Multiple sequence alignment - TraesCS3B01G297400

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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 TraesCS3B01G297400 chr3B 100.000 3152 0 0 548 3699 476948617 476951768 0.000000e+00 5821
1 TraesCS3B01G297400 chr3B 100.000 252 0 0 1 252 476948070 476948321 2.010000e-127 466
2 TraesCS3B01G297400 chr3D 91.559 2014 93 34 548 2499 365908996 365910994 0.000000e+00 2706
3 TraesCS3B01G297400 chr3D 92.134 1195 53 18 2513 3697 365910978 365912141 0.000000e+00 1648
4 TraesCS3B01G297400 chr3D 92.126 254 17 3 1 252 365908680 365908932 4.540000e-94 355
5 TraesCS3B01G297400 chr3A 89.337 2035 117 40 548 2499 487857221 487859238 0.000000e+00 2464
6 TraesCS3B01G297400 chr3A 93.651 1197 55 8 2513 3697 487859222 487860409 0.000000e+00 1770
7 TraesCS3B01G297400 chr3A 88.940 217 14 6 20 227 487856915 487857130 3.660000e-65 259


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 TraesCS3B01G297400 chr3B 476948070 476951768 3698 False 3143.500000 5821 100.000000 1 3699 2 chr3B.!!$F1 3698
1 TraesCS3B01G297400 chr3D 365908680 365912141 3461 False 1569.666667 2706 91.939667 1 3697 3 chr3D.!!$F1 3696
2 TraesCS3B01G297400 chr3A 487856915 487860409 3494 False 1497.666667 2464 90.642667 20 3697 3 chr3A.!!$F1 3677

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
773 857 0.248377 GCGCATCACATGGCTCTTTC 60.248 55.0 0.3 0.0 0.00 2.62 F
2489 2632 0.036388 ATCGGTACAGCCAACACCAG 60.036 55.0 0.0 0.0 36.97 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2612 2757 0.400594 ACAGGTTCTGTAACTGGGGC 59.599 55.000 4.34 0.0 43.46 5.80 R
3417 3585 2.011222 TCGGTATGCGGAAATTTGGTC 58.989 47.619 0.00 0.0 0.00 4.02 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
37 38 2.101917 CCCAACGATATCAGTTACCGGT 59.898 50.000 13.98 13.98 0.00 5.28
100 101 0.749649 CGGCAGTCAGGCTATTCTCT 59.250 55.000 0.00 0.00 41.46 3.10
229 288 0.469144 CCCTGCTCCTACTCTCCTCC 60.469 65.000 0.00 0.00 0.00 4.30
230 289 0.469144 CCTGCTCCTACTCTCCTCCC 60.469 65.000 0.00 0.00 0.00 4.30
231 290 0.469144 CTGCTCCTACTCTCCTCCCC 60.469 65.000 0.00 0.00 0.00 4.81
232 291 0.926720 TGCTCCTACTCTCCTCCCCT 60.927 60.000 0.00 0.00 0.00 4.79
233 292 0.263468 GCTCCTACTCTCCTCCCCTT 59.737 60.000 0.00 0.00 0.00 3.95
234 293 2.032151 GCTCCTACTCTCCTCCCCTTG 61.032 61.905 0.00 0.00 0.00 3.61
245 304 2.044946 CCCCTTGCCTTCTTCCCG 60.045 66.667 0.00 0.00 0.00 5.14
246 305 2.757077 CCCTTGCCTTCTTCCCGT 59.243 61.111 0.00 0.00 0.00 5.28
247 306 1.074951 CCCTTGCCTTCTTCCCGTT 59.925 57.895 0.00 0.00 0.00 4.44
248 307 1.244019 CCCTTGCCTTCTTCCCGTTG 61.244 60.000 0.00 0.00 0.00 4.10
250 309 1.318576 CTTGCCTTCTTCCCGTTGTT 58.681 50.000 0.00 0.00 0.00 2.83
251 310 1.001378 CTTGCCTTCTTCCCGTTGTTG 60.001 52.381 0.00 0.00 0.00 3.33
567 626 2.959421 ATCATATCCTCCCTCCCTCC 57.041 55.000 0.00 0.00 0.00 4.30
581 640 2.849318 CTCCCTCCCTTCCTTTCTTCAT 59.151 50.000 0.00 0.00 0.00 2.57
590 649 4.082354 CCTTCCTTTCTTCATTCAAGCCAG 60.082 45.833 0.00 0.00 31.26 4.85
595 654 0.731417 CTTCATTCAAGCCAGGCTCG 59.269 55.000 16.53 2.69 38.25 5.03
596 655 0.324614 TTCATTCAAGCCAGGCTCGA 59.675 50.000 16.53 6.07 38.25 4.04
597 656 0.391661 TCATTCAAGCCAGGCTCGAC 60.392 55.000 16.53 0.00 38.25 4.20
599 658 2.172483 ATTCAAGCCAGGCTCGACGT 62.172 55.000 16.53 0.00 38.25 4.34
600 659 3.114616 CAAGCCAGGCTCGACGTG 61.115 66.667 16.53 4.83 38.25 4.49
607 672 2.661866 GGCTCGACGTGTGTTGCT 60.662 61.111 0.00 0.00 0.00 3.91
611 676 1.698165 CTCGACGTGTGTTGCTATGT 58.302 50.000 0.00 0.00 0.00 2.29
631 699 1.066152 TCTCATCTCATTCTCACGGCG 59.934 52.381 4.80 4.80 0.00 6.46
635 703 0.601057 TCTCATTCTCACGGCGTGAA 59.399 50.000 37.97 27.32 42.26 3.18
645 713 0.601841 ACGGCGTGAAAAAGGATCGT 60.602 50.000 13.76 0.00 0.00 3.73
658 726 0.603065 GGATCGTGCCTTGCCTTTTT 59.397 50.000 0.00 0.00 0.00 1.94
693 769 2.436824 GCCTTCGTCTCCCTTGCC 60.437 66.667 0.00 0.00 0.00 4.52
764 848 2.440613 TGCATGGGCGCATCACAT 60.441 55.556 14.18 4.92 45.35 3.21
765 849 2.027024 GCATGGGCGCATCACATG 59.973 61.111 21.52 21.52 43.58 3.21
766 850 2.725641 CATGGGCGCATCACATGG 59.274 61.111 14.18 0.00 38.58 3.66
767 851 3.221389 ATGGGCGCATCACATGGC 61.221 61.111 11.00 0.00 0.00 4.40
769 853 3.589881 GGGCGCATCACATGGCTC 61.590 66.667 10.83 0.00 0.00 4.70
770 854 2.515523 GGCGCATCACATGGCTCT 60.516 61.111 10.83 0.00 0.00 4.09
773 857 0.248377 GCGCATCACATGGCTCTTTC 60.248 55.000 0.30 0.00 0.00 2.62
774 858 1.089112 CGCATCACATGGCTCTTTCA 58.911 50.000 0.00 0.00 0.00 2.69
775 859 1.063616 CGCATCACATGGCTCTTTCAG 59.936 52.381 0.00 0.00 0.00 3.02
804 888 6.478512 TTTTCTGTAAGCAAAGGGAATGTT 57.521 33.333 0.00 0.00 0.00 2.71
853 942 1.081892 CTTTCCTGCCATCTCGTGTG 58.918 55.000 0.00 0.00 0.00 3.82
854 943 0.396435 TTTCCTGCCATCTCGTGTGT 59.604 50.000 0.00 0.00 0.00 3.72
855 944 0.320683 TTCCTGCCATCTCGTGTGTG 60.321 55.000 0.00 0.00 0.00 3.82
856 945 1.004560 CCTGCCATCTCGTGTGTGT 60.005 57.895 0.00 0.00 0.00 3.72
862 951 1.995484 CCATCTCGTGTGTGTGATGTC 59.005 52.381 0.00 0.00 35.76 3.06
868 957 0.531974 GTGTGTGTGATGTCCGTGGT 60.532 55.000 0.00 0.00 0.00 4.16
871 960 1.271379 GTGTGTGATGTCCGTGGTCTA 59.729 52.381 0.00 0.00 0.00 2.59
889 979 5.221823 TGGTCTAATTCTTGTCATGTGGTGA 60.222 40.000 0.00 0.00 0.00 4.02
892 982 6.650807 GTCTAATTCTTGTCATGTGGTGAGAA 59.349 38.462 0.00 0.00 37.73 2.87
909 1000 5.295787 GGTGAGAATTAACATGGATTGCGTA 59.704 40.000 0.00 0.00 0.00 4.42
910 1001 6.422223 GTGAGAATTAACATGGATTGCGTAG 58.578 40.000 0.00 0.00 0.00 3.51
911 1002 6.257849 GTGAGAATTAACATGGATTGCGTAGA 59.742 38.462 0.00 0.00 0.00 2.59
912 1003 6.257849 TGAGAATTAACATGGATTGCGTAGAC 59.742 38.462 0.00 0.00 0.00 2.59
913 1004 6.112734 AGAATTAACATGGATTGCGTAGACA 58.887 36.000 0.00 0.00 0.00 3.41
921 1031 3.267483 GGATTGCGTAGACAGCCTTTTA 58.733 45.455 0.00 0.00 0.00 1.52
969 1083 2.945008 TGCTTATGTTATCCACAGCTGC 59.055 45.455 15.27 0.00 39.40 5.25
971 1085 1.581934 TATGTTATCCACAGCTGCGC 58.418 50.000 15.27 0.00 39.40 6.09
1260 1374 0.469070 CTCCTCTCCCAGCTTGATGG 59.531 60.000 0.00 0.00 40.29 3.51
1275 1389 4.157289 GCTTGATGGTTCCATATGCTATGG 59.843 45.833 13.20 13.20 40.48 2.74
1322 1436 8.164070 ACTCTAAACACCAGAAATAACCTCAAT 58.836 33.333 0.00 0.00 0.00 2.57
1348 1462 8.506168 TTGAGAACCCACTTATTATTCATCAC 57.494 34.615 0.00 0.00 0.00 3.06
1350 1464 6.055588 AGAACCCACTTATTATTCATCACCG 58.944 40.000 0.00 0.00 0.00 4.94
1367 1481 1.545582 ACCGCATCTTCAAACAATGGG 59.454 47.619 0.00 0.00 34.24 4.00
1387 1501 0.801067 ACACGGCTCGCTTTCGTATC 60.801 55.000 0.00 0.00 35.23 2.24
1588 1711 3.113824 TGCCCATTTATTCCTGCCAATT 58.886 40.909 0.00 0.00 0.00 2.32
1736 1863 2.645838 ACCAGAAAGAAGCAGCTGAA 57.354 45.000 20.43 0.00 0.00 3.02
1760 1887 3.137544 TCAGTTTGCCCTTTACTTCCTGA 59.862 43.478 0.00 0.00 0.00 3.86
1815 1942 9.463443 AAGATAGTTTGTTGACTAATTTGTTGC 57.537 29.630 0.00 0.00 35.86 4.17
1847 1974 0.595588 TGGCACAGCAATTTACACCG 59.404 50.000 0.00 0.00 0.00 4.94
2139 2267 0.107897 ATTGCCATCGCCGTAAGTGA 60.108 50.000 0.00 0.00 39.91 3.41
2142 2270 1.343142 TGCCATCGCCGTAAGTGATAT 59.657 47.619 0.00 0.00 44.03 1.63
2143 2271 2.559231 TGCCATCGCCGTAAGTGATATA 59.441 45.455 0.00 0.00 44.03 0.86
2144 2272 2.921754 GCCATCGCCGTAAGTGATATAC 59.078 50.000 0.00 0.00 44.03 1.47
2145 2273 3.168963 CCATCGCCGTAAGTGATATACG 58.831 50.000 0.00 0.00 44.03 3.06
2169 2312 3.941483 AGAATGTAAACCTTCCATGCTCG 59.059 43.478 0.00 0.00 0.00 5.03
2185 2328 1.284657 CTCGTGCTGCATCCAACTAG 58.715 55.000 5.27 0.00 0.00 2.57
2193 2336 2.810274 CTGCATCCAACTAGCGCATATT 59.190 45.455 11.47 0.00 31.10 1.28
2200 2343 3.243068 CCAACTAGCGCATATTTGTTCCC 60.243 47.826 11.47 0.00 0.00 3.97
2323 2466 5.350504 AGAGACTGAATCATGTAACCTGG 57.649 43.478 0.00 0.00 0.00 4.45
2329 2472 6.407202 ACTGAATCATGTAACCTGGTTAGAC 58.593 40.000 19.25 12.04 0.00 2.59
2424 2567 1.689813 TGTTCAGAACAGCCGGAGTTA 59.310 47.619 12.24 0.00 36.25 2.24
2480 2623 0.940126 CATTGCTCCATCGGTACAGC 59.060 55.000 0.00 0.00 0.00 4.40
2487 2630 1.024579 CCATCGGTACAGCCAACACC 61.025 60.000 0.00 0.00 36.97 4.16
2488 2631 0.321210 CATCGGTACAGCCAACACCA 60.321 55.000 0.00 0.00 36.97 4.17
2489 2632 0.036388 ATCGGTACAGCCAACACCAG 60.036 55.000 0.00 0.00 36.97 4.00
2490 2633 1.671054 CGGTACAGCCAACACCAGG 60.671 63.158 0.00 0.00 36.97 4.45
2491 2634 1.454539 GGTACAGCCAACACCAGGT 59.545 57.895 0.00 0.00 37.17 4.00
2492 2635 0.605589 GGTACAGCCAACACCAGGTC 60.606 60.000 0.00 0.00 37.17 3.85
2493 2636 0.396811 GTACAGCCAACACCAGGTCT 59.603 55.000 0.00 0.00 0.00 3.85
2494 2637 0.396435 TACAGCCAACACCAGGTCTG 59.604 55.000 4.07 4.07 36.78 3.51
2495 2638 1.149174 CAGCCAACACCAGGTCTGT 59.851 57.895 0.00 0.00 0.00 3.41
2496 2639 0.886490 CAGCCAACACCAGGTCTGTC 60.886 60.000 0.00 0.00 0.00 3.51
2497 2640 1.056700 AGCCAACACCAGGTCTGTCT 61.057 55.000 0.00 0.00 0.00 3.41
2498 2641 0.179018 GCCAACACCAGGTCTGTCTT 60.179 55.000 0.00 0.00 0.00 3.01
2499 2642 1.750682 GCCAACACCAGGTCTGTCTTT 60.751 52.381 0.00 0.00 0.00 2.52
2500 2643 2.654863 CCAACACCAGGTCTGTCTTTT 58.345 47.619 0.00 0.00 0.00 2.27
2501 2644 3.023832 CCAACACCAGGTCTGTCTTTTT 58.976 45.455 0.00 0.00 0.00 1.94
2554 2697 5.694910 CCCATGTCCAGTCACGTATATAAAC 59.305 44.000 0.00 0.00 0.00 2.01
2579 2724 6.881065 CCCTCAGTTTCAATCAGAATGTAAGA 59.119 38.462 0.00 0.00 35.83 2.10
2658 2803 1.534959 AGGACTCACAGAGCCTGCA 60.535 57.895 8.52 0.00 35.82 4.41
2729 2874 2.092914 CAGGGAGAATGGTGGTTAGGTC 60.093 54.545 0.00 0.00 0.00 3.85
2770 2918 3.706389 TGGATGAGGTTAGGGAGATCA 57.294 47.619 0.00 0.00 0.00 2.92
2777 2925 1.207329 GGTTAGGGAGATCAACGCTGT 59.793 52.381 15.76 0.00 32.98 4.40
2779 2927 1.847328 TAGGGAGATCAACGCTGTCA 58.153 50.000 15.76 0.00 32.98 3.58
2780 2928 1.198713 AGGGAGATCAACGCTGTCAT 58.801 50.000 8.26 0.00 0.00 3.06
2849 3000 4.449743 TCCGTAGAATTGTACACAAAGCAC 59.550 41.667 12.72 0.00 39.55 4.40
2959 3112 0.533755 AGGCAAGTGTGAGTGAGTGC 60.534 55.000 0.00 0.00 0.00 4.40
3001 3155 2.941720 GCAGTGAAAATTTTGTGCCCAA 59.058 40.909 8.47 0.00 0.00 4.12
3005 3159 5.990996 CAGTGAAAATTTTGTGCCCAACTAT 59.009 36.000 8.47 0.00 0.00 2.12
3006 3160 5.990996 AGTGAAAATTTTGTGCCCAACTATG 59.009 36.000 8.47 0.00 0.00 2.23
3031 3185 1.301953 ACCGGGCACTAAAACGTCC 60.302 57.895 6.32 0.00 0.00 4.79
3051 3205 3.888930 TCCGCATTCTCTTTGGAAAAAGT 59.111 39.130 0.00 0.00 0.00 2.66
3059 3213 7.964666 TTCTCTTTGGAAAAAGTAGGGAAAA 57.035 32.000 0.00 0.00 0.00 2.29
3078 3234 6.316140 GGGAAAATCTATGAAAATGGGCAAAC 59.684 38.462 0.00 0.00 0.00 2.93
3115 3271 9.472361 ACATAAATAATACAGTACATCGTGTCC 57.528 33.333 0.00 0.00 0.00 4.02
3116 3272 8.922676 CATAAATAATACAGTACATCGTGTCCC 58.077 37.037 0.00 0.00 0.00 4.46
3117 3273 6.726490 AATAATACAGTACATCGTGTCCCT 57.274 37.500 0.00 0.00 0.00 4.20
3118 3274 4.650754 AATACAGTACATCGTGTCCCTC 57.349 45.455 0.00 0.00 0.00 4.30
3119 3275 2.217510 ACAGTACATCGTGTCCCTCT 57.782 50.000 0.00 0.00 0.00 3.69
3129 3297 1.260561 CGTGTCCCTCTTGTTCGTTTG 59.739 52.381 0.00 0.00 0.00 2.93
3135 3303 3.074412 CCCTCTTGTTCGTTTGCACTAT 58.926 45.455 0.00 0.00 0.00 2.12
3136 3304 3.120199 CCCTCTTGTTCGTTTGCACTATG 60.120 47.826 0.00 0.00 0.00 2.23
3241 3409 6.825721 ACCTGAGGATAAAATTGAGCTACAAG 59.174 38.462 4.99 0.00 42.02 3.16
3243 3411 7.226325 CCTGAGGATAAAATTGAGCTACAAGAG 59.774 40.741 0.00 0.00 42.02 2.85
3262 3430 7.671302 ACAAGAGCTACAACATAGAGAGAAAA 58.329 34.615 0.00 0.00 0.00 2.29
3417 3585 1.510383 CTCTGTCTGCGTCCTCCTG 59.490 63.158 0.00 0.00 0.00 3.86
3537 3705 4.283978 TCAATTCTACGGGACTGGTGTAAA 59.716 41.667 0.00 0.00 0.00 2.01
3633 3811 6.590068 AGATTCCCAATACATCACTCTGAAG 58.410 40.000 0.00 0.00 0.00 3.02
3634 3812 4.142609 TCCCAATACATCACTCTGAAGC 57.857 45.455 0.00 0.00 0.00 3.86
3698 3876 9.546428 TCAACATGATACTGATTATTGAATCGT 57.454 29.630 0.00 0.00 43.92 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.668419 AACTGATATCGTTGGGCAGC 58.332 50.000 10.71 0.00 0.00 5.25
85 86 3.445008 TGGTTGAGAGAATAGCCTGACT 58.555 45.455 0.00 0.00 0.00 3.41
86 87 3.895232 TGGTTGAGAGAATAGCCTGAC 57.105 47.619 0.00 0.00 0.00 3.51
93 94 7.302524 GTTGCGTTTATTTGGTTGAGAGAATA 58.697 34.615 0.00 0.00 0.00 1.75
100 101 2.617308 TCCGTTGCGTTTATTTGGTTGA 59.383 40.909 0.00 0.00 0.00 3.18
229 288 1.074951 AACGGGAAGAAGGCAAGGG 59.925 57.895 0.00 0.00 0.00 3.95
230 289 0.537371 ACAACGGGAAGAAGGCAAGG 60.537 55.000 0.00 0.00 0.00 3.61
231 290 1.001378 CAACAACGGGAAGAAGGCAAG 60.001 52.381 0.00 0.00 0.00 4.01
232 291 1.028905 CAACAACGGGAAGAAGGCAA 58.971 50.000 0.00 0.00 0.00 4.52
233 292 2.714259 CAACAACGGGAAGAAGGCA 58.286 52.632 0.00 0.00 0.00 4.75
564 623 4.157472 GCTTGAATGAAGAAAGGAAGGGAG 59.843 45.833 0.00 0.00 32.82 4.30
566 625 3.194329 GGCTTGAATGAAGAAAGGAAGGG 59.806 47.826 0.00 0.00 32.82 3.95
567 626 3.828451 TGGCTTGAATGAAGAAAGGAAGG 59.172 43.478 0.00 0.00 32.82 3.46
590 649 0.736325 ATAGCAACACACGTCGAGCC 60.736 55.000 0.00 0.00 0.00 4.70
595 654 2.672714 TGAGACATAGCAACACACGTC 58.327 47.619 0.00 0.00 0.00 4.34
596 655 2.812358 TGAGACATAGCAACACACGT 57.188 45.000 0.00 0.00 0.00 4.49
597 656 3.515630 AGATGAGACATAGCAACACACG 58.484 45.455 0.00 0.00 0.00 4.49
599 658 4.806640 TGAGATGAGACATAGCAACACA 57.193 40.909 0.00 0.00 0.00 3.72
600 659 6.047870 AGAATGAGATGAGACATAGCAACAC 58.952 40.000 0.00 0.00 0.00 3.32
607 672 4.261783 GCCGTGAGAATGAGATGAGACATA 60.262 45.833 0.00 0.00 0.00 2.29
611 676 1.066152 CGCCGTGAGAATGAGATGAGA 59.934 52.381 0.00 0.00 0.00 3.27
631 699 2.922335 GCAAGGCACGATCCTTTTTCAC 60.922 50.000 9.60 0.00 43.62 3.18
635 703 0.251341 AGGCAAGGCACGATCCTTTT 60.251 50.000 9.60 0.00 43.62 2.27
693 769 2.046314 CTGCGTGTTACCTGGGGG 60.046 66.667 0.00 0.00 38.88 5.40
706 788 1.062587 CGAAAAGGGCTATGAACTGCG 59.937 52.381 0.00 0.00 0.00 5.18
767 851 6.567511 GCTTACAGAAAAAGGAGCTGAAAGAG 60.568 42.308 0.00 0.00 34.07 2.85
769 853 5.009010 TGCTTACAGAAAAAGGAGCTGAAAG 59.991 40.000 0.00 0.00 33.94 2.62
770 854 4.887071 TGCTTACAGAAAAAGGAGCTGAAA 59.113 37.500 0.00 0.00 33.94 2.69
773 857 4.836125 TTGCTTACAGAAAAAGGAGCTG 57.164 40.909 0.00 0.00 35.81 4.24
774 858 5.444663 CTTTGCTTACAGAAAAAGGAGCT 57.555 39.130 0.00 0.00 0.00 4.09
779 863 6.515832 ACATTCCCTTTGCTTACAGAAAAAG 58.484 36.000 0.00 0.00 0.00 2.27
780 864 6.478512 ACATTCCCTTTGCTTACAGAAAAA 57.521 33.333 0.00 0.00 0.00 1.94
781 865 6.478512 AACATTCCCTTTGCTTACAGAAAA 57.521 33.333 0.00 0.00 0.00 2.29
799 883 2.306847 AGCGTCTTTCCACCAAACATT 58.693 42.857 0.00 0.00 0.00 2.71
804 888 2.045561 TTCAAGCGTCTTTCCACCAA 57.954 45.000 0.00 0.00 0.00 3.67
853 942 2.736144 TTAGACCACGGACATCACAC 57.264 50.000 0.00 0.00 0.00 3.82
854 943 3.513912 AGAATTAGACCACGGACATCACA 59.486 43.478 0.00 0.00 0.00 3.58
855 944 4.124851 AGAATTAGACCACGGACATCAC 57.875 45.455 0.00 0.00 0.00 3.06
856 945 4.020573 ACAAGAATTAGACCACGGACATCA 60.021 41.667 0.00 0.00 0.00 3.07
862 951 4.093408 CACATGACAAGAATTAGACCACGG 59.907 45.833 0.00 0.00 0.00 4.94
868 957 6.358974 TCTCACCACATGACAAGAATTAGA 57.641 37.500 0.00 0.00 32.37 2.10
871 960 6.906157 AATTCTCACCACATGACAAGAATT 57.094 33.333 0.00 9.52 36.01 2.17
889 979 6.112734 TGTCTACGCAATCCATGTTAATTCT 58.887 36.000 0.00 0.00 0.00 2.40
892 982 4.273480 GCTGTCTACGCAATCCATGTTAAT 59.727 41.667 0.00 0.00 0.00 1.40
909 1000 5.279056 GGACGCTATATCTAAAAGGCTGTCT 60.279 44.000 0.00 0.00 0.00 3.41
910 1001 4.924462 GGACGCTATATCTAAAAGGCTGTC 59.076 45.833 0.00 0.00 0.00 3.51
911 1002 4.262506 GGGACGCTATATCTAAAAGGCTGT 60.263 45.833 0.00 0.00 0.00 4.40
912 1003 4.021016 AGGGACGCTATATCTAAAAGGCTG 60.021 45.833 0.00 0.00 0.00 4.85
913 1004 4.021016 CAGGGACGCTATATCTAAAAGGCT 60.021 45.833 0.00 0.00 0.00 4.58
921 1031 5.808366 TGATTTTCAGGGACGCTATATCT 57.192 39.130 0.00 0.00 0.00 1.98
969 1083 2.100991 GCCTTGCCGATTGAAGCG 59.899 61.111 0.00 0.00 0.00 4.68
1008 1122 2.088763 CGTCATGAGCGCGAAGTGT 61.089 57.895 12.10 0.00 41.96 3.55
1112 1226 1.202722 TCCTCCCGTCCTCAAAAACAC 60.203 52.381 0.00 0.00 0.00 3.32
1114 1228 1.520494 GTCCTCCCGTCCTCAAAAAC 58.480 55.000 0.00 0.00 0.00 2.43
1301 1415 8.017418 TCAAATTGAGGTTATTTCTGGTGTTT 57.983 30.769 0.00 0.00 0.00 2.83
1322 1436 8.956426 GTGATGAATAATAAGTGGGTTCTCAAA 58.044 33.333 0.00 0.00 0.00 2.69
1348 1462 1.818060 TCCCATTGTTTGAAGATGCGG 59.182 47.619 0.00 0.00 0.00 5.69
1350 1464 3.578688 GTGTCCCATTGTTTGAAGATGC 58.421 45.455 0.00 0.00 0.00 3.91
1367 1481 0.801067 ATACGAAAGCGAGCCGTGTC 60.801 55.000 7.83 0.00 41.64 3.67
1371 1485 0.248498 TCTGATACGAAAGCGAGCCG 60.248 55.000 0.00 0.00 41.64 5.52
1387 1501 5.469760 TGGCATTTTGATATGGACGTATCTG 59.530 40.000 11.59 4.41 33.26 2.90
1457 1577 3.858238 CGGTTCCGATAACAGAGAAGAAC 59.142 47.826 5.19 0.00 33.16 3.01
1534 1656 5.975693 AAAATAAAAGGGCAGTCGAATCA 57.024 34.783 0.00 0.00 0.00 2.57
1588 1711 9.796120 CAACAAACTAGTTCAAATAAAACCTCA 57.204 29.630 8.95 0.00 0.00 3.86
1736 1863 4.524328 CAGGAAGTAAAGGGCAAACTGAAT 59.476 41.667 0.00 0.00 0.00 2.57
1760 1887 5.821470 CACTGAAGACTGATGATGGCTTTAT 59.179 40.000 0.00 0.00 0.00 1.40
1815 1942 1.069823 CTGTGCCATAGGTAGCAGAGG 59.930 57.143 1.51 0.00 44.33 3.69
1847 1974 2.561478 TCAAAGGGGCACTGTAGTTC 57.439 50.000 0.00 0.00 0.00 3.01
2139 2267 9.706691 CATGGAAGGTTTACATTCTACGTATAT 57.293 33.333 7.15 0.00 36.91 0.86
2142 2270 5.813672 GCATGGAAGGTTTACATTCTACGTA 59.186 40.000 7.15 0.00 36.91 3.57
2143 2271 4.634443 GCATGGAAGGTTTACATTCTACGT 59.366 41.667 7.15 0.00 36.91 3.57
2144 2272 4.876107 AGCATGGAAGGTTTACATTCTACG 59.124 41.667 7.15 0.00 36.91 3.51
2145 2273 5.006746 CGAGCATGGAAGGTTTACATTCTAC 59.993 44.000 7.15 0.00 36.91 2.59
2169 2312 1.717937 CGCTAGTTGGATGCAGCAC 59.282 57.895 3.51 0.00 33.55 4.40
2177 2320 3.625764 GGAACAAATATGCGCTAGTTGGA 59.374 43.478 21.89 0.00 39.22 3.53
2200 2343 3.713858 TCAACTGAAGGTGCATGTTTG 57.286 42.857 0.00 0.00 0.00 2.93
2271 2414 1.066858 CAGTGCCATCGAGTACACCTT 60.067 52.381 9.97 0.00 33.46 3.50
2323 2466 6.659668 AGGGCAAGAAAATAGAAAGGTCTAAC 59.340 38.462 0.00 0.00 39.81 2.34
2329 2472 5.982890 TTCAGGGCAAGAAAATAGAAAGG 57.017 39.130 0.00 0.00 0.00 3.11
2480 2623 2.348411 AAAGACAGACCTGGTGTTGG 57.652 50.000 2.82 0.00 34.19 3.77
2502 2645 7.601856 AGACAGATCTGTTGTTTGTTCAAAAA 58.398 30.769 28.46 0.00 45.05 1.94
2503 2646 7.156876 AGACAGATCTGTTGTTTGTTCAAAA 57.843 32.000 28.46 0.00 45.05 2.44
2504 2647 6.757897 AGACAGATCTGTTGTTTGTTCAAA 57.242 33.333 28.46 0.00 45.05 2.69
2505 2648 6.757897 AAGACAGATCTGTTGTTTGTTCAA 57.242 33.333 28.46 0.00 45.05 2.69
2506 2649 6.260050 GGTAAGACAGATCTGTTGTTTGTTCA 59.740 38.462 28.46 8.19 45.05 3.18
2507 2650 6.293462 GGGTAAGACAGATCTGTTGTTTGTTC 60.293 42.308 28.46 13.50 45.05 3.18
2508 2651 5.531287 GGGTAAGACAGATCTGTTGTTTGTT 59.469 40.000 28.46 16.45 45.05 2.83
2509 2652 5.063880 GGGTAAGACAGATCTGTTGTTTGT 58.936 41.667 28.46 12.90 45.05 2.83
2510 2653 5.063204 TGGGTAAGACAGATCTGTTGTTTG 58.937 41.667 28.46 1.86 45.05 2.93
2511 2654 5.304686 TGGGTAAGACAGATCTGTTGTTT 57.695 39.130 28.46 22.66 45.05 2.83
2512 2655 4.974645 TGGGTAAGACAGATCTGTTGTT 57.025 40.909 28.46 24.35 45.05 2.83
2513 2656 4.287067 ACATGGGTAAGACAGATCTGTTGT 59.713 41.667 28.46 21.56 45.05 3.32
2514 2657 4.836825 ACATGGGTAAGACAGATCTGTTG 58.163 43.478 28.46 20.95 45.05 3.33
2515 2658 4.080863 GGACATGGGTAAGACAGATCTGTT 60.081 45.833 28.46 16.66 45.05 3.16
2520 2663 3.452627 GACTGGACATGGGTAAGACAGAT 59.547 47.826 0.00 0.00 0.00 2.90
2554 2697 6.881065 TCTTACATTCTGATTGAAACTGAGGG 59.119 38.462 6.56 0.00 38.29 4.30
2612 2757 0.400594 ACAGGTTCTGTAACTGGGGC 59.599 55.000 4.34 0.00 43.46 5.80
2614 2759 3.170717 TCCTACAGGTTCTGTAACTGGG 58.829 50.000 4.34 6.90 44.80 4.45
2658 2803 4.681978 GTTGAGGTGGCGTCGGCT 62.682 66.667 20.29 0.00 39.81 5.52
2710 2855 1.212195 GGACCTAACCACCATTCTCCC 59.788 57.143 0.00 0.00 0.00 4.30
2729 2874 8.781196 CATCCAATGAGACTAATATTTGACAGG 58.219 37.037 3.83 1.58 0.00 4.00
2757 2905 1.207329 ACAGCGTTGATCTCCCTAACC 59.793 52.381 6.16 0.00 0.00 2.85
2763 2911 2.621338 TGAATGACAGCGTTGATCTCC 58.379 47.619 6.16 0.00 0.00 3.71
2770 2918 5.069119 TCTGTATCCTATGAATGACAGCGTT 59.931 40.000 0.00 0.00 33.28 4.84
2777 2925 7.307131 TGCATCTTCTGTATCCTATGAATGA 57.693 36.000 0.00 0.00 0.00 2.57
2779 2927 8.985315 TTTTGCATCTTCTGTATCCTATGAAT 57.015 30.769 0.00 0.00 0.00 2.57
2780 2928 8.985315 ATTTTGCATCTTCTGTATCCTATGAA 57.015 30.769 0.00 0.00 0.00 2.57
2849 3000 6.223852 AGTCAAGTGTGTTGTTCCTAGTATG 58.776 40.000 0.00 0.00 0.00 2.39
2959 3112 3.581755 CCATGAATGTTGGAAAGCTGTG 58.418 45.455 0.00 0.00 36.26 3.66
3001 3155 0.907704 TGCCCGGTGTCTTCCATAGT 60.908 55.000 0.00 0.00 0.00 2.12
3005 3159 1.122632 TTAGTGCCCGGTGTCTTCCA 61.123 55.000 0.00 0.00 0.00 3.53
3006 3160 0.035739 TTTAGTGCCCGGTGTCTTCC 59.964 55.000 0.00 0.00 0.00 3.46
3016 3170 1.303091 ATGCGGACGTTTTAGTGCCC 61.303 55.000 0.00 0.00 0.00 5.36
3031 3185 5.393962 CCTACTTTTTCCAAAGAGAATGCG 58.606 41.667 1.73 0.00 41.97 4.73
3051 3205 6.439487 TGCCCATTTTCATAGATTTTCCCTA 58.561 36.000 0.00 0.00 0.00 3.53
3059 3213 5.184864 TGAACGTTTGCCCATTTTCATAGAT 59.815 36.000 0.46 0.00 0.00 1.98
3078 3234 8.810427 ACTGTATTATTTATGTAACCGTGAACG 58.190 33.333 0.00 0.00 39.44 3.95
3108 3264 0.748450 AACGAACAAGAGGGACACGA 59.252 50.000 0.00 0.00 0.00 4.35
3109 3265 1.260561 CAAACGAACAAGAGGGACACG 59.739 52.381 0.00 0.00 0.00 4.49
3110 3266 1.002792 GCAAACGAACAAGAGGGACAC 60.003 52.381 0.00 0.00 0.00 3.67
3111 3267 1.305201 GCAAACGAACAAGAGGGACA 58.695 50.000 0.00 0.00 0.00 4.02
3112 3268 1.002792 GTGCAAACGAACAAGAGGGAC 60.003 52.381 0.00 0.00 0.00 4.46
3113 3269 1.134220 AGTGCAAACGAACAAGAGGGA 60.134 47.619 0.00 0.00 0.00 4.20
3114 3270 1.308998 AGTGCAAACGAACAAGAGGG 58.691 50.000 0.00 0.00 0.00 4.30
3115 3271 3.667960 GCATAGTGCAAACGAACAAGAGG 60.668 47.826 0.00 0.00 44.26 3.69
3116 3272 3.482786 GCATAGTGCAAACGAACAAGAG 58.517 45.455 0.00 0.00 44.26 2.85
3117 3273 3.536158 GCATAGTGCAAACGAACAAGA 57.464 42.857 0.00 0.00 44.26 3.02
3241 3409 8.180317 GAGTTTTTCTCTCTATGTTGTAGCTC 57.820 38.462 0.00 0.00 39.86 4.09
3258 3426 4.855715 AAGGCCAGCTTAAGAGTTTTTC 57.144 40.909 5.01 0.00 0.00 2.29
3262 3430 3.149981 GTGAAAGGCCAGCTTAAGAGTT 58.850 45.455 5.01 0.00 0.00 3.01
3417 3585 2.011222 TCGGTATGCGGAAATTTGGTC 58.989 47.619 0.00 0.00 0.00 4.02
3537 3705 6.073548 CGTGCAAACTCTCTGAAACTCTTATT 60.074 38.462 0.00 0.00 0.00 1.40
3648 3826 9.337396 TGAGTTAACATTGTTCTCTTTATGTGT 57.663 29.630 8.61 0.00 31.98 3.72


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

AutoCloner maintained by Alex Coulton.