Multiple sequence alignment - TraesCS5D01G340500

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 TraesCS5D01G340500 chr5D 100.000 4405 0 0 980 5384 429024747 429029151 0.000000e+00 8135.0
1 TraesCS5D01G340500 chr5D 100.000 461 0 0 1 461 429023768 429024228 0.000000e+00 852.0
2 TraesCS5D01G340500 chr5A 93.802 4050 140 39 980 4956 544609981 544613992 0.000000e+00 5986.0
3 TraesCS5D01G340500 chr5A 92.593 270 7 3 202 461 544609225 544609491 5.090000e-100 375.0
4 TraesCS5D01G340500 chr5B 95.923 2085 73 7 980 3061 518293636 518295711 0.000000e+00 3369.0
5 TraesCS5D01G340500 chr5B 95.475 1746 56 11 3174 4902 518295730 518297469 0.000000e+00 2765.0
6 TraesCS5D01G340500 chr5B 86.825 463 37 10 1 460 518292829 518293270 3.750000e-136 496.0
7 TraesCS5D01G340500 chr5B 87.361 269 32 2 5116 5384 518301339 518301605 1.880000e-79 307.0
8 TraesCS5D01G340500 chr3A 84.908 1418 127 45 2051 3405 22142837 22144230 0.000000e+00 1352.0
9 TraesCS5D01G340500 chr3A 85.714 56 8 0 5227 5282 735897351 735897406 5.820000e-05 60.2
10 TraesCS5D01G340500 chr4B 84.572 1426 127 43 2051 3411 169933123 169934520 0.000000e+00 1328.0
11 TraesCS5D01G340500 chr1A 84.529 1422 131 38 2051 3411 590827697 590829090 0.000000e+00 1325.0
12 TraesCS5D01G340500 chr2A 83.716 1480 135 35 1964 3376 19833849 19835289 0.000000e+00 1301.0
13 TraesCS5D01G340500 chr2A 85.458 949 85 18 1847 2772 734977804 734976886 0.000000e+00 939.0
14 TraesCS5D01G340500 chr2A 85.902 532 64 7 3349 3875 734973931 734973406 1.690000e-154 556.0
15 TraesCS5D01G340500 chr2A 84.014 588 53 13 2779 3336 734974836 734974260 1.330000e-145 527.0
16 TraesCS5D01G340500 chr2A 85.408 466 55 8 3423 3875 19835292 19835757 6.310000e-129 472.0
17 TraesCS5D01G340500 chr6A 83.143 700 60 14 1847 2544 252818295 252817652 2.160000e-163 586.0
18 TraesCS5D01G340500 chr2D 86.216 399 47 5 3479 3875 89206421 89206029 4.980000e-115 425.0
19 TraesCS5D01G340500 chr2D 85.965 399 48 5 3479 3875 104910495 104910887 2.320000e-113 420.0
20 TraesCS5D01G340500 chr2D 100.000 32 0 0 5248 5279 518164953 518164922 5.820000e-05 60.2
21 TraesCS5D01G340500 chr7A 84.461 399 50 7 3479 3875 594575213 594575601 3.040000e-102 383.0


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 TraesCS5D01G340500 chr5D 429023768 429029151 5383 False 4493.50 8135 100.000000 1 5384 2 chr5D.!!$F1 5383
1 TraesCS5D01G340500 chr5A 544609225 544613992 4767 False 3180.50 5986 93.197500 202 4956 2 chr5A.!!$F1 4754
2 TraesCS5D01G340500 chr5B 518292829 518301605 8776 False 1734.25 3369 91.396000 1 5384 4 chr5B.!!$F1 5383
3 TraesCS5D01G340500 chr3A 22142837 22144230 1393 False 1352.00 1352 84.908000 2051 3405 1 chr3A.!!$F1 1354
4 TraesCS5D01G340500 chr4B 169933123 169934520 1397 False 1328.00 1328 84.572000 2051 3411 1 chr4B.!!$F1 1360
5 TraesCS5D01G340500 chr1A 590827697 590829090 1393 False 1325.00 1325 84.529000 2051 3411 1 chr1A.!!$F1 1360
6 TraesCS5D01G340500 chr2A 19833849 19835757 1908 False 886.50 1301 84.562000 1964 3875 2 chr2A.!!$F1 1911
7 TraesCS5D01G340500 chr2A 734973406 734977804 4398 True 674.00 939 85.124667 1847 3875 3 chr2A.!!$R1 2028
8 TraesCS5D01G340500 chr6A 252817652 252818295 643 True 586.00 586 83.143000 1847 2544 1 chr6A.!!$R1 697

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
295 298 2.455557 CTGTCATCAGTCACTCCTCCT 58.544 52.381 0.00 0.00 36.97 3.69 F
1446 1470 1.031571 CGTACTACTACACGCCCCCA 61.032 60.000 0.00 0.00 0.00 4.96 F
1962 2004 0.329261 CCCCATTTCTCTCTGCCACA 59.671 55.000 0.00 0.00 0.00 4.17 F
2277 2328 1.067142 TCGGCTGATGTAATATCCGCC 60.067 52.381 10.99 10.99 42.59 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1388 2.363147 AGTCGTCCTGCTCCTCCC 60.363 66.667 0.0 0.00 0.00 4.30 R
3144 5317 0.250252 TGCTGTTCGAACATGCCAGA 60.250 50.000 31.4 19.94 38.41 3.86 R
3909 6415 0.878523 TCACGCTCCGGTTGAAGTTG 60.879 55.000 0.0 0.00 0.00 3.16 R
4439 6951 3.548818 GCAACACAACTCACTCAATGTCC 60.549 47.826 0.0 0.00 0.00 4.02 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
22 23 5.055642 GGGATTTTTCCGTTAGGTTTGAG 57.944 43.478 0.00 0.00 39.05 3.02
23 24 4.482386 GGATTTTTCCGTTAGGTTTGAGC 58.518 43.478 0.00 0.00 39.05 4.26
57 58 8.592105 TTTTTGCTTTGAAATGTCAAGGATAG 57.408 30.769 11.76 1.61 44.49 2.08
80 81 6.867662 GGAACCAATCCTACACATGAATAG 57.132 41.667 0.00 0.07 45.56 1.73
81 82 5.765182 GGAACCAATCCTACACATGAATAGG 59.235 44.000 16.48 16.48 45.56 2.57
90 92 6.828273 TCCTACACATGAATAGGAACCATTTG 59.172 38.462 20.57 0.00 43.26 2.32
92 94 7.773224 CCTACACATGAATAGGAACCATTTGTA 59.227 37.037 17.27 0.00 40.53 2.41
94 96 6.945435 ACACATGAATAGGAACCATTTGTACA 59.055 34.615 0.00 0.00 31.74 2.90
100 102 7.287927 TGAATAGGAACCATTTGTACAAACCAA 59.712 33.333 22.78 1.32 32.51 3.67
103 105 5.053811 GGAACCATTTGTACAAACCAAAGG 58.946 41.667 22.78 19.32 35.45 3.11
104 106 5.395879 GGAACCATTTGTACAAACCAAAGGT 60.396 40.000 22.78 19.87 36.13 3.50
114 116 8.871629 TGTACAAACCAAAGGTATTGATATGT 57.128 30.769 13.92 0.00 33.12 2.29
115 117 9.303116 TGTACAAACCAAAGGTATTGATATGTT 57.697 29.630 13.92 0.00 33.12 2.71
294 297 2.957491 CTGTCATCAGTCACTCCTCC 57.043 55.000 0.00 0.00 36.97 4.30
295 298 2.455557 CTGTCATCAGTCACTCCTCCT 58.544 52.381 0.00 0.00 36.97 3.69
1446 1470 1.031571 CGTACTACTACACGCCCCCA 61.032 60.000 0.00 0.00 0.00 4.96
1962 2004 0.329261 CCCCATTTCTCTCTGCCACA 59.671 55.000 0.00 0.00 0.00 4.17
2148 2196 6.476378 ACACTGCTCTTTTAATACTCATGGT 58.524 36.000 0.00 0.00 0.00 3.55
2149 2197 7.620880 ACACTGCTCTTTTAATACTCATGGTA 58.379 34.615 0.00 0.00 34.62 3.25
2150 2198 8.267894 ACACTGCTCTTTTAATACTCATGGTAT 58.732 33.333 0.00 0.00 42.38 2.73
2151 2199 8.554528 CACTGCTCTTTTAATACTCATGGTATG 58.445 37.037 7.38 0.00 40.62 2.39
2152 2200 7.716998 ACTGCTCTTTTAATACTCATGGTATGG 59.283 37.037 7.38 0.00 40.62 2.74
2225 2274 1.691434 CCTGGAGATTAGGGAGAGCAC 59.309 57.143 0.00 0.00 0.00 4.40
2277 2328 1.067142 TCGGCTGATGTAATATCCGCC 60.067 52.381 10.99 10.99 42.59 6.13
2335 2393 2.094026 GTCATGTCCTGGCCCAATTTTC 60.094 50.000 0.00 0.00 0.00 2.29
2528 2596 2.760650 TCCATACACTGCAGAGTACAGG 59.239 50.000 23.68 24.86 39.55 4.00
2560 2657 2.693074 GGTGTGTCTTTGGTTGATGGTT 59.307 45.455 0.00 0.00 0.00 3.67
2584 2682 8.725148 GTTTTGACATTGATATCTCTGTCTTGT 58.275 33.333 25.31 11.70 38.98 3.16
2662 2760 6.717084 TCGTCTGTGTCATCTTCATCCTATAT 59.283 38.462 0.00 0.00 0.00 0.86
2732 2830 8.630054 AGAGTGAGACTAATAAGAGCGATATT 57.370 34.615 0.00 0.00 0.00 1.28
2795 4936 3.961408 AGACGTTAGGGAGATTGTATGCT 59.039 43.478 0.00 0.00 0.00 3.79
2810 4951 2.895242 ATGCTTGGGAGAAGAAGCTT 57.105 45.000 0.00 0.00 44.15 3.74
2828 4969 8.554835 AGAAGCTTTATGAAGAAGTTAAGGTC 57.445 34.615 0.00 0.00 34.71 3.85
2858 5001 6.879276 ATATCTGCTGGAGTCATTTGATTG 57.121 37.500 0.00 0.00 0.00 2.67
2868 5011 5.335191 GGAGTCATTTGATTGTTCCTGTGAC 60.335 44.000 0.00 0.00 36.03 3.67
3034 5181 9.436957 CTTTAGTAAATGAGGCTAAGTTGAAGA 57.563 33.333 0.00 0.00 0.00 2.87
3064 5211 5.069251 ACAAGGTCATACTACTGATAGTGCC 59.931 44.000 0.00 0.00 41.92 5.01
3086 5235 5.575606 GCCATCTGTGATTTTTGAACTGATG 59.424 40.000 12.33 12.33 43.91 3.07
3091 5240 8.861033 TCTGTGATTTTTGAACTGATGAAAAG 57.139 30.769 0.00 0.00 0.00 2.27
3092 5241 7.436080 TCTGTGATTTTTGAACTGATGAAAAGC 59.564 33.333 0.00 0.00 0.00 3.51
3094 5243 7.548427 TGTGATTTTTGAACTGATGAAAAGCAA 59.452 29.630 0.00 0.00 38.56 3.91
3095 5244 8.553696 GTGATTTTTGAACTGATGAAAAGCAAT 58.446 29.630 0.00 0.00 38.56 3.56
3096 5245 8.552865 TGATTTTTGAACTGATGAAAAGCAATG 58.447 29.630 0.00 0.00 35.32 2.82
3097 5246 7.846644 TTTTTGAACTGATGAAAAGCAATGT 57.153 28.000 0.00 0.00 0.00 2.71
3123 5289 8.239314 TGATGATCATTTTCTGTAGTTTCTTGC 58.761 33.333 10.14 0.00 0.00 4.01
3186 5359 7.391554 AGCATGTCTCTGTTGTATTGTGTATTT 59.608 33.333 0.00 0.00 0.00 1.40
3465 5960 4.168760 GGTAAGCTGATGTCATGTTTTGC 58.831 43.478 0.00 0.00 0.00 3.68
3469 5964 1.980844 CTGATGTCATGTTTTGCGTGC 59.019 47.619 0.00 0.00 34.19 5.34
3477 5974 3.254411 TCATGTTTTGCGTGCAGGATTTA 59.746 39.130 11.29 0.00 34.19 1.40
3903 6409 3.055719 AAGCGGGTGCCATTCACG 61.056 61.111 0.00 0.00 46.56 4.35
3909 6415 2.277501 GTGCCATTCACGATGCGC 60.278 61.111 0.00 0.00 35.76 6.09
4119 6625 2.048222 CTGTCGGAGCGCAAGGAA 60.048 61.111 11.47 0.00 38.28 3.36
4357 6863 4.827087 CCATCGAGCAGCAGCCGT 62.827 66.667 10.66 0.00 43.56 5.68
4358 6864 3.561213 CATCGAGCAGCAGCCGTG 61.561 66.667 10.66 6.20 43.56 4.94
4439 6951 3.741344 CAGTGTTCTCCGTTTCAGTTAGG 59.259 47.826 0.00 0.00 0.00 2.69
4502 7018 4.021456 GGTTTTGGACCCCTAGAATGTTTG 60.021 45.833 0.00 0.00 43.06 2.93
4710 7235 2.265739 CTGCGGCTCCTGTTGCTA 59.734 61.111 0.00 0.00 0.00 3.49
4798 7332 0.030101 TGTTTGTTGCTGCCTAACGC 59.970 50.000 0.00 0.00 38.31 4.84
4885 7419 1.267121 GTGAACTGTAGGGCCTGAGA 58.733 55.000 18.53 0.00 0.00 3.27
4902 7436 0.242286 AGAATCGGATCGGAGATGCG 59.758 55.000 15.91 15.91 45.12 4.73
4905 7439 2.206515 ATCGGATCGGAGATGCGCTC 62.207 60.000 16.96 3.60 45.12 5.03
4945 7479 0.039798 GACGGTGCGTAGACTTCACA 60.040 55.000 0.00 0.00 41.37 3.58
4956 7490 1.202818 AGACTTCACAAGGAACCAGGC 60.203 52.381 0.00 0.00 0.00 4.85
4957 7491 0.550914 ACTTCACAAGGAACCAGGCA 59.449 50.000 0.00 0.00 0.00 4.75
4958 7492 1.242076 CTTCACAAGGAACCAGGCAG 58.758 55.000 0.00 0.00 0.00 4.85
4959 7493 0.178992 TTCACAAGGAACCAGGCAGG 60.179 55.000 0.00 0.00 45.67 4.85
4960 7494 1.604593 CACAAGGAACCAGGCAGGG 60.605 63.158 0.00 0.00 43.89 4.45
4961 7495 1.774217 ACAAGGAACCAGGCAGGGA 60.774 57.895 0.00 0.00 43.89 4.20
4962 7496 1.303643 CAAGGAACCAGGCAGGGAC 60.304 63.158 0.00 0.00 43.89 4.46
4963 7497 1.464198 AAGGAACCAGGCAGGGACT 60.464 57.895 0.00 0.00 43.89 3.85
4964 7498 1.068352 AAGGAACCAGGCAGGGACTT 61.068 55.000 0.00 0.00 43.89 3.01
4965 7499 1.303643 GGAACCAGGCAGGGACTTG 60.304 63.158 0.00 0.00 43.89 3.16
4966 7500 1.303643 GAACCAGGCAGGGACTTGG 60.304 63.158 0.00 0.00 43.89 3.61
4967 7501 2.450502 ACCAGGCAGGGACTTGGT 60.451 61.111 0.00 0.00 41.76 3.67
4968 7502 0.770557 AACCAGGCAGGGACTTGGTA 60.771 55.000 0.00 0.00 45.35 3.25
4969 7503 0.770557 ACCAGGCAGGGACTTGGTAA 60.771 55.000 0.00 0.00 44.39 2.85
4970 7504 0.322546 CCAGGCAGGGACTTGGTAAC 60.323 60.000 0.00 0.00 34.60 2.50
4984 7518 1.439679 GGTAACAAGAGCGAACCAGG 58.560 55.000 0.00 0.00 0.00 4.45
4985 7519 0.796927 GTAACAAGAGCGAACCAGGC 59.203 55.000 0.00 0.00 0.00 4.85
4986 7520 0.394938 TAACAAGAGCGAACCAGGCA 59.605 50.000 0.00 0.00 0.00 4.75
4987 7521 0.886490 AACAAGAGCGAACCAGGCAG 60.886 55.000 0.00 0.00 0.00 4.85
4988 7522 2.037136 CAAGAGCGAACCAGGCAGG 61.037 63.158 0.00 0.00 45.67 4.85
4989 7523 3.259633 AAGAGCGAACCAGGCAGGG 62.260 63.158 0.00 0.00 43.89 4.45
4990 7524 4.785453 GAGCGAACCAGGCAGGGG 62.785 72.222 0.00 0.00 43.89 4.79
4993 7527 4.351054 CGAACCAGGCAGGGGCTT 62.351 66.667 0.00 0.00 43.89 4.35
4994 7528 2.677875 GAACCAGGCAGGGGCTTG 60.678 66.667 0.00 0.00 45.91 4.01
4998 7532 2.763215 CAGGCAGGGGCTTGGTAA 59.237 61.111 0.00 0.00 42.90 2.85
4999 7533 1.678970 CAGGCAGGGGCTTGGTAAC 60.679 63.158 0.00 0.00 42.90 2.50
5000 7534 2.160171 AGGCAGGGGCTTGGTAACA 61.160 57.895 0.00 0.00 42.87 2.41
5019 7553 2.659897 GAGCATCTACAGCCGCCG 60.660 66.667 0.00 0.00 0.00 6.46
5020 7554 4.227134 AGCATCTACAGCCGCCGG 62.227 66.667 0.00 0.00 0.00 6.13
5038 7572 4.388499 GCTCCTCAAACGCCCGGA 62.388 66.667 0.73 0.00 0.00 5.14
5039 7573 2.584608 CTCCTCAAACGCCCGGAT 59.415 61.111 0.73 0.00 0.00 4.18
5040 7574 1.815421 CTCCTCAAACGCCCGGATG 60.815 63.158 0.73 0.00 0.00 3.51
5041 7575 2.824041 CCTCAAACGCCCGGATGG 60.824 66.667 0.73 0.00 37.09 3.51
5042 7576 2.267642 CTCAAACGCCCGGATGGA 59.732 61.111 0.73 0.00 37.49 3.41
5043 7577 2.046700 TCAAACGCCCGGATGGAC 60.047 61.111 0.73 0.00 37.49 4.02
5044 7578 3.496131 CAAACGCCCGGATGGACG 61.496 66.667 0.73 0.51 38.88 4.79
5072 7606 2.287393 CGTGACCGGTGAACATATCA 57.713 50.000 14.63 0.00 35.05 2.15
5073 7607 2.821546 CGTGACCGGTGAACATATCAT 58.178 47.619 14.63 0.00 40.97 2.45
5074 7608 2.539688 CGTGACCGGTGAACATATCATG 59.460 50.000 14.63 2.06 40.97 3.07
5075 7609 3.736740 CGTGACCGGTGAACATATCATGA 60.737 47.826 14.63 0.00 40.97 3.07
5076 7610 3.555956 GTGACCGGTGAACATATCATGAC 59.444 47.826 14.63 0.00 40.97 3.06
5077 7611 3.131396 GACCGGTGAACATATCATGACC 58.869 50.000 14.63 0.00 40.97 4.02
5078 7612 2.771943 ACCGGTGAACATATCATGACCT 59.228 45.455 6.12 0.00 40.97 3.85
5079 7613 3.133691 CCGGTGAACATATCATGACCTG 58.866 50.000 0.00 0.65 40.97 4.00
5107 7641 2.128535 TCCTCAAACCGGCCCAATATA 58.871 47.619 0.00 0.00 0.00 0.86
5120 7654 3.738281 GCCCAATATATCCGGACTGATCG 60.738 52.174 6.12 0.00 0.00 3.69
5121 7655 3.699538 CCCAATATATCCGGACTGATCGA 59.300 47.826 6.12 0.00 0.00 3.59
5126 7660 1.392710 ATCCGGACTGATCGACACCC 61.393 60.000 6.12 0.00 0.00 4.61
5127 7661 2.052690 CCGGACTGATCGACACCCT 61.053 63.158 0.00 0.00 0.00 4.34
5140 11501 2.621998 CGACACCCTTCGTATACATCCT 59.378 50.000 3.32 0.00 34.16 3.24
5170 11531 1.878656 CGGATATGAGGAGGGGTCGC 61.879 65.000 0.00 0.00 0.00 5.19
5188 11549 2.932663 CACAAATGTGCGGGACTCT 58.067 52.632 0.00 0.00 39.39 3.24
5199 11560 2.584391 GGGACTCTTGCGGACACCT 61.584 63.158 0.00 0.00 0.00 4.00
5202 11563 1.202428 GGACTCTTGCGGACACCTATC 60.202 57.143 0.00 0.00 0.00 2.08
5206 11567 2.093890 TCTTGCGGACACCTATCGTTA 58.906 47.619 0.00 0.00 0.00 3.18
5211 11572 1.477700 CGGACACCTATCGTTACCCAA 59.522 52.381 0.00 0.00 0.00 4.12
5261 11622 1.890174 GGTTGAGGGGCCAAATTCG 59.110 57.895 4.39 0.00 0.00 3.34
5296 11657 2.748350 GCGGCCCCTAACCCTATC 59.252 66.667 0.00 0.00 0.00 2.08
5298 11659 1.460689 CGGCCCCTAACCCTATCCA 60.461 63.158 0.00 0.00 0.00 3.41
5305 11666 2.330216 CCTAACCCTATCCAGTCCCAG 58.670 57.143 0.00 0.00 0.00 4.45
5337 11698 4.676951 CGCCACCAACCCCCACAT 62.677 66.667 0.00 0.00 0.00 3.21
5339 11700 2.037208 CCACCAACCCCCACATCC 59.963 66.667 0.00 0.00 0.00 3.51
5340 11701 2.850290 CACCAACCCCCACATCCA 59.150 61.111 0.00 0.00 0.00 3.41
5341 11702 1.606313 CACCAACCCCCACATCCAC 60.606 63.158 0.00 0.00 0.00 4.02
5343 11704 1.000896 CCAACCCCCACATCCACTC 60.001 63.158 0.00 0.00 0.00 3.51
5344 11705 1.377202 CAACCCCCACATCCACTCG 60.377 63.158 0.00 0.00 0.00 4.18
5345 11706 3.268103 AACCCCCACATCCACTCGC 62.268 63.158 0.00 0.00 0.00 5.03
5346 11707 4.838152 CCCCCACATCCACTCGCG 62.838 72.222 0.00 0.00 0.00 5.87
5352 11713 4.193334 CATCCACTCGCGGCTCGA 62.193 66.667 6.13 0.00 46.29 4.04
5360 11721 1.443872 TCGCGGCTCGAAACTCTTC 60.444 57.895 6.13 0.00 45.36 2.87
5363 11724 1.960994 GCGGCTCGAAACTCTTCTGC 61.961 60.000 0.00 0.00 0.00 4.26
5366 11727 1.355066 GCTCGAAACTCTTCTGCCCG 61.355 60.000 0.00 0.00 0.00 6.13
5368 11729 1.374758 CGAAACTCTTCTGCCCGCT 60.375 57.895 0.00 0.00 0.00 5.52
5371 11732 1.518903 AAACTCTTCTGCCCGCTTGC 61.519 55.000 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.569355 TCCTATCCTTGACATTTCAAAGCA 58.431 37.500 0.00 0.00 41.34 3.91
37 38 6.325596 GTTCCTATCCTTGACATTTCAAAGC 58.674 40.000 0.00 0.00 41.34 3.51
38 39 6.434028 TGGTTCCTATCCTTGACATTTCAAAG 59.566 38.462 0.00 0.00 41.34 2.77
57 58 5.765182 CCTATTCATGTGTAGGATTGGTTCC 59.235 44.000 16.37 0.00 45.85 3.62
72 73 7.759433 GGTTTGTACAAATGGTTCCTATTCATG 59.241 37.037 23.11 0.00 32.36 3.07
74 75 6.778069 TGGTTTGTACAAATGGTTCCTATTCA 59.222 34.615 23.11 1.81 32.36 2.57
80 81 5.053811 CCTTTGGTTTGTACAAATGGTTCC 58.946 41.667 23.11 18.46 37.22 3.62
81 82 5.666462 ACCTTTGGTTTGTACAAATGGTTC 58.334 37.500 23.11 10.35 36.68 3.62
84 85 7.437748 TCAATACCTTTGGTTTGTACAAATGG 58.562 34.615 23.11 19.65 37.22 3.16
122 124 6.062095 CGTGGGAATTTTATAGGATGGAACT 58.938 40.000 0.00 0.00 0.00 3.01
123 125 6.059484 TCGTGGGAATTTTATAGGATGGAAC 58.941 40.000 0.00 0.00 0.00 3.62
126 128 6.952773 TTTCGTGGGAATTTTATAGGATGG 57.047 37.500 0.00 0.00 30.88 3.51
127 129 8.629158 TGAATTTCGTGGGAATTTTATAGGATG 58.371 33.333 0.00 0.00 30.88 3.51
129 131 8.629158 CATGAATTTCGTGGGAATTTTATAGGA 58.371 33.333 10.25 0.00 29.96 2.94
130 132 7.382218 GCATGAATTTCGTGGGAATTTTATAGG 59.618 37.037 17.95 0.00 34.08 2.57
131 133 7.920151 TGCATGAATTTCGTGGGAATTTTATAG 59.080 33.333 17.95 0.00 34.08 1.31
132 134 7.776107 TGCATGAATTTCGTGGGAATTTTATA 58.224 30.769 17.95 0.00 34.08 0.98
136 138 4.220382 TCTGCATGAATTTCGTGGGAATTT 59.780 37.500 17.95 0.00 34.08 1.82
137 139 3.763360 TCTGCATGAATTTCGTGGGAATT 59.237 39.130 17.95 0.00 34.08 2.17
138 140 3.129287 GTCTGCATGAATTTCGTGGGAAT 59.871 43.478 17.95 0.00 34.08 3.01
139 141 2.487762 GTCTGCATGAATTTCGTGGGAA 59.512 45.455 17.95 0.00 34.08 3.97
143 145 3.557577 TTGGTCTGCATGAATTTCGTG 57.442 42.857 13.24 13.24 36.50 4.35
187 190 1.412453 AACCACGGTTCCCTGTGCTA 61.412 55.000 0.00 0.00 34.77 3.49
190 193 0.750182 ACAAACCACGGTTCCCTGTG 60.750 55.000 1.05 0.00 37.35 3.66
196 199 2.356695 AGTGCTTAACAAACCACGGTTC 59.643 45.455 1.05 0.00 37.35 3.62
199 202 1.599419 GCAGTGCTTAACAAACCACGG 60.599 52.381 8.18 0.00 33.62 4.94
200 203 1.333619 AGCAGTGCTTAACAAACCACG 59.666 47.619 13.14 0.00 33.89 4.94
294 297 2.107552 TGTAGGTTTTGGGACTTGGGAG 59.892 50.000 0.00 0.00 0.00 4.30
295 298 2.136863 TGTAGGTTTTGGGACTTGGGA 58.863 47.619 0.00 0.00 0.00 4.37
434 448 3.339093 GTTGTGGGAGGGGAGGGG 61.339 72.222 0.00 0.00 0.00 4.79
435 449 3.339093 GGTTGTGGGAGGGGAGGG 61.339 72.222 0.00 0.00 0.00 4.30
436 450 2.160171 TTGGTTGTGGGAGGGGAGG 61.160 63.158 0.00 0.00 0.00 4.30
437 451 1.074951 GTTGGTTGTGGGAGGGGAG 59.925 63.158 0.00 0.00 0.00 4.30
438 452 1.289982 TTGTTGGTTGTGGGAGGGGA 61.290 55.000 0.00 0.00 0.00 4.81
1364 1388 2.363147 AGTCGTCCTGCTCCTCCC 60.363 66.667 0.00 0.00 0.00 4.30
2129 2172 7.041098 CCACCATACCATGAGTATTAAAAGAGC 60.041 40.741 0.00 0.00 39.79 4.09
2148 2196 6.041865 CCATCTAAAAATTCCATGCCACCATA 59.958 38.462 0.00 0.00 0.00 2.74
2149 2197 5.163280 CCATCTAAAAATTCCATGCCACCAT 60.163 40.000 0.00 0.00 0.00 3.55
2150 2198 4.161942 CCATCTAAAAATTCCATGCCACCA 59.838 41.667 0.00 0.00 0.00 4.17
2151 2199 4.162131 ACCATCTAAAAATTCCATGCCACC 59.838 41.667 0.00 0.00 0.00 4.61
2152 2200 5.111293 CACCATCTAAAAATTCCATGCCAC 58.889 41.667 0.00 0.00 0.00 5.01
2277 2328 5.964958 AGGTGATAACAAATTGACTGTGG 57.035 39.130 0.00 0.00 0.00 4.17
2335 2393 4.016444 TGGTAGCATCAAAAGGGCTAAAG 58.984 43.478 0.00 0.00 41.37 1.85
2528 2596 4.631813 CCAAAGACACACCTAATCTGTAGC 59.368 45.833 0.00 0.00 0.00 3.58
2560 2657 8.724229 CAACAAGACAGAGATATCAATGTCAAA 58.276 33.333 28.09 0.00 43.55 2.69
2584 2682 2.492449 CTTCGACGGGCTCTCTGCAA 62.492 60.000 0.00 0.00 45.15 4.08
2662 2760 3.306595 CTTGCTCCCAGCTCGCTCA 62.307 63.158 0.00 0.00 42.97 4.26
2732 2830 5.449297 TCATCCCACCATAGTCATCAAAA 57.551 39.130 0.00 0.00 0.00 2.44
2735 2833 4.040047 ACTTCATCCCACCATAGTCATCA 58.960 43.478 0.00 0.00 0.00 3.07
2795 4936 6.126863 TCTTCATAAAGCTTCTTCTCCCAA 57.873 37.500 0.00 0.00 32.18 4.12
2828 4969 5.644977 TGACTCCAGCAGATATATAACCG 57.355 43.478 0.00 0.00 0.00 4.44
2857 5000 3.701205 ATGTATGCAGTCACAGGAACA 57.299 42.857 0.00 0.00 0.00 3.18
2858 5001 6.280643 TGTATATGTATGCAGTCACAGGAAC 58.719 40.000 0.00 0.00 0.00 3.62
3034 5181 7.667575 ATCAGTAGTATGACCTTGTCAAGAT 57.332 36.000 14.42 0.00 45.96 2.40
3064 5211 8.806177 TTTCATCAGTTCAAAAATCACAGATG 57.194 30.769 0.00 0.00 33.51 2.90
3086 5235 8.380644 CAGAAAATGATCATCACATTGCTTTTC 58.619 33.333 9.06 12.00 37.89 2.29
3091 5240 7.478322 ACTACAGAAAATGATCATCACATTGC 58.522 34.615 9.06 0.00 37.89 3.56
3092 5241 9.850628 AAACTACAGAAAATGATCATCACATTG 57.149 29.630 9.06 7.08 37.89 2.82
3094 5243 9.458727 AGAAACTACAGAAAATGATCATCACAT 57.541 29.630 9.06 0.00 0.00 3.21
3095 5244 8.853077 AGAAACTACAGAAAATGATCATCACA 57.147 30.769 9.06 0.00 0.00 3.58
3096 5245 9.552114 CAAGAAACTACAGAAAATGATCATCAC 57.448 33.333 9.06 3.83 0.00 3.06
3097 5246 8.239314 GCAAGAAACTACAGAAAATGATCATCA 58.761 33.333 9.06 0.00 0.00 3.07
3142 5315 1.400242 GCTGTTCGAACATGCCAGAAC 60.400 52.381 29.79 16.20 42.19 3.01
3144 5317 0.250252 TGCTGTTCGAACATGCCAGA 60.250 50.000 31.40 19.94 38.41 3.86
3465 5960 2.945008 ACCACATCATAAATCCTGCACG 59.055 45.455 0.00 0.00 0.00 5.34
3469 5964 6.375174 TCAGTGAAACCACATCATAAATCCTG 59.625 38.462 0.00 0.00 37.80 3.86
3477 5974 5.563592 TCTGATTCAGTGAAACCACATCAT 58.436 37.500 10.14 0.00 37.80 2.45
3612 6110 3.290710 GCAGAATTTCCCATAAGCAGGA 58.709 45.455 0.00 0.00 0.00 3.86
3897 6403 1.155889 TGAAGTTGCGCATCGTGAAT 58.844 45.000 12.75 0.00 0.00 2.57
3903 6409 1.154225 CCGGTTGAAGTTGCGCATC 60.154 57.895 12.75 11.46 0.00 3.91
3909 6415 0.878523 TCACGCTCCGGTTGAAGTTG 60.879 55.000 0.00 0.00 0.00 3.16
4439 6951 3.548818 GCAACACAACTCACTCAATGTCC 60.549 47.826 0.00 0.00 0.00 4.02
4502 7018 4.025647 GCCTAATTGTAATCAGCGTCAGAC 60.026 45.833 0.00 0.00 0.00 3.51
4767 7292 1.334556 CAACAAACACTGCTGCTGCTA 59.665 47.619 17.00 2.62 40.48 3.49
4841 7375 4.351938 TCGTGTCGTTCCCCAGCG 62.352 66.667 0.00 0.00 0.00 5.18
4885 7419 1.373497 GCGCATCTCCGATCCGATT 60.373 57.895 0.30 0.00 0.00 3.34
4905 7439 0.032678 AGTCCAACGACAGCTGTCTG 59.967 55.000 36.78 31.10 45.71 3.51
4908 7442 1.269998 GTCTAGTCCAACGACAGCTGT 59.730 52.381 21.88 21.88 41.87 4.40
4945 7479 1.068352 AAGTCCCTGCCTGGTTCCTT 61.068 55.000 0.00 0.00 0.00 3.36
4956 7490 2.427506 GCTCTTGTTACCAAGTCCCTG 58.572 52.381 0.00 0.00 46.70 4.45
4957 7491 1.002087 CGCTCTTGTTACCAAGTCCCT 59.998 52.381 0.00 0.00 46.70 4.20
4958 7492 1.001633 TCGCTCTTGTTACCAAGTCCC 59.998 52.381 0.00 0.00 46.70 4.46
4959 7493 2.450609 TCGCTCTTGTTACCAAGTCC 57.549 50.000 0.00 0.00 46.70 3.85
4960 7494 2.479275 GGTTCGCTCTTGTTACCAAGTC 59.521 50.000 0.00 0.00 46.70 3.01
4961 7495 2.158871 TGGTTCGCTCTTGTTACCAAGT 60.159 45.455 0.00 0.00 46.70 3.16
4963 7497 2.489971 CTGGTTCGCTCTTGTTACCAA 58.510 47.619 0.00 0.00 38.33 3.67
4964 7498 1.270625 CCTGGTTCGCTCTTGTTACCA 60.271 52.381 0.00 0.00 37.34 3.25
4965 7499 1.439679 CCTGGTTCGCTCTTGTTACC 58.560 55.000 0.00 0.00 0.00 2.85
4966 7500 0.796927 GCCTGGTTCGCTCTTGTTAC 59.203 55.000 0.00 0.00 0.00 2.50
4967 7501 0.394938 TGCCTGGTTCGCTCTTGTTA 59.605 50.000 0.00 0.00 0.00 2.41
4968 7502 0.886490 CTGCCTGGTTCGCTCTTGTT 60.886 55.000 0.00 0.00 0.00 2.83
4969 7503 1.302033 CTGCCTGGTTCGCTCTTGT 60.302 57.895 0.00 0.00 0.00 3.16
4970 7504 2.037136 CCTGCCTGGTTCGCTCTTG 61.037 63.158 0.00 0.00 0.00 3.02
4971 7505 2.348998 CCTGCCTGGTTCGCTCTT 59.651 61.111 0.00 0.00 0.00 2.85
4972 7506 3.710722 CCCTGCCTGGTTCGCTCT 61.711 66.667 0.00 0.00 0.00 4.09
4973 7507 4.785453 CCCCTGCCTGGTTCGCTC 62.785 72.222 0.00 0.00 0.00 5.03
4976 7510 4.351054 AAGCCCCTGCCTGGTTCG 62.351 66.667 0.00 0.00 38.69 3.95
4977 7511 2.677875 CAAGCCCCTGCCTGGTTC 60.678 66.667 0.00 0.00 38.69 3.62
4978 7512 4.305956 CCAAGCCCCTGCCTGGTT 62.306 66.667 0.00 0.00 43.04 3.67
4981 7515 1.678970 GTTACCAAGCCCCTGCCTG 60.679 63.158 0.00 0.00 38.69 4.85
4982 7516 1.725169 TTGTTACCAAGCCCCTGCCT 61.725 55.000 0.00 0.00 38.69 4.75
4983 7517 1.228737 TTGTTACCAAGCCCCTGCC 60.229 57.895 0.00 0.00 38.69 4.85
4984 7518 0.251165 TCTTGTTACCAAGCCCCTGC 60.251 55.000 0.00 0.00 46.33 4.85
4985 7519 1.826385 CTCTTGTTACCAAGCCCCTG 58.174 55.000 0.00 0.00 46.33 4.45
4986 7520 0.038310 GCTCTTGTTACCAAGCCCCT 59.962 55.000 0.00 0.00 46.33 4.79
4987 7521 0.251165 TGCTCTTGTTACCAAGCCCC 60.251 55.000 0.00 0.00 46.33 5.80
4988 7522 1.745653 GATGCTCTTGTTACCAAGCCC 59.254 52.381 0.00 0.00 46.33 5.19
4989 7523 2.716217 AGATGCTCTTGTTACCAAGCC 58.284 47.619 0.00 0.00 46.33 4.35
4990 7524 4.253685 TGTAGATGCTCTTGTTACCAAGC 58.746 43.478 0.00 0.00 46.33 4.01
4992 7526 4.253685 GCTGTAGATGCTCTTGTTACCAA 58.746 43.478 0.00 0.00 0.00 3.67
4993 7527 3.369471 GGCTGTAGATGCTCTTGTTACCA 60.369 47.826 0.00 0.00 0.00 3.25
4994 7528 3.198872 GGCTGTAGATGCTCTTGTTACC 58.801 50.000 0.00 0.00 0.00 2.85
4995 7529 2.860735 CGGCTGTAGATGCTCTTGTTAC 59.139 50.000 0.00 0.00 0.00 2.50
4996 7530 2.738643 GCGGCTGTAGATGCTCTTGTTA 60.739 50.000 0.00 0.00 0.00 2.41
4997 7531 2.009042 GCGGCTGTAGATGCTCTTGTT 61.009 52.381 0.00 0.00 0.00 2.83
4998 7532 0.460987 GCGGCTGTAGATGCTCTTGT 60.461 55.000 0.00 0.00 0.00 3.16
4999 7533 1.156645 GGCGGCTGTAGATGCTCTTG 61.157 60.000 0.00 0.00 0.00 3.02
5000 7534 1.144936 GGCGGCTGTAGATGCTCTT 59.855 57.895 0.00 0.00 0.00 2.85
5001 7535 2.818132 GGCGGCTGTAGATGCTCT 59.182 61.111 0.00 0.00 0.00 4.09
5002 7536 2.659897 CGGCGGCTGTAGATGCTC 60.660 66.667 7.61 0.00 0.00 4.26
5003 7537 4.227134 CCGGCGGCTGTAGATGCT 62.227 66.667 15.42 0.00 0.00 3.79
5021 7555 3.682292 ATCCGGGCGTTTGAGGAGC 62.682 63.158 0.00 0.00 36.08 4.70
5022 7556 1.815421 CATCCGGGCGTTTGAGGAG 60.815 63.158 0.00 0.00 36.08 3.69
5023 7557 2.267642 CATCCGGGCGTTTGAGGA 59.732 61.111 0.00 0.00 37.17 3.71
5024 7558 2.824041 CCATCCGGGCGTTTGAGG 60.824 66.667 0.00 0.00 0.00 3.86
5025 7559 2.106683 GTCCATCCGGGCGTTTGAG 61.107 63.158 0.00 0.00 36.21 3.02
5026 7560 2.046700 GTCCATCCGGGCGTTTGA 60.047 61.111 0.00 0.00 36.21 2.69
5053 7587 2.287393 TGATATGTTCACCGGTCACG 57.713 50.000 2.59 0.00 40.55 4.35
5054 7588 3.555956 GTCATGATATGTTCACCGGTCAC 59.444 47.826 2.59 5.10 37.11 3.67
5055 7589 3.431626 GGTCATGATATGTTCACCGGTCA 60.432 47.826 2.59 0.00 37.11 4.02
5056 7590 3.131396 GGTCATGATATGTTCACCGGTC 58.869 50.000 2.59 0.00 37.11 4.79
5057 7591 2.771943 AGGTCATGATATGTTCACCGGT 59.228 45.455 0.00 0.00 37.11 5.28
5058 7592 3.133691 CAGGTCATGATATGTTCACCGG 58.866 50.000 0.00 0.00 37.11 5.28
5059 7593 3.133691 CCAGGTCATGATATGTTCACCG 58.866 50.000 0.00 0.00 37.11 4.94
5060 7594 2.880890 GCCAGGTCATGATATGTTCACC 59.119 50.000 0.00 0.00 37.11 4.02
5061 7595 2.880890 GGCCAGGTCATGATATGTTCAC 59.119 50.000 0.00 0.00 37.11 3.18
5062 7596 2.485302 CGGCCAGGTCATGATATGTTCA 60.485 50.000 2.24 0.00 39.12 3.18
5063 7597 2.146342 CGGCCAGGTCATGATATGTTC 58.854 52.381 2.24 0.00 0.00 3.18
5064 7598 1.202806 CCGGCCAGGTCATGATATGTT 60.203 52.381 2.24 0.00 34.51 2.71
5065 7599 0.397941 CCGGCCAGGTCATGATATGT 59.602 55.000 2.24 0.00 34.51 2.29
5066 7600 0.321919 CCCGGCCAGGTCATGATATG 60.322 60.000 2.24 0.54 38.74 1.78
5067 7601 1.492133 CCCCGGCCAGGTCATGATAT 61.492 60.000 3.77 0.00 38.74 1.63
5068 7602 2.146724 CCCCGGCCAGGTCATGATA 61.147 63.158 3.77 0.00 38.74 2.15
5069 7603 3.492353 CCCCGGCCAGGTCATGAT 61.492 66.667 3.77 0.00 38.74 2.45
5077 7611 3.646715 TTTGAGGACCCCGGCCAG 61.647 66.667 2.24 0.00 0.00 4.85
5078 7612 3.961414 GTTTGAGGACCCCGGCCA 61.961 66.667 2.24 0.00 0.00 5.36
5079 7613 4.735358 GGTTTGAGGACCCCGGCC 62.735 72.222 0.00 0.00 33.41 6.13
5107 7641 1.392710 GGGTGTCGATCAGTCCGGAT 61.393 60.000 7.81 0.00 0.00 4.18
5120 7654 5.979288 ATAGGATGTATACGAAGGGTGTC 57.021 43.478 0.00 0.00 0.00 3.67
5121 7655 6.318144 CGATATAGGATGTATACGAAGGGTGT 59.682 42.308 0.00 0.00 0.00 4.16
5126 7660 8.004905 CGTCATCGATATAGGATGTATACGAAG 58.995 40.741 16.11 0.00 39.76 3.79
5127 7661 7.042254 CCGTCATCGATATAGGATGTATACGAA 60.042 40.741 19.58 1.65 39.76 3.85
5140 11501 5.998363 CCTCCTCATATCCGTCATCGATATA 59.002 44.000 0.00 0.00 39.71 0.86
5188 11549 1.135024 GGTAACGATAGGTGTCCGCAA 60.135 52.381 0.00 0.00 43.77 4.85
5211 11572 4.870190 GTGTCCTCACCAAACCGT 57.130 55.556 0.00 0.00 38.51 4.83
5240 11601 0.041090 AATTTGGCCCCTCAACCGAT 59.959 50.000 0.00 0.00 0.00 4.18
5242 11603 1.890174 GAATTTGGCCCCTCAACCG 59.110 57.895 0.00 0.00 0.00 4.44
5279 11640 2.748350 GATAGGGTTAGGGGCCGC 59.252 66.667 12.88 12.88 0.00 6.53
5282 11643 1.057471 GACTGGATAGGGTTAGGGGC 58.943 60.000 0.00 0.00 0.00 5.80
5296 11657 1.123928 GAGGATGGTACTGGGACTGG 58.876 60.000 0.00 0.00 0.00 4.00
5298 11659 1.062810 GGAGAGGATGGTACTGGGACT 60.063 57.143 0.00 0.00 0.00 3.85
5305 11666 2.027751 GCGCGGAGAGGATGGTAC 59.972 66.667 8.83 0.00 0.00 3.34
5333 11694 2.887568 GAGCCGCGAGTGGATGTG 60.888 66.667 8.23 0.00 0.00 3.21
5334 11695 4.498520 CGAGCCGCGAGTGGATGT 62.499 66.667 8.23 0.00 44.57 3.06
5335 11696 4.193334 TCGAGCCGCGAGTGGATG 62.193 66.667 8.23 0.00 45.59 3.51
5343 11704 1.444553 AGAAGAGTTTCGAGCCGCG 60.445 57.895 0.00 0.00 38.38 6.46
5344 11705 1.960994 GCAGAAGAGTTTCGAGCCGC 61.961 60.000 0.00 0.00 38.38 6.53
5345 11706 1.355066 GGCAGAAGAGTTTCGAGCCG 61.355 60.000 9.74 0.00 43.94 5.52
5346 11707 2.461416 GGCAGAAGAGTTTCGAGCC 58.539 57.895 9.74 9.74 45.36 4.70
5352 11713 1.518903 GCAAGCGGGCAGAAGAGTTT 61.519 55.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.