Multiple sequence alignment - TraesCS6A01G098500

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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 TraesCS6A01G098500 chr6A 100.000 4755 0 0 1 4755 65685520 65680766 0.000000e+00 8781.0
1 TraesCS6A01G098500 chr6A 94.280 2168 97 21 1601 3765 65798256 65800399 0.000000e+00 3291.0
2 TraesCS6A01G098500 chr6A 92.340 235 16 2 1295 1527 65798027 65798261 2.740000e-87 333.0
3 TraesCS6A01G098500 chr6A 92.029 138 11 0 1095 1232 65797857 65797994 1.350000e-45 195.0
4 TraesCS6A01G098500 chr6B 92.368 4206 176 49 1 4124 121816226 121812084 0.000000e+00 5854.0
5 TraesCS6A01G098500 chr6B 95.214 2194 84 10 1601 3793 122291066 122293239 0.000000e+00 3450.0
6 TraesCS6A01G098500 chr6B 85.625 480 44 20 1054 1527 122290611 122291071 9.250000e-132 481.0
7 TraesCS6A01G098500 chr6B 87.421 318 24 8 4138 4441 121812046 121811731 7.570000e-93 351.0
8 TraesCS6A01G098500 chr6B 95.434 219 6 3 4541 4755 121799437 121799219 3.520000e-91 346.0
9 TraesCS6A01G098500 chr6B 92.308 117 9 0 4436 4552 121799582 121799466 2.940000e-37 167.0
10 TraesCS6A01G098500 chr6D 90.964 4327 211 62 1 4232 49217380 49221621 0.000000e+00 5659.0
11 TraesCS6A01G098500 chr6D 94.396 2195 86 16 1601 3791 48868988 48866827 0.000000e+00 3338.0
12 TraesCS6A01G098500 chr6D 88.776 490 51 4 4263 4749 49221694 49222182 8.810000e-167 597.0
13 TraesCS6A01G098500 chr6D 87.097 434 32 15 1097 1527 48869395 48868983 2.000000e-128 470.0
14 TraesCS6A01G098500 chr5B 94.033 553 27 1 3280 3832 162833188 162833734 0.000000e+00 833.0
15 TraesCS6A01G098500 chr5B 82.412 199 25 6 913 1104 322748839 322749034 1.060000e-36 165.0
16 TraesCS6A01G098500 chr3D 88.235 51 6 0 4181 4231 384867267 384867217 1.430000e-05 62.1
17 TraesCS6A01G098500 chr3D 89.130 46 4 1 4265 4309 290856244 290856289 6.650000e-04 56.5
18 TraesCS6A01G098500 chr1A 89.130 46 4 1 4182 4226 495595602 495595557 6.650000e-04 56.5
19 TraesCS6A01G098500 chr1A 100.000 28 0 0 4265 4292 419032299 419032272 9.000000e-03 52.8
20 TraesCS6A01G098500 chrUn 100.000 28 0 0 4270 4297 60954855 60954828 9.000000e-03 52.8
21 TraesCS6A01G098500 chr7A 100.000 28 0 0 4265 4292 511930653 511930680 9.000000e-03 52.8
22 TraesCS6A01G098500 chr4A 100.000 28 0 0 4270 4297 601184848 601184821 9.000000e-03 52.8
23 TraesCS6A01G098500 chr1B 100.000 28 0 0 4265 4292 491242145 491242172 9.000000e-03 52.8


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 TraesCS6A01G098500 chr6A 65680766 65685520 4754 True 8781.0 8781 100.0000 1 4755 1 chr6A.!!$R1 4754
1 TraesCS6A01G098500 chr6A 65797857 65800399 2542 False 1273.0 3291 92.8830 1095 3765 3 chr6A.!!$F1 2670
2 TraesCS6A01G098500 chr6B 121811731 121816226 4495 True 3102.5 5854 89.8945 1 4441 2 chr6B.!!$R2 4440
3 TraesCS6A01G098500 chr6B 122290611 122293239 2628 False 1965.5 3450 90.4195 1054 3793 2 chr6B.!!$F1 2739
4 TraesCS6A01G098500 chr6D 49217380 49222182 4802 False 3128.0 5659 89.8700 1 4749 2 chr6D.!!$F1 4748
5 TraesCS6A01G098500 chr6D 48866827 48869395 2568 True 1904.0 3338 90.7465 1097 3791 2 chr6D.!!$R1 2694
6 TraesCS6A01G098500 chr5B 162833188 162833734 546 False 833.0 833 94.0330 3280 3832 1 chr5B.!!$F1 552

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
337 352 0.104120 TGCCTCGGTTGATACATCCG 59.896 55.000 13.0 13.0 44.94 4.18 F
671 686 0.599558 TGCCAACAAGCAAGCAGATC 59.400 50.000 0.0 0.0 40.56 2.75 F
672 687 0.599558 GCCAACAAGCAAGCAGATCA 59.400 50.000 0.0 0.0 0.00 2.92 F
788 803 1.052124 TTCTTCCACGGGTCACCACT 61.052 55.000 0.0 0.0 36.13 4.00 F
1317 1354 1.133790 GTGAATTGAGCTGCCATGTCC 59.866 52.381 0.0 0.0 0.00 4.02 F
2960 3051 1.002544 CTCACCAACAACCTCCTCCTC 59.997 57.143 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1354 0.029433 TCGTTCTCGATGATCCTGCG 59.971 55.000 0.00 0.0 41.35 5.18 R
1560 1605 0.107017 ATCAATTCCCCGACCAGCAG 60.107 55.000 0.00 0.0 0.00 4.24 R
2645 2736 1.014044 TGGAGAAGATGTTGCGCGTC 61.014 55.000 8.43 0.0 0.00 5.19 R
2960 3051 0.464373 CGAACATGGTCATGGGGAGG 60.464 60.000 12.13 0.0 42.91 4.30 R
3149 3240 4.554163 GTGGACACCTTCTCGACG 57.446 61.111 0.00 0.0 0.00 5.12 R
4446 4658 1.204704 ACGCATGAAGAATCCTGTCGA 59.795 47.619 0.00 0.0 31.10 4.20 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
28 29 2.544685 CTTTTGATCGACGGAGAGCAT 58.455 47.619 1.43 0.00 36.36 3.79
56 57 1.047002 CCCTCGCCATCTGAAGATCT 58.953 55.000 0.00 0.00 31.21 2.75
61 62 1.202348 CGCCATCTGAAGATCTGACGT 60.202 52.381 0.00 0.00 31.21 4.34
78 79 3.781307 TTCGCCACCAGGGATCCG 61.781 66.667 5.45 0.00 40.01 4.18
102 105 1.663379 CCACCGTCTCGATGCTACCA 61.663 60.000 0.00 0.00 0.00 3.25
149 152 2.048784 ATCCGCCATCTCGATGCG 60.049 61.111 10.58 10.58 37.49 4.73
161 164 2.765108 TCGATGCGAGAACAGAGATC 57.235 50.000 0.00 0.00 0.00 2.75
163 166 1.336440 CGATGCGAGAACAGAGATCCT 59.664 52.381 0.00 0.00 0.00 3.24
194 197 2.811317 CGCCGCACAGACTTCTCC 60.811 66.667 0.00 0.00 0.00 3.71
203 206 2.619177 CACAGACTTCTCCCGACGATAT 59.381 50.000 0.00 0.00 0.00 1.63
209 212 3.327172 ACTTCTCCCGACGATATCCTCTA 59.673 47.826 0.00 0.00 0.00 2.43
212 215 4.092279 TCTCCCGACGATATCCTCTAGTA 58.908 47.826 0.00 0.00 0.00 1.82
252 267 1.079503 GGAGTTTGTGCAGATCGGAC 58.920 55.000 0.00 0.00 36.27 4.79
297 312 8.944029 GGGTCTAGTGAAAACCTAAATAACTTC 58.056 37.037 0.00 0.00 33.42 3.01
320 335 0.804364 TTGAATGGTCGCTCATGTGC 59.196 50.000 9.72 9.72 0.00 4.57
337 352 0.104120 TGCCTCGGTTGATACATCCG 59.896 55.000 13.00 13.00 44.94 4.18
375 390 3.467374 TTCCTTTTGCCCATGTGAAAC 57.533 42.857 0.00 0.00 37.35 2.78
396 411 4.139786 ACCATGGAGATGAACATGCATAC 58.860 43.478 21.47 0.00 42.31 2.39
441 456 0.756442 TAGCCAAGCCATTGCCCATC 60.756 55.000 0.00 0.00 38.69 3.51
459 474 3.635373 CCATCAGATTCCATGGACCAAAG 59.365 47.826 15.91 3.95 42.11 2.77
500 515 5.649395 AGGGTAAACAACACATGATGAGATG 59.351 40.000 0.00 0.00 31.97 2.90
501 516 5.647658 GGGTAAACAACACATGATGAGATGA 59.352 40.000 7.08 0.00 0.00 2.92
502 517 6.319658 GGGTAAACAACACATGATGAGATGAT 59.680 38.462 7.08 0.00 0.00 2.45
509 524 3.003378 CACATGATGAGATGATGCACCAC 59.997 47.826 0.00 0.00 0.00 4.16
527 542 5.737063 GCACCACAACAAGAAGAACAATGAT 60.737 40.000 0.00 0.00 0.00 2.45
528 543 6.514870 GCACCACAACAAGAAGAACAATGATA 60.515 38.462 0.00 0.00 0.00 2.15
529 544 6.857964 CACCACAACAAGAAGAACAATGATAC 59.142 38.462 0.00 0.00 0.00 2.24
596 611 1.625417 CCCACATGGCATTTTCCCCC 61.625 60.000 0.00 0.00 0.00 5.40
599 614 0.684153 ACATGGCATTTTCCCCCTCG 60.684 55.000 0.00 0.00 0.00 4.63
602 617 1.753078 GGCATTTTCCCCCTCGGTC 60.753 63.158 0.00 0.00 0.00 4.79
629 644 2.099098 CCACGAAGTTAATCATTGCCCC 59.901 50.000 0.00 0.00 41.61 5.80
669 684 4.256462 TGCCAACAAGCAAGCAGA 57.744 50.000 0.00 0.00 40.56 4.26
670 685 2.736197 TGCCAACAAGCAAGCAGAT 58.264 47.368 0.00 0.00 40.56 2.90
671 686 0.599558 TGCCAACAAGCAAGCAGATC 59.400 50.000 0.00 0.00 40.56 2.75
672 687 0.599558 GCCAACAAGCAAGCAGATCA 59.400 50.000 0.00 0.00 0.00 2.92
673 688 1.203994 GCCAACAAGCAAGCAGATCAT 59.796 47.619 0.00 0.00 0.00 2.45
674 689 2.353406 GCCAACAAGCAAGCAGATCATT 60.353 45.455 0.00 0.00 0.00 2.57
689 704 4.032672 CAGATCATTTCACTTCGCTGTCTC 59.967 45.833 0.00 0.00 0.00 3.36
757 772 8.156822 ACAGGAAATAATTCTCTTCCTCTTCT 57.843 34.615 11.03 0.00 44.58 2.85
758 773 8.610369 ACAGGAAATAATTCTCTTCCTCTTCTT 58.390 33.333 11.03 0.00 44.58 2.52
759 774 9.108284 CAGGAAATAATTCTCTTCCTCTTCTTC 57.892 37.037 11.03 0.00 44.58 2.87
760 775 8.271458 AGGAAATAATTCTCTTCCTCTTCTTCC 58.729 37.037 8.97 0.00 44.58 3.46
761 776 8.271458 GGAAATAATTCTCTTCCTCTTCTTCCT 58.729 37.037 6.07 0.00 36.48 3.36
762 777 9.325198 GAAATAATTCTCTTCCTCTTCTTCCTC 57.675 37.037 0.00 0.00 32.57 3.71
780 795 2.354203 CCTCTTCTTCTTCTTCCACGGG 60.354 54.545 0.00 0.00 0.00 5.28
788 803 1.052124 TTCTTCCACGGGTCACCACT 61.052 55.000 0.00 0.00 36.13 4.00
848 863 1.607628 CTGCCAGATAAGAGCATTGCC 59.392 52.381 4.70 0.00 35.64 4.52
968 983 3.429372 AAGAAACAGGCCGGCCACA 62.429 57.895 45.13 0.00 38.92 4.17
977 992 3.058160 CCGGCCACAAAGCTCTGG 61.058 66.667 2.24 0.00 0.00 3.86
1252 1271 1.301244 CGCTCGATCCATCCTTGGG 60.301 63.158 0.00 0.00 43.81 4.12
1259 1278 2.578586 ATCCATCCTTGGGTGCCAGC 62.579 60.000 0.00 0.00 43.81 4.85
1282 1301 5.493133 TTACAACTCTGTTCGTGCAATTT 57.507 34.783 0.00 0.00 36.96 1.82
1315 1337 2.211250 AGTGAATTGAGCTGCCATGT 57.789 45.000 0.00 0.00 0.00 3.21
1317 1354 1.133790 GTGAATTGAGCTGCCATGTCC 59.866 52.381 0.00 0.00 0.00 4.02
1542 1579 3.598299 AGGTACGGCGAGATCTATCTAC 58.402 50.000 16.62 1.45 37.25 2.59
1577 1623 2.409870 GCTGCTGGTCGGGGAATTG 61.410 63.158 0.00 0.00 0.00 2.32
1641 1687 2.171341 ACTTCTCCGGCTTCAACTTC 57.829 50.000 0.00 0.00 0.00 3.01
1817 1908 4.501071 CCTTGATTCCTTTCTGCATTTGG 58.499 43.478 0.00 0.00 0.00 3.28
2342 2433 2.126307 CTCCTGGTCACGCTCGTG 60.126 66.667 15.49 15.49 46.64 4.35
2498 2589 4.814294 GGGCTGTACGTGCTCCCG 62.814 72.222 15.82 0.03 0.00 5.14
2960 3051 1.002544 CTCACCAACAACCTCCTCCTC 59.997 57.143 0.00 0.00 0.00 3.71
3149 3240 1.222936 CACCATCAGCCTCCAGGTC 59.777 63.158 0.00 0.00 37.57 3.85
3568 3661 2.890766 GCCCCGAGGTGAGTCCAAA 61.891 63.158 0.00 0.00 39.02 3.28
3569 3662 1.758592 CCCCGAGGTGAGTCCAAAA 59.241 57.895 0.00 0.00 39.02 2.44
3614 3707 4.793678 GCATCATCAAACTGTTCTTGCACA 60.794 41.667 0.00 0.00 0.00 4.57
3615 3708 5.466819 CATCATCAAACTGTTCTTGCACAT 58.533 37.500 0.00 0.00 0.00 3.21
3616 3709 5.518848 TCATCAAACTGTTCTTGCACATT 57.481 34.783 0.00 0.00 0.00 2.71
3617 3710 5.904941 TCATCAAACTGTTCTTGCACATTT 58.095 33.333 0.00 0.00 0.00 2.32
3618 3711 5.749588 TCATCAAACTGTTCTTGCACATTTG 59.250 36.000 0.00 0.00 32.36 2.32
3619 3712 4.431809 TCAAACTGTTCTTGCACATTTGG 58.568 39.130 0.00 0.00 32.19 3.28
3640 3733 6.659745 TGGATTTGGATTTGATGATGGATC 57.340 37.500 0.00 0.00 0.00 3.36
3641 3734 5.541101 TGGATTTGGATTTGATGATGGATCC 59.459 40.000 4.20 4.20 38.80 3.36
3733 3826 3.119096 GCGTTTCCTCACCTCGCC 61.119 66.667 0.00 0.00 40.83 5.54
3953 4082 7.828223 TGAATAATTTGCTGCCCATGTAAAATT 59.172 29.630 0.00 3.72 33.26 1.82
3965 4094 5.298276 CCCATGTAAAATTACACATACGCCT 59.702 40.000 8.09 0.00 45.47 5.52
4045 4186 9.701355 GTTCCAACATTTTGTAACTGATTTTTG 57.299 29.630 0.00 0.00 30.77 2.44
4077 4218 3.141398 TCATCTTGTTGGCACTTCTGTC 58.859 45.455 0.00 0.00 0.00 3.51
4121 4262 2.485903 TCCACGTTAGAACACGCAATT 58.514 42.857 0.00 0.00 44.37 2.32
4140 4305 2.669910 TGCGCGCACACCCATAAA 60.670 55.556 33.09 2.14 0.00 1.40
4149 4314 4.420168 CGCACACCCATAAATGTTTAAGG 58.580 43.478 0.89 0.89 32.71 2.69
4168 4334 8.398665 GTTTAAGGTGTATATGCTGGAAAGAAG 58.601 37.037 0.00 0.00 0.00 2.85
4250 4448 7.995463 AAACTGTTTAATAATGTGTTTGCGT 57.005 28.000 3.51 0.00 0.00 5.24
4255 4453 7.640852 TGTTTAATAATGTGTTTGCGTACAGT 58.359 30.769 0.00 0.00 0.00 3.55
4326 4538 9.451002 TTTTGTTATGTTTAGATCCACGGAATA 57.549 29.630 0.00 0.00 0.00 1.75
4386 4598 6.816136 TGAAGACATGTACAGAAACTTCTCA 58.184 36.000 22.65 11.22 34.74 3.27
4446 4658 4.953940 ATTGCGGGGCATAAATTTGTAT 57.046 36.364 0.00 0.00 38.76 2.29
4449 4661 2.550606 GCGGGGCATAAATTTGTATCGA 59.449 45.455 0.00 0.00 0.00 3.59
4451 4663 3.562141 CGGGGCATAAATTTGTATCGACA 59.438 43.478 0.00 0.00 0.00 4.35
4452 4664 4.319477 CGGGGCATAAATTTGTATCGACAG 60.319 45.833 0.00 0.00 36.76 3.51
4457 4669 7.078228 GGCATAAATTTGTATCGACAGGATTC 58.922 38.462 0.00 0.00 36.76 2.52
4461 4673 7.921786 AAATTTGTATCGACAGGATTCTTCA 57.078 32.000 0.00 0.00 36.76 3.02
4465 4677 1.926561 TCGACAGGATTCTTCATGCG 58.073 50.000 0.00 0.00 37.15 4.73
4485 4697 8.503196 TCATGCGTTGCAATAGGTTATAAATAG 58.497 33.333 0.59 0.00 43.62 1.73
4500 4712 9.953565 GGTTATAAATAGTCTGGTATATTGGCA 57.046 33.333 0.00 0.00 0.00 4.92
4510 4723 5.071250 TCTGGTATATTGGCACCGATTTAGT 59.929 40.000 0.00 0.00 37.66 2.24
4530 4743 7.841282 TTAGTTTCCCAATTTAATGTGGTCA 57.159 32.000 4.67 0.00 32.60 4.02
4533 4746 6.269769 AGTTTCCCAATTTAATGTGGTCATGT 59.730 34.615 0.00 0.00 34.19 3.21
4604 4817 7.516481 CAATAAGAGATGTGATATTTGAGGCG 58.484 38.462 0.00 0.00 0.00 5.52
4617 4830 9.868277 TGATATTTGAGGCGTTTTTATGAAAAT 57.132 25.926 0.00 0.00 37.12 1.82
4619 4832 9.868277 ATATTTGAGGCGTTTTTATGAAAATCA 57.132 25.926 0.00 0.00 37.12 2.57
4625 4838 7.546358 AGGCGTTTTTATGAAAATCATGATGA 58.454 30.769 9.46 0.00 37.70 2.92
4688 4901 3.630312 GGCAAACAAGAGGAAACACACTA 59.370 43.478 0.00 0.00 0.00 2.74
4695 4908 6.357367 ACAAGAGGAAACACACTAAATCTGT 58.643 36.000 0.00 0.00 0.00 3.41
4700 4913 6.534634 AGGAAACACACTAAATCTGTAAGCT 58.465 36.000 0.00 0.00 0.00 3.74
4713 4926 6.840780 ATCTGTAAGCTAGCACCAATTTTT 57.159 33.333 18.83 1.96 0.00 1.94
4717 4930 8.802267 TCTGTAAGCTAGCACCAATTTTTAAAT 58.198 29.630 18.83 0.00 0.00 1.40
4718 4931 8.980143 TGTAAGCTAGCACCAATTTTTAAATC 57.020 30.769 18.83 0.00 0.00 2.17
4719 4932 8.032451 TGTAAGCTAGCACCAATTTTTAAATCC 58.968 33.333 18.83 0.00 0.00 3.01
4720 4933 6.603940 AGCTAGCACCAATTTTTAAATCCA 57.396 33.333 18.83 0.00 0.00 3.41
4721 4934 7.186570 AGCTAGCACCAATTTTTAAATCCAT 57.813 32.000 18.83 0.00 0.00 3.41
4722 4935 7.043565 AGCTAGCACCAATTTTTAAATCCATG 58.956 34.615 18.83 0.00 0.00 3.66
4723 4936 7.041107 GCTAGCACCAATTTTTAAATCCATGA 58.959 34.615 10.63 0.00 0.00 3.07
4724 4937 7.010460 GCTAGCACCAATTTTTAAATCCATGAC 59.990 37.037 10.63 0.00 0.00 3.06
4726 4939 5.936956 GCACCAATTTTTAAATCCATGACCA 59.063 36.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.372087 CTTCAGATGGCGAGGGTTGC 61.372 60.000 0.00 0.00 0.00 4.17
39 40 2.741612 GTCAGATCTTCAGATGGCGAG 58.258 52.381 0.00 0.00 34.37 5.03
56 57 4.308458 CCCTGGTGGCGAACGTCA 62.308 66.667 0.00 0.00 0.00 4.35
61 62 3.781307 CGGATCCCTGGTGGCGAA 61.781 66.667 6.06 0.00 0.00 4.70
78 79 1.592669 CATCGAGACGGTGGATGGC 60.593 63.158 0.00 0.00 37.65 4.40
115 118 0.392193 GATGGCCGCTCCTCATATGG 60.392 60.000 2.13 0.00 35.26 2.74
117 120 1.986413 GGATGGCCGCTCCTCATAT 59.014 57.895 15.32 0.00 35.26 1.78
118 121 3.471620 GGATGGCCGCTCCTCATA 58.528 61.111 15.32 0.00 35.26 2.15
194 197 3.619483 CAGCTACTAGAGGATATCGTCGG 59.381 52.174 17.35 16.01 36.02 4.79
203 206 2.660572 CTCCTTGCAGCTACTAGAGGA 58.339 52.381 0.00 0.00 0.00 3.71
209 212 0.906756 TGCTCCTCCTTGCAGCTACT 60.907 55.000 0.00 0.00 34.84 2.57
260 275 1.330655 ACTAGACCCCAGGCGTCATG 61.331 60.000 7.03 1.61 32.41 3.07
261 276 1.001760 ACTAGACCCCAGGCGTCAT 59.998 57.895 7.03 0.00 32.41 3.06
264 279 0.834687 TTTCACTAGACCCCAGGCGT 60.835 55.000 0.00 0.00 0.00 5.68
270 285 7.400439 AGTTATTTAGGTTTTCACTAGACCCC 58.600 38.462 0.00 0.00 33.89 4.95
271 286 8.859236 AAGTTATTTAGGTTTTCACTAGACCC 57.141 34.615 0.00 0.00 33.89 4.46
297 312 3.855379 CACATGAGCGACCATTCAATTTG 59.145 43.478 0.00 0.00 0.00 2.32
301 316 0.804364 GCACATGAGCGACCATTCAA 59.196 50.000 0.00 0.00 0.00 2.69
337 352 8.334632 CAAAAGGAATGAACATTTTGGTGTTAC 58.665 33.333 0.00 0.00 43.22 2.50
375 390 3.187842 CGTATGCATGTTCATCTCCATGG 59.812 47.826 10.16 4.97 39.06 3.66
396 411 5.116180 TGTGTTTTATGGAATCTAGGCTCG 58.884 41.667 0.00 0.00 0.00 5.03
430 445 2.076207 TGGAATCTGATGGGCAATGG 57.924 50.000 0.00 0.00 0.00 3.16
431 446 2.299013 CCATGGAATCTGATGGGCAATG 59.701 50.000 5.56 0.00 36.26 2.82
432 447 2.178325 TCCATGGAATCTGATGGGCAAT 59.822 45.455 13.46 0.00 39.81 3.56
433 448 1.570024 TCCATGGAATCTGATGGGCAA 59.430 47.619 13.46 0.00 39.81 4.52
441 456 1.753073 GGCTTTGGTCCATGGAATCTG 59.247 52.381 18.20 7.30 0.00 2.90
459 474 0.036105 CCTTTTGGCATTGGAAGGGC 60.036 55.000 10.06 0.00 35.98 5.19
500 515 3.066621 TGTTCTTCTTGTTGTGGTGCATC 59.933 43.478 0.00 0.00 0.00 3.91
501 516 3.023119 TGTTCTTCTTGTTGTGGTGCAT 58.977 40.909 0.00 0.00 0.00 3.96
502 517 2.441410 TGTTCTTCTTGTTGTGGTGCA 58.559 42.857 0.00 0.00 0.00 4.57
509 524 9.429359 AGAGTAGTATCATTGTTCTTCTTGTTG 57.571 33.333 0.00 0.00 0.00 3.33
527 542 6.714810 TGTTCCAAGTTACGGTTAGAGTAGTA 59.285 38.462 0.00 0.00 0.00 1.82
528 543 5.536161 TGTTCCAAGTTACGGTTAGAGTAGT 59.464 40.000 0.00 0.00 0.00 2.73
529 544 6.017400 TGTTCCAAGTTACGGTTAGAGTAG 57.983 41.667 0.00 0.00 0.00 2.57
539 554 4.782195 GCGATGCTTATGTTCCAAGTTACG 60.782 45.833 0.00 0.00 0.00 3.18
602 617 1.078001 ATTAACTTCGTGGGCCCCG 60.078 57.895 22.27 22.38 0.00 5.73
612 627 3.903467 AGGAGGGGCAATGATTAACTTC 58.097 45.455 0.00 0.00 0.00 3.01
629 644 3.292460 AGAGATAAGACCGTGGAAGGAG 58.708 50.000 0.00 0.00 34.73 3.69
669 684 3.265791 GGAGACAGCGAAGTGAAATGAT 58.734 45.455 0.00 0.00 0.00 2.45
670 685 2.037121 TGGAGACAGCGAAGTGAAATGA 59.963 45.455 0.00 0.00 35.01 2.57
671 686 2.416747 TGGAGACAGCGAAGTGAAATG 58.583 47.619 0.00 0.00 35.01 2.32
672 687 2.839486 TGGAGACAGCGAAGTGAAAT 57.161 45.000 0.00 0.00 35.01 2.17
673 688 2.483876 CTTGGAGACAGCGAAGTGAAA 58.516 47.619 0.00 0.00 44.54 2.69
674 689 1.873903 GCTTGGAGACAGCGAAGTGAA 60.874 52.381 0.00 0.00 44.54 3.18
689 704 1.298859 GAGTACGTGGGCAAGCTTGG 61.299 60.000 27.10 12.81 0.00 3.61
757 772 3.006967 CCGTGGAAGAAGAAGAAGAGGAA 59.993 47.826 0.00 0.00 0.00 3.36
758 773 2.563179 CCGTGGAAGAAGAAGAAGAGGA 59.437 50.000 0.00 0.00 0.00 3.71
759 774 2.354203 CCCGTGGAAGAAGAAGAAGAGG 60.354 54.545 0.00 0.00 0.00 3.69
760 775 2.300437 ACCCGTGGAAGAAGAAGAAGAG 59.700 50.000 0.00 0.00 0.00 2.85
761 776 2.299297 GACCCGTGGAAGAAGAAGAAGA 59.701 50.000 0.00 0.00 0.00 2.87
762 777 2.037251 TGACCCGTGGAAGAAGAAGAAG 59.963 50.000 0.00 0.00 0.00 2.85
788 803 0.950836 CGCAAGTGGATCAACAACCA 59.049 50.000 2.34 0.00 0.00 3.67
946 961 2.626780 GCCGGCCTGTTTCTTGGAC 61.627 63.158 18.11 0.00 0.00 4.02
968 983 0.886490 CGGCAACAGACCAGAGCTTT 60.886 55.000 0.00 0.00 0.00 3.51
977 992 4.329545 TCCTGGCCGGCAACAGAC 62.330 66.667 30.85 10.31 36.86 3.51
1252 1271 1.884235 ACAGAGTTGTAAGCTGGCAC 58.116 50.000 0.00 0.00 35.25 5.01
1259 1278 4.732285 ATTGCACGAACAGAGTTGTAAG 57.268 40.909 0.00 0.00 36.23 2.34
1282 1301 2.356665 TTCACTAAGCAAGCCAACCA 57.643 45.000 0.00 0.00 0.00 3.67
1315 1337 0.385751 GTTCTCGATGATCCTGCGGA 59.614 55.000 0.00 0.00 35.55 5.54
1317 1354 0.029433 TCGTTCTCGATGATCCTGCG 59.971 55.000 0.00 0.00 41.35 5.18
1542 1579 4.135153 CTCTGGTCCCGCCGTCTG 62.135 72.222 0.00 0.00 41.21 3.51
1560 1605 0.107017 ATCAATTCCCCGACCAGCAG 60.107 55.000 0.00 0.00 0.00 4.24
1577 1623 6.291067 TGAATGCACAGATCGAACATAATC 57.709 37.500 0.00 0.00 0.00 1.75
1810 1869 2.640684 CGTCACGCATTCCAAATGC 58.359 52.632 13.35 13.35 41.35 3.56
1832 1923 3.020274 TCTCTCTTGCAGCTTCGAGTAT 58.980 45.455 0.24 0.00 0.00 2.12
1964 2055 4.711949 AGCAGGTTGGCGAGGCAG 62.712 66.667 0.00 0.00 39.27 4.85
2645 2736 1.014044 TGGAGAAGATGTTGCGCGTC 61.014 55.000 8.43 0.00 0.00 5.19
2960 3051 0.464373 CGAACATGGTCATGGGGAGG 60.464 60.000 12.13 0.00 42.91 4.30
3149 3240 4.554163 GTGGACACCTTCTCGACG 57.446 61.111 0.00 0.00 0.00 5.12
3568 3661 5.544650 CTTGAAAAGCCATTGGAGTTGATT 58.455 37.500 6.95 0.00 36.98 2.57
3569 3662 5.143376 CTTGAAAAGCCATTGGAGTTGAT 57.857 39.130 6.95 0.00 36.98 2.57
3601 3694 4.942761 AATCCAAATGTGCAAGAACAGT 57.057 36.364 0.00 0.00 32.52 3.55
3614 3707 7.440505 TCCATCATCAAATCCAAATCCAAAT 57.559 32.000 0.00 0.00 0.00 2.32
3615 3708 6.870895 TCCATCATCAAATCCAAATCCAAA 57.129 33.333 0.00 0.00 0.00 3.28
3616 3709 6.042322 GGATCCATCATCAAATCCAAATCCAA 59.958 38.462 6.95 0.00 38.05 3.53
3617 3710 5.541101 GGATCCATCATCAAATCCAAATCCA 59.459 40.000 6.95 0.00 38.05 3.41
3618 3711 5.541101 TGGATCCATCATCAAATCCAAATCC 59.459 40.000 11.44 0.00 43.52 3.01
3619 3712 6.659745 TGGATCCATCATCAAATCCAAATC 57.340 37.500 11.44 0.00 43.52 2.17
3640 3733 4.037208 GGAGATATCTGCACACCAAAATGG 59.963 45.833 18.47 0.00 37.65 3.16
3641 3734 4.260907 CGGAGATATCTGCACACCAAAATG 60.261 45.833 22.29 0.29 33.58 2.32
3733 3826 1.194098 CAGTGCGTCTTGCTCTTCTTG 59.806 52.381 0.00 0.00 44.69 3.02
3953 4082 4.394439 TTGCATCTTAGGCGTATGTGTA 57.606 40.909 0.00 0.00 0.00 2.90
4002 4141 2.430694 GGAACACCTTGCTTTCCAAAGT 59.569 45.455 1.14 0.00 38.98 2.66
4003 4142 2.430332 TGGAACACCTTGCTTTCCAAAG 59.570 45.455 0.00 0.00 44.65 2.77
4004 4143 2.461695 TGGAACACCTTGCTTTCCAAA 58.538 42.857 0.00 0.00 44.65 3.28
4063 4204 1.523758 AATCCGACAGAAGTGCCAAC 58.476 50.000 0.00 0.00 0.00 3.77
4077 4218 2.223144 TCAAAGCTGACAACGAAATCCG 59.777 45.455 0.00 0.00 45.44 4.18
4134 4275 9.897744 CAGCATATACACCTTAAACATTTATGG 57.102 33.333 12.49 12.49 41.32 2.74
4140 4305 8.052748 TCTTTCCAGCATATACACCTTAAACAT 58.947 33.333 0.00 0.00 0.00 2.71
4149 4314 6.341316 TGACTCTTCTTTCCAGCATATACAC 58.659 40.000 0.00 0.00 0.00 2.90
4168 4334 9.296400 GAATGAAGAGAGTACTGTATTTGACTC 57.704 37.037 0.00 0.00 38.89 3.36
4232 4402 7.010606 CGACTGTACGCAAACACATTATTAAA 58.989 34.615 0.00 0.00 0.00 1.52
4233 4403 6.365518 TCGACTGTACGCAAACACATTATTAA 59.634 34.615 0.00 0.00 0.00 1.40
4237 4435 3.640592 TCGACTGTACGCAAACACATTA 58.359 40.909 0.00 0.00 0.00 1.90
4245 4443 2.717580 AGTGAATCGACTGTACGCAA 57.282 45.000 0.00 0.00 0.00 4.85
4247 4445 3.609475 CTCTAGTGAATCGACTGTACGC 58.391 50.000 0.00 0.00 0.00 4.42
4248 4446 3.063588 TGCTCTAGTGAATCGACTGTACG 59.936 47.826 0.00 0.00 0.00 3.67
4250 4448 5.126779 AGATGCTCTAGTGAATCGACTGTA 58.873 41.667 7.06 0.00 0.00 2.74
4255 4453 9.631452 CAAATATAAGATGCTCTAGTGAATCGA 57.369 33.333 7.06 0.00 0.00 3.59
4366 4578 6.844696 TGTTGAGAAGTTTCTGTACATGTC 57.155 37.500 0.00 0.00 37.73 3.06
4446 4658 1.204704 ACGCATGAAGAATCCTGTCGA 59.795 47.619 0.00 0.00 31.10 4.20
4449 4661 1.470098 GCAACGCATGAAGAATCCTGT 59.530 47.619 0.00 0.00 0.00 4.00
4451 4663 1.825090 TGCAACGCATGAAGAATCCT 58.175 45.000 0.00 0.00 31.71 3.24
4452 4664 2.634982 TTGCAACGCATGAAGAATCC 57.365 45.000 0.00 0.00 38.76 3.01
4457 4669 3.492421 AACCTATTGCAACGCATGAAG 57.508 42.857 0.00 0.00 38.76 3.02
4461 4673 8.391075 ACTATTTATAACCTATTGCAACGCAT 57.609 30.769 0.00 0.00 38.76 4.73
4465 4677 9.338622 ACCAGACTATTTATAACCTATTGCAAC 57.661 33.333 0.00 0.00 0.00 4.17
4485 4697 2.902705 TCGGTGCCAATATACCAGAC 57.097 50.000 0.00 0.00 36.76 3.51
4500 4712 8.032451 CACATTAAATTGGGAAACTAAATCGGT 58.968 33.333 0.00 0.00 33.13 4.69
4510 4723 6.678568 ACATGACCACATTAAATTGGGAAA 57.321 33.333 0.00 0.00 37.18 3.13
4570 4783 4.473196 TCACATCTCTTATTGCCTTACCCA 59.527 41.667 0.00 0.00 0.00 4.51
4576 4789 7.664731 CCTCAAATATCACATCTCTTATTGCCT 59.335 37.037 0.00 0.00 0.00 4.75
4578 4791 7.303998 GCCTCAAATATCACATCTCTTATTGC 58.696 38.462 0.00 0.00 0.00 3.56
4586 4799 6.515272 AAAAACGCCTCAAATATCACATCT 57.485 33.333 0.00 0.00 0.00 2.90
4617 4830 7.772292 CCCTCTCTTATTCTTTTGTCATCATGA 59.228 37.037 0.00 0.00 0.00 3.07
4618 4831 7.013083 CCCCTCTCTTATTCTTTTGTCATCATG 59.987 40.741 0.00 0.00 0.00 3.07
4619 4832 7.059156 CCCCTCTCTTATTCTTTTGTCATCAT 58.941 38.462 0.00 0.00 0.00 2.45
4625 4838 5.190726 CCTCTCCCCTCTCTTATTCTTTTGT 59.809 44.000 0.00 0.00 0.00 2.83
4631 4844 3.621682 TCCCTCTCCCCTCTCTTATTC 57.378 52.381 0.00 0.00 0.00 1.75
4636 4849 2.743131 TTTTTCCCTCTCCCCTCTCT 57.257 50.000 0.00 0.00 0.00 3.10
4688 4901 6.840780 AAATTGGTGCTAGCTTACAGATTT 57.159 33.333 17.23 12.53 0.00 2.17
4695 4908 8.128322 TGGATTTAAAAATTGGTGCTAGCTTA 57.872 30.769 17.23 0.34 0.00 3.09
4700 4913 7.038729 TGGTCATGGATTTAAAAATTGGTGCTA 60.039 33.333 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.