Multiple sequence alignment - TraesCS5D01G201700

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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 TraesCS5D01G201700 chr5D 100.000 3571 0 0 1 3571 305775693 305779263 0.000000e+00 6595
1 TraesCS5D01G201700 chr5D 94.602 704 37 1 2869 3571 380087871 380088574 0.000000e+00 1088
2 TraesCS5D01G201700 chr5D 86.239 218 20 6 2629 2837 157690709 157690493 9.970000e-56 228
3 TraesCS5D01G201700 chr5B 97.141 1959 50 5 658 2613 350497085 350499040 0.000000e+00 3302
4 TraesCS5D01G201700 chr5B 92.186 819 54 7 2762 3571 677810870 677811687 0.000000e+00 1149
5 TraesCS5D01G201700 chr5B 91.265 332 23 4 201 527 350496132 350496462 7.030000e-122 448
6 TraesCS5D01G201700 chr5B 97.414 116 3 0 3 118 350496017 350496132 7.820000e-47 198
7 TraesCS5D01G201700 chr5B 96.591 88 3 0 2258 2345 498069115 498069202 2.870000e-31 147
8 TraesCS5D01G201700 chr5B 87.879 99 4 2 527 622 350496541 350496634 3.770000e-20 110
9 TraesCS5D01G201700 chr5A 95.867 1960 61 10 660 2603 391979309 391977354 0.000000e+00 3153
10 TraesCS5D01G201700 chr5A 93.365 211 11 1 3 210 391979532 391979322 3.460000e-80 309
11 TraesCS5D01G201700 chr2D 94.744 780 31 5 2796 3571 539155855 539155082 0.000000e+00 1205
12 TraesCS5D01G201700 chr2D 95.150 701 31 3 2872 3571 176586831 176587529 0.000000e+00 1103
13 TraesCS5D01G201700 chr2D 90.217 644 51 8 2629 3264 102729425 102728786 0.000000e+00 830
14 TraesCS5D01G201700 chr2D 89.888 267 17 3 2076 2342 651289496 651289752 5.710000e-88 335
15 TraesCS5D01G201700 chr4D 93.274 788 37 10 2796 3571 12301325 12300542 0.000000e+00 1147
16 TraesCS5D01G201700 chr6D 88.667 953 69 18 2629 3571 441785836 441784913 0.000000e+00 1125
17 TraesCS5D01G201700 chr6D 89.431 123 13 0 2629 2751 427268356 427268478 4.770000e-34 156
18 TraesCS5D01G201700 chr7D 88.538 951 73 18 2629 3571 90635755 90634833 0.000000e+00 1120
19 TraesCS5D01G201700 chr7D 95.435 701 30 2 2872 3571 532628998 532629697 0.000000e+00 1116
20 TraesCS5D01G201700 chr7D 95.170 704 33 1 2869 3571 504249216 504248513 0.000000e+00 1110
21 TraesCS5D01G201700 chr7D 95.007 701 33 2 2872 3571 135438439 135439138 0.000000e+00 1099
22 TraesCS5D01G201700 chr7D 83.163 980 116 23 2629 3571 165480760 165479793 0.000000e+00 850
23 TraesCS5D01G201700 chr7D 86.087 115 8 4 2629 2743 17342627 17342733 2.250000e-22 117
24 TraesCS5D01G201700 chr2A 88.339 283 27 5 8 285 98580985 98581266 5.710000e-88 335
25 TraesCS5D01G201700 chr1D 86.486 296 29 9 2629 2914 359788882 359788588 7.440000e-82 315
26 TraesCS5D01G201700 chr1D 90.244 123 8 4 3 121 352537710 352537832 1.330000e-34 158
27 TraesCS5D01G201700 chr3B 88.745 231 11 7 1955 2183 29376368 29376151 5.880000e-68 268
28 TraesCS5D01G201700 chr3B 85.837 233 25 5 33 258 410616017 410616248 1.280000e-59 241
29 TraesCS5D01G201700 chr3B 92.405 158 11 1 2220 2376 29376149 29375992 1.290000e-54 224
30 TraesCS5D01G201700 chr7B 89.516 124 10 2 2629 2751 654710224 654710103 1.720000e-33 154
31 TraesCS5D01G201700 chr3A 84.615 156 15 6 108 258 421717264 421717415 2.870000e-31 147
32 TraesCS5D01G201700 chr3A 91.429 105 7 1 3 105 421716995 421717099 3.720000e-30 143


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 TraesCS5D01G201700 chr5D 305775693 305779263 3570 False 6595.0 6595 100.00000 1 3571 1 chr5D.!!$F1 3570
1 TraesCS5D01G201700 chr5D 380087871 380088574 703 False 1088.0 1088 94.60200 2869 3571 1 chr5D.!!$F2 702
2 TraesCS5D01G201700 chr5B 677810870 677811687 817 False 1149.0 1149 92.18600 2762 3571 1 chr5B.!!$F2 809
3 TraesCS5D01G201700 chr5B 350496017 350499040 3023 False 1014.5 3302 93.42475 3 2613 4 chr5B.!!$F3 2610
4 TraesCS5D01G201700 chr5A 391977354 391979532 2178 True 1731.0 3153 94.61600 3 2603 2 chr5A.!!$R1 2600
5 TraesCS5D01G201700 chr2D 539155082 539155855 773 True 1205.0 1205 94.74400 2796 3571 1 chr2D.!!$R2 775
6 TraesCS5D01G201700 chr2D 176586831 176587529 698 False 1103.0 1103 95.15000 2872 3571 1 chr2D.!!$F1 699
7 TraesCS5D01G201700 chr2D 102728786 102729425 639 True 830.0 830 90.21700 2629 3264 1 chr2D.!!$R1 635
8 TraesCS5D01G201700 chr4D 12300542 12301325 783 True 1147.0 1147 93.27400 2796 3571 1 chr4D.!!$R1 775
9 TraesCS5D01G201700 chr6D 441784913 441785836 923 True 1125.0 1125 88.66700 2629 3571 1 chr6D.!!$R1 942
10 TraesCS5D01G201700 chr7D 90634833 90635755 922 True 1120.0 1120 88.53800 2629 3571 1 chr7D.!!$R1 942
11 TraesCS5D01G201700 chr7D 532628998 532629697 699 False 1116.0 1116 95.43500 2872 3571 1 chr7D.!!$F3 699
12 TraesCS5D01G201700 chr7D 504248513 504249216 703 True 1110.0 1110 95.17000 2869 3571 1 chr7D.!!$R3 702
13 TraesCS5D01G201700 chr7D 135438439 135439138 699 False 1099.0 1099 95.00700 2872 3571 1 chr7D.!!$F2 699
14 TraesCS5D01G201700 chr7D 165479793 165480760 967 True 850.0 850 83.16300 2629 3571 1 chr7D.!!$R2 942

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
537 625 0.107654 CCCCACCGTTCTTCCTCATC 60.108 60.0 0.00 0.0 0.00 2.92 F
552 640 0.174845 TCATCCCAACTAAGACGCCG 59.825 55.0 0.00 0.0 0.00 6.46 F
887 1407 0.245539 CTGGCCTGCTGGATTGTTTG 59.754 55.0 14.77 0.0 34.57 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1904 0.103937 GGGATCAGAGCTCTGGAACG 59.896 60.000 36.92 16.75 43.91 3.95 R
2527 3049 0.397816 CTCCTCCCCTTCATCCTCGT 60.398 60.000 0.00 0.00 0.00 4.18 R
2608 3130 1.135170 TGCTGTCGAAGATGCTCTCAG 60.135 52.381 0.00 0.00 40.67 3.35 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
46 47 9.840427 AAAGTTATGAGTCATTTAACATTTCGG 57.160 29.630 11.68 0.00 0.00 4.30
111 112 0.532862 AGCTATGCATGCACCGTACC 60.533 55.000 25.37 8.43 0.00 3.34
118 119 1.575244 CATGCACCGTACCATCTCTG 58.425 55.000 0.00 0.00 0.00 3.35
132 133 2.001076 TCTCTGCACTCTCTTCCACA 57.999 50.000 0.00 0.00 0.00 4.17
138 139 5.809001 TCTGCACTCTCTTCCACATTTATT 58.191 37.500 0.00 0.00 0.00 1.40
145 146 9.846248 CACTCTCTTCCACATTTATTTAAAAGG 57.154 33.333 0.00 0.00 0.00 3.11
154 155 7.818930 CCACATTTATTTAAAAGGCTGACACAT 59.181 33.333 0.00 0.00 0.00 3.21
160 161 2.831685 AAAGGCTGACACATGTACGA 57.168 45.000 0.00 0.00 0.00 3.43
168 169 2.741517 TGACACATGTACGAATGCAAGG 59.258 45.455 0.00 0.00 0.00 3.61
228 232 5.759506 TTGTGGTGTATTGACAATTTCGT 57.240 34.783 5.89 0.00 37.31 3.85
289 294 0.533531 TCGGATCATGATGCAGGCAC 60.534 55.000 24.65 4.09 0.00 5.01
303 308 4.309950 GCACGTGAGGTCCCGGTT 62.310 66.667 22.23 0.00 0.00 4.44
304 309 2.048503 CACGTGAGGTCCCGGTTC 60.049 66.667 10.90 0.00 0.00 3.62
305 310 3.308705 ACGTGAGGTCCCGGTTCC 61.309 66.667 0.00 1.81 0.00 3.62
306 311 4.078516 CGTGAGGTCCCGGTTCCC 62.079 72.222 0.00 0.00 0.00 3.97
335 341 2.363306 TGTGCTTGATGTCCTTTGGT 57.637 45.000 0.00 0.00 0.00 3.67
346 352 5.601313 TGATGTCCTTTGGTACTCCCTATAC 59.399 44.000 0.00 0.00 0.00 1.47
375 381 2.804212 GCCTGCAAACACTTTCAGCATT 60.804 45.455 0.00 0.00 34.35 3.56
457 466 2.359107 CTCTTGCGGCTCCTTGCA 60.359 61.111 0.00 0.00 45.15 4.08
494 503 3.056328 GCCAAACCGCCAGTCTCC 61.056 66.667 0.00 0.00 0.00 3.71
496 505 3.423154 CAAACCGCCAGTCTCCGC 61.423 66.667 0.00 0.00 0.00 5.54
507 516 4.153330 TCTCCGCCCTACCCTCCC 62.153 72.222 0.00 0.00 0.00 4.30
508 517 4.475444 CTCCGCCCTACCCTCCCA 62.475 72.222 0.00 0.00 0.00 4.37
511 520 3.616721 CGCCCTACCCTCCCATCG 61.617 72.222 0.00 0.00 0.00 3.84
516 525 1.551452 CCTACCCTCCCATCGATCTC 58.449 60.000 0.00 0.00 0.00 2.75
536 624 1.991230 CCCCACCGTTCTTCCTCAT 59.009 57.895 0.00 0.00 0.00 2.90
537 625 0.107654 CCCCACCGTTCTTCCTCATC 60.108 60.000 0.00 0.00 0.00 2.92
548 636 5.179533 GTTCTTCCTCATCCCAACTAAGAC 58.820 45.833 0.00 0.00 0.00 3.01
549 637 3.447586 TCTTCCTCATCCCAACTAAGACG 59.552 47.826 0.00 0.00 0.00 4.18
550 638 1.480954 TCCTCATCCCAACTAAGACGC 59.519 52.381 0.00 0.00 0.00 5.19
551 639 1.473434 CCTCATCCCAACTAAGACGCC 60.473 57.143 0.00 0.00 0.00 5.68
552 640 0.174845 TCATCCCAACTAAGACGCCG 59.825 55.000 0.00 0.00 0.00 6.46
581 669 3.318555 CGCTCGCAGCATCGTCTC 61.319 66.667 8.52 0.00 42.58 3.36
583 671 2.405191 CTCGCAGCATCGTCTCGA 59.595 61.111 0.00 0.00 41.13 4.04
622 713 2.676748 ACCAATGTCCTTTTCAGGCAA 58.323 42.857 0.00 0.00 40.58 4.52
623 714 2.365293 ACCAATGTCCTTTTCAGGCAAC 59.635 45.455 0.00 0.00 40.58 4.17
637 728 2.553079 GGCAACTCACGAACAACAAA 57.447 45.000 0.00 0.00 0.00 2.83
638 729 2.182014 GGCAACTCACGAACAACAAAC 58.818 47.619 0.00 0.00 0.00 2.93
639 730 2.182014 GCAACTCACGAACAACAAACC 58.818 47.619 0.00 0.00 0.00 3.27
640 731 2.436670 CAACTCACGAACAACAAACCG 58.563 47.619 0.00 0.00 0.00 4.44
641 732 2.012937 ACTCACGAACAACAAACCGA 57.987 45.000 0.00 0.00 0.00 4.69
642 733 2.348660 ACTCACGAACAACAAACCGAA 58.651 42.857 0.00 0.00 0.00 4.30
643 734 2.350498 ACTCACGAACAACAAACCGAAG 59.650 45.455 0.00 0.00 0.00 3.79
656 747 3.083997 CGAAGGGGGAGGAGGTGG 61.084 72.222 0.00 0.00 0.00 4.61
887 1407 0.245539 CTGGCCTGCTGGATTGTTTG 59.754 55.000 14.77 0.00 34.57 2.93
1330 1850 1.002746 TTTGCGCAGGCTGGTGATA 60.003 52.632 17.64 0.00 40.82 2.15
1364 1884 2.743664 CGTTTCCATTCATGCTCACTCA 59.256 45.455 0.00 0.00 0.00 3.41
1404 1924 0.467804 GTTCCAGAGCTCTGATCCCC 59.532 60.000 39.34 20.34 46.59 4.81
1410 1931 1.836802 AGAGCTCTGATCCCCTGAAAC 59.163 52.381 17.42 0.00 0.00 2.78
1420 1942 3.370840 TCCCCTGAAACTGAATGATGG 57.629 47.619 0.00 0.00 0.00 3.51
1613 2135 4.864334 CTCATGGCGCCCACCTCC 62.864 72.222 26.77 0.00 35.80 4.30
1655 2177 2.186384 CTCGCCTTCCTCCTGCTG 59.814 66.667 0.00 0.00 0.00 4.41
1997 2519 1.975327 CGGGAGGCTCAAGAACTCA 59.025 57.895 17.69 0.00 32.98 3.41
2019 2541 3.344215 GCATCATCCTCGCGCAGG 61.344 66.667 16.84 16.84 45.15 4.85
2589 3111 3.360168 GTGAGCGTCGTTTGACTTACTAC 59.640 47.826 0.00 0.00 43.21 2.73
2590 3112 3.251729 TGAGCGTCGTTTGACTTACTACT 59.748 43.478 0.00 0.00 43.21 2.57
2591 3113 4.452114 TGAGCGTCGTTTGACTTACTACTA 59.548 41.667 0.00 0.00 43.21 1.82
2615 3137 9.296400 CTAGTAGTGTTTTATCTTTCTGAGAGC 57.704 37.037 0.00 0.00 37.93 4.09
2616 3138 7.671302 AGTAGTGTTTTATCTTTCTGAGAGCA 58.329 34.615 0.00 0.00 37.93 4.26
2617 3139 8.317679 AGTAGTGTTTTATCTTTCTGAGAGCAT 58.682 33.333 0.00 0.00 37.93 3.79
2618 3140 7.608308 AGTGTTTTATCTTTCTGAGAGCATC 57.392 36.000 0.00 0.00 37.93 3.91
2644 3166 4.449068 CGACAGCAAAAGTCAGAATACAGT 59.551 41.667 0.00 0.00 35.77 3.55
2711 3233 0.375803 CCGCCGTAAAATAAAGCGCT 59.624 50.000 2.64 2.64 45.17 5.92
2730 3252 2.829003 CCGAGCCGCTCCAGTAGA 60.829 66.667 14.85 0.00 0.00 2.59
2732 3254 2.407428 CGAGCCGCTCCAGTAGACA 61.407 63.158 14.85 0.00 0.00 3.41
2822 3422 7.096884 TGCGTACATAGTTCATAGTCTTCTT 57.903 36.000 0.00 0.00 0.00 2.52
2970 3606 2.820479 CTCGTCGCGGGAGTCTCT 60.820 66.667 16.67 0.00 0.00 3.10
2982 3618 1.015109 GAGTCTCTGGACGACGCATA 58.985 55.000 0.00 0.00 46.29 3.14
3153 3794 1.001764 CAGTGCCATGGCTTCCTCA 60.002 57.895 35.53 13.42 42.51 3.86
3252 3893 2.672996 GCCAACTCATGTGCCCGT 60.673 61.111 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 2.233186 TGTGGAAGAGAGTGCAGAGATG 59.767 50.000 0.00 0.00 0.00 2.90
118 119 9.346725 CTTTTAAATAAATGTGGAAGAGAGTGC 57.653 33.333 0.00 0.00 0.00 4.40
132 133 9.855021 GTACATGTGTCAGCCTTTTAAATAAAT 57.145 29.630 9.11 0.00 0.00 1.40
138 139 4.633175 TCGTACATGTGTCAGCCTTTTAA 58.367 39.130 9.11 0.00 0.00 1.52
145 146 1.731709 TGCATTCGTACATGTGTCAGC 59.268 47.619 9.11 5.79 0.00 4.26
154 155 2.805671 CAGTTGTCCTTGCATTCGTACA 59.194 45.455 0.00 0.00 0.00 2.90
160 161 3.077359 GTCTAGCAGTTGTCCTTGCATT 58.923 45.455 0.00 0.00 42.67 3.56
168 169 4.387256 GTGTCAGATTGTCTAGCAGTTGTC 59.613 45.833 0.00 0.00 0.00 3.18
199 203 9.823647 AAATTGTCAATACACCACAATACAAAA 57.176 25.926 0.00 0.00 39.34 2.44
263 267 1.270199 GCATCATGATCCGAGCTCTGT 60.270 52.381 12.85 0.00 0.00 3.41
264 268 1.270147 TGCATCATGATCCGAGCTCTG 60.270 52.381 12.85 5.31 0.00 3.35
265 269 1.001068 CTGCATCATGATCCGAGCTCT 59.999 52.381 12.85 0.00 0.00 4.09
289 294 4.078516 GGGAACCGGGACCTCACG 62.079 72.222 6.32 0.00 40.86 4.35
301 306 2.433436 AGCACAAAATCTACCGGGAAC 58.567 47.619 6.32 0.00 0.00 3.62
302 307 2.817258 CAAGCACAAAATCTACCGGGAA 59.183 45.455 6.32 0.00 0.00 3.97
303 308 2.039216 TCAAGCACAAAATCTACCGGGA 59.961 45.455 6.32 0.00 0.00 5.14
304 309 2.432444 TCAAGCACAAAATCTACCGGG 58.568 47.619 6.32 0.00 0.00 5.73
305 310 3.440173 ACATCAAGCACAAAATCTACCGG 59.560 43.478 0.00 0.00 0.00 5.28
306 311 4.437390 GGACATCAAGCACAAAATCTACCG 60.437 45.833 0.00 0.00 0.00 4.02
317 322 3.412386 AGTACCAAAGGACATCAAGCAC 58.588 45.455 0.00 0.00 0.00 4.40
335 341 2.889045 GGCACATGACGTATAGGGAGTA 59.111 50.000 0.00 0.00 0.00 2.59
346 352 0.661187 GTGTTTGCAGGCACATGACG 60.661 55.000 15.07 0.00 35.81 4.35
375 381 1.887854 TGTTGATCGGACGGTCTGTTA 59.112 47.619 16.14 0.00 0.00 2.41
412 421 2.045926 ATGAAGAGGTGGCGGCAC 60.046 61.111 32.17 32.17 0.00 5.01
421 430 1.827969 AGGTGGAAGACGATGAAGAGG 59.172 52.381 0.00 0.00 0.00 3.69
490 499 4.153330 GGGAGGGTAGGGCGGAGA 62.153 72.222 0.00 0.00 0.00 3.71
494 503 3.616721 CGATGGGAGGGTAGGGCG 61.617 72.222 0.00 0.00 0.00 6.13
496 505 0.115349 AGATCGATGGGAGGGTAGGG 59.885 60.000 0.54 0.00 0.00 3.53
498 507 1.169577 CGAGATCGATGGGAGGGTAG 58.830 60.000 0.54 0.00 43.02 3.18
507 516 2.029666 GGTGGGGCGAGATCGATG 59.970 66.667 0.54 0.00 43.02 3.84
508 517 3.606662 CGGTGGGGCGAGATCGAT 61.607 66.667 6.39 0.00 43.02 3.59
511 520 2.202892 GAACGGTGGGGCGAGATC 60.203 66.667 0.00 0.00 0.00 2.75
516 525 3.952628 GAGGAAGAACGGTGGGGCG 62.953 68.421 0.00 0.00 0.00 6.13
536 624 2.263540 GCGGCGTCTTAGTTGGGA 59.736 61.111 9.37 0.00 0.00 4.37
537 625 2.047655 TGCGGCGTCTTAGTTGGG 60.048 61.111 9.37 0.00 0.00 4.12
581 669 3.781079 TTTGCTAATTGGAAGGCATCG 57.219 42.857 0.00 0.00 34.59 3.84
583 671 3.582208 TGGTTTTGCTAATTGGAAGGCAT 59.418 39.130 0.00 0.00 34.59 4.40
622 713 2.012937 TCGGTTTGTTGTTCGTGAGT 57.987 45.000 0.00 0.00 0.00 3.41
623 714 2.286184 CCTTCGGTTTGTTGTTCGTGAG 60.286 50.000 0.00 0.00 0.00 3.51
624 715 1.666700 CCTTCGGTTTGTTGTTCGTGA 59.333 47.619 0.00 0.00 0.00 4.35
625 716 1.268335 CCCTTCGGTTTGTTGTTCGTG 60.268 52.381 0.00 0.00 0.00 4.35
626 717 1.018910 CCCTTCGGTTTGTTGTTCGT 58.981 50.000 0.00 0.00 0.00 3.85
627 718 0.309612 CCCCTTCGGTTTGTTGTTCG 59.690 55.000 0.00 0.00 0.00 3.95
628 719 0.671796 CCCCCTTCGGTTTGTTGTTC 59.328 55.000 0.00 0.00 0.00 3.18
629 720 0.259356 TCCCCCTTCGGTTTGTTGTT 59.741 50.000 0.00 0.00 0.00 2.83
630 721 0.179001 CTCCCCCTTCGGTTTGTTGT 60.179 55.000 0.00 0.00 0.00 3.32
631 722 0.893727 CCTCCCCCTTCGGTTTGTTG 60.894 60.000 0.00 0.00 0.00 3.33
632 723 1.063654 TCCTCCCCCTTCGGTTTGTT 61.064 55.000 0.00 0.00 0.00 2.83
633 724 1.462627 TCCTCCCCCTTCGGTTTGT 60.463 57.895 0.00 0.00 0.00 2.83
634 725 1.299976 CTCCTCCCCCTTCGGTTTG 59.700 63.158 0.00 0.00 0.00 2.93
635 726 1.923909 CCTCCTCCCCCTTCGGTTT 60.924 63.158 0.00 0.00 0.00 3.27
636 727 2.285442 CCTCCTCCCCCTTCGGTT 60.285 66.667 0.00 0.00 0.00 4.44
637 728 3.612607 ACCTCCTCCCCCTTCGGT 61.613 66.667 0.00 0.00 0.00 4.69
638 729 3.083997 CACCTCCTCCCCCTTCGG 61.084 72.222 0.00 0.00 0.00 4.30
639 730 3.083997 CCACCTCCTCCCCCTTCG 61.084 72.222 0.00 0.00 0.00 3.79
640 731 2.692741 CCCACCTCCTCCCCCTTC 60.693 72.222 0.00 0.00 0.00 3.46
641 732 4.371231 CCCCACCTCCTCCCCCTT 62.371 72.222 0.00 0.00 0.00 3.95
645 736 4.791069 TACGCCCCACCTCCTCCC 62.791 72.222 0.00 0.00 0.00 4.30
646 737 2.446036 ATACGCCCCACCTCCTCC 60.446 66.667 0.00 0.00 0.00 4.30
647 738 2.822399 CATACGCCCCACCTCCTC 59.178 66.667 0.00 0.00 0.00 3.71
648 739 3.480133 GCATACGCCCCACCTCCT 61.480 66.667 0.00 0.00 0.00 3.69
649 740 3.792736 TGCATACGCCCCACCTCC 61.793 66.667 0.00 0.00 37.32 4.30
650 741 2.513897 GTGCATACGCCCCACCTC 60.514 66.667 0.00 0.00 37.32 3.85
651 742 4.109675 GGTGCATACGCCCCACCT 62.110 66.667 0.00 0.00 44.32 4.00
652 743 3.929334 TTGGTGCATACGCCCCACC 62.929 63.158 7.85 7.85 46.22 4.61
653 744 1.752694 ATTGGTGCATACGCCCCAC 60.753 57.895 0.00 0.00 46.22 4.61
654 745 1.752310 CATTGGTGCATACGCCCCA 60.752 57.895 0.00 0.00 44.75 4.96
655 746 3.119193 CATTGGTGCATACGCCCC 58.881 61.111 0.00 0.00 46.63 5.80
718 1224 6.588719 TTGTGTAGCAAGAAGGCAATAAAT 57.411 33.333 0.00 0.00 35.83 1.40
721 1227 5.070001 ACTTTGTGTAGCAAGAAGGCAATA 58.930 37.500 0.00 0.00 38.47 1.90
1110 1630 1.663379 CGATCTCCCTGTACACCGCA 61.663 60.000 0.00 0.00 0.00 5.69
1375 1895 2.525629 TCTGGAACGGGGCACTGA 60.526 61.111 0.00 0.00 33.92 3.41
1384 1904 0.103937 GGGATCAGAGCTCTGGAACG 59.896 60.000 36.92 16.75 43.91 3.95
1404 1924 6.040054 TGCAATATCCCATCATTCAGTTTCAG 59.960 38.462 0.00 0.00 0.00 3.02
1410 1931 5.125578 CCATCTGCAATATCCCATCATTCAG 59.874 44.000 0.00 0.00 0.00 3.02
1420 1942 0.877071 CACGGCCATCTGCAATATCC 59.123 55.000 2.24 0.00 43.89 2.59
1470 1992 2.108976 GATCGCCGGGATCTGCAA 59.891 61.111 19.79 0.00 46.66 4.08
1514 2036 3.965258 ATGCCCCTGTTCGTGCCA 61.965 61.111 0.00 0.00 0.00 4.92
1613 2135 1.336755 CAACCCGGAACACCAAAGAAG 59.663 52.381 0.73 0.00 0.00 2.85
1997 2519 4.615815 GCGAGGATGATGCGGCCT 62.616 66.667 0.00 0.00 33.97 5.19
2527 3049 0.397816 CTCCTCCCCTTCATCCTCGT 60.398 60.000 0.00 0.00 0.00 4.18
2589 3111 9.296400 GCTCTCAGAAAGATAAAACACTACTAG 57.704 37.037 0.00 0.00 32.19 2.57
2590 3112 8.803235 TGCTCTCAGAAAGATAAAACACTACTA 58.197 33.333 0.00 0.00 32.19 1.82
2591 3113 7.671302 TGCTCTCAGAAAGATAAAACACTACT 58.329 34.615 0.00 0.00 32.19 2.57
2605 3127 3.842820 CTGTCGAAGATGCTCTCAGAAA 58.157 45.455 0.00 0.00 40.67 2.52
2608 3130 1.135170 TGCTGTCGAAGATGCTCTCAG 60.135 52.381 0.00 0.00 40.67 3.35
2610 3132 2.001812 TTGCTGTCGAAGATGCTCTC 57.998 50.000 0.00 0.00 40.67 3.20
2611 3133 2.462456 TTTGCTGTCGAAGATGCTCT 57.538 45.000 0.00 0.00 40.67 4.09
2612 3134 2.481952 ACTTTTGCTGTCGAAGATGCTC 59.518 45.455 0.00 0.00 40.67 4.26
2613 3135 2.481952 GACTTTTGCTGTCGAAGATGCT 59.518 45.455 0.00 0.00 40.67 3.79
2614 3136 2.224079 TGACTTTTGCTGTCGAAGATGC 59.776 45.455 0.00 0.00 40.67 3.91
2615 3137 3.742882 TCTGACTTTTGCTGTCGAAGATG 59.257 43.478 0.00 0.00 40.67 2.90
2616 3138 3.995199 TCTGACTTTTGCTGTCGAAGAT 58.005 40.909 0.00 0.00 40.67 2.40
2617 3139 3.452755 TCTGACTTTTGCTGTCGAAGA 57.547 42.857 0.00 0.00 37.26 2.87
2618 3140 4.739046 ATTCTGACTTTTGCTGTCGAAG 57.261 40.909 0.00 0.00 37.26 3.79
2619 3141 5.053811 TGTATTCTGACTTTTGCTGTCGAA 58.946 37.500 0.00 0.00 37.26 3.71
2620 3142 4.627058 TGTATTCTGACTTTTGCTGTCGA 58.373 39.130 0.00 0.00 37.26 4.20
2621 3143 4.449068 ACTGTATTCTGACTTTTGCTGTCG 59.551 41.667 0.00 0.00 37.26 4.35
2622 3144 5.683859 CACTGTATTCTGACTTTTGCTGTC 58.316 41.667 0.00 0.00 35.21 3.51
2623 3145 4.023707 GCACTGTATTCTGACTTTTGCTGT 60.024 41.667 0.00 0.00 0.00 4.40
2624 3146 4.470462 GCACTGTATTCTGACTTTTGCTG 58.530 43.478 0.00 0.00 0.00 4.41
2625 3147 3.503748 GGCACTGTATTCTGACTTTTGCT 59.496 43.478 0.00 0.00 0.00 3.91
2626 3148 3.667960 CGGCACTGTATTCTGACTTTTGC 60.668 47.826 0.00 0.00 0.00 3.68
2627 3149 3.120199 CCGGCACTGTATTCTGACTTTTG 60.120 47.826 0.00 0.00 0.00 2.44
2698 3220 1.937899 GCTCGGGAGCGCTTTATTTTA 59.062 47.619 13.26 0.00 45.29 1.52
2711 3233 4.435970 TACTGGAGCGGCTCGGGA 62.436 66.667 22.63 12.48 0.00 5.14
2751 3273 3.001736 GTGCCGAACTATCATTGCTCTTC 59.998 47.826 0.00 0.00 0.00 2.87
2756 3283 3.365832 CAATGTGCCGAACTATCATTGC 58.634 45.455 0.00 0.00 38.83 3.56
2858 3492 9.880157 TGACAAGTAGTAGTAGTTTTTCAGTTT 57.120 29.630 0.00 0.00 0.00 2.66
2968 3604 2.152016 CTAGGATATGCGTCGTCCAGA 58.848 52.381 11.62 0.73 34.42 3.86
2970 3606 0.596577 GCTAGGATATGCGTCGTCCA 59.403 55.000 11.62 0.00 34.42 4.02
2982 3618 3.386768 AATACAACATCGCGCTAGGAT 57.613 42.857 5.56 0.00 0.00 3.24
3153 3794 2.447379 AGCCTGGCCGAGATGGAT 60.447 61.111 16.57 0.00 42.00 3.41
3261 3902 1.300697 GAACTTCACCGACGTGGCT 60.301 57.895 0.00 0.00 43.94 4.75
3455 4096 4.790962 CCACCATGCTGCCTCGCT 62.791 66.667 0.00 0.00 0.00 4.93


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

AutoCloner maintained by Alex Coulton.