Multiple sequence alignment - TraesCS2B01G383500

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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 TraesCS2B01G383500 chr2B 100.000 3674 0 0 1 3674 547059622 547055949 0.000000e+00 6785
1 TraesCS2B01G383500 chr2D 92.526 3305 126 47 1 3236 468858732 468855480 0.000000e+00 4623
2 TraesCS2B01G383500 chr2D 93.494 415 21 3 3262 3674 468855017 468854607 2.430000e-171 612
3 TraesCS2B01G383500 chr2A 90.682 3327 160 62 1 3234 608873623 608870354 0.000000e+00 4289
4 TraesCS2B01G383500 chr2A 91.327 196 15 2 3260 3454 608865832 608865638 2.180000e-67 267
5 TraesCS2B01G383500 chr6A 88.181 1396 158 7 1154 2544 426966091 426967484 0.000000e+00 1657
6 TraesCS2B01G383500 chr6B 88.037 1396 160 7 1154 2544 458487539 458486146 0.000000e+00 1646
7 TraesCS2B01G383500 chr6D 87.894 1396 162 7 1154 2544 293803361 293801968 0.000000e+00 1635


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 TraesCS2B01G383500 chr2B 547055949 547059622 3673 True 6785.0 6785 100.000 1 3674 1 chr2B.!!$R1 3673
1 TraesCS2B01G383500 chr2D 468854607 468858732 4125 True 2617.5 4623 93.010 1 3674 2 chr2D.!!$R1 3673
2 TraesCS2B01G383500 chr2A 608870354 608873623 3269 True 4289.0 4289 90.682 1 3234 1 chr2A.!!$R2 3233
3 TraesCS2B01G383500 chr6A 426966091 426967484 1393 False 1657.0 1657 88.181 1154 2544 1 chr6A.!!$F1 1390
4 TraesCS2B01G383500 chr6B 458486146 458487539 1393 True 1646.0 1646 88.037 1154 2544 1 chr6B.!!$R1 1390
5 TraesCS2B01G383500 chr6D 293801968 293803361 1393 True 1635.0 1635 87.894 1154 2544 1 chr6D.!!$R1 1390

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
373 410 0.178964 TCTGGCCCAAAACTGAAGGG 60.179 55.0 0.0 0.0 45.68 3.95 F
961 1026 1.130777 AAAGCATTGGCCCAAACAGT 58.869 45.0 0.0 0.0 42.56 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1317 1.423395 CTTCTTCGCGCTCAAGAAGT 58.577 50.0 31.45 0.0 46.44 3.01 R
2839 2938 0.250234 CCAGAGATTCCAGAACGGCA 59.750 55.0 0.00 0.0 33.14 5.69 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
62 80 1.810151 CCACCCGGTGACATTGTTTAG 59.190 52.381 19.81 0.00 35.23 1.85
64 82 1.700739 ACCCGGTGACATTGTTTAGGA 59.299 47.619 0.00 0.00 0.00 2.94
111 129 1.294659 GCTCGGCAACTTGGTGAGAG 61.295 60.000 7.05 7.05 0.00 3.20
114 132 0.671781 CGGCAACTTGGTGAGAGGAG 60.672 60.000 0.00 0.00 0.00 3.69
224 258 1.386533 CATGATTGAGCCCGCTTTCT 58.613 50.000 0.00 0.00 0.00 2.52
243 277 6.090358 GCTTTCTGTTAGTATACGAGCACAAA 59.910 38.462 0.00 1.74 0.00 2.83
272 306 8.749026 TGGAGACAGGAAATAGTAGTAGTAAG 57.251 38.462 0.00 0.00 35.01 2.34
284 321 9.759473 AATAGTAGTAGTAAGTTACCAACAGGA 57.241 33.333 9.46 0.00 0.00 3.86
285 322 7.700022 AGTAGTAGTAAGTTACCAACAGGAG 57.300 40.000 9.46 0.00 0.00 3.69
286 323 7.237255 AGTAGTAGTAAGTTACCAACAGGAGT 58.763 38.462 9.46 0.18 0.00 3.85
287 324 8.386264 AGTAGTAGTAAGTTACCAACAGGAGTA 58.614 37.037 9.46 0.00 0.00 2.59
288 325 9.183368 GTAGTAGTAAGTTACCAACAGGAGTAT 57.817 37.037 9.46 0.00 0.00 2.12
289 326 8.064336 AGTAGTAAGTTACCAACAGGAGTATG 57.936 38.462 9.46 0.00 0.00 2.39
336 373 7.281040 TGTACTACTAGCACAGTTTTGTACT 57.719 36.000 18.27 0.00 37.69 2.73
337 374 8.394971 TGTACTACTAGCACAGTTTTGTACTA 57.605 34.615 18.27 0.00 37.69 1.82
338 375 8.292448 TGTACTACTAGCACAGTTTTGTACTAC 58.708 37.037 18.27 0.00 37.69 2.73
360 397 1.561542 TCTGATCCCTCTTTTCTGGCC 59.438 52.381 0.00 0.00 0.00 5.36
373 410 0.178964 TCTGGCCCAAAACTGAAGGG 60.179 55.000 0.00 0.00 45.68 3.95
381 419 3.031013 CCAAAACTGAAGGGAGGTTTGT 58.969 45.455 9.54 0.00 45.50 2.83
395 433 4.580167 GGAGGTTTGTATATGATTGCTGCA 59.420 41.667 0.00 0.00 0.00 4.41
449 487 2.423538 CGGCTCATTTAAAACAGGGAGG 59.576 50.000 0.00 0.00 0.00 4.30
503 541 1.624336 TGTAGGTGTAGCCGTCAGTT 58.376 50.000 0.00 0.00 43.70 3.16
519 560 6.133392 CCGTCAGTTGTGTGTAAACTAAATG 58.867 40.000 0.00 0.00 35.70 2.32
524 565 8.339714 TCAGTTGTGTGTAAACTAAATGTAAGC 58.660 33.333 0.00 0.00 35.70 3.09
549 590 3.089284 CACAAAGAACCAACCCCCTATC 58.911 50.000 0.00 0.00 0.00 2.08
637 690 3.921119 ACGTCAGGAACATACGTAACA 57.079 42.857 0.00 0.00 46.83 2.41
638 691 3.568538 ACGTCAGGAACATACGTAACAC 58.431 45.455 0.00 0.00 46.83 3.32
640 693 4.171005 CGTCAGGAACATACGTAACACAT 58.829 43.478 0.00 0.00 34.76 3.21
714 768 2.483188 GGCCCGTACTAGAGGACAAATG 60.483 54.545 0.00 0.00 0.00 2.32
792 846 6.018832 CAGAATTCCACCACAAAAATGACAAC 60.019 38.462 0.65 0.00 0.00 3.32
961 1026 1.130777 AAAGCATTGGCCCAAACAGT 58.869 45.000 0.00 0.00 42.56 3.55
964 1029 1.203050 AGCATTGGCCCAAACAGTACT 60.203 47.619 0.00 0.00 42.56 2.73
971 1036 2.035449 GGCCCAAACAGTACTGGAAAAC 59.965 50.000 26.12 10.94 34.35 2.43
974 1039 4.558697 GCCCAAACAGTACTGGAAAACATC 60.559 45.833 26.12 5.37 34.35 3.06
979 1045 2.666508 CAGTACTGGAAAACATCGTCCG 59.333 50.000 15.49 0.00 36.65 4.79
1002 1068 6.697892 CCGATGATCAGATCACATATGAGATG 59.302 42.308 18.80 8.55 43.01 2.90
1003 1069 6.697892 CGATGATCAGATCACATATGAGATGG 59.302 42.308 18.80 11.36 43.01 3.51
1004 1070 7.416438 CGATGATCAGATCACATATGAGATGGA 60.416 40.741 18.80 15.46 43.01 3.41
1005 1071 7.735326 TGATCAGATCACATATGAGATGGAT 57.265 36.000 18.80 18.64 38.57 3.41
1006 1072 8.834004 TGATCAGATCACATATGAGATGGATA 57.166 34.615 18.80 8.75 38.57 2.59
1007 1073 9.435570 TGATCAGATCACATATGAGATGGATAT 57.564 33.333 18.80 8.03 38.57 1.63
1020 1092 5.304357 TGAGATGGATATAACAGAAAGGCGA 59.696 40.000 0.00 0.00 0.00 5.54
1021 1093 6.174720 AGATGGATATAACAGAAAGGCGAA 57.825 37.500 0.00 0.00 0.00 4.70
1022 1094 5.992217 AGATGGATATAACAGAAAGGCGAAC 59.008 40.000 0.00 0.00 0.00 3.95
1023 1095 4.116961 TGGATATAACAGAAAGGCGAACG 58.883 43.478 0.00 0.00 0.00 3.95
1024 1096 4.142116 TGGATATAACAGAAAGGCGAACGA 60.142 41.667 0.00 0.00 0.00 3.85
1047 1119 7.176690 ACGAATTTCCACTGGATTTCTTGTTAT 59.823 33.333 14.74 0.00 0.00 1.89
1398 1473 3.204526 CGTAGATCTCCTCCACGTACTT 58.795 50.000 0.00 0.00 0.00 2.24
1401 1476 3.283751 AGATCTCCTCCACGTACTTCTG 58.716 50.000 0.00 0.00 0.00 3.02
1537 1612 3.608662 ACCCACGCCGAGACGAAA 61.609 61.111 0.00 0.00 36.70 3.46
1672 1747 1.210931 CTTCCCGAACAGCGTCGTA 59.789 57.895 6.72 0.00 39.43 3.43
1753 1828 4.856801 CCGTTGATGCTCCCGGGG 62.857 72.222 23.50 13.02 36.84 5.73
2251 2326 4.601621 GAAGAAGTGCTTCCCGATAAAC 57.398 45.455 0.00 0.00 45.90 2.01
2498 2573 1.904865 AGGTAGTCCGTGGCGTTCA 60.905 57.895 0.00 0.00 39.05 3.18
2499 2574 1.217244 GGTAGTCCGTGGCGTTCAT 59.783 57.895 0.00 0.00 0.00 2.57
2606 2681 1.447838 TTCAGCGATCGGAACTGGC 60.448 57.895 18.30 0.00 32.19 4.85
2616 2691 1.299976 GGAACTGGCAAGTCGGGAT 59.700 57.895 0.00 0.00 34.77 3.85
2617 2692 0.322546 GGAACTGGCAAGTCGGGATT 60.323 55.000 0.00 0.00 34.77 3.01
2618 2693 0.804989 GAACTGGCAAGTCGGGATTG 59.195 55.000 0.00 0.00 34.77 2.67
2619 2694 0.609131 AACTGGCAAGTCGGGATTGG 60.609 55.000 0.00 0.00 34.77 3.16
2621 2696 3.508840 GGCAAGTCGGGATTGGCG 61.509 66.667 6.11 0.00 42.36 5.69
2723 2809 2.105528 GCGAAATAGGCGGACGGA 59.894 61.111 0.00 0.00 0.00 4.69
2725 2811 0.878961 GCGAAATAGGCGGACGGATT 60.879 55.000 0.00 0.00 0.00 3.01
2737 2824 2.222953 CGGACGGATTGGATTTCGTTTC 60.223 50.000 0.00 0.00 35.91 2.78
2752 2839 2.094597 TCGTTTCGGAATATCGTGTGGT 60.095 45.455 0.00 0.00 0.00 4.16
2813 2902 1.682451 CCCGCCCGGAGTGAATCTTA 61.682 60.000 0.73 0.00 37.50 2.10
2839 2938 4.458829 TCTCGGATCAGGGGCGGT 62.459 66.667 0.00 0.00 0.00 5.68
2878 2977 3.581770 TGGATTCTGGAGATCATAGCTGG 59.418 47.826 0.00 0.00 0.00 4.85
2971 3073 7.324935 ACTATTTCGGTTTGTTTTTGGAGTTT 58.675 30.769 0.00 0.00 0.00 2.66
3003 3106 6.017026 GGCTGTATAAATCCTTGGCTAGTTTC 60.017 42.308 0.00 0.00 0.00 2.78
3015 3131 2.094442 GGCTAGTTTCTCGCACTCTTCT 60.094 50.000 0.00 0.00 0.00 2.85
3021 3137 4.705507 AGTTTCTCGCACTCTTCTGGTATA 59.294 41.667 0.00 0.00 0.00 1.47
3022 3138 4.902443 TTCTCGCACTCTTCTGGTATAG 57.098 45.455 0.00 0.00 0.00 1.31
3039 3158 8.404000 TCTGGTATAGTTCTGTTACTCGATTTC 58.596 37.037 0.00 0.00 0.00 2.17
3056 3175 6.924111 TCGATTTCTTTTACGGGTAGTACTT 58.076 36.000 0.00 0.00 34.56 2.24
3058 3177 6.808212 CGATTTCTTTTACGGGTAGTACTTCA 59.192 38.462 0.00 0.00 34.56 3.02
3059 3178 7.201384 CGATTTCTTTTACGGGTAGTACTTCAC 60.201 40.741 0.00 0.00 34.56 3.18
3060 3179 6.403866 TTCTTTTACGGGTAGTACTTCACA 57.596 37.500 0.00 0.00 34.56 3.58
3061 3180 6.594788 TCTTTTACGGGTAGTACTTCACAT 57.405 37.500 0.00 0.00 34.56 3.21
3062 3181 6.996509 TCTTTTACGGGTAGTACTTCACATT 58.003 36.000 0.00 0.00 34.56 2.71
3063 3182 6.869913 TCTTTTACGGGTAGTACTTCACATTG 59.130 38.462 0.00 0.00 34.56 2.82
3064 3183 3.604875 ACGGGTAGTACTTCACATTGG 57.395 47.619 0.00 0.00 0.00 3.16
3078 3201 0.888736 CATTGGCACGTTGGGACTGA 60.889 55.000 0.00 0.00 0.00 3.41
3113 3236 8.696410 TTGAAACTTTTAACCTTTGATGACAC 57.304 30.769 0.00 0.00 0.00 3.67
3127 3253 5.029807 TGATGACACTTATTAATGCCCGA 57.970 39.130 0.00 0.00 0.00 5.14
3146 3272 0.831307 AGGATCTCGGGTTTACAGCC 59.169 55.000 0.00 0.00 37.19 4.85
3166 3299 2.047939 GCAATTGTGGTGCTGCCC 60.048 61.111 7.40 0.00 39.00 5.36
3178 3311 0.332293 TGCTGCCCATGGAATCTTGA 59.668 50.000 15.22 0.00 0.00 3.02
3183 3316 4.070716 CTGCCCATGGAATCTTGATAGTC 58.929 47.826 15.22 0.00 0.00 2.59
3190 3323 5.114764 TGGAATCTTGATAGTCATGGCAA 57.885 39.130 0.00 0.00 0.00 4.52
3243 3381 1.690893 GCCTCTAGAGATGGTGATGCA 59.309 52.381 21.76 0.00 0.00 3.96
3244 3382 2.288948 GCCTCTAGAGATGGTGATGCAG 60.289 54.545 21.76 0.73 0.00 4.41
3245 3383 2.288948 CCTCTAGAGATGGTGATGCAGC 60.289 54.545 21.76 0.00 0.00 5.25
3246 3384 1.339291 TCTAGAGATGGTGATGCAGCG 59.661 52.381 0.00 0.00 34.27 5.18
3248 3386 0.538584 AGAGATGGTGATGCAGCGAA 59.461 50.000 0.00 0.00 34.27 4.70
3249 3387 0.654683 GAGATGGTGATGCAGCGAAC 59.345 55.000 0.00 0.00 34.27 3.95
3250 3388 0.745845 AGATGGTGATGCAGCGAACC 60.746 55.000 4.58 4.58 34.27 3.62
3252 3390 0.394762 ATGGTGATGCAGCGAACCAT 60.395 50.000 18.43 18.43 45.95 3.55
3255 3393 1.742831 GGTGATGCAGCGAACCATTTA 59.257 47.619 6.59 0.00 32.69 1.40
3256 3394 2.223340 GGTGATGCAGCGAACCATTTAG 60.223 50.000 6.59 0.00 32.69 1.85
3257 3395 2.677836 GTGATGCAGCGAACCATTTAGA 59.322 45.455 0.00 0.00 0.00 2.10
3258 3396 3.313526 GTGATGCAGCGAACCATTTAGAT 59.686 43.478 0.00 0.00 0.00 1.98
3259 3397 4.511454 GTGATGCAGCGAACCATTTAGATA 59.489 41.667 0.00 0.00 0.00 1.98
3264 3834 5.466728 TGCAGCGAACCATTTAGATATTCTC 59.533 40.000 0.00 0.00 0.00 2.87
3275 3845 7.437748 CATTTAGATATTCTCAGTCGTTCCCT 58.562 38.462 0.00 0.00 0.00 4.20
3299 3869 2.668550 GGTGGTGGGAGCGAACAC 60.669 66.667 0.00 0.00 36.89 3.32
3302 3872 0.818040 GTGGTGGGAGCGAACACTTT 60.818 55.000 7.45 0.00 37.72 2.66
3315 3885 3.545633 GAACACTTTGAGATTCACGTGC 58.454 45.455 11.67 0.00 33.74 5.34
3318 3888 2.061773 ACTTTGAGATTCACGTGCGAG 58.938 47.619 11.67 1.66 0.00 5.03
3323 3893 2.115595 GAGATTCACGTGCGAGATCTG 58.884 52.381 20.44 0.00 0.00 2.90
3325 3895 1.849219 GATTCACGTGCGAGATCTGAC 59.151 52.381 11.67 0.00 0.00 3.51
3331 3901 0.733729 GTGCGAGATCTGACGTACCT 59.266 55.000 12.17 0.00 38.67 3.08
3429 3999 2.096069 CACACTTGCATCTCTGTTTCCG 60.096 50.000 0.00 0.00 0.00 4.30
3430 4000 1.135859 CACTTGCATCTCTGTTTCCGC 60.136 52.381 0.00 0.00 0.00 5.54
3447 4018 1.468520 CCGCTGGGTGTTTGTCTATTG 59.531 52.381 0.00 0.00 0.00 1.90
3472 4043 2.505819 GTCTCACTCTCCCTCTCTCTCT 59.494 54.545 0.00 0.00 0.00 3.10
3473 4044 2.771943 TCTCACTCTCCCTCTCTCTCTC 59.228 54.545 0.00 0.00 0.00 3.20
3474 4045 2.774234 CTCACTCTCCCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
3475 4046 2.771943 TCACTCTCCCTCTCTCTCTCTC 59.228 54.545 0.00 0.00 0.00 3.20
3520 4091 3.297134 TCTGTGTTCTGGCCTCTTTTT 57.703 42.857 3.32 0.00 0.00 1.94
3528 4099 4.380843 TCTGGCCTCTTTTTGTTCCATA 57.619 40.909 3.32 0.00 0.00 2.74
3548 4119 6.607198 TCCATAACCATTCATCTTCTTTTCCC 59.393 38.462 0.00 0.00 0.00 3.97
3595 4167 6.040504 ACCTTTATTCTTTGAACGAAAAGGCT 59.959 34.615 19.44 11.11 37.67 4.58
3611 4183 0.792640 GGCTGAACACATCTGACACG 59.207 55.000 0.00 0.00 35.20 4.49
3631 4203 5.046591 ACACGAGAGATTGTCCAAGGAATTA 60.047 40.000 0.00 0.00 0.00 1.40
3669 4241 1.152290 TCAACCGGGTCACCCACTA 60.152 57.895 15.17 0.00 45.83 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 129 2.587473 GCTTGCGAGCTAGCCTCC 60.587 66.667 19.25 0.00 45.65 4.30
208 242 1.168714 AACAGAAAGCGGGCTCAATC 58.831 50.000 0.00 0.00 0.00 2.67
224 258 8.198778 TCCAATATTTGTGCTCGTATACTAACA 58.801 33.333 0.56 0.00 0.00 2.41
243 277 9.884814 ACTACTACTATTTCCTGTCTCCAATAT 57.115 33.333 0.00 0.00 0.00 1.28
270 304 5.045578 AGCATCATACTCCTGTTGGTAACTT 60.046 40.000 0.00 0.00 37.61 2.66
272 306 4.770795 AGCATCATACTCCTGTTGGTAAC 58.229 43.478 0.00 0.00 34.23 2.50
284 321 8.043710 GCTATAATTAACCTGGAGCATCATACT 58.956 37.037 0.00 0.00 36.25 2.12
285 322 8.043710 AGCTATAATTAACCTGGAGCATCATAC 58.956 37.037 0.00 0.00 36.25 2.39
286 323 8.150827 AGCTATAATTAACCTGGAGCATCATA 57.849 34.615 0.00 0.00 36.25 2.15
287 324 7.025520 AGCTATAATTAACCTGGAGCATCAT 57.974 36.000 0.00 0.00 36.25 2.45
288 325 6.439636 AGCTATAATTAACCTGGAGCATCA 57.560 37.500 0.00 0.00 36.25 3.07
289 326 6.712547 ACAAGCTATAATTAACCTGGAGCATC 59.287 38.462 0.00 0.00 0.00 3.91
336 373 4.033709 CCAGAAAAGAGGGATCAGAGGTA 58.966 47.826 0.00 0.00 0.00 3.08
337 374 2.843113 CCAGAAAAGAGGGATCAGAGGT 59.157 50.000 0.00 0.00 0.00 3.85
338 375 2.421248 GCCAGAAAAGAGGGATCAGAGG 60.421 54.545 0.00 0.00 0.00 3.69
360 397 3.031013 ACAAACCTCCCTTCAGTTTTGG 58.969 45.455 0.00 0.00 31.54 3.28
373 410 5.756195 TGCAGCAATCATATACAAACCTC 57.244 39.130 0.00 0.00 0.00 3.85
381 419 7.763071 GTCATGTAGAGATGCAGCAATCATATA 59.237 37.037 4.07 0.00 0.00 0.86
449 487 6.762661 CCTCACAAGAGTACTCTACCTACTAC 59.237 46.154 25.42 0.00 39.39 2.73
503 541 6.651308 CACGCTTACATTTAGTTTACACACA 58.349 36.000 0.00 0.00 0.00 3.72
519 560 1.332375 TGGTTCTTTGTGCACGCTTAC 59.668 47.619 13.13 6.38 0.00 2.34
524 565 0.248866 GGGTTGGTTCTTTGTGCACG 60.249 55.000 13.13 0.00 0.00 5.34
549 590 9.709495 TCTTCATTTTGATGTTCCCTAAAAATG 57.291 29.630 11.17 11.17 44.13 2.32
635 688 6.238103 CGATCGAATGGCTTTAGTTTATGTGT 60.238 38.462 10.26 0.00 0.00 3.72
637 690 6.046593 TCGATCGAATGGCTTTAGTTTATGT 58.953 36.000 16.99 0.00 0.00 2.29
638 691 6.420903 TCTCGATCGAATGGCTTTAGTTTATG 59.579 38.462 19.92 1.03 0.00 1.90
640 693 5.898174 TCTCGATCGAATGGCTTTAGTTTA 58.102 37.500 19.92 0.00 0.00 2.01
714 768 4.293415 CTGCTGAAGGTTGAATTGTTGAC 58.707 43.478 0.00 0.00 0.00 3.18
819 877 0.729116 GTGTGTGGATGGAATCTGCG 59.271 55.000 0.00 0.00 44.71 5.18
923 988 1.082756 GCCGCTCTTGTGTTCGTTG 60.083 57.895 0.00 0.00 0.00 4.10
961 1026 3.517602 CATCGGACGATGTTTTCCAGTA 58.482 45.455 22.64 0.00 44.93 2.74
974 1039 2.781945 TGTGATCTGATCATCGGACG 57.218 50.000 22.09 0.00 42.04 4.79
979 1045 7.783042 TCCATCTCATATGTGATCTGATCATC 58.217 38.462 22.09 15.72 42.04 2.92
1002 1068 4.365723 TCGTTCGCCTTTCTGTTATATCC 58.634 43.478 0.00 0.00 0.00 2.59
1003 1069 5.961395 TTCGTTCGCCTTTCTGTTATATC 57.039 39.130 0.00 0.00 0.00 1.63
1004 1070 6.920569 AATTCGTTCGCCTTTCTGTTATAT 57.079 33.333 0.00 0.00 0.00 0.86
1005 1071 6.183360 GGAAATTCGTTCGCCTTTCTGTTATA 60.183 38.462 13.98 0.00 37.08 0.98
1006 1072 5.391629 GGAAATTCGTTCGCCTTTCTGTTAT 60.392 40.000 13.98 0.00 37.08 1.89
1007 1073 4.083696 GGAAATTCGTTCGCCTTTCTGTTA 60.084 41.667 13.98 0.00 37.08 2.41
1020 1092 5.301805 ACAAGAAATCCAGTGGAAATTCGTT 59.698 36.000 24.39 18.66 36.99 3.85
1021 1093 4.827284 ACAAGAAATCCAGTGGAAATTCGT 59.173 37.500 24.39 21.19 36.99 3.85
1022 1094 5.376854 ACAAGAAATCCAGTGGAAATTCG 57.623 39.130 24.39 17.71 36.99 3.34
1023 1095 8.306761 ACATAACAAGAAATCCAGTGGAAATTC 58.693 33.333 23.81 23.81 34.34 2.17
1024 1096 8.193953 ACATAACAAGAAATCCAGTGGAAATT 57.806 30.769 17.71 14.42 34.34 1.82
1047 1119 0.981183 ACCAATCAAGCCGGAGTACA 59.019 50.000 5.05 0.00 0.00 2.90
1245 1317 1.423395 CTTCTTCGCGCTCAAGAAGT 58.577 50.000 31.45 0.00 46.44 3.01
1398 1473 3.043713 CGCTGTTCGCCAAGCAGA 61.044 61.111 2.31 0.00 34.21 4.26
1753 1828 2.183555 CTCAAGTCGTACGGCCCC 59.816 66.667 17.68 1.64 0.00 5.80
2606 2681 1.501741 CAACGCCAATCCCGACTTG 59.498 57.895 0.00 0.00 0.00 3.16
2616 2691 4.243008 TCCTCACGCCAACGCCAA 62.243 61.111 0.00 0.00 45.53 4.52
2617 2692 4.680237 CTCCTCACGCCAACGCCA 62.680 66.667 0.00 0.00 45.53 5.69
2621 2696 2.743928 CAGCCTCCTCACGCCAAC 60.744 66.667 0.00 0.00 0.00 3.77
2698 2784 2.189499 GCCTATTTCGCCTGGCCAG 61.189 63.158 26.87 26.87 39.49 4.85
2723 2809 5.526111 ACGATATTCCGAAACGAAATCCAAT 59.474 36.000 10.93 0.00 0.00 3.16
2725 2811 4.269123 CACGATATTCCGAAACGAAATCCA 59.731 41.667 10.93 0.00 0.00 3.41
2737 2824 1.197055 CGTCACCACACGATATTCCG 58.803 55.000 0.00 0.00 42.69 4.30
2766 2853 2.308570 TCTCCAGCCAAAAGCCAAGATA 59.691 45.455 0.00 0.00 45.47 1.98
2767 2854 1.076024 TCTCCAGCCAAAAGCCAAGAT 59.924 47.619 0.00 0.00 45.47 2.40
2769 2856 1.000171 GTTCTCCAGCCAAAAGCCAAG 60.000 52.381 0.00 0.00 45.47 3.61
2799 2888 3.198068 CACCACATAAGATTCACTCCGG 58.802 50.000 0.00 0.00 0.00 5.14
2813 2902 0.826715 CTGATCCGAGACCACCACAT 59.173 55.000 0.00 0.00 0.00 3.21
2839 2938 0.250234 CCAGAGATTCCAGAACGGCA 59.750 55.000 0.00 0.00 33.14 5.69
2971 3073 2.775384 AGGATTTATACAGCCCCGAACA 59.225 45.455 0.00 0.00 0.00 3.18
3003 3106 4.336993 AGAACTATACCAGAAGAGTGCGAG 59.663 45.833 0.00 0.00 0.00 5.03
3015 3131 8.289939 AGAAATCGAGTAACAGAACTATACCA 57.710 34.615 0.00 0.00 0.00 3.25
3021 3137 7.115947 CCGTAAAAGAAATCGAGTAACAGAACT 59.884 37.037 0.00 0.00 0.00 3.01
3022 3138 7.225397 CCGTAAAAGAAATCGAGTAACAGAAC 58.775 38.462 0.00 0.00 0.00 3.01
3039 3158 6.091713 CCAATGTGAAGTACTACCCGTAAAAG 59.908 42.308 0.00 0.00 0.00 2.27
3056 3175 1.149401 TCCCAACGTGCCAATGTGA 59.851 52.632 0.00 0.00 0.00 3.58
3058 3177 1.150536 AGTCCCAACGTGCCAATGT 59.849 52.632 0.00 0.00 0.00 2.71
3059 3178 0.888736 TCAGTCCCAACGTGCCAATG 60.889 55.000 0.00 0.00 0.00 2.82
3060 3179 0.606401 CTCAGTCCCAACGTGCCAAT 60.606 55.000 0.00 0.00 0.00 3.16
3061 3180 1.227823 CTCAGTCCCAACGTGCCAA 60.228 57.895 0.00 0.00 0.00 4.52
3062 3181 2.425592 CTCAGTCCCAACGTGCCA 59.574 61.111 0.00 0.00 0.00 4.92
3063 3182 3.050275 GCTCAGTCCCAACGTGCC 61.050 66.667 0.00 0.00 0.00 5.01
3064 3183 2.031163 AGCTCAGTCCCAACGTGC 59.969 61.111 0.00 0.00 0.00 5.34
3078 3201 8.465273 AGGTTAAAAGTTTCAAAGATACAGCT 57.535 30.769 0.00 0.00 0.00 4.24
3127 3253 0.831307 GGCTGTAAACCCGAGATCCT 59.169 55.000 0.00 0.00 0.00 3.24
3146 3272 0.947180 GGCAGCACCACAATTGCAAG 60.947 55.000 4.94 0.00 42.83 4.01
3166 3299 5.067954 TGCCATGACTATCAAGATTCCATG 58.932 41.667 0.00 0.00 0.00 3.66
3178 3311 7.498900 TCGAAATGTAAATCTTGCCATGACTAT 59.501 33.333 0.00 0.00 0.00 2.12
3183 3316 5.883661 ACTCGAAATGTAAATCTTGCCATG 58.116 37.500 0.00 0.00 0.00 3.66
3243 3381 6.821388 ACTGAGAATATCTAAATGGTTCGCT 58.179 36.000 0.00 0.00 0.00 4.93
3244 3382 6.129062 CGACTGAGAATATCTAAATGGTTCGC 60.129 42.308 0.00 0.00 0.00 4.70
3245 3383 6.918569 ACGACTGAGAATATCTAAATGGTTCG 59.081 38.462 0.00 0.00 0.00 3.95
3246 3384 8.649973 AACGACTGAGAATATCTAAATGGTTC 57.350 34.615 0.00 0.00 0.00 3.62
3248 3386 7.210873 GGAACGACTGAGAATATCTAAATGGT 58.789 38.462 0.00 0.00 0.00 3.55
3249 3387 6.647067 GGGAACGACTGAGAATATCTAAATGG 59.353 42.308 0.00 0.00 0.00 3.16
3250 3388 7.437748 AGGGAACGACTGAGAATATCTAAATG 58.562 38.462 0.00 0.00 0.00 2.32
3252 3390 8.529424 TTAGGGAACGACTGAGAATATCTAAA 57.471 34.615 0.00 0.00 0.00 1.85
3255 3393 5.536916 CCTTAGGGAACGACTGAGAATATCT 59.463 44.000 0.00 0.00 33.58 1.98
3256 3394 5.535406 TCCTTAGGGAACGACTGAGAATATC 59.465 44.000 0.00 0.00 38.93 1.63
3257 3395 5.455872 TCCTTAGGGAACGACTGAGAATAT 58.544 41.667 0.00 0.00 38.93 1.28
3258 3396 4.863548 TCCTTAGGGAACGACTGAGAATA 58.136 43.478 0.00 0.00 38.93 1.75
3259 3397 3.702045 CTCCTTAGGGAACGACTGAGAAT 59.298 47.826 0.00 0.00 41.69 2.40
3275 3845 1.615424 GCTCCCACCACCCTCCTTA 60.615 63.158 0.00 0.00 0.00 2.69
3299 3869 2.328473 TCTCGCACGTGAATCTCAAAG 58.672 47.619 22.23 3.87 0.00 2.77
3302 3872 1.745653 AGATCTCGCACGTGAATCTCA 59.254 47.619 22.23 0.00 0.00 3.27
3315 3885 1.600013 CCTCAGGTACGTCAGATCTCG 59.400 57.143 0.00 0.00 0.00 4.04
3318 3888 1.950909 CTCCCTCAGGTACGTCAGATC 59.049 57.143 0.00 0.00 0.00 2.75
3323 3893 0.450983 CGAACTCCCTCAGGTACGTC 59.549 60.000 0.00 0.00 0.00 4.34
3325 3895 1.139095 GCGAACTCCCTCAGGTACG 59.861 63.158 0.00 0.00 0.00 3.67
3429 3999 1.885887 TGCAATAGACAAACACCCAGC 59.114 47.619 0.00 0.00 0.00 4.85
3430 4000 3.569701 ACTTGCAATAGACAAACACCCAG 59.430 43.478 0.00 0.00 0.00 4.45
3447 4018 1.476488 GAGAGGGAGAGTGAGACTTGC 59.524 57.143 0.00 0.00 0.00 4.01
3489 4060 4.578928 GCCAGAACACAGAACTTCCTAAAA 59.421 41.667 0.00 0.00 0.00 1.52
3528 4099 4.096681 GGGGGAAAAGAAGATGAATGGTT 58.903 43.478 0.00 0.00 0.00 3.67
3591 4163 1.606480 CGTGTCAGATGTGTTCAGCCT 60.606 52.381 0.00 0.00 0.00 4.58
3595 4167 2.884639 TCTCTCGTGTCAGATGTGTTCA 59.115 45.455 0.00 0.00 0.00 3.18
3611 4183 5.240403 GCCATAATTCCTTGGACAATCTCTC 59.760 44.000 6.26 0.00 34.81 3.20
3631 4203 4.663334 TGAGTATCTAGGTACGATGCCAT 58.337 43.478 7.52 0.00 34.92 4.40


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

AutoCloner maintained by Alex Coulton.