Multiple sequence alignment - TraesCS5D01G215700

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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 TraesCS5D01G215700 chr5D 100.000 4791 0 0 1 4791 324757624 324762414 0.000000e+00 8848.0
1 TraesCS5D01G215700 chr5D 86.789 598 62 14 4204 4791 54831951 54832541 0.000000e+00 651.0
2 TraesCS5D01G215700 chr5D 82.993 588 89 10 4211 4791 92148056 92147473 5.490000e-144 521.0
3 TraesCS5D01G215700 chr5B 93.044 2214 77 40 1987 4187 377204837 377206986 0.000000e+00 3164.0
4 TraesCS5D01G215700 chr5B 96.443 759 15 5 1208 1966 377204094 377204840 0.000000e+00 1242.0
5 TraesCS5D01G215700 chr5B 93.398 621 28 7 563 1176 377203481 377204095 0.000000e+00 907.0
6 TraesCS5D01G215700 chr5B 86.940 536 65 4 1 533 377195660 377196193 8.870000e-167 597.0
7 TraesCS5D01G215700 chr5A 95.577 1221 31 11 752 1966 423007504 423008707 0.000000e+00 1934.0
8 TraesCS5D01G215700 chr5A 93.460 1101 56 8 3006 4097 423009752 423010845 0.000000e+00 1620.0
9 TraesCS5D01G215700 chr5A 88.321 1096 72 31 1987 3056 423008704 423009769 0.000000e+00 1264.0
10 TraesCS5D01G215700 chr5A 84.803 737 102 9 1 730 423006599 423007332 0.000000e+00 732.0
11 TraesCS5D01G215700 chr5A 95.000 60 3 0 4080 4139 423010870 423010929 1.420000e-15 95.3
12 TraesCS5D01G215700 chr7A 88.380 611 60 10 4189 4791 67990529 67991136 0.000000e+00 725.0
13 TraesCS5D01G215700 chr7D 87.825 616 51 16 4186 4791 177123028 177123629 0.000000e+00 701.0
14 TraesCS5D01G215700 chr7D 87.059 595 62 14 4204 4791 602800962 602801548 0.000000e+00 658.0
15 TraesCS5D01G215700 chr1B 85.473 592 76 9 4203 4791 420208603 420208019 4.100000e-170 608.0
16 TraesCS5D01G215700 chr1A 85.042 595 69 17 4208 4791 49648358 49647773 5.340000e-164 588.0
17 TraesCS5D01G215700 chr2A 83.418 591 78 17 4204 4785 670691070 670691649 9.130000e-147 531.0
18 TraesCS5D01G215700 chr4A 83.110 598 80 18 4207 4791 497861221 497861810 4.250000e-145 525.0
19 TraesCS5D01G215700 chr3D 83.735 166 27 0 207 372 68052052 68051887 1.780000e-34 158.0
20 TraesCS5D01G215700 chr3B 80.105 191 36 2 287 476 113946091 113946280 1.800000e-29 141.0


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 TraesCS5D01G215700 chr5D 324757624 324762414 4790 False 8848.00 8848 100.0000 1 4791 1 chr5D.!!$F2 4790
1 TraesCS5D01G215700 chr5D 54831951 54832541 590 False 651.00 651 86.7890 4204 4791 1 chr5D.!!$F1 587
2 TraesCS5D01G215700 chr5D 92147473 92148056 583 True 521.00 521 82.9930 4211 4791 1 chr5D.!!$R1 580
3 TraesCS5D01G215700 chr5B 377203481 377206986 3505 False 1771.00 3164 94.2950 563 4187 3 chr5B.!!$F2 3624
4 TraesCS5D01G215700 chr5B 377195660 377196193 533 False 597.00 597 86.9400 1 533 1 chr5B.!!$F1 532
5 TraesCS5D01G215700 chr5A 423006599 423010929 4330 False 1129.06 1934 91.4322 1 4139 5 chr5A.!!$F1 4138
6 TraesCS5D01G215700 chr7A 67990529 67991136 607 False 725.00 725 88.3800 4189 4791 1 chr7A.!!$F1 602
7 TraesCS5D01G215700 chr7D 177123028 177123629 601 False 701.00 701 87.8250 4186 4791 1 chr7D.!!$F1 605
8 TraesCS5D01G215700 chr7D 602800962 602801548 586 False 658.00 658 87.0590 4204 4791 1 chr7D.!!$F2 587
9 TraesCS5D01G215700 chr1B 420208019 420208603 584 True 608.00 608 85.4730 4203 4791 1 chr1B.!!$R1 588
10 TraesCS5D01G215700 chr1A 49647773 49648358 585 True 588.00 588 85.0420 4208 4791 1 chr1A.!!$R1 583
11 TraesCS5D01G215700 chr2A 670691070 670691649 579 False 531.00 531 83.4180 4204 4785 1 chr2A.!!$F1 581
12 TraesCS5D01G215700 chr4A 497861221 497861810 589 False 525.00 525 83.1100 4207 4791 1 chr4A.!!$F1 584

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
72 74 0.319986 TGGCGCAGACACGTTTGATA 60.320 50.0 10.83 0.0 34.89 2.15 F
1881 2046 0.179062 CCAGCAGCAACCCTAGCTAG 60.179 60.0 14.20 14.2 41.14 3.42 F
2465 2638 0.030908 CCGGTCGAGAAGGTAGATGC 59.969 60.0 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2143 0.038166 GCAGATCCAACCCAACAGGA 59.962 55.0 0.00 0.0 39.89 3.86 R
3189 3417 0.034863 TAATGGGGGCGAAGGTGAAC 60.035 55.0 0.00 0.0 0.00 3.18 R
4116 4397 0.249699 TGTAGCACTTGTGTGGACCG 60.250 55.0 2.61 0.0 43.97 4.79 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
70 72 2.202946 TGGCGCAGACACGTTTGA 60.203 55.556 10.83 0.00 34.89 2.69
72 74 0.319986 TGGCGCAGACACGTTTGATA 60.320 50.000 10.83 0.00 34.89 2.15
92 94 0.539438 GTTGTTGGTGGGCATCTGGA 60.539 55.000 0.00 0.00 0.00 3.86
94 96 1.294041 TGTTGGTGGGCATCTGGATA 58.706 50.000 0.00 0.00 0.00 2.59
158 160 1.091771 CATCAAACTCGGCGGCATCT 61.092 55.000 10.53 0.00 0.00 2.90
181 185 2.761208 CCTCTGTTCATAGGAAGGACGT 59.239 50.000 0.00 0.00 34.58 4.34
246 251 3.018973 GCCGTTGTGAAGCGACAA 58.981 55.556 0.00 0.00 33.36 3.18
247 252 1.574428 GCCGTTGTGAAGCGACAAT 59.426 52.632 2.89 0.00 38.11 2.71
250 255 0.586319 CGTTGTGAAGCGACAATGGT 59.414 50.000 9.44 0.00 38.62 3.55
262 267 3.067106 CGACAATGGTTAGTTCTGCACT 58.933 45.455 0.00 0.00 39.87 4.40
263 268 4.242475 CGACAATGGTTAGTTCTGCACTA 58.758 43.478 0.00 0.00 36.88 2.74
274 279 1.079197 CTGCACTACGGCATGGTCA 60.079 57.895 0.00 0.00 43.97 4.02
286 291 3.957435 ATGGTCAGCCTCCCGACGA 62.957 63.158 0.00 0.00 35.27 4.20
307 312 5.163488 ACGACCACGATAATGATCTTTGGTA 60.163 40.000 11.56 0.00 42.24 3.25
328 335 1.546323 GGCATACATCCCACCCATCTG 60.546 57.143 0.00 0.00 0.00 2.90
335 342 1.153086 CCCACCCATCTGCTAGTGC 60.153 63.158 0.00 0.00 40.20 4.40
362 370 0.543749 GCCTAGCATGGAGAACTGGT 59.456 55.000 0.00 0.00 0.00 4.00
372 380 2.832129 TGGAGAACTGGTAGATGTGACC 59.168 50.000 0.00 0.00 37.49 4.02
383 391 1.825474 AGATGTGACCGTCGGAAGATT 59.175 47.619 20.51 0.00 45.19 2.40
431 439 2.844348 ACTTCATATCCGGGGTGAAAGT 59.156 45.455 0.00 4.09 32.08 2.66
462 470 1.612726 GCCTTTGCTGGTCAGACTCAT 60.613 52.381 0.00 0.00 33.53 2.90
476 484 0.530744 ACTCATCAGCGGCGAACTTA 59.469 50.000 12.98 0.00 0.00 2.24
477 485 1.203928 CTCATCAGCGGCGAACTTAG 58.796 55.000 12.98 0.00 0.00 2.18
515 523 2.562738 AGACATTGTCTCCGTGATGACA 59.437 45.455 13.61 0.00 38.71 3.58
521 529 1.472878 GTCTCCGTGATGACAGTAGCA 59.527 52.381 0.00 0.00 33.75 3.49
524 532 1.824852 TCCGTGATGACAGTAGCATGT 59.175 47.619 0.00 0.00 35.68 3.21
534 542 3.694072 GACAGTAGCATGTGGGCATTTAA 59.306 43.478 0.00 0.00 35.83 1.52
536 544 3.023832 AGTAGCATGTGGGCATTTAACC 58.976 45.455 0.00 0.00 35.83 2.85
548 556 3.832490 GGCATTTAACCCTTCTTGAAGGT 59.168 43.478 23.12 11.71 38.28 3.50
556 564 2.301346 CCTTCTTGAAGGTGTTGCTGT 58.699 47.619 18.52 0.00 35.22 4.40
558 566 1.679139 TCTTGAAGGTGTTGCTGTGG 58.321 50.000 0.00 0.00 0.00 4.17
561 569 2.136298 TGAAGGTGTTGCTGTGGAAA 57.864 45.000 0.00 0.00 0.00 3.13
566 574 2.166254 AGGTGTTGCTGTGGAAAAAGTG 59.834 45.455 0.00 0.00 0.00 3.16
653 661 5.443185 ACTCCATTTGTTGATGTTGTCTG 57.557 39.130 0.00 0.00 0.00 3.51
655 663 3.573538 TCCATTTGTTGATGTTGTCTGGG 59.426 43.478 0.00 0.00 0.00 4.45
673 681 3.006940 TGGGTGTCTCGCATCATTTAAC 58.993 45.455 0.00 0.00 34.08 2.01
681 689 7.114811 GTGTCTCGCATCATTTAACAAAAATGT 59.885 33.333 9.56 0.00 38.44 2.71
774 934 4.887748 TGATTCACTTGGTCTCTCTCAAC 58.112 43.478 0.00 0.00 0.00 3.18
805 965 7.090319 TCTAAATGTGATAGCCCATGGTAAT 57.910 36.000 11.73 0.30 0.00 1.89
956 1116 1.474077 GACCTTCCATGCATTTTCGCT 59.526 47.619 0.00 0.00 0.00 4.93
1132 1293 2.131709 CCGGCCTCCATCTCCGTTA 61.132 63.158 0.00 0.00 41.46 3.18
1200 1365 1.623311 TGTTGTGATCACCTGACCGAT 59.377 47.619 22.85 0.00 0.00 4.18
1642 1807 4.008933 GGTCGAGCTGCACCTGGT 62.009 66.667 7.51 0.00 0.00 4.00
1659 1824 4.226168 ACCTGGTCTTTTCCCTTCTCTATG 59.774 45.833 0.00 0.00 0.00 2.23
1660 1825 4.471386 CCTGGTCTTTTCCCTTCTCTATGA 59.529 45.833 0.00 0.00 0.00 2.15
1872 2037 0.669318 TACGTAGCACCAGCAGCAAC 60.669 55.000 0.00 0.00 45.49 4.17
1879 2044 2.227036 ACCAGCAGCAACCCTAGCT 61.227 57.895 0.00 0.00 44.62 3.32
1880 2045 0.909610 ACCAGCAGCAACCCTAGCTA 60.910 55.000 0.00 0.00 41.14 3.32
1881 2046 0.179062 CCAGCAGCAACCCTAGCTAG 60.179 60.000 14.20 14.20 41.14 3.42
1882 2047 0.539051 CAGCAGCAACCCTAGCTAGT 59.461 55.000 19.31 0.00 41.14 2.57
1901 2066 7.158021 AGCTAGTAATCAATCCTATGTCAAGC 58.842 38.462 0.00 0.00 0.00 4.01
1902 2067 7.016072 AGCTAGTAATCAATCCTATGTCAAGCT 59.984 37.037 0.00 0.00 0.00 3.74
1903 2068 8.307483 GCTAGTAATCAATCCTATGTCAAGCTA 58.693 37.037 0.00 0.00 0.00 3.32
1905 2070 8.256356 AGTAATCAATCCTATGTCAAGCTAGT 57.744 34.615 0.00 0.00 0.00 2.57
1906 2071 8.147058 AGTAATCAATCCTATGTCAAGCTAGTG 58.853 37.037 0.00 0.00 0.00 2.74
1907 2072 5.939764 TCAATCCTATGTCAAGCTAGTGT 57.060 39.130 0.00 0.00 0.00 3.55
1908 2073 5.664457 TCAATCCTATGTCAAGCTAGTGTG 58.336 41.667 0.00 0.00 0.00 3.82
1909 2074 3.526931 TCCTATGTCAAGCTAGTGTGC 57.473 47.619 0.00 0.00 0.00 4.57
1910 2075 3.099905 TCCTATGTCAAGCTAGTGTGCT 58.900 45.455 0.00 0.00 46.40 4.40
1911 2076 3.118992 TCCTATGTCAAGCTAGTGTGCTG 60.119 47.826 0.00 0.00 43.24 4.41
1912 2077 3.118992 CCTATGTCAAGCTAGTGTGCTGA 60.119 47.826 0.00 0.00 43.24 4.26
1913 2078 3.623906 ATGTCAAGCTAGTGTGCTGAT 57.376 42.857 0.00 0.00 43.24 2.90
1935 2100 7.700505 TGATTGATTGCAGTCAATTCATCTAC 58.299 34.615 30.73 19.48 46.02 2.59
1938 2103 5.939296 TGATTGCAGTCAATTCATCTACACA 59.061 36.000 9.78 0.00 42.60 3.72
1939 2104 6.600427 TGATTGCAGTCAATTCATCTACACAT 59.400 34.615 9.78 0.00 42.60 3.21
1940 2105 7.769970 TGATTGCAGTCAATTCATCTACACATA 59.230 33.333 9.78 0.00 42.60 2.29
1951 2116 9.730705 AATTCATCTACACATAACATCCCTATG 57.269 33.333 0.00 0.00 39.17 2.23
1962 2127 9.273016 ACATAACATCCCTATGAAACGAATAAG 57.727 33.333 0.00 0.00 36.54 1.73
1963 2128 8.721478 CATAACATCCCTATGAAACGAATAAGG 58.279 37.037 0.00 0.00 36.54 2.69
1964 2129 6.248569 ACATCCCTATGAAACGAATAAGGT 57.751 37.500 0.00 0.00 36.54 3.50
1965 2130 6.659824 ACATCCCTATGAAACGAATAAGGTT 58.340 36.000 0.00 0.00 36.54 3.50
1966 2131 7.798071 ACATCCCTATGAAACGAATAAGGTTA 58.202 34.615 0.00 0.00 36.54 2.85
1967 2132 8.269317 ACATCCCTATGAAACGAATAAGGTTAA 58.731 33.333 0.00 0.00 36.54 2.01
1968 2133 9.116067 CATCCCTATGAAACGAATAAGGTTAAA 57.884 33.333 0.00 0.00 34.84 1.52
1969 2134 8.726870 TCCCTATGAAACGAATAAGGTTAAAG 57.273 34.615 0.00 0.00 0.00 1.85
1970 2135 8.542080 TCCCTATGAAACGAATAAGGTTAAAGA 58.458 33.333 0.00 0.00 0.00 2.52
1971 2136 9.169592 CCCTATGAAACGAATAAGGTTAAAGAA 57.830 33.333 0.00 0.00 0.00 2.52
1972 2137 9.983804 CCTATGAAACGAATAAGGTTAAAGAAC 57.016 33.333 0.00 0.00 34.56 3.01
1980 2145 9.597170 ACGAATAAGGTTAAAGAACTTATCTCC 57.403 33.333 0.00 0.00 37.42 3.71
1981 2146 9.819267 CGAATAAGGTTAAAGAACTTATCTCCT 57.181 33.333 0.00 0.00 37.42 3.69
1985 2150 8.622948 AAGGTTAAAGAACTTATCTCCTGTTG 57.377 34.615 0.00 0.00 37.42 3.33
2107 2272 0.106868 TTCATGAGCCCCTCTGCATG 60.107 55.000 0.00 0.00 39.47 4.06
2108 2273 2.194212 CATGAGCCCCTCTGCATGC 61.194 63.158 11.82 11.82 32.73 4.06
2465 2638 0.030908 CCGGTCGAGAAGGTAGATGC 59.969 60.000 0.00 0.00 0.00 3.91
2502 2675 1.344763 GCCACGGTATATCTCTTGGCT 59.655 52.381 14.48 0.00 45.07 4.75
2542 2719 9.979270 GATGGAAGCTAAAATGTATATGATTCG 57.021 33.333 0.00 0.00 0.00 3.34
2662 2839 3.193691 CCCGTGATGGACAGAGGTATATC 59.806 52.174 0.00 0.00 42.00 1.63
2665 2842 7.066233 CCGTGATGGACAGAGGTATATCCTG 62.066 52.000 0.00 0.00 43.91 3.86
2687 2867 4.403752 TGTGTGCTATGCAGAGTAGAAGAT 59.596 41.667 10.55 0.00 40.08 2.40
2713 2893 4.910195 TGGCAACTTGTCACTCAGATATT 58.090 39.130 0.00 0.00 37.61 1.28
2719 2899 9.265901 GCAACTTGTCACTCAGATATTACATAT 57.734 33.333 0.00 0.00 0.00 1.78
2764 2956 2.232941 AGACGGTTCCATCGTGTGTATT 59.767 45.455 0.00 0.00 41.22 1.89
2767 2959 2.093625 CGGTTCCATCGTGTGTATTGTG 59.906 50.000 0.00 0.00 0.00 3.33
2774 2966 0.162933 CGTGTGTATTGTGGACGTGC 59.837 55.000 0.00 0.00 0.00 5.34
2820 3012 4.828829 TCCATCGTAAGTCCTCCTTTTTC 58.171 43.478 0.00 0.00 34.46 2.29
2847 3039 6.094048 CAGAAGACAGAAAAGGTTTGAGTTGA 59.906 38.462 0.00 0.00 0.00 3.18
2873 3068 4.029520 AGATGTCTCCTACTGATTGCACT 58.970 43.478 0.00 0.00 0.00 4.40
2874 3069 3.876274 TGTCTCCTACTGATTGCACTC 57.124 47.619 0.00 0.00 0.00 3.51
2876 3071 3.578282 TGTCTCCTACTGATTGCACTCAA 59.422 43.478 8.22 0.00 36.51 3.02
2877 3072 4.040339 TGTCTCCTACTGATTGCACTCAAA 59.960 41.667 8.22 0.00 35.56 2.69
2878 3073 4.997395 GTCTCCTACTGATTGCACTCAAAA 59.003 41.667 8.22 0.00 35.56 2.44
2879 3074 5.470098 GTCTCCTACTGATTGCACTCAAAAA 59.530 40.000 8.22 0.00 35.56 1.94
2880 3075 6.150140 GTCTCCTACTGATTGCACTCAAAAAT 59.850 38.462 8.22 0.00 35.56 1.82
2881 3076 6.716628 TCTCCTACTGATTGCACTCAAAAATT 59.283 34.615 8.22 0.00 35.56 1.82
2882 3077 7.882791 TCTCCTACTGATTGCACTCAAAAATTA 59.117 33.333 8.22 0.00 35.56 1.40
2974 3169 2.514824 GCCTTGGGCTCGATGGAC 60.515 66.667 0.80 0.00 46.69 4.02
3192 3420 4.955774 ACCGACCGTGCCGTGTTC 62.956 66.667 0.00 0.00 0.00 3.18
3193 3421 4.953868 CCGACCGTGCCGTGTTCA 62.954 66.667 0.00 0.00 0.00 3.18
3194 3422 3.698463 CGACCGTGCCGTGTTCAC 61.698 66.667 0.00 0.00 0.00 3.18
3195 3423 3.343421 GACCGTGCCGTGTTCACC 61.343 66.667 0.00 0.00 0.00 4.02
3212 3440 1.212250 ACCTTCGCCCCCATTAACCT 61.212 55.000 0.00 0.00 0.00 3.50
3347 3575 0.756294 TGGTGAGTGGTTCATCACGT 59.244 50.000 0.00 0.00 41.98 4.49
3360 3588 2.058798 CATCACGTACGGGATACATGC 58.941 52.381 31.13 0.00 35.85 4.06
3554 3782 1.399727 GGCATCACGAAACTTGTTCCG 60.400 52.381 0.00 0.00 0.00 4.30
3693 3928 2.668632 GACGATGGACCTGGCCAA 59.331 61.111 7.01 0.00 42.16 4.52
3944 4181 1.081641 ACGCAACGTCTACTCACGG 60.082 57.895 0.00 0.00 44.41 4.94
3945 4182 1.208358 CGCAACGTCTACTCACGGA 59.792 57.895 0.00 0.00 44.41 4.69
3949 4186 1.135746 CAACGTCTACTCACGGAGACC 60.136 57.143 7.76 0.00 44.41 3.85
3997 4234 1.303799 ATGAAGAAGGCACAGCTGCG 61.304 55.000 15.27 5.22 45.31 5.18
4040 4277 3.438360 CGCCCTGCTGAAAATTTATCAC 58.562 45.455 0.00 0.00 0.00 3.06
4061 4300 6.314018 TCACGCTTTAACAAAATGCATAGAG 58.686 36.000 0.00 0.00 0.00 2.43
4116 4397 0.729690 GGTTCATCTTGCTTCGCCTC 59.270 55.000 0.00 0.00 0.00 4.70
4147 4428 4.700213 ACAAGTGCTACATAACCATGGTTC 59.300 41.667 33.06 17.96 39.31 3.62
4148 4429 3.886123 AGTGCTACATAACCATGGTTCC 58.114 45.455 33.06 15.32 39.31 3.62
4149 4430 2.612212 GTGCTACATAACCATGGTTCCG 59.388 50.000 33.06 25.34 39.31 4.30
4152 4433 2.018542 ACATAACCATGGTTCCGTCG 57.981 50.000 33.06 19.00 39.31 5.12
4182 4463 3.270877 AGGCACCGACAATTGTAGATTC 58.729 45.455 18.97 7.62 0.00 2.52
4187 4468 5.118990 CACCGACAATTGTAGATTCTGGAT 58.881 41.667 18.97 0.00 0.00 3.41
4240 4526 1.659794 GAGGGATGAGCGAGAGAGC 59.340 63.158 0.00 0.00 37.41 4.09
4298 4592 4.017126 GGAAGGATTGGGTTACAGGAAAG 58.983 47.826 0.00 0.00 0.00 2.62
4317 4614 1.626654 GGTTCACACACGCATCCTCG 61.627 60.000 0.00 0.00 0.00 4.63
4353 4651 1.003812 CCACCCTTTATCGTCACCCAA 59.996 52.381 0.00 0.00 0.00 4.12
4402 4701 0.747852 GACCCACTAGCCAGCTCTAC 59.252 60.000 0.00 0.00 0.00 2.59
4467 4767 0.737715 ACGCTGCGTCATCTTCTTCC 60.738 55.000 23.57 0.00 33.69 3.46
4468 4768 0.737367 CGCTGCGTCATCTTCTTCCA 60.737 55.000 14.93 0.00 0.00 3.53
4471 4771 0.389817 TGCGTCATCTTCTTCCACCG 60.390 55.000 0.00 0.00 0.00 4.94
4536 4839 3.691342 CGGTGGCGGAGAACCTCA 61.691 66.667 0.00 0.00 34.20 3.86
4552 4855 2.039418 CCTCATAATCCTCCCACGTCA 58.961 52.381 0.00 0.00 0.00 4.35
4558 4861 0.106369 ATCCTCCCACGTCATCGGTA 60.106 55.000 0.00 0.00 41.85 4.02
4648 4951 1.561769 ATCCAGGATGCGTGTTGGGA 61.562 55.000 0.00 0.00 31.97 4.37
4734 5037 2.260844 TGAAGGGCTTCAACTGTGAG 57.739 50.000 0.00 0.00 45.56 3.51
4735 5038 1.768275 TGAAGGGCTTCAACTGTGAGA 59.232 47.619 0.00 0.00 45.56 3.27
4736 5039 2.147150 GAAGGGCTTCAACTGTGAGAC 58.853 52.381 0.00 0.00 39.31 3.36
4737 5040 0.034059 AGGGCTTCAACTGTGAGACG 59.966 55.000 0.00 0.00 34.49 4.18
4738 5041 0.249911 GGGCTTCAACTGTGAGACGT 60.250 55.000 0.00 0.00 34.49 4.34
4739 5042 0.861837 GGCTTCAACTGTGAGACGTG 59.138 55.000 0.00 0.00 34.49 4.49
4740 5043 0.861837 GCTTCAACTGTGAGACGTGG 59.138 55.000 0.00 0.00 34.49 4.94
4741 5044 1.538204 GCTTCAACTGTGAGACGTGGA 60.538 52.381 0.00 0.00 34.49 4.02
4785 5107 0.108138 GTGGCAGGTCGAGCTTGTAT 60.108 55.000 15.83 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.674441 CACAGGGCTGATAAGCATGTG 59.326 52.381 19.71 19.71 42.86 3.21
13 14 1.450134 CGCACAGGGCTGATAAGCA 60.450 57.895 3.95 0.00 41.67 3.91
47 48 4.996434 GTGTCTGCGCCACAGCCT 62.996 66.667 4.18 0.00 46.76 4.58
70 72 2.621407 CCAGATGCCCACCAACAACTAT 60.621 50.000 0.00 0.00 0.00 2.12
72 74 0.540365 CCAGATGCCCACCAACAACT 60.540 55.000 0.00 0.00 0.00 3.16
92 94 3.419793 CCCAATCATGGCACGGTAT 57.580 52.632 0.00 0.00 46.09 2.73
128 130 2.609491 CGAGTTTGATGTCGACTGGGAA 60.609 50.000 17.92 4.15 38.50 3.97
158 160 2.501723 GTCCTTCCTATGAACAGAGGCA 59.498 50.000 10.22 0.00 39.58 4.75
181 185 2.111999 CTCTGAGGTCGTTGCCCCAA 62.112 60.000 0.00 0.00 0.00 4.12
241 246 3.067106 AGTGCAGAACTAACCATTGTCG 58.933 45.455 0.00 0.00 37.36 4.35
243 248 3.994392 CGTAGTGCAGAACTAACCATTGT 59.006 43.478 0.00 0.00 43.08 2.71
246 251 2.677037 GCCGTAGTGCAGAACTAACCAT 60.677 50.000 0.00 0.00 43.08 3.55
247 252 1.337447 GCCGTAGTGCAGAACTAACCA 60.337 52.381 0.00 0.00 43.08 3.67
250 255 2.616960 CATGCCGTAGTGCAGAACTAA 58.383 47.619 0.00 0.00 45.93 2.24
307 312 0.773644 GATGGGTGGGATGTATGCCT 59.226 55.000 4.03 0.00 39.30 4.75
335 342 1.147824 CCATGCTAGGCCAGAGTGG 59.852 63.158 5.01 8.45 41.55 4.00
362 370 2.118313 TCTTCCGACGGTCACATCTA 57.882 50.000 14.79 0.00 0.00 1.98
372 380 3.676091 GGCAACAAATCTTCCGACG 57.324 52.632 0.00 0.00 0.00 5.12
431 439 1.003580 CAGCAAAGGCCAGAACTAGGA 59.996 52.381 5.01 0.00 42.56 2.94
462 470 1.214589 GACCTAAGTTCGCCGCTGA 59.785 57.895 0.00 0.00 0.00 4.26
476 484 7.667219 ACAATGTCTTCAACAAGATAATGACCT 59.333 33.333 4.20 0.00 42.37 3.85
477 485 7.820648 ACAATGTCTTCAACAAGATAATGACC 58.179 34.615 4.20 0.00 42.37 4.02
515 523 3.023832 GGTTAAATGCCCACATGCTACT 58.976 45.455 0.00 0.00 36.36 2.57
548 556 2.165437 GTCCACTTTTTCCACAGCAACA 59.835 45.455 0.00 0.00 0.00 3.33
598 606 8.671921 CAGAAGCAACTATGACAGAAACATTAT 58.328 33.333 0.00 0.00 0.00 1.28
603 611 5.931441 ACAGAAGCAACTATGACAGAAAC 57.069 39.130 0.00 0.00 0.00 2.78
653 661 3.006940 TGTTAAATGATGCGAGACACCC 58.993 45.455 0.00 0.00 0.00 4.61
655 663 6.984740 TTTTTGTTAAATGATGCGAGACAC 57.015 33.333 0.00 0.00 0.00 3.67
673 681 7.821595 ATTGATGCACACATAGACATTTTTG 57.178 32.000 0.00 0.00 36.35 2.44
731 739 5.759963 TCAAGCGCGTTTATCCTTTAAAAA 58.240 33.333 8.18 0.00 0.00 1.94
732 740 5.359716 TCAAGCGCGTTTATCCTTTAAAA 57.640 34.783 8.18 0.00 0.00 1.52
733 741 5.554822 ATCAAGCGCGTTTATCCTTTAAA 57.445 34.783 8.18 0.00 0.00 1.52
734 742 5.122554 TGAATCAAGCGCGTTTATCCTTTAA 59.877 36.000 8.18 0.00 0.00 1.52
735 743 4.632251 TGAATCAAGCGCGTTTATCCTTTA 59.368 37.500 8.18 0.00 0.00 1.85
774 934 5.540337 TGGGCTATCACATTTAGAGTAGAGG 59.460 44.000 0.00 0.00 0.00 3.69
805 965 5.381757 GGAGTGATCTCTAGGAGAAGCTAA 58.618 45.833 0.00 0.00 42.27 3.09
956 1116 0.830648 CTAGCCGTCTGGGAAATGGA 59.169 55.000 0.00 0.00 38.47 3.41
1116 1277 0.539986 TTGTAACGGAGATGGAGGCC 59.460 55.000 0.00 0.00 0.00 5.19
1132 1293 6.176975 CATGCATGCAAAGAAATTGATTGT 57.823 33.333 26.68 0.00 41.85 2.71
1200 1365 2.658268 CGATGCATGCTACGGCGA 60.658 61.111 20.33 0.00 42.25 5.54
1659 1824 9.943163 GGAGCAATTAATTAATCAACTCTTCTC 57.057 33.333 21.91 12.16 0.00 2.87
1660 1825 8.616076 CGGAGCAATTAATTAATCAACTCTTCT 58.384 33.333 21.91 6.27 0.00 2.85
1798 1963 2.291043 GCCTTCCCCTTCTCGGACA 61.291 63.158 0.00 0.00 33.16 4.02
1872 2037 7.397476 TGACATAGGATTGATTACTAGCTAGGG 59.603 40.741 24.35 1.84 0.00 3.53
1879 2044 9.368416 ACTAGCTTGACATAGGATTGATTACTA 57.632 33.333 1.04 0.00 0.00 1.82
1880 2045 8.147058 CACTAGCTTGACATAGGATTGATTACT 58.853 37.037 1.04 0.00 0.00 2.24
1881 2046 7.928706 ACACTAGCTTGACATAGGATTGATTAC 59.071 37.037 1.04 0.00 0.00 1.89
1882 2047 7.928167 CACACTAGCTTGACATAGGATTGATTA 59.072 37.037 1.04 0.00 0.00 1.75
1901 2066 3.688185 ACTGCAATCAATCAGCACACTAG 59.312 43.478 0.00 0.00 34.13 2.57
1902 2067 3.678289 ACTGCAATCAATCAGCACACTA 58.322 40.909 0.00 0.00 34.13 2.74
1903 2068 2.486982 GACTGCAATCAATCAGCACACT 59.513 45.455 0.00 0.00 34.13 3.55
1905 2070 2.506444 TGACTGCAATCAATCAGCACA 58.494 42.857 0.00 0.00 34.13 4.57
1906 2071 3.564235 TTGACTGCAATCAATCAGCAC 57.436 42.857 6.47 0.00 33.62 4.40
1907 2072 4.218852 TGAATTGACTGCAATCAATCAGCA 59.781 37.500 22.44 17.25 46.35 4.41
1908 2073 4.740268 TGAATTGACTGCAATCAATCAGC 58.260 39.130 22.44 15.19 46.35 4.26
1909 2074 6.796426 AGATGAATTGACTGCAATCAATCAG 58.204 36.000 22.44 0.00 46.35 2.90
1910 2075 6.769134 AGATGAATTGACTGCAATCAATCA 57.231 33.333 22.44 20.06 46.35 2.57
1911 2076 7.642978 GTGTAGATGAATTGACTGCAATCAATC 59.357 37.037 22.44 15.85 46.35 2.67
1913 2078 6.430616 TGTGTAGATGAATTGACTGCAATCAA 59.569 34.615 13.64 13.64 43.71 2.57
1927 2092 8.491045 TCATAGGGATGTTATGTGTAGATGAA 57.509 34.615 0.00 0.00 34.41 2.57
1935 2100 6.918892 TTCGTTTCATAGGGATGTTATGTG 57.081 37.500 0.00 0.00 34.41 3.21
1938 2103 8.437575 ACCTTATTCGTTTCATAGGGATGTTAT 58.562 33.333 0.00 0.00 34.41 1.89
1939 2104 7.798071 ACCTTATTCGTTTCATAGGGATGTTA 58.202 34.615 0.00 0.00 34.41 2.41
1940 2105 6.659824 ACCTTATTCGTTTCATAGGGATGTT 58.340 36.000 0.00 0.00 34.41 2.71
1962 2127 6.374613 CCCAACAGGAGATAAGTTCTTTAACC 59.625 42.308 0.00 0.00 38.24 2.85
1963 2128 6.940867 ACCCAACAGGAGATAAGTTCTTTAAC 59.059 38.462 0.00 0.00 39.89 2.01
1964 2129 7.086685 ACCCAACAGGAGATAAGTTCTTTAA 57.913 36.000 0.00 0.00 39.89 1.52
1965 2130 6.697641 ACCCAACAGGAGATAAGTTCTTTA 57.302 37.500 0.00 0.00 39.89 1.85
1966 2131 5.584551 ACCCAACAGGAGATAAGTTCTTT 57.415 39.130 0.00 0.00 39.89 2.52
1967 2132 5.316987 CAACCCAACAGGAGATAAGTTCTT 58.683 41.667 0.00 0.00 39.89 2.52
1968 2133 4.263506 CCAACCCAACAGGAGATAAGTTCT 60.264 45.833 0.00 0.00 39.89 3.01
1969 2134 4.010349 CCAACCCAACAGGAGATAAGTTC 58.990 47.826 0.00 0.00 39.89 3.01
1970 2135 3.655777 TCCAACCCAACAGGAGATAAGTT 59.344 43.478 0.00 0.00 39.89 2.66
1971 2136 3.256704 TCCAACCCAACAGGAGATAAGT 58.743 45.455 0.00 0.00 39.89 2.24
1972 2137 4.164988 AGATCCAACCCAACAGGAGATAAG 59.835 45.833 0.00 0.00 39.89 1.73
1973 2138 4.080356 CAGATCCAACCCAACAGGAGATAA 60.080 45.833 0.00 0.00 39.89 1.75
1974 2139 3.455910 CAGATCCAACCCAACAGGAGATA 59.544 47.826 0.00 0.00 39.89 1.98
1975 2140 2.240667 CAGATCCAACCCAACAGGAGAT 59.759 50.000 0.00 0.00 39.89 2.75
1976 2141 1.630369 CAGATCCAACCCAACAGGAGA 59.370 52.381 0.00 0.00 39.89 3.71
1977 2142 1.952367 GCAGATCCAACCCAACAGGAG 60.952 57.143 0.00 0.00 39.89 3.69
1978 2143 0.038166 GCAGATCCAACCCAACAGGA 59.962 55.000 0.00 0.00 39.89 3.86
1979 2144 0.251297 TGCAGATCCAACCCAACAGG 60.251 55.000 0.00 0.00 43.78 4.00
1980 2145 1.171308 CTGCAGATCCAACCCAACAG 58.829 55.000 8.42 0.00 0.00 3.16
1981 2146 0.251297 CCTGCAGATCCAACCCAACA 60.251 55.000 17.39 0.00 0.00 3.33
1982 2147 0.251341 ACCTGCAGATCCAACCCAAC 60.251 55.000 17.39 0.00 0.00 3.77
1983 2148 1.367346 TACCTGCAGATCCAACCCAA 58.633 50.000 17.39 0.00 0.00 4.12
1984 2149 1.004277 GTTACCTGCAGATCCAACCCA 59.996 52.381 17.39 0.00 0.00 4.51
1985 2150 1.682087 GGTTACCTGCAGATCCAACCC 60.682 57.143 17.39 1.60 31.28 4.11
2107 2272 2.598439 CGCAGATAACTGAATGAAGCGC 60.598 50.000 0.00 0.00 46.03 5.92
2108 2273 2.598439 GCGCAGATAACTGAATGAAGCG 60.598 50.000 0.30 0.00 46.03 4.68
2465 2638 1.595093 GGCGGTTGGAGTTGGAATGG 61.595 60.000 0.00 0.00 0.00 3.16
2494 2667 1.134367 CATTCACATGGCAGCCAAGAG 59.866 52.381 23.58 15.50 36.95 2.85
2502 2675 2.510928 TCCATCACATTCACATGGCA 57.489 45.000 0.00 0.00 37.57 4.92
2542 2719 0.035630 AAGAGTCATGACCTGCAGGC 60.036 55.000 33.06 24.14 39.32 4.85
2582 2759 0.597637 CATCCAGTATCGGCGTGTCC 60.598 60.000 6.85 0.00 0.00 4.02
2662 2839 2.428530 TCTACTCTGCATAGCACACAGG 59.571 50.000 0.00 0.00 33.79 4.00
2665 2842 4.377839 TCTTCTACTCTGCATAGCACAC 57.622 45.455 0.00 0.00 33.79 3.82
2687 2867 4.713553 TCTGAGTGACAAGTTGCCATTTA 58.286 39.130 1.81 0.00 0.00 1.40
2764 2956 1.080772 GATGTCGAGCACGTCCACA 60.081 57.895 2.86 1.01 40.69 4.17
2767 2959 3.768632 GTGATGTCGAGCACGTCC 58.231 61.111 2.86 0.00 40.01 4.79
2774 2966 3.009140 GGCATGCGTGATGTCGAG 58.991 61.111 12.44 0.00 34.14 4.04
2820 3012 5.819901 ACTCAAACCTTTTCTGTCTTCTGAG 59.180 40.000 0.00 0.00 34.22 3.35
2847 3039 4.022416 GCAATCAGTAGGAGACATCTCGAT 60.022 45.833 2.86 0.00 43.76 3.59
2873 3068 8.840321 GCTGCTCTCAACCTATATAATTTTTGA 58.160 33.333 0.00 0.00 0.00 2.69
2874 3069 7.800380 CGCTGCTCTCAACCTATATAATTTTTG 59.200 37.037 0.00 0.00 0.00 2.44
2876 3071 6.428159 CCGCTGCTCTCAACCTATATAATTTT 59.572 38.462 0.00 0.00 0.00 1.82
2877 3072 5.934625 CCGCTGCTCTCAACCTATATAATTT 59.065 40.000 0.00 0.00 0.00 1.82
2878 3073 5.482908 CCGCTGCTCTCAACCTATATAATT 58.517 41.667 0.00 0.00 0.00 1.40
2879 3074 4.621747 GCCGCTGCTCTCAACCTATATAAT 60.622 45.833 0.00 0.00 33.53 1.28
2880 3075 3.306088 GCCGCTGCTCTCAACCTATATAA 60.306 47.826 0.00 0.00 33.53 0.98
2881 3076 2.231478 GCCGCTGCTCTCAACCTATATA 59.769 50.000 0.00 0.00 33.53 0.86
2882 3077 1.001406 GCCGCTGCTCTCAACCTATAT 59.999 52.381 0.00 0.00 33.53 0.86
2920 3115 4.764308 CAGAACCTCTGGATCATCGAGATA 59.236 45.833 0.00 0.00 40.71 1.98
2974 3169 1.443872 CTGGGTTTCGGTCTCGTCG 60.444 63.158 0.00 0.00 37.69 5.12
3103 3331 1.277557 TGGAGCTTGAAGGAGAAGAGC 59.722 52.381 0.00 0.00 0.00 4.09
3189 3417 0.034863 TAATGGGGGCGAAGGTGAAC 60.035 55.000 0.00 0.00 0.00 3.18
3190 3418 0.699399 TTAATGGGGGCGAAGGTGAA 59.301 50.000 0.00 0.00 0.00 3.18
3191 3419 0.034863 GTTAATGGGGGCGAAGGTGA 60.035 55.000 0.00 0.00 0.00 4.02
3192 3420 1.035385 GGTTAATGGGGGCGAAGGTG 61.035 60.000 0.00 0.00 0.00 4.00
3193 3421 1.212250 AGGTTAATGGGGGCGAAGGT 61.212 55.000 0.00 0.00 0.00 3.50
3194 3422 0.751643 CAGGTTAATGGGGGCGAAGG 60.752 60.000 0.00 0.00 0.00 3.46
3195 3423 1.384222 GCAGGTTAATGGGGGCGAAG 61.384 60.000 0.00 0.00 0.00 3.79
3212 3440 2.159114 TGCATGCAGACGATAAGTAGCA 60.159 45.455 18.46 0.00 44.41 3.49
3347 3575 2.823154 TCATCATCGCATGTATCCCGTA 59.177 45.455 0.00 0.00 0.00 4.02
3360 3588 3.441163 CATTTGCCCAGTTTCATCATCG 58.559 45.455 0.00 0.00 0.00 3.84
3554 3782 0.741915 TCAAACCAAACCGGCTGAAC 59.258 50.000 0.00 0.00 39.03 3.18
3791 4026 7.736881 TGGGATTACTACATGGTAAGTACAA 57.263 36.000 0.00 0.00 35.52 2.41
3894 4131 1.373812 GCCCGTGTTACCCTCTGTT 59.626 57.895 0.00 0.00 0.00 3.16
3897 4134 0.907704 TCATGCCCGTGTTACCCTCT 60.908 55.000 0.00 0.00 0.00 3.69
3944 4181 2.061773 CGACACATTGACACTGGTCTC 58.938 52.381 10.47 0.00 44.61 3.36
3945 4182 1.412710 ACGACACATTGACACTGGTCT 59.587 47.619 0.00 0.49 44.61 3.85
3972 4209 2.816087 GCTGTGCCTTCTTCATTTCTGA 59.184 45.455 0.00 0.00 0.00 3.27
3997 4234 0.865769 ATGTTCTCGTCGTTTGCCAC 59.134 50.000 0.00 0.00 0.00 5.01
4021 4258 3.129287 AGCGTGATAAATTTTCAGCAGGG 59.871 43.478 0.00 0.00 0.00 4.45
4040 4277 4.202959 CGCTCTATGCATTTTGTTAAAGCG 59.797 41.667 3.54 10.36 43.06 4.68
4053 4292 2.610433 CTCTGTTTGACGCTCTATGCA 58.390 47.619 0.00 0.00 43.06 3.96
4061 4300 1.865865 TCAACTCCTCTGTTTGACGC 58.134 50.000 0.00 0.00 0.00 5.19
4116 4397 0.249699 TGTAGCACTTGTGTGGACCG 60.250 55.000 2.61 0.00 43.97 4.79
4147 4428 3.967335 GCCTCTCGGGATCGACGG 61.967 72.222 8.32 0.00 40.88 4.79
4148 4429 3.209812 TGCCTCTCGGGATCGACG 61.210 66.667 0.00 2.38 40.88 5.12
4149 4430 2.413765 GTGCCTCTCGGGATCGAC 59.586 66.667 0.00 0.00 40.88 4.20
4152 4433 2.833582 TCGGTGCCTCTCGGGATC 60.834 66.667 0.00 0.00 37.23 3.36
4197 4478 1.282157 CTCGATCCCCTTTCCTTTGGT 59.718 52.381 0.00 0.00 0.00 3.67
4201 4482 0.833949 GCTCTCGATCCCCTTTCCTT 59.166 55.000 0.00 0.00 0.00 3.36
4240 4526 3.169099 TCCTTCTTCCTCTCCAAGTCTG 58.831 50.000 0.00 0.00 0.00 3.51
4298 4592 1.626654 CGAGGATGCGTGTGTGAACC 61.627 60.000 0.00 0.00 0.00 3.62
4384 4683 1.038130 CGTAGAGCTGGCTAGTGGGT 61.038 60.000 0.00 0.00 0.00 4.51
4402 4701 0.884704 AACCAGCTGTTAGTGTGCCG 60.885 55.000 13.81 0.00 34.69 5.69
4536 4839 1.618837 CCGATGACGTGGGAGGATTAT 59.381 52.381 0.00 0.00 37.88 1.28
4552 4855 1.296056 GCAAGCAACACCGTACCGAT 61.296 55.000 0.00 0.00 0.00 4.18
4558 4861 2.594592 GGGAGCAAGCAACACCGT 60.595 61.111 0.00 0.00 0.00 4.83
4565 4868 2.853542 TCCAGTGGGGAGCAAGCA 60.854 61.111 9.92 0.00 42.15 3.91
4737 5040 2.346365 GTCCACCCCGTCTTCCAC 59.654 66.667 0.00 0.00 0.00 4.02
4738 5041 2.926242 GGTCCACCCCGTCTTCCA 60.926 66.667 0.00 0.00 0.00 3.53
4739 5042 2.606826 AGGTCCACCCCGTCTTCC 60.607 66.667 0.00 0.00 36.42 3.46
4740 5043 2.663196 CAGGTCCACCCCGTCTTC 59.337 66.667 0.00 0.00 36.42 2.87
4741 5044 2.928396 CCAGGTCCACCCCGTCTT 60.928 66.667 0.00 0.00 36.42 3.01


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

AutoCloner maintained by Alex Coulton.