Multiple sequence alignment - TraesCS3B01G003200

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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 TraesCS3B01G003200 chr3B 100.000 4741 0 0 1 4741 2295690 2300430 0.000000e+00 8756.0
1 TraesCS3B01G003200 chr3B 95.812 2101 77 7 2022 4113 2171235 2169137 0.000000e+00 3382.0
2 TraesCS3B01G003200 chr3B 80.010 2051 287 66 2114 4086 2309400 2311405 0.000000e+00 1402.0
3 TraesCS3B01G003200 chr3B 91.309 1001 49 15 665 1654 2172557 2171584 0.000000e+00 1332.0
4 TraesCS3B01G003200 chr3B 98.116 637 11 1 4106 4741 2169095 2168459 0.000000e+00 1109.0
5 TraesCS3B01G003200 chr3B 81.513 1309 190 32 2457 3730 2161961 2160670 0.000000e+00 1029.0
6 TraesCS3B01G003200 chr3B 93.375 317 17 4 1710 2023 2171586 2171271 2.580000e-127 466.0
7 TraesCS3B01G003200 chr3B 91.346 312 22 4 1 312 2173428 2173122 5.670000e-114 422.0
8 TraesCS3B01G003200 chr3B 87.189 281 33 3 390 668 2172992 2172713 2.750000e-82 316.0
9 TraesCS3B01G003200 chr3B 74.393 906 128 64 996 1830 2163429 2162557 4.640000e-75 292.0
10 TraesCS3B01G003200 chr3B 89.855 69 5 2 1654 1720 554585993 554585925 2.350000e-13 87.9
11 TraesCS3B01G003200 chr3B 92.000 50 4 0 1645 1694 822869980 822870029 2.370000e-08 71.3
12 TraesCS3B01G003200 chr3B 94.286 35 1 1 1687 1720 44000372 44000338 9.000000e-03 52.8
13 TraesCS3B01G003200 chr3D 90.767 2296 153 31 2482 4741 3223489 3221217 0.000000e+00 3011.0
14 TraesCS3B01G003200 chr3D 84.915 1538 118 47 1 1448 3225534 3224021 0.000000e+00 1450.0
15 TraesCS3B01G003200 chr3D 83.480 1023 131 28 2114 3110 3198305 3197295 0.000000e+00 918.0
16 TraesCS3B01G003200 chr3D 77.476 919 122 48 774 1647 3199353 3198475 5.550000e-129 472.0
17 TraesCS3B01G003200 chr3D 83.621 464 70 6 3283 3745 3197168 3196710 9.430000e-117 431.0
18 TraesCS3B01G003200 chr3D 90.615 309 24 4 1710 2015 3223912 3223606 5.710000e-109 405.0
19 TraesCS3B01G003200 chr3D 77.778 513 93 14 2715 3222 3179927 3179431 3.590000e-76 296.0
20 TraesCS3B01G003200 chr3D 95.098 102 5 0 1554 1655 3224010 3223909 1.370000e-35 161.0
21 TraesCS3B01G003200 chr3D 86.486 111 15 0 2702 2812 3152032 3151922 6.440000e-24 122.0
22 TraesCS3B01G003200 chr3D 89.231 65 5 2 1652 1715 84581511 84581574 3.930000e-11 80.5
23 TraesCS3B01G003200 chr3A 88.508 1166 98 24 3179 4316 398620 397463 0.000000e+00 1378.0
24 TraesCS3B01G003200 chr3A 81.112 1816 249 59 2126 3867 373000 371205 0.000000e+00 1367.0
25 TraesCS3B01G003200 chr3A 87.769 1210 96 28 264 1446 401474 400290 0.000000e+00 1367.0
26 TraesCS3B01G003200 chr3A 94.086 744 39 4 2440 3180 399645 398904 0.000000e+00 1125.0
27 TraesCS3B01G003200 chr3A 92.093 430 30 3 4314 4741 397219 396792 1.890000e-168 603.0
28 TraesCS3B01G003200 chr3A 91.205 307 19 6 1712 2012 400055 399751 1.230000e-110 411.0
29 TraesCS3B01G003200 chr3A 77.542 708 92 41 996 1657 373863 373177 9.700000e-97 364.0
30 TraesCS3B01G003200 chr3A 88.210 229 14 3 1431 1657 400272 400055 1.310000e-65 261.0
31 TraesCS3B01G003200 chr3A 76.071 397 67 17 4199 4578 269882 269497 1.050000e-41 182.0
32 TraesCS3B01G003200 chr3A 85.965 114 16 0 3976 4089 270176 270063 6.440000e-24 122.0
33 TraesCS3B01G003200 chr3A 88.889 54 5 1 1641 1694 8012215 8012163 1.100000e-06 65.8
34 TraesCS3B01G003200 chr3A 100.000 28 0 0 1693 1720 376217695 376217668 9.000000e-03 52.8
35 TraesCS3B01G003200 chr4B 81.092 238 21 16 3632 3861 653428036 653427815 8.160000e-38 169.0
36 TraesCS3B01G003200 chr4B 80.952 210 25 10 3658 3861 653012796 653012996 8.220000e-33 152.0
37 TraesCS3B01G003200 chrUn 80.303 198 29 7 3658 3851 126950718 126950527 1.780000e-29 141.0
38 TraesCS3B01G003200 chr5A 78.974 195 31 9 3671 3861 690565582 690565770 1.790000e-24 124.0
39 TraesCS3B01G003200 chr1D 94.340 53 3 0 1642 1694 404263463 404263515 1.090000e-11 82.4
40 TraesCS3B01G003200 chr1D 100.000 28 0 0 1693 1720 295954236 295954209 9.000000e-03 52.8
41 TraesCS3B01G003200 chr2D 97.674 43 1 0 1652 1694 605638829 605638871 1.830000e-09 75.0
42 TraesCS3B01G003200 chr2B 95.652 46 2 0 1650 1695 764060872 764060827 1.830000e-09 75.0
43 TraesCS3B01G003200 chr1B 87.879 66 2 2 1654 1713 112863355 112863290 6.580000e-09 73.1
44 TraesCS3B01G003200 chr6B 92.000 50 4 0 1645 1694 187829240 187829289 2.370000e-08 71.3
45 TraesCS3B01G003200 chr4D 100.000 28 0 0 1692 1719 317063919 317063946 9.000000e-03 52.8


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 TraesCS3B01G003200 chr3B 2295690 2300430 4740 False 8756.000000 8756 100.000000 1 4741 1 chr3B.!!$F1 4740
1 TraesCS3B01G003200 chr3B 2309400 2311405 2005 False 1402.000000 1402 80.010000 2114 4086 1 chr3B.!!$F2 1972
2 TraesCS3B01G003200 chr3B 2168459 2173428 4969 True 1171.166667 3382 92.857833 1 4741 6 chr3B.!!$R4 4740
3 TraesCS3B01G003200 chr3B 2160670 2163429 2759 True 660.500000 1029 77.953000 996 3730 2 chr3B.!!$R3 2734
4 TraesCS3B01G003200 chr3D 3221217 3225534 4317 True 1256.750000 3011 90.348750 1 4741 4 chr3D.!!$R4 4740
5 TraesCS3B01G003200 chr3D 3196710 3199353 2643 True 607.000000 918 81.525667 774 3745 3 chr3D.!!$R3 2971
6 TraesCS3B01G003200 chr3A 371205 373863 2658 True 865.500000 1367 79.327000 996 3867 2 chr3A.!!$R4 2871
7 TraesCS3B01G003200 chr3A 396792 401474 4682 True 857.500000 1378 90.311833 264 4741 6 chr3A.!!$R5 4477

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
250 257 0.323725 CAACCTAGCCTGGCCACAAT 60.324 55.0 16.57 0.0 0.0 2.71 F
1668 2122 0.110104 ATAGTACTCCCTCCGTCCCG 59.890 60.0 0.00 0.0 0.0 5.14 F
1671 2125 0.394352 GTACTCCCTCCGTCCCGTAA 60.394 60.0 0.00 0.0 0.0 3.18 F
1672 2126 0.552848 TACTCCCTCCGTCCCGTAAT 59.447 55.0 0.00 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 2151 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.0 0.0 4.37 R
3075 3943 3.572255 GGTGTAGAAGATTTTGTGGCCAA 59.428 43.478 7.24 0.0 0.0 4.52 R
3491 4680 5.370880 ACATAAATTCTAGCAGATGGAGGGT 59.629 40.000 0.00 0.0 0.0 4.34 R
3969 5203 3.334691 TCTGAAAATACTCCAGCAACGG 58.665 45.455 0.00 0.0 0.0 4.44 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
27 29 3.354472 TAGAGGCGGGCCGAGAAGA 62.354 63.158 33.44 8.30 41.95 2.87
47 49 2.815647 CGGAAGAGGAACTGCGGC 60.816 66.667 0.00 0.00 41.55 6.53
101 103 1.559682 GAGATGGAGGCCACCAACTAA 59.440 52.381 27.86 5.31 41.83 2.24
169 175 3.480133 CTACGGAGGGCCCCTTGG 61.480 72.222 21.43 8.32 31.76 3.61
186 192 3.274288 CTTGGTGCAAGACCTAGGAATC 58.726 50.000 17.98 3.07 46.32 2.52
190 196 3.307762 GGTGCAAGACCTAGGAATCTGTT 60.308 47.826 17.98 0.00 42.25 3.16
250 257 0.323725 CAACCTAGCCTGGCCACAAT 60.324 55.000 16.57 0.00 0.00 2.71
254 261 2.047061 CCTAGCCTGGCCACAATACTA 58.953 52.381 16.57 0.00 0.00 1.82
310 346 7.931578 TTTAGAAGTATTATTGTGGGGTGTG 57.068 36.000 0.00 0.00 0.00 3.82
312 348 5.253330 AGAAGTATTATTGTGGGGTGTGTG 58.747 41.667 0.00 0.00 0.00 3.82
316 352 2.264005 TATTGTGGGGTGTGTGTGTC 57.736 50.000 0.00 0.00 0.00 3.67
319 355 1.822186 GTGGGGTGTGTGTGTCCAC 60.822 63.158 0.00 0.00 40.63 4.02
384 464 4.373116 TTCCGGCCAGTCTGTCGC 62.373 66.667 2.24 0.00 0.00 5.19
423 519 2.223340 GGCTATTTGATGGTGTTGCTCG 60.223 50.000 0.00 0.00 0.00 5.03
440 537 3.003897 TGCTCGTACAACCACATTTTTCC 59.996 43.478 0.00 0.00 0.00 3.13
457 554 6.678568 TTTTTCCAATCTATGGCAAAAGGA 57.321 33.333 0.00 0.00 45.48 3.36
476 573 0.771127 AACCCAGCTGCTACAAAGGA 59.229 50.000 8.66 0.00 0.00 3.36
484 581 3.960755 AGCTGCTACAAAGGAAAACCTTT 59.039 39.130 0.00 8.23 40.19 3.11
531 632 3.919223 TTTGGTGCGGTGGTAAATTAC 57.081 42.857 0.00 0.00 0.00 1.89
539 640 3.236005 CGGTGGTAAATTACGTTTTGGC 58.764 45.455 0.00 0.00 0.00 4.52
551 652 4.116747 ACGTTTTGGCTGTGAATCAAAA 57.883 36.364 0.00 0.00 37.83 2.44
574 675 3.275999 ACCCGTCGATATTTCCCAAAAG 58.724 45.455 0.00 0.00 0.00 2.27
579 680 6.027749 CCGTCGATATTTCCCAAAAGAAAAG 58.972 40.000 0.00 0.00 39.11 2.27
637 741 0.374758 GCATGCATGTGTACTCACCG 59.625 55.000 26.79 0.00 43.26 4.94
740 1015 5.057149 AGCTACTTAGGCATATTTTCCACG 58.943 41.667 0.00 0.00 0.00 4.94
747 1027 1.676006 GCATATTTTCCACGTCCTGGG 59.324 52.381 0.00 0.00 41.06 4.45
1158 1501 1.918957 ACCTCCCTCATCCCAAAAGAG 59.081 52.381 0.00 0.00 0.00 2.85
1229 1575 6.883744 ACAATTTGTTTCCCTTTTAGCTGAA 58.116 32.000 0.00 0.00 0.00 3.02
1230 1576 7.508687 ACAATTTGTTTCCCTTTTAGCTGAAT 58.491 30.769 0.00 0.00 0.00 2.57
1264 1636 0.979665 AGTTAGCTGCTTCTCTGGCA 59.020 50.000 7.79 0.00 38.10 4.92
1288 1661 7.035004 CACAGAAAAAGGAACAAGATGAACAA 58.965 34.615 0.00 0.00 0.00 2.83
1317 1691 7.308782 AGTATTCTGAAATCTTTTAGTGGCG 57.691 36.000 0.00 0.00 0.00 5.69
1318 1692 7.103641 AGTATTCTGAAATCTTTTAGTGGCGA 58.896 34.615 0.00 0.00 0.00 5.54
1319 1693 5.607119 TTCTGAAATCTTTTAGTGGCGAC 57.393 39.130 0.00 0.00 0.00 5.19
1320 1694 4.894784 TCTGAAATCTTTTAGTGGCGACT 58.105 39.130 6.61 6.61 36.07 4.18
1321 1695 6.032956 TCTGAAATCTTTTAGTGGCGACTA 57.967 37.500 4.24 4.24 33.21 2.59
1322 1696 6.640518 TCTGAAATCTTTTAGTGGCGACTAT 58.359 36.000 9.57 0.00 34.53 2.12
1323 1697 7.778083 TCTGAAATCTTTTAGTGGCGACTATA 58.222 34.615 9.57 2.08 34.53 1.31
1324 1698 8.255206 TCTGAAATCTTTTAGTGGCGACTATAA 58.745 33.333 9.57 10.06 34.53 0.98
1402 1791 8.820831 CCAATTCAGTATCCAGTAGATCCTATT 58.179 37.037 0.00 0.00 36.33 1.73
1433 1824 6.662865 AGTATAGTCCTTCTCATCACATGG 57.337 41.667 0.00 0.00 0.00 3.66
1440 1831 6.328410 AGTCCTTCTCATCACATGGAATATCA 59.672 38.462 0.00 0.00 0.00 2.15
1452 1876 6.654582 CACATGGAATATCATAATCAACGGGA 59.345 38.462 0.00 0.00 0.00 5.14
1471 1895 4.273318 GGGACAAGGCAATTGAGTTCTAT 58.727 43.478 10.34 0.00 41.83 1.98
1502 1934 6.153067 CGGCATTTAGTTTTGTTGGAATGTA 58.847 36.000 0.00 0.00 0.00 2.29
1520 1952 6.096001 GGAATGTATTGCTTTCCTCATGAACT 59.904 38.462 10.83 0.00 43.92 3.01
1521 1953 5.885230 TGTATTGCTTTCCTCATGAACTG 57.115 39.130 0.00 0.00 31.05 3.16
1527 1962 3.755378 GCTTTCCTCATGAACTGTGTGAT 59.245 43.478 0.00 0.00 31.05 3.06
1535 1970 6.053632 TCATGAACTGTGTGATGTAGGAAT 57.946 37.500 0.00 0.00 0.00 3.01
1656 2110 5.244626 ACGTCCAGGTGTACAAAATAGTACT 59.755 40.000 0.00 0.00 43.65 2.73
1657 2111 5.803967 CGTCCAGGTGTACAAAATAGTACTC 59.196 44.000 0.00 2.57 43.65 2.59
1662 2116 5.668471 GGTGTACAAAATAGTACTCCCTCC 58.332 45.833 0.00 0.00 45.84 4.30
1663 2117 5.346522 GTGTACAAAATAGTACTCCCTCCG 58.653 45.833 0.00 0.00 43.65 4.63
1664 2118 5.018809 TGTACAAAATAGTACTCCCTCCGT 58.981 41.667 0.00 0.00 43.65 4.69
1665 2119 4.732672 ACAAAATAGTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
1666 2120 3.450096 ACAAAATAGTACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
1667 2121 2.378378 AATAGTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
1668 2122 0.110104 ATAGTACTCCCTCCGTCCCG 59.890 60.000 0.00 0.00 0.00 5.14
1669 2123 1.274703 TAGTACTCCCTCCGTCCCGT 61.275 60.000 0.00 0.00 0.00 5.28
1670 2124 1.224592 GTACTCCCTCCGTCCCGTA 59.775 63.158 0.00 0.00 0.00 4.02
1671 2125 0.394352 GTACTCCCTCCGTCCCGTAA 60.394 60.000 0.00 0.00 0.00 3.18
1672 2126 0.552848 TACTCCCTCCGTCCCGTAAT 59.447 55.000 0.00 0.00 0.00 1.89
1673 2127 0.552848 ACTCCCTCCGTCCCGTAATA 59.447 55.000 0.00 0.00 0.00 0.98
1674 2128 1.146566 ACTCCCTCCGTCCCGTAATAT 59.853 52.381 0.00 0.00 0.00 1.28
1675 2129 2.376518 ACTCCCTCCGTCCCGTAATATA 59.623 50.000 0.00 0.00 0.00 0.86
1676 2130 3.181429 ACTCCCTCCGTCCCGTAATATAA 60.181 47.826 0.00 0.00 0.00 0.98
1677 2131 3.424703 TCCCTCCGTCCCGTAATATAAG 58.575 50.000 0.00 0.00 0.00 1.73
1678 2132 3.074390 TCCCTCCGTCCCGTAATATAAGA 59.926 47.826 0.00 0.00 0.00 2.10
1679 2133 3.828451 CCCTCCGTCCCGTAATATAAGAA 59.172 47.826 0.00 0.00 0.00 2.52
1680 2134 4.321527 CCCTCCGTCCCGTAATATAAGAAC 60.322 50.000 0.00 0.00 0.00 3.01
1681 2135 4.470462 CTCCGTCCCGTAATATAAGAACG 58.530 47.826 0.00 0.00 36.42 3.95
1682 2136 3.882888 TCCGTCCCGTAATATAAGAACGT 59.117 43.478 0.00 0.00 34.90 3.99
1683 2137 4.338118 TCCGTCCCGTAATATAAGAACGTT 59.662 41.667 0.00 0.00 34.90 3.99
1684 2138 5.043248 CCGTCCCGTAATATAAGAACGTTT 58.957 41.667 0.46 0.00 34.90 3.60
1685 2139 5.519927 CCGTCCCGTAATATAAGAACGTTTT 59.480 40.000 0.46 0.00 34.90 2.43
1686 2140 6.035975 CCGTCCCGTAATATAAGAACGTTTTT 59.964 38.462 9.22 9.22 34.90 1.94
1708 2162 6.862469 TTTATACTATTATGGGACGGAGGG 57.138 41.667 0.00 0.00 0.00 4.30
1709 2163 4.687262 ATACTATTATGGGACGGAGGGA 57.313 45.455 0.00 0.00 0.00 4.20
1710 2164 2.890814 ACTATTATGGGACGGAGGGAG 58.109 52.381 0.00 0.00 0.00 4.30
1783 2308 6.596309 TCTGGCATACTCTGAATATACAGG 57.404 41.667 8.93 0.00 38.31 4.00
1834 2359 6.809689 ACAGTGTCATGTTTGAAATGCATATG 59.190 34.615 0.00 0.00 32.48 1.78
1962 2490 0.908910 TGTGCCTCCATTGGACGTAT 59.091 50.000 0.00 0.00 0.00 3.06
2072 2648 4.667519 ATATGTGACGGAGGGAAAGTAC 57.332 45.455 0.00 0.00 0.00 2.73
2089 2665 9.239551 GGGAAAGTACATTAACTAAAGGTCAAT 57.760 33.333 0.00 0.00 33.36 2.57
2175 2775 9.915629 ATATCTCACTCGTTGAAATTACTATCC 57.084 33.333 0.00 0.00 32.21 2.59
2229 2838 6.346758 CGTACTAGACAGCTAGAAATAGGACG 60.347 46.154 11.55 11.55 45.71 4.79
2321 3033 8.047310 GGATTAAGAACCAACTAAGGATGAAGA 58.953 37.037 0.00 0.00 0.00 2.87
2474 3327 6.145696 GCGTATCAAACTCTTTGTCAAGTAGT 59.854 38.462 0.00 0.00 41.36 2.73
2479 3332 8.420374 TCAAACTCTTTGTCAAGTAGTAACAG 57.580 34.615 3.17 0.00 41.36 3.16
2480 3333 7.494625 TCAAACTCTTTGTCAAGTAGTAACAGG 59.505 37.037 3.17 0.00 41.36 4.00
2492 3345 8.794553 TCAAGTAGTAACAGGAAGTCTAAAGAG 58.205 37.037 0.00 0.00 0.00 2.85
2606 3466 6.696411 AGATCCAGAAAATATAGCTCTTCCG 58.304 40.000 0.00 0.00 0.00 4.30
3075 3943 1.541147 CAATGCCAATCACTCCGTTGT 59.459 47.619 0.00 0.00 0.00 3.32
3107 3975 6.620877 AAATCTTCTACACCATACACTCCA 57.379 37.500 0.00 0.00 0.00 3.86
3191 4345 9.489084 GTTGTATAATATTAGGCACACATGAGA 57.511 33.333 0.00 0.00 0.00 3.27
3255 4411 7.092444 TGTCCATATATATTGGAGGGATTCACC 60.092 40.741 13.65 0.00 43.78 4.02
3437 4624 8.730680 GCTAGATAAAGAGTTTGAAAATGACCA 58.269 33.333 0.00 0.00 0.00 4.02
3491 4680 4.699925 TCCTTTCTTTTTCTCTTCCCGA 57.300 40.909 0.00 0.00 0.00 5.14
3554 4743 5.065602 ACCGTGACTGGAAAAAGTCTTTAAC 59.934 40.000 0.00 0.00 45.69 2.01
3854 5054 0.481128 ACGGGATGGAAACACCCTTT 59.519 50.000 0.00 0.00 46.91 3.11
3920 5136 7.999679 TGATCAATGTATGGAAAAGGATGTTC 58.000 34.615 0.00 0.00 0.00 3.18
3969 5203 0.242017 GGCTGTCATGGCTTGTTGTC 59.758 55.000 0.00 0.00 0.00 3.18
3999 5235 8.514594 TGCTGGAGTATTTTCAGAATAAGTTTG 58.485 33.333 0.00 0.00 0.00 2.93
4073 5309 5.280470 GCCCAAAATTATCCCCAACTTTCTT 60.280 40.000 0.00 0.00 0.00 2.52
4111 5398 9.540538 ACTTCTACTATATGGTCTGCTCAATAT 57.459 33.333 0.00 0.00 0.00 1.28
4239 5526 4.383850 TGAACTTTGTTCCCACAACATG 57.616 40.909 7.81 0.00 42.87 3.21
4328 5870 9.295825 ACAGAAGAAAATACAATATGTGGACAA 57.704 29.630 0.00 0.00 0.00 3.18
4632 6175 2.668212 TTGGCCGAAAGCTCACCG 60.668 61.111 0.00 0.00 43.05 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 29 2.665603 GCAGTTCCTCTTCCGCCT 59.334 61.111 0.00 0.00 0.00 5.52
33 35 2.348998 CCTGCCGCAGTTCCTCTT 59.651 61.111 18.98 0.00 0.00 2.85
47 49 3.682885 TTGCAATGCCGGTGCCTG 61.683 61.111 12.53 2.24 41.49 4.85
101 103 4.754114 TGAAGCAACAAAAACAAACAGCTT 59.246 33.333 0.00 0.00 43.03 3.74
137 139 2.225068 CGTAGGTCATCGGAGCATTT 57.775 50.000 0.00 0.00 43.97 2.32
138 140 3.967886 CGTAGGTCATCGGAGCATT 57.032 52.632 0.00 0.00 43.97 3.56
169 175 3.618690 ACAGATTCCTAGGTCTTGCAC 57.381 47.619 9.08 0.00 0.00 4.57
190 196 2.366301 TTATCGGAGCCCAGCCCA 60.366 61.111 0.00 0.00 0.00 5.36
288 322 6.013206 ACACACACCCCACAATAATACTTCTA 60.013 38.462 0.00 0.00 0.00 2.10
290 324 5.007682 ACACACACCCCACAATAATACTTC 58.992 41.667 0.00 0.00 0.00 3.01
298 334 0.467290 GGACACACACACCCCACAAT 60.467 55.000 0.00 0.00 0.00 2.71
302 338 2.592864 GTGGACACACACACCCCA 59.407 61.111 0.00 0.00 46.90 4.96
341 377 7.015292 AGCTCGAAATGTCCCTGAATATAGTTA 59.985 37.037 0.00 0.00 0.00 2.24
423 519 8.687824 CATAGATTGGAAAAATGTGGTTGTAC 57.312 34.615 0.00 0.00 0.00 2.90
440 537 3.768757 TGGGTTCCTTTTGCCATAGATTG 59.231 43.478 0.00 0.00 0.00 2.67
457 554 0.771127 TCCTTTGTAGCAGCTGGGTT 59.229 50.000 17.12 0.00 0.00 4.11
476 573 9.733556 GAATTATATTTGGTTGGGAAAGGTTTT 57.266 29.630 0.00 0.00 0.00 2.43
484 581 6.256819 TGTGGTGAATTATATTTGGTTGGGA 58.743 36.000 0.00 0.00 0.00 4.37
531 632 5.118510 GGTATTTTGATTCACAGCCAAAACG 59.881 40.000 0.00 0.00 40.94 3.60
539 640 3.930229 TCGACGGGTATTTTGATTCACAG 59.070 43.478 0.00 0.00 0.00 3.66
551 652 4.693042 TTTGGGAAATATCGACGGGTAT 57.307 40.909 0.00 0.00 0.00 2.73
579 680 8.047310 ACCCAGAAATATCCACGAATATTATCC 58.953 37.037 0.00 0.00 32.72 2.59
588 691 1.837439 AGCACCCAGAAATATCCACGA 59.163 47.619 0.00 0.00 0.00 4.35
637 741 9.762933 AAATTATGAAATATATGTGGTTGCACC 57.237 29.630 0.00 0.00 39.22 5.01
677 950 8.140677 ACACTGTATACGAACACTAGAGTATC 57.859 38.462 0.00 0.00 32.71 2.24
696 971 5.835819 AGCTAGATATATGTGTGGACACTGT 59.164 40.000 11.09 3.17 46.55 3.55
698 973 7.235079 AGTAGCTAGATATATGTGTGGACACT 58.765 38.462 11.09 0.33 46.55 3.55
1062 1402 3.282745 CTCCACCACCCTCGTCGTG 62.283 68.421 0.00 0.00 31.52 4.35
1063 1403 2.989824 CTCCACCACCCTCGTCGT 60.990 66.667 0.00 0.00 0.00 4.34
1158 1501 2.038557 TCTTACAGGGTTGGAGAAGTGC 59.961 50.000 0.00 0.00 0.00 4.40
1215 1561 7.147213 TGTCCCATTATATTCAGCTAAAAGGGA 60.147 37.037 0.00 0.00 35.02 4.20
1229 1575 7.016661 AGCAGCTAACTAAGTGTCCCATTATAT 59.983 37.037 0.00 0.00 0.00 0.86
1230 1576 6.326583 AGCAGCTAACTAAGTGTCCCATTATA 59.673 38.462 0.00 0.00 0.00 0.98
1264 1636 6.773976 TGTTCATCTTGTTCCTTTTTCTGT 57.226 33.333 0.00 0.00 0.00 3.41
1318 1692 9.449719 CAACAAACCCTCTTGACTAATTATAGT 57.550 33.333 0.00 0.00 45.10 2.12
1319 1693 9.449719 ACAACAAACCCTCTTGACTAATTATAG 57.550 33.333 0.00 0.00 35.14 1.31
1320 1694 9.226606 CACAACAAACCCTCTTGACTAATTATA 57.773 33.333 0.00 0.00 0.00 0.98
1321 1695 7.724061 ACACAACAAACCCTCTTGACTAATTAT 59.276 33.333 0.00 0.00 0.00 1.28
1322 1696 7.012894 CACACAACAAACCCTCTTGACTAATTA 59.987 37.037 0.00 0.00 0.00 1.40
1323 1697 5.891551 ACACAACAAACCCTCTTGACTAATT 59.108 36.000 0.00 0.00 0.00 1.40
1324 1698 5.299279 CACACAACAAACCCTCTTGACTAAT 59.701 40.000 0.00 0.00 0.00 1.73
1332 1706 7.054124 CCATATATACACACAACAAACCCTCT 58.946 38.462 0.00 0.00 0.00 3.69
1433 1824 6.348540 GCCTTGTCCCGTTGATTATGATATTC 60.349 42.308 0.00 0.00 0.00 1.75
1440 1831 2.799126 TGCCTTGTCCCGTTGATTAT 57.201 45.000 0.00 0.00 0.00 1.28
1452 1876 5.351465 CGTACATAGAACTCAATTGCCTTGT 59.649 40.000 0.00 0.71 36.20 3.16
1471 1895 1.810959 AAACTAAATGCCGCCGTACA 58.189 45.000 0.00 0.00 0.00 2.90
1502 1934 4.022589 CACACAGTTCATGAGGAAAGCAAT 60.023 41.667 0.00 0.00 37.23 3.56
1520 1952 5.012664 AGGTTGTACATTCCTACATCACACA 59.987 40.000 15.59 0.00 0.00 3.72
1521 1953 5.488341 AGGTTGTACATTCCTACATCACAC 58.512 41.667 15.59 0.00 0.00 3.82
1527 1962 9.263446 AGAGTTAATAGGTTGTACATTCCTACA 57.737 33.333 21.68 13.81 36.78 2.74
1573 2015 2.009042 GCTGTCCATCTCAACGGGAAG 61.009 57.143 0.00 0.00 31.32 3.46
1683 2137 7.513436 TCCCTCCGTCCCATAATAGTATAAAAA 59.487 37.037 0.00 0.00 0.00 1.94
1684 2138 7.018150 TCCCTCCGTCCCATAATAGTATAAAA 58.982 38.462 0.00 0.00 0.00 1.52
1685 2139 6.564099 TCCCTCCGTCCCATAATAGTATAAA 58.436 40.000 0.00 0.00 0.00 1.40
1686 2140 6.156554 TCCCTCCGTCCCATAATAGTATAA 57.843 41.667 0.00 0.00 0.00 0.98
1687 2141 5.254737 ACTCCCTCCGTCCCATAATAGTATA 59.745 44.000 0.00 0.00 0.00 1.47
1688 2142 4.045590 ACTCCCTCCGTCCCATAATAGTAT 59.954 45.833 0.00 0.00 0.00 2.12
1689 2143 3.400322 ACTCCCTCCGTCCCATAATAGTA 59.600 47.826 0.00 0.00 0.00 1.82
1690 2144 2.179424 ACTCCCTCCGTCCCATAATAGT 59.821 50.000 0.00 0.00 0.00 2.12
1691 2145 2.890814 ACTCCCTCCGTCCCATAATAG 58.109 52.381 0.00 0.00 0.00 1.73
1692 2146 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
1693 2147 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
1694 2148 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
1695 2149 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
1696 2150 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
1697 2151 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
1698 2152 2.378378 ATTACTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
1699 2153 5.075493 TCAATATTACTACTCCCTCCGTCC 58.925 45.833 0.00 0.00 0.00 4.79
1700 2154 6.645790 TTCAATATTACTACTCCCTCCGTC 57.354 41.667 0.00 0.00 0.00 4.79
1701 2155 6.381994 TGTTTCAATATTACTACTCCCTCCGT 59.618 38.462 0.00 0.00 0.00 4.69
1702 2156 6.812998 TGTTTCAATATTACTACTCCCTCCG 58.187 40.000 0.00 0.00 0.00 4.63
1703 2157 9.930693 CTATGTTTCAATATTACTACTCCCTCC 57.069 37.037 0.00 0.00 0.00 4.30
1783 2308 1.213296 TATCTCCTGGGAACTTGGGC 58.787 55.000 0.00 0.00 0.00 5.36
1841 2367 5.717078 AATGATTCTTGCAAGCTCAGAAA 57.283 34.783 25.60 14.99 0.00 2.52
1845 2371 5.204409 ACAAAATGATTCTTGCAAGCTCA 57.796 34.783 24.57 24.57 0.00 4.26
1962 2490 3.055819 GTGAAGAGCCACATAAGACCTCA 60.056 47.826 0.00 0.00 37.04 3.86
2015 2543 2.865079 ACGGATGTATCTCGATGGAGT 58.135 47.619 4.53 0.00 41.26 3.85
2175 2775 1.890876 TGAGTTCCATTTGTCACCCG 58.109 50.000 0.00 0.00 0.00 5.28
2229 2838 3.910648 ACGGAGTTGTACTTGCTACTTC 58.089 45.455 0.00 0.00 37.78 3.01
2474 3327 7.792364 TGGATTCTCTTTAGACTTCCTGTTA 57.208 36.000 0.00 0.00 36.14 2.41
2479 3332 5.995446 ACCATGGATTCTCTTTAGACTTCC 58.005 41.667 21.47 0.00 35.88 3.46
2480 3333 8.261522 ACTAACCATGGATTCTCTTTAGACTTC 58.738 37.037 21.47 0.00 0.00 3.01
2492 3345 8.561738 TCTCTTGTAAAACTAACCATGGATTC 57.438 34.615 21.47 0.00 0.00 2.52
3075 3943 3.572255 GGTGTAGAAGATTTTGTGGCCAA 59.428 43.478 7.24 0.00 0.00 4.52
3191 4345 7.562135 AGTTATGGTCAAAATGTATACTCGGT 58.438 34.615 4.17 0.00 0.00 4.69
3238 4394 5.472301 ACAAAGGTGAATCCCTCCAATAT 57.528 39.130 0.00 0.00 36.75 1.28
3368 4553 6.785076 TCCCTACATAGAGAGGAATCTACTG 58.215 44.000 0.00 0.00 34.68 2.74
3369 4554 6.795507 TCTCCCTACATAGAGAGGAATCTACT 59.204 42.308 0.00 0.00 34.68 2.57
3437 4624 6.173427 TGTGTGGCACATGTGTATATCTAT 57.827 37.500 24.95 0.00 44.52 1.98
3491 4680 5.370880 ACATAAATTCTAGCAGATGGAGGGT 59.629 40.000 0.00 0.00 0.00 4.34
3969 5203 3.334691 TCTGAAAATACTCCAGCAACGG 58.665 45.455 0.00 0.00 0.00 4.44
3999 5235 8.598924 CCAGAATATCGAGCAATACATGAATAC 58.401 37.037 0.00 0.00 0.00 1.89
4096 5332 9.632638 AATAACTTACAATATTGAGCAGACCAT 57.367 29.630 22.16 0.00 0.00 3.55
4098 5334 9.331282 AGAATAACTTACAATATTGAGCAGACC 57.669 33.333 22.16 3.76 0.00 3.85
4102 5338 9.830975 TGCTAGAATAACTTACAATATTGAGCA 57.169 29.630 22.16 16.84 36.12 4.26
4239 5526 6.205658 ACTTAACTTTCAATCTCAAGGTCTGC 59.794 38.462 0.00 0.00 0.00 4.26
4328 5870 0.179032 TGTTTGACATGACGCCCACT 60.179 50.000 0.00 0.00 0.00 4.00
4632 6175 1.003223 CAAACGGACGTGTTCTTTCCC 60.003 52.381 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.