Multiple sequence alignment - TraesCS6D01G016100

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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 TraesCS6D01G016100 chr6D 100.000 5331 0 0 1 5331 6494973 6500303 0.000000e+00 9845
1 TraesCS6D01G016100 chr6D 86.642 2141 267 11 2235 4371 6371092 6373217 0.000000e+00 2351
2 TraesCS6D01G016100 chr6D 85.714 1946 254 16 2461 4399 6352914 6354842 0.000000e+00 2032
3 TraesCS6D01G016100 chr6D 86.128 1658 211 13 2717 4369 6426496 6428139 0.000000e+00 1770
4 TraesCS6D01G016100 chr6D 90.539 1057 100 0 3260 4316 6465690 6466746 0.000000e+00 1399
5 TraesCS6D01G016100 chr6D 98.367 796 11 2 1 794 456364525 456365320 0.000000e+00 1397
6 TraesCS6D01G016100 chr6D 84.444 1440 144 37 795 2174 6424636 6426055 0.000000e+00 1345
7 TraesCS6D01G016100 chr6D 93.827 810 32 9 1770 2562 6352136 6352944 0.000000e+00 1203
8 TraesCS6D01G016100 chr6D 84.027 1033 115 29 1186 2174 6441657 6442683 0.000000e+00 948
9 TraesCS6D01G016100 chr6D 80.920 1174 183 15 1318 2478 7032265 7033410 0.000000e+00 889
10 TraesCS6D01G016100 chr6D 84.615 845 90 17 1303 2129 6370241 6371063 0.000000e+00 804
11 TraesCS6D01G016100 chr6D 89.239 539 45 9 1273 1807 6351572 6352101 0.000000e+00 662
12 TraesCS6D01G016100 chr6D 89.666 329 33 1 2235 2562 6442714 6443042 8.260000e-113 418
13 TraesCS6D01G016100 chr6D 86.239 327 45 0 2228 2554 6426079 6426405 6.570000e-94 355
14 TraesCS6D01G016100 chr6D 98.658 149 2 0 4797 4945 6504907 6505055 1.140000e-66 265
15 TraesCS6D01G016100 chr6D 76.677 313 71 2 2661 2972 6497417 6497728 7.100000e-39 172
16 TraesCS6D01G016100 chr6D 76.677 313 71 2 2445 2756 6497633 6497944 7.100000e-39 172
17 TraesCS6D01G016100 chr6D 84.768 151 15 3 1100 1242 6441447 6441597 1.550000e-30 145
18 TraesCS6D01G016100 chr6D 93.407 91 5 1 4707 4797 6354603 6354692 3.350000e-27 134
19 TraesCS6D01G016100 chr6D 92.045 88 6 1 4710 4797 6466592 6466678 7.250000e-24 122
20 TraesCS6D01G016100 chr6D 89.535 86 8 1 4713 4797 6427933 6428018 2.030000e-19 108
21 TraesCS6D01G016100 chr6B 95.327 2996 114 8 1804 4797 11792764 11795735 0.000000e+00 4734
22 TraesCS6D01G016100 chr6B 90.644 1614 143 5 3185 4797 11599607 11601213 0.000000e+00 2137
23 TraesCS6D01G016100 chr6B 87.855 774 73 14 1278 2036 11592811 11593578 0.000000e+00 889
24 TraesCS6D01G016100 chr6B 90.737 475 35 4 1277 1745 11792306 11792777 4.530000e-175 625
25 TraesCS6D01G016100 chr6B 87.281 228 19 3 1027 1245 11764533 11764759 8.860000e-63 252
26 TraesCS6D01G016100 chr6B 84.074 270 21 11 1027 1280 11792016 11792279 1.920000e-59 241
27 TraesCS6D01G016100 chr6B 82.857 245 38 2 4941 5183 46942159 46942401 3.230000e-52 217
28 TraesCS6D01G016100 chr6A 87.891 1916 213 15 2461 4371 5917642 5919543 0.000000e+00 2235
29 TraesCS6D01G016100 chr6A 86.671 1688 214 9 2717 4399 5901909 5903590 0.000000e+00 1860
30 TraesCS6D01G016100 chr6A 86.068 1658 212 13 2717 4369 5940863 5942506 0.000000e+00 1764
31 TraesCS6D01G016100 chr6A 82.681 1201 133 29 1032 2174 5939239 5940422 0.000000e+00 996
32 TraesCS6D01G016100 chr6A 80.153 1174 179 20 1318 2478 6698706 6699838 0.000000e+00 828
33 TraesCS6D01G016100 chr6A 88.619 536 55 3 1273 1808 5900678 5901207 0.000000e+00 647
34 TraesCS6D01G016100 chr6A 87.263 581 56 8 1321 1889 5916509 5917083 0.000000e+00 647
35 TraesCS6D01G016100 chr6A 89.296 355 36 2 1820 2174 5901260 5901612 1.360000e-120 444
36 TraesCS6D01G016100 chr6A 88.450 329 32 3 2235 2562 5917349 5917672 5.010000e-105 392
37 TraesCS6D01G016100 chr6A 86.239 327 45 0 2228 2554 5940446 5940772 6.570000e-94 355
38 TraesCS6D01G016100 chr6A 98.324 179 2 1 795 973 5938868 5939045 4.010000e-81 313
39 TraesCS6D01G016100 chr6A 85.430 151 14 3 1100 1242 5916183 5916333 3.330000e-32 150
40 TraesCS6D01G016100 chr6A 92.045 88 6 1 4710 4797 5919334 5919420 7.250000e-24 122
41 TraesCS6D01G016100 chr6A 89.535 86 8 1 4713 4797 5942300 5942385 2.030000e-19 108
42 TraesCS6D01G016100 chr5D 98.618 796 9 2 1 794 472422902 472423697 0.000000e+00 1408
43 TraesCS6D01G016100 chr3D 98.375 800 10 3 1 797 57196622 57195823 0.000000e+00 1402
44 TraesCS6D01G016100 chr3D 98.367 796 11 2 1 794 559551027 559550232 0.000000e+00 1397
45 TraesCS6D01G016100 chr2D 98.369 797 11 2 1 795 609280063 609280859 0.000000e+00 1399
46 TraesCS6D01G016100 chr2D 98.367 796 11 2 1 794 633509192 633508397 0.000000e+00 1397
47 TraesCS6D01G016100 chr2D 98.246 798 11 3 1 796 381553179 381553975 0.000000e+00 1393
48 TraesCS6D01G016100 chr2D 98.243 797 12 2 1 795 642887856 642888652 0.000000e+00 1393
49 TraesCS6D01G016100 chr2D 99.439 535 3 0 4797 5331 426933088 426933622 0.000000e+00 972
50 TraesCS6D01G016100 chr2D 98.026 152 2 1 4797 4948 426938230 426938380 4.090000e-66 263
51 TraesCS6D01G016100 chr7D 98.367 796 11 2 1 794 591623314 591624109 0.000000e+00 1397
52 TraesCS6D01G016100 chr7D 99.072 539 5 0 4793 5331 92592934 92593472 0.000000e+00 968
53 TraesCS6D01G016100 chr7D 98.667 150 2 0 4797 4946 92598079 92598228 3.170000e-67 267
54 TraesCS6D01G016100 chr2A 98.327 538 8 1 4794 5331 739695702 739696238 0.000000e+00 942
55 TraesCS6D01G016100 chr2A 97.987 149 3 0 4797 4945 739700844 739700992 5.300000e-65 259
56 TraesCS6D01G016100 chr3A 97.383 535 14 0 4797 5331 644823444 644823978 0.000000e+00 911
57 TraesCS6D01G016100 chr1B 94.486 399 22 0 4809 5207 34604213 34603815 2.730000e-172 616
58 TraesCS6D01G016100 chr1B 78.680 394 78 5 4941 5331 624024052 624024442 1.900000e-64 257
59 TraesCS6D01G016100 chr1B 78.535 396 77 6 4941 5331 121000037 120999645 2.460000e-63 254
60 TraesCS6D01G016100 chr1B 94.615 130 7 0 5202 5331 34594317 34594188 9.050000e-48 202
61 TraesCS6D01G016100 chr1A 78.680 394 78 5 4941 5331 11723155 11723545 1.900000e-64 257
62 TraesCS6D01G016100 chr7A 85.811 148 20 1 4574 4720 164653758 164653611 7.150000e-34 156


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 TraesCS6D01G016100 chr6D 6494973 6500303 5330 False 3396.333333 9845 84.451333 1 5331 3 chr6D.!!$F9 5330
1 TraesCS6D01G016100 chr6D 6370241 6373217 2976 False 1577.500000 2351 85.628500 1303 4371 2 chr6D.!!$F5 3068
2 TraesCS6D01G016100 chr6D 456364525 456365320 795 False 1397.000000 1397 98.367000 1 794 1 chr6D.!!$F3 793
3 TraesCS6D01G016100 chr6D 6351572 6354842 3270 False 1007.750000 2032 90.546750 1273 4797 4 chr6D.!!$F4 3524
4 TraesCS6D01G016100 chr6D 6424636 6428139 3503 False 894.500000 1770 86.586500 795 4797 4 chr6D.!!$F6 4002
5 TraesCS6D01G016100 chr6D 7032265 7033410 1145 False 889.000000 889 80.920000 1318 2478 1 chr6D.!!$F2 1160
6 TraesCS6D01G016100 chr6D 6465690 6466746 1056 False 760.500000 1399 91.292000 3260 4797 2 chr6D.!!$F8 1537
7 TraesCS6D01G016100 chr6D 6441447 6443042 1595 False 503.666667 948 86.153667 1100 2562 3 chr6D.!!$F7 1462
8 TraesCS6D01G016100 chr6B 11599607 11601213 1606 False 2137.000000 2137 90.644000 3185 4797 1 chr6B.!!$F2 1612
9 TraesCS6D01G016100 chr6B 11792016 11795735 3719 False 1866.666667 4734 90.046000 1027 4797 3 chr6B.!!$F5 3770
10 TraesCS6D01G016100 chr6B 11592811 11593578 767 False 889.000000 889 87.855000 1278 2036 1 chr6B.!!$F1 758
11 TraesCS6D01G016100 chr6A 5900678 5903590 2912 False 983.666667 1860 88.195333 1273 4399 3 chr6A.!!$F2 3126
12 TraesCS6D01G016100 chr6A 6698706 6699838 1132 False 828.000000 828 80.153000 1318 2478 1 chr6A.!!$F1 1160
13 TraesCS6D01G016100 chr6A 5916183 5919543 3360 False 709.200000 2235 88.215800 1100 4797 5 chr6A.!!$F3 3697
14 TraesCS6D01G016100 chr6A 5938868 5942506 3638 False 707.200000 1764 88.569400 795 4797 5 chr6A.!!$F4 4002
15 TraesCS6D01G016100 chr5D 472422902 472423697 795 False 1408.000000 1408 98.618000 1 794 1 chr5D.!!$F1 793
16 TraesCS6D01G016100 chr3D 57195823 57196622 799 True 1402.000000 1402 98.375000 1 797 1 chr3D.!!$R1 796
17 TraesCS6D01G016100 chr3D 559550232 559551027 795 True 1397.000000 1397 98.367000 1 794 1 chr3D.!!$R2 793
18 TraesCS6D01G016100 chr2D 609280063 609280859 796 False 1399.000000 1399 98.369000 1 795 1 chr2D.!!$F4 794
19 TraesCS6D01G016100 chr2D 633508397 633509192 795 True 1397.000000 1397 98.367000 1 794 1 chr2D.!!$R1 793
20 TraesCS6D01G016100 chr2D 381553179 381553975 796 False 1393.000000 1393 98.246000 1 796 1 chr2D.!!$F1 795
21 TraesCS6D01G016100 chr2D 642887856 642888652 796 False 1393.000000 1393 98.243000 1 795 1 chr2D.!!$F5 794
22 TraesCS6D01G016100 chr2D 426933088 426933622 534 False 972.000000 972 99.439000 4797 5331 1 chr2D.!!$F2 534
23 TraesCS6D01G016100 chr7D 591623314 591624109 795 False 1397.000000 1397 98.367000 1 794 1 chr7D.!!$F3 793
24 TraesCS6D01G016100 chr7D 92592934 92593472 538 False 968.000000 968 99.072000 4793 5331 1 chr7D.!!$F1 538
25 TraesCS6D01G016100 chr2A 739695702 739696238 536 False 942.000000 942 98.327000 4794 5331 1 chr2A.!!$F1 537
26 TraesCS6D01G016100 chr3A 644823444 644823978 534 False 911.000000 911 97.383000 4797 5331 1 chr3A.!!$F1 534

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
741 745 0.037605 GTCCCGGTTCGTGACTGAAT 60.038 55.0 0.00 0.00 36.72 2.57 F
743 747 0.037697 CCCGGTTCGTGACTGAATCA 60.038 55.0 0.00 0.00 36.72 2.57 F
1249 1459 0.038166 ACTCTACGTACGAACCCCCA 59.962 55.0 24.41 0.00 0.00 4.96 F
1767 2166 0.179018 ATGCCTTTCTCCGGTATGGC 60.179 55.0 17.58 17.58 40.62 4.40 F
2481 3035 1.249407 ACTGGAGCTATACCGCTAGC 58.751 55.0 4.06 4.06 43.65 3.42 F
3733 4359 2.427095 TGTGATCAGTATGGACCTGTCG 59.573 50.0 0.00 0.00 36.16 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 2090 1.143073 ACCCAAGAACTCTGGAACACC 59.857 52.381 0.00 0.0 0.00 4.16 R
2586 3212 4.855715 TTGAGACTGTTACTGGTGAGAG 57.144 45.455 0.00 0.0 0.00 3.20 R
3214 3840 4.559862 ATCCAAGACAACTAGGTTCCAG 57.440 45.455 0.00 0.0 0.00 3.86 R
3716 4342 1.683917 GAGCGACAGGTCCATACTGAT 59.316 52.381 0.00 0.0 39.24 2.90 R
3965 4591 0.036765 CGTCCCGGTGGAATTCTTCA 60.037 55.000 5.23 0.0 44.07 3.02 R
4607 5234 0.462759 ATTGCGAGGCCAGCTCTAAC 60.463 55.000 21.29 0.0 35.28 2.34 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
305 307 1.953231 GACGGGCCGCTAAACCTAGT 61.953 60.000 28.71 0.84 0.00 2.57
431 433 1.003839 TAGAGCACCACAAAGCCCG 60.004 57.895 0.00 0.00 0.00 6.13
741 745 0.037605 GTCCCGGTTCGTGACTGAAT 60.038 55.000 0.00 0.00 36.72 2.57
743 747 0.037697 CCCGGTTCGTGACTGAATCA 60.038 55.000 0.00 0.00 36.72 2.57
1000 1008 1.872197 GCTGCTCTCCGTCACTCACT 61.872 60.000 0.00 0.00 0.00 3.41
1001 1009 0.109365 CTGCTCTCCGTCACTCACTG 60.109 60.000 0.00 0.00 0.00 3.66
1002 1010 0.537371 TGCTCTCCGTCACTCACTGA 60.537 55.000 0.00 0.00 0.00 3.41
1005 1013 2.621055 GCTCTCCGTCACTCACTGATAT 59.379 50.000 0.00 0.00 0.00 1.63
1010 1018 5.638234 TCTCCGTCACTCACTGATATATACG 59.362 44.000 0.00 0.00 0.00 3.06
1012 1020 6.458210 TCCGTCACTCACTGATATATACGTA 58.542 40.000 0.00 0.00 0.00 3.57
1013 1021 6.367149 TCCGTCACTCACTGATATATACGTAC 59.633 42.308 0.00 0.00 0.00 3.67
1016 1024 8.585436 CGTCACTCACTGATATATACGTACTAG 58.415 40.741 0.00 0.00 0.00 2.57
1059 1236 4.395854 ACACACACCACATGCTACATTATG 59.604 41.667 0.00 0.00 0.00 1.90
1060 1239 4.635324 CACACACCACATGCTACATTATGA 59.365 41.667 0.00 0.00 0.00 2.15
1074 1253 3.007506 ACATTATGAACGTCCAGTGACCA 59.992 43.478 0.00 0.00 38.32 4.02
1077 1256 1.301479 GAACGTCCAGTGACCACCC 60.301 63.158 0.00 0.00 38.32 4.61
1165 1355 3.531538 TCTTGACCGGCAAATATGACTC 58.468 45.455 0.00 0.00 35.74 3.36
1166 1356 3.055458 TCTTGACCGGCAAATATGACTCA 60.055 43.478 0.00 0.00 35.74 3.41
1167 1357 2.627945 TGACCGGCAAATATGACTCAC 58.372 47.619 0.00 0.00 29.70 3.51
1169 1359 1.066430 ACCGGCAAATATGACTCACGT 60.066 47.619 0.00 0.00 29.70 4.49
1181 1387 1.956170 CTCACGTCTGCCCACACAC 60.956 63.158 0.00 0.00 0.00 3.82
1205 1412 2.432444 CCATGGAAAAACGAGCACCTA 58.568 47.619 5.56 0.00 0.00 3.08
1230 1439 4.662961 CACACGTCCGCAGCTCCA 62.663 66.667 0.00 0.00 0.00 3.86
1243 1453 1.736126 CAGCTCCACTCTACGTACGAA 59.264 52.381 24.41 5.93 0.00 3.85
1247 1457 0.453390 CCACTCTACGTACGAACCCC 59.547 60.000 24.41 0.00 0.00 4.95
1248 1458 0.453390 CACTCTACGTACGAACCCCC 59.547 60.000 24.41 0.00 0.00 5.40
1249 1459 0.038166 ACTCTACGTACGAACCCCCA 59.962 55.000 24.41 0.00 0.00 4.96
1269 1479 2.054799 ACCTTCTTAAGAGCACCACCA 58.945 47.619 5.12 0.00 0.00 4.17
1294 1662 2.089854 GCACGAAGCAACCGATCAT 58.910 52.632 0.00 0.00 44.79 2.45
1314 1687 2.391130 ACCACCACCACCACACCAT 61.391 57.895 0.00 0.00 0.00 3.55
1315 1688 1.063070 ACCACCACCACCACACCATA 61.063 55.000 0.00 0.00 0.00 2.74
1383 1769 4.711949 AGCGGCAACCTGGAGCTG 62.712 66.667 16.61 16.61 40.08 4.24
1471 1857 0.962356 CCTTCAAGCAAGGCATCCGT 60.962 55.000 0.00 0.00 45.76 4.69
1472 1858 0.449388 CTTCAAGCAAGGCATCCGTC 59.551 55.000 0.00 0.00 0.00 4.79
1479 1865 2.579657 AAGGCATCCGTCACGACCA 61.580 57.895 0.00 0.00 0.00 4.02
1485 1871 0.674581 ATCCGTCACGACCACTACGA 60.675 55.000 0.00 0.00 37.53 3.43
1486 1872 1.154338 CCGTCACGACCACTACGAC 60.154 63.158 0.00 0.00 37.53 4.34
1487 1873 1.570967 CGTCACGACCACTACGACA 59.429 57.895 0.00 0.00 37.53 4.35
1490 1876 0.311790 TCACGACCACTACGACAACC 59.688 55.000 0.00 0.00 34.70 3.77
1536 1922 1.187974 CAAGATTGCTGCCAATGGGA 58.812 50.000 0.00 0.00 41.60 4.37
1598 1984 2.620251 TGACCTTGGCGGAAGATATG 57.380 50.000 0.00 0.00 32.82 1.78
1691 2090 1.676635 CTGTGTGGGCCTGATGGTG 60.677 63.158 4.53 0.00 35.27 4.17
1767 2166 0.179018 ATGCCTTTCTCCGGTATGGC 60.179 55.000 17.58 17.58 40.62 4.40
1808 2207 5.574188 ACCTGTCAAAGCTGGAATATCTTT 58.426 37.500 0.00 0.00 0.00 2.52
1890 2444 2.169561 TGGCGCATCTTGGTATGAGTTA 59.830 45.455 10.83 0.00 0.00 2.24
2148 2702 5.205821 TCTCTATGGTCCGTTTCCTAATGA 58.794 41.667 0.00 0.00 0.00 2.57
2481 3035 1.249407 ACTGGAGCTATACCGCTAGC 58.751 55.000 4.06 4.06 43.65 3.42
2601 3227 7.413438 GCAATATGTTTCTCTCACCAGTAACAG 60.413 40.741 0.00 0.00 0.00 3.16
2622 3248 5.104900 ACAGTCTCAATGGACCTATACAACC 60.105 44.000 0.00 0.00 36.95 3.77
2634 3260 6.353255 GGACCTATACAACCAGGGATACAAAA 60.353 42.308 0.00 0.00 36.15 2.44
2635 3261 6.420638 ACCTATACAACCAGGGATACAAAAC 58.579 40.000 0.00 0.00 36.15 2.43
2658 3284 6.485171 ACTGCAATAGATTACAGGACCTTTT 58.515 36.000 7.28 0.00 35.86 2.27
2659 3285 6.375455 ACTGCAATAGATTACAGGACCTTTTG 59.625 38.462 7.28 0.00 35.86 2.44
3383 4009 5.246656 AGTTTGGCATTCATGGATCTTTCAA 59.753 36.000 0.00 0.00 0.00 2.69
3716 4342 6.839124 ATGGTGCTAGAATTTTTGATGTGA 57.161 33.333 0.00 0.00 0.00 3.58
3733 4359 2.427095 TGTGATCAGTATGGACCTGTCG 59.573 50.000 0.00 0.00 36.16 4.35
3948 4574 6.214819 ACTTATTTAAGCTCCTTGGACCTGTA 59.785 38.462 0.00 0.00 36.79 2.74
3965 4591 8.713971 TGGACCTGTAATATAACAATCTCACAT 58.286 33.333 0.00 0.00 0.00 3.21
4034 4660 2.807967 CAGTCCATATACACGGGCAATG 59.192 50.000 0.00 0.00 0.00 2.82
4112 4738 6.208007 AGAGCATGACAATCAACAGAAAATCA 59.792 34.615 0.00 0.00 0.00 2.57
4145 4771 3.630312 TGAGCCTGTGTTGTTCTTTTACC 59.370 43.478 0.00 0.00 0.00 2.85
4158 4784 4.529716 TCTTTTACCTTGGACTTGGGTT 57.470 40.909 0.00 0.00 34.86 4.11
4168 4794 1.834896 GGACTTGGGTTTGGGTTTGTT 59.165 47.619 0.00 0.00 0.00 2.83
4267 4893 7.109501 ACAAGTTGTATGACAAGGCATATGTA 58.890 34.615 6.75 0.00 39.00 2.29
4410 5037 5.528043 AATGAAGGTGCACATGTTAAACA 57.472 34.783 20.43 6.69 0.00 2.83
4424 5051 7.651304 CACATGTTAAACAATAGGCTTGTTCAA 59.349 33.333 5.11 0.00 41.30 2.69
4539 5166 5.266709 ACCACCTACCTCTGTAACTCTTA 57.733 43.478 0.00 0.00 0.00 2.10
4602 5229 4.212425 CACTTCCACGCATACAGTTTTACA 59.788 41.667 0.00 0.00 0.00 2.41
4607 5234 5.579119 TCCACGCATACAGTTTTACATAGTG 59.421 40.000 0.00 0.00 0.00 2.74
4666 5293 2.843113 CAAGTTCCTTCCCCTCATCTCT 59.157 50.000 0.00 0.00 0.00 3.10
4728 5355 1.374947 GTGTTGTGGCTGGCCTCTA 59.625 57.895 13.05 3.59 36.94 2.43
4765 5392 4.163458 ACCCTACTGTTCAAGAAAGTGTGA 59.837 41.667 0.00 0.00 0.00 3.58
4781 5408 5.234466 AGTGTGAAGAGTTGCCTATTTCT 57.766 39.130 0.00 0.00 0.00 2.52
4906 5533 5.374071 AGGTGAGTTTTACATTTTCGTCCT 58.626 37.500 0.00 0.00 0.00 3.85
4930 5557 7.493971 CCTTCTATTCTTGTTCATGTCACTAGG 59.506 40.741 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 307 3.941483 GCTCCATTTTCCTCGAGATTTGA 59.059 43.478 15.71 0.00 0.00 2.69
513 516 1.671054 CCGGTTCATGCCACGAACT 60.671 57.895 3.46 0.00 41.99 3.01
589 592 3.991924 ATGGTCCTCGCTCCTGGCT 62.992 63.158 0.00 0.00 39.13 4.75
741 745 4.072131 GACAGTTTTCACATTAGCCCTGA 58.928 43.478 0.00 0.00 0.00 3.86
743 747 3.074538 AGGACAGTTTTCACATTAGCCCT 59.925 43.478 0.00 0.00 0.00 5.19
911 915 0.899720 ACCGGCGGTTTAGAATCTGA 59.100 50.000 28.83 0.00 27.29 3.27
1025 1033 3.244078 TGTGGTGTGTGTTGATAGGAGAC 60.244 47.826 0.00 0.00 0.00 3.36
1059 1236 1.301479 GGGTGGTCACTGGACGTTC 60.301 63.158 0.00 0.00 45.28 3.95
1060 1239 2.826702 GGGTGGTCACTGGACGTT 59.173 61.111 0.00 0.00 45.28 3.99
1165 1355 2.972505 GGTGTGTGGGCAGACGTG 60.973 66.667 0.00 0.00 39.50 4.49
1166 1356 3.161450 AGGTGTGTGGGCAGACGT 61.161 61.111 0.00 0.00 39.50 4.34
1167 1357 2.666190 CAGGTGTGTGGGCAGACG 60.666 66.667 0.00 0.00 39.50 4.18
1169 1359 4.269523 GGCAGGTGTGTGGGCAGA 62.270 66.667 0.00 0.00 0.00 4.26
1181 1387 0.109132 GCTCGTTTTTCCATGGCAGG 60.109 55.000 6.96 0.00 0.00 4.85
1205 1412 1.449601 GCGGACGTGTGGATGGATT 60.450 57.895 0.00 0.00 0.00 3.01
1229 1438 0.453390 GGGGGTTCGTACGTAGAGTG 59.547 60.000 16.05 0.00 0.00 3.51
1230 1439 0.038166 TGGGGGTTCGTACGTAGAGT 59.962 55.000 16.05 0.00 0.00 3.24
1243 1453 0.992695 GCTCTTAAGAAGGTGGGGGT 59.007 55.000 6.63 0.00 0.00 4.95
1247 1457 2.427506 GTGGTGCTCTTAAGAAGGTGG 58.572 52.381 6.63 0.00 0.00 4.61
1248 1458 2.224523 TGGTGGTGCTCTTAAGAAGGTG 60.225 50.000 6.63 0.00 0.00 4.00
1249 1459 2.039084 CTGGTGGTGCTCTTAAGAAGGT 59.961 50.000 6.63 0.00 0.00 3.50
1294 1662 2.592864 GTGTGGTGGTGGTGGTGA 59.407 61.111 0.00 0.00 0.00 4.02
1314 1687 1.829456 CGATCCATGGTGGTGGCTA 59.171 57.895 12.58 0.00 39.03 3.93
1315 1688 2.591753 CGATCCATGGTGGTGGCT 59.408 61.111 12.58 0.00 39.03 4.75
1469 1855 0.041047 TTGTCGTAGTGGTCGTGACG 60.041 55.000 0.00 0.00 36.66 4.35
1471 1857 0.311790 GGTTGTCGTAGTGGTCGTGA 59.688 55.000 0.00 0.00 0.00 4.35
1472 1858 0.031043 TGGTTGTCGTAGTGGTCGTG 59.969 55.000 0.00 0.00 0.00 4.35
1479 1865 1.530013 CCCGAGGTGGTTGTCGTAGT 61.530 60.000 0.00 0.00 34.27 2.73
1485 1871 2.841044 ACGACCCGAGGTGGTTGT 60.841 61.111 5.18 0.94 41.73 3.32
1486 1872 2.357034 CACGACCCGAGGTGGTTG 60.357 66.667 7.76 1.75 41.73 3.77
1487 1873 3.622826 CCACGACCCGAGGTGGTT 61.623 66.667 7.76 0.00 41.73 3.67
1490 1876 4.308458 TTGCCACGACCCGAGGTG 62.308 66.667 0.00 0.00 39.64 4.00
1691 2090 1.143073 ACCCAAGAACTCTGGAACACC 59.857 52.381 0.00 0.00 0.00 4.16
2148 2702 5.892119 TGGAGAGACGTCATATTTCCTAGTT 59.108 40.000 19.50 0.00 0.00 2.24
2481 3035 9.912634 TTTCTAAACAAGAAAGATTGCTTATGG 57.087 29.630 0.00 0.00 46.88 2.74
2586 3212 4.855715 TTGAGACTGTTACTGGTGAGAG 57.144 45.455 0.00 0.00 0.00 3.20
2601 3227 5.353394 TGGTTGTATAGGTCCATTGAGAC 57.647 43.478 0.00 0.00 35.95 3.36
2622 3248 6.949352 ATCTATTGCAGTTTTGTATCCCTG 57.051 37.500 0.00 0.00 0.00 4.45
2634 3260 5.700402 AAGGTCCTGTAATCTATTGCAGT 57.300 39.130 16.35 0.00 45.31 4.40
2635 3261 6.678900 GCAAAAGGTCCTGTAATCTATTGCAG 60.679 42.308 12.29 12.29 46.01 4.41
2659 3285 7.553881 TCCAGTAATGCTATTGTAAGAAAGC 57.446 36.000 0.00 0.00 35.51 3.51
2723 3349 7.227156 AGATGGTTGTTAGAAAGATCAAGTGT 58.773 34.615 0.00 0.00 0.00 3.55
2724 3350 7.678947 AGATGGTTGTTAGAAAGATCAAGTG 57.321 36.000 0.00 0.00 0.00 3.16
2725 3351 9.220767 GTAAGATGGTTGTTAGAAAGATCAAGT 57.779 33.333 0.00 0.00 0.00 3.16
2864 3490 6.126409 TGTTGTAAGAAAGGTCAAGGTCATT 58.874 36.000 0.00 0.00 0.00 2.57
3214 3840 4.559862 ATCCAAGACAACTAGGTTCCAG 57.440 45.455 0.00 0.00 0.00 3.86
3716 4342 1.683917 GAGCGACAGGTCCATACTGAT 59.316 52.381 0.00 0.00 39.24 2.90
3733 4359 5.689383 TTTCACCTGTTAGATTGTTGAGC 57.311 39.130 0.00 0.00 0.00 4.26
3802 4428 4.320546 TCCACTCAATTGGTTCCATGAT 57.679 40.909 5.42 0.00 37.93 2.45
3965 4591 0.036765 CGTCCCGGTGGAATTCTTCA 60.037 55.000 5.23 0.00 44.07 3.02
4034 4660 1.600916 GAGGGCCACACAGACCAAC 60.601 63.158 6.18 0.00 0.00 3.77
4112 4738 2.173569 ACACAGGCTCAGAAACCTTCTT 59.826 45.455 0.00 0.00 38.11 2.52
4145 4771 1.788229 AACCCAAACCCAAGTCCAAG 58.212 50.000 0.00 0.00 0.00 3.61
4158 4784 0.827368 GAGGCCAACAACAAACCCAA 59.173 50.000 5.01 0.00 0.00 4.12
4168 4794 2.847234 ACGACCCAGAGGCCAACA 60.847 61.111 5.01 0.00 36.11 3.33
4267 4893 2.821625 GCCCCAGGTAACAACCAGAAAT 60.822 50.000 0.00 0.00 41.41 2.17
4297 4923 5.010282 ACTCAAGTTTTTGTCTCCTTGTGT 58.990 37.500 0.00 0.00 37.03 3.72
4410 5037 6.403866 TGTGAACAATTGAACAAGCCTATT 57.596 33.333 13.59 0.00 0.00 1.73
4424 5051 4.701651 CCTGGTACATGACATGTGAACAAT 59.298 41.667 27.66 4.68 44.60 2.71
4539 5166 5.523916 GGACACGTGCATGTTAAATAGATCT 59.476 40.000 17.22 0.00 31.24 2.75
4602 5229 1.683917 CGAGGCCAGCTCTAACACTAT 59.316 52.381 5.01 0.00 0.00 2.12
4607 5234 0.462759 ATTGCGAGGCCAGCTCTAAC 60.463 55.000 21.29 0.00 35.28 2.34
4781 5408 2.997980 TCAACACTTGTCAAAGAGGCA 58.002 42.857 0.00 0.00 36.84 4.75
4906 5533 8.134202 TCCTAGTGACATGAACAAGAATAGAA 57.866 34.615 0.00 0.00 0.00 2.10
4930 5557 0.899019 GGGAGTGTTGAGAGGACCTC 59.101 60.000 14.15 14.15 42.30 3.85


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

AutoCloner maintained by Alex Coulton.