Multiple sequence alignment - TraesCS2A01G377400

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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 TraesCS2A01G377400 chr2A 100.000 3749 0 0 1 3749 619755474 619759222 0.000000e+00 6924.0
1 TraesCS2A01G377400 chr2A 89.391 1461 148 6 1302 2756 619766544 619768003 0.000000e+00 1832.0
2 TraesCS2A01G377400 chr2A 88.824 170 17 2 367 535 619765861 619766029 1.360000e-49 207.0
3 TraesCS2A01G377400 chr2A 89.720 107 11 0 534 640 619766400 619766506 1.820000e-28 137.0
4 TraesCS2A01G377400 chr2D 93.133 3160 121 33 534 3618 477271352 477274490 0.000000e+00 4545.0
5 TraesCS2A01G377400 chr2D 89.086 1466 153 4 1297 2756 477395477 477396941 0.000000e+00 1814.0
6 TraesCS2A01G377400 chr2D 83.200 375 35 16 165 535 477270663 477271013 6.040000e-83 318.0
7 TraesCS2A01G377400 chr2D 88.415 164 16 2 99 260 477270562 477270724 1.060000e-45 195.0
8 TraesCS2A01G377400 chr2D 86.471 170 22 1 366 535 477394794 477394962 6.390000e-43 185.0
9 TraesCS2A01G377400 chr2D 88.112 143 15 2 534 676 477395333 477395473 6.440000e-38 169.0
10 TraesCS2A01G377400 chr2D 78.846 104 20 2 2133 2235 493004995 493004893 6.720000e-08 69.4
11 TraesCS2A01G377400 chr2B 93.932 2439 117 19 534 2958 559307566 559309987 0.000000e+00 3655.0
12 TraesCS2A01G377400 chr2B 89.759 1455 141 8 1308 2756 559417441 559418893 0.000000e+00 1855.0
13 TraesCS2A01G377400 chr2B 87.817 788 43 23 2950 3693 559310009 559310787 0.000000e+00 874.0
14 TraesCS2A01G377400 chr2B 87.410 278 14 11 276 535 559306953 559307227 2.190000e-77 300.0
15 TraesCS2A01G377400 chr2B 89.349 169 17 1 366 534 559416746 559416913 1.050000e-50 211.0
16 TraesCS2A01G377400 chr2B 82.041 245 15 15 1 238 559306732 559306954 8.270000e-42 182.0
17 TraesCS2A01G377400 chr2B 88.732 142 14 2 534 675 559417286 559417425 4.980000e-39 172.0
18 TraesCS2A01G377400 chr2B 79.808 104 19 2 2133 2235 579572123 579572021 1.440000e-09 75.0
19 TraesCS2A01G377400 chr7D 83.459 133 11 4 1151 1282 504829467 504829589 3.060000e-21 113.0


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 TraesCS2A01G377400 chr2A 619755474 619759222 3748 False 6924.000000 6924 100.000000 1 3749 1 chr2A.!!$F1 3748
1 TraesCS2A01G377400 chr2A 619765861 619768003 2142 False 725.333333 1832 89.311667 367 2756 3 chr2A.!!$F2 2389
2 TraesCS2A01G377400 chr2D 477270562 477274490 3928 False 1686.000000 4545 88.249333 99 3618 3 chr2D.!!$F1 3519
3 TraesCS2A01G377400 chr2D 477394794 477396941 2147 False 722.666667 1814 87.889667 366 2756 3 chr2D.!!$F2 2390
4 TraesCS2A01G377400 chr2B 559306732 559310787 4055 False 1252.750000 3655 87.800000 1 3693 4 chr2B.!!$F1 3692
5 TraesCS2A01G377400 chr2B 559416746 559418893 2147 False 746.000000 1855 89.280000 366 2756 3 chr2B.!!$F2 2390

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
130 138 0.404040 AAAGACCAAAGGCCCGATCA 59.596 50.000 0.00 0.0 0.0 2.92 F
731 1164 1.269448 CGTTGCACACCTTAAGCCAAT 59.731 47.619 0.00 0.0 0.0 3.16 F
1471 1922 0.252881 TCCTTGGAGGCATCCTGTCT 60.253 55.000 19.75 0.0 46.8 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1220 1669 1.333636 GCTGGAGAAGGCTGAGGCTA 61.334 60.0 9.60 0.0 37.50 3.93 R
2577 3034 0.386731 CCGGTGCAAATGTTTCCGAC 60.387 55.0 10.89 0.0 43.22 4.79 R
3180 3681 0.320374 CCTGTTCCTGAGGTACGCAA 59.680 55.0 3.76 0.0 37.93 4.85 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
38 39 9.651913 ACATACTTTTTCTTTTTGAACACATGT 57.348 25.926 0.00 0.00 33.88 3.21
78 79 4.718940 AAGTCACCCTTCAAACAACTTG 57.281 40.909 0.00 0.00 36.25 3.16
81 82 3.442273 GTCACCCTTCAAACAACTTGACA 59.558 43.478 0.00 0.00 43.90 3.58
93 94 8.519526 TCAAACAACTTGACAGATTACAAACTT 58.480 29.630 0.00 0.00 39.20 2.66
94 95 8.586273 CAAACAACTTGACAGATTACAAACTTG 58.414 33.333 0.00 0.00 37.17 3.16
98 99 9.139174 CAACTTGACAGATTACAAACTTGTTTT 57.861 29.630 0.00 0.00 42.35 2.43
125 133 0.467804 TGCAAAAAGACCAAAGGCCC 59.532 50.000 0.00 0.00 0.00 5.80
130 138 0.404040 AAAGACCAAAGGCCCGATCA 59.596 50.000 0.00 0.00 0.00 2.92
147 155 7.152645 GCCCGATCAAATTACAGACTCTATAA 58.847 38.462 0.00 0.00 0.00 0.98
172 180 7.790027 ACCCATAATATGCAAATTGTAAAGCA 58.210 30.769 0.00 0.00 41.73 3.91
193 201 8.523915 AAGCATGTTAGATATTTCCACATGAA 57.476 30.769 20.91 0.00 41.96 2.57
255 295 9.890629 ATGTCAAGCTTGTTAGATATTTCTACA 57.109 29.630 25.19 16.80 34.15 2.74
261 301 9.495572 AGCTTGTTAGATATTTCTACAATAGGC 57.504 33.333 0.00 0.00 34.15 3.93
297 337 6.627395 TGCGAATTTCTCTTTTGGAACTAA 57.373 33.333 0.00 0.00 0.00 2.24
298 338 6.435428 TGCGAATTTCTCTTTTGGAACTAAC 58.565 36.000 0.00 0.00 0.00 2.34
299 339 5.856986 GCGAATTTCTCTTTTGGAACTAACC 59.143 40.000 0.00 0.00 0.00 2.85
363 404 8.589338 TGATATTAACTAGCAAAGAGAGGATCC 58.411 37.037 2.48 2.48 33.66 3.36
364 405 5.615925 TTAACTAGCAAAGAGAGGATCCC 57.384 43.478 8.55 0.00 33.66 3.85
387 445 5.753921 CCTCCCTATTTCACGATTAACTCAC 59.246 44.000 0.00 0.00 0.00 3.51
644 1077 4.042187 AGAACAGGTAAAGATTGCAGACCT 59.958 41.667 0.00 0.00 41.28 3.85
695 1128 3.242543 CCAAAGAGTGATGCGTCATTAGC 60.243 47.826 12.67 0.00 36.60 3.09
696 1129 3.533606 AAGAGTGATGCGTCATTAGCT 57.466 42.857 12.67 4.05 36.60 3.32
721 1154 3.685836 AACTTAAACTCGTTGCACACC 57.314 42.857 0.00 0.00 0.00 4.16
726 1159 3.963383 AAACTCGTTGCACACCTTAAG 57.037 42.857 0.00 0.00 0.00 1.85
731 1164 1.269448 CGTTGCACACCTTAAGCCAAT 59.731 47.619 0.00 0.00 0.00 3.16
788 1225 4.849383 CGTTTATTTGTTCAGTTAAGGCCG 59.151 41.667 0.00 0.00 0.00 6.13
947 1391 3.764434 GACACCTCTGACCACTAGAATGA 59.236 47.826 0.00 0.00 0.00 2.57
951 1395 4.021016 ACCTCTGACCACTAGAATGAACAC 60.021 45.833 0.00 0.00 0.00 3.32
1071 1518 6.903883 TTATTTATGTCTTCTCGAACCTGC 57.096 37.500 0.00 0.00 0.00 4.85
1081 1528 2.939261 CGAACCTGCACCCTACGGT 61.939 63.158 0.00 0.00 46.31 4.83
1118 1567 3.264104 CCGACCTAGAACGGCAAATTAA 58.736 45.455 12.89 0.00 42.55 1.40
1220 1669 2.702592 TTGACGTGTTGGAGTCCTTT 57.297 45.000 11.33 0.00 36.61 3.11
1240 1689 2.964310 GCCTCAGCCTTCTCCAGCA 61.964 63.158 0.00 0.00 0.00 4.41
1242 1691 1.675801 CTCAGCCTTCTCCAGCACA 59.324 57.895 0.00 0.00 0.00 4.57
1271 1720 2.167900 ACTTAATTAGGCGAGGCGAACT 59.832 45.455 0.00 0.00 0.00 3.01
1285 1734 5.276461 AGGCGAACTGTCATTACATCATA 57.724 39.130 0.00 0.00 34.37 2.15
1288 1737 6.767902 AGGCGAACTGTCATTACATCATATTT 59.232 34.615 0.00 0.00 34.37 1.40
1471 1922 0.252881 TCCTTGGAGGCATCCTGTCT 60.253 55.000 19.75 0.00 46.80 3.41
1520 1971 4.321675 CCAAGAAAAGGGGTATTTGGTTCG 60.322 45.833 0.00 0.00 32.44 3.95
1526 1977 0.963355 GGGTATTTGGTTCGCTGCCA 60.963 55.000 0.00 0.00 0.00 4.92
1598 2050 1.468127 GCTCTTTCTTGAAGCCTGAGC 59.532 52.381 13.79 13.79 38.58 4.26
1905 2362 2.102420 CGTATCTATTGGCACTGTCCCA 59.898 50.000 0.00 0.00 0.00 4.37
2043 2500 4.333926 ACTTATGGAAAGCTCGCAATCTTC 59.666 41.667 0.00 0.00 0.00 2.87
2520 2977 4.894784 ACATAGGATCGTATTTCGCCATT 58.105 39.130 5.18 0.00 39.67 3.16
2577 3034 1.268899 CAAAAGCTGGACAGAGCCAAG 59.731 52.381 3.00 0.00 40.08 3.61
2772 3229 6.502158 AGAATCTTCAGGGAAAAGGAGAAGTA 59.498 38.462 0.00 0.00 37.53 2.24
2808 3265 5.713389 TCAAAGATTCAGATTGATGCCAACT 59.287 36.000 0.00 0.00 34.72 3.16
2809 3266 5.831702 AAGATTCAGATTGATGCCAACTC 57.168 39.130 0.00 0.00 34.72 3.01
2810 3267 4.205587 AGATTCAGATTGATGCCAACTCC 58.794 43.478 0.00 0.00 34.72 3.85
2811 3268 3.726557 TTCAGATTGATGCCAACTCCT 57.273 42.857 0.00 0.00 34.72 3.69
2812 3269 2.995283 TCAGATTGATGCCAACTCCTG 58.005 47.619 0.00 0.00 34.72 3.86
2813 3270 1.404391 CAGATTGATGCCAACTCCTGC 59.596 52.381 0.00 0.00 34.72 4.85
2814 3271 0.743097 GATTGATGCCAACTCCTGCC 59.257 55.000 0.00 0.00 34.72 4.85
2815 3272 0.040058 ATTGATGCCAACTCCTGCCA 59.960 50.000 0.00 0.00 34.72 4.92
2816 3273 0.895100 TTGATGCCAACTCCTGCCAC 60.895 55.000 0.00 0.00 0.00 5.01
2817 3274 1.303561 GATGCCAACTCCTGCCACA 60.304 57.895 0.00 0.00 0.00 4.17
2818 3275 1.303888 ATGCCAACTCCTGCCACAG 60.304 57.895 0.00 0.00 0.00 3.66
2819 3276 2.072874 ATGCCAACTCCTGCCACAGT 62.073 55.000 0.00 0.00 0.00 3.55
2820 3277 2.263741 GCCAACTCCTGCCACAGTG 61.264 63.158 0.00 0.00 0.00 3.66
2821 3278 1.601759 CCAACTCCTGCCACAGTGG 60.602 63.158 16.16 16.16 41.55 4.00
2862 3319 9.283768 CTGTTATTAAGAACATACATATGGGCA 57.716 33.333 15.54 0.00 38.60 5.36
2958 3448 0.840617 TTTGCTCCCCTGTGTGTGTA 59.159 50.000 0.00 0.00 0.00 2.90
2960 3450 1.945580 TGCTCCCCTGTGTGTGTATA 58.054 50.000 0.00 0.00 0.00 1.47
2992 3482 2.907910 CAGGAGTTGCAGCAATGTAC 57.092 50.000 11.96 2.68 0.00 2.90
2993 3483 2.153645 CAGGAGTTGCAGCAATGTACA 58.846 47.619 11.96 0.00 0.00 2.90
2994 3484 2.751259 CAGGAGTTGCAGCAATGTACAT 59.249 45.455 11.96 1.41 0.00 2.29
2996 3486 3.828451 AGGAGTTGCAGCAATGTACATTT 59.172 39.130 18.50 2.52 0.00 2.32
2997 3487 5.009631 AGGAGTTGCAGCAATGTACATTTA 58.990 37.500 18.50 0.89 0.00 1.40
2998 3488 5.653769 AGGAGTTGCAGCAATGTACATTTAT 59.346 36.000 18.50 7.37 0.00 1.40
2999 3489 5.973565 GGAGTTGCAGCAATGTACATTTATC 59.026 40.000 18.50 10.56 0.00 1.75
3000 3490 6.183360 GGAGTTGCAGCAATGTACATTTATCT 60.183 38.462 18.50 12.49 0.00 1.98
3001 3491 7.012327 GGAGTTGCAGCAATGTACATTTATCTA 59.988 37.037 18.50 3.27 0.00 1.98
3039 3535 6.615264 ATGCTGCATATAAGAACAGAAGTG 57.385 37.500 14.52 0.00 31.67 3.16
3040 3536 5.491070 TGCTGCATATAAGAACAGAAGTGT 58.509 37.500 0.00 0.00 39.19 3.55
3049 3545 3.996480 AGAACAGAAGTGTCAGGCTAAC 58.004 45.455 0.00 0.00 35.08 2.34
3050 3546 3.388024 AGAACAGAAGTGTCAGGCTAACA 59.612 43.478 0.00 0.00 35.08 2.41
3051 3547 3.113260 ACAGAAGTGTCAGGCTAACAC 57.887 47.619 13.23 13.23 45.86 3.32
3104 3600 8.630054 TTTACTGAAAACATTGCCAGTAGTAT 57.370 30.769 0.00 0.00 41.39 2.12
3167 3668 9.959749 ATTCTTCTTTTGCAATTAGTACGAAAA 57.040 25.926 0.00 0.00 0.00 2.29
3238 3739 1.883732 GGATCAGATAGCGCGCCTA 59.116 57.895 30.33 19.48 0.00 3.93
3287 3796 3.452786 CTCTCCCTCTGCCGCGAA 61.453 66.667 8.23 0.00 0.00 4.70
3371 3880 4.847444 GAAGCTGCGCCTCCCTCC 62.847 72.222 4.18 0.00 0.00 4.30
3489 4016 3.839293 ACGAAGTGACAAGCTAGACATC 58.161 45.455 0.00 0.00 42.51 3.06
3537 4064 7.673810 AAGTCGTTTGTAAAATCCGAAAAAG 57.326 32.000 0.00 0.00 0.00 2.27
3538 4065 6.788243 AGTCGTTTGTAAAATCCGAAAAAGT 58.212 32.000 0.00 0.00 0.00 2.66
3539 4066 6.689669 AGTCGTTTGTAAAATCCGAAAAAGTG 59.310 34.615 0.00 0.00 0.00 3.16
3550 4093 2.482839 CCGAAAAAGTGCACCACCAAAT 60.483 45.455 14.63 0.00 34.49 2.32
3652 4195 8.856490 TTTTGAATTTACTGTTCTTCAAGAGC 57.144 30.769 0.00 0.00 38.45 4.09
3653 4196 6.228273 TGAATTTACTGTTCTTCAAGAGCG 57.772 37.500 0.00 0.00 0.00 5.03
3656 4199 4.537135 TTACTGTTCTTCAAGAGCGGAT 57.463 40.909 16.45 4.19 35.66 4.18
3662 4205 2.451490 TCTTCAAGAGCGGATGAGTCT 58.549 47.619 0.00 0.00 0.00 3.24
3663 4206 3.621558 TCTTCAAGAGCGGATGAGTCTA 58.378 45.455 0.00 0.00 0.00 2.59
3674 4217 2.036992 GGATGAGTCTAGGCTCACATGG 59.963 54.545 28.65 0.00 46.72 3.66
3678 4221 1.842562 AGTCTAGGCTCACATGGCAAT 59.157 47.619 0.00 0.00 34.73 3.56
3693 4236 4.752661 TGGCAATTACCGTGTTAAGAAC 57.247 40.909 0.00 0.00 0.00 3.01
3694 4237 4.391155 TGGCAATTACCGTGTTAAGAACT 58.609 39.130 0.00 0.00 0.00 3.01
3695 4238 5.549347 TGGCAATTACCGTGTTAAGAACTA 58.451 37.500 0.00 0.00 0.00 2.24
3696 4239 5.409214 TGGCAATTACCGTGTTAAGAACTAC 59.591 40.000 0.00 0.00 0.00 2.73
3697 4240 5.409214 GGCAATTACCGTGTTAAGAACTACA 59.591 40.000 0.00 0.00 0.00 2.74
3698 4241 6.301861 GCAATTACCGTGTTAAGAACTACAC 58.698 40.000 0.00 0.00 40.89 2.90
3699 4242 6.073657 GCAATTACCGTGTTAAGAACTACACA 60.074 38.462 0.00 0.00 43.69 3.72
3700 4243 7.518689 GCAATTACCGTGTTAAGAACTACACAA 60.519 37.037 0.00 0.00 43.69 3.33
3701 4244 8.336806 CAATTACCGTGTTAAGAACTACACAAA 58.663 33.333 0.00 0.00 43.69 2.83
3702 4245 8.611654 ATTACCGTGTTAAGAACTACACAAAT 57.388 30.769 0.00 0.00 43.69 2.32
3703 4246 6.930667 ACCGTGTTAAGAACTACACAAATT 57.069 33.333 0.00 0.00 43.69 1.82
3704 4247 6.951643 ACCGTGTTAAGAACTACACAAATTC 58.048 36.000 0.00 0.00 43.69 2.17
3705 4248 6.068931 CCGTGTTAAGAACTACACAAATTCG 58.931 40.000 0.00 0.00 43.69 3.34
3706 4249 6.074195 CCGTGTTAAGAACTACACAAATTCGA 60.074 38.462 0.00 0.00 43.69 3.71
3707 4250 6.784227 CGTGTTAAGAACTACACAAATTCGAC 59.216 38.462 0.00 0.00 43.69 4.20
3708 4251 7.515528 CGTGTTAAGAACTACACAAATTCGACA 60.516 37.037 0.00 0.00 43.69 4.35
3709 4252 7.581600 GTGTTAAGAACTACACAAATTCGACAC 59.418 37.037 0.00 0.00 43.15 3.67
3710 4253 7.278203 TGTTAAGAACTACACAAATTCGACACA 59.722 33.333 0.00 0.00 0.00 3.72
3711 4254 6.671614 AAGAACTACACAAATTCGACACAA 57.328 33.333 0.00 0.00 0.00 3.33
3712 4255 6.044512 AGAACTACACAAATTCGACACAAC 57.955 37.500 0.00 0.00 0.00 3.32
3713 4256 4.806342 ACTACACAAATTCGACACAACC 57.194 40.909 0.00 0.00 0.00 3.77
3714 4257 4.193090 ACTACACAAATTCGACACAACCA 58.807 39.130 0.00 0.00 0.00 3.67
3715 4258 4.636648 ACTACACAAATTCGACACAACCAA 59.363 37.500 0.00 0.00 0.00 3.67
3716 4259 3.765026 ACACAAATTCGACACAACCAAC 58.235 40.909 0.00 0.00 0.00 3.77
3717 4260 2.781101 CACAAATTCGACACAACCAACG 59.219 45.455 0.00 0.00 0.00 4.10
3718 4261 1.778591 CAAATTCGACACAACCAACGC 59.221 47.619 0.00 0.00 0.00 4.84
3719 4262 0.309612 AATTCGACACAACCAACGCC 59.690 50.000 0.00 0.00 0.00 5.68
3720 4263 1.512156 ATTCGACACAACCAACGCCC 61.512 55.000 0.00 0.00 0.00 6.13
3721 4264 2.590575 CGACACAACCAACGCCCT 60.591 61.111 0.00 0.00 0.00 5.19
3722 4265 2.184167 CGACACAACCAACGCCCTT 61.184 57.895 0.00 0.00 0.00 3.95
3723 4266 1.358759 GACACAACCAACGCCCTTG 59.641 57.895 0.00 0.00 0.00 3.61
3724 4267 1.077357 ACACAACCAACGCCCTTGA 60.077 52.632 0.00 0.00 30.42 3.02
3725 4268 1.358759 CACAACCAACGCCCTTGAC 59.641 57.895 0.00 0.00 30.42 3.18
3726 4269 1.101049 CACAACCAACGCCCTTGACT 61.101 55.000 0.00 0.00 30.42 3.41
3727 4270 0.470766 ACAACCAACGCCCTTGACTA 59.529 50.000 0.00 0.00 30.42 2.59
3728 4271 1.134037 ACAACCAACGCCCTTGACTAA 60.134 47.619 0.00 0.00 30.42 2.24
3729 4272 1.535462 CAACCAACGCCCTTGACTAAG 59.465 52.381 0.00 0.00 30.42 2.18
3730 4273 1.053424 ACCAACGCCCTTGACTAAGA 58.947 50.000 0.00 0.00 35.92 2.10
3731 4274 1.628846 ACCAACGCCCTTGACTAAGAT 59.371 47.619 0.00 0.00 35.92 2.40
3732 4275 2.835764 ACCAACGCCCTTGACTAAGATA 59.164 45.455 0.00 0.00 35.92 1.98
3733 4276 3.118738 ACCAACGCCCTTGACTAAGATAG 60.119 47.826 0.00 0.00 35.92 2.08
3734 4277 3.132289 CCAACGCCCTTGACTAAGATAGA 59.868 47.826 0.00 0.00 35.92 1.98
3735 4278 4.382685 CCAACGCCCTTGACTAAGATAGAA 60.383 45.833 0.00 0.00 35.92 2.10
3736 4279 5.360591 CAACGCCCTTGACTAAGATAGAAT 58.639 41.667 0.00 0.00 35.92 2.40
3737 4280 4.950050 ACGCCCTTGACTAAGATAGAATG 58.050 43.478 0.00 0.00 35.92 2.67
3738 4281 4.649674 ACGCCCTTGACTAAGATAGAATGA 59.350 41.667 0.00 0.00 35.92 2.57
3739 4282 5.221342 ACGCCCTTGACTAAGATAGAATGAG 60.221 44.000 0.00 0.00 35.92 2.90
3740 4283 5.546526 GCCCTTGACTAAGATAGAATGAGG 58.453 45.833 0.00 0.00 35.92 3.86
3741 4284 5.546526 CCCTTGACTAAGATAGAATGAGGC 58.453 45.833 0.00 0.00 35.92 4.70
3742 4285 5.226396 CCTTGACTAAGATAGAATGAGGCG 58.774 45.833 0.00 0.00 35.92 5.52
3743 4286 5.010112 CCTTGACTAAGATAGAATGAGGCGA 59.990 44.000 0.00 0.00 35.92 5.54
3744 4287 6.461648 CCTTGACTAAGATAGAATGAGGCGAA 60.462 42.308 0.00 0.00 35.92 4.70
3745 4288 6.465439 TGACTAAGATAGAATGAGGCGAAA 57.535 37.500 0.00 0.00 0.00 3.46
3746 4289 7.055667 TGACTAAGATAGAATGAGGCGAAAT 57.944 36.000 0.00 0.00 0.00 2.17
3747 4290 8.178313 TGACTAAGATAGAATGAGGCGAAATA 57.822 34.615 0.00 0.00 0.00 1.40
3748 4291 8.082852 TGACTAAGATAGAATGAGGCGAAATAC 58.917 37.037 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 8.400947 GGTGACTTAGTATGTACTCGTAATGAA 58.599 37.037 0.00 0.00 37.73 2.57
43 44 5.994250 AGGGTGACTTAGTATGTACTCGTA 58.006 41.667 0.00 0.00 37.73 3.43
44 45 4.853007 AGGGTGACTTAGTATGTACTCGT 58.147 43.478 0.00 0.00 37.73 4.18
45 46 5.356190 TGAAGGGTGACTTAGTATGTACTCG 59.644 44.000 0.00 0.00 40.21 4.18
46 47 6.770746 TGAAGGGTGACTTAGTATGTACTC 57.229 41.667 0.00 0.00 40.21 2.59
47 48 7.015877 TGTTTGAAGGGTGACTTAGTATGTACT 59.984 37.037 0.00 0.00 40.21 2.73
48 49 7.156673 TGTTTGAAGGGTGACTTAGTATGTAC 58.843 38.462 0.00 0.00 40.21 2.90
104 112 2.212652 GGCCTTTGGTCTTTTTGCAAG 58.787 47.619 0.00 0.00 0.00 4.01
125 133 8.141909 TGGGTTATAGAGTCTGTAATTTGATCG 58.858 37.037 11.94 0.00 0.00 3.69
147 155 7.790027 TGCTTTACAATTTGCATATTATGGGT 58.210 30.769 1.85 0.00 0.00 4.51
193 201 3.334583 ACCAACAAGCTCGACATGTAT 57.665 42.857 0.00 0.00 28.03 2.29
255 295 5.433526 TCGCAAATAGTTAAGGTGCCTATT 58.566 37.500 0.00 0.00 33.86 1.73
261 301 7.752695 AGAGAAATTCGCAAATAGTTAAGGTG 58.247 34.615 0.00 0.00 0.00 4.00
344 385 3.709141 GAGGGATCCTCTCTTTGCTAGTT 59.291 47.826 12.58 0.00 46.41 2.24
345 386 3.304829 GAGGGATCCTCTCTTTGCTAGT 58.695 50.000 12.58 0.00 46.41 2.57
358 399 2.326428 TCGTGAAATAGGGAGGGATCC 58.674 52.381 1.92 1.92 0.00 3.36
359 400 4.625607 AATCGTGAAATAGGGAGGGATC 57.374 45.455 0.00 0.00 0.00 3.36
360 401 5.607171 AGTTAATCGTGAAATAGGGAGGGAT 59.393 40.000 0.00 0.00 0.00 3.85
362 403 5.163343 TGAGTTAATCGTGAAATAGGGAGGG 60.163 44.000 0.00 0.00 0.00 4.30
363 404 5.753921 GTGAGTTAATCGTGAAATAGGGAGG 59.246 44.000 0.00 0.00 0.00 4.30
364 405 5.753921 GGTGAGTTAATCGTGAAATAGGGAG 59.246 44.000 0.00 0.00 0.00 4.30
387 445 1.966451 GCCACCTGAAAGACGTGGG 60.966 63.158 0.00 0.00 43.79 4.61
644 1077 0.468226 ACTGGAGACGTCCTTTGCAA 59.532 50.000 13.01 0.00 44.30 4.08
695 1128 6.573725 GTGTGCAACGAGTTTAAGTTAATGAG 59.426 38.462 0.00 0.00 42.39 2.90
696 1129 6.423862 GTGTGCAACGAGTTTAAGTTAATGA 58.576 36.000 0.00 0.00 42.39 2.57
721 1154 4.332819 CACTTCCCGAGTTATTGGCTTAAG 59.667 45.833 0.00 0.00 36.10 1.85
726 1159 2.396590 TCACTTCCCGAGTTATTGGC 57.603 50.000 0.00 0.00 36.10 4.52
731 1164 4.730949 AAATCGATCACTTCCCGAGTTA 57.269 40.909 0.00 0.00 38.54 2.24
788 1225 5.986004 TTTTTCTCTTCCGAGTCAGTTTC 57.014 39.130 0.00 0.00 38.45 2.78
947 1391 7.552459 ACCTGCTTTATAAACAAAACAGTGTT 58.448 30.769 1.64 1.64 43.58 3.32
951 1395 8.816640 ATTGACCTGCTTTATAAACAAAACAG 57.183 30.769 0.00 0.00 0.00 3.16
1081 1528 5.864418 AGGTCGGCAAGTCATATTACTTA 57.136 39.130 2.00 0.00 37.61 2.24
1220 1669 1.333636 GCTGGAGAAGGCTGAGGCTA 61.334 60.000 9.60 0.00 37.50 3.93
1240 1689 4.710375 TCGCCTAATTAAGTTCTCTCCTGT 59.290 41.667 0.00 0.00 0.00 4.00
1242 1691 4.342665 CCTCGCCTAATTAAGTTCTCTCCT 59.657 45.833 0.00 0.00 0.00 3.69
1247 1696 2.429610 TCGCCTCGCCTAATTAAGTTCT 59.570 45.455 0.00 0.00 0.00 3.01
1248 1697 2.817901 TCGCCTCGCCTAATTAAGTTC 58.182 47.619 0.00 0.00 0.00 3.01
1249 1698 2.934553 GTTCGCCTCGCCTAATTAAGTT 59.065 45.455 0.00 0.00 0.00 2.66
1288 1737 8.924511 ACTTCAAAATCAGGAATCAGAGTAAA 57.075 30.769 0.00 0.00 0.00 2.01
1471 1922 1.929494 AGAGGCCACATTATTCCCCAA 59.071 47.619 5.01 0.00 0.00 4.12
1520 1971 2.295885 AGTATCAGCAAGATTGGCAGC 58.704 47.619 0.00 0.00 38.19 5.25
1526 1977 6.269315 CGTGAAGACTAGTATCAGCAAGATT 58.731 40.000 10.32 0.00 38.19 2.40
1789 2246 5.294799 GTCGCTCCTCATCGTATGATATAGT 59.705 44.000 0.00 0.00 38.85 2.12
1905 2362 4.036518 ACTTCAGCTGAGGGAATATCTGT 58.963 43.478 27.37 2.57 0.00 3.41
2043 2500 2.244436 CTGTCCATGCACCGAAAGCG 62.244 60.000 0.00 0.00 33.85 4.68
2520 2977 1.623311 ACTGTCCCGATGAACATGTCA 59.377 47.619 0.00 0.00 41.67 3.58
2577 3034 0.386731 CCGGTGCAAATGTTTCCGAC 60.387 55.000 10.89 0.00 43.22 4.79
2679 3136 6.466812 TCTTGACAGAAACTTCATGCAGATA 58.533 36.000 0.00 0.00 0.00 1.98
2808 3265 2.107378 TGTAAATTCCACTGTGGCAGGA 59.893 45.455 22.02 8.06 37.47 3.86
2809 3266 2.513753 TGTAAATTCCACTGTGGCAGG 58.486 47.619 22.02 0.00 37.47 4.85
2810 3267 4.789012 AATGTAAATTCCACTGTGGCAG 57.211 40.909 22.02 0.00 37.47 4.85
2811 3268 4.343526 ACAAATGTAAATTCCACTGTGGCA 59.656 37.500 22.02 12.25 37.47 4.92
2812 3269 4.881920 ACAAATGTAAATTCCACTGTGGC 58.118 39.130 22.02 7.40 37.47 5.01
2813 3270 5.243730 AGGACAAATGTAAATTCCACTGTGG 59.756 40.000 20.86 20.86 39.43 4.17
2814 3271 6.151691 CAGGACAAATGTAAATTCCACTGTG 58.848 40.000 0.00 0.00 0.00 3.66
2815 3272 5.833131 ACAGGACAAATGTAAATTCCACTGT 59.167 36.000 0.00 0.00 0.00 3.55
2816 3273 6.331369 ACAGGACAAATGTAAATTCCACTG 57.669 37.500 0.00 0.00 0.00 3.66
2817 3274 6.976934 AACAGGACAAATGTAAATTCCACT 57.023 33.333 0.00 0.00 0.00 4.00
2862 3319 1.820519 TCGACTACACCGGCTTATTGT 59.179 47.619 0.00 0.00 0.00 2.71
2958 3448 5.765182 GCAACTCCTGCCACACTATTTATAT 59.235 40.000 0.00 0.00 46.13 0.86
2960 3450 3.947834 GCAACTCCTGCCACACTATTTAT 59.052 43.478 0.00 0.00 46.13 1.40
2993 3483 9.132521 GCATTGCAAGCGAATTTATAGATAAAT 57.867 29.630 4.94 2.29 42.91 1.40
2994 3484 8.352201 AGCATTGCAAGCGAATTTATAGATAAA 58.648 29.630 11.91 0.00 35.55 1.40
2996 3486 7.300320 CAGCATTGCAAGCGAATTTATAGATA 58.700 34.615 11.91 0.00 37.01 1.98
2997 3487 6.147581 CAGCATTGCAAGCGAATTTATAGAT 58.852 36.000 11.91 0.00 37.01 1.98
2998 3488 5.513376 CAGCATTGCAAGCGAATTTATAGA 58.487 37.500 11.91 0.00 37.01 1.98
2999 3489 5.801176 CAGCATTGCAAGCGAATTTATAG 57.199 39.130 11.91 0.00 37.01 1.31
3026 3521 5.069914 TGTTAGCCTGACACTTCTGTTCTTA 59.930 40.000 0.00 0.00 0.00 2.10
3037 3533 3.662247 ACTACAGTGTTAGCCTGACAC 57.338 47.619 11.52 11.52 45.92 3.67
3039 3535 4.884247 AGAAACTACAGTGTTAGCCTGAC 58.116 43.478 0.00 0.00 34.04 3.51
3040 3536 6.659745 TTAGAAACTACAGTGTTAGCCTGA 57.340 37.500 0.00 0.00 34.04 3.86
3049 3545 8.322906 TGGTGATGAATTTAGAAACTACAGTG 57.677 34.615 0.00 0.00 0.00 3.66
3050 3546 8.918202 TTGGTGATGAATTTAGAAACTACAGT 57.082 30.769 0.00 0.00 0.00 3.55
3090 3586 8.487970 CGAGTATGTTTAATACTACTGGCAATG 58.512 37.037 0.00 0.00 35.20 2.82
3167 3668 3.881688 AGGTACGCAACGTCTGAGTATAT 59.118 43.478 13.84 6.65 41.58 0.86
3180 3681 0.320374 CCTGTTCCTGAGGTACGCAA 59.680 55.000 3.76 0.00 37.93 4.85
3287 3796 4.423209 GGGCTCCAGGAGAGGGGT 62.423 72.222 21.89 0.00 43.46 4.95
3371 3880 0.462047 GGAATACAGGAGTGGTGCGG 60.462 60.000 0.00 0.00 0.00 5.69
3375 3884 1.623542 GCCCGGAATACAGGAGTGGT 61.624 60.000 0.73 0.00 33.26 4.16
3378 3887 0.325296 TCTGCCCGGAATACAGGAGT 60.325 55.000 0.73 0.00 33.26 3.85
3476 4003 2.028130 CTCCTCGGATGTCTAGCTTGT 58.972 52.381 0.00 0.00 0.00 3.16
3514 4041 6.689669 CACTTTTTCGGATTTTACAAACGACT 59.310 34.615 0.00 0.00 32.85 4.18
3518 4045 6.407623 GTGCACTTTTTCGGATTTTACAAAC 58.592 36.000 10.32 0.00 0.00 2.93
3524 4051 3.453424 GTGGTGCACTTTTTCGGATTTT 58.547 40.909 17.98 0.00 0.00 1.82
3528 4055 0.394488 TGGTGGTGCACTTTTTCGGA 60.394 50.000 17.98 0.00 34.40 4.55
3529 4056 0.457851 TTGGTGGTGCACTTTTTCGG 59.542 50.000 17.98 0.00 34.40 4.30
3530 4057 2.285827 TTTGGTGGTGCACTTTTTCG 57.714 45.000 17.98 0.00 34.40 3.46
3531 4058 3.530535 ACATTTGGTGGTGCACTTTTTC 58.469 40.909 17.98 0.00 34.40 2.29
3532 4059 3.625649 ACATTTGGTGGTGCACTTTTT 57.374 38.095 17.98 0.00 34.40 1.94
3550 4093 1.082169 GCGCAAGATTCGTGCAACA 60.082 52.632 21.59 0.00 42.33 3.33
3642 4185 2.451490 AGACTCATCCGCTCTTGAAGA 58.549 47.619 0.00 0.00 0.00 2.87
3649 4192 0.596082 GAGCCTAGACTCATCCGCTC 59.404 60.000 0.51 0.00 36.65 5.03
3656 4199 0.826715 GCCATGTGAGCCTAGACTCA 59.173 55.000 4.41 4.41 44.32 3.41
3662 4205 2.744823 CGGTAATTGCCATGTGAGCCTA 60.745 50.000 13.39 0.00 0.00 3.93
3663 4206 1.767759 GGTAATTGCCATGTGAGCCT 58.232 50.000 7.82 0.00 0.00 4.58
3674 4217 6.301861 GTGTAGTTCTTAACACGGTAATTGC 58.698 40.000 0.00 0.00 36.92 3.56
3693 4236 4.804608 TGGTTGTGTCGAATTTGTGTAG 57.195 40.909 0.00 0.00 0.00 2.74
3694 4237 4.494362 CGTTGGTTGTGTCGAATTTGTGTA 60.494 41.667 0.00 0.00 0.00 2.90
3695 4238 3.729462 CGTTGGTTGTGTCGAATTTGTGT 60.729 43.478 0.00 0.00 0.00 3.72
3696 4239 2.781101 CGTTGGTTGTGTCGAATTTGTG 59.219 45.455 0.00 0.00 0.00 3.33
3697 4240 2.793237 GCGTTGGTTGTGTCGAATTTGT 60.793 45.455 0.00 0.00 0.00 2.83
3698 4241 1.778591 GCGTTGGTTGTGTCGAATTTG 59.221 47.619 0.00 0.00 0.00 2.32
3699 4242 1.268845 GGCGTTGGTTGTGTCGAATTT 60.269 47.619 0.00 0.00 0.00 1.82
3700 4243 0.309612 GGCGTTGGTTGTGTCGAATT 59.690 50.000 0.00 0.00 0.00 2.17
3701 4244 1.512156 GGGCGTTGGTTGTGTCGAAT 61.512 55.000 0.00 0.00 0.00 3.34
3702 4245 2.181521 GGGCGTTGGTTGTGTCGAA 61.182 57.895 0.00 0.00 0.00 3.71
3703 4246 2.589442 GGGCGTTGGTTGTGTCGA 60.589 61.111 0.00 0.00 0.00 4.20
3704 4247 2.184167 AAGGGCGTTGGTTGTGTCG 61.184 57.895 0.00 0.00 0.00 4.35
3705 4248 1.098712 TCAAGGGCGTTGGTTGTGTC 61.099 55.000 18.76 0.00 36.71 3.67
3706 4249 1.077357 TCAAGGGCGTTGGTTGTGT 60.077 52.632 18.76 0.00 36.71 3.72
3707 4250 1.101049 AGTCAAGGGCGTTGGTTGTG 61.101 55.000 18.76 0.00 36.71 3.33
3708 4251 0.470766 TAGTCAAGGGCGTTGGTTGT 59.529 50.000 18.76 5.11 36.71 3.32
3709 4252 1.535462 CTTAGTCAAGGGCGTTGGTTG 59.465 52.381 18.76 0.00 36.71 3.77
3710 4253 1.418637 TCTTAGTCAAGGGCGTTGGTT 59.581 47.619 18.76 10.36 36.71 3.67
3711 4254 1.053424 TCTTAGTCAAGGGCGTTGGT 58.947 50.000 18.76 9.87 36.71 3.67
3712 4255 2.403252 ATCTTAGTCAAGGGCGTTGG 57.597 50.000 18.76 3.75 36.71 3.77
3713 4256 4.386867 TCTATCTTAGTCAAGGGCGTTG 57.613 45.455 13.49 13.49 37.52 4.10
3714 4257 5.128827 TCATTCTATCTTAGTCAAGGGCGTT 59.871 40.000 0.00 0.00 32.22 4.84
3715 4258 4.649674 TCATTCTATCTTAGTCAAGGGCGT 59.350 41.667 0.00 0.00 32.22 5.68
3716 4259 5.201713 TCATTCTATCTTAGTCAAGGGCG 57.798 43.478 0.00 0.00 32.22 6.13
3717 4260 5.546526 CCTCATTCTATCTTAGTCAAGGGC 58.453 45.833 0.00 0.00 32.22 5.19
3718 4261 5.546526 GCCTCATTCTATCTTAGTCAAGGG 58.453 45.833 0.00 0.00 32.22 3.95
3719 4262 5.010112 TCGCCTCATTCTATCTTAGTCAAGG 59.990 44.000 0.00 0.00 32.22 3.61
3720 4263 6.078202 TCGCCTCATTCTATCTTAGTCAAG 57.922 41.667 0.00 0.00 0.00 3.02
3721 4264 6.465439 TTCGCCTCATTCTATCTTAGTCAA 57.535 37.500 0.00 0.00 0.00 3.18
3722 4265 6.465439 TTTCGCCTCATTCTATCTTAGTCA 57.535 37.500 0.00 0.00 0.00 3.41
3723 4266 8.455598 GTATTTCGCCTCATTCTATCTTAGTC 57.544 38.462 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.