Multiple sequence alignment - TraesCS4D01G209500

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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 TraesCS4D01G209500 chr4D 100.000 3127 0 0 1 3127 360944146 360941020 0.000000e+00 5775.0
1 TraesCS4D01G209500 chr4B 93.052 2634 78 50 583 3126 446342501 446345119 0.000000e+00 3753.0
2 TraesCS4D01G209500 chr4B 94.937 474 22 1 1985 2458 560292808 560292337 0.000000e+00 741.0
3 TraesCS4D01G209500 chr4B 94.783 230 12 0 2228 2457 648942480 648942709 2.970000e-95 359.0
4 TraesCS4D01G209500 chr4B 97.000 100 3 0 1890 1989 560294617 560294518 5.360000e-38 169.0
5 TraesCS4D01G209500 chr4B 96.341 82 3 0 1 82 446341801 446341882 5.440000e-28 135.0
6 TraesCS4D01G209500 chr4B 75.493 355 45 19 231 562 446342185 446342520 5.440000e-28 135.0
7 TraesCS4D01G209500 chr4A 92.248 2593 94 51 582 3124 103766680 103769215 0.000000e+00 3576.0
8 TraesCS4D01G209500 chr4A 93.074 231 16 0 2228 2458 695669120 695668890 3.860000e-89 339.0
9 TraesCS4D01G209500 chr4A 77.403 593 79 29 1 562 103766132 103766700 5.070000e-78 302.0
10 TraesCS4D01G209500 chr3B 94.860 642 29 3 1817 2458 356022087 356022724 0.000000e+00 1000.0
11 TraesCS4D01G209500 chr3B 94.704 642 31 2 1817 2458 661974731 661975369 0.000000e+00 994.0
12 TraesCS4D01G209500 chr3B 93.162 117 8 0 1224 1340 116690152 116690036 4.150000e-39 172.0
13 TraesCS4D01G209500 chr3B 100.000 41 0 0 3087 3127 179948707 179948667 3.340000e-10 76.8
14 TraesCS4D01G209500 chr3B 100.000 38 0 0 1169 1206 116690192 116690155 1.560000e-08 71.3
15 TraesCS4D01G209500 chr6B 94.246 643 32 4 1817 2458 251103294 251103932 0.000000e+00 977.0
16 TraesCS4D01G209500 chr6B 94.106 526 27 3 1934 2458 306015091 306014569 0.000000e+00 797.0
17 TraesCS4D01G209500 chr1B 86.957 207 19 5 978 1184 42067455 42067257 3.140000e-55 226.0
18 TraesCS4D01G209500 chr2D 91.667 96 6 2 1210 1304 102626735 102626641 7.040000e-27 132.0
19 TraesCS4D01G209500 chr2A 90.805 87 8 0 1 87 776462947 776462861 1.970000e-22 117.0


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 TraesCS4D01G209500 chr4D 360941020 360944146 3126 True 5775 5775 100.000000 1 3127 1 chr4D.!!$R1 3126
1 TraesCS4D01G209500 chr4B 446341801 446345119 3318 False 1341 3753 88.295333 1 3126 3 chr4B.!!$F2 3125
2 TraesCS4D01G209500 chr4B 560292337 560294617 2280 True 455 741 95.968500 1890 2458 2 chr4B.!!$R1 568
3 TraesCS4D01G209500 chr4A 103766132 103769215 3083 False 1939 3576 84.825500 1 3124 2 chr4A.!!$F1 3123
4 TraesCS4D01G209500 chr3B 356022087 356022724 637 False 1000 1000 94.860000 1817 2458 1 chr3B.!!$F1 641
5 TraesCS4D01G209500 chr3B 661974731 661975369 638 False 994 994 94.704000 1817 2458 1 chr3B.!!$F2 641
6 TraesCS4D01G209500 chr6B 251103294 251103932 638 False 977 977 94.246000 1817 2458 1 chr6B.!!$F1 641
7 TraesCS4D01G209500 chr6B 306014569 306015091 522 True 797 797 94.106000 1934 2458 1 chr6B.!!$R1 524

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
399 612 1.000283 CTATCCAGATGTCCGAGCACC 60.000 57.143 0.0 0.0 0.0 5.01 F
410 623 1.073125 TCCGAGCACCCTGAAAATTGA 59.927 47.619 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 4075 1.068055 GTTTGCTCATGGCCAACTCTG 60.068 52.381 10.96 2.87 41.53 3.35 R
2161 4158 3.297134 TTCCCCCATAATTCACTGCTC 57.703 47.619 0.00 0.00 0.00 4.26 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
73 74 3.645975 GTGTGGGCACGTCAACGG 61.646 66.667 7.53 0.00 44.95 4.44
141 171 5.834239 AAAACAAACGATGGAGTAGTACG 57.166 39.130 0.00 0.00 0.00 3.67
143 173 4.088823 ACAAACGATGGAGTAGTACGTC 57.911 45.455 0.00 0.00 36.20 4.34
145 176 4.157289 ACAAACGATGGAGTAGTACGTCAT 59.843 41.667 9.97 9.97 36.20 3.06
159 190 2.115348 CGTCATCGTGTAGCGGTATT 57.885 50.000 0.00 0.00 41.72 1.89
161 192 3.620761 CGTCATCGTGTAGCGGTATTTA 58.379 45.455 0.00 0.00 41.72 1.40
164 195 5.507180 CGTCATCGTGTAGCGGTATTTATAG 59.493 44.000 0.00 0.00 41.72 1.31
168 199 6.005583 TCGTGTAGCGGTATTTATAGAAGG 57.994 41.667 0.00 0.00 41.72 3.46
186 217 4.962362 AGAAGGAAAAGAAAAAGGCCTTGA 59.038 37.500 21.33 0.00 35.99 3.02
192 223 1.882623 AGAAAAAGGCCTTGAAGAGCG 59.117 47.619 21.33 0.00 0.00 5.03
207 238 3.279875 GCGGCTAAATGGCTCCCG 61.280 66.667 0.00 0.00 41.72 5.14
260 442 4.037565 ACACGAGAGATGTTTGAGTGTGTA 59.962 41.667 0.00 0.00 39.49 2.90
295 477 2.697431 TTTAGCGTGTTTGCACATCC 57.303 45.000 0.00 0.00 45.50 3.51
306 488 2.052782 TGCACATCCGAGTAGCTCTA 57.947 50.000 0.00 0.00 0.00 2.43
318 504 6.002704 CCGAGTAGCTCTAAGAAATAGGGTA 58.997 44.000 0.00 0.00 34.29 3.69
340 553 9.059260 GGGTATGTGAAAAAGTTTACTAGTTCA 57.941 33.333 0.00 0.00 30.87 3.18
347 560 9.332502 TGAAAAAGTTTACTAGTTCATGCACTA 57.667 29.630 0.00 5.10 29.36 2.74
351 564 7.757097 AGTTTACTAGTTCATGCACTAATCG 57.243 36.000 0.00 0.00 0.00 3.34
353 566 6.459670 TTACTAGTTCATGCACTAATCGGA 57.540 37.500 0.00 0.00 0.00 4.55
355 568 5.533482 ACTAGTTCATGCACTAATCGGATC 58.467 41.667 6.67 0.00 0.00 3.36
356 569 4.679373 AGTTCATGCACTAATCGGATCT 57.321 40.909 0.00 0.00 0.00 2.75
358 571 6.352016 AGTTCATGCACTAATCGGATCTAT 57.648 37.500 0.00 0.00 0.00 1.98
362 575 8.988934 GTTCATGCACTAATCGGATCTATTTTA 58.011 33.333 0.00 0.00 0.00 1.52
363 576 8.534333 TCATGCACTAATCGGATCTATTTTAC 57.466 34.615 0.00 0.00 0.00 2.01
364 577 8.367911 TCATGCACTAATCGGATCTATTTTACT 58.632 33.333 0.00 0.00 0.00 2.24
365 578 8.993121 CATGCACTAATCGGATCTATTTTACTT 58.007 33.333 0.00 0.00 0.00 2.24
366 579 8.589335 TGCACTAATCGGATCTATTTTACTTC 57.411 34.615 0.00 0.00 0.00 3.01
374 587 8.197988 TCGGATCTATTTTACTTCTTTTGCTC 57.802 34.615 0.00 0.00 0.00 4.26
382 595 7.986085 TTTTACTTCTTTTGCTCAGAGCTAT 57.014 32.000 23.15 2.51 42.97 2.97
383 596 7.602517 TTTACTTCTTTTGCTCAGAGCTATC 57.397 36.000 23.15 0.00 42.97 2.08
399 612 1.000283 CTATCCAGATGTCCGAGCACC 60.000 57.143 0.00 0.00 0.00 5.01
408 621 1.202879 TGTCCGAGCACCCTGAAAATT 60.203 47.619 0.00 0.00 0.00 1.82
410 623 1.073125 TCCGAGCACCCTGAAAATTGA 59.927 47.619 0.00 0.00 0.00 2.57
447 660 4.281688 CACCCAAACATCTTCCATTCAAGT 59.718 41.667 0.00 0.00 0.00 3.16
448 661 4.524328 ACCCAAACATCTTCCATTCAAGTC 59.476 41.667 0.00 0.00 0.00 3.01
462 688 8.519799 TCCATTCAAGTCTTTTTAGTGTTTCT 57.480 30.769 0.00 0.00 0.00 2.52
481 707 9.556030 GTGTTTCTATTATTTTTACTGCTCACC 57.444 33.333 0.00 0.00 0.00 4.02
482 708 9.290988 TGTTTCTATTATTTTTACTGCTCACCA 57.709 29.630 0.00 0.00 0.00 4.17
486 712 9.905713 TCTATTATTTTTACTGCTCACCAAGAT 57.094 29.630 0.00 0.00 0.00 2.40
488 714 7.994425 TTATTTTTACTGCTCACCAAGATCA 57.006 32.000 0.00 0.00 0.00 2.92
489 715 5.947228 TTTTTACTGCTCACCAAGATCAG 57.053 39.130 0.00 0.00 44.20 2.90
490 716 4.890158 TTTACTGCTCACCAAGATCAGA 57.110 40.909 3.30 0.00 41.85 3.27
491 717 5.426689 TTTACTGCTCACCAAGATCAGAT 57.573 39.130 3.30 0.00 41.85 2.90
493 719 6.544928 TTACTGCTCACCAAGATCAGATAA 57.455 37.500 3.30 0.00 41.85 1.75
494 720 5.021033 ACTGCTCACCAAGATCAGATAAG 57.979 43.478 3.30 0.00 41.85 1.73
497 723 5.423015 TGCTCACCAAGATCAGATAAGTTC 58.577 41.667 0.00 0.00 0.00 3.01
499 725 4.433615 TCACCAAGATCAGATAAGTTCGC 58.566 43.478 0.00 0.00 0.00 4.70
500 726 3.243877 CACCAAGATCAGATAAGTTCGCG 59.756 47.826 0.00 0.00 0.00 5.87
501 727 3.119101 ACCAAGATCAGATAAGTTCGCGT 60.119 43.478 5.77 0.00 0.00 6.01
503 729 3.357166 AGATCAGATAAGTTCGCGTCC 57.643 47.619 5.77 0.00 0.00 4.79
504 730 2.688446 AGATCAGATAAGTTCGCGTCCA 59.312 45.455 5.77 0.00 0.00 4.02
505 731 3.319405 AGATCAGATAAGTTCGCGTCCAT 59.681 43.478 5.77 0.00 0.00 3.41
544 770 2.033299 CCTTGCTGCTTTTCACTTCGAA 59.967 45.455 0.00 0.00 0.00 3.71
545 771 3.304928 CCTTGCTGCTTTTCACTTCGAAT 60.305 43.478 0.00 0.00 32.32 3.34
546 772 4.083324 CCTTGCTGCTTTTCACTTCGAATA 60.083 41.667 0.00 0.00 32.32 1.75
547 773 5.431420 TTGCTGCTTTTCACTTCGAATAA 57.569 34.783 0.00 0.00 32.32 1.40
548 774 5.627499 TGCTGCTTTTCACTTCGAATAAT 57.373 34.783 0.00 0.00 32.32 1.28
549 775 5.631026 TGCTGCTTTTCACTTCGAATAATC 58.369 37.500 0.00 0.00 32.32 1.75
550 776 5.181056 TGCTGCTTTTCACTTCGAATAATCA 59.819 36.000 0.00 0.00 32.32 2.57
551 777 5.736358 GCTGCTTTTCACTTCGAATAATCAG 59.264 40.000 0.00 1.80 32.32 2.90
552 778 6.402550 GCTGCTTTTCACTTCGAATAATCAGA 60.403 38.462 0.00 0.00 32.32 3.27
553 779 7.433708 TGCTTTTCACTTCGAATAATCAGAA 57.566 32.000 0.00 0.00 32.32 3.02
554 780 7.521529 TGCTTTTCACTTCGAATAATCAGAAG 58.478 34.615 0.00 9.43 44.86 2.85
555 781 6.963805 GCTTTTCACTTCGAATAATCAGAAGG 59.036 38.462 0.00 6.20 43.95 3.46
556 782 6.985188 TTTCACTTCGAATAATCAGAAGGG 57.015 37.500 0.00 10.69 44.36 3.95
558 784 6.485830 TCACTTCGAATAATCAGAAGGGAT 57.514 37.500 11.06 0.00 45.96 3.85
559 785 6.516718 TCACTTCGAATAATCAGAAGGGATC 58.483 40.000 11.06 0.00 45.96 3.36
560 786 5.698545 CACTTCGAATAATCAGAAGGGATCC 59.301 44.000 1.92 1.92 45.46 3.36
561 787 4.891992 TCGAATAATCAGAAGGGATCCC 57.108 45.455 24.59 24.59 0.00 3.85
562 788 3.583086 TCGAATAATCAGAAGGGATCCCC 59.417 47.826 28.11 13.27 45.90 4.81
571 797 2.036572 GGGATCCCCAACCGCAAA 59.963 61.111 21.42 0.00 44.65 3.68
572 798 1.608046 GGGATCCCCAACCGCAAAA 60.608 57.895 21.42 0.00 44.65 2.44
573 799 1.188871 GGGATCCCCAACCGCAAAAA 61.189 55.000 21.42 0.00 44.65 1.94
701 934 1.599240 GATCCCGCATCTCCCTTGC 60.599 63.158 0.00 0.00 36.74 4.01
702 935 2.049627 GATCCCGCATCTCCCTTGCT 62.050 60.000 0.00 0.00 37.96 3.91
703 936 2.049627 ATCCCGCATCTCCCTTGCTC 62.050 60.000 0.00 0.00 37.96 4.26
810 1062 3.220658 TCACCAGCGACGTCACCA 61.221 61.111 17.16 0.00 0.00 4.17
1000 1280 3.245315 CACGTCCGATCCGCGTTC 61.245 66.667 4.92 0.05 36.67 3.95
1061 1341 2.360600 TCCGGGGGATTTGTTGCG 60.361 61.111 0.00 0.00 0.00 4.85
1369 1649 3.164269 CTCCTCATGGGGTCGGGG 61.164 72.222 12.53 0.00 35.33 5.73
1397 1677 1.587043 CCTGCTCGACCAGTTCTCGA 61.587 60.000 6.97 0.00 37.82 4.04
2054 4050 1.305213 GAAGGGCTTGCATTCCCCA 60.305 57.895 17.45 0.00 43.67 4.96
2078 4075 7.378728 CCACCTTTTGTCTCGTTTTAAGAATTC 59.621 37.037 0.00 0.00 0.00 2.17
2150 4147 1.688735 GAAGAACAAGCCCAAGCCTTT 59.311 47.619 0.00 0.00 41.25 3.11
2367 4365 3.983044 TCCTCTGGCTAAACCTCTTTC 57.017 47.619 0.00 0.00 40.22 2.62
2415 4414 7.492352 AGTTCTGTCATAAGTTGTAACAACC 57.508 36.000 2.07 0.00 0.00 3.77
2473 4498 6.350110 GGGCTGCTAAGTGATGTTTTGATTTA 60.350 38.462 0.00 0.00 0.00 1.40
2474 4499 7.260603 GGCTGCTAAGTGATGTTTTGATTTAT 58.739 34.615 0.00 0.00 0.00 1.40
2510 4539 3.131223 GTGCTTCTACATGCTGGACTCTA 59.869 47.826 0.00 0.00 0.00 2.43
2540 4569 7.594758 TGTTTTCATTTGCACTGCTAAATAGAC 59.405 33.333 1.98 0.30 0.00 2.59
2571 4600 5.701224 AGAAGTCCATTACAGGGTTTTGAA 58.299 37.500 0.00 0.00 0.00 2.69
2589 4618 4.265904 TGAAGCTCAACCGATTCAAGTA 57.734 40.909 0.00 0.00 36.48 2.24
2657 4686 3.650942 TGAATTGAACTAGTGTGAGGGGT 59.349 43.478 0.00 0.00 0.00 4.95
2668 4697 2.501723 GTGTGAGGGGTCATATGAGTGT 59.498 50.000 5.42 0.00 0.00 3.55
2675 4704 4.835615 AGGGGTCATATGAGTGTAGTGATC 59.164 45.833 5.42 0.00 0.00 2.92
2703 4732 9.962783 ATGAAGAAATGTCTACCGTATTAGTAC 57.037 33.333 0.00 0.00 32.16 2.73
2824 4853 3.991121 GGAGTTCTCTGTTCCTTTCTTCG 59.009 47.826 0.00 0.00 0.00 3.79
2903 4932 4.201822 GCTGGATTCCGAACAATGTTAGTC 60.202 45.833 0.00 0.00 0.00 2.59
2927 4956 2.670635 GCAGTAGGCATGACACTCG 58.329 57.895 0.00 0.00 43.97 4.18
2955 4984 7.275560 TGTCTGTATGTTCATCATTGTAGTTCG 59.724 37.037 0.00 0.00 37.91 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 2.481952 CGCCCGGTGTATACTACTCTAC 59.518 54.545 0.00 0.00 0.00 2.59
151 182 9.457436 TTTTCTTTTCCTTCTATAAATACCGCT 57.543 29.630 0.00 0.00 0.00 5.52
159 190 8.585018 CAAGGCCTTTTTCTTTTCCTTCTATAA 58.415 33.333 17.61 0.00 32.11 0.98
161 192 6.782494 TCAAGGCCTTTTTCTTTTCCTTCTAT 59.218 34.615 17.61 0.00 32.11 1.98
164 195 5.276461 TCAAGGCCTTTTTCTTTTCCTTC 57.724 39.130 17.61 0.00 32.11 3.46
168 199 4.747108 GCTCTTCAAGGCCTTTTTCTTTTC 59.253 41.667 17.61 0.00 0.00 2.29
186 217 0.464554 GGAGCCATTTAGCCGCTCTT 60.465 55.000 0.00 0.00 46.60 2.85
192 223 2.561478 TTATCGGGAGCCATTTAGCC 57.439 50.000 0.00 0.00 0.00 3.93
221 400 7.368833 TCTCTCGTGTAAAGAAAGAAACCTAG 58.631 38.462 0.00 0.00 0.00 3.02
223 402 6.158023 TCTCTCGTGTAAAGAAAGAAACCT 57.842 37.500 0.00 0.00 0.00 3.50
224 403 6.424207 ACATCTCTCGTGTAAAGAAAGAAACC 59.576 38.462 0.00 0.00 0.00 3.27
225 404 7.409465 ACATCTCTCGTGTAAAGAAAGAAAC 57.591 36.000 0.00 0.00 0.00 2.78
226 405 8.335356 CAAACATCTCTCGTGTAAAGAAAGAAA 58.665 33.333 0.00 0.00 0.00 2.52
227 406 7.709182 TCAAACATCTCTCGTGTAAAGAAAGAA 59.291 33.333 0.00 0.00 0.00 2.52
228 407 7.207383 TCAAACATCTCTCGTGTAAAGAAAGA 58.793 34.615 0.00 0.00 0.00 2.52
233 415 5.692204 ACACTCAAACATCTCTCGTGTAAAG 59.308 40.000 0.00 0.00 32.94 1.85
240 422 5.863935 TCATTACACACTCAAACATCTCTCG 59.136 40.000 0.00 0.00 0.00 4.04
260 442 5.914635 CACGCTAAAAATTGACACAGTCATT 59.085 36.000 0.12 0.00 42.40 2.57
295 477 7.175293 ACATACCCTATTTCTTAGAGCTACTCG 59.825 40.741 0.00 0.00 35.36 4.18
318 504 8.629158 TGCATGAACTAGTAAACTTTTTCACAT 58.371 29.630 0.00 0.00 32.13 3.21
340 553 9.209175 GAAGTAAAATAGATCCGATTAGTGCAT 57.791 33.333 0.00 0.00 0.00 3.96
347 560 9.178758 AGCAAAAGAAGTAAAATAGATCCGATT 57.821 29.630 0.00 0.00 0.00 3.34
350 563 7.974675 TGAGCAAAAGAAGTAAAATAGATCCG 58.025 34.615 0.00 0.00 0.00 4.18
351 564 9.167311 TCTGAGCAAAAGAAGTAAAATAGATCC 57.833 33.333 0.00 0.00 0.00 3.36
353 566 8.672815 GCTCTGAGCAAAAGAAGTAAAATAGAT 58.327 33.333 24.02 0.00 41.89 1.98
355 568 8.038492 AGCTCTGAGCAAAAGAAGTAAAATAG 57.962 34.615 29.49 0.00 45.56 1.73
356 569 7.986085 AGCTCTGAGCAAAAGAAGTAAAATA 57.014 32.000 29.49 0.00 45.56 1.40
358 571 7.119846 GGATAGCTCTGAGCAAAAGAAGTAAAA 59.880 37.037 29.49 1.35 45.56 1.52
362 575 4.019860 TGGATAGCTCTGAGCAAAAGAAGT 60.020 41.667 29.49 10.35 45.56 3.01
363 576 4.511527 TGGATAGCTCTGAGCAAAAGAAG 58.488 43.478 29.49 0.00 45.56 2.85
364 577 4.223700 TCTGGATAGCTCTGAGCAAAAGAA 59.776 41.667 29.49 10.82 45.56 2.52
365 578 3.771479 TCTGGATAGCTCTGAGCAAAAGA 59.229 43.478 29.49 20.10 45.56 2.52
366 579 4.134379 TCTGGATAGCTCTGAGCAAAAG 57.866 45.455 29.49 18.42 45.56 2.27
371 584 2.029110 GGACATCTGGATAGCTCTGAGC 60.029 54.545 21.72 21.72 42.84 4.26
374 587 2.228582 CTCGGACATCTGGATAGCTCTG 59.771 54.545 0.00 0.00 0.00 3.35
382 595 2.359169 GGGTGCTCGGACATCTGGA 61.359 63.158 0.00 0.00 0.00 3.86
383 596 2.187946 GGGTGCTCGGACATCTGG 59.812 66.667 0.00 0.00 0.00 3.86
399 612 4.332819 GTGAGGTCCGTATCAATTTTCAGG 59.667 45.833 0.00 0.00 0.00 3.86
408 621 1.509463 GTGCGTGAGGTCCGTATCA 59.491 57.895 0.00 0.00 0.00 2.15
410 623 2.718073 GGGTGCGTGAGGTCCGTAT 61.718 63.158 0.00 0.00 0.00 3.06
462 688 9.679661 TGATCTTGGTGAGCAGTAAAAATAATA 57.320 29.630 0.00 0.00 36.01 0.98
474 700 5.423015 GAACTTATCTGATCTTGGTGAGCA 58.577 41.667 0.00 0.00 38.94 4.26
476 702 4.505922 GCGAACTTATCTGATCTTGGTGAG 59.494 45.833 0.00 0.00 0.00 3.51
477 703 4.433615 GCGAACTTATCTGATCTTGGTGA 58.566 43.478 0.00 0.00 0.00 4.02
478 704 3.243877 CGCGAACTTATCTGATCTTGGTG 59.756 47.826 0.00 0.00 0.00 4.17
479 705 3.119101 ACGCGAACTTATCTGATCTTGGT 60.119 43.478 15.93 0.00 0.00 3.67
481 707 3.487574 GGACGCGAACTTATCTGATCTTG 59.512 47.826 15.93 0.00 0.00 3.02
482 708 3.130516 TGGACGCGAACTTATCTGATCTT 59.869 43.478 15.93 0.00 0.00 2.40
483 709 2.688446 TGGACGCGAACTTATCTGATCT 59.312 45.455 15.93 0.00 0.00 2.75
486 712 4.642445 TTATGGACGCGAACTTATCTGA 57.358 40.909 15.93 0.00 0.00 3.27
487 713 5.670097 CATTTATGGACGCGAACTTATCTG 58.330 41.667 15.93 0.00 0.00 2.90
488 714 5.907197 CATTTATGGACGCGAACTTATCT 57.093 39.130 15.93 0.00 0.00 1.98
503 729 6.128172 GCAAGGTCCTCGAATATCCATTTATG 60.128 42.308 0.00 0.00 0.00 1.90
504 730 5.940470 GCAAGGTCCTCGAATATCCATTTAT 59.060 40.000 0.00 0.00 0.00 1.40
505 731 5.071788 AGCAAGGTCCTCGAATATCCATTTA 59.928 40.000 0.00 0.00 0.00 1.40
544 770 3.399305 GGTTGGGGATCCCTTCTGATTAT 59.601 47.826 30.08 0.00 45.70 1.28
545 771 2.783510 GGTTGGGGATCCCTTCTGATTA 59.216 50.000 30.08 4.39 45.70 1.75
546 772 1.570979 GGTTGGGGATCCCTTCTGATT 59.429 52.381 30.08 0.00 45.70 2.57
547 773 1.226311 GGTTGGGGATCCCTTCTGAT 58.774 55.000 30.08 0.00 45.70 2.90
548 774 1.271840 CGGTTGGGGATCCCTTCTGA 61.272 60.000 30.08 9.15 45.70 3.27
549 775 1.224592 CGGTTGGGGATCCCTTCTG 59.775 63.158 30.08 19.71 45.70 3.02
550 776 2.680370 GCGGTTGGGGATCCCTTCT 61.680 63.158 30.08 0.00 45.70 2.85
551 777 2.124278 GCGGTTGGGGATCCCTTC 60.124 66.667 30.08 18.90 45.70 3.46
552 778 2.087857 TTTGCGGTTGGGGATCCCTT 62.088 55.000 30.08 0.00 45.70 3.95
553 779 2.087857 TTTTGCGGTTGGGGATCCCT 62.088 55.000 30.08 0.00 45.70 4.20
554 780 1.188871 TTTTTGCGGTTGGGGATCCC 61.189 55.000 23.95 23.95 45.71 3.85
555 781 2.356992 TTTTTGCGGTTGGGGATCC 58.643 52.632 1.92 1.92 0.00 3.36
574 800 8.708378 GGGATCCCTTCTGATTTTTCATTTTAT 58.292 33.333 24.69 0.00 0.00 1.40
575 801 7.147915 CGGGATCCCTTCTGATTTTTCATTTTA 60.148 37.037 28.42 0.00 0.00 1.52
576 802 6.351286 CGGGATCCCTTCTGATTTTTCATTTT 60.351 38.462 28.42 0.00 0.00 1.82
577 803 5.127682 CGGGATCCCTTCTGATTTTTCATTT 59.872 40.000 28.42 0.00 0.00 2.32
578 804 4.646492 CGGGATCCCTTCTGATTTTTCATT 59.354 41.667 28.42 0.00 0.00 2.57
579 805 4.210331 CGGGATCCCTTCTGATTTTTCAT 58.790 43.478 28.42 0.00 0.00 2.57
580 806 3.620488 CGGGATCCCTTCTGATTTTTCA 58.380 45.455 28.42 0.00 0.00 2.69
581 807 2.359214 GCGGGATCCCTTCTGATTTTTC 59.641 50.000 28.42 0.00 0.00 2.29
584 810 0.918983 TGCGGGATCCCTTCTGATTT 59.081 50.000 28.42 0.00 0.00 2.17
683 914 1.599240 GCAAGGGAGATGCGGGATC 60.599 63.158 0.65 0.65 33.57 3.36
691 922 3.225235 GCCTCGAGCAAGGGAGAT 58.775 61.111 6.99 0.00 42.97 2.75
701 934 2.636412 TTGACCGGTCAGCCTCGAG 61.636 63.158 34.25 5.13 41.13 4.04
702 935 2.599281 TTGACCGGTCAGCCTCGA 60.599 61.111 34.25 18.28 41.13 4.04
703 936 2.432628 GTTGACCGGTCAGCCTCG 60.433 66.667 34.08 0.00 41.13 4.63
840 1092 3.318557 GGGTGGTTTCGTTTTTATGTGGA 59.681 43.478 0.00 0.00 0.00 4.02
984 1264 4.824166 CGAACGCGGATCGGACGT 62.824 66.667 23.47 13.87 43.86 4.34
1369 1649 4.373116 TCGAGCAGGCGGTGGAAC 62.373 66.667 0.00 0.00 0.00 3.62
1444 1724 3.823330 ACGGACGGCATCGACTCC 61.823 66.667 0.00 0.00 40.11 3.85
1696 1976 4.084888 GCGAACCTTCCAACGGCG 62.085 66.667 4.80 4.80 0.00 6.46
2054 4050 7.992008 TGAATTCTTAAAACGAGACAAAAGGT 58.008 30.769 7.05 0.00 0.00 3.50
2078 4075 1.068055 GTTTGCTCATGGCCAACTCTG 60.068 52.381 10.96 2.87 41.53 3.35
2150 4147 5.441718 AATTCACTGCTCTCCCATTCTTA 57.558 39.130 0.00 0.00 0.00 2.10
2161 4158 3.297134 TTCCCCCATAATTCACTGCTC 57.703 47.619 0.00 0.00 0.00 4.26
2415 4414 2.523015 ACTACAAGTAAATCGACGGCG 58.477 47.619 2.87 2.87 39.35 6.46
2484 4509 1.945394 CCAGCATGTAGAAGCACATCC 59.055 52.381 0.00 0.00 37.02 3.51
2485 4510 2.611292 GTCCAGCATGTAGAAGCACATC 59.389 50.000 0.00 0.00 37.02 3.06
2486 4511 2.238144 AGTCCAGCATGTAGAAGCACAT 59.762 45.455 0.00 0.00 39.76 3.21
2487 4512 1.625315 AGTCCAGCATGTAGAAGCACA 59.375 47.619 0.00 0.00 0.00 4.57
2488 4513 2.093764 AGAGTCCAGCATGTAGAAGCAC 60.094 50.000 0.00 0.00 0.00 4.40
2510 4539 8.830201 TTTAGCAGTGCAAATGAAAACATTAT 57.170 26.923 19.20 0.00 30.28 1.28
2540 4569 6.183360 ACCCTGTAATGGACTTCTTTTGTTTG 60.183 38.462 0.00 0.00 0.00 2.93
2571 4600 6.349300 ACATAATACTTGAATCGGTTGAGCT 58.651 36.000 0.00 0.00 0.00 4.09
2657 4686 8.917088 TCTTCATTGATCACTACACTCATATGA 58.083 33.333 5.07 5.07 0.00 2.15
2668 4697 7.706607 CGGTAGACATTTCTTCATTGATCACTA 59.293 37.037 0.00 0.00 32.75 2.74
2675 4704 9.314321 ACTAATACGGTAGACATTTCTTCATTG 57.686 33.333 0.00 0.00 32.75 2.82
2753 4782 9.201989 ACTCCACTTCAACATCTCTTATACATA 57.798 33.333 0.00 0.00 0.00 2.29
2788 4817 4.219288 AGAGAACTCCATTTGGATTTGCAC 59.781 41.667 6.90 0.07 44.46 4.57
2789 4818 4.219070 CAGAGAACTCCATTTGGATTTGCA 59.781 41.667 6.90 0.00 44.46 4.08
2927 4956 8.256611 ACTACAATGATGAACATACAGACAAC 57.743 34.615 0.00 0.00 38.38 3.32
2933 4962 7.899178 AACGAACTACAATGATGAACATACA 57.101 32.000 0.00 0.00 38.38 2.29
2934 4963 8.656849 AGAAACGAACTACAATGATGAACATAC 58.343 33.333 0.00 0.00 38.38 2.39


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

AutoCloner maintained by Alex Coulton.