Multiple sequence alignment - TraesCS3B01G031600

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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 TraesCS3B01G031600 chr3B 100.000 3065 0 0 1 3065 14347553 14344489 0.000000e+00 5661
1 TraesCS3B01G031600 chr3B 93.836 2385 89 18 734 3065 27035391 27037770 0.000000e+00 3537
2 TraesCS3B01G031600 chr3D 94.286 1680 76 1 809 2468 10220823 10219144 0.000000e+00 2553
3 TraesCS3B01G031600 chr3D 97.321 560 15 0 2506 3065 10219145 10218586 0.000000e+00 952
4 TraesCS3B01G031600 chr3D 85.326 368 24 10 1 338 508333085 508333452 1.350000e-93 353
5 TraesCS3B01G031600 chr3D 88.710 124 4 2 592 708 10222190 10222070 3.190000e-30 143
6 TraesCS3B01G031600 chr3A 93.918 1529 86 4 842 2367 16889149 16890673 0.000000e+00 2302
7 TraesCS3B01G031600 chr3A 84.699 732 67 17 2379 3065 16890779 16891510 0.000000e+00 689
8 TraesCS3B01G031600 chr2B 96.926 553 16 1 1 552 92607475 92608027 0.000000e+00 926
9 TraesCS3B01G031600 chr2B 95.161 372 16 2 181 552 686053529 686053160 1.220000e-163 586
10 TraesCS3B01G031600 chr5D 90.000 580 29 12 1 552 513012798 513012220 0.000000e+00 723
11 TraesCS3B01G031600 chr5B 89.399 566 36 19 1 553 101349378 101348824 0.000000e+00 691
12 TraesCS3B01G031600 chr1D 88.468 581 37 15 1 552 319925098 319924519 0.000000e+00 675
13 TraesCS3B01G031600 chr1D 77.161 937 197 13 1136 2068 462359131 462358208 2.090000e-146 529
14 TraesCS3B01G031600 chr6B 90.631 491 19 9 1 464 584049855 584050345 7.210000e-176 627
15 TraesCS3B01G031600 chr1B 79.730 814 158 7 1298 2108 637478358 637477549 1.580000e-162 582
16 TraesCS3B01G031600 chr1B 77.790 941 186 17 1151 2084 637388656 637387732 2.670000e-155 558
17 TraesCS3B01G031600 chr1B 84.926 544 55 14 28 551 583954461 583953925 2.710000e-145 525
18 TraesCS3B01G031600 chr1B 83.112 527 67 16 25 542 630915077 630915590 7.740000e-126 460
19 TraesCS3B01G031600 chr5A 85.426 446 37 13 1 418 658302896 658302451 3.630000e-119 438
20 TraesCS3B01G031600 chr5A 85.946 370 51 1 181 550 475463509 475463141 7.970000e-106 394


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 TraesCS3B01G031600 chr3B 14344489 14347553 3064 True 5661.0 5661 100.0000 1 3065 1 chr3B.!!$R1 3064
1 TraesCS3B01G031600 chr3B 27035391 27037770 2379 False 3537.0 3537 93.8360 734 3065 1 chr3B.!!$F1 2331
2 TraesCS3B01G031600 chr3D 10218586 10222190 3604 True 1216.0 2553 93.4390 592 3065 3 chr3D.!!$R1 2473
3 TraesCS3B01G031600 chr3A 16889149 16891510 2361 False 1495.5 2302 89.3085 842 3065 2 chr3A.!!$F1 2223
4 TraesCS3B01G031600 chr2B 92607475 92608027 552 False 926.0 926 96.9260 1 552 1 chr2B.!!$F1 551
5 TraesCS3B01G031600 chr5D 513012220 513012798 578 True 723.0 723 90.0000 1 552 1 chr5D.!!$R1 551
6 TraesCS3B01G031600 chr5B 101348824 101349378 554 True 691.0 691 89.3990 1 553 1 chr5B.!!$R1 552
7 TraesCS3B01G031600 chr1D 319924519 319925098 579 True 675.0 675 88.4680 1 552 1 chr1D.!!$R1 551
8 TraesCS3B01G031600 chr1D 462358208 462359131 923 True 529.0 529 77.1610 1136 2068 1 chr1D.!!$R2 932
9 TraesCS3B01G031600 chr1B 637477549 637478358 809 True 582.0 582 79.7300 1298 2108 1 chr1B.!!$R3 810
10 TraesCS3B01G031600 chr1B 637387732 637388656 924 True 558.0 558 77.7900 1151 2084 1 chr1B.!!$R2 933
11 TraesCS3B01G031600 chr1B 583953925 583954461 536 True 525.0 525 84.9260 28 551 1 chr1B.!!$R1 523
12 TraesCS3B01G031600 chr1B 630915077 630915590 513 False 460.0 460 83.1120 25 542 1 chr1B.!!$F1 517

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
577 636 0.17576 TGGGATGCGTGCTAGAGAAC 59.824 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 3863 0.179037 ATCATGTGGGAGACGCCATG 60.179 55.0 0.0 0.0 38.95 3.66 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
26 28 1.133482 CAAACTCACCTCCCCAAACCT 60.133 52.381 0.00 0.00 0.00 3.50
295 354 2.747855 CGGAGCAAGGGAGCAACC 60.748 66.667 0.00 0.00 36.85 3.77
430 489 3.947041 ACCCTCCCTGGAGCCAGT 61.947 66.667 14.97 2.25 42.15 4.00
563 622 2.772622 GGGTCGGGTGGATGGGAT 60.773 66.667 0.00 0.00 0.00 3.85
564 623 2.510906 GGTCGGGTGGATGGGATG 59.489 66.667 0.00 0.00 0.00 3.51
565 624 2.203209 GTCGGGTGGATGGGATGC 60.203 66.667 0.00 0.00 0.00 3.91
566 625 3.860605 TCGGGTGGATGGGATGCG 61.861 66.667 0.00 0.00 0.00 4.73
567 626 4.175337 CGGGTGGATGGGATGCGT 62.175 66.667 0.00 0.00 0.00 5.24
568 627 2.516930 GGGTGGATGGGATGCGTG 60.517 66.667 0.00 0.00 0.00 5.34
569 628 3.211963 GGTGGATGGGATGCGTGC 61.212 66.667 0.00 0.00 0.00 5.34
570 629 2.124570 GTGGATGGGATGCGTGCT 60.125 61.111 0.00 0.00 0.00 4.40
571 630 1.146041 GTGGATGGGATGCGTGCTA 59.854 57.895 0.00 0.00 0.00 3.49
572 631 0.882042 GTGGATGGGATGCGTGCTAG 60.882 60.000 0.00 0.00 0.00 3.42
573 632 1.048160 TGGATGGGATGCGTGCTAGA 61.048 55.000 0.00 0.00 0.00 2.43
574 633 0.320247 GGATGGGATGCGTGCTAGAG 60.320 60.000 0.00 0.00 0.00 2.43
575 634 0.676184 GATGGGATGCGTGCTAGAGA 59.324 55.000 0.00 0.00 0.00 3.10
576 635 1.069204 GATGGGATGCGTGCTAGAGAA 59.931 52.381 0.00 0.00 0.00 2.87
577 636 0.175760 TGGGATGCGTGCTAGAGAAC 59.824 55.000 0.00 0.00 0.00 3.01
578 637 0.461961 GGGATGCGTGCTAGAGAACT 59.538 55.000 0.00 0.00 0.00 3.01
579 638 1.681793 GGGATGCGTGCTAGAGAACTA 59.318 52.381 0.00 0.00 0.00 2.24
580 639 2.297597 GGGATGCGTGCTAGAGAACTAT 59.702 50.000 0.00 0.00 0.00 2.12
581 640 3.312828 GGATGCGTGCTAGAGAACTATG 58.687 50.000 0.00 0.00 0.00 2.23
582 641 2.871182 TGCGTGCTAGAGAACTATGG 57.129 50.000 0.00 0.00 0.00 2.74
583 642 1.409064 TGCGTGCTAGAGAACTATGGG 59.591 52.381 0.00 0.00 0.00 4.00
584 643 1.409427 GCGTGCTAGAGAACTATGGGT 59.591 52.381 0.00 0.00 0.00 4.51
585 644 2.799917 GCGTGCTAGAGAACTATGGGTG 60.800 54.545 0.00 0.00 0.00 4.61
586 645 2.427453 CGTGCTAGAGAACTATGGGTGT 59.573 50.000 0.00 0.00 0.00 4.16
587 646 3.119101 CGTGCTAGAGAACTATGGGTGTT 60.119 47.826 0.00 0.00 0.00 3.32
588 647 4.620803 CGTGCTAGAGAACTATGGGTGTTT 60.621 45.833 0.00 0.00 0.00 2.83
589 648 4.870991 GTGCTAGAGAACTATGGGTGTTTC 59.129 45.833 0.00 0.00 0.00 2.78
590 649 4.530553 TGCTAGAGAACTATGGGTGTTTCA 59.469 41.667 0.00 0.00 0.00 2.69
643 702 5.683876 ACTTATTGATGTGCTACAGAGGT 57.316 39.130 0.00 0.00 0.00 3.85
680 746 0.247736 AGCGTTCGATCTTGGAAGCT 59.752 50.000 0.00 0.00 0.00 3.74
681 747 1.476891 AGCGTTCGATCTTGGAAGCTA 59.523 47.619 0.00 0.00 31.10 3.32
682 748 1.855360 GCGTTCGATCTTGGAAGCTAG 59.145 52.381 0.00 0.00 0.00 3.42
708 774 7.893124 ATGATTTTCAGAATATGGAGTTGCT 57.107 32.000 0.00 0.00 0.00 3.91
709 775 7.707624 TGATTTTCAGAATATGGAGTTGCTT 57.292 32.000 0.00 0.00 0.00 3.91
710 776 8.806429 TGATTTTCAGAATATGGAGTTGCTTA 57.194 30.769 0.00 0.00 0.00 3.09
711 777 9.412460 TGATTTTCAGAATATGGAGTTGCTTAT 57.588 29.630 0.00 0.00 0.00 1.73
715 781 9.679661 TTTCAGAATATGGAGTTGCTTATAACA 57.320 29.630 0.00 0.00 33.02 2.41
716 782 9.679661 TTCAGAATATGGAGTTGCTTATAACAA 57.320 29.630 0.00 0.00 33.02 2.83
717 783 9.851686 TCAGAATATGGAGTTGCTTATAACAAT 57.148 29.630 4.52 0.00 33.02 2.71
804 2019 4.134563 CCGGTGTTCCTTTCCCAATATAG 58.865 47.826 0.00 0.00 0.00 1.31
966 2210 1.098129 CCGCCTCAGATCGTCAGAGA 61.098 60.000 8.32 0.00 32.48 3.10
979 2223 3.383505 TCGTCAGAGAAGTTGGAGTTGAA 59.616 43.478 0.00 0.00 0.00 2.69
993 2237 4.261801 GGAGTTGAATTGCTGCCTAGTTA 58.738 43.478 0.00 0.00 0.00 2.24
999 2243 6.588719 TGAATTGCTGCCTAGTTACAAAAT 57.411 33.333 0.00 0.00 0.00 1.82
1131 2375 5.048504 TGGTGACTCTTCAAAATCTGCAATC 60.049 40.000 0.00 0.00 31.90 2.67
1293 2537 1.596934 CTACCTCTCCGCCTTTGCA 59.403 57.895 0.00 0.00 37.32 4.08
1296 2540 2.665000 CTCTCCGCCTTTGCAGGA 59.335 61.111 0.00 0.00 44.19 3.86
1468 2712 2.415010 CCGAGATGGAGGTCTGCG 59.585 66.667 0.00 0.00 42.00 5.18
1711 2955 1.153745 GAGCGCATCGACTCTTGGT 60.154 57.895 11.47 0.00 31.32 3.67
1968 3212 1.542547 GGTTTTGAGGTCTTGAGCGGA 60.543 52.381 0.00 0.00 0.00 5.54
2240 3484 0.249280 CCAACGTCTTTGTTTGCCCC 60.249 55.000 0.00 0.00 32.71 5.80
2284 3530 0.108804 AACCATCAGTACCGTCGCTG 60.109 55.000 0.00 0.00 0.00 5.18
2323 3569 2.268298 GTGTGTCGCCTCGTCAAATAT 58.732 47.619 0.00 0.00 0.00 1.28
2325 3571 3.124636 GTGTGTCGCCTCGTCAAATATTT 59.875 43.478 0.00 0.00 0.00 1.40
2337 3583 7.148423 CCTCGTCAAATATTTCTTGTGTGATGA 60.148 37.037 0.00 2.26 0.00 2.92
2427 3767 1.582502 GAATCACGTTTCTAGGCGACG 59.417 52.381 10.47 10.47 42.13 5.12
2476 3856 9.435688 ACGCATCATATATGAATAAAGTTAGCA 57.564 29.630 19.03 0.00 40.69 3.49
2486 3866 8.867112 ATGAATAAAGTTAGCAAATGAGCATG 57.133 30.769 0.00 0.00 36.85 4.06
2487 3867 7.259882 TGAATAAAGTTAGCAAATGAGCATGG 58.740 34.615 0.00 0.00 36.85 3.66
2488 3868 3.515330 AAGTTAGCAAATGAGCATGGC 57.485 42.857 0.00 0.00 36.85 4.40
2489 3869 1.402968 AGTTAGCAAATGAGCATGGCG 59.597 47.619 0.00 0.00 36.85 5.69
2490 3870 1.133025 GTTAGCAAATGAGCATGGCGT 59.867 47.619 0.00 0.00 36.85 5.68
2491 3871 1.016627 TAGCAAATGAGCATGGCGTC 58.983 50.000 0.00 0.00 36.85 5.19
2492 3872 0.679002 AGCAAATGAGCATGGCGTCT 60.679 50.000 0.00 0.00 36.85 4.18
2493 3873 0.248377 GCAAATGAGCATGGCGTCTC 60.248 55.000 0.00 0.00 0.00 3.36
2494 3874 0.379669 CAAATGAGCATGGCGTCTCC 59.620 55.000 0.00 0.00 0.00 3.71
2495 3875 0.749454 AAATGAGCATGGCGTCTCCC 60.749 55.000 0.00 0.00 0.00 4.30
2496 3876 1.913951 AATGAGCATGGCGTCTCCCA 61.914 55.000 0.00 0.00 39.65 4.37
2497 3877 2.512515 GAGCATGGCGTCTCCCAC 60.513 66.667 0.00 0.00 37.79 4.61
2498 3878 3.315142 GAGCATGGCGTCTCCCACA 62.315 63.158 0.00 0.00 37.79 4.17
2499 3879 2.124570 GCATGGCGTCTCCCACAT 60.125 61.111 0.00 0.00 37.79 3.21
2500 3880 2.475466 GCATGGCGTCTCCCACATG 61.475 63.158 0.00 0.00 42.61 3.21
2501 3881 1.221566 CATGGCGTCTCCCACATGA 59.778 57.895 0.00 0.00 42.39 3.07
2502 3882 0.179037 CATGGCGTCTCCCACATGAT 60.179 55.000 0.00 0.00 42.39 2.45
2503 3883 1.070601 CATGGCGTCTCCCACATGATA 59.929 52.381 0.00 0.00 42.39 2.15
2504 3884 0.752658 TGGCGTCTCCCACATGATAG 59.247 55.000 0.00 0.00 0.00 2.08
2505 3885 0.753262 GGCGTCTCCCACATGATAGT 59.247 55.000 0.00 0.00 0.00 2.12
2506 3886 1.961394 GGCGTCTCCCACATGATAGTA 59.039 52.381 0.00 0.00 0.00 1.82
2555 3935 9.561069 GTATGACCCAGAATATGTTCAAACTAT 57.439 33.333 4.92 0.00 36.79 2.12
2651 4031 7.445121 TGCACAATCCTCCTAACATCTTATAG 58.555 38.462 0.00 0.00 0.00 1.31
2670 4050 8.960591 TCTTATAGCACTTAAAGTACGTACCTT 58.039 33.333 21.80 17.53 0.00 3.50
2727 4118 0.453793 CAGTTCGACCTGAGCGAGAT 59.546 55.000 3.48 0.00 39.14 2.75
2918 4329 1.138266 CCGTATCCAGGTCATCGGTTT 59.862 52.381 0.00 0.00 34.38 3.27
2973 4396 0.179018 CCCCTTTGTCCCCATCGATC 60.179 60.000 0.00 0.00 0.00 3.69
2986 4409 3.261643 CCCATCGATCCTCATGGTGATAA 59.738 47.826 0.00 0.00 38.37 1.75
3050 4496 6.350949 GGGACAATACATAGGCAACATTTTGT 60.351 38.462 0.00 0.00 41.41 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.069165 GCAGGTTTGGGGAGGTGAGT 62.069 60.000 0.00 0.00 0.00 3.41
193 227 3.782443 GTCGGATTCGGTGGGGCT 61.782 66.667 0.00 0.00 36.95 5.19
197 231 1.740285 CCTAGGTCGGATTCGGTGG 59.260 63.158 0.00 0.00 36.95 4.61
276 335 4.722700 TTGCTCCCTTGCTCCGGC 62.723 66.667 0.00 0.00 39.26 6.13
277 336 2.747855 GTTGCTCCCTTGCTCCGG 60.748 66.667 0.00 0.00 0.00 5.14
278 337 2.747855 GGTTGCTCCCTTGCTCCG 60.748 66.667 0.00 0.00 0.00 4.63
279 338 1.377856 GAGGTTGCTCCCTTGCTCC 60.378 63.158 0.00 0.00 34.03 4.70
280 339 1.743252 CGAGGTTGCTCCCTTGCTC 60.743 63.158 0.00 0.00 34.03 4.26
281 340 2.177594 CTCGAGGTTGCTCCCTTGCT 62.178 60.000 3.91 0.00 36.14 3.91
282 341 1.743252 CTCGAGGTTGCTCCCTTGC 60.743 63.158 3.91 0.00 36.14 4.01
283 342 1.078848 CCTCGAGGTTGCTCCCTTG 60.079 63.158 24.04 3.71 37.35 3.61
553 612 0.882042 CTAGCACGCATCCCATCCAC 60.882 60.000 0.00 0.00 0.00 4.02
554 613 1.048160 TCTAGCACGCATCCCATCCA 61.048 55.000 0.00 0.00 0.00 3.41
555 614 0.320247 CTCTAGCACGCATCCCATCC 60.320 60.000 0.00 0.00 0.00 3.51
556 615 0.676184 TCTCTAGCACGCATCCCATC 59.324 55.000 0.00 0.00 0.00 3.51
557 616 1.123077 TTCTCTAGCACGCATCCCAT 58.877 50.000 0.00 0.00 0.00 4.00
558 617 0.175760 GTTCTCTAGCACGCATCCCA 59.824 55.000 0.00 0.00 0.00 4.37
559 618 0.461961 AGTTCTCTAGCACGCATCCC 59.538 55.000 0.00 0.00 0.00 3.85
560 619 3.312828 CATAGTTCTCTAGCACGCATCC 58.687 50.000 0.00 0.00 0.00 3.51
561 620 3.312828 CCATAGTTCTCTAGCACGCATC 58.687 50.000 0.00 0.00 0.00 3.91
562 621 2.036475 CCCATAGTTCTCTAGCACGCAT 59.964 50.000 0.00 0.00 0.00 4.73
563 622 1.409064 CCCATAGTTCTCTAGCACGCA 59.591 52.381 0.00 0.00 0.00 5.24
564 623 1.409427 ACCCATAGTTCTCTAGCACGC 59.591 52.381 0.00 0.00 0.00 5.34
565 624 2.427453 ACACCCATAGTTCTCTAGCACG 59.573 50.000 0.00 0.00 0.00 5.34
566 625 4.473477 AACACCCATAGTTCTCTAGCAC 57.527 45.455 0.00 0.00 0.00 4.40
567 626 4.530553 TGAAACACCCATAGTTCTCTAGCA 59.469 41.667 0.00 0.00 0.00 3.49
568 627 5.086104 TGAAACACCCATAGTTCTCTAGC 57.914 43.478 0.00 0.00 0.00 3.42
569 628 6.287589 ACTGAAACACCCATAGTTCTCTAG 57.712 41.667 0.00 0.00 0.00 2.43
570 629 6.681729 AACTGAAACACCCATAGTTCTCTA 57.318 37.500 0.00 0.00 0.00 2.43
571 630 5.568620 AACTGAAACACCCATAGTTCTCT 57.431 39.130 0.00 0.00 0.00 3.10
572 631 6.635030 AAAACTGAAACACCCATAGTTCTC 57.365 37.500 0.00 0.00 31.71 2.87
643 702 6.347079 CGAACGCTTCTAAACTTGGTGAAATA 60.347 38.462 0.00 0.00 0.00 1.40
656 715 3.861276 TCCAAGATCGAACGCTTCTAA 57.139 42.857 0.00 0.00 0.00 2.10
657 716 3.770666 CTTCCAAGATCGAACGCTTCTA 58.229 45.455 0.00 0.00 0.00 2.10
681 747 8.844244 GCAACTCCATATTCTGAAAATCATACT 58.156 33.333 0.00 0.00 0.00 2.12
682 748 8.844244 AGCAACTCCATATTCTGAAAATCATAC 58.156 33.333 0.00 0.00 0.00 2.39
718 784 8.749354 GGGAAAAGGACATCAATAAGTAATTGT 58.251 33.333 0.00 0.00 44.58 2.71
719 785 8.748412 TGGGAAAAGGACATCAATAAGTAATTG 58.252 33.333 0.00 0.00 45.47 2.32
720 786 8.893563 TGGGAAAAGGACATCAATAAGTAATT 57.106 30.769 0.00 0.00 0.00 1.40
721 787 8.336235 TCTGGGAAAAGGACATCAATAAGTAAT 58.664 33.333 0.00 0.00 0.00 1.89
722 788 7.695055 TCTGGGAAAAGGACATCAATAAGTAA 58.305 34.615 0.00 0.00 0.00 2.24
723 789 7.265599 TCTGGGAAAAGGACATCAATAAGTA 57.734 36.000 0.00 0.00 0.00 2.24
724 790 6.139679 TCTGGGAAAAGGACATCAATAAGT 57.860 37.500 0.00 0.00 0.00 2.24
725 791 6.434028 TGTTCTGGGAAAAGGACATCAATAAG 59.566 38.462 0.00 0.00 30.35 1.73
726 792 6.208599 GTGTTCTGGGAAAAGGACATCAATAA 59.791 38.462 0.00 0.00 37.98 1.40
727 793 5.710099 GTGTTCTGGGAAAAGGACATCAATA 59.290 40.000 0.00 0.00 37.98 1.90
728 794 4.524328 GTGTTCTGGGAAAAGGACATCAAT 59.476 41.667 0.00 0.00 37.98 2.57
729 795 3.888930 GTGTTCTGGGAAAAGGACATCAA 59.111 43.478 0.00 0.00 37.98 2.57
730 796 3.486383 GTGTTCTGGGAAAAGGACATCA 58.514 45.455 0.00 0.00 37.98 3.07
731 797 2.484264 CGTGTTCTGGGAAAAGGACATC 59.516 50.000 0.00 0.00 37.98 3.06
732 798 2.158667 ACGTGTTCTGGGAAAAGGACAT 60.159 45.455 0.00 0.00 37.98 3.06
768 840 0.675522 CACCGGTATGTTCCCGCTTT 60.676 55.000 6.87 0.00 44.13 3.51
804 2019 8.126700 ACGCACCAGTATTTTGCTATTTTATAC 58.873 33.333 0.00 0.00 33.90 1.47
820 2060 1.337074 CCGGTAAGAAACGCACCAGTA 60.337 52.381 0.00 0.00 32.32 2.74
966 2210 2.036346 GGCAGCAATTCAACTCCAACTT 59.964 45.455 0.00 0.00 0.00 2.66
979 2223 6.040842 CCCATATTTTGTAACTAGGCAGCAAT 59.959 38.462 0.00 0.00 0.00 3.56
993 2237 3.943671 TCCGACCATCCCATATTTTGT 57.056 42.857 0.00 0.00 0.00 2.83
999 2243 2.168458 TGACTTCCGACCATCCCATA 57.832 50.000 0.00 0.00 0.00 2.74
1052 2296 1.058748 CTATCAACACGGTTGCGCG 59.941 57.895 0.00 0.00 0.00 6.86
1076 2320 0.608130 GGTTCTTTGGCCCCATTCAC 59.392 55.000 0.00 0.00 0.00 3.18
1205 2449 2.485582 CGACGATCTCGCCAGTGT 59.514 61.111 0.00 0.00 44.43 3.55
1273 2517 1.596934 CAAAGGCGGAGAGGTAGCA 59.403 57.895 0.00 0.00 0.00 3.49
1293 2537 2.284258 AAGGCGCTGACCTCTCCT 60.284 61.111 7.64 0.00 39.93 3.69
1296 2540 2.604686 TCCAAGGCGCTGACCTCT 60.605 61.111 7.64 0.00 39.93 3.69
1359 2603 4.819761 GCCTCGCCGTCATGCTCA 62.820 66.667 0.00 0.00 0.00 4.26
1468 2712 0.469070 AGGAGCTGCCTCATCATCAC 59.531 55.000 0.00 0.00 46.97 3.06
1711 2955 0.462581 GCCATCATGACGCCAAGAGA 60.463 55.000 0.00 0.00 0.00 3.10
1867 3111 1.467883 GCGCAAACTGCTATGCAATGA 60.468 47.619 0.30 0.00 42.25 2.57
1968 3212 0.391661 CAGGGTTGCATCGCAGTAGT 60.392 55.000 13.60 0.00 40.61 2.73
2240 3484 1.668101 GACGCAGGAGGGACAGTAGG 61.668 65.000 0.00 0.00 0.00 3.18
2284 3530 3.062639 ACACGACAATTTCATCGAGCATC 59.937 43.478 9.79 0.00 40.86 3.91
2323 3569 1.425066 AGGGGCTCATCACACAAGAAA 59.575 47.619 0.00 0.00 0.00 2.52
2325 3571 0.615331 GAGGGGCTCATCACACAAGA 59.385 55.000 0.00 0.00 0.00 3.02
2337 3583 2.525381 CTCGGCATAGGAGGGGCT 60.525 66.667 0.00 0.00 0.00 5.19
2427 3767 5.151297 ACATTTCCATTTGTTGATGGTCC 57.849 39.130 4.02 0.00 45.53 4.46
2468 3848 2.159338 CGCCATGCTCATTTGCTAACTT 60.159 45.455 0.00 0.00 0.00 2.66
2469 3849 1.402968 CGCCATGCTCATTTGCTAACT 59.597 47.619 0.00 0.00 0.00 2.24
2470 3850 1.133025 ACGCCATGCTCATTTGCTAAC 59.867 47.619 0.00 0.00 0.00 2.34
2471 3851 1.401552 GACGCCATGCTCATTTGCTAA 59.598 47.619 0.00 0.00 0.00 3.09
2472 3852 1.016627 GACGCCATGCTCATTTGCTA 58.983 50.000 0.00 0.00 0.00 3.49
2473 3853 0.679002 AGACGCCATGCTCATTTGCT 60.679 50.000 0.00 0.00 0.00 3.91
2474 3854 0.248377 GAGACGCCATGCTCATTTGC 60.248 55.000 0.00 0.00 0.00 3.68
2475 3855 0.379669 GGAGACGCCATGCTCATTTG 59.620 55.000 0.00 0.00 36.34 2.32
2476 3856 0.749454 GGGAGACGCCATGCTCATTT 60.749 55.000 0.00 0.00 38.95 2.32
2477 3857 1.153086 GGGAGACGCCATGCTCATT 60.153 57.895 0.00 0.00 38.95 2.57
2478 3858 2.369633 TGGGAGACGCCATGCTCAT 61.370 57.895 0.00 0.00 38.95 2.90
2479 3859 3.002583 TGGGAGACGCCATGCTCA 61.003 61.111 0.00 0.00 38.95 4.26
2480 3860 2.512515 GTGGGAGACGCCATGCTC 60.513 66.667 0.00 0.00 38.95 4.26
2481 3861 2.673200 ATGTGGGAGACGCCATGCT 61.673 57.895 0.00 0.00 38.95 3.79
2482 3862 2.124570 ATGTGGGAGACGCCATGC 60.125 61.111 0.00 0.00 38.95 4.06
2483 3863 0.179037 ATCATGTGGGAGACGCCATG 60.179 55.000 0.00 0.00 38.95 3.66
2484 3864 1.345741 CTATCATGTGGGAGACGCCAT 59.654 52.381 0.00 0.00 38.95 4.40
2485 3865 0.752658 CTATCATGTGGGAGACGCCA 59.247 55.000 0.00 0.00 38.95 5.69
2486 3866 0.753262 ACTATCATGTGGGAGACGCC 59.247 55.000 0.00 0.00 0.00 5.68
2487 3867 2.623889 AGTACTATCATGTGGGAGACGC 59.376 50.000 0.00 0.00 0.00 5.19
2488 3868 5.306394 TCTAGTACTATCATGTGGGAGACG 58.694 45.833 2.33 0.00 0.00 4.18
2489 3869 7.768807 ATTCTAGTACTATCATGTGGGAGAC 57.231 40.000 2.33 0.00 0.00 3.36
2490 3870 8.783660 AAATTCTAGTACTATCATGTGGGAGA 57.216 34.615 2.33 0.00 0.00 3.71
2491 3871 9.265901 CAAAATTCTAGTACTATCATGTGGGAG 57.734 37.037 2.33 0.00 0.00 4.30
2492 3872 8.210946 CCAAAATTCTAGTACTATCATGTGGGA 58.789 37.037 2.33 0.00 0.00 4.37
2493 3873 7.993183 ACCAAAATTCTAGTACTATCATGTGGG 59.007 37.037 18.10 12.38 0.00 4.61
2494 3874 8.964476 ACCAAAATTCTAGTACTATCATGTGG 57.036 34.615 2.33 11.29 0.00 4.17
2497 3877 9.722056 GCAAACCAAAATTCTAGTACTATCATG 57.278 33.333 2.33 0.00 0.00 3.07
2498 3878 9.461312 TGCAAACCAAAATTCTAGTACTATCAT 57.539 29.630 2.33 0.00 0.00 2.45
2499 3879 8.726988 GTGCAAACCAAAATTCTAGTACTATCA 58.273 33.333 2.33 0.00 0.00 2.15
2500 3880 8.182227 GGTGCAAACCAAAATTCTAGTACTATC 58.818 37.037 2.33 0.00 0.00 2.08
2501 3881 7.148306 CGGTGCAAACCAAAATTCTAGTACTAT 60.148 37.037 2.33 0.00 0.00 2.12
2502 3882 6.148150 CGGTGCAAACCAAAATTCTAGTACTA 59.852 38.462 1.89 1.89 0.00 1.82
2503 3883 5.048991 CGGTGCAAACCAAAATTCTAGTACT 60.049 40.000 0.00 0.00 0.00 2.73
2504 3884 5.049267 TCGGTGCAAACCAAAATTCTAGTAC 60.049 40.000 0.00 0.00 0.00 2.73
2505 3885 5.064558 TCGGTGCAAACCAAAATTCTAGTA 58.935 37.500 0.00 0.00 0.00 1.82
2506 3886 3.886505 TCGGTGCAAACCAAAATTCTAGT 59.113 39.130 0.00 0.00 0.00 2.57
2613 3993 1.914531 TTGTGCAGCGCAGTAGCATG 61.915 55.000 11.47 0.00 40.08 4.06
2651 4031 7.042925 CCATATGAAGGTACGTACTTTAAGTGC 60.043 40.741 21.39 10.41 0.00 4.40
2670 4050 5.958380 AGAGTTTGTAGAGTGGACCATATGA 59.042 40.000 3.65 0.00 0.00 2.15
2727 4118 2.417924 GCCTCGAAGAAGCAGAAGATCA 60.418 50.000 0.00 0.00 44.63 2.92
2918 4329 1.806542 GCAAGAAGGACGATGAAAGCA 59.193 47.619 0.00 0.00 0.00 3.91
2973 4396 2.804527 CGTGCTCATTATCACCATGAGG 59.195 50.000 11.03 0.00 45.45 3.86


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

AutoCloner maintained by Alex Coulton.