Multiple sequence alignment - TraesCS6B01G023300

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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 TraesCS6B01G023300 chr6B 100.000 2637 0 0 1 2637 14332374 14335010 0.000000e+00 4870.0
1 TraesCS6B01G023300 chr6B 89.318 1788 151 28 869 2637 14545580 14543814 0.000000e+00 2207.0
2 TraesCS6B01G023300 chr6B 100.000 594 0 0 2834 3427 14335207 14335800 0.000000e+00 1098.0
3 TraesCS6B01G023300 chr6B 81.010 1327 209 27 922 2218 14550361 14549048 0.000000e+00 1014.0
4 TraesCS6B01G023300 chr6B 95.446 549 23 1 2834 3382 14543769 14543223 0.000000e+00 874.0
5 TraesCS6B01G023300 chr6B 79.053 1098 202 18 1135 2218 15750932 15749849 0.000000e+00 728.0
6 TraesCS6B01G023300 chr6B 82.545 613 101 4 1609 2218 14629182 14628573 5.030000e-148 534.0
7 TraesCS6B01G023300 chr6B 84.836 244 18 9 39 280 14620792 14620566 9.570000e-56 228.0
8 TraesCS6B01G023300 chr6B 83.607 244 19 10 39 280 14548205 14547981 3.470000e-50 209.0
9 TraesCS6B01G023300 chr6B 80.000 105 16 4 979 1078 53077163 53077059 4.740000e-09 73.1
10 TraesCS6B01G023300 chr6A 92.817 1768 96 8 876 2637 7991105 7992847 0.000000e+00 2532.0
11 TraesCS6B01G023300 chr6A 90.503 1074 77 9 1565 2637 8197967 8196918 0.000000e+00 1395.0
12 TraesCS6B01G023300 chr6A 95.993 549 22 0 2834 3382 7992892 7993440 0.000000e+00 893.0
13 TraesCS6B01G023300 chr6A 85.196 716 62 20 861 1554 8199042 8198349 0.000000e+00 695.0
14 TraesCS6B01G023300 chr6A 89.031 547 39 3 2842 3382 8196889 8196358 0.000000e+00 658.0
15 TraesCS6B01G023300 chr6A 78.190 1050 191 27 1135 2165 9336110 9337140 1.340000e-178 636.0
16 TraesCS6B01G023300 chr6A 85.830 247 12 11 39 283 8200363 8200138 1.230000e-59 241.0
17 TraesCS6B01G023300 chr6A 85.577 208 15 4 271 475 7990459 7990654 1.610000e-48 204.0
18 TraesCS6B01G023300 chr6A 91.358 81 6 1 39 118 7988951 7989031 3.620000e-20 110.0
19 TraesCS6B01G023300 chr6A 79.851 134 26 1 970 1102 9473089 9473222 2.820000e-16 97.1
20 TraesCS6B01G023300 chr6A 100.000 46 0 0 3382 3427 7993512 7993557 6.090000e-13 86.1
21 TraesCS6B01G023300 chr6A 97.826 46 1 0 3382 3427 8193958 8193913 2.840000e-11 80.5
22 TraesCS6B01G023300 chr6A 97.826 46 0 1 3382 3427 8196285 8196241 1.020000e-10 78.7
23 TraesCS6B01G023300 chr6D 90.541 1924 131 12 730 2637 7718534 7720422 0.000000e+00 2497.0
24 TraesCS6B01G023300 chr6D 85.804 1909 203 30 730 2624 7990239 7988385 0.000000e+00 1962.0
25 TraesCS6B01G023300 chr6D 79.711 1109 188 26 1130 2218 7998997 7997906 0.000000e+00 767.0
26 TraesCS6B01G023300 chr6D 96.269 402 15 0 2834 3235 7720467 7720868 0.000000e+00 660.0
27 TraesCS6B01G023300 chr6D 83.534 249 16 11 39 283 7992299 7992072 3.470000e-50 209.0
28 TraesCS6B01G023300 chr6D 100.000 46 0 0 3382 3427 7720955 7721000 6.090000e-13 86.1
29 TraesCS6B01G023300 chr1B 88.782 731 44 18 884 1586 27364784 27364064 0.000000e+00 861.0
30 TraesCS6B01G023300 chr1B 79.289 1294 209 40 960 2218 27753059 27751790 0.000000e+00 850.0
31 TraesCS6B01G023300 chr1B 96.479 284 3 5 1 283 27676024 27675747 2.410000e-126 462.0
32 TraesCS6B01G023300 chr1B 89.305 187 13 4 97 283 27750965 27750786 9.570000e-56 228.0
33 TraesCS6B01G023300 chr1B 81.818 176 13 6 285 460 27673955 27673799 2.780000e-26 130.0
34 TraesCS6B01G023300 chr2D 78.025 314 41 15 3080 3378 588164208 588164508 4.550000e-39 172.0
35 TraesCS6B01G023300 chr5A 92.188 64 1 2 220 283 650826459 650826518 1.690000e-13 87.9
36 TraesCS6B01G023300 chr5D 90.625 64 2 2 220 283 524579434 524579493 7.880000e-12 82.4


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 TraesCS6B01G023300 chr6B 14332374 14335800 3426 False 2984.000000 4870 100.000000 1 3427 2 chr6B.!!$F1 3426
1 TraesCS6B01G023300 chr6B 14543223 14550361 7138 True 1076.000000 2207 87.345250 39 3382 4 chr6B.!!$R5 3343
2 TraesCS6B01G023300 chr6B 15749849 15750932 1083 True 728.000000 728 79.053000 1135 2218 1 chr6B.!!$R3 1083
3 TraesCS6B01G023300 chr6B 14628573 14629182 609 True 534.000000 534 82.545000 1609 2218 1 chr6B.!!$R2 609
4 TraesCS6B01G023300 chr6A 7988951 7993557 4606 False 765.020000 2532 93.149000 39 3427 5 chr6A.!!$F3 3388
5 TraesCS6B01G023300 chr6A 9336110 9337140 1030 False 636.000000 636 78.190000 1135 2165 1 chr6A.!!$F1 1030
6 TraesCS6B01G023300 chr6A 8193913 8200363 6450 True 524.700000 1395 91.035333 39 3427 6 chr6A.!!$R1 3388
7 TraesCS6B01G023300 chr6D 7988385 7992299 3914 True 1085.500000 1962 84.669000 39 2624 2 chr6D.!!$R2 2585
8 TraesCS6B01G023300 chr6D 7718534 7721000 2466 False 1081.033333 2497 95.603333 730 3427 3 chr6D.!!$F1 2697
9 TraesCS6B01G023300 chr6D 7997906 7998997 1091 True 767.000000 767 79.711000 1130 2218 1 chr6D.!!$R1 1088
10 TraesCS6B01G023300 chr1B 27364064 27364784 720 True 861.000000 861 88.782000 884 1586 1 chr1B.!!$R1 702
11 TraesCS6B01G023300 chr1B 27750786 27753059 2273 True 539.000000 850 84.297000 97 2218 2 chr1B.!!$R3 2121
12 TraesCS6B01G023300 chr1B 27673799 27676024 2225 True 296.000000 462 89.148500 1 460 2 chr1B.!!$R2 459

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
479 5063 0.033781 TCGACCGGACCGATGTTTTT 59.966 50.0 17.49 0.0 0.00 1.94 F
858 6565 0.253327 AGAGAAAAGACGGGGCATCC 59.747 55.0 0.00 0.0 0.00 3.51 F
1812 7997 0.026414 TCGACGAGAAGAAGATCGCG 59.974 55.0 0.00 0.0 46.16 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 7997 0.038166 TCAGGTGATCCACTTTGGCC 59.962 55.0 0.00 0.0 37.47 5.36 R
1840 8025 0.750546 TCGACATCCGACCACCCTAG 60.751 60.0 0.00 0.0 43.23 3.02 R
3143 9554 0.102300 GTAAATGCGGGTGCCCATTC 59.898 55.0 8.14 0.0 41.78 2.67 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
149 2270 4.708177 TGCAGAGGGAAATGCTATCTAAC 58.292 43.478 0.00 0.00 42.98 2.34
153 2274 6.687647 GCAGAGGGAAATGCTATCTAACTTCT 60.688 42.308 0.00 0.00 39.38 2.85
327 4870 3.087031 ACACCCAGCATTTCTGAAGATG 58.913 45.455 7.67 7.67 45.72 2.90
346 4891 5.994250 AGATGCATACACCTACAGTTTCAT 58.006 37.500 0.00 0.00 0.00 2.57
371 4916 3.730715 GTGAAGTTCTGTTTCCAATTGCG 59.269 43.478 4.17 0.00 0.00 4.85
378 4923 4.331968 TCTGTTTCCAATTGCGATAAGGT 58.668 39.130 0.00 0.00 0.00 3.50
398 4943 6.067217 AGGTTTGGTTACTTATCAGCTGAT 57.933 37.500 30.85 30.85 38.51 2.90
403 4948 7.843490 TTGGTTACTTATCAGCTGATTACAC 57.157 36.000 32.94 20.69 36.05 2.90
404 4949 6.941857 TGGTTACTTATCAGCTGATTACACA 58.058 36.000 32.94 19.14 36.05 3.72
405 4950 6.816640 TGGTTACTTATCAGCTGATTACACAC 59.183 38.462 32.94 22.23 36.05 3.82
406 4951 6.816640 GGTTACTTATCAGCTGATTACACACA 59.183 38.462 32.94 11.68 36.05 3.72
407 4952 7.201530 GGTTACTTATCAGCTGATTACACACAC 60.202 40.741 32.94 19.47 36.05 3.82
408 4953 5.793817 ACTTATCAGCTGATTACACACACA 58.206 37.500 32.94 10.16 36.05 3.72
409 4954 5.639506 ACTTATCAGCTGATTACACACACAC 59.360 40.000 32.94 0.00 36.05 3.82
410 4955 3.467374 TCAGCTGATTACACACACACA 57.533 42.857 13.74 0.00 0.00 3.72
411 4956 3.130633 TCAGCTGATTACACACACACAC 58.869 45.455 13.74 0.00 0.00 3.82
412 4957 2.871633 CAGCTGATTACACACACACACA 59.128 45.455 8.42 0.00 0.00 3.72
413 4958 2.872245 AGCTGATTACACACACACACAC 59.128 45.455 0.00 0.00 0.00 3.82
414 4959 2.032030 GCTGATTACACACACACACACC 60.032 50.000 0.00 0.00 0.00 4.16
440 5016 2.678336 GGAGATTGACCGGTGTTGAATC 59.322 50.000 14.63 13.92 0.00 2.52
475 5059 3.138798 CCTCGACCGGACCGATGT 61.139 66.667 17.49 5.29 35.35 3.06
476 5060 2.707849 CCTCGACCGGACCGATGTT 61.708 63.158 17.49 0.00 35.35 2.71
478 5062 0.389426 CTCGACCGGACCGATGTTTT 60.389 55.000 17.49 0.00 35.35 2.43
479 5063 0.033781 TCGACCGGACCGATGTTTTT 59.966 50.000 17.49 0.00 0.00 1.94
506 5651 8.485578 TTTTTCCTTCTTCCTTTATTTAGGCA 57.514 30.769 0.00 0.00 35.15 4.75
511 5656 6.071391 CCTTCTTCCTTTATTTAGGCAAGCAA 60.071 38.462 0.00 0.00 35.15 3.91
542 5687 7.450323 AGGTTTAACAAGTGGCTAATTATGTGT 59.550 33.333 0.00 0.00 0.00 3.72
543 5688 7.753580 GGTTTAACAAGTGGCTAATTATGTGTC 59.246 37.037 0.00 0.00 0.00 3.67
557 5702 0.391528 TGTGTCATCACCATGCCTCG 60.392 55.000 0.00 0.00 43.26 4.63
572 5717 0.603707 CCTCGAGCTCACTTGGCAAA 60.604 55.000 15.40 0.00 0.00 3.68
573 5718 1.229428 CTCGAGCTCACTTGGCAAAA 58.771 50.000 15.40 0.00 0.00 2.44
574 5719 1.603802 CTCGAGCTCACTTGGCAAAAA 59.396 47.619 15.40 0.00 0.00 1.94
602 5748 1.029681 AAGAAAGGAAAGCGCCGTTT 58.970 45.000 2.29 2.79 29.58 3.60
603 5749 0.310854 AGAAAGGAAAGCGCCGTTTG 59.689 50.000 2.29 0.00 29.58 2.93
604 5750 0.309612 GAAAGGAAAGCGCCGTTTGA 59.690 50.000 2.29 0.00 29.58 2.69
609 5755 1.052287 GAAAGCGCCGTTTGATTGTG 58.948 50.000 2.29 0.00 0.00 3.33
619 5765 2.415776 GTTTGATTGTGGGCAATGTGG 58.584 47.619 0.00 0.00 44.61 4.17
629 5775 3.882288 GTGGGCAATGTGGTTTCAATTTT 59.118 39.130 0.00 0.00 0.00 1.82
652 6273 3.684628 TCCTTCCCGGCCCTCTCT 61.685 66.667 0.00 0.00 0.00 3.10
676 6298 3.518303 ACTAGGGAAAAGCGTATCAGGTT 59.482 43.478 0.00 0.00 0.00 3.50
678 6300 4.563140 AGGGAAAAGCGTATCAGGTTTA 57.437 40.909 0.00 0.00 40.43 2.01
679 6301 4.913784 AGGGAAAAGCGTATCAGGTTTAA 58.086 39.130 0.00 0.00 40.43 1.52
683 6305 6.084277 GGAAAAGCGTATCAGGTTTAACAAG 58.916 40.000 0.00 0.00 40.43 3.16
684 6306 6.293790 GGAAAAGCGTATCAGGTTTAACAAGT 60.294 38.462 0.00 0.00 40.43 3.16
685 6307 5.607119 AAGCGTATCAGGTTTAACAAGTG 57.393 39.130 0.00 0.00 0.00 3.16
686 6308 4.000988 AGCGTATCAGGTTTAACAAGTGG 58.999 43.478 0.00 0.00 0.00 4.00
688 6310 4.000988 CGTATCAGGTTTAACAAGTGGCT 58.999 43.478 0.00 0.00 0.00 4.75
689 6311 5.172934 CGTATCAGGTTTAACAAGTGGCTA 58.827 41.667 0.00 0.00 0.00 3.93
691 6313 6.315393 CGTATCAGGTTTAACAAGTGGCTAAT 59.685 38.462 0.00 0.00 0.00 1.73
692 6314 7.148306 CGTATCAGGTTTAACAAGTGGCTAATT 60.148 37.037 0.00 0.00 0.00 1.40
694 6316 8.823220 ATCAGGTTTAACAAGTGGCTAATTAT 57.177 30.769 0.00 0.00 0.00 1.28
695 6317 8.276252 TCAGGTTTAACAAGTGGCTAATTATC 57.724 34.615 0.00 0.00 0.00 1.75
697 6319 8.739972 CAGGTTTAACAAGTGGCTAATTATCTT 58.260 33.333 0.00 0.00 0.00 2.40
698 6320 8.957466 AGGTTTAACAAGTGGCTAATTATCTTC 58.043 33.333 0.00 0.00 0.00 2.87
699 6321 8.188799 GGTTTAACAAGTGGCTAATTATCTTCC 58.811 37.037 0.00 0.00 0.00 3.46
706 6329 6.538263 AGTGGCTAATTATCTTCCATTCTCC 58.462 40.000 0.00 0.00 0.00 3.71
707 6330 5.707764 GTGGCTAATTATCTTCCATTCTCCC 59.292 44.000 0.00 0.00 0.00 4.30
710 6333 7.007116 GGCTAATTATCTTCCATTCTCCCTTT 58.993 38.462 0.00 0.00 0.00 3.11
712 6335 8.572185 GCTAATTATCTTCCATTCTCCCTTTTC 58.428 37.037 0.00 0.00 0.00 2.29
724 6347 8.614469 CATTCTCCCTTTTCCTAGAATGTATC 57.386 38.462 13.27 0.00 45.22 2.24
725 6348 6.749036 TCTCCCTTTTCCTAGAATGTATCC 57.251 41.667 0.00 0.00 0.00 2.59
726 6349 6.453476 TCTCCCTTTTCCTAGAATGTATCCT 58.547 40.000 0.00 0.00 0.00 3.24
727 6350 6.327626 TCTCCCTTTTCCTAGAATGTATCCTG 59.672 42.308 0.00 0.00 0.00 3.86
732 6424 7.070571 CCTTTTCCTAGAATGTATCCTGAGACT 59.929 40.741 0.00 0.00 0.00 3.24
756 6448 2.591571 TGATGCTCAATCTCAGGTCG 57.408 50.000 0.00 0.00 36.15 4.79
762 6454 2.165437 GCTCAATCTCAGGTCGTCTTCT 59.835 50.000 0.00 0.00 0.00 2.85
773 6465 2.411547 GGTCGTCTTCTTTGCAATCACG 60.412 50.000 0.00 4.97 0.00 4.35
775 6467 2.475111 TCGTCTTCTTTGCAATCACGAC 59.525 45.455 0.00 4.79 30.28 4.34
795 6487 9.967245 TCACGACGAAAAATAAAGAAAGATATG 57.033 29.630 0.00 0.00 0.00 1.78
858 6565 0.253327 AGAGAAAAGACGGGGCATCC 59.747 55.000 0.00 0.00 0.00 3.51
873 6613 2.414691 GGCATCCGAAAGAAAAGAGTGC 60.415 50.000 0.00 0.00 0.00 4.40
933 6690 4.023707 GCCCAATTGTATATGTCTGTCAGC 60.024 45.833 4.43 0.00 0.00 4.26
1034 6809 3.833645 CCGCGTCCTCATCCGGAA 61.834 66.667 9.01 0.00 43.20 4.30
1085 6860 1.338484 CCCTCTCCACCGCATCATATG 60.338 57.143 0.00 0.00 0.00 1.78
1411 7212 3.399181 GCCTGTCCCCCATCGTCA 61.399 66.667 0.00 0.00 0.00 4.35
1530 7332 2.188817 CACTACTACCTGCCCCTCTTT 58.811 52.381 0.00 0.00 0.00 2.52
1812 7997 0.026414 TCGACGAGAAGAAGATCGCG 59.974 55.000 0.00 0.00 46.16 5.87
1840 8025 1.066858 TGGATCACCTGAAGAAGACGC 60.067 52.381 0.00 0.00 37.04 5.19
1856 8041 2.423898 CGCTAGGGTGGTCGGATGT 61.424 63.158 0.00 0.00 0.00 3.06
1908 8093 1.234821 TTTTGCTCGCCAAGTCGAAT 58.765 45.000 0.00 0.00 38.08 3.34
2218 8403 5.177696 GTGCCCGCTAGATTTAGATTTACAG 59.822 44.000 0.00 0.00 0.00 2.74
2219 8404 4.691216 GCCCGCTAGATTTAGATTTACAGG 59.309 45.833 0.00 0.00 0.00 4.00
2220 8405 5.742255 GCCCGCTAGATTTAGATTTACAGGT 60.742 44.000 0.00 0.00 0.00 4.00
2221 8406 5.927115 CCCGCTAGATTTAGATTTACAGGTC 59.073 44.000 0.00 0.00 0.00 3.85
2222 8407 6.239345 CCCGCTAGATTTAGATTTACAGGTCT 60.239 42.308 0.00 0.00 0.00 3.85
2223 8408 7.039923 CCCGCTAGATTTAGATTTACAGGTCTA 60.040 40.741 0.00 0.00 0.00 2.59
2224 8409 8.358148 CCGCTAGATTTAGATTTACAGGTCTAA 58.642 37.037 0.00 0.00 35.69 2.10
2225 8410 9.182933 CGCTAGATTTAGATTTACAGGTCTAAC 57.817 37.037 0.00 0.00 36.84 2.34
2291 8495 2.983229 AGTTCTGAAGCCAGCTATGTG 58.017 47.619 0.00 0.00 40.20 3.21
2317 8521 9.353999 GTTGGTCATTATTTTGTAATGGAGAAC 57.646 33.333 7.66 5.19 36.03 3.01
2472 8688 6.480763 TGGGAAGTTCACTGCTTCATAAATA 58.519 36.000 6.69 0.00 42.88 1.40
2474 8690 7.615365 TGGGAAGTTCACTGCTTCATAAATATT 59.385 33.333 6.69 0.00 42.88 1.28
2475 8691 8.131731 GGGAAGTTCACTGCTTCATAAATATTC 58.868 37.037 5.01 0.00 42.88 1.75
2477 8693 9.713740 GAAGTTCACTGCTTCATAAATATTCAG 57.286 33.333 0.00 0.00 41.29 3.02
2479 8695 9.453572 AGTTCACTGCTTCATAAATATTCAGAA 57.546 29.630 5.38 0.00 0.00 3.02
2542 8926 7.987458 GTCATGGTTATCTTGACTTTCAGGATA 59.013 37.037 4.52 4.38 40.75 2.59
2552 8936 3.074412 ACTTTCAGGATAGTTGGTTGCG 58.926 45.455 0.00 0.00 0.00 4.85
2990 9374 2.568062 TGCCCATCATCTTTTTGTGCAT 59.432 40.909 0.00 0.00 0.00 3.96
3071 9455 7.116075 TGATATAAGCTTGCTAAAGGAAACCA 58.884 34.615 9.86 0.00 33.68 3.67
3072 9456 7.613801 TGATATAAGCTTGCTAAAGGAAACCAA 59.386 33.333 9.86 0.00 33.68 3.67
3073 9457 6.857437 ATAAGCTTGCTAAAGGAAACCAAT 57.143 33.333 9.86 0.00 33.68 3.16
3076 9462 7.954666 AAGCTTGCTAAAGGAAACCAATATA 57.045 32.000 0.00 0.00 33.68 0.86
3208 9619 3.548818 GGTTTCAGTTGCACACATCACTC 60.549 47.826 0.00 0.00 0.00 3.51
3248 9660 5.065859 TCACTTTCTTTTGTGAATTCTGCGA 59.934 36.000 7.05 0.00 39.82 5.10
3334 9746 6.532657 GTCAAAAATTTGCCCACTATCTGATG 59.467 38.462 0.00 0.00 38.05 3.07
3335 9747 6.436847 TCAAAAATTTGCCCACTATCTGATGA 59.563 34.615 0.00 0.00 38.05 2.92
3344 9756 4.164988 CCCACTATCTGATGAAACTCCCTT 59.835 45.833 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.624452 GCTTGAGCAATCAATTTCCTTGAC 59.376 41.667 0.00 0.00 42.82 3.18
327 4870 5.063944 CACTGATGAAACTGTAGGTGTATGC 59.936 44.000 0.00 0.00 0.00 3.14
346 4891 5.450412 GCAATTGGAAACAGAACTTCACTGA 60.450 40.000 7.72 0.00 44.54 3.41
371 4916 7.769044 TCAGCTGATAAGTAACCAAACCTTATC 59.231 37.037 13.74 10.29 43.59 1.75
378 4923 7.880713 TGTGTAATCAGCTGATAAGTAACCAAA 59.119 33.333 28.92 10.38 33.73 3.28
398 4943 3.431068 CCACTAGGTGTGTGTGTGTGTAA 60.431 47.826 0.00 0.00 44.81 2.41
403 4948 1.686587 TCTCCACTAGGTGTGTGTGTG 59.313 52.381 0.00 0.00 44.81 3.82
404 4949 2.082140 TCTCCACTAGGTGTGTGTGT 57.918 50.000 0.00 0.00 44.81 3.72
405 4950 3.006859 TCAATCTCCACTAGGTGTGTGTG 59.993 47.826 0.00 0.00 44.81 3.82
406 4951 3.006967 GTCAATCTCCACTAGGTGTGTGT 59.993 47.826 0.00 0.00 44.81 3.72
407 4952 3.589988 GTCAATCTCCACTAGGTGTGTG 58.410 50.000 0.00 0.00 44.81 3.82
408 4953 2.567615 GGTCAATCTCCACTAGGTGTGT 59.432 50.000 0.00 0.00 44.81 3.72
409 4954 2.417379 CGGTCAATCTCCACTAGGTGTG 60.417 54.545 0.00 0.00 45.80 3.82
410 4955 1.825474 CGGTCAATCTCCACTAGGTGT 59.175 52.381 0.00 0.00 35.89 4.16
411 4956 1.137086 CCGGTCAATCTCCACTAGGTG 59.863 57.143 0.00 0.00 35.89 4.00
412 4957 1.273098 ACCGGTCAATCTCCACTAGGT 60.273 52.381 0.00 0.00 35.89 3.08
413 4958 1.137086 CACCGGTCAATCTCCACTAGG 59.863 57.143 2.59 0.00 0.00 3.02
414 4959 1.825474 ACACCGGTCAATCTCCACTAG 59.175 52.381 2.59 0.00 0.00 2.57
454 5030 2.905935 ATCGGTCCGGTCGAGGTCAT 62.906 60.000 22.11 7.65 40.09 3.06
481 5065 8.485578 TGCCTAAATAAAGGAAGAAGGAAAAA 57.514 30.769 0.00 0.00 39.15 1.94
482 5066 8.485578 TTGCCTAAATAAAGGAAGAAGGAAAA 57.514 30.769 0.00 0.00 39.15 2.29
486 5123 5.418840 TGCTTGCCTAAATAAAGGAAGAAGG 59.581 40.000 0.00 0.00 39.15 3.46
505 5650 5.459762 CACTTGTTAAACCTGATGTTGCTTG 59.540 40.000 0.00 0.00 37.23 4.01
506 5651 5.451798 CCACTTGTTAAACCTGATGTTGCTT 60.452 40.000 0.00 0.00 37.23 3.91
511 5656 3.832527 AGCCACTTGTTAAACCTGATGT 58.167 40.909 0.00 0.00 0.00 3.06
542 5687 1.144716 GCTCGAGGCATGGTGATGA 59.855 57.895 15.58 0.00 41.35 2.92
543 5688 0.879400 GAGCTCGAGGCATGGTGATG 60.879 60.000 15.58 0.00 44.79 3.07
574 5719 5.007626 GGCGCTTTCCTTTCTTTTCATTTTT 59.992 36.000 7.64 0.00 0.00 1.94
575 5720 4.511454 GGCGCTTTCCTTTCTTTTCATTTT 59.489 37.500 7.64 0.00 0.00 1.82
595 5741 2.126502 GCCCACAATCAAACGGCG 60.127 61.111 4.80 4.80 0.00 6.46
602 5748 1.714541 AACCACATTGCCCACAATCA 58.285 45.000 0.00 0.00 44.83 2.57
603 5749 2.036992 TGAAACCACATTGCCCACAATC 59.963 45.455 0.00 0.00 44.83 2.67
609 5755 3.882288 ACAAAATTGAAACCACATTGCCC 59.118 39.130 0.00 0.00 0.00 5.36
619 5765 4.743151 GGGAAGGACGAACAAAATTGAAAC 59.257 41.667 0.00 0.00 0.00 2.78
629 5775 4.011517 GGCCGGGAAGGACGAACA 62.012 66.667 2.18 0.00 45.00 3.18
652 6273 4.713321 ACCTGATACGCTTTTCCCTAGTAA 59.287 41.667 0.00 0.00 0.00 2.24
676 6298 9.474313 AATGGAAGATAATTAGCCACTTGTTAA 57.526 29.630 0.00 0.00 0.00 2.01
678 6300 7.836183 AGAATGGAAGATAATTAGCCACTTGTT 59.164 33.333 0.00 0.00 0.00 2.83
679 6301 7.349598 AGAATGGAAGATAATTAGCCACTTGT 58.650 34.615 0.00 0.00 0.00 3.16
683 6305 5.707764 GGGAGAATGGAAGATAATTAGCCAC 59.292 44.000 0.00 0.00 0.00 5.01
684 6306 5.612688 AGGGAGAATGGAAGATAATTAGCCA 59.387 40.000 0.00 0.00 0.00 4.75
685 6307 6.133253 AGGGAGAATGGAAGATAATTAGCC 57.867 41.667 0.00 0.00 0.00 3.93
686 6308 8.470657 AAAAGGGAGAATGGAAGATAATTAGC 57.529 34.615 0.00 0.00 0.00 3.09
688 6310 8.791749 AGGAAAAGGGAGAATGGAAGATAATTA 58.208 33.333 0.00 0.00 0.00 1.40
689 6311 7.656354 AGGAAAAGGGAGAATGGAAGATAATT 58.344 34.615 0.00 0.00 0.00 1.40
691 6313 6.658555 AGGAAAAGGGAGAATGGAAGATAA 57.341 37.500 0.00 0.00 0.00 1.75
692 6314 7.139619 TCTAGGAAAAGGGAGAATGGAAGATA 58.860 38.462 0.00 0.00 0.00 1.98
694 6316 5.350547 TCTAGGAAAAGGGAGAATGGAAGA 58.649 41.667 0.00 0.00 0.00 2.87
695 6317 5.700402 TCTAGGAAAAGGGAGAATGGAAG 57.300 43.478 0.00 0.00 0.00 3.46
697 6319 6.006275 CATTCTAGGAAAAGGGAGAATGGA 57.994 41.667 13.28 0.00 46.02 3.41
706 6329 7.070571 AGTCTCAGGATACATTCTAGGAAAAGG 59.929 40.741 0.00 0.00 41.41 3.11
707 6330 7.925483 CAGTCTCAGGATACATTCTAGGAAAAG 59.075 40.741 0.00 0.00 41.41 2.27
710 6333 6.673583 TCAGTCTCAGGATACATTCTAGGAA 58.326 40.000 0.00 0.00 41.41 3.36
712 6335 6.968263 TTCAGTCTCAGGATACATTCTAGG 57.032 41.667 0.00 0.00 41.41 3.02
720 6343 5.609423 AGCATCAATTCAGTCTCAGGATAC 58.391 41.667 0.00 0.00 0.00 2.24
722 6345 4.163649 TGAGCATCAATTCAGTCTCAGGAT 59.836 41.667 0.00 0.00 45.97 3.24
724 6347 3.870274 TGAGCATCAATTCAGTCTCAGG 58.130 45.455 0.00 0.00 45.97 3.86
756 6448 2.475111 TCGTCGTGATTGCAAAGAAGAC 59.525 45.455 1.71 9.85 0.00 3.01
762 6454 6.913132 TCTTTATTTTTCGTCGTGATTGCAAA 59.087 30.769 1.71 0.00 0.00 3.68
795 6487 6.480320 AGTGGCTGACAATATTTCGATTAGTC 59.520 38.462 0.00 0.00 0.00 2.59
799 6491 5.431765 AGAGTGGCTGACAATATTTCGATT 58.568 37.500 0.00 0.00 0.00 3.34
833 6525 2.484651 GCCCCGTCTTTTCTCTTTTCTC 59.515 50.000 0.00 0.00 0.00 2.87
834 6526 2.158667 TGCCCCGTCTTTTCTCTTTTCT 60.159 45.455 0.00 0.00 0.00 2.52
835 6527 2.227194 TGCCCCGTCTTTTCTCTTTTC 58.773 47.619 0.00 0.00 0.00 2.29
836 6528 2.358322 TGCCCCGTCTTTTCTCTTTT 57.642 45.000 0.00 0.00 0.00 2.27
837 6529 2.437413 GATGCCCCGTCTTTTCTCTTT 58.563 47.619 0.00 0.00 0.00 2.52
838 6530 1.340114 GGATGCCCCGTCTTTTCTCTT 60.340 52.381 0.00 0.00 0.00 2.85
839 6531 0.253327 GGATGCCCCGTCTTTTCTCT 59.747 55.000 0.00 0.00 0.00 3.10
858 6565 2.605580 GGGCTTGCACTCTTTTCTTTCG 60.606 50.000 0.00 0.00 0.00 3.46
933 6690 2.093764 GGGTCAGTCTCTCTCACATTGG 60.094 54.545 0.00 0.00 0.00 3.16
1031 6806 1.334384 GGAGGGAGTGGAGAGCTTCC 61.334 65.000 7.71 7.71 46.98 3.46
1034 6809 2.043450 CGGAGGGAGTGGAGAGCT 60.043 66.667 0.00 0.00 0.00 4.09
1183 6976 3.691342 CTCCACGGCGAACCCAGA 61.691 66.667 16.62 0.00 0.00 3.86
1812 7997 0.038166 TCAGGTGATCCACTTTGGCC 59.962 55.000 0.00 0.00 37.47 5.36
1840 8025 0.750546 TCGACATCCGACCACCCTAG 60.751 60.000 0.00 0.00 43.23 3.02
1908 8093 3.120385 CCGTGCTGCAGCGATTCA 61.120 61.111 32.11 13.09 45.83 2.57
2218 8403 6.575162 ATTCTTGGTTCATGTTGTTAGACC 57.425 37.500 0.00 0.00 0.00 3.85
2219 8404 7.805071 CAGAATTCTTGGTTCATGTTGTTAGAC 59.195 37.037 4.86 0.00 0.00 2.59
2220 8405 7.719193 TCAGAATTCTTGGTTCATGTTGTTAGA 59.281 33.333 4.86 0.00 0.00 2.10
2221 8406 7.874940 TCAGAATTCTTGGTTCATGTTGTTAG 58.125 34.615 4.86 0.00 0.00 2.34
2222 8407 7.502226 ACTCAGAATTCTTGGTTCATGTTGTTA 59.498 33.333 4.86 0.00 0.00 2.41
2223 8408 6.322201 ACTCAGAATTCTTGGTTCATGTTGTT 59.678 34.615 4.86 0.00 0.00 2.83
2224 8409 5.829924 ACTCAGAATTCTTGGTTCATGTTGT 59.170 36.000 4.86 0.00 0.00 3.32
2225 8410 6.323203 ACTCAGAATTCTTGGTTCATGTTG 57.677 37.500 4.86 0.00 0.00 3.33
2226 8411 8.641498 ATTACTCAGAATTCTTGGTTCATGTT 57.359 30.769 4.86 0.00 0.00 2.71
2227 8412 9.911788 ATATTACTCAGAATTCTTGGTTCATGT 57.088 29.630 4.86 0.00 0.00 3.21
2265 8451 2.568956 AGCTGGCTTCAGAACTACATCA 59.431 45.455 0.00 0.00 40.86 3.07
2291 8495 9.353999 GTTCTCCATTACAAAATAATGACCAAC 57.646 33.333 7.99 4.45 37.15 3.77
2344 8550 6.153340 TCAAAGGATAGATTTTGGAAAGCCAG 59.847 38.462 0.00 0.00 46.91 4.85
2507 8891 4.537135 AGATAACCATGACGTGAACTGT 57.463 40.909 0.00 0.00 0.00 3.55
2542 8926 0.957395 CTCTGATGCCGCAACCAACT 60.957 55.000 0.00 0.00 0.00 3.16
2552 8936 2.501723 TGACCTACCTTTCTCTGATGCC 59.498 50.000 0.00 0.00 0.00 4.40
3076 9462 9.495382 AAAGGTCTCTAGATTATGAAGTACCTT 57.505 33.333 0.00 0.00 43.54 3.50
3143 9554 0.102300 GTAAATGCGGGTGCCCATTC 59.898 55.000 8.14 0.00 41.78 2.67
3208 9619 2.173519 AGTGAGGCCACCAATGAATTG 58.826 47.619 5.01 0.00 44.22 2.32
3248 9660 6.533730 TGAACTAATCACAACCTCAACAGAT 58.466 36.000 0.00 0.00 31.50 2.90
3312 9724 6.855763 TCATCAGATAGTGGGCAAATTTTT 57.144 33.333 0.00 0.00 0.00 1.94
3317 9729 4.922206 AGTTTCATCAGATAGTGGGCAAA 58.078 39.130 0.00 0.00 0.00 3.68
3344 9756 7.027874 AGGTTTACCTCCTTCATAACATTGA 57.972 36.000 0.00 0.00 44.77 2.57
3374 9786 1.656587 TTCTACACAGGATGCCCAGT 58.343 50.000 0.00 0.00 42.53 4.00


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

AutoCloner maintained by Alex Coulton.