Multiple sequence alignment - TraesCS7A01G148500

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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 TraesCS7A01G148500 chr7A 100.000 2615 0 0 1 2615 101624256 101621642 0.000000e+00 4830.0
1 TraesCS7A01G148500 chr7A 96.222 794 28 2 1 793 559412379 559411587 0.000000e+00 1299.0
2 TraesCS7A01G148500 chr7A 91.667 516 39 4 989 1503 445550515 445551027 0.000000e+00 712.0
3 TraesCS7A01G148500 chr7A 90.541 518 45 4 989 1505 445558536 445559050 0.000000e+00 682.0
4 TraesCS7A01G148500 chr7A 92.944 411 26 3 1094 1503 423886318 423885910 1.730000e-166 595.0
5 TraesCS7A01G148500 chr7A 86.957 115 7 5 1915 2028 359168478 359168585 3.530000e-24 122.0
6 TraesCS7A01G148500 chr7A 91.954 87 6 1 1902 1987 110174459 110174373 1.270000e-23 121.0
7 TraesCS7A01G148500 chr4A 92.905 1198 84 1 941 2138 395981406 395982602 0.000000e+00 1740.0
8 TraesCS7A01G148500 chr4A 94.194 844 42 7 1 841 138728470 138727631 0.000000e+00 1280.0
9 TraesCS7A01G148500 chr4A 89.019 938 89 13 1 935 333581048 333580122 0.000000e+00 1149.0
10 TraesCS7A01G148500 chr4A 89.019 938 89 13 1 935 357623096 357622170 0.000000e+00 1149.0
11 TraesCS7A01G148500 chr4A 84.966 1031 103 33 1 1018 366387914 366386923 0.000000e+00 998.0
12 TraesCS7A01G148500 chr4A 84.481 1031 106 35 1 1018 304722247 304723236 0.000000e+00 968.0
13 TraesCS7A01G148500 chr4A 82.263 1043 124 32 1 1018 356326764 356327770 0.000000e+00 845.0
14 TraesCS7A01G148500 chr4A 93.243 518 33 2 989 1505 266989444 266989960 0.000000e+00 761.0
15 TraesCS7A01G148500 chr4A 91.845 515 39 3 992 1505 561080230 561079718 0.000000e+00 715.0
16 TraesCS7A01G148500 chr4A 92.351 353 26 1 1507 1859 506057434 506057785 3.890000e-138 501.0
17 TraesCS7A01G148500 chr4A 90.652 353 32 1 1507 1859 506068010 506068361 3.940000e-128 468.0
18 TraesCS7A01G148500 chr4A 89.493 276 28 1 1584 1859 506108784 506109058 5.360000e-92 348.0
19 TraesCS7A01G148500 chr4A 87.719 114 13 1 912 1024 466907841 466907728 5.870000e-27 132.0
20 TraesCS7A01G148500 chr4A 81.457 151 26 2 1710 1859 401231061 401230912 3.530000e-24 122.0
21 TraesCS7A01G148500 chr4A 83.193 119 19 1 912 1029 72109440 72109322 9.900000e-20 108.0
22 TraesCS7A01G148500 chr4A 95.833 48 1 1 2019 2066 274395039 274394993 2.790000e-10 76.8
23 TraesCS7A01G148500 chr6A 93.471 919 60 0 941 1859 378454306 378453388 0.000000e+00 1365.0
24 TraesCS7A01G148500 chr6A 92.088 910 70 2 951 1859 378422127 378421219 0.000000e+00 1280.0
25 TraesCS7A01G148500 chr6A 93.502 831 50 4 1 829 529889680 529890508 0.000000e+00 1232.0
26 TraesCS7A01G148500 chr6A 93.269 832 50 6 1 829 529853360 529854188 0.000000e+00 1221.0
27 TraesCS7A01G148500 chr6A 93.243 518 34 1 989 1505 253447216 253446699 0.000000e+00 761.0
28 TraesCS7A01G148500 chr6A 86.815 493 54 10 2130 2615 511361483 511361971 8.230000e-150 540.0
29 TraesCS7A01G148500 chr6A 89.970 329 33 0 1531 1859 378429596 378429268 2.410000e-115 425.0
30 TraesCS7A01G148500 chr6A 79.639 609 84 28 2016 2596 509629185 509629781 4.050000e-108 401.0
31 TraesCS7A01G148500 chr6A 78.982 609 89 25 2016 2596 509614604 509615201 1.900000e-101 379.0
32 TraesCS7A01G148500 chr6A 77.052 597 86 34 2046 2605 259131889 259132471 1.970000e-76 296.0
33 TraesCS7A01G148500 chr6A 92.969 128 8 1 2019 2146 486083593 486083467 4.440000e-43 185.0
34 TraesCS7A01G148500 chr6A 93.023 129 6 3 2019 2146 486109177 486109051 4.440000e-43 185.0
35 TraesCS7A01G148500 chr6A 86.667 75 6 4 1930 2003 492909805 492909876 2.160000e-11 80.5
36 TraesCS7A01G148500 chr1A 89.913 1031 79 16 1 1018 184686194 184687212 0.000000e+00 1304.0
37 TraesCS7A01G148500 chr1A 89.894 940 80 14 2 935 233463281 233464211 0.000000e+00 1195.0
38 TraesCS7A01G148500 chr3A 88.711 939 91 13 1 935 22102944 22103871 0.000000e+00 1133.0
39 TraesCS7A01G148500 chr3A 85.000 80 5 6 1909 1987 250701447 250701374 1.000000e-09 75.0
40 TraesCS7A01G148500 chr2A 95.302 447 20 1 2170 2615 386866759 386866313 0.000000e+00 708.0
41 TraesCS7A01G148500 chr2A 94.407 447 24 1 2170 2615 386874926 386874480 0.000000e+00 686.0
42 TraesCS7A01G148500 chr2A 94.407 447 24 1 2170 2615 386882562 386882116 0.000000e+00 686.0
43 TraesCS7A01G148500 chr2A 94.407 447 24 1 2170 2615 386903778 386903332 0.000000e+00 686.0
44 TraesCS7A01G148500 chr2A 87.627 493 49 11 2130 2615 500977956 500977469 1.760000e-156 562.0
45 TraesCS7A01G148500 chr2A 90.196 255 24 1 941 1194 309403545 309403291 5.390000e-87 331.0
46 TraesCS7A01G148500 chr2A 89.691 194 16 4 1955 2146 120941039 120940848 7.230000e-61 244.0
47 TraesCS7A01G148500 chr2A 84.496 258 20 12 1955 2194 120923409 120923154 1.210000e-58 237.0
48 TraesCS7A01G148500 chr2A 84.264 197 22 2 1495 1683 57671339 57671534 1.600000e-42 183.0
49 TraesCS7A01G148500 chr2A 89.333 75 2 4 1930 2003 477065915 477065984 3.580000e-14 89.8
50 TraesCS7A01G148500 chr2A 84.507 71 11 0 1744 1814 431626188 431626118 1.300000e-08 71.3
51 TraesCS7A01G148500 chrUn 94.407 447 24 1 2170 2615 354783228 354783674 0.000000e+00 686.0
52 TraesCS7A01G148500 chrUn 92.308 143 10 1 1507 1649 74767184 74767325 4.410000e-48 202.0
53 TraesCS7A01G148500 chr5A 87.755 490 49 10 2133 2615 448130319 448129834 1.760000e-156 562.0
54 TraesCS7A01G148500 chr5A 87.551 490 50 10 2133 2615 448122329 448121844 8.180000e-155 556.0
55 TraesCS7A01G148500 chr5A 84.047 257 23 11 1955 2194 114369140 114368885 5.630000e-57 231.0
56 TraesCS7A01G148500 chr5A 89.333 75 3 3 1930 2003 260137646 260137716 3.580000e-14 89.8


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 TraesCS7A01G148500 chr7A 101621642 101624256 2614 True 4830 4830 100.000 1 2615 1 chr7A.!!$R1 2614
1 TraesCS7A01G148500 chr7A 559411587 559412379 792 True 1299 1299 96.222 1 793 1 chr7A.!!$R4 792
2 TraesCS7A01G148500 chr7A 445550515 445551027 512 False 712 712 91.667 989 1503 1 chr7A.!!$F2 514
3 TraesCS7A01G148500 chr7A 445558536 445559050 514 False 682 682 90.541 989 1505 1 chr7A.!!$F3 516
4 TraesCS7A01G148500 chr4A 395981406 395982602 1196 False 1740 1740 92.905 941 2138 1 chr4A.!!$F4 1197
5 TraesCS7A01G148500 chr4A 138727631 138728470 839 True 1280 1280 94.194 1 841 1 chr4A.!!$R2 840
6 TraesCS7A01G148500 chr4A 333580122 333581048 926 True 1149 1149 89.019 1 935 1 chr4A.!!$R4 934
7 TraesCS7A01G148500 chr4A 357622170 357623096 926 True 1149 1149 89.019 1 935 1 chr4A.!!$R5 934
8 TraesCS7A01G148500 chr4A 366386923 366387914 991 True 998 998 84.966 1 1018 1 chr4A.!!$R6 1017
9 TraesCS7A01G148500 chr4A 304722247 304723236 989 False 968 968 84.481 1 1018 1 chr4A.!!$F2 1017
10 TraesCS7A01G148500 chr4A 356326764 356327770 1006 False 845 845 82.263 1 1018 1 chr4A.!!$F3 1017
11 TraesCS7A01G148500 chr4A 266989444 266989960 516 False 761 761 93.243 989 1505 1 chr4A.!!$F1 516
12 TraesCS7A01G148500 chr4A 561079718 561080230 512 True 715 715 91.845 992 1505 1 chr4A.!!$R9 513
13 TraesCS7A01G148500 chr6A 378453388 378454306 918 True 1365 1365 93.471 941 1859 1 chr6A.!!$R4 918
14 TraesCS7A01G148500 chr6A 378421219 378422127 908 True 1280 1280 92.088 951 1859 1 chr6A.!!$R2 908
15 TraesCS7A01G148500 chr6A 529889680 529890508 828 False 1232 1232 93.502 1 829 1 chr6A.!!$F7 828
16 TraesCS7A01G148500 chr6A 529853360 529854188 828 False 1221 1221 93.269 1 829 1 chr6A.!!$F6 828
17 TraesCS7A01G148500 chr6A 253446699 253447216 517 True 761 761 93.243 989 1505 1 chr6A.!!$R1 516
18 TraesCS7A01G148500 chr6A 509629185 509629781 596 False 401 401 79.639 2016 2596 1 chr6A.!!$F4 580
19 TraesCS7A01G148500 chr6A 509614604 509615201 597 False 379 379 78.982 2016 2596 1 chr6A.!!$F3 580
20 TraesCS7A01G148500 chr6A 259131889 259132471 582 False 296 296 77.052 2046 2605 1 chr6A.!!$F1 559
21 TraesCS7A01G148500 chr1A 184686194 184687212 1018 False 1304 1304 89.913 1 1018 1 chr1A.!!$F1 1017
22 TraesCS7A01G148500 chr1A 233463281 233464211 930 False 1195 1195 89.894 2 935 1 chr1A.!!$F2 933
23 TraesCS7A01G148500 chr3A 22102944 22103871 927 False 1133 1133 88.711 1 935 1 chr3A.!!$F1 934

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
883 901 0.95396 CTTTCCGGTCCCGTTCTTGG 60.954 60.0 0.0 0.0 37.81 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2042 0.322726 TTGCCTAAACCTAACCGGCC 60.323 55.0 0.0 0.0 39.97 6.13 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
360 369 6.432936 AGCATATCATGAAGCATTTGTTACG 58.567 36.000 17.04 0.00 0.00 3.18
361 370 6.038603 AGCATATCATGAAGCATTTGTTACGT 59.961 34.615 17.04 0.00 0.00 3.57
362 371 6.141211 GCATATCATGAAGCATTTGTTACGTG 59.859 38.462 0.00 0.00 0.00 4.49
365 374 4.154015 TCATGAAGCATTTGTTACGTGGAG 59.846 41.667 0.00 0.00 0.00 3.86
370 379 3.252458 AGCATTTGTTACGTGGAGGAAAC 59.748 43.478 0.00 0.00 0.00 2.78
371 380 3.805823 CATTTGTTACGTGGAGGAAACG 58.194 45.455 0.00 0.00 46.32 3.60
431 442 2.592287 GGCAACGTTCCGGTTCCA 60.592 61.111 0.00 0.00 0.00 3.53
700 716 1.483415 GATGCGGTGTAGGGGAAGTAA 59.517 52.381 0.00 0.00 0.00 2.24
839 857 2.472861 CGTAGATGTTCATGTCATCGGC 59.527 50.000 19.43 16.29 44.20 5.54
883 901 0.953960 CTTTCCGGTCCCGTTCTTGG 60.954 60.000 0.00 0.00 37.81 3.61
948 975 2.053627 CAACGTCACGGTAGTTGTACC 58.946 52.381 0.35 0.00 44.99 3.34
1021 1048 1.414919 TGAAGTGGTACTTGGCGAGTT 59.585 47.619 13.65 0.00 38.80 3.01
1064 1091 1.075542 GCACATGTGACGAATCCGAA 58.924 50.000 29.80 0.00 39.50 4.30
1097 1124 1.573108 GTCTTGGAGAGGGATGGTCA 58.427 55.000 0.00 0.00 0.00 4.02
1124 1151 2.281692 TTGTCGGTCTCGGTCGGA 60.282 61.111 0.00 0.00 36.95 4.55
1182 1211 0.467290 TCCCAAAAACGCTCCTGCTT 60.467 50.000 0.00 0.00 36.97 3.91
1208 1237 2.096248 GGTCTCTGTCTCGGTCTTCAT 58.904 52.381 0.00 0.00 0.00 2.57
1256 1285 1.002792 CACGAATGCGATAGTCCTCGA 60.003 52.381 0.00 0.00 41.12 4.04
1307 1336 1.798735 CCTTGGCAGTGATTCGCAG 59.201 57.895 0.00 0.00 0.00 5.18
1622 1653 4.899239 CGCGGCCTAGAGCAAGGG 62.899 72.222 0.00 0.00 46.50 3.95
1625 1656 1.758514 CGGCCTAGAGCAAGGGAGA 60.759 63.158 0.00 0.00 46.50 3.71
1629 1660 1.834263 GCCTAGAGCAAGGGAGAAGAA 59.166 52.381 0.00 0.00 42.97 2.52
1631 1662 3.103742 CCTAGAGCAAGGGAGAAGAAGT 58.896 50.000 0.00 0.00 32.55 3.01
1644 1675 4.415332 GAAGTCGGTGGCGCGAGA 62.415 66.667 12.10 0.00 0.00 4.04
1654 1685 2.261671 GCGCGAGAGAAGTTCCCA 59.738 61.111 12.10 0.00 0.00 4.37
1683 1714 4.155733 ACCGGCGAATGGATGCGA 62.156 61.111 9.30 0.00 0.00 5.10
1808 1839 4.467084 GGCCATGGCGACGGAGAA 62.467 66.667 29.90 0.00 43.06 2.87
1811 1842 1.375396 CCATGGCGACGGAGAAACA 60.375 57.895 0.00 0.00 0.00 2.83
1874 1905 1.153469 CGGCAAGAGGAAGGAGAGC 60.153 63.158 0.00 0.00 0.00 4.09
1878 1909 1.687493 AAGAGGAAGGAGAGCCCGG 60.687 63.158 0.00 0.00 40.87 5.73
1913 1944 3.411517 CCTGTTGCGGGAGGGGAT 61.412 66.667 0.00 0.00 29.82 3.85
1955 1986 1.200020 GAATCAAACGTGGGGCTTCTG 59.800 52.381 0.00 0.00 0.00 3.02
2145 2190 9.936759 AAAACAAAACAATGAAAGAGAAGGTAA 57.063 25.926 0.00 0.00 0.00 2.85
2184 2236 1.313091 GGACATTTTCCCGGGCTCAC 61.313 60.000 18.49 2.88 38.70 3.51
2195 2247 0.314935 CGGGCTCACAAAAATGTGCT 59.685 50.000 4.13 0.00 38.75 4.40
2200 2252 3.622612 GGCTCACAAAAATGTGCTTGTTT 59.377 39.130 4.13 0.00 38.75 2.83
2202 2254 4.548726 GCTCACAAAAATGTGCTTGTTTCG 60.549 41.667 4.13 0.00 39.49 3.46
2209 2261 7.064490 ACAAAAATGTGCTTGTTTCGAGAAAAT 59.936 29.630 0.00 0.00 31.76 1.82
2210 2262 8.538856 CAAAAATGTGCTTGTTTCGAGAAAATA 58.461 29.630 0.00 0.00 31.33 1.40
2211 2263 7.858052 AAATGTGCTTGTTTCGAGAAAATAG 57.142 32.000 0.00 2.60 31.33 1.73
2212 2264 6.801539 ATGTGCTTGTTTCGAGAAAATAGA 57.198 33.333 0.00 0.00 31.33 1.98
2215 2267 6.481976 TGTGCTTGTTTCGAGAAAATAGAGAA 59.518 34.615 0.00 0.00 31.33 2.87
2218 2270 6.521477 GCTTGTTTCGAGAAAATAGAGAAAGC 59.479 38.462 0.00 0.00 32.39 3.51
2228 2280 8.278729 AGAAAATAGAGAAAGCCAAGATTGAG 57.721 34.615 0.00 0.00 0.00 3.02
2230 2282 8.820153 AAAATAGAGAAAGCCAAGATTGAGAT 57.180 30.769 0.00 0.00 0.00 2.75
2231 2283 7.804843 AATAGAGAAAGCCAAGATTGAGATG 57.195 36.000 0.00 0.00 0.00 2.90
2233 2285 5.568392 AGAGAAAGCCAAGATTGAGATGTT 58.432 37.500 0.00 0.00 0.00 2.71
2235 2287 7.170965 AGAGAAAGCCAAGATTGAGATGTTTA 58.829 34.615 0.00 0.00 0.00 2.01
2304 2358 9.581289 TTCAAGGTAATGAAGAGTCCAAAAATA 57.419 29.630 0.00 0.00 34.50 1.40
2335 2389 0.035439 GGTGGAGCTCCGGAAAATGA 60.035 55.000 27.43 4.53 39.43 2.57
2336 2390 1.087501 GTGGAGCTCCGGAAAATGAC 58.912 55.000 27.43 13.62 39.43 3.06
2346 2400 5.163794 GCTCCGGAAAATGACGAAAGAATAA 60.164 40.000 5.23 0.00 0.00 1.40
2354 2408 7.816945 AAATGACGAAAGAATAAATGGCAAG 57.183 32.000 0.00 0.00 0.00 4.01
2362 2416 7.065803 CGAAAGAATAAATGGCAAGGTTAGAGA 59.934 37.037 0.00 0.00 0.00 3.10
2363 2417 7.872113 AAGAATAAATGGCAAGGTTAGAGAG 57.128 36.000 0.00 0.00 0.00 3.20
2367 2421 2.185004 TGGCAAGGTTAGAGAGCAAC 57.815 50.000 0.00 0.00 0.00 4.17
2368 2422 1.699634 TGGCAAGGTTAGAGAGCAACT 59.300 47.619 0.00 0.00 0.00 3.16
2369 2423 2.289694 TGGCAAGGTTAGAGAGCAACTC 60.290 50.000 3.25 3.25 45.22 3.01
2381 2435 2.805099 AGAGCAACTCGAAGCAGAAAAG 59.195 45.455 6.89 0.00 35.36 2.27
2383 2437 2.545946 AGCAACTCGAAGCAGAAAAGAC 59.454 45.455 6.89 0.00 0.00 3.01
2384 2438 2.545946 GCAACTCGAAGCAGAAAAGACT 59.454 45.455 0.00 0.00 0.00 3.24
2385 2439 3.002759 GCAACTCGAAGCAGAAAAGACTT 59.997 43.478 0.00 0.00 0.00 3.01
2386 2440 4.521943 CAACTCGAAGCAGAAAAGACTTG 58.478 43.478 0.00 0.00 0.00 3.16
2387 2441 4.060038 ACTCGAAGCAGAAAAGACTTGA 57.940 40.909 0.00 0.00 0.00 3.02
2389 2443 4.202161 ACTCGAAGCAGAAAAGACTTGAGA 60.202 41.667 0.00 0.00 0.00 3.27
2391 2445 4.054671 CGAAGCAGAAAAGACTTGAGAGT 58.945 43.478 0.00 0.00 39.32 3.24
2392 2446 4.509600 CGAAGCAGAAAAGACTTGAGAGTT 59.490 41.667 0.00 0.00 35.88 3.01
2394 2448 6.201044 CGAAGCAGAAAAGACTTGAGAGTTTA 59.799 38.462 0.00 0.00 35.88 2.01
2411 2465 7.913297 TGAGAGTTTAAATTGCAAGTGTGTTAC 59.087 33.333 4.94 0.00 0.00 2.50
2422 2477 4.612033 GCAAGTGTGTTACGGTAATTCCAC 60.612 45.833 3.59 10.58 35.57 4.02
2520 2583 1.972872 AATGGACCGAAGATCCATGC 58.027 50.000 7.27 0.00 42.83 4.06
2521 2584 0.839277 ATGGACCGAAGATCCATGCA 59.161 50.000 5.73 0.00 42.14 3.96
2522 2585 0.617935 TGGACCGAAGATCCATGCAA 59.382 50.000 0.00 0.00 0.00 4.08
2527 2590 4.261197 GGACCGAAGATCCATGCAATTTAC 60.261 45.833 0.00 0.00 0.00 2.01
2531 2594 6.601613 ACCGAAGATCCATGCAATTTACTTAA 59.398 34.615 0.00 0.00 0.00 1.85
2532 2595 7.134815 CCGAAGATCCATGCAATTTACTTAAG 58.865 38.462 0.00 0.00 0.00 1.85
2553 2616 9.884465 CTTAAGTGAGTTTTAGTTGGATTTGAG 57.116 33.333 0.00 0.00 0.00 3.02
2554 2617 9.621629 TTAAGTGAGTTTTAGTTGGATTTGAGA 57.378 29.630 0.00 0.00 0.00 3.27
2555 2618 8.519799 AAGTGAGTTTTAGTTGGATTTGAGAA 57.480 30.769 0.00 0.00 0.00 2.87
2565 2628 5.482878 AGTTGGATTTGAGAAAATGATGGCT 59.517 36.000 0.00 0.00 0.00 4.75
2603 2666 2.702898 CACATGATGCAACGAACCAA 57.297 45.000 0.00 0.00 0.00 3.67
2604 2667 3.010624 CACATGATGCAACGAACCAAA 57.989 42.857 0.00 0.00 0.00 3.28
2605 2668 3.379240 CACATGATGCAACGAACCAAAA 58.621 40.909 0.00 0.00 0.00 2.44
2606 2669 3.182173 CACATGATGCAACGAACCAAAAC 59.818 43.478 0.00 0.00 0.00 2.43
2607 2670 2.112475 TGATGCAACGAACCAAAACG 57.888 45.000 0.00 0.00 0.00 3.60
2608 2671 1.671328 TGATGCAACGAACCAAAACGA 59.329 42.857 0.00 0.00 0.00 3.85
2609 2672 2.097629 TGATGCAACGAACCAAAACGAA 59.902 40.909 0.00 0.00 0.00 3.85
2611 2674 2.251893 TGCAACGAACCAAAACGAAAC 58.748 42.857 0.00 0.00 0.00 2.78
2612 2675 2.251893 GCAACGAACCAAAACGAAACA 58.748 42.857 0.00 0.00 0.00 2.83
2614 2677 2.547913 ACGAACCAAAACGAAACACC 57.452 45.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
431 442 4.778534 TCGGTTTCTCAATCGAGTTACT 57.221 40.909 0.00 0.00 40.71 2.24
700 716 2.762535 ATGAACGTCCCGAGAATGTT 57.237 45.000 0.00 0.00 0.00 2.71
839 857 1.080298 GACCCCAAGTACCACGACG 60.080 63.158 0.00 0.00 0.00 5.12
883 901 2.858344 CGAACGTGAATGACTACCATCC 59.142 50.000 0.00 0.00 33.53 3.51
948 975 4.456253 CGACGTCTCGTGGACCGG 62.456 72.222 14.70 0.00 41.37 5.28
1021 1048 0.458889 GCCCATGTACAACTACGCGA 60.459 55.000 15.93 0.00 0.00 5.87
1097 1124 2.681848 CGAGACCGACAAGTACCACTAT 59.318 50.000 0.00 0.00 38.22 2.12
1124 1151 0.598158 TTCGACTACGTTTTGCCGCT 60.598 50.000 0.00 0.00 40.69 5.52
1182 1211 0.034960 CCGAGACAGAGACCTCCTCA 60.035 60.000 0.00 0.00 44.40 3.86
1208 1237 2.652530 GCCAAGTACCACGACCGA 59.347 61.111 0.00 0.00 0.00 4.69
1527 1558 3.390521 CAGCGCCCACAGGTCCTA 61.391 66.667 2.29 0.00 34.57 2.94
1555 1586 3.148279 GTCATCGCCCGAGGACCT 61.148 66.667 20.74 0.00 46.37 3.85
1613 1644 1.548269 CGACTTCTTCTCCCTTGCTCT 59.452 52.381 0.00 0.00 0.00 4.09
1622 1653 2.095252 GCGCCACCGACTTCTTCTC 61.095 63.158 0.00 0.00 36.29 2.87
1625 1656 3.916392 CTCGCGCCACCGACTTCTT 62.916 63.158 0.00 0.00 36.29 2.52
1631 1662 4.116328 CTTCTCTCGCGCCACCGA 62.116 66.667 0.00 0.00 36.29 4.69
1644 1675 2.342648 GTCGCCGTGGGAACTTCT 59.657 61.111 0.00 0.00 0.00 2.85
1700 1731 3.121030 CACCTCGCCGCAAGAAGG 61.121 66.667 0.00 0.00 43.02 3.46
1760 1791 0.456824 CTTCTGCTGCTTCGTCGCTA 60.457 55.000 0.00 0.00 0.00 4.26
1761 1792 1.735920 CTTCTGCTGCTTCGTCGCT 60.736 57.895 0.00 0.00 0.00 4.93
1808 1839 3.850098 CTGTCGCCCCAGCCTTGTT 62.850 63.158 0.00 0.00 34.57 2.83
1811 1842 3.710722 CTCTGTCGCCCCAGCCTT 61.711 66.667 0.00 0.00 34.57 4.35
1886 1917 2.031163 GCAACAGGGAGTCACGCT 59.969 61.111 0.00 0.00 42.55 5.07
1887 1918 3.414700 CGCAACAGGGAGTCACGC 61.415 66.667 0.00 0.00 0.00 5.34
1911 1942 2.166907 TCCAACCTCTCCCTCTCATC 57.833 55.000 0.00 0.00 0.00 2.92
1913 1944 1.686428 CGATCCAACCTCTCCCTCTCA 60.686 57.143 0.00 0.00 0.00 3.27
1961 1992 2.760385 CTCCCTCGTCTCCACCCC 60.760 72.222 0.00 0.00 0.00 4.95
2011 2042 0.322726 TTGCCTAAACCTAACCGGCC 60.323 55.000 0.00 0.00 39.97 6.13
2017 2048 1.683629 CCGCCCATTGCCTAAACCTAA 60.684 52.381 0.00 0.00 36.24 2.69
2131 2176 1.278127 CCGCCCTTACCTTCTCTTTCA 59.722 52.381 0.00 0.00 0.00 2.69
2145 2190 3.099170 ATGCCCAGATTCCGCCCT 61.099 61.111 0.00 0.00 0.00 5.19
2179 2231 4.548726 CGAAACAAGCACATTTTTGTGAGC 60.549 41.667 10.14 0.00 42.02 4.26
2184 2236 5.947503 TTCTCGAAACAAGCACATTTTTG 57.052 34.783 0.00 0.00 0.00 2.44
2195 2247 6.485313 TGGCTTTCTCTATTTTCTCGAAACAA 59.515 34.615 0.00 0.00 0.00 2.83
2200 2252 6.037786 TCTTGGCTTTCTCTATTTTCTCGA 57.962 37.500 0.00 0.00 0.00 4.04
2202 2254 8.273780 TCAATCTTGGCTTTCTCTATTTTCTC 57.726 34.615 0.00 0.00 0.00 2.87
2209 2261 6.305272 ACATCTCAATCTTGGCTTTCTCTA 57.695 37.500 0.00 0.00 0.00 2.43
2210 2262 5.176741 ACATCTCAATCTTGGCTTTCTCT 57.823 39.130 0.00 0.00 0.00 3.10
2211 2263 5.893897 AACATCTCAATCTTGGCTTTCTC 57.106 39.130 0.00 0.00 0.00 2.87
2212 2264 7.765695 TTAAACATCTCAATCTTGGCTTTCT 57.234 32.000 0.00 0.00 0.00 2.52
2215 2267 8.587608 TGAATTTAAACATCTCAATCTTGGCTT 58.412 29.630 0.00 0.00 0.00 4.35
2279 2331 9.753674 ATATTTTTGGACTCTTCATTACCTTGA 57.246 29.630 0.00 0.00 0.00 3.02
2286 2340 7.938140 TCCGAATATTTTTGGACTCTTCATT 57.062 32.000 0.94 0.00 40.00 2.57
2287 2341 8.525290 AATCCGAATATTTTTGGACTCTTCAT 57.475 30.769 7.00 0.00 46.18 2.57
2304 2358 2.755103 GAGCTCCACCAAAAATCCGAAT 59.245 45.455 0.87 0.00 0.00 3.34
2335 2389 5.722021 AACCTTGCCATTTATTCTTTCGT 57.278 34.783 0.00 0.00 0.00 3.85
2336 2390 7.065803 TCTCTAACCTTGCCATTTATTCTTTCG 59.934 37.037 0.00 0.00 0.00 3.46
2346 2400 3.084786 GTTGCTCTCTAACCTTGCCATT 58.915 45.455 0.00 0.00 0.00 3.16
2354 2408 2.263945 GCTTCGAGTTGCTCTCTAACC 58.736 52.381 7.61 0.00 40.75 2.85
2362 2416 2.545946 GTCTTTTCTGCTTCGAGTTGCT 59.454 45.455 8.23 0.00 0.00 3.91
2363 2417 2.545946 AGTCTTTTCTGCTTCGAGTTGC 59.454 45.455 0.00 0.00 0.00 4.17
2367 2421 4.302455 TCTCAAGTCTTTTCTGCTTCGAG 58.698 43.478 0.00 0.00 0.00 4.04
2368 2422 4.202161 ACTCTCAAGTCTTTTCTGCTTCGA 60.202 41.667 0.00 0.00 0.00 3.71
2369 2423 4.054671 ACTCTCAAGTCTTTTCTGCTTCG 58.945 43.478 0.00 0.00 0.00 3.79
2370 2424 6.370433 AAACTCTCAAGTCTTTTCTGCTTC 57.630 37.500 0.00 0.00 33.48 3.86
2371 2425 7.865706 TTAAACTCTCAAGTCTTTTCTGCTT 57.134 32.000 0.00 0.00 33.48 3.91
2372 2426 7.865706 TTTAAACTCTCAAGTCTTTTCTGCT 57.134 32.000 0.00 0.00 33.48 4.24
2373 2427 8.962111 CAATTTAAACTCTCAAGTCTTTTCTGC 58.038 33.333 0.00 0.00 33.48 4.26
2374 2428 8.962111 GCAATTTAAACTCTCAAGTCTTTTCTG 58.038 33.333 0.00 0.00 33.48 3.02
2376 2430 8.856490 TGCAATTTAAACTCTCAAGTCTTTTC 57.144 30.769 0.00 0.00 33.48 2.29
2381 2435 7.166473 CACACTTGCAATTTAAACTCTCAAGTC 59.834 37.037 17.04 0.00 40.13 3.01
2383 2437 6.974622 ACACACTTGCAATTTAAACTCTCAAG 59.025 34.615 0.00 14.52 36.48 3.02
2384 2438 6.862209 ACACACTTGCAATTTAAACTCTCAA 58.138 32.000 0.00 0.00 0.00 3.02
2385 2439 6.449635 ACACACTTGCAATTTAAACTCTCA 57.550 33.333 0.00 0.00 0.00 3.27
2386 2440 7.111593 CGTAACACACTTGCAATTTAAACTCTC 59.888 37.037 0.00 0.00 0.00 3.20
2387 2441 6.910433 CGTAACACACTTGCAATTTAAACTCT 59.090 34.615 0.00 0.00 0.00 3.24
2389 2443 5.974751 CCGTAACACACTTGCAATTTAAACT 59.025 36.000 0.00 0.00 0.00 2.66
2391 2445 5.892568 ACCGTAACACACTTGCAATTTAAA 58.107 33.333 0.00 0.00 0.00 1.52
2392 2446 5.502153 ACCGTAACACACTTGCAATTTAA 57.498 34.783 0.00 0.00 0.00 1.52
2394 2448 5.502153 TTACCGTAACACACTTGCAATTT 57.498 34.783 0.00 0.00 0.00 1.82
2481 2539 1.961133 TAAACCGAGGGAAGGGTGAT 58.039 50.000 0.00 0.00 36.45 3.06
2482 2540 1.732117 TTAAACCGAGGGAAGGGTGA 58.268 50.000 0.00 0.00 36.45 4.02
2484 2542 2.291346 CCATTTAAACCGAGGGAAGGGT 60.291 50.000 0.00 0.00 38.44 4.34
2486 2544 3.014623 GTCCATTTAAACCGAGGGAAGG 58.985 50.000 0.00 0.00 0.00 3.46
2487 2545 3.014623 GGTCCATTTAAACCGAGGGAAG 58.985 50.000 0.00 0.00 0.00 3.46
2527 2590 9.884465 CTCAAATCCAACTAAAACTCACTTAAG 57.116 33.333 0.00 0.00 0.00 1.85
2531 2594 8.519799 TTTCTCAAATCCAACTAAAACTCACT 57.480 30.769 0.00 0.00 0.00 3.41
2532 2595 9.750125 ATTTTCTCAAATCCAACTAAAACTCAC 57.250 29.630 0.00 0.00 0.00 3.51
2543 2606 6.014413 TCAAGCCATCATTTTCTCAAATCCAA 60.014 34.615 0.00 0.00 29.41 3.53
2544 2607 5.481122 TCAAGCCATCATTTTCTCAAATCCA 59.519 36.000 0.00 0.00 29.41 3.41
2545 2608 5.969423 TCAAGCCATCATTTTCTCAAATCC 58.031 37.500 0.00 0.00 29.41 3.01
2547 2610 7.039882 GTCATCAAGCCATCATTTTCTCAAAT 58.960 34.615 0.00 0.00 32.36 2.32
2548 2611 6.015265 TGTCATCAAGCCATCATTTTCTCAAA 60.015 34.615 0.00 0.00 0.00 2.69
2553 2616 5.898174 TCATGTCATCAAGCCATCATTTTC 58.102 37.500 0.00 0.00 0.00 2.29
2554 2617 5.925506 TCATGTCATCAAGCCATCATTTT 57.074 34.783 0.00 0.00 0.00 1.82
2555 2618 5.739070 GCATCATGTCATCAAGCCATCATTT 60.739 40.000 0.00 0.00 0.00 2.32
2565 2628 3.193691 TGTGCATTGCATCATGTCATCAA 59.806 39.130 15.49 0.00 41.91 2.57


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

AutoCloner maintained by Alex Coulton.