Multiple sequence alignment - TraesCS1B01G262500

Loading Multiple Alignment...

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 TraesCS1B01G262500 chr1B 100.000 4109 0 0 1 4109 461294492 461298600 0.000000e+00 7589.0
1 TraesCS1B01G262500 chr1B 98.023 354 6 1 2589 2941 461236891 461237244 7.550000e-172 614.0
2 TraesCS1B01G262500 chr1D 96.068 3408 63 22 739 4109 343885567 343888940 0.000000e+00 5485.0
3 TraesCS1B01G262500 chr4B 88.415 656 63 9 1 645 501350576 501351229 0.000000e+00 778.0
4 TraesCS1B01G262500 chr4B 81.618 680 103 11 3 664 585740530 585739855 1.000000e-150 544.0
5 TraesCS1B01G262500 chr4B 88.742 151 8 5 2 143 25825023 25824873 4.220000e-40 176.0
6 TraesCS1B01G262500 chr6B 87.805 656 75 5 1 653 120840312 120840965 0.000000e+00 763.0
7 TraesCS1B01G262500 chr6B 87.387 666 70 5 1 653 693810773 693811437 0.000000e+00 752.0
8 TraesCS1B01G262500 chr6B 85.444 687 77 11 1 669 45569878 45569197 0.000000e+00 693.0
9 TraesCS1B01G262500 chr6B 85.897 234 28 4 3444 3672 688619751 688619518 1.140000e-60 244.0
10 TraesCS1B01G262500 chr3B 87.176 655 67 9 1 645 461057815 461058462 0.000000e+00 728.0
11 TraesCS1B01G262500 chr3B 86.624 628 64 12 54 664 498060359 498059735 0.000000e+00 676.0
12 TraesCS1B01G262500 chr3D 86.280 656 73 7 1 645 104139856 104140505 0.000000e+00 697.0
13 TraesCS1B01G262500 chr3D 78.395 486 88 12 2618 3099 435293047 435292575 2.400000e-77 300.0
14 TraesCS1B01G262500 chr7D 84.862 687 81 12 1 671 552311102 552310423 0.000000e+00 671.0
15 TraesCS1B01G262500 chr7D 88.671 459 49 3 2 459 187260887 187260431 1.290000e-154 556.0
16 TraesCS1B01G262500 chrUn 88.802 384 32 3 4 378 117317933 117317552 1.040000e-125 460.0
17 TraesCS1B01G262500 chr7B 89.412 255 26 1 4 258 3702909 3702656 1.840000e-83 320.0
18 TraesCS1B01G262500 chr7B 87.342 237 23 6 3442 3672 464645388 464645153 8.760000e-67 265.0
19 TraesCS1B01G262500 chr7B 86.207 232 28 3 3445 3672 140467473 140467242 8.820000e-62 248.0
20 TraesCS1B01G262500 chr5D 88.696 230 20 5 3445 3668 257855807 257855578 4.050000e-70 276.0
21 TraesCS1B01G262500 chr5B 89.401 217 23 0 1 217 81212559 81212775 1.460000e-69 274.0
22 TraesCS1B01G262500 chr5B 87.446 231 19 9 3445 3668 543221206 543221433 1.470000e-64 257.0
23 TraesCS1B01G262500 chr3A 77.207 487 93 13 2618 3100 574011354 574010882 6.770000e-68 268.0
24 TraesCS1B01G262500 chr4D 87.931 232 21 5 3446 3672 362196457 362196686 2.440000e-67 267.0
25 TraesCS1B01G262500 chr4D 85.833 240 28 5 3444 3679 440410143 440410380 2.450000e-62 250.0
26 TraesCS1B01G262500 chr2B 85.062 241 30 5 3444 3678 590664685 590664445 1.480000e-59 241.0
27 TraesCS1B01G262500 chr1A 88.889 162 10 3 3952 4109 443199032 443199189 4.190000e-45 193.0
28 TraesCS1B01G262500 chr5A 100.000 28 0 0 3198 3225 619446909 619446936 7.000000e-03 52.8


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 TraesCS1B01G262500 chr1B 461294492 461298600 4108 False 7589 7589 100.000 1 4109 1 chr1B.!!$F2 4108
1 TraesCS1B01G262500 chr1D 343885567 343888940 3373 False 5485 5485 96.068 739 4109 1 chr1D.!!$F1 3370
2 TraesCS1B01G262500 chr4B 501350576 501351229 653 False 778 778 88.415 1 645 1 chr4B.!!$F1 644
3 TraesCS1B01G262500 chr4B 585739855 585740530 675 True 544 544 81.618 3 664 1 chr4B.!!$R2 661
4 TraesCS1B01G262500 chr6B 120840312 120840965 653 False 763 763 87.805 1 653 1 chr6B.!!$F1 652
5 TraesCS1B01G262500 chr6B 693810773 693811437 664 False 752 752 87.387 1 653 1 chr6B.!!$F2 652
6 TraesCS1B01G262500 chr6B 45569197 45569878 681 True 693 693 85.444 1 669 1 chr6B.!!$R1 668
7 TraesCS1B01G262500 chr3B 461057815 461058462 647 False 728 728 87.176 1 645 1 chr3B.!!$F1 644
8 TraesCS1B01G262500 chr3B 498059735 498060359 624 True 676 676 86.624 54 664 1 chr3B.!!$R1 610
9 TraesCS1B01G262500 chr3D 104139856 104140505 649 False 697 697 86.280 1 645 1 chr3D.!!$F1 644
10 TraesCS1B01G262500 chr7D 552310423 552311102 679 True 671 671 84.862 1 671 1 chr7D.!!$R2 670

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
615 633 0.176910 TCATCGCCGACCTGCATTTA 59.823 50.000 0.00 0.0 0.00 1.40 F
655 677 0.970937 GGGCCTTTTTGGGGTCTAGC 60.971 60.000 0.84 0.0 36.00 3.42 F
666 688 1.206371 GGGGTCTAGCGTTGCTCTTAA 59.794 52.381 0.00 0.0 40.44 1.85 F
1941 1978 0.251832 TCCTCGTCTTCTCCAAGGCT 60.252 55.000 0.00 0.0 31.36 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 1870 0.827925 ACTTGGAGTGGAGCGACTCA 60.828 55.000 13.4 0.0 43.70 3.41 R
1941 1978 1.003839 CTTGTAGCGTCCCTTGCCA 60.004 57.895 0.0 0.0 0.00 4.92 R
2897 2934 2.060980 AGCCTCCACCGCTTCCTAG 61.061 63.158 0.0 0.0 30.57 3.02 R
3668 3727 0.247736 GGACGAATCACTGCCACTCT 59.752 55.000 0.0 0.0 0.00 3.24 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
62 63 0.877071 ATGTCTGCTGCCGAAAGTTG 59.123 50.000 0.00 0.00 0.00 3.16
82 83 3.805207 TGGAGAGCATCATCTCAACATG 58.195 45.455 6.12 0.00 46.31 3.21
83 84 3.199289 TGGAGAGCATCATCTCAACATGT 59.801 43.478 6.12 0.00 46.31 3.21
135 145 1.728490 GCACGGGCTCAATTCCATCC 61.728 60.000 0.00 0.00 36.96 3.51
385 399 3.950794 GAATCGGCGGCAGTGGACA 62.951 63.158 10.53 0.00 0.00 4.02
446 462 1.579429 GGGCGCGAGTTGAAATGTT 59.421 52.632 12.10 0.00 0.00 2.71
461 477 1.779061 ATGTTCCTCCCGCCAACTGT 61.779 55.000 0.00 0.00 0.00 3.55
468 484 0.759959 TCCCGCCAACTGTTTCACTA 59.240 50.000 0.00 0.00 0.00 2.74
470 486 0.872388 CCGCCAACTGTTTCACTACC 59.128 55.000 0.00 0.00 0.00 3.18
475 491 3.439129 GCCAACTGTTTCACTACCATACC 59.561 47.826 0.00 0.00 0.00 2.73
532 548 0.601057 CGGGTTAGGGCCAAGTTTTG 59.399 55.000 6.18 0.00 0.00 2.44
542 558 2.203294 AAGTTTTGGTCGCGCCCT 60.203 55.556 8.05 0.00 36.04 5.19
598 616 1.345089 TCTGTTCGGACGGGATTTTCA 59.655 47.619 1.96 0.00 32.78 2.69
615 633 0.176910 TCATCGCCGACCTGCATTTA 59.823 50.000 0.00 0.00 0.00 1.40
650 668 3.513566 TCGGGGCCTTTTTGGGGT 61.514 61.111 0.84 0.00 36.00 4.95
655 677 0.970937 GGGCCTTTTTGGGGTCTAGC 60.971 60.000 0.84 0.00 36.00 3.42
666 688 1.206371 GGGGTCTAGCGTTGCTCTTAA 59.794 52.381 0.00 0.00 40.44 1.85
669 691 3.586892 GGTCTAGCGTTGCTCTTAAACT 58.413 45.455 0.00 0.00 40.44 2.66
670 692 3.613299 GGTCTAGCGTTGCTCTTAAACTC 59.387 47.826 0.00 0.00 40.44 3.01
671 693 4.487019 GTCTAGCGTTGCTCTTAAACTCT 58.513 43.478 0.00 0.00 40.44 3.24
672 694 5.392811 GGTCTAGCGTTGCTCTTAAACTCTA 60.393 44.000 0.00 0.00 40.44 2.43
673 695 6.267070 GTCTAGCGTTGCTCTTAAACTCTAT 58.733 40.000 0.00 0.00 40.44 1.98
674 696 6.197468 GTCTAGCGTTGCTCTTAAACTCTATG 59.803 42.308 0.00 0.00 40.44 2.23
675 697 5.073311 AGCGTTGCTCTTAAACTCTATGA 57.927 39.130 0.00 0.00 30.62 2.15
676 698 5.479306 AGCGTTGCTCTTAAACTCTATGAA 58.521 37.500 0.00 0.00 30.62 2.57
677 699 5.932303 AGCGTTGCTCTTAAACTCTATGAAA 59.068 36.000 0.00 0.00 30.62 2.69
678 700 6.016111 GCGTTGCTCTTAAACTCTATGAAAC 58.984 40.000 0.00 0.00 0.00 2.78
679 701 6.128526 GCGTTGCTCTTAAACTCTATGAAACT 60.129 38.462 0.00 0.00 0.00 2.66
680 702 7.063074 GCGTTGCTCTTAAACTCTATGAAACTA 59.937 37.037 0.00 0.00 0.00 2.24
681 703 8.587950 CGTTGCTCTTAAACTCTATGAAACTAG 58.412 37.037 0.00 0.00 0.00 2.57
682 704 8.384365 GTTGCTCTTAAACTCTATGAAACTAGC 58.616 37.037 0.00 0.00 0.00 3.42
683 705 7.841956 TGCTCTTAAACTCTATGAAACTAGCT 58.158 34.615 0.00 0.00 0.00 3.32
684 706 7.761704 TGCTCTTAAACTCTATGAAACTAGCTG 59.238 37.037 0.00 0.00 0.00 4.24
685 707 7.762159 GCTCTTAAACTCTATGAAACTAGCTGT 59.238 37.037 0.00 0.00 0.00 4.40
688 710 8.928270 TTAAACTCTATGAAACTAGCTGTAGC 57.072 34.615 0.00 0.00 42.49 3.58
689 711 6.531503 AACTCTATGAAACTAGCTGTAGCA 57.468 37.500 6.65 0.00 45.16 3.49
690 712 6.723298 ACTCTATGAAACTAGCTGTAGCAT 57.277 37.500 6.65 3.29 45.16 3.79
691 713 7.118496 ACTCTATGAAACTAGCTGTAGCATT 57.882 36.000 6.65 0.00 45.16 3.56
692 714 6.983307 ACTCTATGAAACTAGCTGTAGCATTG 59.017 38.462 6.65 2.40 45.16 2.82
693 715 4.889832 ATGAAACTAGCTGTAGCATTGC 57.110 40.909 6.65 0.00 45.16 3.56
694 716 3.942829 TGAAACTAGCTGTAGCATTGCT 58.057 40.909 16.63 16.63 45.16 3.91
695 717 5.084818 TGAAACTAGCTGTAGCATTGCTA 57.915 39.130 14.33 14.33 45.16 3.49
733 755 7.787725 ACTATATAAGTGCTTTTTCGGAAGG 57.212 36.000 0.00 0.00 36.93 3.46
734 756 7.562135 ACTATATAAGTGCTTTTTCGGAAGGA 58.438 34.615 0.00 0.00 36.93 3.36
735 757 8.044908 ACTATATAAGTGCTTTTTCGGAAGGAA 58.955 33.333 0.00 0.00 36.93 3.36
736 758 7.696992 ATATAAGTGCTTTTTCGGAAGGAAA 57.303 32.000 0.00 0.00 42.75 3.13
768 790 9.834628 GAAGACACAAATCCGTTATTTTAATGA 57.165 29.630 0.00 0.00 35.54 2.57
785 807 2.169832 TGAGAGAAACTTGAAGGCGG 57.830 50.000 0.00 0.00 0.00 6.13
786 808 1.270839 TGAGAGAAACTTGAAGGCGGG 60.271 52.381 0.00 0.00 0.00 6.13
832 854 2.548480 CACTTTTCTTTGGAGACGACCC 59.452 50.000 0.00 0.00 0.00 4.46
833 855 2.152016 CTTTTCTTTGGAGACGACCCC 58.848 52.381 0.00 0.00 0.00 4.95
846 872 2.363276 ACCCCTGTATGGCGTCGA 60.363 61.111 0.00 0.00 0.00 4.20
875 901 2.687935 GTCTCTAGAGGCAGGTTCAGAG 59.312 54.545 19.57 0.00 32.23 3.35
909 943 2.484770 GCACACTGTGGGTACTCTGAAA 60.485 50.000 12.28 0.00 33.64 2.69
918 952 3.055094 TGGGTACTCTGAAAGCATCTTCC 60.055 47.826 0.00 0.00 0.00 3.46
924 958 1.399791 CTGAAAGCATCTTCCCTTCGC 59.600 52.381 0.00 0.00 0.00 4.70
1113 1150 4.214383 CTCCGCAAGCGCATCGTG 62.214 66.667 11.47 3.45 38.40 4.35
1152 1189 2.811101 CTCTGGCTCGCCTACCTG 59.189 66.667 9.65 0.00 36.94 4.00
1266 1303 2.650778 CTTTTGTGGGCGCCCTTC 59.349 61.111 43.34 33.87 36.94 3.46
1395 1432 5.554637 CGCTGTACGTCTACTGGAAGTCC 62.555 56.522 0.00 0.00 42.01 3.85
1465 1502 1.220749 GGCGTCCTCAAGTATGCCA 59.779 57.895 1.27 0.00 42.03 4.92
1941 1978 0.251832 TCCTCGTCTTCTCCAAGGCT 60.252 55.000 0.00 0.00 31.36 4.58
2084 2121 1.737735 GGAAGTTGCGCAAATGCCC 60.738 57.895 32.86 26.32 37.91 5.36
2554 2591 2.066393 TCCTCAGATCTTGCCCCCG 61.066 63.158 0.00 0.00 0.00 5.73
2605 2642 1.077716 ATAAACAGCGGGTCCAGGC 60.078 57.895 0.00 0.00 0.00 4.85
2733 2770 1.443802 CGGAGGCCAAGAACTTCTTC 58.556 55.000 5.01 0.00 33.78 2.87
3075 3112 4.051167 TACAGGGTCGAGGCCGGA 62.051 66.667 5.05 0.00 36.24 5.14
3134 3171 1.944709 AGTTCGTTTTGCGCCTTAACT 59.055 42.857 4.18 3.38 41.07 2.24
3196 3233 7.272084 GCTATTTGTTCACACTTTTCTGCTATG 59.728 37.037 0.00 0.00 0.00 2.23
3201 3238 5.738619 TCACACTTTTCTGCTATGTCCTA 57.261 39.130 0.00 0.00 0.00 2.94
3240 3277 8.090788 TCCCTAGTTTAGAGCTCACATTTAAT 57.909 34.615 17.77 0.00 0.00 1.40
3270 3307 9.364989 GATTTTCAATTAAAATTCGGTCATCCA 57.635 29.630 0.00 0.00 45.70 3.41
3288 3341 8.037166 GGTCATCCAATATTTCTCAAAGCTTTT 58.963 33.333 9.53 0.00 0.00 2.27
3335 3391 3.575965 CCTTTGTAAGGCCACACAATC 57.424 47.619 19.36 0.00 42.78 2.67
3336 3392 2.890311 CCTTTGTAAGGCCACACAATCA 59.110 45.455 19.36 7.95 42.78 2.57
3337 3393 3.320541 CCTTTGTAAGGCCACACAATCAA 59.679 43.478 19.36 7.36 42.78 2.57
3366 3422 7.713942 GGTATTTACTCTCGTAATCCAATTGGT 59.286 37.037 23.76 8.60 35.65 3.67
3408 3464 2.351418 CAGCGACAAACTGAACAGTGAA 59.649 45.455 8.25 0.00 41.58 3.18
3411 3467 3.354397 CGACAAACTGAACAGTGAAAGC 58.646 45.455 8.25 0.00 41.58 3.51
3420 3476 1.429463 ACAGTGAAAGCGATTCGTCC 58.571 50.000 8.03 0.00 41.18 4.79
3451 3507 6.006275 TCTACCGACCAAATACTACTACCT 57.994 41.667 0.00 0.00 0.00 3.08
3452 3508 7.136822 TCTACCGACCAAATACTACTACCTA 57.863 40.000 0.00 0.00 0.00 3.08
3648 3706 6.092533 GGTCAAATTTTGGCATGGAATACAAG 59.907 38.462 15.12 0.00 36.88 3.16
3668 3727 5.546499 ACAAGGAGACTAATAAACCAGGACA 59.454 40.000 0.00 0.00 42.68 4.02
3673 3732 6.287589 AGACTAATAAACCAGGACAGAGTG 57.712 41.667 0.00 0.00 0.00 3.51
3674 3733 5.187967 AGACTAATAAACCAGGACAGAGTGG 59.812 44.000 0.00 0.00 39.98 4.00
3675 3734 2.789409 ATAAACCAGGACAGAGTGGC 57.211 50.000 0.00 0.00 37.34 5.01
3676 3735 1.429930 TAAACCAGGACAGAGTGGCA 58.570 50.000 0.00 0.00 37.34 4.92
3677 3736 0.109342 AAACCAGGACAGAGTGGCAG 59.891 55.000 0.00 0.00 37.34 4.85
3678 3737 1.056700 AACCAGGACAGAGTGGCAGT 61.057 55.000 0.00 0.00 37.34 4.40
3679 3738 1.004080 CCAGGACAGAGTGGCAGTG 60.004 63.158 0.00 0.00 0.00 3.66
3680 3739 1.475169 CCAGGACAGAGTGGCAGTGA 61.475 60.000 0.00 0.00 0.00 3.41
3681 3740 0.612229 CAGGACAGAGTGGCAGTGAT 59.388 55.000 0.00 0.00 0.00 3.06
3682 3741 1.002888 CAGGACAGAGTGGCAGTGATT 59.997 52.381 0.00 0.00 0.00 2.57
3683 3742 1.277557 AGGACAGAGTGGCAGTGATTC 59.722 52.381 0.00 0.00 0.00 2.52
3684 3743 1.354040 GACAGAGTGGCAGTGATTCG 58.646 55.000 0.00 0.00 0.00 3.34
3685 3744 0.681733 ACAGAGTGGCAGTGATTCGT 59.318 50.000 0.00 0.00 0.00 3.85
3686 3745 1.337260 ACAGAGTGGCAGTGATTCGTC 60.337 52.381 0.00 0.00 0.00 4.20
3687 3746 0.247736 AGAGTGGCAGTGATTCGTCC 59.752 55.000 0.00 0.00 0.00 4.79
3688 3747 0.037326 GAGTGGCAGTGATTCGTCCA 60.037 55.000 0.00 0.00 0.00 4.02
3689 3748 0.396435 AGTGGCAGTGATTCGTCCAA 59.604 50.000 0.00 0.00 0.00 3.53
3690 3749 1.003580 AGTGGCAGTGATTCGTCCAAT 59.996 47.619 0.00 0.00 0.00 3.16
3691 3750 1.812571 GTGGCAGTGATTCGTCCAATT 59.187 47.619 0.00 0.00 0.00 2.32
3692 3751 2.228822 GTGGCAGTGATTCGTCCAATTT 59.771 45.455 0.00 0.00 0.00 1.82
3773 3832 4.709397 CCAAAGTATACCTGCCAAATGGAA 59.291 41.667 2.98 0.00 37.39 3.53
3903 3962 7.039434 TCGAGAGACTGCAATATCAAATAGGAT 60.039 37.037 0.00 0.00 33.31 3.24
3967 4026 2.093711 TCGGTGTGTCCTCAATGGTATG 60.094 50.000 0.00 0.00 37.07 2.39
4008 4067 6.318648 GTCATCATTAGCACAAGGTATGGAAA 59.681 38.462 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 3.560481 CACATGTTGAGATGATGCTCTCC 59.440 47.826 0.00 0.00 40.85 3.71
135 145 1.678360 GTGCGCTTCTTGTTCATGTG 58.322 50.000 9.73 0.00 0.00 3.21
292 305 3.329889 CTAGGCTGCACCACCCCA 61.330 66.667 0.50 0.00 43.14 4.96
344 358 1.412343 GCCAAATATGTGGGCGGAATT 59.588 47.619 14.08 0.00 39.26 2.17
435 451 1.534729 GCGGGAGGAACATTTCAACT 58.465 50.000 0.00 0.00 0.00 3.16
437 453 0.111446 TGGCGGGAGGAACATTTCAA 59.889 50.000 0.00 0.00 0.00 2.69
446 462 1.072505 GAAACAGTTGGCGGGAGGA 59.927 57.895 0.00 0.00 0.00 3.71
461 477 1.065998 GTGCCCGGTATGGTAGTGAAA 60.066 52.381 0.00 0.00 35.15 2.69
532 548 3.035727 TTTTTGAAGGGCGCGACC 58.964 55.556 27.87 27.87 37.93 4.79
598 616 0.464036 TCTAAATGCAGGTCGGCGAT 59.536 50.000 14.79 0.00 36.28 4.58
615 633 1.445871 GACCCGCAAAATAACCGTCT 58.554 50.000 0.00 0.00 0.00 4.18
645 663 1.192146 AAGAGCAACGCTAGACCCCA 61.192 55.000 0.00 0.00 39.88 4.96
650 668 4.785511 AGAGTTTAAGAGCAACGCTAGA 57.214 40.909 0.00 0.00 39.88 2.43
655 677 7.352719 AGTTTCATAGAGTTTAAGAGCAACG 57.647 36.000 0.00 0.00 0.00 4.10
666 688 6.531503 TGCTACAGCTAGTTTCATAGAGTT 57.468 37.500 2.44 0.00 42.66 3.01
669 691 5.755375 GCAATGCTACAGCTAGTTTCATAGA 59.245 40.000 0.00 0.00 42.66 1.98
670 692 5.757320 AGCAATGCTACAGCTAGTTTCATAG 59.243 40.000 5.69 0.00 42.66 2.23
671 693 5.674525 AGCAATGCTACAGCTAGTTTCATA 58.325 37.500 5.69 0.00 42.66 2.15
672 694 4.521146 AGCAATGCTACAGCTAGTTTCAT 58.479 39.130 5.69 0.00 42.66 2.57
673 695 3.942829 AGCAATGCTACAGCTAGTTTCA 58.057 40.909 5.69 0.00 42.66 2.69
685 707 8.573885 AGTTATATTACTCACGTAGCAATGCTA 58.426 33.333 11.40 11.40 40.44 3.49
686 708 7.434492 AGTTATATTACTCACGTAGCAATGCT 58.566 34.615 13.92 13.92 43.41 3.79
687 709 7.639162 AGTTATATTACTCACGTAGCAATGC 57.361 36.000 0.00 0.00 0.00 3.56
707 729 9.321562 CCTTCCGAAAAAGCACTTATATAGTTA 57.678 33.333 0.00 0.00 33.85 2.24
708 730 8.044908 TCCTTCCGAAAAAGCACTTATATAGTT 58.955 33.333 0.00 0.00 33.85 2.24
709 731 7.562135 TCCTTCCGAAAAAGCACTTATATAGT 58.438 34.615 0.00 0.00 37.68 2.12
710 732 8.433421 TTCCTTCCGAAAAAGCACTTATATAG 57.567 34.615 0.00 0.00 0.00 1.31
711 733 8.795842 TTTCCTTCCGAAAAAGCACTTATATA 57.204 30.769 0.00 0.00 37.53 0.86
712 734 7.696992 TTTCCTTCCGAAAAAGCACTTATAT 57.303 32.000 0.00 0.00 37.53 0.86
713 735 7.513371 TTTTCCTTCCGAAAAAGCACTTATA 57.487 32.000 0.00 0.00 45.38 0.98
714 736 6.399639 TTTTCCTTCCGAAAAAGCACTTAT 57.600 33.333 0.00 0.00 45.38 1.73
715 737 5.838531 TTTTCCTTCCGAAAAAGCACTTA 57.161 34.783 0.00 0.00 45.38 2.24
716 738 4.729227 TTTTCCTTCCGAAAAAGCACTT 57.271 36.364 0.00 0.00 45.38 3.16
735 757 5.576447 ACGGATTTGTGTCTTCACTTTTT 57.424 34.783 0.00 0.00 44.14 1.94
736 758 5.576447 AACGGATTTGTGTCTTCACTTTT 57.424 34.783 0.00 0.00 44.14 2.27
737 759 6.877611 ATAACGGATTTGTGTCTTCACTTT 57.122 33.333 0.00 0.00 44.14 2.66
753 775 9.496873 TCAAGTTTCTCTCATTAAAATAACGGA 57.503 29.630 0.00 0.00 0.00 4.69
768 790 0.606673 GCCCGCCTTCAAGTTTCTCT 60.607 55.000 0.00 0.00 0.00 3.10
808 830 4.374399 GTCGTCTCCAAAGAAAAGTGGTA 58.626 43.478 0.00 0.00 36.23 3.25
817 839 0.471211 ACAGGGGTCGTCTCCAAAGA 60.471 55.000 0.25 0.00 0.00 2.52
832 854 0.527817 GGAAGTCGACGCCATACAGG 60.528 60.000 20.96 0.00 41.84 4.00
833 855 0.172578 TGGAAGTCGACGCCATACAG 59.827 55.000 23.58 0.00 0.00 2.74
846 872 3.096092 CTGCCTCTAGAGACTTGGAAGT 58.904 50.000 21.76 0.00 43.16 3.01
859 885 0.978146 GCCCTCTGAACCTGCCTCTA 60.978 60.000 0.00 0.00 0.00 2.43
875 901 0.603975 AGTGTGCTCTTTTCTCGCCC 60.604 55.000 0.00 0.00 0.00 6.13
909 943 1.153549 GACGCGAAGGGAAGATGCT 60.154 57.895 15.93 0.00 46.37 3.79
918 952 1.289109 AATCACCGTTGACGCGAAGG 61.289 55.000 15.93 10.79 38.18 3.46
924 958 0.725784 GCAGCAAATCACCGTTGACG 60.726 55.000 0.00 0.00 33.38 4.35
957 991 2.047443 GGTCGAGAGGAAGACGCCT 61.047 63.158 0.00 0.00 42.17 5.52
1266 1303 2.801631 GCCGAGGTGGAGGATGAGG 61.802 68.421 0.00 0.00 42.00 3.86
1833 1870 0.827925 ACTTGGAGTGGAGCGACTCA 60.828 55.000 13.40 0.00 43.70 3.41
1941 1978 1.003839 CTTGTAGCGTCCCTTGCCA 60.004 57.895 0.00 0.00 0.00 4.92
2897 2934 2.060980 AGCCTCCACCGCTTCCTAG 61.061 63.158 0.00 0.00 30.57 3.02
3075 3112 3.951769 GAGCTTGGCCCTGGCATGT 62.952 63.158 10.86 0.00 44.11 3.21
3196 3233 7.889600 ACTAGGGAGCTTAGTGTTATATAGGAC 59.110 40.741 0.00 0.00 30.46 3.85
3201 3238 9.878737 TCTAAACTAGGGAGCTTAGTGTTATAT 57.121 33.333 0.00 0.00 31.96 0.86
3240 3277 9.973450 TGACCGAATTTTAATTGAAAATCTCAA 57.027 25.926 8.58 0.00 45.21 3.02
3261 3298 5.297776 AGCTTTGAGAAATATTGGATGACCG 59.702 40.000 0.00 0.00 39.42 4.79
3328 3384 7.606456 ACGAGAGTAAATACCAATTGATTGTGT 59.394 33.333 7.12 0.00 46.88 3.72
3329 3385 7.974675 ACGAGAGTAAATACCAATTGATTGTG 58.025 34.615 7.12 0.00 46.88 3.33
3366 3422 5.586243 GCTGATCCTAAGACAAATGCTACAA 59.414 40.000 0.00 0.00 0.00 2.41
3408 3464 4.504858 AGAGTAATTTGGACGAATCGCTT 58.495 39.130 1.15 0.00 0.00 4.68
3411 3467 4.440103 CGGTAGAGTAATTTGGACGAATCG 59.560 45.833 0.00 0.00 0.00 3.34
3420 3476 9.028185 GTAGTATTTGGTCGGTAGAGTAATTTG 57.972 37.037 0.00 0.00 0.00 2.32
3451 3507 7.989947 AAGAGGACTTATAAACCAGGATGTA 57.010 36.000 0.00 0.00 34.28 2.29
3452 3508 6.893020 AAGAGGACTTATAAACCAGGATGT 57.107 37.500 0.00 0.00 34.28 3.06
3624 3682 6.092533 CCTTGTATTCCATGCCAAAATTTGAC 59.907 38.462 7.37 0.00 0.00 3.18
3630 3688 4.462483 GTCTCCTTGTATTCCATGCCAAAA 59.538 41.667 0.00 0.00 0.00 2.44
3648 3706 5.422650 ACTCTGTCCTGGTTTATTAGTCTCC 59.577 44.000 0.00 0.00 0.00 3.71
3668 3727 0.247736 GGACGAATCACTGCCACTCT 59.752 55.000 0.00 0.00 0.00 3.24
3673 3732 3.575965 AAAATTGGACGAATCACTGCC 57.424 42.857 0.00 0.00 0.00 4.85
3674 3733 4.083003 TGGTAAAATTGGACGAATCACTGC 60.083 41.667 0.00 0.00 0.00 4.40
3675 3734 5.621197 TGGTAAAATTGGACGAATCACTG 57.379 39.130 0.00 0.00 0.00 3.66
3676 3735 5.710099 ACATGGTAAAATTGGACGAATCACT 59.290 36.000 0.00 0.00 0.00 3.41
3677 3736 5.799936 CACATGGTAAAATTGGACGAATCAC 59.200 40.000 0.00 0.00 0.00 3.06
3678 3737 5.105957 CCACATGGTAAAATTGGACGAATCA 60.106 40.000 0.00 0.00 0.00 2.57
3679 3738 5.124776 TCCACATGGTAAAATTGGACGAATC 59.875 40.000 0.00 0.00 36.34 2.52
3680 3739 5.013547 TCCACATGGTAAAATTGGACGAAT 58.986 37.500 0.00 0.00 36.34 3.34
3681 3740 4.399219 TCCACATGGTAAAATTGGACGAA 58.601 39.130 0.00 0.00 36.34 3.85
3682 3741 4.022413 TCCACATGGTAAAATTGGACGA 57.978 40.909 0.00 0.00 36.34 4.20
3683 3742 4.775058 TTCCACATGGTAAAATTGGACG 57.225 40.909 0.00 0.00 36.06 4.79
3684 3743 6.989759 AGTTTTTCCACATGGTAAAATTGGAC 59.010 34.615 15.75 6.30 43.19 4.02
3685 3744 7.130681 AGTTTTTCCACATGGTAAAATTGGA 57.869 32.000 15.75 0.00 43.19 3.53
3686 3745 7.714813 AGAAGTTTTTCCACATGGTAAAATTGG 59.285 33.333 15.75 0.00 43.19 3.16
3687 3746 8.661352 AGAAGTTTTTCCACATGGTAAAATTG 57.339 30.769 15.75 0.00 43.19 2.32
3688 3747 9.758651 GTAGAAGTTTTTCCACATGGTAAAATT 57.241 29.630 15.75 13.23 43.19 1.82
3689 3748 8.079809 CGTAGAAGTTTTTCCACATGGTAAAAT 58.920 33.333 15.75 6.94 43.19 1.82
3690 3749 7.419204 CGTAGAAGTTTTTCCACATGGTAAAA 58.581 34.615 10.41 10.41 40.55 1.52
3691 3750 6.513720 GCGTAGAAGTTTTTCCACATGGTAAA 60.514 38.462 0.00 0.00 33.51 2.01
3692 3751 5.049267 GCGTAGAAGTTTTTCCACATGGTAA 60.049 40.000 0.00 0.00 33.64 2.85
3773 3832 7.975616 GTGGAAGTGTATATGATGTGCAATTTT 59.024 33.333 0.00 0.00 0.00 1.82
3863 3922 2.439701 TCGAGGACCTGCTACCCG 60.440 66.667 0.00 0.00 0.00 5.28
3903 3962 8.531982 AGTCATCTGTCTGCTGTTATAAGTTAA 58.468 33.333 0.00 0.00 0.00 2.01
3967 4026 9.556030 CTAATGATGACATGAATATGCATGAAC 57.444 33.333 27.49 19.86 46.64 3.18
4008 4067 4.664688 ATGGAGGGTCAGAATTTTCAGT 57.335 40.909 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.