Multiple sequence alignment - TraesCS4D01G286100

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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 TraesCS4D01G286100 chr4D 100.000 4569 0 0 1 4569 456497852 456493284 0.000000e+00 8438
1 TraesCS4D01G286100 chr4B 95.205 1710 68 4 1367 3074 570738512 570736815 0.000000e+00 2691
2 TraesCS4D01G286100 chr4B 95.881 1408 46 5 3058 4464 570736794 570735398 0.000000e+00 2268
3 TraesCS4D01G286100 chr4B 92.761 1119 48 16 4 1101 570740799 570739693 0.000000e+00 1587
4 TraesCS4D01G286100 chr4B 82.759 203 19 8 1138 1338 570739576 570739388 2.830000e-37 167
5 TraesCS4D01G286100 chr4B 97.403 77 2 0 4493 4569 570735398 570735322 1.030000e-26 132
6 TraesCS4D01G286100 chr4A 95.333 1607 58 10 1466 3069 11361731 11363323 0.000000e+00 2536
7 TraesCS4D01G286100 chr4A 88.244 1412 94 33 1 1369 11360294 11361676 0.000000e+00 1622
8 TraesCS4D01G286100 chr4A 94.385 748 32 6 3826 4569 11364087 11364828 0.000000e+00 1140
9 TraesCS4D01G286100 chr4A 96.215 687 26 0 3056 3742 11363358 11364044 0.000000e+00 1125
10 TraesCS4D01G286100 chr4A 89.806 206 11 4 1 203 11326982 11327180 5.870000e-64 255


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 TraesCS4D01G286100 chr4D 456493284 456497852 4568 True 8438.00 8438 100.00000 1 4569 1 chr4D.!!$R1 4568
1 TraesCS4D01G286100 chr4B 570735322 570740799 5477 True 1369.00 2691 92.80180 4 4569 5 chr4B.!!$R1 4565
2 TraesCS4D01G286100 chr4A 11360294 11364828 4534 False 1605.75 2536 93.54425 1 4569 4 chr4A.!!$F2 4568

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
298 326 0.963856 TACGTCGAGGTCCTGCATGT 60.964 55.0 15.00 0.0 0.00 3.21 F
1089 1137 0.178873 TCTCTTACCACTTGCCCCCT 60.179 55.0 0.00 0.0 0.00 4.79 F
1872 2885 0.320697 CTCCTTCGAAACCGGGAAGT 59.679 55.0 6.32 0.0 38.34 3.01 F
3205 4281 0.390472 CTCTGGACAAGTCGAAGCCC 60.390 60.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 1369 0.111639 TTGCCCCAGACAAGGTTACC 59.888 55.0 0.00 0.00 0.00 2.85 R
2780 3805 0.326264 GGGCTTCACCATGACTCTGT 59.674 55.0 0.00 0.00 42.05 3.41 R
3250 4326 0.038159 GGTACAGTCTGCGCTTGTCT 60.038 55.0 9.73 1.74 0.00 3.41 R
4488 5567 0.179103 CGTGGGGGTATCGTACAACC 60.179 60.0 0.00 0.00 34.85 3.77 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
53 54 7.658525 TGGAGTGTAATTGGAATTGCATATT 57.341 32.000 0.00 6.55 41.75 1.28
103 106 6.985188 TCTTCCAATTATGTGTAGCAACTC 57.015 37.500 0.00 0.00 0.00 3.01
109 112 6.422223 CAATTATGTGTAGCAACTCGAATCC 58.578 40.000 0.00 0.00 0.00 3.01
130 133 5.646215 TCCCATACTTTTGGCTTTAAGGAA 58.354 37.500 0.00 0.00 35.29 3.36
131 134 5.714806 TCCCATACTTTTGGCTTTAAGGAAG 59.285 40.000 0.00 0.00 38.45 3.46
132 135 5.480422 CCCATACTTTTGGCTTTAAGGAAGT 59.520 40.000 0.00 0.00 37.69 3.01
133 136 6.661805 CCCATACTTTTGGCTTTAAGGAAGTA 59.338 38.462 0.00 0.00 37.69 2.24
134 137 7.148069 CCCATACTTTTGGCTTTAAGGAAGTAG 60.148 40.741 0.00 0.00 37.69 2.57
135 138 7.148069 CCATACTTTTGGCTTTAAGGAAGTAGG 60.148 40.741 0.00 0.00 37.69 3.18
194 201 4.537135 TGACTGGTCTACCATTCTGTTC 57.463 45.455 17.35 3.66 46.46 3.18
227 234 3.264450 CCCCCTGTACAATCTCAGAGTTT 59.736 47.826 0.00 0.00 34.02 2.66
236 264 7.602644 TGTACAATCTCAGAGTTTTACATCCAC 59.397 37.037 0.00 0.00 0.00 4.02
240 268 4.279922 TCTCAGAGTTTTACATCCACACGA 59.720 41.667 0.00 0.00 0.00 4.35
259 287 1.197430 AGTCTTCTCTGCACAGGGGG 61.197 60.000 0.00 0.00 0.00 5.40
260 288 2.045536 CTTCTCTGCACAGGGGGC 60.046 66.667 0.00 0.00 0.00 5.80
266 294 1.531365 CTGCACAGGGGGCAAAGAA 60.531 57.895 0.00 0.00 41.39 2.52
267 295 1.809567 CTGCACAGGGGGCAAAGAAC 61.810 60.000 0.00 0.00 41.39 3.01
268 296 1.832167 GCACAGGGGGCAAAGAACA 60.832 57.895 0.00 0.00 0.00 3.18
271 299 1.693606 CACAGGGGGCAAAGAACAAAT 59.306 47.619 0.00 0.00 0.00 2.32
275 303 3.056607 CAGGGGGCAAAGAACAAATACTG 60.057 47.826 0.00 0.00 0.00 2.74
279 307 5.279960 GGGGGCAAAGAACAAATACTGAAAT 60.280 40.000 0.00 0.00 0.00 2.17
281 309 6.811665 GGGGCAAAGAACAAATACTGAAATAC 59.188 38.462 0.00 0.00 0.00 1.89
296 324 1.112113 AATACGTCGAGGTCCTGCAT 58.888 50.000 15.00 0.00 0.00 3.96
298 326 0.963856 TACGTCGAGGTCCTGCATGT 60.964 55.000 15.00 0.00 0.00 3.21
646 678 2.197324 CGGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
647 679 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
683 724 2.290641 TGACTTTTTGAAGCTTCTCGCC 59.709 45.455 26.09 10.05 40.39 5.54
782 824 2.415010 CGGAGATCAGCTGGACCG 59.585 66.667 15.13 18.32 34.77 4.79
783 825 2.121538 CGGAGATCAGCTGGACCGA 61.122 63.158 25.23 5.40 42.40 4.69
869 911 1.235696 GCTCCTCCTGATCCCTCCT 59.764 63.158 0.00 0.00 0.00 3.69
878 920 4.473520 ATCCCTCCTGTTGCCGCG 62.474 66.667 0.00 0.00 0.00 6.46
932 974 2.124487 ACGGAGGAGAGAGGAGCG 60.124 66.667 0.00 0.00 0.00 5.03
952 994 1.339151 GGAGTTCGCCTGTGGATCTTT 60.339 52.381 0.00 0.00 0.00 2.52
971 1013 5.178797 TCTTTAGGAAAGGAAGCTCATTCG 58.821 41.667 0.00 0.00 38.95 3.34
1078 1126 1.205893 CCTGTGAGTGCCTCTCTTACC 59.794 57.143 7.37 0.00 43.13 2.85
1089 1137 0.178873 TCTCTTACCACTTGCCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
1096 1144 2.256306 ACCACTTGCCCCCTAATTTTG 58.744 47.619 0.00 0.00 0.00 2.44
1097 1145 1.554617 CCACTTGCCCCCTAATTTTGG 59.445 52.381 0.00 0.00 0.00 3.28
1101 1236 3.326588 ACTTGCCCCCTAATTTTGGTTTC 59.673 43.478 0.00 0.00 0.00 2.78
1103 1238 3.169908 TGCCCCCTAATTTTGGTTTCTC 58.830 45.455 0.00 0.00 0.00 2.87
1111 1246 8.593679 CCCCTAATTTTGGTTTCTCTGTATTTT 58.406 33.333 0.00 0.00 0.00 1.82
1127 1265 8.677148 TCTGTATTTTTCAGTTTCTACTTGCT 57.323 30.769 0.00 0.00 34.86 3.91
1128 1266 8.774586 TCTGTATTTTTCAGTTTCTACTTGCTC 58.225 33.333 0.00 0.00 34.86 4.26
1133 1271 3.239449 TCAGTTTCTACTTGCTCCCTGA 58.761 45.455 0.00 0.00 30.26 3.86
1190 1334 8.147058 TGTTTTGGTTATTCGTACTGGTAGTAA 58.853 33.333 0.00 0.00 31.62 2.24
1214 1358 5.867903 TCTTGGATTTGGTTTGTGTTGAT 57.132 34.783 0.00 0.00 0.00 2.57
1218 1362 5.121811 TGGATTTGGTTTGTGTTGATTTGG 58.878 37.500 0.00 0.00 0.00 3.28
1219 1363 5.122519 GGATTTGGTTTGTGTTGATTTGGT 58.877 37.500 0.00 0.00 0.00 3.67
1220 1364 5.588246 GGATTTGGTTTGTGTTGATTTGGTT 59.412 36.000 0.00 0.00 0.00 3.67
1221 1365 6.238347 GGATTTGGTTTGTGTTGATTTGGTTC 60.238 38.462 0.00 0.00 0.00 3.62
1223 1367 3.444034 TGGTTTGTGTTGATTTGGTTCGA 59.556 39.130 0.00 0.00 0.00 3.71
1224 1368 4.098654 TGGTTTGTGTTGATTTGGTTCGAT 59.901 37.500 0.00 0.00 0.00 3.59
1225 1369 4.444056 GGTTTGTGTTGATTTGGTTCGATG 59.556 41.667 0.00 0.00 0.00 3.84
1226 1370 3.913548 TGTGTTGATTTGGTTCGATGG 57.086 42.857 0.00 0.00 0.00 3.51
1227 1371 3.218453 TGTGTTGATTTGGTTCGATGGT 58.782 40.909 0.00 0.00 0.00 3.55
1228 1372 4.390264 TGTGTTGATTTGGTTCGATGGTA 58.610 39.130 0.00 0.00 0.00 3.25
1232 1376 4.295141 TGATTTGGTTCGATGGTAACCT 57.705 40.909 4.92 0.00 45.53 3.50
1246 1391 2.312390 GTAACCTTGTCTGGGGCAAAA 58.688 47.619 0.00 0.00 0.00 2.44
1255 1400 4.360889 TGTCTGGGGCAAAATTTGGATAT 58.639 39.130 7.89 0.00 0.00 1.63
1262 1410 5.528320 GGGGCAAAATTTGGATATCATGTTG 59.472 40.000 7.89 2.93 0.00 3.33
1284 1432 7.661437 TGTTGTGCATCTTACACTTCTATTTCT 59.339 33.333 0.00 0.00 38.86 2.52
1309 1458 9.472361 CTGTCACTAGTTTTAGCTACTTTGTTA 57.528 33.333 0.00 0.00 0.00 2.41
1338 1489 2.732282 GCACCTTCGCCTCTATTTTTGC 60.732 50.000 0.00 0.00 0.00 3.68
1339 1490 2.749621 CACCTTCGCCTCTATTTTTGCT 59.250 45.455 0.00 0.00 0.00 3.91
1346 2351 2.690497 GCCTCTATTTTTGCTCCCCTTC 59.310 50.000 0.00 0.00 0.00 3.46
1352 2357 6.365520 TCTATTTTTGCTCCCCTTCCTTATC 58.634 40.000 0.00 0.00 0.00 1.75
1395 2408 6.920817 CATGCTGCATGGATAAGAACATTAT 58.079 36.000 30.12 0.00 38.11 1.28
1403 2416 9.468532 GCATGGATAAGAACATTATTTTCTTCC 57.531 33.333 9.30 7.12 41.43 3.46
1431 2444 8.458843 AGGTTTGATATACTTCAAATTTCACGG 58.541 33.333 5.11 0.00 44.80 4.94
1432 2445 8.241367 GGTTTGATATACTTCAAATTTCACGGT 58.759 33.333 5.11 0.00 44.80 4.83
1435 2448 8.138365 TGATATACTTCAAATTTCACGGTAGC 57.862 34.615 0.00 0.00 0.00 3.58
1440 2453 5.920273 ACTTCAAATTTCACGGTAGCAAATG 59.080 36.000 0.00 0.00 0.00 2.32
1445 2458 5.705609 ATTTCACGGTAGCAAATGAAACT 57.294 34.783 14.59 5.76 42.22 2.66
1446 2459 6.811253 ATTTCACGGTAGCAAATGAAACTA 57.189 33.333 14.59 0.00 42.22 2.24
1449 2462 6.236017 TCACGGTAGCAAATGAAACTAAAG 57.764 37.500 0.00 0.00 0.00 1.85
1568 2581 6.801575 TCTTACACACATTTCCTTTGTTTCC 58.198 36.000 0.00 0.00 0.00 3.13
1576 2589 2.838637 TCCTTTGTTTCCTGTTGGGT 57.161 45.000 0.00 0.00 36.25 4.51
1740 2753 1.272490 TCATCGTCGAACTTGAAGGCT 59.728 47.619 0.00 0.00 0.00 4.58
1872 2885 0.320697 CTCCTTCGAAACCGGGAAGT 59.679 55.000 6.32 0.00 38.34 3.01
1890 2903 2.229792 AGTGGTATGGTTGTTGCTGTG 58.770 47.619 0.00 0.00 0.00 3.66
1945 2958 1.561542 AGGAATGGCTGGTAGGTTCAG 59.438 52.381 0.00 0.00 35.49 3.02
1955 2968 4.094476 CTGGTAGGTTCAGGACTCCTTAA 58.906 47.826 0.00 0.00 33.34 1.85
1956 2969 4.495565 TGGTAGGTTCAGGACTCCTTAAA 58.504 43.478 0.00 0.00 33.34 1.52
1961 2974 8.272889 GGTAGGTTCAGGACTCCTTAAAAATAT 58.727 37.037 0.00 0.00 33.34 1.28
2005 3018 8.250332 GCTATTTTTCATGTTTCCTGATGGTTA 58.750 33.333 0.00 0.00 34.23 2.85
2498 3511 1.202114 TCAATGCAGGAATTCAACGCC 59.798 47.619 7.93 0.00 0.00 5.68
2618 3631 7.148641 CAGAGTATATCGCAACAGGTTAGAAT 58.851 38.462 0.00 0.00 0.00 2.40
2697 3710 6.441274 GTCATGTGACATCAGTTTTGACAAT 58.559 36.000 8.22 0.00 44.18 2.71
2698 3711 7.584108 GTCATGTGACATCAGTTTTGACAATA 58.416 34.615 8.22 0.00 44.18 1.90
2719 3733 4.647564 AGATGTTGATGTTGGGTCTTCT 57.352 40.909 0.00 0.00 0.00 2.85
2739 3753 8.132995 GTCTTCTCTCTGTATTAGCTAAACCTC 58.867 40.741 10.85 2.39 0.00 3.85
2740 3754 8.056400 TCTTCTCTCTGTATTAGCTAAACCTCT 58.944 37.037 10.85 0.00 0.00 3.69
2780 3805 5.191722 GGCCTAAATCATCCCATACCTATGA 59.808 44.000 0.00 0.00 35.75 2.15
2781 3806 6.116126 GCCTAAATCATCCCATACCTATGAC 58.884 44.000 0.00 0.00 35.75 3.06
2782 3807 6.296432 GCCTAAATCATCCCATACCTATGACA 60.296 42.308 0.00 0.00 35.75 3.58
2783 3808 7.334090 CCTAAATCATCCCATACCTATGACAG 58.666 42.308 0.00 0.00 35.75 3.51
2784 3809 7.180946 CCTAAATCATCCCATACCTATGACAGA 59.819 40.741 0.00 0.00 35.75 3.41
2785 3810 6.617782 AATCATCCCATACCTATGACAGAG 57.382 41.667 0.00 0.00 35.75 3.35
2786 3811 5.079998 TCATCCCATACCTATGACAGAGT 57.920 43.478 0.00 0.00 35.75 3.24
2787 3812 5.080337 TCATCCCATACCTATGACAGAGTC 58.920 45.833 0.00 0.00 35.75 3.36
2788 3813 4.536295 TCCCATACCTATGACAGAGTCA 57.464 45.455 1.95 1.95 46.90 3.41
2847 3872 3.018856 TCATGGTGTTCTCCAATCATGC 58.981 45.455 0.00 0.00 41.09 4.06
2880 3905 4.203226 GGAATTGTTTCCTGATCTCCCTC 58.797 47.826 0.00 0.00 46.80 4.30
2891 3916 2.879026 TGATCTCCCTCGATAGTCAACG 59.121 50.000 0.00 0.00 37.40 4.10
3025 4053 6.767524 TTAAATTCGACACTGGCCATATTT 57.232 33.333 5.51 6.69 0.00 1.40
3127 4203 0.898326 TTACAGGTCGCCTCTCTGCA 60.898 55.000 0.00 0.00 32.19 4.41
3199 4275 0.455295 GACGAGCTCTGGACAAGTCG 60.455 60.000 12.85 0.00 0.00 4.18
3205 4281 0.390472 CTCTGGACAAGTCGAAGCCC 60.390 60.000 0.00 0.00 0.00 5.19
3428 4504 3.758554 GCTCCAAGACTCCAAAAGCAATA 59.241 43.478 0.00 0.00 0.00 1.90
3704 4780 3.068307 GGAATATGACTACGGCACTCTGT 59.932 47.826 0.00 0.00 35.61 3.41
3725 4801 6.979817 TCTGTGATGAATTGTTTTTCACCAAG 59.020 34.615 0.00 0.00 38.37 3.61
3726 4802 5.523188 TGTGATGAATTGTTTTTCACCAAGC 59.477 36.000 0.00 0.00 38.37 4.01
3795 4871 0.742990 TGCCGGGTTTATCTTCTGCG 60.743 55.000 2.18 0.00 0.00 5.18
3796 4872 0.461339 GCCGGGTTTATCTTCTGCGA 60.461 55.000 2.18 0.00 0.00 5.10
3797 4873 1.287425 CCGGGTTTATCTTCTGCGAC 58.713 55.000 0.00 0.00 0.00 5.19
3798 4874 1.404986 CCGGGTTTATCTTCTGCGACA 60.405 52.381 0.00 0.00 0.00 4.35
3799 4875 2.550978 CGGGTTTATCTTCTGCGACAT 58.449 47.619 0.00 0.00 0.00 3.06
3800 4876 2.285220 CGGGTTTATCTTCTGCGACATG 59.715 50.000 0.00 0.00 0.00 3.21
3801 4877 3.531538 GGGTTTATCTTCTGCGACATGA 58.468 45.455 0.00 0.00 0.00 3.07
3802 4878 4.130118 GGGTTTATCTTCTGCGACATGAT 58.870 43.478 0.00 0.00 0.00 2.45
3803 4879 5.297547 GGGTTTATCTTCTGCGACATGATA 58.702 41.667 0.00 0.00 0.00 2.15
3806 4882 6.701841 GGTTTATCTTCTGCGACATGATAGAA 59.298 38.462 0.00 2.90 0.00 2.10
3817 4893 5.468072 GCGACATGATAGAAACTGGATGATT 59.532 40.000 0.00 0.00 0.00 2.57
3818 4894 6.017605 GCGACATGATAGAAACTGGATGATTT 60.018 38.462 0.00 0.00 0.00 2.17
3819 4895 7.350467 CGACATGATAGAAACTGGATGATTTG 58.650 38.462 0.00 0.00 0.00 2.32
3832 4908 6.209986 ACTGGATGATTTGTTGTTGACATGAT 59.790 34.615 0.00 0.00 38.26 2.45
4100 5179 5.416952 AGCCTTGAATTTCAGGAATGTACAG 59.583 40.000 9.88 0.00 0.00 2.74
4101 5180 5.415701 GCCTTGAATTTCAGGAATGTACAGA 59.584 40.000 9.88 0.00 0.00 3.41
4215 5294 2.038387 CTGCTAAGGCGGGTAAATGT 57.962 50.000 0.00 0.00 40.90 2.71
4216 5295 1.940613 CTGCTAAGGCGGGTAAATGTC 59.059 52.381 0.00 0.00 40.90 3.06
4295 5374 2.045536 GCCCTGCTTCCTCACCAG 60.046 66.667 0.00 0.00 0.00 4.00
4372 5451 8.146412 CAGATCCTACATCAGACAATCATACAA 58.854 37.037 0.00 0.00 0.00 2.41
4463 5542 8.808092 CCTTAACTAAATCTAGGGGAGTATCAG 58.192 40.741 0.00 0.00 36.25 2.90
4464 5543 9.589461 CTTAACTAAATCTAGGGGAGTATCAGA 57.411 37.037 0.00 0.00 36.25 3.27
4465 5544 9.589461 TTAACTAAATCTAGGGGAGTATCAGAG 57.411 37.037 0.00 0.00 36.25 3.35
4466 5545 7.409408 ACTAAATCTAGGGGAGTATCAGAGA 57.591 40.000 0.00 0.00 36.25 3.10
4467 5546 7.827787 ACTAAATCTAGGGGAGTATCAGAGAA 58.172 38.462 0.00 0.00 36.25 2.87
4468 5547 6.987403 AAATCTAGGGGAGTATCAGAGAAC 57.013 41.667 0.00 0.00 36.25 3.01
4469 5548 5.941146 ATCTAGGGGAGTATCAGAGAACT 57.059 43.478 0.00 0.00 36.25 3.01
4470 5549 5.313280 TCTAGGGGAGTATCAGAGAACTC 57.687 47.826 7.04 7.04 41.16 3.01
4471 5550 4.727332 TCTAGGGGAGTATCAGAGAACTCA 59.273 45.833 14.66 0.00 43.21 3.41
4472 5551 3.909732 AGGGGAGTATCAGAGAACTCAG 58.090 50.000 14.66 0.00 43.21 3.35
4473 5552 2.364002 GGGGAGTATCAGAGAACTCAGC 59.636 54.545 14.66 2.38 43.21 4.26
4474 5553 3.027412 GGGAGTATCAGAGAACTCAGCA 58.973 50.000 14.66 0.00 43.21 4.41
4475 5554 3.449018 GGGAGTATCAGAGAACTCAGCAA 59.551 47.826 14.66 0.00 43.21 3.91
4476 5555 4.081420 GGGAGTATCAGAGAACTCAGCAAA 60.081 45.833 14.66 0.00 43.21 3.68
4477 5556 5.482908 GGAGTATCAGAGAACTCAGCAAAA 58.517 41.667 14.66 0.00 43.21 2.44
4478 5557 5.934625 GGAGTATCAGAGAACTCAGCAAAAA 59.065 40.000 14.66 0.00 43.21 1.94
4479 5558 6.128418 GGAGTATCAGAGAACTCAGCAAAAAC 60.128 42.308 14.66 0.00 43.21 2.43
4480 5559 6.291377 AGTATCAGAGAACTCAGCAAAAACA 58.709 36.000 4.64 0.00 0.00 2.83
4481 5560 6.939163 AGTATCAGAGAACTCAGCAAAAACAT 59.061 34.615 4.64 0.00 0.00 2.71
4482 5561 6.645790 ATCAGAGAACTCAGCAAAAACATT 57.354 33.333 4.64 0.00 0.00 2.71
4483 5562 5.824429 TCAGAGAACTCAGCAAAAACATTG 58.176 37.500 4.64 0.00 0.00 2.82
4484 5563 4.443394 CAGAGAACTCAGCAAAAACATTGC 59.557 41.667 5.06 5.06 45.22 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.439129 ACACTCCATTTAGCCGCTTAAAC 59.561 43.478 0.00 0.00 0.00 2.01
77 78 6.714810 AGTTGCTACACATAATTGGAAGAACA 59.285 34.615 0.13 0.00 0.00 3.18
103 106 4.718940 AAAGCCAAAAGTATGGGATTCG 57.281 40.909 0.00 0.00 41.01 3.34
109 112 6.590234 ACTTCCTTAAAGCCAAAAGTATGG 57.410 37.500 0.00 0.00 43.70 2.74
130 133 4.286032 TGGTTGTTGATTGCTACTCCTACT 59.714 41.667 0.00 0.00 0.00 2.57
131 134 4.575885 TGGTTGTTGATTGCTACTCCTAC 58.424 43.478 0.00 0.00 0.00 3.18
132 135 4.901197 TGGTTGTTGATTGCTACTCCTA 57.099 40.909 0.00 0.00 0.00 2.94
133 136 3.788227 TGGTTGTTGATTGCTACTCCT 57.212 42.857 0.00 0.00 0.00 3.69
134 137 5.048083 TGAATTGGTTGTTGATTGCTACTCC 60.048 40.000 0.00 0.00 0.00 3.85
135 138 6.012658 TGAATTGGTTGTTGATTGCTACTC 57.987 37.500 0.00 0.00 0.00 2.59
194 201 2.092323 GTACAGGGGGCTTTAAGCAAG 58.908 52.381 19.10 5.67 44.75 4.01
227 234 4.079970 AGAGAAGACTCGTGTGGATGTAA 58.920 43.478 0.00 0.00 46.64 2.41
236 264 1.668337 CCTGTGCAGAGAAGACTCGTG 60.668 57.143 13.38 0.00 46.64 4.35
240 268 1.197430 CCCCCTGTGCAGAGAAGACT 61.197 60.000 13.38 0.00 0.00 3.24
259 287 7.006210 CGACGTATTTCAGTATTTGTTCTTTGC 59.994 37.037 0.00 0.00 0.00 3.68
260 288 8.218441 TCGACGTATTTCAGTATTTGTTCTTTG 58.782 33.333 0.00 0.00 0.00 2.77
266 294 5.717119 ACCTCGACGTATTTCAGTATTTGT 58.283 37.500 0.00 0.00 0.00 2.83
267 295 5.231568 GGACCTCGACGTATTTCAGTATTTG 59.768 44.000 0.00 0.00 0.00 2.32
268 296 5.126707 AGGACCTCGACGTATTTCAGTATTT 59.873 40.000 0.00 0.00 0.00 1.40
271 299 3.376234 CAGGACCTCGACGTATTTCAGTA 59.624 47.826 0.00 0.00 0.00 2.74
275 303 1.135199 TGCAGGACCTCGACGTATTTC 60.135 52.381 0.00 0.00 0.00 2.17
279 307 0.963856 ACATGCAGGACCTCGACGTA 60.964 55.000 4.84 0.00 0.00 3.57
281 309 0.172578 TTACATGCAGGACCTCGACG 59.827 55.000 4.84 0.00 0.00 5.12
296 324 0.752009 TTGGTGGCGGCAACTTTACA 60.752 50.000 28.38 3.89 0.00 2.41
298 326 1.787057 CGTTGGTGGCGGCAACTTTA 61.787 55.000 28.38 10.65 0.00 1.85
639 671 4.565850 ATCCCCTCCGCCTCCTCC 62.566 72.222 0.00 0.00 0.00 4.30
640 672 2.073101 AAATCCCCTCCGCCTCCTC 61.073 63.158 0.00 0.00 0.00 3.71
641 673 2.042930 AAATCCCCTCCGCCTCCT 59.957 61.111 0.00 0.00 0.00 3.69
642 674 1.709994 ATCAAATCCCCTCCGCCTCC 61.710 60.000 0.00 0.00 0.00 4.30
643 675 0.183731 AATCAAATCCCCTCCGCCTC 59.816 55.000 0.00 0.00 0.00 4.70
644 676 0.106519 CAATCAAATCCCCTCCGCCT 60.107 55.000 0.00 0.00 0.00 5.52
645 677 0.106719 TCAATCAAATCCCCTCCGCC 60.107 55.000 0.00 0.00 0.00 6.13
646 678 1.025041 GTCAATCAAATCCCCTCCGC 58.975 55.000 0.00 0.00 0.00 5.54
647 679 2.717639 AGTCAATCAAATCCCCTCCG 57.282 50.000 0.00 0.00 0.00 4.63
683 724 1.151668 CAACGCCAGGAGAGAAACAG 58.848 55.000 0.00 0.00 0.00 3.16
782 824 1.335964 GGTTTCTGGCGAGGCTTTTTC 60.336 52.381 0.00 0.00 0.00 2.29
783 825 0.673985 GGTTTCTGGCGAGGCTTTTT 59.326 50.000 0.00 0.00 0.00 1.94
878 920 3.137687 GCTAGAGAGAGCTGGCCC 58.862 66.667 0.00 0.00 39.50 5.80
898 940 3.691342 TCCCGGGTCAAGTCAGCG 61.691 66.667 22.86 0.00 0.00 5.18
932 974 0.250513 AAGATCCACAGGCGAACTCC 59.749 55.000 0.00 0.00 0.00 3.85
952 994 3.118738 GGACGAATGAGCTTCCTTTCCTA 60.119 47.826 0.00 0.00 0.00 2.94
971 1013 0.614979 TACCTCCCAGCTGACAGGAC 60.615 60.000 28.46 0.00 0.00 3.85
1078 1126 2.256306 ACCAAAATTAGGGGGCAAGTG 58.744 47.619 2.32 0.00 0.00 3.16
1096 1144 9.880064 GTAGAAACTGAAAAATACAGAGAAACC 57.120 33.333 0.00 0.00 38.55 3.27
1101 1236 8.778358 AGCAAGTAGAAACTGAAAAATACAGAG 58.222 33.333 0.00 0.00 38.55 3.35
1103 1238 8.017946 GGAGCAAGTAGAAACTGAAAAATACAG 58.982 37.037 0.00 0.00 40.68 2.74
1111 1246 3.646162 TCAGGGAGCAAGTAGAAACTGAA 59.354 43.478 0.00 0.00 35.62 3.02
1157 1295 5.538849 ACGAATAACCAAAACAACCCAAT 57.461 34.783 0.00 0.00 0.00 3.16
1163 1301 6.991531 ACTACCAGTACGAATAACCAAAACAA 59.008 34.615 0.00 0.00 0.00 2.83
1190 1334 6.232581 TCAACACAAACCAAATCCAAGAAT 57.767 33.333 0.00 0.00 0.00 2.40
1218 1362 3.000727 CCAGACAAGGTTACCATCGAAC 58.999 50.000 3.51 0.00 0.00 3.95
1219 1363 2.027561 CCCAGACAAGGTTACCATCGAA 60.028 50.000 3.51 0.00 0.00 3.71
1220 1364 1.553248 CCCAGACAAGGTTACCATCGA 59.447 52.381 3.51 0.00 0.00 3.59
1221 1365 1.406887 CCCCAGACAAGGTTACCATCG 60.407 57.143 3.51 0.00 0.00 3.84
1223 1367 0.331616 GCCCCAGACAAGGTTACCAT 59.668 55.000 3.51 0.00 0.00 3.55
1224 1368 1.063070 TGCCCCAGACAAGGTTACCA 61.063 55.000 3.51 0.00 0.00 3.25
1225 1369 0.111639 TTGCCCCAGACAAGGTTACC 59.888 55.000 0.00 0.00 0.00 2.85
1226 1370 1.989706 TTTGCCCCAGACAAGGTTAC 58.010 50.000 0.00 0.00 0.00 2.50
1227 1371 2.757894 TTTTGCCCCAGACAAGGTTA 57.242 45.000 0.00 0.00 0.00 2.85
1228 1372 2.101640 ATTTTGCCCCAGACAAGGTT 57.898 45.000 0.00 0.00 0.00 3.50
1232 1376 2.402564 TCCAAATTTTGCCCCAGACAA 58.597 42.857 3.50 0.00 0.00 3.18
1246 1391 6.971726 AGATGCACAACATGATATCCAAAT 57.028 33.333 0.00 0.00 39.84 2.32
1255 1400 5.308014 AGAAGTGTAAGATGCACAACATGA 58.692 37.500 0.00 0.00 39.84 3.07
1262 1410 7.331934 TGACAGAAATAGAAGTGTAAGATGCAC 59.668 37.037 0.00 0.00 37.13 4.57
1284 1432 9.252962 GTAACAAAGTAGCTAAAACTAGTGACA 57.747 33.333 0.00 0.00 0.00 3.58
1297 1445 3.071023 TGCACCAGAGTAACAAAGTAGCT 59.929 43.478 0.00 0.00 0.00 3.32
1298 1446 3.186613 GTGCACCAGAGTAACAAAGTAGC 59.813 47.826 5.22 0.00 0.00 3.58
1309 1458 2.031163 GCGAAGGTGCACCAGAGT 59.969 61.111 36.39 18.95 38.89 3.24
1346 2351 4.623932 TGCTATGCTTACCCTGATAAGG 57.376 45.455 0.00 0.00 33.48 2.69
1426 2439 5.761234 ACTTTAGTTTCATTTGCTACCGTGA 59.239 36.000 0.00 0.00 0.00 4.35
1428 2441 6.628919 AACTTTAGTTTCATTTGCTACCGT 57.371 33.333 0.00 0.00 33.93 4.83
1461 2474 4.654091 GCTCTCTGCTATCTGAAACTCT 57.346 45.455 0.00 0.00 38.95 3.24
1568 2581 3.474600 GATGGATCTGATGACCCAACAG 58.525 50.000 0.00 0.00 35.94 3.16
1576 2589 4.442052 GGTCACTTTCGATGGATCTGATGA 60.442 45.833 0.00 0.00 0.00 2.92
1872 2885 2.647683 TCACAGCAACAACCATACCA 57.352 45.000 0.00 0.00 0.00 3.25
1955 2968 9.314133 AGCCAGAGGAAAGTAGAAAAATATTTT 57.686 29.630 7.64 7.64 0.00 1.82
1956 2969 8.885693 AGCCAGAGGAAAGTAGAAAAATATTT 57.114 30.769 0.00 0.00 0.00 1.40
1961 2974 8.706322 AAAATAGCCAGAGGAAAGTAGAAAAA 57.294 30.769 0.00 0.00 0.00 1.94
2005 3018 2.616510 CCTCCGTCTGAGCAGGAAAATT 60.617 50.000 0.00 0.00 39.98 1.82
2220 3233 6.854496 TTGGTTACTTGATAGTTGACACAC 57.146 37.500 0.00 0.00 35.78 3.82
2498 3511 5.514204 CGCTAATCCAAAATCTGAAAGCTTG 59.486 40.000 0.00 0.00 0.00 4.01
2690 3703 6.009589 ACCCAACATCAACATCTATTGTCAA 58.990 36.000 0.00 0.00 37.68 3.18
2697 3710 5.485353 AGAGAAGACCCAACATCAACATCTA 59.515 40.000 0.00 0.00 0.00 1.98
2698 3711 4.288105 AGAGAAGACCCAACATCAACATCT 59.712 41.667 0.00 0.00 0.00 2.90
2719 3733 7.396339 TCAACAGAGGTTTAGCTAATACAGAGA 59.604 37.037 7.08 0.00 34.21 3.10
2739 3753 4.718940 AGGCCGGAAAATAATTCAACAG 57.281 40.909 5.05 0.00 0.00 3.16
2740 3754 6.591750 TTTAGGCCGGAAAATAATTCAACA 57.408 33.333 5.05 0.00 0.00 3.33
2780 3805 0.326264 GGGCTTCACCATGACTCTGT 59.674 55.000 0.00 0.00 42.05 3.41
2781 3806 0.617413 AGGGCTTCACCATGACTCTG 59.383 55.000 0.00 0.00 42.05 3.35
2782 3807 2.254152 TAGGGCTTCACCATGACTCT 57.746 50.000 0.00 0.00 42.05 3.24
2783 3808 3.567478 AATAGGGCTTCACCATGACTC 57.433 47.619 0.00 0.00 42.05 3.36
2784 3809 3.010584 ACAAATAGGGCTTCACCATGACT 59.989 43.478 0.00 0.00 42.05 3.41
2785 3810 3.356290 ACAAATAGGGCTTCACCATGAC 58.644 45.455 0.00 0.00 42.05 3.06
2786 3811 3.737559 ACAAATAGGGCTTCACCATGA 57.262 42.857 0.00 0.00 42.05 3.07
2787 3812 4.806640 AAACAAATAGGGCTTCACCATG 57.193 40.909 0.00 0.00 42.05 3.66
2788 3813 6.496911 ACTTTAAACAAATAGGGCTTCACCAT 59.503 34.615 0.00 0.00 42.05 3.55
2789 3814 5.836358 ACTTTAAACAAATAGGGCTTCACCA 59.164 36.000 0.00 0.00 42.05 4.17
2790 3815 6.340962 ACTTTAAACAAATAGGGCTTCACC 57.659 37.500 0.00 0.00 37.93 4.02
2874 3899 0.738975 TGCGTTGACTATCGAGGGAG 59.261 55.000 0.00 0.00 0.00 4.30
2880 3905 0.370273 GGCAAGTGCGTTGACTATCG 59.630 55.000 2.88 0.00 41.61 2.92
2891 3916 2.099756 AGACAAAACAGAAGGCAAGTGC 59.900 45.455 0.00 0.00 41.14 4.40
2974 4000 6.434340 GGAATAAAGTGGAGTGGAACATTTCT 59.566 38.462 0.00 0.00 44.52 2.52
3105 4181 2.678190 GCAGAGAGGCGACCTGTAAATT 60.678 50.000 2.98 0.00 31.76 1.82
3109 4185 0.898326 TTGCAGAGAGGCGACCTGTA 60.898 55.000 2.98 0.00 31.76 2.74
3127 4203 0.969894 AGCTGTAGACGTCTGCCTTT 59.030 50.000 28.12 11.21 0.00 3.11
3187 4263 1.671742 GGGCTTCGACTTGTCCAGA 59.328 57.895 0.00 0.00 0.00 3.86
3199 4275 1.596477 CTGCTCTATGCCGGGCTTC 60.596 63.158 21.46 2.52 42.00 3.86
3205 4281 1.683917 ACTAGGTTCTGCTCTATGCCG 59.316 52.381 0.00 0.00 42.00 5.69
3250 4326 0.038159 GGTACAGTCTGCGCTTGTCT 60.038 55.000 9.73 1.74 0.00 3.41
3262 4338 1.334160 TGTCCATGACACGGTACAGT 58.666 50.000 0.00 0.00 37.67 3.55
3428 4504 1.447838 CAACCTGCGGCGACACTAT 60.448 57.895 12.98 0.00 0.00 2.12
3704 4780 5.055812 GGCTTGGTGAAAAACAATTCATCA 58.944 37.500 0.00 0.00 46.00 3.07
3795 4871 8.218338 ACAAATCATCCAGTTTCTATCATGTC 57.782 34.615 0.00 0.00 0.00 3.06
3796 4872 8.464404 CAACAAATCATCCAGTTTCTATCATGT 58.536 33.333 0.00 0.00 0.00 3.21
3797 4873 8.464404 ACAACAAATCATCCAGTTTCTATCATG 58.536 33.333 0.00 0.00 0.00 3.07
3798 4874 8.585471 ACAACAAATCATCCAGTTTCTATCAT 57.415 30.769 0.00 0.00 0.00 2.45
3799 4875 8.298854 CAACAACAAATCATCCAGTTTCTATCA 58.701 33.333 0.00 0.00 0.00 2.15
3800 4876 8.514594 TCAACAACAAATCATCCAGTTTCTATC 58.485 33.333 0.00 0.00 0.00 2.08
3801 4877 8.299570 GTCAACAACAAATCATCCAGTTTCTAT 58.700 33.333 0.00 0.00 0.00 1.98
3802 4878 7.284261 TGTCAACAACAAATCATCCAGTTTCTA 59.716 33.333 0.00 0.00 34.03 2.10
3803 4879 6.096705 TGTCAACAACAAATCATCCAGTTTCT 59.903 34.615 0.00 0.00 34.03 2.52
3806 4882 5.850557 TGTCAACAACAAATCATCCAGTT 57.149 34.783 0.00 0.00 34.03 3.16
3817 4893 7.416817 CACAGTTTCTATCATGTCAACAACAA 58.583 34.615 0.00 0.00 42.37 2.83
3818 4894 6.017192 CCACAGTTTCTATCATGTCAACAACA 60.017 38.462 0.00 0.00 43.51 3.33
3819 4895 6.204688 TCCACAGTTTCTATCATGTCAACAAC 59.795 38.462 0.00 0.00 0.00 3.32
3848 4924 1.202915 TGACAAGCCTGGAAATGCTCA 60.203 47.619 0.00 0.00 36.66 4.26
3947 5023 4.579340 CCTGAGAAATATGCAGCTGTGATT 59.421 41.667 16.64 9.56 0.00 2.57
3948 5024 4.135306 CCTGAGAAATATGCAGCTGTGAT 58.865 43.478 16.64 10.39 0.00 3.06
4109 5188 5.068234 TCACTAAACCCAAGAGACATACG 57.932 43.478 0.00 0.00 0.00 3.06
4215 5294 3.317993 TCGAGAAATGAGACACACTGTGA 59.682 43.478 16.30 0.00 36.96 3.58
4216 5295 3.426859 GTCGAGAAATGAGACACACTGTG 59.573 47.826 7.68 7.68 39.75 3.66
4372 5451 2.005370 TGACCAACTTACTCCCGAGT 57.995 50.000 2.41 2.41 45.02 4.18
4463 5542 4.362279 TGCAATGTTTTTGCTGAGTTCTC 58.638 39.130 11.18 0.00 45.13 2.87
4464 5543 4.142093 ACTGCAATGTTTTTGCTGAGTTCT 60.142 37.500 19.57 0.00 45.13 3.01
4465 5544 4.026310 CACTGCAATGTTTTTGCTGAGTTC 60.026 41.667 19.57 0.00 45.13 3.01
4466 5545 3.866910 CACTGCAATGTTTTTGCTGAGTT 59.133 39.130 19.57 0.22 45.13 3.01
4467 5546 3.450578 CACTGCAATGTTTTTGCTGAGT 58.549 40.909 19.57 9.85 45.13 3.41
4468 5547 2.798283 CCACTGCAATGTTTTTGCTGAG 59.202 45.455 19.57 13.34 45.13 3.35
4469 5548 2.168106 ACCACTGCAATGTTTTTGCTGA 59.832 40.909 19.57 0.00 45.13 4.26
4470 5549 2.553086 ACCACTGCAATGTTTTTGCTG 58.447 42.857 13.44 13.44 45.13 4.41
4471 5550 2.937799 CAACCACTGCAATGTTTTTGCT 59.062 40.909 11.18 0.00 45.13 3.91
4472 5551 2.677337 ACAACCACTGCAATGTTTTTGC 59.323 40.909 3.44 3.44 45.11 3.68
4473 5552 4.026968 CGTACAACCACTGCAATGTTTTTG 60.027 41.667 0.00 0.00 0.00 2.44
4474 5553 4.109050 CGTACAACCACTGCAATGTTTTT 58.891 39.130 0.00 0.00 0.00 1.94
4475 5554 3.378742 TCGTACAACCACTGCAATGTTTT 59.621 39.130 0.00 0.00 0.00 2.43
4476 5555 2.946329 TCGTACAACCACTGCAATGTTT 59.054 40.909 0.00 0.00 0.00 2.83
4477 5556 2.566913 TCGTACAACCACTGCAATGTT 58.433 42.857 0.00 0.00 0.00 2.71
4478 5557 2.248280 TCGTACAACCACTGCAATGT 57.752 45.000 0.00 0.00 0.00 2.71
4479 5558 3.063452 GGTATCGTACAACCACTGCAATG 59.937 47.826 4.57 0.00 35.73 2.82
4480 5559 3.267483 GGTATCGTACAACCACTGCAAT 58.733 45.455 4.57 0.00 35.73 3.56
4481 5560 2.613474 GGGTATCGTACAACCACTGCAA 60.613 50.000 10.29 0.00 37.51 4.08
4482 5561 1.066716 GGGTATCGTACAACCACTGCA 60.067 52.381 10.29 0.00 37.51 4.41
4483 5562 1.648504 GGGTATCGTACAACCACTGC 58.351 55.000 10.29 0.00 37.51 4.40
4484 5563 1.134610 GGGGGTATCGTACAACCACTG 60.135 57.143 10.24 0.00 39.29 3.66
4485 5564 1.197812 GGGGGTATCGTACAACCACT 58.802 55.000 10.24 0.00 39.29 4.00
4486 5565 0.903942 TGGGGGTATCGTACAACCAC 59.096 55.000 10.29 6.97 38.54 4.16
4487 5566 0.903942 GTGGGGGTATCGTACAACCA 59.096 55.000 10.29 0.00 37.51 3.67
4488 5567 0.179103 CGTGGGGGTATCGTACAACC 60.179 60.000 0.00 0.00 34.85 3.77
4489 5568 0.817013 TCGTGGGGGTATCGTACAAC 59.183 55.000 0.00 0.00 0.00 3.32
4490 5569 1.409790 CATCGTGGGGGTATCGTACAA 59.590 52.381 0.00 0.00 0.00 2.41
4491 5570 1.034356 CATCGTGGGGGTATCGTACA 58.966 55.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.