Multiple sequence alignment - TraesCS3D01G003000

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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 TraesCS3D01G003000 chr3D 100.000 2817 0 0 1 2817 1298871 1296055 0.000000e+00 5203
1 TraesCS3D01G003000 chrUn 88.548 1921 103 50 560 2421 34530189 34528327 0.000000e+00 2220
2 TraesCS3D01G003000 chrUn 77.990 418 33 22 2418 2816 34528282 34527905 1.020000e-49 207
3 TraesCS3D01G003000 chr3A 90.902 1220 77 12 845 2045 7781429 7782633 0.000000e+00 1607
4 TraesCS3D01G003000 chr3A 82.312 718 50 33 2089 2771 7782729 7783404 4.100000e-153 551
5 TraesCS3D01G003000 chr3A 82.289 463 52 16 1 454 7780428 7780869 9.530000e-100 374
6 TraesCS3D01G003000 chr3A 95.506 89 4 0 694 782 7781125 7781213 2.930000e-30 143


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 TraesCS3D01G003000 chr3D 1296055 1298871 2816 True 5203.00 5203 100.00000 1 2817 1 chr3D.!!$R1 2816
1 TraesCS3D01G003000 chrUn 34527905 34530189 2284 True 1213.50 2220 83.26900 560 2816 2 chrUn.!!$R1 2256
2 TraesCS3D01G003000 chr3A 7780428 7783404 2976 False 668.75 1607 87.75225 1 2771 4 chr3A.!!$F1 2770

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
523 533 0.031043 TCGAGCGGAGTGTTTTTCGA 59.969 50.0 0.0 0.0 35.05 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 2872 0.638746 GTGTGCATGTACGTACTCGC 59.361 55.0 25.12 24.6 41.18 5.03 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
46 47 4.847367 CCCCTTGCCCCTGCCATC 62.847 72.222 0.00 0.00 36.33 3.51
48 49 4.113815 CCTTGCCCCTGCCATCGA 62.114 66.667 0.00 0.00 36.33 3.59
50 51 4.776322 TTGCCCCTGCCATCGACG 62.776 66.667 0.00 0.00 36.33 5.12
53 54 3.770040 CCCCTGCCATCGACGACA 61.770 66.667 0.00 0.00 0.00 4.35
55 56 2.887568 CCTGCCATCGACGACAGC 60.888 66.667 12.71 12.71 0.00 4.40
56 57 3.250323 CTGCCATCGACGACAGCG 61.250 66.667 14.19 7.20 44.79 5.18
86 93 1.806568 GCTGAGAGACCACTCCTCG 59.193 63.158 0.00 0.00 43.53 4.63
116 123 3.073735 AGCTCCCTGTCGAGGCAG 61.074 66.667 0.00 0.00 38.17 4.85
123 130 1.213013 CTGTCGAGGCAGCGTAGTT 59.787 57.895 0.00 0.00 0.00 2.24
141 148 0.737367 TTGTCGCATGCTCGAAGGAG 60.737 55.000 17.13 0.00 43.46 3.69
151 158 4.060038 TGCTCGAAGGAGATTACAATCC 57.940 45.455 0.00 0.00 43.27 3.01
193 203 3.721706 CTGTGGAGGTGGAGGGGC 61.722 72.222 0.00 0.00 0.00 5.80
205 215 4.095400 AGGGGCCGGGAGAGTGAT 62.095 66.667 2.18 0.00 0.00 3.06
212 222 1.360551 CGGGAGAGTGATAGTGGCG 59.639 63.158 0.00 0.00 0.00 5.69
229 239 2.598632 CGGCGCCAAGATTCGGATC 61.599 63.158 28.98 0.00 0.00 3.36
233 243 0.104855 CGCCAAGATTCGGATCTGGA 59.895 55.000 20.27 0.00 41.78 3.86
236 246 2.547642 GCCAAGATTCGGATCTGGAGAG 60.548 54.545 20.27 3.16 41.78 3.20
252 262 4.841617 AGAGATCCGGAGCCGCCA 62.842 66.667 17.84 0.00 38.24 5.69
253 263 3.620785 GAGATCCGGAGCCGCCAT 61.621 66.667 17.84 0.00 38.24 4.40
271 281 1.134995 CATCTGCTGGCGTAGAGAACA 60.135 52.381 4.01 0.00 35.30 3.18
273 283 1.071605 CTGCTGGCGTAGAGAACAAC 58.928 55.000 0.00 0.00 0.00 3.32
289 299 1.070786 AACGACTTCGGCATGGTGT 59.929 52.632 3.30 0.00 44.95 4.16
290 300 0.534203 AACGACTTCGGCATGGTGTT 60.534 50.000 3.30 0.00 44.95 3.32
292 302 0.948623 CGACTTCGGCATGGTGTTGA 60.949 55.000 0.00 0.00 35.37 3.18
293 303 0.517316 GACTTCGGCATGGTGTTGAC 59.483 55.000 0.00 0.00 0.00 3.18
296 306 4.101790 CGGCATGGTGTTGACGGC 62.102 66.667 0.00 0.00 44.46 5.68
297 307 4.101790 GGCATGGTGTTGACGGCG 62.102 66.667 4.80 4.80 0.00 6.46
299 309 4.101790 CATGGTGTTGACGGCGCC 62.102 66.667 19.07 19.07 37.06 6.53
319 329 4.445699 AGCTGTGCTTATAGGCGC 57.554 55.556 13.08 13.08 42.34 6.53
320 330 1.592669 AGCTGTGCTTATAGGCGCG 60.593 57.895 14.73 0.00 44.60 6.86
321 331 1.591594 GCTGTGCTTATAGGCGCGA 60.592 57.895 12.10 4.58 44.60 5.87
324 334 1.227147 GTGCTTATAGGCGCGACCA 60.227 57.895 9.25 0.00 43.14 4.02
369 379 0.739813 AATGCGGCGACTGGAGTAAC 60.740 55.000 12.98 0.00 0.00 2.50
385 395 2.981909 ACCTTCTCGGTCGTCGCA 60.982 61.111 0.00 0.00 44.93 5.10
386 396 2.504244 CCTTCTCGGTCGTCGCAC 60.504 66.667 0.00 0.00 39.05 5.34
394 404 2.507547 GTCGTCGCACCGGCATTA 60.508 61.111 0.00 0.00 41.24 1.90
398 408 1.226295 GTCGCACCGGCATTAAAGC 60.226 57.895 0.00 0.00 41.24 3.51
399 409 2.277247 CGCACCGGCATTAAAGCG 60.277 61.111 0.00 2.30 41.24 4.68
400 410 2.874751 GCACCGGCATTAAAGCGT 59.125 55.556 0.00 0.00 40.72 5.07
454 464 2.745821 CCGGCATCAATATCATGGAGTG 59.254 50.000 0.00 0.00 0.00 3.51
459 469 5.123502 GGCATCAATATCATGGAGTGATGTC 59.876 44.000 25.80 23.11 46.85 3.06
460 470 5.123502 GCATCAATATCATGGAGTGATGTCC 59.876 44.000 25.80 14.92 46.85 4.02
461 471 4.886579 TCAATATCATGGAGTGATGTCCG 58.113 43.478 0.00 0.00 46.85 4.79
462 472 2.820059 TATCATGGAGTGATGTCCGC 57.180 50.000 0.00 0.00 46.85 5.54
463 473 1.126488 ATCATGGAGTGATGTCCGCT 58.874 50.000 0.00 0.00 45.76 5.52
464 474 1.069823 ATCATGGAGTGATGTCCGCTC 59.930 52.381 0.00 0.00 45.76 5.03
465 475 4.005113 TATCATGGAGTGATGTCCGCTCT 61.005 47.826 0.00 0.00 46.85 4.09
466 476 4.749785 TATCATGGAGTGATGTCCGCTCTA 60.750 45.833 0.00 0.00 46.85 2.43
467 477 6.550870 TATCATGGAGTGATGTCCGCTCTAG 61.551 48.000 0.00 0.00 46.85 2.43
468 478 8.658330 TATCATGGAGTGATGTCCGCTCTAGA 62.658 46.154 0.00 0.00 46.85 2.43
478 488 3.201494 GCTCTAGAGCGGCACTGA 58.799 61.111 28.04 5.06 45.29 3.41
479 489 1.226831 GCTCTAGAGCGGCACTGAC 60.227 63.158 28.04 0.70 45.29 3.51
480 490 1.063327 CTCTAGAGCGGCACTGACG 59.937 63.158 6.86 0.00 36.98 4.35
481 491 1.369839 CTCTAGAGCGGCACTGACGA 61.370 60.000 8.96 3.50 35.20 4.20
482 492 1.063327 CTAGAGCGGCACTGACGAG 59.937 63.158 8.96 0.00 35.20 4.18
483 493 2.928313 CTAGAGCGGCACTGACGAGC 62.928 65.000 8.96 0.00 35.20 5.03
485 495 3.997064 GAGCGGCACTGACGAGCAT 62.997 63.158 8.96 0.00 35.20 3.79
486 496 3.857854 GCGGCACTGACGAGCATG 61.858 66.667 8.96 0.00 35.20 4.06
487 497 3.190849 CGGCACTGACGAGCATGG 61.191 66.667 0.00 0.00 35.20 3.66
490 500 0.745845 GGCACTGACGAGCATGGATT 60.746 55.000 0.00 0.00 0.00 3.01
493 503 1.089920 ACTGACGAGCATGGATTTGC 58.910 50.000 0.00 0.00 43.09 3.68
500 510 3.034569 GCATGGATTTGCGACAACC 57.965 52.632 0.00 0.00 32.06 3.77
501 511 0.243365 GCATGGATTTGCGACAACCA 59.757 50.000 0.00 0.00 32.06 3.67
502 512 1.981254 CATGGATTTGCGACAACCAC 58.019 50.000 0.00 0.00 33.38 4.16
503 513 1.541147 CATGGATTTGCGACAACCACT 59.459 47.619 0.00 0.00 33.38 4.00
504 514 1.686355 TGGATTTGCGACAACCACTT 58.314 45.000 0.00 0.00 0.00 3.16
506 516 1.399727 GGATTTGCGACAACCACTTCG 60.400 52.381 0.00 0.00 38.31 3.79
507 517 1.529438 GATTTGCGACAACCACTTCGA 59.471 47.619 0.00 0.00 37.43 3.71
508 518 0.934496 TTTGCGACAACCACTTCGAG 59.066 50.000 0.00 0.00 37.43 4.04
509 519 1.495584 TTGCGACAACCACTTCGAGC 61.496 55.000 0.00 0.00 37.43 5.03
510 520 3.000080 GCGACAACCACTTCGAGCG 62.000 63.158 0.00 0.00 37.43 5.03
511 521 2.372690 CGACAACCACTTCGAGCGG 61.373 63.158 0.00 0.00 37.43 5.52
512 522 1.006571 GACAACCACTTCGAGCGGA 60.007 57.895 4.07 0.00 0.00 5.54
514 524 1.006102 CAACCACTTCGAGCGGAGT 60.006 57.895 0.00 0.00 0.00 3.85
515 525 1.006102 AACCACTTCGAGCGGAGTG 60.006 57.895 21.31 21.31 0.00 3.51
516 526 1.745320 AACCACTTCGAGCGGAGTGT 61.745 55.000 24.81 13.35 0.00 3.55
517 527 1.006102 CCACTTCGAGCGGAGTGTT 60.006 57.895 24.81 0.00 0.00 3.32
518 528 0.600255 CCACTTCGAGCGGAGTGTTT 60.600 55.000 24.81 0.00 0.00 2.83
519 529 1.217882 CACTTCGAGCGGAGTGTTTT 58.782 50.000 20.28 0.00 0.00 2.43
521 531 1.865340 ACTTCGAGCGGAGTGTTTTTC 59.135 47.619 2.51 0.00 0.00 2.29
522 532 0.856641 TTCGAGCGGAGTGTTTTTCG 59.143 50.000 0.00 0.00 0.00 3.46
523 533 0.031043 TCGAGCGGAGTGTTTTTCGA 59.969 50.000 0.00 0.00 35.05 3.71
524 534 0.435008 CGAGCGGAGTGTTTTTCGAG 59.565 55.000 0.00 0.00 0.00 4.04
525 535 0.164002 GAGCGGAGTGTTTTTCGAGC 59.836 55.000 0.00 0.00 0.00 5.03
526 536 1.154654 GCGGAGTGTTTTTCGAGCG 60.155 57.895 0.00 0.00 0.00 5.03
529 539 1.136611 CGGAGTGTTTTTCGAGCGAAG 60.137 52.381 5.42 0.00 35.38 3.79
530 540 2.132762 GGAGTGTTTTTCGAGCGAAGA 58.867 47.619 5.42 0.00 35.38 2.87
533 543 1.865340 GTGTTTTTCGAGCGAAGAGGT 59.135 47.619 5.42 0.00 35.38 3.85
535 545 2.940410 TGTTTTTCGAGCGAAGAGGTTT 59.060 40.909 5.42 0.00 35.38 3.27
537 547 4.142556 TGTTTTTCGAGCGAAGAGGTTTTT 60.143 37.500 5.42 0.00 35.38 1.94
539 549 1.508632 TCGAGCGAAGAGGTTTTTGG 58.491 50.000 0.00 0.00 0.00 3.28
541 551 1.605753 GAGCGAAGAGGTTTTTGGGT 58.394 50.000 0.00 0.00 0.00 4.51
542 552 1.266989 GAGCGAAGAGGTTTTTGGGTG 59.733 52.381 0.00 0.00 0.00 4.61
543 553 1.029681 GCGAAGAGGTTTTTGGGTGT 58.970 50.000 0.00 0.00 0.00 4.16
544 554 1.269051 GCGAAGAGGTTTTTGGGTGTG 60.269 52.381 0.00 0.00 0.00 3.82
546 556 2.032924 CGAAGAGGTTTTTGGGTGTGTC 59.967 50.000 0.00 0.00 0.00 3.67
547 557 2.067365 AGAGGTTTTTGGGTGTGTCC 57.933 50.000 0.00 0.00 0.00 4.02
548 558 0.666374 GAGGTTTTTGGGTGTGTCCG 59.334 55.000 0.00 0.00 37.00 4.79
549 559 0.256464 AGGTTTTTGGGTGTGTCCGA 59.744 50.000 0.00 0.00 37.00 4.55
550 560 0.666374 GGTTTTTGGGTGTGTCCGAG 59.334 55.000 0.00 0.00 37.00 4.63
551 561 0.666374 GTTTTTGGGTGTGTCCGAGG 59.334 55.000 0.00 0.00 37.00 4.63
552 562 0.256464 TTTTTGGGTGTGTCCGAGGT 59.744 50.000 0.00 0.00 37.00 3.85
553 563 0.464735 TTTTGGGTGTGTCCGAGGTG 60.465 55.000 0.00 0.00 37.00 4.00
554 564 1.628238 TTTGGGTGTGTCCGAGGTGT 61.628 55.000 0.00 0.00 37.00 4.16
555 565 2.035237 TTGGGTGTGTCCGAGGTGTC 62.035 60.000 0.00 0.00 37.00 3.67
556 566 2.504274 GGGTGTGTCCGAGGTGTCA 61.504 63.158 0.00 0.00 37.00 3.58
558 568 0.179067 GGTGTGTCCGAGGTGTCAAA 60.179 55.000 0.00 0.00 0.00 2.69
564 574 1.372004 CCGAGGTGTCAAACGCGTA 60.372 57.895 14.46 0.00 0.00 4.42
576 586 4.082192 CGCGTACGTGGTAGCATT 57.918 55.556 20.84 0.00 33.53 3.56
579 589 0.458889 GCGTACGTGGTAGCATTCCA 60.459 55.000 17.90 0.00 0.00 3.53
596 606 1.379044 CAGATGCCCACAAGTCCCC 60.379 63.158 0.00 0.00 0.00 4.81
599 609 3.590466 ATGCCCACAAGTCCCCTGC 62.590 63.158 0.00 0.00 0.00 4.85
604 614 1.662044 CACAAGTCCCCTGCTTTGC 59.338 57.895 0.00 0.00 0.00 3.68
623 633 1.398390 GCACCAGGTTTGCGAGATTAG 59.602 52.381 0.00 0.00 0.00 1.73
630 640 4.396166 CAGGTTTGCGAGATTAGGAACAAT 59.604 41.667 0.00 0.00 0.00 2.71
642 652 6.241648 GATTAGGAACAATCAGACCGGTACG 61.242 48.000 7.34 0.51 42.13 3.67
658 675 2.095364 GGTACGCGGGTAGATGATGTAG 60.095 54.545 13.20 0.00 0.00 2.74
662 679 2.812591 CGCGGGTAGATGATGTAGTACT 59.187 50.000 0.00 0.00 0.00 2.73
663 680 3.999001 CGCGGGTAGATGATGTAGTACTA 59.001 47.826 0.00 0.00 0.00 1.82
664 681 4.453478 CGCGGGTAGATGATGTAGTACTAA 59.547 45.833 3.61 0.00 0.00 2.24
665 682 5.390673 CGCGGGTAGATGATGTAGTACTAAG 60.391 48.000 3.61 0.00 0.00 2.18
666 683 5.472820 GCGGGTAGATGATGTAGTACTAAGT 59.527 44.000 3.61 0.00 0.00 2.24
667 684 6.016443 GCGGGTAGATGATGTAGTACTAAGTT 60.016 42.308 3.61 0.00 0.00 2.66
668 685 7.361127 CGGGTAGATGATGTAGTACTAAGTTG 58.639 42.308 3.61 0.00 0.00 3.16
669 686 7.521748 CGGGTAGATGATGTAGTACTAAGTTGG 60.522 44.444 3.61 0.00 0.00 3.77
683 700 1.463674 AGTTGGATTGGATGGCGAAC 58.536 50.000 0.00 0.00 0.00 3.95
703 737 1.607178 TCCGGACGGCTTTACAGGA 60.607 57.895 0.00 0.00 34.68 3.86
715 749 3.253432 GCTTTACAGGAGTTTTGAGGGTG 59.747 47.826 0.00 0.00 0.00 4.61
723 757 1.963515 AGTTTTGAGGGTGTGGATTGC 59.036 47.619 0.00 0.00 0.00 3.56
910 1129 7.705912 TTCCATCCTCCTCTCCAATTATAAA 57.294 36.000 0.00 0.00 0.00 1.40
973 1197 1.517832 CCCTCACGTCTCCATCACC 59.482 63.158 0.00 0.00 0.00 4.02
975 1199 0.898320 CCTCACGTCTCCATCACCTT 59.102 55.000 0.00 0.00 0.00 3.50
978 1202 3.017442 CTCACGTCTCCATCACCTTCTA 58.983 50.000 0.00 0.00 0.00 2.10
1043 1267 0.618968 ACACTCCCACTCCCATCTCC 60.619 60.000 0.00 0.00 0.00 3.71
1051 1275 0.117140 ACTCCCATCTCCCTCACACA 59.883 55.000 0.00 0.00 0.00 3.72
1081 1321 2.680352 GCACTCCCGTCCCTCTCA 60.680 66.667 0.00 0.00 0.00 3.27
1082 1322 2.716017 GCACTCCCGTCCCTCTCAG 61.716 68.421 0.00 0.00 0.00 3.35
1083 1323 2.055042 CACTCCCGTCCCTCTCAGG 61.055 68.421 0.00 0.00 34.30 3.86
1084 1324 2.360980 CTCCCGTCCCTCTCAGGT 59.639 66.667 0.00 0.00 31.93 4.00
1085 1325 1.755008 CTCCCGTCCCTCTCAGGTC 60.755 68.421 0.00 0.00 31.93 3.85
1086 1326 2.218115 CTCCCGTCCCTCTCAGGTCT 62.218 65.000 0.00 0.00 31.93 3.85
1087 1327 1.755008 CCCGTCCCTCTCAGGTCTC 60.755 68.421 0.00 0.00 31.93 3.36
1088 1328 1.000771 CCGTCCCTCTCAGGTCTCA 60.001 63.158 0.00 0.00 31.93 3.27
1097 1344 1.907222 CTCAGGTCTCAGCCATGGCA 61.907 60.000 37.18 18.01 44.88 4.92
1121 1368 1.227205 CAGGCTGCTCGTGATCCTC 60.227 63.158 0.00 0.00 32.56 3.71
1382 1629 2.284331 TTCTACCAGCCTCCCGCA 60.284 61.111 0.00 0.00 41.38 5.69
1383 1630 1.899437 CTTCTACCAGCCTCCCGCAA 61.899 60.000 0.00 0.00 41.38 4.85
1563 1822 2.183300 CCGTAACTGCCGCTGCTA 59.817 61.111 0.70 0.00 38.71 3.49
1582 1841 1.844687 ACCCTGGTCGGTTACTAGTC 58.155 55.000 0.00 0.00 34.98 2.59
1593 1852 4.144534 GGTTACTAGTCCGATCATCGAC 57.855 50.000 9.16 5.09 43.74 4.20
1602 1865 2.357952 TCCGATCATCGACCAGTTACTG 59.642 50.000 9.16 5.22 43.74 2.74
1629 1896 3.084786 GCTAGCACTCCCACATTTTTCT 58.915 45.455 10.63 0.00 0.00 2.52
1840 2110 4.380974 GCAAGAATCTTGTGCTTTTTCTCG 59.619 41.667 22.28 0.00 35.36 4.04
1919 2193 4.116961 CGATCGTTGCTATTACTTTCCCA 58.883 43.478 7.03 0.00 0.00 4.37
1920 2194 4.750098 CGATCGTTGCTATTACTTTCCCAT 59.250 41.667 7.03 0.00 0.00 4.00
1921 2195 5.236478 CGATCGTTGCTATTACTTTCCCATT 59.764 40.000 7.03 0.00 0.00 3.16
1922 2196 6.238374 CGATCGTTGCTATTACTTTCCCATTT 60.238 38.462 7.03 0.00 0.00 2.32
1923 2197 6.431198 TCGTTGCTATTACTTTCCCATTTC 57.569 37.500 0.00 0.00 0.00 2.17
1924 2198 5.355910 TCGTTGCTATTACTTTCCCATTTCC 59.644 40.000 0.00 0.00 0.00 3.13
1925 2199 5.449999 CGTTGCTATTACTTTCCCATTTCCC 60.450 44.000 0.00 0.00 0.00 3.97
1965 2239 1.072666 CGCGTACTACGTTTGGTCCC 61.073 60.000 10.23 0.00 44.73 4.46
1973 2247 2.880963 ACGTTTGGTCCCAACATTTG 57.119 45.000 6.64 0.00 35.46 2.32
2014 2288 1.873591 ACTCGCTTGTTGGAATGACAC 59.126 47.619 0.00 0.00 0.00 3.67
2015 2289 0.865111 TCGCTTGTTGGAATGACACG 59.135 50.000 0.00 0.00 0.00 4.49
2016 2290 0.865111 CGCTTGTTGGAATGACACGA 59.135 50.000 0.00 0.00 0.00 4.35
2017 2291 1.464608 CGCTTGTTGGAATGACACGAT 59.535 47.619 0.00 0.00 0.00 3.73
2030 2304 2.159379 TGACACGATCGAGTGATTGAGG 60.159 50.000 22.89 1.14 44.43 3.86
2100 2425 1.662309 CGATCCACGTACATACTCGCC 60.662 57.143 0.00 0.00 37.22 5.54
2164 2490 8.413309 TGTAGAAGCTAGTACTAGTTTTCCAA 57.587 34.615 26.65 18.49 36.86 3.53
2249 2583 3.674682 CGTGACTTGCAACTTCCCAAAAA 60.675 43.478 0.00 0.00 0.00 1.94
2250 2584 3.865164 GTGACTTGCAACTTCCCAAAAAG 59.135 43.478 0.00 0.00 0.00 2.27
2263 2597 1.758783 CAAAAAGTGGAGAGCGTTGC 58.241 50.000 0.00 0.00 0.00 4.17
2264 2598 0.307760 AAAAAGTGGAGAGCGTTGCG 59.692 50.000 0.00 0.00 0.00 4.85
2265 2599 0.531974 AAAAGTGGAGAGCGTTGCGA 60.532 50.000 0.00 0.00 0.00 5.10
2362 2701 5.584251 AGAATCGATCAGAAAAGAGGAAAGC 59.416 40.000 0.00 0.00 0.00 3.51
2363 2702 3.254060 TCGATCAGAAAAGAGGAAAGCG 58.746 45.455 0.00 0.00 0.00 4.68
2386 2727 2.665000 GCAGGTCACAGCTGGCTA 59.335 61.111 19.93 0.00 43.49 3.93
2387 2728 1.222936 GCAGGTCACAGCTGGCTAT 59.777 57.895 19.93 0.00 43.49 2.97
2439 2828 2.366590 ACTGTCATGCTGAGTGAGTGAA 59.633 45.455 0.00 0.00 0.00 3.18
2444 2833 3.260128 TCATGCTGAGTGAGTGAATGAGT 59.740 43.478 0.00 0.00 0.00 3.41
2449 2838 4.439974 GCTGAGTGAGTGAATGAGTAGGAG 60.440 50.000 0.00 0.00 0.00 3.69
2453 2842 4.099266 AGTGAGTGAATGAGTAGGAGCATC 59.901 45.833 0.00 0.00 0.00 3.91
2464 2853 2.824546 GAGCATCCGAGCATCCCA 59.175 61.111 0.00 0.00 36.85 4.37
2465 2854 1.374190 GAGCATCCGAGCATCCCAT 59.626 57.895 0.00 0.00 36.85 4.00
2466 2855 0.954449 GAGCATCCGAGCATCCCATG 60.954 60.000 0.00 0.00 36.85 3.66
2483 2872 1.544246 CATGCATGCATCATGGTAGGG 59.456 52.381 30.07 12.02 41.64 3.53
2500 2892 1.143969 GGGCGAGTACGTACATGCAC 61.144 60.000 30.49 27.01 41.98 4.57
2524 2916 2.320587 CGTGTCCAAGAGCAGGTGC 61.321 63.158 0.00 0.00 42.49 5.01
2529 2921 1.200948 GTCCAAGAGCAGGTGCATTTC 59.799 52.381 4.48 0.00 45.16 2.17
2530 2922 1.202915 TCCAAGAGCAGGTGCATTTCA 60.203 47.619 4.48 0.00 45.16 2.69
2533 2925 0.250467 AGAGCAGGTGCATTTCACGT 60.250 50.000 4.48 0.00 46.56 4.49
2537 2931 2.031157 AGCAGGTGCATTTCACGTAAAC 60.031 45.455 4.48 0.00 46.56 2.01
2549 2944 8.015658 GCATTTCACGTAAACAAGAAGAAGTAT 58.984 33.333 0.00 0.00 0.00 2.12
2550 2945 9.878599 CATTTCACGTAAACAAGAAGAAGTATT 57.121 29.630 0.00 0.00 0.00 1.89
2553 2948 9.970395 TTCACGTAAACAAGAAGAAGTATTAGA 57.030 29.630 0.00 0.00 0.00 2.10
2556 2951 8.870879 ACGTAAACAAGAAGAAGTATTAGATGC 58.129 33.333 0.00 0.00 0.00 3.91
2557 2952 8.050750 CGTAAACAAGAAGAAGTATTAGATGCG 58.949 37.037 0.00 0.00 0.00 4.73
2558 2953 5.975410 ACAAGAAGAAGTATTAGATGCGC 57.025 39.130 0.00 0.00 0.00 6.09
2559 2954 5.419542 ACAAGAAGAAGTATTAGATGCGCA 58.580 37.500 14.96 14.96 0.00 6.09
2576 2979 1.132436 CATGTGCGTACGTTGGCTG 59.868 57.895 17.90 5.00 0.00 4.85
2581 2984 2.860293 CGTACGTTGGCTGCTTGG 59.140 61.111 7.22 0.00 0.00 3.61
2613 3034 4.295119 GTCCACCGACACCGCACT 62.295 66.667 0.00 0.00 38.99 4.40
2647 3077 2.159973 CGTCGCAACTAACACATCACAG 60.160 50.000 0.00 0.00 0.00 3.66
2716 3146 0.530744 TGCTCGTCAAACTAGCCGAT 59.469 50.000 1.74 0.00 36.22 4.18
2717 3147 1.746787 TGCTCGTCAAACTAGCCGATA 59.253 47.619 1.74 0.00 36.22 2.92
2720 3150 3.802685 GCTCGTCAAACTAGCCGATAATT 59.197 43.478 0.00 0.00 31.50 1.40
2721 3151 4.085004 GCTCGTCAAACTAGCCGATAATTC 60.085 45.833 0.00 0.00 31.50 2.17
2767 3201 2.112815 GCTTGCTAATCCCGCCGTT 61.113 57.895 0.00 0.00 0.00 4.44
2776 3210 2.561478 ATCCCGCCGTTTTAGCATAT 57.439 45.000 0.00 0.00 0.00 1.78
2786 3220 5.909610 GCCGTTTTAGCATATCTGATGAAAC 59.090 40.000 6.65 6.65 41.31 2.78
2799 3233 5.329493 TCTGATGAAACGTACGTAGTCATG 58.671 41.667 34.34 25.60 43.93 3.07
2816 3250 5.687780 AGTCATGCATCATGGAGTTATCAA 58.312 37.500 0.00 0.00 41.66 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.661648 GGCAAGGGGAAGGCTCCA 61.662 66.667 0.00 0.00 44.51 3.86
29 30 4.847367 GATGGCAGGGGCAAGGGG 62.847 72.222 0.00 0.00 42.43 4.79
44 45 4.692129 GACATCGCTGTCGTCGAT 57.308 55.556 3.30 0.00 46.27 3.59
86 93 0.109504 GGGAGCTCGCTATGATCGAC 60.110 60.000 22.62 0.00 32.08 4.20
123 130 1.153765 CTCCTTCGAGCATGCGACA 60.154 57.895 13.01 0.00 40.42 4.35
129 136 4.503991 GGGATTGTAATCTCCTTCGAGCAT 60.504 45.833 4.75 0.00 35.94 3.79
141 148 2.300437 CGAGGAGGAGGGGATTGTAATC 59.700 54.545 0.00 0.00 34.66 1.75
173 183 4.087892 CCTCCACCTCCACAGCGG 62.088 72.222 0.00 0.00 0.00 5.52
188 198 2.664835 CTATCACTCTCCCGGCCCCT 62.665 65.000 0.00 0.00 0.00 4.79
193 203 1.742768 GCCACTATCACTCTCCCGG 59.257 63.158 0.00 0.00 0.00 5.73
196 206 1.068250 GCCGCCACTATCACTCTCC 59.932 63.158 0.00 0.00 0.00 3.71
212 222 1.227674 AGATCCGAATCTTGGCGCC 60.228 57.895 22.73 22.73 39.27 6.53
229 239 1.178534 GGCTCCGGATCTCTCTCCAG 61.179 65.000 3.57 0.00 34.78 3.86
233 243 2.909965 GCGGCTCCGGATCTCTCT 60.910 66.667 3.57 0.00 40.19 3.10
236 246 3.581687 GATGGCGGCTCCGGATCTC 62.582 68.421 3.57 0.00 40.19 2.75
252 262 1.186200 TGTTCTCTACGCCAGCAGAT 58.814 50.000 0.00 0.00 0.00 2.90
253 263 0.966179 TTGTTCTCTACGCCAGCAGA 59.034 50.000 0.00 0.00 0.00 4.26
259 269 1.984297 GAAGTCGTTGTTCTCTACGCC 59.016 52.381 0.00 0.00 41.10 5.68
262 272 1.984297 GCCGAAGTCGTTGTTCTCTAC 59.016 52.381 0.00 0.00 37.74 2.59
263 273 1.610038 TGCCGAAGTCGTTGTTCTCTA 59.390 47.619 0.00 0.00 37.74 2.43
271 281 0.534203 AACACCATGCCGAAGTCGTT 60.534 50.000 0.00 0.00 37.74 3.85
273 283 0.948623 TCAACACCATGCCGAAGTCG 60.949 55.000 0.00 0.00 39.44 4.18
296 306 0.855349 CTATAAGCACAGCTTCGGCG 59.145 55.000 7.62 0.00 46.77 6.46
297 307 1.221414 CCTATAAGCACAGCTTCGGC 58.779 55.000 7.62 0.00 46.77 5.54
299 309 0.855349 CGCCTATAAGCACAGCTTCG 59.145 55.000 7.62 1.70 46.77 3.79
302 312 1.592669 CGCGCCTATAAGCACAGCT 60.593 57.895 0.00 0.00 42.56 4.24
303 313 1.591594 TCGCGCCTATAAGCACAGC 60.592 57.895 0.00 0.00 0.00 4.40
304 314 1.215655 GGTCGCGCCTATAAGCACAG 61.216 60.000 0.00 0.00 0.00 3.66
305 315 1.227147 GGTCGCGCCTATAAGCACA 60.227 57.895 0.00 0.00 0.00 4.57
306 316 1.215655 CTGGTCGCGCCTATAAGCAC 61.216 60.000 18.14 1.04 38.35 4.40
307 317 1.067416 CTGGTCGCGCCTATAAGCA 59.933 57.895 18.14 7.86 38.35 3.91
308 318 1.664965 CCTGGTCGCGCCTATAAGC 60.665 63.158 18.14 3.55 38.35 3.09
309 319 1.664965 GCCTGGTCGCGCCTATAAG 60.665 63.158 18.14 8.75 38.35 1.73
310 320 2.420043 GCCTGGTCGCGCCTATAA 59.580 61.111 18.14 0.28 38.35 0.98
311 321 3.973516 CGCCTGGTCGCGCCTATA 61.974 66.667 18.14 0.60 46.47 1.31
319 329 4.796231 CGTCCCTTCGCCTGGTCG 62.796 72.222 0.00 0.00 0.00 4.79
320 330 4.452733 CCGTCCCTTCGCCTGGTC 62.453 72.222 0.00 0.00 0.00 4.02
324 334 3.391382 CTTCCCGTCCCTTCGCCT 61.391 66.667 0.00 0.00 0.00 5.52
342 352 3.126879 TCGCCGCATTGAAGCCAG 61.127 61.111 0.00 0.00 0.00 4.85
354 364 0.458025 GAAGGTTACTCCAGTCGCCG 60.458 60.000 0.00 0.00 39.02 6.46
385 395 1.211709 GCAACGCTTTAATGCCGGT 59.788 52.632 1.90 0.00 34.03 5.28
386 396 4.071374 GCAACGCTTTAATGCCGG 57.929 55.556 0.00 0.00 34.03 6.13
408 418 3.607987 GATGCGAACGGACGAGCG 61.608 66.667 7.62 2.75 35.09 5.03
412 422 2.726691 AAAGCGATGCGAACGGACG 61.727 57.895 0.00 0.00 0.00 4.79
420 430 4.520846 GCCGGTCAAAGCGATGCG 62.521 66.667 1.90 0.00 42.41 4.73
421 431 2.652893 GATGCCGGTCAAAGCGATGC 62.653 60.000 1.90 0.00 42.41 3.91
462 472 1.063327 CGTCAGTGCCGCTCTAGAG 59.937 63.158 15.85 15.85 0.00 2.43
463 473 1.369839 CTCGTCAGTGCCGCTCTAGA 61.370 60.000 0.00 0.00 0.00 2.43
464 474 1.063327 CTCGTCAGTGCCGCTCTAG 59.937 63.158 0.00 0.00 0.00 2.43
465 475 3.052620 GCTCGTCAGTGCCGCTCTA 62.053 63.158 0.00 0.00 0.00 2.43
466 476 4.427661 GCTCGTCAGTGCCGCTCT 62.428 66.667 0.00 0.00 0.00 4.09
467 477 3.997064 ATGCTCGTCAGTGCCGCTC 62.997 63.158 0.00 0.00 36.14 5.03
468 478 4.074526 ATGCTCGTCAGTGCCGCT 62.075 61.111 0.00 0.00 36.14 5.52
470 480 2.913054 ATCCATGCTCGTCAGTGCCG 62.913 60.000 0.00 0.00 36.14 5.69
471 481 0.745845 AATCCATGCTCGTCAGTGCC 60.746 55.000 0.00 0.00 36.14 5.01
472 482 1.089920 AAATCCATGCTCGTCAGTGC 58.910 50.000 0.00 0.00 37.38 4.40
473 483 1.202110 GCAAATCCATGCTCGTCAGTG 60.202 52.381 0.00 0.00 43.06 3.66
475 485 0.027194 CGCAAATCCATGCTCGTCAG 59.973 55.000 0.00 0.00 44.21 3.51
477 487 0.026803 GTCGCAAATCCATGCTCGTC 59.973 55.000 0.00 0.00 44.21 4.20
478 488 0.673333 TGTCGCAAATCCATGCTCGT 60.673 50.000 0.00 0.00 44.21 4.18
479 489 0.447406 TTGTCGCAAATCCATGCTCG 59.553 50.000 0.00 0.00 44.21 5.03
480 490 1.468054 GGTTGTCGCAAATCCATGCTC 60.468 52.381 0.00 0.00 44.21 4.26
481 491 0.527565 GGTTGTCGCAAATCCATGCT 59.472 50.000 0.00 0.00 44.21 3.79
482 492 0.243365 TGGTTGTCGCAAATCCATGC 59.757 50.000 0.00 0.00 42.94 4.06
483 493 1.541147 AGTGGTTGTCGCAAATCCATG 59.459 47.619 5.62 0.00 0.00 3.66
485 495 1.606668 GAAGTGGTTGTCGCAAATCCA 59.393 47.619 0.00 0.00 0.00 3.41
486 496 1.399727 CGAAGTGGTTGTCGCAAATCC 60.400 52.381 0.00 0.00 0.00 3.01
487 497 1.529438 TCGAAGTGGTTGTCGCAAATC 59.471 47.619 0.00 0.00 37.19 2.17
490 500 1.495584 GCTCGAAGTGGTTGTCGCAA 61.496 55.000 0.00 0.00 37.19 4.85
493 503 2.372690 CCGCTCGAAGTGGTTGTCG 61.373 63.158 6.37 0.00 40.92 4.35
494 504 1.006571 TCCGCTCGAAGTGGTTGTC 60.007 57.895 12.27 0.00 45.85 3.18
496 506 1.006102 ACTCCGCTCGAAGTGGTTG 60.006 57.895 12.27 9.77 45.85 3.77
497 507 1.006102 CACTCCGCTCGAAGTGGTT 60.006 57.895 7.02 0.00 45.85 3.67
500 510 1.217882 AAAACACTCCGCTCGAAGTG 58.782 50.000 12.36 12.36 38.17 3.16
501 511 1.865340 GAAAAACACTCCGCTCGAAGT 59.135 47.619 0.00 0.00 0.00 3.01
502 512 1.136611 CGAAAAACACTCCGCTCGAAG 60.137 52.381 0.00 0.00 0.00 3.79
503 513 0.856641 CGAAAAACACTCCGCTCGAA 59.143 50.000 0.00 0.00 0.00 3.71
504 514 0.031043 TCGAAAAACACTCCGCTCGA 59.969 50.000 0.00 0.00 33.29 4.04
506 516 0.164002 GCTCGAAAAACACTCCGCTC 59.836 55.000 0.00 0.00 0.00 5.03
507 517 1.557443 CGCTCGAAAAACACTCCGCT 61.557 55.000 0.00 0.00 0.00 5.52
508 518 1.154654 CGCTCGAAAAACACTCCGC 60.155 57.895 0.00 0.00 0.00 5.54
509 519 0.856641 TTCGCTCGAAAAACACTCCG 59.143 50.000 1.86 0.00 0.00 4.63
510 520 2.132762 TCTTCGCTCGAAAAACACTCC 58.867 47.619 6.18 0.00 33.34 3.85
511 521 2.155924 CCTCTTCGCTCGAAAAACACTC 59.844 50.000 6.18 0.00 33.34 3.51
512 522 2.135933 CCTCTTCGCTCGAAAAACACT 58.864 47.619 6.18 0.00 33.34 3.55
514 524 2.234300 ACCTCTTCGCTCGAAAAACA 57.766 45.000 6.18 0.00 33.34 2.83
515 525 3.604065 AAACCTCTTCGCTCGAAAAAC 57.396 42.857 6.18 0.00 33.34 2.43
516 526 4.347813 CAAAAACCTCTTCGCTCGAAAAA 58.652 39.130 6.18 0.00 33.34 1.94
517 527 3.242936 CCAAAAACCTCTTCGCTCGAAAA 60.243 43.478 6.18 0.00 33.34 2.29
518 528 2.289547 CCAAAAACCTCTTCGCTCGAAA 59.710 45.455 6.18 0.00 33.34 3.46
519 529 1.871039 CCAAAAACCTCTTCGCTCGAA 59.129 47.619 4.58 4.58 0.00 3.71
521 531 0.517316 CCCAAAAACCTCTTCGCTCG 59.483 55.000 0.00 0.00 0.00 5.03
522 532 1.266989 CACCCAAAAACCTCTTCGCTC 59.733 52.381 0.00 0.00 0.00 5.03
523 533 1.318576 CACCCAAAAACCTCTTCGCT 58.681 50.000 0.00 0.00 0.00 4.93
524 534 1.029681 ACACCCAAAAACCTCTTCGC 58.970 50.000 0.00 0.00 0.00 4.70
525 535 2.021457 ACACACCCAAAAACCTCTTCG 58.979 47.619 0.00 0.00 0.00 3.79
526 536 2.361119 GGACACACCCAAAAACCTCTTC 59.639 50.000 0.00 0.00 0.00 2.87
529 539 0.666374 CGGACACACCCAAAAACCTC 59.334 55.000 0.00 0.00 34.64 3.85
530 540 0.256464 TCGGACACACCCAAAAACCT 59.744 50.000 0.00 0.00 34.64 3.50
533 543 0.256464 ACCTCGGACACACCCAAAAA 59.744 50.000 0.00 0.00 34.64 1.94
535 545 1.147376 CACCTCGGACACACCCAAA 59.853 57.895 0.00 0.00 34.64 3.28
537 547 2.445085 ACACCTCGGACACACCCA 60.445 61.111 0.00 0.00 34.64 4.51
539 549 0.179067 TTTGACACCTCGGACACACC 60.179 55.000 0.00 0.00 0.00 4.16
541 551 0.528901 CGTTTGACACCTCGGACACA 60.529 55.000 0.00 0.00 0.00 3.72
542 552 1.828331 GCGTTTGACACCTCGGACAC 61.828 60.000 0.00 0.00 0.00 3.67
543 553 1.593209 GCGTTTGACACCTCGGACA 60.593 57.895 0.00 0.00 0.00 4.02
544 554 2.654912 CGCGTTTGACACCTCGGAC 61.655 63.158 0.00 0.00 0.00 4.79
546 556 1.372004 TACGCGTTTGACACCTCGG 60.372 57.895 20.78 0.00 0.00 4.63
547 557 1.771044 GTACGCGTTTGACACCTCG 59.229 57.895 20.78 0.00 0.00 4.63
548 558 1.771044 CGTACGCGTTTGACACCTC 59.229 57.895 20.78 0.00 0.00 3.85
549 559 3.926497 CGTACGCGTTTGACACCT 58.074 55.556 20.78 0.00 0.00 4.00
564 574 1.743772 GCATCTGGAATGCTACCACGT 60.744 52.381 2.84 0.00 41.52 4.49
569 579 1.312815 GTGGGCATCTGGAATGCTAC 58.687 55.000 9.62 6.19 44.02 3.58
574 584 1.341383 GGACTTGTGGGCATCTGGAAT 60.341 52.381 0.00 0.00 0.00 3.01
576 586 1.685224 GGACTTGTGGGCATCTGGA 59.315 57.895 0.00 0.00 0.00 3.86
579 589 1.542375 AGGGGACTTGTGGGCATCT 60.542 57.895 0.00 0.00 37.44 2.90
596 606 0.877213 GCAAACCTGGTGCAAAGCAG 60.877 55.000 0.00 0.00 40.08 4.24
599 609 0.318107 CTCGCAAACCTGGTGCAAAG 60.318 55.000 0.00 0.00 42.33 2.77
604 614 2.009774 CCTAATCTCGCAAACCTGGTG 58.990 52.381 0.00 0.00 0.00 4.17
623 633 1.636988 CGTACCGGTCTGATTGTTCC 58.363 55.000 12.40 0.00 0.00 3.62
642 652 5.472820 ACTTAGTACTACATCATCTACCCGC 59.527 44.000 0.91 0.00 0.00 6.13
658 675 3.560068 CGCCATCCAATCCAACTTAGTAC 59.440 47.826 0.00 0.00 0.00 2.73
662 679 3.013921 GTTCGCCATCCAATCCAACTTA 58.986 45.455 0.00 0.00 0.00 2.24
663 680 1.818674 GTTCGCCATCCAATCCAACTT 59.181 47.619 0.00 0.00 0.00 2.66
664 681 1.463674 GTTCGCCATCCAATCCAACT 58.536 50.000 0.00 0.00 0.00 3.16
665 682 0.098728 CGTTCGCCATCCAATCCAAC 59.901 55.000 0.00 0.00 0.00 3.77
666 683 0.322098 ACGTTCGCCATCCAATCCAA 60.322 50.000 0.00 0.00 0.00 3.53
667 684 0.742990 GACGTTCGCCATCCAATCCA 60.743 55.000 0.00 0.00 0.00 3.41
668 685 1.436983 GGACGTTCGCCATCCAATCC 61.437 60.000 0.00 0.00 32.35 3.01
669 686 1.762222 CGGACGTTCGCCATCCAATC 61.762 60.000 1.83 0.00 32.35 2.67
703 737 1.963515 GCAATCCACACCCTCAAAACT 59.036 47.619 0.00 0.00 0.00 2.66
723 757 2.622942 GAGTAGTCTCAGGGCATCTCTG 59.377 54.545 0.00 0.00 40.18 3.35
840 1056 2.981859 AGTGTACCTGCTAAATCCCG 57.018 50.000 0.00 0.00 0.00 5.14
841 1057 5.493809 TGTTAAGTGTACCTGCTAAATCCC 58.506 41.667 0.00 0.00 0.00 3.85
842 1058 6.428771 TGTTGTTAAGTGTACCTGCTAAATCC 59.571 38.462 0.00 0.00 0.00 3.01
843 1059 7.041644 TGTGTTGTTAAGTGTACCTGCTAAATC 60.042 37.037 0.00 0.00 0.00 2.17
973 1197 0.895530 TGCGGGAGAAGTGGTAGAAG 59.104 55.000 0.00 0.00 0.00 2.85
975 1199 1.568504 AATGCGGGAGAAGTGGTAGA 58.431 50.000 0.00 0.00 0.00 2.59
978 1202 1.349688 TGTAAATGCGGGAGAAGTGGT 59.650 47.619 0.00 0.00 0.00 4.16
1043 1267 2.972505 GCGGTGGTGTGTGTGAGG 60.973 66.667 0.00 0.00 0.00 3.86
1051 1275 4.175337 AGTGCAGTGCGGTGGTGT 62.175 61.111 11.20 0.00 0.00 4.16
1075 1315 0.464870 CATGGCTGAGACCTGAGAGG 59.535 60.000 0.00 0.00 42.49 3.69
1081 1321 1.530771 GATGCCATGGCTGAGACCT 59.469 57.895 35.53 12.50 42.51 3.85
1082 1322 1.527844 GGATGCCATGGCTGAGACC 60.528 63.158 35.53 24.82 42.51 3.85
1083 1323 0.761187 TAGGATGCCATGGCTGAGAC 59.239 55.000 35.53 20.81 42.51 3.36
1084 1324 0.761187 GTAGGATGCCATGGCTGAGA 59.239 55.000 35.53 17.68 42.51 3.27
1085 1325 0.471191 TGTAGGATGCCATGGCTGAG 59.529 55.000 35.53 0.00 42.51 3.35
1086 1326 0.471191 CTGTAGGATGCCATGGCTGA 59.529 55.000 35.53 18.88 42.51 4.26
1087 1327 0.536687 CCTGTAGGATGCCATGGCTG 60.537 60.000 35.53 15.14 38.71 4.85
1088 1328 1.842007 CCTGTAGGATGCCATGGCT 59.158 57.895 35.53 21.86 38.71 4.75
1097 1344 0.684479 TCACGAGCAGCCTGTAGGAT 60.684 55.000 1.17 0.00 37.39 3.24
1121 1368 3.743091 GAGGAGCGCGGAGAAGACG 62.743 68.421 8.83 0.00 0.00 4.18
1352 1599 2.169769 CTGGTAGAAGCCGGGAATGTAA 59.830 50.000 2.18 0.00 0.00 2.41
1442 1698 4.463788 GGCAGGATGGGGTTGGGG 62.464 72.222 0.00 0.00 35.86 4.96
1516 1775 4.405671 AGAGGACGACCGCCGAGA 62.406 66.667 3.80 0.00 41.76 4.04
1563 1822 1.618074 GGACTAGTAACCGACCAGGGT 60.618 57.143 0.00 0.00 46.96 4.34
1582 1841 2.543861 CCAGTAACTGGTCGATGATCGG 60.544 54.545 15.48 0.97 45.82 4.18
1712 1979 6.417258 TGAGCAATGAATCAATACAGAGGAA 58.583 36.000 0.00 0.00 0.00 3.36
1832 2102 1.420138 AGGAAGAGGCACCGAGAAAAA 59.580 47.619 0.00 0.00 0.00 1.94
1836 2106 1.056660 AAAAGGAAGAGGCACCGAGA 58.943 50.000 0.00 0.00 0.00 4.04
1840 2110 2.959030 ACAAGAAAAAGGAAGAGGCACC 59.041 45.455 0.00 0.00 0.00 5.01
1924 2198 1.604604 AACAATCACTCCCAACACGG 58.395 50.000 0.00 0.00 0.00 4.94
1925 2199 3.628017 GAAAACAATCACTCCCAACACG 58.372 45.455 0.00 0.00 0.00 4.49
2014 2288 2.145958 ATGCCTCAATCACTCGATCG 57.854 50.000 9.36 9.36 0.00 3.69
2015 2289 4.889832 AAAATGCCTCAATCACTCGATC 57.110 40.909 0.00 0.00 0.00 3.69
2016 2290 5.240183 CCATAAAATGCCTCAATCACTCGAT 59.760 40.000 0.00 0.00 0.00 3.59
2017 2291 4.576053 CCATAAAATGCCTCAATCACTCGA 59.424 41.667 0.00 0.00 0.00 4.04
2030 2304 9.505995 CAAATTAATTTTGAGGCCATAAAATGC 57.494 29.630 22.78 0.00 46.36 3.56
2060 2363 3.491639 TCGTTAATTGTCTCAACGTGGTG 59.508 43.478 9.54 0.00 44.02 4.17
2164 2490 2.010582 GCACCACGCTAGCTAGCTCT 62.011 60.000 36.02 22.00 46.85 4.09
2249 2583 2.088674 AACTCGCAACGCTCTCCACT 62.089 55.000 0.00 0.00 0.00 4.00
2250 2584 1.664965 AACTCGCAACGCTCTCCAC 60.665 57.895 0.00 0.00 0.00 4.02
2253 2587 2.472049 GCAACTCGCAACGCTCTC 59.528 61.111 0.00 0.00 41.79 3.20
2262 2596 1.335051 GGAAACTTTCCTGCAACTCGC 60.335 52.381 12.69 0.00 46.57 5.03
2263 2597 2.688364 GGAAACTTTCCTGCAACTCG 57.312 50.000 12.69 0.00 46.57 4.18
2362 2701 2.328099 GCTGTGACCTGCCTTTCCG 61.328 63.158 0.00 0.00 0.00 4.30
2363 2702 1.073897 AGCTGTGACCTGCCTTTCC 59.926 57.895 0.00 0.00 36.27 3.13
2386 2727 2.236395 CTCTCCCCAAACTCCAACGTAT 59.764 50.000 0.00 0.00 0.00 3.06
2387 2728 1.621814 CTCTCCCCAAACTCCAACGTA 59.378 52.381 0.00 0.00 0.00 3.57
2439 2828 0.965439 GCTCGGATGCTCCTACTCAT 59.035 55.000 1.51 0.00 33.30 2.90
2444 2833 1.188219 GGGATGCTCGGATGCTCCTA 61.188 60.000 12.58 0.00 33.30 2.94
2449 2838 3.664495 CATGGGATGCTCGGATGC 58.336 61.111 0.00 0.00 0.00 3.91
2458 2847 2.368655 CATGATGCATGCATGGGATG 57.631 50.000 36.73 27.19 39.48 3.51
2464 2853 1.919240 CCCTACCATGATGCATGCAT 58.081 50.000 32.66 32.66 40.20 3.96
2465 2854 0.824595 GCCCTACCATGATGCATGCA 60.825 55.000 25.04 25.04 40.20 3.96
2466 2855 1.859427 CGCCCTACCATGATGCATGC 61.859 60.000 11.82 11.82 40.20 4.06
2483 2872 0.638746 GTGTGCATGTACGTACTCGC 59.361 55.000 25.12 24.60 41.18 5.03
2524 2916 9.878599 AATACTTCTTCTTGTTTACGTGAAATG 57.121 29.630 0.00 0.00 0.00 2.32
2530 2922 8.870879 GCATCTAATACTTCTTCTTGTTTACGT 58.129 33.333 0.00 0.00 0.00 3.57
2533 2925 7.547722 TGCGCATCTAATACTTCTTCTTGTTTA 59.452 33.333 5.66 0.00 0.00 2.01
2537 2931 5.973651 TGCGCATCTAATACTTCTTCTTG 57.026 39.130 5.66 0.00 0.00 3.02
2557 2952 2.202298 GCCAACGTACGCACATGC 60.202 61.111 16.72 7.62 37.78 4.06
2558 2953 1.132436 CAGCCAACGTACGCACATG 59.868 57.895 16.72 9.41 0.00 3.21
2559 2954 2.677003 GCAGCCAACGTACGCACAT 61.677 57.895 16.72 0.00 0.00 3.21
2576 2979 2.908073 CGGTCCAAGCACACCAAGC 61.908 63.158 0.00 0.00 32.33 4.01
2581 2984 3.330275 GACACGGTCCAAGCACAC 58.670 61.111 0.00 0.00 0.00 3.82
2613 3034 1.068417 GCGACGGTACATATGGCCA 59.932 57.895 8.56 8.56 0.00 5.36
2647 3077 0.108804 TTAGCTAGCCTCGTGTGTGC 60.109 55.000 12.13 0.00 0.00 4.57
2695 3125 1.687494 CGGCTAGTTTGACGAGCAGC 61.687 60.000 13.69 0.00 46.63 5.25
2701 3131 4.356162 CGAATTATCGGCTAGTTTGACG 57.644 45.455 0.00 0.00 45.32 4.35
2739 3173 2.479219 GGATTAGCAAGCAAGCAAGAGC 60.479 50.000 3.19 0.00 42.56 4.09
2740 3174 2.098770 GGGATTAGCAAGCAAGCAAGAG 59.901 50.000 3.19 0.00 36.85 2.85
2741 3175 2.094675 GGGATTAGCAAGCAAGCAAGA 58.905 47.619 3.19 0.00 36.85 3.02
2767 3201 6.976349 ACGTACGTTTCATCAGATATGCTAAA 59.024 34.615 16.72 0.00 0.00 1.85
2776 3210 5.329493 CATGACTACGTACGTTTCATCAGA 58.671 41.667 28.72 11.34 31.46 3.27
2786 3220 2.726241 CCATGATGCATGACTACGTACG 59.274 50.000 15.01 15.01 43.81 3.67


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

AutoCloner maintained by Alex Coulton.