Multiple sequence alignment - TraesCS7D01G104200

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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 TraesCS7D01G104200 chr7D 100.000 3825 0 0 1 3825 63461157 63464981 0.000000e+00 7064.0
1 TraesCS7D01G104200 chr7D 75.882 340 38 21 2781 3114 20427150 20426849 2.400000e-27 134.0
2 TraesCS7D01G104200 chr7B 93.928 1795 79 16 1393 3187 3882037 3883801 0.000000e+00 2684.0
3 TraesCS7D01G104200 chr7B 93.878 490 22 3 912 1399 3866718 3867201 0.000000e+00 732.0
4 TraesCS7D01G104200 chr7B 92.604 338 21 3 6 340 3866334 3866670 2.070000e-132 483.0
5 TraesCS7D01G104200 chr7B 85.551 263 14 9 3463 3724 3883798 3884037 1.760000e-63 254.0
6 TraesCS7D01G104200 chr4D 84.875 2314 232 70 1026 3305 505359046 505356817 0.000000e+00 2226.0
7 TraesCS7D01G104200 chr4D 81.800 1522 218 32 1208 2710 435198936 435197455 0.000000e+00 1221.0
8 TraesCS7D01G104200 chr4D 95.207 605 13 2 992 1593 418854649 418854058 0.000000e+00 942.0
9 TraesCS7D01G104200 chr4B 82.113 1571 224 35 1157 2710 535331734 535330204 0.000000e+00 1291.0
10 TraesCS7D01G104200 chr4B 79.310 1595 260 34 1160 2709 139593889 139592320 0.000000e+00 1053.0
11 TraesCS7D01G104200 chr4B 79.210 1443 243 31 1159 2591 460156847 460155452 0.000000e+00 950.0
12 TraesCS7D01G104200 chr4A 80.292 1573 244 36 1163 2710 36608008 36606477 0.000000e+00 1127.0
13 TraesCS7D01G104200 chr4A 79.183 1518 250 37 1160 2638 478191182 478192672 0.000000e+00 992.0
14 TraesCS7D01G104200 chr3B 79.571 1444 247 34 1175 2595 706028920 706027502 0.000000e+00 989.0
15 TraesCS7D01G104200 chr3B 79.107 1455 230 47 1190 2599 706754685 706756110 0.000000e+00 935.0
16 TraesCS7D01G104200 chr3B 78.760 1436 246 42 1176 2592 706182869 706184264 0.000000e+00 907.0
17 TraesCS7D01G104200 chr7A 92.857 686 22 3 948 1626 66251190 66251855 0.000000e+00 970.0
18 TraesCS7D01G104200 chr7A 93.439 503 28 5 415 915 661857051 661856552 0.000000e+00 741.0
19 TraesCS7D01G104200 chr7A 89.522 544 34 14 3151 3686 66251853 66252381 0.000000e+00 667.0
20 TraesCS7D01G104200 chr7A 93.662 142 7 1 3686 3825 66252523 66252664 1.080000e-50 211.0
21 TraesCS7D01G104200 chr3D 79.308 1445 246 38 1175 2595 533960118 533958703 0.000000e+00 963.0
22 TraesCS7D01G104200 chr3D 92.969 512 27 9 415 922 280409074 280408568 0.000000e+00 737.0
23 TraesCS7D01G104200 chr3D 99.359 312 2 0 992 1303 141356970 141356659 1.990000e-157 566.0
24 TraesCS7D01G104200 chr3D 98.980 294 3 0 992 1285 560962352 560962645 9.410000e-146 527.0
25 TraesCS7D01G104200 chr1D 94.212 501 27 2 414 912 283421598 283421098 0.000000e+00 763.0
26 TraesCS7D01G104200 chr1D 92.650 517 30 8 413 924 493775621 493775108 0.000000e+00 737.0
27 TraesCS7D01G104200 chr6D 93.491 507 30 3 407 910 104330408 104329902 0.000000e+00 750.0
28 TraesCS7D01G104200 chr6D 93.110 508 33 2 407 912 94520672 94521179 0.000000e+00 743.0
29 TraesCS7D01G104200 chr1B 93.613 501 28 4 415 911 256912827 256912327 0.000000e+00 745.0
30 TraesCS7D01G104200 chr5A 93.254 504 31 3 414 914 620282876 620283379 0.000000e+00 739.0
31 TraesCS7D01G104200 chr5A 80.584 994 130 34 1848 2819 689631005 689630053 0.000000e+00 708.0
32 TraesCS7D01G104200 chr5A 89.130 46 5 0 342 387 104083795 104083840 1.480000e-04 58.4
33 TraesCS7D01G104200 chr2D 92.927 509 31 5 408 914 613428102 613427597 0.000000e+00 736.0
34 TraesCS7D01G104200 chr2D 100.000 29 0 0 359 387 200250287 200250259 2.000000e-03 54.7
35 TraesCS7D01G104200 chr6B 76.930 1192 200 40 1141 2284 134838398 134839562 3.270000e-170 608.0
36 TraesCS7D01G104200 chr2A 94.118 34 2 0 355 388 738780779 738780812 7.000000e-03 52.8


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 TraesCS7D01G104200 chr7D 63461157 63464981 3824 False 7064.0 7064 100.000000 1 3825 1 chr7D.!!$F1 3824
1 TraesCS7D01G104200 chr7B 3882037 3884037 2000 False 1469.0 2684 89.739500 1393 3724 2 chr7B.!!$F2 2331
2 TraesCS7D01G104200 chr7B 3866334 3867201 867 False 607.5 732 93.241000 6 1399 2 chr7B.!!$F1 1393
3 TraesCS7D01G104200 chr4D 505356817 505359046 2229 True 2226.0 2226 84.875000 1026 3305 1 chr4D.!!$R3 2279
4 TraesCS7D01G104200 chr4D 435197455 435198936 1481 True 1221.0 1221 81.800000 1208 2710 1 chr4D.!!$R2 1502
5 TraesCS7D01G104200 chr4D 418854058 418854649 591 True 942.0 942 95.207000 992 1593 1 chr4D.!!$R1 601
6 TraesCS7D01G104200 chr4B 535330204 535331734 1530 True 1291.0 1291 82.113000 1157 2710 1 chr4B.!!$R3 1553
7 TraesCS7D01G104200 chr4B 139592320 139593889 1569 True 1053.0 1053 79.310000 1160 2709 1 chr4B.!!$R1 1549
8 TraesCS7D01G104200 chr4B 460155452 460156847 1395 True 950.0 950 79.210000 1159 2591 1 chr4B.!!$R2 1432
9 TraesCS7D01G104200 chr4A 36606477 36608008 1531 True 1127.0 1127 80.292000 1163 2710 1 chr4A.!!$R1 1547
10 TraesCS7D01G104200 chr4A 478191182 478192672 1490 False 992.0 992 79.183000 1160 2638 1 chr4A.!!$F1 1478
11 TraesCS7D01G104200 chr3B 706027502 706028920 1418 True 989.0 989 79.571000 1175 2595 1 chr3B.!!$R1 1420
12 TraesCS7D01G104200 chr3B 706754685 706756110 1425 False 935.0 935 79.107000 1190 2599 1 chr3B.!!$F2 1409
13 TraesCS7D01G104200 chr3B 706182869 706184264 1395 False 907.0 907 78.760000 1176 2592 1 chr3B.!!$F1 1416
14 TraesCS7D01G104200 chr7A 66251190 66252664 1474 False 616.0 970 92.013667 948 3825 3 chr7A.!!$F1 2877
15 TraesCS7D01G104200 chr3D 533958703 533960118 1415 True 963.0 963 79.308000 1175 2595 1 chr3D.!!$R3 1420
16 TraesCS7D01G104200 chr3D 280408568 280409074 506 True 737.0 737 92.969000 415 922 1 chr3D.!!$R2 507
17 TraesCS7D01G104200 chr1D 283421098 283421598 500 True 763.0 763 94.212000 414 912 1 chr1D.!!$R1 498
18 TraesCS7D01G104200 chr1D 493775108 493775621 513 True 737.0 737 92.650000 413 924 1 chr1D.!!$R2 511
19 TraesCS7D01G104200 chr6D 104329902 104330408 506 True 750.0 750 93.491000 407 910 1 chr6D.!!$R1 503
20 TraesCS7D01G104200 chr6D 94520672 94521179 507 False 743.0 743 93.110000 407 912 1 chr6D.!!$F1 505
21 TraesCS7D01G104200 chr1B 256912327 256912827 500 True 745.0 745 93.613000 415 911 1 chr1B.!!$R1 496
22 TraesCS7D01G104200 chr5A 620282876 620283379 503 False 739.0 739 93.254000 414 914 1 chr5A.!!$F2 500
23 TraesCS7D01G104200 chr5A 689630053 689631005 952 True 708.0 708 80.584000 1848 2819 1 chr5A.!!$R1 971
24 TraesCS7D01G104200 chr2D 613427597 613428102 505 True 736.0 736 92.927000 408 914 1 chr2D.!!$R2 506
25 TraesCS7D01G104200 chr6B 134838398 134839562 1164 False 608.0 608 76.930000 1141 2284 1 chr6B.!!$F1 1143

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
371 375 0.195096 GGTACCCCCTCCATCCCATA 59.805 60.0 0.0 0.0 0.0 2.74 F
2038 2120 0.179100 ATCATCAAGGTGCCTCGACG 60.179 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 2273 0.038744 CATGGTTCTTGGGCTCACCT 59.961 55.0 0.0 0.0 41.11 4.00 R
2923 3157 0.258774 ACTTGGACACTTGGGCACTT 59.741 50.0 0.0 0.0 0.00 3.16 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
34 35 8.845227 CAAGCAAAACAATATTTTTACCCCTTT 58.155 29.630 0.00 0.00 0.00 3.11
73 74 2.923655 CACACAATCATCGTCGTTAGCT 59.076 45.455 0.00 0.00 0.00 3.32
134 137 1.490910 GTTACTGGGGATGGAGAAGGG 59.509 57.143 0.00 0.00 0.00 3.95
165 168 2.197324 CGAGAGGGGGAGGAGGAG 59.803 72.222 0.00 0.00 0.00 3.69
170 173 3.695825 GGGGGAGGAGGAGTGGGA 61.696 72.222 0.00 0.00 0.00 4.37
173 176 2.037527 GGAGGAGGAGTGGGACGT 59.962 66.667 0.00 0.00 0.00 4.34
179 182 3.986006 GGAGTGGGACGTGACGCA 61.986 66.667 4.25 0.00 0.00 5.24
180 183 2.028484 GAGTGGGACGTGACGCAA 59.972 61.111 4.25 0.00 34.73 4.85
281 285 1.600636 ACGGGATGTGTTGTGCTGG 60.601 57.895 0.00 0.00 0.00 4.85
309 313 3.263602 TGCTTCGATTCGTATCTACCG 57.736 47.619 5.89 0.00 0.00 4.02
311 315 2.667724 GCTTCGATTCGTATCTACCGGG 60.668 54.545 6.32 0.00 0.00 5.73
328 332 1.003812 CGGGGTGGATGTGAAAGGTAA 59.996 52.381 0.00 0.00 0.00 2.85
333 337 5.506708 GGGTGGATGTGAAAGGTAAGTTAT 58.493 41.667 0.00 0.00 0.00 1.89
340 344 8.803235 GGATGTGAAAGGTAAGTTATTTTCCTT 58.197 33.333 14.93 7.98 39.75 3.36
360 364 5.443283 CCTTTTACATAGAAAGGTACCCCC 58.557 45.833 8.74 0.00 45.17 5.40
362 366 5.963214 TTTACATAGAAAGGTACCCCCTC 57.037 43.478 8.74 2.66 45.47 4.30
363 367 2.772930 ACATAGAAAGGTACCCCCTCC 58.227 52.381 8.74 0.00 45.47 4.30
364 368 2.046729 ACATAGAAAGGTACCCCCTCCA 59.953 50.000 8.74 0.00 45.47 3.86
365 369 3.312155 ACATAGAAAGGTACCCCCTCCAT 60.312 47.826 8.74 0.00 45.47 3.41
366 370 1.894699 AGAAAGGTACCCCCTCCATC 58.105 55.000 8.74 0.00 45.47 3.51
367 371 0.844660 GAAAGGTACCCCCTCCATCC 59.155 60.000 8.74 0.00 45.47 3.51
368 372 0.626574 AAAGGTACCCCCTCCATCCC 60.627 60.000 8.74 0.00 45.47 3.85
369 373 1.844296 AAGGTACCCCCTCCATCCCA 61.844 60.000 8.74 0.00 45.47 4.37
370 374 1.072930 GGTACCCCCTCCATCCCAT 60.073 63.158 0.00 0.00 0.00 4.00
371 375 0.195096 GGTACCCCCTCCATCCCATA 59.805 60.000 0.00 0.00 0.00 2.74
372 376 1.416907 GGTACCCCCTCCATCCCATAA 60.417 57.143 0.00 0.00 0.00 1.90
373 377 2.644151 GTACCCCCTCCATCCCATAAT 58.356 52.381 0.00 0.00 0.00 1.28
374 378 3.507166 GGTACCCCCTCCATCCCATAATA 60.507 52.174 0.00 0.00 0.00 0.98
375 379 3.621173 ACCCCCTCCATCCCATAATAT 57.379 47.619 0.00 0.00 0.00 1.28
376 380 4.746206 ACCCCCTCCATCCCATAATATA 57.254 45.455 0.00 0.00 0.00 0.86
377 381 5.062844 ACCCCCTCCATCCCATAATATAA 57.937 43.478 0.00 0.00 0.00 0.98
378 382 4.794067 ACCCCCTCCATCCCATAATATAAC 59.206 45.833 0.00 0.00 0.00 1.89
379 383 4.793520 CCCCCTCCATCCCATAATATAACA 59.206 45.833 0.00 0.00 0.00 2.41
380 384 5.255207 CCCCCTCCATCCCATAATATAACAA 59.745 44.000 0.00 0.00 0.00 2.83
381 385 6.187682 CCCCTCCATCCCATAATATAACAAC 58.812 44.000 0.00 0.00 0.00 3.32
382 386 5.880332 CCCTCCATCCCATAATATAACAACG 59.120 44.000 0.00 0.00 0.00 4.10
383 387 6.472887 CCTCCATCCCATAATATAACAACGT 58.527 40.000 0.00 0.00 0.00 3.99
384 388 6.940298 CCTCCATCCCATAATATAACAACGTT 59.060 38.462 0.00 0.00 0.00 3.99
385 389 7.447238 CCTCCATCCCATAATATAACAACGTTT 59.553 37.037 0.00 0.00 0.00 3.60
410 414 5.941948 ATGGAACGGAAAGAGTAAGTTTG 57.058 39.130 0.00 0.00 0.00 2.93
423 427 8.890124 AAGAGTAAGTTTGTTTTCTCTACTCC 57.110 34.615 0.00 0.00 34.84 3.85
591 598 3.580458 CCTCGTTCATCCTTATCTCCCAT 59.420 47.826 0.00 0.00 0.00 4.00
639 648 5.815233 AGGAAGTCTCTGAAACAATCTGA 57.185 39.130 0.00 0.00 35.08 3.27
687 697 4.431131 CCATGCCTCCGCCCAGTT 62.431 66.667 0.00 0.00 0.00 3.16
702 712 0.389391 CAGTTCGACCACCAGTCACT 59.611 55.000 0.00 0.00 46.69 3.41
755 766 9.345517 CTCTCATCTTTCTCGAGATATCATTTC 57.654 37.037 17.44 0.00 35.35 2.17
915 930 3.879295 GCATAGGCATCTTGCTAGTTTCA 59.121 43.478 0.00 0.00 44.28 2.69
916 931 4.260948 GCATAGGCATCTTGCTAGTTTCAC 60.261 45.833 0.00 0.00 44.28 3.18
917 932 3.423539 AGGCATCTTGCTAGTTTCACA 57.576 42.857 0.00 0.00 44.28 3.58
918 933 3.960571 AGGCATCTTGCTAGTTTCACAT 58.039 40.909 0.00 0.00 44.28 3.21
922 937 6.434028 AGGCATCTTGCTAGTTTCACATTAAA 59.566 34.615 0.00 0.00 44.28 1.52
923 938 6.749118 GGCATCTTGCTAGTTTCACATTAAAG 59.251 38.462 0.00 0.00 44.28 1.85
924 939 7.362056 GGCATCTTGCTAGTTTCACATTAAAGA 60.362 37.037 0.00 0.00 44.28 2.52
1713 1782 2.683859 TACAGCGTCGTCGTGGAGG 61.684 63.158 3.66 0.00 39.49 4.30
2007 2089 0.611062 ACGGAATCACGTCCTGGAGA 60.611 55.000 0.00 0.00 45.08 3.71
2038 2120 0.179100 ATCATCAAGGTGCCTCGACG 60.179 55.000 0.00 0.00 0.00 5.12
2043 2125 2.722201 AAGGTGCCTCGACGGATCC 61.722 63.158 0.00 0.00 33.16 3.36
2140 2273 1.255882 CATTGGCAGGCTGGTACAAA 58.744 50.000 17.64 0.00 38.70 2.83
2323 2519 1.072173 TCTGCCCATTATCATCCCGTG 59.928 52.381 0.00 0.00 0.00 4.94
2385 2587 4.987408 TCATGTGCATTTAACTGATGGG 57.013 40.909 0.00 0.00 0.00 4.00
2391 2601 6.767456 TGTGCATTTAACTGATGGGATTTTT 58.233 32.000 0.00 0.00 0.00 1.94
2392 2602 7.901029 TGTGCATTTAACTGATGGGATTTTTA 58.099 30.769 0.00 0.00 0.00 1.52
2393 2603 8.538701 TGTGCATTTAACTGATGGGATTTTTAT 58.461 29.630 0.00 0.00 0.00 1.40
2394 2604 9.382275 GTGCATTTAACTGATGGGATTTTTATT 57.618 29.630 0.00 0.00 0.00 1.40
2395 2605 9.956640 TGCATTTAACTGATGGGATTTTTATTT 57.043 25.926 0.00 0.00 0.00 1.40
2595 2805 0.400213 GGTGGTGATCCTGTTGTCCA 59.600 55.000 0.00 0.00 34.23 4.02
2610 2820 1.228245 TCCACTGGCTCCACTTTGC 60.228 57.895 0.00 0.00 0.00 3.68
2813 3032 1.371635 GCGACGCAAATTGCCTTGT 60.372 52.632 16.42 4.48 41.12 3.16
2820 3039 4.542735 ACGCAAATTGCCTTGTAAGTTAC 58.457 39.130 12.80 6.06 41.12 2.50
2894 3116 4.457603 TGTTTTCAGTGTTTGGATATCCGG 59.542 41.667 17.04 0.00 39.43 5.14
2908 3130 4.065281 CCGGCCCGTCGACTCTTT 62.065 66.667 14.70 0.00 0.00 2.52
2922 3156 4.876107 TCGACTCTTTTTCCATGATTAGCC 59.124 41.667 0.00 0.00 0.00 3.93
2923 3157 4.635765 CGACTCTTTTTCCATGATTAGCCA 59.364 41.667 0.00 0.00 0.00 4.75
2924 3158 5.123820 CGACTCTTTTTCCATGATTAGCCAA 59.876 40.000 0.00 0.00 0.00 4.52
2925 3159 6.521151 ACTCTTTTTCCATGATTAGCCAAG 57.479 37.500 0.00 0.00 0.00 3.61
2926 3160 6.012745 ACTCTTTTTCCATGATTAGCCAAGT 58.987 36.000 0.00 0.00 0.00 3.16
2927 3161 6.071728 ACTCTTTTTCCATGATTAGCCAAGTG 60.072 38.462 0.00 0.00 0.00 3.16
2928 3162 4.454728 TTTTCCATGATTAGCCAAGTGC 57.545 40.909 0.00 0.00 41.71 4.40
2929 3163 2.057137 TCCATGATTAGCCAAGTGCC 57.943 50.000 0.00 0.00 42.71 5.01
2930 3164 1.035139 CCATGATTAGCCAAGTGCCC 58.965 55.000 0.00 0.00 42.71 5.36
2954 3188 7.093640 CCCAAGTGTCCAAGTTAGTATACTACA 60.094 40.741 12.25 5.29 0.00 2.74
2955 3189 7.758528 CCAAGTGTCCAAGTTAGTATACTACAC 59.241 40.741 18.73 18.73 36.26 2.90
2956 3190 8.521176 CAAGTGTCCAAGTTAGTATACTACACT 58.479 37.037 21.54 21.54 42.73 3.55
2957 3191 9.745018 AAGTGTCCAAGTTAGTATACTACACTA 57.255 33.333 24.97 6.80 41.29 2.74
2958 3192 9.171877 AGTGTCCAAGTTAGTATACTACACTAC 57.828 37.037 24.09 15.38 40.78 2.73
2959 3193 9.171877 GTGTCCAAGTTAGTATACTACACTACT 57.828 37.037 18.95 14.15 34.54 2.57
2975 3209 5.373222 ACACTACTTACCATTCTGTTGCAA 58.627 37.500 0.00 0.00 0.00 4.08
2976 3210 5.470098 ACACTACTTACCATTCTGTTGCAAG 59.530 40.000 0.00 0.00 0.00 4.01
2977 3211 5.470098 CACTACTTACCATTCTGTTGCAAGT 59.530 40.000 0.00 0.00 0.00 3.16
2978 3212 6.017109 CACTACTTACCATTCTGTTGCAAGTT 60.017 38.462 0.00 0.00 0.00 2.66
2979 3213 5.186996 ACTTACCATTCTGTTGCAAGTTG 57.813 39.130 0.00 0.00 0.00 3.16
2980 3214 2.514205 ACCATTCTGTTGCAAGTTGC 57.486 45.000 21.17 21.17 45.29 4.17
3002 3236 7.230849 TGCAACCATGAAGTAATTGATCTTT 57.769 32.000 0.00 0.00 0.00 2.52
3028 3262 1.204941 GCAATCACGGACCTCTGTACT 59.795 52.381 0.00 0.00 33.39 2.73
3082 3317 0.948678 ACCGTGGTGTTACATTGCAC 59.051 50.000 0.00 0.00 35.07 4.57
3115 3350 3.093814 TGACATTTGAGGCTTGATGCAT 58.906 40.909 0.00 0.00 45.15 3.96
3124 3359 4.202080 TGAGGCTTGATGCATGCTAATTTC 60.202 41.667 20.33 8.48 45.15 2.17
3125 3360 3.958798 AGGCTTGATGCATGCTAATTTCT 59.041 39.130 20.33 5.74 45.15 2.52
3128 3363 4.976731 GCTTGATGCATGCTAATTTCTCTG 59.023 41.667 20.33 0.31 42.31 3.35
3149 3384 8.801299 TCTCTGTGCATTAACATGGAAATAAAA 58.199 29.630 0.00 0.00 31.56 1.52
3167 3402 3.825908 AAATTCCTTCCCAGCTGGTTA 57.174 42.857 30.63 16.19 34.77 2.85
3197 3442 3.131933 TGCTGTGGTTGTTTTGCATAGTT 59.868 39.130 0.00 0.00 0.00 2.24
3198 3443 4.339530 TGCTGTGGTTGTTTTGCATAGTTA 59.660 37.500 0.00 0.00 0.00 2.24
3199 3444 5.010516 TGCTGTGGTTGTTTTGCATAGTTAT 59.989 36.000 0.00 0.00 0.00 1.89
3200 3445 5.345741 GCTGTGGTTGTTTTGCATAGTTATG 59.654 40.000 0.00 0.00 36.78 1.90
3236 3481 2.126031 GTCGCAGGTCGGTTCTCC 60.126 66.667 0.00 0.00 39.05 3.71
3242 3487 2.280628 GCAGGTCGGTTCTCCTTTATG 58.719 52.381 0.00 0.00 30.91 1.90
3243 3488 2.354805 GCAGGTCGGTTCTCCTTTATGT 60.355 50.000 0.00 0.00 30.91 2.29
3244 3489 3.868754 GCAGGTCGGTTCTCCTTTATGTT 60.869 47.826 0.00 0.00 30.91 2.71
3307 3561 0.680618 CTTGCTGGGGTGCATTTCAA 59.319 50.000 0.00 0.00 42.96 2.69
3332 3586 3.454375 ACATAACTCCGAATAGCCAACG 58.546 45.455 0.00 0.00 0.00 4.10
3352 3609 7.065085 GCCAACGAGCTGAATCATTGTATATAT 59.935 37.037 0.00 0.00 0.00 0.86
3397 3654 3.525268 GGCCCACTTGGACATATTTTG 57.475 47.619 0.00 0.00 44.36 2.44
3398 3655 2.418609 GGCCCACTTGGACATATTTTGC 60.419 50.000 0.00 0.00 44.36 3.68
3406 3663 6.532657 CACTTGGACATATTTTGCTGAAATCC 59.467 38.462 2.55 0.00 38.80 3.01
3465 3722 3.648545 GCACCCTCCTCCTAGATAATTGT 59.351 47.826 0.00 0.00 0.00 2.71
3484 3741 5.499139 TTGTGTGCTTACTTCTTCCTTTG 57.501 39.130 0.00 0.00 0.00 2.77
3581 3838 2.094442 GTCTACTGTGTCTCCTCCAAGC 60.094 54.545 0.00 0.00 0.00 4.01
3603 3860 2.437897 CCCCTTCAAGCTGTGCCT 59.562 61.111 0.00 0.00 0.00 4.75
3635 3892 3.484953 TCTCCATGGTTGGTAGGTACT 57.515 47.619 12.58 0.00 44.06 2.73
3636 3893 3.104512 TCTCCATGGTTGGTAGGTACTG 58.895 50.000 12.58 0.00 44.06 2.74
3637 3894 2.838202 CTCCATGGTTGGTAGGTACTGT 59.162 50.000 12.58 0.00 44.06 3.55
3638 3895 4.028131 CTCCATGGTTGGTAGGTACTGTA 58.972 47.826 12.58 0.00 44.06 2.74
3639 3896 3.770933 TCCATGGTTGGTAGGTACTGTAC 59.229 47.826 12.58 9.46 44.06 2.90
3714 4113 4.151689 AGTCAAACATCATAAACCGTGTCG 59.848 41.667 0.00 0.00 0.00 4.35
3735 4134 0.321298 TTTAGGTGGAACTGAGCGGC 60.321 55.000 0.00 0.00 36.74 6.53
3791 4192 1.374758 GAAGCACACAGGGGACTCG 60.375 63.158 0.00 0.00 40.21 4.18
3803 4204 1.895131 GGGGACTCGTTTGTACCACTA 59.105 52.381 8.86 0.00 42.69 2.74
3811 4212 4.491676 TCGTTTGTACCACTAGAATGAGC 58.508 43.478 0.00 0.00 0.00 4.26
3814 4215 2.453521 TGTACCACTAGAATGAGCGGT 58.546 47.619 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.443323 GGGTAAAAATATTGTTTTGCTTGGTAT 57.557 29.630 0.00 0.00 34.60 2.73
8 9 7.977789 AGGGGTAAAAATATTGTTTTGCTTG 57.022 32.000 0.00 0.00 34.60 4.01
41 42 1.071542 TGATTGTGTGGTGACCGACAT 59.928 47.619 7.07 0.00 0.00 3.06
44 45 1.671556 CGATGATTGTGTGGTGACCGA 60.672 52.381 0.00 0.00 0.00 4.69
159 162 2.971452 GTCACGTCCCACTCCTCC 59.029 66.667 0.00 0.00 0.00 4.30
165 168 3.698463 CGTTGCGTCACGTCCCAC 61.698 66.667 0.00 0.00 35.34 4.61
170 173 4.903010 AAGGCCGTTGCGTCACGT 62.903 61.111 0.00 0.00 38.57 4.49
173 176 3.515611 AAAAAGGCCGTTGCGTCA 58.484 50.000 4.14 0.00 38.85 4.35
289 293 2.031420 CCGGTAGATACGAATCGAAGCA 60.031 50.000 10.55 0.00 37.19 3.91
290 294 2.582687 CCGGTAGATACGAATCGAAGC 58.417 52.381 10.55 0.00 37.19 3.86
294 298 1.068748 CACCCCGGTAGATACGAATCG 60.069 57.143 0.00 0.00 37.19 3.34
309 313 2.041216 ACTTACCTTTCACATCCACCCC 59.959 50.000 0.00 0.00 0.00 4.95
311 315 7.462571 AAATAACTTACCTTTCACATCCACC 57.537 36.000 0.00 0.00 0.00 4.61
353 357 2.127651 TTATGGGATGGAGGGGGTAC 57.872 55.000 0.00 0.00 0.00 3.34
355 359 3.621173 ATATTATGGGATGGAGGGGGT 57.379 47.619 0.00 0.00 0.00 4.95
356 360 4.793520 TGTTATATTATGGGATGGAGGGGG 59.206 45.833 0.00 0.00 0.00 5.40
357 361 6.187682 GTTGTTATATTATGGGATGGAGGGG 58.812 44.000 0.00 0.00 0.00 4.79
358 362 5.880332 CGTTGTTATATTATGGGATGGAGGG 59.120 44.000 0.00 0.00 0.00 4.30
359 363 6.472887 ACGTTGTTATATTATGGGATGGAGG 58.527 40.000 0.00 0.00 0.00 4.30
360 364 7.979444 AACGTTGTTATATTATGGGATGGAG 57.021 36.000 0.00 0.00 0.00 3.86
361 365 8.754991 AAAACGTTGTTATATTATGGGATGGA 57.245 30.769 0.00 0.00 0.00 3.41
370 374 9.985318 CCGTTCCATAAAAACGTTGTTATATTA 57.015 29.630 20.64 8.71 46.03 0.98
371 375 8.728833 TCCGTTCCATAAAAACGTTGTTATATT 58.271 29.630 20.64 0.62 46.03 1.28
372 376 8.266392 TCCGTTCCATAAAAACGTTGTTATAT 57.734 30.769 20.64 2.30 46.03 0.86
373 377 7.664082 TCCGTTCCATAAAAACGTTGTTATA 57.336 32.000 20.64 6.51 46.03 0.98
374 378 6.557291 TCCGTTCCATAAAAACGTTGTTAT 57.443 33.333 16.45 16.45 46.03 1.89
375 379 5.998454 TCCGTTCCATAAAAACGTTGTTA 57.002 34.783 13.17 13.17 46.03 2.41
376 380 4.897025 TCCGTTCCATAAAAACGTTGTT 57.103 36.364 9.06 9.06 46.03 2.83
377 381 4.897025 TTCCGTTCCATAAAAACGTTGT 57.103 36.364 0.00 0.00 46.03 3.32
378 382 5.512473 TCTTTCCGTTCCATAAAAACGTTG 58.488 37.500 0.00 0.00 46.03 4.10
379 383 5.297527 ACTCTTTCCGTTCCATAAAAACGTT 59.702 36.000 0.00 0.00 46.03 3.99
380 384 4.818005 ACTCTTTCCGTTCCATAAAAACGT 59.182 37.500 7.51 0.00 46.03 3.99
381 385 5.352643 ACTCTTTCCGTTCCATAAAAACG 57.647 39.130 1.64 1.64 46.79 3.60
382 386 7.868775 ACTTACTCTTTCCGTTCCATAAAAAC 58.131 34.615 0.00 0.00 0.00 2.43
383 387 8.454570 AACTTACTCTTTCCGTTCCATAAAAA 57.545 30.769 0.00 0.00 0.00 1.94
384 388 8.347035 CAAACTTACTCTTTCCGTTCCATAAAA 58.653 33.333 0.00 0.00 0.00 1.52
385 389 7.499895 ACAAACTTACTCTTTCCGTTCCATAAA 59.500 33.333 0.00 0.00 0.00 1.40
389 393 4.773013 ACAAACTTACTCTTTCCGTTCCA 58.227 39.130 0.00 0.00 0.00 3.53
434 440 2.781923 CACACCATCATCACCAACTCA 58.218 47.619 0.00 0.00 0.00 3.41
660 670 1.402896 GGAGGCATGGAGATGGACGA 61.403 60.000 0.00 0.00 0.00 4.20
702 712 2.682494 GAGGAGTGGGGCGTGGTA 60.682 66.667 0.00 0.00 0.00 3.25
755 766 7.776933 TGGTATCTCGAGAATTTCATTGAAG 57.223 36.000 20.91 0.00 0.00 3.02
824 837 3.737559 TTGACCCATGCAGGAGTAATT 57.262 42.857 0.00 0.00 41.22 1.40
922 937 7.746703 AGGGAAAGTCACAAACTAACTTATCT 58.253 34.615 0.00 0.00 37.17 1.98
923 938 7.981102 AGGGAAAGTCACAAACTAACTTATC 57.019 36.000 0.00 0.00 37.17 1.75
924 939 7.881751 GGTAGGGAAAGTCACAAACTAACTTAT 59.118 37.037 0.00 0.00 37.17 1.73
931 946 3.974642 AGAGGTAGGGAAAGTCACAAACT 59.025 43.478 0.00 0.00 41.10 2.66
943 958 1.568504 ACGAAATGCAGAGGTAGGGA 58.431 50.000 0.00 0.00 0.00 4.20
1694 1763 1.511464 CTCCACGACGACGCTGTAC 60.511 63.158 7.30 0.00 43.96 2.90
1713 1782 1.700042 ATGAAGTCCAGATCCCGGCC 61.700 60.000 0.00 0.00 0.00 6.13
2007 2089 2.424601 CCTTGATGATTGTGTTGCCGAT 59.575 45.455 0.00 0.00 0.00 4.18
2038 2120 2.945668 CTCCGAACAAATGGAAGGATCC 59.054 50.000 2.48 2.48 46.76 3.36
2043 2125 3.403038 ACAGTCTCCGAACAAATGGAAG 58.597 45.455 0.00 0.00 32.89 3.46
2140 2273 0.038744 CATGGTTCTTGGGCTCACCT 59.961 55.000 0.00 0.00 41.11 4.00
2813 3032 4.081862 CAGGAACAGGACATCGGTAACTTA 60.082 45.833 0.00 0.00 0.00 2.24
2820 3039 0.391661 CCACAGGAACAGGACATCGG 60.392 60.000 0.00 0.00 0.00 4.18
2865 3087 4.561105 TCCAAACACTGAAAACAAACCAC 58.439 39.130 0.00 0.00 0.00 4.16
2866 3088 4.873746 TCCAAACACTGAAAACAAACCA 57.126 36.364 0.00 0.00 0.00 3.67
2867 3089 6.645003 GGATATCCAAACACTGAAAACAAACC 59.355 38.462 17.34 0.00 35.64 3.27
2894 3116 0.601841 TGGAAAAAGAGTCGACGGGC 60.602 55.000 10.46 3.92 0.00 6.13
2908 3130 2.760092 GGCACTTGGCTAATCATGGAAA 59.240 45.455 0.00 0.00 44.01 3.13
2922 3156 0.670162 CTTGGACACTTGGGCACTTG 59.330 55.000 0.00 0.00 0.00 3.16
2923 3157 0.258774 ACTTGGACACTTGGGCACTT 59.741 50.000 0.00 0.00 0.00 3.16
2924 3158 0.258774 AACTTGGACACTTGGGCACT 59.741 50.000 0.00 0.00 0.00 4.40
2925 3159 1.880027 CTAACTTGGACACTTGGGCAC 59.120 52.381 0.00 0.00 0.00 5.01
2926 3160 1.493022 ACTAACTTGGACACTTGGGCA 59.507 47.619 0.00 0.00 0.00 5.36
2927 3161 2.271944 ACTAACTTGGACACTTGGGC 57.728 50.000 0.00 0.00 0.00 5.36
2928 3162 6.295719 AGTATACTAACTTGGACACTTGGG 57.704 41.667 2.75 0.00 0.00 4.12
2929 3163 7.758528 GTGTAGTATACTAACTTGGACACTTGG 59.241 40.741 18.95 0.00 43.54 3.61
2930 3164 8.521176 AGTGTAGTATACTAACTTGGACACTTG 58.479 37.037 21.54 0.00 41.02 3.16
2954 3188 5.621193 ACTTGCAACAGAATGGTAAGTAGT 58.379 37.500 0.00 0.00 43.62 2.73
2955 3189 6.373779 CAACTTGCAACAGAATGGTAAGTAG 58.626 40.000 0.00 0.00 43.62 2.57
2956 3190 5.278266 GCAACTTGCAACAGAATGGTAAGTA 60.278 40.000 8.97 0.00 44.26 2.24
2957 3191 4.499696 GCAACTTGCAACAGAATGGTAAGT 60.500 41.667 8.97 0.00 44.26 2.24
2958 3192 3.983344 GCAACTTGCAACAGAATGGTAAG 59.017 43.478 8.97 0.00 44.26 2.34
2959 3193 3.976169 GCAACTTGCAACAGAATGGTAA 58.024 40.909 8.97 0.00 44.26 2.85
2975 3209 6.435277 AGATCAATTACTTCATGGTTGCAACT 59.565 34.615 27.64 7.56 0.00 3.16
2976 3210 6.624423 AGATCAATTACTTCATGGTTGCAAC 58.376 36.000 21.59 21.59 0.00 4.17
2977 3211 6.839124 AGATCAATTACTTCATGGTTGCAA 57.161 33.333 0.00 0.00 0.00 4.08
2978 3212 6.839124 AAGATCAATTACTTCATGGTTGCA 57.161 33.333 0.00 0.00 0.00 4.08
2979 3213 6.532657 CCAAAGATCAATTACTTCATGGTTGC 59.467 38.462 0.00 0.00 0.00 4.17
2980 3214 7.605449 ACCAAAGATCAATTACTTCATGGTTG 58.395 34.615 0.00 0.00 35.20 3.77
2981 3215 7.781324 ACCAAAGATCAATTACTTCATGGTT 57.219 32.000 0.00 0.00 35.20 3.67
2990 3224 6.311200 GTGATTGCCAACCAAAGATCAATTAC 59.689 38.462 0.00 0.00 36.92 1.89
3002 3236 1.602323 GGTCCGTGATTGCCAACCA 60.602 57.895 0.00 0.00 0.00 3.67
3028 3262 2.033675 CACAGCAAGCATGAAACACAGA 59.966 45.455 0.00 0.00 0.00 3.41
3095 3330 3.444916 CATGCATCAAGCCTCAAATGTC 58.555 45.455 0.00 0.00 44.83 3.06
3100 3335 2.423446 TAGCATGCATCAAGCCTCAA 57.577 45.000 21.98 0.00 44.83 3.02
3115 3350 6.816134 TGTTAATGCACAGAGAAATTAGCA 57.184 33.333 0.00 0.00 36.34 3.49
3124 3359 8.984891 TTTTATTTCCATGTTAATGCACAGAG 57.015 30.769 0.00 0.00 31.93 3.35
3125 3360 9.941325 AATTTTATTTCCATGTTAATGCACAGA 57.059 25.926 0.00 0.00 31.93 3.41
3128 3363 9.382275 AGGAATTTTATTTCCATGTTAATGCAC 57.618 29.630 6.05 0.00 46.40 4.57
3149 3384 1.285078 GGTAACCAGCTGGGAAGGAAT 59.715 52.381 35.42 11.03 41.15 3.01
3171 3406 1.393196 GCAAAACAACCACAGCACAAC 59.607 47.619 0.00 0.00 0.00 3.32
3197 3442 7.330946 GCGACAATAATTGACTAGGCATACATA 59.669 37.037 0.00 0.00 0.00 2.29
3198 3443 6.147821 GCGACAATAATTGACTAGGCATACAT 59.852 38.462 0.00 0.00 0.00 2.29
3199 3444 5.465390 GCGACAATAATTGACTAGGCATACA 59.535 40.000 0.00 0.00 0.00 2.29
3200 3445 5.465390 TGCGACAATAATTGACTAGGCATAC 59.535 40.000 0.00 0.00 0.00 2.39
3207 3452 4.109766 CGACCTGCGACAATAATTGACTA 58.890 43.478 0.00 0.00 44.57 2.59
3259 3504 8.641498 AATTTCACAACTGAAGAACCAGATAT 57.359 30.769 0.00 0.00 37.70 1.63
3307 3561 3.646162 TGGCTATTCGGAGTTATGTCCAT 59.354 43.478 0.00 0.00 36.23 3.41
3352 3609 7.390440 CCTAGTTTGACAACCTCAACATGATAA 59.610 37.037 0.00 0.00 38.70 1.75
3377 3634 2.418609 GCAAAATATGTCCAAGTGGGCC 60.419 50.000 0.00 0.00 39.61 5.80
3397 3654 8.992835 AATAGTGATTTCAAAAGGATTTCAGC 57.007 30.769 0.00 0.00 37.28 4.26
3465 3722 3.486383 CCCAAAGGAAGAAGTAAGCACA 58.514 45.455 0.00 0.00 33.47 4.57
3484 3741 3.956744 ACTGTTTTAGAAGGAGATGCCC 58.043 45.455 0.00 0.00 37.37 5.36
3581 3838 2.036256 CAGCTTGAAGGGGGTGGG 59.964 66.667 0.00 0.00 0.00 4.61
3657 3914 9.760660 GTAGCTTATCAGTTGAAACATGTAAAG 57.239 33.333 0.00 0.00 0.00 1.85
3714 4113 1.439679 CGCTCAGTTCCACCTAAACC 58.560 55.000 0.00 0.00 0.00 3.27
3735 4134 3.447742 TCAGTTGCATCTACGTAGCATG 58.552 45.455 18.00 19.96 38.19 4.06
3778 4177 1.069668 GTACAAACGAGTCCCCTGTGT 59.930 52.381 0.00 0.00 0.00 3.72
3783 4182 0.683412 AGTGGTACAAACGAGTCCCC 59.317 55.000 0.00 0.00 44.16 4.81
3784 4183 2.821969 TCTAGTGGTACAAACGAGTCCC 59.178 50.000 0.00 0.00 44.16 4.46
3791 4192 3.617263 CCGCTCATTCTAGTGGTACAAAC 59.383 47.826 0.00 0.00 44.16 2.93


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

AutoCloner maintained by Alex Coulton.