Multiple sequence alignment - TraesCS5D01G335800

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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 TraesCS5D01G335800 chr5D 100.000 4089 0 0 1 4089 425085167 425089255 0.000000e+00 7552.0
1 TraesCS5D01G335800 chr5A 92.273 3598 145 44 1 3546 539100666 539104182 0.000000e+00 4981.0
2 TraesCS5D01G335800 chr5A 93.188 367 13 5 3730 4089 539104718 539105079 2.800000e-146 529.0
3 TraesCS5D01G335800 chr5A 79.167 192 31 7 3889 4074 552787799 552787987 1.540000e-24 124.0
4 TraesCS5D01G335800 chr5A 94.286 35 2 0 3552 3586 539104368 539104402 2.000000e-03 54.7
5 TraesCS5D01G335800 chr5B 90.694 3342 144 57 372 3626 514287568 514290829 0.000000e+00 4294.0
6 TraesCS5D01G335800 chr5B 85.333 600 49 17 1055 1653 415393472 415394033 5.890000e-163 584.0
7 TraesCS5D01G335800 chr5B 89.041 365 20 5 3730 4089 514291071 514291420 6.280000e-118 435.0
8 TraesCS5D01G335800 chr5B 100.000 34 0 0 3643 3676 514290862 514290895 3.410000e-06 63.9
9 TraesCS5D01G335800 chr5B 100.000 29 0 0 2788 2816 514290870 514290898 2.000000e-03 54.7
10 TraesCS5D01G335800 chr7A 87.562 603 47 9 1052 1653 617958015 617958590 0.000000e+00 673.0
11 TraesCS5D01G335800 chr3B 87.333 600 49 6 1055 1653 782859207 782859780 0.000000e+00 662.0
12 TraesCS5D01G335800 chr2A 88.180 533 34 9 1122 1653 3343505 3343001 3.490000e-170 608.0
13 TraesCS5D01G335800 chr2A 80.000 210 21 9 1050 1252 577480648 577480453 7.130000e-28 135.0
14 TraesCS5D01G335800 chr2A 80.000 190 33 3 3904 4089 732956253 732956065 7.130000e-28 135.0
15 TraesCS5D01G335800 chr2A 78.523 149 29 2 3944 4089 699412514 699412662 1.210000e-15 95.3
16 TraesCS5D01G335800 chr2A 75.393 191 38 7 3901 4089 524966062 524966245 2.620000e-12 84.2
17 TraesCS5D01G335800 chr1A 82.096 229 39 1 1449 1677 514691046 514691272 1.160000e-45 195.0
18 TraesCS5D01G335800 chr7B 92.969 128 9 0 1055 1182 381893345 381893218 1.940000e-43 187.0
19 TraesCS5D01G335800 chr6A 79.791 287 32 15 1016 1293 426863412 426863143 6.980000e-43 185.0
20 TraesCS5D01G335800 chr1D 80.349 229 43 1 1449 1677 418044694 418044920 5.430000e-39 172.0
21 TraesCS5D01G335800 chr4B 89.844 128 13 0 1055 1182 180292720 180292847 9.090000e-37 165.0
22 TraesCS5D01G335800 chr4B 85.714 56 8 0 3730 3785 636642328 636642273 4.410000e-05 60.2
23 TraesCS5D01G335800 chrUn 79.688 192 34 4 3900 4087 20500288 20500478 2.560000e-27 134.0
24 TraesCS5D01G335800 chr4A 89.362 94 10 0 3996 4089 584037641 584037548 7.180000e-23 119.0
25 TraesCS5D01G335800 chr2B 77.249 189 40 3 3900 4087 634609367 634609553 1.550000e-19 108.0
26 TraesCS5D01G335800 chr2D 76.963 191 41 2 3900 4087 145394608 145394418 5.590000e-19 106.0
27 TraesCS5D01G335800 chr6B 80.303 132 14 6 3736 3855 204111650 204111781 5.630000e-14 89.8
28 TraesCS5D01G335800 chr7D 90.196 51 5 0 3730 3780 30761820 30761870 2.640000e-07 67.6
29 TraesCS5D01G335800 chr1B 100.000 31 0 0 1623 1653 627842917 627842947 1.590000e-04 58.4


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 TraesCS5D01G335800 chr5D 425085167 425089255 4088 False 7552.0 7552 100.00000 1 4089 1 chr5D.!!$F1 4088
1 TraesCS5D01G335800 chr5A 539100666 539105079 4413 False 1854.9 4981 93.24900 1 4089 3 chr5A.!!$F2 4088
2 TraesCS5D01G335800 chr5B 514287568 514291420 3852 False 1211.9 4294 94.93375 372 4089 4 chr5B.!!$F2 3717
3 TraesCS5D01G335800 chr5B 415393472 415394033 561 False 584.0 584 85.33300 1055 1653 1 chr5B.!!$F1 598
4 TraesCS5D01G335800 chr7A 617958015 617958590 575 False 673.0 673 87.56200 1052 1653 1 chr7A.!!$F1 601
5 TraesCS5D01G335800 chr3B 782859207 782859780 573 False 662.0 662 87.33300 1055 1653 1 chr3B.!!$F1 598
6 TraesCS5D01G335800 chr2A 3343001 3343505 504 True 608.0 608 88.18000 1122 1653 1 chr2A.!!$R1 531

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
350 355 0.179702 ATGCTCATCGCCACATCAGT 59.820 50.0 0.0 0.0 38.05 3.41 F
1372 1426 0.040067 GCGTCCTCTTTTTGTGCTGG 60.040 55.0 0.0 0.0 0.00 4.85 F
1938 2018 0.258194 TCCTCGTAAGTCCCTCCCTC 59.742 60.0 0.0 0.0 39.48 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2113 0.035152 AGCACAATCCAATCGAGCCA 60.035 50.0 0.00 0.0 0.0 4.75 R
2680 2778 0.879400 CGTGATGCATCTGAGAGGGC 60.879 60.0 26.32 0.0 0.0 5.19 R
3714 4068 0.106708 GCAGGCCGAGAATATGTCCA 59.893 55.0 0.00 0.0 0.0 4.02 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
24 25 2.624029 CCAGCCATACCTGGTTTCCAAT 60.624 50.000 3.84 0.00 45.87 3.16
47 48 2.159407 TCGCACGTGTTATTCCGATACA 60.159 45.455 18.38 0.00 0.00 2.29
54 55 4.547587 CGTGTTATTCCGATACAGAAACGC 60.548 45.833 0.00 0.00 0.00 4.84
102 103 5.737860 TCAGCATACTTGACATTCATCACT 58.262 37.500 0.00 0.00 0.00 3.41
139 140 4.564782 ACTGAGCAGATGAAGATTTCCA 57.435 40.909 4.21 0.00 0.00 3.53
151 152 6.001449 TGAAGATTTCCATTACCCGAATCT 57.999 37.500 0.00 0.00 38.36 2.40
154 155 7.715249 TGAAGATTTCCATTACCCGAATCTAAG 59.285 37.037 0.00 0.00 36.38 2.18
173 174 2.280797 GAACGGCACAGGTGAGCA 60.281 61.111 3.10 0.00 33.19 4.26
179 180 1.064505 CGGCACAGGTGAGCATAATTG 59.935 52.381 3.10 0.00 33.19 2.32
189 190 7.094634 ACAGGTGAGCATAATTGAAGTTTGTAG 60.095 37.037 0.00 0.00 0.00 2.74
191 192 5.734498 GTGAGCATAATTGAAGTTTGTAGCG 59.266 40.000 0.00 0.00 0.00 4.26
229 230 0.400213 AATGCCCTTTCCGTCTCACA 59.600 50.000 0.00 0.00 0.00 3.58
247 252 1.602377 ACACGCTTTTAGCCAGTCAAC 59.398 47.619 0.00 0.00 38.18 3.18
249 254 0.521735 CGCTTTTAGCCAGTCAACCC 59.478 55.000 0.00 0.00 38.18 4.11
275 280 0.928229 GAATCCGCACGCGTTATTCT 59.072 50.000 10.22 0.00 37.16 2.40
340 345 2.191802 GTCTGACACTCATGCTCATCG 58.808 52.381 2.24 0.00 0.00 3.84
350 355 0.179702 ATGCTCATCGCCACATCAGT 59.820 50.000 0.00 0.00 38.05 3.41
365 370 2.203788 AGTTCGGCCCTCCTCACA 60.204 61.111 0.00 0.00 0.00 3.58
397 402 0.608130 TCACTAACTCACCGCTGCAT 59.392 50.000 0.00 0.00 0.00 3.96
449 454 1.949257 CGGCAAAGAACACCCACTC 59.051 57.895 0.00 0.00 0.00 3.51
461 466 2.892852 ACACCCACTCAAACATCCATTG 59.107 45.455 0.00 0.00 0.00 2.82
473 478 2.897207 CCATTGGCCATGGCACTG 59.103 61.111 36.56 27.14 46.59 3.66
474 479 1.683025 CCATTGGCCATGGCACTGA 60.683 57.895 36.56 19.46 46.59 3.41
491 496 1.153958 GAAGCTTGGCATGCGGAAC 60.154 57.895 18.23 1.17 35.28 3.62
503 508 3.794270 CGGAACACGCGATTCCAT 58.206 55.556 31.58 8.89 45.15 3.41
513 518 3.289128 CGATTCCATCGCCTTGCTA 57.711 52.632 0.00 0.00 46.55 3.49
514 519 1.143305 CGATTCCATCGCCTTGCTAG 58.857 55.000 0.00 0.00 46.55 3.42
526 531 4.504596 TGCTAGGCCCCGGCATTG 62.505 66.667 8.23 2.48 44.11 2.82
679 685 2.125673 GCGAAACCGAGGCAGCTA 60.126 61.111 0.00 0.00 0.00 3.32
716 728 3.826754 CGACCGGCTGCTGCTAGA 61.827 66.667 15.64 0.00 39.59 2.43
717 729 2.105930 GACCGGCTGCTGCTAGAG 59.894 66.667 15.64 4.60 39.59 2.43
748 763 0.373716 GCGAGGCGGTCTATGTTTTG 59.626 55.000 0.00 0.00 0.00 2.44
752 767 3.058501 CGAGGCGGTCTATGTTTTGTTTT 60.059 43.478 0.00 0.00 0.00 2.43
754 769 4.866921 AGGCGGTCTATGTTTTGTTTTTC 58.133 39.130 0.00 0.00 0.00 2.29
755 770 4.339814 AGGCGGTCTATGTTTTGTTTTTCA 59.660 37.500 0.00 0.00 0.00 2.69
756 771 4.679654 GGCGGTCTATGTTTTGTTTTTCAG 59.320 41.667 0.00 0.00 0.00 3.02
757 772 5.506649 GGCGGTCTATGTTTTGTTTTTCAGA 60.507 40.000 0.00 0.00 0.00 3.27
759 774 6.088085 GCGGTCTATGTTTTGTTTTTCAGATG 59.912 38.462 0.00 0.00 0.00 2.90
760 775 7.359595 CGGTCTATGTTTTGTTTTTCAGATGA 58.640 34.615 0.00 0.00 0.00 2.92
761 776 7.860373 CGGTCTATGTTTTGTTTTTCAGATGAA 59.140 33.333 0.00 0.00 0.00 2.57
810 851 1.080705 ACGCGAAGGAGAAGGAACG 60.081 57.895 15.93 0.00 0.00 3.95
932 973 1.447314 GACCCCAACGGCTAGTTCG 60.447 63.158 6.17 6.17 42.02 3.95
1013 1054 0.259938 AATCCAATGCCACCTCCCTC 59.740 55.000 0.00 0.00 0.00 4.30
1014 1055 1.649271 ATCCAATGCCACCTCCCTCC 61.649 60.000 0.00 0.00 0.00 4.30
1015 1056 2.276740 CAATGCCACCTCCCTCCC 59.723 66.667 0.00 0.00 0.00 4.30
1016 1057 3.023735 AATGCCACCTCCCTCCCC 61.024 66.667 0.00 0.00 0.00 4.81
1017 1058 3.603330 AATGCCACCTCCCTCCCCT 62.603 63.158 0.00 0.00 0.00 4.79
1018 1059 4.741239 TGCCACCTCCCTCCCCTC 62.741 72.222 0.00 0.00 0.00 4.30
1020 1061 4.825679 CCACCTCCCTCCCCTCCC 62.826 77.778 0.00 0.00 0.00 4.30
1038 1079 4.803908 CTCCCTCCCCCAAAGCGC 62.804 72.222 0.00 0.00 0.00 5.92
1057 1102 4.148825 CGTCCGCTTCCTCCCCTG 62.149 72.222 0.00 0.00 0.00 4.45
1128 1173 0.114560 GGGGGAGATCTGATCCGGTA 59.885 60.000 13.83 0.00 37.75 4.02
1158 1203 1.317431 CCATGATGCACCACCACCAG 61.317 60.000 0.00 0.00 0.00 4.00
1368 1422 1.002468 CAGGTGCGTCCTCTTTTTGTG 60.002 52.381 0.00 0.00 46.24 3.33
1369 1423 0.317854 GGTGCGTCCTCTTTTTGTGC 60.318 55.000 0.00 0.00 0.00 4.57
1370 1424 0.663153 GTGCGTCCTCTTTTTGTGCT 59.337 50.000 0.00 0.00 0.00 4.40
1371 1425 0.662619 TGCGTCCTCTTTTTGTGCTG 59.337 50.000 0.00 0.00 0.00 4.41
1372 1426 0.040067 GCGTCCTCTTTTTGTGCTGG 60.040 55.000 0.00 0.00 0.00 4.85
1373 1427 1.593196 CGTCCTCTTTTTGTGCTGGA 58.407 50.000 0.00 0.00 0.00 3.86
1374 1428 1.532868 CGTCCTCTTTTTGTGCTGGAG 59.467 52.381 0.00 0.00 0.00 3.86
1375 1429 1.268079 GTCCTCTTTTTGTGCTGGAGC 59.732 52.381 0.00 0.00 42.50 4.70
1376 1430 1.143684 TCCTCTTTTTGTGCTGGAGCT 59.856 47.619 0.00 0.00 42.66 4.09
1377 1431 1.959282 CCTCTTTTTGTGCTGGAGCTT 59.041 47.619 0.00 0.00 42.66 3.74
1378 1432 2.363359 CCTCTTTTTGTGCTGGAGCTTT 59.637 45.455 0.00 0.00 42.66 3.51
1379 1433 3.378339 CTCTTTTTGTGCTGGAGCTTTG 58.622 45.455 0.00 0.00 42.66 2.77
1380 1434 1.862827 CTTTTTGTGCTGGAGCTTTGC 59.137 47.619 0.00 0.00 42.66 3.68
1381 1435 1.113788 TTTTGTGCTGGAGCTTTGCT 58.886 45.000 0.00 0.00 43.88 3.91
1382 1436 1.113788 TTTGTGCTGGAGCTTTGCTT 58.886 45.000 0.00 0.00 39.88 3.91
1383 1437 1.113788 TTGTGCTGGAGCTTTGCTTT 58.886 45.000 0.00 0.00 39.88 3.51
1384 1438 1.113788 TGTGCTGGAGCTTTGCTTTT 58.886 45.000 0.00 0.00 39.88 2.27
1385 1439 1.481772 TGTGCTGGAGCTTTGCTTTTT 59.518 42.857 0.00 0.00 39.88 1.94
1429 1495 4.559063 CTGATGGCCGGGGCTGAG 62.559 72.222 22.12 10.47 41.60 3.35
1435 1501 4.344865 GCCGGGGCTGAGGTTTGA 62.345 66.667 2.18 0.00 38.26 2.69
1436 1502 2.677228 CCGGGGCTGAGGTTTGAT 59.323 61.111 0.00 0.00 0.00 2.57
1476 1546 1.001641 GCAGCTGGTGGACAAGGAT 60.002 57.895 17.12 0.00 0.00 3.24
1758 1834 7.154656 GGATGGCAACTCAATATTTTAATCCC 58.845 38.462 0.00 0.00 37.61 3.85
1761 1837 6.438741 TGGCAACTCAATATTTTAATCCCACA 59.561 34.615 0.00 0.00 37.61 4.17
1931 2011 0.971447 ACCAGGCTCCTCGTAAGTCC 60.971 60.000 0.00 0.00 39.48 3.85
1934 2014 0.396001 AGGCTCCTCGTAAGTCCCTC 60.396 60.000 0.00 0.00 39.48 4.30
1935 2015 1.393487 GGCTCCTCGTAAGTCCCTCC 61.393 65.000 0.00 0.00 39.48 4.30
1936 2016 1.393487 GCTCCTCGTAAGTCCCTCCC 61.393 65.000 0.00 0.00 39.48 4.30
1937 2017 0.259356 CTCCTCGTAAGTCCCTCCCT 59.741 60.000 0.00 0.00 39.48 4.20
1938 2018 0.258194 TCCTCGTAAGTCCCTCCCTC 59.742 60.000 0.00 0.00 39.48 4.30
1939 2019 0.259356 CCTCGTAAGTCCCTCCCTCT 59.741 60.000 0.00 0.00 39.48 3.69
1940 2020 1.682740 CTCGTAAGTCCCTCCCTCTC 58.317 60.000 0.00 0.00 39.48 3.20
1941 2021 1.213430 CTCGTAAGTCCCTCCCTCTCT 59.787 57.143 0.00 0.00 39.48 3.10
1942 2022 1.212441 TCGTAAGTCCCTCCCTCTCTC 59.788 57.143 0.00 0.00 39.48 3.20
1943 2023 1.213430 CGTAAGTCCCTCCCTCTCTCT 59.787 57.143 0.00 0.00 0.00 3.10
1944 2024 2.747135 CGTAAGTCCCTCCCTCTCTCTC 60.747 59.091 0.00 0.00 0.00 3.20
1969 2049 6.720748 CCCCCTTCCATTCAAAATTTCAAATT 59.279 34.615 0.00 0.00 0.00 1.82
1984 2064 7.912056 ATTTCAAATTCAGTTCAGATCGAGA 57.088 32.000 0.00 0.00 0.00 4.04
2026 2106 9.378551 GATATGGTAAGAATCAATGGCGTAATA 57.621 33.333 0.00 0.00 0.00 0.98
2028 2108 8.635765 ATGGTAAGAATCAATGGCGTAATAAT 57.364 30.769 0.00 0.00 0.00 1.28
2029 2109 9.733556 ATGGTAAGAATCAATGGCGTAATAATA 57.266 29.630 0.00 0.00 0.00 0.98
2030 2110 9.562408 TGGTAAGAATCAATGGCGTAATAATAA 57.438 29.630 0.00 0.00 0.00 1.40
2031 2111 9.821662 GGTAAGAATCAATGGCGTAATAATAAC 57.178 33.333 0.00 0.00 0.00 1.89
2034 2114 9.950680 AAGAATCAATGGCGTAATAATAACTTG 57.049 29.630 0.00 0.00 0.00 3.16
2035 2115 8.567948 AGAATCAATGGCGTAATAATAACTTGG 58.432 33.333 0.00 0.00 0.00 3.61
2551 2631 3.880846 GGCAAGAAGATGGCCGCG 61.881 66.667 0.00 0.00 39.79 6.46
3034 3147 1.079057 GGCGGTGAAGGAGAAGGTC 60.079 63.158 0.00 0.00 0.00 3.85
3037 3150 1.248785 CGGTGAAGGAGAAGGTCGGA 61.249 60.000 0.00 0.00 0.00 4.55
3306 3431 3.398406 TCAGTTTGCTGCTGATTCGTTA 58.602 40.909 0.00 0.00 42.29 3.18
3307 3432 4.002982 TCAGTTTGCTGCTGATTCGTTAT 58.997 39.130 0.00 0.00 42.29 1.89
3309 3434 5.641636 TCAGTTTGCTGCTGATTCGTTATTA 59.358 36.000 0.00 0.00 42.29 0.98
3312 3443 8.122330 CAGTTTGCTGCTGATTCGTTATTATTA 58.878 33.333 0.00 0.00 35.77 0.98
3556 3720 6.459066 TCAGAAATTTAGCTCTGGATATCGG 58.541 40.000 0.00 0.00 39.67 4.18
3626 3949 1.528129 GAGGTCCAAGTTCAGGCAAG 58.472 55.000 0.00 0.00 0.00 4.01
3627 3950 0.538287 AGGTCCAAGTTCAGGCAAGC 60.538 55.000 0.00 0.00 0.00 4.01
3628 3951 0.538287 GGTCCAAGTTCAGGCAAGCT 60.538 55.000 0.00 0.00 0.00 3.74
3633 3956 2.361737 GTTCAGGCAAGCTCCCCC 60.362 66.667 0.00 0.00 0.00 5.40
3695 4049 1.864711 CAGGACGACGACAACAACAAT 59.135 47.619 0.00 0.00 0.00 2.71
3704 4058 1.270550 GACAACAACAATGGCAGGAGG 59.729 52.381 0.00 0.00 0.00 4.30
3705 4059 1.133513 ACAACAACAATGGCAGGAGGA 60.134 47.619 0.00 0.00 0.00 3.71
3706 4060 1.962807 CAACAACAATGGCAGGAGGAA 59.037 47.619 0.00 0.00 0.00 3.36
3707 4061 2.364970 CAACAACAATGGCAGGAGGAAA 59.635 45.455 0.00 0.00 0.00 3.13
3708 4062 2.676748 ACAACAATGGCAGGAGGAAAA 58.323 42.857 0.00 0.00 0.00 2.29
3710 4064 2.629617 CAACAATGGCAGGAGGAAAAGT 59.370 45.455 0.00 0.00 0.00 2.66
3711 4065 2.519013 ACAATGGCAGGAGGAAAAGTC 58.481 47.619 0.00 0.00 0.00 3.01
3712 4066 2.108952 ACAATGGCAGGAGGAAAAGTCT 59.891 45.455 0.00 0.00 0.00 3.24
3713 4067 3.160269 CAATGGCAGGAGGAAAAGTCTT 58.840 45.455 0.00 0.00 0.00 3.01
3714 4068 3.532641 ATGGCAGGAGGAAAAGTCTTT 57.467 42.857 0.00 0.00 0.00 2.52
3715 4069 2.586425 TGGCAGGAGGAAAAGTCTTTG 58.414 47.619 0.00 0.00 0.00 2.77
3716 4070 1.889170 GGCAGGAGGAAAAGTCTTTGG 59.111 52.381 0.00 0.00 0.00 3.28
3717 4071 2.489073 GGCAGGAGGAAAAGTCTTTGGA 60.489 50.000 0.00 0.00 0.00 3.53
3719 4073 3.820557 CAGGAGGAAAAGTCTTTGGACA 58.179 45.455 0.00 0.00 44.36 4.02
3720 4074 4.401925 CAGGAGGAAAAGTCTTTGGACAT 58.598 43.478 0.00 0.00 44.36 3.06
3721 4075 5.560724 CAGGAGGAAAAGTCTTTGGACATA 58.439 41.667 0.00 0.00 44.36 2.29
3722 4076 6.183347 CAGGAGGAAAAGTCTTTGGACATAT 58.817 40.000 0.00 0.00 44.36 1.78
3723 4077 6.660949 CAGGAGGAAAAGTCTTTGGACATATT 59.339 38.462 0.00 0.00 44.36 1.28
3724 4078 6.887002 AGGAGGAAAAGTCTTTGGACATATTC 59.113 38.462 0.00 0.00 44.36 1.75
3725 4079 6.887002 GGAGGAAAAGTCTTTGGACATATTCT 59.113 38.462 0.00 0.00 44.36 2.40
3728 4082 6.183360 GGAAAAGTCTTTGGACATATTCTCGG 60.183 42.308 0.00 0.00 44.36 4.63
3790 4315 1.533469 CCGACTCCTTCTCACCGGTT 61.533 60.000 2.97 0.00 33.02 4.44
3810 4335 0.398318 GCCATATTCTCGGCCTCCTT 59.602 55.000 0.00 0.00 42.82 3.36
3852 4377 0.670546 AACATCTTGACACGGAGGCG 60.671 55.000 0.00 0.00 0.00 5.52
3884 4416 8.561738 AGATTATTTTTACTCCTTCGAAGCAA 57.438 30.769 19.99 8.82 0.00 3.91
3889 4421 1.667830 CTCCTTCGAAGCAACGGCA 60.668 57.895 19.99 0.00 44.61 5.69
3896 4428 1.208614 GAAGCAACGGCAAGCTCAG 59.791 57.895 0.00 0.00 44.61 3.35
3917 4449 2.364632 CTCTCCTCTCTTCGAGCTTGA 58.635 52.381 0.00 0.00 38.49 3.02
3961 4493 3.073356 TCAAGATGTTAAACTTCCCCGGT 59.927 43.478 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.780806 TCGGAATAACACGTGCGAAA 58.219 45.000 17.22 0.00 34.51 3.46
47 48 1.589716 GCTGATTGCAGGGCGTTTCT 61.590 55.000 0.00 0.00 42.53 2.52
102 103 4.081917 TGCTCAGTAATTATGGTGTCGTGA 60.082 41.667 0.00 0.00 0.00 4.35
139 140 3.070590 CCGTTCCCTTAGATTCGGGTAAT 59.929 47.826 0.00 0.00 41.40 1.89
151 152 1.122632 TCACCTGTGCCGTTCCCTTA 61.123 55.000 0.00 0.00 0.00 2.69
154 155 2.358737 CTCACCTGTGCCGTTCCC 60.359 66.667 0.00 0.00 0.00 3.97
173 174 7.372451 TGTAAGCGCTACAAACTTCAATTAT 57.628 32.000 12.05 0.00 37.58 1.28
179 180 3.125316 AGCATGTAAGCGCTACAAACTTC 59.875 43.478 12.05 5.14 43.75 3.01
189 190 0.109597 ACTTTGCAGCATGTAAGCGC 60.110 50.000 0.00 0.00 42.90 5.92
191 192 4.032104 GCATTAACTTTGCAGCATGTAAGC 59.968 41.667 0.00 0.00 42.90 3.09
229 230 1.235724 GGTTGACTGGCTAAAAGCGT 58.764 50.000 0.00 0.00 43.62 5.07
236 237 1.335132 GGATCCGGGTTGACTGGCTA 61.335 60.000 0.00 0.00 45.92 3.93
237 238 2.670148 GGATCCGGGTTGACTGGCT 61.670 63.158 0.00 0.00 45.92 4.75
265 270 2.468040 GTCTCCGAATCAGAATAACGCG 59.532 50.000 3.53 3.53 0.00 6.01
275 280 1.191489 TGCAGGGTGTCTCCGAATCA 61.191 55.000 0.00 0.00 37.00 2.57
321 326 2.573941 CGATGAGCATGAGTGTCAGA 57.426 50.000 0.00 0.00 0.00 3.27
340 345 3.134127 GGGCCGAACTGATGTGGC 61.134 66.667 0.00 0.00 46.82 5.01
350 355 1.841556 AACTGTGAGGAGGGCCGAA 60.842 57.895 0.00 0.00 39.96 4.30
374 379 2.416836 GCAGCGGTGAGTTAGTGATACA 60.417 50.000 20.69 0.00 0.00 2.29
379 384 2.196749 CTATGCAGCGGTGAGTTAGTG 58.803 52.381 20.69 0.00 0.00 2.74
405 410 3.762293 GGCCATGCCGCATGATTA 58.238 55.556 30.86 0.00 43.81 1.75
461 466 1.980772 AAGCTTCAGTGCCATGGCC 60.981 57.895 33.44 23.56 41.09 5.36
471 476 1.588824 TTCCGCATGCCAAGCTTCAG 61.589 55.000 13.15 0.00 0.00 3.02
473 478 1.153958 GTTCCGCATGCCAAGCTTC 60.154 57.895 13.15 0.00 0.00 3.86
474 479 1.902918 TGTTCCGCATGCCAAGCTT 60.903 52.632 13.15 0.00 0.00 3.74
517 522 4.160635 GTTCGACGCAATGCCGGG 62.161 66.667 2.18 0.00 0.00 5.73
518 523 3.418913 TGTTCGACGCAATGCCGG 61.419 61.111 0.00 0.00 0.00 6.13
540 545 4.072088 CGTTTGACGCTGACCCGC 62.072 66.667 0.00 0.00 33.65 6.13
711 723 4.615834 CTCGTCGGGCGCTCTAGC 62.616 72.222 5.36 0.00 41.07 3.42
748 763 2.478894 TCGCCTCGTTCATCTGAAAAAC 59.521 45.455 0.00 0.00 35.58 2.43
752 767 0.173481 CCTCGCCTCGTTCATCTGAA 59.827 55.000 0.00 0.00 0.00 3.02
754 769 1.880340 GCCTCGCCTCGTTCATCTG 60.880 63.158 0.00 0.00 0.00 2.90
755 770 2.496817 GCCTCGCCTCGTTCATCT 59.503 61.111 0.00 0.00 0.00 2.90
756 771 2.956964 CGCCTCGCCTCGTTCATC 60.957 66.667 0.00 0.00 0.00 2.92
757 772 4.514577 CCGCCTCGCCTCGTTCAT 62.515 66.667 0.00 0.00 0.00 2.57
777 815 0.793478 CGCGTGTCGTTCGAATCTCT 60.793 55.000 0.00 0.00 0.00 3.10
778 816 0.791983 TCGCGTGTCGTTCGAATCTC 60.792 55.000 5.77 0.00 39.67 2.75
1016 1057 3.596459 TTTGGGGGAGGGAGGGGAG 62.596 68.421 0.00 0.00 0.00 4.30
1017 1058 3.558124 TTTGGGGGAGGGAGGGGA 61.558 66.667 0.00 0.00 0.00 4.81
1018 1059 3.023735 CTTTGGGGGAGGGAGGGG 61.024 72.222 0.00 0.00 0.00 4.79
1019 1060 3.744155 GCTTTGGGGGAGGGAGGG 61.744 72.222 0.00 0.00 0.00 4.30
1020 1061 4.115199 CGCTTTGGGGGAGGGAGG 62.115 72.222 0.00 0.00 0.00 4.30
1038 1079 3.839432 GGGGAGGAAGCGGACGAG 61.839 72.222 0.00 0.00 0.00 4.18
1158 1203 4.385405 AGCCACTGGTCGAGCTGC 62.385 66.667 19.73 14.29 33.41 5.25
1360 1414 1.862827 GCAAAGCTCCAGCACAAAAAG 59.137 47.619 0.48 0.00 45.16 2.27
1429 1495 3.829601 TCCATTACAACCACCATCAAACC 59.170 43.478 0.00 0.00 0.00 3.27
1430 1496 5.410067 CATCCATTACAACCACCATCAAAC 58.590 41.667 0.00 0.00 0.00 2.93
1431 1497 4.465660 CCATCCATTACAACCACCATCAAA 59.534 41.667 0.00 0.00 0.00 2.69
1432 1498 4.022603 CCATCCATTACAACCACCATCAA 58.977 43.478 0.00 0.00 0.00 2.57
1433 1499 3.268072 TCCATCCATTACAACCACCATCA 59.732 43.478 0.00 0.00 0.00 3.07
1434 1500 3.897239 TCCATCCATTACAACCACCATC 58.103 45.455 0.00 0.00 0.00 3.51
1435 1501 4.217510 CATCCATCCATTACAACCACCAT 58.782 43.478 0.00 0.00 0.00 3.55
1436 1502 3.626983 CCATCCATCCATTACAACCACCA 60.627 47.826 0.00 0.00 0.00 4.17
1476 1546 2.186903 GCAATCGCCTTCTCCGGA 59.813 61.111 2.93 2.93 0.00 5.14
1682 1752 9.830294 AATTTGAACTTTGAAAAGAAAAGCTTG 57.170 25.926 9.71 0.00 38.03 4.01
1685 1755 9.824534 TGAAATTTGAACTTTGAAAAGAAAAGC 57.175 25.926 9.71 3.38 38.03 3.51
1758 1834 2.734723 CCGCACCTCTGTCGTGTG 60.735 66.667 0.00 0.00 40.61 3.82
1931 2011 1.598856 AAGGGGGAGAGAGAGGGAGG 61.599 65.000 0.00 0.00 0.00 4.30
1934 2014 1.074850 GGAAGGGGGAGAGAGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
1935 2015 0.267356 ATGGAAGGGGGAGAGAGAGG 59.733 60.000 0.00 0.00 0.00 3.69
1936 2016 2.046292 GAATGGAAGGGGGAGAGAGAG 58.954 57.143 0.00 0.00 0.00 3.20
1937 2017 1.366082 TGAATGGAAGGGGGAGAGAGA 59.634 52.381 0.00 0.00 0.00 3.10
1938 2018 1.885049 TGAATGGAAGGGGGAGAGAG 58.115 55.000 0.00 0.00 0.00 3.20
1939 2019 2.359376 TTGAATGGAAGGGGGAGAGA 57.641 50.000 0.00 0.00 0.00 3.10
1940 2020 3.456380 TTTTGAATGGAAGGGGGAGAG 57.544 47.619 0.00 0.00 0.00 3.20
1941 2021 4.418395 AATTTTGAATGGAAGGGGGAGA 57.582 40.909 0.00 0.00 0.00 3.71
1942 2022 4.531732 TGAAATTTTGAATGGAAGGGGGAG 59.468 41.667 0.00 0.00 0.00 4.30
1943 2023 4.497516 TGAAATTTTGAATGGAAGGGGGA 58.502 39.130 0.00 0.00 0.00 4.81
1944 2024 4.906747 TGAAATTTTGAATGGAAGGGGG 57.093 40.909 0.00 0.00 0.00 5.40
2026 2106 4.949856 ACAATCCAATCGAGCCAAGTTATT 59.050 37.500 0.00 0.00 0.00 1.40
2028 2108 3.689161 CACAATCCAATCGAGCCAAGTTA 59.311 43.478 0.00 0.00 0.00 2.24
2029 2109 2.489329 CACAATCCAATCGAGCCAAGTT 59.511 45.455 0.00 0.00 0.00 2.66
2030 2110 2.086869 CACAATCCAATCGAGCCAAGT 58.913 47.619 0.00 0.00 0.00 3.16
2031 2111 1.202222 GCACAATCCAATCGAGCCAAG 60.202 52.381 0.00 0.00 0.00 3.61
2032 2112 0.810648 GCACAATCCAATCGAGCCAA 59.189 50.000 0.00 0.00 0.00 4.52
2033 2113 0.035152 AGCACAATCCAATCGAGCCA 60.035 50.000 0.00 0.00 0.00 4.75
2034 2114 0.659957 GAGCACAATCCAATCGAGCC 59.340 55.000 0.00 0.00 0.00 4.70
2035 2115 0.302890 CGAGCACAATCCAATCGAGC 59.697 55.000 0.00 0.00 35.47 5.03
2596 2688 1.281899 GCATGCGGTGAGAGTAGAAC 58.718 55.000 0.00 0.00 0.00 3.01
2678 2776 1.960250 GATGCATCTGAGAGGGCGC 60.960 63.158 19.70 0.00 0.00 6.53
2680 2778 0.879400 CGTGATGCATCTGAGAGGGC 60.879 60.000 26.32 0.00 0.00 5.19
2683 2781 2.609984 GGGATCGTGATGCATCTGAGAG 60.610 54.545 26.32 13.13 0.00 3.20
2686 2784 1.122227 TGGGATCGTGATGCATCTGA 58.878 50.000 26.32 22.67 0.00 3.27
3034 3147 1.118838 AGATCCTCAGCCTCTTTCCG 58.881 55.000 0.00 0.00 0.00 4.30
3037 3150 2.504996 CTGGAAGATCCTCAGCCTCTTT 59.495 50.000 0.00 0.00 37.46 2.52
3197 3313 2.697425 CGCGATGCAGAAACTCCG 59.303 61.111 0.00 0.00 0.00 4.63
3235 3356 2.018515 GTCGATCGATCCCTCCCTATC 58.981 57.143 22.50 0.00 0.00 2.08
3389 3520 8.680903 AGCTTTGAAGTGATTATCGAAATCAAT 58.319 29.630 18.32 15.98 38.27 2.57
3556 3720 5.283060 ACAGAACTTGCATCGACAAATAC 57.717 39.130 0.00 0.00 0.00 1.89
3695 4049 2.586425 CAAAGACTTTTCCTCCTGCCA 58.414 47.619 0.00 0.00 0.00 4.92
3704 4058 6.675728 GCCGAGAATATGTCCAAAGACTTTTC 60.676 42.308 0.00 0.00 43.91 2.29
3705 4059 5.123979 GCCGAGAATATGTCCAAAGACTTTT 59.876 40.000 0.00 0.00 43.91 2.27
3706 4060 4.636206 GCCGAGAATATGTCCAAAGACTTT 59.364 41.667 0.00 0.00 43.91 2.66
3707 4061 4.192317 GCCGAGAATATGTCCAAAGACTT 58.808 43.478 0.00 0.00 43.91 3.01
3708 4062 3.432326 GGCCGAGAATATGTCCAAAGACT 60.432 47.826 0.00 0.00 43.91 3.24
3710 4064 2.771943 AGGCCGAGAATATGTCCAAAGA 59.228 45.455 0.00 0.00 0.00 2.52
3711 4065 2.874701 CAGGCCGAGAATATGTCCAAAG 59.125 50.000 0.00 0.00 0.00 2.77
3712 4066 2.917933 CAGGCCGAGAATATGTCCAAA 58.082 47.619 0.00 0.00 0.00 3.28
3713 4067 1.475034 GCAGGCCGAGAATATGTCCAA 60.475 52.381 0.00 0.00 0.00 3.53
3714 4068 0.106708 GCAGGCCGAGAATATGTCCA 59.893 55.000 0.00 0.00 0.00 4.02
3715 4069 0.603975 GGCAGGCCGAGAATATGTCC 60.604 60.000 0.00 0.00 0.00 4.02
3716 4070 0.106708 TGGCAGGCCGAGAATATGTC 59.893 55.000 5.74 0.00 39.42 3.06
3717 4071 0.107456 CTGGCAGGCCGAGAATATGT 59.893 55.000 6.61 0.00 39.42 2.29
3719 4073 0.394565 GTCTGGCAGGCCGAGAATAT 59.605 55.000 15.73 0.00 39.42 1.28
3720 4074 1.686325 GGTCTGGCAGGCCGAGAATA 61.686 60.000 24.30 0.00 39.42 1.75
3721 4075 2.586792 GTCTGGCAGGCCGAGAAT 59.413 61.111 15.73 0.00 39.42 2.40
3722 4076 3.706373 GGTCTGGCAGGCCGAGAA 61.706 66.667 24.30 0.00 39.42 2.87
3852 4377 5.880341 AGGAGTAAAAATAATCTTGTGCGC 58.120 37.500 0.00 0.00 0.00 6.09
3884 4416 2.264166 GAGAGCTGAGCTTGCCGT 59.736 61.111 9.00 0.00 39.88 5.68
3889 4421 2.102578 GAAGAGAGGAGAGCTGAGCTT 58.897 52.381 9.00 0.00 39.88 3.74
3917 4449 1.144057 CAGCGGCCGATAAGAAGGT 59.856 57.895 33.48 0.00 0.00 3.50
3961 4493 7.718272 CTCCAAAATGAATGAGCAAAAGAAA 57.282 32.000 0.00 0.00 0.00 2.52
3991 4523 1.996191 GCGAAGAAGGAGACATGTGTC 59.004 52.381 14.43 14.43 45.08 3.67
4059 4591 3.389656 GTGGGAGGAGGAGAAGATAAAGG 59.610 52.174 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.