Multiple sequence alignment - TraesCS2D01G092700

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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 TraesCS2D01G092700 chr2D 100.000 2252 0 0 1 2252 44081701 44083952 0.000000e+00 4159
1 TraesCS2D01G092700 chr2B 89.019 1712 66 58 613 2243 69417082 69418752 0.000000e+00 2008
2 TraesCS2D01G092700 chr2B 88.471 425 19 13 23 419 69416635 69417057 9.350000e-134 486
3 TraesCS2D01G092700 chr2B 91.525 118 4 4 2096 2213 68622054 68621943 8.330000e-35 158
4 TraesCS2D01G092700 chr2A 85.023 1095 60 43 613 1651 47913300 47914346 0.000000e+00 1018
5 TraesCS2D01G092700 chr2A 92.394 447 26 2 1 445 47912841 47913281 4.080000e-177 630
6 TraesCS2D01G092700 chr2A 91.379 116 8 2 2138 2252 47914717 47914831 8.330000e-35 158
7 TraesCS2D01G092700 chr2A 86.713 143 12 3 1835 1970 47914502 47914644 3.870000e-33 152
8 TraesCS2D01G092700 chr5B 85.256 156 17 3 449 600 177644132 177644285 2.990000e-34 156
9 TraesCS2D01G092700 chr5B 85.806 155 11 8 449 597 659402763 659402912 1.080000e-33 154
10 TraesCS2D01G092700 chr5B 88.000 125 7 8 2094 2213 563122901 563123022 8.390000e-30 141
11 TraesCS2D01G092700 chr4A 92.035 113 6 2 2105 2214 655448609 655448721 2.990000e-34 156
12 TraesCS2D01G092700 chr4A 90.991 111 7 2 2105 2212 655568665 655568775 1.800000e-31 147
13 TraesCS2D01G092700 chr4A 89.167 120 7 5 2094 2211 647382098 647382213 6.480000e-31 145
14 TraesCS2D01G092700 chr7D 90.991 111 6 4 2106 2213 44403247 44403356 1.800000e-31 147
15 TraesCS2D01G092700 chr7D 90.991 111 6 4 2106 2213 44571464 44571573 1.800000e-31 147
16 TraesCS2D01G092700 chr5D 84.416 154 18 3 451 600 482642463 482642312 1.800000e-31 147
17 TraesCS2D01G092700 chr6B 84.177 158 16 5 448 600 499005493 499005340 6.480000e-31 145
18 TraesCS2D01G092700 chr3A 83.974 156 19 3 449 600 596005708 596005861 6.480000e-31 145
19 TraesCS2D01G092700 chr6D 98.750 80 1 0 1 80 335166280 335166201 2.330000e-30 143
20 TraesCS2D01G092700 chr4D 98.750 80 1 0 1 80 38580525 38580604 2.330000e-30 143
21 TraesCS2D01G092700 chr4D 98.750 80 1 0 1 80 54782892 54782813 2.330000e-30 143
22 TraesCS2D01G092700 chr4D 98.750 80 1 0 1 80 231624566 231624645 2.330000e-30 143
23 TraesCS2D01G092700 chr4D 83.974 156 18 4 449 600 364544286 364544438 2.330000e-30 143
24 TraesCS2D01G092700 chr4D 82.530 166 22 4 439 600 483092906 483093068 3.020000e-29 139
25 TraesCS2D01G092700 chr3D 98.750 80 1 0 1 80 8765861 8765782 2.330000e-30 143
26 TraesCS2D01G092700 chr3D 83.974 156 18 4 449 600 488387504 488387656 2.330000e-30 143
27 TraesCS2D01G092700 chr3D 98.750 80 1 0 1 80 515325297 515325218 2.330000e-30 143
28 TraesCS2D01G092700 chr1D 98.750 80 1 0 1 80 293923995 293923916 2.330000e-30 143
29 TraesCS2D01G092700 chr1D 98.750 80 1 0 1 80 368919281 368919360 2.330000e-30 143
30 TraesCS2D01G092700 chr1A 83.871 155 20 3 449 600 538381627 538381779 2.330000e-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 TraesCS2D01G092700 chr2D 44081701 44083952 2251 False 4159.0 4159 100.00000 1 2252 1 chr2D.!!$F1 2251
1 TraesCS2D01G092700 chr2B 69416635 69418752 2117 False 1247.0 2008 88.74500 23 2243 2 chr2B.!!$F1 2220
2 TraesCS2D01G092700 chr2A 47912841 47914831 1990 False 489.5 1018 88.87725 1 2252 4 chr2A.!!$F1 2251

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
266 295 0.17907 GAAAGATGCCTCCGGTCTCC 60.179 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1285 1359 0.034186 CAGAGCAGGGCCAATACCAA 60.034 55.0 6.18 0.0 0.0 3.67 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
87 88 6.016276 TCCTGGCACAAAAGAAGAGAATAAAC 60.016 38.462 0.00 0.00 38.70 2.01
98 99 8.846423 AAGAAGAGAATAAACATCTCCCTCTA 57.154 34.615 0.00 0.00 43.52 2.43
135 159 4.454504 AGACAATAAAGCAACACCCTAACG 59.545 41.667 0.00 0.00 0.00 3.18
137 161 2.554370 TAAAGCAACACCCTAACGCT 57.446 45.000 0.00 0.00 33.45 5.07
179 208 1.547372 AGGCATGCATGTGTTCCTTTC 59.453 47.619 26.79 7.51 0.00 2.62
243 272 0.868406 CCTTTGTTGTCGTCCTCAGC 59.132 55.000 0.00 0.00 0.00 4.26
255 284 1.821332 CCTCAGCGGGGAAAGATGC 60.821 63.158 0.00 0.00 0.00 3.91
266 295 0.179070 GAAAGATGCCTCCGGTCTCC 60.179 60.000 0.00 0.00 0.00 3.71
405 434 4.452455 GGACAAGTTGAACATCGATCTGTT 59.548 41.667 10.54 4.10 41.92 3.16
451 480 8.888579 ACTACTCCAGTAAAATATTCATTCCG 57.111 34.615 0.00 0.00 34.98 4.30
452 481 8.483758 ACTACTCCAGTAAAATATTCATTCCGT 58.516 33.333 0.00 0.00 34.98 4.69
453 482 9.326413 CTACTCCAGTAAAATATTCATTCCGTT 57.674 33.333 0.00 0.00 0.00 4.44
454 483 8.209917 ACTCCAGTAAAATATTCATTCCGTTC 57.790 34.615 0.00 0.00 0.00 3.95
455 484 7.282450 ACTCCAGTAAAATATTCATTCCGTTCC 59.718 37.037 0.00 0.00 0.00 3.62
456 485 7.343357 TCCAGTAAAATATTCATTCCGTTCCT 58.657 34.615 0.00 0.00 0.00 3.36
457 486 8.487848 TCCAGTAAAATATTCATTCCGTTCCTA 58.512 33.333 0.00 0.00 0.00 2.94
458 487 9.116067 CCAGTAAAATATTCATTCCGTTCCTAA 57.884 33.333 0.00 0.00 0.00 2.69
497 526 9.958234 TTTTAAGATTTCAAATGAATCGTCACA 57.042 25.926 0.00 0.00 36.31 3.58
515 550 6.604930 CGTCACATACGGATGTATATACACA 58.395 40.000 14.23 0.00 44.82 3.72
516 551 7.248437 CGTCACATACGGATGTATATACACAT 58.752 38.462 14.23 4.21 44.82 3.21
517 552 7.218204 CGTCACATACGGATGTATATACACATG 59.782 40.741 14.23 15.99 44.82 3.21
518 553 8.027189 GTCACATACGGATGTATATACACATGT 58.973 37.037 14.23 16.51 44.82 3.21
519 554 8.581578 TCACATACGGATGTATATACACATGTT 58.418 33.333 14.23 1.59 44.82 2.71
520 555 9.203421 CACATACGGATGTATATACACATGTTT 57.797 33.333 14.23 8.54 44.82 2.83
521 556 9.772973 ACATACGGATGTATATACACATGTTTT 57.227 29.630 12.79 0.08 44.77 2.43
537 572 9.507329 ACACATGTTTTAGAATGTAGATTCACT 57.493 29.630 14.46 0.00 40.59 3.41
538 573 9.979270 CACATGTTTTAGAATGTAGATTCACTC 57.021 33.333 14.46 2.09 40.59 3.51
539 574 9.725019 ACATGTTTTAGAATGTAGATTCACTCA 57.275 29.630 14.46 6.83 40.59 3.41
549 584 9.855361 GAATGTAGATTCACTCATTTTGTATCG 57.145 33.333 7.69 0.00 38.33 2.92
550 585 8.948631 ATGTAGATTCACTCATTTTGTATCGT 57.051 30.769 0.00 0.00 0.00 3.73
581 616 9.956720 AGTCATTTGTTGAAATTTTCTAGACAG 57.043 29.630 10.33 2.96 35.70 3.51
582 617 9.950680 GTCATTTGTTGAAATTTTCTAGACAGA 57.049 29.630 10.33 8.08 35.70 3.41
598 633 8.167605 TCTAGACAGATATTTAGAAACGGAGG 57.832 38.462 0.00 0.00 0.00 4.30
599 634 6.163135 AGACAGATATTTAGAAACGGAGGG 57.837 41.667 0.00 0.00 0.00 4.30
600 635 5.070580 AGACAGATATTTAGAAACGGAGGGG 59.929 44.000 0.00 0.00 0.00 4.79
601 636 4.102681 ACAGATATTTAGAAACGGAGGGGG 59.897 45.833 0.00 0.00 0.00 5.40
602 637 4.347000 CAGATATTTAGAAACGGAGGGGGA 59.653 45.833 0.00 0.00 0.00 4.81
603 638 4.593634 AGATATTTAGAAACGGAGGGGGAG 59.406 45.833 0.00 0.00 0.00 4.30
604 639 1.282382 TTTAGAAACGGAGGGGGAGG 58.718 55.000 0.00 0.00 0.00 4.30
605 640 0.619543 TTAGAAACGGAGGGGGAGGG 60.620 60.000 0.00 0.00 0.00 4.30
606 641 1.521119 TAGAAACGGAGGGGGAGGGA 61.521 60.000 0.00 0.00 0.00 4.20
607 642 2.285442 AAACGGAGGGGGAGGGAG 60.285 66.667 0.00 0.00 0.00 4.30
608 643 2.817420 GAAACGGAGGGGGAGGGAGA 62.817 65.000 0.00 0.00 0.00 3.71
609 644 2.824388 AAACGGAGGGGGAGGGAGAG 62.824 65.000 0.00 0.00 0.00 3.20
610 645 3.430497 CGGAGGGGGAGGGAGAGA 61.430 72.222 0.00 0.00 0.00 3.10
611 646 2.612251 GGAGGGGGAGGGAGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
612 647 2.329399 GGAGGGGGAGGGAGAGAGT 61.329 68.421 0.00 0.00 0.00 3.24
613 648 1.000041 GGAGGGGGAGGGAGAGAGTA 61.000 65.000 0.00 0.00 0.00 2.59
614 649 1.163408 GAGGGGGAGGGAGAGAGTAT 58.837 60.000 0.00 0.00 0.00 2.12
628 663 9.853177 AGGGAGAGAGTATTATAAAATTGTTGG 57.147 33.333 0.00 0.00 0.00 3.77
691 726 1.682684 GCCGAGGACCTTGAGAGGA 60.683 63.158 10.67 0.00 46.74 3.71
705 741 1.450134 GAGGATGGCATGTGACGCA 60.450 57.895 3.81 0.00 0.00 5.24
740 776 1.914634 CGACTATCTGGACACACAGC 58.085 55.000 0.00 0.00 38.36 4.40
968 1024 1.075600 CCACCTCCCTCTCCTCTCC 60.076 68.421 0.00 0.00 0.00 3.71
976 1035 1.541672 CTCTCCTCTCCCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
978 1037 2.018086 CTCCTCTCCCCTCTCCCCT 61.018 68.421 0.00 0.00 0.00 4.79
979 1038 2.015726 TCCTCTCCCCTCTCCCCTC 61.016 68.421 0.00 0.00 0.00 4.30
994 1067 2.262915 CTCGCGGAGGAGCAAAGT 59.737 61.111 6.13 0.00 36.85 2.66
1280 1354 0.458716 CCGCCGTCTTCTTCTTCCTC 60.459 60.000 0.00 0.00 0.00 3.71
1281 1355 0.458716 CGCCGTCTTCTTCTTCCTCC 60.459 60.000 0.00 0.00 0.00 4.30
1282 1356 0.899019 GCCGTCTTCTTCTTCCTCCT 59.101 55.000 0.00 0.00 0.00 3.69
1283 1357 1.134936 GCCGTCTTCTTCTTCCTCCTC 60.135 57.143 0.00 0.00 0.00 3.71
1284 1358 1.478916 CCGTCTTCTTCTTCCTCCTCC 59.521 57.143 0.00 0.00 0.00 4.30
1285 1359 2.452505 CGTCTTCTTCTTCCTCCTCCT 58.547 52.381 0.00 0.00 0.00 3.69
1343 1423 4.250305 GCTCCACCACCACCGTGT 62.250 66.667 0.00 0.00 38.41 4.49
1499 1594 1.374343 CGAGGGACGGACTCATCGAA 61.374 60.000 0.00 0.00 38.46 3.71
1543 1638 6.511416 AGTCACTAGTGTAAGATCATCATGC 58.489 40.000 21.99 0.00 0.00 4.06
1558 1653 3.310352 ATGCATGCATGGGTCCTTT 57.690 47.368 31.74 5.52 35.03 3.11
1602 1712 2.554462 TGTTCTGTTGTCGAGAGAGAGG 59.446 50.000 0.00 0.00 43.49 3.69
1604 1714 0.814457 CTGTTGTCGAGAGAGAGGGG 59.186 60.000 0.00 0.00 43.49 4.79
1625 1749 0.966179 AGAATGTTTGTTTCCGGGGC 59.034 50.000 0.00 0.00 0.00 5.80
1649 1773 0.527565 AGCAACGTTGGCCATCAATC 59.472 50.000 28.33 9.29 37.73 2.67
1650 1774 0.243365 GCAACGTTGGCCATCAATCA 59.757 50.000 28.33 0.00 37.73 2.57
1652 1776 2.598589 CAACGTTGGCCATCAATCAAG 58.401 47.619 20.71 0.00 37.73 3.02
1664 1788 0.521867 CAATCAAGCATCACACGCGG 60.522 55.000 12.47 1.27 0.00 6.46
1693 1817 5.936686 TCTTTCTGCTTCAGTTTCAGATG 57.063 39.130 0.00 0.00 36.81 2.90
1694 1818 5.614308 TCTTTCTGCTTCAGTTTCAGATGA 58.386 37.500 0.00 0.00 36.81 2.92
1737 1861 2.358898 TGCTTCACTTCAGTTTGCTTCC 59.641 45.455 0.00 0.00 0.00 3.46
1751 1875 1.539388 TGCTTCCGCAAAACATACCTG 59.461 47.619 0.00 0.00 44.62 4.00
1752 1876 1.135402 GCTTCCGCAAAACATACCTGG 60.135 52.381 0.00 0.00 35.78 4.45
1753 1877 2.159382 CTTCCGCAAAACATACCTGGT 58.841 47.619 4.05 4.05 0.00 4.00
1852 2009 2.531508 GCGCACGAATGAAAATGAATCC 59.468 45.455 0.30 0.00 0.00 3.01
1941 2137 2.738521 CGCTGGTCCCAGTCAACG 60.739 66.667 14.56 6.02 45.24 4.10
1942 2138 3.050275 GCTGGTCCCAGTCAACGC 61.050 66.667 14.56 0.00 45.24 4.84
1944 2140 4.980805 TGGTCCCAGTCAACGCGC 62.981 66.667 5.73 0.00 0.00 6.86
1994 2190 1.216710 CCGTCAGAGGCTCAGAACC 59.783 63.158 18.26 2.38 0.00 3.62
1995 2191 1.536073 CCGTCAGAGGCTCAGAACCA 61.536 60.000 18.26 0.00 0.00 3.67
1996 2192 0.534412 CGTCAGAGGCTCAGAACCAT 59.466 55.000 18.26 0.00 0.00 3.55
1997 2193 1.066573 CGTCAGAGGCTCAGAACCATT 60.067 52.381 18.26 0.00 0.00 3.16
1998 2194 2.613977 CGTCAGAGGCTCAGAACCATTT 60.614 50.000 18.26 0.00 0.00 2.32
1999 2195 3.416156 GTCAGAGGCTCAGAACCATTTT 58.584 45.455 18.26 0.00 0.00 1.82
2000 2196 3.823304 GTCAGAGGCTCAGAACCATTTTT 59.177 43.478 18.26 0.00 0.00 1.94
2001 2197 3.822735 TCAGAGGCTCAGAACCATTTTTG 59.177 43.478 18.26 1.37 0.00 2.44
2002 2198 3.057033 CAGAGGCTCAGAACCATTTTTGG 60.057 47.826 18.26 0.00 0.00 3.28
2003 2199 1.620323 AGGCTCAGAACCATTTTTGGC 59.380 47.619 0.00 0.00 0.00 4.52
2004 2200 1.669795 GGCTCAGAACCATTTTTGGCG 60.670 52.381 0.00 0.00 0.00 5.69
2006 2202 2.922335 GCTCAGAACCATTTTTGGCGTC 60.922 50.000 0.00 0.00 0.00 5.19
2057 2254 1.478105 GCCACATCCCCTCACAATTTC 59.522 52.381 0.00 0.00 0.00 2.17
2213 2428 2.180086 ACCATCTGAGCTACATCCCCTA 59.820 50.000 0.00 0.00 0.00 3.53
2214 2429 3.242867 CCATCTGAGCTACATCCCCTAA 58.757 50.000 0.00 0.00 0.00 2.69
2221 2436 7.479579 TCTGAGCTACATCCCCTAACTATAAT 58.520 38.462 0.00 0.00 0.00 1.28
2245 2460 7.601073 TGTAATCTTGTCTTCAGCTTATGTG 57.399 36.000 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 208 1.442526 CTTCAGCTTGGCGGCTATGG 61.443 60.000 11.43 0.00 41.00 2.74
243 272 2.203070 CGGAGGCATCTTTCCCCG 60.203 66.667 0.00 0.00 33.46 5.73
428 457 9.321562 GAACGGAATGAATATTTTACTGGAGTA 57.678 33.333 0.00 0.00 0.00 2.59
471 500 9.958234 TGTGACGATTCATTTGAAATCTTAAAA 57.042 25.926 0.00 0.00 37.61 1.52
488 517 7.966753 GTGTATATACATCCGTATGTGACGATT 59.033 37.037 18.27 0.00 45.99 3.34
489 518 7.120138 TGTGTATATACATCCGTATGTGACGAT 59.880 37.037 18.27 0.00 45.99 3.73
490 519 6.427547 TGTGTATATACATCCGTATGTGACGA 59.572 38.462 18.27 0.00 45.99 4.20
491 520 6.604930 TGTGTATATACATCCGTATGTGACG 58.395 40.000 18.27 0.00 45.99 4.35
492 521 8.027189 ACATGTGTATATACATCCGTATGTGAC 58.973 37.037 18.27 2.36 45.99 3.67
493 522 8.117813 ACATGTGTATATACATCCGTATGTGA 57.882 34.615 18.27 0.00 45.99 3.58
494 523 8.757164 AACATGTGTATATACATCCGTATGTG 57.243 34.615 18.27 10.53 45.99 3.21
512 547 9.979270 GAGTGAATCTACATTCTAAAACATGTG 57.021 33.333 0.00 0.00 39.49 3.21
513 548 9.725019 TGAGTGAATCTACATTCTAAAACATGT 57.275 29.630 0.00 0.00 39.49 3.21
523 558 9.855361 CGATACAAAATGAGTGAATCTACATTC 57.145 33.333 0.00 0.00 39.24 2.67
524 559 9.383519 ACGATACAAAATGAGTGAATCTACATT 57.616 29.630 0.00 0.00 34.99 2.71
525 560 8.948631 ACGATACAAAATGAGTGAATCTACAT 57.051 30.769 0.00 0.00 0.00 2.29
555 590 9.956720 CTGTCTAGAAAATTTCAACAAATGACT 57.043 29.630 8.55 0.00 37.92 3.41
556 591 9.950680 TCTGTCTAGAAAATTTCAACAAATGAC 57.049 29.630 8.55 5.87 37.92 3.06
572 607 8.630917 CCTCCGTTTCTAAATATCTGTCTAGAA 58.369 37.037 0.00 0.00 36.32 2.10
573 608 7.230913 CCCTCCGTTTCTAAATATCTGTCTAGA 59.769 40.741 0.00 0.00 37.35 2.43
574 609 7.371936 CCCTCCGTTTCTAAATATCTGTCTAG 58.628 42.308 0.00 0.00 0.00 2.43
575 610 6.267014 CCCCTCCGTTTCTAAATATCTGTCTA 59.733 42.308 0.00 0.00 0.00 2.59
576 611 5.070580 CCCCTCCGTTTCTAAATATCTGTCT 59.929 44.000 0.00 0.00 0.00 3.41
577 612 5.298347 CCCCTCCGTTTCTAAATATCTGTC 58.702 45.833 0.00 0.00 0.00 3.51
578 613 4.102681 CCCCCTCCGTTTCTAAATATCTGT 59.897 45.833 0.00 0.00 0.00 3.41
579 614 4.347000 TCCCCCTCCGTTTCTAAATATCTG 59.653 45.833 0.00 0.00 0.00 2.90
580 615 4.563782 TCCCCCTCCGTTTCTAAATATCT 58.436 43.478 0.00 0.00 0.00 1.98
581 616 4.262938 CCTCCCCCTCCGTTTCTAAATATC 60.263 50.000 0.00 0.00 0.00 1.63
582 617 3.651423 CCTCCCCCTCCGTTTCTAAATAT 59.349 47.826 0.00 0.00 0.00 1.28
583 618 3.043418 CCTCCCCCTCCGTTTCTAAATA 58.957 50.000 0.00 0.00 0.00 1.40
584 619 1.844497 CCTCCCCCTCCGTTTCTAAAT 59.156 52.381 0.00 0.00 0.00 1.40
585 620 1.282382 CCTCCCCCTCCGTTTCTAAA 58.718 55.000 0.00 0.00 0.00 1.85
586 621 0.619543 CCCTCCCCCTCCGTTTCTAA 60.620 60.000 0.00 0.00 0.00 2.10
587 622 1.002533 CCCTCCCCCTCCGTTTCTA 59.997 63.158 0.00 0.00 0.00 2.10
588 623 2.285442 CCCTCCCCCTCCGTTTCT 60.285 66.667 0.00 0.00 0.00 2.52
589 624 2.285144 TCCCTCCCCCTCCGTTTC 60.285 66.667 0.00 0.00 0.00 2.78
590 625 2.285442 CTCCCTCCCCCTCCGTTT 60.285 66.667 0.00 0.00 0.00 3.60
591 626 3.281787 TCTCCCTCCCCCTCCGTT 61.282 66.667 0.00 0.00 0.00 4.44
592 627 3.756783 CTCTCCCTCCCCCTCCGT 61.757 72.222 0.00 0.00 0.00 4.69
593 628 3.430497 TCTCTCCCTCCCCCTCCG 61.430 72.222 0.00 0.00 0.00 4.63
594 629 1.000041 TACTCTCTCCCTCCCCCTCC 61.000 65.000 0.00 0.00 0.00 4.30
595 630 1.163408 ATACTCTCTCCCTCCCCCTC 58.837 60.000 0.00 0.00 0.00 4.30
596 631 1.638959 AATACTCTCTCCCTCCCCCT 58.361 55.000 0.00 0.00 0.00 4.79
597 632 3.856747 ATAATACTCTCTCCCTCCCCC 57.143 52.381 0.00 0.00 0.00 5.40
598 633 7.816300 ATTTTATAATACTCTCTCCCTCCCC 57.184 40.000 0.00 0.00 0.00 4.81
599 634 8.661345 ACAATTTTATAATACTCTCTCCCTCCC 58.339 37.037 0.00 0.00 0.00 4.30
602 637 9.853177 CCAACAATTTTATAATACTCTCTCCCT 57.147 33.333 0.00 0.00 0.00 4.20
603 638 9.847224 TCCAACAATTTTATAATACTCTCTCCC 57.153 33.333 0.00 0.00 0.00 4.30
607 642 9.931210 CCGTTCCAACAATTTTATAATACTCTC 57.069 33.333 0.00 0.00 0.00 3.20
608 643 9.675464 TCCGTTCCAACAATTTTATAATACTCT 57.325 29.630 0.00 0.00 0.00 3.24
609 644 9.712359 GTCCGTTCCAACAATTTTATAATACTC 57.288 33.333 0.00 0.00 0.00 2.59
610 645 9.233649 TGTCCGTTCCAACAATTTTATAATACT 57.766 29.630 0.00 0.00 0.00 2.12
628 663 2.866762 GAGACAAGCCATATGTCCGTTC 59.133 50.000 1.24 0.00 46.60 3.95
640 675 3.173240 GTCGCGTCGAGACAAGCC 61.173 66.667 22.04 0.00 36.23 4.35
691 726 0.806868 CTTTCTGCGTCACATGCCAT 59.193 50.000 0.00 0.00 0.00 4.40
705 741 7.148641 CAGATAGTCGCATTGTATACCTTTCT 58.851 38.462 0.00 0.00 0.00 2.52
740 776 1.078567 GGAAGCAGGGCTCACTCAG 60.079 63.158 0.00 0.00 38.25 3.35
904 940 2.354103 CGACAATGAAGGCCAGAGAGAA 60.354 50.000 5.01 0.00 0.00 2.87
978 1037 2.048222 CACTTTGCTCCTCCGCGA 60.048 61.111 8.23 0.00 0.00 5.87
979 1038 2.048222 TCACTTTGCTCCTCCGCG 60.048 61.111 0.00 0.00 0.00 6.46
983 1042 1.407989 CCATCCCTCACTTTGCTCCTC 60.408 57.143 0.00 0.00 0.00 3.71
1144 1217 2.606587 CCTTGTAGCTGGCCACCCT 61.607 63.158 0.00 3.47 0.00 4.34
1280 1354 0.106519 CAGGGCCAATACCAAGGAGG 60.107 60.000 6.18 0.00 45.67 4.30
1281 1355 0.753111 GCAGGGCCAATACCAAGGAG 60.753 60.000 6.18 0.00 0.00 3.69
1282 1356 1.214305 AGCAGGGCCAATACCAAGGA 61.214 55.000 6.18 0.00 0.00 3.36
1283 1357 0.753111 GAGCAGGGCCAATACCAAGG 60.753 60.000 6.18 0.00 0.00 3.61
1284 1358 0.257039 AGAGCAGGGCCAATACCAAG 59.743 55.000 6.18 0.00 0.00 3.61
1285 1359 0.034186 CAGAGCAGGGCCAATACCAA 60.034 55.000 6.18 0.00 0.00 3.67
1340 1420 2.959357 GAGCAGCACGCAAGGACAC 61.959 63.158 0.00 0.00 46.13 3.67
1343 1423 1.227943 AAAGAGCAGCACGCAAGGA 60.228 52.632 0.00 0.00 46.13 3.36
1443 1538 2.885644 CGTTCTCGCCACCATCGG 60.886 66.667 0.00 0.00 0.00 4.18
1499 1594 3.442977 ACTAATCTACTCGCAAGGAACGT 59.557 43.478 0.00 0.00 38.47 3.99
1565 1675 9.626045 ACAACAGAACAACTAGAAAAAGAAAAG 57.374 29.630 0.00 0.00 0.00 2.27
1567 1677 7.960738 CGACAACAGAACAACTAGAAAAAGAAA 59.039 33.333 0.00 0.00 0.00 2.52
1582 1692 2.094957 CCCTCTCTCTCGACAACAGAAC 60.095 54.545 0.00 0.00 0.00 3.01
1602 1712 1.544246 CCGGAAACAAACATTCTCCCC 59.456 52.381 0.00 0.00 0.00 4.81
1604 1714 1.544246 CCCCGGAAACAAACATTCTCC 59.456 52.381 0.73 0.00 0.00 3.71
1625 1749 2.355009 GGCCAACGTTGCTTGCAG 60.355 61.111 22.93 9.07 0.00 4.41
1649 1773 1.154413 GAACCGCGTGTGATGCTTG 60.154 57.895 4.92 0.00 0.00 4.01
1650 1774 2.325082 GGAACCGCGTGTGATGCTT 61.325 57.895 4.92 0.00 0.00 3.91
1652 1776 1.852067 AAAGGAACCGCGTGTGATGC 61.852 55.000 4.92 0.00 0.00 3.91
1664 1788 5.506686 AACTGAAGCAGAAAGAAAGGAAC 57.493 39.130 0.82 0.00 35.18 3.62
1693 1817 3.451141 AAGGAATCTCACGAGCAGATC 57.549 47.619 0.00 0.00 29.82 2.75
1694 1818 3.450457 AGAAAGGAATCTCACGAGCAGAT 59.550 43.478 0.00 0.00 31.51 2.90
1746 1870 2.290464 CGGACACAACAAAACCAGGTA 58.710 47.619 0.00 0.00 0.00 3.08
1747 1871 1.099689 CGGACACAACAAAACCAGGT 58.900 50.000 0.00 0.00 0.00 4.00
1749 1873 0.738389 AGCGGACACAACAAAACCAG 59.262 50.000 0.00 0.00 0.00 4.00
1751 1875 1.133407 TCAAGCGGACACAACAAAACC 59.867 47.619 0.00 0.00 0.00 3.27
1752 1876 2.553079 TCAAGCGGACACAACAAAAC 57.447 45.000 0.00 0.00 0.00 2.43
1753 1877 3.880490 AGTATCAAGCGGACACAACAAAA 59.120 39.130 0.00 0.00 0.00 2.44
1827 1953 1.386412 CATTTTCATTCGTGCGCCAAC 59.614 47.619 4.18 0.00 0.00 3.77
1994 2190 1.444212 CGCAGGGACGCCAAAAATG 60.444 57.895 0.00 0.00 0.00 2.32
1995 2191 2.961768 CGCAGGGACGCCAAAAAT 59.038 55.556 0.00 0.00 0.00 1.82
2030 2227 0.842635 GAGGGGATGTGGCTCAGATT 59.157 55.000 0.00 0.00 0.00 2.40
2131 2328 4.675063 ACCCCACTTCTCCAATGTATTT 57.325 40.909 0.00 0.00 0.00 1.40
2133 2330 4.040461 CGATACCCCACTTCTCCAATGTAT 59.960 45.833 0.00 0.00 0.00 2.29
2221 2436 6.092670 GCACATAAGCTGAAGACAAGATTACA 59.907 38.462 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.