Multiple sequence alignment - TraesCS4D01G016700

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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 TraesCS4D01G016700 chr4D 100.000 2360 0 0 1 2360 7586288 7588647 0.000000e+00 4359.0
1 TraesCS4D01G016700 chr4A 90.363 2096 77 35 2 2042 596003413 596001388 0.000000e+00 2636.0
2 TraesCS4D01G016700 chr4A 93.814 194 12 0 2119 2312 596001385 596001192 2.290000e-75 292.0
3 TraesCS4D01G016700 chr4A 80.469 128 23 2 1010 1136 21631975 21632101 1.930000e-16 97.1
4 TraesCS4D01G016700 chr4B 89.756 1396 72 31 649 2006 13395107 13396469 0.000000e+00 1720.0
5 TraesCS4D01G016700 chr4B 91.542 603 22 4 1 575 13394398 13394999 0.000000e+00 804.0
6 TraesCS4D01G016700 chr4B 91.192 193 13 2 878 1066 291450801 291450993 2.330000e-65 259.0
7 TraesCS4D01G016700 chr4B 80.315 127 25 0 1010 1136 556069781 556069655 1.930000e-16 97.1
8 TraesCS4D01G016700 chr3B 90.686 204 13 5 878 1076 727081904 727081702 1.390000e-67 267.0
9 TraesCS4D01G016700 chr5B 90.196 204 14 5 878 1076 711785547 711785749 6.470000e-66 261.0
10 TraesCS4D01G016700 chr5B 91.192 193 13 2 878 1066 544816087 544816279 2.330000e-65 259.0
11 TraesCS4D01G016700 chr1B 89.119 193 17 3 878 1066 588928656 588928848 1.090000e-58 237.0
12 TraesCS4D01G016700 chr1A 81.768 181 28 4 1025 1201 559886837 559886658 1.890000e-31 147.0
13 TraesCS4D01G016700 chr1A 78.099 242 41 9 1025 1257 559941803 559941565 2.440000e-30 143.0
14 TraesCS4D01G016700 chrUn 77.273 242 43 9 1025 1257 67087903 67087665 5.290000e-27 132.0
15 TraesCS4D01G016700 chrUn 76.613 248 52 5 1025 1266 199465921 199465674 5.290000e-27 132.0
16 TraesCS4D01G016700 chrUn 76.955 243 48 6 1022 1257 307431728 307431969 5.290000e-27 132.0
17 TraesCS4D01G016700 chrUn 76.860 242 50 5 1022 1257 343570822 343571063 5.290000e-27 132.0
18 TraesCS4D01G016700 chrUn 76.860 242 50 5 1022 1257 343624734 343624975 5.290000e-27 132.0


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 TraesCS4D01G016700 chr4D 7586288 7588647 2359 False 4359 4359 100.0000 1 2360 1 chr4D.!!$F1 2359
1 TraesCS4D01G016700 chr4A 596001192 596003413 2221 True 1464 2636 92.0885 2 2312 2 chr4A.!!$R1 2310
2 TraesCS4D01G016700 chr4B 13394398 13396469 2071 False 1262 1720 90.6490 1 2006 2 chr4B.!!$F2 2005

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
944 1035 1.298953 AATAGCCTCCCAAGAAGCCA 58.701 50.0 0.0 0.0 28.87 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 2407 0.039618 TGACCCTGGAATCTTTGGCC 59.96 55.0 0.0 0.0 0.0 5.36 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
133 135 6.039047 TGTCAACCGACTAAAGCTATACCTAG 59.961 42.308 0.00 0.00 43.06 3.02
141 143 7.861872 CGACTAAAGCTATACCTAGACCTTTTC 59.138 40.741 0.00 0.00 0.00 2.29
146 148 9.755122 AAAGCTATACCTAGACCTTTTCAAAAT 57.245 29.630 0.00 0.00 0.00 1.82
201 204 2.270434 TGCCCTCCACCTCTAAATCT 57.730 50.000 0.00 0.00 0.00 2.40
236 239 4.392940 GCTGCTGGAATCTGTATGGTAAT 58.607 43.478 0.00 0.00 0.00 1.89
536 565 2.821366 GGCTGGCTCATGTCACCG 60.821 66.667 0.00 0.00 0.00 4.94
566 595 1.342174 CTGCCTGGCTCAAACATTTGT 59.658 47.619 21.03 0.00 39.18 2.83
586 615 6.494666 TTGTAGAAATCCATACCTACAGGG 57.505 41.667 0.00 0.00 41.39 4.45
587 616 5.784023 TGTAGAAATCCATACCTACAGGGA 58.216 41.667 0.00 0.00 37.25 4.20
588 617 6.206787 TGTAGAAATCCATACCTACAGGGAA 58.793 40.000 0.00 0.00 37.25 3.97
589 618 6.674861 TGTAGAAATCCATACCTACAGGGAAA 59.325 38.462 0.00 0.00 37.25 3.13
590 619 6.652205 AGAAATCCATACCTACAGGGAAAA 57.348 37.500 0.00 0.00 40.27 2.29
591 620 7.039722 AGAAATCCATACCTACAGGGAAAAA 57.960 36.000 0.00 0.00 40.27 1.94
592 621 6.890268 AGAAATCCATACCTACAGGGAAAAAC 59.110 38.462 0.00 0.00 40.27 2.43
593 622 6.402981 AATCCATACCTACAGGGAAAAACT 57.597 37.500 0.00 0.00 40.27 2.66
594 623 5.174037 TCCATACCTACAGGGAAAAACTG 57.826 43.478 0.00 0.00 41.64 3.16
595 624 4.018779 TCCATACCTACAGGGAAAAACTGG 60.019 45.833 0.00 0.00 40.23 4.00
597 626 3.790089 ACCTACAGGGAAAAACTGGAG 57.210 47.619 0.00 0.00 44.78 3.86
609 638 6.351033 GGGAAAAACTGGAGAAAACTGAAACT 60.351 38.462 0.00 0.00 0.00 2.66
794 875 1.541015 CCAGGAAAAAGGCCAGCAAAC 60.541 52.381 5.01 0.00 0.00 2.93
938 1029 2.158608 CCCCTACAAATAGCCTCCCAAG 60.159 54.545 0.00 0.00 0.00 3.61
939 1030 2.777692 CCCTACAAATAGCCTCCCAAGA 59.222 50.000 0.00 0.00 0.00 3.02
940 1031 3.202151 CCCTACAAATAGCCTCCCAAGAA 59.798 47.826 0.00 0.00 0.00 2.52
941 1032 4.455606 CCTACAAATAGCCTCCCAAGAAG 58.544 47.826 0.00 0.00 0.00 2.85
942 1033 2.728007 ACAAATAGCCTCCCAAGAAGC 58.272 47.619 0.00 0.00 0.00 3.86
943 1034 2.027385 CAAATAGCCTCCCAAGAAGCC 58.973 52.381 0.00 0.00 28.87 4.35
944 1035 1.298953 AATAGCCTCCCAAGAAGCCA 58.701 50.000 0.00 0.00 28.87 4.75
945 1036 1.298953 ATAGCCTCCCAAGAAGCCAA 58.701 50.000 0.00 0.00 28.87 4.52
971 1062 1.890510 CAGCACAGCACAGCACAGA 60.891 57.895 0.00 0.00 0.00 3.41
972 1063 1.597302 AGCACAGCACAGCACAGAG 60.597 57.895 0.00 0.00 0.00 3.35
1055 1155 3.403558 GAGGGAGGACTGCACCCC 61.404 72.222 5.73 0.00 44.21 4.95
1341 1444 0.936764 CGCAGGTCGGAGATGATTCG 60.937 60.000 0.00 0.00 40.67 3.34
1342 1445 1.218230 GCAGGTCGGAGATGATTCGC 61.218 60.000 0.00 0.00 40.67 4.70
1355 1458 0.039798 GATTCGCCCGTGTCGCTATA 60.040 55.000 0.00 0.00 0.00 1.31
1356 1459 0.601558 ATTCGCCCGTGTCGCTATAT 59.398 50.000 0.00 0.00 0.00 0.86
1357 1460 0.386476 TTCGCCCGTGTCGCTATATT 59.614 50.000 0.00 0.00 0.00 1.28
1358 1461 1.237533 TCGCCCGTGTCGCTATATTA 58.762 50.000 0.00 0.00 0.00 0.98
1374 1477 6.527023 CGCTATATTAATTGAGGAGTACACCG 59.473 42.308 3.50 0.00 34.73 4.94
1399 1502 4.422073 CCATTCTATGGCTTGTAGACCA 57.578 45.455 0.00 0.00 44.70 4.02
1402 1505 5.221803 CCATTCTATGGCTTGTAGACCATCT 60.222 44.000 0.00 0.00 43.26 2.90
1403 1506 6.014242 CCATTCTATGGCTTGTAGACCATCTA 60.014 42.308 0.00 0.00 43.26 1.98
1404 1507 6.656632 TTCTATGGCTTGTAGACCATCTAG 57.343 41.667 0.00 0.00 43.26 2.43
1405 1508 5.706447 TCTATGGCTTGTAGACCATCTAGT 58.294 41.667 0.00 0.00 43.26 2.57
1406 1509 4.679373 ATGGCTTGTAGACCATCTAGTG 57.321 45.455 0.00 0.00 43.26 2.74
1407 1510 2.168521 TGGCTTGTAGACCATCTAGTGC 59.831 50.000 0.00 0.00 28.01 4.40
1408 1511 2.432510 GGCTTGTAGACCATCTAGTGCT 59.567 50.000 0.00 0.00 28.01 4.40
1453 1558 5.462034 TGTTTCTTTTGTCATTTTTGGCG 57.538 34.783 0.00 0.00 0.00 5.69
1457 1562 6.761731 TTCTTTTGTCATTTTTGGCGTATG 57.238 33.333 0.00 0.00 0.00 2.39
1465 1570 7.598278 TGTCATTTTTGGCGTATGTTCTTATT 58.402 30.769 0.00 0.00 0.00 1.40
1466 1571 7.540400 TGTCATTTTTGGCGTATGTTCTTATTG 59.460 33.333 0.00 0.00 0.00 1.90
1470 1575 4.209307 TGGCGTATGTTCTTATTGTGGA 57.791 40.909 0.00 0.00 0.00 4.02
1548 1657 3.005155 GCTTGGCTTTGAAATGAGACTGT 59.995 43.478 0.00 0.00 0.00 3.55
1658 1776 4.992688 TGTTGCAACCTAACAAAGACAAG 58.007 39.130 26.14 0.00 35.29 3.16
1777 1902 7.277981 GGCAATCTATTTATCTATGTACCGGTG 59.722 40.741 19.93 0.00 0.00 4.94
1899 2031 6.183360 CCCCCTTTCCAATGTTCACATTATAC 60.183 42.308 4.85 0.00 44.10 1.47
2038 2170 1.971357 TCCTGAAGACAAGGACAGACC 59.029 52.381 0.00 0.00 39.35 3.85
2042 2174 4.020218 CCTGAAGACAAGGACAGACCATTA 60.020 45.833 0.00 0.00 42.04 1.90
2043 2175 5.152623 TGAAGACAAGGACAGACCATTAG 57.847 43.478 0.00 0.00 42.04 1.73
2044 2176 4.020218 TGAAGACAAGGACAGACCATTAGG 60.020 45.833 0.00 0.00 42.04 2.69
2045 2177 2.840651 AGACAAGGACAGACCATTAGGG 59.159 50.000 0.00 0.00 42.04 3.53
2061 2193 7.849804 CCATTAGGGTGTATCTATGTATTGC 57.150 40.000 0.00 0.00 0.00 3.56
2062 2194 7.394016 CCATTAGGGTGTATCTATGTATTGCA 58.606 38.462 0.00 0.00 0.00 4.08
2063 2195 7.882791 CCATTAGGGTGTATCTATGTATTGCAA 59.117 37.037 0.00 0.00 0.00 4.08
2064 2196 9.283768 CATTAGGGTGTATCTATGTATTGCAAA 57.716 33.333 1.71 0.00 0.00 3.68
2065 2197 8.902540 TTAGGGTGTATCTATGTATTGCAAAG 57.097 34.615 1.71 0.00 0.00 2.77
2066 2198 5.765182 AGGGTGTATCTATGTATTGCAAAGC 59.235 40.000 1.71 0.00 0.00 3.51
2067 2199 5.048713 GGGTGTATCTATGTATTGCAAAGCC 60.049 44.000 1.71 0.00 0.00 4.35
2068 2200 5.048713 GGTGTATCTATGTATTGCAAAGCCC 60.049 44.000 1.71 0.00 0.00 5.19
2069 2201 5.530915 GTGTATCTATGTATTGCAAAGCCCA 59.469 40.000 1.71 0.00 0.00 5.36
2070 2202 6.207417 GTGTATCTATGTATTGCAAAGCCCAT 59.793 38.462 1.71 6.02 0.00 4.00
2071 2203 5.972107 ATCTATGTATTGCAAAGCCCATC 57.028 39.130 1.71 0.00 0.00 3.51
2072 2204 5.052693 TCTATGTATTGCAAAGCCCATCT 57.947 39.130 1.71 0.00 0.00 2.90
2073 2205 5.448654 TCTATGTATTGCAAAGCCCATCTT 58.551 37.500 1.71 0.00 36.34 2.40
2074 2206 5.893255 TCTATGTATTGCAAAGCCCATCTTT 59.107 36.000 1.71 0.00 45.43 2.52
2075 2207 7.059788 TCTATGTATTGCAAAGCCCATCTTTA 58.940 34.615 1.71 0.00 42.82 1.85
2076 2208 5.323371 TGTATTGCAAAGCCCATCTTTAC 57.677 39.130 1.71 0.00 42.82 2.01
2077 2209 4.769488 TGTATTGCAAAGCCCATCTTTACA 59.231 37.500 1.71 0.33 42.82 2.41
2078 2210 3.940209 TTGCAAAGCCCATCTTTACAG 57.060 42.857 0.00 0.00 42.82 2.74
2079 2211 2.875296 TGCAAAGCCCATCTTTACAGT 58.125 42.857 0.00 0.00 42.82 3.55
2080 2212 3.230134 TGCAAAGCCCATCTTTACAGTT 58.770 40.909 0.00 0.00 42.82 3.16
2081 2213 3.005684 TGCAAAGCCCATCTTTACAGTTG 59.994 43.478 0.00 0.00 42.82 3.16
2082 2214 3.578688 CAAAGCCCATCTTTACAGTTGC 58.421 45.455 0.00 0.00 42.82 4.17
2083 2215 2.887151 AGCCCATCTTTACAGTTGCT 57.113 45.000 0.00 0.00 0.00 3.91
2084 2216 3.160679 AGCCCATCTTTACAGTTGCTT 57.839 42.857 0.00 0.00 0.00 3.91
2085 2217 4.301072 AGCCCATCTTTACAGTTGCTTA 57.699 40.909 0.00 0.00 0.00 3.09
2086 2218 4.265073 AGCCCATCTTTACAGTTGCTTAG 58.735 43.478 0.00 0.00 0.00 2.18
2087 2219 3.378427 GCCCATCTTTACAGTTGCTTAGG 59.622 47.826 0.00 0.00 0.00 2.69
2088 2220 4.843728 CCCATCTTTACAGTTGCTTAGGA 58.156 43.478 0.00 0.00 0.00 2.94
2089 2221 5.253330 CCCATCTTTACAGTTGCTTAGGAA 58.747 41.667 0.00 0.00 0.00 3.36
2090 2222 5.355350 CCCATCTTTACAGTTGCTTAGGAAG 59.645 44.000 0.00 0.00 0.00 3.46
2091 2223 6.173339 CCATCTTTACAGTTGCTTAGGAAGA 58.827 40.000 0.00 0.00 0.00 2.87
2092 2224 6.655003 CCATCTTTACAGTTGCTTAGGAAGAA 59.345 38.462 0.00 0.00 0.00 2.52
2093 2225 7.174946 CCATCTTTACAGTTGCTTAGGAAGAAA 59.825 37.037 0.00 0.00 0.00 2.52
2094 2226 8.734386 CATCTTTACAGTTGCTTAGGAAGAAAT 58.266 33.333 0.00 0.00 0.00 2.17
2095 2227 8.324163 TCTTTACAGTTGCTTAGGAAGAAATC 57.676 34.615 0.00 0.00 0.00 2.17
2096 2228 8.157476 TCTTTACAGTTGCTTAGGAAGAAATCT 58.843 33.333 0.00 0.00 0.00 2.40
2097 2229 7.672983 TTACAGTTGCTTAGGAAGAAATCTG 57.327 36.000 0.00 0.00 34.29 2.90
2098 2230 5.869579 ACAGTTGCTTAGGAAGAAATCTGA 58.130 37.500 7.73 0.00 33.30 3.27
2099 2231 5.936956 ACAGTTGCTTAGGAAGAAATCTGAG 59.063 40.000 7.73 0.00 33.30 3.35
2100 2232 6.169094 CAGTTGCTTAGGAAGAAATCTGAGA 58.831 40.000 0.00 0.00 31.94 3.27
2101 2233 6.091986 CAGTTGCTTAGGAAGAAATCTGAGAC 59.908 42.308 0.00 0.00 31.94 3.36
2102 2234 5.745312 TGCTTAGGAAGAAATCTGAGACA 57.255 39.130 0.00 0.00 0.00 3.41
2103 2235 5.728471 TGCTTAGGAAGAAATCTGAGACAG 58.272 41.667 0.00 0.00 0.00 3.51
2104 2236 5.247110 TGCTTAGGAAGAAATCTGAGACAGT 59.753 40.000 0.00 0.00 32.61 3.55
2105 2237 5.580297 GCTTAGGAAGAAATCTGAGACAGTG 59.420 44.000 0.00 0.00 32.61 3.66
2106 2238 3.936564 AGGAAGAAATCTGAGACAGTGC 58.063 45.455 0.00 0.00 32.61 4.40
2107 2239 3.006247 GGAAGAAATCTGAGACAGTGCC 58.994 50.000 0.00 0.00 32.61 5.01
2108 2240 3.557898 GGAAGAAATCTGAGACAGTGCCA 60.558 47.826 0.00 0.00 32.61 4.92
2109 2241 3.996921 AGAAATCTGAGACAGTGCCAT 57.003 42.857 0.00 0.00 32.61 4.40
2110 2242 5.423015 GAAGAAATCTGAGACAGTGCCATA 58.577 41.667 0.00 0.00 32.61 2.74
2111 2243 5.021033 AGAAATCTGAGACAGTGCCATAG 57.979 43.478 0.00 0.00 32.61 2.23
2112 2244 2.906691 ATCTGAGACAGTGCCATAGC 57.093 50.000 0.00 0.00 40.48 2.97
2113 2245 1.857965 TCTGAGACAGTGCCATAGCT 58.142 50.000 0.00 0.00 40.80 3.32
2114 2246 3.018423 TCTGAGACAGTGCCATAGCTA 57.982 47.619 0.00 0.00 40.80 3.32
2115 2247 3.570540 TCTGAGACAGTGCCATAGCTAT 58.429 45.455 0.00 0.00 40.80 2.97
2116 2248 4.729868 TCTGAGACAGTGCCATAGCTATA 58.270 43.478 5.77 0.00 40.80 1.31
2117 2249 4.764308 TCTGAGACAGTGCCATAGCTATAG 59.236 45.833 5.77 0.00 40.80 1.31
2149 2281 4.202357 ACTGCTTAAGTGGAGTTGTGATGA 60.202 41.667 4.02 0.00 37.88 2.92
2151 2283 4.696877 TGCTTAAGTGGAGTTGTGATGATG 59.303 41.667 4.02 0.00 0.00 3.07
2188 2320 5.168569 TCATGACCAAGTTCTACGAACATC 58.831 41.667 9.16 2.67 0.00 3.06
2202 2334 2.282555 CGAACATCGGACAGTGCATAAG 59.717 50.000 0.00 0.00 36.00 1.73
2211 2343 4.677584 GGACAGTGCATAAGACTAGACAG 58.322 47.826 0.00 0.00 0.00 3.51
2273 2405 9.543783 GGATGGAACGTTATTTTACTCTATCTT 57.456 33.333 0.00 0.00 0.00 2.40
2299 2431 3.897505 CCAAAGATTCCAGGGTCAAAAGT 59.102 43.478 0.00 0.00 0.00 2.66
2300 2432 4.344968 CCAAAGATTCCAGGGTCAAAAGTT 59.655 41.667 0.00 0.00 0.00 2.66
2303 2435 5.319043 AGATTCCAGGGTCAAAAGTTGTA 57.681 39.130 0.00 0.00 0.00 2.41
2312 2444 6.540914 CAGGGTCAAAAGTTGTAGAACTGTTA 59.459 38.462 7.80 0.00 41.87 2.41
2313 2445 6.541278 AGGGTCAAAAGTTGTAGAACTGTTAC 59.459 38.462 7.80 7.12 41.87 2.50
2314 2446 6.541278 GGGTCAAAAGTTGTAGAACTGTTACT 59.459 38.462 7.80 0.00 41.87 2.24
2315 2447 7.712205 GGGTCAAAAGTTGTAGAACTGTTACTA 59.288 37.037 7.80 0.00 41.87 1.82
2316 2448 9.101655 GGTCAAAAGTTGTAGAACTGTTACTAA 57.898 33.333 7.80 0.00 41.87 2.24
2334 2466 9.497030 TGTTACTAAAATATTTGCTTATGTGCG 57.503 29.630 0.39 0.00 35.36 5.34
2335 2467 9.710979 GTTACTAAAATATTTGCTTATGTGCGA 57.289 29.630 0.39 0.00 35.36 5.10
2336 2468 9.710979 TTACTAAAATATTTGCTTATGTGCGAC 57.289 29.630 0.39 0.00 35.36 5.19
2337 2469 6.905076 ACTAAAATATTTGCTTATGTGCGACG 59.095 34.615 0.39 0.00 35.36 5.12
2338 2470 2.730183 TATTTGCTTATGTGCGACGC 57.270 45.000 14.19 14.19 35.36 5.19
2339 2471 0.801872 ATTTGCTTATGTGCGACGCA 59.198 45.000 20.50 20.50 35.60 5.24
2340 2472 0.801872 TTTGCTTATGTGCGACGCAT 59.198 45.000 27.23 13.78 41.91 4.73
2341 2473 1.646189 TTGCTTATGTGCGACGCATA 58.354 45.000 27.23 24.33 41.91 3.14
2342 2474 1.646189 TGCTTATGTGCGACGCATAA 58.354 45.000 27.23 19.24 42.21 1.90
2343 2475 2.209273 TGCTTATGTGCGACGCATAAT 58.791 42.857 27.23 23.05 43.04 1.28
2344 2476 2.032979 TGCTTATGTGCGACGCATAATG 60.033 45.455 27.23 17.13 43.04 1.90
2345 2477 2.032894 GCTTATGTGCGACGCATAATGT 60.033 45.455 27.23 11.07 43.04 2.71
2346 2478 3.183574 GCTTATGTGCGACGCATAATGTA 59.816 43.478 27.23 9.99 43.04 2.29
2347 2479 4.688063 CTTATGTGCGACGCATAATGTAC 58.312 43.478 27.23 11.59 43.04 2.90
2348 2480 2.287393 TGTGCGACGCATAATGTACT 57.713 45.000 27.23 0.00 41.91 2.73
2349 2481 1.923864 TGTGCGACGCATAATGTACTG 59.076 47.619 27.23 0.00 41.91 2.74
2350 2482 1.924524 GTGCGACGCATAATGTACTGT 59.075 47.619 27.23 0.00 41.91 3.55
2351 2483 2.347452 GTGCGACGCATAATGTACTGTT 59.653 45.455 27.23 0.00 41.91 3.16
2352 2484 2.997303 TGCGACGCATAATGTACTGTTT 59.003 40.909 20.50 0.00 31.71 2.83
2353 2485 4.031991 GTGCGACGCATAATGTACTGTTTA 59.968 41.667 27.23 0.00 41.91 2.01
2354 2486 4.806775 TGCGACGCATAATGTACTGTTTAT 59.193 37.500 20.50 0.00 31.71 1.40
2355 2487 5.978322 TGCGACGCATAATGTACTGTTTATA 59.022 36.000 20.50 0.00 31.71 0.98
2356 2488 6.476053 TGCGACGCATAATGTACTGTTTATAA 59.524 34.615 20.50 0.00 31.71 0.98
2357 2489 7.001922 GCGACGCATAATGTACTGTTTATAAG 58.998 38.462 16.42 0.00 0.00 1.73
2358 2490 7.096353 GCGACGCATAATGTACTGTTTATAAGA 60.096 37.037 16.42 0.00 0.00 2.10
2359 2491 8.912658 CGACGCATAATGTACTGTTTATAAGAT 58.087 33.333 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 155 8.508875 ACGGTAGTACCAATTTTGTAGATTTTG 58.491 33.333 19.41 0.00 38.47 2.44
161 164 5.448089 GGCATACACGGTAGTACCAATTTTG 60.448 44.000 19.41 11.18 38.47 2.44
169 172 1.339291 GGAGGGCATACACGGTAGTAC 59.661 57.143 0.00 0.00 0.00 2.73
201 204 1.614051 CCAGCAGCCACCTGTGATTAA 60.614 52.381 0.00 0.00 41.26 1.40
536 565 2.924105 GCCAGGCAGTGCTGTTTCC 61.924 63.158 16.11 0.00 0.00 3.13
566 595 7.758820 TTTTCCCTGTAGGTATGGATTTCTA 57.241 36.000 0.00 0.00 36.75 2.10
586 615 7.812669 TCAAGTTTCAGTTTTCTCCAGTTTTTC 59.187 33.333 0.00 0.00 0.00 2.29
587 616 7.598869 GTCAAGTTTCAGTTTTCTCCAGTTTTT 59.401 33.333 0.00 0.00 0.00 1.94
588 617 7.090808 GTCAAGTTTCAGTTTTCTCCAGTTTT 58.909 34.615 0.00 0.00 0.00 2.43
589 618 6.208599 TGTCAAGTTTCAGTTTTCTCCAGTTT 59.791 34.615 0.00 0.00 0.00 2.66
590 619 5.710099 TGTCAAGTTTCAGTTTTCTCCAGTT 59.290 36.000 0.00 0.00 0.00 3.16
591 620 5.253330 TGTCAAGTTTCAGTTTTCTCCAGT 58.747 37.500 0.00 0.00 0.00 4.00
592 621 5.818136 TGTCAAGTTTCAGTTTTCTCCAG 57.182 39.130 0.00 0.00 0.00 3.86
593 622 6.432783 TCTTTGTCAAGTTTCAGTTTTCTCCA 59.567 34.615 0.00 0.00 0.00 3.86
594 623 6.852664 TCTTTGTCAAGTTTCAGTTTTCTCC 58.147 36.000 0.00 0.00 0.00 3.71
595 624 7.273598 GGTTCTTTGTCAAGTTTCAGTTTTCTC 59.726 37.037 0.00 0.00 0.00 2.87
597 626 6.866248 TGGTTCTTTGTCAAGTTTCAGTTTTC 59.134 34.615 0.00 0.00 0.00 2.29
609 638 4.229304 TCAGGAGTTGGTTCTTTGTCAA 57.771 40.909 0.00 0.00 0.00 3.18
794 875 4.767255 GGGTGTGAGCCTGCCTCG 62.767 72.222 0.00 0.00 43.82 4.63
942 1033 2.521465 TGTGCTGGCCTTGGTTGG 60.521 61.111 3.32 0.00 0.00 3.77
943 1034 3.045142 CTGTGCTGGCCTTGGTTG 58.955 61.111 3.32 0.00 0.00 3.77
944 1035 2.914097 GCTGTGCTGGCCTTGGTT 60.914 61.111 3.32 0.00 0.00 3.67
945 1036 4.208403 TGCTGTGCTGGCCTTGGT 62.208 61.111 3.32 0.00 0.00 3.67
975 1066 2.306805 TGCTGGCTATGGCTATTGCTAT 59.693 45.455 15.28 3.26 42.98 2.97
976 1067 1.699083 TGCTGGCTATGGCTATTGCTA 59.301 47.619 15.28 9.17 39.59 3.49
1055 1155 1.516386 ACGCTCGCAATGTAGTCCG 60.516 57.895 0.00 0.00 0.00 4.79
1341 1444 3.991773 TCAATTAATATAGCGACACGGGC 59.008 43.478 0.00 0.00 0.00 6.13
1342 1445 4.625742 CCTCAATTAATATAGCGACACGGG 59.374 45.833 0.00 0.00 0.00 5.28
1355 1458 6.070653 TGGTAACGGTGTACTCCTCAATTAAT 60.071 38.462 11.98 0.00 42.51 1.40
1356 1459 5.245751 TGGTAACGGTGTACTCCTCAATTAA 59.754 40.000 11.98 0.00 42.51 1.40
1357 1460 4.771577 TGGTAACGGTGTACTCCTCAATTA 59.228 41.667 11.98 3.40 42.51 1.40
1358 1461 3.579586 TGGTAACGGTGTACTCCTCAATT 59.420 43.478 11.98 4.23 42.51 2.32
1422 1527 8.652810 AAATGACAAAAGAAACAGGAGATTTG 57.347 30.769 0.00 0.00 34.75 2.32
1423 1528 9.671279 AAAAATGACAAAAGAAACAGGAGATTT 57.329 25.926 0.00 0.00 0.00 2.17
1465 1570 5.441500 TGTACATTCCAAGTTCTTTCCACA 58.558 37.500 0.00 0.00 0.00 4.17
1466 1571 5.763204 TCTGTACATTCCAAGTTCTTTCCAC 59.237 40.000 0.00 0.00 0.00 4.02
1470 1575 7.556275 TGACTTTCTGTACATTCCAAGTTCTTT 59.444 33.333 0.00 0.00 0.00 2.52
1506 1611 6.425114 CCAAGCACTATTAGCATCTATTTCGT 59.575 38.462 0.00 0.00 0.00 3.85
1513 1618 3.853355 AGCCAAGCACTATTAGCATCT 57.147 42.857 0.00 0.00 0.00 2.90
1548 1657 7.930462 CGTTCTTAAAACGAACAAAAAGAACA 58.070 30.769 19.75 0.00 46.66 3.18
1613 1731 7.989826 ACAAGAAACCAATTAGCACATCTATC 58.010 34.615 0.00 0.00 0.00 2.08
1614 1732 7.944729 ACAAGAAACCAATTAGCACATCTAT 57.055 32.000 0.00 0.00 0.00 1.98
1615 1733 7.592938 CAACAAGAAACCAATTAGCACATCTA 58.407 34.615 0.00 0.00 0.00 1.98
1616 1734 6.449698 CAACAAGAAACCAATTAGCACATCT 58.550 36.000 0.00 0.00 0.00 2.90
1621 1739 4.662468 TGCAACAAGAAACCAATTAGCA 57.338 36.364 0.00 0.00 0.00 3.49
1658 1776 1.133976 ACATGCATGCTAACCTCCTCC 60.134 52.381 26.53 0.00 0.00 4.30
1899 2031 1.937278 CTGTGGTCAGCAGCTATCAG 58.063 55.000 0.00 0.00 34.79 2.90
2038 2170 8.846943 TTGCAATACATAGATACACCCTAATG 57.153 34.615 0.00 0.00 0.00 1.90
2042 2174 5.765182 GCTTTGCAATACATAGATACACCCT 59.235 40.000 0.00 0.00 29.47 4.34
2043 2175 5.048713 GGCTTTGCAATACATAGATACACCC 60.049 44.000 0.00 0.00 29.47 4.61
2044 2176 5.048713 GGGCTTTGCAATACATAGATACACC 60.049 44.000 0.00 0.00 29.47 4.16
2045 2177 5.530915 TGGGCTTTGCAATACATAGATACAC 59.469 40.000 0.00 0.00 29.47 2.90
2046 2178 5.689835 TGGGCTTTGCAATACATAGATACA 58.310 37.500 0.00 0.00 29.47 2.29
2047 2179 6.656693 AGATGGGCTTTGCAATACATAGATAC 59.343 38.462 0.00 0.00 29.47 2.24
2048 2180 6.782986 AGATGGGCTTTGCAATACATAGATA 58.217 36.000 0.00 0.00 29.47 1.98
2049 2181 5.638133 AGATGGGCTTTGCAATACATAGAT 58.362 37.500 0.00 0.00 29.47 1.98
2050 2182 5.052693 AGATGGGCTTTGCAATACATAGA 57.947 39.130 0.00 0.00 29.47 1.98
2051 2183 5.779529 AAGATGGGCTTTGCAATACATAG 57.220 39.130 0.00 0.00 31.11 2.23
2052 2184 7.038154 GTAAAGATGGGCTTTGCAATACATA 57.962 36.000 0.00 0.00 46.03 2.29
2053 2185 5.906073 GTAAAGATGGGCTTTGCAATACAT 58.094 37.500 0.00 2.62 46.03 2.29
2054 2186 5.323371 GTAAAGATGGGCTTTGCAATACA 57.677 39.130 0.00 0.00 46.03 2.29
2060 2192 3.578688 CAACTGTAAAGATGGGCTTTGC 58.421 45.455 0.00 0.00 46.03 3.68
2061 2193 3.256631 AGCAACTGTAAAGATGGGCTTTG 59.743 43.478 0.00 0.00 46.03 2.77
2063 2195 3.160679 AGCAACTGTAAAGATGGGCTT 57.839 42.857 0.00 0.00 38.88 4.35
2064 2196 2.887151 AGCAACTGTAAAGATGGGCT 57.113 45.000 0.00 0.00 0.00 5.19
2065 2197 3.378427 CCTAAGCAACTGTAAAGATGGGC 59.622 47.826 0.00 0.00 0.00 5.36
2066 2198 4.843728 TCCTAAGCAACTGTAAAGATGGG 58.156 43.478 0.00 0.00 0.00 4.00
2067 2199 6.173339 TCTTCCTAAGCAACTGTAAAGATGG 58.827 40.000 0.00 0.00 0.00 3.51
2068 2200 7.672983 TTCTTCCTAAGCAACTGTAAAGATG 57.327 36.000 0.00 0.00 0.00 2.90
2069 2201 8.870075 ATTTCTTCCTAAGCAACTGTAAAGAT 57.130 30.769 0.00 0.00 0.00 2.40
2070 2202 8.157476 AGATTTCTTCCTAAGCAACTGTAAAGA 58.843 33.333 0.00 0.00 0.00 2.52
2071 2203 8.233190 CAGATTTCTTCCTAAGCAACTGTAAAG 58.767 37.037 0.00 0.00 0.00 1.85
2072 2204 7.936847 TCAGATTTCTTCCTAAGCAACTGTAAA 59.063 33.333 0.00 0.00 0.00 2.01
2073 2205 7.450074 TCAGATTTCTTCCTAAGCAACTGTAA 58.550 34.615 0.00 0.00 0.00 2.41
2074 2206 7.004555 TCAGATTTCTTCCTAAGCAACTGTA 57.995 36.000 0.00 0.00 0.00 2.74
2075 2207 5.869579 TCAGATTTCTTCCTAAGCAACTGT 58.130 37.500 0.00 0.00 0.00 3.55
2076 2208 6.091986 GTCTCAGATTTCTTCCTAAGCAACTG 59.908 42.308 0.00 0.00 0.00 3.16
2077 2209 6.169800 GTCTCAGATTTCTTCCTAAGCAACT 58.830 40.000 0.00 0.00 0.00 3.16
2078 2210 5.934625 TGTCTCAGATTTCTTCCTAAGCAAC 59.065 40.000 0.00 0.00 0.00 4.17
2079 2211 6.114187 TGTCTCAGATTTCTTCCTAAGCAA 57.886 37.500 0.00 0.00 0.00 3.91
2080 2212 5.247110 ACTGTCTCAGATTTCTTCCTAAGCA 59.753 40.000 3.70 0.00 35.18 3.91
2081 2213 5.580297 CACTGTCTCAGATTTCTTCCTAAGC 59.420 44.000 3.70 0.00 35.18 3.09
2082 2214 5.580297 GCACTGTCTCAGATTTCTTCCTAAG 59.420 44.000 3.70 0.00 35.18 2.18
2083 2215 5.482908 GCACTGTCTCAGATTTCTTCCTAA 58.517 41.667 3.70 0.00 35.18 2.69
2084 2216 4.081420 GGCACTGTCTCAGATTTCTTCCTA 60.081 45.833 3.70 0.00 35.18 2.94
2085 2217 3.307339 GGCACTGTCTCAGATTTCTTCCT 60.307 47.826 3.70 0.00 35.18 3.36
2086 2218 3.006247 GGCACTGTCTCAGATTTCTTCC 58.994 50.000 3.70 0.00 35.18 3.46
2087 2219 3.668447 TGGCACTGTCTCAGATTTCTTC 58.332 45.455 3.70 0.00 35.18 2.87
2088 2220 3.777106 TGGCACTGTCTCAGATTTCTT 57.223 42.857 3.70 0.00 35.18 2.52
2089 2221 3.996921 ATGGCACTGTCTCAGATTTCT 57.003 42.857 3.70 0.00 35.18 2.52
2090 2222 3.559242 GCTATGGCACTGTCTCAGATTTC 59.441 47.826 0.00 0.00 38.54 2.17
2091 2223 3.199508 AGCTATGGCACTGTCTCAGATTT 59.800 43.478 3.10 0.00 41.70 2.17
2092 2224 2.770802 AGCTATGGCACTGTCTCAGATT 59.229 45.455 3.10 0.00 41.70 2.40
2093 2225 2.396608 AGCTATGGCACTGTCTCAGAT 58.603 47.619 3.10 0.00 41.70 2.90
2094 2226 1.857965 AGCTATGGCACTGTCTCAGA 58.142 50.000 3.10 0.00 41.70 3.27
2095 2227 4.764308 TCTATAGCTATGGCACTGTCTCAG 59.236 45.833 16.77 1.19 41.70 3.35
2096 2228 4.729868 TCTATAGCTATGGCACTGTCTCA 58.270 43.478 16.77 0.00 41.70 3.27
2097 2229 4.764823 ACTCTATAGCTATGGCACTGTCTC 59.235 45.833 16.77 0.00 41.70 3.36
2098 2230 4.522405 CACTCTATAGCTATGGCACTGTCT 59.478 45.833 16.77 0.00 41.70 3.41
2099 2231 4.520874 TCACTCTATAGCTATGGCACTGTC 59.479 45.833 16.77 0.00 41.70 3.51
2100 2232 4.474394 TCACTCTATAGCTATGGCACTGT 58.526 43.478 16.77 7.57 41.70 3.55
2101 2233 5.459536 TTCACTCTATAGCTATGGCACTG 57.540 43.478 16.77 8.84 41.70 3.66
2102 2234 5.363868 TGTTTCACTCTATAGCTATGGCACT 59.636 40.000 16.77 0.00 41.70 4.40
2103 2235 5.463724 GTGTTTCACTCTATAGCTATGGCAC 59.536 44.000 16.77 10.49 41.70 5.01
2104 2236 5.363868 AGTGTTTCACTCTATAGCTATGGCA 59.636 40.000 16.77 2.16 41.21 4.92
2105 2237 5.694006 CAGTGTTTCACTCTATAGCTATGGC 59.306 44.000 16.77 0.00 43.43 4.40
2106 2238 5.694006 GCAGTGTTTCACTCTATAGCTATGG 59.306 44.000 16.77 13.68 43.43 2.74
2107 2239 6.511416 AGCAGTGTTTCACTCTATAGCTATG 58.489 40.000 16.77 6.66 43.43 2.23
2108 2240 6.723298 AGCAGTGTTTCACTCTATAGCTAT 57.277 37.500 11.77 11.77 43.43 2.97
2109 2241 6.531503 AAGCAGTGTTTCACTCTATAGCTA 57.468 37.500 0.00 0.00 43.43 3.32
2110 2242 5.413309 AAGCAGTGTTTCACTCTATAGCT 57.587 39.130 0.00 0.00 43.43 3.32
2111 2243 6.814146 ACTTAAGCAGTGTTTCACTCTATAGC 59.186 38.462 1.29 1.02 43.43 2.97
2149 2281 7.071069 TGGTCATGAATAGAAGTGATAGCAT 57.929 36.000 0.00 0.00 0.00 3.79
2151 2283 6.989169 ACTTGGTCATGAATAGAAGTGATAGC 59.011 38.462 0.00 0.00 0.00 2.97
2161 2293 6.811665 TGTTCGTAGAACTTGGTCATGAATAG 59.188 38.462 13.17 0.00 45.90 1.73
2188 2320 3.128764 TGTCTAGTCTTATGCACTGTCCG 59.871 47.826 0.00 0.00 0.00 4.79
2202 2334 5.331876 AGTCCACAATAAGCTGTCTAGTC 57.668 43.478 0.00 0.00 0.00 2.59
2211 2343 4.636206 CCCAAAGAGTAGTCCACAATAAGC 59.364 45.833 0.00 0.00 0.00 3.09
2273 2405 0.486879 ACCCTGGAATCTTTGGCCAA 59.513 50.000 16.05 16.05 0.00 4.52
2275 2407 0.039618 TGACCCTGGAATCTTTGGCC 59.960 55.000 0.00 0.00 0.00 5.36
2289 2421 5.830000 AACAGTTCTACAACTTTTGACCC 57.170 39.130 0.00 0.00 41.24 4.46
2312 2444 6.905076 CGTCGCACATAAGCAAATATTTTAGT 59.095 34.615 0.00 0.00 0.00 2.24
2313 2445 6.129717 GCGTCGCACATAAGCAAATATTTTAG 60.130 38.462 13.44 0.00 0.00 1.85
2314 2446 5.679355 GCGTCGCACATAAGCAAATATTTTA 59.321 36.000 13.44 0.00 0.00 1.52
2315 2447 4.499040 GCGTCGCACATAAGCAAATATTTT 59.501 37.500 13.44 0.00 0.00 1.82
2316 2448 4.035017 GCGTCGCACATAAGCAAATATTT 58.965 39.130 13.44 0.00 0.00 1.40
2317 2449 3.064682 TGCGTCGCACATAAGCAAATATT 59.935 39.130 17.58 0.00 34.66 1.28
2318 2450 2.611751 TGCGTCGCACATAAGCAAATAT 59.388 40.909 17.58 0.00 34.66 1.28
2319 2451 2.003301 TGCGTCGCACATAAGCAAATA 58.997 42.857 17.58 0.00 34.66 1.40
2320 2452 0.801872 TGCGTCGCACATAAGCAAAT 59.198 45.000 17.58 0.00 34.66 2.32
2321 2453 0.801872 ATGCGTCGCACATAAGCAAA 59.198 45.000 24.34 0.00 43.04 3.68
2322 2454 1.646189 TATGCGTCGCACATAAGCAA 58.354 45.000 24.34 0.00 43.04 3.91
2323 2455 1.646189 TTATGCGTCGCACATAAGCA 58.354 45.000 24.34 0.00 43.04 3.91
2324 2456 2.032894 ACATTATGCGTCGCACATAAGC 60.033 45.455 24.34 0.00 43.04 3.09
2325 2457 3.859745 ACATTATGCGTCGCACATAAG 57.140 42.857 24.34 13.84 43.04 1.73
2326 2458 4.208253 CAGTACATTATGCGTCGCACATAA 59.792 41.667 24.34 18.19 43.04 1.90
2327 2459 3.733727 CAGTACATTATGCGTCGCACATA 59.266 43.478 24.34 9.44 43.04 2.29
2328 2460 2.539688 CAGTACATTATGCGTCGCACAT 59.460 45.455 24.34 14.85 43.04 3.21
2329 2461 1.923864 CAGTACATTATGCGTCGCACA 59.076 47.619 24.34 8.54 43.04 4.57
2330 2462 1.924524 ACAGTACATTATGCGTCGCAC 59.075 47.619 24.34 7.91 43.04 5.34
2331 2463 2.287393 ACAGTACATTATGCGTCGCA 57.713 45.000 24.05 24.05 44.86 5.10
2332 2464 3.651562 AAACAGTACATTATGCGTCGC 57.348 42.857 11.10 11.10 0.00 5.19
2333 2465 8.277270 TCTTATAAACAGTACATTATGCGTCG 57.723 34.615 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.