Multiple sequence alignment - TraesCS7A01G105100

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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 TraesCS7A01G105100 chr7A 100.000 4845 0 0 1 4845 63780955 63785799 0.000000e+00 8948.0
1 TraesCS7A01G105100 chr7A 81.445 1509 229 38 2779 4251 13833867 13835360 0.000000e+00 1188.0
2 TraesCS7A01G105100 chr7A 81.777 878 146 9 934 1799 13832279 13833154 0.000000e+00 723.0
3 TraesCS7A01G105100 chr7A 77.598 433 68 17 1357 1772 20513330 20512910 8.110000e-58 235.0
4 TraesCS7A01G105100 chr7A 96.825 63 1 1 4314 4375 63785212 63785274 2.390000e-18 104.0
5 TraesCS7A01G105100 chr7A 96.825 63 1 1 4258 4320 63785268 63785329 2.390000e-18 104.0
6 TraesCS7A01G105100 chr7A 76.048 167 22 9 4381 4529 18174342 18174176 2.420000e-08 71.3
7 TraesCS7A01G105100 chr7D 93.670 2654 123 21 1 2625 59465938 59468575 0.000000e+00 3928.0
8 TraesCS7A01G105100 chr7D 96.389 1274 39 2 3148 4420 59469035 59470302 0.000000e+00 2091.0
9 TraesCS7A01G105100 chr7D 81.692 1513 224 40 2776 4251 14592083 14593579 0.000000e+00 1210.0
10 TraesCS7A01G105100 chr7D 98.069 466 8 1 2656 3121 59468572 59469036 0.000000e+00 809.0
11 TraesCS7A01G105100 chr7D 81.385 881 138 19 934 1799 14590501 14591370 0.000000e+00 695.0
12 TraesCS7A01G105100 chr7D 84.505 626 37 30 4258 4845 59470194 59470797 9.100000e-157 564.0
13 TraesCS7A01G105100 chr7D 94.595 333 17 1 212 543 59417998 59418330 9.300000e-142 514.0
14 TraesCS7A01G105100 chr7D 93.355 301 13 4 546 839 59418723 59419023 5.760000e-119 438.0
15 TraesCS7A01G105100 chr7D 84.545 110 10 5 1921 2028 599810441 599810545 8.580000e-18 102.0
16 TraesCS7A01G105100 chr2D 78.728 1368 253 28 2781 4129 2449701 2448353 0.000000e+00 880.0
17 TraesCS7A01G105100 chr2D 85.321 109 11 3 1921 2029 376051415 376051312 1.840000e-19 108.0
18 TraesCS7A01G105100 chr2D 87.500 56 7 0 4376 4431 48392107 48392162 1.130000e-06 65.8
19 TraesCS7A01G105100 chrUn 77.717 1454 263 44 2699 4117 15723004 15724431 0.000000e+00 833.0
20 TraesCS7A01G105100 chrUn 77.369 1467 270 47 2699 4129 15441836 15440396 0.000000e+00 813.0
21 TraesCS7A01G105100 chrUn 77.373 1454 265 47 2699 4117 357011193 357012617 0.000000e+00 804.0
22 TraesCS7A01G105100 chrUn 85.821 670 81 11 2779 3441 335447183 335446521 0.000000e+00 699.0
23 TraesCS7A01G105100 chrUn 77.625 581 95 25 2699 3256 358520110 358519542 2.180000e-83 320.0
24 TraesCS7A01G105100 chrUn 84.259 108 12 3 1921 2028 86734336 86734234 3.090000e-17 100.0
25 TraesCS7A01G105100 chr4A 79.830 1175 191 33 3112 4254 722288448 722287288 0.000000e+00 815.0
26 TraesCS7A01G105100 chr4A 79.746 1101 193 25 3093 4179 722331523 722330439 0.000000e+00 771.0
27 TraesCS7A01G105100 chr4A 84.241 349 49 5 2779 3122 722293090 722292743 7.770000e-88 335.0
28 TraesCS7A01G105100 chr4A 78.605 215 24 17 4380 4589 546623377 546623574 6.590000e-24 122.0
29 TraesCS7A01G105100 chr4A 77.381 168 34 4 2075 2242 722293734 722293571 3.990000e-16 97.1
30 TraesCS7A01G105100 chr3D 79.290 845 151 15 3148 3984 15387850 15387022 1.960000e-158 569.0
31 TraesCS7A01G105100 chr3D 84.940 166 23 2 3516 3680 590043673 590043837 3.000000e-37 167.0
32 TraesCS7A01G105100 chr3D 85.000 60 8 1 4375 4433 45947477 45947418 5.240000e-05 60.2
33 TraesCS7A01G105100 chr3B 78.681 849 155 18 3148 3984 22518402 22519236 4.270000e-150 542.0
34 TraesCS7A01G105100 chr3B 83.636 110 13 3 1920 2029 1417382 1417278 1.110000e-16 99.0
35 TraesCS7A01G105100 chr3B 82.569 109 19 0 1570 1678 22524058 22524166 3.990000e-16 97.1
36 TraesCS7A01G105100 chr3A 76.705 777 139 32 998 1740 20914067 20914835 1.260000e-105 394.0
37 TraesCS7A01G105100 chr3A 86.726 113 8 5 1921 2031 604326460 604326567 8.520000e-23 119.0
38 TraesCS7A01G105100 chr3A 85.586 111 11 4 1920 2029 67576166 67576060 1.430000e-20 111.0
39 TraesCS7A01G105100 chr3A 82.203 118 20 1 1566 1683 20834999 20835115 3.090000e-17 100.0
40 TraesCS7A01G105100 chr3A 84.314 102 16 0 1570 1671 20932142 20932243 3.090000e-17 100.0
41 TraesCS7A01G105100 chr3A 82.609 69 3 3 4403 4462 20485220 20485152 9.000000e-03 52.8
42 TraesCS7A01G105100 chr2B 79.888 179 17 9 4383 4547 98979232 98979405 3.960000e-21 113.0
43 TraesCS7A01G105100 chr2B 100.000 29 0 0 4436 4464 41863674 41863646 2.000000e-03 54.7
44 TraesCS7A01G105100 chr7B 87.629 97 8 2 1933 2029 594770900 594770808 5.130000e-20 110.0
45 TraesCS7A01G105100 chr5B 83.784 111 10 6 1920 2028 689227382 689227486 1.110000e-16 99.0
46 TraesCS7A01G105100 chr6A 84.783 92 14 0 1580 1671 528351720 528351811 5.160000e-15 93.5
47 TraesCS7A01G105100 chr6A 82.143 112 8 7 4372 4473 24011958 24011849 8.640000e-13 86.1


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 TraesCS7A01G105100 chr7A 63780955 63785799 4844 False 3052.00 8948 97.883333 1 4845 3 chr7A.!!$F2 4844
1 TraesCS7A01G105100 chr7A 13832279 13835360 3081 False 955.50 1188 81.611000 934 4251 2 chr7A.!!$F1 3317
2 TraesCS7A01G105100 chr7D 59465938 59470797 4859 False 1848.00 3928 93.158250 1 4845 4 chr7D.!!$F4 4844
3 TraesCS7A01G105100 chr7D 14590501 14593579 3078 False 952.50 1210 81.538500 934 4251 2 chr7D.!!$F2 3317
4 TraesCS7A01G105100 chr7D 59417998 59419023 1025 False 476.00 514 93.975000 212 839 2 chr7D.!!$F3 627
5 TraesCS7A01G105100 chr2D 2448353 2449701 1348 True 880.00 880 78.728000 2781 4129 1 chr2D.!!$R1 1348
6 TraesCS7A01G105100 chrUn 15723004 15724431 1427 False 833.00 833 77.717000 2699 4117 1 chrUn.!!$F1 1418
7 TraesCS7A01G105100 chrUn 15440396 15441836 1440 True 813.00 813 77.369000 2699 4129 1 chrUn.!!$R1 1430
8 TraesCS7A01G105100 chrUn 357011193 357012617 1424 False 804.00 804 77.373000 2699 4117 1 chrUn.!!$F2 1418
9 TraesCS7A01G105100 chrUn 335446521 335447183 662 True 699.00 699 85.821000 2779 3441 1 chrUn.!!$R3 662
10 TraesCS7A01G105100 chrUn 358519542 358520110 568 True 320.00 320 77.625000 2699 3256 1 chrUn.!!$R4 557
11 TraesCS7A01G105100 chr4A 722287288 722288448 1160 True 815.00 815 79.830000 3112 4254 1 chr4A.!!$R1 1142
12 TraesCS7A01G105100 chr4A 722330439 722331523 1084 True 771.00 771 79.746000 3093 4179 1 chr4A.!!$R2 1086
13 TraesCS7A01G105100 chr4A 722292743 722293734 991 True 216.05 335 80.811000 2075 3122 2 chr4A.!!$R3 1047
14 TraesCS7A01G105100 chr3D 15387022 15387850 828 True 569.00 569 79.290000 3148 3984 1 chr3D.!!$R1 836
15 TraesCS7A01G105100 chr3B 22518402 22519236 834 False 542.00 542 78.681000 3148 3984 1 chr3B.!!$F1 836
16 TraesCS7A01G105100 chr3A 20914067 20914835 768 False 394.00 394 76.705000 998 1740 1 chr3A.!!$F2 742

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
887 1292 0.038166 ACAGGTGGCACCGATGATTT 59.962 50.0 29.76 8.85 44.90 2.17 F
1725 2171 0.318784 GCAACGTCAGGTTCGAGACT 60.319 55.0 0.00 0.00 36.49 3.24 F
2164 2658 0.040958 CTGGTTGCTTTCTGCGTCAC 60.041 55.0 0.00 0.00 46.63 3.67 F
2194 2688 0.243907 CGTCGCCTCAGAGGAAGAAA 59.756 55.0 21.89 0.00 37.67 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2658 0.097325 GAGGCGACGACAGTAGACAG 59.903 60.0 2.19 0.0 33.04 3.51 R
2906 3534 6.314917 ACATCCCAAGAGTCTAACCAAATTT 58.685 36.0 0.00 0.0 0.00 1.82 R
3764 4423 2.173356 CCTCATCCCATAACTGCCAAGA 59.827 50.0 0.00 0.0 0.00 3.02 R
4005 4674 2.567615 ACTGTAGGAGTGGGTAGCAAAG 59.432 50.0 0.00 0.0 31.75 2.77 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
64 65 1.648467 GATTCTTCCACGGCAGCCAC 61.648 60.000 13.30 0.00 0.00 5.01
163 164 6.878923 ACATCGAGAATTGACATTTGGACTAA 59.121 34.615 0.00 0.00 0.00 2.24
184 185 7.565680 ACTAATTCATTGTTCTATTCGGTCCT 58.434 34.615 0.00 0.00 0.00 3.85
192 193 6.737254 TGTTCTATTCGGTCCTGATTTTTC 57.263 37.500 0.00 0.00 0.00 2.29
201 202 2.875933 GTCCTGATTTTTCGTGTGGACA 59.124 45.455 0.00 0.00 41.29 4.02
202 203 2.875933 TCCTGATTTTTCGTGTGGACAC 59.124 45.455 0.00 0.00 43.15 3.67
358 360 5.808540 TGATTGAACGTTTCTAATCTACGGG 59.191 40.000 22.74 0.00 39.45 5.28
384 386 2.345641 CGGACTGATACTGAAAGCAACG 59.654 50.000 0.00 0.00 37.60 4.10
452 454 5.061721 GGGGGAAAGCTATAATTCCTGAA 57.938 43.478 13.35 0.00 43.75 3.02
492 494 7.764443 GGGGAAAGGCTAATTGAGTTTAATTTC 59.236 37.037 0.00 0.00 32.79 2.17
493 495 7.488150 GGGAAAGGCTAATTGAGTTTAATTTCG 59.512 37.037 0.00 0.00 32.79 3.46
512 514 5.670149 TTCGTAAACGGTTTTCTTATGCA 57.330 34.783 11.87 0.00 40.29 3.96
579 971 5.016245 TGTCCTTTTCCCATTAATCTCCCTT 59.984 40.000 0.00 0.00 0.00 3.95
777 1175 8.523915 AAGAAACAATGATAAGCATGTGGATA 57.476 30.769 0.00 0.00 37.28 2.59
808 1213 2.096417 CACCGGAAAAGTTTAGTCGCTG 60.096 50.000 9.46 0.00 0.00 5.18
887 1292 0.038166 ACAGGTGGCACCGATGATTT 59.962 50.000 29.76 8.85 44.90 2.17
914 1319 4.702131 GCTTCAAATCTATGGACTGTTGGT 59.298 41.667 0.00 0.00 0.00 3.67
945 1350 3.633951 GCAACAAGCAAGCAAGGC 58.366 55.556 0.00 0.00 44.79 4.35
947 1354 1.219522 GCAACAAGCAAGCAAGGCAG 61.220 55.000 0.00 0.00 44.79 4.85
958 1365 1.168714 GCAAGGCAGTTAGGACAAGG 58.831 55.000 0.00 0.00 0.00 3.61
1023 1433 4.828925 GGCGTCCTGCTGCTCCTC 62.829 72.222 0.00 0.00 45.43 3.71
1068 1487 2.974698 GCAACGGCACAGCTCTGT 60.975 61.111 0.00 0.00 46.17 3.41
1182 1601 4.749310 CTCTTCGCTGCCGCCACT 62.749 66.667 0.00 0.00 0.00 4.00
1203 1637 4.424711 GGCCAATCCCCAGACGCA 62.425 66.667 0.00 0.00 0.00 5.24
1406 1846 4.659172 CCTCAACCCAGCGGCCAA 62.659 66.667 2.24 0.00 0.00 4.52
1725 2171 0.318784 GCAACGTCAGGTTCGAGACT 60.319 55.000 0.00 0.00 36.49 3.24
1740 2186 5.060662 TCGAGACTTTCATGTTCTTCGAT 57.939 39.130 0.00 0.00 0.00 3.59
1743 2189 5.518128 CGAGACTTTCATGTTCTTCGATCAT 59.482 40.000 0.00 0.00 0.00 2.45
1882 2332 1.327303 TCATTTGCTGGTGGTGGTTC 58.673 50.000 0.00 0.00 0.00 3.62
1914 2364 7.053498 TGATTTAGTTGGCATGCTATCAGTAA 58.947 34.615 18.92 8.20 0.00 2.24
1917 2367 8.972458 TTTAGTTGGCATGCTATCAGTAATTA 57.028 30.769 18.92 0.00 0.00 1.40
1930 2380 5.138758 TCAGTAATTAGCTACTCCCTCCA 57.861 43.478 0.00 0.00 29.36 3.86
1939 2389 5.622346 AGCTACTCCCTCCATTTTCTAAG 57.378 43.478 0.00 0.00 0.00 2.18
1942 2392 6.847036 AGCTACTCCCTCCATTTTCTAAGTAT 59.153 38.462 0.00 0.00 0.00 2.12
1987 2437 7.911651 ACTAAAGACTACATATGGATGGATGG 58.088 38.462 7.80 0.00 37.39 3.51
1988 2438 7.734865 ACTAAAGACTACATATGGATGGATGGA 59.265 37.037 7.80 0.00 37.39 3.41
1989 2439 7.579940 AAAGACTACATATGGATGGATGGAT 57.420 36.000 7.80 0.00 37.39 3.41
1990 2440 6.556974 AGACTACATATGGATGGATGGATG 57.443 41.667 7.80 0.00 37.39 3.51
2049 2499 9.932207 TTGCTTTGACAATAGATTCATTCATTT 57.068 25.926 0.00 0.00 0.00 2.32
2081 2575 4.085261 CCGTACGATAATTTGTGGATGTCG 60.085 45.833 18.76 0.00 0.00 4.35
2125 2619 4.156739 GCAGCCTTGGGTAATTGCTATATC 59.843 45.833 0.00 0.00 0.00 1.63
2164 2658 0.040958 CTGGTTGCTTTCTGCGTCAC 60.041 55.000 0.00 0.00 46.63 3.67
2178 2672 1.725292 GCGTCACTGTCTACTGTCGTC 60.725 57.143 0.00 0.00 0.00 4.20
2194 2688 0.243907 CGTCGCCTCAGAGGAAGAAA 59.756 55.000 21.89 0.00 37.67 2.52
2400 2900 6.147164 CAGGTGCAAAGATACTACGAGAAAAA 59.853 38.462 0.00 0.00 0.00 1.94
2473 2976 2.487934 CAGGATTATCCGGCTTCACAG 58.512 52.381 5.50 0.00 42.75 3.66
2477 2980 4.163458 AGGATTATCCGGCTTCACAGTTTA 59.837 41.667 5.50 0.00 42.75 2.01
2487 2990 5.569059 CGGCTTCACAGTTTATGATTTTCAC 59.431 40.000 0.00 0.00 0.00 3.18
2570 3073 6.862469 TGGCCCTGTATATAAGGTACATAC 57.138 41.667 0.00 0.00 32.13 2.39
2633 3167 9.896645 TCTAATCAAGAGAAACAAGAATATGCT 57.103 29.630 0.00 0.00 0.00 3.79
2634 3168 9.932699 CTAATCAAGAGAAACAAGAATATGCTG 57.067 33.333 0.00 0.00 0.00 4.41
2635 3169 7.934855 ATCAAGAGAAACAAGAATATGCTGT 57.065 32.000 0.00 0.00 0.00 4.40
2636 3170 9.453572 AATCAAGAGAAACAAGAATATGCTGTA 57.546 29.630 0.00 0.00 0.00 2.74
2637 3171 9.624373 ATCAAGAGAAACAAGAATATGCTGTAT 57.376 29.630 0.00 0.00 0.00 2.29
2638 3172 8.886719 TCAAGAGAAACAAGAATATGCTGTATG 58.113 33.333 0.00 0.00 0.00 2.39
2639 3173 8.671921 CAAGAGAAACAAGAATATGCTGTATGT 58.328 33.333 0.00 0.00 0.00 2.29
2640 3174 9.890629 AAGAGAAACAAGAATATGCTGTATGTA 57.109 29.630 0.00 0.00 0.00 2.29
2729 3350 7.970102 TCCTTGTACTCATTACTTGGTAGTTT 58.030 34.615 0.00 0.00 35.78 2.66
2906 3534 5.586243 GCTCATAGCCAAACTTCAACATAGA 59.414 40.000 0.00 0.00 34.48 1.98
2936 3564 1.280421 AGACTCTTGGGATGTTGCTCC 59.720 52.381 0.00 0.00 34.31 4.70
3123 3759 3.398406 TGCGTAATTGCACTCTCTTGAA 58.602 40.909 0.00 0.00 40.62 2.69
3125 3761 4.455533 TGCGTAATTGCACTCTCTTGAAAT 59.544 37.500 0.00 0.00 40.62 2.17
3138 3775 6.127647 ACTCTCTTGAAATTTGAGTGTGCAAA 60.128 34.615 7.18 0.00 41.49 3.68
3431 4078 4.073293 CACAAGAAGAGTGGTTGGTACT 57.927 45.455 0.00 0.00 33.43 2.73
3503 4154 5.833082 AGTCAGCCATATAGTAACTTGACG 58.167 41.667 0.00 0.00 0.00 4.35
3539 4195 2.684001 TTAGTGGTTACATGGCTCCG 57.316 50.000 0.00 0.00 0.00 4.63
3705 4363 9.950680 GTTCATAAACACCCATATAACATGAAG 57.049 33.333 0.00 0.00 35.36 3.02
3759 4418 9.284968 GTACCTAACTATATGGTGAAATTGCAT 57.715 33.333 0.00 0.00 35.48 3.96
3953 4622 2.825836 GACAATGCTCCTGCGGGG 60.826 66.667 12.87 3.48 43.34 5.73
4005 4674 2.289133 GGTAGGCGATGAAGAGGATTCC 60.289 54.545 0.00 0.00 0.00 3.01
4017 4689 2.239907 AGAGGATTCCTTTGCTACCCAC 59.760 50.000 6.68 0.00 31.76 4.61
4163 4850 6.909550 TTTTGAGGGTTATGTAAGCACAAT 57.090 33.333 4.58 0.00 38.42 2.71
4238 4928 9.044150 AGTCAATCAAAACCATAATTGTGTTTG 57.956 29.630 10.28 10.28 32.85 2.93
4366 5056 9.901172 TTCTAAAAACTATTATCAACCTCCTCC 57.099 33.333 0.00 0.00 0.00 4.30
4371 5061 8.437274 AAACTATTATCAACCTCCTCCGATAT 57.563 34.615 0.00 0.00 0.00 1.63
4401 5091 5.187967 TCAAGACCCAAAAGTTTTGGCTTTA 59.812 36.000 33.28 22.35 37.68 1.85
4450 5192 1.551430 TCGGGGCTAGAAATTTCGACA 59.449 47.619 12.42 1.81 0.00 4.35
4451 5193 1.933853 CGGGGCTAGAAATTTCGACAG 59.066 52.381 12.42 11.65 0.00 3.51
4452 5194 1.671328 GGGGCTAGAAATTTCGACAGC 59.329 52.381 23.29 23.29 33.53 4.40
4453 5195 2.356135 GGGCTAGAAATTTCGACAGCA 58.644 47.619 28.10 8.94 34.92 4.41
4454 5196 2.945668 GGGCTAGAAATTTCGACAGCAT 59.054 45.455 28.10 10.44 34.92 3.79
4455 5197 4.127171 GGGCTAGAAATTTCGACAGCATA 58.873 43.478 28.10 10.90 34.92 3.14
4456 5198 4.574828 GGGCTAGAAATTTCGACAGCATAA 59.425 41.667 28.10 6.17 34.92 1.90
4457 5199 5.502606 GGCTAGAAATTTCGACAGCATAAC 58.497 41.667 28.10 16.06 34.92 1.89
4458 5200 5.191059 GCTAGAAATTTCGACAGCATAACG 58.809 41.667 25.00 6.05 34.07 3.18
4459 5201 4.003519 AGAAATTTCGACAGCATAACGC 57.996 40.909 12.42 0.00 42.91 4.84
4495 5237 3.308438 AATCAACAAGAATGGTGCAGC 57.692 42.857 9.47 9.47 44.26 5.25
4513 5258 5.348451 GTGCAGCGTTCATTCCAAAATTAAT 59.652 36.000 0.00 0.00 0.00 1.40
4526 5271 8.859236 TTCCAAAATTAATTCATGCAATCCAA 57.141 26.923 0.10 0.00 0.00 3.53
4558 5303 5.934043 TCAGTCAATACACTGGATGAAACAG 59.066 40.000 0.91 0.00 43.59 3.16
4573 5318 7.375106 GATGAAACAGTCCATATCATCATCC 57.625 40.000 8.70 0.00 43.61 3.51
4576 5321 8.211030 TGAAACAGTCCATATCATCATCCTAT 57.789 34.615 0.00 0.00 0.00 2.57
4590 5335 6.950041 TCATCATCCTATCAAATCATTTCCCC 59.050 38.462 0.00 0.00 0.00 4.81
4595 5340 4.275936 CCTATCAAATCATTTCCCCGACAC 59.724 45.833 0.00 0.00 0.00 3.67
4629 5374 2.941064 GCCTAGGGCTAAAACTAAACGG 59.059 50.000 11.72 0.00 46.69 4.44
4630 5375 3.620719 GCCTAGGGCTAAAACTAAACGGT 60.621 47.826 11.72 0.00 46.69 4.83
4774 5534 3.073101 GAGGGAACTACGGCGGGT 61.073 66.667 13.24 6.93 44.43 5.28
4823 5593 9.608617 GTTTAACAGAGTATTTACAAAGAAGGC 57.391 33.333 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.535462 CTGCCGTGGAAGAATCGTTTT 59.465 47.619 0.00 0.00 0.00 2.43
41 42 1.156736 CTGCCGTGGAAGAATCGTTT 58.843 50.000 0.00 0.00 0.00 3.60
42 43 1.298859 GCTGCCGTGGAAGAATCGTT 61.299 55.000 0.00 0.00 0.00 3.85
43 44 1.741770 GCTGCCGTGGAAGAATCGT 60.742 57.895 0.00 0.00 0.00 3.73
44 45 2.464459 GGCTGCCGTGGAAGAATCG 61.464 63.158 1.35 0.00 0.00 3.34
163 164 5.989477 TCAGGACCGAATAGAACAATGAAT 58.011 37.500 0.00 0.00 0.00 2.57
201 202 3.474920 AGATTAGGTGGAATTCAGGGGT 58.525 45.455 7.93 0.00 0.00 4.95
202 203 4.210331 CAAGATTAGGTGGAATTCAGGGG 58.790 47.826 7.93 0.00 0.00 4.79
358 360 3.368236 GCTTTCAGTATCAGTCCGACAAC 59.632 47.826 0.40 0.00 0.00 3.32
452 454 4.408921 GCCTTTCCCCCAAAGCTTATTATT 59.591 41.667 0.00 0.00 40.40 1.40
492 494 6.735263 TTTTGCATAAGAAAACCGTTTACG 57.265 33.333 0.00 0.00 39.44 3.18
493 495 7.529185 GCATTTTTGCATAAGAAAACCGTTTAC 59.471 33.333 0.00 0.00 34.41 2.01
512 514 4.671766 GCTCGTCCTACATTTCGCATTTTT 60.672 41.667 0.00 0.00 0.00 1.94
579 971 1.418264 TGGGAAGGACGTGAACATCAA 59.582 47.619 0.00 0.00 0.00 2.57
688 1083 6.524490 CAATGTCGGTTTTTCATTTATGTGC 58.476 36.000 0.00 0.00 30.74 4.57
777 1175 8.252417 ACTAAACTTTTCCGGTGTTTTGTAAAT 58.748 29.630 19.76 6.26 37.67 1.40
855 1260 5.185056 GGTGCCACCTGTTTACTTCATTAAT 59.815 40.000 6.63 0.00 34.73 1.40
856 1261 4.521256 GGTGCCACCTGTTTACTTCATTAA 59.479 41.667 6.63 0.00 34.73 1.40
887 1292 4.161565 ACAGTCCATAGATTTGAAGCCGTA 59.838 41.667 0.00 0.00 0.00 4.02
914 1319 2.168326 TGTTGCTTTCAGCGATCAGA 57.832 45.000 0.00 0.00 46.26 3.27
945 1350 5.073311 TCGATTTCTCCTTGTCCTAACTG 57.927 43.478 0.00 0.00 0.00 3.16
947 1354 3.866327 GCTCGATTTCTCCTTGTCCTAAC 59.134 47.826 0.00 0.00 0.00 2.34
958 1365 2.962253 CCGGCCGCTCGATTTCTC 60.962 66.667 22.85 0.00 0.00 2.87
1023 1433 4.172512 AGCGGCATGAGCAGGAGG 62.173 66.667 14.56 0.00 44.61 4.30
1291 1725 4.408821 GTCGCTGGGGCATGTCCA 62.409 66.667 20.13 13.67 38.60 4.02
1339 1773 1.534235 AGCCTGGTCTCTGGTCGTT 60.534 57.895 0.00 0.00 34.83 3.85
1740 2186 3.535629 GATCCGCCGCATGGGATGA 62.536 63.158 12.02 4.92 43.00 2.92
1743 2189 4.240103 CTGATCCGCCGCATGGGA 62.240 66.667 12.02 0.52 38.47 4.37
1882 2332 4.807304 GCATGCCAACTAAATCAAGATTGG 59.193 41.667 6.36 0.00 42.31 3.16
1914 2364 7.348537 ACTTAGAAAATGGAGGGAGTAGCTAAT 59.651 37.037 0.00 0.00 0.00 1.73
1917 2367 5.033522 ACTTAGAAAATGGAGGGAGTAGCT 58.966 41.667 0.00 0.00 0.00 3.32
1983 2433 8.136165 ACACTCTAAAATACGTCTACATCCATC 58.864 37.037 0.00 0.00 0.00 3.51
1986 2436 8.834465 TCTACACTCTAAAATACGTCTACATCC 58.166 37.037 0.00 0.00 0.00 3.51
2049 2499 7.403421 CACAAATTATCGTACGGAGCAAAATA 58.597 34.615 16.52 0.80 0.00 1.40
2081 2575 5.465935 TGCGTTCCATGACCTTTAAAATTC 58.534 37.500 0.00 0.00 0.00 2.17
2164 2658 0.097325 GAGGCGACGACAGTAGACAG 59.903 60.000 2.19 0.00 33.04 3.51
2178 2672 2.289072 TGTTCTTTCTTCCTCTGAGGCG 60.289 50.000 19.08 12.01 34.61 5.52
2194 2688 8.257602 ACTAATTTACCCACCATTTTTGTTCT 57.742 30.769 0.00 0.00 0.00 3.01
2346 2845 1.000274 GGAATTGACCCAATATGCGCC 60.000 52.381 4.18 0.00 32.43 6.53
2347 2846 2.422276 GGAATTGACCCAATATGCGC 57.578 50.000 0.00 0.00 32.43 6.09
2400 2900 4.510340 CCTTCTTGCAACTTGTAACTACGT 59.490 41.667 0.00 0.00 0.00 3.57
2477 2980 6.769822 AGCTTCCAATATCTCGTGAAAATCAT 59.230 34.615 0.00 0.00 0.00 2.45
2487 2990 7.203910 AGTTACTTGTAGCTTCCAATATCTCG 58.796 38.462 0.00 0.00 0.00 4.04
2651 3185 8.739039 CCTCCACAGTTTCAAATAATTGTATGA 58.261 33.333 0.00 0.00 37.79 2.15
2652 3186 8.739039 TCCTCCACAGTTTCAAATAATTGTATG 58.261 33.333 0.00 0.00 37.79 2.39
2653 3187 8.877864 TCCTCCACAGTTTCAAATAATTGTAT 57.122 30.769 0.00 0.00 37.79 2.29
2654 3188 8.698973 TTCCTCCACAGTTTCAAATAATTGTA 57.301 30.769 0.00 0.00 37.79 2.41
2655 3189 7.595819 TTCCTCCACAGTTTCAAATAATTGT 57.404 32.000 0.00 0.00 37.79 2.71
2906 3534 6.314917 ACATCCCAAGAGTCTAACCAAATTT 58.685 36.000 0.00 0.00 0.00 1.82
3759 4418 5.843969 TCATCCCATAACTGCCAAGACTATA 59.156 40.000 0.00 0.00 0.00 1.31
3764 4423 2.173356 CCTCATCCCATAACTGCCAAGA 59.827 50.000 0.00 0.00 0.00 3.02
3859 4528 2.933495 TGCACACATAGTAGTCCGAC 57.067 50.000 0.00 0.00 0.00 4.79
4005 4674 2.567615 ACTGTAGGAGTGGGTAGCAAAG 59.432 50.000 0.00 0.00 31.75 2.77
4294 4984 7.763528 GCACATATCTGAGGAGGTTGATAATAG 59.236 40.741 0.00 0.00 0.00 1.73
4295 4985 7.577616 CGCACATATCTGAGGAGGTTGATAATA 60.578 40.741 0.00 0.00 0.00 0.98
4296 4986 6.471146 GCACATATCTGAGGAGGTTGATAAT 58.529 40.000 0.00 0.00 0.00 1.28
4297 4987 5.509670 CGCACATATCTGAGGAGGTTGATAA 60.510 44.000 0.00 0.00 0.00 1.75
4298 4988 4.021981 CGCACATATCTGAGGAGGTTGATA 60.022 45.833 0.00 0.00 0.00 2.15
4299 4989 3.244009 CGCACATATCTGAGGAGGTTGAT 60.244 47.826 0.00 0.00 0.00 2.57
4355 5045 3.026707 TCACATATCGGAGGAGGTTGA 57.973 47.619 0.00 0.00 0.00 3.18
4366 5056 6.094048 ACTTTTGGGTCTTGATTCACATATCG 59.906 38.462 0.00 0.00 0.00 2.92
4371 5061 5.930837 AAACTTTTGGGTCTTGATTCACA 57.069 34.783 0.00 0.00 0.00 3.58
4401 5091 6.631971 CCAAATTTTGGCCTTGTTTGTAAT 57.368 33.333 14.96 0.00 45.17 1.89
4430 5172 1.551430 TGTCGAAATTTCTAGCCCCGA 59.449 47.619 15.92 4.37 0.00 5.14
4433 5175 2.356135 TGCTGTCGAAATTTCTAGCCC 58.644 47.619 23.96 10.38 0.00 5.19
4450 5192 2.267188 TCTTTACGACGCGTTATGCT 57.733 45.000 15.53 0.00 41.54 3.79
4451 5193 3.519497 GATTCTTTACGACGCGTTATGC 58.481 45.455 15.53 0.00 41.54 3.14
4452 5194 3.548668 TGGATTCTTTACGACGCGTTATG 59.451 43.478 15.53 9.55 41.54 1.90
4453 5195 3.772932 TGGATTCTTTACGACGCGTTAT 58.227 40.909 15.53 7.40 41.54 1.89
4454 5196 3.214697 TGGATTCTTTACGACGCGTTA 57.785 42.857 15.53 0.00 41.54 3.18
4455 5197 2.068837 TGGATTCTTTACGACGCGTT 57.931 45.000 15.53 0.00 41.54 4.84
4456 5198 2.068837 TTGGATTCTTTACGACGCGT 57.931 45.000 13.85 13.85 44.35 6.01
4457 5199 3.061563 TGATTTGGATTCTTTACGACGCG 59.938 43.478 3.53 3.53 0.00 6.01
4458 5200 4.593597 TGATTTGGATTCTTTACGACGC 57.406 40.909 0.00 0.00 0.00 5.19
4459 5201 5.922546 TGTTGATTTGGATTCTTTACGACG 58.077 37.500 0.00 0.00 0.00 5.12
4460 5202 7.581476 TCTTGTTGATTTGGATTCTTTACGAC 58.419 34.615 0.00 0.00 0.00 4.34
4461 5203 7.737972 TCTTGTTGATTTGGATTCTTTACGA 57.262 32.000 0.00 0.00 0.00 3.43
4462 5204 8.853345 CATTCTTGTTGATTTGGATTCTTTACG 58.147 33.333 0.00 0.00 0.00 3.18
4463 5205 9.143631 CCATTCTTGTTGATTTGGATTCTTTAC 57.856 33.333 0.00 0.00 32.91 2.01
4464 5206 8.869109 ACCATTCTTGTTGATTTGGATTCTTTA 58.131 29.630 0.00 0.00 34.37 1.85
4495 5237 7.961855 TGCATGAATTAATTTTGGAATGAACG 58.038 30.769 1.43 0.00 0.00 3.95
4526 5271 4.060900 CAGTGTATTGACTGACTTGCACT 58.939 43.478 0.00 0.00 45.39 4.40
4558 5303 9.848710 ATGATTTGATAGGATGATGATATGGAC 57.151 33.333 0.00 0.00 0.00 4.02
4573 5318 4.275936 GGTGTCGGGGAAATGATTTGATAG 59.724 45.833 0.00 0.00 0.00 2.08
4576 5321 2.224892 TGGTGTCGGGGAAATGATTTGA 60.225 45.455 0.00 0.00 0.00 2.69
4590 5335 1.954146 CTTCGTGGTGGTGGTGTCG 60.954 63.158 0.00 0.00 0.00 4.35
4595 5340 1.079127 CTAGGCTTCGTGGTGGTGG 60.079 63.158 0.00 0.00 0.00 4.61
4625 5370 8.881743 TGTTCATTAGCGTTATTTATAACCGTT 58.118 29.630 6.96 0.00 39.49 4.44
4627 5372 8.545420 AGTGTTCATTAGCGTTATTTATAACCG 58.455 33.333 6.96 4.40 39.49 4.44
4752 5508 1.515081 CGCCGTAGTTCCCTCAAAAA 58.485 50.000 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.