Multiple sequence alignment - TraesCS6B01G312500

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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 TraesCS6B01G312500 chr6B 100.000 3062 0 0 1 3062 560180200 560183261 0.000000e+00 5655
1 TraesCS6B01G312500 chr6B 94.308 773 36 6 4 771 540604517 540603748 0.000000e+00 1177
2 TraesCS6B01G312500 chr6B 76.715 1108 231 25 1967 3062 94010679 94009587 2.630000e-165 592
3 TraesCS6B01G312500 chr1D 80.493 2312 415 30 771 3061 476594089 476596385 0.000000e+00 1738
4 TraesCS6B01G312500 chr1D 82.249 338 47 12 34 364 356284553 356284222 2.320000e-71 279
5 TraesCS6B01G312500 chr1A 79.016 2297 452 25 771 3047 510526379 510528665 0.000000e+00 1544
6 TraesCS6B01G312500 chr1A 82.498 1377 226 10 1696 3061 12017275 12015903 0.000000e+00 1194
7 TraesCS6B01G312500 chr1A 82.604 937 153 10 771 1701 12026904 12025972 0.000000e+00 819
8 TraesCS6B01G312500 chr1A 78.947 228 35 13 4 223 12575309 12575531 3.180000e-30 143
9 TraesCS6B01G312500 chr2A 78.377 2317 459 37 771 3061 771803791 771801491 0.000000e+00 1465
10 TraesCS6B01G312500 chr6A 81.267 1799 320 13 1274 3061 560579141 560580933 0.000000e+00 1439
11 TraesCS6B01G312500 chr6A 81.250 768 100 22 12 771 500516181 500515450 5.690000e-162 580
12 TraesCS6B01G312500 chr3A 81.914 1609 270 16 771 2365 143489493 143487892 0.000000e+00 1339
13 TraesCS6B01G312500 chr3A 81.613 310 42 13 392 692 471580175 471580478 3.050000e-60 243
14 TraesCS6B01G312500 chr2B 77.355 2314 486 33 771 3061 247600687 247598389 0.000000e+00 1336
15 TraesCS6B01G312500 chr7B 77.955 1066 224 10 2000 3061 497229602 497228544 0.000000e+00 656
16 TraesCS6B01G312500 chr7B 76.176 978 207 24 2098 3062 732586651 732587615 2.740000e-135 492
17 TraesCS6B01G312500 chr6D 83.197 732 97 19 12 734 359009025 359008311 0.000000e+00 647
18 TraesCS6B01G312500 chr6D 77.761 661 97 31 12 652 353101238 353100608 8.070000e-96 361
19 TraesCS6B01G312500 chr4D 79.104 536 73 29 41 552 8198172 8197652 1.760000e-87 333
20 TraesCS6B01G312500 chr7A 78.517 526 80 30 40 552 679823960 679824465 6.370000e-82 315
21 TraesCS6B01G312500 chr5B 74.242 726 182 5 971 1694 399032953 399032231 1.780000e-77 300
22 TraesCS6B01G312500 chr5B 82.203 236 42 0 2824 3059 700302733 700302968 1.440000e-48 204
23 TraesCS6B01G312500 chr7D 84.880 291 37 5 400 686 37424028 37424315 1.390000e-73 287
24 TraesCS6B01G312500 chr7D 81.163 361 53 12 12 365 29310469 29310117 3.010000e-70 276
25 TraesCS6B01G312500 chr7D 82.006 339 44 13 358 685 160658410 160658078 3.890000e-69 272
26 TraesCS6B01G312500 chr3D 81.534 352 54 10 12 358 342811259 342811604 2.320000e-71 279
27 TraesCS6B01G312500 chr3D 80.833 360 57 12 12 363 1649470 1649825 3.890000e-69 272
28 TraesCS6B01G312500 chr5D 81.449 345 54 8 352 689 14744080 14744421 1.080000e-69 274
29 TraesCS6B01G312500 chr2D 80.663 362 55 13 12 364 572259095 572258740 1.810000e-67 267
30 TraesCS6B01G312500 chr2D 81.667 300 45 7 357 647 55317877 55317579 1.100000e-59 241
31 TraesCS6B01G312500 chr2D 78.932 337 57 12 355 683 147424349 147424019 1.850000e-52 217
32 TraesCS6B01G312500 chrUn 79.641 334 51 13 357 681 33903767 33903442 1.100000e-54 224
33 TraesCS6B01G312500 chrUn 79.403 335 50 15 357 681 365856568 365856893 5.140000e-53 219
34 TraesCS6B01G312500 chrUn 81.513 238 44 0 2824 3061 339841407 339841644 2.410000e-46 196
35 TraesCS6B01G312500 chr4A 82.353 238 42 0 2824 3061 620175329 620175566 1.110000e-49 207


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 TraesCS6B01G312500 chr6B 560180200 560183261 3061 False 5655 5655 100.000 1 3062 1 chr6B.!!$F1 3061
1 TraesCS6B01G312500 chr6B 540603748 540604517 769 True 1177 1177 94.308 4 771 1 chr6B.!!$R2 767
2 TraesCS6B01G312500 chr6B 94009587 94010679 1092 True 592 592 76.715 1967 3062 1 chr6B.!!$R1 1095
3 TraesCS6B01G312500 chr1D 476594089 476596385 2296 False 1738 1738 80.493 771 3061 1 chr1D.!!$F1 2290
4 TraesCS6B01G312500 chr1A 510526379 510528665 2286 False 1544 1544 79.016 771 3047 1 chr1A.!!$F2 2276
5 TraesCS6B01G312500 chr1A 12015903 12017275 1372 True 1194 1194 82.498 1696 3061 1 chr1A.!!$R1 1365
6 TraesCS6B01G312500 chr1A 12025972 12026904 932 True 819 819 82.604 771 1701 1 chr1A.!!$R2 930
7 TraesCS6B01G312500 chr2A 771801491 771803791 2300 True 1465 1465 78.377 771 3061 1 chr2A.!!$R1 2290
8 TraesCS6B01G312500 chr6A 560579141 560580933 1792 False 1439 1439 81.267 1274 3061 1 chr6A.!!$F1 1787
9 TraesCS6B01G312500 chr6A 500515450 500516181 731 True 580 580 81.250 12 771 1 chr6A.!!$R1 759
10 TraesCS6B01G312500 chr3A 143487892 143489493 1601 True 1339 1339 81.914 771 2365 1 chr3A.!!$R1 1594
11 TraesCS6B01G312500 chr2B 247598389 247600687 2298 True 1336 1336 77.355 771 3061 1 chr2B.!!$R1 2290
12 TraesCS6B01G312500 chr7B 497228544 497229602 1058 True 656 656 77.955 2000 3061 1 chr7B.!!$R1 1061
13 TraesCS6B01G312500 chr7B 732586651 732587615 964 False 492 492 76.176 2098 3062 1 chr7B.!!$F1 964
14 TraesCS6B01G312500 chr6D 359008311 359009025 714 True 647 647 83.197 12 734 1 chr6D.!!$R2 722
15 TraesCS6B01G312500 chr6D 353100608 353101238 630 True 361 361 77.761 12 652 1 chr6D.!!$R1 640
16 TraesCS6B01G312500 chr4D 8197652 8198172 520 True 333 333 79.104 41 552 1 chr4D.!!$R1 511
17 TraesCS6B01G312500 chr7A 679823960 679824465 505 False 315 315 78.517 40 552 1 chr7A.!!$F1 512
18 TraesCS6B01G312500 chr5B 399032231 399032953 722 True 300 300 74.242 971 1694 1 chr5B.!!$R1 723

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
790 870 0.905337 ACGCTCAGGCTAGGGTTTCT 60.905 55.0 7.52 0.0 39.4 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2567 2666 0.322008 CCTGAGAAGCCCAAGTCCAC 60.322 60.0 0.0 0.0 0.0 4.02 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
93 94 9.491934 AAAATGTTTGCGGTTTTGTATAAAAAC 57.508 25.926 2.81 2.81 39.54 2.43
378 442 2.163818 TGTTCGCCGATTCAAGAGTT 57.836 45.000 0.00 0.00 0.00 3.01
379 443 2.489971 TGTTCGCCGATTCAAGAGTTT 58.510 42.857 0.00 0.00 0.00 2.66
502 581 5.317733 AGTGTCCACGAATTTGAAAAACA 57.682 34.783 0.00 0.00 36.20 2.83
552 631 9.993881 GAGTTTAACAAAATGTTCATGATTTCG 57.006 29.630 0.00 0.00 40.22 3.46
776 856 1.706443 AACAAGTAGCCGTTACGCTC 58.294 50.000 0.00 0.00 40.39 5.03
790 870 0.905337 ACGCTCAGGCTAGGGTTTCT 60.905 55.000 7.52 0.00 39.40 2.52
807 887 3.703001 TTCTTTTCCTCTCTGGCGATT 57.297 42.857 0.00 0.00 35.26 3.34
808 888 4.819105 TTCTTTTCCTCTCTGGCGATTA 57.181 40.909 0.00 0.00 35.26 1.75
809 889 5.359194 TTCTTTTCCTCTCTGGCGATTAT 57.641 39.130 0.00 0.00 35.26 1.28
810 890 4.697514 TCTTTTCCTCTCTGGCGATTATG 58.302 43.478 0.00 0.00 35.26 1.90
833 913 1.608717 CCTGAGAGTTCCCTGTCCGG 61.609 65.000 0.00 0.00 30.77 5.14
842 922 2.115266 CCTGTCCGGCCAAAACCT 59.885 61.111 2.24 0.00 0.00 3.50
844 924 1.971695 CTGTCCGGCCAAAACCTCC 60.972 63.158 2.24 0.00 0.00 4.30
852 933 2.361230 CAAAACCTCCCTCCGGCC 60.361 66.667 0.00 0.00 0.00 6.13
853 934 2.531942 AAAACCTCCCTCCGGCCT 60.532 61.111 0.00 0.00 0.00 5.19
858 940 2.840102 CTCCCTCCGGCCTCGATT 60.840 66.667 0.00 0.00 39.00 3.34
860 942 4.241555 CCCTCCGGCCTCGATTGG 62.242 72.222 0.00 0.00 39.00 3.16
875 957 2.035632 GATTGGGAGATCGAGACCTGT 58.964 52.381 0.00 0.00 0.00 4.00
878 960 1.395826 GGGAGATCGAGACCTGTGGG 61.396 65.000 0.00 0.00 38.88 4.61
893 975 4.250305 GGGTCGTGCCACTGTGGT 62.250 66.667 26.48 0.00 40.46 4.16
894 976 2.665185 GGTCGTGCCACTGTGGTC 60.665 66.667 26.48 18.86 40.46 4.02
895 977 3.036084 GTCGTGCCACTGTGGTCG 61.036 66.667 26.48 26.95 40.46 4.79
915 998 3.702048 TCCTTCCGGCCGACCTTG 61.702 66.667 30.73 9.82 0.00 3.61
920 1003 1.880819 TTCCGGCCGACCTTGTAGAC 61.881 60.000 30.73 0.00 0.00 2.59
921 1004 2.202570 CGGCCGACCTTGTAGACG 60.203 66.667 24.07 0.00 0.00 4.18
922 1005 2.693762 CGGCCGACCTTGTAGACGA 61.694 63.158 24.07 0.00 0.00 4.20
923 1006 1.814527 GGCCGACCTTGTAGACGAT 59.185 57.895 0.00 0.00 0.00 3.73
924 1007 1.027357 GGCCGACCTTGTAGACGATA 58.973 55.000 0.00 0.00 0.00 2.92
992 1077 4.182744 CGGGAGATCGGATCTGGT 57.817 61.111 24.43 1.34 40.38 4.00
993 1078 3.341263 CGGGAGATCGGATCTGGTA 57.659 57.895 24.43 0.00 40.38 3.25
996 1081 2.164338 GGGAGATCGGATCTGGTAGAC 58.836 57.143 24.43 9.11 40.38 2.59
1089 1174 2.435059 GAAGGTGTCCGCTGGCTC 60.435 66.667 0.00 0.00 0.00 4.70
1090 1175 3.240134 GAAGGTGTCCGCTGGCTCA 62.240 63.158 0.00 0.00 0.00 4.26
1117 1202 2.752903 GCCAAGGTTCACACGGATAAAT 59.247 45.455 0.00 0.00 0.00 1.40
1122 1207 6.294508 CCAAGGTTCACACGGATAAATCTTTT 60.295 38.462 0.00 0.00 0.00 2.27
1127 1212 7.333672 GGTTCACACGGATAAATCTTTTAGTCT 59.666 37.037 0.00 0.00 0.00 3.24
1151 1236 3.255888 ACAACGTTCTACAGAGAGATGCA 59.744 43.478 0.00 0.00 31.77 3.96
1176 1261 0.958382 CCTGGAATCCGGCGAAACAA 60.958 55.000 9.30 0.00 0.00 2.83
1181 1266 1.533731 GAATCCGGCGAAACAAGTGAA 59.466 47.619 9.30 0.00 0.00 3.18
1215 1300 0.942252 GACCGAACCTGTTTGTGGTC 59.058 55.000 11.63 11.63 39.10 4.02
1269 1354 1.367346 TGGAACTTGGTCCATGGCTA 58.633 50.000 6.96 0.00 42.97 3.93
1307 1392 0.102300 CTCATGTGCCCATACGACGA 59.898 55.000 0.00 0.00 0.00 4.20
1308 1393 0.179121 TCATGTGCCCATACGACGAC 60.179 55.000 0.00 0.00 0.00 4.34
1320 1405 5.338365 CCATACGACGACTTTACTAAAGCT 58.662 41.667 0.00 0.00 42.27 3.74
1329 1414 6.421202 ACGACTTTACTAAAGCTGAAGAAGTG 59.579 38.462 8.26 2.33 42.27 3.16
1332 1417 3.492102 ACTAAAGCTGAAGAAGTGCCA 57.508 42.857 2.72 0.00 0.00 4.92
1377 1462 2.165437 GCAAATCCATAAACTGCCGGAA 59.835 45.455 5.05 0.00 0.00 4.30
1407 1492 5.875224 TGTAGAAGGAACATTGTGGAATCA 58.125 37.500 0.00 0.00 0.00 2.57
1452 1537 8.904099 AGATTTTAGATATGAGGTTAAACGGG 57.096 34.615 0.00 0.00 0.00 5.28
1459 1544 6.557633 AGATATGAGGTTAAACGGGAATACCT 59.442 38.462 0.00 0.00 41.74 3.08
1464 1549 1.215140 TAAACGGGAATACCTGGGGG 58.785 55.000 0.00 0.00 46.20 5.40
1502 1587 1.270094 GGTTCGTCATGATATCCGCCA 60.270 52.381 0.00 0.00 0.00 5.69
1516 1601 1.362355 CGCCAACCCCTCACAAAAC 59.638 57.895 0.00 0.00 0.00 2.43
1518 1603 1.119684 GCCAACCCCTCACAAAACTT 58.880 50.000 0.00 0.00 0.00 2.66
1538 1623 2.644676 TGTGAGTATCGTCAGAGGAGG 58.355 52.381 0.00 0.00 38.61 4.30
1539 1624 1.335496 GTGAGTATCGTCAGAGGAGGC 59.665 57.143 0.00 0.00 38.61 4.70
1611 1696 0.395586 TATGTGGGCTGATTGGGCAC 60.396 55.000 0.00 0.00 0.00 5.01
1645 1730 1.123077 CGGATCTGGGGTTCATGAGA 58.877 55.000 0.00 0.00 0.00 3.27
1646 1731 1.202580 CGGATCTGGGGTTCATGAGAC 60.203 57.143 0.00 0.00 0.00 3.36
1665 1750 4.936891 AGACAAAAGACATGAAGTTTGGC 58.063 39.130 17.61 15.89 38.94 4.52
1687 1772 2.020694 GCTGGCTGTATGCAGATGGTT 61.021 52.381 15.68 0.00 45.28 3.67
1707 1792 4.260948 GGTTCAAACAGAGCAAGAACTGAG 60.261 45.833 0.00 0.00 38.78 3.35
1715 1800 1.072965 AGCAAGAACTGAGGAGGTTGG 59.927 52.381 0.00 0.00 0.00 3.77
1723 1808 0.471211 TGAGGAGGTTGGTCGAGGTT 60.471 55.000 0.00 0.00 0.00 3.50
1724 1809 0.685660 GAGGAGGTTGGTCGAGGTTT 59.314 55.000 0.00 0.00 0.00 3.27
1737 1822 4.758165 GGTCGAGGTTTTGATAACCAGAAA 59.242 41.667 7.53 0.00 42.69 2.52
1809 1897 1.337384 ACCTGGCCGATACTGCATCA 61.337 55.000 0.00 0.00 32.71 3.07
1816 1904 0.249447 CGATACTGCATCAAGCCCGA 60.249 55.000 0.00 0.00 44.83 5.14
1818 1906 0.833287 ATACTGCATCAAGCCCGACT 59.167 50.000 0.00 0.00 44.83 4.18
1822 1910 0.107703 TGCATCAAGCCCGACTAAGG 60.108 55.000 0.00 0.00 44.83 2.69
1823 1911 0.107654 GCATCAAGCCCGACTAAGGT 60.108 55.000 0.00 0.00 37.23 3.50
1824 1912 1.656652 CATCAAGCCCGACTAAGGTG 58.343 55.000 0.00 0.00 0.00 4.00
1825 1913 1.066143 CATCAAGCCCGACTAAGGTGT 60.066 52.381 0.00 0.00 0.00 4.16
1829 1917 1.861982 AGCCCGACTAAGGTGTGTAT 58.138 50.000 0.00 0.00 0.00 2.29
1836 1924 3.181489 CGACTAAGGTGTGTATCAGGGAC 60.181 52.174 0.00 0.00 0.00 4.46
1843 1931 2.093500 GTGTGTATCAGGGACATGCAGA 60.093 50.000 0.00 0.00 0.00 4.26
1889 1981 2.224281 TGGCTATGGATAGTTCGCAAGG 60.224 50.000 0.00 0.00 33.20 3.61
1913 2005 4.177026 CAGCCTAGCACAACAACTACTAG 58.823 47.826 0.00 0.00 0.00 2.57
1946 2038 1.475403 CAAGGGCTAGGAGAAGACGA 58.525 55.000 0.00 0.00 0.00 4.20
1949 2041 1.063567 AGGGCTAGGAGAAGACGATGT 60.064 52.381 0.00 0.00 0.00 3.06
1962 2057 2.893398 GATGTTCCCTCGTCGCCT 59.107 61.111 0.00 0.00 0.00 5.52
1998 2093 6.715347 AACAGTAAGAAGGCAAAGTTTGAT 57.285 33.333 19.82 3.90 0.00 2.57
2009 2104 4.301628 GCAAAGTTTGATTCCCAAGAGTG 58.698 43.478 19.82 0.00 35.94 3.51
2153 2252 1.506028 TTCCCCGGGGCTGATTTTCT 61.506 55.000 36.68 0.00 34.68 2.52
2245 2344 1.453155 GTGTATCCAGTGTTGGCCTG 58.547 55.000 3.32 0.00 44.63 4.85
2260 2359 3.007920 CTGAGTGGAGGGCTGGCT 61.008 66.667 0.00 0.00 0.00 4.75
2272 2371 1.527433 GGCTGGCTCTGTTTTGGGAC 61.527 60.000 0.00 0.00 0.00 4.46
2275 2374 0.400213 TGGCTCTGTTTTGGGACGAT 59.600 50.000 0.00 0.00 0.00 3.73
2284 2383 5.046159 TCTGTTTTGGGACGATAACCTACAT 60.046 40.000 0.00 0.00 0.00 2.29
2303 2402 1.812235 TGTAACCGTGCTCGACTCTA 58.188 50.000 10.21 0.00 39.71 2.43
2308 2407 1.226435 CGTGCTCGACTCTAGTGCC 60.226 63.158 1.00 0.00 39.71 5.01
2313 2412 1.178276 CTCGACTCTAGTGCCAGGTT 58.822 55.000 0.00 0.00 0.00 3.50
2317 2416 3.380637 TCGACTCTAGTGCCAGGTTTATC 59.619 47.826 0.00 0.00 0.00 1.75
2340 2439 5.469760 TCGATGTGAGAATTGTTGACAATGT 59.530 36.000 9.90 1.58 45.06 2.71
2341 2440 6.648725 TCGATGTGAGAATTGTTGACAATGTA 59.351 34.615 9.90 0.00 45.06 2.29
2362 2461 4.983671 AAGTGACAAAACTTGGAGAACC 57.016 40.909 0.00 0.00 38.95 3.62
2365 2464 3.442273 GTGACAAAACTTGGAGAACCACA 59.558 43.478 0.00 0.00 46.80 4.17
2403 2502 3.468063 GGTGGAGAACCGTCACCT 58.532 61.111 0.00 0.00 45.36 4.00
2414 2513 2.811410 ACCGTCACCTTATGTGGAGTA 58.189 47.619 0.00 0.00 45.48 2.59
2504 2603 2.302733 TGGCAGCATGAACACTTCTCTA 59.697 45.455 0.00 0.00 39.69 2.43
2533 2632 3.138304 TCGGTCTGAGAACCAAATGTTG 58.862 45.455 0.00 0.00 39.43 3.33
2545 2644 3.823873 ACCAAATGTTGCTATTCCGTGAA 59.176 39.130 0.00 0.00 0.00 3.18
2565 2664 1.538047 TGCTTGGAAGATTGTGAGCC 58.462 50.000 0.00 0.00 0.00 4.70
2567 2666 1.089920 CTTGGAAGATTGTGAGCCGG 58.910 55.000 0.00 0.00 0.00 6.13
2605 2704 4.137543 CAGGAGCCCCTTTTACATATGAC 58.862 47.826 10.38 0.00 42.02 3.06
2641 2740 1.069513 ACAAGGAATGTTCGTGTCCGA 59.930 47.619 0.00 0.00 40.06 4.55
2671 2770 1.795768 CCTGTGCAGACGAAGCTTTA 58.204 50.000 0.00 0.00 0.00 1.85
2674 2773 3.003275 CCTGTGCAGACGAAGCTTTAAAA 59.997 43.478 0.00 0.00 0.00 1.52
2677 2776 4.515191 TGTGCAGACGAAGCTTTAAAAGAT 59.485 37.500 0.00 0.00 0.00 2.40
2737 2836 1.598962 CTCCGATCATGCGCCCATT 60.599 57.895 4.18 0.00 0.00 3.16
2782 2881 2.676839 ACCACGACGTACTCAGAGTATG 59.323 50.000 23.33 23.33 42.07 2.39
2797 2896 6.705302 TCAGAGTATGCCCAGATATGAAATC 58.295 40.000 0.00 0.00 0.00 2.17
2807 2906 6.014647 CCCAGATATGAAATCATGTGGGAAT 58.985 40.000 23.27 4.74 46.00 3.01
2862 2961 1.479730 CTGGGGTAGGAGTAAACCGAC 59.520 57.143 0.00 0.00 36.57 4.79
2873 2972 1.756408 TAAACCGACCGGGCACTTGA 61.756 55.000 8.76 0.00 40.62 3.02
2874 2973 2.612095 AAACCGACCGGGCACTTGAA 62.612 55.000 8.76 0.00 40.62 2.69
2907 3006 3.908643 TGCTCTCAAAGAGATGATGCT 57.091 42.857 8.14 0.00 45.07 3.79
2920 3019 3.100862 GATGCTTCGGTTGCGAGCC 62.101 63.158 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
502 581 5.156355 GTGCACATCTTTGAAATCGTGAAT 58.844 37.500 13.17 0.00 0.00 2.57
586 665 4.343814 TCCTGCATCACCGAGATACATTAA 59.656 41.667 0.00 0.00 34.43 1.40
643 722 4.340950 CCCTTACTTGCAACAGGAGAAAAA 59.659 41.667 13.90 0.00 0.00 1.94
776 856 3.009584 AGAGGAAAAGAAACCCTAGCCTG 59.990 47.826 0.00 0.00 0.00 4.85
790 870 4.442706 GACATAATCGCCAGAGAGGAAAA 58.557 43.478 0.00 0.00 41.22 2.29
807 887 1.112113 GGGAACTCTCAGGCGACATA 58.888 55.000 0.00 0.00 0.00 2.29
808 888 0.616111 AGGGAACTCTCAGGCGACAT 60.616 55.000 0.00 0.00 32.90 3.06
809 889 1.228894 AGGGAACTCTCAGGCGACA 60.229 57.895 0.00 0.00 32.90 4.35
810 890 1.216710 CAGGGAACTCTCAGGCGAC 59.783 63.158 0.00 0.00 40.21 5.19
858 940 0.684479 CCACAGGTCTCGATCTCCCA 60.684 60.000 0.00 0.00 0.00 4.37
860 942 0.684805 ACCCACAGGTCTCGATCTCC 60.685 60.000 0.00 0.00 46.45 3.71
875 957 4.248842 CCACAGTGGCACGACCCA 62.249 66.667 12.71 0.00 37.83 4.51
878 960 3.036084 CGACCACAGTGGCACGAC 61.036 66.667 26.06 11.04 42.67 4.34
909 992 4.686554 GCCATCAATATCGTCTACAAGGTC 59.313 45.833 0.00 0.00 0.00 3.85
910 993 4.632153 GCCATCAATATCGTCTACAAGGT 58.368 43.478 0.00 0.00 0.00 3.50
911 994 3.675225 CGCCATCAATATCGTCTACAAGG 59.325 47.826 0.00 0.00 0.00 3.61
915 998 3.570926 TCCGCCATCAATATCGTCTAC 57.429 47.619 0.00 0.00 0.00 2.59
920 1003 1.730501 AGCATCCGCCATCAATATCG 58.269 50.000 0.00 0.00 39.83 2.92
921 1004 4.194640 ACATAGCATCCGCCATCAATATC 58.805 43.478 0.00 0.00 39.83 1.63
922 1005 4.194640 GACATAGCATCCGCCATCAATAT 58.805 43.478 0.00 0.00 39.83 1.28
923 1006 3.599343 GACATAGCATCCGCCATCAATA 58.401 45.455 0.00 0.00 39.83 1.90
924 1007 2.430465 GACATAGCATCCGCCATCAAT 58.570 47.619 0.00 0.00 39.83 2.57
978 1063 4.138290 TGAAGTCTACCAGATCCGATCTC 58.862 47.826 8.00 0.00 37.58 2.75
992 1077 2.460669 TGAGCTGCTCCATGAAGTCTA 58.539 47.619 25.61 1.03 0.00 2.59
993 1078 1.273759 TGAGCTGCTCCATGAAGTCT 58.726 50.000 25.61 0.00 0.00 3.24
996 1081 1.093159 GGTTGAGCTGCTCCATGAAG 58.907 55.000 25.61 0.00 0.00 3.02
1044 1129 4.819610 TCACAGGATCATCCTCCTCAATA 58.180 43.478 1.94 0.00 45.66 1.90
1071 1156 4.379243 AGCCAGCGGACACCTTCG 62.379 66.667 0.00 0.00 0.00 3.79
1089 1174 0.400213 TGTGAACCTTGGCTAGGGTG 59.600 55.000 19.14 0.00 46.92 4.61
1098 1183 5.880054 AAGATTTATCCGTGTGAACCTTG 57.120 39.130 0.00 0.00 0.00 3.61
1100 1185 7.166167 ACTAAAAGATTTATCCGTGTGAACCT 58.834 34.615 0.00 0.00 0.00 3.50
1117 1202 6.798482 TGTAGAACGTTGTCAGACTAAAAGA 58.202 36.000 5.00 0.00 0.00 2.52
1122 1207 5.303165 TCTCTGTAGAACGTTGTCAGACTA 58.697 41.667 5.00 0.00 32.77 2.59
1127 1212 4.616143 GCATCTCTCTGTAGAACGTTGTCA 60.616 45.833 5.00 1.37 0.00 3.58
1176 1261 1.578583 CGACGGGTTTGAACTTCACT 58.421 50.000 0.00 0.00 0.00 3.41
1181 1266 1.070275 GGTCCGACGGGTTTGAACT 59.930 57.895 15.25 0.00 33.83 3.01
1269 1354 5.779241 TGAGAACTACCCAATTCCTGAAT 57.221 39.130 0.00 0.00 0.00 2.57
1307 1392 5.470437 GGCACTTCTTCAGCTTTAGTAAAGT 59.530 40.000 20.95 7.88 40.64 2.66
1308 1393 5.470098 TGGCACTTCTTCAGCTTTAGTAAAG 59.530 40.000 16.87 16.87 41.46 1.85
1320 1405 4.334552 TGAATAGCATTGGCACTTCTTCA 58.665 39.130 0.00 0.00 44.61 3.02
1329 1414 2.894763 TTGGCATGAATAGCATTGGC 57.105 45.000 0.00 0.00 34.15 4.52
1332 1417 5.362105 ACCAAATTGGCATGAATAGCATT 57.638 34.783 12.67 0.00 42.67 3.56
1377 1462 5.301805 CACAATGTTCCTTCTACAAAACCCT 59.698 40.000 0.00 0.00 0.00 4.34
1389 1474 5.707298 CAGTAGTGATTCCACAATGTTCCTT 59.293 40.000 0.00 0.00 45.54 3.36
1419 1504 7.028131 ACCTCATATCTAAAATCTCCCCAGAT 58.972 38.462 0.00 0.00 41.59 2.90
1434 1519 6.557633 AGGTATTCCCGTTTAACCTCATATCT 59.442 38.462 0.00 0.00 35.67 1.98
1464 1549 2.760581 ACCCTAACCCTCACATAGTCC 58.239 52.381 0.00 0.00 0.00 3.85
1516 1601 3.066064 CCTCCTCTGACGATACTCACAAG 59.934 52.174 0.00 0.00 0.00 3.16
1518 1603 2.644676 CCTCCTCTGACGATACTCACA 58.355 52.381 0.00 0.00 0.00 3.58
1538 1623 1.080705 AAGTACACCTGTCTCGCGC 60.081 57.895 0.00 0.00 0.00 6.86
1539 1624 0.732880 CCAAGTACACCTGTCTCGCG 60.733 60.000 0.00 0.00 0.00 5.87
1593 1678 1.683365 GTGCCCAATCAGCCCACAT 60.683 57.895 0.00 0.00 0.00 3.21
1599 1684 1.448985 TAAAGTCGTGCCCAATCAGC 58.551 50.000 0.00 0.00 0.00 4.26
1611 1696 2.159226 AGATCCGCACTCCTTAAAGTCG 60.159 50.000 0.00 0.00 0.00 4.18
1645 1730 4.685924 CTGCCAAACTTCATGTCTTTTGT 58.314 39.130 11.84 0.00 0.00 2.83
1646 1731 3.492011 GCTGCCAAACTTCATGTCTTTTG 59.508 43.478 0.00 1.05 0.00 2.44
1687 1772 3.134623 TCCTCAGTTCTTGCTCTGTTTGA 59.865 43.478 0.00 0.00 33.89 2.69
1707 1792 1.202722 TCAAAACCTCGACCAACCTCC 60.203 52.381 0.00 0.00 0.00 4.30
1715 1800 5.237779 TGTTTCTGGTTATCAAAACCTCGAC 59.762 40.000 8.29 3.44 40.88 4.20
1723 1808 3.888323 TGCTGCTGTTTCTGGTTATCAAA 59.112 39.130 0.00 0.00 0.00 2.69
1724 1809 3.485394 TGCTGCTGTTTCTGGTTATCAA 58.515 40.909 0.00 0.00 0.00 2.57
1737 1822 2.262915 GGAGTACGCTGCTGCTGT 59.737 61.111 14.03 14.50 36.97 4.40
1792 1880 1.224075 CTTGATGCAGTATCGGCCAG 58.776 55.000 2.24 0.00 38.71 4.85
1809 1897 1.636148 TACACACCTTAGTCGGGCTT 58.364 50.000 0.00 0.00 0.00 4.35
1816 1904 3.786553 TGTCCCTGATACACACCTTAGT 58.213 45.455 0.00 0.00 0.00 2.24
1818 1906 3.118408 GCATGTCCCTGATACACACCTTA 60.118 47.826 0.00 0.00 0.00 2.69
1822 1910 2.093500 TCTGCATGTCCCTGATACACAC 60.093 50.000 0.00 0.00 0.00 3.82
1823 1911 2.187100 TCTGCATGTCCCTGATACACA 58.813 47.619 0.00 0.00 0.00 3.72
1824 1912 2.988010 TCTGCATGTCCCTGATACAC 57.012 50.000 0.00 0.00 0.00 2.90
1825 1913 2.036346 CGATCTGCATGTCCCTGATACA 59.964 50.000 0.00 0.00 0.00 2.29
1829 1917 0.461548 GTCGATCTGCATGTCCCTGA 59.538 55.000 0.00 0.00 0.00 3.86
1889 1981 1.884235 AGTTGTTGTGCTAGGCTGTC 58.116 50.000 0.00 0.00 0.00 3.51
1892 1984 3.833070 ACTAGTAGTTGTTGTGCTAGGCT 59.167 43.478 0.00 0.00 34.94 4.58
1913 2005 1.950954 GCCCTTGGGTCAGAGCTAAAC 60.951 57.143 7.61 0.00 0.00 2.01
1946 2038 2.017559 GCTAGGCGACGAGGGAACAT 62.018 60.000 0.00 0.00 33.10 2.71
1949 2041 1.980232 TTGCTAGGCGACGAGGGAA 60.980 57.895 0.00 0.00 33.10 3.97
1998 2093 1.974957 TCATCCGAACACTCTTGGGAA 59.025 47.619 0.00 0.00 30.18 3.97
2009 2104 1.618861 CGCCGATCTATCATCCGAAC 58.381 55.000 0.00 0.00 0.00 3.95
2096 2195 2.285083 CAAAACCTCACGAACTGTCCA 58.715 47.619 0.00 0.00 0.00 4.02
2153 2252 4.220821 AGAGGCTTGACGAGTTTCTGATAA 59.779 41.667 0.00 0.00 0.00 1.75
2245 2344 2.686835 AGAGCCAGCCCTCCACTC 60.687 66.667 0.00 0.00 32.17 3.51
2257 2356 2.396590 TATCGTCCCAAAACAGAGCC 57.603 50.000 0.00 0.00 0.00 4.70
2260 2359 4.283978 TGTAGGTTATCGTCCCAAAACAGA 59.716 41.667 0.00 0.00 0.00 3.41
2272 2371 3.488310 GCACGGTTACATGTAGGTTATCG 59.512 47.826 5.56 6.06 0.00 2.92
2275 2374 3.427909 CGAGCACGGTTACATGTAGGTTA 60.428 47.826 5.56 0.00 35.72 2.85
2284 2383 1.736126 CTAGAGTCGAGCACGGTTACA 59.264 52.381 3.11 0.00 40.21 2.41
2303 2402 2.236146 TCACATCGATAAACCTGGCACT 59.764 45.455 0.00 0.00 0.00 4.40
2308 2407 6.668541 ACAATTCTCACATCGATAAACCTG 57.331 37.500 0.00 0.00 0.00 4.00
2313 2412 7.665561 TTGTCAACAATTCTCACATCGATAA 57.334 32.000 0.00 0.00 0.00 1.75
2317 2416 5.692814 ACATTGTCAACAATTCTCACATCG 58.307 37.500 5.64 0.00 43.48 3.84
2340 2439 5.355910 GTGGTTCTCCAAGTTTTGTCACTTA 59.644 40.000 0.00 0.00 46.15 2.24
2341 2440 4.157840 GTGGTTCTCCAAGTTTTGTCACTT 59.842 41.667 0.00 0.00 46.15 3.16
2362 2461 3.118364 TGGTTCACCGTACACGAATGTG 61.118 50.000 2.76 3.53 45.13 3.21
2365 2464 2.409975 CTTGGTTCACCGTACACGAAT 58.590 47.619 2.76 0.00 43.02 3.34
2403 2502 6.010850 AGACTTGACAGAGTACTCCACATAA 58.989 40.000 19.38 7.90 0.00 1.90
2414 2513 0.889306 GCCCGTAGACTTGACAGAGT 59.111 55.000 0.00 0.00 0.00 3.24
2504 2603 2.752238 CTCAGACCGAGGCGACCT 60.752 66.667 0.00 0.00 38.18 3.85
2531 2630 2.423185 CCAAGCATTCACGGAATAGCAA 59.577 45.455 15.72 0.00 32.65 3.91
2533 2632 2.288666 TCCAAGCATTCACGGAATAGC 58.711 47.619 0.00 6.10 30.44 2.97
2545 2644 2.097825 GGCTCACAATCTTCCAAGCAT 58.902 47.619 0.00 0.00 0.00 3.79
2565 2664 1.376037 GAGAAGCCCAAGTCCACCG 60.376 63.158 0.00 0.00 0.00 4.94
2567 2666 0.322008 CCTGAGAAGCCCAAGTCCAC 60.322 60.000 0.00 0.00 0.00 4.02
2605 2704 3.573538 TCCTTGTTCCATGTTGTCCATTG 59.426 43.478 0.00 0.00 0.00 2.82
2638 2737 4.087892 CAGGCCCTGTCCAGTCGG 62.088 72.222 1.39 0.00 0.00 4.79
2641 2740 3.958860 GCACAGGCCCTGTCCAGT 61.959 66.667 15.03 0.00 43.43 4.00
2653 2752 3.878086 TTTAAAGCTTCGTCTGCACAG 57.122 42.857 0.00 0.00 0.00 3.66
2659 2758 7.065923 GGGAACATATCTTTTAAAGCTTCGTCT 59.934 37.037 0.00 0.00 0.00 4.18
2671 2770 3.672241 GCGCAAACGGGAACATATCTTTT 60.672 43.478 0.30 0.00 40.57 2.27
2674 2773 1.014352 GCGCAAACGGGAACATATCT 58.986 50.000 0.30 0.00 40.57 1.98
2677 2776 0.519519 CTTGCGCAAACGGGAACATA 59.480 50.000 25.01 0.00 40.57 2.29
2782 2881 3.508793 CCCACATGATTTCATATCTGGGC 59.491 47.826 0.00 0.00 37.66 5.36
2797 2896 1.000739 AGGGTGCCATTCCCACATG 59.999 57.895 3.79 0.00 46.82 3.21
2850 2949 2.125391 GCCCGGTCGGTTTACTCC 60.125 66.667 8.67 0.00 0.00 3.85
2862 2961 1.674322 ACCGAATTCAAGTGCCCGG 60.674 57.895 6.22 0.00 42.30 5.73
2883 2982 4.744259 GCATCATCTCTTTGAGAGCATCCT 60.744 45.833 3.64 0.00 42.26 3.24
2893 2992 3.730061 GCAACCGAAGCATCATCTCTTTG 60.730 47.826 0.00 0.00 0.00 2.77
2907 3006 3.589654 CTCCAGGCTCGCAACCGAA 62.590 63.158 0.00 0.00 43.87 4.30
2920 3019 2.544486 GCCAAAGTTTGACTTGCTCCAG 60.544 50.000 17.33 0.00 38.66 3.86
2930 3029 3.005684 GTCATGACATGGCCAAAGTTTGA 59.994 43.478 21.07 15.32 0.00 2.69
2995 3094 2.821366 GCCCTGTCTGCGTCATGG 60.821 66.667 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.