Multiple sequence alignment - TraesCS3A01G035100

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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 TraesCS3A01G035100 chr3A 100.000 2879 0 0 1 2879 19487274 19484396 0.000000e+00 5317.0
1 TraesCS3A01G035100 chr3A 88.723 1206 116 9 716 1911 19357137 19358332 0.000000e+00 1456.0
2 TraesCS3A01G035100 chr3A 79.171 941 147 28 919 1824 19286263 19287189 8.820000e-170 606.0
3 TraesCS3A01G035100 chr3A 78.008 1014 169 36 907 1893 25959775 25958789 3.200000e-164 588.0
4 TraesCS3A01G035100 chr3A 79.661 531 85 15 1429 1943 26449973 26450496 7.580000e-96 361.0
5 TraesCS3A01G035100 chr3A 96.774 93 3 0 311 403 19356031 19356123 3.840000e-34 156.0
6 TraesCS3A01G035100 chr3A 83.750 80 13 0 1742 1821 26448839 26448918 3.080000e-10 76.8
7 TraesCS3A01G035100 chr3D 89.649 1710 114 23 777 2455 17361604 17363281 0.000000e+00 2119.0
8 TraesCS3A01G035100 chr3D 87.634 1213 120 17 716 1911 17533295 17532096 0.000000e+00 1382.0
9 TraesCS3A01G035100 chr3D 86.963 698 73 17 24 707 17528504 17527811 0.000000e+00 769.0
10 TraesCS3A01G035100 chr3D 88.564 411 46 1 297 707 17533849 17533440 5.540000e-137 497.0
11 TraesCS3A01G035100 chr3D 86.635 419 42 10 2465 2879 17363386 17363794 4.370000e-123 451.0
12 TraesCS3A01G035100 chr3D 84.352 409 41 15 757 1164 17527633 17527247 2.090000e-101 379.0
13 TraesCS3A01G035100 chr3D 90.323 155 13 1 30 182 17361019 17361173 4.860000e-48 202.0
14 TraesCS3A01G035100 chr3D 84.615 195 26 3 1633 1827 11340219 11340409 1.050000e-44 191.0
15 TraesCS3A01G035100 chr3D 86.598 97 13 0 1266 1362 11343985 11344081 1.090000e-19 108.0
16 TraesCS3A01G035100 chr3B 85.613 1404 125 31 843 2222 24933006 24934356 0.000000e+00 1402.0
17 TraesCS3A01G035100 chr3B 84.268 642 85 9 1188 1825 30363600 30364229 1.900000e-171 612.0
18 TraesCS3A01G035100 chr3B 83.048 643 91 10 1188 1825 29976624 29977253 4.160000e-158 568.0
19 TraesCS3A01G035100 chr3B 82.277 694 78 18 19 707 24932178 24932831 2.510000e-155 558.0
20 TraesCS3A01G035100 chr3B 91.020 245 18 2 2639 2879 24934376 24934620 7.690000e-86 327.0
21 TraesCS3A01G035100 chr2D 85.281 231 15 9 2246 2458 569346940 569346711 1.340000e-53 220.0
22 TraesCS3A01G035100 chr2D 89.209 139 14 1 2456 2593 607078433 607078295 3.810000e-39 172.0
23 TraesCS3A01G035100 chr2D 90.000 60 6 0 2534 2593 2496685 2496626 8.550000e-11 78.7
24 TraesCS3A01G035100 chr7B 90.580 138 13 0 2456 2593 228919424 228919287 1.760000e-42 183.0
25 TraesCS3A01G035100 chr7B 91.509 106 8 1 142 247 740164868 740164972 8.310000e-31 145.0
26 TraesCS3A01G035100 chr7B 89.623 106 9 1 142 247 285340315 285340212 1.800000e-27 134.0
27 TraesCS3A01G035100 chr7B 84.375 128 19 1 2466 2593 610479637 610479511 1.080000e-24 124.0
28 TraesCS3A01G035100 chr7B 81.600 125 19 3 23 144 680288097 680288220 1.830000e-17 100.0
29 TraesCS3A01G035100 chr4D 92.453 106 8 0 142 247 248926511 248926406 4.970000e-33 152.0
30 TraesCS3A01G035100 chr4D 88.785 107 11 1 142 247 493929130 493929024 2.330000e-26 130.0
31 TraesCS3A01G035100 chr7A 86.331 139 16 2 2455 2593 646478646 646478511 6.430000e-32 148.0
32 TraesCS3A01G035100 chr7A 92.157 102 8 0 146 247 121882652 121882753 8.310000e-31 145.0
33 TraesCS3A01G035100 chr7A 84.783 138 19 2 2457 2593 74140034 74140170 1.390000e-28 137.0
34 TraesCS3A01G035100 chr7D 91.509 106 8 1 142 247 228982763 228982659 8.310000e-31 145.0
35 TraesCS3A01G035100 chr7D 82.171 129 20 2 18 144 601281417 601281290 1.090000e-19 108.0
36 TraesCS3A01G035100 chr7D 82.540 126 19 2 18 141 601316767 601316891 1.090000e-19 108.0
37 TraesCS3A01G035100 chr2B 91.509 106 8 1 142 247 406443785 406443681 8.310000e-31 145.0
38 TraesCS3A01G035100 chr2A 91.176 102 9 0 146 247 136735609 136735508 3.870000e-29 139.0
39 TraesCS3A01G035100 chr6D 90.196 102 9 1 146 247 436380834 436380934 6.470000e-27 132.0
40 TraesCS3A01G035100 chr6A 85.185 108 6 6 2496 2593 23895264 23895371 5.080000e-18 102.0
41 TraesCS3A01G035100 chr4B 90.909 66 5 1 2529 2593 664762112 664762177 1.420000e-13 87.9


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 TraesCS3A01G035100 chr3A 19484396 19487274 2878 True 5317.000000 5317 100.000000 1 2879 1 chr3A.!!$R1 2878
1 TraesCS3A01G035100 chr3A 19356031 19358332 2301 False 806.000000 1456 92.748500 311 1911 2 chr3A.!!$F2 1600
2 TraesCS3A01G035100 chr3A 19286263 19287189 926 False 606.000000 606 79.171000 919 1824 1 chr3A.!!$F1 905
3 TraesCS3A01G035100 chr3A 25958789 25959775 986 True 588.000000 588 78.008000 907 1893 1 chr3A.!!$R2 986
4 TraesCS3A01G035100 chr3A 26448839 26450496 1657 False 218.900000 361 81.705500 1429 1943 2 chr3A.!!$F3 514
5 TraesCS3A01G035100 chr3D 17361019 17363794 2775 False 924.000000 2119 88.869000 30 2879 3 chr3D.!!$F2 2849
6 TraesCS3A01G035100 chr3D 17527247 17533849 6602 True 756.750000 1382 86.878250 24 1911 4 chr3D.!!$R1 1887
7 TraesCS3A01G035100 chr3B 24932178 24934620 2442 False 762.333333 1402 86.303333 19 2879 3 chr3B.!!$F3 2860
8 TraesCS3A01G035100 chr3B 30363600 30364229 629 False 612.000000 612 84.268000 1188 1825 1 chr3B.!!$F2 637
9 TraesCS3A01G035100 chr3B 29976624 29977253 629 False 568.000000 568 83.048000 1188 1825 1 chr3B.!!$F1 637

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
286 291 0.249699 CGGCCCTTTGTTTTTCACCC 60.25 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 3300 0.623723 TAGCCACTCCCAATCCAACC 59.376 55.0 0.0 0.0 0.0 3.77 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
40 41 9.145865 ACAAAAACGAAACAAGACAATAACATT 57.854 25.926 0.00 0.00 0.00 2.71
108 109 8.996024 TTCAACTCGAACAACTGATAATATCA 57.004 30.769 2.68 2.68 37.76 2.15
153 156 6.942576 AGCCCAGTGATATTGATTATTGGTAC 59.057 38.462 0.00 0.00 29.22 3.34
182 185 4.921515 GCATCGCGTCTAGTTGGAATATAA 59.078 41.667 5.77 0.00 0.00 0.98
230 233 8.709386 TGCTTTTATTGTTTTCTGTTTAAGCA 57.291 26.923 0.00 0.00 41.10 3.91
267 272 5.784578 ACATACCTTGAAACTGGGTTTTC 57.215 39.130 0.00 0.00 35.77 2.29
275 280 0.397957 AACTGGGTTTTCGGCCCTTT 60.398 50.000 0.00 0.00 46.22 3.11
281 286 2.634600 GGTTTTCGGCCCTTTGTTTTT 58.365 42.857 0.00 0.00 0.00 1.94
282 287 2.610374 GGTTTTCGGCCCTTTGTTTTTC 59.390 45.455 0.00 0.00 0.00 2.29
284 289 2.588027 TTCGGCCCTTTGTTTTTCAC 57.412 45.000 0.00 0.00 0.00 3.18
285 290 0.747852 TCGGCCCTTTGTTTTTCACC 59.252 50.000 0.00 0.00 0.00 4.02
286 291 0.249699 CGGCCCTTTGTTTTTCACCC 60.250 55.000 0.00 0.00 0.00 4.61
287 292 1.128200 GGCCCTTTGTTTTTCACCCT 58.872 50.000 0.00 0.00 0.00 4.34
288 293 1.202639 GGCCCTTTGTTTTTCACCCTG 60.203 52.381 0.00 0.00 0.00 4.45
289 294 1.202639 GCCCTTTGTTTTTCACCCTGG 60.203 52.381 0.00 0.00 0.00 4.45
291 296 2.102420 CCCTTTGTTTTTCACCCTGGTC 59.898 50.000 0.00 0.00 0.00 4.02
292 297 2.763448 CCTTTGTTTTTCACCCTGGTCA 59.237 45.455 0.00 0.00 0.00 4.02
426 669 2.386661 AGTATTTCTGTCAGGCACCG 57.613 50.000 0.00 0.00 0.00 4.94
492 735 5.178797 GCTAATCTGTGTGTCCTGTAACAT 58.821 41.667 0.00 0.00 0.00 2.71
511 754 3.231736 ACCGTGAGACGCACCCTT 61.232 61.111 3.58 0.00 44.85 3.95
528 771 2.311841 CCCTTGGTTTACTCCCCTCAAT 59.688 50.000 0.00 0.00 0.00 2.57
533 776 3.913799 TGGTTTACTCCCCTCAATTCTGA 59.086 43.478 0.00 0.00 0.00 3.27
545 788 2.093288 TCAATTCTGAGAAGGCTGCGAT 60.093 45.455 0.00 0.00 0.00 4.58
560 803 1.303074 CGATGCTGCCAGCCCATAT 60.303 57.895 15.29 0.00 41.51 1.78
598 841 3.136750 CCTCGCCTGAGATGGAGG 58.863 66.667 0.00 0.31 45.57 4.30
599 842 2.506061 CCTCGCCTGAGATGGAGGG 61.506 68.421 5.77 0.00 45.57 4.30
601 844 0.468214 CTCGCCTGAGATGGAGGGTA 60.468 60.000 0.00 0.00 45.57 3.69
608 851 4.265073 CCTGAGATGGAGGGTAGTTTTTG 58.735 47.826 0.00 0.00 0.00 2.44
652 899 6.820335 TCTTTACACACCTATCATGATCCAG 58.180 40.000 12.53 4.92 0.00 3.86
669 916 4.868172 TCCAGGAATCCATGAACAAGAT 57.132 40.909 0.61 0.00 0.00 2.40
700 948 7.792925 TGAAAGACAAAGTACGTGAATATGTG 58.207 34.615 0.00 0.00 0.00 3.21
701 949 7.654116 TGAAAGACAAAGTACGTGAATATGTGA 59.346 33.333 0.00 0.00 0.00 3.58
703 951 7.757097 AGACAAAGTACGTGAATATGTGATC 57.243 36.000 0.00 0.00 0.00 2.92
706 954 8.547967 ACAAAGTACGTGAATATGTGATCTTT 57.452 30.769 0.00 0.00 0.00 2.52
707 955 9.647797 ACAAAGTACGTGAATATGTGATCTTTA 57.352 29.630 0.00 0.00 0.00 1.85
733 1447 8.194104 ACACACATATTCTTTAACTTGCACAAA 58.806 29.630 0.00 0.00 0.00 2.83
884 1620 2.746362 GCTGACAAAAGCATGAGTAGCT 59.254 45.455 0.00 0.00 45.97 3.32
972 1712 1.308998 GATGGCTTACCCGTCAATGG 58.691 55.000 0.00 0.00 46.97 3.16
973 1713 0.623723 ATGGCTTACCCGTCAATGGT 59.376 50.000 0.00 0.00 39.97 3.55
1072 1813 0.322546 AGCCCCGATTTTCCAGTCAC 60.323 55.000 0.00 0.00 0.00 3.67
1074 1815 1.739067 CCCCGATTTTCCAGTCACTC 58.261 55.000 0.00 0.00 0.00 3.51
1222 1993 2.165167 TGGTGTTCGTCTGGGTAGTAG 58.835 52.381 0.00 0.00 0.00 2.57
1223 1994 1.135170 GGTGTTCGTCTGGGTAGTAGC 60.135 57.143 0.00 0.00 0.00 3.58
1224 1995 1.542915 GTGTTCGTCTGGGTAGTAGCA 59.457 52.381 1.13 0.00 0.00 3.49
1229 2000 1.789523 GTCTGGGTAGTAGCATGGGA 58.210 55.000 1.13 0.00 0.00 4.37
1251 2022 3.991051 CCACTGACGGTCGCTGGT 61.991 66.667 13.29 3.72 0.00 4.00
1368 2142 1.829222 GGAAGATCGTGTGGTCCCTTA 59.171 52.381 0.00 0.00 0.00 2.69
1494 2277 5.559991 GCGTGTCATTGATGTACACAAAGAA 60.560 40.000 18.08 6.21 38.02 2.52
1533 2316 2.981302 GGCACCTGCAATTTCCCC 59.019 61.111 0.00 0.00 44.36 4.81
1647 2463 2.265739 GTGGAGGTGAGATGCGCA 59.734 61.111 14.96 14.96 0.00 6.09
1766 2584 4.593864 GATGGGCTCGTCGGGCTC 62.594 72.222 18.16 14.80 0.00 4.70
1870 2695 5.186797 ACCGGCCAATCATCTTTTAATCAAA 59.813 36.000 0.00 0.00 0.00 2.69
1990 2838 9.620259 GAGGATTAGGATGAAGTTGATAGTTTT 57.380 33.333 0.00 0.00 0.00 2.43
1991 2839 9.981460 AGGATTAGGATGAAGTTGATAGTTTTT 57.019 29.630 0.00 0.00 0.00 1.94
1996 2844 8.697507 AGGATGAAGTTGATAGTTTTTGTTCT 57.302 30.769 0.00 0.00 0.00 3.01
1997 2845 9.136323 AGGATGAAGTTGATAGTTTTTGTTCTT 57.864 29.630 0.00 0.00 0.00 2.52
2057 3123 3.131400 GGCCCTAGTTAGTCTGAACTGAG 59.869 52.174 0.00 0.00 39.96 3.35
2062 3128 2.829120 AGTTAGTCTGAACTGAGCTCCC 59.171 50.000 12.15 0.00 38.25 4.30
2139 3212 3.068873 AGTCAGAGACCAGTCACACTTTC 59.931 47.826 0.00 0.00 32.18 2.62
2140 3213 3.031013 TCAGAGACCAGTCACACTTTCA 58.969 45.455 0.00 0.00 0.00 2.69
2141 3214 3.068732 TCAGAGACCAGTCACACTTTCAG 59.931 47.826 0.00 0.00 0.00 3.02
2142 3215 3.068732 CAGAGACCAGTCACACTTTCAGA 59.931 47.826 0.00 0.00 0.00 3.27
2143 3216 3.706594 AGAGACCAGTCACACTTTCAGAA 59.293 43.478 0.00 0.00 0.00 3.02
2144 3217 4.346418 AGAGACCAGTCACACTTTCAGAAT 59.654 41.667 0.00 0.00 0.00 2.40
2145 3218 5.041191 AGACCAGTCACACTTTCAGAATT 57.959 39.130 0.00 0.00 0.00 2.17
2146 3219 5.440610 AGACCAGTCACACTTTCAGAATTT 58.559 37.500 0.00 0.00 0.00 1.82
2147 3220 5.888161 AGACCAGTCACACTTTCAGAATTTT 59.112 36.000 0.00 0.00 0.00 1.82
2148 3221 6.038714 AGACCAGTCACACTTTCAGAATTTTC 59.961 38.462 0.00 0.00 0.00 2.29
2149 3222 5.067805 ACCAGTCACACTTTCAGAATTTTCC 59.932 40.000 0.00 0.00 0.00 3.13
2150 3223 5.067674 CCAGTCACACTTTCAGAATTTTCCA 59.932 40.000 0.00 0.00 0.00 3.53
2161 3234 8.647143 TTTCAGAATTTTCCATTTTGAGACAC 57.353 30.769 0.00 0.00 0.00 3.67
2270 3363 6.510879 AATTTAAAGGGTCAGTCGATTTCC 57.489 37.500 0.00 0.00 0.00 3.13
2273 3366 3.721087 AAGGGTCAGTCGATTTCCAAT 57.279 42.857 0.00 0.00 0.00 3.16
2274 3367 3.721087 AGGGTCAGTCGATTTCCAATT 57.279 42.857 0.00 0.00 0.00 2.32
2317 3410 3.208747 AGATCCAACGTCCACAACTTT 57.791 42.857 0.00 0.00 0.00 2.66
2329 3422 5.107065 CGTCCACAACTTTATCTTCAACCTC 60.107 44.000 0.00 0.00 0.00 3.85
2362 3455 6.681368 GCACTGTTTCTCTTCAACCTCAAATT 60.681 38.462 0.00 0.00 0.00 1.82
2370 3463 3.611025 TCAACCTCAAATTTGACCCCT 57.389 42.857 16.91 0.00 32.90 4.79
2371 3464 3.230134 TCAACCTCAAATTTGACCCCTG 58.770 45.455 16.91 11.42 32.90 4.45
2458 3563 2.204151 CCCTCCCCTGAACCACCT 60.204 66.667 0.00 0.00 0.00 4.00
2459 3564 1.852626 CCCTCCCCTGAACCACCTT 60.853 63.158 0.00 0.00 0.00 3.50
2460 3565 1.380302 CCTCCCCTGAACCACCTTG 59.620 63.158 0.00 0.00 0.00 3.61
2461 3566 1.133809 CCTCCCCTGAACCACCTTGA 61.134 60.000 0.00 0.00 0.00 3.02
2462 3567 0.771127 CTCCCCTGAACCACCTTGAA 59.229 55.000 0.00 0.00 0.00 2.69
2463 3568 1.355720 CTCCCCTGAACCACCTTGAAT 59.644 52.381 0.00 0.00 0.00 2.57
2485 3685 8.982723 TGAATCCTAAGATAGATAATAGGGTGC 58.017 37.037 0.00 0.00 36.41 5.01
2512 3713 1.681486 GAGCCCCTTCCTTCTCTCCG 61.681 65.000 0.00 0.00 0.00 4.63
2513 3714 1.686110 GCCCCTTCCTTCTCTCCGA 60.686 63.158 0.00 0.00 0.00 4.55
2514 3715 1.962321 GCCCCTTCCTTCTCTCCGAC 61.962 65.000 0.00 0.00 0.00 4.79
2533 3734 4.012721 AGGCCCTTCCTCCTCCGT 62.013 66.667 0.00 0.00 43.20 4.69
2534 3735 3.471806 GGCCCTTCCTCCTCCGTC 61.472 72.222 0.00 0.00 0.00 4.79
2535 3736 3.471806 GCCCTTCCTCCTCCGTCC 61.472 72.222 0.00 0.00 0.00 4.79
2540 3741 1.490574 CTTCCTCCTCCGTCCTTCAT 58.509 55.000 0.00 0.00 0.00 2.57
2544 3745 1.555075 CCTCCTCCGTCCTTCATTCAA 59.445 52.381 0.00 0.00 0.00 2.69
2548 3749 4.261801 TCCTCCGTCCTTCATTCAAAATC 58.738 43.478 0.00 0.00 0.00 2.17
2556 3757 5.409826 GTCCTTCATTCAAAATCGACTGACT 59.590 40.000 0.00 0.00 0.00 3.41
2574 3775 5.471456 ACTGACTCGAAATCAAAATTCAGCT 59.529 36.000 1.10 0.00 0.00 4.24
2592 3793 4.808414 AGCTGACTGACATGTAGCTAAA 57.192 40.909 16.61 0.00 42.45 1.85
2593 3794 4.753233 AGCTGACTGACATGTAGCTAAAG 58.247 43.478 16.61 4.34 42.45 1.85
2594 3795 3.308323 GCTGACTGACATGTAGCTAAAGC 59.692 47.826 9.79 6.70 42.49 3.51
2595 3796 3.861840 TGACTGACATGTAGCTAAAGCC 58.138 45.455 0.00 0.00 43.38 4.35
2596 3797 3.198872 GACTGACATGTAGCTAAAGCCC 58.801 50.000 0.00 0.00 43.38 5.19
2607 3808 2.026636 AGCTAAAGCCCGTTGGATTACA 60.027 45.455 0.00 0.00 40.02 2.41
2608 3809 2.750712 GCTAAAGCCCGTTGGATTACAA 59.249 45.455 0.00 0.00 40.02 2.41
2736 3941 0.808755 CCCATGTTAGCCCGTGTTTC 59.191 55.000 0.00 0.00 0.00 2.78
2756 3961 9.142993 GTGTTTCTTTTTGCGAAAAATGTATTC 57.857 29.630 12.84 5.23 39.43 1.75
2818 4055 6.942532 TTTAAGAAGTGCACAAGAGATTGT 57.057 33.333 21.04 0.00 35.14 2.71
2832 4069 6.723052 ACAAGAGATTGTGGGAAATGAAAGAT 59.277 34.615 0.00 0.00 33.23 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.360093 TGTCTTGTTTCGTTTTTGTTTATTCAT 57.640 25.926 0.00 0.00 0.00 2.57
12 13 8.979574 TGTTATTGTCTTGTTTCGTTTTTGTTT 58.020 25.926 0.00 0.00 0.00 2.83
13 14 8.522178 TGTTATTGTCTTGTTTCGTTTTTGTT 57.478 26.923 0.00 0.00 0.00 2.83
14 15 8.696410 ATGTTATTGTCTTGTTTCGTTTTTGT 57.304 26.923 0.00 0.00 0.00 2.83
15 16 9.965748 AAATGTTATTGTCTTGTTTCGTTTTTG 57.034 25.926 0.00 0.00 0.00 2.44
18 19 9.581099 AGAAAATGTTATTGTCTTGTTTCGTTT 57.419 25.926 0.00 0.00 0.00 3.60
19 20 9.581099 AAGAAAATGTTATTGTCTTGTTTCGTT 57.419 25.926 6.25 0.00 0.00 3.85
20 21 9.581099 AAAGAAAATGTTATTGTCTTGTTTCGT 57.419 25.926 7.53 0.00 0.00 3.85
40 41 7.908453 TCCCTTGGTTTGAACTTAAAAAGAAA 58.092 30.769 0.00 0.00 0.00 2.52
48 49 4.403734 GTGGATCCCTTGGTTTGAACTTA 58.596 43.478 9.90 0.00 0.00 2.24
78 79 3.132289 TCAGTTGTTCGAGTTGAAGGACT 59.868 43.478 0.00 0.00 37.23 3.85
108 109 4.381718 GGCTTGAGTTGGACTAATACGAGT 60.382 45.833 0.00 0.00 0.00 4.18
119 122 1.067295 ATCACTGGGCTTGAGTTGGA 58.933 50.000 0.00 0.00 0.00 3.53
153 156 1.845266 ACTAGACGCGATGCTCATTG 58.155 50.000 15.93 0.00 0.00 2.82
159 162 1.571919 ATTCCAACTAGACGCGATGC 58.428 50.000 15.93 0.85 0.00 3.91
199 202 8.839947 AACAGAAAACAATAAAAGCAAAATGC 57.160 26.923 0.00 0.00 45.46 3.56
219 222 3.565482 CAGCTCTTGGTTGCTTAAACAGA 59.435 43.478 0.00 0.00 40.86 3.41
230 233 4.729868 AGGTATGTTTTCAGCTCTTGGTT 58.270 39.130 0.00 0.00 0.00 3.67
267 272 0.249699 GGGTGAAAAACAAAGGGCCG 60.250 55.000 0.00 0.00 0.00 6.13
275 280 3.221771 CTGATGACCAGGGTGAAAAACA 58.778 45.455 0.00 0.00 39.23 2.83
281 286 2.300967 GGGCTGATGACCAGGGTGA 61.301 63.158 0.00 0.00 42.34 4.02
282 287 2.273449 GGGCTGATGACCAGGGTG 59.727 66.667 0.00 0.00 42.34 4.61
288 293 4.894201 CAGGATGGGCTGATGACC 57.106 61.111 0.00 0.00 43.36 4.02
315 320 0.528924 GCATGTTGCATCTCAGCCAA 59.471 50.000 0.00 0.00 44.26 4.52
403 409 4.680708 CGGTGCCTGACAGAAATACTACAT 60.681 45.833 3.32 0.00 0.00 2.29
426 669 6.058183 AGTTGGTTGGAGCATATAGATCAAC 58.942 40.000 0.00 0.00 33.23 3.18
468 711 4.039852 TGTTACAGGACACACAGATTAGCA 59.960 41.667 0.00 0.00 0.00 3.49
492 735 3.986006 GGGTGCGTCTCACGGTGA 61.986 66.667 10.88 10.88 46.56 4.02
511 754 3.913799 TCAGAATTGAGGGGAGTAAACCA 59.086 43.478 0.00 0.00 0.00 3.67
528 771 0.742281 GCATCGCAGCCTTCTCAGAA 60.742 55.000 0.00 0.00 0.00 3.02
533 776 2.823147 GCAGCATCGCAGCCTTCT 60.823 61.111 0.00 0.00 35.03 2.85
545 788 1.149854 CTGATATGGGCTGGCAGCA 59.850 57.895 37.49 21.31 44.75 4.41
598 841 7.908827 TTTTTCAGGGAAAACAAAAACTACC 57.091 32.000 3.79 0.00 40.56 3.18
599 842 8.941977 ACATTTTTCAGGGAAAACAAAAACTAC 58.058 29.630 3.79 0.00 40.56 2.73
601 844 7.663493 TCACATTTTTCAGGGAAAACAAAAACT 59.337 29.630 3.79 0.00 40.56 2.66
608 851 8.978539 GTAAAGATCACATTTTTCAGGGAAAAC 58.021 33.333 3.79 0.00 40.56 2.43
644 891 4.801521 TGTTCATGGATTCCTGGATCAT 57.198 40.909 3.95 0.00 0.00 2.45
652 899 6.789262 CAAGTACATCTTGTTCATGGATTCC 58.211 40.000 0.00 0.00 45.89 3.01
669 916 6.331845 TCACGTACTTTGTCTTTCAAGTACA 58.668 36.000 17.84 1.50 38.71 2.90
703 951 9.891828 TGCAAGTTAAAGAATATGTGTGTAAAG 57.108 29.630 0.00 0.00 0.00 1.85
706 954 8.384607 TGTGCAAGTTAAAGAATATGTGTGTA 57.615 30.769 0.00 0.00 0.00 2.90
707 955 7.270757 TGTGCAAGTTAAAGAATATGTGTGT 57.729 32.000 0.00 0.00 0.00 3.72
725 1439 4.696479 ATTGGGTTATTGGTTTGTGCAA 57.304 36.364 0.00 0.00 0.00 4.08
733 1447 9.492730 AAGAAGATCATTTATTGGGTTATTGGT 57.507 29.630 0.00 0.00 0.00 3.67
829 1562 5.015178 ACAAGATCCCTTTGACCCTTTATCA 59.985 40.000 0.56 0.00 0.00 2.15
840 1573 8.997323 CAGCTATCTAAATACAAGATCCCTTTG 58.003 37.037 0.00 0.00 35.36 2.77
884 1620 3.237268 AGGCTGTTTGTTTCCATACCA 57.763 42.857 0.00 0.00 0.00 3.25
972 1712 9.827411 GTTTCTGAATTTCTAATCCTAACACAC 57.173 33.333 0.00 0.00 0.00 3.82
973 1713 9.010029 GGTTTCTGAATTTCTAATCCTAACACA 57.990 33.333 0.00 0.00 0.00 3.72
1072 1813 2.019249 TCCTATGGTGGTACGAACGAG 58.981 52.381 0.14 0.00 0.00 4.18
1074 1815 2.288030 GGATCCTATGGTGGTACGAACG 60.288 54.545 3.84 0.00 0.00 3.95
1222 1993 1.099879 GTCAGTGGCATCTCCCATGC 61.100 60.000 0.00 0.00 43.85 4.06
1223 1994 0.812811 CGTCAGTGGCATCTCCCATG 60.813 60.000 0.00 0.00 37.20 3.66
1224 1995 1.524002 CGTCAGTGGCATCTCCCAT 59.476 57.895 0.00 0.00 37.20 4.00
1229 2000 2.573869 CGACCGTCAGTGGCATCT 59.426 61.111 0.00 0.00 0.00 2.90
1264 2035 2.124942 CGAGCAGCCTTCCCCTTC 60.125 66.667 0.00 0.00 0.00 3.46
1368 2142 4.090761 TGAGCAACTGACCTCAAAATCT 57.909 40.909 0.00 0.00 35.32 2.40
1477 2260 8.682936 AAGTCTTCTTCTTTGTGTACATCAAT 57.317 30.769 0.00 0.00 0.00 2.57
1494 2277 3.195661 GTTGGTGACGTTGAAGTCTTCT 58.804 45.455 13.67 0.00 41.47 2.85
1647 2463 1.426223 AAACACGTTGCTCGCGTTT 59.574 47.368 5.77 12.42 45.66 3.60
1870 2695 2.613133 CGTCCTAGCTTAGCTACGAACT 59.387 50.000 19.47 0.00 40.44 3.01
2001 2849 9.753674 TTCACTGGATTTCTAAAATGTAGGAAT 57.246 29.630 0.00 0.00 0.00 3.01
2003 2851 9.396022 GATTCACTGGATTTCTAAAATGTAGGA 57.604 33.333 0.00 0.00 0.00 2.94
2007 2855 9.696917 GTTTGATTCACTGGATTTCTAAAATGT 57.303 29.630 0.00 0.00 0.00 2.71
2008 2856 9.695526 TGTTTGATTCACTGGATTTCTAAAATG 57.304 29.630 0.00 0.00 0.00 2.32
2009 2857 9.918630 CTGTTTGATTCACTGGATTTCTAAAAT 57.081 29.630 0.00 0.00 0.00 1.82
2010 2858 8.359642 CCTGTTTGATTCACTGGATTTCTAAAA 58.640 33.333 0.00 0.00 35.72 1.52
2011 2859 7.523709 GCCTGTTTGATTCACTGGATTTCTAAA 60.524 37.037 4.88 0.00 35.72 1.85
2013 2861 5.415701 GCCTGTTTGATTCACTGGATTTCTA 59.584 40.000 4.88 0.00 35.72 2.10
2062 3128 1.850441 CTGTTTATACGGCCGACTTCG 59.150 52.381 35.90 3.66 39.44 3.79
2085 3151 2.224018 ACAAGTGCGTGATGCCAATTTT 60.224 40.909 0.00 0.00 45.60 1.82
2139 3212 7.205297 ACTGTGTCTCAAAATGGAAAATTCTG 58.795 34.615 0.00 0.00 0.00 3.02
2140 3213 7.068593 TGACTGTGTCTCAAAATGGAAAATTCT 59.931 33.333 0.00 0.00 33.15 2.40
2141 3214 7.168135 GTGACTGTGTCTCAAAATGGAAAATTC 59.832 37.037 0.00 0.00 33.15 2.17
2142 3215 6.980397 GTGACTGTGTCTCAAAATGGAAAATT 59.020 34.615 0.00 0.00 33.15 1.82
2143 3216 6.096705 TGTGACTGTGTCTCAAAATGGAAAAT 59.903 34.615 0.77 0.00 33.95 1.82
2144 3217 5.417266 TGTGACTGTGTCTCAAAATGGAAAA 59.583 36.000 0.77 0.00 33.95 2.29
2145 3218 4.946772 TGTGACTGTGTCTCAAAATGGAAA 59.053 37.500 0.77 0.00 33.95 3.13
2146 3219 4.335315 GTGTGACTGTGTCTCAAAATGGAA 59.665 41.667 4.39 0.00 37.70 3.53
2147 3220 3.876914 GTGTGACTGTGTCTCAAAATGGA 59.123 43.478 4.39 0.00 37.70 3.41
2148 3221 3.879295 AGTGTGACTGTGTCTCAAAATGG 59.121 43.478 4.39 0.00 37.70 3.16
2149 3222 5.490139 AAGTGTGACTGTGTCTCAAAATG 57.510 39.130 4.39 0.00 37.70 2.32
2150 3223 5.647658 TGAAAGTGTGACTGTGTCTCAAAAT 59.352 36.000 4.39 0.00 37.70 1.82
2161 3234 3.247173 GTCTGAAGCTGAAAGTGTGACTG 59.753 47.826 0.00 0.00 35.30 3.51
2205 3279 2.497273 CTCCCAATCCAACCATCCAAAC 59.503 50.000 0.00 0.00 0.00 2.93
2213 3300 0.623723 TAGCCACTCCCAATCCAACC 59.376 55.000 0.00 0.00 0.00 3.77
2270 3363 7.812191 TGATCCAACGGTTGAAATAGAAAATTG 59.188 33.333 21.88 0.95 0.00 2.32
2273 3366 6.885952 TGATCCAACGGTTGAAATAGAAAA 57.114 33.333 21.88 1.23 0.00 2.29
2274 3367 6.712998 TCTTGATCCAACGGTTGAAATAGAAA 59.287 34.615 21.88 9.25 0.00 2.52
2317 3410 3.198417 TGCATGCTCAGAGGTTGAAGATA 59.802 43.478 20.33 0.00 34.81 1.98
2329 3422 2.424557 AGAGAAACAGTGCATGCTCAG 58.575 47.619 20.33 14.80 0.00 3.35
2441 3546 1.852626 AAGGTGGTTCAGGGGAGGG 60.853 63.158 0.00 0.00 0.00 4.30
2459 3564 8.982723 GCACCCTATTATCTATCTTAGGATTCA 58.017 37.037 0.00 0.00 34.36 2.57
2460 3565 9.207868 AGCACCCTATTATCTATCTTAGGATTC 57.792 37.037 0.00 0.00 34.36 2.52
2461 3566 8.986991 CAGCACCCTATTATCTATCTTAGGATT 58.013 37.037 0.00 0.00 34.36 3.01
2462 3567 8.347591 TCAGCACCCTATTATCTATCTTAGGAT 58.652 37.037 0.00 0.00 34.36 3.24
2463 3568 7.616150 GTCAGCACCCTATTATCTATCTTAGGA 59.384 40.741 0.00 0.00 34.36 2.94
2485 3685 4.821589 GAAGGGGCTCGCCGTCAG 62.822 72.222 12.51 0.00 36.85 3.51
2526 3727 3.780804 TTTTGAATGAAGGACGGAGGA 57.219 42.857 0.00 0.00 0.00 3.71
2527 3728 3.063997 CGATTTTGAATGAAGGACGGAGG 59.936 47.826 0.00 0.00 0.00 4.30
2528 3729 3.932710 TCGATTTTGAATGAAGGACGGAG 59.067 43.478 0.00 0.00 0.00 4.63
2529 3730 3.682858 GTCGATTTTGAATGAAGGACGGA 59.317 43.478 0.00 0.00 0.00 4.69
2530 3731 3.684788 AGTCGATTTTGAATGAAGGACGG 59.315 43.478 0.00 0.00 0.00 4.79
2531 3732 4.388773 TCAGTCGATTTTGAATGAAGGACG 59.611 41.667 0.00 0.00 39.72 4.79
2532 3733 5.409826 AGTCAGTCGATTTTGAATGAAGGAC 59.590 40.000 0.00 0.00 43.64 3.85
2533 3734 5.551233 AGTCAGTCGATTTTGAATGAAGGA 58.449 37.500 0.00 0.00 43.64 3.36
2534 3735 5.862811 GAGTCAGTCGATTTTGAATGAAGG 58.137 41.667 0.00 0.00 43.64 3.46
2556 3757 5.692814 CAGTCAGCTGAATTTTGATTTCGA 58.307 37.500 20.19 0.00 45.28 3.71
2574 3775 3.369471 GGGCTTTAGCTACATGTCAGTCA 60.369 47.826 0.00 0.00 41.70 3.41
2592 3793 1.102978 GCATTGTAATCCAACGGGCT 58.897 50.000 0.00 0.00 35.44 5.19
2593 3794 0.248458 CGCATTGTAATCCAACGGGC 60.248 55.000 0.00 0.00 35.44 6.13
2594 3795 1.091537 ACGCATTGTAATCCAACGGG 58.908 50.000 0.00 0.00 35.44 5.28
2595 3796 2.514902 CAACGCATTGTAATCCAACGG 58.485 47.619 0.00 0.00 35.44 4.44
2596 3797 2.514902 CCAACGCATTGTAATCCAACG 58.485 47.619 0.00 0.00 35.44 4.10
2607 3808 2.733945 GTTGTGGGCCAACGCATT 59.266 55.556 8.40 0.00 43.71 3.56
2653 3854 3.101437 TCCACCTATTTGACGCCTAAGA 58.899 45.455 0.00 0.00 0.00 2.10
2686 3887 1.325476 GCTGGCCCAAATAGCTGCTT 61.325 55.000 7.79 0.00 34.70 3.91
2687 3888 1.755783 GCTGGCCCAAATAGCTGCT 60.756 57.895 7.57 7.57 34.70 4.24


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

AutoCloner maintained by Alex Coulton.