Multiple sequence alignment - TraesCS2B01G310600

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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 TraesCS2B01G310600 chr2B 100.000 2279 0 0 1 2279 443761892 443764170 0.000000e+00 4209.0
1 TraesCS2B01G310600 chr2D 92.130 1474 63 26 621 2084 373879198 373880628 0.000000e+00 2030.0
2 TraesCS2B01G310600 chr2D 89.174 351 20 10 34 379 373878596 373878933 2.710000e-114 422.0
3 TraesCS2B01G310600 chr2D 95.755 212 1 3 2068 2279 373882032 373882235 3.630000e-88 335.0
4 TraesCS2B01G310600 chr2D 84.536 97 4 3 544 636 373879085 373879174 4.030000e-13 86.1
5 TraesCS2B01G310600 chrUn 86.995 1807 118 54 10 1783 229268544 229266822 0.000000e+00 1927.0
6 TraesCS2B01G310600 chrUn 86.192 449 13 10 1857 2279 229266832 229266407 7.470000e-120 440.0


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 TraesCS2B01G310600 chr2B 443761892 443764170 2278 False 4209.000 4209 100.00000 1 2279 1 chr2B.!!$F1 2278
1 TraesCS2B01G310600 chr2D 373878596 373882235 3639 False 718.275 2030 90.39875 34 2279 4 chr2D.!!$F1 2245
2 TraesCS2B01G310600 chrUn 229266407 229268544 2137 True 1183.500 1927 86.59350 10 2279 2 chrUn.!!$R1 2269

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
396 410 0.034337 CAACTGCAATTTGCTGGCCT 59.966 50.0 25.76 11.72 45.06 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1801 0.98423 TCGAAGCCAGGATTCAAGGT 59.016 50.0 17.68 0.0 0.0 3.5 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 286 1.099689 CCGAGTTCCTCTGGTCTCTC 58.900 60.000 0.00 0.00 0.00 3.20
280 287 1.340600 CCGAGTTCCTCTGGTCTCTCT 60.341 57.143 0.00 0.00 0.00 3.10
281 288 2.014128 CGAGTTCCTCTGGTCTCTCTC 58.986 57.143 0.00 0.00 0.00 3.20
282 289 2.355716 CGAGTTCCTCTGGTCTCTCTCT 60.356 54.545 0.00 0.00 0.00 3.10
283 290 3.279434 GAGTTCCTCTGGTCTCTCTCTC 58.721 54.545 0.00 0.00 0.00 3.20
284 291 2.014128 GTTCCTCTGGTCTCTCTCTCG 58.986 57.143 0.00 0.00 0.00 4.04
285 292 0.107410 TCCTCTGGTCTCTCTCTCGC 60.107 60.000 0.00 0.00 0.00 5.03
286 293 0.393673 CCTCTGGTCTCTCTCTCGCA 60.394 60.000 0.00 0.00 0.00 5.10
287 294 1.016627 CTCTGGTCTCTCTCTCGCAG 58.983 60.000 0.00 0.00 0.00 5.18
288 295 1.029408 TCTGGTCTCTCTCTCGCAGC 61.029 60.000 0.00 0.00 0.00 5.25
289 296 1.303643 TGGTCTCTCTCTCGCAGCA 60.304 57.895 0.00 0.00 0.00 4.41
290 297 1.311651 TGGTCTCTCTCTCGCAGCAG 61.312 60.000 0.00 0.00 0.00 4.24
291 298 1.226660 GTCTCTCTCTCGCAGCAGC 60.227 63.158 0.00 0.00 37.42 5.25
292 299 1.676967 TCTCTCTCTCGCAGCAGCA 60.677 57.895 0.82 0.00 42.27 4.41
313 320 2.440409 AGCAGCTCCAACAAGGTAATG 58.560 47.619 0.00 0.00 39.02 1.90
314 321 2.162681 GCAGCTCCAACAAGGTAATGT 58.837 47.619 0.00 0.00 39.02 2.71
319 333 3.864921 GCTCCAACAAGGTAATGTCTCGT 60.865 47.826 0.00 0.00 39.02 4.18
336 350 0.865218 CGTCTCTGCTCGATGTGCTC 60.865 60.000 0.00 0.00 0.00 4.26
379 393 3.494573 ACAATCATGTGTGCCAATTGCAA 60.495 39.130 0.00 0.00 42.60 4.08
380 394 5.565451 ACAATCATGTGTGCCAATTGCAAC 61.565 41.667 0.00 0.80 42.60 4.17
381 395 7.705255 ACAATCATGTGTGCCAATTGCAACT 62.705 40.000 0.00 0.00 42.60 3.16
394 408 1.864176 GCAACTGCAATTTGCTGGC 59.136 52.632 25.76 18.51 45.06 4.85
395 409 1.571215 GCAACTGCAATTTGCTGGCC 61.571 55.000 25.76 13.39 45.06 5.36
396 410 0.034337 CAACTGCAATTTGCTGGCCT 59.966 50.000 25.76 11.72 45.06 5.19
413 427 1.902141 GCCTCTCCCCTTTCCTAGTGT 60.902 57.143 0.00 0.00 0.00 3.55
435 479 4.561735 TGCCCTTTTTGTTCGTTTCTAG 57.438 40.909 0.00 0.00 0.00 2.43
437 481 4.399934 TGCCCTTTTTGTTCGTTTCTAGTT 59.600 37.500 0.00 0.00 0.00 2.24
439 483 4.738252 CCCTTTTTGTTCGTTTCTAGTTGC 59.262 41.667 0.00 0.00 0.00 4.17
441 485 5.977129 CCTTTTTGTTCGTTTCTAGTTGCAT 59.023 36.000 0.00 0.00 0.00 3.96
445 489 4.130857 TGTTCGTTTCTAGTTGCATTCCA 58.869 39.130 0.00 0.00 0.00 3.53
447 491 5.240623 TGTTCGTTTCTAGTTGCATTCCATT 59.759 36.000 0.00 0.00 0.00 3.16
448 492 5.545658 TCGTTTCTAGTTGCATTCCATTC 57.454 39.130 0.00 0.00 0.00 2.67
469 516 3.929002 GCAATCTGCTGCATCCCA 58.071 55.556 1.31 0.00 42.17 4.37
470 517 1.436336 GCAATCTGCTGCATCCCAC 59.564 57.895 1.31 0.00 42.17 4.61
494 541 4.333372 CCCATGCCTTTGATTTGTTTATGC 59.667 41.667 0.00 0.00 0.00 3.14
495 542 4.936411 CCATGCCTTTGATTTGTTTATGCA 59.064 37.500 0.00 0.00 0.00 3.96
497 544 6.482835 CATGCCTTTGATTTGTTTATGCATG 58.517 36.000 10.16 0.00 44.89 4.06
498 545 5.549347 TGCCTTTGATTTGTTTATGCATGT 58.451 33.333 10.16 0.00 0.00 3.21
499 546 5.638657 TGCCTTTGATTTGTTTATGCATGTC 59.361 36.000 10.16 0.00 0.00 3.06
500 547 5.870978 GCCTTTGATTTGTTTATGCATGTCT 59.129 36.000 10.16 0.00 0.00 3.41
501 548 6.035327 GCCTTTGATTTGTTTATGCATGTCTC 59.965 38.462 10.16 0.00 0.00 3.36
503 550 6.587206 TTGATTTGTTTATGCATGTCTCCA 57.413 33.333 10.16 0.00 0.00 3.86
507 554 3.261580 TGTTTATGCATGTCTCCACGAG 58.738 45.455 10.16 0.00 0.00 4.18
508 555 1.939974 TTATGCATGTCTCCACGAGC 58.060 50.000 10.16 0.00 0.00 5.03
509 556 0.104855 TATGCATGTCTCCACGAGCC 59.895 55.000 10.16 0.00 0.00 4.70
510 557 1.620739 ATGCATGTCTCCACGAGCCT 61.621 55.000 0.00 0.00 0.00 4.58
511 558 1.078848 GCATGTCTCCACGAGCCTT 60.079 57.895 0.00 0.00 0.00 4.35
512 559 1.364626 GCATGTCTCCACGAGCCTTG 61.365 60.000 0.00 0.00 0.00 3.61
513 560 1.078848 ATGTCTCCACGAGCCTTGC 60.079 57.895 0.00 0.00 0.00 4.01
514 561 1.548357 ATGTCTCCACGAGCCTTGCT 61.548 55.000 0.00 0.00 43.88 3.91
515 562 1.004440 GTCTCCACGAGCCTTGCTT 60.004 57.895 0.00 0.00 39.88 3.91
516 563 1.004560 TCTCCACGAGCCTTGCTTG 60.005 57.895 1.77 1.77 44.94 4.01
517 564 1.004560 CTCCACGAGCCTTGCTTGA 60.005 57.895 10.22 0.00 42.27 3.02
518 565 1.294659 CTCCACGAGCCTTGCTTGAC 61.295 60.000 10.22 0.00 42.27 3.18
519 566 1.597854 CCACGAGCCTTGCTTGACA 60.598 57.895 10.22 0.00 42.27 3.58
520 567 1.571460 CACGAGCCTTGCTTGACAC 59.429 57.895 10.22 0.00 42.27 3.67
521 568 1.146041 ACGAGCCTTGCTTGACACA 59.854 52.632 10.22 0.00 42.27 3.72
522 569 0.250467 ACGAGCCTTGCTTGACACAT 60.250 50.000 10.22 0.00 42.27 3.21
545 592 5.869753 ATCTTTGCAAGTTGCTAGTACTG 57.130 39.130 27.17 11.13 45.31 2.74
546 593 4.956085 TCTTTGCAAGTTGCTAGTACTGA 58.044 39.130 27.17 12.98 45.31 3.41
580 644 6.248420 GCAATAGCGTTAACATGTGTGTAAAG 59.752 38.462 0.00 0.00 37.67 1.85
581 645 7.295201 CAATAGCGTTAACATGTGTGTAAAGT 58.705 34.615 0.00 0.00 37.67 2.66
582 646 5.090652 AGCGTTAACATGTGTGTAAAGTG 57.909 39.130 0.00 0.00 37.67 3.16
583 647 4.573201 AGCGTTAACATGTGTGTAAAGTGT 59.427 37.500 0.00 0.00 37.67 3.55
584 648 5.754406 AGCGTTAACATGTGTGTAAAGTGTA 59.246 36.000 0.00 0.00 37.67 2.90
585 649 6.258287 AGCGTTAACATGTGTGTAAAGTGTAA 59.742 34.615 0.00 0.00 37.67 2.41
619 683 1.978542 TTGCTTAGAACGAGCGAGTC 58.021 50.000 0.00 0.00 43.02 3.36
627 691 3.062466 CGAGCGAGTCACCCTCCA 61.062 66.667 0.00 0.00 36.82 3.86
628 692 2.574399 GAGCGAGTCACCCTCCAC 59.426 66.667 0.00 0.00 36.82 4.02
636 700 3.006537 CGAGTCACCCTCCACTTTCTTTA 59.993 47.826 0.00 0.00 36.82 1.85
637 701 4.570930 GAGTCACCCTCCACTTTCTTTAG 58.429 47.826 0.00 0.00 33.79 1.85
638 702 3.974642 AGTCACCCTCCACTTTCTTTAGT 59.025 43.478 0.00 0.00 0.00 2.24
641 705 6.100714 AGTCACCCTCCACTTTCTTTAGTTTA 59.899 38.462 0.00 0.00 0.00 2.01
645 709 9.292195 CACCCTCCACTTTCTTTAGTTTATTTA 57.708 33.333 0.00 0.00 0.00 1.40
723 823 9.497030 GTTCTGTTTTTCTTCTTCTTCTTCTTC 57.503 33.333 0.00 0.00 0.00 2.87
724 824 9.454859 TTCTGTTTTTCTTCTTCTTCTTCTTCT 57.545 29.630 0.00 0.00 0.00 2.85
725 825 9.454859 TCTGTTTTTCTTCTTCTTCTTCTTCTT 57.545 29.630 0.00 0.00 0.00 2.52
726 826 9.715123 CTGTTTTTCTTCTTCTTCTTCTTCTTC 57.285 33.333 0.00 0.00 0.00 2.87
727 827 9.454859 TGTTTTTCTTCTTCTTCTTCTTCTTCT 57.545 29.630 0.00 0.00 0.00 2.85
731 831 9.549078 TTTCTTCTTCTTCTTCTTCTTCTTACC 57.451 33.333 0.00 0.00 0.00 2.85
732 832 8.485578 TCTTCTTCTTCTTCTTCTTCTTACCT 57.514 34.615 0.00 0.00 0.00 3.08
733 833 8.581578 TCTTCTTCTTCTTCTTCTTCTTACCTC 58.418 37.037 0.00 0.00 0.00 3.85
734 834 7.234661 TCTTCTTCTTCTTCTTCTTACCTCC 57.765 40.000 0.00 0.00 0.00 4.30
735 835 6.782988 TCTTCTTCTTCTTCTTCTTACCTCCA 59.217 38.462 0.00 0.00 0.00 3.86
736 836 6.996180 TCTTCTTCTTCTTCTTACCTCCAA 57.004 37.500 0.00 0.00 0.00 3.53
737 837 6.998802 TCTTCTTCTTCTTCTTACCTCCAAG 58.001 40.000 0.00 0.00 0.00 3.61
738 838 5.746990 TCTTCTTCTTCTTACCTCCAAGG 57.253 43.478 0.00 0.00 42.49 3.61
752 852 0.038744 CCAAGGAGGATGTTGCCACT 59.961 55.000 0.00 0.00 41.22 4.00
790 890 3.430790 GGGTATCCTGGAATTTTTGCTGC 60.431 47.826 0.00 0.00 0.00 5.25
803 903 3.349006 GCTGCCACACGACCACAG 61.349 66.667 0.00 0.00 0.00 3.66
827 927 2.291741 CACTTCACTGTTTCTGCTTCCC 59.708 50.000 0.00 0.00 0.00 3.97
861 961 3.429547 CCTGCACTCATAGTAGGACACAC 60.430 52.174 0.00 0.00 40.83 3.82
949 1052 2.116125 GGCCCCCACATATGGCTC 59.884 66.667 7.80 0.00 45.76 4.70
1014 1120 1.528824 CGGGATGGACAGGCTCAAT 59.471 57.895 0.00 0.00 0.00 2.57
1299 1405 1.526575 GCAGCTTGCTTGCTTGGGTA 61.527 55.000 1.40 0.00 41.98 3.69
1399 1511 0.178984 TGCCATGCCATCATGTAGGG 60.179 55.000 8.00 2.72 46.64 3.53
1404 1516 2.897271 TGCCATCATGTAGGGTTTGT 57.103 45.000 8.00 0.00 0.00 2.83
1405 1517 2.445427 TGCCATCATGTAGGGTTTGTG 58.555 47.619 8.00 0.00 0.00 3.33
1578 1691 3.737172 GTTGGGTCAATGCGCGCT 61.737 61.111 33.29 15.19 0.00 5.92
1640 1753 5.711976 CAGTCCTGGGAAAATGTCATTTACT 59.288 40.000 11.18 6.53 0.00 2.24
1649 1762 6.088085 GGAAAATGTCATTTACTGCTCGTTTG 59.912 38.462 11.18 0.00 0.00 2.93
1662 1775 2.420022 GCTCGTTTGATGGCAATGTACT 59.580 45.455 0.00 0.00 33.25 2.73
1663 1776 3.621268 GCTCGTTTGATGGCAATGTACTA 59.379 43.478 0.00 0.00 33.25 1.82
1664 1777 4.494199 GCTCGTTTGATGGCAATGTACTAC 60.494 45.833 0.00 0.00 33.25 2.73
1673 1786 3.772572 TGGCAATGTACTACCAGCTCTAA 59.227 43.478 0.00 0.00 0.00 2.10
1679 1792 3.767131 TGTACTACCAGCTCTAATGCACA 59.233 43.478 0.00 0.00 34.99 4.57
1686 1799 3.250280 CCAGCTCTAATGCACAATGCTAG 59.750 47.826 2.02 0.00 45.31 3.42
1687 1800 3.875727 CAGCTCTAATGCACAATGCTAGT 59.124 43.478 2.02 0.00 45.31 2.57
1688 1801 5.052481 CAGCTCTAATGCACAATGCTAGTA 58.948 41.667 2.02 0.00 45.31 1.82
1697 1810 4.635765 TGCACAATGCTAGTACCTTGAATC 59.364 41.667 2.02 0.00 45.31 2.52
1708 1821 1.351017 ACCTTGAATCCTGGCTTCGAA 59.649 47.619 5.86 0.00 0.00 3.71
1785 1898 6.542005 ACCACAAGCATCGAATATATGACAAA 59.458 34.615 0.00 0.00 0.00 2.83
1830 1943 0.391597 AAGGTCGGTCACACGTCAAT 59.608 50.000 0.00 0.00 34.94 2.57
1908 2026 0.659957 GCCTTCACATCGAGCATTCC 59.340 55.000 0.00 0.00 0.00 3.01
1909 2027 2.013563 GCCTTCACATCGAGCATTCCA 61.014 52.381 0.00 0.00 0.00 3.53
1913 2031 3.333029 TCACATCGAGCATTCCAAAGA 57.667 42.857 0.00 0.00 0.00 2.52
1934 2052 2.027745 AGAATCAGTCGCCACACTTCAT 60.028 45.455 0.00 0.00 0.00 2.57
1935 2053 2.479566 ATCAGTCGCCACACTTCATT 57.520 45.000 0.00 0.00 0.00 2.57
1959 2077 6.753107 TCATCATGCATATTAATCTGCCAG 57.247 37.500 19.64 13.31 37.59 4.85
2142 3680 8.934023 AAAAGGAAACATGATTGGTTCTAGTA 57.066 30.769 0.00 0.00 46.76 1.82
2143 3681 8.567285 AAAGGAAACATGATTGGTTCTAGTAG 57.433 34.615 0.00 0.00 46.76 2.57
2144 3682 7.496346 AGGAAACATGATTGGTTCTAGTAGA 57.504 36.000 0.00 0.00 46.76 2.59
2145 3683 7.918076 AGGAAACATGATTGGTTCTAGTAGAA 58.082 34.615 8.59 8.59 46.76 2.10
2146 3684 8.383175 AGGAAACATGATTGGTTCTAGTAGAAA 58.617 33.333 14.20 0.00 46.76 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.524621 GGATGGATCAGCGGTGTGG 60.525 63.158 15.22 0.00 0.00 4.17
1 2 0.812811 CAGGATGGATCAGCGGTGTG 60.813 60.000 15.22 0.00 0.00 3.82
2 3 1.524002 CAGGATGGATCAGCGGTGT 59.476 57.895 15.22 1.68 0.00 4.16
3 4 4.451241 CAGGATGGATCAGCGGTG 57.549 61.111 8.67 8.67 0.00 4.94
290 297 1.288127 CCTTGTTGGAGCTGCTTGC 59.712 57.895 6.82 0.00 43.29 4.01
291 298 1.896220 TACCTTGTTGGAGCTGCTTG 58.104 50.000 6.82 0.00 39.71 4.01
292 299 2.656947 TTACCTTGTTGGAGCTGCTT 57.343 45.000 6.82 0.00 39.71 3.91
313 320 0.730265 ACATCGAGCAGAGACGAGAC 59.270 55.000 0.00 0.00 41.63 3.36
314 321 0.729690 CACATCGAGCAGAGACGAGA 59.270 55.000 0.00 0.00 41.63 4.04
319 333 1.135170 CAAGAGCACATCGAGCAGAGA 60.135 52.381 0.00 0.00 0.00 3.10
382 396 1.514553 GGAGAGGCCAGCAAATTGC 59.485 57.895 10.41 10.41 45.46 3.56
383 397 1.325476 GGGGAGAGGCCAGCAAATTG 61.325 60.000 5.01 0.00 38.95 2.32
384 398 1.000866 GGGGAGAGGCCAGCAAATT 59.999 57.895 5.01 0.00 38.95 1.82
385 399 1.513087 AAGGGGAGAGGCCAGCAAAT 61.513 55.000 5.01 0.00 38.95 2.32
386 400 1.729267 AAAGGGGAGAGGCCAGCAAA 61.729 55.000 5.01 0.00 38.95 3.68
387 401 2.142292 GAAAGGGGAGAGGCCAGCAA 62.142 60.000 5.01 0.00 38.95 3.91
388 402 2.532715 AAAGGGGAGAGGCCAGCA 60.533 61.111 5.01 0.00 38.95 4.41
389 403 2.273776 GAAAGGGGAGAGGCCAGC 59.726 66.667 5.01 0.00 38.95 4.85
390 404 0.326618 TAGGAAAGGGGAGAGGCCAG 60.327 60.000 5.01 0.00 38.95 4.85
391 405 0.326618 CTAGGAAAGGGGAGAGGCCA 60.327 60.000 5.01 0.00 38.95 5.36
392 406 0.326713 ACTAGGAAAGGGGAGAGGCC 60.327 60.000 0.00 0.00 0.00 5.19
393 407 0.833949 CACTAGGAAAGGGGAGAGGC 59.166 60.000 0.00 0.00 0.00 4.70
394 408 2.237392 CAACACTAGGAAAGGGGAGAGG 59.763 54.545 0.00 0.00 30.24 3.69
395 409 2.355209 GCAACACTAGGAAAGGGGAGAG 60.355 54.545 0.00 0.00 30.24 3.20
396 410 1.628846 GCAACACTAGGAAAGGGGAGA 59.371 52.381 0.00 0.00 30.24 3.71
413 427 3.878160 AGAAACGAACAAAAAGGGCAA 57.122 38.095 0.00 0.00 0.00 4.52
469 516 2.028561 ACAAATCAAAGGCATGGGGT 57.971 45.000 0.00 0.00 0.00 4.95
470 517 3.421919 AAACAAATCAAAGGCATGGGG 57.578 42.857 0.00 0.00 0.00 4.96
495 542 1.078848 GCAAGGCTCGTGGAGACAT 60.079 57.895 0.72 0.00 40.81 3.06
497 544 1.004440 AAGCAAGGCTCGTGGAGAC 60.004 57.895 0.00 0.00 38.25 3.36
498 545 1.004560 CAAGCAAGGCTCGTGGAGA 60.005 57.895 0.00 0.00 38.25 3.71
499 546 1.004560 TCAAGCAAGGCTCGTGGAG 60.005 57.895 0.00 0.00 38.25 3.86
500 547 1.301716 GTCAAGCAAGGCTCGTGGA 60.302 57.895 0.00 0.00 38.25 4.02
501 548 1.597854 TGTCAAGCAAGGCTCGTGG 60.598 57.895 0.00 0.00 38.25 4.94
503 550 0.250467 ATGTGTCAAGCAAGGCTCGT 60.250 50.000 0.00 0.00 38.25 4.18
507 554 4.418392 CAAAGATATGTGTCAAGCAAGGC 58.582 43.478 0.00 0.00 0.00 4.35
508 555 4.082625 TGCAAAGATATGTGTCAAGCAAGG 60.083 41.667 0.00 0.00 0.00 3.61
509 556 5.050644 TGCAAAGATATGTGTCAAGCAAG 57.949 39.130 0.00 0.00 0.00 4.01
510 557 5.450592 TTGCAAAGATATGTGTCAAGCAA 57.549 34.783 0.00 0.00 37.15 3.91
545 592 3.951979 AACGCTATTGCAACTGCTATC 57.048 42.857 19.03 0.00 42.66 2.08
546 593 4.634004 TGTTAACGCTATTGCAACTGCTAT 59.366 37.500 19.03 3.61 42.66 2.97
580 644 6.158598 AGCAAATCATGATGGTTGTTTACAC 58.841 36.000 17.39 4.41 0.00 2.90
581 645 6.343716 AGCAAATCATGATGGTTGTTTACA 57.656 33.333 17.39 0.00 0.00 2.41
582 646 8.243426 TCTAAGCAAATCATGATGGTTGTTTAC 58.757 33.333 19.22 5.93 37.76 2.01
583 647 8.347004 TCTAAGCAAATCATGATGGTTGTTTA 57.653 30.769 19.22 19.48 37.76 2.01
584 648 7.230849 TCTAAGCAAATCATGATGGTTGTTT 57.769 32.000 19.60 19.60 37.76 2.83
585 649 6.839124 TCTAAGCAAATCATGATGGTTGTT 57.161 33.333 19.22 12.12 37.76 2.83
619 683 7.761038 AATAAACTAAAGAAAGTGGAGGGTG 57.239 36.000 0.00 0.00 0.00 4.61
672 772 5.995282 ACTAGCAGTAGAGTGTAGCATAGAG 59.005 44.000 0.00 0.00 0.00 2.43
673 773 5.760743 CACTAGCAGTAGAGTGTAGCATAGA 59.239 44.000 0.00 0.00 38.61 1.98
674 774 5.996219 CACTAGCAGTAGAGTGTAGCATAG 58.004 45.833 0.00 0.00 38.61 2.23
769 869 3.430790 GGCAGCAAAAATTCCAGGATACC 60.431 47.826 0.00 0.00 37.17 2.73
779 879 1.537990 GGTCGTGTGGCAGCAAAAATT 60.538 47.619 0.00 0.00 0.00 1.82
790 890 2.203001 TGTGCTGTGGTCGTGTGG 60.203 61.111 0.00 0.00 0.00 4.17
803 903 1.672881 AGCAGAAACAGTGAAGTGTGC 59.327 47.619 0.00 1.80 0.00 4.57
827 927 5.702349 ATGAGTGCAGGAAAAGAAGAAAG 57.298 39.130 0.00 0.00 0.00 2.62
861 961 3.532213 CGCGACTCGTATTAACTTGTG 57.468 47.619 0.00 0.00 0.00 3.33
949 1052 2.755103 GCAACAGGGTAAGGAAATCAGG 59.245 50.000 0.00 0.00 0.00 3.86
1014 1120 0.036590 TCTGCATGTACAGCTTGGCA 59.963 50.000 15.28 11.70 37.59 4.92
1294 1400 4.002256 TGGATATGTTCTCCAGTACCCA 57.998 45.455 0.00 0.00 37.87 4.51
1399 1511 4.284485 CCTTAGCGGTTACAAACACAAAC 58.716 43.478 0.00 0.00 0.00 2.93
1404 1516 2.369532 AGACCCTTAGCGGTTACAAACA 59.630 45.455 0.00 0.00 35.79 2.83
1405 1517 3.049708 AGACCCTTAGCGGTTACAAAC 57.950 47.619 0.00 0.00 35.79 2.93
1578 1691 1.682702 CCAATGCCACAGCCATGTAGA 60.683 52.381 0.00 0.00 37.65 2.59
1629 1742 5.163723 CCATCAAACGAGCAGTAAATGACAT 60.164 40.000 0.00 0.00 0.00 3.06
1640 1753 1.246649 ACATTGCCATCAAACGAGCA 58.753 45.000 0.00 0.00 35.56 4.26
1649 1762 3.134458 GAGCTGGTAGTACATTGCCATC 58.866 50.000 2.06 0.00 0.00 3.51
1662 1775 2.945008 GCATTGTGCATTAGAGCTGGTA 59.055 45.455 0.00 0.00 44.26 3.25
1663 1776 1.747355 GCATTGTGCATTAGAGCTGGT 59.253 47.619 0.00 0.00 44.26 4.00
1664 1777 2.486951 GCATTGTGCATTAGAGCTGG 57.513 50.000 0.00 0.00 44.26 4.85
1673 1786 4.220693 TCAAGGTACTAGCATTGTGCAT 57.779 40.909 4.61 0.00 43.04 3.96
1679 1792 4.687219 GCCAGGATTCAAGGTACTAGCATT 60.687 45.833 0.00 0.00 38.49 3.56
1686 1799 2.093658 TCGAAGCCAGGATTCAAGGTAC 60.094 50.000 17.68 0.00 0.00 3.34
1687 1800 2.184533 TCGAAGCCAGGATTCAAGGTA 58.815 47.619 17.68 0.00 0.00 3.08
1688 1801 0.984230 TCGAAGCCAGGATTCAAGGT 59.016 50.000 17.68 0.00 0.00 3.50
1697 1810 2.029838 ACTTAGCATTCGAAGCCAGG 57.970 50.000 3.35 0.25 0.00 4.45
1708 1821 5.189736 TCACCTCCATTAGTCAACTTAGCAT 59.810 40.000 0.00 0.00 0.00 3.79
1830 1943 3.244112 TGCATGAACCATTGCATTGTTGA 60.244 39.130 7.75 0.00 31.84 3.18
1908 2026 2.158449 GTGTGGCGACTGATTCTCTTTG 59.842 50.000 0.00 0.00 0.00 2.77
1909 2027 2.037772 AGTGTGGCGACTGATTCTCTTT 59.962 45.455 0.00 0.00 0.00 2.52
1913 2031 1.344438 TGAAGTGTGGCGACTGATTCT 59.656 47.619 0.00 0.00 0.00 2.40
1934 2052 7.231925 ACTGGCAGATTAATATGCATGATGAAA 59.768 33.333 30.21 9.13 46.19 2.69
1935 2053 6.717997 ACTGGCAGATTAATATGCATGATGAA 59.282 34.615 30.21 10.25 46.19 2.57
2142 3680 6.747414 AATAACTTGGCCCTTTTCTTTTCT 57.253 33.333 0.00 0.00 0.00 2.52
2143 3681 7.667557 AGTAATAACTTGGCCCTTTTCTTTTC 58.332 34.615 0.00 0.00 29.00 2.29
2144 3682 7.612065 AGTAATAACTTGGCCCTTTTCTTTT 57.388 32.000 0.00 0.00 29.00 2.27
2145 3683 7.612065 AAGTAATAACTTGGCCCTTTTCTTT 57.388 32.000 0.00 0.00 44.40 2.52
2146 3684 7.612065 AAAGTAATAACTTGGCCCTTTTCTT 57.388 32.000 0.00 0.00 45.37 2.52
2235 3773 7.933577 CCTTGTTATGCTATCCTGAATGTTAGA 59.066 37.037 0.00 0.00 0.00 2.10
2236 3774 7.933577 TCCTTGTTATGCTATCCTGAATGTTAG 59.066 37.037 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.