Multiple sequence alignment - TraesCS5D01G407100

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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 TraesCS5D01G407100 chr5D 100.000 3476 0 0 1 3476 472433814 472437289 0.000000e+00 6420.0
1 TraesCS5D01G407100 chr5D 96.023 176 7 0 3301 3476 456384976 456384801 1.580000e-73 287.0
2 TraesCS5D01G407100 chr5D 93.333 180 11 1 3083 3261 456385150 456384971 7.400000e-67 265.0
3 TraesCS5D01G407100 chr5B 92.319 1341 59 11 1361 2662 579383358 579384693 0.000000e+00 1866.0
4 TraesCS5D01G407100 chr5B 81.764 669 97 20 2010 2660 579150045 579150706 1.420000e-148 536.0
5 TraesCS5D01G407100 chr5B 80.241 663 83 25 1361 1990 579143225 579143872 4.090000e-124 455.0
6 TraesCS5D01G407100 chr5B 82.471 348 27 19 778 1119 578996181 578996500 1.230000e-69 274.0
7 TraesCS5D01G407100 chr5B 86.022 186 23 3 1382 1564 579078875 579079060 2.740000e-46 196.0
8 TraesCS5D01G407100 chr5B 85.165 182 14 3 991 1159 579076978 579077159 1.280000e-39 174.0
9 TraesCS5D01G407100 chr5B 86.184 152 13 5 880 1029 579382825 579382970 1.290000e-34 158.0
10 TraesCS5D01G407100 chr5B 89.773 88 7 1 1234 1319 578938454 578938541 1.020000e-20 111.0
11 TraesCS5D01G407100 chr5B 80.986 142 16 9 889 1027 579142774 579142907 6.140000e-18 102.0
12 TraesCS5D01G407100 chr5B 84.615 104 11 4 9 110 579140925 579141025 7.940000e-17 99.0
13 TraesCS5D01G407100 chr5B 85.437 103 1 5 1579 1668 579079147 579079248 1.030000e-15 95.3
14 TraesCS5D01G407100 chr5A 92.622 1274 58 15 1387 2659 591976593 591977831 0.000000e+00 1799.0
15 TraesCS5D01G407100 chr5A 91.443 783 35 9 411 1180 591975387 591976150 0.000000e+00 1046.0
16 TraesCS5D01G407100 chr5A 91.722 302 16 6 71 370 591974861 591975155 8.980000e-111 411.0
17 TraesCS5D01G407100 chr5A 84.466 206 16 4 991 1180 591867843 591868048 4.580000e-44 189.0
18 TraesCS5D01G407100 chr5A 97.531 81 2 0 1 81 591954379 591954459 4.680000e-29 139.0
19 TraesCS5D01G407100 chr5A 82.895 76 8 3 1247 1320 591976242 591976314 2.900000e-06 63.9
20 TraesCS5D01G407100 chr2D 92.154 803 57 6 2679 3476 39614309 39615110 0.000000e+00 1129.0
21 TraesCS5D01G407100 chr1D 92.264 698 49 5 2784 3476 323605574 323604877 0.000000e+00 985.0
22 TraesCS5D01G407100 chr4D 88.739 817 63 16 2679 3476 414822781 414821975 0.000000e+00 972.0
23 TraesCS5D01G407100 chr2A 88.265 801 89 5 2679 3476 349627652 349628450 0.000000e+00 953.0
24 TraesCS5D01G407100 chr2A 86.443 804 90 9 2679 3476 115966551 115965761 0.000000e+00 863.0
25 TraesCS5D01G407100 chr1B 86.725 806 92 7 2679 3476 53939297 53940095 0.000000e+00 881.0
26 TraesCS5D01G407100 chr3B 88.104 538 55 8 2679 3207 437650307 437649770 6.330000e-177 630.0
27 TraesCS5D01G407100 chr6D 87.091 519 60 7 2679 3192 264780089 264779573 6.470000e-162 580.0
28 TraesCS5D01G407100 chr6D 91.480 223 17 1 3254 3476 264779579 264779359 4.360000e-79 305.0
29 TraesCS5D01G407100 chr6D 86.486 111 15 0 2060 2170 448810583 448810693 4.710000e-24 122.0
30 TraesCS5D01G407100 chr7B 85.565 478 56 11 2679 3152 453267194 453266726 4.030000e-134 488.0
31 TraesCS5D01G407100 chr6A 87.387 111 14 0 2060 2170 594959121 594959231 1.010000e-25 128.0


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 TraesCS5D01G407100 chr5D 472433814 472437289 3475 False 6420.000000 6420 100.000000 1 3476 1 chr5D.!!$F1 3475
1 TraesCS5D01G407100 chr5B 579382825 579384693 1868 False 1012.000000 1866 89.251500 880 2662 2 chr5B.!!$F6 1782
2 TraesCS5D01G407100 chr5B 579150045 579150706 661 False 536.000000 536 81.764000 2010 2660 1 chr5B.!!$F3 650
3 TraesCS5D01G407100 chr5B 579140925 579143872 2947 False 218.666667 455 81.947333 9 1990 3 chr5B.!!$F5 1981
4 TraesCS5D01G407100 chr5A 591974861 591977831 2970 False 829.975000 1799 89.670500 71 2659 4 chr5A.!!$F3 2588
5 TraesCS5D01G407100 chr2D 39614309 39615110 801 False 1129.000000 1129 92.154000 2679 3476 1 chr2D.!!$F1 797
6 TraesCS5D01G407100 chr1D 323604877 323605574 697 True 985.000000 985 92.264000 2784 3476 1 chr1D.!!$R1 692
7 TraesCS5D01G407100 chr4D 414821975 414822781 806 True 972.000000 972 88.739000 2679 3476 1 chr4D.!!$R1 797
8 TraesCS5D01G407100 chr2A 349627652 349628450 798 False 953.000000 953 88.265000 2679 3476 1 chr2A.!!$F1 797
9 TraesCS5D01G407100 chr2A 115965761 115966551 790 True 863.000000 863 86.443000 2679 3476 1 chr2A.!!$R1 797
10 TraesCS5D01G407100 chr1B 53939297 53940095 798 False 881.000000 881 86.725000 2679 3476 1 chr1B.!!$F1 797
11 TraesCS5D01G407100 chr3B 437649770 437650307 537 True 630.000000 630 88.104000 2679 3207 1 chr3B.!!$R1 528
12 TraesCS5D01G407100 chr6D 264779359 264780089 730 True 442.500000 580 89.285500 2679 3476 2 chr6D.!!$R1 797

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
267 268 0.107654 GAACAATCCGCTAGGGCTGT 60.108 55.0 0.19 1.76 38.33 4.40 F
1071 2412 0.391263 GAGTTCCGGTGGTGTCCATC 60.391 60.0 0.00 0.00 35.28 3.51 F
1346 2751 0.313987 CGCGCCAGTCATATGTAGGA 59.686 55.0 0.00 0.00 0.00 2.94 F
2180 3867 0.449388 CGGCAGAAGTTCATGGAAGC 59.551 55.0 5.50 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 2641 0.941542 TAAATCGGGCTTGCGCATAC 59.058 50.000 12.75 6.22 38.10 2.39 R
2314 4004 0.036952 CACTGCTGGAGACCGTGATT 60.037 55.000 2.24 0.00 0.00 2.57 R
2356 4055 0.255890 TAATGCTGGACCTCCAAGCC 59.744 55.000 11.13 0.00 46.97 4.35 R
3192 4937 1.152030 TGTCAGCCTCCTTGGGACT 60.152 57.895 0.00 0.00 36.00 3.85 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 2.873525 GCCTCGCCTCCCTACATCC 61.874 68.421 0.00 0.00 0.00 3.51
44 45 2.832498 GCCTCCCTACATCCTGCC 59.168 66.667 0.00 0.00 0.00 4.85
45 46 2.823758 GCCTCCCTACATCCTGCCC 61.824 68.421 0.00 0.00 0.00 5.36
50 51 1.281925 CCCTACATCCTGCCCCAGTT 61.282 60.000 0.00 0.00 0.00 3.16
54 55 2.036256 ATCCTGCCCCAGTTGCAC 59.964 61.111 0.00 0.00 34.46 4.57
66 67 0.396435 AGTTGCACCACCTTCGATCA 59.604 50.000 0.00 0.00 0.00 2.92
68 69 0.605319 TTGCACCACCTTCGATCACC 60.605 55.000 0.00 0.00 0.00 4.02
69 70 1.745489 GCACCACCTTCGATCACCC 60.745 63.158 0.00 0.00 0.00 4.61
91 92 2.750237 CGAAAAAGGGAGGGGCGG 60.750 66.667 0.00 0.00 0.00 6.13
137 138 4.411540 ACTCACCTCATCCATGCTAAGATT 59.588 41.667 0.00 0.00 0.00 2.40
141 142 5.181433 CACCTCATCCATGCTAAGATTCATG 59.819 44.000 0.00 0.00 39.67 3.07
158 159 0.827507 ATGTTTTGACCGCCAAGCCT 60.828 50.000 0.00 0.00 35.94 4.58
177 178 3.056465 GCCTAGAGCTCGGCTAATAACAT 60.056 47.826 21.52 0.00 42.98 2.71
178 179 4.739195 CCTAGAGCTCGGCTAATAACATC 58.261 47.826 8.37 0.00 39.88 3.06
224 225 2.362397 GCACCATCGTCTTCTCCTATCA 59.638 50.000 0.00 0.00 0.00 2.15
241 242 0.461548 TCATGTCGGTGAGGAGCATC 59.538 55.000 0.00 0.00 0.00 3.91
248 249 3.149899 GTGAGGAGCATCACCACAG 57.850 57.895 4.06 0.00 43.12 3.66
259 260 0.396435 TCACCACAGAACAATCCGCT 59.604 50.000 0.00 0.00 0.00 5.52
267 268 0.107654 GAACAATCCGCTAGGGCTGT 60.108 55.000 0.19 1.76 38.33 4.40
343 345 3.054802 GCAAAGAGAGAGAAATCCCCTGA 60.055 47.826 0.00 0.00 0.00 3.86
345 351 5.564550 CAAAGAGAGAGAAATCCCCTGAAA 58.435 41.667 0.00 0.00 0.00 2.69
347 353 3.521531 AGAGAGAGAAATCCCCTGAAACC 59.478 47.826 0.00 0.00 0.00 3.27
350 356 1.357761 GAGAAATCCCCTGAAACCCCA 59.642 52.381 0.00 0.00 0.00 4.96
355 361 1.392407 TCCCCTGAAACCCCATTGAT 58.608 50.000 0.00 0.00 0.00 2.57
358 364 1.832998 CCCTGAAACCCCATTGATTGG 59.167 52.381 0.00 0.00 46.00 3.16
371 377 1.453928 GATTGGGCGGGCTTAGCTT 60.454 57.895 3.59 0.00 34.52 3.74
375 381 2.189521 GGCGGGCTTAGCTTGCTA 59.810 61.111 17.33 0.00 34.52 3.49
376 382 1.451387 GGCGGGCTTAGCTTGCTAA 60.451 57.895 17.33 13.52 34.52 3.09
380 386 1.470285 CGGGCTTAGCTTGCTAACGTA 60.470 52.381 10.62 0.00 0.00 3.57
495 729 5.013704 TGTTTACCCCAGATCAACTACACAT 59.986 40.000 0.00 0.00 0.00 3.21
524 758 9.009327 GCATACATGTAAATATCACAAACACAC 57.991 33.333 10.14 0.00 0.00 3.82
527 761 8.165239 ACATGTAAATATCACAAACACACAGT 57.835 30.769 0.00 0.00 0.00 3.55
533 767 7.849804 AATATCACAAACACACAGTAGATCC 57.150 36.000 0.00 0.00 0.00 3.36
534 768 4.955811 TCACAAACACACAGTAGATCCT 57.044 40.909 0.00 0.00 0.00 3.24
567 801 3.242413 CCGAAGGCATGTCTCGTATTTTG 60.242 47.826 0.00 0.00 46.14 2.44
570 804 2.939103 AGGCATGTCTCGTATTTTGCTC 59.061 45.455 0.00 0.00 0.00 4.26
571 805 2.032178 GGCATGTCTCGTATTTTGCTCC 59.968 50.000 0.00 0.00 0.00 4.70
614 849 6.665248 TGGAGACAGATAGATACCATGTATGG 59.335 42.308 9.31 9.31 44.60 2.74
655 890 6.431543 ACTCAGAAACTTCTATCTCTCACGAA 59.568 38.462 0.00 0.00 35.34 3.85
729 968 2.271944 TCAAGTCCGTCTCAGTCTCA 57.728 50.000 0.00 0.00 0.00 3.27
870 1603 2.441750 TGGTGCACCTTCTTCCTTAGTT 59.558 45.455 34.75 0.00 36.82 2.24
949 2247 4.451096 GCTGCAGCTACTTGTAAACTTGTA 59.549 41.667 31.33 0.00 38.21 2.41
1011 2318 0.687427 AGCCAAGCAAAACCACTGGT 60.687 50.000 0.00 0.00 37.65 4.00
1068 2409 2.048503 CGAGTTCCGGTGGTGTCC 60.049 66.667 0.00 0.00 33.91 4.02
1069 2410 2.863346 CGAGTTCCGGTGGTGTCCA 61.863 63.158 0.00 0.00 33.91 4.02
1070 2411 1.677552 GAGTTCCGGTGGTGTCCAT 59.322 57.895 0.00 0.00 35.28 3.41
1071 2412 0.391263 GAGTTCCGGTGGTGTCCATC 60.391 60.000 0.00 0.00 35.28 3.51
1072 2413 1.125093 AGTTCCGGTGGTGTCCATCA 61.125 55.000 0.00 0.00 33.50 3.07
1175 2535 1.345415 GGGTAAGGTTTCAGACACCGA 59.655 52.381 0.00 0.00 39.56 4.69
1182 2551 0.742505 TTTCAGACACCGACGACAGT 59.257 50.000 0.00 0.00 0.00 3.55
1212 2581 0.392706 ATCGGCCGAAGCATATCACA 59.607 50.000 34.66 4.17 42.56 3.58
1244 2641 8.393366 CAACAAGATTGACTGGTATGTTATCTG 58.607 37.037 0.00 0.00 31.64 2.90
1346 2751 0.313987 CGCGCCAGTCATATGTAGGA 59.686 55.000 0.00 0.00 0.00 2.94
1348 2753 2.408050 GCGCCAGTCATATGTAGGAAG 58.592 52.381 0.00 8.00 0.00 3.46
1349 2754 2.224066 GCGCCAGTCATATGTAGGAAGT 60.224 50.000 0.00 0.00 0.00 3.01
1350 2755 3.005472 GCGCCAGTCATATGTAGGAAGTA 59.995 47.826 0.00 0.00 0.00 2.24
1351 2756 4.799678 CGCCAGTCATATGTAGGAAGTAG 58.200 47.826 12.77 0.00 0.00 2.57
1352 2757 4.321304 CGCCAGTCATATGTAGGAAGTAGG 60.321 50.000 12.77 0.00 0.00 3.18
1354 2759 5.304614 GCCAGTCATATGTAGGAAGTAGGAA 59.695 44.000 12.77 0.00 0.00 3.36
1355 2760 6.739008 GCCAGTCATATGTAGGAAGTAGGAAC 60.739 46.154 12.77 0.00 0.00 3.62
1356 2761 6.551601 CCAGTCATATGTAGGAAGTAGGAACT 59.448 42.308 1.90 0.00 46.37 3.01
1357 2762 7.724506 CCAGTCATATGTAGGAAGTAGGAACTA 59.275 40.741 1.90 0.00 41.75 2.24
1702 3380 5.821995 AGTATTCGAGACTACTACCTTGACC 59.178 44.000 0.47 0.00 0.00 4.02
1781 3459 3.592059 TGGTCGACCAACTTATTACTGC 58.408 45.455 34.60 3.18 44.35 4.40
1854 3541 3.071206 GGGCACTCTCTCGGAGCA 61.071 66.667 0.00 0.00 45.48 4.26
2180 3867 0.449388 CGGCAGAAGTTCATGGAAGC 59.551 55.000 5.50 0.00 0.00 3.86
2188 3875 2.679342 TTCATGGAAGCCTCCCCCG 61.679 63.158 0.00 0.00 41.64 5.73
2219 3906 2.849966 CGTTCGCGGCATTCTCTCG 61.850 63.158 6.13 0.00 36.88 4.04
2356 4055 1.347817 GAAACAGGACAGCGAGCTCG 61.348 60.000 31.37 31.37 43.27 5.03
2366 4065 3.764466 CGAGCTCGGCTTGGAGGT 61.764 66.667 28.40 4.74 46.68 3.85
2368 4067 3.394836 AGCTCGGCTTGGAGGTCC 61.395 66.667 0.00 0.00 40.55 4.46
2662 4392 2.200373 TCTAGCTTGGGTTCAAAGCC 57.800 50.000 4.01 4.01 46.58 4.35
2663 4393 1.705186 TCTAGCTTGGGTTCAAAGCCT 59.295 47.619 11.89 0.00 46.54 4.58
2664 4394 2.087646 CTAGCTTGGGTTCAAAGCCTC 58.912 52.381 11.89 2.41 46.54 4.70
2665 4395 0.185901 AGCTTGGGTTCAAAGCCTCA 59.814 50.000 11.89 0.00 46.54 3.86
2666 4396 0.315251 GCTTGGGTTCAAAGCCTCAC 59.685 55.000 11.89 0.00 46.54 3.51
2667 4397 1.986882 CTTGGGTTCAAAGCCTCACT 58.013 50.000 11.89 0.00 46.54 3.41
2668 4398 1.882623 CTTGGGTTCAAAGCCTCACTC 59.117 52.381 11.89 0.00 46.54 3.51
2669 4399 0.843309 TGGGTTCAAAGCCTCACTCA 59.157 50.000 11.89 0.00 46.54 3.41
2670 4400 1.202806 TGGGTTCAAAGCCTCACTCAG 60.203 52.381 11.89 0.00 46.54 3.35
2671 4401 1.528129 GGTTCAAAGCCTCACTCAGG 58.472 55.000 0.00 0.00 46.82 3.86
2687 4417 3.245658 ACTCAGGCTAGTCAAACCCTAGA 60.246 47.826 0.00 0.00 35.01 2.43
2712 4442 5.751990 CCTCCGGTGTGTTATATAAACTGAC 59.248 44.000 0.00 0.00 0.00 3.51
2714 4444 5.104374 CCGGTGTGTTATATAAACTGACGT 58.896 41.667 0.00 0.00 0.00 4.34
2730 4460 2.688446 TGACGTCAGGCTAGTCAATAGG 59.312 50.000 15.76 0.00 41.30 2.57
2789 4520 4.931914 ACATGTACTCTGTACTACACCCT 58.068 43.478 0.00 0.00 0.00 4.34
2832 4564 6.043706 AGCAGCATGTAGGGTATTATCTCTTT 59.956 38.462 0.00 0.00 39.31 2.52
2909 4643 4.801164 CTTAGCTTAGGACCCCTACTACA 58.199 47.826 0.00 0.00 35.63 2.74
2922 4656 3.635373 CCCTACTACAAGATACGCTGGAA 59.365 47.826 0.00 0.00 0.00 3.53
2938 4672 3.938963 GCTGGAAATAGAACCGACATTGA 59.061 43.478 0.00 0.00 0.00 2.57
2949 4683 5.647658 AGAACCGACATTGATGCTTTCATTA 59.352 36.000 0.00 0.00 33.34 1.90
2959 4693 2.094675 TGCTTTCATTAAGAGCCTGCC 58.905 47.619 0.00 0.00 35.80 4.85
3174 4919 1.069227 GGAGCTTTGTTGCAGTTACGG 60.069 52.381 0.00 0.00 34.99 4.02
3192 4937 2.965147 GCTCACGTGCGCCATGAAA 61.965 57.895 19.57 0.00 0.00 2.69
3283 5028 1.821061 CGCTCCGGCATAGGAATCCT 61.821 60.000 7.13 7.13 40.25 3.24
3339 5084 3.357203 GGGAGATTTGACCCTTCCTTTC 58.643 50.000 0.00 0.00 42.56 2.62
3423 5181 6.947644 TCCATGCACGAATTACTACTAGTA 57.052 37.500 1.89 1.89 0.00 1.82
3467 5225 9.667107 TCTTTACCTCTGGTTGTTTATTCTATG 57.333 33.333 0.00 0.00 37.09 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.737793 CTCAACCTATTTCCGGTGCAC 59.262 52.381 8.80 8.80 34.33 4.57
1 2 1.339631 CCTCAACCTATTTCCGGTGCA 60.340 52.381 0.00 0.00 34.33 4.57
2 3 1.379527 CCTCAACCTATTTCCGGTGC 58.620 55.000 0.00 0.00 34.33 5.01
3 4 2.017113 GCCCTCAACCTATTTCCGGTG 61.017 57.143 0.00 0.00 34.33 4.94
4 5 0.255033 GCCCTCAACCTATTTCCGGT 59.745 55.000 0.00 0.00 35.97 5.28
5 6 0.465642 GGCCCTCAACCTATTTCCGG 60.466 60.000 0.00 0.00 0.00 5.14
6 7 0.546598 AGGCCCTCAACCTATTTCCG 59.453 55.000 0.00 0.00 35.10 4.30
7 8 1.475213 CGAGGCCCTCAACCTATTTCC 60.475 57.143 12.13 0.00 37.77 3.13
40 41 3.297620 GTGGTGCAACTGGGGCAG 61.298 66.667 2.04 0.00 42.85 4.85
44 45 2.260869 CGAAGGTGGTGCAACTGGG 61.261 63.158 2.04 0.00 36.74 4.45
45 46 0.606401 ATCGAAGGTGGTGCAACTGG 60.606 55.000 2.04 0.00 36.74 4.00
50 51 1.003839 GGTGATCGAAGGTGGTGCA 60.004 57.895 0.00 0.00 0.00 4.57
54 55 1.221840 CCAGGGTGATCGAAGGTGG 59.778 63.158 0.00 0.00 0.00 4.61
66 67 2.117423 CCCTTTTTCGGCCAGGGT 59.883 61.111 15.69 0.00 42.36 4.34
68 69 1.678970 CCTCCCTTTTTCGGCCAGG 60.679 63.158 2.24 0.23 0.00 4.45
69 70 1.678970 CCCTCCCTTTTTCGGCCAG 60.679 63.158 2.24 0.00 0.00 4.85
91 92 4.162320 TGAAGTGGTAGATCCTTCATCCAC 59.838 45.833 7.12 0.00 42.72 4.02
137 138 0.313672 GCTTGGCGGTCAAAACATGA 59.686 50.000 0.00 0.00 34.56 3.07
141 142 0.521735 CTAGGCTTGGCGGTCAAAAC 59.478 55.000 0.00 0.00 34.56 2.43
158 159 4.154375 CGAGATGTTATTAGCCGAGCTCTA 59.846 45.833 12.85 0.00 40.44 2.43
173 174 1.924731 TCTGGGACTGACGAGATGTT 58.075 50.000 0.00 0.00 0.00 2.71
174 175 1.546476 GTTCTGGGACTGACGAGATGT 59.454 52.381 0.00 0.00 35.62 3.06
177 178 3.747735 AGTTCTGGGACTGACGAGA 57.252 52.632 0.00 0.00 35.62 4.04
224 225 0.176680 GTGATGCTCCTCACCGACAT 59.823 55.000 4.02 0.00 39.72 3.06
241 242 2.002586 CTAGCGGATTGTTCTGTGGTG 58.997 52.381 0.00 0.00 0.00 4.17
248 249 0.107654 ACAGCCCTAGCGGATTGTTC 60.108 55.000 1.75 0.00 46.67 3.18
350 356 1.109323 GCTAAGCCCGCCCAATCAAT 61.109 55.000 0.00 0.00 0.00 2.57
355 361 2.361104 CAAGCTAAGCCCGCCCAA 60.361 61.111 0.00 0.00 0.00 4.12
358 364 1.451387 TTAGCAAGCTAAGCCCGCC 60.451 57.895 10.29 0.00 34.02 6.13
362 368 4.877323 AAATACGTTAGCAAGCTAAGCC 57.123 40.909 14.34 3.94 38.95 4.35
371 377 3.304794 GCCACCACAAAAATACGTTAGCA 60.305 43.478 0.00 0.00 0.00 3.49
373 379 4.759516 AGCCACCACAAAAATACGTTAG 57.240 40.909 0.00 0.00 0.00 2.34
375 381 3.057806 GCTAGCCACCACAAAAATACGTT 60.058 43.478 2.29 0.00 0.00 3.99
376 382 2.486592 GCTAGCCACCACAAAAATACGT 59.513 45.455 2.29 0.00 0.00 3.57
416 649 4.057432 TGAAATTTTGCTTGTGCTTAGGC 58.943 39.130 0.00 0.00 40.48 3.93
524 758 5.105473 TCGGTCCAAAGTTTAGGATCTACTG 60.105 44.000 12.57 6.20 36.11 2.74
525 759 5.021458 TCGGTCCAAAGTTTAGGATCTACT 58.979 41.667 12.57 0.00 36.11 2.57
526 760 5.334724 TCGGTCCAAAGTTTAGGATCTAC 57.665 43.478 12.57 2.48 36.11 2.59
527 761 5.105064 CCTTCGGTCCAAAGTTTAGGATCTA 60.105 44.000 12.57 3.10 36.11 1.98
533 767 2.500229 TGCCTTCGGTCCAAAGTTTAG 58.500 47.619 0.00 0.00 0.00 1.85
534 768 2.642154 TGCCTTCGGTCCAAAGTTTA 57.358 45.000 0.00 0.00 0.00 2.01
567 801 2.229784 CACATTGTGGGAGAAAAGGAGC 59.770 50.000 9.00 0.00 0.00 4.70
570 804 3.648339 CACACATTGTGGGAGAAAAGG 57.352 47.619 20.33 0.00 44.27 3.11
598 833 7.287696 TCGCATATGTCCATACATGGTATCTAT 59.712 37.037 8.09 0.50 45.99 1.98
599 834 6.605594 TCGCATATGTCCATACATGGTATCTA 59.394 38.462 8.09 0.00 45.99 1.98
614 849 4.363138 TCTGAGTCACATTCGCATATGTC 58.637 43.478 4.29 0.00 36.64 3.06
655 890 4.141251 AGCCAGGGTATAATGACCGAAAAT 60.141 41.667 0.00 0.00 40.76 1.82
751 1484 7.834068 TGTAAGTACGTACTCTTCGAATACT 57.166 36.000 27.51 11.07 34.99 2.12
832 1565 2.993899 CACCATGACTGAACTCGTAACC 59.006 50.000 0.00 0.00 0.00 2.85
870 1603 2.373836 TCCAATCTTTGTTCTTCGGGGA 59.626 45.455 0.00 0.00 0.00 4.81
949 2247 7.636150 TGCTTACTTATAGAGTACTCCGTTT 57.364 36.000 19.38 3.39 40.51 3.60
1030 2337 3.815401 CGAGCTTCTTCTTTTCTTTGGGA 59.185 43.478 0.00 0.00 0.00 4.37
1068 2409 4.750952 CAAGCCTTGCTATGATCTGATG 57.249 45.455 0.00 0.00 38.25 3.07
1182 2551 2.089936 CGGCCGATTGTCGTCGAAA 61.090 57.895 24.07 0.00 44.06 3.46
1190 2559 1.202639 TGATATGCTTCGGCCGATTGT 60.203 47.619 31.56 17.52 40.91 2.71
1195 2564 1.224069 CCTGTGATATGCTTCGGCCG 61.224 60.000 22.12 22.12 40.91 6.13
1244 2641 0.941542 TAAATCGGGCTTGCGCATAC 59.058 50.000 12.75 6.22 38.10 2.39
1341 2746 4.819088 CCTACCGTAGTTCCTACTTCCTAC 59.181 50.000 4.86 0.00 35.06 3.18
1346 2751 3.022406 CAGCCTACCGTAGTTCCTACTT 58.978 50.000 4.86 0.00 35.06 2.24
1348 2753 2.648059 TCAGCCTACCGTAGTTCCTAC 58.352 52.381 4.86 0.00 33.99 3.18
1349 2754 3.589951 ATCAGCCTACCGTAGTTCCTA 57.410 47.619 4.86 0.00 0.00 2.94
1350 2755 2.456073 ATCAGCCTACCGTAGTTCCT 57.544 50.000 4.86 0.00 0.00 3.36
1351 2756 3.132467 AGAAATCAGCCTACCGTAGTTCC 59.868 47.826 4.86 0.00 0.00 3.62
1352 2757 4.098196 AGAGAAATCAGCCTACCGTAGTTC 59.902 45.833 4.86 1.42 0.00 3.01
1354 2759 3.381908 CAGAGAAATCAGCCTACCGTAGT 59.618 47.826 4.86 0.00 0.00 2.73
1355 2760 3.381908 ACAGAGAAATCAGCCTACCGTAG 59.618 47.826 0.00 0.00 0.00 3.51
1356 2761 3.362706 ACAGAGAAATCAGCCTACCGTA 58.637 45.455 0.00 0.00 0.00 4.02
1357 2762 2.180276 ACAGAGAAATCAGCCTACCGT 58.820 47.619 0.00 0.00 0.00 4.83
1359 2764 5.283457 ACATACAGAGAAATCAGCCTACC 57.717 43.478 0.00 0.00 0.00 3.18
1702 3380 7.874940 TCCAGTTTGTTGATCACTATTTTCAG 58.125 34.615 0.00 0.00 0.00 3.02
1776 3454 3.961408 GGTCCTCCTTTCTCATAGCAGTA 59.039 47.826 0.00 0.00 0.00 2.74
1778 3456 2.768527 TGGTCCTCCTTTCTCATAGCAG 59.231 50.000 0.00 0.00 34.23 4.24
1779 3457 2.832838 TGGTCCTCCTTTCTCATAGCA 58.167 47.619 0.00 0.00 34.23 3.49
1781 3459 3.198635 TGCTTGGTCCTCCTTTCTCATAG 59.801 47.826 0.00 0.00 34.23 2.23
1882 3569 1.028868 GGCTTCTCCTGCACCATCAC 61.029 60.000 0.00 0.00 0.00 3.06
2188 3875 1.298041 CGAACGTTGTGCCAACACC 60.298 57.895 5.00 5.56 46.86 4.16
2284 3974 0.746659 AACCTGCTTTTCCACAGCAC 59.253 50.000 0.00 0.00 42.49 4.40
2285 3975 1.032014 GAACCTGCTTTTCCACAGCA 58.968 50.000 0.00 0.00 45.21 4.41
2313 4003 1.204704 CACTGCTGGAGACCGTGATTA 59.795 52.381 2.24 0.00 0.00 1.75
2314 4004 0.036952 CACTGCTGGAGACCGTGATT 60.037 55.000 2.24 0.00 0.00 2.57
2315 4005 1.593787 CACTGCTGGAGACCGTGAT 59.406 57.895 2.24 0.00 0.00 3.06
2356 4055 0.255890 TAATGCTGGACCTCCAAGCC 59.744 55.000 11.13 0.00 46.97 4.35
2366 4065 3.587498 ACAGGGTAGCTATAATGCTGGA 58.413 45.455 0.00 0.00 43.87 3.86
2368 4067 4.528596 AGGTACAGGGTAGCTATAATGCTG 59.471 45.833 6.33 0.00 43.87 4.41
2437 4157 5.061920 AGAGATAAACTGACTTCGACCAC 57.938 43.478 0.00 0.00 0.00 4.16
2662 4392 2.354203 GGGTTTGACTAGCCTGAGTGAG 60.354 54.545 0.00 0.00 32.89 3.51
2663 4393 1.623811 GGGTTTGACTAGCCTGAGTGA 59.376 52.381 0.00 0.00 32.89 3.41
2664 4394 1.625818 AGGGTTTGACTAGCCTGAGTG 59.374 52.381 0.00 0.00 44.08 3.51
2665 4395 2.031495 AGGGTTTGACTAGCCTGAGT 57.969 50.000 0.00 0.00 44.08 3.41
2666 4396 3.131400 GTCTAGGGTTTGACTAGCCTGAG 59.869 52.174 4.72 0.03 45.27 3.35
2667 4397 3.097614 GTCTAGGGTTTGACTAGCCTGA 58.902 50.000 4.72 0.00 45.27 3.86
2668 4398 2.168728 GGTCTAGGGTTTGACTAGCCTG 59.831 54.545 4.72 0.00 45.27 4.85
2670 4400 2.431419 GAGGTCTAGGGTTTGACTAGCC 59.569 54.545 0.00 0.00 38.21 3.93
2671 4401 2.431419 GGAGGTCTAGGGTTTGACTAGC 59.569 54.545 0.00 0.00 38.21 3.42
2672 4402 2.688958 CGGAGGTCTAGGGTTTGACTAG 59.311 54.545 0.00 0.00 39.38 2.57
2673 4403 2.731572 CGGAGGTCTAGGGTTTGACTA 58.268 52.381 0.00 0.00 34.01 2.59
2674 4404 1.558233 CGGAGGTCTAGGGTTTGACT 58.442 55.000 0.00 0.00 34.01 3.41
2712 4442 4.913335 TTACCTATTGACTAGCCTGACG 57.087 45.455 0.00 0.00 0.00 4.35
2714 4444 6.373759 TGAGATTACCTATTGACTAGCCTGA 58.626 40.000 0.00 0.00 0.00 3.86
2751 4481 8.155510 AGAGTACATGTATCTACCACGAGATTA 58.844 37.037 9.18 0.00 37.38 1.75
2789 4520 9.902196 CATGCTGCTTTTGATTGTATTCATATA 57.098 29.630 0.00 0.00 0.00 0.86
2851 4583 3.181447 TGGTAACATGGACACGGGTTTTA 60.181 43.478 0.00 0.00 46.17 1.52
2855 4589 2.454369 TGGTAACATGGACACGGGT 58.546 52.632 0.00 0.00 46.17 5.28
2909 4643 4.098960 TCGGTTCTATTTCCAGCGTATCTT 59.901 41.667 0.00 0.00 33.25 2.40
2922 4656 5.647658 TGAAAGCATCAATGTCGGTTCTATT 59.352 36.000 0.00 0.00 34.30 1.73
2938 4672 2.692041 GGCAGGCTCTTAATGAAAGCAT 59.308 45.455 0.00 0.00 37.78 3.79
3042 4779 7.156876 AGCGACAATGATTTGGAAAAAGATA 57.843 32.000 0.00 0.00 37.15 1.98
3043 4780 6.029346 AGCGACAATGATTTGGAAAAAGAT 57.971 33.333 0.00 0.00 37.15 2.40
3174 4919 2.839324 CTTTCATGGCGCACGTGAGC 62.839 60.000 32.62 32.62 45.35 4.26
3192 4937 1.152030 TGTCAGCCTCCTTGGGACT 60.152 57.895 0.00 0.00 36.00 3.85
3270 5015 1.902508 TCCGATCAGGATTCCTATGCC 59.097 52.381 4.51 0.00 45.98 4.40
3339 5084 5.803461 GGCCGTTTTAGCTAAACAATAAAGG 59.197 40.000 18.45 15.05 45.20 3.11
3359 5104 1.153647 TTAGAGACGTGCATGGCCG 60.154 57.895 8.55 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.