Multiple sequence alignment - TraesCS3A01G500100

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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 TraesCS3A01G500100 chr3A 100.000 3551 0 0 1 3551 724696140 724699690 0.000000e+00 6558.0
1 TraesCS3A01G500100 chr3A 85.053 2636 306 39 2 2556 724559766 724562394 0.000000e+00 2604.0
2 TraesCS3A01G500100 chr3A 82.788 947 132 15 1630 2556 724542974 724543909 0.000000e+00 817.0
3 TraesCS3A01G500100 chr3A 76.190 1323 238 36 4 1271 724541398 724542698 8.370000e-176 627.0
4 TraesCS3A01G500100 chr3D 94.899 2568 126 2 2 2567 593706463 593709027 0.000000e+00 4012.0
5 TraesCS3A01G500100 chr3D 94.684 696 27 2 2662 3357 593709390 593710075 0.000000e+00 1072.0
6 TraesCS3A01G500100 chr3D 81.833 1233 196 20 1355 2567 593654814 593653590 0.000000e+00 1011.0
7 TraesCS3A01G500100 chr3D 80.885 1266 191 30 1324 2550 593689299 593690552 0.000000e+00 950.0
8 TraesCS3A01G500100 chr3D 77.519 1330 219 42 4 1280 593687995 593689297 0.000000e+00 726.0
9 TraesCS3A01G500100 chr3D 95.238 84 4 0 2580 2663 593709080 593709163 2.220000e-27 134.0
10 TraesCS3A01G500100 chr3D 96.970 66 2 0 1 66 593683834 593683899 1.040000e-20 111.0
11 TraesCS3A01G500100 chrUn 92.766 2585 165 9 1 2567 41910552 41907972 0.000000e+00 3718.0
12 TraesCS3A01G500100 chrUn 82.157 1233 192 16 1355 2567 41926539 41927763 0.000000e+00 1033.0
13 TraesCS3A01G500100 chrUn 77.091 1279 211 39 4 1224 41925196 41926450 0.000000e+00 664.0
14 TraesCS3A01G500100 chrUn 92.457 464 26 6 3059 3521 41900177 41899722 0.000000e+00 654.0
15 TraesCS3A01G500100 chrUn 94.704 321 14 2 2750 3069 41907422 41907104 2.460000e-136 496.0
16 TraesCS3A01G500100 chrUn 93.182 88 6 0 2665 2752 41907592 41907505 2.880000e-26 130.0
17 TraesCS3A01G500100 chrUn 91.667 84 6 1 2580 2663 41907916 41907834 8.060000e-22 115.0
18 TraesCS3A01G500100 chr7B 74.368 1147 226 40 1460 2552 518676753 518675621 9.110000e-116 427.0
19 TraesCS3A01G500100 chr4B 85.366 82 12 0 3371 3452 13988091 13988172 6.320000e-13 86.1
20 TraesCS3A01G500100 chr4B 85.366 82 8 2 3371 3452 29333068 29332991 8.170000e-12 82.4
21 TraesCS3A01G500100 chr1B 84.507 71 9 2 3370 3439 677026445 677026376 6.360000e-08 69.4
22 TraesCS3A01G500100 chr5D 93.182 44 3 0 3409 3452 218641679 218641636 8.230000e-07 65.8
23 TraesCS3A01G500100 chr2D 95.000 40 2 0 3413 3452 119845018 119845057 2.960000e-06 63.9


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 TraesCS3A01G500100 chr3A 724696140 724699690 3550 False 6558.000000 6558 100.000000 1 3551 1 chr3A.!!$F2 3550
1 TraesCS3A01G500100 chr3A 724559766 724562394 2628 False 2604.000000 2604 85.053000 2 2556 1 chr3A.!!$F1 2554
2 TraesCS3A01G500100 chr3A 724541398 724543909 2511 False 722.000000 817 79.489000 4 2556 2 chr3A.!!$F3 2552
3 TraesCS3A01G500100 chr3D 593706463 593710075 3612 False 1739.333333 4012 94.940333 2 3357 3 chr3D.!!$F3 3355
4 TraesCS3A01G500100 chr3D 593653590 593654814 1224 True 1011.000000 1011 81.833000 1355 2567 1 chr3D.!!$R1 1212
5 TraesCS3A01G500100 chr3D 593687995 593690552 2557 False 838.000000 950 79.202000 4 2550 2 chr3D.!!$F2 2546
6 TraesCS3A01G500100 chrUn 41907104 41910552 3448 True 1114.750000 3718 93.079750 1 3069 4 chrUn.!!$R2 3068
7 TraesCS3A01G500100 chrUn 41925196 41927763 2567 False 848.500000 1033 79.624000 4 2567 2 chrUn.!!$F1 2563
8 TraesCS3A01G500100 chr7B 518675621 518676753 1132 True 427.000000 427 74.368000 1460 2552 1 chr7B.!!$R1 1092


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
130 136 0.108945 GTCGACGACCCCTACAAAGG 60.109 60.0 17.25 0.0 43.25 3.11 F
921 981 0.602372 GATCGGGATGAGCTTCTGGC 60.602 60.0 0.00 0.0 42.19 4.85 F
1393 1509 0.039978 CATACGCTACTCCGCTCCAG 60.040 60.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1509 1.021390 CGCACCCTGATCTTGTCACC 61.021 60.000 0.00 0.00 32.22 4.02 R
2324 2571 1.000955 GGGCCCTGACTACATCATACG 59.999 57.143 17.04 0.00 36.48 3.06 R
3360 3980 0.108329 GAGTTGCCCTTGTAGCGCTA 60.108 55.000 14.45 14.45 0.00 4.26 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
112 115 4.653888 CGGCCTGTTTTCCCCCGT 62.654 66.667 0.00 0.00 34.56 5.28
130 136 0.108945 GTCGACGACCCCTACAAAGG 60.109 60.000 17.25 0.00 43.25 3.11
379 400 0.721718 GTCAAGCAGTACCATGACGC 59.278 55.000 0.00 0.00 33.62 5.19
513 534 1.874562 CGACCACTACAAGTACGACG 58.125 55.000 0.00 0.00 0.00 5.12
514 535 1.460743 CGACCACTACAAGTACGACGA 59.539 52.381 0.00 0.00 0.00 4.20
515 536 2.723010 CGACCACTACAAGTACGACGAC 60.723 54.545 0.00 0.00 0.00 4.34
520 541 1.061711 CTACAAGTACGACGACTCCGG 59.938 57.143 0.00 0.00 40.78 5.14
861 909 3.883744 CTCAGAGCGTGCCGGGTTT 62.884 63.158 2.18 0.00 0.00 3.27
921 981 0.602372 GATCGGGATGAGCTTCTGGC 60.602 60.000 0.00 0.00 42.19 4.85
948 1008 0.762418 AGTGTGGACGATGTGGGAAA 59.238 50.000 0.00 0.00 0.00 3.13
949 1009 1.142060 AGTGTGGACGATGTGGGAAAA 59.858 47.619 0.00 0.00 0.00 2.29
991 1059 1.295423 GGAACTAGCCAAGCCGACA 59.705 57.895 0.00 0.00 0.00 4.35
1068 1166 3.317149 TGAAGTACAGCTACAACGACACT 59.683 43.478 0.00 0.00 0.00 3.55
1110 1208 4.232188 ACATCACCAGAAGATCAGCAAT 57.768 40.909 0.00 0.00 0.00 3.56
1185 1286 3.184581 GTGACGCTGAGTTTAGTTTCCAG 59.815 47.826 0.00 0.00 0.00 3.86
1203 1307 2.423446 GCGCTAGACATCAGGGGG 59.577 66.667 0.00 0.00 0.00 5.40
1224 1328 1.004745 CAGGCCTACCCAGTCACAATT 59.995 52.381 3.98 0.00 36.11 2.32
1292 1396 4.636435 CCGGCGTTGGGTGGTCTT 62.636 66.667 6.01 0.00 0.00 3.01
1393 1509 0.039978 CATACGCTACTCCGCTCCAG 60.040 60.000 0.00 0.00 0.00 3.86
1853 2037 3.770040 CGCCGTCCTCACCATGGA 61.770 66.667 21.47 0.00 0.00 3.41
1915 2099 1.268283 AAGCAGGAGGAGCCAGTACC 61.268 60.000 0.00 0.00 40.02 3.34
2324 2571 1.783031 CTCCGCTTGATGCCTCATGC 61.783 60.000 16.63 16.63 44.80 4.06
2441 2688 1.339644 ATGGTTATACCGTGCGGGGT 61.340 55.000 15.44 3.80 42.58 4.95
2514 2764 0.739112 CACTTCCTTCGCAGAGGAGC 60.739 60.000 5.32 0.00 38.43 4.70
2530 2780 3.088532 AGGAGCAGATCGAGTGGATATC 58.911 50.000 0.00 0.00 34.82 1.63
2538 2788 4.462132 AGATCGAGTGGATATCAGATGGTG 59.538 45.833 4.83 0.00 34.82 4.17
2608 2901 9.515226 TGTACCTTACTAGCATTTCTTTTTCAT 57.485 29.630 0.00 0.00 0.00 2.57
2642 2935 7.380536 TCTGGTTACGTTTGTATACTTCACAT 58.619 34.615 4.17 0.00 0.00 3.21
2663 2956 7.011773 CACATCTTCTATGTCAGTGAAAAACG 58.988 38.462 0.00 0.00 0.00 3.60
2687 3221 5.491982 GAGGAATTCCAAGACAGTGTATGT 58.508 41.667 26.22 0.00 41.51 2.29
2738 3272 7.578310 AATACAGTAGCAAAGCATTGATGAT 57.422 32.000 5.73 0.00 38.94 2.45
2743 3277 7.972277 ACAGTAGCAAAGCATTGATGATTAAAG 59.028 33.333 5.73 0.00 38.94 1.85
2808 3427 4.328983 CACAAATCCACAGTACGTCCATAC 59.671 45.833 0.00 0.00 0.00 2.39
2809 3428 4.020928 ACAAATCCACAGTACGTCCATACA 60.021 41.667 0.00 0.00 0.00 2.29
2819 3438 7.972277 CACAGTACGTCCATACAAAACTACTAT 59.028 37.037 0.00 0.00 0.00 2.12
2823 3442 6.032094 ACGTCCATACAAAACTACTATGACG 58.968 40.000 0.00 0.00 33.05 4.35
2932 3551 7.620880 TGATTATATACTTGGCCTCCACATAC 58.379 38.462 3.32 0.00 30.78 2.39
2957 3576 2.501881 CTGCAACCGTAAATACAACGC 58.498 47.619 0.00 0.00 39.00 4.84
3035 3654 0.722799 GCAAGCAAACGAAGAGCGAC 60.723 55.000 0.00 0.00 44.57 5.19
3079 3699 7.735917 TCTCTTTTACAGGTTGATGAGAGAAA 58.264 34.615 0.00 0.00 36.43 2.52
3156 3776 1.005097 TGTGGAGGATTCTGCAATGCT 59.995 47.619 6.82 0.00 42.92 3.79
3162 3782 2.948840 GATTCTGCAATGCTGGCGGC 62.949 60.000 12.43 12.43 37.56 6.53
3214 3834 5.030874 AGATGCTTTGCGTTAGTTACAAC 57.969 39.130 0.00 0.00 0.00 3.32
3254 3874 8.165239 AGATTTGTGTTTATTACAAGCAGTGA 57.835 30.769 0.00 0.00 39.03 3.41
3255 3875 8.292448 AGATTTGTGTTTATTACAAGCAGTGAG 58.708 33.333 0.00 0.00 39.03 3.51
3256 3876 5.356882 TGTGTTTATTACAAGCAGTGAGC 57.643 39.130 0.00 0.00 46.19 4.26
3326 3946 4.531332 GTGACAGCACAAAGAATCTTGAC 58.469 43.478 0.00 0.00 44.51 3.18
3366 3986 9.855021 ATTAAAAATTTACAATCAGTTAGCGCT 57.145 25.926 17.26 17.26 0.00 5.92
3368 3988 8.669394 AAAAATTTACAATCAGTTAGCGCTAC 57.331 30.769 18.63 12.48 0.00 3.58
3369 3989 6.978343 AATTTACAATCAGTTAGCGCTACA 57.022 33.333 18.63 5.91 0.00 2.74
3370 3990 6.978343 ATTTACAATCAGTTAGCGCTACAA 57.022 33.333 18.63 1.65 0.00 2.41
3371 3991 6.403333 TTTACAATCAGTTAGCGCTACAAG 57.597 37.500 18.63 9.69 0.00 3.16
3372 3992 3.262420 ACAATCAGTTAGCGCTACAAGG 58.738 45.455 18.63 7.42 0.00 3.61
3373 3993 2.604046 ATCAGTTAGCGCTACAAGGG 57.396 50.000 18.63 5.55 0.00 3.95
3382 4002 2.380084 CGCTACAAGGGCAACTCTAA 57.620 50.000 0.00 0.00 0.00 2.10
3383 4003 2.000447 CGCTACAAGGGCAACTCTAAC 59.000 52.381 0.00 0.00 0.00 2.34
3384 4004 2.357075 GCTACAAGGGCAACTCTAACC 58.643 52.381 0.00 0.00 0.00 2.85
3385 4005 2.618053 CTACAAGGGCAACTCTAACCG 58.382 52.381 0.00 0.00 0.00 4.44
3386 4006 1.053424 ACAAGGGCAACTCTAACCGA 58.947 50.000 0.00 0.00 0.00 4.69
3387 4007 1.628846 ACAAGGGCAACTCTAACCGAT 59.371 47.619 0.00 0.00 0.00 4.18
3388 4008 2.039879 ACAAGGGCAACTCTAACCGATT 59.960 45.455 0.00 0.00 0.00 3.34
3389 4009 3.081804 CAAGGGCAACTCTAACCGATTT 58.918 45.455 0.00 0.00 0.00 2.17
3390 4010 2.987232 AGGGCAACTCTAACCGATTTC 58.013 47.619 0.00 0.00 0.00 2.17
3391 4011 2.014857 GGGCAACTCTAACCGATTTCC 58.985 52.381 0.00 0.00 0.00 3.13
3392 4012 2.355818 GGGCAACTCTAACCGATTTCCT 60.356 50.000 0.00 0.00 0.00 3.36
3393 4013 3.118519 GGGCAACTCTAACCGATTTCCTA 60.119 47.826 0.00 0.00 0.00 2.94
3394 4014 4.510571 GGCAACTCTAACCGATTTCCTAA 58.489 43.478 0.00 0.00 0.00 2.69
3395 4015 4.939439 GGCAACTCTAACCGATTTCCTAAA 59.061 41.667 0.00 0.00 0.00 1.85
3396 4016 5.413523 GGCAACTCTAACCGATTTCCTAAAA 59.586 40.000 0.00 0.00 0.00 1.52
3397 4017 6.403309 GGCAACTCTAACCGATTTCCTAAAAG 60.403 42.308 0.00 0.00 0.00 2.27
3398 4018 6.148976 GCAACTCTAACCGATTTCCTAAAAGT 59.851 38.462 0.00 0.00 0.00 2.66
3399 4019 7.308408 GCAACTCTAACCGATTTCCTAAAAGTT 60.308 37.037 0.00 0.00 0.00 2.66
3400 4020 9.211485 CAACTCTAACCGATTTCCTAAAAGTTA 57.789 33.333 0.00 0.00 0.00 2.24
3401 4021 9.783081 AACTCTAACCGATTTCCTAAAAGTTAA 57.217 29.630 0.00 0.00 0.00 2.01
3402 4022 9.783081 ACTCTAACCGATTTCCTAAAAGTTAAA 57.217 29.630 0.00 0.00 0.00 1.52
3407 4027 8.107399 ACCGATTTCCTAAAAGTTAAAGAAGG 57.893 34.615 0.00 0.00 0.00 3.46
3408 4028 7.940688 ACCGATTTCCTAAAAGTTAAAGAAGGA 59.059 33.333 0.00 0.00 0.00 3.36
3409 4029 8.957466 CCGATTTCCTAAAAGTTAAAGAAGGAT 58.043 33.333 0.00 0.00 33.33 3.24
3410 4030 9.989869 CGATTTCCTAAAAGTTAAAGAAGGATC 57.010 33.333 0.00 0.00 33.33 3.36
3412 4032 7.916914 TTCCTAAAAGTTAAAGAAGGATCCG 57.083 36.000 5.98 0.00 33.33 4.18
3413 4033 6.412214 TCCTAAAAGTTAAAGAAGGATCCGG 58.588 40.000 5.98 0.00 0.00 5.14
3414 4034 5.066117 CCTAAAAGTTAAAGAAGGATCCGGC 59.934 44.000 5.98 2.12 0.00 6.13
3415 4035 2.711978 AGTTAAAGAAGGATCCGGCC 57.288 50.000 5.98 0.00 0.00 6.13
3416 4036 1.134491 AGTTAAAGAAGGATCCGGCCG 60.134 52.381 21.04 21.04 0.00 6.13
3417 4037 1.134610 GTTAAAGAAGGATCCGGCCGA 60.135 52.381 30.73 13.82 0.00 5.54
3418 4038 0.750850 TAAAGAAGGATCCGGCCGAG 59.249 55.000 30.73 17.53 0.00 4.63
3419 4039 1.265454 AAAGAAGGATCCGGCCGAGT 61.265 55.000 30.73 15.27 0.00 4.18
3420 4040 0.396695 AAGAAGGATCCGGCCGAGTA 60.397 55.000 30.73 12.51 0.00 2.59
3421 4041 0.396695 AGAAGGATCCGGCCGAGTAA 60.397 55.000 30.73 9.56 0.00 2.24
3422 4042 0.462789 GAAGGATCCGGCCGAGTAAA 59.537 55.000 30.73 6.66 0.00 2.01
3423 4043 0.464452 AAGGATCCGGCCGAGTAAAG 59.536 55.000 30.73 8.93 0.00 1.85
3424 4044 0.686769 AGGATCCGGCCGAGTAAAGT 60.687 55.000 30.73 3.41 0.00 2.66
3425 4045 0.177373 GGATCCGGCCGAGTAAAGTT 59.823 55.000 30.73 2.96 0.00 2.66
3426 4046 1.410153 GGATCCGGCCGAGTAAAGTTA 59.590 52.381 30.73 0.00 0.00 2.24
3427 4047 2.545322 GGATCCGGCCGAGTAAAGTTAG 60.545 54.545 30.73 5.39 0.00 2.34
3428 4048 1.549203 TCCGGCCGAGTAAAGTTAGT 58.451 50.000 30.73 0.00 0.00 2.24
3429 4049 1.203052 TCCGGCCGAGTAAAGTTAGTG 59.797 52.381 30.73 4.53 0.00 2.74
3430 4050 1.636988 CGGCCGAGTAAAGTTAGTGG 58.363 55.000 24.07 0.00 0.00 4.00
3431 4051 1.203052 CGGCCGAGTAAAGTTAGTGGA 59.797 52.381 24.07 0.00 0.00 4.02
3432 4052 2.734492 CGGCCGAGTAAAGTTAGTGGAG 60.734 54.545 24.07 0.00 0.00 3.86
3433 4053 2.233186 GGCCGAGTAAAGTTAGTGGAGT 59.767 50.000 0.00 0.00 0.00 3.85
3434 4054 3.445096 GGCCGAGTAAAGTTAGTGGAGTA 59.555 47.826 0.00 0.00 0.00 2.59
3435 4055 4.082026 GGCCGAGTAAAGTTAGTGGAGTAA 60.082 45.833 0.00 0.00 0.00 2.24
3436 4056 5.473039 GCCGAGTAAAGTTAGTGGAGTAAA 58.527 41.667 0.00 0.00 0.00 2.01
3437 4057 6.104665 GCCGAGTAAAGTTAGTGGAGTAAAT 58.895 40.000 0.00 0.00 0.00 1.40
3438 4058 6.592994 GCCGAGTAAAGTTAGTGGAGTAAATT 59.407 38.462 0.00 0.00 0.00 1.82
3439 4059 7.118825 GCCGAGTAAAGTTAGTGGAGTAAATTT 59.881 37.037 0.00 0.00 35.16 1.82
3440 4060 8.996271 CCGAGTAAAGTTAGTGGAGTAAATTTT 58.004 33.333 0.00 0.00 33.50 1.82
3446 4066 7.997773 AGTTAGTGGAGTAAATTTTTCCTCC 57.002 36.000 17.77 17.77 43.13 4.30
3447 4067 7.756614 AGTTAGTGGAGTAAATTTTTCCTCCT 58.243 34.615 21.91 17.47 43.21 3.69
3448 4068 7.883833 AGTTAGTGGAGTAAATTTTTCCTCCTC 59.116 37.037 21.91 19.50 43.21 3.71
3449 4069 6.455690 AGTGGAGTAAATTTTTCCTCCTCT 57.544 37.500 21.91 20.72 43.21 3.69
3450 4070 7.569599 AGTGGAGTAAATTTTTCCTCCTCTA 57.430 36.000 21.76 8.60 42.87 2.43
3451 4071 8.164057 AGTGGAGTAAATTTTTCCTCCTCTAT 57.836 34.615 21.76 9.52 42.87 1.98
3452 4072 8.615705 AGTGGAGTAAATTTTTCCTCCTCTATT 58.384 33.333 21.76 9.08 42.87 1.73
3453 4073 9.901172 GTGGAGTAAATTTTTCCTCCTCTATTA 57.099 33.333 21.91 7.30 43.21 0.98
3459 4079 8.950007 AAATTTTTCCTCCTCTATTAACCACA 57.050 30.769 0.00 0.00 0.00 4.17
3460 4080 8.950007 AATTTTTCCTCCTCTATTAACCACAA 57.050 30.769 0.00 0.00 0.00 3.33
3461 4081 8.950007 ATTTTTCCTCCTCTATTAACCACAAA 57.050 30.769 0.00 0.00 0.00 2.83
3462 4082 8.770010 TTTTTCCTCCTCTATTAACCACAAAA 57.230 30.769 0.00 0.00 0.00 2.44
3463 4083 7.996098 TTTCCTCCTCTATTAACCACAAAAG 57.004 36.000 0.00 0.00 0.00 2.27
3464 4084 6.062258 TCCTCCTCTATTAACCACAAAAGG 57.938 41.667 0.00 0.00 0.00 3.11
3465 4085 5.788533 TCCTCCTCTATTAACCACAAAAGGA 59.211 40.000 0.00 0.00 0.00 3.36
3466 4086 6.070194 TCCTCCTCTATTAACCACAAAAGGAG 60.070 42.308 7.89 7.89 45.34 3.69
3467 4087 6.062258 TCCTCTATTAACCACAAAAGGAGG 57.938 41.667 0.00 0.00 39.12 4.30
3468 4088 5.788533 TCCTCTATTAACCACAAAAGGAGGA 59.211 40.000 0.00 0.00 42.73 3.71
3469 4089 6.447084 TCCTCTATTAACCACAAAAGGAGGAT 59.553 38.462 0.00 0.00 40.93 3.24
3470 4090 6.768381 CCTCTATTAACCACAAAAGGAGGATC 59.232 42.308 0.00 0.00 39.87 3.36
3471 4091 7.265599 TCTATTAACCACAAAAGGAGGATCA 57.734 36.000 0.00 0.00 36.25 2.92
3472 4092 7.872138 TCTATTAACCACAAAAGGAGGATCAT 58.128 34.615 0.00 0.00 36.25 2.45
3473 4093 6.780457 ATTAACCACAAAAGGAGGATCATG 57.220 37.500 0.00 0.00 36.25 3.07
3474 4094 2.450476 ACCACAAAAGGAGGATCATGC 58.550 47.619 0.00 0.00 36.25 4.06
3475 4095 1.753073 CCACAAAAGGAGGATCATGCC 59.247 52.381 0.00 0.00 36.25 4.40
3476 4096 2.449464 CACAAAAGGAGGATCATGCCA 58.551 47.619 0.00 0.00 36.25 4.92
3477 4097 2.165030 CACAAAAGGAGGATCATGCCAC 59.835 50.000 0.00 0.00 36.25 5.01
3478 4098 2.042162 ACAAAAGGAGGATCATGCCACT 59.958 45.455 0.00 0.00 36.25 4.00
3479 4099 3.266772 ACAAAAGGAGGATCATGCCACTA 59.733 43.478 0.00 0.00 36.25 2.74
3480 4100 3.853355 AAAGGAGGATCATGCCACTAG 57.147 47.619 0.00 0.00 36.25 2.57
3481 4101 1.055040 AGGAGGATCATGCCACTAGC 58.945 55.000 0.00 0.00 38.70 3.42
3491 4111 3.688553 GCCACTAGCACCATAGTCC 57.311 57.895 0.00 0.00 42.97 3.85
3492 4112 1.123928 GCCACTAGCACCATAGTCCT 58.876 55.000 0.00 0.00 42.97 3.85
3493 4113 1.069358 GCCACTAGCACCATAGTCCTC 59.931 57.143 0.00 0.00 42.97 3.71
3494 4114 2.672098 CCACTAGCACCATAGTCCTCT 58.328 52.381 0.00 0.00 33.68 3.69
3495 4115 2.625790 CCACTAGCACCATAGTCCTCTC 59.374 54.545 0.00 0.00 33.68 3.20
3496 4116 2.292016 CACTAGCACCATAGTCCTCTCG 59.708 54.545 0.00 0.00 33.68 4.04
3497 4117 1.883275 CTAGCACCATAGTCCTCTCGG 59.117 57.143 0.00 0.00 0.00 4.63
3498 4118 1.068250 GCACCATAGTCCTCTCGGC 59.932 63.158 0.00 0.00 0.00 5.54
3499 4119 1.742768 CACCATAGTCCTCTCGGCC 59.257 63.158 0.00 0.00 0.00 6.13
3500 4120 1.457831 ACCATAGTCCTCTCGGCCC 60.458 63.158 0.00 0.00 0.00 5.80
3501 4121 2.210711 CCATAGTCCTCTCGGCCCC 61.211 68.421 0.00 0.00 0.00 5.80
3502 4122 1.457643 CATAGTCCTCTCGGCCCCA 60.458 63.158 0.00 0.00 0.00 4.96
3503 4123 1.457831 ATAGTCCTCTCGGCCCCAC 60.458 63.158 0.00 0.00 0.00 4.61
3504 4124 2.948801 ATAGTCCTCTCGGCCCCACC 62.949 65.000 0.00 0.00 0.00 4.61
3521 4141 4.659172 CGCCACCACCACCACCAT 62.659 66.667 0.00 0.00 0.00 3.55
3522 4142 2.676471 GCCACCACCACCACCATC 60.676 66.667 0.00 0.00 0.00 3.51
3523 4143 2.035626 CCACCACCACCACCATCC 59.964 66.667 0.00 0.00 0.00 3.51
3524 4144 2.538141 CCACCACCACCACCATCCT 61.538 63.158 0.00 0.00 0.00 3.24
3525 4145 1.002134 CACCACCACCACCATCCTC 60.002 63.158 0.00 0.00 0.00 3.71
3526 4146 1.151810 ACCACCACCACCATCCTCT 60.152 57.895 0.00 0.00 0.00 3.69
3527 4147 1.201429 ACCACCACCACCATCCTCTC 61.201 60.000 0.00 0.00 0.00 3.20
3528 4148 1.219124 CACCACCACCATCCTCTCG 59.781 63.158 0.00 0.00 0.00 4.04
3529 4149 2.187946 CCACCACCATCCTCTCGC 59.812 66.667 0.00 0.00 0.00 5.03
3530 4150 2.187946 CACCACCATCCTCTCGCC 59.812 66.667 0.00 0.00 0.00 5.54
3531 4151 3.083997 ACCACCATCCTCTCGCCC 61.084 66.667 0.00 0.00 0.00 6.13
3532 4152 4.227134 CCACCATCCTCTCGCCCG 62.227 72.222 0.00 0.00 0.00 6.13
3533 4153 4.899239 CACCATCCTCTCGCCCGC 62.899 72.222 0.00 0.00 0.00 6.13
3536 4156 4.899239 CATCCTCTCGCCCGCCAC 62.899 72.222 0.00 0.00 0.00 5.01
3547 4167 4.885270 CCGCCACCACCAACACCA 62.885 66.667 0.00 0.00 0.00 4.17
3548 4168 2.830827 CGCCACCACCAACACCAA 60.831 61.111 0.00 0.00 0.00 3.67
3549 4169 2.811799 GCCACCACCAACACCAAC 59.188 61.111 0.00 0.00 0.00 3.77
3550 4170 2.055042 GCCACCACCAACACCAACA 61.055 57.895 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 115 1.880819 GCCTTTGTAGGGGTCGTCGA 61.881 60.000 0.00 0.00 42.25 4.20
349 370 1.737201 TGCTTGACAGAACCGTCGA 59.263 52.632 0.00 0.00 38.84 4.20
360 381 0.721718 GCGTCATGGTACTGCTTGAC 59.278 55.000 0.00 7.61 36.09 3.18
379 400 4.227134 CATGGAGGCGGAGGACGG 62.227 72.222 0.00 0.00 44.51 4.79
490 511 0.108472 GTACTTGTAGTGGTCGCCCC 60.108 60.000 0.00 0.00 0.00 5.80
822 870 2.959071 GAGCATGCGCCGAGACTC 60.959 66.667 13.01 0.67 39.83 3.36
921 981 1.892819 ATCGTCCACACTGCTGGGAG 61.893 60.000 0.00 0.00 31.41 4.30
991 1059 3.085443 GATGATCGACATCGGTTCAGT 57.915 47.619 10.73 0.00 44.46 3.41
1068 1166 3.976593 CTGGCCTCCTCCAGCATA 58.023 61.111 3.32 0.00 46.11 3.14
1110 1208 3.969976 CTGACCCTATCATCTTCTTCCCA 59.030 47.826 0.00 0.00 36.48 4.37
1185 1286 2.423446 CCCCTGATGTCTAGCGCC 59.577 66.667 2.29 0.00 0.00 6.53
1203 1307 2.124507 TTGTGACTGGGTAGGCCTGC 62.125 60.000 17.99 15.51 34.45 4.85
1224 1328 2.580276 GCGACCATCCGTAACCCA 59.420 61.111 0.00 0.00 0.00 4.51
1227 1331 1.875364 GTCGGCGACCATCCGTAAC 60.875 63.158 28.72 0.00 46.49 2.50
1229 1333 1.669049 ATTGTCGGCGACCATCCGTA 61.669 55.000 34.28 13.56 46.49 4.02
1230 1334 1.669049 TATTGTCGGCGACCATCCGT 61.669 55.000 34.28 16.87 46.49 4.69
1393 1509 1.021390 CGCACCCTGATCTTGTCACC 61.021 60.000 0.00 0.00 32.22 4.02
1542 1682 1.758280 ACCGTTACCAGTGTCTGACAA 59.242 47.619 12.81 0.00 32.44 3.18
1608 1792 2.588314 CTGAGGCTGCTGATCGCC 60.588 66.667 0.00 1.37 46.65 5.54
1915 2099 3.129502 CGTGGGGTGCAGCTCATG 61.130 66.667 23.32 22.95 0.00 3.07
2324 2571 1.000955 GGGCCCTGACTACATCATACG 59.999 57.143 17.04 0.00 36.48 3.06
2411 2658 2.218603 GTATAACCATGTCCCAAGCGG 58.781 52.381 0.00 0.00 0.00 5.52
2514 2764 4.462132 ACCATCTGATATCCACTCGATCTG 59.538 45.833 0.00 0.00 31.92 2.90
2538 2788 9.871238 TCTCCAGTCTTATGTTAAATGTTAGAC 57.129 33.333 0.00 0.00 0.00 2.59
2608 2901 5.180271 ACAAACGTAACCAGAGTCTTGAAA 58.820 37.500 0.00 0.00 0.00 2.69
2613 2906 6.830873 AGTATACAAACGTAACCAGAGTCT 57.169 37.500 5.50 0.00 0.00 3.24
2642 2935 5.849510 TCCGTTTTTCACTGACATAGAAGA 58.150 37.500 0.00 0.00 0.00 2.87
2663 2956 3.425162 ACACTGTCTTGGAATTCCTCC 57.575 47.619 24.73 10.47 45.64 4.30
2687 3221 5.784578 ATGTGTCCACGCTTATATAGTGA 57.215 39.130 2.92 0.00 38.06 3.41
2743 3277 9.891828 TGTGATGATGATTGTTTTGTAGTTTAC 57.108 29.630 0.00 0.00 0.00 2.01
2819 3438 8.035165 TGCTTTATGAAGTAAAATTAGCGTCA 57.965 30.769 0.00 0.00 35.25 4.35
2932 3551 1.400494 GTATTTACGGTTGCAGGCCTG 59.600 52.381 29.34 29.34 0.00 4.85
2957 3576 3.757745 AATGAAATTAACACTCGGCGG 57.242 42.857 7.21 0.00 32.46 6.13
3085 3705 8.268605 TCACCATGGTATACACTAATTTTAGCA 58.731 33.333 19.28 0.00 34.09 3.49
3357 3977 0.323629 TTGCCCTTGTAGCGCTAACT 59.676 50.000 20.73 0.00 0.00 2.24
3358 3978 0.446616 GTTGCCCTTGTAGCGCTAAC 59.553 55.000 20.73 13.83 0.00 2.34
3359 3979 0.323629 AGTTGCCCTTGTAGCGCTAA 59.676 50.000 20.73 5.43 0.00 3.09
3360 3980 0.108329 GAGTTGCCCTTGTAGCGCTA 60.108 55.000 14.45 14.45 0.00 4.26
3361 3981 1.376037 GAGTTGCCCTTGTAGCGCT 60.376 57.895 17.26 17.26 0.00 5.92
3362 3982 0.108329 TAGAGTTGCCCTTGTAGCGC 60.108 55.000 0.00 0.00 0.00 5.92
3363 3983 2.000447 GTTAGAGTTGCCCTTGTAGCG 59.000 52.381 0.00 0.00 0.00 4.26
3364 3984 2.357075 GGTTAGAGTTGCCCTTGTAGC 58.643 52.381 0.00 0.00 0.00 3.58
3365 3985 2.232941 TCGGTTAGAGTTGCCCTTGTAG 59.767 50.000 0.00 0.00 0.00 2.74
3366 3986 2.250031 TCGGTTAGAGTTGCCCTTGTA 58.750 47.619 0.00 0.00 0.00 2.41
3367 3987 1.053424 TCGGTTAGAGTTGCCCTTGT 58.947 50.000 0.00 0.00 0.00 3.16
3368 3988 2.403252 ATCGGTTAGAGTTGCCCTTG 57.597 50.000 0.00 0.00 0.00 3.61
3369 3989 3.344515 GAAATCGGTTAGAGTTGCCCTT 58.655 45.455 0.00 0.00 37.28 3.95
3370 3990 2.355818 GGAAATCGGTTAGAGTTGCCCT 60.356 50.000 0.00 0.00 38.96 5.19
3371 3991 2.014857 GGAAATCGGTTAGAGTTGCCC 58.985 52.381 0.00 0.00 38.96 5.36
3372 3992 2.987232 AGGAAATCGGTTAGAGTTGCC 58.013 47.619 0.00 0.00 44.55 4.52
3373 3993 6.148976 ACTTTTAGGAAATCGGTTAGAGTTGC 59.851 38.462 0.00 0.00 43.95 4.17
3374 3994 7.668525 ACTTTTAGGAAATCGGTTAGAGTTG 57.331 36.000 0.00 0.00 37.28 3.16
3375 3995 9.783081 TTAACTTTTAGGAAATCGGTTAGAGTT 57.217 29.630 0.00 0.00 40.18 3.01
3376 3996 9.783081 TTTAACTTTTAGGAAATCGGTTAGAGT 57.217 29.630 0.00 0.00 0.00 3.24
3381 4001 8.573885 CCTTCTTTAACTTTTAGGAAATCGGTT 58.426 33.333 0.00 0.00 0.00 4.44
3382 4002 7.940688 TCCTTCTTTAACTTTTAGGAAATCGGT 59.059 33.333 0.00 0.00 0.00 4.69
3383 4003 8.331730 TCCTTCTTTAACTTTTAGGAAATCGG 57.668 34.615 0.00 0.00 0.00 4.18
3384 4004 9.989869 GATCCTTCTTTAACTTTTAGGAAATCG 57.010 33.333 0.00 0.00 35.58 3.34
3386 4006 8.957466 CGGATCCTTCTTTAACTTTTAGGAAAT 58.043 33.333 10.75 0.00 35.58 2.17
3387 4007 7.392393 CCGGATCCTTCTTTAACTTTTAGGAAA 59.608 37.037 10.75 0.00 35.58 3.13
3388 4008 6.882678 CCGGATCCTTCTTTAACTTTTAGGAA 59.117 38.462 10.75 0.00 35.58 3.36
3389 4009 6.412214 CCGGATCCTTCTTTAACTTTTAGGA 58.588 40.000 10.75 0.00 36.33 2.94
3390 4010 5.066117 GCCGGATCCTTCTTTAACTTTTAGG 59.934 44.000 5.05 0.00 0.00 2.69
3391 4011 5.066117 GGCCGGATCCTTCTTTAACTTTTAG 59.934 44.000 5.05 0.00 0.00 1.85
3392 4012 4.945543 GGCCGGATCCTTCTTTAACTTTTA 59.054 41.667 5.05 0.00 0.00 1.52
3393 4013 3.762288 GGCCGGATCCTTCTTTAACTTTT 59.238 43.478 5.05 0.00 0.00 2.27
3394 4014 3.353557 GGCCGGATCCTTCTTTAACTTT 58.646 45.455 5.05 0.00 0.00 2.66
3395 4015 2.679930 CGGCCGGATCCTTCTTTAACTT 60.680 50.000 20.10 0.00 0.00 2.66
3396 4016 1.134491 CGGCCGGATCCTTCTTTAACT 60.134 52.381 20.10 0.00 0.00 2.24
3397 4017 1.134610 TCGGCCGGATCCTTCTTTAAC 60.135 52.381 27.83 0.00 0.00 2.01
3398 4018 1.138266 CTCGGCCGGATCCTTCTTTAA 59.862 52.381 27.83 0.00 0.00 1.52
3399 4019 0.750850 CTCGGCCGGATCCTTCTTTA 59.249 55.000 27.83 0.00 0.00 1.85
3400 4020 1.265454 ACTCGGCCGGATCCTTCTTT 61.265 55.000 27.83 0.00 0.00 2.52
3401 4021 0.396695 TACTCGGCCGGATCCTTCTT 60.397 55.000 27.83 1.52 0.00 2.52
3402 4022 0.396695 TTACTCGGCCGGATCCTTCT 60.397 55.000 27.83 0.65 0.00 2.85
3403 4023 0.462789 TTTACTCGGCCGGATCCTTC 59.537 55.000 27.83 0.56 0.00 3.46
3404 4024 0.464452 CTTTACTCGGCCGGATCCTT 59.536 55.000 27.83 5.81 0.00 3.36
3405 4025 0.686769 ACTTTACTCGGCCGGATCCT 60.687 55.000 27.83 5.74 0.00 3.24
3406 4026 0.177373 AACTTTACTCGGCCGGATCC 59.823 55.000 27.83 0.00 0.00 3.36
3407 4027 2.100418 ACTAACTTTACTCGGCCGGATC 59.900 50.000 27.83 0.00 0.00 3.36
3408 4028 2.105766 ACTAACTTTACTCGGCCGGAT 58.894 47.619 27.83 16.52 0.00 4.18
3409 4029 1.203052 CACTAACTTTACTCGGCCGGA 59.797 52.381 27.83 11.38 0.00 5.14
3410 4030 1.636988 CACTAACTTTACTCGGCCGG 58.363 55.000 27.83 18.67 0.00 6.13
3411 4031 1.203052 TCCACTAACTTTACTCGGCCG 59.797 52.381 22.12 22.12 0.00 6.13
3412 4032 2.233186 ACTCCACTAACTTTACTCGGCC 59.767 50.000 0.00 0.00 0.00 6.13
3413 4033 3.589495 ACTCCACTAACTTTACTCGGC 57.411 47.619 0.00 0.00 0.00 5.54
3414 4034 8.543862 AAATTTACTCCACTAACTTTACTCGG 57.456 34.615 0.00 0.00 0.00 4.63
3434 4054 8.950007 TGTGGTTAATAGAGGAGGAAAAATTT 57.050 30.769 0.00 0.00 0.00 1.82
3435 4055 8.950007 TTGTGGTTAATAGAGGAGGAAAAATT 57.050 30.769 0.00 0.00 0.00 1.82
3436 4056 8.950007 TTTGTGGTTAATAGAGGAGGAAAAAT 57.050 30.769 0.00 0.00 0.00 1.82
3437 4057 8.770010 TTTTGTGGTTAATAGAGGAGGAAAAA 57.230 30.769 0.00 0.00 0.00 1.94
3438 4058 7.450323 CCTTTTGTGGTTAATAGAGGAGGAAAA 59.550 37.037 0.00 0.00 0.00 2.29
3439 4059 6.946009 CCTTTTGTGGTTAATAGAGGAGGAAA 59.054 38.462 0.00 0.00 0.00 3.13
3440 4060 6.273730 TCCTTTTGTGGTTAATAGAGGAGGAA 59.726 38.462 0.00 0.00 0.00 3.36
3441 4061 5.788533 TCCTTTTGTGGTTAATAGAGGAGGA 59.211 40.000 0.00 0.00 0.00 3.71
3442 4062 6.062258 TCCTTTTGTGGTTAATAGAGGAGG 57.938 41.667 0.00 0.00 0.00 4.30
3443 4063 6.070194 TCCTCCTTTTGTGGTTAATAGAGGAG 60.070 42.308 8.70 8.70 45.41 3.69
3444 4064 5.788533 TCCTCCTTTTGTGGTTAATAGAGGA 59.211 40.000 0.00 0.00 0.00 3.71
3445 4065 6.062258 TCCTCCTTTTGTGGTTAATAGAGG 57.938 41.667 0.00 0.00 0.00 3.69
3446 4066 7.338710 TGATCCTCCTTTTGTGGTTAATAGAG 58.661 38.462 0.00 0.00 0.00 2.43
3447 4067 7.265599 TGATCCTCCTTTTGTGGTTAATAGA 57.734 36.000 0.00 0.00 0.00 1.98
3448 4068 7.469181 GCATGATCCTCCTTTTGTGGTTAATAG 60.469 40.741 0.00 0.00 0.00 1.73
3449 4069 6.321181 GCATGATCCTCCTTTTGTGGTTAATA 59.679 38.462 0.00 0.00 0.00 0.98
3450 4070 5.127682 GCATGATCCTCCTTTTGTGGTTAAT 59.872 40.000 0.00 0.00 0.00 1.40
3451 4071 4.462483 GCATGATCCTCCTTTTGTGGTTAA 59.538 41.667 0.00 0.00 0.00 2.01
3452 4072 4.016444 GCATGATCCTCCTTTTGTGGTTA 58.984 43.478 0.00 0.00 0.00 2.85
3453 4073 2.827921 GCATGATCCTCCTTTTGTGGTT 59.172 45.455 0.00 0.00 0.00 3.67
3454 4074 2.450476 GCATGATCCTCCTTTTGTGGT 58.550 47.619 0.00 0.00 0.00 4.16
3455 4075 1.753073 GGCATGATCCTCCTTTTGTGG 59.247 52.381 0.00 0.00 0.00 4.17
3456 4076 2.165030 GTGGCATGATCCTCCTTTTGTG 59.835 50.000 0.00 0.00 0.00 3.33
3457 4077 2.042162 AGTGGCATGATCCTCCTTTTGT 59.958 45.455 0.00 0.00 0.00 2.83
3458 4078 2.731572 AGTGGCATGATCCTCCTTTTG 58.268 47.619 0.00 0.00 0.00 2.44
3459 4079 3.686691 GCTAGTGGCATGATCCTCCTTTT 60.687 47.826 0.00 0.00 41.35 2.27
3460 4080 2.158696 GCTAGTGGCATGATCCTCCTTT 60.159 50.000 0.00 0.00 41.35 3.11
3461 4081 1.419387 GCTAGTGGCATGATCCTCCTT 59.581 52.381 0.00 0.00 41.35 3.36
3462 4082 1.055040 GCTAGTGGCATGATCCTCCT 58.945 55.000 0.00 0.00 41.35 3.69
3463 4083 3.621953 GCTAGTGGCATGATCCTCC 57.378 57.895 0.00 0.00 41.35 4.30
3473 4093 1.069358 GAGGACTATGGTGCTAGTGGC 59.931 57.143 2.49 0.00 44.07 5.01
3474 4094 2.625790 GAGAGGACTATGGTGCTAGTGG 59.374 54.545 2.49 0.00 44.07 4.00
3475 4095 2.292016 CGAGAGGACTATGGTGCTAGTG 59.708 54.545 2.49 0.00 44.07 2.74
3476 4096 2.577700 CGAGAGGACTATGGTGCTAGT 58.422 52.381 2.49 0.00 44.07 2.57
3504 4124 4.659172 ATGGTGGTGGTGGTGGCG 62.659 66.667 0.00 0.00 0.00 5.69
3505 4125 2.676471 GATGGTGGTGGTGGTGGC 60.676 66.667 0.00 0.00 0.00 5.01
3506 4126 2.035626 GGATGGTGGTGGTGGTGG 59.964 66.667 0.00 0.00 0.00 4.61
3507 4127 1.002134 GAGGATGGTGGTGGTGGTG 60.002 63.158 0.00 0.00 0.00 4.17
3508 4128 1.151810 AGAGGATGGTGGTGGTGGT 60.152 57.895 0.00 0.00 0.00 4.16
3509 4129 1.604378 GAGAGGATGGTGGTGGTGG 59.396 63.158 0.00 0.00 0.00 4.61
3510 4130 1.219124 CGAGAGGATGGTGGTGGTG 59.781 63.158 0.00 0.00 0.00 4.17
3511 4131 2.660064 GCGAGAGGATGGTGGTGGT 61.660 63.158 0.00 0.00 0.00 4.16
3512 4132 2.187946 GCGAGAGGATGGTGGTGG 59.812 66.667 0.00 0.00 0.00 4.61
3513 4133 2.187946 GGCGAGAGGATGGTGGTG 59.812 66.667 0.00 0.00 0.00 4.17
3514 4134 3.083997 GGGCGAGAGGATGGTGGT 61.084 66.667 0.00 0.00 0.00 4.16
3515 4135 4.227134 CGGGCGAGAGGATGGTGG 62.227 72.222 0.00 0.00 0.00 4.61
3516 4136 4.899239 GCGGGCGAGAGGATGGTG 62.899 72.222 0.00 0.00 0.00 4.17
3519 4139 4.899239 GTGGCGGGCGAGAGGATG 62.899 72.222 0.00 0.00 0.00 3.51
3530 4150 4.885270 TGGTGTTGGTGGTGGCGG 62.885 66.667 0.00 0.00 0.00 6.13
3531 4151 2.830827 TTGGTGTTGGTGGTGGCG 60.831 61.111 0.00 0.00 0.00 5.69
3532 4152 2.055042 TGTTGGTGTTGGTGGTGGC 61.055 57.895 0.00 0.00 0.00 5.01
3533 4153 4.346049 TGTTGGTGTTGGTGGTGG 57.654 55.556 0.00 0.00 0.00 4.61



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

AutoCloner maintained by Alex Coulton.