Multiple sequence alignment - TraesCS3D01G125500

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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 TraesCS3D01G125500 chr3D 100.000 5719 0 0 1 5719 83924654 83918936 0.000000e+00 10562.0
1 TraesCS3D01G125500 chr3D 96.108 1182 29 5 404 1575 83943710 83942536 0.000000e+00 1912.0
2 TraesCS3D01G125500 chr3D 94.891 411 18 3 1 408 83944211 83943801 1.740000e-179 640.0
3 TraesCS3D01G125500 chr3D 81.950 482 68 16 1 473 83973542 83973071 1.930000e-104 390.0
4 TraesCS3D01G125500 chr3D 91.534 189 16 0 4054 4242 83940248 83940060 1.580000e-65 261.0
5 TraesCS3D01G125500 chr3D 89.506 162 13 3 2427 2586 83940802 83940643 9.720000e-48 202.0
6 TraesCS3D01G125500 chr3D 88.976 127 9 5 2040 2166 83942507 83942386 9.920000e-33 152.0
7 TraesCS3D01G125500 chr3D 91.525 59 5 0 2236 2294 83942348 83942290 1.320000e-11 82.4
8 TraesCS3D01G125500 chr3D 96.970 33 0 1 3609 3640 23203860 23203892 3.000000e-03 54.7
9 TraesCS3D01G125500 chr3A 93.072 2324 132 16 3408 5714 100016301 100013990 0.000000e+00 3373.0
10 TraesCS3D01G125500 chr3A 92.628 1370 58 18 614 1953 100019410 100018054 0.000000e+00 1930.0
11 TraesCS3D01G125500 chr3A 90.397 958 62 18 2552 3491 100017247 100016302 0.000000e+00 1232.0
12 TraesCS3D01G125500 chr3A 89.427 454 16 11 2114 2555 100017863 100017430 1.400000e-150 544.0
13 TraesCS3D01G125500 chr3A 82.828 198 27 6 4191 4387 40842623 40842814 2.740000e-38 171.0
14 TraesCS3D01G125500 chr3B 90.930 1742 91 22 4002 5719 132625632 132627330 0.000000e+00 2279.0
15 TraesCS3D01G125500 chr3B 92.708 1536 75 15 406 1913 132621644 132623170 0.000000e+00 2182.0
16 TraesCS3D01G125500 chr3B 94.898 784 30 2 783 1566 131495720 131496493 0.000000e+00 1218.0
17 TraesCS3D01G125500 chr3B 91.842 760 38 11 4002 4755 131514851 131515592 0.000000e+00 1038.0
18 TraesCS3D01G125500 chr3B 89.439 767 51 13 4974 5719 131515789 131516546 0.000000e+00 941.0
19 TraesCS3D01G125500 chr3B 82.825 885 60 36 2114 2957 132623330 132624163 0.000000e+00 708.0
20 TraesCS3D01G125500 chr3B 92.010 413 27 6 1 407 132621149 132621561 4.970000e-160 575.0
21 TraesCS3D01G125500 chr3B 87.742 465 28 10 2114 2551 131500595 131501057 3.060000e-142 516.0
22 TraesCS3D01G125500 chr3B 81.070 486 61 24 1 473 132616964 132617431 5.450000e-95 359.0
23 TraesCS3D01G125500 chr3B 84.290 331 14 19 1561 1872 131497728 131498039 7.250000e-74 289.0
24 TraesCS3D01G125500 chr3B 83.258 221 21 12 2552 2770 131501838 131502044 7.560000e-44 189.0
25 TraesCS3D01G125500 chr3B 90.756 119 10 1 3081 3199 131513463 131513580 2.130000e-34 158.0
26 TraesCS3D01G125500 chr3B 90.909 99 7 2 1854 1950 131498057 131498155 1.290000e-26 132.0
27 TraesCS3D01G125500 chr3B 94.737 76 2 2 2004 2079 132623178 132623251 3.620000e-22 117.0
28 TraesCS3D01G125500 chr1D 83.436 326 44 7 1210 1527 115366801 115367124 1.560000e-75 294.0
29 TraesCS3D01G125500 chr1D 83.838 198 24 7 4191 4387 452252804 452252614 1.270000e-41 182.0
30 TraesCS3D01G125500 chr1B 83.436 326 44 7 1210 1527 176784189 176784512 1.560000e-75 294.0
31 TraesCS3D01G125500 chr7D 86.700 203 23 2 4143 4344 101575277 101575476 7.460000e-54 222.0
32 TraesCS3D01G125500 chr7D 85.859 198 21 6 4191 4387 83321770 83321961 2.700000e-48 204.0
33 TraesCS3D01G125500 chr5D 86.364 198 20 6 4191 4387 9073980 9074171 5.810000e-50 209.0
34 TraesCS3D01G125500 chr5D 75.862 174 29 8 3540 3710 3069617 3069780 6.140000e-10 76.8
35 TraesCS3D01G125500 chr5D 81.633 98 12 2 3541 3638 499065666 499065575 6.140000e-10 76.8
36 TraesCS3D01G125500 chr2D 82.828 198 27 6 4191 4387 575974130 575973939 2.740000e-38 171.0
37 TraesCS3D01G125500 chr2D 76.506 166 28 6 3541 3704 644387700 644387856 4.750000e-11 80.5
38 TraesCS3D01G125500 chr6A 76.667 180 30 9 3564 3741 538037222 538037391 7.890000e-14 89.8
39 TraesCS3D01G125500 chr1A 82.692 104 14 4 3608 3710 520777017 520776917 7.890000e-14 89.8
40 TraesCS3D01G125500 chr7B 85.294 68 8 2 4140 4206 126162161 126162095 1.030000e-07 69.4
41 TraesCS3D01G125500 chr7B 86.441 59 6 2 4140 4197 126192816 126192873 4.780000e-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 TraesCS3D01G125500 chr3D 83918936 83924654 5718 True 10562.000000 10562 100.000000 1 5719 1 chr3D.!!$R1 5718
1 TraesCS3D01G125500 chr3D 83940060 83944211 4151 True 541.566667 1912 92.090000 1 4242 6 chr3D.!!$R3 4241
2 TraesCS3D01G125500 chr3A 100013990 100019410 5420 True 1769.750000 3373 91.381000 614 5714 4 chr3A.!!$R1 5100
3 TraesCS3D01G125500 chr3B 132616964 132627330 10366 False 1036.666667 2279 89.046667 1 5719 6 chr3B.!!$F3 5718
4 TraesCS3D01G125500 chr3B 131513463 131516546 3083 False 712.333333 1038 90.679000 3081 5719 3 chr3B.!!$F2 2638
5 TraesCS3D01G125500 chr3B 131495720 131502044 6324 False 468.800000 1218 88.219400 783 2770 5 chr3B.!!$F1 1987

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
291 4484 1.300963 GGGTGCAGATGAGCCTCAA 59.699 57.895 0.00 0.00 0.00 3.02 F
573 4864 1.731613 CGTGTACGTGCATCGGTGT 60.732 57.895 10.21 0.00 44.69 4.16 F
1878 7471 1.082104 CGTGAAAACTTGCGAGGCC 60.082 57.895 5.79 0.00 0.00 5.19 F
2587 12764 0.861450 GCCGCATGCGTATCACAAAC 60.861 55.000 35.55 11.53 37.81 2.93 F
3786 14698 0.038526 GTGTGTCTACGGGTGGAGTG 60.039 60.000 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 7440 1.221466 TTTCACGCAGTCTTCTGGCG 61.221 55.0 3.51 3.51 41.61 5.69 R
2309 11225 0.524862 GCACCGGACTAGAGACGAAA 59.475 55.0 9.46 0.00 0.00 3.46 R
2727 13059 0.030101 GCGAATCCGTCTCTCTCAGG 59.970 60.0 0.00 0.00 38.24 3.86 R
4163 15272 0.035630 AGAAGAGCACCTGCATCACC 60.036 55.0 0.00 0.00 45.16 4.02 R
5263 16495 0.321919 AGCAGGCGATCAAGAAAGCA 60.322 50.0 0.00 0.00 0.00 3.91 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
291 4484 1.300963 GGGTGCAGATGAGCCTCAA 59.699 57.895 0.00 0.00 0.00 3.02
373 4566 2.548480 GGCATACCTCAAGCGGAAATAC 59.452 50.000 0.00 0.00 0.00 1.89
569 4860 2.390288 GTGCGTGTACGTGCATCG 59.610 61.111 10.21 15.56 43.96 3.84
573 4864 1.731613 CGTGTACGTGCATCGGTGT 60.732 57.895 10.21 0.00 44.69 4.16
689 4985 4.769345 TGAACATATGCATACACCCAGA 57.231 40.909 8.99 0.00 0.00 3.86
873 5178 2.970974 GACACGCAGCTCCAAAGGC 61.971 63.158 0.00 0.00 0.00 4.35
940 5252 4.673298 TCCGATGCACGCACCGTT 62.673 61.111 4.87 0.00 38.32 4.44
941 5253 4.444024 CCGATGCACGCACCGTTG 62.444 66.667 4.87 0.00 38.32 4.10
1008 5327 2.438434 CGCCCCACCATGAAGTCC 60.438 66.667 0.00 0.00 0.00 3.85
1116 5435 2.892425 GAGCCATGGGTTCTCGCG 60.892 66.667 19.39 0.00 30.11 5.87
1329 5651 4.504916 CGCCTGCTCCTGGAGACG 62.505 72.222 27.53 18.69 33.10 4.18
1798 7369 2.715749 CCTCAAGGTGACCATGCATA 57.284 50.000 3.63 0.00 0.00 3.14
1817 7410 9.888878 CATGCATACATTTTTATCTTTCTCGAT 57.111 29.630 0.00 0.00 32.87 3.59
1847 7440 5.587289 TGCACTTTGTACTTTTGGTCAATC 58.413 37.500 0.00 0.00 0.00 2.67
1878 7471 1.082104 CGTGAAAACTTGCGAGGCC 60.082 57.895 5.79 0.00 0.00 5.19
1930 7563 3.682529 GCATTTTGCATGGGACAGCGT 62.683 52.381 0.00 0.00 44.26 5.07
1955 7749 4.382040 CCAGAGTGGTAGAAGTACATGGTG 60.382 50.000 0.00 0.00 31.35 4.17
1974 7768 5.577100 TGGTGAACCACTATAGAGTACTGT 58.423 41.667 6.78 0.00 42.01 3.55
2073 7867 2.158449 CGATGTCAAACTGTGAGAAGCC 59.842 50.000 0.00 0.00 36.74 4.35
2094 7888 5.895534 AGCCATAACCAAAGATCATTCATGT 59.104 36.000 0.00 0.00 0.00 3.21
2103 10053 4.729227 AGATCATTCATGTGCATGCAAA 57.271 36.364 24.58 19.43 38.65 3.68
2104 10054 5.079689 AGATCATTCATGTGCATGCAAAA 57.920 34.783 24.58 14.69 38.65 2.44
2105 10055 5.670485 AGATCATTCATGTGCATGCAAAAT 58.330 33.333 24.58 16.45 38.65 1.82
2106 10056 6.811954 AGATCATTCATGTGCATGCAAAATA 58.188 32.000 24.58 9.81 38.65 1.40
2107 10057 6.700081 AGATCATTCATGTGCATGCAAAATAC 59.300 34.615 24.58 10.34 38.65 1.89
2108 10058 5.968254 TCATTCATGTGCATGCAAAATACT 58.032 33.333 24.58 0.00 38.65 2.12
2109 10059 6.037726 TCATTCATGTGCATGCAAAATACTC 58.962 36.000 24.58 8.72 38.65 2.59
2110 10060 4.374843 TCATGTGCATGCAAAATACTCC 57.625 40.909 24.58 7.90 38.65 3.85
2111 10061 3.762823 TCATGTGCATGCAAAATACTCCA 59.237 39.130 24.58 13.94 38.65 3.86
2112 10062 3.574284 TGTGCATGCAAAATACTCCAC 57.426 42.857 24.58 6.29 0.00 4.02
2300 11216 3.194861 GCCTGTTGTCACGCATATCTAA 58.805 45.455 0.00 0.00 0.00 2.10
2301 11217 3.809832 GCCTGTTGTCACGCATATCTAAT 59.190 43.478 0.00 0.00 0.00 1.73
2302 11218 4.273480 GCCTGTTGTCACGCATATCTAATT 59.727 41.667 0.00 0.00 0.00 1.40
2303 11219 5.465390 GCCTGTTGTCACGCATATCTAATTA 59.535 40.000 0.00 0.00 0.00 1.40
2304 11220 6.018262 GCCTGTTGTCACGCATATCTAATTAA 60.018 38.462 0.00 0.00 0.00 1.40
2305 11221 7.307989 GCCTGTTGTCACGCATATCTAATTAAT 60.308 37.037 0.00 0.00 0.00 1.40
2306 11222 8.223769 CCTGTTGTCACGCATATCTAATTAATC 58.776 37.037 0.00 0.00 0.00 1.75
2307 11223 8.083462 TGTTGTCACGCATATCTAATTAATCC 57.917 34.615 0.00 0.00 0.00 3.01
2308 11224 7.172532 TGTTGTCACGCATATCTAATTAATCCC 59.827 37.037 0.00 0.00 0.00 3.85
2309 11225 7.004555 TGTCACGCATATCTAATTAATCCCT 57.995 36.000 0.00 0.00 0.00 4.20
2310 11226 7.450074 TGTCACGCATATCTAATTAATCCCTT 58.550 34.615 0.00 0.00 0.00 3.95
2311 11227 7.936847 TGTCACGCATATCTAATTAATCCCTTT 59.063 33.333 0.00 0.00 0.00 3.11
2312 11228 8.443937 GTCACGCATATCTAATTAATCCCTTTC 58.556 37.037 0.00 0.00 0.00 2.62
2313 11229 7.330946 TCACGCATATCTAATTAATCCCTTTCG 59.669 37.037 0.00 0.00 0.00 3.46
2314 11230 7.117812 CACGCATATCTAATTAATCCCTTTCGT 59.882 37.037 0.00 0.00 0.00 3.85
2315 11231 7.331193 ACGCATATCTAATTAATCCCTTTCGTC 59.669 37.037 0.00 0.00 0.00 4.20
2316 11232 7.545965 CGCATATCTAATTAATCCCTTTCGTCT 59.454 37.037 0.00 0.00 0.00 4.18
2317 11233 8.874816 GCATATCTAATTAATCCCTTTCGTCTC 58.125 37.037 0.00 0.00 0.00 3.36
2373 11291 2.826725 TGTTTGTCCTTTGTTTTCCCGT 59.173 40.909 0.00 0.00 0.00 5.28
2414 11776 5.353938 TCACACTCAACAGTACAACTTACC 58.646 41.667 0.00 0.00 0.00 2.85
2417 11779 5.105064 ACACTCAACAGTACAACTTACCACT 60.105 40.000 0.00 0.00 0.00 4.00
2418 11780 6.097270 ACACTCAACAGTACAACTTACCACTA 59.903 38.462 0.00 0.00 0.00 2.74
2419 11781 6.420008 CACTCAACAGTACAACTTACCACTAC 59.580 42.308 0.00 0.00 0.00 2.73
2586 12763 1.301677 TGCCGCATGCGTATCACAAA 61.302 50.000 35.55 11.10 45.60 2.83
2587 12764 0.861450 GCCGCATGCGTATCACAAAC 60.861 55.000 35.55 11.53 37.81 2.93
2727 13059 1.305219 TTGGTATGCGTTGCTGCTCC 61.305 55.000 0.00 0.00 35.36 4.70
2758 13092 2.095668 ACGGATTCGCGTGCAAAATTAA 60.096 40.909 5.77 0.00 40.63 1.40
2828 13163 3.282021 AGCATGTTCAGTTCAGTGTTGT 58.718 40.909 0.00 0.00 0.00 3.32
2845 13180 7.335673 TCAGTGTTGTCATTTTACAGTTTCTCA 59.664 33.333 0.00 0.00 0.00 3.27
2859 13194 9.760077 TTACAGTTTCTCAGTCTTTTAACTAGG 57.240 33.333 0.00 0.00 0.00 3.02
2860 13195 8.019656 ACAGTTTCTCAGTCTTTTAACTAGGA 57.980 34.615 0.00 0.00 0.00 2.94
2905 13246 5.892348 AGTTGGTGACCCTTCTGAATTTAT 58.108 37.500 0.00 0.00 0.00 1.40
2906 13247 7.027874 AGTTGGTGACCCTTCTGAATTTATA 57.972 36.000 0.00 0.00 0.00 0.98
2907 13248 6.884836 AGTTGGTGACCCTTCTGAATTTATAC 59.115 38.462 0.00 0.00 0.00 1.47
2908 13249 5.424757 TGGTGACCCTTCTGAATTTATACG 58.575 41.667 0.00 0.00 0.00 3.06
2941 13282 9.528489 AATATCAGGTTTATCTCTCTCTACTCC 57.472 37.037 0.00 0.00 0.00 3.85
3068 13447 2.642154 TAAACTCCTGACCCGCAAAA 57.358 45.000 0.00 0.00 0.00 2.44
3218 13600 2.017049 CCATAAGCAAAGTCGGGGAAG 58.983 52.381 0.00 0.00 0.00 3.46
3245 13634 2.171003 ACCATGCAAAAGTTAGGCCTC 58.829 47.619 9.68 0.00 0.00 4.70
3261 14064 2.450476 GCCTCTGGACCATTCACATTT 58.550 47.619 0.00 0.00 0.00 2.32
3307 14110 5.065914 CCCTATATTGTGTCAATGGAGGTG 58.934 45.833 16.13 9.09 0.00 4.00
3308 14111 5.397899 CCCTATATTGTGTCAATGGAGGTGT 60.398 44.000 16.13 0.00 0.00 4.16
3309 14112 6.183361 CCCTATATTGTGTCAATGGAGGTGTA 60.183 42.308 16.13 0.00 0.00 2.90
3310 14113 6.706270 CCTATATTGTGTCAATGGAGGTGTAC 59.294 42.308 5.40 0.00 0.00 2.90
3354 14157 4.609301 TCCAGGGAAATTATCAAAGTGGG 58.391 43.478 0.00 0.00 0.00 4.61
3359 14168 4.780554 GGGAAATTATCAAAGTGGGGGAAA 59.219 41.667 0.00 0.00 0.00 3.13
3360 14169 5.249622 GGGAAATTATCAAAGTGGGGGAAAA 59.750 40.000 0.00 0.00 0.00 2.29
3376 14185 2.689983 GGAAAAGTGGCGGATGATCAAT 59.310 45.455 0.00 0.00 0.00 2.57
3383 14192 1.341209 GGCGGATGATCAATTTTCCCC 59.659 52.381 0.00 2.45 0.00 4.81
3411 14304 7.907214 AAACCGATATATGCTCCTTATTGTC 57.093 36.000 0.00 0.00 0.00 3.18
3532 14428 0.179034 GAATCCCAGCTCTTGCCGAT 60.179 55.000 0.00 0.00 40.80 4.18
3623 14534 2.370445 ACCGGCTCCCTGAAGATGG 61.370 63.158 0.00 0.00 0.00 3.51
3678 14589 1.278238 CGGTGCATTTAGAGTCGTCC 58.722 55.000 0.00 0.00 0.00 4.79
3690 14601 2.203379 TCGTCCGAGGGTGTGTGA 60.203 61.111 0.00 0.00 0.00 3.58
3741 14653 3.130633 CAGTCGATGTTGTCTTTGGTGA 58.869 45.455 0.00 0.00 0.00 4.02
3764 14676 2.686405 TCCGCTTAGATCTAGTTTGCGA 59.314 45.455 27.16 17.40 43.81 5.10
3773 14685 2.592194 TCTAGTTTGCGATCGTGTGTC 58.408 47.619 17.81 0.00 0.00 3.67
3776 14688 2.325761 AGTTTGCGATCGTGTGTCTAC 58.674 47.619 17.81 5.86 0.00 2.59
3782 14694 0.179145 GATCGTGTGTCTACGGGTGG 60.179 60.000 0.00 0.00 43.85 4.61
3783 14695 0.609957 ATCGTGTGTCTACGGGTGGA 60.610 55.000 0.00 0.00 43.85 4.02
3784 14696 1.211969 CGTGTGTCTACGGGTGGAG 59.788 63.158 0.00 0.00 40.22 3.86
3785 14697 1.521450 CGTGTGTCTACGGGTGGAGT 61.521 60.000 0.00 0.00 40.22 3.85
3786 14698 0.038526 GTGTGTCTACGGGTGGAGTG 60.039 60.000 0.00 0.00 0.00 3.51
3788 14700 1.183549 GTGTCTACGGGTGGAGTGAT 58.816 55.000 0.00 0.00 0.00 3.06
3815 14758 5.178061 TGCTATTCTAGTGTGTTGGTCATG 58.822 41.667 0.00 0.00 0.00 3.07
3819 14762 1.806542 CTAGTGTGTTGGTCATGTGCC 59.193 52.381 0.00 0.00 0.00 5.01
3828 14771 0.322456 GGTCATGTGCCACCTTAGCA 60.322 55.000 0.00 0.00 38.08 3.49
3829 14772 1.683011 GGTCATGTGCCACCTTAGCAT 60.683 52.381 0.00 0.00 43.29 3.79
3831 14774 1.281577 TCATGTGCCACCTTAGCATGA 59.718 47.619 0.00 0.00 43.29 3.07
3832 14775 2.092267 TCATGTGCCACCTTAGCATGAT 60.092 45.455 0.00 0.00 43.29 2.45
3833 14776 2.512692 TGTGCCACCTTAGCATGATT 57.487 45.000 0.00 0.00 43.29 2.57
3915 14865 3.003480 CGACTTCCTTCTGTTCATTCCC 58.997 50.000 0.00 0.00 0.00 3.97
3932 14882 2.683968 TCCCGTGCTTATATTCATCGC 58.316 47.619 0.00 0.00 0.00 4.58
3941 14891 5.479027 TGCTTATATTCATCGCTAGGTGGTA 59.521 40.000 0.00 0.00 0.00 3.25
3949 14899 3.589951 TCGCTAGGTGGTATAAGGACT 57.410 47.619 0.00 0.00 0.00 3.85
4070 15178 4.176752 GGCGCCGGGAAAGAGGAT 62.177 66.667 12.58 0.00 0.00 3.24
4112 15221 3.003763 GACCCCCGGAAGCTGTCT 61.004 66.667 0.73 0.00 0.00 3.41
4370 15479 4.459089 GTCGCCAGGCTCCAGGTC 62.459 72.222 10.54 0.00 0.00 3.85
4376 15485 2.203788 AGGCTCCAGGTCCGTTCA 60.204 61.111 0.00 0.00 0.00 3.18
4395 15504 4.286297 TCATCGGACATTTTCCAACTCT 57.714 40.909 0.00 0.00 46.29 3.24
4397 15506 2.778299 TCGGACATTTTCCAACTCTGG 58.222 47.619 0.00 0.00 46.29 3.86
4448 15557 1.200760 ACATGTCTGGGCTGCAGGTA 61.201 55.000 17.12 0.00 0.00 3.08
4535 15644 3.597728 GGCGTTGGCGGGTTCAAA 61.598 61.111 0.00 0.00 41.24 2.69
4755 15880 1.226295 GCGGCGCTCAATGTTTACC 60.226 57.895 26.86 0.00 0.00 2.85
4970 16165 5.067805 AGAGTTCTTCAAACCTTTGCGAAAT 59.932 36.000 0.00 0.00 38.05 2.17
4971 16166 5.281727 AGTTCTTCAAACCTTTGCGAAATC 58.718 37.500 0.00 0.00 38.05 2.17
4972 16167 4.909696 TCTTCAAACCTTTGCGAAATCA 57.090 36.364 0.00 0.00 38.05 2.57
4973 16168 4.858935 TCTTCAAACCTTTGCGAAATCAG 58.141 39.130 0.00 0.00 38.05 2.90
4974 16169 4.578516 TCTTCAAACCTTTGCGAAATCAGA 59.421 37.500 0.00 0.00 38.05 3.27
4975 16170 4.223320 TCAAACCTTTGCGAAATCAGAC 57.777 40.909 0.00 0.00 38.05 3.51
4982 16177 4.461405 CTTTGCGAAATCAGACAGAGTTG 58.539 43.478 0.00 0.00 34.14 3.16
4987 16182 4.024893 GCGAAATCAGACAGAGTTGTTCAA 60.025 41.667 0.00 0.00 37.76 2.69
4997 16192 5.133221 ACAGAGTTGTTCAAACTATGCCTT 58.867 37.500 11.61 0.00 41.67 4.35
5074 16273 5.744666 ACAAATAGTTGTACACACACACC 57.255 39.130 6.80 0.00 46.33 4.16
5120 16341 8.691661 ATCACTAAACTAACCACAAATGTTCT 57.308 30.769 0.00 0.00 0.00 3.01
5141 16365 5.016831 TCTACAGGCAGAACTTCAGATACA 58.983 41.667 0.00 0.00 0.00 2.29
5148 16372 4.629200 GCAGAACTTCAGATACAAGTCTGG 59.371 45.833 4.28 0.00 44.51 3.86
5247 16479 5.957771 AGAATAAACACAGGGCTGAGATA 57.042 39.130 0.00 0.00 0.00 1.98
5263 16495 5.939764 TGAGATAGCCTCATTTGTGTACT 57.060 39.130 0.00 0.00 46.38 2.73
5365 16597 3.310860 ATCGTCGCCACCCACCTTC 62.311 63.158 0.00 0.00 0.00 3.46
5400 16632 0.817013 CAGTCTGAGCCTCTCCTCAC 59.183 60.000 0.00 0.00 36.96 3.51
5452 16684 2.059786 CCGGAAACCCCTACCGCTA 61.060 63.158 0.00 0.00 44.45 4.26
5539 16771 0.106268 TTGGTGTGCCATGGTGAGTT 60.106 50.000 14.67 0.00 45.56 3.01
5542 16774 2.260154 TGTGCCATGGTGAGTTGCG 61.260 57.895 14.67 0.00 0.00 4.85
5550 16782 2.320587 GGTGAGTTGCGGCACTCTG 61.321 63.158 23.33 0.00 43.32 3.35
5560 16792 2.734591 GCACTCTGACCACCGACA 59.265 61.111 0.00 0.00 0.00 4.35
5572 16804 0.377203 CACCGACATCGACGATCTCA 59.623 55.000 7.54 0.00 43.02 3.27
5639 16874 0.179150 GCAGCTCTCGTCTTCGTCAT 60.179 55.000 0.00 0.00 38.33 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 4354 8.502161 AACTCTGTGCAAATTTTCGTAAATAC 57.498 30.769 0.08 0.00 32.85 1.89
291 4484 0.486879 TGGGGAGGACATTTTGGCTT 59.513 50.000 0.00 0.00 0.00 4.35
569 4860 3.768468 TTTTCAGAAACACCGAACACC 57.232 42.857 0.00 0.00 0.00 4.16
689 4985 1.603802 CTTGTTGGACGTGATGTGCTT 59.396 47.619 0.00 0.00 40.08 3.91
940 5252 2.035961 AGCTACTTCAAGTTCACGCTCA 59.964 45.455 0.00 0.00 0.00 4.26
941 5253 2.664085 GAGCTACTTCAAGTTCACGCTC 59.336 50.000 12.22 12.22 36.32 5.03
990 5309 2.351276 GACTTCATGGTGGGGCGT 59.649 61.111 0.00 0.00 0.00 5.68
991 5310 2.438434 GGACTTCATGGTGGGGCG 60.438 66.667 0.00 0.00 0.00 6.13
992 5311 1.077429 GAGGACTTCATGGTGGGGC 60.077 63.158 0.00 0.00 0.00 5.80
993 5312 1.221840 CGAGGACTTCATGGTGGGG 59.778 63.158 0.00 0.00 0.00 4.96
994 5313 0.108138 GACGAGGACTTCATGGTGGG 60.108 60.000 0.00 0.00 0.00 4.61
997 5316 1.821753 CTGAGACGAGGACTTCATGGT 59.178 52.381 0.00 0.00 0.00 3.55
1008 5327 1.153862 GCTGTGGCTCTGAGACGAG 60.154 63.158 9.28 6.92 35.22 4.18
1798 7369 8.425577 ACATCGATCGAGAAAGATAAAAATGT 57.574 30.769 23.84 14.22 0.00 2.71
1817 7410 5.270083 CAAAAGTACAAAGTGCAACATCGA 58.730 37.500 0.00 0.00 41.43 3.59
1847 7440 1.221466 TTTCACGCAGTCTTCTGGCG 61.221 55.000 3.51 3.51 41.61 5.69
1878 7471 3.059461 ACGCAAAAACACATGTACTACGG 60.059 43.478 0.00 0.00 0.00 4.02
1936 7569 4.020485 GGTTCACCATGTACTTCTACCACT 60.020 45.833 0.00 0.00 35.64 4.00
1964 7758 7.445707 CAGCATGGAGATTACTACAGTACTCTA 59.554 40.741 8.71 3.37 40.62 2.43
1965 7759 6.264292 CAGCATGGAGATTACTACAGTACTCT 59.736 42.308 8.52 8.52 40.62 3.24
1966 7760 6.442952 CAGCATGGAGATTACTACAGTACTC 58.557 44.000 0.00 0.00 40.62 2.59
2073 7867 6.566141 TGCACATGAATGATCTTTGGTTATG 58.434 36.000 0.00 1.97 0.00 1.90
2094 7888 2.230992 GTGGTGGAGTATTTTGCATGCA 59.769 45.455 18.46 18.46 0.00 3.96
2103 10053 5.067283 GTGTTTTCAACTGTGGTGGAGTATT 59.933 40.000 0.00 0.00 0.00 1.89
2104 10054 4.578928 GTGTTTTCAACTGTGGTGGAGTAT 59.421 41.667 0.00 0.00 0.00 2.12
2105 10055 3.942748 GTGTTTTCAACTGTGGTGGAGTA 59.057 43.478 0.00 0.00 0.00 2.59
2106 10056 2.752903 GTGTTTTCAACTGTGGTGGAGT 59.247 45.455 0.00 0.00 0.00 3.85
2107 10057 3.016736 AGTGTTTTCAACTGTGGTGGAG 58.983 45.455 0.00 0.00 0.00 3.86
2108 10058 2.752354 CAGTGTTTTCAACTGTGGTGGA 59.248 45.455 0.00 0.00 0.00 4.02
2109 10059 2.491693 ACAGTGTTTTCAACTGTGGTGG 59.508 45.455 8.33 0.00 39.11 4.61
2110 10060 3.848272 ACAGTGTTTTCAACTGTGGTG 57.152 42.857 8.33 0.00 39.11 4.17
2111 10061 4.864704 AAACAGTGTTTTCAACTGTGGT 57.135 36.364 15.58 0.00 39.83 4.16
2112 10062 7.644986 TTTAAAACAGTGTTTTCAACTGTGG 57.355 32.000 31.73 0.00 39.83 4.17
2135 10085 2.868583 CAGATGAATGCGGACGAGAATT 59.131 45.455 0.00 0.00 0.00 2.17
2300 11216 5.009811 CGGACTAGAGACGAAAGGGATTAAT 59.990 44.000 0.00 0.00 0.00 1.40
2301 11217 4.337555 CGGACTAGAGACGAAAGGGATTAA 59.662 45.833 0.00 0.00 0.00 1.40
2302 11218 3.881688 CGGACTAGAGACGAAAGGGATTA 59.118 47.826 0.00 0.00 0.00 1.75
2303 11219 2.688958 CGGACTAGAGACGAAAGGGATT 59.311 50.000 0.00 0.00 0.00 3.01
2304 11220 2.299521 CGGACTAGAGACGAAAGGGAT 58.700 52.381 0.00 0.00 0.00 3.85
2305 11221 1.681166 CCGGACTAGAGACGAAAGGGA 60.681 57.143 0.00 0.00 0.00 4.20
2306 11222 0.739561 CCGGACTAGAGACGAAAGGG 59.260 60.000 0.00 0.00 0.00 3.95
2307 11223 1.132643 CACCGGACTAGAGACGAAAGG 59.867 57.143 9.46 0.00 0.00 3.11
2308 11224 1.467713 GCACCGGACTAGAGACGAAAG 60.468 57.143 9.46 0.00 0.00 2.62
2309 11225 0.524862 GCACCGGACTAGAGACGAAA 59.475 55.000 9.46 0.00 0.00 3.46
2310 11226 1.310933 GGCACCGGACTAGAGACGAA 61.311 60.000 9.46 0.00 0.00 3.85
2311 11227 1.748122 GGCACCGGACTAGAGACGA 60.748 63.158 9.46 0.00 0.00 4.20
2312 11228 2.772691 GGGCACCGGACTAGAGACG 61.773 68.421 9.46 0.00 40.86 4.18
2313 11229 3.208335 GGGCACCGGACTAGAGAC 58.792 66.667 9.46 0.00 40.86 3.36
2373 11291 2.872245 GTGAGCACTGAAGTTGCTTACA 59.128 45.455 12.76 0.00 42.35 2.41
2400 11744 5.972107 ATCGTAGTGGTAAGTTGTACTGT 57.028 39.130 0.00 0.00 0.00 3.55
2532 11903 6.749923 ACTAAAAGATGAATCTTGTCTGCC 57.250 37.500 6.32 0.00 45.83 4.85
2540 11911 6.664816 TGCCCATGAAACTAAAAGATGAATCT 59.335 34.615 0.00 0.00 39.22 2.40
2586 12763 1.819288 TCGATCCGAAAAGCTCTGAGT 59.181 47.619 6.53 0.00 31.06 3.41
2587 12764 2.568696 TCGATCCGAAAAGCTCTGAG 57.431 50.000 0.00 0.00 31.06 3.35
2712 13044 1.450134 CAGGGAGCAGCAACGCATA 60.450 57.895 0.00 0.00 0.00 3.14
2727 13059 0.030101 GCGAATCCGTCTCTCTCAGG 59.970 60.000 0.00 0.00 38.24 3.86
2822 13157 7.472543 ACTGAGAAACTGTAAAATGACAACAC 58.527 34.615 0.00 0.00 0.00 3.32
2845 13180 6.990798 AGCGTTTACTCCTAGTTAAAAGACT 58.009 36.000 0.00 0.00 0.00 3.24
2859 13194 2.479275 GAGGTGAACCAAGCGTTTACTC 59.521 50.000 1.62 0.00 40.07 2.59
2860 13195 2.104281 AGAGGTGAACCAAGCGTTTACT 59.896 45.455 1.62 0.00 40.07 2.24
2941 13282 1.996292 TTCAGAGAATTGAGGCGTCG 58.004 50.000 1.39 0.00 0.00 5.12
3088 13467 3.838244 TCGGGGATTCTTAGGATTGTG 57.162 47.619 0.00 0.00 0.00 3.33
3203 13584 1.073199 CACCTTCCCCGACTTTGCT 59.927 57.895 0.00 0.00 0.00 3.91
3206 13587 1.071228 GTACACACCTTCCCCGACTTT 59.929 52.381 0.00 0.00 0.00 2.66
3207 13588 0.683412 GTACACACCTTCCCCGACTT 59.317 55.000 0.00 0.00 0.00 3.01
3209 13590 1.294459 GGTACACACCTTCCCCGAC 59.706 63.158 0.00 0.00 42.11 4.79
3210 13591 1.152290 TGGTACACACCTTCCCCGA 60.152 57.895 0.00 0.00 45.98 5.14
3211 13592 3.474000 TGGTACACACCTTCCCCG 58.526 61.111 0.00 0.00 45.98 5.73
3236 13625 1.559682 TGAATGGTCCAGAGGCCTAAC 59.440 52.381 4.42 1.32 0.00 2.34
3261 14064 5.454897 GGCAAACTATTAAACACCCCCAAAA 60.455 40.000 0.00 0.00 0.00 2.44
3265 14068 2.498481 GGGCAAACTATTAAACACCCCC 59.502 50.000 0.00 0.00 0.00 5.40
3266 14069 3.437213 AGGGCAAACTATTAAACACCCC 58.563 45.455 0.00 0.00 36.74 4.95
3354 14157 1.025041 GATCATCCGCCACTTTTCCC 58.975 55.000 0.00 0.00 0.00 3.97
3359 14168 3.131046 GGAAAATTGATCATCCGCCACTT 59.869 43.478 0.00 0.00 0.00 3.16
3360 14169 2.689983 GGAAAATTGATCATCCGCCACT 59.310 45.455 0.00 0.00 0.00 4.00
3376 14185 1.906990 TATCGGTTTTGCGGGGAAAA 58.093 45.000 0.00 0.00 0.00 2.29
3383 14192 3.067106 AGGAGCATATATCGGTTTTGCG 58.933 45.455 0.00 0.00 38.32 4.85
3623 14534 4.141482 TGCCAAGTAGGGAGAACCATATTC 60.141 45.833 0.00 0.00 43.89 1.75
3678 14589 0.880278 CACACCTTCACACACCCTCG 60.880 60.000 0.00 0.00 0.00 4.63
3741 14653 4.051922 CGCAAACTAGATCTAAGCGGATT 58.948 43.478 21.29 4.33 40.00 3.01
3764 14676 0.609957 TCCACCCGTAGACACACGAT 60.610 55.000 0.00 0.00 44.69 3.73
3773 14685 0.902531 AACCATCACTCCACCCGTAG 59.097 55.000 0.00 0.00 0.00 3.51
3776 14688 2.040544 GCAACCATCACTCCACCCG 61.041 63.158 0.00 0.00 0.00 5.28
3782 14694 5.521735 CACACTAGAATAGCAACCATCACTC 59.478 44.000 0.00 0.00 44.39 3.51
3783 14695 5.046304 ACACACTAGAATAGCAACCATCACT 60.046 40.000 0.00 0.00 44.39 3.41
3784 14696 5.178797 ACACACTAGAATAGCAACCATCAC 58.821 41.667 0.00 0.00 44.39 3.06
3785 14697 5.420725 ACACACTAGAATAGCAACCATCA 57.579 39.130 0.00 0.00 44.39 3.07
3786 14698 5.065218 CCAACACACTAGAATAGCAACCATC 59.935 44.000 0.00 0.00 44.39 3.51
3788 14700 4.202419 ACCAACACACTAGAATAGCAACCA 60.202 41.667 0.00 0.00 44.39 3.67
3815 14758 5.067674 TGAATTAATCATGCTAAGGTGGCAC 59.932 40.000 9.70 9.70 42.69 5.01
3819 14762 6.603237 TCGTGAATTAATCATGCTAAGGTG 57.397 37.500 0.00 0.00 43.53 4.00
3898 14845 2.778299 CACGGGAATGAACAGAAGGAA 58.222 47.619 0.00 0.00 0.00 3.36
3899 14846 1.610624 GCACGGGAATGAACAGAAGGA 60.611 52.381 0.00 0.00 0.00 3.36
3915 14865 4.324669 CACCTAGCGATGAATATAAGCACG 59.675 45.833 0.00 0.00 0.00 5.34
3932 14882 5.069251 CCACTCAAGTCCTTATACCACCTAG 59.931 48.000 0.00 0.00 0.00 3.02
3941 14891 7.259088 AGTACAAATCCACTCAAGTCCTTAT 57.741 36.000 0.00 0.00 0.00 1.73
3949 14899 4.927267 ATGGGAGTACAAATCCACTCAA 57.073 40.909 0.00 0.00 42.45 3.02
4163 15272 0.035630 AGAAGAGCACCTGCATCACC 60.036 55.000 0.00 0.00 45.16 4.02
4398 15507 1.674764 CTGGCGGATGAGAGCTGTCT 61.675 60.000 12.66 0.00 34.86 3.41
4523 15632 1.976474 GCTCCATTTGAACCCGCCA 60.976 57.895 0.00 0.00 0.00 5.69
4535 15644 1.078848 GAACCAGAGCGTGCTCCAT 60.079 57.895 17.76 1.49 43.70 3.41
4637 15761 2.437359 CTCGCCCTGCCCTTCTTG 60.437 66.667 0.00 0.00 0.00 3.02
4755 15880 5.246307 AGAGACAAATTAAGAAGAACCCCG 58.754 41.667 0.00 0.00 0.00 5.73
4862 16046 8.454106 GTGCTACTATTTCATGATTTGTGAAGT 58.546 33.333 0.00 0.00 36.96 3.01
4886 16070 1.730121 GCAATCAGATTGGCGTGTGTG 60.730 52.381 22.25 0.00 40.57 3.82
4970 16165 5.466728 GCATAGTTTGAACAACTCTGTCTGA 59.533 40.000 0.00 0.00 33.45 3.27
4971 16166 5.334414 GGCATAGTTTGAACAACTCTGTCTG 60.334 44.000 0.00 0.00 33.45 3.51
4972 16167 4.757149 GGCATAGTTTGAACAACTCTGTCT 59.243 41.667 0.00 0.00 33.45 3.41
4973 16168 4.757149 AGGCATAGTTTGAACAACTCTGTC 59.243 41.667 0.00 0.00 33.45 3.51
4974 16169 4.718961 AGGCATAGTTTGAACAACTCTGT 58.281 39.130 0.00 0.00 37.39 3.41
4975 16170 5.695851 AAGGCATAGTTTGAACAACTCTG 57.304 39.130 0.00 0.00 0.00 3.35
4982 16177 5.932303 TCTGTGAGTAAGGCATAGTTTGAAC 59.068 40.000 0.00 0.00 0.00 3.18
4987 16182 5.865085 TGTTTCTGTGAGTAAGGCATAGTT 58.135 37.500 0.00 0.00 0.00 2.24
5090 16297 4.901868 TGTGGTTAGTTTAGTGATCACCC 58.098 43.478 22.21 13.50 0.00 4.61
5091 16298 6.870971 TTTGTGGTTAGTTTAGTGATCACC 57.129 37.500 22.21 6.97 0.00 4.02
5120 16341 5.246203 ACTTGTATCTGAAGTTCTGCCTGTA 59.754 40.000 4.17 0.00 28.94 2.74
5138 16359 3.834813 AGTGATGAGCTTCCAGACTTGTA 59.165 43.478 0.00 0.00 0.00 2.41
5141 16365 4.530161 AGTTAGTGATGAGCTTCCAGACTT 59.470 41.667 0.00 0.00 0.00 3.01
5148 16372 6.760770 AGCTGAATAAGTTAGTGATGAGCTTC 59.239 38.462 0.00 0.00 28.78 3.86
5198 16426 7.531857 TCCATGTGGTGTGTTATTATTTGTT 57.468 32.000 0.00 0.00 36.34 2.83
5205 16433 6.723298 TTCTTTTCCATGTGGTGTGTTATT 57.277 33.333 0.00 0.00 36.34 1.40
5206 16434 6.916360 ATTCTTTTCCATGTGGTGTGTTAT 57.084 33.333 0.00 0.00 36.34 1.89
5207 16435 7.825331 TTATTCTTTTCCATGTGGTGTGTTA 57.175 32.000 0.00 0.00 36.34 2.41
5209 16437 6.097554 TGTTTATTCTTTTCCATGTGGTGTGT 59.902 34.615 0.00 0.00 36.34 3.72
5210 16438 6.420604 GTGTTTATTCTTTTCCATGTGGTGTG 59.579 38.462 0.00 0.00 36.34 3.82
5247 16479 2.867109 AGCAGTACACAAATGAGGCT 57.133 45.000 0.00 0.00 0.00 4.58
5263 16495 0.321919 AGCAGGCGATCAAGAAAGCA 60.322 50.000 0.00 0.00 0.00 3.91
5365 16597 2.594303 TGTGCAGGCAGGAAACCG 60.594 61.111 0.00 0.00 0.00 4.44
5400 16632 1.767681 CTCCTTCCAAGATCCTGGGAG 59.232 57.143 11.40 11.40 41.34 4.30
5452 16684 1.887797 TATGGTTCCCAAGGTCCGAT 58.112 50.000 0.00 0.00 36.95 4.18
5461 16693 5.015178 AGTGGAAAAGAAGATATGGTTCCCA 59.985 40.000 0.00 0.00 38.19 4.37
5477 16709 4.788925 TCAAGGAGGAGAAAGTGGAAAA 57.211 40.909 0.00 0.00 0.00 2.29
5539 16771 4.314440 GGTGGTCAGAGTGCCGCA 62.314 66.667 0.00 0.00 37.02 5.69
5542 16774 2.048127 GTCGGTGGTCAGAGTGCC 60.048 66.667 0.00 0.00 0.00 5.01
5550 16782 0.591741 GATCGTCGATGTCGGTGGTC 60.592 60.000 13.54 0.00 40.29 4.02
5560 16792 3.782889 TGTGTTGATGAGATCGTCGAT 57.217 42.857 7.63 7.63 34.69 3.59
5572 16804 4.825422 ACGAGATCACTGAATGTGTTGAT 58.175 39.130 0.00 0.00 46.27 2.57
5593 16825 3.325870 TGAGATCACCGAATGTGTTGAC 58.674 45.455 0.00 0.00 45.61 3.18
5639 16874 4.876107 GCAGGAAATCCAAAGTAGAATCGA 59.124 41.667 1.67 0.00 38.89 3.59


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

AutoCloner maintained by Alex Coulton.