Multiple sequence alignment - TraesCS3D01G078300

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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 TraesCS3D01G078300 chr3D 100.000 5709 0 0 1 5709 38753563 38747855 0.000000e+00 10543.0
1 TraesCS3D01G078300 chr3A 94.378 5763 171 68 6 5709 49985761 49980093 0.000000e+00 8706.0
2 TraesCS3D01G078300 chr3B 94.136 5491 163 79 6 5423 61565542 61560138 0.000000e+00 8209.0
3 TraesCS3D01G078300 chr3B 95.392 217 7 3 5484 5698 61560138 61559923 5.480000e-90 342.0
4 TraesCS3D01G078300 chr1B 100.000 33 0 0 462 494 661058058 661058026 1.720000e-05 62.1


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 TraesCS3D01G078300 chr3D 38747855 38753563 5708 True 10543.0 10543 100.000 1 5709 1 chr3D.!!$R1 5708
1 TraesCS3D01G078300 chr3A 49980093 49985761 5668 True 8706.0 8706 94.378 6 5709 1 chr3A.!!$R1 5703
2 TraesCS3D01G078300 chr3B 61559923 61565542 5619 True 4275.5 8209 94.764 6 5698 2 chr3B.!!$R1 5692

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
706 714 0.047176 AGAGGAGAGAGGGGAGAGGA 59.953 60.000 0.0 0.0 0.00 3.71 F
708 716 0.047176 AGGAGAGAGGGGAGAGGAGA 59.953 60.000 0.0 0.0 0.00 3.71 F
1116 1129 0.174389 TCGCTCCAGCTCTTCATCAC 59.826 55.000 0.0 0.0 39.32 3.06 F
2469 2520 0.543277 CTGCTAGGTGGCTGAATGGA 59.457 55.000 0.0 0.0 33.89 3.41 F
3191 3268 1.073923 TCCTCCCTTCTTTCAAGGTGC 59.926 52.381 0.0 0.0 35.65 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2252 0.041238 ACGATGAACAGGAGGAGGGA 59.959 55.0 0.0 0.0 0.0 4.20 R
2660 2715 0.325933 GCCATCGATCCATCCATCCA 59.674 55.0 0.0 0.0 0.0 3.41 R
2661 2716 0.325933 TGCCATCGATCCATCCATCC 59.674 55.0 0.0 0.0 0.0 3.51 R
3304 3406 1.024046 ACACACACGCACACACACAT 61.024 50.0 0.0 0.0 0.0 3.21 R
5119 5277 0.400594 ACACTTAACTGCTCACCCCC 59.599 55.0 0.0 0.0 0.0 5.40 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
90 93 8.718734 GTTAAATCGGTGATCAAAGTTAGACTT 58.281 33.333 0.00 0.00 40.80 3.01
199 202 9.065871 GCAATGCAATTTCTAAGTAGTTTAGTG 57.934 33.333 0.00 0.00 36.15 2.74
212 215 7.153217 AGTAGTTTAGTGTGTGCTTGTTTTT 57.847 32.000 0.00 0.00 0.00 1.94
382 386 5.399596 CGTACATCTATCAACCTGTCATTCG 59.600 44.000 0.00 0.00 0.00 3.34
529 533 2.165641 CTGACACGTACAGCTTATGGGA 59.834 50.000 8.57 0.00 0.00 4.37
539 543 7.440255 ACGTACAGCTTATGGGAAATAATACAC 59.560 37.037 0.00 0.00 0.00 2.90
699 707 2.936202 CAAGAGAGAGAGGAGAGAGGG 58.064 57.143 0.00 0.00 0.00 4.30
705 713 0.478507 GAGAGGAGAGAGGGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
706 714 0.047176 AGAGGAGAGAGGGGAGAGGA 59.953 60.000 0.00 0.00 0.00 3.71
707 715 0.478507 GAGGAGAGAGGGGAGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
708 716 0.047176 AGGAGAGAGGGGAGAGGAGA 59.953 60.000 0.00 0.00 0.00 3.71
709 717 0.478507 GGAGAGAGGGGAGAGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
710 718 1.518367 GAGAGAGGGGAGAGGAGAGA 58.482 60.000 0.00 0.00 0.00 3.10
733 741 5.393866 AGAGAGAGAGAGTCACCTTTCTTT 58.606 41.667 6.94 0.84 32.58 2.52
738 746 2.810852 GAGAGTCACCTTTCTTTGCTGG 59.189 50.000 0.00 0.00 0.00 4.85
1008 1018 0.620030 AGTGTAGCACCATGATGGCA 59.380 50.000 12.25 0.00 42.67 4.92
1116 1129 0.174389 TCGCTCCAGCTCTTCATCAC 59.826 55.000 0.00 0.00 39.32 3.06
1210 1230 3.819368 TCAGCAGTTTTCATCTTCACCA 58.181 40.909 0.00 0.00 0.00 4.17
1248 1281 6.039717 TGTTGAGAAAATGTTGAAAGAGAGGG 59.960 38.462 0.00 0.00 0.00 4.30
1310 1343 0.604780 AGGTGTGCTCACAGTCATGC 60.605 55.000 19.67 1.60 45.45 4.06
1323 1356 3.047796 CAGTCATGCTGTTTGAGTTTGC 58.952 45.455 8.46 0.00 40.27 3.68
1426 1459 3.818121 TTCTGGTTGTCCCGGTGCG 62.818 63.158 0.00 0.00 40.86 5.34
1459 1492 3.197265 GGCACAGCAAAATGACAAGTTT 58.803 40.909 0.00 0.00 0.00 2.66
1972 2016 1.809619 CGATGACGACATGGCCGTT 60.810 57.895 14.91 2.58 40.67 4.44
2187 2231 1.648302 CCATTGCTGGGGATGGGAGA 61.648 60.000 0.00 0.00 39.30 3.71
2206 2250 1.816835 GAGCATCATGTGGCATATGGG 59.183 52.381 21.85 15.76 33.17 4.00
2208 2252 1.919240 CATCATGTGGCATATGGGCT 58.081 50.000 21.85 6.70 43.83 5.19
2209 2253 1.816835 CATCATGTGGCATATGGGCTC 59.183 52.381 21.85 0.05 43.83 4.70
2308 2354 5.221130 CCGTCCTCCTCGATCTAATTAAAC 58.779 45.833 0.00 0.00 0.00 2.01
2335 2381 3.006217 GGGGAATTAATTGAGAGCCATGC 59.994 47.826 5.17 0.00 0.00 4.06
2466 2517 2.887151 AAACTGCTAGGTGGCTGAAT 57.113 45.000 0.00 0.00 35.59 2.57
2469 2520 0.543277 CTGCTAGGTGGCTGAATGGA 59.457 55.000 0.00 0.00 33.89 3.41
2538 2593 4.459337 GCCTAGCTTAGCTGAAAGGAAAAA 59.541 41.667 21.83 0.00 40.10 1.94
2579 2634 5.221722 CCCATTTGCAAGAGGTAGCTAGATA 60.222 44.000 15.51 0.00 0.00 1.98
2580 2635 5.931146 CCATTTGCAAGAGGTAGCTAGATAG 59.069 44.000 10.25 0.00 0.00 2.08
2660 2715 2.305009 GCAAGCAGCTTTAGGATGGAT 58.695 47.619 4.38 0.00 41.15 3.41
2661 2716 2.034305 GCAAGCAGCTTTAGGATGGATG 59.966 50.000 4.38 0.00 41.15 3.51
2662 2717 2.621998 CAAGCAGCTTTAGGATGGATGG 59.378 50.000 4.38 0.00 0.00 3.51
2663 2718 2.130193 AGCAGCTTTAGGATGGATGGA 58.870 47.619 0.00 0.00 0.00 3.41
2706 2761 1.281899 GGTCATCTTTTCTCTCGCCG 58.718 55.000 0.00 0.00 0.00 6.46
2760 2817 3.497103 TGCAGTTCCATCCATCCATAG 57.503 47.619 0.00 0.00 0.00 2.23
2896 2969 9.672673 ATTATTACAATGTAGCCAGTATCCATC 57.327 33.333 0.00 0.00 0.00 3.51
2897 2970 6.493189 TTACAATGTAGCCAGTATCCATCA 57.507 37.500 0.00 0.00 0.00 3.07
2946 3021 9.029243 CATGCAAAAATTTGTGTACAAGACTAA 57.971 29.630 10.07 0.00 40.24 2.24
2947 3022 9.762933 ATGCAAAAATTTGTGTACAAGACTAAT 57.237 25.926 10.07 0.00 40.24 1.73
2948 3023 9.593134 TGCAAAAATTTGTGTACAAGACTAATT 57.407 25.926 10.07 0.00 40.24 1.40
2993 3070 7.036996 TGGATACATAATTTGGTACGACGTA 57.963 36.000 2.97 2.97 46.17 3.57
3077 3154 1.415126 GGAGATCATCAGGAGGGGGAA 60.415 57.143 0.00 0.00 0.00 3.97
3088 3165 4.785453 GGGGGAAGCCTGCACGAG 62.785 72.222 0.00 0.00 0.00 4.18
3190 3267 3.728385 ATCCTCCCTTCTTTCAAGGTG 57.272 47.619 0.00 0.00 35.65 4.00
3191 3268 1.073923 TCCTCCCTTCTTTCAAGGTGC 59.926 52.381 0.00 0.00 35.65 5.01
3222 3324 5.734720 TCCTGACTACATCTCCAACATTTC 58.265 41.667 0.00 0.00 0.00 2.17
3223 3325 5.485353 TCCTGACTACATCTCCAACATTTCT 59.515 40.000 0.00 0.00 0.00 2.52
3224 3326 6.667848 TCCTGACTACATCTCCAACATTTCTA 59.332 38.462 0.00 0.00 0.00 2.10
3225 3327 6.758886 CCTGACTACATCTCCAACATTTCTAC 59.241 42.308 0.00 0.00 0.00 2.59
3226 3328 7.239763 TGACTACATCTCCAACATTTCTACA 57.760 36.000 0.00 0.00 0.00 2.74
3227 3329 7.097192 TGACTACATCTCCAACATTTCTACAC 58.903 38.462 0.00 0.00 0.00 2.90
3228 3330 7.004555 ACTACATCTCCAACATTTCTACACA 57.995 36.000 0.00 0.00 0.00 3.72
3229 3331 7.624549 ACTACATCTCCAACATTTCTACACAT 58.375 34.615 0.00 0.00 0.00 3.21
3230 3332 6.748333 ACATCTCCAACATTTCTACACATG 57.252 37.500 0.00 0.00 0.00 3.21
3231 3333 5.124457 ACATCTCCAACATTTCTACACATGC 59.876 40.000 0.00 0.00 0.00 4.06
3232 3334 4.650734 TCTCCAACATTTCTACACATGCA 58.349 39.130 0.00 0.00 0.00 3.96
3233 3335 5.255687 TCTCCAACATTTCTACACATGCAT 58.744 37.500 0.00 0.00 0.00 3.96
3234 3336 5.711506 TCTCCAACATTTCTACACATGCATT 59.288 36.000 0.00 0.00 0.00 3.56
3235 3337 5.712004 TCCAACATTTCTACACATGCATTG 58.288 37.500 0.00 1.69 0.00 2.82
3236 3338 4.327898 CCAACATTTCTACACATGCATTGC 59.672 41.667 0.00 0.46 0.00 3.56
3237 3339 4.787260 ACATTTCTACACATGCATTGCA 57.213 36.364 14.72 14.72 44.86 4.08
3304 3406 7.615757 TGTCTTGTCAAGTCTATTCTCCTCATA 59.384 37.037 12.30 0.00 0.00 2.15
3315 3423 3.251479 TCTCCTCATATGTGTGTGTGC 57.749 47.619 1.90 0.00 0.00 4.57
3316 3424 1.929169 CTCCTCATATGTGTGTGTGCG 59.071 52.381 1.90 0.00 0.00 5.34
3317 3425 1.275010 TCCTCATATGTGTGTGTGCGT 59.725 47.619 1.90 0.00 0.00 5.24
3318 3426 1.394572 CCTCATATGTGTGTGTGCGTG 59.605 52.381 1.90 0.00 0.00 5.34
3319 3427 2.068519 CTCATATGTGTGTGTGCGTGT 58.931 47.619 1.90 0.00 0.00 4.49
3320 3428 1.797635 TCATATGTGTGTGTGCGTGTG 59.202 47.619 1.90 0.00 0.00 3.82
3321 3429 1.530720 CATATGTGTGTGTGCGTGTGT 59.469 47.619 0.00 0.00 0.00 3.72
3322 3430 0.933796 TATGTGTGTGTGCGTGTGTG 59.066 50.000 0.00 0.00 0.00 3.82
3323 3431 1.024046 ATGTGTGTGTGCGTGTGTGT 61.024 50.000 0.00 0.00 0.00 3.72
3324 3432 1.225991 GTGTGTGTGCGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
3325 3433 1.669437 TGTGTGTGCGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
3326 3434 1.225991 GTGTGTGCGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
3332 3440 1.231296 TGCGTGTGTGTGTGTTGTGT 61.231 50.000 0.00 0.00 0.00 3.72
3339 3447 2.723658 GTGTGTGTGTTGTGTTGTGTTG 59.276 45.455 0.00 0.00 0.00 3.33
3346 3454 2.362397 TGTTGTGTTGTGTTGTGTTGGT 59.638 40.909 0.00 0.00 0.00 3.67
3359 3467 2.744741 TGTGTTGGTTAGTGTGTGTGTG 59.255 45.455 0.00 0.00 0.00 3.82
3361 3469 2.744741 TGTTGGTTAGTGTGTGTGTGTG 59.255 45.455 0.00 0.00 0.00 3.82
3362 3470 2.745281 GTTGGTTAGTGTGTGTGTGTGT 59.255 45.455 0.00 0.00 0.00 3.72
3363 3471 2.351455 TGGTTAGTGTGTGTGTGTGTG 58.649 47.619 0.00 0.00 0.00 3.82
3426 3534 4.074259 ACTGAGCATGTGTTTATCTGCAA 58.926 39.130 0.00 0.00 37.09 4.08
3531 3655 2.039480 AGGATTGCTGCTCTTCAACAGA 59.961 45.455 0.00 0.00 35.90 3.41
3561 3685 1.067354 CCTTCGGCAAGGTACGTACTT 60.067 52.381 24.07 15.22 44.11 2.24
3562 3686 2.164219 CCTTCGGCAAGGTACGTACTTA 59.836 50.000 24.07 0.00 44.11 2.24
3563 3687 2.919666 TCGGCAAGGTACGTACTTAC 57.080 50.000 24.07 12.90 0.00 2.34
3564 3688 2.436417 TCGGCAAGGTACGTACTTACT 58.564 47.619 24.07 11.02 0.00 2.24
3565 3689 2.162208 TCGGCAAGGTACGTACTTACTG 59.838 50.000 24.07 16.86 0.00 2.74
3566 3690 2.733227 CGGCAAGGTACGTACTTACTGG 60.733 54.545 24.07 12.19 0.00 4.00
3567 3691 2.232208 GGCAAGGTACGTACTTACTGGT 59.768 50.000 24.07 0.00 0.00 4.00
3568 3692 3.443681 GGCAAGGTACGTACTTACTGGTA 59.556 47.826 24.07 0.00 0.00 3.25
3569 3693 4.082245 GGCAAGGTACGTACTTACTGGTAA 60.082 45.833 24.07 0.00 0.00 2.85
3570 3694 4.859245 GCAAGGTACGTACTTACTGGTAAC 59.141 45.833 24.07 4.60 0.00 2.50
3704 3838 5.350504 ACTCATGGTCACAAGAATAGAGG 57.649 43.478 0.00 0.00 0.00 3.69
3710 3844 7.391554 TCATGGTCACAAGAATAGAGGAAAAAG 59.608 37.037 0.00 0.00 0.00 2.27
3853 3987 4.886579 TGGTTTAGTCCTTTTCGTACCTC 58.113 43.478 0.00 0.00 0.00 3.85
3945 4089 7.388776 AGACTTAAACGGTATTTAAGGTCAACC 59.611 37.037 18.51 0.00 42.96 3.77
3974 4118 2.434336 TGTATGTATGCACAGACCCTCC 59.566 50.000 0.00 0.00 44.56 4.30
4024 4175 5.122396 CAGAGTACAGTTGGGCAAAAGATAC 59.878 44.000 0.00 0.00 0.00 2.24
4082 4233 7.661536 TTACCTCTTAGATGCTTCTACATGT 57.338 36.000 8.76 2.69 34.15 3.21
4083 4234 8.762481 TTACCTCTTAGATGCTTCTACATGTA 57.238 34.615 8.76 5.25 34.15 2.29
4084 4235 7.045126 ACCTCTTAGATGCTTCTACATGTAC 57.955 40.000 8.76 0.00 34.15 2.90
4243 4394 3.103080 AGACCAGGTCGAGGTAATTCT 57.897 47.619 14.32 0.00 40.09 2.40
4296 4450 2.094026 TGCCTCTATGTGCCATATAGCG 60.094 50.000 3.75 0.00 34.65 4.26
4325 4479 4.040829 TCCTGACCATCATCGCTCATTTAT 59.959 41.667 0.00 0.00 0.00 1.40
4569 4727 1.371558 GTTTCTGTCGACAGGGGCT 59.628 57.895 37.82 0.00 43.91 5.19
4583 4741 2.048127 GGCTGTCAGACACCGGAC 60.048 66.667 9.46 0.00 37.88 4.79
4625 4783 2.145397 TGATCTTCGCAGTAGAGGGT 57.855 50.000 0.00 0.00 0.00 4.34
4868 5026 7.938490 ACATATTTCCTTTGCTTTCACCATTTT 59.062 29.630 0.00 0.00 0.00 1.82
4903 5061 3.278668 AGCCAAGTGAATCATCTGGAG 57.721 47.619 15.19 0.00 0.00 3.86
4960 5118 1.263484 GCAGATCATGGAAGCATGACG 59.737 52.381 0.00 0.00 43.42 4.35
5119 5277 2.363359 AGGCAGGAAAACAGAAAAGCAG 59.637 45.455 0.00 0.00 0.00 4.24
5443 5601 6.941857 TCATTAAGTTGCTCATGTACTGGTA 58.058 36.000 0.00 0.00 0.00 3.25
5594 5752 6.317140 ACTTGATCTCACATTGCGAATACAAT 59.683 34.615 0.00 0.00 40.90 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.571080 AAAACATCTTTCAAATGCAACCAAT 57.429 28.000 0.00 0.00 0.00 3.16
1 2 6.998968 AAAACATCTTTCAAATGCAACCAA 57.001 29.167 0.00 0.00 0.00 3.67
2 3 8.498054 TTTAAAACATCTTTCAAATGCAACCA 57.502 26.923 0.00 0.00 0.00 3.67
3 4 9.780413 TTTTTAAAACATCTTTCAAATGCAACC 57.220 25.926 0.00 0.00 0.00 3.77
60 63 6.548441 ACTTTGATCACCGATTTAACGAAA 57.452 33.333 0.00 0.00 35.09 3.46
64 67 8.252964 AGTCTAACTTTGATCACCGATTTAAC 57.747 34.615 0.00 0.00 0.00 2.01
90 93 1.072266 ACAAGGCCCCACACTATTCA 58.928 50.000 0.00 0.00 0.00 2.57
115 118 1.229723 TTAAAGGTCCTCCCGGCCT 60.230 57.895 0.00 0.00 38.11 5.19
153 156 7.414540 GCATTGCAGAACAAAACTAGCTACTAT 60.415 37.037 3.15 0.00 42.86 2.12
154 157 6.128282 GCATTGCAGAACAAAACTAGCTACTA 60.128 38.462 3.15 0.00 42.86 1.82
155 158 5.335191 GCATTGCAGAACAAAACTAGCTACT 60.335 40.000 3.15 0.00 42.86 2.57
156 159 4.853743 GCATTGCAGAACAAAACTAGCTAC 59.146 41.667 3.15 0.00 42.86 3.58
199 202 5.288804 ACATATGTCCAAAAACAAGCACAC 58.711 37.500 1.41 0.00 31.81 3.82
212 215 5.715279 GGTGGAGTAGCTATACATATGTCCA 59.285 44.000 12.68 7.31 31.98 4.02
382 386 6.857964 GCTTGTATTTGTCCACATATATGCAC 59.142 38.462 12.79 7.70 0.00 4.57
529 533 2.767644 GCCCTGGGGGTGTATTATTT 57.232 50.000 16.03 0.00 46.51 1.40
699 707 3.309296 TCTCTCTCTCTCTCTCCTCTCC 58.691 54.545 0.00 0.00 0.00 3.71
705 713 3.452627 AGGTGACTCTCTCTCTCTCTCTC 59.547 52.174 0.00 0.00 32.90 3.20
706 714 3.454858 AGGTGACTCTCTCTCTCTCTCT 58.545 50.000 0.00 0.00 32.90 3.10
707 715 3.914426 AGGTGACTCTCTCTCTCTCTC 57.086 52.381 0.00 0.00 32.90 3.20
708 716 4.289672 AGAAAGGTGACTCTCTCTCTCTCT 59.710 45.833 0.00 0.00 29.58 3.10
709 717 4.589908 AGAAAGGTGACTCTCTCTCTCTC 58.410 47.826 0.00 0.00 29.58 3.20
710 718 4.657814 AGAAAGGTGACTCTCTCTCTCT 57.342 45.455 0.00 0.00 29.58 3.10
733 741 1.531365 CCCTTTCAAGGCACCAGCA 60.531 57.895 0.00 0.00 45.10 4.41
738 746 2.039879 TCTCTTACCCCTTTCAAGGCAC 59.960 50.000 0.00 0.00 45.10 5.01
988 998 1.019673 GCCATCATGGTGCTACACTG 58.980 55.000 5.31 0.00 40.46 3.66
1008 1018 0.466555 CGGAGGAGGAAGACGAGGAT 60.467 60.000 0.00 0.00 0.00 3.24
1116 1129 4.680237 TGGTTGCCTCCGACAGCG 62.680 66.667 0.00 0.00 37.24 5.18
1221 1241 8.139989 CCTCTCTTTCAACATTTTCTCAACAAT 58.860 33.333 0.00 0.00 0.00 2.71
1285 1318 0.394192 CTGTGAGCACACCTTCCTCA 59.606 55.000 11.92 0.00 45.40 3.86
1310 1343 3.152341 AGAGGGATGCAAACTCAAACAG 58.848 45.455 15.25 0.00 33.76 3.16
1323 1356 6.324254 TCATATATGCATCTGAGAGAGGGATG 59.676 42.308 0.19 0.00 37.62 3.51
1426 1459 0.319813 GCTGTGCCACAATTCCCAAC 60.320 55.000 0.00 0.00 0.00 3.77
1459 1492 9.548631 TTCTTCCCTTCTTTTATTCTCTCTCTA 57.451 33.333 0.00 0.00 0.00 2.43
1657 1694 4.614946 GCTCACTGCAAAGAGTTCAATTT 58.385 39.130 14.45 0.00 42.31 1.82
1917 1961 1.413767 CGATGACGGTCTTGGAAGCG 61.414 60.000 9.88 0.00 45.19 4.68
1948 1992 1.209128 CCATGTCGTCATCGTAAGCC 58.791 55.000 0.00 0.00 38.33 4.35
1977 2021 4.980805 TTGGGAGCACGACGGCAC 62.981 66.667 10.28 4.58 35.83 5.01
1978 2022 4.680237 CTTGGGAGCACGACGGCA 62.680 66.667 10.28 0.00 35.83 5.69
2002 2046 3.921767 CTTCTGCAGCCGCGAGACA 62.922 63.158 8.23 0.00 42.97 3.41
2187 2231 1.919240 CCCATATGCCACATGATGCT 58.081 50.000 0.00 0.00 0.00 3.79
2206 2250 0.467804 GATGAACAGGAGGAGGGAGC 59.532 60.000 0.00 0.00 0.00 4.70
2208 2252 0.041238 ACGATGAACAGGAGGAGGGA 59.959 55.000 0.00 0.00 0.00 4.20
2209 2253 0.461961 GACGATGAACAGGAGGAGGG 59.538 60.000 0.00 0.00 0.00 4.30
2308 2354 4.522022 GGCTCTCAATTAATTCCCCATCTG 59.478 45.833 0.00 0.00 0.00 2.90
2335 2381 7.141100 ACCTCGTTAATTGTACATTTTCCAG 57.859 36.000 8.20 2.19 0.00 3.86
2538 2593 5.488262 AATGGGTCAGCAAAATTAAGCTT 57.512 34.783 3.48 3.48 39.50 3.74
2579 2634 4.060900 GCATGCATATGTACTGTACTGCT 58.939 43.478 22.85 11.64 36.65 4.24
2580 2635 3.809279 TGCATGCATATGTACTGTACTGC 59.191 43.478 18.46 18.22 36.65 4.40
2581 2636 4.084171 GCTGCATGCATATGTACTGTACTG 60.084 45.833 22.97 5.09 42.31 2.74
2582 2637 4.060900 GCTGCATGCATATGTACTGTACT 58.939 43.478 22.97 7.21 42.31 2.73
2660 2715 0.325933 GCCATCGATCCATCCATCCA 59.674 55.000 0.00 0.00 0.00 3.41
2661 2716 0.325933 TGCCATCGATCCATCCATCC 59.674 55.000 0.00 0.00 0.00 3.51
2662 2717 2.014857 CATGCCATCGATCCATCCATC 58.985 52.381 0.00 0.00 0.00 3.51
2663 2718 1.340697 CCATGCCATCGATCCATCCAT 60.341 52.381 0.00 0.00 0.00 3.41
2706 2761 5.286267 TGCTATAGTAGTACTTTTGGGCC 57.714 43.478 8.40 0.00 0.00 5.80
2915 2990 9.339492 CTTGTACACAAATTTTTGCATGTTTTT 57.661 25.926 4.23 0.00 41.79 1.94
2946 3021 6.072508 CCAGACAGTAAGCACACACAATTAAT 60.073 38.462 0.00 0.00 0.00 1.40
2947 3022 5.238432 CCAGACAGTAAGCACACACAATTAA 59.762 40.000 0.00 0.00 0.00 1.40
2948 3023 4.754618 CCAGACAGTAAGCACACACAATTA 59.245 41.667 0.00 0.00 0.00 1.40
2952 3027 1.760029 TCCAGACAGTAAGCACACACA 59.240 47.619 0.00 0.00 0.00 3.72
2953 3028 2.526304 TCCAGACAGTAAGCACACAC 57.474 50.000 0.00 0.00 0.00 3.82
2993 3070 1.379443 CAGGCACACCCATCTGCAT 60.379 57.895 0.00 0.00 36.11 3.96
3052 3129 1.825281 CTCCTGATGATCTCCCCGCC 61.825 65.000 0.00 0.00 0.00 6.13
3151 3228 1.528292 TATTGTTGTTGGTGGCGGGC 61.528 55.000 0.00 0.00 0.00 6.13
3190 3267 4.128643 AGATGTAGTCAGGAGTAGTACGC 58.871 47.826 0.00 0.00 0.00 4.42
3191 3268 4.751098 GGAGATGTAGTCAGGAGTAGTACG 59.249 50.000 0.00 0.00 0.00 3.67
3229 3331 7.278135 AGAGTAGATAGAGAAAATGCAATGCA 58.722 34.615 11.44 11.44 44.86 3.96
3230 3332 7.727331 AGAGTAGATAGAGAAAATGCAATGC 57.273 36.000 0.00 0.00 0.00 3.56
3231 3333 9.979578 AGTAGAGTAGATAGAGAAAATGCAATG 57.020 33.333 0.00 0.00 0.00 2.82
3233 3335 8.634444 GGAGTAGAGTAGATAGAGAAAATGCAA 58.366 37.037 0.00 0.00 0.00 4.08
3234 3336 7.231722 GGGAGTAGAGTAGATAGAGAAAATGCA 59.768 40.741 0.00 0.00 0.00 3.96
3235 3337 7.231722 TGGGAGTAGAGTAGATAGAGAAAATGC 59.768 40.741 0.00 0.00 0.00 3.56
3236 3338 8.698973 TGGGAGTAGAGTAGATAGAGAAAATG 57.301 38.462 0.00 0.00 0.00 2.32
3237 3339 9.362151 CTTGGGAGTAGAGTAGATAGAGAAAAT 57.638 37.037 0.00 0.00 0.00 1.82
3238 3340 8.558312 TCTTGGGAGTAGAGTAGATAGAGAAAA 58.442 37.037 0.00 0.00 0.00 2.29
3239 3341 8.103660 TCTTGGGAGTAGAGTAGATAGAGAAA 57.896 38.462 0.00 0.00 0.00 2.52
3240 3342 7.569485 TCTCTTGGGAGTAGAGTAGATAGAGAA 59.431 40.741 0.00 0.00 40.04 2.87
3304 3406 1.024046 ACACACACGCACACACACAT 61.024 50.000 0.00 0.00 0.00 3.21
3315 3423 1.069568 ACAACACAACACACACACACG 60.070 47.619 0.00 0.00 0.00 4.49
3316 3424 2.287308 ACACAACACAACACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
3317 3425 1.950216 ACACAACACAACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
3318 3426 2.697431 ACACAACACAACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
3319 3427 2.359214 ACAACACAACACAACACACACA 59.641 40.909 0.00 0.00 0.00 3.72
3320 3428 2.723658 CACAACACAACACAACACACAC 59.276 45.455 0.00 0.00 0.00 3.82
3321 3429 2.359214 ACACAACACAACACAACACACA 59.641 40.909 0.00 0.00 0.00 3.72
3322 3430 3.006659 ACACAACACAACACAACACAC 57.993 42.857 0.00 0.00 0.00 3.82
3323 3431 3.375642 CAACACAACACAACACAACACA 58.624 40.909 0.00 0.00 0.00 3.72
3324 3432 2.728839 CCAACACAACACAACACAACAC 59.271 45.455 0.00 0.00 0.00 3.32
3325 3433 2.362397 ACCAACACAACACAACACAACA 59.638 40.909 0.00 0.00 0.00 3.33
3326 3434 3.019933 ACCAACACAACACAACACAAC 57.980 42.857 0.00 0.00 0.00 3.32
3332 3440 3.821600 ACACACTAACCAACACAACACAA 59.178 39.130 0.00 0.00 0.00 3.33
3339 3447 2.745281 ACACACACACACTAACCAACAC 59.255 45.455 0.00 0.00 0.00 3.32
3346 3454 2.739379 CACACACACACACACACACTAA 59.261 45.455 0.00 0.00 0.00 2.24
3359 3467 4.119862 AGTGATCAGTACAACACACACAC 58.880 43.478 0.00 0.00 35.97 3.82
3361 3469 7.170828 TGAATTAGTGATCAGTACAACACACAC 59.829 37.037 9.87 0.00 35.97 3.82
3362 3470 7.170828 GTGAATTAGTGATCAGTACAACACACA 59.829 37.037 21.92 10.95 35.97 3.72
3363 3471 7.385205 AGTGAATTAGTGATCAGTACAACACAC 59.615 37.037 25.16 20.84 35.97 3.82
3426 3534 8.893727 GGTACTCACTCATTAATTAACAAGCAT 58.106 33.333 0.00 0.00 0.00 3.79
3561 3685 4.650754 GCTAGCTAGCTTGTTACCAGTA 57.349 45.455 33.71 0.00 45.62 2.74
3562 3686 3.528597 GCTAGCTAGCTTGTTACCAGT 57.471 47.619 33.71 0.00 45.62 4.00
3683 3817 5.604758 TCCTCTATTCTTGTGACCATGAG 57.395 43.478 0.00 0.00 0.00 2.90
3945 4089 5.923114 GTCTGTGCATACATACATAGGACAG 59.077 44.000 0.00 0.00 34.90 3.51
3954 4098 2.700897 AGGAGGGTCTGTGCATACATAC 59.299 50.000 0.00 0.00 35.97 2.39
3974 4118 4.082571 CCCCAAAGAGTAAATTCAGCACAG 60.083 45.833 0.00 0.00 0.00 3.66
4296 4450 1.236628 GATGATGGTCAGGATGCAGC 58.763 55.000 0.00 0.00 34.76 5.25
4325 4479 2.487762 CCCGCTTAAAGTCTGCATGAAA 59.512 45.455 0.00 0.00 0.00 2.69
4448 4604 8.196378 ACCCATTGCTTATTAACAGGTTTTAA 57.804 30.769 0.00 0.00 0.00 1.52
4569 4727 0.603065 CTGATGTCCGGTGTCTGACA 59.397 55.000 6.36 6.36 44.86 3.58
4583 4741 3.015327 CCTTTGCTTCCTCCTTCTGATG 58.985 50.000 0.00 0.00 0.00 3.07
4868 5026 7.365497 TCACTTGGCTATAGAGATTTGATCA 57.635 36.000 3.21 0.00 0.00 2.92
5119 5277 0.400594 ACACTTAACTGCTCACCCCC 59.599 55.000 0.00 0.00 0.00 5.40
5306 5464 8.642432 CCCTGTCTACTCTGAACATTATTCATA 58.358 37.037 0.00 0.00 0.00 2.15
5438 5596 9.176181 GTATTTGTTGTGTATTGTTGTTACCAG 57.824 33.333 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.