Multiple sequence alignment - TraesCS7B01G225100

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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 TraesCS7B01G225100 chr7B 100.000 4493 0 0 1 4493 425472646 425477138 0.000000e+00 8298.0
1 TraesCS7B01G225100 chr7A 93.820 2605 105 23 382 2983 472121486 472124037 0.000000e+00 3868.0
2 TraesCS7B01G225100 chr7A 93.134 670 28 5 3350 4009 472124534 472125195 0.000000e+00 966.0
3 TraesCS7B01G225100 chr7A 85.676 377 27 7 2975 3351 472124102 472124451 5.490000e-99 372.0
4 TraesCS7B01G225100 chr7A 90.850 153 14 0 4007 4159 472159525 472159677 5.890000e-49 206.0
5 TraesCS7B01G225100 chr7D 96.392 2328 72 5 633 2959 410060912 410058596 0.000000e+00 3823.0
6 TraesCS7B01G225100 chr7D 91.327 1326 54 10 2975 4250 410058231 410056917 0.000000e+00 1755.0
7 TraesCS7B01G225100 chr7D 91.772 632 50 2 3 634 410067264 410066635 0.000000e+00 878.0
8 TraesCS7B01G225100 chr7D 88.205 195 11 7 4161 4353 410054409 410054225 5.850000e-54 222.0
9 TraesCS7B01G225100 chr7D 93.103 116 6 2 4350 4464 127694687 127694801 7.730000e-38 169.0
10 TraesCS7B01G225100 chr7D 91.892 111 9 0 4354 4464 556638096 556637986 6.020000e-34 156.0
11 TraesCS7B01G225100 chr7D 91.358 81 4 2 4251 4331 410056798 410056721 1.710000e-19 108.0
12 TraesCS7B01G225100 chr6A 93.966 116 5 2 4350 4464 270601645 270601759 1.660000e-39 174.0
13 TraesCS7B01G225100 chr4B 92.174 115 8 1 4350 4464 591928538 591928425 1.290000e-35 161.0
14 TraesCS7B01G225100 chr4B 94.175 103 6 0 4353 4455 173177183 173177285 1.670000e-34 158.0
15 TraesCS7B01G225100 chr2D 92.105 114 5 4 4353 4464 118039446 118039557 1.670000e-34 158.0
16 TraesCS7B01G225100 chr1D 91.964 112 7 2 4353 4464 482306376 482306267 6.020000e-34 156.0
17 TraesCS7B01G225100 chr1D 93.333 105 6 1 4350 4454 263196271 263196168 2.160000e-33 154.0
18 TraesCS7B01G225100 chr2A 91.818 110 9 0 4355 4464 680295289 680295398 2.160000e-33 154.0
19 TraesCS7B01G225100 chr3A 97.561 41 1 0 3256 3296 224372099 224372059 2.240000e-08 71.3
20 TraesCS7B01G225100 chrUn 97.143 35 1 0 3255 3289 83375585 83375551 4.850000e-05 60.2
21 TraesCS7B01G225100 chr2B 97.059 34 1 0 3256 3289 200019305 200019338 1.750000e-04 58.4


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 TraesCS7B01G225100 chr7B 425472646 425477138 4492 False 8298.000000 8298 100.000000 1 4493 1 chr7B.!!$F1 4492
1 TraesCS7B01G225100 chr7A 472121486 472125195 3709 False 1735.333333 3868 90.876667 382 4009 3 chr7A.!!$F2 3627
2 TraesCS7B01G225100 chr7D 410054225 410060912 6687 True 1477.000000 3823 91.820500 633 4353 4 chr7D.!!$R3 3720
3 TraesCS7B01G225100 chr7D 410066635 410067264 629 True 878.000000 878 91.772000 3 634 1 chr7D.!!$R1 631

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
572 573 0.313043 GCGCCAGCTCATTGCATTAT 59.687 50.0 0.00 0.0 45.94 1.28 F
2368 2371 0.323302 TTCCCGCAGTGTGAGCATTA 59.677 50.0 4.93 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2515 2518 0.108233 CTCAGCAGCTCCTCCAAGTC 60.108 60.0 0.0 0.0 0.0 3.01 R
3783 4252 0.463295 ATGACAGGCAGCTCATTCCG 60.463 55.0 0.0 0.0 0.0 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
33 34 4.837972 TCCACCAAACACGATCATTGATA 58.162 39.130 0.00 0.00 0.00 2.15
35 36 5.353956 TCCACCAAACACGATCATTGATAAG 59.646 40.000 0.00 0.00 0.00 1.73
56 57 1.895798 GGATCCTCCGCATCTATCACA 59.104 52.381 3.84 0.00 0.00 3.58
75 76 6.317789 TCACAAAGTCATCAAATTCCTCAC 57.682 37.500 0.00 0.00 0.00 3.51
76 77 5.827267 TCACAAAGTCATCAAATTCCTCACA 59.173 36.000 0.00 0.00 0.00 3.58
119 120 4.576330 AAAAACATCTAGGTGAGGGAGG 57.424 45.455 10.76 0.00 0.00 4.30
139 140 4.101448 GCTCCAGACCCACCGCAT 62.101 66.667 0.00 0.00 0.00 4.73
153 154 3.807538 GCATGTGGCCGAGTGCTG 61.808 66.667 16.15 1.82 40.92 4.41
161 162 1.670949 GGCCGAGTGCTGATCAGAGA 61.671 60.000 27.04 8.85 40.92 3.10
182 183 1.800315 GTCGTCATCGTCGTGTGGG 60.800 63.158 0.00 0.00 38.33 4.61
189 190 4.920112 CGTCGTGTGGGTGGGCAA 62.920 66.667 0.00 0.00 0.00 4.52
194 195 4.514585 TGTGGGTGGGCAAAGCGT 62.515 61.111 0.00 0.00 0.00 5.07
199 200 3.799755 GTGGGCAAAGCGTAGGCG 61.800 66.667 1.05 0.00 46.35 5.52
228 229 3.944250 AAGGCGGGCAACTGGATGG 62.944 63.158 3.78 0.00 45.89 3.51
326 327 3.712907 GCTAGGCCACGAACCCCA 61.713 66.667 5.01 0.00 0.00 4.96
336 337 0.469144 ACGAACCCCAAAGGCAACAT 60.469 50.000 0.00 0.00 40.58 2.71
348 349 1.164411 GGCAACATGTTCGATCCACA 58.836 50.000 8.48 0.00 0.00 4.17
402 403 2.681778 CACGGGAGCTCAGGGACT 60.682 66.667 17.19 0.00 43.88 3.85
435 436 2.899339 GAGCAAGGAGATGGCGGC 60.899 66.667 0.00 0.00 0.00 6.53
474 475 2.231215 ATACGATGCAGCAGAAGACC 57.769 50.000 1.53 0.00 0.00 3.85
510 511 3.054503 CGTCGAGGGAGTCACCGT 61.055 66.667 0.00 0.00 40.11 4.83
513 514 1.001269 TCGAGGGAGTCACCGTGAT 60.001 57.895 4.13 0.00 40.11 3.06
533 534 5.701290 GTGATGATATTAAACCTTAGCCGCT 59.299 40.000 0.00 0.00 0.00 5.52
557 558 1.735973 GGGATCCATTTCAAGCGCC 59.264 57.895 15.23 0.00 0.00 6.53
572 573 0.313043 GCGCCAGCTCATTGCATTAT 59.687 50.000 0.00 0.00 45.94 1.28
591 592 9.027129 TGCATTATAGAATATTATTACCGCGAC 57.973 33.333 8.23 0.00 0.00 5.19
623 624 4.764823 CCCAGACAAGCCTTATTGTTGTAA 59.235 41.667 0.00 0.00 43.32 2.41
704 707 5.538813 ACCTTGTTTCCCAAAGAAATAGGAC 59.461 40.000 18.39 0.00 45.99 3.85
870 873 3.352524 ACCTCGTCGGTCACTCAC 58.647 61.111 0.00 0.00 44.93 3.51
1140 1143 2.997897 GCCCTATCCGCCTCCGAT 60.998 66.667 0.00 0.00 36.29 4.18
1311 1314 2.048127 GAGCTCGGCAACCTCGTT 60.048 61.111 0.00 0.00 0.00 3.85
1312 1315 2.357517 AGCTCGGCAACCTCGTTG 60.358 61.111 0.08 0.08 45.24 4.10
1551 1554 0.682855 CTGTCTCCTCCGAGCCTTCT 60.683 60.000 0.00 0.00 35.94 2.85
1552 1555 0.967887 TGTCTCCTCCGAGCCTTCTG 60.968 60.000 0.00 0.00 35.94 3.02
1575 1578 0.545548 AGTTCTCCCGCCTCTCCTTT 60.546 55.000 0.00 0.00 0.00 3.11
1620 1623 4.039357 CTCGTGGCCTCGTGTCGT 62.039 66.667 25.10 0.00 0.00 4.34
1625 1628 2.261671 GGCCTCGTGTCGTGTCAT 59.738 61.111 0.00 0.00 0.00 3.06
1945 1948 3.494378 CGGACAGCAAGCATCTGG 58.506 61.111 0.00 0.00 35.94 3.86
2295 2298 3.315765 TGGGTCGTCCATGTTTGTC 57.684 52.632 0.04 0.00 41.46 3.18
2307 2310 4.178169 TTTGTCGTGCGGGTGGGT 62.178 61.111 0.00 0.00 0.00 4.51
2311 2314 4.308458 TCGTGCGGGTGGGTGAAG 62.308 66.667 0.00 0.00 0.00 3.02
2333 2336 3.737047 GCATCAACAGAGGCATTTCCATG 60.737 47.826 0.00 0.00 38.81 3.66
2334 2337 2.449464 TCAACAGAGGCATTTCCATGG 58.551 47.619 4.97 4.97 37.29 3.66
2343 2346 1.451387 ATTTCCATGGCCGACCGAC 60.451 57.895 6.96 0.00 39.70 4.79
2368 2371 0.323302 TTCCCGCAGTGTGAGCATTA 59.677 50.000 4.93 0.00 0.00 1.90
2538 2541 0.837691 TGGAGGAGCTGCTGAGGAAA 60.838 55.000 14.48 0.00 0.00 3.13
2571 2574 0.393673 CCACATTGCCACCGATACCA 60.394 55.000 0.00 0.00 0.00 3.25
2577 2580 2.279935 TGCCACCGATACCAAACTTT 57.720 45.000 0.00 0.00 0.00 2.66
2691 2694 8.695456 TCTGCTGTCATAGTTGATTACAGATTA 58.305 33.333 5.03 0.00 40.78 1.75
2692 2695 9.317936 CTGCTGTCATAGTTGATTACAGATTAA 57.682 33.333 5.03 0.00 40.78 1.40
2714 2717 6.670695 AAAGACTTCCAATTGCTGGTTAAT 57.329 33.333 0.00 0.00 46.51 1.40
2715 2718 5.904362 AGACTTCCAATTGCTGGTTAATC 57.096 39.130 0.00 0.00 46.51 1.75
2716 2719 4.706962 AGACTTCCAATTGCTGGTTAATCC 59.293 41.667 0.00 0.00 46.51 3.01
2717 2720 4.415596 ACTTCCAATTGCTGGTTAATCCA 58.584 39.130 0.00 0.00 46.51 3.41
2718 2721 4.220602 ACTTCCAATTGCTGGTTAATCCAC 59.779 41.667 0.00 0.00 46.51 4.02
2730 2733 6.368791 GCTGGTTAATCCACTTTGAAAAATCC 59.631 38.462 0.00 0.00 41.93 3.01
2756 2759 1.640428 ATCTGTTGCGACATGTACCG 58.360 50.000 7.38 0.00 34.72 4.02
2774 2777 5.825507 GTACCGAACTATAACTGGTACCAG 58.174 45.833 35.54 35.54 45.91 4.00
2805 2808 7.482169 TCTTATCAGTTGTTAGACCATCTGT 57.518 36.000 0.00 0.00 34.95 3.41
2824 2827 5.579047 TCTGTGGTCACCCATTTCATATTT 58.421 37.500 0.00 0.00 44.35 1.40
2849 2852 0.599558 CTTGCACAACCATGTCCCAG 59.400 55.000 0.00 0.00 37.82 4.45
2855 2858 2.692557 CACAACCATGTCCCAGAACAAA 59.307 45.455 0.00 0.00 37.82 2.83
2866 2869 4.000325 TCCCAGAACAAACATGATGTACG 59.000 43.478 0.00 0.00 0.00 3.67
2867 2870 3.126858 CCCAGAACAAACATGATGTACGG 59.873 47.826 0.00 5.84 0.00 4.02
2875 2878 5.121768 ACAAACATGATGTACGGAGTTAAGC 59.878 40.000 0.00 0.00 37.78 3.09
2883 2886 7.959175 TGATGTACGGAGTTAAGCCTAAATAT 58.041 34.615 0.00 0.00 37.78 1.28
2886 2889 9.623000 ATGTACGGAGTTAAGCCTAAATATTTT 57.377 29.630 5.91 0.00 37.78 1.82
2914 2917 6.865834 TGGGCAAATTTCCATATTAGTTGT 57.134 33.333 8.36 0.00 0.00 3.32
2915 2918 6.638610 TGGGCAAATTTCCATATTAGTTGTG 58.361 36.000 8.36 0.00 0.00 3.33
2940 2944 0.536006 AACCCTGTGCTCTGAACAGC 60.536 55.000 4.34 0.00 43.06 4.40
2942 2946 1.071987 CCTGTGCTCTGAACAGCCA 59.928 57.895 4.34 0.00 43.06 4.75
2945 2949 0.107263 TGTGCTCTGAACAGCCAACA 60.107 50.000 0.00 0.00 38.80 3.33
2946 2950 0.308993 GTGCTCTGAACAGCCAACAC 59.691 55.000 0.00 0.15 38.80 3.32
2948 2952 0.819259 GCTCTGAACAGCCAACACCA 60.819 55.000 0.00 0.00 32.76 4.17
2959 2963 4.158394 ACAGCCAACACCATCATGATTAAC 59.842 41.667 5.16 0.00 0.00 2.01
2960 2964 4.158209 CAGCCAACACCATCATGATTAACA 59.842 41.667 5.16 0.00 0.00 2.41
2966 2970 6.748333 ACACCATCATGATTAACAGAGTTG 57.252 37.500 5.16 0.00 0.00 3.16
2967 2971 5.124457 ACACCATCATGATTAACAGAGTTGC 59.876 40.000 5.16 0.00 0.00 4.17
2972 3325 5.961272 TCATGATTAACAGAGTTGCGACTA 58.039 37.500 6.58 0.00 35.88 2.59
2973 3326 6.394809 TCATGATTAACAGAGTTGCGACTAA 58.605 36.000 6.58 0.00 35.88 2.24
2987 3340 4.584874 TGCGACTAAATCTTTTGATCCCA 58.415 39.130 0.00 0.00 38.40 4.37
2988 3341 5.007034 TGCGACTAAATCTTTTGATCCCAA 58.993 37.500 0.00 0.00 38.40 4.12
2992 3345 7.023575 CGACTAAATCTTTTGATCCCAACAAG 58.976 38.462 0.00 0.00 38.40 3.16
2998 3351 6.537453 TCTTTTGATCCCAACAAGTTTCAA 57.463 33.333 0.00 0.00 30.88 2.69
2999 3352 7.123355 TCTTTTGATCCCAACAAGTTTCAAT 57.877 32.000 0.00 0.00 30.88 2.57
3004 3357 7.537596 TGATCCCAACAAGTTTCAATATGTT 57.462 32.000 0.00 0.00 36.49 2.71
3006 3359 8.087750 TGATCCCAACAAGTTTCAATATGTTTC 58.912 33.333 0.00 0.00 33.97 2.78
3077 3430 6.546034 ACCAATTTATAGCTTACCATGACACC 59.454 38.462 0.00 0.00 0.00 4.16
3078 3431 6.545666 CCAATTTATAGCTTACCATGACACCA 59.454 38.462 0.00 0.00 0.00 4.17
3079 3432 7.231317 CCAATTTATAGCTTACCATGACACCAT 59.769 37.037 0.00 0.00 0.00 3.55
3080 3433 8.632679 CAATTTATAGCTTACCATGACACCATT 58.367 33.333 0.00 0.00 0.00 3.16
3081 3434 9.860650 AATTTATAGCTTACCATGACACCATTA 57.139 29.630 0.00 0.00 0.00 1.90
3082 3435 8.671384 TTTATAGCTTACCATGACACCATTAC 57.329 34.615 0.00 0.00 0.00 1.89
3083 3436 4.844349 AGCTTACCATGACACCATTACT 57.156 40.909 0.00 0.00 0.00 2.24
3084 3437 5.950544 AGCTTACCATGACACCATTACTA 57.049 39.130 0.00 0.00 0.00 1.82
3085 3438 6.500589 AGCTTACCATGACACCATTACTAT 57.499 37.500 0.00 0.00 0.00 2.12
3167 3520 6.236017 TGTTCTGAAACCTTAGTTATTGCG 57.764 37.500 0.00 0.00 34.19 4.85
3198 3551 8.976986 AAAAAGAGCAGCAGATACATTTTTAG 57.023 30.769 0.00 0.00 29.54 1.85
3203 3556 6.054295 AGCAGCAGATACATTTTTAGAGAGG 58.946 40.000 0.00 0.00 0.00 3.69
3266 3640 7.759489 TCACTAATGTAAGAACTGCCAAAAT 57.241 32.000 0.00 0.00 0.00 1.82
3311 3685 7.586349 AGGGTGTATTTCTTATGTGATTCCAT 58.414 34.615 0.00 0.00 0.00 3.41
3315 3689 9.722056 GTGTATTTCTTATGTGATTCCATTCAC 57.278 33.333 0.00 0.00 45.05 3.18
3339 3713 5.391203 CGCTGTTCTTCAATTGATGACATGA 60.391 40.000 20.34 6.47 37.92 3.07
3346 3720 7.988737 TCTTCAATTGATGACATGATGTAACC 58.011 34.615 17.55 0.00 37.92 2.85
3418 3876 3.003394 TGCATTGTCCAACATCCTAGG 57.997 47.619 0.82 0.82 0.00 3.02
3444 3902 5.247507 TCAGTTCACTGTTTCATTGTTGG 57.752 39.130 6.84 0.00 44.12 3.77
3461 3919 2.681344 GTTGGGCTACTCATTTAACGGG 59.319 50.000 0.00 0.00 0.00 5.28
3564 4022 1.748122 AGCGAGCAATGCTTCTGGG 60.748 57.895 9.91 0.00 40.48 4.45
3620 4088 2.561419 GCTTGCAATGATATGATGCCCT 59.439 45.455 0.00 0.00 39.31 5.19
3632 4100 1.818959 GATGCCCTGTTGCTGCCAAA 61.819 55.000 0.00 0.00 31.68 3.28
3698 4166 6.039829 GGAAATGCCACTTTCCCTAAGAATAG 59.960 42.308 10.08 0.00 45.63 1.73
3701 4169 5.030147 TGCCACTTTCCCTAAGAATAGAGA 58.970 41.667 0.00 0.00 37.30 3.10
3711 4179 7.000472 TCCCTAAGAATAGAGAAAATGGCATG 59.000 38.462 0.00 0.00 0.00 4.06
3724 4192 8.938801 AGAAAATGGCATGGATATACATAACA 57.061 30.769 0.00 3.22 0.00 2.41
3966 4435 7.870509 AGCTCATTTGTGTCATACATTATGT 57.129 32.000 2.58 2.58 39.48 2.29
4019 4488 9.559732 TCTTGAAGAACTATTGATTGTTCAGAA 57.440 29.630 16.58 7.99 42.36 3.02
4021 4490 8.675705 TGAAGAACTATTGATTGTTCAGAACA 57.324 30.769 12.24 12.24 42.36 3.18
4086 4555 0.610687 AGTAACCTCAGCTGTGCCTC 59.389 55.000 14.67 1.84 0.00 4.70
4099 4568 2.086869 TGTGCCTCTAAGAGCATTTGC 58.913 47.619 0.00 0.00 41.86 3.68
4146 4615 2.297698 TCTAGGAACTTCGGTGGTCA 57.702 50.000 0.00 0.00 41.75 4.02
4159 4628 3.257127 TCGGTGGTCATCGCATAATATCA 59.743 43.478 0.00 0.00 34.38 2.15
4190 4677 3.180891 TCCACATTCACACAACGTACA 57.819 42.857 0.00 0.00 0.00 2.90
4257 4862 9.635520 ACAGATTATAAAATACTCCGTATTCCG 57.364 33.333 0.25 0.00 37.69 4.30
4261 4866 8.836268 TTATAAAATACTCCGTATTCCGCATT 57.164 30.769 0.25 0.00 37.69 3.56
4269 4874 6.228258 ACTCCGTATTCCGCATTAACAATAT 58.772 36.000 0.00 0.00 34.38 1.28
4270 4875 6.708949 ACTCCGTATTCCGCATTAACAATATT 59.291 34.615 0.00 0.00 34.38 1.28
4271 4876 7.874016 ACTCCGTATTCCGCATTAACAATATTA 59.126 33.333 0.00 0.00 34.38 0.98
4272 4877 8.246908 TCCGTATTCCGCATTAACAATATTAG 57.753 34.615 0.00 0.00 34.38 1.73
4336 4941 8.147704 ACAACCAAAATCCAACTTATACAAAGG 58.852 33.333 0.00 0.00 0.00 3.11
4337 4942 8.364142 CAACCAAAATCCAACTTATACAAAGGA 58.636 33.333 0.00 0.00 0.00 3.36
4338 4943 8.485578 ACCAAAATCCAACTTATACAAAGGAA 57.514 30.769 0.00 0.00 0.00 3.36
4339 4944 8.585018 ACCAAAATCCAACTTATACAAAGGAAG 58.415 33.333 0.00 0.00 0.00 3.46
4340 4945 7.545615 CCAAAATCCAACTTATACAAAGGAAGC 59.454 37.037 0.00 0.00 0.00 3.86
4341 4946 6.436843 AATCCAACTTATACAAAGGAAGCG 57.563 37.500 0.00 0.00 0.00 4.68
4342 4947 4.258543 TCCAACTTATACAAAGGAAGCGG 58.741 43.478 0.00 0.00 0.00 5.52
4343 4948 4.020039 TCCAACTTATACAAAGGAAGCGGA 60.020 41.667 0.00 0.00 0.00 5.54
4344 4949 4.881850 CCAACTTATACAAAGGAAGCGGAT 59.118 41.667 0.00 0.00 0.00 4.18
4345 4950 6.053005 CCAACTTATACAAAGGAAGCGGATA 58.947 40.000 0.00 0.00 0.00 2.59
4346 4951 6.540914 CCAACTTATACAAAGGAAGCGGATAA 59.459 38.462 0.00 0.00 0.00 1.75
4347 4952 7.066525 CCAACTTATACAAAGGAAGCGGATAAA 59.933 37.037 0.00 0.00 0.00 1.40
4348 4953 7.549615 ACTTATACAAAGGAAGCGGATAAAC 57.450 36.000 0.00 0.00 0.00 2.01
4349 4954 6.541278 ACTTATACAAAGGAAGCGGATAAACC 59.459 38.462 0.00 0.00 0.00 3.27
4350 4955 3.434940 ACAAAGGAAGCGGATAAACCT 57.565 42.857 0.00 0.00 36.31 3.50
4351 4956 3.763057 ACAAAGGAAGCGGATAAACCTT 58.237 40.909 0.00 0.00 41.83 3.50
4352 4957 4.913784 ACAAAGGAAGCGGATAAACCTTA 58.086 39.130 0.00 0.00 39.59 2.69
4353 4958 4.941873 ACAAAGGAAGCGGATAAACCTTAG 59.058 41.667 0.00 0.00 39.59 2.18
4354 4959 5.183228 CAAAGGAAGCGGATAAACCTTAGA 58.817 41.667 0.00 0.00 39.59 2.10
4355 4960 4.674281 AGGAAGCGGATAAACCTTAGAG 57.326 45.455 0.00 0.00 36.31 2.43
4356 4961 3.132160 GGAAGCGGATAAACCTTAGAGC 58.868 50.000 0.00 0.00 36.31 4.09
4357 4962 3.431766 GGAAGCGGATAAACCTTAGAGCA 60.432 47.826 0.00 0.00 36.31 4.26
4358 4963 4.381411 GAAGCGGATAAACCTTAGAGCAT 58.619 43.478 0.00 0.00 36.31 3.79
4359 4964 3.996480 AGCGGATAAACCTTAGAGCATC 58.004 45.455 0.00 0.00 36.31 3.91
4360 4965 3.643792 AGCGGATAAACCTTAGAGCATCT 59.356 43.478 0.00 0.00 42.72 2.90
4361 4966 4.101741 AGCGGATAAACCTTAGAGCATCTT 59.898 41.667 0.00 0.00 41.07 2.40
4362 4967 4.449405 GCGGATAAACCTTAGAGCATCTTC 59.551 45.833 0.00 0.00 41.07 2.87
4363 4968 5.601662 CGGATAAACCTTAGAGCATCTTCA 58.398 41.667 0.00 0.00 41.07 3.02
4364 4969 6.049149 CGGATAAACCTTAGAGCATCTTCAA 58.951 40.000 0.00 0.00 41.07 2.69
4365 4970 6.708054 CGGATAAACCTTAGAGCATCTTCAAT 59.292 38.462 0.00 0.00 41.07 2.57
4366 4971 7.872993 CGGATAAACCTTAGAGCATCTTCAATA 59.127 37.037 0.00 0.00 41.07 1.90
4367 4972 9.213799 GGATAAACCTTAGAGCATCTTCAATAG 57.786 37.037 0.00 0.00 40.44 1.73
4374 4979 3.385577 GAGCATCTTCAATAGACGGTCC 58.614 50.000 4.14 0.00 37.56 4.46
4375 4980 2.766263 AGCATCTTCAATAGACGGTCCA 59.234 45.455 4.14 0.00 35.19 4.02
4378 4983 5.247110 AGCATCTTCAATAGACGGTCCATAT 59.753 40.000 4.14 0.00 35.19 1.78
4448 5053 6.726379 TCCAACAGATGGTCCATATGTAAAA 58.274 36.000 28.06 15.44 44.05 1.52
4449 5054 7.178573 TCCAACAGATGGTCCATATGTAAAAA 58.821 34.615 28.06 13.92 44.05 1.94
4484 5089 4.496840 CCGAAAAATTACATAACCGCCTCC 60.497 45.833 0.00 0.00 0.00 4.30
4485 5090 4.334481 CGAAAAATTACATAACCGCCTCCT 59.666 41.667 0.00 0.00 0.00 3.69
4487 5092 4.497291 AAATTACATAACCGCCTCCTGA 57.503 40.909 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.617263 GTGTTTGGTGGATAGCTCTTACG 59.383 47.826 0.00 0.00 0.00 3.18
1 2 3.617263 CGTGTTTGGTGGATAGCTCTTAC 59.383 47.826 0.00 0.00 0.00 2.34
56 57 6.461509 GGTTGTGTGAGGAATTTGATGACTTT 60.462 38.462 0.00 0.00 0.00 2.66
102 103 0.266152 CCCCTCCCTCACCTAGATGT 59.734 60.000 0.00 0.00 0.00 3.06
139 140 2.265739 GATCAGCACTCGGCCACA 59.734 61.111 2.24 0.00 46.50 4.17
152 153 2.869192 CGATGACGACTCTCTCTGATCA 59.131 50.000 0.00 0.00 42.66 2.92
153 154 2.869801 ACGATGACGACTCTCTCTGATC 59.130 50.000 0.00 0.00 42.66 2.92
161 162 0.166161 CACACGACGATGACGACTCT 59.834 55.000 0.00 0.00 42.66 3.24
182 183 3.799755 CGCCTACGCTTTGCCCAC 61.800 66.667 0.00 0.00 0.00 4.61
189 190 1.226888 GATCGTTCCGCCTACGCTT 60.227 57.895 0.00 0.00 38.81 4.68
211 212 4.431131 CCATCCAGTTGCCCGCCT 62.431 66.667 0.00 0.00 0.00 5.52
224 225 2.741747 GCCTACGCCCTACCCATC 59.258 66.667 0.00 0.00 0.00 3.51
228 229 3.149648 TTCCGCCTACGCCCTACC 61.150 66.667 0.00 0.00 38.22 3.18
326 327 2.228822 GTGGATCGAACATGTTGCCTTT 59.771 45.455 17.58 0.00 0.00 3.11
336 337 3.534554 CATGAATCCTGTGGATCGAACA 58.465 45.455 0.00 0.52 42.27 3.18
388 389 2.993853 CCAAGTCCCTGAGCTCCC 59.006 66.667 12.15 0.00 0.00 4.30
461 462 2.431683 GGTGGGTCTTCTGCTGCA 59.568 61.111 0.88 0.88 0.00 4.41
474 475 0.460311 GTGAGTCTACCCATCGGTGG 59.540 60.000 8.08 8.08 44.40 4.61
510 511 5.700832 CAGCGGCTAAGGTTTAATATCATCA 59.299 40.000 0.26 0.00 0.00 3.07
513 514 3.813166 GCAGCGGCTAAGGTTTAATATCA 59.187 43.478 0.26 0.00 36.96 2.15
533 534 2.423373 GCTTGAAATGGATCCCCTAGCA 60.423 50.000 9.90 0.00 0.00 3.49
572 573 9.350357 GAAGAATGTCGCGGTAATAATATTCTA 57.650 33.333 6.13 0.00 33.81 2.10
591 592 2.026449 AGGCTTGTCTGGGAGAAGAATG 60.026 50.000 8.31 0.00 35.34 2.67
623 624 8.250143 AGAAAGGGTATCATTTTTCAACTGTT 57.750 30.769 0.00 0.00 33.19 3.16
658 661 9.944376 AAGGTGACGCTGTATATGATATTTTAT 57.056 29.630 0.00 0.00 0.00 1.40
659 662 9.203421 CAAGGTGACGCTGTATATGATATTTTA 57.797 33.333 0.00 0.00 0.00 1.52
704 707 0.373716 GCTTATCGGCCAACTTGTCG 59.626 55.000 2.24 0.00 0.00 4.35
867 870 5.011125 CACCTAGAAAGAAGAAGAGTGGTGA 59.989 44.000 0.00 0.00 42.46 4.02
868 871 5.233988 CACCTAGAAAGAAGAAGAGTGGTG 58.766 45.833 0.00 0.00 35.89 4.17
869 872 4.284746 CCACCTAGAAAGAAGAAGAGTGGT 59.715 45.833 0.00 0.00 37.93 4.16
870 873 4.323104 CCCACCTAGAAAGAAGAAGAGTGG 60.323 50.000 0.00 0.00 41.50 4.00
1535 1538 2.055042 GCAGAAGGCTCGGAGGAGA 61.055 63.158 7.20 0.00 43.27 3.71
1945 1948 0.179215 CGCAAGAACTCGTCCAATGC 60.179 55.000 0.00 0.00 43.02 3.56
2307 2310 2.502142 ATGCCTCTGTTGATGCTTCA 57.498 45.000 0.00 0.00 35.35 3.02
2311 2314 1.820519 TGGAAATGCCTCTGTTGATGC 59.179 47.619 0.00 0.00 37.63 3.91
2333 2336 3.769875 GAATCCTCGTCGGTCGGCC 62.770 68.421 0.00 0.00 40.32 6.13
2334 2337 2.278661 GAATCCTCGTCGGTCGGC 60.279 66.667 0.00 0.00 40.32 5.54
2343 2346 1.811266 CACACTGCGGGAATCCTCG 60.811 63.158 0.00 2.36 0.00 4.63
2368 2371 2.355920 CCTCTCCAGCAAAGCATCTCTT 60.356 50.000 0.00 0.00 36.34 2.85
2515 2518 0.108233 CTCAGCAGCTCCTCCAAGTC 60.108 60.000 0.00 0.00 0.00 3.01
2577 2580 5.386958 AGTAAGACTTTGTGAGATACGCA 57.613 39.130 0.00 0.00 37.22 5.24
2714 2717 5.584253 TTTGTCGGATTTTTCAAAGTGGA 57.416 34.783 0.00 0.00 0.00 4.02
2715 2718 6.701400 AGATTTTGTCGGATTTTTCAAAGTGG 59.299 34.615 0.00 0.00 32.67 4.00
2716 2719 7.222611 ACAGATTTTGTCGGATTTTTCAAAGTG 59.777 33.333 0.00 0.00 33.87 3.16
2717 2720 7.264947 ACAGATTTTGTCGGATTTTTCAAAGT 58.735 30.769 0.00 0.00 33.87 2.66
2718 2721 7.698836 ACAGATTTTGTCGGATTTTTCAAAG 57.301 32.000 0.00 0.00 33.87 2.77
2730 2733 2.661504 TGTCGCAACAGATTTTGTCG 57.338 45.000 0.00 0.00 39.73 4.35
2756 2759 6.041069 AGCTCATCTGGTACCAGTTATAGTTC 59.959 42.308 35.34 19.68 43.96 3.01
2771 2774 5.021033 ACAACTGATAAGAGCTCATCTGG 57.979 43.478 17.77 10.35 38.67 3.86
2774 2777 6.699642 GGTCTAACAACTGATAAGAGCTCATC 59.300 42.308 17.77 11.64 0.00 2.92
2849 2852 5.607119 AACTCCGTACATCATGTTTGTTC 57.393 39.130 0.00 4.40 0.00 3.18
2855 2858 3.451178 AGGCTTAACTCCGTACATCATGT 59.549 43.478 0.00 0.00 0.00 3.21
2891 2894 6.212388 ACACAACTAATATGGAAATTTGCCCA 59.788 34.615 7.27 4.15 36.79 5.36
2940 2944 5.649395 ACTCTGTTAATCATGATGGTGTTGG 59.351 40.000 9.46 1.35 0.00 3.77
2942 2946 6.349611 GCAACTCTGTTAATCATGATGGTGTT 60.350 38.462 9.46 7.87 0.00 3.32
2945 2949 4.333649 CGCAACTCTGTTAATCATGATGGT 59.666 41.667 9.46 0.00 0.00 3.55
2946 2950 4.571984 TCGCAACTCTGTTAATCATGATGG 59.428 41.667 9.46 0.00 0.00 3.51
2948 2952 5.423015 AGTCGCAACTCTGTTAATCATGAT 58.577 37.500 1.18 1.18 0.00 2.45
2959 2963 6.228273 TCAAAAGATTTAGTCGCAACTCTG 57.772 37.500 0.00 0.00 36.92 3.35
2960 2964 6.092807 GGATCAAAAGATTTAGTCGCAACTCT 59.907 38.462 0.00 0.00 36.92 3.24
2966 2970 5.106317 TGTTGGGATCAAAAGATTTAGTCGC 60.106 40.000 0.00 0.00 34.28 5.19
2967 2971 6.494893 TGTTGGGATCAAAAGATTTAGTCG 57.505 37.500 0.00 0.00 34.28 4.18
2972 3325 7.563906 TGAAACTTGTTGGGATCAAAAGATTT 58.436 30.769 0.00 0.00 34.28 2.17
2973 3326 7.123355 TGAAACTTGTTGGGATCAAAAGATT 57.877 32.000 0.00 0.00 34.28 2.40
3077 3430 6.477033 GTGTGACCTTCAGCAGTATAGTAATG 59.523 42.308 0.00 0.00 0.00 1.90
3078 3431 6.381420 AGTGTGACCTTCAGCAGTATAGTAAT 59.619 38.462 0.00 0.00 0.00 1.89
3079 3432 5.715279 AGTGTGACCTTCAGCAGTATAGTAA 59.285 40.000 0.00 0.00 0.00 2.24
3080 3433 5.262009 AGTGTGACCTTCAGCAGTATAGTA 58.738 41.667 0.00 0.00 0.00 1.82
3081 3434 4.090090 AGTGTGACCTTCAGCAGTATAGT 58.910 43.478 0.00 0.00 0.00 2.12
3082 3435 4.158579 TGAGTGTGACCTTCAGCAGTATAG 59.841 45.833 0.00 0.00 0.00 1.31
3083 3436 4.082190 GTGAGTGTGACCTTCAGCAGTATA 60.082 45.833 0.00 0.00 0.00 1.47
3084 3437 2.899900 TGAGTGTGACCTTCAGCAGTAT 59.100 45.455 0.00 0.00 0.00 2.12
3085 3438 2.035961 GTGAGTGTGACCTTCAGCAGTA 59.964 50.000 0.00 0.00 0.00 2.74
3140 3493 9.308318 GCAATAACTAAGGTTTCAGAACAAAAA 57.692 29.630 0.00 0.00 37.51 1.94
3181 3534 7.011857 GGTTCCTCTCTAAAAATGTATCTGCTG 59.988 40.741 0.00 0.00 0.00 4.41
3198 3551 7.440523 AATATTATCGCAAATGGTTCCTCTC 57.559 36.000 0.00 0.00 0.00 3.20
3266 3640 6.485313 CACCCTTTGTTCACTAATGTAAGACA 59.515 38.462 0.00 0.00 0.00 3.41
3311 3685 4.514816 TCATCAATTGAAGAACAGCGTGAA 59.485 37.500 13.09 0.00 0.00 3.18
3315 3689 4.408993 TGTCATCAATTGAAGAACAGCG 57.591 40.909 14.54 0.00 35.70 5.18
3339 3713 7.497909 CCAATGGTTACTTTCTATCGGTTACAT 59.502 37.037 0.00 0.00 0.00 2.29
3346 3720 7.549488 AGAAGAACCAATGGTTACTTTCTATCG 59.451 37.037 24.85 0.00 46.95 2.92
3418 3876 5.640732 ACAATGAAACAGTGAACTGAACAC 58.359 37.500 17.11 6.21 46.59 3.32
3444 3902 2.327200 AGCCCGTTAAATGAGTAGCC 57.673 50.000 0.00 0.00 0.00 3.93
3461 3919 2.789409 AGGGTGTTCATCCAGTTAGC 57.211 50.000 4.86 0.00 0.00 3.09
3524 3982 0.980231 ACCTCTGCCTCAGGTGGATC 60.980 60.000 0.00 0.00 43.10 3.36
3620 4088 1.682854 CTTCTTCCTTTGGCAGCAACA 59.317 47.619 0.00 0.00 0.00 3.33
3632 4100 2.164624 CACTACTGCTACGCTTCTTCCT 59.835 50.000 0.00 0.00 0.00 3.36
3698 4166 9.013229 TGTTATGTATATCCATGCCATTTTCTC 57.987 33.333 0.00 0.00 0.00 2.87
3701 4169 8.710749 ACTGTTATGTATATCCATGCCATTTT 57.289 30.769 0.00 0.00 0.00 1.82
3724 4192 8.052748 TGCAAATAACCAAGATAAGGACATACT 58.947 33.333 0.00 0.00 0.00 2.12
3783 4252 0.463295 ATGACAGGCAGCTCATTCCG 60.463 55.000 0.00 0.00 0.00 4.30
3880 4349 2.158986 CCAGCCGAGAATCTCACTCAAT 60.159 50.000 11.18 0.00 34.47 2.57
3966 4435 2.125147 GCACTAGGCACATCCGCA 60.125 61.111 0.00 0.00 43.97 5.69
4017 4486 1.208052 TCTGGAGCTGCCTACATGTTC 59.792 52.381 2.30 0.00 37.63 3.18
4019 4488 0.829333 CTCTGGAGCTGCCTACATGT 59.171 55.000 2.69 2.69 37.63 3.21
4146 4615 7.284034 GGAATCTTGGGATTGATATTATGCGAT 59.716 37.037 0.00 0.00 41.68 4.58
4159 4628 4.463891 GTGTGAATGTGGAATCTTGGGATT 59.536 41.667 0.00 0.00 43.99 3.01
4190 4677 3.563808 ACATAGTGTGCACGTTTTCATGT 59.436 39.130 13.13 11.95 36.20 3.21
4213 4700 2.993899 CTGTTGTGATACCGACCTTGTC 59.006 50.000 0.00 0.00 0.00 3.18
4283 4888 9.490083 AAAGACCCTAGTTGTATAAGATACTGT 57.510 33.333 0.00 0.00 0.00 3.55
4300 4905 5.954757 TGGATTTTGGTTGTAAAGACCCTA 58.045 37.500 0.00 0.00 36.30 3.53
4331 4936 5.183228 TCTAAGGTTTATCCGCTTCCTTTG 58.817 41.667 0.00 0.00 41.99 2.77
4332 4937 5.429130 CTCTAAGGTTTATCCGCTTCCTTT 58.571 41.667 0.00 0.00 41.99 3.11
4333 4938 4.683671 GCTCTAAGGTTTATCCGCTTCCTT 60.684 45.833 0.00 0.00 41.99 3.36
4334 4939 3.181464 GCTCTAAGGTTTATCCGCTTCCT 60.181 47.826 0.00 0.00 41.99 3.36
4335 4940 3.132160 GCTCTAAGGTTTATCCGCTTCC 58.868 50.000 0.00 0.00 41.99 3.46
4336 4941 3.793559 TGCTCTAAGGTTTATCCGCTTC 58.206 45.455 0.00 0.00 41.99 3.86
4337 4942 3.906720 TGCTCTAAGGTTTATCCGCTT 57.093 42.857 0.00 0.00 41.99 4.68
4338 4943 3.643792 AGATGCTCTAAGGTTTATCCGCT 59.356 43.478 0.00 0.00 41.99 5.52
4339 4944 3.996480 AGATGCTCTAAGGTTTATCCGC 58.004 45.455 0.00 0.00 41.99 5.54
4340 4945 5.601662 TGAAGATGCTCTAAGGTTTATCCG 58.398 41.667 0.00 0.00 41.99 4.18
4341 4946 9.213799 CTATTGAAGATGCTCTAAGGTTTATCC 57.786 37.037 0.00 0.00 0.00 2.59
4342 4947 9.988815 TCTATTGAAGATGCTCTAAGGTTTATC 57.011 33.333 0.00 0.00 0.00 1.75
4343 4948 9.771534 GTCTATTGAAGATGCTCTAAGGTTTAT 57.228 33.333 0.00 0.00 36.36 1.40
4344 4949 7.921214 CGTCTATTGAAGATGCTCTAAGGTTTA 59.079 37.037 0.00 0.00 36.36 2.01
4345 4950 6.758886 CGTCTATTGAAGATGCTCTAAGGTTT 59.241 38.462 0.00 0.00 36.36 3.27
4346 4951 6.276847 CGTCTATTGAAGATGCTCTAAGGTT 58.723 40.000 0.00 0.00 36.36 3.50
4347 4952 5.221342 CCGTCTATTGAAGATGCTCTAAGGT 60.221 44.000 0.00 0.00 39.56 3.50
4348 4953 5.221342 ACCGTCTATTGAAGATGCTCTAAGG 60.221 44.000 0.00 0.00 39.56 2.69
4349 4954 5.837437 ACCGTCTATTGAAGATGCTCTAAG 58.163 41.667 0.00 0.00 39.56 2.18
4350 4955 5.221263 GGACCGTCTATTGAAGATGCTCTAA 60.221 44.000 0.00 0.00 39.56 2.10
4351 4956 4.278669 GGACCGTCTATTGAAGATGCTCTA 59.721 45.833 0.00 0.00 39.56 2.43
4352 4957 3.068873 GGACCGTCTATTGAAGATGCTCT 59.931 47.826 0.00 0.00 39.56 4.09
4353 4958 3.181475 TGGACCGTCTATTGAAGATGCTC 60.181 47.826 0.00 0.00 39.56 4.26
4354 4959 2.766263 TGGACCGTCTATTGAAGATGCT 59.234 45.455 0.00 0.00 39.56 3.79
4355 4960 3.179443 TGGACCGTCTATTGAAGATGC 57.821 47.619 0.00 0.00 39.56 3.91
4356 4961 6.459066 ACATATGGACCGTCTATTGAAGATG 58.541 40.000 7.80 3.38 40.44 2.90
4357 4962 6.672266 ACATATGGACCGTCTATTGAAGAT 57.328 37.500 7.80 0.00 36.36 2.40
4358 4963 7.591421 TTACATATGGACCGTCTATTGAAGA 57.409 36.000 7.80 0.00 0.00 2.87
4359 4964 8.657074 TTTTACATATGGACCGTCTATTGAAG 57.343 34.615 7.80 0.00 0.00 3.02
4360 4965 9.621629 ATTTTTACATATGGACCGTCTATTGAA 57.378 29.630 7.80 0.00 0.00 2.69
4388 4993 6.873997 TGCTCTCGAATATCCAAAAGTTAGA 58.126 36.000 0.00 0.00 0.00 2.10
4453 5058 9.985318 CGGTTATGTAATTTTTCGGTTATGTAA 57.015 29.630 0.00 0.00 0.00 2.41
4454 5059 8.121708 GCGGTTATGTAATTTTTCGGTTATGTA 58.878 33.333 0.00 0.00 0.00 2.29
4455 5060 6.968335 GCGGTTATGTAATTTTTCGGTTATGT 59.032 34.615 0.00 0.00 0.00 2.29
4456 5061 6.415573 GGCGGTTATGTAATTTTTCGGTTATG 59.584 38.462 0.00 0.00 0.00 1.90
4457 5062 6.319405 AGGCGGTTATGTAATTTTTCGGTTAT 59.681 34.615 0.00 0.00 0.00 1.89
4458 5063 5.647225 AGGCGGTTATGTAATTTTTCGGTTA 59.353 36.000 0.00 0.00 0.00 2.85
4459 5064 4.460034 AGGCGGTTATGTAATTTTTCGGTT 59.540 37.500 0.00 0.00 0.00 4.44
4460 5065 4.011698 AGGCGGTTATGTAATTTTTCGGT 58.988 39.130 0.00 0.00 0.00 4.69
4461 5066 4.496840 GGAGGCGGTTATGTAATTTTTCGG 60.497 45.833 0.00 0.00 0.00 4.30
4462 5067 4.334481 AGGAGGCGGTTATGTAATTTTTCG 59.666 41.667 0.00 0.00 0.00 3.46
4463 5068 5.355910 TCAGGAGGCGGTTATGTAATTTTTC 59.644 40.000 0.00 0.00 0.00 2.29
4464 5069 5.258051 TCAGGAGGCGGTTATGTAATTTTT 58.742 37.500 0.00 0.00 0.00 1.94
4465 5070 4.850680 TCAGGAGGCGGTTATGTAATTTT 58.149 39.130 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.