Multiple sequence alignment - TraesCS3B01G199700

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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 TraesCS3B01G199700 chr3B 100.000 2419 0 0 1 2419 228301607 228299189 0.000000e+00 4468.0
1 TraesCS3B01G199700 chr3B 95.352 839 34 5 3 838 289553076 289553912 0.000000e+00 1328.0
2 TraesCS3B01G199700 chr3B 81.326 573 89 14 873 1430 228209344 228208775 1.320000e-122 449.0
3 TraesCS3B01G199700 chr3D 95.600 841 32 5 3 839 379797771 379796932 0.000000e+00 1343.0
4 TraesCS3B01G199700 chr3D 87.275 833 77 20 1531 2336 308231965 308231135 0.000000e+00 924.0
5 TraesCS3B01G199700 chr3D 90.749 681 55 6 1543 2215 308260835 308260155 0.000000e+00 902.0
6 TraesCS3B01G199700 chr3D 85.578 631 64 6 839 1466 157180009 157179403 9.430000e-179 636.0
7 TraesCS3B01G199700 chr3D 81.152 573 81 18 873 1431 157102663 157102104 3.690000e-118 435.0
8 TraesCS3B01G199700 chr7B 95.595 840 31 6 3 838 79704344 79705181 0.000000e+00 1341.0
9 TraesCS3B01G199700 chr7B 95.579 837 30 7 3 835 188921004 188920171 0.000000e+00 1334.0
10 TraesCS3B01G199700 chr1D 95.590 839 30 7 3 836 485892918 485893754 0.000000e+00 1338.0
11 TraesCS3B01G199700 chr6B 95.482 841 31 7 3 838 455347370 455346532 0.000000e+00 1336.0
12 TraesCS3B01G199700 chr6B 87.698 756 82 10 1588 2339 631940794 631941542 0.000000e+00 870.0
13 TraesCS3B01G199700 chr6B 97.297 37 1 0 1480 1516 483862802 483862838 2.010000e-06 63.9
14 TraesCS3B01G199700 chr2B 95.471 839 34 4 3 838 481969792 481970629 0.000000e+00 1336.0
15 TraesCS3B01G199700 chr2B 84.917 842 110 15 1588 2419 378442297 378441463 0.000000e+00 835.0
16 TraesCS3B01G199700 chr7D 95.471 839 33 5 3 838 632271871 632272707 0.000000e+00 1334.0
17 TraesCS3B01G199700 chr5D 95.471 839 33 5 3 838 248069292 248068456 0.000000e+00 1334.0
18 TraesCS3B01G199700 chr5D 86.581 313 42 0 871 1183 62528171 62528483 1.780000e-91 346.0
19 TraesCS3B01G199700 chr2D 89.532 812 67 11 1525 2324 305000804 304999999 0.000000e+00 1013.0
20 TraesCS3B01G199700 chr2D 88.294 803 77 11 1516 2305 347818049 347817251 0.000000e+00 946.0
21 TraesCS3B01G199700 chr6D 88.116 791 79 7 1531 2308 368720834 368720046 0.000000e+00 926.0
22 TraesCS3B01G199700 chr4D 85.081 925 105 23 1516 2415 65571364 65572280 0.000000e+00 913.0
23 TraesCS3B01G199700 chr6A 85.981 856 102 12 1540 2382 156740225 156741075 0.000000e+00 900.0
24 TraesCS3B01G199700 chr6A 97.297 37 1 0 1480 1516 6377236 6377200 2.010000e-06 63.9
25 TraesCS3B01G199700 chr6A 97.297 37 1 0 1480 1516 495863992 495863956 2.010000e-06 63.9
26 TraesCS3B01G199700 chr3A 86.564 521 63 4 839 1355 171137904 171138421 3.490000e-158 568.0
27 TraesCS3B01G199700 chr3A 83.066 561 77 14 873 1417 171173804 171174362 6.010000e-136 494.0
28 TraesCS3B01G199700 chr5A 97.297 37 1 0 1480 1516 322600242 322600278 2.010000e-06 63.9
29 TraesCS3B01G199700 chr5A 97.297 37 1 0 1480 1516 423306774 423306738 2.010000e-06 63.9
30 TraesCS3B01G199700 chr5A 97.297 37 1 0 1480 1516 423404367 423404331 2.010000e-06 63.9
31 TraesCS3B01G199700 chr4A 97.297 37 1 0 1480 1516 151362071 151362035 2.010000e-06 63.9
32 TraesCS3B01G199700 chr4A 97.297 37 1 0 1480 1516 514065751 514065787 2.010000e-06 63.9
33 TraesCS3B01G199700 chr1A 97.297 37 1 0 1480 1516 586247529 586247565 2.010000e-06 63.9


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 TraesCS3B01G199700 chr3B 228299189 228301607 2418 True 4468 4468 100.000 1 2419 1 chr3B.!!$R2 2418
1 TraesCS3B01G199700 chr3B 289553076 289553912 836 False 1328 1328 95.352 3 838 1 chr3B.!!$F1 835
2 TraesCS3B01G199700 chr3B 228208775 228209344 569 True 449 449 81.326 873 1430 1 chr3B.!!$R1 557
3 TraesCS3B01G199700 chr3D 379796932 379797771 839 True 1343 1343 95.600 3 839 1 chr3D.!!$R5 836
4 TraesCS3B01G199700 chr3D 308231135 308231965 830 True 924 924 87.275 1531 2336 1 chr3D.!!$R3 805
5 TraesCS3B01G199700 chr3D 308260155 308260835 680 True 902 902 90.749 1543 2215 1 chr3D.!!$R4 672
6 TraesCS3B01G199700 chr3D 157179403 157180009 606 True 636 636 85.578 839 1466 1 chr3D.!!$R2 627
7 TraesCS3B01G199700 chr3D 157102104 157102663 559 True 435 435 81.152 873 1431 1 chr3D.!!$R1 558
8 TraesCS3B01G199700 chr7B 79704344 79705181 837 False 1341 1341 95.595 3 838 1 chr7B.!!$F1 835
9 TraesCS3B01G199700 chr7B 188920171 188921004 833 True 1334 1334 95.579 3 835 1 chr7B.!!$R1 832
10 TraesCS3B01G199700 chr1D 485892918 485893754 836 False 1338 1338 95.590 3 836 1 chr1D.!!$F1 833
11 TraesCS3B01G199700 chr6B 455346532 455347370 838 True 1336 1336 95.482 3 838 1 chr6B.!!$R1 835
12 TraesCS3B01G199700 chr6B 631940794 631941542 748 False 870 870 87.698 1588 2339 1 chr6B.!!$F2 751
13 TraesCS3B01G199700 chr2B 481969792 481970629 837 False 1336 1336 95.471 3 838 1 chr2B.!!$F1 835
14 TraesCS3B01G199700 chr2B 378441463 378442297 834 True 835 835 84.917 1588 2419 1 chr2B.!!$R1 831
15 TraesCS3B01G199700 chr7D 632271871 632272707 836 False 1334 1334 95.471 3 838 1 chr7D.!!$F1 835
16 TraesCS3B01G199700 chr5D 248068456 248069292 836 True 1334 1334 95.471 3 838 1 chr5D.!!$R1 835
17 TraesCS3B01G199700 chr2D 304999999 305000804 805 True 1013 1013 89.532 1525 2324 1 chr2D.!!$R1 799
18 TraesCS3B01G199700 chr2D 347817251 347818049 798 True 946 946 88.294 1516 2305 1 chr2D.!!$R2 789
19 TraesCS3B01G199700 chr6D 368720046 368720834 788 True 926 926 88.116 1531 2308 1 chr6D.!!$R1 777
20 TraesCS3B01G199700 chr4D 65571364 65572280 916 False 913 913 85.081 1516 2415 1 chr4D.!!$F1 899
21 TraesCS3B01G199700 chr6A 156740225 156741075 850 False 900 900 85.981 1540 2382 1 chr6A.!!$F1 842
22 TraesCS3B01G199700 chr3A 171137904 171138421 517 False 568 568 86.564 839 1355 1 chr3A.!!$F1 516
23 TraesCS3B01G199700 chr3A 171173804 171174362 558 False 494 494 83.066 873 1417 1 chr3A.!!$F2 544

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
996 1005 0.173708 GCAAGGAGACGGACGATTCT 59.826 55.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2390 0.036671 GGCAGCGGTAGTACAACCTT 60.037 55.0 2.06 0.0 37.39 3.5 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
99 101 7.466590 GCCTACTAGATTGATCTTTCTTGCAAC 60.467 40.741 0.00 0.00 38.32 4.17
134 136 1.269448 GCTTTGGGTTCAATCTTGCGA 59.731 47.619 0.00 0.00 32.28 5.10
282 284 4.820897 TGCGTTACTCTGTTCTTCATGAT 58.179 39.130 0.00 0.00 0.00 2.45
649 657 3.692593 ACTTTTGCAAGTTACGTGAAGGT 59.307 39.130 1.88 0.00 40.66 3.50
707 715 4.571580 TCTTGTTTGTTTGTGTAGGTACGG 59.428 41.667 0.00 0.00 0.00 4.02
798 806 1.614903 CTTTGCTGCATCACCCTTTCA 59.385 47.619 1.84 0.00 0.00 2.69
842 850 1.517257 CTCAAGAGGTAGCACGCGG 60.517 63.158 12.47 0.00 0.00 6.46
855 863 1.003262 CACGCGGCACTCAAAAATGG 61.003 55.000 12.47 0.00 0.00 3.16
862 870 3.611530 CGGCACTCAAAAATGGAACGAAT 60.612 43.478 0.00 0.00 0.00 3.34
864 872 4.545610 GCACTCAAAAATGGAACGAATCA 58.454 39.130 0.00 0.00 0.00 2.57
865 873 5.163513 GCACTCAAAAATGGAACGAATCAT 58.836 37.500 0.00 0.00 0.00 2.45
866 874 5.061311 GCACTCAAAAATGGAACGAATCATG 59.939 40.000 0.00 0.00 0.00 3.07
867 875 5.061311 CACTCAAAAATGGAACGAATCATGC 59.939 40.000 0.00 0.00 0.00 4.06
869 877 3.525268 AAAATGGAACGAATCATGCCC 57.475 42.857 0.00 0.00 0.00 5.36
870 878 2.142356 AATGGAACGAATCATGCCCA 57.858 45.000 0.00 0.00 0.00 5.36
894 903 0.972134 CAGGACTGAAGCCTCTGACA 59.028 55.000 0.00 0.00 32.12 3.58
908 917 0.972983 CTGACACGGGAGGAGGTGAT 60.973 60.000 0.00 0.00 37.58 3.06
916 925 1.402896 GGAGGAGGTGATCGCCATCA 61.403 60.000 26.71 0.00 37.84 3.07
918 927 0.689080 AGGAGGTGATCGCCATCAGT 60.689 55.000 26.71 5.85 39.86 3.41
949 958 4.954118 TCCTGGCGACCACCCTGT 62.954 66.667 0.00 0.00 0.00 4.00
951 960 3.625897 CTGGCGACCACCCTGTCA 61.626 66.667 0.00 0.00 34.88 3.58
955 964 3.299977 CGACCACCCTGTCACCGA 61.300 66.667 0.00 0.00 34.88 4.69
970 979 1.153647 CCGAAGCACCGCATCTACA 60.154 57.895 0.00 0.00 0.00 2.74
973 982 1.726853 GAAGCACCGCATCTACAACT 58.273 50.000 0.00 0.00 0.00 3.16
977 986 0.806102 CACCGCATCTACAACTCGGG 60.806 60.000 4.00 0.00 43.93 5.14
989 998 3.068691 CTCGGGCAAGGAGACGGA 61.069 66.667 0.00 0.00 33.27 4.69
993 1002 2.722201 GGGCAAGGAGACGGACGAT 61.722 63.158 0.00 0.00 0.00 3.73
996 1005 0.173708 GCAAGGAGACGGACGATTCT 59.826 55.000 0.00 0.00 0.00 2.40
1004 1013 0.036388 ACGGACGATTCTGGCATGTT 60.036 50.000 0.00 0.00 31.53 2.71
1007 1016 2.292267 GGACGATTCTGGCATGTTGAT 58.708 47.619 0.00 0.00 0.00 2.57
1061 1070 2.232399 TGAGGTGCTAGACGTGTACAA 58.768 47.619 0.00 0.00 0.00 2.41
1062 1071 2.823747 TGAGGTGCTAGACGTGTACAAT 59.176 45.455 0.00 0.00 0.00 2.71
1092 1101 0.536460 GGGTTGCCTTCAAGTTCCGA 60.536 55.000 0.00 0.00 31.93 4.55
1144 1153 4.954118 ACCCTCCACACGGCCAGA 62.954 66.667 2.24 0.00 0.00 3.86
1146 1155 4.087892 CCTCCACACGGCCAGAGG 62.088 72.222 2.24 5.95 40.00 3.69
1177 1186 0.616395 TGGGGTCTGCGTCTTCCATA 60.616 55.000 0.00 0.00 0.00 2.74
1222 1243 6.919662 GTGTGTCATTGTCATTCAAAGTTCAT 59.080 34.615 0.00 0.00 39.62 2.57
1253 1274 3.418684 AGCCAGTAACCGAGAAAACAT 57.581 42.857 0.00 0.00 0.00 2.71
1254 1275 3.335579 AGCCAGTAACCGAGAAAACATC 58.664 45.455 0.00 0.00 0.00 3.06
1255 1276 3.071479 GCCAGTAACCGAGAAAACATCA 58.929 45.455 0.00 0.00 0.00 3.07
1266 1289 5.220739 CCGAGAAAACATCATCATGGTTCTC 60.221 44.000 12.45 12.45 39.16 2.87
1345 1368 0.249911 GAGTGTGGCAACTTCCTCGT 60.250 55.000 0.00 0.00 37.61 4.18
1355 1378 2.734079 CAACTTCCTCGTGAGCTTCTTC 59.266 50.000 0.00 0.00 0.00 2.87
1376 1408 4.326507 ACGCCTGCTTCTGCTGCT 62.327 61.111 0.00 0.00 40.48 4.24
1377 1409 3.800863 CGCCTGCTTCTGCTGCTG 61.801 66.667 0.00 0.00 40.48 4.41
1378 1410 2.672307 GCCTGCTTCTGCTGCTGT 60.672 61.111 0.00 0.00 40.48 4.40
1390 1425 3.762293 TGCTGTTGCATCGGCTTT 58.238 50.000 25.01 0.00 45.31 3.51
1401 1436 0.107165 ATCGGCTTTAGGTTGCCCTC 60.107 55.000 0.00 0.00 45.90 4.30
1411 1446 0.908198 GGTTGCCCTCTGATGAGAGT 59.092 55.000 8.46 0.00 43.98 3.24
1418 1453 4.646945 TGCCCTCTGATGAGAGTAAACTAG 59.353 45.833 8.46 0.00 43.98 2.57
1421 1456 6.361433 CCCTCTGATGAGAGTAAACTAGAGA 58.639 44.000 8.46 0.00 43.98 3.10
1427 1462 2.683867 GAGAGTAAACTAGAGAGCGGCA 59.316 50.000 1.45 0.00 0.00 5.69
1450 1485 6.086765 GCAAAATTGACGAAACATGTCACTAG 59.913 38.462 0.00 0.00 45.42 2.57
1451 1486 4.928661 ATTGACGAAACATGTCACTAGC 57.071 40.909 0.00 0.00 45.42 3.42
1455 1490 4.022676 TGACGAAACATGTCACTAGCAGTA 60.023 41.667 0.00 0.00 41.20 2.74
1476 1511 8.494236 CAGTATCACTGTACTTTTTCTTTTGC 57.506 34.615 0.00 0.00 41.19 3.68
1477 1512 7.321271 CAGTATCACTGTACTTTTTCTTTTGCG 59.679 37.037 0.00 0.00 41.19 4.85
1478 1513 4.915704 TCACTGTACTTTTTCTTTTGCGG 58.084 39.130 0.00 0.00 0.00 5.69
1479 1514 4.396790 TCACTGTACTTTTTCTTTTGCGGT 59.603 37.500 0.00 0.00 0.00 5.68
1480 1515 5.099575 CACTGTACTTTTTCTTTTGCGGTT 58.900 37.500 0.00 0.00 0.00 4.44
1481 1516 5.004345 CACTGTACTTTTTCTTTTGCGGTTG 59.996 40.000 0.00 0.00 0.00 3.77
1482 1517 5.106078 ACTGTACTTTTTCTTTTGCGGTTGA 60.106 36.000 0.00 0.00 0.00 3.18
1483 1518 5.710984 TGTACTTTTTCTTTTGCGGTTGAA 58.289 33.333 0.00 0.00 0.00 2.69
1484 1519 6.157211 TGTACTTTTTCTTTTGCGGTTGAAA 58.843 32.000 0.00 0.00 0.00 2.69
1485 1520 5.524511 ACTTTTTCTTTTGCGGTTGAAAC 57.475 34.783 0.00 0.00 0.00 2.78
1486 1521 4.090786 ACTTTTTCTTTTGCGGTTGAAACG 59.909 37.500 0.00 0.00 0.00 3.60
1487 1522 3.489180 TTTCTTTTGCGGTTGAAACGA 57.511 38.095 6.88 0.00 0.00 3.85
1488 1523 3.701532 TTCTTTTGCGGTTGAAACGAT 57.298 38.095 6.88 0.00 0.00 3.73
1489 1524 3.262135 TCTTTTGCGGTTGAAACGATC 57.738 42.857 6.88 0.00 0.00 3.69
1490 1525 1.969256 CTTTTGCGGTTGAAACGATCG 59.031 47.619 14.88 14.88 0.00 3.69
1491 1526 1.218763 TTTGCGGTTGAAACGATCGA 58.781 45.000 24.34 0.00 0.00 3.59
1492 1527 1.434555 TTGCGGTTGAAACGATCGAT 58.565 45.000 24.34 7.21 0.00 3.59
1493 1528 2.281140 TGCGGTTGAAACGATCGATA 57.719 45.000 24.34 1.52 0.00 2.92
1494 1529 2.816689 TGCGGTTGAAACGATCGATAT 58.183 42.857 24.34 6.96 0.00 1.63
1495 1530 2.538037 TGCGGTTGAAACGATCGATATG 59.462 45.455 24.34 4.03 0.00 1.78
1496 1531 2.792674 GCGGTTGAAACGATCGATATGA 59.207 45.455 24.34 1.44 0.00 2.15
1497 1532 3.428870 GCGGTTGAAACGATCGATATGAT 59.571 43.478 24.34 0.00 41.06 2.45
1498 1533 4.084537 GCGGTTGAAACGATCGATATGATT 60.085 41.667 24.34 0.59 37.47 2.57
1499 1534 5.365942 CGGTTGAAACGATCGATATGATTG 58.634 41.667 24.34 1.89 43.22 2.67
1500 1535 5.174943 CGGTTGAAACGATCGATATGATTGA 59.825 40.000 24.34 0.00 40.46 2.57
1501 1536 6.355638 GGTTGAAACGATCGATATGATTGAC 58.644 40.000 24.34 7.92 40.46 3.18
1502 1537 6.201044 GGTTGAAACGATCGATATGATTGACT 59.799 38.462 24.34 0.00 40.46 3.41
1503 1538 7.381408 GGTTGAAACGATCGATATGATTGACTA 59.619 37.037 24.34 0.00 40.46 2.59
1504 1539 8.420945 GTTGAAACGATCGATATGATTGACTAG 58.579 37.037 24.34 0.00 40.46 2.57
1505 1540 7.871853 TGAAACGATCGATATGATTGACTAGA 58.128 34.615 24.34 0.00 40.46 2.43
1506 1541 8.017946 TGAAACGATCGATATGATTGACTAGAG 58.982 37.037 24.34 0.00 40.46 2.43
1507 1542 6.429791 ACGATCGATATGATTGACTAGAGG 57.570 41.667 24.34 0.00 40.46 3.69
1508 1543 5.355630 ACGATCGATATGATTGACTAGAGGG 59.644 44.000 24.34 0.00 40.46 4.30
1509 1544 5.220951 CGATCGATATGATTGACTAGAGGGG 60.221 48.000 10.26 0.00 40.46 4.79
1510 1545 4.344978 TCGATATGATTGACTAGAGGGGG 58.655 47.826 0.00 0.00 0.00 5.40
1570 1606 3.253230 ACAACAAGTGCAAGCAAAGAAC 58.747 40.909 0.00 0.00 0.00 3.01
1571 1607 2.193306 ACAAGTGCAAGCAAAGAACG 57.807 45.000 0.00 0.00 0.00 3.95
1574 1610 0.670162 AGTGCAAGCAAAGAACGCAT 59.330 45.000 0.00 0.00 34.66 4.73
1614 1659 6.697641 AAAGGGAAGAGATAACCACAAGTA 57.302 37.500 0.00 0.00 0.00 2.24
1641 1686 3.070159 CGGTGGAGATGAGGATGTGTTAT 59.930 47.826 0.00 0.00 0.00 1.89
1804 1851 2.443016 AAGGCGGCAACCAAACCA 60.443 55.556 13.08 0.00 0.00 3.67
1892 1939 1.843368 CACAATGGAATGTGGCTCCT 58.157 50.000 0.00 0.00 45.47 3.69
1899 1946 1.771255 GGAATGTGGCTCCTAGGTGAT 59.229 52.381 15.10 0.00 0.00 3.06
1905 1952 2.703007 GTGGCTCCTAGGTGATCTCAAT 59.297 50.000 15.10 0.00 0.00 2.57
1909 1956 3.068873 GCTCCTAGGTGATCTCAATCGTT 59.931 47.826 15.10 0.00 34.39 3.85
1962 2009 1.632018 CGCAAGGGATTAGTGGGGGA 61.632 60.000 0.00 0.00 0.00 4.81
2028 2078 6.840780 ACCAATCCTAGAAAATCAACAAGG 57.159 37.500 0.00 0.00 0.00 3.61
2101 2154 0.196118 AGTTTGGGGGAGGAAGAGGA 59.804 55.000 0.00 0.00 0.00 3.71
2104 2157 1.841334 TTGGGGGAGGAAGAGGAAAA 58.159 50.000 0.00 0.00 0.00 2.29
2140 2194 3.519370 AGACCCCCTTTTATAGTGGGA 57.481 47.619 0.00 0.00 43.91 4.37
2141 2195 3.822880 AGACCCCCTTTTATAGTGGGAA 58.177 45.455 0.00 0.00 43.91 3.97
2148 2204 6.014012 CCCCTTTTATAGTGGGAAGACAAAA 58.986 40.000 7.96 0.00 43.47 2.44
2155 2211 2.104170 GTGGGAAGACAAAACCAACCA 58.896 47.619 0.00 0.00 34.26 3.67
2165 2221 4.227197 ACAAAACCAACCATTATCCACCA 58.773 39.130 0.00 0.00 0.00 4.17
2173 2229 0.552848 CATTATCCACCACCCAGCCT 59.447 55.000 0.00 0.00 0.00 4.58
2222 2299 1.814527 GGTACTACCGCACCCTGAG 59.185 63.158 0.00 0.00 0.00 3.35
2265 2345 1.376649 ACAGGGGGAAAAGCAGAGAT 58.623 50.000 0.00 0.00 0.00 2.75
2270 2350 1.485066 GGGGAAAAGCAGAGATACGGA 59.515 52.381 0.00 0.00 0.00 4.69
2305 2385 3.199880 GTAGTAGGAGCGGTACTACCA 57.800 52.381 28.91 16.53 43.69 3.25
2329 2409 0.036671 AAGGTTGTACTACCGCTGCC 60.037 55.000 18.87 0.00 43.21 4.85
2342 2434 1.079405 GCTGCCACAACCGCTAGTA 60.079 57.895 0.00 0.00 0.00 1.82
2346 2438 1.296727 GCCACAACCGCTAGTATTCC 58.703 55.000 0.00 0.00 0.00 3.01
2352 2444 0.263765 ACCGCTAGTATTCCAGGGGA 59.736 55.000 11.18 0.00 45.31 4.81
2359 2451 4.080526 GCTAGTATTCCAGGGGAAAACAGA 60.081 45.833 1.25 0.00 45.41 3.41
2366 2458 2.290896 CCAGGGGAAAACAGATAGCACA 60.291 50.000 0.00 0.00 0.00 4.57
2367 2459 3.624777 CAGGGGAAAACAGATAGCACAT 58.375 45.455 0.00 0.00 0.00 3.21
2402 2495 7.215085 GGAGGTTATACCGTAAAATCTGACAT 58.785 38.462 0.00 0.00 44.90 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 101 1.734465 CAAAGCTAAGCACTTCTCCCG 59.266 52.381 0.00 0.00 0.00 5.14
134 136 1.407437 GCTGTCATCGGGAAAGGACAT 60.407 52.381 0.00 0.00 39.33 3.06
282 284 5.244851 CCTGCCTGCATCTAGAGTATTAAGA 59.755 44.000 0.00 0.00 0.00 2.10
315 317 7.069950 TGCATCTCTACTATTACTCCACACATT 59.930 37.037 0.00 0.00 0.00 2.71
481 484 4.383770 GCCATAGGTTTCACTAGTGGCTTA 60.384 45.833 22.48 13.37 40.50 3.09
649 657 3.199677 CGCGATAAAGGGGTTGTCAATA 58.800 45.455 0.00 0.00 0.00 1.90
707 715 1.756430 GAGGATCCTCAAAAGTGCCC 58.244 55.000 32.90 5.47 42.31 5.36
798 806 3.243737 GCGTTGGTTTTTCCCTTGAAGAT 60.244 43.478 0.00 0.00 34.77 2.40
842 850 4.545610 TGATTCGTTCCATTTTTGAGTGC 58.454 39.130 0.00 0.00 0.00 4.40
844 852 5.163513 GCATGATTCGTTCCATTTTTGAGT 58.836 37.500 0.00 0.00 0.00 3.41
855 863 1.468054 GCAAGTGGGCATGATTCGTTC 60.468 52.381 0.00 0.00 0.00 3.95
862 870 1.303561 GTCCTGCAAGTGGGCATGA 60.304 57.895 0.00 0.00 43.97 3.07
864 872 1.303888 CAGTCCTGCAAGTGGGCAT 60.304 57.895 0.00 0.00 43.97 4.40
865 873 1.993701 TTCAGTCCTGCAAGTGGGCA 61.994 55.000 0.00 0.00 42.53 5.36
866 874 1.228245 TTCAGTCCTGCAAGTGGGC 60.228 57.895 0.00 0.00 0.00 5.36
867 875 1.239968 GCTTCAGTCCTGCAAGTGGG 61.240 60.000 0.00 0.00 0.00 4.61
869 877 0.250640 AGGCTTCAGTCCTGCAAGTG 60.251 55.000 0.00 0.00 31.53 3.16
870 878 0.036022 GAGGCTTCAGTCCTGCAAGT 59.964 55.000 0.00 0.00 33.24 3.16
879 888 1.668294 CCGTGTCAGAGGCTTCAGT 59.332 57.895 0.00 0.00 0.00 3.41
894 903 3.148279 GCGATCACCTCCTCCCGT 61.148 66.667 0.00 0.00 0.00 5.28
916 925 0.822164 AGGAACGCGTTATAGCCACT 59.178 50.000 26.68 11.24 0.00 4.00
918 927 0.179094 CCAGGAACGCGTTATAGCCA 60.179 55.000 26.68 0.00 0.00 4.75
949 958 1.600511 TAGATGCGGTGCTTCGGTGA 61.601 55.000 1.94 0.00 37.70 4.02
951 960 1.153628 GTAGATGCGGTGCTTCGGT 60.154 57.895 1.94 0.00 37.70 4.69
955 964 1.726853 GAGTTGTAGATGCGGTGCTT 58.273 50.000 0.00 0.00 0.00 3.91
970 979 2.657237 CGTCTCCTTGCCCGAGTT 59.343 61.111 0.00 0.00 0.00 3.01
973 982 3.379445 GTCCGTCTCCTTGCCCGA 61.379 66.667 0.00 0.00 0.00 5.14
977 986 0.173708 AGAATCGTCCGTCTCCTTGC 59.826 55.000 0.00 0.00 0.00 4.01
989 998 2.715046 ACATCAACATGCCAGAATCGT 58.285 42.857 0.00 0.00 32.57 3.73
993 1002 3.084039 GAGGAACATCAACATGCCAGAA 58.916 45.455 0.00 0.00 32.57 3.02
996 1005 2.161855 GTGAGGAACATCAACATGCCA 58.838 47.619 0.00 0.00 32.57 4.92
1041 1050 1.900245 TGTACACGTCTAGCACCTCA 58.100 50.000 0.00 0.00 0.00 3.86
1050 1059 1.079405 CGGGCCATTGTACACGTCT 60.079 57.895 4.39 0.00 0.00 4.18
1077 1086 0.468226 AGTGTCGGAACTTGAAGGCA 59.532 50.000 0.00 0.00 0.00 4.75
1092 1101 0.991920 CCTCCATGTAACCCCAGTGT 59.008 55.000 0.00 0.00 0.00 3.55
1144 1153 0.767060 ACCCCAAAGAACTCGACCCT 60.767 55.000 0.00 0.00 0.00 4.34
1146 1155 0.685660 AGACCCCAAAGAACTCGACC 59.314 55.000 0.00 0.00 0.00 4.79
1177 1186 9.162764 GACACACAATTATACTGTGGAACTTAT 57.837 33.333 15.32 0.00 46.89 1.73
1229 1250 3.323751 TTTCTCGGTTACTGGCTTACC 57.676 47.619 0.00 0.00 0.00 2.85
1253 1274 4.460034 CACATTGTTGGAGAACCATGATGA 59.540 41.667 0.00 0.00 46.34 2.92
1254 1275 4.460034 TCACATTGTTGGAGAACCATGATG 59.540 41.667 0.00 0.00 46.34 3.07
1255 1276 4.665451 TCACATTGTTGGAGAACCATGAT 58.335 39.130 0.00 0.00 46.34 2.45
1266 1289 5.447683 CGTCAACCTATCATCACATTGTTGG 60.448 44.000 0.00 0.00 34.06 3.77
1299 1322 2.449967 TACTCCGCCTTCTCCACCCA 62.450 60.000 0.00 0.00 0.00 4.51
1329 1352 0.249868 CTCACGAGGAAGTTGCCACA 60.250 55.000 0.00 0.00 0.00 4.17
1359 1382 4.326507 AGCAGCAGAAGCAGGCGT 62.327 61.111 0.00 0.00 44.74 5.68
1368 1400 2.036571 CCGATGCAACAGCAGCAGA 61.037 57.895 6.53 0.00 44.50 4.26
1376 1408 1.539388 CAACCTAAAGCCGATGCAACA 59.461 47.619 0.00 0.00 41.13 3.33
1377 1409 1.732405 GCAACCTAAAGCCGATGCAAC 60.732 52.381 0.00 0.00 41.13 4.17
1378 1410 0.525761 GCAACCTAAAGCCGATGCAA 59.474 50.000 0.00 0.00 41.13 4.08
1401 1436 5.277779 CCGCTCTCTAGTTTACTCTCATCAG 60.278 48.000 0.00 0.00 0.00 2.90
1411 1446 5.121768 GTCAATTTTGCCGCTCTCTAGTTTA 59.878 40.000 0.00 0.00 0.00 2.01
1418 1453 0.796312 TCGTCAATTTTGCCGCTCTC 59.204 50.000 0.00 0.00 28.49 3.20
1421 1456 1.066303 TGTTTCGTCAATTTTGCCGCT 59.934 42.857 0.00 0.00 28.49 5.52
1427 1462 6.142817 GCTAGTGACATGTTTCGTCAATTTT 58.857 36.000 0.00 0.00 44.58 1.82
1455 1490 5.067283 ACCGCAAAAGAAAAAGTACAGTGAT 59.933 36.000 0.00 0.00 0.00 3.06
1466 1501 3.834610 TCGTTTCAACCGCAAAAGAAAA 58.165 36.364 0.00 0.00 32.44 2.29
1467 1502 3.489180 TCGTTTCAACCGCAAAAGAAA 57.511 38.095 0.00 0.00 0.00 2.52
1468 1503 3.623863 GATCGTTTCAACCGCAAAAGAA 58.376 40.909 0.00 0.00 0.00 2.52
1469 1504 2.349060 CGATCGTTTCAACCGCAAAAGA 60.349 45.455 7.03 0.00 0.00 2.52
1470 1505 1.969256 CGATCGTTTCAACCGCAAAAG 59.031 47.619 7.03 0.00 0.00 2.27
1471 1506 1.598132 TCGATCGTTTCAACCGCAAAA 59.402 42.857 15.94 0.00 0.00 2.44
1472 1507 1.218763 TCGATCGTTTCAACCGCAAA 58.781 45.000 15.94 0.00 0.00 3.68
1473 1508 1.434555 ATCGATCGTTTCAACCGCAA 58.565 45.000 15.94 0.00 0.00 4.85
1474 1509 2.281140 TATCGATCGTTTCAACCGCA 57.719 45.000 15.94 0.00 0.00 5.69
1475 1510 2.792674 TCATATCGATCGTTTCAACCGC 59.207 45.455 15.94 0.00 0.00 5.68
1476 1511 5.174943 TCAATCATATCGATCGTTTCAACCG 59.825 40.000 15.94 0.20 31.11 4.44
1477 1512 6.201044 AGTCAATCATATCGATCGTTTCAACC 59.799 38.462 15.94 0.00 31.11 3.77
1478 1513 7.166628 AGTCAATCATATCGATCGTTTCAAC 57.833 36.000 15.94 3.73 31.11 3.18
1479 1514 8.349983 TCTAGTCAATCATATCGATCGTTTCAA 58.650 33.333 15.94 0.00 31.11 2.69
1480 1515 7.871853 TCTAGTCAATCATATCGATCGTTTCA 58.128 34.615 15.94 0.00 31.11 2.69
1481 1516 7.483375 CCTCTAGTCAATCATATCGATCGTTTC 59.517 40.741 15.94 0.00 31.11 2.78
1482 1517 7.309177 CCTCTAGTCAATCATATCGATCGTTT 58.691 38.462 15.94 6.78 31.11 3.60
1483 1518 6.127869 CCCTCTAGTCAATCATATCGATCGTT 60.128 42.308 15.94 9.65 31.11 3.85
1484 1519 5.355630 CCCTCTAGTCAATCATATCGATCGT 59.644 44.000 15.94 5.23 31.11 3.73
1485 1520 5.220951 CCCCTCTAGTCAATCATATCGATCG 60.221 48.000 9.36 9.36 31.11 3.69
1486 1521 5.068460 CCCCCTCTAGTCAATCATATCGATC 59.932 48.000 0.00 0.00 31.11 3.69
1487 1522 4.959210 CCCCCTCTAGTCAATCATATCGAT 59.041 45.833 2.16 2.16 35.12 3.59
1488 1523 4.344978 CCCCCTCTAGTCAATCATATCGA 58.655 47.826 0.00 0.00 0.00 3.59
1489 1524 4.727507 CCCCCTCTAGTCAATCATATCG 57.272 50.000 0.00 0.00 0.00 2.92
1507 1542 4.141914 TGTTGTTATTGTTGTTTCACCCCC 60.142 41.667 0.00 0.00 0.00 5.40
1508 1543 5.012328 TGTTGTTATTGTTGTTTCACCCC 57.988 39.130 0.00 0.00 0.00 4.95
1509 1544 5.869888 TGTTGTTGTTATTGTTGTTTCACCC 59.130 36.000 0.00 0.00 0.00 4.61
1510 1545 6.952935 TGTTGTTGTTATTGTTGTTTCACC 57.047 33.333 0.00 0.00 0.00 4.02
1511 1546 7.788055 TGTTGTTGTTGTTATTGTTGTTTCAC 58.212 30.769 0.00 0.00 0.00 3.18
1512 1547 7.946655 TGTTGTTGTTGTTATTGTTGTTTCA 57.053 28.000 0.00 0.00 0.00 2.69
1513 1548 8.276325 TGTTGTTGTTGTTGTTATTGTTGTTTC 58.724 29.630 0.00 0.00 0.00 2.78
1514 1549 8.142994 TGTTGTTGTTGTTGTTATTGTTGTTT 57.857 26.923 0.00 0.00 0.00 2.83
1523 1558 6.533723 TGTTGTTGTTGTTGTTGTTGTTGTTA 59.466 30.769 0.00 0.00 0.00 2.41
1570 1606 3.476295 ACTTGCTATTGTTGTGATGCG 57.524 42.857 0.00 0.00 0.00 4.73
1571 1607 5.801947 CCTTTACTTGCTATTGTTGTGATGC 59.198 40.000 0.00 0.00 0.00 3.91
1574 1610 5.626142 TCCCTTTACTTGCTATTGTTGTGA 58.374 37.500 0.00 0.00 0.00 3.58
1614 1659 1.760086 CCTCATCTCCACCGGCTCT 60.760 63.158 0.00 0.00 0.00 4.09
1687 1734 1.076485 GGGAGCATTGTGCCTCCAT 60.076 57.895 16.56 0.00 46.52 3.41
1784 1831 1.007387 GTTTGGTTGCCGCCTTCAG 60.007 57.895 0.00 0.00 0.00 3.02
1804 1851 2.683768 TGCCCCAACCTTGTTTGTAAT 58.316 42.857 0.00 0.00 0.00 1.89
1892 1939 4.960469 ACCCTAAACGATTGAGATCACCTA 59.040 41.667 0.00 0.00 32.33 3.08
1899 1946 2.565391 TGAGCACCCTAAACGATTGAGA 59.435 45.455 0.00 0.00 0.00 3.27
1905 1952 2.215196 GTGTTTGAGCACCCTAAACGA 58.785 47.619 0.00 0.00 37.17 3.85
1962 2009 7.177878 ACACTTCCACCAAGAGATATTTGATT 58.822 34.615 0.00 0.00 35.82 2.57
2028 2078 4.744795 TCTCTCTTCCTAGCCAATCAAC 57.255 45.455 0.00 0.00 0.00 3.18
2140 2194 5.011635 GGTGGATAATGGTTGGTTTTGTCTT 59.988 40.000 0.00 0.00 0.00 3.01
2141 2195 4.526650 GGTGGATAATGGTTGGTTTTGTCT 59.473 41.667 0.00 0.00 0.00 3.41
2148 2204 1.006639 GGGTGGTGGATAATGGTTGGT 59.993 52.381 0.00 0.00 0.00 3.67
2155 2211 0.552848 CAGGCTGGGTGGTGGATAAT 59.447 55.000 6.61 0.00 0.00 1.28
2173 2229 2.361483 TAGTACCGCCCGTCTGCA 60.361 61.111 0.00 0.00 0.00 4.41
2227 2304 3.487372 TGTTTCTCGTTCTCTCCTGAGA 58.513 45.455 0.00 0.00 46.58 3.27
2229 2306 2.558795 CCTGTTTCTCGTTCTCTCCTGA 59.441 50.000 0.00 0.00 0.00 3.86
2238 2315 2.583143 CTTTTCCCCCTGTTTCTCGTT 58.417 47.619 0.00 0.00 0.00 3.85
2239 2316 1.818131 GCTTTTCCCCCTGTTTCTCGT 60.818 52.381 0.00 0.00 0.00 4.18
2240 2317 0.881796 GCTTTTCCCCCTGTTTCTCG 59.118 55.000 0.00 0.00 0.00 4.04
2247 2326 2.743183 CGTATCTCTGCTTTTCCCCCTG 60.743 54.545 0.00 0.00 0.00 4.45
2270 2350 2.931105 TACCATGGCCACCACCGT 60.931 61.111 8.16 2.00 35.80 4.83
2282 2362 3.749226 GTAGTACCGCTCCTACTACCAT 58.251 50.000 9.65 0.00 39.99 3.55
2310 2390 0.036671 GGCAGCGGTAGTACAACCTT 60.037 55.000 2.06 0.00 37.39 3.50
2314 2394 0.393448 TTGTGGCAGCGGTAGTACAA 59.607 50.000 2.06 5.86 0.00 2.41
2315 2395 0.320073 GTTGTGGCAGCGGTAGTACA 60.320 55.000 2.06 0.00 0.00 2.90
2329 2409 2.550978 CCTGGAATACTAGCGGTTGTG 58.449 52.381 11.94 0.00 0.00 3.33
2339 2431 5.398012 GCTATCTGTTTTCCCCTGGAATACT 60.398 44.000 14.64 1.76 41.71 2.12
2342 2434 3.269381 TGCTATCTGTTTTCCCCTGGAAT 59.731 43.478 0.00 0.00 41.71 3.01
2346 2438 3.071874 TGTGCTATCTGTTTTCCCCTG 57.928 47.619 0.00 0.00 0.00 4.45
2352 2444 6.116126 GGGTCTCTAATGTGCTATCTGTTTT 58.884 40.000 0.00 0.00 0.00 2.43
2359 2451 2.894126 CTCCGGGTCTCTAATGTGCTAT 59.106 50.000 0.00 0.00 0.00 2.97
2366 2458 4.414677 GGTATAACCTCCGGGTCTCTAAT 58.585 47.826 0.00 0.00 46.67 1.73
2367 2459 3.748668 CGGTATAACCTCCGGGTCTCTAA 60.749 52.174 0.00 0.00 46.67 2.10
2383 2475 9.661563 ACTTTTCATGTCAGATTTTACGGTATA 57.338 29.630 0.00 0.00 0.00 1.47
2384 2476 8.561738 ACTTTTCATGTCAGATTTTACGGTAT 57.438 30.769 0.00 0.00 0.00 2.73
2397 2490 2.238521 GGGCCTTGACTTTTCATGTCA 58.761 47.619 0.84 0.00 41.94 3.58


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

AutoCloner maintained by Alex Coulton.