Multiple sequence alignment - TraesCS4D01G020000

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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 TraesCS4D01G020000 chr4D 100.000 2204 0 0 1 2204 8651797 8654000 0.000000e+00 4071.0
1 TraesCS4D01G020000 chr4A 86.056 961 88 14 305 1237 594701576 594700634 0.000000e+00 990.0
2 TraesCS4D01G020000 chr4A 95.596 545 19 2 1664 2204 594686520 594685977 0.000000e+00 869.0
3 TraesCS4D01G020000 chr4A 88.172 372 41 2 155 523 563249535 563249906 7.220000e-120 440.0
4 TraesCS4D01G020000 chr4A 87.903 372 42 2 155 523 563289382 563289753 3.360000e-118 435.0
5 TraesCS4D01G020000 chr4A 80.519 385 48 19 1051 1419 594687395 594687022 1.000000e-68 270.0
6 TraesCS4D01G020000 chr4A 88.043 92 4 3 941 1028 594687473 594687385 3.870000e-18 102.0
7 TraesCS4D01G020000 chr4B 91.570 605 36 3 1601 2204 16056550 16057140 0.000000e+00 821.0
8 TraesCS4D01G020000 chr4B 89.877 652 39 7 1564 2204 17044439 17043804 0.000000e+00 813.0
9 TraesCS4D01G020000 chr4B 86.283 452 35 13 787 1220 17045053 17044611 1.190000e-127 466.0
10 TraesCS4D01G020000 chr4B 79.597 397 26 28 760 1141 16056094 16056450 1.320000e-57 233.0
11 TraesCS4D01G020000 chr7D 83.840 526 68 9 1 517 136870659 136871176 3.290000e-133 484.0
12 TraesCS4D01G020000 chr7D 78.172 536 68 27 1 524 571235241 571234743 1.650000e-76 296.0
13 TraesCS4D01G020000 chr2D 81.952 543 75 17 1 523 399351721 399352260 2.600000e-119 438.0
14 TraesCS4D01G020000 chr2D 79.381 194 17 6 25 195 71642964 71642771 4.970000e-22 115.0
15 TraesCS4D01G020000 chr2D 95.455 44 2 0 1497 1540 621124734 621124777 1.090000e-08 71.3
16 TraesCS4D01G020000 chr2A 82.157 510 77 6 1 499 603733877 603733371 2.020000e-115 425.0
17 TraesCS4D01G020000 chr3D 80.403 546 83 15 2 534 309774586 309774052 5.700000e-106 394.0
18 TraesCS4D01G020000 chr3D 80.073 547 83 12 1 524 352643176 352642633 1.230000e-102 383.0
19 TraesCS4D01G020000 chr3D 85.714 56 7 1 1480 1534 64676071 64676126 8.500000e-05 58.4
20 TraesCS4D01G020000 chr1B 80.150 534 94 5 1 523 334439994 334440526 2.650000e-104 388.0
21 TraesCS4D01G020000 chr1B 80.896 424 72 5 108 523 106906444 106906022 2.110000e-85 326.0
22 TraesCS4D01G020000 chr2B 79.643 560 73 10 1 522 107958217 107957661 4.470000e-97 364.0
23 TraesCS4D01G020000 chr7A 78.300 447 60 21 85 517 207888660 207889083 1.010000e-63 254.0
24 TraesCS4D01G020000 chr5D 78.297 364 53 14 5 345 40186057 40185697 6.170000e-51 211.0
25 TraesCS4D01G020000 chr1D 74.589 547 87 30 3 521 252906542 252907064 2.230000e-45 193.0
26 TraesCS4D01G020000 chr1D 96.970 33 1 0 576 608 481664228 481664260 3.060000e-04 56.5
27 TraesCS4D01G020000 chrUn 83.898 118 19 0 1 118 477191750 477191867 1.790000e-21 113.0
28 TraesCS4D01G020000 chrUn 93.182 44 3 0 1497 1540 110700240 110700197 5.080000e-07 65.8
29 TraesCS4D01G020000 chrUn 93.182 44 3 0 1497 1540 143995229 143995272 5.080000e-07 65.8
30 TraesCS4D01G020000 chr5A 95.455 44 2 0 1497 1540 16043459 16043416 1.090000e-08 71.3
31 TraesCS4D01G020000 chr5A 90.385 52 4 1 1490 1541 11079253 11079203 1.410000e-07 67.6
32 TraesCS4D01G020000 chr5A 97.143 35 1 0 575 609 513717594 513717560 2.360000e-05 60.2
33 TraesCS4D01G020000 chr5B 88.136 59 4 2 1484 1539 488254632 488254690 1.410000e-07 67.6
34 TraesCS4D01G020000 chr3B 93.333 45 3 0 1497 1541 736305121 736305077 1.410000e-07 67.6
35 TraesCS4D01G020000 chr3B 97.059 34 0 1 577 609 347924167 347924134 3.060000e-04 56.5
36 TraesCS4D01G020000 chr3A 93.333 45 3 0 1497 1541 368744896 368744940 1.410000e-07 67.6


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 TraesCS4D01G020000 chr4D 8651797 8654000 2203 False 4071.000000 4071 100.000000 1 2204 1 chr4D.!!$F1 2203
1 TraesCS4D01G020000 chr4A 594700634 594701576 942 True 990.000000 990 86.056000 305 1237 1 chr4A.!!$R1 932
2 TraesCS4D01G020000 chr4A 594685977 594687473 1496 True 413.666667 869 88.052667 941 2204 3 chr4A.!!$R2 1263
3 TraesCS4D01G020000 chr4B 17043804 17045053 1249 True 639.500000 813 88.080000 787 2204 2 chr4B.!!$R1 1417
4 TraesCS4D01G020000 chr4B 16056094 16057140 1046 False 527.000000 821 85.583500 760 2204 2 chr4B.!!$F1 1444
5 TraesCS4D01G020000 chr7D 136870659 136871176 517 False 484.000000 484 83.840000 1 517 1 chr7D.!!$F1 516
6 TraesCS4D01G020000 chr2D 399351721 399352260 539 False 438.000000 438 81.952000 1 523 1 chr2D.!!$F1 522
7 TraesCS4D01G020000 chr2A 603733371 603733877 506 True 425.000000 425 82.157000 1 499 1 chr2A.!!$R1 498
8 TraesCS4D01G020000 chr3D 309774052 309774586 534 True 394.000000 394 80.403000 2 534 1 chr3D.!!$R1 532
9 TraesCS4D01G020000 chr3D 352642633 352643176 543 True 383.000000 383 80.073000 1 524 1 chr3D.!!$R2 523
10 TraesCS4D01G020000 chr1B 334439994 334440526 532 False 388.000000 388 80.150000 1 523 1 chr1B.!!$F1 522
11 TraesCS4D01G020000 chr2B 107957661 107958217 556 True 364.000000 364 79.643000 1 522 1 chr2B.!!$R1 521

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
547 625 0.163788 GATGTGGACGACGCAACTTG 59.836 55.0 0.0 0.0 43.88 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 2214 0.109132 GACCCTTGAATTGCTTGCCG 60.109 55.0 0.0 0.0 0.0 5.69 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
36 37 0.592637 TCGCTTACAACGACGGAGAA 59.407 50.000 0.00 0.00 33.96 2.87
47 48 3.441290 CGGAGAAGGACGCTCGGT 61.441 66.667 0.00 0.00 33.19 4.69
92 93 1.760192 GCTCCAGATTGCCATTGAGT 58.240 50.000 0.00 0.00 0.00 3.41
188 227 1.535028 CTCATCATCCTCTCCGACTCG 59.465 57.143 0.00 0.00 0.00 4.18
197 236 1.222387 CTCCGACTCGTCCTCCTCT 59.778 63.158 0.00 0.00 0.00 3.69
245 302 0.613777 ACTCGGACAATTCTCCACCC 59.386 55.000 0.39 0.00 0.00 4.61
312 370 1.340248 TGACGAGGAAGTGGTGAAGAC 59.660 52.381 0.00 0.00 0.00 3.01
376 437 7.510428 TTAAACTTGTCCGTCGTATTATGTC 57.490 36.000 0.00 0.00 0.00 3.06
378 439 2.761392 TGTCCGTCGTATTATGTCCG 57.239 50.000 0.00 0.00 0.00 4.79
439 500 5.180492 GTGATCTTTTGGTGAACGGATTGTA 59.820 40.000 0.00 0.00 0.00 2.41
453 514 7.173390 TGAACGGATTGTACATTTGTATGTTCA 59.827 33.333 15.39 15.39 42.29 3.18
499 565 4.070224 CGTAGTTTTTATCGACGTTGCAC 58.930 43.478 0.00 0.00 31.49 4.57
544 622 1.626654 CTGGATGTGGACGACGCAAC 61.627 60.000 0.00 0.00 43.88 4.17
547 625 0.163788 GATGTGGACGACGCAACTTG 59.836 55.000 0.00 0.00 43.88 3.16
549 627 0.874175 TGTGGACGACGCAACTTGAG 60.874 55.000 0.00 0.00 36.47 3.02
554 632 1.190323 GACGACGCAACTTGAGAACTG 59.810 52.381 0.00 0.00 0.00 3.16
556 634 2.061773 CGACGCAACTTGAGAACTGAT 58.938 47.619 0.00 0.00 0.00 2.90
557 635 2.091277 CGACGCAACTTGAGAACTGATC 59.909 50.000 0.00 0.00 0.00 2.92
561 639 2.413453 GCAACTTGAGAACTGATCGGTC 59.587 50.000 7.86 0.81 0.00 4.79
563 641 4.058124 CAACTTGAGAACTGATCGGTCAA 58.942 43.478 7.86 7.33 33.05 3.18
566 644 2.621338 TGAGAACTGATCGGTCAATGC 58.379 47.619 7.86 0.00 33.05 3.56
568 646 1.556911 AGAACTGATCGGTCAATGCCT 59.443 47.619 7.86 0.00 33.05 4.75
569 647 2.766263 AGAACTGATCGGTCAATGCCTA 59.234 45.455 7.86 0.00 33.05 3.93
614 702 4.459331 CCGGATTTGCCACGCGTG 62.459 66.667 31.77 31.77 35.94 5.34
643 731 3.533606 TGCTCTGATGGCTTTAGACTC 57.466 47.619 0.00 0.00 0.00 3.36
644 732 2.159184 TGCTCTGATGGCTTTAGACTCG 60.159 50.000 0.00 0.00 0.00 4.18
665 753 0.529119 GTCGTCACGTGTCCCTTGTT 60.529 55.000 16.51 0.00 0.00 2.83
693 781 7.436970 TCGCTGAACACATACGATAATTACAAT 59.563 33.333 0.00 0.00 0.00 2.71
734 822 1.676967 GCATAGCATAGGCCAGCCC 60.677 63.158 5.01 0.00 43.66 5.19
735 823 1.763120 CATAGCATAGGCCAGCCCA 59.237 57.895 5.01 0.00 42.56 5.36
742 830 0.630673 ATAGGCCAGCCCATGTTTCA 59.369 50.000 5.01 0.00 36.58 2.69
777 865 1.512926 TCTTCTGCTTCTTCGCCAAC 58.487 50.000 0.00 0.00 0.00 3.77
895 1003 1.740285 CCCGTCCATAAGTAGCGCT 59.260 57.895 17.26 17.26 0.00 5.92
972 1110 4.463879 CCACCGGAGAGCCAGCAG 62.464 72.222 9.46 0.00 0.00 4.24
987 1125 3.099438 CAGCAGCAGAGCAATCGG 58.901 61.111 0.00 0.00 36.85 4.18
1208 1353 2.475466 GCGCCATCCTGTGATGTGG 61.475 63.158 0.00 0.00 45.78 4.17
1209 1354 1.078214 CGCCATCCTGTGATGTGGT 60.078 57.895 2.24 0.00 45.78 4.16
1220 1365 3.932580 GATGTGGTGTGAGGCGCGA 62.933 63.158 12.10 0.00 0.00 5.87
1221 1366 3.315142 ATGTGGTGTGAGGCGCGAT 62.315 57.895 12.10 0.00 0.00 4.58
1222 1367 2.742372 GTGGTGTGAGGCGCGATT 60.742 61.111 12.10 0.00 0.00 3.34
1223 1368 2.434185 TGGTGTGAGGCGCGATTC 60.434 61.111 12.10 6.84 0.00 2.52
1224 1369 3.554692 GGTGTGAGGCGCGATTCG 61.555 66.667 12.10 0.62 42.12 3.34
1250 1395 3.554692 CGTGGTCGGCGAATCAGC 61.555 66.667 12.92 0.00 0.00 4.26
1251 1396 2.434185 GTGGTCGGCGAATCAGCA 60.434 61.111 12.92 1.84 39.27 4.41
1252 1397 1.815421 GTGGTCGGCGAATCAGCAT 60.815 57.895 12.92 0.00 39.27 3.79
1253 1398 1.521457 TGGTCGGCGAATCAGCATC 60.521 57.895 12.92 0.00 39.27 3.91
1254 1399 2.589492 GGTCGGCGAATCAGCATCG 61.589 63.158 12.92 0.00 42.99 3.84
1255 1400 1.588932 GTCGGCGAATCAGCATCGA 60.589 57.895 12.92 0.00 42.76 3.59
1256 1401 0.941463 GTCGGCGAATCAGCATCGAT 60.941 55.000 12.92 0.00 42.76 3.59
1257 1402 0.664466 TCGGCGAATCAGCATCGATC 60.664 55.000 7.35 0.00 42.76 3.69
1262 1407 0.320247 GAATCAGCATCGATCGGCCT 60.320 55.000 16.41 6.28 0.00 5.19
1266 1411 3.654020 GCATCGATCGGCCTTGCC 61.654 66.667 16.41 0.00 46.75 4.52
1293 1451 2.520979 GATCGTTGACTTCCTCGTCTG 58.479 52.381 0.00 0.00 35.00 3.51
1296 1515 1.199327 CGTTGACTTCCTCGTCTGCTA 59.801 52.381 0.00 0.00 35.00 3.49
1297 1516 2.729467 CGTTGACTTCCTCGTCTGCTAG 60.729 54.545 0.00 0.00 35.00 3.42
1298 1517 2.201921 TGACTTCCTCGTCTGCTAGT 57.798 50.000 0.00 0.00 35.00 2.57
1299 1518 3.345508 TGACTTCCTCGTCTGCTAGTA 57.654 47.619 0.00 0.00 35.00 1.82
1300 1519 3.008330 TGACTTCCTCGTCTGCTAGTAC 58.992 50.000 0.00 0.00 35.00 2.73
1301 1520 3.272581 GACTTCCTCGTCTGCTAGTACT 58.727 50.000 0.00 0.00 0.00 2.73
1302 1521 4.081254 TGACTTCCTCGTCTGCTAGTACTA 60.081 45.833 1.89 1.89 35.00 1.82
1303 1522 4.444536 ACTTCCTCGTCTGCTAGTACTAG 58.555 47.826 23.25 23.25 36.29 2.57
1304 1523 4.080975 ACTTCCTCGTCTGCTAGTACTAGT 60.081 45.833 26.76 0.00 35.65 2.57
1305 1524 5.128499 ACTTCCTCGTCTGCTAGTACTAGTA 59.872 44.000 26.76 22.60 35.65 1.82
1306 1525 5.804944 TCCTCGTCTGCTAGTACTAGTAT 57.195 43.478 26.76 0.00 35.65 2.12
1307 1526 5.782047 TCCTCGTCTGCTAGTACTAGTATC 58.218 45.833 26.76 17.86 35.65 2.24
1308 1527 5.539574 TCCTCGTCTGCTAGTACTAGTATCT 59.460 44.000 26.76 7.87 35.65 1.98
1309 1528 5.865552 CCTCGTCTGCTAGTACTAGTATCTC 59.134 48.000 26.76 15.63 35.65 2.75
1310 1529 6.294899 CCTCGTCTGCTAGTACTAGTATCTCT 60.295 46.154 26.76 1.36 35.65 3.10
1311 1530 7.053316 TCGTCTGCTAGTACTAGTATCTCTT 57.947 40.000 26.76 0.00 35.65 2.85
1312 1531 7.499292 TCGTCTGCTAGTACTAGTATCTCTTT 58.501 38.462 26.76 0.00 35.65 2.52
1313 1532 7.438757 TCGTCTGCTAGTACTAGTATCTCTTTG 59.561 40.741 26.76 11.89 35.65 2.77
1314 1533 7.225145 CGTCTGCTAGTACTAGTATCTCTTTGT 59.775 40.741 26.76 0.00 35.65 2.83
1315 1534 9.545105 GTCTGCTAGTACTAGTATCTCTTTGTA 57.455 37.037 26.76 1.29 35.65 2.41
1316 1535 9.545105 TCTGCTAGTACTAGTATCTCTTTGTAC 57.455 37.037 26.76 9.37 36.31 2.90
1317 1536 9.550406 CTGCTAGTACTAGTATCTCTTTGTACT 57.450 37.037 26.76 0.00 42.18 2.73
1318 1537 9.545105 TGCTAGTACTAGTATCTCTTTGTACTC 57.455 37.037 26.76 8.45 41.10 2.59
1319 1538 8.992073 GCTAGTACTAGTATCTCTTTGTACTCC 58.008 40.741 26.76 4.54 41.10 3.85
1321 1540 8.967664 AGTACTAGTATCTCTTTGTACTCCAG 57.032 38.462 5.75 0.00 39.01 3.86
1322 1541 8.550585 AGTACTAGTATCTCTTTGTACTCCAGT 58.449 37.037 5.75 0.00 39.01 4.00
1323 1542 9.176460 GTACTAGTATCTCTTTGTACTCCAGTT 57.824 37.037 5.75 0.00 34.86 3.16
1324 1543 8.653036 ACTAGTATCTCTTTGTACTCCAGTTT 57.347 34.615 0.00 0.00 33.48 2.66
1325 1544 8.524487 ACTAGTATCTCTTTGTACTCCAGTTTG 58.476 37.037 0.00 0.00 33.48 2.93
1326 1545 7.304497 AGTATCTCTTTGTACTCCAGTTTGT 57.696 36.000 0.00 0.00 0.00 2.83
1327 1546 8.418597 AGTATCTCTTTGTACTCCAGTTTGTA 57.581 34.615 0.00 0.00 0.00 2.41
1328 1547 9.036980 AGTATCTCTTTGTACTCCAGTTTGTAT 57.963 33.333 0.00 0.00 0.00 2.29
1329 1548 9.088512 GTATCTCTTTGTACTCCAGTTTGTATG 57.911 37.037 0.00 0.00 0.00 2.39
1330 1549 6.464222 TCTCTTTGTACTCCAGTTTGTATGG 58.536 40.000 0.00 0.00 39.33 2.74
1370 1589 5.220228 GGATTGGAACTAATAATCGATCGCG 60.220 44.000 11.09 0.00 39.35 5.87
1401 1620 0.179215 GCTCTTCGTTTGGCATCGTG 60.179 55.000 11.18 7.06 0.00 4.35
1428 1689 3.114616 CTCTGTGGAACTGCGCCG 61.115 66.667 4.18 0.00 38.04 6.46
1448 1709 1.126488 TTGCCAATTCCCAACAGCAA 58.874 45.000 0.00 0.00 37.85 3.91
1451 1712 1.873486 GCCAATTCCCAACAGCAACAC 60.873 52.381 0.00 0.00 0.00 3.32
1452 1713 1.270252 CCAATTCCCAACAGCAACACC 60.270 52.381 0.00 0.00 0.00 4.16
1472 1738 0.457851 ACCTTCCTCTGCTCGATTCG 59.542 55.000 0.00 0.00 0.00 3.34
1480 1746 0.721718 CTGCTCGATTCGGTTTCACC 59.278 55.000 6.18 0.00 34.05 4.02
1495 1761 6.711194 TCGGTTTCACCACTCAAAATTATACA 59.289 34.615 0.00 0.00 38.47 2.29
1512 1779 6.989155 TTATACACCTCCGTCCAGAATTAT 57.011 37.500 0.00 0.00 0.00 1.28
1536 1803 8.846943 ATTTGTCGCAGAAATGGATGTATATA 57.153 30.769 0.00 0.00 39.69 0.86
1557 1826 2.299297 AGACAAGTAAGTTGGGACGGAG 59.701 50.000 0.00 0.00 40.90 4.63
1558 1827 2.036862 GACAAGTAAGTTGGGACGGAGT 59.963 50.000 0.00 0.00 42.69 3.85
1559 1828 3.233507 ACAAGTAAGTTGGGACGGAGTA 58.766 45.455 0.00 0.00 40.59 2.59
1669 2167 1.947456 GGACCGCTTTCTTTCACAACT 59.053 47.619 0.00 0.00 0.00 3.16
1670 2168 2.357952 GGACCGCTTTCTTTCACAACTT 59.642 45.455 0.00 0.00 0.00 2.66
1674 2172 4.201920 ACCGCTTTCTTTCACAACTTCTTC 60.202 41.667 0.00 0.00 0.00 2.87
1696 2205 4.693566 TCTTTAACCGAGGTTACAATGCAG 59.306 41.667 13.75 4.80 39.90 4.41
1697 2206 1.165270 AACCGAGGTTACAATGCAGC 58.835 50.000 5.60 0.00 36.46 5.25
1698 2207 0.036164 ACCGAGGTTACAATGCAGCA 59.964 50.000 0.00 0.00 0.00 4.41
1699 2208 1.164411 CCGAGGTTACAATGCAGCAA 58.836 50.000 0.00 0.00 0.00 3.91
1700 2209 1.539388 CCGAGGTTACAATGCAGCAAA 59.461 47.619 0.00 0.00 0.00 3.68
1701 2210 2.414559 CCGAGGTTACAATGCAGCAAAG 60.415 50.000 0.00 0.00 0.00 2.77
1702 2211 2.599659 GAGGTTACAATGCAGCAAAGC 58.400 47.619 0.00 0.00 0.00 3.51
1703 2212 1.273327 AGGTTACAATGCAGCAAAGCC 59.727 47.619 0.00 0.00 0.00 4.35
1704 2213 1.339711 GTTACAATGCAGCAAAGCCG 58.660 50.000 0.00 0.00 0.00 5.52
1705 2214 0.388391 TTACAATGCAGCAAAGCCGC 60.388 50.000 0.00 0.00 0.00 6.53
1706 2215 2.526091 TACAATGCAGCAAAGCCGCG 62.526 55.000 0.00 0.00 36.85 6.46
1729 2238 1.212751 GCAATTCAAGGGTCCGTGC 59.787 57.895 0.00 0.00 0.00 5.34
1730 2239 1.523154 GCAATTCAAGGGTCCGTGCA 61.523 55.000 0.00 0.00 0.00 4.57
1731 2240 1.176527 CAATTCAAGGGTCCGTGCAT 58.823 50.000 0.00 0.00 0.00 3.96
1792 2309 5.235186 CGATTTAAACACAAAATTGCACCCA 59.765 36.000 0.00 0.00 0.00 4.51
1935 2456 4.201802 TGTTCTATGTGCACATTGTATGCG 60.202 41.667 35.45 15.63 46.49 4.73
2069 2590 0.387929 TGTCGGGTGAGACAAGTCAC 59.612 55.000 2.72 0.00 46.81 3.67
2098 2619 0.591659 GTCCGACACTTTCTTTGCCC 59.408 55.000 0.00 0.00 0.00 5.36
2107 2628 2.084546 CTTTCTTTGCCCCTAGGTTCG 58.915 52.381 8.29 0.00 34.57 3.95
2179 2700 1.895798 TCCAGAGATATGTCATCGGCC 59.104 52.381 2.30 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 2.903547 GCGCCTTGGCGTTCTTTCA 61.904 57.895 30.53 0.00 35.43 2.69
92 93 3.506096 CGCCTCGCACTCGGACTA 61.506 66.667 0.00 0.00 36.13 2.59
128 153 2.740055 CTGCCGCTTGAGCTTCGT 60.740 61.111 1.07 0.00 39.32 3.85
188 227 0.741915 GGTCATCGTCAGAGGAGGAC 59.258 60.000 23.53 23.53 41.37 3.85
197 236 2.048597 GTGCCGTGGTCATCGTCA 60.049 61.111 0.00 0.00 0.00 4.35
234 291 2.267961 GACGGCGGGTGGAGAATT 59.732 61.111 13.24 0.00 0.00 2.17
282 339 1.125093 TTCCTCGTCAGCCCTTTCCA 61.125 55.000 0.00 0.00 0.00 3.53
312 370 2.194201 TTTAAAGTGGAGAAGGCGGG 57.806 50.000 0.00 0.00 0.00 6.13
345 406 4.504097 ACGACGGACAAGTTTAAACTACAC 59.496 41.667 20.83 13.76 38.57 2.90
376 437 1.801771 TCGCCAAAGTTCACATAACGG 59.198 47.619 0.00 0.00 0.00 4.44
378 439 4.946784 AGATCGCCAAAGTTCACATAAC 57.053 40.909 0.00 0.00 0.00 1.89
453 514 7.089538 CGTAGATCATGAGCTGACATAGAAAT 58.910 38.462 23.45 0.00 36.48 2.17
524 590 2.509336 GCGTCGTCCACATCCAGG 60.509 66.667 0.00 0.00 0.00 4.45
525 591 1.374125 TTGCGTCGTCCACATCCAG 60.374 57.895 0.00 0.00 0.00 3.86
531 609 0.596600 TCTCAAGTTGCGTCGTCCAC 60.597 55.000 0.00 0.00 0.00 4.02
544 622 3.063180 GCATTGACCGATCAGTTCTCAAG 59.937 47.826 0.00 0.00 35.83 3.02
547 625 1.936547 GGCATTGACCGATCAGTTCTC 59.063 52.381 0.00 0.00 35.83 2.87
549 627 2.029838 AGGCATTGACCGATCAGTTC 57.970 50.000 0.00 0.00 35.83 3.01
554 632 2.900528 CCGTAGGCATTGACCGATC 58.099 57.895 0.00 0.00 46.14 3.69
575 663 1.200839 CTCAAACGTCCGTGAACGC 59.799 57.895 0.00 0.00 46.40 4.84
579 667 2.738480 CCCCTCAAACGTCCGTGA 59.262 61.111 0.00 0.00 0.00 4.35
581 669 4.324991 GGCCCCTCAAACGTCCGT 62.325 66.667 0.00 0.00 0.00 4.69
585 673 2.420466 AAATCCGGCCCCTCAAACGT 62.420 55.000 0.00 0.00 0.00 3.99
586 674 1.677633 AAATCCGGCCCCTCAAACG 60.678 57.895 0.00 0.00 0.00 3.60
611 699 2.104859 CAGAGCATCCACAGCCACG 61.105 63.158 0.00 0.00 33.66 4.94
612 700 0.107312 ATCAGAGCATCCACAGCCAC 60.107 55.000 0.00 0.00 33.66 5.01
614 702 0.818445 CCATCAGAGCATCCACAGCC 60.818 60.000 0.00 0.00 33.66 4.85
654 742 0.531974 TCAGCGACAACAAGGGACAC 60.532 55.000 0.00 0.00 0.00 3.67
665 753 2.647529 ATCGTATGTGTTCAGCGACA 57.352 45.000 0.00 0.00 37.58 4.35
693 781 3.241067 AGGCGTTCGTTTAGATGCTTA 57.759 42.857 0.00 0.00 32.97 3.09
742 830 4.320494 GCAGAAGAATTGAAATGGTCGTGT 60.320 41.667 0.00 0.00 0.00 4.49
822 930 0.179015 TGGCCTGCTGTTCGGTTTAA 60.179 50.000 3.32 0.00 0.00 1.52
972 1110 3.885521 GGCCGATTGCTCTGCTGC 61.886 66.667 0.00 0.00 40.92 5.25
1233 1378 3.554692 GCTGATTCGCCGACCACG 61.555 66.667 0.00 0.00 39.43 4.94
1234 1379 1.766143 GATGCTGATTCGCCGACCAC 61.766 60.000 0.00 0.00 0.00 4.16
1235 1380 1.521457 GATGCTGATTCGCCGACCA 60.521 57.895 0.00 0.00 0.00 4.02
1236 1381 2.589492 CGATGCTGATTCGCCGACC 61.589 63.158 0.00 0.00 0.00 4.79
1237 1382 0.941463 ATCGATGCTGATTCGCCGAC 60.941 55.000 0.00 0.00 36.56 4.79
1238 1383 0.664466 GATCGATGCTGATTCGCCGA 60.664 55.000 0.54 0.00 36.56 5.54
1239 1384 1.777819 GATCGATGCTGATTCGCCG 59.222 57.895 0.54 0.00 36.56 6.46
1240 1385 1.621301 CCGATCGATGCTGATTCGCC 61.621 60.000 18.66 0.00 36.56 5.54
1241 1386 1.777819 CCGATCGATGCTGATTCGC 59.222 57.895 18.66 0.00 36.56 4.70
1242 1387 1.621301 GGCCGATCGATGCTGATTCG 61.621 60.000 18.66 0.00 37.94 3.34
1243 1388 0.320247 AGGCCGATCGATGCTGATTC 60.320 55.000 18.66 0.00 0.00 2.52
1244 1389 0.107456 AAGGCCGATCGATGCTGATT 59.893 50.000 18.66 6.46 0.00 2.57
1245 1390 0.602106 CAAGGCCGATCGATGCTGAT 60.602 55.000 18.66 0.38 0.00 2.90
1246 1391 1.227350 CAAGGCCGATCGATGCTGA 60.227 57.895 18.66 0.00 0.00 4.26
1247 1392 2.890109 GCAAGGCCGATCGATGCTG 61.890 63.158 18.66 8.77 34.29 4.41
1248 1393 2.590007 GCAAGGCCGATCGATGCT 60.590 61.111 18.66 0.00 34.29 3.79
1249 1394 3.654020 GGCAAGGCCGATCGATGC 61.654 66.667 18.66 19.36 39.62 3.91
1266 1411 3.659089 AAGTCAACGATCGGCCGGG 62.659 63.158 27.83 17.46 0.00 5.73
1293 1451 8.992073 GGAGTACAAAGAGATACTAGTACTAGC 58.008 40.741 26.54 12.76 43.71 3.42
1296 1515 8.550585 ACTGGAGTACAAAGAGATACTAGTACT 58.449 37.037 4.31 0.00 44.97 2.73
1297 1516 8.735692 ACTGGAGTACAAAGAGATACTAGTAC 57.264 38.462 4.31 0.00 38.92 2.73
1298 1517 9.750783 AAACTGGAGTACAAAGAGATACTAGTA 57.249 33.333 4.77 4.77 31.69 1.82
1299 1518 8.524487 CAAACTGGAGTACAAAGAGATACTAGT 58.476 37.037 0.00 0.00 31.69 2.57
1300 1519 8.524487 ACAAACTGGAGTACAAAGAGATACTAG 58.476 37.037 0.00 0.00 31.69 2.57
1301 1520 8.418597 ACAAACTGGAGTACAAAGAGATACTA 57.581 34.615 0.00 0.00 31.69 1.82
1302 1521 7.304497 ACAAACTGGAGTACAAAGAGATACT 57.696 36.000 0.00 0.00 34.28 2.12
1303 1522 9.088512 CATACAAACTGGAGTACAAAGAGATAC 57.911 37.037 0.00 0.00 0.00 2.24
1304 1523 8.258007 CCATACAAACTGGAGTACAAAGAGATA 58.742 37.037 0.00 0.00 35.70 1.98
1305 1524 7.106239 CCATACAAACTGGAGTACAAAGAGAT 58.894 38.462 0.00 0.00 35.70 2.75
1306 1525 6.042781 ACCATACAAACTGGAGTACAAAGAGA 59.957 38.462 0.00 0.00 37.22 3.10
1307 1526 6.147821 CACCATACAAACTGGAGTACAAAGAG 59.852 42.308 0.00 0.00 37.22 2.85
1308 1527 5.995282 CACCATACAAACTGGAGTACAAAGA 59.005 40.000 0.00 0.00 37.22 2.52
1309 1528 5.763204 ACACCATACAAACTGGAGTACAAAG 59.237 40.000 0.00 0.00 36.07 2.77
1310 1529 5.686753 ACACCATACAAACTGGAGTACAAA 58.313 37.500 0.00 0.00 36.07 2.83
1311 1530 5.298989 ACACCATACAAACTGGAGTACAA 57.701 39.130 0.00 0.00 36.07 2.41
1312 1531 4.967084 ACACCATACAAACTGGAGTACA 57.033 40.909 0.00 0.00 36.07 2.90
1313 1532 9.609346 ATTATTACACCATACAAACTGGAGTAC 57.391 33.333 0.00 0.00 38.85 2.73
1328 1547 9.928618 TTCCAATCCAGAATTATTATTACACCA 57.071 29.630 0.00 0.00 0.00 4.17
1370 1589 2.329379 ACGAAGAGCAACGAATGAGTC 58.671 47.619 0.00 0.00 0.00 3.36
1372 1591 3.473367 CAAACGAAGAGCAACGAATGAG 58.527 45.455 0.00 0.00 0.00 2.90
1379 1598 1.725931 CGATGCCAAACGAAGAGCAAC 60.726 52.381 0.00 0.00 38.99 4.17
1383 1602 1.148310 ACACGATGCCAAACGAAGAG 58.852 50.000 0.00 0.00 0.00 2.85
1428 1689 0.392336 TGCTGTTGGGAATTGGCAAC 59.608 50.000 0.00 0.00 0.00 4.17
1448 1709 1.821061 CGAGCAGAGGAAGGTGGTGT 61.821 60.000 0.00 0.00 0.00 4.16
1451 1712 0.539051 AATCGAGCAGAGGAAGGTGG 59.461 55.000 0.00 0.00 0.00 4.61
1452 1713 1.800655 CGAATCGAGCAGAGGAAGGTG 60.801 57.143 0.00 0.00 0.00 4.00
1480 1746 5.293569 GGACGGAGGTGTATAATTTTGAGTG 59.706 44.000 0.00 0.00 0.00 3.51
1495 1761 4.514401 GACAAATAATTCTGGACGGAGGT 58.486 43.478 0.00 0.00 0.00 3.85
1512 1779 8.147704 TCTATATACATCCATTTCTGCGACAAA 58.852 33.333 0.00 0.00 0.00 2.83
1536 1803 2.299297 CTCCGTCCCAACTTACTTGTCT 59.701 50.000 0.00 0.00 0.00 3.41
1567 1836 7.365741 GCTGAACTATGTATGCATGCTTTTAT 58.634 34.615 20.33 12.27 36.58 1.40
1578 1847 2.811873 GCCCTGGGCTGAACTATGTATG 60.812 54.545 30.42 0.00 46.69 2.39
1579 1848 1.421646 GCCCTGGGCTGAACTATGTAT 59.578 52.381 30.42 0.00 46.69 2.29
1602 1871 0.719465 GTTCGACTGTTATGTGCCCG 59.281 55.000 0.00 0.00 0.00 6.13
1652 1926 3.971032 AGAAGTTGTGAAAGAAAGCGG 57.029 42.857 0.00 0.00 0.00 5.52
1653 1927 5.162000 AGAAGAAGTTGTGAAAGAAAGCG 57.838 39.130 0.00 0.00 0.00 4.68
1669 2167 6.072893 GCATTGTAACCTCGGTTAAAGAAGAA 60.073 38.462 9.96 0.00 41.51 2.52
1670 2168 5.410439 GCATTGTAACCTCGGTTAAAGAAGA 59.590 40.000 9.96 0.00 41.51 2.87
1674 2172 4.671766 GCTGCATTGTAACCTCGGTTAAAG 60.672 45.833 9.96 2.87 41.51 1.85
1697 2206 3.919973 ATTGCTTGCCGCGGCTTTG 62.920 57.895 45.79 34.35 43.27 2.77
1698 2207 3.225069 AATTGCTTGCCGCGGCTTT 62.225 52.632 45.79 26.76 43.27 3.51
1699 2208 3.631487 GAATTGCTTGCCGCGGCTT 62.631 57.895 45.79 32.50 43.27 4.35
1700 2209 4.120331 GAATTGCTTGCCGCGGCT 62.120 61.111 45.79 27.95 43.27 5.52
1701 2210 3.912820 TTGAATTGCTTGCCGCGGC 62.913 57.895 42.35 42.35 43.27 6.53
1702 2211 1.802715 CTTGAATTGCTTGCCGCGG 60.803 57.895 24.05 24.05 43.27 6.46
1703 2212 1.802715 CCTTGAATTGCTTGCCGCG 60.803 57.895 0.00 0.00 43.27 6.46
1704 2213 1.446618 CCCTTGAATTGCTTGCCGC 60.447 57.895 0.00 0.00 39.77 6.53
1705 2214 0.109132 GACCCTTGAATTGCTTGCCG 60.109 55.000 0.00 0.00 0.00 5.69
1706 2215 0.247460 GGACCCTTGAATTGCTTGCC 59.753 55.000 0.00 0.00 0.00 4.52
1792 2309 1.209019 TGTTTGCCTGTTTGGTTGCAT 59.791 42.857 0.00 0.00 38.35 3.96
2069 2590 2.814280 AGTGTCGGACAACCAGTAAG 57.186 50.000 13.23 0.00 35.59 2.34


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

AutoCloner maintained by Alex Coulton.