Multiple sequence alignment - TraesCS6D01G110800

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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 TraesCS6D01G110800 chr6D 100.000 2790 0 0 1 2790 77526112 77523323 0.000000e+00 5153
1 TraesCS6D01G110800 chr6B 93.829 794 33 8 1467 2255 150151628 150150846 0.000000e+00 1181
2 TraesCS6D01G110800 chr6B 91.725 713 39 13 384 1086 150152647 150151945 0.000000e+00 972
3 TraesCS6D01G110800 chr6B 96.034 353 14 0 1104 1456 150151957 150151605 2.410000e-160 575
4 TraesCS6D01G110800 chr6B 90.657 396 29 5 1 390 150153076 150152683 1.150000e-143 520
5 TraesCS6D01G110800 chr6A 92.847 713 35 5 1557 2253 92853207 92852495 0.000000e+00 1020
6 TraesCS6D01G110800 chr6A 92.479 585 20 10 878 1456 92853886 92853320 0.000000e+00 815
7 TraesCS6D01G110800 chr6A 95.789 95 2 2 1 94 92853980 92853887 4.810000e-33 152
8 TraesCS6D01G110800 chr6A 98.750 80 1 0 1476 1555 92853332 92853253 2.900000e-30 143
9 TraesCS6D01G110800 chr6A 88.043 92 10 1 169 260 359152871 359152961 1.060000e-19 108
10 TraesCS6D01G110800 chr6A 85.714 98 12 2 169 266 535854798 535854893 4.920000e-18 102
11 TraesCS6D01G110800 chr2B 87.037 324 31 7 2258 2580 420609179 420609492 3.420000e-94 355
12 TraesCS6D01G110800 chr2B 89.151 212 22 1 2580 2790 420609525 420609736 2.130000e-66 263
13 TraesCS6D01G110800 chr2B 78.543 247 38 12 1837 2076 770660768 770660530 6.230000e-32 148
14 TraesCS6D01G110800 chr7A 77.333 300 54 10 1838 2130 37374870 37374578 6.180000e-37 165
15 TraesCS6D01G110800 chr7A 78.481 237 30 12 1835 2067 638488910 638489129 4.850000e-28 135
16 TraesCS6D01G110800 chr7A 90.217 92 8 1 169 260 486925671 486925761 4.880000e-23 119
17 TraesCS6D01G110800 chr3B 78.058 278 42 14 1835 2099 673137857 673137586 1.030000e-34 158
18 TraesCS6D01G110800 chr4A 82.081 173 24 5 1838 2007 167305722 167305890 1.040000e-29 141
19 TraesCS6D01G110800 chr1B 77.974 227 43 5 1836 2059 659726162 659726384 4.850000e-28 135
20 TraesCS6D01G110800 chr5D 82.692 156 21 4 1838 1990 426475629 426475781 1.740000e-27 134
21 TraesCS6D01G110800 chr4B 89.130 92 9 1 169 260 5927360 5927450 2.270000e-21 113
22 TraesCS6D01G110800 chr3A 87.629 97 11 1 165 261 383471678 383471773 8.170000e-21 111
23 TraesCS6D01G110800 chr2A 86.139 101 12 2 166 266 707748303 707748401 1.060000e-19 108
24 TraesCS6D01G110800 chr7B 86.316 95 12 1 169 263 664917079 664916986 4.920000e-18 102
25 TraesCS6D01G110800 chr2D 89.157 83 7 2 184 266 63908274 63908194 4.920000e-18 102


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 TraesCS6D01G110800 chr6D 77523323 77526112 2789 True 5153.0 5153 100.00000 1 2790 1 chr6D.!!$R1 2789
1 TraesCS6D01G110800 chr6B 150150846 150153076 2230 True 812.0 1181 93.06125 1 2255 4 chr6B.!!$R1 2254
2 TraesCS6D01G110800 chr6A 92852495 92853980 1485 True 532.5 1020 94.96625 1 2253 4 chr6A.!!$R1 2252
3 TraesCS6D01G110800 chr2B 420609179 420609736 557 False 309.0 355 88.09400 2258 2790 2 chr2B.!!$F1 532

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
526 575 0.249657 TTTGGGTGGCATTTGCGAAC 60.25 50.0 0.0 0.0 43.26 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 2143 0.03779 GTCCTCACTCAGTGACAGGC 60.038 60.0 2.36 0.0 37.67 4.85 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
36 37 3.264450 AGACCTCCCAACATCGATCTTTT 59.736 43.478 0.00 0.00 0.00 2.27
37 38 3.610911 ACCTCCCAACATCGATCTTTTC 58.389 45.455 0.00 0.00 0.00 2.29
39 40 3.624861 CCTCCCAACATCGATCTTTTCTG 59.375 47.826 0.00 0.00 0.00 3.02
84 86 4.888326 TTTGTGGAGATTTGGATTTGGG 57.112 40.909 0.00 0.00 0.00 4.12
123 125 5.365619 ACCGAAAAGACTTGTGAATGTACT 58.634 37.500 0.00 0.00 0.00 2.73
165 167 3.575256 TGACGTTTGGGTCACTACAGTAT 59.425 43.478 0.00 0.00 41.76 2.12
176 178 6.781507 GGGTCACTACAGTATATTACTCCCTT 59.218 42.308 0.00 0.00 36.76 3.95
193 195 3.521937 TCCCTTCATCCCGAATTACTTGT 59.478 43.478 0.00 0.00 31.69 3.16
217 221 7.142021 GTCACATATATGGATGTATCTAGGCG 58.858 42.308 16.96 0.00 37.99 5.52
228 232 8.426489 TGGATGTATCTAGGCGTATTTTAGTTT 58.574 33.333 0.00 0.00 0.00 2.66
296 300 9.184523 CATGGAGGGAGTAGTTTATAGAGATAG 57.815 40.741 0.00 0.00 0.00 2.08
319 323 7.617041 AGTATTTACAAAGCTCATCCTGAAC 57.383 36.000 0.00 0.00 0.00 3.18
340 344 8.506168 TGAACGAAGCAAAATTAGAGGAATAT 57.494 30.769 0.00 0.00 0.00 1.28
345 349 7.530861 CGAAGCAAAATTAGAGGAATATAACGC 59.469 37.037 0.00 0.00 0.00 4.84
360 364 2.341318 AACGCGATTTTGTTTAGGCC 57.659 45.000 15.93 0.00 0.00 5.19
363 367 1.613270 GCGATTTTGTTTAGGCCACG 58.387 50.000 5.01 0.00 0.00 4.94
368 372 3.907894 TTTTGTTTAGGCCACGTGATC 57.092 42.857 19.30 8.60 0.00 2.92
378 382 2.231235 GGCCACGTGATCTTGGAAAAAT 59.769 45.455 19.30 0.00 35.33 1.82
379 383 3.306019 GGCCACGTGATCTTGGAAAAATT 60.306 43.478 19.30 0.00 35.33 1.82
380 384 3.674753 GCCACGTGATCTTGGAAAAATTG 59.325 43.478 19.30 0.00 35.33 2.32
386 390 8.183536 CACGTGATCTTGGAAAAATTGATGATA 58.816 33.333 10.90 0.00 0.00 2.15
387 391 8.184192 ACGTGATCTTGGAAAAATTGATGATAC 58.816 33.333 0.00 0.00 0.00 2.24
388 392 8.183536 CGTGATCTTGGAAAAATTGATGATACA 58.816 33.333 0.00 0.00 0.00 2.29
494 543 4.631377 TGCAATGGACTTTCTTATCTCACG 59.369 41.667 0.00 0.00 0.00 4.35
497 546 4.451629 TGGACTTTCTTATCTCACGGAC 57.548 45.455 0.00 0.00 0.00 4.79
501 550 4.879598 ACTTTCTTATCTCACGGACGTTT 58.120 39.130 0.00 0.00 0.00 3.60
522 571 0.603439 CTGGTTTGGGTGGCATTTGC 60.603 55.000 0.00 0.00 41.14 3.68
526 575 0.249657 TTTGGGTGGCATTTGCGAAC 60.250 50.000 0.00 0.00 43.26 3.95
557 606 8.999431 TGATGACTATTTTAGTTGTTTGGAGAC 58.001 33.333 0.00 0.00 39.59 3.36
561 610 5.684550 ATTTTAGTTGTTTGGAGACCGAC 57.315 39.130 0.00 0.00 0.00 4.79
562 611 4.411256 TTTAGTTGTTTGGAGACCGACT 57.589 40.909 0.00 0.00 0.00 4.18
582 631 5.365403 ACTGTTTCTTCAAAACAACACGA 57.635 34.783 5.03 0.00 39.36 4.35
583 632 5.151389 ACTGTTTCTTCAAAACAACACGAC 58.849 37.500 5.03 0.00 39.36 4.34
630 679 8.565855 TTTTGAGTAAAAACGAGCAGAAACTGC 61.566 37.037 14.74 14.74 43.64 4.40
646 695 1.945394 ACTGCCATCATTTGATCTCGC 59.055 47.619 0.00 0.00 31.21 5.03
662 711 2.158143 CTCGCGTCGCAACTAAAATTG 58.842 47.619 18.75 0.00 0.00 2.32
728 777 7.412137 ACCGATTTGTAATACCTTTATACGC 57.588 36.000 0.00 0.00 0.00 4.42
777 826 6.425721 GGCGAGTATTTTTGTATGTGCCTATA 59.574 38.462 0.00 0.00 35.92 1.31
778 827 7.119262 GGCGAGTATTTTTGTATGTGCCTATAT 59.881 37.037 0.00 0.00 35.92 0.86
808 857 6.441093 ACGTGATTCACATCTATGCATTTT 57.559 33.333 16.61 0.00 33.40 1.82
809 858 6.489675 ACGTGATTCACATCTATGCATTTTC 58.510 36.000 16.61 0.00 33.40 2.29
810 859 6.317140 ACGTGATTCACATCTATGCATTTTCT 59.683 34.615 16.61 0.00 33.40 2.52
811 860 6.631636 CGTGATTCACATCTATGCATTTTCTG 59.368 38.462 16.61 0.46 33.40 3.02
812 861 7.466320 CGTGATTCACATCTATGCATTTTCTGA 60.466 37.037 16.61 0.00 33.40 3.27
813 862 7.856398 GTGATTCACATCTATGCATTTTCTGAG 59.144 37.037 3.54 0.00 34.08 3.35
815 864 8.693120 ATTCACATCTATGCATTTTCTGAGAT 57.307 30.769 3.54 2.70 0.00 2.75
816 865 8.515695 TTCACATCTATGCATTTTCTGAGATT 57.484 30.769 3.54 0.00 0.00 2.40
842 891 3.380471 AGTGCATAATTGGGTAAGCCA 57.620 42.857 0.00 0.00 36.17 4.75
850 899 2.684001 TTGGGTAAGCCATGTACTCG 57.316 50.000 0.00 0.00 36.17 4.18
855 904 3.381949 GGTAAGCCATGTACTCGATGAC 58.618 50.000 0.00 0.00 34.09 3.06
856 905 3.068307 GGTAAGCCATGTACTCGATGACT 59.932 47.826 0.00 0.00 34.09 3.41
859 908 2.099921 AGCCATGTACTCGATGACTCAC 59.900 50.000 0.00 0.00 0.00 3.51
860 909 2.799917 GCCATGTACTCGATGACTCACC 60.800 54.545 0.00 0.00 0.00 4.02
861 910 2.690497 CCATGTACTCGATGACTCACCT 59.310 50.000 0.00 0.00 0.00 4.00
885 941 7.168302 CCTTTGCACGTACATGTTTTATCAAAA 59.832 33.333 2.30 0.00 0.00 2.44
888 944 8.581057 TGCACGTACATGTTTTATCAAAATTT 57.419 26.923 2.30 0.00 32.22 1.82
889 945 8.695284 TGCACGTACATGTTTTATCAAAATTTC 58.305 29.630 2.30 0.00 32.22 2.17
890 946 8.695284 GCACGTACATGTTTTATCAAAATTTCA 58.305 29.630 2.30 0.00 32.22 2.69
928 985 8.201464 ACACTATATGATCGATGTGGTTTTACA 58.799 33.333 0.54 0.00 34.63 2.41
937 994 7.124347 TCGATGTGGTTTTACATTTGTAGAC 57.876 36.000 0.00 0.00 41.15 2.59
1019 1076 2.035449 TGACCGGCCTAACATAGATTCG 59.965 50.000 0.00 0.00 0.00 3.34
1036 1093 5.059833 AGATTCGGTAGGATTTGATTCAGC 58.940 41.667 0.00 0.00 0.00 4.26
1058 1115 2.640332 AGAAACTTCTTCTCCCCCACTC 59.360 50.000 0.00 0.00 32.55 3.51
1073 1130 2.393768 ACTCAGCATTTGCCGCGAG 61.394 57.895 8.23 10.84 43.38 5.03
1085 1142 3.782244 CGCGAGCAGGCAACACTC 61.782 66.667 0.00 0.00 38.34 3.51
1086 1143 3.426568 GCGAGCAGGCAACACTCC 61.427 66.667 0.00 0.00 38.45 3.85
1087 1144 2.345244 CGAGCAGGCAACACTCCT 59.655 61.111 0.00 0.00 38.45 3.69
1091 1148 3.664495 CAGGCAACACTCCTGCAG 58.336 61.111 6.78 6.78 43.88 4.41
1092 1149 1.228063 CAGGCAACACTCCTGCAGT 60.228 57.895 13.81 0.00 43.88 4.40
1093 1150 1.072159 AGGCAACACTCCTGCAGTC 59.928 57.895 13.81 0.00 41.78 3.51
1094 1151 1.968540 GGCAACACTCCTGCAGTCC 60.969 63.158 13.81 0.00 41.78 3.85
1095 1152 1.072159 GCAACACTCCTGCAGTCCT 59.928 57.895 13.81 0.00 39.69 3.85
1096 1153 1.233285 GCAACACTCCTGCAGTCCTG 61.233 60.000 13.81 6.59 39.69 3.86
1106 1163 4.421515 CAGTCCTGCTGGCCCCAG 62.422 72.222 9.98 9.98 46.15 4.45
1212 1299 4.379143 CTCGTCGTCGTGGTCGCA 62.379 66.667 1.33 0.00 38.33 5.10
1238 1325 1.817941 GTGCGGGCGTACCATCATT 60.818 57.895 0.00 0.00 40.22 2.57
1349 1436 2.594592 GAAAGCCGGTGGTGCAGT 60.595 61.111 1.90 0.00 0.00 4.40
1444 1535 1.154016 AACAGATGAGACGTCGCGG 60.154 57.895 14.68 6.66 0.00 6.46
1445 1536 2.951745 CAGATGAGACGTCGCGGC 60.952 66.667 14.68 1.93 33.59 6.53
1446 1537 4.538283 AGATGAGACGTCGCGGCG 62.538 66.667 33.66 33.66 41.28 6.46
1447 1538 4.531912 GATGAGACGTCGCGGCGA 62.532 66.667 41.68 22.69 41.28 5.54
1456 1547 2.666862 TCGCGGCGACCATGTTTT 60.667 55.556 22.69 0.00 0.00 2.43
1457 1548 2.254051 CGCGGCGACCATGTTTTT 59.746 55.556 19.16 0.00 0.00 1.94
1535 1626 2.690367 GAGGTCAAAGCTCCCTCCT 58.310 57.895 9.45 5.57 39.10 3.69
1669 1812 0.545646 ATCTCTCCCTGCTGCCTTTC 59.454 55.000 0.00 0.00 0.00 2.62
1722 1866 7.061905 CGTCTTTCTGAAGATATTGTGTACGTT 59.938 37.037 0.00 0.00 43.41 3.99
1807 1951 0.683973 AAATGGCGCATGGGAAACAA 59.316 45.000 14.90 0.00 0.00 2.83
1809 1953 0.176219 ATGGCGCATGGGAAACAATG 59.824 50.000 14.90 0.00 0.00 2.82
1857 2001 8.367660 TCAAAGAGGTAATATCACTGAGAGTT 57.632 34.615 0.00 0.00 0.00 3.01
1861 2005 8.458573 AGAGGTAATATCACTGAGAGTTACAG 57.541 38.462 11.93 0.00 40.68 2.74
1955 2107 4.630069 ACTCAAGCGTGTAAATATGGTCAC 59.370 41.667 0.00 0.00 0.00 3.67
1969 2121 0.441145 GGTCACGAACGTAATGTGGC 59.559 55.000 12.87 11.45 37.49 5.01
2033 2185 1.481819 CGGGCTATGCATTTTTGCGC 61.482 55.000 3.54 11.84 37.69 6.09
2132 2290 4.846779 TTTATTTGCAGAAAAGTCGCCT 57.153 36.364 0.00 0.00 0.00 5.52
2153 2311 1.001406 ACTGGCTACTGTTCTGCTCAC 59.999 52.381 0.00 0.00 0.00 3.51
2174 2333 6.028368 TCACGATGCGAAAAGTAAAACAAAA 58.972 32.000 0.00 0.00 0.00 2.44
2180 2339 4.260456 GCGAAAAGTAAAACAAAAAGGGCC 60.260 41.667 0.00 0.00 0.00 5.80
2301 2460 4.282195 GTCAATCCTATCTCTTCCCACGAT 59.718 45.833 0.00 0.00 0.00 3.73
2302 2461 5.477291 GTCAATCCTATCTCTTCCCACGATA 59.523 44.000 0.00 0.00 0.00 2.92
2308 2467 6.782988 TCCTATCTCTTCCCACGATAATTCTT 59.217 38.462 0.00 0.00 0.00 2.52
2310 2469 5.277857 TCTCTTCCCACGATAATTCTTCC 57.722 43.478 0.00 0.00 0.00 3.46
2319 2478 2.222027 GATAATTCTTCCCCCACGCAG 58.778 52.381 0.00 0.00 0.00 5.18
2371 2530 1.153469 CTCTTCCCTTCCTCGCAGC 60.153 63.158 0.00 0.00 0.00 5.25
2374 2533 3.254024 TTCCCTTCCTCGCAGCCAC 62.254 63.158 0.00 0.00 0.00 5.01
2380 2539 3.869272 CCTCGCAGCCACGCATTC 61.869 66.667 0.00 0.00 0.00 2.67
2387 2546 0.806868 CAGCCACGCATTCAGTCAAT 59.193 50.000 0.00 0.00 0.00 2.57
2397 2556 4.367386 CATTCAGTCAATGCCCTTCTTC 57.633 45.455 0.00 0.00 35.66 2.87
2415 2574 2.757077 CCCACCTCTCCCCAACAC 59.243 66.667 0.00 0.00 0.00 3.32
2417 2576 2.153401 CCACCTCTCCCCAACACCA 61.153 63.158 0.00 0.00 0.00 4.17
2422 2581 1.903877 CTCTCCCCAACACCAGCGAT 61.904 60.000 0.00 0.00 0.00 4.58
2430 2589 0.107508 AACACCAGCGATGGATCCAG 60.108 55.000 29.47 12.52 0.00 3.86
2436 2595 3.125376 GCGATGGATCCAGCCCCTT 62.125 63.158 23.90 3.38 0.00 3.95
2440 2599 1.659035 ATGGATCCAGCCCCTTTCCC 61.659 60.000 21.33 0.00 0.00 3.97
2462 2621 4.828296 CCACCCCCATGCAGCCTC 62.828 72.222 0.00 0.00 0.00 4.70
2468 2627 2.372890 CCCATGCAGCCTCTCTCCA 61.373 63.158 0.00 0.00 0.00 3.86
2480 2639 2.465813 CTCTCTCCACATCCTCACCTT 58.534 52.381 0.00 0.00 0.00 3.50
2481 2640 3.628513 CCTCTCTCCACATCCTCACCTTA 60.629 52.174 0.00 0.00 0.00 2.69
2482 2641 3.366396 TCTCTCCACATCCTCACCTTAC 58.634 50.000 0.00 0.00 0.00 2.34
2483 2642 2.432510 CTCTCCACATCCTCACCTTACC 59.567 54.545 0.00 0.00 0.00 2.85
2484 2643 2.044492 TCTCCACATCCTCACCTTACCT 59.956 50.000 0.00 0.00 0.00 3.08
2485 2644 2.840651 CTCCACATCCTCACCTTACCTT 59.159 50.000 0.00 0.00 0.00 3.50
2486 2645 3.256704 TCCACATCCTCACCTTACCTTT 58.743 45.455 0.00 0.00 0.00 3.11
2497 2656 1.271163 CCTTACCTTTGCTCGTTCCCA 60.271 52.381 0.00 0.00 0.00 4.37
2498 2657 2.618045 CCTTACCTTTGCTCGTTCCCAT 60.618 50.000 0.00 0.00 0.00 4.00
2499 2658 2.107950 TACCTTTGCTCGTTCCCATG 57.892 50.000 0.00 0.00 0.00 3.66
2500 2659 0.400213 ACCTTTGCTCGTTCCCATGA 59.600 50.000 0.00 0.00 0.00 3.07
2502 2661 0.443869 CTTTGCTCGTTCCCATGACG 59.556 55.000 0.00 0.00 41.62 4.35
2503 2662 0.953471 TTTGCTCGTTCCCATGACGG 60.953 55.000 5.69 0.00 40.70 4.79
2504 2663 2.107041 TTGCTCGTTCCCATGACGGT 62.107 55.000 5.69 0.00 40.70 4.83
2507 2666 1.868519 GCTCGTTCCCATGACGGTATC 60.869 57.143 5.69 0.00 40.70 2.24
2511 2670 0.468226 TTCCCATGACGGTATCAGGC 59.532 55.000 0.00 0.00 41.91 4.85
2517 2676 1.299468 GACGGTATCAGGCTCTGCG 60.299 63.158 0.00 0.00 0.00 5.18
2529 2688 3.788616 CTCTGCGCTGCTAGAGCCC 62.789 68.421 9.73 0.00 46.01 5.19
2574 2733 0.179006 GACATGGATGGGAAGAGGGC 60.179 60.000 0.00 0.00 0.00 5.19
2589 2781 4.176752 GGCGTGGAGGGGATGGTC 62.177 72.222 0.00 0.00 0.00 4.02
2597 2789 0.466124 GAGGGGATGGTCTGTGCTAC 59.534 60.000 0.00 0.00 0.00 3.58
2617 2809 4.400961 AGCTGCGCTCCCTTCCAC 62.401 66.667 9.73 0.00 30.62 4.02
2625 2817 1.817099 CTCCCTTCCACATCGCAGC 60.817 63.158 0.00 0.00 0.00 5.25
2629 2821 0.531532 CCTTCCACATCGCAGCTAGG 60.532 60.000 0.00 0.00 0.00 3.02
2653 2845 2.573869 CCCATCGACACTCGTGCT 59.426 61.111 0.00 0.00 41.35 4.40
2671 2863 0.248843 CTGAGGTGTTCCTGGCTCTC 59.751 60.000 0.00 0.00 45.24 3.20
2680 2872 0.614697 TCCTGGCTCTCCATCGTCAA 60.615 55.000 0.00 0.00 42.51 3.18
2681 2873 0.250234 CCTGGCTCTCCATCGTCAAA 59.750 55.000 0.00 0.00 42.51 2.69
2684 2876 1.079503 GGCTCTCCATCGTCAAACAC 58.920 55.000 0.00 0.00 0.00 3.32
2686 2878 2.143122 GCTCTCCATCGTCAAACACAA 58.857 47.619 0.00 0.00 0.00 3.33
2690 2882 1.606668 TCCATCGTCAAACACAAAGGC 59.393 47.619 0.00 0.00 0.00 4.35
2691 2883 1.662876 CCATCGTCAAACACAAAGGCG 60.663 52.381 0.00 0.00 0.00 5.52
2718 2911 3.003378 GGAAATTACACGGGATAAGCTGC 59.997 47.826 0.00 0.00 0.00 5.25
2752 2945 2.558378 CATCGACCACATGCTCATCTT 58.442 47.619 0.00 0.00 0.00 2.40
2756 2949 1.131883 GACCACATGCTCATCTTGCAC 59.868 52.381 0.00 0.00 43.59 4.57
2757 2950 0.098200 CCACATGCTCATCTTGCACG 59.902 55.000 0.00 0.00 43.59 5.34
2759 2952 1.081892 ACATGCTCATCTTGCACGAC 58.918 50.000 0.00 0.00 43.59 4.34
2760 2953 1.338484 ACATGCTCATCTTGCACGACT 60.338 47.619 0.00 0.00 43.59 4.18
2784 2977 2.877866 TCTTCGACCTTTCTCTCTGGT 58.122 47.619 0.00 0.00 36.70 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 7.324935 TGAACACTAACAAGAAACAGTACAGA 58.675 34.615 0.00 0.00 0.00 3.41
37 38 7.534085 TGAACACTAACAAGAAACAGTACAG 57.466 36.000 0.00 0.00 0.00 2.74
39 40 9.783256 AAAATGAACACTAACAAGAAACAGTAC 57.217 29.630 0.00 0.00 0.00 2.73
94 96 4.124238 TCACAAGTCTTTTCGGTACAAGG 58.876 43.478 0.00 0.00 0.00 3.61
102 104 5.107065 GGGAGTACATTCACAAGTCTTTTCG 60.107 44.000 0.00 0.00 0.00 3.46
104 106 5.941788 AGGGAGTACATTCACAAGTCTTTT 58.058 37.500 0.00 0.00 0.00 2.27
146 148 7.486647 AGTAATATACTGTAGTGACCCAAACG 58.513 38.462 0.00 0.00 37.69 3.60
151 153 6.313324 AGGGAGTAATATACTGTAGTGACCC 58.687 44.000 0.00 0.00 39.59 4.46
161 163 5.900437 TCGGGATGAAGGGAGTAATATACT 58.100 41.667 0.00 0.00 42.86 2.12
165 167 6.785963 AGTAATTCGGGATGAAGGGAGTAATA 59.214 38.462 0.00 0.00 40.65 0.98
176 178 4.545208 TGTGACAAGTAATTCGGGATGA 57.455 40.909 0.00 0.00 0.00 2.92
193 195 6.833933 ACGCCTAGATACATCCATATATGTGA 59.166 38.462 11.73 8.77 40.29 3.58
251 255 7.337942 CCTCCATGCTACTTCTGAAATTACTTT 59.662 37.037 0.00 0.00 0.00 2.66
261 265 2.114616 ACTCCCTCCATGCTACTTCTG 58.885 52.381 0.00 0.00 0.00 3.02
265 269 3.406512 AACTACTCCCTCCATGCTACT 57.593 47.619 0.00 0.00 0.00 2.57
267 271 6.860034 TCTATAAACTACTCCCTCCATGCTA 58.140 40.000 0.00 0.00 0.00 3.49
319 323 7.530861 GCGTTATATTCCTCTAATTTTGCTTCG 59.469 37.037 0.00 0.00 0.00 3.79
340 344 2.812591 TGGCCTAAACAAAATCGCGTTA 59.187 40.909 5.77 0.00 0.00 3.18
345 349 2.224549 TCACGTGGCCTAAACAAAATCG 59.775 45.455 17.00 0.00 0.00 3.34
360 364 6.380995 TCATCAATTTTTCCAAGATCACGTG 58.619 36.000 9.94 9.94 0.00 4.49
363 367 9.859427 TTGTATCATCAATTTTTCCAAGATCAC 57.141 29.630 0.00 0.00 0.00 3.06
390 394 9.331282 GGCTTCATTACATACTTCTAAGTGAAT 57.669 33.333 5.62 0.00 40.07 2.57
391 395 7.491372 CGGCTTCATTACATACTTCTAAGTGAA 59.509 37.037 5.62 0.00 40.07 3.18
392 396 6.978659 CGGCTTCATTACATACTTCTAAGTGA 59.021 38.462 5.62 0.00 40.07 3.41
440 489 3.610911 CTGACAGGTTCCCCTTAACATC 58.389 50.000 0.00 0.00 39.89 3.06
466 515 8.587608 TGAGATAAGAAAGTCCATTGCAAATTT 58.412 29.630 1.71 0.00 0.00 1.82
473 522 5.292101 GTCCGTGAGATAAGAAAGTCCATTG 59.708 44.000 0.00 0.00 0.00 2.82
494 543 1.362355 CCCAAACCAGCAAACGTCC 59.638 57.895 0.00 0.00 0.00 4.79
497 546 1.067250 CCACCCAAACCAGCAAACG 59.933 57.895 0.00 0.00 0.00 3.60
501 550 1.053264 AAATGCCACCCAAACCAGCA 61.053 50.000 0.00 0.00 37.94 4.41
522 571 8.827599 CAACTAAAATAGTCATCAAAACGTTCG 58.172 33.333 0.00 0.00 38.26 3.95
551 600 2.036387 TGAAGAAACAGTCGGTCTCCA 58.964 47.619 0.00 0.00 0.00 3.86
557 606 4.557301 GTGTTGTTTTGAAGAAACAGTCGG 59.443 41.667 4.75 0.00 40.70 4.79
561 610 5.150683 TGTCGTGTTGTTTTGAAGAAACAG 58.849 37.500 4.75 0.00 40.70 3.16
562 611 5.109662 TGTCGTGTTGTTTTGAAGAAACA 57.890 34.783 0.55 0.55 38.26 2.83
582 631 9.578439 CAAAATCTCTTTCTTCTCAAAAACTGT 57.422 29.630 0.00 0.00 0.00 3.55
583 632 9.793252 TCAAAATCTCTTTCTTCTCAAAAACTG 57.207 29.630 0.00 0.00 0.00 3.16
630 679 1.190984 CGACGCGAGATCAAATGATGG 59.809 52.381 15.93 0.00 34.37 3.51
635 684 0.370273 GTTGCGACGCGAGATCAAAT 59.630 50.000 15.93 0.00 0.00 2.32
662 711 1.939934 GTTGGAAAAGGGTTTGCTTGC 59.060 47.619 0.00 0.00 36.14 4.01
728 777 2.490328 AATTGGCACACACAAACTCG 57.510 45.000 0.00 0.00 39.29 4.18
777 826 8.712363 GCATAGATGTGAATCACGTTATAACAT 58.288 33.333 15.67 9.52 37.14 2.71
778 827 7.708752 TGCATAGATGTGAATCACGTTATAACA 59.291 33.333 15.67 3.92 37.14 2.41
833 882 2.364324 TCATCGAGTACATGGCTTACCC 59.636 50.000 0.00 0.00 33.59 3.69
842 891 4.748892 CAAAGGTGAGTCATCGAGTACAT 58.251 43.478 0.00 0.00 0.00 2.29
850 899 1.512926 ACGTGCAAAGGTGAGTCATC 58.487 50.000 0.00 0.00 0.00 2.92
855 904 2.143122 ACATGTACGTGCAAAGGTGAG 58.857 47.619 11.22 0.00 0.00 3.51
856 905 2.248280 ACATGTACGTGCAAAGGTGA 57.752 45.000 11.22 0.00 0.00 4.02
859 908 5.694816 TGATAAAACATGTACGTGCAAAGG 58.305 37.500 11.22 6.12 0.00 3.11
860 909 7.616103 TTTGATAAAACATGTACGTGCAAAG 57.384 32.000 11.22 9.11 0.00 2.77
861 910 7.987268 TTTTGATAAAACATGTACGTGCAAA 57.013 28.000 11.22 12.30 0.00 3.68
885 941 9.547753 CATATAGTGTACTAAGCCAACTGAAAT 57.452 33.333 0.00 0.00 31.39 2.17
888 944 7.891498 TCATATAGTGTACTAAGCCAACTGA 57.109 36.000 0.00 0.00 31.39 3.41
889 945 7.539022 CGATCATATAGTGTACTAAGCCAACTG 59.461 40.741 0.00 0.00 31.39 3.16
890 946 7.447545 TCGATCATATAGTGTACTAAGCCAACT 59.552 37.037 0.00 0.00 31.39 3.16
891 947 7.591165 TCGATCATATAGTGTACTAAGCCAAC 58.409 38.462 0.00 0.00 31.39 3.77
928 985 2.264005 TGTTGCCACCGTCTACAAAT 57.736 45.000 0.00 0.00 0.00 2.32
1019 1076 5.649831 AGTTTCTGCTGAATCAAATCCTACC 59.350 40.000 14.51 0.00 31.56 3.18
1036 1093 2.373502 AGTGGGGGAGAAGAAGTTTCTG 59.626 50.000 0.00 0.00 37.65 3.02
1089 1146 4.421515 CTGGGGCCAGCAGGACTG 62.422 72.222 4.39 0.00 45.05 3.51
1104 1161 4.803426 GTCGGAGAGCGTGGCCTG 62.803 72.222 3.32 0.00 36.95 4.85
1107 1164 4.415332 TTCGTCGGAGAGCGTGGC 62.415 66.667 0.00 0.00 36.95 5.01
1108 1165 2.504244 GTTCGTCGGAGAGCGTGG 60.504 66.667 0.00 0.00 36.95 4.94
1109 1166 2.870161 CGTTCGTCGGAGAGCGTG 60.870 66.667 8.54 0.00 39.45 5.34
1110 1167 4.755614 GCGTTCGTCGGAGAGCGT 62.756 66.667 15.40 0.00 44.69 5.07
1236 1323 1.809619 CGACGCCATCACGGACAAT 60.810 57.895 0.00 0.00 36.56 2.71
1363 1450 2.184830 CCTCGTCCTCATCGCCGTA 61.185 63.158 0.00 0.00 0.00 4.02
1458 1549 1.332375 CGCCCACGTTTCAGAAAGAAA 59.668 47.619 0.00 0.00 43.71 2.52
1459 1550 0.941542 CGCCCACGTTTCAGAAAGAA 59.058 50.000 0.00 0.00 33.53 2.52
1460 1551 0.105224 TCGCCCACGTTTCAGAAAGA 59.895 50.000 0.00 0.00 41.18 2.52
1461 1552 0.234884 GTCGCCCACGTTTCAGAAAG 59.765 55.000 0.00 0.00 41.18 2.62
1462 1553 1.161563 GGTCGCCCACGTTTCAGAAA 61.162 55.000 0.00 0.00 41.18 2.52
1463 1554 1.595929 GGTCGCCCACGTTTCAGAA 60.596 57.895 0.00 0.00 41.18 3.02
1464 1555 2.029964 GGTCGCCCACGTTTCAGA 59.970 61.111 0.00 0.00 41.18 3.27
1465 1556 1.671054 ATGGTCGCCCACGTTTCAG 60.671 57.895 0.00 0.00 45.65 3.02
1466 1557 1.963855 CATGGTCGCCCACGTTTCA 60.964 57.895 0.00 0.00 45.65 2.69
1467 1558 1.512156 AACATGGTCGCCCACGTTTC 61.512 55.000 0.00 0.00 44.38 2.78
1468 1559 1.104577 AAACATGGTCGCCCACGTTT 61.105 50.000 3.51 3.51 45.94 3.60
1469 1560 2.112297 AACATGGTCGCCCACGTT 59.888 55.556 0.00 0.00 45.65 3.99
1470 1561 2.112297 AAACATGGTCGCCCACGT 59.888 55.556 0.00 0.00 45.65 4.49
1471 1562 2.182614 GACAAACATGGTCGCCCACG 62.183 60.000 0.00 0.00 45.65 4.94
1472 1563 0.889186 AGACAAACATGGTCGCCCAC 60.889 55.000 0.00 0.00 45.65 4.61
1474 1565 1.875963 CAGACAAACATGGTCGCCC 59.124 57.895 0.00 0.00 40.20 6.13
1475 1566 1.210155 GCAGACAAACATGGTCGCC 59.790 57.895 0.00 0.00 40.20 5.54
1722 1866 4.507710 GTGCCATGTGATAGAAACAGAGA 58.492 43.478 0.00 0.00 0.00 3.10
1832 1976 7.962995 ACTCTCAGTGATATTACCTCTTTGA 57.037 36.000 0.00 0.00 0.00 2.69
1857 2001 5.611796 GAACATGTGATGCAAGTTCTGTA 57.388 39.130 0.00 0.00 46.40 2.74
1955 2107 1.519758 GATACGGCCACATTACGTTCG 59.480 52.381 2.24 0.00 41.53 3.95
1956 2108 1.862827 GGATACGGCCACATTACGTTC 59.137 52.381 2.24 0.00 41.53 3.95
1957 2109 1.207570 TGGATACGGCCACATTACGTT 59.792 47.619 2.24 0.00 41.53 3.99
1958 2110 0.825410 TGGATACGGCCACATTACGT 59.175 50.000 2.24 0.00 43.88 3.57
1959 2111 1.798223 CATGGATACGGCCACATTACG 59.202 52.381 2.24 0.00 41.56 3.18
1960 2112 2.548057 CACATGGATACGGCCACATTAC 59.452 50.000 2.24 0.00 41.56 1.89
1961 2113 2.171659 ACACATGGATACGGCCACATTA 59.828 45.455 2.24 0.00 41.56 1.90
1962 2114 1.064758 ACACATGGATACGGCCACATT 60.065 47.619 2.24 0.00 41.56 2.71
1991 2143 0.037790 GTCCTCACTCAGTGACAGGC 60.038 60.000 2.36 0.00 37.67 4.85
2132 2290 2.231478 GTGAGCAGAACAGTAGCCAGTA 59.769 50.000 0.00 0.00 0.00 2.74
2153 2311 6.344032 CCTTTTTGTTTTACTTTTCGCATCG 58.656 36.000 0.00 0.00 0.00 3.84
2174 2333 0.106918 TGAGTTTTGACGTGGCCCTT 60.107 50.000 0.00 0.00 0.00 3.95
2180 2339 5.022021 GTCTCTTGTTTGAGTTTTGACGTG 58.978 41.667 0.00 0.00 35.68 4.49
2255 2414 1.269988 CGGCCTCACGATGAAGATCAT 60.270 52.381 0.00 0.00 40.34 2.45
2256 2415 0.103026 CGGCCTCACGATGAAGATCA 59.897 55.000 0.00 0.00 35.47 2.92
2282 2441 6.957020 AGAATTATCGTGGGAAGAGATAGGAT 59.043 38.462 0.00 0.00 0.00 3.24
2301 2460 0.393808 GCTGCGTGGGGGAAGAATTA 60.394 55.000 0.00 0.00 0.00 1.40
2302 2461 1.678970 GCTGCGTGGGGGAAGAATT 60.679 57.895 0.00 0.00 0.00 2.17
2310 2469 3.969250 AATACGTGGCTGCGTGGGG 62.969 63.158 15.55 0.00 45.33 4.96
2319 2478 0.824759 AGGAGAGGTGAATACGTGGC 59.175 55.000 0.00 0.00 0.00 5.01
2380 2539 1.467920 GGGAAGAAGGGCATTGACTG 58.532 55.000 0.00 0.00 0.00 3.51
2387 2546 2.121506 AGGTGGGGAAGAAGGGCA 60.122 61.111 0.00 0.00 0.00 5.36
2397 2556 2.531685 TGTTGGGGAGAGGTGGGG 60.532 66.667 0.00 0.00 0.00 4.96
2415 2574 2.281345 GGCTGGATCCATCGCTGG 60.281 66.667 21.58 8.70 44.64 4.85
2417 2576 3.564218 GGGGCTGGATCCATCGCT 61.564 66.667 26.10 0.00 0.00 4.93
2422 2581 2.316586 GGGAAAGGGGCTGGATCCA 61.317 63.158 15.27 15.27 31.63 3.41
2454 2613 1.620739 GGATGTGGAGAGAGGCTGCA 61.621 60.000 0.50 0.00 43.20 4.41
2455 2614 1.145819 GGATGTGGAGAGAGGCTGC 59.854 63.158 0.00 0.00 35.18 5.25
2456 2615 0.752054 GAGGATGTGGAGAGAGGCTG 59.248 60.000 0.00 0.00 0.00 4.85
2462 2621 2.432510 GGTAAGGTGAGGATGTGGAGAG 59.567 54.545 0.00 0.00 0.00 3.20
2468 2627 2.644798 AGCAAAGGTAAGGTGAGGATGT 59.355 45.455 0.00 0.00 0.00 3.06
2480 2639 1.626321 TCATGGGAACGAGCAAAGGTA 59.374 47.619 0.00 0.00 0.00 3.08
2481 2640 0.400213 TCATGGGAACGAGCAAAGGT 59.600 50.000 0.00 0.00 0.00 3.50
2482 2641 0.804989 GTCATGGGAACGAGCAAAGG 59.195 55.000 0.00 0.00 0.00 3.11
2483 2642 0.443869 CGTCATGGGAACGAGCAAAG 59.556 55.000 0.00 0.00 0.00 2.77
2484 2643 0.953471 CCGTCATGGGAACGAGCAAA 60.953 55.000 6.97 0.00 0.00 3.68
2485 2644 1.375396 CCGTCATGGGAACGAGCAA 60.375 57.895 6.97 0.00 0.00 3.91
2486 2645 1.252215 TACCGTCATGGGAACGAGCA 61.252 55.000 6.97 0.00 44.64 4.26
2497 2656 0.390860 GCAGAGCCTGATACCGTCAT 59.609 55.000 6.40 0.00 35.97 3.06
2498 2657 1.816537 GCAGAGCCTGATACCGTCA 59.183 57.895 6.40 0.00 32.44 4.35
2499 2658 1.299468 CGCAGAGCCTGATACCGTC 60.299 63.158 6.40 0.00 32.44 4.79
2500 2659 2.808315 CGCAGAGCCTGATACCGT 59.192 61.111 6.40 0.00 32.44 4.83
2529 2688 1.710816 CTAGACCTTAGAGCAGGGGG 58.289 60.000 0.00 0.00 38.42 5.40
2545 2704 1.271762 CCATCCATGTCCCCATGCTAG 60.272 57.143 0.00 0.00 45.90 3.42
2574 2733 1.990060 ACAGACCATCCCCTCCACG 60.990 63.158 0.00 0.00 0.00 4.94
2603 2795 2.268920 GATGTGGAAGGGAGCGCA 59.731 61.111 11.47 0.00 0.00 6.09
2653 2845 1.194781 GGAGAGCCAGGAACACCTCA 61.195 60.000 0.00 0.00 30.75 3.86
2671 2863 1.662876 CGCCTTTGTGTTTGACGATGG 60.663 52.381 0.00 0.00 36.65 3.51
2680 2872 2.520741 CCCCACCGCCTTTGTGTT 60.521 61.111 0.00 0.00 31.71 3.32
2681 2873 2.575455 TTTCCCCACCGCCTTTGTGT 62.575 55.000 0.00 0.00 31.71 3.72
2684 2876 1.203758 GTAATTTCCCCACCGCCTTTG 59.796 52.381 0.00 0.00 0.00 2.77
2686 2878 0.406361 TGTAATTTCCCCACCGCCTT 59.594 50.000 0.00 0.00 0.00 4.35
2690 2882 1.027792 CCCGTGTAATTTCCCCACCG 61.028 60.000 0.00 0.00 0.00 4.94
2691 2883 0.328926 TCCCGTGTAATTTCCCCACC 59.671 55.000 0.00 0.00 0.00 4.61
2752 2945 1.602165 GGTCGAAGAAGAAGTCGTGCA 60.602 52.381 0.00 0.00 39.69 4.57
2756 2949 3.903360 AGAAAGGTCGAAGAAGAAGTCG 58.097 45.455 0.00 0.00 39.69 4.18
2757 2950 5.048294 AGAGAGAAAGGTCGAAGAAGAAGTC 60.048 44.000 0.00 0.00 39.69 3.01
2759 2952 5.160641 CAGAGAGAAAGGTCGAAGAAGAAG 58.839 45.833 0.00 0.00 39.69 2.85
2760 2953 4.021894 CCAGAGAGAAAGGTCGAAGAAGAA 60.022 45.833 0.00 0.00 39.69 2.52


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

AutoCloner maintained by Alex Coulton.