Multiple sequence alignment - TraesCS5B01G255400

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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 TraesCS5B01G255400 chr5B 100.000 2198 0 0 1 2198 438038764 438036567 0.000000e+00 4060
1 TraesCS5B01G255400 chr5B 89.099 477 48 4 151 623 646063345 646063821 6.760000e-165 590
2 TraesCS5B01G255400 chr5D 88.537 1230 53 19 698 1880 369339755 369338567 0.000000e+00 1410
3 TraesCS5B01G255400 chr5D 89.922 129 10 2 2070 2198 369338409 369338284 1.750000e-36 163
4 TraesCS5B01G255400 chr5A 84.553 738 62 21 642 1343 471818649 471817928 0.000000e+00 684
5 TraesCS5B01G255400 chr5A 82.051 702 60 30 1405 2062 471817929 471817250 2.480000e-149 538
6 TraesCS5B01G255400 chr5A 88.148 135 16 0 2064 2198 471817213 471817079 6.280000e-36 161
7 TraesCS5B01G255400 chr2B 84.466 618 76 12 1 615 397267627 397268227 1.880000e-165 592
8 TraesCS5B01G255400 chr2B 85.593 472 42 15 164 623 184411115 184410658 2.550000e-129 472
9 TraesCS5B01G255400 chr2B 86.957 92 9 3 536 624 671888063 671887972 1.390000e-17 100
10 TraesCS5B01G255400 chr1B 83.740 615 82 10 1 612 476694117 476694716 1.140000e-157 566
11 TraesCS5B01G255400 chr1B 82.646 461 73 3 38 493 502077789 502078247 3.400000e-108 401
12 TraesCS5B01G255400 chr2A 84.444 585 67 15 38 616 130726462 130725896 2.470000e-154 555
13 TraesCS5B01G255400 chr3B 82.683 589 75 13 38 616 16323770 16324341 4.210000e-137 497
14 TraesCS5B01G255400 chr3B 81.188 606 81 21 36 624 581095372 581095961 7.150000e-125 457
15 TraesCS5B01G255400 chr7B 86.866 434 55 2 151 582 238381419 238381852 3.280000e-133 484
16 TraesCS5B01G255400 chr7B 78.505 535 64 27 1 497 329859764 329859243 9.860000e-79 303
17 TraesCS5B01G255400 chr6B 86.571 350 39 6 279 621 161270011 161269663 1.590000e-101 379
18 TraesCS5B01G255400 chr6B 90.830 229 21 0 1 229 161270253 161270025 7.620000e-80 307


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 TraesCS5B01G255400 chr5B 438036567 438038764 2197 True 4060.0 4060 100.000000 1 2198 1 chr5B.!!$R1 2197
1 TraesCS5B01G255400 chr5D 369338284 369339755 1471 True 786.5 1410 89.229500 698 2198 2 chr5D.!!$R1 1500
2 TraesCS5B01G255400 chr5A 471817079 471818649 1570 True 461.0 684 84.917333 642 2198 3 chr5A.!!$R1 1556
3 TraesCS5B01G255400 chr2B 397267627 397268227 600 False 592.0 592 84.466000 1 615 1 chr2B.!!$F1 614
4 TraesCS5B01G255400 chr1B 476694117 476694716 599 False 566.0 566 83.740000 1 612 1 chr1B.!!$F1 611
5 TraesCS5B01G255400 chr2A 130725896 130726462 566 True 555.0 555 84.444000 38 616 1 chr2A.!!$R1 578
6 TraesCS5B01G255400 chr3B 16323770 16324341 571 False 497.0 497 82.683000 38 616 1 chr3B.!!$F1 578
7 TraesCS5B01G255400 chr3B 581095372 581095961 589 False 457.0 457 81.188000 36 624 1 chr3B.!!$F2 588
8 TraesCS5B01G255400 chr7B 329859243 329859764 521 True 303.0 303 78.505000 1 497 1 chr7B.!!$R1 496
9 TraesCS5B01G255400 chr6B 161269663 161270253 590 True 343.0 379 88.700500 1 621 2 chr6B.!!$R1 620

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
926 1033 0.036671 CCTCGCCTTTTCCGTTACCT 60.037 55.0 0.0 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 1992 0.034186 GGCCATGACCCAGAATGTCA 60.034 55.0 0.0 0.0 45.98 3.58 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
23 24 1.639722 TCGATGAACTGACCTGGGAA 58.360 50.000 0.00 0.00 0.00 3.97
72 73 1.421485 CAACAGCACGGCGATTCTC 59.579 57.895 16.62 0.00 0.00 2.87
89 91 4.514577 CCTCCTCCGCGCGAACAT 62.515 66.667 34.63 0.00 0.00 2.71
185 206 0.955428 ATGCTGCGGTTGTAGTGGTG 60.955 55.000 0.00 0.00 0.00 4.17
190 211 1.227704 CGGTTGTAGTGGTGTGGCA 60.228 57.895 0.00 0.00 0.00 4.92
270 291 0.618968 ATCCCTTTCTCACTCCGGCT 60.619 55.000 0.00 0.00 0.00 5.52
338 370 3.855668 TGGTGGATTTGGAAGGAAATGT 58.144 40.909 0.00 0.00 0.00 2.71
441 502 1.301874 CCGCCTAAACACCCAACGA 60.302 57.895 0.00 0.00 0.00 3.85
444 505 1.337074 CGCCTAAACACCCAACGAGTA 60.337 52.381 0.00 0.00 0.00 2.59
499 563 2.246739 CGCATCGATGGAACGGCAT 61.247 57.895 26.00 0.00 0.00 4.40
513 582 2.511373 GCATGGTCGGACGCATCA 60.511 61.111 1.43 0.00 0.00 3.07
515 584 1.715585 CATGGTCGGACGCATCAAC 59.284 57.895 1.43 0.00 0.00 3.18
523 592 1.234821 GGACGCATCAACAAACCTGA 58.765 50.000 0.00 0.00 0.00 3.86
557 626 1.496403 CGAGATGACGATCGGACGGA 61.496 60.000 20.98 0.00 35.33 4.69
560 629 2.734756 GATGACGATCGGACGGAGCC 62.735 65.000 20.98 0.00 37.61 4.70
607 678 2.260844 AGCACAGCTGCACTTTTAGA 57.739 45.000 15.27 0.00 46.97 2.10
922 1029 3.047877 CGCCTCGCCTTTTCCGTT 61.048 61.111 0.00 0.00 0.00 4.44
923 1030 1.738830 CGCCTCGCCTTTTCCGTTA 60.739 57.895 0.00 0.00 0.00 3.18
924 1031 1.792301 GCCTCGCCTTTTCCGTTAC 59.208 57.895 0.00 0.00 0.00 2.50
925 1032 1.642037 GCCTCGCCTTTTCCGTTACC 61.642 60.000 0.00 0.00 0.00 2.85
926 1033 0.036671 CCTCGCCTTTTCCGTTACCT 60.037 55.000 0.00 0.00 0.00 3.08
927 1034 1.609841 CCTCGCCTTTTCCGTTACCTT 60.610 52.381 0.00 0.00 0.00 3.50
928 1035 2.148768 CTCGCCTTTTCCGTTACCTTT 58.851 47.619 0.00 0.00 0.00 3.11
929 1036 2.551032 CTCGCCTTTTCCGTTACCTTTT 59.449 45.455 0.00 0.00 0.00 2.27
930 1037 2.549329 TCGCCTTTTCCGTTACCTTTTC 59.451 45.455 0.00 0.00 0.00 2.29
931 1038 2.551032 CGCCTTTTCCGTTACCTTTTCT 59.449 45.455 0.00 0.00 0.00 2.52
932 1039 3.004002 CGCCTTTTCCGTTACCTTTTCTT 59.996 43.478 0.00 0.00 0.00 2.52
933 1040 4.543692 GCCTTTTCCGTTACCTTTTCTTC 58.456 43.478 0.00 0.00 0.00 2.87
934 1041 4.558095 GCCTTTTCCGTTACCTTTTCTTCC 60.558 45.833 0.00 0.00 0.00 3.46
935 1042 4.825634 CCTTTTCCGTTACCTTTTCTTCCT 59.174 41.667 0.00 0.00 0.00 3.36
936 1043 5.301045 CCTTTTCCGTTACCTTTTCTTCCTT 59.699 40.000 0.00 0.00 0.00 3.36
937 1044 5.761165 TTTCCGTTACCTTTTCTTCCTTG 57.239 39.130 0.00 0.00 0.00 3.61
938 1045 4.426736 TCCGTTACCTTTTCTTCCTTGT 57.573 40.909 0.00 0.00 0.00 3.16
939 1046 4.383173 TCCGTTACCTTTTCTTCCTTGTC 58.617 43.478 0.00 0.00 0.00 3.18
940 1047 3.501062 CCGTTACCTTTTCTTCCTTGTCC 59.499 47.826 0.00 0.00 0.00 4.02
958 1065 3.414193 TCCCCTACCTCGGAGCGA 61.414 66.667 0.00 0.00 0.00 4.93
960 1067 2.056223 CCCCTACCTCGGAGCGAAA 61.056 63.158 0.00 0.00 34.74 3.46
961 1068 1.437986 CCCTACCTCGGAGCGAAAG 59.562 63.158 0.00 0.00 34.74 2.62
962 1069 1.035932 CCCTACCTCGGAGCGAAAGA 61.036 60.000 0.00 0.00 34.74 2.52
963 1070 0.382515 CCTACCTCGGAGCGAAAGAG 59.617 60.000 0.00 0.00 34.74 2.85
1121 1228 1.349026 CTTCCACAAGCTCTCCTCCAA 59.651 52.381 0.00 0.00 0.00 3.53
1228 1348 1.144093 CTCCCCCGAGATCTACTCTGT 59.856 57.143 0.00 0.00 42.92 3.41
1254 1374 2.831742 CGGCATGCATTGGGCTCT 60.832 61.111 21.36 0.00 45.15 4.09
1261 1385 1.452833 GCATTGGGCTCTGTCTCCC 60.453 63.158 0.00 0.00 42.93 4.30
1263 1387 1.613630 ATTGGGCTCTGTCTCCCGT 60.614 57.895 0.00 0.00 45.60 5.28
1345 1469 2.586914 CGGGGCCGGTCGATTTAC 60.587 66.667 1.90 0.00 35.56 2.01
1346 1470 2.585698 GGGGCCGGTCGATTTACA 59.414 61.111 1.90 0.00 0.00 2.41
1347 1471 1.147600 GGGGCCGGTCGATTTACAT 59.852 57.895 1.90 0.00 0.00 2.29
1348 1472 0.464916 GGGGCCGGTCGATTTACATT 60.465 55.000 1.90 0.00 0.00 2.71
1349 1473 0.661020 GGGCCGGTCGATTTACATTG 59.339 55.000 1.90 0.00 0.00 2.82
1350 1474 1.658994 GGCCGGTCGATTTACATTGA 58.341 50.000 1.90 0.00 0.00 2.57
1351 1475 2.218603 GGCCGGTCGATTTACATTGAT 58.781 47.619 1.90 0.00 0.00 2.57
1352 1476 2.616842 GGCCGGTCGATTTACATTGATT 59.383 45.455 1.90 0.00 0.00 2.57
1353 1477 3.066203 GGCCGGTCGATTTACATTGATTT 59.934 43.478 1.90 0.00 0.00 2.17
1354 1478 4.279659 GCCGGTCGATTTACATTGATTTC 58.720 43.478 1.90 0.00 0.00 2.17
1355 1479 4.788521 GCCGGTCGATTTACATTGATTTCC 60.789 45.833 1.90 0.00 0.00 3.13
1356 1480 4.574828 CCGGTCGATTTACATTGATTTCCT 59.425 41.667 0.00 0.00 0.00 3.36
1357 1481 5.501715 CGGTCGATTTACATTGATTTCCTG 58.498 41.667 0.00 0.00 0.00 3.86
1358 1482 5.273944 GGTCGATTTACATTGATTTCCTGC 58.726 41.667 0.00 0.00 0.00 4.85
1359 1483 5.066505 GGTCGATTTACATTGATTTCCTGCT 59.933 40.000 0.00 0.00 0.00 4.24
1360 1484 5.967674 GTCGATTTACATTGATTTCCTGCTG 59.032 40.000 0.00 0.00 0.00 4.41
1361 1485 5.879777 TCGATTTACATTGATTTCCTGCTGA 59.120 36.000 0.00 0.00 0.00 4.26
1362 1486 6.374053 TCGATTTACATTGATTTCCTGCTGAA 59.626 34.615 0.00 0.00 0.00 3.02
1363 1487 7.067372 TCGATTTACATTGATTTCCTGCTGAAT 59.933 33.333 0.00 0.00 31.67 2.57
1364 1488 7.703621 CGATTTACATTGATTTCCTGCTGAATT 59.296 33.333 0.00 0.00 31.67 2.17
1369 1493 8.937634 ACATTGATTTCCTGCTGAATTAATTC 57.062 30.769 19.37 19.37 37.31 2.17
1370 1494 7.983484 ACATTGATTTCCTGCTGAATTAATTCC 59.017 33.333 22.42 10.71 35.97 3.01
1371 1495 6.469782 TGATTTCCTGCTGAATTAATTCCC 57.530 37.500 22.42 14.84 35.97 3.97
1372 1496 4.981806 TTTCCTGCTGAATTAATTCCCG 57.018 40.909 22.42 15.30 35.97 5.14
1373 1497 3.644966 TCCTGCTGAATTAATTCCCGT 57.355 42.857 22.42 0.00 35.97 5.28
1374 1498 3.963129 TCCTGCTGAATTAATTCCCGTT 58.037 40.909 22.42 0.00 35.97 4.44
1375 1499 4.340617 TCCTGCTGAATTAATTCCCGTTT 58.659 39.130 22.42 0.00 35.97 3.60
1376 1500 4.157656 TCCTGCTGAATTAATTCCCGTTTG 59.842 41.667 22.42 9.24 35.97 2.93
1377 1501 4.082245 CCTGCTGAATTAATTCCCGTTTGT 60.082 41.667 22.42 0.00 35.97 2.83
1378 1502 5.461032 TGCTGAATTAATTCCCGTTTGTT 57.539 34.783 22.42 0.00 35.97 2.83
1379 1503 5.226396 TGCTGAATTAATTCCCGTTTGTTG 58.774 37.500 22.42 5.67 35.97 3.33
1380 1504 4.091365 GCTGAATTAATTCCCGTTTGTTGC 59.909 41.667 22.42 10.44 35.97 4.17
1381 1505 5.461032 TGAATTAATTCCCGTTTGTTGCT 57.539 34.783 22.42 0.00 35.97 3.91
1382 1506 5.848406 TGAATTAATTCCCGTTTGTTGCTT 58.152 33.333 22.42 0.00 35.97 3.91
1383 1507 5.923684 TGAATTAATTCCCGTTTGTTGCTTC 59.076 36.000 22.42 0.00 35.97 3.86
1384 1508 2.415697 AATTCCCGTTTGTTGCTTCG 57.584 45.000 0.00 0.00 0.00 3.79
1385 1509 0.039527 ATTCCCGTTTGTTGCTTCGC 60.040 50.000 0.00 0.00 0.00 4.70
1386 1510 1.098712 TTCCCGTTTGTTGCTTCGCT 61.099 50.000 0.00 0.00 0.00 4.93
1387 1511 1.082104 CCCGTTTGTTGCTTCGCTC 60.082 57.895 0.00 0.00 0.00 5.03
1388 1512 1.082104 CCGTTTGTTGCTTCGCTCC 60.082 57.895 0.00 0.00 0.00 4.70
1389 1513 1.438710 CGTTTGTTGCTTCGCTCCG 60.439 57.895 0.00 0.00 0.00 4.63
1390 1514 1.827315 CGTTTGTTGCTTCGCTCCGA 61.827 55.000 0.00 0.00 0.00 4.55
1391 1515 0.517316 GTTTGTTGCTTCGCTCCGAT 59.483 50.000 0.00 0.00 35.23 4.18
1392 1516 0.516877 TTTGTTGCTTCGCTCCGATG 59.483 50.000 0.00 0.00 35.23 3.84
1393 1517 0.320334 TTGTTGCTTCGCTCCGATGA 60.320 50.000 4.93 0.00 35.23 2.92
1394 1518 0.108186 TGTTGCTTCGCTCCGATGAT 60.108 50.000 4.93 0.00 35.23 2.45
1395 1519 0.302890 GTTGCTTCGCTCCGATGATG 59.697 55.000 4.93 0.00 35.23 3.07
1396 1520 0.108186 TTGCTTCGCTCCGATGATGT 60.108 50.000 4.93 0.00 35.23 3.06
1397 1521 0.528466 TGCTTCGCTCCGATGATGTC 60.528 55.000 4.93 0.00 35.23 3.06
1514 1720 3.019564 GTTTAGTGCTCCATCATGCCTT 58.980 45.455 0.00 0.00 0.00 4.35
1534 1740 5.151389 CCTTCGTTTGTGCCTGTTTATTAC 58.849 41.667 0.00 0.00 0.00 1.89
1535 1741 5.048991 CCTTCGTTTGTGCCTGTTTATTACT 60.049 40.000 0.00 0.00 0.00 2.24
1536 1742 5.351233 TCGTTTGTGCCTGTTTATTACTG 57.649 39.130 0.00 0.00 0.00 2.74
1560 1766 6.183360 TGCTGCTCATTAGTTTAGCAAATACC 60.183 38.462 0.00 0.00 45.04 2.73
1730 1951 2.430921 GTGACGTCCACGCTCCTG 60.431 66.667 14.12 0.00 44.43 3.86
1741 1973 1.009675 CGCTCCTGTGTTGTTGTGC 60.010 57.895 0.00 0.00 0.00 4.57
1754 1986 2.858839 TGTTGTGCACTCTACGATACG 58.141 47.619 19.41 0.00 0.00 3.06
1756 1988 3.436359 TGTTGTGCACTCTACGATACGTA 59.564 43.478 19.41 0.00 41.54 3.57
1757 1989 3.663464 TGTGCACTCTACGATACGTAC 57.337 47.619 19.41 0.00 41.54 3.67
1758 1990 3.264947 TGTGCACTCTACGATACGTACT 58.735 45.455 19.41 0.00 41.54 2.73
1759 1991 3.308053 TGTGCACTCTACGATACGTACTC 59.692 47.826 19.41 0.00 41.54 2.59
1760 1992 3.555139 GTGCACTCTACGATACGTACTCT 59.445 47.826 10.32 0.00 41.54 3.24
1761 1993 3.554731 TGCACTCTACGATACGTACTCTG 59.445 47.826 0.00 0.00 41.54 3.35
1762 1994 3.801050 GCACTCTACGATACGTACTCTGA 59.199 47.826 0.00 0.00 41.54 3.27
1763 1995 4.317980 GCACTCTACGATACGTACTCTGAC 60.318 50.000 0.00 0.00 41.54 3.51
1764 1996 4.802563 CACTCTACGATACGTACTCTGACA 59.197 45.833 0.00 0.00 41.54 3.58
1765 1997 5.462729 CACTCTACGATACGTACTCTGACAT 59.537 44.000 0.00 0.00 41.54 3.06
1766 1998 6.018913 CACTCTACGATACGTACTCTGACATT 60.019 42.308 0.00 0.00 41.54 2.71
1767 1999 6.200665 ACTCTACGATACGTACTCTGACATTC 59.799 42.308 0.00 0.00 41.54 2.67
1778 2010 1.065199 TCTGACATTCTGGGTCATGGC 60.065 52.381 0.00 0.00 43.72 4.40
1780 2012 1.077501 ACATTCTGGGTCATGGCCG 60.078 57.895 10.95 0.00 0.00 6.13
1807 2039 1.873270 GATTTGGTTGCCCGTCCACC 61.873 60.000 0.00 0.00 33.12 4.61
1808 2040 4.589675 TTGGTTGCCCGTCCACCC 62.590 66.667 0.00 0.00 33.12 4.61
1850 2082 1.522806 TTGCCTTGCACGTTCGACT 60.523 52.632 0.00 0.00 38.71 4.18
1852 2084 1.092921 TGCCTTGCACGTTCGACTTT 61.093 50.000 0.00 0.00 31.71 2.66
1854 2086 0.234884 CCTTGCACGTTCGACTTTCC 59.765 55.000 0.00 0.00 0.00 3.13
1876 2108 0.725784 GTTGAAACGGCGATGCAGTG 60.726 55.000 16.62 0.00 37.01 3.66
1918 2153 2.167693 TCACTCTAACTGCCCCGTAATG 59.832 50.000 0.00 0.00 0.00 1.90
1949 2184 2.026641 GGCAAAAGCCTGATAGATGCA 58.973 47.619 0.00 0.00 34.14 3.96
1952 2187 3.317149 GCAAAAGCCTGATAGATGCATGA 59.683 43.478 2.46 0.00 32.80 3.07
1962 2197 6.315642 CCTGATAGATGCATGATATGTGGTTC 59.684 42.308 2.46 0.00 0.00 3.62
1965 2200 5.300411 AGATGCATGATATGTGGTTCAGA 57.700 39.130 2.46 0.00 0.00 3.27
1967 2202 6.124340 AGATGCATGATATGTGGTTCAGAAA 58.876 36.000 2.46 0.00 0.00 2.52
1968 2203 6.776116 AGATGCATGATATGTGGTTCAGAAAT 59.224 34.615 2.46 0.00 0.00 2.17
1969 2204 6.778834 TGCATGATATGTGGTTCAGAAATT 57.221 33.333 0.00 0.00 0.00 1.82
1970 2205 6.566141 TGCATGATATGTGGTTCAGAAATTG 58.434 36.000 0.00 0.00 0.00 2.32
1972 2207 5.233957 TGATATGTGGTTCAGAAATTGCG 57.766 39.130 0.00 0.00 0.00 4.85
1975 2213 1.001487 TGTGGTTCAGAAATTGCGCAG 60.001 47.619 11.31 0.00 0.00 5.18
1977 2215 0.109132 GGTTCAGAAATTGCGCAGGG 60.109 55.000 11.31 0.00 0.00 4.45
1995 2233 2.358737 CCTCCCAAGCCACACGAC 60.359 66.667 0.00 0.00 0.00 4.34
1999 2238 1.961277 CCCAAGCCACACGACTGTC 60.961 63.158 0.00 0.00 0.00 3.51
2024 2263 4.759693 TGTGATTCGCAAAGTAGTTGGATT 59.240 37.500 0.00 0.00 37.73 3.01
2025 2264 5.240623 TGTGATTCGCAAAGTAGTTGGATTT 59.759 36.000 0.00 0.00 37.73 2.17
2026 2265 5.795441 GTGATTCGCAAAGTAGTTGGATTTC 59.205 40.000 0.00 0.00 37.73 2.17
2029 2268 4.130857 TCGCAAAGTAGTTGGATTTCACA 58.869 39.130 0.00 0.00 37.73 3.58
2034 2273 4.866508 AGTAGTTGGATTTCACACGAGA 57.133 40.909 0.00 0.00 0.00 4.04
2044 2283 7.782049 TGGATTTCACACGAGAGAATAGTAAT 58.218 34.615 0.00 0.00 0.00 1.89
2076 2350 6.543465 TCTCTGAAACTCTGAAATTTCAAGCA 59.457 34.615 20.82 11.51 42.62 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.320771 AGAATCGCCGTGAGCAAACT 60.321 50.000 0.00 0.00 44.04 2.66
72 73 4.514577 ATGTTCGCGCGGAGGAGG 62.515 66.667 31.69 0.00 0.00 4.30
155 157 1.014044 CCGCAGCATACAACAGTCGT 61.014 55.000 0.00 0.00 0.00 4.34
394 454 1.662686 CCTCCAGTTCTTCTCCCCTT 58.337 55.000 0.00 0.00 0.00 3.95
499 563 0.533085 TTTGTTGATGCGTCCGACCA 60.533 50.000 2.83 0.00 0.00 4.02
513 582 1.941812 CGCGCTTCTCAGGTTTGTT 59.058 52.632 5.56 0.00 0.00 2.83
515 584 2.174349 GCGCGCTTCTCAGGTTTG 59.826 61.111 26.67 0.00 0.00 2.93
634 705 4.918588 ACGATGGTATCTGGTTCCTTTTT 58.081 39.130 0.00 0.00 0.00 1.94
635 706 4.569719 ACGATGGTATCTGGTTCCTTTT 57.430 40.909 0.00 0.00 0.00 2.27
636 707 5.687166 TTACGATGGTATCTGGTTCCTTT 57.313 39.130 0.00 0.00 0.00 3.11
637 708 5.687166 TTTACGATGGTATCTGGTTCCTT 57.313 39.130 0.00 0.00 0.00 3.36
638 709 5.425630 GTTTTACGATGGTATCTGGTTCCT 58.574 41.667 0.00 0.00 0.00 3.36
639 710 4.573607 GGTTTTACGATGGTATCTGGTTCC 59.426 45.833 0.00 0.00 0.00 3.62
640 711 4.269363 CGGTTTTACGATGGTATCTGGTTC 59.731 45.833 0.00 0.00 35.47 3.62
647 718 2.282407 GGCACGGTTTTACGATGGTAT 58.718 47.619 0.00 0.00 37.61 2.73
711 788 1.866853 CTTTTCAAGGGCGAGGTGGC 61.867 60.000 0.00 0.00 43.88 5.01
756 837 3.670377 GGTCCGTGGTTTGGCTGC 61.670 66.667 0.00 0.00 0.00 5.25
894 1001 3.357079 CGAGGCGCTTTTGCTGGT 61.357 61.111 7.64 0.00 44.80 4.00
920 1027 4.760715 GGAGGACAAGGAAGAAAAGGTAAC 59.239 45.833 0.00 0.00 0.00 2.50
921 1028 4.202535 GGGAGGACAAGGAAGAAAAGGTAA 60.203 45.833 0.00 0.00 0.00 2.85
922 1029 3.329814 GGGAGGACAAGGAAGAAAAGGTA 59.670 47.826 0.00 0.00 0.00 3.08
923 1030 2.108425 GGGAGGACAAGGAAGAAAAGGT 59.892 50.000 0.00 0.00 0.00 3.50
924 1031 2.555448 GGGGAGGACAAGGAAGAAAAGG 60.555 54.545 0.00 0.00 0.00 3.11
925 1032 2.376855 AGGGGAGGACAAGGAAGAAAAG 59.623 50.000 0.00 0.00 0.00 2.27
926 1033 2.428901 AGGGGAGGACAAGGAAGAAAA 58.571 47.619 0.00 0.00 0.00 2.29
927 1034 2.133858 AGGGGAGGACAAGGAAGAAA 57.866 50.000 0.00 0.00 0.00 2.52
928 1035 2.547990 GTAGGGGAGGACAAGGAAGAA 58.452 52.381 0.00 0.00 0.00 2.52
929 1036 1.273666 GGTAGGGGAGGACAAGGAAGA 60.274 57.143 0.00 0.00 0.00 2.87
930 1037 1.205055 GGTAGGGGAGGACAAGGAAG 58.795 60.000 0.00 0.00 0.00 3.46
931 1038 0.797579 AGGTAGGGGAGGACAAGGAA 59.202 55.000 0.00 0.00 0.00 3.36
932 1039 0.338814 GAGGTAGGGGAGGACAAGGA 59.661 60.000 0.00 0.00 0.00 3.36
933 1040 1.043673 CGAGGTAGGGGAGGACAAGG 61.044 65.000 0.00 0.00 0.00 3.61
934 1041 1.043673 CCGAGGTAGGGGAGGACAAG 61.044 65.000 0.00 0.00 0.00 3.16
935 1042 1.001248 CCGAGGTAGGGGAGGACAA 59.999 63.158 0.00 0.00 0.00 3.18
936 1043 1.932231 TCCGAGGTAGGGGAGGACA 60.932 63.158 0.00 0.00 0.00 4.02
937 1044 1.152715 CTCCGAGGTAGGGGAGGAC 60.153 68.421 0.00 0.00 44.94 3.85
938 1045 3.343505 CTCCGAGGTAGGGGAGGA 58.656 66.667 0.00 0.00 44.94 3.71
958 1065 2.664081 CCTCCGGCTCCTGCTCTTT 61.664 63.158 0.00 0.00 39.59 2.52
1121 1228 1.990060 CCGTCCTGGAGGTGGATGT 60.990 63.158 14.71 0.00 42.00 3.06
1185 1292 3.590182 GGAGGGAGCTCTAGTAGTAGGAT 59.410 52.174 14.64 0.00 0.00 3.24
1186 1293 2.981081 GGAGGGAGCTCTAGTAGTAGGA 59.019 54.545 14.64 0.00 0.00 2.94
1244 1364 1.153289 CGGGAGACAGAGCCCAATG 60.153 63.158 0.00 0.00 44.94 2.82
1344 1468 7.983484 GGAATTAATTCAGCAGGAAATCAATGT 59.017 33.333 25.55 0.00 39.39 2.71
1345 1469 7.440255 GGGAATTAATTCAGCAGGAAATCAATG 59.560 37.037 25.55 0.00 39.39 2.82
1346 1470 7.503549 GGGAATTAATTCAGCAGGAAATCAAT 58.496 34.615 25.55 0.00 39.39 2.57
1347 1471 6.405731 CGGGAATTAATTCAGCAGGAAATCAA 60.406 38.462 25.55 0.00 39.39 2.57
1348 1472 5.067674 CGGGAATTAATTCAGCAGGAAATCA 59.932 40.000 25.55 0.00 39.39 2.57
1349 1473 5.067805 ACGGGAATTAATTCAGCAGGAAATC 59.932 40.000 25.55 7.61 39.39 2.17
1350 1474 4.956075 ACGGGAATTAATTCAGCAGGAAAT 59.044 37.500 25.55 3.30 39.39 2.17
1351 1475 4.340617 ACGGGAATTAATTCAGCAGGAAA 58.659 39.130 25.55 0.00 39.39 3.13
1352 1476 3.963129 ACGGGAATTAATTCAGCAGGAA 58.037 40.909 25.55 0.00 38.53 3.36
1353 1477 3.644966 ACGGGAATTAATTCAGCAGGA 57.355 42.857 25.55 0.00 38.53 3.86
1354 1478 4.082245 ACAAACGGGAATTAATTCAGCAGG 60.082 41.667 25.55 14.15 38.53 4.85
1355 1479 5.059404 ACAAACGGGAATTAATTCAGCAG 57.941 39.130 25.55 16.35 38.53 4.24
1356 1480 5.226396 CAACAAACGGGAATTAATTCAGCA 58.774 37.500 25.55 0.00 38.53 4.41
1357 1481 4.091365 GCAACAAACGGGAATTAATTCAGC 59.909 41.667 25.55 11.96 38.53 4.26
1358 1482 5.469479 AGCAACAAACGGGAATTAATTCAG 58.531 37.500 25.55 20.66 38.53 3.02
1359 1483 5.461032 AGCAACAAACGGGAATTAATTCA 57.539 34.783 25.55 0.00 38.53 2.57
1360 1484 5.060446 CGAAGCAACAAACGGGAATTAATTC 59.940 40.000 18.22 18.22 36.08 2.17
1361 1485 4.920927 CGAAGCAACAAACGGGAATTAATT 59.079 37.500 0.00 0.00 0.00 1.40
1362 1486 4.481463 CGAAGCAACAAACGGGAATTAAT 58.519 39.130 0.00 0.00 0.00 1.40
1363 1487 3.891324 CGAAGCAACAAACGGGAATTAA 58.109 40.909 0.00 0.00 0.00 1.40
1364 1488 3.546002 CGAAGCAACAAACGGGAATTA 57.454 42.857 0.00 0.00 0.00 1.40
1365 1489 2.415697 CGAAGCAACAAACGGGAATT 57.584 45.000 0.00 0.00 0.00 2.17
1389 1513 8.700722 ATCTCTGCTAAAATATCGACATCATC 57.299 34.615 0.00 0.00 0.00 2.92
1451 1637 0.536460 AAACGCAAACGGAGGGACAT 60.536 50.000 0.00 0.00 46.04 3.06
1453 1639 0.317519 CAAAACGCAAACGGAGGGAC 60.318 55.000 0.00 0.00 46.04 4.46
1514 1720 4.319911 GCAGTAATAAACAGGCACAAACGA 60.320 41.667 0.00 0.00 32.61 3.85
1534 1740 4.952262 TTGCTAAACTAATGAGCAGCAG 57.048 40.909 0.00 0.00 46.29 4.24
1535 1741 5.902613 ATTTGCTAAACTAATGAGCAGCA 57.097 34.783 0.00 0.00 46.29 4.41
1536 1742 6.202226 GGTATTTGCTAAACTAATGAGCAGC 58.798 40.000 0.00 0.00 46.29 5.25
1560 1766 0.826256 CCATGTGCCTCCATGATGGG 60.826 60.000 12.26 2.25 43.99 4.00
1727 1948 1.382522 AGAGTGCACAACAACACAGG 58.617 50.000 21.04 0.00 39.30 4.00
1728 1949 2.033747 CGTAGAGTGCACAACAACACAG 60.034 50.000 21.04 0.00 39.30 3.66
1730 1951 2.198406 TCGTAGAGTGCACAACAACAC 58.802 47.619 21.04 10.50 37.05 3.32
1741 1973 4.802563 TGTCAGAGTACGTATCGTAGAGTG 59.197 45.833 0.00 1.55 43.06 3.51
1754 1986 4.437239 CATGACCCAGAATGTCAGAGTAC 58.563 47.826 0.00 0.00 45.20 2.73
1756 1988 2.238144 CCATGACCCAGAATGTCAGAGT 59.762 50.000 0.00 0.00 45.20 3.24
1757 1989 2.915349 CCATGACCCAGAATGTCAGAG 58.085 52.381 0.00 0.00 45.20 3.35
1758 1990 1.065199 GCCATGACCCAGAATGTCAGA 60.065 52.381 0.00 0.00 45.20 3.27
1759 1991 1.386533 GCCATGACCCAGAATGTCAG 58.613 55.000 0.00 0.00 45.20 3.51
1760 1992 0.034186 GGCCATGACCCAGAATGTCA 60.034 55.000 0.00 0.00 45.98 3.58
1761 1993 1.097547 CGGCCATGACCCAGAATGTC 61.098 60.000 2.24 0.00 0.00 3.06
1762 1994 1.077501 CGGCCATGACCCAGAATGT 60.078 57.895 2.24 0.00 0.00 2.71
1763 1995 1.825191 CCGGCCATGACCCAGAATG 60.825 63.158 2.24 0.00 0.00 2.67
1764 1996 2.270874 GACCGGCCATGACCCAGAAT 62.271 60.000 0.00 0.00 0.00 2.40
1765 1997 2.933287 ACCGGCCATGACCCAGAA 60.933 61.111 0.00 0.00 0.00 3.02
1766 1998 3.399181 GACCGGCCATGACCCAGA 61.399 66.667 0.00 0.00 0.00 3.86
1767 1999 3.687321 CTGACCGGCCATGACCCAG 62.687 68.421 0.00 0.00 0.00 4.45
1778 2010 0.523072 CAACCAAATCTGCTGACCGG 59.477 55.000 0.00 0.00 0.00 5.28
1780 2012 0.244721 GGCAACCAAATCTGCTGACC 59.755 55.000 0.00 0.00 38.65 4.02
1808 2040 5.166398 CGGAACCACTACTACTACCTTTTG 58.834 45.833 0.00 0.00 0.00 2.44
1816 2048 1.274447 GGCAACGGAACCACTACTACT 59.726 52.381 0.00 0.00 0.00 2.57
1817 2049 1.274447 AGGCAACGGAACCACTACTAC 59.726 52.381 0.00 0.00 46.39 2.73
1818 2050 1.636148 AGGCAACGGAACCACTACTA 58.364 50.000 0.00 0.00 46.39 1.82
1819 2051 0.763035 AAGGCAACGGAACCACTACT 59.237 50.000 0.00 0.00 46.39 2.57
1854 2086 1.225745 GCATCGCCGTTTCAACTCG 60.226 57.895 0.00 0.00 0.00 4.18
1876 2108 6.765036 AGTGATTATGAGTGGTTCACATCATC 59.235 38.462 12.58 0.00 39.37 2.92
1918 2153 0.388520 GCTTTTGCCGTCATGGGTTC 60.389 55.000 0.00 0.00 40.15 3.62
1949 2184 5.734220 GCGCAATTTCTGAACCACATATCAT 60.734 40.000 0.30 0.00 0.00 2.45
1952 2187 3.443329 TGCGCAATTTCTGAACCACATAT 59.557 39.130 8.16 0.00 0.00 1.78
1962 2197 2.182537 GGCCCTGCGCAATTTCTG 59.817 61.111 13.05 0.00 40.31 3.02
1965 2200 3.070576 GGAGGCCCTGCGCAATTT 61.071 61.111 13.05 0.00 40.31 1.82
1990 2228 1.125021 GCGAATCACAAGACAGTCGTG 59.875 52.381 14.29 14.29 31.90 4.35
1991 2229 1.269569 TGCGAATCACAAGACAGTCGT 60.270 47.619 0.00 0.00 31.90 4.34
1995 2233 3.885484 ACTTTGCGAATCACAAGACAG 57.115 42.857 0.00 0.00 0.00 3.51
1999 2238 4.213270 TCCAACTACTTTGCGAATCACAAG 59.787 41.667 0.00 0.00 33.34 3.16
2053 2292 6.698008 TGCTTGAAATTTCAGAGTTTCAGA 57.302 33.333 19.64 2.52 43.03 3.27
2054 2293 7.941795 ATTGCTTGAAATTTCAGAGTTTCAG 57.058 32.000 19.64 13.65 43.03 3.02
2097 2371 7.707035 ACTTAGTATGAGTGATCGACAAAATCC 59.293 37.037 0.00 0.00 0.00 3.01
2153 2427 8.934023 TGAATACATTTGGAGGAGTTTTACTT 57.066 30.769 0.00 0.00 0.00 2.24
2154 2428 8.934023 TTGAATACATTTGGAGGAGTTTTACT 57.066 30.769 0.00 0.00 0.00 2.24
2155 2429 9.974980 TTTTGAATACATTTGGAGGAGTTTTAC 57.025 29.630 0.00 0.00 0.00 2.01
2158 2432 8.096414 CCATTTTGAATACATTTGGAGGAGTTT 58.904 33.333 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.