Multiple sequence alignment - TraesCS4A01G070800

Loading Multiple Alignment...

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 TraesCS4A01G070800 chr4A 100.000 3800 0 0 1 3800 68140278 68144077 0.000000e+00 7018.0
1 TraesCS4A01G070800 chr4B 88.402 3242 175 78 10 3148 474377399 474380542 0.000000e+00 3718.0
2 TraesCS4A01G070800 chr4B 86.330 673 56 22 3150 3798 474380571 474381231 0.000000e+00 701.0
3 TraesCS4A01G070800 chr4B 74.517 569 96 30 1302 1835 494692231 494691677 6.440000e-48 202.0
4 TraesCS4A01G070800 chr4D 89.405 3077 144 50 10 2981 386829996 386832995 0.000000e+00 3709.0
5 TraesCS4A01G070800 chr4D 86.028 866 70 25 2966 3798 386833141 386833988 0.000000e+00 881.0
6 TraesCS4A01G070800 chr2D 82.296 723 94 27 1157 1853 131777776 131777062 2.530000e-166 595.0
7 TraesCS4A01G070800 chr2D 92.308 39 2 1 2691 2728 131776486 131776448 2.000000e-03 54.7
8 TraesCS4A01G070800 chr2B 81.906 724 95 26 1157 1853 186311856 186312570 2.540000e-161 579.0
9 TraesCS4A01G070800 chr2B 88.070 285 32 2 1570 1853 185776816 185776533 1.690000e-88 337.0
10 TraesCS4A01G070800 chr2B 92.308 39 3 0 2688 2726 186313105 186313143 5.300000e-04 56.5
11 TraesCS4A01G070800 chr2B 96.875 32 1 0 2691 2722 185775988 185775957 2.000000e-03 54.7
12 TraesCS4A01G070800 chr2A 81.717 722 100 25 1157 1853 138827332 138826618 1.180000e-159 573.0
13 TraesCS4A01G070800 chr2A 100.000 29 0 0 2691 2719 138826121 138826093 2.000000e-03 54.7
14 TraesCS4A01G070800 chr5D 76.364 660 117 26 1207 1836 520910025 520910675 6.130000e-83 318.0
15 TraesCS4A01G070800 chr5A 75.261 671 120 29 1207 1836 649441485 649442150 1.040000e-70 278.0
16 TraesCS4A01G070800 chr5B 74.265 680 120 34 1207 1836 656925821 656926495 6.350000e-58 235.0
17 TraesCS4A01G070800 chr7D 72.321 560 107 36 1302 1836 547458020 547457484 8.570000e-27 132.0
18 TraesCS4A01G070800 chr7A 71.658 561 112 33 1301 1836 631365246 631365784 1.120000e-20 111.0
19 TraesCS4A01G070800 chr7B 71.429 560 115 34 1301 1836 590500947 590500409 5.190000e-19 106.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G070800 chr4A 68140278 68144077 3799 False 7018.00 7018 100.0000 1 3800 1 chr4A.!!$F1 3799
1 TraesCS4A01G070800 chr4B 474377399 474381231 3832 False 2209.50 3718 87.3660 10 3798 2 chr4B.!!$F1 3788
2 TraesCS4A01G070800 chr4B 494691677 494692231 554 True 202.00 202 74.5170 1302 1835 1 chr4B.!!$R1 533
3 TraesCS4A01G070800 chr4D 386829996 386833988 3992 False 2295.00 3709 87.7165 10 3798 2 chr4D.!!$F1 3788
4 TraesCS4A01G070800 chr2D 131776448 131777776 1328 True 324.85 595 87.3020 1157 2728 2 chr2D.!!$R1 1571
5 TraesCS4A01G070800 chr2B 186311856 186313143 1287 False 317.75 579 87.1070 1157 2726 2 chr2B.!!$F1 1569
6 TraesCS4A01G070800 chr2A 138826093 138827332 1239 True 313.85 573 90.8585 1157 2719 2 chr2A.!!$R1 1562
7 TraesCS4A01G070800 chr5D 520910025 520910675 650 False 318.00 318 76.3640 1207 1836 1 chr5D.!!$F1 629
8 TraesCS4A01G070800 chr5A 649441485 649442150 665 False 278.00 278 75.2610 1207 1836 1 chr5A.!!$F1 629
9 TraesCS4A01G070800 chr5B 656925821 656926495 674 False 235.00 235 74.2650 1207 1836 1 chr5B.!!$F1 629

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
965 1021 0.036388 CGCCATTAGTGACCACCAGT 60.036 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2829 3242 0.034756 TTGGATGGACGGATATGGCG 59.965 55.0 0.0 0.0 0.0 5.69 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
25 26 3.598019 ACGGGCGAGTTATTCAGTTTA 57.402 42.857 0.00 0.00 0.00 2.01
32 33 5.234543 GGCGAGTTATTCAGTTTATCAGTCC 59.765 44.000 0.00 0.00 0.00 3.85
41 42 8.785329 ATTCAGTTTATCAGTCCTCTCTTTTC 57.215 34.615 0.00 0.00 0.00 2.29
57 61 6.888430 TCTCTTTTCGCACTGAATTAACTTC 58.112 36.000 0.00 0.00 36.22 3.01
65 69 5.164012 CGCACTGAATTAACTTCACTCTCTG 60.164 44.000 0.00 0.00 38.97 3.35
105 109 1.076533 CACACATACGCCACCGAGAC 61.077 60.000 0.00 0.00 38.29 3.36
118 122 1.177401 CCGAGACATGACAGTCCAGA 58.823 55.000 0.00 0.00 39.34 3.86
149 153 4.878439 AGCACACAGTACGTCATTTAAGA 58.122 39.130 0.00 0.00 0.00 2.10
154 158 7.063456 CACACAGTACGTCATTTAAGAAACAG 58.937 38.462 0.00 0.00 0.00 3.16
163 167 6.575201 CGTCATTTAAGAAACAGCACTCTTTC 59.425 38.462 0.00 0.00 33.89 2.62
170 174 5.075493 AGAAACAGCACTCTTTCATTGGAT 58.925 37.500 2.01 0.00 0.00 3.41
171 175 6.240894 AGAAACAGCACTCTTTCATTGGATA 58.759 36.000 2.01 0.00 0.00 2.59
177 181 4.513318 GCACTCTTTCATTGGATAGTAGCC 59.487 45.833 0.00 0.00 0.00 3.93
249 253 3.257393 ACATTTACTGCTCGCTTCAGAG 58.743 45.455 5.61 0.00 41.03 3.35
295 311 2.427232 GCACATGCAAGAGCTTTCAA 57.573 45.000 4.03 0.00 42.74 2.69
297 313 3.125316 GCACATGCAAGAGCTTTCAAAA 58.875 40.909 4.03 0.00 42.74 2.44
315 331 4.932799 TCAAAAATCAGCTTGGATGCATTG 59.067 37.500 0.00 0.00 34.99 2.82
321 348 0.179119 GCTTGGATGCATTGAGCCAC 60.179 55.000 15.14 0.00 44.83 5.01
344 371 4.553323 CAAGATTTTCAGCAAGGTTCCTG 58.447 43.478 0.00 0.00 0.00 3.86
345 372 2.560105 AGATTTTCAGCAAGGTTCCTGC 59.440 45.455 0.00 0.00 0.00 4.85
346 373 1.774110 TTTTCAGCAAGGTTCCTGCA 58.226 45.000 12.86 0.00 0.00 4.41
351 378 0.963962 AGCAAGGTTCCTGCACATTG 59.036 50.000 12.86 0.00 40.62 2.82
370 397 7.380602 GCACATTGCATTATCTTATCCTTCAAC 59.619 37.037 0.00 0.00 44.26 3.18
421 448 1.384502 CCATCCTGGCCCTCCACTA 60.385 63.158 0.00 0.00 37.47 2.74
438 465 4.391830 TCCACTAAAATCTCATCGCACAAC 59.608 41.667 0.00 0.00 0.00 3.32
450 477 4.038080 CACAACCCGCGCCTTTCC 62.038 66.667 0.00 0.00 0.00 3.13
469 496 0.532862 CGCCAGAAGATACGGCCATT 60.533 55.000 2.24 0.00 43.17 3.16
470 497 1.230324 GCCAGAAGATACGGCCATTC 58.770 55.000 2.24 0.00 40.07 2.67
506 535 3.429547 CCCGATACAATCCTGATCGATCC 60.430 52.174 22.31 5.50 44.04 3.36
507 536 3.430008 CGATACAATCCTGATCGATCCG 58.570 50.000 22.31 15.91 44.04 4.18
581 623 7.559590 AGAAAAGGTTATCTGAATCCAATCG 57.440 36.000 0.00 0.00 0.00 3.34
596 638 0.748005 AATCGAGCCCCATTCCGTTG 60.748 55.000 0.00 0.00 0.00 4.10
611 653 4.806342 TCCGTTGTTTCTTCAGTAAAGC 57.194 40.909 0.00 0.00 34.76 3.51
651 698 2.357517 AGTGAACGGCCGCTCTTG 60.358 61.111 28.58 0.00 0.00 3.02
740 793 2.042404 CTGCCTCTGCCTCTCATCCC 62.042 65.000 0.00 0.00 36.33 3.85
767 820 2.240921 TGATAGTTTATGGGTGGCTGCA 59.759 45.455 0.50 0.00 0.00 4.41
785 838 1.687493 ACCCTGCACCTCTCCTAGC 60.687 63.158 0.00 0.00 0.00 3.42
788 841 1.687146 CTGCACCTCTCCTAGCCCA 60.687 63.158 0.00 0.00 0.00 5.36
799 855 2.430332 CTCCTAGCCCAAGACTTCTCTG 59.570 54.545 0.00 0.00 0.00 3.35
811 867 1.342574 ACTTCTCTGCCTCCCTCTACC 60.343 57.143 0.00 0.00 0.00 3.18
828 884 1.251527 ACCGTCTCCCACTGCTGTAG 61.252 60.000 0.00 0.00 0.00 2.74
831 887 1.132643 CGTCTCCCACTGCTGTAGTAC 59.867 57.143 0.00 0.00 37.60 2.73
832 888 2.448453 GTCTCCCACTGCTGTAGTACT 58.552 52.381 0.00 0.00 37.60 2.73
834 890 1.751924 CTCCCACTGCTGTAGTACTCC 59.248 57.143 0.00 0.00 37.60 3.85
835 891 1.358103 TCCCACTGCTGTAGTACTCCT 59.642 52.381 0.00 0.00 37.60 3.69
836 892 2.579400 TCCCACTGCTGTAGTACTCCTA 59.421 50.000 0.00 0.00 37.60 2.94
837 893 2.688958 CCCACTGCTGTAGTACTCCTAC 59.311 54.545 0.00 0.00 45.36 3.18
838 894 3.622630 CCACTGCTGTAGTACTCCTACT 58.377 50.000 0.00 0.00 45.36 2.57
839 895 4.384978 CCCACTGCTGTAGTACTCCTACTA 60.385 50.000 0.00 0.00 45.36 1.82
840 896 5.191426 CCACTGCTGTAGTACTCCTACTAA 58.809 45.833 0.00 0.00 45.36 2.24
841 897 5.651139 CCACTGCTGTAGTACTCCTACTAAA 59.349 44.000 0.00 0.00 45.36 1.85
842 898 6.404513 CCACTGCTGTAGTACTCCTACTAAAC 60.405 46.154 0.00 0.00 45.36 2.01
858 914 0.249398 AAACTAGTACTGCAGCCGGG 59.751 55.000 15.27 3.17 0.00 5.73
884 940 3.101643 TGGACTGCCAGTACTGATACT 57.898 47.619 24.68 3.69 42.74 2.12
965 1021 0.036388 CGCCATTAGTGACCACCAGT 60.036 55.000 0.00 0.00 0.00 4.00
966 1022 1.453155 GCCATTAGTGACCACCAGTG 58.547 55.000 0.00 0.00 0.00 3.66
986 1042 3.064324 AACCCGAGCTGCATTGCC 61.064 61.111 6.12 0.00 0.00 4.52
1004 1060 1.200948 GCCTCAAGAACAGAACATGGC 59.799 52.381 0.00 0.00 0.00 4.40
1010 1066 2.086869 AGAACAGAACATGGCAATCCG 58.913 47.619 0.00 0.00 34.14 4.18
1014 1070 2.086869 CAGAACATGGCAATCCGAAGT 58.913 47.619 0.00 0.00 34.14 3.01
1050 1106 1.069636 GCGCTGCTTTGTATATGCCTC 60.070 52.381 0.00 0.00 0.00 4.70
1068 1124 3.633235 CCTCAGAGGTAATTCGATCGTG 58.367 50.000 15.94 2.51 0.00 4.35
1116 1172 5.677319 TGTAGGAGGAGTTCTTGTAATGG 57.323 43.478 0.00 0.00 0.00 3.16
1133 1189 4.713824 AATGGTGAGCTGAATTGACATG 57.286 40.909 0.00 0.00 0.00 3.21
1136 1192 2.421424 GGTGAGCTGAATTGACATGGTC 59.579 50.000 0.00 0.00 0.00 4.02
1137 1193 2.421424 GTGAGCTGAATTGACATGGTCC 59.579 50.000 0.00 0.00 0.00 4.46
1868 2033 2.683768 AGGTCCATACTCCTGCCTTAG 58.316 52.381 0.00 0.00 32.29 2.18
2002 2173 2.418334 CGATGATGAGATCGGCATGGAT 60.418 50.000 8.55 0.00 41.29 3.41
2003 2174 2.467566 TGATGAGATCGGCATGGATG 57.532 50.000 8.55 0.00 0.00 3.51
2021 2197 4.709840 CTCTGGTTGGTGCCTGAG 57.290 61.111 4.96 4.96 44.31 3.35
2064 2241 5.237344 ACCTTATCTCGCATACAAAATGCTC 59.763 40.000 8.22 0.00 42.50 4.26
2106 2283 0.947180 TGAGGTGCTTACGAAACGGC 60.947 55.000 0.00 0.00 0.00 5.68
2145 2322 5.118990 CGAGAGGCTTGAAAATGGAAGATA 58.881 41.667 0.00 0.00 0.00 1.98
2199 2381 7.773149 CCAGTATATTAGTGGGTAGTAGATGC 58.227 42.308 1.13 0.00 44.00 3.91
2237 2419 0.036875 AGTGGGTGCTTAGCTTGTCC 59.963 55.000 5.60 3.04 0.00 4.02
2267 2478 2.608988 CCCCCTGTGGCTCTCACT 60.609 66.667 0.00 0.00 46.20 3.41
2353 2573 7.244886 TCTTATCTTGTGATGAAGTCAGGAA 57.755 36.000 0.00 0.00 37.56 3.36
2409 2629 4.499019 CCATGAAACTGCCGTAACACTTTT 60.499 41.667 0.00 0.00 0.00 2.27
2434 2654 1.069775 AGGCGGGAAAGGGTAAAAGA 58.930 50.000 0.00 0.00 0.00 2.52
2467 2689 5.438761 AACAACTTTCAGTGCTGGATTAC 57.561 39.130 0.00 0.00 0.00 1.89
2488 2710 5.740290 ACGTTTCTCCTGATCCTCTTTTA 57.260 39.130 0.00 0.00 0.00 1.52
2495 2719 9.547753 TTTCTCCTGATCCTCTTTTATTATTCG 57.452 33.333 0.00 0.00 0.00 3.34
2497 2721 8.580720 TCTCCTGATCCTCTTTTATTATTCGAG 58.419 37.037 0.00 0.00 0.00 4.04
2498 2722 7.155328 TCCTGATCCTCTTTTATTATTCGAGC 58.845 38.462 0.00 0.00 0.00 5.03
2499 2723 6.931281 CCTGATCCTCTTTTATTATTCGAGCA 59.069 38.462 0.00 0.00 0.00 4.26
2520 2776 3.775661 TTCGCATCTGATCGTGAACTA 57.224 42.857 10.12 0.00 0.00 2.24
2679 3080 2.590092 GGCCAGGGCGTGATACTT 59.410 61.111 9.09 0.00 43.06 2.24
2779 3189 4.180946 CGCCGCTCGCACTACTCT 62.181 66.667 0.00 0.00 37.30 3.24
2820 3233 4.960938 AGCATCACGCCATTATTAGAAGA 58.039 39.130 0.00 0.00 44.04 2.87
2829 3242 5.309638 GCCATTATTAGAAGAGAAGGACCC 58.690 45.833 0.00 0.00 0.00 4.46
2985 3573 1.745489 GCTCGCGGAAAGAATGGGT 60.745 57.895 6.13 0.00 0.00 4.51
2991 3579 0.168128 CGGAAAGAATGGGTCGTTGC 59.832 55.000 0.00 0.00 33.67 4.17
3058 3646 5.380043 AGATCGCCATTGTAAAATCCATCT 58.620 37.500 0.00 0.00 0.00 2.90
3059 3647 5.829924 AGATCGCCATTGTAAAATCCATCTT 59.170 36.000 0.00 0.00 0.00 2.40
3061 3649 6.279513 TCGCCATTGTAAAATCCATCTTTT 57.720 33.333 0.00 0.00 33.17 2.27
3062 3650 6.696411 TCGCCATTGTAAAATCCATCTTTTT 58.304 32.000 0.00 0.00 31.15 1.94
3063 3651 6.811170 TCGCCATTGTAAAATCCATCTTTTTC 59.189 34.615 0.00 0.00 31.15 2.29
3100 3701 2.809601 GCACGGCTGTGGAGTACG 60.810 66.667 26.55 0.00 46.51 3.67
3101 3702 2.959372 CACGGCTGTGGAGTACGA 59.041 61.111 18.43 0.00 42.59 3.43
3102 3703 1.154016 CACGGCTGTGGAGTACGAG 60.154 63.158 18.43 0.00 42.59 4.18
3103 3704 1.602888 ACGGCTGTGGAGTACGAGT 60.603 57.895 0.00 0.00 0.00 4.18
3104 3705 0.321919 ACGGCTGTGGAGTACGAGTA 60.322 55.000 0.00 0.00 0.00 2.59
3105 3706 0.098376 CGGCTGTGGAGTACGAGTAC 59.902 60.000 5.32 5.32 36.35 2.73
3148 3749 7.097192 AGTAGAAAAGATTCTTACACGCATGA 58.903 34.615 0.00 0.00 43.43 3.07
3177 3815 2.268920 CCGCTGCCCAAGAGCTAA 59.731 61.111 0.00 0.00 34.03 3.09
3209 3847 1.386525 TATACCCACTCGCCGTCCAC 61.387 60.000 0.00 0.00 0.00 4.02
3246 3884 4.430908 GCTAGTGGCGAACAAACTATAGT 58.569 43.478 0.00 0.00 0.00 2.12
3247 3885 5.585390 GCTAGTGGCGAACAAACTATAGTA 58.415 41.667 5.65 0.00 0.00 1.82
3248 3886 5.686397 GCTAGTGGCGAACAAACTATAGTAG 59.314 44.000 5.65 4.81 0.00 2.57
3249 3887 5.909621 AGTGGCGAACAAACTATAGTAGA 57.090 39.130 5.65 0.00 0.00 2.59
3250 3888 5.892568 AGTGGCGAACAAACTATAGTAGAG 58.107 41.667 5.65 1.87 0.00 2.43
3251 3889 5.041940 GTGGCGAACAAACTATAGTAGAGG 58.958 45.833 5.65 0.00 0.00 3.69
3252 3890 4.049869 GGCGAACAAACTATAGTAGAGGC 58.950 47.826 5.65 5.55 0.00 4.70
3253 3891 4.202131 GGCGAACAAACTATAGTAGAGGCT 60.202 45.833 5.65 0.00 0.00 4.58
3254 3892 4.977347 GCGAACAAACTATAGTAGAGGCTC 59.023 45.833 6.34 6.34 0.00 4.70
3255 3893 5.450137 GCGAACAAACTATAGTAGAGGCTCA 60.450 44.000 18.26 0.00 0.00 4.26
3256 3894 6.202937 CGAACAAACTATAGTAGAGGCTCAG 58.797 44.000 18.26 6.51 0.00 3.35
3257 3895 6.472686 AACAAACTATAGTAGAGGCTCAGG 57.527 41.667 18.26 1.04 0.00 3.86
3258 3896 4.342665 ACAAACTATAGTAGAGGCTCAGGC 59.657 45.833 18.26 6.09 37.82 4.85
3259 3897 4.463050 AACTATAGTAGAGGCTCAGGCT 57.537 45.455 18.26 0.00 42.48 4.58
3260 3898 5.586155 AACTATAGTAGAGGCTCAGGCTA 57.414 43.478 18.26 14.85 38.98 3.93
3261 3899 5.586155 ACTATAGTAGAGGCTCAGGCTAA 57.414 43.478 18.26 0.00 38.98 3.09
3355 4018 5.862924 AGTTCACATCGTTTCAGTAATGG 57.137 39.130 0.00 0.00 0.00 3.16
3376 4039 2.094762 ACAGGACGTACAAATGCCTC 57.905 50.000 0.00 0.00 0.00 4.70
3401 4064 4.377839 TGTTATCTCTGCTCTGTAGTGC 57.622 45.455 0.00 0.00 35.32 4.40
3412 4075 1.151668 CTGTAGTGCCACAGTGCTTC 58.848 55.000 0.00 0.00 40.89 3.86
3454 4118 3.814842 TCGCTGATTTGCCATAACCATAG 59.185 43.478 0.00 0.00 0.00 2.23
3466 4130 4.502259 CCATAACCATAGCCAGTCAGAGAC 60.502 50.000 0.00 0.00 0.00 3.36
3474 4138 1.735920 CAGTCAGAGACGTGGCAGC 60.736 63.158 0.00 0.00 37.67 5.25
3512 4176 0.457509 CAGTCTAGCTGCCAGACACG 60.458 60.000 25.86 14.86 44.03 4.49
3522 4186 3.607775 GCTGCCAGACACGCATAATAATG 60.608 47.826 0.00 0.00 35.25 1.90
3551 4215 1.028130 TCACCAAACATTTGCTCGCA 58.972 45.000 0.00 0.00 36.86 5.10
3552 4216 1.001487 TCACCAAACATTTGCTCGCAG 60.001 47.619 0.00 0.00 36.86 5.18
3553 4217 0.318955 ACCAAACATTTGCTCGCAGC 60.319 50.000 0.00 1.70 42.82 5.25
3554 4218 0.038892 CCAAACATTTGCTCGCAGCT 60.039 50.000 9.12 0.00 42.97 4.24
3594 4258 6.205658 ACTCAATCAACAGCTAAAAGGAAGAC 59.794 38.462 0.00 0.00 0.00 3.01
3634 4298 2.819595 CCGAGTTGGCGACATGGG 60.820 66.667 7.78 1.09 42.32 4.00
3638 4302 2.359850 GTTGGCGACATGGGCTGA 60.360 61.111 0.00 0.00 42.32 4.26
3642 4306 1.212751 GGCGACATGGGCTGAAAAC 59.787 57.895 10.32 0.00 0.00 2.43
3671 4335 1.069668 ACCACTCCTACCACGACAAAC 59.930 52.381 0.00 0.00 0.00 2.93
3674 4338 1.270147 ACTCCTACCACGACAAACTGC 60.270 52.381 0.00 0.00 0.00 4.40
3773 4450 4.778143 ACCGGCGGACAAGATGCC 62.778 66.667 35.78 0.00 45.39 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.461135 GAATAACTCGCCCGTACCCA 59.539 55.000 0.00 0.00 0.00 4.51
1 2 0.461135 TGAATAACTCGCCCGTACCC 59.539 55.000 0.00 0.00 0.00 3.69
3 4 2.573941 ACTGAATAACTCGCCCGTAC 57.426 50.000 0.00 0.00 0.00 3.67
4 5 3.598019 AAACTGAATAACTCGCCCGTA 57.402 42.857 0.00 0.00 0.00 4.02
5 6 2.467566 AAACTGAATAACTCGCCCGT 57.532 45.000 0.00 0.00 0.00 5.28
7 8 5.116882 ACTGATAAACTGAATAACTCGCCC 58.883 41.667 0.00 0.00 0.00 6.13
8 9 5.234543 GGACTGATAAACTGAATAACTCGCC 59.765 44.000 0.00 0.00 0.00 5.54
16 17 7.547370 CGAAAAGAGAGGACTGATAAACTGAAT 59.453 37.037 0.00 0.00 0.00 2.57
25 26 2.564947 AGTGCGAAAAGAGAGGACTGAT 59.435 45.455 0.00 0.00 35.28 2.90
32 33 6.473397 AGTTAATTCAGTGCGAAAAGAGAG 57.527 37.500 0.00 0.00 37.12 3.20
65 69 0.959372 AGCCTGACTTGCTGATGTGC 60.959 55.000 0.00 0.00 37.76 4.57
105 109 3.743521 TCAGGTTTTCTGGACTGTCATG 58.256 45.455 10.38 1.68 43.53 3.07
118 122 2.612212 CGTACTGTGTGCTTCAGGTTTT 59.388 45.455 0.00 0.00 37.25 2.43
149 153 6.006449 ACTATCCAATGAAAGAGTGCTGTTT 58.994 36.000 0.00 0.00 0.00 2.83
154 158 4.513318 GGCTACTATCCAATGAAAGAGTGC 59.487 45.833 0.00 0.00 0.00 4.40
163 167 2.744202 GGCAATCGGCTACTATCCAATG 59.256 50.000 0.00 0.00 44.01 2.82
177 181 1.331756 GATGGTTAGTGCTGGCAATCG 59.668 52.381 0.00 0.00 0.00 3.34
249 253 0.872388 AATCCGGTTGTTGCTTCGTC 59.128 50.000 0.00 0.00 0.00 4.20
295 311 4.755411 CTCAATGCATCCAAGCTGATTTT 58.245 39.130 0.00 0.00 34.99 1.82
297 313 2.100916 GCTCAATGCATCCAAGCTGATT 59.899 45.455 16.47 0.00 42.31 2.57
315 331 1.888512 TGCTGAAAATCTTGGTGGCTC 59.111 47.619 0.00 0.00 0.00 4.70
321 348 3.575687 AGGAACCTTGCTGAAAATCTTGG 59.424 43.478 0.00 0.00 0.00 3.61
344 371 6.973843 TGAAGGATAAGATAATGCAATGTGC 58.026 36.000 0.00 0.00 45.29 4.57
345 372 8.407832 TGTTGAAGGATAAGATAATGCAATGTG 58.592 33.333 0.00 0.00 0.00 3.21
346 373 8.523915 TGTTGAAGGATAAGATAATGCAATGT 57.476 30.769 0.00 0.00 0.00 2.71
370 397 2.288152 CCGACACTTGTGGGGATTTTTG 60.288 50.000 2.56 0.00 39.82 2.44
421 448 1.468520 CGGGTTGTGCGATGAGATTTT 59.531 47.619 0.00 0.00 0.00 1.82
455 482 2.222027 CTTGGGAATGGCCGTATCTTC 58.778 52.381 0.00 0.00 37.63 2.87
469 496 2.200092 GGGGTTTGGTGCTTGGGA 59.800 61.111 0.00 0.00 0.00 4.37
470 497 3.302344 CGGGGTTTGGTGCTTGGG 61.302 66.667 0.00 0.00 0.00 4.12
506 535 0.953471 TCCCTGCAATTTCCACGACG 60.953 55.000 0.00 0.00 0.00 5.12
507 536 1.068541 GTTCCCTGCAATTTCCACGAC 60.069 52.381 0.00 0.00 0.00 4.34
518 547 1.340991 GGAGGCTAATTGTTCCCTGCA 60.341 52.381 0.00 0.00 36.04 4.41
581 623 0.526211 GAAACAACGGAATGGGGCTC 59.474 55.000 0.00 0.00 0.00 4.70
596 638 4.844267 TGCTTTCGCTTTACTGAAGAAAC 58.156 39.130 0.00 0.00 37.57 2.78
611 653 1.002468 CCGGCCTTTATCATGCTTTCG 60.002 52.381 0.00 0.00 0.00 3.46
651 698 3.055385 TCCATGGCCGTATTTATAGCCTC 60.055 47.826 6.96 0.00 45.94 4.70
740 793 4.520492 GCCACCCATAAACTATCAGGATTG 59.480 45.833 0.00 0.00 0.00 2.67
767 820 1.687493 GCTAGGAGAGGTGCAGGGT 60.687 63.158 0.00 0.00 0.00 4.34
770 823 1.267574 TTGGGCTAGGAGAGGTGCAG 61.268 60.000 0.00 0.00 0.00 4.41
771 824 1.229496 TTGGGCTAGGAGAGGTGCA 60.229 57.895 0.00 0.00 0.00 4.57
772 825 0.978146 TCTTGGGCTAGGAGAGGTGC 60.978 60.000 0.00 0.00 0.00 5.01
773 826 0.827368 GTCTTGGGCTAGGAGAGGTG 59.173 60.000 0.00 0.00 0.00 4.00
774 827 0.713579 AGTCTTGGGCTAGGAGAGGT 59.286 55.000 0.00 0.00 0.00 3.85
775 828 1.760029 GAAGTCTTGGGCTAGGAGAGG 59.240 57.143 0.00 0.00 0.00 3.69
776 829 2.693074 GAGAAGTCTTGGGCTAGGAGAG 59.307 54.545 0.00 0.00 0.00 3.20
777 830 2.313342 AGAGAAGTCTTGGGCTAGGAGA 59.687 50.000 0.00 0.00 0.00 3.71
785 838 0.251634 GGAGGCAGAGAAGTCTTGGG 59.748 60.000 0.00 0.00 0.00 4.12
788 841 1.078656 AGAGGGAGGCAGAGAAGTCTT 59.921 52.381 0.00 0.00 0.00 3.01
799 855 1.829096 GGAGACGGTAGAGGGAGGC 60.829 68.421 0.00 0.00 0.00 4.70
811 867 1.132643 GTACTACAGCAGTGGGAGACG 59.867 57.143 0.00 0.00 38.24 4.18
828 884 7.467131 GCTGCAGTACTAGTTTAGTAGGAGTAC 60.467 44.444 16.64 0.00 41.59 2.73
831 887 5.221087 GGCTGCAGTACTAGTTTAGTAGGAG 60.221 48.000 16.64 0.00 41.59 3.69
832 888 4.643784 GGCTGCAGTACTAGTTTAGTAGGA 59.356 45.833 16.64 0.00 41.59 2.94
834 890 4.497674 CCGGCTGCAGTACTAGTTTAGTAG 60.498 50.000 16.64 1.39 41.59 2.57
835 891 3.379372 CCGGCTGCAGTACTAGTTTAGTA 59.621 47.826 16.64 0.00 40.14 1.82
836 892 2.165845 CCGGCTGCAGTACTAGTTTAGT 59.834 50.000 16.64 0.00 42.68 2.24
837 893 2.481449 CCCGGCTGCAGTACTAGTTTAG 60.481 54.545 16.64 0.00 0.00 1.85
838 894 1.479323 CCCGGCTGCAGTACTAGTTTA 59.521 52.381 16.64 0.00 0.00 2.01
839 895 0.249398 CCCGGCTGCAGTACTAGTTT 59.751 55.000 16.64 0.00 0.00 2.66
840 896 1.614241 CCCCGGCTGCAGTACTAGTT 61.614 60.000 16.64 0.00 0.00 2.24
841 897 2.058595 CCCCGGCTGCAGTACTAGT 61.059 63.158 16.64 0.00 0.00 2.57
842 898 1.614241 AACCCCGGCTGCAGTACTAG 61.614 60.000 16.64 4.64 0.00 2.57
879 935 4.045104 CGCAACCTGTCAGTATCAGTATC 58.955 47.826 0.00 0.00 0.00 2.24
880 936 3.447586 ACGCAACCTGTCAGTATCAGTAT 59.552 43.478 0.00 0.00 0.00 2.12
881 937 2.823747 ACGCAACCTGTCAGTATCAGTA 59.176 45.455 0.00 0.00 0.00 2.74
882 938 1.618837 ACGCAACCTGTCAGTATCAGT 59.381 47.619 0.00 0.00 0.00 3.41
883 939 2.094494 AGACGCAACCTGTCAGTATCAG 60.094 50.000 0.00 0.00 38.83 2.90
884 940 1.893137 AGACGCAACCTGTCAGTATCA 59.107 47.619 0.00 0.00 38.83 2.15
965 1021 3.866379 AATGCAGCTCGGGTTGGCA 62.866 57.895 0.00 0.15 0.00 4.92
966 1022 3.064324 AATGCAGCTCGGGTTGGC 61.064 61.111 0.00 0.00 0.00 4.52
986 1042 4.380233 GGATTGCCATGTTCTGTTCTTGAG 60.380 45.833 0.00 0.00 0.00 3.02
1004 1060 1.721489 CGACGCAAACACTTCGGATTG 60.721 52.381 0.00 0.00 0.00 2.67
1010 1066 0.935196 AAGGACGACGCAAACACTTC 59.065 50.000 0.00 0.00 0.00 3.01
1014 1070 2.876879 CGCAAGGACGACGCAAACA 61.877 57.895 0.00 0.00 34.06 2.83
1050 1106 3.438297 ACCACGATCGAATTACCTCTG 57.562 47.619 24.34 5.83 0.00 3.35
1068 1124 3.025262 ACCTCACTCGATTTCCTCTACC 58.975 50.000 0.00 0.00 0.00 3.18
1116 1172 2.421424 GGACCATGTCAATTCAGCTCAC 59.579 50.000 0.00 0.00 33.68 3.51
1133 1189 1.476488 AGCAAACACAACACAAGGACC 59.524 47.619 0.00 0.00 0.00 4.46
1136 1192 2.270047 CCAAGCAAACACAACACAAGG 58.730 47.619 0.00 0.00 0.00 3.61
1137 1193 2.667481 CACCAAGCAAACACAACACAAG 59.333 45.455 0.00 0.00 0.00 3.16
1166 1222 0.667487 ACGTGAATGTCACTGCTCCG 60.667 55.000 6.80 0.00 44.85 4.63
1172 1228 3.131396 GTTCAGGAACGTGAATGTCACT 58.869 45.455 11.93 0.00 44.85 3.41
1868 2033 3.629398 AGCTAGTGATTAAATGCAGTGGC 59.371 43.478 9.82 9.82 40.80 5.01
2002 2173 2.113774 CAGGCACCAACCAGAGCA 59.886 61.111 0.00 0.00 0.00 4.26
2003 2174 1.673665 CTCAGGCACCAACCAGAGC 60.674 63.158 0.00 0.00 36.66 4.09
2004 2175 1.673665 GCTCAGGCACCAACCAGAG 60.674 63.158 0.00 0.00 44.10 3.35
2005 2176 2.431683 GCTCAGGCACCAACCAGA 59.568 61.111 0.00 0.00 38.54 3.86
2006 2177 2.113774 TGCTCAGGCACCAACCAG 59.886 61.111 0.00 0.00 44.28 4.00
2089 2266 0.949105 CTGCCGTTTCGTAAGCACCT 60.949 55.000 0.00 0.00 37.18 4.00
2090 2267 1.495951 CTGCCGTTTCGTAAGCACC 59.504 57.895 0.00 0.00 37.18 5.01
2106 2283 1.943116 CTCGCTCTCACTGTCCCCTG 61.943 65.000 0.00 0.00 0.00 4.45
2131 2308 7.838884 TCACAATGCATTATCTTCCATTTTCA 58.161 30.769 12.53 0.00 0.00 2.69
2132 2309 8.761497 CATCACAATGCATTATCTTCCATTTTC 58.239 33.333 12.53 0.00 0.00 2.29
2133 2310 8.479689 TCATCACAATGCATTATCTTCCATTTT 58.520 29.630 12.53 0.00 32.58 1.82
2134 2311 8.014070 TCATCACAATGCATTATCTTCCATTT 57.986 30.769 12.53 0.00 32.58 2.32
2135 2312 7.591421 TCATCACAATGCATTATCTTCCATT 57.409 32.000 12.53 0.00 32.58 3.16
2136 2313 7.450323 TGATCATCACAATGCATTATCTTCCAT 59.550 33.333 12.53 0.00 32.58 3.41
2145 2322 4.338400 CCAGACTGATCATCACAATGCATT 59.662 41.667 5.99 5.99 32.58 3.56
2199 2381 5.345702 CCACTAAATGCAACATGAATGAGG 58.654 41.667 0.00 0.00 0.00 3.86
2353 2573 5.813383 CCATCATTCATATGGCCTAGTCTT 58.187 41.667 3.32 0.00 37.67 3.01
2409 2629 4.715523 CCTTTCCCGCCTTCCGCA 62.716 66.667 0.00 0.00 37.30 5.69
2467 2689 8.894768 ATAATAAAAGAGGATCAGGAGAAACG 57.105 34.615 0.00 0.00 37.82 3.60
2488 2710 4.309933 TCAGATGCGAATGCTCGAATAAT 58.690 39.130 0.00 0.00 43.78 1.28
2495 2719 1.191868 CACGATCAGATGCGAATGCTC 59.808 52.381 8.64 0.00 43.34 4.26
2497 2721 1.211743 TCACGATCAGATGCGAATGC 58.788 50.000 8.64 0.00 43.20 3.56
2498 2722 2.862536 AGTTCACGATCAGATGCGAATG 59.137 45.455 8.64 0.27 0.00 2.67
2499 2723 3.170791 AGTTCACGATCAGATGCGAAT 57.829 42.857 8.64 0.00 0.00 3.34
2679 3080 2.121963 AGCCAGGAGTTGTCCCCA 60.122 61.111 0.00 0.00 45.26 4.96
2805 3215 4.991687 GGTCCTTCTCTTCTAATAATGGCG 59.008 45.833 0.00 0.00 0.00 5.69
2806 3216 5.309638 GGGTCCTTCTCTTCTAATAATGGC 58.690 45.833 0.00 0.00 0.00 4.40
2807 3217 5.542779 CGGGTCCTTCTCTTCTAATAATGG 58.457 45.833 0.00 0.00 0.00 3.16
2808 3218 4.991687 GCGGGTCCTTCTCTTCTAATAATG 59.008 45.833 0.00 0.00 0.00 1.90
2811 3224 2.963782 GGCGGGTCCTTCTCTTCTAATA 59.036 50.000 0.00 0.00 0.00 0.98
2813 3226 1.192428 GGCGGGTCCTTCTCTTCTAA 58.808 55.000 0.00 0.00 0.00 2.10
2820 3233 1.472662 CGGATATGGCGGGTCCTTCT 61.473 60.000 0.00 0.00 35.26 2.85
2829 3242 0.034756 TTGGATGGACGGATATGGCG 59.965 55.000 0.00 0.00 0.00 5.69
2867 3280 5.303078 TCTGTTCAGCTTCTAACTTCTCTGT 59.697 40.000 5.29 0.00 0.00 3.41
2883 3302 5.327091 CAAACAGTGTGTTCTTCTGTTCAG 58.673 41.667 9.61 0.00 46.95 3.02
2991 3579 2.433145 ACTCGCCGTGCACATCAG 60.433 61.111 18.64 8.95 0.00 2.90
3058 3646 8.436970 GCAAACTAGAAAAAGGAAAACGAAAAA 58.563 29.630 0.00 0.00 0.00 1.94
3059 3647 7.599245 TGCAAACTAGAAAAAGGAAAACGAAAA 59.401 29.630 0.00 0.00 0.00 2.29
3061 3649 6.528774 GTGCAAACTAGAAAAAGGAAAACGAA 59.471 34.615 0.00 0.00 0.00 3.85
3062 3650 6.031471 GTGCAAACTAGAAAAAGGAAAACGA 58.969 36.000 0.00 0.00 0.00 3.85
3063 3651 5.052633 CGTGCAAACTAGAAAAAGGAAAACG 60.053 40.000 0.00 0.00 0.00 3.60
3177 3815 7.201920 GGCGAGTGGGTATATACAATCATAGAT 60.202 40.741 14.70 0.00 31.72 1.98
3195 3833 2.432628 GAAGTGGACGGCGAGTGG 60.433 66.667 16.62 0.00 0.00 4.00
3209 3847 2.465097 CTAGCGATCGGCCGGAGAAG 62.465 65.000 27.83 13.58 45.17 2.85
3245 3883 2.605837 GGTTTAGCCTGAGCCTCTAC 57.394 55.000 0.00 0.00 41.25 2.59
3256 3894 1.599542 GTGCATCGATCAGGTTTAGCC 59.400 52.381 0.00 0.00 37.58 3.93
3257 3895 2.555199 AGTGCATCGATCAGGTTTAGC 58.445 47.619 0.00 0.00 0.00 3.09
3258 3896 6.703607 AGAATAAGTGCATCGATCAGGTTTAG 59.296 38.462 0.00 0.00 0.00 1.85
3259 3897 6.479990 CAGAATAAGTGCATCGATCAGGTTTA 59.520 38.462 0.00 0.00 0.00 2.01
3260 3898 5.295292 CAGAATAAGTGCATCGATCAGGTTT 59.705 40.000 0.00 0.00 0.00 3.27
3261 3899 4.813161 CAGAATAAGTGCATCGATCAGGTT 59.187 41.667 0.00 0.00 0.00 3.50
3270 3908 4.340381 AGCAAATCCCAGAATAAGTGCATC 59.660 41.667 0.00 0.00 33.21 3.91
3355 4018 2.415512 GAGGCATTTGTACGTCCTGTTC 59.584 50.000 0.00 0.00 0.00 3.18
3372 4035 3.321682 AGAGCAGAGATAACATGAGAGGC 59.678 47.826 0.00 0.00 0.00 4.70
3376 4039 6.207928 CACTACAGAGCAGAGATAACATGAG 58.792 44.000 0.00 0.00 0.00 2.90
3454 4118 2.433318 GCCACGTCTCTGACTGGC 60.433 66.667 18.01 18.01 43.53 4.85
3474 4138 5.070180 AGACTGTCAGTGATAATGGATGGAG 59.930 44.000 11.04 0.00 0.00 3.86
3522 4186 3.665745 ATGTTTGGTGAATGTTCCAGC 57.334 42.857 0.00 0.00 35.05 4.85
3551 4215 3.450096 TGAGTGTCAATCATCAGCTAGCT 59.550 43.478 12.68 12.68 0.00 3.32
3552 4216 3.790091 TGAGTGTCAATCATCAGCTAGC 58.210 45.455 6.62 6.62 0.00 3.42
3594 4258 2.768503 TTACCGGGCCACTCGTTTCG 62.769 60.000 6.32 0.00 0.00 3.46
3618 4282 3.499737 GCCCATGTCGCCAACTCG 61.500 66.667 0.00 0.00 0.00 4.18
3628 4292 3.788227 TCTAGTGTTTTCAGCCCATGT 57.212 42.857 0.00 0.00 0.00 3.21
3634 4298 5.351740 GGAGTGGTATTCTAGTGTTTTCAGC 59.648 44.000 0.00 0.00 0.00 4.26
3638 4302 6.499350 TGGTAGGAGTGGTATTCTAGTGTTTT 59.501 38.462 0.00 0.00 0.00 2.43
3642 4306 4.036498 CGTGGTAGGAGTGGTATTCTAGTG 59.964 50.000 0.00 0.00 0.00 2.74
3671 4335 3.363378 CGCTACTGACTTTTCTTGTGCAG 60.363 47.826 0.00 0.00 0.00 4.41
3674 4338 3.604772 GCACGCTACTGACTTTTCTTGTG 60.605 47.826 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.