Multiple sequence alignment - TraesCS6D01G270700

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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 TraesCS6D01G270700 chr6D 100.000 3023 0 0 1 3023 380365587 380368609 0.000000e+00 5583.0
1 TraesCS6D01G270700 chr6D 92.707 2276 102 18 670 2928 380254571 380256799 0.000000e+00 3225.0
2 TraesCS6D01G270700 chr6D 89.938 1123 101 7 942 2055 380177548 380178667 0.000000e+00 1437.0
3 TraesCS6D01G270700 chr6B 92.888 1631 83 11 670 2300 566039281 566037684 0.000000e+00 2338.0
4 TraesCS6D01G270700 chr6B 95.383 1213 49 3 1 1208 566028885 566027675 0.000000e+00 1923.0
5 TraesCS6D01G270700 chr6B 95.545 1010 44 1 1203 2212 566027192 566026184 0.000000e+00 1615.0
6 TraesCS6D01G270700 chr6B 90.357 1120 96 6 945 2055 566122444 566121328 0.000000e+00 1459.0
7 TraesCS6D01G270700 chr6B 89.385 650 30 10 2297 2928 566034288 566033660 0.000000e+00 782.0
8 TraesCS6D01G270700 chr6B 91.481 270 23 0 2657 2926 565708220 565707951 3.680000e-99 372.0
9 TraesCS6D01G270700 chr6A 95.759 1297 55 0 821 2117 520650537 520649241 0.000000e+00 2091.0
10 TraesCS6D01G270700 chr6A 89.707 1127 101 9 946 2061 520670613 520669491 0.000000e+00 1424.0
11 TraesCS6D01G270700 chr6A 83.836 365 27 8 2300 2653 520622191 520621848 4.860000e-83 318.0
12 TraesCS6D01G270700 chr6A 91.489 188 15 1 2657 2844 520621728 520621542 1.080000e-64 257.0
13 TraesCS6D01G270700 chr7B 87.480 623 78 0 5 627 300134445 300133823 0.000000e+00 719.0
14 TraesCS6D01G270700 chr7B 90.625 96 8 1 2929 3023 111899935 111899840 3.160000e-25 126.0
15 TraesCS6D01G270700 chr1B 87.040 625 77 4 5 627 272835563 272836185 0.000000e+00 702.0
16 TraesCS6D01G270700 chr1B 85.106 94 13 1 2931 3023 453769017 453769110 8.920000e-16 95.3
17 TraesCS6D01G270700 chr2D 86.783 628 77 6 1 626 242048577 242049200 0.000000e+00 695.0
18 TraesCS6D01G270700 chr2A 87.055 618 75 5 7 622 414425626 414426240 0.000000e+00 693.0
19 TraesCS6D01G270700 chr2A 86.548 617 74 9 7 618 297047990 297048602 0.000000e+00 671.0
20 TraesCS6D01G270700 chr2A 86.905 84 10 1 2929 3011 138901881 138901964 3.210000e-15 93.5
21 TraesCS6D01G270700 chr7D 86.817 622 74 7 1 618 259382932 259383549 0.000000e+00 688.0
22 TraesCS6D01G270700 chr3D 86.356 623 79 3 1 618 234800138 234800759 0.000000e+00 675.0
23 TraesCS6D01G270700 chr4D 85.918 632 79 9 1 627 207560712 207561338 0.000000e+00 665.0
24 TraesCS6D01G270700 chr5D 94.681 94 4 1 2931 3023 507614179 507614272 8.730000e-31 145.0
25 TraesCS6D01G270700 chr3A 89.247 93 9 1 2932 3023 700039209 700039117 6.850000e-22 115.0
26 TraesCS6D01G270700 chr7A 88.421 95 10 1 2930 3023 69717601 69717695 2.460000e-21 113.0
27 TraesCS6D01G270700 chr3B 84.615 91 14 0 1555 1645 684617269 684617359 1.150000e-14 91.6
28 TraesCS6D01G270700 chrUn 84.375 64 9 1 1175 1237 24657914 24657851 9.050000e-06 62.1
29 TraesCS6D01G270700 chr1D 97.059 34 1 0 1184 1217 72498134 72498167 1.170000e-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 TraesCS6D01G270700 chr6D 380365587 380368609 3022 False 5583.0 5583 100.0000 1 3023 1 chr6D.!!$F3 3022
1 TraesCS6D01G270700 chr6D 380254571 380256799 2228 False 3225.0 3225 92.7070 670 2928 1 chr6D.!!$F2 2258
2 TraesCS6D01G270700 chr6D 380177548 380178667 1119 False 1437.0 1437 89.9380 942 2055 1 chr6D.!!$F1 1113
3 TraesCS6D01G270700 chr6B 566026184 566028885 2701 True 1769.0 1923 95.4640 1 2212 2 chr6B.!!$R3 2211
4 TraesCS6D01G270700 chr6B 566033660 566039281 5621 True 1560.0 2338 91.1365 670 2928 2 chr6B.!!$R4 2258
5 TraesCS6D01G270700 chr6B 566121328 566122444 1116 True 1459.0 1459 90.3570 945 2055 1 chr6B.!!$R2 1110
6 TraesCS6D01G270700 chr6A 520649241 520650537 1296 True 2091.0 2091 95.7590 821 2117 1 chr6A.!!$R1 1296
7 TraesCS6D01G270700 chr6A 520669491 520670613 1122 True 1424.0 1424 89.7070 946 2061 1 chr6A.!!$R2 1115
8 TraesCS6D01G270700 chr6A 520621542 520622191 649 True 287.5 318 87.6625 2300 2844 2 chr6A.!!$R3 544
9 TraesCS6D01G270700 chr7B 300133823 300134445 622 True 719.0 719 87.4800 5 627 1 chr7B.!!$R2 622
10 TraesCS6D01G270700 chr1B 272835563 272836185 622 False 702.0 702 87.0400 5 627 1 chr1B.!!$F1 622
11 TraesCS6D01G270700 chr2D 242048577 242049200 623 False 695.0 695 86.7830 1 626 1 chr2D.!!$F1 625
12 TraesCS6D01G270700 chr2A 414425626 414426240 614 False 693.0 693 87.0550 7 622 1 chr2A.!!$F3 615
13 TraesCS6D01G270700 chr2A 297047990 297048602 612 False 671.0 671 86.5480 7 618 1 chr2A.!!$F2 611
14 TraesCS6D01G270700 chr7D 259382932 259383549 617 False 688.0 688 86.8170 1 618 1 chr7D.!!$F1 617
15 TraesCS6D01G270700 chr3D 234800138 234800759 621 False 675.0 675 86.3560 1 618 1 chr3D.!!$F1 617
16 TraesCS6D01G270700 chr4D 207560712 207561338 626 False 665.0 665 85.9180 1 627 1 chr4D.!!$F1 626

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
585 594 0.745845 AAGGAGCAAGCGCAATCGAT 60.746 50.0 11.47 0.0 42.27 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 6346 0.938008 GTGCGCCCTAATTGTAGAGC 59.062 55.0 4.18 0.0 0.0 4.09 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
237 239 6.808212 GCTACAACAACAATGCATACAAGATT 59.192 34.615 0.00 0.00 0.00 2.40
243 245 8.054152 ACAACAATGCATACAAGATTGACATA 57.946 30.769 0.00 0.00 32.47 2.29
248 250 4.881273 TGCATACAAGATTGACATACCACC 59.119 41.667 0.00 0.00 0.00 4.61
331 333 3.181449 TGAGGTTTTCGATCCAAGGTCAA 60.181 43.478 0.00 0.00 0.00 3.18
541 550 6.116126 GGAGAAACTTTGCATACTCAGGTAT 58.884 40.000 0.00 0.00 39.02 2.73
585 594 0.745845 AAGGAGCAAGCGCAATCGAT 60.746 50.000 11.47 0.00 42.27 3.59
640 649 4.526650 AGAGGACAAGGAGAGAAGAAAGAC 59.473 45.833 0.00 0.00 0.00 3.01
655 664 2.464157 AAGACGGAGAAGCAAAGGAG 57.536 50.000 0.00 0.00 0.00 3.69
811 820 8.454106 AGTCAATATTGTCAGTGCACTATTTTC 58.546 33.333 21.20 9.34 0.00 2.29
824 838 5.769662 TGCACTATTTTCTTTGACAGGTCAT 59.230 36.000 2.52 0.00 39.64 3.06
891 905 4.248058 CAATCAAAACCCAAATGCTCTCC 58.752 43.478 0.00 0.00 0.00 3.71
984 1000 4.637534 TCAGTCTATGCAAAATCTCAAGCC 59.362 41.667 0.00 0.00 0.00 4.35
1008 1024 2.481104 GCTATATCTCGAGATGGCAGCC 60.481 54.545 33.22 18.74 36.05 4.85
1068 1084 0.310232 GACGCTACATACTCCCGGTC 59.690 60.000 0.00 0.00 0.00 4.79
2117 2630 4.986659 GCGTCAGTAAAGTTCTTCCAAGTA 59.013 41.667 0.00 0.00 0.00 2.24
2118 2631 5.118817 GCGTCAGTAAAGTTCTTCCAAGTAG 59.881 44.000 0.00 0.00 0.00 2.57
2231 2745 1.143305 GACATTATCAGCGCTGCGAT 58.857 50.000 32.44 22.97 0.00 4.58
2262 2776 9.958234 TTATTTCGTCAATTTCAAGATTTGTCA 57.042 25.926 0.00 0.00 0.00 3.58
2286 2800 4.756502 CTCAGTCTCTTCTCATGCATTCA 58.243 43.478 0.00 0.00 0.00 2.57
2346 6259 6.294731 GCAATTCTGGTTCATAAGAGTGGTTT 60.295 38.462 0.00 0.00 0.00 3.27
2348 6261 7.839680 ATTCTGGTTCATAAGAGTGGTTTTT 57.160 32.000 0.00 0.00 0.00 1.94
2416 6346 1.661480 CACATGCACACCCCAACAG 59.339 57.895 0.00 0.00 0.00 3.16
2518 6448 1.063492 TGTGGGCCTATCCGAAGACTA 60.063 52.381 4.53 0.00 34.94 2.59
2519 6449 1.340568 GTGGGCCTATCCGAAGACTAC 59.659 57.143 4.53 0.00 34.94 2.73
2520 6450 0.597072 GGGCCTATCCGAAGACTACG 59.403 60.000 0.84 0.00 34.94 3.51
2521 6451 1.316651 GGCCTATCCGAAGACTACGT 58.683 55.000 0.00 0.00 0.00 3.57
2522 6452 1.266446 GGCCTATCCGAAGACTACGTC 59.734 57.143 0.00 0.00 0.00 4.34
2523 6453 1.266446 GCCTATCCGAAGACTACGTCC 59.734 57.143 0.00 0.00 32.18 4.79
2524 6454 2.569059 CCTATCCGAAGACTACGTCCA 58.431 52.381 0.00 0.00 32.18 4.02
2525 6455 3.147629 CCTATCCGAAGACTACGTCCAT 58.852 50.000 0.00 0.00 32.18 3.41
2526 6456 4.321718 CCTATCCGAAGACTACGTCCATA 58.678 47.826 0.00 0.00 32.18 2.74
2527 6457 4.942483 CCTATCCGAAGACTACGTCCATAT 59.058 45.833 0.00 0.00 32.18 1.78
2528 6458 4.768130 ATCCGAAGACTACGTCCATATG 57.232 45.455 0.00 0.00 32.18 1.78
2529 6459 2.882761 TCCGAAGACTACGTCCATATGG 59.117 50.000 16.25 16.25 32.18 2.74
2530 6460 2.621998 CCGAAGACTACGTCCATATGGT 59.378 50.000 21.28 5.10 36.34 3.55
2531 6461 3.550233 CCGAAGACTACGTCCATATGGTG 60.550 52.174 21.28 16.67 36.34 4.17
2532 6462 3.066342 CGAAGACTACGTCCATATGGTGT 59.934 47.826 21.28 20.98 36.34 4.16
2533 6463 4.274214 CGAAGACTACGTCCATATGGTGTA 59.726 45.833 21.28 20.97 36.34 2.90
2534 6464 5.048921 CGAAGACTACGTCCATATGGTGTAT 60.049 44.000 21.28 13.68 36.34 2.29
2535 6465 6.148315 CGAAGACTACGTCCATATGGTGTATA 59.852 42.308 21.28 9.08 36.34 1.47
2536 6466 7.308169 CGAAGACTACGTCCATATGGTGTATAA 60.308 40.741 21.28 6.23 36.34 0.98
2742 6788 7.438160 GGCATAGCAACAAAATAAAGGATAACC 59.562 37.037 0.00 0.00 0.00 2.85
2930 6976 8.749841 TGATGAAAACAACATTATTTTACCCG 57.250 30.769 0.00 0.00 0.00 5.28
2931 6977 8.577296 TGATGAAAACAACATTATTTTACCCGA 58.423 29.630 0.00 0.00 0.00 5.14
2932 6978 9.413048 GATGAAAACAACATTATTTTACCCGAA 57.587 29.630 0.00 0.00 0.00 4.30
2933 6979 9.765795 ATGAAAACAACATTATTTTACCCGAAA 57.234 25.926 0.00 0.00 0.00 3.46
2934 6980 9.595823 TGAAAACAACATTATTTTACCCGAAAA 57.404 25.926 0.00 0.00 41.24 2.29
2936 6982 7.646446 AACAACATTATTTTACCCGAAAAGC 57.354 32.000 0.00 0.00 40.34 3.51
2937 6983 6.988522 ACAACATTATTTTACCCGAAAAGCT 58.011 32.000 0.00 0.00 40.34 3.74
2938 6984 7.088272 ACAACATTATTTTACCCGAAAAGCTC 58.912 34.615 0.00 0.00 40.34 4.09
2939 6985 6.203808 ACATTATTTTACCCGAAAAGCTCC 57.796 37.500 0.00 0.00 40.34 4.70
2940 6986 5.949952 ACATTATTTTACCCGAAAAGCTCCT 59.050 36.000 0.00 0.00 40.34 3.69
2941 6987 6.436218 ACATTATTTTACCCGAAAAGCTCCTT 59.564 34.615 0.00 0.00 40.34 3.36
2942 6988 4.783764 ATTTTACCCGAAAAGCTCCTTG 57.216 40.909 0.00 0.00 40.34 3.61
2943 6989 2.194201 TTACCCGAAAAGCTCCTTGG 57.806 50.000 0.00 0.00 0.00 3.61
2944 6990 1.061546 TACCCGAAAAGCTCCTTGGT 58.938 50.000 0.00 0.00 0.00 3.67
2945 6991 0.537371 ACCCGAAAAGCTCCTTGGTG 60.537 55.000 0.00 0.00 0.00 4.17
2946 6992 1.581447 CCGAAAAGCTCCTTGGTGC 59.419 57.895 5.65 5.65 0.00 5.01
2947 6993 1.172180 CCGAAAAGCTCCTTGGTGCA 61.172 55.000 14.87 0.00 0.00 4.57
2948 6994 0.040067 CGAAAAGCTCCTTGGTGCAC 60.040 55.000 8.80 8.80 0.00 4.57
2949 6995 0.040067 GAAAAGCTCCTTGGTGCACG 60.040 55.000 11.45 0.00 0.00 5.34
2950 6996 1.455383 AAAAGCTCCTTGGTGCACGG 61.455 55.000 11.45 6.85 0.00 4.94
2953 6999 4.988598 CTCCTTGGTGCACGGCGT 62.989 66.667 6.77 6.77 0.00 5.68
2954 7000 4.980805 TCCTTGGTGCACGGCGTC 62.981 66.667 10.85 6.01 0.00 5.19
2955 7001 4.988598 CCTTGGTGCACGGCGTCT 62.989 66.667 10.85 0.00 0.00 4.18
2956 7002 2.048597 CTTGGTGCACGGCGTCTA 60.049 61.111 10.85 0.00 0.00 2.59
2957 7003 2.048597 TTGGTGCACGGCGTCTAG 60.049 61.111 10.85 0.00 0.00 2.43
2958 7004 2.765250 CTTGGTGCACGGCGTCTAGT 62.765 60.000 10.85 0.00 0.00 2.57
2959 7005 2.809601 GGTGCACGGCGTCTAGTG 60.810 66.667 10.85 0.00 41.01 2.74
2960 7006 2.809601 GTGCACGGCGTCTAGTGG 60.810 66.667 10.85 0.00 38.68 4.00
2961 7007 3.299977 TGCACGGCGTCTAGTGGT 61.300 61.111 10.85 0.00 38.68 4.16
2962 7008 1.972752 TGCACGGCGTCTAGTGGTA 60.973 57.895 10.85 0.00 38.68 3.25
2963 7009 1.317431 TGCACGGCGTCTAGTGGTAT 61.317 55.000 10.85 0.00 38.68 2.73
2964 7010 0.870307 GCACGGCGTCTAGTGGTATG 60.870 60.000 10.85 0.00 38.68 2.39
2965 7011 0.870307 CACGGCGTCTAGTGGTATGC 60.870 60.000 10.85 0.00 34.93 3.14
2966 7012 1.035932 ACGGCGTCTAGTGGTATGCT 61.036 55.000 6.77 0.00 0.00 3.79
2967 7013 0.102481 CGGCGTCTAGTGGTATGCTT 59.898 55.000 0.00 0.00 0.00 3.91
2968 7014 1.335810 CGGCGTCTAGTGGTATGCTTA 59.664 52.381 0.00 0.00 0.00 3.09
2969 7015 2.030185 CGGCGTCTAGTGGTATGCTTAT 60.030 50.000 0.00 0.00 0.00 1.73
2970 7016 3.576648 GGCGTCTAGTGGTATGCTTATC 58.423 50.000 0.00 0.00 0.00 1.75
2971 7017 3.235195 GCGTCTAGTGGTATGCTTATCG 58.765 50.000 0.00 0.00 0.00 2.92
2972 7018 3.822996 CGTCTAGTGGTATGCTTATCGG 58.177 50.000 0.00 0.00 0.00 4.18
2973 7019 3.576648 GTCTAGTGGTATGCTTATCGGC 58.423 50.000 0.00 0.00 0.00 5.54
2974 7020 3.005472 GTCTAGTGGTATGCTTATCGGCA 59.995 47.826 0.00 0.00 46.63 5.69
2975 7021 2.240493 AGTGGTATGCTTATCGGCAC 57.760 50.000 0.00 0.00 45.36 5.01
2976 7022 1.202651 AGTGGTATGCTTATCGGCACC 60.203 52.381 0.00 0.00 45.36 5.01
2977 7023 0.833949 TGGTATGCTTATCGGCACCA 59.166 50.000 0.00 0.00 45.36 4.17
2978 7024 1.419762 TGGTATGCTTATCGGCACCAT 59.580 47.619 0.00 0.00 45.36 3.55
2979 7025 2.158682 TGGTATGCTTATCGGCACCATT 60.159 45.455 0.00 0.00 45.36 3.16
2980 7026 2.484264 GGTATGCTTATCGGCACCATTC 59.516 50.000 0.00 0.00 45.36 2.67
2981 7027 1.229428 ATGCTTATCGGCACCATTCG 58.771 50.000 0.00 0.00 45.36 3.34
2982 7028 0.107897 TGCTTATCGGCACCATTCGT 60.108 50.000 0.00 0.00 37.29 3.85
2983 7029 0.582005 GCTTATCGGCACCATTCGTC 59.418 55.000 0.00 0.00 0.00 4.20
2984 7030 1.806623 GCTTATCGGCACCATTCGTCT 60.807 52.381 0.00 0.00 0.00 4.18
2985 7031 1.860950 CTTATCGGCACCATTCGTCTG 59.139 52.381 0.00 0.00 0.00 3.51
2986 7032 0.529773 TATCGGCACCATTCGTCTGC 60.530 55.000 0.00 0.00 0.00 4.26
2987 7033 2.520465 ATCGGCACCATTCGTCTGCA 62.520 55.000 0.00 0.00 32.20 4.41
2988 7034 2.108514 CGGCACCATTCGTCTGCAT 61.109 57.895 0.00 0.00 32.20 3.96
2989 7035 1.430632 GGCACCATTCGTCTGCATG 59.569 57.895 0.00 0.00 32.20 4.06
2990 7036 1.308069 GGCACCATTCGTCTGCATGT 61.308 55.000 0.00 0.00 32.20 3.21
2991 7037 0.179181 GCACCATTCGTCTGCATGTG 60.179 55.000 0.00 0.00 0.00 3.21
2992 7038 0.448990 CACCATTCGTCTGCATGTGG 59.551 55.000 0.00 0.00 0.00 4.17
2993 7039 0.324614 ACCATTCGTCTGCATGTGGA 59.675 50.000 2.04 0.00 0.00 4.02
2994 7040 1.065199 ACCATTCGTCTGCATGTGGAT 60.065 47.619 2.04 0.00 0.00 3.41
2995 7041 1.600957 CCATTCGTCTGCATGTGGATC 59.399 52.381 0.00 0.00 0.00 3.36
2996 7042 1.259770 CATTCGTCTGCATGTGGATCG 59.740 52.381 0.00 1.18 0.00 3.69
2997 7043 0.246360 TTCGTCTGCATGTGGATCGT 59.754 50.000 0.00 0.00 0.00 3.73
2998 7044 0.179137 TCGTCTGCATGTGGATCGTC 60.179 55.000 0.00 0.00 0.00 4.20
2999 7045 0.458370 CGTCTGCATGTGGATCGTCA 60.458 55.000 0.00 0.00 0.00 4.35
3000 7046 1.803998 CGTCTGCATGTGGATCGTCAT 60.804 52.381 0.00 0.00 0.00 3.06
3001 7047 1.863454 GTCTGCATGTGGATCGTCATC 59.137 52.381 0.00 0.00 0.00 2.92
3002 7048 1.758862 TCTGCATGTGGATCGTCATCT 59.241 47.619 0.00 0.00 0.00 2.90
3003 7049 2.133553 CTGCATGTGGATCGTCATCTC 58.866 52.381 0.00 0.00 0.00 2.75
3004 7050 1.135046 GCATGTGGATCGTCATCTCG 58.865 55.000 0.00 0.00 0.00 4.04
3005 7051 1.135046 CATGTGGATCGTCATCTCGC 58.865 55.000 0.00 0.00 0.00 5.03
3006 7052 0.746659 ATGTGGATCGTCATCTCGCA 59.253 50.000 0.00 0.00 0.00 5.10
3007 7053 0.746659 TGTGGATCGTCATCTCGCAT 59.253 50.000 0.00 0.00 0.00 4.73
3008 7054 1.136891 TGTGGATCGTCATCTCGCATT 59.863 47.619 0.00 0.00 0.00 3.56
3009 7055 2.205074 GTGGATCGTCATCTCGCATTT 58.795 47.619 0.00 0.00 0.00 2.32
3010 7056 3.181480 TGTGGATCGTCATCTCGCATTTA 60.181 43.478 0.00 0.00 0.00 1.40
3011 7057 3.182572 GTGGATCGTCATCTCGCATTTAC 59.817 47.826 0.00 0.00 0.00 2.01
3012 7058 2.405357 GGATCGTCATCTCGCATTTACG 59.595 50.000 0.00 0.00 0.00 3.18
3013 7059 2.836479 TCGTCATCTCGCATTTACGA 57.164 45.000 0.00 0.00 40.36 3.43
3014 7060 3.139603 TCGTCATCTCGCATTTACGAA 57.860 42.857 0.00 0.00 42.39 3.85
3015 7061 2.850060 TCGTCATCTCGCATTTACGAAC 59.150 45.455 0.00 0.00 42.39 3.95
3016 7062 2.034842 CGTCATCTCGCATTTACGAACC 60.035 50.000 0.00 0.00 42.39 3.62
3017 7063 2.927477 GTCATCTCGCATTTACGAACCA 59.073 45.455 0.00 0.00 42.39 3.67
3018 7064 3.369756 GTCATCTCGCATTTACGAACCAA 59.630 43.478 0.00 0.00 42.39 3.67
3019 7065 4.034048 GTCATCTCGCATTTACGAACCAAT 59.966 41.667 0.00 0.00 42.39 3.16
3020 7066 4.033932 TCATCTCGCATTTACGAACCAATG 59.966 41.667 0.00 0.00 42.39 2.82
3021 7067 3.331150 TCTCGCATTTACGAACCAATGT 58.669 40.909 0.00 0.00 42.39 2.71
3022 7068 4.496360 TCTCGCATTTACGAACCAATGTA 58.504 39.130 0.00 0.00 42.39 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 239 1.344065 ACTTGTCGGGTGGTATGTCA 58.656 50.000 0.00 0.00 0.00 3.58
243 245 0.249573 CGTTGTACTTGTCGGGTGGT 60.250 55.000 0.00 0.00 0.00 4.16
248 250 0.782384 GCTCACGTTGTACTTGTCGG 59.218 55.000 0.00 0.00 0.00 4.79
385 394 1.214673 ACTAGGTGAGCCGATGGTAGA 59.785 52.381 0.00 0.00 40.50 2.59
395 404 0.674895 CCACTTGGCACTAGGTGAGC 60.675 60.000 1.57 0.00 35.23 4.26
541 550 1.126488 CTCCATGGCTAGCTCCTTGA 58.874 55.000 15.72 4.67 34.28 3.02
585 594 1.153568 CCGCGATTGCTTCTCTCCA 60.154 57.895 8.23 0.00 39.65 3.86
640 649 2.232452 TCTTCTCTCCTTTGCTTCTCCG 59.768 50.000 0.00 0.00 0.00 4.63
811 820 6.765036 AGATATAGTGCAATGACCTGTCAAAG 59.235 38.462 3.79 1.44 43.58 2.77
891 905 4.633126 TCAAGAGAAGCATCTTTGGATTCG 59.367 41.667 11.33 0.00 37.43 3.34
984 1000 4.422840 CTGCCATCTCGAGATATAGCTTG 58.577 47.826 29.37 22.23 32.63 4.01
1008 1024 2.587194 CCATTGGAGAGCGGCTCG 60.587 66.667 23.15 8.66 44.91 5.03
1040 1056 0.973496 TATGTAGCGTCCAGGCACCA 60.973 55.000 0.00 0.00 34.64 4.17
1068 1084 0.035458 AAGAAGACGGCCTCTTGTGG 59.965 55.000 18.52 0.00 39.53 4.17
1344 1857 3.736224 AGGACCTCCTCGCCGGTA 61.736 66.667 1.90 0.00 44.77 4.02
1546 2059 2.218603 GTTCACGTTCATCAACCCACT 58.781 47.619 0.00 0.00 0.00 4.00
1552 2065 3.395639 GGTAGTGGTTCACGTTCATCAA 58.604 45.455 0.00 0.00 39.64 2.57
1711 2224 1.671054 CCACGTCCACCCACATCAC 60.671 63.158 0.00 0.00 0.00 3.06
1967 2480 2.125673 CACCCTCGGCAAGGTACG 60.126 66.667 3.90 0.00 44.56 3.67
2262 2776 2.177734 TGCATGAGAAGAGACTGAGCT 58.822 47.619 0.00 0.00 0.00 4.09
2315 6228 8.370182 ACTCTTATGAACCAGAATTGCAAAAAT 58.630 29.630 1.71 0.00 0.00 1.82
2352 6265 9.705290 TTGCATTAATAAAGAACCCTTTTTCTC 57.295 29.630 0.00 0.00 42.26 2.87
2380 6300 5.691305 GCATGTGCTTTTGTATTCACTTGAA 59.309 36.000 10.08 0.00 37.00 2.69
2416 6346 0.938008 GTGCGCCCTAATTGTAGAGC 59.062 55.000 4.18 0.00 0.00 4.09
2518 6448 5.266733 ACGTTTATACACCATATGGACGT 57.733 39.130 28.77 25.18 38.94 4.34
2519 6449 4.682860 GGACGTTTATACACCATATGGACG 59.317 45.833 28.77 24.56 38.94 4.79
2520 6450 5.603596 TGGACGTTTATACACCATATGGAC 58.396 41.667 28.77 12.59 38.94 4.02
2521 6451 5.873146 TGGACGTTTATACACCATATGGA 57.127 39.130 28.77 6.40 38.94 3.41
2524 6454 7.822334 CACCATATGGACGTTTATACACCATAT 59.178 37.037 28.77 13.96 44.97 1.78
2525 6455 7.156000 CACCATATGGACGTTTATACACCATA 58.844 38.462 28.77 11.10 42.23 2.74
2526 6456 5.995282 CACCATATGGACGTTTATACACCAT 59.005 40.000 28.77 7.70 41.10 3.55
2527 6457 5.104859 ACACCATATGGACGTTTATACACCA 60.105 40.000 28.77 0.00 38.94 4.17
2528 6458 5.362263 ACACCATATGGACGTTTATACACC 58.638 41.667 28.77 0.00 38.94 4.16
2529 6459 9.695526 TTATACACCATATGGACGTTTATACAC 57.304 33.333 28.77 0.00 38.94 2.90
2532 6462 9.709495 GGTTTATACACCATATGGACGTTTATA 57.291 33.333 28.77 15.34 36.73 0.98
2533 6463 8.434392 AGGTTTATACACCATATGGACGTTTAT 58.566 33.333 28.77 16.21 39.62 1.40
2534 6464 7.794041 AGGTTTATACACCATATGGACGTTTA 58.206 34.615 28.77 18.43 39.62 2.01
2535 6465 6.655930 AGGTTTATACACCATATGGACGTTT 58.344 36.000 28.77 19.33 39.62 3.60
2536 6466 6.243216 AGGTTTATACACCATATGGACGTT 57.757 37.500 28.77 15.46 39.62 3.99
2742 6788 3.763360 TGCTTGTTGATTATGGTTGGAGG 59.237 43.478 0.00 0.00 0.00 4.30
2908 6954 9.595823 TTTTCGGGTAAAATAATGTTGTTTTCA 57.404 25.926 3.91 0.00 34.17 2.69
2928 6974 1.172180 TGCACCAAGGAGCTTTTCGG 61.172 55.000 9.84 0.00 33.00 4.30
2929 6975 0.040067 GTGCACCAAGGAGCTTTTCG 60.040 55.000 5.22 0.00 33.00 3.46
2930 6976 0.040067 CGTGCACCAAGGAGCTTTTC 60.040 55.000 12.15 0.00 33.00 2.29
2931 6977 1.455383 CCGTGCACCAAGGAGCTTTT 61.455 55.000 12.15 0.00 35.05 2.27
2932 6978 1.898574 CCGTGCACCAAGGAGCTTT 60.899 57.895 12.15 0.00 35.05 3.51
2933 6979 2.281761 CCGTGCACCAAGGAGCTT 60.282 61.111 12.15 0.00 35.05 3.74
2936 6982 4.988598 ACGCCGTGCACCAAGGAG 62.989 66.667 12.15 11.23 38.51 3.69
2937 6983 4.980805 GACGCCGTGCACCAAGGA 62.981 66.667 12.15 0.00 35.05 3.36
2938 6984 3.583276 TAGACGCCGTGCACCAAGG 62.583 63.158 12.15 8.15 36.14 3.61
2939 6985 2.048597 TAGACGCCGTGCACCAAG 60.049 61.111 12.15 4.87 0.00 3.61
2940 6986 2.048597 CTAGACGCCGTGCACCAA 60.049 61.111 12.15 0.00 0.00 3.67
2941 6987 3.299977 ACTAGACGCCGTGCACCA 61.300 61.111 12.15 0.00 0.00 4.17
2942 6988 2.809601 CACTAGACGCCGTGCACC 60.810 66.667 12.15 0.00 0.00 5.01
2943 6989 2.203972 TACCACTAGACGCCGTGCAC 62.204 60.000 6.82 6.82 0.00 4.57
2944 6990 1.317431 ATACCACTAGACGCCGTGCA 61.317 55.000 0.00 0.00 0.00 4.57
2945 6991 0.870307 CATACCACTAGACGCCGTGC 60.870 60.000 0.00 0.00 0.00 5.34
2946 6992 0.870307 GCATACCACTAGACGCCGTG 60.870 60.000 0.00 0.00 0.00 4.94
2947 6993 1.035932 AGCATACCACTAGACGCCGT 61.036 55.000 0.00 0.00 0.00 5.68
2948 6994 0.102481 AAGCATACCACTAGACGCCG 59.898 55.000 0.00 0.00 0.00 6.46
2949 6995 3.576648 GATAAGCATACCACTAGACGCC 58.423 50.000 0.00 0.00 0.00 5.68
2950 6996 3.235195 CGATAAGCATACCACTAGACGC 58.765 50.000 0.00 0.00 0.00 5.19
2951 6997 3.822996 CCGATAAGCATACCACTAGACG 58.177 50.000 0.00 0.00 0.00 4.18
2952 6998 3.005472 TGCCGATAAGCATACCACTAGAC 59.995 47.826 0.00 0.00 38.00 2.59
2953 6999 3.005472 GTGCCGATAAGCATACCACTAGA 59.995 47.826 0.00 0.00 46.24 2.43
2954 7000 3.318017 GTGCCGATAAGCATACCACTAG 58.682 50.000 0.00 0.00 46.24 2.57
2955 7001 2.036733 GGTGCCGATAAGCATACCACTA 59.963 50.000 0.00 0.00 46.24 2.74
2956 7002 1.202651 GGTGCCGATAAGCATACCACT 60.203 52.381 0.00 0.00 46.24 4.00
2957 7003 1.226746 GGTGCCGATAAGCATACCAC 58.773 55.000 0.00 0.00 46.24 4.16
2958 7004 0.833949 TGGTGCCGATAAGCATACCA 59.166 50.000 0.00 0.00 46.24 3.25
2959 7005 2.185004 ATGGTGCCGATAAGCATACC 57.815 50.000 0.00 0.00 46.24 2.73
2960 7006 2.157668 CGAATGGTGCCGATAAGCATAC 59.842 50.000 0.00 0.00 46.24 2.39
2961 7007 2.224185 ACGAATGGTGCCGATAAGCATA 60.224 45.455 0.00 0.00 46.24 3.14
2962 7008 1.229428 CGAATGGTGCCGATAAGCAT 58.771 50.000 0.00 0.00 46.24 3.79
2963 7009 0.107897 ACGAATGGTGCCGATAAGCA 60.108 50.000 0.00 0.00 41.46 3.91
2964 7010 0.582005 GACGAATGGTGCCGATAAGC 59.418 55.000 0.00 0.00 0.00 3.09
2965 7011 1.860950 CAGACGAATGGTGCCGATAAG 59.139 52.381 0.00 0.00 0.00 1.73
2966 7012 1.934589 CAGACGAATGGTGCCGATAA 58.065 50.000 0.00 0.00 0.00 1.75
2967 7013 0.529773 GCAGACGAATGGTGCCGATA 60.530 55.000 0.00 0.00 0.00 2.92
2968 7014 1.815421 GCAGACGAATGGTGCCGAT 60.815 57.895 0.00 0.00 0.00 4.18
2969 7015 2.434185 GCAGACGAATGGTGCCGA 60.434 61.111 0.00 0.00 0.00 5.54
2970 7016 2.108514 ATGCAGACGAATGGTGCCG 61.109 57.895 0.00 0.00 36.31 5.69
2971 7017 1.308069 ACATGCAGACGAATGGTGCC 61.308 55.000 0.00 0.00 36.31 5.01
2972 7018 0.179181 CACATGCAGACGAATGGTGC 60.179 55.000 0.00 0.00 37.73 5.01
2973 7019 0.448990 CCACATGCAGACGAATGGTG 59.551 55.000 0.00 0.00 0.00 4.17
2974 7020 0.324614 TCCACATGCAGACGAATGGT 59.675 50.000 0.00 0.00 0.00 3.55
2975 7021 1.600957 GATCCACATGCAGACGAATGG 59.399 52.381 0.00 0.00 0.00 3.16
2976 7022 1.259770 CGATCCACATGCAGACGAATG 59.740 52.381 0.00 0.00 0.00 2.67
2977 7023 1.134699 ACGATCCACATGCAGACGAAT 60.135 47.619 0.00 0.00 0.00 3.34
2978 7024 0.246360 ACGATCCACATGCAGACGAA 59.754 50.000 0.00 0.00 0.00 3.85
2979 7025 0.179137 GACGATCCACATGCAGACGA 60.179 55.000 0.00 0.00 0.00 4.20
2980 7026 0.458370 TGACGATCCACATGCAGACG 60.458 55.000 0.00 0.00 0.00 4.18
2981 7027 1.863454 GATGACGATCCACATGCAGAC 59.137 52.381 0.00 0.00 0.00 3.51
2982 7028 1.758862 AGATGACGATCCACATGCAGA 59.241 47.619 0.00 0.00 0.00 4.26
2983 7029 2.133553 GAGATGACGATCCACATGCAG 58.866 52.381 0.00 0.00 0.00 4.41
2984 7030 1.536709 CGAGATGACGATCCACATGCA 60.537 52.381 0.00 0.00 35.09 3.96
2985 7031 1.135046 CGAGATGACGATCCACATGC 58.865 55.000 0.00 0.00 35.09 4.06
2986 7032 1.135046 GCGAGATGACGATCCACATG 58.865 55.000 4.37 0.00 35.09 3.21
2987 7033 0.746659 TGCGAGATGACGATCCACAT 59.253 50.000 0.00 0.00 35.09 3.21
2988 7034 0.746659 ATGCGAGATGACGATCCACA 59.253 50.000 0.00 0.00 35.09 4.17
2989 7035 1.858091 AATGCGAGATGACGATCCAC 58.142 50.000 0.00 0.00 35.09 4.02
2990 7036 2.602257 AAATGCGAGATGACGATCCA 57.398 45.000 0.00 0.00 35.09 3.41
2991 7037 2.405357 CGTAAATGCGAGATGACGATCC 59.595 50.000 0.00 0.00 35.09 3.36
2992 7038 3.297472 TCGTAAATGCGAGATGACGATC 58.703 45.455 0.00 0.00 34.66 3.69
2993 7039 3.349488 TCGTAAATGCGAGATGACGAT 57.651 42.857 0.00 0.00 34.66 3.73
2994 7040 2.836479 TCGTAAATGCGAGATGACGA 57.164 45.000 0.00 0.00 37.01 4.20
2995 7041 2.034842 GGTTCGTAAATGCGAGATGACG 60.035 50.000 0.00 0.00 42.10 4.35
2996 7042 2.927477 TGGTTCGTAAATGCGAGATGAC 59.073 45.455 0.00 0.00 42.10 3.06
2997 7043 3.239587 TGGTTCGTAAATGCGAGATGA 57.760 42.857 0.00 0.00 42.10 2.92
2998 7044 4.201812 ACATTGGTTCGTAAATGCGAGATG 60.202 41.667 0.00 1.78 42.10 2.90
2999 7045 3.938963 ACATTGGTTCGTAAATGCGAGAT 59.061 39.130 0.00 0.00 42.10 2.75
3000 7046 3.331150 ACATTGGTTCGTAAATGCGAGA 58.669 40.909 0.00 0.00 42.10 4.04
3001 7047 3.740044 ACATTGGTTCGTAAATGCGAG 57.260 42.857 0.00 0.00 42.10 5.03


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

AutoCloner maintained by Alex Coulton.