Multiple sequence alignment - TraesCS1B01G195300

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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 TraesCS1B01G195300 chr1B 100.000 3975 0 0 1 3975 350400362 350396388 0.000000e+00 7341
1 TraesCS1B01G195300 chr1B 85.756 344 40 5 3640 3975 614794492 614794150 4.890000e-94 355
2 TraesCS1B01G195300 chr1B 87.500 88 9 2 487 574 593520112 593520027 2.530000e-17 100
3 TraesCS1B01G195300 chr1D 96.992 3324 79 10 657 3975 261733895 261737202 0.000000e+00 5565
4 TraesCS1B01G195300 chr1D 86.047 344 39 5 3640 3975 449280218 449279876 1.050000e-95 361
5 TraesCS1B01G195300 chr1A 93.573 3314 130 39 676 3975 338591108 338587864 0.000000e+00 4863
6 TraesCS1B01G195300 chr1A 87.425 334 33 5 3650 3975 544475132 544474800 3.750000e-100 375
7 TraesCS1B01G195300 chr1A 95.181 83 4 0 573 655 472211515 472211597 8.960000e-27 132
8 TraesCS1B01G195300 chr6B 91.738 581 39 3 1 572 661839143 661839723 0.000000e+00 798
9 TraesCS1B01G195300 chr6A 90.345 580 48 1 1 572 598248987 598249566 0.000000e+00 754
10 TraesCS1B01G195300 chr5B 89.673 581 46 5 1 573 563920284 563919710 0.000000e+00 728
11 TraesCS1B01G195300 chr5B 88.336 583 57 4 1 573 50064179 50063598 0.000000e+00 689
12 TraesCS1B01G195300 chr3A 89.329 581 54 1 1 573 434921814 434922394 0.000000e+00 723
13 TraesCS1B01G195300 chr2A 88.103 580 60 2 1 572 463933846 463933268 0.000000e+00 680
14 TraesCS1B01G195300 chr2A 86.919 581 68 1 1 573 261181881 261182461 0.000000e+00 645
15 TraesCS1B01G195300 chr2A 90.090 333 25 1 249 573 14709453 14709785 3.670000e-115 425
16 TraesCS1B01G195300 chr3B 87.113 582 66 2 1 573 528050008 528049427 0.000000e+00 651
17 TraesCS1B01G195300 chr5A 85.531 622 82 6 1240 1854 683233552 683232932 0.000000e+00 643
18 TraesCS1B01G195300 chr5A 86.379 580 71 1 1 572 495147608 495148187 9.380000e-176 627
19 TraesCS1B01G195300 chr5A 83.019 583 83 12 2268 2839 683232308 683231731 7.620000e-142 514
20 TraesCS1B01G195300 chr5A 88.081 344 35 5 1879 2219 683232807 683232467 1.720000e-108 403
21 TraesCS1B01G195300 chr5A 88.506 87 6 3 488 573 195627849 195627932 7.030000e-18 102
22 TraesCS1B01G195300 chr4D 84.591 623 86 8 1240 1854 500851803 500851183 9.440000e-171 610
23 TraesCS1B01G195300 chr4D 82.333 583 87 12 2268 2839 500850558 500849981 3.570000e-135 492
24 TraesCS1B01G195300 chr4D 86.765 340 41 3 1882 2219 500851055 500850718 3.750000e-100 375
25 TraesCS1B01G195300 chr4D 83.111 225 38 0 2615 2839 500924639 500924415 5.210000e-49 206
26 TraesCS1B01G195300 chr4D 83.111 225 38 0 2615 2839 500961070 500960846 5.210000e-49 206
27 TraesCS1B01G195300 chr4B 84.084 622 89 6 1241 1854 644828282 644827663 3.420000e-165 592
28 TraesCS1B01G195300 chr4B 82.474 582 86 11 2269 2839 644827051 644826475 2.760000e-136 496
29 TraesCS1B01G195300 chr4B 85.714 392 49 4 1879 2268 644827558 644827172 1.330000e-109 407
30 TraesCS1B01G195300 chr7B 93.156 263 9 2 320 573 531434378 531434116 1.040000e-100 377
31 TraesCS1B01G195300 chr2D 78.141 581 119 8 2269 2845 507826125 507825549 2.920000e-96 363
32 TraesCS1B01G195300 chr2B 78.238 579 114 9 2269 2841 596650466 596649894 1.050000e-95 361
33 TraesCS1B01G195300 chr2B 92.941 85 6 0 573 657 744317541 744317625 1.500000e-24 124
34 TraesCS1B01G195300 chr2B 89.535 86 5 3 488 572 211883792 211883874 5.430000e-19 106
35 TraesCS1B01G195300 chr7D 95.455 88 4 0 573 660 45202234 45202147 1.490000e-29 141


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 TraesCS1B01G195300 chr1B 350396388 350400362 3974 True 7341.000000 7341 100.000000 1 3975 1 chr1B.!!$R1 3974
1 TraesCS1B01G195300 chr1D 261733895 261737202 3307 False 5565.000000 5565 96.992000 657 3975 1 chr1D.!!$F1 3318
2 TraesCS1B01G195300 chr1A 338587864 338591108 3244 True 4863.000000 4863 93.573000 676 3975 1 chr1A.!!$R1 3299
3 TraesCS1B01G195300 chr6B 661839143 661839723 580 False 798.000000 798 91.738000 1 572 1 chr6B.!!$F1 571
4 TraesCS1B01G195300 chr6A 598248987 598249566 579 False 754.000000 754 90.345000 1 572 1 chr6A.!!$F1 571
5 TraesCS1B01G195300 chr5B 563919710 563920284 574 True 728.000000 728 89.673000 1 573 1 chr5B.!!$R2 572
6 TraesCS1B01G195300 chr5B 50063598 50064179 581 True 689.000000 689 88.336000 1 573 1 chr5B.!!$R1 572
7 TraesCS1B01G195300 chr3A 434921814 434922394 580 False 723.000000 723 89.329000 1 573 1 chr3A.!!$F1 572
8 TraesCS1B01G195300 chr2A 463933268 463933846 578 True 680.000000 680 88.103000 1 572 1 chr2A.!!$R1 571
9 TraesCS1B01G195300 chr2A 261181881 261182461 580 False 645.000000 645 86.919000 1 573 1 chr2A.!!$F2 572
10 TraesCS1B01G195300 chr3B 528049427 528050008 581 True 651.000000 651 87.113000 1 573 1 chr3B.!!$R1 572
11 TraesCS1B01G195300 chr5A 495147608 495148187 579 False 627.000000 627 86.379000 1 572 1 chr5A.!!$F2 571
12 TraesCS1B01G195300 chr5A 683231731 683233552 1821 True 520.000000 643 85.543667 1240 2839 3 chr5A.!!$R1 1599
13 TraesCS1B01G195300 chr4D 500849981 500851803 1822 True 492.333333 610 84.563000 1240 2839 3 chr4D.!!$R3 1599
14 TraesCS1B01G195300 chr4B 644826475 644828282 1807 True 498.333333 592 84.090667 1241 2839 3 chr4B.!!$R1 1598
15 TraesCS1B01G195300 chr2D 507825549 507826125 576 True 363.000000 363 78.141000 2269 2845 1 chr2D.!!$R1 576
16 TraesCS1B01G195300 chr2B 596649894 596650466 572 True 361.000000 361 78.238000 2269 2841 1 chr2B.!!$R1 572

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
609 621 0.035036 TGTCGTGGCCGGTGATTTAA 59.965 50.000 1.90 0.0 33.95 1.52 F
1715 1751 0.034896 ACAACGGCTTCACCTTCGAT 59.965 50.000 0.00 0.0 35.61 3.59 F
1841 1877 2.181021 CTCTACGCCACGGTGTCC 59.819 66.667 5.35 0.0 39.72 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 1877 0.462759 GGCTTCTGAACAGGATCCGG 60.463 60.0 10.69 10.69 0.00 5.14 R
2768 3040 0.532573 TGAAGGTGGAGCTGTCGATC 59.467 55.0 0.00 0.00 0.00 3.69 R
3175 3449 0.615544 ACCACCATCATGCCTTTGGG 60.616 55.0 7.79 0.00 34.72 4.12 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
210 211 1.342074 CAGGTCACAGTTCCCTCAGA 58.658 55.000 0.00 0.00 0.00 3.27
255 256 1.748493 ACGCCTCAAAGTTGCAGAAAA 59.252 42.857 0.00 0.00 0.00 2.29
292 293 1.421268 TGTTGCTGATCACTTGGGAGT 59.579 47.619 0.00 0.00 36.25 3.85
318 319 0.956633 AAGAGAGGAACGCGTGTGTA 59.043 50.000 14.98 0.00 0.00 2.90
336 337 4.456566 TGTGTATTTAGAGGAAAAACGCCC 59.543 41.667 0.00 0.00 0.00 6.13
438 447 4.801891 TGTTCTGTAGCGAGATAAAACGT 58.198 39.130 0.00 0.00 0.00 3.99
441 450 4.581493 TCTGTAGCGAGATAAAACGTACG 58.419 43.478 15.01 15.01 0.00 3.67
443 452 1.553308 AGCGAGATAAAACGTACGGC 58.447 50.000 21.06 9.65 0.00 5.68
545 557 7.040201 ACTGCTTTCTTCTAAATCAATGAAGCA 60.040 33.333 6.75 6.75 37.63 3.91
597 609 2.868662 CTGATGTACTCAGTGTCGTGG 58.131 52.381 11.84 0.00 45.42 4.94
598 610 1.067846 TGATGTACTCAGTGTCGTGGC 60.068 52.381 0.00 0.00 0.00 5.01
599 611 0.246635 ATGTACTCAGTGTCGTGGCC 59.753 55.000 0.00 0.00 0.00 5.36
600 612 1.443872 GTACTCAGTGTCGTGGCCG 60.444 63.158 0.00 0.00 0.00 6.13
601 613 2.632544 TACTCAGTGTCGTGGCCGG 61.633 63.158 0.00 0.00 33.95 6.13
602 614 3.991051 CTCAGTGTCGTGGCCGGT 61.991 66.667 1.90 0.00 33.95 5.28
603 615 4.293648 TCAGTGTCGTGGCCGGTG 62.294 66.667 1.90 0.00 33.95 4.94
604 616 4.293648 CAGTGTCGTGGCCGGTGA 62.294 66.667 1.90 0.00 33.95 4.02
605 617 3.311110 AGTGTCGTGGCCGGTGAT 61.311 61.111 1.90 0.00 33.95 3.06
606 618 2.358247 GTGTCGTGGCCGGTGATT 60.358 61.111 1.90 0.00 33.95 2.57
607 619 1.964373 GTGTCGTGGCCGGTGATTT 60.964 57.895 1.90 0.00 33.95 2.17
608 620 0.671163 GTGTCGTGGCCGGTGATTTA 60.671 55.000 1.90 0.00 33.95 1.40
609 621 0.035036 TGTCGTGGCCGGTGATTTAA 59.965 50.000 1.90 0.00 33.95 1.52
610 622 0.445043 GTCGTGGCCGGTGATTTAAC 59.555 55.000 1.90 0.00 33.95 2.01
611 623 0.674269 TCGTGGCCGGTGATTTAACC 60.674 55.000 1.90 0.00 36.82 2.85
620 632 2.774687 GGTGATTTAACCGTGTCCACT 58.225 47.619 0.00 0.00 0.00 4.00
621 633 2.482721 GGTGATTTAACCGTGTCCACTG 59.517 50.000 0.00 0.00 0.00 3.66
622 634 3.395639 GTGATTTAACCGTGTCCACTGA 58.604 45.455 0.00 0.00 0.00 3.41
623 635 4.000988 GTGATTTAACCGTGTCCACTGAT 58.999 43.478 0.00 0.00 0.00 2.90
624 636 4.454504 GTGATTTAACCGTGTCCACTGATT 59.545 41.667 0.00 0.00 0.00 2.57
625 637 5.640357 GTGATTTAACCGTGTCCACTGATTA 59.360 40.000 0.00 0.00 0.00 1.75
626 638 6.148150 GTGATTTAACCGTGTCCACTGATTAA 59.852 38.462 0.00 0.00 0.00 1.40
627 639 6.882140 TGATTTAACCGTGTCCACTGATTAAT 59.118 34.615 0.00 0.00 0.00 1.40
628 640 7.392113 TGATTTAACCGTGTCCACTGATTAATT 59.608 33.333 0.00 0.00 0.00 1.40
629 641 6.489127 TTAACCGTGTCCACTGATTAATTG 57.511 37.500 0.00 0.00 0.00 2.32
630 642 3.343617 ACCGTGTCCACTGATTAATTGG 58.656 45.455 0.00 0.00 0.00 3.16
631 643 3.008594 ACCGTGTCCACTGATTAATTGGA 59.991 43.478 3.63 3.63 37.07 3.53
632 644 4.006989 CCGTGTCCACTGATTAATTGGAA 58.993 43.478 8.61 0.00 41.15 3.53
633 645 4.640201 CCGTGTCCACTGATTAATTGGAAT 59.360 41.667 8.61 0.00 41.15 3.01
634 646 5.449041 CCGTGTCCACTGATTAATTGGAATG 60.449 44.000 8.61 5.85 41.15 2.67
635 647 5.123820 CGTGTCCACTGATTAATTGGAATGT 59.876 40.000 8.61 0.00 41.15 2.71
636 648 6.315144 CGTGTCCACTGATTAATTGGAATGTA 59.685 38.462 8.61 0.00 41.15 2.29
637 649 7.012327 CGTGTCCACTGATTAATTGGAATGTAT 59.988 37.037 8.61 0.00 41.15 2.29
638 650 8.131100 GTGTCCACTGATTAATTGGAATGTATG 58.869 37.037 8.61 0.00 41.15 2.39
639 651 7.285172 TGTCCACTGATTAATTGGAATGTATGG 59.715 37.037 8.61 0.00 41.15 2.74
640 652 7.285401 GTCCACTGATTAATTGGAATGTATGGT 59.715 37.037 8.61 0.00 41.15 3.55
641 653 7.285172 TCCACTGATTAATTGGAATGTATGGTG 59.715 37.037 5.09 0.00 36.45 4.17
642 654 7.068593 CCACTGATTAATTGGAATGTATGGTGT 59.931 37.037 0.00 0.00 31.39 4.16
643 655 8.469200 CACTGATTAATTGGAATGTATGGTGTT 58.531 33.333 0.00 0.00 0.00 3.32
644 656 8.686334 ACTGATTAATTGGAATGTATGGTGTTC 58.314 33.333 0.00 0.00 0.00 3.18
645 657 8.006298 TGATTAATTGGAATGTATGGTGTTCC 57.994 34.615 0.00 0.00 41.37 3.62
733 746 2.279173 AGATTGGCCAGTAAACCCTCT 58.721 47.619 5.11 0.00 0.00 3.69
747 760 2.884685 CTCTCGCTTGCTGCTCCG 60.885 66.667 0.00 0.96 40.11 4.63
813 831 4.083643 AGTTCATCACTTCTGCATTTCACG 60.084 41.667 0.00 0.00 27.32 4.35
862 880 8.102484 ACCATTCCCTTTCTATAGTAACACAT 57.898 34.615 0.00 0.00 0.00 3.21
880 898 0.532862 ATGTTTATGGGCTCCTCGCG 60.533 55.000 0.00 0.00 40.44 5.87
953 971 4.197498 TACCCGCGCGCTAACTCC 62.197 66.667 30.48 0.00 0.00 3.85
964 982 3.489785 CGCGCTAACTCCAGGTTTATAAG 59.510 47.826 5.56 0.00 39.17 1.73
966 984 3.489785 CGCTAACTCCAGGTTTATAAGCG 59.510 47.826 8.31 8.31 45.89 4.68
1087 1105 4.986645 TTCTTGGCGCGCTCTGCA 62.987 61.111 32.29 17.83 46.97 4.41
1183 1213 5.411053 TGCGTGTGTCTTTTATCATGATCAA 59.589 36.000 12.53 4.64 0.00 2.57
1199 1229 2.696989 TCAATGGACGCTGTGATGAT 57.303 45.000 0.00 0.00 0.00 2.45
1715 1751 0.034896 ACAACGGCTTCACCTTCGAT 59.965 50.000 0.00 0.00 35.61 3.59
1841 1877 2.181021 CTCTACGCCACGGTGTCC 59.819 66.667 5.35 0.00 39.72 4.02
1877 2018 2.768344 CAGGAGGGGGTGCCGTAT 60.768 66.667 0.00 0.00 0.00 3.06
2768 3040 3.721706 GTGAGGGGGCTCAGGGTG 61.722 72.222 0.00 0.00 33.58 4.61
2861 3133 1.813513 CGCAAGTCTGAAATGACCCT 58.186 50.000 0.00 0.00 37.66 4.34
2895 3167 9.848710 ATACTGATCTGAATGAATGAATCAACT 57.151 29.630 6.60 0.00 42.54 3.16
2896 3168 8.211116 ACTGATCTGAATGAATGAATCAACTC 57.789 34.615 6.60 0.00 42.54 3.01
2897 3169 7.827729 ACTGATCTGAATGAATGAATCAACTCA 59.172 33.333 6.60 1.64 42.54 3.41
2898 3170 8.570068 TGATCTGAATGAATGAATCAACTCAA 57.430 30.769 3.07 0.00 42.54 3.02
3119 3392 9.874205 CTGTTTGTTGATTATTATGAAACCCAT 57.126 29.630 0.00 0.00 39.25 4.00
3270 3547 5.186409 ACCAATTTCCATTGATGACAAGAGG 59.814 40.000 0.00 0.00 42.35 3.69
3303 3580 3.181483 GGCCCAACATTGCTTCAGAATAG 60.181 47.826 0.00 0.00 0.00 1.73
3308 3585 5.181811 CCAACATTGCTTCAGAATAGTGTGA 59.818 40.000 0.00 0.00 0.00 3.58
3341 3618 9.301153 CATTTACAGTTTTGCACTAGAAACTTT 57.699 29.630 10.78 8.17 42.47 2.66
3446 3723 6.233434 GGATCCAGCATGTAATCATCTTACA 58.767 40.000 6.95 0.74 38.99 2.41
3523 3800 4.590222 ACCAAAAGGCAGAAATGACTTGAT 59.410 37.500 0.00 0.00 37.20 2.57
3646 3925 0.904649 TCGGCATCTCTGTTGTCCAT 59.095 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 0.040336 ATATCTACGCGACACTGCCG 60.040 55.000 15.93 0.00 0.00 5.69
210 211 1.882352 GCGGTCAGTCTTTCCCAATGT 60.882 52.381 0.00 0.00 0.00 2.71
255 256 0.978146 ACAGCATCGACCTTAGCCCT 60.978 55.000 0.00 0.00 0.00 5.19
292 293 1.871039 CGCGTTCCTCTCTTTCCAAAA 59.129 47.619 0.00 0.00 0.00 2.44
318 319 3.089284 CTGGGGCGTTTTTCCTCTAAAT 58.911 45.455 0.00 0.00 0.00 1.40
336 337 0.460987 GCTGAACATCCTCCGTCTGG 60.461 60.000 0.00 0.00 0.00 3.86
443 452 3.550437 AAACTAGGCCAGCTACATGAG 57.450 47.619 5.01 0.00 0.00 2.90
506 518 4.019174 AGAAAGCAGTGGGAAATACATGG 58.981 43.478 0.00 0.00 0.00 3.66
545 557 1.358152 TGAAAGATCCGGGTTCACCT 58.642 50.000 0.00 0.00 36.97 4.00
578 590 1.067846 GCCACGACACTGAGTACATCA 60.068 52.381 0.00 0.00 36.21 3.07
579 591 1.630148 GCCACGACACTGAGTACATC 58.370 55.000 0.00 0.00 0.00 3.06
580 592 0.246635 GGCCACGACACTGAGTACAT 59.753 55.000 0.00 0.00 0.00 2.29
581 593 1.663739 GGCCACGACACTGAGTACA 59.336 57.895 0.00 0.00 0.00 2.90
582 594 1.443872 CGGCCACGACACTGAGTAC 60.444 63.158 2.24 0.00 44.60 2.73
583 595 2.632544 CCGGCCACGACACTGAGTA 61.633 63.158 2.24 0.00 44.60 2.59
584 596 3.991051 CCGGCCACGACACTGAGT 61.991 66.667 2.24 0.00 44.60 3.41
585 597 3.991051 ACCGGCCACGACACTGAG 61.991 66.667 0.00 0.00 44.60 3.35
586 598 4.293648 CACCGGCCACGACACTGA 62.294 66.667 0.00 0.00 44.60 3.41
587 599 3.589654 ATCACCGGCCACGACACTG 62.590 63.158 0.00 0.00 44.60 3.66
588 600 2.391724 AAATCACCGGCCACGACACT 62.392 55.000 0.00 0.00 44.60 3.55
589 601 0.671163 TAAATCACCGGCCACGACAC 60.671 55.000 0.00 0.00 44.60 3.67
590 602 0.035036 TTAAATCACCGGCCACGACA 59.965 50.000 0.00 0.00 44.60 4.35
591 603 0.445043 GTTAAATCACCGGCCACGAC 59.555 55.000 0.00 0.00 44.60 4.34
592 604 0.674269 GGTTAAATCACCGGCCACGA 60.674 55.000 0.00 0.00 44.60 4.35
593 605 1.798087 GGTTAAATCACCGGCCACG 59.202 57.895 0.00 0.00 40.55 4.94
600 612 2.482721 CAGTGGACACGGTTAAATCACC 59.517 50.000 0.00 0.00 36.20 4.02
601 613 3.395639 TCAGTGGACACGGTTAAATCAC 58.604 45.455 2.72 0.00 36.20 3.06
602 614 3.755112 TCAGTGGACACGGTTAAATCA 57.245 42.857 2.72 0.00 36.20 2.57
603 615 6.730960 TTAATCAGTGGACACGGTTAAATC 57.269 37.500 2.72 0.00 36.20 2.17
604 616 7.362574 CCAATTAATCAGTGGACACGGTTAAAT 60.363 37.037 12.84 6.11 34.05 1.40
605 617 6.072397 CCAATTAATCAGTGGACACGGTTAAA 60.072 38.462 12.84 4.10 34.05 1.52
606 618 5.413213 CCAATTAATCAGTGGACACGGTTAA 59.587 40.000 11.88 11.88 34.05 2.01
607 619 4.938832 CCAATTAATCAGTGGACACGGTTA 59.061 41.667 0.00 0.52 34.05 2.85
608 620 3.756434 CCAATTAATCAGTGGACACGGTT 59.244 43.478 0.00 1.35 34.05 4.44
609 621 3.008594 TCCAATTAATCAGTGGACACGGT 59.991 43.478 3.63 0.00 36.51 4.83
610 622 3.605634 TCCAATTAATCAGTGGACACGG 58.394 45.455 3.63 0.00 36.51 4.94
611 623 5.123820 ACATTCCAATTAATCAGTGGACACG 59.876 40.000 6.82 2.55 41.15 4.49
612 624 6.515272 ACATTCCAATTAATCAGTGGACAC 57.485 37.500 6.82 0.00 41.15 3.67
613 625 7.285172 CCATACATTCCAATTAATCAGTGGACA 59.715 37.037 6.82 1.14 41.15 4.02
614 626 7.285401 ACCATACATTCCAATTAATCAGTGGAC 59.715 37.037 6.82 0.00 41.15 4.02
615 627 7.285172 CACCATACATTCCAATTAATCAGTGGA 59.715 37.037 3.63 3.63 39.70 4.02
616 628 7.068593 ACACCATACATTCCAATTAATCAGTGG 59.931 37.037 0.00 0.00 0.00 4.00
617 629 7.999679 ACACCATACATTCCAATTAATCAGTG 58.000 34.615 0.00 0.00 0.00 3.66
618 630 8.593945 AACACCATACATTCCAATTAATCAGT 57.406 30.769 0.00 0.00 0.00 3.41
619 631 8.137437 GGAACACCATACATTCCAATTAATCAG 58.863 37.037 0.00 0.00 41.40 2.90
620 632 7.617329 TGGAACACCATACATTCCAATTAATCA 59.383 33.333 2.48 0.00 46.93 2.57
621 633 8.006298 TGGAACACCATACATTCCAATTAATC 57.994 34.615 2.48 0.00 46.93 1.75
622 634 7.969690 TGGAACACCATACATTCCAATTAAT 57.030 32.000 2.48 0.00 46.93 1.40
629 641 3.279434 GACCTGGAACACCATACATTCC 58.721 50.000 0.00 0.00 42.00 3.01
630 642 3.950397 TGACCTGGAACACCATACATTC 58.050 45.455 0.00 0.00 32.90 2.67
631 643 4.380843 TTGACCTGGAACACCATACATT 57.619 40.909 0.00 0.00 32.90 2.71
632 644 4.380843 TTTGACCTGGAACACCATACAT 57.619 40.909 0.00 0.00 32.90 2.29
633 645 3.866703 TTTGACCTGGAACACCATACA 57.133 42.857 0.00 0.00 32.90 2.29
655 667 8.792633 TCCGAAAGAATTACATTTGACATTCTT 58.207 29.630 12.17 12.17 44.32 2.52
862 880 1.153449 CGCGAGGAGCCCATAAACA 60.153 57.895 0.00 0.00 44.76 2.83
880 898 0.670162 TTGCAGTGCAAAGAAGAGCC 59.330 50.000 27.79 0.00 45.96 4.70
953 971 3.617263 AGTTCGCTTCGCTTATAAACCTG 59.383 43.478 0.00 0.00 0.00 4.00
994 1012 1.227263 GCGAGCTCGGCATCCTTTA 60.227 57.895 35.10 0.00 40.23 1.85
1071 1089 4.765449 ATGCAGAGCGCGCCAAGA 62.765 61.111 30.33 8.86 46.97 3.02
1087 1105 2.473760 CCTCCGAGAGTGCGACGAT 61.474 63.158 0.00 0.00 0.00 3.73
1183 1213 2.696989 TTGATCATCACAGCGTCCAT 57.303 45.000 0.00 0.00 0.00 3.41
1199 1229 3.353029 CACGCACGGCACCATTGA 61.353 61.111 0.00 0.00 0.00 2.57
1529 1565 2.186903 CTGGCCCGCGTGTAGAAT 59.813 61.111 4.92 0.00 0.00 2.40
1715 1751 2.838693 TTGGTCCCCGTGACGTGA 60.839 61.111 3.64 0.00 45.46 4.35
1841 1877 0.462759 GGCTTCTGAACAGGATCCGG 60.463 60.000 10.69 10.69 0.00 5.14
2033 2174 4.758251 TGGATGCCGTGTGCCTCG 62.758 66.667 0.00 0.00 40.16 4.63
2768 3040 0.532573 TGAAGGTGGAGCTGTCGATC 59.467 55.000 0.00 0.00 0.00 3.69
2861 3133 8.715088 CATTCATTCAGATCAGTATAATTGCGA 58.285 33.333 0.00 0.00 0.00 5.10
2894 3166 7.946655 TCATAGTTGTGTTAGTTGAGTTGAG 57.053 36.000 0.00 0.00 0.00 3.02
2895 3167 9.990360 TTATCATAGTTGTGTTAGTTGAGTTGA 57.010 29.630 0.00 0.00 0.00 3.18
3119 3392 7.067372 CAGAGAAATGCATGTTAAAGGGATGTA 59.933 37.037 0.00 0.00 0.00 2.29
3175 3449 0.615544 ACCACCATCATGCCTTTGGG 60.616 55.000 7.79 0.00 34.72 4.12
3176 3450 1.205417 GAACCACCATCATGCCTTTGG 59.795 52.381 0.00 0.00 36.56 3.28
3270 3547 1.367471 GTTGGGCCTTGGTTTGCTC 59.633 57.895 4.53 0.00 0.00 4.26
3303 3580 5.376854 AACTGTAAATGCATCCTTCACAC 57.623 39.130 0.00 0.00 0.00 3.82
3308 3585 5.212532 TGCAAAACTGTAAATGCATCCTT 57.787 34.783 0.00 0.00 43.32 3.36
3446 3723 7.786046 TTACATGTATTCGGTCCCTGTATAT 57.214 36.000 6.36 0.00 0.00 0.86
3492 3769 1.118838 CTGCCTTTTGGTTGTTCCCA 58.881 50.000 0.00 0.00 42.99 4.37
3646 3925 5.570205 TGTTGGTGACTTCTTGGGTATTA 57.430 39.130 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.