Multiple sequence alignment - TraesCS2B01G360200

Loading Multiple Alignment...

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 TraesCS2B01G360200 chr2B 100.000 3992 0 0 1 3992 513476161 513472170 0.000000e+00 7372
1 TraesCS2B01G360200 chr2A 91.361 1933 98 29 8 1908 551811867 551813762 0.000000e+00 2580
2 TraesCS2B01G360200 chr2D 95.686 1298 46 6 1370 2663 435048858 435047567 0.000000e+00 2078
3 TraesCS2B01G360200 chr2D 94.296 1350 53 15 2661 3992 435047487 435046144 0.000000e+00 2045
4 TraesCS2B01G360200 chr2D 89.364 771 45 14 581 1320 435049645 435048881 0.000000e+00 935
5 TraesCS2B01G360200 chr2D 85.546 595 47 22 8 584 435050331 435049758 1.600000e-163 586


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 TraesCS2B01G360200 chr2B 513472170 513476161 3991 True 7372 7372 100.000 1 3992 1 chr2B.!!$R1 3991
1 TraesCS2B01G360200 chr2A 551811867 551813762 1895 False 2580 2580 91.361 8 1908 1 chr2A.!!$F1 1900
2 TraesCS2B01G360200 chr2D 435046144 435050331 4187 True 1411 2078 91.223 8 3992 4 chr2D.!!$R1 3984

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
408 426 0.250234 ATGTCGGCACTGCAGTACAT 59.750 50.0 21.20 21.59 0.00 2.29 F
474 494 0.321210 TTGGCGAACATGTGGATCGT 60.321 50.0 17.19 0.00 38.75 3.73 F
1773 1953 0.321671 TGTAGGTCTCTGCAAGGCAC 59.678 55.0 0.00 0.00 32.73 5.01 F
2745 3009 0.256464 ACGAGGACGAGGAGGAGAAT 59.744 55.0 0.00 0.00 42.66 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2147 0.038526 GACAGAACCGCCGAGAAGAA 60.039 55.000 0.00 0.00 0.00 2.52 R
2138 2318 0.392595 GTGGGCTGGTAGGCTAACAC 60.393 60.000 8.51 5.92 41.09 3.32 R
2886 3150 0.511221 CTCCAAACGCGTACACCTTG 59.489 55.000 14.46 13.23 0.00 3.61 R
3897 4177 2.030562 AACCCTTGCGACCAGACG 59.969 61.111 0.00 0.00 0.00 4.18 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
93 94 1.745489 GTTCGATCACACAGCCCCC 60.745 63.158 0.00 0.00 0.00 5.40
141 142 1.820906 CCATGTGATCCCAGCACCG 60.821 63.158 0.00 0.00 35.43 4.94
157 158 0.613260 ACCGCTGACCTTGCAATCTA 59.387 50.000 0.00 0.00 0.00 1.98
205 206 1.221021 GGGTGGAGTTCGTGGGATC 59.779 63.158 0.00 0.00 0.00 3.36
206 207 1.153628 GGTGGAGTTCGTGGGATCG 60.154 63.158 0.00 0.00 0.00 3.69
222 231 2.419713 GGATCGGGAAGGTTTGGTAGAC 60.420 54.545 0.00 0.00 0.00 2.59
223 232 0.604578 TCGGGAAGGTTTGGTAGACG 59.395 55.000 0.00 0.00 0.00 4.18
274 289 1.264295 GTCTTCGTGTAGGGAAGGGT 58.736 55.000 2.12 0.00 40.95 4.34
302 317 4.470602 AGGAAGGATCTTCCGTTTTTGTT 58.529 39.130 17.78 0.00 42.75 2.83
317 332 4.963237 TTTTGTTCATGAAAATTCCGCG 57.037 36.364 10.35 0.00 0.00 6.46
347 364 2.093394 TGTTCGTCAGTTCTTGGTTGGA 60.093 45.455 0.00 0.00 0.00 3.53
356 373 1.672356 CTTGGTTGGAGACTGCGGG 60.672 63.158 0.00 0.00 0.00 6.13
408 426 0.250234 ATGTCGGCACTGCAGTACAT 59.750 50.000 21.20 21.59 0.00 2.29
445 465 5.106396 CCACTTTGTGATCTTGACCTTGATC 60.106 44.000 0.00 0.00 39.43 2.92
458 478 3.282021 ACCTTGATCGGATTGTGATTGG 58.718 45.455 0.00 0.00 0.00 3.16
467 487 2.164219 GGATTGTGATTGGCGAACATGT 59.836 45.455 0.00 0.00 0.00 3.21
468 488 2.702898 TTGTGATTGGCGAACATGTG 57.297 45.000 0.00 0.00 0.00 3.21
469 489 0.880441 TGTGATTGGCGAACATGTGG 59.120 50.000 0.00 0.00 0.00 4.17
470 490 1.164411 GTGATTGGCGAACATGTGGA 58.836 50.000 0.00 0.00 0.00 4.02
471 491 1.745087 GTGATTGGCGAACATGTGGAT 59.255 47.619 0.00 0.00 0.00 3.41
472 492 2.016318 TGATTGGCGAACATGTGGATC 58.984 47.619 0.00 0.00 0.00 3.36
473 493 1.003545 GATTGGCGAACATGTGGATCG 60.004 52.381 12.91 12.91 39.47 3.69
474 494 0.321210 TTGGCGAACATGTGGATCGT 60.321 50.000 17.19 0.00 38.75 3.73
475 495 0.739462 TGGCGAACATGTGGATCGTC 60.739 55.000 14.48 14.48 41.28 4.20
476 496 0.460284 GGCGAACATGTGGATCGTCT 60.460 55.000 17.19 0.00 38.12 4.18
477 497 0.647410 GCGAACATGTGGATCGTCTG 59.353 55.000 17.19 1.79 38.75 3.51
478 498 1.996292 CGAACATGTGGATCGTCTGT 58.004 50.000 9.71 0.00 0.00 3.41
479 499 2.337583 CGAACATGTGGATCGTCTGTT 58.662 47.619 9.71 2.43 33.02 3.16
480 500 2.736721 CGAACATGTGGATCGTCTGTTT 59.263 45.455 9.71 0.00 30.63 2.83
481 501 3.186409 CGAACATGTGGATCGTCTGTTTT 59.814 43.478 9.71 0.00 30.63 2.43
482 502 4.319477 CGAACATGTGGATCGTCTGTTTTT 60.319 41.667 9.71 0.00 30.63 1.94
522 545 3.455990 TTGTTGGTTGAGTGCGTAGTA 57.544 42.857 0.00 0.00 0.00 1.82
606 745 5.144100 CCATAGACCTGTAAGATCAGAGGT 58.856 45.833 1.83 1.83 44.49 3.85
607 746 5.010516 CCATAGACCTGTAAGATCAGAGGTG 59.989 48.000 6.61 0.00 42.01 4.00
650 791 5.742453 CCAATTTCATCTTCAGAATTGCTCG 59.258 40.000 0.00 0.00 0.00 5.03
678 830 7.732140 ACTTAGGATCACATCTCTCCATTCATA 59.268 37.037 0.00 0.00 0.00 2.15
687 839 8.028354 CACATCTCTCCATTCATACTCTATGAC 58.972 40.741 0.00 0.00 44.32 3.06
813 971 5.874895 ACAATGTGTGATCTGACTGATTG 57.125 39.130 0.00 0.00 35.14 2.67
861 1041 7.873739 AAACAATGCATTGCTTAGTTACTTC 57.126 32.000 33.94 0.00 41.38 3.01
866 1046 4.937620 TGCATTGCTTAGTTACTTCCTCTG 59.062 41.667 10.49 0.00 0.00 3.35
886 1066 0.609662 CAAGAATGGGGTTGCCTTGG 59.390 55.000 0.00 0.00 32.80 3.61
891 1071 3.989787 GGGGTTGCCTTGGTTGCG 61.990 66.667 0.00 0.00 0.00 4.85
938 1118 3.441572 AGCCATTTGACAACTCAGTATGC 59.558 43.478 0.00 0.00 34.76 3.14
1243 1423 4.582701 TTGGAGGCAAGTTGTACAATTG 57.417 40.909 12.26 16.38 0.00 2.32
1358 1538 7.965107 CAGGCTACATGTAAATTCTTCAGAAAC 59.035 37.037 7.06 0.00 37.61 2.78
1367 1547 1.604604 TCTTCAGAAACCCCGCAAAG 58.395 50.000 0.00 0.00 0.00 2.77
1427 1607 0.736636 CATTCGACATGTGCCAGCAT 59.263 50.000 1.15 0.00 0.00 3.79
1454 1634 5.646606 CCCATGTTTAACCTAATGAAACCG 58.353 41.667 0.00 0.00 33.11 4.44
1542 1722 2.109126 GGCGAGAAGAATTGCCGCT 61.109 57.895 0.00 0.00 42.58 5.52
1561 1741 0.690192 TGCGGGAAATCTCAGGTCAA 59.310 50.000 0.00 0.00 0.00 3.18
1695 1875 5.070446 CCATGCCTTATCAGGTAAGAGTACA 59.930 44.000 1.55 0.00 43.18 2.90
1721 1901 5.931146 TGATTTGGTTGAATTTTGGGAATCG 59.069 36.000 0.00 0.00 0.00 3.34
1742 1922 1.795872 TGTCTGCCGATGTAACAAACG 59.204 47.619 0.00 0.00 0.00 3.60
1773 1953 0.321671 TGTAGGTCTCTGCAAGGCAC 59.678 55.000 0.00 0.00 32.73 5.01
1822 2002 2.146342 AGTCGAACAATGCTTGTGAGG 58.854 47.619 2.88 0.00 44.59 3.86
1867 2047 1.304134 AATCGACACCTTTGGGGGC 60.304 57.895 0.00 0.00 40.38 5.80
1873 2053 0.551396 ACACCTTTGGGGGCTATAGC 59.449 55.000 16.78 16.78 40.38 2.97
1885 2065 3.760684 GGGGCTATAGCTTGAATGGAATG 59.239 47.826 23.53 0.00 41.70 2.67
1957 2137 3.304928 GCATCTTTGTAGTGCAAGCAACT 60.305 43.478 0.00 0.00 38.47 3.16
1967 2147 1.839994 TGCAAGCAACTATAGGAGGCT 59.160 47.619 4.43 6.94 36.13 4.58
1987 2167 1.446272 CTTCTCGGCGGTTCTGTCC 60.446 63.158 7.21 0.00 0.00 4.02
2086 2266 0.682855 CTCGTCTTCTCTCTGGGCCT 60.683 60.000 4.53 0.00 0.00 5.19
2100 2280 1.559682 TGGGCCTCTTGAGAATGTACC 59.440 52.381 4.53 0.00 0.00 3.34
2138 2318 1.472480 CCGGCAATTGTTACCTCCTTG 59.528 52.381 7.40 0.00 0.00 3.61
2213 2393 6.040209 TGCTTTTCTTATCCAATTGCATGT 57.960 33.333 0.00 0.00 0.00 3.21
2214 2394 6.101332 TGCTTTTCTTATCCAATTGCATGTC 58.899 36.000 0.00 0.00 0.00 3.06
2215 2395 5.521372 GCTTTTCTTATCCAATTGCATGTCC 59.479 40.000 0.00 0.00 0.00 4.02
2216 2396 6.602410 TTTTCTTATCCAATTGCATGTCCA 57.398 33.333 0.00 0.00 0.00 4.02
2218 2398 6.795144 TTCTTATCCAATTGCATGTCCATT 57.205 33.333 0.00 0.00 0.00 3.16
2221 2401 6.380560 TCTTATCCAATTGCATGTCCATTCAA 59.619 34.615 0.00 0.00 0.00 2.69
2222 2402 4.886496 TCCAATTGCATGTCCATTCAAA 57.114 36.364 0.00 0.00 28.59 2.69
2223 2403 5.423704 TCCAATTGCATGTCCATTCAAAT 57.576 34.783 0.00 0.00 28.59 2.32
2322 2504 3.777910 GCAAGCTTGGGCATGGGG 61.778 66.667 27.10 0.00 41.70 4.96
2354 2536 2.134287 GGGCGTCCCTCAGCTGATA 61.134 63.158 18.63 2.95 41.34 2.15
2355 2537 1.476007 GGGCGTCCCTCAGCTGATAT 61.476 60.000 18.63 0.00 41.34 1.63
2363 2545 3.386078 TCCCTCAGCTGATATCACACTTC 59.614 47.826 18.63 0.00 0.00 3.01
2365 2547 3.067320 CCTCAGCTGATATCACACTTCGA 59.933 47.826 18.63 0.00 0.00 3.71
2373 2555 4.649218 TGATATCACACTTCGAGGGAATCA 59.351 41.667 0.00 0.00 0.00 2.57
2459 2641 2.286425 CTCACCTGGGGATGGGGT 60.286 66.667 0.00 0.00 0.00 4.95
2460 2642 1.930656 CTCACCTGGGGATGGGGTT 60.931 63.158 0.00 0.00 0.00 4.11
2612 2794 0.402861 ACTCCTTTGGGTGGAAGGGA 60.403 55.000 3.30 0.00 43.13 4.20
2613 2795 0.329596 CTCCTTTGGGTGGAAGGGAG 59.670 60.000 3.30 0.00 43.13 4.30
2614 2796 1.304464 CCTTTGGGTGGAAGGGAGC 60.304 63.158 0.00 0.00 39.99 4.70
2640 2822 2.047274 TAGGCTTGCAGGTGCGAC 60.047 61.111 0.00 0.00 45.83 5.19
2664 2928 5.500290 CGAATGAATCGTGTAAACTGGTAGC 60.500 44.000 0.00 0.00 46.52 3.58
2679 2943 4.018415 ACTGGTAGCACCCAACTATTCATT 60.018 41.667 0.00 0.00 37.50 2.57
2680 2944 4.929479 TGGTAGCACCCAACTATTCATTT 58.071 39.130 0.00 0.00 37.50 2.32
2684 2948 4.568956 AGCACCCAACTATTCATTTTTGC 58.431 39.130 0.00 0.00 0.00 3.68
2694 2958 8.702438 CAACTATTCATTTTTGCCAAAGTACTG 58.298 33.333 0.00 0.00 0.00 2.74
2702 2966 9.206870 CATTTTTGCCAAAGTACTGAAATGTAT 57.793 29.630 0.00 0.00 31.86 2.29
2739 3003 0.677098 TTCAGGACGAGGACGAGGAG 60.677 60.000 0.00 0.00 42.66 3.69
2745 3009 0.256464 ACGAGGACGAGGAGGAGAAT 59.744 55.000 0.00 0.00 42.66 2.40
2794 3058 0.736325 CTCACTCACCGGGCTAAACG 60.736 60.000 6.32 0.00 0.00 3.60
2898 3162 4.728102 TCCGGCAAGGTGTACGCG 62.728 66.667 3.53 3.53 41.99 6.01
2929 3193 4.704833 GCTCGGGTCAGCTTGGCA 62.705 66.667 0.00 0.00 36.38 4.92
2977 3241 2.660064 CCCCCTCTCCAGGTTGACG 61.660 68.421 0.00 0.00 38.30 4.35
2999 3263 1.816183 CGATCTCGCCTAGTTCCTCCT 60.816 57.143 0.00 0.00 0.00 3.69
3003 3267 0.687757 TCGCCTAGTTCCTCCTGCAT 60.688 55.000 0.00 0.00 0.00 3.96
3005 3269 1.127343 GCCTAGTTCCTCCTGCATCT 58.873 55.000 0.00 0.00 0.00 2.90
3006 3270 1.202627 GCCTAGTTCCTCCTGCATCTG 60.203 57.143 0.00 0.00 0.00 2.90
3008 3272 0.833287 TAGTTCCTCCTGCATCTGCC 59.167 55.000 0.00 0.00 41.18 4.85
3009 3273 0.913451 AGTTCCTCCTGCATCTGCCT 60.913 55.000 0.00 0.00 41.18 4.75
3010 3274 0.747283 GTTCCTCCTGCATCTGCCTG 60.747 60.000 0.00 0.00 41.18 4.85
3011 3275 0.911045 TTCCTCCTGCATCTGCCTGA 60.911 55.000 0.00 0.00 41.18 3.86
3012 3276 0.911045 TCCTCCTGCATCTGCCTGAA 60.911 55.000 0.00 0.00 41.18 3.02
3013 3277 0.034767 CCTCCTGCATCTGCCTGAAA 60.035 55.000 0.00 0.00 41.18 2.69
3026 3296 6.299805 TCTGCCTGAAACTTCATACTGTAT 57.700 37.500 0.00 0.00 36.46 2.29
3034 3304 8.239038 TGAAACTTCATACTGTATAGGGAGAG 57.761 38.462 0.00 0.00 31.01 3.20
3036 3306 8.840200 AAACTTCATACTGTATAGGGAGAGAA 57.160 34.615 0.00 0.00 0.00 2.87
3038 3308 8.472007 ACTTCATACTGTATAGGGAGAGAAAG 57.528 38.462 0.00 0.00 0.00 2.62
3040 3310 9.137459 CTTCATACTGTATAGGGAGAGAAAGAA 57.863 37.037 0.00 0.00 0.00 2.52
3108 3385 5.278315 CCTTGGTTGGTTACTTTTGAGTAGC 60.278 44.000 0.00 0.00 0.00 3.58
3119 3396 5.352284 ACTTTTGAGTAGCGGACAGATATG 58.648 41.667 0.00 0.00 0.00 1.78
3120 3397 3.371102 TTGAGTAGCGGACAGATATGC 57.629 47.619 0.00 0.00 0.00 3.14
3134 3411 3.687698 CAGATATGCGATGATGCCATGAA 59.312 43.478 0.00 0.00 32.09 2.57
3191 3468 6.643388 TGCTTAGCTCTTCATTCTTCATACA 58.357 36.000 5.60 0.00 0.00 2.29
3279 3556 8.598202 TTGTTACATAGTCTCCCATTACAGTA 57.402 34.615 0.00 0.00 0.00 2.74
3280 3557 8.598202 TGTTACATAGTCTCCCATTACAGTAA 57.402 34.615 0.00 0.00 0.00 2.24
3361 3639 0.749454 AAGATGGAGCATGAACCGGC 60.749 55.000 0.00 0.00 0.00 6.13
3375 3653 2.341846 ACCGGCACTTGAAGAAAAGA 57.658 45.000 0.00 0.00 0.00 2.52
3398 3676 2.411547 GGTCAACGCTTTTGATCTCACG 60.412 50.000 0.00 0.00 0.00 4.35
3402 3680 1.195448 ACGCTTTTGATCTCACGCTTG 59.805 47.619 0.00 0.00 0.00 4.01
3418 3696 2.712057 CTTGCAAAGCGGACAGAAAT 57.288 45.000 0.00 0.00 36.98 2.17
3542 3820 1.375140 ACCGCAGCAGTCATGACAG 60.375 57.895 27.02 20.37 0.00 3.51
3599 3878 4.215742 CCGCCGAGTAATGCCCGA 62.216 66.667 0.00 0.00 0.00 5.14
3613 3892 0.651031 GCCCGAAAGTCGTATGCTTC 59.349 55.000 0.00 0.00 38.40 3.86
3662 3941 4.876679 TGTTAAGATGGACGTCAACACAAA 59.123 37.500 18.91 1.73 0.00 2.83
3668 3947 5.937540 AGATGGACGTCAACACAAAATATCA 59.062 36.000 18.91 1.14 0.00 2.15
3710 3989 2.631160 TGTTGTCGAAGGACCAATGT 57.369 45.000 0.00 0.00 42.73 2.71
3870 4150 0.305617 CATTGCCGATGGTGATGACG 59.694 55.000 0.00 0.00 31.83 4.35
3897 4177 6.772716 TGGAAGCATAGAATAAATCAAGGTCC 59.227 38.462 0.00 0.00 0.00 4.46
3902 4182 6.073548 GCATAGAATAAATCAAGGTCCGTCTG 60.074 42.308 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.641192 GGGGGATGGAGGAGAAAGTTT 59.359 52.381 0.00 0.00 0.00 2.66
1 2 1.299939 GGGGGATGGAGGAGAAAGTT 58.700 55.000 0.00 0.00 0.00 2.66
2 3 0.121197 TGGGGGATGGAGGAGAAAGT 59.879 55.000 0.00 0.00 0.00 2.66
3 4 1.298953 TTGGGGGATGGAGGAGAAAG 58.701 55.000 0.00 0.00 0.00 2.62
4 5 1.766951 TTTGGGGGATGGAGGAGAAA 58.233 50.000 0.00 0.00 0.00 2.52
5 6 1.357761 GTTTTGGGGGATGGAGGAGAA 59.642 52.381 0.00 0.00 0.00 2.87
6 7 0.999712 GTTTTGGGGGATGGAGGAGA 59.000 55.000 0.00 0.00 0.00 3.71
141 142 3.314635 CCTGAATAGATTGCAAGGTCAGC 59.685 47.826 4.94 0.00 31.69 4.26
151 152 5.620205 CGGACGGAGATACCTGAATAGATTG 60.620 48.000 0.00 0.00 36.31 2.67
157 158 1.329256 CCGGACGGAGATACCTGAAT 58.671 55.000 4.40 0.00 37.50 2.57
205 206 0.390735 CCGTCTACCAAACCTTCCCG 60.391 60.000 0.00 0.00 0.00 5.14
206 207 0.035725 CCCGTCTACCAAACCTTCCC 60.036 60.000 0.00 0.00 0.00 3.97
222 231 1.070758 CTGATCTGATAACCACCCCCG 59.929 57.143 0.00 0.00 0.00 5.73
223 232 2.127708 ACTGATCTGATAACCACCCCC 58.872 52.381 6.60 0.00 0.00 5.40
274 289 5.757099 AACGGAAGATCCTTCCTTTTCTA 57.243 39.130 19.81 0.00 36.45 2.10
302 317 5.365403 AAACTAACGCGGAATTTTCATGA 57.635 34.783 12.47 0.00 0.00 3.07
317 332 6.468000 CCAAGAACTGACGAACAAAAACTAAC 59.532 38.462 0.00 0.00 0.00 2.34
356 373 3.357079 CCCAACTCCACACTGCGC 61.357 66.667 0.00 0.00 0.00 6.09
396 414 3.461061 CCTCCACATATGTACTGCAGTG 58.539 50.000 29.57 13.72 0.00 3.66
445 465 0.801872 TGTTCGCCAATCACAATCCG 59.198 50.000 0.00 0.00 0.00 4.18
458 478 0.647410 CAGACGATCCACATGTTCGC 59.353 55.000 16.30 10.29 36.37 4.70
503 526 2.101082 TGTACTACGCACTCAACCAACA 59.899 45.455 0.00 0.00 0.00 3.33
522 545 0.612229 AGTCAGCAGCAGCATACTGT 59.388 50.000 3.17 0.00 46.30 3.55
525 548 1.865970 GATCAGTCAGCAGCAGCATAC 59.134 52.381 3.17 0.48 45.49 2.39
530 553 1.066358 TCAAGGATCAGTCAGCAGCAG 60.066 52.381 0.00 0.00 0.00 4.24
606 745 1.390383 TTACGACGGACCCACACACA 61.390 55.000 0.00 0.00 0.00 3.72
607 746 0.940991 GTTACGACGGACCCACACAC 60.941 60.000 0.00 0.00 0.00 3.82
650 791 4.219115 TGGAGAGATGTGATCCTAAGTCC 58.781 47.826 0.00 0.00 34.04 3.85
798 956 2.706339 AGGCCAATCAGTCAGATCAC 57.294 50.000 5.01 0.00 35.39 3.06
839 1019 5.711976 AGGAAGTAACTAAGCAATGCATTGT 59.288 36.000 33.67 21.12 39.88 2.71
848 1028 4.283467 TCTTGCAGAGGAAGTAACTAAGCA 59.717 41.667 0.00 0.00 0.00 3.91
861 1041 1.180029 CAACCCCATTCTTGCAGAGG 58.820 55.000 0.00 0.00 0.00 3.69
866 1046 0.037046 CAAGGCAACCCCATTCTTGC 60.037 55.000 0.00 0.00 41.79 4.01
886 1066 3.192103 AACCCAGGGTCCTCGCAAC 62.192 63.158 13.17 0.00 33.12 4.17
891 1071 1.580059 TGTATGAACCCAGGGTCCTC 58.420 55.000 13.17 7.58 33.12 3.71
1026 1206 7.993183 ACTATGTTGTGGAATTCTATAACCAGG 59.007 37.037 22.57 15.85 32.89 4.45
1080 1260 2.279784 GCTTCTGGATCCGGCGAG 60.280 66.667 16.48 16.01 0.00 5.03
1243 1423 5.847670 AAAGTCGTGAGAACTAAGAATGC 57.152 39.130 0.00 0.00 45.01 3.56
1358 1538 2.989253 GGTGGGAACTTTGCGGGG 60.989 66.667 0.00 0.00 0.00 5.73
1367 1547 2.586648 ATTCCAAGTCTGGTGGGAAC 57.413 50.000 0.00 0.00 43.97 3.62
1427 1607 5.718801 TCATTAGGTTAAACATGGGCCTA 57.281 39.130 4.53 0.00 0.00 3.93
1454 1634 1.270907 TCAGCCACTCCTTCTCTTCC 58.729 55.000 0.00 0.00 0.00 3.46
1542 1722 0.690192 TTGACCTGAGATTTCCCGCA 59.310 50.000 0.00 0.00 0.00 5.69
1561 1741 3.259314 TGTGGCCTGGTCCAGCAT 61.259 61.111 13.99 0.00 36.67 3.79
1695 1875 7.119553 CGATTCCCAAAATTCAACCAAATCAAT 59.880 33.333 0.00 0.00 0.00 2.57
1721 1901 2.411031 CGTTTGTTACATCGGCAGACAC 60.411 50.000 0.00 0.00 0.00 3.67
1742 1922 2.162408 GAGACCTACAAATGCAGCAACC 59.838 50.000 0.00 0.00 0.00 3.77
1773 1953 3.274586 CGGCATGCGTGATCCTGG 61.275 66.667 12.44 0.00 0.00 4.45
1867 2047 4.082895 GCAGGCATTCCATTCAAGCTATAG 60.083 45.833 0.00 0.00 33.74 1.31
1873 2053 3.066342 CAGTAGCAGGCATTCCATTCAAG 59.934 47.826 0.00 0.00 33.74 3.02
1885 2065 3.177487 GTTAACGTAGTCAGTAGCAGGC 58.823 50.000 0.00 0.00 45.00 4.85
1930 2110 2.436417 TGCACTACAAAGATGCCCTTC 58.564 47.619 0.00 0.00 38.63 3.46
1957 2137 2.240279 GCCGAGAAGAAGCCTCCTATA 58.760 52.381 0.00 0.00 0.00 1.31
1967 2147 0.038526 GACAGAACCGCCGAGAAGAA 60.039 55.000 0.00 0.00 0.00 2.52
1987 2167 3.297736 AGTATAAACCCGACCCTCTCTG 58.702 50.000 0.00 0.00 0.00 3.35
2052 2232 4.933064 GAGGCTCGACATCGGCGG 62.933 72.222 7.21 0.00 40.29 6.13
2086 2266 3.325870 CGCAACAGGTACATTCTCAAGA 58.674 45.455 0.00 0.00 0.00 3.02
2138 2318 0.392595 GTGGGCTGGTAGGCTAACAC 60.393 60.000 8.51 5.92 41.09 3.32
2259 2441 2.897326 ACACCGACCTGCATATATAGCA 59.103 45.455 8.79 8.79 40.19 3.49
2322 2504 2.383527 CGCCCTCGCTGTTCTTGTC 61.384 63.158 0.00 0.00 0.00 3.18
2354 2536 3.600388 GTTGATTCCCTCGAAGTGTGAT 58.400 45.455 0.00 0.00 0.00 3.06
2355 2537 2.609491 CGTTGATTCCCTCGAAGTGTGA 60.609 50.000 0.00 0.00 0.00 3.58
2363 2545 1.982073 GCCTTGCGTTGATTCCCTCG 61.982 60.000 0.00 0.00 0.00 4.63
2365 2547 1.678970 GGCCTTGCGTTGATTCCCT 60.679 57.895 0.00 0.00 0.00 4.20
2373 2555 0.823356 ATTGACACTGGCCTTGCGTT 60.823 50.000 3.32 0.00 0.00 4.84
2452 2634 1.607801 GCAGCCTTGGAAACCCCATC 61.608 60.000 0.00 0.00 46.10 3.51
2614 2796 2.029838 CTGCAAGCCTAGGTTGTAGG 57.970 55.000 22.64 0.70 45.15 3.18
2650 2832 2.551032 GTTGGGTGCTACCAGTTTACAC 59.449 50.000 7.49 0.00 42.47 2.90
2654 2836 4.202524 TGAATAGTTGGGTGCTACCAGTTT 60.203 41.667 7.49 0.00 42.47 2.66
2659 2841 5.914898 AAAATGAATAGTTGGGTGCTACC 57.085 39.130 0.00 0.00 37.60 3.18
2664 2928 4.892433 TGGCAAAAATGAATAGTTGGGTG 58.108 39.130 0.00 0.00 0.00 4.61
2679 2943 9.853555 CATATACATTTCAGTACTTTGGCAAAA 57.146 29.630 14.43 0.00 0.00 2.44
2680 2944 9.019656 ACATATACATTTCAGTACTTTGGCAAA 57.980 29.630 12.79 12.79 0.00 3.68
2694 2958 6.425114 ACCAAGAGCGATCACATATACATTTC 59.575 38.462 2.38 0.00 0.00 2.17
2702 2966 4.183865 CTGAAACCAAGAGCGATCACATA 58.816 43.478 2.38 0.00 0.00 2.29
2758 3022 1.827399 GAGGCGACCAACTTGGGAGA 61.827 60.000 12.62 0.00 43.37 3.71
2794 3058 2.352127 GGCTGATCTGCACAAACCTTTC 60.352 50.000 23.84 1.31 34.04 2.62
2847 3111 1.006281 ACCGTATGAGACACCCCTGTA 59.994 52.381 0.00 0.00 0.00 2.74
2850 3114 0.902531 CAACCGTATGAGACACCCCT 59.097 55.000 0.00 0.00 0.00 4.79
2886 3150 0.511221 CTCCAAACGCGTACACCTTG 59.489 55.000 14.46 13.23 0.00 3.61
2898 3162 1.376037 CGAGCCACCTCCTCCAAAC 60.376 63.158 0.00 0.00 34.49 2.93
2977 3241 1.264826 GAGGAACTAGGCGAGATCGAC 59.735 57.143 6.39 2.45 45.38 4.20
2999 3263 2.275134 TGAAGTTTCAGGCAGATGCA 57.725 45.000 7.19 0.00 35.94 3.96
3003 3267 4.623932 ACAGTATGAAGTTTCAGGCAGA 57.376 40.909 0.74 0.00 41.08 4.26
3005 3269 6.408092 CCCTATACAGTATGAAGTTTCAGGCA 60.408 42.308 3.03 0.00 41.08 4.75
3006 3270 5.992217 CCCTATACAGTATGAAGTTTCAGGC 59.008 44.000 3.03 0.00 41.08 4.85
3008 3272 8.239038 TCTCCCTATACAGTATGAAGTTTCAG 57.761 38.462 3.03 0.00 41.08 3.02
3009 3273 8.059461 TCTCTCCCTATACAGTATGAAGTTTCA 58.941 37.037 3.03 0.00 39.69 2.69
3010 3274 8.466617 TCTCTCCCTATACAGTATGAAGTTTC 57.533 38.462 3.03 0.00 39.69 2.78
3011 3275 8.840200 TTCTCTCCCTATACAGTATGAAGTTT 57.160 34.615 3.03 0.00 39.69 2.66
3012 3276 8.840200 TTTCTCTCCCTATACAGTATGAAGTT 57.160 34.615 3.03 0.00 39.69 2.66
3013 3277 8.282982 TCTTTCTCTCCCTATACAGTATGAAGT 58.717 37.037 3.03 0.00 39.69 3.01
3073 3345 1.687996 CCAACCAAGGGTCCAAACACT 60.688 52.381 0.00 0.00 42.47 3.55
3074 3346 0.750249 CCAACCAAGGGTCCAAACAC 59.250 55.000 0.00 0.00 33.12 3.32
3076 3348 1.491668 AACCAACCAAGGGTCCAAAC 58.508 50.000 0.00 0.00 37.77 2.93
3078 3350 1.854280 AGTAACCAACCAAGGGTCCAA 59.146 47.619 0.00 0.00 37.77 3.53
3079 3351 1.525175 AGTAACCAACCAAGGGTCCA 58.475 50.000 0.00 0.00 37.77 4.02
3080 3352 2.670019 AAGTAACCAACCAAGGGTCC 57.330 50.000 0.00 0.00 37.77 4.46
3108 3385 1.657594 GCATCATCGCATATCTGTCCG 59.342 52.381 0.00 0.00 0.00 4.79
3134 3411 7.527568 TTCGGTTCAGTTTAAAACCCATAAT 57.472 32.000 1.98 0.00 41.59 1.28
3142 3419 7.913297 CAGTTGAGATTTCGGTTCAGTTTAAAA 59.087 33.333 0.00 0.00 0.00 1.52
3279 3556 6.206498 GCATTTGAAGAGTAACGACCTTTTT 58.794 36.000 0.00 0.00 0.00 1.94
3280 3557 5.278315 GGCATTTGAAGAGTAACGACCTTTT 60.278 40.000 0.00 0.00 0.00 2.27
3317 3594 1.075601 TATGATCCAGGAATGGCCCC 58.924 55.000 0.00 0.00 37.37 5.80
3346 3624 2.359850 GTGCCGGTTCATGCTCCA 60.360 61.111 1.90 0.00 0.00 3.86
3361 3639 5.207768 CGTTGACCATCTTTTCTTCAAGTG 58.792 41.667 0.00 0.00 0.00 3.16
3375 3653 3.189287 GTGAGATCAAAAGCGTTGACCAT 59.811 43.478 7.88 0.00 0.00 3.55
3402 3680 0.794605 GCGATTTCTGTCCGCTTTGC 60.795 55.000 0.00 0.00 44.83 3.68
3418 3696 1.173043 CAAGGGTGGCTAAATTGCGA 58.827 50.000 0.00 0.00 0.00 5.10
3424 3702 3.050089 CCAAGCAAGGGTGGCTAAA 57.950 52.632 0.00 0.00 41.66 1.85
3444 3722 2.709125 TTTGGACCGGCGACAGACTG 62.709 60.000 9.30 0.00 0.00 3.51
3467 3745 3.057596 TGCTCGTTTGTCCATCCAAAATC 60.058 43.478 0.00 0.00 36.17 2.17
3506 3784 2.116125 GTGGAAGGCTTGGGTGCT 59.884 61.111 3.46 0.00 0.00 4.40
3599 3878 4.002906 TCACTTGGAAGCATACGACTTT 57.997 40.909 0.00 0.00 0.00 2.66
3613 3892 3.268330 CACTGAGGATGACATCACTTGG 58.732 50.000 17.08 10.14 33.27 3.61
3662 3941 8.328758 TGTTAGGTCATTCCTCTTTGTGATATT 58.671 33.333 0.00 0.00 44.42 1.28
3668 3947 6.777580 ACATTTGTTAGGTCATTCCTCTTTGT 59.222 34.615 0.00 0.00 44.42 2.83
3710 3989 5.355910 GGCTATCAAAAATTAACTCCCGTCA 59.644 40.000 0.00 0.00 0.00 4.35
3773 4053 3.181434 TGTTTGTTTATGAGGCCTCCACT 60.181 43.478 29.95 16.55 0.00 4.00
3867 4147 5.758296 TGATTTATTCTATGCTTCCACCGTC 59.242 40.000 0.00 0.00 0.00 4.79
3870 4150 6.547510 ACCTTGATTTATTCTATGCTTCCACC 59.452 38.462 0.00 0.00 0.00 4.61
3897 4177 2.030562 AACCCTTGCGACCAGACG 59.969 61.111 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.