Multiple sequence alignment - TraesCS2D01G198200

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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 TraesCS2D01G198200 chr2D 100.000 3668 0 0 1 3668 145896671 145893004 0.000000e+00 6774
1 TraesCS2D01G198200 chr2A 92.835 2917 134 39 798 3668 156364630 156367517 0.000000e+00 4159
2 TraesCS2D01G198200 chr2A 85.767 815 68 26 17 805 156363812 156364604 0.000000e+00 819
3 TraesCS2D01G198200 chr2B 91.143 3150 150 54 1 3072 206121955 206118857 0.000000e+00 4152
4 TraesCS2D01G198200 chr2B 90.169 356 27 5 3314 3668 206117663 206117315 1.200000e-124 457
5 TraesCS2D01G198200 chr5D 82.395 1119 195 2 1551 2668 423070407 423071524 0.000000e+00 974
6 TraesCS2D01G198200 chr5B 82.127 1119 195 3 1551 2668 510704580 510705694 0.000000e+00 953


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 TraesCS2D01G198200 chr2D 145893004 145896671 3667 True 6774.0 6774 100.000 1 3668 1 chr2D.!!$R1 3667
1 TraesCS2D01G198200 chr2A 156363812 156367517 3705 False 2489.0 4159 89.301 17 3668 2 chr2A.!!$F1 3651
2 TraesCS2D01G198200 chr2B 206117315 206121955 4640 True 2304.5 4152 90.656 1 3668 2 chr2B.!!$R1 3667
3 TraesCS2D01G198200 chr5D 423070407 423071524 1117 False 974.0 974 82.395 1551 2668 1 chr5D.!!$F1 1117
4 TraesCS2D01G198200 chr5B 510704580 510705694 1114 False 953.0 953 82.127 1551 2668 1 chr5B.!!$F1 1117

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
376 393 0.182537 TGCAGCTGGTTTGGTGTACT 59.817 50.0 17.12 0.0 37.70 2.73 F
1297 1377 0.101399 CTTCACTCCTCCGTCCATCG 59.899 60.0 0.00 0.0 39.52 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1481 0.793250 GCTTCTGCTTCAGGTCGTTC 59.207 55.0 0.00 0.00 36.03 3.95 R
3193 3381 0.843309 TCCTTGCAAGACAGGTTGGA 59.157 50.0 28.05 11.76 0.00 3.53 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 4.676471 CGTAGTACTTTTTGTGCGACAGTA 59.324 41.667 0.00 0.00 36.90 2.74
111 118 2.139118 GTACGGCCTCGGTACTACTAG 58.861 57.143 11.05 0.00 41.39 2.57
174 185 1.081509 CGCGTCAAATGGTTGGTGG 60.082 57.895 0.00 0.00 35.29 4.61
188 199 3.773119 GGTTGGTGGTAGATTAGACCTCA 59.227 47.826 0.00 0.00 37.88 3.86
207 218 0.314935 ACGATTTGTGCCTGCCAAAG 59.685 50.000 10.16 3.16 35.45 2.77
269 282 8.230486 GCGATCTTGTATATTTATTTCAGTGGG 58.770 37.037 0.00 0.00 0.00 4.61
326 339 1.681264 GAAAGGGAGTGTGGTTGGTTG 59.319 52.381 0.00 0.00 0.00 3.77
329 342 2.200337 GGAGTGTGGTTGGTTGGGC 61.200 63.158 0.00 0.00 0.00 5.36
330 343 2.123468 AGTGTGGTTGGTTGGGCC 60.123 61.111 0.00 0.00 37.90 5.80
332 345 3.810188 TGTGGTTGGTTGGGCCGA 61.810 61.111 0.00 0.00 41.21 5.54
373 390 2.480610 CGTGCAGCTGGTTTGGTGT 61.481 57.895 17.12 0.00 37.70 4.16
375 392 0.310854 GTGCAGCTGGTTTGGTGTAC 59.689 55.000 17.12 0.00 41.86 2.90
376 393 0.182537 TGCAGCTGGTTTGGTGTACT 59.817 50.000 17.12 0.00 37.70 2.73
377 394 0.593128 GCAGCTGGTTTGGTGTACTG 59.407 55.000 17.12 0.00 37.70 2.74
378 395 1.967319 CAGCTGGTTTGGTGTACTGT 58.033 50.000 5.57 0.00 0.00 3.55
379 396 2.808933 GCAGCTGGTTTGGTGTACTGTA 60.809 50.000 17.12 0.00 37.70 2.74
387 404 5.533154 TGGTTTGGTGTACTGTAGGAAATTG 59.467 40.000 0.00 0.00 0.00 2.32
547 577 1.646189 GATCTTCTTCGGTCAGCACC 58.354 55.000 0.00 0.00 39.69 5.01
562 594 0.321564 GCACCACTACACCATGCTCA 60.322 55.000 0.00 0.00 33.44 4.26
566 598 1.575244 CACTACACCATGCTCATCCG 58.425 55.000 0.00 0.00 0.00 4.18
599 631 5.537300 TCTTGTTATCTGTAGGATGCCTC 57.463 43.478 0.00 0.00 34.61 4.70
601 633 2.972713 TGTTATCTGTAGGATGCCTCCC 59.027 50.000 4.15 0.00 43.21 4.30
617 652 2.234908 CCTCCCAGTAGTTGGTTCTCTG 59.765 54.545 0.00 0.00 46.25 3.35
621 656 3.118956 CCCAGTAGTTGGTTCTCTGCTAG 60.119 52.174 0.00 0.00 46.25 3.42
622 657 3.764434 CCAGTAGTTGGTTCTCTGCTAGA 59.236 47.826 0.00 0.00 42.41 2.43
623 658 4.381079 CCAGTAGTTGGTTCTCTGCTAGAC 60.381 50.000 0.00 0.00 42.41 2.59
624 659 4.461081 CAGTAGTTGGTTCTCTGCTAGACT 59.539 45.833 0.00 0.00 32.51 3.24
625 660 3.951775 AGTTGGTTCTCTGCTAGACTG 57.048 47.619 0.00 0.00 32.51 3.51
627 662 1.930251 TGGTTCTCTGCTAGACTGCT 58.070 50.000 0.00 0.00 32.51 4.24
628 663 3.087370 TGGTTCTCTGCTAGACTGCTA 57.913 47.619 0.00 0.00 32.51 3.49
629 664 2.755655 TGGTTCTCTGCTAGACTGCTAC 59.244 50.000 0.00 0.00 32.51 3.58
630 665 3.020984 GGTTCTCTGCTAGACTGCTACT 58.979 50.000 0.00 0.00 32.51 2.57
631 666 3.181491 GGTTCTCTGCTAGACTGCTACTG 60.181 52.174 0.00 0.00 32.51 2.74
660 695 6.306837 GTGTTCTCTTCAGACTAACTTGATCG 59.693 42.308 0.00 0.00 0.00 3.69
671 706 9.227490 CAGACTAACTTGATCGTCTGTTTATAG 57.773 37.037 14.51 3.72 45.01 1.31
672 707 8.958506 AGACTAACTTGATCGTCTGTTTATAGT 58.041 33.333 0.00 0.00 35.56 2.12
673 708 8.912787 ACTAACTTGATCGTCTGTTTATAGTG 57.087 34.615 0.00 0.00 0.00 2.74
699 734 9.277783 GTATGCCTTGTATGTGATCTTCTAATT 57.722 33.333 0.00 0.00 0.00 1.40
751 790 3.561143 TGGTTGCTTGTGATTGTTAGGT 58.439 40.909 0.00 0.00 0.00 3.08
774 813 6.417930 GGTTCTTGTACTTTTGCATGTCTTTC 59.582 38.462 0.00 0.00 0.00 2.62
778 817 7.701924 TCTTGTACTTTTGCATGTCTTTCTTTG 59.298 33.333 0.00 0.00 0.00 2.77
818 889 9.607988 TTTAGTTCCATGTATACATTACACCAG 57.392 33.333 15.85 3.14 33.61 4.00
936 1012 6.255215 TGTCTTGTTTCAGATTTCGTTTCAC 58.745 36.000 0.00 0.00 0.00 3.18
947 1023 5.770162 AGATTTCGTTTCACCTGGATTTCTT 59.230 36.000 0.00 0.00 0.00 2.52
999 1079 3.433615 GTCAGATTCTTCACCGAACAAGG 59.566 47.826 0.00 0.00 37.30 3.61
1008 1088 2.106683 CCGAACAAGGATGGCCGAC 61.107 63.158 0.00 0.00 39.96 4.79
1236 1316 2.363147 ACTCTGGACTCCTCGGCC 60.363 66.667 0.00 0.00 0.00 6.13
1297 1377 0.101399 CTTCACTCCTCCGTCCATCG 59.899 60.000 0.00 0.00 39.52 3.84
1401 1481 2.324332 CTGTGACGACCGAGGATCCG 62.324 65.000 5.98 0.00 0.00 4.18
1407 1487 1.063811 GACCGAGGATCCGAACGAC 59.936 63.158 23.13 15.37 0.00 4.34
2073 2153 2.436109 GGGCTCTGCAAGGTTCCA 59.564 61.111 0.00 0.00 0.00 3.53
2680 2760 1.333619 GGCACTAGTGTTGTGGTGTTG 59.666 52.381 23.44 0.00 36.08 3.33
2808 2892 4.251268 GTTGTAATGCCGAACTTAGGTCT 58.749 43.478 0.00 0.00 0.00 3.85
2849 2938 6.398095 TGATGAGATGTAGTGGTACAAGTTG 58.602 40.000 0.00 0.00 44.16 3.16
2871 2960 4.347000 TGGAGGGCTACAGTATATGTTTCC 59.653 45.833 0.00 0.00 39.96 3.13
2872 2961 4.347000 GGAGGGCTACAGTATATGTTTCCA 59.653 45.833 0.00 0.00 39.96 3.53
2921 3019 0.689055 TGTCTCAATCAGCACTGCCT 59.311 50.000 0.00 0.00 0.00 4.75
2928 3026 0.108138 ATCAGCACTGCCTCGTAACC 60.108 55.000 0.00 0.00 0.00 2.85
2932 3030 0.517316 GCACTGCCTCGTAACCAAAG 59.483 55.000 0.00 0.00 0.00 2.77
2945 3043 7.710907 CCTCGTAACCAAAGATGATTTGAGATA 59.289 37.037 2.01 0.00 0.00 1.98
2978 3077 4.991056 GGTGCCTTTGGAGATTTCTTTTTC 59.009 41.667 0.00 0.00 0.00 2.29
2979 3078 4.681483 GTGCCTTTGGAGATTTCTTTTTCG 59.319 41.667 0.00 0.00 0.00 3.46
3053 3162 8.890472 TCCACCAGGCTAGATATACAAAATAAT 58.110 33.333 0.00 0.00 33.74 1.28
3135 3317 2.412847 GCCGAAGATTTGGTCGTTGAAG 60.413 50.000 0.87 0.00 35.48 3.02
3137 3319 3.496884 CCGAAGATTTGGTCGTTGAAGAA 59.503 43.478 0.00 0.00 35.48 2.52
3138 3320 4.024387 CCGAAGATTTGGTCGTTGAAGAAA 60.024 41.667 0.00 0.00 35.48 2.52
3148 3336 4.091424 GTCGTTGAAGAAACATGCATAGC 58.909 43.478 0.00 0.00 38.84 2.97
3163 3351 3.053693 TGCATAGCCTAAACCACTTCCAT 60.054 43.478 0.00 0.00 0.00 3.41
3164 3352 4.165180 TGCATAGCCTAAACCACTTCCATA 59.835 41.667 0.00 0.00 0.00 2.74
3165 3353 4.515567 GCATAGCCTAAACCACTTCCATAC 59.484 45.833 0.00 0.00 0.00 2.39
3166 3354 5.680619 CATAGCCTAAACCACTTCCATACA 58.319 41.667 0.00 0.00 0.00 2.29
3167 3355 4.862641 AGCCTAAACCACTTCCATACAT 57.137 40.909 0.00 0.00 0.00 2.29
3168 3356 4.781934 AGCCTAAACCACTTCCATACATC 58.218 43.478 0.00 0.00 0.00 3.06
3169 3357 3.883489 GCCTAAACCACTTCCATACATCC 59.117 47.826 0.00 0.00 0.00 3.51
3170 3358 4.127171 CCTAAACCACTTCCATACATCCG 58.873 47.826 0.00 0.00 0.00 4.18
3171 3359 2.710096 AACCACTTCCATACATCCGG 57.290 50.000 0.00 0.00 0.00 5.14
3172 3360 1.874129 ACCACTTCCATACATCCGGA 58.126 50.000 6.61 6.61 0.00 5.14
3173 3361 2.408565 ACCACTTCCATACATCCGGAT 58.591 47.619 12.38 12.38 0.00 4.18
3174 3362 2.777692 ACCACTTCCATACATCCGGATT 59.222 45.455 16.19 9.22 0.00 3.01
3175 3363 3.971305 ACCACTTCCATACATCCGGATTA 59.029 43.478 16.19 11.21 0.00 1.75
3176 3364 4.410883 ACCACTTCCATACATCCGGATTAA 59.589 41.667 16.19 6.02 0.00 1.40
3177 3365 5.073144 ACCACTTCCATACATCCGGATTAAT 59.927 40.000 16.19 8.41 0.00 1.40
3178 3366 6.003950 CCACTTCCATACATCCGGATTAATT 58.996 40.000 16.19 1.82 0.00 1.40
3179 3367 7.165485 CCACTTCCATACATCCGGATTAATTA 58.835 38.462 16.19 4.24 0.00 1.40
3180 3368 7.829211 CCACTTCCATACATCCGGATTAATTAT 59.171 37.037 16.19 6.52 0.00 1.28
3181 3369 8.668353 CACTTCCATACATCCGGATTAATTATG 58.332 37.037 16.19 17.20 0.00 1.90
3182 3370 8.602424 ACTTCCATACATCCGGATTAATTATGA 58.398 33.333 16.19 3.01 0.00 2.15
3183 3371 9.618890 CTTCCATACATCCGGATTAATTATGAT 57.381 33.333 16.19 0.00 0.00 2.45
3190 3378 9.534565 ACATCCGGATTAATTATGATATTCTCG 57.465 33.333 16.19 0.00 0.00 4.04
3191 3379 8.491152 CATCCGGATTAATTATGATATTCTCGC 58.509 37.037 16.19 0.00 0.00 5.03
3192 3380 7.552459 TCCGGATTAATTATGATATTCTCGCA 58.448 34.615 0.00 0.00 0.00 5.10
3193 3381 8.204160 TCCGGATTAATTATGATATTCTCGCAT 58.796 33.333 0.00 0.00 0.00 4.73
3194 3382 8.491152 CCGGATTAATTATGATATTCTCGCATC 58.509 37.037 0.00 0.00 0.00 3.91
3195 3383 8.491152 CGGATTAATTATGATATTCTCGCATCC 58.509 37.037 0.00 0.00 0.00 3.51
3196 3384 9.330063 GGATTAATTATGATATTCTCGCATCCA 57.670 33.333 0.00 0.00 0.00 3.41
3199 3387 6.992063 ATTATGATATTCTCGCATCCAACC 57.008 37.500 0.00 0.00 0.00 3.77
3200 3388 4.630644 ATGATATTCTCGCATCCAACCT 57.369 40.909 0.00 0.00 0.00 3.50
3201 3389 3.732212 TGATATTCTCGCATCCAACCTG 58.268 45.455 0.00 0.00 0.00 4.00
3202 3390 3.134623 TGATATTCTCGCATCCAACCTGT 59.865 43.478 0.00 0.00 0.00 4.00
3203 3391 2.029838 ATTCTCGCATCCAACCTGTC 57.970 50.000 0.00 0.00 0.00 3.51
3204 3392 0.976641 TTCTCGCATCCAACCTGTCT 59.023 50.000 0.00 0.00 0.00 3.41
3243 3474 6.207417 CCATCCTTGAAAGTTCTAGCTTTTGA 59.793 38.462 0.00 0.00 38.64 2.69
3255 3486 0.109735 GCTTTTGAAGTAGGTGCCGC 60.110 55.000 0.00 0.00 0.00 6.53
3256 3487 1.234821 CTTTTGAAGTAGGTGCCGCA 58.765 50.000 0.00 0.00 0.00 5.69
3262 3493 1.326548 GAAGTAGGTGCCGCATTTACG 59.673 52.381 0.00 0.00 0.00 3.18
3342 4507 2.826488 ACTCCAGTAGCACCAATCTCT 58.174 47.619 0.00 0.00 0.00 3.10
3418 4583 1.308069 CGACCACCCATGCTTCTTGG 61.308 60.000 0.00 0.00 0.00 3.61
3466 4634 6.702716 TTTTGTAGGGTTGGAACTTGTAAG 57.297 37.500 0.00 0.00 0.00 2.34
3467 4635 3.746940 TGTAGGGTTGGAACTTGTAAGC 58.253 45.455 0.00 0.00 0.00 3.09
3474 4642 4.304939 GTTGGAACTTGTAAGCGAGTAGT 58.695 43.478 0.00 0.00 38.35 2.73
3558 4732 5.991328 ACGAGCATCCATAAATAACAGTG 57.009 39.130 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.433274 GCACAAAAAGTACTACGTACCCC 59.567 47.826 0.00 0.00 39.58 4.95
11 12 4.440758 TGTCGCACAAAAAGTACTACGTAC 59.559 41.667 0.00 0.00 39.10 3.67
15 16 5.118203 CCTACTGTCGCACAAAAAGTACTAC 59.882 44.000 0.00 0.00 0.00 2.73
37 38 2.352503 CTTGCAAGCAAAATACGCCT 57.647 45.000 14.65 0.00 35.33 5.52
74 75 2.079020 TACGGGTGCTATGCGGCTAC 62.079 60.000 0.00 0.00 0.00 3.58
83 84 3.142838 GAGGCCGTACGGGTGCTA 61.143 66.667 33.98 0.00 38.44 3.49
111 118 1.027357 CAAGCATGGTCATGGCCTAC 58.973 55.000 19.09 6.81 39.16 3.18
141 148 0.391263 ACGCGGTCTGAGGAAATTCC 60.391 55.000 12.47 3.29 36.58 3.01
188 199 0.314935 CTTTGGCAGGCACAAATCGT 59.685 50.000 0.00 0.00 37.22 3.73
207 218 2.832201 GCCCCTGGATCTGCTTGC 60.832 66.667 0.00 0.00 0.00 4.01
269 282 6.316390 CAGGGACAGGATTAATTAACTGACAC 59.684 42.308 17.98 14.14 35.08 3.67
334 347 4.324991 AGTTTGACCCGCCCGTCC 62.325 66.667 0.00 0.00 31.35 4.79
373 390 6.406370 CACCTCATCACAATTTCCTACAGTA 58.594 40.000 0.00 0.00 0.00 2.74
375 392 4.637534 CCACCTCATCACAATTTCCTACAG 59.362 45.833 0.00 0.00 0.00 2.74
376 393 4.567537 CCCACCTCATCACAATTTCCTACA 60.568 45.833 0.00 0.00 0.00 2.74
377 394 3.947834 CCCACCTCATCACAATTTCCTAC 59.052 47.826 0.00 0.00 0.00 3.18
378 395 3.053693 CCCCACCTCATCACAATTTCCTA 60.054 47.826 0.00 0.00 0.00 2.94
379 396 2.291800 CCCCACCTCATCACAATTTCCT 60.292 50.000 0.00 0.00 0.00 3.36
387 404 3.933861 AAGTAATCCCCACCTCATCAC 57.066 47.619 0.00 0.00 0.00 3.06
547 577 1.134699 ACGGATGAGCATGGTGTAGTG 60.135 52.381 0.00 0.00 0.00 2.74
562 594 2.851195 ACAAGAAGCAAGTGAACGGAT 58.149 42.857 0.00 0.00 0.00 4.18
566 598 6.305693 ACAGATAACAAGAAGCAAGTGAAC 57.694 37.500 0.00 0.00 0.00 3.18
601 633 4.461081 AGTCTAGCAGAGAACCAACTACTG 59.539 45.833 0.00 0.00 35.37 2.74
617 652 4.181309 ACACTTTCAGTAGCAGTCTAGC 57.819 45.455 0.00 0.00 0.00 3.42
621 656 4.877282 AGAGAACACTTTCAGTAGCAGTC 58.123 43.478 0.00 0.00 33.72 3.51
622 657 4.946478 AGAGAACACTTTCAGTAGCAGT 57.054 40.909 0.00 0.00 33.72 4.40
623 658 5.292765 TGAAGAGAACACTTTCAGTAGCAG 58.707 41.667 0.00 0.00 33.72 4.24
624 659 5.069119 TCTGAAGAGAACACTTTCAGTAGCA 59.931 40.000 11.77 0.00 33.72 3.49
625 660 5.404066 GTCTGAAGAGAACACTTTCAGTAGC 59.596 44.000 11.77 3.03 33.72 3.58
627 662 6.716934 AGTCTGAAGAGAACACTTTCAGTA 57.283 37.500 11.77 0.00 33.72 2.74
628 663 5.606348 AGTCTGAAGAGAACACTTTCAGT 57.394 39.130 11.77 0.00 33.72 3.41
629 664 7.206687 AGTTAGTCTGAAGAGAACACTTTCAG 58.793 38.462 7.04 7.04 33.72 3.02
630 665 7.113658 AGTTAGTCTGAAGAGAACACTTTCA 57.886 36.000 7.45 0.00 33.72 2.69
631 666 7.707035 TCAAGTTAGTCTGAAGAGAACACTTTC 59.293 37.037 7.45 0.00 28.25 2.62
640 675 6.189677 AGACGATCAAGTTAGTCTGAAGAG 57.810 41.667 0.00 0.00 41.77 2.85
660 695 8.765219 CATACAAGGCATACACTATAAACAGAC 58.235 37.037 0.00 0.00 0.00 3.51
671 706 6.051717 AGAAGATCACATACAAGGCATACAC 58.948 40.000 0.00 0.00 0.00 2.90
672 707 6.239217 AGAAGATCACATACAAGGCATACA 57.761 37.500 0.00 0.00 0.00 2.29
673 708 8.839310 ATTAGAAGATCACATACAAGGCATAC 57.161 34.615 0.00 0.00 0.00 2.39
732 771 5.438761 AGAACCTAACAATCACAAGCAAC 57.561 39.130 0.00 0.00 0.00 4.17
734 773 4.887071 ACAAGAACCTAACAATCACAAGCA 59.113 37.500 0.00 0.00 0.00 3.91
751 790 7.333528 AGAAAGACATGCAAAAGTACAAGAA 57.666 32.000 0.00 0.00 0.00 2.52
778 817 9.998106 ACATGGAACTAAATACATACTGTATCC 57.002 33.333 0.00 0.00 42.29 2.59
792 831 9.607988 CTGGTGTAATGTATACATGGAACTAAA 57.392 33.333 18.94 0.06 36.56 1.85
796 835 7.769044 AGAACTGGTGTAATGTATACATGGAAC 59.231 37.037 18.94 16.40 36.56 3.62
810 881 7.093902 CCAGTAACAGAGATAGAACTGGTGTAA 60.094 40.741 10.46 0.00 45.74 2.41
818 889 6.926313 ACACTTCCAGTAACAGAGATAGAAC 58.074 40.000 0.00 0.00 0.00 3.01
886 960 9.945904 AGTAATAAGACTGTAAGAAGAAAAGGG 57.054 33.333 0.00 0.00 37.43 3.95
936 1012 4.494091 TCTTCTAGCCAAGAAATCCAGG 57.506 45.455 1.22 0.00 43.66 4.45
999 1079 0.321653 AAGTTGGAGTGTCGGCCATC 60.322 55.000 2.24 0.00 33.46 3.51
1008 1088 0.613260 TCATCCGGGAAGTTGGAGTG 59.387 55.000 0.00 0.00 37.76 3.51
1362 1442 1.284297 TGACGCATGAAGCACTCACG 61.284 55.000 0.00 0.00 46.13 4.35
1401 1481 0.793250 GCTTCTGCTTCAGGTCGTTC 59.207 55.000 0.00 0.00 36.03 3.95
1458 1538 2.490115 CTCGAGGCTGTTAACTGTCTCT 59.510 50.000 31.56 18.90 42.17 3.10
1463 1543 1.203523 AGCTCTCGAGGCTGTTAACTG 59.796 52.381 22.47 7.67 38.73 3.16
1500 1580 2.994995 TTCTCCGGCTCCAGCGAA 60.995 61.111 0.00 0.00 43.26 4.70
1845 1925 1.880340 CTTGACGGCCTCAGCGATC 60.880 63.158 0.00 0.00 41.24 3.69
1851 1931 4.649705 TCCCCCTTGACGGCCTCA 62.650 66.667 0.00 0.26 0.00 3.86
2680 2760 1.963338 AGCGAGGTCACAAAGCAGC 60.963 57.895 0.00 0.00 0.00 5.25
2849 2938 4.347000 TGGAAACATATACTGTAGCCCTCC 59.653 45.833 0.00 0.00 36.98 4.30
2921 3019 9.613428 ATTATCTCAAATCATCTTTGGTTACGA 57.387 29.630 0.00 0.00 0.00 3.43
2932 3030 8.517878 CACCAATACCCATTATCTCAAATCATC 58.482 37.037 0.00 0.00 0.00 2.92
2945 3043 2.187100 CCAAAGGCACCAATACCCATT 58.813 47.619 0.00 0.00 0.00 3.16
3121 3303 4.202101 TGCATGTTTCTTCAACGACCAAAT 60.202 37.500 0.00 0.00 38.36 2.32
3135 3317 4.399303 AGTGGTTTAGGCTATGCATGTTTC 59.601 41.667 10.16 0.00 0.00 2.78
3137 3319 3.968265 AGTGGTTTAGGCTATGCATGTT 58.032 40.909 10.16 0.00 0.00 2.71
3138 3320 3.652057 AGTGGTTTAGGCTATGCATGT 57.348 42.857 10.16 0.00 0.00 3.21
3148 3336 4.127171 CGGATGTATGGAAGTGGTTTAGG 58.873 47.826 0.00 0.00 0.00 2.69
3164 3352 9.534565 CGAGAATATCATAATTAATCCGGATGT 57.465 33.333 19.95 10.85 0.00 3.06
3165 3353 8.491152 GCGAGAATATCATAATTAATCCGGATG 58.509 37.037 19.95 4.99 0.00 3.51
3166 3354 8.204160 TGCGAGAATATCATAATTAATCCGGAT 58.796 33.333 12.38 12.38 0.00 4.18
3167 3355 7.552459 TGCGAGAATATCATAATTAATCCGGA 58.448 34.615 6.61 6.61 0.00 5.14
3168 3356 7.770801 TGCGAGAATATCATAATTAATCCGG 57.229 36.000 0.00 0.00 0.00 5.14
3169 3357 8.491152 GGATGCGAGAATATCATAATTAATCCG 58.509 37.037 0.00 0.00 0.00 4.18
3170 3358 9.330063 TGGATGCGAGAATATCATAATTAATCC 57.670 33.333 0.00 0.00 0.00 3.01
3173 3361 8.946085 GGTTGGATGCGAGAATATCATAATTAA 58.054 33.333 0.00 0.00 0.00 1.40
3174 3362 8.321353 AGGTTGGATGCGAGAATATCATAATTA 58.679 33.333 0.00 0.00 0.00 1.40
3175 3363 7.120285 CAGGTTGGATGCGAGAATATCATAATT 59.880 37.037 0.00 0.00 0.00 1.40
3176 3364 6.596888 CAGGTTGGATGCGAGAATATCATAAT 59.403 38.462 0.00 0.00 0.00 1.28
3177 3365 5.934043 CAGGTTGGATGCGAGAATATCATAA 59.066 40.000 0.00 0.00 0.00 1.90
3178 3366 5.012046 ACAGGTTGGATGCGAGAATATCATA 59.988 40.000 0.00 0.00 0.00 2.15
3179 3367 4.202398 ACAGGTTGGATGCGAGAATATCAT 60.202 41.667 0.00 0.00 0.00 2.45
3180 3368 3.134623 ACAGGTTGGATGCGAGAATATCA 59.865 43.478 0.00 0.00 0.00 2.15
3181 3369 3.733337 ACAGGTTGGATGCGAGAATATC 58.267 45.455 0.00 0.00 0.00 1.63
3182 3370 3.389329 AGACAGGTTGGATGCGAGAATAT 59.611 43.478 0.00 0.00 0.00 1.28
3183 3371 2.766263 AGACAGGTTGGATGCGAGAATA 59.234 45.455 0.00 0.00 0.00 1.75
3184 3372 1.556911 AGACAGGTTGGATGCGAGAAT 59.443 47.619 0.00 0.00 0.00 2.40
3185 3373 0.976641 AGACAGGTTGGATGCGAGAA 59.023 50.000 0.00 0.00 0.00 2.87
3186 3374 0.976641 AAGACAGGTTGGATGCGAGA 59.023 50.000 0.00 0.00 0.00 4.04
3187 3375 1.081892 CAAGACAGGTTGGATGCGAG 58.918 55.000 0.00 0.00 0.00 5.03
3188 3376 0.955428 GCAAGACAGGTTGGATGCGA 60.955 55.000 0.00 0.00 0.00 5.10
3189 3377 1.236616 TGCAAGACAGGTTGGATGCG 61.237 55.000 0.00 0.00 36.62 4.73
3190 3378 0.961019 TTGCAAGACAGGTTGGATGC 59.039 50.000 0.00 0.00 0.00 3.91
3191 3379 1.542915 CCTTGCAAGACAGGTTGGATG 59.457 52.381 28.05 2.25 0.00 3.51
3192 3380 1.425066 TCCTTGCAAGACAGGTTGGAT 59.575 47.619 28.05 0.00 0.00 3.41
3193 3381 0.843309 TCCTTGCAAGACAGGTTGGA 59.157 50.000 28.05 11.76 0.00 3.53
3194 3382 1.915141 ATCCTTGCAAGACAGGTTGG 58.085 50.000 28.05 9.40 0.00 3.77
3195 3383 4.154918 GTCTAATCCTTGCAAGACAGGTTG 59.845 45.833 28.05 9.08 38.56 3.77
3196 3384 4.327680 GTCTAATCCTTGCAAGACAGGTT 58.672 43.478 28.05 15.42 38.56 3.50
3197 3385 3.307762 GGTCTAATCCTTGCAAGACAGGT 60.308 47.826 28.05 4.45 40.09 4.00
3198 3386 3.274288 GGTCTAATCCTTGCAAGACAGG 58.726 50.000 28.05 12.19 40.09 4.00
3199 3387 3.942829 TGGTCTAATCCTTGCAAGACAG 58.057 45.455 28.05 16.86 40.09 3.51
3200 3388 4.517285 GATGGTCTAATCCTTGCAAGACA 58.483 43.478 28.05 13.94 40.09 3.41
3201 3389 3.879892 GGATGGTCTAATCCTTGCAAGAC 59.120 47.826 28.05 16.11 42.57 3.01
3202 3390 4.156455 GGATGGTCTAATCCTTGCAAGA 57.844 45.455 28.05 13.93 42.57 3.02
3243 3474 1.338389 ACGTAAATGCGGCACCTACTT 60.338 47.619 4.03 0.54 35.98 2.24
3262 3493 6.144175 GGCGAGTAACAGTAGAATAGATCAC 58.856 44.000 0.00 0.00 0.00 3.06
3342 4507 0.037303 CTGCCTTCAGCCTTCAGGAA 59.963 55.000 0.00 0.00 42.71 3.36
3384 4549 1.203013 TGGTCGAAACCTCCTGAGAGA 60.203 52.381 0.00 0.00 46.60 3.10
3418 4583 3.094386 TGGACAACCAGAAGTGCAC 57.906 52.632 9.40 9.40 41.77 4.57
3466 4634 4.559153 TGGGTTTACTTTGTACTACTCGC 58.441 43.478 0.00 0.00 0.00 5.03
3467 4635 6.869913 TGATTGGGTTTACTTTGTACTACTCG 59.130 38.462 0.00 0.00 0.00 4.18
3503 4677 5.040635 GCTTAGTCTCTGTGCTTACATCTC 58.959 45.833 0.00 0.00 0.00 2.75
3558 4732 6.207221 TGGTAATTTTCTTTCCCGTTAAGACC 59.793 38.462 0.00 0.00 31.68 3.85


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

AutoCloner maintained by Alex Coulton.