Multiple sequence alignment - TraesCS2A01G445500

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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 TraesCS2A01G445500 chr2A 100.000 3291 0 0 1 3291 695149181 695152471 0.000000e+00 6078
1 TraesCS2A01G445500 chr2B 86.265 3320 213 103 54 3219 662372176 662375406 0.000000e+00 3380
2 TraesCS2A01G445500 chr2B 85.973 2260 176 57 23 2208 661850305 661852497 0.000000e+00 2287
3 TraesCS2A01G445500 chr2D 85.525 3323 221 114 51 3224 555575576 555578787 0.000000e+00 3232
4 TraesCS2A01G445500 chr2D 84.936 1487 97 48 1 1414 555394214 555395646 0.000000e+00 1387
5 TraesCS2A01G445500 chr2D 94.092 677 33 2 1444 2120 555395714 555396383 0.000000e+00 1022
6 TraesCS2A01G445500 chr6D 93.023 129 8 1 1001 1129 352835526 352835653 1.560000e-43 187
7 TraesCS2A01G445500 chr6D 88.281 128 11 3 1242 1367 296993419 296993294 2.050000e-32 150
8 TraesCS2A01G445500 chr6D 88.281 128 11 3 1242 1367 298207144 298207019 2.050000e-32 150
9 TraesCS2A01G445500 chr6D 95.556 90 4 0 1450 1539 352835881 352835970 9.520000e-31 145
10 TraesCS2A01G445500 chr6A 93.023 129 8 1 1001 1129 490301789 490301916 1.560000e-43 187
11 TraesCS2A01G445500 chr6A 96.512 86 3 0 1450 1535 490302137 490302222 3.420000e-30 143
12 TraesCS2A01G445500 chr6B 90.909 132 11 1 1001 1132 526101297 526101167 3.380000e-40 176
13 TraesCS2A01G445500 chr6B 94.186 86 5 0 1450 1535 526100919 526100834 7.410000e-27 132
14 TraesCS2A01G445500 chr1D 87.597 129 16 0 1242 1370 364625136 364625008 2.050000e-32 150
15 TraesCS2A01G445500 chr3D 86.822 129 17 0 1242 1370 492131560 492131688 9.520000e-31 145
16 TraesCS2A01G445500 chr1A 86.822 129 17 0 1242 1370 463461561 463461433 9.520000e-31 145


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 TraesCS2A01G445500 chr2A 695149181 695152471 3290 False 6078.0 6078 100.000 1 3291 1 chr2A.!!$F1 3290
1 TraesCS2A01G445500 chr2B 662372176 662375406 3230 False 3380.0 3380 86.265 54 3219 1 chr2B.!!$F2 3165
2 TraesCS2A01G445500 chr2B 661850305 661852497 2192 False 2287.0 2287 85.973 23 2208 1 chr2B.!!$F1 2185
3 TraesCS2A01G445500 chr2D 555575576 555578787 3211 False 3232.0 3232 85.525 51 3224 1 chr2D.!!$F1 3173
4 TraesCS2A01G445500 chr2D 555394214 555396383 2169 False 1204.5 1387 89.514 1 2120 2 chr2D.!!$F2 2119

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
360 366 0.109913 GCCAGATCATGAGCCATGGA 59.890 55.0 20.15 0.0 41.66 3.41 F
1370 1539 0.311790 AACATGCTCGGCAACAAGTG 59.688 50.0 2.68 0.0 43.62 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1552 0.106268 TTCAGGGTGCTGCAAAAGGA 60.106 50.0 2.77 0.0 0.00 3.36 R
3227 3496 0.109597 GTTGCTGTTGCGCTATGCTT 60.110 50.0 9.73 0.0 46.63 3.91 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
45 46 0.891904 CCCCGCGGGTTATAATTGGG 60.892 60.000 40.52 18.92 38.25 4.12
55 56 6.407639 GCGGGTTATAATTGGGGAAGAAAAAT 60.408 38.462 0.00 0.00 0.00 1.82
66 68 5.221481 TGGGGAAGAAAAATAAAAACGGGAC 60.221 40.000 0.00 0.00 0.00 4.46
79 81 3.719214 GGGACGAATTAGGCAGCG 58.281 61.111 0.00 0.00 0.00 5.18
103 105 4.345257 AGTCTAATGAATCGTAGGGTGCAT 59.655 41.667 0.00 0.00 0.00 3.96
109 113 2.240493 ATCGTAGGGTGCATGCTAAC 57.760 50.000 20.33 9.56 0.00 2.34
113 117 0.461870 TAGGGTGCATGCTAACGCTG 60.462 55.000 27.63 0.00 39.61 5.18
114 118 2.100991 GGTGCATGCTAACGCTGC 59.899 61.111 20.33 0.00 39.29 5.25
123 127 1.270968 CTAACGCTGCGCTGATTCG 59.729 57.895 23.51 14.16 0.00 3.34
150 154 3.368571 GCCTCCCAACAGTGCTGC 61.369 66.667 0.00 0.00 0.00 5.25
169 173 1.087771 CGCGTACTGTTCCCCAATCC 61.088 60.000 0.00 0.00 0.00 3.01
188 192 1.066454 CCCGGCGATAAATTTGGTTCC 59.934 52.381 9.30 0.00 0.00 3.62
228 233 1.407712 GCTAACTGTTCCCCGCCATTA 60.408 52.381 0.00 0.00 0.00 1.90
230 235 1.834188 AACTGTTCCCCGCCATTAAG 58.166 50.000 0.00 0.00 0.00 1.85
239 244 2.618709 CCCCGCCATTAAGAAACTGATC 59.381 50.000 0.00 0.00 0.00 2.92
314 320 4.388485 TGTCCCGGTTAACCTACTTTTTC 58.612 43.478 22.12 5.57 0.00 2.29
317 323 5.049198 GTCCCGGTTAACCTACTTTTTCTTG 60.049 44.000 22.12 2.21 0.00 3.02
320 326 5.278120 CCGGTTAACCTACTTTTTCTTGTGG 60.278 44.000 22.12 7.02 0.00 4.17
327 333 3.866883 ACTTTTTCTTGTGGGTGTGTG 57.133 42.857 0.00 0.00 0.00 3.82
328 334 3.161866 ACTTTTTCTTGTGGGTGTGTGT 58.838 40.909 0.00 0.00 0.00 3.72
329 335 3.056891 ACTTTTTCTTGTGGGTGTGTGTG 60.057 43.478 0.00 0.00 0.00 3.82
353 359 0.591659 CGCCATTGCCAGATCATGAG 59.408 55.000 0.09 0.00 0.00 2.90
360 366 0.109913 GCCAGATCATGAGCCATGGA 59.890 55.000 20.15 0.00 41.66 3.41
469 489 2.278596 CCAGCCGGACATCGTACG 60.279 66.667 5.05 9.53 39.92 3.67
481 501 1.210931 TCGTACGAGGCACGAAAGG 59.789 57.895 15.28 4.74 44.79 3.11
500 528 1.645710 GAGAGAAGAGAACCCCACCA 58.354 55.000 0.00 0.00 0.00 4.17
504 542 1.700186 AGAAGAGAACCCCACCAAGAC 59.300 52.381 0.00 0.00 0.00 3.01
553 607 2.897350 CGGCCGAGGAAATCAGGC 60.897 66.667 24.07 0.00 42.96 4.85
565 619 0.834612 AATCAGGCGACCGGGAAATA 59.165 50.000 6.32 0.00 0.00 1.40
568 622 0.730840 CAGGCGACCGGGAAATAAAC 59.269 55.000 6.32 0.00 0.00 2.01
571 625 2.159000 AGGCGACCGGGAAATAAACTAG 60.159 50.000 6.32 0.00 0.00 2.57
581 635 4.510571 GGAAATAAACTAGCCCGACAGAA 58.489 43.478 0.00 0.00 0.00 3.02
625 679 2.572284 CACCTTCTCGTCGGGGAC 59.428 66.667 0.00 0.00 0.00 4.46
671 730 2.859032 GCTCAGGTGTATAGTGTAGCGC 60.859 54.545 0.00 0.00 0.00 5.92
693 752 0.321671 CCCAGGTGTAGTGGTGACAG 59.678 60.000 0.00 0.00 44.46 3.51
695 754 0.320771 CAGGTGTAGTGGTGACAGGC 60.321 60.000 0.00 0.00 44.46 4.85
746 850 2.747822 GCAGCGGCAGACACATGAG 61.748 63.158 3.18 0.00 40.72 2.90
799 904 4.631740 TGTCGCAGGGTCAGGGGA 62.632 66.667 0.00 0.00 0.00 4.81
800 905 4.083862 GTCGCAGGGTCAGGGGAC 62.084 72.222 0.00 0.00 43.55 4.46
832 937 2.642700 CCAAAGTTTCACCCCGCG 59.357 61.111 0.00 0.00 0.00 6.46
892 1003 4.148825 ATCTCGCACACCTCCGGC 62.149 66.667 0.00 0.00 0.00 6.13
902 1013 2.125350 CCTCCGGCACAAGAGAGC 60.125 66.667 0.00 0.00 30.84 4.09
989 1136 1.710996 TTTGAAGCGGTGGGAGGGAA 61.711 55.000 0.00 0.00 0.00 3.97
1196 1365 5.702209 AGTTCATGCCAATTTTTGCTTAAGG 59.298 36.000 4.29 0.00 0.00 2.69
1212 1381 4.677584 CTTAAGGGAGAACTCGACTGATG 58.322 47.826 0.00 0.00 0.00 3.07
1370 1539 0.311790 AACATGCTCGGCAACAAGTG 59.688 50.000 2.68 0.00 43.62 3.16
1379 1548 2.699910 GCAACAAGTGCGTTCATCG 58.300 52.632 0.00 0.00 45.10 3.84
1422 1621 6.048732 TGAAGAAAGCTCCATACATGTGTA 57.951 37.500 9.11 0.00 34.67 2.90
1602 1812 0.668535 AAGAAGAAAACCACCTGCGC 59.331 50.000 0.00 0.00 0.00 6.09
1642 1858 1.186200 CGTCTCCATCCTCTTCCACA 58.814 55.000 0.00 0.00 0.00 4.17
1713 1929 0.535780 CAGAGCAACACCAGCAAGGA 60.536 55.000 1.83 0.00 41.22 3.36
1714 1930 0.183492 AGAGCAACACCAGCAAGGAA 59.817 50.000 1.83 0.00 41.22 3.36
1715 1931 0.312102 GAGCAACACCAGCAAGGAAC 59.688 55.000 1.83 0.00 41.22 3.62
1717 1933 1.142870 AGCAACACCAGCAAGGAACTA 59.857 47.619 1.83 0.00 38.49 2.24
1718 1934 1.537202 GCAACACCAGCAAGGAACTAG 59.463 52.381 1.83 0.00 38.49 2.57
1825 2041 3.790437 CACTGCCCGGCCATCTCT 61.790 66.667 7.03 0.00 0.00 3.10
2123 2342 1.664321 GCCCATCGACGACTACCAGT 61.664 60.000 0.00 0.00 0.00 4.00
2242 2467 1.745115 CGCCACGTCAACCATCCAT 60.745 57.895 0.00 0.00 0.00 3.41
2305 2530 6.123651 GGGTCTATGAGATCACTCGGTATAT 58.876 44.000 0.00 0.00 45.25 0.86
2306 2531 7.092578 TGGGTCTATGAGATCACTCGGTATATA 60.093 40.741 0.00 0.00 45.25 0.86
2307 2532 7.940137 GGGTCTATGAGATCACTCGGTATATAT 59.060 40.741 0.00 0.00 45.25 0.86
2308 2533 9.999660 GGTCTATGAGATCACTCGGTATATATA 57.000 37.037 0.00 0.00 45.25 0.86
2341 2566 7.380065 CCGATCTCTTAGTATAGAAACAAGCAC 59.620 40.741 0.00 0.00 0.00 4.40
2375 2600 2.798680 CCACGACTGATGCTAGTACAC 58.201 52.381 0.00 0.00 0.00 2.90
2376 2601 2.163613 CCACGACTGATGCTAGTACACA 59.836 50.000 0.00 0.00 0.00 3.72
2378 2603 3.608506 CACGACTGATGCTAGTACACAAC 59.391 47.826 0.00 0.00 0.00 3.32
2415 2642 1.068474 GTACAACTGTACGCCTGCAG 58.932 55.000 6.78 6.78 41.06 4.41
2430 2657 1.239296 TGCAGCAGGAGTACGTACGT 61.239 55.000 25.98 25.98 0.00 3.57
2451 2686 1.404391 ACCCAGCACGAAGACTATACG 59.596 52.381 0.00 0.00 0.00 3.06
2479 2714 8.577164 AAAAAGGGATATAGTTAGGCTAGGAA 57.423 34.615 0.00 0.00 32.45 3.36
2492 2727 2.175878 CTAGGAAGCACACACAAGCT 57.824 50.000 0.00 0.00 44.31 3.74
2493 2728 2.072298 CTAGGAAGCACACACAAGCTC 58.928 52.381 0.00 0.00 40.90 4.09
2494 2729 0.882042 AGGAAGCACACACAAGCTCG 60.882 55.000 0.00 0.00 40.90 5.03
2521 2756 8.523658 AGGAGATGCTTAAAATAACTTTTCCAC 58.476 33.333 0.00 0.00 36.09 4.02
2531 2778 0.951558 ACTTTTCCACACATGCGACC 59.048 50.000 0.00 0.00 0.00 4.79
2538 2785 2.127270 CACATGCGACCACGTTGC 60.127 61.111 0.00 0.00 42.77 4.17
2569 2816 1.649390 AAAGTGGTGCGACGCAAACA 61.649 50.000 26.29 22.84 41.47 2.83
2575 2822 0.654472 GTGCGACGCAAACAAGTCAG 60.654 55.000 26.29 0.00 41.47 3.51
2603 2850 2.161609 GTCAAGGTTTCCGGTGCTAATG 59.838 50.000 0.00 0.00 0.00 1.90
2639 2886 4.925068 ACTCAACTTCAACTGTCAAATGC 58.075 39.130 0.00 0.00 0.00 3.56
2640 2887 4.202050 ACTCAACTTCAACTGTCAAATGCC 60.202 41.667 0.00 0.00 0.00 4.40
2665 2912 0.319211 CAACAGCGACCAAGTACGGA 60.319 55.000 0.00 0.00 0.00 4.69
2666 2913 0.606604 AACAGCGACCAAGTACGGAT 59.393 50.000 0.00 0.00 0.00 4.18
2671 2932 2.508439 ACCAAGTACGGATGCGCG 60.508 61.111 6.51 0.00 0.00 6.86
2704 2965 1.160329 ACGCCAGCGCTTTATCATCC 61.160 55.000 7.50 0.00 44.19 3.51
2705 2966 1.159713 CGCCAGCGCTTTATCATCCA 61.160 55.000 7.50 0.00 0.00 3.41
2706 2967 1.024271 GCCAGCGCTTTATCATCCAA 58.976 50.000 7.50 0.00 0.00 3.53
2716 2977 6.204359 CGCTTTATCATCCAAGAAATTCCTG 58.796 40.000 0.00 0.00 0.00 3.86
2800 3062 0.035915 GGTGAAGCCTGTCTCCTTCC 60.036 60.000 0.00 0.00 37.29 3.46
2837 3099 4.142730 GCTGCTCATGTTTTCTACTTCCTG 60.143 45.833 0.00 0.00 0.00 3.86
2838 3100 4.973168 TGCTCATGTTTTCTACTTCCTGT 58.027 39.130 0.00 0.00 0.00 4.00
2911 3173 4.506654 GGCTGCATGATTGATTCATTTGTC 59.493 41.667 0.50 0.00 42.62 3.18
2922 3184 2.851263 TCATTTGTCAGTAGGGCGTT 57.149 45.000 0.00 0.00 0.00 4.84
2923 3185 2.422597 TCATTTGTCAGTAGGGCGTTG 58.577 47.619 0.00 0.00 0.00 4.10
3001 3263 0.461135 GGGTCGTATTGGGCGAGTAA 59.539 55.000 0.00 0.00 39.14 2.24
3015 3277 7.136289 TGGGCGAGTAAAGTTTTATTTGTAG 57.864 36.000 0.00 0.00 0.00 2.74
3047 3309 1.996798 AAGGTGACTCTTGGACTCGA 58.003 50.000 0.00 0.00 42.68 4.04
3055 3317 1.543802 CTCTTGGACTCGAAGTGCTCT 59.456 52.381 7.71 0.00 37.46 4.09
3077 3339 3.836562 TGGGAAGAAACTAGAGTACCACC 59.163 47.826 0.00 0.00 0.00 4.61
3080 3342 4.527427 GGAAGAAACTAGAGTACCACCACT 59.473 45.833 0.00 0.00 0.00 4.00
3086 3348 1.558233 AGAGTACCACCACTGCCTAC 58.442 55.000 0.00 0.00 0.00 3.18
3093 3355 1.899814 CCACCACTGCCTACTTGTCTA 59.100 52.381 0.00 0.00 0.00 2.59
3094 3356 2.501723 CCACCACTGCCTACTTGTCTAT 59.498 50.000 0.00 0.00 0.00 1.98
3095 3357 3.430929 CCACCACTGCCTACTTGTCTATC 60.431 52.174 0.00 0.00 0.00 2.08
3096 3358 3.449018 CACCACTGCCTACTTGTCTATCT 59.551 47.826 0.00 0.00 0.00 1.98
3097 3359 4.645136 CACCACTGCCTACTTGTCTATCTA 59.355 45.833 0.00 0.00 0.00 1.98
3098 3360 5.303078 CACCACTGCCTACTTGTCTATCTAT 59.697 44.000 0.00 0.00 0.00 1.98
3099 3361 6.490381 CACCACTGCCTACTTGTCTATCTATA 59.510 42.308 0.00 0.00 0.00 1.31
3138 3400 0.669318 TGCTTCGTTGTCGATGGACC 60.669 55.000 5.33 0.00 45.65 4.46
3211 3480 1.142097 GCGTCCCTCACCTAAGCTC 59.858 63.158 0.00 0.00 0.00 4.09
3224 3493 5.422012 TCACCTAAGCTCAAGTACATCATCA 59.578 40.000 0.00 0.00 0.00 3.07
3225 3494 6.098838 TCACCTAAGCTCAAGTACATCATCAT 59.901 38.462 0.00 0.00 0.00 2.45
3226 3495 6.423302 CACCTAAGCTCAAGTACATCATCATC 59.577 42.308 0.00 0.00 0.00 2.92
3227 3496 6.098838 ACCTAAGCTCAAGTACATCATCATCA 59.901 38.462 0.00 0.00 0.00 3.07
3228 3497 6.988580 CCTAAGCTCAAGTACATCATCATCAA 59.011 38.462 0.00 0.00 0.00 2.57
3229 3498 6.922247 AAGCTCAAGTACATCATCATCAAG 57.078 37.500 0.00 0.00 0.00 3.02
3230 3499 4.815308 AGCTCAAGTACATCATCATCAAGC 59.185 41.667 0.00 0.00 0.00 4.01
3231 3500 4.573607 GCTCAAGTACATCATCATCAAGCA 59.426 41.667 0.00 0.00 0.00 3.91
3232 3501 5.238868 GCTCAAGTACATCATCATCAAGCAT 59.761 40.000 0.00 0.00 0.00 3.79
3233 3502 6.426025 GCTCAAGTACATCATCATCAAGCATA 59.574 38.462 0.00 0.00 0.00 3.14
3234 3503 7.360185 GCTCAAGTACATCATCATCAAGCATAG 60.360 40.741 0.00 0.00 0.00 2.23
3235 3504 6.426025 TCAAGTACATCATCATCAAGCATAGC 59.574 38.462 0.00 0.00 0.00 2.97
3236 3505 4.928020 AGTACATCATCATCAAGCATAGCG 59.072 41.667 0.00 0.00 0.00 4.26
3237 3506 2.483106 ACATCATCATCAAGCATAGCGC 59.517 45.455 0.00 0.00 42.91 5.92
3238 3507 2.243602 TCATCATCAAGCATAGCGCA 57.756 45.000 11.47 0.00 46.13 6.09
3239 3508 2.563702 TCATCATCAAGCATAGCGCAA 58.436 42.857 11.47 0.00 46.13 4.85
3240 3509 2.288729 TCATCATCAAGCATAGCGCAAC 59.711 45.455 11.47 0.00 46.13 4.17
3241 3510 1.736612 TCATCAAGCATAGCGCAACA 58.263 45.000 11.47 0.00 46.13 3.33
3242 3511 1.667212 TCATCAAGCATAGCGCAACAG 59.333 47.619 11.47 0.00 46.13 3.16
3243 3512 0.379669 ATCAAGCATAGCGCAACAGC 59.620 50.000 11.47 8.22 46.13 4.40
3244 3513 0.954938 TCAAGCATAGCGCAACAGCA 60.955 50.000 11.47 0.00 46.13 4.41
3245 3514 0.109643 CAAGCATAGCGCAACAGCAA 60.110 50.000 11.47 0.00 46.13 3.91
3246 3515 0.109597 AAGCATAGCGCAACAGCAAC 60.110 50.000 11.47 0.00 46.13 4.17
3247 3516 1.514873 GCATAGCGCAACAGCAACC 60.515 57.895 11.47 0.00 41.79 3.77
3248 3517 1.137404 CATAGCGCAACAGCAACCC 59.863 57.895 11.47 0.00 40.15 4.11
3249 3518 1.002134 ATAGCGCAACAGCAACCCT 60.002 52.632 11.47 0.00 40.15 4.34
3250 3519 0.609131 ATAGCGCAACAGCAACCCTT 60.609 50.000 11.47 0.00 40.15 3.95
3251 3520 1.514678 TAGCGCAACAGCAACCCTTG 61.515 55.000 11.47 0.00 40.15 3.61
3252 3521 3.119193 CGCAACAGCAACCCTTGT 58.881 55.556 0.00 0.00 0.00 3.16
3253 3522 1.437160 CGCAACAGCAACCCTTGTT 59.563 52.632 0.00 0.00 34.14 2.83
3254 3523 0.179113 CGCAACAGCAACCCTTGTTT 60.179 50.000 0.00 0.00 30.42 2.83
3255 3524 1.570813 GCAACAGCAACCCTTGTTTC 58.429 50.000 0.00 0.00 30.42 2.78
3256 3525 1.838913 CAACAGCAACCCTTGTTTCG 58.161 50.000 0.00 0.00 30.42 3.46
3257 3526 1.134175 CAACAGCAACCCTTGTTTCGT 59.866 47.619 0.00 0.00 30.42 3.85
3258 3527 1.021968 ACAGCAACCCTTGTTTCGTC 58.978 50.000 0.00 0.00 30.42 4.20
3259 3528 1.021202 CAGCAACCCTTGTTTCGTCA 58.979 50.000 0.00 0.00 30.42 4.35
3260 3529 1.608590 CAGCAACCCTTGTTTCGTCAT 59.391 47.619 0.00 0.00 30.42 3.06
3261 3530 1.880027 AGCAACCCTTGTTTCGTCATC 59.120 47.619 0.00 0.00 30.42 2.92
3262 3531 1.068541 GCAACCCTTGTTTCGTCATCC 60.069 52.381 0.00 0.00 30.42 3.51
3263 3532 2.226330 CAACCCTTGTTTCGTCATCCA 58.774 47.619 0.00 0.00 30.42 3.41
3264 3533 1.892209 ACCCTTGTTTCGTCATCCAC 58.108 50.000 0.00 0.00 0.00 4.02
3265 3534 1.420138 ACCCTTGTTTCGTCATCCACT 59.580 47.619 0.00 0.00 0.00 4.00
3266 3535 1.806542 CCCTTGTTTCGTCATCCACTG 59.193 52.381 0.00 0.00 0.00 3.66
3267 3536 1.806542 CCTTGTTTCGTCATCCACTGG 59.193 52.381 0.00 0.00 0.00 4.00
3268 3537 2.494059 CTTGTTTCGTCATCCACTGGT 58.506 47.619 0.00 0.00 0.00 4.00
3269 3538 3.556213 CCTTGTTTCGTCATCCACTGGTA 60.556 47.826 0.00 0.00 0.00 3.25
3270 3539 3.034721 TGTTTCGTCATCCACTGGTAC 57.965 47.619 0.00 0.00 0.00 3.34
3271 3540 2.289195 TGTTTCGTCATCCACTGGTACC 60.289 50.000 4.43 4.43 0.00 3.34
3272 3541 0.528924 TTCGTCATCCACTGGTACCG 59.471 55.000 7.57 4.79 0.00 4.02
3273 3542 1.141019 CGTCATCCACTGGTACCGG 59.859 63.158 19.74 19.74 0.00 5.28
3274 3543 1.317431 CGTCATCCACTGGTACCGGA 61.317 60.000 27.93 18.06 0.00 5.14
3275 3544 0.460311 GTCATCCACTGGTACCGGAG 59.540 60.000 27.93 19.24 30.84 4.63
3276 3545 1.144057 CATCCACTGGTACCGGAGC 59.856 63.158 27.93 1.71 30.84 4.70
3277 3546 1.305802 ATCCACTGGTACCGGAGCA 60.306 57.895 27.93 5.89 30.84 4.26
3278 3547 0.907704 ATCCACTGGTACCGGAGCAA 60.908 55.000 27.93 10.48 34.44 3.91
3279 3548 1.079127 CCACTGGTACCGGAGCAAG 60.079 63.158 27.93 10.43 34.44 4.01
3280 3549 1.541310 CCACTGGTACCGGAGCAAGA 61.541 60.000 27.93 0.00 34.44 3.02
3281 3550 0.320374 CACTGGTACCGGAGCAAGAA 59.680 55.000 27.93 0.00 34.44 2.52
3282 3551 1.053424 ACTGGTACCGGAGCAAGAAA 58.947 50.000 27.93 0.00 34.44 2.52
3283 3552 1.418637 ACTGGTACCGGAGCAAGAAAA 59.581 47.619 27.93 0.00 34.44 2.29
3284 3553 2.039879 ACTGGTACCGGAGCAAGAAAAT 59.960 45.455 27.93 0.00 34.44 1.82
3285 3554 2.420022 CTGGTACCGGAGCAAGAAAATG 59.580 50.000 16.40 0.00 34.44 2.32
3286 3555 1.743394 GGTACCGGAGCAAGAAAATGG 59.257 52.381 9.46 0.00 0.00 3.16
3287 3556 1.743394 GTACCGGAGCAAGAAAATGGG 59.257 52.381 9.46 0.00 0.00 4.00
3288 3557 1.250840 ACCGGAGCAAGAAAATGGGC 61.251 55.000 9.46 0.00 0.00 5.36
3289 3558 0.967380 CCGGAGCAAGAAAATGGGCT 60.967 55.000 0.00 0.00 39.75 5.19
3290 3559 0.890683 CGGAGCAAGAAAATGGGCTT 59.109 50.000 0.00 0.00 36.59 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.877443 CTTCCCCAATTATAACCCGCG 59.123 52.381 0.00 0.00 0.00 6.46
45 46 5.761003 TCGTCCCGTTTTTATTTTTCTTCC 58.239 37.500 0.00 0.00 0.00 3.46
55 56 3.672808 TGCCTAATTCGTCCCGTTTTTA 58.327 40.909 0.00 0.00 0.00 1.52
66 68 2.776312 TAGACTCGCTGCCTAATTCG 57.224 50.000 0.00 0.00 0.00 3.34
79 81 4.202121 TGCACCCTACGATTCATTAGACTC 60.202 45.833 0.00 0.00 0.00 3.36
150 154 1.087771 GGATTGGGGAACAGTACGCG 61.088 60.000 3.53 3.53 0.00 6.01
169 173 1.746220 TGGAACCAAATTTATCGCCGG 59.254 47.619 0.00 0.00 0.00 6.13
228 233 5.152623 TGATTCGTCCAGATCAGTTTCTT 57.847 39.130 0.00 0.00 0.00 2.52
230 235 4.260538 GCATGATTCGTCCAGATCAGTTTC 60.261 45.833 0.00 0.00 0.00 2.78
239 244 2.353889 CTCCTTTGCATGATTCGTCCAG 59.646 50.000 0.00 0.00 0.00 3.86
287 293 1.196766 AGGTTAACCGGGACAGGGAC 61.197 60.000 18.91 0.00 42.08 4.46
314 320 2.730715 CGAAAACACACACACCCACAAG 60.731 50.000 0.00 0.00 0.00 3.16
317 323 0.524604 GCGAAAACACACACACCCAC 60.525 55.000 0.00 0.00 0.00 4.61
320 326 0.383949 ATGGCGAAAACACACACACC 59.616 50.000 0.00 0.00 0.00 4.16
327 333 0.313672 TCTGGCAATGGCGAAAACAC 59.686 50.000 1.51 0.00 42.47 3.32
328 334 1.202114 GATCTGGCAATGGCGAAAACA 59.798 47.619 1.51 0.00 42.47 2.83
329 335 1.202114 TGATCTGGCAATGGCGAAAAC 59.798 47.619 1.51 1.04 42.47 2.43
353 359 1.377725 CACCCAGACAGTCCATGGC 60.378 63.158 6.96 2.00 37.09 4.40
465 485 0.524862 TCTCCTTTCGTGCCTCGTAC 59.475 55.000 0.00 0.00 40.80 3.67
466 486 0.809385 CTCTCCTTTCGTGCCTCGTA 59.191 55.000 0.00 0.00 40.80 3.43
469 489 1.546476 TCTTCTCTCCTTTCGTGCCTC 59.454 52.381 0.00 0.00 0.00 4.70
481 501 1.645710 TGGTGGGGTTCTCTTCTCTC 58.354 55.000 0.00 0.00 0.00 3.20
533 587 4.830765 TGATTTCCTCGGCCGCGG 62.831 66.667 28.44 28.44 0.00 6.46
553 607 2.207590 GGCTAGTTTATTTCCCGGTCG 58.792 52.381 0.00 0.00 0.00 4.79
565 619 2.301870 TGTGATTCTGTCGGGCTAGTTT 59.698 45.455 0.00 0.00 0.00 2.66
568 622 1.751351 TCTGTGATTCTGTCGGGCTAG 59.249 52.381 0.00 0.00 0.00 3.42
571 625 0.037326 TGTCTGTGATTCTGTCGGGC 60.037 55.000 0.00 0.00 0.00 6.13
581 635 1.230635 GCCTTGCGTGTGTCTGTGAT 61.231 55.000 0.00 0.00 0.00 3.06
625 679 1.213013 GTCCCGATCGATCCATCCG 59.787 63.158 18.66 8.09 0.00 4.18
626 680 1.213013 CGTCCCGATCGATCCATCC 59.787 63.158 18.66 4.97 0.00 3.51
650 704 2.859032 GCGCTACACTATACACCTGAGC 60.859 54.545 0.00 0.00 0.00 4.26
671 730 1.003355 CACCACTACACCTGGGCTG 60.003 63.158 0.00 0.00 32.45 4.85
674 733 0.321671 CTGTCACCACTACACCTGGG 59.678 60.000 0.00 0.00 32.45 4.45
678 737 1.374252 CGCCTGTCACCACTACACC 60.374 63.158 0.00 0.00 0.00 4.16
741 842 1.742880 CCTGGTCCGTGTGCTCATG 60.743 63.158 0.86 0.86 0.00 3.07
803 908 4.748679 CTTTGGCTGCTGCGCGTC 62.749 66.667 8.43 0.00 40.82 5.19
816 921 2.050442 GCGCGGGGTGAAACTTTG 60.050 61.111 8.83 0.00 36.74 2.77
832 937 1.194495 GCCGGTATATATACACGCGC 58.806 55.000 21.56 19.89 34.98 6.86
892 1003 1.206072 GCTGTTGCGCTCTCTTGTG 59.794 57.895 9.73 0.00 0.00 3.33
944 1067 4.215742 TAGCCCGAATGGTCGCCG 62.216 66.667 0.00 0.00 46.28 6.46
945 1068 2.280186 CTAGCCCGAATGGTCGCC 60.280 66.667 0.00 0.00 46.28 5.54
946 1069 2.083835 TAGCTAGCCCGAATGGTCGC 62.084 60.000 12.13 0.00 46.28 5.19
947 1070 3.929672 GCTAGCTAGCCCGAATGGTCG 62.930 61.905 31.67 0.00 43.39 4.79
1188 1357 2.231478 CAGTCGAGTTCTCCCTTAAGCA 59.769 50.000 0.00 0.00 0.00 3.91
1189 1358 2.492484 TCAGTCGAGTTCTCCCTTAAGC 59.508 50.000 0.00 0.00 0.00 3.09
1196 1365 2.200067 CATGCATCAGTCGAGTTCTCC 58.800 52.381 0.00 0.00 0.00 3.71
1212 1381 2.725723 CGAACCAAAACACATCACATGC 59.274 45.455 0.00 0.00 0.00 4.06
1379 1548 0.601046 GGGTGCTGCAAAAGGAAAGC 60.601 55.000 2.77 0.00 36.18 3.51
1383 1552 0.106268 TTCAGGGTGCTGCAAAAGGA 60.106 50.000 2.77 0.00 0.00 3.36
1387 1556 1.682854 CTTTCTTCAGGGTGCTGCAAA 59.317 47.619 2.77 0.00 0.00 3.68
1422 1621 2.162681 GTTAGCCCACTGCAGTTGATT 58.837 47.619 18.94 7.93 44.83 2.57
1642 1858 2.191109 GTGGTGGTCGTGGTGGTT 59.809 61.111 0.00 0.00 0.00 3.67
1713 1929 5.721960 TCCAGCTCCAATTCTAGTTCTAGTT 59.278 40.000 6.73 0.00 0.00 2.24
1714 1930 5.273208 TCCAGCTCCAATTCTAGTTCTAGT 58.727 41.667 6.73 0.00 0.00 2.57
1715 1931 5.596361 TCTCCAGCTCCAATTCTAGTTCTAG 59.404 44.000 0.83 0.83 0.00 2.43
1716 1932 5.519808 TCTCCAGCTCCAATTCTAGTTCTA 58.480 41.667 0.00 0.00 0.00 2.10
1717 1933 4.357325 TCTCCAGCTCCAATTCTAGTTCT 58.643 43.478 0.00 0.00 0.00 3.01
1718 1934 4.744795 TCTCCAGCTCCAATTCTAGTTC 57.255 45.455 0.00 0.00 0.00 3.01
1980 2196 4.776322 CCGCATTGCTCCACGGGA 62.776 66.667 7.12 0.00 41.95 5.14
2006 2222 2.266055 CTCTGGTCCCTTGCCGTC 59.734 66.667 0.00 0.00 0.00 4.79
2123 2342 2.742403 CGGGTCCGGTTGTTGGTA 59.258 61.111 0.00 0.00 35.56 3.25
2199 2421 2.124695 GGCCGGCTTGGAAGTAGG 60.125 66.667 28.56 0.00 42.00 3.18
2233 2458 2.572333 CTTCGGGCCCATGGATGGTT 62.572 60.000 24.92 0.00 46.65 3.67
2234 2459 3.020647 TTCGGGCCCATGGATGGT 61.021 61.111 24.92 0.00 46.65 3.55
2245 2470 3.909086 AACTGCAGAGGCTTCGGGC 62.909 63.158 23.35 8.27 41.91 6.13
2305 2530 9.376075 CTATACTAAGAGATCGGACGGTTTATA 57.624 37.037 0.00 0.00 0.00 0.98
2306 2531 8.099537 TCTATACTAAGAGATCGGACGGTTTAT 58.900 37.037 0.00 0.00 0.00 1.40
2307 2532 7.445121 TCTATACTAAGAGATCGGACGGTTTA 58.555 38.462 0.00 0.00 0.00 2.01
2308 2533 6.294473 TCTATACTAAGAGATCGGACGGTTT 58.706 40.000 0.00 0.00 0.00 3.27
2358 2583 3.833442 TGTTGTGTACTAGCATCAGTCG 58.167 45.455 0.00 0.00 0.00 4.18
2402 2629 2.816958 CCTGCTGCAGGCGTACAG 60.817 66.667 33.52 13.16 45.13 2.74
2430 2657 2.615447 CGTATAGTCTTCGTGCTGGGTA 59.385 50.000 0.00 0.00 0.00 3.69
2479 2714 1.301244 CCTCGAGCTTGTGTGTGCT 60.301 57.895 6.99 0.00 42.82 4.40
2491 2726 7.778470 AAGTTATTTTAAGCATCTCCTCGAG 57.222 36.000 5.13 5.13 0.00 4.04
2492 2727 8.561738 AAAAGTTATTTTAAGCATCTCCTCGA 57.438 30.769 0.00 0.00 36.85 4.04
2493 2728 7.910683 GGAAAAGTTATTTTAAGCATCTCCTCG 59.089 37.037 0.00 0.00 38.74 4.63
2494 2729 8.739972 TGGAAAAGTTATTTTAAGCATCTCCTC 58.260 33.333 0.00 0.00 38.74 3.71
2521 2756 2.127270 GCAACGTGGTCGCATGTG 60.127 61.111 0.00 0.00 41.18 3.21
2531 2778 4.724697 CTGCTTCGGCGCAACGTG 62.725 66.667 10.83 3.75 45.37 4.49
2538 2785 2.127118 CACTTTGCTGCTTCGGCG 60.127 61.111 0.00 0.00 45.37 6.46
2560 2807 2.363220 CGTTTCTGACTTGTTTGCGTC 58.637 47.619 0.00 0.00 0.00 5.19
2569 2816 1.489230 ACCTTGACCCGTTTCTGACTT 59.511 47.619 0.00 0.00 0.00 3.01
2575 2822 0.589708 CGGAAACCTTGACCCGTTTC 59.410 55.000 4.48 4.48 44.58 2.78
2603 2850 2.027469 AGTTGAGTTACATCCCGGGTTC 60.027 50.000 22.86 8.52 0.00 3.62
2704 2965 4.766404 AAACCGTAGCAGGAATTTCTTG 57.234 40.909 4.25 4.25 34.73 3.02
2705 2966 4.022329 CCAAAACCGTAGCAGGAATTTCTT 60.022 41.667 0.00 0.00 34.73 2.52
2706 2967 3.506067 CCAAAACCGTAGCAGGAATTTCT 59.494 43.478 0.00 0.00 34.73 2.52
2778 3040 0.689623 AGGAGACAGGCTTCACCAAG 59.310 55.000 12.75 0.00 43.14 3.61
2800 3062 0.962356 AGCAGCGAATGGGAAAGGTG 60.962 55.000 0.00 0.00 35.47 4.00
2837 3099 5.993441 TGTAAACTAGAGCCAAAGTGGTTAC 59.007 40.000 0.00 0.00 40.46 2.50
2838 3100 6.177310 TGTAAACTAGAGCCAAAGTGGTTA 57.823 37.500 0.00 0.00 40.46 2.85
2922 3184 0.530431 CCATGTCATGATCCGCGACA 60.530 55.000 14.67 1.36 43.35 4.35
2923 3185 0.249447 TCCATGTCATGATCCGCGAC 60.249 55.000 14.67 0.00 0.00 5.19
2974 3236 1.299620 CAATACGACCCGGCCGTAG 60.300 63.158 26.12 17.81 44.27 3.51
3038 3300 0.318441 CCAGAGCACTTCGAGTCCAA 59.682 55.000 0.00 0.00 0.00 3.53
3045 3307 1.801178 GTTTCTTCCCAGAGCACTTCG 59.199 52.381 0.00 0.00 0.00 3.79
3047 3309 3.904339 TCTAGTTTCTTCCCAGAGCACTT 59.096 43.478 0.00 0.00 30.47 3.16
3055 3317 3.836562 GGTGGTACTCTAGTTTCTTCCCA 59.163 47.826 0.00 0.00 0.00 4.37
3077 3339 8.341892 TCATATAGATAGACAAGTAGGCAGTG 57.658 38.462 0.00 0.00 0.00 3.66
3097 3359 9.799106 AAGCAGCTTACATAGGTTTTATCATAT 57.201 29.630 5.62 0.00 30.51 1.78
3098 3360 9.273016 GAAGCAGCTTACATAGGTTTTATCATA 57.727 33.333 7.92 0.00 30.51 2.15
3099 3361 7.041780 CGAAGCAGCTTACATAGGTTTTATCAT 60.042 37.037 7.92 0.00 30.51 2.45
3109 3371 3.000674 CGACAACGAAGCAGCTTACATAG 60.001 47.826 7.92 0.14 42.66 2.23
3138 3400 1.399440 CACGTGAGATTTGGAGCCATG 59.601 52.381 10.90 0.00 0.00 3.66
3211 3480 6.600350 GCTATGCTTGATGATGATGTACTTG 58.400 40.000 0.00 0.00 0.00 3.16
3224 3493 0.379669 GCTGTTGCGCTATGCTTGAT 59.620 50.000 9.73 0.00 46.63 2.57
3225 3494 0.954938 TGCTGTTGCGCTATGCTTGA 60.955 50.000 9.73 0.00 46.63 3.02
3226 3495 0.109643 TTGCTGTTGCGCTATGCTTG 60.110 50.000 9.73 0.00 46.63 4.01
3227 3496 0.109597 GTTGCTGTTGCGCTATGCTT 60.110 50.000 9.73 0.00 46.63 3.91
3228 3497 1.503542 GTTGCTGTTGCGCTATGCT 59.496 52.632 9.73 0.00 46.63 3.79
3229 3498 1.514873 GGTTGCTGTTGCGCTATGC 60.515 57.895 9.73 10.77 43.34 3.14
3230 3499 1.137404 GGGTTGCTGTTGCGCTATG 59.863 57.895 9.73 0.00 43.34 2.23
3231 3500 0.609131 AAGGGTTGCTGTTGCGCTAT 60.609 50.000 9.73 0.00 43.34 2.97
3232 3501 1.228124 AAGGGTTGCTGTTGCGCTA 60.228 52.632 9.73 0.00 43.34 4.26
3233 3502 2.519302 AAGGGTTGCTGTTGCGCT 60.519 55.556 9.73 0.00 43.34 5.92
3234 3503 2.355009 CAAGGGTTGCTGTTGCGC 60.355 61.111 0.00 0.00 43.34 6.09
3235 3504 0.179113 AAACAAGGGTTGCTGTTGCG 60.179 50.000 0.00 0.00 43.34 4.85
3236 3505 1.570813 GAAACAAGGGTTGCTGTTGC 58.429 50.000 0.00 0.00 37.30 4.17
3237 3506 1.134175 ACGAAACAAGGGTTGCTGTTG 59.866 47.619 0.00 0.00 37.30 3.33
3238 3507 1.404035 GACGAAACAAGGGTTGCTGTT 59.596 47.619 0.00 0.00 37.30 3.16
3239 3508 1.021968 GACGAAACAAGGGTTGCTGT 58.978 50.000 0.00 0.00 37.30 4.40
3240 3509 1.021202 TGACGAAACAAGGGTTGCTG 58.979 50.000 0.00 0.00 37.30 4.41
3241 3510 1.880027 GATGACGAAACAAGGGTTGCT 59.120 47.619 0.00 0.00 37.30 3.91
3242 3511 1.068541 GGATGACGAAACAAGGGTTGC 60.069 52.381 0.00 0.00 37.30 4.17
3243 3512 2.031157 GTGGATGACGAAACAAGGGTTG 60.031 50.000 0.00 0.00 37.30 3.77
3244 3513 2.158667 AGTGGATGACGAAACAAGGGTT 60.159 45.455 0.00 0.00 39.43 4.11
3245 3514 1.420138 AGTGGATGACGAAACAAGGGT 59.580 47.619 0.00 0.00 0.00 4.34
3246 3515 1.806542 CAGTGGATGACGAAACAAGGG 59.193 52.381 0.00 0.00 0.00 3.95
3247 3516 1.806542 CCAGTGGATGACGAAACAAGG 59.193 52.381 1.68 0.00 0.00 3.61
3248 3517 2.494059 ACCAGTGGATGACGAAACAAG 58.506 47.619 18.40 0.00 0.00 3.16
3249 3518 2.631160 ACCAGTGGATGACGAAACAA 57.369 45.000 18.40 0.00 0.00 2.83
3250 3519 2.289195 GGTACCAGTGGATGACGAAACA 60.289 50.000 18.40 0.00 0.00 2.83
3251 3520 2.344025 GGTACCAGTGGATGACGAAAC 58.656 52.381 18.40 0.66 0.00 2.78
3252 3521 1.067425 CGGTACCAGTGGATGACGAAA 60.067 52.381 18.40 0.00 0.00 3.46
3253 3522 0.528924 CGGTACCAGTGGATGACGAA 59.471 55.000 18.40 0.00 0.00 3.85
3254 3523 1.317431 CCGGTACCAGTGGATGACGA 61.317 60.000 18.40 0.00 0.00 4.20
3255 3524 1.141019 CCGGTACCAGTGGATGACG 59.859 63.158 18.40 13.97 0.00 4.35
3256 3525 0.460311 CTCCGGTACCAGTGGATGAC 59.540 60.000 18.40 10.46 0.00 3.06
3257 3526 1.327690 GCTCCGGTACCAGTGGATGA 61.328 60.000 18.40 3.58 0.00 2.92
3258 3527 1.144057 GCTCCGGTACCAGTGGATG 59.856 63.158 18.40 6.15 0.00 3.51
3259 3528 0.907704 TTGCTCCGGTACCAGTGGAT 60.908 55.000 18.40 2.54 0.00 3.41
3260 3529 1.534476 TTGCTCCGGTACCAGTGGA 60.534 57.895 18.40 9.73 0.00 4.02
3261 3530 1.079127 CTTGCTCCGGTACCAGTGG 60.079 63.158 13.54 7.91 0.00 4.00
3262 3531 0.320374 TTCTTGCTCCGGTACCAGTG 59.680 55.000 13.54 2.41 0.00 3.66
3263 3532 1.053424 TTTCTTGCTCCGGTACCAGT 58.947 50.000 13.54 0.00 0.00 4.00
3264 3533 2.178912 TTTTCTTGCTCCGGTACCAG 57.821 50.000 13.54 3.57 0.00 4.00
3265 3534 2.432444 CATTTTCTTGCTCCGGTACCA 58.568 47.619 13.54 0.00 0.00 3.25
3266 3535 1.743394 CCATTTTCTTGCTCCGGTACC 59.257 52.381 0.16 0.16 0.00 3.34
3267 3536 1.743394 CCCATTTTCTTGCTCCGGTAC 59.257 52.381 0.00 0.00 0.00 3.34
3268 3537 1.953311 GCCCATTTTCTTGCTCCGGTA 60.953 52.381 0.00 0.00 0.00 4.02
3269 3538 1.250840 GCCCATTTTCTTGCTCCGGT 61.251 55.000 0.00 0.00 0.00 5.28
3270 3539 0.967380 AGCCCATTTTCTTGCTCCGG 60.967 55.000 0.00 0.00 0.00 5.14
3271 3540 0.890683 AAGCCCATTTTCTTGCTCCG 59.109 50.000 0.00 0.00 32.62 4.63


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

AutoCloner maintained by Alex Coulton.