3.33
3116 6323 1.691196 CTGTTGGTCAGCTTTCCCAA 58.309 50.000 4.73 4.73 37.36 4.12
3118 6325 1.214175 TGTTGGTCAGCTTTCCCAAGA 59.786 47.619 8.40 5.40 38.84 3.02
3332 6546 9.838339 TGTTAAAAATTTAAAAATCCAGCTGGA 57.162 25.926 36.73 36.73 40.19 3.86
3334 6548 9.278978 TTAAAAATTTAAAAATCCAGCTGGACC 57.721 29.630 37.39 0.00 37.06 4.46
3345 6559 4.704833 CTGGACCGTGGCCCAGTG 62.705 72.222 12.70 0.00 43.71 3.66
3347 6561 4.699522 GGACCGTGGCCCAGTGTC 62.700 72.222 0.00 1.38 0.00 3.67
3348 6562 3.626924 GACCGTGGCCCAGTGTCT 61.627 66.667 0.00 0.00 0.00 3.41
3349 6563 3.591254 GACCGTGGCCCAGTGTCTC 62.591 68.421 0.00 0.00 0.00 3.36
3350 6564 3.625897 CCGTGGCCCAGTGTCTCA 61.626 66.667 0.00 0.00 0.00 3.27
3351 6565 2.357517 CGTGGCCCAGTGTCTCAC 60.358 66.667 0.00 0.00 34.10 3.51
3352 6566 2.032681 GTGGCCCAGTGTCTCACC 59.967 66.667 0.00 0.00 34.49 4.02
3353 6567 3.249189 TGGCCCAGTGTCTCACCC 61.249 66.667 0.00 0.00 34.49 4.61
3354 6568 3.249189 GGCCCAGTGTCTCACCCA 61.249 66.667 0.00 0.00 34.49 4.51
3355 6569 2.032681 GCCCAGTGTCTCACCCAC 59.967 66.667 0.00 0.00 34.49 4.61
3356 6570 2.343758 CCCAGTGTCTCACCCACG 59.656 66.667 0.00 0.00 37.88 4.94
3357 6571 2.357517 CCAGTGTCTCACCCACGC 60.358 66.667 0.00 0.00 37.88 5.34
3358 6572 2.421314 CAGTGTCTCACCCACGCA 59.579 61.111 0.00 0.00 37.88 5.24
3359 6573 1.956170 CAGTGTCTCACCCACGCAC 60.956 63.158 0.00 0.00 37.88 5.34
3360 6574 2.134287 AGTGTCTCACCCACGCACT 61.134 57.895 0.00 0.00 37.88 4.40
3361 6575 1.956170 GTGTCTCACCCACGCACTG 60.956 63.158 0.00 0.00 0.00 3.66
3362 6576 2.357517 GTCTCACCCACGCACTGG 60.358 66.667 0.00 0.00 40.26 4.00
3363 6577 4.314440 TCTCACCCACGCACTGGC 62.314 66.667 0.00 0.00 39.01 4.85
3364 6578 4.320456 CTCACCCACGCACTGGCT 62.320 66.667 0.00 0.00 39.01 4.75
3365 6579 4.314440 TCACCCACGCACTGGCTC 62.314 66.667 0.00 0.00 39.01 4.70
3366 6580 4.624364 CACCCACGCACTGGCTCA 62.624 66.667 0.00 0.00 39.01 4.26
3367 6581 3.640407 ACCCACGCACTGGCTCAT 61.640 61.111 0.00 0.00 39.01 2.90
3368 6582 2.290287 ACCCACGCACTGGCTCATA 61.290 57.895 0.00 0.00 39.01 2.15
3369 6583 1.078497 CCCACGCACTGGCTCATAA 60.078 57.895 0.00 0.00 39.01 1.90
3370 6584 0.676466 CCCACGCACTGGCTCATAAA 60.676 55.000 0.00 0.00 39.01 1.40
3371 6585 0.447801 CCACGCACTGGCTCATAAAC 59.552 55.000 0.00 0.00 38.10 2.01
3372 6586 1.442769 CACGCACTGGCTCATAAACT 58.557 50.000 0.00 0.00 38.10 2.66
3373 6587 1.394917 CACGCACTGGCTCATAAACTC 59.605 52.381 0.00 0.00 38.10 3.01
3374 6588 0.647410 CGCACTGGCTCATAAACTCG 59.353 55.000 0.00 0.00 38.10 4.18
3375 6589 1.726853 GCACTGGCTCATAAACTCGT 58.273 50.000 0.00 0.00 36.96 4.18
3376 6590 2.076863 GCACTGGCTCATAAACTCGTT 58.923 47.619 0.00 0.00 36.96 3.85
3377 6591 2.484264 GCACTGGCTCATAAACTCGTTT 59.516 45.455 0.35 0.35 36.96 3.60
3378 6592 3.667960 GCACTGGCTCATAAACTCGTTTG 60.668 47.826 5.35 0.00 36.96 2.93
3379 6593 2.484264 ACTGGCTCATAAACTCGTTTGC 59.516 45.455 5.35 0.52 34.23 3.68
3380 6594 1.810151 TGGCTCATAAACTCGTTTGCC 59.190 47.619 12.20 12.20 37.99 4.52
3381 6595 1.132453 GGCTCATAAACTCGTTTGCCC 59.868 52.381 5.35 0.00 34.03 5.36
3382 6596 1.810151 GCTCATAAACTCGTTTGCCCA 59.190 47.619 5.35 0.00 34.23 5.36
3383 6597 2.423538 GCTCATAAACTCGTTTGCCCAT 59.576 45.455 5.35 0.00 34.23 4.00
3384 6598 3.487544 GCTCATAAACTCGTTTGCCCATC 60.488 47.826 5.35 0.00 34.23 3.51
3385 6599 3.941483 CTCATAAACTCGTTTGCCCATCT 59.059 43.478 5.35 0.00 34.23 2.90
3386 6600 3.689161 TCATAAACTCGTTTGCCCATCTG 59.311 43.478 5.35 0.00 34.23 2.90
3387 6601 0.598065 AAACTCGTTTGCCCATCTGC 59.402 50.000 0.00 0.00 0.00 4.26
3388 6602 0.250901 AACTCGTTTGCCCATCTGCT 60.251 50.000 0.00 0.00 0.00 4.24
3389 6603 0.250901 ACTCGTTTGCCCATCTGCTT 60.251 50.000 0.00 0.00 0.00 3.91
3390 6604 0.169672 CTCGTTTGCCCATCTGCTTG 59.830 55.000 0.00 0.00 0.00 4.01
3391 6605 1.444895 CGTTTGCCCATCTGCTTGC 60.445 57.895 0.00 0.00 0.00 4.01
3392 6606 1.870055 CGTTTGCCCATCTGCTTGCT 61.870 55.000 0.00 0.00 0.00 3.91
3393 6607 0.108945 GTTTGCCCATCTGCTTGCTC 60.109 55.000 0.00 0.00 0.00 4.26
3394 6608 1.588824 TTTGCCCATCTGCTTGCTCG 61.589 55.000 0.00 0.00 0.00 5.03
3395 6609 2.437359 GCCCATCTGCTTGCTCGT 60.437 61.111 0.00 0.00 0.00 4.18
3396 6610 2.758089 GCCCATCTGCTTGCTCGTG 61.758 63.158 0.00 0.00 0.00 4.35
3397 6611 2.110967 CCCATCTGCTTGCTCGTGG 61.111 63.158 0.00 0.00 0.00 4.94
3398 6612 1.376424 CCATCTGCTTGCTCGTGGT 60.376 57.895 0.00 0.00 0.00 4.16
3399 6613 0.957395 CCATCTGCTTGCTCGTGGTT 60.957 55.000 0.00 0.00 0.00 3.67
3400 6614 0.877071 CATCTGCTTGCTCGTGGTTT 59.123 50.000 0.00 0.00 0.00 3.27
3401 6615 1.267806 CATCTGCTTGCTCGTGGTTTT 59.732 47.619 0.00 0.00 0.00 2.43
3402 6616 0.944386 TCTGCTTGCTCGTGGTTTTC 59.056 50.000 0.00 0.00 0.00 2.29
3403 6617 0.947244 CTGCTTGCTCGTGGTTTTCT 59.053 50.000 0.00 0.00 0.00 2.52
3404 6618 1.334869 CTGCTTGCTCGTGGTTTTCTT 59.665 47.619 0.00 0.00 0.00 2.52
3405 6619 1.333619 TGCTTGCTCGTGGTTTTCTTC 59.666 47.619 0.00 0.00 0.00 2.87
3406 6620 1.604278 GCTTGCTCGTGGTTTTCTTCT 59.396 47.619 0.00 0.00 0.00 2.85
3407 6621 2.033424 GCTTGCTCGTGGTTTTCTTCTT 59.967 45.455 0.00 0.00 0.00 2.52
3408 6622 3.489229 GCTTGCTCGTGGTTTTCTTCTTT 60.489 43.478 0.00 0.00 0.00 2.52
3409 6623 4.672409 CTTGCTCGTGGTTTTCTTCTTTT 58.328 39.130 0.00 0.00 0.00 2.27
3410 6624 4.712122 TGCTCGTGGTTTTCTTCTTTTT 57.288 36.364 0.00 0.00 0.00 1.94
3411 6625 4.668289 TGCTCGTGGTTTTCTTCTTTTTC 58.332 39.130 0.00 0.00 0.00 2.29
3412 6626 3.724257 GCTCGTGGTTTTCTTCTTTTTCG 59.276 43.478 0.00 0.00 0.00 3.46
3413 6627 3.687200 TCGTGGTTTTCTTCTTTTTCGC 58.313 40.909 0.00 0.00 0.00 4.70
3414 6628 3.375922 TCGTGGTTTTCTTCTTTTTCGCT 59.624 39.130 0.00 0.00 0.00 4.93
3415 6629 4.102649 CGTGGTTTTCTTCTTTTTCGCTT 58.897 39.130 0.00 0.00 0.00 4.68
3416 6630 4.027702 CGTGGTTTTCTTCTTTTTCGCTTG 60.028 41.667 0.00 0.00 0.00 4.01
3417 6631 3.862845 TGGTTTTCTTCTTTTTCGCTTGC 59.137 39.130 0.00 0.00 0.00 4.01
3418 6632 3.245284 GGTTTTCTTCTTTTTCGCTTGCC 59.755 43.478 0.00 0.00 0.00 4.52
3419 6633 3.791973 TTTCTTCTTTTTCGCTTGCCA 57.208 38.095 0.00 0.00 0.00 4.92
3420 6634 4.320608 TTTCTTCTTTTTCGCTTGCCAT 57.679 36.364 0.00 0.00 0.00 4.40
3421 6635 4.320608 TTCTTCTTTTTCGCTTGCCATT 57.679 36.364 0.00 0.00 0.00 3.16
3422 6636 3.641648 TCTTCTTTTTCGCTTGCCATTG 58.358 40.909 0.00 0.00 0.00 2.82
3423 6637 3.317711 TCTTCTTTTTCGCTTGCCATTGA 59.682 39.130 0.00 0.00 0.00 2.57
3424 6638 3.940209 TCTTTTTCGCTTGCCATTGAT 57.060 38.095 0.00 0.00 0.00 2.57
3425 6639 3.836949 TCTTTTTCGCTTGCCATTGATC 58.163 40.909 0.00 0.00 0.00 2.92
3426 6640 3.255395 TCTTTTTCGCTTGCCATTGATCA 59.745 39.130 0.00 0.00 0.00 2.92
3427 6641 3.657015 TTTTCGCTTGCCATTGATCAA 57.343 38.095 11.26 11.26 0.00 2.57
3428 6642 2.634982 TTCGCTTGCCATTGATCAAC 57.365 45.000 11.07 0.00 0.00 3.18
3429 6643 0.810648 TCGCTTGCCATTGATCAACC 59.189 50.000 11.07 3.03 0.00 3.77
3430 6644 0.813184 CGCTTGCCATTGATCAACCT 59.187 50.000 11.07 0.00 0.00 3.50
3431 6645 1.203052 CGCTTGCCATTGATCAACCTT 59.797 47.619 11.07 0.00 0.00 3.50
3432 6646 2.733227 CGCTTGCCATTGATCAACCTTC 60.733 50.000 11.07 1.30 0.00 3.46
3433 6647 2.417787 GCTTGCCATTGATCAACCTTCC 60.418 50.000 11.07 0.00 0.00 3.46
3434 6648 1.851304 TGCCATTGATCAACCTTCCC 58.149 50.000 11.07 0.00 0.00 3.97
3435 6649 1.114627 GCCATTGATCAACCTTCCCC 58.885 55.000 11.07 0.00 0.00 4.81
3436 6650 1.392589 CCATTGATCAACCTTCCCCG 58.607 55.000 11.07 0.00 0.00 5.73
3437 6651 1.392589 CATTGATCAACCTTCCCCGG 58.607 55.000 11.07 0.00 0.00 5.73
3438 6652 1.064758 CATTGATCAACCTTCCCCGGA 60.065 52.381 11.07 0.00 0.00 5.14
3439 6653 1.068948 TTGATCAACCTTCCCCGGAA 58.931 50.000 0.73 0.00 0.00 4.30
3440 6654 1.068948 TGATCAACCTTCCCCGGAAA 58.931 50.000 0.73 0.00 33.34 3.13
3441 6655 1.638589 TGATCAACCTTCCCCGGAAAT 59.361 47.619 0.73 0.00 33.34 2.17
3442 6656 2.847449 TGATCAACCTTCCCCGGAAATA 59.153 45.455 0.73 0.00 33.34 1.40
3443 6657 3.267291 TGATCAACCTTCCCCGGAAATAA 59.733 43.478 0.73 0.00 33.34 1.40
3444 6658 3.810721 TCAACCTTCCCCGGAAATAAA 57.189 42.857 0.73 0.00 33.34 1.40
3445 6659 4.325084 TCAACCTTCCCCGGAAATAAAT 57.675 40.909 0.73 0.00 33.34 1.40
3446 6660 5.453866 TCAACCTTCCCCGGAAATAAATA 57.546 39.130 0.73 0.00 33.34 1.40
3447 6661 5.442391 TCAACCTTCCCCGGAAATAAATAG 58.558 41.667 0.73 0.00 33.34 1.73
3448 6662 5.192121 TCAACCTTCCCCGGAAATAAATAGA 59.808 40.000 0.73 0.00 33.34 1.98
3449 6663 5.924769 ACCTTCCCCGGAAATAAATAGAT 57.075 39.130 0.73 0.00 33.34 1.98
3450 6664 6.275692 ACCTTCCCCGGAAATAAATAGATT 57.724 37.500 0.73 0.00 33.34 2.40
3451 6665 7.396906 ACCTTCCCCGGAAATAAATAGATTA 57.603 36.000 0.73 0.00 33.34 1.75
3452 6666 7.459234 ACCTTCCCCGGAAATAAATAGATTAG 58.541 38.462 0.73 0.00 33.34 1.73
3453 6667 6.884836 CCTTCCCCGGAAATAAATAGATTAGG 59.115 42.308 0.73 0.00 33.34 2.69
3454 6668 7.396906 TTCCCCGGAAATAAATAGATTAGGT 57.603 36.000 0.73 0.00 0.00 3.08
3455 6669 7.396906 TCCCCGGAAATAAATAGATTAGGTT 57.603 36.000 0.73 0.00 0.00 3.50
3456 6670 7.818469 TCCCCGGAAATAAATAGATTAGGTTT 58.182 34.615 0.73 0.00 0.00 3.27
3457 6671 7.940688 TCCCCGGAAATAAATAGATTAGGTTTC 59.059 37.037 0.73 0.00 0.00 2.78
3458 6672 7.942894 CCCCGGAAATAAATAGATTAGGTTTCT 59.057 37.037 0.73 0.00 0.00 2.52
3459 6673 9.350951 CCCGGAAATAAATAGATTAGGTTTCTT 57.649 33.333 0.73 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.753009 TATCATCAGCGGGGGCATGC 62.753 60.000 9.90 9.90 0.00 4.06
25 26 6.828273 CCCTTCTATTGTTGTGGTTATCATCA 59.172 38.462 0.00 0.00 0.00 3.07
27 28 6.129179 CCCCTTCTATTGTTGTGGTTATCAT 58.871 40.000 0.00 0.00 0.00 2.45
34 35 3.449746 TTCCCCCTTCTATTGTTGTGG 57.550 47.619 0.00 0.00 0.00 4.17
206 666 0.815615 GGGAGTCGATGCATGGTTCC 60.816 60.000 19.18 19.18 0.00 3.62
275 2624 1.792757 TTCCTTGGGCAGTGCTCCAT 61.793 55.000 21.38 0.00 31.26 3.41
331 2680 2.422945 GGAGGAGTTGAAGGGTTGTTGT 60.423 50.000 0.00 0.00 0.00 3.32
334 2683 1.143073 GTGGAGGAGTTGAAGGGTTGT 59.857 52.381 0.00 0.00 0.00 3.32
454 2804 2.535331 AAAACCCTAGCCACCGCCT 61.535 57.895 0.00 0.00 34.57 5.52
484 2834 0.178767 TTCATGGAGATGCAGGACCG 59.821 55.000 0.00 0.00 0.00 4.79
491 2841 2.098770 GCTCACCTTTTCATGGAGATGC 59.901 50.000 0.00 0.00 0.00 3.91
576 3231 7.442364 GCATGTAGAGAGCTGTATTATGGAAAA 59.558 37.037 0.00 0.00 0.00 2.29
769 3628 2.425668 TGGCTGCATTTCACTGATGATG 59.574 45.455 0.50 0.61 33.85 3.07
770 3629 2.730382 TGGCTGCATTTCACTGATGAT 58.270 42.857 0.50 0.00 33.85 2.45
771 3630 2.203470 TGGCTGCATTTCACTGATGA 57.797 45.000 0.50 0.00 0.00 2.92
829 3690 5.167845 CAAAGAGGTGAGAGTAAAGAGAGC 58.832 45.833 0.00 0.00 0.00 4.09
830 3691 5.719173 CCAAAGAGGTGAGAGTAAAGAGAG 58.281 45.833 0.00 0.00 0.00 3.20
915 3945 6.506147 CAGCAGGCACAATTTATAGCAAATA 58.494 36.000 0.00 0.00 0.00 1.40
981 4051 2.203337 GCAGTGGAGGGTGCAACA 60.203 61.111 3.06 0.00 39.98 3.33
1125 4205 1.671379 GAAGAAGGTCACGGTGGCC 60.671 63.158 23.94 23.94 44.07 5.36
1217 4297 4.238654 AAACGTCGGCGGGGAACA 62.239 61.111 16.39 0.00 43.45 3.18
1651 4753 4.372999 GGCCTTCCCCAGCTTGCT 62.373 66.667 0.00 0.00 0.00 3.91
1792 4894 2.126965 CGACGAAGAAGACGCGGT 60.127 61.111 12.47 0.00 0.00 5.68
1908 5019 1.374190 CTTCAGCTGCACCTCTGGT 59.626 57.895 9.47 0.00 35.62 4.00
2049 5164 0.789687 TTCCCAATTGGTCCACCCAT 59.210 50.000 22.91 0.00 44.74 4.00
2127 5242 1.302351 GCCAGCTGCAACACTCTCT 60.302 57.895 8.66 0.00 40.77 3.10
2190 5365 1.067693 CATCGACTACAAACGCTGCA 58.932 50.000 0.00 0.00 0.00 4.41
2362 5544 0.531200 CCCTTCAGTACGGACTCCAC 59.469 60.000 0.00 0.00 31.73 4.02
2374 5556 0.908198 CAAGAGGACCCTCCCTTCAG 59.092 60.000 12.19 0.00 43.70 3.02
2377 5559 0.196118 TTCCAAGAGGACCCTCCCTT 59.804 55.000 12.19 0.00 45.73 3.95
2416 5598 0.034574 TTGGGTGCACACAACTCACT 60.035 50.000 30.23 0.00 33.72 3.41
2598 5794 9.734620 CAACCGTGTTCAATCAATTTCATATAT 57.265 29.630 0.00 0.00 0.00 0.86
2647 5846 6.426633 CCAAAACAGAATTAAATGGTCCCAAC 59.573 38.462 0.00 0.00 0.00 3.77
2690 5893 4.647611 TGGTTTCGACTACCATTCAACAT 58.352 39.130 13.24 0.00 40.65 2.71
2747 5954 4.081476 AGGAAAAGAAAGCATTATGTGGCC 60.081 41.667 0.00 0.00 0.00 5.36
2784 5991 6.015856 TCGTTTGAGCAATTAAATGGAAAGGA 60.016 34.615 0.00 0.00 0.00 3.36
2819 6026 4.842531 TCTCTATGGCTGGTTGAATGAA 57.157 40.909 0.00 0.00 0.00 2.57
2822 6029 3.117776 TGCATCTCTATGGCTGGTTGAAT 60.118 43.478 0.00 0.00 33.38 2.57
2830 6037 6.373774 GCTATTTAATGTGCATCTCTATGGCT 59.626 38.462 0.00 0.00 33.38 4.75
2841 6048 4.394610 TCTTTCGCTGCTATTTAATGTGCA 59.605 37.500 0.00 7.10 0.00 4.57
2854 6061 0.167689 CTTGCTTCCTCTTTCGCTGC 59.832 55.000 0.00 0.00 0.00 5.25
2887 6094 0.113190 ACTTTTGGCCCCTTCTCCAG 59.887 55.000 0.00 0.00 33.32 3.86
2904 6111 4.021925 GCCCCAACTCGCTCCACT 62.022 66.667 0.00 0.00 0.00 4.00
2940 6147 7.670364 TGAGAGTTGTCAATATCACTTTCTCA 58.330 34.615 0.00 0.00 0.00 3.27
2976 6183 0.179001 CCCGAACACACCCCTTTTCT 60.179 55.000 0.00 0.00 0.00 2.52
2977 6184 1.802337 GCCCGAACACACCCCTTTTC 61.802 60.000 0.00 0.00 0.00 2.29
3099 6306 1.981256 TCTTGGGAAAGCTGACCAAC 58.019 50.000 11.69 0.00 39.22 3.77
3128 6335 9.777575 ACGTATTATTCAAAAATAGAAAACCCG 57.222 29.630 0.00 0.00 0.00 5.28
3240 6454 9.423061 GCACTAAATTCCATTAAAACTGTGATT 57.577 29.630 0.00 0.00 0.00 2.57
3242 6456 8.177119 AGCACTAAATTCCATTAAAACTGTGA 57.823 30.769 0.00 0.00 0.00 3.58
3243 6457 8.816640 AAGCACTAAATTCCATTAAAACTGTG 57.183 30.769 0.00 0.00 0.00 3.66
3276 6490 9.040939 CCTTGATTTTTAAATTTCCTGAACGTT 57.959 29.630 0.00 0.00 0.00 3.99
3277 6491 8.417884 TCCTTGATTTTTAAATTTCCTGAACGT 58.582 29.630 0.00 0.00 0.00 3.99
3278 6492 8.810652 TCCTTGATTTTTAAATTTCCTGAACG 57.189 30.769 0.00 0.00 0.00 3.95
3330 6544 4.699522 GACACTGGGCCACGGTCC 62.700 72.222 17.87 0.00 41.01 4.46
3331 6545 3.591254 GAGACACTGGGCCACGGTC 62.591 68.421 20.02 20.02 36.23 4.79
3332 6546 3.626924 GAGACACTGGGCCACGGT 61.627 66.667 0.00 2.95 40.00 4.83
3333 6547 3.625897 TGAGACACTGGGCCACGG 61.626 66.667 0.00 0.00 0.00 4.94
3334 6548 2.357517 GTGAGACACTGGGCCACG 60.358 66.667 0.00 1.10 0.00 4.94
3335 6549 2.032681 GGTGAGACACTGGGCCAC 59.967 66.667 0.00 0.00 34.40 5.01
3336 6550 3.249189 GGGTGAGACACTGGGCCA 61.249 66.667 5.85 5.85 34.40 5.36
3337 6551 3.249189 TGGGTGAGACACTGGGCC 61.249 66.667 0.00 0.00 34.40 5.80
3338 6552 2.032681 GTGGGTGAGACACTGGGC 59.967 66.667 0.00 0.00 35.98 5.36
3339 6553 2.343758 CGTGGGTGAGACACTGGG 59.656 66.667 0.00 0.00 36.71 4.45
3340 6554 2.357517 GCGTGGGTGAGACACTGG 60.358 66.667 0.00 0.00 36.71 4.00
3341 6555 1.956170 GTGCGTGGGTGAGACACTG 60.956 63.158 0.00 0.00 36.71 3.66
3342 6556 2.134287 AGTGCGTGGGTGAGACACT 61.134 57.895 0.00 0.00 36.78 3.55
3343 6557 1.956170 CAGTGCGTGGGTGAGACAC 60.956 63.158 0.00 0.00 35.55 3.67
3344 6558 2.421314 CAGTGCGTGGGTGAGACA 59.579 61.111 0.00 0.00 0.00 3.41
3345 6559 2.357517 CCAGTGCGTGGGTGAGAC 60.358 66.667 0.00 0.00 43.63 3.36
3353 6567 1.394917 GAGTTTATGAGCCAGTGCGTG 59.605 52.381 0.00 0.00 44.33 5.34
3354 6568 1.726853 GAGTTTATGAGCCAGTGCGT 58.273 50.000 0.00 0.00 44.33 5.24
3355 6569 0.647410 CGAGTTTATGAGCCAGTGCG 59.353 55.000 0.00 0.00 44.33 5.34
3356 6570 1.726853 ACGAGTTTATGAGCCAGTGC 58.273 50.000 0.00 0.00 37.95 4.40
3357 6571 3.667960 GCAAACGAGTTTATGAGCCAGTG 60.668 47.826 0.50 0.00 0.00 3.66
3358 6572 2.484264 GCAAACGAGTTTATGAGCCAGT 59.516 45.455 0.50 0.00 0.00 4.00
3359 6573 2.159517 GGCAAACGAGTTTATGAGCCAG 60.160 50.000 17.44 0.40 37.65 4.85
3360 6574 1.810151 GGCAAACGAGTTTATGAGCCA 59.190 47.619 17.44 0.00 37.65 4.75
3361 6575 1.132453 GGGCAAACGAGTTTATGAGCC 59.868 52.381 15.28 15.28 37.25 4.70
3362 6576 1.810151 TGGGCAAACGAGTTTATGAGC 59.190 47.619 0.50 1.14 0.00 4.26
3363 6577 3.941483 AGATGGGCAAACGAGTTTATGAG 59.059 43.478 0.50 0.00 0.00 2.90
3364 6578 3.689161 CAGATGGGCAAACGAGTTTATGA 59.311 43.478 0.50 0.00 0.00 2.15
3365 6579 3.731867 GCAGATGGGCAAACGAGTTTATG 60.732 47.826 0.50 0.00 0.00 1.90
3366 6580 2.423538 GCAGATGGGCAAACGAGTTTAT 59.576 45.455 0.50 0.00 0.00 1.40
3367 6581 1.810151 GCAGATGGGCAAACGAGTTTA 59.190 47.619 0.50 0.00 0.00 2.01
3368 6582 0.598065 GCAGATGGGCAAACGAGTTT 59.402 50.000 0.00 0.00 0.00 2.66
3369 6583 0.250901 AGCAGATGGGCAAACGAGTT 60.251 50.000 0.00 0.00 35.83 3.01
3370 6584 0.250901 AAGCAGATGGGCAAACGAGT 60.251 50.000 0.00 0.00 35.83 4.18
3371 6585 0.169672 CAAGCAGATGGGCAAACGAG 59.830 55.000 0.00 0.00 35.83 4.18
3372 6586 1.865788 GCAAGCAGATGGGCAAACGA 61.866 55.000 0.00 0.00 35.83 3.85
3373 6587 1.444895 GCAAGCAGATGGGCAAACG 60.445 57.895 0.00 0.00 35.83 3.60
3374 6588 0.108945 GAGCAAGCAGATGGGCAAAC 60.109 55.000 0.00 0.00 35.83 2.93
3375 6589 1.588824 CGAGCAAGCAGATGGGCAAA 61.589 55.000 0.00 0.00 35.83 3.68
3376 6590 2.042259 CGAGCAAGCAGATGGGCAA 61.042 57.895 0.00 0.00 35.83 4.52
3377 6591 2.437180 CGAGCAAGCAGATGGGCA 60.437 61.111 0.00 0.00 35.83 5.36
3378 6592 2.437359 ACGAGCAAGCAGATGGGC 60.437 61.111 0.00 0.00 0.00 5.36
3379 6593 2.110967 CCACGAGCAAGCAGATGGG 61.111 63.158 0.00 0.00 0.00 4.00
3380 6594 0.957395 AACCACGAGCAAGCAGATGG 60.957 55.000 0.00 6.86 0.00 3.51
3381 6595 0.877071 AAACCACGAGCAAGCAGATG 59.123 50.000 0.00 0.00 0.00 2.90
3382 6596 1.537202 GAAAACCACGAGCAAGCAGAT 59.463 47.619 0.00 0.00 0.00 2.90
3383 6597 0.944386 GAAAACCACGAGCAAGCAGA 59.056 50.000 0.00 0.00 0.00 4.26
3384 6598 0.947244 AGAAAACCACGAGCAAGCAG 59.053 50.000 0.00 0.00 0.00 4.24
3385 6599 1.333619 GAAGAAAACCACGAGCAAGCA 59.666 47.619 0.00 0.00 0.00 3.91
3386 6600 1.604278 AGAAGAAAACCACGAGCAAGC 59.396 47.619 0.00 0.00 0.00 4.01
3387 6601 3.971032 AAGAAGAAAACCACGAGCAAG 57.029 42.857 0.00 0.00 0.00 4.01
3388 6602 4.712122 AAAAGAAGAAAACCACGAGCAA 57.288 36.364 0.00 0.00 0.00 3.91
3389 6603 4.668289 GAAAAAGAAGAAAACCACGAGCA 58.332 39.130 0.00 0.00 0.00 4.26
3390 6604 3.724257 CGAAAAAGAAGAAAACCACGAGC 59.276 43.478 0.00 0.00 0.00 5.03
3391 6605 3.724257 GCGAAAAAGAAGAAAACCACGAG 59.276 43.478 0.00 0.00 0.00 4.18
3392 6606 3.375922 AGCGAAAAAGAAGAAAACCACGA 59.624 39.130 0.00 0.00 0.00 4.35
3393 6607 3.691498 AGCGAAAAAGAAGAAAACCACG 58.309 40.909 0.00 0.00 0.00 4.94
3394 6608 4.259810 GCAAGCGAAAAAGAAGAAAACCAC 60.260 41.667 0.00 0.00 0.00 4.16
3395 6609 3.862845 GCAAGCGAAAAAGAAGAAAACCA 59.137 39.130 0.00 0.00 0.00 3.67
3396 6610 3.245284 GGCAAGCGAAAAAGAAGAAAACC 59.755 43.478 0.00 0.00 0.00 3.27
3397 6611 3.862845 TGGCAAGCGAAAAAGAAGAAAAC 59.137 39.130 0.00 0.00 0.00 2.43
3398 6612 4.116747 TGGCAAGCGAAAAAGAAGAAAA 57.883 36.364 0.00 0.00 0.00 2.29
3399 6613 3.791973 TGGCAAGCGAAAAAGAAGAAA 57.208 38.095 0.00 0.00 0.00 2.52
3400 6614 4.050553 CAATGGCAAGCGAAAAAGAAGAA 58.949 39.130 0.00 0.00 0.00 2.52
3401 6615 3.317711 TCAATGGCAAGCGAAAAAGAAGA 59.682 39.130 0.00 0.00 0.00 2.87
3402 6616 3.641648 TCAATGGCAAGCGAAAAAGAAG 58.358 40.909 0.00 0.00 0.00 2.85
3403 6617 3.724508 TCAATGGCAAGCGAAAAAGAA 57.275 38.095 0.00 0.00 0.00 2.52
3404 6618 3.255395 TGATCAATGGCAAGCGAAAAAGA 59.745 39.130 0.00 0.00 0.00 2.52
3405 6619 3.577667 TGATCAATGGCAAGCGAAAAAG 58.422 40.909 0.00 0.00 0.00 2.27
3406 6620 3.657015 TGATCAATGGCAAGCGAAAAA 57.343 38.095 0.00 0.00 0.00 1.94
3407 6621 3.316283 GTTGATCAATGGCAAGCGAAAA 58.684 40.909 12.12 0.00 0.00 2.29
3408 6622 2.352617 GGTTGATCAATGGCAAGCGAAA 60.353 45.455 12.12 0.00 33.57 3.46
3409 6623 1.202114 GGTTGATCAATGGCAAGCGAA 59.798 47.619 12.12 0.00 33.57 4.70
3410 6624 0.810648 GGTTGATCAATGGCAAGCGA 59.189 50.000 12.12 0.00 33.57 4.93
3411 6625 0.813184 AGGTTGATCAATGGCAAGCG 59.187 50.000 12.12 0.00 44.63 4.68
3412 6626 2.417787 GGAAGGTTGATCAATGGCAAGC 60.418 50.000 12.12 9.66 41.43 4.01
3413 6627 2.167075 GGGAAGGTTGATCAATGGCAAG 59.833 50.000 12.12 0.00 0.00 4.01
3414 6628 2.178580 GGGAAGGTTGATCAATGGCAA 58.821 47.619 12.12 0.00 0.00 4.52
3415 6629 1.619432 GGGGAAGGTTGATCAATGGCA 60.619 52.381 12.12 0.00 0.00 4.92
3416 6630 1.114627 GGGGAAGGTTGATCAATGGC 58.885 55.000 12.12 0.00 0.00 4.40
3417 6631 1.392589 CGGGGAAGGTTGATCAATGG 58.607 55.000 12.12 0.00 0.00 3.16
3418 6632 1.064758 TCCGGGGAAGGTTGATCAATG 60.065 52.381 12.12 0.00 0.00 2.82
3419 6633 1.295020 TCCGGGGAAGGTTGATCAAT 58.705 50.000 12.12 0.00 0.00 2.57
3420 6634 1.068948 TTCCGGGGAAGGTTGATCAA 58.931 50.000 3.38 3.38 0.00 2.57
3421 6635 1.068948 TTTCCGGGGAAGGTTGATCA 58.931 50.000 0.00 0.00 35.38 2.92
3422 6636 2.437085 ATTTCCGGGGAAGGTTGATC 57.563 50.000 0.00 0.00 35.38 2.92
3423 6637 4.325084 TTTATTTCCGGGGAAGGTTGAT 57.675 40.909 0.00 0.00 35.38 2.57
3424 6638 3.810721 TTTATTTCCGGGGAAGGTTGA 57.189 42.857 0.00 0.00 35.38 3.18
3425 6639 5.442391 TCTATTTATTTCCGGGGAAGGTTG 58.558 41.667 0.00 0.00 35.38 3.77
3426 6640 5.720486 TCTATTTATTTCCGGGGAAGGTT 57.280 39.130 0.00 0.00 35.38 3.50
3427 6641 5.924769 ATCTATTTATTTCCGGGGAAGGT 57.075 39.130 0.00 0.00 35.38 3.50
3428 6642 6.884836 CCTAATCTATTTATTTCCGGGGAAGG 59.115 42.308 0.00 0.00 35.38 3.46
3429 6643 7.459234 ACCTAATCTATTTATTTCCGGGGAAG 58.541 38.462 0.00 0.00 35.38 3.46
3430 6644 7.396906 ACCTAATCTATTTATTTCCGGGGAA 57.603 36.000 0.00 0.00 0.00 3.97
3431 6645 7.396906 AACCTAATCTATTTATTTCCGGGGA 57.603 36.000 0.00 0.00 0.00 4.81
3432 6646 7.942894 AGAAACCTAATCTATTTATTTCCGGGG 59.057 37.037 0.00 0.00 0.00 5.73
3433 6647 8.919777 AGAAACCTAATCTATTTATTTCCGGG 57.080 34.615 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.