Multiple sequence alignment - TraesCS2D01G393300

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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 TraesCS2D01G393300 chr2D 100.000 3523 0 0 1 3523 502573120 502576642 0.000000e+00 6506.0
1 TraesCS2D01G393300 chr2A 95.911 1394 55 1 931 2324 648027134 648028525 0.000000e+00 2257.0
2 TraesCS2D01G393300 chr2A 89.492 1142 70 24 2386 3523 648106987 648108082 0.000000e+00 1399.0
3 TraesCS2D01G393300 chr2A 84.087 1150 120 28 2386 3523 648029082 648030180 0.000000e+00 1051.0
4 TraesCS2D01G393300 chr2A 88.088 319 27 9 608 925 648026768 648027076 5.560000e-98 368.0
5 TraesCS2D01G393300 chr2A 93.151 146 10 0 2185 2330 648104680 648104825 7.660000e-52 215.0
6 TraesCS2D01G393300 chr2A 85.417 144 21 0 518 661 15269119 15269262 2.190000e-32 150.0
7 TraesCS2D01G393300 chr2B 95.282 1399 66 0 931 2329 590228292 590229690 0.000000e+00 2218.0
8 TraesCS2D01G393300 chr2B 91.230 935 67 10 1 931 590227332 590228255 0.000000e+00 1258.0
9 TraesCS2D01G393300 chr2B 86.321 753 60 22 2391 3115 590230268 590231005 0.000000e+00 780.0
10 TraesCS2D01G393300 chr2B 87.048 332 38 5 3196 3523 590231004 590231334 1.540000e-98 370.0
11 TraesCS2D01G393300 chr3D 76.442 815 146 34 2723 3520 276519267 276520052 1.970000e-107 399.0
12 TraesCS2D01G393300 chr3D 83.333 384 56 5 1081 1457 414629242 414629624 7.240000e-92 348.0
13 TraesCS2D01G393300 chr3D 86.111 144 20 0 518 661 584164963 584165106 4.710000e-34 156.0
14 TraesCS2D01G393300 chr1D 73.871 1041 224 31 1114 2120 470190148 470191174 4.290000e-99 372.0
15 TraesCS2D01G393300 chr1D 76.323 718 139 26 1111 1808 470084783 470085489 4.330000e-94 355.0
16 TraesCS2D01G393300 chr1A 73.842 1036 223 31 1119 2120 563783660 563784681 5.560000e-98 368.0
17 TraesCS2D01G393300 chr3B 83.073 384 57 5 1081 1457 540456792 540457174 3.370000e-90 342.0
18 TraesCS2D01G393300 chr3B 74.811 794 154 37 2754 3522 492212122 492212894 2.040000e-82 316.0
19 TraesCS2D01G393300 chr3B 79.845 129 22 4 2669 2795 492214039 492214165 1.350000e-14 91.6
20 TraesCS2D01G393300 chr3A 82.812 384 58 5 1081 1457 535823913 535823531 1.570000e-88 337.0
21 TraesCS2D01G393300 chr3A 73.996 523 110 20 1612 2121 535823328 535822819 4.640000e-44 189.0
22 TraesCS2D01G393300 chr4A 73.068 906 157 50 2576 3444 2534571 2535426 1.260000e-59 241.0
23 TraesCS2D01G393300 chr4D 78.049 328 55 14 3136 3454 469181909 469181590 1.290000e-44 191.0
24 TraesCS2D01G393300 chr5D 84.722 144 22 0 518 661 320450888 320450745 1.020000e-30 145.0
25 TraesCS2D01G393300 chrUn 97.059 34 1 0 27 60 313365951 313365984 1.370000e-04 58.4
26 TraesCS2D01G393300 chrUn 97.059 34 1 0 27 60 313373497 313373530 1.370000e-04 58.4


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 TraesCS2D01G393300 chr2D 502573120 502576642 3522 False 6506.000000 6506 100.00000 1 3523 1 chr2D.!!$F1 3522
1 TraesCS2D01G393300 chr2A 648026768 648030180 3412 False 1225.333333 2257 89.36200 608 3523 3 chr2A.!!$F2 2915
2 TraesCS2D01G393300 chr2A 648104680 648108082 3402 False 807.000000 1399 91.32150 2185 3523 2 chr2A.!!$F3 1338
3 TraesCS2D01G393300 chr2B 590227332 590231334 4002 False 1156.500000 2218 89.97025 1 3523 4 chr2B.!!$F1 3522
4 TraesCS2D01G393300 chr3D 276519267 276520052 785 False 399.000000 399 76.44200 2723 3520 1 chr3D.!!$F1 797
5 TraesCS2D01G393300 chr1D 470190148 470191174 1026 False 372.000000 372 73.87100 1114 2120 1 chr1D.!!$F2 1006
6 TraesCS2D01G393300 chr1D 470084783 470085489 706 False 355.000000 355 76.32300 1111 1808 1 chr1D.!!$F1 697
7 TraesCS2D01G393300 chr1A 563783660 563784681 1021 False 368.000000 368 73.84200 1119 2120 1 chr1A.!!$F1 1001
8 TraesCS2D01G393300 chr3B 492212122 492214165 2043 False 203.800000 316 77.32800 2669 3522 2 chr3B.!!$F2 853
9 TraesCS2D01G393300 chr3A 535822819 535823913 1094 True 263.000000 337 78.40400 1081 2121 2 chr3A.!!$R1 1040
10 TraesCS2D01G393300 chr4A 2534571 2535426 855 False 241.000000 241 73.06800 2576 3444 1 chr4A.!!$F1 868

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
825 830 0.251165 GGCTGTCCTGTGCCCTTAAA 60.251 55.0 0.0 0.0 43.11 1.52 F
2090 2214 0.105039 CTCAGTACGGGATGAAGGGC 59.895 60.0 0.0 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 2511 0.382515 TTACAAAAGCCCGTGTGTGC 59.617 50.000 0.0 0.00 0.00 4.57 R
3497 6299 4.416516 AGGTCATATCATGATACCGTGGA 58.583 43.478 17.6 7.89 42.04 4.02 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
30 31 3.486375 GCACAACCATCGACATCTTCATG 60.486 47.826 0.00 0.00 35.92 3.07
32 33 4.869861 CACAACCATCGACATCTTCATGTA 59.130 41.667 0.00 0.00 43.79 2.29
37 38 5.755375 ACCATCGACATCTTCATGTATTGTC 59.245 40.000 0.00 2.12 43.79 3.18
51 52 2.793278 ATTGTCGCCACCACTTTTTC 57.207 45.000 0.00 0.00 0.00 2.29
52 53 0.378962 TTGTCGCCACCACTTTTTCG 59.621 50.000 0.00 0.00 0.00 3.46
53 54 0.745128 TGTCGCCACCACTTTTTCGT 60.745 50.000 0.00 0.00 0.00 3.85
54 55 0.316689 GTCGCCACCACTTTTTCGTG 60.317 55.000 0.00 0.00 34.71 4.35
65 66 5.080969 CACTTTTTCGTGGTCCCTATAGA 57.919 43.478 0.00 0.00 0.00 1.98
67 68 6.812998 CACTTTTTCGTGGTCCCTATAGATA 58.187 40.000 0.00 0.00 0.00 1.98
78 79 8.634444 GTGGTCCCTATAGATATATGTGATGTC 58.366 40.741 0.00 0.00 0.00 3.06
103 105 2.438434 CCATCCCCCGTGTCAAGC 60.438 66.667 0.00 0.00 0.00 4.01
111 113 1.300620 CCGTGTCAAGCCTTCGTCA 60.301 57.895 0.00 0.00 0.00 4.35
112 114 0.670546 CCGTGTCAAGCCTTCGTCAT 60.671 55.000 0.00 0.00 0.00 3.06
113 115 0.716108 CGTGTCAAGCCTTCGTCATC 59.284 55.000 0.00 0.00 0.00 2.92
114 116 1.079503 GTGTCAAGCCTTCGTCATCC 58.920 55.000 0.00 0.00 0.00 3.51
132 135 0.602106 CCTGCATCTCACCGCCATAG 60.602 60.000 0.00 0.00 0.00 2.23
135 138 1.665916 CATCTCACCGCCATAGCCG 60.666 63.158 0.00 0.00 34.57 5.52
197 201 2.543653 GGTGGCCATCATAATTCGCAAC 60.544 50.000 12.38 0.00 0.00 4.17
207 211 1.586154 AATTCGCAACAAGCCTCCCG 61.586 55.000 0.00 0.00 41.38 5.14
226 230 2.554272 CGCACCGCACAAACCTAC 59.446 61.111 0.00 0.00 0.00 3.18
236 240 2.227194 CACAAACCTACCAGAACCACC 58.773 52.381 0.00 0.00 0.00 4.61
259 263 2.619849 CCTCCTTCTGATGTGCAACCAT 60.620 50.000 0.00 0.00 34.36 3.55
260 264 3.087031 CTCCTTCTGATGTGCAACCATT 58.913 45.455 0.00 0.00 34.36 3.16
278 282 5.027293 CCATTGTGGTCATCACTGAGATA 57.973 43.478 0.00 0.00 46.20 1.98
348 352 2.156917 CAATGGCACACAGACATCAGT 58.843 47.619 0.00 0.00 44.97 3.41
351 355 1.270465 TGGCACACAGACATCAGTGAG 60.270 52.381 10.97 4.71 36.92 3.51
357 361 0.900421 CAGACATCAGTGAGGAGGCA 59.100 55.000 12.53 0.00 0.00 4.75
369 373 1.376553 GGAGGCACTGCTTGAGTCC 60.377 63.158 0.00 0.00 45.87 3.85
370 374 1.676384 GAGGCACTGCTTGAGTCCT 59.324 57.895 0.00 0.00 41.55 3.85
379 383 1.833630 TGCTTGAGTCCTGATCCGATT 59.166 47.619 0.00 0.00 0.00 3.34
438 443 4.769063 CACCGCCGCCCATACACA 62.769 66.667 0.00 0.00 0.00 3.72
439 444 4.770874 ACCGCCGCCCATACACAC 62.771 66.667 0.00 0.00 0.00 3.82
440 445 4.467084 CCGCCGCCCATACACACT 62.467 66.667 0.00 0.00 0.00 3.55
441 446 3.195002 CGCCGCCCATACACACTG 61.195 66.667 0.00 0.00 0.00 3.66
442 447 2.046314 GCCGCCCATACACACTGT 60.046 61.111 0.00 0.00 0.00 3.55
454 459 0.806868 CACACTGTGCCACATCCATC 59.193 55.000 7.90 0.00 0.00 3.51
458 463 0.393944 CTGTGCCACATCCATCTGCT 60.394 55.000 0.00 0.00 0.00 4.24
505 510 2.124151 GCCGGATCCAAGCACCAT 60.124 61.111 16.93 0.00 0.00 3.55
512 517 1.600957 GATCCAAGCACCATCATCACG 59.399 52.381 0.00 0.00 0.00 4.35
565 570 3.311110 GTGTCCGAGAGCCACCCA 61.311 66.667 0.00 0.00 0.00 4.51
566 571 2.284625 TGTCCGAGAGCCACCCAT 60.285 61.111 0.00 0.00 0.00 4.00
591 596 1.852157 AGCAAGATCCCCACCACCA 60.852 57.895 0.00 0.00 0.00 4.17
592 597 1.678970 GCAAGATCCCCACCACCAC 60.679 63.158 0.00 0.00 0.00 4.16
593 598 1.000896 CAAGATCCCCACCACCACC 60.001 63.158 0.00 0.00 0.00 4.61
605 610 3.148963 ACCACCGTCGACCACACA 61.149 61.111 10.58 0.00 0.00 3.72
734 739 6.544038 ACCGTTAACATTGTAGGTTTACAC 57.456 37.500 6.39 0.00 39.44 2.90
824 829 1.378762 GGCTGTCCTGTGCCCTTAA 59.621 57.895 0.00 0.00 43.11 1.85
825 830 0.251165 GGCTGTCCTGTGCCCTTAAA 60.251 55.000 0.00 0.00 43.11 1.52
826 831 1.616994 GGCTGTCCTGTGCCCTTAAAT 60.617 52.381 0.00 0.00 43.11 1.40
827 832 2.171003 GCTGTCCTGTGCCCTTAAATT 58.829 47.619 0.00 0.00 0.00 1.82
1115 1176 2.438434 CAACCACCCTCGCCATCC 60.438 66.667 0.00 0.00 0.00 3.51
1826 1938 4.201657 TCAATTGCGATCCATGTGATCTT 58.798 39.130 16.99 6.60 46.52 2.40
2025 2149 0.898789 GACGACCTTGGGAGAGGACA 60.899 60.000 0.00 0.00 39.25 4.02
2026 2150 0.252284 ACGACCTTGGGAGAGGACAT 60.252 55.000 0.00 0.00 39.25 3.06
2090 2214 0.105039 CTCAGTACGGGATGAAGGGC 59.895 60.000 0.00 0.00 0.00 5.19
2101 2225 1.819288 GATGAAGGGCGATCGGATCTA 59.181 52.381 18.30 0.00 0.00 1.98
2154 2278 1.990799 TAGCCACGAGAACAATGACG 58.009 50.000 0.00 0.00 0.00 4.35
2168 2292 0.821517 ATGACGCTTCCATCGGTGTA 59.178 50.000 0.00 0.00 0.00 2.90
2178 2302 2.295070 TCCATCGGTGTATACGACATGG 59.705 50.000 13.19 13.19 43.78 3.66
2179 2303 2.058798 CATCGGTGTATACGACATGGC 58.941 52.381 0.00 0.00 43.78 4.40
2330 2454 3.082548 GGCGTCAGTATCTATCTGGCTA 58.917 50.000 0.00 0.00 35.66 3.93
2331 2455 3.119779 GGCGTCAGTATCTATCTGGCTAC 60.120 52.174 0.00 0.00 35.66 3.58
2340 2490 4.160642 TCTATCTGGCTACGGTGAGTTA 57.839 45.455 0.00 0.00 0.00 2.24
2353 2503 1.624336 TGAGTTACACACGGGCTACT 58.376 50.000 0.00 0.00 0.00 2.57
2356 2506 3.765511 TGAGTTACACACGGGCTACTATT 59.234 43.478 0.00 0.00 0.00 1.73
2358 2508 3.131755 AGTTACACACGGGCTACTATTCC 59.868 47.826 0.00 0.00 0.00 3.01
2359 2509 1.861982 ACACACGGGCTACTATTCCT 58.138 50.000 0.00 0.00 0.00 3.36
2360 2510 2.185387 ACACACGGGCTACTATTCCTT 58.815 47.619 0.00 0.00 0.00 3.36
2361 2511 2.093658 ACACACGGGCTACTATTCCTTG 60.094 50.000 0.00 0.00 0.00 3.61
2362 2512 1.134491 ACACGGGCTACTATTCCTTGC 60.134 52.381 0.00 0.00 0.00 4.01
2363 2513 1.134521 CACGGGCTACTATTCCTTGCA 60.135 52.381 0.00 0.00 0.00 4.08
2428 4666 4.074259 AGTGTGTGATACATTGCACATGT 58.926 39.130 15.56 15.56 45.59 3.21
2429 4667 4.520111 AGTGTGTGATACATTGCACATGTT 59.480 37.500 16.19 7.62 45.59 2.71
2430 4668 5.009911 AGTGTGTGATACATTGCACATGTTT 59.990 36.000 16.19 10.64 45.59 2.83
2431 4669 5.691305 GTGTGTGATACATTGCACATGTTTT 59.309 36.000 16.19 7.80 45.59 2.43
2456 4694 3.309961 TGCAAAATTGTGTGTGTGTGT 57.690 38.095 0.00 0.00 0.00 3.72
2457 4695 2.991866 TGCAAAATTGTGTGTGTGTGTG 59.008 40.909 0.00 0.00 0.00 3.82
2536 4780 3.124578 TGTGTGACACATAGCACATGT 57.875 42.857 15.39 0.00 45.59 3.21
2537 4781 3.475575 TGTGTGACACATAGCACATGTT 58.524 40.909 15.39 0.00 45.59 2.71
2538 4782 3.882288 TGTGTGACACATAGCACATGTTT 59.118 39.130 15.39 0.00 45.59 2.83
2539 4783 4.337836 TGTGTGACACATAGCACATGTTTT 59.662 37.500 15.39 0.00 45.59 2.43
2540 4784 5.163571 TGTGTGACACATAGCACATGTTTTT 60.164 36.000 15.39 0.00 45.59 1.94
2603 4847 4.025813 ACACAGTTTGAAAAATGCAATCGC 60.026 37.500 3.32 0.00 37.49 4.58
2605 4849 2.155539 AGTTTGAAAAATGCAATCGCGC 59.844 40.909 0.00 0.00 42.97 6.86
2736 5002 7.758076 TCATTCATGCTCAATTTTGACATTCTC 59.242 33.333 0.00 0.00 31.39 2.87
2800 5066 8.947055 TTTAGGTGTTTAACGGATATAACTCC 57.053 34.615 0.00 0.00 35.46 3.85
2922 5198 6.478512 TTTTAAAGATCTTTGTGGCAAGGT 57.521 33.333 27.37 2.82 34.23 3.50
3100 5383 7.764443 CCTTAGAAACCGATACATCTTTTGAGA 59.236 37.037 0.00 0.00 0.00 3.27
3132 5918 0.457853 TTTCGAGAGGGAATGCGTCG 60.458 55.000 0.00 0.00 0.00 5.12
3230 6024 7.716123 AGAATCAATGAAGTTCAAATTTGGCAA 59.284 29.630 17.90 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.115446 ACAATACATGAAGATGTCGATGGTT 58.885 36.000 0.00 0.00 42.14 3.67
30 31 3.561503 GAAAAAGTGGTGGCGACAATAC 58.438 45.455 0.00 0.00 46.06 1.89
32 33 1.001815 CGAAAAAGTGGTGGCGACAAT 60.002 47.619 0.00 0.00 46.06 2.71
37 38 4.607024 CACGAAAAAGTGGTGGCG 57.393 55.556 0.00 0.00 38.40 5.69
51 52 7.285629 ACATCACATATATCTATAGGGACCACG 59.714 40.741 0.00 0.00 0.00 4.94
52 53 8.540507 ACATCACATATATCTATAGGGACCAC 57.459 38.462 0.00 0.00 0.00 4.16
53 54 8.569596 AGACATCACATATATCTATAGGGACCA 58.430 37.037 0.00 0.00 0.00 4.02
54 55 8.855110 CAGACATCACATATATCTATAGGGACC 58.145 40.741 0.00 0.00 0.00 4.46
55 56 8.356657 GCAGACATCACATATATCTATAGGGAC 58.643 40.741 0.00 0.00 0.00 4.46
56 57 8.061304 TGCAGACATCACATATATCTATAGGGA 58.939 37.037 0.00 0.00 0.00 4.20
60 61 9.860898 GTTGTGCAGACATCACATATATCTATA 57.139 33.333 0.00 0.00 43.12 1.31
65 66 5.683681 TGGTTGTGCAGACATCACATATAT 58.316 37.500 0.00 0.00 43.12 0.86
67 68 3.954200 TGGTTGTGCAGACATCACATAT 58.046 40.909 0.00 0.00 43.12 1.78
78 79 2.751436 CGGGGGATGGTTGTGCAG 60.751 66.667 0.00 0.00 0.00 4.41
103 105 1.137675 TGAGATGCAGGATGACGAAGG 59.862 52.381 0.00 0.00 39.69 3.46
111 113 1.703014 ATGGCGGTGAGATGCAGGAT 61.703 55.000 0.00 0.00 0.00 3.24
112 114 1.048160 TATGGCGGTGAGATGCAGGA 61.048 55.000 0.00 0.00 0.00 3.86
113 115 0.602106 CTATGGCGGTGAGATGCAGG 60.602 60.000 0.00 0.00 0.00 4.85
114 116 1.226686 GCTATGGCGGTGAGATGCAG 61.227 60.000 0.00 0.00 0.00 4.41
135 138 3.866582 CCTCCAGATCCGGTGGCC 61.867 72.222 0.00 0.00 33.14 5.36
165 168 1.434513 ATGGCCACCAAAGGTCCTCA 61.435 55.000 8.16 0.00 36.95 3.86
166 169 0.681243 GATGGCCACCAAAGGTCCTC 60.681 60.000 8.16 0.00 36.95 3.71
222 226 2.240162 GAGGCGGTGGTTCTGGTAGG 62.240 65.000 0.00 0.00 0.00 3.18
226 230 2.804828 GAAGGAGGCGGTGGTTCTGG 62.805 65.000 0.00 0.00 0.00 3.86
236 240 0.674581 TTGCACATCAGAAGGAGGCG 60.675 55.000 0.00 0.00 0.00 5.52
278 282 1.880027 GGCACACGTTGGATTCTTCTT 59.120 47.619 0.00 0.00 0.00 2.52
327 331 1.471287 CTGATGTCTGTGTGCCATTGG 59.529 52.381 0.00 0.00 0.00 3.16
331 335 0.758123 TCACTGATGTCTGTGTGCCA 59.242 50.000 16.31 0.00 43.48 4.92
348 352 1.123861 ACTCAAGCAGTGCCTCCTCA 61.124 55.000 12.58 0.00 32.26 3.86
351 355 1.376553 GGACTCAAGCAGTGCCTCC 60.377 63.158 12.58 4.63 37.49 4.30
357 361 0.534412 CGGATCAGGACTCAAGCAGT 59.466 55.000 0.00 0.00 38.45 4.40
359 363 1.489481 ATCGGATCAGGACTCAAGCA 58.511 50.000 0.00 0.00 0.00 3.91
427 432 3.177600 GCACAGTGTGTATGGGCG 58.822 61.111 23.73 0.00 37.33 6.13
428 433 1.303236 TGGCACAGTGTGTATGGGC 60.303 57.895 23.73 10.80 46.61 5.36
436 441 0.694771 AGATGGATGTGGCACAGTGT 59.305 50.000 26.04 9.40 41.80 3.55
438 443 0.679002 GCAGATGGATGTGGCACAGT 60.679 55.000 26.04 13.76 41.80 3.55
439 444 0.393944 AGCAGATGGATGTGGCACAG 60.394 55.000 26.04 11.23 41.80 3.66
440 445 0.393402 GAGCAGATGGATGTGGCACA 60.393 55.000 24.36 24.36 0.00 4.57
441 446 0.393402 TGAGCAGATGGATGTGGCAC 60.393 55.000 11.55 11.55 0.00 5.01
442 447 0.107361 CTGAGCAGATGGATGTGGCA 60.107 55.000 0.00 0.00 0.00 4.92
481 486 1.451504 CTTGGATCCGGCATGGCTA 59.548 57.895 18.09 5.65 37.80 3.93
483 488 3.599704 GCTTGGATCCGGCATGGC 61.600 66.667 20.24 9.69 37.80 4.40
551 556 3.785859 GCATGGGTGGCTCTCGGA 61.786 66.667 0.00 0.00 0.00 4.55
591 596 2.694829 GAAGCTGTGTGGTCGACGGT 62.695 60.000 9.92 0.00 0.00 4.83
592 597 2.022129 GAAGCTGTGTGGTCGACGG 61.022 63.158 9.92 0.00 0.00 4.79
593 598 2.365068 CGAAGCTGTGTGGTCGACG 61.365 63.158 9.92 0.00 0.00 5.12
778 783 1.687494 GCGGCATGACAACGACTCTC 61.687 60.000 0.00 0.00 0.00 3.20
1270 1334 1.218316 CTGTAGAAGGTGCCGTCCC 59.782 63.158 0.65 0.00 0.00 4.46
1458 1522 3.869272 CTTCAGGTCCGCATGCGC 61.869 66.667 34.00 21.07 38.24 6.09
1515 1591 1.730064 GTCCGCGTTTCTGATAAGCAA 59.270 47.619 4.92 0.00 0.00 3.91
1716 1828 0.824759 AGGTCCTCGCCATAGTCAAC 59.175 55.000 0.00 0.00 0.00 3.18
1826 1938 0.821301 TGTTGCTTGGCGTCCAATCA 60.821 50.000 10.99 10.43 43.07 2.57
2025 2149 1.272212 CCGCCCAACAAAAAGCACTAT 59.728 47.619 0.00 0.00 0.00 2.12
2026 2150 0.671251 CCGCCCAACAAAAAGCACTA 59.329 50.000 0.00 0.00 0.00 2.74
2090 2214 3.914966 CGTCCAAGAAATAGATCCGATCG 59.085 47.826 8.51 8.51 0.00 3.69
2101 2225 9.559732 TGTAATATTCATCATCGTCCAAGAAAT 57.440 29.630 0.00 0.00 0.00 2.17
2142 2266 2.029728 CGATGGAAGCGTCATTGTTCTC 59.970 50.000 1.14 0.00 43.21 2.87
2154 2278 2.223641 TGTCGTATACACCGATGGAAGC 60.224 50.000 3.32 0.00 36.62 3.86
2168 2292 1.227263 GCCGTCTGCCATGTCGTAT 60.227 57.895 0.00 0.00 0.00 3.06
2178 2302 2.945398 GATGAGACCTCGCCGTCTGC 62.945 65.000 8.71 2.84 43.22 4.26
2179 2303 1.064946 GATGAGACCTCGCCGTCTG 59.935 63.158 8.71 0.00 43.22 3.51
2330 2454 1.364901 CCCGTGTGTAACTCACCGT 59.635 57.895 0.00 0.00 45.61 4.83
2331 2455 2.025418 GCCCGTGTGTAACTCACCG 61.025 63.158 0.00 3.90 45.61 4.94
2340 2490 1.861982 AGGAATAGTAGCCCGTGTGT 58.138 50.000 0.00 0.00 0.00 3.72
2344 2494 1.134491 GTGCAAGGAATAGTAGCCCGT 60.134 52.381 0.00 0.00 0.00 5.28
2346 2496 2.289565 GTGTGCAAGGAATAGTAGCCC 58.710 52.381 0.00 0.00 0.00 5.19
2347 2497 2.678336 GTGTGTGCAAGGAATAGTAGCC 59.322 50.000 0.00 0.00 0.00 3.93
2349 2499 2.930040 CCGTGTGTGCAAGGAATAGTAG 59.070 50.000 0.00 0.00 45.31 2.57
2352 2502 1.086696 CCCGTGTGTGCAAGGAATAG 58.913 55.000 0.00 0.00 45.31 1.73
2353 2503 0.958382 GCCCGTGTGTGCAAGGAATA 60.958 55.000 0.00 0.00 45.31 1.75
2356 2506 2.902423 AAAGCCCGTGTGTGCAAGGA 62.902 55.000 0.00 0.00 45.31 3.36
2358 2508 0.871163 CAAAAGCCCGTGTGTGCAAG 60.871 55.000 0.00 0.00 0.00 4.01
2359 2509 1.140589 CAAAAGCCCGTGTGTGCAA 59.859 52.632 0.00 0.00 0.00 4.08
2360 2510 0.748367 TACAAAAGCCCGTGTGTGCA 60.748 50.000 0.00 0.00 0.00 4.57
2361 2511 0.382515 TTACAAAAGCCCGTGTGTGC 59.617 50.000 0.00 0.00 0.00 4.57
2362 2512 2.853731 TTTACAAAAGCCCGTGTGTG 57.146 45.000 0.00 0.00 0.00 3.82
2363 2513 3.870633 TTTTTACAAAAGCCCGTGTGT 57.129 38.095 0.00 0.00 0.00 3.72
2456 4694 6.836242 TGTTGTGCAATGATAGGGTATATCA 58.164 36.000 0.00 0.40 38.20 2.15
2457 4695 7.928307 ATGTTGTGCAATGATAGGGTATATC 57.072 36.000 0.00 0.00 0.00 1.63
2603 4847 1.267532 GGTAATGCAAGACATCACGCG 60.268 52.381 3.53 3.53 38.34 6.01
2605 4849 4.685169 AAAGGTAATGCAAGACATCACG 57.315 40.909 0.00 0.00 38.34 4.35
2680 4946 6.281405 AGTTGTAGGTTGAGTGTAGAAACAG 58.719 40.000 0.00 0.00 35.91 3.16
2788 5054 9.537192 TGTACTTGTAATTTGGAGTTATATCCG 57.463 33.333 0.00 0.00 42.77 4.18
2800 5066 9.838975 TGCACTATTTCATGTACTTGTAATTTG 57.161 29.630 15.53 13.93 0.00 2.32
2922 5198 8.037758 ACATTAAACTCAATGTTTGTGGTTGAA 58.962 29.630 4.30 3.39 44.75 2.69
2968 5244 7.860872 GGTTCGTGTTTTTCAGACTTCATTTAT 59.139 33.333 0.00 0.00 0.00 1.40
3132 5918 8.375506 AGGAAATTTTAATTCTCCTTCAAACCC 58.624 33.333 0.00 0.00 32.42 4.11
3205 5998 7.424227 TGCCAAATTTGAACTTCATTGATTC 57.576 32.000 19.86 0.00 0.00 2.52
3352 6150 9.561069 GACATACAAATATACTCAAGACCCAAT 57.439 33.333 0.00 0.00 0.00 3.16
3460 6262 5.916318 TCCACACTTCATTTGCAATTTCTT 58.084 33.333 0.00 0.00 0.00 2.52
3497 6299 4.416516 AGGTCATATCATGATACCGTGGA 58.583 43.478 17.60 7.89 42.04 4.02


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

AutoCloner maintained by Alex Coulton.