Multiple sequence alignment - TraesCS6A01G039900

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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 TraesCS6A01G039900 chr6A 100.000 3181 0 0 1 3181 20523320 20520140 0.000000e+00 5875.0
1 TraesCS6A01G039900 chr6A 82.897 1491 223 19 726 2198 16530983 16532459 0.000000e+00 1312.0
2 TraesCS6A01G039900 chr6A 80.968 1240 218 11 1018 2245 20310456 20309223 0.000000e+00 966.0
3 TraesCS6A01G039900 chr6D 92.116 3057 178 28 7 3018 20603589 20600551 0.000000e+00 4252.0
4 TraesCS6A01G039900 chr6D 83.604 1476 211 17 740 2198 16242667 16244128 0.000000e+00 1356.0
5 TraesCS6A01G039900 chr6D 79.663 1544 276 27 727 2246 20312487 20310958 0.000000e+00 1077.0
6 TraesCS6A01G039900 chr6B 92.050 2478 138 30 570 3018 35529740 35527293 0.000000e+00 3430.0
7 TraesCS6A01G039900 chr6B 83.005 1471 211 19 735 2198 27992654 27991216 0.000000e+00 1295.0
8 TraesCS6A01G039900 chr6B 79.871 1545 271 30 727 2246 34341696 34340167 0.000000e+00 1094.0
9 TraesCS6A01G039900 chr6B 80.383 1305 219 23 960 2245 34685373 34684087 0.000000e+00 957.0
10 TraesCS6A01G039900 chr6B 82.394 142 18 5 2484 2618 51336424 51336283 2.000000e-22 117.0
11 TraesCS6A01G039900 chrUn 80.052 1544 270 28 727 2246 273854545 273856074 0.000000e+00 1110.0
12 TraesCS6A01G039900 chrUn 91.608 143 11 1 3039 3181 455531476 455531335 2.500000e-46 196.0
13 TraesCS6A01G039900 chr3B 93.007 143 10 0 3039 3181 663571686 663571828 3.220000e-50 209.0
14 TraesCS6A01G039900 chr3B 89.051 137 15 0 3045 3181 560893144 560893008 1.520000e-38 171.0
15 TraesCS6A01G039900 chr5D 91.608 143 11 1 3039 3181 557340334 557340193 2.500000e-46 196.0
16 TraesCS6A01G039900 chr5D 91.608 143 11 1 3039 3181 557349057 557348916 2.500000e-46 196.0
17 TraesCS6A01G039900 chr5D 91.608 143 11 1 3039 3181 564742881 564742740 2.500000e-46 196.0
18 TraesCS6A01G039900 chr5D 82.843 204 26 5 2482 2679 539019600 539019800 1.170000e-39 174.0
19 TraesCS6A01G039900 chr2A 80.930 215 31 6 2479 2686 163671808 163671597 9.130000e-36 161.0
20 TraesCS6A01G039900 chr5B 83.234 167 21 3 2479 2638 8901203 8901369 2.560000e-31 147.0
21 TraesCS6A01G039900 chr1B 84.507 142 17 2 2482 2618 553144914 553144773 5.530000e-28 135.0
22 TraesCS6A01G039900 chr1A 84.507 142 17 2 2482 2618 506545515 506545374 5.530000e-28 135.0
23 TraesCS6A01G039900 chr7A 82.550 149 16 6 2479 2618 439809149 439809296 4.310000e-24 122.0
24 TraesCS6A01G039900 chr4D 83.607 61 10 0 2626 2686 26525559 26525619 1.230000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G039900 chr6A 20520140 20523320 3180 True 5875 5875 100.000 1 3181 1 chr6A.!!$R2 3180
1 TraesCS6A01G039900 chr6A 16530983 16532459 1476 False 1312 1312 82.897 726 2198 1 chr6A.!!$F1 1472
2 TraesCS6A01G039900 chr6A 20309223 20310456 1233 True 966 966 80.968 1018 2245 1 chr6A.!!$R1 1227
3 TraesCS6A01G039900 chr6D 20600551 20603589 3038 True 4252 4252 92.116 7 3018 1 chr6D.!!$R2 3011
4 TraesCS6A01G039900 chr6D 16242667 16244128 1461 False 1356 1356 83.604 740 2198 1 chr6D.!!$F1 1458
5 TraesCS6A01G039900 chr6D 20310958 20312487 1529 True 1077 1077 79.663 727 2246 1 chr6D.!!$R1 1519
6 TraesCS6A01G039900 chr6B 35527293 35529740 2447 True 3430 3430 92.050 570 3018 1 chr6B.!!$R4 2448
7 TraesCS6A01G039900 chr6B 27991216 27992654 1438 True 1295 1295 83.005 735 2198 1 chr6B.!!$R1 1463
8 TraesCS6A01G039900 chr6B 34340167 34341696 1529 True 1094 1094 79.871 727 2246 1 chr6B.!!$R2 1519
9 TraesCS6A01G039900 chr6B 34684087 34685373 1286 True 957 957 80.383 960 2245 1 chr6B.!!$R3 1285
10 TraesCS6A01G039900 chrUn 273854545 273856074 1529 False 1110 1110 80.052 727 2246 1 chrUn.!!$F1 1519

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
126 127 0.392336 GATCTGGAGGCCACTAGCTG 59.608 60.0 5.01 0.0 43.05 4.24 F
1225 1301 0.320771 GGACGCAACCTCAGTGACAT 60.321 55.0 0.00 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1807 0.105593 AGTAGTCATGCTCATGGGCG 59.894 55.0 14.07 0.0 39.24 6.13 R
2915 3026 0.036875 GAAGTGGGACCCAAGGTGAG 59.963 60.0 16.98 0.0 35.25 3.51 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
28 29 1.153628 GCTCGCAGGGTGAATACGT 60.154 57.895 0.00 0.00 0.00 3.57
40 41 0.997726 GAATACGTCGCCGAGCTAGC 60.998 60.000 6.62 6.62 37.88 3.42
42 43 2.119147 ATACGTCGCCGAGCTAGCTG 62.119 60.000 24.99 14.20 37.88 4.24
44 45 2.278271 GTCGCCGAGCTAGCTGTC 60.278 66.667 24.99 8.07 0.00 3.51
49 50 1.063327 CCGAGCTAGCTGTCTCACG 59.937 63.158 24.99 17.73 0.00 4.35
77 78 2.403252 GCTCTAGCAAGGTTTAGCCA 57.597 50.000 0.00 0.00 41.59 4.75
91 92 4.865865 GCCAGTGGCTAGGCTTAG 57.134 61.111 27.48 0.00 46.69 2.18
126 127 0.392336 GATCTGGAGGCCACTAGCTG 59.608 60.000 5.01 0.00 43.05 4.24
173 174 3.910817 GGCACCATTGTTGCAATGA 57.089 47.368 19.69 0.00 0.00 2.57
184 185 2.514824 GCAATGAGGGAGGGCGTC 60.515 66.667 0.00 0.00 0.00 5.19
205 210 0.741221 GGTCCGTCTTGAGTCATGCC 60.741 60.000 0.00 0.00 0.00 4.40
206 211 0.741221 GTCCGTCTTGAGTCATGCCC 60.741 60.000 0.00 0.00 0.00 5.36
211 216 1.002430 GTCTTGAGTCATGCCCACTGA 59.998 52.381 0.00 0.00 0.00 3.41
255 260 0.667453 TGTCACATTGCAACGCACAT 59.333 45.000 0.00 0.00 38.71 3.21
279 284 3.383546 TGTTTGCTAGCGAAATTAGCG 57.616 42.857 19.11 0.00 45.05 4.26
301 309 5.088739 CGCAGATGATGAAGGTAAACAAAC 58.911 41.667 0.00 0.00 0.00 2.93
315 323 5.454554 GGTAAACAAACGCTTCAAAGAAGAC 59.545 40.000 10.72 1.92 0.00 3.01
317 325 4.016113 ACAAACGCTTCAAAGAAGACAC 57.984 40.909 10.72 0.00 0.00 3.67
330 338 6.643770 TCAAAGAAGACACTACGGTGAATTAC 59.356 38.462 3.06 0.00 45.61 1.89
344 356 4.082733 GGTGAATTACTCTCCCTTTGCAAC 60.083 45.833 0.00 0.00 32.37 4.17
351 363 4.999939 CCCTTTGCAACGCACGGC 63.000 66.667 0.00 0.00 38.71 5.68
352 364 3.964875 CCTTTGCAACGCACGGCT 61.965 61.111 0.00 0.00 38.71 5.52
366 378 2.128035 CACGGCTATGCTTGCTAGTAC 58.872 52.381 0.00 0.00 0.00 2.73
407 419 9.294030 CATTGATTTAGTAAATGGAGAGTTTGC 57.706 33.333 12.86 0.00 0.00 3.68
408 420 7.994425 TGATTTAGTAAATGGAGAGTTTGCA 57.006 32.000 12.86 0.00 0.00 4.08
409 421 8.579850 TGATTTAGTAAATGGAGAGTTTGCAT 57.420 30.769 12.86 0.00 39.86 3.96
413 425 6.422776 AGTAAATGGAGAGTTTGCATTACG 57.577 37.500 0.70 0.00 45.78 3.18
448 460 2.973224 GCTTGTGTAGACGTTGCAAATG 59.027 45.455 0.00 0.00 39.23 2.32
459 471 1.805943 GTTGCAAATGATTTGGGTGCC 59.194 47.619 18.52 3.21 40.94 5.01
474 486 1.547675 GGTGCCTCCCAAATCTCACAA 60.548 52.381 0.00 0.00 0.00 3.33
487 499 5.613358 AATCTCACAATGAAGTCGTTTCC 57.387 39.130 0.00 0.00 34.77 3.13
526 538 4.037446 AGTCTCGATCCAGAATAGAGCAAC 59.963 45.833 0.00 0.00 37.12 4.17
666 678 2.080286 TCTGCAACTCTTAGGAACGC 57.920 50.000 0.00 0.00 0.00 4.84
830 888 9.264719 TGTGTGCTAGATATGAACAAATATCTG 57.735 33.333 14.21 7.62 45.37 2.90
884 949 2.092699 AGCTCCAAATCTTCTAGTGGCC 60.093 50.000 0.00 0.00 0.00 5.36
929 994 5.169295 ACTACTTCAGCATTTCCGAGTTAC 58.831 41.667 0.00 0.00 0.00 2.50
933 1008 3.734463 TCAGCATTTCCGAGTTACACAA 58.266 40.909 0.00 0.00 0.00 3.33
978 1054 7.122055 ACGAGAATTCTGCTATATAAGGAGGAG 59.878 40.741 14.00 0.00 43.57 3.69
1155 1231 1.207089 CAGATAGGGACTTGGCGTCAA 59.793 52.381 0.91 0.91 44.68 3.18
1225 1301 0.320771 GGACGCAACCTCAGTGACAT 60.321 55.000 0.00 0.00 0.00 3.06
1435 1514 0.389948 GGAGACGTTACTGTGCCTGG 60.390 60.000 0.00 0.00 0.00 4.45
1436 1515 0.601558 GAGACGTTACTGTGCCTGGA 59.398 55.000 0.00 0.00 0.00 3.86
1440 1519 1.134340 ACGTTACTGTGCCTGGAAACA 60.134 47.619 0.00 0.00 39.59 2.83
1446 1525 0.539438 TGTGCCTGGAAACATCCCAC 60.539 55.000 0.00 0.00 41.51 4.61
1652 1732 0.878961 GAAGTTTCGGCTGTCGTGGT 60.879 55.000 0.09 0.00 40.32 4.16
1727 1807 3.058639 CGGCTACTAACTACCCATACGTC 60.059 52.174 0.00 0.00 0.00 4.34
1803 1886 1.002502 GGCTTTAAGGAGGTGCCGT 60.003 57.895 0.00 0.00 43.43 5.68
1853 1936 2.048603 GGCAGCCCAACCTGTCATC 61.049 63.158 0.00 0.00 37.40 2.92
1979 2062 1.861574 ACCCATGATCATGACCCCAAT 59.138 47.619 32.71 10.03 41.20 3.16
2018 2101 2.396590 TCATAAAGAACTCGTGGGGC 57.603 50.000 0.00 0.00 0.00 5.80
2253 2350 7.865385 CAGCTAGACTTACTATTGACCAGAATC 59.135 40.741 0.00 0.00 0.00 2.52
2261 2358 6.240549 ACTATTGACCAGAATCTAAGGTGG 57.759 41.667 0.00 0.00 35.36 4.61
2271 2368 8.560903 ACCAGAATCTAAGGTGGATAAATTTCT 58.439 33.333 0.00 0.00 33.57 2.52
2333 2430 7.156876 AGAATAAAATGTGAAGATCCGCAAA 57.843 32.000 0.00 0.00 0.00 3.68
2446 2551 6.266168 TGCAGAAGTTTGACTTTTCAGAAA 57.734 33.333 0.00 0.00 38.80 2.52
2447 2552 6.324819 TGCAGAAGTTTGACTTTTCAGAAAG 58.675 36.000 0.00 0.00 46.17 2.62
2496 2601 7.550712 AGGGGAGTACTACTTATAAAAACACG 58.449 38.462 4.77 0.00 0.00 4.49
2835 2946 8.481974 TGTTTCTTTTAAACTTTTAGGTTGCC 57.518 30.769 0.00 0.00 0.00 4.52
2868 2979 4.636648 CGCTAGACTCTACTCTCCTTTTCA 59.363 45.833 0.00 0.00 0.00 2.69
2889 3000 6.572167 TCACTAATGAAATGAACATGTGCA 57.428 33.333 9.52 9.52 0.00 4.57
2892 3003 5.808540 ACTAATGAAATGAACATGTGCATGC 59.191 36.000 20.38 15.14 42.39 4.06
2896 3007 2.267188 ATGAACATGTGCATGCGTTC 57.733 45.000 19.01 22.01 42.39 3.95
2901 3012 0.806868 CATGTGCATGCGTTCTCCTT 59.193 50.000 14.09 0.00 31.39 3.36
2915 3026 4.613850 CGTTCTCCTTAAGAAAAAGCAGCC 60.614 45.833 3.36 0.00 45.50 4.85
2941 3052 2.534042 TGGGTCCCACTTCTAGAGAG 57.466 55.000 6.47 0.00 0.00 3.20
2979 3090 7.098477 CCCCACATATGTAAAATGCATAATGG 58.902 38.462 8.32 0.69 38.06 3.16
3018 3129 4.336889 TCTCTGGGAACTACAACACTTG 57.663 45.455 0.00 0.00 0.00 3.16
3019 3130 3.071023 TCTCTGGGAACTACAACACTTGG 59.929 47.826 0.00 0.00 34.12 3.61
3020 3131 2.775384 TCTGGGAACTACAACACTTGGT 59.225 45.455 0.00 0.00 34.12 3.67
3021 3132 2.878406 CTGGGAACTACAACACTTGGTG 59.122 50.000 0.00 0.00 39.75 4.17
3023 3134 2.616842 GGGAACTACAACACTTGGTGTG 59.383 50.000 10.26 3.18 46.79 3.82
3033 3144 2.596452 CACTTGGTGTGTCTAGTAGCG 58.404 52.381 0.00 0.00 41.53 4.26
3034 3145 2.030185 CACTTGGTGTGTCTAGTAGCGT 60.030 50.000 0.00 0.00 41.53 5.07
3035 3146 2.228343 ACTTGGTGTGTCTAGTAGCGTC 59.772 50.000 0.00 0.00 0.00 5.19
3036 3147 1.900245 TGGTGTGTCTAGTAGCGTCA 58.100 50.000 0.00 0.00 0.00 4.35
3037 3148 2.443416 TGGTGTGTCTAGTAGCGTCAT 58.557 47.619 0.00 0.00 0.00 3.06
3038 3149 3.613030 TGGTGTGTCTAGTAGCGTCATA 58.387 45.455 0.00 0.00 0.00 2.15
3039 3150 3.376234 TGGTGTGTCTAGTAGCGTCATAC 59.624 47.826 0.00 1.22 0.00 2.39
3040 3151 3.545624 GGTGTGTCTAGTAGCGTCATACG 60.546 52.174 0.00 0.00 45.88 3.06
3061 3172 4.873129 CCGTGTCGCCCCGATCTG 62.873 72.222 0.00 0.00 38.42 2.90
3062 3173 4.873129 CGTGTCGCCCCGATCTGG 62.873 72.222 0.00 0.00 38.42 3.86
3068 3179 4.241555 GCCCCGATCTGGCGACAT 62.242 66.667 7.30 0.00 41.51 3.06
3069 3180 2.280389 CCCCGATCTGGCGACATG 60.280 66.667 0.00 0.00 41.51 3.21
3070 3181 2.280389 CCCGATCTGGCGACATGG 60.280 66.667 0.00 0.00 41.51 3.66
3071 3182 2.280389 CCGATCTGGCGACATGGG 60.280 66.667 0.00 0.00 41.51 4.00
3072 3183 2.280389 CGATCTGGCGACATGGGG 60.280 66.667 0.00 0.00 41.51 4.96
3073 3184 2.111878 GATCTGGCGACATGGGGG 59.888 66.667 0.00 0.00 41.51 5.40
3074 3185 2.366837 ATCTGGCGACATGGGGGA 60.367 61.111 0.00 0.00 41.51 4.81
3075 3186 1.983119 GATCTGGCGACATGGGGGAA 61.983 60.000 0.00 0.00 41.51 3.97
3076 3187 1.570857 ATCTGGCGACATGGGGGAAA 61.571 55.000 0.00 0.00 41.51 3.13
3077 3188 2.034999 TGGCGACATGGGGGAAAC 59.965 61.111 0.00 0.00 33.40 2.78
3078 3189 3.131478 GGCGACATGGGGGAAACG 61.131 66.667 0.00 0.00 0.00 3.60
3079 3190 3.810896 GCGACATGGGGGAAACGC 61.811 66.667 0.00 0.00 43.79 4.84
3099 3210 4.760047 CCGCCGGTGACTCCCAAG 62.760 72.222 18.79 0.00 0.00 3.61
3100 3211 3.691342 CGCCGGTGACTCCCAAGA 61.691 66.667 10.20 0.00 0.00 3.02
3101 3212 2.047179 GCCGGTGACTCCCAAGAC 60.047 66.667 1.90 0.00 0.00 3.01
3102 3213 2.663196 CCGGTGACTCCCAAGACC 59.337 66.667 0.00 0.00 0.00 3.85
3103 3214 2.214216 CCGGTGACTCCCAAGACCA 61.214 63.158 0.00 0.00 0.00 4.02
3104 3215 1.004918 CGGTGACTCCCAAGACCAC 60.005 63.158 0.00 0.00 0.00 4.16
3105 3216 1.375326 GGTGACTCCCAAGACCACC 59.625 63.158 0.00 0.00 40.08 4.61
3106 3217 1.128188 GGTGACTCCCAAGACCACCT 61.128 60.000 0.00 0.00 41.80 4.00
3107 3218 0.321996 GTGACTCCCAAGACCACCTC 59.678 60.000 0.00 0.00 0.00 3.85
3108 3219 0.191064 TGACTCCCAAGACCACCTCT 59.809 55.000 0.00 0.00 0.00 3.69
3109 3220 0.899019 GACTCCCAAGACCACCTCTC 59.101 60.000 0.00 0.00 0.00 3.20
3110 3221 0.545548 ACTCCCAAGACCACCTCTCC 60.546 60.000 0.00 0.00 0.00 3.71
3111 3222 0.252467 CTCCCAAGACCACCTCTCCT 60.252 60.000 0.00 0.00 0.00 3.69
3112 3223 0.193574 TCCCAAGACCACCTCTCCTT 59.806 55.000 0.00 0.00 0.00 3.36
3113 3224 0.615850 CCCAAGACCACCTCTCCTTC 59.384 60.000 0.00 0.00 0.00 3.46
3114 3225 0.615850 CCAAGACCACCTCTCCTTCC 59.384 60.000 0.00 0.00 0.00 3.46
3115 3226 0.615850 CAAGACCACCTCTCCTTCCC 59.384 60.000 0.00 0.00 0.00 3.97
3116 3227 0.547954 AAGACCACCTCTCCTTCCCC 60.548 60.000 0.00 0.00 0.00 4.81
3117 3228 1.081277 GACCACCTCTCCTTCCCCT 59.919 63.158 0.00 0.00 0.00 4.79
3118 3229 0.978667 GACCACCTCTCCTTCCCCTC 60.979 65.000 0.00 0.00 0.00 4.30
3119 3230 2.060980 CCACCTCTCCTTCCCCTCG 61.061 68.421 0.00 0.00 0.00 4.63
3120 3231 1.305381 CACCTCTCCTTCCCCTCGT 60.305 63.158 0.00 0.00 0.00 4.18
3121 3232 1.000612 ACCTCTCCTTCCCCTCGTC 59.999 63.158 0.00 0.00 0.00 4.20
3122 3233 1.308326 CCTCTCCTTCCCCTCGTCT 59.692 63.158 0.00 0.00 0.00 4.18
3123 3234 0.324830 CCTCTCCTTCCCCTCGTCTT 60.325 60.000 0.00 0.00 0.00 3.01
3124 3235 0.820871 CTCTCCTTCCCCTCGTCTTG 59.179 60.000 0.00 0.00 0.00 3.02
3125 3236 1.219393 CTCCTTCCCCTCGTCTTGC 59.781 63.158 0.00 0.00 0.00 4.01
3126 3237 2.245438 CTCCTTCCCCTCGTCTTGCC 62.245 65.000 0.00 0.00 0.00 4.52
3127 3238 2.125512 CTTCCCCTCGTCTTGCCG 60.126 66.667 0.00 0.00 0.00 5.69
3128 3239 4.388499 TTCCCCTCGTCTTGCCGC 62.388 66.667 0.00 0.00 0.00 6.53
3133 3244 4.749310 CTCGTCTTGCCGCTGCCT 62.749 66.667 0.00 0.00 36.33 4.75
3136 3247 3.123620 GTCTTGCCGCTGCCTGAG 61.124 66.667 0.00 0.00 36.33 3.35
3137 3248 4.399395 TCTTGCCGCTGCCTGAGG 62.399 66.667 0.00 0.00 38.75 3.86
3154 3265 2.044946 GGGACCATCGGCAAAGCT 60.045 61.111 0.00 0.00 0.00 3.74
3155 3266 2.115291 GGGACCATCGGCAAAGCTC 61.115 63.158 0.00 0.00 0.00 4.09
3156 3267 2.464459 GGACCATCGGCAAAGCTCG 61.464 63.158 0.00 0.00 0.00 5.03
3157 3268 3.100862 GACCATCGGCAAAGCTCGC 62.101 63.158 0.00 0.00 0.00 5.03
3158 3269 4.228097 CCATCGGCAAAGCTCGCG 62.228 66.667 0.00 0.00 0.00 5.87
3159 3270 4.876081 CATCGGCAAAGCTCGCGC 62.876 66.667 0.00 0.00 0.00 6.86
3165 3276 3.929948 CAAAGCTCGCGCGGGATC 61.930 66.667 37.54 22.17 42.32 3.36
3169 3280 4.057428 GCTCGCGCGGGATCCTAT 62.057 66.667 37.54 0.00 0.00 2.57
3170 3281 2.126307 CTCGCGCGGGATCCTATG 60.126 66.667 29.20 9.88 0.00 2.23
3171 3282 2.596338 TCGCGCGGGATCCTATGA 60.596 61.111 31.69 2.53 0.00 2.15
3172 3283 2.430921 CGCGCGGGATCCTATGAC 60.431 66.667 24.84 0.00 0.00 3.06
3173 3284 2.430921 GCGCGGGATCCTATGACG 60.431 66.667 12.58 7.37 0.00 4.35
3174 3285 2.258591 CGCGGGATCCTATGACGG 59.741 66.667 12.58 0.00 0.00 4.79
3175 3286 2.048127 GCGGGATCCTATGACGGC 60.048 66.667 12.58 0.67 0.00 5.68
3176 3287 2.258591 CGGGATCCTATGACGGCG 59.741 66.667 12.58 4.80 0.00 6.46
3177 3288 2.657237 GGGATCCTATGACGGCGG 59.343 66.667 13.24 0.00 0.00 6.13
3178 3289 2.048127 GGATCCTATGACGGCGGC 60.048 66.667 13.24 9.67 0.00 6.53
3179 3290 2.430921 GATCCTATGACGGCGGCG 60.431 66.667 31.06 31.06 0.00 6.46
3180 3291 3.916392 GATCCTATGACGGCGGCGG 62.916 68.421 35.05 16.70 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.690762 ACCCTGCGAGCTTTTCCTTA 59.309 50.000 0.00 0.00 0.00 2.69
3 4 1.302832 CACCCTGCGAGCTTTTCCT 60.303 57.895 0.00 0.00 0.00 3.36
4 5 0.889186 TTCACCCTGCGAGCTTTTCC 60.889 55.000 0.00 0.00 0.00 3.13
5 6 1.168714 ATTCACCCTGCGAGCTTTTC 58.831 50.000 0.00 0.00 0.00 2.29
28 29 2.438614 AGACAGCTAGCTCGGCGA 60.439 61.111 16.15 10.14 34.52 5.54
44 45 2.048312 TAGAGCATCCGCGTCGTGAG 62.048 60.000 7.51 0.00 45.49 3.51
87 88 0.592754 GAGTGCTACTCGCGGCTAAG 60.593 60.000 6.13 0.00 43.27 2.18
88 89 1.432251 GAGTGCTACTCGCGGCTAA 59.568 57.895 6.13 0.00 43.27 3.09
89 90 3.108343 GAGTGCTACTCGCGGCTA 58.892 61.111 6.13 0.00 43.27 3.93
96 97 1.606668 CCTCCAGATCGAGTGCTACTC 59.393 57.143 6.31 6.31 41.71 2.59
97 98 1.686355 CCTCCAGATCGAGTGCTACT 58.314 55.000 0.00 0.00 0.00 2.57
98 99 0.031449 GCCTCCAGATCGAGTGCTAC 59.969 60.000 0.00 0.00 0.00 3.58
99 100 1.109920 GGCCTCCAGATCGAGTGCTA 61.110 60.000 0.00 0.00 0.00 3.49
100 101 2.430610 GGCCTCCAGATCGAGTGCT 61.431 63.158 0.00 0.00 0.00 4.40
101 102 2.107953 GGCCTCCAGATCGAGTGC 59.892 66.667 0.00 0.00 0.00 4.40
103 104 0.259065 TAGTGGCCTCCAGATCGAGT 59.741 55.000 3.32 0.00 32.34 4.18
104 105 0.958091 CTAGTGGCCTCCAGATCGAG 59.042 60.000 3.32 0.00 32.34 4.04
105 106 1.109920 GCTAGTGGCCTCCAGATCGA 61.110 60.000 3.32 0.00 32.34 3.59
108 109 1.694133 GCAGCTAGTGGCCTCCAGAT 61.694 60.000 3.32 0.00 43.05 2.90
110 111 2.188994 GCAGCTAGTGGCCTCCAG 59.811 66.667 3.32 0.00 43.05 3.86
126 127 2.888414 TGTTTTAACTTACTGCCCTGGC 59.112 45.455 0.00 0.00 42.35 4.85
128 129 3.810941 TCGTGTTTTAACTTACTGCCCTG 59.189 43.478 0.00 0.00 0.00 4.45
141 142 2.307768 TGGTGCCCAAATCGTGTTTTA 58.692 42.857 0.00 0.00 0.00 1.52
143 144 1.337118 ATGGTGCCCAAATCGTGTTT 58.663 45.000 0.00 0.00 36.95 2.83
184 185 0.458543 CATGACTCAAGACGGACCCG 60.459 60.000 6.94 6.94 46.03 5.28
189 190 1.021390 GTGGGCATGACTCAAGACGG 61.021 60.000 0.00 0.00 0.00 4.79
190 191 0.036952 AGTGGGCATGACTCAAGACG 60.037 55.000 0.00 0.00 0.00 4.18
205 210 5.543507 ATCAGATAACCTTAGCTCAGTGG 57.456 43.478 0.00 0.00 0.00 4.00
206 211 9.553064 AAAATATCAGATAACCTTAGCTCAGTG 57.447 33.333 0.00 0.00 0.00 3.66
239 244 0.940047 TGCATGTGCGTTGCAATGTG 60.940 50.000 19.49 10.96 46.48 3.21
240 245 1.363080 TGCATGTGCGTTGCAATGT 59.637 47.368 19.49 0.00 46.48 2.71
255 260 3.574284 AATTTCGCTAGCAAACATGCA 57.426 38.095 16.45 0.00 37.25 3.96
272 277 3.813443 ACCTTCATCATCTGCGCTAATT 58.187 40.909 9.73 0.00 0.00 1.40
279 284 5.088739 CGTTTGTTTACCTTCATCATCTGC 58.911 41.667 0.00 0.00 0.00 4.26
301 309 2.408704 CCGTAGTGTCTTCTTTGAAGCG 59.591 50.000 2.71 0.53 0.00 4.68
315 323 3.700038 AGGGAGAGTAATTCACCGTAGTG 59.300 47.826 0.00 0.00 46.00 2.74
317 325 5.109903 CAAAGGGAGAGTAATTCACCGTAG 58.890 45.833 0.00 0.00 37.42 3.51
330 338 1.576421 GTGCGTTGCAAAGGGAGAG 59.424 57.895 14.31 0.00 41.47 3.20
407 419 6.759827 ACAAGCCTAACTATAACACCGTAATG 59.240 38.462 0.00 0.00 0.00 1.90
408 420 6.759827 CACAAGCCTAACTATAACACCGTAAT 59.240 38.462 0.00 0.00 0.00 1.89
409 421 6.101332 CACAAGCCTAACTATAACACCGTAA 58.899 40.000 0.00 0.00 0.00 3.18
410 422 5.185635 ACACAAGCCTAACTATAACACCGTA 59.814 40.000 0.00 0.00 0.00 4.02
411 423 4.020839 ACACAAGCCTAACTATAACACCGT 60.021 41.667 0.00 0.00 0.00 4.83
412 424 4.501071 ACACAAGCCTAACTATAACACCG 58.499 43.478 0.00 0.00 0.00 4.94
413 425 6.755607 GTCTACACAAGCCTAACTATAACACC 59.244 42.308 0.00 0.00 0.00 4.16
459 471 4.093998 CGACTTCATTGTGAGATTTGGGAG 59.906 45.833 0.00 0.00 0.00 4.30
463 475 5.853282 GGAAACGACTTCATTGTGAGATTTG 59.147 40.000 0.00 0.00 35.55 2.32
497 509 4.674281 ATTCTGGATCGAGACTTAACCC 57.326 45.455 6.97 0.00 0.00 4.11
502 514 4.211125 TGCTCTATTCTGGATCGAGACTT 58.789 43.478 6.97 1.11 31.01 3.01
504 516 4.202060 TGTTGCTCTATTCTGGATCGAGAC 60.202 45.833 6.97 0.00 31.01 3.36
629 641 6.482898 TGCAGAATAAATTGTAATGCCCAT 57.517 33.333 0.00 0.00 0.00 4.00
666 678 4.939052 AGGTACCAATATCCTCAACTCG 57.061 45.455 15.94 0.00 0.00 4.18
675 687 5.054477 ACACACGCATAAGGTACCAATATC 58.946 41.667 15.94 6.04 0.00 1.63
681 693 2.419667 ACAACACACGCATAAGGTACC 58.580 47.619 2.73 2.73 0.00 3.34
850 915 1.583556 TGGAGCTACATGGTCATGGT 58.416 50.000 14.49 4.22 44.40 3.55
851 916 2.715749 TTGGAGCTACATGGTCATGG 57.284 50.000 0.00 0.37 44.40 3.66
852 917 4.458397 AGATTTGGAGCTACATGGTCATG 58.542 43.478 0.00 9.19 44.40 3.07
853 918 4.785346 AGATTTGGAGCTACATGGTCAT 57.215 40.909 0.00 0.00 44.40 3.06
854 919 4.225942 AGAAGATTTGGAGCTACATGGTCA 59.774 41.667 0.00 0.00 44.40 4.02
855 920 4.775236 AGAAGATTTGGAGCTACATGGTC 58.225 43.478 0.00 0.00 42.07 4.02
884 949 2.260869 CCGAACCACAGGCAAGGTG 61.261 63.158 0.00 0.00 38.37 4.00
950 1026 6.390721 TCCTTATATAGCAGAATTCTCGTGC 58.609 40.000 4.57 7.54 37.48 5.34
1345 1424 0.947244 GCAGCTACCATACATGTGGC 59.053 55.000 9.11 3.41 43.27 5.01
1427 1506 0.539438 GTGGGATGTTTCCAGGCACA 60.539 55.000 0.00 0.00 44.60 4.57
1446 1525 3.807538 GCGCCAGTCCACATGCAG 61.808 66.667 0.00 0.00 0.00 4.41
1652 1732 2.183300 GCCGATGACACGTAGCCA 59.817 61.111 0.00 0.00 0.00 4.75
1727 1807 0.105593 AGTAGTCATGCTCATGGGCG 59.894 55.000 14.07 0.00 39.24 6.13
1793 1876 0.734889 CATCATTTGACGGCACCTCC 59.265 55.000 0.00 0.00 0.00 4.30
1803 1886 1.811965 CAACGCCACCTCATCATTTGA 59.188 47.619 0.00 0.00 0.00 2.69
1979 2062 3.069443 TGATCCAGTATTGCATGCGTCTA 59.931 43.478 14.09 1.23 0.00 2.59
2018 2101 1.135867 CGTTTTCACCCCATTTTGCG 58.864 50.000 0.00 0.00 0.00 4.85
2124 2211 6.828273 TGATATCATTCCCACCTTTGTTACTG 59.172 38.462 0.00 0.00 0.00 2.74
2170 2257 7.087409 TGTGCACCTGTTTGATTATTAGATG 57.913 36.000 15.69 0.00 0.00 2.90
2222 2319 7.039293 TGGTCAATAGTAAGTCTAGCTGTTCAA 60.039 37.037 0.00 0.00 31.67 2.69
2253 2350 8.306761 ACTTTTGCAGAAATTTATCCACCTTAG 58.693 33.333 0.00 0.00 0.00 2.18
2462 2567 5.280998 AGTAGTACTCCCCTAGTCCAAAA 57.719 43.478 0.00 0.00 39.80 2.44
2835 2946 2.010582 GAGTCTAGCGAGTGGGCCAG 62.011 65.000 6.40 0.00 0.00 4.85
2868 2979 5.808540 GCATGCACATGTTCATTTCATTAGT 59.191 36.000 14.21 0.00 40.80 2.24
2885 2996 2.346803 TCTTAAGGAGAACGCATGCAC 58.653 47.619 19.57 8.42 0.00 4.57
2889 3000 4.518970 TGCTTTTTCTTAAGGAGAACGCAT 59.481 37.500 1.85 0.00 43.90 4.73
2892 3003 4.467735 GCTGCTTTTTCTTAAGGAGAACG 58.532 43.478 8.76 0.00 43.79 3.95
2896 3007 4.074970 TGAGGCTGCTTTTTCTTAAGGAG 58.925 43.478 1.85 0.00 43.87 3.69
2901 3012 3.508845 AGGTGAGGCTGCTTTTTCTTA 57.491 42.857 0.00 0.00 0.00 2.10
2915 3026 0.036875 GAAGTGGGACCCAAGGTGAG 59.963 60.000 16.98 0.00 35.25 3.51
2941 3052 6.303839 ACATATGTGGGGTGTTGTTATATCC 58.696 40.000 7.78 0.00 0.00 2.59
2979 3090 4.503734 CAGAGAAGAAGCATCGAGATGTTC 59.496 45.833 13.79 14.29 40.80 3.18
2987 3098 2.093764 AGTTCCCAGAGAAGAAGCATCG 60.094 50.000 0.00 0.00 34.29 3.84
3018 3129 3.545624 CGTATGACGCTACTAGACACACC 60.546 52.174 0.00 0.00 33.65 4.16
3019 3130 3.605406 CGTATGACGCTACTAGACACAC 58.395 50.000 0.00 0.00 33.65 3.82
3020 3131 3.938778 CGTATGACGCTACTAGACACA 57.061 47.619 0.00 0.00 33.65 3.72
3032 3143 4.137872 ACACGGGGGCGTATGACG 62.138 66.667 0.00 0.00 45.88 4.35
3033 3144 2.202837 GACACGGGGGCGTATGAC 60.203 66.667 0.00 0.00 0.00 3.06
3034 3145 3.829044 CGACACGGGGGCGTATGA 61.829 66.667 0.00 0.00 0.00 2.15
3053 3164 2.280389 CCATGTCGCCAGATCGGG 60.280 66.667 7.64 7.64 34.06 5.14
3054 3165 2.280389 CCCATGTCGCCAGATCGG 60.280 66.667 0.00 0.00 38.11 4.18
3055 3166 2.280389 CCCCATGTCGCCAGATCG 60.280 66.667 0.00 0.00 0.00 3.69
3056 3167 1.983119 TTCCCCCATGTCGCCAGATC 61.983 60.000 0.00 0.00 0.00 2.75
3057 3168 1.570857 TTTCCCCCATGTCGCCAGAT 61.571 55.000 0.00 0.00 0.00 2.90
3058 3169 2.227757 TTTCCCCCATGTCGCCAGA 61.228 57.895 0.00 0.00 0.00 3.86
3059 3170 2.046285 GTTTCCCCCATGTCGCCAG 61.046 63.158 0.00 0.00 0.00 4.85
3060 3171 2.034999 GTTTCCCCCATGTCGCCA 59.965 61.111 0.00 0.00 0.00 5.69
3061 3172 3.131478 CGTTTCCCCCATGTCGCC 61.131 66.667 0.00 0.00 0.00 5.54
3062 3173 3.810896 GCGTTTCCCCCATGTCGC 61.811 66.667 0.00 0.00 37.17 5.19
3063 3174 3.131478 GGCGTTTCCCCCATGTCG 61.131 66.667 0.00 0.00 0.00 4.35
3064 3175 2.034999 TGGCGTTTCCCCCATGTC 59.965 61.111 0.00 0.00 0.00 3.06
3065 3176 2.282887 GTGGCGTTTCCCCCATGT 60.283 61.111 0.00 0.00 32.95 3.21
3066 3177 3.068064 GGTGGCGTTTCCCCCATG 61.068 66.667 0.00 0.00 32.95 3.66
3067 3178 4.733542 CGGTGGCGTTTCCCCCAT 62.734 66.667 0.00 0.00 32.95 4.00
3082 3193 4.760047 CTTGGGAGTCACCGGCGG 62.760 72.222 27.06 27.06 40.11 6.13
3083 3194 3.691342 TCTTGGGAGTCACCGGCG 61.691 66.667 0.00 0.00 40.11 6.46
3084 3195 2.047179 GTCTTGGGAGTCACCGGC 60.047 66.667 0.00 0.00 40.11 6.13
3085 3196 2.214216 TGGTCTTGGGAGTCACCGG 61.214 63.158 0.00 0.00 40.11 5.28
3086 3197 1.004918 GTGGTCTTGGGAGTCACCG 60.005 63.158 0.00 0.00 40.11 4.94
3087 3198 1.128188 AGGTGGTCTTGGGAGTCACC 61.128 60.000 0.00 0.00 42.70 4.02
3088 3199 0.321996 GAGGTGGTCTTGGGAGTCAC 59.678 60.000 0.00 0.00 0.00 3.67
3089 3200 0.191064 AGAGGTGGTCTTGGGAGTCA 59.809 55.000 0.00 0.00 27.07 3.41
3090 3201 0.899019 GAGAGGTGGTCTTGGGAGTC 59.101 60.000 0.00 0.00 34.71 3.36
3091 3202 0.545548 GGAGAGGTGGTCTTGGGAGT 60.546 60.000 0.00 0.00 34.71 3.85
3092 3203 0.252467 AGGAGAGGTGGTCTTGGGAG 60.252 60.000 0.00 0.00 34.71 4.30
3093 3204 0.193574 AAGGAGAGGTGGTCTTGGGA 59.806 55.000 0.00 0.00 34.71 4.37
3094 3205 0.615850 GAAGGAGAGGTGGTCTTGGG 59.384 60.000 0.00 0.00 34.71 4.12
3095 3206 0.615850 GGAAGGAGAGGTGGTCTTGG 59.384 60.000 0.00 0.00 34.71 3.61
3096 3207 0.615850 GGGAAGGAGAGGTGGTCTTG 59.384 60.000 0.00 0.00 34.71 3.02
3097 3208 0.547954 GGGGAAGGAGAGGTGGTCTT 60.548 60.000 0.00 0.00 34.71 3.01
3098 3209 1.081277 GGGGAAGGAGAGGTGGTCT 59.919 63.158 0.00 0.00 38.71 3.85
3099 3210 0.978667 GAGGGGAAGGAGAGGTGGTC 60.979 65.000 0.00 0.00 0.00 4.02
3100 3211 1.081277 GAGGGGAAGGAGAGGTGGT 59.919 63.158 0.00 0.00 0.00 4.16
3101 3212 2.060980 CGAGGGGAAGGAGAGGTGG 61.061 68.421 0.00 0.00 0.00 4.61
3102 3213 1.305381 ACGAGGGGAAGGAGAGGTG 60.305 63.158 0.00 0.00 0.00 4.00
3103 3214 1.000612 GACGAGGGGAAGGAGAGGT 59.999 63.158 0.00 0.00 0.00 3.85
3104 3215 0.324830 AAGACGAGGGGAAGGAGAGG 60.325 60.000 0.00 0.00 0.00 3.69
3105 3216 0.820871 CAAGACGAGGGGAAGGAGAG 59.179 60.000 0.00 0.00 0.00 3.20
3106 3217 1.258445 GCAAGACGAGGGGAAGGAGA 61.258 60.000 0.00 0.00 0.00 3.71
3107 3218 1.219393 GCAAGACGAGGGGAAGGAG 59.781 63.158 0.00 0.00 0.00 3.69
3108 3219 2.291043 GGCAAGACGAGGGGAAGGA 61.291 63.158 0.00 0.00 0.00 3.36
3109 3220 2.269241 GGCAAGACGAGGGGAAGG 59.731 66.667 0.00 0.00 0.00 3.46
3110 3221 2.125512 CGGCAAGACGAGGGGAAG 60.126 66.667 0.00 0.00 35.47 3.46
3111 3222 4.388499 GCGGCAAGACGAGGGGAA 62.388 66.667 0.00 0.00 35.47 3.97
3116 3227 4.749310 AGGCAGCGGCAAGACGAG 62.749 66.667 11.88 0.00 43.71 4.18
3119 3230 3.123620 CTCAGGCAGCGGCAAGAC 61.124 66.667 11.88 0.00 43.71 3.01
3120 3231 4.399395 CCTCAGGCAGCGGCAAGA 62.399 66.667 11.88 6.72 43.71 3.02
3127 3238 3.412624 GATGGTCCCCTCAGGCAGC 62.413 68.421 0.00 0.00 34.51 5.25
3128 3239 2.914289 GATGGTCCCCTCAGGCAG 59.086 66.667 0.00 0.00 34.51 4.85
3129 3240 3.083349 CGATGGTCCCCTCAGGCA 61.083 66.667 0.00 0.00 34.51 4.75
3130 3241 3.866582 CCGATGGTCCCCTCAGGC 61.867 72.222 0.00 0.00 34.51 4.85
3131 3242 3.866582 GCCGATGGTCCCCTCAGG 61.867 72.222 0.00 0.00 0.00 3.86
3132 3243 2.196997 TTTGCCGATGGTCCCCTCAG 62.197 60.000 0.00 0.00 0.00 3.35
3133 3244 2.196997 CTTTGCCGATGGTCCCCTCA 62.197 60.000 0.00 0.00 0.00 3.86
3134 3245 1.452108 CTTTGCCGATGGTCCCCTC 60.452 63.158 0.00 0.00 0.00 4.30
3135 3246 2.677228 CTTTGCCGATGGTCCCCT 59.323 61.111 0.00 0.00 0.00 4.79
3136 3247 3.140814 GCTTTGCCGATGGTCCCC 61.141 66.667 0.00 0.00 0.00 4.81
3137 3248 2.044946 AGCTTTGCCGATGGTCCC 60.045 61.111 0.00 0.00 0.00 4.46
3138 3249 2.464459 CGAGCTTTGCCGATGGTCC 61.464 63.158 0.00 0.00 0.00 4.46
3139 3250 3.093278 CGAGCTTTGCCGATGGTC 58.907 61.111 0.00 0.00 0.00 4.02
3140 3251 3.127533 GCGAGCTTTGCCGATGGT 61.128 61.111 0.64 0.00 0.00 3.55
3141 3252 4.228097 CGCGAGCTTTGCCGATGG 62.228 66.667 0.00 0.00 0.00 3.51
3153 3264 2.126307 CATAGGATCCCGCGCGAG 60.126 66.667 34.63 20.97 0.00 5.03
3154 3265 2.596338 TCATAGGATCCCGCGCGA 60.596 61.111 34.63 13.72 0.00 5.87
3155 3266 2.430921 GTCATAGGATCCCGCGCG 60.431 66.667 25.67 25.67 0.00 6.86
3156 3267 2.430921 CGTCATAGGATCCCGCGC 60.431 66.667 8.55 0.00 0.00 6.86
3157 3268 2.258591 CCGTCATAGGATCCCGCG 59.741 66.667 8.55 0.00 0.00 6.46
3158 3269 2.048127 GCCGTCATAGGATCCCGC 60.048 66.667 8.55 0.00 0.00 6.13
3159 3270 2.258591 CGCCGTCATAGGATCCCG 59.741 66.667 8.55 4.07 0.00 5.14
3160 3271 2.657237 CCGCCGTCATAGGATCCC 59.343 66.667 8.55 0.00 0.00 3.85
3161 3272 2.048127 GCCGCCGTCATAGGATCC 60.048 66.667 2.48 2.48 0.00 3.36
3162 3273 2.430921 CGCCGCCGTCATAGGATC 60.431 66.667 0.00 0.00 0.00 3.36
3163 3274 3.991051 CCGCCGCCGTCATAGGAT 61.991 66.667 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.