Multiple sequence alignment - TraesCS5B01G338200

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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 TraesCS5B01G338200 chr5B 100.000 1636 0 0 1 1636 522084714 522086349 0.000000e+00 3022
1 TraesCS5B01G338200 chr5B 100.000 1366 0 0 2013 3378 522086726 522088091 0.000000e+00 2523
2 TraesCS5B01G338200 chr2A 93.289 1639 106 3 1 1636 718358437 718356800 0.000000e+00 2414
3 TraesCS5B01G338200 chr2A 91.024 635 51 5 2207 2839 718356370 718355740 0.000000e+00 852
4 TraesCS5B01G338200 chr2A 90.171 468 37 8 2836 3298 718355713 718355250 4.820000e-168 601
5 TraesCS5B01G338200 chr2A 94.907 216 10 1 2013 2227 718356768 718356553 1.500000e-88 337
6 TraesCS5B01G338200 chr3D 86.663 1642 207 9 1 1636 561020261 561018626 0.000000e+00 1808
7 TraesCS5B01G338200 chr1D 85.888 1644 220 10 1 1636 78393859 78395498 0.000000e+00 1740
8 TraesCS5B01G338200 chr2D 85.636 1643 224 10 1 1636 534505282 534503645 0.000000e+00 1716
9 TraesCS5B01G338200 chr2D 79.661 767 138 15 2015 2769 534503612 534502852 1.380000e-148 536


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 TraesCS5B01G338200 chr5B 522084714 522088091 3377 False 2772.5 3022 100.00000 1 3378 2 chr5B.!!$F1 3377
1 TraesCS5B01G338200 chr2A 718355250 718358437 3187 True 1051.0 2414 92.34775 1 3298 4 chr2A.!!$R1 3297
2 TraesCS5B01G338200 chr3D 561018626 561020261 1635 True 1808.0 1808 86.66300 1 1636 1 chr3D.!!$R1 1635
3 TraesCS5B01G338200 chr1D 78393859 78395498 1639 False 1740.0 1740 85.88800 1 1636 1 chr1D.!!$F1 1635
4 TraesCS5B01G338200 chr2D 534502852 534505282 2430 True 1126.0 1716 82.64850 1 2769 2 chr2D.!!$R1 2768

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
221 223 0.173708 GCTGTCCTCAGGTACCTTCG 59.826 60.0 13.15 5.93 41.57 3.79 F
1329 1339 0.249114 TGCACTAACAACTCGACGCA 60.249 50.0 0.00 0.00 0.00 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1502 1513 0.749649 TTGCACGGCCTTCATGTTTT 59.250 45.0 0.0 0.0 0.00 2.43 R
3298 3555 0.108992 TCAGGTGACGTTGTATCGCC 60.109 55.0 0.0 0.0 45.51 5.54 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
53 54 2.090760 TGATTGCCGCAAAAGCATAGA 58.909 42.857 10.42 0.00 40.59 1.98
55 56 3.882288 TGATTGCCGCAAAAGCATAGATA 59.118 39.130 10.42 0.00 40.59 1.98
59 60 2.350197 GCCGCAAAAGCATAGATAGCAG 60.350 50.000 0.00 0.00 0.00 4.24
97 98 9.605275 CTCTTGTCATTCATTTGATTCCTAGTA 57.395 33.333 0.00 0.00 0.00 1.82
135 136 2.161012 GTCGTCTGACACAGATACGGAA 59.839 50.000 8.73 0.00 42.73 4.30
162 163 2.231618 GGCTCGTCGAAGCGGATTC 61.232 63.158 3.13 0.00 43.45 2.52
178 179 4.399219 CGGATTCTCCTCTGTAGATGGTA 58.601 47.826 0.00 0.00 33.30 3.25
197 198 3.979495 GGTAGTAAGGCATCGACATTACG 59.021 47.826 5.33 0.00 40.69 3.18
212 214 2.724977 TTACGACAAGCTGTCCTCAG 57.275 50.000 9.71 0.00 44.20 3.35
221 223 0.173708 GCTGTCCTCAGGTACCTTCG 59.826 60.000 13.15 5.93 41.57 3.79
222 224 0.818296 CTGTCCTCAGGTACCTTCGG 59.182 60.000 13.15 15.49 37.97 4.30
239 241 0.391661 CGGAGTTGTAGCAGTGCCAT 60.392 55.000 12.58 0.00 0.00 4.40
242 244 1.021390 AGTTGTAGCAGTGCCATCGC 61.021 55.000 12.58 0.00 0.00 4.58
245 247 3.770040 TAGCAGTGCCATCGCGGT 61.770 61.111 12.58 0.00 38.08 5.68
252 257 1.899054 TGCCATCGCGGTTGGAAAA 60.899 52.632 26.53 12.25 36.26 2.29
308 313 0.944311 GTGAGCTCGTCGGAAGCAAA 60.944 55.000 9.64 0.00 0.00 3.68
311 316 0.320771 AGCTCGTCGGAAGCAAATGT 60.321 50.000 8.45 0.00 0.00 2.71
335 340 2.688666 TCCTACAGCTGCCAGGGG 60.689 66.667 26.67 16.36 0.00 4.79
402 407 2.129607 GATGTGCAAACAAACTGCCAG 58.870 47.619 0.00 0.00 39.13 4.85
482 487 9.539139 CTGATATCTCAATATGAATTTCGTTGC 57.461 33.333 3.98 0.00 0.00 4.17
513 518 3.658709 TGATTGTTGCACGTGACTATGA 58.341 40.909 22.23 3.25 0.00 2.15
516 521 0.713883 GTTGCACGTGACTATGACGG 59.286 55.000 22.23 0.00 41.21 4.79
676 681 6.036517 GGAGACACATAATCCATCGCATATTC 59.963 42.308 0.00 0.00 33.08 1.75
725 730 4.080356 TGACAGGAAAGATTGGGGTGATAG 60.080 45.833 0.00 0.00 0.00 2.08
764 769 2.238521 GTTGAACCATTCAGAGCCCAA 58.761 47.619 0.00 0.00 41.38 4.12
769 774 1.837439 ACCATTCAGAGCCCAACGATA 59.163 47.619 0.00 0.00 0.00 2.92
785 790 7.010923 GCCCAACGATAAATGCATTTTGAAATA 59.989 33.333 28.45 11.02 0.00 1.40
830 835 4.037684 CGAAGGACCGATACTGAATAGGTT 59.962 45.833 0.00 0.00 43.04 3.50
849 854 6.382919 AGGTTAGCATTTAAACTACCTGGA 57.617 37.500 0.00 0.00 0.00 3.86
861 867 6.441088 AAACTACCTGGACTCATTCTTTCT 57.559 37.500 0.00 0.00 0.00 2.52
869 875 5.181009 TGGACTCATTCTTTCTGTGCATAG 58.819 41.667 3.68 3.68 0.00 2.23
981 989 6.263842 GGCAAGATATCAAGGATGAATTGACA 59.736 38.462 5.32 0.00 39.36 3.58
1025 1033 2.296792 CATGTGGAGGTGTGTTCAACA 58.703 47.619 0.00 0.00 33.26 3.33
1053 1061 3.947196 TGTGCGAGAAAGATAATGGCATT 59.053 39.130 18.01 18.01 0.00 3.56
1116 1124 6.109359 CCCCAAATTTGTTGTGAGTAAAACA 58.891 36.000 16.73 0.00 34.57 2.83
1154 1162 7.837689 AGTTGGTACTGGATGTGAGTAATAGTA 59.162 37.037 0.00 0.00 31.99 1.82
1178 1186 6.542574 ACTATAGTATCGTACAGCAGTGAC 57.457 41.667 2.75 0.00 0.00 3.67
1189 1198 5.176774 CGTACAGCAGTGACAAAATCTGTAA 59.823 40.000 0.00 0.00 38.84 2.41
1248 1257 4.506802 GGAGAAACTGACTGGGGTTACATT 60.507 45.833 0.00 0.00 0.00 2.71
1320 1330 7.099764 TGAAAAAGGTGAATTTGCACTAACAA 58.900 30.769 0.00 0.00 38.78 2.83
1329 1339 0.249114 TGCACTAACAACTCGACGCA 60.249 50.000 0.00 0.00 0.00 5.24
1333 1343 1.856597 ACTAACAACTCGACGCACAAC 59.143 47.619 0.00 0.00 0.00 3.32
1342 1352 4.491676 ACTCGACGCACAACTGTTATAAT 58.508 39.130 0.00 0.00 0.00 1.28
1475 1486 2.298661 GGTCCTGGACCCAACGGAT 61.299 63.158 31.73 0.00 46.19 4.18
1502 1513 9.636789 ACAGATGAAATGGATGAGATGAAAATA 57.363 29.630 0.00 0.00 0.00 1.40
2121 2133 1.254026 CTACACTGAGTTCACCGGGA 58.746 55.000 6.32 0.00 0.00 5.14
2224 2441 8.253810 TGAAGATATCTAAGTTGTTCAGTCCAG 58.746 37.037 5.46 0.00 0.00 3.86
2230 2447 5.997746 TCTAAGTTGTTCAGTCCAGAATTGG 59.002 40.000 0.00 0.00 46.49 3.16
2273 2491 3.181467 TGCTTTGGTTGCTTGCATTTAGT 60.181 39.130 0.00 0.00 0.00 2.24
2274 2492 3.809279 GCTTTGGTTGCTTGCATTTAGTT 59.191 39.130 0.00 0.00 0.00 2.24
2294 2512 2.362736 TGCAGATAGAACGTCTACGGT 58.637 47.619 7.50 0.00 44.92 4.83
2305 2523 0.731417 GTCTACGGTCGAAGCTAGCA 59.269 55.000 18.83 0.00 0.00 3.49
2327 2545 6.149308 AGCATACGAGATTGTGACAATGAAAA 59.851 34.615 16.52 0.00 0.00 2.29
2409 2627 1.701704 CGGTTTGGGTGACTACGTAC 58.298 55.000 0.00 0.00 0.00 3.67
2425 2643 3.277211 TACGAGCGAACGCAGCCTT 62.277 57.895 20.66 0.00 44.88 4.35
2463 2681 6.090358 GCTAGTCATCGTGTTACTGCTAAAAA 59.910 38.462 0.00 0.00 0.00 1.94
2499 2717 1.715519 CGACGTATCGTTTTGGTTCGT 59.284 47.619 0.00 0.00 43.66 3.85
2531 2749 3.658757 TGGATTGCAAAAACCTAGCAC 57.341 42.857 1.71 0.00 38.11 4.40
2545 2763 0.030773 TAGCACGATGTGAGCGATCC 59.969 55.000 0.00 0.00 39.39 3.36
2590 2808 6.071165 AGTGGTATGTAAAACCTAAGTAGCGT 60.071 38.462 0.00 0.00 37.91 5.07
2611 2829 4.620184 CGTTTAAGACCTAAGTGGAACGAG 59.380 45.833 0.00 0.00 45.86 4.18
2621 2839 3.299340 AGTGGAACGAGTGTGATGTAC 57.701 47.619 0.00 0.00 45.86 2.90
2625 2843 3.166657 GGAACGAGTGTGATGTACGTAC 58.833 50.000 18.90 18.90 36.20 3.67
2626 2844 3.365264 GGAACGAGTGTGATGTACGTACA 60.365 47.826 29.15 29.15 40.98 2.90
2658 2876 0.169009 GAATTCACACCTGCGCCTTC 59.831 55.000 4.18 0.00 0.00 3.46
2666 2884 0.251341 ACCTGCGCCTTCTGGATTTT 60.251 50.000 4.18 0.00 34.57 1.82
2671 2889 2.487762 TGCGCCTTCTGGATTTTAGTTG 59.512 45.455 4.18 0.00 34.57 3.16
2675 2893 3.670627 GCCTTCTGGATTTTAGTTGTGCG 60.671 47.826 0.00 0.00 34.57 5.34
2695 2919 2.159448 CGACCTTGCAAGTGTTGTTGAA 60.159 45.455 24.35 0.00 0.00 2.69
2725 2949 6.260050 AGTTGACGTAAATACATTATGGCTGG 59.740 38.462 0.00 0.00 39.03 4.85
2785 3009 3.076621 CTGCAAAGCTGATAACTCCACA 58.923 45.455 0.00 0.00 0.00 4.17
2794 3018 8.494016 AAGCTGATAACTCCACATAAGTAAAC 57.506 34.615 0.00 0.00 0.00 2.01
2796 3020 7.982354 AGCTGATAACTCCACATAAGTAAACTC 59.018 37.037 0.00 0.00 0.00 3.01
2801 3025 3.592059 TCCACATAAGTAAACTCGGTGC 58.408 45.455 0.00 0.00 0.00 5.01
2813 3037 1.269726 ACTCGGTGCCTTGCAAAAATG 60.270 47.619 0.00 0.00 41.47 2.32
2818 3042 2.550639 GGTGCCTTGCAAAAATGACCAT 60.551 45.455 0.00 0.00 41.47 3.55
2826 3050 3.949754 TGCAAAAATGACCATGGCAAAAA 59.050 34.783 13.04 0.00 0.00 1.94
2827 3051 4.036498 TGCAAAAATGACCATGGCAAAAAG 59.964 37.500 13.04 3.68 0.00 2.27
2831 3055 7.256286 CAAAAATGACCATGGCAAAAAGAAAA 58.744 30.769 13.04 0.00 0.00 2.29
2832 3056 7.585579 AAAATGACCATGGCAAAAAGAAAAT 57.414 28.000 13.04 0.00 0.00 1.82
2843 3096 6.096695 GGCAAAAAGAAAATCCGTAGCATTA 58.903 36.000 0.00 0.00 0.00 1.90
2886 3141 8.902540 AAAAGAAAACAAAGAGTTGGAACTTT 57.097 26.923 0.00 0.00 41.19 2.66
2924 3179 3.839293 CAGTGTGGACTAGTAAGTGAGC 58.161 50.000 0.00 0.00 35.56 4.26
2936 3191 5.948992 AGTAAGTGAGCCAAACTTCATTC 57.051 39.130 0.00 0.00 38.73 2.67
2940 3195 1.879380 TGAGCCAAACTTCATTCACGG 59.121 47.619 0.00 0.00 0.00 4.94
2941 3196 2.151202 GAGCCAAACTTCATTCACGGA 58.849 47.619 0.00 0.00 0.00 4.69
2992 3247 3.873361 CACATTGCAGATCATACGGTCTT 59.127 43.478 0.00 0.00 0.00 3.01
2993 3248 3.873361 ACATTGCAGATCATACGGTCTTG 59.127 43.478 0.00 0.00 0.00 3.02
2997 3252 2.479730 GCAGATCATACGGTCTTGTCGT 60.480 50.000 0.00 0.00 43.64 4.34
2998 3253 3.364062 CAGATCATACGGTCTTGTCGTC 58.636 50.000 0.00 0.00 41.38 4.20
3000 3255 3.632604 AGATCATACGGTCTTGTCGTCAT 59.367 43.478 0.00 0.00 41.38 3.06
3017 3272 4.406069 CGTCATAACGTAGAACTTCGGAA 58.594 43.478 5.91 0.00 43.94 4.30
3023 3278 4.629251 ACGTAGAACTTCGGAATCCTAC 57.371 45.455 0.00 11.23 0.00 3.18
3053 3308 2.080286 AAGTGATCGTAGTTGCGCTT 57.920 45.000 9.73 0.00 0.00 4.68
3068 3323 2.682836 GCGCTTGGCATTTAGGAAAAA 58.317 42.857 0.00 0.00 42.87 1.94
3070 3325 3.860754 GCGCTTGGCATTTAGGAAAAAGT 60.861 43.478 0.00 0.00 42.87 2.66
3073 3328 5.344933 CGCTTGGCATTTAGGAAAAAGTTAC 59.655 40.000 0.00 0.00 0.00 2.50
3079 3334 9.050601 TGGCATTTAGGAAAAAGTTACAATTTG 57.949 29.630 0.00 0.00 0.00 2.32
3101 3356 6.902224 TGATGTATGTAGAAAATGGACACG 57.098 37.500 0.00 0.00 0.00 4.49
3108 3363 5.301555 TGTAGAAAATGGACACGTTGATGA 58.698 37.500 0.00 0.00 0.00 2.92
3119 3374 0.519792 CGTTGATGATGCGTGCTGTG 60.520 55.000 0.00 0.00 0.00 3.66
3120 3375 0.179181 GTTGATGATGCGTGCTGTGG 60.179 55.000 0.00 0.00 0.00 4.17
3134 3389 1.399714 CTGTGGGAGCATGCATGATT 58.600 50.000 30.64 16.89 0.00 2.57
3142 3397 4.098349 GGGAGCATGCATGATTTTAGTTCA 59.902 41.667 30.64 0.00 0.00 3.18
3145 3400 5.597806 AGCATGCATGATTTTAGTTCATGG 58.402 37.500 30.64 0.00 46.81 3.66
3151 3406 6.096705 TGCATGATTTTAGTTCATGGTTAGGG 59.903 38.462 13.72 0.00 46.81 3.53
3161 3416 1.400494 CATGGTTAGGGCTTTACGTGC 59.600 52.381 0.00 0.00 0.00 5.34
3195 3450 0.609131 ACTTCGATGCAAAGTGGGGG 60.609 55.000 1.47 0.00 35.68 5.40
3203 3458 1.665442 CAAAGTGGGGGAAAAGGCG 59.335 57.895 0.00 0.00 0.00 5.52
3219 3474 1.226267 GCGCGGATCGAATTTGCAA 60.226 52.632 8.83 0.00 41.67 4.08
3244 3499 4.523173 ACTTGAAATAGTCGAGACTGTCCA 59.477 41.667 15.36 8.09 42.52 4.02
3245 3500 4.703645 TGAAATAGTCGAGACTGTCCAG 57.296 45.455 15.36 0.00 42.52 3.86
3246 3501 4.079970 TGAAATAGTCGAGACTGTCCAGT 58.920 43.478 15.36 0.00 45.84 4.00
3306 3563 8.873215 TTTTTATTTCTTGTTTTGGCGATACA 57.127 26.923 0.00 0.00 0.00 2.29
3307 3564 8.873215 TTTTATTTCTTGTTTTGGCGATACAA 57.127 26.923 9.88 9.88 0.00 2.41
3308 3565 7.861176 TTATTTCTTGTTTTGGCGATACAAC 57.139 32.000 6.65 0.00 0.00 3.32
3309 3566 3.529634 TCTTGTTTTGGCGATACAACG 57.470 42.857 6.65 4.57 0.00 4.10
3310 3567 2.873472 TCTTGTTTTGGCGATACAACGT 59.127 40.909 6.65 0.00 35.59 3.99
3311 3568 2.953640 TGTTTTGGCGATACAACGTC 57.046 45.000 0.00 0.00 38.42 4.34
3312 3569 2.210961 TGTTTTGGCGATACAACGTCA 58.789 42.857 0.00 0.00 45.89 4.35
3314 3571 4.582760 TGGCGATACAACGTCACC 57.417 55.556 0.00 0.00 42.82 4.02
3315 3572 1.969085 TGGCGATACAACGTCACCT 59.031 52.632 0.00 0.00 42.82 4.00
3316 3573 0.389296 TGGCGATACAACGTCACCTG 60.389 55.000 0.00 0.00 42.82 4.00
3317 3574 0.108992 GGCGATACAACGTCACCTGA 60.109 55.000 0.00 0.00 37.83 3.86
3318 3575 1.670674 GGCGATACAACGTCACCTGAA 60.671 52.381 0.00 0.00 37.83 3.02
3319 3576 2.063266 GCGATACAACGTCACCTGAAA 58.937 47.619 0.00 0.00 35.59 2.69
3320 3577 2.477375 GCGATACAACGTCACCTGAAAA 59.523 45.455 0.00 0.00 35.59 2.29
3321 3578 3.059461 GCGATACAACGTCACCTGAAAAA 60.059 43.478 0.00 0.00 35.59 1.94
3322 3579 4.698276 CGATACAACGTCACCTGAAAAAG 58.302 43.478 0.00 0.00 0.00 2.27
3323 3580 7.795707 GCGATACAACGTCACCTGAAAAAGG 62.796 48.000 0.00 0.00 42.72 3.11
3333 3590 3.078594 CCTGAAAAAGGTTTGGTCGTG 57.921 47.619 0.00 0.00 41.74 4.35
3334 3591 2.459934 CTGAAAAAGGTTTGGTCGTGC 58.540 47.619 0.00 0.00 0.00 5.34
3335 3592 1.819288 TGAAAAAGGTTTGGTCGTGCA 59.181 42.857 0.00 0.00 0.00 4.57
3336 3593 2.231478 TGAAAAAGGTTTGGTCGTGCAA 59.769 40.909 0.00 0.00 0.00 4.08
3337 3594 3.254892 GAAAAAGGTTTGGTCGTGCAAA 58.745 40.909 0.00 0.00 0.00 3.68
3338 3595 3.320673 AAAAGGTTTGGTCGTGCAAAA 57.679 38.095 0.00 0.00 0.00 2.44
3339 3596 2.287393 AAGGTTTGGTCGTGCAAAAC 57.713 45.000 2.90 2.90 39.67 2.43
3340 3597 1.470051 AGGTTTGGTCGTGCAAAACT 58.530 45.000 10.01 0.00 40.14 2.66
3341 3598 1.822371 AGGTTTGGTCGTGCAAAACTT 59.178 42.857 10.01 1.18 40.14 2.66
3342 3599 3.018149 AGGTTTGGTCGTGCAAAACTTA 58.982 40.909 10.01 0.00 40.14 2.24
3343 3600 3.110358 GGTTTGGTCGTGCAAAACTTAC 58.890 45.455 10.01 2.50 40.14 2.34
3344 3601 2.741122 TTGGTCGTGCAAAACTTACG 57.259 45.000 0.00 0.00 39.04 3.18
3345 3602 0.938713 TGGTCGTGCAAAACTTACGG 59.061 50.000 0.00 0.00 38.29 4.02
3346 3603 0.385098 GGTCGTGCAAAACTTACGGC 60.385 55.000 0.00 0.00 41.28 5.68
3347 3604 0.305313 GTCGTGCAAAACTTACGGCA 59.695 50.000 0.00 0.00 41.60 5.69
3352 3609 3.889196 TGCAAAACTTACGGCACTAAG 57.111 42.857 0.00 0.00 0.00 2.18
3353 3610 2.550606 TGCAAAACTTACGGCACTAAGG 59.449 45.455 5.02 0.00 0.00 2.69
3354 3611 2.809696 GCAAAACTTACGGCACTAAGGA 59.190 45.455 5.02 0.00 0.00 3.36
3355 3612 3.251487 GCAAAACTTACGGCACTAAGGAA 59.749 43.478 5.02 0.00 0.00 3.36
3356 3613 4.082949 GCAAAACTTACGGCACTAAGGAAT 60.083 41.667 5.02 0.00 0.00 3.01
3357 3614 5.390613 CAAAACTTACGGCACTAAGGAATG 58.609 41.667 5.02 0.00 0.00 2.67
3358 3615 3.975168 ACTTACGGCACTAAGGAATGT 57.025 42.857 5.02 0.00 0.00 2.71
3359 3616 3.596214 ACTTACGGCACTAAGGAATGTG 58.404 45.455 5.02 0.00 37.26 3.21
3360 3617 3.259876 ACTTACGGCACTAAGGAATGTGA 59.740 43.478 0.00 0.00 36.38 3.58
3361 3618 2.851263 ACGGCACTAAGGAATGTGAA 57.149 45.000 0.00 0.00 36.38 3.18
3362 3619 2.423577 ACGGCACTAAGGAATGTGAAC 58.576 47.619 0.00 0.00 36.38 3.18
3363 3620 2.038557 ACGGCACTAAGGAATGTGAACT 59.961 45.455 0.00 0.00 36.38 3.01
3364 3621 3.074412 CGGCACTAAGGAATGTGAACTT 58.926 45.455 0.00 0.00 36.38 2.66
3365 3622 3.125316 CGGCACTAAGGAATGTGAACTTC 59.875 47.826 0.00 0.00 36.38 3.01
3366 3623 3.440522 GGCACTAAGGAATGTGAACTTCC 59.559 47.826 0.00 0.00 42.13 3.46
3371 3628 2.997485 GGAATGTGAACTTCCTGTGC 57.003 50.000 0.00 0.00 39.30 4.57
3372 3629 1.197721 GGAATGTGAACTTCCTGTGCG 59.802 52.381 0.00 0.00 39.30 5.34
3373 3630 1.197721 GAATGTGAACTTCCTGTGCGG 59.802 52.381 0.00 0.00 0.00 5.69
3374 3631 1.237285 ATGTGAACTTCCTGTGCGGC 61.237 55.000 0.00 0.00 0.00 6.53
3375 3632 1.598130 GTGAACTTCCTGTGCGGCT 60.598 57.895 0.00 0.00 0.00 5.52
3376 3633 1.301716 TGAACTTCCTGTGCGGCTC 60.302 57.895 0.00 0.00 0.00 4.70
3377 3634 2.357517 AACTTCCTGTGCGGCTCG 60.358 61.111 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.468072 CCTCCATTATCACGATGAAAGGAAG 59.532 44.000 0.00 0.00 33.03 3.46
53 54 5.129485 ACAAGAGGCATACACTAACTGCTAT 59.871 40.000 0.00 0.00 36.18 2.97
55 56 3.261897 ACAAGAGGCATACACTAACTGCT 59.738 43.478 0.00 0.00 36.18 4.24
59 60 5.874810 TGAATGACAAGAGGCATACACTAAC 59.125 40.000 0.00 0.00 0.00 2.34
97 98 6.878923 TCAGACGACCAAATCATCAGTTTTAT 59.121 34.615 0.00 0.00 0.00 1.40
98 99 6.147164 GTCAGACGACCAAATCATCAGTTTTA 59.853 38.462 0.00 0.00 36.02 1.52
144 145 2.202756 AATCCGCTTCGACGAGCC 60.203 61.111 3.57 1.35 39.51 4.70
162 163 4.521256 GCCTTACTACCATCTACAGAGGAG 59.479 50.000 0.00 0.00 0.00 3.69
178 179 3.129813 TGTCGTAATGTCGATGCCTTACT 59.870 43.478 0.00 0.00 41.78 2.24
197 198 1.066787 GGTACCTGAGGACAGCTTGTC 60.067 57.143 4.99 7.52 46.23 3.18
221 223 1.373570 GATGGCACTGCTACAACTCC 58.626 55.000 0.00 0.00 0.00 3.85
222 224 1.002366 CGATGGCACTGCTACAACTC 58.998 55.000 0.00 0.00 0.00 3.01
239 241 1.670791 AGTTCTTTTTCCAACCGCGA 58.329 45.000 8.23 0.00 0.00 5.87
242 244 3.564225 AGCTGTAGTTCTTTTTCCAACCG 59.436 43.478 0.00 0.00 0.00 4.44
245 247 3.951037 TGCAGCTGTAGTTCTTTTTCCAA 59.049 39.130 16.64 0.00 0.00 3.53
252 257 2.430465 CCATGTGCAGCTGTAGTTCTT 58.570 47.619 16.64 0.00 0.00 2.52
308 313 1.759445 CAGCTGTAGGAGGTGCTACAT 59.241 52.381 11.28 0.00 43.06 2.29
335 340 1.079819 TGCTCTGTAAGGCTGACGC 60.080 57.895 0.00 0.00 32.37 5.19
344 349 2.420642 CTGCTTCTTGCTGCTCTGTAA 58.579 47.619 0.00 0.00 43.37 2.41
402 407 0.673956 GACGGAAAGAAGGACCAGGC 60.674 60.000 0.00 0.00 0.00 4.85
482 487 3.925913 CGTGCAACAATCATTAAAAGGGG 59.074 43.478 0.00 0.00 35.74 4.79
513 518 2.994995 TCACCGCCATCTGTCCGT 60.995 61.111 0.00 0.00 0.00 4.69
516 521 2.509336 CCGTCACCGCCATCTGTC 60.509 66.667 0.00 0.00 0.00 3.51
652 657 6.591448 TGAATATGCGATGGATTATGTGTCTC 59.409 38.462 0.00 0.00 0.00 3.36
676 681 7.862372 AGTTGTATTTACAGTTTTCAGTGCATG 59.138 33.333 0.00 0.00 37.52 4.06
683 688 7.771361 TCCTGTCAGTTGTATTTACAGTTTTCA 59.229 33.333 0.00 0.00 37.52 2.69
684 689 8.149973 TCCTGTCAGTTGTATTTACAGTTTTC 57.850 34.615 0.00 0.00 37.52 2.29
693 698 6.209391 CCCAATCTTTCCTGTCAGTTGTATTT 59.791 38.462 0.00 0.00 0.00 1.40
785 790 5.008911 TCGCATGCAAGCAAATTAGATATGT 59.991 36.000 19.57 0.00 0.00 2.29
788 793 5.497635 TTCGCATGCAAGCAAATTAGATA 57.502 34.783 19.57 0.00 0.00 1.98
789 794 4.357142 CTTCGCATGCAAGCAAATTAGAT 58.643 39.130 19.57 0.00 0.00 1.98
830 835 6.614694 TGAGTCCAGGTAGTTTAAATGCTA 57.385 37.500 0.00 0.00 0.00 3.49
841 846 5.174395 CACAGAAAGAATGAGTCCAGGTAG 58.826 45.833 0.00 0.00 0.00 3.18
843 848 3.808618 GCACAGAAAGAATGAGTCCAGGT 60.809 47.826 0.00 0.00 0.00 4.00
849 854 3.944015 GCCTATGCACAGAAAGAATGAGT 59.056 43.478 0.00 0.00 37.47 3.41
892 900 6.656632 TTTCCTGCATACAAATGTGGTTAA 57.343 33.333 0.00 0.00 35.38 2.01
897 905 4.081531 ACCCATTTCCTGCATACAAATGTG 60.082 41.667 17.38 12.07 36.27 3.21
904 912 3.699038 TGCTTAACCCATTTCCTGCATAC 59.301 43.478 0.00 0.00 0.00 2.39
981 989 4.624913 TCATTGTTATCTCTCCTCCTGGT 58.375 43.478 0.00 0.00 34.23 4.00
1033 1041 5.008613 GGTAAATGCCATTATCTTTCTCGCA 59.991 40.000 0.00 0.00 0.00 5.10
1053 1061 0.759812 TATCCATCCACCCGCGGTAA 60.760 55.000 26.12 6.42 32.11 2.85
1132 1140 8.235359 AGTTACTATTACTCACATCCAGTACC 57.765 38.462 0.00 0.00 0.00 3.34
1154 1162 6.541278 TGTCACTGCTGTACGATACTATAGTT 59.459 38.462 11.40 0.00 0.00 2.24
1161 1169 5.577164 AGATTTTGTCACTGCTGTACGATAC 59.423 40.000 0.00 0.00 0.00 2.24
1167 1175 7.744087 AATTACAGATTTTGTCACTGCTGTA 57.256 32.000 0.00 0.00 41.29 2.74
1189 1198 8.031277 GCAGACTTCATCCTGTAATTTCAAAAT 58.969 33.333 0.00 0.00 33.19 1.82
1209 1218 1.129917 CTCCATCATCCCTGCAGACT 58.870 55.000 17.39 0.00 0.00 3.24
1248 1257 8.045507 GCCTTATCTGAATTCATCATATCCTCA 58.954 37.037 8.96 0.00 37.44 3.86
1320 1330 2.433868 ATAACAGTTGTGCGTCGAGT 57.566 45.000 0.00 0.00 0.00 4.18
1342 1352 8.762481 TGTCAGCTATAGGTTAAGACAATAGA 57.238 34.615 16.79 0.60 32.26 1.98
1475 1486 9.636789 ATTTTCATCTCATCCATTTCATCTGTA 57.363 29.630 0.00 0.00 0.00 2.74
1502 1513 0.749649 TTGCACGGCCTTCATGTTTT 59.250 45.000 0.00 0.00 0.00 2.43
2121 2133 3.096852 TCAGTGATGAACGGAGGTACAT 58.903 45.455 0.00 0.00 0.00 2.29
2196 2210 9.039870 GGACTGAACAACTTAGATATCTTCATG 57.960 37.037 11.25 8.04 0.00 3.07
2237 2454 5.275067 ACCAAAGCAGCATCAGTTTTAAA 57.725 34.783 0.00 0.00 0.00 1.52
2238 2455 4.935352 ACCAAAGCAGCATCAGTTTTAA 57.065 36.364 0.00 0.00 0.00 1.52
2241 2458 2.804212 GCAACCAAAGCAGCATCAGTTT 60.804 45.455 0.00 0.00 0.00 2.66
2273 2491 2.751259 ACCGTAGACGTTCTATCTGCAA 59.249 45.455 0.85 0.00 37.74 4.08
2274 2492 2.353889 GACCGTAGACGTTCTATCTGCA 59.646 50.000 0.85 0.00 37.74 4.41
2284 2502 1.005340 CTAGCTTCGACCGTAGACGT 58.995 55.000 0.00 0.00 37.74 4.34
2294 2512 3.315470 ACAATCTCGTATGCTAGCTTCGA 59.685 43.478 17.23 19.53 0.00 3.71
2305 2523 6.878923 TCCTTTTCATTGTCACAATCTCGTAT 59.121 34.615 0.00 0.00 0.00 3.06
2362 2580 5.104817 TGTTGCTCCTCAATCTATGATCACA 60.105 40.000 0.00 0.00 37.44 3.58
2409 2627 2.506217 TAAGGCTGCGTTCGCTCG 60.506 61.111 17.63 10.02 0.00 5.03
2481 2699 2.472816 ACACGAACCAAAACGATACGT 58.527 42.857 0.00 0.00 43.97 3.57
2499 2717 1.568123 TGCAATCCATGGGACCATACA 59.432 47.619 13.02 0.00 32.98 2.29
2531 2749 0.947660 CCCATGGATCGCTCACATCG 60.948 60.000 15.22 0.00 0.00 3.84
2545 2763 3.756434 ACTTGTTCCGAATTACACCCATG 59.244 43.478 0.00 0.00 0.00 3.66
2590 2808 5.069516 ACACTCGTTCCACTTAGGTCTTAAA 59.930 40.000 0.00 0.00 39.02 1.52
2621 2839 7.753580 TGTGAATTCAGATACTTAGTGTGTACG 59.246 37.037 8.80 0.00 0.00 3.67
2625 2843 7.063898 CAGGTGTGAATTCAGATACTTAGTGTG 59.936 40.741 8.80 0.00 0.00 3.82
2626 2844 7.099764 CAGGTGTGAATTCAGATACTTAGTGT 58.900 38.462 8.80 0.00 0.00 3.55
2658 2876 3.074412 AGGTCGCACAACTAAAATCCAG 58.926 45.455 0.00 0.00 0.00 3.86
2666 2884 1.225855 CTTGCAAGGTCGCACAACTA 58.774 50.000 19.14 0.00 42.87 2.24
2671 2889 0.592247 CAACACTTGCAAGGTCGCAC 60.592 55.000 29.18 0.00 42.87 5.34
2675 2893 3.502191 TTCAACAACACTTGCAAGGTC 57.498 42.857 29.18 0.00 0.00 3.85
2686 2910 5.804692 ACGTCAACTACAATTCAACAACA 57.195 34.783 0.00 0.00 0.00 3.33
2725 2949 1.070108 GTTCAAAAACTCCGTCTCGCC 60.070 52.381 0.00 0.00 32.36 5.54
2738 2962 9.615295 GCCATAAAGTTATAAACTCGTTCAAAA 57.385 29.630 0.00 0.00 41.91 2.44
2739 2963 9.005777 AGCCATAAAGTTATAAACTCGTTCAAA 57.994 29.630 0.00 0.00 41.91 2.69
2785 3009 3.007635 GCAAGGCACCGAGTTTACTTAT 58.992 45.455 0.00 0.00 0.00 1.73
2794 3018 1.000385 TCATTTTTGCAAGGCACCGAG 60.000 47.619 0.00 0.00 38.71 4.63
2796 3020 1.139163 GTCATTTTTGCAAGGCACCG 58.861 50.000 0.00 0.00 38.71 4.94
2801 3025 2.078392 GCCATGGTCATTTTTGCAAGG 58.922 47.619 14.67 0.00 0.00 3.61
2813 3037 3.679502 CGGATTTTCTTTTTGCCATGGTC 59.320 43.478 14.67 6.41 0.00 4.02
2818 3042 3.319405 TGCTACGGATTTTCTTTTTGCCA 59.681 39.130 0.00 0.00 0.00 4.92
2826 3050 3.131396 CGCCTAATGCTACGGATTTTCT 58.869 45.455 0.00 0.00 38.05 2.52
2827 3051 2.870411 ACGCCTAATGCTACGGATTTTC 59.130 45.455 0.00 0.00 38.05 2.29
2831 3055 1.037493 TCACGCCTAATGCTACGGAT 58.963 50.000 0.00 0.00 38.05 4.18
2832 3056 0.818938 TTCACGCCTAATGCTACGGA 59.181 50.000 0.00 0.00 38.05 4.69
2857 3110 7.227049 TCCAACTCTTTGTTTTCTTTTCACT 57.773 32.000 0.00 0.00 36.63 3.41
2878 3133 0.850100 TCCCAAGCCTCAAAGTTCCA 59.150 50.000 0.00 0.00 0.00 3.53
2886 3141 2.401699 CTGCAGTGTCCCAAGCCTCA 62.402 60.000 5.25 0.00 0.00 3.86
2888 3143 2.433446 CTGCAGTGTCCCAAGCCT 59.567 61.111 5.25 0.00 0.00 4.58
2924 3179 3.366273 CCACATCCGTGAATGAAGTTTGG 60.366 47.826 0.00 0.00 46.80 3.28
2940 3195 1.064060 GCATGTTTACTCGGCCACATC 59.936 52.381 2.24 0.00 0.00 3.06
2941 3196 1.094785 GCATGTTTACTCGGCCACAT 58.905 50.000 2.24 0.00 0.00 3.21
2955 3210 6.772233 TCTGCAATGTGGTATATTAAGCATGT 59.228 34.615 0.00 0.00 0.00 3.21
2997 3252 5.359009 AGGATTCCGAAGTTCTACGTTATGA 59.641 40.000 0.00 0.00 0.00 2.15
2998 3253 5.589192 AGGATTCCGAAGTTCTACGTTATG 58.411 41.667 0.00 0.00 0.00 1.90
3000 3255 5.647658 TGTAGGATTCCGAAGTTCTACGTTA 59.352 40.000 0.00 0.00 32.28 3.18
3023 3278 9.586150 GCAACTACGATCACTTTGATATTAATG 57.414 33.333 0.00 0.00 37.20 1.90
3053 3308 9.050601 CAAATTGTAACTTTTTCCTAAATGCCA 57.949 29.630 0.00 0.00 0.00 4.92
3079 3334 6.903883 ACGTGTCCATTTTCTACATACATC 57.096 37.500 0.00 0.00 0.00 3.06
3101 3356 0.179181 CCACAGCACGCATCATCAAC 60.179 55.000 0.00 0.00 0.00 3.18
3119 3374 4.098349 TGAACTAAAATCATGCATGCTCCC 59.902 41.667 22.25 4.57 0.00 4.30
3120 3375 5.252969 TGAACTAAAATCATGCATGCTCC 57.747 39.130 22.25 4.00 0.00 4.70
3131 3386 6.775594 AAGCCCTAACCATGAACTAAAATC 57.224 37.500 0.00 0.00 0.00 2.17
3134 3389 5.644636 CGTAAAGCCCTAACCATGAACTAAA 59.355 40.000 0.00 0.00 0.00 1.85
3142 3397 1.280998 AGCACGTAAAGCCCTAACCAT 59.719 47.619 0.00 0.00 0.00 3.55
3145 3400 1.084289 CCAGCACGTAAAGCCCTAAC 58.916 55.000 0.00 0.00 0.00 2.34
3151 3406 1.226746 ACTTGTCCAGCACGTAAAGC 58.773 50.000 0.00 0.00 0.00 3.51
3161 3416 5.446473 GCATCGAAGTTCATTACTTGTCCAG 60.446 44.000 3.32 0.00 47.00 3.86
3195 3450 0.377203 AATTCGATCCGCGCCTTTTC 59.623 50.000 0.00 0.00 40.61 2.29
3203 3458 1.398390 AGTCTTGCAAATTCGATCCGC 59.602 47.619 0.00 0.00 0.00 5.54
3219 3474 5.106078 GGACAGTCTCGACTATTTCAAGTCT 60.106 44.000 0.00 0.00 43.11 3.24
3244 3499 3.194968 CGGGACACTTAGTATCCAACACT 59.805 47.826 12.09 0.00 33.87 3.55
3245 3500 3.518590 CGGGACACTTAGTATCCAACAC 58.481 50.000 12.09 0.00 33.87 3.32
3246 3501 2.498481 CCGGGACACTTAGTATCCAACA 59.502 50.000 12.09 0.00 33.87 3.33
3289 3546 2.873472 ACGTTGTATCGCCAAAACAAGA 59.127 40.909 0.00 0.00 34.01 3.02
3290 3547 3.223157 GACGTTGTATCGCCAAAACAAG 58.777 45.455 0.00 0.00 34.01 3.16
3292 3549 2.032722 GTGACGTTGTATCGCCAAAACA 60.033 45.455 0.00 0.00 0.00 2.83
3293 3550 2.567067 GTGACGTTGTATCGCCAAAAC 58.433 47.619 0.00 0.00 0.00 2.43
3297 3554 4.582760 GGTGACGTTGTATCGCCA 57.417 55.556 0.00 0.00 44.69 5.69
3298 3555 0.108992 TCAGGTGACGTTGTATCGCC 60.109 55.000 0.00 0.00 45.51 5.54
3299 3556 1.705256 TTCAGGTGACGTTGTATCGC 58.295 50.000 0.00 0.00 0.00 4.58
3300 3557 4.377022 CCTTTTTCAGGTGACGTTGTATCG 60.377 45.833 0.00 0.00 37.99 2.92
3301 3558 5.030874 CCTTTTTCAGGTGACGTTGTATC 57.969 43.478 0.00 0.00 37.99 2.24
3314 3571 2.159310 TGCACGACCAAACCTTTTTCAG 60.159 45.455 0.00 0.00 0.00 3.02
3315 3572 1.819288 TGCACGACCAAACCTTTTTCA 59.181 42.857 0.00 0.00 0.00 2.69
3316 3573 2.570442 TGCACGACCAAACCTTTTTC 57.430 45.000 0.00 0.00 0.00 2.29
3317 3574 3.320673 TTTGCACGACCAAACCTTTTT 57.679 38.095 0.00 0.00 30.28 1.94
3318 3575 2.997303 GTTTTGCACGACCAAACCTTTT 59.003 40.909 0.00 0.00 34.68 2.27
3319 3576 2.232696 AGTTTTGCACGACCAAACCTTT 59.767 40.909 7.21 0.00 34.68 3.11
3320 3577 1.822371 AGTTTTGCACGACCAAACCTT 59.178 42.857 7.21 0.00 34.68 3.50
3321 3578 1.470051 AGTTTTGCACGACCAAACCT 58.530 45.000 7.21 0.00 34.68 3.50
3322 3579 2.287393 AAGTTTTGCACGACCAAACC 57.713 45.000 7.21 0.00 34.68 3.27
3323 3580 2.779471 CGTAAGTTTTGCACGACCAAAC 59.221 45.455 3.27 3.27 37.89 2.93
3324 3581 2.223294 CCGTAAGTTTTGCACGACCAAA 60.223 45.455 0.00 0.00 37.89 3.28
3325 3582 1.331138 CCGTAAGTTTTGCACGACCAA 59.669 47.619 0.00 0.00 37.89 3.67
3326 3583 0.938713 CCGTAAGTTTTGCACGACCA 59.061 50.000 0.00 0.00 37.89 4.02
3327 3584 0.385098 GCCGTAAGTTTTGCACGACC 60.385 55.000 0.00 0.00 37.89 4.79
3328 3585 0.305313 TGCCGTAAGTTTTGCACGAC 59.695 50.000 0.00 0.00 37.89 4.34
3329 3586 0.305313 GTGCCGTAAGTTTTGCACGA 59.695 50.000 7.91 0.00 43.83 4.35
3330 3587 2.778372 GTGCCGTAAGTTTTGCACG 58.222 52.632 7.91 0.00 43.83 5.34
3332 3589 2.550606 CCTTAGTGCCGTAAGTTTTGCA 59.449 45.455 0.00 0.00 0.00 4.08
3333 3590 2.809696 TCCTTAGTGCCGTAAGTTTTGC 59.190 45.455 2.48 0.00 0.00 3.68
3334 3591 5.048991 ACATTCCTTAGTGCCGTAAGTTTTG 60.049 40.000 2.48 0.41 0.00 2.44
3335 3592 5.048991 CACATTCCTTAGTGCCGTAAGTTTT 60.049 40.000 2.48 0.00 0.00 2.43
3336 3593 4.454504 CACATTCCTTAGTGCCGTAAGTTT 59.545 41.667 2.48 0.00 0.00 2.66
3337 3594 4.000988 CACATTCCTTAGTGCCGTAAGTT 58.999 43.478 2.48 0.00 0.00 2.66
3338 3595 3.259876 TCACATTCCTTAGTGCCGTAAGT 59.740 43.478 0.00 0.00 35.76 2.24
3339 3596 3.857052 TCACATTCCTTAGTGCCGTAAG 58.143 45.455 0.00 0.00 35.76 2.34
3340 3597 3.965379 TCACATTCCTTAGTGCCGTAA 57.035 42.857 0.00 0.00 35.76 3.18
3341 3598 3.259876 AGTTCACATTCCTTAGTGCCGTA 59.740 43.478 0.00 0.00 35.76 4.02
3342 3599 2.038557 AGTTCACATTCCTTAGTGCCGT 59.961 45.455 0.00 0.00 35.76 5.68
3343 3600 2.699954 AGTTCACATTCCTTAGTGCCG 58.300 47.619 0.00 0.00 35.76 5.69
3344 3601 3.440522 GGAAGTTCACATTCCTTAGTGCC 59.559 47.826 5.01 0.00 42.52 5.01
3345 3602 4.686839 GGAAGTTCACATTCCTTAGTGC 57.313 45.455 5.01 0.00 42.52 4.40
3352 3609 1.197721 CGCACAGGAAGTTCACATTCC 59.802 52.381 5.01 0.00 45.56 3.01
3353 3610 1.197721 CCGCACAGGAAGTTCACATTC 59.802 52.381 5.01 0.00 45.00 2.67
3354 3611 1.238439 CCGCACAGGAAGTTCACATT 58.762 50.000 5.01 0.00 45.00 2.71
3355 3612 1.237285 GCCGCACAGGAAGTTCACAT 61.237 55.000 5.01 0.00 45.00 3.21
3356 3613 1.891919 GCCGCACAGGAAGTTCACA 60.892 57.895 5.01 0.00 45.00 3.58
3357 3614 1.569479 GAGCCGCACAGGAAGTTCAC 61.569 60.000 5.01 0.00 45.00 3.18
3358 3615 1.301716 GAGCCGCACAGGAAGTTCA 60.302 57.895 5.01 0.00 45.00 3.18
3359 3616 2.383527 CGAGCCGCACAGGAAGTTC 61.384 63.158 0.00 0.00 45.00 3.01
3360 3617 2.357517 CGAGCCGCACAGGAAGTT 60.358 61.111 0.00 0.00 45.00 2.66


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

AutoCloner maintained by Alex Coulton.