Multiple sequence alignment - TraesCS7B01G073700

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 TraesCS7B01G073700 chr7B 100.000 3356 0 0 1 3356 83023238 83026593 0.000000e+00 6198.0
1 TraesCS7B01G073700 chr7B 82.731 249 40 2 337 584 494497806 494497560 5.640000e-53 219.0
2 TraesCS7B01G073700 chr7D 92.011 2591 135 30 586 3155 121931061 121933600 0.000000e+00 3572.0
3 TraesCS7B01G073700 chr7A 93.340 1997 80 18 586 2556 125478623 125480592 0.000000e+00 2902.0
4 TraesCS7B01G073700 chr7A 88.043 736 75 8 2628 3356 125483058 125483787 0.000000e+00 859.0
5 TraesCS7B01G073700 chr7A 86.458 96 10 1 1261 1353 19547377 19547282 5.920000e-18 102.0
6 TraesCS7B01G073700 chr7A 89.024 82 8 1 520 600 508091727 508091646 2.130000e-17 100.0
7 TraesCS7B01G073700 chr7A 88.136 59 6 1 535 592 282942556 282942614 6.010000e-08 69.4
8 TraesCS7B01G073700 chr4A 87.963 432 29 9 174 582 209307936 209307505 3.890000e-134 488.0
9 TraesCS7B01G073700 chr4A 91.803 183 10 1 1 178 209308342 209308160 2.000000e-62 250.0
10 TraesCS7B01G073700 chr6B 87.037 432 33 9 174 582 673541202 673541633 1.820000e-127 466.0
11 TraesCS7B01G073700 chr6B 92.778 180 8 1 1 175 673540796 673540975 4.300000e-64 255.0
12 TraesCS7B01G073700 chr3A 87.901 405 26 9 174 555 701237631 701238035 3.950000e-124 455.0
13 TraesCS7B01G073700 chr3A 87.724 391 25 8 174 541 572651879 572651489 5.140000e-118 435.0
14 TraesCS7B01G073700 chr3A 96.753 154 5 0 22 175 701237251 701237404 1.190000e-64 257.0
15 TraesCS7B01G073700 chr3A 91.803 183 10 1 1 178 572652284 572652102 2.000000e-62 250.0
16 TraesCS7B01G073700 chr4B 86.765 408 31 9 174 558 142850436 142850843 1.850000e-117 433.0
17 TraesCS7B01G073700 chr4B 92.778 180 8 1 1 175 142850029 142850208 4.300000e-64 255.0
18 TraesCS7B01G073700 chr4B 92.350 183 9 1 1 178 420964789 420964607 4.300000e-64 255.0
19 TraesCS7B01G073700 chr4B 94.479 163 9 0 174 336 420964383 420964221 5.560000e-63 252.0
20 TraesCS7B01G073700 chr4B 92.638 163 12 0 174 336 187553740 187553902 5.600000e-58 235.0
21 TraesCS7B01G073700 chr4B 91.304 69 3 3 1286 1351 625380958 625381026 1.280000e-14 91.6
22 TraesCS7B01G073700 chr4B 88.406 69 5 3 1286 1351 625401295 625401363 2.780000e-11 80.5
23 TraesCS7B01G073700 chrUn 85.682 440 26 15 182 584 88054497 88054058 2.390000e-116 429.0
24 TraesCS7B01G073700 chrUn 92.350 183 9 1 1 178 88054909 88054727 4.300000e-64 255.0
25 TraesCS7B01G073700 chr1D 88.267 375 21 9 174 525 89984714 89984340 8.600000e-116 427.0
26 TraesCS7B01G073700 chr1D 91.257 183 11 1 1 178 89985120 89984938 9.300000e-61 244.0
27 TraesCS7B01G073700 chr3B 92.778 180 8 1 1 175 517862471 517862650 4.300000e-64 255.0
28 TraesCS7B01G073700 chr3B 93.252 163 11 0 174 336 517862877 517863039 1.200000e-59 241.0
29 TraesCS7B01G073700 chr3B 87.273 220 14 5 384 589 517863036 517863255 4.330000e-59 239.0
30 TraesCS7B01G073700 chr5B 80.488 246 41 5 2053 2292 58839531 58839287 7.400000e-42 182.0
31 TraesCS7B01G073700 chr5B 90.566 53 0 5 2698 2746 374366639 374366690 7.770000e-07 65.8
32 TraesCS7B01G073700 chr5D 91.954 87 3 4 2693 2776 322768738 322768823 5.880000e-23 119.0
33 TraesCS7B01G073700 chr5D 83.333 102 13 4 1261 1360 406198437 406198536 1.280000e-14 91.6
34 TraesCS7B01G073700 chr5A 76.126 222 45 8 2124 2341 670401937 670402154 3.540000e-20 110.0


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 TraesCS7B01G073700 chr7B 83023238 83026593 3355 False 6198.0 6198 100.0000 1 3356 1 chr7B.!!$F1 3355
1 TraesCS7B01G073700 chr7D 121931061 121933600 2539 False 3572.0 3572 92.0110 586 3155 1 chr7D.!!$F1 2569
2 TraesCS7B01G073700 chr7A 125478623 125483787 5164 False 1880.5 2902 90.6915 586 3356 2 chr7A.!!$F2 2770
3 TraesCS7B01G073700 chr4A 209307505 209308342 837 True 369.0 488 89.8830 1 582 2 chr4A.!!$R1 581
4 TraesCS7B01G073700 chr6B 673540796 673541633 837 False 360.5 466 89.9075 1 582 2 chr6B.!!$F1 581
5 TraesCS7B01G073700 chr3A 701237251 701238035 784 False 356.0 455 92.3270 22 555 2 chr3A.!!$F1 533
6 TraesCS7B01G073700 chr3A 572651489 572652284 795 True 342.5 435 89.7635 1 541 2 chr3A.!!$R1 540
7 TraesCS7B01G073700 chr4B 142850029 142850843 814 False 344.0 433 89.7715 1 558 2 chr4B.!!$F4 557
8 TraesCS7B01G073700 chr4B 420964221 420964789 568 True 253.5 255 93.4145 1 336 2 chr4B.!!$R1 335
9 TraesCS7B01G073700 chrUn 88054058 88054909 851 True 342.0 429 89.0160 1 584 2 chrUn.!!$R1 583
10 TraesCS7B01G073700 chr1D 89984340 89985120 780 True 335.5 427 89.7620 1 525 2 chr1D.!!$R1 524
11 TraesCS7B01G073700 chr3B 517862471 517863255 784 False 245.0 255 91.1010 1 589 3 chr3B.!!$F1 588

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
855 1130 0.538057 AGTGGCACATCACCCAACTG 60.538 55.0 21.41 0.0 44.52 3.16 F
904 1179 0.647410 CCAATCACGACTAAGCAGCG 59.353 55.0 0.00 0.0 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 2091 0.035056 GGGGTGGACTGGAAGACATG 60.035 60.0 0.0 0.0 37.43 3.21 R
2887 5594 0.036765 TTCCTAGCCGTTGCGTCAAT 60.037 50.0 0.0 0.0 44.33 2.57 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
38 44 4.600111 ACCTTGTTCAAGGGGAGTACATAA 59.400 41.667 28.01 0.00 44.27 1.90
138 144 3.723764 CCTTCGAAATGTTGTTGAACGTG 59.276 43.478 0.00 0.00 34.49 4.49
175 181 3.894759 AGCAGAAGTGGTGCATATTGAT 58.105 40.909 0.00 0.00 43.82 2.57
178 184 4.818546 GCAGAAGTGGTGCATATTGATAGT 59.181 41.667 0.00 0.00 40.86 2.12
201 436 2.305405 GCTTGTCTAGCGATGGCAG 58.695 57.895 1.50 0.00 43.41 4.85
222 457 6.425504 GCAGCATAAGTTTAGCTATGTTGAG 58.574 40.000 11.55 0.00 36.73 3.02
225 460 6.989169 AGCATAAGTTTAGCTATGTTGAGAGG 59.011 38.462 0.00 0.00 36.73 3.69
256 491 8.572855 TCATCATGTGAACCATATGTGTTTTA 57.427 30.769 1.24 0.00 35.12 1.52
332 567 6.598525 CAACATCAAAGTATAGTCGTTTGCA 58.401 36.000 0.00 0.00 32.30 4.08
336 571 9.109393 ACATCAAAGTATAGTCGTTTGCATATT 57.891 29.630 0.00 0.00 32.30 1.28
340 575 9.210426 CAAAGTATAGTCGTTTGCATATTTGTC 57.790 33.333 0.00 0.00 0.00 3.18
343 601 9.758651 AGTATAGTCGTTTGCATATTTGTCATA 57.241 29.630 0.00 0.00 0.00 2.15
355 613 8.733458 TGCATATTTGTCATATATCTCCTTTGC 58.267 33.333 0.00 0.00 0.00 3.68
362 620 7.944061 TGTCATATATCTCCTTTGCAAAATGG 58.056 34.615 13.84 11.98 0.00 3.16
504 762 5.647225 ACAGTCGTTTTAACCAAACAACCTA 59.353 36.000 0.00 0.00 44.63 3.08
507 765 6.150809 AGTCGTTTTAACCAAACAACCTACAA 59.849 34.615 0.00 0.00 44.63 2.41
525 783 6.819146 ACCTACAACTTTTCTATAGCAGCTTC 59.181 38.462 0.00 0.00 0.00 3.86
527 785 6.976636 ACAACTTTTCTATAGCAGCTTCTC 57.023 37.500 0.00 0.00 0.00 2.87
545 803 2.031516 CCACAGCAGCTTCTCCACG 61.032 63.158 0.00 0.00 0.00 4.94
584 856 1.027357 CAGCTCAACCAAACACAGCT 58.973 50.000 0.00 0.00 41.20 4.24
589 861 3.632189 CTCAACCAAACACAGCTTTAGC 58.368 45.455 0.00 0.00 42.49 3.09
590 862 3.020274 TCAACCAAACACAGCTTTAGCA 58.980 40.909 4.33 0.00 45.16 3.49
591 863 3.636300 TCAACCAAACACAGCTTTAGCAT 59.364 39.130 4.33 0.00 45.16 3.79
592 864 3.923017 ACCAAACACAGCTTTAGCATC 57.077 42.857 4.33 0.00 45.16 3.91
604 876 3.564644 GCTTTAGCATCTGAGATGCACAT 59.435 43.478 39.13 25.80 46.77 3.21
606 878 5.237996 GCTTTAGCATCTGAGATGCACATAA 59.762 40.000 39.13 28.14 46.77 1.90
617 889 8.407832 TCTGAGATGCACATAACCAAATTATTG 58.592 33.333 0.00 0.00 30.54 1.90
621 893 6.035368 TGCACATAACCAAATTATTGCACT 57.965 33.333 0.00 0.00 39.58 4.40
625 897 7.621841 GCACATAACCAAATTATTGCACTGTTG 60.622 37.037 0.00 0.00 37.31 3.33
626 898 7.384660 CACATAACCAAATTATTGCACTGTTGT 59.615 33.333 0.00 0.00 35.10 3.32
648 920 6.867550 TGTTACAAATGTCACCAAAACATGA 58.132 32.000 0.00 0.00 37.42 3.07
677 951 9.903682 CTTGTGAGTCATAAAAACATGAATTCT 57.096 29.630 7.05 0.00 36.71 2.40
713 987 2.671619 ATCACACAAACGGGGGCG 60.672 61.111 0.00 0.00 0.00 6.13
716 990 4.493049 ACACAAACGGGGGCGTGT 62.493 61.111 0.00 0.00 37.76 4.49
720 994 1.376166 CAAACGGGGGCGTGTATCA 60.376 57.895 0.00 0.00 0.00 2.15
727 1002 1.053424 GGGGCGTGTATCAATCCCTA 58.947 55.000 0.00 0.00 37.16 3.53
731 1006 3.131396 GGCGTGTATCAATCCCTAACAG 58.869 50.000 0.00 0.00 0.00 3.16
732 1007 2.544267 GCGTGTATCAATCCCTAACAGC 59.456 50.000 0.00 0.00 0.00 4.40
736 1011 3.455910 TGTATCAATCCCTAACAGCTGCT 59.544 43.478 15.27 3.62 0.00 4.24
855 1130 0.538057 AGTGGCACATCACCCAACTG 60.538 55.000 21.41 0.00 44.52 3.16
883 1158 6.234177 GTCCCCTGAATTATCCAATGACTAG 58.766 44.000 0.00 0.00 0.00 2.57
904 1179 0.647410 CCAATCACGACTAAGCAGCG 59.353 55.000 0.00 0.00 0.00 5.18
905 1180 1.629013 CAATCACGACTAAGCAGCGA 58.371 50.000 0.00 0.00 0.00 4.93
906 1181 1.585668 CAATCACGACTAAGCAGCGAG 59.414 52.381 0.00 0.00 0.00 5.03
961 1236 0.953003 GTAATCCCGCGACTAGCTCT 59.047 55.000 8.23 0.00 45.59 4.09
1036 1311 4.007644 CCACGCTGCTGGTCCTGA 62.008 66.667 0.00 0.00 0.00 3.86
1734 2015 2.811317 GGCGTCACCAGCTTCTCG 60.811 66.667 0.00 0.00 38.86 4.04
1872 2153 1.370609 CGTCGCTCTACTTCCTCTCA 58.629 55.000 0.00 0.00 0.00 3.27
1953 2234 3.484742 GATCATCGACTCGGGCGCA 62.485 63.158 10.83 0.00 0.00 6.09
2355 2636 3.653855 GCTCGTAGCGTCGGTATAG 57.346 57.895 7.51 9.44 0.00 1.31
2364 2645 1.922545 GCGTCGGTATAGTGGTGAAAC 59.077 52.381 0.00 0.00 0.00 2.78
2371 2652 5.243507 TCGGTATAGTGGTGAAACTGTACAA 59.756 40.000 11.65 0.00 43.04 2.41
2451 2732 3.434299 CGGTAGAGTAAATTTTGTGCGGT 59.566 43.478 0.00 0.00 0.00 5.68
2491 2772 1.313091 TGTAGCTGATCTGACGGCGT 61.313 55.000 14.65 14.65 45.57 5.68
2594 2893 2.846039 TAGGAGCGTTCTTAAGCGAG 57.154 50.000 6.67 0.00 38.61 5.03
2616 5315 0.745845 CAAGCCGATGGGTCTCAAGG 60.746 60.000 0.00 0.00 34.97 3.61
2676 5381 6.017852 GTGTTGCTCTTCTTTAAGCTTGTACT 60.018 38.462 9.86 0.00 39.31 2.73
2803 5508 4.250464 GTGTCATTATTGGAGGAACGACA 58.750 43.478 0.00 0.00 0.00 4.35
2824 5529 2.761208 ACCATCTTTCCTCCTACACTCG 59.239 50.000 0.00 0.00 0.00 4.18
2874 5581 2.303022 TCATCTCTGGTCCTCCAAACAC 59.697 50.000 0.00 0.00 43.81 3.32
2887 5594 5.016173 CCTCCAAACACCATCAGGAAAATA 58.984 41.667 0.00 0.00 38.69 1.40
2924 5631 2.267681 AAGTCGTCGATCCGAGCCAC 62.268 60.000 0.00 0.00 37.56 5.01
2930 5637 1.337071 GTCGATCCGAGCCACAAGATA 59.663 52.381 0.00 0.00 36.23 1.98
2932 5639 1.609072 CGATCCGAGCCACAAGATAGA 59.391 52.381 0.00 0.00 0.00 1.98
2961 5668 9.064706 TGGTAGTGATTTGAAAAATAAACCGTA 57.935 29.630 0.00 0.00 0.00 4.02
2967 5674 3.764218 TGAAAAATAAACCGTAGCCCCA 58.236 40.909 0.00 0.00 0.00 4.96
2968 5675 4.345854 TGAAAAATAAACCGTAGCCCCAT 58.654 39.130 0.00 0.00 0.00 4.00
2976 5683 2.690840 ACCGTAGCCCCATAGAAGAAT 58.309 47.619 0.00 0.00 0.00 2.40
3008 5715 2.707791 CACCCCATATCCAGTCAGACAT 59.292 50.000 2.66 0.00 0.00 3.06
3010 5717 2.551721 CCCCATATCCAGTCAGACATGC 60.552 54.545 2.66 0.00 0.00 4.06
3012 5719 3.181447 CCCATATCCAGTCAGACATGCTT 60.181 47.826 2.66 0.00 0.00 3.91
3036 5743 2.838813 GGGACCTAACCTTACAAGCTCT 59.161 50.000 0.00 0.00 0.00 4.09
3055 5762 3.628008 TCTCCTATGACGCCTAAACTGA 58.372 45.455 0.00 0.00 0.00 3.41
3067 5774 3.125316 GCCTAAACTGAAGGAACATCACG 59.875 47.826 0.00 0.00 36.08 4.35
3085 5792 2.970639 CGTCGGAGAAGGAGCCAA 59.029 61.111 0.00 0.00 39.69 4.52
3098 5805 3.126453 AGGAGCCAAAGGACCAAGATAT 58.874 45.455 0.00 0.00 0.00 1.63
3104 5811 3.117738 CCAAAGGACCAAGATATGAGGCT 60.118 47.826 0.00 0.00 0.00 4.58
3119 5826 1.071814 GGCTTCGTTGTGTACCCCA 59.928 57.895 0.00 0.00 0.00 4.96
3165 5876 6.285224 CACCTGTATAACATCAATAACCGGA 58.715 40.000 9.46 0.00 0.00 5.14
3184 5895 4.562347 CCGGATCCATCACTTCATAAGAGG 60.562 50.000 13.41 0.00 0.00 3.69
3189 5900 4.466370 TCCATCACTTCATAAGAGGAACGT 59.534 41.667 0.00 0.00 0.00 3.99
3210 5921 3.056465 GTCCAGACGATCCATTATCCTCC 60.056 52.174 0.00 0.00 0.00 4.30
3211 5922 3.169099 CCAGACGATCCATTATCCTCCT 58.831 50.000 0.00 0.00 0.00 3.69
3218 5930 5.780282 ACGATCCATTATCCTCCTTATGTCA 59.220 40.000 0.00 0.00 0.00 3.58
3221 5933 7.526192 CGATCCATTATCCTCCTTATGTCACTT 60.526 40.741 0.00 0.00 0.00 3.16
3227 5939 5.677319 TCCTCCTTATGTCACTTGTTAGG 57.323 43.478 0.00 0.00 0.00 2.69
3243 5955 1.503401 TAGGTGACCAGGACTCGGGA 61.503 60.000 3.63 0.00 32.37 5.14
3255 5967 5.246307 CAGGACTCGGGAAAACTTTATTCT 58.754 41.667 0.00 0.00 0.00 2.40
3262 5974 5.353123 TCGGGAAAACTTTATTCTTGATCCG 59.647 40.000 0.00 0.00 31.86 4.18
3263 5975 5.340803 GGGAAAACTTTATTCTTGATCCGC 58.659 41.667 0.00 0.00 0.00 5.54
3265 5977 6.030228 GGAAAACTTTATTCTTGATCCGCAG 58.970 40.000 0.00 0.00 0.00 5.18
3274 5986 3.127533 GATCCGCAGTGCACCACC 61.128 66.667 16.83 0.68 34.49 4.61
3279 5991 2.669569 GCAGTGCACCACCATCGT 60.670 61.111 14.63 0.00 34.49 3.73
3293 6005 0.235665 CATCGTCACCACAACACTGC 59.764 55.000 0.00 0.00 0.00 4.40
3322 6034 9.346005 CTAAGGAACCAAACTCTAACCTTAAAA 57.654 33.333 0.00 0.00 37.82 1.52
3327 6039 5.761726 ACCAAACTCTAACCTTAAAAGACCG 59.238 40.000 0.00 0.00 0.00 4.79
3340 6052 2.851263 AAGACCGAACTACAATGCCA 57.149 45.000 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 67 1.183030 TTGAGGTGGACGGTCACGAT 61.183 55.000 10.76 0.00 44.60 3.73
138 144 1.005748 GCTTGAGCACCCCAAAAGC 60.006 57.895 0.00 0.00 41.59 3.51
165 171 5.299949 ACAAGCATCGACTATCAATATGCA 58.700 37.500 8.17 0.00 44.18 3.96
201 436 6.203723 CCCTCTCAACATAGCTAAACTTATGC 59.796 42.308 0.00 0.00 0.00 3.14
222 457 3.209410 GTTCACATGATGATGACCCCTC 58.791 50.000 0.00 0.00 37.11 4.30
225 460 3.003394 TGGTTCACATGATGATGACCC 57.997 47.619 0.00 2.27 37.40 4.46
336 571 8.415553 CCATTTTGCAAAGGAGATATATGACAA 58.584 33.333 12.41 0.00 0.00 3.18
340 575 9.071276 ACTACCATTTTGCAAAGGAGATATATG 57.929 33.333 20.92 14.50 0.00 1.78
343 601 7.615365 TGAACTACCATTTTGCAAAGGAGATAT 59.385 33.333 20.92 5.35 0.00 1.63
345 603 5.774690 TGAACTACCATTTTGCAAAGGAGAT 59.225 36.000 20.92 7.84 0.00 2.75
409 667 8.391106 CCTAAGTGAGTTTGTTTATATGCTGAC 58.609 37.037 0.00 0.00 0.00 3.51
504 762 5.877564 GGAGAAGCTGCTATAGAAAAGTTGT 59.122 40.000 0.90 0.00 0.00 3.32
507 765 5.046304 TGTGGAGAAGCTGCTATAGAAAAGT 60.046 40.000 0.90 0.00 0.00 2.66
525 783 0.673022 GTGGAGAAGCTGCTGTGGAG 60.673 60.000 0.00 0.00 0.00 3.86
527 785 2.031516 CGTGGAGAAGCTGCTGTGG 61.032 63.158 0.00 0.00 0.00 4.17
545 803 4.474113 CTGCAGATTCTGAAAAAGCTGAC 58.526 43.478 17.87 0.00 43.62 3.51
584 856 5.528690 GGTTATGTGCATCTCAGATGCTAAA 59.471 40.000 34.25 22.08 44.79 1.85
589 861 5.823209 TTTGGTTATGTGCATCTCAGATG 57.177 39.130 10.64 10.64 30.58 2.90
590 862 8.701908 ATAATTTGGTTATGTGCATCTCAGAT 57.298 30.769 0.00 0.00 31.80 2.90
591 863 8.407832 CAATAATTTGGTTATGTGCATCTCAGA 58.592 33.333 0.00 0.00 33.32 3.27
592 864 7.168637 GCAATAATTTGGTTATGTGCATCTCAG 59.831 37.037 0.00 0.00 37.10 3.35
604 876 8.414003 TGTAACAACAGTGCAATAATTTGGTTA 58.586 29.630 0.00 0.00 33.22 2.85
606 878 6.810911 TGTAACAACAGTGCAATAATTTGGT 58.189 32.000 0.00 0.00 33.22 3.67
617 889 4.041723 GGTGACATTTGTAACAACAGTGC 58.958 43.478 0.77 0.00 30.77 4.40
621 893 6.455647 TGTTTTGGTGACATTTGTAACAACA 58.544 32.000 0.77 0.72 42.32 3.33
625 897 7.763172 TTCATGTTTTGGTGACATTTGTAAC 57.237 32.000 0.00 0.00 42.32 2.50
626 898 8.037758 AGTTTCATGTTTTGGTGACATTTGTAA 58.962 29.630 0.00 0.00 42.32 2.41
713 987 3.561725 GCAGCTGTTAGGGATTGATACAC 59.438 47.826 16.64 0.00 0.00 2.90
716 990 5.147767 TCTAGCAGCTGTTAGGGATTGATA 58.852 41.667 30.13 11.41 30.96 2.15
720 994 2.103941 GCTCTAGCAGCTGTTAGGGATT 59.896 50.000 34.12 6.52 45.83 3.01
736 1011 4.291540 CAACAGCACTTTTGTTGCTCTA 57.708 40.909 5.32 0.00 45.97 2.43
793 1068 3.159298 CGGAAGCCAGTAACAGCAT 57.841 52.632 0.00 0.00 0.00 3.79
883 1158 1.661112 GCTGCTTAGTCGTGATTGGAC 59.339 52.381 0.00 0.00 34.62 4.02
906 1181 0.099436 CCATTTAGCAAGCACCTCGC 59.901 55.000 0.00 0.00 42.91 5.03
908 1183 2.819608 TGTTCCATTTAGCAAGCACCTC 59.180 45.455 0.00 0.00 0.00 3.85
909 1184 2.875296 TGTTCCATTTAGCAAGCACCT 58.125 42.857 0.00 0.00 0.00 4.00
911 1186 8.925161 TTATTTATGTTCCATTTAGCAAGCAC 57.075 30.769 0.00 0.00 0.00 4.40
961 1236 1.014044 GCAGTGACAAAGATCGCCGA 61.014 55.000 0.00 0.00 0.00 5.54
1608 1889 4.722855 CCGAACGTTACCCGCCGT 62.723 66.667 0.00 0.00 41.42 5.68
1615 1896 4.143363 GCCGCAGCCGAACGTTAC 62.143 66.667 0.00 0.00 36.29 2.50
1734 2015 2.080286 ACATGGACGTGAAGCAGTAC 57.920 50.000 0.00 0.00 0.00 2.73
1810 2091 0.035056 GGGGTGGACTGGAAGACATG 60.035 60.000 0.00 0.00 37.43 3.21
1811 2092 1.553690 CGGGGTGGACTGGAAGACAT 61.554 60.000 0.00 0.00 37.43 3.06
1812 2093 2.214216 CGGGGTGGACTGGAAGACA 61.214 63.158 0.00 0.00 37.43 3.41
1872 2153 1.078848 GACGCTGATGCCCTTCAGT 60.079 57.895 11.36 0.00 44.10 3.41
2335 2616 1.126479 CTATACCGACGCTACGAGCTC 59.874 57.143 2.73 2.73 39.60 4.09
2346 2627 4.184079 ACAGTTTCACCACTATACCGAC 57.816 45.455 0.00 0.00 0.00 4.79
2350 2631 7.156673 TCCTTTGTACAGTTTCACCACTATAC 58.843 38.462 0.00 0.00 28.79 1.47
2352 2633 6.182507 TCCTTTGTACAGTTTCACCACTAT 57.817 37.500 0.00 0.00 0.00 2.12
2355 2636 4.196971 ACTCCTTTGTACAGTTTCACCAC 58.803 43.478 0.00 0.00 0.00 4.16
2364 2645 6.149142 ACGAGTTCTACTACTCCTTTGTACAG 59.851 42.308 0.00 0.00 41.18 2.74
2371 2652 4.635324 GTGCTACGAGTTCTACTACTCCTT 59.365 45.833 0.00 0.00 41.18 3.36
2422 2703 0.388294 ATTTACTCTACCGCCTCGCC 59.612 55.000 0.00 0.00 0.00 5.54
2423 2704 2.220479 AATTTACTCTACCGCCTCGC 57.780 50.000 0.00 0.00 0.00 5.03
2424 2705 3.930848 ACAAAATTTACTCTACCGCCTCG 59.069 43.478 0.00 0.00 0.00 4.63
2425 2706 4.436986 GCACAAAATTTACTCTACCGCCTC 60.437 45.833 0.00 0.00 0.00 4.70
2426 2707 3.439129 GCACAAAATTTACTCTACCGCCT 59.561 43.478 0.00 0.00 0.00 5.52
2451 2732 1.005867 GACGGCCCAGTTTACACGA 60.006 57.895 0.00 0.00 0.00 4.35
2491 2772 1.341976 GGCCTTCCATTGGAAAGGCTA 60.342 52.381 33.68 13.02 45.90 3.93
2594 2893 1.522580 GAGACCCATCGGCTTGCTC 60.523 63.158 0.00 0.00 0.00 4.26
2644 5343 3.498774 AAGAAGAGCAACACCTCATGT 57.501 42.857 0.00 0.00 46.42 3.21
2779 5484 4.876107 GTCGTTCCTCCAATAATGACACAT 59.124 41.667 0.00 0.00 40.04 3.21
2780 5485 4.250464 GTCGTTCCTCCAATAATGACACA 58.750 43.478 0.00 0.00 40.04 3.72
2803 5508 2.761208 CGAGTGTAGGAGGAAAGATGGT 59.239 50.000 0.00 0.00 0.00 3.55
2835 5540 1.792367 TGACATCGAGCTTTGTTCACG 59.208 47.619 0.00 0.00 0.00 4.35
2836 5541 3.681897 AGATGACATCGAGCTTTGTTCAC 59.318 43.478 9.77 0.00 0.00 3.18
2840 5547 3.519579 CAGAGATGACATCGAGCTTTGT 58.480 45.455 9.77 0.00 0.00 2.83
2842 5549 2.499289 ACCAGAGATGACATCGAGCTTT 59.501 45.455 9.77 0.00 0.00 3.51
2874 5581 4.898829 TGCGTCAATATTTTCCTGATGG 57.101 40.909 0.00 0.00 0.00 3.51
2887 5594 0.036765 TTCCTAGCCGTTGCGTCAAT 60.037 50.000 0.00 0.00 44.33 2.57
2924 5631 8.777865 TTCAAATCACTACCACTTCTATCTTG 57.222 34.615 0.00 0.00 0.00 3.02
2932 5639 9.758651 GGTTTATTTTTCAAATCACTACCACTT 57.241 29.630 0.00 0.00 0.00 3.16
2937 5644 9.058424 GCTACGGTTTATTTTTCAAATCACTAC 57.942 33.333 0.00 0.00 0.00 2.73
2961 5668 6.495526 GTCTTCTAGTATTCTTCTATGGGGCT 59.504 42.308 0.00 0.00 0.00 5.19
2967 5674 6.783482 GGGGTGGTCTTCTAGTATTCTTCTAT 59.217 42.308 0.00 0.00 0.00 1.98
2968 5675 6.134754 GGGGTGGTCTTCTAGTATTCTTCTA 58.865 44.000 0.00 0.00 0.00 2.10
2976 5683 4.171243 TGGATATGGGGTGGTCTTCTAGTA 59.829 45.833 0.00 0.00 0.00 1.82
3010 5717 4.383880 GCTTGTAAGGTTAGGTCCCCTAAG 60.384 50.000 2.99 0.00 45.42 2.18
3012 5719 3.109928 GCTTGTAAGGTTAGGTCCCCTA 58.890 50.000 0.00 0.00 34.61 3.53
3027 5734 1.681793 GGCGTCATAGGAGAGCTTGTA 59.318 52.381 5.04 0.00 0.00 2.41
3036 5743 3.132289 CCTTCAGTTTAGGCGTCATAGGA 59.868 47.826 0.00 0.00 0.00 2.94
3055 5762 1.736645 CCGACGCGTGATGTTCCTT 60.737 57.895 20.70 0.00 0.00 3.36
3067 5774 2.781595 TTTGGCTCCTTCTCCGACGC 62.782 60.000 0.00 0.00 0.00 5.19
3085 5792 3.181461 CGAAGCCTCATATCTTGGTCCTT 60.181 47.826 0.00 0.00 0.00 3.36
3098 5805 0.034337 GGGTACACAACGAAGCCTCA 59.966 55.000 0.00 0.00 0.00 3.86
3104 5811 4.223255 TCTTATGATGGGGTACACAACGAA 59.777 41.667 0.00 0.00 0.00 3.85
3119 5826 3.689649 GGTGTTTGAAGGCGTCTTATGAT 59.310 43.478 0.17 0.00 32.52 2.45
3165 5876 5.129485 ACGTTCCTCTTATGAAGTGATGGAT 59.871 40.000 0.00 0.00 0.00 3.41
3189 5900 3.165875 GGAGGATAATGGATCGTCTGGA 58.834 50.000 7.07 0.00 45.13 3.86
3202 5913 7.402071 ACCTAACAAGTGACATAAGGAGGATAA 59.598 37.037 0.00 0.00 0.00 1.75
3205 5916 5.046591 CACCTAACAAGTGACATAAGGAGGA 60.047 44.000 0.00 0.00 37.42 3.71
3218 5930 2.633481 GAGTCCTGGTCACCTAACAAGT 59.367 50.000 0.00 0.00 0.00 3.16
3221 5933 1.254026 CGAGTCCTGGTCACCTAACA 58.746 55.000 0.00 0.00 0.00 2.41
3227 5939 0.395312 TTTTCCCGAGTCCTGGTCAC 59.605 55.000 0.00 0.00 0.00 3.67
3234 5946 5.704053 TCAAGAATAAAGTTTTCCCGAGTCC 59.296 40.000 0.00 0.00 0.00 3.85
3243 5955 6.381801 CACTGCGGATCAAGAATAAAGTTTT 58.618 36.000 0.00 0.00 0.00 2.43
3255 5967 1.965930 GTGGTGCACTGCGGATCAA 60.966 57.895 17.98 0.00 0.00 2.57
3262 5974 2.669569 ACGATGGTGGTGCACTGC 60.670 61.111 17.98 9.63 34.40 4.40
3263 5975 1.301637 TGACGATGGTGGTGCACTG 60.302 57.895 17.98 0.99 34.40 3.66
3265 5977 2.325082 GGTGACGATGGTGGTGCAC 61.325 63.158 8.80 8.80 0.00 4.57
3274 5986 0.235665 GCAGTGTTGTGGTGACGATG 59.764 55.000 0.00 0.00 0.00 3.84
3279 5991 2.034048 TAGCGGCAGTGTTGTGGTGA 62.034 55.000 1.45 0.00 0.00 4.02
3293 6005 2.474410 AGAGTTTGGTTCCTTAGCGG 57.526 50.000 0.00 0.00 0.00 5.52
3322 6034 1.346395 TGTGGCATTGTAGTTCGGTCT 59.654 47.619 0.00 0.00 0.00 3.85
3327 6039 2.226330 TGTGGTGTGGCATTGTAGTTC 58.774 47.619 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.