Multiple sequence alignment - TraesCS5B01G350200

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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 TraesCS5B01G350200 chr5B 100.000 4103 0 0 1 4103 531203686 531207788 0.000000e+00 7577.0
1 TraesCS5B01G350200 chr5B 82.231 771 115 11 2128 2878 543281420 543280652 0.000000e+00 645.0
2 TraesCS5B01G350200 chr5B 82.524 515 80 9 1016 1522 543282493 543281981 1.050000e-120 444.0
3 TraesCS5B01G350200 chr5B 88.013 317 38 0 3015 3331 543270190 543269874 3.870000e-100 375.0
4 TraesCS5B01G350200 chr5B 84.146 328 46 6 3029 3351 543297743 543297417 3.080000e-81 313.0
5 TraesCS5B01G350200 chr5B 89.000 100 11 0 2141 2240 543245153 543245054 1.550000e-24 124.0
6 TraesCS5B01G350200 chr5B 85.567 97 13 1 999 1095 531197691 531197786 2.610000e-17 100.0
7 TraesCS5B01G350200 chr5D 93.492 3411 148 30 618 3987 437014814 437018191 0.000000e+00 5001.0
8 TraesCS5B01G350200 chr5D 86.792 530 70 0 1008 1537 553910509 553911038 3.530000e-165 592.0
9 TraesCS5B01G350200 chr5D 77.519 1032 178 32 1834 2823 553911488 553912507 4.600000e-159 571.0
10 TraesCS5B01G350200 chr5D 85.569 589 28 9 61 595 437014136 437014721 7.700000e-157 564.0
11 TraesCS5B01G350200 chr5D 80.561 535 102 2 1001 1534 445486030 445485497 1.060000e-110 411.0
12 TraesCS5B01G350200 chr5D 82.276 457 70 10 2877 3324 553912498 553912952 6.430000e-103 385.0
13 TraesCS5B01G350200 chr5D 84.451 328 45 6 3029 3351 445489966 445489640 6.620000e-83 318.0
14 TraesCS5B01G350200 chr5D 80.702 342 51 7 3499 3830 436983748 436984084 6.810000e-63 252.0
15 TraesCS5B01G350200 chr5D 89.000 100 11 0 2141 2240 445404561 445404462 1.550000e-24 124.0
16 TraesCS5B01G350200 chr5D 93.421 76 5 0 2 77 437014045 437014120 3.350000e-21 113.0
17 TraesCS5B01G350200 chr5A 90.751 3449 199 51 599 3995 552298008 552301388 0.000000e+00 4492.0
18 TraesCS5B01G350200 chr5A 83.920 653 27 20 9 595 552282611 552283251 1.670000e-153 553.0
19 TraesCS5B01G350200 chr5A 83.144 528 78 8 1000 1517 563256423 563255897 4.800000e-129 472.0
20 TraesCS5B01G350200 chr5A 88.000 100 12 0 2141 2240 563255237 563255138 7.200000e-23 119.0
21 TraesCS5B01G350200 chr5A 91.667 60 5 0 3593 3652 552276105 552276164 2.630000e-12 84.2
22 TraesCS5B01G350200 chr4B 79.728 735 102 30 2119 2840 2206419 2207119 4.770000e-134 488.0
23 TraesCS5B01G350200 chr4B 85.330 409 49 8 2119 2518 2235828 2236234 2.950000e-111 412.0
24 TraesCS5B01G350200 chr4B 80.000 515 95 6 1001 1511 2205415 2205925 1.390000e-99 374.0
25 TraesCS5B01G350200 chr4B 79.401 267 42 11 2579 2840 2236292 2236550 4.220000e-40 176.0
26 TraesCS5B01G350200 chr1D 81.887 530 92 4 1005 1533 410460392 410459866 1.050000e-120 444.0
27 TraesCS5B01G350200 chr1A 74.368 1147 242 37 2708 3830 506278027 506276909 3.760000e-120 442.0
28 TraesCS5B01G350200 chr2B 82.236 501 83 6 1020 1517 794611699 794611202 1.050000e-115 427.0
29 TraesCS5B01G350200 chr7A 81.395 516 91 4 1008 1522 7817266 7817777 2.280000e-112 416.0
30 TraesCS5B01G350200 chr7A 80.992 121 21 2 2097 2216 7818514 7818633 1.210000e-15 95.3
31 TraesCS5B01G350200 chr4D 82.527 372 54 10 2958 3322 1689534 1689901 2.380000e-82 316.0
32 TraesCS5B01G350200 chr3A 81.395 387 59 9 2877 3252 13552401 13552785 1.850000e-78 303.0
33 TraesCS5B01G350200 chr3A 81.766 351 61 3 2475 2823 13552061 13552410 1.440000e-74 291.0
34 TraesCS5B01G350200 chrUn 79.401 267 42 11 2579 2840 51689370 51689628 4.220000e-40 176.0
35 TraesCS5B01G350200 chrUn 91.667 72 6 0 2671 2742 310057553 310057482 2.610000e-17 100.0


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 TraesCS5B01G350200 chr5B 531203686 531207788 4102 False 7577.000000 7577 100.000000 1 4103 1 chr5B.!!$F2 4102
1 TraesCS5B01G350200 chr5B 543280652 543282493 1841 True 544.500000 645 82.377500 1016 2878 2 chr5B.!!$R4 1862
2 TraesCS5B01G350200 chr5D 437014045 437018191 4146 False 1892.666667 5001 90.827333 2 3987 3 chr5D.!!$F2 3985
3 TraesCS5B01G350200 chr5D 553910509 553912952 2443 False 516.000000 592 82.195667 1008 3324 3 chr5D.!!$F3 2316
4 TraesCS5B01G350200 chr5D 445485497 445489966 4469 True 364.500000 411 82.506000 1001 3351 2 chr5D.!!$R2 2350
5 TraesCS5B01G350200 chr5A 552298008 552301388 3380 False 4492.000000 4492 90.751000 599 3995 1 chr5A.!!$F3 3396
6 TraesCS5B01G350200 chr5A 552282611 552283251 640 False 553.000000 553 83.920000 9 595 1 chr5A.!!$F2 586
7 TraesCS5B01G350200 chr5A 563255138 563256423 1285 True 295.500000 472 85.572000 1000 2240 2 chr5A.!!$R1 1240
8 TraesCS5B01G350200 chr4B 2205415 2207119 1704 False 431.000000 488 79.864000 1001 2840 2 chr4B.!!$F1 1839
9 TraesCS5B01G350200 chr4B 2235828 2236550 722 False 294.000000 412 82.365500 2119 2840 2 chr4B.!!$F2 721
10 TraesCS5B01G350200 chr1D 410459866 410460392 526 True 444.000000 444 81.887000 1005 1533 1 chr1D.!!$R1 528
11 TraesCS5B01G350200 chr1A 506276909 506278027 1118 True 442.000000 442 74.368000 2708 3830 1 chr1A.!!$R1 1122
12 TraesCS5B01G350200 chr7A 7817266 7818633 1367 False 255.650000 416 81.193500 1008 2216 2 chr7A.!!$F1 1208
13 TraesCS5B01G350200 chr3A 13552061 13552785 724 False 297.000000 303 81.580500 2475 3252 2 chr3A.!!$F1 777

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
335 392 0.179056 CCATTCCTCGTTGGCCGTAT 60.179 55.0 0.0 0.0 37.94 3.06 F
597 702 0.456312 CGTTCCACTGCGTCCTAGTC 60.456 60.0 0.0 0.0 0.00 2.59 F
1522 4474 1.506493 CTTCAATAGCCTAGCCAGCG 58.494 55.0 0.0 0.0 34.64 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 5881 0.102481 GGATCCGCGTCTTCTTGCTA 59.898 55.000 4.92 0.0 0.00 3.49 R
2345 5892 1.136305 TGAAGGAACTAAGGATCCGCG 59.864 52.381 5.98 0.0 38.49 6.46 R
3274 6856 0.108585 GCCGGCATATCCTTCTCCAA 59.891 55.000 24.80 0.0 0.00 3.53 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
55 59 3.244814 GTGAATGCATCGTCATCTCAGTC 59.755 47.826 0.00 0.00 0.00 3.51
108 151 8.911662 ACATACATCGCACTAAAAACAAAAATC 58.088 29.630 0.00 0.00 0.00 2.17
182 225 3.440173 CCCAACACCAATTACAGCTACAG 59.560 47.826 0.00 0.00 0.00 2.74
335 392 0.179056 CCATTCCTCGTTGGCCGTAT 60.179 55.000 0.00 0.00 37.94 3.06
393 472 4.680237 CTCAAGGTGGCGGCGACA 62.680 66.667 13.60 13.60 0.00 4.35
494 599 1.819229 CGTCCACTCCTCCATCAGG 59.181 63.158 0.00 0.00 45.15 3.86
596 701 1.585006 CGTTCCACTGCGTCCTAGT 59.415 57.895 0.00 0.00 0.00 2.57
597 702 0.456312 CGTTCCACTGCGTCCTAGTC 60.456 60.000 0.00 0.00 0.00 2.59
614 771 3.423539 AGTCCTAACATGCTTGCTTGA 57.576 42.857 14.07 0.00 0.00 3.02
650 825 1.876156 CAGAGTCACAAAGAAGTGGGC 59.124 52.381 0.00 0.00 39.93 5.36
655 830 1.771854 TCACAAAGAAGTGGGCCTGTA 59.228 47.619 4.53 0.00 39.93 2.74
716 891 3.187432 GGAAAGTGAAAAGAAGAGAGGCG 59.813 47.826 0.00 0.00 0.00 5.52
810 985 1.933021 ACACGGGAGGAATGTAGTCA 58.067 50.000 0.00 0.00 0.00 3.41
860 1035 3.430895 GGCACATCAACATCAAAAAGCAG 59.569 43.478 0.00 0.00 0.00 4.24
949 1130 4.030913 CTGTGACCCCCAGAGAAATAGTA 58.969 47.826 0.00 0.00 38.35 1.82
985 1166 4.194720 CGAGGGGACGAGGAAGCG 62.195 72.222 0.00 0.00 35.09 4.68
1311 4257 1.692519 GGTCAGGATGGTATAACCGCT 59.307 52.381 0.00 0.00 42.58 5.52
1522 4474 1.506493 CTTCAATAGCCTAGCCAGCG 58.494 55.000 0.00 0.00 34.64 5.18
1537 4489 1.816835 CCAGCGTATCCGAGCCTTATA 59.183 52.381 0.00 0.00 35.63 0.98
1555 4507 6.296145 GCCTTATAGCCATCTAAAGAGGATGT 60.296 42.308 0.00 0.00 38.95 3.06
1560 4512 2.223829 CCATCTAAAGAGGATGTCGCGT 60.224 50.000 5.77 0.00 38.95 6.01
1676 4655 3.935203 GCTCTCCGTTTGATGATCAGAAA 59.065 43.478 0.09 0.00 0.00 2.52
1677 4656 4.033817 GCTCTCCGTTTGATGATCAGAAAG 59.966 45.833 0.09 0.00 0.00 2.62
1684 4663 7.065085 TCCGTTTGATGATCAGAAAGAAGATTC 59.935 37.037 0.09 0.00 0.00 2.52
1697 4676 6.314896 AGAAAGAAGATTCGCAAGGACATTAG 59.685 38.462 0.00 0.00 34.46 1.73
1717 4696 1.661112 GGCTTGAAGACTATGTGCGAC 59.339 52.381 0.00 0.00 0.00 5.19
1760 4790 3.887716 GGCAATTGTCATCCTCAAGCTAT 59.112 43.478 4.85 0.00 0.00 2.97
1821 4851 2.301296 TCCTCAAGTGCAAGGAGAAGAG 59.699 50.000 11.03 2.40 36.75 2.85
2099 5628 6.925165 AGAGAAATTACACTGGTGCAAATTTG 59.075 34.615 21.25 14.03 38.47 2.32
2105 5634 4.432712 ACACTGGTGCAAATTTGTTCTTC 58.567 39.130 19.03 3.17 0.00 2.87
2151 5680 2.554142 CTGTCATTTGCAGCTATCGGA 58.446 47.619 0.00 0.00 0.00 4.55
2334 5881 2.343387 GCCCGCAACAAAAGGCAT 59.657 55.556 0.00 0.00 45.07 4.40
2345 5892 4.773323 ACAAAAGGCATAGCAAGAAGAC 57.227 40.909 0.00 0.00 0.00 3.01
2349 5896 1.638467 GCATAGCAAGAAGACGCGG 59.362 57.895 12.47 0.00 0.00 6.46
2825 6395 1.918262 ACTCAAGGCCATCCTCAATGA 59.082 47.619 5.01 0.00 43.40 2.57
2871 6441 2.494870 CCTCAAGGGAAAGAAGCCATTG 59.505 50.000 0.00 0.00 45.73 2.82
3018 6589 0.588252 CGGTTGAAAGCAGTGTCCAG 59.412 55.000 0.00 0.00 0.00 3.86
3274 6856 1.677217 GCAGAGGACGGAGCTTTCAAT 60.677 52.381 0.00 0.00 0.00 2.57
3392 6977 9.050601 CCATTTCTACTTCTACATTTCCATCTC 57.949 37.037 0.00 0.00 0.00 2.75
3508 7099 3.355378 TGCCAACAAGGTTGGAGATATG 58.645 45.455 27.43 4.08 42.06 1.78
3588 7179 1.880340 GACGCTCGAAGCCTCATGG 60.880 63.158 0.00 0.00 38.18 3.66
3592 7195 0.176680 GCTCGAAGCCTCATGGAGAA 59.823 55.000 0.00 0.00 34.48 2.87
3712 7315 6.918022 TCTCATGTCTGTATTACTTGTATGCG 59.082 38.462 0.00 0.00 0.00 4.73
3747 7350 4.520111 TCTTTTCTTGATTTGCAGCAGCTA 59.480 37.500 1.76 0.00 42.74 3.32
3776 7379 2.548178 CGGAGCTTGATGCACTTGT 58.452 52.632 0.00 0.00 45.94 3.16
3777 7380 0.445436 CGGAGCTTGATGCACTTGTC 59.555 55.000 0.00 0.00 45.94 3.18
3778 7381 0.807496 GGAGCTTGATGCACTTGTCC 59.193 55.000 0.00 0.00 45.94 4.02
3779 7382 1.527034 GAGCTTGATGCACTTGTCCA 58.473 50.000 0.00 0.00 45.94 4.02
3780 7383 1.467734 GAGCTTGATGCACTTGTCCAG 59.532 52.381 0.00 0.00 45.94 3.86
3781 7384 1.202855 AGCTTGATGCACTTGTCCAGT 60.203 47.619 0.00 0.00 45.94 4.00
3782 7385 1.610522 GCTTGATGCACTTGTCCAGTT 59.389 47.619 0.00 0.00 42.31 3.16
3783 7386 2.035066 GCTTGATGCACTTGTCCAGTTT 59.965 45.455 0.00 0.00 42.31 2.66
3784 7387 3.635331 CTTGATGCACTTGTCCAGTTTG 58.365 45.455 0.00 0.00 30.92 2.93
3832 7449 4.254492 GTTGGAACTGTCAGATTACCCTC 58.746 47.826 6.91 0.00 0.00 4.30
3833 7450 3.791320 TGGAACTGTCAGATTACCCTCT 58.209 45.455 6.91 0.00 0.00 3.69
3834 7451 4.168101 TGGAACTGTCAGATTACCCTCTT 58.832 43.478 6.91 0.00 0.00 2.85
3835 7452 5.338632 TGGAACTGTCAGATTACCCTCTTA 58.661 41.667 6.91 0.00 0.00 2.10
3836 7453 5.964477 TGGAACTGTCAGATTACCCTCTTAT 59.036 40.000 6.91 0.00 0.00 1.73
3837 7454 6.098409 TGGAACTGTCAGATTACCCTCTTATC 59.902 42.308 6.91 0.00 0.00 1.75
3848 7465 3.875571 ACCCTCTTATCCTTATCCCCAG 58.124 50.000 0.00 0.00 0.00 4.45
3853 7470 5.151454 CTCTTATCCTTATCCCCAGAGTGT 58.849 45.833 0.00 0.00 0.00 3.55
3859 7476 3.209410 CTTATCCCCAGAGTGTTCATGC 58.791 50.000 0.00 0.00 0.00 4.06
3876 7493 5.760484 TCATGCCTGTAATATGGATGCTA 57.240 39.130 0.00 0.00 0.00 3.49
3930 7547 5.649395 AGTGGATTTGGTGTGATAGTCATTG 59.351 40.000 0.00 0.00 0.00 2.82
3961 7579 6.220930 TCGCTTACCCTATTGATGTGATTAC 58.779 40.000 0.00 0.00 0.00 1.89
3969 7587 7.347222 ACCCTATTGATGTGATTACCTGTCTTA 59.653 37.037 0.00 0.00 0.00 2.10
3972 7590 9.254133 CTATTGATGTGATTACCTGTCTTACTG 57.746 37.037 0.00 0.00 0.00 2.74
3987 7605 4.023963 GTCTTACTGCCCAAAGTTCAGAAC 60.024 45.833 5.00 5.00 0.00 3.01
3988 7606 2.736670 ACTGCCCAAAGTTCAGAACT 57.263 45.000 10.27 10.27 45.46 3.01
3989 7607 2.301346 ACTGCCCAAAGTTCAGAACTG 58.699 47.619 16.85 6.10 41.91 3.16
3990 7608 1.000938 CTGCCCAAAGTTCAGAACTGC 60.001 52.381 16.85 15.13 41.91 4.40
3991 7609 1.032014 GCCCAAAGTTCAGAACTGCA 58.968 50.000 16.85 0.00 41.91 4.41
3992 7610 1.000938 GCCCAAAGTTCAGAACTGCAG 60.001 52.381 16.85 13.48 41.91 4.41
3993 7611 2.301346 CCCAAAGTTCAGAACTGCAGT 58.699 47.619 15.25 15.25 41.91 4.40
3994 7612 2.033801 CCCAAAGTTCAGAACTGCAGTG 59.966 50.000 22.49 8.45 41.91 3.66
3995 7613 2.684881 CCAAAGTTCAGAACTGCAGTGT 59.315 45.455 22.49 10.75 41.91 3.55
3996 7614 3.129287 CCAAAGTTCAGAACTGCAGTGTT 59.871 43.478 22.49 5.18 41.91 3.32
3997 7615 4.380867 CCAAAGTTCAGAACTGCAGTGTTT 60.381 41.667 22.49 4.26 41.91 2.83
3998 7616 5.163513 CAAAGTTCAGAACTGCAGTGTTTT 58.836 37.500 22.49 3.80 41.91 2.43
3999 7617 5.391312 AAGTTCAGAACTGCAGTGTTTTT 57.609 34.783 22.49 3.33 41.91 1.94
4021 7639 6.987403 TTTTATTTTTAGGGGAACTGCAGT 57.013 33.333 15.25 15.25 0.00 4.40
4022 7640 5.975693 TTATTTTTAGGGGAACTGCAGTG 57.024 39.130 22.49 0.00 0.00 3.66
4023 7641 1.616159 TTTTAGGGGAACTGCAGTGC 58.384 50.000 22.49 19.82 0.00 4.40
4024 7642 0.771127 TTTAGGGGAACTGCAGTGCT 59.229 50.000 24.24 7.89 0.00 4.40
4025 7643 0.036732 TTAGGGGAACTGCAGTGCTG 59.963 55.000 24.24 19.32 0.00 4.41
4026 7644 1.127567 TAGGGGAACTGCAGTGCTGT 61.128 55.000 24.24 20.68 42.21 4.40
4066 7684 9.515226 TTTTACAATAGTGCTGTTATTCTTCCT 57.485 29.630 0.00 0.00 0.00 3.36
4067 7685 8.718102 TTACAATAGTGCTGTTATTCTTCCTC 57.282 34.615 0.00 0.00 0.00 3.71
4068 7686 6.711277 ACAATAGTGCTGTTATTCTTCCTCA 58.289 36.000 0.00 0.00 0.00 3.86
4069 7687 7.168219 ACAATAGTGCTGTTATTCTTCCTCAA 58.832 34.615 0.00 0.00 0.00 3.02
4070 7688 7.831193 ACAATAGTGCTGTTATTCTTCCTCAAT 59.169 33.333 0.00 0.00 0.00 2.57
4071 7689 9.330063 CAATAGTGCTGTTATTCTTCCTCAATA 57.670 33.333 0.00 0.00 0.00 1.90
4073 7691 9.717942 ATAGTGCTGTTATTCTTCCTCAATATC 57.282 33.333 0.00 0.00 0.00 1.63
4074 7692 6.995091 AGTGCTGTTATTCTTCCTCAATATCC 59.005 38.462 0.00 0.00 0.00 2.59
4075 7693 6.767902 GTGCTGTTATTCTTCCTCAATATCCA 59.232 38.462 0.00 0.00 0.00 3.41
4076 7694 6.767902 TGCTGTTATTCTTCCTCAATATCCAC 59.232 38.462 0.00 0.00 0.00 4.02
4077 7695 6.995091 GCTGTTATTCTTCCTCAATATCCACT 59.005 38.462 0.00 0.00 0.00 4.00
4078 7696 8.150945 GCTGTTATTCTTCCTCAATATCCACTA 58.849 37.037 0.00 0.00 0.00 2.74
4079 7697 9.482627 CTGTTATTCTTCCTCAATATCCACTAC 57.517 37.037 0.00 0.00 0.00 2.73
4080 7698 9.213777 TGTTATTCTTCCTCAATATCCACTACT 57.786 33.333 0.00 0.00 0.00 2.57
4081 7699 9.482627 GTTATTCTTCCTCAATATCCACTACTG 57.517 37.037 0.00 0.00 0.00 2.74
4082 7700 7.682787 ATTCTTCCTCAATATCCACTACTGT 57.317 36.000 0.00 0.00 0.00 3.55
4083 7701 8.783660 ATTCTTCCTCAATATCCACTACTGTA 57.216 34.615 0.00 0.00 0.00 2.74
4084 7702 8.603898 TTCTTCCTCAATATCCACTACTGTAA 57.396 34.615 0.00 0.00 0.00 2.41
4085 7703 8.008513 TCTTCCTCAATATCCACTACTGTAAC 57.991 38.462 0.00 0.00 0.00 2.50
4086 7704 7.839705 TCTTCCTCAATATCCACTACTGTAACT 59.160 37.037 0.00 0.00 0.00 2.24
4087 7705 7.584122 TCCTCAATATCCACTACTGTAACTC 57.416 40.000 0.00 0.00 0.00 3.01
4088 7706 7.355101 TCCTCAATATCCACTACTGTAACTCT 58.645 38.462 0.00 0.00 0.00 3.24
4089 7707 7.502895 TCCTCAATATCCACTACTGTAACTCTC 59.497 40.741 0.00 0.00 0.00 3.20
4090 7708 7.504238 CCTCAATATCCACTACTGTAACTCTCT 59.496 40.741 0.00 0.00 0.00 3.10
4091 7709 8.226819 TCAATATCCACTACTGTAACTCTCTG 57.773 38.462 0.00 0.00 0.00 3.35
4092 7710 7.834681 TCAATATCCACTACTGTAACTCTCTGT 59.165 37.037 0.00 0.00 0.00 3.41
4093 7711 5.906113 ATCCACTACTGTAACTCTCTGTG 57.094 43.478 0.00 0.00 0.00 3.66
4094 7712 4.981812 TCCACTACTGTAACTCTCTGTGA 58.018 43.478 0.00 0.00 0.00 3.58
4095 7713 5.571285 TCCACTACTGTAACTCTCTGTGAT 58.429 41.667 0.00 0.00 0.00 3.06
4096 7714 5.416013 TCCACTACTGTAACTCTCTGTGATG 59.584 44.000 0.00 0.00 0.00 3.07
4097 7715 5.184096 CCACTACTGTAACTCTCTGTGATGT 59.816 44.000 0.00 0.00 0.00 3.06
4098 7716 6.374613 CCACTACTGTAACTCTCTGTGATGTA 59.625 42.308 0.00 0.00 0.00 2.29
4099 7717 7.244898 CACTACTGTAACTCTCTGTGATGTAC 58.755 42.308 0.00 0.00 0.00 2.90
4100 7718 5.646577 ACTGTAACTCTCTGTGATGTACC 57.353 43.478 0.00 0.00 0.00 3.34
4101 7719 5.077564 ACTGTAACTCTCTGTGATGTACCA 58.922 41.667 0.00 0.00 0.00 3.25
4102 7720 5.184096 ACTGTAACTCTCTGTGATGTACCAG 59.816 44.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.131709 TCCAGATTATTGCTAGCAGGC 57.868 47.619 18.45 6.86 0.00 4.85
43 47 2.222976 GCATGCTTTGACTGAGATGACG 60.223 50.000 11.37 0.00 0.00 4.35
46 50 3.427638 CCTTGCATGCTTTGACTGAGATG 60.428 47.826 20.33 0.00 0.00 2.90
55 59 2.288334 TGTTAGTGCCTTGCATGCTTTG 60.288 45.455 20.33 7.86 41.91 2.77
79 83 9.549509 TTTTGTTTTTAGTGCGATGTATGTATC 57.450 29.630 0.00 0.00 0.00 2.24
80 84 9.900710 TTTTTGTTTTTAGTGCGATGTATGTAT 57.099 25.926 0.00 0.00 0.00 2.29
82 86 8.810652 ATTTTTGTTTTTAGTGCGATGTATGT 57.189 26.923 0.00 0.00 0.00 2.29
83 87 8.095512 CGATTTTTGTTTTTAGTGCGATGTATG 58.904 33.333 0.00 0.00 0.00 2.39
84 88 7.806014 ACGATTTTTGTTTTTAGTGCGATGTAT 59.194 29.630 0.00 0.00 0.00 2.29
182 225 4.778143 ACTGACGGCGGGCCATTC 62.778 66.667 13.24 5.97 35.37 2.67
349 406 2.853914 GTTGAGGTTGCTCGTCGC 59.146 61.111 0.00 0.00 39.77 5.19
467 572 2.420568 GGAGTGGACGCCGGTCATA 61.421 63.158 1.90 0.00 45.28 2.15
596 701 2.436417 GGTCAAGCAAGCATGTTAGGA 58.564 47.619 0.00 0.00 0.00 2.94
597 702 1.474077 GGGTCAAGCAAGCATGTTAGG 59.526 52.381 0.00 0.00 0.00 2.69
614 771 0.900182 TCTGTCTCACATCGCAGGGT 60.900 55.000 0.00 0.00 0.00 4.34
645 820 1.269569 GCAACACTTTTACAGGCCCAC 60.270 52.381 0.00 0.00 0.00 4.61
686 861 0.741915 TTTTCACTTTCCACCACGCC 59.258 50.000 0.00 0.00 0.00 5.68
716 891 5.123227 TCGGACCCATGATTTTACTTGATC 58.877 41.667 0.00 0.00 0.00 2.92
860 1035 0.593128 GAATGGGGTGCGATGTATGC 59.407 55.000 0.00 0.00 0.00 3.14
949 1130 1.738030 CGAGGTCGGCGGTTATTTTCT 60.738 52.381 7.21 0.00 35.37 2.52
1311 4257 3.427528 GCTCGTTGTCTTCGATGTTGTAA 59.572 43.478 0.00 0.00 36.73 2.41
1522 4474 3.702045 AGATGGCTATAAGGCTCGGATAC 59.298 47.826 2.01 0.00 41.96 2.24
1537 4489 2.224161 GCGACATCCTCTTTAGATGGCT 60.224 50.000 5.16 0.00 45.92 4.75
1585 4549 5.335426 GCATCATCATTGGTTGCTTATCGAT 60.335 40.000 2.16 2.16 32.78 3.59
1676 4655 4.446371 CCTAATGTCCTTGCGAATCTTCT 58.554 43.478 0.00 0.00 0.00 2.85
1677 4656 3.002759 GCCTAATGTCCTTGCGAATCTTC 59.997 47.826 0.00 0.00 0.00 2.87
1684 4663 1.737838 TCAAGCCTAATGTCCTTGCG 58.262 50.000 0.00 0.00 36.72 4.85
1697 4676 1.661112 GTCGCACATAGTCTTCAAGCC 59.339 52.381 0.00 0.00 0.00 4.35
1760 4790 2.565391 TCAATTGTGGCGTCTCTTCCTA 59.435 45.455 5.13 0.00 0.00 2.94
1821 4851 0.464554 GGTTGGGCTCAGCTGTATCC 60.465 60.000 14.67 13.42 0.00 2.59
1906 5201 3.262405 ACAAATAACTTACGGGCCTCAGA 59.738 43.478 0.84 0.00 0.00 3.27
2034 5338 5.296780 TGCTTTTGTGTAGAGAAGACCAAAG 59.703 40.000 0.00 0.00 37.24 2.77
2075 5412 6.701400 ACAAATTTGCACCAGTGTAATTTCTC 59.299 34.615 18.12 0.00 36.15 2.87
2099 5628 2.919859 GCTTCCCGTACGTAAGAAGAAC 59.080 50.000 29.18 16.65 38.38 3.01
2105 5634 6.663172 ACGTAGTTGCTTCCCGTACGTAAG 62.663 50.000 15.21 17.10 45.72 2.34
2334 5881 0.102481 GGATCCGCGTCTTCTTGCTA 59.898 55.000 4.92 0.00 0.00 3.49
2345 5892 1.136305 TGAAGGAACTAAGGATCCGCG 59.864 52.381 5.98 0.00 38.49 6.46
2349 5896 4.579869 TGCACTTGAAGGAACTAAGGATC 58.420 43.478 0.00 0.00 38.49 3.36
3018 6589 3.255642 TGGATAAAACCTTCTTGTGCAGC 59.744 43.478 0.00 0.00 0.00 5.25
3274 6856 0.108585 GCCGGCATATCCTTCTCCAA 59.891 55.000 24.80 0.00 0.00 3.53
3547 7138 4.269183 TGAAGCGTGTTGGATATTGGAAT 58.731 39.130 0.00 0.00 0.00 3.01
3548 7139 3.680490 TGAAGCGTGTTGGATATTGGAA 58.320 40.909 0.00 0.00 0.00 3.53
3705 7308 2.088423 GATGGAACCAAACCGCATACA 58.912 47.619 0.00 0.00 0.00 2.29
3712 7315 5.529581 TCAAGAAAAGATGGAACCAAACC 57.470 39.130 0.00 0.00 0.00 3.27
3771 7374 1.967319 ACGCATCAAACTGGACAAGT 58.033 45.000 0.00 0.00 42.60 3.16
3772 7375 2.159653 GCTACGCATCAAACTGGACAAG 60.160 50.000 0.00 0.00 0.00 3.16
3773 7376 1.804151 GCTACGCATCAAACTGGACAA 59.196 47.619 0.00 0.00 0.00 3.18
3774 7377 1.270571 TGCTACGCATCAAACTGGACA 60.271 47.619 0.00 0.00 31.71 4.02
3775 7378 1.394917 CTGCTACGCATCAAACTGGAC 59.605 52.381 0.00 0.00 38.13 4.02
3776 7379 1.001974 ACTGCTACGCATCAAACTGGA 59.998 47.619 0.00 0.00 38.13 3.86
3777 7380 1.394917 GACTGCTACGCATCAAACTGG 59.605 52.381 0.00 0.00 38.13 4.00
3778 7381 2.093310 CAGACTGCTACGCATCAAACTG 59.907 50.000 0.00 0.00 38.13 3.16
3779 7382 2.289072 ACAGACTGCTACGCATCAAACT 60.289 45.455 1.25 0.00 38.13 2.66
3780 7383 2.069273 ACAGACTGCTACGCATCAAAC 58.931 47.619 1.25 0.00 38.13 2.93
3781 7384 2.455674 ACAGACTGCTACGCATCAAA 57.544 45.000 1.25 0.00 38.13 2.69
3782 7385 2.029020 AGAACAGACTGCTACGCATCAA 60.029 45.455 1.25 0.00 38.13 2.57
3783 7386 1.546029 AGAACAGACTGCTACGCATCA 59.454 47.619 1.25 0.00 38.13 3.07
3784 7387 2.285827 AGAACAGACTGCTACGCATC 57.714 50.000 1.25 0.00 38.13 3.91
3807 7424 4.567747 GGGTAATCTGACAGTTCCAACCAT 60.568 45.833 1.59 0.00 0.00 3.55
3809 7426 3.009143 AGGGTAATCTGACAGTTCCAACC 59.991 47.826 1.59 4.82 0.00 3.77
3832 7449 5.366768 TGAACACTCTGGGGATAAGGATAAG 59.633 44.000 0.00 0.00 0.00 1.73
3833 7450 5.285401 TGAACACTCTGGGGATAAGGATAA 58.715 41.667 0.00 0.00 0.00 1.75
3834 7451 4.890988 TGAACACTCTGGGGATAAGGATA 58.109 43.478 0.00 0.00 0.00 2.59
3835 7452 3.736094 TGAACACTCTGGGGATAAGGAT 58.264 45.455 0.00 0.00 0.00 3.24
3836 7453 3.199442 TGAACACTCTGGGGATAAGGA 57.801 47.619 0.00 0.00 0.00 3.36
3837 7454 3.813443 CATGAACACTCTGGGGATAAGG 58.187 50.000 0.00 0.00 0.00 2.69
3848 7465 5.368145 TCCATATTACAGGCATGAACACTC 58.632 41.667 4.84 0.00 0.00 3.51
3853 7470 4.989277 AGCATCCATATTACAGGCATGAA 58.011 39.130 4.84 0.00 0.00 2.57
3859 7476 6.936335 TCAACATGTAGCATCCATATTACAGG 59.064 38.462 0.00 0.00 34.88 4.00
3876 7493 4.645535 ACATGCTACAGAGTTCAACATGT 58.354 39.130 0.00 0.00 41.17 3.21
3930 7547 4.448210 TCAATAGGGTAAGCGATTGTTCC 58.552 43.478 0.00 0.00 32.33 3.62
3948 7565 6.540189 GCAGTAAGACAGGTAATCACATCAAT 59.460 38.462 0.00 0.00 0.00 2.57
3961 7579 2.568623 ACTTTGGGCAGTAAGACAGG 57.431 50.000 0.00 0.00 0.00 4.00
3969 7587 2.301346 CAGTTCTGAACTTTGGGCAGT 58.699 47.619 19.89 0.00 40.46 4.40
3972 7590 1.000938 CTGCAGTTCTGAACTTTGGGC 60.001 52.381 19.89 19.02 40.46 5.36
3997 7615 7.213678 CACTGCAGTTCCCCTAAAAATAAAAA 58.786 34.615 18.94 0.00 0.00 1.94
3998 7616 6.740122 GCACTGCAGTTCCCCTAAAAATAAAA 60.740 38.462 18.94 0.00 0.00 1.52
3999 7617 5.279256 GCACTGCAGTTCCCCTAAAAATAAA 60.279 40.000 18.94 0.00 0.00 1.40
4000 7618 4.219725 GCACTGCAGTTCCCCTAAAAATAA 59.780 41.667 18.94 0.00 0.00 1.40
4001 7619 3.761752 GCACTGCAGTTCCCCTAAAAATA 59.238 43.478 18.94 0.00 0.00 1.40
4002 7620 2.562738 GCACTGCAGTTCCCCTAAAAAT 59.437 45.455 18.94 0.00 0.00 1.82
4003 7621 1.960689 GCACTGCAGTTCCCCTAAAAA 59.039 47.619 18.94 0.00 0.00 1.94
4004 7622 1.144913 AGCACTGCAGTTCCCCTAAAA 59.855 47.619 18.94 0.00 0.00 1.52
4005 7623 0.771127 AGCACTGCAGTTCCCCTAAA 59.229 50.000 18.94 0.00 0.00 1.85
4006 7624 0.036732 CAGCACTGCAGTTCCCCTAA 59.963 55.000 18.94 0.00 0.00 2.69
4007 7625 1.127567 ACAGCACTGCAGTTCCCCTA 61.128 55.000 18.94 0.00 0.00 3.53
4008 7626 1.999634 AACAGCACTGCAGTTCCCCT 62.000 55.000 18.94 8.41 33.14 4.79
4009 7627 0.250727 TAACAGCACTGCAGTTCCCC 60.251 55.000 18.94 6.04 38.98 4.81
4010 7628 1.604604 TTAACAGCACTGCAGTTCCC 58.395 50.000 18.94 8.74 38.98 3.97
4011 7629 3.923017 AATTAACAGCACTGCAGTTCC 57.077 42.857 18.94 11.50 38.98 3.62
4040 7658 9.515226 AGGAAGAATAACAGCACTATTGTAAAA 57.485 29.630 0.00 0.00 0.00 1.52
4041 7659 9.162764 GAGGAAGAATAACAGCACTATTGTAAA 57.837 33.333 0.00 0.00 0.00 2.01
4042 7660 8.318412 TGAGGAAGAATAACAGCACTATTGTAA 58.682 33.333 0.00 0.00 0.00 2.41
4043 7661 7.847096 TGAGGAAGAATAACAGCACTATTGTA 58.153 34.615 0.00 0.00 0.00 2.41
4044 7662 6.711277 TGAGGAAGAATAACAGCACTATTGT 58.289 36.000 0.00 0.00 0.00 2.71
4045 7663 7.615582 TTGAGGAAGAATAACAGCACTATTG 57.384 36.000 0.00 0.00 0.00 1.90
4047 7665 9.717942 GATATTGAGGAAGAATAACAGCACTAT 57.282 33.333 0.00 0.00 0.00 2.12
4048 7666 8.150945 GGATATTGAGGAAGAATAACAGCACTA 58.849 37.037 0.00 0.00 0.00 2.74
4049 7667 6.995091 GGATATTGAGGAAGAATAACAGCACT 59.005 38.462 0.00 0.00 0.00 4.40
4050 7668 6.767902 TGGATATTGAGGAAGAATAACAGCAC 59.232 38.462 0.00 0.00 0.00 4.40
4051 7669 6.767902 GTGGATATTGAGGAAGAATAACAGCA 59.232 38.462 0.00 0.00 0.00 4.41
4052 7670 6.995091 AGTGGATATTGAGGAAGAATAACAGC 59.005 38.462 0.00 0.00 0.00 4.40
4053 7671 9.482627 GTAGTGGATATTGAGGAAGAATAACAG 57.517 37.037 0.00 0.00 0.00 3.16
4054 7672 9.213777 AGTAGTGGATATTGAGGAAGAATAACA 57.786 33.333 0.00 0.00 0.00 2.41
4055 7673 9.482627 CAGTAGTGGATATTGAGGAAGAATAAC 57.517 37.037 0.00 0.00 0.00 1.89
4056 7674 9.213777 ACAGTAGTGGATATTGAGGAAGAATAA 57.786 33.333 1.92 0.00 0.00 1.40
4057 7675 8.783660 ACAGTAGTGGATATTGAGGAAGAATA 57.216 34.615 1.92 0.00 0.00 1.75
4058 7676 7.682787 ACAGTAGTGGATATTGAGGAAGAAT 57.317 36.000 1.92 0.00 0.00 2.40
4059 7677 8.475639 GTTACAGTAGTGGATATTGAGGAAGAA 58.524 37.037 1.92 0.00 0.00 2.52
4060 7678 7.839705 AGTTACAGTAGTGGATATTGAGGAAGA 59.160 37.037 1.92 0.00 0.00 2.87
4061 7679 8.012957 AGTTACAGTAGTGGATATTGAGGAAG 57.987 38.462 1.92 0.00 0.00 3.46
4062 7680 7.839705 AGAGTTACAGTAGTGGATATTGAGGAA 59.160 37.037 1.92 0.00 0.00 3.36
4063 7681 7.355101 AGAGTTACAGTAGTGGATATTGAGGA 58.645 38.462 1.92 0.00 0.00 3.71
4064 7682 7.504238 AGAGAGTTACAGTAGTGGATATTGAGG 59.496 40.741 1.92 0.00 0.00 3.86
4065 7683 8.349245 CAGAGAGTTACAGTAGTGGATATTGAG 58.651 40.741 1.92 0.00 0.00 3.02
4066 7684 7.834681 ACAGAGAGTTACAGTAGTGGATATTGA 59.165 37.037 1.92 0.00 0.00 2.57
4067 7685 7.918033 CACAGAGAGTTACAGTAGTGGATATTG 59.082 40.741 1.92 0.00 0.00 1.90
4068 7686 7.834681 TCACAGAGAGTTACAGTAGTGGATATT 59.165 37.037 1.92 0.00 0.00 1.28
4069 7687 7.347252 TCACAGAGAGTTACAGTAGTGGATAT 58.653 38.462 1.92 0.00 0.00 1.63
4070 7688 6.718294 TCACAGAGAGTTACAGTAGTGGATA 58.282 40.000 1.92 0.00 0.00 2.59
4071 7689 5.571285 TCACAGAGAGTTACAGTAGTGGAT 58.429 41.667 1.92 0.00 0.00 3.41
4072 7690 4.981812 TCACAGAGAGTTACAGTAGTGGA 58.018 43.478 1.92 0.00 0.00 4.02
4073 7691 5.184096 ACATCACAGAGAGTTACAGTAGTGG 59.816 44.000 1.92 0.00 0.00 4.00
4074 7692 6.260870 ACATCACAGAGAGTTACAGTAGTG 57.739 41.667 0.00 0.00 0.00 2.74
4075 7693 6.374894 GGTACATCACAGAGAGTTACAGTAGT 59.625 42.308 0.00 0.00 0.00 2.73
4076 7694 6.374613 TGGTACATCACAGAGAGTTACAGTAG 59.625 42.308 0.00 0.00 0.00 2.57
4077 7695 6.243148 TGGTACATCACAGAGAGTTACAGTA 58.757 40.000 0.00 0.00 0.00 2.74
4078 7696 5.077564 TGGTACATCACAGAGAGTTACAGT 58.922 41.667 0.00 0.00 0.00 3.55
4079 7697 5.644977 TGGTACATCACAGAGAGTTACAG 57.355 43.478 0.00 0.00 0.00 2.74
4080 7698 5.644977 CTGGTACATCACAGAGAGTTACA 57.355 43.478 0.00 0.00 38.20 2.41


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

AutoCloner maintained by Alex Coulton.