Multiple sequence alignment - TraesCS7A01G115000

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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 TraesCS7A01G115000 chr7A 100.000 2258 0 0 1 2258 71117736 71119993 0.000000e+00 4170.0
1 TraesCS7A01G115000 chr7A 94.336 459 15 6 788 1235 70893989 70894447 0.000000e+00 693.0
2 TraesCS7A01G115000 chr7A 92.798 361 19 6 888 1242 74596574 74596215 1.200000e-142 516.0
3 TraesCS7A01G115000 chr7A 95.033 302 15 0 934 1235 74610821 74610520 2.030000e-130 475.0
4 TraesCS7A01G115000 chr7A 89.655 232 17 3 2023 2251 74604480 74604253 2.840000e-74 289.0
5 TraesCS7A01G115000 chr7A 79.116 249 37 11 1987 2225 74595378 74595135 8.350000e-35 158.0
6 TraesCS7A01G115000 chr7A 94.915 59 3 0 788 846 74611001 74610943 2.390000e-15 93.5
7 TraesCS7A01G115000 chr7D 90.058 865 44 17 484 1329 68924653 68923812 0.000000e+00 1083.0
8 TraesCS7A01G115000 chr7D 89.407 472 21 4 1 460 68925288 68924834 3.250000e-158 568.0
9 TraesCS7A01G115000 chr7D 89.673 397 37 4 57 451 4740245 4739851 9.310000e-139 503.0
10 TraesCS7A01G115000 chr7D 84.601 526 52 18 782 1294 66513325 66513834 1.560000e-136 496.0
11 TraesCS7A01G115000 chr7D 85.918 490 36 22 782 1242 66484559 66485044 2.020000e-135 492.0
12 TraesCS7A01G115000 chr7D 93.569 311 18 2 933 1242 68935192 68934883 1.580000e-126 462.0
13 TraesCS7A01G115000 chr7D 84.400 500 33 19 811 1294 68914199 68913729 1.230000e-122 449.0
14 TraesCS7A01G115000 chr7D 84.946 465 44 20 789 1242 68806170 68805721 4.420000e-122 448.0
15 TraesCS7A01G115000 chr7D 84.100 478 19 26 1485 1936 68923771 68923325 2.090000e-110 409.0
16 TraesCS7A01G115000 chr7D 92.620 271 17 1 1991 2258 68922979 68922709 9.780000e-104 387.0
17 TraesCS7A01G115000 chr7D 89.888 267 23 2 1988 2251 66514215 66514480 7.720000e-90 340.0
18 TraesCS7A01G115000 chr7D 97.541 122 3 0 1998 2119 68804658 68804537 2.270000e-50 209.0
19 TraesCS7A01G115000 chr7D 80.444 225 35 6 2008 2226 68911477 68911256 1.790000e-36 163.0
20 TraesCS7A01G115000 chr7D 91.262 103 9 0 2156 2258 68804539 68804437 8.410000e-30 141.0
21 TraesCS7A01G115000 chr7D 85.827 127 15 3 1813 1936 68911903 68911777 5.060000e-27 132.0
22 TraesCS7A01G115000 chr3B 88.771 472 40 7 2 460 10736393 10735922 1.170000e-157 566.0
23 TraesCS7A01G115000 chr7B 87.140 521 31 19 1448 1934 10105643 10105125 1.960000e-155 558.0
24 TraesCS7A01G115000 chr7B 86.653 472 49 3 1 460 34681760 34681291 5.560000e-141 510.0
25 TraesCS7A01G115000 chr7B 95.053 283 12 1 953 1235 10241552 10241272 5.720000e-121 444.0
26 TraesCS7A01G115000 chr7B 93.284 268 16 2 976 1242 7727898 7728164 5.850000e-106 394.0
27 TraesCS7A01G115000 chr7B 90.299 268 20 2 1994 2258 10104834 10104570 1.660000e-91 346.0
28 TraesCS7A01G115000 chr7B 82.186 247 40 2 1988 2230 7558555 7558801 2.270000e-50 209.0
29 TraesCS7A01G115000 chr7B 92.857 140 7 1 881 1017 8446104 8446243 1.370000e-47 200.0
30 TraesCS7A01G115000 chr7B 100.000 53 0 0 794 846 10241767 10241715 5.130000e-17 99.0
31 TraesCS7A01G115000 chr7B 88.095 84 4 2 788 871 8445978 8446055 6.640000e-16 95.3
32 TraesCS7A01G115000 chr7B 86.486 74 4 3 798 871 10190834 10190767 2.400000e-10 76.8
33 TraesCS7A01G115000 chr4B 88.136 472 44 2 1 460 17032171 17032642 3.280000e-153 551.0
34 TraesCS7A01G115000 chr4B 79.126 206 42 1 2023 2228 258794054 258794258 8.410000e-30 141.0
35 TraesCS7A01G115000 chr3A 87.924 472 45 2 1 460 154028715 154028244 1.530000e-151 545.0
36 TraesCS7A01G115000 chr3A 88.608 395 45 0 57 451 42446069 42446463 4.360000e-132 481.0
37 TraesCS7A01G115000 chr5B 87.021 470 50 4 2 460 405706783 405707252 9.240000e-144 520.0
38 TraesCS7A01G115000 chr5A 85.381 472 57 5 1 460 572834797 572835268 1.570000e-131 479.0


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 TraesCS7A01G115000 chr7A 71117736 71119993 2257 False 4170.00 4170 100.000000 1 2258 1 chr7A.!!$F2 2257
1 TraesCS7A01G115000 chr7A 74595135 74596574 1439 True 337.00 516 85.957000 888 2225 2 chr7A.!!$R2 1337
2 TraesCS7A01G115000 chr7D 68922709 68925288 2579 True 611.75 1083 89.046250 1 2258 4 chr7D.!!$R5 2257
3 TraesCS7A01G115000 chr7D 66513325 66514480 1155 False 418.00 496 87.244500 782 2251 2 chr7D.!!$F2 1469
4 TraesCS7A01G115000 chr7D 68804437 68806170 1733 True 266.00 448 91.249667 789 2258 3 chr7D.!!$R3 1469
5 TraesCS7A01G115000 chr7D 68911256 68914199 2943 True 248.00 449 83.557000 811 2226 3 chr7D.!!$R4 1415
6 TraesCS7A01G115000 chr7B 10104570 10105643 1073 True 452.00 558 88.719500 1448 2258 2 chr7B.!!$R3 810

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
924 1123 0.321653 CCTACCAACACACAGCCTCC 60.322 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 4322 0.251121 ACCCGGATGTCAATGCAACA 60.251 50.0 0.73 0.0 0.0 3.33 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
29 30 1.437573 CTAACATCAGCCGCCTCGA 59.562 57.895 0.00 0.00 0.00 4.04
94 107 0.875059 GCCTTCGCAACAACTAGCTT 59.125 50.000 0.00 0.00 34.03 3.74
95 108 1.400242 GCCTTCGCAACAACTAGCTTG 60.400 52.381 0.00 0.00 33.46 4.01
96 109 1.873591 CCTTCGCAACAACTAGCTTGT 59.126 47.619 0.00 0.00 45.68 3.16
142 155 1.270625 CCTTGTTGCGAAGGTCCACTA 60.271 52.381 0.00 0.00 38.19 2.74
222 235 2.637383 GGAGTCGTCGCACCTCCTT 61.637 63.158 14.50 0.00 41.31 3.36
230 243 1.738099 CGCACCTCCTTCGAACCAG 60.738 63.158 0.00 0.00 0.00 4.00
277 290 1.387084 GCACGACAACGATGAAGTCTC 59.613 52.381 0.00 0.00 42.66 3.36
323 336 3.146066 TCTGCAACCGAAGCTATGTTTT 58.854 40.909 0.00 0.00 0.00 2.43
363 376 0.324943 AATGCTTGCCCTCGTACACT 59.675 50.000 0.00 0.00 0.00 3.55
364 377 1.191535 ATGCTTGCCCTCGTACACTA 58.808 50.000 0.00 0.00 0.00 2.74
365 378 1.191535 TGCTTGCCCTCGTACACTAT 58.808 50.000 0.00 0.00 0.00 2.12
366 379 1.134818 TGCTTGCCCTCGTACACTATG 60.135 52.381 0.00 0.00 0.00 2.23
367 380 1.136305 GCTTGCCCTCGTACACTATGA 59.864 52.381 0.00 0.00 0.00 2.15
368 381 2.810650 CTTGCCCTCGTACACTATGAC 58.189 52.381 0.00 0.00 0.00 3.06
369 382 1.842052 TGCCCTCGTACACTATGACA 58.158 50.000 0.00 0.00 0.00 3.58
434 447 6.757897 TCTGAAATAATACCCTTGTTGCAG 57.242 37.500 0.00 0.00 30.20 4.41
439 452 7.121168 TGAAATAATACCCTTGTTGCAGAAGAG 59.879 37.037 8.71 0.00 0.00 2.85
451 464 9.286946 CTTGTTGCAGAAGAGAAAATATTCATC 57.713 33.333 2.11 0.00 38.06 2.92
452 465 8.339344 TGTTGCAGAAGAGAAAATATTCATCA 57.661 30.769 0.00 0.00 38.06 3.07
455 468 8.741603 TGCAGAAGAGAAAATATTCATCATCA 57.258 30.769 0.00 0.00 38.06 3.07
460 473 9.443283 GAAGAGAAAATATTCATCATCAAACCG 57.557 33.333 0.00 0.00 38.06 4.44
461 474 7.934457 AGAGAAAATATTCATCATCAAACCGG 58.066 34.615 0.00 0.00 38.06 5.28
462 475 7.013655 AGAGAAAATATTCATCATCAAACCGGG 59.986 37.037 6.32 0.00 38.06 5.73
463 476 6.833416 AGAAAATATTCATCATCAAACCGGGA 59.167 34.615 6.32 0.00 38.06 5.14
464 477 6.391227 AAATATTCATCATCAAACCGGGAC 57.609 37.500 6.32 0.00 0.00 4.46
466 479 3.433306 TTCATCATCAAACCGGGACTT 57.567 42.857 6.32 0.00 0.00 3.01
467 480 2.710377 TCATCATCAAACCGGGACTTG 58.290 47.619 6.32 6.63 0.00 3.16
468 481 1.133025 CATCATCAAACCGGGACTTGC 59.867 52.381 6.32 0.00 0.00 4.01
470 483 1.674322 ATCAAACCGGGACTTGCCG 60.674 57.895 6.32 1.54 37.63 5.69
471 484 4.038080 CAAACCGGGACTTGCCGC 62.038 66.667 6.32 0.00 37.63 6.53
505 675 4.614555 TTGATCAAAATCAATCCGACGG 57.385 40.909 7.84 7.84 44.94 4.79
514 684 1.079681 AATCCGACGGCTACGCAAA 60.080 52.632 9.66 0.00 46.04 3.68
516 686 2.495366 ATCCGACGGCTACGCAAACA 62.495 55.000 9.66 0.00 46.04 2.83
534 704 3.364441 GCGGATGTTGTGCCTGCA 61.364 61.111 0.00 0.00 0.00 4.41
555 725 4.794655 GCATTGAAGGTTAGCGTTTTCCAA 60.795 41.667 0.00 0.00 0.00 3.53
556 726 5.469479 CATTGAAGGTTAGCGTTTTCCAAT 58.531 37.500 0.00 0.00 0.00 3.16
562 733 8.145122 TGAAGGTTAGCGTTTTCCAATAAAAAT 58.855 29.630 0.00 0.00 31.29 1.82
563 734 9.628746 GAAGGTTAGCGTTTTCCAATAAAAATA 57.371 29.630 0.00 0.00 31.29 1.40
577 748 8.856103 TCCAATAAAAATAGGCCAAATACTAGC 58.144 33.333 5.01 0.00 0.00 3.42
583 754 3.127425 AGGCCAAATACTAGCGAATCC 57.873 47.619 5.01 0.00 0.00 3.01
586 757 3.189287 GGCCAAATACTAGCGAATCCATG 59.811 47.826 0.00 0.00 0.00 3.66
718 889 2.191513 CAGCCGCCAATGCATAGCT 61.192 57.895 16.91 10.16 38.20 3.32
721 892 1.947013 CCGCCAATGCATAGCTCAG 59.053 57.895 16.91 4.62 37.32 3.35
733 904 0.820074 TAGCTCAGGCGGACTAGCTC 60.820 60.000 15.19 0.00 43.96 4.09
739 910 4.175489 GCGGACTAGCTCGCGTCA 62.175 66.667 5.77 0.00 42.48 4.35
742 913 1.777030 CGGACTAGCTCGCGTCATCT 61.777 60.000 5.77 1.64 31.88 2.90
745 916 1.284408 CTAGCTCGCGTCATCTCCC 59.716 63.158 5.77 0.00 0.00 4.30
753 924 1.519455 CGTCATCTCCCGGCTGTTC 60.519 63.158 0.00 0.00 0.00 3.18
754 925 1.519455 GTCATCTCCCGGCTGTTCG 60.519 63.158 0.00 0.00 0.00 3.95
755 926 1.982395 TCATCTCCCGGCTGTTCGT 60.982 57.895 0.00 0.00 0.00 3.85
756 927 1.811266 CATCTCCCGGCTGTTCGTG 60.811 63.158 0.00 0.00 0.00 4.35
757 928 3.665675 ATCTCCCGGCTGTTCGTGC 62.666 63.158 0.00 0.00 0.00 5.34
871 1042 2.050168 CCACACCACGCAATGCAC 60.050 61.111 5.91 0.00 0.00 4.57
872 1043 2.720605 CACACCACGCAATGCACA 59.279 55.556 5.91 0.00 0.00 4.57
924 1123 0.321653 CCTACCAACACACAGCCTCC 60.322 60.000 0.00 0.00 0.00 4.30
952 1155 0.595095 CAAGTTGTGCTCCCAGAAGC 59.405 55.000 0.00 0.00 42.82 3.86
953 1156 0.475906 AAGTTGTGCTCCCAGAAGCT 59.524 50.000 0.00 0.00 42.94 3.74
1247 1463 2.035237 AACCAAGAAGTCGACGCCCA 62.035 55.000 10.46 0.00 0.00 5.36
1324 1559 2.294791 AGACAAGGATCCATCGATCGAC 59.705 50.000 22.06 7.07 45.16 4.20
1329 1564 0.039978 GATCCATCGATCGACACGCT 60.040 55.000 22.06 0.09 35.83 5.07
1333 1568 0.028110 CATCGATCGACACGCTCTGA 59.972 55.000 22.06 0.00 0.00 3.27
1337 1572 1.531883 CGATCGACACGCTCTGAATGA 60.532 52.381 10.26 0.00 0.00 2.57
1338 1573 1.849219 GATCGACACGCTCTGAATGAC 59.151 52.381 0.00 0.00 0.00 3.06
1339 1574 0.881796 TCGACACGCTCTGAATGACT 59.118 50.000 0.00 0.00 0.00 3.41
1340 1575 0.987715 CGACACGCTCTGAATGACTG 59.012 55.000 0.00 0.00 0.00 3.51
1341 1576 1.401539 CGACACGCTCTGAATGACTGA 60.402 52.381 0.00 0.00 0.00 3.41
1342 1577 2.677199 GACACGCTCTGAATGACTGAA 58.323 47.619 0.00 0.00 0.00 3.02
1343 1578 3.257393 GACACGCTCTGAATGACTGAAT 58.743 45.455 0.00 0.00 0.00 2.57
1344 1579 3.257393 ACACGCTCTGAATGACTGAATC 58.743 45.455 0.00 0.00 0.00 2.52
1345 1580 3.056250 ACACGCTCTGAATGACTGAATCT 60.056 43.478 0.00 0.00 0.00 2.40
1346 1581 4.158579 ACACGCTCTGAATGACTGAATCTA 59.841 41.667 0.00 0.00 0.00 1.98
1347 1582 5.163468 ACACGCTCTGAATGACTGAATCTAT 60.163 40.000 0.00 0.00 0.00 1.98
1348 1583 5.175308 CACGCTCTGAATGACTGAATCTATG 59.825 44.000 0.00 0.00 0.00 2.23
1349 1584 4.150274 CGCTCTGAATGACTGAATCTATGC 59.850 45.833 0.00 0.00 0.00 3.14
1350 1585 5.299148 GCTCTGAATGACTGAATCTATGCT 58.701 41.667 0.00 0.00 0.00 3.79
1358 1593 1.524355 CTGAATCTATGCTTGCGTCCG 59.476 52.381 0.00 0.00 0.00 4.79
1366 1601 2.089349 GCTTGCGTCCGTGTCTCTC 61.089 63.158 0.00 0.00 0.00 3.20
1379 1614 0.793250 GTCTCTCGAGTTTTGGCAGC 59.207 55.000 13.13 0.00 0.00 5.25
1382 1617 1.196354 CTCTCGAGTTTTGGCAGCTTG 59.804 52.381 13.13 0.00 0.00 4.01
1397 1632 3.923017 AGCTTGGCTGAAATTGTACAC 57.077 42.857 0.00 0.00 37.57 2.90
1399 1634 3.004734 AGCTTGGCTGAAATTGTACACAC 59.995 43.478 0.00 0.00 37.57 3.82
1400 1635 3.243367 GCTTGGCTGAAATTGTACACACA 60.243 43.478 0.00 0.00 0.00 3.72
1401 1636 6.898603 AGCTTGGCTGAAATTGTACACACAA 61.899 40.000 0.00 0.00 42.59 3.33
1402 1637 8.136267 AGCTTGGCTGAAATTGTACACACAAT 62.136 38.462 0.00 0.00 46.35 2.71
1414 1649 4.642437 TGTACACACAATTCCTTTCTTGCA 59.358 37.500 0.00 0.00 0.00 4.08
1415 1650 4.311816 ACACACAATTCCTTTCTTGCAG 57.688 40.909 0.00 0.00 0.00 4.41
1416 1651 3.701040 ACACACAATTCCTTTCTTGCAGT 59.299 39.130 0.00 0.00 0.00 4.40
1417 1652 4.202050 ACACACAATTCCTTTCTTGCAGTC 60.202 41.667 0.00 0.00 0.00 3.51
1418 1653 3.003689 ACACAATTCCTTTCTTGCAGTCG 59.996 43.478 0.00 0.00 0.00 4.18
1419 1654 3.250762 CACAATTCCTTTCTTGCAGTCGA 59.749 43.478 0.00 0.00 0.00 4.20
1421 1656 4.520492 ACAATTCCTTTCTTGCAGTCGAAT 59.480 37.500 0.00 0.00 0.00 3.34
1422 1657 4.691860 ATTCCTTTCTTGCAGTCGAATG 57.308 40.909 8.83 8.83 0.00 2.67
1425 1660 2.095567 CCTTTCTTGCAGTCGAATGTGG 60.096 50.000 15.06 5.26 0.00 4.17
1426 1661 2.542020 TTCTTGCAGTCGAATGTGGA 57.458 45.000 15.06 7.49 0.00 4.02
1427 1662 2.542020 TCTTGCAGTCGAATGTGGAA 57.458 45.000 15.06 6.13 0.00 3.53
1430 1665 2.254546 TGCAGTCGAATGTGGAACTT 57.745 45.000 15.06 0.00 38.04 2.66
1431 1666 1.872952 TGCAGTCGAATGTGGAACTTG 59.127 47.619 15.06 0.00 38.04 3.16
1432 1667 2.143122 GCAGTCGAATGTGGAACTTGA 58.857 47.619 15.06 0.00 38.04 3.02
1433 1668 2.744202 GCAGTCGAATGTGGAACTTGAT 59.256 45.455 15.06 0.00 38.04 2.57
1434 1669 3.425359 GCAGTCGAATGTGGAACTTGATG 60.425 47.826 15.06 0.00 38.04 3.07
1437 1672 3.002791 TCGAATGTGGAACTTGATGAGC 58.997 45.455 0.00 0.00 38.04 4.26
1439 1674 3.063180 CGAATGTGGAACTTGATGAGCTC 59.937 47.826 6.82 6.82 38.04 4.09
1440 1675 3.708403 ATGTGGAACTTGATGAGCTCA 57.292 42.857 20.79 20.79 38.04 4.26
1441 1676 3.049708 TGTGGAACTTGATGAGCTCAG 57.950 47.619 22.96 10.82 38.04 3.35
1443 1678 3.262660 TGTGGAACTTGATGAGCTCAGAT 59.737 43.478 22.96 5.97 38.04 2.90
1444 1679 3.622163 GTGGAACTTGATGAGCTCAGATG 59.378 47.826 22.96 14.67 34.68 2.90
1445 1680 3.516700 TGGAACTTGATGAGCTCAGATGA 59.483 43.478 22.96 7.09 34.68 2.92
1446 1681 4.121317 GGAACTTGATGAGCTCAGATGAG 58.879 47.826 22.96 17.68 44.75 2.90
1508 2366 9.452065 GTTAAAATTCTCTTCTTCGCTTCTTTT 57.548 29.630 0.00 0.00 0.00 2.27
1514 2372 5.010112 TCTCTTCTTCGCTTCTTTTCTCTGA 59.990 40.000 0.00 0.00 0.00 3.27
1632 3401 5.025826 CACACGTACAAAACCAGAGAAAAC 58.974 41.667 0.00 0.00 0.00 2.43
1685 3454 5.445964 AGTTCTGTCCCAAAGTTGTTATGT 58.554 37.500 0.00 0.00 0.00 2.29
1686 3455 5.299279 AGTTCTGTCCCAAAGTTGTTATGTG 59.701 40.000 0.00 0.00 0.00 3.21
1693 3462 3.562141 CCAAAGTTGTTATGTGACCGTCA 59.438 43.478 0.00 0.00 0.00 4.35
1713 3491 4.453136 GTCACGGCAGATAAAAACCTTACA 59.547 41.667 0.00 0.00 0.00 2.41
1739 3517 6.826893 TTTGCTAACAAAAAGAAGACATGC 57.173 33.333 0.00 0.00 42.73 4.06
1757 3539 3.510388 TGCGATGTAGAAACCTGAGAG 57.490 47.619 0.00 0.00 0.00 3.20
1766 3552 6.688578 TGTAGAAACCTGAGAGTGTAATGTC 58.311 40.000 0.00 0.00 0.00 3.06
1792 3583 7.011482 CCAGAAACTAGTATCTTATGGTGTTGC 59.989 40.741 10.15 0.00 28.85 4.17
1793 3584 7.011482 CAGAAACTAGTATCTTATGGTGTTGCC 59.989 40.741 0.00 0.00 37.90 4.52
1802 3598 2.710096 ATGGTGTTGCCGCTATAACT 57.290 45.000 0.00 0.00 41.21 2.24
1867 3716 3.134127 GCCGCCATCACTTGTCCC 61.134 66.667 0.00 0.00 0.00 4.46
1934 4071 9.630098 AAACACAAATTTATTCTCTGCTGTATG 57.370 29.630 0.00 0.00 0.00 2.39
1989 4154 3.447742 CAAAGGCAAAACAGACAGGTTC 58.552 45.455 0.00 0.00 0.00 3.62
2065 4236 5.916318 TGCAAATTGTGGTTCTGAATTCTT 58.084 33.333 7.05 0.00 0.00 2.52
2119 4291 1.816863 GAGGTGGACTGTCAGGCGAA 61.817 60.000 10.38 0.00 0.00 4.70
2147 4322 8.168058 GGGAGTCCTACTCTTATCTTTCTCTAT 58.832 40.741 9.58 0.00 44.46 1.98
2149 4324 9.569122 GAGTCCTACTCTTATCTTTCTCTATGT 57.431 37.037 0.00 0.00 41.88 2.29
2191 4366 0.606401 AACTCGGTGTGGGCTGAATG 60.606 55.000 0.00 0.00 0.00 2.67
2196 4371 0.326264 GGTGTGGGCTGAATGAGACT 59.674 55.000 0.00 0.00 0.00 3.24
2234 4409 3.705051 AGGAATCATGTCACAGGCAATT 58.295 40.909 0.00 0.00 0.00 2.32
2236 4411 2.953466 ATCATGTCACAGGCAATTGC 57.047 45.000 22.47 22.47 41.14 3.56
2251 4426 4.455190 GGCAATTGCTGGAGAAGATCTATC 59.545 45.833 28.42 3.55 41.70 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.511600 GCGGCTGATGTTAGCGGT 60.512 61.111 0.00 0.00 44.60 5.68
15 16 2.125552 TTGTCGAGGCGGCTGATG 60.126 61.111 19.63 6.13 30.55 3.07
100 113 1.425412 CTTGTTGCAAAGCCATGAGC 58.575 50.000 0.00 0.00 44.25 4.26
101 114 1.614903 TCCTTGTTGCAAAGCCATGAG 59.385 47.619 0.00 0.00 0.00 2.90
102 115 1.340889 GTCCTTGTTGCAAAGCCATGA 59.659 47.619 0.00 0.00 0.00 3.07
103 116 1.606224 GGTCCTTGTTGCAAAGCCATG 60.606 52.381 0.00 0.00 0.00 3.66
104 117 0.681175 GGTCCTTGTTGCAAAGCCAT 59.319 50.000 0.00 0.00 0.00 4.40
203 216 4.477975 GGAGGTGCGACGACTCCG 62.478 72.222 14.92 0.00 41.15 4.63
213 226 2.035442 GCTGGTTCGAAGGAGGTGC 61.035 63.158 0.00 0.00 0.00 5.01
215 228 1.371558 GTGCTGGTTCGAAGGAGGT 59.628 57.895 0.00 0.00 0.00 3.85
293 306 0.886938 TCGGTTGCAGAAATCGCCAA 60.887 50.000 0.00 0.00 42.36 4.52
323 336 1.858000 GCAACACGACGCATGTTTCAA 60.858 47.619 1.44 0.00 38.22 2.69
363 376 1.966901 AATGAGCGCCCCGTGTCATA 61.967 55.000 2.29 0.00 33.79 2.15
364 377 3.329542 AATGAGCGCCCCGTGTCAT 62.330 57.895 2.29 2.13 35.40 3.06
365 378 3.950794 GAATGAGCGCCCCGTGTCA 62.951 63.158 2.29 0.00 0.00 3.58
366 379 3.195698 GAATGAGCGCCCCGTGTC 61.196 66.667 2.29 0.00 0.00 3.67
367 380 3.706373 AGAATGAGCGCCCCGTGT 61.706 61.111 2.29 0.00 0.00 4.49
368 381 3.197790 CAGAATGAGCGCCCCGTG 61.198 66.667 2.29 0.00 39.69 4.94
434 447 9.443283 CGGTTTGATGATGAATATTTTCTCTTC 57.557 33.333 0.00 0.00 32.78 2.87
439 452 6.918022 GTCCCGGTTTGATGATGAATATTTTC 59.082 38.462 0.00 0.00 0.00 2.29
451 464 1.883021 GGCAAGTCCCGGTTTGATG 59.117 57.895 13.02 1.77 0.00 3.07
452 465 1.674322 CGGCAAGTCCCGGTTTGAT 60.674 57.895 13.02 0.00 44.46 2.57
470 483 1.975363 GATCAAGCACTCGCACTGGC 61.975 60.000 0.00 0.00 42.27 4.85
471 484 0.671472 TGATCAAGCACTCGCACTGG 60.671 55.000 0.00 0.00 42.27 4.00
472 485 1.150827 TTGATCAAGCACTCGCACTG 58.849 50.000 3.38 0.00 42.27 3.66
473 486 1.882912 TTTGATCAAGCACTCGCACT 58.117 45.000 8.41 0.00 42.27 4.40
474 487 2.686558 TTTTGATCAAGCACTCGCAC 57.313 45.000 8.41 0.00 42.27 5.34
475 488 2.813172 TGATTTTGATCAAGCACTCGCA 59.187 40.909 8.41 0.00 42.27 5.10
476 489 3.476295 TGATTTTGATCAAGCACTCGC 57.524 42.857 8.41 0.00 38.99 5.03
477 490 5.032863 GGATTGATTTTGATCAAGCACTCG 58.967 41.667 16.26 0.00 45.67 4.18
478 491 5.032863 CGGATTGATTTTGATCAAGCACTC 58.967 41.667 16.26 11.19 45.67 3.51
479 492 4.701651 TCGGATTGATTTTGATCAAGCACT 59.298 37.500 16.26 3.34 45.67 4.40
480 493 4.795278 GTCGGATTGATTTTGATCAAGCAC 59.205 41.667 16.26 4.81 45.67 4.40
481 494 4.437255 CGTCGGATTGATTTTGATCAAGCA 60.437 41.667 16.26 6.00 45.67 3.91
514 684 1.968017 CAGGCACAACATCCGCTGT 60.968 57.895 0.00 0.00 40.84 4.40
516 686 3.058160 GCAGGCACAACATCCGCT 61.058 61.111 0.00 0.00 0.00 5.52
530 700 3.559238 AAACGCTAACCTTCAATGCAG 57.441 42.857 0.00 0.00 0.00 4.41
534 704 5.722021 ATTGGAAAACGCTAACCTTCAAT 57.278 34.783 0.00 0.00 0.00 2.57
555 725 8.685838 TTCGCTAGTATTTGGCCTATTTTTAT 57.314 30.769 3.32 0.00 0.00 1.40
556 726 8.685838 ATTCGCTAGTATTTGGCCTATTTTTA 57.314 30.769 3.32 0.00 0.00 1.52
562 733 3.644265 TGGATTCGCTAGTATTTGGCCTA 59.356 43.478 3.32 0.00 0.00 3.93
563 734 2.438021 TGGATTCGCTAGTATTTGGCCT 59.562 45.455 3.32 0.00 0.00 5.19
577 748 5.764686 TGGATTACCTCATTTCATGGATTCG 59.235 40.000 0.00 0.00 37.04 3.34
583 754 6.375174 TGTGTTCTGGATTACCTCATTTCATG 59.625 38.462 0.00 0.00 37.04 3.07
586 757 5.705441 TGTGTGTTCTGGATTACCTCATTTC 59.295 40.000 0.00 0.00 37.04 2.17
619 790 4.081972 TGTCTGAGTTGGTAGATCTTGAGC 60.082 45.833 0.00 0.00 0.00 4.26
718 889 3.518998 GCGAGCTAGTCCGCCTGA 61.519 66.667 16.45 0.00 45.06 3.86
736 907 1.519455 CGAACAGCCGGGAGATGAC 60.519 63.158 2.18 0.00 0.00 3.06
737 908 1.982395 ACGAACAGCCGGGAGATGA 60.982 57.895 2.18 0.00 0.00 2.92
738 909 1.811266 CACGAACAGCCGGGAGATG 60.811 63.158 2.18 0.00 34.30 2.90
739 910 2.579201 CACGAACAGCCGGGAGAT 59.421 61.111 2.18 0.00 34.30 2.75
786 957 2.436646 CCAGTCGAAATGGCCGCT 60.437 61.111 5.07 0.00 0.00 5.52
924 1123 1.154413 GCACAACTTGCGATCACGG 60.154 57.895 0.00 0.00 42.79 4.94
944 1147 0.249657 GATCGCAGGTAGCTTCTGGG 60.250 60.000 20.33 20.33 43.67 4.45
952 1155 0.179100 CACCACCAGATCGCAGGTAG 60.179 60.000 7.13 3.69 36.07 3.18
953 1156 0.613572 TCACCACCAGATCGCAGGTA 60.614 55.000 7.13 0.00 36.07 3.08
1144 1354 1.067776 CGTGGTGTGGTAGAACTCCTC 60.068 57.143 0.00 0.00 35.25 3.71
1272 1507 0.299895 GATCAAGCATCGCTGTCGTG 59.700 55.000 0.00 0.00 39.62 4.35
1324 1559 3.519579 AGATTCAGTCATTCAGAGCGTG 58.480 45.455 0.00 0.00 0.00 5.34
1329 1564 5.526479 GCAAGCATAGATTCAGTCATTCAGA 59.474 40.000 0.00 0.00 0.00 3.27
1333 1568 4.194640 ACGCAAGCATAGATTCAGTCATT 58.805 39.130 0.00 0.00 45.62 2.57
1337 1572 2.555199 GGACGCAAGCATAGATTCAGT 58.445 47.619 0.00 0.00 45.62 3.41
1338 1573 1.524355 CGGACGCAAGCATAGATTCAG 59.476 52.381 0.00 0.00 45.62 3.02
1339 1574 1.134818 ACGGACGCAAGCATAGATTCA 60.135 47.619 0.00 0.00 45.62 2.57
1340 1575 1.258982 CACGGACGCAAGCATAGATTC 59.741 52.381 0.00 0.00 45.62 2.52
1341 1576 1.290203 CACGGACGCAAGCATAGATT 58.710 50.000 0.00 0.00 45.62 2.40
1342 1577 0.175760 ACACGGACGCAAGCATAGAT 59.824 50.000 0.00 0.00 45.62 1.98
1343 1578 0.457853 GACACGGACGCAAGCATAGA 60.458 55.000 0.00 0.00 45.62 1.98
1344 1579 0.458543 AGACACGGACGCAAGCATAG 60.459 55.000 0.00 0.00 45.62 2.23
1345 1580 0.457853 GAGACACGGACGCAAGCATA 60.458 55.000 0.00 0.00 45.62 3.14
1346 1581 1.738099 GAGACACGGACGCAAGCAT 60.738 57.895 0.00 0.00 45.62 3.79
1347 1582 2.355837 GAGACACGGACGCAAGCA 60.356 61.111 0.00 0.00 45.62 3.91
1348 1583 2.049063 AGAGACACGGACGCAAGC 60.049 61.111 0.00 0.00 45.62 4.01
1349 1584 2.183858 TCGAGAGACACGGACGCAAG 62.184 60.000 0.00 0.00 38.54 4.01
1350 1585 2.183858 CTCGAGAGACACGGACGCAA 62.184 60.000 6.58 0.00 35.39 4.85
1358 1593 1.795286 CTGCCAAAACTCGAGAGACAC 59.205 52.381 21.68 4.35 35.39 3.67
1366 1601 1.372128 GCCAAGCTGCCAAAACTCG 60.372 57.895 0.00 0.00 0.00 4.18
1379 1614 4.566545 TGTGTGTACAATTTCAGCCAAG 57.433 40.909 0.00 0.00 32.88 3.61
1392 1627 5.181690 TGCAAGAAAGGAATTGTGTGTAC 57.818 39.130 0.00 0.00 0.00 2.90
1393 1628 4.887071 ACTGCAAGAAAGGAATTGTGTGTA 59.113 37.500 0.00 0.00 37.43 2.90
1395 1630 4.293415 GACTGCAAGAAAGGAATTGTGTG 58.707 43.478 0.00 0.00 37.43 3.82
1396 1631 3.003689 CGACTGCAAGAAAGGAATTGTGT 59.996 43.478 0.00 0.00 37.43 3.72
1397 1632 3.250762 TCGACTGCAAGAAAGGAATTGTG 59.749 43.478 0.00 0.00 37.43 3.33
1399 1634 4.488126 TTCGACTGCAAGAAAGGAATTG 57.512 40.909 0.00 0.00 37.43 2.32
1400 1635 4.520492 ACATTCGACTGCAAGAAAGGAATT 59.480 37.500 2.19 0.00 37.43 2.17
1401 1636 4.074970 ACATTCGACTGCAAGAAAGGAAT 58.925 39.130 2.19 0.00 37.43 3.01
1402 1637 3.250762 CACATTCGACTGCAAGAAAGGAA 59.749 43.478 2.19 0.00 37.43 3.36
1403 1638 2.807967 CACATTCGACTGCAAGAAAGGA 59.192 45.455 2.19 0.00 37.43 3.36
1404 1639 2.095567 CCACATTCGACTGCAAGAAAGG 60.096 50.000 2.19 3.42 37.43 3.11
1405 1640 2.807967 TCCACATTCGACTGCAAGAAAG 59.192 45.455 2.19 2.49 37.43 2.62
1406 1641 2.844946 TCCACATTCGACTGCAAGAAA 58.155 42.857 2.19 0.00 37.43 2.52
1408 1643 2.143122 GTTCCACATTCGACTGCAAGA 58.857 47.619 2.19 0.00 37.43 3.02
1409 1644 2.146342 AGTTCCACATTCGACTGCAAG 58.854 47.619 2.19 0.00 42.29 4.01
1411 1646 1.872952 CAAGTTCCACATTCGACTGCA 59.127 47.619 2.19 0.00 0.00 4.41
1412 1647 2.143122 TCAAGTTCCACATTCGACTGC 58.857 47.619 2.19 0.00 0.00 4.40
1414 1649 4.248859 CTCATCAAGTTCCACATTCGACT 58.751 43.478 0.00 0.00 0.00 4.18
1415 1650 3.181516 GCTCATCAAGTTCCACATTCGAC 60.182 47.826 0.00 0.00 0.00 4.20
1416 1651 3.002791 GCTCATCAAGTTCCACATTCGA 58.997 45.455 0.00 0.00 0.00 3.71
1417 1652 3.005554 AGCTCATCAAGTTCCACATTCG 58.994 45.455 0.00 0.00 0.00 3.34
1418 1653 4.005650 TGAGCTCATCAAGTTCCACATTC 58.994 43.478 13.74 0.00 34.50 2.67
1419 1654 4.008330 CTGAGCTCATCAAGTTCCACATT 58.992 43.478 18.63 0.00 37.52 2.71
1421 1656 2.634453 TCTGAGCTCATCAAGTTCCACA 59.366 45.455 18.63 0.00 37.52 4.17
1422 1657 3.325293 TCTGAGCTCATCAAGTTCCAC 57.675 47.619 18.63 0.00 37.52 4.02
1425 1660 5.008619 TCTCATCTGAGCTCATCAAGTTC 57.991 43.478 18.63 0.00 41.80 3.01
1426 1661 5.603596 GATCTCATCTGAGCTCATCAAGTT 58.396 41.667 18.63 7.70 41.80 2.66
1427 1662 4.261698 CGATCTCATCTGAGCTCATCAAGT 60.262 45.833 18.63 0.26 41.80 3.16
1430 1665 2.030096 GCGATCTCATCTGAGCTCATCA 60.030 50.000 18.63 7.47 41.80 3.07
1431 1666 2.030096 TGCGATCTCATCTGAGCTCATC 60.030 50.000 18.63 9.02 41.80 2.92
1432 1667 1.962100 TGCGATCTCATCTGAGCTCAT 59.038 47.619 18.63 0.00 41.80 2.90
1433 1668 1.066757 GTGCGATCTCATCTGAGCTCA 59.933 52.381 17.19 17.19 41.80 4.26
1434 1669 1.602668 GGTGCGATCTCATCTGAGCTC 60.603 57.143 6.82 6.82 41.80 4.09
1437 1672 2.591571 TTGGTGCGATCTCATCTGAG 57.408 50.000 0.56 0.56 43.36 3.35
1439 1674 2.287103 CACATTGGTGCGATCTCATCTG 59.713 50.000 0.00 0.00 38.37 2.90
1440 1675 2.558378 CACATTGGTGCGATCTCATCT 58.442 47.619 0.00 0.00 38.37 2.90
1508 2366 7.398618 AGACAAATTCAACTATCCTCTCAGAGA 59.601 37.037 2.09 0.00 0.00 3.10
1514 2372 9.442047 CTTACAAGACAAATTCAACTATCCTCT 57.558 33.333 0.00 0.00 0.00 3.69
1632 3401 0.788995 CTTGTGCTCGCTTCTCTGTG 59.211 55.000 0.00 0.00 0.00 3.66
1693 3462 6.584185 AATTGTAAGGTTTTTATCTGCCGT 57.416 33.333 0.00 0.00 0.00 5.68
1694 3463 7.621219 GCAAAATTGTAAGGTTTTTATCTGCCG 60.621 37.037 0.00 0.00 0.00 5.69
1737 3515 2.826128 ACTCTCAGGTTTCTACATCGCA 59.174 45.455 0.00 0.00 0.00 5.10
1738 3516 3.182967 CACTCTCAGGTTTCTACATCGC 58.817 50.000 0.00 0.00 0.00 4.58
1739 3517 4.442375 ACACTCTCAGGTTTCTACATCG 57.558 45.455 0.00 0.00 0.00 3.84
1766 3552 7.011482 GCAACACCATAAGATACTAGTTTCTGG 59.989 40.741 15.48 14.95 0.00 3.86
1792 3583 5.398169 TGCACAAAATTCAAGTTATAGCGG 58.602 37.500 0.00 0.00 0.00 5.52
1793 3584 6.314018 TCTGCACAAAATTCAAGTTATAGCG 58.686 36.000 0.00 0.00 0.00 4.26
1802 3598 4.629200 GTGGTGTTTCTGCACAAAATTCAA 59.371 37.500 0.00 0.00 40.89 2.69
1867 3716 1.227031 ATGGCCATTTCAATGCGCG 60.227 52.632 14.09 0.00 35.09 6.86
1934 4071 9.683069 AAACTTCAGAACATGTATGAACAAATC 57.317 29.630 17.90 2.05 39.58 2.17
1989 4154 3.873952 GCTCTTGTTATTCTGCTACCTGG 59.126 47.826 0.00 0.00 0.00 4.45
2065 4236 1.470805 CGCCTCCGACACAATGACATA 60.471 52.381 0.00 0.00 36.29 2.29
2119 4291 5.196984 AGAAAGATAAGAGTAGGACTCCCCT 59.803 44.000 3.00 0.00 46.18 4.79
2130 4305 9.107177 CAATGCAACATAGAGAAAGATAAGAGT 57.893 33.333 0.00 0.00 0.00 3.24
2147 4322 0.251121 ACCCGGATGTCAATGCAACA 60.251 50.000 0.73 0.00 0.00 3.33
2149 4324 1.680555 GGTACCCGGATGTCAATGCAA 60.681 52.381 0.73 0.00 0.00 4.08
2191 4366 6.655848 TCCTTACTCTTTCACTGTCTAGTCTC 59.344 42.308 0.00 0.00 34.07 3.36
2196 4371 7.776618 TGATTCCTTACTCTTTCACTGTCTA 57.223 36.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.