Multiple sequence alignment - TraesCS3D01G389200

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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 TraesCS3D01G389200 chr3D 100.000 3650 0 0 318 3967 504738896 504742545 0.000000e+00 6741.0
1 TraesCS3D01G389200 chr3D 92.611 203 12 1 2755 2957 504741219 504741418 5.020000e-74 289.0
2 TraesCS3D01G389200 chr3D 92.611 203 12 1 2641 2840 504741333 504741535 5.020000e-74 289.0
3 TraesCS3D01G389200 chr3D 100.000 139 0 0 1 139 504738579 504738717 1.410000e-64 257.0
4 TraesCS3D01G389200 chr3D 93.103 58 4 0 2628 2685 504741158 504741215 7.060000e-13 86.1
5 TraesCS3D01G389200 chr3D 93.103 58 4 0 2580 2637 504741206 504741263 7.060000e-13 86.1
6 TraesCS3D01G389200 chr3B 93.319 3293 158 33 319 3561 666449282 666452562 0.000000e+00 4806.0
7 TraesCS3D01G389200 chr3B 90.160 376 28 8 3594 3967 666452871 666453239 7.710000e-132 481.0
8 TraesCS3D01G389200 chr3B 91.626 203 14 1 2641 2840 666451728 666451930 1.090000e-70 278.0
9 TraesCS3D01G389200 chr3B 90.640 203 16 1 2755 2957 666451614 666451813 2.350000e-67 267.0
10 TraesCS3D01G389200 chr3B 90.647 139 13 0 1 139 666449107 666449245 6.770000e-43 185.0
11 TraesCS3D01G389200 chr3A 92.940 2153 112 20 497 2637 642924937 642927061 0.000000e+00 3097.0
12 TraesCS3D01G389200 chr3A 87.293 724 57 11 3272 3967 642927859 642928575 0.000000e+00 795.0
13 TraesCS3D01G389200 chr3A 81.371 569 52 22 2755 3272 642927179 642927744 7.930000e-112 414.0
14 TraesCS3D01G389200 chr3A 95.082 244 12 0 2593 2836 642927131 642927374 6.220000e-103 385.0
15 TraesCS3D01G389200 chr3A 93.939 165 10 0 2632 2796 642927008 642927172 2.370000e-62 250.0
16 TraesCS3D01G389200 chr3A 88.333 180 17 2 319 498 642924657 642924832 3.110000e-51 213.0
17 TraesCS3D01G389200 chr3A 85.185 189 20 4 2726 2913 642926991 642927172 1.880000e-43 187.0
18 TraesCS3D01G389200 chr3A 89.474 95 10 0 1 95 642924245 642924339 1.940000e-23 121.0
19 TraesCS3D01G389200 chr3A 96.000 50 2 0 2588 2637 642927174 642927223 9.140000e-12 82.4


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 TraesCS3D01G389200 chr3D 504738579 504742545 3966 False 1291.366667 6741 95.238000 1 3967 6 chr3D.!!$F1 3966
1 TraesCS3D01G389200 chr3B 666449107 666453239 4132 False 1203.400000 4806 91.278400 1 3967 5 chr3B.!!$F1 3966
2 TraesCS3D01G389200 chr3A 642924245 642928575 4330 False 616.044444 3097 89.957444 1 3967 9 chr3A.!!$F1 3966

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
342 436 0.750546 TCACCACCTCGATCTACCCG 60.751 60.0 0.00 0.00 0.0 5.28 F
1003 1220 0.963962 AAAGCACTGTTCAGCCATGG 59.036 50.0 7.63 7.63 0.0 3.66 F
2125 2346 0.394352 AATTCACCGCCACTCCCATC 60.394 55.0 0.00 0.00 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 1665 0.313043 CTTGTGCAGACTTTGGCAGG 59.687 55.0 0.00 0.0 41.35 4.85 R
2648 2869 0.178873 AGGGGTAAAGAGGCTGTGGA 60.179 55.0 0.00 0.0 0.00 4.02 R
3660 4390 0.538746 TGCTGACCGGTAGTGACTCA 60.539 55.0 7.34 0.0 0.00 3.41 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
73 74 3.520290 TTGATACCGTAGCCTGACAAG 57.480 47.619 0.00 0.00 0.00 3.16
74 75 1.136305 TGATACCGTAGCCTGACAAGC 59.864 52.381 0.00 0.00 0.00 4.01
79 80 1.709147 CGTAGCCTGACAAGCCATGC 61.709 60.000 0.00 0.00 0.00 4.06
118 119 1.686052 TGGACACACCTGGAAATTTGC 59.314 47.619 0.00 2.22 39.86 3.68
342 436 0.750546 TCACCACCTCGATCTACCCG 60.751 60.000 0.00 0.00 0.00 5.28
343 437 1.455217 ACCACCTCGATCTACCCGG 60.455 63.158 0.00 0.00 0.00 5.73
360 454 2.637872 CCCGGGTGGTCAGATGTTATAT 59.362 50.000 14.18 0.00 0.00 0.86
403 500 2.706723 TGGGTTTACACAGCTCAGGTTA 59.293 45.455 0.00 0.00 0.00 2.85
412 509 6.759497 ACACAGCTCAGGTTAAATATTTCC 57.241 37.500 3.39 0.72 0.00 3.13
414 511 6.891908 ACACAGCTCAGGTTAAATATTTCCAT 59.108 34.615 3.39 0.00 0.00 3.41
461 558 7.759489 TCACAAACTTCCAGTTTATGCTATT 57.241 32.000 3.25 0.00 45.84 1.73
464 561 8.246180 CACAAACTTCCAGTTTATGCTATTGAT 58.754 33.333 1.60 0.00 45.84 2.57
540 743 3.753272 TCTGCTCTTTTACATTCAGGTGC 59.247 43.478 0.00 0.00 0.00 5.01
629 832 6.200808 CAACTGAATAAATATGCGCATCACA 58.799 36.000 29.11 10.50 0.00 3.58
631 834 5.528690 ACTGAATAAATATGCGCATCACACT 59.471 36.000 29.11 4.88 0.00 3.55
657 862 8.196771 TGGTGATTTTTCATGGCTAACATAATC 58.803 33.333 0.00 0.00 37.84 1.75
658 863 8.196771 GGTGATTTTTCATGGCTAACATAATCA 58.803 33.333 0.00 0.00 37.97 2.57
661 866 8.597662 ATTTTTCATGGCTAACATAATCATGC 57.402 30.769 0.00 0.00 37.84 4.06
688 893 7.739295 TCTGCGATTACTTCAAAATCTACAAC 58.261 34.615 0.00 0.00 32.29 3.32
691 896 6.466097 GCGATTACTTCAAAATCTACAACAGC 59.534 38.462 0.00 0.00 32.29 4.40
692 897 7.624344 GCGATTACTTCAAAATCTACAACAGCT 60.624 37.037 0.00 0.00 32.29 4.24
794 1010 1.909700 TGTCCCTGAAATCAAGTGGC 58.090 50.000 0.00 0.00 0.00 5.01
815 1032 4.025647 GGCGACAAAGTACATGCTCTAATC 60.026 45.833 0.00 0.00 0.00 1.75
849 1066 4.202172 GGAAGTACAGGCTCTAATCACTCC 60.202 50.000 0.00 0.00 0.00 3.85
851 1068 4.551671 AGTACAGGCTCTAATCACTCCAT 58.448 43.478 0.00 0.00 0.00 3.41
901 1118 3.721706 CCCCAGAGACCCTGCCAC 61.722 72.222 0.00 0.00 41.57 5.01
903 1120 4.767255 CCAGAGACCCTGCCACGC 62.767 72.222 0.00 0.00 41.57 5.34
972 1189 3.120468 TCACATTCTCCCATCTCCTCA 57.880 47.619 0.00 0.00 0.00 3.86
1003 1220 0.963962 AAAGCACTGTTCAGCCATGG 59.036 50.000 7.63 7.63 0.00 3.66
1019 1236 1.393539 CATGGAAGTAAGCGTTGGACG 59.606 52.381 0.00 0.00 45.88 4.79
1369 1586 9.632638 AGAAAAGTGTATTCAAGCATACCATAT 57.367 29.630 0.00 0.00 0.00 1.78
1400 1617 4.952335 CCAAGAACATGGCTAGAGGAAAAT 59.048 41.667 0.00 0.00 32.78 1.82
1405 1622 8.829373 AGAACATGGCTAGAGGAAAATTTTAT 57.171 30.769 2.75 0.00 0.00 1.40
1584 1803 2.275466 ACCAGGTAGGCCAAAGTACAT 58.725 47.619 5.01 0.00 43.14 2.29
1684 1905 8.336806 TCATCGAAGCGAAAAAGTACTTAAAAA 58.663 29.630 8.92 0.00 39.99 1.94
1685 1906 9.113876 CATCGAAGCGAAAAAGTACTTAAAAAT 57.886 29.630 8.92 0.00 39.99 1.82
1687 1908 8.336806 TCGAAGCGAAAAAGTACTTAAAAATGA 58.663 29.630 8.92 0.00 31.06 2.57
1731 1952 9.171877 GTTCATTCTTCCTGAATATCTTTCAGT 57.828 33.333 12.81 0.00 43.00 3.41
2054 2275 6.870769 AGTAATGGCATTTGGATCAAAGAAG 58.129 36.000 19.21 0.00 36.76 2.85
2104 2325 8.879227 TCACATTCTACCATCAATGTATCCATA 58.121 33.333 0.00 0.00 40.52 2.74
2113 2334 9.466497 ACCATCAATGTATCCATATAATTCACC 57.534 33.333 0.00 0.00 0.00 4.02
2125 2346 0.394352 AATTCACCGCCACTCCCATC 60.394 55.000 0.00 0.00 0.00 3.51
2133 2354 1.616921 CCACTCCCATCCCAGCATT 59.383 57.895 0.00 0.00 0.00 3.56
2144 2365 1.153289 CCAGCATTCCTCACCTCCG 60.153 63.158 0.00 0.00 0.00 4.63
2166 2387 2.041081 TCCAACTACAAATCCCCACCAG 59.959 50.000 0.00 0.00 0.00 4.00
2171 2392 1.451449 ACAAATCCCCACCAGTACCA 58.549 50.000 0.00 0.00 0.00 3.25
2172 2393 2.000048 ACAAATCCCCACCAGTACCAT 59.000 47.619 0.00 0.00 0.00 3.55
2264 2485 4.124351 TACTCTTCGCCGCCACCG 62.124 66.667 0.00 0.00 0.00 4.94
2320 2541 4.009675 GCTCCACCAACATCTAACAATCA 58.990 43.478 0.00 0.00 0.00 2.57
2333 2554 3.817709 AACAATCAAACACCAACCCAG 57.182 42.857 0.00 0.00 0.00 4.45
2605 2826 4.503817 GCTACCAGCATCAATATCTCCACA 60.504 45.833 0.00 0.00 41.89 4.17
2607 2828 2.812591 CCAGCATCAATATCTCCACAGC 59.187 50.000 0.00 0.00 0.00 4.40
2612 2833 4.746089 GCATCAATATCTCCACAGCCTCTT 60.746 45.833 0.00 0.00 0.00 2.85
2648 2869 2.779430 TCCACCACCAGCATCAATATCT 59.221 45.455 0.00 0.00 0.00 1.98
2696 2917 3.708631 CTCCACCACCATATCTGAACTCT 59.291 47.826 0.00 0.00 0.00 3.24
2759 2980 0.041312 CGCCACCAGTTTCTTCAACG 60.041 55.000 0.00 0.00 40.75 4.10
2876 3145 0.041312 CGCCACCAGTTTCTTCAACG 60.041 55.000 0.00 0.00 40.75 4.10
2942 3211 1.490910 CTGAACTCCTACCAATCCCCC 59.509 57.143 0.00 0.00 0.00 5.40
2979 3249 3.474600 CTGTCATAAGCATCAGGAAGGG 58.525 50.000 0.00 0.00 0.00 3.95
3010 3280 6.884295 TGAAATGTAAGTTTCCTAGTGGGATG 59.116 38.462 0.00 0.00 44.66 3.51
3065 3364 4.794169 ACAAAATGCCGTAATGTGAAGTC 58.206 39.130 0.00 0.00 0.00 3.01
3072 3371 5.057819 TGCCGTAATGTGAAGTCTTAAACA 58.942 37.500 3.68 3.68 0.00 2.83
3135 3435 5.435686 TGGTTAGATGACTGCCAAGTAAT 57.564 39.130 0.00 0.00 36.52 1.89
3206 3528 3.691609 GTGGGCAGAATAAACAGAAGAGG 59.308 47.826 0.00 0.00 0.00 3.69
3212 3534 5.391416 GCAGAATAAACAGAAGAGGTGAAGC 60.391 44.000 0.00 0.00 0.00 3.86
3256 3578 1.949525 GCAGCTGGAGTTTTCAACTGA 59.050 47.619 17.12 0.00 43.03 3.41
3288 3725 8.639761 TCAGTCTCTAGTATTATTTACCCAAGC 58.360 37.037 0.00 0.00 0.00 4.01
3309 3746 4.214971 AGCATCTAGTGTTGTTTCAGCTTG 59.785 41.667 0.00 0.00 0.00 4.01
3311 3748 3.540617 TCTAGTGTTGTTTCAGCTTGCA 58.459 40.909 0.00 0.00 0.00 4.08
3314 3751 2.098117 AGTGTTGTTTCAGCTTGCACTC 59.902 45.455 0.00 0.00 31.04 3.51
3315 3752 1.405105 TGTTGTTTCAGCTTGCACTCC 59.595 47.619 0.00 0.00 0.00 3.85
3319 3756 0.662619 TTTCAGCTTGCACTCCGTTG 59.337 50.000 0.00 0.00 0.00 4.10
3332 3769 2.766828 ACTCCGTTGCCTAGAGCTATTT 59.233 45.455 0.00 0.00 44.23 1.40
3367 3807 8.409358 AACCATAAGTTGTATGAGCTTTTCTT 57.591 30.769 0.00 0.00 37.29 2.52
3368 3808 9.515226 AACCATAAGTTGTATGAGCTTTTCTTA 57.485 29.630 0.00 0.00 37.29 2.10
3369 3809 9.167311 ACCATAAGTTGTATGAGCTTTTCTTAG 57.833 33.333 0.00 0.00 0.00 2.18
3375 3815 9.857957 AGTTGTATGAGCTTTTCTTAGTAGTAC 57.142 33.333 0.00 0.00 0.00 2.73
3454 3895 7.975866 AAATATTTTCTACTGCGCATTTCTG 57.024 32.000 12.24 0.00 0.00 3.02
3486 3928 7.609532 AGAAACTGGAACAAAATAGAGAGATGG 59.390 37.037 0.00 0.00 38.70 3.51
3499 3941 2.497675 GAGAGATGGTGTGGCTTGACTA 59.502 50.000 0.00 0.00 0.00 2.59
3525 3967 5.355350 CCACTCCACTTATTCCAGATTTGTC 59.645 44.000 0.00 0.00 0.00 3.18
3563 4016 4.561530 GCGGCATCTATCCAAGATAGAACA 60.562 45.833 16.11 0.00 43.42 3.18
3575 4028 3.474920 AGATAGAACAAATCCAGGGGGT 58.525 45.455 0.00 0.00 34.93 4.95
3576 4029 4.641868 AGATAGAACAAATCCAGGGGGTA 58.358 43.478 0.00 0.00 34.93 3.69
3601 4330 3.118408 TCTCCACCGTGAAATTCTATGGG 60.118 47.826 0.00 0.00 0.00 4.00
3660 4390 0.961857 TTGGAATGCAGTGCGCTCAT 60.962 50.000 9.73 1.40 43.06 2.90
3802 4544 1.145738 AGGCACATTTCTTCAGTGGGT 59.854 47.619 0.00 0.00 33.98 4.51
3803 4545 1.541588 GGCACATTTCTTCAGTGGGTC 59.458 52.381 0.00 0.00 33.98 4.46
3835 4577 2.079158 TCAGAGAAATTTCGGCTGCTG 58.921 47.619 26.14 20.74 35.72 4.41
3842 4584 2.748058 ATTTCGGCTGCTGAACGGGT 62.748 55.000 22.72 7.46 0.00 5.28
3851 4593 2.552315 CTGCTGAACGGGTGTAAACAAT 59.448 45.455 0.00 0.00 0.00 2.71
3856 4598 5.676532 TGAACGGGTGTAAACAATAACAG 57.323 39.130 0.00 0.00 0.00 3.16
3877 4619 2.126850 CGCTCGACTGCTCAACGA 60.127 61.111 0.00 0.00 34.90 3.85
3878 4620 1.729484 CGCTCGACTGCTCAACGAA 60.729 57.895 0.00 0.00 35.70 3.85
3912 4654 2.430921 GCCGGATCTCGCGGTATG 60.431 66.667 5.05 0.00 37.59 2.39
3924 4666 3.151554 TCGCGGTATGTATCTACCATGT 58.848 45.455 6.13 0.00 41.12 3.21
3940 4682 4.890088 ACCATGTATTGTTCGTGTACAGT 58.110 39.130 0.00 0.00 32.45 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.480224 TCGACTTCGACGACAAAACT 57.520 45.000 0.00 0.00 44.22 2.66
73 74 2.262211 GAATTGGAAGAAACGCATGGC 58.738 47.619 0.00 0.00 0.00 4.40
74 75 2.230992 TGGAATTGGAAGAAACGCATGG 59.769 45.455 0.00 0.00 0.00 3.66
79 80 3.568007 TCCACTTGGAATTGGAAGAAACG 59.432 43.478 0.00 0.00 42.18 3.60
113 114 5.937540 GCCTTATTTACCAAAACTGGCAAAT 59.062 36.000 7.36 7.36 38.22 2.32
317 318 3.771577 AGATCGAGGTGGTGAAGTTTT 57.228 42.857 0.00 0.00 0.00 2.43
318 319 3.056035 GGTAGATCGAGGTGGTGAAGTTT 60.056 47.826 0.00 0.00 0.00 2.66
321 415 1.409427 GGGTAGATCGAGGTGGTGAAG 59.591 57.143 0.00 0.00 0.00 3.02
342 436 8.758829 TGTATCATATATAACATCTGACCACCC 58.241 37.037 0.00 0.00 0.00 4.61
343 437 9.587772 GTGTATCATATATAACATCTGACCACC 57.412 37.037 0.00 0.00 0.00 4.61
360 454 6.406370 CCAGTGTCTTTGAAGGTGTATCATA 58.594 40.000 0.00 0.00 0.00 2.15
412 509 8.687824 ATGCAAATTTTCCTACGTTTCTTATG 57.312 30.769 0.00 0.00 0.00 1.90
414 511 7.806014 GTGATGCAAATTTTCCTACGTTTCTTA 59.194 33.333 0.00 0.00 0.00 2.10
540 743 7.172190 AGTTTATCCTGCATACTGAATTCATCG 59.828 37.037 8.96 0.48 0.00 3.84
629 832 4.832266 TGTTAGCCATGAAAAATCACCAGT 59.168 37.500 0.00 0.00 0.00 4.00
631 834 5.999205 ATGTTAGCCATGAAAAATCACCA 57.001 34.783 0.00 0.00 30.69 4.17
657 862 4.541085 TTGAAGTAATCGCAGATGCATG 57.459 40.909 2.46 0.00 45.12 4.06
658 863 5.565592 TTTTGAAGTAATCGCAGATGCAT 57.434 34.783 0.00 0.00 45.12 3.96
661 866 7.909267 TGTAGATTTTGAAGTAATCGCAGATG 58.091 34.615 0.00 0.00 45.12 2.90
711 916 7.439157 TGCATGGTGTATATAAATCTGCTTC 57.561 36.000 0.00 0.00 0.00 3.86
760 973 7.880160 TTCAGGGACAATATGGAATTAGTTG 57.120 36.000 0.00 0.00 0.00 3.16
772 986 4.016444 GCCACTTGATTTCAGGGACAATA 58.984 43.478 0.00 0.00 0.00 1.90
776 990 0.804989 CGCCACTTGATTTCAGGGAC 59.195 55.000 0.00 0.00 0.00 4.46
794 1010 6.893958 AAGATTAGAGCATGTACTTTGTCG 57.106 37.500 0.00 0.00 0.00 4.35
822 1039 3.468071 TTAGAGCCTGTACTTCCCTCA 57.532 47.619 0.00 0.00 0.00 3.86
823 1040 3.961408 TGATTAGAGCCTGTACTTCCCTC 59.039 47.826 0.00 0.00 0.00 4.30
849 1066 4.389374 CTGGTAAGGTAGTATGGCCAATG 58.611 47.826 10.96 0.00 0.00 2.82
851 1068 2.171870 GCTGGTAAGGTAGTATGGCCAA 59.828 50.000 10.96 0.00 0.00 4.52
901 1118 1.229428 ATAATGTTCAGGATGGCGCG 58.771 50.000 0.00 0.00 36.16 6.86
903 1120 6.128007 GGGTATTTATAATGTTCAGGATGGCG 60.128 42.308 0.00 0.00 36.16 5.69
908 1125 8.051468 TGGATGGGTATTTATAATGTTCAGGA 57.949 34.615 0.00 0.00 0.00 3.86
994 1211 0.613260 ACGCTTACTTCCATGGCTGA 59.387 50.000 6.96 0.00 0.00 4.26
1019 1236 2.484287 TAGCTGACCCTTTGGCTGGC 62.484 60.000 0.00 0.00 36.40 4.85
1369 1586 4.038271 AGCCATGTTCTTGGATCTTCAA 57.962 40.909 8.59 0.00 39.25 2.69
1405 1622 7.720957 ACAGCAGATAATAATGATAACCAAGCA 59.279 33.333 0.00 0.00 0.00 3.91
1448 1665 0.313043 CTTGTGCAGACTTTGGCAGG 59.687 55.000 0.00 0.00 41.35 4.85
1495 1712 6.267699 AGGCTTCTAAAACACTAAAAATGGCT 59.732 34.615 0.00 0.00 0.00 4.75
2054 2275 4.448732 GGTTTTGAACATCCAGCAAATGTC 59.551 41.667 0.00 0.00 36.35 3.06
2104 2325 0.916086 TGGGAGTGGCGGTGAATTAT 59.084 50.000 0.00 0.00 0.00 1.28
2113 2334 4.864334 GCTGGGATGGGAGTGGCG 62.864 72.222 0.00 0.00 0.00 5.69
2125 2346 1.225704 GGAGGTGAGGAATGCTGGG 59.774 63.158 0.00 0.00 0.00 4.45
2133 2354 0.406750 TAGTTGGACGGAGGTGAGGA 59.593 55.000 0.00 0.00 0.00 3.71
2144 2365 2.224917 TGGTGGGGATTTGTAGTTGGAC 60.225 50.000 0.00 0.00 0.00 4.02
2166 2387 2.943033 GTGGTGAATGCTGGTATGGTAC 59.057 50.000 0.00 0.00 0.00 3.34
2171 2392 1.212935 GGAGGTGGTGAATGCTGGTAT 59.787 52.381 0.00 0.00 0.00 2.73
2172 2393 0.618458 GGAGGTGGTGAATGCTGGTA 59.382 55.000 0.00 0.00 0.00 3.25
2264 2485 2.158871 TGAAGGTGTGGACTGTTGGTAC 60.159 50.000 0.00 0.00 0.00 3.34
2320 2541 5.537295 GGTAAATACTTCTGGGTTGGTGTTT 59.463 40.000 0.00 0.00 0.00 2.83
2333 2554 5.641789 AGTATGGGGGTGGTAAATACTTC 57.358 43.478 0.00 0.00 31.59 3.01
2605 2826 1.141185 GCCATAGGGGTAAAGAGGCT 58.859 55.000 0.00 0.00 39.65 4.58
2648 2869 0.178873 AGGGGTAAAGAGGCTGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
2696 2917 0.406361 GTGGTGGTGGGGATTGGTAA 59.594 55.000 0.00 0.00 0.00 2.85
2759 2980 1.375268 GTGCAGAGGCTGTGGAGAC 60.375 63.158 14.04 0.00 41.91 3.36
2876 3145 4.025858 TGCAGAGGCTGTGGAGGC 62.026 66.667 14.04 0.00 45.31 4.70
2942 3211 2.923035 AGGTGACTCGGTGGTGGG 60.923 66.667 0.00 0.00 32.90 4.61
2979 3249 9.665264 CACTAGGAAACTTACATTTCAAGAAAC 57.335 33.333 0.00 0.00 43.67 2.78
3010 3280 7.549839 TGAATGGTACTATACTGTTACCACAC 58.450 38.462 10.43 8.59 42.74 3.82
3072 3371 8.887717 GTTGAGTTTATATGAGCTCTTGTGAAT 58.112 33.333 16.19 0.96 0.00 2.57
3109 3409 3.719268 TGGCAGTCATCTAACCAATGT 57.281 42.857 0.00 0.00 0.00 2.71
3206 3528 2.577700 TCCTCTCGAGATAGGCTTCAC 58.422 52.381 17.03 0.00 32.55 3.18
3212 3534 2.225491 CGCTTCTTCCTCTCGAGATAGG 59.775 54.545 17.03 14.90 0.00 2.57
3288 3725 4.023792 TGCAAGCTGAAACAACACTAGATG 60.024 41.667 0.00 0.00 0.00 2.90
3309 3746 1.811679 GCTCTAGGCAACGGAGTGC 60.812 63.158 0.00 0.00 45.00 4.40
3311 3748 2.074729 ATAGCTCTAGGCAACGGAGT 57.925 50.000 0.00 0.00 44.79 3.85
3314 3751 3.126831 CTGAAATAGCTCTAGGCAACGG 58.873 50.000 0.00 0.00 44.79 4.44
3332 3769 7.826744 TCATACAACTTATGGTTACATTGCTGA 59.173 33.333 0.00 0.00 38.53 4.26
3380 3820 9.878599 CCGTATATTGGATTGAAAATAGAACAC 57.121 33.333 0.00 0.00 0.00 3.32
3445 3886 2.989840 AGTTTCTCGAGACAGAAATGCG 59.010 45.455 16.36 0.00 42.88 4.73
3454 3895 5.674933 ATTTTGTTCCAGTTTCTCGAGAC 57.325 39.130 16.36 5.26 0.00 3.36
3499 3941 2.551270 TCTGGAATAAGTGGAGTGGCT 58.449 47.619 0.00 0.00 0.00 4.75
3525 3967 2.760159 CCGCAGCATAAACGGTGGG 61.760 63.158 0.00 0.00 44.32 4.61
3563 4016 2.206223 GGAGAAGTACCCCCTGGATTT 58.794 52.381 0.00 0.00 34.81 2.17
3575 4028 4.884668 AGAATTTCACGGTGGAGAAGTA 57.115 40.909 8.50 0.00 0.00 2.24
3576 4029 3.771577 AGAATTTCACGGTGGAGAAGT 57.228 42.857 8.50 0.75 0.00 3.01
3629 4358 1.620323 GCATTCCAAGCCCAGTTTTCT 59.380 47.619 0.00 0.00 0.00 2.52
3636 4365 2.277591 GCACTGCATTCCAAGCCCA 61.278 57.895 0.00 0.00 0.00 5.36
3637 4366 2.575461 GCACTGCATTCCAAGCCC 59.425 61.111 0.00 0.00 0.00 5.19
3660 4390 0.538746 TGCTGACCGGTAGTGACTCA 60.539 55.000 7.34 0.00 0.00 3.41
3753 4490 0.965363 GCGTGGTTGGGTGATGGATT 60.965 55.000 0.00 0.00 0.00 3.01
3802 4544 4.302509 TCTGAAAACCCGCCGCGA 62.303 61.111 15.93 0.00 0.00 5.87
3803 4545 3.788766 CTCTGAAAACCCGCCGCG 61.789 66.667 5.59 5.59 0.00 6.46
3835 4577 4.023878 TGCTGTTATTGTTTACACCCGTTC 60.024 41.667 0.00 0.00 0.00 3.95
3842 4584 2.811431 AGCGCTGCTGTTATTGTTTACA 59.189 40.909 10.39 0.00 37.57 2.41
3851 4593 1.444383 CAGTCGAGCGCTGCTGTTA 60.444 57.895 18.48 0.00 39.88 2.41
3877 4619 4.224370 TCCGGCAGGAAGATAAACTACTTT 59.776 41.667 1.89 0.00 45.12 2.66
3878 4620 3.773119 TCCGGCAGGAAGATAAACTACTT 59.227 43.478 1.89 0.00 45.12 2.24
3912 4654 7.916977 TGTACACGAACAATACATGGTAGATAC 59.083 37.037 0.00 0.00 0.00 2.24
3924 4666 5.299582 TCATCGACTGTACACGAACAATA 57.700 39.130 11.94 0.00 41.65 1.90
3940 4682 0.631753 AGGTCTCCTCCCTTCATCGA 59.368 55.000 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.