Multiple sequence alignment - TraesCS3A01G117200

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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 TraesCS3A01G117200 chr3A 100.000 7239 0 0 1 7239 86624183 86631421 0.000000e+00 13369.0
1 TraesCS3A01G117200 chr3A 79.391 1446 238 42 697 2103 55563414 55561990 0.000000e+00 965.0
2 TraesCS3A01G117200 chr3A 80.563 355 50 9 2460 2807 55561546 55561204 9.320000e-64 255.0
3 TraesCS3A01G117200 chr3A 80.282 355 51 9 2460 2807 55603298 55602956 4.340000e-62 250.0
4 TraesCS3A01G117200 chr3A 80.282 355 51 9 2460 2807 55605021 55604679 4.340000e-62 250.0
5 TraesCS3A01G117200 chr3D 92.105 4851 302 41 2436 7239 73761424 73766240 0.000000e+00 6761.0
6 TraesCS3A01G117200 chr3D 94.251 2435 124 9 1 2433 73758968 73761388 0.000000e+00 3707.0
7 TraesCS3A01G117200 chr3D 78.678 1604 275 50 544 2103 43781238 43782818 0.000000e+00 1005.0
8 TraesCS3A01G117200 chr3D 82.836 268 40 5 2544 2807 43783345 43783610 1.210000e-57 235.0
9 TraesCS3A01G117200 chr3D 96.364 55 2 0 5890 5944 73764844 73764898 2.780000e-14 91.6
10 TraesCS3A01G117200 chr3D 80.734 109 19 2 217 324 21715188 21715295 4.650000e-12 84.2
11 TraesCS3A01G117200 chr3B 89.949 3502 288 35 2436 5890 119086481 119089965 0.000000e+00 4458.0
12 TraesCS3A01G117200 chr3B 90.361 2407 196 19 2436 4813 136487249 136484850 0.000000e+00 3127.0
13 TraesCS3A01G117200 chr3B 93.595 2061 118 7 1 2050 119083750 119085807 0.000000e+00 3062.0
14 TraesCS3A01G117200 chr3B 93.350 2060 124 6 1 2050 136489979 136487923 0.000000e+00 3033.0
15 TraesCS3A01G117200 chr3B 93.063 1355 83 9 5889 7239 119089910 119091257 0.000000e+00 1971.0
16 TraesCS3A01G117200 chr3B 79.289 1463 248 39 619 2042 68403997 68402551 0.000000e+00 972.0
17 TraesCS3A01G117200 chr3B 94.148 393 21 2 2049 2441 136487677 136487287 1.340000e-166 597.0
18 TraesCS3A01G117200 chr3B 93.333 390 24 2 2049 2438 119086053 119086440 6.300000e-160 575.0
19 TraesCS3A01G117200 chr3B 88.889 171 19 0 2637 2807 68401879 68401709 2.050000e-50 211.0
20 TraesCS3A01G117200 chrUn 83.072 573 86 10 1301 1869 471930996 471931561 1.800000e-140 510.0
21 TraesCS3A01G117200 chr6A 88.934 244 23 4 3484 3724 601961128 601961370 1.530000e-76 298.0
22 TraesCS3A01G117200 chr2D 87.654 243 27 3 3484 3724 620601550 620601791 5.530000e-71 279.0
23 TraesCS3A01G117200 chr2D 80.198 101 14 6 229 325 313635677 313635775 3.620000e-08 71.3
24 TraesCS3A01G117200 chr2A 86.640 247 28 5 3484 3727 737498046 737498290 1.200000e-67 268.0
25 TraesCS3A01G117200 chr7D 85.950 242 31 3 3485 3724 64691313 64691073 9.320000e-64 255.0
26 TraesCS3A01G117200 chr4D 86.207 232 27 5 3485 3713 109270136 109270365 5.610000e-61 246.0
27 TraesCS3A01G117200 chr4D 83.333 78 13 0 247 324 417622978 417622901 1.010000e-08 73.1
28 TraesCS3A01G117200 chr1A 84.836 244 33 4 3485 3726 112946732 112946491 7.260000e-60 243.0
29 TraesCS3A01G117200 chr5D 80.469 128 20 4 186 313 362880549 362880671 7.730000e-15 93.5
30 TraesCS3A01G117200 chr6D 79.817 109 20 2 217 324 49450635 49450742 2.170000e-10 78.7
31 TraesCS3A01G117200 chr6B 78.512 121 16 8 217 332 123245079 123245194 3.620000e-08 71.3


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 TraesCS3A01G117200 chr3A 86624183 86631421 7238 False 13369.000000 13369 100.000000 1 7239 1 chr3A.!!$F1 7238
1 TraesCS3A01G117200 chr3A 55561204 55563414 2210 True 610.000000 965 79.977000 697 2807 2 chr3A.!!$R1 2110
2 TraesCS3A01G117200 chr3A 55602956 55605021 2065 True 250.000000 250 80.282000 2460 2807 2 chr3A.!!$R2 347
3 TraesCS3A01G117200 chr3D 73758968 73766240 7272 False 3519.866667 6761 94.240000 1 7239 3 chr3D.!!$F3 7238
4 TraesCS3A01G117200 chr3D 43781238 43783610 2372 False 620.000000 1005 80.757000 544 2807 2 chr3D.!!$F2 2263
5 TraesCS3A01G117200 chr3B 119083750 119091257 7507 False 2516.500000 4458 92.485000 1 7239 4 chr3B.!!$F1 7238
6 TraesCS3A01G117200 chr3B 136484850 136489979 5129 True 2252.333333 3127 92.619667 1 4813 3 chr3B.!!$R2 4812
7 TraesCS3A01G117200 chr3B 68401709 68403997 2288 True 591.500000 972 84.089000 619 2807 2 chr3B.!!$R1 2188
8 TraesCS3A01G117200 chrUn 471930996 471931561 565 False 510.000000 510 83.072000 1301 1869 1 chrUn.!!$F1 568

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
295 305 2.407340 TTGGCCCAAAATACAAGGGT 57.593 45.000 0.00 0.0 44.69 4.34 F
1151 1194 1.344763 GATCGGGGAACTACTGGATGG 59.655 57.143 0.00 0.0 0.00 3.51 F
1820 1870 0.109342 AGGTGGTGGCAGAAACTGAG 59.891 55.000 2.81 0.0 32.44 3.35 F
3117 5276 0.035739 GACCCGGTGAGCCTTTTGTA 59.964 55.000 0.00 0.0 0.00 2.41 F
4663 6856 0.106894 TACATTGTGTGTGTGGGCGA 59.893 50.000 0.00 0.0 42.24 5.54 F
5325 7529 1.000385 TCTTGGGAAATTGTTGCAGCG 60.000 47.619 0.00 0.0 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1235 1278 1.500474 TGAGGCCTTACCAGATGAGG 58.500 55.000 6.77 0.0 43.14 3.86 R
2475 2906 0.531532 GCTCCATGACGATGTCCCAG 60.532 60.000 0.00 0.0 0.00 4.45 R
3197 5357 0.107081 CCGGGGCCACATAATTACGA 59.893 55.000 5.46 0.0 0.00 3.43 R
4828 7024 0.173255 CATTTGCGGGGAATGGACAC 59.827 55.000 0.00 0.0 32.24 3.67 R
5605 7816 0.755698 GGCCCCACTCTCTACGATGA 60.756 60.000 0.00 0.0 0.00 2.92 R
6726 8949 1.008327 TGGAGCCAGTGAGGATTAGGA 59.992 52.381 0.00 0.0 41.22 2.94 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
78 87 5.753744 CCACGTTGTACACACAAAATACAT 58.246 37.500 0.00 0.00 45.99 2.29
98 107 4.715297 ACATTATTTGTACTCCCTCCGTCT 59.285 41.667 0.00 0.00 36.57 4.18
110 119 4.346730 TCCCTCCGTCTGTGTTTATTAGA 58.653 43.478 0.00 0.00 0.00 2.10
130 139 4.147321 AGACACATTCACATTTTGAGCCT 58.853 39.130 0.00 0.00 34.94 4.58
188 198 8.172484 TGAATTATATGTAGCAAAACGTGTCAC 58.828 33.333 0.00 0.00 0.00 3.67
208 218 8.352942 GTGTCACTGAAAACTTCCTTTGAATAT 58.647 33.333 0.00 0.00 0.00 1.28
295 305 2.407340 TTGGCCCAAAATACAAGGGT 57.593 45.000 0.00 0.00 44.69 4.34
368 378 6.530019 TCTAAATGACAGTCTGCACTATCA 57.470 37.500 1.31 0.00 40.41 2.15
411 421 4.300189 AGCGTTCAACAAACAAATGCTA 57.700 36.364 0.00 0.00 42.00 3.49
446 456 5.893687 TGATTTGTTTCGATGCTATGCAAT 58.106 33.333 0.00 0.00 43.62 3.56
666 683 4.836125 AAATTGGCCAAGTAGCATATCG 57.164 40.909 24.94 0.00 0.00 2.92
896 930 6.951062 TTTAAAGGTGTGTCATGTTCATCA 57.049 33.333 0.00 0.00 0.00 3.07
924 958 6.772360 TCTTGAAATTGTAGCATTATGGCA 57.228 33.333 0.00 0.00 35.83 4.92
999 1042 8.143193 CCATTTATATTATTGCAGCAACCTCAA 58.857 33.333 10.85 2.93 0.00 3.02
1004 1047 5.465532 TTATTGCAGCAACCTCAAATGAA 57.534 34.783 10.85 0.00 0.00 2.57
1151 1194 1.344763 GATCGGGGAACTACTGGATGG 59.655 57.143 0.00 0.00 0.00 3.51
1235 1278 4.725556 TGCGGAAAAATAGATATGACGC 57.274 40.909 0.00 0.00 44.14 5.19
1642 1688 1.002033 GAAGCCATATTGGAGCTTGCG 60.002 52.381 0.51 0.00 46.44 4.85
1710 1756 9.112725 GTTAAAAGAGGTCACCTTGTAAGTTTA 57.887 33.333 0.00 0.00 31.76 2.01
1711 1757 9.856162 TTAAAAGAGGTCACCTTGTAAGTTTAT 57.144 29.630 0.00 0.00 31.76 1.40
1793 1843 9.520515 AAGAATTCCAACTGACTTATGTTATGT 57.479 29.630 0.65 0.00 0.00 2.29
1818 1868 1.347707 TCTAGGTGGTGGCAGAAACTG 59.652 52.381 0.00 0.00 34.12 3.16
1820 1870 0.109342 AGGTGGTGGCAGAAACTGAG 59.891 55.000 2.81 0.00 32.44 3.35
1821 1871 1.518903 GGTGGTGGCAGAAACTGAGC 61.519 60.000 2.81 0.00 32.44 4.26
2002 2052 1.538512 GCACTGAAGAGAGCATGCAAA 59.461 47.619 21.98 0.00 35.96 3.68
2006 2056 3.825014 ACTGAAGAGAGCATGCAAATTGT 59.175 39.130 21.98 5.19 0.00 2.71
2038 2088 9.640952 CAATTAATAGGTTAAATCCTCCTTCCA 57.359 33.333 0.00 0.00 38.86 3.53
2355 2744 9.709495 TTGTCTACGTAATAAACATTGTACCTT 57.291 29.630 0.00 0.00 0.00 3.50
2427 2816 9.869757 AACTATAAGTAATTCCATTTTGGCAAC 57.130 29.630 0.00 0.00 37.47 4.17
2475 2906 7.860373 TGCACATGTAAACATTAGAGTGAAAAC 59.140 33.333 12.79 0.44 33.61 2.43
2498 2929 1.269723 GGACATCGTCATGGAGCGATA 59.730 52.381 16.09 0.00 44.68 2.92
2677 4832 0.251297 CAGGTGGGATGAAGGTGCAA 60.251 55.000 0.00 0.00 0.00 4.08
2775 4930 0.101579 GACCTGAGAAGAGCTACCGC 59.898 60.000 0.00 0.00 0.00 5.68
2817 4972 9.162764 GAATCGGCAAGTATTATATGTTACCAT 57.837 33.333 0.00 0.00 34.97 3.55
2892 5047 9.547753 TGCATTCTCTTACTAATATTTGGTCTC 57.452 33.333 0.00 0.00 0.00 3.36
2893 5048 8.994170 GCATTCTCTTACTAATATTTGGTCTCC 58.006 37.037 0.00 0.00 0.00 3.71
2900 5056 3.350219 AATATTTGGTCTCCGTGTGCT 57.650 42.857 0.00 0.00 0.00 4.40
3096 5255 7.068348 GTGGAACTAGAACATGTAGGACTATGA 59.932 40.741 0.00 0.00 0.00 2.15
3097 5256 7.785028 TGGAACTAGAACATGTAGGACTATGAT 59.215 37.037 0.00 0.00 0.00 2.45
3104 5263 2.594131 TGTAGGACTATGATGACCCGG 58.406 52.381 0.00 0.00 0.00 5.73
3117 5276 0.035739 GACCCGGTGAGCCTTTTGTA 59.964 55.000 0.00 0.00 0.00 2.41
3167 5327 9.929180 GAGCCAGTTATAAATAGTCATCACATA 57.071 33.333 0.00 0.00 0.00 2.29
3197 5357 6.709281 TGTCATTATTGCAACAATCCCATTT 58.291 32.000 0.00 0.00 0.00 2.32
3199 5359 6.019640 GTCATTATTGCAACAATCCCATTTCG 60.020 38.462 0.00 0.00 0.00 3.46
3221 5381 2.279037 ATTATGTGGCCCCGGGTGAC 62.279 60.000 21.85 14.21 0.00 3.67
3244 5404 0.383231 GCCCGAGATCCAAATTGCAG 59.617 55.000 0.00 0.00 0.00 4.41
3302 5471 8.937207 ACTTAAGTCGATACCTATAGATGGTT 57.063 34.615 1.12 0.00 38.88 3.67
3323 5492 2.026729 TGGATACAGGTTGCGATTCCAA 60.027 45.455 0.00 0.00 46.17 3.53
3338 5507 2.917713 TCCAACCCTATGCATTTGGT 57.082 45.000 21.66 17.49 39.69 3.67
3384 5553 9.275398 ACAAAATTAATGAGACGGTGTACTAAA 57.725 29.630 0.00 0.00 0.00 1.85
3388 5557 9.886132 AATTAATGAGACGGTGTACTAAAATCT 57.114 29.630 0.00 0.00 0.00 2.40
3410 5579 1.133792 AACCAAGTCCTGGGTGAACTG 60.134 52.381 0.00 0.00 46.64 3.16
3413 5582 2.571653 CCAAGTCCTGGGTGAACTGATA 59.428 50.000 0.00 0.00 42.17 2.15
3414 5583 3.200825 CCAAGTCCTGGGTGAACTGATAT 59.799 47.826 0.00 0.00 42.17 1.63
3426 5595 6.147821 GGGTGAACTGATATAATGACCAATCG 59.852 42.308 0.00 0.00 0.00 3.34
3557 5729 8.519492 ACTTTGATTCATAATTTTGGTCAACG 57.481 30.769 13.08 13.42 0.00 4.10
3617 5791 8.579682 AGAAAGTCTTTAAAATGTGCATTCAC 57.420 30.769 0.00 0.00 43.40 3.18
3770 5945 8.553459 AACTCATTGACTCGTAGAATTTCAAT 57.447 30.769 0.00 0.00 39.58 2.57
3809 5984 7.534723 ACTAGTGGTTAATAACTGACACTCA 57.465 36.000 13.93 4.58 39.59 3.41
3826 6001 5.930135 ACACTCAGGAAGTTAATCTTGTGT 58.070 37.500 0.00 0.00 35.45 3.72
3827 6002 7.062749 ACACTCAGGAAGTTAATCTTGTGTA 57.937 36.000 0.00 0.00 36.89 2.90
3855 6030 4.210537 CGGGTGATAACGGTTAAGCATTAG 59.789 45.833 4.47 0.00 0.00 1.73
3863 6038 6.569179 AACGGTTAAGCATTAGAACAATGT 57.431 33.333 5.38 0.00 0.00 2.71
3872 6047 8.748380 AAGCATTAGAACAATGTTAAGCTTTC 57.252 30.769 3.20 0.00 35.30 2.62
3896 6071 3.798878 CACCTGCTATAAGATGTGTCACG 59.201 47.826 0.00 0.00 0.00 4.35
3898 6073 2.797156 CTGCTATAAGATGTGTCACGCC 59.203 50.000 0.00 0.00 0.00 5.68
3899 6074 2.135933 GCTATAAGATGTGTCACGCCC 58.864 52.381 0.00 0.00 0.00 6.13
3913 6090 2.814919 TCACGCCCGATACAATTTGTTT 59.185 40.909 7.45 0.00 0.00 2.83
3920 6097 8.838365 ACGCCCGATACAATTTGTTTTATAATA 58.162 29.630 7.45 0.00 0.00 0.98
3952 6129 6.840780 ACTTGAATCATTAGGAACCTTTGG 57.159 37.500 0.00 0.00 0.00 3.28
4002 6179 6.588373 GTGTGGTCTCTTCTTCTCTTATTCAC 59.412 42.308 0.00 0.00 0.00 3.18
4003 6180 5.802956 GTGGTCTCTTCTTCTCTTATTCACG 59.197 44.000 0.00 0.00 0.00 4.35
4029 6206 6.212388 TGGGTGACTGCCAATAACATTAATTT 59.788 34.615 0.00 0.00 0.00 1.82
4164 6341 5.621197 TGAAACAATTTGGATGTAGGTCG 57.379 39.130 0.78 0.00 0.00 4.79
4257 6436 9.007901 AGGTCTTCAGTTTAGAAAAATCAGATG 57.992 33.333 0.00 0.00 0.00 2.90
4355 6534 6.989759 ACAAAATTAACCCACCAATTGACTTC 59.010 34.615 7.12 0.00 0.00 3.01
4359 6538 2.597455 ACCCACCAATTGACTTCTTGG 58.403 47.619 7.12 3.48 46.03 3.61
4363 6542 2.624838 CACCAATTGACTTCTTGGCACT 59.375 45.455 7.12 0.00 44.74 4.40
4437 6616 3.004839 CGAATTGAGGATAGCTCGGAAGA 59.995 47.826 0.00 0.00 39.12 2.87
4473 6652 1.706305 TGAACCTATCAACCGGGGTTT 59.294 47.619 6.32 0.00 41.44 3.27
4546 6725 4.537015 CTTTTTGTTCATTGGGAGTCGAC 58.463 43.478 7.70 7.70 0.00 4.20
4563 6754 2.056577 CGACGTTCCCTACAAGTTGTC 58.943 52.381 12.82 0.00 0.00 3.18
4564 6755 2.410939 GACGTTCCCTACAAGTTGTCC 58.589 52.381 12.82 0.00 0.00 4.02
4592 6783 9.300681 TGGTAACTTCATTGATCTCAAGATTTT 57.699 29.630 0.00 0.00 36.98 1.82
4636 6827 0.767375 CATAGGGCTAGGGTGTGCAT 59.233 55.000 0.00 0.00 0.00 3.96
4661 6854 1.001815 GTGTACATTGTGTGTGTGGGC 60.002 52.381 0.00 0.00 42.24 5.36
4663 6856 0.106894 TACATTGTGTGTGTGGGCGA 59.893 50.000 0.00 0.00 42.24 5.54
4665 6858 1.148273 ATTGTGTGTGTGGGCGAGT 59.852 52.632 0.00 0.00 0.00 4.18
4680 6873 1.863662 CGAGTGGGCTCTACGTGTGT 61.864 60.000 0.00 0.00 39.53 3.72
4713 6906 5.066764 GCTGTGTTTGTACTAGGTTTCCAAA 59.933 40.000 0.00 0.00 0.00 3.28
4820 7016 9.148879 TCATGAAAACCAAATTCCCTAGTAAAA 57.851 29.630 0.00 0.00 0.00 1.52
4828 7024 9.996554 ACCAAATTCCCTAGTAAAATTTTCTTG 57.003 29.630 6.72 5.92 31.91 3.02
5006 7203 8.845227 ACATTTTGGGTGATTAATTTTGAAACC 58.155 29.630 0.00 0.00 0.00 3.27
5031 7235 8.514594 CCTCAAGAAATTAGTTCAAGCATACAA 58.485 33.333 0.00 0.00 38.86 2.41
5068 7272 3.428725 GGCGTGATGAAAAATATGTGCCA 60.429 43.478 0.00 0.00 38.60 4.92
5208 7412 2.925306 GCGAGGCGAAACTTCTCAAGTA 60.925 50.000 0.00 0.00 41.91 2.24
5232 7436 5.984233 TTTGCTATATTTGTACGGCTCAG 57.016 39.130 0.00 0.00 0.00 3.35
5290 7494 8.777865 TTAGAGATGTACTTGACTTCAAATGG 57.222 34.615 0.00 0.00 35.20 3.16
5311 7515 4.202274 TGGATATTTTGCATGCATCTTGGG 60.202 41.667 23.37 0.00 0.00 4.12
5315 7519 3.985019 TTTGCATGCATCTTGGGAAAT 57.015 38.095 23.37 0.00 0.00 2.17
5325 7529 1.000385 TCTTGGGAAATTGTTGCAGCG 60.000 47.619 0.00 0.00 0.00 5.18
5328 7532 1.617850 TGGGAAATTGTTGCAGCGATT 59.382 42.857 10.04 10.04 0.00 3.34
5341 7545 6.526325 TGTTGCAGCGATTTGAACATAATTAC 59.474 34.615 0.00 0.00 0.00 1.89
5435 7639 7.306399 GCACATATGTATCTTTTTGCATGCTTC 60.306 37.037 20.33 0.00 0.00 3.86
5538 7746 7.466746 AACCATTTTCAATCTTGCTTAGCTA 57.533 32.000 5.60 0.00 0.00 3.32
5539 7747 7.651027 ACCATTTTCAATCTTGCTTAGCTAT 57.349 32.000 5.60 0.00 0.00 2.97
5605 7816 3.727726 TGACGATGAATACGATGGCATT 58.272 40.909 0.00 0.00 34.70 3.56
5606 7817 3.740832 TGACGATGAATACGATGGCATTC 59.259 43.478 0.00 0.00 34.70 2.67
5607 7818 3.727726 ACGATGAATACGATGGCATTCA 58.272 40.909 0.00 5.90 43.34 2.57
5750 7969 4.524328 AGAAAGGTGAAACATAGCCCTTTG 59.476 41.667 6.70 0.00 43.63 2.77
5775 7994 5.528043 TTATGAGATCTCAAGTGAGGAGC 57.472 43.478 28.40 0.00 43.58 4.70
5836 8056 3.525862 AGAGGTCTTCTGAACATCCCTT 58.474 45.455 0.00 0.00 33.93 3.95
6032 8253 1.717113 CGACAAAAGATGACGCGTGTA 59.283 47.619 20.70 5.70 40.05 2.90
6035 8256 4.128554 ACAAAAGATGACGCGTGTAAAG 57.871 40.909 20.70 0.78 0.00 1.85
6186 8407 4.210537 GCATACCGACGCATACACTAATTT 59.789 41.667 0.00 0.00 0.00 1.82
6193 8414 5.398711 CGACGCATACACTAATTTAGAGACC 59.601 44.000 10.39 0.00 0.00 3.85
6230 8451 9.512435 CTATAAGAATGCTTTTTGTTGATCCAG 57.488 33.333 0.00 0.00 35.56 3.86
6309 8530 3.745332 GCTTTTGCAACAATAATGCCC 57.255 42.857 0.00 0.00 46.58 5.36
6338 8559 4.937620 TGTTAGAATGGTGATCAAGAGCAC 59.062 41.667 9.81 9.81 46.13 4.40
6400 8622 1.080298 AAACAAACGTGTCGTGCTCA 58.920 45.000 0.00 0.00 39.99 4.26
6432 8654 8.398665 GGGAATGTATGAGTGACATTAAACTTC 58.601 37.037 1.21 0.00 45.33 3.01
6488 8710 6.154445 TGCTTTCTTTCATTCATTTGCTCTC 58.846 36.000 0.00 0.00 0.00 3.20
6594 8816 5.789574 ATCCAATCAAGGGGTAAGTTACA 57.210 39.130 14.81 0.00 0.00 2.41
6602 8824 5.824097 TCAAGGGGTAAGTTACACTTCAAAC 59.176 40.000 14.80 0.00 39.51 2.93
6670 8893 3.587923 TGCATTTTTGTAAGGAGCATGC 58.412 40.909 10.51 10.51 36.82 4.06
6708 8931 6.095440 GCCAACATTGTGATAATACAAGTCCT 59.905 38.462 0.00 0.00 43.14 3.85
6726 8949 0.255318 CTTGCATCTTGCTCCTCCCT 59.745 55.000 0.75 0.00 45.31 4.20
6738 8961 2.604139 CTCCTCCCTCCTAATCCTCAC 58.396 57.143 0.00 0.00 0.00 3.51
6798 9021 4.336153 CACAATCGTCATCCCAATCATGAA 59.664 41.667 0.00 0.00 31.98 2.57
6896 9119 0.517316 GTCATCAACCCGTGCAACTC 59.483 55.000 0.00 0.00 31.75 3.01
6925 9148 6.591001 TGGCTAGCAATTAATGAGACACATA 58.409 36.000 18.24 0.00 38.38 2.29
7033 9258 6.038936 TCAAATGATGCATCAAGGTGATACAG 59.961 38.462 31.79 13.00 40.69 2.74
7048 9273 5.756347 GGTGATACAGCCGTACATAATTCAA 59.244 40.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.183360 TGTGATTGTCATGTTTTCACGAGAAA 60.183 34.615 3.76 3.76 41.78 2.52
78 87 4.081862 CACAGACGGAGGGAGTACAAATAA 60.082 45.833 0.00 0.00 0.00 1.40
110 119 5.536161 ACTTAGGCTCAAAATGTGAATGTGT 59.464 36.000 0.00 0.00 35.22 3.72
130 139 9.121658 TGTTACACAAATGTATGGTCAAACTTA 57.878 29.630 0.00 0.00 41.02 2.24
181 190 4.094294 TCAAAGGAAGTTTTCAGTGACACG 59.906 41.667 0.00 0.00 0.00 4.49
259 269 5.779771 TGGGCCAAATTTTGACTCTAGATTT 59.220 36.000 2.13 0.00 0.00 2.17
295 305 0.178533 CCGTCCGGGTTTATTAGGCA 59.821 55.000 0.00 0.00 0.00 4.75
368 378 7.283127 ACGCTATTTGTGATAACAAATCCTCAT 59.717 33.333 22.14 3.77 44.25 2.90
389 399 4.300189 AGCATTTGTTTGTTGAACGCTA 57.700 36.364 0.00 0.00 41.29 4.26
393 403 7.897800 GTGTTTTCTAGCATTTGTTTGTTGAAC 59.102 33.333 0.00 0.00 38.78 3.18
411 421 5.068460 TCGAAACAAATCATGGGTGTTTTCT 59.932 36.000 17.57 3.09 43.60 2.52
446 456 5.486063 ACCTATACCCATCACACAGTAAACA 59.514 40.000 0.00 0.00 0.00 2.83
518 528 6.652245 ACTATTGTTGTAAAAGTTTCGACCG 58.348 36.000 0.00 0.00 0.00 4.79
666 683 3.129638 TGGTGTGCAACTCTTGGTTTTAC 59.870 43.478 0.00 0.00 38.04 2.01
878 912 3.181451 ACTGTGATGAACATGACACACCT 60.181 43.478 0.00 0.00 38.39 4.00
895 929 9.069078 CATAATGCTACAATTTCAAGAACTGTG 57.931 33.333 6.88 0.00 0.00 3.66
896 930 8.246180 CCATAATGCTACAATTTCAAGAACTGT 58.754 33.333 3.19 3.19 0.00 3.55
1004 1047 8.090831 GCTCCAATAAAACTTCCATTCTTTCTT 58.909 33.333 0.00 0.00 0.00 2.52
1076 1119 6.697455 TCGTTCAAGCAAGAGTATAAGCTATG 59.303 38.462 0.00 0.00 36.07 2.23
1078 1121 6.034591 GTCGTTCAAGCAAGAGTATAAGCTA 58.965 40.000 0.00 0.00 36.07 3.32
1091 1134 0.662619 CAAGCCAAGTCGTTCAAGCA 59.337 50.000 0.00 0.00 0.00 3.91
1151 1194 6.775088 TCATCATAATCAGAGTTCAAAACGC 58.225 36.000 0.00 0.00 36.23 4.84
1235 1278 1.500474 TGAGGCCTTACCAGATGAGG 58.500 55.000 6.77 0.00 43.14 3.86
1663 1709 6.773976 AACTCCTCACAAAAATGAAGTTGA 57.226 33.333 0.00 0.00 0.00 3.18
1762 1811 9.167311 ACATAAGTCAGTTGGAATTCTTATGAC 57.833 33.333 21.41 18.41 42.99 3.06
1793 1843 2.265367 TCTGCCACCACCTAGAATGAA 58.735 47.619 0.00 0.00 0.00 2.57
1818 1868 2.673368 ACTCAAATTTGATCCGACGCTC 59.327 45.455 20.76 0.00 36.46 5.03
1820 1870 3.471495 AACTCAAATTTGATCCGACGC 57.529 42.857 20.76 0.00 36.46 5.19
1821 1871 5.029650 TGAAACTCAAATTTGATCCGACG 57.970 39.130 20.76 10.76 36.46 5.12
2139 2512 9.694520 CTTTTCTGTTTGTATGACTCGATATTG 57.305 33.333 0.00 0.00 0.00 1.90
2450 2881 8.076178 AGTTTTCACTCTAATGTTTACATGTGC 58.924 33.333 9.11 0.00 36.56 4.57
2457 2888 7.284074 TGTCCCAGTTTTCACTCTAATGTTTA 58.716 34.615 0.00 0.00 0.00 2.01
2475 2906 0.531532 GCTCCATGACGATGTCCCAG 60.532 60.000 0.00 0.00 0.00 4.45
2677 4832 7.071069 TCATGTATTCTGGAAGCACATCTAT 57.929 36.000 9.12 0.00 0.00 1.98
2775 4930 5.064198 TGCCGATTCTTTAAGATAAACCACG 59.936 40.000 0.00 0.00 0.00 4.94
2810 4965 7.443259 TGCCAAACTAGTTTTCTATGGTAAC 57.557 36.000 18.25 5.49 34.37 2.50
2891 5046 1.672030 CATCTTGGCAGCACACGGA 60.672 57.895 0.00 0.00 0.00 4.69
2892 5047 1.236616 TTCATCTTGGCAGCACACGG 61.237 55.000 0.00 0.00 0.00 4.94
2893 5048 0.592637 TTTCATCTTGGCAGCACACG 59.407 50.000 0.00 0.00 0.00 4.49
2900 5056 5.698104 AGATCATGGTATTTCATCTTGGCA 58.302 37.500 0.00 0.00 0.00 4.92
3013 5169 7.928167 TGTAGACTTGCAAACAGATCTATATGG 59.072 37.037 0.00 0.00 30.89 2.74
3014 5170 8.877808 TGTAGACTTGCAAACAGATCTATATG 57.122 34.615 0.00 0.00 30.89 1.78
3016 5172 8.749354 TCTTGTAGACTTGCAAACAGATCTATA 58.251 33.333 0.00 0.00 30.89 1.31
3096 5255 0.609131 CAAAAGGCTCACCGGGTCAT 60.609 55.000 6.32 0.00 42.76 3.06
3097 5256 1.228124 CAAAAGGCTCACCGGGTCA 60.228 57.895 6.32 0.00 42.76 4.02
3117 5276 2.806244 ACGCTAAGAAACACGAAGCATT 59.194 40.909 0.00 0.00 33.10 3.56
3167 5327 7.550196 GGGATTGTTGCAATAATGACAATTTCT 59.450 33.333 24.00 0.00 41.37 2.52
3197 5357 0.107081 CCGGGGCCACATAATTACGA 59.893 55.000 5.46 0.00 0.00 3.43
3199 5359 0.184211 ACCCGGGGCCACATAATTAC 59.816 55.000 27.92 0.00 0.00 1.89
3221 5381 1.094785 AATTTGGATCTCGGGCAACG 58.905 50.000 0.00 0.00 46.11 4.10
3302 5471 1.557371 TGGAATCGCAACCTGTATCCA 59.443 47.619 0.00 0.00 33.32 3.41
3323 5492 5.137551 GGTTATGTACCAAATGCATAGGGT 58.862 41.667 21.70 21.70 46.92 4.34
3338 5507 8.749026 TTTTGTAGAAGTGTTTGGGTTATGTA 57.251 30.769 0.00 0.00 0.00 2.29
3373 5542 7.148523 GGACTTGGTTTAGATTTTAGTACACCG 60.149 40.741 0.00 0.00 0.00 4.94
3384 5553 3.655777 TCACCCAGGACTTGGTTTAGATT 59.344 43.478 2.53 0.00 46.25 2.40
3388 5557 2.781174 AGTTCACCCAGGACTTGGTTTA 59.219 45.455 2.53 0.00 46.25 2.01
3403 5572 7.946655 TCGATTGGTCATTATATCAGTTCAC 57.053 36.000 0.00 0.00 0.00 3.18
3410 5579 9.689976 CCATCTAGATCGATTGGTCATTATATC 57.310 37.037 1.03 0.00 0.00 1.63
3413 5582 7.724490 TCCATCTAGATCGATTGGTCATTAT 57.276 36.000 11.81 0.00 0.00 1.28
3414 5583 7.539034 TTCCATCTAGATCGATTGGTCATTA 57.461 36.000 11.81 0.00 0.00 1.90
3484 5655 2.579624 TAAGGGCATTGGAGGGAGTA 57.420 50.000 0.00 0.00 0.00 2.59
3485 5656 1.496429 CATAAGGGCATTGGAGGGAGT 59.504 52.381 0.00 0.00 0.00 3.85
3487 5658 0.185901 GCATAAGGGCATTGGAGGGA 59.814 55.000 0.00 0.00 0.00 4.20
3489 5660 1.684983 CTTGCATAAGGGCATTGGAGG 59.315 52.381 0.00 0.00 44.48 4.30
3517 5688 6.863645 TGAATCAAAGTTTGACACGAAAAACA 59.136 30.769 20.26 7.60 43.48 2.83
3587 5760 9.643693 ATGCACATTTTAAAGACTTTCTAATGG 57.356 29.630 24.34 18.28 32.40 3.16
3617 5791 8.677300 AGTTATATGCCACAAAAAGTATGTCAG 58.323 33.333 0.00 0.00 0.00 3.51
3705 5879 0.181350 GTACTCCCTGCATCCCCTTG 59.819 60.000 0.00 0.00 0.00 3.61
3711 5885 4.461081 CACTATCCTAGTACTCCCTGCATC 59.539 50.000 0.00 0.00 37.23 3.91
3750 5924 8.877779 CAGAAGATTGAAATTCTACGAGTCAAT 58.122 33.333 0.00 0.00 40.65 2.57
3809 5984 6.331061 CGTAGCTACACAAGATTAACTTCCT 58.669 40.000 23.21 0.00 36.61 3.36
3826 6001 2.057137 ACCGTTATCACCCGTAGCTA 57.943 50.000 0.00 0.00 0.00 3.32
3827 6002 1.188863 AACCGTTATCACCCGTAGCT 58.811 50.000 0.00 0.00 0.00 3.32
3855 6030 6.145535 CAGGTGAGAAAGCTTAACATTGTTC 58.854 40.000 5.07 0.00 33.14 3.18
3863 6038 7.182817 TCTTATAGCAGGTGAGAAAGCTTAA 57.817 36.000 0.00 0.00 38.47 1.85
3872 6047 5.046529 GTGACACATCTTATAGCAGGTGAG 58.953 45.833 0.00 0.00 0.00 3.51
4002 6179 0.802494 GTTATTGGCAGTCACCCACG 59.198 55.000 0.00 0.00 30.65 4.94
4003 6180 1.904287 TGTTATTGGCAGTCACCCAC 58.096 50.000 0.00 0.00 30.65 4.61
4029 6206 8.780846 TTGTGTTTCAACTCTAACAACTAGAA 57.219 30.769 0.00 0.00 36.17 2.10
4164 6341 6.395629 TGTGAACTAGCTAGGTTTATCACAC 58.604 40.000 26.71 22.00 29.98 3.82
4217 6396 3.652869 TGAAGACCTTGTCCCATTTCTCT 59.347 43.478 0.00 0.00 32.18 3.10
4218 6397 4.006319 CTGAAGACCTTGTCCCATTTCTC 58.994 47.826 0.00 0.00 32.18 2.87
4219 6398 3.395941 ACTGAAGACCTTGTCCCATTTCT 59.604 43.478 0.00 0.00 32.18 2.52
4293 6472 9.541143 AATGTTTAAAGGTGTGTTCTATTTTGG 57.459 29.630 0.00 0.00 0.00 3.28
4341 6520 1.962807 TGCCAAGAAGTCAATTGGTGG 59.037 47.619 5.42 5.42 46.36 4.61
4355 6534 9.643693 AAAATGAAAGATAATTACAGTGCCAAG 57.356 29.630 0.00 0.00 0.00 3.61
4359 6538 8.250332 TGGGAAAATGAAAGATAATTACAGTGC 58.750 33.333 0.00 0.00 0.00 4.40
4404 6583 8.031864 AGCTATCCTCAATTCGTTGATACTATG 58.968 37.037 0.00 0.00 0.00 2.23
4424 6603 6.524101 AGGAATCTAATCTTCCGAGCTATC 57.476 41.667 0.00 0.00 45.63 2.08
4437 6616 5.520748 AGGTTCACCACAAGGAATCTAAT 57.479 39.130 0.00 0.00 32.89 1.73
4546 6725 1.269936 ACGGACAACTTGTAGGGAACG 60.270 52.381 0.00 0.00 0.00 3.95
4563 6754 4.503910 TGAGATCAATGAAGTTACCACGG 58.496 43.478 0.00 0.00 0.00 4.94
4564 6755 5.869344 TCTTGAGATCAATGAAGTTACCACG 59.131 40.000 0.00 0.00 35.02 4.94
4636 6827 3.013219 ACACACACAATGTACACAAGCA 58.987 40.909 0.00 0.00 40.64 3.91
4663 6856 1.113517 ACACACACGTAGAGCCCACT 61.114 55.000 0.00 0.00 0.00 4.00
4665 6858 1.475280 GATACACACACGTAGAGCCCA 59.525 52.381 0.00 0.00 0.00 5.36
4680 6873 5.468540 AGTACAAACACAGCTCAGATACA 57.531 39.130 0.00 0.00 0.00 2.29
4820 7016 2.825532 CGGGGAATGGACACAAGAAAAT 59.174 45.455 0.00 0.00 0.00 1.82
4828 7024 0.173255 CATTTGCGGGGAATGGACAC 59.827 55.000 0.00 0.00 32.24 3.67
4830 7026 1.757682 TACATTTGCGGGGAATGGAC 58.242 50.000 0.00 0.00 38.50 4.02
4886 7082 6.547141 CCATTGTCCATCTACATGTTTGGTAT 59.453 38.462 2.30 3.28 0.00 2.73
5006 7203 9.334693 GTTGTATGCTTGAACTAATTTCTTGAG 57.665 33.333 0.00 0.00 34.97 3.02
5068 7272 8.352942 ACTTCAAGATGTTCGCTTATTTTCTTT 58.647 29.630 0.00 0.00 0.00 2.52
5077 7281 5.273944 GTTGAAACTTCAAGATGTTCGCTT 58.726 37.500 5.13 0.00 46.80 4.68
5138 7342 6.142798 GCATTTATGTTATCCATGCAAACGAG 59.857 38.462 0.00 0.00 40.06 4.18
5144 7348 4.140536 TCCGCATTTATGTTATCCATGCA 58.859 39.130 0.00 0.00 40.28 3.96
5192 7396 5.452777 AGCAAAATACTTGAGAAGTTTCGC 58.547 37.500 0.00 0.00 42.81 4.70
5208 7412 6.017109 CCTGAGCCGTACAAATATAGCAAAAT 60.017 38.462 0.00 0.00 0.00 1.82
5232 7436 1.131126 CTGTTGATGCCATGTCGTTCC 59.869 52.381 0.00 0.00 0.00 3.62
5290 7494 5.204409 TCCCAAGATGCATGCAAAATATC 57.796 39.130 26.68 17.18 0.00 1.63
5311 7515 4.208873 TGTTCAAATCGCTGCAACAATTTC 59.791 37.500 0.00 0.00 0.00 2.17
5315 7519 2.859526 TGTTCAAATCGCTGCAACAA 57.140 40.000 0.00 0.00 0.00 2.83
5439 7643 7.817418 ACCATAACAATATGTGGTTATCACC 57.183 36.000 0.00 0.00 45.48 4.02
5538 7746 3.243636 CCAGTTTCACTTCAAGCTTGCAT 60.244 43.478 21.99 6.35 0.00 3.96
5539 7747 2.099592 CCAGTTTCACTTCAAGCTTGCA 59.900 45.455 21.99 10.41 0.00 4.08
5605 7816 0.755698 GGCCCCACTCTCTACGATGA 60.756 60.000 0.00 0.00 0.00 2.92
5606 7817 1.742768 GGCCCCACTCTCTACGATG 59.257 63.158 0.00 0.00 0.00 3.84
5607 7818 1.457831 GGGCCCCACTCTCTACGAT 60.458 63.158 12.23 0.00 0.00 3.73
5658 7869 5.278758 GGAAACTTGTAAACATAGCAGCCAA 60.279 40.000 0.00 0.00 0.00 4.52
5659 7870 4.217550 GGAAACTTGTAAACATAGCAGCCA 59.782 41.667 0.00 0.00 0.00 4.75
5750 7969 5.851720 TCCTCACTTGAGATCTCATAATGC 58.148 41.667 25.64 0.00 44.74 3.56
5775 7994 2.126467 CATTTGTGTTCCACTTTGCCG 58.874 47.619 0.00 0.00 35.11 5.69
5820 8040 7.944554 AGTTTAATCAAAGGGATGTTCAGAAGA 59.055 33.333 0.00 0.00 36.02 2.87
5866 8086 9.342308 CACATATAATGGTAGAAGGTGTCAATT 57.658 33.333 0.00 0.00 33.60 2.32
5928 8148 7.700234 CACGCTGCAAAATATAATGGTAGAAAA 59.300 33.333 0.00 0.00 0.00 2.29
5961 8182 2.180946 AGATGCACAGTGGATCCCTA 57.819 50.000 26.66 0.00 44.93 3.53
5966 8187 4.226384 TGGATAGTAGATGCACAGTGGAT 58.774 43.478 7.37 7.37 0.00 3.41
6145 8366 5.050363 GGTATGCTTGTACATGTTATCCACG 60.050 44.000 2.30 0.00 0.00 4.94
6226 8447 4.202121 GCTTCGTACATCTATTCCACTGGA 60.202 45.833 0.00 0.00 0.00 3.86
6230 8451 4.084328 GCATGCTTCGTACATCTATTCCAC 60.084 45.833 11.37 0.00 0.00 4.02
6309 8530 6.820152 TCTTGATCACCATTCTAACATGACTG 59.180 38.462 0.00 0.00 0.00 3.51
6338 8559 5.028549 ACATGGTGGCAATCTAAGTAGAG 57.971 43.478 0.00 0.00 35.50 2.43
6400 8622 4.532126 TGTCACTCATACATTCCCAGAAGT 59.468 41.667 0.00 0.00 0.00 3.01
6432 8654 5.983475 TCAAAAAGCCAATGCATAAAAACG 58.017 33.333 0.00 0.00 41.13 3.60
6488 8710 2.100989 GACTAGGGTAGGACCACACAG 58.899 57.143 0.00 0.00 41.02 3.66
6670 8893 4.083003 ACAATGTTGGCGTTAACCATACAG 60.083 41.667 0.00 0.00 40.13 2.74
6726 8949 1.008327 TGGAGCCAGTGAGGATTAGGA 59.992 52.381 0.00 0.00 41.22 2.94
6738 8961 7.881751 TGATATTGAAAATCTATCTGGAGCCAG 59.118 37.037 10.29 10.29 44.86 4.85
6831 9054 9.905713 AACAATGTCTATAACCAATACTGATGT 57.094 29.630 0.00 0.00 0.00 3.06
6896 9119 4.823442 TCTCATTAATTGCTAGCCATGTGG 59.177 41.667 13.29 0.00 38.53 4.17
6970 9194 9.022884 TCTTCATATCATGTTTTTCAACCATGA 57.977 29.630 0.00 4.25 36.11 3.07
7006 9231 3.129813 TCACCTTGATGCATCATTTGAGC 59.870 43.478 29.13 0.12 36.56 4.26


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

AutoCloner maintained by Alex Coulton.