Multiple sequence alignment - TraesCS5D01G403000

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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 TraesCS5D01G403000 chr5D 100.000 3493 0 0 1 3493 468842741 468839249 0.000000e+00 6451.0
1 TraesCS5D01G403000 chr5D 80.000 110 16 4 45 148 501085769 501085660 3.740000e-10 76.8
2 TraesCS5D01G403000 chr5D 100.000 28 0 0 3136 3163 496016892 496016919 6.000000e-03 52.8
3 TraesCS5D01G403000 chr5B 90.964 2313 111 36 729 3017 575631548 575629310 0.000000e+00 3024.0
4 TraesCS5D01G403000 chr5B 87.664 916 56 23 903 1784 576523432 576524324 0.000000e+00 1013.0
5 TraesCS5D01G403000 chr5B 88.504 635 45 15 1789 2417 576524633 576525245 0.000000e+00 743.0
6 TraesCS5D01G403000 chr5B 90.431 418 25 9 1861 2272 576447891 576448299 1.430000e-148 536.0
7 TraesCS5D01G403000 chr5B 84.536 485 68 4 4 487 576521998 576522476 1.130000e-129 473.0
8 TraesCS5D01G403000 chr5B 93.506 308 12 5 1815 2122 104905707 104905408 5.320000e-123 451.0
9 TraesCS5D01G403000 chr5B 82.958 311 19 15 3186 3493 575629312 575629033 2.080000e-62 250.0
10 TraesCS5D01G403000 chr5B 89.055 201 13 5 2260 2454 576448315 576448512 1.250000e-59 241.0
11 TraesCS5D01G403000 chr5B 99.074 108 1 0 1718 1825 576447445 576447552 9.890000e-46 195.0
12 TraesCS5D01G403000 chr5B 88.889 135 13 2 475 608 576522809 576522942 7.760000e-37 165.0
13 TraesCS5D01G403000 chr5B 88.793 116 10 3 604 717 575631749 575631635 4.700000e-29 139.0
14 TraesCS5D01G403000 chr5A 90.108 1759 69 46 604 2292 589062704 589060981 0.000000e+00 2187.0
15 TraesCS5D01G403000 chr5A 89.370 762 45 13 2323 3066 589060983 589060240 0.000000e+00 926.0
16 TraesCS5D01G403000 chr5A 85.921 483 60 7 2 481 589063426 589062949 3.110000e-140 508.0
17 TraesCS5D01G403000 chr5A 92.812 320 16 4 3174 3493 589060165 589059853 1.140000e-124 457.0
18 TraesCS5D01G403000 chr5A 84.807 441 28 11 1285 1724 673966290 673965888 1.170000e-109 407.0
19 TraesCS5D01G403000 chr5A 85.185 81 12 0 1211 1291 702504757 702504677 2.230000e-12 84.2
20 TraesCS5D01G403000 chr5A 75.294 170 33 6 1211 1374 702459604 702459770 4.840000e-09 73.1
21 TraesCS5D01G403000 chr3B 86.318 899 45 24 1253 2122 454137317 454138166 0.000000e+00 907.0
22 TraesCS5D01G403000 chr3B 85.984 899 48 24 1253 2122 454344588 454345437 0.000000e+00 891.0
23 TraesCS5D01G403000 chr3B 90.566 318 19 5 1285 1602 196634334 196634640 9.020000e-111 411.0
24 TraesCS5D01G403000 chr3B 84.354 441 30 11 1285 1724 197090229 197090631 2.530000e-106 396.0
25 TraesCS5D01G403000 chr7B 86.034 895 49 21 1253 2119 421243672 421244518 0.000000e+00 891.0
26 TraesCS5D01G403000 chr7B 85.714 441 25 11 1285 1724 728162639 728163042 6.930000e-117 431.0
27 TraesCS5D01G403000 chr4A 84.586 785 44 21 1368 2122 651457161 651457898 0.000000e+00 708.0
28 TraesCS5D01G403000 chr7A 85.488 441 25 18 1285 1724 578922546 578922144 1.160000e-114 424.0
29 TraesCS5D01G403000 chr7A 85.488 441 25 18 1285 1724 578926246 578925844 1.160000e-114 424.0
30 TraesCS5D01G403000 chr4B 77.647 170 29 6 1211 1374 662409321 662409155 1.030000e-15 95.3
31 TraesCS5D01G403000 chr4D 77.193 171 28 8 1211 1374 506217040 506216874 4.800000e-14 89.8


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 TraesCS5D01G403000 chr5D 468839249 468842741 3492 True 6451.000000 6451 100.000000 1 3493 1 chr5D.!!$R1 3492
1 TraesCS5D01G403000 chr5B 575629033 575631749 2716 True 1137.666667 3024 87.571667 604 3493 3 chr5B.!!$R2 2889
2 TraesCS5D01G403000 chr5B 576521998 576525245 3247 False 598.500000 1013 87.398250 4 2417 4 chr5B.!!$F2 2413
3 TraesCS5D01G403000 chr5B 576447445 576448512 1067 False 324.000000 536 92.853333 1718 2454 3 chr5B.!!$F1 736
4 TraesCS5D01G403000 chr5A 589059853 589063426 3573 True 1019.500000 2187 89.552750 2 3493 4 chr5A.!!$R3 3491
5 TraesCS5D01G403000 chr3B 454137317 454138166 849 False 907.000000 907 86.318000 1253 2122 1 chr3B.!!$F3 869
6 TraesCS5D01G403000 chr3B 454344588 454345437 849 False 891.000000 891 85.984000 1253 2122 1 chr3B.!!$F4 869
7 TraesCS5D01G403000 chr7B 421243672 421244518 846 False 891.000000 891 86.034000 1253 2119 1 chr7B.!!$F1 866
8 TraesCS5D01G403000 chr4A 651457161 651457898 737 False 708.000000 708 84.586000 1368 2122 1 chr4A.!!$F1 754
9 TraesCS5D01G403000 chr7A 578922144 578926246 4102 True 424.000000 424 85.488000 1285 1724 2 chr7A.!!$R1 439

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
552 959 0.034089 CTGATCCTGGTTTGGGGTCC 60.034 60.0 0.0 0.0 33.28 4.46 F
1121 1988 0.108585 TTTTTCACCCGAGAGCTGCT 59.891 50.0 0.0 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 3508 1.041447 ATGAGGCAAGGCAATGAGGC 61.041 55.0 0.0 0.0 44.61 4.70 R
2928 7404 0.529119 GGTTGTTCCACGACGACACT 60.529 55.0 0.0 0.0 35.94 3.55 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
30 31 8.918202 TCCTATGTGATGTAACTTCAAAGTTT 57.082 30.769 12.95 0.00 46.52 2.66
128 130 3.756117 AGTTAGGTTTCTTTGAGGGCTG 58.244 45.455 0.00 0.00 0.00 4.85
131 133 0.600057 GGTTTCTTTGAGGGCTGCAG 59.400 55.000 10.11 10.11 0.00 4.41
154 156 5.939883 AGTTTGCCAAAAGAAAAAGCTCTTT 59.060 32.000 0.00 0.00 45.49 2.52
163 165 3.001330 AGAAAAAGCTCTTTGACACGTCG 59.999 43.478 0.00 0.00 32.36 5.12
167 169 1.000955 AGCTCTTTGACACGTCGGAAT 59.999 47.619 0.00 0.00 0.00 3.01
177 179 1.065764 CGTCGGAATCGAGCATCCA 59.934 57.895 13.27 1.01 46.91 3.41
184 186 1.137872 GAATCGAGCATCCAGTCAGGT 59.862 52.381 0.00 0.00 39.02 4.00
244 246 2.094957 GTCTGGACTCCTCTCTTTGTCG 60.095 54.545 0.00 0.00 0.00 4.35
245 247 1.203523 CTGGACTCCTCTCTTTGTCGG 59.796 57.143 0.00 0.00 0.00 4.79
246 248 1.203013 TGGACTCCTCTCTTTGTCGGA 60.203 52.381 0.00 0.00 0.00 4.55
247 249 1.893801 GGACTCCTCTCTTTGTCGGAA 59.106 52.381 0.00 0.00 0.00 4.30
248 250 2.094442 GGACTCCTCTCTTTGTCGGAAG 60.094 54.545 0.00 0.00 0.00 3.46
251 253 3.835395 ACTCCTCTCTTTGTCGGAAGAAT 59.165 43.478 0.00 0.00 45.01 2.40
294 302 5.963865 AGCTAATCTTCTTCTTCTCCCTCTT 59.036 40.000 0.00 0.00 0.00 2.85
311 319 0.320374 CTTCTTCACACACCGGGCTA 59.680 55.000 6.32 0.00 0.00 3.93
315 323 0.034337 TTCACACACCGGGCTAACTC 59.966 55.000 6.32 0.00 0.00 3.01
327 335 2.038557 GGGCTAACTCTTTGACAGTCCA 59.961 50.000 0.00 0.00 31.14 4.02
328 336 3.307762 GGGCTAACTCTTTGACAGTCCAT 60.308 47.826 0.00 0.00 31.14 3.41
340 348 4.028490 GTCCATGGTCACGGGGCA 62.028 66.667 12.58 0.00 0.00 5.36
345 353 2.300967 ATGGTCACGGGGCAGACAT 61.301 57.895 0.00 0.00 36.50 3.06
347 355 2.347490 GTCACGGGGCAGACATGT 59.653 61.111 0.00 0.00 34.93 3.21
349 357 2.815211 CACGGGGCAGACATGTCG 60.815 66.667 19.85 15.27 34.09 4.35
357 365 2.283676 AGACATGTCGGGTCCGGT 60.284 61.111 19.85 0.00 40.25 5.28
359 367 3.659089 GACATGTCGGGTCCGGTGG 62.659 68.421 10.69 0.38 40.25 4.61
458 466 5.280654 AGAGGGTTGTAAAAGTACACGAA 57.719 39.130 0.00 0.00 40.00 3.85
459 467 5.861727 AGAGGGTTGTAAAAGTACACGAAT 58.138 37.500 0.00 0.00 40.00 3.34
460 468 6.293698 AGAGGGTTGTAAAAGTACACGAATT 58.706 36.000 0.00 0.00 40.00 2.17
474 501 5.957842 ACACGAATTTCAGCTGGATTTTA 57.042 34.783 15.13 0.00 0.00 1.52
487 514 4.712476 CTGGATTTTAGATGGGTCAGGAG 58.288 47.826 0.00 0.00 0.00 3.69
503 875 2.279918 AGTGTCGGACGCCAACAC 60.280 61.111 17.47 10.85 42.80 3.32
549 956 0.698238 TCACTGATCCTGGTTTGGGG 59.302 55.000 0.00 0.00 0.00 4.96
552 959 0.034089 CTGATCCTGGTTTGGGGTCC 60.034 60.000 0.00 0.00 33.28 4.46
576 991 4.202441 ACTGGGAAATTTCATCGATCCAG 58.798 43.478 25.25 25.25 44.24 3.86
579 994 2.951642 GGAAATTTCATCGATCCAGCCA 59.048 45.455 19.49 0.00 0.00 4.75
599 1042 6.650390 CAGCCAAAAATAAAGGTGCTATTTGT 59.350 34.615 0.00 0.00 31.02 2.83
772 1336 2.890474 CCCCATGCTACGCGACAC 60.890 66.667 15.93 0.74 0.00 3.67
959 1799 2.032528 CTGACGCCACCACACCAT 59.967 61.111 0.00 0.00 0.00 3.55
962 1802 1.295423 GACGCCACCACACCATACT 59.705 57.895 0.00 0.00 0.00 2.12
963 1803 1.003839 ACGCCACCACACCATACTG 60.004 57.895 0.00 0.00 0.00 2.74
965 1805 2.046285 GCCACCACACCATACTGGC 61.046 63.158 0.00 0.00 42.67 4.85
967 1807 1.378378 CACCACACCATACTGGCCA 59.622 57.895 4.71 4.71 42.67 5.36
968 1808 0.251121 CACCACACCATACTGGCCAA 60.251 55.000 7.01 0.00 42.67 4.52
1112 1979 4.134563 TCTTCTTCTTCCTTTTTCACCCG 58.865 43.478 0.00 0.00 0.00 5.28
1114 1981 3.740115 TCTTCTTCCTTTTTCACCCGAG 58.260 45.455 0.00 0.00 0.00 4.63
1120 1987 0.519077 CTTTTTCACCCGAGAGCTGC 59.481 55.000 0.00 0.00 0.00 5.25
1121 1988 0.108585 TTTTTCACCCGAGAGCTGCT 59.891 50.000 0.00 0.00 0.00 4.24
1122 1989 0.320771 TTTTCACCCGAGAGCTGCTC 60.321 55.000 21.72 21.72 40.38 4.26
1123 1990 2.172483 TTTCACCCGAGAGCTGCTCC 62.172 60.000 25.09 15.54 40.70 4.70
1124 1991 3.385384 CACCCGAGAGCTGCTCCA 61.385 66.667 25.09 0.00 40.70 3.86
1130 1998 1.227615 GAGAGCTGCTCCATCTGGC 60.228 63.158 25.09 0.00 37.69 4.85
1181 2053 3.338249 GCTTACTGCTGTTCTTGATGGA 58.662 45.455 0.09 0.00 38.95 3.41
1480 2363 0.969894 CTCACTCACCGTTTCCTCCT 59.030 55.000 0.00 0.00 0.00 3.69
1497 2387 2.168728 CTCCTTCCTTTCCTTCCCTACG 59.831 54.545 0.00 0.00 0.00 3.51
1645 2544 5.245075 AGAGTTCATCGTCCTCTCTTTTCTT 59.755 40.000 0.00 0.00 32.52 2.52
1951 3506 1.380785 CAGCCCAGCAATGGTCCAT 60.381 57.895 0.00 0.00 0.00 3.41
1952 3507 0.974010 CAGCCCAGCAATGGTCCATT 60.974 55.000 11.59 11.59 34.04 3.16
2188 5000 5.234543 CCTATACGCTCCTTTTGAAACTAGC 59.765 44.000 0.00 0.00 0.00 3.42
2226 5836 2.681097 GCCATTAGGTGTGAAGGGAGTC 60.681 54.545 0.00 0.00 37.19 3.36
2246 5856 2.360165 TCCTAGCCGTTTCGATTAGTCC 59.640 50.000 0.00 0.00 0.00 3.85
2602 7054 4.982241 AGGAAGAGAACCTTTGTGATGA 57.018 40.909 0.00 0.00 34.68 2.92
2603 7055 5.511386 AGGAAGAGAACCTTTGTGATGAT 57.489 39.130 0.00 0.00 34.68 2.45
2604 7056 5.251764 AGGAAGAGAACCTTTGTGATGATG 58.748 41.667 0.00 0.00 34.68 3.07
2628 7080 0.616371 TGGTATTCCGTTCTGGTGGG 59.384 55.000 0.00 0.00 39.52 4.61
2632 7084 0.613777 ATTCCGTTCTGGTGGGAGAC 59.386 55.000 0.00 0.00 39.52 3.36
2699 7157 4.141711 GGTTTAGGGCTGATGTAGTGATGA 60.142 45.833 0.00 0.00 0.00 2.92
2792 7260 1.466856 TCTTTGGTGCAGATCATGGC 58.533 50.000 0.00 0.00 0.00 4.40
2819 7287 0.036671 CAGATCAGTGGAGTGCAGCA 60.037 55.000 0.00 0.00 0.00 4.41
2820 7288 0.910338 AGATCAGTGGAGTGCAGCAT 59.090 50.000 0.00 0.00 0.00 3.79
2821 7289 1.015109 GATCAGTGGAGTGCAGCATG 58.985 55.000 0.00 0.00 40.87 4.06
2852 7320 4.392445 TGTACGAAAATCCGGTAACATTGG 59.608 41.667 0.00 0.00 0.00 3.16
2886 7354 4.177026 CTGTTCTATGTCTTCCCTTCGTG 58.823 47.826 0.00 0.00 0.00 4.35
2902 7378 0.800683 CGTGAAAGCGATGCCTCGTA 60.801 55.000 13.00 0.00 46.71 3.43
2907 7383 0.528684 AAGCGATGCCTCGTAGCTTC 60.529 55.000 13.00 0.00 43.70 3.86
2928 7404 9.177608 AGCTTCTCAAAATTTAGTATGTATGCA 57.822 29.630 0.00 0.00 0.00 3.96
2966 7442 3.173965 ACCAGCCAGACTAAGAAGCTAA 58.826 45.455 0.00 0.00 31.23 3.09
2968 7444 3.935828 CCAGCCAGACTAAGAAGCTAAAC 59.064 47.826 0.00 0.00 31.23 2.01
2969 7445 3.935828 CAGCCAGACTAAGAAGCTAAACC 59.064 47.826 0.00 0.00 31.23 3.27
2970 7446 3.583086 AGCCAGACTAAGAAGCTAAACCA 59.417 43.478 0.00 0.00 30.46 3.67
3061 7539 4.326826 CTCAGGATGTTGTGGTACATGTT 58.673 43.478 2.30 0.00 38.80 2.71
3066 7544 3.847671 TGTTGTGGTACATGTTCCTCA 57.152 42.857 20.70 19.72 44.52 3.86
3068 7546 3.389656 TGTTGTGGTACATGTTCCTCAGA 59.610 43.478 20.83 12.35 44.52 3.27
3069 7547 3.961480 TGTGGTACATGTTCCTCAGAG 57.039 47.619 20.70 0.00 44.52 3.35
3072 7550 4.102524 TGTGGTACATGTTCCTCAGAGTTT 59.897 41.667 20.70 0.00 44.52 2.66
3073 7551 4.691216 GTGGTACATGTTCCTCAGAGTTTC 59.309 45.833 20.70 0.00 44.52 2.78
3075 7553 4.262894 GGTACATGTTCCTCAGAGTTTCCA 60.263 45.833 13.89 0.00 0.00 3.53
3076 7554 4.647564 ACATGTTCCTCAGAGTTTCCAT 57.352 40.909 0.00 0.00 0.00 3.41
3077 7555 4.583871 ACATGTTCCTCAGAGTTTCCATC 58.416 43.478 0.00 0.00 0.00 3.51
3079 7557 4.543590 TGTTCCTCAGAGTTTCCATCTC 57.456 45.455 0.00 0.00 0.00 2.75
3084 7562 5.090139 TCCTCAGAGTTTCCATCTCTTTCT 58.910 41.667 0.00 0.00 39.84 2.52
3088 7591 7.230309 CCTCAGAGTTTCCATCTCTTTCTTTTT 59.770 37.037 0.00 0.00 39.84 1.94
3128 7631 9.141400 GAAAACTAGTTAGAGTAGGATGTTGTG 57.859 37.037 8.92 0.00 0.00 3.33
3130 7633 6.254522 ACTAGTTAGAGTAGGATGTTGTGGT 58.745 40.000 0.00 0.00 0.00 4.16
3132 7635 6.527057 AGTTAGAGTAGGATGTTGTGGTAC 57.473 41.667 0.00 0.00 0.00 3.34
3133 7636 6.014647 AGTTAGAGTAGGATGTTGTGGTACA 58.985 40.000 0.00 0.00 0.00 2.90
3134 7637 6.668283 AGTTAGAGTAGGATGTTGTGGTACAT 59.332 38.462 0.00 0.00 44.52 2.29
3135 7638 5.344743 AGAGTAGGATGTTGTGGTACATG 57.655 43.478 0.00 0.00 44.52 3.21
3136 7639 3.871594 GAGTAGGATGTTGTGGTACATGC 59.128 47.826 0.00 0.00 44.52 4.06
3139 7642 1.665679 GGATGTTGTGGTACATGCTCG 59.334 52.381 0.00 0.00 44.52 5.03
3141 7644 0.321210 TGTTGTGGTACATGCTCGGG 60.321 55.000 0.00 0.00 44.52 5.14
3142 7645 0.321298 GTTGTGGTACATGCTCGGGT 60.321 55.000 0.00 0.00 44.52 5.28
3143 7646 0.321210 TTGTGGTACATGCTCGGGTG 60.321 55.000 0.00 0.00 44.52 4.61
3144 7647 2.106683 GTGGTACATGCTCGGGTGC 61.107 63.158 0.00 0.00 44.52 5.01
3146 7649 1.815421 GGTACATGCTCGGGTGCAG 60.815 63.158 0.00 0.00 46.71 4.41
3148 7651 0.807667 GTACATGCTCGGGTGCAGAG 60.808 60.000 0.00 0.00 46.71 3.35
3149 7652 0.970427 TACATGCTCGGGTGCAGAGA 60.970 55.000 5.67 0.00 46.71 3.10
3151 7654 1.145598 ATGCTCGGGTGCAGAGATG 59.854 57.895 5.67 0.00 46.71 2.90
3152 7655 2.202987 GCTCGGGTGCAGAGATGG 60.203 66.667 5.67 0.00 37.93 3.51
3153 7656 2.725312 GCTCGGGTGCAGAGATGGA 61.725 63.158 5.67 0.00 37.93 3.41
3157 7660 1.281867 TCGGGTGCAGAGATGGATTTT 59.718 47.619 0.00 0.00 0.00 1.82
3158 7661 1.672881 CGGGTGCAGAGATGGATTTTC 59.327 52.381 0.00 0.00 0.00 2.29
3159 7662 1.672881 GGGTGCAGAGATGGATTTTCG 59.327 52.381 0.00 0.00 0.00 3.46
3160 7663 2.359900 GGTGCAGAGATGGATTTTCGT 58.640 47.619 0.00 0.00 0.00 3.85
3161 7664 2.749621 GGTGCAGAGATGGATTTTCGTT 59.250 45.455 0.00 0.00 0.00 3.85
3162 7665 3.938963 GGTGCAGAGATGGATTTTCGTTA 59.061 43.478 0.00 0.00 0.00 3.18
3163 7666 4.201822 GGTGCAGAGATGGATTTTCGTTAC 60.202 45.833 0.00 0.00 0.00 2.50
3164 7667 3.938963 TGCAGAGATGGATTTTCGTTACC 59.061 43.478 0.00 0.00 0.00 2.85
3165 7668 3.312697 GCAGAGATGGATTTTCGTTACCC 59.687 47.826 0.00 0.00 0.00 3.69
3166 7669 4.513442 CAGAGATGGATTTTCGTTACCCA 58.487 43.478 0.00 0.00 0.00 4.51
3167 7670 4.941263 CAGAGATGGATTTTCGTTACCCAA 59.059 41.667 0.00 0.00 0.00 4.12
3168 7671 5.414454 CAGAGATGGATTTTCGTTACCCAAA 59.586 40.000 0.00 0.00 0.00 3.28
3169 7672 6.095440 CAGAGATGGATTTTCGTTACCCAAAT 59.905 38.462 0.00 0.00 0.00 2.32
3170 7673 6.318900 AGAGATGGATTTTCGTTACCCAAATC 59.681 38.462 5.71 5.71 36.55 2.17
3172 7675 4.023739 GGATTTTCGTTACCCAAATCCG 57.976 45.455 13.75 0.00 43.70 4.18
3288 7791 4.456535 TCTAACAAAGCCAACAAGCTACA 58.543 39.130 0.00 0.00 44.11 2.74
3293 7796 0.884704 AGCCAACAAGCTACACACGG 60.885 55.000 0.00 0.00 42.70 4.94
3303 7806 4.308899 AGCTACACACGGATTATGTCTC 57.691 45.455 0.00 0.00 0.00 3.36
3304 7807 3.699538 AGCTACACACGGATTATGTCTCA 59.300 43.478 0.00 0.00 0.00 3.27
3334 7837 2.867109 AGCTACACAGGCATTTGTCT 57.133 45.000 0.00 0.00 0.00 3.41
3423 7933 2.563261 ATATCCCTCATGCTGCACTG 57.437 50.000 3.57 5.11 0.00 3.66
3424 7934 0.179037 TATCCCTCATGCTGCACTGC 60.179 55.000 3.57 0.00 0.00 4.40
3426 7936 2.697761 CCCTCATGCTGCACTGCAC 61.698 63.158 3.57 0.00 46.33 4.57
3427 7937 1.674651 CCTCATGCTGCACTGCACT 60.675 57.895 3.57 0.00 46.33 4.40
3469 7979 0.040067 CTTGCAGGTTTCGCCAAGAC 60.040 55.000 0.00 0.00 40.61 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.777865 TTTGAAGTTACATCACATAGGAAGAG 57.222 34.615 0.00 0.00 0.00 2.85
2 3 8.375506 ACTTTGAAGTTACATCACATAGGAAGA 58.624 33.333 5.01 0.00 35.21 2.87
77 79 8.397575 TCATTAACAACCTAAGCAATGTACAA 57.602 30.769 0.00 0.00 0.00 2.41
113 115 1.322442 ACTGCAGCCCTCAAAGAAAC 58.678 50.000 15.27 0.00 0.00 2.78
115 117 1.682854 CAAACTGCAGCCCTCAAAGAA 59.317 47.619 15.27 0.00 0.00 2.52
128 130 3.374988 AGCTTTTTCTTTTGGCAAACTGC 59.625 39.130 13.10 9.04 44.08 4.40
131 133 5.801350 AAGAGCTTTTTCTTTTGGCAAAC 57.199 34.783 13.10 0.00 33.74 2.93
154 156 1.154093 GCTCGATTCCGACGTGTCA 60.154 57.895 0.00 0.00 40.30 3.58
163 165 1.539929 CCTGACTGGATGCTCGATTCC 60.540 57.143 0.00 2.98 38.35 3.01
167 169 0.900182 ACACCTGACTGGATGCTCGA 60.900 55.000 5.22 0.00 39.71 4.04
177 179 3.117888 AGTTGAATGGTTGACACCTGACT 60.118 43.478 0.00 0.00 44.61 3.41
184 186 2.174639 AGGGACAGTTGAATGGTTGACA 59.825 45.455 0.00 0.00 0.00 3.58
273 275 7.676043 TGAAGAAGAGGGAGAAGAAGAAGATTA 59.324 37.037 0.00 0.00 0.00 1.75
294 302 0.034337 GTTAGCCCGGTGTGTGAAGA 59.966 55.000 0.00 0.00 0.00 2.87
311 319 3.136443 TGACCATGGACTGTCAAAGAGTT 59.864 43.478 21.47 0.00 38.48 3.01
315 323 1.800586 CGTGACCATGGACTGTCAAAG 59.199 52.381 21.47 5.66 42.67 2.77
327 335 2.300967 ATGTCTGCCCCGTGACCAT 61.301 57.895 0.00 0.00 32.67 3.55
328 336 2.927856 ATGTCTGCCCCGTGACCA 60.928 61.111 0.00 0.00 32.67 4.02
340 348 2.283676 ACCGGACCCGACATGTCT 60.284 61.111 22.95 4.97 42.83 3.41
357 365 1.068417 CACAAGGTTCGTCGTCCCA 59.932 57.895 5.88 0.00 0.00 4.37
359 367 1.068474 CATCACAAGGTTCGTCGTCC 58.932 55.000 0.00 0.00 0.00 4.79
458 466 5.522641 ACCCATCTAAAATCCAGCTGAAAT 58.477 37.500 17.39 5.44 0.00 2.17
459 467 4.934356 ACCCATCTAAAATCCAGCTGAAA 58.066 39.130 17.39 2.78 0.00 2.69
460 468 4.018506 TGACCCATCTAAAATCCAGCTGAA 60.019 41.667 17.39 0.00 0.00 3.02
474 501 0.972983 CCGACACTCCTGACCCATCT 60.973 60.000 0.00 0.00 0.00 2.90
503 875 2.511600 GAGCCCGGACGTCCATTG 60.512 66.667 32.80 20.77 35.14 2.82
549 956 2.351726 CGATGAAATTTCCCAGTCGGAC 59.648 50.000 15.48 0.00 41.83 4.79
552 959 3.248602 GGATCGATGAAATTTCCCAGTCG 59.751 47.826 15.48 17.24 0.00 4.18
562 977 5.603170 ATTTTTGGCTGGATCGATGAAAT 57.397 34.783 0.54 0.00 0.00 2.17
576 991 7.172361 TCAACAAATAGCACCTTTATTTTTGGC 59.828 33.333 0.00 0.00 30.41 4.52
579 994 7.116233 CGCTCAACAAATAGCACCTTTATTTTT 59.884 33.333 0.00 0.00 38.70 1.94
626 1101 2.351276 CTCCACGGGGTGAAAGGG 59.649 66.667 2.12 0.00 35.23 3.95
884 1454 2.897207 GGGGCGGGGTTTTAATGC 59.103 61.111 0.00 0.00 0.00 3.56
959 1799 2.038863 TCTTCCTTCCTTGGCCAGTA 57.961 50.000 5.11 0.00 0.00 2.74
962 1802 0.251341 GCTTCTTCCTTCCTTGGCCA 60.251 55.000 0.00 0.00 0.00 5.36
963 1803 0.251341 TGCTTCTTCCTTCCTTGGCC 60.251 55.000 0.00 0.00 0.00 5.36
965 1805 2.165998 CCTTGCTTCTTCCTTCCTTGG 58.834 52.381 0.00 0.00 0.00 3.61
967 1807 3.491342 GTTCCTTGCTTCTTCCTTCCTT 58.509 45.455 0.00 0.00 0.00 3.36
968 1808 2.224892 GGTTCCTTGCTTCTTCCTTCCT 60.225 50.000 0.00 0.00 0.00 3.36
1112 1979 1.227615 GCCAGATGGAGCAGCTCTC 60.228 63.158 21.99 12.56 41.15 3.20
1114 1981 1.227615 GAGCCAGATGGAGCAGCTC 60.228 63.158 14.69 14.69 42.74 4.09
1120 1987 0.539051 AAGAACCGAGCCAGATGGAG 59.461 55.000 2.18 0.00 37.39 3.86
1121 1988 0.250234 CAAGAACCGAGCCAGATGGA 59.750 55.000 2.18 0.00 37.39 3.41
1122 1989 0.745845 CCAAGAACCGAGCCAGATGG 60.746 60.000 0.00 0.00 38.53 3.51
1123 1990 0.250234 TCCAAGAACCGAGCCAGATG 59.750 55.000 0.00 0.00 0.00 2.90
1124 1991 0.984230 TTCCAAGAACCGAGCCAGAT 59.016 50.000 0.00 0.00 0.00 2.90
1130 1998 5.438761 AAAACAGATTTCCAAGAACCGAG 57.561 39.130 0.00 0.00 0.00 4.63
1181 2053 2.573869 CTGCTCATCGTCCCACGT 59.426 61.111 0.00 0.00 43.14 4.49
1497 2387 2.676471 AACTGTGCGATTGGGGCC 60.676 61.111 0.00 0.00 0.00 5.80
1678 2578 7.416731 ACAATCCTCCTACACCTTACTAGTAA 58.583 38.462 14.52 14.52 0.00 2.24
1679 2579 6.978261 ACAATCCTCCTACACCTTACTAGTA 58.022 40.000 0.00 0.00 0.00 1.82
1689 2589 7.865706 ATAATGTTCAACAATCCTCCTACAC 57.134 36.000 0.00 0.00 0.00 2.90
1942 3497 1.483415 GCAATGAGGCAATGGACCATT 59.517 47.619 14.28 14.28 34.04 3.16
1953 3508 1.041447 ATGAGGCAAGGCAATGAGGC 61.041 55.000 0.00 0.00 44.61 4.70
1954 3509 1.136305 CAATGAGGCAAGGCAATGAGG 59.864 52.381 0.00 0.00 0.00 3.86
1955 3510 1.136305 CCAATGAGGCAAGGCAATGAG 59.864 52.381 0.00 0.00 0.00 2.90
2075 3631 2.895372 GGAACCCCACGCGCATAG 60.895 66.667 5.73 0.00 0.00 2.23
2096 3652 1.608801 GCAGCCAAATGTGGGAAAAGG 60.609 52.381 3.47 0.00 46.09 3.11
2188 5000 1.728490 GGCCTGCTAATTTGCGAGGG 61.728 60.000 21.80 17.08 34.30 4.30
2226 5836 2.740452 GGACTAATCGAAACGGCTAGG 58.260 52.381 0.00 0.00 0.00 3.02
2228 5838 1.745087 ACGGACTAATCGAAACGGCTA 59.255 47.619 0.00 0.00 0.00 3.93
2246 5856 1.804748 GCTGTAAAAGGGACCAGAACG 59.195 52.381 0.00 0.00 0.00 3.95
2360 6596 2.435938 TTCGGACCTTGCGCCATC 60.436 61.111 4.18 0.00 0.00 3.51
2386 6826 4.379243 CGCCGCTGGTGTCCTTCT 62.379 66.667 0.71 0.00 0.00 2.85
2443 6883 2.611800 AGCAGGCCAGGATCACCA 60.612 61.111 5.01 0.00 38.94 4.17
2602 7054 4.103153 ACCAGAACGGAATACCATCATCAT 59.897 41.667 0.00 0.00 38.63 2.45
2603 7055 3.454447 ACCAGAACGGAATACCATCATCA 59.546 43.478 0.00 0.00 38.63 3.07
2604 7056 3.809832 CACCAGAACGGAATACCATCATC 59.190 47.826 0.00 0.00 38.63 2.92
2628 7080 5.101628 CACTGACAAGCTATCTTCAGTCTC 58.898 45.833 13.65 0.00 36.08 3.36
2632 7084 5.101628 GTCTCACTGACAAGCTATCTTCAG 58.898 45.833 10.65 10.65 44.73 3.02
2699 7157 4.080695 AGACACAGCATCAGGTCATAACAT 60.081 41.667 0.00 0.00 32.79 2.71
2766 7224 2.957402 TCTGCACCAAAGAACCAGAT 57.043 45.000 0.00 0.00 0.00 2.90
2792 7260 3.087031 ACTCCACTGATCTGCCAATTTG 58.913 45.455 0.00 0.00 0.00 2.32
2819 7287 3.375299 GGATTTTCGTACAGCAAGAGCAT 59.625 43.478 0.00 0.00 45.49 3.79
2820 7288 2.742053 GGATTTTCGTACAGCAAGAGCA 59.258 45.455 0.00 0.00 45.49 4.26
2821 7289 2.222819 CGGATTTTCGTACAGCAAGAGC 60.223 50.000 0.00 0.00 42.56 4.09
2822 7290 2.348666 CCGGATTTTCGTACAGCAAGAG 59.651 50.000 0.00 0.00 0.00 2.85
2823 7291 2.289195 ACCGGATTTTCGTACAGCAAGA 60.289 45.455 9.46 0.00 0.00 3.02
2824 7292 2.073816 ACCGGATTTTCGTACAGCAAG 58.926 47.619 9.46 0.00 0.00 4.01
2902 7378 9.177608 TGCATACATACTAAATTTTGAGAAGCT 57.822 29.630 6.63 0.00 0.00 3.74
2907 7383 9.708222 GACACTGCATACATACTAAATTTTGAG 57.292 33.333 6.63 0.00 0.00 3.02
2925 7401 1.590525 GTTCCACGACGACACTGCA 60.591 57.895 0.00 0.00 0.00 4.41
2928 7404 0.529119 GGTTGTTCCACGACGACACT 60.529 55.000 0.00 0.00 35.94 3.55
2951 7427 6.274157 TCTCTGGTTTAGCTTCTTAGTCTG 57.726 41.667 0.00 0.00 0.00 3.51
3032 7510 2.617276 CCACAACATCCTGAGCATCTGT 60.617 50.000 0.00 0.00 34.92 3.41
3044 7522 4.323417 TGAGGAACATGTACCACAACATC 58.677 43.478 0.00 0.00 38.01 3.06
3061 7539 5.090139 AGAAAGAGATGGAAACTCTGAGGA 58.910 41.667 9.85 0.00 46.20 3.71
3068 7546 8.525290 TTCTCAAAAAGAAAGAGATGGAAACT 57.475 30.769 0.00 0.00 41.10 2.66
3114 7617 3.871594 GCATGTACCACAACATCCTACTC 59.128 47.826 0.00 0.00 38.01 2.59
3116 7619 3.871594 GAGCATGTACCACAACATCCTAC 59.128 47.826 0.00 0.00 38.01 3.18
3117 7620 3.430236 CGAGCATGTACCACAACATCCTA 60.430 47.826 0.00 0.00 38.01 2.94
3118 7621 2.677902 CGAGCATGTACCACAACATCCT 60.678 50.000 0.00 0.00 38.01 3.24
3119 7622 1.665679 CGAGCATGTACCACAACATCC 59.334 52.381 0.00 0.00 38.01 3.51
3121 7624 1.678728 CCCGAGCATGTACCACAACAT 60.679 52.381 0.00 0.00 40.75 2.71
3122 7625 0.321210 CCCGAGCATGTACCACAACA 60.321 55.000 0.00 0.00 0.00 3.33
3124 7627 0.321210 CACCCGAGCATGTACCACAA 60.321 55.000 0.00 0.00 0.00 3.33
3128 7631 1.815421 CTGCACCCGAGCATGTACC 60.815 63.158 0.00 0.00 44.68 3.34
3130 7633 0.970427 TCTCTGCACCCGAGCATGTA 60.970 55.000 0.00 0.00 44.68 2.29
3132 7635 1.145598 ATCTCTGCACCCGAGCATG 59.854 57.895 0.00 0.00 44.68 4.06
3133 7636 1.145598 CATCTCTGCACCCGAGCAT 59.854 57.895 0.00 0.00 44.68 3.79
3134 7637 2.580815 CATCTCTGCACCCGAGCA 59.419 61.111 0.00 0.00 43.35 4.26
3135 7638 2.037620 ATCCATCTCTGCACCCGAGC 62.038 60.000 0.00 0.00 0.00 5.03
3136 7639 0.467384 AATCCATCTCTGCACCCGAG 59.533 55.000 0.00 0.00 0.00 4.63
3137 7640 0.911769 AAATCCATCTCTGCACCCGA 59.088 50.000 0.00 0.00 0.00 5.14
3138 7641 1.672881 GAAAATCCATCTCTGCACCCG 59.327 52.381 0.00 0.00 0.00 5.28
3139 7642 1.672881 CGAAAATCCATCTCTGCACCC 59.327 52.381 0.00 0.00 0.00 4.61
3141 7644 4.201822 GGTAACGAAAATCCATCTCTGCAC 60.202 45.833 0.00 0.00 0.00 4.57
3142 7645 3.938963 GGTAACGAAAATCCATCTCTGCA 59.061 43.478 0.00 0.00 0.00 4.41
3143 7646 3.312697 GGGTAACGAAAATCCATCTCTGC 59.687 47.826 0.00 0.00 37.60 4.26
3144 7647 4.513442 TGGGTAACGAAAATCCATCTCTG 58.487 43.478 0.00 0.00 37.60 3.35
3145 7648 4.837093 TGGGTAACGAAAATCCATCTCT 57.163 40.909 0.00 0.00 37.60 3.10
3146 7649 5.890424 TTTGGGTAACGAAAATCCATCTC 57.110 39.130 0.00 0.00 41.61 2.75
3157 7660 0.036448 TTGGCGGATTTGGGTAACGA 59.964 50.000 0.00 0.00 37.60 3.85
3158 7661 0.882474 TTTGGCGGATTTGGGTAACG 59.118 50.000 0.00 0.00 37.60 3.18
3159 7662 2.887337 CATTTGGCGGATTTGGGTAAC 58.113 47.619 0.00 0.00 0.00 2.50
3160 7663 1.205893 GCATTTGGCGGATTTGGGTAA 59.794 47.619 0.00 0.00 0.00 2.85
3161 7664 0.820871 GCATTTGGCGGATTTGGGTA 59.179 50.000 0.00 0.00 0.00 3.69
3162 7665 1.596408 GCATTTGGCGGATTTGGGT 59.404 52.632 0.00 0.00 0.00 4.51
3163 7666 1.153389 GGCATTTGGCGGATTTGGG 60.153 57.895 0.00 0.00 46.16 4.12
3164 7667 0.036577 TTGGCATTTGGCGGATTTGG 60.037 50.000 0.00 0.00 46.16 3.28
3165 7668 1.805869 TTTGGCATTTGGCGGATTTG 58.194 45.000 0.00 0.00 46.16 2.32
3166 7669 2.785540 ATTTGGCATTTGGCGGATTT 57.214 40.000 0.00 0.00 46.16 2.17
3167 7670 2.027377 TGAATTTGGCATTTGGCGGATT 60.027 40.909 0.00 2.66 46.16 3.01
3168 7671 1.554160 TGAATTTGGCATTTGGCGGAT 59.446 42.857 0.00 0.00 46.16 4.18
3169 7672 0.972134 TGAATTTGGCATTTGGCGGA 59.028 45.000 0.00 0.00 46.16 5.54
3170 7673 1.361793 CTGAATTTGGCATTTGGCGG 58.638 50.000 0.00 0.00 46.16 6.13
3171 7674 0.722848 GCTGAATTTGGCATTTGGCG 59.277 50.000 0.00 0.00 46.16 5.69
3172 7675 1.089112 GGCTGAATTTGGCATTTGGC 58.911 50.000 0.00 0.00 43.74 4.52
3269 7772 2.757868 TGTGTAGCTTGTTGGCTTTGTT 59.242 40.909 0.00 0.00 42.97 2.83
3270 7773 2.099098 GTGTGTAGCTTGTTGGCTTTGT 59.901 45.455 0.00 0.00 42.97 2.83
3311 7814 4.342092 AGACAAATGCCTGTGTAGCTTTTT 59.658 37.500 0.00 0.00 35.97 1.94
3324 7827 5.402398 GTGATGAACCTTTAGACAAATGCC 58.598 41.667 0.00 0.00 0.00 4.40
3365 7875 0.739112 GCAGTTCAGCTTCCTCTCCG 60.739 60.000 0.00 0.00 0.00 4.63
3423 7933 3.491267 GCCTTACGTCTGATATTCAGTGC 59.509 47.826 0.00 0.00 44.58 4.40
3424 7934 4.938080 AGCCTTACGTCTGATATTCAGTG 58.062 43.478 0.00 2.18 44.58 3.66
3425 7935 4.038162 GGAGCCTTACGTCTGATATTCAGT 59.962 45.833 0.00 0.00 44.58 3.41
3426 7936 4.551388 GGAGCCTTACGTCTGATATTCAG 58.449 47.826 0.00 0.00 45.59 3.02
3427 7937 3.321111 GGGAGCCTTACGTCTGATATTCA 59.679 47.826 0.00 0.00 0.00 2.57
3469 7979 4.778415 CTCCTGCGTCGACGTGGG 62.778 72.222 34.08 32.49 42.22 4.61


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

AutoCloner maintained by Alex Coulton.