Multiple sequence alignment - TraesCS7A01G258400

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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 TraesCS7A01G258400 chr7A 100.000 3570 0 0 1 3570 249593737 249590168 0.000000e+00 6593
1 TraesCS7A01G258400 chr7D 93.510 1926 76 12 1 1918 234806061 234804177 0.000000e+00 2819
2 TraesCS7A01G258400 chr7D 93.546 1503 54 13 1916 3409 234804095 234802627 0.000000e+00 2198
3 TraesCS7A01G258400 chr7B 91.061 1734 85 25 1710 3409 210860102 210858405 0.000000e+00 2279
4 TraesCS7A01G258400 chr7B 92.366 1179 51 20 515 1679 210861256 210860103 0.000000e+00 1642
5 TraesCS7A01G258400 chr7B 95.281 445 21 0 1 445 210861725 210861281 0.000000e+00 706
6 TraesCS7A01G258400 chr1D 90.361 166 13 3 3405 3570 221889418 221889256 7.760000e-52 215
7 TraesCS7A01G258400 chr1B 90.419 167 10 3 3405 3570 688760189 688760350 7.760000e-52 215
8 TraesCS7A01G258400 chr1B 96.629 89 3 0 3482 3570 635545153 635545065 7.990000e-32 148
9 TraesCS7A01G258400 chr6A 97.753 89 2 0 3482 3570 32582955 32583043 1.720000e-33 154
10 TraesCS7A01G258400 chr6A 96.629 89 3 0 3482 3570 543392399 543392311 7.990000e-32 148
11 TraesCS7A01G258400 chr2B 97.753 89 2 0 3482 3570 776250588 776250676 1.720000e-33 154
12 TraesCS7A01G258400 chr2B 95.294 85 3 1 3398 3481 33847661 33847577 2.240000e-27 134
13 TraesCS7A01G258400 chr2B 93.333 90 3 3 3394 3481 11578874 11578962 2.890000e-26 130
14 TraesCS7A01G258400 chr2B 90.722 97 4 5 3386 3481 209752492 209752584 1.350000e-24 124
15 TraesCS7A01G258400 chr6B 96.629 89 3 0 3482 3570 42350220 42350308 7.990000e-32 148
16 TraesCS7A01G258400 chr5B 96.629 89 3 0 3482 3570 596082263 596082351 7.990000e-32 148
17 TraesCS7A01G258400 chr5B 94.253 87 1 4 3396 3481 689032448 689032365 2.890000e-26 130
18 TraesCS7A01G258400 chr5A 96.629 89 3 0 3482 3570 577567861 577567949 7.990000e-32 148
19 TraesCS7A01G258400 chr4A 97.500 80 1 1 3403 3481 11180470 11180549 6.220000e-28 135
20 TraesCS7A01G258400 chr3B 96.386 83 2 1 3400 3481 606376361 606376279 6.220000e-28 135
21 TraesCS7A01G258400 chr3A 94.253 87 4 1 3396 3481 741191132 741191046 8.040000e-27 132


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 TraesCS7A01G258400 chr7A 249590168 249593737 3569 True 6593.000000 6593 100.000000 1 3570 1 chr7A.!!$R1 3569
1 TraesCS7A01G258400 chr7D 234802627 234806061 3434 True 2508.500000 2819 93.528000 1 3409 2 chr7D.!!$R1 3408
2 TraesCS7A01G258400 chr7B 210858405 210861725 3320 True 1542.333333 2279 92.902667 1 3409 3 chr7B.!!$R1 3408

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
898 913 0.447801 ACAGCATGGCGATCGTTTTC 59.552 50.0 17.81 5.08 43.62 2.29 F
1663 1687 0.627469 AGGGTGGTCTATGCCCCAAT 60.627 55.0 0.00 0.00 43.32 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2510 1.335689 GGCAGCTTGTTTGCAGAGAAG 60.336 52.381 9.54 9.54 43.28 2.85 R
3447 3596 0.032130 ATAGGGTGAGTGTATGCGCG 59.968 55.000 0.00 0.00 0.00 6.86 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
89 90 6.084326 TCACAGAAAAGCCAGGTTTATTTC 57.916 37.500 0.00 0.00 0.00 2.17
95 96 1.359130 AGCCAGGTTTATTTCAGCCCT 59.641 47.619 0.00 0.00 0.00 5.19
98 99 2.943033 CCAGGTTTATTTCAGCCCTACG 59.057 50.000 0.00 0.00 0.00 3.51
164 165 1.871080 AACCTCGTCAAAGTGCTCAG 58.129 50.000 0.00 0.00 0.00 3.35
206 207 3.495100 CCTGATAGGATCCCCGTTTCTTG 60.495 52.174 8.55 0.00 37.67 3.02
234 235 9.722184 CTCCAGATCATACAAAGATATCACATT 57.278 33.333 5.32 0.00 0.00 2.71
285 286 3.472652 TCCATTTTGCTGTAGTCGTGTT 58.527 40.909 0.00 0.00 0.00 3.32
286 287 3.496884 TCCATTTTGCTGTAGTCGTGTTC 59.503 43.478 0.00 0.00 0.00 3.18
318 319 1.693083 CTAGCTGTAAACCACGCGCC 61.693 60.000 5.73 0.00 33.65 6.53
331 332 1.019278 ACGCGCCGATGATTCTTTGT 61.019 50.000 5.73 0.00 0.00 2.83
463 464 2.104622 TGTTGAGTGTTGAGGATGCTGA 59.895 45.455 0.00 0.00 0.00 4.26
674 683 2.647683 TGTATGTTCAACCCACTGCA 57.352 45.000 0.00 0.00 0.00 4.41
698 707 2.385315 CATATGCAACGTCGAGTCGAT 58.615 47.619 19.75 0.00 38.42 3.59
766 781 9.565213 TGCATTTTTCCTTTGTTTAACAAATTG 57.435 25.926 21.33 15.83 45.79 2.32
818 833 4.679197 TGCGTTGAGAAATTTGTAATGCAC 59.321 37.500 15.83 0.00 38.07 4.57
847 862 7.582667 TTGCACTACACTAGAAGAGCATATA 57.417 36.000 13.68 2.23 0.00 0.86
848 863 6.971602 TGCACTACACTAGAAGAGCATATAC 58.028 40.000 0.00 0.00 0.00 1.47
856 871 8.709308 ACACTAGAAGAGCATATACCATTTTCT 58.291 33.333 0.00 0.00 0.00 2.52
882 897 7.248437 TGTACTAGACGAACACATTATCACAG 58.752 38.462 0.00 0.00 0.00 3.66
898 913 0.447801 ACAGCATGGCGATCGTTTTC 59.552 50.000 17.81 5.08 43.62 2.29
925 941 2.357637 CCGCGTGGACAAATTTGGATAT 59.642 45.455 21.74 0.74 37.49 1.63
926 942 3.562141 CCGCGTGGACAAATTTGGATATA 59.438 43.478 21.74 1.53 37.49 0.86
966 982 8.762426 AGAAACAAGACTGTAAATAAACTCGTC 58.238 33.333 0.00 0.00 33.45 4.20
1051 1067 2.811799 GCAAAGTGCAACGGGGTT 59.188 55.556 0.00 0.00 45.86 4.11
1052 1068 1.591327 GCAAAGTGCAACGGGGTTG 60.591 57.895 4.19 4.19 45.86 3.77
1053 1069 1.067250 CAAAGTGCAACGGGGTTGG 59.933 57.895 10.19 0.00 45.86 3.77
1054 1070 1.380650 AAAGTGCAACGGGGTTGGT 60.381 52.632 10.19 0.00 45.86 3.67
1055 1071 0.973496 AAAGTGCAACGGGGTTGGTT 60.973 50.000 10.19 0.00 45.86 3.67
1073 1089 1.406860 TTTTGGTTCCCCTTGCTGCC 61.407 55.000 0.00 0.00 0.00 4.85
1144 1160 1.383456 GCCGGCAATTGCATAGTCCA 61.383 55.000 30.32 0.00 44.36 4.02
1179 1195 2.446036 GAGCCCACCCTATCCGGT 60.446 66.667 0.00 0.00 36.18 5.28
1353 1372 2.125350 GCTTCAGGGAGGCAGTCG 60.125 66.667 0.00 0.00 34.72 4.18
1354 1373 2.650116 GCTTCAGGGAGGCAGTCGA 61.650 63.158 0.00 0.00 34.72 4.20
1355 1374 1.515020 CTTCAGGGAGGCAGTCGAG 59.485 63.158 0.00 0.00 0.00 4.04
1356 1375 1.954362 CTTCAGGGAGGCAGTCGAGG 61.954 65.000 0.00 0.00 0.00 4.63
1357 1376 2.681778 CAGGGAGGCAGTCGAGGT 60.682 66.667 0.00 0.00 0.00 3.85
1358 1377 2.363147 AGGGAGGCAGTCGAGGTC 60.363 66.667 0.00 0.00 0.00 3.85
1514 1533 3.443145 TCCTCTTCGTCCTCTTCTTCT 57.557 47.619 0.00 0.00 0.00 2.85
1600 1619 4.323417 TGAACATTTCGCACCTGACTAAT 58.677 39.130 0.00 0.00 0.00 1.73
1618 1639 5.393866 ACTAATGGGTCAAAATTCTGGTGT 58.606 37.500 0.00 0.00 0.00 4.16
1663 1687 0.627469 AGGGTGGTCTATGCCCCAAT 60.627 55.000 0.00 0.00 43.32 3.16
1698 1722 3.624777 CCTGCCTTTATGGTGATTGAGT 58.375 45.455 0.00 0.00 38.35 3.41
1768 1792 3.942130 AGCTTGGAATTTGGCAAGTAC 57.058 42.857 0.00 0.00 0.00 2.73
1806 1830 3.586100 ATTTGGGCGGTGTTGAATAAC 57.414 42.857 0.00 0.00 37.32 1.89
1827 1851 3.055094 ACAGAGGTCGAATGTAGGCATTT 60.055 43.478 0.00 0.00 44.61 2.32
1846 1870 2.949177 TGTGTCCATGGTTACTGCTT 57.051 45.000 12.58 0.00 0.00 3.91
2075 2192 7.023575 GGAATTTGCTATATTATGGTCTTGCG 58.976 38.462 0.00 0.00 0.00 4.85
2181 2298 2.478292 CTGGCCTTAGAGGGTAGGAAA 58.522 52.381 3.32 0.00 35.37 3.13
2392 2510 6.515272 TTTGTATGAGCCCTGATTTTTCTC 57.485 37.500 0.00 0.00 0.00 2.87
2808 2926 6.480320 GGTGTGTGACTATCAGATAAATGTCC 59.520 42.308 6.05 0.70 0.00 4.02
2813 2931 6.703607 GTGACTATCAGATAAATGTCCCACAG 59.296 42.308 6.05 0.00 0.00 3.66
2905 3023 7.920682 ACAAGTGGATATTTTGTTTTGAGACAC 59.079 33.333 0.00 0.00 31.38 3.67
2908 3026 8.084073 AGTGGATATTTTGTTTTGAGACACATG 58.916 33.333 0.00 0.00 0.00 3.21
3026 3174 4.942761 TGAGCAAAGAAAATTGAAGGCT 57.057 36.364 0.00 0.00 31.84 4.58
3027 3175 6.403866 TTGAGCAAAGAAAATTGAAGGCTA 57.596 33.333 0.00 0.00 31.84 3.93
3028 3176 5.772521 TGAGCAAAGAAAATTGAAGGCTAC 58.227 37.500 0.00 0.00 31.84 3.58
3029 3177 5.536161 TGAGCAAAGAAAATTGAAGGCTACT 59.464 36.000 0.00 0.00 31.84 2.57
3030 3178 6.018589 AGCAAAGAAAATTGAAGGCTACTC 57.981 37.500 0.00 0.00 31.84 2.59
3031 3179 5.047731 AGCAAAGAAAATTGAAGGCTACTCC 60.048 40.000 0.00 0.00 31.84 3.85
3197 3346 8.637281 TTTGACATGCACATATCAATTCATTC 57.363 30.769 5.25 0.00 34.60 2.67
3258 3407 6.280855 TCGGAGTTCTCACATATCTGAAAA 57.719 37.500 2.24 0.00 0.00 2.29
3259 3408 6.333416 TCGGAGTTCTCACATATCTGAAAAG 58.667 40.000 2.24 0.00 0.00 2.27
3269 3418 8.565896 TCACATATCTGAAAAGTAGCACATTT 57.434 30.769 0.00 0.00 0.00 2.32
3276 3425 7.990917 TCTGAAAAGTAGCACATTTAAACACA 58.009 30.769 0.00 0.00 0.00 3.72
3289 3438 5.814764 TTTAAACACACGGCAGTTTTCTA 57.185 34.783 6.67 0.00 38.71 2.10
3292 3441 1.414919 ACACACGGCAGTTTTCTAGGA 59.585 47.619 0.00 0.00 0.00 2.94
3337 3486 6.538381 ACGAAGTTTTTGGCATCAATCTTTTT 59.462 30.769 0.00 0.00 37.78 1.94
3338 3487 6.847289 CGAAGTTTTTGGCATCAATCTTTTTG 59.153 34.615 0.00 0.00 32.28 2.44
3339 3488 7.465781 CGAAGTTTTTGGCATCAATCTTTTTGT 60.466 33.333 0.00 0.00 32.28 2.83
3340 3489 7.250445 AGTTTTTGGCATCAATCTTTTTGTC 57.750 32.000 0.00 0.00 32.28 3.18
3346 3495 4.097892 GGCATCAATCTTTTTGTCGGGTAT 59.902 41.667 0.00 0.00 0.00 2.73
3391 3540 8.732746 AGATAACCAACATGATAAACACCTAC 57.267 34.615 0.00 0.00 0.00 3.18
3434 3583 3.917988 TGAGCATCAGTACAGACACAAG 58.082 45.455 0.00 0.00 42.56 3.16
3435 3584 2.670414 GAGCATCAGTACAGACACAAGC 59.330 50.000 0.00 0.00 33.17 4.01
3436 3585 1.391485 GCATCAGTACAGACACAAGCG 59.609 52.381 0.00 0.00 0.00 4.68
3437 3586 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
3438 3587 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
3439 3588 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
3440 3589 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
3441 3590 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
3442 3591 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
3443 3592 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
3444 3593 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
3445 3594 3.448686 ACAGACACAAGCGCTCATATAC 58.551 45.455 12.06 1.00 0.00 1.47
3446 3595 3.119137 ACAGACACAAGCGCTCATATACA 60.119 43.478 12.06 0.00 0.00 2.29
3447 3596 3.243877 CAGACACAAGCGCTCATATACAC 59.756 47.826 12.06 0.00 0.00 2.90
3448 3597 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
3452 3601 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
3453 3602 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
3454 3603 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
3455 3604 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
3456 3605 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
3457 3606 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
3458 3607 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
3459 3608 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
3460 3609 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
3461 3610 1.556564 ATACACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
3462 3611 0.457166 TACACGCGCATACACTCACC 60.457 55.000 5.73 0.00 0.00 4.02
3463 3612 2.125673 ACGCGCATACACTCACCC 60.126 61.111 5.73 0.00 0.00 4.61
3464 3613 2.184322 CGCGCATACACTCACCCT 59.816 61.111 8.75 0.00 0.00 4.34
3465 3614 1.317431 ACGCGCATACACTCACCCTA 61.317 55.000 5.73 0.00 0.00 3.53
3466 3615 0.032130 CGCGCATACACTCACCCTAT 59.968 55.000 8.75 0.00 0.00 2.57
3467 3616 1.502231 GCGCATACACTCACCCTATG 58.498 55.000 0.30 0.00 0.00 2.23
3468 3617 1.068588 GCGCATACACTCACCCTATGA 59.931 52.381 0.30 0.00 35.45 2.15
3469 3618 2.483013 GCGCATACACTCACCCTATGAA 60.483 50.000 0.30 0.00 36.69 2.57
3470 3619 3.123804 CGCATACACTCACCCTATGAAC 58.876 50.000 0.00 0.00 36.69 3.18
3471 3620 3.123804 GCATACACTCACCCTATGAACG 58.876 50.000 0.00 0.00 36.69 3.95
3472 3621 2.953466 TACACTCACCCTATGAACGC 57.047 50.000 0.00 0.00 36.69 4.84
3473 3622 0.973632 ACACTCACCCTATGAACGCA 59.026 50.000 0.00 0.00 36.69 5.24
3474 3623 1.337823 ACACTCACCCTATGAACGCAC 60.338 52.381 0.00 0.00 36.69 5.34
3475 3624 0.973632 ACTCACCCTATGAACGCACA 59.026 50.000 0.00 0.00 36.69 4.57
3476 3625 1.337823 ACTCACCCTATGAACGCACAC 60.338 52.381 0.00 0.00 36.69 3.82
3477 3626 0.682292 TCACCCTATGAACGCACACA 59.318 50.000 0.00 0.00 33.02 3.72
3478 3627 0.796312 CACCCTATGAACGCACACAC 59.204 55.000 0.00 0.00 0.00 3.82
3479 3628 0.669318 ACCCTATGAACGCACACACG 60.669 55.000 0.00 0.00 39.50 4.49
3480 3629 1.419922 CCTATGAACGCACACACGC 59.580 57.895 0.00 0.00 36.19 5.34
3481 3630 1.014044 CCTATGAACGCACACACGCT 61.014 55.000 0.00 0.00 36.19 5.07
3482 3631 0.790207 CTATGAACGCACACACGCTT 59.210 50.000 0.00 0.00 36.19 4.68
3483 3632 1.194547 CTATGAACGCACACACGCTTT 59.805 47.619 0.00 0.00 36.19 3.51
3484 3633 1.222300 ATGAACGCACACACGCTTTA 58.778 45.000 0.00 0.00 36.19 1.85
3485 3634 0.302288 TGAACGCACACACGCTTTAC 59.698 50.000 0.00 0.00 36.19 2.01
3500 3649 4.260334 GCTTTACGAAGTCATTGTAGGC 57.740 45.455 0.00 0.00 43.93 3.93
3501 3650 3.241995 GCTTTACGAAGTCATTGTAGGCG 60.242 47.826 0.00 0.00 43.93 5.52
3502 3651 1.917273 TACGAAGTCATTGTAGGCGC 58.083 50.000 0.00 0.00 43.93 6.53
3503 3652 0.739813 ACGAAGTCATTGTAGGCGCC 60.740 55.000 21.89 21.89 29.74 6.53
3504 3653 0.460284 CGAAGTCATTGTAGGCGCCT 60.460 55.000 34.85 34.85 0.00 5.52
3505 3654 1.291132 GAAGTCATTGTAGGCGCCTC 58.709 55.000 36.73 24.38 0.00 4.70
3506 3655 0.460284 AAGTCATTGTAGGCGCCTCG 60.460 55.000 36.73 17.43 0.00 4.63
3507 3656 1.153628 GTCATTGTAGGCGCCTCGT 60.154 57.895 36.73 13.13 0.00 4.18
3508 3657 1.141019 TCATTGTAGGCGCCTCGTC 59.859 57.895 36.73 24.11 0.00 4.20
3509 3658 2.104331 ATTGTAGGCGCCTCGTCG 59.896 61.111 36.73 0.00 36.23 5.12
3510 3659 2.707849 ATTGTAGGCGCCTCGTCGT 61.708 57.895 36.73 14.07 36.23 4.34
3511 3660 2.221906 ATTGTAGGCGCCTCGTCGTT 62.222 55.000 36.73 10.36 36.23 3.85
3512 3661 2.879462 GTAGGCGCCTCGTCGTTG 60.879 66.667 36.73 0.00 36.23 4.10
3513 3662 3.057548 TAGGCGCCTCGTCGTTGA 61.058 61.111 36.73 10.36 36.23 3.18
3514 3663 3.332493 TAGGCGCCTCGTCGTTGAC 62.332 63.158 36.73 0.00 36.23 3.18
3533 3682 4.115270 GGAACGTCTCCTCCCACT 57.885 61.111 8.87 0.00 41.61 4.00
3534 3683 1.592223 GGAACGTCTCCTCCCACTG 59.408 63.158 8.87 0.00 41.61 3.66
3535 3684 0.898789 GGAACGTCTCCTCCCACTGA 60.899 60.000 8.87 0.00 41.61 3.41
3536 3685 0.966920 GAACGTCTCCTCCCACTGAA 59.033 55.000 0.00 0.00 0.00 3.02
3537 3686 1.343465 GAACGTCTCCTCCCACTGAAA 59.657 52.381 0.00 0.00 0.00 2.69
3538 3687 0.969894 ACGTCTCCTCCCACTGAAAG 59.030 55.000 0.00 0.00 42.29 2.62
3539 3688 0.390472 CGTCTCCTCCCACTGAAAGC 60.390 60.000 0.00 0.00 37.60 3.51
3540 3689 0.390472 GTCTCCTCCCACTGAAAGCG 60.390 60.000 0.00 0.00 37.60 4.68
3541 3690 1.743252 CTCCTCCCACTGAAAGCGC 60.743 63.158 0.00 0.00 37.60 5.92
3542 3691 2.032528 CCTCCCACTGAAAGCGCA 59.967 61.111 11.47 0.00 37.60 6.09
3543 3692 1.377725 CCTCCCACTGAAAGCGCAT 60.378 57.895 11.47 0.00 37.60 4.73
3544 3693 1.372087 CCTCCCACTGAAAGCGCATC 61.372 60.000 11.47 8.39 37.60 3.91
3545 3694 1.699656 CTCCCACTGAAAGCGCATCG 61.700 60.000 11.47 6.82 37.60 3.84
3556 3705 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
3557 3706 2.885676 CGCATCGCCGGAAATCCTG 61.886 63.158 5.05 0.00 0.00 3.86
3558 3707 1.523711 GCATCGCCGGAAATCCTGA 60.524 57.895 5.05 0.00 0.00 3.86
3559 3708 1.095228 GCATCGCCGGAAATCCTGAA 61.095 55.000 5.05 0.00 0.00 3.02
3560 3709 1.378531 CATCGCCGGAAATCCTGAAA 58.621 50.000 5.05 0.00 0.00 2.69
3561 3710 1.949525 CATCGCCGGAAATCCTGAAAT 59.050 47.619 5.05 0.00 0.00 2.17
3562 3711 2.992124 TCGCCGGAAATCCTGAAATA 57.008 45.000 5.05 0.00 0.00 1.40
3563 3712 3.269538 TCGCCGGAAATCCTGAAATAA 57.730 42.857 5.05 0.00 0.00 1.40
3564 3713 3.611970 TCGCCGGAAATCCTGAAATAAA 58.388 40.909 5.05 0.00 0.00 1.40
3565 3714 3.375922 TCGCCGGAAATCCTGAAATAAAC 59.624 43.478 5.05 0.00 0.00 2.01
3566 3715 3.488553 CGCCGGAAATCCTGAAATAAACC 60.489 47.826 5.05 0.00 0.00 3.27
3567 3716 3.181479 GCCGGAAATCCTGAAATAAACCC 60.181 47.826 5.05 0.00 0.00 4.11
3568 3717 4.020543 CCGGAAATCCTGAAATAAACCCA 58.979 43.478 0.00 0.00 0.00 4.51
3569 3718 4.097892 CCGGAAATCCTGAAATAAACCCAG 59.902 45.833 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 2.225382 TCATGTTGGAGGAGACCGTA 57.775 50.000 0.00 0.00 0.00 4.02
98 99 4.398319 TCTTTTTCATGTTGGAGGAGACC 58.602 43.478 0.00 0.00 0.00 3.85
206 207 8.363390 TGTGATATCTTTGTATGATCTGGAGAC 58.637 37.037 3.98 0.00 0.00 3.36
286 287 9.811995 TGGTTTACAGCTAGTATACATTTACAG 57.188 33.333 5.50 0.00 36.66 2.74
318 319 7.164826 GCTAATGTTAAGCACAAAGAATCATCG 59.835 37.037 0.00 0.00 39.50 3.84
331 332 6.655003 GGGAATATGCTAGCTAATGTTAAGCA 59.345 38.462 17.23 7.50 42.62 3.91
463 464 1.625818 ACAGAATCTTGGTCTTCGCCT 59.374 47.619 0.00 0.00 0.00 5.52
690 699 9.995957 ATAGAATCATACAAAGATATCGACTCG 57.004 33.333 0.00 0.00 0.00 4.18
790 805 7.484641 GCATTACAAATTTCTCAACGCAGATAA 59.515 33.333 0.00 0.00 0.00 1.75
818 833 4.894784 TCTTCTAGTGTAGTGCAAAAGGG 58.105 43.478 0.00 0.00 0.00 3.95
847 862 6.423001 GTGTTCGTCTAGTACAAGAAAATGGT 59.577 38.462 0.00 0.00 31.92 3.55
848 863 6.422701 TGTGTTCGTCTAGTACAAGAAAATGG 59.577 38.462 0.00 0.00 31.92 3.16
856 871 7.595604 TGTGATAATGTGTTCGTCTAGTACAA 58.404 34.615 0.00 0.00 31.92 2.41
882 897 2.201732 TCTAGAAAACGATCGCCATGC 58.798 47.619 16.60 0.00 0.00 4.06
898 913 1.722011 ATTTGTCCACGCGGTTCTAG 58.278 50.000 12.47 0.00 0.00 2.43
925 941 9.342308 AGTCTTGTTTCTCATTTGATTTGACTA 57.658 29.630 0.00 0.00 0.00 2.59
926 942 8.133627 CAGTCTTGTTTCTCATTTGATTTGACT 58.866 33.333 0.00 0.00 0.00 3.41
945 961 5.118050 TGCGACGAGTTTATTTACAGTCTTG 59.882 40.000 0.00 0.00 0.00 3.02
1073 1089 2.048503 ACGGCGGGAAAAGTCGAG 60.049 61.111 13.24 0.00 39.29 4.04
1173 1189 3.735251 GAGGAGGGACGGACCGGAT 62.735 68.421 20.00 0.00 40.11 4.18
1229 1246 3.680786 CAGCGTGGGTGAGACGGA 61.681 66.667 0.00 0.00 37.30 4.69
1514 1533 2.501316 TGAAGAGGATGAAGGCGATGAA 59.499 45.455 0.00 0.00 0.00 2.57
1600 1619 2.315176 CCACACCAGAATTTTGACCCA 58.685 47.619 0.00 0.00 0.00 4.51
1618 1639 1.194121 TCTCTTGCTAGCAGGTGCCA 61.194 55.000 24.36 5.56 43.38 4.92
1768 1792 2.486472 ATTCCAAGCCACAGACAGAG 57.514 50.000 0.00 0.00 0.00 3.35
1806 1830 2.898729 ATGCCTACATTCGACCTCTG 57.101 50.000 0.00 0.00 30.07 3.35
1827 1851 2.105649 TCAAGCAGTAACCATGGACACA 59.894 45.455 21.47 0.00 0.00 3.72
1846 1870 4.164030 TGAATAGCATAGTTGGAGGCTTCA 59.836 41.667 0.00 0.00 37.66 3.02
1931 2046 4.370049 CTCCAAGTAGCATGATCTGACTG 58.630 47.826 0.00 0.00 0.00 3.51
2067 2184 5.682862 CACATTCAATAATTAGCGCAAGACC 59.317 40.000 11.47 0.00 43.02 3.85
2392 2510 1.335689 GGCAGCTTGTTTGCAGAGAAG 60.336 52.381 9.54 9.54 43.28 2.85
2446 2564 3.309954 GTCATGCCGTGGAGAAGAAATAC 59.690 47.826 0.00 0.00 0.00 1.89
2491 2609 2.323599 CTCAGAGCTCATGGGGATGTA 58.676 52.381 17.77 0.00 0.00 2.29
2808 2926 7.290110 TGAATCTATGTAGTGGATACTGTGG 57.710 40.000 0.00 0.00 37.78 4.17
2813 2931 7.482169 TCCCATGAATCTATGTAGTGGATAC 57.518 40.000 0.00 0.00 34.72 2.24
2899 3017 3.127548 CCAATGCACCTTACATGTGTCTC 59.872 47.826 9.11 0.00 36.11 3.36
2900 3018 3.084039 CCAATGCACCTTACATGTGTCT 58.916 45.455 9.11 0.00 36.11 3.41
2902 3020 2.170166 CCCAATGCACCTTACATGTGT 58.830 47.619 9.11 0.00 36.11 3.72
3052 3201 5.835113 AAGCTGTACAACAACATTTGTCT 57.165 34.783 0.00 0.00 44.59 3.41
3197 3346 5.878406 ATCCCAGAACTATCCAGTTGTAG 57.122 43.478 0.00 0.00 45.18 2.74
3258 3407 3.058501 GCCGTGTGTTTAAATGTGCTACT 60.059 43.478 0.00 0.00 0.00 2.57
3259 3408 3.231160 GCCGTGTGTTTAAATGTGCTAC 58.769 45.455 0.00 0.00 0.00 3.58
3269 3418 3.810941 CCTAGAAAACTGCCGTGTGTTTA 59.189 43.478 0.00 0.00 35.63 2.01
3274 3423 2.922740 TTCCTAGAAAACTGCCGTGT 57.077 45.000 0.00 0.00 0.00 4.49
3275 3424 3.314080 TGTTTTCCTAGAAAACTGCCGTG 59.686 43.478 25.14 0.00 39.97 4.94
3276 3425 3.547746 TGTTTTCCTAGAAAACTGCCGT 58.452 40.909 25.14 0.00 39.97 5.68
3292 3441 7.383843 ACTTCGTTTCACAAGAAAACATGTTTT 59.616 29.630 31.40 31.40 44.75 2.43
3325 3474 5.581605 CCATACCCGACAAAAAGATTGATG 58.418 41.667 0.00 0.00 0.00 3.07
3326 3475 4.097892 GCCATACCCGACAAAAAGATTGAT 59.902 41.667 0.00 0.00 0.00 2.57
3329 3478 3.426615 TGCCATACCCGACAAAAAGATT 58.573 40.909 0.00 0.00 0.00 2.40
3331 3480 2.224670 ACTGCCATACCCGACAAAAAGA 60.225 45.455 0.00 0.00 0.00 2.52
3332 3481 2.159382 ACTGCCATACCCGACAAAAAG 58.841 47.619 0.00 0.00 0.00 2.27
3337 3486 1.783071 TGATACTGCCATACCCGACA 58.217 50.000 0.00 0.00 0.00 4.35
3338 3487 2.563179 AGATGATACTGCCATACCCGAC 59.437 50.000 0.00 0.00 0.00 4.79
3339 3488 2.562738 CAGATGATACTGCCATACCCGA 59.437 50.000 0.00 0.00 0.00 5.14
3340 3489 2.300152 ACAGATGATACTGCCATACCCG 59.700 50.000 0.00 0.00 41.06 5.28
3346 3495 6.737720 ATCTAGAAACAGATGATACTGCCA 57.262 37.500 0.00 0.00 41.06 4.92
3375 3524 7.103641 CAGTTAGGTGTAGGTGTTTATCATGT 58.896 38.462 0.00 0.00 0.00 3.21
3409 3558 5.122519 TGTGTCTGTACTGATGCTCAAAAA 58.877 37.500 5.69 0.00 0.00 1.94
3410 3559 4.702831 TGTGTCTGTACTGATGCTCAAAA 58.297 39.130 5.69 0.00 0.00 2.44
3411 3560 4.335400 TGTGTCTGTACTGATGCTCAAA 57.665 40.909 5.69 0.00 0.00 2.69
3412 3561 4.309933 CTTGTGTCTGTACTGATGCTCAA 58.690 43.478 5.69 6.69 0.00 3.02
3413 3562 3.862264 GCTTGTGTCTGTACTGATGCTCA 60.862 47.826 5.69 0.00 0.00 4.26
3414 3563 2.670414 GCTTGTGTCTGTACTGATGCTC 59.330 50.000 5.69 0.00 0.00 4.26
3415 3564 2.693069 GCTTGTGTCTGTACTGATGCT 58.307 47.619 5.69 0.00 0.00 3.79
3416 3565 1.391485 CGCTTGTGTCTGTACTGATGC 59.609 52.381 5.69 3.20 0.00 3.91
3417 3566 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
3418 3567 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
3419 3568 0.673985 AGCGCTTGTGTCTGTACTGA 59.326 50.000 2.64 0.00 0.00 3.41
3420 3569 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
3421 3570 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
3422 3571 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
3423 3572 3.801114 ATATGAGCGCTTGTGTCTGTA 57.199 42.857 13.26 0.00 0.00 2.74
3424 3573 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
3425 3574 3.243877 GTGTATATGAGCGCTTGTGTCTG 59.756 47.826 13.26 0.00 0.00 3.51
3426 3575 3.448686 GTGTATATGAGCGCTTGTGTCT 58.551 45.455 13.26 0.00 0.00 3.41
3427 3576 2.216488 CGTGTATATGAGCGCTTGTGTC 59.784 50.000 13.26 0.00 0.00 3.67
3428 3577 2.193447 CGTGTATATGAGCGCTTGTGT 58.807 47.619 13.26 4.27 0.00 3.72
3429 3578 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
3430 3579 1.209128 GCGTGTATATGAGCGCTTGT 58.791 50.000 13.26 5.98 45.48 3.16
3431 3580 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
3432 3581 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
3433 3582 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
3436 3585 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
3437 3586 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
3438 3587 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
3439 3588 3.119628 GTGAGTGTATGCGCGTGTATATG 59.880 47.826 13.61 0.00 0.00 1.78
3440 3589 3.305964 GTGAGTGTATGCGCGTGTATAT 58.694 45.455 13.61 0.00 0.00 0.86
3441 3590 2.542205 GGTGAGTGTATGCGCGTGTATA 60.542 50.000 13.61 2.40 0.00 1.47
3442 3591 1.556564 GTGAGTGTATGCGCGTGTAT 58.443 50.000 13.61 4.63 0.00 2.29
3443 3592 0.457166 GGTGAGTGTATGCGCGTGTA 60.457 55.000 13.61 0.00 0.00 2.90
3444 3593 1.736645 GGTGAGTGTATGCGCGTGT 60.737 57.895 13.61 0.00 0.00 4.49
3445 3594 2.452813 GGGTGAGTGTATGCGCGTG 61.453 63.158 13.61 0.00 0.00 5.34
3446 3595 1.317431 TAGGGTGAGTGTATGCGCGT 61.317 55.000 8.43 7.55 0.00 6.01
3447 3596 0.032130 ATAGGGTGAGTGTATGCGCG 59.968 55.000 0.00 0.00 0.00 6.86
3448 3597 1.068588 TCATAGGGTGAGTGTATGCGC 59.931 52.381 0.00 0.00 31.80 6.09
3449 3598 3.123804 GTTCATAGGGTGAGTGTATGCG 58.876 50.000 0.00 0.00 38.29 4.73
3450 3599 3.123804 CGTTCATAGGGTGAGTGTATGC 58.876 50.000 0.00 0.00 38.29 3.14
3451 3600 3.123804 GCGTTCATAGGGTGAGTGTATG 58.876 50.000 0.00 0.00 38.29 2.39
3452 3601 2.764010 TGCGTTCATAGGGTGAGTGTAT 59.236 45.455 0.00 0.00 38.29 2.29
3453 3602 2.094390 GTGCGTTCATAGGGTGAGTGTA 60.094 50.000 0.00 0.00 38.29 2.90
3454 3603 0.973632 TGCGTTCATAGGGTGAGTGT 59.026 50.000 0.00 0.00 38.29 3.55
3455 3604 1.337728 TGTGCGTTCATAGGGTGAGTG 60.338 52.381 0.00 0.00 38.29 3.51
3456 3605 0.973632 TGTGCGTTCATAGGGTGAGT 59.026 50.000 0.00 0.00 38.29 3.41
3457 3606 1.337728 TGTGTGCGTTCATAGGGTGAG 60.338 52.381 0.00 0.00 38.29 3.51
3458 3607 0.682292 TGTGTGCGTTCATAGGGTGA 59.318 50.000 0.00 0.00 34.25 4.02
3459 3608 0.796312 GTGTGTGCGTTCATAGGGTG 59.204 55.000 0.00 0.00 0.00 4.61
3460 3609 0.669318 CGTGTGTGCGTTCATAGGGT 60.669 55.000 0.00 0.00 0.00 4.34
3461 3610 1.966493 GCGTGTGTGCGTTCATAGGG 61.966 60.000 0.00 0.00 0.00 3.53
3462 3611 1.014044 AGCGTGTGTGCGTTCATAGG 61.014 55.000 0.00 0.00 40.67 2.57
3463 3612 0.790207 AAGCGTGTGTGCGTTCATAG 59.210 50.000 0.00 0.00 40.67 2.23
3464 3613 1.222300 AAAGCGTGTGTGCGTTCATA 58.778 45.000 0.00 0.00 40.67 2.15
3465 3614 1.070175 GTAAAGCGTGTGTGCGTTCAT 60.070 47.619 0.00 0.00 37.69 2.57
3466 3615 0.302288 GTAAAGCGTGTGTGCGTTCA 59.698 50.000 0.00 0.00 37.69 3.18
3467 3616 0.716926 CGTAAAGCGTGTGTGCGTTC 60.717 55.000 0.00 0.00 37.69 3.95
3468 3617 1.146957 TCGTAAAGCGTGTGTGCGTT 61.147 50.000 0.00 0.00 42.13 4.84
3469 3618 1.146957 TTCGTAAAGCGTGTGTGCGT 61.147 50.000 0.00 0.00 42.13 5.24
3470 3619 0.448861 CTTCGTAAAGCGTGTGTGCG 60.449 55.000 0.00 0.00 42.13 5.34
3471 3620 0.580104 ACTTCGTAAAGCGTGTGTGC 59.420 50.000 0.00 0.00 42.13 4.57
3472 3621 1.855978 TGACTTCGTAAAGCGTGTGTG 59.144 47.619 0.00 0.00 42.13 3.82
3473 3622 2.212869 TGACTTCGTAAAGCGTGTGT 57.787 45.000 0.00 0.00 42.13 3.72
3474 3623 3.059868 ACAATGACTTCGTAAAGCGTGTG 60.060 43.478 0.00 0.00 42.13 3.82
3475 3624 3.128349 ACAATGACTTCGTAAAGCGTGT 58.872 40.909 0.00 0.00 42.13 4.49
3476 3625 3.788434 ACAATGACTTCGTAAAGCGTG 57.212 42.857 0.00 0.00 42.13 5.34
3477 3626 3.924686 CCTACAATGACTTCGTAAAGCGT 59.075 43.478 0.00 0.00 42.13 5.07
3478 3627 3.241995 GCCTACAATGACTTCGTAAAGCG 60.242 47.826 0.00 0.00 43.01 4.68
3479 3628 3.241995 CGCCTACAATGACTTCGTAAAGC 60.242 47.826 0.00 0.00 35.81 3.51
3480 3629 3.241995 GCGCCTACAATGACTTCGTAAAG 60.242 47.826 0.00 0.00 38.54 1.85
3481 3630 2.669434 GCGCCTACAATGACTTCGTAAA 59.331 45.455 0.00 0.00 0.00 2.01
3482 3631 2.264813 GCGCCTACAATGACTTCGTAA 58.735 47.619 0.00 0.00 0.00 3.18
3483 3632 1.470285 GGCGCCTACAATGACTTCGTA 60.470 52.381 22.15 0.00 0.00 3.43
3484 3633 0.739813 GGCGCCTACAATGACTTCGT 60.740 55.000 22.15 0.00 0.00 3.85
3485 3634 0.460284 AGGCGCCTACAATGACTTCG 60.460 55.000 31.86 0.00 0.00 3.79
3486 3635 1.291132 GAGGCGCCTACAATGACTTC 58.709 55.000 32.97 9.38 0.00 3.01
3487 3636 0.460284 CGAGGCGCCTACAATGACTT 60.460 55.000 32.97 2.04 0.00 3.01
3488 3637 1.141881 CGAGGCGCCTACAATGACT 59.858 57.895 32.97 3.02 0.00 3.41
3489 3638 1.146358 GACGAGGCGCCTACAATGAC 61.146 60.000 32.97 14.51 0.00 3.06
3490 3639 1.141019 GACGAGGCGCCTACAATGA 59.859 57.895 32.97 0.00 0.00 2.57
3491 3640 2.230940 CGACGAGGCGCCTACAATG 61.231 63.158 32.97 18.94 0.00 2.82
3492 3641 2.104331 CGACGAGGCGCCTACAAT 59.896 61.111 32.97 15.46 0.00 2.71
3493 3642 2.922950 AACGACGAGGCGCCTACAA 61.923 57.895 32.97 0.00 33.86 2.41
3494 3643 3.367743 AACGACGAGGCGCCTACA 61.368 61.111 32.97 0.00 33.86 2.74
3495 3644 2.879462 CAACGACGAGGCGCCTAC 60.879 66.667 32.97 22.05 33.86 3.18
3496 3645 3.057548 TCAACGACGAGGCGCCTA 61.058 61.111 32.97 8.37 33.86 3.93
3497 3646 4.719369 GTCAACGACGAGGCGCCT 62.719 66.667 33.48 33.48 33.86 5.52
3517 3666 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
3518 3667 1.344763 CTTTCAGTGGGAGGAGACGTT 59.655 52.381 0.00 0.00 0.00 3.99
3519 3668 0.969894 CTTTCAGTGGGAGGAGACGT 59.030 55.000 0.00 0.00 0.00 4.34
3520 3669 0.390472 GCTTTCAGTGGGAGGAGACG 60.390 60.000 0.00 0.00 0.00 4.18
3521 3670 0.390472 CGCTTTCAGTGGGAGGAGAC 60.390 60.000 0.00 0.00 0.00 3.36
3522 3671 1.975327 CGCTTTCAGTGGGAGGAGA 59.025 57.895 0.00 0.00 0.00 3.71
3523 3672 1.743252 GCGCTTTCAGTGGGAGGAG 60.743 63.158 0.00 0.00 0.00 3.69
3524 3673 1.841302 ATGCGCTTTCAGTGGGAGGA 61.841 55.000 9.73 0.00 0.00 3.71
3525 3674 1.372087 GATGCGCTTTCAGTGGGAGG 61.372 60.000 9.73 0.00 0.00 4.30
3526 3675 1.699656 CGATGCGCTTTCAGTGGGAG 61.700 60.000 9.73 0.00 0.00 4.30
3527 3676 1.741401 CGATGCGCTTTCAGTGGGA 60.741 57.895 9.73 0.00 0.00 4.37
3528 3677 2.787249 CGATGCGCTTTCAGTGGG 59.213 61.111 9.73 0.00 0.00 4.61
3539 3688 2.588877 AGGATTTCCGGCGATGCG 60.589 61.111 9.30 0.00 42.08 4.73
3540 3689 1.095228 TTCAGGATTTCCGGCGATGC 61.095 55.000 9.30 0.00 42.08 3.91
3541 3690 1.378531 TTTCAGGATTTCCGGCGATG 58.621 50.000 9.30 0.00 42.08 3.84
3542 3691 2.348411 ATTTCAGGATTTCCGGCGAT 57.652 45.000 9.30 0.00 42.08 4.58
3543 3692 2.992124 TATTTCAGGATTTCCGGCGA 57.008 45.000 9.30 0.00 42.08 5.54
3544 3693 3.488553 GGTTTATTTCAGGATTTCCGGCG 60.489 47.826 0.00 0.00 42.08 6.46
3545 3694 3.181479 GGGTTTATTTCAGGATTTCCGGC 60.181 47.826 0.00 0.00 42.08 6.13
3546 3695 4.020543 TGGGTTTATTTCAGGATTTCCGG 58.979 43.478 0.00 0.00 42.08 5.14
3547 3696 5.248870 CTGGGTTTATTTCAGGATTTCCG 57.751 43.478 0.00 0.00 42.08 4.30


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

AutoCloner maintained by Alex Coulton.