Multiple sequence alignment - TraesCS3B01G462300

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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 TraesCS3B01G462300 chr3B 100.000 4018 0 0 1 4018 705183799 705187816 0.000000e+00 7420.0
1 TraesCS3B01G462300 chr3D 88.262 3527 266 70 7 3442 533373966 533377435 0.000000e+00 4084.0
2 TraesCS3B01G462300 chr3D 88.114 3542 260 75 6 3442 533391718 533395203 0.000000e+00 4060.0
3 TraesCS3B01G462300 chr3D 87.321 3557 279 77 1 3442 533313601 533317100 0.000000e+00 3912.0
4 TraesCS3B01G462300 chr3D 87.313 2010 163 48 1492 3442 532991979 532993955 0.000000e+00 2215.0
5 TraesCS3B01G462300 chr3D 87.484 1518 122 31 1 1496 532976951 532978422 0.000000e+00 1688.0
6 TraesCS3B01G462300 chr3D 86.910 1398 131 26 2049 3415 533411069 533412445 0.000000e+00 1520.0
7 TraesCS3B01G462300 chr3D 87.289 771 66 15 1 757 533406831 533407583 0.000000e+00 852.0
8 TraesCS3B01G462300 chr3D 92.555 591 26 5 993 1583 533407781 533408353 0.000000e+00 832.0
9 TraesCS3B01G462300 chr3D 85.860 587 72 9 3438 4015 533377612 533378196 7.380000e-172 614.0
10 TraesCS3B01G462300 chr3D 85.860 587 72 9 3438 4015 533395380 533395964 7.380000e-172 614.0
11 TraesCS3B01G462300 chr3D 84.394 660 58 16 1584 2213 533410396 533411040 1.230000e-169 606.0
12 TraesCS3B01G462300 chr3D 92.113 355 19 5 3667 4018 532994382 532994730 3.610000e-135 492.0
13 TraesCS3B01G462300 chr3D 88.000 425 33 7 1 407 533401870 533402294 1.680000e-133 486.0
14 TraesCS3B01G462300 chr3D 88.391 379 38 5 3643 4015 533317464 533317842 6.120000e-123 451.0
15 TraesCS3B01G462300 chr3D 90.395 177 10 7 3438 3610 533317296 533317469 4.040000e-55 226.0
16 TraesCS3B01G462300 chr3D 88.298 188 10 7 745 929 533407604 533407782 8.750000e-52 215.0
17 TraesCS3B01G462300 chr3D 91.176 136 11 1 3438 3572 533412674 533412809 2.470000e-42 183.0
18 TraesCS3B01G462300 chr3A 87.007 2432 190 46 1075 3442 668817704 668820073 0.000000e+00 2625.0
19 TraesCS3B01G462300 chr3A 87.446 2079 162 44 1428 3442 668867781 668869824 0.000000e+00 2302.0
20 TraesCS3B01G462300 chr3A 88.323 1884 146 35 1 1860 668923273 668925106 0.000000e+00 2193.0
21 TraesCS3B01G462300 chr3A 86.327 1631 160 30 1856 3442 668981606 668983217 0.000000e+00 1718.0
22 TraesCS3B01G462300 chr3A 86.205 1631 161 31 1856 3442 668985957 668987567 0.000000e+00 1707.0
23 TraesCS3B01G462300 chr3A 86.213 1632 160 30 1856 3442 668990301 668991912 0.000000e+00 1707.0
24 TraesCS3B01G462300 chr3A 85.714 1211 109 29 2049 3227 669054771 669055949 0.000000e+00 1219.0
25 TraesCS3B01G462300 chr3A 87.599 758 70 17 1 745 668816412 668817158 0.000000e+00 857.0
26 TraesCS3B01G462300 chr3A 86.184 760 83 14 1 747 669052902 669053652 0.000000e+00 802.0
27 TraesCS3B01G462300 chr3A 84.848 726 60 21 1520 2213 669054035 669054742 0.000000e+00 686.0
28 TraesCS3B01G462300 chr3A 89.173 508 47 6 1 500 668863499 668864006 9.480000e-176 627.0
29 TraesCS3B01G462300 chr3A 92.722 371 18 4 1075 1440 668867393 668867759 9.890000e-146 527.0
30 TraesCS3B01G462300 chr3A 90.423 355 28 6 3667 4018 668983653 668984004 2.830000e-126 462.0
31 TraesCS3B01G462300 chr3A 89.859 355 30 6 3667 4018 668992342 668992693 6.120000e-123 451.0
32 TraesCS3B01G462300 chr3A 89.577 355 31 6 3667 4018 668987997 668988348 2.850000e-121 446.0
33 TraesCS3B01G462300 chr3A 89.045 356 35 3 3667 4018 668820806 668821161 4.770000e-119 438.0
34 TraesCS3B01G462300 chr3A 88.154 363 29 4 3667 4015 669056587 669056949 1.730000e-113 420.0
35 TraesCS3B01G462300 chr3A 85.477 241 22 7 737 976 668817401 668817629 5.190000e-59 239.0
36 TraesCS3B01G462300 chr3A 88.557 201 18 4 737 936 668866713 668866909 5.190000e-59 239.0
37 TraesCS3B01G462300 chr3A 83.262 233 23 12 520 747 668865466 668865687 2.450000e-47 200.0
38 TraesCS3B01G462300 chr3A 93.548 62 1 1 1018 1079 668867318 668867376 5.530000e-14 89.8
39 TraesCS3B01G462300 chr3A 95.652 46 2 0 1034 1079 668817634 668817679 1.550000e-09 75.0


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 TraesCS3B01G462300 chr3B 705183799 705187816 4017 False 7420.000000 7420 100.000000 1 4018 1 chr3B.!!$F1 4017
1 TraesCS3B01G462300 chr3D 533373966 533378196 4230 False 2349.000000 4084 87.061000 7 4015 2 chr3D.!!$F5 4008
2 TraesCS3B01G462300 chr3D 533391718 533395964 4246 False 2337.000000 4060 86.987000 6 4015 2 chr3D.!!$F6 4009
3 TraesCS3B01G462300 chr3D 532976951 532978422 1471 False 1688.000000 1688 87.484000 1 1496 1 chr3D.!!$F1 1495
4 TraesCS3B01G462300 chr3D 533313601 533317842 4241 False 1529.666667 3912 88.702333 1 4015 3 chr3D.!!$F4 4014
5 TraesCS3B01G462300 chr3D 532991979 532994730 2751 False 1353.500000 2215 89.713000 1492 4018 2 chr3D.!!$F3 2526
6 TraesCS3B01G462300 chr3D 533406831 533412809 5978 False 701.333333 1520 88.437000 1 3572 6 chr3D.!!$F7 3571
7 TraesCS3B01G462300 chr3A 668923273 668925106 1833 False 2193.000000 2193 88.323000 1 1860 1 chr3A.!!$F1 1859
8 TraesCS3B01G462300 chr3A 668981606 668992693 11087 False 1081.833333 1718 88.100667 1856 4018 6 chr3A.!!$F4 2162
9 TraesCS3B01G462300 chr3A 668816412 668821161 4749 False 846.800000 2625 88.956000 1 4018 5 chr3A.!!$F2 4017
10 TraesCS3B01G462300 chr3A 669052902 669056949 4047 False 781.750000 1219 86.225000 1 4015 4 chr3A.!!$F5 4014
11 TraesCS3B01G462300 chr3A 668863499 668869824 6325 False 664.133333 2302 89.118000 1 3442 6 chr3A.!!$F3 3441

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
468 506 0.537371 CCTCGGCTTCAAGGGTGTTT 60.537 55.0 0.0 0.0 0.00 2.83 F
1770 6763 0.311790 ACAAGCGATGGTGTTTGCTG 59.688 50.0 0.0 0.0 37.81 4.41 F
2772 8041 0.756903 TGTATCCCTAAAGCTCCGCC 59.243 55.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 6825 0.475475 CATAGCCAGGGGAAGATGCA 59.525 55.0 0.0 0.0 0.0 3.96 R
2863 8132 0.163788 CGACGCATCAACCAACTCAC 59.836 55.0 0.0 0.0 0.0 3.51 R
3691 13934 0.398098 AGGGTGATGGTACGGTAGGG 60.398 60.0 0.0 0.0 0.0 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
31 32 6.569127 TTACTGTATTAAGGGAGGCATGAA 57.431 37.500 0.00 0.00 0.00 2.57
150 166 4.760047 GCGCGGTGGAGATGGTGT 62.760 66.667 8.83 0.00 0.00 4.16
259 279 1.139058 GCGACATGGAGGGTGACTTAT 59.861 52.381 0.00 0.00 0.00 1.73
261 281 2.565841 GACATGGAGGGTGACTTATGC 58.434 52.381 0.00 0.00 31.21 3.14
290 310 1.229209 TGTCCCACCTGGAGGAGAC 60.229 63.158 12.14 15.94 46.38 3.36
308 340 5.059833 GGAGACTGAGTGTTTTGACTTGAT 58.940 41.667 0.00 0.00 0.00 2.57
311 343 3.002656 ACTGAGTGTTTTGACTTGATGCG 59.997 43.478 0.00 0.00 0.00 4.73
394 426 4.158786 TGCCCAATTCATCCTTTTCTTGA 58.841 39.130 0.00 0.00 0.00 3.02
395 427 4.021192 TGCCCAATTCATCCTTTTCTTGAC 60.021 41.667 0.00 0.00 0.00 3.18
430 467 4.943705 TCTTTGCTATGGTCAAGGTGATTC 59.056 41.667 0.00 0.00 0.00 2.52
446 483 6.064060 AGGTGATTCTTTGTCTCAACAATGA 58.936 36.000 3.57 3.57 44.59 2.57
452 490 7.672983 TTCTTTGTCTCAACAATGATACCTC 57.327 36.000 7.45 0.00 44.38 3.85
468 506 0.537371 CCTCGGCTTCAAGGGTGTTT 60.537 55.000 0.00 0.00 0.00 2.83
469 507 0.593128 CTCGGCTTCAAGGGTGTTTG 59.407 55.000 0.00 0.00 0.00 2.93
502 540 1.204704 ACGGATCGATCTTTGCTCACA 59.795 47.619 23.96 0.00 0.00 3.58
504 544 2.736719 CGGATCGATCTTTGCTCACAGT 60.737 50.000 23.96 0.00 0.00 3.55
514 554 2.359107 CTCACAGTGCGCCACCAT 60.359 61.111 4.18 0.00 34.49 3.55
547 2027 2.288273 GGAAGACGGCAGCGATATACTT 60.288 50.000 0.00 0.00 0.00 2.24
551 2033 1.605710 ACGGCAGCGATATACTTACGT 59.394 47.619 0.00 0.00 0.00 3.57
552 2034 2.807967 ACGGCAGCGATATACTTACGTA 59.192 45.455 0.00 0.00 0.00 3.57
553 2035 3.438087 ACGGCAGCGATATACTTACGTAT 59.562 43.478 0.00 0.00 39.56 3.06
609 2091 6.428083 TGGTCTTGTAAGAGTTGGACAATA 57.572 37.500 0.00 0.00 35.32 1.90
624 2106 7.602644 AGTTGGACAATATTAGTATGTATGGCG 59.397 37.037 0.00 0.00 0.00 5.69
667 2156 5.445964 AGAAAAGAAGTCCCAACAAGCTTA 58.554 37.500 0.00 0.00 0.00 3.09
728 2219 2.275380 CCAAAACCAAGAGGGGCCG 61.275 63.158 0.00 0.00 42.91 6.13
730 2221 2.774633 AAAACCAAGAGGGGCCGGT 61.775 57.895 1.90 0.00 42.91 5.28
757 3287 1.068333 GCACACCAACCAGCTGTATTG 60.068 52.381 13.81 15.84 0.00 1.90
849 3380 1.262640 AATAGAACGGGGAGCACGGT 61.263 55.000 0.00 0.00 35.23 4.83
967 3502 2.363795 CGGCCACCTCCTAGTCCA 60.364 66.667 2.24 0.00 0.00 4.02
1091 3990 2.123428 GGATGCAGGATGTGGTGGC 61.123 63.158 0.00 0.00 39.31 5.01
1261 4167 3.704566 TCAGTGACCTACTCAACAACAGT 59.295 43.478 0.00 0.00 37.60 3.55
1262 4168 4.891168 TCAGTGACCTACTCAACAACAGTA 59.109 41.667 0.00 0.00 37.60 2.74
1263 4169 4.982916 CAGTGACCTACTCAACAACAGTAC 59.017 45.833 0.00 0.00 37.60 2.73
1347 4260 5.376854 GTGGACTACGTACCTGAAACTTA 57.623 43.478 4.09 0.00 0.00 2.24
1373 4286 3.494251 GGGGCTTGCATATAAATTTTGCG 59.506 43.478 8.41 0.00 39.23 4.85
1419 4332 9.533831 AATCCCTGTATCAGTTACAAAAAGATT 57.466 29.630 0.00 0.00 40.27 2.40
1446 4393 8.209584 TCTTCTGCTCTATCAAAGCTAATGATT 58.790 33.333 17.25 5.39 40.50 2.57
1487 4434 7.169158 TGACAGATTCAAGTTTTTGGAAAGT 57.831 32.000 0.00 0.00 34.97 2.66
1504 4451 1.079612 GTTTGCCATTGCTGCCTCC 60.080 57.895 0.00 0.00 38.71 4.30
1589 6582 2.695585 ACCAAGGTGTTCCTCTCTCTT 58.304 47.619 0.00 0.00 44.35 2.85
1590 6583 3.049344 ACCAAGGTGTTCCTCTCTCTTT 58.951 45.455 0.00 0.00 44.35 2.52
1591 6584 3.071747 ACCAAGGTGTTCCTCTCTCTTTC 59.928 47.826 0.00 0.00 44.35 2.62
1592 6585 3.558109 CCAAGGTGTTCCTCTCTCTTTCC 60.558 52.174 0.00 0.00 44.35 3.13
1593 6586 3.268034 AGGTGTTCCTCTCTCTTTCCT 57.732 47.619 0.00 0.00 40.58 3.36
1594 6587 3.592865 AGGTGTTCCTCTCTCTTTCCTT 58.407 45.455 0.00 0.00 40.58 3.36
1595 6588 3.580895 AGGTGTTCCTCTCTCTTTCCTTC 59.419 47.826 0.00 0.00 40.58 3.46
1596 6589 3.307129 GGTGTTCCTCTCTCTTTCCTTCC 60.307 52.174 0.00 0.00 0.00 3.46
1597 6590 3.580895 GTGTTCCTCTCTCTTTCCTTCCT 59.419 47.826 0.00 0.00 0.00 3.36
1636 6629 2.380064 TTCAGGCAACCAAGTCCATT 57.620 45.000 0.00 0.00 37.17 3.16
1637 6630 2.380064 TCAGGCAACCAAGTCCATTT 57.620 45.000 0.00 0.00 37.17 2.32
1638 6631 3.517296 TCAGGCAACCAAGTCCATTTA 57.483 42.857 0.00 0.00 37.17 1.40
1639 6632 3.838565 TCAGGCAACCAAGTCCATTTAA 58.161 40.909 0.00 0.00 37.17 1.52
1662 6655 9.778741 TTAATTCCGAGCAAGATATCAAATACT 57.221 29.630 5.32 0.00 0.00 2.12
1692 6685 6.735063 CCGTTTAATTAATCACGTGAGTTGTC 59.265 38.462 24.73 7.25 46.40 3.18
1730 6723 6.069905 TGTTTGGGCAGATGGAGTACTATAAA 60.070 38.462 0.00 0.00 0.00 1.40
1770 6763 0.311790 ACAAGCGATGGTGTTTGCTG 59.688 50.000 0.00 0.00 37.81 4.41
1826 6819 6.367421 TCGACAAATTCAACAATCGTTAAGG 58.633 36.000 0.00 0.00 32.75 2.69
1832 6825 5.957842 TTCAACAATCGTTAAGGCAGATT 57.042 34.783 0.00 0.00 35.24 2.40
1861 6857 1.681666 CTGGCTATGGGGCGATGAT 59.318 57.895 0.00 0.00 44.11 2.45
1938 6935 2.056985 GGCAATGTTGGCCCTTTGA 58.943 52.632 0.00 0.00 46.85 2.69
1952 6949 2.093973 CCCTTTGACGTCTAGTGCAGAT 60.094 50.000 17.92 0.00 35.17 2.90
2000 6997 2.389715 ACCTCACTGCCAGGTATAGAC 58.610 52.381 0.00 0.00 42.91 2.59
2078 7102 4.108336 AGATATGATATTAGCTGCGCGTG 58.892 43.478 8.43 1.88 0.00 5.34
2120 7147 7.920160 TTGTGCATCAATTCTGTAGTAATCA 57.080 32.000 0.00 0.00 0.00 2.57
2121 7148 7.920160 TGTGCATCAATTCTGTAGTAATCAA 57.080 32.000 0.00 0.00 0.00 2.57
2122 7149 8.334263 TGTGCATCAATTCTGTAGTAATCAAA 57.666 30.769 0.00 0.00 0.00 2.69
2123 7150 8.236586 TGTGCATCAATTCTGTAGTAATCAAAC 58.763 33.333 0.00 0.00 0.00 2.93
2124 7151 8.454106 GTGCATCAATTCTGTAGTAATCAAACT 58.546 33.333 0.00 0.00 0.00 2.66
2187 7407 1.497991 ACATGTTCAACGACTCACCG 58.502 50.000 0.00 0.00 0.00 4.94
2208 7428 3.628017 GTTGCAGCAATGTAAGTCGTTT 58.372 40.909 11.96 0.00 0.00 3.60
2264 7484 7.344612 AGTTGGATATGTAGACATTAGTGTGGA 59.655 37.037 0.00 0.00 39.09 4.02
2276 7496 1.650528 AGTGTGGAGCTTCTAGCCTT 58.349 50.000 0.00 0.00 43.77 4.35
2348 7593 2.036604 TCCAGCACGTGTGTTCAGAATA 59.963 45.455 18.38 0.00 0.00 1.75
2376 7621 5.410746 CCATGCATCCACTAAGTAGCTATTG 59.589 44.000 0.00 0.00 0.00 1.90
2541 7792 5.829391 ACCATGTTTCCCGTTTACTAACTTT 59.171 36.000 0.00 0.00 31.89 2.66
2553 7804 7.013529 CGTTTACTAACTTTGTATGTCTTGCC 58.986 38.462 0.00 0.00 31.89 4.52
2583 7840 1.203287 GAAGGAGCTTTTGATGGGCAC 59.797 52.381 0.00 0.00 0.00 5.01
2601 7858 2.541588 GCACGTGAACACAATGCTTTCT 60.542 45.455 22.23 0.00 38.98 2.52
2602 7859 3.694734 CACGTGAACACAATGCTTTCTT 58.305 40.909 10.90 0.00 0.00 2.52
2604 7861 4.027458 CACGTGAACACAATGCTTTCTTTG 60.027 41.667 10.90 0.00 34.58 2.77
2635 7892 5.030147 ACCCTACACCACATGATCTTTCTA 58.970 41.667 0.00 0.00 0.00 2.10
2653 7910 2.101750 TCTAGAGCGTCCAACAACAACA 59.898 45.455 0.00 0.00 0.00 3.33
2656 7914 2.033299 AGAGCGTCCAACAACAACATTG 59.967 45.455 0.00 0.00 0.00 2.82
2663 7921 4.801516 GTCCAACAACAACATTGTAACACC 59.198 41.667 0.00 0.00 41.31 4.16
2666 7924 4.647424 ACAACAACATTGTAACACCCAG 57.353 40.909 0.00 0.00 41.31 4.45
2667 7925 4.274147 ACAACAACATTGTAACACCCAGA 58.726 39.130 0.00 0.00 41.31 3.86
2730 7994 6.701432 ATAACTCTACAACGTGCTTTACAC 57.299 37.500 0.00 0.00 46.45 2.90
2772 8041 0.756903 TGTATCCCTAAAGCTCCGCC 59.243 55.000 0.00 0.00 0.00 6.13
2793 8062 2.113774 CACTGCAGCCCAAGGTGA 59.886 61.111 15.27 0.00 44.53 4.02
2803 8072 2.591429 CAAGGTGACGCAGGCACA 60.591 61.111 14.87 0.00 37.99 4.57
2816 8085 2.585247 GCACACCCGACGCCTATC 60.585 66.667 0.00 0.00 0.00 2.08
2820 8089 0.968901 ACACCCGACGCCTATCAAGA 60.969 55.000 0.00 0.00 0.00 3.02
2863 8132 1.451567 CCTGCCCAGTCTGCATCAG 60.452 63.158 0.00 1.29 38.22 2.90
2868 8137 0.612229 CCCAGTCTGCATCAGTGAGT 59.388 55.000 0.00 0.00 32.61 3.41
2873 8142 2.105477 AGTCTGCATCAGTGAGTTGGTT 59.895 45.455 0.00 0.00 32.61 3.67
2888 8157 0.108992 TGGTTGATGCGTCGTCTACC 60.109 55.000 18.38 18.38 42.58 3.18
2935 8204 0.400381 TGCATAGAGGCCTCCATCCA 60.400 55.000 29.54 15.50 0.00 3.41
3006 8275 2.125326 CACCGCATCTACCTCCCGA 61.125 63.158 0.00 0.00 0.00 5.14
3076 8345 1.597461 CGACCCTTCCTCCTCAACC 59.403 63.158 0.00 0.00 0.00 3.77
3092 8362 2.625314 TCAACCGCATTTTGGTGATTCA 59.375 40.909 0.00 0.00 40.35 2.57
3126 8396 6.485830 TTCTTCATGGGGTTATCACTAGAG 57.514 41.667 0.00 0.00 0.00 2.43
3164 8434 7.166970 CGCTACAATTTAATAAGTGCTCGACTA 59.833 37.037 0.00 0.00 32.78 2.59
3227 12847 0.682852 ACCGTTCTCGTGGGAATTCA 59.317 50.000 7.93 0.00 35.01 2.57
3324 12949 3.053455 GTTCACGCACTCTAGGATATGC 58.947 50.000 0.00 0.00 34.66 3.14
3339 12964 3.343972 TGCGTCTTTGCAAGGCTC 58.656 55.556 3.19 0.00 43.02 4.70
3353 12978 4.757657 TGCAAGGCTCTCACGTTTAATTAA 59.242 37.500 0.00 0.00 0.00 1.40
3360 12985 8.038944 AGGCTCTCACGTTTAATTAACAATAGA 58.961 33.333 0.00 0.00 36.50 1.98
3361 12986 8.114905 GGCTCTCACGTTTAATTAACAATAGAC 58.885 37.037 0.00 0.00 36.50 2.59
3363 12988 8.969121 TCTCACGTTTAATTAACAATAGACGA 57.031 30.769 19.34 3.26 36.50 4.20
3461 13386 4.021544 TCCATTATGTGTGCCTTGGTTTTC 60.022 41.667 0.00 0.00 0.00 2.29
3545 13785 7.492352 TCAAACTAGCAGTAAAAACTCTTCC 57.508 36.000 0.00 0.00 0.00 3.46
3581 13822 8.511604 AAAGAAACATCGAAATACATGGAGAT 57.488 30.769 0.00 0.00 0.00 2.75
3603 13844 0.984230 ACCTTCTTCATCTGCCCGAA 59.016 50.000 0.00 0.00 0.00 4.30
3612 13853 1.762522 ATCTGCCCGAATGAGCCGAT 61.763 55.000 0.00 0.00 0.00 4.18
3619 13860 1.148157 CGAATGAGCCGATTGAGCGT 61.148 55.000 0.00 0.00 34.64 5.07
3641 13882 1.430632 CACATGTTGCTCCATCGCC 59.569 57.895 0.00 0.00 0.00 5.54
3660 13901 2.280628 CCTGAGCCAACCTATCGTTTC 58.719 52.381 0.00 0.00 29.93 2.78
3661 13902 2.354704 CCTGAGCCAACCTATCGTTTCA 60.355 50.000 0.00 0.00 29.93 2.69
3662 13903 3.535561 CTGAGCCAACCTATCGTTTCAT 58.464 45.455 0.00 0.00 29.93 2.57
3663 13904 3.531538 TGAGCCAACCTATCGTTTCATC 58.468 45.455 0.00 0.00 29.93 2.92
3664 13905 2.540101 GAGCCAACCTATCGTTTCATCG 59.460 50.000 0.00 0.00 29.93 3.84
3666 13907 3.131577 AGCCAACCTATCGTTTCATCGTA 59.868 43.478 0.00 0.00 29.93 3.43
3678 13921 4.031426 CGTTTCATCGTAGGCAGAAAGTAC 59.969 45.833 0.00 0.00 31.35 2.73
3681 13924 4.270834 TCATCGTAGGCAGAAAGTACTCT 58.729 43.478 0.00 0.00 0.00 3.24
3691 13934 4.789784 CAGAAAGTACTCTAGGCTATCGC 58.210 47.826 0.00 0.00 0.00 4.58
3834 14091 2.404215 CGGCTGGGATAGTTTGATACG 58.596 52.381 0.00 0.00 0.00 3.06
3920 18524 6.098409 GGTTCATAGGACCAGAAATCTAGTCA 59.902 42.308 10.43 0.00 36.53 3.41
3926 18530 4.407296 GGACCAGAAATCTAGTCAGGATGT 59.593 45.833 10.43 0.00 36.53 3.06
3975 18586 3.887621 TTCTTTAGTGAGACCATCCCG 57.112 47.619 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 7.928307 TTTGTAGTCCACTCGTATAGTAGTT 57.072 36.000 0.00 0.00 35.76 2.24
93 108 1.202222 CGCCTCTGCCATTTCATTCAC 60.202 52.381 0.00 0.00 0.00 3.18
150 166 1.315690 CCTAGGGTCGACGCTAATGA 58.684 55.000 33.47 19.64 40.24 2.57
174 190 1.480789 TGACAATACCGCCTCTAGCA 58.519 50.000 0.00 0.00 44.04 3.49
259 279 4.819783 GGACACATCCCACAAGCA 57.180 55.556 0.00 0.00 39.39 3.91
290 310 3.248363 TCGCATCAAGTCAAAACACTCAG 59.752 43.478 0.00 0.00 0.00 3.35
308 340 4.815269 CCAAGATTTGGGTAAAAATCGCA 58.185 39.130 0.00 0.00 46.58 5.10
311 343 7.320399 ACGAATCCAAGATTTGGGTAAAAATC 58.680 34.615 7.91 2.19 45.46 2.17
394 426 5.361857 CCATAGCAAAGAAATGGATCCAAGT 59.638 40.000 20.67 9.62 42.36 3.16
395 427 5.361857 ACCATAGCAAAGAAATGGATCCAAG 59.638 40.000 20.67 4.19 42.36 3.61
446 483 0.541863 CACCCTTGAAGCCGAGGTAT 59.458 55.000 0.00 0.00 41.58 2.73
452 490 0.593128 CTCAAACACCCTTGAAGCCG 59.407 55.000 0.00 0.00 34.96 5.52
502 540 3.640407 ACTGGATGGTGGCGCACT 61.640 61.111 10.83 0.00 34.40 4.40
514 554 0.318441 CGTCTTCCTCTTGCACTGGA 59.682 55.000 0.00 0.00 0.00 3.86
547 2027 8.367943 AGAAAACAACACACATGTAATACGTA 57.632 30.769 0.00 0.00 38.45 3.57
645 2134 4.655762 AAGCTTGTTGGGACTTCTTTTC 57.344 40.909 0.00 0.00 0.00 2.29
650 2139 5.705609 TGAAATAAGCTTGTTGGGACTTC 57.294 39.130 9.86 2.75 0.00 3.01
651 2140 6.478512 TTTGAAATAAGCTTGTTGGGACTT 57.521 33.333 9.86 0.00 0.00 3.01
652 2141 6.670695 ATTTGAAATAAGCTTGTTGGGACT 57.329 33.333 9.86 0.00 0.00 3.85
653 2142 6.147656 CCAATTTGAAATAAGCTTGTTGGGAC 59.852 38.462 9.86 2.93 32.13 4.46
654 2143 6.229733 CCAATTTGAAATAAGCTTGTTGGGA 58.770 36.000 9.86 0.00 32.13 4.37
655 2144 5.106594 GCCAATTTGAAATAAGCTTGTTGGG 60.107 40.000 9.86 4.42 35.36 4.12
656 2145 5.389725 CGCCAATTTGAAATAAGCTTGTTGG 60.390 40.000 9.86 6.35 37.29 3.77
657 2146 5.389725 CCGCCAATTTGAAATAAGCTTGTTG 60.390 40.000 9.86 0.00 0.00 3.33
658 2147 4.690280 CCGCCAATTTGAAATAAGCTTGTT 59.310 37.500 9.86 5.80 0.00 2.83
659 2148 4.244862 CCGCCAATTTGAAATAAGCTTGT 58.755 39.130 9.86 0.00 0.00 3.16
663 2152 3.843999 TCACCGCCAATTTGAAATAAGC 58.156 40.909 0.00 0.00 0.00 3.09
667 2156 2.035321 ACGTTCACCGCCAATTTGAAAT 59.965 40.909 0.00 0.00 41.42 2.17
735 2226 3.663176 CAGCTGGTTGGTGTGCGG 61.663 66.667 5.57 0.00 39.17 5.69
1261 4167 5.593095 AGGCAGAGTGATAAACGTGATAGTA 59.407 40.000 0.00 0.00 0.00 1.82
1262 4168 4.402793 AGGCAGAGTGATAAACGTGATAGT 59.597 41.667 0.00 0.00 0.00 2.12
1263 4169 4.938080 AGGCAGAGTGATAAACGTGATAG 58.062 43.478 0.00 0.00 0.00 2.08
1347 4260 5.955961 AAATTTATATGCAAGCCCCTGTT 57.044 34.783 0.00 0.00 0.00 3.16
1373 4286 2.713877 TCAACCGCACCCCTTAAATAC 58.286 47.619 0.00 0.00 0.00 1.89
1419 4332 7.559486 TCATTAGCTTTGATAGAGCAGAAGAA 58.441 34.615 0.00 0.00 42.56 2.52
1487 4434 2.285024 GGGAGGCAGCAATGGCAAA 61.285 57.895 0.00 0.00 44.61 3.68
1534 4481 2.840066 AAGATCTCCTCGAGCCGCG 61.840 63.158 6.99 0.00 42.69 6.46
1547 4494 8.117813 TGGTTGGGTATTTTCTAAACAAGATC 57.882 34.615 0.00 0.00 33.05 2.75
1614 6607 2.676748 TGGACTTGGTTGCCTGAAAAT 58.323 42.857 0.00 0.00 0.00 1.82
1636 6629 9.778741 AGTATTTGATATCTTGCTCGGAATTAA 57.221 29.630 3.98 0.00 0.00 1.40
1638 6631 9.950496 ATAGTATTTGATATCTTGCTCGGAATT 57.050 29.630 3.98 0.00 0.00 2.17
1639 6632 9.950496 AATAGTATTTGATATCTTGCTCGGAAT 57.050 29.630 3.98 0.00 0.00 3.01
1662 6655 9.585099 ACTCACGTGATTAATTAAACGGTAATA 57.415 29.630 20.40 6.10 40.25 0.98
1663 6656 8.483307 ACTCACGTGATTAATTAAACGGTAAT 57.517 30.769 20.40 6.57 40.25 1.89
1682 6675 6.913132 ACAATAAGAGATATCGACAACTCACG 59.087 38.462 3.69 0.00 32.59 4.35
1692 6685 5.991606 TCTGCCCAAACAATAAGAGATATCG 59.008 40.000 0.00 0.00 0.00 2.92
1730 6723 1.369091 GCATTGGTCGCCTCGTCATT 61.369 55.000 0.00 0.00 0.00 2.57
1753 6746 0.593128 GACAGCAAACACCATCGCTT 59.407 50.000 0.00 0.00 30.72 4.68
1757 6750 2.030805 GGTCTTGACAGCAAACACCATC 60.031 50.000 3.08 0.00 37.15 3.51
1761 6754 3.002348 GTGTAGGTCTTGACAGCAAACAC 59.998 47.826 3.08 5.64 35.12 3.32
1770 6763 0.601558 TGAGCCGTGTAGGTCTTGAC 59.398 55.000 0.00 0.00 43.70 3.18
1802 6795 6.367421 CCTTAACGATTGTTGAATTTGTCGA 58.633 36.000 8.70 0.00 39.12 4.20
1810 6803 5.698832 CAATCTGCCTTAACGATTGTTGAA 58.301 37.500 8.70 0.00 39.25 2.69
1832 6825 0.475475 CATAGCCAGGGGAAGATGCA 59.525 55.000 0.00 0.00 0.00 3.96
1861 6857 2.433970 TGCATGATACTGGATGTCGGAA 59.566 45.455 0.00 0.00 0.00 4.30
1938 6935 3.954904 AGAACCATATCTGCACTAGACGT 59.045 43.478 0.00 0.00 38.49 4.34
2074 7098 8.656849 CACAATTAATATTCTACCTATCCACGC 58.343 37.037 0.00 0.00 0.00 5.34
2187 7407 2.969443 ACGACTTACATTGCTGCAAC 57.031 45.000 18.51 1.93 0.00 4.17
2276 7496 3.513768 TTGACGCTGCTCGCTTCCA 62.514 57.895 0.00 0.00 43.23 3.53
2283 7510 1.929836 CCAGATAACTTGACGCTGCTC 59.070 52.381 0.00 0.00 0.00 4.26
2348 7593 3.091633 ACTTAGTGGATGCATGGCTTT 57.908 42.857 2.46 0.00 0.00 3.51
2573 7830 0.464554 TGTGTTCACGTGCCCATCAA 60.465 50.000 11.67 0.00 0.00 2.57
2583 7840 3.486841 CCAAAGAAAGCATTGTGTTCACG 59.513 43.478 0.00 0.00 0.00 4.35
2635 7892 1.967319 ATGTTGTTGTTGGACGCTCT 58.033 45.000 0.00 0.00 0.00 4.09
2653 7910 4.534500 TGTATCCAGTCTGGGTGTTACAAT 59.466 41.667 19.11 4.98 38.32 2.71
2656 7914 4.504858 CTTGTATCCAGTCTGGGTGTTAC 58.495 47.826 19.11 14.63 38.32 2.50
2663 7921 4.872691 CACTTAAGCTTGTATCCAGTCTGG 59.127 45.833 13.21 13.21 39.43 3.86
2666 7924 6.654793 CTTCACTTAAGCTTGTATCCAGTC 57.345 41.667 9.86 0.00 0.00 3.51
2679 7937 6.175712 GAGAATCTGTTGGCTTCACTTAAG 57.824 41.667 0.00 0.00 38.32 1.85
2772 8041 1.364901 CCTTGGGCTGCAGTGTTTG 59.635 57.895 16.64 3.51 0.00 2.93
2803 8072 1.068741 GATTCTTGATAGGCGTCGGGT 59.931 52.381 0.00 0.00 0.00 5.28
2808 8077 2.398588 TGGGAGATTCTTGATAGGCGT 58.601 47.619 0.00 0.00 0.00 5.68
2816 8085 2.041620 TGGTTCCCTTGGGAGATTCTTG 59.958 50.000 8.55 0.00 0.00 3.02
2820 8089 2.450886 ACTTTGGTTCCCTTGGGAGATT 59.549 45.455 8.55 0.00 0.00 2.40
2863 8132 0.163788 CGACGCATCAACCAACTCAC 59.836 55.000 0.00 0.00 0.00 3.51
2868 8137 1.670674 GGTAGACGACGCATCAACCAA 60.671 52.381 0.00 0.00 0.00 3.67
2873 8142 1.065551 CAGATGGTAGACGACGCATCA 59.934 52.381 12.77 0.00 37.81 3.07
2888 8157 0.463295 AGAAGATGTGGCCGCAGATG 60.463 55.000 25.48 0.00 0.00 2.90
2935 8204 5.248380 AGTAGGGCACTTCTTCTGAAATT 57.752 39.130 0.00 0.00 31.59 1.82
2965 8234 2.322355 ATTTCTCATGGTCAGCCTCG 57.678 50.000 0.00 0.00 35.27 4.63
3006 8275 1.764723 TGGATCAGCTCAATCCATCGT 59.235 47.619 19.17 0.00 46.05 3.73
3036 8305 0.473755 TGTTGATGCTCCACCACACT 59.526 50.000 0.00 0.00 0.00 3.55
3038 8307 0.537143 GGTGTTGATGCTCCACCACA 60.537 55.000 3.28 0.00 46.33 4.17
3076 8345 3.189080 TCAGACTGAATCACCAAAATGCG 59.811 43.478 1.64 0.00 0.00 4.73
3092 8362 4.785376 ACCCCATGAAGAATAGTTCAGACT 59.215 41.667 0.00 0.00 39.78 3.24
3137 8407 6.020121 GTCGAGCACTTATTAAATTGTAGCGA 60.020 38.462 0.00 0.00 0.00 4.93
3164 8434 7.271511 TGCAGATTAAAAGTTTGTTCACCATT 58.728 30.769 0.00 0.00 0.00 3.16
3167 8437 6.366061 GGATGCAGATTAAAAGTTTGTTCACC 59.634 38.462 0.00 0.00 0.00 4.02
3227 12847 6.647334 TCACAATACCATGACACATGTTTT 57.353 33.333 0.00 0.00 0.00 2.43
3339 12964 9.671521 CTTCGTCTATTGTTAATTAAACGTGAG 57.328 33.333 14.24 10.94 41.30 3.51
3353 12978 6.590292 CCAATAACAGTGTCTTCGTCTATTGT 59.410 38.462 15.42 0.00 0.00 2.71
3360 12985 4.330944 TGACCAATAACAGTGTCTTCGT 57.669 40.909 0.00 0.00 0.00 3.85
3361 12986 4.084013 GGTTGACCAATAACAGTGTCTTCG 60.084 45.833 0.00 0.00 35.64 3.79
3363 12988 3.813166 CGGTTGACCAATAACAGTGTCTT 59.187 43.478 0.00 0.00 35.14 3.01
3446 13371 1.362355 CCCGAAAACCAAGGCACAC 59.638 57.895 0.00 0.00 0.00 3.82
3461 13386 4.252878 TGACACATATATGCTATTGCCCG 58.747 43.478 12.79 0.00 38.71 6.13
3521 13761 6.202188 CGGAAGAGTTTTTACTGCTAGTTTGA 59.798 38.462 0.00 0.00 0.00 2.69
3572 13813 4.916041 TGAAGAAGGTTGATCTCCATGT 57.084 40.909 9.47 0.00 0.00 3.21
3576 13817 3.876320 GCAGATGAAGAAGGTTGATCTCC 59.124 47.826 0.00 0.00 0.00 3.71
3578 13819 3.371380 GGGCAGATGAAGAAGGTTGATCT 60.371 47.826 0.00 0.00 0.00 2.75
3581 13822 1.339055 CGGGCAGATGAAGAAGGTTGA 60.339 52.381 0.00 0.00 0.00 3.18
3603 13844 1.709147 GCAACGCTCAATCGGCTCAT 61.709 55.000 0.00 0.00 0.00 2.90
3619 13860 0.889994 GATGGAGCAACATGTGGCAA 59.110 50.000 26.79 12.39 0.00 4.52
3660 13901 4.640789 AGAGTACTTTCTGCCTACGATG 57.359 45.455 0.00 0.00 0.00 3.84
3661 13902 4.822896 CCTAGAGTACTTTCTGCCTACGAT 59.177 45.833 0.00 0.00 0.00 3.73
3662 13903 4.197750 CCTAGAGTACTTTCTGCCTACGA 58.802 47.826 0.00 0.00 0.00 3.43
3663 13904 3.243134 GCCTAGAGTACTTTCTGCCTACG 60.243 52.174 0.00 0.00 0.00 3.51
3664 13905 3.955551 AGCCTAGAGTACTTTCTGCCTAC 59.044 47.826 0.00 0.00 0.00 3.18
3666 13907 3.108847 AGCCTAGAGTACTTTCTGCCT 57.891 47.619 0.00 0.00 0.00 4.75
3691 13934 0.398098 AGGGTGATGGTACGGTAGGG 60.398 60.000 0.00 0.00 0.00 3.53
3823 14080 9.946165 CTAGTCATATGTGAACGTATCAAACTA 57.054 33.333 1.90 0.00 40.50 2.24
3860 14122 5.357032 ACACCTTGTTTGCCTTATATACTGC 59.643 40.000 0.00 0.00 0.00 4.40
3876 14138 4.230745 ACCTACTTCAACAACACCTTGT 57.769 40.909 0.00 0.00 42.81 3.16
3879 14141 4.497291 TGAACCTACTTCAACAACACCT 57.503 40.909 0.00 0.00 35.84 4.00
3920 18524 1.204941 GCTACGTCCAGTTCACATCCT 59.795 52.381 0.00 0.00 0.00 3.24
3926 18530 2.750948 GTTTGAGCTACGTCCAGTTCA 58.249 47.619 0.00 0.00 34.42 3.18
3975 18586 1.066071 GTCCAGGACTTCAACCCTAGC 60.066 57.143 12.94 0.00 0.00 3.42
3984 18595 6.959522 ACACTAGTGTCAAGTCCAGGACTTC 61.960 48.000 29.39 20.20 43.55 3.01


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

AutoCloner maintained by Alex Coulton.