Multiple sequence alignment - TraesCS5A01G090800

Loading Multiple Alignment...

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 TraesCS5A01G090800 chr5A 100.000 5614 0 0 1 5614 123714316 123708703 0.000000e+00 10368
1 TraesCS5A01G090800 chr5D 95.885 5030 154 24 613 5614 116175789 116170785 0.000000e+00 8093
2 TraesCS5A01G090800 chr5D 88.124 581 54 13 1 572 116176371 116175797 0.000000e+00 676
3 TraesCS5A01G090800 chr5B 95.019 4477 180 26 1023 5478 128219503 128215049 0.000000e+00 6992
4 TraesCS5A01G090800 chr5B 88.018 434 42 3 1 424 128220378 128219945 6.490000e-139 505
5 TraesCS5A01G090800 chr5B 87.500 432 54 0 613 1044 128219946 128219515 3.020000e-137 499
6 TraesCS5A01G090800 chr5B 88.889 99 3 6 5518 5614 128215051 128214959 1.280000e-21 115
7 TraesCS5A01G090800 chr4B 79.814 322 50 6 3608 3928 53449626 53449319 2.630000e-53 220
8 TraesCS5A01G090800 chr4B 84.404 218 34 0 1898 2115 195464293 195464076 1.220000e-51 215
9 TraesCS5A01G090800 chr4B 79.077 325 50 8 3608 3928 53474643 53474333 2.050000e-49 207
10 TraesCS5A01G090800 chr4B 83.621 116 19 0 3028 3143 195463262 195463147 5.950000e-20 110
11 TraesCS5A01G090800 chr4D 83.945 218 35 0 1898 2115 136187128 136186911 5.700000e-50 209
12 TraesCS5A01G090800 chr4D 74.046 393 83 13 3028 3414 136186098 136185719 5.860000e-30 143
13 TraesCS5A01G090800 chr4A 83.636 220 36 0 1898 2117 423155672 423155891 2.050000e-49 207
14 TraesCS5A01G090800 chr4A 74.046 393 84 13 3028 3414 423156566 423156946 1.630000e-30 145


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 TraesCS5A01G090800 chr5A 123708703 123714316 5613 True 10368.00 10368 100.0000 1 5614 1 chr5A.!!$R1 5613
1 TraesCS5A01G090800 chr5D 116170785 116176371 5586 True 4384.50 8093 92.0045 1 5614 2 chr5D.!!$R1 5613
2 TraesCS5A01G090800 chr5B 128214959 128220378 5419 True 2027.75 6992 89.8565 1 5614 4 chr5B.!!$R1 5613

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
366 377 0.036388 GTTCCTCCTTGACGATGGCA 60.036 55.0 0.00 0.00 0.00 4.92 F
544 555 0.107459 GCTGCTTGGGACCCTTCTAG 60.107 60.0 13.00 6.57 0.00 2.43 F
860 871 0.179000 CCACCTTCCTTCTCCCATCG 59.821 60.0 0.00 0.00 0.00 3.84 F
2118 2164 0.179076 CGCTGTCATCATAGGCACCA 60.179 55.0 0.00 0.00 0.00 4.17 F
2838 2892 1.347320 GGAATGGACGACGTCTTGTC 58.653 55.0 25.87 18.72 44.53 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2157 0.178990 GGAGAACAACCTTGGTGCCT 60.179 55.000 0.00 0.0 0.00 4.75 R
2232 2279 0.822164 ACGAAAGCGGTAGGTATGCT 59.178 50.000 0.00 0.0 43.17 3.79 R
2674 2728 0.462759 GGCCTCACATGGACAGCTAC 60.463 60.000 0.00 0.0 34.56 3.58 R
3295 3356 3.214328 AGGCCGGCTATAGTTCAATTTG 58.786 45.455 28.56 0.0 0.00 2.32 R
4783 4848 0.388907 CAAGGACGCCAGCCAAATTG 60.389 55.000 0.00 0.0 0.00 2.32 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
47 51 4.079443 CCCAATTCCAATGGTTAGGAGGTA 60.079 45.833 0.00 0.00 36.14 3.08
59 63 4.409247 GGTTAGGAGGTACTTCATCACCAT 59.591 45.833 15.66 0.00 41.55 3.55
71 75 3.066380 TCATCACCATTGACACTCGTTG 58.934 45.455 0.00 0.00 33.38 4.10
72 76 2.613026 TCACCATTGACACTCGTTGT 57.387 45.000 0.00 0.00 43.10 3.32
99 110 1.078759 CGAGCTTCGACGCCTTTGAT 61.079 55.000 10.66 0.00 43.74 2.57
106 117 4.607955 CTTCGACGCCTTTGATATCACTA 58.392 43.478 4.48 0.00 0.00 2.74
125 136 1.430369 AAGGGGAGTTGCAAGAGGCT 61.430 55.000 0.00 0.00 45.15 4.58
126 137 0.547712 AGGGGAGTTGCAAGAGGCTA 60.548 55.000 0.00 0.00 45.15 3.93
169 180 1.980765 TCACTGGTGATTCTTCTGGCT 59.019 47.619 0.00 0.00 34.14 4.75
276 287 2.351738 GGGGCGATTCAACTTTGTCTTG 60.352 50.000 0.00 0.00 0.00 3.02
294 305 7.718334 TGTCTTGGAGTACATATCTTCTTCA 57.282 36.000 0.00 0.00 0.00 3.02
305 316 7.673641 ACATATCTTCTTCATCTGGTTCTCT 57.326 36.000 0.00 0.00 0.00 3.10
324 335 1.227853 GGTGTTGGAGAAGCGTGGT 60.228 57.895 0.00 0.00 0.00 4.16
335 346 3.343421 GCGTGGTGGTGGTTCGAC 61.343 66.667 0.00 0.00 0.00 4.20
355 366 1.072930 ACCCCAAGTGGTTCCTCCT 60.073 57.895 0.00 0.00 33.91 3.69
356 367 0.701310 ACCCCAAGTGGTTCCTCCTT 60.701 55.000 0.00 0.00 33.91 3.36
366 377 0.036388 GTTCCTCCTTGACGATGGCA 60.036 55.000 0.00 0.00 0.00 4.92
368 379 0.614697 TCCTCCTTGACGATGGCAGA 60.615 55.000 0.00 0.00 0.00 4.26
391 402 8.266392 AGAAGCAAATCTGAATAGAAGTTGAG 57.734 34.615 0.00 0.00 35.56 3.02
403 414 8.717717 TGAATAGAAGTTGAGATTATGACCCAT 58.282 33.333 0.00 0.00 0.00 4.00
420 431 7.872113 TGACCCATTTGCAATTTTACTTTTT 57.128 28.000 0.00 0.00 0.00 1.94
430 441 6.183360 TGCAATTTTACTTTTTGGTCTACGGT 60.183 34.615 0.00 0.00 0.00 4.83
431 442 6.698329 GCAATTTTACTTTTTGGTCTACGGTT 59.302 34.615 0.00 0.00 0.00 4.44
432 443 7.306341 GCAATTTTACTTTTTGGTCTACGGTTG 60.306 37.037 0.00 0.00 0.00 3.77
455 466 6.372104 TGTCCATGCATATTTTAGGGATTGA 58.628 36.000 0.00 0.00 0.00 2.57
524 535 2.912967 CGCTTTGACTTAATGCAGCTTG 59.087 45.455 0.00 0.00 38.87 4.01
525 536 3.248266 GCTTTGACTTAATGCAGCTTGG 58.752 45.455 0.00 0.00 38.80 3.61
526 537 3.248266 CTTTGACTTAATGCAGCTTGGC 58.752 45.455 0.00 0.00 0.00 4.52
527 538 2.205022 TGACTTAATGCAGCTTGGCT 57.795 45.000 0.00 0.00 40.77 4.75
542 553 2.759795 GCTGCTTGGGACCCTTCT 59.240 61.111 13.00 0.00 0.00 2.85
544 555 0.107459 GCTGCTTGGGACCCTTCTAG 60.107 60.000 13.00 6.57 0.00 2.43
550 561 3.676093 CTTGGGACCCTTCTAGTTGTTC 58.324 50.000 13.00 0.00 0.00 3.18
552 563 3.050089 TGGGACCCTTCTAGTTGTTCAA 58.950 45.455 13.00 0.00 0.00 2.69
582 593 9.206690 TGGAAAAATAAATGTAAGCCATATCCA 57.793 29.630 0.00 0.00 31.97 3.41
591 602 9.705103 AAATGTAAGCCATATCCATATAGCATT 57.295 29.630 0.72 0.00 31.15 3.56
592 603 8.687292 ATGTAAGCCATATCCATATAGCATTG 57.313 34.615 0.72 0.00 31.15 2.82
593 604 7.860584 TGTAAGCCATATCCATATAGCATTGA 58.139 34.615 0.72 0.00 31.15 2.57
594 605 8.496916 TGTAAGCCATATCCATATAGCATTGAT 58.503 33.333 0.72 0.00 31.15 2.57
596 607 8.915057 AAGCCATATCCATATAGCATTGATAC 57.085 34.615 0.72 0.00 31.15 2.24
597 608 8.272659 AGCCATATCCATATAGCATTGATACT 57.727 34.615 0.72 0.00 31.15 2.12
598 609 8.721479 AGCCATATCCATATAGCATTGATACTT 58.279 33.333 0.72 0.00 31.15 2.24
628 639 3.756933 ACCCGTGTTAGTTTTAGCTCA 57.243 42.857 0.00 0.00 0.00 4.26
636 647 6.736853 CGTGTTAGTTTTAGCTCAAGCATTAC 59.263 38.462 4.59 0.00 45.16 1.89
640 651 4.755123 AGTTTTAGCTCAAGCATTACGTGT 59.245 37.500 0.00 0.00 45.16 4.49
643 654 2.069273 AGCTCAAGCATTACGTGTCAC 58.931 47.619 0.00 0.00 45.16 3.67
651 662 3.743911 AGCATTACGTGTCACGATTTTGA 59.256 39.130 30.95 6.51 46.05 2.69
666 677 5.699458 ACGATTTTGACTCACCTACGATTTT 59.301 36.000 0.00 0.00 0.00 1.82
714 725 2.670148 GGCAGGACGATCCCTTGGT 61.670 63.158 0.00 0.00 37.19 3.67
718 729 1.745489 GGACGATCCCTTGGTGCAC 60.745 63.158 8.80 8.80 0.00 4.57
719 730 1.296715 GACGATCCCTTGGTGCACT 59.703 57.895 17.98 0.00 0.00 4.40
764 775 3.299340 TCCGTCTTTCTTTCTCCTTCG 57.701 47.619 0.00 0.00 0.00 3.79
766 777 2.987821 CCGTCTTTCTTTCTCCTTCGAC 59.012 50.000 0.00 0.00 0.00 4.20
770 781 0.981943 TTCTTTCTCCTTCGACCCCC 59.018 55.000 0.00 0.00 0.00 5.40
798 809 4.019681 TCCCGCCATCTTCTTCTTTCTTTA 60.020 41.667 0.00 0.00 0.00 1.85
860 871 0.179000 CCACCTTCCTTCTCCCATCG 59.821 60.000 0.00 0.00 0.00 3.84
861 872 0.905357 CACCTTCCTTCTCCCATCGT 59.095 55.000 0.00 0.00 0.00 3.73
864 875 3.055385 CACCTTCCTTCTCCCATCGTTTA 60.055 47.826 0.00 0.00 0.00 2.01
889 900 0.313043 GACCTTGTCGTCGACCTCAA 59.687 55.000 22.05 13.84 0.00 3.02
891 902 0.314302 CCTTGTCGTCGACCTCAACT 59.686 55.000 22.05 0.00 0.00 3.16
920 931 2.973899 CCACTAGTGGCAGCGAGT 59.026 61.111 28.48 0.00 44.73 4.18
940 951 1.226575 CGAGCGCCGACACTAATCA 60.227 57.895 2.29 0.00 41.76 2.57
943 954 0.249489 AGCGCCGACACTAATCATCC 60.249 55.000 2.29 0.00 0.00 3.51
971 982 3.099905 TCGAGAGAGAATGTGAACCCAT 58.900 45.455 0.00 0.00 34.84 4.00
984 995 2.897207 CCCATTAGGTCGTCGGCA 59.103 61.111 0.00 0.00 0.00 5.69
992 1003 1.375013 GGTCGTCGGCAAGCCTTTA 60.375 57.895 9.73 0.00 0.00 1.85
996 1007 1.948145 TCGTCGGCAAGCCTTTAAAAA 59.052 42.857 9.73 0.00 0.00 1.94
1045 1089 3.376078 GCCACTGCCACCACCATG 61.376 66.667 0.00 0.00 0.00 3.66
1054 1098 1.742880 CACCACCATGTGAGCTCGG 60.743 63.158 9.64 6.53 38.55 4.63
1057 1101 2.046892 ACCATGTGAGCTCGGTGC 60.047 61.111 9.64 0.00 43.29 5.01
1075 1119 1.590610 GCTCACTCGTCAGCCTCTCA 61.591 60.000 0.00 0.00 0.00 3.27
1087 1131 4.630940 GTCAGCCTCTCATCTTCTTTCTTG 59.369 45.833 0.00 0.00 0.00 3.02
1112 1156 7.558444 TGTAAGATTTACTTCTCCCTCTCTCTC 59.442 40.741 1.24 0.00 39.72 3.20
1182 1227 5.129485 TCTTTCATGCCTAAAGTCTAGAGGG 59.871 44.000 0.00 0.00 35.79 4.30
1295 1340 7.450014 TGCTTCTTCTTCTTCTTCTTCTCTCTA 59.550 37.037 0.00 0.00 0.00 2.43
1296 1341 8.470002 GCTTCTTCTTCTTCTTCTTCTCTCTAT 58.530 37.037 0.00 0.00 0.00 1.98
1341 1386 0.967887 CCTCTCTCAGTCCGAAGCCA 60.968 60.000 0.00 0.00 0.00 4.75
1348 1393 2.932614 CTCAGTCCGAAGCCAATTACTG 59.067 50.000 0.00 0.00 36.52 2.74
1400 1445 2.217510 TCCTGGAGCTACGTCTTCTT 57.782 50.000 0.00 0.00 0.00 2.52
1470 1515 2.187946 GGGACACTCATGGCGAGG 59.812 66.667 0.00 0.00 46.98 4.63
1576 1621 2.030274 CCGGATTGGTTCAGTTTGGTTC 60.030 50.000 0.00 0.00 0.00 3.62
1643 1688 3.322466 CCGCTTGGTGTCCTCCCT 61.322 66.667 0.00 0.00 0.00 4.20
1732 1778 5.831525 TGATTCCCTGATTGATCTGGAATTG 59.168 40.000 19.78 6.98 45.58 2.32
1751 1797 4.427096 TTGTTTTGAAGCTTCGTGTTGA 57.573 36.364 21.11 0.00 0.00 3.18
2084 2130 2.930562 ACCAGCCACCTCACCCTC 60.931 66.667 0.00 0.00 0.00 4.30
2111 2157 2.362397 GGAGAAGGACGCTGTCATCATA 59.638 50.000 10.14 0.00 33.68 2.15
2118 2164 0.179076 CGCTGTCATCATAGGCACCA 60.179 55.000 0.00 0.00 0.00 4.17
2135 2181 2.554032 CACCAAGGTTGTTCTCCACATC 59.446 50.000 0.00 0.00 34.43 3.06
2139 2185 4.504864 CCAAGGTTGTTCTCCACATCAGTA 60.505 45.833 0.00 0.00 34.43 2.74
2144 2190 6.042781 AGGTTGTTCTCCACATCAGTAACTTA 59.957 38.462 0.00 0.00 34.43 2.24
2159 2206 6.810182 TCAGTAACTTATAAACGCCTTCTCAC 59.190 38.462 0.00 0.00 0.00 3.51
2220 2267 5.974156 TGGATTGGATGTTCTCCTATTCA 57.026 39.130 0.00 0.00 45.21 2.57
2221 2268 6.520021 TGGATTGGATGTTCTCCTATTCAT 57.480 37.500 0.00 0.00 45.21 2.57
2226 2273 6.119240 TGGATGTTCTCCTATTCATGGATC 57.881 41.667 0.00 0.00 45.21 3.36
2232 2279 6.493458 TGTTCTCCTATTCATGGATCGATGTA 59.507 38.462 16.21 8.38 32.56 2.29
2241 2288 5.261216 TCATGGATCGATGTAGCATACCTA 58.739 41.667 16.21 0.00 42.12 3.08
2535 2587 3.129852 TCATTATTTTGGTCTTGCGCG 57.870 42.857 0.00 0.00 0.00 6.86
2544 2596 2.536365 TGGTCTTGCGCGTATTTAGAG 58.464 47.619 8.43 0.00 0.00 2.43
2595 2648 9.120422 GGGTTTCCGCGTATATAAAATTTTATG 57.880 33.333 26.61 14.74 35.20 1.90
2674 2728 2.173669 GGGCATCGGATGTGACACG 61.174 63.158 18.54 0.00 0.00 4.49
2838 2892 1.347320 GGAATGGACGACGTCTTGTC 58.653 55.000 25.87 18.72 44.53 3.18
3184 3244 8.299570 AGACATCAGAATTTTATGTGGTTTGTC 58.700 33.333 6.12 0.00 34.09 3.18
3295 3356 3.049912 GTGGAATTGGTTTCGCTCAAAC 58.950 45.455 0.57 0.57 43.43 2.93
3594 3658 4.393062 GCTCTTCATGTGCTGCTACTTTAA 59.607 41.667 0.00 0.00 32.89 1.52
3604 3668 4.095782 TGCTGCTACTTTAATAAAAGCCCG 59.904 41.667 0.00 1.26 45.06 6.13
4453 4517 6.060136 TCTGCCTCTCCAATATCAATTTCAG 58.940 40.000 0.00 0.00 0.00 3.02
4517 4581 4.023980 ACATTTCTGGATACTCCGAGTCA 58.976 43.478 3.74 0.00 40.17 3.41
4526 4590 4.828387 GGATACTCCGAGTCAGTATTTCCT 59.172 45.833 3.74 0.00 37.22 3.36
4667 4731 7.619965 TCATGTTTCTGTCCATGTACAATCTA 58.380 34.615 0.00 0.00 39.53 1.98
4753 4818 3.348647 TCAAAGAATCATCGGGCTTCA 57.651 42.857 0.00 0.00 0.00 3.02
4783 4848 5.586243 TCAGCTTTGAGGCTCATAATACAAC 59.414 40.000 19.50 3.90 41.00 3.32
5192 5258 4.202151 TGTCGCAAGCTCATACTATCATGT 60.202 41.667 0.00 0.00 37.18 3.21
5323 5390 2.202623 CCTGTACTCGTCTGGCGC 60.203 66.667 0.00 0.00 41.07 6.53
5362 5429 3.604667 CAACCTGCCGCCTTTGCA 61.605 61.111 0.00 0.00 37.32 4.08
5472 5539 0.948678 GCAGTGGCCGTTTTCACTTA 59.051 50.000 0.00 0.00 41.71 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.312890 ACCATTGGAATTGGGTTCAACA 58.687 40.909 10.37 0.00 38.64 3.33
22 23 4.352893 CTCCTAACCATTGGAATTGGGTT 58.647 43.478 10.37 0.00 45.15 4.11
23 24 3.309848 CCTCCTAACCATTGGAATTGGGT 60.310 47.826 10.37 0.00 34.43 4.51
47 51 3.244215 ACGAGTGTCAATGGTGATGAAGT 60.244 43.478 0.00 0.00 35.80 3.01
59 63 3.748530 TCGTGCCACAACGAGTGTCAA 62.749 52.381 10.80 0.00 46.99 3.18
71 75 3.470567 CGAAGCTCGTCGTGCCAC 61.471 66.667 15.17 8.97 36.26 5.01
72 76 3.666253 TCGAAGCTCGTCGTGCCA 61.666 61.111 15.17 0.00 41.35 4.92
73 77 3.173240 GTCGAAGCTCGTCGTGCC 61.173 66.667 15.17 1.00 41.35 5.01
81 92 1.922570 TATCAAAGGCGTCGAAGCTC 58.077 50.000 22.38 12.70 37.29 4.09
99 110 4.101114 TCTTGCAACTCCCCTTAGTGATA 58.899 43.478 0.00 0.00 0.00 2.15
106 117 1.075659 GCCTCTTGCAACTCCCCTT 59.924 57.895 0.00 0.00 40.77 3.95
125 136 0.619255 TTGAAGAGGGGGCATCGGTA 60.619 55.000 0.00 0.00 0.00 4.02
126 137 1.497309 TTTGAAGAGGGGGCATCGGT 61.497 55.000 0.00 0.00 0.00 4.69
169 180 1.558167 TTCCATTAGACCGCCCTGCA 61.558 55.000 0.00 0.00 0.00 4.41
179 190 6.707440 TTGACAAGCAAAAGTTCCATTAGA 57.293 33.333 0.00 0.00 32.46 2.10
217 228 2.240921 GGCCAGGAAGAAGAAGAGGAAT 59.759 50.000 0.00 0.00 0.00 3.01
276 287 7.296628 ACCAGATGAAGAAGATATGTACTCC 57.703 40.000 0.00 0.00 0.00 3.85
294 305 2.304180 CTCCAACACCAGAGAACCAGAT 59.696 50.000 0.00 0.00 31.43 2.90
305 316 1.227823 CCACGCTTCTCCAACACCA 60.228 57.895 0.00 0.00 0.00 4.17
324 335 3.618750 GGGGTCGTCGAACCACCA 61.619 66.667 29.68 0.00 42.10 4.17
355 366 1.603456 TTTGCTTCTGCCATCGTCAA 58.397 45.000 0.00 0.00 38.71 3.18
356 367 1.739466 GATTTGCTTCTGCCATCGTCA 59.261 47.619 0.00 0.00 38.71 4.35
366 377 8.099537 TCTCAACTTCTATTCAGATTTGCTTCT 58.900 33.333 0.00 0.00 29.85 2.85
368 379 8.804912 ATCTCAACTTCTATTCAGATTTGCTT 57.195 30.769 0.00 0.00 29.85 3.91
380 391 9.347240 CAAATGGGTCATAATCTCAACTTCTAT 57.653 33.333 0.00 0.00 0.00 1.98
391 402 8.947055 AGTAAAATTGCAAATGGGTCATAATC 57.053 30.769 1.71 0.00 0.00 1.75
396 407 7.201767 CCAAAAAGTAAAATTGCAAATGGGTCA 60.202 33.333 1.71 0.00 0.00 4.02
403 414 7.222999 CCGTAGACCAAAAAGTAAAATTGCAAA 59.777 33.333 1.71 0.00 0.00 3.68
420 431 0.036765 GCATGGACAACCGTAGACCA 60.037 55.000 0.00 0.00 39.42 4.02
430 441 6.838090 TCAATCCCTAAAATATGCATGGACAA 59.162 34.615 10.16 0.00 0.00 3.18
431 442 6.372104 TCAATCCCTAAAATATGCATGGACA 58.628 36.000 10.16 0.00 0.00 4.02
432 443 6.491403 ACTCAATCCCTAAAATATGCATGGAC 59.509 38.462 10.16 0.00 0.00 4.02
455 466 8.403236 GGACTCGGCAAATTTAATATTACAACT 58.597 33.333 0.00 0.00 0.00 3.16
464 475 8.062065 TCATAAAAGGACTCGGCAAATTTAAT 57.938 30.769 0.00 0.00 0.00 1.40
469 480 4.843728 TCTCATAAAAGGACTCGGCAAAT 58.156 39.130 0.00 0.00 0.00 2.32
473 484 3.798202 ACATCTCATAAAAGGACTCGGC 58.202 45.455 0.00 0.00 0.00 5.54
486 497 3.533606 AGCGCTGAAAGTACATCTCAT 57.466 42.857 10.39 0.00 35.30 2.90
524 535 1.562672 TAGAAGGGTCCCAAGCAGCC 61.563 60.000 11.55 0.00 0.00 4.85
525 536 0.107459 CTAGAAGGGTCCCAAGCAGC 60.107 60.000 11.55 0.00 0.00 5.25
526 537 1.280457 ACTAGAAGGGTCCCAAGCAG 58.720 55.000 11.55 4.41 0.00 4.24
527 538 1.351017 CAACTAGAAGGGTCCCAAGCA 59.649 52.381 11.55 0.00 0.00 3.91
528 539 1.351350 ACAACTAGAAGGGTCCCAAGC 59.649 52.381 11.55 0.00 0.00 4.01
529 540 3.072476 TGAACAACTAGAAGGGTCCCAAG 59.928 47.826 11.55 4.40 0.00 3.61
566 577 9.128404 CAATGCTATATGGATATGGCTTACATT 57.872 33.333 14.02 5.09 44.54 2.71
567 578 8.496916 TCAATGCTATATGGATATGGCTTACAT 58.503 33.333 14.02 0.06 44.54 2.29
569 580 8.915057 ATCAATGCTATATGGATATGGCTTAC 57.085 34.615 14.02 0.00 44.54 2.34
572 583 8.272659 AGTATCAATGCTATATGGATATGGCT 57.727 34.615 14.02 0.00 44.54 4.75
573 584 8.915057 AAGTATCAATGCTATATGGATATGGC 57.085 34.615 7.79 7.79 44.51 4.40
586 597 8.188139 CGGGTTTATTGTTTAAGTATCAATGCT 58.812 33.333 0.00 0.00 34.35 3.79
587 598 7.971722 ACGGGTTTATTGTTTAAGTATCAATGC 59.028 33.333 0.00 0.00 34.35 3.56
588 599 9.284594 CACGGGTTTATTGTTTAAGTATCAATG 57.715 33.333 0.00 0.00 34.35 2.82
589 600 9.016438 ACACGGGTTTATTGTTTAAGTATCAAT 57.984 29.630 0.00 0.00 36.12 2.57
590 601 8.393671 ACACGGGTTTATTGTTTAAGTATCAA 57.606 30.769 0.00 0.00 0.00 2.57
591 602 7.982761 ACACGGGTTTATTGTTTAAGTATCA 57.017 32.000 0.00 0.00 0.00 2.15
592 603 9.977762 CTAACACGGGTTTATTGTTTAAGTATC 57.022 33.333 9.10 0.00 38.45 2.24
593 604 9.506018 ACTAACACGGGTTTATTGTTTAAGTAT 57.494 29.630 9.10 0.00 38.45 2.12
594 605 8.900983 ACTAACACGGGTTTATTGTTTAAGTA 57.099 30.769 9.10 0.00 38.45 2.24
595 606 7.806409 ACTAACACGGGTTTATTGTTTAAGT 57.194 32.000 9.10 0.00 38.45 2.24
596 607 9.518906 AAAACTAACACGGGTTTATTGTTTAAG 57.481 29.630 9.10 0.00 38.45 1.85
599 610 7.648908 GCTAAAACTAACACGGGTTTATTGTTT 59.351 33.333 9.10 12.32 38.45 2.83
600 611 7.013559 AGCTAAAACTAACACGGGTTTATTGTT 59.986 33.333 9.10 6.72 38.45 2.83
601 612 6.487668 AGCTAAAACTAACACGGGTTTATTGT 59.512 34.615 9.10 1.00 38.45 2.71
602 613 6.905578 AGCTAAAACTAACACGGGTTTATTG 58.094 36.000 9.10 0.00 38.45 1.90
603 614 6.711645 TGAGCTAAAACTAACACGGGTTTATT 59.288 34.615 9.10 0.00 38.45 1.40
604 615 6.232692 TGAGCTAAAACTAACACGGGTTTAT 58.767 36.000 9.10 0.00 38.45 1.40
605 616 5.609423 TGAGCTAAAACTAACACGGGTTTA 58.391 37.500 9.10 0.00 38.45 2.01
606 617 4.453751 TGAGCTAAAACTAACACGGGTTT 58.546 39.130 9.10 0.00 38.45 3.27
607 618 4.075963 TGAGCTAAAACTAACACGGGTT 57.924 40.909 8.72 8.72 41.06 4.11
608 619 3.756933 TGAGCTAAAACTAACACGGGT 57.243 42.857 0.00 0.00 0.00 5.28
609 620 3.120304 GCTTGAGCTAAAACTAACACGGG 60.120 47.826 0.00 0.00 38.21 5.28
610 621 3.496884 TGCTTGAGCTAAAACTAACACGG 59.503 43.478 4.44 0.00 42.66 4.94
611 622 4.725556 TGCTTGAGCTAAAACTAACACG 57.274 40.909 4.44 0.00 42.66 4.49
628 639 4.212425 TCAAAATCGTGACACGTAATGCTT 59.788 37.500 26.01 10.34 43.14 3.91
640 651 3.253921 TCGTAGGTGAGTCAAAATCGTGA 59.746 43.478 0.00 0.00 0.00 4.35
643 654 5.779806 AAATCGTAGGTGAGTCAAAATCG 57.220 39.130 0.00 0.00 0.00 3.34
689 700 2.434884 ATCGTCCTGCCGCAACAG 60.435 61.111 0.00 0.00 37.42 3.16
700 711 1.745489 GTGCACCAAGGGATCGTCC 60.745 63.158 5.22 0.00 35.23 4.79
770 781 1.745653 GAAGAAGATGGCGGGAAAAGG 59.254 52.381 0.00 0.00 0.00 3.11
771 782 2.716217 AGAAGAAGATGGCGGGAAAAG 58.284 47.619 0.00 0.00 0.00 2.27
798 809 3.841255 AGAGAGTCGGGAAAGAAAGGAAT 59.159 43.478 0.00 0.00 0.00 3.01
889 900 3.357203 ACTAGTGGTGACGATCATCAGT 58.643 45.455 11.57 11.57 43.16 3.41
929 940 2.363680 AGCTCAGGGATGATTAGTGTCG 59.636 50.000 0.00 0.00 0.00 4.35
936 947 1.962807 CTCTCGAGCTCAGGGATGATT 59.037 52.381 15.40 0.00 0.00 2.57
940 951 0.843309 TCTCTCTCGAGCTCAGGGAT 59.157 55.000 15.40 0.00 37.19 3.85
943 954 2.023673 ACATTCTCTCTCGAGCTCAGG 58.976 52.381 15.40 5.54 37.19 3.86
971 982 1.823169 AAGGCTTGCCGACGACCTAA 61.823 55.000 0.00 0.00 0.00 2.69
996 1007 1.746615 AGCATTCGGCGACATGCTT 60.747 52.632 33.37 24.15 46.94 3.91
1006 1017 3.869272 GCAGTGGCGAGCATTCGG 61.869 66.667 0.00 0.00 46.76 4.30
1009 1020 3.058160 GTGGCAGTGGCGAGCATT 61.058 61.111 12.58 0.00 42.47 3.56
1034 1078 2.034687 AGCTCACATGGTGGTGGC 59.965 61.111 0.00 0.00 39.27 5.01
1054 1098 1.445238 GAGGCTGACGAGTGAGCAC 60.445 63.158 15.83 6.26 41.71 4.40
1057 1101 1.065401 GATGAGAGGCTGACGAGTGAG 59.935 57.143 0.00 0.00 0.00 3.51
1063 1107 2.957491 AAGAAGATGAGAGGCTGACG 57.043 50.000 0.00 0.00 0.00 4.35
1087 1131 7.778382 AGAGAGAGAGGGAGAAGTAAATCTTAC 59.222 40.741 0.00 0.00 36.40 2.34
1097 1141 4.510167 AGAAGAGAGAGAGAGGGAGAAG 57.490 50.000 0.00 0.00 0.00 2.85
1099 1143 4.631234 ACTAGAAGAGAGAGAGAGGGAGA 58.369 47.826 0.00 0.00 0.00 3.71
1112 1156 3.280295 TCTACGCTTGGGACTAGAAGAG 58.720 50.000 0.00 0.00 0.00 2.85
1182 1227 7.605410 TGGCTTGTACTAGTATTTGTTTAGC 57.395 36.000 5.75 7.37 0.00 3.09
1263 1308 2.149578 GAAGAAGAAGAAGCAGCAGCA 58.850 47.619 3.17 0.00 45.49 4.41
1264 1309 2.425539 AGAAGAAGAAGAAGCAGCAGC 58.574 47.619 0.00 0.00 42.56 5.25
1265 1310 4.317488 AGAAGAAGAAGAAGAAGCAGCAG 58.683 43.478 0.00 0.00 0.00 4.24
1266 1311 4.348863 AGAAGAAGAAGAAGAAGCAGCA 57.651 40.909 0.00 0.00 0.00 4.41
1267 1312 4.996758 AGAAGAAGAAGAAGAAGAAGCAGC 59.003 41.667 0.00 0.00 0.00 5.25
1268 1313 6.458210 AGAGAAGAAGAAGAAGAAGAAGCAG 58.542 40.000 0.00 0.00 0.00 4.24
1269 1314 6.267471 AGAGAGAAGAAGAAGAAGAAGAAGCA 59.733 38.462 0.00 0.00 0.00 3.91
1270 1315 6.691508 AGAGAGAAGAAGAAGAAGAAGAAGC 58.308 40.000 0.00 0.00 0.00 3.86
1272 1317 8.966868 GGATAGAGAGAAGAAGAAGAAGAAGAA 58.033 37.037 0.00 0.00 0.00 2.52
1273 1318 8.112822 TGGATAGAGAGAAGAAGAAGAAGAAGA 58.887 37.037 0.00 0.00 0.00 2.87
1274 1319 8.190784 GTGGATAGAGAGAAGAAGAAGAAGAAG 58.809 40.741 0.00 0.00 0.00 2.85
1295 1340 4.760220 AAGGGGGAGGCGGTGGAT 62.760 66.667 0.00 0.00 0.00 3.41
1315 1360 0.750182 GGACTGAGAGAGGAGGACGG 60.750 65.000 0.00 0.00 0.00 4.79
1341 1386 3.181503 CGAATGCAAGCTGCTCAGTAATT 60.182 43.478 1.00 4.08 45.31 1.40
1348 1393 0.801251 AAGACGAATGCAAGCTGCTC 59.199 50.000 1.00 0.00 45.31 4.26
1359 1404 0.457851 CGCAGGAGAGGAAGACGAAT 59.542 55.000 0.00 0.00 0.00 3.34
1436 1481 2.034066 CCCTTTGCGGCAGAAGGA 59.966 61.111 29.30 6.40 44.15 3.36
1470 1515 4.439123 GCGGTGATAAACGTACTTACTAGC 59.561 45.833 0.00 0.00 0.00 3.42
1552 1597 2.446435 CAAACTGAACCAATCCGGGAT 58.554 47.619 2.97 2.97 40.22 3.85
1643 1688 5.656859 TCTCAACAGGAGGATCTCGAATTTA 59.343 40.000 0.00 0.00 44.19 1.40
1732 1778 5.514914 TGAATTCAACACGAAGCTTCAAAAC 59.485 36.000 25.47 9.93 36.95 2.43
1751 1797 2.241160 TGCACTGCAACTCCATGAATT 58.759 42.857 0.00 0.00 34.76 2.17
2111 2157 0.178990 GGAGAACAACCTTGGTGCCT 60.179 55.000 0.00 0.00 0.00 4.75
2118 2164 3.864789 ACTGATGTGGAGAACAACCTT 57.135 42.857 0.00 0.00 43.61 3.50
2135 2181 6.812160 AGTGAGAAGGCGTTTATAAGTTACTG 59.188 38.462 0.00 0.00 0.00 2.74
2139 2185 8.788325 ATAAAGTGAGAAGGCGTTTATAAGTT 57.212 30.769 0.00 0.00 0.00 2.66
2144 2190 5.294552 GCTGATAAAGTGAGAAGGCGTTTAT 59.705 40.000 0.00 0.00 0.00 1.40
2159 2206 4.820173 TGCAGAATCCTCATGCTGATAAAG 59.180 41.667 0.00 0.00 37.88 1.85
2220 2267 4.402793 GGTAGGTATGCTACATCGATCCAT 59.597 45.833 0.00 0.00 0.00 3.41
2221 2268 3.762288 GGTAGGTATGCTACATCGATCCA 59.238 47.826 0.00 0.00 0.00 3.41
2226 2273 1.540267 AGCGGTAGGTATGCTACATCG 59.460 52.381 0.00 0.00 37.15 3.84
2232 2279 0.822164 ACGAAAGCGGTAGGTATGCT 59.178 50.000 0.00 0.00 43.17 3.79
2241 2288 1.145377 AGTGTGGAACGAAAGCGGT 59.855 52.632 0.00 0.00 42.39 5.68
2475 2527 4.210537 ACGTCTTTCAAGGTAAACATCACG 59.789 41.667 0.00 0.00 0.00 4.35
2544 2596 9.622004 CCATGCATAAGAAAATTCATAGTGATC 57.378 33.333 0.00 0.00 0.00 2.92
2565 2617 1.519408 ATATACGCGGAAACCCATGC 58.481 50.000 12.47 0.00 0.00 4.06
2595 2648 3.364964 CGAATATTGGGCCGCTAATGTTC 60.365 47.826 17.68 17.68 33.64 3.18
2674 2728 0.462759 GGCCTCACATGGACAGCTAC 60.463 60.000 0.00 0.00 34.56 3.58
3157 3217 9.295825 ACAAACCACATAAAATTCTGATGTCTA 57.704 29.630 0.00 0.00 31.44 2.59
3295 3356 3.214328 AGGCCGGCTATAGTTCAATTTG 58.786 45.455 28.56 0.00 0.00 2.32
3696 3760 7.221838 GCAACTCAAATTAAGTAGCAAAACACA 59.778 33.333 0.00 0.00 0.00 3.72
4058 4122 7.287696 TGCAGATCCACTCTACTAATGTGAATA 59.712 37.037 0.00 0.00 33.95 1.75
4412 4476 4.166725 AGGCAGATATTGGTGAAAGGATCA 59.833 41.667 0.00 0.00 35.05 2.92
4475 4539 1.743252 GGAGCAAGACCAAGAGGCG 60.743 63.158 0.00 0.00 39.06 5.52
4517 4581 3.619979 CGGAACAAGCCTCAGGAAATACT 60.620 47.826 0.00 0.00 0.00 2.12
4526 4590 1.671742 GAGGTCGGAACAAGCCTCA 59.328 57.895 6.71 0.00 45.00 3.86
4753 4818 2.568956 TGAGCCTCAAAGCTGACTGTAT 59.431 45.455 0.00 0.00 45.15 2.29
4783 4848 0.388907 CAAGGACGCCAGCCAAATTG 60.389 55.000 0.00 0.00 0.00 2.32
5226 5293 2.569853 TCCGGTGATTTGGTACTGATGT 59.430 45.455 0.00 0.00 0.00 3.06
5323 5390 2.967397 CACATGCTGCCCAAGTGG 59.033 61.111 0.00 0.00 38.99 4.00
5362 5429 2.812011 GTTCCCAGCGTGTACAATCTTT 59.188 45.455 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.