Multiple sequence alignment - TraesCS3D01G280600

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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 TraesCS3D01G280600 chr3D 100.000 2864 0 0 1 2864 388535501 388532638 0.000000e+00 5289.0
1 TraesCS3D01G280600 chr3D 86.022 186 25 1 2168 2352 303791378 303791563 6.260000e-47 198.0
2 TraesCS3D01G280600 chr3B 91.474 1642 47 26 447 2062 505836881 505835307 0.000000e+00 2170.0
3 TraesCS3D01G280600 chr3B 84.362 729 85 19 2146 2864 505834943 505834234 0.000000e+00 688.0
4 TraesCS3D01G280600 chr3B 95.427 328 5 3 1 323 505837719 505837397 5.470000e-142 514.0
5 TraesCS3D01G280600 chr3B 95.588 136 6 0 326 461 505837031 505836896 4.800000e-53 219.0
6 TraesCS3D01G280600 chr3B 80.749 187 28 8 1050 1232 799860575 799860393 3.850000e-29 139.0
7 TraesCS3D01G280600 chr3A 88.449 1567 113 35 1314 2864 509798700 509797186 0.000000e+00 1829.0
8 TraesCS3D01G280600 chr3A 88.227 739 41 25 535 1245 509799452 509798732 0.000000e+00 841.0
9 TraesCS3D01G280600 chr3A 86.571 350 27 12 2 344 509799880 509799544 4.510000e-98 368.0
10 TraesCS3D01G280600 chr3A 81.452 124 22 1 1367 1489 428569856 428569733 1.820000e-17 100.0
11 TraesCS3D01G280600 chr3A 97.727 44 1 0 425 468 509799530 509799487 3.060000e-10 76.8
12 TraesCS3D01G280600 chr2A 82.284 429 61 10 2445 2864 165870122 165870544 9.760000e-95 357.0
13 TraesCS3D01G280600 chr2D 81.352 429 64 9 2446 2862 608654376 608653952 4.570000e-88 335.0
14 TraesCS3D01G280600 chr2D 91.176 102 9 0 2350 2451 106163521 106163622 3.850000e-29 139.0
15 TraesCS3D01G280600 chr2D 88.571 105 12 0 2350 2454 353576862 353576758 8.330000e-26 128.0
16 TraesCS3D01G280600 chr7B 80.607 428 69 10 2448 2862 100353000 100352574 4.600000e-83 318.0
17 TraesCS3D01G280600 chr2B 80.645 434 59 19 2445 2864 263649242 263649664 2.140000e-81 313.0
18 TraesCS3D01G280600 chr1A 80.000 435 72 10 2445 2864 336871724 336871290 9.970000e-80 307.0
19 TraesCS3D01G280600 chr1A 81.818 187 28 6 1050 1233 550314199 550314016 4.940000e-33 152.0
20 TraesCS3D01G280600 chr7A 78.391 435 80 8 2444 2864 482321547 482321981 1.310000e-68 270.0
21 TraesCS3D01G280600 chr6B 78.472 432 80 9 2445 2864 507791866 507791436 1.310000e-68 270.0
22 TraesCS3D01G280600 chr6B 91.176 102 8 1 2350 2450 658653242 658653343 1.380000e-28 137.0
23 TraesCS3D01G280600 chr7D 75.076 662 118 30 2165 2809 602558028 602557397 6.080000e-67 265.0
24 TraesCS3D01G280600 chr7D 85.789 190 27 0 2163 2352 505372473 505372284 4.840000e-48 202.0
25 TraesCS3D01G280600 chr4D 88.298 188 22 0 2165 2352 507884340 507884153 2.870000e-55 226.0
26 TraesCS3D01G280600 chr4D 87.701 187 23 0 2166 2352 64370368 64370554 4.800000e-53 219.0
27 TraesCS3D01G280600 chr4D 91.667 96 8 0 2350 2445 507884181 507884086 1.790000e-27 134.0
28 TraesCS3D01G280600 chr4B 86.631 187 25 0 2166 2352 291803822 291804008 1.040000e-49 207.0
29 TraesCS3D01G280600 chr4A 85.075 201 28 2 2152 2352 729680195 729679997 1.350000e-48 204.0
30 TraesCS3D01G280600 chr4A 80.978 184 35 0 1050 1233 19622495 19622312 2.300000e-31 147.0
31 TraesCS3D01G280600 chr1B 86.486 185 25 0 2168 2352 154638308 154638124 1.350000e-48 204.0
32 TraesCS3D01G280600 chr1B 80.000 200 33 7 1050 1245 627929050 627928854 1.070000e-29 141.0
33 TraesCS3D01G280600 chr1B 85.841 113 16 0 2350 2462 154638152 154638040 1.390000e-23 121.0
34 TraesCS3D01G280600 chr5D 85.263 190 28 0 2163 2352 456706146 456706335 2.250000e-46 196.0
35 TraesCS3D01G280600 chr5D 77.895 190 38 4 1050 1237 461440808 461440621 6.480000e-22 115.0
36 TraesCS3D01G280600 chr6A 77.817 284 37 15 2168 2451 200925005 200925262 4.940000e-33 152.0
37 TraesCS3D01G280600 chr1D 82.286 175 25 6 1062 1233 457852038 457851867 2.300000e-31 147.0
38 TraesCS3D01G280600 chr1D 85.075 67 8 2 2017 2081 477428899 477428833 1.840000e-07 67.6
39 TraesCS3D01G280600 chr5B 90.426 94 9 0 2350 2443 536517219 536517312 1.080000e-24 124.0
40 TraesCS3D01G280600 chr5A 78.723 188 36 4 1052 1237 581488106 581487921 3.880000e-24 122.0


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 TraesCS3D01G280600 chr3D 388532638 388535501 2863 True 5289.00 5289 100.00000 1 2864 1 chr3D.!!$R1 2863
1 TraesCS3D01G280600 chr3B 505834234 505837719 3485 True 897.75 2170 91.71275 1 2864 4 chr3B.!!$R2 2863
2 TraesCS3D01G280600 chr3A 509797186 509799880 2694 True 778.70 1829 90.24350 2 2864 4 chr3A.!!$R2 2862
3 TraesCS3D01G280600 chr7D 602557397 602558028 631 True 265.00 265 75.07600 2165 2809 1 chr7D.!!$R2 644

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
495 898 0.248377 GCATTTGAGCAGCATCCGTC 60.248 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 3103 0.249657 GATCTGAGGCCATCCGTCAC 60.25 60.0 5.01 0.0 37.47 3.67 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
96 98 2.433145 CGTGACAGCGGCTGTGAT 60.433 61.111 37.72 15.94 45.44 3.06
143 146 1.378378 TCCGCTTTGGATCAAGGCA 59.622 52.632 13.57 0.00 44.80 4.75
257 264 1.601162 GGTGACACGAAGAGCAACGTA 60.601 52.381 0.00 0.00 40.76 3.57
289 296 1.048601 TCGTGGAAGCCTTGAAGAGT 58.951 50.000 0.00 0.00 0.00 3.24
290 297 2.029290 GTCGTGGAAGCCTTGAAGAGTA 60.029 50.000 0.00 0.00 0.00 2.59
317 325 2.650778 GGCGCCCCTTCTTGTTTG 59.349 61.111 18.11 0.00 0.00 2.93
321 329 1.866853 CGCCCCTTCTTGTTTGAGGC 61.867 60.000 0.00 0.00 35.55 4.70
322 330 0.827507 GCCCCTTCTTGTTTGAGGCA 60.828 55.000 0.00 0.00 38.79 4.75
324 332 2.038659 CCCCTTCTTGTTTGAGGCAAA 58.961 47.619 0.00 0.00 0.00 3.68
347 719 0.962356 ATCCACAGCAAAGCGGAAGG 60.962 55.000 0.00 0.00 0.00 3.46
367 739 1.493772 CCAAACGTTGAGAGCGTGTA 58.506 50.000 0.00 0.00 42.10 2.90
393 765 2.674380 GCCTGTTCCACCCTGCAG 60.674 66.667 6.78 6.78 0.00 4.41
422 794 3.060615 CTGCCAAGCTGCTCCCAC 61.061 66.667 1.00 0.00 0.00 4.61
423 795 3.564345 CTGCCAAGCTGCTCCCACT 62.564 63.158 1.00 0.00 0.00 4.00
489 892 1.286570 CCAACGCATTTGAGCAGCA 59.713 52.632 0.00 0.00 37.39 4.41
494 897 1.805254 GCATTTGAGCAGCATCCGT 59.195 52.632 0.00 0.00 0.00 4.69
495 898 0.248377 GCATTTGAGCAGCATCCGTC 60.248 55.000 0.00 0.00 0.00 4.79
497 900 0.749454 ATTTGAGCAGCATCCGTCCC 60.749 55.000 0.00 0.00 0.00 4.46
581 984 2.223572 ACTGCACGCTGAAAAGGAAAAG 60.224 45.455 2.69 0.00 0.00 2.27
784 1189 1.304381 CCCAACACCCCATCACCTG 60.304 63.158 0.00 0.00 0.00 4.00
848 1255 1.302033 GCGGGGTGAGGCAGATATG 60.302 63.158 0.00 0.00 0.00 1.78
862 1269 6.136857 AGGCAGATATGTACTTTCTCACCTA 58.863 40.000 0.00 0.00 0.00 3.08
863 1270 6.266558 AGGCAGATATGTACTTTCTCACCTAG 59.733 42.308 0.00 0.00 0.00 3.02
905 1312 2.495551 GAAATATCTGCGCGCGCG 60.496 61.111 45.73 45.73 45.51 6.86
920 1330 3.871574 GCGCACACACACGTTGGT 61.872 61.111 0.30 0.00 0.00 3.67
921 1331 2.526993 GCGCACACACACGTTGGTA 61.527 57.895 0.30 0.00 0.00 3.25
986 1415 1.436983 CGGCTTCCTTATCCGGTTGC 61.437 60.000 0.00 0.00 39.52 4.17
987 1416 1.436983 GGCTTCCTTATCCGGTTGCG 61.437 60.000 0.00 0.00 0.00 4.85
1238 1670 2.160417 AGCTCAACACCTACGTACGTAC 59.840 50.000 23.60 15.90 0.00 3.67
1239 1671 2.729156 GCTCAACACCTACGTACGTACC 60.729 54.545 23.60 2.84 0.00 3.34
1240 1672 1.810151 TCAACACCTACGTACGTACCC 59.190 52.381 23.60 0.00 0.00 3.69
1241 1673 1.539388 CAACACCTACGTACGTACCCA 59.461 52.381 23.60 6.22 0.00 4.51
1242 1674 1.165270 ACACCTACGTACGTACCCAC 58.835 55.000 23.60 0.00 0.00 4.61
1303 1735 0.315568 GTATGCCTACTCTGCTCCGG 59.684 60.000 0.00 0.00 0.00 5.14
1309 1741 2.329678 CTACTCTGCTCCGGTCAGCG 62.330 65.000 17.63 15.04 42.92 5.18
1310 1742 4.504916 CTCTGCTCCGGTCAGCGG 62.505 72.222 16.14 16.14 45.90 5.52
1314 1746 4.577246 GCTCCGGTCAGCGGCTAG 62.577 72.222 11.45 4.83 0.00 3.42
1324 1756 2.025441 GCGGCTAGCTCTCGAGTG 59.975 66.667 15.72 11.53 44.04 3.51
1325 1757 2.766400 GCGGCTAGCTCTCGAGTGT 61.766 63.158 15.72 3.81 44.04 3.55
1326 1758 1.803943 CGGCTAGCTCTCGAGTGTT 59.196 57.895 15.72 10.76 0.00 3.32
1327 1759 0.171455 CGGCTAGCTCTCGAGTGTTT 59.829 55.000 15.72 5.69 0.00 2.83
1362 1799 3.599792 CTCGCCGTTGCTGCTTTGG 62.600 63.158 0.00 0.53 34.43 3.28
1756 2193 1.874129 TTCAAGCCCGGATAAGAGGA 58.126 50.000 0.73 0.00 0.00 3.71
1836 2273 4.397832 GCCGTGCCGTTCCCCTTA 62.398 66.667 0.00 0.00 0.00 2.69
1877 2314 3.567397 TCTACTGATAGACCTTGGGAGC 58.433 50.000 0.00 0.00 32.16 4.70
1921 2363 3.057174 ACACGTGTGATGTTTTGGTGTTT 60.057 39.130 22.71 0.00 33.77 2.83
1922 2364 4.156190 ACACGTGTGATGTTTTGGTGTTTA 59.844 37.500 22.71 0.00 33.77 2.01
1923 2365 5.163602 ACACGTGTGATGTTTTGGTGTTTAT 60.164 36.000 22.71 0.00 33.77 1.40
1924 2366 5.172951 CACGTGTGATGTTTTGGTGTTTATG 59.827 40.000 7.58 0.00 0.00 1.90
1925 2367 5.163602 ACGTGTGATGTTTTGGTGTTTATGT 60.164 36.000 0.00 0.00 0.00 2.29
1926 2368 6.038382 ACGTGTGATGTTTTGGTGTTTATGTA 59.962 34.615 0.00 0.00 0.00 2.29
1927 2369 7.081349 CGTGTGATGTTTTGGTGTTTATGTAT 58.919 34.615 0.00 0.00 0.00 2.29
1928 2370 7.060518 CGTGTGATGTTTTGGTGTTTATGTATG 59.939 37.037 0.00 0.00 0.00 2.39
1929 2371 7.865385 GTGTGATGTTTTGGTGTTTATGTATGT 59.135 33.333 0.00 0.00 0.00 2.29
1930 2372 8.417106 TGTGATGTTTTGGTGTTTATGTATGTT 58.583 29.630 0.00 0.00 0.00 2.71
1931 2373 9.255304 GTGATGTTTTGGTGTTTATGTATGTTT 57.745 29.630 0.00 0.00 0.00 2.83
1983 2428 4.023107 GCATAGTTGCTATCTGACCGTCTA 60.023 45.833 0.00 0.00 45.77 2.59
2035 2480 8.447833 CCACGAGTTTTAGCATTTAGAAATGTA 58.552 33.333 14.72 5.44 45.77 2.29
2068 2515 5.048224 AGTGGGTTCATATATACCGAGTTCG 60.048 44.000 0.00 0.00 35.19 3.95
2069 2516 4.171754 GGGTTCATATATACCGAGTTCGC 58.828 47.826 0.00 0.00 38.18 4.70
2081 2528 1.465689 CGAGTTCGCCGATGCATTTTT 60.466 47.619 0.00 0.00 37.32 1.94
2085 2532 1.173043 TCGCCGATGCATTTTTCCTT 58.827 45.000 0.00 0.00 37.32 3.36
2094 2541 1.970640 GCATTTTTCCTTCACCCACCT 59.029 47.619 0.00 0.00 0.00 4.00
2096 2543 2.375014 TTTTTCCTTCACCCACCTCC 57.625 50.000 0.00 0.00 0.00 4.30
2097 2544 1.529744 TTTTCCTTCACCCACCTCCT 58.470 50.000 0.00 0.00 0.00 3.69
2098 2545 1.064825 TTTCCTTCACCCACCTCCTC 58.935 55.000 0.00 0.00 0.00 3.71
2099 2546 0.104672 TTCCTTCACCCACCTCCTCA 60.105 55.000 0.00 0.00 0.00 3.86
2109 2562 1.620798 CCACCTCCTCACCTCTCATGA 60.621 57.143 0.00 0.00 0.00 3.07
2142 2595 5.824904 TTTAAGAGCATGCTGGAAATCTC 57.175 39.130 28.27 8.18 0.00 2.75
2143 2596 1.950828 AGAGCATGCTGGAAATCTCG 58.049 50.000 28.27 0.00 0.00 4.04
2144 2597 0.942962 GAGCATGCTGGAAATCTCGG 59.057 55.000 28.27 0.00 0.00 4.63
2183 2909 1.095228 CGGCCCTTCATATGTTGCGT 61.095 55.000 1.90 0.00 0.00 5.24
2201 2927 2.798499 GCGTCGCACATCTACATACCTT 60.798 50.000 13.44 0.00 0.00 3.50
2212 2938 8.889717 CACATCTACATACCTTAAATTCCGTTT 58.110 33.333 0.00 0.00 0.00 3.60
2243 2978 6.745116 TCTATTCAATCCATACACGTCGATT 58.255 36.000 0.00 0.00 0.00 3.34
2299 3034 9.928236 TTTAAAACAAAGCAAAGCAAATCATAC 57.072 25.926 0.00 0.00 0.00 2.39
2346 3081 1.359848 AATCAATGTCCGAGCGTGAC 58.640 50.000 0.00 0.00 0.00 3.67
2347 3082 0.802222 ATCAATGTCCGAGCGTGACG 60.802 55.000 0.00 0.00 35.46 4.35
2354 3089 4.162640 CGAGCGTGACGGATGAAA 57.837 55.556 7.25 0.00 0.00 2.69
2355 3090 2.665777 CGAGCGTGACGGATGAAAT 58.334 52.632 7.25 0.00 0.00 2.17
2356 3091 0.572590 CGAGCGTGACGGATGAAATC 59.427 55.000 7.25 0.00 44.55 2.17
2368 3103 3.244670 GATGAAATCAATGTCCGAGCG 57.755 47.619 0.00 0.00 44.70 5.03
2369 3104 2.093306 TGAAATCAATGTCCGAGCGT 57.907 45.000 0.00 0.00 0.00 5.07
2370 3105 1.731709 TGAAATCAATGTCCGAGCGTG 59.268 47.619 0.00 0.00 0.00 5.34
2371 3106 1.999735 GAAATCAATGTCCGAGCGTGA 59.000 47.619 0.00 0.00 0.00 4.35
2449 3205 3.940640 CGGAATGCGTCATGCCCG 61.941 66.667 10.24 12.56 45.60 6.13
2467 3223 2.125552 TGCTCATTCACGCCCGAG 60.126 61.111 0.00 0.00 0.00 4.63
2490 3246 2.202557 TGCGGCGAGTCACATACG 60.203 61.111 12.98 0.00 0.00 3.06
2497 3254 1.256652 CGAGTCACATACGTCAACCG 58.743 55.000 0.00 0.00 44.03 4.44
2505 3262 2.018727 ATACGTCAACCGCCGGCATA 62.019 55.000 28.98 2.79 41.42 3.14
2508 3265 1.817941 GTCAACCGCCGGCATATGT 60.818 57.895 28.98 14.67 0.00 2.29
2522 3279 2.445427 CATATGTGTGGGTGGAAAGCA 58.555 47.619 0.00 0.00 0.00 3.91
2534 3291 0.171231 GGAAAGCACTCCGAAATGGC 59.829 55.000 0.00 0.00 37.80 4.40
2560 3320 2.303022 TCGCCTCAAATTCTCCTCTGTT 59.697 45.455 0.00 0.00 0.00 3.16
2627 3392 4.933064 GGATCCGAGCGCGACAGG 62.933 72.222 12.10 9.32 40.82 4.00
2633 3398 3.760035 GAGCGCGACAGGGGAGAA 61.760 66.667 12.10 0.00 0.00 2.87
2639 3404 1.674057 CGACAGGGGAGAAAGCTGT 59.326 57.895 0.00 0.00 0.00 4.40
2736 3506 3.020026 CTCTGCCTTGCAAGTCGCG 62.020 63.158 24.35 16.23 46.97 5.87
2757 3527 3.745803 GACGAAGGGACGCCGACT 61.746 66.667 0.00 0.00 36.70 4.18
2763 3533 4.047059 GGGACGCCGACTGACGAA 62.047 66.667 0.22 0.00 45.77 3.85
2826 3596 1.956869 ACATCTCTGGTGGTGGATCA 58.043 50.000 0.00 0.00 0.00 2.92
2850 3620 0.833287 CGATGGTGAGGATTGGGAGT 59.167 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 98 2.776526 AGGGTGGCACCTTGTGGA 60.777 61.111 33.87 0.00 37.69 4.02
143 146 1.004918 CTTTCGTCCCGAGCCAACT 60.005 57.895 0.00 0.00 37.14 3.16
257 264 0.327924 TCCACGACTGAATGGCCAAT 59.672 50.000 10.96 0.00 35.81 3.16
324 332 1.686052 TCCGCTTTGCTGTGGATTTTT 59.314 42.857 3.73 0.00 41.18 1.94
347 719 1.082756 CACGCTCTCAACGTTTGGC 60.083 57.895 0.00 0.00 42.96 4.52
367 739 2.525368 GGTGGAACAGGCCTAAAATGT 58.475 47.619 3.98 0.00 41.80 2.71
393 765 1.787012 CTTGGCAGCATGTTGAAACC 58.213 50.000 14.38 5.77 39.31 3.27
494 897 1.757118 GTTGAGATCAGATCACCGGGA 59.243 52.381 13.14 0.00 0.00 5.14
495 898 1.202580 GGTTGAGATCAGATCACCGGG 60.203 57.143 13.14 0.00 0.00 5.73
497 900 2.967599 TGGTTGAGATCAGATCACCG 57.032 50.000 13.14 0.00 0.00 4.94
501 904 2.877168 GGTGCATGGTTGAGATCAGATC 59.123 50.000 1.64 1.64 0.00 2.75
502 905 2.240414 TGGTGCATGGTTGAGATCAGAT 59.760 45.455 0.00 0.00 0.00 2.90
503 906 1.629861 TGGTGCATGGTTGAGATCAGA 59.370 47.619 0.00 0.00 0.00 3.27
504 907 2.118313 TGGTGCATGGTTGAGATCAG 57.882 50.000 0.00 0.00 0.00 2.90
505 908 2.812836 ATGGTGCATGGTTGAGATCA 57.187 45.000 0.00 0.00 0.00 2.92
506 909 3.181483 GGAAATGGTGCATGGTTGAGATC 60.181 47.826 0.00 0.00 0.00 2.75
581 984 4.467062 GCTCAAAAGCGCTCGGCC 62.467 66.667 12.06 0.00 45.17 6.13
710 1115 1.398390 GATTTGCTCGGTGATGTGTCC 59.602 52.381 0.00 0.00 0.00 4.02
712 1117 1.078709 CGATTTGCTCGGTGATGTGT 58.921 50.000 0.00 0.00 43.82 3.72
760 1165 0.178947 GATGGGGTGTTGGGGTTCAA 60.179 55.000 0.00 0.00 0.00 2.69
834 1241 5.163405 TGAGAAAGTACATATCTGCCTCACC 60.163 44.000 0.00 0.00 0.00 4.02
836 1243 5.163405 GGTGAGAAAGTACATATCTGCCTCA 60.163 44.000 0.00 0.00 0.00 3.86
838 1245 4.965532 AGGTGAGAAAGTACATATCTGCCT 59.034 41.667 0.00 3.19 0.00 4.75
848 1255 7.479150 ACGCTTTATACTAGGTGAGAAAGTAC 58.521 38.462 0.00 0.00 0.00 2.73
905 1312 1.730064 CCTATACCAACGTGTGTGTGC 59.270 52.381 0.00 0.00 0.00 4.57
906 1313 3.306917 TCCTATACCAACGTGTGTGTG 57.693 47.619 0.00 0.00 0.00 3.82
907 1314 3.306502 CCTTCCTATACCAACGTGTGTGT 60.307 47.826 0.00 0.00 0.00 3.72
908 1315 3.056393 TCCTTCCTATACCAACGTGTGTG 60.056 47.826 0.00 0.00 0.00 3.82
1284 1716 0.315568 CCGGAGCAGAGTAGGCATAC 59.684 60.000 0.00 0.00 0.00 2.39
1285 1717 0.106167 ACCGGAGCAGAGTAGGCATA 60.106 55.000 9.46 0.00 0.00 3.14
1309 1741 1.067495 ACAAACACTCGAGAGCTAGCC 60.067 52.381 21.68 2.81 0.00 3.93
1310 1742 2.355717 ACAAACACTCGAGAGCTAGC 57.644 50.000 21.68 6.62 0.00 3.42
1311 1743 3.426859 CACAACAAACACTCGAGAGCTAG 59.573 47.826 21.68 8.34 0.00 3.42
1313 1745 2.205074 CACAACAAACACTCGAGAGCT 58.795 47.619 21.68 0.00 0.00 4.09
1314 1746 1.333258 GCACAACAAACACTCGAGAGC 60.333 52.381 21.68 3.31 0.00 4.09
1317 1749 1.933181 TGAGCACAACAAACACTCGAG 59.067 47.619 11.84 11.84 0.00 4.04
1319 1751 3.363970 GGTATGAGCACAACAAACACTCG 60.364 47.826 0.00 0.00 0.00 4.18
1320 1752 3.815401 AGGTATGAGCACAACAAACACTC 59.185 43.478 0.00 0.00 0.00 3.51
1321 1753 3.565482 CAGGTATGAGCACAACAAACACT 59.435 43.478 0.00 0.00 0.00 3.55
1322 1754 3.853307 GCAGGTATGAGCACAACAAACAC 60.853 47.826 0.00 0.00 0.00 3.32
1323 1755 2.293122 GCAGGTATGAGCACAACAAACA 59.707 45.455 0.00 0.00 0.00 2.83
1324 1756 2.554032 AGCAGGTATGAGCACAACAAAC 59.446 45.455 0.00 0.00 0.00 2.93
1325 1757 2.813754 GAGCAGGTATGAGCACAACAAA 59.186 45.455 0.00 0.00 0.00 2.83
1326 1758 2.426522 GAGCAGGTATGAGCACAACAA 58.573 47.619 0.00 0.00 0.00 2.83
1327 1759 1.672737 CGAGCAGGTATGAGCACAACA 60.673 52.381 0.00 0.00 0.00 3.33
1362 1799 0.875059 CCTTGCGAAAACCCTGAGAC 59.125 55.000 0.00 0.00 0.00 3.36
1735 2172 3.578716 CTCCTCTTATCCGGGCTTGAATA 59.421 47.826 0.00 0.00 0.00 1.75
1836 2273 4.366267 AGAACACCTGTCCCAGATTAGAT 58.634 43.478 0.00 0.00 32.44 1.98
1877 2314 5.763698 TGTACACCTATCTATCAACTCTCGG 59.236 44.000 0.00 0.00 0.00 4.63
1930 2372 8.863086 GGGGAAGTACACTGTACATACATATAA 58.137 37.037 19.34 0.00 35.36 0.98
1931 2373 8.229605 AGGGGAAGTACACTGTACATACATATA 58.770 37.037 19.34 0.00 35.36 0.86
1932 2374 7.073854 AGGGGAAGTACACTGTACATACATAT 58.926 38.462 19.34 0.00 35.36 1.78
1983 2428 2.170607 AGTGACTACTATGGCGGCAATT 59.829 45.455 18.31 2.22 34.74 2.32
2057 2503 1.299926 GCATCGGCGAACTCGGTAT 60.300 57.895 15.93 0.00 40.23 2.73
2068 2515 2.262211 GTGAAGGAAAAATGCATCGGC 58.738 47.619 0.00 0.00 41.68 5.54
2069 2516 2.417243 GGGTGAAGGAAAAATGCATCGG 60.417 50.000 0.00 0.00 0.00 4.18
2081 2528 0.836400 GTGAGGAGGTGGGTGAAGGA 60.836 60.000 0.00 0.00 0.00 3.36
2085 2532 1.229209 GAGGTGAGGAGGTGGGTGA 60.229 63.158 0.00 0.00 0.00 4.02
2094 2541 2.037901 GCTGATCATGAGAGGTGAGGA 58.962 52.381 0.09 0.00 0.00 3.71
2096 2543 2.694109 TGAGCTGATCATGAGAGGTGAG 59.306 50.000 12.62 0.00 31.12 3.51
2097 2544 2.743553 TGAGCTGATCATGAGAGGTGA 58.256 47.619 12.62 3.42 31.12 4.02
2133 2586 1.975680 GTATAGGGGCCGAGATTTCCA 59.024 52.381 0.00 0.00 0.00 3.53
2142 2595 1.194781 AGGCAGATGTATAGGGGCCG 61.195 60.000 0.00 0.00 45.79 6.13
2143 2596 0.326264 CAGGCAGATGTATAGGGGCC 59.674 60.000 0.00 0.00 41.65 5.80
2144 2597 0.322008 GCAGGCAGATGTATAGGGGC 60.322 60.000 0.00 0.00 0.00 5.80
2170 2896 1.433534 TGTGCGACGCAACATATGAA 58.566 45.000 26.29 0.00 41.47 2.57
2183 2909 6.704493 GGAATTTAAGGTATGTAGATGTGCGA 59.296 38.462 0.00 0.00 0.00 5.10
2212 2938 9.996554 ACGTGTATGGATTGAATAGATTTGATA 57.003 29.630 0.00 0.00 0.00 2.15
2221 2947 9.563898 GTATAATCGACGTGTATGGATTGAATA 57.436 33.333 0.00 0.00 31.95 1.75
2222 2948 8.085909 TGTATAATCGACGTGTATGGATTGAAT 58.914 33.333 0.00 0.00 31.95 2.57
2223 2949 7.427214 TGTATAATCGACGTGTATGGATTGAA 58.573 34.615 0.00 0.00 31.95 2.69
2224 2950 6.972722 TGTATAATCGACGTGTATGGATTGA 58.027 36.000 0.00 0.00 31.95 2.57
2225 2951 7.631915 TTGTATAATCGACGTGTATGGATTG 57.368 36.000 0.00 0.00 31.95 2.67
2226 2952 9.350357 GTATTGTATAATCGACGTGTATGGATT 57.650 33.333 0.00 0.00 33.91 3.01
2227 2953 8.517056 TGTATTGTATAATCGACGTGTATGGAT 58.483 33.333 0.00 0.00 0.00 3.41
2228 2954 7.873910 TGTATTGTATAATCGACGTGTATGGA 58.126 34.615 0.00 0.00 0.00 3.41
2229 2955 8.510132 TTGTATTGTATAATCGACGTGTATGG 57.490 34.615 0.00 0.00 0.00 2.74
2299 3034 2.361757 TGGCATGTCTGGTTTGTTCAAG 59.638 45.455 0.00 0.00 0.00 3.02
2347 3082 2.032549 CGCTCGGACATTGATTTCATCC 60.033 50.000 0.00 0.00 0.00 3.51
2348 3083 2.609459 ACGCTCGGACATTGATTTCATC 59.391 45.455 0.00 0.00 0.00 2.92
2349 3084 2.352651 CACGCTCGGACATTGATTTCAT 59.647 45.455 0.00 0.00 0.00 2.57
2350 3085 1.731709 CACGCTCGGACATTGATTTCA 59.268 47.619 0.00 0.00 0.00 2.69
2351 3086 1.999735 TCACGCTCGGACATTGATTTC 59.000 47.619 0.00 0.00 0.00 2.17
2352 3087 1.732259 GTCACGCTCGGACATTGATTT 59.268 47.619 0.00 0.00 35.36 2.17
2353 3088 1.359848 GTCACGCTCGGACATTGATT 58.640 50.000 0.00 0.00 35.36 2.57
2354 3089 0.802222 CGTCACGCTCGGACATTGAT 60.802 55.000 0.00 0.00 34.97 2.57
2355 3090 1.443702 CGTCACGCTCGGACATTGA 60.444 57.895 0.00 0.00 34.97 2.57
2356 3091 3.072598 CGTCACGCTCGGACATTG 58.927 61.111 0.00 0.00 34.97 2.82
2364 3099 4.148825 AGGCCATCCGTCACGCTC 62.149 66.667 5.01 0.00 37.47 5.03
2365 3100 4.148825 GAGGCCATCCGTCACGCT 62.149 66.667 5.01 0.00 37.47 5.07
2366 3101 4.451150 TGAGGCCATCCGTCACGC 62.451 66.667 5.01 0.00 37.47 5.34
2367 3102 2.021068 ATCTGAGGCCATCCGTCACG 62.021 60.000 5.01 0.00 37.47 4.35
2368 3103 0.249657 GATCTGAGGCCATCCGTCAC 60.250 60.000 5.01 0.00 37.47 3.67
2369 3104 0.687427 TGATCTGAGGCCATCCGTCA 60.687 55.000 5.01 0.00 37.47 4.35
2370 3105 0.249657 GTGATCTGAGGCCATCCGTC 60.250 60.000 5.01 0.00 37.47 4.79
2371 3106 0.689080 AGTGATCTGAGGCCATCCGT 60.689 55.000 5.01 0.00 37.47 4.69
2449 3205 2.434185 TCGGGCGTGAATGAGCAC 60.434 61.111 0.00 0.00 35.46 4.40
2490 3246 1.817941 ACATATGCCGGCGGTTGAC 60.818 57.895 28.82 11.33 0.00 3.18
2497 3254 2.124320 ACCCACACATATGCCGGC 60.124 61.111 22.73 22.73 0.00 6.13
2505 3262 0.185901 AGTGCTTTCCACCCACACAT 59.814 50.000 0.00 0.00 45.83 3.21
2508 3265 1.150536 GGAGTGCTTTCCACCCACA 59.849 57.895 2.64 0.00 45.83 4.17
2522 3279 1.299976 GACTGGGCCATTTCGGAGT 59.700 57.895 6.72 0.00 36.56 3.85
2534 3291 1.373570 GAGAATTTGAGGCGACTGGG 58.626 55.000 0.00 0.00 44.43 4.45
2560 3320 2.966732 GCTGTCCGACCCCATTGGA 61.967 63.158 3.62 0.00 38.75 3.53
2588 3348 1.448540 CTTCTGTCCGAGCGCCAAT 60.449 57.895 2.29 0.00 0.00 3.16
2625 3390 0.402121 GTGGAACAGCTTTCTCCCCT 59.598 55.000 3.58 0.00 41.80 4.79
2639 3404 0.323629 GAGGTTCGGACATGGTGGAA 59.676 55.000 0.00 0.00 0.00 3.53
2707 3476 0.894184 AAGGCAGAGAACGTCCTCGA 60.894 55.000 0.00 0.00 40.62 4.04
2710 3479 1.004440 GCAAGGCAGAGAACGTCCT 60.004 57.895 0.00 0.00 0.00 3.85
2757 3527 4.961511 ACGCAAGCCGCTTCGTCA 62.962 61.111 18.67 0.00 45.62 4.35
2826 3596 0.833287 CAATCCTCACCATCGGTCCT 59.167 55.000 0.00 0.00 31.02 3.85


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

AutoCloner maintained by Alex Coulton.