Multiple sequence alignment - TraesCS2B01G134300

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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 TraesCS2B01G134300 chr2B 100.000 3121 0 0 1 3121 100344270 100341150 0.000000e+00 5764.0
1 TraesCS2B01G134300 chr2B 77.174 276 46 12 1001 1269 29005775 29005510 9.020000e-31 145.0
2 TraesCS2B01G134300 chr2B 87.500 48 6 0 463 510 225436036 225436083 4.350000e-04 56.5
3 TraesCS2B01G134300 chr2D 93.398 2484 128 21 375 2845 64192155 64189695 0.000000e+00 3646.0
4 TraesCS2B01G134300 chr2D 94.038 369 22 0 1 369 64192559 64192191 7.560000e-156 560.0
5 TraesCS2B01G134300 chr2D 91.873 283 10 2 2846 3115 64189658 64189376 1.760000e-102 383.0
6 TraesCS2B01G134300 chr2A 91.784 2349 152 23 504 2845 65674757 65672443 0.000000e+00 3230.0
7 TraesCS2B01G134300 chr2A 86.059 373 47 3 1 369 65675257 65674886 2.260000e-106 396.0
8 TraesCS2B01G134300 chr2A 88.112 286 15 4 2844 3115 65672408 65672128 3.880000e-84 322.0
9 TraesCS2B01G134300 chr2A 91.765 85 7 0 380 464 65674845 65674761 5.470000e-23 119.0
10 TraesCS2B01G134300 chr2A 88.679 53 6 0 465 517 605168561 605168509 7.220000e-07 65.8
11 TraesCS2B01G134300 chr2A 89.796 49 3 2 463 510 581481416 581481369 9.350000e-06 62.1
12 TraesCS2B01G134300 chr4A 78.966 290 50 10 988 1269 211000041 211000327 1.480000e-43 187.0
13 TraesCS2B01G134300 chr4D 78.983 295 42 15 985 1269 291737042 291736758 1.910000e-42 183.0
14 TraesCS2B01G134300 chr4B 85.714 147 21 0 1123 1269 273688491 273688637 4.170000e-34 156.0
15 TraesCS2B01G134300 chr4B 76.897 290 54 10 985 1269 565112011 565112292 5.390000e-33 152.0
16 TraesCS2B01G134300 chr7B 84.722 144 22 0 1126 1269 613375179 613375036 9.020000e-31 145.0
17 TraesCS2B01G134300 chr7B 76.207 290 56 10 985 1269 709129001 709129282 1.170000e-29 141.0
18 TraesCS2B01G134300 chr6A 100.000 37 0 0 463 499 205095210 205095174 5.590000e-08 69.4
19 TraesCS2B01G134300 chr5B 95.238 42 2 0 463 504 259541744 259541703 2.010000e-07 67.6
20 TraesCS2B01G134300 chr5B 97.297 37 1 0 463 499 8543965 8543929 2.600000e-06 63.9
21 TraesCS2B01G134300 chr1A 97.297 37 1 0 463 499 572016786 572016822 2.600000e-06 63.9
22 TraesCS2B01G134300 chr6D 89.362 47 5 0 465 511 26757906 26757860 3.360000e-05 60.2


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 TraesCS2B01G134300 chr2B 100341150 100344270 3120 True 5764.000000 5764 100.000 1 3121 1 chr2B.!!$R2 3120
1 TraesCS2B01G134300 chr2D 64189376 64192559 3183 True 1529.666667 3646 93.103 1 3115 3 chr2D.!!$R1 3114
2 TraesCS2B01G134300 chr2A 65672128 65675257 3129 True 1016.750000 3230 89.430 1 3115 4 chr2A.!!$R3 3114

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
749 791 0.250338 GACCACTTTCCTGTTCGGCT 60.25 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2383 2430 1.134995 CAGGTCATAAGAGCAGCGACA 60.135 52.381 0.0 0.0 44.6 4.35 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
76 77 0.697079 CCATCCTCCCCAGATCCATG 59.303 60.000 0.00 0.00 0.00 3.66
84 85 1.386533 CCCAGATCCATGCACTGTTC 58.613 55.000 0.00 0.00 0.00 3.18
90 91 2.097160 CATGCACTGTTCGCGCTC 59.903 61.111 5.56 0.00 0.00 5.03
139 140 1.721664 CGAGTTATCGCCGGACCTGA 61.722 60.000 5.05 0.00 42.97 3.86
142 143 1.485066 AGTTATCGCCGGACCTGAATT 59.515 47.619 5.05 0.00 0.00 2.17
162 163 2.512692 TGGGGATGATTTGTGTCCTG 57.487 50.000 0.00 0.00 32.55 3.86
267 269 1.413445 CAGAGGATGCCAGAGAGAAGG 59.587 57.143 0.00 0.00 0.00 3.46
281 283 5.604650 CAGAGAGAAGGGATAGGGTTTATGT 59.395 44.000 0.00 0.00 0.00 2.29
288 290 6.749036 AGGGATAGGGTTTATGTCTGTAAG 57.251 41.667 0.00 0.00 0.00 2.34
290 293 6.677076 AGGGATAGGGTTTATGTCTGTAAGTT 59.323 38.462 0.00 0.00 33.76 2.66
295 298 9.901172 ATAGGGTTTATGTCTGTAAGTTTTAGG 57.099 33.333 0.00 0.00 33.76 2.69
313 316 8.251026 AGTTTTAGGCATTTTTAGTAATGAGGC 58.749 33.333 0.00 0.00 37.65 4.70
329 332 3.911868 TGAGGCAATTTCCGATTGTTTG 58.088 40.909 1.30 0.00 0.00 2.93
343 349 0.821711 TGTTTGGTGCCAGTGGTAGC 60.822 55.000 21.13 21.13 36.39 3.58
369 375 4.145876 TGTTGCGATTGATTTCACTGAC 57.854 40.909 0.00 0.00 0.00 3.51
371 377 4.153986 GTTGCGATTGATTTCACTGACAG 58.846 43.478 0.00 0.00 0.00 3.51
373 379 3.433274 TGCGATTGATTTCACTGACAGTC 59.567 43.478 4.74 0.00 0.00 3.51
378 414 6.977502 CGATTGATTTCACTGACAGTCTAGAT 59.022 38.462 4.74 0.00 0.00 1.98
384 420 5.042463 TCACTGACAGTCTAGATCCTAGG 57.958 47.826 4.74 0.82 0.00 3.02
403 439 2.062636 GGGGATTATAGGCTGGTTGGA 58.937 52.381 0.00 0.00 0.00 3.53
415 451 1.806542 CTGGTTGGATGTTTGGTCGAG 59.193 52.381 0.00 0.00 0.00 4.04
627 663 3.378427 CCTACTATGCTTGCCTGGTTTTC 59.622 47.826 0.00 0.00 0.00 2.29
651 688 3.495331 TCAAAAACTATGCTTGCCTGGA 58.505 40.909 0.00 0.00 0.00 3.86
675 712 0.899720 GGTCGGGGTACTGATCAACA 59.100 55.000 0.00 0.00 33.11 3.33
735 777 3.430453 TCTTGAATGGGAATTGGACCAC 58.570 45.455 0.00 0.00 40.05 4.16
745 787 3.255888 GGAATTGGACCACTTTCCTGTTC 59.744 47.826 21.01 5.84 36.51 3.18
749 791 0.250338 GACCACTTTCCTGTTCGGCT 60.250 55.000 0.00 0.00 0.00 5.52
789 831 1.209898 GCTATGTTGCGCAGTTGCA 59.790 52.632 11.31 9.32 44.61 4.08
877 919 7.931015 TCTGGGTTTGATATATGGAACTAGT 57.069 36.000 0.00 0.00 0.00 2.57
935 979 2.037251 TCCTTTGCAACTAGTCTCGCTT 59.963 45.455 0.00 0.00 0.00 4.68
950 994 7.938563 AGTCTCGCTTCTAAATATGAATGTC 57.061 36.000 0.00 0.00 0.00 3.06
973 1017 1.703438 CTTCGATGACCTGCAGCAGC 61.703 60.000 17.81 4.92 42.57 5.25
1065 1109 5.899299 AGGAAGTGGTACGTATTGATGTAC 58.101 41.667 0.00 0.00 44.30 2.90
1069 1113 6.276832 AGTGGTACGTATTGATGTACTGTT 57.723 37.500 0.00 0.00 44.41 3.16
1100 1144 1.881973 CAGTACTGTGGCATTGCAACT 59.118 47.619 16.86 0.62 32.93 3.16
1260 1304 1.038130 CCCTCTCTGGATTCGTCCGT 61.038 60.000 0.00 0.00 38.35 4.69
1293 1337 6.157994 TGTTTTACCCTTGCTATATCCTGACT 59.842 38.462 0.00 0.00 0.00 3.41
1296 1340 2.232452 CCCTTGCTATATCCTGACTCCG 59.768 54.545 0.00 0.00 0.00 4.63
1318 1362 6.038382 TCCGTTTATTTGTCTTAAAGCACACA 59.962 34.615 0.00 0.00 0.00 3.72
1377 1421 4.274950 TCTCACGAAATGGGTTGTTTTCTC 59.725 41.667 0.00 0.00 31.20 2.87
1403 1447 3.616956 TTGTCTGTCTAGCTGATTGGG 57.383 47.619 0.00 0.00 0.00 4.12
1433 1477 3.710326 ATCATGACATTGACATGCTGC 57.290 42.857 19.86 0.00 43.03 5.25
1460 1504 8.543774 CAGTAGTTTCTTAAGATATCCTTTGCG 58.456 37.037 5.89 0.00 36.34 4.85
1507 1551 9.967346 GTAGTATTCTCTATTCTGCACACATTA 57.033 33.333 0.00 0.00 0.00 1.90
1667 1712 6.206634 AGGTTCATTCACTAATTCGCTTCAAA 59.793 34.615 0.00 0.00 0.00 2.69
1684 1729 5.344396 GCTTCAAACTTCTTTTATCTGCAGC 59.656 40.000 9.47 0.00 0.00 5.25
1730 1775 5.163258 ACACAGTTTGAGATTCTCCAGAACT 60.163 40.000 11.12 13.92 36.80 3.01
1835 1880 3.047718 CTTGGTCAGCTGCGCATGG 62.048 63.158 12.24 0.00 0.00 3.66
1868 1914 4.873827 ACTTGACTGCTGAAACGTTTTCTA 59.126 37.500 15.89 3.78 0.00 2.10
1872 1918 6.791303 TGACTGCTGAAACGTTTTCTATTTT 58.209 32.000 15.89 0.00 0.00 1.82
1974 2021 5.986936 TCTGTACGACGATAATGACTGATC 58.013 41.667 0.00 0.00 0.00 2.92
2003 2050 4.759782 AGTGGTGGTGAGATCTTAATTCG 58.240 43.478 0.00 0.00 0.00 3.34
2129 2176 5.655974 TGAGATCAAGCAGTAGATGAGTTCT 59.344 40.000 0.00 0.00 38.57 3.01
2153 2200 5.057149 GCGAGGAAGATTTTGCTAGGATAA 58.943 41.667 0.49 0.00 34.85 1.75
2249 2296 3.066291 TGATAAAACCGTGGACTGCAT 57.934 42.857 0.00 0.00 0.00 3.96
2320 2367 6.259608 CCATGAATGGTCTATGTTTCTCAGAC 59.740 42.308 0.82 0.00 43.05 3.51
2383 2430 8.149647 TGTACCTGAATTCTGAAATGCATTTTT 58.850 29.630 24.81 14.91 29.72 1.94
2399 2446 4.672542 GCATTTTTGTCGCTGCTCTTATGA 60.673 41.667 0.00 0.00 0.00 2.15
2400 2447 4.404507 TTTTTGTCGCTGCTCTTATGAC 57.595 40.909 0.00 0.00 0.00 3.06
2431 2478 4.440663 GGATTATTGTGCTTGCTTTCTCCC 60.441 45.833 0.00 0.00 0.00 4.30
2469 2516 3.120041 GCTGTTTGCCGTTAAATGTGTT 58.880 40.909 0.00 0.00 35.15 3.32
2478 2525 5.650266 TGCCGTTAAATGTGTTGGATTCTAT 59.350 36.000 0.00 0.00 0.00 1.98
2519 2566 9.274206 AGAAGTCTCTTTACAAACTAAACCATC 57.726 33.333 0.00 0.00 0.00 3.51
2551 2598 6.285329 ACATGGGGGAGATTCATAGAAATT 57.715 37.500 0.00 0.00 0.00 1.82
2554 2601 4.140947 TGGGGGAGATTCATAGAAATTGGG 60.141 45.833 0.00 0.00 0.00 4.12
2555 2602 3.829026 GGGGAGATTCATAGAAATTGGGC 59.171 47.826 0.00 0.00 0.00 5.36
2557 2604 4.895297 GGGAGATTCATAGAAATTGGGCAA 59.105 41.667 0.00 0.00 0.00 4.52
2558 2605 5.010415 GGGAGATTCATAGAAATTGGGCAAG 59.990 44.000 0.00 0.00 0.00 4.01
2559 2606 5.829924 GGAGATTCATAGAAATTGGGCAAGA 59.170 40.000 0.00 0.00 0.00 3.02
2564 2612 5.192927 TCATAGAAATTGGGCAAGATTCGT 58.807 37.500 0.00 0.00 0.00 3.85
2575 2623 5.116882 GGGCAAGATTCGTGTATCTAACTT 58.883 41.667 1.61 0.00 33.81 2.66
2702 2750 4.570369 ACAAATGTGTAAAAGCAACTTGCC 59.430 37.500 10.25 0.00 39.44 4.52
2719 2770 5.263599 ACTTGCCATGGTTGATTCTTGATA 58.736 37.500 14.67 0.00 0.00 2.15
2720 2771 5.359009 ACTTGCCATGGTTGATTCTTGATAG 59.641 40.000 14.67 0.00 0.00 2.08
2721 2772 4.209538 TGCCATGGTTGATTCTTGATAGG 58.790 43.478 14.67 0.00 0.00 2.57
2723 2774 4.689705 GCCATGGTTGATTCTTGATAGGGA 60.690 45.833 14.67 0.00 0.00 4.20
2724 2775 5.068636 CCATGGTTGATTCTTGATAGGGAG 58.931 45.833 2.57 0.00 0.00 4.30
2725 2776 5.398353 CCATGGTTGATTCTTGATAGGGAGT 60.398 44.000 2.57 0.00 0.00 3.85
2726 2777 5.779241 TGGTTGATTCTTGATAGGGAGTT 57.221 39.130 0.00 0.00 0.00 3.01
2727 2778 5.745227 TGGTTGATTCTTGATAGGGAGTTC 58.255 41.667 0.00 0.00 0.00 3.01
2728 2779 5.126779 GGTTGATTCTTGATAGGGAGTTCC 58.873 45.833 0.00 0.00 0.00 3.62
2737 2788 2.854253 AGGGAGTTCCTGTTGCAGA 58.146 52.632 0.00 0.00 46.07 4.26
2738 2789 1.366319 AGGGAGTTCCTGTTGCAGAT 58.634 50.000 0.00 0.00 46.07 2.90
2739 2790 1.004044 AGGGAGTTCCTGTTGCAGATG 59.996 52.381 0.00 0.00 46.07 2.90
2740 2791 1.271597 GGGAGTTCCTGTTGCAGATGT 60.272 52.381 0.00 0.00 32.44 3.06
2741 2792 2.508526 GGAGTTCCTGTTGCAGATGTT 58.491 47.619 0.00 0.00 32.44 2.71
2747 2798 3.489355 TCCTGTTGCAGATGTTTGATGT 58.511 40.909 0.00 0.00 32.44 3.06
2753 2804 4.888038 TGCAGATGTTTGATGTGCTATC 57.112 40.909 5.52 0.00 38.85 2.08
2757 2808 5.277393 GCAGATGTTTGATGTGCTATCTGAG 60.277 44.000 14.24 0.00 42.38 3.35
2780 2831 1.490490 ACAGAAGGCTCACAGGAAACA 59.510 47.619 0.00 0.00 0.00 2.83
2784 2835 1.680338 AGGCTCACAGGAAACAACAC 58.320 50.000 0.00 0.00 0.00 3.32
2801 2852 5.034152 ACAACACACTGCATTTAAAACTCG 58.966 37.500 0.00 0.00 0.00 4.18
2805 2856 6.503524 ACACACTGCATTTAAAACTCGAAAT 58.496 32.000 0.00 0.00 0.00 2.17
2823 2876 7.052565 TCGAAATAAACCGTTAGAACATCAC 57.947 36.000 0.00 0.00 0.00 3.06
2830 2883 1.135083 CGTTAGAACATCACGAGCCCT 60.135 52.381 0.00 0.00 35.93 5.19
2831 2884 2.674177 CGTTAGAACATCACGAGCCCTT 60.674 50.000 0.00 0.00 35.93 3.95
2848 2937 3.960755 GCCCTTGGTAGATAAAATTGCCT 59.039 43.478 0.00 0.00 0.00 4.75
2861 2950 2.557920 ATTGCCTAGTATCAGCAGCC 57.442 50.000 0.00 0.00 37.89 4.85
2890 2979 4.339814 AGCTGCTATAACTGTAGGAGACAC 59.660 45.833 0.00 0.00 41.17 3.67
2898 2987 4.644163 ACTGTAGGAGACACTGAGTACT 57.356 45.455 0.00 0.00 33.31 2.73
3056 3145 3.459710 AGGTGCTCTCCTACTTACAGT 57.540 47.619 0.00 0.00 35.87 3.55
3057 3146 3.093057 AGGTGCTCTCCTACTTACAGTG 58.907 50.000 0.00 0.00 35.87 3.66
3059 3148 3.090037 GTGCTCTCCTACTTACAGTGGA 58.910 50.000 0.00 0.00 0.00 4.02
3115 3217 2.278245 TCCACCATCATCCTCCAAAGT 58.722 47.619 0.00 0.00 0.00 2.66
3116 3218 2.239654 TCCACCATCATCCTCCAAAGTC 59.760 50.000 0.00 0.00 0.00 3.01
3117 3219 2.648059 CACCATCATCCTCCAAAGTCC 58.352 52.381 0.00 0.00 0.00 3.85
3118 3220 2.025981 CACCATCATCCTCCAAAGTCCA 60.026 50.000 0.00 0.00 0.00 4.02
3119 3221 2.649312 ACCATCATCCTCCAAAGTCCAA 59.351 45.455 0.00 0.00 0.00 3.53
3120 3222 3.075882 ACCATCATCCTCCAAAGTCCAAA 59.924 43.478 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 0.104777 TGGATCTGGGGAGGATGGAG 60.105 60.000 0.00 0.00 0.00 3.86
139 140 4.223477 CAGGACACAAATCATCCCCAAATT 59.777 41.667 0.00 0.00 32.47 1.82
142 143 2.806434 CAGGACACAAATCATCCCCAA 58.194 47.619 0.00 0.00 32.47 4.12
162 163 4.578601 GCGGATGCTAATCGTATAAATGC 58.421 43.478 0.00 0.00 38.39 3.56
267 269 8.803397 AAAACTTACAGACATAAACCCTATCC 57.197 34.615 0.00 0.00 0.00 2.59
288 290 8.032451 TGCCTCATTACTAAAAATGCCTAAAAC 58.968 33.333 0.00 0.00 36.89 2.43
290 293 7.710676 TGCCTCATTACTAAAAATGCCTAAA 57.289 32.000 0.00 0.00 36.89 1.85
295 298 7.254084 CGGAAATTGCCTCATTACTAAAAATGC 60.254 37.037 0.00 0.00 36.89 3.56
304 307 5.248870 ACAATCGGAAATTGCCTCATTAC 57.751 39.130 0.00 0.00 32.55 1.89
313 316 2.736192 GGCACCAAACAATCGGAAATTG 59.264 45.455 0.00 0.00 35.29 2.32
329 332 0.537371 AAACAGCTACCACTGGCACC 60.537 55.000 0.00 0.00 42.21 5.01
343 349 4.977963 AGTGAAATCAATCGCAACAAACAG 59.022 37.500 0.00 0.00 32.22 3.16
384 420 3.074538 ACATCCAACCAGCCTATAATCCC 59.925 47.826 0.00 0.00 0.00 3.85
403 439 3.815809 TCCAAGAAACTCGACCAAACAT 58.184 40.909 0.00 0.00 0.00 2.71
415 451 2.558359 CACCTGAACCCATCCAAGAAAC 59.442 50.000 0.00 0.00 0.00 2.78
493 529 6.795098 TTTAGCCAAATACACACACTGTAG 57.205 37.500 0.00 0.00 38.80 2.74
627 663 4.628333 CCAGGCAAGCATAGTTTTTGAATG 59.372 41.667 0.00 0.00 0.00 2.67
651 688 3.379445 CAGTACCCCGACCGTGCT 61.379 66.667 0.00 0.00 0.00 4.40
655 692 0.179119 GTTGATCAGTACCCCGACCG 60.179 60.000 0.00 0.00 0.00 4.79
718 755 3.195610 GGAAAGTGGTCCAATTCCCATTC 59.804 47.826 20.26 8.69 37.65 2.67
735 777 1.363744 CTAGCAGCCGAACAGGAAAG 58.636 55.000 0.00 0.00 45.00 2.62
745 787 3.854669 CCAGACCCCTAGCAGCCG 61.855 72.222 0.00 0.00 0.00 5.52
749 791 0.984230 CAGAAACCAGACCCCTAGCA 59.016 55.000 0.00 0.00 0.00 3.49
801 843 7.120726 GTGGTTTATTCCAAATAGTACAGCTGT 59.879 37.037 25.12 25.12 39.34 4.40
895 939 9.555727 GCAAAGGACACTATGGTATAAAGATAA 57.444 33.333 0.00 0.00 0.00 1.75
896 940 8.710239 TGCAAAGGACACTATGGTATAAAGATA 58.290 33.333 0.00 0.00 0.00 1.98
950 994 1.396301 GCTGCAGGTCATCGAAGAAAG 59.604 52.381 17.12 0.00 43.58 2.62
973 1017 0.397254 ACTGGAGGGATACTGGGACG 60.397 60.000 0.00 0.00 0.00 4.79
1065 1109 5.234329 CACAGTACTGTAACCAAGACAACAG 59.766 44.000 27.48 6.98 42.83 3.16
1069 1113 3.493699 GCCACAGTACTGTAACCAAGACA 60.494 47.826 27.48 0.00 42.83 3.41
1100 1144 5.927689 CCAATACAAAGCAAGAATGAGCAAA 59.072 36.000 0.00 0.00 0.00 3.68
1143 1187 3.629398 CCTTGGCAGTTATGATCCTGTTC 59.371 47.826 0.00 0.00 0.00 3.18
1285 1329 5.422214 AGACAAATAAACGGAGTCAGGAT 57.578 39.130 0.00 0.00 45.00 3.24
1286 1330 4.884668 AGACAAATAAACGGAGTCAGGA 57.115 40.909 0.00 0.00 45.00 3.86
1293 1337 6.038382 TGTGTGCTTTAAGACAAATAAACGGA 59.962 34.615 0.00 0.00 0.00 4.69
1296 1340 7.700656 ACACTGTGTGCTTTAAGACAAATAAAC 59.299 33.333 13.50 0.00 36.98 2.01
1318 1362 3.450457 GGAGAATCTGGATCACTCACACT 59.550 47.826 14.44 0.00 33.73 3.55
1386 1430 8.441311 AATATTATCCCAATCAGCTAGACAGA 57.559 34.615 0.00 0.00 0.00 3.41
1433 1477 8.831550 GCAAAGGATATCTTAAGAAACTACTGG 58.168 37.037 9.71 1.76 34.78 4.00
1481 1525 8.879342 AATGTGTGCAGAATAGAGAATACTAC 57.121 34.615 0.00 0.00 0.00 2.73
1507 1551 2.863809 ACCGCTGAAATTCAAGGACTT 58.136 42.857 19.42 0.25 31.36 3.01
1592 1636 8.817100 TCATGCTACTGATCTAATAACAAAACG 58.183 33.333 0.00 0.00 0.00 3.60
1667 1712 8.970859 AATGTATAGCTGCAGATAAAAGAAGT 57.029 30.769 20.43 0.47 0.00 3.01
1835 1880 4.575885 TCAGCAGTCAAGTTACCAATACC 58.424 43.478 0.00 0.00 0.00 2.73
1868 1914 2.370849 ACACCCTACGACCAGTCAAAAT 59.629 45.455 0.00 0.00 0.00 1.82
1872 1918 2.519771 ATACACCCTACGACCAGTCA 57.480 50.000 0.00 0.00 0.00 3.41
1974 2021 5.350504 AGATCTCACCACCACTTAATCAG 57.649 43.478 0.00 0.00 0.00 2.90
2003 2050 4.083110 AGAGTTGCAGCAACAATCATGTAC 60.083 41.667 34.38 15.86 45.66 2.90
2129 2176 2.236146 TCCTAGCAAAATCTTCCTCGCA 59.764 45.455 0.00 0.00 0.00 5.10
2249 2296 2.557924 CAAGGTTTCCATAAGCACTGCA 59.442 45.455 3.30 0.00 0.00 4.41
2316 2363 4.331717 ACACCAAGTTTAGTGTTTCGTCTG 59.668 41.667 3.13 0.00 44.65 3.51
2320 2367 7.480542 GCATATTACACCAAGTTTAGTGTTTCG 59.519 37.037 12.43 1.91 44.65 3.46
2330 2377 4.949856 CCAGGAAGCATATTACACCAAGTT 59.050 41.667 0.00 0.00 0.00 2.66
2383 2430 1.134995 CAGGTCATAAGAGCAGCGACA 60.135 52.381 0.00 0.00 44.60 4.35
2399 2446 4.307032 AGCACAATAATCCAAGACAGGT 57.693 40.909 0.00 0.00 0.00 4.00
2400 2447 4.676196 GCAAGCACAATAATCCAAGACAGG 60.676 45.833 0.00 0.00 0.00 4.00
2431 2478 2.025887 ACAGCCCCTTCTCCAACTTATG 60.026 50.000 0.00 0.00 0.00 1.90
2457 2504 7.009174 GCCAAATAGAATCCAACACATTTAACG 59.991 37.037 0.00 0.00 0.00 3.18
2469 2516 4.139786 GAGCTGATGCCAAATAGAATCCA 58.860 43.478 0.00 0.00 40.80 3.41
2478 2525 3.517100 AGACTTCTAGAGCTGATGCCAAA 59.483 43.478 0.00 0.00 40.80 3.28
2541 2588 5.066375 CACGAATCTTGCCCAATTTCTATGA 59.934 40.000 0.00 0.00 0.00 2.15
2546 2593 3.575965 ACACGAATCTTGCCCAATTTC 57.424 42.857 0.00 0.00 0.00 2.17
2551 2598 4.161565 AGTTAGATACACGAATCTTGCCCA 59.838 41.667 0.00 0.00 37.41 5.36
2554 2601 9.851043 GATTAAAGTTAGATACACGAATCTTGC 57.149 33.333 0.00 0.00 37.41 4.01
2575 2623 5.199723 TGGTTGCTGGCTAATGATGATTAA 58.800 37.500 0.00 0.00 0.00 1.40
2678 2726 5.491973 GCAAGTTGCTTTTACACATTTGTG 58.508 37.500 20.71 9.10 45.02 3.33
2679 2727 4.570369 GGCAAGTTGCTTTTACACATTTGT 59.430 37.500 26.16 0.00 44.28 2.83
2688 2736 3.386078 TCAACCATGGCAAGTTGCTTTTA 59.614 39.130 26.16 11.60 44.28 1.52
2698 2746 4.646040 CCTATCAAGAATCAACCATGGCAA 59.354 41.667 13.04 0.00 0.00 4.52
2700 2748 3.571401 CCCTATCAAGAATCAACCATGGC 59.429 47.826 13.04 0.00 0.00 4.40
2702 2750 5.688807 ACTCCCTATCAAGAATCAACCATG 58.311 41.667 0.00 0.00 0.00 3.66
2720 2771 1.271597 ACATCTGCAACAGGAACTCCC 60.272 52.381 0.00 0.00 34.60 4.30
2721 2772 2.191128 ACATCTGCAACAGGAACTCC 57.809 50.000 0.00 0.00 34.60 3.85
2723 2774 3.554934 TCAAACATCTGCAACAGGAACT 58.445 40.909 0.00 0.00 43.88 3.01
2724 2775 3.988379 TCAAACATCTGCAACAGGAAC 57.012 42.857 0.00 0.00 31.51 3.62
2725 2776 3.890756 ACATCAAACATCTGCAACAGGAA 59.109 39.130 0.00 0.00 31.51 3.36
2726 2777 3.253921 CACATCAAACATCTGCAACAGGA 59.746 43.478 0.00 0.00 31.51 3.86
2727 2778 3.571571 CACATCAAACATCTGCAACAGG 58.428 45.455 0.00 0.00 31.51 4.00
2728 2779 2.984471 GCACATCAAACATCTGCAACAG 59.016 45.455 0.00 0.00 0.00 3.16
2729 2780 2.624364 AGCACATCAAACATCTGCAACA 59.376 40.909 0.00 0.00 0.00 3.33
2730 2781 3.293311 AGCACATCAAACATCTGCAAC 57.707 42.857 0.00 0.00 0.00 4.17
2731 2782 4.945543 AGATAGCACATCAAACATCTGCAA 59.054 37.500 0.00 0.00 0.00 4.08
2732 2783 4.334481 CAGATAGCACATCAAACATCTGCA 59.666 41.667 0.00 0.00 34.73 4.41
2733 2784 4.573607 TCAGATAGCACATCAAACATCTGC 59.426 41.667 4.83 0.00 39.34 4.26
2734 2785 6.047231 TCTCAGATAGCACATCAAACATCTG 58.953 40.000 0.00 0.00 40.34 2.90
2735 2786 6.231258 TCTCAGATAGCACATCAAACATCT 57.769 37.500 1.70 0.00 0.00 2.90
2736 2787 6.915544 TTCTCAGATAGCACATCAAACATC 57.084 37.500 1.70 0.00 0.00 3.06
2737 2788 6.656270 TGTTTCTCAGATAGCACATCAAACAT 59.344 34.615 9.01 0.00 0.00 2.71
2738 2789 5.997129 TGTTTCTCAGATAGCACATCAAACA 59.003 36.000 9.01 9.01 0.00 2.83
2739 2790 6.369890 TCTGTTTCTCAGATAGCACATCAAAC 59.630 38.462 1.70 4.04 46.77 2.93
2740 2791 6.466812 TCTGTTTCTCAGATAGCACATCAAA 58.533 36.000 1.70 0.00 46.77 2.69
2741 2792 6.041423 TCTGTTTCTCAGATAGCACATCAA 57.959 37.500 1.70 0.00 46.77 2.57
2753 2804 3.065655 CTGTGAGCCTTCTGTTTCTCAG 58.934 50.000 0.00 0.00 44.85 3.35
2757 2808 2.550830 TCCTGTGAGCCTTCTGTTTC 57.449 50.000 0.00 0.00 0.00 2.78
2780 2831 5.493133 TCGAGTTTTAAATGCAGTGTGTT 57.507 34.783 0.00 0.00 0.00 3.32
2784 2835 8.424731 GGTTTATTTCGAGTTTTAAATGCAGTG 58.575 33.333 0.00 0.00 0.00 3.66
2801 2852 7.052565 TCGTGATGTTCTAACGGTTTATTTC 57.947 36.000 0.00 0.00 37.87 2.17
2805 2856 3.922240 GCTCGTGATGTTCTAACGGTTTA 59.078 43.478 0.00 0.00 37.87 2.01
2823 2876 4.261197 GCAATTTTATCTACCAAGGGCTCG 60.261 45.833 0.00 0.00 0.00 5.03
2830 2883 9.778741 CTGATACTAGGCAATTTTATCTACCAA 57.221 33.333 0.00 0.00 0.00 3.67
2831 2884 7.878127 GCTGATACTAGGCAATTTTATCTACCA 59.122 37.037 0.00 0.00 0.00 3.25
2848 2937 2.910199 CTTGCTTGGCTGCTGATACTA 58.090 47.619 0.00 0.00 0.00 1.82
2882 2971 3.417101 CACAGAGTACTCAGTGTCTCCT 58.583 50.000 30.23 5.15 40.71 3.69
2890 2979 1.341209 TGTGGTGCACAGAGTACTCAG 59.659 52.381 24.44 18.88 39.62 3.35
2911 3000 1.074775 TGGATGGTGCTCACAACCC 59.925 57.895 2.21 0.00 29.81 4.11
3009 3098 1.866601 GCAACCTGGATTTTTGTGTGC 59.133 47.619 0.00 0.00 0.00 4.57
3057 3146 4.445019 GGGACATCAAGGAAGGAACTATCC 60.445 50.000 0.00 0.00 46.98 2.59
3059 3148 3.459969 GGGGACATCAAGGAAGGAACTAT 59.540 47.826 0.00 0.00 38.49 2.12


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

AutoCloner maintained by Alex Coulton.