Multiple sequence alignment - TraesCS1B01G293400

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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 TraesCS1B01G293400 chr1B 100.000 2669 0 0 1 2669 511189531 511192199 0.000000e+00 4929
1 TraesCS1B01G293400 chr1D 91.636 2750 103 52 1 2669 381045857 381048560 0.000000e+00 3687
2 TraesCS1B01G293400 chr1A 92.624 2115 68 34 1 2054 481756328 481758415 0.000000e+00 2961
3 TraesCS1B01G293400 chr1A 91.176 306 14 7 2135 2434 481758428 481758726 1.150000e-108 403
4 TraesCS1B01G293400 chr1A 96.000 100 3 1 2570 2669 481758883 481758981 7.650000e-36 161
5 TraesCS1B01G293400 chr4D 83.156 469 45 18 1834 2290 481401165 481400719 5.350000e-107 398
6 TraesCS1B01G293400 chr4D 82.600 477 47 19 1826 2290 458010988 458010536 3.220000e-104 388
7 TraesCS1B01G293400 chr2D 82.773 476 46 21 1826 2290 614004671 614005121 2.490000e-105 392
8 TraesCS1B01G293400 chr7D 82.390 477 48 20 1826 2290 592850765 592850313 1.500000e-102 383
9 TraesCS1B01G293400 chr6A 82.180 477 49 19 1826 2290 601566860 601566408 6.970000e-101 377
10 TraesCS1B01G293400 chr5D 82.008 478 48 25 1826 2290 523096073 523095621 3.240000e-99 372
11 TraesCS1B01G293400 chr5D 80.825 485 53 16 1826 2290 524290408 524290872 7.070000e-91 344
12 TraesCS1B01G293400 chr7B 82.128 470 47 22 1834 2290 723873155 723872710 4.200000e-98 368
13 TraesCS1B01G293400 chr5B 87.892 223 17 7 1826 2043 699305264 699305047 1.230000e-63 254


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 TraesCS1B01G293400 chr1B 511189531 511192199 2668 False 4929 4929 100.000000 1 2669 1 chr1B.!!$F1 2668
1 TraesCS1B01G293400 chr1D 381045857 381048560 2703 False 3687 3687 91.636000 1 2669 1 chr1D.!!$F1 2668
2 TraesCS1B01G293400 chr1A 481756328 481758981 2653 False 1175 2961 93.266667 1 2669 3 chr1A.!!$F1 2668

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
577 590 1.034292 GCATCAGGGAGGGAAAGCAC 61.034 60.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2555 2701 0.028505 GACCATGATGACGCACATGC 59.971 55.0 0.0 0.0 41.43 4.06 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
101 102 4.008074 TGTTTGTCAAGATCCTCACCTC 57.992 45.455 0.00 0.00 0.00 3.85
108 109 4.081198 GTCAAGATCCTCACCTCATCAGTT 60.081 45.833 0.00 0.00 0.00 3.16
123 124 1.202486 TCAGTTTCCGACAGGTCACAC 60.202 52.381 0.00 0.00 39.05 3.82
278 291 6.038271 ACATGTTTTCGAGGGAGTATAATTGC 59.962 38.462 0.00 0.00 0.00 3.56
299 312 2.271800 GATCGAATTCTGTCGTTGGCT 58.728 47.619 3.52 0.00 41.80 4.75
323 336 7.042523 GCTGCTCTAGATTGATCTTCTTCTTTC 60.043 40.741 0.00 0.00 38.32 2.62
333 346 9.730705 ATTGATCTTCTTCTTTCATTACTCACA 57.269 29.630 0.00 0.00 0.00 3.58
334 347 9.730705 TTGATCTTCTTCTTTCATTACTCACAT 57.269 29.630 0.00 0.00 0.00 3.21
435 448 3.488047 CCAGATTTAGAAATGCGCACCAG 60.488 47.826 14.90 0.00 0.00 4.00
452 465 2.513738 ACCAGCAGGGCCTCATTATTAA 59.486 45.455 0.95 0.00 42.05 1.40
496 509 1.451067 GGCAGAGCCTATGATCATGC 58.549 55.000 18.72 13.69 46.69 4.06
508 521 2.016318 TGATCATGCGCCACCTTTTAG 58.984 47.619 4.18 0.00 0.00 1.85
569 582 2.424956 GCACTAAAAAGCATCAGGGAGG 59.575 50.000 0.00 0.00 0.00 4.30
577 590 1.034292 GCATCAGGGAGGGAAAGCAC 61.034 60.000 0.00 0.00 0.00 4.40
588 601 5.193679 GGAGGGAAAGCACACACTAATTAT 58.806 41.667 0.00 0.00 0.00 1.28
589 602 5.652452 GGAGGGAAAGCACACACTAATTATT 59.348 40.000 0.00 0.00 0.00 1.40
590 603 6.826741 GGAGGGAAAGCACACACTAATTATTA 59.173 38.462 0.00 0.00 0.00 0.98
591 604 7.502561 GGAGGGAAAGCACACACTAATTATTAT 59.497 37.037 0.00 0.00 0.00 1.28
651 666 2.376956 GTGCGCGTGTTTAAACAATCA 58.623 42.857 22.14 13.91 41.21 2.57
652 667 2.784380 GTGCGCGTGTTTAAACAATCAA 59.216 40.909 22.14 5.40 41.21 2.57
653 668 3.423867 GTGCGCGTGTTTAAACAATCAAT 59.576 39.130 22.14 0.00 41.21 2.57
767 782 7.248437 CCAACCGAAGAGATTACAAAAATACC 58.752 38.462 0.00 0.00 0.00 2.73
771 786 7.664318 ACCGAAGAGATTACAAAAATACCAAGT 59.336 33.333 0.00 0.00 0.00 3.16
772 787 9.158233 CCGAAGAGATTACAAAAATACCAAGTA 57.842 33.333 0.00 0.00 0.00 2.24
838 856 1.676014 GGTGAAGTGGATGGTCCTTCG 60.676 57.143 0.00 0.00 37.90 3.79
1031 1072 3.484407 AGAAGAAGAAGCACAAGCACAT 58.516 40.909 0.00 0.00 45.49 3.21
1058 1111 3.049344 ACAAGGAGAAGAAGGACAAGGT 58.951 45.455 0.00 0.00 0.00 3.50
1673 1729 1.526917 CCGTGGCCCAATGATCCTC 60.527 63.158 0.00 0.00 0.00 3.71
1675 1731 1.152673 GTGGCCCAATGATCCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
1676 1732 1.309013 TGGCCCAATGATCCTCCCT 60.309 57.895 0.00 0.00 0.00 4.20
1713 1769 1.065926 TGCTCGATCCATTTCTGCAGT 60.066 47.619 14.67 0.00 0.00 4.40
1751 1807 0.109781 GGCTCGCAATTCGCAAAGAA 60.110 50.000 0.00 0.00 42.60 2.52
1958 2014 4.851843 TCATCAATGAAGAAGCCATCTGT 58.148 39.130 0.00 0.00 38.79 3.41
1966 2022 3.777106 AGAAGCCATCTGTTCTGTTCA 57.223 42.857 0.00 0.00 36.88 3.18
1967 2023 4.298103 AGAAGCCATCTGTTCTGTTCAT 57.702 40.909 0.00 0.00 36.88 2.57
2001 2063 2.929398 TCATGTAGCATTGTACAGCACG 59.071 45.455 9.50 0.00 36.36 5.34
2027 2092 2.618709 GCCACAGCTCTTTTTGTACAGT 59.381 45.455 0.00 0.00 35.50 3.55
2079 2144 2.163010 GTGTTCCTCCATGCACTCATTG 59.837 50.000 0.00 0.00 0.00 2.82
2256 2359 2.680339 GAGAAAGTGGGTGCTGCTTATC 59.320 50.000 0.00 0.00 0.00 1.75
2257 2360 2.307098 AGAAAGTGGGTGCTGCTTATCT 59.693 45.455 0.00 0.00 0.00 1.98
2258 2361 2.119801 AAGTGGGTGCTGCTTATCTG 57.880 50.000 0.00 0.00 0.00 2.90
2271 2374 1.594862 CTTATCTGCTGCTTACGTGGC 59.405 52.381 0.00 3.00 0.00 5.01
2298 2401 4.386867 ACCATCTCGTGTAGTATTGGTG 57.613 45.455 0.00 0.00 34.75 4.17
2348 2451 2.675844 TGTTTTTCACCTGTGACGTGAG 59.324 45.455 0.00 0.00 41.10 3.51
2409 2512 1.007721 AGGCAGATCCACAGAGGTAGT 59.992 52.381 0.00 0.00 39.02 2.73
2429 2535 2.551270 TCCTGCTTGGACTGGAATAGT 58.449 47.619 0.00 0.00 44.02 2.12
2430 2536 3.719871 TCCTGCTTGGACTGGAATAGTA 58.280 45.455 0.00 0.00 40.53 1.82
2431 2537 3.451178 TCCTGCTTGGACTGGAATAGTAC 59.549 47.826 0.00 0.00 40.53 2.73
2441 2547 8.461249 TGGACTGGAATAGTACATACTAAGAC 57.539 38.462 2.96 0.00 45.42 3.01
2443 2549 7.504911 GGACTGGAATAGTACATACTAAGACCA 59.495 40.741 15.12 15.12 41.64 4.02
2444 2550 8.834004 ACTGGAATAGTACATACTAAGACCAA 57.166 34.615 15.97 7.14 41.64 3.67
2445 2551 9.435570 ACTGGAATAGTACATACTAAGACCAAT 57.564 33.333 15.97 9.03 41.64 3.16
2447 2553 8.647796 TGGAATAGTACATACTAAGACCAATGG 58.352 37.037 0.00 0.00 41.64 3.16
2448 2554 7.603024 GGAATAGTACATACTAAGACCAATGGC 59.397 40.741 0.00 0.00 41.64 4.40
2450 2556 5.671493 AGTACATACTAAGACCAATGGCAC 58.329 41.667 0.00 0.00 34.13 5.01
2454 2560 0.729116 CTAAGACCAATGGCACTGCG 59.271 55.000 0.00 0.00 0.00 5.18
2455 2561 0.323302 TAAGACCAATGGCACTGCGA 59.677 50.000 0.00 0.00 0.00 5.10
2457 2563 1.672356 GACCAATGGCACTGCGAGT 60.672 57.895 0.00 0.00 0.00 4.18
2458 2564 1.639298 GACCAATGGCACTGCGAGTC 61.639 60.000 0.00 0.00 0.00 3.36
2459 2565 1.376424 CCAATGGCACTGCGAGTCT 60.376 57.895 0.00 0.00 0.00 3.24
2460 2566 0.957395 CCAATGGCACTGCGAGTCTT 60.957 55.000 0.00 0.00 0.00 3.01
2461 2567 0.167470 CAATGGCACTGCGAGTCTTG 59.833 55.000 0.00 0.00 0.00 3.02
2463 2569 0.671781 ATGGCACTGCGAGTCTTGAC 60.672 55.000 0.00 0.00 0.00 3.18
2464 2570 2.029844 GGCACTGCGAGTCTTGACC 61.030 63.158 0.00 0.00 0.00 4.02
2466 2572 1.287730 GCACTGCGAGTCTTGACCAG 61.288 60.000 0.00 1.32 0.00 4.00
2467 2573 0.668706 CACTGCGAGTCTTGACCAGG 60.669 60.000 9.23 0.00 0.00 4.45
2469 2575 0.108898 CTGCGAGTCTTGACCAGGAG 60.109 60.000 0.00 0.00 0.00 3.69
2470 2576 0.827925 TGCGAGTCTTGACCAGGAGT 60.828 55.000 0.00 0.00 0.00 3.85
2472 2578 1.670380 GCGAGTCTTGACCAGGAGTTC 60.670 57.143 0.00 0.00 0.00 3.01
2473 2579 1.613925 CGAGTCTTGACCAGGAGTTCA 59.386 52.381 0.00 0.00 0.00 3.18
2474 2580 2.232452 CGAGTCTTGACCAGGAGTTCAT 59.768 50.000 0.00 0.00 0.00 2.57
2475 2581 3.594134 GAGTCTTGACCAGGAGTTCATG 58.406 50.000 0.00 0.00 0.00 3.07
2476 2582 2.079925 GTCTTGACCAGGAGTTCATGC 58.920 52.381 0.00 0.00 0.00 4.06
2481 2618 2.079925 GACCAGGAGTTCATGCTTCAC 58.920 52.381 0.00 0.00 0.00 3.18
2492 2629 0.677731 ATGCTTCACACCGTGGATGG 60.678 55.000 3.03 0.00 33.87 3.51
2498 2644 0.108329 CACACCGTGGATGGGTACTC 60.108 60.000 3.03 0.00 35.58 2.59
2500 2646 2.056223 ACCGTGGATGGGTACTCGG 61.056 63.158 0.00 0.00 42.94 4.63
2501 2647 2.056223 CCGTGGATGGGTACTCGGT 61.056 63.158 0.00 0.00 34.38 4.69
2502 2648 1.610554 CCGTGGATGGGTACTCGGTT 61.611 60.000 0.00 0.00 34.38 4.44
2503 2649 0.248289 CGTGGATGGGTACTCGGTTT 59.752 55.000 0.00 0.00 0.00 3.27
2504 2650 1.738030 CGTGGATGGGTACTCGGTTTC 60.738 57.143 0.00 0.00 0.00 2.78
2505 2651 1.276989 GTGGATGGGTACTCGGTTTCA 59.723 52.381 0.00 0.00 0.00 2.69
2506 2652 1.276989 TGGATGGGTACTCGGTTTCAC 59.723 52.381 0.00 0.00 0.00 3.18
2507 2653 1.276989 GGATGGGTACTCGGTTTCACA 59.723 52.381 0.00 0.00 0.00 3.58
2509 2655 1.416243 TGGGTACTCGGTTTCACACT 58.584 50.000 0.00 0.00 0.00 3.55
2510 2656 1.764134 TGGGTACTCGGTTTCACACTT 59.236 47.619 0.00 0.00 0.00 3.16
2512 2658 2.546789 GGGTACTCGGTTTCACACTTTG 59.453 50.000 0.00 0.00 0.00 2.77
2513 2659 3.460103 GGTACTCGGTTTCACACTTTGA 58.540 45.455 0.00 0.00 0.00 2.69
2515 2661 3.536956 ACTCGGTTTCACACTTTGAGA 57.463 42.857 0.00 0.00 34.94 3.27
2529 2675 9.871238 TCACACTTTGAGAAAATATACTAGACC 57.129 33.333 0.00 0.00 0.00 3.85
2537 2683 7.789831 TGAGAAAATATACTAGACCAGACCCAT 59.210 37.037 0.00 0.00 0.00 4.00
2547 2693 0.829333 CCAGACCCATGAGGACAGAG 59.171 60.000 7.17 0.00 39.89 3.35
2549 2695 0.712979 AGACCCATGAGGACAGAGGA 59.287 55.000 7.17 0.00 39.89 3.71
2550 2696 0.827368 GACCCATGAGGACAGAGGAC 59.173 60.000 7.17 0.00 39.89 3.85
2551 2697 0.117140 ACCCATGAGGACAGAGGACA 59.883 55.000 7.17 0.00 39.89 4.02
2553 2699 1.620798 CCCATGAGGACAGAGGACAGA 60.621 57.143 0.00 0.00 38.24 3.41
2554 2700 2.396608 CCATGAGGACAGAGGACAGAT 58.603 52.381 0.00 0.00 36.89 2.90
2555 2701 2.102757 CCATGAGGACAGAGGACAGATG 59.897 54.545 0.00 0.00 36.89 2.90
2556 2702 1.189752 TGAGGACAGAGGACAGATGC 58.810 55.000 0.00 0.00 0.00 3.91
2557 2703 1.189752 GAGGACAGAGGACAGATGCA 58.810 55.000 0.00 0.00 0.00 3.96
2558 2704 1.761784 GAGGACAGAGGACAGATGCAT 59.238 52.381 0.00 0.00 0.00 3.96
2559 2705 1.485480 AGGACAGAGGACAGATGCATG 59.515 52.381 2.46 0.00 0.00 4.06
2560 2706 1.209019 GGACAGAGGACAGATGCATGT 59.791 52.381 2.46 0.00 35.68 3.21
2561 2707 2.277969 GACAGAGGACAGATGCATGTG 58.722 52.381 21.42 21.42 32.25 3.21
2562 2708 1.015109 CAGAGGACAGATGCATGTGC 58.985 55.000 22.79 13.47 41.42 4.57
2563 2709 0.461516 AGAGGACAGATGCATGTGCG 60.462 55.000 22.79 1.55 45.27 5.34
2564 2710 0.742281 GAGGACAGATGCATGTGCGT 60.742 55.000 22.79 16.22 45.27 5.24
2589 2735 3.006003 TCATGGTCGTGTTGTAGCAGTTA 59.994 43.478 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 2.069273 GTGACCTGTCGGAAACTGATG 58.931 52.381 0.00 0.00 0.00 3.07
123 124 0.890683 AAAGCGAATGCCCTTGAAGG 59.109 50.000 3.69 3.69 44.31 3.46
229 232 4.448866 ACGTACCCGATCCTGAAGGAAAT 61.449 47.826 2.51 0.00 42.05 2.17
278 291 1.005975 GCCAACGACAGAATTCGATCG 60.006 52.381 24.15 24.15 41.78 3.69
299 312 7.845037 TGAAAGAAGAAGATCAATCTAGAGCA 58.155 34.615 0.00 0.00 35.76 4.26
329 342 9.679661 TCTTGGAGCAATATAAAAAGTATGTGA 57.320 29.630 0.00 0.00 0.00 3.58
347 360 9.193133 CATGATGATTGATTAATTTCTTGGAGC 57.807 33.333 0.00 0.00 0.00 4.70
359 372 5.829391 CCTGGGTGTTCATGATGATTGATTA 59.171 40.000 0.00 0.00 0.00 1.75
435 448 3.817647 CAGACTTAATAATGAGGCCCTGC 59.182 47.826 0.00 0.00 0.00 4.85
441 454 9.239002 CGAGTAGTTTCAGACTTAATAATGAGG 57.761 37.037 0.00 0.00 39.86 3.86
452 465 3.890147 AGAACACCGAGTAGTTTCAGACT 59.110 43.478 0.00 0.00 42.55 3.24
496 509 2.169769 TCATACTCCCTAAAAGGTGGCG 59.830 50.000 0.00 0.00 31.93 5.69
508 521 5.203060 ACGAAGCTAAAGATCATACTCCC 57.797 43.478 0.00 0.00 0.00 4.30
588 601 9.482175 ACTTTGGCCCATTTGTATTAGTAATAA 57.518 29.630 0.00 0.00 0.00 1.40
590 603 7.971368 ACTTTGGCCCATTTGTATTAGTAAT 57.029 32.000 0.00 0.17 0.00 1.89
591 604 8.880991 TTACTTTGGCCCATTTGTATTAGTAA 57.119 30.769 0.00 0.00 0.00 2.24
682 697 3.739300 CCGCCTCGTCATATAAAACGATT 59.261 43.478 11.84 0.00 45.81 3.34
683 698 3.314553 CCGCCTCGTCATATAAAACGAT 58.685 45.455 11.84 0.00 45.81 3.73
797 815 3.623060 CCACTTGGACATTATTCAGGACG 59.377 47.826 0.00 0.00 37.39 4.79
838 856 2.413453 CCGCAAAGTTTCTAGTCAGAGC 59.587 50.000 0.00 0.00 30.73 4.09
1031 1072 2.705658 TCCTTCTTCTCCTTGTGCTTGA 59.294 45.455 0.00 0.00 0.00 3.02
1317 1373 0.895559 CCTTGGACTTCTTGGTGCCC 60.896 60.000 0.00 0.00 0.00 5.36
1552 1608 2.423446 GGCCTGCAGTATCCTCCG 59.577 66.667 13.81 0.00 0.00 4.63
1675 1731 0.319383 CAAGAGGCCATCGATCGGAG 60.319 60.000 16.41 7.99 0.00 4.63
1676 1732 1.742146 CAAGAGGCCATCGATCGGA 59.258 57.895 16.41 2.25 0.00 4.55
1713 1769 5.110814 AGCCAATAATAACAGTACCTGCA 57.889 39.130 0.00 0.00 34.37 4.41
1751 1807 5.147032 TCCAACCCAAAAGAATCAGACATT 58.853 37.500 0.00 0.00 0.00 2.71
1955 2011 3.405831 TGCCTCTCAATGAACAGAACAG 58.594 45.455 0.00 0.00 0.00 3.16
1958 2014 5.535783 TGAAAATGCCTCTCAATGAACAGAA 59.464 36.000 0.00 0.00 0.00 3.02
1966 2022 4.951715 TGCTACATGAAAATGCCTCTCAAT 59.048 37.500 0.00 0.00 0.00 2.57
1967 2023 4.334552 TGCTACATGAAAATGCCTCTCAA 58.665 39.130 0.00 0.00 0.00 3.02
2027 2092 2.429971 TGTGCACAGCAATTTCCAGAAA 59.570 40.909 17.42 0.00 41.47 2.52
2101 2166 9.689976 CATGTGGTTTACAATCTCATACAAAAA 57.310 29.630 0.00 0.00 43.77 1.94
2140 2209 8.458843 CAACAGAGTTTTTCCAGAAGAAGTTAA 58.541 33.333 0.00 0.00 35.40 2.01
2141 2210 7.610305 ACAACAGAGTTTTTCCAGAAGAAGTTA 59.390 33.333 0.00 0.00 35.40 2.24
2142 2211 6.434340 ACAACAGAGTTTTTCCAGAAGAAGTT 59.566 34.615 0.00 0.00 35.40 2.66
2271 2374 1.066858 ACTACACGAGATGGTTGCCTG 60.067 52.381 0.00 0.00 0.00 4.85
2298 2401 7.418025 GCATATATTCATCCTCACTACCTACCC 60.418 44.444 0.00 0.00 0.00 3.69
2348 2451 1.807573 CGAAGCAGAGTTCGCTCCC 60.808 63.158 0.00 0.00 45.16 4.30
2409 2512 2.551270 ACTATTCCAGTCCAAGCAGGA 58.449 47.619 0.00 0.00 46.75 3.86
2422 2528 7.603024 GCCATTGGTCTTAGTATGTACTATTCC 59.397 40.741 4.26 5.31 38.48 3.01
2424 2530 7.931948 GTGCCATTGGTCTTAGTATGTACTATT 59.068 37.037 4.26 0.00 38.48 1.73
2426 2532 6.610020 AGTGCCATTGGTCTTAGTATGTACTA 59.390 38.462 4.26 0.00 37.73 1.82
2427 2533 5.425539 AGTGCCATTGGTCTTAGTATGTACT 59.574 40.000 4.26 0.00 40.24 2.73
2428 2534 5.523916 CAGTGCCATTGGTCTTAGTATGTAC 59.476 44.000 4.26 0.00 0.00 2.90
2429 2535 5.670485 CAGTGCCATTGGTCTTAGTATGTA 58.330 41.667 4.26 0.00 0.00 2.29
2430 2536 4.517285 CAGTGCCATTGGTCTTAGTATGT 58.483 43.478 4.26 0.00 0.00 2.29
2431 2537 3.313526 GCAGTGCCATTGGTCTTAGTATG 59.686 47.826 2.85 0.00 0.00 2.39
2433 2539 2.676750 CGCAGTGCCATTGGTCTTAGTA 60.677 50.000 10.11 0.00 0.00 1.82
2435 2541 0.729116 CGCAGTGCCATTGGTCTTAG 59.271 55.000 10.11 0.00 0.00 2.18
2438 2544 1.376424 CTCGCAGTGCCATTGGTCT 60.376 57.895 10.11 0.81 0.00 3.85
2439 2545 1.639298 GACTCGCAGTGCCATTGGTC 61.639 60.000 10.11 7.12 0.00 4.02
2440 2546 1.672356 GACTCGCAGTGCCATTGGT 60.672 57.895 10.11 1.20 0.00 3.67
2441 2547 0.957395 AAGACTCGCAGTGCCATTGG 60.957 55.000 10.11 0.00 0.00 3.16
2443 2549 0.035317 TCAAGACTCGCAGTGCCATT 59.965 50.000 10.11 0.00 0.00 3.16
2444 2550 0.671781 GTCAAGACTCGCAGTGCCAT 60.672 55.000 10.11 0.00 0.00 4.40
2445 2551 1.300931 GTCAAGACTCGCAGTGCCA 60.301 57.895 10.11 0.00 0.00 4.92
2447 2553 1.287730 CTGGTCAAGACTCGCAGTGC 61.288 60.000 4.58 4.58 0.00 4.40
2448 2554 0.668706 CCTGGTCAAGACTCGCAGTG 60.669 60.000 0.00 0.00 0.00 3.66
2450 2556 0.108898 CTCCTGGTCAAGACTCGCAG 60.109 60.000 0.00 0.00 0.00 5.18
2454 2560 3.594134 CATGAACTCCTGGTCAAGACTC 58.406 50.000 0.00 0.00 0.00 3.36
2455 2561 2.289945 GCATGAACTCCTGGTCAAGACT 60.290 50.000 0.00 0.00 0.00 3.24
2457 2563 1.980765 AGCATGAACTCCTGGTCAAGA 59.019 47.619 0.00 0.00 0.00 3.02
2458 2564 2.486472 AGCATGAACTCCTGGTCAAG 57.514 50.000 0.00 0.00 0.00 3.02
2459 2565 2.106338 TGAAGCATGAACTCCTGGTCAA 59.894 45.455 0.00 0.00 0.00 3.18
2460 2566 1.699083 TGAAGCATGAACTCCTGGTCA 59.301 47.619 0.00 0.00 0.00 4.02
2461 2567 2.079925 GTGAAGCATGAACTCCTGGTC 58.920 52.381 0.00 0.00 0.00 4.02
2463 2569 1.808945 GTGTGAAGCATGAACTCCTGG 59.191 52.381 0.00 0.00 0.00 4.45
2464 2570 1.808945 GGTGTGAAGCATGAACTCCTG 59.191 52.381 0.00 0.00 0.00 3.86
2466 2572 0.798776 CGGTGTGAAGCATGAACTCC 59.201 55.000 0.00 0.00 0.00 3.85
2467 2573 1.195448 CACGGTGTGAAGCATGAACTC 59.805 52.381 0.00 0.00 35.23 3.01
2469 2575 0.238289 CCACGGTGTGAAGCATGAAC 59.762 55.000 7.45 0.00 35.23 3.18
2470 2576 0.107643 TCCACGGTGTGAAGCATGAA 59.892 50.000 7.45 0.00 35.23 2.57
2472 2578 0.448990 CATCCACGGTGTGAAGCATG 59.551 55.000 7.45 0.00 35.23 4.06
2473 2579 0.677731 CCATCCACGGTGTGAAGCAT 60.678 55.000 7.45 0.00 35.23 3.79
2474 2580 1.302431 CCATCCACGGTGTGAAGCA 60.302 57.895 7.45 0.00 35.23 3.91
2475 2581 2.040544 CCCATCCACGGTGTGAAGC 61.041 63.158 7.45 0.00 35.23 3.86
2476 2582 0.611200 TACCCATCCACGGTGTGAAG 59.389 55.000 7.45 1.70 35.23 3.02
2481 2618 1.141019 CGAGTACCCATCCACGGTG 59.859 63.158 0.00 0.00 34.66 4.94
2492 2629 3.460103 TCAAAGTGTGAAACCGAGTACC 58.540 45.455 0.00 0.00 34.36 3.34
2498 2644 8.504005 AGTATATTTTCTCAAAGTGTGAAACCG 58.496 33.333 5.28 0.00 38.90 4.44
2503 2649 9.871238 GGTCTAGTATATTTTCTCAAAGTGTGA 57.129 33.333 0.00 0.00 34.17 3.58
2504 2650 9.653287 TGGTCTAGTATATTTTCTCAAAGTGTG 57.347 33.333 0.00 0.00 0.00 3.82
2505 2651 9.877178 CTGGTCTAGTATATTTTCTCAAAGTGT 57.123 33.333 0.00 0.00 0.00 3.55
2509 2655 8.483758 GGGTCTGGTCTAGTATATTTTCTCAAA 58.516 37.037 0.00 0.00 0.00 2.69
2510 2656 7.622081 TGGGTCTGGTCTAGTATATTTTCTCAA 59.378 37.037 0.00 0.00 0.00 3.02
2512 2658 7.598759 TGGGTCTGGTCTAGTATATTTTCTC 57.401 40.000 0.00 0.00 0.00 2.87
2513 2659 7.789831 TCATGGGTCTGGTCTAGTATATTTTCT 59.210 37.037 0.00 0.00 0.00 2.52
2515 2661 7.016661 CCTCATGGGTCTGGTCTAGTATATTTT 59.983 40.741 0.00 0.00 0.00 1.82
2528 2674 0.829333 CTCTGTCCTCATGGGTCTGG 59.171 60.000 0.00 0.00 36.25 3.86
2529 2675 0.829333 CCTCTGTCCTCATGGGTCTG 59.171 60.000 0.00 0.00 36.25 3.51
2537 2683 1.189752 GCATCTGTCCTCTGTCCTCA 58.810 55.000 0.00 0.00 0.00 3.86
2547 2693 1.020861 TGACGCACATGCATCTGTCC 61.021 55.000 0.00 0.00 42.21 4.02
2549 2695 1.012086 GATGACGCACATGCATCTGT 58.988 50.000 0.00 0.00 42.21 3.41
2550 2696 1.011333 TGATGACGCACATGCATCTG 58.989 50.000 0.00 0.00 42.21 2.90
2551 2697 1.602377 CATGATGACGCACATGCATCT 59.398 47.619 0.00 0.00 42.21 2.90
2553 2699 0.666374 CCATGATGACGCACATGCAT 59.334 50.000 4.49 0.00 41.43 3.96
2554 2700 0.677414 ACCATGATGACGCACATGCA 60.677 50.000 4.49 0.00 41.43 3.96
2555 2701 0.028505 GACCATGATGACGCACATGC 59.971 55.000 0.00 0.00 41.43 4.06
2556 2702 0.302589 CGACCATGATGACGCACATG 59.697 55.000 0.00 0.00 42.12 3.21
2557 2703 0.108186 ACGACCATGATGACGCACAT 60.108 50.000 10.63 0.00 42.47 3.21
2558 2704 1.013524 CACGACCATGATGACGCACA 61.014 55.000 10.63 0.00 0.00 4.57
2559 2705 1.014044 ACACGACCATGATGACGCAC 61.014 55.000 10.63 0.00 0.00 5.34
2560 2706 0.320334 AACACGACCATGATGACGCA 60.320 50.000 10.63 0.00 0.00 5.24
2561 2707 0.095245 CAACACGACCATGATGACGC 59.905 55.000 10.63 0.00 0.00 5.19
2562 2708 1.428448 ACAACACGACCATGATGACG 58.572 50.000 0.00 9.52 0.00 4.35
2563 2709 2.348666 GCTACAACACGACCATGATGAC 59.651 50.000 0.00 0.00 0.00 3.06
2564 2710 2.028567 TGCTACAACACGACCATGATGA 60.029 45.455 0.00 0.00 0.00 2.92
2565 2711 2.345876 TGCTACAACACGACCATGATG 58.654 47.619 0.00 0.00 0.00 3.07
2566 2712 2.028112 ACTGCTACAACACGACCATGAT 60.028 45.455 0.00 0.00 0.00 2.45
2567 2713 1.343142 ACTGCTACAACACGACCATGA 59.657 47.619 0.00 0.00 0.00 3.07
2568 2714 1.795768 ACTGCTACAACACGACCATG 58.204 50.000 0.00 0.00 0.00 3.66
2589 2735 2.104622 CCTGGATGCCCAACAAACTTTT 59.895 45.455 0.00 0.00 42.98 2.27


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

AutoCloner maintained by Alex Coulton.