Multiple sequence alignment - TraesCS5B01G384900

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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 TraesCS5B01G384900 chr5B 100.000 3818 0 0 1 3818 563545969 563542152 0.000000e+00 7051
1 TraesCS5B01G384900 chr5B 94.086 1471 60 10 1670 3117 563464143 563465609 0.000000e+00 2209
2 TraesCS5B01G384900 chr5B 90.326 951 49 23 658 1594 563463187 563464108 0.000000e+00 1206
3 TraesCS5B01G384900 chr5B 93.290 462 22 6 3304 3763 563465631 563466085 0.000000e+00 673
4 TraesCS5B01G384900 chr5B 88.362 464 29 10 1 461 563462403 563462844 5.610000e-148 534
5 TraesCS5B01G384900 chr5A 92.552 2296 100 34 645 2889 578835826 578838101 0.000000e+00 3227
6 TraesCS5B01G384900 chr5A 92.123 292 17 5 3254 3543 578841842 578842129 1.280000e-109 407
7 TraesCS5B01G384900 chr5A 90.351 228 18 4 3540 3763 578842253 578842480 2.880000e-76 296
8 TraesCS5B01G384900 chr5A 86.220 254 23 9 398 648 578835492 578835736 8.130000e-67 265
9 TraesCS5B01G384900 chr5A 85.401 274 17 7 1 259 578834110 578834375 2.920000e-66 263
10 TraesCS5B01G384900 chr5A 87.273 110 10 2 3151 3256 578839166 578839275 5.180000e-24 122
11 TraesCS5B01G384900 chr5D 94.679 1184 54 6 1657 2836 459315051 459316229 0.000000e+00 1829
12 TraesCS5B01G384900 chr5D 88.777 793 36 26 734 1507 459314255 459315013 0.000000e+00 922
13 TraesCS5B01G384900 chr5D 82.810 669 66 24 1 648 459310379 459311019 1.550000e-153 553
14 TraesCS5B01G384900 chr5D 92.453 106 8 0 645 750 459312618 459312723 6.610000e-33 152
15 TraesCS5B01G384900 chr3D 91.912 1088 88 0 1748 2835 37969939 37968852 0.000000e+00 1522
16 TraesCS5B01G384900 chr3D 91.793 463 38 0 1000 1462 37970902 37970440 0.000000e+00 645
17 TraesCS5B01G384900 chr3B 91.575 1092 92 0 1748 2839 60366537 60365446 0.000000e+00 1507
18 TraesCS5B01G384900 chr3B 88.304 513 52 4 954 1462 60368109 60367601 3.260000e-170 608
19 TraesCS5B01G384900 chr7A 86.606 1090 142 3 1751 2836 4515760 4516849 0.000000e+00 1201
20 TraesCS5B01G384900 chr7A 86.434 1091 142 5 1751 2836 4556977 4555888 0.000000e+00 1190
21 TraesCS5B01G384900 chr7A 87.905 463 56 0 1000 1462 4559792 4559330 2.590000e-151 545
22 TraesCS5B01G384900 chr7A 87.619 420 49 1 1046 1462 4511363 4511782 5.730000e-133 484
23 TraesCS5B01G384900 chr3A 93.109 595 41 0 2245 2839 48663772 48663178 0.000000e+00 872
24 TraesCS5B01G384900 chr3A 91.023 479 43 0 1748 2226 48664334 48663856 0.000000e+00 647
25 TraesCS5B01G384900 chr3A 88.694 513 50 4 954 1462 48665200 48664692 1.510000e-173 619
26 TraesCS5B01G384900 chr4A 85.073 757 107 5 1751 2502 738980734 738979979 0.000000e+00 767
27 TraesCS5B01G384900 chr4A 87.473 463 58 0 1000 1462 738983793 738983331 5.610000e-148 534
28 TraesCS5B01G384900 chr2B 82.629 213 37 0 2593 2805 439916536 439916324 5.040000e-44 189
29 TraesCS5B01G384900 chrUn 94.872 117 3 2 3544 3658 445191417 445191302 3.030000e-41 180
30 TraesCS5B01G384900 chr6B 94.872 117 3 2 3544 3658 712507437 712507322 3.030000e-41 180
31 TraesCS5B01G384900 chr6B 94.872 117 3 2 3544 3658 712508242 712508127 3.030000e-41 180
32 TraesCS5B01G384900 chr6B 94.872 117 3 2 3544 3658 712513458 712513343 3.030000e-41 180
33 TraesCS5B01G384900 chr6B 94.872 117 3 2 3544 3658 712528271 712528156 3.030000e-41 180
34 TraesCS5B01G384900 chr2D 91.129 124 9 1 3537 3658 405617784 405617661 2.360000e-37 167
35 TraesCS5B01G384900 chr6A 82.822 163 22 3 3538 3695 153507956 153508117 1.430000e-29 141


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 TraesCS5B01G384900 chr5B 563542152 563545969 3817 True 7051.000000 7051 100.000000 1 3818 1 chr5B.!!$R1 3817
1 TraesCS5B01G384900 chr5B 563462403 563466085 3682 False 1155.500000 2209 91.516000 1 3763 4 chr5B.!!$F1 3762
2 TraesCS5B01G384900 chr5A 578834110 578842480 8370 False 763.333333 3227 88.986667 1 3763 6 chr5A.!!$F1 3762
3 TraesCS5B01G384900 chr5D 459310379 459316229 5850 False 864.000000 1829 89.679750 1 2836 4 chr5D.!!$F1 2835
4 TraesCS5B01G384900 chr3D 37968852 37970902 2050 True 1083.500000 1522 91.852500 1000 2835 2 chr3D.!!$R1 1835
5 TraesCS5B01G384900 chr3B 60365446 60368109 2663 True 1057.500000 1507 89.939500 954 2839 2 chr3B.!!$R1 1885
6 TraesCS5B01G384900 chr7A 4555888 4559792 3904 True 867.500000 1190 87.169500 1000 2836 2 chr7A.!!$R1 1836
7 TraesCS5B01G384900 chr7A 4511363 4516849 5486 False 842.500000 1201 87.112500 1046 2836 2 chr7A.!!$F1 1790
8 TraesCS5B01G384900 chr3A 48663178 48665200 2022 True 712.666667 872 90.942000 954 2839 3 chr3A.!!$R1 1885
9 TraesCS5B01G384900 chr4A 738979979 738983793 3814 True 650.500000 767 86.273000 1000 2502 2 chr4A.!!$R1 1502

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
555 1622 0.244450 TAGCTGGTACGTTTGTCCCG 59.756 55.0 0.0 0.0 0.00 5.14 F
1580 9342 0.035739 ACACCTACACGGCCGAAAAT 59.964 50.0 35.9 16.1 35.61 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 9861 0.232303 GACGAAGCAAACACTGTCCG 59.768 55.0 0.0 0.0 0.0 4.79 R
3277 17919 0.033011 CTCTCCCCCTTCTTCTCCGA 60.033 60.0 0.0 0.0 0.0 4.55 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
94 95 1.135286 GCCAATCAAAGTGTGCTAGCC 60.135 52.381 13.29 4.15 0.00 3.93
95 96 2.440409 CCAATCAAAGTGTGCTAGCCT 58.560 47.619 13.29 0.00 0.00 4.58
96 97 3.609853 CCAATCAAAGTGTGCTAGCCTA 58.390 45.455 13.29 0.00 0.00 3.93
97 98 3.624861 CCAATCAAAGTGTGCTAGCCTAG 59.375 47.826 13.29 0.00 0.00 3.02
368 478 6.648879 AGTGTAAAATATTGTGTTGGCAGT 57.351 33.333 0.00 0.00 0.00 4.40
402 1402 5.063817 GCATGCATAAAAACAGGGAAACATC 59.936 40.000 14.21 0.00 0.00 3.06
444 1450 8.624877 CGGAGTTTTACGATTTACTATACATCG 58.375 37.037 0.00 3.50 44.37 3.84
465 1499 4.459337 TCGTCGGCTCATCTATAACATGAT 59.541 41.667 0.00 0.00 29.78 2.45
487 1521 8.980143 TGATTTTATGATGCATGCATGATTAG 57.020 30.769 36.73 3.47 36.70 1.73
492 1526 5.366829 TGATGCATGCATGATTAGTAAGC 57.633 39.130 36.73 18.23 36.70 3.09
494 1528 4.556942 TGCATGCATGATTAGTAAGCAC 57.443 40.909 30.64 8.14 38.12 4.40
507 1541 8.194769 TGATTAGTAAGCACGTCAAGAATGATA 58.805 33.333 0.00 0.00 38.01 2.15
509 1543 5.352284 AGTAAGCACGTCAAGAATGATAGG 58.648 41.667 0.00 0.00 38.01 2.57
510 1544 3.895232 AGCACGTCAAGAATGATAGGT 57.105 42.857 0.00 0.00 38.01 3.08
516 1550 6.037172 GCACGTCAAGAATGATAGGTATTGTT 59.963 38.462 0.00 0.00 38.01 2.83
517 1551 7.621991 CACGTCAAGAATGATAGGTATTGTTC 58.378 38.462 0.00 0.00 38.01 3.18
518 1552 6.475727 ACGTCAAGAATGATAGGTATTGTTCG 59.524 38.462 0.00 0.00 38.01 3.95
555 1622 0.244450 TAGCTGGTACGTTTGTCCCG 59.756 55.000 0.00 0.00 0.00 5.14
574 1641 2.164219 CCGTGCACTTCCAATATGCTTT 59.836 45.455 16.19 0.00 40.13 3.51
575 1642 3.376859 CCGTGCACTTCCAATATGCTTTA 59.623 43.478 16.19 0.00 40.13 1.85
576 1643 4.342772 CGTGCACTTCCAATATGCTTTAC 58.657 43.478 16.19 0.00 40.13 2.01
577 1644 4.142708 CGTGCACTTCCAATATGCTTTACA 60.143 41.667 16.19 0.00 40.13 2.41
578 1645 5.095490 GTGCACTTCCAATATGCTTTACAC 58.905 41.667 10.32 0.00 40.13 2.90
664 3352 5.747675 GGAACTATTCGACCTTACTTACAGC 59.252 44.000 0.00 0.00 0.00 4.40
700 3388 5.163405 ACTGTTGAGCTTAGAGAAGACAACA 60.163 40.000 19.39 19.39 46.49 3.33
783 5025 2.970379 ATGGGCTGCGTCACCATCA 61.970 57.895 2.76 0.00 40.90 3.07
828 5075 2.272471 GCCCACTTGCCCCTACTC 59.728 66.667 0.00 0.00 0.00 2.59
859 5120 6.126768 GGATTGCTATATATACCTCCTGCCAA 60.127 42.308 0.00 0.00 0.00 4.52
860 5121 5.939764 TGCTATATATACCTCCTGCCAAG 57.060 43.478 0.00 0.00 0.00 3.61
861 5122 4.162320 TGCTATATATACCTCCTGCCAAGC 59.838 45.833 0.00 0.00 0.00 4.01
862 5123 4.162320 GCTATATATACCTCCTGCCAAGCA 59.838 45.833 0.00 0.00 36.92 3.91
885 5146 1.849976 GCAGAGCAACTCACACCAGC 61.850 60.000 0.00 0.00 32.06 4.85
888 5149 0.607489 GAGCAACTCACACCAGCCAT 60.607 55.000 0.00 0.00 0.00 4.40
906 5167 0.677731 ATCACCAATCACCACCAGCG 60.678 55.000 0.00 0.00 0.00 5.18
941 5203 5.472478 AGTGCATGCTTATCATTGGTGATAG 59.528 40.000 20.33 0.00 45.44 2.08
942 5204 4.216902 TGCATGCTTATCATTGGTGATAGC 59.783 41.667 20.33 10.32 45.44 2.97
945 5207 3.395607 TGCTTATCATTGGTGATAGCCCT 59.604 43.478 12.72 0.00 45.44 5.19
946 5208 4.597075 TGCTTATCATTGGTGATAGCCCTA 59.403 41.667 12.72 0.00 45.44 3.53
947 5209 5.181748 GCTTATCATTGGTGATAGCCCTAG 58.818 45.833 0.00 0.00 45.44 3.02
948 5210 3.710209 ATCATTGGTGATAGCCCTAGC 57.290 47.619 0.00 0.00 43.18 3.42
949 5211 2.407562 TCATTGGTGATAGCCCTAGCA 58.592 47.619 0.00 0.00 43.56 3.49
957 5219 0.980423 ATAGCCCTAGCAAGCTAGCC 59.020 55.000 20.83 14.26 44.36 3.93
968 5230 2.105930 GCTAGCCGCTGGAGAGTG 59.894 66.667 8.12 0.00 35.14 3.51
1070 5351 3.060615 GCTGCAGGTGCTGAAGGG 61.061 66.667 17.12 0.00 37.60 3.95
1421 5705 2.506061 CCGAGATCCTCAGCCCCAG 61.506 68.421 0.00 0.00 0.00 4.45
1440 5724 4.116328 CGCGTGCTCTCCTTCCGA 62.116 66.667 0.00 0.00 0.00 4.55
1482 9196 6.655848 AGGTAATTAATTAACTCAACGTGGCA 59.344 34.615 18.25 0.00 35.46 4.92
1483 9197 7.338449 AGGTAATTAATTAACTCAACGTGGCAT 59.662 33.333 18.25 0.00 35.46 4.40
1521 9283 4.452455 GCCAGAGTATCCCATAATTGAACG 59.548 45.833 0.00 0.00 33.66 3.95
1527 9289 8.429641 AGAGTATCCCATAATTGAACGTACAAT 58.570 33.333 0.00 0.00 37.74 2.71
1564 9326 4.621068 TGGTACACAGCTACGTATACAC 57.379 45.455 3.32 0.00 0.00 2.90
1580 9342 0.035739 ACACCTACACGGCCGAAAAT 59.964 50.000 35.90 16.10 35.61 1.82
1612 9386 5.512788 CGTAACGTCACGTGGAAAATATACT 59.487 40.000 17.00 0.00 39.99 2.12
1717 9894 0.458543 TGCTTCGTCTGCTCGATTCC 60.459 55.000 0.00 0.00 39.57 3.01
1730 11593 0.247814 CGATTCCTGTTGACGCATGC 60.248 55.000 7.91 7.91 0.00 4.06
1731 11594 0.804364 GATTCCTGTTGACGCATGCA 59.196 50.000 19.57 0.00 0.00 3.96
1732 11595 1.402968 GATTCCTGTTGACGCATGCAT 59.597 47.619 19.57 0.36 0.00 3.96
1733 11596 0.522626 TTCCTGTTGACGCATGCATG 59.477 50.000 22.70 22.70 0.00 4.06
2148 13327 3.710722 CTGCAGGAGAAGGGCGGT 61.711 66.667 5.57 0.00 0.00 5.68
2181 13360 0.684535 TGGACGACAGCAGGATGAAA 59.315 50.000 0.00 0.00 39.69 2.69
2208 13387 2.047274 CTGGACATGTTCGCGGGT 60.047 61.111 6.13 0.00 0.00 5.28
2610 13854 0.245813 GCTACGAGTTCCTCCCGTTT 59.754 55.000 0.00 0.00 37.69 3.60
2799 14043 4.760047 CTCGCCACCCCCTTCGTG 62.760 72.222 0.00 0.00 0.00 4.35
2890 14148 4.748679 GTGTCCGTCGGTCCGTCG 62.749 72.222 21.65 21.65 38.02 5.12
2892 14150 3.118454 GTCCGTCGGTCCGTCGTA 61.118 66.667 25.25 10.84 36.79 3.43
2894 14152 2.099062 CCGTCGGTCCGTCGTAAG 59.901 66.667 25.25 10.03 36.79 2.34
2895 14153 2.680913 CCGTCGGTCCGTCGTAAGT 61.681 63.158 25.25 0.00 36.79 2.24
2896 14154 1.358725 CCGTCGGTCCGTCGTAAGTA 61.359 60.000 25.25 0.00 36.79 2.24
2927 14259 3.796717 CGCGTGTGTACAGTATCATTGAT 59.203 43.478 4.28 4.28 0.00 2.57
2952 14284 3.242576 CGTTGCTTGTGTTGATGTGTGTA 60.243 43.478 0.00 0.00 0.00 2.90
3035 14367 2.296190 CTGGCCGTACTGTATCTGCATA 59.704 50.000 0.00 0.00 0.00 3.14
3036 14368 2.897326 TGGCCGTACTGTATCTGCATAT 59.103 45.455 0.00 0.00 0.00 1.78
3091 14427 5.044428 AGTACGTACTACTGCTGTTTGAG 57.956 43.478 26.36 0.00 34.08 3.02
3120 14456 5.356882 TTCTGTTCTTTGTTTATCCAGCG 57.643 39.130 0.00 0.00 0.00 5.18
3121 14457 4.637276 TCTGTTCTTTGTTTATCCAGCGA 58.363 39.130 0.00 0.00 0.00 4.93
3122 14458 5.245531 TCTGTTCTTTGTTTATCCAGCGAT 58.754 37.500 0.00 0.00 0.00 4.58
3123 14459 5.351465 TCTGTTCTTTGTTTATCCAGCGATC 59.649 40.000 0.00 0.00 0.00 3.69
3139 14515 5.086727 CAGCGATCGACGAGCTAATTATTA 58.913 41.667 21.57 0.00 45.77 0.98
3140 14516 5.567915 CAGCGATCGACGAGCTAATTATTAA 59.432 40.000 21.57 0.00 45.77 1.40
3141 14517 5.568296 AGCGATCGACGAGCTAATTATTAAC 59.432 40.000 21.57 0.00 45.77 2.01
3142 14518 5.341462 GCGATCGACGAGCTAATTATTAACA 59.659 40.000 21.57 0.00 45.77 2.41
3143 14519 6.033619 GCGATCGACGAGCTAATTATTAACAT 59.966 38.462 21.57 0.00 45.77 2.71
3144 14520 7.376535 CGATCGACGAGCTAATTATTAACATG 58.623 38.462 10.26 0.00 45.77 3.21
3145 14521 7.461546 CGATCGACGAGCTAATTATTAACATGG 60.462 40.741 10.26 0.00 45.77 3.66
3146 14522 6.509656 TCGACGAGCTAATTATTAACATGGT 58.490 36.000 0.00 0.00 0.00 3.55
3147 14523 6.982141 TCGACGAGCTAATTATTAACATGGTT 59.018 34.615 0.00 0.00 0.00 3.67
3148 14524 7.493320 TCGACGAGCTAATTATTAACATGGTTT 59.507 33.333 0.00 0.00 0.00 3.27
3188 15257 8.586273 CGATTAGTTGCATGAAACAAAATTAGG 58.414 33.333 18.97 7.72 32.21 2.69
3212 15281 6.672147 GCATTAGCCGATTTCATAGTGAAAT 58.328 36.000 15.55 15.55 45.67 2.17
3213 15282 7.141363 GCATTAGCCGATTTCATAGTGAAATT 58.859 34.615 16.41 6.13 44.40 1.82
3229 15302 5.098211 GTGAAATTAGAATGCTTGTGAGGC 58.902 41.667 0.00 0.00 0.00 4.70
3238 15311 0.514691 GCTTGTGAGGCGAAGAGTTG 59.485 55.000 0.00 0.00 0.00 3.16
3240 15313 2.693069 CTTGTGAGGCGAAGAGTTGAT 58.307 47.619 0.00 0.00 0.00 2.57
3252 15325 4.479619 GAAGAGTTGATTGTTGTGGATGC 58.520 43.478 0.00 0.00 0.00 3.91
3256 17898 0.804364 TGATTGTTGTGGATGCGAGC 59.196 50.000 0.00 0.00 0.00 5.03
3296 17938 0.033011 TCGGAGAAGAAGGGGGAGAG 60.033 60.000 0.00 0.00 0.00 3.20
3304 17946 1.369983 AGAAGGGGGAGAGGGTTACAT 59.630 52.381 0.00 0.00 0.00 2.29
3351 17993 2.337583 CGTGACTTGGTGAGGTACATG 58.662 52.381 0.00 0.00 0.00 3.21
3488 18130 4.935205 TCAAACAGCAAAGCATCTACGTAT 59.065 37.500 0.00 0.00 0.00 3.06
3494 18136 5.007039 CAGCAAAGCATCTACGTATTGACAT 59.993 40.000 8.20 0.00 0.00 3.06
3515 18162 1.816224 TGACATAGACGCTGCACTGTA 59.184 47.619 0.00 0.00 0.00 2.74
3670 18449 8.097038 ACTTCAGACTTTGAAATCTAGTATGCA 58.903 33.333 0.00 0.00 44.84 3.96
3671 18450 9.107177 CTTCAGACTTTGAAATCTAGTATGCAT 57.893 33.333 3.79 3.79 44.84 3.96
3672 18451 8.654230 TCAGACTTTGAAATCTAGTATGCATC 57.346 34.615 0.19 0.00 32.64 3.91
3773 18553 4.883026 CTGAAAGCCAGCATGCAC 57.117 55.556 21.98 8.95 35.89 4.57
3774 18554 2.264124 CTGAAAGCCAGCATGCACT 58.736 52.632 21.98 11.33 35.89 4.40
3775 18555 0.601558 CTGAAAGCCAGCATGCACTT 59.398 50.000 21.98 16.78 35.89 3.16
3776 18556 1.000506 CTGAAAGCCAGCATGCACTTT 59.999 47.619 24.56 24.56 41.61 2.66
3777 18557 1.413445 TGAAAGCCAGCATGCACTTTT 59.587 42.857 24.89 17.35 39.86 2.27
3778 18558 1.796459 GAAAGCCAGCATGCACTTTTG 59.204 47.619 24.89 13.83 39.86 2.44
3781 18561 0.601841 GCCAGCATGCACTTTTGCTT 60.602 50.000 21.98 0.00 46.71 3.91
3782 18562 1.144969 CCAGCATGCACTTTTGCTTG 58.855 50.000 21.98 5.61 46.71 4.01
3789 18569 2.292103 GCACTTTTGCTTGTGTTGGA 57.708 45.000 0.00 0.00 46.17 3.53
3790 18570 1.926510 GCACTTTTGCTTGTGTTGGAC 59.073 47.619 0.00 0.00 46.17 4.02
3791 18571 2.184448 CACTTTTGCTTGTGTTGGACG 58.816 47.619 0.00 0.00 0.00 4.79
3792 18572 1.816224 ACTTTTGCTTGTGTTGGACGT 59.184 42.857 0.00 0.00 0.00 4.34
3793 18573 3.011119 ACTTTTGCTTGTGTTGGACGTA 58.989 40.909 0.00 0.00 0.00 3.57
3794 18574 3.181504 ACTTTTGCTTGTGTTGGACGTAC 60.182 43.478 0.00 0.00 0.00 3.67
3795 18575 1.301423 TTGCTTGTGTTGGACGTACC 58.699 50.000 0.00 0.00 39.54 3.34
3796 18576 0.876777 TGCTTGTGTTGGACGTACCG 60.877 55.000 0.00 0.00 42.61 4.02
3797 18577 1.562575 GCTTGTGTTGGACGTACCGG 61.563 60.000 0.00 0.00 42.61 5.28
3798 18578 0.032403 CTTGTGTTGGACGTACCGGA 59.968 55.000 9.46 0.00 42.61 5.14
3799 18579 0.463204 TTGTGTTGGACGTACCGGAA 59.537 50.000 9.46 0.00 42.61 4.30
3800 18580 0.463204 TGTGTTGGACGTACCGGAAA 59.537 50.000 9.46 0.00 42.61 3.13
3801 18581 1.070445 TGTGTTGGACGTACCGGAAAT 59.930 47.619 9.46 0.00 42.61 2.17
3802 18582 2.145536 GTGTTGGACGTACCGGAAATT 58.854 47.619 9.46 0.00 42.61 1.82
3803 18583 2.549329 GTGTTGGACGTACCGGAAATTT 59.451 45.455 9.46 0.00 42.61 1.82
3804 18584 3.003585 GTGTTGGACGTACCGGAAATTTT 59.996 43.478 9.46 0.00 42.61 1.82
3805 18585 3.250521 TGTTGGACGTACCGGAAATTTTC 59.749 43.478 9.46 0.24 42.61 2.29
3806 18586 2.425539 TGGACGTACCGGAAATTTTCC 58.574 47.619 16.80 16.80 46.62 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.905337 AGCCTAGCTTCACGGAACCT 60.905 55.000 0.00 0.00 33.89 3.50
94 95 3.495001 GCGGCAAAAGGAACTATAGCTAG 59.505 47.826 0.00 0.00 38.49 3.42
95 96 3.463944 GCGGCAAAAGGAACTATAGCTA 58.536 45.455 0.00 0.00 38.49 3.32
96 97 2.289565 GCGGCAAAAGGAACTATAGCT 58.710 47.619 0.00 0.00 38.49 3.32
97 98 1.333931 GGCGGCAAAAGGAACTATAGC 59.666 52.381 3.07 0.00 38.49 2.97
98 99 1.947456 GGGCGGCAAAAGGAACTATAG 59.053 52.381 12.47 0.00 38.49 1.31
99 100 1.282447 TGGGCGGCAAAAGGAACTATA 59.718 47.619 12.47 0.00 38.49 1.31
100 101 0.039035 TGGGCGGCAAAAGGAACTAT 59.961 50.000 12.47 0.00 38.49 2.12
177 183 8.519526 AGATTGAGAGAGTCTGTAACTGTTTAG 58.480 37.037 0.00 0.00 38.74 1.85
368 478 5.247110 TGTTTTTATGCATGCCCCTAGAAAA 59.753 36.000 16.68 9.55 0.00 2.29
444 1450 7.426929 AAAATCATGTTATAGATGAGCCGAC 57.573 36.000 0.00 0.00 33.38 4.79
465 1499 9.902196 CTTACTAATCATGCATGCATCATAAAA 57.098 29.630 30.07 16.17 33.90 1.52
487 1521 5.109903 ACCTATCATTCTTGACGTGCTTAC 58.890 41.667 0.00 0.00 33.85 2.34
490 1524 3.895232 ACCTATCATTCTTGACGTGCT 57.105 42.857 0.00 0.00 33.85 4.40
492 1526 7.515215 CGAACAATACCTATCATTCTTGACGTG 60.515 40.741 0.00 0.00 33.85 4.49
494 1528 6.475727 ACGAACAATACCTATCATTCTTGACG 59.524 38.462 0.00 0.00 33.85 4.35
507 1541 6.827727 AGGAGCAATATAACGAACAATACCT 58.172 36.000 0.00 0.00 0.00 3.08
509 1543 7.916552 ACAAGGAGCAATATAACGAACAATAC 58.083 34.615 0.00 0.00 0.00 1.89
510 1544 9.772973 ATACAAGGAGCAATATAACGAACAATA 57.227 29.630 0.00 0.00 0.00 1.90
516 1550 7.090808 CAGCTATACAAGGAGCAATATAACGA 58.909 38.462 0.00 0.00 41.36 3.85
517 1551 6.311445 CCAGCTATACAAGGAGCAATATAACG 59.689 42.308 0.00 0.00 41.36 3.18
518 1552 7.162082 ACCAGCTATACAAGGAGCAATATAAC 58.838 38.462 0.00 0.00 41.36 1.89
555 1622 5.095490 GTGTAAAGCATATTGGAAGTGCAC 58.905 41.667 9.40 9.40 41.19 4.57
614 1681 3.006940 TGCAAGTGGAAAGGTATAAGCG 58.993 45.455 0.00 0.00 0.00 4.68
700 3388 3.503363 CACTGTGTGATGGTTAGTGCAAT 59.497 43.478 0.00 0.00 35.23 3.56
783 5025 2.047274 CGAGTTGGCCCACGTCAT 60.047 61.111 0.00 0.00 0.00 3.06
804 5046 4.424711 GGCAAGTGGGCGATGGGA 62.425 66.667 0.00 0.00 33.57 4.37
828 5075 7.566879 AGGAGGTATATATAGCAATCCTTGAGG 59.433 40.741 19.66 0.00 33.99 3.86
859 5120 1.671704 GAGTTGCTCTGCTGCTGCT 60.672 57.895 17.00 0.00 40.48 4.24
860 5121 1.964891 TGAGTTGCTCTGCTGCTGC 60.965 57.895 8.89 8.89 40.20 5.25
861 5122 0.883370 TGTGAGTTGCTCTGCTGCTG 60.883 55.000 0.00 0.00 0.00 4.41
862 5123 0.883814 GTGTGAGTTGCTCTGCTGCT 60.884 55.000 0.00 0.00 0.00 4.24
885 5146 1.466856 CTGGTGGTGATTGGTGATGG 58.533 55.000 0.00 0.00 0.00 3.51
888 5149 1.302431 CGCTGGTGGTGATTGGTGA 60.302 57.895 0.00 0.00 0.00 4.02
906 5167 1.012841 GCATGCACTGGTAGAAGAGC 58.987 55.000 14.21 0.00 34.72 4.09
941 5203 2.280457 CGGCTAGCTTGCTAGGGC 60.280 66.667 25.23 18.09 39.26 5.19
942 5204 2.280457 GCGGCTAGCTTGCTAGGG 60.280 66.667 25.23 8.11 44.04 3.53
957 5219 1.153862 GCTCACTCACTCTCCAGCG 60.154 63.158 0.00 0.00 0.00 5.18
989 5266 2.501723 AGCTCGTCCATGTTCTACCAAT 59.498 45.455 0.00 0.00 0.00 3.16
997 5274 0.601558 ACGTACAGCTCGTCCATGTT 59.398 50.000 0.00 0.00 36.85 2.71
998 5275 2.264124 ACGTACAGCTCGTCCATGT 58.736 52.632 0.00 0.00 36.85 3.21
1070 5351 1.520787 CGCATCGGGTTCAGGTACC 60.521 63.158 2.73 2.73 37.47 3.34
1125 5409 3.135457 TGGTGCATGCTGCCGATG 61.135 61.111 20.33 0.00 44.23 3.84
1440 5724 0.972983 CCTCGTCCTCCCTGATGTGT 60.973 60.000 0.00 0.00 0.00 3.72
1527 9289 8.627403 GCTGTGTACCACTATATACTTGACTAA 58.373 37.037 0.00 0.00 35.11 2.24
1540 9302 5.294306 GTGTATACGTAGCTGTGTACCACTA 59.706 44.000 16.38 1.87 36.09 2.74
1557 9319 1.024271 TCGGCCGTGTAGGTGTATAC 58.976 55.000 27.15 0.00 43.70 1.47
1563 9325 1.900245 AAATTTTCGGCCGTGTAGGT 58.100 45.000 27.15 5.08 43.70 3.08
1564 9326 4.422546 TTTAAATTTTCGGCCGTGTAGG 57.577 40.909 27.15 0.00 44.97 3.18
1607 9381 1.700186 TGTGGTTGTGGTGCCAGTATA 59.300 47.619 0.00 0.00 35.14 1.47
1612 9386 0.256177 TAGTTGTGGTTGTGGTGCCA 59.744 50.000 0.00 0.00 0.00 4.92
1687 9861 0.232303 GACGAAGCAAACACTGTCCG 59.768 55.000 0.00 0.00 0.00 4.79
1717 9894 4.066769 GCATGCATGCGTCAACAG 57.933 55.556 33.99 3.05 44.67 3.16
1730 11593 4.167554 TGCATATATGTGTGCATGCATG 57.832 40.909 25.64 22.70 45.84 4.06
2181 13360 1.219773 ACATGTCCAGGATGATGGCT 58.780 50.000 13.57 0.00 39.69 4.75
2238 13417 2.040464 AGCTCCGACATCCCCCAT 60.040 61.111 0.00 0.00 0.00 4.00
2487 13731 2.823829 GATGGCCCACGCGTTGATC 61.824 63.158 10.22 1.42 35.02 2.92
2508 13752 2.666098 CCAGTACTTGGGGTCCCGG 61.666 68.421 0.48 0.00 43.75 5.73
2890 14148 4.532903 GCGCGCGCACGTACTTAC 62.533 66.667 46.11 15.61 42.83 2.34
2927 14259 3.375610 ACACATCAACACAAGCAACGTAA 59.624 39.130 0.00 0.00 0.00 3.18
3004 14336 3.249973 TACGGCCAGATCGATCGCG 62.250 63.158 19.33 14.24 39.35 5.87
3005 14337 1.729838 GTACGGCCAGATCGATCGC 60.730 63.158 19.33 16.80 0.00 4.58
3035 14367 7.147846 GGGAGTAACAACAATCCAATCATTCAT 60.148 37.037 0.00 0.00 33.24 2.57
3036 14368 6.152661 GGGAGTAACAACAATCCAATCATTCA 59.847 38.462 0.00 0.00 33.24 2.57
3113 14449 0.885150 TAGCTCGTCGATCGCTGGAT 60.885 55.000 16.76 1.87 39.67 3.41
3117 14453 3.833545 ATAATTAGCTCGTCGATCGCT 57.166 42.857 11.09 12.88 39.67 4.93
3120 14456 7.328737 ACCATGTTAATAATTAGCTCGTCGATC 59.671 37.037 0.00 0.00 0.00 3.69
3121 14457 7.152645 ACCATGTTAATAATTAGCTCGTCGAT 58.847 34.615 0.00 0.00 0.00 3.59
3122 14458 6.509656 ACCATGTTAATAATTAGCTCGTCGA 58.490 36.000 0.00 0.00 0.00 4.20
3123 14459 6.764877 ACCATGTTAATAATTAGCTCGTCG 57.235 37.500 0.00 0.00 0.00 5.12
3139 14515 1.408702 AGCAAACGCAGAAACCATGTT 59.591 42.857 0.00 0.00 0.00 2.71
3140 14516 1.032014 AGCAAACGCAGAAACCATGT 58.968 45.000 0.00 0.00 0.00 3.21
3141 14517 2.987413 TAGCAAACGCAGAAACCATG 57.013 45.000 0.00 0.00 0.00 3.66
3142 14518 2.095853 CGATAGCAAACGCAGAAACCAT 59.904 45.455 0.00 0.00 0.00 3.55
3143 14519 1.463056 CGATAGCAAACGCAGAAACCA 59.537 47.619 0.00 0.00 0.00 3.67
3144 14520 1.730064 TCGATAGCAAACGCAGAAACC 59.270 47.619 0.00 0.00 0.00 3.27
3145 14521 3.658351 ATCGATAGCAAACGCAGAAAC 57.342 42.857 0.00 0.00 0.00 2.78
3146 14522 4.868171 ACTAATCGATAGCAAACGCAGAAA 59.132 37.500 0.00 0.00 34.78 2.52
3147 14523 4.430007 ACTAATCGATAGCAAACGCAGAA 58.570 39.130 0.00 0.00 34.78 3.02
3148 14524 4.041740 ACTAATCGATAGCAAACGCAGA 57.958 40.909 0.00 0.00 34.78 4.26
3188 15257 5.673337 TTCACTATGAAATCGGCTAATGC 57.327 39.130 0.00 0.00 32.71 3.56
3212 15281 2.760634 TCGCCTCACAAGCATTCTAA 57.239 45.000 0.00 0.00 0.00 2.10
3213 15282 2.233676 TCTTCGCCTCACAAGCATTCTA 59.766 45.455 0.00 0.00 0.00 2.10
3215 15284 1.396301 CTCTTCGCCTCACAAGCATTC 59.604 52.381 0.00 0.00 0.00 2.67
3217 15286 0.322975 ACTCTTCGCCTCACAAGCAT 59.677 50.000 0.00 0.00 0.00 3.79
3218 15287 0.106708 AACTCTTCGCCTCACAAGCA 59.893 50.000 0.00 0.00 0.00 3.91
3229 15302 4.715896 CATCCACAACAATCAACTCTTCG 58.284 43.478 0.00 0.00 0.00 3.79
3238 15311 0.247814 CGCTCGCATCCACAACAATC 60.248 55.000 0.00 0.00 0.00 2.67
3240 15313 2.965147 GCGCTCGCATCCACAACAA 61.965 57.895 9.59 0.00 41.49 2.83
3277 17919 0.033011 CTCTCCCCCTTCTTCTCCGA 60.033 60.000 0.00 0.00 0.00 4.55
3278 17920 1.045911 CCTCTCCCCCTTCTTCTCCG 61.046 65.000 0.00 0.00 0.00 4.63
3280 17922 0.043485 ACCCTCTCCCCCTTCTTCTC 59.957 60.000 0.00 0.00 0.00 2.87
3286 17928 1.082194 TCATGTAACCCTCTCCCCCTT 59.918 52.381 0.00 0.00 0.00 3.95
3287 17929 0.722676 TCATGTAACCCTCTCCCCCT 59.277 55.000 0.00 0.00 0.00 4.79
3296 17938 0.036765 TCACTGCCGTCATGTAACCC 60.037 55.000 0.00 0.00 0.00 4.11
3304 17946 2.910479 ACCGAGTCACTGCCGTCA 60.910 61.111 0.00 0.00 0.00 4.35
3488 18130 2.672874 GCAGCGTCTATGTCAATGTCAA 59.327 45.455 0.00 0.00 0.00 3.18
3494 18136 1.000843 ACAGTGCAGCGTCTATGTCAA 59.999 47.619 0.00 0.00 0.00 3.18
3670 18449 4.101119 ACTCCCTCCGATCATTTTTACGAT 59.899 41.667 0.00 0.00 0.00 3.73
3671 18450 3.449737 ACTCCCTCCGATCATTTTTACGA 59.550 43.478 0.00 0.00 0.00 3.43
3672 18451 3.793559 ACTCCCTCCGATCATTTTTACG 58.206 45.455 0.00 0.00 0.00 3.18
3771 18551 2.184448 CGTCCAACACAAGCAAAAGTG 58.816 47.619 0.00 0.00 41.40 3.16
3772 18552 1.816224 ACGTCCAACACAAGCAAAAGT 59.184 42.857 0.00 0.00 0.00 2.66
3773 18553 2.559998 ACGTCCAACACAAGCAAAAG 57.440 45.000 0.00 0.00 0.00 2.27
3774 18554 2.097791 GGTACGTCCAACACAAGCAAAA 59.902 45.455 0.00 0.00 35.97 2.44
3775 18555 1.671845 GGTACGTCCAACACAAGCAAA 59.328 47.619 0.00 0.00 35.97 3.68
3776 18556 1.301423 GGTACGTCCAACACAAGCAA 58.699 50.000 0.00 0.00 35.97 3.91
3777 18557 2.994990 GGTACGTCCAACACAAGCA 58.005 52.632 0.00 0.00 35.97 3.91


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

AutoCloner maintained by Alex Coulton.