Multiple sequence alignment - TraesCS1A01G309200

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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 TraesCS1A01G309200 chr1A 100.000 4193 0 0 1 4193 499982785 499978593 0.000000e+00 7744.0
1 TraesCS1A01G309200 chr1A 95.192 104 5 0 1284 1387 499981450 499981347 9.330000e-37 165.0
2 TraesCS1A01G309200 chr1A 95.192 104 5 0 1336 1439 499981502 499981399 9.330000e-37 165.0
3 TraesCS1A01G309200 chr1A 94.231 52 3 0 1284 1335 499981398 499981347 3.480000e-11 80.5
4 TraesCS1A01G309200 chr1A 94.231 52 3 0 1388 1439 499981502 499981451 3.480000e-11 80.5
5 TraesCS1A01G309200 chr1D 94.246 2833 117 18 1336 4145 404492196 404489387 0.000000e+00 4287.0
6 TraesCS1A01G309200 chr1D 85.004 1407 119 43 14 1387 404493437 404492090 0.000000e+00 1345.0
7 TraesCS1A01G309200 chr1B 93.136 2739 132 29 1327 4040 544132241 544129534 0.000000e+00 3965.0
8 TraesCS1A01G309200 chr1B 87.643 1311 90 34 115 1387 544133408 544132132 0.000000e+00 1458.0
9 TraesCS1A01G309200 chr1B 98.077 52 1 0 1284 1335 544132183 544132132 1.610000e-14 91.6
10 TraesCS1A01G309200 chr1B 97.826 46 1 0 4027 4072 544114144 544114099 3.480000e-11 80.5
11 TraesCS1A01G309200 chr1B 86.885 61 5 2 1379 1439 544132241 544132184 9.730000e-07 65.8


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 TraesCS1A01G309200 chr1A 499978593 499982785 4192 True 1647.0 7744 95.76920 1 4193 5 chr1A.!!$R1 4192
1 TraesCS1A01G309200 chr1D 404489387 404493437 4050 True 2816.0 4287 89.62500 14 4145 2 chr1D.!!$R1 4131
2 TraesCS1A01G309200 chr1B 544129534 544133408 3874 True 1395.1 3965 91.43525 115 4040 4 chr1B.!!$R2 3925

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
176 189 0.036022 GAAGCTTGGTCTGGTGAGCT 59.964 55.000 2.10 0.00 46.71 4.09 F
422 436 0.099436 GTGACTTCGATTGGCATGGC 59.901 55.000 13.29 13.29 0.00 4.40 F
441 455 0.107017 CATTTGGGGACGGCTGAGAT 60.107 55.000 0.00 0.00 0.00 2.75 F
574 606 0.169009 GCCTGCGATGAACTTTGTCC 59.831 55.000 0.00 0.00 0.00 4.02 F
754 801 0.519077 CAGTTTCGCCCTCTTTGCTC 59.481 55.000 0.00 0.00 0.00 4.26 F
1890 1946 1.066858 ACAAGGTACAGTGCATCGGAG 60.067 52.381 0.00 0.00 0.00 4.63 F
2712 2770 0.391661 TGTCCTCGATTGCCTCTTGC 60.392 55.000 0.00 0.00 41.77 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 1814 1.604278 GCAGACACAGTTCCAAAGGAC 59.396 52.381 0.00 0.00 0.00 3.85 R
2213 2270 0.955919 GAACCTACACCAGCTGCCAC 60.956 60.000 8.66 0.00 0.00 5.01 R
2222 2279 0.971386 TCGTCCTTGGAACCTACACC 59.029 55.000 0.00 0.00 0.00 4.16 R
2543 2601 3.171528 TGGATGTGGCAAAATCCATTGA 58.828 40.909 22.81 6.60 45.86 2.57 R
2581 2639 0.255890 TAAATCCCCAGCTGACAGCC 59.744 55.000 23.74 6.31 43.77 4.85 R
3093 3156 0.033208 GTTCTTGATCCCATGGGCCA 60.033 55.000 27.41 22.10 34.68 5.36 R
4030 4132 0.249953 TGTGCTGGCAAATGCTTTGG 60.250 50.000 5.25 0.00 40.94 3.28 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
32 33 6.461640 AGGCGTAGTTAGTGTGAATTTTACT 58.538 36.000 0.00 0.00 0.00 2.24
37 38 6.780706 AGTTAGTGTGAATTTTACTGACCG 57.219 37.500 0.00 0.00 33.06 4.79
62 63 4.080863 GGAGTGGATTTTCTGGAGCTTCTA 60.081 45.833 0.00 0.00 0.00 2.10
63 64 5.096443 AGTGGATTTTCTGGAGCTTCTAG 57.904 43.478 0.00 0.00 0.00 2.43
77 78 5.033589 AGCTTCTAGTGAGATTCCATTGG 57.966 43.478 0.00 0.00 0.00 3.16
81 82 1.760192 AGTGAGATTCCATTGGCTGC 58.240 50.000 0.00 0.00 0.00 5.25
82 83 0.379669 GTGAGATTCCATTGGCTGCG 59.620 55.000 0.00 0.00 0.00 5.18
106 107 1.625315 TGTGGGTGGATGTGAGAAGAG 59.375 52.381 0.00 0.00 0.00 2.85
111 112 0.247460 TGGATGTGAGAAGAGCGGTG 59.753 55.000 0.00 0.00 0.00 4.94
112 113 0.460987 GGATGTGAGAAGAGCGGTGG 60.461 60.000 0.00 0.00 0.00 4.61
174 187 2.832931 CGAAGCTTGGTCTGGTGAG 58.167 57.895 2.10 0.00 0.00 3.51
175 188 1.294659 CGAAGCTTGGTCTGGTGAGC 61.295 60.000 2.10 0.00 40.79 4.26
176 189 0.036022 GAAGCTTGGTCTGGTGAGCT 59.964 55.000 2.10 0.00 46.71 4.09
186 199 2.224314 GTCTGGTGAGCTAGTGTTTTGC 59.776 50.000 0.00 0.00 0.00 3.68
196 209 3.670627 GCTAGTGTTTTGCCGATTTCCTG 60.671 47.826 0.00 0.00 0.00 3.86
208 221 2.618709 CGATTTCCTGGCTCATAAACCC 59.381 50.000 0.00 0.00 0.00 4.11
212 225 1.065709 TCCTGGCTCATAAACCCGTTC 60.066 52.381 0.00 0.00 0.00 3.95
229 243 0.739462 TTCCGGTTATGAGCTGTGCG 60.739 55.000 0.00 0.00 0.00 5.34
233 247 1.156736 GGTTATGAGCTGTGCGTTGT 58.843 50.000 0.00 0.00 0.00 3.32
254 268 1.566563 CTGTGCTGACTTGTGCGAC 59.433 57.895 0.00 0.00 0.00 5.19
301 315 1.074775 CTTGTGCTGGCCCTGGTAA 59.925 57.895 0.00 0.00 0.00 2.85
304 318 0.114168 TGTGCTGGCCCTGGTAATTT 59.886 50.000 0.00 0.00 0.00 1.82
306 320 1.257055 TGCTGGCCCTGGTAATTTGC 61.257 55.000 0.00 0.00 0.00 3.68
327 341 1.487976 ACATGGCCTGTGATCTCGATT 59.512 47.619 14.47 0.00 36.48 3.34
348 362 2.029739 TGATTCGACCTGTAGCGTGAAA 60.030 45.455 0.00 0.00 0.00 2.69
352 366 3.395639 TCGACCTGTAGCGTGAAATTTT 58.604 40.909 0.00 0.00 0.00 1.82
353 367 3.185594 TCGACCTGTAGCGTGAAATTTTG 59.814 43.478 0.00 0.00 0.00 2.44
354 368 3.234386 GACCTGTAGCGTGAAATTTTGC 58.766 45.455 0.00 0.00 0.00 3.68
355 369 2.030274 ACCTGTAGCGTGAAATTTTGCC 60.030 45.455 7.21 0.00 0.00 4.52
394 408 0.825410 TGTGGATCATTTGCCATGGC 59.175 50.000 30.54 30.54 42.35 4.40
395 409 0.105408 GTGGATCATTTGCCATGGCC 59.895 55.000 33.44 15.93 41.09 5.36
420 434 3.553511 GTCTAGTGACTTCGATTGGCATG 59.446 47.826 0.00 0.00 39.94 4.06
421 435 1.742761 AGTGACTTCGATTGGCATGG 58.257 50.000 0.00 0.00 0.00 3.66
422 436 0.099436 GTGACTTCGATTGGCATGGC 59.901 55.000 13.29 13.29 0.00 4.40
424 438 1.027357 GACTTCGATTGGCATGGCAT 58.973 50.000 23.96 12.99 0.00 4.40
425 439 1.406539 GACTTCGATTGGCATGGCATT 59.593 47.619 23.96 19.50 0.00 3.56
426 440 1.826720 ACTTCGATTGGCATGGCATTT 59.173 42.857 23.96 13.74 0.00 2.32
427 441 2.198406 CTTCGATTGGCATGGCATTTG 58.802 47.619 23.96 21.67 0.00 2.32
429 443 0.531090 CGATTGGCATGGCATTTGGG 60.531 55.000 23.96 9.16 0.00 4.12
430 444 0.179040 GATTGGCATGGCATTTGGGG 60.179 55.000 23.96 0.00 0.00 4.96
431 445 0.620990 ATTGGCATGGCATTTGGGGA 60.621 50.000 23.96 6.39 0.00 4.81
432 446 1.551908 TTGGCATGGCATTTGGGGAC 61.552 55.000 23.96 0.00 0.00 4.46
433 447 2.495866 GCATGGCATTTGGGGACG 59.504 61.111 0.00 0.00 0.00 4.79
434 448 3.080045 GCATGGCATTTGGGGACGG 62.080 63.158 0.00 0.00 0.00 4.79
435 449 2.759560 ATGGCATTTGGGGACGGC 60.760 61.111 0.00 0.00 0.00 5.68
436 450 3.301222 ATGGCATTTGGGGACGGCT 62.301 57.895 0.00 0.00 0.00 5.52
437 451 3.451894 GGCATTTGGGGACGGCTG 61.452 66.667 0.00 0.00 0.00 4.85
438 452 2.361104 GCATTTGGGGACGGCTGA 60.361 61.111 0.00 0.00 0.00 4.26
439 453 2.409870 GCATTTGGGGACGGCTGAG 61.410 63.158 0.00 0.00 0.00 3.35
440 454 1.299648 CATTTGGGGACGGCTGAGA 59.700 57.895 0.00 0.00 0.00 3.27
441 455 0.107017 CATTTGGGGACGGCTGAGAT 60.107 55.000 0.00 0.00 0.00 2.75
442 456 0.625849 ATTTGGGGACGGCTGAGATT 59.374 50.000 0.00 0.00 0.00 2.40
443 457 1.281419 TTTGGGGACGGCTGAGATTA 58.719 50.000 0.00 0.00 0.00 1.75
448 462 0.389757 GGACGGCTGAGATTACCTCC 59.610 60.000 0.00 0.00 41.25 4.30
455 469 2.122768 CTGAGATTACCTCCAGGGCTT 58.877 52.381 0.00 0.00 41.25 4.35
464 478 1.208293 CCTCCAGGGCTTCAGTTCTAC 59.792 57.143 0.00 0.00 0.00 2.59
465 479 2.183679 CTCCAGGGCTTCAGTTCTACT 58.816 52.381 0.00 0.00 0.00 2.57
507 537 3.006967 GCTCAACTGGTCTTCCTCTGTTA 59.993 47.826 0.00 0.00 34.23 2.41
515 545 4.202461 TGGTCTTCCTCTGTTACTTGCAAT 60.202 41.667 0.00 0.00 34.23 3.56
548 580 7.297936 TGTCTTTCTACCATGTAGAGTTCAA 57.702 36.000 4.34 0.00 0.00 2.69
550 582 9.031537 TGTCTTTCTACCATGTAGAGTTCAATA 57.968 33.333 4.34 0.00 0.00 1.90
560 592 2.363683 AGAGTTCAATAAGCAGCCTGC 58.636 47.619 9.13 9.13 45.46 4.85
574 606 0.169009 GCCTGCGATGAACTTTGTCC 59.831 55.000 0.00 0.00 0.00 4.02
601 633 7.391554 TCTTCATGTGATTTGGAGAGGTTAAAG 59.608 37.037 0.00 0.00 0.00 1.85
603 635 6.655003 TCATGTGATTTGGAGAGGTTAAAGTC 59.345 38.462 0.00 0.00 0.00 3.01
605 637 4.700692 GTGATTTGGAGAGGTTAAAGTCCC 59.299 45.833 0.00 0.00 0.00 4.46
614 646 5.695424 GAGGTTAAAGTCCCTCCATAAGT 57.305 43.478 0.00 0.00 41.22 2.24
615 647 5.672503 GAGGTTAAAGTCCCTCCATAAGTC 58.327 45.833 0.00 0.00 41.22 3.01
616 648 4.161754 AGGTTAAAGTCCCTCCATAAGTCG 59.838 45.833 0.00 0.00 0.00 4.18
632 664 8.316214 TCCATAAGTCGTCTGTAACCTTAAAAT 58.684 33.333 0.00 0.00 0.00 1.82
662 694 7.322664 ACAAGTGTTGGCTATTTGGATATTTG 58.677 34.615 0.00 0.00 34.12 2.32
663 695 7.178274 ACAAGTGTTGGCTATTTGGATATTTGA 59.822 33.333 0.00 0.00 34.12 2.69
664 696 7.902920 AGTGTTGGCTATTTGGATATTTGAT 57.097 32.000 0.00 0.00 0.00 2.57
665 697 8.995027 AGTGTTGGCTATTTGGATATTTGATA 57.005 30.769 0.00 0.00 0.00 2.15
666 698 8.850156 AGTGTTGGCTATTTGGATATTTGATAC 58.150 33.333 0.00 0.00 0.00 2.24
667 699 8.850156 GTGTTGGCTATTTGGATATTTGATACT 58.150 33.333 0.00 0.00 0.00 2.12
710 757 3.492011 CAGATTTGTTTTTGGTGCTCTGC 59.508 43.478 0.00 0.00 0.00 4.26
727 774 4.201792 GCTCTGCTGTGTCAATATTGTCTG 60.202 45.833 14.97 11.21 0.00 3.51
754 801 0.519077 CAGTTTCGCCCTCTTTGCTC 59.481 55.000 0.00 0.00 0.00 4.26
762 809 3.259876 TCGCCCTCTTTGCTCTTTTACTA 59.740 43.478 0.00 0.00 0.00 1.82
764 811 3.375610 GCCCTCTTTGCTCTTTTACTAGC 59.624 47.826 0.00 0.00 39.25 3.42
772 819 3.997021 TGCTCTTTTACTAGCAGCAGAAC 59.003 43.478 0.00 0.00 43.56 3.01
781 829 4.570930 ACTAGCAGCAGAACTCCTTTAAC 58.429 43.478 0.00 0.00 0.00 2.01
809 857 3.974642 ACCAGGAGACTTACCAACTTCTT 59.025 43.478 0.00 0.00 40.21 2.52
853 909 7.530863 GGGATTTCATGAACTGTCTAAGAAAC 58.469 38.462 7.89 0.00 0.00 2.78
865 921 7.807680 ACTGTCTAAGAAACGATGAAATTTCC 58.192 34.615 15.48 0.25 35.77 3.13
868 924 7.659799 TGTCTAAGAAACGATGAAATTTCCTCA 59.340 33.333 19.43 2.91 35.77 3.86
879 935 7.698130 CGATGAAATTTCCTCATACCAGAAAAC 59.302 37.037 19.43 0.00 33.63 2.43
887 943 4.381612 CCTCATACCAGAAAACGCTCAGTA 60.382 45.833 0.00 0.00 0.00 2.74
905 961 8.547894 CGCTCAGTATGCTGTATTTACATTTTA 58.452 33.333 10.80 0.00 43.05 1.52
924 980 8.234546 ACATTTTACCGTCAACTTGATATGTTC 58.765 33.333 0.00 0.00 0.00 3.18
948 1004 7.977818 TCTGTTTAGATATACAGGATGGCATT 58.022 34.615 0.00 0.00 43.62 3.56
959 1015 6.252599 ACAGGATGGCATTAGAAATGTAGA 57.747 37.500 0.00 0.00 43.62 2.59
961 1017 6.126652 ACAGGATGGCATTAGAAATGTAGACT 60.127 38.462 0.00 0.00 43.62 3.24
1113 1169 8.346476 CTCAGAATAGTGAGCATGTAAGTAAC 57.654 38.462 0.00 0.00 37.74 2.50
1325 1381 9.804758 ATAAGTTTCGTTTATTTTGTTGGTTCA 57.195 25.926 0.00 0.00 0.00 3.18
1326 1382 8.710835 AAGTTTCGTTTATTTTGTTGGTTCAT 57.289 26.923 0.00 0.00 0.00 2.57
1327 1383 8.710835 AGTTTCGTTTATTTTGTTGGTTCATT 57.289 26.923 0.00 0.00 0.00 2.57
1328 1384 8.813282 AGTTTCGTTTATTTTGTTGGTTCATTC 58.187 29.630 0.00 0.00 0.00 2.67
1329 1385 8.813282 GTTTCGTTTATTTTGTTGGTTCATTCT 58.187 29.630 0.00 0.00 0.00 2.40
1330 1386 7.922505 TCGTTTATTTTGTTGGTTCATTCTG 57.077 32.000 0.00 0.00 0.00 3.02
1331 1387 6.419413 TCGTTTATTTTGTTGGTTCATTCTGC 59.581 34.615 0.00 0.00 0.00 4.26
1332 1388 6.420604 CGTTTATTTTGTTGGTTCATTCTGCT 59.579 34.615 0.00 0.00 0.00 4.24
1333 1389 7.042791 CGTTTATTTTGTTGGTTCATTCTGCTT 60.043 33.333 0.00 0.00 0.00 3.91
1334 1390 7.712264 TTATTTTGTTGGTTCATTCTGCTTG 57.288 32.000 0.00 0.00 0.00 4.01
1335 1391 4.734398 TTTGTTGGTTCATTCTGCTTGT 57.266 36.364 0.00 0.00 0.00 3.16
1336 1392 4.734398 TTGTTGGTTCATTCTGCTTGTT 57.266 36.364 0.00 0.00 0.00 2.83
1337 1393 5.843673 TTGTTGGTTCATTCTGCTTGTTA 57.156 34.783 0.00 0.00 0.00 2.41
1338 1394 5.181690 TGTTGGTTCATTCTGCTTGTTAC 57.818 39.130 0.00 0.00 0.00 2.50
1339 1395 4.887071 TGTTGGTTCATTCTGCTTGTTACT 59.113 37.500 0.00 0.00 0.00 2.24
1340 1396 5.359576 TGTTGGTTCATTCTGCTTGTTACTT 59.640 36.000 0.00 0.00 0.00 2.24
1341 1397 6.544197 TGTTGGTTCATTCTGCTTGTTACTTA 59.456 34.615 0.00 0.00 0.00 2.24
1342 1398 7.067615 TGTTGGTTCATTCTGCTTGTTACTTAA 59.932 33.333 0.00 0.00 0.00 1.85
1343 1399 7.759489 TGGTTCATTCTGCTTGTTACTTAAT 57.241 32.000 0.00 0.00 0.00 1.40
1344 1400 8.856153 TGGTTCATTCTGCTTGTTACTTAATA 57.144 30.769 0.00 0.00 0.00 0.98
1345 1401 9.461312 TGGTTCATTCTGCTTGTTACTTAATAT 57.539 29.630 0.00 0.00 0.00 1.28
1346 1402 9.722056 GGTTCATTCTGCTTGTTACTTAATATG 57.278 33.333 0.00 0.00 0.00 1.78
1349 1405 9.109393 TCATTCTGCTTGTTACTTAATATGACC 57.891 33.333 0.00 0.00 0.00 4.02
1350 1406 9.113838 CATTCTGCTTGTTACTTAATATGACCT 57.886 33.333 0.00 0.00 0.00 3.85
1393 1449 6.544197 TGTTGGTTCATTCTGCTTGTTACTTA 59.456 34.615 0.00 0.00 0.00 2.24
1524 1580 5.439721 ACAATGCATATCTAGAACCTGCAA 58.560 37.500 22.93 12.12 45.03 4.08
1535 1591 2.771372 AGAACCTGCAATTTGGTGGTTT 59.229 40.909 5.82 0.00 40.60 3.27
1567 1623 8.667463 CGAATCCATTGTGTATCATGCATATTA 58.333 33.333 0.00 0.00 0.00 0.98
1570 1626 8.688747 TCCATTGTGTATCATGCATATTAACA 57.311 30.769 0.00 0.00 0.00 2.41
1667 1723 3.946606 TGCTGCATATATCAGGTCATGG 58.053 45.455 0.00 0.00 32.41 3.66
1673 1729 4.934001 GCATATATCAGGTCATGGACTGTG 59.066 45.833 14.44 8.32 32.47 3.66
1696 1752 2.509964 ACACACAAGTTTCTCTTCCCCT 59.490 45.455 0.00 0.00 33.63 4.79
1703 1759 4.519906 AGTTTCTCTTCCCCTCAAAACA 57.480 40.909 0.00 0.00 0.00 2.83
1722 1778 5.505173 AACACAAGTTCCTCATGTTTCAG 57.495 39.130 0.00 0.00 30.46 3.02
1758 1814 9.469807 CTAGTCTGCTAGAAGTTGTTAATATGG 57.530 37.037 0.00 0.00 45.77 2.74
1887 1943 1.795768 ACACAAGGTACAGTGCATCG 58.204 50.000 10.96 0.00 39.62 3.84
1890 1946 1.066858 ACAAGGTACAGTGCATCGGAG 60.067 52.381 0.00 0.00 0.00 4.63
2116 2172 5.882557 CCTTGCAAAGTACATACCAGAATCT 59.117 40.000 0.00 0.00 44.25 2.40
2196 2253 2.771943 TGCCTTCCTTCATACCGAGAAT 59.228 45.455 0.00 0.00 0.00 2.40
2208 2265 3.643159 ACCGAGAATGCTTTGGTTTTC 57.357 42.857 0.00 0.00 31.44 2.29
2209 2266 3.222603 ACCGAGAATGCTTTGGTTTTCT 58.777 40.909 0.00 0.00 31.44 2.52
2213 2270 5.858581 CCGAGAATGCTTTGGTTTTCTAAAG 59.141 40.000 0.00 0.00 46.49 1.85
2222 2279 2.622942 TGGTTTTCTAAAGTGGCAGCTG 59.377 45.455 10.11 10.11 0.00 4.24
2351 2408 6.900194 TCCTCTGCTAACATAGGCTTTTTAT 58.100 36.000 0.00 0.00 39.46 1.40
2359 2416 7.201785 GCTAACATAGGCTTTTTATGCTGGTTA 60.202 37.037 0.00 0.00 32.90 2.85
2628 2686 4.098894 ACAATCAGATTTCTTGCCCCATT 58.901 39.130 0.00 0.00 0.00 3.16
2629 2687 4.161001 ACAATCAGATTTCTTGCCCCATTC 59.839 41.667 0.00 0.00 0.00 2.67
2630 2688 3.744940 TCAGATTTCTTGCCCCATTCT 57.255 42.857 0.00 0.00 0.00 2.40
2631 2689 4.860802 TCAGATTTCTTGCCCCATTCTA 57.139 40.909 0.00 0.00 0.00 2.10
2632 2690 4.526970 TCAGATTTCTTGCCCCATTCTAC 58.473 43.478 0.00 0.00 0.00 2.59
2633 2691 4.018506 TCAGATTTCTTGCCCCATTCTACA 60.019 41.667 0.00 0.00 0.00 2.74
2634 2692 4.891756 CAGATTTCTTGCCCCATTCTACAT 59.108 41.667 0.00 0.00 0.00 2.29
2635 2693 5.361857 CAGATTTCTTGCCCCATTCTACATT 59.638 40.000 0.00 0.00 0.00 2.71
2711 2769 2.099141 TTGTCCTCGATTGCCTCTTG 57.901 50.000 0.00 0.00 0.00 3.02
2712 2770 0.391661 TGTCCTCGATTGCCTCTTGC 60.392 55.000 0.00 0.00 41.77 4.01
2733 2791 7.651704 TCTTGCTAACAGTTCTTTTATTTTGCC 59.348 33.333 0.00 0.00 0.00 4.52
2797 2860 4.830600 TCTTCGGAGCCAACCTAAATTTTT 59.169 37.500 0.00 0.00 0.00 1.94
2810 2873 6.288294 ACCTAAATTTTTGTTCCAAGCCTTC 58.712 36.000 0.00 0.00 0.00 3.46
2841 2904 8.758829 ACTAGACTAAATCATCACATGTTACCA 58.241 33.333 0.00 0.00 0.00 3.25
3064 3127 3.004354 ATGCGGTCCGGGGTGTTA 61.004 61.111 14.38 0.00 0.00 2.41
3093 3156 5.211201 CCAGGGTTTGAATCCCATCTTATT 58.789 41.667 13.51 0.00 46.82 1.40
3228 3292 5.751243 TTACAAAGGAAACACTTCTGAGC 57.249 39.130 0.00 0.00 0.00 4.26
3291 3355 3.673338 TCGTCTTAACAACAGAATGAGCG 59.327 43.478 0.00 0.00 39.69 5.03
3306 3370 0.884704 GAGCGCTGTTTGGACCTTCA 60.885 55.000 18.48 0.00 0.00 3.02
3426 3490 4.089361 CCAGTTAGCAATCCCCTTCTTTT 58.911 43.478 0.00 0.00 0.00 2.27
3470 3534 3.499918 ACATGTAGCAAGAAACAGAGCAC 59.500 43.478 0.00 0.00 0.00 4.40
3508 3572 4.016444 CAAGGCCCTAAAGCTACATGAAA 58.984 43.478 0.00 0.00 0.00 2.69
3536 3600 9.436957 CTATCTGGTAGTTGTACATTTCTGTTT 57.563 33.333 0.00 0.00 36.79 2.83
3576 3640 5.071788 TCTGCTTACCTTATATTGACCCCTG 59.928 44.000 0.00 0.00 0.00 4.45
3637 3701 3.157087 ACAAATCAACTTGGCTACTGGG 58.843 45.455 0.00 0.00 0.00 4.45
3639 3703 4.202524 ACAAATCAACTTGGCTACTGGGTA 60.203 41.667 0.00 0.00 0.00 3.69
3643 3707 3.393278 TCAACTTGGCTACTGGGTAACTT 59.607 43.478 0.00 0.00 0.00 2.66
3667 3731 3.120095 GCATTTACGAGGTTGGTTGTACC 60.120 47.826 0.00 0.00 39.22 3.34
3752 3835 7.230913 TCAAGGAGTAATAGTCCATACAGTAGC 59.769 40.741 15.88 0.00 40.24 3.58
3821 3904 1.114627 TCGATGCTAGTGGTGCTCAT 58.885 50.000 0.00 0.00 0.00 2.90
3825 3908 3.431233 CGATGCTAGTGGTGCTCATAATG 59.569 47.826 0.00 0.00 0.00 1.90
3902 4004 5.369699 AGCTATGAATTAAAGGGCTACTCCA 59.630 40.000 0.00 0.00 36.21 3.86
3955 4057 0.770499 TGTGGAGGTGGATGCTTTGA 59.230 50.000 0.00 0.00 0.00 2.69
3957 4059 1.747355 GTGGAGGTGGATGCTTTGATG 59.253 52.381 0.00 0.00 0.00 3.07
3975 4077 2.160221 GCATGCATTTGGCCGTTCG 61.160 57.895 14.21 0.00 43.89 3.95
3990 4092 2.542595 CCGTTCGTGCCAGATAATAACC 59.457 50.000 0.00 0.00 0.00 2.85
4113 4216 4.792068 TGTTTGGATTGAGGGATATGGTC 58.208 43.478 0.00 0.00 0.00 4.02
4136 4239 1.413445 TGCAGCTCAAAGCCATGTTTT 59.587 42.857 0.00 0.00 43.77 2.43
4137 4240 2.064014 GCAGCTCAAAGCCATGTTTTC 58.936 47.619 0.00 0.00 43.77 2.29
4140 4243 4.374399 CAGCTCAAAGCCATGTTTTCTTT 58.626 39.130 0.00 0.00 43.77 2.52
4141 4244 4.210537 CAGCTCAAAGCCATGTTTTCTTTG 59.789 41.667 15.14 15.14 43.77 2.77
4147 4250 7.950512 TCAAAGCCATGTTTTCTTTGATAAGA 58.049 30.769 17.85 0.00 46.01 2.10
4148 4251 8.420222 TCAAAGCCATGTTTTCTTTGATAAGAA 58.580 29.630 17.85 0.00 46.01 2.52
4155 4258 2.754946 TCTTTGATAAGAACGGCGGT 57.245 45.000 13.24 3.35 37.45 5.68
4156 4259 3.872511 TCTTTGATAAGAACGGCGGTA 57.127 42.857 13.24 0.00 37.45 4.02
4157 4260 4.395959 TCTTTGATAAGAACGGCGGTAT 57.604 40.909 13.24 0.00 37.45 2.73
4158 4261 5.518848 TCTTTGATAAGAACGGCGGTATA 57.481 39.130 13.24 1.44 37.45 1.47
4159 4262 5.904941 TCTTTGATAAGAACGGCGGTATAA 58.095 37.500 13.24 0.00 37.45 0.98
4160 4263 5.750067 TCTTTGATAAGAACGGCGGTATAAC 59.250 40.000 13.24 0.98 37.45 1.89
4161 4264 3.981211 TGATAAGAACGGCGGTATAACC 58.019 45.455 13.24 0.00 34.05 2.85
4162 4265 3.638160 TGATAAGAACGGCGGTATAACCT 59.362 43.478 13.24 0.00 35.66 3.50
4163 4266 2.591571 AAGAACGGCGGTATAACCTC 57.408 50.000 13.24 0.00 35.66 3.85
4164 4267 0.383231 AGAACGGCGGTATAACCTCG 59.617 55.000 13.24 7.01 38.12 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.097825 ACTAACTACGCCTACCACCAG 58.902 52.381 0.00 0.00 0.00 4.00
1 2 1.820519 CACTAACTACGCCTACCACCA 59.179 52.381 0.00 0.00 0.00 4.17
2 3 1.821136 ACACTAACTACGCCTACCACC 59.179 52.381 0.00 0.00 0.00 4.61
3 4 2.489329 TCACACTAACTACGCCTACCAC 59.511 50.000 0.00 0.00 0.00 4.16
4 5 2.794103 TCACACTAACTACGCCTACCA 58.206 47.619 0.00 0.00 0.00 3.25
5 6 3.855689 TTCACACTAACTACGCCTACC 57.144 47.619 0.00 0.00 0.00 3.18
6 7 6.716898 AAAATTCACACTAACTACGCCTAC 57.283 37.500 0.00 0.00 0.00 3.18
7 8 7.543172 CAGTAAAATTCACACTAACTACGCCTA 59.457 37.037 0.00 0.00 0.00 3.93
8 9 6.367969 CAGTAAAATTCACACTAACTACGCCT 59.632 38.462 0.00 0.00 0.00 5.52
9 10 6.366877 TCAGTAAAATTCACACTAACTACGCC 59.633 38.462 0.00 0.00 0.00 5.68
10 11 7.225397 GTCAGTAAAATTCACACTAACTACGC 58.775 38.462 0.00 0.00 0.00 4.42
11 12 7.410087 CGGTCAGTAAAATTCACACTAACTACG 60.410 40.741 0.00 0.00 0.00 3.51
12 13 7.620806 GCGGTCAGTAAAATTCACACTAACTAC 60.621 40.741 0.00 0.00 0.00 2.73
32 33 0.672401 GAAAATCCACTCCGCGGTCA 60.672 55.000 27.15 5.52 0.00 4.02
37 38 1.373570 CTCCAGAAAATCCACTCCGC 58.626 55.000 0.00 0.00 0.00 5.54
62 63 1.760192 GCAGCCAATGGAATCTCACT 58.240 50.000 2.05 0.00 0.00 3.41
63 64 0.379669 CGCAGCCAATGGAATCTCAC 59.620 55.000 2.05 0.00 0.00 3.51
81 82 4.033776 ACATCCACCCACAGGCCG 62.034 66.667 0.00 0.00 36.11 6.13
82 83 2.361610 CACATCCACCCACAGGCC 60.362 66.667 0.00 0.00 36.11 5.19
91 92 0.247736 ACCGCTCTTCTCACATCCAC 59.752 55.000 0.00 0.00 0.00 4.02
106 107 1.206578 CAAACGTGATCACCACCGC 59.793 57.895 20.03 0.00 42.76 5.68
111 112 1.862602 GCCACCCAAACGTGATCACC 61.863 60.000 20.03 2.90 35.68 4.02
112 113 1.579429 GCCACCCAAACGTGATCAC 59.421 57.895 16.21 16.21 35.68 3.06
167 180 1.537202 GGCAAAACACTAGCTCACCAG 59.463 52.381 0.00 0.00 0.00 4.00
171 184 2.472695 ATCGGCAAAACACTAGCTCA 57.527 45.000 0.00 0.00 0.00 4.26
174 187 2.488153 AGGAAATCGGCAAAACACTAGC 59.512 45.455 0.00 0.00 0.00 3.42
175 188 3.119849 CCAGGAAATCGGCAAAACACTAG 60.120 47.826 0.00 0.00 0.00 2.57
176 189 2.817258 CCAGGAAATCGGCAAAACACTA 59.183 45.455 0.00 0.00 0.00 2.74
186 199 2.618709 GGTTTATGAGCCAGGAAATCGG 59.381 50.000 0.00 0.00 0.00 4.18
212 225 1.019278 AACGCACAGCTCATAACCGG 61.019 55.000 0.00 0.00 0.00 5.28
229 243 1.133025 ACAAGTCAGCACAGCAACAAC 59.867 47.619 0.00 0.00 0.00 3.32
233 247 1.729276 GCACAAGTCAGCACAGCAA 59.271 52.632 0.00 0.00 0.00 3.91
327 341 1.170442 TCACGCTACAGGTCGAATCA 58.830 50.000 0.00 0.00 0.00 2.57
355 369 2.299867 CAACAAATGAAACTGGAGGGGG 59.700 50.000 0.00 0.00 0.00 5.40
359 373 4.916983 TCCACAACAAATGAAACTGGAG 57.083 40.909 0.00 0.00 0.00 3.86
365 379 5.469421 GGCAAATGATCCACAACAAATGAAA 59.531 36.000 0.00 0.00 0.00 2.69
420 434 3.451894 CAGCCGTCCCCAAATGCC 61.452 66.667 0.00 0.00 0.00 4.40
421 435 2.361104 TCAGCCGTCCCCAAATGC 60.361 61.111 0.00 0.00 0.00 3.56
422 436 0.107017 ATCTCAGCCGTCCCCAAATG 60.107 55.000 0.00 0.00 0.00 2.32
424 438 1.065709 GTAATCTCAGCCGTCCCCAAA 60.066 52.381 0.00 0.00 0.00 3.28
425 439 0.539986 GTAATCTCAGCCGTCCCCAA 59.460 55.000 0.00 0.00 0.00 4.12
426 440 1.335132 GGTAATCTCAGCCGTCCCCA 61.335 60.000 0.00 0.00 0.00 4.96
427 441 1.049289 AGGTAATCTCAGCCGTCCCC 61.049 60.000 0.00 0.00 0.00 4.81
429 443 0.389757 GGAGGTAATCTCAGCCGTCC 59.610 60.000 0.00 0.00 44.19 4.79
430 444 1.067821 CTGGAGGTAATCTCAGCCGTC 59.932 57.143 0.00 0.00 44.19 4.79
431 445 1.115467 CTGGAGGTAATCTCAGCCGT 58.885 55.000 0.00 0.00 44.19 5.68
432 446 0.390860 CCTGGAGGTAATCTCAGCCG 59.609 60.000 0.00 0.00 44.19 5.52
433 447 0.761802 CCCTGGAGGTAATCTCAGCC 59.238 60.000 0.00 0.00 44.19 4.85
434 448 0.107643 GCCCTGGAGGTAATCTCAGC 59.892 60.000 0.00 0.00 44.19 4.26
435 449 1.799933 AGCCCTGGAGGTAATCTCAG 58.200 55.000 0.00 0.00 44.19 3.35
436 450 2.119495 GAAGCCCTGGAGGTAATCTCA 58.881 52.381 0.00 0.00 44.19 3.27
437 451 2.103941 CTGAAGCCCTGGAGGTAATCTC 59.896 54.545 0.00 0.00 41.71 2.75
438 452 2.122768 CTGAAGCCCTGGAGGTAATCT 58.877 52.381 0.00 0.00 38.26 2.40
439 453 1.840635 ACTGAAGCCCTGGAGGTAATC 59.159 52.381 0.00 0.00 38.26 1.75
440 454 1.972588 ACTGAAGCCCTGGAGGTAAT 58.027 50.000 0.00 0.00 38.26 1.89
441 455 1.628846 GAACTGAAGCCCTGGAGGTAA 59.371 52.381 0.00 0.00 38.26 2.85
442 456 1.203313 AGAACTGAAGCCCTGGAGGTA 60.203 52.381 0.00 0.00 38.26 3.08
443 457 0.474660 AGAACTGAAGCCCTGGAGGT 60.475 55.000 0.00 0.00 38.26 3.85
464 478 3.244044 GCTAGCTTCCCCATAAGAGTCAG 60.244 52.174 7.70 0.00 0.00 3.51
465 479 2.700897 GCTAGCTTCCCCATAAGAGTCA 59.299 50.000 7.70 0.00 0.00 3.41
467 481 2.969262 GAGCTAGCTTCCCCATAAGAGT 59.031 50.000 20.42 0.00 0.00 3.24
468 482 2.968574 TGAGCTAGCTTCCCCATAAGAG 59.031 50.000 20.42 0.00 0.00 2.85
469 483 3.046283 TGAGCTAGCTTCCCCATAAGA 57.954 47.619 20.42 0.00 0.00 2.10
471 485 3.115390 AGTTGAGCTAGCTTCCCCATAA 58.885 45.455 20.42 3.47 0.00 1.90
474 488 0.615331 CAGTTGAGCTAGCTTCCCCA 59.385 55.000 20.42 9.36 0.00 4.96
475 489 0.107459 CCAGTTGAGCTAGCTTCCCC 60.107 60.000 20.42 6.44 0.00 4.81
476 490 0.615850 ACCAGTTGAGCTAGCTTCCC 59.384 55.000 20.42 6.84 0.00 3.97
530 560 7.418337 TGCTTATTGAACTCTACATGGTAGA 57.582 36.000 6.01 6.01 0.00 2.59
540 570 2.363683 GCAGGCTGCTTATTGAACTCT 58.636 47.619 31.37 0.00 40.96 3.24
548 580 1.134280 AGTTCATCGCAGGCTGCTTAT 60.134 47.619 34.17 24.50 42.25 1.73
550 582 0.607489 AAGTTCATCGCAGGCTGCTT 60.607 50.000 34.17 20.36 42.25 3.91
560 592 4.692625 ACATGAAGAGGACAAAGTTCATCG 59.307 41.667 0.00 0.00 37.50 3.84
567 599 5.474532 TCCAAATCACATGAAGAGGACAAAG 59.525 40.000 0.00 0.00 0.00 2.77
574 606 4.841422 ACCTCTCCAAATCACATGAAGAG 58.159 43.478 0.00 1.95 0.00 2.85
601 633 2.100989 ACAGACGACTTATGGAGGGAC 58.899 52.381 0.00 0.00 0.00 4.46
603 635 3.181478 GGTTACAGACGACTTATGGAGGG 60.181 52.174 0.00 0.00 0.00 4.30
605 637 4.985538 AGGTTACAGACGACTTATGGAG 57.014 45.455 0.00 0.00 0.00 3.86
613 645 9.934190 TGTTAAAATTTTAAGGTTACAGACGAC 57.066 29.630 20.94 8.19 33.66 4.34
632 664 7.113658 TCCAAATAGCCAACACTTGTTAAAA 57.886 32.000 0.00 0.00 36.32 1.52
636 668 7.480760 AATATCCAAATAGCCAACACTTGTT 57.519 32.000 0.00 0.00 39.12 2.83
637 669 7.178274 TCAAATATCCAAATAGCCAACACTTGT 59.822 33.333 0.00 0.00 0.00 3.16
638 670 7.546358 TCAAATATCCAAATAGCCAACACTTG 58.454 34.615 0.00 0.00 0.00 3.16
640 672 7.902920 ATCAAATATCCAAATAGCCAACACT 57.097 32.000 0.00 0.00 0.00 3.55
673 705 9.662947 AAAACAAATCTGTATACCTAGTGGTAC 57.337 33.333 0.00 0.00 42.45 3.34
688 720 3.492011 GCAGAGCACCAAAAACAAATCTG 59.508 43.478 0.00 0.00 36.78 2.90
690 722 3.492011 CAGCAGAGCACCAAAAACAAATC 59.508 43.478 0.00 0.00 0.00 2.17
691 723 3.118665 ACAGCAGAGCACCAAAAACAAAT 60.119 39.130 0.00 0.00 0.00 2.32
696 743 1.405105 GACACAGCAGAGCACCAAAAA 59.595 47.619 0.00 0.00 0.00 1.94
699 746 0.107263 TTGACACAGCAGAGCACCAA 60.107 50.000 0.00 0.00 0.00 3.67
710 757 9.101655 TGAATATGACAGACAATATTGACACAG 57.898 33.333 22.16 11.75 0.00 3.66
727 774 3.798202 AGAGGGCGAAACTGAATATGAC 58.202 45.455 0.00 0.00 0.00 3.06
754 801 4.826556 AGGAGTTCTGCTGCTAGTAAAAG 58.173 43.478 0.00 0.00 44.41 2.27
764 811 7.606456 TGGTTTATAGTTAAAGGAGTTCTGCTG 59.394 37.037 0.00 0.00 0.00 4.41
772 819 8.080363 AGTCTCCTGGTTTATAGTTAAAGGAG 57.920 38.462 9.12 9.12 37.98 3.69
781 829 7.184067 AGTTGGTAAGTCTCCTGGTTTATAG 57.816 40.000 0.00 0.00 0.00 1.31
809 857 6.550938 ATCCCGATCAGCATATTTATCTCA 57.449 37.500 0.00 0.00 0.00 3.27
853 909 6.925610 TTCTGGTATGAGGAAATTTCATCG 57.074 37.500 23.45 11.26 40.61 3.84
865 921 3.589988 ACTGAGCGTTTTCTGGTATGAG 58.410 45.455 0.00 0.00 0.00 2.90
868 924 3.871594 GCATACTGAGCGTTTTCTGGTAT 59.128 43.478 0.00 0.00 0.00 2.73
887 943 7.618502 TGACGGTAAAATGTAAATACAGCAT 57.381 32.000 0.00 0.00 39.92 3.79
905 961 4.894784 ACAGAACATATCAAGTTGACGGT 58.105 39.130 7.96 3.95 0.00 4.83
924 980 9.376075 CTAATGCCATCCTGTATATCTAAACAG 57.624 37.037 0.00 0.00 42.25 3.16
990 1046 2.042686 TCATACACATGAGCAAGGCC 57.957 50.000 0.00 0.00 36.22 5.19
1010 1066 9.118236 GAGTACTGCAACAATTGTAAGAAATTC 57.882 33.333 12.39 6.98 0.00 2.17
1013 1069 7.497579 TGAGAGTACTGCAACAATTGTAAGAAA 59.502 33.333 12.39 2.38 0.00 2.52
1019 1075 5.308014 TCATGAGAGTACTGCAACAATTGT 58.692 37.500 4.92 4.92 0.00 2.71
1113 1169 1.672881 GATCCACCGAAAGCTCCAATG 59.327 52.381 0.00 0.00 0.00 2.82
1170 1226 4.315803 AGGTCCATCTTAGACGTTGTTTG 58.684 43.478 0.00 0.00 34.97 2.93
1312 1368 5.673514 ACAAGCAGAATGAACCAACAAAAT 58.326 33.333 0.00 0.00 39.69 1.82
1313 1369 5.083533 ACAAGCAGAATGAACCAACAAAA 57.916 34.783 0.00 0.00 39.69 2.44
1314 1370 4.734398 ACAAGCAGAATGAACCAACAAA 57.266 36.364 0.00 0.00 39.69 2.83
1315 1371 4.734398 AACAAGCAGAATGAACCAACAA 57.266 36.364 0.00 0.00 39.69 2.83
1316 1372 4.887071 AGTAACAAGCAGAATGAACCAACA 59.113 37.500 0.00 0.00 39.69 3.33
1317 1373 5.438761 AGTAACAAGCAGAATGAACCAAC 57.561 39.130 0.00 0.00 39.69 3.77
1318 1374 7.575414 TTAAGTAACAAGCAGAATGAACCAA 57.425 32.000 0.00 0.00 39.69 3.67
1319 1375 7.759489 ATTAAGTAACAAGCAGAATGAACCA 57.241 32.000 0.00 0.00 39.69 3.67
1320 1376 9.722056 CATATTAAGTAACAAGCAGAATGAACC 57.278 33.333 0.00 0.00 39.69 3.62
1323 1379 9.109393 GGTCATATTAAGTAACAAGCAGAATGA 57.891 33.333 0.00 0.00 39.69 2.57
1324 1380 9.113838 AGGTCATATTAAGTAACAAGCAGAATG 57.886 33.333 0.00 0.00 40.87 2.67
1355 1411 9.541143 AGAATGAACCAACAAAATAAACGAAAT 57.459 25.926 0.00 0.00 0.00 2.17
1356 1412 8.812329 CAGAATGAACCAACAAAATAAACGAAA 58.188 29.630 0.00 0.00 39.69 3.46
1357 1413 7.043059 GCAGAATGAACCAACAAAATAAACGAA 60.043 33.333 0.00 0.00 39.69 3.85
1358 1414 6.419413 GCAGAATGAACCAACAAAATAAACGA 59.581 34.615 0.00 0.00 39.69 3.85
1524 1580 5.478679 TGGATTCGACATAAAACCACCAAAT 59.521 36.000 0.00 0.00 0.00 2.32
1535 1591 7.307930 GCATGATACACAATGGATTCGACATAA 60.308 37.037 0.00 0.00 0.00 1.90
1637 1693 6.113411 CCTGATATATGCAGCAATCTCATCA 58.887 40.000 0.00 3.98 32.06 3.07
1638 1694 6.114089 ACCTGATATATGCAGCAATCTCATC 58.886 40.000 0.00 0.00 32.06 2.92
1656 1712 2.639347 TGTTCACAGTCCATGACCTGAT 59.361 45.455 15.75 1.49 32.18 2.90
1673 1729 3.315470 GGGGAAGAGAAACTTGTGTGTTC 59.685 47.826 0.00 0.00 39.13 3.18
1696 1752 5.913137 AACATGAGGAACTTGTGTTTTGA 57.087 34.783 0.00 0.00 41.26 2.69
1703 1759 4.780815 TCACTGAAACATGAGGAACTTGT 58.219 39.130 0.00 0.00 41.55 3.16
1722 1778 5.193663 TCTAGCAGACTAGCATGAATCAC 57.806 43.478 0.00 0.00 44.83 3.06
1758 1814 1.604278 GCAGACACAGTTCCAAAGGAC 59.396 52.381 0.00 0.00 0.00 3.85
1880 1936 5.235305 ACATTAACAAATCTCCGATGCAC 57.765 39.130 0.00 0.00 0.00 4.57
2196 2253 3.449018 TGCCACTTTAGAAAACCAAAGCA 59.551 39.130 0.00 0.00 35.58 3.91
2208 2265 2.350522 CTACACCAGCTGCCACTTTAG 58.649 52.381 8.66 0.00 0.00 1.85
2209 2266 1.003118 CCTACACCAGCTGCCACTTTA 59.997 52.381 8.66 0.00 0.00 1.85
2213 2270 0.955919 GAACCTACACCAGCTGCCAC 60.956 60.000 8.66 0.00 0.00 5.01
2222 2279 0.971386 TCGTCCTTGGAACCTACACC 59.029 55.000 0.00 0.00 0.00 4.16
2411 2469 5.365025 TCATTGATTTGTGAACCCCTGAAAA 59.635 36.000 0.00 0.00 0.00 2.29
2543 2601 3.171528 TGGATGTGGCAAAATCCATTGA 58.828 40.909 22.81 6.60 45.86 2.57
2544 2602 3.613494 TGGATGTGGCAAAATCCATTG 57.387 42.857 22.81 0.00 45.86 2.82
2581 2639 0.255890 TAAATCCCCAGCTGACAGCC 59.744 55.000 23.74 6.31 43.77 4.85
2612 2670 4.591321 TGTAGAATGGGGCAAGAAATCT 57.409 40.909 0.00 0.00 0.00 2.40
2631 2689 8.889717 CGGTGAATAATGGTTTAGTAGAAATGT 58.110 33.333 0.00 0.00 0.00 2.71
2632 2690 9.104965 TCGGTGAATAATGGTTTAGTAGAAATG 57.895 33.333 0.00 0.00 0.00 2.32
2633 2691 9.675464 TTCGGTGAATAATGGTTTAGTAGAAAT 57.325 29.630 0.00 0.00 0.00 2.17
2634 2692 9.158233 CTTCGGTGAATAATGGTTTAGTAGAAA 57.842 33.333 0.00 0.00 0.00 2.52
2635 2693 8.316214 ACTTCGGTGAATAATGGTTTAGTAGAA 58.684 33.333 0.00 0.00 0.00 2.10
2711 2769 6.128822 GCAGGCAAAATAAAAGAACTGTTAGC 60.129 38.462 0.00 0.00 0.00 3.09
2712 2770 6.922957 TGCAGGCAAAATAAAAGAACTGTTAG 59.077 34.615 0.00 0.00 0.00 2.34
2733 2791 7.760794 TGGCAGATTCAAAAATAAATAGTGCAG 59.239 33.333 0.00 0.00 31.30 4.41
2797 2860 1.494721 AGTCTTGGAAGGCTTGGAACA 59.505 47.619 3.46 0.00 37.85 3.18
2810 2873 7.984050 ACATGTGATGATTTAGTCTAGTCTTGG 59.016 37.037 0.00 0.00 0.00 3.61
2841 2904 3.491447 GCAACTGCTTTTGAACCTGACAT 60.491 43.478 2.42 0.00 38.21 3.06
3064 3127 1.620822 GATTCAAACCCTGGCTGTGT 58.379 50.000 0.00 0.00 0.00 3.72
3093 3156 0.033208 GTTCTTGATCCCATGGGCCA 60.033 55.000 27.41 22.10 34.68 5.36
3285 3349 0.250901 AAGGTCCAAACAGCGCTCAT 60.251 50.000 7.13 0.00 0.00 2.90
3291 3355 2.746362 CAGATCTGAAGGTCCAAACAGC 59.254 50.000 18.34 0.00 0.00 4.40
3306 3370 1.544917 AAGGGGTTGGGGCAGATCT 60.545 57.895 0.00 0.00 0.00 2.75
3470 3534 1.062002 CCTTGGTATTGCGTGTAAGCG 59.938 52.381 0.00 0.00 40.67 4.68
3508 3572 7.093289 ACAGAAATGTACAACTACCAGATAGCT 60.093 37.037 0.00 0.00 33.73 3.32
3536 3600 6.818644 GGTAAGCAGATTCAATGACTGAACTA 59.181 38.462 5.21 0.00 46.80 2.24
3576 3640 3.144506 CAACATCCCAGATCTATGGCAC 58.855 50.000 8.48 0.00 39.17 5.01
3626 3690 2.158593 TGCAAAGTTACCCAGTAGCCAA 60.159 45.455 0.00 0.00 0.00 4.52
3629 3693 4.783764 AAATGCAAAGTTACCCAGTAGC 57.216 40.909 0.00 0.00 0.00 3.58
3637 3701 5.151389 CCAACCTCGTAAATGCAAAGTTAC 58.849 41.667 0.00 0.00 0.00 2.50
3639 3703 3.634910 ACCAACCTCGTAAATGCAAAGTT 59.365 39.130 0.00 0.00 0.00 2.66
3643 3707 2.952978 ACAACCAACCTCGTAAATGCAA 59.047 40.909 0.00 0.00 0.00 4.08
3667 3731 2.386829 ATCCCCCAATATGGCAACTG 57.613 50.000 0.00 0.00 35.79 3.16
3669 3733 3.421844 GACTATCCCCCAATATGGCAAC 58.578 50.000 0.00 0.00 35.79 4.17
3739 3803 9.326413 AGTAACAAAATATGCTACTGTATGGAC 57.674 33.333 0.00 0.00 39.03 4.02
3804 3887 4.450419 GTCATTATGAGCACCACTAGCATC 59.550 45.833 0.00 0.00 0.00 3.91
3821 3904 6.381498 TTCTCAACCCAAGGTATGTCATTA 57.619 37.500 0.00 0.00 33.12 1.90
3856 3958 8.934023 AGCTATCTGATCTTTTACTAGCTACT 57.066 34.615 5.70 0.00 38.82 2.57
3928 4030 3.509575 GCATCCACCTCCACAAAATGTAA 59.490 43.478 0.00 0.00 0.00 2.41
3929 4031 3.088532 GCATCCACCTCCACAAAATGTA 58.911 45.455 0.00 0.00 0.00 2.29
3936 4038 0.770499 TCAAAGCATCCACCTCCACA 59.230 50.000 0.00 0.00 0.00 4.17
3955 4057 0.460635 GAACGGCCAAATGCATGCAT 60.461 50.000 27.46 27.46 43.89 3.96
3957 4059 2.160221 CGAACGGCCAAATGCATGC 61.160 57.895 11.82 11.82 43.89 4.06
3975 4077 2.618709 GCTGTGGGTTATTATCTGGCAC 59.381 50.000 0.00 0.00 0.00 5.01
3990 4092 1.280746 CAGAAACGCACAGCTGTGG 59.719 57.895 39.92 31.82 45.72 4.17
4030 4132 0.249953 TGTGCTGGCAAATGCTTTGG 60.250 50.000 5.25 0.00 40.94 3.28
4046 4148 7.856145 AAATAGTTGCCTAGAAGAGAATGTG 57.144 36.000 0.00 0.00 0.00 3.21
4076 4178 5.798125 TCCAAACATTGCCTTGACAATAA 57.202 34.783 0.00 0.00 38.19 1.40
4079 4181 4.100653 TCAATCCAAACATTGCCTTGACAA 59.899 37.500 1.63 0.00 34.26 3.18
4081 4183 4.240096 CTCAATCCAAACATTGCCTTGAC 58.760 43.478 1.63 0.00 34.26 3.18
4083 4185 3.592059 CCTCAATCCAAACATTGCCTTG 58.408 45.455 0.00 0.00 34.26 3.61
4113 4216 1.067142 ACATGGCTTTGAGCTGCAATG 60.067 47.619 9.09 9.09 43.98 2.82
4136 4239 2.754946 ACCGCCGTTCTTATCAAAGA 57.245 45.000 0.00 0.00 40.03 2.52
4137 4240 5.050567 GGTTATACCGCCGTTCTTATCAAAG 60.051 44.000 0.00 0.00 0.00 2.77
4140 4243 3.638160 AGGTTATACCGCCGTTCTTATCA 59.362 43.478 0.00 0.00 44.90 2.15
4141 4244 4.233005 GAGGTTATACCGCCGTTCTTATC 58.767 47.826 0.00 0.00 44.90 1.75
4142 4245 3.304928 CGAGGTTATACCGCCGTTCTTAT 60.305 47.826 0.00 0.00 44.90 1.73
4143 4246 2.033299 CGAGGTTATACCGCCGTTCTTA 59.967 50.000 0.00 0.00 44.90 2.10
4144 4247 1.202336 CGAGGTTATACCGCCGTTCTT 60.202 52.381 0.00 0.00 44.90 2.52
4145 4248 0.383231 CGAGGTTATACCGCCGTTCT 59.617 55.000 0.00 0.00 44.90 3.01
4146 4249 1.211181 GCGAGGTTATACCGCCGTTC 61.211 60.000 12.57 0.00 44.90 3.95
4147 4250 1.227060 GCGAGGTTATACCGCCGTT 60.227 57.895 12.57 0.00 44.90 4.44
4148 4251 2.414594 GCGAGGTTATACCGCCGT 59.585 61.111 12.57 0.00 44.90 5.68


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

AutoCloner maintained by Alex Coulton.