Multiple sequence alignment - TraesCS4B01G196900

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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 TraesCS4B01G196900 chr4B 100.000 4015 0 0 1 4015 424059254 424063268 0.000000e+00 7415.0
1 TraesCS4B01G196900 chr4B 96.711 973 31 1 2040 3011 423776187 423775215 0.000000e+00 1618.0
2 TraesCS4B01G196900 chr4B 97.835 508 11 0 996 1503 423777152 423776645 0.000000e+00 878.0
3 TraesCS4B01G196900 chr4D 96.480 1676 55 3 1616 3289 341923522 341925195 0.000000e+00 2765.0
4 TraesCS4B01G196900 chr4D 92.909 1650 63 31 4 1618 341921799 341923429 0.000000e+00 2350.0
5 TraesCS4B01G196900 chr4D 93.003 1129 61 15 1897 3011 341696240 341695116 0.000000e+00 1631.0
6 TraesCS4B01G196900 chr4D 98.211 503 9 0 996 1498 341697082 341696580 0.000000e+00 880.0
7 TraesCS4B01G196900 chr4A 90.579 1624 87 37 1897 3484 124405092 124403499 0.000000e+00 2091.0
8 TraesCS4B01G196900 chr4A 92.691 1464 48 24 136 1562 124406748 124405307 0.000000e+00 2056.0
9 TraesCS4B01G196900 chr4A 92.609 1123 67 11 1901 3011 125028781 125029899 0.000000e+00 1600.0
10 TraesCS4B01G196900 chr4A 97.813 503 11 0 996 1498 125027942 125028444 0.000000e+00 869.0
11 TraesCS4B01G196900 chr4A 92.029 138 5 5 3 135 124406932 124406796 5.300000e-44 189.0
12 TraesCS4B01G196900 chr4A 96.000 75 3 0 1547 1621 125028553 125028627 5.450000e-24 122.0
13 TraesCS4B01G196900 chr5B 94.564 883 48 0 2132 3014 593659272 593658390 0.000000e+00 1365.0
14 TraesCS4B01G196900 chr5B 93.977 880 53 0 2132 3011 593944221 593943342 0.000000e+00 1332.0
15 TraesCS4B01G196900 chr5B 96.444 478 16 1 994 1471 593945333 593944857 0.000000e+00 787.0
16 TraesCS4B01G196900 chr5B 90.395 354 28 3 3667 4015 56593180 56592828 1.020000e-125 460.0
17 TraesCS4B01G196900 chr5D 94.451 883 49 0 2132 3014 483227761 483226879 0.000000e+00 1360.0
18 TraesCS4B01G196900 chr5D 94.545 880 48 0 2132 3011 483371377 483370498 0.000000e+00 1360.0
19 TraesCS4B01G196900 chr5D 95.842 481 19 1 992 1472 483228785 483228306 0.000000e+00 776.0
20 TraesCS4B01G196900 chr5D 95.816 478 19 1 994 1471 483372420 483371944 0.000000e+00 771.0
21 TraesCS4B01G196900 chr5D 92.330 339 24 1 3679 4015 377296308 377296646 7.800000e-132 481.0
22 TraesCS4B01G196900 chr5D 91.860 86 7 0 3516 3601 377295456 377295541 1.960000e-23 121.0
23 TraesCS4B01G196900 chr5D 96.154 52 2 0 3628 3679 377295594 377295645 7.150000e-13 86.1
24 TraesCS4B01G196900 chr5A 95.643 482 20 1 994 1475 604312716 604312236 0.000000e+00 773.0
25 TraesCS4B01G196900 chr3B 94.985 339 14 2 3679 4015 647231966 647231629 2.750000e-146 529.0
26 TraesCS4B01G196900 chr3B 96.809 94 3 0 3508 3601 647232827 647232734 1.490000e-34 158.0
27 TraesCS4B01G196900 chr6B 93.510 339 20 1 3679 4015 27117618 27117956 1.670000e-138 503.0
28 TraesCS4B01G196900 chr6B 91.489 94 8 0 3508 3601 27116760 27116853 3.260000e-26 130.0
29 TraesCS4B01G196900 chr6B 92.308 52 4 0 3628 3679 27116906 27116957 1.550000e-09 75.0
30 TraesCS4B01G196900 chr6D 93.215 339 21 1 3679 4015 106666461 106666799 7.750000e-137 497.0
31 TraesCS4B01G196900 chr6D 92.553 94 7 0 3508 3601 106665602 106665695 7.000000e-28 135.0
32 TraesCS4B01G196900 chr6D 96.154 52 2 0 3628 3679 106665748 106665799 7.150000e-13 86.1
33 TraesCS4B01G196900 chr1B 93.215 339 21 1 3679 4015 569705202 569704864 7.750000e-137 497.0
34 TraesCS4B01G196900 chr1B 94.466 253 12 1 3765 4015 13964480 13964228 4.870000e-104 388.0
35 TraesCS4B01G196900 chr1B 92.045 88 7 0 3514 3601 569706057 569705970 1.520000e-24 124.0
36 TraesCS4B01G196900 chr1B 97.959 49 1 0 3631 3679 569705914 569705866 7.150000e-13 86.1
37 TraesCS4B01G196900 chr2A 92.625 339 23 1 3679 4015 733426138 733425800 1.680000e-133 486.0
38 TraesCS4B01G196900 chr2A 94.318 88 5 0 3514 3601 733426993 733426906 7.000000e-28 135.0
39 TraesCS4B01G196900 chr7D 80.906 309 28 13 3226 3510 580551632 580551933 8.740000e-52 215.0
40 TraesCS4B01G196900 chr7D 93.976 83 5 0 3933 4015 50746077 50746159 4.210000e-25 126.0


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 TraesCS4B01G196900 chr4B 424059254 424063268 4014 False 7415.000000 7415 100.000000 1 4015 1 chr4B.!!$F1 4014
1 TraesCS4B01G196900 chr4B 423775215 423777152 1937 True 1248.000000 1618 97.273000 996 3011 2 chr4B.!!$R1 2015
2 TraesCS4B01G196900 chr4D 341921799 341925195 3396 False 2557.500000 2765 94.694500 4 3289 2 chr4D.!!$F1 3285
3 TraesCS4B01G196900 chr4D 341695116 341697082 1966 True 1255.500000 1631 95.607000 996 3011 2 chr4D.!!$R1 2015
4 TraesCS4B01G196900 chr4A 124403499 124406932 3433 True 1445.333333 2091 91.766333 3 3484 3 chr4A.!!$R1 3481
5 TraesCS4B01G196900 chr4A 125027942 125029899 1957 False 863.666667 1600 95.474000 996 3011 3 chr4A.!!$F1 2015
6 TraesCS4B01G196900 chr5B 593658390 593659272 882 True 1365.000000 1365 94.564000 2132 3014 1 chr5B.!!$R2 882
7 TraesCS4B01G196900 chr5B 593943342 593945333 1991 True 1059.500000 1332 95.210500 994 3011 2 chr5B.!!$R3 2017
8 TraesCS4B01G196900 chr5D 483226879 483228785 1906 True 1068.000000 1360 95.146500 992 3014 2 chr5D.!!$R1 2022
9 TraesCS4B01G196900 chr5D 483370498 483372420 1922 True 1065.500000 1360 95.180500 994 3011 2 chr5D.!!$R2 2017
10 TraesCS4B01G196900 chr5D 377295456 377296646 1190 False 229.366667 481 93.448000 3516 4015 3 chr5D.!!$F1 499
11 TraesCS4B01G196900 chr3B 647231629 647232827 1198 True 343.500000 529 95.897000 3508 4015 2 chr3B.!!$R1 507
12 TraesCS4B01G196900 chr6B 27116760 27117956 1196 False 236.000000 503 92.435667 3508 4015 3 chr6B.!!$F1 507
13 TraesCS4B01G196900 chr6D 106665602 106666799 1197 False 239.366667 497 93.974000 3508 4015 3 chr6D.!!$F1 507
14 TraesCS4B01G196900 chr1B 569704864 569706057 1193 True 235.700000 497 94.406333 3514 4015 3 chr1B.!!$R2 501
15 TraesCS4B01G196900 chr2A 733425800 733426993 1193 True 310.500000 486 93.471500 3514 4015 2 chr2A.!!$R1 501

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
890 975 0.030705 TTCCTGGATCTAGGCCTGCT 60.031 55.000 19.97 0.0 37.76 4.24 F
1699 2196 1.674441 TCTCGTACTGCCATTCCTACG 59.326 52.381 0.00 0.0 34.59 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 2251 2.036089 TGCAAAGCAGCAATGATCACAA 59.964 40.909 0.0 0.0 42.46 3.33 R
3148 3790 0.179045 GGCACAAGACAGACACCACT 60.179 55.000 0.0 0.0 0.00 4.00 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
188 242 1.685421 GCCTCCTGCTCCAGTCTCT 60.685 63.158 0.00 0.00 36.87 3.10
210 264 3.116531 GGAACGTGCACCCTACGC 61.117 66.667 12.15 0.00 44.87 4.42
369 425 0.719623 AGGAAGGAACCCTAGAGCCT 59.280 55.000 0.00 0.00 31.13 4.58
401 457 6.013293 GTCAGTATAAATAGGGGAGCCATTCT 60.013 42.308 0.00 0.00 0.00 2.40
421 479 4.377760 TCGCCCGAACCCTCCTCT 62.378 66.667 0.00 0.00 0.00 3.69
422 480 3.839432 CGCCCGAACCCTCCTCTC 61.839 72.222 0.00 0.00 0.00 3.20
423 481 2.683933 GCCCGAACCCTCCTCTCA 60.684 66.667 0.00 0.00 0.00 3.27
424 482 2.726351 GCCCGAACCCTCCTCTCAG 61.726 68.421 0.00 0.00 0.00 3.35
425 483 1.305381 CCCGAACCCTCCTCTCAGT 60.305 63.158 0.00 0.00 0.00 3.41
426 484 1.324005 CCCGAACCCTCCTCTCAGTC 61.324 65.000 0.00 0.00 0.00 3.51
502 566 2.579873 TCCTTCGAGGTTAGTATCCCG 58.420 52.381 0.00 0.00 36.53 5.14
503 567 2.173356 TCCTTCGAGGTTAGTATCCCGA 59.827 50.000 0.00 6.70 36.53 5.14
504 568 2.292845 CCTTCGAGGTTAGTATCCCGAC 59.707 54.545 9.17 0.00 31.41 4.79
505 569 3.212685 CTTCGAGGTTAGTATCCCGACT 58.787 50.000 9.17 0.00 31.41 4.18
565 629 3.862124 CGAAGCTCCCGTGTTCTG 58.138 61.111 0.00 0.00 0.00 3.02
576 640 0.792640 CGTGTTCTGCGCTCATCTTT 59.207 50.000 9.73 0.00 0.00 2.52
585 649 2.014068 GCGCTCATCTTTGGTAGCCTT 61.014 52.381 0.00 0.00 0.00 4.35
640 705 0.857311 CGCGGATGCATCGTTTGTTC 60.857 55.000 20.15 3.83 42.97 3.18
693 763 4.645136 ACTGTTGCCTCGATCTGTAGATTA 59.355 41.667 0.00 0.00 34.37 1.75
694 764 4.933330 TGTTGCCTCGATCTGTAGATTAC 58.067 43.478 0.00 0.00 34.37 1.89
695 765 3.898517 TGCCTCGATCTGTAGATTACG 57.101 47.619 0.00 0.00 34.37 3.18
696 766 3.473625 TGCCTCGATCTGTAGATTACGA 58.526 45.455 0.00 5.81 34.37 3.43
776 849 5.386060 TGAATCTGTCGGTAGATGGACTAT 58.614 41.667 3.61 0.00 37.48 2.12
778 851 5.713792 ATCTGTCGGTAGATGGACTATTG 57.286 43.478 2.20 0.00 36.12 1.90
805 885 8.404000 TCTCAATTTCGTAGACTGAGTATAACC 58.596 37.037 0.00 0.00 38.43 2.85
876 957 1.521423 GTCTTCGTGTCGTGTTTCCTG 59.479 52.381 0.00 0.00 0.00 3.86
890 975 0.030705 TTCCTGGATCTAGGCCTGCT 60.031 55.000 19.97 0.00 37.76 4.24
931 1017 8.267894 ACTGCTGATATATTAGTGTTCCAGTTT 58.732 33.333 6.40 0.00 0.00 2.66
979 1066 9.030301 CCGTTTTTGTCTAATTTTTCTGATTGT 57.970 29.630 0.00 0.00 0.00 2.71
1509 1621 4.060038 CTGAAAGGCCGTGTATAGATGT 57.940 45.455 0.00 0.00 0.00 3.06
1699 2196 1.674441 TCTCGTACTGCCATTCCTACG 59.326 52.381 0.00 0.00 34.59 3.51
1714 2211 2.173143 TCCTACGGTTTTTGGGTTCACT 59.827 45.455 0.00 0.00 0.00 3.41
1715 2212 2.292292 CCTACGGTTTTTGGGTTCACTG 59.708 50.000 0.00 0.00 0.00 3.66
1739 2236 6.145535 GGTTGATTGTTCTGCTGTTCTAAAG 58.854 40.000 0.00 0.00 0.00 1.85
1754 2251 7.862873 GCTGTTCTAAAGTTTATGCTCACTTTT 59.137 33.333 2.82 0.00 39.69 2.27
1771 2268 4.952460 ACTTTTTGTGATCATTGCTGCTT 58.048 34.783 0.00 0.00 0.00 3.91
1797 2294 7.361127 TGCAATTTCATTTTTGTTTATGCCTG 58.639 30.769 0.00 0.00 0.00 4.85
1839 2340 2.030007 TGCTGTTTTCTGCTGGCAATAC 60.030 45.455 0.00 0.00 43.59 1.89
1987 2586 3.927142 AGTTTATGCTCACTTAGTGCGAC 59.073 43.478 7.61 0.05 39.54 5.19
2014 2613 5.344128 GTGCTGTTGTGCAATTTCTTATCTG 59.656 40.000 0.00 0.00 45.12 2.90
2108 2748 8.451908 AGCTGTGAGTTTCATTTAACTAAAGT 57.548 30.769 0.00 0.00 38.43 2.66
2912 3553 2.103432 TCCTCTTGGTCGTTTTGCTGTA 59.897 45.455 0.00 0.00 34.23 2.74
3017 3658 5.105595 GGCTGCCATCAAGAAGAAGTAATTT 60.106 40.000 15.17 0.00 0.00 1.82
3022 3664 7.014134 TGCCATCAAGAAGAAGTAATTTGACAA 59.986 33.333 0.00 0.00 31.34 3.18
3024 3666 9.565213 CCATCAAGAAGAAGTAATTTGACAATC 57.435 33.333 0.00 0.00 31.34 2.67
3047 3689 5.817296 TCGATATCCAAATCACTGTTTCAGG 59.183 40.000 0.00 0.00 35.51 3.86
3093 3735 3.988819 TGAGTTTTGTTAAGGGCATTGC 58.011 40.909 0.00 0.00 0.00 3.56
3110 3752 4.389077 GCATTGCTCGTACTGGGTATATTC 59.611 45.833 0.16 0.00 0.00 1.75
3170 3813 1.230324 GGTGTCTGTCTTGTGCCTTC 58.770 55.000 0.00 0.00 0.00 3.46
3220 3865 5.491982 GTGAAACCTGGATGTTATGAGACT 58.508 41.667 0.00 0.00 0.00 3.24
3243 3889 9.269453 GACTTGGTTGTGTCTTTTAATACTAGT 57.731 33.333 0.00 0.00 0.00 2.57
3289 3935 7.486647 AGATGCTTTATCTAGTGCATTTTTGG 58.513 34.615 0.00 0.00 44.32 3.28
3291 3937 7.408756 TGCTTTATCTAGTGCATTTTTGGAT 57.591 32.000 0.00 0.00 0.00 3.41
3310 3971 5.698832 TGGATGCATCTAAACGTTCTTTTG 58.301 37.500 25.28 0.00 0.00 2.44
3323 3984 5.158494 ACGTTCTTTTGTTTTGAAGGTGTC 58.842 37.500 0.00 0.00 37.40 3.67
3330 3991 8.536175 TCTTTTGTTTTGAAGGTGTCCTTTTAT 58.464 29.630 2.48 0.00 44.82 1.40
3338 3999 7.519032 TGAAGGTGTCCTTTTATTTACAAGG 57.481 36.000 2.48 0.00 44.82 3.61
3340 4001 8.219178 TGAAGGTGTCCTTTTATTTACAAGGTA 58.781 33.333 2.48 0.00 44.82 3.08
3344 4005 8.084073 GGTGTCCTTTTATTTACAAGGTAAACC 58.916 37.037 3.88 0.00 40.59 3.27
3355 4016 8.722622 TTTACAAGGTAAACCATTTATTCCCA 57.277 30.769 1.26 0.00 38.89 4.37
3374 4037 3.308402 CCCACTACTGATGGTTCATTGGT 60.308 47.826 0.00 0.00 35.23 3.67
3375 4038 3.691118 CCACTACTGATGGTTCATTGGTG 59.309 47.826 3.80 3.80 41.04 4.17
3377 4040 5.487433 CACTACTGATGGTTCATTGGTGTA 58.513 41.667 2.92 0.00 38.43 2.90
3382 4045 4.780815 TGATGGTTCATTGGTGTATCCTC 58.219 43.478 0.00 0.00 37.07 3.71
3383 4046 4.227073 TGATGGTTCATTGGTGTATCCTCA 59.773 41.667 0.00 0.00 37.07 3.86
3396 4059 4.020128 GTGTATCCTCACCTCTGTTTCCTT 60.020 45.833 0.00 0.00 32.81 3.36
3409 4072 4.511454 TCTGTTTCCTTGACAACGAAGATG 59.489 41.667 0.00 0.00 35.98 2.90
3411 4074 4.638421 TGTTTCCTTGACAACGAAGATGTT 59.362 37.500 0.00 0.00 45.60 2.71
3412 4075 5.818336 TGTTTCCTTGACAACGAAGATGTTA 59.182 36.000 0.00 0.00 45.60 2.41
3413 4076 5.917541 TTCCTTGACAACGAAGATGTTAC 57.082 39.130 0.00 0.00 45.60 2.50
3414 4077 5.209818 TCCTTGACAACGAAGATGTTACT 57.790 39.130 0.00 0.00 45.60 2.24
3415 4078 5.227908 TCCTTGACAACGAAGATGTTACTC 58.772 41.667 0.00 0.00 45.60 2.59
3416 4079 4.988540 CCTTGACAACGAAGATGTTACTCA 59.011 41.667 0.00 0.00 45.60 3.41
3417 4080 5.119279 CCTTGACAACGAAGATGTTACTCAG 59.881 44.000 0.00 0.00 45.60 3.35
3418 4081 5.447624 TGACAACGAAGATGTTACTCAGA 57.552 39.130 0.00 0.00 45.60 3.27
3419 4082 5.220381 TGACAACGAAGATGTTACTCAGAC 58.780 41.667 0.00 0.00 45.60 3.51
3422 4085 5.221263 ACAACGAAGATGTTACTCAGACACT 60.221 40.000 0.00 0.00 42.04 3.55
3426 4089 5.393569 CGAAGATGTTACTCAGACACTCCAT 60.394 44.000 0.00 0.00 0.00 3.41
3431 4094 6.222038 TGTTACTCAGACACTCCATATTCC 57.778 41.667 0.00 0.00 0.00 3.01
3436 4099 5.013079 ACTCAGACACTCCATATTCCAAACA 59.987 40.000 0.00 0.00 0.00 2.83
3445 4108 6.721208 ACTCCATATTCCAAACAGTCACATTT 59.279 34.615 0.00 0.00 0.00 2.32
3447 4110 6.152661 TCCATATTCCAAACAGTCACATTTCC 59.847 38.462 0.00 0.00 0.00 3.13
3448 4111 6.071447 CCATATTCCAAACAGTCACATTTCCA 60.071 38.462 0.00 0.00 0.00 3.53
3449 4112 4.647424 TTCCAAACAGTCACATTTCCAC 57.353 40.909 0.00 0.00 0.00 4.02
3451 4114 5.042463 TCCAAACAGTCACATTTCCACTA 57.958 39.130 0.00 0.00 0.00 2.74
3452 4115 4.819630 TCCAAACAGTCACATTTCCACTAC 59.180 41.667 0.00 0.00 0.00 2.73
3470 4135 7.373493 TCCACTACTTCTACTTTTTACTTCCG 58.627 38.462 0.00 0.00 0.00 4.30
3480 4145 4.989168 ACTTTTTACTTCCGAGTGTAGCAG 59.011 41.667 0.00 0.00 36.60 4.24
3484 4149 1.961394 ACTTCCGAGTGTAGCAGAACA 59.039 47.619 0.00 0.00 33.99 3.18
3485 4150 2.364324 ACTTCCGAGTGTAGCAGAACAA 59.636 45.455 0.00 0.00 33.99 2.83
3486 4151 3.006967 ACTTCCGAGTGTAGCAGAACAAT 59.993 43.478 0.00 0.00 33.99 2.71
3487 4152 3.678056 TCCGAGTGTAGCAGAACAATT 57.322 42.857 0.00 0.00 0.00 2.32
3488 4153 4.002906 TCCGAGTGTAGCAGAACAATTT 57.997 40.909 0.00 0.00 0.00 1.82
3489 4154 4.385825 TCCGAGTGTAGCAGAACAATTTT 58.614 39.130 0.00 0.00 0.00 1.82
3490 4155 4.819630 TCCGAGTGTAGCAGAACAATTTTT 59.180 37.500 0.00 0.00 0.00 1.94
3555 4220 2.092049 TGAATGGGATGAGCAGCTGATT 60.092 45.455 20.43 5.21 0.00 2.57
3601 4266 2.389059 CAGAACGCATCCTACAGATCG 58.611 52.381 0.00 0.00 30.59 3.69
3602 4267 2.033424 CAGAACGCATCCTACAGATCGA 59.967 50.000 0.00 0.00 30.59 3.59
3603 4268 2.887783 AGAACGCATCCTACAGATCGAT 59.112 45.455 0.00 0.00 30.59 3.59
3605 4270 1.542030 ACGCATCCTACAGATCGATCC 59.458 52.381 21.66 4.34 30.59 3.36
3606 4271 1.135257 CGCATCCTACAGATCGATCCC 60.135 57.143 21.66 0.00 30.59 3.85
3608 4273 2.813907 CATCCTACAGATCGATCCCCT 58.186 52.381 21.66 7.02 30.59 4.79
3609 4274 3.169099 CATCCTACAGATCGATCCCCTT 58.831 50.000 21.66 6.37 30.59 3.95
3610 4275 4.344978 CATCCTACAGATCGATCCCCTTA 58.655 47.826 21.66 7.16 30.59 2.69
3611 4276 4.035612 TCCTACAGATCGATCCCCTTAG 57.964 50.000 21.66 15.14 0.00 2.18
3612 4277 3.398292 TCCTACAGATCGATCCCCTTAGT 59.602 47.826 21.66 12.64 0.00 2.24
3613 4278 4.140994 TCCTACAGATCGATCCCCTTAGTT 60.141 45.833 21.66 0.00 0.00 2.24
3614 4279 4.589374 CCTACAGATCGATCCCCTTAGTTT 59.411 45.833 21.66 0.00 0.00 2.66
3615 4280 5.070580 CCTACAGATCGATCCCCTTAGTTTT 59.929 44.000 21.66 0.00 0.00 2.43
3617 4282 4.130118 CAGATCGATCCCCTTAGTTTTGG 58.870 47.826 21.66 0.00 0.00 3.28
3618 4283 2.413310 TCGATCCCCTTAGTTTTGGC 57.587 50.000 0.00 0.00 0.00 4.52
3625 4316 3.589735 TCCCCTTAGTTTTGGCACATAGA 59.410 43.478 0.00 0.00 39.30 1.98
3626 4317 4.229582 TCCCCTTAGTTTTGGCACATAGAT 59.770 41.667 0.00 0.00 39.30 1.98
3728 5086 2.609459 CAGACGTTGTCTTTGCTGAAGT 59.391 45.455 0.00 0.00 41.37 3.01
3858 5216 0.116940 AATCAATGGTGGTTGGCCCT 59.883 50.000 0.00 0.00 0.00 5.19
3867 5225 1.045911 TGGTTGGCCCTGTTTTGGAC 61.046 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 40 6.846283 CCTCGACATAATAAAAATTCTCGCAC 59.154 38.462 0.00 0.00 0.00 5.34
123 128 7.826918 AAATGTTTTACCCACTACTTGCTAA 57.173 32.000 0.00 0.00 0.00 3.09
188 242 2.745037 GGGTGCACGTTCCCTGTA 59.255 61.111 11.45 0.00 40.48 2.74
210 264 1.755179 AGTTCGGCATCCTGGATTTG 58.245 50.000 6.42 0.00 0.00 2.32
369 425 4.039973 CCCCTATTTATACTGACAGCGGAA 59.960 45.833 1.25 0.00 0.00 4.30
377 433 6.013379 CAGAATGGCTCCCCTATTTATACTGA 60.013 42.308 0.00 0.00 0.00 3.41
421 479 0.845102 GGGGAAGAAAGGGGGACTGA 60.845 60.000 0.00 0.00 0.00 3.41
422 480 1.691823 GGGGAAGAAAGGGGGACTG 59.308 63.158 0.00 0.00 0.00 3.51
423 481 1.544151 GGGGGAAGAAAGGGGGACT 60.544 63.158 0.00 0.00 0.00 3.85
424 482 3.097293 GGGGGAAGAAAGGGGGAC 58.903 66.667 0.00 0.00 0.00 4.46
502 566 1.330655 TGGAGATGGCTCGGGAAGTC 61.331 60.000 0.00 0.00 42.25 3.01
503 567 1.306141 TGGAGATGGCTCGGGAAGT 60.306 57.895 0.00 0.00 42.25 3.01
504 568 1.333636 ACTGGAGATGGCTCGGGAAG 61.334 60.000 0.00 0.00 42.25 3.46
505 569 1.306141 ACTGGAGATGGCTCGGGAA 60.306 57.895 0.00 0.00 42.25 3.97
565 629 0.462759 AGGCTACCAAAGATGAGCGC 60.463 55.000 0.00 0.00 35.71 5.92
576 640 1.153449 CGCGGATTGAAGGCTACCA 60.153 57.895 0.00 0.00 0.00 3.25
585 649 2.184322 GACCAGCTCGCGGATTGA 59.816 61.111 6.13 0.00 0.00 2.57
606 670 1.264826 TCCGCGAAAAAGTGCCTAAAC 59.735 47.619 8.23 0.00 0.00 2.01
640 705 6.074782 GAGAAAATCCTTCTCAACGCTATACG 60.075 42.308 9.15 0.00 44.74 3.06
776 849 6.085555 ACTCAGTCTACGAAATTGAGACAA 57.914 37.500 12.89 0.00 41.73 3.18
778 851 9.224058 GTTATACTCAGTCTACGAAATTGAGAC 57.776 37.037 12.89 0.00 38.81 3.36
805 885 9.317936 TCTATAACAGATAGTTTGCAATCACTG 57.682 33.333 13.00 16.37 41.64 3.66
836 917 4.081862 AGACGATTTACAAACTGATCGGGA 60.082 41.667 6.47 0.00 44.02 5.14
876 957 1.751563 GGACAGCAGGCCTAGATCC 59.248 63.158 3.98 6.87 0.00 3.36
890 975 0.175760 GCAGTCAAGGCTATCGGACA 59.824 55.000 10.00 0.00 32.79 4.02
931 1017 2.972625 CCAGAACGAAGAACTGGCATA 58.027 47.619 0.00 0.00 43.44 3.14
1466 1553 6.486657 TCAGGGATGAAGAGTTTTAACAAGTG 59.513 38.462 0.00 0.00 0.00 3.16
1498 1594 4.700213 ACCAACCAGCAAACATCTATACAC 59.300 41.667 0.00 0.00 0.00 2.90
1509 1621 6.065374 TCAAATAAGTCTACCAACCAGCAAA 58.935 36.000 0.00 0.00 0.00 3.68
1632 2128 3.857157 AAAACTACAGGTGAAGCTGGA 57.143 42.857 13.62 4.39 0.00 3.86
1699 2196 2.498078 TCAACCAGTGAACCCAAAAACC 59.502 45.455 0.00 0.00 31.51 3.27
1714 2211 3.554934 AGAACAGCAGAACAATCAACCA 58.445 40.909 0.00 0.00 0.00 3.67
1715 2212 5.689383 TTAGAACAGCAGAACAATCAACC 57.311 39.130 0.00 0.00 0.00 3.77
1754 2251 2.036089 TGCAAAGCAGCAATGATCACAA 59.964 40.909 0.00 0.00 42.46 3.33
1771 2268 7.861372 CAGGCATAAACAAAAATGAAATTGCAA 59.139 29.630 0.00 0.00 36.10 4.08
1797 2294 7.020010 CAGCAAGAGACATGATTACTTTGAAC 58.980 38.462 0.00 0.00 0.00 3.18
1839 2340 3.452627 AGAACTAAGATGGCACTGTAGGG 59.547 47.826 0.00 0.00 0.00 3.53
1987 2586 2.129607 GAAATTGCACAACAGCACTGG 58.870 47.619 2.21 0.00 45.61 4.00
2108 2748 8.394971 TCTAAAAATGAGAAGCAGAATGACAA 57.605 30.769 0.00 0.00 39.69 3.18
2807 3448 4.219288 GCATCACCATTCTTGAGGAACTTT 59.781 41.667 0.00 0.00 41.55 2.66
2912 3553 1.229428 CAGTTTGCCTCATGTCACGT 58.771 50.000 0.00 0.00 0.00 4.49
2981 3622 1.378762 GGCAGCCTTGGTCACCTTA 59.621 57.895 3.29 0.00 0.00 2.69
3017 3658 6.348498 ACAGTGATTTGGATATCGATTGTCA 58.652 36.000 1.71 0.00 0.00 3.58
3022 3664 6.484643 CCTGAAACAGTGATTTGGATATCGAT 59.515 38.462 2.16 2.16 0.00 3.59
3024 3666 5.504665 GCCTGAAACAGTGATTTGGATATCG 60.505 44.000 0.00 0.00 0.00 2.92
3047 3689 4.923281 CCAATACTAAAAACTGCTTGGTGC 59.077 41.667 0.00 0.00 43.25 5.01
3093 3735 5.706369 ACAGCTAGAATATACCCAGTACGAG 59.294 44.000 0.00 0.00 0.00 4.18
3148 3790 0.179045 GGCACAAGACAGACACCACT 60.179 55.000 0.00 0.00 0.00 4.00
3243 3889 9.624697 GCATCTACACAGATAAAATTCAACAAA 57.375 29.630 0.00 0.00 39.62 2.83
3289 3935 7.623268 AAACAAAAGAACGTTTAGATGCATC 57.377 32.000 19.37 19.37 33.68 3.91
3291 3937 7.030165 TCAAAACAAAAGAACGTTTAGATGCA 58.970 30.769 0.46 0.00 34.32 3.96
3293 3939 8.531530 CCTTCAAAACAAAAGAACGTTTAGATG 58.468 33.333 0.46 2.94 34.32 2.90
3294 3940 8.248253 ACCTTCAAAACAAAAGAACGTTTAGAT 58.752 29.630 0.46 0.00 34.32 1.98
3295 3941 7.539366 CACCTTCAAAACAAAAGAACGTTTAGA 59.461 33.333 0.46 0.00 34.32 2.10
3297 3943 7.146648 ACACCTTCAAAACAAAAGAACGTTTA 58.853 30.769 0.46 0.00 34.32 2.01
3300 3946 5.128992 ACACCTTCAAAACAAAAGAACGT 57.871 34.783 0.00 0.00 0.00 3.99
3301 3947 4.561213 GGACACCTTCAAAACAAAAGAACG 59.439 41.667 0.00 0.00 0.00 3.95
3310 3971 9.589111 TTGTAAATAAAAGGACACCTTCAAAAC 57.411 29.630 3.45 0.34 43.92 2.43
3330 3991 8.586744 GTGGGAATAAATGGTTTACCTTGTAAA 58.413 33.333 0.00 0.00 36.82 2.01
3333 3994 6.319715 AGTGGGAATAAATGGTTTACCTTGT 58.680 36.000 0.00 0.00 36.82 3.16
3338 3999 8.621286 CATCAGTAGTGGGAATAAATGGTTTAC 58.379 37.037 0.00 0.00 0.00 2.01
3340 4001 6.607198 CCATCAGTAGTGGGAATAAATGGTTT 59.393 38.462 0.00 0.00 32.98 3.27
3344 4005 6.828273 TGAACCATCAGTAGTGGGAATAAATG 59.172 38.462 0.00 0.00 41.14 2.32
3355 4016 4.640771 ACACCAATGAACCATCAGTAGT 57.359 40.909 0.00 0.00 39.39 2.73
3374 4037 3.791320 AGGAAACAGAGGTGAGGATACA 58.209 45.455 0.00 0.00 41.41 2.29
3375 4038 4.223032 TCAAGGAAACAGAGGTGAGGATAC 59.777 45.833 0.00 0.00 0.00 2.24
3377 4040 3.008485 GTCAAGGAAACAGAGGTGAGGAT 59.992 47.826 0.00 0.00 0.00 3.24
3382 4045 2.287915 CGTTGTCAAGGAAACAGAGGTG 59.712 50.000 0.00 0.00 0.00 4.00
3383 4046 2.169769 TCGTTGTCAAGGAAACAGAGGT 59.830 45.455 5.50 0.00 0.00 3.85
3389 4052 4.813296 ACATCTTCGTTGTCAAGGAAAC 57.187 40.909 18.50 0.00 35.17 2.78
3396 4059 5.220381 GTCTGAGTAACATCTTCGTTGTCA 58.780 41.667 0.00 0.00 0.00 3.58
3409 4072 6.222038 TGGAATATGGAGTGTCTGAGTAAC 57.778 41.667 0.00 0.00 0.00 2.50
3410 4073 6.867519 TTGGAATATGGAGTGTCTGAGTAA 57.132 37.500 0.00 0.00 0.00 2.24
3411 4074 6.212589 TGTTTGGAATATGGAGTGTCTGAGTA 59.787 38.462 0.00 0.00 0.00 2.59
3412 4075 5.013079 TGTTTGGAATATGGAGTGTCTGAGT 59.987 40.000 0.00 0.00 0.00 3.41
3413 4076 5.491070 TGTTTGGAATATGGAGTGTCTGAG 58.509 41.667 0.00 0.00 0.00 3.35
3414 4077 5.013079 ACTGTTTGGAATATGGAGTGTCTGA 59.987 40.000 0.00 0.00 0.00 3.27
3415 4078 5.248640 ACTGTTTGGAATATGGAGTGTCTG 58.751 41.667 0.00 0.00 0.00 3.51
3416 4079 5.013079 TGACTGTTTGGAATATGGAGTGTCT 59.987 40.000 0.00 0.00 0.00 3.41
3417 4080 5.122396 GTGACTGTTTGGAATATGGAGTGTC 59.878 44.000 0.00 0.00 0.00 3.67
3418 4081 5.003804 GTGACTGTTTGGAATATGGAGTGT 58.996 41.667 0.00 0.00 0.00 3.55
3419 4082 5.003160 TGTGACTGTTTGGAATATGGAGTG 58.997 41.667 0.00 0.00 0.00 3.51
3422 4085 6.152661 GGAAATGTGACTGTTTGGAATATGGA 59.847 38.462 0.00 0.00 0.00 3.41
3426 4089 6.068010 AGTGGAAATGTGACTGTTTGGAATA 58.932 36.000 0.00 0.00 0.00 1.75
3431 4094 6.260936 AGAAGTAGTGGAAATGTGACTGTTTG 59.739 38.462 0.00 0.00 0.00 2.93
3436 4099 6.919775 AGTAGAAGTAGTGGAAATGTGACT 57.080 37.500 0.00 0.00 0.00 3.41
3445 4108 7.231317 TCGGAAGTAAAAAGTAGAAGTAGTGGA 59.769 37.037 0.00 0.00 0.00 4.02
3447 4110 8.081025 ACTCGGAAGTAAAAAGTAGAAGTAGTG 58.919 37.037 0.00 0.00 32.59 2.74
3448 4111 8.081025 CACTCGGAAGTAAAAAGTAGAAGTAGT 58.919 37.037 0.00 0.00 33.25 2.73
3449 4112 8.081025 ACACTCGGAAGTAAAAAGTAGAAGTAG 58.919 37.037 0.00 0.00 33.25 2.57
3451 4114 6.814043 ACACTCGGAAGTAAAAAGTAGAAGT 58.186 36.000 0.00 0.00 33.25 3.01
3452 4115 7.062022 GCTACACTCGGAAGTAAAAAGTAGAAG 59.938 40.741 0.00 0.00 32.62 2.85
3468 4133 4.749245 AAAATTGTTCTGCTACACTCGG 57.251 40.909 0.00 0.00 0.00 4.63
3501 4166 4.455877 GGGTCTATGAGTCCACTTTTTGTG 59.544 45.833 0.00 0.00 45.80 3.33
3502 4167 4.652822 GGGTCTATGAGTCCACTTTTTGT 58.347 43.478 0.00 0.00 0.00 2.83
3503 4168 3.684788 CGGGTCTATGAGTCCACTTTTTG 59.315 47.826 0.00 0.00 0.00 2.44
3504 4169 3.581332 TCGGGTCTATGAGTCCACTTTTT 59.419 43.478 0.00 0.00 0.00 1.94
3505 4170 3.170717 TCGGGTCTATGAGTCCACTTTT 58.829 45.455 0.00 0.00 0.00 2.27
3506 4171 2.816411 TCGGGTCTATGAGTCCACTTT 58.184 47.619 0.00 0.00 0.00 2.66
3507 4172 2.526888 TCGGGTCTATGAGTCCACTT 57.473 50.000 0.00 0.00 0.00 3.16
3508 4173 2.757894 ATCGGGTCTATGAGTCCACT 57.242 50.000 0.00 0.00 0.00 4.00
3509 4174 3.635373 TGTAATCGGGTCTATGAGTCCAC 59.365 47.826 0.00 0.00 0.00 4.02
3510 4175 3.889538 CTGTAATCGGGTCTATGAGTCCA 59.110 47.826 0.00 0.00 0.00 4.02
3511 4176 3.256136 CCTGTAATCGGGTCTATGAGTCC 59.744 52.174 0.00 0.00 35.48 3.85
3512 4177 4.506886 CCTGTAATCGGGTCTATGAGTC 57.493 50.000 0.00 0.00 35.48 3.36
3555 4220 3.791973 ATGTGCCAAAAGTTTTCACGA 57.208 38.095 12.80 5.70 0.00 4.35
3601 4266 2.802719 TGTGCCAAAACTAAGGGGATC 58.197 47.619 0.00 0.00 0.00 3.36
3602 4267 2.990740 TGTGCCAAAACTAAGGGGAT 57.009 45.000 0.00 0.00 0.00 3.85
3603 4268 2.990740 ATGTGCCAAAACTAAGGGGA 57.009 45.000 0.00 0.00 0.00 4.81
3605 4270 4.202050 GCATCTATGTGCCAAAACTAAGGG 60.202 45.833 0.00 0.00 39.18 3.95
3606 4271 4.398988 TGCATCTATGTGCCAAAACTAAGG 59.601 41.667 0.00 0.00 44.43 2.69
3608 4273 5.252547 TCTGCATCTATGTGCCAAAACTAA 58.747 37.500 0.00 0.00 44.43 2.24
3609 4274 4.842574 TCTGCATCTATGTGCCAAAACTA 58.157 39.130 0.00 0.00 44.43 2.24
3610 4275 3.689347 TCTGCATCTATGTGCCAAAACT 58.311 40.909 0.00 0.00 44.43 2.66
3611 4276 4.439305 TTCTGCATCTATGTGCCAAAAC 57.561 40.909 0.00 0.00 44.43 2.43
3612 4277 5.664294 AATTCTGCATCTATGTGCCAAAA 57.336 34.783 0.00 0.00 44.43 2.44
3613 4278 5.664294 AAATTCTGCATCTATGTGCCAAA 57.336 34.783 0.00 0.00 44.43 3.28
3614 4279 5.664294 AAAATTCTGCATCTATGTGCCAA 57.336 34.783 0.00 0.00 44.43 4.52
3615 4280 5.664294 AAAAATTCTGCATCTATGTGCCA 57.336 34.783 0.00 0.00 44.43 4.92
3728 5086 0.834687 ACCTTCCCGGAGTGCTACAA 60.835 55.000 0.73 0.00 36.31 2.41
3858 5216 2.807967 CTCTCTGCATTCGTCCAAAACA 59.192 45.455 0.00 0.00 0.00 2.83
3867 5225 5.163602 ACCTCTTAGTAACTCTCTGCATTCG 60.164 44.000 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.