Multiple sequence alignment - TraesCS4D01G279800

Loading Multiple Alignment...

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 TraesCS4D01G279800 chr4D 100.000 3411 0 0 1 3411 451037022 451040432 0.000000e+00 6300
1 TraesCS4D01G279800 chr4D 90.960 885 56 18 994 1857 472682700 472681819 0.000000e+00 1170
2 TraesCS4D01G279800 chr4D 87.184 593 71 3 402 990 472683325 472682734 0.000000e+00 669
3 TraesCS4D01G279800 chr4D 90.074 272 21 6 1389 1657 220337292 220337560 7.010000e-92 348
4 TraesCS4D01G279800 chr4D 91.228 228 17 2 3185 3410 262390676 262390450 1.190000e-79 307
5 TraesCS4D01G279800 chr4D 94.262 122 6 1 2963 3084 80469911 80470031 5.810000e-43 185
6 TraesCS4D01G279800 chr3D 93.963 2998 119 27 1 2967 562558019 562560985 0.000000e+00 4477
7 TraesCS4D01G279800 chr3D 89.146 562 41 12 2403 2955 266652316 266652866 0.000000e+00 682
8 TraesCS4D01G279800 chr3D 96.793 343 7 4 3071 3410 562560984 562561325 1.370000e-158 569
9 TraesCS4D01G279800 chr3D 92.453 318 22 2 3071 3386 266652874 266653191 1.440000e-123 453
10 TraesCS4D01G279800 chr4A 94.942 1997 69 21 994 2967 15920385 15918398 0.000000e+00 3099
11 TraesCS4D01G279800 chr4A 95.338 1866 47 15 1132 2967 682751396 682753251 0.000000e+00 2928
12 TraesCS4D01G279800 chr4A 94.282 857 44 5 77 929 682750310 682751165 0.000000e+00 1306
13 TraesCS4D01G279800 chr4A 91.525 885 51 15 994 1857 581495494 581494613 0.000000e+00 1197
14 TraesCS4D01G279800 chr4A 93.083 665 37 7 1 658 15922156 15921494 0.000000e+00 965
15 TraesCS4D01G279800 chr4A 93.705 556 32 3 1855 2407 581494578 581494023 0.000000e+00 830
16 TraesCS4D01G279800 chr4A 91.472 598 50 1 402 998 15921026 15920429 0.000000e+00 821
17 TraesCS4D01G279800 chr4A 95.602 432 15 3 1 429 15921491 15921061 0.000000e+00 689
18 TraesCS4D01G279800 chr4A 97.093 344 7 3 3071 3411 15918399 15918056 8.210000e-161 577
19 TraesCS4D01G279800 chr4A 95.640 344 7 4 3071 3411 682753250 682753588 2.310000e-151 545
20 TraesCS4D01G279800 chr4A 96.610 118 2 2 2962 3078 628491121 628491005 9.660000e-46 195
21 TraesCS4D01G279800 chr4A 78.453 181 30 6 2409 2581 671922774 671922595 3.600000e-20 110
22 TraesCS4D01G279800 chr7D 88.836 1478 124 22 402 1857 44720111 44718653 0.000000e+00 1777
23 TraesCS4D01G279800 chr7D 93.750 128 5 3 2959 3085 379324243 379324118 4.490000e-44 189
24 TraesCS4D01G279800 chr7D 88.321 137 11 5 994 1125 114147674 114147538 3.520000e-35 159
25 TraesCS4D01G279800 chr5A 86.273 1508 127 52 402 1857 611981409 611979930 0.000000e+00 1565
26 TraesCS4D01G279800 chr5A 92.334 887 44 15 989 1854 124618281 124619164 0.000000e+00 1240
27 TraesCS4D01G279800 chr5A 93.874 555 29 4 1855 2407 611979895 611979344 0.000000e+00 832
28 TraesCS4D01G279800 chr5A 88.448 554 56 8 402 951 124617731 124618280 0.000000e+00 662
29 TraesCS4D01G279800 chr5A 83.716 522 68 9 3 511 124605688 124606205 8.560000e-131 477
30 TraesCS4D01G279800 chr5A 83.784 518 67 9 3 507 124602822 124603335 3.080000e-130 475
31 TraesCS4D01G279800 chr5A 97.391 115 3 0 2966 3080 69844894 69844780 2.690000e-46 196
32 TraesCS4D01G279800 chr7A 89.438 1193 94 19 402 1568 47298103 47296917 0.000000e+00 1476
33 TraesCS4D01G279800 chr7A 89.179 268 12 8 1607 1857 47296922 47296655 5.490000e-83 318
34 TraesCS4D01G279800 chr7A 85.490 255 21 11 2527 2770 354946883 354947132 5.650000e-63 252
35 TraesCS4D01G279800 chr7A 97.345 113 3 0 2966 3078 269960426 269960314 3.470000e-45 193
36 TraesCS4D01G279800 chr7A 93.651 126 8 0 2963 3088 535535483 535535358 4.490000e-44 189
37 TraesCS4D01G279800 chr6D 91.818 880 47 11 999 1857 420230892 420230017 0.000000e+00 1203
38 TraesCS4D01G279800 chr6D 94.234 555 30 2 1855 2407 420229982 420229428 0.000000e+00 846
39 TraesCS4D01G279800 chr6D 89.552 603 56 4 402 998 420231542 420230941 0.000000e+00 758
40 TraesCS4D01G279800 chr6D 88.806 536 46 9 402 932 420234339 420233813 0.000000e+00 645
41 TraesCS4D01G279800 chr5D 91.053 883 53 5 994 1857 441571959 441571084 0.000000e+00 1170
42 TraesCS4D01G279800 chr5D 90.990 677 39 11 1200 1857 490439530 490438857 0.000000e+00 893
43 TraesCS4D01G279800 chr5D 93.694 555 29 5 1855 2407 490438822 490438272 0.000000e+00 826
44 TraesCS4D01G279800 chr5D 93.381 559 30 4 1855 2407 441571049 441570492 0.000000e+00 821
45 TraesCS4D01G279800 chr5D 88.688 442 35 8 3 431 490440678 490440239 3.020000e-145 525
46 TraesCS4D01G279800 chr5D 81.029 680 84 30 5 658 441572844 441572184 1.830000e-137 499
47 TraesCS4D01G279800 chr5D 90.583 223 16 2 994 1215 490439765 490439547 1.200000e-74 291
48 TraesCS4D01G279800 chr5D 87.615 218 20 4 1426 1642 62235003 62235214 2.630000e-61 246
49 TraesCS4D01G279800 chr5B 90.827 883 51 6 994 1854 604870093 604870967 0.000000e+00 1155
50 TraesCS4D01G279800 chr5B 81.341 686 82 36 3 658 604869183 604869852 1.810000e-142 516
51 TraesCS4D01G279800 chr1D 90.225 890 59 8 994 1857 439791090 439790203 0.000000e+00 1136
52 TraesCS4D01G279800 chr1D 88.040 602 64 6 402 998 439791726 439791128 0.000000e+00 706
53 TraesCS4D01G279800 chr4B 95.813 621 18 4 1940 2559 564152535 564153148 0.000000e+00 996
54 TraesCS4D01G279800 chr4B 93.695 571 15 11 1304 1854 564151536 564152105 0.000000e+00 835
55 TraesCS4D01G279800 chr4B 95.139 432 15 5 1 429 564150283 564150711 0.000000e+00 676
56 TraesCS4D01G279800 chr4B 97.305 371 5 4 2589 2955 564155407 564155776 2.890000e-175 625
57 TraesCS4D01G279800 chr4B 96.793 343 7 4 3071 3409 564155784 564156126 1.370000e-158 569
58 TraesCS4D01G279800 chr4B 92.887 239 11 2 1007 1241 564151300 564151536 3.260000e-90 342
59 TraesCS4D01G279800 chr4B 78.723 188 31 5 2404 2583 338507240 338507054 2.150000e-22 117
60 TraesCS4D01G279800 chr2B 93.502 554 25 8 2403 2955 733164559 733165102 0.000000e+00 813
61 TraesCS4D01G279800 chr2B 95.335 343 14 2 3071 3411 733165111 733165453 8.320000e-151 544
62 TraesCS4D01G279800 chr2A 93.613 501 26 5 1161 1658 743368927 743369424 0.000000e+00 743
63 TraesCS4D01G279800 chr2A 98.182 110 2 0 2966 3075 16796694 16796585 3.470000e-45 193
64 TraesCS4D01G279800 chr2A 96.552 116 4 0 2959 3074 209894279 209894164 3.470000e-45 193
65 TraesCS4D01G279800 chr1A 92.169 332 14 3 1306 1635 538399454 538399775 3.100000e-125 459
66 TraesCS4D01G279800 chr1A 84.615 312 21 16 994 1305 538399000 538399284 5.570000e-73 285
67 TraesCS4D01G279800 chr1A 82.979 329 22 16 2451 2770 335873075 335873378 2.020000e-67 267
68 TraesCS4D01G279800 chr7B 86.405 331 24 13 2454 2770 530665624 530665947 3.260000e-90 342
69 TraesCS4D01G279800 chrUn 86.765 272 28 7 3113 3377 87853778 87853508 2.570000e-76 296
70 TraesCS4D01G279800 chr3B 86.973 261 29 4 3113 3369 18216528 18216787 4.310000e-74 289
71 TraesCS4D01G279800 chr3B 79.006 181 29 5 2409 2581 279752788 279752967 7.730000e-22 115
72 TraesCS4D01G279800 chr6A 84.091 308 24 21 1570 1857 203220466 203220768 1.210000e-69 274
73 TraesCS4D01G279800 chr3A 91.667 132 8 3 2945 3074 684705875 684705745 2.700000e-41 180


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 TraesCS4D01G279800 chr4D 451037022 451040432 3410 False 6300.000000 6300 100.000000 1 3411 1 chr4D.!!$F3 3410
1 TraesCS4D01G279800 chr4D 472681819 472683325 1506 True 919.500000 1170 89.072000 402 1857 2 chr4D.!!$R2 1455
2 TraesCS4D01G279800 chr3D 562558019 562561325 3306 False 2523.000000 4477 95.378000 1 3410 2 chr3D.!!$F2 3409
3 TraesCS4D01G279800 chr3D 266652316 266653191 875 False 567.500000 682 90.799500 2403 3386 2 chr3D.!!$F1 983
4 TraesCS4D01G279800 chr4A 682750310 682753588 3278 False 1593.000000 2928 95.086667 77 3411 3 chr4A.!!$F1 3334
5 TraesCS4D01G279800 chr4A 15918056 15922156 4100 True 1230.200000 3099 94.438400 1 3411 5 chr4A.!!$R3 3410
6 TraesCS4D01G279800 chr4A 581494023 581495494 1471 True 1013.500000 1197 92.615000 994 2407 2 chr4A.!!$R4 1413
7 TraesCS4D01G279800 chr7D 44718653 44720111 1458 True 1777.000000 1777 88.836000 402 1857 1 chr7D.!!$R1 1455
8 TraesCS4D01G279800 chr5A 611979344 611981409 2065 True 1198.500000 1565 90.073500 402 2407 2 chr5A.!!$R2 2005
9 TraesCS4D01G279800 chr5A 124617731 124619164 1433 False 951.000000 1240 90.391000 402 1854 2 chr5A.!!$F2 1452
10 TraesCS4D01G279800 chr5A 124602822 124606205 3383 False 476.000000 477 83.750000 3 511 2 chr5A.!!$F1 508
11 TraesCS4D01G279800 chr7A 47296655 47298103 1448 True 897.000000 1476 89.308500 402 1857 2 chr7A.!!$R3 1455
12 TraesCS4D01G279800 chr6D 420229428 420234339 4911 True 863.000000 1203 91.102500 402 2407 4 chr6D.!!$R1 2005
13 TraesCS4D01G279800 chr5D 441570492 441572844 2352 True 830.000000 1170 88.487667 5 2407 3 chr5D.!!$R1 2402
14 TraesCS4D01G279800 chr5D 490438272 490440678 2406 True 633.750000 893 90.988750 3 2407 4 chr5D.!!$R2 2404
15 TraesCS4D01G279800 chr5B 604869183 604870967 1784 False 835.500000 1155 86.084000 3 1854 2 chr5B.!!$F1 1851
16 TraesCS4D01G279800 chr1D 439790203 439791726 1523 True 921.000000 1136 89.132500 402 1857 2 chr1D.!!$R1 1455
17 TraesCS4D01G279800 chr4B 564150283 564156126 5843 False 673.833333 996 95.272000 1 3409 6 chr4B.!!$F1 3408
18 TraesCS4D01G279800 chr2B 733164559 733165453 894 False 678.500000 813 94.418500 2403 3411 2 chr2B.!!$F1 1008
19 TraesCS4D01G279800 chr1A 538399000 538399775 775 False 372.000000 459 88.392000 994 1635 2 chr1A.!!$F2 641

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
971 6345 1.980765 TCTTCCTTGAGGAGCATGTGT 59.019 47.619 0.0 0.0 46.36 3.72 F
2097 8681 0.254178 AGCTGGGCGTTGAGATTCAT 59.746 50.000 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 8731 0.179009 ACCATGAGGGCAATGGATCG 60.179 55.0 17.04 0.0 42.05 3.69 R
3054 11901 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.0 0.00 0.0 0.00 4.30 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
420 903 9.788960 GAACAATTTGGATTTAGTTAGGTGATC 57.211 33.333 0.78 0.00 0.00 2.92
421 904 9.533831 AACAATTTGGATTTAGTTAGGTGATCT 57.466 29.630 0.78 0.00 0.00 2.75
446 1264 5.744819 GGATCTTGACGAGCTAGTAAAAGAC 59.255 44.000 19.94 15.16 32.94 3.01
460 1279 4.925646 AGTAAAAGACGTTCGGTGGATTAC 59.074 41.667 0.00 0.00 0.00 1.89
493 1315 2.766263 TCTAGTAGGTGAGCATGTTGGG 59.234 50.000 0.00 0.00 0.00 4.12
507 1329 6.609876 AGCATGTTGGGTATTATATTGGTGA 58.390 36.000 0.00 0.00 0.00 4.02
669 5505 8.215926 TGTTCGGTGTATTAATTAATCTTGGG 57.784 34.615 13.95 3.63 0.00 4.12
723 5691 7.873739 ATTGAACCAAATTTCTTCGTGATTC 57.126 32.000 0.00 0.00 0.00 2.52
831 6204 7.706607 GTCTAATAGATGCGCATGGTGATTATA 59.293 37.037 30.76 14.00 0.00 0.98
902 6275 8.954950 ATTTAGTTATCTGACTGTGATCTTGG 57.045 34.615 0.00 0.00 0.00 3.61
971 6345 1.980765 TCTTCCTTGAGGAGCATGTGT 59.019 47.619 0.00 0.00 46.36 3.72
976 6350 2.027745 CCTTGAGGAGCATGTGTAGTGT 60.028 50.000 0.00 0.00 37.39 3.55
1095 6564 2.200337 GGCGGTTCAGGTTTGCCTT 61.200 57.895 0.00 0.00 44.18 4.35
1137 6711 1.552792 CTCACTCTGGTCTCCCCTTTC 59.447 57.143 0.00 0.00 0.00 2.62
1209 6969 7.122501 GGTATTCCAGGTAGTTAGCCTATCTAC 59.877 44.444 10.32 10.32 34.74 2.59
1412 7610 2.843730 TGCAGAACTATTTGGGCTCCTA 59.156 45.455 0.00 0.00 0.00 2.94
1512 7719 2.398588 TCTGGACCTCAAGTTCACTGT 58.601 47.619 0.00 0.00 28.07 3.55
1552 7759 1.064357 CGCGAGGAAGAGTAGGAAGAC 59.936 57.143 0.00 0.00 0.00 3.01
1884 8152 6.042093 CCTGAAGTATGCCTAATCTTGGACTA 59.958 42.308 0.00 0.00 0.00 2.59
1957 8534 7.993758 GGGTTCTAAGCTATTGAATTAGGAAGT 59.006 37.037 0.00 0.00 0.00 3.01
2050 8628 0.750249 TCCGCACAGTGACAAGAGAA 59.250 50.000 4.15 0.00 0.00 2.87
2064 8642 3.830755 ACAAGAGAATTGCTGGCTTCAAT 59.169 39.130 0.00 0.17 35.83 2.57
2076 8654 6.186957 TGCTGGCTTCAATAAGGATAAGAAA 58.813 36.000 0.00 0.00 32.98 2.52
2097 8681 0.254178 AGCTGGGCGTTGAGATTCAT 59.746 50.000 0.00 0.00 0.00 2.57
2147 8731 3.929610 GCTGACTACATGAAGGTGAGTTC 59.070 47.826 0.00 0.00 0.00 3.01
2162 8746 0.911769 AGTTCGATCCATTGCCCTCA 59.088 50.000 0.00 0.00 0.00 3.86
2368 8959 6.328672 AGTCAATAGCTGATGAGGAACCTAAT 59.671 38.462 0.00 0.00 36.14 1.73
2446 9037 6.264518 GGTGATTTTTCTCCCTCTTGTTAACA 59.735 38.462 3.59 3.59 0.00 2.41
2583 11415 9.836076 CATATCTTGATTGCACGATTGATTATT 57.164 29.630 0.00 0.00 35.06 1.40
2955 11802 3.631686 TCGTTTTGGAATGGGCTATGATG 59.368 43.478 0.00 0.00 0.00 3.07
2956 11803 3.631686 CGTTTTGGAATGGGCTATGATGA 59.368 43.478 0.00 0.00 0.00 2.92
2959 11806 6.218746 GTTTTGGAATGGGCTATGATGATTC 58.781 40.000 0.00 0.00 0.00 2.52
2960 11807 4.038271 TGGAATGGGCTATGATGATTCC 57.962 45.455 0.00 0.00 41.65 3.01
2963 11810 5.082425 GGAATGGGCTATGATGATTCCTTT 58.918 41.667 0.00 0.00 39.27 3.11
2964 11811 5.541484 GGAATGGGCTATGATGATTCCTTTT 59.459 40.000 0.00 0.00 39.27 2.27
2965 11812 6.042437 GGAATGGGCTATGATGATTCCTTTTT 59.958 38.462 0.00 0.00 39.27 1.94
2966 11813 7.233348 GGAATGGGCTATGATGATTCCTTTTTA 59.767 37.037 0.00 0.00 39.27 1.52
2967 11814 6.959639 TGGGCTATGATGATTCCTTTTTAC 57.040 37.500 0.00 0.00 0.00 2.01
2968 11815 6.672593 TGGGCTATGATGATTCCTTTTTACT 58.327 36.000 0.00 0.00 0.00 2.24
2969 11816 6.772716 TGGGCTATGATGATTCCTTTTTACTC 59.227 38.462 0.00 0.00 0.00 2.59
2970 11817 6.207614 GGGCTATGATGATTCCTTTTTACTCC 59.792 42.308 0.00 0.00 0.00 3.85
2971 11818 6.207614 GGCTATGATGATTCCTTTTTACTCCC 59.792 42.308 0.00 0.00 0.00 4.30
2972 11819 7.001073 GCTATGATGATTCCTTTTTACTCCCT 58.999 38.462 0.00 0.00 0.00 4.20
2973 11820 7.174080 GCTATGATGATTCCTTTTTACTCCCTC 59.826 40.741 0.00 0.00 0.00 4.30
2974 11821 5.755849 TGATGATTCCTTTTTACTCCCTCC 58.244 41.667 0.00 0.00 0.00 4.30
2975 11822 4.216411 TGATTCCTTTTTACTCCCTCCG 57.784 45.455 0.00 0.00 0.00 4.63
2976 11823 3.585732 TGATTCCTTTTTACTCCCTCCGT 59.414 43.478 0.00 0.00 0.00 4.69
2977 11824 4.042435 TGATTCCTTTTTACTCCCTCCGTT 59.958 41.667 0.00 0.00 0.00 4.44
2978 11825 3.690475 TCCTTTTTACTCCCTCCGTTC 57.310 47.619 0.00 0.00 0.00 3.95
2979 11826 2.303890 TCCTTTTTACTCCCTCCGTTCC 59.696 50.000 0.00 0.00 0.00 3.62
2980 11827 2.039348 CCTTTTTACTCCCTCCGTTCCA 59.961 50.000 0.00 0.00 0.00 3.53
2981 11828 3.497227 CCTTTTTACTCCCTCCGTTCCAA 60.497 47.826 0.00 0.00 0.00 3.53
2982 11829 3.860968 TTTTACTCCCTCCGTTCCAAA 57.139 42.857 0.00 0.00 0.00 3.28
2983 11830 4.376225 TTTTACTCCCTCCGTTCCAAAT 57.624 40.909 0.00 0.00 0.00 2.32
2984 11831 4.376225 TTTACTCCCTCCGTTCCAAATT 57.624 40.909 0.00 0.00 0.00 1.82
2985 11832 5.502089 TTTACTCCCTCCGTTCCAAATTA 57.498 39.130 0.00 0.00 0.00 1.40
2986 11833 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2987 11834 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2988 11835 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2989 11836 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2990 11837 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2991 11838 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2992 11839 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2993 11840 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
2994 11841 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2995 11842 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
2996 11843 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
2997 11844 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
2998 11845 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
2999 11846 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
3000 11847 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
3001 11848 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
3002 11849 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
3003 11850 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
3004 11851 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
3005 11852 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
3006 11853 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
3007 11854 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
3008 11855 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
3009 11856 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
3010 11857 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
3011 11858 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
3012 11859 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
3013 11860 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
3014 11861 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
3015 11862 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
3016 11863 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
3017 11864 7.327275 CGCAGAAATGGATGTATCTAGAACTAC 59.673 40.741 0.00 0.00 0.00 2.73
3018 11865 8.144478 GCAGAAATGGATGTATCTAGAACTACA 58.856 37.037 8.32 8.32 32.75 2.74
3042 11889 9.381038 ACAATACAACTAGATACATCCATACCT 57.619 33.333 0.00 0.00 0.00 3.08
3043 11890 9.645059 CAATACAACTAGATACATCCATACCTG 57.355 37.037 0.00 0.00 0.00 4.00
3044 11891 6.102897 ACAACTAGATACATCCATACCTGC 57.897 41.667 0.00 0.00 0.00 4.85
3045 11892 5.164233 CAACTAGATACATCCATACCTGCG 58.836 45.833 0.00 0.00 0.00 5.18
3046 11893 4.663334 ACTAGATACATCCATACCTGCGA 58.337 43.478 0.00 0.00 0.00 5.10
3047 11894 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
3048 11895 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
3049 11896 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
3050 11897 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
3051 11898 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
3052 11899 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
3053 11900 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
3054 11901 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
3055 11902 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
3056 11903 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
3057 11904 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
3058 11905 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
3059 11906 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
3060 11907 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
3061 11908 2.093783 CCTGCGACAAGTAATTCGGAAC 59.906 50.000 0.00 0.00 35.02 3.62
3312 12172 0.405585 ACACTTTCCCACTCCCCATG 59.594 55.000 0.00 0.00 0.00 3.66
3369 12229 2.937519 CTCCCTATTTTCCTTGCTCCC 58.062 52.381 0.00 0.00 0.00 4.30
3374 12234 4.325816 CCCTATTTTCCTTGCTCCCCTAAA 60.326 45.833 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 628 8.799367 CATCTCTGACTATCTTCTCAAGATCAT 58.201 37.037 1.96 0.00 44.79 2.45
420 903 4.902443 TTACTAGCTCGTCAAGATCCAG 57.098 45.455 0.00 0.00 0.00 3.86
421 904 5.417894 TCTTTTACTAGCTCGTCAAGATCCA 59.582 40.000 8.21 0.00 0.00 3.41
446 1264 1.072116 TTCGCGTAATCCACCGAACG 61.072 55.000 5.77 0.00 35.96 3.95
460 1279 4.036027 TCACCTACTAGACCTAAATTCGCG 59.964 45.833 0.00 0.00 0.00 5.87
635 5471 7.915293 ATTAATACACCGAACATCTTTGACA 57.085 32.000 0.00 0.00 0.00 3.58
669 5505 7.331687 ACAATCACCTAACTAAATGCAAATTGC 59.668 33.333 11.58 11.58 45.29 3.56
971 6345 3.632080 CCCCGCACCACCACACTA 61.632 66.667 0.00 0.00 0.00 2.74
1095 6564 3.110552 GGGGGAGAGAGGAGGTGA 58.889 66.667 0.00 0.00 0.00 4.02
1137 6711 2.696506 TGAAGCTGCAGAATGAGACAG 58.303 47.619 20.43 0.00 39.69 3.51
1209 6969 4.755411 ACATCAAATGTAGGTGTAGTCCG 58.245 43.478 0.00 0.00 42.78 4.79
1412 7610 5.621193 ACTAAAACCAACTGATACAGCTGT 58.379 37.500 25.12 25.12 34.37 4.40
1512 7719 4.290155 GCGACTGCAGATGAAAAGAAAAA 58.710 39.130 23.35 0.00 42.15 1.94
1552 7759 0.322008 GTGAAACCCTCTCTGCCTGG 60.322 60.000 0.00 0.00 0.00 4.45
1957 8534 6.576185 GGGTCTCAAACGGATAAACTGTATA 58.424 40.000 0.00 0.00 37.07 1.47
1987 8565 0.254178 CCCTGCAGTAGCCAACAGAT 59.746 55.000 13.81 0.00 41.13 2.90
2050 8628 6.367983 TCTTATCCTTATTGAAGCCAGCAAT 58.632 36.000 0.00 0.00 39.20 3.56
2064 8642 3.681594 CGCCCAGCTGTTTCTTATCCTTA 60.682 47.826 13.81 0.00 0.00 2.69
2076 8654 0.674895 GAATCTCAACGCCCAGCTGT 60.675 55.000 13.81 0.00 0.00 4.40
2097 8681 8.708378 ACATGACCTTCATAGATGTATTTGAGA 58.292 33.333 0.00 0.00 34.28 3.27
2147 8731 0.179009 ACCATGAGGGCAATGGATCG 60.179 55.000 17.04 0.00 42.05 3.69
2583 11415 4.159506 GCATTCCTAACATACCCAGCAAAA 59.840 41.667 0.00 0.00 0.00 2.44
2955 11802 4.217836 ACGGAGGGAGTAAAAAGGAATC 57.782 45.455 0.00 0.00 0.00 2.52
2956 11803 4.567116 GGAACGGAGGGAGTAAAAAGGAAT 60.567 45.833 0.00 0.00 0.00 3.01
2959 11806 2.039348 TGGAACGGAGGGAGTAAAAAGG 59.961 50.000 0.00 0.00 0.00 3.11
2960 11807 3.412237 TGGAACGGAGGGAGTAAAAAG 57.588 47.619 0.00 0.00 0.00 2.27
2963 11810 4.376225 AATTTGGAACGGAGGGAGTAAA 57.624 40.909 0.00 0.00 0.00 2.01
2964 11811 4.533311 AGTAATTTGGAACGGAGGGAGTAA 59.467 41.667 0.00 0.00 0.00 2.24
2965 11812 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2966 11813 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2967 11814 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2968 11815 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2969 11816 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2970 11817 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2971 11818 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2972 11819 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
2973 11820 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
2974 11821 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
2975 11822 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
2976 11823 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
2977 11824 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
2978 11825 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
2979 11826 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
2980 11827 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
2981 11828 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
2982 11829 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
2983 11830 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
2984 11831 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
2985 11832 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
2986 11833 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
2987 11834 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
2988 11835 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
2989 11836 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
2990 11837 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
2991 11838 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
2992 11839 8.144478 TGTAGTTCTAGATACATCCATTTCTGC 58.856 37.037 2.64 0.00 0.00 4.26
3016 11863 9.381038 AGGTATGGATGTATCTAGTTGTATTGT 57.619 33.333 0.00 0.00 0.00 2.71
3017 11864 9.645059 CAGGTATGGATGTATCTAGTTGTATTG 57.355 37.037 0.00 0.00 0.00 1.90
3018 11865 8.314751 GCAGGTATGGATGTATCTAGTTGTATT 58.685 37.037 0.00 0.00 0.00 1.89
3019 11866 7.363007 CGCAGGTATGGATGTATCTAGTTGTAT 60.363 40.741 0.00 0.00 0.00 2.29
3020 11867 6.072119 CGCAGGTATGGATGTATCTAGTTGTA 60.072 42.308 0.00 0.00 0.00 2.41
3021 11868 5.279006 CGCAGGTATGGATGTATCTAGTTGT 60.279 44.000 0.00 0.00 0.00 3.32
3022 11869 5.048013 TCGCAGGTATGGATGTATCTAGTTG 60.048 44.000 0.00 0.00 0.00 3.16
3023 11870 5.047943 GTCGCAGGTATGGATGTATCTAGTT 60.048 44.000 0.00 0.00 0.00 2.24
3024 11871 4.459685 GTCGCAGGTATGGATGTATCTAGT 59.540 45.833 0.00 0.00 0.00 2.57
3025 11872 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
3026 11873 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
3027 11874 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
3028 11875 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
3029 11876 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
3030 11877 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
3031 11878 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
3032 11879 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
3033 11880 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
3034 11881 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
3035 11882 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
3036 11883 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
3037 11884 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
3038 11885 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
3039 11886 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
3040 11887 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
3041 11888 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
3042 11889 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
3043 11890 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
3044 11891 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
3045 11892 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3046 11893 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3047 11894 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3048 11895 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
3049 11896 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3050 11897 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3051 11898 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
3052 11899 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
3053 11900 1.341778 ACTACTCCCTCCGTTCCGAAT 60.342 52.381 0.00 0.00 0.00 3.34
3054 11901 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
3055 11902 0.911769 TACTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
3056 11903 1.978454 ATACTACTCCCTCCGTTCCG 58.022 55.000 0.00 0.00 0.00 4.30
3057 11904 4.750021 AAAATACTACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
3058 11905 5.362143 ACCTAAAATACTACTCCCTCCGTTC 59.638 44.000 0.00 0.00 0.00 3.95
3059 11906 5.275630 ACCTAAAATACTACTCCCTCCGTT 58.724 41.667 0.00 0.00 0.00 4.44
3060 11907 4.876580 ACCTAAAATACTACTCCCTCCGT 58.123 43.478 0.00 0.00 0.00 4.69
3061 11908 5.866159 AACCTAAAATACTACTCCCTCCG 57.134 43.478 0.00 0.00 0.00 4.63
3062 11909 7.124750 TGTGTAACCTAAAATACTACTCCCTCC 59.875 40.741 0.00 0.00 34.36 4.30
3063 11910 8.071177 TGTGTAACCTAAAATACTACTCCCTC 57.929 38.462 0.00 0.00 34.36 4.30
3064 11911 8.619683 ATGTGTAACCTAAAATACTACTCCCT 57.380 34.615 0.00 0.00 34.36 4.20
3065 11912 9.676861 AAATGTGTAACCTAAAATACTACTCCC 57.323 33.333 0.00 0.00 34.36 4.30
3312 12172 4.804108 CTCATACAGGAAGATCGTCATCC 58.196 47.826 10.88 6.41 34.63 3.51
3369 12229 8.087750 TCAACAGTTAATGGCTTCATTTTTAGG 58.912 33.333 0.00 0.00 41.04 2.69
3374 12234 6.040842 ACAGTCAACAGTTAATGGCTTCATTT 59.959 34.615 0.00 0.00 41.04 2.32


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

AutoCloner maintained by Alex Coulton.