Multiple sequence alignment - TraesCS5B01G052300

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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 TraesCS5B01G052300 chr5B 100.000 2652 0 0 318 2969 57495326 57492675 0.000000e+00 4898.0
1 TraesCS5B01G052300 chr5B 100.000 41 0 0 1 41 57495643 57495603 3.170000e-10 76.8
2 TraesCS5B01G052300 chr5A 94.126 1447 52 22 800 2233 43253799 43252373 0.000000e+00 2170.0
3 TraesCS5B01G052300 chr5A 94.638 1380 44 20 823 2189 42696540 42695178 0.000000e+00 2111.0
4 TraesCS5B01G052300 chr5A 93.179 733 34 5 2230 2962 42693461 42692745 0.000000e+00 1062.0
5 TraesCS5B01G052300 chr5A 94.145 649 27 6 2230 2878 43252257 43251620 0.000000e+00 977.0
6 TraesCS5B01G052300 chr5A 84.739 249 16 6 580 816 42696825 42696587 2.300000e-56 230.0
7 TraesCS5B01G052300 chr5D 94.224 1160 39 15 823 1972 54784723 54785864 0.000000e+00 1746.0
8 TraesCS5B01G052300 chr5D 84.697 379 34 7 2460 2818 54693678 54693304 1.010000e-94 357.0
9 TraesCS5B01G052300 chr5D 89.051 274 19 2 1682 1955 54720459 54720197 2.210000e-86 329.0
10 TraesCS5B01G052300 chr5D 90.749 227 14 4 2007 2233 54710070 54709851 2.240000e-76 296.0
11 TraesCS5B01G052300 chr5D 90.086 232 16 3 2230 2460 54708907 54708682 8.050000e-76 294.0
12 TraesCS5B01G052300 chr5D 93.519 108 5 2 710 816 54784570 54784676 3.060000e-35 159.0
13 TraesCS5B01G052300 chr5D 97.436 39 1 0 3 41 54783879 54783917 1.910000e-07 67.6
14 TraesCS5B01G052300 chr1A 86.515 482 46 15 2343 2819 536363849 536364316 2.040000e-141 512.0
15 TraesCS5B01G052300 chr1D 83.034 501 48 18 2343 2819 442153872 442153385 1.270000e-113 420.0
16 TraesCS5B01G052300 chr3B 82.152 409 50 6 2342 2729 258169503 258169909 2.210000e-86 329.0
17 TraesCS5B01G052300 chr2B 81.446 415 47 11 2380 2766 707600737 707600325 2.220000e-81 313.0
18 TraesCS5B01G052300 chr7D 76.800 500 77 17 2342 2818 611883943 611884426 8.220000e-61 244.0
19 TraesCS5B01G052300 chr7B 77.747 364 66 15 2461 2819 619133255 619132902 3.000000e-50 209.0
20 TraesCS5B01G052300 chr7B 83.482 224 32 5 2344 2566 619144809 619144590 1.400000e-48 204.0
21 TraesCS5B01G052300 chr4A 74.560 511 84 23 2342 2819 733667115 733666618 6.540000e-42 182.0
22 TraesCS5B01G052300 chr7A 97.619 42 1 0 2339 2380 648659176 648659217 4.110000e-09 73.1


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 TraesCS5B01G052300 chr5B 57492675 57495643 2968 True 2487.400000 4898 100.000000 1 2969 2 chr5B.!!$R1 2968
1 TraesCS5B01G052300 chr5A 43251620 43253799 2179 True 1573.500000 2170 94.135500 800 2878 2 chr5A.!!$R2 2078
2 TraesCS5B01G052300 chr5A 42692745 42696825 4080 True 1134.333333 2111 90.852000 580 2962 3 chr5A.!!$R1 2382
3 TraesCS5B01G052300 chr5D 54783879 54785864 1985 False 657.533333 1746 95.059667 3 1972 3 chr5D.!!$F1 1969
4 TraesCS5B01G052300 chr5D 54708682 54710070 1388 True 295.000000 296 90.417500 2007 2460 2 chr5D.!!$R3 453

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
529 530 0.105964 GTGTGTGTAGTGTGCCCTCA 59.894 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2316 0.249489 AACTCGCGGCCTAAGCATAG 60.249 55.0 6.13 0.0 42.56 2.23 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
343 344 3.806521 CAGTCTTCCGGAAATGCTCATAG 59.193 47.826 19.39 2.73 0.00 2.23
346 347 1.801242 TCCGGAAATGCTCATAGGGA 58.199 50.000 0.00 0.00 0.00 4.20
353 354 5.623368 CGGAAATGCTCATAGGGATAGAGTC 60.623 48.000 0.00 0.00 0.00 3.36
365 366 1.321743 GATAGAGTCTGCGTTTGTGCG 59.678 52.381 1.86 0.00 37.81 5.34
370 371 0.247894 GTCTGCGTTTGTGCGTTCAA 60.248 50.000 0.00 0.00 37.81 2.69
374 375 0.502275 GCGTTTGTGCGTTCAAATGG 59.498 50.000 19.74 12.45 41.68 3.16
388 389 6.620733 GCGTTCAAATGGGTGAGTATATATGC 60.621 42.308 0.00 0.00 0.00 3.14
394 395 5.006153 TGGGTGAGTATATATGCGTATGC 57.994 43.478 8.77 0.00 43.20 3.14
407 408 3.651771 GCGTATGCATAAGCGTCTGCG 62.652 57.143 25.24 14.93 46.23 5.18
418 419 2.696076 GCGTCTGCGTATGTACTTTG 57.304 50.000 0.00 0.00 40.81 2.77
425 426 6.522761 GTCTGCGTATGTACTTTGTTACAAG 58.477 40.000 0.00 0.00 0.00 3.16
429 430 7.346695 TGCGTATGTACTTTGTTACAAGAAAC 58.653 34.615 0.00 0.00 0.00 2.78
440 441 5.221880 TGTTACAAGAAACTACGCACGTAT 58.778 37.500 3.01 0.00 0.00 3.06
456 457 4.432503 GCACGTATGAAACAGAAGTACACG 60.433 45.833 0.00 0.00 0.00 4.49
468 469 3.874543 AGAAGTACACGCACAAAACATGA 59.125 39.130 0.00 0.00 0.00 3.07
497 498 3.906475 CGCAATGTGTGTGTGTGC 58.094 55.556 0.00 0.00 32.74 4.57
500 501 1.201722 GCAATGTGTGTGTGTGCGTG 61.202 55.000 0.00 0.00 0.00 5.34
501 502 1.063972 AATGTGTGTGTGTGCGTGC 59.936 52.632 0.00 0.00 0.00 5.34
502 503 2.645281 AATGTGTGTGTGTGCGTGCG 62.645 55.000 0.00 0.00 0.00 5.34
504 505 3.858989 TGTGTGTGTGCGTGCGTG 61.859 61.111 0.00 0.00 0.00 5.34
519 520 2.544359 GTGCGTGCGTGTGTGTAG 59.456 61.111 0.00 0.00 0.00 2.74
524 525 1.275657 GTGCGTGTGTGTAGTGTGC 59.724 57.895 0.00 0.00 0.00 4.57
525 526 1.885388 TGCGTGTGTGTAGTGTGCC 60.885 57.895 0.00 0.00 0.00 5.01
526 527 2.604174 GCGTGTGTGTAGTGTGCCC 61.604 63.158 0.00 0.00 0.00 5.36
527 528 1.069090 CGTGTGTGTAGTGTGCCCT 59.931 57.895 0.00 0.00 0.00 5.19
528 529 0.944311 CGTGTGTGTAGTGTGCCCTC 60.944 60.000 0.00 0.00 0.00 4.30
529 530 0.105964 GTGTGTGTAGTGTGCCCTCA 59.894 55.000 0.00 0.00 0.00 3.86
530 531 0.833949 TGTGTGTAGTGTGCCCTCAA 59.166 50.000 0.00 0.00 0.00 3.02
531 532 1.210722 TGTGTGTAGTGTGCCCTCAAA 59.789 47.619 0.00 0.00 0.00 2.69
532 533 2.158682 TGTGTGTAGTGTGCCCTCAAAT 60.159 45.455 0.00 0.00 0.00 2.32
534 535 3.317993 GTGTGTAGTGTGCCCTCAAATTT 59.682 43.478 0.00 0.00 0.00 1.82
535 536 3.317711 TGTGTAGTGTGCCCTCAAATTTG 59.682 43.478 12.15 12.15 0.00 2.32
536 537 3.317993 GTGTAGTGTGCCCTCAAATTTGT 59.682 43.478 17.47 0.00 0.00 2.83
537 538 4.517453 GTGTAGTGTGCCCTCAAATTTGTA 59.483 41.667 17.47 4.40 0.00 2.41
538 539 5.183140 GTGTAGTGTGCCCTCAAATTTGTAT 59.817 40.000 17.47 0.00 0.00 2.29
542 543 9.284968 GTAGTGTGCCCTCAAATTTGTATATAT 57.715 33.333 17.47 0.00 0.00 0.86
543 544 8.396272 AGTGTGCCCTCAAATTTGTATATATC 57.604 34.615 17.47 5.75 0.00 1.63
545 546 7.230510 GTGTGCCCTCAAATTTGTATATATCCA 59.769 37.037 17.47 4.55 0.00 3.41
546 547 7.949565 TGTGCCCTCAAATTTGTATATATCCAT 59.050 33.333 17.47 0.00 0.00 3.41
548 549 8.805175 TGCCCTCAAATTTGTATATATCCATTG 58.195 33.333 17.47 0.00 0.00 2.82
550 551 8.805175 CCCTCAAATTTGTATATATCCATTGCA 58.195 33.333 17.47 0.00 0.00 4.08
560 561 9.869757 TGTATATATCCATTGCATAGTGTACAC 57.130 33.333 18.56 18.56 0.00 2.90
561 562 9.869757 GTATATATCCATTGCATAGTGTACACA 57.130 33.333 27.06 13.77 0.00 3.72
567 568 9.964354 ATCCATTGCATAGTGTACACATTATAT 57.036 29.630 27.06 13.28 29.30 0.86
568 569 9.791801 TCCATTGCATAGTGTACACATTATATT 57.208 29.630 27.06 7.78 29.30 1.28
572 573 9.620259 TTGCATAGTGTACACATTATATTTGGA 57.380 29.630 27.06 9.50 29.30 3.53
573 574 9.620259 TGCATAGTGTACACATTATATTTGGAA 57.380 29.630 27.06 0.00 29.30 3.53
578 579 9.801873 AGTGTACACATTATATTTGGAAATTGC 57.198 29.630 27.06 0.00 0.00 3.56
605 606 1.447838 CATGTCTCGGTTCGGGTGG 60.448 63.158 0.00 0.00 0.00 4.61
724 976 0.248565 CACTAGGAGCTTGCAGCAGA 59.751 55.000 10.16 0.00 45.56 4.26
729 981 0.733729 GGAGCTTGCAGCAGATTGAG 59.266 55.000 10.16 0.00 45.56 3.02
816 1078 4.586235 AACAGGGCGCCACTGCTT 62.586 61.111 32.22 24.46 39.55 3.91
898 1200 1.225704 CCACTCCATGCCTTCCTCC 59.774 63.158 0.00 0.00 0.00 4.30
924 1226 1.403679 CCGTGCAAGAAACAGACCAAA 59.596 47.619 0.00 0.00 0.00 3.28
925 1227 2.450160 CGTGCAAGAAACAGACCAAAC 58.550 47.619 0.00 0.00 0.00 2.93
926 1228 2.159448 CGTGCAAGAAACAGACCAAACA 60.159 45.455 0.00 0.00 0.00 2.83
927 1229 3.438360 GTGCAAGAAACAGACCAAACAG 58.562 45.455 0.00 0.00 0.00 3.16
928 1230 3.128589 GTGCAAGAAACAGACCAAACAGA 59.871 43.478 0.00 0.00 0.00 3.41
929 1231 3.128589 TGCAAGAAACAGACCAAACAGAC 59.871 43.478 0.00 0.00 0.00 3.51
930 1232 3.489229 GCAAGAAACAGACCAAACAGACC 60.489 47.826 0.00 0.00 0.00 3.85
931 1233 3.644966 AGAAACAGACCAAACAGACCA 57.355 42.857 0.00 0.00 0.00 4.02
932 1234 3.963129 AGAAACAGACCAAACAGACCAA 58.037 40.909 0.00 0.00 0.00 3.67
938 1240 0.678366 ACCAAACAGACCAACGCACA 60.678 50.000 0.00 0.00 0.00 4.57
950 1252 3.442273 ACCAACGCACAACCCATATAAAG 59.558 43.478 0.00 0.00 0.00 1.85
951 1253 3.442273 CCAACGCACAACCCATATAAAGT 59.558 43.478 0.00 0.00 0.00 2.66
956 1259 4.014847 CACAACCCATATAAAGTGCACG 57.985 45.455 12.01 0.00 0.00 5.34
983 1289 2.629050 TAGCTCCGCTGCATTCCGTC 62.629 60.000 0.00 0.00 40.10 4.79
1416 1731 4.383861 CAGGTCGAGCAGCTGGCA 62.384 66.667 17.12 0.00 45.53 4.92
1945 2260 4.812476 TGCTCGATCCCGCCAACG 62.812 66.667 0.00 0.00 39.67 4.10
1950 2265 2.582498 GATCCCGCCAACGACTCG 60.582 66.667 0.00 0.00 43.93 4.18
2001 2316 6.698329 ACAAACCAAGCCGTTTAATTAACTTC 59.302 34.615 0.00 0.00 34.21 3.01
2005 2320 7.758495 ACCAAGCCGTTTAATTAACTTCTATG 58.242 34.615 0.00 0.00 34.46 2.23
2071 2386 2.726832 GGTAGGCACCGATCTACATC 57.273 55.000 0.00 0.00 38.00 3.06
2201 4074 7.336931 AGCAACGGTGTGATTAGAATTAATCTT 59.663 33.333 0.66 0.00 43.62 2.40
2202 4075 7.968405 GCAACGGTGTGATTAGAATTAATCTTT 59.032 33.333 0.66 0.00 43.62 2.52
2204 4077 9.840427 AACGGTGTGATTAGAATTAATCTTTTG 57.160 29.630 8.31 0.13 43.62 2.44
2311 5132 5.791336 TGATGGATGTAGTGATACTGACC 57.209 43.478 0.00 0.00 0.00 4.02
2426 5247 0.963962 CACCTTTTGCTGCATCACCT 59.036 50.000 1.84 0.00 0.00 4.00
2599 5420 8.715191 TGCAAACATTTTTCTAAAACTGTGAT 57.285 26.923 10.69 3.05 39.76 3.06
2644 5466 3.809832 CGGCGAACATTTCTAGAATGGAT 59.190 43.478 5.89 0.00 32.14 3.41
2733 5555 8.744923 CGATCATTTTTCGAAATGCATGATTAA 58.255 29.630 25.99 12.54 39.39 1.40
2878 5700 1.283793 CAAAGCCCAGACGCACTTG 59.716 57.895 0.00 0.00 0.00 3.16
2914 5736 2.096614 CGTGTAACAAATCGAGCGGTTT 60.097 45.455 0.00 0.00 35.74 3.27
2915 5737 3.223157 GTGTAACAAATCGAGCGGTTTG 58.777 45.455 22.62 22.62 40.29 2.93
2916 5738 2.239201 GTAACAAATCGAGCGGTTTGC 58.761 47.619 23.75 8.32 46.98 3.68
2953 5775 1.812571 GCCCAATACCACAAGTGACTG 59.187 52.381 0.94 0.00 0.00 3.51
2962 5784 4.451900 ACCACAAGTGACTGGAGTAAAAG 58.548 43.478 0.94 0.00 0.00 2.27
2963 5785 4.163458 ACCACAAGTGACTGGAGTAAAAGA 59.837 41.667 0.94 0.00 0.00 2.52
2964 5786 5.123227 CCACAAGTGACTGGAGTAAAAGAA 58.877 41.667 0.94 0.00 0.00 2.52
2965 5787 5.588648 CCACAAGTGACTGGAGTAAAAGAAA 59.411 40.000 0.94 0.00 0.00 2.52
2966 5788 6.263168 CCACAAGTGACTGGAGTAAAAGAAAT 59.737 38.462 0.94 0.00 0.00 2.17
2967 5789 7.355778 CACAAGTGACTGGAGTAAAAGAAATC 58.644 38.462 0.00 0.00 0.00 2.17
2968 5790 6.486993 ACAAGTGACTGGAGTAAAAGAAATCC 59.513 38.462 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.256383 TGCTGCATTGCTTTGATTGTACT 59.744 39.130 10.49 0.00 0.00 2.73
1 2 3.577667 TGCTGCATTGCTTTGATTGTAC 58.422 40.909 10.49 0.00 0.00 2.90
317 318 1.373570 CATTTCCGGAAGACTGAGCC 58.626 55.000 17.97 0.00 0.00 4.70
318 319 0.729690 GCATTTCCGGAAGACTGAGC 59.270 55.000 17.97 12.05 0.00 4.26
319 320 2.275318 GAGCATTTCCGGAAGACTGAG 58.725 52.381 17.97 6.17 0.00 3.35
320 321 1.623311 TGAGCATTTCCGGAAGACTGA 59.377 47.619 17.97 7.57 0.00 3.41
321 322 2.099141 TGAGCATTTCCGGAAGACTG 57.901 50.000 17.97 16.41 0.00 3.51
322 323 3.181461 CCTATGAGCATTTCCGGAAGACT 60.181 47.826 17.97 15.46 0.00 3.24
323 324 3.134458 CCTATGAGCATTTCCGGAAGAC 58.866 50.000 17.97 10.79 0.00 3.01
324 325 2.104792 CCCTATGAGCATTTCCGGAAGA 59.895 50.000 17.97 9.16 0.00 2.87
325 326 2.104792 TCCCTATGAGCATTTCCGGAAG 59.895 50.000 17.97 8.09 0.00 3.46
326 327 2.123589 TCCCTATGAGCATTTCCGGAA 58.876 47.619 14.35 14.35 0.00 4.30
327 328 1.801242 TCCCTATGAGCATTTCCGGA 58.199 50.000 0.00 0.00 0.00 5.14
328 329 2.867109 ATCCCTATGAGCATTTCCGG 57.133 50.000 0.00 0.00 0.00 5.14
329 330 4.221703 ACTCTATCCCTATGAGCATTTCCG 59.778 45.833 0.00 0.00 0.00 4.30
330 331 5.483583 AGACTCTATCCCTATGAGCATTTCC 59.516 44.000 0.00 0.00 0.00 3.13
331 332 6.397272 CAGACTCTATCCCTATGAGCATTTC 58.603 44.000 0.00 0.00 0.00 2.17
343 344 2.271800 CACAAACGCAGACTCTATCCC 58.728 52.381 0.00 0.00 0.00 3.85
346 347 1.336887 ACGCACAAACGCAGACTCTAT 60.337 47.619 0.00 0.00 36.19 1.98
353 354 1.187704 CATTTGAACGCACAAACGCAG 59.812 47.619 9.21 0.00 41.49 5.18
365 366 6.426937 ACGCATATATACTCACCCATTTGAAC 59.573 38.462 0.00 0.00 0.00 3.18
370 371 6.049149 GCATACGCATATATACTCACCCATT 58.951 40.000 0.00 0.00 38.36 3.16
388 389 0.159554 CGCAGACGCTTATGCATACG 59.840 55.000 10.58 10.44 42.68 3.06
407 408 9.999883 CGTAGTTTCTTGTAACAAAGTACATAC 57.000 33.333 0.00 0.00 37.90 2.39
409 410 7.225145 TGCGTAGTTTCTTGTAACAAAGTACAT 59.775 33.333 0.00 0.00 37.90 2.29
415 416 4.329528 ACGTGCGTAGTTTCTTGTAACAAA 59.670 37.500 0.00 0.00 0.00 2.83
418 419 5.343058 TCATACGTGCGTAGTTTCTTGTAAC 59.657 40.000 10.23 0.00 33.77 2.50
425 426 4.383649 TCTGTTTCATACGTGCGTAGTTTC 59.616 41.667 10.23 1.63 33.77 2.78
429 430 3.918591 ACTTCTGTTTCATACGTGCGTAG 59.081 43.478 10.23 3.47 33.77 3.51
440 441 2.894902 TGTGCGTGTACTTCTGTTTCA 58.105 42.857 0.00 0.00 0.00 2.69
456 457 4.983538 TGTGTCATTGATCATGTTTTGTGC 59.016 37.500 0.00 0.00 34.06 4.57
501 502 3.263171 CTACACACACGCACGCACG 62.263 63.158 0.00 0.00 39.50 5.34
502 503 2.235016 ACTACACACACGCACGCAC 61.235 57.895 0.00 0.00 0.00 5.34
504 505 2.235016 ACACTACACACACGCACGC 61.235 57.895 0.00 0.00 0.00 5.34
506 507 1.275657 GCACACTACACACACGCAC 59.724 57.895 0.00 0.00 0.00 5.34
510 511 0.105964 TGAGGGCACACTACACACAC 59.894 55.000 0.00 0.00 0.00 3.82
512 513 1.961793 TTTGAGGGCACACTACACAC 58.038 50.000 0.00 0.00 0.00 3.82
513 514 2.949177 ATTTGAGGGCACACTACACA 57.051 45.000 0.00 0.00 0.00 3.72
516 517 5.897377 ATACAAATTTGAGGGCACACTAC 57.103 39.130 24.64 0.00 0.00 2.73
517 518 9.502091 GATATATACAAATTTGAGGGCACACTA 57.498 33.333 24.64 3.70 0.00 2.74
519 520 7.230510 TGGATATATACAAATTTGAGGGCACAC 59.769 37.037 24.64 9.31 0.00 3.82
524 525 8.805175 TGCAATGGATATATACAAATTTGAGGG 58.195 33.333 24.64 0.00 0.00 4.30
534 535 9.869757 GTGTACACTATGCAATGGATATATACA 57.130 33.333 18.92 0.00 0.00 2.29
535 536 9.869757 TGTGTACACTATGCAATGGATATATAC 57.130 33.333 25.60 0.28 0.00 1.47
537 538 9.964354 AATGTGTACACTATGCAATGGATATAT 57.036 29.630 25.60 3.30 0.00 0.86
542 543 9.791801 AATATAATGTGTACACTATGCAATGGA 57.208 29.630 25.60 2.74 0.00 3.41
546 547 9.620259 TCCAAATATAATGTGTACACTATGCAA 57.380 29.630 25.60 5.74 0.00 4.08
552 553 9.801873 GCAATTTCCAAATATAATGTGTACACT 57.198 29.630 25.60 10.10 0.00 3.55
553 554 9.801873 AGCAATTTCCAAATATAATGTGTACAC 57.198 29.630 19.36 19.36 0.00 2.90
572 573 6.375455 ACCGAGACATGAGAAATAAGCAATTT 59.625 34.615 0.00 0.00 40.59 1.82
573 574 5.882557 ACCGAGACATGAGAAATAAGCAATT 59.117 36.000 0.00 0.00 0.00 2.32
574 575 5.431765 ACCGAGACATGAGAAATAAGCAAT 58.568 37.500 0.00 0.00 0.00 3.56
575 576 4.832248 ACCGAGACATGAGAAATAAGCAA 58.168 39.130 0.00 0.00 0.00 3.91
576 577 4.471904 ACCGAGACATGAGAAATAAGCA 57.528 40.909 0.00 0.00 0.00 3.91
577 578 4.026475 CGAACCGAGACATGAGAAATAAGC 60.026 45.833 0.00 0.00 0.00 3.09
578 579 4.504461 CCGAACCGAGACATGAGAAATAAG 59.496 45.833 0.00 0.00 0.00 1.73
605 606 1.312815 AAGTTCCAACACAGAGCAGC 58.687 50.000 0.00 0.00 0.00 5.25
724 976 3.777106 TGAACTCCAAGCTGTCTCAAT 57.223 42.857 0.00 0.00 0.00 2.57
729 981 1.338200 ACGGATGAACTCCAAGCTGTC 60.338 52.381 0.00 0.00 45.24 3.51
778 1040 5.435686 TTGGGATACAACAGCATAGAGTT 57.564 39.130 0.00 0.00 33.18 3.01
816 1078 1.382629 GGCAGGTTTAGGCCTTCCA 59.617 57.895 12.58 0.00 46.74 3.53
817 1079 4.338815 GGCAGGTTTAGGCCTTCC 57.661 61.111 12.58 12.06 46.74 3.46
898 1200 0.817634 TGTTTCTTGCACGGGTGGAG 60.818 55.000 0.43 0.00 31.08 3.86
924 1226 1.822186 GGGTTGTGCGTTGGTCTGT 60.822 57.895 0.00 0.00 0.00 3.41
925 1227 1.172180 ATGGGTTGTGCGTTGGTCTG 61.172 55.000 0.00 0.00 0.00 3.51
926 1228 0.398696 TATGGGTTGTGCGTTGGTCT 59.601 50.000 0.00 0.00 0.00 3.85
927 1229 1.459450 ATATGGGTTGTGCGTTGGTC 58.541 50.000 0.00 0.00 0.00 4.02
928 1230 2.791347 TATATGGGTTGTGCGTTGGT 57.209 45.000 0.00 0.00 0.00 3.67
929 1231 3.442273 ACTTTATATGGGTTGTGCGTTGG 59.558 43.478 0.00 0.00 0.00 3.77
930 1232 4.411327 CACTTTATATGGGTTGTGCGTTG 58.589 43.478 0.00 0.00 0.00 4.10
931 1233 3.119637 GCACTTTATATGGGTTGTGCGTT 60.120 43.478 0.00 0.00 40.67 4.84
932 1234 2.422127 GCACTTTATATGGGTTGTGCGT 59.578 45.455 0.00 0.00 40.67 5.24
938 1240 4.142469 GCTTTCGTGCACTTTATATGGGTT 60.142 41.667 16.19 0.00 0.00 4.11
1074 1380 3.449227 TACAGGGAGGACGCGCAG 61.449 66.667 5.73 2.42 0.00 5.18
1275 1590 2.262915 GTCTCCCACCACTGAGCG 59.737 66.667 0.00 0.00 0.00 5.03
1651 1966 4.049817 ACGGAGCGGAGTCTCCCT 62.050 66.667 13.54 11.03 44.18 4.20
1827 2142 2.504519 GGGTAGCCAGGGTAAGCG 59.495 66.667 5.96 0.00 0.00 4.68
2001 2316 0.249489 AACTCGCGGCCTAAGCATAG 60.249 55.000 6.13 0.00 42.56 2.23
2005 2320 0.582005 CATAAACTCGCGGCCTAAGC 59.418 55.000 6.13 0.00 38.76 3.09
2075 2390 1.371758 CAGCTGCTACACGTCACGT 60.372 57.895 0.00 0.00 42.36 4.49
2076 2391 2.720758 GCAGCTGCTACACGTCACG 61.721 63.158 31.33 0.00 38.21 4.35
2077 2392 2.720758 CGCAGCTGCTACACGTCAC 61.721 63.158 34.22 3.85 39.32 3.67
2078 2393 2.430751 CGCAGCTGCTACACGTCA 60.431 61.111 34.22 0.00 39.32 4.35
2079 2394 2.430921 ACGCAGCTGCTACACGTC 60.431 61.111 34.22 5.37 39.32 4.34
2153 2468 5.462729 GCTCTGCATCGATATCCATGAATAG 59.537 44.000 13.79 6.87 0.00 1.73
2157 2472 2.564062 TGCTCTGCATCGATATCCATGA 59.436 45.455 13.79 0.00 31.71 3.07
2168 2483 0.950555 TCACACCGTTGCTCTGCATC 60.951 55.000 0.00 0.00 38.76 3.91
2201 4074 5.701224 ACCTGATTACCCTTTGAAGTCAAA 58.299 37.500 6.33 6.33 42.90 2.69
2202 4075 5.073144 AGACCTGATTACCCTTTGAAGTCAA 59.927 40.000 0.00 0.00 0.00 3.18
2204 4077 5.167303 AGACCTGATTACCCTTTGAAGTC 57.833 43.478 0.00 0.00 0.00 3.01
2213 4086 9.852091 CGTAAATAAGTATAGACCTGATTACCC 57.148 37.037 0.00 0.00 0.00 3.69
2300 5121 2.991250 ACAATGCCAGGTCAGTATCAC 58.009 47.619 0.00 0.00 0.00 3.06
2389 5210 2.621998 GGTGATCATGGCCATTGAAGAG 59.378 50.000 17.92 3.44 0.00 2.85
2644 5466 8.187913 TCCACCAATTTACAAAATGATCTTCA 57.812 30.769 0.00 0.00 0.00 3.02
2770 5592 8.876275 AACTGTTCGTGACTTACAAAATACTA 57.124 30.769 0.00 0.00 0.00 1.82
2771 5593 7.781548 AACTGTTCGTGACTTACAAAATACT 57.218 32.000 0.00 0.00 0.00 2.12
2772 5594 8.831000 AAAACTGTTCGTGACTTACAAAATAC 57.169 30.769 0.00 0.00 0.00 1.89
2878 5700 0.738412 ACACGGGCTAATACACACGC 60.738 55.000 0.00 0.00 0.00 5.34
2923 5745 4.823419 TATTGGGCCGCCACGTCG 62.823 66.667 12.58 0.00 0.00 5.12
2924 5746 3.199891 GTATTGGGCCGCCACGTC 61.200 66.667 12.58 0.00 0.00 4.34
2925 5747 4.789123 GGTATTGGGCCGCCACGT 62.789 66.667 12.58 0.00 0.00 4.49
2926 5748 4.787286 TGGTATTGGGCCGCCACG 62.787 66.667 12.58 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.