Multiple sequence alignment - TraesCS2D01G396500

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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 TraesCS2D01G396500 chr2D 100.000 6315 0 0 1 6315 507757204 507750890 0.000000e+00 11662.0
1 TraesCS2D01G396500 chr2A 94.545 3831 119 28 1019 4812 652295233 652291456 0.000000e+00 5834.0
2 TraesCS2D01G396500 chr2A 96.571 1458 41 3 4866 6315 652291303 652289847 0.000000e+00 2407.0
3 TraesCS2D01G396500 chr2A 86.126 764 69 16 5 756 652298766 652298028 0.000000e+00 789.0
4 TraesCS2D01G396500 chr2A 85.766 274 20 8 779 1034 652297699 652297427 8.070000e-69 272.0
5 TraesCS2D01G396500 chr2A 94.118 68 4 0 4480 4547 652291831 652291764 3.110000e-18 104.0
6 TraesCS2D01G396500 chr2B 95.934 1451 55 2 4866 6315 596413341 596411894 0.000000e+00 2350.0
7 TraesCS2D01G396500 chr2B 95.043 807 28 6 4010 4812 596414291 596413493 0.000000e+00 1258.0
8 TraesCS2D01G396500 chr2B 92.343 875 32 10 765 1635 596418044 596417201 0.000000e+00 1212.0
9 TraesCS2D01G396500 chr2B 91.057 861 64 9 2376 3229 596416183 596415329 0.000000e+00 1151.0
10 TraesCS2D01G396500 chr2B 95.296 574 21 3 3233 3806 596415262 596414695 0.000000e+00 905.0
11 TraesCS2D01G396500 chr2B 87.059 255 24 8 1705 1957 596417011 596416764 4.820000e-71 279.0
12 TraesCS2D01G396500 chr2B 92.073 164 13 0 2212 2375 596416423 596416260 1.370000e-56 231.0
13 TraesCS2D01G396500 chr2B 88.827 179 6 5 3800 3970 596414465 596414293 2.310000e-49 207.0
14 TraesCS2D01G396500 chr2B 96.610 59 1 1 4810 4868 596413452 596413395 5.210000e-16 97.1
15 TraesCS2D01G396500 chr6D 76.667 360 74 9 5899 6253 427568677 427569031 2.320000e-44 191.0
16 TraesCS2D01G396500 chr7A 87.970 133 15 1 4927 5058 65461566 65461698 8.480000e-34 156.0
17 TraesCS2D01G396500 chr7A 76.923 221 41 8 6027 6242 556299832 556299617 4.000000e-22 117.0
18 TraesCS2D01G396500 chr7A 87.037 54 7 0 6198 6251 33606899 33606952 1.900000e-05 62.1
19 TraesCS2D01G396500 chr4D 74.595 370 67 24 5899 6253 387756775 387756418 3.070000e-28 137.0
20 TraesCS2D01G396500 chr7B 78.281 221 38 8 6027 6242 517394351 517394136 3.970000e-27 134.0
21 TraesCS2D01G396500 chr7D 77.376 221 40 8 6027 6242 489114706 489114491 8.600000e-24 122.0
22 TraesCS2D01G396500 chr6B 77.193 228 40 11 6032 6253 219571081 219570860 8.600000e-24 122.0
23 TraesCS2D01G396500 chr6A 81.481 135 23 2 6026 6159 156751569 156751702 6.690000e-20 110.0


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 TraesCS2D01G396500 chr2D 507750890 507757204 6314 True 11662.000000 11662 100.000000 1 6315 1 chr2D.!!$R1 6314
1 TraesCS2D01G396500 chr2A 652289847 652295233 5386 True 2781.666667 5834 95.078000 1019 6315 3 chr2A.!!$R1 5296
2 TraesCS2D01G396500 chr2A 652297427 652298766 1339 True 530.500000 789 85.946000 5 1034 2 chr2A.!!$R2 1029
3 TraesCS2D01G396500 chr2B 596411894 596418044 6150 True 854.455556 2350 92.693556 765 6315 9 chr2B.!!$R1 5550


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
125 127 0.250513 ATCCTGAGGGCGTTGAAGTC 59.749 55.000 0.00 0.00 0.00 3.01 F
1268 1619 0.257616 CCTCCTCGTCCTCCTCTTCT 59.742 60.000 0.00 0.00 0.00 2.85 F
1706 2071 0.931005 GTACGATGGCTGCTGTTAGC 59.069 55.000 0.00 0.00 42.82 3.09 F
3257 4146 0.251742 TTAAGCTGCAACATGCCCCT 60.252 50.000 1.02 0.00 44.23 4.79 F
3258 4147 0.251742 TAAGCTGCAACATGCCCCTT 60.252 50.000 1.02 5.12 44.23 3.95 F
4492 5627 2.227036 AGGTCCACTTGGGCTCCAG 61.227 63.158 0.00 0.00 40.38 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 2054 0.036010 AAGCTAACAGCAGCCATCGT 60.036 50.000 0.38 0.0 45.56 3.73 R
2834 3660 2.088423 AGAAAAGGCACACACAAACGA 58.912 42.857 0.00 0.0 0.00 3.85 R
3331 4220 3.693085 ACTAAACATGGCAGCAATCAGAG 59.307 43.478 0.00 0.0 0.00 3.35 R
4912 6148 0.260230 TCACCAAGGGGCTGTTTCAA 59.740 50.000 0.00 0.0 37.90 2.69 R
4959 6195 1.160137 CTGAAAACTGGGCTTCTCCG 58.840 55.000 0.00 0.0 34.94 4.63 R
5421 6664 0.460459 GTTCTGCCTTAGTCGAGGGC 60.460 60.000 10.50 10.5 45.45 5.19 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
30 31 2.124860 ACCGCCGCAATCCTAACC 60.125 61.111 0.00 0.00 0.00 2.85
34 35 1.076995 GCCGCAATCCTAACCCCTT 60.077 57.895 0.00 0.00 0.00 3.95
38 39 1.064685 CGCAATCCTAACCCCTTCCTT 60.065 52.381 0.00 0.00 0.00 3.36
41 42 3.952323 GCAATCCTAACCCCTTCCTTTAC 59.048 47.826 0.00 0.00 0.00 2.01
55 57 3.140623 TCCTTTACGCACCAAAACCTAC 58.859 45.455 0.00 0.00 0.00 3.18
57 59 4.040217 TCCTTTACGCACCAAAACCTACTA 59.960 41.667 0.00 0.00 0.00 1.82
70 72 6.717997 CCAAAACCTACTATTTTACACCACCT 59.282 38.462 0.00 0.00 0.00 4.00
78 80 7.220890 ACTATTTTACACCACCTAATCCCAT 57.779 36.000 0.00 0.00 0.00 4.00
83 85 2.637872 ACACCACCTAATCCCATATCGG 59.362 50.000 0.00 0.00 0.00 4.18
86 88 2.615493 CCACCTAATCCCATATCGGTGC 60.615 54.545 0.00 0.00 40.32 5.01
87 89 2.303022 CACCTAATCCCATATCGGTGCT 59.697 50.000 0.00 0.00 35.96 4.40
88 90 2.567615 ACCTAATCCCATATCGGTGCTC 59.432 50.000 0.00 0.00 0.00 4.26
109 111 1.202533 CCTCACATCCACACGGTATCC 60.203 57.143 0.00 0.00 0.00 2.59
110 112 1.757118 CTCACATCCACACGGTATCCT 59.243 52.381 0.00 0.00 0.00 3.24
125 127 0.250513 ATCCTGAGGGCGTTGAAGTC 59.749 55.000 0.00 0.00 0.00 3.01
126 128 1.738099 CCTGAGGGCGTTGAAGTCG 60.738 63.158 0.00 0.00 0.00 4.18
127 129 1.738099 CTGAGGGCGTTGAAGTCGG 60.738 63.158 0.00 0.00 0.00 4.79
128 130 2.434359 GAGGGCGTTGAAGTCGGG 60.434 66.667 0.00 0.00 0.00 5.14
129 131 4.699522 AGGGCGTTGAAGTCGGGC 62.700 66.667 0.00 0.00 0.00 6.13
132 134 3.479269 GCGTTGAAGTCGGGCGAG 61.479 66.667 0.00 0.00 0.00 5.03
133 135 2.809601 CGTTGAAGTCGGGCGAGG 60.810 66.667 0.00 0.00 0.00 4.63
134 136 2.434359 GTTGAAGTCGGGCGAGGG 60.434 66.667 0.00 0.00 0.00 4.30
186 188 2.094338 CAGAGGAAATGAAAGCCTTGCC 60.094 50.000 0.00 0.00 30.70 4.52
196 198 2.811542 AAGCCTTGCCTTCGCCTCTC 62.812 60.000 0.00 0.00 0.00 3.20
212 214 2.280628 CTCTCAACCGCCTTTATCACC 58.719 52.381 0.00 0.00 0.00 4.02
246 248 6.604735 AACATATATGCTCGAGTTTTGGTC 57.395 37.500 15.13 0.00 0.00 4.02
254 256 4.213270 TGCTCGAGTTTTGGTCTTTACATG 59.787 41.667 15.13 0.00 0.00 3.21
255 257 4.712763 CTCGAGTTTTGGTCTTTACATGC 58.287 43.478 3.62 0.00 0.00 4.06
266 268 4.380867 GGTCTTTACATGCTTGGTTGGATG 60.381 45.833 4.44 0.00 40.80 3.51
286 288 5.707764 GGATGTAATTAGAGGAAGGGAATGC 59.292 44.000 0.00 0.00 0.00 3.56
297 299 3.563479 GGAAGGGAATGCAAACTTAGGGA 60.563 47.826 0.00 0.00 0.00 4.20
298 300 4.281657 GAAGGGAATGCAAACTTAGGGAT 58.718 43.478 0.00 0.00 0.00 3.85
303 313 5.598417 GGGAATGCAAACTTAGGGATTACAT 59.402 40.000 0.00 0.00 28.16 2.29
307 317 5.565509 TGCAAACTTAGGGATTACATGACA 58.434 37.500 0.00 0.00 0.00 3.58
310 320 7.498900 TGCAAACTTAGGGATTACATGACATAG 59.501 37.037 0.00 0.00 0.00 2.23
336 346 6.710744 AGTCACCTGTGGTTTTAGATAGTTTG 59.289 38.462 0.00 0.00 31.02 2.93
382 392 3.257624 GGGAGTTTAGAGTCGAACTTCCA 59.742 47.826 24.08 0.00 46.49 3.53
414 424 1.884235 CAGTGAAGTGGTGGGAACTC 58.116 55.000 0.00 0.00 0.00 3.01
416 426 0.391597 GTGAAGTGGTGGGAACTCGA 59.608 55.000 0.00 0.00 0.00 4.04
424 434 1.407025 GGTGGGAACTCGAAGGGAATC 60.407 57.143 0.00 0.00 0.00 2.52
441 451 4.035675 GGGAATCGATTCACATGGAACTTC 59.964 45.833 32.92 14.94 39.94 3.01
482 492 6.825610 AGAATAAATGTCTCCTCAGATGGTC 58.174 40.000 0.00 0.00 0.00 4.02
489 499 3.769844 GTCTCCTCAGATGGTCAAACCTA 59.230 47.826 0.00 0.00 39.58 3.08
555 566 7.955185 AGATCTATCCACTTCTAATCTCACCAT 59.045 37.037 0.00 0.00 0.00 3.55
556 567 9.249053 GATCTATCCACTTCTAATCTCACCATA 57.751 37.037 0.00 0.00 0.00 2.74
565 576 8.646900 ACTTCTAATCTCACCATAATTCTCTCC 58.353 37.037 0.00 0.00 0.00 3.71
573 584 7.841729 TCTCACCATAATTCTCTCCTAACTCTT 59.158 37.037 0.00 0.00 0.00 2.85
593 604 8.115490 ACTCTTATTCATCTTCCCAAAAGTTG 57.885 34.615 0.00 0.00 0.00 3.16
594 605 7.725844 ACTCTTATTCATCTTCCCAAAAGTTGT 59.274 33.333 0.00 0.00 0.00 3.32
601 612 5.576447 TCTTCCCAAAAGTTGTCAAACTC 57.424 39.130 0.00 0.00 46.15 3.01
631 644 8.905850 TCATTGTCGTGTCCTTATACAACTATA 58.094 33.333 0.00 0.00 33.27 1.31
639 652 6.097270 TGTCCTTATACAACTATACAAGGCGT 59.903 38.462 0.00 0.00 0.00 5.68
640 653 7.285172 TGTCCTTATACAACTATACAAGGCGTA 59.715 37.037 0.00 0.00 0.00 4.42
641 654 8.137437 GTCCTTATACAACTATACAAGGCGTAA 58.863 37.037 0.00 0.00 32.59 3.18
642 655 8.863086 TCCTTATACAACTATACAAGGCGTAAT 58.137 33.333 0.00 0.00 32.59 1.89
643 656 9.485206 CCTTATACAACTATACAAGGCGTAATT 57.515 33.333 0.00 0.00 32.59 1.40
647 660 5.756833 ACAACTATACAAGGCGTAATTAGGC 59.243 40.000 19.46 19.46 32.59 3.93
656 669 4.400036 GGCGTAATTAGGCCGAAATTAG 57.600 45.455 28.09 16.15 45.77 1.73
669 682 5.613358 CCGAAATTAGGCCTATCATTGAC 57.387 43.478 14.74 8.52 0.00 3.18
670 683 4.455877 CCGAAATTAGGCCTATCATTGACC 59.544 45.833 14.74 4.30 0.00 4.02
673 686 6.263168 CGAAATTAGGCCTATCATTGACCTTT 59.737 38.462 14.74 2.97 31.79 3.11
708 721 7.846644 CTCTGATGAGCTTGTATTTTCTTCT 57.153 36.000 0.00 0.00 33.12 2.85
709 722 7.606858 TCTGATGAGCTTGTATTTTCTTCTG 57.393 36.000 0.00 0.00 0.00 3.02
725 738 5.298989 TCTTCTGGTACACTTTGGCTTTA 57.701 39.130 0.00 0.00 0.00 1.85
727 740 6.123651 TCTTCTGGTACACTTTGGCTTTAAA 58.876 36.000 0.00 0.00 0.00 1.52
730 743 4.538738 TGGTACACTTTGGCTTTAAACCT 58.461 39.130 0.00 0.00 0.00 3.50
731 744 4.339814 TGGTACACTTTGGCTTTAAACCTG 59.660 41.667 0.00 2.26 0.00 4.00
733 746 4.918810 ACACTTTGGCTTTAAACCTGAG 57.081 40.909 7.89 7.75 0.00 3.35
743 756 4.462834 GCTTTAAACCTGAGGGCTTTACAT 59.537 41.667 2.38 0.00 35.63 2.29
748 761 3.185455 ACCTGAGGGCTTTACATCTCTT 58.815 45.455 2.38 0.00 35.63 2.85
903 1245 1.313091 GGTTGCGGATTTCAGTCCCC 61.313 60.000 0.00 0.00 34.67 4.81
904 1246 0.608035 GTTGCGGATTTCAGTCCCCA 60.608 55.000 0.00 0.00 34.67 4.96
905 1247 0.608035 TTGCGGATTTCAGTCCCCAC 60.608 55.000 0.00 0.00 34.67 4.61
906 1248 1.749258 GCGGATTTCAGTCCCCACC 60.749 63.158 0.00 0.00 34.67 4.61
907 1249 1.077716 CGGATTTCAGTCCCCACCC 60.078 63.158 0.00 0.00 34.67 4.61
1268 1619 0.257616 CCTCCTCGTCCTCCTCTTCT 59.742 60.000 0.00 0.00 0.00 2.85
1537 1888 6.040278 TGTGATTCTACTAGAGCAGGAAGATG 59.960 42.308 0.00 0.00 0.00 2.90
1584 1935 6.812879 TGAGAGATTACGTAACTGACTCAA 57.187 37.500 22.10 13.82 0.00 3.02
1585 1936 6.609533 TGAGAGATTACGTAACTGACTCAAC 58.390 40.000 22.10 18.12 0.00 3.18
1614 1965 2.028748 GTGCTTGAGATGTGGGCAATTT 60.029 45.455 0.00 0.00 34.65 1.82
1654 2012 5.886474 GCTCTAGGTTTAAATTAGTTGGCCT 59.114 40.000 3.32 0.00 0.00 5.19
1657 2015 7.043565 TCTAGGTTTAAATTAGTTGGCCTACG 58.956 38.462 11.80 0.00 0.00 3.51
1670 2035 1.353076 GCCTACGGTGTTTCTAACGG 58.647 55.000 0.00 0.00 0.00 4.44
1689 2054 2.810164 GGTGCCCAATTAGGTTTGGTA 58.190 47.619 2.81 0.00 43.92 3.25
1705 2070 1.134818 TGGTACGATGGCTGCTGTTAG 60.135 52.381 0.00 0.00 0.00 2.34
1706 2071 0.931005 GTACGATGGCTGCTGTTAGC 59.069 55.000 0.00 0.00 42.82 3.09
1806 2276 2.380084 TTGGGAGTTACAGCGATCAC 57.620 50.000 0.00 0.00 0.00 3.06
1807 2277 1.262417 TGGGAGTTACAGCGATCACA 58.738 50.000 0.00 0.00 0.00 3.58
1842 2312 6.863126 AGCTATTAGTGTGTTTGCATCAAAAC 59.137 34.615 0.00 0.00 39.90 2.43
1905 2375 4.196971 GCGGAGGTTTGATGTATTAGGTT 58.803 43.478 0.00 0.00 0.00 3.50
1983 2464 7.684937 ATGATCTGCCAAAGCTTAGATAATC 57.315 36.000 9.02 5.42 40.80 1.75
1984 2465 6.000219 TGATCTGCCAAAGCTTAGATAATCC 59.000 40.000 9.02 0.00 40.80 3.01
2005 2490 4.044191 TCCATAGATATCGAAGGACCAGGA 59.956 45.833 5.78 0.00 0.00 3.86
2053 2538 8.348285 AGCTATTCTCTCTCATACCAACTATC 57.652 38.462 0.00 0.00 0.00 2.08
2064 2549 7.824289 TCTCATACCAACTATCTGTTTTTCAGG 59.176 37.037 0.00 0.00 43.76 3.86
2116 2601 4.875544 GCTTTACGCCATTACTTGATGA 57.124 40.909 0.00 0.00 0.00 2.92
2156 2641 1.605451 GGGTAAAGTGGTGGGGCAC 60.605 63.158 0.00 0.00 0.00 5.01
2197 2682 5.547465 TCCCTTAACTGTACATGACTTGTG 58.453 41.667 0.00 0.00 39.48 3.33
2309 3053 1.518431 CCCCATCCCCAAGGTTTCCT 61.518 60.000 0.00 0.00 33.87 3.36
2320 3064 6.387220 TCCCCAAGGTTTCCTTTTTGAATTTA 59.613 34.615 0.00 0.00 41.69 1.40
2438 3258 1.614996 TGCTGTTACATGGGGTTGTG 58.385 50.000 0.00 0.00 0.00 3.33
2449 3269 1.216678 TGGGGTTGTGTTTCCTCACAT 59.783 47.619 0.47 0.00 45.73 3.21
2521 3341 9.485206 GACTTAGGAAATTAGTTGTACTGTTCA 57.515 33.333 0.00 0.00 0.00 3.18
2587 3407 8.931568 GGAACTAATACTAAAATGGTCTCCCTA 58.068 37.037 0.00 0.00 0.00 3.53
2672 3494 4.400845 CTGCACATTTCTTTGAGATGTCG 58.599 43.478 1.50 0.76 35.63 4.35
2673 3495 3.166657 GCACATTTCTTTGAGATGTCGC 58.833 45.455 1.50 5.71 35.63 5.19
2708 3534 9.672086 TCAGTGCAAACAATTATTTAACAGTAC 57.328 29.630 0.00 0.00 0.00 2.73
2887 3713 4.274147 TCCTGTTGGTTTTAAAGACTGCA 58.726 39.130 0.00 0.00 34.23 4.41
2933 3759 6.432783 ACATCGAAGTGGATTTGAATAACCAA 59.567 34.615 0.00 0.00 34.88 3.67
3107 3933 6.986250 TCATATCAGCCTACTAACACAGATG 58.014 40.000 0.00 0.00 0.00 2.90
3256 4145 0.607620 TTTAAGCTGCAACATGCCCC 59.392 50.000 1.02 0.00 44.23 5.80
3257 4146 0.251742 TTAAGCTGCAACATGCCCCT 60.252 50.000 1.02 0.00 44.23 4.79
3258 4147 0.251742 TAAGCTGCAACATGCCCCTT 60.252 50.000 1.02 5.12 44.23 3.95
3331 4220 7.278135 TGGCAAATGCTATCATAGATCTATCC 58.722 38.462 12.50 6.95 41.70 2.59
3343 4232 4.540359 AGATCTATCCTCTGATTGCTGC 57.460 45.455 0.00 0.00 32.18 5.25
3503 4392 6.152661 CCAAGTTAACATGGAATTGGCTAGAA 59.847 38.462 22.56 0.00 36.89 2.10
3678 4567 6.486657 ACTGCAGCGGTTGATAAATTATGTAT 59.513 34.615 15.27 0.00 0.00 2.29
3798 4687 6.934645 TGGGGTCGATTCTTTATGATATTGTC 59.065 38.462 0.00 0.00 0.00 3.18
3823 4948 9.378551 TCGTATTACAATTTAGAAAGTCATGCT 57.621 29.630 0.00 0.00 0.00 3.79
3842 4967 6.379417 TCATGCTTTCTCAGAGAAGATAGTGA 59.621 38.462 12.74 11.51 35.37 3.41
3847 4972 7.416664 GCTTTCTCAGAGAAGATAGTGATGTCT 60.417 40.741 12.74 0.00 35.37 3.41
3999 5132 4.440250 GCGCTGTCTATCTCTGTTTCCTAA 60.440 45.833 0.00 0.00 0.00 2.69
4100 5234 3.328505 AGGCATATTGTTTTGCAGTTGC 58.671 40.909 0.00 0.00 40.66 4.17
4378 5513 5.647658 TGCGATTCTTTTGAACCTGTATCAT 59.352 36.000 0.00 0.00 41.77 2.45
4455 5590 7.551262 CACCTATCGCTAGACTAGATCTGTTAT 59.449 40.741 13.91 0.00 38.49 1.89
4456 5591 8.104566 ACCTATCGCTAGACTAGATCTGTTATT 58.895 37.037 13.91 0.00 38.49 1.40
4457 5592 9.602568 CCTATCGCTAGACTAGATCTGTTATTA 57.397 37.037 13.91 0.00 38.49 0.98
4492 5627 2.227036 AGGTCCACTTGGGCTCCAG 61.227 63.158 0.00 0.00 40.38 3.86
4612 5747 5.473504 ACAATGACCAGATTCACCAAACTAC 59.526 40.000 0.00 0.00 0.00 2.73
4829 6009 2.897326 GGTAACCATCCTGTTTTTGGCT 59.103 45.455 0.00 0.00 33.66 4.75
4959 6195 4.452795 GGAACACTAGAAGCTGGAGAAAAC 59.547 45.833 0.00 0.00 0.00 2.43
5139 6375 1.576451 GCACATGCGATGGTGTCACA 61.576 55.000 5.12 0.00 37.35 3.58
5165 6401 1.531578 GGAATCGAGCTAAATTCGCCC 59.468 52.381 12.15 0.00 37.94 6.13
5176 6412 2.044123 AATTCGCCCTGATGGAGTTC 57.956 50.000 0.00 0.00 35.07 3.01
5180 6416 1.617018 CGCCCTGATGGAGTTCTCCA 61.617 60.000 21.55 21.55 44.85 3.86
5195 6431 4.248842 CCACACCGCTGGGTCACA 62.249 66.667 0.00 0.00 46.01 3.58
5336 6579 1.734465 CTTTCTTCCGGCAAGTGCTAG 59.266 52.381 0.00 0.00 41.70 3.42
5345 6588 0.603707 GCAAGTGCTAGTCCTGTGCA 60.604 55.000 0.00 0.00 38.21 4.57
5391 6634 2.565391 TCATCAACCTCGCTTACCAAGA 59.435 45.455 0.00 0.00 0.00 3.02
5396 6639 1.519455 CTCGCTTACCAAGAGGCCG 60.519 63.158 0.00 0.00 39.06 6.13
5421 6664 2.438075 GCTGCTTCTGCTCCCAGG 60.438 66.667 0.00 0.00 39.61 4.45
5433 6677 1.381327 TCCCAGGCCCTCGACTAAG 60.381 63.158 0.00 0.00 0.00 2.18
5576 6820 3.672295 GAGCGGCCTTGGTCCTCAG 62.672 68.421 0.00 0.00 0.00 3.35
5848 7092 3.909086 AAGCCCTTGAGCTGCGTCC 62.909 63.158 0.00 0.00 44.11 4.79
6279 7523 2.532199 TAGTTTGGCCCCCGGGAA 60.532 61.111 26.32 4.79 37.50 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.076995 AAGGGGTTAGGATTGCGGC 60.077 57.895 0.00 0.00 0.00 6.53
18 19 0.546598 AGGAAGGGGTTAGGATTGCG 59.453 55.000 0.00 0.00 0.00 4.85
21 22 3.371273 GCGTAAAGGAAGGGGTTAGGATT 60.371 47.826 0.00 0.00 0.00 3.01
30 31 1.611519 TTTGGTGCGTAAAGGAAGGG 58.388 50.000 0.00 0.00 0.00 3.95
34 35 2.351706 AGGTTTTGGTGCGTAAAGGA 57.648 45.000 0.00 0.00 0.00 3.36
38 39 6.880942 AAAATAGTAGGTTTTGGTGCGTAA 57.119 33.333 0.00 0.00 0.00 3.18
41 42 6.081693 GTGTAAAATAGTAGGTTTTGGTGCG 58.918 40.000 0.00 0.00 31.71 5.34
55 57 9.449719 GATATGGGATTAGGTGGTGTAAAATAG 57.550 37.037 0.00 0.00 0.00 1.73
57 59 6.940298 CGATATGGGATTAGGTGGTGTAAAAT 59.060 38.462 0.00 0.00 0.00 1.82
70 72 1.906574 GGGAGCACCGATATGGGATTA 59.093 52.381 11.20 0.00 44.64 1.75
78 80 1.040646 GATGTGAGGGAGCACCGATA 58.959 55.000 0.00 0.00 46.96 2.92
83 85 0.674895 GTGTGGATGTGAGGGAGCAC 60.675 60.000 0.00 0.00 39.22 4.40
86 88 1.219124 CCGTGTGGATGTGAGGGAG 59.781 63.158 0.00 0.00 37.49 4.30
87 89 0.251877 TACCGTGTGGATGTGAGGGA 60.252 55.000 0.00 0.00 39.21 4.20
88 90 0.830648 ATACCGTGTGGATGTGAGGG 59.169 55.000 0.00 0.00 39.21 4.30
109 111 1.738099 CCGACTTCAACGCCCTCAG 60.738 63.158 0.00 0.00 0.00 3.35
110 112 2.342279 CCGACTTCAACGCCCTCA 59.658 61.111 0.00 0.00 0.00 3.86
143 145 4.217035 CGTCATCGGGATTGGCAA 57.783 55.556 0.68 0.68 0.00 4.52
161 163 1.747924 GGCTTTCATTTCCTCTGCTCC 59.252 52.381 0.00 0.00 0.00 4.70
169 171 2.672195 CGAAGGCAAGGCTTTCATTTCC 60.672 50.000 10.35 0.00 43.32 3.13
186 188 2.788191 AAGGCGGTTGAGAGGCGAAG 62.788 60.000 0.00 0.00 38.03 3.79
196 198 1.094785 CAGGGTGATAAAGGCGGTTG 58.905 55.000 0.00 0.00 0.00 3.77
212 214 6.319911 TCGAGCATATATGTTAGGATCTCAGG 59.680 42.308 14.14 0.40 0.00 3.86
246 248 4.789012 ACATCCAACCAAGCATGTAAAG 57.211 40.909 0.00 0.00 0.00 1.85
254 256 5.437060 TCCTCTAATTACATCCAACCAAGC 58.563 41.667 0.00 0.00 0.00 4.01
255 257 6.543831 CCTTCCTCTAATTACATCCAACCAAG 59.456 42.308 0.00 0.00 0.00 3.61
266 268 6.603599 AGTTTGCATTCCCTTCCTCTAATTAC 59.396 38.462 0.00 0.00 0.00 1.89
286 288 9.265901 CTCTATGTCATGTAATCCCTAAGTTTG 57.734 37.037 0.00 0.00 0.00 2.93
307 317 6.875972 ATCTAAAACCACAGGTGACTCTAT 57.124 37.500 0.00 0.00 40.21 1.98
310 320 6.038997 ACTATCTAAAACCACAGGTGACTC 57.961 41.667 0.00 0.00 40.21 3.36
317 327 8.166422 AGTTTCCAAACTATCTAAAACCACAG 57.834 34.615 2.74 0.00 46.75 3.66
336 346 4.999311 ACCCGTTATCACTTGTAAGTTTCC 59.001 41.667 0.00 0.00 37.08 3.13
355 365 0.172803 CGACTCTAAACTCCCACCCG 59.827 60.000 0.00 0.00 0.00 5.28
382 392 4.460382 CCACTTCACTGCTAATGAAATGGT 59.540 41.667 13.89 2.01 44.62 3.55
414 424 2.545526 CCATGTGAATCGATTCCCTTCG 59.454 50.000 30.16 16.81 40.46 3.79
416 426 3.931907 TCCATGTGAATCGATTCCCTT 57.068 42.857 30.16 17.34 35.97 3.95
424 434 7.201530 GGTTAGTAAGAAGTTCCATGTGAATCG 60.202 40.741 0.00 0.00 34.90 3.34
464 474 4.566488 GGTTTGACCATCTGAGGAGACATT 60.566 45.833 0.00 0.00 38.42 2.71
529 540 7.301420 TGGTGAGATTAGAAGTGGATAGATCT 58.699 38.462 0.00 0.00 0.00 2.75
530 541 7.531857 TGGTGAGATTAGAAGTGGATAGATC 57.468 40.000 0.00 0.00 0.00 2.75
532 543 9.607333 ATTATGGTGAGATTAGAAGTGGATAGA 57.393 33.333 0.00 0.00 0.00 1.98
536 547 8.324191 AGAATTATGGTGAGATTAGAAGTGGA 57.676 34.615 0.00 0.00 0.00 4.02
565 576 9.454859 ACTTTTGGGAAGATGAATAAGAGTTAG 57.545 33.333 0.00 0.00 0.00 2.34
573 584 7.831691 TTGACAACTTTTGGGAAGATGAATA 57.168 32.000 3.53 0.00 34.12 1.75
593 604 2.538449 ACGACAATGACACGAGTTTGAC 59.462 45.455 4.70 0.00 0.00 3.18
594 605 2.538037 CACGACAATGACACGAGTTTGA 59.462 45.455 4.70 0.00 0.00 2.69
601 612 1.497991 AAGGACACGACAATGACACG 58.502 50.000 0.00 0.00 0.00 4.49
631 644 0.538118 TCGGCCTAATTACGCCTTGT 59.462 50.000 19.29 0.00 43.38 3.16
646 659 4.072131 TCAATGATAGGCCTAATTTCGGC 58.928 43.478 18.42 9.34 46.83 5.54
647 660 4.455877 GGTCAATGATAGGCCTAATTTCGG 59.544 45.833 18.42 5.50 0.00 4.30
648 661 5.308825 AGGTCAATGATAGGCCTAATTTCG 58.691 41.667 18.42 6.05 0.00 3.46
649 662 7.588497 AAAGGTCAATGATAGGCCTAATTTC 57.412 36.000 18.42 10.84 0.00 2.17
687 700 6.240894 ACCAGAAGAAAATACAAGCTCATCA 58.759 36.000 0.00 0.00 0.00 3.07
690 703 6.426937 GTGTACCAGAAGAAAATACAAGCTCA 59.573 38.462 0.00 0.00 0.00 4.26
691 704 6.651225 AGTGTACCAGAAGAAAATACAAGCTC 59.349 38.462 0.00 0.00 0.00 4.09
708 721 4.339814 CAGGTTTAAAGCCAAAGTGTACCA 59.660 41.667 13.60 0.00 0.00 3.25
709 722 4.581409 TCAGGTTTAAAGCCAAAGTGTACC 59.419 41.667 13.60 0.00 0.00 3.34
727 740 2.839228 AGAGATGTAAAGCCCTCAGGT 58.161 47.619 0.00 0.00 34.57 4.00
730 743 6.560003 TCATTAAGAGATGTAAAGCCCTCA 57.440 37.500 0.00 0.00 0.00 3.86
731 744 8.457238 AAATCATTAAGAGATGTAAAGCCCTC 57.543 34.615 0.00 0.00 0.00 4.30
772 795 8.284435 TCCTCCTCAATTTCATTAAGGAATCAT 58.716 33.333 3.00 0.00 35.77 2.45
774 797 8.525290 TTCCTCCTCAATTTCATTAAGGAATC 57.475 34.615 3.00 0.00 36.89 2.52
980 1323 4.393371 GGCTGTTCCAGTAGAATTCAGAAC 59.607 45.833 8.44 11.89 36.69 3.01
1174 1519 3.767044 GAGGGGGAGGAGGAGGAGC 62.767 73.684 0.00 0.00 0.00 4.70
1316 1667 2.841988 GGGGCAGAGAGATCGGCT 60.842 66.667 0.68 0.00 0.00 5.52
1507 1858 5.301551 CCTGCTCTAGTAGAATCACAGACAT 59.698 44.000 15.55 0.00 0.00 3.06
1510 1861 5.117406 TCCTGCTCTAGTAGAATCACAGA 57.883 43.478 15.55 6.76 0.00 3.41
1526 1877 1.493871 CCTCCCAATCATCTTCCTGCT 59.506 52.381 0.00 0.00 0.00 4.24
1537 1888 2.409570 ACTAGTAAGGCCCTCCCAATC 58.590 52.381 0.00 0.00 35.39 2.67
1577 1928 3.213206 AGCACCAATTGAGTTGAGTCA 57.787 42.857 7.12 0.00 40.37 3.41
1580 1931 4.156664 CTCAAGCACCAATTGAGTTGAG 57.843 45.455 7.12 13.98 45.58 3.02
1614 1965 9.569122 AAACCTAGAGCAATGTTCTTTTAACTA 57.431 29.630 4.66 0.00 0.00 2.24
1654 2012 1.605202 GGCACCGTTAGAAACACCGTA 60.605 52.381 0.00 0.00 0.00 4.02
1657 2015 2.250646 GGGCACCGTTAGAAACACC 58.749 57.895 0.00 0.00 40.86 4.16
1689 2054 0.036010 AAGCTAACAGCAGCCATCGT 60.036 50.000 0.38 0.00 45.56 3.73
1705 2070 4.760204 ACGATATACCCAGGCAATAAAAGC 59.240 41.667 0.00 0.00 0.00 3.51
1706 2071 6.877611 AACGATATACCCAGGCAATAAAAG 57.122 37.500 0.00 0.00 0.00 2.27
1846 2316 9.407380 ACCATTACATTCAACATGCTAATAAGA 57.593 29.630 0.00 0.00 0.00 2.10
1905 2375 4.515191 GTGAACACAGCAGTCCTTTTGATA 59.485 41.667 0.00 0.00 0.00 2.15
1983 2464 4.344978 TCCTGGTCCTTCGATATCTATGG 58.655 47.826 0.34 2.13 0.00 2.74
1984 2465 5.257262 TCTCCTGGTCCTTCGATATCTATG 58.743 45.833 0.34 0.00 0.00 2.23
2005 2490 0.114954 TTGGGCATTTGGGCTCTTCT 59.885 50.000 0.00 0.00 42.84 2.85
2053 2538 8.099364 TCTCAAAGTATTAGCCTGAAAAACAG 57.901 34.615 0.00 0.00 45.36 3.16
2113 2598 9.533253 CCAACTTTCTGTACTGAAAATTTTCAT 57.467 29.630 28.86 21.21 45.26 2.57
2114 2599 7.978975 CCCAACTTTCTGTACTGAAAATTTTCA 59.021 33.333 27.39 27.39 44.31 2.69
2115 2600 7.979537 ACCCAACTTTCTGTACTGAAAATTTTC 59.020 33.333 23.09 21.60 35.79 2.29
2116 2601 7.847096 ACCCAACTTTCTGTACTGAAAATTTT 58.153 30.769 23.09 15.50 35.79 1.82
2309 3053 9.558396 AGCACCTCATTTCAATAAATTCAAAAA 57.442 25.926 0.00 0.00 32.87 1.94
2320 3064 5.688807 AGCAGTATAGCACCTCATTTCAAT 58.311 37.500 0.00 0.00 36.85 2.57
2325 3069 4.202264 GGTGTAGCAGTATAGCACCTCATT 60.202 45.833 0.00 0.00 44.35 2.57
2438 3258 3.434940 ACCCCACTTATGTGAGGAAAC 57.565 47.619 15.13 0.00 43.77 2.78
2449 3269 9.819267 CTTATTAAAACAAAACAACCCCACTTA 57.181 29.630 0.00 0.00 0.00 2.24
2672 3494 3.968649 TGTTTGCACTGAGAAATCAAGC 58.031 40.909 0.00 0.00 0.00 4.01
2673 3495 8.752766 ATAATTGTTTGCACTGAGAAATCAAG 57.247 30.769 0.00 0.00 0.00 3.02
2708 3534 4.994852 TCGGTCTTCAGACATACAAAAAGG 59.005 41.667 9.18 0.00 46.47 3.11
2720 3546 3.599343 CACCATGAATTCGGTCTTCAGA 58.401 45.455 2.32 0.00 36.16 3.27
2834 3660 2.088423 AGAAAAGGCACACACAAACGA 58.912 42.857 0.00 0.00 0.00 3.85
2843 3669 6.323739 AGGAAATAGTTGAAAGAAAAGGCACA 59.676 34.615 0.00 0.00 0.00 4.57
2887 3713 9.314321 CGATGTTTTGTATTCCTGTAGTAAGAT 57.686 33.333 0.00 0.00 0.00 2.40
2933 3759 4.009002 GAGACCCACGAACTCTAACTACT 58.991 47.826 0.00 0.00 0.00 2.57
3107 3933 9.372369 ACAGAGCATTAGAGATTTTACACTAAC 57.628 33.333 0.00 0.00 0.00 2.34
3111 3937 6.531948 ACGACAGAGCATTAGAGATTTTACAC 59.468 38.462 0.00 0.00 0.00 2.90
3168 3994 9.307121 CAGTTGTAGGAATGAAAGTCTAGTATG 57.693 37.037 0.00 0.00 0.00 2.39
3256 4145 6.036953 GCCAGATAACAGAATGAGTTCAGAAG 59.963 42.308 0.00 0.00 39.69 2.85
3257 4146 5.877012 GCCAGATAACAGAATGAGTTCAGAA 59.123 40.000 0.00 0.00 39.69 3.02
3258 4147 5.046376 TGCCAGATAACAGAATGAGTTCAGA 60.046 40.000 0.00 0.00 39.69 3.27
3331 4220 3.693085 ACTAAACATGGCAGCAATCAGAG 59.307 43.478 0.00 0.00 0.00 3.35
3343 4232 4.930963 TGCAGAACACAAACTAAACATGG 58.069 39.130 0.00 0.00 0.00 3.66
3503 4392 5.763876 AGACCACTAAAAGTAGCCTCAAT 57.236 39.130 0.00 0.00 0.00 2.57
3678 4567 9.345254 TCCATTTATCCCATGTTATCATAGGTA 57.655 33.333 0.00 0.00 35.04 3.08
3798 4687 9.988350 AAGCATGACTTTCTAAATTGTAATACG 57.012 29.630 0.00 0.00 33.71 3.06
3823 4948 7.953005 AGACATCACTATCTTCTCTGAGAAA 57.047 36.000 19.73 11.79 33.19 2.52
3842 4967 7.603180 TGTGGATGTAAGAAGCTATAGACAT 57.397 36.000 3.21 3.05 0.00 3.06
3847 4972 7.948357 ACGTAATGTGGATGTAAGAAGCTATA 58.052 34.615 0.00 0.00 0.00 1.31
3999 5132 5.431731 TGAATAATAGACACCAGGGACCATT 59.568 40.000 0.00 0.00 0.00 3.16
4039 5172 3.698539 TCAGTTTGTTCAATTGTCTGGCA 59.301 39.130 5.13 0.00 0.00 4.92
4100 5234 6.623486 TGACCAAATATGAAGAACTGCATTG 58.377 36.000 0.32 0.00 0.00 2.82
4209 5343 7.541783 TGTTTTAGATCAGCACATTTATGTTGC 59.458 33.333 0.00 8.34 39.39 4.17
4240 5374 0.731417 CTGGATAGTGTTGCTGCTGC 59.269 55.000 8.89 8.89 40.20 5.25
4347 5481 4.026062 GGTTCAAAAGAATCGCAACCAAAC 60.026 41.667 0.00 0.00 34.57 2.93
4388 5523 9.262358 GCCCAAGTTATCTCTTTATTACTGTAG 57.738 37.037 0.00 0.00 0.00 2.74
4389 5524 8.989131 AGCCCAAGTTATCTCTTTATTACTGTA 58.011 33.333 0.00 0.00 0.00 2.74
4390 5525 7.862675 AGCCCAAGTTATCTCTTTATTACTGT 58.137 34.615 0.00 0.00 0.00 3.55
4391 5526 8.207545 AGAGCCCAAGTTATCTCTTTATTACTG 58.792 37.037 0.00 0.00 32.44 2.74
4492 5627 5.008118 GTCTAGCAATAGGTGATTTTGGCTC 59.992 44.000 0.00 0.00 29.64 4.70
4612 5747 5.969435 CAGTGTGTCAATATTTGCAGCTATG 59.031 40.000 0.00 0.00 0.00 2.23
4827 6007 5.803020 ATTTAAAGGATCGAACACTCAGC 57.197 39.130 0.00 0.00 0.00 4.26
4829 6009 7.444183 AGAACAATTTAAAGGATCGAACACTCA 59.556 33.333 0.00 0.00 0.00 3.41
4868 6048 4.223923 ACTTGCTGCTGAACCTCTATACTT 59.776 41.667 0.00 0.00 0.00 2.24
4869 6049 3.772025 ACTTGCTGCTGAACCTCTATACT 59.228 43.478 0.00 0.00 0.00 2.12
4870 6050 4.130286 ACTTGCTGCTGAACCTCTATAC 57.870 45.455 0.00 0.00 0.00 1.47
4871 6051 4.826274 AACTTGCTGCTGAACCTCTATA 57.174 40.909 0.00 0.00 0.00 1.31
4912 6148 0.260230 TCACCAAGGGGCTGTTTCAA 59.740 50.000 0.00 0.00 37.90 2.69
4959 6195 1.160137 CTGAAAACTGGGCTTCTCCG 58.840 55.000 0.00 0.00 34.94 4.63
5094 6330 3.396260 TTCTTGTAGTTCTCCCCAACG 57.604 47.619 0.00 0.00 0.00 4.10
5139 6375 5.733373 GCGAATTTAGCTCGATTCCCAAATT 60.733 40.000 13.42 7.54 38.61 1.82
5176 6412 3.625897 TGACCCAGCGGTGTGGAG 61.626 66.667 23.30 8.86 44.88 3.86
5180 6416 4.250305 GGTGTGACCCAGCGGTGT 62.250 66.667 14.40 0.00 44.88 4.16
5195 6431 4.720046 TGTGTGTGTACAACATATTGGGT 58.280 39.130 0.00 0.00 41.97 4.51
5336 6579 3.054503 CAGCCAGCTGCACAGGAC 61.055 66.667 8.66 0.00 44.83 3.85
5421 6664 0.460459 GTTCTGCCTTAGTCGAGGGC 60.460 60.000 10.50 10.50 45.45 5.19
5433 6677 3.846360 AGTACTGTATCGTTGTTCTGCC 58.154 45.455 0.00 0.00 0.00 4.85
5576 6820 1.067071 AGCTCGCCTACAAGGTTACAC 60.067 52.381 0.00 0.00 37.80 2.90
5746 6990 1.227089 CCATCTCCGCCGTCTTCAG 60.227 63.158 0.00 0.00 0.00 3.02
5877 7121 1.927487 TTGGGCAGAACGAGTACCTA 58.073 50.000 0.00 0.00 0.00 3.08
6279 7523 4.719369 GTGGTCGCCGCGTTCTCT 62.719 66.667 13.39 0.00 0.00 3.10



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

AutoCloner maintained by Alex Coulton.