Multiple sequence alignment - TraesCS7B01G286100

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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 TraesCS7B01G286100 chr7B 100.000 3352 0 0 1 3352 521198835 521195484 0.000000e+00 6191.0
1 TraesCS7B01G286100 chr7B 91.477 2417 123 45 626 3016 521151566 521149207 0.000000e+00 3245.0
2 TraesCS7B01G286100 chr7B 90.098 1424 93 32 1604 3012 522142075 522143465 0.000000e+00 1805.0
3 TraesCS7B01G286100 chr7B 91.667 636 46 3 1 629 652302498 652303133 0.000000e+00 874.0
4 TraesCS7B01G286100 chr7B 83.918 827 56 28 690 1464 522141247 522142048 0.000000e+00 719.0
5 TraesCS7B01G286100 chr7B 100.000 257 0 0 3549 3805 521195287 521195031 3.440000e-130 475.0
6 TraesCS7B01G286100 chr7B 89.540 239 17 1 3557 3795 521148955 521148725 2.870000e-76 296.0
7 TraesCS7B01G286100 chr7B 87.571 177 20 2 3150 3324 521149143 521148967 1.790000e-48 204.0
8 TraesCS7B01G286100 chr7D 93.026 2151 83 25 945 3067 491874027 491871916 0.000000e+00 3079.0
9 TraesCS7B01G286100 chr7D 91.673 1405 87 22 1600 2987 493203681 493205072 0.000000e+00 1919.0
10 TraesCS7B01G286100 chr7D 88.123 1465 126 35 1563 3012 493560511 493561942 0.000000e+00 1698.0
11 TraesCS7B01G286100 chr7D 85.276 815 57 27 690 1459 493202856 493203652 0.000000e+00 782.0
12 TraesCS7B01G286100 chr7D 93.921 329 13 3 626 948 491877637 491877310 1.230000e-134 490.0
13 TraesCS7B01G286100 chr7D 85.821 268 20 6 1166 1418 493559980 493560244 6.270000e-68 268.0
14 TraesCS7B01G286100 chr7A 94.684 1505 64 6 1559 3049 558109982 558108480 0.000000e+00 2322.0
15 TraesCS7B01G286100 chr7A 91.422 1399 96 20 1602 2987 559361783 559363170 0.000000e+00 1897.0
16 TraesCS7B01G286100 chr7A 92.027 903 62 5 1556 2449 559386809 559387710 0.000000e+00 1260.0
17 TraesCS7B01G286100 chr7A 92.308 637 39 4 1 630 58214057 58213424 0.000000e+00 896.0
18 TraesCS7B01G286100 chr7A 87.516 785 58 19 626 1396 558110895 558110137 0.000000e+00 870.0
19 TraesCS7B01G286100 chr7A 84.753 446 35 18 690 1109 559361022 559361460 2.110000e-112 416.0
20 TraesCS7B01G286100 chr7A 88.110 328 35 4 2486 2811 559388039 559388364 1.660000e-103 387.0
21 TraesCS7B01G286100 chr7A 90.155 193 18 1 1204 1396 559361519 559361710 2.270000e-62 250.0
22 TraesCS7B01G286100 chr7A 86.772 189 20 2 1166 1354 559386014 559386197 4.980000e-49 206.0
23 TraesCS7B01G286100 chr7A 92.553 94 5 2 3060 3151 473897584 473897491 2.380000e-27 134.0
24 TraesCS7B01G286100 chr4B 95.880 631 24 2 1 630 145839581 145840210 0.000000e+00 1020.0
25 TraesCS7B01G286100 chr4B 89.412 85 7 2 3068 3150 105348601 105348685 5.200000e-19 106.0
26 TraesCS7B01G286100 chr6B 94.921 630 30 2 1 629 686218297 686218925 0.000000e+00 985.0
27 TraesCS7B01G286100 chr6B 91.693 638 43 5 1 629 461972278 461971642 0.000000e+00 876.0
28 TraesCS7B01G286100 chr3D 95.440 614 27 1 1 613 508579165 508579778 0.000000e+00 977.0
29 TraesCS7B01G286100 chr2D 94.286 630 31 5 1 629 481970617 481971242 0.000000e+00 959.0
30 TraesCS7B01G286100 chr2B 92.628 624 39 3 1 617 779060228 779060851 0.000000e+00 891.0
31 TraesCS7B01G286100 chr6A 91.195 636 45 6 1 629 48503481 48502850 0.000000e+00 854.0
32 TraesCS7B01G286100 chr6A 82.847 822 132 7 1625 2443 564975151 564975966 0.000000e+00 728.0
33 TraesCS7B01G286100 chr5A 94.118 85 3 2 3068 3150 590871679 590871595 1.110000e-25 128.0
34 TraesCS7B01G286100 chr4D 83.088 136 21 2 1208 1342 455693547 455693681 5.160000e-24 122.0
35 TraesCS7B01G286100 chr3B 91.209 91 6 2 3062 3150 676214712 676214622 5.160000e-24 122.0
36 TraesCS7B01G286100 chr1A 91.111 90 6 2 3063 3150 84793910 84793821 1.860000e-23 121.0
37 TraesCS7B01G286100 chr2A 89.535 86 7 2 3067 3150 264300126 264300041 1.450000e-19 108.0
38 TraesCS7B01G286100 chr2A 85.106 94 13 1 3068 3160 15617194 15617101 1.130000e-15 95.3
39 TraesCS7B01G286100 chr4A 84.375 96 11 4 3058 3150 437609353 437609447 1.460000e-14 91.6
40 TraesCS7B01G286100 chr4A 83.871 93 13 2 3060 3150 113714482 113714390 1.880000e-13 87.9


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 TraesCS7B01G286100 chr7B 521195031 521198835 3804 True 3333.000000 6191 100.000000 1 3805 2 chr7B.!!$R2 3804
1 TraesCS7B01G286100 chr7B 522141247 522143465 2218 False 1262.000000 1805 87.008000 690 3012 2 chr7B.!!$F2 2322
2 TraesCS7B01G286100 chr7B 521148725 521151566 2841 True 1248.333333 3245 89.529333 626 3795 3 chr7B.!!$R1 3169
3 TraesCS7B01G286100 chr7B 652302498 652303133 635 False 874.000000 874 91.667000 1 629 1 chr7B.!!$F1 628
4 TraesCS7B01G286100 chr7D 491871916 491877637 5721 True 1784.500000 3079 93.473500 626 3067 2 chr7D.!!$R1 2441
5 TraesCS7B01G286100 chr7D 493202856 493205072 2216 False 1350.500000 1919 88.474500 690 2987 2 chr7D.!!$F1 2297
6 TraesCS7B01G286100 chr7D 493559980 493561942 1962 False 983.000000 1698 86.972000 1166 3012 2 chr7D.!!$F2 1846
7 TraesCS7B01G286100 chr7A 558108480 558110895 2415 True 1596.000000 2322 91.100000 626 3049 2 chr7A.!!$R3 2423
8 TraesCS7B01G286100 chr7A 58213424 58214057 633 True 896.000000 896 92.308000 1 630 1 chr7A.!!$R1 629
9 TraesCS7B01G286100 chr7A 559361022 559363170 2148 False 854.333333 1897 88.776667 690 2987 3 chr7A.!!$F1 2297
10 TraesCS7B01G286100 chr7A 559386014 559388364 2350 False 617.666667 1260 88.969667 1166 2811 3 chr7A.!!$F2 1645
11 TraesCS7B01G286100 chr4B 145839581 145840210 629 False 1020.000000 1020 95.880000 1 630 1 chr4B.!!$F2 629
12 TraesCS7B01G286100 chr6B 686218297 686218925 628 False 985.000000 985 94.921000 1 629 1 chr6B.!!$F1 628
13 TraesCS7B01G286100 chr6B 461971642 461972278 636 True 876.000000 876 91.693000 1 629 1 chr6B.!!$R1 628
14 TraesCS7B01G286100 chr3D 508579165 508579778 613 False 977.000000 977 95.440000 1 613 1 chr3D.!!$F1 612
15 TraesCS7B01G286100 chr2D 481970617 481971242 625 False 959.000000 959 94.286000 1 629 1 chr2D.!!$F1 628
16 TraesCS7B01G286100 chr2B 779060228 779060851 623 False 891.000000 891 92.628000 1 617 1 chr2B.!!$F1 616
17 TraesCS7B01G286100 chr6A 48502850 48503481 631 True 854.000000 854 91.195000 1 629 1 chr6A.!!$R1 628
18 TraesCS7B01G286100 chr6A 564975151 564975966 815 False 728.000000 728 82.847000 1625 2443 1 chr6A.!!$F1 818

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
995 4363 0.378962 GTGAGATCGACAGTAGCGCT 59.621 55.0 17.26 17.26 0.00 5.92 F
1360 4756 0.494095 AAGGTCCTCCTCCCTCTTGT 59.506 55.0 0.00 0.00 44.35 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2803 7039 1.078143 GTGGATCGCTGGAGGCTTT 60.078 57.895 0.0 0.0 39.13 3.51 R
3317 7577 0.247736 GGCGACATGGAGACTGAAGT 59.752 55.000 0.0 0.0 0.00 3.01 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
36 38 1.892474 CCATGTTGGGGACATTTCGTT 59.108 47.619 0.00 0.00 46.80 3.85
53 55 0.388649 GTTGTCGATGTCTGCCTCGT 60.389 55.000 0.00 0.00 34.95 4.18
62 64 4.767255 CTGCCTCGTCCCCTGTGC 62.767 72.222 0.00 0.00 0.00 4.57
224 226 4.716287 TGTGTGAGGGAGATGATTCATGTA 59.284 41.667 3.32 0.00 0.00 2.29
310 312 2.281484 GATGTGGCCGGTGTGTGT 60.281 61.111 1.90 0.00 0.00 3.72
442 457 1.419762 TGTGCAAGTGTGGTGAGGTAT 59.580 47.619 0.00 0.00 0.00 2.73
450 465 5.755409 AGTGTGGTGAGGTATGATTGTTA 57.245 39.130 0.00 0.00 0.00 2.41
510 525 0.878523 TGTTTCGTGCTTCCCGAGTG 60.879 55.000 0.00 0.00 35.49 3.51
620 638 4.812626 GCAAATATTTTGCCTCCATTCTGG 59.187 41.667 12.74 0.00 39.38 3.86
659 677 1.686355 TCGTTTGCAAATGTCACCCT 58.314 45.000 26.39 0.00 0.00 4.34
720 745 2.626780 GGCAAGGCTGGGTTTCGAC 61.627 63.158 0.00 0.00 0.00 4.20
734 759 3.617284 GTTTCGACCCCAACTTGGATAT 58.383 45.455 9.61 0.00 40.96 1.63
735 760 4.384427 GGTTTCGACCCCAACTTGGATATA 60.384 45.833 9.61 0.00 40.96 0.86
995 4363 0.378962 GTGAGATCGACAGTAGCGCT 59.621 55.000 17.26 17.26 0.00 5.92
1010 4378 2.279784 GCTCGCGATGGGGAAGAG 60.280 66.667 10.36 0.00 34.39 2.85
1097 4468 1.546476 AGTCCTCTTTCAGGTACGCAG 59.454 52.381 0.00 0.00 43.95 5.18
1128 4499 9.657419 ATGGTTTCCTTTTGATTCATGTATTTC 57.343 29.630 0.00 0.00 0.00 2.17
1134 4505 9.709495 TCCTTTTGATTCATGTATTTCTTTTGG 57.291 29.630 0.00 0.00 0.00 3.28
1179 4553 5.764192 AGAAGAATCTGAGCTTAATGGATGC 59.236 40.000 0.00 0.00 33.59 3.91
1190 4564 4.142093 GCTTAATGGATGCTTGTTCATGGT 60.142 41.667 0.00 0.00 0.00 3.55
1192 4566 2.291209 TGGATGCTTGTTCATGGTGT 57.709 45.000 0.00 0.00 0.00 4.16
1193 4567 2.596346 TGGATGCTTGTTCATGGTGTT 58.404 42.857 0.00 0.00 0.00 3.32
1194 4568 2.964464 TGGATGCTTGTTCATGGTGTTT 59.036 40.909 0.00 0.00 0.00 2.83
1195 4569 3.005684 TGGATGCTTGTTCATGGTGTTTC 59.994 43.478 0.00 0.00 0.00 2.78
1196 4570 3.578688 GATGCTTGTTCATGGTGTTTCC 58.421 45.455 0.00 0.00 0.00 3.13
1360 4756 0.494095 AAGGTCCTCCTCCCTCTTGT 59.506 55.000 0.00 0.00 44.35 3.16
1441 4877 2.250939 CGTGGCGGTGACAACATGT 61.251 57.895 0.00 0.00 0.00 3.21
1539 5430 6.780706 TCCTACTCTGTTTTTCGATGAAAC 57.219 37.500 14.57 14.57 37.48 2.78
1555 5448 1.394917 GAAACTGTACCAGCTGCGATG 59.605 52.381 8.66 0.00 34.37 3.84
1575 5468 6.293618 CGATGAAGAACAAAATGTGCAAATG 58.706 36.000 0.00 0.00 0.00 2.32
1615 5514 6.971184 ACAGTATACAAACTAAACCGATCGAG 59.029 38.462 18.66 8.44 0.00 4.04
1643 5552 1.198759 AGGTTACATGCCTGGTCGGT 61.199 55.000 0.00 0.00 34.56 4.69
1993 5905 2.492090 CTCAAGAGCGACCTCGGG 59.508 66.667 0.00 0.00 43.05 5.14
2642 6878 1.198713 AGATCCTCATGCACGAAGGT 58.801 50.000 9.90 0.00 0.00 3.50
2803 7039 1.227999 GCAACAGCACAACGGAGCTA 61.228 55.000 0.00 0.00 39.02 3.32
2813 7049 0.250513 AACGGAGCTAAAGCCTCCAG 59.749 55.000 15.89 12.12 43.38 3.86
2855 7097 9.161629 TCGAGCATGAATTTTCTGAAGTAAATA 57.838 29.630 0.00 0.00 0.00 1.40
2897 7144 7.391148 TGCTATAGACACGCAGATATTATCA 57.609 36.000 3.21 0.00 0.00 2.15
2898 7145 7.826690 TGCTATAGACACGCAGATATTATCAA 58.173 34.615 3.21 0.00 0.00 2.57
2899 7146 8.470002 TGCTATAGACACGCAGATATTATCAAT 58.530 33.333 3.21 0.00 0.00 2.57
2900 7147 8.963130 GCTATAGACACGCAGATATTATCAATC 58.037 37.037 3.21 0.00 0.00 2.67
2939 7186 5.559770 TGTCCAAAATTGATGAGCTCTACA 58.440 37.500 16.19 11.92 0.00 2.74
2972 7219 5.636543 ACACGACTGTAGTAAATAAAGCACC 59.363 40.000 0.00 0.00 0.00 5.01
2976 7223 6.034161 ACTGTAGTAAATAAAGCACCGAGT 57.966 37.500 0.00 0.00 0.00 4.18
2987 7234 5.599999 AAAGCACCGAGTATATGAAGAGT 57.400 39.130 0.00 0.00 0.00 3.24
3032 7290 1.265095 CCATGTGCATGATAAGACGCC 59.735 52.381 13.21 0.00 41.20 5.68
3040 7298 1.179152 TGATAAGACGCCGAGTTGGA 58.821 50.000 0.00 0.00 42.00 3.53
3049 7307 1.797025 GCCGAGTTGGATATGGCTAC 58.203 55.000 0.00 0.00 42.44 3.58
3068 7326 6.071051 TGGCTACTCAAGTGACATAACATGTA 60.071 38.462 0.00 0.00 45.03 2.29
3069 7327 6.255887 GGCTACTCAAGTGACATAACATGTAC 59.744 42.308 0.00 0.00 45.03 2.90
3070 7328 7.036220 GCTACTCAAGTGACATAACATGTACT 58.964 38.462 0.00 0.00 45.03 2.73
3071 7329 7.221067 GCTACTCAAGTGACATAACATGTACTC 59.779 40.741 0.00 0.00 45.03 2.59
3072 7330 6.398918 ACTCAAGTGACATAACATGTACTCC 58.601 40.000 0.00 0.00 45.03 3.85
3073 7331 5.730550 TCAAGTGACATAACATGTACTCCC 58.269 41.667 0.00 0.00 45.03 4.30
3074 7332 5.483937 TCAAGTGACATAACATGTACTCCCT 59.516 40.000 0.00 0.00 45.03 4.20
3075 7333 5.599999 AGTGACATAACATGTACTCCCTC 57.400 43.478 0.00 0.00 45.03 4.30
3076 7334 4.406003 AGTGACATAACATGTACTCCCTCC 59.594 45.833 0.00 0.00 45.03 4.30
3077 7335 3.383505 TGACATAACATGTACTCCCTCCG 59.616 47.826 0.00 0.00 45.03 4.63
3078 7336 3.371965 ACATAACATGTACTCCCTCCGT 58.628 45.455 0.00 0.00 42.78 4.69
3079 7337 3.383825 ACATAACATGTACTCCCTCCGTC 59.616 47.826 0.00 0.00 42.78 4.79
3080 7338 1.192428 AACATGTACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
3081 7339 0.686769 ACATGTACTCCCTCCGTCCC 60.687 60.000 0.00 0.00 0.00 4.46
3082 7340 0.686441 CATGTACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
3083 7341 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
3084 7342 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
3085 7343 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3086 7344 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3087 7345 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3088 7346 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3089 7347 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
3090 7348 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
3091 7349 4.663592 ACTCCCTCCGTCCCAAAATATAAT 59.336 41.667 0.00 0.00 0.00 1.28
3092 7350 5.847817 ACTCCCTCCGTCCCAAAATATAATA 59.152 40.000 0.00 0.00 0.00 0.98
3093 7351 6.330778 ACTCCCTCCGTCCCAAAATATAATAA 59.669 38.462 0.00 0.00 0.00 1.40
3094 7352 6.536447 TCCCTCCGTCCCAAAATATAATAAC 58.464 40.000 0.00 0.00 0.00 1.89
3095 7353 5.410439 CCCTCCGTCCCAAAATATAATAACG 59.590 44.000 0.00 0.00 0.00 3.18
3096 7354 5.993441 CCTCCGTCCCAAAATATAATAACGT 59.007 40.000 0.00 0.00 0.00 3.99
3097 7355 6.484308 CCTCCGTCCCAAAATATAATAACGTT 59.516 38.462 5.88 5.88 0.00 3.99
3098 7356 7.012610 CCTCCGTCCCAAAATATAATAACGTTT 59.987 37.037 5.91 0.00 0.00 3.60
3099 7357 8.278729 TCCGTCCCAAAATATAATAACGTTTT 57.721 30.769 5.91 3.53 0.00 2.43
3100 7358 9.388506 TCCGTCCCAAAATATAATAACGTTTTA 57.611 29.630 5.91 5.78 0.00 1.52
3144 7402 8.970859 AAACATTCTAATATTCTGGACAGAGG 57.029 34.615 1.92 0.00 38.88 3.69
3145 7403 7.072263 ACATTCTAATATTCTGGACAGAGGG 57.928 40.000 1.92 0.00 38.88 4.30
3146 7404 6.846505 ACATTCTAATATTCTGGACAGAGGGA 59.153 38.462 1.92 0.00 38.88 4.20
3147 7405 6.985653 TTCTAATATTCTGGACAGAGGGAG 57.014 41.667 1.92 0.00 38.88 4.30
3148 7406 6.031964 TCTAATATTCTGGACAGAGGGAGT 57.968 41.667 1.92 0.00 38.88 3.85
3154 7412 2.920271 TCTGGACAGAGGGAGTAAGAGA 59.080 50.000 0.00 0.00 32.82 3.10
3161 7419 5.646215 ACAGAGGGAGTAAGAGAGAAGAAA 58.354 41.667 0.00 0.00 0.00 2.52
3199 7459 6.698008 ATTTTGCATGGATCTCGATGTAAA 57.302 33.333 12.10 12.10 41.74 2.01
3206 7466 6.370994 GCATGGATCTCGATGTAAAATCTCAT 59.629 38.462 0.00 0.00 35.00 2.90
3212 7472 9.814899 GATCTCGATGTAAAATCTCATGGATAT 57.185 33.333 0.00 0.00 33.71 1.63
3224 7484 9.887629 AAATCTCATGGATATAGCATTGACTAG 57.112 33.333 0.00 0.00 33.71 2.57
3232 7492 2.969628 AGCATTGACTAGGACTTCGG 57.030 50.000 0.00 0.00 0.00 4.30
3245 7505 2.005370 ACTTCGGTAAGTCCCAGTCA 57.995 50.000 0.00 0.00 42.42 3.41
3257 7517 4.181309 GTCCCAGTCAACTGAGACTTAG 57.819 50.000 15.21 0.00 46.26 2.18
3266 7526 4.342378 TCAACTGAGACTTAGCAAGACTGT 59.658 41.667 5.85 0.00 33.75 3.55
3268 7528 3.639094 ACTGAGACTTAGCAAGACTGTGT 59.361 43.478 5.85 0.00 33.75 3.72
3311 7571 6.035327 GCTCATGCATAATCTTGTTTTGGAAC 59.965 38.462 0.00 0.00 39.41 3.62
3328 7588 4.451900 TGGAACAAGAAACTTCAGTCTCC 58.548 43.478 0.00 0.00 31.92 3.71
3329 7589 4.080582 TGGAACAAGAAACTTCAGTCTCCA 60.081 41.667 10.87 10.87 31.92 3.86
3330 7590 5.066593 GGAACAAGAAACTTCAGTCTCCAT 58.933 41.667 0.00 0.00 0.00 3.41
3331 7591 5.049129 GGAACAAGAAACTTCAGTCTCCATG 60.049 44.000 0.00 0.00 0.00 3.66
3332 7592 5.041191 ACAAGAAACTTCAGTCTCCATGT 57.959 39.130 0.00 0.00 0.00 3.21
3333 7593 5.059833 ACAAGAAACTTCAGTCTCCATGTC 58.940 41.667 0.00 0.00 0.00 3.06
3334 7594 3.919216 AGAAACTTCAGTCTCCATGTCG 58.081 45.455 0.00 0.00 0.00 4.35
3335 7595 2.086054 AACTTCAGTCTCCATGTCGC 57.914 50.000 0.00 0.00 0.00 5.19
3336 7596 0.247736 ACTTCAGTCTCCATGTCGCC 59.752 55.000 0.00 0.00 0.00 5.54
3337 7597 0.460987 CTTCAGTCTCCATGTCGCCC 60.461 60.000 0.00 0.00 0.00 6.13
3338 7598 2.202797 CAGTCTCCATGTCGCCCG 60.203 66.667 0.00 0.00 0.00 6.13
3339 7599 2.362503 AGTCTCCATGTCGCCCGA 60.363 61.111 0.00 0.00 0.00 5.14
3340 7600 2.105128 GTCTCCATGTCGCCCGAG 59.895 66.667 0.00 0.00 0.00 4.63
3341 7601 3.147595 TCTCCATGTCGCCCGAGG 61.148 66.667 0.00 0.00 0.00 4.63
3342 7602 4.227134 CTCCATGTCGCCCGAGGG 62.227 72.222 3.22 3.22 38.57 4.30
3587 7847 0.103208 CTTTATCCTCTGCTCGCCGT 59.897 55.000 0.00 0.00 0.00 5.68
3631 7891 2.344950 CTGCTCAGTGGTGAATGAGTC 58.655 52.381 0.00 0.00 43.94 3.36
3633 7893 2.001812 CTCAGTGGTGAATGAGTCGG 57.998 55.000 0.00 0.00 38.49 4.79
3638 7898 1.450312 GGTGAATGAGTCGGCTGGG 60.450 63.158 0.00 0.00 0.00 4.45
3747 8007 4.856801 ATGGTGGCGGCGGCTAAG 62.857 66.667 33.21 0.00 39.81 2.18
3757 8017 2.588877 CGGCTAAGGATGGGCACG 60.589 66.667 0.00 0.00 32.43 5.34
3761 8021 1.972660 GCTAAGGATGGGCACGACCT 61.973 60.000 0.00 0.00 39.10 3.85
3801 8061 3.124921 CGGGTGGCGTGATCCAAC 61.125 66.667 0.00 0.00 43.08 3.77
3802 8062 2.033448 GGGTGGCGTGATCCAACA 59.967 61.111 0.00 0.00 45.60 3.33
3803 8063 1.378514 GGGTGGCGTGATCCAACAT 60.379 57.895 0.00 0.00 45.60 2.71
3804 8064 0.107410 GGGTGGCGTGATCCAACATA 60.107 55.000 0.00 0.00 45.60 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 38 1.506718 GACGAGGCAGACATCGACA 59.493 57.895 7.14 0.00 41.40 4.35
53 55 1.291033 AGAGGTACATAGCACAGGGGA 59.709 52.381 0.00 0.00 0.00 4.81
224 226 2.158798 CCTCTGGATGCTCACATGACAT 60.159 50.000 0.00 0.00 36.35 3.06
310 312 0.107703 CAGACGCCTTCCCATTAGCA 60.108 55.000 0.00 0.00 0.00 3.49
442 457 7.392953 TCACATGCTCCTAAAACATAACAATCA 59.607 33.333 0.00 0.00 0.00 2.57
450 465 3.009723 CCGTCACATGCTCCTAAAACAT 58.990 45.455 0.00 0.00 0.00 2.71
510 525 0.313987 CAAAGAACCCGAAACAGGCC 59.686 55.000 0.00 0.00 0.00 5.19
558 576 7.544804 AAGAAGAAGAAAATTGCCCAGTTAT 57.455 32.000 0.00 0.00 0.00 1.89
572 590 7.222224 GCCTCGTCGATTAATTAAGAAGAAGAA 59.778 37.037 3.94 0.00 0.00 2.52
645 663 1.067295 AGGAGAGGGTGACATTTGCA 58.933 50.000 0.00 0.00 0.00 4.08
659 677 4.910956 CGAATGTTCGCCAGGAGA 57.089 55.556 1.90 0.00 44.26 3.71
720 745 5.463154 TGGGAAAATATATCCAAGTTGGGG 58.537 41.667 21.85 0.00 38.32 4.96
734 759 4.533707 TGGCACAAATTCCATGGGAAAATA 59.466 37.500 13.02 0.00 39.85 1.40
735 760 3.330110 TGGCACAAATTCCATGGGAAAAT 59.670 39.130 13.02 1.10 39.85 1.82
995 4363 4.207281 CGCTCTTCCCCATCGCGA 62.207 66.667 13.09 13.09 45.99 5.87
1097 4468 4.021192 TGAATCAAAAGGAAACCATGAGCC 60.021 41.667 0.00 0.00 0.00 4.70
1128 4499 5.808030 TCGGAAAAACAAACTAAGCCAAAAG 59.192 36.000 0.00 0.00 0.00 2.27
1134 4505 4.514066 TCTCCTCGGAAAAACAAACTAAGC 59.486 41.667 0.00 0.00 0.00 3.09
1179 4553 6.824305 AGATTAGGAAACACCATGAACAAG 57.176 37.500 0.00 0.00 42.04 3.16
1190 4564 3.826157 CCCTGCAACAAGATTAGGAAACA 59.174 43.478 0.00 0.00 0.00 2.83
1192 4566 3.181423 ACCCCTGCAACAAGATTAGGAAA 60.181 43.478 0.00 0.00 0.00 3.13
1193 4567 2.378547 ACCCCTGCAACAAGATTAGGAA 59.621 45.455 0.00 0.00 0.00 3.36
1194 4568 1.992557 ACCCCTGCAACAAGATTAGGA 59.007 47.619 0.00 0.00 0.00 2.94
1195 4569 2.514458 ACCCCTGCAACAAGATTAGG 57.486 50.000 0.00 0.00 0.00 2.69
1196 4570 3.420893 TGAACCCCTGCAACAAGATTAG 58.579 45.455 0.00 0.00 0.00 1.73
1360 4756 6.220201 TGTTGAGACACGAATGATTTAGTGA 58.780 36.000 17.34 0.00 39.88 3.41
1495 5114 4.021981 GGAAAATGCTTTTGGTAGCTGTCT 60.022 41.667 0.00 0.00 41.76 3.41
1555 5448 4.208873 TCGCATTTGCACATTTTGTTCTTC 59.791 37.500 3.13 0.00 42.21 2.87
1575 5468 6.596703 TGTATACTGTATACTTCGTGATCGC 58.403 40.000 28.56 0.00 41.21 4.58
1615 5514 1.937546 GCATGTAACCTGCACCCAGC 61.938 60.000 0.00 0.00 45.96 4.85
1643 5552 0.790495 GACGCGTCGATGTCGTACAA 60.790 55.000 25.19 0.00 40.80 2.41
2803 7039 1.078143 GTGGATCGCTGGAGGCTTT 60.078 57.895 0.00 0.00 39.13 3.51
2896 7143 7.200455 TGGACAGACGTATACATAGTTGATTG 58.800 38.462 3.32 0.00 0.00 2.67
2897 7144 7.342769 TGGACAGACGTATACATAGTTGATT 57.657 36.000 3.32 0.00 0.00 2.57
2898 7145 6.954487 TGGACAGACGTATACATAGTTGAT 57.046 37.500 3.32 0.00 0.00 2.57
2899 7146 6.762702 TTGGACAGACGTATACATAGTTGA 57.237 37.500 3.32 0.00 0.00 3.18
2900 7147 7.821595 TTTTGGACAGACGTATACATAGTTG 57.178 36.000 3.32 0.00 0.00 3.16
2918 7165 7.707624 ATTTGTAGAGCTCATCAATTTTGGA 57.292 32.000 17.77 5.06 0.00 3.53
2939 7186 3.728845 ACTACAGTCGTGTGAGCAATTT 58.271 40.909 0.00 0.00 37.52 1.82
2972 7219 8.731605 TGCCTCTTATAACTCTTCATATACTCG 58.268 37.037 0.00 0.00 0.00 4.18
3032 7290 4.202161 ACTTGAGTAGCCATATCCAACTCG 60.202 45.833 0.00 0.00 39.52 4.18
3040 7298 7.124573 TGTTATGTCACTTGAGTAGCCATAT 57.875 36.000 0.00 0.00 0.00 1.78
3049 7307 5.812642 GGGAGTACATGTTATGTCACTTGAG 59.187 44.000 2.30 0.00 43.67 3.02
3067 7325 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3068 7326 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3069 7327 4.699925 TTATATTTTGGGACGGAGGGAG 57.300 45.455 0.00 0.00 0.00 4.30
3070 7328 6.536447 GTTATTATATTTTGGGACGGAGGGA 58.464 40.000 0.00 0.00 0.00 4.20
3071 7329 5.410439 CGTTATTATATTTTGGGACGGAGGG 59.590 44.000 0.00 0.00 0.00 4.30
3072 7330 5.993441 ACGTTATTATATTTTGGGACGGAGG 59.007 40.000 0.00 0.00 33.95 4.30
3073 7331 7.486802 AACGTTATTATATTTTGGGACGGAG 57.513 36.000 0.00 0.00 33.95 4.63
3074 7332 7.862512 AAACGTTATTATATTTTGGGACGGA 57.137 32.000 0.00 0.00 33.95 4.69
3092 7350 8.991243 TGATACTATGCTAGTGTTAAAACGTT 57.009 30.769 0.00 0.00 39.81 3.99
3093 7351 8.991243 TTGATACTATGCTAGTGTTAAAACGT 57.009 30.769 6.21 0.00 39.81 3.99
3101 7359 9.672673 AGAATGTTTTTGATACTATGCTAGTGT 57.327 29.630 6.21 0.61 39.81 3.55
3118 7376 9.401058 CCTCTGTCCAGAATATTAGAATGTTTT 57.599 33.333 0.00 0.00 36.94 2.43
3119 7377 7.995488 CCCTCTGTCCAGAATATTAGAATGTTT 59.005 37.037 0.00 0.00 36.94 2.83
3120 7378 7.348274 TCCCTCTGTCCAGAATATTAGAATGTT 59.652 37.037 0.00 0.00 36.94 2.71
3121 7379 6.846505 TCCCTCTGTCCAGAATATTAGAATGT 59.153 38.462 0.00 0.00 36.94 2.71
3122 7380 7.016072 ACTCCCTCTGTCCAGAATATTAGAATG 59.984 40.741 0.00 0.00 36.94 2.67
3123 7381 7.079048 ACTCCCTCTGTCCAGAATATTAGAAT 58.921 38.462 0.00 0.00 36.94 2.40
3124 7382 6.444704 ACTCCCTCTGTCCAGAATATTAGAA 58.555 40.000 0.00 0.00 36.94 2.10
3125 7383 6.031964 ACTCCCTCTGTCCAGAATATTAGA 57.968 41.667 0.00 0.00 36.94 2.10
3126 7384 7.726291 TCTTACTCCCTCTGTCCAGAATATTAG 59.274 40.741 0.00 0.00 36.94 1.73
3127 7385 7.592736 TCTTACTCCCTCTGTCCAGAATATTA 58.407 38.462 0.00 0.00 36.94 0.98
3128 7386 6.444704 TCTTACTCCCTCTGTCCAGAATATT 58.555 40.000 0.00 0.00 36.94 1.28
3129 7387 6.031964 TCTTACTCCCTCTGTCCAGAATAT 57.968 41.667 0.00 0.00 36.94 1.28
3130 7388 5.193930 TCTCTTACTCCCTCTGTCCAGAATA 59.806 44.000 0.00 0.00 36.94 1.75
3131 7389 4.017037 TCTCTTACTCCCTCTGTCCAGAAT 60.017 45.833 0.00 0.00 36.94 2.40
3132 7390 3.333980 TCTCTTACTCCCTCTGTCCAGAA 59.666 47.826 0.00 0.00 36.94 3.02
3133 7391 2.920271 TCTCTTACTCCCTCTGTCCAGA 59.080 50.000 0.00 0.00 35.85 3.86
3134 7392 3.053991 TCTCTCTTACTCCCTCTGTCCAG 60.054 52.174 0.00 0.00 0.00 3.86
3135 7393 2.920271 TCTCTCTTACTCCCTCTGTCCA 59.080 50.000 0.00 0.00 0.00 4.02
3136 7394 3.655615 TCTCTCTTACTCCCTCTGTCC 57.344 52.381 0.00 0.00 0.00 4.02
3137 7395 4.850680 TCTTCTCTCTTACTCCCTCTGTC 58.149 47.826 0.00 0.00 0.00 3.51
3138 7396 4.938575 TCTTCTCTCTTACTCCCTCTGT 57.061 45.455 0.00 0.00 0.00 3.41
3139 7397 6.597832 TTTTCTTCTCTCTTACTCCCTCTG 57.402 41.667 0.00 0.00 0.00 3.35
3170 7430 8.199449 ACATCGAGATCCATGCAAAATTTTATT 58.801 29.630 2.44 0.00 0.00 1.40
3172 7432 7.099266 ACATCGAGATCCATGCAAAATTTTA 57.901 32.000 2.44 0.00 0.00 1.52
3199 7459 8.484575 CCTAGTCAATGCTATATCCATGAGATT 58.515 37.037 0.00 0.00 36.33 2.40
3206 7466 6.071896 CGAAGTCCTAGTCAATGCTATATCCA 60.072 42.308 0.00 0.00 0.00 3.41
3212 7472 3.362706 ACCGAAGTCCTAGTCAATGCTA 58.637 45.455 0.00 0.00 0.00 3.49
3245 7505 4.100189 ACACAGTCTTGCTAAGTCTCAGTT 59.900 41.667 0.00 0.00 0.00 3.16
3257 7517 4.752101 ACAGATAACTCAACACAGTCTTGC 59.248 41.667 0.00 0.00 0.00 4.01
3266 7526 4.910195 AGCATCCAACAGATAACTCAACA 58.090 39.130 0.00 0.00 32.37 3.33
3268 7528 5.164620 TGAGCATCCAACAGATAACTCAA 57.835 39.130 5.55 0.00 41.19 3.02
3311 7571 4.151335 CGACATGGAGACTGAAGTTTCTTG 59.849 45.833 0.00 3.11 30.73 3.02
3317 7577 0.247736 GGCGACATGGAGACTGAAGT 59.752 55.000 0.00 0.00 0.00 3.01
3320 7580 2.710902 CGGGCGACATGGAGACTGA 61.711 63.158 0.00 0.00 0.00 3.41
3324 7584 3.147595 CCTCGGGCGACATGGAGA 61.148 66.667 4.93 0.00 0.00 3.71
3325 7585 4.227134 CCCTCGGGCGACATGGAG 62.227 72.222 0.00 0.00 0.00 3.86
3549 7809 3.215587 AAGGGAGGTTGCCTGGCAG 62.216 63.158 22.17 7.75 37.13 4.85
3550 7810 3.185203 AAGGGAGGTTGCCTGGCA 61.185 61.111 19.30 19.30 37.13 4.92
3551 7811 2.361737 GAAGGGAGGTTGCCTGGC 60.362 66.667 12.87 12.87 37.13 4.85
3552 7812 0.113190 AAAGAAGGGAGGTTGCCTGG 59.887 55.000 0.00 0.00 37.13 4.45
3553 7813 2.879103 TAAAGAAGGGAGGTTGCCTG 57.121 50.000 0.00 0.00 37.13 4.85
3554 7814 2.242452 GGATAAAGAAGGGAGGTTGCCT 59.758 50.000 0.00 0.00 41.29 4.75
3555 7815 2.242452 AGGATAAAGAAGGGAGGTTGCC 59.758 50.000 0.00 0.00 0.00 4.52
3587 7847 3.249189 AAGAGGTCCTGGCGGCAA 61.249 61.111 14.48 0.00 0.00 4.52
3648 7908 3.058160 GCCTGCCATCACGCTGTT 61.058 61.111 0.00 0.00 0.00 3.16
3706 7966 1.709147 AAGATCCAGCGTTGCGATGC 61.709 55.000 10.40 10.40 42.12 3.91
3712 7972 1.033746 ATGGGCAAGATCCAGCGTTG 61.034 55.000 0.00 0.00 37.75 4.10
3714 7974 1.452651 CATGGGCAAGATCCAGCGT 60.453 57.895 1.41 0.00 37.75 5.07
3742 8002 1.523938 GGTCGTGCCCATCCTTAGC 60.524 63.158 0.00 0.00 0.00 3.09
3746 8006 3.402681 CCAGGTCGTGCCCATCCT 61.403 66.667 0.00 0.00 38.26 3.24
3747 8007 2.666596 GATCCAGGTCGTGCCCATCC 62.667 65.000 0.00 0.00 38.26 3.51
3757 8017 1.142748 CAGACGCCAGATCCAGGTC 59.857 63.158 3.95 0.61 0.00 3.85
3761 8021 2.293318 AAGCCAGACGCCAGATCCA 61.293 57.895 0.00 0.00 38.78 3.41
3785 8045 0.107410 TATGTTGGATCACGCCACCC 60.107 55.000 0.00 0.00 37.75 4.61


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

AutoCloner maintained by Alex Coulton.