Multiple sequence alignment - TraesCS2B01G448100

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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 TraesCS2B01G448100 chr2B 100.000 2660 0 0 1 2660 640766377 640763718 0.000000e+00 4913
1 TraesCS2B01G448100 chr2A 87.545 2754 129 82 1 2660 680358773 680356140 0.000000e+00 2988
2 TraesCS2B01G448100 chr2D 91.710 1713 66 35 562 2253 538055756 538054099 0.000000e+00 2307
3 TraesCS2B01G448100 chr2D 85.324 586 39 24 5 552 538056461 538055885 1.790000e-156 562
4 TraesCS2B01G448100 chr2D 87.467 383 20 10 2288 2660 538054093 538053729 1.470000e-112 416
5 TraesCS2B01G448100 chr2D 81.034 174 25 7 1065 1234 367089163 367089332 5.970000e-27 132
6 TraesCS2B01G448100 chr6D 90.659 182 14 3 1057 1237 139916316 139916495 3.420000e-59 239
7 TraesCS2B01G448100 chr6B 91.379 174 13 2 1065 1237 239729260 239729432 1.230000e-58 237
8 TraesCS2B01G448100 chr6A 91.379 174 13 2 1065 1237 183188186 183188358 1.230000e-58 237
9 TraesCS2B01G448100 chr1B 82.061 262 30 14 1069 1323 552474257 552474006 9.650000e-50 207
10 TraesCS2B01G448100 chr1D 86.631 187 23 2 1069 1254 410072045 410071860 3.470000e-49 206
11 TraesCS2B01G448100 chr1A 81.298 262 35 11 1069 1323 505925841 505925587 1.610000e-47 200


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 TraesCS2B01G448100 chr2B 640763718 640766377 2659 True 4913 4913 100.000 1 2660 1 chr2B.!!$R1 2659
1 TraesCS2B01G448100 chr2A 680356140 680358773 2633 True 2988 2988 87.545 1 2660 1 chr2A.!!$R1 2659
2 TraesCS2B01G448100 chr2D 538053729 538056461 2732 True 1095 2307 88.167 5 2660 3 chr2D.!!$R1 2655

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
623 809 0.399075 ACCTCACCCTAACCAAACCG 59.601 55.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 2648 0.039346 TTCAACGACGCGTATCACCA 60.039 50.0 13.97 0.0 39.99 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
35 36 2.359169 GGGTGGTGGAGAGCGATCA 61.359 63.158 2.38 0.00 0.00 2.92
71 72 2.185867 GGCGATACCGTTGGCTCA 59.814 61.111 0.00 0.00 38.24 4.26
129 132 4.752879 GGGCGCACGGAACTAGCA 62.753 66.667 10.83 0.00 0.00 3.49
222 229 1.008329 GAAAACACACGACCGACCAA 58.992 50.000 0.00 0.00 0.00 3.67
257 273 1.529948 AGTCAGTGGACCGAACCGA 60.530 57.895 0.00 0.00 45.48 4.69
259 275 0.666577 GTCAGTGGACCGAACCGAAG 60.667 60.000 0.00 0.00 38.12 3.79
260 276 3.939573 GTCAGTGGACCGAACCGAAGG 62.940 61.905 0.00 0.00 46.77 3.46
274 301 0.721718 CGAAGGCACGGAAAGCTAAG 59.278 55.000 0.00 0.00 0.00 2.18
282 309 1.826096 ACGGAAAGCTAAGGAGACTCC 59.174 52.381 14.15 14.15 42.68 3.85
306 333 2.530700 CGTAGAAGGAGACGCGATTTTC 59.469 50.000 15.93 9.16 31.49 2.29
313 340 2.456989 GAGACGCGATTTTCCGTATGA 58.543 47.619 15.93 0.00 37.87 2.15
343 390 2.802414 CTTTCGCCGCTGCAAAGC 60.802 61.111 0.00 0.00 37.32 3.51
344 391 3.541093 CTTTCGCCGCTGCAAAGCA 62.541 57.895 0.00 0.00 37.32 3.91
394 441 2.764010 TGCTCTCGGTATAAGCCAAGAA 59.236 45.455 0.00 0.00 35.12 2.52
411 458 2.490993 GAAGGGCCACGTGCATTTGG 62.491 60.000 10.91 11.37 43.89 3.28
418 466 2.668279 GCCACGTGCATTTGGTCTAAAG 60.668 50.000 10.91 0.00 40.77 1.85
420 468 3.364964 CCACGTGCATTTGGTCTAAAGAC 60.365 47.826 10.91 1.30 44.04 3.01
421 469 2.478894 ACGTGCATTTGGTCTAAAGACG 59.521 45.455 4.13 8.29 45.65 4.18
422 470 2.159707 CGTGCATTTGGTCTAAAGACGG 60.160 50.000 4.13 0.00 45.65 4.79
429 479 0.743345 GGTCTAAAGACGGGCGCAAT 60.743 55.000 10.83 0.00 45.65 3.56
435 485 4.160635 GACGGGCGCAATTCGTGG 62.161 66.667 18.67 0.00 41.07 4.94
524 588 0.943673 TGCGCGATTACCATTCCATG 59.056 50.000 12.10 0.00 0.00 3.66
559 745 8.512138 GCCAGAATAAAAAGTTGTAAAGAGCTA 58.488 33.333 0.00 0.00 0.00 3.32
601 787 1.596260 CACTACGCGTAGAGAATCGGA 59.404 52.381 43.57 11.97 42.67 4.55
623 809 0.399075 ACCTCACCCTAACCAAACCG 59.601 55.000 0.00 0.00 0.00 4.44
646 837 4.498345 GGCACTGCTCAGTATAGTACAGAC 60.498 50.000 1.79 0.00 40.20 3.51
689 880 3.282157 CGCACCTGCACTGCACTT 61.282 61.111 11.29 0.00 42.21 3.16
706 897 1.841663 CTTGCGCACCAGTACACACC 61.842 60.000 11.12 0.00 0.00 4.16
725 916 3.761752 CACCCCACCAAATAATCGAAAGT 59.238 43.478 0.00 0.00 0.00 2.66
726 917 3.761752 ACCCCACCAAATAATCGAAAGTG 59.238 43.478 0.00 0.00 0.00 3.16
727 918 3.428862 CCCCACCAAATAATCGAAAGTGC 60.429 47.826 0.00 0.00 0.00 4.40
728 919 3.192422 CCCACCAAATAATCGAAAGTGCA 59.808 43.478 0.00 0.00 0.00 4.57
729 920 4.321601 CCCACCAAATAATCGAAAGTGCAA 60.322 41.667 0.00 0.00 0.00 4.08
730 921 5.226396 CCACCAAATAATCGAAAGTGCAAA 58.774 37.500 0.00 0.00 0.00 3.68
731 922 5.694006 CCACCAAATAATCGAAAGTGCAAAA 59.306 36.000 0.00 0.00 0.00 2.44
732 923 6.128849 CCACCAAATAATCGAAAGTGCAAAAG 60.129 38.462 0.00 0.00 0.00 2.27
743 934 8.077836 TCGAAAGTGCAAAAGAAAAAGAAAAA 57.922 26.923 0.00 0.00 0.00 1.94
783 974 4.373116 GGAGGAACAGACGGCGCA 62.373 66.667 10.83 0.00 0.00 6.09
936 1127 1.040339 GCCAGACCAACCAACCAACA 61.040 55.000 0.00 0.00 0.00 3.33
944 1135 3.959975 CCAACCAACACCGCACCG 61.960 66.667 0.00 0.00 0.00 4.94
984 1196 3.764049 GCGCACGGTCGAACACTC 61.764 66.667 0.30 0.00 0.00 3.51
986 1198 3.103911 GCACGGTCGAACACTCGG 61.104 66.667 0.00 0.00 45.49 4.63
991 1203 3.173240 GTCGAACACTCGGCGCTC 61.173 66.667 7.64 0.00 45.49 5.03
992 1204 4.415332 TCGAACACTCGGCGCTCC 62.415 66.667 7.64 0.00 45.49 4.70
1323 1535 4.406173 AGCAGCACCGTCGAGTCG 62.406 66.667 6.09 6.09 0.00 4.18
1372 1599 3.429141 CCGCTCCTGCTGTTGCTG 61.429 66.667 0.00 0.00 40.48 4.41
1373 1600 4.099170 CGCTCCTGCTGTTGCTGC 62.099 66.667 0.00 0.00 40.48 5.25
1374 1601 3.745803 GCTCCTGCTGTTGCTGCC 61.746 66.667 0.00 0.00 40.48 4.85
1375 1602 3.060615 CTCCTGCTGTTGCTGCCC 61.061 66.667 0.00 0.00 40.48 5.36
1376 1603 4.666253 TCCTGCTGTTGCTGCCCC 62.666 66.667 0.00 0.00 40.48 5.80
1550 1777 2.063015 ATGAACAAGGTGGCGTCCCA 62.063 55.000 0.00 0.00 39.32 4.37
1933 2169 5.227569 ACAATTTCCTTAAAAGCAAGGGG 57.772 39.130 2.23 0.00 44.53 4.79
1938 2174 5.545063 TTCCTTAAAAGCAAGGGGAAAAG 57.455 39.130 2.23 0.00 44.53 2.27
2055 2299 4.641094 TCCATTCTTAACCGTGTGTTGTTT 59.359 37.500 0.00 0.00 37.83 2.83
2058 2302 6.973474 CCATTCTTAACCGTGTGTTGTTTTTA 59.027 34.615 0.00 0.00 37.83 1.52
2059 2303 7.650104 CCATTCTTAACCGTGTGTTGTTTTTAT 59.350 33.333 0.00 0.00 37.83 1.40
2083 2327 0.953471 TCGGTGTATGGCTGTTGTGC 60.953 55.000 0.00 0.00 0.00 4.57
2085 2329 1.176527 GGTGTATGGCTGTTGTGCAT 58.823 50.000 0.00 0.00 34.04 3.96
2086 2330 1.135315 GGTGTATGGCTGTTGTGCATG 60.135 52.381 0.00 0.00 34.04 4.06
2087 2331 1.811965 GTGTATGGCTGTTGTGCATGA 59.188 47.619 0.00 0.00 34.04 3.07
2088 2332 2.424601 GTGTATGGCTGTTGTGCATGAT 59.575 45.455 0.00 0.00 34.04 2.45
2089 2333 3.090790 TGTATGGCTGTTGTGCATGATT 58.909 40.909 0.00 0.00 34.04 2.57
2090 2334 4.096231 GTGTATGGCTGTTGTGCATGATTA 59.904 41.667 0.00 0.00 34.04 1.75
2091 2335 4.888823 TGTATGGCTGTTGTGCATGATTAT 59.111 37.500 0.00 0.00 34.04 1.28
2092 2336 3.786516 TGGCTGTTGTGCATGATTATG 57.213 42.857 0.00 0.00 37.36 1.90
2093 2337 2.427812 TGGCTGTTGTGCATGATTATGG 59.572 45.455 0.00 0.00 34.79 2.74
2094 2338 2.428171 GGCTGTTGTGCATGATTATGGT 59.572 45.455 0.00 0.00 34.79 3.55
2095 2339 3.119029 GGCTGTTGTGCATGATTATGGTT 60.119 43.478 0.00 0.00 34.79 3.67
2096 2340 4.497300 GCTGTTGTGCATGATTATGGTTT 58.503 39.130 0.00 0.00 34.79 3.27
2097 2341 5.394005 GGCTGTTGTGCATGATTATGGTTTA 60.394 40.000 0.00 0.00 34.79 2.01
2098 2342 6.275335 GCTGTTGTGCATGATTATGGTTTAT 58.725 36.000 0.00 0.00 34.79 1.40
2099 2343 6.418819 GCTGTTGTGCATGATTATGGTTTATC 59.581 38.462 0.00 0.00 34.79 1.75
2100 2344 7.643569 TGTTGTGCATGATTATGGTTTATCT 57.356 32.000 0.00 0.00 34.79 1.98
2101 2345 7.706159 TGTTGTGCATGATTATGGTTTATCTC 58.294 34.615 0.00 0.00 34.79 2.75
2123 2378 6.037720 TCTCTGATTAGTCGATCTGTCTTGAC 59.962 42.308 0.00 0.00 0.00 3.18
2192 2450 8.992073 GGGTATCTACTAACTTGTTTTTCGAAA 58.008 33.333 6.47 6.47 0.00 3.46
2240 2498 4.273148 AGCAAGTTCTTATGTTCGGACT 57.727 40.909 0.00 0.00 0.00 3.85
2253 2511 4.193090 TGTTCGGACTAGCAAAAGAAACA 58.807 39.130 0.00 0.00 0.00 2.83
2265 2523 5.067283 AGCAAAAGAAACAACTCCGTGTTAT 59.933 36.000 0.00 0.00 40.86 1.89
2272 2530 6.539464 AGAAACAACTCCGTGTTATTGTGTTA 59.461 34.615 0.00 0.00 40.86 2.41
2275 2533 6.514947 ACAACTCCGTGTTATTGTGTTAGTA 58.485 36.000 0.00 0.00 37.07 1.82
2276 2534 6.421801 ACAACTCCGTGTTATTGTGTTAGTAC 59.578 38.462 0.00 0.00 37.07 2.73
2324 2582 3.567478 ATGACTGCTGAAGATTACCCC 57.433 47.619 0.00 0.00 0.00 4.95
2328 2590 3.450904 ACTGCTGAAGATTACCCCTACA 58.549 45.455 0.00 0.00 0.00 2.74
2352 2614 3.193757 CGTTCATCGTCCTCCCGA 58.806 61.111 0.00 0.00 41.73 5.14
2388 2650 2.787249 CAGAATTGCGGACGCTGG 59.213 61.111 18.04 0.00 42.51 4.85
2389 2651 2.034879 CAGAATTGCGGACGCTGGT 61.035 57.895 18.04 2.39 42.51 4.00
2390 2652 2.034879 AGAATTGCGGACGCTGGTG 61.035 57.895 18.04 0.00 42.51 4.17
2391 2653 2.031919 AATTGCGGACGCTGGTGA 59.968 55.556 18.04 0.00 42.51 4.02
2416 2682 0.872388 GTCGTTGAATTGAACGGCCT 59.128 50.000 26.10 0.00 45.92 5.19
2417 2683 1.136057 GTCGTTGAATTGAACGGCCTC 60.136 52.381 26.10 12.89 45.92 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 130 4.147322 CGTGCGATTCGGTGGTGC 62.147 66.667 8.34 0.00 0.00 5.01
128 131 4.147322 GCGTGCGATTCGGTGGTG 62.147 66.667 8.34 0.00 0.00 4.17
129 132 4.673298 TGCGTGCGATTCGGTGGT 62.673 61.111 8.34 0.00 0.00 4.16
194 201 0.025770 CGTGTGTTTTCGCGTCAAGT 59.974 50.000 5.77 0.00 36.71 3.16
222 229 0.711184 ACTGGGCCTGAGGTACTACT 59.289 55.000 18.12 0.00 41.55 2.57
257 273 0.690762 TCCTTAGCTTTCCGTGCCTT 59.309 50.000 0.00 0.00 0.00 4.35
259 275 0.249398 TCTCCTTAGCTTTCCGTGCC 59.751 55.000 0.00 0.00 0.00 5.01
260 276 1.066787 AGTCTCCTTAGCTTTCCGTGC 60.067 52.381 0.00 0.00 0.00 5.34
261 277 2.417515 GGAGTCTCCTTAGCTTTCCGTG 60.418 54.545 12.02 0.00 32.53 4.94
262 278 1.826096 GGAGTCTCCTTAGCTTTCCGT 59.174 52.381 12.02 0.00 32.53 4.69
263 279 2.104170 AGGAGTCTCCTTAGCTTTCCG 58.896 52.381 16.28 0.00 46.91 4.30
285 312 2.190325 AAATCGCGTCTCCTTCTACG 57.810 50.000 5.77 0.00 41.92 3.51
293 320 2.456989 TCATACGGAAAATCGCGTCTC 58.543 47.619 5.77 0.00 0.00 3.36
343 390 4.640201 ACCAATGTCCACGGATTTAATCTG 59.360 41.667 11.83 11.83 41.49 2.90
344 391 4.855340 ACCAATGTCCACGGATTTAATCT 58.145 39.130 4.87 0.00 0.00 2.40
394 441 2.990967 CCAAATGCACGTGGCCCT 60.991 61.111 18.88 0.00 43.89 5.19
411 458 1.062148 GAATTGCGCCCGTCTTTAGAC 59.938 52.381 4.18 0.00 41.47 2.59
418 466 4.160635 CCACGAATTGCGCCCGTC 62.161 66.667 4.18 0.00 46.04 4.79
421 469 4.776647 GTGCCACGAATTGCGCCC 62.777 66.667 4.18 0.00 46.04 6.13
422 470 1.987704 TATGTGCCACGAATTGCGCC 61.988 55.000 4.18 0.00 46.04 6.53
435 485 2.542597 TGGTTCGGTATTCGTATGTGC 58.457 47.619 0.00 0.00 40.32 4.57
479 532 2.656560 ACATCTCGTTTTCCTCTCGG 57.343 50.000 0.00 0.00 0.00 4.63
484 537 4.319261 GCACGTTTTACATCTCGTTTTCCT 60.319 41.667 0.00 0.00 34.30 3.36
494 547 2.153680 AATCGCGCACGTTTTACATC 57.846 45.000 8.75 0.00 41.18 3.06
496 549 1.126479 GGTAATCGCGCACGTTTTACA 59.874 47.619 8.75 0.00 39.00 2.41
524 588 2.341846 TTTATTCTGGCCGTGGATCC 57.658 50.000 4.20 4.20 0.00 3.36
559 745 1.664016 CGTTAGTTCACGGCGTGTACT 60.664 52.381 40.05 40.05 44.13 2.73
560 746 0.704551 CGTTAGTTCACGGCGTGTAC 59.295 55.000 33.32 33.32 36.47 2.90
561 747 3.090598 CGTTAGTTCACGGCGTGTA 57.909 52.632 35.65 26.39 36.47 2.90
580 766 1.386961 CGATTCTCTACGCGTAGTGC 58.613 55.000 37.32 23.67 45.12 4.40
582 768 1.865970 CTCCGATTCTCTACGCGTAGT 59.134 52.381 37.32 23.45 34.84 2.73
583 769 1.865970 ACTCCGATTCTCTACGCGTAG 59.134 52.381 34.93 34.93 34.56 3.51
584 770 1.945387 ACTCCGATTCTCTACGCGTA 58.055 50.000 19.40 19.40 0.00 4.42
585 771 1.596727 GTACTCCGATTCTCTACGCGT 59.403 52.381 19.17 19.17 0.00 6.01
586 772 1.070041 GGTACTCCGATTCTCTACGCG 60.070 57.143 3.53 3.53 0.00 6.01
623 809 3.632604 TCTGTACTATACTGAGCAGTGCC 59.367 47.826 12.58 3.92 42.52 5.01
646 837 0.817634 TTGGTTGGTCGCTTGGTCAG 60.818 55.000 0.00 0.00 0.00 3.51
689 880 2.280524 GGTGTGTACTGGTGCGCA 60.281 61.111 5.66 5.66 33.47 6.09
706 897 3.192422 TGCACTTTCGATTATTTGGTGGG 59.808 43.478 0.00 0.00 0.00 4.61
743 934 3.707102 GCTAATACCTCTGTCCCTCTGTT 59.293 47.826 0.00 0.00 0.00 3.16
744 935 3.301274 GCTAATACCTCTGTCCCTCTGT 58.699 50.000 0.00 0.00 0.00 3.41
745 936 2.294791 CGCTAATACCTCTGTCCCTCTG 59.705 54.545 0.00 0.00 0.00 3.35
753 944 2.693591 TGTTCCTCCGCTAATACCTCTG 59.306 50.000 0.00 0.00 0.00 3.35
887 1078 3.237741 GGGGAGGAGAGGCGATGG 61.238 72.222 0.00 0.00 0.00 3.51
944 1135 4.560856 TTGTTGTTGCGGTGGCGC 62.561 61.111 0.00 0.00 44.10 6.53
989 1201 4.247380 GAGCCATGGGGAGCGGAG 62.247 72.222 15.13 0.00 35.59 4.63
993 1205 3.728292 CTTGGGAGCCATGGGGAGC 62.728 68.421 15.13 0.00 35.59 4.70
994 1206 1.574526 TTCTTGGGAGCCATGGGGAG 61.575 60.000 15.13 0.00 35.59 4.30
995 1207 1.543642 TTCTTGGGAGCCATGGGGA 60.544 57.895 15.13 0.00 35.59 4.81
996 1208 1.380380 GTTCTTGGGAGCCATGGGG 60.380 63.158 15.13 0.00 31.53 4.96
997 1209 1.750399 CGTTCTTGGGAGCCATGGG 60.750 63.158 15.13 0.00 31.53 4.00
1224 1436 2.358247 CCGACGGGGAAGTTGGTG 60.358 66.667 5.81 0.00 40.12 4.17
1256 1468 4.760047 GGAGCGGGATGTGCGTGT 62.760 66.667 0.00 0.00 37.44 4.49
1359 1586 4.666253 GGGGCAGCAACAGCAGGA 62.666 66.667 0.00 0.00 0.00 3.86
1550 1777 1.675972 TCGCTCTGCTCTTCCTCGT 60.676 57.895 0.00 0.00 0.00 4.18
1623 1850 4.329545 GGCGGCAGGTTCAGGTCA 62.330 66.667 3.07 0.00 0.00 4.02
1656 1883 2.717390 CGAGATCGGTCCATCTCCTAT 58.283 52.381 18.23 0.00 44.24 2.57
1807 2040 9.531158 GATCTATGTACACCTACTTACCCTTAT 57.469 37.037 0.00 0.00 0.00 1.73
1878 2111 4.202398 TGGGAGCAGATAGATGGATGTTTC 60.202 45.833 0.00 0.00 0.00 2.78
2041 2285 6.251801 CGAAGAAATAAAAACAACACACGGTT 59.748 34.615 0.00 0.00 41.47 4.44
2055 2299 5.250200 ACAGCCATACACCGAAGAAATAAA 58.750 37.500 0.00 0.00 0.00 1.40
2058 2302 3.350219 ACAGCCATACACCGAAGAAAT 57.650 42.857 0.00 0.00 0.00 2.17
2059 2303 2.811431 CAACAGCCATACACCGAAGAAA 59.189 45.455 0.00 0.00 0.00 2.52
2085 2329 9.914131 CGACTAATCAGAGATAAACCATAATCA 57.086 33.333 0.00 0.00 0.00 2.57
2089 2333 9.521841 AGATCGACTAATCAGAGATAAACCATA 57.478 33.333 0.00 0.00 0.00 2.74
2090 2334 8.303156 CAGATCGACTAATCAGAGATAAACCAT 58.697 37.037 0.00 0.00 0.00 3.55
2091 2335 7.285629 ACAGATCGACTAATCAGAGATAAACCA 59.714 37.037 0.00 0.00 0.00 3.67
2092 2336 7.653647 ACAGATCGACTAATCAGAGATAAACC 58.346 38.462 0.00 0.00 0.00 3.27
2093 2337 8.564574 AGACAGATCGACTAATCAGAGATAAAC 58.435 37.037 0.00 0.00 0.00 2.01
2094 2338 8.684386 AGACAGATCGACTAATCAGAGATAAA 57.316 34.615 0.00 0.00 0.00 1.40
2095 2339 8.563732 CAAGACAGATCGACTAATCAGAGATAA 58.436 37.037 0.00 0.00 0.00 1.75
2096 2340 7.934120 TCAAGACAGATCGACTAATCAGAGATA 59.066 37.037 0.00 0.00 0.00 1.98
2097 2341 6.770303 TCAAGACAGATCGACTAATCAGAGAT 59.230 38.462 0.00 0.00 0.00 2.75
2098 2342 6.037720 GTCAAGACAGATCGACTAATCAGAGA 59.962 42.308 0.00 0.00 0.00 3.10
2099 2343 6.038161 AGTCAAGACAGATCGACTAATCAGAG 59.962 42.308 2.72 0.00 36.97 3.35
2100 2344 5.883115 AGTCAAGACAGATCGACTAATCAGA 59.117 40.000 2.72 0.00 36.97 3.27
2101 2345 6.130298 AGTCAAGACAGATCGACTAATCAG 57.870 41.667 2.72 0.00 36.97 2.90
2110 2365 5.574082 CCAGTAAGTAGTCAAGACAGATCG 58.426 45.833 2.72 0.00 0.00 3.69
2123 2378 4.759782 ACTGTTAGCATGCCAGTAAGTAG 58.240 43.478 21.84 13.78 37.66 2.57
2214 2472 4.935808 CCGAACATAAGAACTTGCTACCTT 59.064 41.667 0.00 0.00 0.00 3.50
2216 2474 4.329256 GTCCGAACATAAGAACTTGCTACC 59.671 45.833 0.00 0.00 0.00 3.18
2240 2498 3.942748 ACACGGAGTTGTTTCTTTTGCTA 59.057 39.130 0.00 0.00 41.61 3.49
2253 2511 5.928264 GGTACTAACACAATAACACGGAGTT 59.072 40.000 0.00 1.20 41.61 3.01
2265 2523 2.624364 TCTCTGCACGGTACTAACACAA 59.376 45.455 0.00 0.00 0.00 3.33
2272 2530 1.961394 TGAACTTCTCTGCACGGTACT 59.039 47.619 0.00 0.00 0.00 2.73
2275 2533 0.753262 ACTGAACTTCTCTGCACGGT 59.247 50.000 0.00 0.00 0.00 4.83
2276 2534 1.423395 GACTGAACTTCTCTGCACGG 58.577 55.000 0.00 0.00 0.00 4.94
2324 2582 2.787723 CGATGAACGTGCCTTTGTAG 57.212 50.000 0.00 0.00 37.22 2.74
2346 2608 3.827898 GCAGTCGGGACTCGGGAG 61.828 72.222 0.00 0.00 40.20 4.30
2347 2609 4.671590 TGCAGTCGGGACTCGGGA 62.672 66.667 0.00 0.00 40.20 5.14
2348 2610 2.725203 TTTTGCAGTCGGGACTCGGG 62.725 60.000 0.00 0.00 40.20 5.14
2349 2611 1.291877 CTTTTGCAGTCGGGACTCGG 61.292 60.000 0.00 0.00 40.20 4.63
2350 2612 1.901650 GCTTTTGCAGTCGGGACTCG 61.902 60.000 0.00 0.00 46.58 4.18
2351 2613 1.869690 GCTTTTGCAGTCGGGACTC 59.130 57.895 0.00 0.00 46.58 3.36
2352 2614 4.065110 GCTTTTGCAGTCGGGACT 57.935 55.556 0.00 0.00 46.58 3.85
2376 2638 1.447140 GTATCACCAGCGTCCGCAA 60.447 57.895 14.70 0.00 44.88 4.85
2384 2646 1.804326 AACGACGCGTATCACCAGC 60.804 57.895 13.97 0.00 39.99 4.85
2385 2647 0.455464 TCAACGACGCGTATCACCAG 60.455 55.000 13.97 0.00 39.99 4.00
2386 2648 0.039346 TTCAACGACGCGTATCACCA 60.039 50.000 13.97 0.00 39.99 4.17
2388 2650 2.343246 TCAATTCAACGACGCGTATCAC 59.657 45.455 13.97 0.00 39.99 3.06
2389 2651 2.597520 TCAATTCAACGACGCGTATCA 58.402 42.857 13.97 0.00 39.99 2.15
2390 2652 3.331178 GTTCAATTCAACGACGCGTATC 58.669 45.455 13.97 0.00 39.99 2.24
2391 2653 3.363788 GTTCAATTCAACGACGCGTAT 57.636 42.857 13.97 0.00 39.99 3.06
2416 2682 1.204228 GCAGTTTCGTCGACACACGA 61.204 55.000 17.16 4.48 46.91 4.35
2417 2683 1.198397 GCAGTTTCGTCGACACACG 59.802 57.895 17.16 1.66 41.36 4.49
2421 2687 1.000233 GCTACGCAGTTTCGTCGACA 61.000 55.000 17.16 0.00 37.78 4.35
2588 2873 1.372623 GCGGACTCGTTCGTTCCTT 60.373 57.895 0.00 0.00 38.89 3.36
2600 2885 2.913578 TGTGTGTACGGGCGGACT 60.914 61.111 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.