Multiple sequence alignment - TraesCS3B01G264500

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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 TraesCS3B01G264500 chr3B 100.000 3301 0 0 1 3301 423498750 423495450 0.000000e+00 6096.0
1 TraesCS3B01G264500 chr3D 90.548 2994 156 49 346 3301 326121706 326118802 0.000000e+00 3843.0
2 TraesCS3B01G264500 chr3D 87.848 395 37 3 1 395 326122342 326121959 1.400000e-123 453.0
3 TraesCS3B01G264500 chr3D 97.872 47 1 0 2476 2522 56336968 56336922 7.590000e-12 82.4
4 TraesCS3B01G264500 chr3A 91.736 2045 71 33 489 2481 438809693 438811691 0.000000e+00 2750.0
5 TraesCS3B01G264500 chr3A 85.696 797 78 18 2522 3301 438811699 438812476 0.000000e+00 808.0
6 TraesCS3B01G264500 chr3A 88.943 407 43 2 3 409 438788821 438789225 4.920000e-138 501.0
7 TraesCS3B01G264500 chr7D 76.119 402 66 20 399 782 159875376 159874987 2.020000e-42 183.0
8 TraesCS3B01G264500 chr7D 90.000 50 5 0 628 677 588690653 588690702 7.650000e-07 65.8
9 TraesCS3B01G264500 chr4B 77.567 263 45 10 520 775 597035127 597034872 2.650000e-31 147.0
10 TraesCS3B01G264500 chr1A 93.478 92 6 0 1328 1419 461523594 461523503 1.600000e-28 137.0
11 TraesCS3B01G264500 chr1D 87.395 119 13 2 1333 1450 362132129 362132012 5.750000e-28 135.0
12 TraesCS3B01G264500 chr1D 92.391 92 7 0 1328 1419 362012774 362012683 7.430000e-27 132.0
13 TraesCS3B01G264500 chr1D 86.325 117 12 4 1326 1440 476872306 476872192 1.240000e-24 124.0
14 TraesCS3B01G264500 chr1D 94.231 52 2 1 2471 2522 174151278 174151228 9.820000e-11 78.7
15 TraesCS3B01G264500 chr1B 73.621 417 80 27 1023 1419 484465107 484464701 2.070000e-27 134.0
16 TraesCS3B01G264500 chr1B 86.290 124 15 2 1328 1450 484692420 484692298 2.070000e-27 134.0
17 TraesCS3B01G264500 chr1B 89.011 91 10 0 1326 1416 664318207 664318297 2.690000e-21 113.0
18 TraesCS3B01G264500 chr5D 77.465 213 38 9 475 683 462998730 462998936 5.790000e-23 119.0
19 TraesCS3B01G264500 chr5D 97.872 47 1 0 2476 2522 312854069 312854023 7.590000e-12 82.4
20 TraesCS3B01G264500 chr5D 94.340 53 2 1 2470 2522 465008137 465008086 2.730000e-11 80.5
21 TraesCS3B01G264500 chr5A 86.000 100 11 3 569 668 582974063 582974159 1.620000e-18 104.0
22 TraesCS3B01G264500 chr5B 75.556 225 46 9 504 723 569559031 569559251 5.830000e-18 102.0
23 TraesCS3B01G264500 chr5B 90.769 65 3 3 2458 2521 125481515 125481577 2.110000e-12 84.2
24 TraesCS3B01G264500 chr2D 76.796 181 35 6 539 714 425989932 425990110 9.750000e-16 95.3
25 TraesCS3B01G264500 chr7A 90.625 64 6 0 719 782 158378290 158378353 5.870000e-13 86.1
26 TraesCS3B01G264500 chr7A 97.917 48 1 0 2475 2522 308450904 308450857 2.110000e-12 84.2
27 TraesCS3B01G264500 chr4D 97.872 47 1 0 2476 2522 306239614 306239568 7.590000e-12 82.4
28 TraesCS3B01G264500 chr4D 88.406 69 4 4 2453 2521 116822022 116821958 2.730000e-11 80.5
29 TraesCS3B01G264500 chr2B 83.951 81 12 1 627 706 17344346 17344426 3.530000e-10 76.8
30 TraesCS3B01G264500 chr7B 86.957 69 3 6 2455 2522 682374529 682374592 4.570000e-09 73.1


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 TraesCS3B01G264500 chr3B 423495450 423498750 3300 True 6096 6096 100.000 1 3301 1 chr3B.!!$R1 3300
1 TraesCS3B01G264500 chr3D 326118802 326122342 3540 True 2148 3843 89.198 1 3301 2 chr3D.!!$R2 3300
2 TraesCS3B01G264500 chr3A 438809693 438812476 2783 False 1779 2750 88.716 489 3301 2 chr3A.!!$F2 2812

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
103 104 0.537653 ACGCTAGGCTTTCCTCTTCC 59.462 55.0 0.00 0.00 43.06 3.46 F
1545 1886 0.455633 GGTACCTGTCGCTGTACACG 60.456 60.0 4.06 10.39 39.23 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 2123 0.881118 AATTTGCGGCAATGTCGACT 59.119 45.0 17.19 0.0 29.41 4.18 R
3195 3572 0.534877 ATGTTGCAGAAGCGTCACCA 60.535 50.0 1.61 0.0 46.23 4.17 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
31 32 1.524621 GACATGGGTGGAGATGGCG 60.525 63.158 0.00 0.00 0.00 5.69
34 35 0.816825 CATGGGTGGAGATGGCGAAG 60.817 60.000 0.00 0.00 0.00 3.79
51 52 4.338682 GGCGAAGAAGAGTAGGAGTGATAA 59.661 45.833 0.00 0.00 0.00 1.75
75 76 1.562008 GAAGGAGAGGGGAAGGAAAGG 59.438 57.143 0.00 0.00 0.00 3.11
102 103 1.799548 CGACGCTAGGCTTTCCTCTTC 60.800 57.143 0.00 0.00 43.06 2.87
103 104 0.537653 ACGCTAGGCTTTCCTCTTCC 59.462 55.000 0.00 0.00 43.06 3.46
175 176 1.533338 CGAGGTGGTTAGAATCGTCCG 60.533 57.143 0.00 0.00 0.00 4.79
182 183 2.159282 GGTTAGAATCGTCCGCTTGAGA 60.159 50.000 0.00 0.00 0.00 3.27
183 184 2.846039 TAGAATCGTCCGCTTGAGAC 57.154 50.000 0.00 0.00 0.00 3.36
195 196 2.346847 CGCTTGAGACTAGCAATGTGAC 59.653 50.000 0.00 0.00 38.55 3.67
196 197 3.329386 GCTTGAGACTAGCAATGTGACA 58.671 45.455 0.00 0.00 38.51 3.58
199 200 5.714047 CTTGAGACTAGCAATGTGACAGTA 58.286 41.667 0.00 0.00 0.00 2.74
217 218 9.901724 GTGACAGTAAGTAAATTATCATTGTCG 57.098 33.333 0.00 0.00 0.00 4.35
219 220 9.309516 GACAGTAAGTAAATTATCATTGTCGGA 57.690 33.333 0.00 0.00 0.00 4.55
234 235 3.881220 TGTCGGATATTTTGTTCCCTCC 58.119 45.455 0.00 0.00 0.00 4.30
235 236 2.870411 GTCGGATATTTTGTTCCCTCCG 59.130 50.000 2.51 2.51 45.27 4.63
236 237 2.158871 TCGGATATTTTGTTCCCTCCGG 60.159 50.000 8.72 0.00 44.32 5.14
237 238 2.158871 CGGATATTTTGTTCCCTCCGGA 60.159 50.000 2.93 2.93 41.38 5.14
238 239 3.683281 CGGATATTTTGTTCCCTCCGGAA 60.683 47.826 5.23 0.00 46.38 4.30
282 283 6.810911 AGATGCTCGTGTAGTGAAATTCTAT 58.189 36.000 0.00 0.00 0.00 1.98
343 344 6.709018 AAAAACTACAAGCCAACACTACAT 57.291 33.333 0.00 0.00 0.00 2.29
364 365 9.313323 CTACATTAACAACATGTAAAGAACACG 57.687 33.333 0.00 0.00 42.09 4.49
365 366 7.136119 ACATTAACAACATGTAAAGAACACGG 58.864 34.615 0.00 0.00 42.09 4.94
369 672 4.753107 ACAACATGTAAAGAACACGGGTAG 59.247 41.667 0.00 0.00 42.09 3.18
378 681 8.916062 TGTAAAGAACACGGGTAGATTGATATA 58.084 33.333 0.00 0.00 31.43 0.86
380 683 7.598759 AAGAACACGGGTAGATTGATATAGT 57.401 36.000 0.00 0.00 0.00 2.12
385 688 6.948886 ACACGGGTAGATTGATATAGTGAGAT 59.051 38.462 0.00 0.00 0.00 2.75
387 690 6.948886 ACGGGTAGATTGATATAGTGAGATGT 59.051 38.462 0.00 0.00 0.00 3.06
388 691 7.451877 ACGGGTAGATTGATATAGTGAGATGTT 59.548 37.037 0.00 0.00 0.00 2.71
402 705 1.701847 AGATGTTTGGACTGTCAGGCT 59.298 47.619 5.47 0.00 0.00 4.58
420 723 1.136891 GCTTGCTTTGGTTCACAGGTT 59.863 47.619 0.00 0.00 0.00 3.50
427 730 4.261614 GCTTTGGTTCACAGGTTCCTAAAG 60.262 45.833 0.00 0.00 0.00 1.85
530 833 3.957497 ACATGCTTGAGTGTTTGGGTTAA 59.043 39.130 6.60 0.00 0.00 2.01
531 834 4.037923 ACATGCTTGAGTGTTTGGGTTAAG 59.962 41.667 6.60 0.00 0.00 1.85
533 836 2.288213 GCTTGAGTGTTTGGGTTAAGGC 60.288 50.000 0.00 0.00 0.00 4.35
535 838 3.237268 TGAGTGTTTGGGTTAAGGCAT 57.763 42.857 0.00 0.00 0.00 4.40
536 839 4.374689 TGAGTGTTTGGGTTAAGGCATA 57.625 40.909 0.00 0.00 0.00 3.14
537 840 4.331968 TGAGTGTTTGGGTTAAGGCATAG 58.668 43.478 0.00 0.00 0.00 2.23
539 842 3.332485 AGTGTTTGGGTTAAGGCATAGGA 59.668 43.478 0.00 0.00 0.00 2.94
547 850 4.525100 GGGTTAAGGCATAGGAAAAACACA 59.475 41.667 0.00 0.00 0.00 3.72
584 887 6.515272 ACACAGTCAAATCAAAGACAAACT 57.485 33.333 0.00 0.00 37.23 2.66
598 901 8.617809 TCAAAGACAAACTACATGAAAAGGTAC 58.382 33.333 0.00 0.00 0.00 3.34
600 903 7.730364 AGACAAACTACATGAAAAGGTACAG 57.270 36.000 0.00 0.00 0.00 2.74
629 932 7.156673 GCATGTTATTATGCCATCAAGGATTT 58.843 34.615 0.00 0.00 45.93 2.17
643 946 3.662247 AGGATTTGTCTCGTTCTTCGT 57.338 42.857 0.00 0.00 40.80 3.85
646 949 1.929230 TTTGTCTCGTTCTTCGTGCA 58.071 45.000 0.00 0.00 40.80 4.57
662 965 5.309323 TCGTGCATAGGAATTTGAAAAGG 57.691 39.130 0.00 0.00 0.00 3.11
668 974 5.418840 GCATAGGAATTTGAAAAGGAGGTCA 59.581 40.000 0.00 0.00 0.00 4.02
683 989 9.588096 AAAAGGAGGTCAAAGTAGATTGTAAAT 57.412 29.630 0.00 0.00 0.00 1.40
719 1025 5.130350 TCTCTGAAACGGACCAAAAGAAAT 58.870 37.500 0.00 0.00 0.00 2.17
727 1033 5.984725 ACGGACCAAAAGAAATTTTCCTTT 58.015 33.333 5.52 2.99 34.39 3.11
728 1034 5.815222 ACGGACCAAAAGAAATTTTCCTTTG 59.185 36.000 19.55 19.55 39.59 2.77
729 1035 5.277297 CGGACCAAAAGAAATTTTCCTTTGC 60.277 40.000 20.50 12.01 38.92 3.68
775 1097 7.702348 GGCTTAAACAATGTCATCATAGGAAAC 59.298 37.037 0.00 0.00 33.49 2.78
807 1132 9.280174 TCCTATGTGTTTTGTAAGAAGTTTAGG 57.720 33.333 0.00 0.00 0.00 2.69
808 1133 9.280174 CCTATGTGTTTTGTAAGAAGTTTAGGA 57.720 33.333 0.00 0.00 0.00 2.94
852 1177 5.152623 TCAAAGGAGGTTAGTCTGTCATG 57.847 43.478 0.00 0.00 0.00 3.07
853 1178 4.593206 TCAAAGGAGGTTAGTCTGTCATGT 59.407 41.667 0.00 0.00 0.00 3.21
854 1179 5.778241 TCAAAGGAGGTTAGTCTGTCATGTA 59.222 40.000 0.00 0.00 0.00 2.29
891 1216 0.620556 ATGCCCTCCACTTGTACCTG 59.379 55.000 0.00 0.00 0.00 4.00
926 1251 2.394930 AAAACAAACAGGTTGGCACC 57.605 45.000 2.51 0.00 44.67 5.01
965 1290 2.032681 ACAAGGCCGAACCAGAGC 59.967 61.111 0.00 0.00 43.14 4.09
979 1320 1.102154 CAGAGCTCAGATCGACCACT 58.898 55.000 17.77 0.00 0.00 4.00
1545 1886 0.455633 GGTACCTGTCGCTGTACACG 60.456 60.000 4.06 10.39 39.23 4.49
1551 1892 4.746951 TCGCTGTACACGTCCGCG 62.747 66.667 17.47 17.47 44.63 6.46
1733 2078 2.163390 CGAGCAGACCAGCATCACG 61.163 63.158 0.00 0.00 36.85 4.35
1915 2260 2.822643 ATCTTCCACCGCCTCCCAGA 62.823 60.000 0.00 0.00 0.00 3.86
2118 2463 3.319198 GGGAGCACGGGGAGTTCA 61.319 66.667 0.00 0.00 0.00 3.18
2119 2464 2.670148 GGGAGCACGGGGAGTTCAT 61.670 63.158 0.00 0.00 0.00 2.57
2416 2767 6.371809 ACGTGTGCTCTTTTTCTTTATCAA 57.628 33.333 0.00 0.00 0.00 2.57
2419 2770 7.920682 ACGTGTGCTCTTTTTCTTTATCAATTT 59.079 29.630 0.00 0.00 0.00 1.82
2420 2771 8.420189 CGTGTGCTCTTTTTCTTTATCAATTTC 58.580 33.333 0.00 0.00 0.00 2.17
2483 2834 8.567948 CATTTCTTCCTCTCTAGTCATCTACTC 58.432 40.741 0.00 0.00 39.80 2.59
2485 2836 4.986054 TCCTCTCTAGTCATCTACTCCC 57.014 50.000 0.00 0.00 39.80 4.30
2488 2839 4.349636 CCTCTCTAGTCATCTACTCCCTCA 59.650 50.000 0.00 0.00 39.80 3.86
2492 2843 5.686753 TCTAGTCATCTACTCCCTCAGTTC 58.313 45.833 0.00 0.00 39.80 3.01
2500 2851 6.546428 TCTACTCCCTCAGTTCCAAAATAG 57.454 41.667 0.00 0.00 36.43 1.73
2502 2853 6.903534 TCTACTCCCTCAGTTCCAAAATAGAT 59.096 38.462 0.00 0.00 36.43 1.98
2506 2857 4.884164 CCCTCAGTTCCAAAATAGATGACC 59.116 45.833 0.00 0.00 0.00 4.02
2507 2858 4.884164 CCTCAGTTCCAAAATAGATGACCC 59.116 45.833 0.00 0.00 0.00 4.46
2508 2859 5.500234 CTCAGTTCCAAAATAGATGACCCA 58.500 41.667 0.00 0.00 0.00 4.51
2509 2860 5.886609 TCAGTTCCAAAATAGATGACCCAA 58.113 37.500 0.00 0.00 0.00 4.12
2510 2861 5.710099 TCAGTTCCAAAATAGATGACCCAAC 59.290 40.000 0.00 0.00 0.00 3.77
2511 2862 5.711976 CAGTTCCAAAATAGATGACCCAACT 59.288 40.000 0.00 0.00 0.00 3.16
2512 2863 6.209391 CAGTTCCAAAATAGATGACCCAACTT 59.791 38.462 0.00 0.00 0.00 2.66
2515 2866 8.749354 GTTCCAAAATAGATGACCCAACTTTAT 58.251 33.333 0.00 0.00 0.00 1.40
2517 2868 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
2518 2869 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
2606 2968 4.780815 TGATAGAAATCAACCGGCTGATT 58.219 39.130 24.20 24.20 45.82 2.57
2608 2970 5.758296 TGATAGAAATCAACCGGCTGATTAC 59.242 40.000 28.53 18.35 43.65 1.89
2609 2971 4.222124 AGAAATCAACCGGCTGATTACT 57.778 40.909 28.53 17.00 43.65 2.24
2610 2972 4.192317 AGAAATCAACCGGCTGATTACTC 58.808 43.478 28.53 23.03 43.65 2.59
2611 2973 2.225068 ATCAACCGGCTGATTACTCG 57.775 50.000 14.68 0.00 31.84 4.18
2612 2974 0.892755 TCAACCGGCTGATTACTCGT 59.107 50.000 2.67 0.00 0.00 4.18
2614 2976 1.393539 CAACCGGCTGATTACTCGTTG 59.606 52.381 0.00 0.00 0.00 4.10
2615 2977 0.739813 ACCGGCTGATTACTCGTTGC 60.740 55.000 0.00 0.00 0.00 4.17
2616 2978 1.631072 CGGCTGATTACTCGTTGCG 59.369 57.895 0.00 0.00 0.00 4.85
2622 2984 1.749609 GATTACTCGTTGCGTCCGCC 61.750 60.000 9.43 0.00 41.09 6.13
2623 2985 4.764336 TACTCGTTGCGTCCGCCG 62.764 66.667 9.43 6.61 41.09 6.46
2657 3020 4.443394 GCGTTCGATCCTATTTTATCGTGT 59.557 41.667 0.00 0.00 44.11 4.49
2661 3024 7.325338 CGTTCGATCCTATTTTATCGTGTGTAT 59.675 37.037 0.00 0.00 44.11 2.29
2690 3053 2.714250 TCCCACTTGTCTAACCACCATT 59.286 45.455 0.00 0.00 0.00 3.16
2695 3058 4.761739 CACTTGTCTAACCACCATTCACAT 59.238 41.667 0.00 0.00 0.00 3.21
2700 3063 8.415950 TTGTCTAACCACCATTCACATAAATT 57.584 30.769 0.00 0.00 0.00 1.82
2727 3090 1.078918 CAGGCAGCCATCGTCTTCA 60.079 57.895 15.80 0.00 0.00 3.02
2744 3115 4.393371 GTCTTCATCTTTTCCTGTAGGCAC 59.607 45.833 0.00 0.00 34.44 5.01
2749 3120 0.696501 TTTTCCTGTAGGCACCTCCC 59.303 55.000 0.00 0.00 34.51 4.30
2768 3139 2.159099 CCCGAATCAATCTCTCGTCCAA 60.159 50.000 0.00 0.00 0.00 3.53
2825 3196 4.351054 AAGCCGCTCCTTGGGTGG 62.351 66.667 0.00 0.00 37.28 4.61
2864 3235 3.173953 TCACCATTGCAATCCCTTTCT 57.826 42.857 9.53 0.00 0.00 2.52
2874 3245 3.566351 CAATCCCTTTCTTATCCCACCC 58.434 50.000 0.00 0.00 0.00 4.61
2954 3325 2.030946 GCGGAGATGTTGATACTGCAAC 59.969 50.000 0.00 0.00 46.33 4.17
2956 3327 4.682787 CGGAGATGTTGATACTGCAACTA 58.317 43.478 0.00 0.00 46.31 2.24
2960 3331 5.911752 AGATGTTGATACTGCAACTAGAGG 58.088 41.667 0.00 0.00 46.31 3.69
3017 3388 2.676471 GGTGCTGCAATCCCGGTT 60.676 61.111 2.77 0.00 0.00 4.44
3027 3398 1.895020 AATCCCGGTTAGCGCTCACA 61.895 55.000 22.30 3.07 0.00 3.58
3080 3457 2.416547 AGACACACAATTGTAGATGCGC 59.583 45.455 11.53 0.00 33.30 6.09
3081 3458 1.468520 ACACACAATTGTAGATGCGCC 59.531 47.619 11.53 0.00 33.30 6.53
3084 3461 1.009675 CAATTGTAGATGCGCCGCC 60.010 57.895 6.63 0.00 0.00 6.13
3087 3464 4.865761 TGTAGATGCGCCGCCGTC 62.866 66.667 6.63 4.89 36.67 4.79
3141 3518 2.567169 CAGGACCTCAACATCACCACTA 59.433 50.000 0.00 0.00 0.00 2.74
3151 3528 5.711506 TCAACATCACCACTATTGCAGAAAT 59.288 36.000 0.00 0.00 0.00 2.17
3195 3572 2.330440 TGATACATCAATGCAGGCGT 57.670 45.000 0.00 0.00 33.08 5.68
3196 3573 1.941975 TGATACATCAATGCAGGCGTG 59.058 47.619 1.01 1.01 33.08 5.34
3197 3574 1.265095 GATACATCAATGCAGGCGTGG 59.735 52.381 8.72 0.00 0.00 4.94
3198 3575 0.035534 TACATCAATGCAGGCGTGGT 60.036 50.000 8.72 0.00 0.00 4.16
3220 3600 3.618594 TGACGCTTCTGCAACATAATCTC 59.381 43.478 0.00 0.00 39.64 2.75
3291 3671 3.070429 CAACAAGACCTCTGTTGCAAC 57.930 47.619 22.83 22.83 36.86 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.748591 GCCATCTCCACCCATGTCTTC 60.749 57.143 0.00 0.00 0.00 2.87
31 32 6.093771 TCACGTTATCACTCCTACTCTTCTTC 59.906 42.308 0.00 0.00 0.00 2.87
34 35 5.814764 TCACGTTATCACTCCTACTCTTC 57.185 43.478 0.00 0.00 0.00 2.87
51 52 0.905337 CCTTCCCCTCTCCTTCACGT 60.905 60.000 0.00 0.00 0.00 4.49
114 115 2.019156 GCAGAGGCCATTACCTTGGTC 61.019 57.143 5.01 0.00 41.32 4.02
172 173 1.550524 ACATTGCTAGTCTCAAGCGGA 59.449 47.619 0.00 0.00 43.11 5.54
175 176 3.329386 TGTCACATTGCTAGTCTCAAGC 58.671 45.455 0.00 0.00 40.50 4.01
182 183 8.848474 AATTTACTTACTGTCACATTGCTAGT 57.152 30.769 0.00 0.00 0.00 2.57
241 242 9.601217 ACGAGCATCTTAGAAAACAATACTTAT 57.399 29.630 0.00 0.00 0.00 1.73
242 243 8.869897 CACGAGCATCTTAGAAAACAATACTTA 58.130 33.333 0.00 0.00 0.00 2.24
263 264 9.447040 TCGAAATATAGAATTTCACTACACGAG 57.553 33.333 10.20 0.00 37.76 4.18
324 325 6.292923 TGTTAATGTAGTGTTGGCTTGTAGT 58.707 36.000 0.00 0.00 0.00 2.73
325 326 6.795098 TGTTAATGTAGTGTTGGCTTGTAG 57.205 37.500 0.00 0.00 0.00 2.74
326 327 6.542735 TGTTGTTAATGTAGTGTTGGCTTGTA 59.457 34.615 0.00 0.00 0.00 2.41
327 328 5.358442 TGTTGTTAATGTAGTGTTGGCTTGT 59.642 36.000 0.00 0.00 0.00 3.16
328 329 5.826586 TGTTGTTAATGTAGTGTTGGCTTG 58.173 37.500 0.00 0.00 0.00 4.01
330 331 5.534654 ACATGTTGTTAATGTAGTGTTGGCT 59.465 36.000 0.00 0.00 36.50 4.75
331 332 5.768317 ACATGTTGTTAATGTAGTGTTGGC 58.232 37.500 0.00 0.00 36.50 4.52
332 333 9.393249 CTTTACATGTTGTTAATGTAGTGTTGG 57.607 33.333 2.30 0.00 40.59 3.77
343 344 5.589452 ACCCGTGTTCTTTACATGTTGTTAA 59.411 36.000 2.30 0.00 41.35 2.01
363 364 7.397892 ACATCTCACTATATCAATCTACCCG 57.602 40.000 0.00 0.00 0.00 5.28
364 365 9.429359 CAAACATCTCACTATATCAATCTACCC 57.571 37.037 0.00 0.00 0.00 3.69
365 366 9.429359 CCAAACATCTCACTATATCAATCTACC 57.571 37.037 0.00 0.00 0.00 3.18
369 672 8.986847 CAGTCCAAACATCTCACTATATCAATC 58.013 37.037 0.00 0.00 0.00 2.67
378 681 3.244353 CCTGACAGTCCAAACATCTCACT 60.244 47.826 0.93 0.00 0.00 3.41
380 683 2.550855 GCCTGACAGTCCAAACATCTCA 60.551 50.000 0.93 0.00 0.00 3.27
385 688 1.679139 CAAGCCTGACAGTCCAAACA 58.321 50.000 0.93 0.00 0.00 2.83
387 690 0.183492 AGCAAGCCTGACAGTCCAAA 59.817 50.000 0.93 0.00 0.00 3.28
388 691 0.183492 AAGCAAGCCTGACAGTCCAA 59.817 50.000 0.93 0.00 0.00 3.53
402 705 1.754226 GGAACCTGTGAACCAAAGCAA 59.246 47.619 0.00 0.00 0.00 3.91
420 723 7.537596 TTTTTCCTTTCATGCATCTTTAGGA 57.462 32.000 0.00 4.24 0.00 2.94
447 750 7.707624 TGCAATCCTATTCAATTCTTGTCTT 57.292 32.000 0.00 0.00 0.00 3.01
449 752 8.814235 CAAATGCAATCCTATTCAATTCTTGTC 58.186 33.333 0.00 0.00 0.00 3.18
451 754 8.712285 ACAAATGCAATCCTATTCAATTCTTG 57.288 30.769 0.00 0.00 0.00 3.02
511 814 2.955660 CCTTAACCCAAACACTCAAGCA 59.044 45.455 0.00 0.00 0.00 3.91
530 833 5.652452 GGATTACTGTGTTTTTCCTATGCCT 59.348 40.000 0.00 0.00 0.00 4.75
531 834 5.652452 AGGATTACTGTGTTTTTCCTATGCC 59.348 40.000 0.00 0.00 31.93 4.40
564 867 8.344831 TCATGTAGTTTGTCTTTGATTTGACTG 58.655 33.333 0.00 0.00 34.57 3.51
584 887 7.165485 ACATGCTAACTGTACCTTTTCATGTA 58.835 34.615 15.09 0.00 39.80 2.29
629 932 2.415491 CCTATGCACGAAGAACGAGACA 60.415 50.000 0.00 0.00 45.77 3.41
643 946 5.332743 ACCTCCTTTTCAAATTCCTATGCA 58.667 37.500 0.00 0.00 0.00 3.96
646 949 7.730332 ACTTTGACCTCCTTTTCAAATTCCTAT 59.270 33.333 0.00 0.00 40.16 2.57
719 1025 8.311109 GGTTCAAAGGAATATAGCAAAGGAAAA 58.689 33.333 0.00 0.00 35.05 2.29
812 1137 8.940397 TCCTTTGATTCATAGGAAAACTTCTT 57.060 30.769 19.76 0.00 38.33 2.52
813 1138 7.613411 CCTCCTTTGATTCATAGGAAAACTTCT 59.387 37.037 21.55 0.00 40.12 2.85
814 1139 7.394641 ACCTCCTTTGATTCATAGGAAAACTTC 59.605 37.037 21.55 0.00 40.12 3.01
852 1177 4.334443 CATTTTGACGCACATGCTACTAC 58.666 43.478 1.82 0.00 39.32 2.73
853 1178 3.181511 GCATTTTGACGCACATGCTACTA 60.182 43.478 1.82 0.00 39.32 1.82
854 1179 2.414559 GCATTTTGACGCACATGCTACT 60.415 45.455 1.82 0.00 39.32 2.57
891 1216 6.316890 TGTTTGTTTTAGTAGTTGACCTGGTC 59.683 38.462 19.96 19.96 0.00 4.02
926 1251 2.203139 TTGTGGTGTGCCTCCGTG 60.203 61.111 0.00 0.00 35.27 4.94
938 1263 3.977244 GGCCTTGTGCGGTTGTGG 61.977 66.667 0.00 0.00 42.61 4.17
1551 1892 3.453679 AGCTCCGAGCCTTCGTCC 61.454 66.667 16.99 0.00 43.77 4.79
1778 2123 0.881118 AATTTGCGGCAATGTCGACT 59.119 45.000 17.19 0.00 29.41 4.18
2099 2444 4.658786 AACTCCCCGTGCTCCCCT 62.659 66.667 0.00 0.00 0.00 4.79
2244 2589 0.178876 TGATCCTCCAAGACCCACCA 60.179 55.000 0.00 0.00 0.00 4.17
2449 2800 7.694093 ACTAGAGAGGAAGAAATGAAATTGGT 58.306 34.615 0.00 0.00 36.10 3.67
2465 2816 4.349636 TGAGGGAGTAGATGACTAGAGAGG 59.650 50.000 0.00 0.00 39.06 3.69
2483 2834 4.884164 GGTCATCTATTTTGGAACTGAGGG 59.116 45.833 0.00 0.00 0.00 4.30
2485 2836 5.500234 TGGGTCATCTATTTTGGAACTGAG 58.500 41.667 0.00 0.00 0.00 3.35
2488 2839 5.892348 AGTTGGGTCATCTATTTTGGAACT 58.108 37.500 0.00 0.00 0.00 3.01
2492 2843 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
2500 2851 8.038944 TCAGTGTTAGTATAAAGTTGGGTCATC 58.961 37.037 0.00 0.00 0.00 2.92
2502 2853 7.156673 GTCAGTGTTAGTATAAAGTTGGGTCA 58.843 38.462 0.00 0.00 0.00 4.02
2506 2857 8.603242 AACTGTCAGTGTTAGTATAAAGTTGG 57.397 34.615 6.18 0.00 0.00 3.77
2515 2866 9.826574 AATGAAGTAAAACTGTCAGTGTTAGTA 57.173 29.630 19.43 8.94 31.93 1.82
2517 2868 8.826710 TCAATGAAGTAAAACTGTCAGTGTTAG 58.173 33.333 14.80 3.49 35.26 2.34
2518 2869 8.725405 TCAATGAAGTAAAACTGTCAGTGTTA 57.275 30.769 11.02 11.02 35.26 2.41
2519 2870 7.624360 TCAATGAAGTAAAACTGTCAGTGTT 57.376 32.000 13.02 13.02 35.26 3.32
2581 2943 4.816385 TCAGCCGGTTGATTTCTATCATTC 59.184 41.667 17.98 0.00 40.37 2.67
2606 2968 4.764336 CGGCGGACGCAACGAGTA 62.764 66.667 18.95 0.00 44.11 2.59
2622 2984 3.554692 GAACGCTGATGGACGCCG 61.555 66.667 0.00 0.00 0.00 6.46
2623 2985 3.554692 CGAACGCTGATGGACGCC 61.555 66.667 0.00 0.00 0.00 5.68
2634 2996 4.443394 ACACGATAAAATAGGATCGAACGC 59.557 41.667 10.92 0.00 46.19 4.84
2690 3053 6.430864 TGCCTGGAGGATAAAATTTATGTGA 58.569 36.000 2.58 0.00 37.39 3.58
2695 3058 4.215109 GGCTGCCTGGAGGATAAAATTTA 58.785 43.478 12.43 0.00 37.39 1.40
2700 3063 1.143684 GATGGCTGCCTGGAGGATAAA 59.856 52.381 21.03 0.00 37.39 1.40
2727 3090 2.239907 GGAGGTGCCTACAGGAAAAGAT 59.760 50.000 0.00 0.00 37.39 2.40
2744 3115 1.683917 ACGAGAGATTGATTCGGGAGG 59.316 52.381 0.00 0.00 38.58 4.30
2749 3120 3.775202 AGTTGGACGAGAGATTGATTCG 58.225 45.455 0.00 0.00 40.02 3.34
2768 3139 4.008933 GCAGTGTGCCCTCGGAGT 62.009 66.667 4.02 0.00 37.42 3.85
2787 3158 2.499693 TGCTTGCAGCCATAGTAGTACA 59.500 45.455 2.52 0.00 41.51 2.90
2788 3159 3.179443 TGCTTGCAGCCATAGTAGTAC 57.821 47.619 5.82 0.00 41.51 2.73
2813 3184 0.755327 AACAACACCACCCAAGGAGC 60.755 55.000 0.00 0.00 0.00 4.70
2825 3196 2.116366 GATGACGGTTTGCAACAACAC 58.884 47.619 0.00 0.00 0.00 3.32
2864 3235 1.691482 CGAAGGAGAGGGGTGGGATAA 60.691 57.143 0.00 0.00 0.00 1.75
2874 3245 3.502123 ATAGGAGAGACGAAGGAGAGG 57.498 52.381 0.00 0.00 0.00 3.69
3027 3398 1.000060 GCAATATGCCAACATCGCCAT 60.000 47.619 0.00 0.00 37.42 4.40
3089 3466 2.176273 ATCATCGACCGCTTGCAGC 61.176 57.895 0.00 0.00 38.02 5.25
3103 3480 2.321263 CTGCCCGAGCTCCACATCAT 62.321 60.000 8.47 0.00 40.80 2.45
3141 3518 7.269316 TGCAACATTGATGATATTTCTGCAAT 58.731 30.769 0.00 0.00 31.20 3.56
3151 3528 7.878547 TTGTATTCCTGCAACATTGATGATA 57.121 32.000 0.00 0.00 0.00 2.15
3195 3572 0.534877 ATGTTGCAGAAGCGTCACCA 60.535 50.000 1.61 0.00 46.23 4.17
3196 3573 1.438651 TATGTTGCAGAAGCGTCACC 58.561 50.000 1.61 0.00 46.23 4.02
3197 3574 3.372206 AGATTATGTTGCAGAAGCGTCAC 59.628 43.478 1.61 0.00 46.23 3.67
3198 3575 3.599343 AGATTATGTTGCAGAAGCGTCA 58.401 40.909 1.61 0.00 46.23 4.35
3233 3613 4.385358 AACAGTCTTGTTGCGGATTTTT 57.615 36.364 0.00 0.00 45.54 1.94


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

AutoCloner maintained by Alex Coulton.