Multiple sequence alignment - TraesCS3D01G105300

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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 TraesCS3D01G105300 chr3D 100.000 4228 0 0 1 4228 57508466 57504239 0.000000e+00 7808.0
1 TraesCS3D01G105300 chr3D 93.636 110 7 0 3882 3991 463716974 463716865 9.400000e-37 165.0
2 TraesCS3D01G105300 chr3B 93.990 3910 161 33 2 3883 90473712 90469849 0.000000e+00 5851.0
3 TraesCS3D01G105300 chr3B 85.714 238 12 9 3990 4205 90469850 90469613 9.140000e-57 231.0
4 TraesCS3D01G105300 chr3B 94.444 108 6 0 3885 3992 505264678 505264571 2.610000e-37 167.0
5 TraesCS3D01G105300 chr3B 92.793 111 8 0 3882 3992 8054771 8054661 1.220000e-35 161.0
6 TraesCS3D01G105300 chr3A 92.233 2060 96 22 1836 3877 66508804 66506791 0.000000e+00 2859.0
7 TraesCS3D01G105300 chr3A 93.472 1348 68 8 498 1842 66510160 66508830 0.000000e+00 1984.0
8 TraesCS3D01G105300 chr3A 87.158 475 46 8 1 466 66510630 66510162 3.740000e-145 525.0
9 TraesCS3D01G105300 chr3A 87.356 261 11 10 3990 4228 66506618 66506358 3.220000e-71 279.0
10 TraesCS3D01G105300 chr3A 100.000 36 0 0 3977 4012 711494102 711494137 2.730000e-07 67.6
11 TraesCS3D01G105300 chr5D 94.545 110 6 0 3882 3991 282007121 282007012 2.020000e-38 171.0
12 TraesCS3D01G105300 chr6A 94.444 108 6 0 3885 3992 222554899 222555006 2.610000e-37 167.0
13 TraesCS3D01G105300 chr5B 94.393 107 6 0 3885 3991 364132666 364132772 9.400000e-37 165.0
14 TraesCS3D01G105300 chr2D 93.636 110 7 0 3882 3991 388818754 388818863 9.400000e-37 165.0
15 TraesCS3D01G105300 chr2D 89.474 57 4 2 3674 3729 43945954 43946009 2.110000e-08 71.3
16 TraesCS3D01G105300 chr7D 93.578 109 7 0 3885 3993 74592409 74592517 3.380000e-36 163.0
17 TraesCS3D01G105300 chr7D 91.453 117 10 0 3875 3991 550233657 550233541 1.220000e-35 161.0
18 TraesCS3D01G105300 chr7D 97.561 41 1 0 3685 3725 204247186 204247226 2.110000e-08 71.3
19 TraesCS3D01G105300 chr1A 88.525 61 5 2 3670 3729 75916366 75916425 5.860000e-09 73.1
20 TraesCS3D01G105300 chr1A 97.059 34 1 0 3976 4009 177523883 177523916 1.640000e-04 58.4
21 TraesCS3D01G105300 chr7A 97.561 41 1 0 3685 3725 216344332 216344372 2.110000e-08 71.3
22 TraesCS3D01G105300 chr6D 88.525 61 4 3 3688 3746 24554633 24554574 2.110000e-08 71.3
23 TraesCS3D01G105300 chr6D 93.617 47 3 0 3686 3732 405119633 405119587 2.110000e-08 71.3
24 TraesCS3D01G105300 chr6D 93.023 43 3 0 3688 3730 371534722 371534764 3.530000e-06 63.9


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 TraesCS3D01G105300 chr3D 57504239 57508466 4227 True 7808.00 7808 100.00000 1 4228 1 chr3D.!!$R1 4227
1 TraesCS3D01G105300 chr3B 90469613 90473712 4099 True 3041.00 5851 89.85200 2 4205 2 chr3B.!!$R3 4203
2 TraesCS3D01G105300 chr3A 66506358 66510630 4272 True 1411.75 2859 90.05475 1 4228 4 chr3A.!!$R1 4227

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
235 250 0.179018 AATCCCTGGCACCGATAAGC 60.179 55.0 0.00 0.0 0.00 3.09 F
1325 1373 0.107752 TCGCACTGCAATATCCAGCA 60.108 50.0 1.11 0.0 39.25 4.41 F
2350 2440 0.178932 AGCTACGGCCATCCATCCTA 60.179 55.0 2.24 0.0 39.73 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1455 0.251634 CTCCACTGAAGGAAGGAGGC 59.748 60.0 0.0 0.00 43.07 4.70 R
2461 2551 0.467384 ATGCCTAGAAGATGCAGCGT 59.533 50.0 0.0 0.00 38.58 5.07 R
3905 4007 0.108804 ACATCCGTTCGAGCGACAAT 60.109 50.0 23.8 10.39 0.00 2.71 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
60 64 1.738830 GTTAGGCGCCGTGTAGCAA 60.739 57.895 23.20 4.79 34.54 3.91
108 123 2.223180 GGTACCGCATCCAACGAATTTC 60.223 50.000 0.00 0.00 0.00 2.17
131 146 0.584396 TTTTACTCGCGCACCTGTTG 59.416 50.000 8.75 0.00 0.00 3.33
177 192 9.461312 TTTTTATTTATCACCTGCTGTATCTGT 57.539 29.630 0.00 0.00 0.00 3.41
229 244 0.251916 TTGTAGAATCCCTGGCACCG 59.748 55.000 0.00 0.00 0.00 4.94
230 245 0.616395 TGTAGAATCCCTGGCACCGA 60.616 55.000 0.00 0.00 0.00 4.69
231 246 0.759346 GTAGAATCCCTGGCACCGAT 59.241 55.000 0.00 0.00 0.00 4.18
232 247 1.968493 GTAGAATCCCTGGCACCGATA 59.032 52.381 0.00 0.00 0.00 2.92
233 248 1.507140 AGAATCCCTGGCACCGATAA 58.493 50.000 0.00 0.00 0.00 1.75
234 249 1.417890 AGAATCCCTGGCACCGATAAG 59.582 52.381 0.00 0.00 0.00 1.73
235 250 0.179018 AATCCCTGGCACCGATAAGC 60.179 55.000 0.00 0.00 0.00 3.09
261 282 1.207089 TGGTCGTGGATTGATCTGTCC 59.793 52.381 9.28 9.28 35.02 4.02
265 286 4.051922 GTCGTGGATTGATCTGTCCATAC 58.948 47.826 18.48 15.91 45.57 2.39
310 331 6.806739 GGGATGCTTGTTTGTATTGTTTAGTC 59.193 38.462 0.00 0.00 0.00 2.59
311 332 7.367285 GGATGCTTGTTTGTATTGTTTAGTCA 58.633 34.615 0.00 0.00 0.00 3.41
312 333 7.538678 GGATGCTTGTTTGTATTGTTTAGTCAG 59.461 37.037 0.00 0.00 0.00 3.51
313 334 6.734137 TGCTTGTTTGTATTGTTTAGTCAGG 58.266 36.000 0.00 0.00 0.00 3.86
314 335 6.320164 TGCTTGTTTGTATTGTTTAGTCAGGT 59.680 34.615 0.00 0.00 0.00 4.00
315 336 6.636850 GCTTGTTTGTATTGTTTAGTCAGGTG 59.363 38.462 0.00 0.00 0.00 4.00
320 341 3.508845 ATTGTTTAGTCAGGTGTGGCT 57.491 42.857 0.00 0.00 42.88 4.75
380 405 1.225704 GCATGCTAGGTTGCTCCCT 59.774 57.895 11.37 0.38 38.70 4.20
381 406 0.817229 GCATGCTAGGTTGCTCCCTC 60.817 60.000 11.37 0.00 35.97 4.30
389 414 0.248843 GGTTGCTCCCTCTCTGACAG 59.751 60.000 0.00 0.00 0.00 3.51
402 427 6.462552 CTCTCTGACAGAGGAAACATATGA 57.537 41.667 28.13 7.86 44.75 2.15
477 504 3.509967 CCAGATTGGTCCCTTTGGTTAAC 59.490 47.826 0.00 0.00 31.35 2.01
486 513 5.278808 GGTCCCTTTGGTTAACTGATCAAAC 60.279 44.000 5.42 0.00 0.00 2.93
496 523 7.911205 TGGTTAACTGATCAAACAAAACTTACG 59.089 33.333 5.42 0.00 0.00 3.18
534 561 6.101650 TCCGTGCATCTATTGACTGATAAT 57.898 37.500 0.00 0.00 0.00 1.28
552 579 6.299141 TGATAATCTTGCCCTGTTTCTATCC 58.701 40.000 0.00 0.00 0.00 2.59
563 606 5.105752 CCTGTTTCTATCCGCTGCTATATC 58.894 45.833 0.00 0.00 0.00 1.63
564 607 5.105554 CCTGTTTCTATCCGCTGCTATATCT 60.106 44.000 0.00 0.00 0.00 1.98
565 608 6.095580 CCTGTTTCTATCCGCTGCTATATCTA 59.904 42.308 0.00 0.00 0.00 1.98
566 609 7.089770 TGTTTCTATCCGCTGCTATATCTAG 57.910 40.000 0.00 0.00 0.00 2.43
567 610 6.095580 TGTTTCTATCCGCTGCTATATCTAGG 59.904 42.308 0.00 0.00 0.00 3.02
568 611 4.720046 TCTATCCGCTGCTATATCTAGGG 58.280 47.826 0.00 0.00 0.00 3.53
569 612 2.145397 TCCGCTGCTATATCTAGGGG 57.855 55.000 0.00 0.00 43.61 4.79
570 613 2.145397 CCGCTGCTATATCTAGGGGA 57.855 55.000 9.83 0.00 44.64 4.81
571 614 2.042569 TCCGCTGCTATATCTAGGGGAA 59.957 50.000 13.68 2.97 46.50 3.97
572 615 2.166664 CCGCTGCTATATCTAGGGGAAC 59.833 54.545 9.83 0.00 44.64 3.62
634 677 3.026694 ACTCCATTTAGAAGGGCAATGC 58.973 45.455 0.00 0.00 30.92 3.56
665 711 3.941483 CGTCCTAATTCCTCACATTTGCT 59.059 43.478 0.00 0.00 0.00 3.91
699 745 7.552687 TGACCTTCAAGTGCTAATTACCTAATG 59.447 37.037 0.00 0.00 0.00 1.90
724 770 9.023962 TGATATAGCACAAAGTCCATTTCTTTT 57.976 29.630 0.00 0.00 33.58 2.27
772 818 9.435570 ACTAATCAATCTACCTTCCTAGCTTTA 57.564 33.333 0.00 0.00 0.00 1.85
839 886 2.297597 GCGGTAGCTCAGTCCATAATCT 59.702 50.000 0.00 0.00 41.01 2.40
857 904 7.699391 CCATAATCTGTGTTCAACTTAATGCTG 59.301 37.037 0.00 0.00 0.00 4.41
872 919 2.975732 TGCTGGCACATTGTTTTCAA 57.024 40.000 0.00 0.00 44.33 2.69
997 1045 1.144708 TGAACCATCTCCAAGTGCCAA 59.855 47.619 0.00 0.00 0.00 4.52
1097 1145 7.545965 GCTCTGTTCTGCTGTTTATCTTAGTTA 59.454 37.037 0.00 0.00 0.00 2.24
1168 1216 0.530650 AGCATTCGGGTAGTGATGCG 60.531 55.000 0.00 0.00 39.71 4.73
1216 1264 2.628178 TGGGAGTATGGCAAGTAGATCG 59.372 50.000 0.00 0.00 0.00 3.69
1268 1316 5.163195 ACACAGTTTCCAGGTCATAGAGTTT 60.163 40.000 0.00 0.00 0.00 2.66
1274 1322 4.566004 TCCAGGTCATAGAGTTTTGAACG 58.434 43.478 0.00 0.00 34.70 3.95
1294 1342 2.677037 CGTAGGGACCTCACATGTTTCC 60.677 54.545 0.00 0.00 0.00 3.13
1317 1365 1.065491 TGTTCCCTATCGCACTGCAAT 60.065 47.619 1.11 0.00 0.00 3.56
1325 1373 0.107752 TCGCACTGCAATATCCAGCA 60.108 50.000 1.11 0.00 39.25 4.41
1407 1455 2.030893 TGGTTGCAATGAAGCGAAAGAG 60.031 45.455 0.59 0.00 37.31 2.85
1453 1501 4.430007 TGGACGCTGTTGACTATTATGTC 58.570 43.478 0.00 0.00 37.47 3.06
1612 1660 1.747924 TCTCAGAGGAATGTCAGAGCG 59.252 52.381 0.00 0.00 31.75 5.03
1690 1738 2.283298 AGTAACAATCATCAGCTGCCG 58.717 47.619 9.47 1.89 0.00 5.69
1751 1799 2.035961 GGAAGGAACCAAGCACCTTTTC 59.964 50.000 0.00 0.00 42.98 2.29
1826 1874 4.693095 TGTGCTTGATGCGTCTTTATTGTA 59.307 37.500 7.58 0.00 46.63 2.41
1918 1997 7.336176 ACTTTATTTTAGTAGTTACCTGCTGCC 59.664 37.037 0.00 0.00 35.13 4.85
2022 2101 7.748847 AGCGTATGAGGTTGTTGTTTTTATAG 58.251 34.615 0.00 0.00 0.00 1.31
2098 2182 1.679311 GTGGCACTGGGATCACTGA 59.321 57.895 11.13 0.00 0.00 3.41
2350 2440 0.178932 AGCTACGGCCATCCATCCTA 60.179 55.000 2.24 0.00 39.73 2.94
2461 2551 5.840693 TCAATCTGCCATCTCCTATCAGTAA 59.159 40.000 0.00 0.00 0.00 2.24
2462 2552 5.736951 ATCTGCCATCTCCTATCAGTAAC 57.263 43.478 0.00 0.00 0.00 2.50
2497 2587 1.755265 GCATGCAAGGGTATCCATGGT 60.755 52.381 14.21 1.59 36.47 3.55
2552 2642 6.850234 AGATAGGAGCTCATTCCATTTGATT 58.150 36.000 17.19 0.00 39.84 2.57
2577 2667 1.896465 AGACACAGGTAGAGGTCTTGC 59.104 52.381 0.00 0.00 37.31 4.01
2580 2670 2.706190 ACACAGGTAGAGGTCTTGCTTT 59.294 45.455 0.00 0.00 0.00 3.51
2593 2683 4.354587 GTCTTGCTTTCTGTTTTCAGGTG 58.645 43.478 0.00 0.00 46.94 4.00
2594 2684 4.016444 TCTTGCTTTCTGTTTTCAGGTGT 58.984 39.130 0.00 0.00 46.94 4.16
2612 2702 3.632145 GGTGTTTTAGCTGGTATCCATGG 59.368 47.826 4.97 4.97 30.82 3.66
2613 2703 3.632145 GTGTTTTAGCTGGTATCCATGGG 59.368 47.826 13.02 0.00 30.82 4.00
2765 2855 6.930164 TGAGATGAGTTACGAGGTATAGAGAC 59.070 42.308 0.00 0.00 0.00 3.36
2809 2900 5.143369 AGGAAACTGCAGGATCTTTTCTTT 58.857 37.500 19.93 5.75 41.13 2.52
2820 2911 7.471399 GCAGGATCTTTTCTTTAACCTTTTCCA 60.471 37.037 0.00 0.00 0.00 3.53
2933 3024 1.261619 GAAGTGGTCTGTTGCAGTTCG 59.738 52.381 0.00 0.00 32.61 3.95
3004 3095 6.513180 TGGTACGAATTTCTTATGCTCCTAG 58.487 40.000 0.00 0.00 0.00 3.02
3041 3132 6.757237 TGTTGAACAATTCATTACAGCCATT 58.243 32.000 0.00 0.00 39.84 3.16
3044 3135 5.716228 TGAACAATTCATTACAGCCATTCCT 59.284 36.000 0.00 0.00 34.08 3.36
3059 3150 3.441572 CCATTCCTTGAATCGTTTGCTCT 59.558 43.478 0.00 0.00 28.87 4.09
3064 3155 3.120060 CCTTGAATCGTTTGCTCTTCCAG 60.120 47.826 0.00 0.00 0.00 3.86
3072 3163 3.120408 CGTTTGCTCTTCCAGTTCTGATG 60.120 47.826 1.00 0.00 0.00 3.07
3084 3175 8.634335 TTCCAGTTCTGATGTATGATTTTTGA 57.366 30.769 1.00 0.00 0.00 2.69
3085 3176 8.634335 TCCAGTTCTGATGTATGATTTTTGAA 57.366 30.769 1.00 0.00 0.00 2.69
3086 3177 8.514594 TCCAGTTCTGATGTATGATTTTTGAAC 58.485 33.333 1.00 0.00 33.64 3.18
3087 3178 8.517878 CCAGTTCTGATGTATGATTTTTGAACT 58.482 33.333 1.00 0.00 41.15 3.01
3122 3213 5.551233 CAGGAGGAGTACAAAGACAATGAA 58.449 41.667 0.00 0.00 0.00 2.57
3302 3393 2.588034 GAGTTATGCCGGTCGCCC 60.588 66.667 1.90 0.00 36.24 6.13
3323 3414 1.815003 GTCCATTCTTTGGTGCCTGAG 59.185 52.381 0.00 0.00 46.52 3.35
3324 3415 1.704628 TCCATTCTTTGGTGCCTGAGA 59.295 47.619 0.00 0.00 46.52 3.27
3375 3466 1.944709 GTTTCGTGGGTTTGCTGTAGT 59.055 47.619 0.00 0.00 0.00 2.73
3568 3667 1.882912 TGGCATGAGACCGATAATGC 58.117 50.000 0.00 0.00 43.71 3.56
3608 3707 3.857854 GCATGTCGTCGCTGGCTG 61.858 66.667 0.00 0.00 0.00 4.85
3659 3758 3.690460 ACTTGCTCTGGTAATTCCCTTG 58.310 45.455 0.00 0.00 34.77 3.61
3899 4001 6.855763 TTTATTACTACTCCCTCCGTTTCA 57.144 37.500 0.00 0.00 0.00 2.69
3900 4002 7.427989 TTTATTACTACTCCCTCCGTTTCAT 57.572 36.000 0.00 0.00 0.00 2.57
3902 4004 8.716674 TTATTACTACTCCCTCCGTTTCATAT 57.283 34.615 0.00 0.00 0.00 1.78
3905 4007 8.537728 TTACTACTCCCTCCGTTTCATATTAA 57.462 34.615 0.00 0.00 0.00 1.40
3906 4008 7.613551 ACTACTCCCTCCGTTTCATATTAAT 57.386 36.000 0.00 0.00 0.00 1.40
3907 4009 8.030913 ACTACTCCCTCCGTTTCATATTAATT 57.969 34.615 0.00 0.00 0.00 1.40
3911 4013 5.756347 TCCCTCCGTTTCATATTAATTGTCG 59.244 40.000 0.00 1.18 0.00 4.35
3912 4014 5.440685 CCTCCGTTTCATATTAATTGTCGC 58.559 41.667 0.00 0.00 0.00 5.19
3914 4016 6.281848 TCCGTTTCATATTAATTGTCGCTC 57.718 37.500 0.00 0.00 0.00 5.03
3915 4017 5.051307 TCCGTTTCATATTAATTGTCGCTCG 60.051 40.000 0.00 0.00 0.00 5.03
3917 4019 6.407623 CGTTTCATATTAATTGTCGCTCGAA 58.592 36.000 0.00 0.00 0.00 3.71
3918 4020 6.351000 CGTTTCATATTAATTGTCGCTCGAAC 59.649 38.462 0.00 0.00 0.00 3.95
3919 4021 5.555190 TCATATTAATTGTCGCTCGAACG 57.445 39.130 0.82 0.82 0.00 3.95
3920 4022 4.443063 TCATATTAATTGTCGCTCGAACGG 59.557 41.667 8.55 0.00 0.00 4.44
3921 4023 2.350899 TTAATTGTCGCTCGAACGGA 57.649 45.000 8.55 0.00 0.00 4.69
3923 4025 0.999406 AATTGTCGCTCGAACGGATG 59.001 50.000 8.55 0.00 0.00 3.51
3924 4026 0.108804 ATTGTCGCTCGAACGGATGT 60.109 50.000 8.55 0.00 0.00 3.06
3926 4028 0.736636 TGTCGCTCGAACGGATGTAT 59.263 50.000 8.55 0.00 0.00 2.29
3927 4029 1.268386 TGTCGCTCGAACGGATGTATC 60.268 52.381 8.55 0.00 0.00 2.24
3928 4030 1.002684 GTCGCTCGAACGGATGTATCT 60.003 52.381 8.55 0.00 0.00 1.98
3929 4031 2.222678 GTCGCTCGAACGGATGTATCTA 59.777 50.000 8.55 0.00 0.00 1.98
3932 4067 3.547413 CGCTCGAACGGATGTATCTAACA 60.547 47.826 0.00 0.00 43.86 2.41
3935 4070 4.916870 TCGAACGGATGTATCTAACACTG 58.083 43.478 0.00 0.00 42.09 3.66
3940 4075 7.646526 CGAACGGATGTATCTAACACTGAAATA 59.353 37.037 0.00 0.00 42.09 1.40
3941 4076 8.644318 AACGGATGTATCTAACACTGAAATAC 57.356 34.615 0.00 0.00 42.09 1.89
3942 4077 6.916387 ACGGATGTATCTAACACTGAAATACG 59.084 38.462 0.00 0.00 42.09 3.06
3944 4079 7.096599 CGGATGTATCTAACACTGAAATACGTG 60.097 40.741 0.00 0.00 42.09 4.49
3947 4082 9.731819 ATGTATCTAACACTGAAATACGTGTAG 57.268 33.333 0.00 0.00 43.05 2.74
3956 4091 7.147966 ACACTGAAATACGTGTAGATACATCCA 60.148 37.037 0.00 0.00 42.14 3.41
3958 4093 8.421784 ACTGAAATACGTGTAGATACATCCATT 58.578 33.333 0.00 0.00 38.63 3.16
3962 4119 8.818141 AATACGTGTAGATACATCCATTTCAG 57.182 34.615 0.00 0.00 38.63 3.02
3963 4120 5.050490 ACGTGTAGATACATCCATTTCAGC 58.950 41.667 0.00 0.00 38.63 4.26
3967 4124 4.406648 AGATACATCCATTTCAGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
3968 4125 4.769688 AGATACATCCATTTCAGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
3969 4126 4.572389 AGATACATCCATTTCAGCGACAAC 59.428 41.667 0.00 0.00 0.00 3.32
3972 4129 4.323417 ACATCCATTTCAGCGACAACTAA 58.677 39.130 0.00 0.00 0.00 2.24
3974 4131 6.112734 ACATCCATTTCAGCGACAACTAATA 58.887 36.000 0.00 0.00 0.00 0.98
3975 4132 6.767902 ACATCCATTTCAGCGACAACTAATAT 59.232 34.615 0.00 0.00 0.00 1.28
3981 4138 4.109766 TCAGCGACAACTAATATGGAACG 58.890 43.478 0.00 0.00 0.00 3.95
4018 4188 2.228480 GGGAGTACTTGCCACCCCA 61.228 63.158 9.65 0.00 37.22 4.96
4019 4189 1.765074 GGAGTACTTGCCACCCCAA 59.235 57.895 0.00 0.00 0.00 4.12
4020 4190 0.322546 GGAGTACTTGCCACCCCAAG 60.323 60.000 0.00 0.72 45.90 3.61
4022 4192 1.282157 GAGTACTTGCCACCCCAAGAT 59.718 52.381 8.71 0.00 43.79 2.40
4023 4193 1.282157 AGTACTTGCCACCCCAAGATC 59.718 52.381 8.71 0.00 43.79 2.75
4025 4195 1.668826 ACTTGCCACCCCAAGATCTA 58.331 50.000 8.71 0.00 43.79 1.98
4026 4196 2.208872 ACTTGCCACCCCAAGATCTAT 58.791 47.619 8.71 0.00 43.79 1.98
4043 4220 6.327934 AGATCTATGCTTCACAAAATTGCAC 58.672 36.000 0.00 0.00 36.44 4.57
4059 4236 4.846779 TTGCACCCAGTTCATAAACTTC 57.153 40.909 0.00 0.00 43.28 3.01
4081 4258 7.444183 ACTTCGATTACCAAGTCATTTTCTCAA 59.556 33.333 0.00 0.00 0.00 3.02
4124 4302 8.851541 TTCTTTTTCTATTTACGTGTGGGTAT 57.148 30.769 0.00 0.00 0.00 2.73
4219 4411 4.715713 AGAAGAACCCAAGGTCTAACAAC 58.284 43.478 0.00 0.00 33.12 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 64 1.000896 CCAAAATGGTCGCTCCCCT 60.001 57.895 0.00 0.00 34.77 4.79
80 95 1.377987 GGATGCGGTACCCAAAGCA 60.378 57.895 13.61 13.61 44.13 3.91
108 123 2.241722 CAGGTGCGCGAGTAAAATTTG 58.758 47.619 12.10 0.00 0.00 2.32
143 158 6.189567 CAGGTGATAAATAAAAACTACGGCG 58.810 40.000 4.80 4.80 0.00 6.46
177 192 1.691196 CAGAGTTTTGAACCTGGCCA 58.309 50.000 4.71 4.71 0.00 5.36
229 244 3.531538 TCCACGACCAAGAATGCTTATC 58.468 45.455 0.00 0.00 31.81 1.75
230 245 3.627395 TCCACGACCAAGAATGCTTAT 57.373 42.857 0.00 0.00 31.81 1.73
231 246 3.627395 ATCCACGACCAAGAATGCTTA 57.373 42.857 0.00 0.00 31.81 3.09
232 247 2.489329 CAATCCACGACCAAGAATGCTT 59.511 45.455 0.00 0.00 33.74 3.91
233 248 2.086869 CAATCCACGACCAAGAATGCT 58.913 47.619 0.00 0.00 0.00 3.79
234 249 2.083774 TCAATCCACGACCAAGAATGC 58.916 47.619 0.00 0.00 0.00 3.56
235 250 4.034858 CAGATCAATCCACGACCAAGAATG 59.965 45.833 0.00 0.00 0.00 2.67
282 303 3.057596 ACAATACAAACAAGCATCCCGTG 60.058 43.478 0.00 0.00 0.00 4.94
301 322 3.290948 AAGCCACACCTGACTAAACAA 57.709 42.857 0.00 0.00 0.00 2.83
310 331 8.682936 AATTAATCTTATCTAAGCCACACCTG 57.317 34.615 0.00 0.00 33.40 4.00
311 332 9.125026 CAAATTAATCTTATCTAAGCCACACCT 57.875 33.333 0.00 0.00 33.40 4.00
312 333 9.120538 TCAAATTAATCTTATCTAAGCCACACC 57.879 33.333 0.00 0.00 33.40 4.16
351 375 3.430565 TAGCATGCGCAGGACCGAG 62.431 63.158 28.37 5.44 42.27 4.63
354 378 2.590007 CCTAGCATGCGCAGGACC 60.590 66.667 28.37 9.13 42.27 4.46
358 382 2.044832 GAGCAACCTAGCATGCGCAG 62.045 60.000 18.32 13.37 46.98 5.18
380 405 5.954752 ACTCATATGTTTCCTCTGTCAGAGA 59.045 40.000 28.19 13.31 45.07 3.10
381 406 6.219417 ACTCATATGTTTCCTCTGTCAGAG 57.781 41.667 21.18 21.18 41.96 3.35
459 485 4.463050 TCAGTTAACCAAAGGGACCAAT 57.537 40.909 0.88 0.00 38.05 3.16
466 492 7.763985 AGTTTTGTTTGATCAGTTAACCAAAGG 59.236 33.333 0.88 0.00 0.00 3.11
477 504 9.658475 TGTTATTCGTAAGTTTTGTTTGATCAG 57.342 29.630 0.00 0.00 39.48 2.90
496 523 7.417612 AGATGCACGGATAAAACATGTTATTC 58.582 34.615 12.39 8.90 0.00 1.75
511 538 5.529581 TTATCAGTCAATAGATGCACGGA 57.470 39.130 0.00 0.00 0.00 4.69
534 561 1.406887 GCGGATAGAAACAGGGCAAGA 60.407 52.381 0.00 0.00 0.00 3.02
552 579 2.166664 GGTTCCCCTAGATATAGCAGCG 59.833 54.545 0.00 0.00 0.00 5.18
563 606 7.433537 TGTTCTAGAATTTAGGTTCCCCTAG 57.566 40.000 8.75 0.00 44.21 3.02
564 607 7.681168 TCTTGTTCTAGAATTTAGGTTCCCCTA 59.319 37.037 8.75 0.00 42.66 3.53
565 608 6.504279 TCTTGTTCTAGAATTTAGGTTCCCCT 59.496 38.462 8.75 0.00 45.51 4.79
566 609 6.718294 TCTTGTTCTAGAATTTAGGTTCCCC 58.282 40.000 8.75 0.00 0.00 4.81
567 610 8.809468 ATTCTTGTTCTAGAATTTAGGTTCCC 57.191 34.615 8.75 0.00 40.99 3.97
595 638 9.646522 AAATGGAGTATATTGGCTTCTAACAAT 57.353 29.630 0.00 0.00 40.21 2.71
640 683 1.200519 TGTGAGGAATTAGGACGGGG 58.799 55.000 0.00 0.00 0.00 5.73
643 686 3.941483 AGCAAATGTGAGGAATTAGGACG 59.059 43.478 0.00 0.00 0.00 4.79
654 700 7.798596 AGGTCAGATATTTAGCAAATGTGAG 57.201 36.000 0.00 0.00 32.38 3.51
665 711 9.905713 AATTAGCACTTGAAGGTCAGATATTTA 57.094 29.630 0.00 0.00 0.00 1.40
674 720 7.769044 TCATTAGGTAATTAGCACTTGAAGGTC 59.231 37.037 16.53 0.00 0.00 3.85
699 745 9.294030 CAAAAGAAATGGACTTTGTGCTATATC 57.706 33.333 0.00 0.00 37.59 1.63
724 770 6.727394 AGTAAATCCACCCATTACTTTAGCA 58.273 36.000 0.00 0.00 36.70 3.49
772 818 7.482169 TGAAACTGACTTCATACACTCCTAT 57.518 36.000 0.00 0.00 30.31 2.57
780 826 7.202016 TCCAAACATGAAACTGACTTCATAC 57.798 36.000 0.00 0.00 42.79 2.39
839 886 2.954989 TGCCAGCATTAAGTTGAACACA 59.045 40.909 0.00 0.00 0.00 3.72
857 904 4.874970 AGTCTCATTGAAAACAATGTGCC 58.125 39.130 18.13 9.35 41.78 5.01
872 919 3.450096 TCAGACAGCAATGCTAGTCTCAT 59.550 43.478 25.92 12.03 41.36 2.90
997 1045 4.103785 CCTGGGTTGAGTATGATCCATCTT 59.896 45.833 0.00 0.00 0.00 2.40
1054 1102 3.099905 AGAGCACAGGTGAAGTATAGCA 58.900 45.455 3.10 0.00 0.00 3.49
1168 1216 0.542333 GAGGACCAAGTCTAAGGGGC 59.458 60.000 0.00 0.00 32.47 5.80
1216 1264 4.690748 TGACTTGAAGATGGAACGTCATTC 59.309 41.667 0.00 0.00 36.48 2.67
1268 1316 1.707106 TGTGAGGTCCCTACGTTCAA 58.293 50.000 0.00 0.00 0.00 2.69
1274 1322 2.572104 AGGAAACATGTGAGGTCCCTAC 59.428 50.000 0.00 0.00 0.00 3.18
1294 1342 1.398390 GCAGTGCGATAGGGAACAAAG 59.602 52.381 0.00 0.00 0.00 2.77
1317 1365 1.506025 TGGTACATGGCTGCTGGATA 58.494 50.000 0.00 0.00 0.00 2.59
1325 1373 3.328637 TGAGCATCATATGGTACATGGCT 59.671 43.478 2.13 0.00 42.99 4.75
1407 1455 0.251634 CTCCACTGAAGGAAGGAGGC 59.748 60.000 0.00 0.00 43.07 4.70
1453 1501 2.435586 CTGTTGGAGGAGCTGCCG 60.436 66.667 0.00 0.00 43.43 5.69
1612 1660 5.122239 TGAAATATTAGCACTATCATGGCGC 59.878 40.000 0.00 0.00 0.00 6.53
1690 1738 2.362077 AGCACTTGTGGTTGAATGGAAC 59.638 45.455 0.00 0.00 0.00 3.62
1751 1799 3.305335 GGTAATGTTCTTGTTGGCACAGG 60.305 47.826 0.00 0.00 42.39 4.00
2035 2114 4.098044 AGACTGTGAGTTTGAAAGACGAGA 59.902 41.667 0.00 0.00 0.00 4.04
2036 2115 4.363999 AGACTGTGAGTTTGAAAGACGAG 58.636 43.478 0.00 0.00 0.00 4.18
2037 2116 4.386867 AGACTGTGAGTTTGAAAGACGA 57.613 40.909 0.00 0.00 0.00 4.20
2038 2117 5.692204 ACATAGACTGTGAGTTTGAAAGACG 59.308 40.000 6.17 0.00 36.48 4.18
2039 2118 8.764524 ATACATAGACTGTGAGTTTGAAAGAC 57.235 34.615 6.17 0.00 38.92 3.01
2461 2551 0.467384 ATGCCTAGAAGATGCAGCGT 59.533 50.000 0.00 0.00 38.58 5.07
2462 2552 0.866427 CATGCCTAGAAGATGCAGCG 59.134 55.000 0.00 0.00 38.58 5.18
2497 2587 1.180456 CCTTCCACTGTTGGCATGCA 61.180 55.000 21.36 2.54 43.56 3.96
2525 2615 6.327365 TCAAATGGAATGAGCTCCTATCTACA 59.673 38.462 12.15 1.71 36.35 2.74
2552 2642 1.203063 ACCTCTACCTGTGTCTCAGCA 60.203 52.381 0.00 0.00 42.38 4.41
2577 2667 6.473455 CAGCTAAAACACCTGAAAACAGAAAG 59.527 38.462 0.00 0.00 0.00 2.62
2580 2670 4.338118 CCAGCTAAAACACCTGAAAACAGA 59.662 41.667 0.00 0.00 0.00 3.41
2593 2683 4.137543 CTCCCATGGATACCAGCTAAAAC 58.862 47.826 15.22 0.00 36.75 2.43
2594 2684 3.785887 ACTCCCATGGATACCAGCTAAAA 59.214 43.478 15.22 0.00 36.75 1.52
2765 2855 3.914312 TGAGTAGAAGAAGCAAAGACCG 58.086 45.455 0.00 0.00 0.00 4.79
2794 2885 6.868864 GGAAAAGGTTAAAGAAAAGATCCTGC 59.131 38.462 0.00 0.00 0.00 4.85
2809 2900 7.827236 CCTGTACATACAAGATGGAAAAGGTTA 59.173 37.037 0.00 0.00 35.50 2.85
2820 2911 6.173339 CCAACAGTTCCTGTACATACAAGAT 58.827 40.000 0.00 0.00 44.62 2.40
2933 3024 1.078759 CGTCGTCTTGTGCCTCATCC 61.079 60.000 0.00 0.00 0.00 3.51
3004 3095 4.647424 TGTTCAACATGGAACTGGAAAC 57.353 40.909 13.72 1.47 45.74 2.78
3041 3132 3.074412 GGAAGAGCAAACGATTCAAGGA 58.926 45.455 0.00 0.00 0.00 3.36
3044 3135 3.476552 ACTGGAAGAGCAAACGATTCAA 58.523 40.909 0.00 0.00 37.43 2.69
3059 3150 8.634335 TCAAAAATCATACATCAGAACTGGAA 57.366 30.769 1.93 0.00 0.00 3.53
3084 3175 5.905913 ACTCCTCCTGCCATAGTTAATAGTT 59.094 40.000 0.00 0.00 0.00 2.24
3085 3176 5.468658 ACTCCTCCTGCCATAGTTAATAGT 58.531 41.667 0.00 0.00 0.00 2.12
3086 3177 6.493802 TGTACTCCTCCTGCCATAGTTAATAG 59.506 42.308 0.00 0.00 0.00 1.73
3087 3178 6.378745 TGTACTCCTCCTGCCATAGTTAATA 58.621 40.000 0.00 0.00 0.00 0.98
3088 3179 5.216622 TGTACTCCTCCTGCCATAGTTAAT 58.783 41.667 0.00 0.00 0.00 1.40
3089 3180 4.616553 TGTACTCCTCCTGCCATAGTTAA 58.383 43.478 0.00 0.00 0.00 2.01
3090 3181 4.259933 TGTACTCCTCCTGCCATAGTTA 57.740 45.455 0.00 0.00 0.00 2.24
3122 3213 2.290577 GCACTTCAGAATTCCCAGGAGT 60.291 50.000 0.65 0.05 0.00 3.85
3230 3321 3.637229 CGGTTATTCTGCTTCCTCTCCTA 59.363 47.826 0.00 0.00 0.00 2.94
3323 3414 1.268743 GCGCACTTATTTCCATGGCTC 60.269 52.381 6.96 0.00 0.00 4.70
3324 3415 0.740737 GCGCACTTATTTCCATGGCT 59.259 50.000 6.96 0.00 0.00 4.75
3366 3457 6.230472 AGACATGATAACACAACTACAGCAA 58.770 36.000 0.00 0.00 0.00 3.91
3375 3466 7.503521 TTTACAGCAAGACATGATAACACAA 57.496 32.000 0.00 0.00 0.00 3.33
3568 3667 0.532417 TACCCACCAACGTCAAACCG 60.532 55.000 0.00 0.00 0.00 4.44
3659 3758 8.975410 AACCTTTTGTTTTACTAGTTTCACAC 57.025 30.769 0.00 0.00 31.47 3.82
3869 3971 9.819754 ACGGAGGGAGTAGTAATAAATATAGTT 57.180 33.333 0.00 0.00 0.00 2.24
3870 3972 9.819754 AACGGAGGGAGTAGTAATAAATATAGT 57.180 33.333 0.00 0.00 0.00 2.12
3873 3975 9.151177 TGAAACGGAGGGAGTAGTAATAAATAT 57.849 33.333 0.00 0.00 0.00 1.28
3877 3979 8.716674 ATATGAAACGGAGGGAGTAGTAATAA 57.283 34.615 0.00 0.00 0.00 1.40
3878 3980 8.716674 AATATGAAACGGAGGGAGTAGTAATA 57.283 34.615 0.00 0.00 0.00 0.98
3879 3981 7.613551 AATATGAAACGGAGGGAGTAGTAAT 57.386 36.000 0.00 0.00 0.00 1.89
3880 3982 8.537728 TTAATATGAAACGGAGGGAGTAGTAA 57.462 34.615 0.00 0.00 0.00 2.24
3881 3983 8.716674 ATTAATATGAAACGGAGGGAGTAGTA 57.283 34.615 0.00 0.00 0.00 1.82
3882 3984 7.613551 ATTAATATGAAACGGAGGGAGTAGT 57.386 36.000 0.00 0.00 0.00 2.73
3883 3985 7.931948 ACAATTAATATGAAACGGAGGGAGTAG 59.068 37.037 0.00 0.00 0.00 2.57
3888 3990 5.560183 GCGACAATTAATATGAAACGGAGGG 60.560 44.000 0.00 0.00 0.00 4.30
3897 3999 4.443063 CCGTTCGAGCGACAATTAATATGA 59.557 41.667 23.80 0.00 0.00 2.15
3899 4001 4.613944 TCCGTTCGAGCGACAATTAATAT 58.386 39.130 23.80 0.00 0.00 1.28
3900 4002 4.031418 TCCGTTCGAGCGACAATTAATA 57.969 40.909 23.80 0.00 0.00 0.98
3902 4004 2.350899 TCCGTTCGAGCGACAATTAA 57.649 45.000 23.80 0.00 0.00 1.40
3905 4007 0.108804 ACATCCGTTCGAGCGACAAT 60.109 50.000 23.80 10.39 0.00 2.71
3906 4008 0.522626 TACATCCGTTCGAGCGACAA 59.477 50.000 23.80 8.44 0.00 3.18
3907 4009 0.736636 ATACATCCGTTCGAGCGACA 59.263 50.000 23.80 9.45 0.00 4.35
3911 4013 3.729716 GTGTTAGATACATCCGTTCGAGC 59.270 47.826 0.00 0.00 39.39 5.03
3912 4014 4.970611 CAGTGTTAGATACATCCGTTCGAG 59.029 45.833 0.00 0.00 39.39 4.04
3914 4016 4.916870 TCAGTGTTAGATACATCCGTTCG 58.083 43.478 0.00 0.00 39.39 3.95
3915 4017 7.772332 ATTTCAGTGTTAGATACATCCGTTC 57.228 36.000 0.00 0.00 39.39 3.95
3917 4019 6.916387 CGTATTTCAGTGTTAGATACATCCGT 59.084 38.462 0.00 0.00 39.39 4.69
3918 4020 6.916387 ACGTATTTCAGTGTTAGATACATCCG 59.084 38.462 0.00 0.00 39.39 4.18
3919 4021 8.062231 CACGTATTTCAGTGTTAGATACATCC 57.938 38.462 0.00 0.00 39.39 3.51
3932 4067 7.342769 TGGATGTATCTACACGTATTTCAGT 57.657 36.000 0.00 0.00 39.30 3.41
3935 4070 9.256477 TGAAATGGATGTATCTACACGTATTTC 57.744 33.333 17.42 17.42 39.33 2.17
3940 4075 5.050490 GCTGAAATGGATGTATCTACACGT 58.950 41.667 0.00 0.00 39.30 4.49
3941 4076 4.148871 CGCTGAAATGGATGTATCTACACG 59.851 45.833 0.00 0.00 39.30 4.49
3942 4077 5.175856 GTCGCTGAAATGGATGTATCTACAC 59.824 44.000 0.00 0.00 39.30 2.90
3944 4079 5.289595 TGTCGCTGAAATGGATGTATCTAC 58.710 41.667 0.00 0.00 0.00 2.59
3947 4082 4.572389 AGTTGTCGCTGAAATGGATGTATC 59.428 41.667 0.00 0.00 0.00 2.24
3956 4091 6.238103 CGTTCCATATTAGTTGTCGCTGAAAT 60.238 38.462 0.00 0.00 0.00 2.17
3958 4093 4.565166 CGTTCCATATTAGTTGTCGCTGAA 59.435 41.667 0.00 0.00 0.00 3.02
3962 4119 3.450578 TCCGTTCCATATTAGTTGTCGC 58.549 45.455 0.00 0.00 0.00 5.19
3963 4120 4.049186 CCTCCGTTCCATATTAGTTGTCG 58.951 47.826 0.00 0.00 0.00 4.35
3967 4124 4.296056 ACTCCCTCCGTTCCATATTAGTT 58.704 43.478 0.00 0.00 0.00 2.24
3968 4125 3.924922 ACTCCCTCCGTTCCATATTAGT 58.075 45.455 0.00 0.00 0.00 2.24
3969 4126 5.078256 ACTACTCCCTCCGTTCCATATTAG 58.922 45.833 0.00 0.00 0.00 1.73
3972 4129 3.614568 ACTACTCCCTCCGTTCCATAT 57.385 47.619 0.00 0.00 0.00 1.78
3974 4131 2.249309 AACTACTCCCTCCGTTCCAT 57.751 50.000 0.00 0.00 0.00 3.41
3975 4132 2.019807 AAACTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
3981 4138 3.032459 CCCTCTGTAAACTACTCCCTCC 58.968 54.545 0.00 0.00 0.00 4.30
4018 4188 6.810182 GTGCAATTTTGTGAAGCATAGATCTT 59.190 34.615 0.00 0.00 37.56 2.40
4019 4189 6.327934 GTGCAATTTTGTGAAGCATAGATCT 58.672 36.000 0.00 0.00 37.56 2.75
4020 4190 5.517770 GGTGCAATTTTGTGAAGCATAGATC 59.482 40.000 0.00 0.00 37.56 2.75
4022 4192 4.321899 GGGTGCAATTTTGTGAAGCATAGA 60.322 41.667 0.00 0.00 37.56 1.98
4023 4193 3.928375 GGGTGCAATTTTGTGAAGCATAG 59.072 43.478 0.00 0.00 37.56 2.23
4025 4195 2.104451 TGGGTGCAATTTTGTGAAGCAT 59.896 40.909 0.00 0.00 37.56 3.79
4026 4196 1.483827 TGGGTGCAATTTTGTGAAGCA 59.516 42.857 0.00 0.00 0.00 3.91
4043 4220 5.878116 TGGTAATCGAAGTTTATGAACTGGG 59.122 40.000 3.30 0.00 45.18 4.45
4059 4236 8.970691 AAATTGAGAAAATGACTTGGTAATCG 57.029 30.769 0.00 0.00 0.00 3.34
4101 4278 8.388103 CAGATACCCACACGTAAATAGAAAAAG 58.612 37.037 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.