Multiple sequence alignment - TraesCS2B01G118500

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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 TraesCS2B01G118500 chr2B 100.000 3375 0 0 1 3375 83956403 83953029 0.000000e+00 6233
1 TraesCS2B01G118500 chr2B 81.838 1850 185 65 884 2693 82851558 82853296 0.000000e+00 1415
2 TraesCS2B01G118500 chr2B 83.100 1071 98 39 1645 2693 82361884 82362893 0.000000e+00 898
3 TraesCS2B01G118500 chr2B 88.966 580 58 3 1001 1580 82361285 82361858 0.000000e+00 712
4 TraesCS2B01G118500 chr2B 82.768 708 81 22 1916 2599 82714847 82715537 8.060000e-166 593
5 TraesCS2B01G118500 chr2B 87.238 478 51 7 1103 1580 82714082 82714549 1.380000e-148 536
6 TraesCS2B01G118500 chr2B 79.685 699 107 25 887 1578 83211076 83211746 3.940000e-129 472
7 TraesCS2B01G118500 chr2B 78.862 246 28 12 2597 2842 82717655 82717876 9.760000e-31 145
8 TraesCS2B01G118500 chr2D 92.293 2660 112 39 245 2858 53648250 53650862 0.000000e+00 3690
9 TraesCS2B01G118500 chr2D 83.199 1863 157 59 909 2693 52851926 52853710 0.000000e+00 1563
10 TraesCS2B01G118500 chr2D 81.616 1931 196 70 970 2842 52646917 52648746 0.000000e+00 1452
11 TraesCS2B01G118500 chr2D 81.157 674 95 22 912 1578 52959419 52960067 2.320000e-141 512
12 TraesCS2B01G118500 chr2D 91.506 259 10 6 1 248 53647807 53648064 2.490000e-91 346
13 TraesCS2B01G118500 chr2A 87.661 2869 201 60 606 3368 54474522 54471701 0.000000e+00 3195
14 TraesCS2B01G118500 chr2A 82.128 1175 113 37 1709 2851 54112545 54113654 0.000000e+00 917
15 TraesCS2B01G118500 chr2A 88.801 634 55 11 970 1598 54012296 54012918 0.000000e+00 763
16 TraesCS2B01G118500 chr2A 80.813 959 89 38 1713 2612 54012980 54013902 0.000000e+00 664
17 TraesCS2B01G118500 chr2A 86.823 554 64 6 1049 1598 54111933 54112481 8.010000e-171 610
18 TraesCS2B01G118500 chr2A 87.477 543 44 16 1 524 54475107 54474570 3.720000e-169 604


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 TraesCS2B01G118500 chr2B 83953029 83956403 3374 True 6233.000000 6233 100.0000 1 3375 1 chr2B.!!$R1 3374
1 TraesCS2B01G118500 chr2B 82851558 82853296 1738 False 1415.000000 1415 81.8380 884 2693 1 chr2B.!!$F1 1809
2 TraesCS2B01G118500 chr2B 82361285 82362893 1608 False 805.000000 898 86.0330 1001 2693 2 chr2B.!!$F3 1692
3 TraesCS2B01G118500 chr2B 83211076 83211746 670 False 472.000000 472 79.6850 887 1578 1 chr2B.!!$F2 691
4 TraesCS2B01G118500 chr2B 82714082 82717876 3794 False 424.666667 593 82.9560 1103 2842 3 chr2B.!!$F4 1739
5 TraesCS2B01G118500 chr2D 53647807 53650862 3055 False 2018.000000 3690 91.8995 1 2858 2 chr2D.!!$F4 2857
6 TraesCS2B01G118500 chr2D 52851926 52853710 1784 False 1563.000000 1563 83.1990 909 2693 1 chr2D.!!$F2 1784
7 TraesCS2B01G118500 chr2D 52646917 52648746 1829 False 1452.000000 1452 81.6160 970 2842 1 chr2D.!!$F1 1872
8 TraesCS2B01G118500 chr2D 52959419 52960067 648 False 512.000000 512 81.1570 912 1578 1 chr2D.!!$F3 666
9 TraesCS2B01G118500 chr2A 54471701 54475107 3406 True 1899.500000 3195 87.5690 1 3368 2 chr2A.!!$R1 3367
10 TraesCS2B01G118500 chr2A 54111933 54113654 1721 False 763.500000 917 84.4755 1049 2851 2 chr2A.!!$F2 1802
11 TraesCS2B01G118500 chr2A 54012296 54013902 1606 False 713.500000 763 84.8070 970 2612 2 chr2A.!!$F1 1642

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
98 110 0.249447 CAGCCAGTGACAGACGACAA 60.249 55.0 0.0 0.0 0.00 3.18 F
357 559 0.597637 ACAGCGGAGAAACTGACGTG 60.598 55.0 0.0 0.0 37.35 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1230 1511 4.681025 GCTGCAAATCAAATCAAAGAACGA 59.319 37.500 0.0 0.0 0.0 3.85 R
2537 3018 1.512364 CACGCATCAACAACAAACACG 59.488 47.619 0.0 0.0 0.0 4.49 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
65 67 4.778415 CGCGCGCTGTCCTGTAGT 62.778 66.667 30.48 0.00 0.00 2.73
93 95 2.427320 TGGCAGCCAGTGACAGAC 59.573 61.111 11.22 0.00 40.35 3.51
94 96 2.740055 GGCAGCCAGTGACAGACG 60.740 66.667 6.55 0.00 32.31 4.18
95 97 2.340078 GCAGCCAGTGACAGACGA 59.660 61.111 0.00 0.00 0.00 4.20
98 110 0.249447 CAGCCAGTGACAGACGACAA 60.249 55.000 0.00 0.00 0.00 3.18
136 148 2.359900 CCCGGTGAGAAAAGGATCTTG 58.640 52.381 0.00 0.00 0.00 3.02
141 153 4.646572 GGTGAGAAAAGGATCTTGACACT 58.353 43.478 0.00 0.00 0.00 3.55
269 470 4.813027 TCGTGGTTACTGGTATCTTTCAC 58.187 43.478 0.00 0.00 0.00 3.18
357 559 0.597637 ACAGCGGAGAAACTGACGTG 60.598 55.000 0.00 0.00 37.35 4.49
358 560 1.006102 AGCGGAGAAACTGACGTGG 60.006 57.895 0.00 0.00 0.00 4.94
359 561 1.006571 GCGGAGAAACTGACGTGGA 60.007 57.895 0.00 0.00 0.00 4.02
425 632 0.952010 CCAACCACCTAACCGGTTCG 60.952 60.000 26.16 18.31 46.37 3.95
450 657 1.134694 GAAATTTTCTCCGCGCGCT 59.865 52.632 30.48 5.54 0.00 5.92
464 671 2.471264 CGCGCGCTTGTAGATAATCATG 60.471 50.000 30.48 3.00 0.00 3.07
500 710 1.869574 CGTCGATGCCGTCTGACAG 60.870 63.158 8.73 0.00 37.05 3.51
501 711 1.213013 GTCGATGCCGTCTGACAGT 59.787 57.895 8.73 0.00 37.05 3.55
524 752 5.606348 AAAAACTAGCTGGAGAGATCGAT 57.394 39.130 3.17 0.00 0.00 3.59
546 792 8.683615 TCGATTTACACTAGATGATTACACAGT 58.316 33.333 0.00 0.00 0.00 3.55
549 795 5.667539 ACACTAGATGATTACACAGTGCT 57.332 39.130 0.00 0.00 37.26 4.40
550 796 6.042638 ACACTAGATGATTACACAGTGCTT 57.957 37.500 0.00 0.00 37.26 3.91
551 797 7.170393 ACACTAGATGATTACACAGTGCTTA 57.830 36.000 0.00 0.00 37.26 3.09
552 798 7.786030 ACACTAGATGATTACACAGTGCTTAT 58.214 34.615 0.00 0.00 37.26 1.73
553 799 7.923344 ACACTAGATGATTACACAGTGCTTATC 59.077 37.037 0.00 2.08 37.26 1.75
554 800 8.140628 CACTAGATGATTACACAGTGCTTATCT 58.859 37.037 0.00 5.81 31.72 1.98
557 803 5.675684 TGATTACACAGTGCTTATCTGGA 57.324 39.130 0.00 0.00 37.25 3.86
558 804 6.048732 TGATTACACAGTGCTTATCTGGAA 57.951 37.500 0.00 0.00 37.25 3.53
559 805 6.108687 TGATTACACAGTGCTTATCTGGAAG 58.891 40.000 0.00 0.00 37.25 3.46
572 818 7.593875 CTTATCTGGAAGCAGTATCATTAGC 57.406 40.000 0.00 0.00 0.00 3.09
573 819 5.557576 ATCTGGAAGCAGTATCATTAGCA 57.442 39.130 0.00 0.00 0.00 3.49
574 820 5.357742 TCTGGAAGCAGTATCATTAGCAA 57.642 39.130 0.00 0.00 0.00 3.91
575 821 5.118990 TCTGGAAGCAGTATCATTAGCAAC 58.881 41.667 0.00 0.00 0.00 4.17
576 822 4.199310 TGGAAGCAGTATCATTAGCAACC 58.801 43.478 0.00 0.00 0.00 3.77
577 823 4.080356 TGGAAGCAGTATCATTAGCAACCT 60.080 41.667 0.00 0.00 0.00 3.50
604 850 5.718649 TTAGCGCTTGATGATTGTAGTTC 57.281 39.130 18.68 0.00 0.00 3.01
610 856 6.201806 GCGCTTGATGATTGTAGTTCTTATCT 59.798 38.462 0.00 0.00 0.00 1.98
656 903 2.015456 TAGGACATGCTCATCCGGAT 57.985 50.000 12.38 12.38 40.20 4.18
674 923 5.820947 TCCGGATGGTAAAGAGCTTTAATTC 59.179 40.000 0.00 3.04 36.86 2.17
688 937 2.116827 TAATTCACCGCCGTTGGATT 57.883 45.000 0.00 0.00 0.00 3.01
719 968 8.567948 CGGAGCAATTAATCACCATTAATTAGT 58.432 33.333 10.81 3.95 46.67 2.24
732 981 5.769662 CCATTAATTAGTGGCTAAGCATGGA 59.230 40.000 13.47 0.00 35.23 3.41
733 982 6.072286 CCATTAATTAGTGGCTAAGCATGGAG 60.072 42.308 13.47 0.00 35.23 3.86
734 983 2.332063 TTAGTGGCTAAGCATGGAGC 57.668 50.000 0.00 0.00 46.19 4.70
757 1006 4.327357 CGAGGTGCAGTAAATAAGTGAGTG 59.673 45.833 0.00 0.00 0.00 3.51
761 1010 6.942576 AGGTGCAGTAAATAAGTGAGTGAAAT 59.057 34.615 0.00 0.00 0.00 2.17
840 1090 2.024414 CAGCTATAAAACCACCCCAGC 58.976 52.381 0.00 0.00 0.00 4.85
1176 1455 2.421131 CGTCGACCTCAACAAGACG 58.579 57.895 10.58 1.99 46.32 4.18
1221 1502 4.545678 AGTACTACTACTCCTCCTCGAGA 58.454 47.826 15.71 0.00 33.83 4.04
1837 2179 1.000060 CGGGTGTTCGACAAGGACTTA 60.000 52.381 0.00 0.00 0.00 2.24
2380 2820 6.320171 CAACATGTGGAAGATCTGATTGAAC 58.680 40.000 0.00 0.00 0.00 3.18
2709 5334 4.141298 GGATGAATTGGAGGGTGAGAGATT 60.141 45.833 0.00 0.00 0.00 2.40
2727 5353 4.205587 AGATTATACCGAGACCGACTTGT 58.794 43.478 0.00 0.00 38.22 3.16
2762 5394 9.681692 TCTGATTGTGTGTTAATTGAAATGAAG 57.318 29.630 0.00 0.00 0.00 3.02
2842 5481 4.437682 TGATTCTGGGGTCATGGTTATC 57.562 45.455 0.00 0.00 0.00 1.75
2858 5497 0.109643 TATCGGACGGTGTTGTGTCG 60.110 55.000 0.00 0.00 35.95 4.35
2860 5499 2.663852 GGACGGTGTTGTGTCGGG 60.664 66.667 0.00 0.00 35.95 5.14
2862 5501 1.363443 GACGGTGTTGTGTCGGGTA 59.637 57.895 0.00 0.00 0.00 3.69
2880 5521 1.465777 GTAACCGTGTTTCCCAATCCG 59.534 52.381 0.00 0.00 0.00 4.18
2881 5522 0.108963 AACCGTGTTTCCCAATCCGA 59.891 50.000 0.00 0.00 0.00 4.55
2882 5523 0.108963 ACCGTGTTTCCCAATCCGAA 59.891 50.000 0.00 0.00 0.00 4.30
2885 5526 3.011119 CCGTGTTTCCCAATCCGAAATA 58.989 45.455 0.00 0.00 32.19 1.40
2886 5527 3.440872 CCGTGTTTCCCAATCCGAAATAA 59.559 43.478 0.00 0.00 32.19 1.40
2887 5528 4.097286 CCGTGTTTCCCAATCCGAAATAAT 59.903 41.667 0.00 0.00 32.19 1.28
2889 5530 5.741982 CGTGTTTCCCAATCCGAAATAATTC 59.258 40.000 0.00 0.00 32.19 2.17
2890 5531 6.040247 GTGTTTCCCAATCCGAAATAATTCC 58.960 40.000 0.00 0.00 32.19 3.01
2891 5532 5.955355 TGTTTCCCAATCCGAAATAATTCCT 59.045 36.000 0.00 0.00 32.19 3.36
2893 5534 4.725490 TCCCAATCCGAAATAATTCCTCC 58.275 43.478 0.00 0.00 31.52 4.30
2894 5535 3.826729 CCCAATCCGAAATAATTCCTCCC 59.173 47.826 0.00 0.00 31.52 4.30
2895 5536 3.826729 CCAATCCGAAATAATTCCTCCCC 59.173 47.826 0.00 0.00 31.52 4.81
2940 5589 0.941936 TCGAAGCGCACAATCACGAA 60.942 50.000 11.47 0.00 0.00 3.85
2977 5627 2.929301 AGTTCAATCCCCTTCCCTGTA 58.071 47.619 0.00 0.00 0.00 2.74
2983 5633 0.338814 TCCCCTTCCCTGTAGAGGTC 59.661 60.000 5.02 0.00 37.73 3.85
2986 5636 0.970937 CCTTCCCTGTAGAGGTCGCA 60.971 60.000 5.02 0.00 37.73 5.10
2988 5638 1.605058 TTCCCTGTAGAGGTCGCAGC 61.605 60.000 5.02 0.00 37.73 5.25
2996 5646 1.731720 AGAGGTCGCAGCTTTGATTC 58.268 50.000 0.00 0.00 0.00 2.52
2998 5648 1.663135 GAGGTCGCAGCTTTGATTCTC 59.337 52.381 0.00 0.00 0.00 2.87
2999 5649 1.277557 AGGTCGCAGCTTTGATTCTCT 59.722 47.619 0.00 0.00 0.00 3.10
3028 5678 0.740737 CAAGAATTGGTCGGGATGGC 59.259 55.000 0.00 0.00 43.94 4.40
3061 5712 7.971168 CCGTGATATGTTTACCAAGCAAAATAA 59.029 33.333 0.00 0.00 0.00 1.40
3086 5737 6.218746 ACTGGAATTGCTTGAAGATTTTGAC 58.781 36.000 0.00 0.00 0.00 3.18
3092 5743 2.226437 GCTTGAAGATTTTGACGCTCCA 59.774 45.455 0.00 0.00 0.00 3.86
3099 5750 2.679355 TTTTGACGCTCCAAATCACG 57.321 45.000 2.01 0.00 36.12 4.35
3111 5762 0.813184 AAATCACGAAGCCATGGCAG 59.187 50.000 37.18 27.99 44.88 4.85
3115 5766 2.124819 CGAAGCCATGGCAGAGCT 60.125 61.111 37.18 14.94 44.88 4.09
3132 5793 0.673985 GCTGTTGTTCCAACCCCTTC 59.326 55.000 4.78 0.00 0.00 3.46
3140 5801 1.069775 TCCAACCCCTTCCCTTGTAC 58.930 55.000 0.00 0.00 0.00 2.90
3141 5802 0.039180 CCAACCCCTTCCCTTGTACC 59.961 60.000 0.00 0.00 0.00 3.34
3145 5806 2.598787 CCCTTCCCTTGTACCGGCA 61.599 63.158 0.00 0.00 0.00 5.69
3146 5807 1.078426 CCTTCCCTTGTACCGGCAG 60.078 63.158 0.00 0.00 0.00 4.85
3153 5814 2.510064 CTTGTACCGGCAGCGGGTTA 62.510 60.000 28.11 15.70 38.10 2.85
3160 5821 1.658994 CGGCAGCGGGTTAGATTTTA 58.341 50.000 0.00 0.00 0.00 1.52
3163 5824 3.738899 CGGCAGCGGGTTAGATTTTACTA 60.739 47.826 0.00 0.00 0.00 1.82
3165 5826 4.637091 GGCAGCGGGTTAGATTTTACTAAA 59.363 41.667 0.00 0.00 34.74 1.85
3166 5827 5.298527 GGCAGCGGGTTAGATTTTACTAAAT 59.701 40.000 0.00 0.00 36.68 1.40
3189 5850 1.271840 TAGCAAGAAGTGGCCGGGAT 61.272 55.000 2.18 0.00 0.00 3.85
3193 5854 0.912487 AAGAAGTGGCCGGGATGGTA 60.912 55.000 2.18 0.00 41.21 3.25
3194 5855 0.694444 AGAAGTGGCCGGGATGGTAT 60.694 55.000 2.18 0.00 41.21 2.73
3195 5856 0.182775 GAAGTGGCCGGGATGGTATT 59.817 55.000 2.18 0.00 41.21 1.89
3196 5857 0.629058 AAGTGGCCGGGATGGTATTT 59.371 50.000 2.18 0.00 41.21 1.40
3197 5858 0.182775 AGTGGCCGGGATGGTATTTC 59.817 55.000 2.18 0.00 41.21 2.17
3198 5859 1.147376 TGGCCGGGATGGTATTTCG 59.853 57.895 2.18 0.00 41.21 3.46
3199 5860 1.338890 TGGCCGGGATGGTATTTCGA 61.339 55.000 2.18 0.00 41.21 3.71
3200 5861 0.883370 GGCCGGGATGGTATTTCGAC 60.883 60.000 2.18 0.00 41.21 4.20
3248 5909 0.798776 GTGTGAAGCCATTCGAGTGG 59.201 55.000 21.86 21.86 42.35 4.00
3269 5930 4.081586 TGGGTTACCAAAACCTTTGTGTTC 60.082 41.667 2.98 0.00 45.87 3.18
3271 5932 4.142425 GGTTACCAAAACCTTTGTGTTCGA 60.142 41.667 0.00 0.00 37.34 3.71
3286 5952 2.552315 TGTTCGATTCCACTTCAAAGCC 59.448 45.455 0.00 0.00 0.00 4.35
3301 5967 3.621268 TCAAAGCCTAATCATTTCCGTCG 59.379 43.478 0.00 0.00 0.00 5.12
3316 5982 4.758773 TCCGTCGGAAATAAACCCTAAT 57.241 40.909 12.68 0.00 0.00 1.73
3318 5984 3.492011 CCGTCGGAAATAAACCCTAATCG 59.508 47.826 4.91 0.00 0.00 3.34
3327 5993 7.147966 GGAAATAAACCCTAATCGTTTCCATGT 60.148 37.037 8.61 0.00 41.53 3.21
3336 6002 7.362920 CCCTAATCGTTTCCATGTTGAAGATTT 60.363 37.037 7.81 0.00 0.00 2.17
3343 6009 8.853345 CGTTTCCATGTTGAAGATTTTGAATAG 58.147 33.333 0.00 0.00 0.00 1.73
3356 6022 6.535150 AGATTTTGAATAGAAATCTCGTGCGA 59.465 34.615 6.33 0.00 45.81 5.10
3363 6029 3.448686 AGAAATCTCGTGCGATTAGTGG 58.551 45.455 0.00 0.00 33.47 4.00
3368 6034 0.107897 TCGTGCGATTAGTGGCCATT 60.108 50.000 9.72 7.59 0.00 3.16
3369 6035 0.732571 CGTGCGATTAGTGGCCATTT 59.267 50.000 9.72 2.75 0.00 2.32
3370 6036 1.132262 CGTGCGATTAGTGGCCATTTT 59.868 47.619 9.72 0.00 0.00 1.82
3371 6037 2.353269 CGTGCGATTAGTGGCCATTTTA 59.647 45.455 9.72 0.00 0.00 1.52
3372 6038 3.546020 CGTGCGATTAGTGGCCATTTTAG 60.546 47.826 9.72 0.11 0.00 1.85
3373 6039 2.948979 TGCGATTAGTGGCCATTTTAGG 59.051 45.455 9.72 0.00 0.00 2.69
3374 6040 2.293399 GCGATTAGTGGCCATTTTAGGG 59.707 50.000 9.72 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 62 1.286570 CCACGTACGTGCCACTACA 59.713 57.895 36.76 0.00 44.16 2.74
91 93 1.922444 GCTCGATCGATCCTTGTCGTC 60.922 57.143 19.78 2.19 42.07 4.20
92 94 0.029567 GCTCGATCGATCCTTGTCGT 59.970 55.000 19.78 0.00 42.07 4.34
93 95 0.661780 GGCTCGATCGATCCTTGTCG 60.662 60.000 26.66 10.97 42.74 4.35
94 96 0.319125 GGGCTCGATCGATCCTTGTC 60.319 60.000 30.79 16.06 31.60 3.18
95 97 1.742768 GGGCTCGATCGATCCTTGT 59.257 57.895 30.79 0.00 31.60 3.16
98 110 2.986413 CCGGGCTCGATCGATCCT 60.986 66.667 30.79 0.00 39.00 3.24
136 148 3.424433 CGAGGGTTAAATCGCAAAGTGTC 60.424 47.826 0.00 0.00 31.42 3.67
141 153 3.062909 CGAATCGAGGGTTAAATCGCAAA 59.937 43.478 0.00 0.00 38.79 3.68
200 212 1.868987 AAAATCGGGAAAACGGCCGG 61.869 55.000 31.76 11.88 0.00 6.13
213 225 0.317770 ACGCAGCCACACAAAAATCG 60.318 50.000 0.00 0.00 0.00 3.34
216 228 1.000827 CCATACGCAGCCACACAAAAA 60.001 47.619 0.00 0.00 0.00 1.94
269 470 1.550130 TTCCCCTTCTACTGTGGCCG 61.550 60.000 0.00 0.00 0.00 6.13
375 577 1.582937 CGGTGCTACGTACGCTCTG 60.583 63.158 16.72 12.92 0.00 3.35
425 632 1.977188 CGGAGAAAATTTCAACGGCC 58.023 50.000 8.55 0.00 0.00 6.13
450 657 6.573434 ACGACTTGCTCATGATTATCTACAA 58.427 36.000 0.00 0.00 0.00 2.41
464 671 1.153997 GGACCGAGACGACTTGCTC 60.154 63.158 0.00 0.00 0.00 4.26
500 710 5.892568 TCGATCTCTCCAGCTAGTTTTTAC 58.107 41.667 0.00 0.00 0.00 2.01
501 711 6.716934 ATCGATCTCTCCAGCTAGTTTTTA 57.283 37.500 0.00 0.00 0.00 1.52
524 752 7.611770 AGCACTGTGTAATCATCTAGTGTAAA 58.388 34.615 9.86 0.00 36.37 2.01
549 795 7.066307 TGCTAATGATACTGCTTCCAGATAA 57.934 36.000 0.00 0.00 41.77 1.75
550 796 6.670695 TGCTAATGATACTGCTTCCAGATA 57.329 37.500 0.00 0.00 41.77 1.98
551 797 5.557576 TGCTAATGATACTGCTTCCAGAT 57.442 39.130 0.00 0.00 41.77 2.90
552 798 5.118990 GTTGCTAATGATACTGCTTCCAGA 58.881 41.667 0.00 0.00 41.77 3.86
553 799 4.274459 GGTTGCTAATGATACTGCTTCCAG 59.726 45.833 0.00 0.00 44.80 3.86
554 800 4.080356 AGGTTGCTAATGATACTGCTTCCA 60.080 41.667 0.00 0.00 0.00 3.53
557 803 6.240549 ACTAGGTTGCTAATGATACTGCTT 57.759 37.500 0.00 0.00 0.00 3.91
558 804 5.878406 ACTAGGTTGCTAATGATACTGCT 57.122 39.130 0.00 0.00 0.00 4.24
559 805 9.360093 CTAATACTAGGTTGCTAATGATACTGC 57.640 37.037 0.00 0.00 0.00 4.40
560 806 9.360093 GCTAATACTAGGTTGCTAATGATACTG 57.640 37.037 0.00 0.00 0.00 2.74
561 807 8.244802 CGCTAATACTAGGTTGCTAATGATACT 58.755 37.037 0.00 0.00 0.00 2.12
562 808 7.009357 GCGCTAATACTAGGTTGCTAATGATAC 59.991 40.741 0.00 0.00 0.00 2.24
563 809 7.033791 GCGCTAATACTAGGTTGCTAATGATA 58.966 38.462 0.00 0.00 0.00 2.15
564 810 5.869888 GCGCTAATACTAGGTTGCTAATGAT 59.130 40.000 0.00 0.00 0.00 2.45
565 811 5.010719 AGCGCTAATACTAGGTTGCTAATGA 59.989 40.000 8.99 0.00 0.00 2.57
566 812 5.230942 AGCGCTAATACTAGGTTGCTAATG 58.769 41.667 8.99 0.00 0.00 1.90
567 813 5.470047 AGCGCTAATACTAGGTTGCTAAT 57.530 39.130 8.99 0.00 0.00 1.73
568 814 4.931661 AGCGCTAATACTAGGTTGCTAA 57.068 40.909 8.99 0.00 0.00 3.09
569 815 4.340097 TCAAGCGCTAATACTAGGTTGCTA 59.660 41.667 12.05 0.00 40.57 3.49
570 816 3.132289 TCAAGCGCTAATACTAGGTTGCT 59.868 43.478 12.05 0.00 40.57 3.91
571 817 3.454375 TCAAGCGCTAATACTAGGTTGC 58.546 45.455 12.05 0.00 40.57 4.17
572 818 5.289595 TCATCAAGCGCTAATACTAGGTTG 58.710 41.667 12.05 0.15 41.67 3.77
573 819 5.531122 TCATCAAGCGCTAATACTAGGTT 57.469 39.130 12.05 0.00 0.00 3.50
574 820 5.730296 ATCATCAAGCGCTAATACTAGGT 57.270 39.130 12.05 0.00 0.00 3.08
575 821 5.928839 ACAATCATCAAGCGCTAATACTAGG 59.071 40.000 12.05 0.29 0.00 3.02
576 822 7.810282 ACTACAATCATCAAGCGCTAATACTAG 59.190 37.037 12.05 3.76 0.00 2.57
577 823 7.658261 ACTACAATCATCAAGCGCTAATACTA 58.342 34.615 12.05 0.00 0.00 1.82
604 850 6.985645 GCTAATGATAGAGCATCCCAGATAAG 59.014 42.308 0.00 0.00 38.62 1.73
610 856 3.165071 TCGCTAATGATAGAGCATCCCA 58.835 45.455 0.97 0.00 38.69 4.37
656 903 4.155280 GCGGTGAATTAAAGCTCTTTACCA 59.845 41.667 10.23 4.29 35.05 3.25
674 923 1.977594 GCAGTAATCCAACGGCGGTG 61.978 60.000 19.91 19.91 31.09 4.94
688 937 3.202906 GGTGATTAATTGCTCCGCAGTA 58.797 45.455 0.00 0.00 40.61 2.74
719 968 1.144716 CTCGCTCCATGCTTAGCCA 59.855 57.895 0.29 0.00 40.11 4.75
732 981 3.056107 TCACTTATTTACTGCACCTCGCT 60.056 43.478 0.00 0.00 43.06 4.93
733 982 3.259064 TCACTTATTTACTGCACCTCGC 58.741 45.455 0.00 0.00 42.89 5.03
734 983 4.327357 CACTCACTTATTTACTGCACCTCG 59.673 45.833 0.00 0.00 0.00 4.63
735 984 5.479306 TCACTCACTTATTTACTGCACCTC 58.521 41.667 0.00 0.00 0.00 3.85
736 985 5.483685 TCACTCACTTATTTACTGCACCT 57.516 39.130 0.00 0.00 0.00 4.00
742 991 6.183360 CGGCGAATTTCACTCACTTATTTACT 60.183 38.462 0.00 0.00 0.00 2.24
757 1006 4.237809 GCGGGCTCGGCGAATTTC 62.238 66.667 12.13 0.08 36.79 2.17
815 1064 2.361789 GGTGGTTTTATAGCTGCGGAA 58.638 47.619 0.00 0.00 0.00 4.30
820 1069 2.024414 GCTGGGGTGGTTTTATAGCTG 58.976 52.381 0.00 0.00 0.00 4.24
878 1128 5.994054 GGGATGATTTTCTCTGATTGATCGA 59.006 40.000 0.00 0.00 0.00 3.59
1230 1511 4.681025 GCTGCAAATCAAATCAAAGAACGA 59.319 37.500 0.00 0.00 0.00 3.85
2537 3018 1.512364 CACGCATCAACAACAAACACG 59.488 47.619 0.00 0.00 0.00 4.49
2709 5334 3.758023 TCAAACAAGTCGGTCTCGGTATA 59.242 43.478 0.00 0.00 36.95 1.47
2842 5481 3.033764 CCGACACAACACCGTCCG 61.034 66.667 0.00 0.00 0.00 4.79
2858 5497 1.814394 GATTGGGAAACACGGTTACCC 59.186 52.381 0.00 0.00 40.79 3.69
2860 5499 1.465777 CGGATTGGGAAACACGGTTAC 59.534 52.381 0.00 0.00 0.00 2.50
2862 5501 0.108963 TCGGATTGGGAAACACGGTT 59.891 50.000 0.00 0.00 0.00 4.44
2875 5516 4.114015 GGGGGAGGAATTATTTCGGATT 57.886 45.455 0.00 0.00 32.28 3.01
2904 5545 4.747810 CTTCGAAATTTTCAATCTGGGGG 58.252 43.478 9.66 0.00 0.00 5.40
2905 5546 4.176271 GCTTCGAAATTTTCAATCTGGGG 58.824 43.478 9.66 0.00 0.00 4.96
2906 5547 3.853671 CGCTTCGAAATTTTCAATCTGGG 59.146 43.478 9.66 0.37 0.00 4.45
2907 5548 3.301642 GCGCTTCGAAATTTTCAATCTGG 59.698 43.478 0.00 0.00 0.00 3.86
2908 5549 3.913763 TGCGCTTCGAAATTTTCAATCTG 59.086 39.130 9.73 0.00 0.00 2.90
2910 5551 3.668191 TGTGCGCTTCGAAATTTTCAATC 59.332 39.130 9.73 0.00 0.00 2.67
2911 5552 3.637432 TGTGCGCTTCGAAATTTTCAAT 58.363 36.364 9.73 0.00 0.00 2.57
2917 5566 2.584791 GTGATTGTGCGCTTCGAAATT 58.415 42.857 9.73 0.00 0.00 1.82
2922 5571 0.517132 CTTCGTGATTGTGCGCTTCG 60.517 55.000 9.73 3.17 0.00 3.79
2940 5589 0.976073 ACTACCGCTGTACCATGGCT 60.976 55.000 13.04 1.45 0.00 4.75
2952 5601 1.664873 GAAGGGGATTGAACTACCGC 58.335 55.000 0.00 0.00 36.99 5.68
2954 5603 2.092375 CAGGGAAGGGGATTGAACTACC 60.092 54.545 0.00 0.00 0.00 3.18
2962 5611 1.369983 ACCTCTACAGGGAAGGGGATT 59.630 52.381 0.00 0.00 45.53 3.01
2977 5627 1.277557 AGAATCAAAGCTGCGACCTCT 59.722 47.619 0.00 0.00 0.00 3.69
2983 5633 7.743838 GCTATATTTAAGAGAATCAAAGCTGCG 59.256 37.037 0.00 0.00 37.82 5.18
2996 5646 8.499162 CCGACCAATTCTTGCTATATTTAAGAG 58.501 37.037 0.00 0.00 32.59 2.85
2998 5648 7.444183 TCCCGACCAATTCTTGCTATATTTAAG 59.556 37.037 0.00 0.00 0.00 1.85
2999 5649 7.284074 TCCCGACCAATTCTTGCTATATTTAA 58.716 34.615 0.00 0.00 0.00 1.52
3028 5678 2.332063 AAACATATCACGGGCCAGAG 57.668 50.000 10.86 0.71 0.00 3.35
3036 5686 8.903570 TTATTTTGCTTGGTAAACATATCACG 57.096 30.769 0.00 0.00 0.00 4.35
3040 5690 9.651913 CCAGTTTATTTTGCTTGGTAAACATAT 57.348 29.630 13.66 0.00 38.72 1.78
3041 5691 8.861086 TCCAGTTTATTTTGCTTGGTAAACATA 58.139 29.630 13.66 2.05 38.72 2.29
3042 5692 7.731054 TCCAGTTTATTTTGCTTGGTAAACAT 58.269 30.769 13.66 2.48 38.72 2.71
3061 5712 6.703165 GTCAAAATCTTCAAGCAATTCCAGTT 59.297 34.615 0.00 0.00 0.00 3.16
3075 5726 4.853743 GTGATTTGGAGCGTCAAAATCTTC 59.146 41.667 19.56 13.11 39.64 2.87
3086 5737 1.298157 TGGCTTCGTGATTTGGAGCG 61.298 55.000 0.00 0.00 0.00 5.03
3092 5743 0.813184 CTGCCATGGCTTCGTGATTT 59.187 50.000 35.53 0.00 42.51 2.17
3099 5750 0.964358 AACAGCTCTGCCATGGCTTC 60.964 55.000 35.53 21.03 42.51 3.86
3141 5802 1.329599 GTAAAATCTAACCCGCTGCCG 59.670 52.381 0.00 0.00 0.00 5.69
3160 5821 6.874134 CGGCCACTTCTTGCTATATATTTAGT 59.126 38.462 2.24 0.00 0.00 2.24
3163 5824 5.003804 CCGGCCACTTCTTGCTATATATTT 58.996 41.667 2.24 0.00 0.00 1.40
3165 5826 3.055094 CCCGGCCACTTCTTGCTATATAT 60.055 47.826 2.24 0.00 0.00 0.86
3166 5827 2.301870 CCCGGCCACTTCTTGCTATATA 59.698 50.000 2.24 0.00 0.00 0.86
3176 5837 0.182775 AATACCATCCCGGCCACTTC 59.817 55.000 2.24 0.00 39.03 3.01
3183 5844 0.599204 CGGTCGAAATACCATCCCGG 60.599 60.000 0.00 0.00 39.71 5.73
3189 5850 0.247185 GGTCACCGGTCGAAATACCA 59.753 55.000 2.59 0.00 39.71 3.25
3214 5875 4.817517 CTTCACACGGTTGTTCTATACCT 58.182 43.478 0.00 0.00 31.66 3.08
3248 5909 4.106909 CGAACACAAAGGTTTTGGTAACC 58.893 43.478 6.51 0.00 40.58 2.85
3253 5914 4.048504 GGAATCGAACACAAAGGTTTTGG 58.951 43.478 6.51 0.00 0.00 3.28
3259 5920 3.563808 TGAAGTGGAATCGAACACAAAGG 59.436 43.478 16.99 0.00 39.99 3.11
3263 5924 3.003275 GCTTTGAAGTGGAATCGAACACA 59.997 43.478 16.99 2.28 39.99 3.72
3264 5925 3.555518 GCTTTGAAGTGGAATCGAACAC 58.444 45.455 9.44 9.44 37.86 3.32
3269 5930 4.635765 TGATTAGGCTTTGAAGTGGAATCG 59.364 41.667 0.00 0.00 0.00 3.34
3271 5932 7.364144 GGAAATGATTAGGCTTTGAAGTGGAAT 60.364 37.037 0.00 0.00 0.00 3.01
3301 5967 6.762702 TGGAAACGATTAGGGTTTATTTCC 57.237 37.500 6.00 6.00 42.52 3.13
3306 5972 6.239396 TCAACATGGAAACGATTAGGGTTTA 58.761 36.000 0.00 0.00 37.70 2.01
3316 5982 6.384258 TCAAAATCTTCAACATGGAAACGA 57.616 33.333 0.00 0.00 0.00 3.85
3318 5984 9.912634 TCTATTCAAAATCTTCAACATGGAAAC 57.087 29.630 0.00 0.00 0.00 2.78
3336 6002 6.978659 ACTAATCGCACGAGATTTCTATTCAA 59.021 34.615 1.30 0.00 40.83 2.69
3343 6009 2.033662 GCCACTAATCGCACGAGATTTC 60.034 50.000 1.30 0.00 40.83 2.17
3349 6015 0.107897 AATGGCCACTAATCGCACGA 60.108 50.000 8.16 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.