Multiple sequence alignment - TraesCS3D01G002900

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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 TraesCS3D01G002900 chr3D 100.000 3604 0 0 1 3604 1278506 1282109 0.000000e+00 6656.0
1 TraesCS3D01G002900 chr3D 90.625 704 56 5 2198 2897 1287927 1288624 0.000000e+00 926.0
2 TraesCS3D01G002900 chr3D 74.138 290 63 11 1110 1390 456641437 456641723 3.800000e-20 110.0
3 TraesCS3D01G002900 chr3A 91.506 1507 72 24 6 1494 7792560 7791092 0.000000e+00 2023.0
4 TraesCS3D01G002900 chr3A 88.651 1542 118 24 1578 3101 7790650 7789148 0.000000e+00 1825.0
5 TraesCS3D01G002900 chr3A 74.828 290 61 10 1110 1390 599528627 599528913 1.760000e-23 121.0
6 TraesCS3D01G002900 chrUn 92.176 1112 60 12 1574 2680 281635851 281634762 0.000000e+00 1546.0
7 TraesCS3D01G002900 chrUn 92.176 1112 60 12 1574 2680 281642725 281641636 0.000000e+00 1546.0
8 TraesCS3D01G002900 chrUn 92.176 1112 60 12 1574 2680 312315709 312314620 0.000000e+00 1546.0
9 TraesCS3D01G002900 chrUn 88.842 950 46 24 573 1494 281636947 281636030 0.000000e+00 1112.0
10 TraesCS3D01G002900 chrUn 88.842 950 46 24 573 1494 281643821 281642904 0.000000e+00 1112.0
11 TraesCS3D01G002900 chrUn 88.842 950 46 24 573 1494 312316805 312315888 0.000000e+00 1112.0
12 TraesCS3D01G002900 chrUn 87.755 196 21 3 2801 2996 281634765 281634573 3.620000e-55 226.0
13 TraesCS3D01G002900 chrUn 87.755 196 21 3 2801 2996 281641639 281641447 3.620000e-55 226.0
14 TraesCS3D01G002900 chrUn 87.755 196 21 3 2801 2996 312314623 312314431 3.620000e-55 226.0
15 TraesCS3D01G002900 chrUn 92.105 114 8 1 2996 3108 281633226 281633113 3.720000e-35 159.0
16 TraesCS3D01G002900 chrUn 92.105 114 8 1 2996 3108 281640102 281639989 3.720000e-35 159.0
17 TraesCS3D01G002900 chrUn 92.105 114 8 1 2996 3108 328118963 328118850 3.720000e-35 159.0
18 TraesCS3D01G002900 chr4D 94.892 509 23 2 3099 3604 502728496 502729004 0.000000e+00 793.0
19 TraesCS3D01G002900 chr4D 93.898 508 24 3 3103 3604 481889345 481888839 0.000000e+00 760.0
20 TraesCS3D01G002900 chr2D 92.927 509 30 1 3102 3604 350068327 350067819 0.000000e+00 736.0
21 TraesCS3D01G002900 chr2D 92.607 514 27 5 3097 3604 16248285 16248793 0.000000e+00 728.0
22 TraesCS3D01G002900 chr2D 92.578 512 29 2 3102 3604 50128130 50128641 0.000000e+00 726.0
23 TraesCS3D01G002900 chr2D 92.070 517 32 5 3094 3602 500589633 500590148 0.000000e+00 719.0
24 TraesCS3D01G002900 chr2B 92.607 514 26 4 3099 3600 394126860 394127373 0.000000e+00 728.0
25 TraesCS3D01G002900 chr2B 75.916 191 40 6 1 187 18117557 18117745 3.830000e-15 93.5
26 TraesCS3D01G002900 chr1D 92.593 513 28 7 3102 3604 254797674 254797162 0.000000e+00 728.0
27 TraesCS3D01G002900 chr6D 92.442 516 28 6 3098 3604 325416553 325417066 0.000000e+00 726.0
28 TraesCS3D01G002900 chr6D 82.550 298 43 7 1105 1396 140156115 140155821 1.660000e-63 254.0
29 TraesCS3D01G002900 chr6D 74.127 487 100 17 10 479 9789762 9790239 1.030000e-40 178.0
30 TraesCS3D01G002900 chr7D 82.373 295 43 7 1105 1396 498495988 498496276 7.730000e-62 248.0
31 TraesCS3D01G002900 chr7D 77.350 234 43 7 247 476 603726637 603726864 2.920000e-26 130.0
32 TraesCS3D01G002900 chr7D 82.075 106 18 1 361 466 63561265 63561369 4.960000e-14 89.8
33 TraesCS3D01G002900 chr6B 82.274 299 42 9 1105 1396 240250360 240250066 7.730000e-62 248.0
34 TraesCS3D01G002900 chr5D 76.471 289 60 5 246 532 464564126 464564408 2.240000e-32 150.0
35 TraesCS3D01G002900 chr5D 78.231 147 29 2 1101 1244 564929344 564929490 1.380000e-14 91.6
36 TraesCS3D01G002900 chr5B 78.243 239 44 5 248 482 626168405 626168639 2.900000e-31 147.0
37 TraesCS3D01G002900 chr5B 78.243 239 44 5 248 482 626179804 626180038 2.900000e-31 147.0
38 TraesCS3D01G002900 chr5B 79.141 163 30 3 335 493 228817365 228817527 3.800000e-20 110.0
39 TraesCS3D01G002900 chr6A 74.884 215 40 9 244 458 476003268 476003068 6.410000e-13 86.1
40 TraesCS3D01G002900 chr4A 76.351 148 30 4 1101 1244 606370520 606370666 1.390000e-09 75.0


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 TraesCS3D01G002900 chr3D 1278506 1282109 3603 False 6656.000000 6656 100.0000 1 3604 1 chr3D.!!$F1 3603
1 TraesCS3D01G002900 chr3D 1287927 1288624 697 False 926.000000 926 90.6250 2198 2897 1 chr3D.!!$F2 699
2 TraesCS3D01G002900 chr3A 7789148 7792560 3412 True 1924.000000 2023 90.0785 6 3101 2 chr3A.!!$R1 3095
3 TraesCS3D01G002900 chrUn 312314431 312316805 2374 True 961.333333 1546 89.5910 573 2996 3 chrUn.!!$R3 2423
4 TraesCS3D01G002900 chrUn 281633113 281643821 10708 True 760.750000 1546 90.2195 573 3108 8 chrUn.!!$R2 2535
5 TraesCS3D01G002900 chr4D 502728496 502729004 508 False 793.000000 793 94.8920 3099 3604 1 chr4D.!!$F1 505
6 TraesCS3D01G002900 chr4D 481888839 481889345 506 True 760.000000 760 93.8980 3103 3604 1 chr4D.!!$R1 501
7 TraesCS3D01G002900 chr2D 350067819 350068327 508 True 736.000000 736 92.9270 3102 3604 1 chr2D.!!$R1 502
8 TraesCS3D01G002900 chr2D 16248285 16248793 508 False 728.000000 728 92.6070 3097 3604 1 chr2D.!!$F1 507
9 TraesCS3D01G002900 chr2D 50128130 50128641 511 False 726.000000 726 92.5780 3102 3604 1 chr2D.!!$F2 502
10 TraesCS3D01G002900 chr2D 500589633 500590148 515 False 719.000000 719 92.0700 3094 3602 1 chr2D.!!$F3 508
11 TraesCS3D01G002900 chr2B 394126860 394127373 513 False 728.000000 728 92.6070 3099 3600 1 chr2B.!!$F2 501
12 TraesCS3D01G002900 chr1D 254797162 254797674 512 True 728.000000 728 92.5930 3102 3604 1 chr1D.!!$R1 502
13 TraesCS3D01G002900 chr6D 325416553 325417066 513 False 726.000000 726 92.4420 3098 3604 1 chr6D.!!$F2 506

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
905 7805 0.101579 CCGTCAACCAACCAACCAAC 59.898 55.000 0.00 0.00 0.00 3.77 F
981 7881 0.237761 CAGCAGCAGCACAGAAGTTC 59.762 55.000 3.17 0.00 45.49 3.01 F
993 7897 0.387878 AGAAGTTCGCTGCGTCTCTG 60.388 55.000 22.48 0.00 0.00 3.35 F
1467 8372 1.004044 AGCTGCTGCAGAAATACCAGT 59.996 47.619 32.30 2.41 42.74 4.00 F
2066 9351 0.250124 TCGGCACCAACGACTTCATT 60.250 50.000 0.00 0.00 35.12 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 9193 0.028242 GACTGCGTCGTCGAGATCAT 59.972 55.0 6.17 0.00 39.71 2.45 R
1915 9200 0.096454 TATCACTGACTGCGTCGTCG 59.904 55.0 0.00 0.00 36.71 5.12 R
1917 9202 0.170561 GGTATCACTGACTGCGTCGT 59.829 55.0 0.00 3.43 34.95 4.34 R
2444 9729 0.252558 ACCCCATCTCGTACAACCCT 60.253 55.0 0.00 0.00 0.00 4.34 R
3231 11874 1.076332 GGTCGGAAATGGTTGTCTCG 58.924 55.0 0.00 0.00 0.00 4.04 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
22 23 2.190488 CTTGAAAGCGGGAGGGCTCT 62.190 60.000 0.00 0.00 43.93 4.09
70 72 1.486310 AGTGTTTGTGTCCTGCTCAGA 59.514 47.619 0.00 0.00 0.00 3.27
84 86 2.045926 CAGAAAGGCGGGGAGGTG 60.046 66.667 0.00 0.00 0.00 4.00
156 158 3.857854 GCGTCTAGCGTCGTCGGA 61.858 66.667 3.90 0.00 43.66 4.55
180 182 2.358737 GTGGAAGTGTGGCTCCGG 60.359 66.667 0.00 0.00 0.00 5.14
184 186 2.847234 AAGTGTGGCTCCGGTGGA 60.847 61.111 0.00 0.00 0.00 4.02
189 191 2.038813 TGGCTCCGGTGGATCTCA 59.961 61.111 0.00 0.00 0.00 3.27
193 195 1.753078 CTCCGGTGGATCTCACGGA 60.753 63.158 18.92 18.92 46.96 4.69
229 231 1.977854 TCTATGATGGATCCGGTTGGG 59.022 52.381 7.39 0.00 35.24 4.12
242 244 2.604079 TTGGGTCCGGCCTTCGTA 60.604 61.111 13.58 0.00 37.43 3.43
254 256 2.182825 GCCTTCGTACATGTGTCTACG 58.817 52.381 9.11 10.65 37.29 3.51
269 271 4.159135 GTGTCTACGGGTTGGATTCTTCTA 59.841 45.833 0.00 0.00 0.00 2.10
273 275 3.793559 ACGGGTTGGATTCTTCTAATCG 58.206 45.455 0.00 0.00 32.47 3.34
274 276 3.131396 CGGGTTGGATTCTTCTAATCGG 58.869 50.000 0.00 0.00 0.00 4.18
276 278 2.544267 GGTTGGATTCTTCTAATCGGCG 59.456 50.000 0.00 0.00 0.00 6.46
277 279 1.865865 TGGATTCTTCTAATCGGCGC 58.134 50.000 0.00 0.00 0.00 6.53
280 282 2.221981 GGATTCTTCTAATCGGCGCTTG 59.778 50.000 7.64 0.00 0.00 4.01
294 296 0.368227 CGCTTGTCTTCATCTGCGAC 59.632 55.000 0.00 0.00 45.15 5.19
312 314 2.553086 GACGGTTGTTGTTCAGGTACA 58.447 47.619 0.00 0.00 0.00 2.90
360 362 5.219987 GCACGACGACTTTTTGATAGTCTAC 60.220 44.000 0.00 0.00 39.86 2.59
361 363 6.084925 CACGACGACTTTTTGATAGTCTACT 58.915 40.000 0.00 0.00 39.86 2.57
363 365 7.909121 CACGACGACTTTTTGATAGTCTACTAT 59.091 37.037 0.00 2.26 41.56 2.12
408 410 1.141881 GAAGGAGCGATGAAGGCGA 59.858 57.895 0.00 0.00 35.00 5.54
446 448 2.496070 TCCAGTGCTTATAGTCGTTGCT 59.504 45.455 0.00 0.00 0.00 3.91
482 484 7.391833 ACAGACCTGGATGAACTTTTATTTCTC 59.608 37.037 0.00 0.00 34.19 2.87
786 7673 5.796935 GCTCGACTACAACAATTTACTACGA 59.203 40.000 0.00 0.00 0.00 3.43
788 7675 6.667370 TCGACTACAACAATTTACTACGACA 58.333 36.000 0.00 0.00 0.00 4.35
902 7802 1.152922 TCCCGTCAACCAACCAACC 60.153 57.895 0.00 0.00 0.00 3.77
903 7803 1.454111 CCCGTCAACCAACCAACCA 60.454 57.895 0.00 0.00 0.00 3.67
904 7804 1.038130 CCCGTCAACCAACCAACCAA 61.038 55.000 0.00 0.00 0.00 3.67
905 7805 0.101579 CCGTCAACCAACCAACCAAC 59.898 55.000 0.00 0.00 0.00 3.77
906 7806 0.101579 CGTCAACCAACCAACCAACC 59.898 55.000 0.00 0.00 0.00 3.77
951 7851 2.160615 CGTCACGTTCTCTCACTCTCAT 59.839 50.000 0.00 0.00 0.00 2.90
952 7852 3.726486 CGTCACGTTCTCTCACTCTCATC 60.726 52.174 0.00 0.00 0.00 2.92
953 7853 3.189495 GTCACGTTCTCTCACTCTCATCA 59.811 47.826 0.00 0.00 0.00 3.07
954 7854 3.821033 TCACGTTCTCTCACTCTCATCAA 59.179 43.478 0.00 0.00 0.00 2.57
955 7855 4.278419 TCACGTTCTCTCACTCTCATCAAA 59.722 41.667 0.00 0.00 0.00 2.69
956 7856 4.384247 CACGTTCTCTCACTCTCATCAAAC 59.616 45.833 0.00 0.00 0.00 2.93
957 7857 4.038042 ACGTTCTCTCACTCTCATCAAACA 59.962 41.667 0.00 0.00 0.00 2.83
979 7879 2.259439 GCAGCAGCAGCACAGAAGT 61.259 57.895 4.63 0.00 45.49 3.01
980 7880 1.793134 GCAGCAGCAGCACAGAAGTT 61.793 55.000 4.63 0.00 45.49 2.66
981 7881 0.237761 CAGCAGCAGCACAGAAGTTC 59.762 55.000 3.17 0.00 45.49 3.01
993 7897 0.387878 AGAAGTTCGCTGCGTCTCTG 60.388 55.000 22.48 0.00 0.00 3.35
994 7898 1.347817 GAAGTTCGCTGCGTCTCTGG 61.348 60.000 22.48 0.00 0.00 3.86
995 7899 3.482783 GTTCGCTGCGTCTCTGGC 61.483 66.667 22.48 2.19 0.00 4.85
999 7903 4.724602 GCTGCGTCTCTGGCGACA 62.725 66.667 0.00 0.00 39.59 4.35
1000 7904 2.049156 CTGCGTCTCTGGCGACAA 60.049 61.111 0.00 0.00 42.06 3.18
1001 7905 1.446792 CTGCGTCTCTGGCGACAAT 60.447 57.895 0.00 0.00 42.06 2.71
1002 7906 1.690283 CTGCGTCTCTGGCGACAATG 61.690 60.000 0.00 0.00 42.06 2.82
1003 7907 2.456119 GCGTCTCTGGCGACAATGG 61.456 63.158 0.00 0.00 42.06 3.16
1004 7908 2.456119 CGTCTCTGGCGACAATGGC 61.456 63.158 0.00 0.00 42.06 4.40
1005 7909 2.125552 TCTCTGGCGACAATGGCG 60.126 61.111 3.09 3.09 42.06 5.69
1006 7910 3.197790 CTCTGGCGACAATGGCGG 61.198 66.667 11.62 0.00 42.06 6.13
1007 7911 4.776322 TCTGGCGACAATGGCGGG 62.776 66.667 11.62 0.00 42.06 6.13
1419 8323 6.263168 TCTTTGTGAGTGATCCCTTTCTTTTC 59.737 38.462 0.00 0.00 0.00 2.29
1420 8324 5.310409 TGTGAGTGATCCCTTTCTTTTCT 57.690 39.130 0.00 0.00 0.00 2.52
1424 8328 6.488344 GTGAGTGATCCCTTTCTTTTCTTTCT 59.512 38.462 0.00 0.00 0.00 2.52
1426 8330 6.605119 AGTGATCCCTTTCTTTTCTTTCTCA 58.395 36.000 0.00 0.00 0.00 3.27
1461 8366 1.830279 TTGCTAGCTGCTGCAGAAAT 58.170 45.000 32.30 18.69 43.37 2.17
1463 8368 2.283298 TGCTAGCTGCTGCAGAAATAC 58.717 47.619 32.30 14.39 43.37 1.89
1464 8369 1.601430 GCTAGCTGCTGCAGAAATACC 59.399 52.381 32.30 13.67 42.74 2.73
1465 8370 2.910199 CTAGCTGCTGCAGAAATACCA 58.090 47.619 32.30 3.32 42.74 3.25
1466 8371 1.747709 AGCTGCTGCAGAAATACCAG 58.252 50.000 32.30 14.81 42.74 4.00
1467 8372 1.004044 AGCTGCTGCAGAAATACCAGT 59.996 47.619 32.30 2.41 42.74 4.00
1472 8377 5.564651 GCTGCTGCAGAAATACCAGTTTTTA 60.565 40.000 32.30 0.00 39.41 1.52
1474 8379 4.859245 GCTGCAGAAATACCAGTTTTTAGC 59.141 41.667 20.43 0.00 0.00 3.09
1475 8380 5.335976 GCTGCAGAAATACCAGTTTTTAGCT 60.336 40.000 20.43 0.00 0.00 3.32
1495 8409 5.422145 AGCTGAAAAACAAGTGCAGAAAAT 58.578 33.333 0.00 0.00 0.00 1.82
1540 8742 9.274206 GCATCATATATACGAGTATCTAGGTCA 57.726 37.037 0.00 0.00 0.00 4.02
1543 8745 9.780186 TCATATATACGAGTATCTAGGTCATGG 57.220 37.037 0.00 0.00 0.00 3.66
1546 8748 8.961294 ATATACGAGTATCTAGGTCATGGTAC 57.039 38.462 0.00 0.00 0.00 3.34
1560 8762 4.453136 GTCATGGTACGTATGTTGTTGGTT 59.547 41.667 0.00 0.00 0.00 3.67
1561 8763 4.452795 TCATGGTACGTATGTTGTTGGTTG 59.547 41.667 0.00 0.00 0.00 3.77
1562 8764 3.806380 TGGTACGTATGTTGTTGGTTGT 58.194 40.909 0.00 0.00 0.00 3.32
1565 8767 4.971220 GGTACGTATGTTGTTGGTTGTTTG 59.029 41.667 0.00 0.00 0.00 2.93
1576 8778 5.059833 TGTTGGTTGTTTGGATTTATTGGC 58.940 37.500 0.00 0.00 0.00 4.52
1684 8958 1.025041 ATACATCACGCTCGCTCTCA 58.975 50.000 0.00 0.00 0.00 3.27
1749 9023 4.087182 ACAGTGTGCTAGTAGTACCATGT 58.913 43.478 14.86 15.14 29.18 3.21
1817 9094 5.519566 TCACTTGCAATCATCAAACAACAAC 59.480 36.000 0.00 0.00 0.00 3.32
1818 9095 5.291371 CACTTGCAATCATCAAACAACAACA 59.709 36.000 0.00 0.00 0.00 3.33
1819 9096 5.521010 ACTTGCAATCATCAAACAACAACAG 59.479 36.000 0.00 0.00 0.00 3.16
1820 9097 3.803231 TGCAATCATCAAACAACAACAGC 59.197 39.130 0.00 0.00 0.00 4.40
1821 9098 3.803231 GCAATCATCAAACAACAACAGCA 59.197 39.130 0.00 0.00 0.00 4.41
1822 9099 4.270566 GCAATCATCAAACAACAACAGCAA 59.729 37.500 0.00 0.00 0.00 3.91
1823 9100 5.220624 GCAATCATCAAACAACAACAGCAAA 60.221 36.000 0.00 0.00 0.00 3.68
1824 9101 6.675002 GCAATCATCAAACAACAACAGCAAAA 60.675 34.615 0.00 0.00 0.00 2.44
1825 9102 6.981762 ATCATCAAACAACAACAGCAAAAA 57.018 29.167 0.00 0.00 0.00 1.94
1920 9205 9.791820 TTTTACTGTTTTATATGATCTCGACGA 57.208 29.630 0.00 0.00 0.00 4.20
1921 9206 8.778141 TTACTGTTTTATATGATCTCGACGAC 57.222 34.615 0.00 0.00 0.00 4.34
1922 9207 5.907945 ACTGTTTTATATGATCTCGACGACG 59.092 40.000 0.00 0.00 41.26 5.12
2066 9351 0.250124 TCGGCACCAACGACTTCATT 60.250 50.000 0.00 0.00 35.12 2.57
2318 9603 4.592192 CTCCGCGCCATGGTCGAT 62.592 66.667 26.00 0.00 0.00 3.59
2402 9687 1.296392 CATCCTGCAGAACCCGTCA 59.704 57.895 17.39 0.00 0.00 4.35
2435 9720 4.621087 AAGGTGGCCAGGGGTTGC 62.621 66.667 5.11 0.00 0.00 4.17
2606 9891 3.181503 CCTTCAGCCATTTCTTGTGATCG 60.182 47.826 0.00 0.00 0.00 3.69
2686 9971 4.406972 TGATTCATGTGCTACTTCTAGGCT 59.593 41.667 0.00 0.00 0.00 4.58
2711 9996 6.524101 TTTTGTGCTTAGTTTGTTCTTCCT 57.476 33.333 0.00 0.00 0.00 3.36
2712 9997 6.524101 TTTGTGCTTAGTTTGTTCTTCCTT 57.476 33.333 0.00 0.00 0.00 3.36
2751 10036 3.128764 GTGCTTAGTTTATTCAGGGTGGC 59.871 47.826 0.00 0.00 0.00 5.01
2753 10038 3.761752 GCTTAGTTTATTCAGGGTGGCAA 59.238 43.478 0.00 0.00 0.00 4.52
2774 10059 3.825328 AGCCATACTCCCATGATTTGAC 58.175 45.455 0.00 0.00 0.00 3.18
2775 10060 2.549754 GCCATACTCCCATGATTTGACG 59.450 50.000 0.00 0.00 0.00 4.35
2840 10125 9.640974 GATGTCATTAATTGTATGCATTTTTGC 57.359 29.630 3.54 0.00 0.00 3.68
2936 10225 6.750963 CCAGCTTTCAGCATAGAAATTTCTTC 59.249 38.462 25.02 14.46 45.56 2.87
2988 10277 8.999431 TGGAGAGAGTACATGTTTATGTTTTTC 58.001 33.333 2.30 0.00 45.01 2.29
3030 11665 5.685841 ACACGTTTTATGTAAGTGTGCATC 58.314 37.500 0.00 0.00 43.39 3.91
3134 11777 1.153107 CATTGCCGATCCAGCCTGA 60.153 57.895 0.00 0.00 0.00 3.86
3170 11813 3.426787 TTTATTGAGCCGGTTTGAGGA 57.573 42.857 1.90 0.00 0.00 3.71
3175 11818 0.250513 GAGCCGGTTTGAGGAGATGT 59.749 55.000 1.90 0.00 0.00 3.06
3231 11874 1.089920 CTGCATGTCCCTAGTTGCAC 58.910 55.000 0.00 0.00 39.98 4.57
3269 11912 2.247267 GACGTTTGGTTGTCCGCG 59.753 61.111 0.00 0.00 36.30 6.46
3378 12021 3.928992 CACAGAATCTGAACATGTAGCGT 59.071 43.478 18.20 0.00 35.18 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.751837 GCCCTCCCGCTTTCAAGG 60.752 66.667 0.00 0.00 0.00 3.61
4 5 2.224159 AGAGCCCTCCCGCTTTCAA 61.224 57.895 0.00 0.00 39.87 2.69
10 11 0.322187 TAAAAACAGAGCCCTCCCGC 60.322 55.000 0.00 0.00 0.00 6.13
56 58 0.250467 GCCTTTCTGAGCAGGACACA 60.250 55.000 8.73 0.00 30.81 3.72
57 59 1.294659 CGCCTTTCTGAGCAGGACAC 61.295 60.000 8.73 0.00 30.81 3.67
84 86 1.267121 TATATCTTCAGGGAGCCGCC 58.733 55.000 0.00 0.00 0.00 6.13
87 89 8.083828 TGATCTTATTATATCTTCAGGGAGCC 57.916 38.462 0.00 0.00 0.00 4.70
147 149 4.695231 ACACGCCTTCCGACGACG 62.695 66.667 0.00 0.00 41.02 5.12
156 158 1.525995 CCACACTTCCACACGCCTT 60.526 57.895 0.00 0.00 0.00 4.35
180 182 2.403252 ACCAATTCCGTGAGATCCAC 57.597 50.000 4.71 4.71 42.30 4.02
184 186 2.224769 ACACCAACCAATTCCGTGAGAT 60.225 45.455 0.00 0.00 0.00 2.75
189 191 2.100087 GACAAACACCAACCAATTCCGT 59.900 45.455 0.00 0.00 0.00 4.69
193 195 6.295236 CCATCATAGACAAACACCAACCAATT 60.295 38.462 0.00 0.00 0.00 2.32
242 244 1.344065 TCCAACCCGTAGACACATGT 58.656 50.000 0.00 0.00 0.00 3.21
254 256 2.879026 GCCGATTAGAAGAATCCAACCC 59.121 50.000 0.00 0.00 0.00 4.11
269 271 1.009829 GATGAAGACAAGCGCCGATT 58.990 50.000 2.29 0.00 0.00 3.34
273 275 1.427020 GCAGATGAAGACAAGCGCC 59.573 57.895 2.29 0.00 0.00 6.53
274 276 1.059994 CGCAGATGAAGACAAGCGC 59.940 57.895 0.00 0.00 38.31 5.92
294 296 2.286833 CAGTGTACCTGAACAACAACCG 59.713 50.000 5.67 0.00 44.49 4.44
312 314 2.683768 CTAAGGCTCCATAGGACCAGT 58.316 52.381 0.00 0.00 0.00 4.00
330 332 2.984471 CAAAAAGTCGTCGTGCTAGCTA 59.016 45.455 17.23 0.00 0.00 3.32
331 333 1.792949 CAAAAAGTCGTCGTGCTAGCT 59.207 47.619 17.23 0.00 0.00 3.32
332 334 1.790623 TCAAAAAGTCGTCGTGCTAGC 59.209 47.619 8.10 8.10 0.00 3.42
333 335 4.857588 ACTATCAAAAAGTCGTCGTGCTAG 59.142 41.667 0.00 0.00 0.00 3.42
339 341 9.926751 TTATAGTAGACTATCAAAAAGTCGTCG 57.073 33.333 5.46 0.00 46.46 5.12
360 362 5.235186 CGGAGCCAGACAAATCTTGTTATAG 59.765 44.000 0.00 0.00 45.52 1.31
361 363 5.105106 TCGGAGCCAGACAAATCTTGTTATA 60.105 40.000 0.00 0.00 45.52 0.98
363 365 3.007506 TCGGAGCCAGACAAATCTTGTTA 59.992 43.478 0.00 0.00 45.52 2.41
428 430 5.508153 CCATCTAGCAACGACTATAAGCACT 60.508 44.000 0.00 0.00 0.00 4.40
508 510 5.642063 TGGAAGAACTTCGGATGTATTTGTC 59.358 40.000 8.20 0.00 40.37 3.18
519 521 5.646606 TCTTTGTTTTTGGAAGAACTTCGG 58.353 37.500 8.20 0.00 40.37 4.30
520 522 5.743872 CCTCTTTGTTTTTGGAAGAACTTCG 59.256 40.000 8.20 0.00 40.37 3.79
561 563 0.895530 ATATAGGCGACATGGGGACG 59.104 55.000 0.00 0.00 0.00 4.79
786 7673 2.123897 GGTGTTGGCCTGTGGTGT 60.124 61.111 3.32 0.00 0.00 4.16
788 7675 1.455587 CTTGGTGTTGGCCTGTGGT 60.456 57.895 3.32 0.00 0.00 4.16
902 7802 4.561735 AGACGGTGTAAATTGTTGGTTG 57.438 40.909 0.00 0.00 0.00 3.77
903 7803 5.344884 CAAAGACGGTGTAAATTGTTGGTT 58.655 37.500 0.00 0.00 0.00 3.67
904 7804 4.735283 GCAAAGACGGTGTAAATTGTTGGT 60.735 41.667 0.00 0.00 0.00 3.67
905 7805 3.733727 GCAAAGACGGTGTAAATTGTTGG 59.266 43.478 0.00 0.00 0.00 3.77
906 7806 3.420576 CGCAAAGACGGTGTAAATTGTTG 59.579 43.478 0.00 0.00 0.00 3.33
951 7851 1.792118 CTGCTGCTGCTGCTGTTTGA 61.792 55.000 27.67 9.42 39.81 2.69
952 7852 1.371758 CTGCTGCTGCTGCTGTTTG 60.372 57.895 27.67 11.95 39.81 2.93
953 7853 3.039988 CTGCTGCTGCTGCTGTTT 58.960 55.556 27.67 0.00 39.81 2.83
1419 8323 2.169663 GTGCATGCACGATGAGAAAG 57.830 50.000 33.20 0.00 37.19 2.62
1467 8372 6.393990 TCTGCACTTGTTTTTCAGCTAAAAA 58.606 32.000 0.00 0.00 43.20 1.94
1472 8377 4.454728 TTTCTGCACTTGTTTTTCAGCT 57.545 36.364 0.00 0.00 0.00 4.24
1513 8594 9.496873 GACCTAGATACTCGTATATATGATGCT 57.503 37.037 5.11 3.96 0.00 3.79
1523 8604 5.873712 CGTACCATGACCTAGATACTCGTAT 59.126 44.000 0.00 0.00 0.00 3.06
1524 8605 5.221521 ACGTACCATGACCTAGATACTCGTA 60.222 44.000 0.00 0.00 0.00 3.43
1525 8606 4.063689 CGTACCATGACCTAGATACTCGT 58.936 47.826 0.00 0.00 0.00 4.18
1526 8607 4.063689 ACGTACCATGACCTAGATACTCG 58.936 47.826 0.00 0.00 0.00 4.18
1527 8608 6.654161 ACATACGTACCATGACCTAGATACTC 59.346 42.308 0.00 0.00 0.00 2.59
1528 8609 6.540995 ACATACGTACCATGACCTAGATACT 58.459 40.000 0.00 0.00 0.00 2.12
1529 8610 6.814506 ACATACGTACCATGACCTAGATAC 57.185 41.667 0.00 0.00 0.00 2.24
1532 8613 4.951715 ACAACATACGTACCATGACCTAGA 59.048 41.667 0.00 0.00 0.00 2.43
1533 8614 5.258456 ACAACATACGTACCATGACCTAG 57.742 43.478 0.00 0.00 0.00 3.02
1540 8742 4.391155 ACAACCAACAACATACGTACCAT 58.609 39.130 0.00 0.00 0.00 3.55
1543 8745 4.971220 CCAAACAACCAACAACATACGTAC 59.029 41.667 0.00 0.00 0.00 3.67
1546 8748 4.294416 TCCAAACAACCAACAACATACG 57.706 40.909 0.00 0.00 0.00 3.06
1560 8762 9.956640 AATGAATAAAGCCAATAAATCCAAACA 57.043 25.926 0.00 0.00 0.00 2.83
1598 8866 2.041301 ATGCATGCATGGGCCCTT 60.041 55.556 31.74 15.22 40.13 3.95
1662 8936 0.030773 GAGCGAGCGTGATGTATGGA 59.969 55.000 0.00 0.00 0.00 3.41
1684 8958 3.632333 TGCTAGCTAGTCCACACAGTAT 58.368 45.455 21.62 0.00 0.00 2.12
1749 9023 2.578480 TGTAAATGCCACTGGGACCATA 59.422 45.455 0.00 0.00 35.59 2.74
1827 9104 8.245195 ACTTCATTAACCATAGGTGTGTTTTT 57.755 30.769 0.00 0.00 35.34 1.94
1894 9179 9.791820 TCGTCGAGATCATATAAAACAGTAAAA 57.208 29.630 0.00 0.00 0.00 1.52
1905 9190 3.064931 ACTGCGTCGTCGAGATCATATA 58.935 45.455 6.17 0.00 39.71 0.86
1908 9193 0.028242 GACTGCGTCGTCGAGATCAT 59.972 55.000 6.17 0.00 39.71 2.45
1909 9194 1.296056 TGACTGCGTCGTCGAGATCA 61.296 55.000 6.17 2.55 39.71 2.92
1910 9195 0.587737 CTGACTGCGTCGTCGAGATC 60.588 60.000 6.17 0.00 39.71 2.75
1911 9196 1.299562 ACTGACTGCGTCGTCGAGAT 61.300 55.000 6.17 0.00 39.71 2.75
1912 9197 1.959738 ACTGACTGCGTCGTCGAGA 60.960 57.895 6.17 0.00 39.71 4.04
1913 9198 1.794003 CACTGACTGCGTCGTCGAG 60.794 63.158 6.17 3.34 39.71 4.04
1914 9199 1.574702 ATCACTGACTGCGTCGTCGA 61.575 55.000 6.17 0.00 39.71 4.20
1915 9200 0.096454 TATCACTGACTGCGTCGTCG 59.904 55.000 0.00 0.00 36.71 5.12
1916 9201 1.536149 GTATCACTGACTGCGTCGTC 58.464 55.000 0.00 0.13 34.95 4.20
1917 9202 0.170561 GGTATCACTGACTGCGTCGT 59.829 55.000 0.00 3.43 34.95 4.34
1918 9203 0.525668 GGGTATCACTGACTGCGTCG 60.526 60.000 4.65 0.00 34.95 5.12
1919 9204 0.818296 AGGGTATCACTGACTGCGTC 59.182 55.000 2.32 2.32 0.00 5.19
1920 9205 1.066858 CAAGGGTATCACTGACTGCGT 60.067 52.381 0.00 0.00 0.00 5.24
1921 9206 1.066858 ACAAGGGTATCACTGACTGCG 60.067 52.381 0.00 0.00 0.00 5.18
1922 9207 2.622436 GACAAGGGTATCACTGACTGC 58.378 52.381 0.00 0.00 0.00 4.40
2009 9294 4.329545 TCAGCAACCACCGCCCTC 62.330 66.667 0.00 0.00 0.00 4.30
2066 9351 1.544691 GTGAGGGCGAAGTAGTTCTCA 59.455 52.381 8.63 2.77 0.00 3.27
2422 9707 4.601794 CACAGCAACCCCTGGCCA 62.602 66.667 4.71 4.71 37.16 5.36
2435 9720 1.227999 CGTACAACCCTGTGCCACAG 61.228 60.000 18.02 18.02 45.53 3.66
2444 9729 0.252558 ACCCCATCTCGTACAACCCT 60.253 55.000 0.00 0.00 0.00 4.34
2636 9921 3.552068 GGGACGTGAATTTCCTGGTTTTG 60.552 47.826 0.00 0.00 31.90 2.44
2641 9926 1.453155 CTGGGACGTGAATTTCCTGG 58.547 55.000 0.00 0.00 31.90 4.45
2642 9927 0.804989 GCTGGGACGTGAATTTCCTG 59.195 55.000 0.00 0.00 31.90 3.86
2751 10036 4.037208 GTCAAATCATGGGAGTATGGCTTG 59.963 45.833 0.00 0.00 0.00 4.01
2753 10038 3.745480 CGTCAAATCATGGGAGTATGGCT 60.745 47.826 0.00 0.00 0.00 4.75
2763 10048 5.818136 AATGGAACTACGTCAAATCATGG 57.182 39.130 0.00 0.00 0.00 3.66
2814 10099 9.640974 GCAAAAATGCATACAATTAATGACATC 57.359 29.630 0.00 0.00 34.41 3.06
2835 10120 5.178797 GCTTCTGGTCTCTACATAGCAAAA 58.821 41.667 0.00 0.00 0.00 2.44
2840 10125 8.948631 TTTAATTGCTTCTGGTCTCTACATAG 57.051 34.615 0.00 0.00 0.00 2.23
2845 10130 6.054860 AGCTTTAATTGCTTCTGGTCTCTA 57.945 37.500 0.00 0.00 37.52 2.43
2880 10169 3.006217 GCTCAGTTTCAAGCCAGGATTTT 59.994 43.478 0.00 0.00 32.22 1.82
2936 10225 4.725556 AGCATAATATAAACGTGTGCCG 57.274 40.909 0.00 0.00 44.03 5.69
3030 11665 2.478134 GCTATATGGTTCTGAGCTTGCG 59.522 50.000 0.00 0.00 0.00 4.85
3085 11728 1.889829 CGCCCCTAGTATCCTCAGAAG 59.110 57.143 0.00 0.00 0.00 2.85
3149 11792 3.756434 CTCCTCAAACCGGCTCAATAAAA 59.244 43.478 0.00 0.00 0.00 1.52
3231 11874 1.076332 GGTCGGAAATGGTTGTCTCG 58.924 55.000 0.00 0.00 0.00 4.04
3269 11912 2.290367 TCATATGTGCGCCTAATGCAAC 59.710 45.455 4.18 0.00 45.23 4.17
3345 11988 2.926200 CAGATTCTGTGTGGTAAGCTCG 59.074 50.000 5.46 0.00 0.00 5.03
3378 12021 9.554395 TGAACTGTCATTTGTTTAAGTAGATGA 57.446 29.630 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.