Multiple sequence alignment - TraesCS1B01G228200

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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 TraesCS1B01G228200 chr1B 100.000 3590 0 0 1 3590 409633608 409630019 0.000000e+00 6630
1 TraesCS1B01G228200 chr1A 95.442 2940 111 13 661 3590 377432597 377429671 0.000000e+00 4665
2 TraesCS1B01G228200 chr1A 87.547 265 17 4 1 259 377444431 377444177 3.510000e-75 292
3 TraesCS1B01G228200 chr1A 89.706 136 5 2 261 396 377444142 377444016 7.970000e-37 165
4 TraesCS1B01G228200 chr1D 94.593 2959 111 19 661 3590 302822509 302819571 0.000000e+00 4532
5 TraesCS1B01G228200 chr1D 87.170 265 19 3 1 259 302823371 302823116 1.630000e-73 287
6 TraesCS1B01G228200 chr1D 86.957 138 7 3 261 396 302823081 302822953 1.040000e-30 145
7 TraesCS1B01G228200 chr3B 81.111 270 32 8 1 259 84737235 84736974 7.860000e-47 198
8 TraesCS1B01G228200 chr3A 80.515 272 32 9 1 259 65350662 65350399 4.730000e-44 189
9 TraesCS1B01G228200 chr3D 80.625 160 23 1 1 160 54386527 54386376 2.260000e-22 117


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 TraesCS1B01G228200 chr1B 409630019 409633608 3589 True 6630.000000 6630 100.000000 1 3590 1 chr1B.!!$R1 3589
1 TraesCS1B01G228200 chr1A 377429671 377432597 2926 True 4665.000000 4665 95.442000 661 3590 1 chr1A.!!$R1 2929
2 TraesCS1B01G228200 chr1D 302819571 302823371 3800 True 1654.666667 4532 89.573333 1 3590 3 chr1D.!!$R1 3589

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
422 464 0.103208 GCTGCTACTGTGCGGACTAT 59.897 55.0 8.99 0.0 41.56 2.12 F
778 1040 0.250081 TTGTTTCCAAATTGCGGCCC 60.250 50.0 0.00 0.0 0.00 5.80 F
1383 1652 0.321671 ACAGCGTGTACTCCTGCAAT 59.678 50.0 11.13 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1652 1.222387 GTACCCCGCTAACATGGCA 59.778 57.895 0.0 0.0 0.0 4.92 R
2422 2691 2.849294 TCACATGAACGGGATGAACA 57.151 45.000 0.0 0.0 0.0 3.18 R
2842 3116 4.019321 TCCCTCTTCCTTCAATTACACCAG 60.019 45.833 0.0 0.0 0.0 4.00 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
24 25 6.924111 TCTAATGCTTTTCCACTCCATTTTC 58.076 36.000 0.00 0.00 0.00 2.29
94 95 2.810870 TGTTAGGTTGGGTGTGTGTT 57.189 45.000 0.00 0.00 0.00 3.32
95 96 2.370349 TGTTAGGTTGGGTGTGTGTTG 58.630 47.619 0.00 0.00 0.00 3.33
96 97 1.679153 GTTAGGTTGGGTGTGTGTTGG 59.321 52.381 0.00 0.00 0.00 3.77
97 98 0.920438 TAGGTTGGGTGTGTGTTGGT 59.080 50.000 0.00 0.00 0.00 3.67
98 99 0.682855 AGGTTGGGTGTGTGTTGGTG 60.683 55.000 0.00 0.00 0.00 4.17
99 100 0.968393 GGTTGGGTGTGTGTTGGTGT 60.968 55.000 0.00 0.00 0.00 4.16
100 101 0.172352 GTTGGGTGTGTGTTGGTGTG 59.828 55.000 0.00 0.00 0.00 3.82
101 102 0.251386 TTGGGTGTGTGTTGGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
108 109 3.032459 TGTGTGTTGGTGTGTCCTACTA 58.968 45.455 0.00 0.00 41.34 1.82
109 110 3.644265 TGTGTGTTGGTGTGTCCTACTAT 59.356 43.478 0.00 0.00 41.34 2.12
111 112 4.021368 GTGTGTTGGTGTGTCCTACTATCT 60.021 45.833 0.00 0.00 41.34 1.98
119 120 3.301274 GTGTCCTACTATCTGGAGCCTT 58.699 50.000 0.00 0.00 32.36 4.35
120 121 4.079385 TGTGTCCTACTATCTGGAGCCTTA 60.079 45.833 0.00 0.00 32.36 2.69
121 122 5.081032 GTGTCCTACTATCTGGAGCCTTAT 58.919 45.833 0.00 0.00 32.36 1.73
122 123 5.540719 GTGTCCTACTATCTGGAGCCTTATT 59.459 44.000 0.00 0.00 32.36 1.40
133 134 4.562767 TGGAGCCTTATTACCCAGACATA 58.437 43.478 0.00 0.00 0.00 2.29
135 136 5.610982 TGGAGCCTTATTACCCAGACATATT 59.389 40.000 0.00 0.00 0.00 1.28
140 141 6.431234 GCCTTATTACCCAGACATATTGAAGG 59.569 42.308 0.00 0.00 33.28 3.46
143 144 3.959495 ACCCAGACATATTGAAGGCAT 57.041 42.857 0.00 0.00 0.00 4.40
194 195 2.707849 GCATGAAGGTGGCTGCAGG 61.708 63.158 17.12 0.00 34.77 4.85
248 255 5.258051 AGCTGGAATTATTTTACGGAACCA 58.742 37.500 0.00 0.00 0.00 3.67
259 266 5.365403 TTTACGGAACCATTTAGCTTGTG 57.635 39.130 0.00 0.00 0.00 3.33
269 309 4.322198 CCATTTAGCTTGTGGCAATGTTCT 60.322 41.667 0.00 0.00 44.79 3.01
274 314 2.351157 GCTTGTGGCAATGTTCTGTCTC 60.351 50.000 0.00 0.00 41.35 3.36
275 315 1.511850 TGTGGCAATGTTCTGTCTCG 58.488 50.000 0.00 0.00 0.00 4.04
276 316 1.202639 TGTGGCAATGTTCTGTCTCGT 60.203 47.619 0.00 0.00 0.00 4.18
349 391 2.357637 TGTGCTGCAACTTAAAGTGGTC 59.642 45.455 2.77 0.00 0.00 4.02
359 401 3.883489 ACTTAAAGTGGTCTGGTGAAAGC 59.117 43.478 0.00 0.00 0.00 3.51
366 408 0.884704 GTCTGGTGAAAGCGCCTTGA 60.885 55.000 2.29 0.00 45.15 3.02
372 414 1.541588 GTGAAAGCGCCTTGAGGAAAT 59.458 47.619 2.29 0.00 37.39 2.17
373 415 2.747446 GTGAAAGCGCCTTGAGGAAATA 59.253 45.455 2.29 0.00 37.39 1.40
374 416 2.747446 TGAAAGCGCCTTGAGGAAATAC 59.253 45.455 2.29 0.00 37.39 1.89
375 417 2.789409 AAGCGCCTTGAGGAAATACT 57.211 45.000 2.29 0.00 37.39 2.12
376 418 2.029838 AGCGCCTTGAGGAAATACTG 57.970 50.000 2.29 0.00 37.39 2.74
416 458 3.075998 CGAAGCTGCTACTGTGCG 58.924 61.111 0.90 0.00 35.36 5.34
417 459 2.447887 CGAAGCTGCTACTGTGCGG 61.448 63.158 0.90 6.67 41.91 5.69
418 460 1.079819 GAAGCTGCTACTGTGCGGA 60.080 57.895 0.90 0.00 41.56 5.54
419 461 1.355066 GAAGCTGCTACTGTGCGGAC 61.355 60.000 0.90 0.00 41.56 4.79
420 462 1.821061 AAGCTGCTACTGTGCGGACT 61.821 55.000 8.99 8.00 41.56 3.85
421 463 0.965866 AGCTGCTACTGTGCGGACTA 60.966 55.000 8.99 0.00 41.56 2.59
422 464 0.103208 GCTGCTACTGTGCGGACTAT 59.897 55.000 8.99 0.00 41.56 2.12
423 465 1.471676 GCTGCTACTGTGCGGACTATT 60.472 52.381 8.99 0.00 41.56 1.73
424 466 2.223735 GCTGCTACTGTGCGGACTATTA 60.224 50.000 8.99 0.00 41.56 0.98
425 467 3.553096 GCTGCTACTGTGCGGACTATTAT 60.553 47.826 8.99 0.00 41.56 1.28
426 468 3.977427 TGCTACTGTGCGGACTATTATG 58.023 45.455 8.99 0.00 35.36 1.90
427 469 3.634910 TGCTACTGTGCGGACTATTATGA 59.365 43.478 8.99 0.00 35.36 2.15
428 470 3.982058 GCTACTGTGCGGACTATTATGAC 59.018 47.826 8.99 0.00 0.00 3.06
429 471 3.454371 ACTGTGCGGACTATTATGACC 57.546 47.619 8.99 0.00 0.00 4.02
430 472 3.031736 ACTGTGCGGACTATTATGACCT 58.968 45.455 8.99 0.00 0.00 3.85
440 482 5.929415 GGACTATTATGACCTAGCTTTGCTC 59.071 44.000 0.00 0.00 40.44 4.26
441 483 5.533482 ACTATTATGACCTAGCTTTGCTCG 58.467 41.667 0.00 0.00 40.44 5.03
460 502 2.610374 TCGTTTGACCCTTTTGTTCTCG 59.390 45.455 0.00 0.00 0.00 4.04
464 506 3.007473 TGACCCTTTTGTTCTCGGTTT 57.993 42.857 0.00 0.00 0.00 3.27
473 515 7.255346 CCCTTTTGTTCTCGGTTTTATGTAACT 60.255 37.037 0.00 0.00 0.00 2.24
474 516 8.776470 CCTTTTGTTCTCGGTTTTATGTAACTA 58.224 33.333 0.00 0.00 0.00 2.24
495 537 5.604231 ACTATATCAGTCCTGGAGATTGCAA 59.396 40.000 0.00 0.00 32.40 4.08
499 541 3.582647 TCAGTCCTGGAGATTGCAAGTTA 59.417 43.478 4.94 0.00 32.40 2.24
500 542 4.225942 TCAGTCCTGGAGATTGCAAGTTAT 59.774 41.667 4.94 0.00 32.40 1.89
501 543 4.574013 CAGTCCTGGAGATTGCAAGTTATC 59.426 45.833 4.94 0.00 0.00 1.75
504 546 5.415701 GTCCTGGAGATTGCAAGTTATCAAA 59.584 40.000 4.94 0.00 0.00 2.69
505 547 5.415701 TCCTGGAGATTGCAAGTTATCAAAC 59.584 40.000 4.94 0.00 35.72 2.93
506 548 5.393461 CCTGGAGATTGCAAGTTATCAAACC 60.393 44.000 4.94 3.94 36.15 3.27
512 554 9.691362 GAGATTGCAAGTTATCAAACCTTTTTA 57.309 29.630 4.94 0.00 36.15 1.52
547 746 8.729805 ATTTCTTTCAAACTTGTAAATGCCAA 57.270 26.923 0.00 0.00 0.00 4.52
548 747 8.553459 TTTCTTTCAAACTTGTAAATGCCAAA 57.447 26.923 0.00 0.00 0.00 3.28
549 748 8.729805 TTCTTTCAAACTTGTAAATGCCAAAT 57.270 26.923 0.00 0.00 0.00 2.32
550 749 8.729805 TCTTTCAAACTTGTAAATGCCAAATT 57.270 26.923 0.00 0.00 0.00 1.82
551 750 9.823647 TCTTTCAAACTTGTAAATGCCAAATTA 57.176 25.926 0.00 0.00 0.00 1.40
552 751 9.862585 CTTTCAAACTTGTAAATGCCAAATTAC 57.137 29.630 0.00 0.00 33.59 1.89
553 752 7.630470 TCAAACTTGTAAATGCCAAATTACG 57.370 32.000 0.00 0.00 35.30 3.18
554 753 6.642950 TCAAACTTGTAAATGCCAAATTACGG 59.357 34.615 0.00 0.00 35.30 4.02
556 755 6.334102 ACTTGTAAATGCCAAATTACGGAA 57.666 33.333 0.00 0.00 35.30 4.30
558 757 6.811170 ACTTGTAAATGCCAAATTACGGAATG 59.189 34.615 0.00 0.00 35.30 2.67
559 758 6.274157 TGTAAATGCCAAATTACGGAATGT 57.726 33.333 0.00 0.00 35.30 2.71
566 778 4.142271 GCCAAATTACGGAATGTGAATGGA 60.142 41.667 12.46 0.00 32.62 3.41
590 802 4.590850 AATTGTGCTGGGTTTCTCTTTC 57.409 40.909 0.00 0.00 0.00 2.62
602 814 8.166422 TGGGTTTCTCTTTCATAAAGTTCTTC 57.834 34.615 0.00 0.00 39.52 2.87
604 816 7.230712 GGGTTTCTCTTTCATAAAGTTCTTCCA 59.769 37.037 0.00 0.00 39.52 3.53
611 831 9.277783 TCTTTCATAAAGTTCTTCCAAGAGAAG 57.722 33.333 0.00 0.00 44.48 2.85
622 842 1.889170 CCAAGAGAAGAAACCCTTGCC 59.111 52.381 0.00 0.00 35.83 4.52
623 843 1.537202 CAAGAGAAGAAACCCTTGCCG 59.463 52.381 0.00 0.00 34.68 5.69
624 844 0.606673 AGAGAAGAAACCCTTGCCGC 60.607 55.000 0.00 0.00 34.68 6.53
648 868 1.665735 CGGCCACCGTTTCAGAAAATG 60.666 52.381 2.24 0.00 42.73 2.32
650 870 2.223947 GGCCACCGTTTCAGAAAATGTT 60.224 45.455 0.00 0.00 30.71 2.71
653 873 4.429108 CCACCGTTTCAGAAAATGTTGTT 58.571 39.130 0.00 0.00 30.71 2.83
671 933 8.718102 ATGTTGTTCTGTGGTATACTGATAAC 57.282 34.615 2.25 2.96 37.15 1.89
695 957 1.027357 CAACACTCAACTGGCAGCTT 58.973 50.000 15.89 5.45 0.00 3.74
712 974 2.620585 AGCTTGGTGAAAGAGAAACTGC 59.379 45.455 0.00 0.00 38.24 4.40
745 1007 1.262950 TGGAACGCAAATCAACACTCG 59.737 47.619 0.00 0.00 0.00 4.18
778 1040 0.250081 TTGTTTCCAAATTGCGGCCC 60.250 50.000 0.00 0.00 0.00 5.80
794 1059 1.547372 GGCCCTGTGTTTCGTAGAGTA 59.453 52.381 0.00 0.00 38.43 2.59
806 1071 1.859703 CGTAGAGTAGATGCTCGTCGT 59.140 52.381 0.00 0.00 40.26 4.34
830 1095 3.433615 CCTGGTCACATTTTTCTCTCGTC 59.566 47.826 0.00 0.00 0.00 4.20
858 1124 4.864334 GGATGGTGGCCTGCGGAG 62.864 72.222 3.32 0.00 0.00 4.63
1383 1652 0.321671 ACAGCGTGTACTCCTGCAAT 59.678 50.000 11.13 0.00 0.00 3.56
1422 1691 3.073735 CACCTCTCCCTCGCAGCT 61.074 66.667 0.00 0.00 0.00 4.24
1443 1712 3.929948 GCGGCGGAGATCTTTGCG 61.930 66.667 9.78 3.20 34.82 4.85
1488 1757 5.011533 CACCTCCTATAACTCTGCTATGCTT 59.988 44.000 0.00 0.00 0.00 3.91
1625 1894 1.910722 CTGGTCTCATGGACAGGGG 59.089 63.158 13.95 0.00 46.16 4.79
1632 1901 2.943265 ATGGACAGGGGCCTTGCT 60.943 61.111 16.58 2.83 0.00 3.91
1653 1922 2.811307 GCAGCTCCATGCCCATTTA 58.189 52.632 0.00 0.00 44.23 1.40
2043 2312 2.965671 ATGGTAAGCAGATCCATGGG 57.034 50.000 13.02 0.00 40.00 4.00
2179 2448 1.044611 GGAGAGGAGGGATACTGTGC 58.955 60.000 0.00 0.00 0.00 4.57
2320 2589 1.005294 GACAGCTTGTTGCCATTGCG 61.005 55.000 0.00 0.00 44.23 4.85
2349 2618 6.395629 AGTTGATGAAGGCATGAATTTCTTG 58.604 36.000 0.00 7.70 34.11 3.02
2352 2621 5.126545 TGATGAAGGCATGAATTTCTTGGAG 59.873 40.000 12.61 0.00 34.11 3.86
2360 2629 6.034591 GCATGAATTTCTTGGAGTTGATGAG 58.965 40.000 12.61 0.00 0.00 2.90
2422 2691 2.224843 TGTGTGGTGGATTTGATCAGCT 60.225 45.455 0.00 0.00 33.13 4.24
2829 3103 2.439156 GGACCTGCAGACATGGGC 60.439 66.667 17.39 0.00 0.00 5.36
2948 3224 5.801947 GCGATTTCACAAATATTGTCAAGCT 59.198 36.000 0.00 0.00 43.23 3.74
3027 3303 4.966366 GCTCAGCATTACTATTTTTCTGCG 59.034 41.667 0.00 0.00 34.89 5.18
3028 3304 4.908736 TCAGCATTACTATTTTTCTGCGC 58.091 39.130 0.00 0.00 34.89 6.09
3029 3305 4.635765 TCAGCATTACTATTTTTCTGCGCT 59.364 37.500 9.73 0.00 34.89 5.92
3030 3306 5.815222 TCAGCATTACTATTTTTCTGCGCTA 59.185 36.000 9.73 0.00 34.89 4.26
3032 3308 5.584649 AGCATTACTATTTTTCTGCGCTACA 59.415 36.000 9.73 0.00 34.89 2.74
3034 3310 6.912591 GCATTACTATTTTTCTGCGCTACATT 59.087 34.615 9.73 0.00 0.00 2.71
3035 3311 7.112148 GCATTACTATTTTTCTGCGCTACATTC 59.888 37.037 9.73 0.00 0.00 2.67
3036 3312 7.603963 TTACTATTTTTCTGCGCTACATTCA 57.396 32.000 9.73 0.00 0.00 2.57
3100 3395 3.213206 TCTGCATCTGTGTCCAGTTTT 57.787 42.857 0.00 0.00 39.82 2.43
3191 3486 1.632920 TGTCCACAGGATTACATGGCA 59.367 47.619 0.00 0.00 32.73 4.92
3280 3575 9.979578 AATCATGTATGTTGTTTGTGTACAAAT 57.020 25.926 12.72 0.55 46.12 2.32
3330 3626 6.598850 ACATGGATGTTGTTTTTCTTTTGCTT 59.401 30.769 0.00 0.00 37.90 3.91
3359 3655 7.019418 CAGGTGATACATTCATTTCATATGCG 58.981 38.462 0.00 0.00 36.54 4.73
3469 3765 3.523606 ACAAACATGTTTCTGCTGCAA 57.476 38.095 20.85 0.00 0.00 4.08
3472 3768 4.877251 ACAAACATGTTTCTGCTGCAAAAT 59.123 33.333 20.85 0.00 0.00 1.82
3491 3787 2.702898 TGCCATCATGTTCAACAACG 57.297 45.000 0.00 0.00 34.95 4.10
3492 3788 1.952990 TGCCATCATGTTCAACAACGT 59.047 42.857 0.00 0.00 34.95 3.99
3493 3789 3.142174 TGCCATCATGTTCAACAACGTA 58.858 40.909 0.00 0.00 34.95 3.57
3494 3790 3.058570 TGCCATCATGTTCAACAACGTAC 60.059 43.478 0.00 0.00 34.95 3.67
3495 3791 3.058570 GCCATCATGTTCAACAACGTACA 60.059 43.478 0.00 0.00 34.95 2.90
3496 3792 4.379394 GCCATCATGTTCAACAACGTACAT 60.379 41.667 0.00 0.00 34.95 2.29
3497 3793 5.088068 CCATCATGTTCAACAACGTACATG 58.912 41.667 17.02 17.02 45.69 3.21
3557 3853 7.567622 TCCCTAGAAAAGCCTAACTATGTATGT 59.432 37.037 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.815856 TGCACTGCAAAATGAGGAAAA 57.184 38.095 0.00 0.00 34.76 2.29
21 22 3.815856 TTGCACTGCAAAATGAGGAAA 57.184 38.095 14.21 0.00 45.96 3.13
65 66 5.838521 ACACCCAACCTAACAAATTTCATCT 59.161 36.000 0.00 0.00 0.00 2.90
80 81 0.968393 ACACCAACACACACCCAACC 60.968 55.000 0.00 0.00 0.00 3.77
94 95 3.632333 CTCCAGATAGTAGGACACACCA 58.368 50.000 0.00 0.00 42.04 4.17
95 96 2.362717 GCTCCAGATAGTAGGACACACC 59.637 54.545 0.00 0.00 39.35 4.16
96 97 2.362717 GGCTCCAGATAGTAGGACACAC 59.637 54.545 0.00 0.00 0.00 3.82
97 98 2.245028 AGGCTCCAGATAGTAGGACACA 59.755 50.000 0.00 0.00 0.00 3.72
98 99 2.952116 AGGCTCCAGATAGTAGGACAC 58.048 52.381 0.00 0.00 0.00 3.67
99 100 3.689872 AAGGCTCCAGATAGTAGGACA 57.310 47.619 0.00 0.00 0.00 4.02
100 101 6.153170 GGTAATAAGGCTCCAGATAGTAGGAC 59.847 46.154 0.00 0.00 0.00 3.85
101 102 6.254522 GGTAATAAGGCTCCAGATAGTAGGA 58.745 44.000 0.00 0.00 0.00 2.94
108 109 3.941629 TCTGGGTAATAAGGCTCCAGAT 58.058 45.455 14.46 0.00 46.13 2.90
111 112 2.840511 TGTCTGGGTAATAAGGCTCCA 58.159 47.619 0.00 0.00 0.00 3.86
119 120 6.508030 TGCCTTCAATATGTCTGGGTAATA 57.492 37.500 0.00 0.00 0.00 0.98
120 121 5.387113 TGCCTTCAATATGTCTGGGTAAT 57.613 39.130 0.00 0.00 0.00 1.89
121 122 4.853468 TGCCTTCAATATGTCTGGGTAA 57.147 40.909 0.00 0.00 0.00 2.85
122 123 5.132502 CAATGCCTTCAATATGTCTGGGTA 58.867 41.667 0.00 0.00 0.00 3.69
133 134 9.193806 AGTAGATCAAAATACAATGCCTTCAAT 57.806 29.630 0.00 0.00 0.00 2.57
135 136 8.579850 AAGTAGATCAAAATACAATGCCTTCA 57.420 30.769 0.00 0.00 0.00 3.02
194 195 8.791429 TTTGTCAGCAATTGGGAAACCTGAAC 62.791 42.308 7.72 6.03 42.47 3.18
222 229 5.243426 TCCGTAAAATAATTCCAGCTTGC 57.757 39.130 0.00 0.00 0.00 4.01
236 243 5.278561 CCACAAGCTAAATGGTTCCGTAAAA 60.279 40.000 3.20 0.00 33.63 1.52
242 249 1.892474 TGCCACAAGCTAAATGGTTCC 59.108 47.619 11.36 0.00 44.23 3.62
248 255 4.281688 ACAGAACATTGCCACAAGCTAAAT 59.718 37.500 0.00 0.00 44.23 1.40
259 266 1.873591 ACAACGAGACAGAACATTGCC 59.126 47.619 0.00 0.00 0.00 4.52
269 309 4.038763 AGACTTTGACCATACAACGAGACA 59.961 41.667 0.00 0.00 0.00 3.41
274 314 8.504005 AGAAATAAAGACTTTGACCATACAACG 58.496 33.333 10.80 0.00 0.00 4.10
275 315 9.612620 CAGAAATAAAGACTTTGACCATACAAC 57.387 33.333 10.80 0.00 0.00 3.32
276 316 8.792633 CCAGAAATAAAGACTTTGACCATACAA 58.207 33.333 10.80 0.00 0.00 2.41
316 358 4.520111 AGTTGCAGCACATCAATAGTTTGA 59.480 37.500 2.55 0.00 45.57 2.69
317 359 4.801891 AGTTGCAGCACATCAATAGTTTG 58.198 39.130 2.55 0.00 0.00 2.93
318 360 5.458041 AAGTTGCAGCACATCAATAGTTT 57.542 34.783 2.55 0.00 0.00 2.66
319 361 6.573664 TTAAGTTGCAGCACATCAATAGTT 57.426 33.333 2.55 0.00 0.00 2.24
329 371 2.618709 AGACCACTTTAAGTTGCAGCAC 59.381 45.455 2.55 0.00 0.00 4.40
349 391 1.580845 CCTCAAGGCGCTTTCACCAG 61.581 60.000 7.64 0.00 0.00 4.00
359 401 4.124851 ACTACAGTATTTCCTCAAGGCG 57.875 45.455 0.00 0.00 34.44 5.52
366 408 7.793948 ACTTCCAGTAACTACAGTATTTCCT 57.206 36.000 0.00 0.00 0.00 3.36
396 438 1.784062 CACAGTAGCAGCTTCGCAC 59.216 57.895 0.00 0.00 0.00 5.34
397 439 2.029288 GCACAGTAGCAGCTTCGCA 61.029 57.895 0.00 0.00 0.00 5.10
398 440 2.781300 GCACAGTAGCAGCTTCGC 59.219 61.111 0.00 0.00 0.00 4.70
399 441 2.447887 CCGCACAGTAGCAGCTTCG 61.448 63.158 0.00 0.00 0.00 3.79
400 442 1.079819 TCCGCACAGTAGCAGCTTC 60.080 57.895 0.00 0.00 0.00 3.86
401 443 1.374758 GTCCGCACAGTAGCAGCTT 60.375 57.895 0.00 0.00 0.00 3.74
402 444 0.965866 TAGTCCGCACAGTAGCAGCT 60.966 55.000 0.00 0.00 0.00 4.24
403 445 0.103208 ATAGTCCGCACAGTAGCAGC 59.897 55.000 0.00 0.00 0.00 5.25
404 446 2.586258 AATAGTCCGCACAGTAGCAG 57.414 50.000 0.00 0.00 0.00 4.24
405 447 3.634910 TCATAATAGTCCGCACAGTAGCA 59.365 43.478 0.00 0.00 0.00 3.49
406 448 3.982058 GTCATAATAGTCCGCACAGTAGC 59.018 47.826 0.00 0.00 0.00 3.58
407 449 4.278669 AGGTCATAATAGTCCGCACAGTAG 59.721 45.833 0.00 0.00 0.00 2.57
408 450 4.212716 AGGTCATAATAGTCCGCACAGTA 58.787 43.478 0.00 0.00 0.00 2.74
409 451 3.031736 AGGTCATAATAGTCCGCACAGT 58.968 45.455 0.00 0.00 0.00 3.55
410 452 3.735237 AGGTCATAATAGTCCGCACAG 57.265 47.619 0.00 0.00 0.00 3.66
411 453 3.005472 GCTAGGTCATAATAGTCCGCACA 59.995 47.826 0.00 0.00 0.00 4.57
412 454 3.256136 AGCTAGGTCATAATAGTCCGCAC 59.744 47.826 0.00 0.00 0.00 5.34
413 455 3.497332 AGCTAGGTCATAATAGTCCGCA 58.503 45.455 0.00 0.00 0.00 5.69
414 456 4.522722 AAGCTAGGTCATAATAGTCCGC 57.477 45.455 0.00 0.00 0.00 5.54
415 457 4.686554 GCAAAGCTAGGTCATAATAGTCCG 59.313 45.833 0.00 0.00 0.00 4.79
416 458 5.859495 AGCAAAGCTAGGTCATAATAGTCC 58.141 41.667 0.00 0.00 36.99 3.85
417 459 5.631512 CGAGCAAAGCTAGGTCATAATAGTC 59.368 44.000 15.75 0.00 39.88 2.59
418 460 5.069251 ACGAGCAAAGCTAGGTCATAATAGT 59.931 40.000 15.75 4.53 39.88 2.12
419 461 5.533482 ACGAGCAAAGCTAGGTCATAATAG 58.467 41.667 15.75 4.03 39.88 1.73
420 462 5.531122 ACGAGCAAAGCTAGGTCATAATA 57.469 39.130 15.75 0.00 39.88 0.98
421 463 4.408182 ACGAGCAAAGCTAGGTCATAAT 57.592 40.909 15.75 0.00 39.88 1.28
422 464 3.887621 ACGAGCAAAGCTAGGTCATAA 57.112 42.857 15.75 0.00 39.88 1.90
423 465 3.887621 AACGAGCAAAGCTAGGTCATA 57.112 42.857 15.75 0.00 39.88 2.15
424 466 2.744202 CAAACGAGCAAAGCTAGGTCAT 59.256 45.455 15.75 0.89 39.88 3.06
425 467 2.143122 CAAACGAGCAAAGCTAGGTCA 58.857 47.619 15.75 0.00 39.88 4.02
426 468 2.157863 GTCAAACGAGCAAAGCTAGGTC 59.842 50.000 7.92 7.92 39.88 3.85
427 469 2.143925 GTCAAACGAGCAAAGCTAGGT 58.856 47.619 4.25 0.00 39.88 3.08
428 470 1.464997 GGTCAAACGAGCAAAGCTAGG 59.535 52.381 4.25 0.00 39.88 3.02
429 471 1.464997 GGGTCAAACGAGCAAAGCTAG 59.535 52.381 0.00 0.00 39.88 3.42
430 472 1.071699 AGGGTCAAACGAGCAAAGCTA 59.928 47.619 0.00 0.00 39.88 3.32
440 482 2.286772 CCGAGAACAAAAGGGTCAAACG 60.287 50.000 0.00 0.00 0.00 3.60
441 483 2.686405 ACCGAGAACAAAAGGGTCAAAC 59.314 45.455 0.00 0.00 0.00 2.93
460 502 9.490379 CCAGGACTGATATAGTTACATAAAACC 57.510 37.037 0.00 0.00 40.53 3.27
473 515 5.604231 ACTTGCAATCTCCAGGACTGATATA 59.396 40.000 0.00 0.00 0.00 0.86
474 516 4.411540 ACTTGCAATCTCCAGGACTGATAT 59.588 41.667 0.00 0.00 0.00 1.63
531 730 6.750148 TCCGTAATTTGGCATTTACAAGTTT 58.250 32.000 16.39 0.00 31.53 2.66
533 732 5.968528 TCCGTAATTTGGCATTTACAAGT 57.031 34.783 16.39 0.00 0.00 3.16
534 733 6.811170 ACATTCCGTAATTTGGCATTTACAAG 59.189 34.615 16.39 9.80 0.00 3.16
538 737 6.516739 TCACATTCCGTAATTTGGCATTTA 57.483 33.333 0.00 0.00 0.00 1.40
539 738 5.398603 TCACATTCCGTAATTTGGCATTT 57.601 34.783 0.00 0.00 0.00 2.32
541 740 5.350633 CATTCACATTCCGTAATTTGGCAT 58.649 37.500 0.00 0.00 0.00 4.40
542 741 4.381398 CCATTCACATTCCGTAATTTGGCA 60.381 41.667 0.00 0.00 0.00 4.92
543 742 4.111916 CCATTCACATTCCGTAATTTGGC 58.888 43.478 0.00 0.00 0.00 4.52
544 743 5.105957 TGTCCATTCACATTCCGTAATTTGG 60.106 40.000 0.00 0.00 0.00 3.28
545 744 5.948588 TGTCCATTCACATTCCGTAATTTG 58.051 37.500 0.00 0.00 0.00 2.32
547 746 6.582677 TTTGTCCATTCACATTCCGTAATT 57.417 33.333 0.00 0.00 0.00 1.40
548 747 6.773976 ATTTGTCCATTCACATTCCGTAAT 57.226 33.333 0.00 0.00 0.00 1.89
549 748 6.015856 ACAATTTGTCCATTCACATTCCGTAA 60.016 34.615 0.00 0.00 0.00 3.18
550 749 5.475220 ACAATTTGTCCATTCACATTCCGTA 59.525 36.000 0.00 0.00 0.00 4.02
551 750 4.280677 ACAATTTGTCCATTCACATTCCGT 59.719 37.500 0.00 0.00 0.00 4.69
552 751 4.622313 CACAATTTGTCCATTCACATTCCG 59.378 41.667 0.00 0.00 0.00 4.30
553 752 4.389687 GCACAATTTGTCCATTCACATTCC 59.610 41.667 0.00 0.00 0.00 3.01
554 753 5.119588 CAGCACAATTTGTCCATTCACATTC 59.880 40.000 0.00 0.00 0.00 2.67
556 755 4.561938 CCAGCACAATTTGTCCATTCACAT 60.562 41.667 0.00 0.00 0.00 3.21
558 757 3.319755 CCAGCACAATTTGTCCATTCAC 58.680 45.455 0.00 0.00 0.00 3.18
559 758 2.299582 CCCAGCACAATTTGTCCATTCA 59.700 45.455 0.00 0.00 0.00 2.57
566 778 3.299503 AGAGAAACCCAGCACAATTTGT 58.700 40.909 0.00 0.00 0.00 2.83
602 814 1.889170 GGCAAGGGTTTCTTCTCTTGG 59.111 52.381 8.13 0.00 37.61 3.61
604 816 1.897560 CGGCAAGGGTTTCTTCTCTT 58.102 50.000 0.00 0.00 32.41 2.85
641 861 7.936847 TCAGTATACCACAGAACAACATTTTCT 59.063 33.333 0.00 0.00 33.38 2.52
642 862 8.094798 TCAGTATACCACAGAACAACATTTTC 57.905 34.615 0.00 0.00 0.00 2.29
648 868 7.277981 CCAGTTATCAGTATACCACAGAACAAC 59.722 40.741 0.00 3.16 0.00 3.32
650 870 6.439375 ACCAGTTATCAGTATACCACAGAACA 59.561 38.462 0.00 0.00 0.00 3.18
653 873 6.192044 TGACCAGTTATCAGTATACCACAGA 58.808 40.000 0.00 0.00 0.00 3.41
656 876 6.534079 GTGTTGACCAGTTATCAGTATACCAC 59.466 42.308 0.00 0.00 0.00 4.16
657 877 6.439375 AGTGTTGACCAGTTATCAGTATACCA 59.561 38.462 0.00 0.00 0.00 3.25
658 878 6.875076 AGTGTTGACCAGTTATCAGTATACC 58.125 40.000 0.00 0.00 0.00 2.73
659 879 7.544622 TGAGTGTTGACCAGTTATCAGTATAC 58.455 38.462 0.00 0.00 0.00 1.47
671 933 0.947244 GCCAGTTGAGTGTTGACCAG 59.053 55.000 0.00 0.00 0.00 4.00
695 957 3.558931 TGAGCAGTTTCTCTTTCACCA 57.441 42.857 0.00 0.00 34.29 4.17
712 974 5.739752 TTGCGTTCCATCTGAATTATGAG 57.260 39.130 0.00 0.00 34.90 2.90
745 1007 4.416620 TGGAAACAATTTGAACACACGAC 58.583 39.130 2.79 0.00 37.44 4.34
778 1040 4.987832 AGCATCTACTCTACGAAACACAG 58.012 43.478 0.00 0.00 0.00 3.66
794 1059 1.251527 ACCAGGAACGACGAGCATCT 61.252 55.000 0.00 0.00 0.00 2.90
806 1071 4.065088 CGAGAGAAAAATGTGACCAGGAA 58.935 43.478 0.00 0.00 0.00 3.36
858 1124 0.744874 TGGTCGATCCAGATCCGAAC 59.255 55.000 0.00 6.38 41.93 3.95
1383 1652 1.222387 GTACCCCGCTAACATGGCA 59.778 57.895 0.00 0.00 0.00 4.92
1443 1712 2.280119 TCGTGATGCGGCATAGCC 60.280 61.111 16.66 4.24 46.75 3.93
1455 1724 3.053842 AGTTATAGGAGGTGAGGTCGTGA 60.054 47.826 0.00 0.00 0.00 4.35
1457 1726 3.202595 AGAGTTATAGGAGGTGAGGTCGT 59.797 47.826 0.00 0.00 0.00 4.34
1466 1735 5.477510 CAAGCATAGCAGAGTTATAGGAGG 58.522 45.833 0.00 0.00 0.00 4.30
1653 1922 4.533707 TCAGACAAGAACCCAAGATGAGAT 59.466 41.667 0.00 0.00 0.00 2.75
2043 2312 5.587289 TCAAAACCAGTTTGTAGCAACATC 58.413 37.500 0.00 0.00 45.83 3.06
2179 2448 4.097437 AGCAGATAACATTGCATTCCACAG 59.903 41.667 0.00 0.00 42.67 3.66
2286 2555 6.340522 ACAAGCTGTCAAAACTAGCAAAAAT 58.659 32.000 0.00 0.00 39.84 1.82
2349 2618 5.016051 TGTATCTCTTGCTCATCAACTCC 57.984 43.478 0.00 0.00 0.00 3.85
2352 2621 5.016051 TCCTGTATCTCTTGCTCATCAAC 57.984 43.478 0.00 0.00 0.00 3.18
2360 2629 4.517285 TGGAACAATCCTGTATCTCTTGC 58.483 43.478 0.00 0.00 46.70 4.01
2422 2691 2.849294 TCACATGAACGGGATGAACA 57.151 45.000 0.00 0.00 0.00 3.18
2574 2843 6.006449 AGCACTCATTTATTTTGGACTGTCT 58.994 36.000 7.85 0.00 0.00 3.41
2829 3103 4.335647 ACCAGGCCCAGCAGAACG 62.336 66.667 0.00 0.00 0.00 3.95
2842 3116 4.019321 TCCCTCTTCCTTCAATTACACCAG 60.019 45.833 0.00 0.00 0.00 4.00
2948 3224 4.061596 TGTGACATGACAAAGCGATGTTA 58.938 39.130 0.00 0.00 32.57 2.41
3027 3303 7.078228 CCTACAAACTTTCAAGTGAATGTAGC 58.922 38.462 21.43 0.00 42.55 3.58
3028 3304 8.154649 ACCTACAAACTTTCAAGTGAATGTAG 57.845 34.615 20.68 20.68 42.94 2.74
3029 3305 9.048446 GTACCTACAAACTTTCAAGTGAATGTA 57.952 33.333 11.63 8.38 40.22 2.29
3030 3306 7.554835 TGTACCTACAAACTTTCAAGTGAATGT 59.445 33.333 6.73 6.73 42.05 2.71
3032 3308 8.514330 TTGTACCTACAAACTTTCAAGTGAAT 57.486 30.769 0.00 0.00 42.66 2.57
3100 3395 8.264347 TGCAAGGTATCTGTACATCATTTTCTA 58.736 33.333 0.00 0.00 32.25 2.10
3280 3575 8.673711 GTTTATGGATTAGCTTTGTCACACATA 58.326 33.333 0.00 0.00 0.00 2.29
3321 3617 6.109156 TGTATCACCTGTAGAAGCAAAAGA 57.891 37.500 0.00 0.00 0.00 2.52
3469 3765 3.989167 CGTTGTTGAACATGATGGCATTT 59.011 39.130 0.00 0.00 30.68 2.32
3472 3768 1.952990 ACGTTGTTGAACATGATGGCA 59.047 42.857 0.00 0.00 31.78 4.92
3496 3792 9.679661 TGCTTCTTTAAGATATTTGATGTACCA 57.320 29.630 0.00 0.00 34.37 3.25


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

AutoCloner maintained by Alex Coulton.