Multiple sequence alignment - TraesCS3A01G485600

Loading Multiple Alignment...

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 TraesCS3A01G485600 chr3A 100.000 4341 0 0 1 4341 714591684 714587344 0.000000e+00 8017
1 TraesCS3A01G485600 chr3A 89.119 2463 190 36 1633 4044 714645540 714647975 0.000000e+00 2992
2 TraesCS3A01G485600 chr3A 90.465 1248 113 5 1 1248 714643673 714644914 0.000000e+00 1640
3 TraesCS3A01G485600 chr3A 87.805 779 82 5 794 1571 714627773 714628539 0.000000e+00 900
4 TraesCS3A01G485600 chr3A 88.757 676 67 5 2717 3391 714602902 714602235 0.000000e+00 819
5 TraesCS3A01G485600 chr3A 90.811 185 15 2 1230 1414 714644930 714645112 3.350000e-61 246
6 TraesCS3A01G485600 chr3D 89.864 3374 293 23 4 3350 579423874 579420523 0.000000e+00 4290
7 TraesCS3A01G485600 chr3D 89.651 2464 185 39 1633 4045 579587107 579589551 0.000000e+00 3073
8 TraesCS3A01G485600 chr3D 94.249 1339 74 3 1 1339 579396187 579394852 0.000000e+00 2043
9 TraesCS3A01G485600 chr3D 91.960 1393 107 5 1 1393 579585292 579586679 0.000000e+00 1947
10 TraesCS3A01G485600 chr3D 91.067 1265 71 15 1364 2609 579394855 579393614 0.000000e+00 1672
11 TraesCS3A01G485600 chr3D 93.868 848 44 6 2605 3449 579383798 579382956 0.000000e+00 1271
12 TraesCS3A01G485600 chr3D 86.622 299 34 6 4046 4341 579379623 579379328 4.190000e-85 326
13 TraesCS3A01G485600 chr3D 91.703 229 7 2 3562 3779 579382959 579382732 1.520000e-79 307
14 TraesCS3A01G485600 chr3D 92.179 179 14 0 3169 3347 579367490 579367312 2.000000e-63 254
15 TraesCS3A01G485600 chr3B 88.419 3402 321 27 24 3390 773761067 773757704 0.000000e+00 4032
16 TraesCS3A01G485600 chr3B 91.165 1777 128 17 1628 3387 773900177 773901941 0.000000e+00 2385
17 TraesCS3A01G485600 chr3B 91.203 1239 106 2 8 1246 773898620 773899855 0.000000e+00 1681
18 TraesCS3A01G485600 chr3B 95.770 662 22 4 2686 3345 773743745 773743088 0.000000e+00 1062
19 TraesCS3A01G485600 chr3B 89.189 185 18 2 1230 1414 773899873 773900055 3.380000e-56 230
20 TraesCS3A01G485600 chr3B 90.722 97 8 1 3384 3479 773730251 773730155 1.270000e-25 128


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 TraesCS3A01G485600 chr3A 714587344 714591684 4340 True 8017.000000 8017 100.000000 1 4341 1 chr3A.!!$R1 4340
1 TraesCS3A01G485600 chr3A 714643673 714647975 4302 False 1626.000000 2992 90.131667 1 4044 3 chr3A.!!$F2 4043
2 TraesCS3A01G485600 chr3A 714627773 714628539 766 False 900.000000 900 87.805000 794 1571 1 chr3A.!!$F1 777
3 TraesCS3A01G485600 chr3A 714602235 714602902 667 True 819.000000 819 88.757000 2717 3391 1 chr3A.!!$R2 674
4 TraesCS3A01G485600 chr3D 579420523 579423874 3351 True 4290.000000 4290 89.864000 4 3350 1 chr3D.!!$R2 3346
5 TraesCS3A01G485600 chr3D 579585292 579589551 4259 False 2510.000000 3073 90.805500 1 4045 2 chr3D.!!$F1 4044
6 TraesCS3A01G485600 chr3D 579393614 579396187 2573 True 1857.500000 2043 92.658000 1 2609 2 chr3D.!!$R4 2608
7 TraesCS3A01G485600 chr3D 579379328 579383798 4470 True 634.666667 1271 90.731000 2605 4341 3 chr3D.!!$R3 1736
8 TraesCS3A01G485600 chr3B 773757704 773761067 3363 True 4032.000000 4032 88.419000 24 3390 1 chr3B.!!$R3 3366
9 TraesCS3A01G485600 chr3B 773898620 773901941 3321 False 1432.000000 2385 90.519000 8 3387 3 chr3B.!!$F1 3379
10 TraesCS3A01G485600 chr3B 773743088 773743745 657 True 1062.000000 1062 95.770000 2686 3345 1 chr3B.!!$R2 659

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
448 449 0.106918 GACCCACAAGACACACCCAA 60.107 55.0 0.00 0.0 0.00 4.12 F
1331 1400 0.316204 GCATGACAACTTGCTGCCTT 59.684 50.0 0.00 0.0 41.77 4.35 F
1778 2272 0.451783 CCTTGTATGGTTCCGCAAGC 59.548 55.0 11.92 0.0 37.56 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1581 0.034574 AACAACATGGGGATAGCGCA 60.035 50.000 11.47 0.0 0.00 6.09 R
2495 3018 2.047274 AATCGTGTCGGCCAGTGG 60.047 61.111 4.20 4.2 0.00 4.00 R
3559 4112 0.034896 AGTGATCACGGGGACACAAC 59.965 55.000 19.85 0.0 35.97 3.32 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 1.070275 CTCTGCACACCTGACAGCA 59.930 57.895 0.00 0.00 35.43 4.41
65 66 4.594920 TCTCACTCCTGGAAAAACTCTCAT 59.405 41.667 0.00 0.00 0.00 2.90
72 73 4.563580 CCTGGAAAAACTCTCATCTCGGAA 60.564 45.833 0.00 0.00 0.00 4.30
84 85 2.607631 TCTCGGAACAAGGTTCGTTT 57.392 45.000 3.30 0.00 0.00 3.60
286 287 2.620367 GGCCACCACATACTTTGGATGA 60.620 50.000 0.00 0.00 37.58 2.92
321 322 1.871772 CAGCAACTCTTCGGCCAAG 59.128 57.895 2.24 6.06 0.00 3.61
355 356 7.066284 ACAATGGCAATCTTGTAGTCTTATCAC 59.934 37.037 3.24 0.00 33.96 3.06
396 397 2.101415 GCAGAGCTTTGAAAACCCAAGT 59.899 45.455 8.73 0.00 0.00 3.16
448 449 0.106918 GACCCACAAGACACACCCAA 60.107 55.000 0.00 0.00 0.00 4.12
474 475 1.765314 CGGATGATCTCTTGGAAGGGT 59.235 52.381 0.00 0.00 0.00 4.34
524 525 1.073763 TGGTGGGAATGACCTTGACAG 59.926 52.381 0.00 0.00 38.98 3.51
609 610 1.580059 ATGTATCCTCCAACGTGGGT 58.420 50.000 9.33 0.00 38.32 4.51
648 649 7.604164 AGTCCACTCATGTATTTGACAGTTTAG 59.396 37.037 0.00 0.00 42.79 1.85
655 656 5.876357 TGTATTTGACAGTTTAGAAGGGCT 58.124 37.500 0.00 0.00 32.86 5.19
656 657 6.303839 TGTATTTGACAGTTTAGAAGGGCTT 58.696 36.000 0.00 0.00 32.86 4.35
858 859 1.497991 GCTACTGCGACAACACAGAA 58.502 50.000 0.00 0.00 37.35 3.02
873 874 2.559668 CACAGAAGCAATTCCCACATGT 59.440 45.455 0.00 0.00 0.00 3.21
901 902 4.202441 CCTTGATGGATTTGACCCTAGTG 58.798 47.826 0.00 0.00 38.35 2.74
910 911 5.300792 GGATTTGACCCTAGTGACAAAACAA 59.699 40.000 6.89 0.00 36.19 2.83
918 919 4.036380 CCTAGTGACAAAACAAAGTGGGTC 59.964 45.833 0.00 0.00 0.00 4.46
946 947 1.988293 TTTTTCTCATGGTTGCCGGA 58.012 45.000 5.05 0.00 0.00 5.14
1054 1055 4.439289 GGAACAAAAGCTATGATGACTGCC 60.439 45.833 6.45 0.00 0.00 4.85
1067 1068 0.819259 GACTGCCAAGTGGAGTGCAA 60.819 55.000 0.18 0.00 36.52 4.08
1183 1184 3.539604 CTGATTGATGTGGAGAAGGGTC 58.460 50.000 0.00 0.00 0.00 4.46
1215 1216 3.612955 GCTATGAGAACCTGTATCTCCGC 60.613 52.174 1.45 0.00 42.14 5.54
1249 1318 5.766222 TGTCAAGTACGTTCCTCTTTCTAC 58.234 41.667 0.00 0.00 0.00 2.59
1262 1331 6.456501 TCCTCTTTCTACTGCTCTTGTTTAC 58.543 40.000 0.00 0.00 0.00 2.01
1274 1343 4.554973 GCTCTTGTTTACGTTCATGAATGC 59.445 41.667 24.48 10.93 0.00 3.56
1329 1398 4.565531 GCATGACAACTTGCTGCC 57.434 55.556 0.00 0.00 41.77 4.85
1331 1400 0.316204 GCATGACAACTTGCTGCCTT 59.684 50.000 0.00 0.00 41.77 4.35
1332 1401 1.541147 GCATGACAACTTGCTGCCTTA 59.459 47.619 0.00 0.00 41.77 2.69
1350 1419 9.750125 GCTGCCTTATAACTTGCTAATAAATTT 57.250 29.630 0.00 0.00 0.00 1.82
1360 1429 8.748380 ACTTGCTAATAAATTTTGAGTTGCTC 57.252 30.769 0.00 0.00 0.00 4.26
1413 1511 7.363968 GCAAAGTCACTAGAGGGTATTAGTTCT 60.364 40.741 0.00 0.00 0.00 3.01
1414 1512 8.532819 CAAAGTCACTAGAGGGTATTAGTTCTT 58.467 37.037 0.00 0.00 0.00 2.52
1415 1513 9.765295 AAAGTCACTAGAGGGTATTAGTTCTTA 57.235 33.333 0.00 0.00 0.00 2.10
1416 1514 8.983702 AGTCACTAGAGGGTATTAGTTCTTAG 57.016 38.462 0.00 0.00 0.00 2.18
1417 1515 8.780003 AGTCACTAGAGGGTATTAGTTCTTAGA 58.220 37.037 0.00 0.00 0.00 2.10
1418 1516 9.406113 GTCACTAGAGGGTATTAGTTCTTAGAA 57.594 37.037 0.00 0.00 0.00 2.10
1421 1519 9.590828 ACTAGAGGGTATTAGTTCTTAGAATCC 57.409 37.037 0.00 0.00 0.00 3.01
1422 1520 9.816787 CTAGAGGGTATTAGTTCTTAGAATCCT 57.183 37.037 0.00 0.00 0.00 3.24
1426 1524 9.725206 AGGGTATTAGTTCTTAGAATCCTAACA 57.275 33.333 0.00 0.00 31.94 2.41
1434 1532 9.771534 AGTTCTTAGAATCCTAACATGCTAATC 57.228 33.333 0.00 0.00 31.94 1.75
1435 1533 9.771534 GTTCTTAGAATCCTAACATGCTAATCT 57.228 33.333 0.00 0.00 31.94 2.40
1436 1534 9.770097 TTCTTAGAATCCTAACATGCTAATCTG 57.230 33.333 0.00 0.00 31.94 2.90
1437 1535 9.147732 TCTTAGAATCCTAACATGCTAATCTGA 57.852 33.333 0.00 0.00 31.94 3.27
1438 1536 9.770097 CTTAGAATCCTAACATGCTAATCTGAA 57.230 33.333 0.00 0.00 31.94 3.02
1441 1539 8.897752 AGAATCCTAACATGCTAATCTGAAAAC 58.102 33.333 0.00 0.00 0.00 2.43
1442 1540 7.573968 ATCCTAACATGCTAATCTGAAAACC 57.426 36.000 0.00 0.00 0.00 3.27
1443 1541 6.721318 TCCTAACATGCTAATCTGAAAACCT 58.279 36.000 0.00 0.00 0.00 3.50
1444 1542 7.857456 TCCTAACATGCTAATCTGAAAACCTA 58.143 34.615 0.00 0.00 0.00 3.08
1445 1543 8.494433 TCCTAACATGCTAATCTGAAAACCTAT 58.506 33.333 0.00 0.00 0.00 2.57
1446 1544 8.562892 CCTAACATGCTAATCTGAAAACCTATG 58.437 37.037 0.00 0.00 0.00 2.23
1447 1545 6.382869 ACATGCTAATCTGAAAACCTATGC 57.617 37.500 0.00 0.00 0.00 3.14
1448 1546 6.125029 ACATGCTAATCTGAAAACCTATGCT 58.875 36.000 0.00 0.00 0.00 3.79
1449 1547 6.604795 ACATGCTAATCTGAAAACCTATGCTT 59.395 34.615 0.00 0.00 0.00 3.91
1450 1548 7.123247 ACATGCTAATCTGAAAACCTATGCTTT 59.877 33.333 0.00 0.00 0.00 3.51
1451 1549 7.088589 TGCTAATCTGAAAACCTATGCTTTC 57.911 36.000 0.00 0.00 33.10 2.62
1452 1550 6.658816 TGCTAATCTGAAAACCTATGCTTTCA 59.341 34.615 0.00 0.00 38.81 2.69
1460 1558 7.950512 TGAAAACCTATGCTTTCAGAATTTCA 58.049 30.769 0.00 0.00 36.79 2.69
1461 1559 8.084073 TGAAAACCTATGCTTTCAGAATTTCAG 58.916 33.333 0.00 0.00 36.79 3.02
1462 1560 7.530426 AAACCTATGCTTTCAGAATTTCAGT 57.470 32.000 0.00 0.00 0.00 3.41
1463 1561 8.635765 AAACCTATGCTTTCAGAATTTCAGTA 57.364 30.769 0.00 0.00 0.00 2.74
1464 1562 8.814038 AACCTATGCTTTCAGAATTTCAGTAT 57.186 30.769 0.00 0.00 0.00 2.12
1465 1563 8.814038 ACCTATGCTTTCAGAATTTCAGTATT 57.186 30.769 0.00 0.00 0.00 1.89
1466 1564 8.897752 ACCTATGCTTTCAGAATTTCAGTATTC 58.102 33.333 0.00 0.00 35.26 1.75
1467 1565 8.896744 CCTATGCTTTCAGAATTTCAGTATTCA 58.103 33.333 0.00 0.00 37.06 2.57
1471 1569 9.985730 TGCTTTCAGAATTTCAGTATTCAAATT 57.014 25.926 0.00 0.00 37.06 1.82
1476 1574 9.611284 TCAGAATTTCAGTATTCAAATTGTTCG 57.389 29.630 0.00 0.00 37.06 3.95
1477 1575 9.611284 CAGAATTTCAGTATTCAAATTGTTCGA 57.389 29.630 0.00 0.00 37.06 3.71
1478 1576 9.612620 AGAATTTCAGTATTCAAATTGTTCGAC 57.387 29.630 0.00 0.00 37.06 4.20
1479 1577 9.612620 GAATTTCAGTATTCAAATTGTTCGACT 57.387 29.630 0.00 0.00 33.31 4.18
1485 1583 9.586150 CAGTATTCAAATTGTTCGACTATATGC 57.414 33.333 0.00 0.00 0.00 3.14
1486 1584 8.487970 AGTATTCAAATTGTTCGACTATATGCG 58.512 33.333 0.00 0.00 0.00 4.73
1487 1585 5.078153 TCAAATTGTTCGACTATATGCGC 57.922 39.130 0.00 0.00 0.00 6.09
1528 1693 6.801862 GTCATTTGCTTGGTGTTTGTACTATC 59.198 38.462 0.00 0.00 0.00 2.08
1556 1724 5.689383 ATGTCAACGTATTTGATATGCCC 57.311 39.130 0.00 0.00 46.14 5.36
1588 1772 2.180276 CAGGTAGTGAGCCCAAGTACT 58.820 52.381 0.00 0.00 0.00 2.73
1618 1809 7.894376 AAAACATTCCTGATGCAATTAACTG 57.106 32.000 0.00 0.00 39.47 3.16
1778 2272 0.451783 CCTTGTATGGTTCCGCAAGC 59.548 55.000 11.92 0.00 37.56 4.01
1790 2284 4.248058 GTTCCGCAAGCTTAAAGGTAGTA 58.752 43.478 0.00 0.00 0.00 1.82
1795 2289 5.220605 CCGCAAGCTTAAAGGTAGTACATTC 60.221 44.000 0.00 0.00 0.00 2.67
1886 2382 4.326826 TCTCTTAGGCAAACATGACAAGG 58.673 43.478 0.00 0.00 0.00 3.61
1895 2391 4.219288 GCAAACATGACAAGGAAGGAAGAT 59.781 41.667 0.00 0.00 0.00 2.40
1975 2471 8.897752 ACTCATGAACTTCCATTTATTAGCTTC 58.102 33.333 0.00 0.00 0.00 3.86
2023 2523 9.574516 AACAACTTCTCTATGTCCAATTTACTT 57.425 29.630 0.00 0.00 0.00 2.24
2105 2605 9.515020 TCTAATTGCACCGAAATATGAAAAATC 57.485 29.630 0.00 0.00 0.00 2.17
2149 2661 8.810652 TTCAAAACTGAACCATAGTATTTTGC 57.189 30.769 0.00 0.00 31.08 3.68
2171 2683 5.772672 TGCAACCTTAATTTTCTTCCTGCTA 59.227 36.000 0.00 0.00 0.00 3.49
2392 2908 2.310538 AGCCTTGACACCTTCCTTTTG 58.689 47.619 0.00 0.00 0.00 2.44
2402 2918 5.070685 ACACCTTCCTTTTGAGTATGTTCC 58.929 41.667 0.00 0.00 0.00 3.62
2421 2937 6.841119 TGTTCCGATCACAAATTAATCAGTG 58.159 36.000 11.88 11.88 0.00 3.66
2443 2959 5.119588 GTGAAAAATCAGTTGATGCCACATG 59.880 40.000 0.00 0.00 34.49 3.21
2465 2988 9.017509 ACATGTGAAATCATAATCCCATACATC 57.982 33.333 0.00 0.00 0.00 3.06
2495 3018 7.022384 CAGATTCTGAAAAGAAGTCAATGCTC 58.978 38.462 8.00 0.00 32.44 4.26
2821 3353 6.665992 TTTATCCAGCGGTTATATGTCTCT 57.334 37.500 0.00 0.00 0.00 3.10
3007 3541 3.319122 GTCTGCAATTCCTTTTGACCACT 59.681 43.478 0.00 0.00 0.00 4.00
3018 3564 7.469537 TCCTTTTGACCACTTGACTTAAAAA 57.530 32.000 0.00 0.00 0.00 1.94
3118 3666 0.107945 AGGGCTGCTCGAATGAAGAC 60.108 55.000 0.00 0.00 0.00 3.01
3270 3818 8.951243 ACTGTATTTTTCTCAGAGAAATAAGGC 58.049 33.333 23.54 14.20 43.06 4.35
3474 4025 2.040278 CACCCCCTCAGTTCAAAGATGA 59.960 50.000 0.00 0.00 0.00 2.92
3476 4027 3.245052 ACCCCCTCAGTTCAAAGATGAAG 60.245 47.826 0.00 0.00 45.88 3.02
3479 4030 4.006319 CCCTCAGTTCAAAGATGAAGTCC 58.994 47.826 0.00 0.00 45.36 3.85
3480 4031 3.681897 CCTCAGTTCAAAGATGAAGTCCG 59.318 47.826 0.00 0.00 45.36 4.79
3506 4059 3.009143 GGAGGACAAGGTTATGGTCAACT 59.991 47.826 0.00 0.00 33.26 3.16
3512 4065 6.331369 ACAAGGTTATGGTCAACTTTGATG 57.669 37.500 15.08 0.00 44.09 3.07
3518 4071 0.109597 GGTCAACTTTGATGCTGCCG 60.110 55.000 0.00 0.00 39.73 5.69
3537 4090 4.631377 TGCCGTCTTCTTACAATCTGAATG 59.369 41.667 0.00 0.00 0.00 2.67
3556 4109 2.660572 TGTATTGGTGCTGGTGTTGTT 58.339 42.857 0.00 0.00 0.00 2.83
3559 4112 1.102154 TTGGTGCTGGTGTTGTTCTG 58.898 50.000 0.00 0.00 0.00 3.02
3566 4119 2.477863 GCTGGTGTTGTTCTGTTGTGTC 60.478 50.000 0.00 0.00 0.00 3.67
3611 4164 0.101399 ACGCTCACCATCGCTTCTAG 59.899 55.000 0.00 0.00 0.00 2.43
3736 4301 0.107017 GGCTAAGCTGAATGCCTCCA 60.107 55.000 10.92 0.00 44.23 3.86
3772 4347 4.334759 TCGTCTACTGGTACTACATCAAGC 59.665 45.833 0.00 0.00 0.00 4.01
3802 6137 5.580297 GCATTGAAGTTTGTTTCAGTTTCCA 59.420 36.000 0.00 0.00 38.25 3.53
3838 6175 0.033642 GTCTGTAATAGGGCGGCTCC 59.966 60.000 9.56 0.00 0.00 4.70
3847 6184 2.746359 GGCGGCTCCTGCTATCAT 59.254 61.111 0.00 0.00 39.59 2.45
3854 6191 1.626747 CTCCTGCTATCATGCGATCG 58.373 55.000 11.69 11.69 35.36 3.69
3906 6243 2.332063 TGAAGCTCCGGATTTCATCC 57.668 50.000 21.29 3.68 46.22 3.51
3939 6276 8.409371 TGCTTTGTAATGAACTTGTTGTGATTA 58.591 29.630 0.00 0.00 0.00 1.75
3996 6350 1.379527 CTAAAGGAATCACACGCCCC 58.620 55.000 0.00 0.00 0.00 5.80
4045 7474 0.804989 AGTTTTGCGGCATGCTACTC 59.195 50.000 18.92 4.95 46.63 2.59
4046 7475 0.521291 GTTTTGCGGCATGCTACTCA 59.479 50.000 18.92 7.57 46.63 3.41
4047 7476 1.133025 GTTTTGCGGCATGCTACTCAT 59.867 47.619 18.92 0.00 46.63 2.90
4061 7490 0.908198 ACTCATGGCTCCAGGAAGTC 59.092 55.000 4.75 0.00 36.28 3.01
4067 7496 2.334977 TGGCTCCAGGAAGTCTTGTTA 58.665 47.619 0.00 0.00 0.00 2.41
4068 7497 2.303022 TGGCTCCAGGAAGTCTTGTTAG 59.697 50.000 0.00 0.00 0.00 2.34
4076 7505 6.003950 CCAGGAAGTCTTGTTAGGAAATTCA 58.996 40.000 0.00 0.00 0.00 2.57
4083 7512 6.655425 AGTCTTGTTAGGAAATTCAGTTAGCC 59.345 38.462 0.00 0.00 0.00 3.93
4088 7517 3.000727 AGGAAATTCAGTTAGCCGAACG 58.999 45.455 0.00 0.00 43.37 3.95
4094 7523 0.796312 CAGTTAGCCGAACGTTGCAT 59.204 50.000 5.00 0.00 43.37 3.96
4106 7535 3.980646 ACGTTGCATGTTAGCTTTTCA 57.019 38.095 0.00 0.00 34.99 2.69
4124 7553 5.867903 TTTCAGCCAATCCAGAAAAGAAA 57.132 34.783 0.00 0.00 0.00 2.52
4126 7555 5.200368 TCAGCCAATCCAGAAAAGAAAAC 57.800 39.130 0.00 0.00 0.00 2.43
4190 7621 6.713762 TCATCCTGTTTTGAAAATGTCTGT 57.286 33.333 0.00 0.00 0.00 3.41
4191 7622 7.111247 TCATCCTGTTTTGAAAATGTCTGTT 57.889 32.000 0.00 0.00 0.00 3.16
4192 7623 6.979817 TCATCCTGTTTTGAAAATGTCTGTTG 59.020 34.615 0.00 0.00 0.00 3.33
4302 7734 9.778993 ATATGTTTTCAGAAAAAGATCATCGTG 57.221 29.630 10.00 0.00 38.74 4.35
4303 7735 7.026631 TGTTTTCAGAAAAAGATCATCGTGT 57.973 32.000 10.00 0.00 35.10 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.179009 ACAAGCATGCTGTCAGGTGT 60.179 50.000 23.48 17.63 0.00 4.16
65 66 2.206750 CAAACGAACCTTGTTCCGAGA 58.793 47.619 0.00 0.00 0.00 4.04
100 101 3.893753 TTCAGTTGAATTTGAGGGGGA 57.106 42.857 0.00 0.00 0.00 4.81
188 189 4.371786 TGAAGCATCAGTGATCGGATTAC 58.628 43.478 1.56 4.84 0.00 1.89
286 287 1.067516 GCTGCCAGTGATTGTGTTTGT 59.932 47.619 0.00 0.00 0.00 2.83
321 322 3.863142 AGATTGCCATTGTTGAGAAGC 57.137 42.857 0.00 0.00 0.00 3.86
355 356 1.958579 CCATAACATGGCACCATCTGG 59.041 52.381 0.00 1.48 44.70 3.86
396 397 2.879233 GCCAGGAAGGACGGTGTCA 61.879 63.158 0.00 0.00 41.22 3.58
448 449 1.202734 CCAAGAGATCATCCGCCATGT 60.203 52.381 0.00 0.00 33.66 3.21
474 475 3.508845 CCTTTTGAAGGGTCTTCAGGA 57.491 47.619 9.81 2.26 45.27 3.86
524 525 2.094649 CAGACGAAGAACTGTAGGGGAC 60.095 54.545 0.00 0.00 33.13 4.46
609 610 1.075050 AGTGGACTAACGGTCTGGAGA 59.925 52.381 0.00 0.00 43.97 3.71
648 649 0.462759 CCTCACCATCGAAGCCCTTC 60.463 60.000 0.00 0.00 36.29 3.46
655 656 0.106708 GCATAGGCCTCACCATCGAA 59.893 55.000 9.68 0.00 43.14 3.71
656 657 1.048160 TGCATAGGCCTCACCATCGA 61.048 55.000 9.68 0.00 43.14 3.59
739 740 2.028112 TGGTATTCCATCTCCATAGCGC 60.028 50.000 0.00 0.00 39.03 5.92
807 808 6.016693 CACCACAGTATCCATAGAGACTACAG 60.017 46.154 0.00 0.00 42.67 2.74
858 859 2.493278 GCACTTACATGTGGGAATTGCT 59.507 45.455 9.11 0.00 38.31 3.91
901 902 3.066760 CCTCTGACCCACTTTGTTTTGTC 59.933 47.826 0.00 0.00 0.00 3.18
910 911 2.683211 AAATTGCCTCTGACCCACTT 57.317 45.000 0.00 0.00 0.00 3.16
918 919 4.796038 ACCATGAGAAAAATTGCCTCTG 57.204 40.909 0.00 0.00 0.00 3.35
946 947 3.209410 CACACTGCAGTTCTTCCTTTCT 58.791 45.455 18.94 0.00 0.00 2.52
1054 1055 5.146482 CAATTTTTGTTGCACTCCACTTG 57.854 39.130 0.00 0.00 0.00 3.16
1067 1068 5.199024 TGCTACACATGAGCAATTTTTGT 57.801 34.783 5.17 0.00 46.71 2.83
1183 1184 0.249447 TTCTCATAGCCGATGGTGCG 60.249 55.000 0.00 0.00 36.08 5.34
1195 1196 2.891580 GGCGGAGATACAGGTTCTCATA 59.108 50.000 3.39 0.00 41.16 2.15
1215 1216 1.537202 GTACTTGACAAGGCAGCAAGG 59.463 52.381 19.16 0.00 42.40 3.61
1249 1318 4.990543 TCATGAACGTAAACAAGAGCAG 57.009 40.909 0.00 0.00 0.00 4.24
1274 1343 9.781834 TGTTACACACAAATTCTTAAACTGAAG 57.218 29.630 0.00 0.00 29.87 3.02
1350 1419 1.405105 GCCAAAGTGTGAGCAACTCAA 59.595 47.619 0.00 0.00 42.46 3.02
1360 1429 4.577152 TGGTGGAGCCAAAGTGTG 57.423 55.556 0.00 0.00 45.94 3.82
1415 1513 8.897752 GTTTTCAGATTAGCATGTTAGGATTCT 58.102 33.333 0.00 0.00 0.00 2.40
1416 1514 8.131731 GGTTTTCAGATTAGCATGTTAGGATTC 58.868 37.037 0.00 0.00 0.00 2.52
1417 1515 7.836183 AGGTTTTCAGATTAGCATGTTAGGATT 59.164 33.333 0.00 0.00 0.00 3.01
1418 1516 7.349598 AGGTTTTCAGATTAGCATGTTAGGAT 58.650 34.615 0.00 0.00 0.00 3.24
1419 1517 6.721318 AGGTTTTCAGATTAGCATGTTAGGA 58.279 36.000 0.00 0.00 0.00 2.94
1420 1518 8.562892 CATAGGTTTTCAGATTAGCATGTTAGG 58.437 37.037 0.00 0.00 0.00 2.69
1421 1519 8.072567 GCATAGGTTTTCAGATTAGCATGTTAG 58.927 37.037 0.00 0.00 0.00 2.34
1422 1520 7.775093 AGCATAGGTTTTCAGATTAGCATGTTA 59.225 33.333 0.00 0.00 0.00 2.41
1423 1521 6.604795 AGCATAGGTTTTCAGATTAGCATGTT 59.395 34.615 0.00 0.00 0.00 2.71
1424 1522 6.125029 AGCATAGGTTTTCAGATTAGCATGT 58.875 36.000 0.00 0.00 0.00 3.21
1425 1523 6.630444 AGCATAGGTTTTCAGATTAGCATG 57.370 37.500 0.00 0.00 0.00 4.06
1426 1524 7.340232 TGAAAGCATAGGTTTTCAGATTAGCAT 59.660 33.333 14.25 0.00 45.47 3.79
1427 1525 6.658816 TGAAAGCATAGGTTTTCAGATTAGCA 59.341 34.615 14.25 0.00 45.47 3.49
1428 1526 7.088589 TGAAAGCATAGGTTTTCAGATTAGC 57.911 36.000 14.25 0.00 45.47 3.09
1436 1534 8.084684 ACTGAAATTCTGAAAGCATAGGTTTTC 58.915 33.333 9.43 9.43 42.52 2.29
1437 1535 7.955918 ACTGAAATTCTGAAAGCATAGGTTTT 58.044 30.769 6.87 0.00 33.25 2.43
1438 1536 7.530426 ACTGAAATTCTGAAAGCATAGGTTT 57.470 32.000 6.87 0.00 35.90 3.27
1439 1537 8.814038 ATACTGAAATTCTGAAAGCATAGGTT 57.186 30.769 6.87 0.00 0.00 3.50
1440 1538 8.814038 AATACTGAAATTCTGAAAGCATAGGT 57.186 30.769 6.87 0.00 0.00 3.08
1441 1539 8.896744 TGAATACTGAAATTCTGAAAGCATAGG 58.103 33.333 6.87 0.00 36.90 2.57
1445 1543 9.985730 AATTTGAATACTGAAATTCTGAAAGCA 57.014 25.926 6.87 0.00 36.90 3.91
1450 1548 9.611284 CGAACAATTTGAATACTGAAATTCTGA 57.389 29.630 6.87 0.00 36.90 3.27
1451 1549 9.611284 TCGAACAATTTGAATACTGAAATTCTG 57.389 29.630 2.79 0.00 36.90 3.02
1452 1550 9.612620 GTCGAACAATTTGAATACTGAAATTCT 57.387 29.630 2.79 0.00 36.90 2.40
1453 1551 9.612620 AGTCGAACAATTTGAATACTGAAATTC 57.387 29.630 2.79 0.00 36.57 2.17
1459 1557 9.586150 GCATATAGTCGAACAATTTGAATACTG 57.414 33.333 2.79 0.00 0.00 2.74
1460 1558 8.487970 CGCATATAGTCGAACAATTTGAATACT 58.512 33.333 2.79 4.03 0.00 2.12
1461 1559 7.266335 GCGCATATAGTCGAACAATTTGAATAC 59.734 37.037 0.30 0.00 0.00 1.89
1462 1560 7.170828 AGCGCATATAGTCGAACAATTTGAATA 59.829 33.333 11.47 0.00 0.00 1.75
1463 1561 6.017934 AGCGCATATAGTCGAACAATTTGAAT 60.018 34.615 11.47 0.00 0.00 2.57
1464 1562 5.293324 AGCGCATATAGTCGAACAATTTGAA 59.707 36.000 11.47 0.00 0.00 2.69
1465 1563 4.808895 AGCGCATATAGTCGAACAATTTGA 59.191 37.500 11.47 0.00 0.00 2.69
1466 1564 5.083136 AGCGCATATAGTCGAACAATTTG 57.917 39.130 11.47 0.00 0.00 2.32
1467 1565 6.090898 GGATAGCGCATATAGTCGAACAATTT 59.909 38.462 11.47 0.00 0.00 1.82
1468 1566 5.577164 GGATAGCGCATATAGTCGAACAATT 59.423 40.000 11.47 0.00 0.00 2.32
1469 1567 5.103000 GGATAGCGCATATAGTCGAACAAT 58.897 41.667 11.47 0.00 0.00 2.71
1470 1568 4.482386 GGATAGCGCATATAGTCGAACAA 58.518 43.478 11.47 0.00 0.00 2.83
1471 1569 3.119602 GGGATAGCGCATATAGTCGAACA 60.120 47.826 11.47 0.00 0.00 3.18
1472 1570 3.436496 GGGATAGCGCATATAGTCGAAC 58.564 50.000 11.47 0.00 0.00 3.95
1473 1571 2.426024 GGGGATAGCGCATATAGTCGAA 59.574 50.000 11.47 0.00 0.00 3.71
1474 1572 2.022195 GGGGATAGCGCATATAGTCGA 58.978 52.381 11.47 0.00 0.00 4.20
1475 1573 1.749063 TGGGGATAGCGCATATAGTCG 59.251 52.381 11.47 0.00 0.00 4.18
1476 1574 3.133003 ACATGGGGATAGCGCATATAGTC 59.867 47.826 11.47 0.00 0.00 2.59
1477 1575 3.107601 ACATGGGGATAGCGCATATAGT 58.892 45.455 11.47 0.00 0.00 2.12
1478 1576 3.827008 ACATGGGGATAGCGCATATAG 57.173 47.619 11.47 0.00 0.00 1.31
1479 1577 3.263170 ACAACATGGGGATAGCGCATATA 59.737 43.478 11.47 0.00 0.00 0.86
1480 1578 2.040278 ACAACATGGGGATAGCGCATAT 59.960 45.455 11.47 4.47 0.00 1.78
1481 1579 1.419762 ACAACATGGGGATAGCGCATA 59.580 47.619 11.47 0.00 0.00 3.14
1482 1580 0.183492 ACAACATGGGGATAGCGCAT 59.817 50.000 11.47 0.06 0.00 4.73
1483 1581 0.034574 AACAACATGGGGATAGCGCA 60.035 50.000 11.47 0.00 0.00 6.09
1484 1582 0.381801 CAACAACATGGGGATAGCGC 59.618 55.000 0.00 0.00 0.00 5.92
1485 1583 1.670811 GACAACAACATGGGGATAGCG 59.329 52.381 0.00 0.00 0.00 4.26
1486 1584 2.722094 TGACAACAACATGGGGATAGC 58.278 47.619 0.00 0.00 0.00 2.97
1487 1585 5.653507 CAAATGACAACAACATGGGGATAG 58.346 41.667 0.00 0.00 0.00 2.08
1543 1711 5.804944 CCACCATTTGGGCATATCAAATA 57.195 39.130 0.96 0.00 41.28 1.40
1556 1724 4.253685 CTCACTACCTGTACCACCATTTG 58.746 47.826 0.00 0.00 0.00 2.32
1588 1772 7.649533 ATTGCATCAGGAATGTTTTAGATGA 57.350 32.000 0.00 0.00 37.71 2.92
1790 2284 9.768662 ACTGCTTCTCAAAAATTAAATGAATGT 57.231 25.926 0.00 0.00 0.00 2.71
1795 2289 9.044150 TCCAAACTGCTTCTCAAAAATTAAATG 57.956 29.630 0.00 0.00 0.00 2.32
1807 2301 3.206150 TGTGTCTTCCAAACTGCTTCTC 58.794 45.455 0.00 0.00 0.00 2.87
1808 2302 3.281727 TGTGTCTTCCAAACTGCTTCT 57.718 42.857 0.00 0.00 0.00 2.85
1886 2382 9.044150 CATTATCAGTCTCTTTGATCTTCCTTC 57.956 37.037 0.00 0.00 36.68 3.46
1895 2391 4.778213 CCCCCATTATCAGTCTCTTTGA 57.222 45.455 0.00 0.00 0.00 2.69
1917 2413 2.420022 AGTCCATCACTAATGCGCAAAC 59.580 45.455 17.11 0.12 31.37 2.93
1975 2471 2.483877 TGTTGCAGCAACTATTTCCTCG 59.516 45.455 32.99 0.00 43.85 4.63
2023 2523 2.034066 CCAAAGCCGCCTTCTCCA 59.966 61.111 0.00 0.00 0.00 3.86
2078 2578 9.868277 ATTTTTCATATTTCGGTGCAATTAGAA 57.132 25.926 0.00 0.00 0.00 2.10
2105 2605 4.923893 TGAATCACAGCAAAAAGTGACAG 58.076 39.130 0.00 0.00 46.38 3.51
2149 2661 7.454260 AGTAGCAGGAAGAAAATTAAGGTTG 57.546 36.000 0.00 0.00 0.00 3.77
2171 2683 3.973973 TGTAAGAGCCCCTGCATTATAGT 59.026 43.478 0.00 0.00 41.13 2.12
2361 2873 3.595173 GTGTCAAGGCTTTTGTTTGGTT 58.405 40.909 0.00 0.00 0.00 3.67
2392 2908 8.826710 TGATTAATTTGTGATCGGAACATACTC 58.173 33.333 0.00 0.00 0.00 2.59
2421 2937 5.119588 CACATGTGGCATCAACTGATTTTTC 59.880 40.000 18.51 0.00 31.21 2.29
2443 2959 9.850628 CAATGATGTATGGGATTATGATTTCAC 57.149 33.333 0.00 0.00 0.00 3.18
2465 2988 6.675026 TGACTTCTTTTCAGAATCTGCAATG 58.325 36.000 5.18 3.88 38.42 2.82
2495 3018 2.047274 AATCGTGTCGGCCAGTGG 60.047 61.111 4.20 4.20 0.00 4.00
2821 3353 4.352001 AGAGGCCTTCCATTGCATATTCTA 59.648 41.667 6.77 0.00 33.74 2.10
3118 3666 2.741612 ACATGGATGCAACACAAAACG 58.258 42.857 0.00 0.00 0.00 3.60
3270 3818 2.257894 CGTAGTCTGCTCTCTTTGCTG 58.742 52.381 0.00 0.00 0.00 4.41
3479 4030 1.968050 ATAACCTTGTCCTCCCGGCG 61.968 60.000 0.00 0.00 0.00 6.46
3480 4031 0.463833 CATAACCTTGTCCTCCCGGC 60.464 60.000 0.00 0.00 0.00 6.13
3506 4059 1.896220 AAGAAGACGGCAGCATCAAA 58.104 45.000 0.00 0.00 0.00 2.69
3512 4065 2.349886 CAGATTGTAAGAAGACGGCAGC 59.650 50.000 0.00 0.00 0.00 5.25
3518 4071 9.167311 ACCAATACATTCAGATTGTAAGAAGAC 57.833 33.333 8.83 0.00 33.55 3.01
3537 4090 2.884639 AGAACAACACCAGCACCAATAC 59.115 45.455 0.00 0.00 0.00 1.89
3556 4109 0.320374 GATCACGGGGACACAACAGA 59.680 55.000 0.00 0.00 0.00 3.41
3559 4112 0.034896 AGTGATCACGGGGACACAAC 59.965 55.000 19.85 0.00 35.97 3.32
3611 4164 1.004745 TCAGGATGGCAAACCTTCTCC 59.995 52.381 12.76 3.60 39.53 3.71
3624 4177 1.372087 GCTTCAGCGGGTTCAGGATG 61.372 60.000 0.00 0.00 37.54 3.51
3736 4301 2.492484 AGTAGACGACCGATCAGCTTTT 59.508 45.455 0.00 0.00 0.00 2.27
3772 4347 6.974622 ACTGAAACAAACTTCAATGCTAACAG 59.025 34.615 0.00 0.00 34.96 3.16
3838 6175 1.681025 CGCCGATCGCATGATAGCAG 61.681 60.000 10.32 0.00 34.95 4.24
3854 6191 3.405592 TACGACGACATGCTCCGCC 62.406 63.158 0.00 0.00 0.00 6.13
3866 6203 1.135199 ACATACCAAGCACCTACGACG 60.135 52.381 0.00 0.00 0.00 5.12
3906 6243 3.681897 AGTTCATTACAAAGCAGAGCTCG 59.318 43.478 8.37 4.60 38.25 5.03
3912 6249 6.264832 TCACAACAAGTTCATTACAAAGCAG 58.735 36.000 0.00 0.00 0.00 4.24
3914 6251 7.698836 AATCACAACAAGTTCATTACAAAGC 57.301 32.000 0.00 0.00 0.00 3.51
3939 6276 1.139520 GGCGGCGCTTCATTGATTT 59.860 52.632 32.30 0.00 0.00 2.17
3978 6332 0.391927 CGGGGCGTGTGATTCCTTTA 60.392 55.000 0.00 0.00 0.00 1.85
3981 6335 4.096003 CCGGGGCGTGTGATTCCT 62.096 66.667 0.00 0.00 0.00 3.36
3996 6350 8.879342 ATCAATATTTGTAAGAGAAGACTCCG 57.121 34.615 0.00 0.00 43.53 4.63
4045 7474 1.004044 ACAAGACTTCCTGGAGCCATG 59.996 52.381 0.00 0.00 0.00 3.66
4046 7475 1.366319 ACAAGACTTCCTGGAGCCAT 58.634 50.000 0.00 0.00 0.00 4.40
4047 7476 1.140312 AACAAGACTTCCTGGAGCCA 58.860 50.000 0.00 0.00 0.00 4.75
4048 7477 2.355209 CCTAACAAGACTTCCTGGAGCC 60.355 54.545 0.00 0.00 0.00 4.70
4049 7478 2.567615 TCCTAACAAGACTTCCTGGAGC 59.432 50.000 0.00 0.00 0.00 4.70
4061 7490 5.642063 TCGGCTAACTGAATTTCCTAACAAG 59.358 40.000 0.00 0.00 0.00 3.16
4067 7496 3.000727 CGTTCGGCTAACTGAATTTCCT 58.999 45.455 0.22 0.00 43.03 3.36
4068 7497 2.740447 ACGTTCGGCTAACTGAATTTCC 59.260 45.455 0.22 0.00 43.03 3.13
4076 7505 0.796312 CATGCAACGTTCGGCTAACT 59.204 50.000 11.37 0.00 35.81 2.24
4083 7512 2.594529 AAGCTAACATGCAACGTTCG 57.405 45.000 8.04 4.23 34.99 3.95
4088 7517 2.989166 GGCTGAAAAGCTAACATGCAAC 59.011 45.455 0.00 0.00 34.99 4.17
4094 7523 3.495331 TGGATTGGCTGAAAAGCTAACA 58.505 40.909 0.00 0.00 38.06 2.41
4106 7535 5.813513 ATGTTTTCTTTTCTGGATTGGCT 57.186 34.783 0.00 0.00 0.00 4.75
4109 7538 9.865321 ACATGATATGTTTTCTTTTCTGGATTG 57.135 29.630 0.00 0.00 41.63 2.67
4166 7597 7.294017 ACAGACATTTTCAAAACAGGATGAT 57.706 32.000 0.00 0.00 39.69 2.45
4172 7603 9.950680 AGTATACAACAGACATTTTCAAAACAG 57.049 29.630 5.50 0.00 0.00 3.16
4212 7643 9.309516 GATGAGCATTTTCAAATACACAATGAT 57.690 29.630 0.00 0.00 0.00 2.45
4217 7648 7.604549 ACATGATGAGCATTTTCAAATACACA 58.395 30.769 0.00 0.00 34.15 3.72


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

AutoCloner maintained by Alex Coulton.