Multiple sequence alignment - TraesCS5B01G029900

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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 TraesCS5B01G029900 chr5B 100.000 4982 0 0 1 4982 32416203 32421184 0.000000e+00 9201.0
1 TraesCS5B01G029900 chr5B 92.479 3683 216 33 1088 4732 32639880 32643539 0.000000e+00 5210.0
2 TraesCS5B01G029900 chr5B 92.375 2046 122 17 2619 4642 8187251 8185218 0.000000e+00 2883.0
3 TraesCS5B01G029900 chr5B 93.386 1270 60 11 274 1530 8188845 8187587 0.000000e+00 1858.0
4 TraesCS5B01G029900 chr5B 91.939 521 30 7 3065 3580 37404427 37403914 0.000000e+00 719.0
5 TraesCS5B01G029900 chr5B 94.722 360 16 1 4315 4674 37403916 37403560 1.570000e-154 556.0
6 TraesCS5B01G029900 chr5B 93.061 245 16 1 4738 4982 32645038 32645281 1.710000e-94 357.0
7 TraesCS5B01G029900 chr5B 88.581 289 20 9 1 277 8189167 8188880 6.180000e-89 339.0
8 TraesCS5B01G029900 chr5B 91.020 245 22 0 4738 4982 32561110 32561354 1.030000e-86 331.0
9 TraesCS5B01G029900 chr5B 74.688 802 132 39 739 1519 8351654 8352405 1.750000e-74 291.0
10 TraesCS5B01G029900 chr5B 85.068 221 21 9 4280 4498 32583732 32583942 1.090000e-51 215.0
11 TraesCS5B01G029900 chr5B 100.000 37 0 0 3163 3199 8186780 8186744 8.950000e-08 69.4
12 TraesCS5B01G029900 chr5D 91.983 2083 124 25 2619 4699 7965876 7963835 0.000000e+00 2881.0
13 TraesCS5B01G029900 chr5D 88.816 760 64 14 781 1530 7966925 7966177 0.000000e+00 913.0
14 TraesCS5B01G029900 chr5D 89.216 714 57 8 4020 4732 7959660 7958966 0.000000e+00 874.0
15 TraesCS5B01G029900 chr5D 92.342 222 16 1 4738 4959 7958531 7958311 1.040000e-81 315.0
16 TraesCS5B01G029900 chr5D 92.093 215 17 0 4745 4959 7960022 7959808 2.250000e-78 303.0
17 TraesCS5B01G029900 chr5D 93.478 46 1 1 2357 2402 461476190 461476233 3.220000e-07 67.6
18 TraesCS5B01G029900 chr5A 93.621 1019 57 1 3319 4337 6288372 6287362 0.000000e+00 1515.0
19 TraesCS5B01G029900 chr5A 92.206 603 35 7 2619 3215 6289567 6288971 0.000000e+00 843.0
20 TraesCS5B01G029900 chr5A 87.500 712 66 11 829 1520 6290599 6289891 0.000000e+00 800.0
21 TraesCS5B01G029900 chr5A 85.802 162 18 5 2251 2407 581923330 581923169 3.080000e-37 167.0
22 TraesCS5B01G029900 chr5A 87.736 106 4 5 708 804 6290704 6290599 1.130000e-21 115.0
23 TraesCS5B01G029900 chr1A 87.273 165 17 2 2255 2418 584290671 584290832 8.520000e-43 185.0
24 TraesCS5B01G029900 chr1A 82.390 159 26 2 2249 2406 29045511 29045668 2.420000e-28 137.0
25 TraesCS5B01G029900 chr1A 85.714 98 14 0 1781 1878 584290768 584290671 2.450000e-18 104.0
26 TraesCS5B01G029900 chr6B 84.656 189 24 2 1780 1966 632286027 632286212 3.060000e-42 183.0
27 TraesCS5B01G029900 chr6B 89.720 107 9 1 2249 2353 632286199 632286305 8.700000e-28 135.0
28 TraesCS5B01G029900 chr6B 100.000 28 0 0 1579 1606 618122999 618123026 9.000000e-03 52.8
29 TraesCS5B01G029900 chr7B 83.626 171 20 1 1805 1967 720479779 720479609 2.400000e-33 154.0
30 TraesCS5B01G029900 chr3D 81.761 159 27 2 2249 2406 594972758 594972915 1.130000e-26 132.0
31 TraesCS5B01G029900 chr2D 81.699 153 22 4 2260 2409 606634385 606634534 6.770000e-24 122.0
32 TraesCS5B01G029900 chr4A 79.487 156 27 5 2249 2402 550466399 550466551 6.820000e-19 106.0
33 TraesCS5B01G029900 chr3A 79.114 158 27 4 2249 2403 82878157 82878311 2.450000e-18 104.0
34 TraesCS5B01G029900 chr6A 84.706 85 13 0 1 85 297670491 297670575 8.890000e-13 86.1
35 TraesCS5B01G029900 chr3B 76.336 131 22 6 399 521 472874880 472875009 1.500000e-05 62.1
36 TraesCS5B01G029900 chr7D 94.595 37 2 0 2212 2248 38625081 38625045 1.940000e-04 58.4


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 TraesCS5B01G029900 chr5B 32416203 32421184 4981 False 9201.00 9201 100.00000 1 4982 1 chr5B.!!$F2 4981
1 TraesCS5B01G029900 chr5B 32639880 32645281 5401 False 2783.50 5210 92.77000 1088 4982 2 chr5B.!!$F5 3894
2 TraesCS5B01G029900 chr5B 8185218 8189167 3949 True 1287.35 2883 93.58550 1 4642 4 chr5B.!!$R1 4641
3 TraesCS5B01G029900 chr5B 37403560 37404427 867 True 637.50 719 93.33050 3065 4674 2 chr5B.!!$R2 1609
4 TraesCS5B01G029900 chr5B 8351654 8352405 751 False 291.00 291 74.68800 739 1519 1 chr5B.!!$F1 780
5 TraesCS5B01G029900 chr5D 7958311 7966925 8614 True 1057.20 2881 90.89000 781 4959 5 chr5D.!!$R1 4178
6 TraesCS5B01G029900 chr5A 6287362 6290704 3342 True 818.25 1515 90.26575 708 4337 4 chr5A.!!$R2 3629

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
187 199 0.250727 CCCCGTTCATTGGTGTGAGT 60.251 55.0 0.00 0.00 0.00 3.41 F
2040 2211 0.109086 CCAGTAGTGTGGAGCGAGTG 60.109 60.0 0.00 0.00 40.44 3.51 F
2712 2905 0.393808 GAATTCCTGGCCGCCTACAA 60.394 55.0 11.61 0.39 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2281 0.247814 GGCACACATCGAGCGAAATG 60.248 55.0 0.0 1.12 0.00 2.32 R
2881 3074 0.033504 GTGTCGCTGAACCTTCCAGA 59.966 55.0 0.0 0.00 33.65 3.86 R
4605 10162 0.540454 GTGTTAGCCCCTCCTACACC 59.460 60.0 0.0 0.00 0.00 4.16 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
51 52 7.395772 TGCTGTACAAATGAATCCTATGGAAAA 59.604 33.333 0.00 0.00 34.34 2.29
84 85 6.406370 AGATTCACATCCTACGAATCAAACA 58.594 36.000 12.42 0.00 44.83 2.83
93 94 1.953686 ACGAATCAAACAACCACCCTG 59.046 47.619 0.00 0.00 0.00 4.45
94 95 1.335872 CGAATCAAACAACCACCCTGC 60.336 52.381 0.00 0.00 0.00 4.85
108 109 3.366985 CCACCCTGCGAAAATTTCCTAAC 60.367 47.826 0.00 0.00 0.00 2.34
109 110 2.823747 ACCCTGCGAAAATTTCCTAACC 59.176 45.455 0.00 0.00 0.00 2.85
126 138 3.611025 AACCATCCAAAACCTCTGGAA 57.389 42.857 0.00 0.00 45.96 3.53
129 141 4.089361 ACCATCCAAAACCTCTGGAATTC 58.911 43.478 0.00 0.00 45.96 2.17
159 171 3.244700 CCAAAGGAGTCCTGATGTGAAGT 60.245 47.826 13.89 0.00 32.13 3.01
182 194 0.536233 TGTGACCCCGTTCATTGGTG 60.536 55.000 0.00 0.00 30.97 4.17
183 195 0.536460 GTGACCCCGTTCATTGGTGT 60.536 55.000 0.00 0.00 30.97 4.16
187 199 0.250727 CCCCGTTCATTGGTGTGAGT 60.251 55.000 0.00 0.00 0.00 3.41
222 234 7.786178 TCCAAATAATACCGAGAAACATGAG 57.214 36.000 0.00 0.00 0.00 2.90
229 241 2.800544 ACCGAGAAACATGAGAAACACG 59.199 45.455 0.00 0.00 0.00 4.49
284 297 2.795175 ACGGAAGTACACACACAGAG 57.205 50.000 0.00 0.00 46.88 3.35
285 298 2.304092 ACGGAAGTACACACACAGAGA 58.696 47.619 0.00 0.00 46.88 3.10
286 299 2.293677 ACGGAAGTACACACACAGAGAG 59.706 50.000 0.00 0.00 46.88 3.20
287 300 2.552743 CGGAAGTACACACACAGAGAGA 59.447 50.000 0.00 0.00 0.00 3.10
288 301 3.365465 CGGAAGTACACACACAGAGAGAG 60.365 52.174 0.00 0.00 0.00 3.20
289 302 3.821600 GGAAGTACACACACAGAGAGAGA 59.178 47.826 0.00 0.00 0.00 3.10
290 303 4.083003 GGAAGTACACACACAGAGAGAGAG 60.083 50.000 0.00 0.00 0.00 3.20
291 304 4.359434 AGTACACACACAGAGAGAGAGA 57.641 45.455 0.00 0.00 0.00 3.10
292 305 4.323417 AGTACACACACAGAGAGAGAGAG 58.677 47.826 0.00 0.00 0.00 3.20
303 354 1.876799 AGAGAGAGAGACACACACACG 59.123 52.381 0.00 0.00 0.00 4.49
375 426 4.701651 ACGGCAGATTTTGAGATTGATGAA 59.298 37.500 0.00 0.00 0.00 2.57
380 431 6.967767 GCAGATTTTGAGATTGATGAAGTCAG 59.032 38.462 0.00 0.00 38.29 3.51
578 629 1.919956 CTCGGCTACGGTCAGTTCGT 61.920 60.000 0.00 0.00 43.64 3.85
579 630 1.800315 CGGCTACGGTCAGTTCGTG 60.800 63.158 0.00 0.00 41.24 4.35
604 655 8.692710 TGGAGAGTATTTACATTCGTAAGTGAT 58.307 33.333 0.00 0.00 38.79 3.06
664 715 6.009115 AGTCCCAAAATGTATGACGTTTTC 57.991 37.500 6.57 0.00 43.26 2.29
679 730 3.400641 CGTTTTCGCGGTTCAGTTGAAC 61.401 50.000 14.98 14.98 43.82 3.18
863 924 2.529151 CTGTCACAAAAACTGCACCAC 58.471 47.619 0.00 0.00 0.00 4.16
880 941 3.679389 ACCACCAGTGACATTCTGATTC 58.321 45.455 0.00 0.00 35.20 2.52
881 942 3.012518 CCACCAGTGACATTCTGATTCC 58.987 50.000 0.00 0.00 35.20 3.01
971 1059 4.001956 AGCCCAGCCCAGCCATTT 62.002 61.111 0.00 0.00 0.00 2.32
986 1078 1.474077 CCATTTTAGGCACCTGCTCAC 59.526 52.381 0.00 0.00 41.70 3.51
1017 1111 0.883833 ACATGGCTTTTGAAGGAGCG 59.116 50.000 0.00 0.00 39.78 5.03
1113 1207 2.208431 CTGCTGTTACTGCTAGCATCC 58.792 52.381 19.72 6.98 45.38 3.51
1125 1219 2.460918 CTAGCATCCGTAAGAACCACG 58.539 52.381 0.00 0.00 43.02 4.94
1143 1249 0.449388 CGGCATCCACAAGAAAGCTC 59.551 55.000 0.00 0.00 32.00 4.09
1268 1374 2.269241 CAACGGCCTCCTCTTCCC 59.731 66.667 0.00 0.00 0.00 3.97
1275 1381 4.148825 CTCCTCTTCCCCCGCACG 62.149 72.222 0.00 0.00 0.00 5.34
1340 1446 3.487202 CGTCATGCGAACCCACGG 61.487 66.667 3.85 0.00 44.77 4.94
1440 1546 2.047274 GGCGAGTACTGGCAGCAA 60.047 61.111 27.96 0.00 35.94 3.91
1451 1557 2.256461 GCAGCAAACCAGGAAGCG 59.744 61.111 0.00 0.00 0.00 4.68
1543 1649 4.797349 GCAACTACACTTACCTACTTAGCG 59.203 45.833 0.00 0.00 0.00 4.26
1547 1653 2.421424 ACACTTACCTACTTAGCGGTCG 59.579 50.000 0.00 0.00 34.76 4.79
1549 1655 2.680339 ACTTACCTACTTAGCGGTCGAC 59.320 50.000 7.13 7.13 34.76 4.20
1557 1663 2.221906 TTAGCGGTCGACCTTCAGCC 62.222 60.000 30.92 12.46 0.00 4.85
1570 1676 1.338337 CTTCAGCCGTACGATCCTGAT 59.662 52.381 23.77 4.19 34.62 2.90
1571 1677 1.399714 TCAGCCGTACGATCCTGATT 58.600 50.000 18.76 0.00 30.00 2.57
1572 1678 1.067060 TCAGCCGTACGATCCTGATTG 59.933 52.381 18.76 0.00 30.00 2.67
1573 1679 1.067060 CAGCCGTACGATCCTGATTGA 59.933 52.381 18.76 0.00 0.00 2.57
1606 1712 6.016108 GCATCTCTAGTAGATCCCGTAAAAGT 60.016 42.308 0.00 0.00 43.42 2.66
1614 1720 4.035112 AGATCCCGTAAAAGTCCATACCA 58.965 43.478 0.00 0.00 0.00 3.25
1880 2030 6.201806 TGCAAAATTTCATCCAAAACTAACGG 59.798 34.615 0.00 0.00 0.00 4.44
1881 2031 6.201997 GCAAAATTTCATCCAAAACTAACGGT 59.798 34.615 0.00 0.00 0.00 4.83
1891 2041 4.024302 CCAAAACTAACGGTGGAGAAACTC 60.024 45.833 0.00 0.00 32.54 3.01
1909 2059 7.666623 AGAAACTCTCACCAAAAAGAACAAAA 58.333 30.769 0.00 0.00 0.00 2.44
1915 2065 4.803088 TCACCAAAAAGAACAAAATCGCTG 59.197 37.500 0.00 0.00 0.00 5.18
1951 2122 2.554462 GTTCTTTTTGGTGAGAGCTCCC 59.446 50.000 10.93 5.22 0.00 4.30
1954 2125 0.401738 TTTTGGTGAGAGCTCCCCAG 59.598 55.000 10.93 0.00 38.34 4.45
1978 2149 4.787551 TGTTAGTTTTGTCATCCACTGGT 58.212 39.130 0.00 0.00 0.00 4.00
1979 2150 4.578516 TGTTAGTTTTGTCATCCACTGGTG 59.421 41.667 0.00 0.00 0.00 4.17
1989 2160 3.215671 CCACTGGTGGGTTTGGAAA 57.784 52.632 11.62 0.00 46.81 3.13
1994 2165 0.821711 TGGTGGGTTTGGAAAGAGCG 60.822 55.000 0.00 0.00 0.00 5.03
2030 2201 2.384828 TGATCATACGGCCAGTAGTGT 58.615 47.619 2.24 0.00 38.94 3.55
2035 2206 1.601419 TACGGCCAGTAGTGTGGAGC 61.601 60.000 2.24 0.00 40.44 4.70
2040 2211 0.109086 CCAGTAGTGTGGAGCGAGTG 60.109 60.000 0.00 0.00 40.44 3.51
2066 2237 7.818930 GCTTGATCTTATTAGAGAAGAGATGGG 59.181 40.741 7.23 0.00 36.41 4.00
2103 2274 4.442052 GCAGGATGTATCACTGACTTAGCA 60.442 45.833 11.87 0.00 39.31 3.49
2110 2281 1.063806 CACTGACTTAGCAGCGTGAC 58.936 55.000 0.00 0.00 39.51 3.67
2135 2306 1.217511 CTCGATGTGTGCCTCTGCT 59.782 57.895 0.00 0.00 38.71 4.24
2258 2431 3.069729 GGCCCTTCGATACAGATGTTAGT 59.930 47.826 0.00 0.00 0.00 2.24
2265 2438 7.201530 CCTTCGATACAGATGTTAGTTTTGGAC 60.202 40.741 0.00 0.00 0.00 4.02
2289 2462 7.653647 ACGAAATTTTGCTAGAACCATAAACA 58.346 30.769 5.27 0.00 0.00 2.83
2410 2583 3.149005 AGCCACACCTTTCCGATTTTA 57.851 42.857 0.00 0.00 0.00 1.52
2569 2762 8.830580 TGACATTTTTCTAAAACTGAGAGTGAG 58.169 33.333 11.18 0.00 34.06 3.51
2587 2780 2.978978 TGAGAACCTCCACTCATTTGGA 59.021 45.455 0.00 0.00 43.83 3.53
2678 2871 0.677731 CACCAACGCTCCATCCACAT 60.678 55.000 0.00 0.00 0.00 3.21
2712 2905 0.393808 GAATTCCTGGCCGCCTACAA 60.394 55.000 11.61 0.39 0.00 2.41
2766 2959 2.125766 GACCCACCGGAAGAAAGGCT 62.126 60.000 9.46 0.00 0.00 4.58
2881 3074 0.980423 GTCCTCTTCAGGCTGGTCTT 59.020 55.000 15.73 0.00 40.12 3.01
2936 3129 1.210478 GCCTTGCTGGAAGAGGTCATA 59.790 52.381 10.73 0.00 38.35 2.15
2949 3142 5.543507 AGAGGTCATAAAGGAGCACATAG 57.456 43.478 0.00 0.00 37.74 2.23
3020 3213 1.269723 CAGCAAGAGTACGGTCTCACA 59.730 52.381 10.74 0.00 36.97 3.58
3023 3216 2.164624 GCAAGAGTACGGTCTCACAGAT 59.835 50.000 10.74 0.00 36.97 2.90
3055 3250 2.401766 CCCTCTTGATGGTGCGTGC 61.402 63.158 0.00 0.00 0.00 5.34
3056 3251 1.376424 CCTCTTGATGGTGCGTGCT 60.376 57.895 0.00 0.00 0.00 4.40
3057 3252 0.957395 CCTCTTGATGGTGCGTGCTT 60.957 55.000 0.00 0.00 0.00 3.91
3058 3253 0.167470 CTCTTGATGGTGCGTGCTTG 59.833 55.000 0.00 0.00 0.00 4.01
3060 3255 0.311790 CTTGATGGTGCGTGCTTGTT 59.688 50.000 0.00 0.00 0.00 2.83
3062 3257 0.310543 TGATGGTGCGTGCTTGTTTC 59.689 50.000 0.00 0.00 0.00 2.78
3157 3359 9.566530 ACAAAGTTTTTCCATTGCAAAATTTAC 57.433 25.926 1.71 0.00 29.29 2.01
3300 3912 7.505258 ACACAACACATATATACATGGCAGTA 58.495 34.615 0.00 0.00 0.00 2.74
3525 4233 2.450320 CCTCAGCAGCCTGCCCTAT 61.450 63.158 14.25 0.00 46.52 2.57
3554 4262 1.000521 CCATGAAAGAGGCCCTGCA 60.001 57.895 0.00 0.00 0.00 4.41
3585 4293 4.803908 GGGCCTTTGCTCCTCCCG 62.804 72.222 0.84 0.00 37.74 5.14
3591 4299 0.179000 CTTTGCTCCTCCCGCACTAT 59.821 55.000 0.00 0.00 37.07 2.12
3675 4383 1.384502 TTGGGCCATCGGGAGAGAT 60.385 57.895 7.26 0.00 45.48 2.75
3756 4464 2.293170 GAGAAATCTAGCAACCTGGGC 58.707 52.381 0.00 0.00 0.00 5.36
3757 4465 1.017387 GAAATCTAGCAACCTGGGCG 58.983 55.000 0.00 0.00 36.08 6.13
3924 4632 4.081087 GGAAAGGTTAGTATGGCTGAGACA 60.081 45.833 0.00 0.00 0.00 3.41
3927 4635 5.700402 AGGTTAGTATGGCTGAGACATTT 57.300 39.130 5.91 0.00 31.56 2.32
4088 4796 3.307242 GTCCATCTATTGTTGCTGTCGAC 59.693 47.826 9.11 9.11 0.00 4.20
4101 4809 1.678627 CTGTCGACCGAGAAGATGGAT 59.321 52.381 14.12 0.00 0.00 3.41
4107 4815 3.181486 CGACCGAGAAGATGGATGAGAAA 60.181 47.826 0.00 0.00 0.00 2.52
4229 4937 6.756542 GGCCATATGGATTTGTCTTTTTGTAC 59.243 38.462 26.47 0.80 37.39 2.90
4278 4986 8.959548 AGTGAATGCATTGTTGTTATGAGATTA 58.040 29.630 18.59 0.00 0.00 1.75
4461 10008 4.381612 CGAATTGGTACACTCTAAGCCAGA 60.382 45.833 0.00 0.00 39.29 3.86
4547 10101 1.071071 TGGTTCCAAAGTACGACCCAG 59.929 52.381 0.00 0.00 0.00 4.45
4585 10139 3.347216 CACCGATTTCAACCATCTTCCT 58.653 45.455 0.00 0.00 0.00 3.36
4599 10156 4.516698 CCATCTTCCTTCATGTTAATCCCG 59.483 45.833 0.00 0.00 0.00 5.14
4605 10162 0.943673 TCATGTTAATCCCGCATGCG 59.056 50.000 32.60 32.60 39.64 4.73
4638 10195 2.699954 CTAACACCTGTGTGATCCCAC 58.300 52.381 3.28 0.79 45.76 4.61
4685 10242 8.585881 TGGGTTAATTTAAATTTCAATCGGTCA 58.414 29.630 18.14 0.75 0.00 4.02
4699 10256 5.943416 TCAATCGGTCATTTCTAAATGGTGT 59.057 36.000 13.89 0.00 44.51 4.16
4703 10260 4.082787 CGGTCATTTCTAAATGGTGTTGCT 60.083 41.667 13.89 0.00 44.51 3.91
4715 10272 1.339631 GGTGTTGCTGGTGCTGGTATA 60.340 52.381 0.00 0.00 40.48 1.47
4729 10286 3.119245 GCTGGTATAGTTCTTCGTGACCA 60.119 47.826 0.00 0.00 34.44 4.02
4730 10287 4.441634 GCTGGTATAGTTCTTCGTGACCAT 60.442 45.833 0.00 0.00 35.08 3.55
4731 10288 5.006153 TGGTATAGTTCTTCGTGACCATG 57.994 43.478 0.00 0.00 30.67 3.66
4732 10289 4.707934 TGGTATAGTTCTTCGTGACCATGA 59.292 41.667 0.00 0.00 30.67 3.07
4733 10290 5.186215 TGGTATAGTTCTTCGTGACCATGAA 59.814 40.000 0.00 4.78 35.28 2.57
4795 11854 4.760220 AGGGGGAAGGATGGCGGT 62.760 66.667 0.00 0.00 0.00 5.68
4850 11909 0.108992 GGTGTTGCTATGACCGTCGA 60.109 55.000 0.00 0.00 0.00 4.20
4864 11923 4.103103 TCGACGGTGAGAGCTGCG 62.103 66.667 0.00 0.00 0.00 5.18
4871 11930 2.755876 TGAGAGCTGCGACCGGAT 60.756 61.111 9.46 0.00 0.00 4.18
4875 11934 3.069980 GAGCTGCGACCGGATGACT 62.070 63.158 9.46 0.00 0.00 3.41
4925 11984 2.425143 ATGACCAAGACAATGGCGAT 57.575 45.000 0.00 0.00 44.75 4.58
4926 11985 3.558931 ATGACCAAGACAATGGCGATA 57.441 42.857 0.00 0.00 44.75 2.92
4945 12004 5.105716 GCGATAGTTGAGCTATGAGGGAATA 60.106 44.000 0.00 0.00 40.30 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.822519 TCCATAGGATTCATTTGTACAGCAC 59.177 40.000 0.00 0.00 0.00 4.40
51 52 9.667107 TTCGTAGGATGTGAATCTTTAAGAATT 57.333 29.630 0.00 0.00 0.00 2.17
59 60 6.878923 TGTTTGATTCGTAGGATGTGAATCTT 59.121 34.615 13.42 0.00 45.16 2.40
60 61 6.406370 TGTTTGATTCGTAGGATGTGAATCT 58.594 36.000 13.42 0.00 45.16 2.40
84 85 1.343142 GGAAATTTTCGCAGGGTGGTT 59.657 47.619 3.17 0.00 0.00 3.67
93 94 4.712122 TGGATGGTTAGGAAATTTTCGC 57.288 40.909 3.17 0.00 0.00 4.70
94 95 6.367695 GGTTTTGGATGGTTAGGAAATTTTCG 59.632 38.462 3.17 0.00 0.00 3.46
108 109 3.448660 GGAATTCCAGAGGTTTTGGATGG 59.551 47.826 20.04 0.00 43.87 3.51
109 110 4.347607 AGGAATTCCAGAGGTTTTGGATG 58.652 43.478 26.22 0.00 43.87 3.51
159 171 1.678627 CAATGAACGGGGTCACAACAA 59.321 47.619 0.00 0.00 0.00 2.83
210 222 2.220824 TGCGTGTTTCTCATGTTTCTCG 59.779 45.455 0.00 0.00 35.64 4.04
256 269 4.337836 TGTGTGTACTTCCGTACTGTGTTA 59.662 41.667 0.00 0.00 44.97 2.41
274 287 3.058293 GTGTCTCTCTCTCTCTGTGTGTG 60.058 52.174 0.00 0.00 0.00 3.82
277 290 3.146066 GTGTGTCTCTCTCTCTCTGTGT 58.854 50.000 0.00 0.00 0.00 3.72
279 292 3.146066 GTGTGTGTCTCTCTCTCTCTGT 58.854 50.000 0.00 0.00 0.00 3.41
281 294 3.146066 GTGTGTGTGTCTCTCTCTCTCT 58.854 50.000 0.00 0.00 0.00 3.10
282 295 2.095969 CGTGTGTGTGTCTCTCTCTCTC 60.096 54.545 0.00 0.00 0.00 3.20
283 296 1.876799 CGTGTGTGTGTCTCTCTCTCT 59.123 52.381 0.00 0.00 0.00 3.10
284 297 1.664588 GCGTGTGTGTGTCTCTCTCTC 60.665 57.143 0.00 0.00 0.00 3.20
285 298 0.312416 GCGTGTGTGTGTCTCTCTCT 59.688 55.000 0.00 0.00 0.00 3.10
286 299 0.030773 TGCGTGTGTGTGTCTCTCTC 59.969 55.000 0.00 0.00 0.00 3.20
287 300 0.249073 GTGCGTGTGTGTGTCTCTCT 60.249 55.000 0.00 0.00 0.00 3.10
288 301 0.527600 TGTGCGTGTGTGTGTCTCTC 60.528 55.000 0.00 0.00 0.00 3.20
289 302 0.806102 GTGTGCGTGTGTGTGTCTCT 60.806 55.000 0.00 0.00 0.00 3.10
290 303 1.081556 TGTGTGCGTGTGTGTGTCTC 61.082 55.000 0.00 0.00 0.00 3.36
291 304 1.079474 TGTGTGCGTGTGTGTGTCT 60.079 52.632 0.00 0.00 0.00 3.41
292 305 1.060308 GTGTGTGCGTGTGTGTGTC 59.940 57.895 0.00 0.00 0.00 3.67
303 354 1.000506 TCCGTTTCTAGGAGTGTGTGC 59.999 52.381 0.00 0.00 33.19 4.57
375 426 1.924320 GCGAGCCGACTGTACTGACT 61.924 60.000 6.77 0.00 0.00 3.41
380 431 0.661552 TCATAGCGAGCCGACTGTAC 59.338 55.000 0.00 0.00 0.00 2.90
578 629 8.058667 TCACTTACGAATGTAAATACTCTCCA 57.941 34.615 0.00 0.00 39.95 3.86
641 692 5.334569 CGAAAACGTCATACATTTTGGGACT 60.335 40.000 0.00 0.00 0.00 3.85
652 703 1.456544 TGAACCGCGAAAACGTCATAC 59.543 47.619 8.23 0.00 0.00 2.39
690 741 4.658901 AGTCCCAATAAATCGTACTCCCAT 59.341 41.667 0.00 0.00 0.00 4.00
848 908 1.204467 CACTGGTGGTGCAGTTTTTGT 59.796 47.619 0.00 0.00 39.22 2.83
863 924 3.947868 ACAGGAATCAGAATGTCACTGG 58.052 45.455 0.00 0.00 37.40 4.00
880 941 7.215789 AGCTCTTCATCAATTATGTCTACAGG 58.784 38.462 0.00 0.00 36.89 4.00
881 942 8.659925 AAGCTCTTCATCAATTATGTCTACAG 57.340 34.615 0.00 0.00 36.89 2.74
971 1059 0.764890 ACAAGTGAGCAGGTGCCTAA 59.235 50.000 0.00 0.00 43.38 2.69
1017 1111 1.571919 CGAGCTGCAGGTAATGGTAC 58.428 55.000 20.22 3.26 0.00 3.34
1069 1163 0.669077 GGTACGACGATGAGGAGCAT 59.331 55.000 0.00 0.00 40.77 3.79
1078 1172 1.404391 CAGCAGTAAGGGTACGACGAT 59.596 52.381 0.00 0.00 35.20 3.73
1113 1207 0.390603 TGGATGCCGTGGTTCTTACG 60.391 55.000 0.00 0.00 40.98 3.18
1125 1219 0.813821 GGAGCTTTCTTGTGGATGCC 59.186 55.000 0.00 0.00 0.00 4.40
1128 1222 0.678048 GCCGGAGCTTTCTTGTGGAT 60.678 55.000 5.05 0.00 35.50 3.41
1332 1438 3.256960 AGGATGTGGCCGTGGGTT 61.257 61.111 0.00 0.00 0.00 4.11
1362 1468 3.410628 TGCGAGGCCATGGACCAT 61.411 61.111 16.13 0.00 0.00 3.55
1440 1546 2.110213 TTGACGCGCTTCCTGGTT 59.890 55.556 11.76 0.00 0.00 3.67
1547 1653 0.248949 GGATCGTACGGCTGAAGGTC 60.249 60.000 16.52 0.00 0.00 3.85
1549 1655 0.249073 CAGGATCGTACGGCTGAAGG 60.249 60.000 16.52 0.00 0.00 3.46
1557 1663 5.758924 TCTAACATCAATCAGGATCGTACG 58.241 41.667 9.53 9.53 0.00 3.67
1570 1676 9.008965 GATCTACTAGAGATGCTCTAACATCAA 57.991 37.037 0.00 0.00 45.48 2.57
1571 1677 7.609918 GGATCTACTAGAGATGCTCTAACATCA 59.390 40.741 12.96 0.00 46.70 3.07
1572 1678 7.985476 GGATCTACTAGAGATGCTCTAACATC 58.015 42.308 12.96 0.00 46.70 3.06
1573 1679 7.938140 GGATCTACTAGAGATGCTCTAACAT 57.062 40.000 12.96 0.00 46.70 2.71
1606 1712 8.090788 ACTCTAAAGCTCTTTTATGGTATGGA 57.909 34.615 0.00 0.00 34.23 3.41
1846 1996 4.622740 GGATGAAATTTTGCAAGAACCTCG 59.377 41.667 0.00 0.00 0.00 4.63
1848 1998 5.549742 TGGATGAAATTTTGCAAGAACCT 57.450 34.783 0.00 0.00 0.00 3.50
1880 2030 4.881850 TCTTTTTGGTGAGAGTTTCTCCAC 59.118 41.667 4.05 4.97 46.31 4.02
1881 2031 5.110814 TCTTTTTGGTGAGAGTTTCTCCA 57.889 39.130 0.50 0.50 45.31 3.86
1891 2041 5.043248 AGCGATTTTGTTCTTTTTGGTGAG 58.957 37.500 0.00 0.00 0.00 3.51
1915 2065 6.237915 CCAAAAAGAACAAAATCACTGCTCAC 60.238 38.462 0.00 0.00 0.00 3.51
1951 2122 5.707298 AGTGGATGACAAAACTAACATCTGG 59.293 40.000 0.00 0.00 39.03 3.86
1954 2125 5.473504 ACCAGTGGATGACAAAACTAACATC 59.526 40.000 18.40 0.00 38.53 3.06
1978 2149 2.642154 TTACGCTCTTTCCAAACCCA 57.358 45.000 0.00 0.00 0.00 4.51
1979 2150 3.756963 AGAATTACGCTCTTTCCAAACCC 59.243 43.478 0.00 0.00 0.00 4.11
1986 2157 7.707035 TCAAAGATCCTAGAATTACGCTCTTTC 59.293 37.037 0.00 0.00 31.32 2.62
1989 2160 6.716934 TCAAAGATCCTAGAATTACGCTCT 57.283 37.500 0.00 0.00 0.00 4.09
1994 2165 9.360093 CCGTATGATCAAAGATCCTAGAATTAC 57.640 37.037 0.00 0.00 0.00 1.89
2010 2181 2.100749 CACACTACTGGCCGTATGATCA 59.899 50.000 0.00 0.00 0.00 2.92
2035 2206 7.421599 TCTTCTCTAATAAGATCAAGCACTCG 58.578 38.462 0.00 0.00 0.00 4.18
2040 2211 7.818930 CCCATCTCTTCTCTAATAAGATCAAGC 59.181 40.741 0.00 0.00 32.72 4.01
2045 2216 8.461033 AGGTACCCATCTCTTCTCTAATAAGAT 58.539 37.037 8.74 0.00 32.72 2.40
2050 2221 5.151454 CCAGGTACCCATCTCTTCTCTAAT 58.849 45.833 8.74 0.00 0.00 1.73
2066 2237 3.121030 CTGCAGCACGCCAGGTAC 61.121 66.667 0.00 0.00 41.33 3.34
2082 2253 4.202202 GCTGCTAAGTCAGTGATACATCCT 60.202 45.833 0.00 0.00 36.49 3.24
2110 2281 0.247814 GGCACACATCGAGCGAAATG 60.248 55.000 0.00 1.12 0.00 2.32
2135 2306 4.802051 GGCCAGCAAGCCGGATCA 62.802 66.667 5.05 0.00 44.57 2.92
2246 2419 7.972832 ATTTCGTCCAAAACTAACATCTGTA 57.027 32.000 0.00 0.00 0.00 2.74
2258 2431 5.980715 GGTTCTAGCAAAATTTCGTCCAAAA 59.019 36.000 0.00 0.00 0.00 2.44
2265 2438 8.687824 ATGTTTATGGTTCTAGCAAAATTTCG 57.312 30.769 0.00 0.00 0.00 3.46
2289 2462 9.466497 ACTTTGTGACATCAAACCTTATCATAT 57.534 29.630 0.00 0.00 34.30 1.78
2295 2468 9.179909 TCTAAAACTTTGTGACATCAAACCTTA 57.820 29.630 0.00 0.40 34.30 2.69
2328 2501 5.432885 AAAACCAGTATCAAACAAGGTCG 57.567 39.130 0.00 0.00 37.67 4.79
2386 2559 0.606604 TCGGAAAGGTGTGGCTACTC 59.393 55.000 0.64 0.00 0.00 2.59
2587 2780 0.897621 GTTAAAAGCCAGCCAGCCAT 59.102 50.000 0.00 0.00 0.00 4.40
2678 2871 2.621338 GAATTCGCTCATGTCCACTGA 58.379 47.619 0.00 0.00 0.00 3.41
2712 2905 2.094182 AGCGACTTACGACATCATTGGT 60.094 45.455 0.00 0.00 45.77 3.67
2881 3074 0.033504 GTGTCGCTGAACCTTCCAGA 59.966 55.000 0.00 0.00 33.65 3.86
2936 3129 4.006319 GCTTCAAGTCTATGTGCTCCTTT 58.994 43.478 0.00 0.00 0.00 3.11
2949 3142 5.576895 GGCAGAATTATCTTGCTTCAAGTC 58.423 41.667 6.47 0.00 41.66 3.01
3020 3213 6.821616 AAGAGGGACTTGACATTATCATCT 57.178 37.500 0.00 0.00 41.55 2.90
3087 3283 7.173047 ACCATGAATTTGCAATGGAAAAACTAC 59.827 33.333 20.24 0.00 36.33 2.73
3132 3334 9.565213 TGTAAATTTTGCAATGGAAAAACTTTG 57.435 25.926 16.09 0.00 34.38 2.77
3153 3355 8.948631 TTTGCAATGGAAAAACTGTATGTAAA 57.051 26.923 0.00 0.00 0.00 2.01
3157 3359 8.085720 TGAATTTGCAATGGAAAAACTGTATG 57.914 30.769 3.64 0.00 0.00 2.39
3254 3855 9.911788 TTGTGTACTAGTAAGTAATACCTAGCT 57.088 33.333 3.61 0.00 39.90 3.32
3270 3871 9.140286 GCCATGTATATATGTGTTGTGTACTAG 57.860 37.037 8.46 0.00 0.00 2.57
3312 3924 9.471084 CGAACAAAGGGTCAAATTTTAATTAGT 57.529 29.630 0.00 0.00 0.00 2.24
3337 4045 5.523916 CCTCAAATATGTTCTGGTAAGACCG 59.476 44.000 0.00 0.00 42.58 4.79
3525 4233 4.335416 CCTCTTTCATGGTTGCCTTTAGA 58.665 43.478 0.00 0.00 0.00 2.10
3585 4293 1.331756 CAATCAGCGGTGGAATAGTGC 59.668 52.381 15.67 0.00 0.00 4.40
3675 4383 1.073923 GGTCTCTCCCAAGCTTTTGGA 59.926 52.381 12.72 12.72 44.82 3.53
4029 4737 2.949644 GCCCTCACCTTAATTATTGCGT 59.050 45.455 0.00 0.00 0.00 5.24
4088 4796 7.792374 TTAAATTTCTCATCCATCTTCTCGG 57.208 36.000 0.00 0.00 0.00 4.63
4101 4809 9.461312 ACTATAACCAGTGCATTAAATTTCTCA 57.539 29.630 0.00 0.00 0.00 3.27
4278 4986 1.806542 CACGGCTATGCTTTCACAACT 59.193 47.619 0.00 0.00 0.00 3.16
4524 10078 2.563702 GGTCGTACTTTGGAACCACAA 58.436 47.619 0.00 0.00 0.00 3.33
4547 10101 8.474006 AAATCGGTGCATTTCCTTTAATTAAC 57.526 30.769 0.00 0.00 0.00 2.01
4585 10139 1.333308 CGCATGCGGGATTAACATGAA 59.667 47.619 31.99 0.00 43.04 2.57
4599 10156 2.203070 CCCTCCTACACCGCATGC 60.203 66.667 7.91 7.91 0.00 4.06
4605 10162 0.540454 GTGTTAGCCCCTCCTACACC 59.460 60.000 0.00 0.00 0.00 4.16
4606 10163 0.540454 GGTGTTAGCCCCTCCTACAC 59.460 60.000 0.00 0.00 0.00 2.90
4638 10195 0.739813 CCTAAAACAGGCCGAGACCG 60.740 60.000 0.00 0.00 37.70 4.79
4659 10216 8.585881 TGACCGATTGAAATTTAAATTAACCCA 58.414 29.630 13.68 7.32 0.00 4.51
4674 10231 6.432783 ACACCATTTAGAAATGACCGATTGAA 59.567 34.615 15.09 0.00 46.72 2.69
4676 10233 6.194796 ACACCATTTAGAAATGACCGATTG 57.805 37.500 15.09 6.07 46.72 2.67
4677 10234 6.620678 CAACACCATTTAGAAATGACCGATT 58.379 36.000 15.09 1.86 46.72 3.34
4680 10237 4.082787 AGCAACACCATTTAGAAATGACCG 60.083 41.667 15.09 6.63 46.72 4.79
4685 10242 4.561326 GCACCAGCAACACCATTTAGAAAT 60.561 41.667 0.00 0.00 41.58 2.17
4699 10256 2.571653 AGAACTATACCAGCACCAGCAA 59.428 45.455 0.00 0.00 45.49 3.91
4703 10260 2.829720 ACGAAGAACTATACCAGCACCA 59.170 45.455 0.00 0.00 0.00 4.17
4715 10272 2.872038 GCCTTCATGGTCACGAAGAACT 60.872 50.000 8.16 0.00 40.94 3.01
4729 10286 2.202703 GTACGTCGGCGCCTTCAT 60.203 61.111 26.68 10.19 42.83 2.57
4730 10287 4.764336 CGTACGTCGGCGCCTTCA 62.764 66.667 26.68 4.99 42.83 3.02
4731 10288 4.766088 ACGTACGTCGGCGCCTTC 62.766 66.667 26.68 15.95 44.69 3.46
4732 10289 4.347453 AACGTACGTCGGCGCCTT 62.347 61.111 26.68 6.12 44.69 4.35
4735 10292 3.397317 AACAACGTACGTCGGCGC 61.397 61.111 23.05 0.00 44.69 6.53
4736 10293 2.462468 CAACAACGTACGTCGGCG 59.538 61.111 23.05 8.42 44.69 6.46
4770 11829 2.446337 ATCCTTCCCCCTTGACCCCA 62.446 60.000 0.00 0.00 0.00 4.96
4784 11843 2.215451 ATTCCAGCACCGCCATCCTT 62.215 55.000 0.00 0.00 0.00 3.36
4795 11854 1.622607 CCGTGGACCCTATTCCAGCA 61.623 60.000 0.00 0.00 46.75 4.41
4850 11909 4.057428 GGTCGCAGCTCTCACCGT 62.057 66.667 0.00 0.00 0.00 4.83
4864 11923 2.105128 CTCCGCAGTCATCCGGTC 59.895 66.667 0.00 0.00 44.63 4.79
4871 11930 1.292223 GGTTGTAGCTCCGCAGTCA 59.708 57.895 0.00 0.00 0.00 3.41
4875 11934 3.307906 ACCGGTTGTAGCTCCGCA 61.308 61.111 0.00 0.00 44.63 5.69
4925 11984 6.467677 GCAATATTCCCTCATAGCTCAACTA 58.532 40.000 0.00 0.00 34.64 2.24
4926 11985 5.312079 GCAATATTCCCTCATAGCTCAACT 58.688 41.667 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.