Multiple sequence alignment - TraesCS1B01G308100

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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 TraesCS1B01G308100 chr1B 100.000 4675 0 0 1 4675 530765279 530760605 0.000000e+00 8634
1 TraesCS1B01G308100 chr1B 98.398 4121 61 3 556 4675 95491441 95495557 0.000000e+00 7239
2 TraesCS1B01G308100 chr1B 98.940 566 3 2 1 565 633166873 633167436 0.000000e+00 1009
3 TraesCS1B01G308100 chr2A 98.083 4120 75 4 556 4675 374483078 374487193 0.000000e+00 7167
4 TraesCS1B01G308100 chr2A 97.960 4118 79 4 560 4675 628648808 628644694 0.000000e+00 7134
5 TraesCS1B01G308100 chr2A 97.889 4121 80 3 556 4675 161526270 161530384 0.000000e+00 7121
6 TraesCS1B01G308100 chr2A 97.816 4120 83 6 560 4675 628569208 628573324 0.000000e+00 7103
7 TraesCS1B01G308100 chr2A 92.511 227 14 2 671 894 756945590 756945364 5.840000e-84 322
8 TraesCS1B01G308100 chr2B 98.012 4124 74 6 556 4675 424685618 424681499 0.000000e+00 7155
9 TraesCS1B01G308100 chr2B 96.156 3616 108 7 1081 4675 244701345 244704950 0.000000e+00 5879
10 TraesCS1B01G308100 chr2B 96.238 3323 93 6 1375 4675 244763240 244759928 0.000000e+00 5415
11 TraesCS1B01G308100 chr2B 98.258 574 5 3 1 569 38880606 38881179 0.000000e+00 1000
12 TraesCS1B01G308100 chr2B 93.213 221 12 2 671 888 244701024 244701244 5.840000e-84 322
13 TraesCS1B01G308100 chr1A 97.914 4123 83 2 556 4675 409608632 409612754 0.000000e+00 7134
14 TraesCS1B01G308100 chr1A 99.286 560 2 2 1 559 3839316 3838758 0.000000e+00 1011
15 TraesCS1B01G308100 chr1A 99.284 559 4 0 1 559 185853698 185854256 0.000000e+00 1011
16 TraesCS1B01G308100 chr1A 99.286 560 2 2 1 559 555109896 555109338 0.000000e+00 1011
17 TraesCS1B01G308100 chr7D 97.403 3235 73 3 1448 4675 474677238 474680468 0.000000e+00 5498
18 TraesCS1B01G308100 chr5A 96.008 2906 106 7 918 3821 272284484 272287381 0.000000e+00 4715
19 TraesCS1B01G308100 chr6B 99.463 559 2 1 1 558 188484661 188485219 0.000000e+00 1014
20 TraesCS1B01G308100 chr5B 99.463 559 2 1 1 558 170536554 170535996 0.000000e+00 1014
21 TraesCS1B01G308100 chr7B 99.461 557 3 0 2 558 714479797 714480353 0.000000e+00 1013
22 TraesCS1B01G308100 chrUn 98.934 563 5 1 1 562 380145919 380145357 0.000000e+00 1005


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 TraesCS1B01G308100 chr1B 530760605 530765279 4674 True 8634.0 8634 100.0000 1 4675 1 chr1B.!!$R1 4674
1 TraesCS1B01G308100 chr1B 95491441 95495557 4116 False 7239.0 7239 98.3980 556 4675 1 chr1B.!!$F1 4119
2 TraesCS1B01G308100 chr1B 633166873 633167436 563 False 1009.0 1009 98.9400 1 565 1 chr1B.!!$F2 564
3 TraesCS1B01G308100 chr2A 374483078 374487193 4115 False 7167.0 7167 98.0830 556 4675 1 chr2A.!!$F2 4119
4 TraesCS1B01G308100 chr2A 628644694 628648808 4114 True 7134.0 7134 97.9600 560 4675 1 chr2A.!!$R1 4115
5 TraesCS1B01G308100 chr2A 161526270 161530384 4114 False 7121.0 7121 97.8890 556 4675 1 chr2A.!!$F1 4119
6 TraesCS1B01G308100 chr2A 628569208 628573324 4116 False 7103.0 7103 97.8160 560 4675 1 chr2A.!!$F3 4115
7 TraesCS1B01G308100 chr2B 424681499 424685618 4119 True 7155.0 7155 98.0120 556 4675 1 chr2B.!!$R2 4119
8 TraesCS1B01G308100 chr2B 244759928 244763240 3312 True 5415.0 5415 96.2380 1375 4675 1 chr2B.!!$R1 3300
9 TraesCS1B01G308100 chr2B 244701024 244704950 3926 False 3100.5 5879 94.6845 671 4675 2 chr2B.!!$F2 4004
10 TraesCS1B01G308100 chr2B 38880606 38881179 573 False 1000.0 1000 98.2580 1 569 1 chr2B.!!$F1 568
11 TraesCS1B01G308100 chr1A 409608632 409612754 4122 False 7134.0 7134 97.9140 556 4675 1 chr1A.!!$F2 4119
12 TraesCS1B01G308100 chr1A 3838758 3839316 558 True 1011.0 1011 99.2860 1 559 1 chr1A.!!$R1 558
13 TraesCS1B01G308100 chr1A 185853698 185854256 558 False 1011.0 1011 99.2840 1 559 1 chr1A.!!$F1 558
14 TraesCS1B01G308100 chr1A 555109338 555109896 558 True 1011.0 1011 99.2860 1 559 1 chr1A.!!$R2 558
15 TraesCS1B01G308100 chr7D 474677238 474680468 3230 False 5498.0 5498 97.4030 1448 4675 1 chr7D.!!$F1 3227
16 TraesCS1B01G308100 chr5A 272284484 272287381 2897 False 4715.0 4715 96.0080 918 3821 1 chr5A.!!$F1 2903
17 TraesCS1B01G308100 chr6B 188484661 188485219 558 False 1014.0 1014 99.4630 1 558 1 chr6B.!!$F1 557
18 TraesCS1B01G308100 chr5B 170535996 170536554 558 True 1014.0 1014 99.4630 1 558 1 chr5B.!!$R1 557
19 TraesCS1B01G308100 chr7B 714479797 714480353 556 False 1013.0 1013 99.4610 2 558 1 chr7B.!!$F1 556
20 TraesCS1B01G308100 chrUn 380145357 380145919 562 True 1005.0 1005 98.9340 1 562 1 chrUn.!!$R1 561

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
489 490 0.165944 CCTTTAGTCGCGCCTGTTTG 59.834 55.0 0.00 0.0 0.00 2.93 F
490 491 0.165944 CTTTAGTCGCGCCTGTTTGG 59.834 55.0 0.00 0.0 39.35 3.28 F
539 540 0.316689 GTTGCGAACCACGACCAAAG 60.317 55.0 0.00 0.0 45.77 2.77 F
550 551 0.317160 CGACCAAAGGCCCTTTTTCC 59.683 55.0 5.84 0.0 30.60 3.13 F
553 554 0.396435 CCAAAGGCCCTTTTTCCACC 59.604 55.0 5.84 0.0 30.60 4.61 F
1929 1938 1.029947 GCCGTCGACCCCAAAATCAT 61.030 55.0 10.58 0.0 0.00 2.45 F
2393 2407 1.056660 GAGGGTCACCAAGGTTGAGA 58.943 55.0 0.00 0.0 40.13 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 1611 1.473677 ACATGTGTCCCATCAATTGCG 59.526 47.619 0.00 0.0 0.00 4.85 R
1822 1831 2.175202 GGCATAACCACCATCAACCAA 58.825 47.619 0.00 0.0 38.86 3.67 R
1949 1958 3.063452 GTGATTTCGTAACACGGCATGAT 59.937 43.478 0.00 0.0 42.81 2.45 R
2093 2102 4.583871 ACGCTCATCTCCTTTTTCAGATT 58.416 39.130 0.00 0.0 0.00 2.40 R
2581 2595 3.895232 TTCCACTGTGCTCTATCTTCC 57.105 47.619 1.29 0.0 0.00 3.46 R
2838 2852 0.179089 CGCTAGAATCCTGCACTGCT 60.179 55.000 1.98 0.0 0.00 4.24 R
4180 4216 1.337260 GCACCTTCGCTCTTCTTCTGA 60.337 52.381 0.00 0.0 0.00 3.27 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
464 465 1.717194 TAAGCAACCGCGACTAAAGG 58.283 50.000 8.23 0.00 45.49 3.11
465 466 0.953960 AAGCAACCGCGACTAAAGGG 60.954 55.000 8.23 0.00 45.49 3.95
466 467 2.396157 GCAACCGCGACTAAAGGGG 61.396 63.158 8.23 0.00 45.85 4.79
467 468 1.743995 CAACCGCGACTAAAGGGGG 60.744 63.158 8.23 0.00 44.84 5.40
484 485 4.468689 GGGCCTTTAGTCGCGCCT 62.469 66.667 0.84 0.00 41.35 5.52
485 486 3.195698 GGCCTTTAGTCGCGCCTG 61.196 66.667 0.00 0.00 38.41 4.85
486 487 2.434359 GCCTTTAGTCGCGCCTGT 60.434 61.111 0.00 0.00 0.00 4.00
487 488 2.033194 GCCTTTAGTCGCGCCTGTT 61.033 57.895 0.00 0.00 0.00 3.16
488 489 1.574702 GCCTTTAGTCGCGCCTGTTT 61.575 55.000 0.00 0.00 0.00 2.83
489 490 0.165944 CCTTTAGTCGCGCCTGTTTG 59.834 55.000 0.00 0.00 0.00 2.93
490 491 0.165944 CTTTAGTCGCGCCTGTTTGG 59.834 55.000 0.00 0.00 39.35 3.28
491 492 0.533308 TTTAGTCGCGCCTGTTTGGT 60.533 50.000 0.00 0.00 38.35 3.67
492 493 0.947180 TTAGTCGCGCCTGTTTGGTC 60.947 55.000 0.00 0.00 38.35 4.02
493 494 4.072088 GTCGCGCCTGTTTGGTCG 62.072 66.667 0.00 0.00 38.35 4.79
498 499 3.284449 GCCTGTTTGGTCGCGGTT 61.284 61.111 6.13 0.00 38.35 4.44
499 500 2.637025 CCTGTTTGGTCGCGGTTG 59.363 61.111 6.13 0.00 0.00 3.77
500 501 2.051345 CTGTTTGGTCGCGGTTGC 60.051 61.111 6.13 0.00 37.91 4.17
518 519 2.403586 GCAACCGCGACTAATGGC 59.596 61.111 8.23 0.00 0.00 4.40
519 520 2.395360 GCAACCGCGACTAATGGCA 61.395 57.895 8.23 0.00 0.00 4.92
520 521 1.715585 CAACCGCGACTAATGGCAG 59.284 57.895 8.23 0.00 0.00 4.85
521 522 1.019278 CAACCGCGACTAATGGCAGT 61.019 55.000 8.23 0.00 0.00 4.40
522 523 0.321298 AACCGCGACTAATGGCAGTT 60.321 50.000 8.23 0.00 0.00 3.16
523 524 1.019278 ACCGCGACTAATGGCAGTTG 61.019 55.000 8.23 0.00 33.66 3.16
525 526 1.060937 GCGACTAATGGCAGTTGCG 59.939 57.895 0.00 0.70 44.02 4.85
526 527 1.358725 GCGACTAATGGCAGTTGCGA 61.359 55.000 14.22 0.00 44.02 5.10
527 528 1.075542 CGACTAATGGCAGTTGCGAA 58.924 50.000 0.00 0.00 43.26 4.70
528 529 1.201921 CGACTAATGGCAGTTGCGAAC 60.202 52.381 0.00 0.00 43.26 3.95
529 530 1.130561 GACTAATGGCAGTTGCGAACC 59.869 52.381 0.00 0.00 43.26 3.62
530 531 1.164411 CTAATGGCAGTTGCGAACCA 58.836 50.000 0.00 0.00 43.26 3.67
531 532 0.878416 TAATGGCAGTTGCGAACCAC 59.122 50.000 0.00 0.00 43.26 4.16
532 533 2.128853 AATGGCAGTTGCGAACCACG 62.129 55.000 0.00 0.00 43.26 4.94
533 534 2.970324 GGCAGTTGCGAACCACGA 60.970 61.111 0.00 0.00 45.77 4.35
534 535 2.248431 GCAGTTGCGAACCACGAC 59.752 61.111 0.00 0.00 45.77 4.34
535 536 2.935955 CAGTTGCGAACCACGACC 59.064 61.111 0.00 0.00 45.77 4.79
536 537 1.885388 CAGTTGCGAACCACGACCA 60.885 57.895 0.00 0.00 45.77 4.02
537 538 1.153329 AGTTGCGAACCACGACCAA 60.153 52.632 0.00 0.00 45.77 3.67
538 539 0.745128 AGTTGCGAACCACGACCAAA 60.745 50.000 0.00 0.00 45.77 3.28
539 540 0.316689 GTTGCGAACCACGACCAAAG 60.317 55.000 0.00 0.00 45.77 2.77
540 541 1.440938 TTGCGAACCACGACCAAAGG 61.441 55.000 0.00 0.00 45.77 3.11
541 542 2.943653 CGAACCACGACCAAAGGC 59.056 61.111 0.00 0.00 45.77 4.35
542 543 2.613506 CGAACCACGACCAAAGGCC 61.614 63.158 0.00 0.00 45.77 5.19
543 544 2.203437 AACCACGACCAAAGGCCC 60.203 61.111 0.00 0.00 0.00 5.80
544 545 2.692273 GAACCACGACCAAAGGCCCT 62.692 60.000 0.00 0.00 0.00 5.19
545 546 2.115266 CCACGACCAAAGGCCCTT 59.885 61.111 0.00 0.00 0.00 3.95
546 547 1.530655 CCACGACCAAAGGCCCTTT 60.531 57.895 1.93 1.93 33.58 3.11
547 548 1.112916 CCACGACCAAAGGCCCTTTT 61.113 55.000 5.84 0.00 30.60 2.27
548 549 0.750249 CACGACCAAAGGCCCTTTTT 59.250 50.000 5.84 0.00 30.60 1.94
549 550 1.037493 ACGACCAAAGGCCCTTTTTC 58.963 50.000 5.84 5.31 30.60 2.29
550 551 0.317160 CGACCAAAGGCCCTTTTTCC 59.683 55.000 5.84 0.00 30.60 3.13
551 552 1.419381 GACCAAAGGCCCTTTTTCCA 58.581 50.000 5.84 0.00 30.60 3.53
552 553 1.070134 GACCAAAGGCCCTTTTTCCAC 59.930 52.381 5.84 0.00 30.60 4.02
553 554 0.396435 CCAAAGGCCCTTTTTCCACC 59.604 55.000 5.84 0.00 30.60 4.61
554 555 1.127343 CAAAGGCCCTTTTTCCACCA 58.873 50.000 5.84 0.00 30.60 4.17
558 559 1.367471 GCCCTTTTTCCACCAGTGC 59.633 57.895 0.00 0.00 0.00 4.40
591 592 6.061441 TCTGTTCTTCATTGGTACACATTGT 58.939 36.000 0.00 0.00 39.29 2.71
902 908 6.804677 TGAAGAATTTTTGCTCTTACTGCAA 58.195 32.000 0.00 0.00 46.90 4.08
950 957 5.784578 TGTAGAACTTGCACTCTTACTGA 57.215 39.130 0.00 0.00 0.00 3.41
979 986 7.396907 TGGTGTAGTAGTAATAACTAGCCACAA 59.603 37.037 0.00 0.00 38.89 3.33
1373 1381 2.539338 TTCGGTTTGGTCACAGCGC 61.539 57.895 0.00 0.00 33.92 5.92
1678 1687 5.509498 CATTCAGAAATAGGAAAGGGACCA 58.491 41.667 0.00 0.00 0.00 4.02
1822 1831 2.597578 ACCTCCGGGCAAGTTTTATT 57.402 45.000 0.00 0.00 35.63 1.40
1929 1938 1.029947 GCCGTCGACCCCAAAATCAT 61.030 55.000 10.58 0.00 0.00 2.45
1949 1958 5.406163 TCATAGGGAGCTATTCAATCTCCA 58.594 41.667 7.31 0.00 46.24 3.86
2093 2102 5.469760 CGGCAATCTTACATAACATCATCCA 59.530 40.000 0.00 0.00 0.00 3.41
2393 2407 1.056660 GAGGGTCACCAAGGTTGAGA 58.943 55.000 0.00 0.00 40.13 3.27
2581 2595 6.751425 ACATTAACATACAATGTGGAAATGCG 59.249 34.615 15.65 0.00 43.27 4.73
3239 3267 2.169352 TGGAGGAGCTAGCAAGAATCAC 59.831 50.000 18.83 3.54 0.00 3.06
3296 3324 4.205587 GAGAAAGGGTGCAGATTGATGAT 58.794 43.478 0.00 0.00 0.00 2.45
3305 3333 5.009710 GGTGCAGATTGATGATGATGTTGAT 59.990 40.000 0.00 0.00 0.00 2.57
4035 4071 8.593945 AAAGGGATGCTTTTAACATAGATCAA 57.406 30.769 0.00 0.00 0.00 2.57
4180 4216 5.819901 GCAGGAGTTCTACATAAGAATGCTT 59.180 40.000 0.00 0.00 45.84 3.91
4453 4574 8.971321 CCTGTTCAAATCTTAGAATTGTTGTTG 58.029 33.333 9.51 0.03 0.00 3.33
4502 4623 6.112734 ACTGTCAGTGTTATTGTCACTTCAA 58.887 36.000 4.21 0.00 43.14 2.69
4590 4718 0.182537 CTGTTGTCCCTGTGGTCCAA 59.817 55.000 0.00 0.00 0.00 3.53
4638 4766 1.141657 AGAGTGGCGTGGATTGCATAT 59.858 47.619 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
467 468 4.468689 AGGCGCGACTAAAGGCCC 62.469 66.667 16.12 0.00 46.75 5.80
468 469 3.195698 CAGGCGCGACTAAAGGCC 61.196 66.667 17.67 0.00 45.91 5.19
469 470 1.574702 AAACAGGCGCGACTAAAGGC 61.575 55.000 17.67 0.00 0.00 4.35
470 471 0.165944 CAAACAGGCGCGACTAAAGG 59.834 55.000 17.67 4.30 0.00 3.11
471 472 0.165944 CCAAACAGGCGCGACTAAAG 59.834 55.000 17.67 4.78 0.00 1.85
472 473 0.533308 ACCAAACAGGCGCGACTAAA 60.533 50.000 17.67 0.00 43.14 1.85
473 474 0.947180 GACCAAACAGGCGCGACTAA 60.947 55.000 17.67 0.00 43.14 2.24
474 475 1.373748 GACCAAACAGGCGCGACTA 60.374 57.895 17.67 0.00 43.14 2.59
475 476 2.665185 GACCAAACAGGCGCGACT 60.665 61.111 9.84 9.84 43.14 4.18
476 477 4.072088 CGACCAAACAGGCGCGAC 62.072 66.667 12.10 7.34 43.14 5.19
481 482 3.284449 AACCGCGACCAAACAGGC 61.284 61.111 8.23 0.00 43.14 4.85
482 483 2.637025 CAACCGCGACCAAACAGG 59.363 61.111 8.23 0.00 45.67 4.00
483 484 2.051345 GCAACCGCGACCAAACAG 60.051 61.111 8.23 0.00 0.00 3.16
501 502 2.309764 CTGCCATTAGTCGCGGTTGC 62.310 60.000 6.13 0.28 37.91 4.17
502 503 1.019278 ACTGCCATTAGTCGCGGTTG 61.019 55.000 6.13 0.00 41.86 3.77
503 504 1.295423 ACTGCCATTAGTCGCGGTT 59.705 52.632 6.13 0.00 41.86 4.44
504 505 1.019278 CAACTGCCATTAGTCGCGGT 61.019 55.000 6.13 0.00 46.47 5.68
505 506 1.715585 CAACTGCCATTAGTCGCGG 59.284 57.895 6.13 0.00 37.39 6.46
506 507 1.060937 GCAACTGCCATTAGTCGCG 59.939 57.895 0.00 0.00 34.31 5.87
507 508 1.060937 CGCAACTGCCATTAGTCGC 59.939 57.895 0.00 0.00 37.91 5.19
508 509 1.075542 TTCGCAACTGCCATTAGTCG 58.924 50.000 0.00 0.00 37.91 4.18
509 510 1.130561 GGTTCGCAACTGCCATTAGTC 59.869 52.381 0.00 0.00 37.91 2.59
510 511 1.165270 GGTTCGCAACTGCCATTAGT 58.835 50.000 0.00 0.00 37.91 2.24
511 512 1.135689 GTGGTTCGCAACTGCCATTAG 60.136 52.381 0.00 0.00 37.91 1.73
512 513 0.878416 GTGGTTCGCAACTGCCATTA 59.122 50.000 0.00 0.00 37.91 1.90
513 514 1.659794 GTGGTTCGCAACTGCCATT 59.340 52.632 0.00 0.00 37.91 3.16
514 515 2.616330 CGTGGTTCGCAACTGCCAT 61.616 57.895 0.00 0.00 37.91 4.40
515 516 3.276091 CGTGGTTCGCAACTGCCA 61.276 61.111 0.00 0.00 37.91 4.92
516 517 2.970324 TCGTGGTTCGCAACTGCC 60.970 61.111 0.00 0.00 39.67 4.85
517 518 2.248431 GTCGTGGTTCGCAACTGC 59.752 61.111 0.00 0.00 39.67 4.40
518 519 1.433053 TTGGTCGTGGTTCGCAACTG 61.433 55.000 0.00 0.00 39.67 3.16
519 520 0.745128 TTTGGTCGTGGTTCGCAACT 60.745 50.000 0.00 0.00 39.67 3.16
520 521 0.316689 CTTTGGTCGTGGTTCGCAAC 60.317 55.000 0.00 0.00 39.67 4.17
521 522 1.440938 CCTTTGGTCGTGGTTCGCAA 61.441 55.000 0.00 0.00 39.67 4.85
522 523 1.890041 CCTTTGGTCGTGGTTCGCA 60.890 57.895 0.00 0.00 39.67 5.10
523 524 2.943653 CCTTTGGTCGTGGTTCGC 59.056 61.111 0.00 0.00 39.67 4.70
524 525 2.613506 GGCCTTTGGTCGTGGTTCG 61.614 63.158 0.00 0.00 41.41 3.95
525 526 2.265904 GGGCCTTTGGTCGTGGTTC 61.266 63.158 0.84 0.00 0.00 3.62
526 527 2.203437 GGGCCTTTGGTCGTGGTT 60.203 61.111 0.84 0.00 0.00 3.67
527 528 2.292785 AAAGGGCCTTTGGTCGTGGT 62.293 55.000 29.99 2.81 31.98 4.16
528 529 1.112916 AAAAGGGCCTTTGGTCGTGG 61.113 55.000 31.06 0.00 33.64 4.94
529 530 0.750249 AAAAAGGGCCTTTGGTCGTG 59.250 50.000 31.06 0.00 33.64 4.35
530 531 1.037493 GAAAAAGGGCCTTTGGTCGT 58.963 50.000 31.06 13.21 33.64 4.34
531 532 0.317160 GGAAAAAGGGCCTTTGGTCG 59.683 55.000 31.06 0.00 33.64 4.79
532 533 1.070134 GTGGAAAAAGGGCCTTTGGTC 59.930 52.381 31.06 27.31 33.64 4.02
533 534 1.128200 GTGGAAAAAGGGCCTTTGGT 58.872 50.000 31.06 21.81 33.64 3.67
534 535 0.396435 GGTGGAAAAAGGGCCTTTGG 59.604 55.000 31.06 0.00 33.64 3.28
535 536 1.070601 CTGGTGGAAAAAGGGCCTTTG 59.929 52.381 31.06 12.80 33.64 2.77
536 537 1.343985 ACTGGTGGAAAAAGGGCCTTT 60.344 47.619 25.68 25.68 34.94 3.11
537 538 0.264657 ACTGGTGGAAAAAGGGCCTT 59.735 50.000 14.48 14.48 0.00 4.35
538 539 0.469892 CACTGGTGGAAAAAGGGCCT 60.470 55.000 0.00 0.00 0.00 5.19
539 540 2.049435 CACTGGTGGAAAAAGGGCC 58.951 57.895 0.00 0.00 0.00 5.80
540 541 1.367471 GCACTGGTGGAAAAAGGGC 59.633 57.895 2.84 0.00 32.30 5.19
541 542 0.821711 TCGCACTGGTGGAAAAAGGG 60.822 55.000 2.84 0.00 0.00 3.95
542 543 1.200020 GATCGCACTGGTGGAAAAAGG 59.800 52.381 2.84 0.00 0.00 3.11
543 544 1.879380 TGATCGCACTGGTGGAAAAAG 59.121 47.619 2.84 0.00 0.00 2.27
544 545 1.974265 TGATCGCACTGGTGGAAAAA 58.026 45.000 2.84 0.00 0.00 1.94
545 546 2.083774 GATGATCGCACTGGTGGAAAA 58.916 47.619 2.84 0.00 0.00 2.29
546 547 1.003003 TGATGATCGCACTGGTGGAAA 59.997 47.619 2.84 0.00 0.00 3.13
547 548 0.612744 TGATGATCGCACTGGTGGAA 59.387 50.000 2.84 0.00 0.00 3.53
548 549 0.832626 ATGATGATCGCACTGGTGGA 59.167 50.000 2.84 0.00 0.00 4.02
549 550 1.202615 AGATGATGATCGCACTGGTGG 60.203 52.381 2.84 0.00 33.34 4.61
550 551 1.865340 CAGATGATGATCGCACTGGTG 59.135 52.381 0.00 0.00 33.34 4.17
551 552 1.483827 ACAGATGATGATCGCACTGGT 59.516 47.619 14.22 3.93 33.34 4.00
552 553 2.235845 ACAGATGATGATCGCACTGG 57.764 50.000 14.22 3.51 33.34 4.00
553 554 3.455327 AGAACAGATGATGATCGCACTG 58.545 45.455 10.21 10.21 35.91 3.66
554 555 3.815856 AGAACAGATGATGATCGCACT 57.184 42.857 0.00 0.00 35.91 4.40
558 559 5.526479 ACCAATGAAGAACAGATGATGATCG 59.474 40.000 0.00 0.00 35.91 3.69
691 692 1.614903 CAATTCAGGGTCTTGCTGCAA 59.385 47.619 15.16 15.16 0.00 4.08
932 939 5.239525 ACCAAATCAGTAAGAGTGCAAGTTC 59.760 40.000 0.00 0.00 0.00 3.01
950 957 8.984855 TGGCTAGTTATTACTACTACACCAAAT 58.015 33.333 0.00 0.00 35.78 2.32
979 986 8.940397 TCCATTCCAAGTCTAAAGAAGAAAAT 57.060 30.769 0.00 0.00 35.47 1.82
1602 1611 1.473677 ACATGTGTCCCATCAATTGCG 59.526 47.619 0.00 0.00 0.00 4.85
1822 1831 2.175202 GGCATAACCACCATCAACCAA 58.825 47.619 0.00 0.00 38.86 3.67
1929 1938 5.406163 TGATGGAGATTGAATAGCTCCCTA 58.594 41.667 9.62 0.00 46.01 3.53
1949 1958 3.063452 GTGATTTCGTAACACGGCATGAT 59.937 43.478 0.00 0.00 42.81 2.45
2093 2102 4.583871 ACGCTCATCTCCTTTTTCAGATT 58.416 39.130 0.00 0.00 0.00 2.40
2581 2595 3.895232 TTCCACTGTGCTCTATCTTCC 57.105 47.619 1.29 0.00 0.00 3.46
2838 2852 0.179089 CGCTAGAATCCTGCACTGCT 60.179 55.000 1.98 0.00 0.00 4.24
3296 3324 3.435327 GCACGTAAACCTCATCAACATCA 59.565 43.478 0.00 0.00 0.00 3.07
3305 3333 3.690139 TGTTTTCTTGCACGTAAACCTCA 59.310 39.130 18.39 2.62 31.25 3.86
3924 3958 6.739331 AAATCAGCCTAGACTAGCTACAAT 57.261 37.500 3.76 0.00 37.18 2.71
4035 4071 9.440761 ACAGTAGGTAAATCAATCTCTATCCTT 57.559 33.333 0.00 0.00 0.00 3.36
4180 4216 1.337260 GCACCTTCGCTCTTCTTCTGA 60.337 52.381 0.00 0.00 0.00 3.27
4502 4623 3.875727 GCAGTAATGACACAGATGCAGAT 59.124 43.478 0.00 0.00 32.58 2.90
4590 4718 0.849094 TGGTTAGTCCCCAAGGGCAT 60.849 55.000 0.00 0.00 43.94 4.40
4638 4766 4.863415 GGACCAAATCCCTGCCAA 57.137 55.556 0.00 0.00 42.46 4.52


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

AutoCloner maintained by Alex Coulton.