Multiple sequence alignment - TraesCS6B01G324200

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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 TraesCS6B01G324200 chr6B 100.000 3615 0 0 1 3615 573416086 573412472 0.000000e+00 6676.0
1 TraesCS6B01G324200 chr6A 93.411 2398 124 18 119 2495 525031991 525029607 0.000000e+00 3522.0
2 TraesCS6B01G324200 chr6A 86.822 774 46 18 2761 3511 525029208 525028468 0.000000e+00 813.0
3 TraesCS6B01G324200 chr6A 90.476 189 14 4 2500 2686 525029516 525029330 2.790000e-61 246.0
4 TraesCS6B01G324200 chr6A 96.667 120 2 2 1273 1392 74321334 74321217 7.920000e-47 198.0
5 TraesCS6B01G324200 chr6A 91.589 107 9 0 10 116 447633442 447633336 8.090000e-32 148.0
6 TraesCS6B01G324200 chr6A 94.340 53 2 1 2689 2741 525029245 525029194 2.990000e-11 80.5
7 TraesCS6B01G324200 chr6D 93.093 2389 120 28 119 2502 383229068 383226720 0.000000e+00 3456.0
8 TraesCS6B01G324200 chr6D 86.776 1157 65 34 2503 3615 383226614 383225502 0.000000e+00 1208.0
9 TraesCS6B01G324200 chr1B 91.109 1316 97 14 1166 2477 645142627 645141328 0.000000e+00 1764.0
10 TraesCS6B01G324200 chr1A 90.150 1330 115 10 1166 2491 559707901 559706584 0.000000e+00 1716.0
11 TraesCS6B01G324200 chr1D 90.335 1314 107 14 1168 2477 467439116 467437819 0.000000e+00 1705.0
12 TraesCS6B01G324200 chr1D 88.793 116 11 2 1 116 42976096 42975983 1.350000e-29 141.0
13 TraesCS6B01G324200 chr7D 84.425 1374 182 22 1134 2487 166514266 166512905 0.000000e+00 1323.0
14 TraesCS6B01G324200 chr7D 90.826 109 7 3 119 226 50897950 50898056 3.760000e-30 143.0
15 TraesCS6B01G324200 chr7D 87.603 121 15 0 9 129 136582335 136582455 1.350000e-29 141.0
16 TraesCS6B01G324200 chr7A 82.591 1482 210 34 1033 2487 167904737 167903277 0.000000e+00 1264.0
17 TraesCS6B01G324200 chr7B 82.517 1470 219 28 1041 2487 130747373 130745919 0.000000e+00 1256.0
18 TraesCS6B01G324200 chr4A 81.924 1289 198 31 1134 2401 24557502 24556228 0.000000e+00 1057.0
19 TraesCS6B01G324200 chr4A 91.667 108 9 0 9 116 38347376 38347483 2.250000e-32 150.0
20 TraesCS6B01G324200 chr3D 79.218 486 57 25 119 573 597188272 597187800 7.590000e-77 298.0
21 TraesCS6B01G324200 chr3D 79.218 486 57 25 119 573 597192381 597191909 7.590000e-77 298.0
22 TraesCS6B01G324200 chr3D 92.593 108 8 0 9 116 423018600 423018493 4.830000e-34 156.0
23 TraesCS6B01G324200 chr3D 91.667 108 9 0 11 118 500655507 500655614 2.250000e-32 150.0
24 TraesCS6B01G324200 chr2D 76.592 534 64 43 9 483 513333034 513333565 1.680000e-58 237.0
25 TraesCS6B01G324200 chr3B 76.240 484 84 20 122 578 12130273 12129794 1.010000e-55 228.0
26 TraesCS6B01G324200 chr3B 75.826 484 86 20 122 578 12152670 12152191 2.190000e-52 217.0
27 TraesCS6B01G324200 chr3B 75.926 486 60 26 2 431 20872778 20872294 2.850000e-46 196.0
28 TraesCS6B01G324200 chr5B 81.463 205 31 6 232 432 559477141 559476940 1.040000e-35 161.0
29 TraesCS6B01G324200 chr2A 91.667 108 9 0 9 116 613050936 613050829 2.250000e-32 150.0
30 TraesCS6B01G324200 chr5D 87.903 124 13 2 9 131 97069835 97069713 1.050000e-30 145.0
31 TraesCS6B01G324200 chr4B 88.288 111 13 0 119 229 25922777 25922887 2.260000e-27 134.0


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 TraesCS6B01G324200 chr6B 573412472 573416086 3614 True 6676.000 6676 100.00000 1 3615 1 chr6B.!!$R1 3614
1 TraesCS6B01G324200 chr6A 525028468 525031991 3523 True 1165.375 3522 91.26225 119 3511 4 chr6A.!!$R3 3392
2 TraesCS6B01G324200 chr6D 383225502 383229068 3566 True 2332.000 3456 89.93450 119 3615 2 chr6D.!!$R1 3496
3 TraesCS6B01G324200 chr1B 645141328 645142627 1299 True 1764.000 1764 91.10900 1166 2477 1 chr1B.!!$R1 1311
4 TraesCS6B01G324200 chr1A 559706584 559707901 1317 True 1716.000 1716 90.15000 1166 2491 1 chr1A.!!$R1 1325
5 TraesCS6B01G324200 chr1D 467437819 467439116 1297 True 1705.000 1705 90.33500 1168 2477 1 chr1D.!!$R2 1309
6 TraesCS6B01G324200 chr7D 166512905 166514266 1361 True 1323.000 1323 84.42500 1134 2487 1 chr7D.!!$R1 1353
7 TraesCS6B01G324200 chr7A 167903277 167904737 1460 True 1264.000 1264 82.59100 1033 2487 1 chr7A.!!$R1 1454
8 TraesCS6B01G324200 chr7B 130745919 130747373 1454 True 1256.000 1256 82.51700 1041 2487 1 chr7B.!!$R1 1446
9 TraesCS6B01G324200 chr4A 24556228 24557502 1274 True 1057.000 1057 81.92400 1134 2401 1 chr4A.!!$R1 1267
10 TraesCS6B01G324200 chr3D 597187800 597192381 4581 True 298.000 298 79.21800 119 573 2 chr3D.!!$R2 454
11 TraesCS6B01G324200 chr2D 513333034 513333565 531 False 237.000 237 76.59200 9 483 1 chr2D.!!$F1 474

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
994 1072 0.041839 CAACACAGACTCAAGCGCAC 60.042 55.0 11.47 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2686 6072 0.179176 CTCACGTCCTCTTCTCAGCG 60.179 60.0 0.0 0.0 0.0 5.18 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
22 23 0.806868 CATCATGTTGCGGTTGAGCT 59.193 50.000 0.00 0.00 38.13 4.09
23 24 0.806868 ATCATGTTGCGGTTGAGCTG 59.193 50.000 0.00 0.00 38.13 4.24
26 27 0.534877 ATGTTGCGGTTGAGCTGTCA 60.535 50.000 0.00 0.00 38.13 3.58
36 37 2.189594 TGAGCTGTCAATGACCCTTG 57.810 50.000 11.24 0.17 0.00 3.61
39 40 3.245016 TGAGCTGTCAATGACCCTTGATT 60.245 43.478 11.24 0.00 37.47 2.57
68 69 6.395629 CCTTGAAATTGAGAACATGCTCATT 58.604 36.000 4.16 0.00 43.84 2.57
69 70 6.872020 CCTTGAAATTGAGAACATGCTCATTT 59.128 34.615 4.16 4.78 43.84 2.32
74 75 2.885894 TGAGAACATGCTCATTTGCACA 59.114 40.909 0.00 0.00 46.33 4.57
92 93 1.009389 CACTCCGCGTCTTCAAGGAC 61.009 60.000 4.92 0.00 0.00 3.85
107 108 3.643978 GACCGCCTGCATCATCGC 61.644 66.667 0.00 0.00 0.00 4.58
249 305 1.481056 CGGAGGACAGGGGTTGAACT 61.481 60.000 0.00 0.00 0.00 3.01
255 311 1.342174 GACAGGGGTTGAACTACGACA 59.658 52.381 0.00 0.00 34.74 4.35
269 325 2.046864 CGACAGAGGAGAAGCGGGA 61.047 63.158 0.00 0.00 0.00 5.14
365 423 2.317609 GCAGCGACGAAGGCAAGAA 61.318 57.895 0.00 0.00 0.00 2.52
412 472 2.435938 GATGAAGGCGCGGGTTCA 60.436 61.111 17.48 17.48 37.10 3.18
415 475 3.431725 GAAGGCGCGGGTTCAAGG 61.432 66.667 8.83 0.00 0.00 3.61
424 484 1.699730 CGGGTTCAAGGAGGGTTTTT 58.300 50.000 0.00 0.00 0.00 1.94
436 496 1.458588 GGTTTTTGGTGGGCTGGGA 60.459 57.895 0.00 0.00 0.00 4.37
473 533 1.304713 TCTGGTGTCCGGACTACCC 60.305 63.158 34.09 29.18 33.41 3.69
474 534 1.608336 CTGGTGTCCGGACTACCCA 60.608 63.158 34.09 31.12 34.08 4.51
477 537 0.616891 GGTGTCCGGACTACCCAAAT 59.383 55.000 33.39 0.00 34.14 2.32
479 539 1.553704 GTGTCCGGACTACCCAAATCT 59.446 52.381 33.39 0.00 34.14 2.40
496 558 5.010922 CCAAATCTCCCATGTTTGTCTTTGA 59.989 40.000 5.36 0.00 32.41 2.69
512 574 6.059484 TGTCTTTGATTTACGGGAGAAAACT 58.941 36.000 0.00 0.00 0.00 2.66
529 591 1.390565 ACTTATCCGGACCGTCTCAG 58.609 55.000 6.12 6.02 0.00 3.35
549 611 1.712018 CGGACCGATACAGTCTCGCA 61.712 60.000 8.64 0.00 34.84 5.10
557 619 4.320567 CCGATACAGTCTCGCATTAGATGT 60.321 45.833 2.83 0.00 34.84 3.06
570 632 0.681887 TAGATGTCTTCGGCGGTCCA 60.682 55.000 7.21 0.00 0.00 4.02
573 635 2.126031 GTCTTCGGCGGTCCAGAC 60.126 66.667 7.21 10.12 31.03 3.51
574 636 2.599281 TCTTCGGCGGTCCAGACA 60.599 61.111 7.21 0.00 0.00 3.41
579 641 2.741092 GGCGGTCCAGACAGTTCA 59.259 61.111 0.00 0.00 0.00 3.18
588 664 3.007398 GTCCAGACAGTTCAATCCAGACT 59.993 47.826 0.00 0.00 0.00 3.24
604 680 0.390735 GACTGACGCGGGTGGTTTAT 60.391 55.000 10.96 0.00 0.00 1.40
614 690 2.110352 GTGGTTTATGGGTCCGCCG 61.110 63.158 0.00 0.00 34.97 6.46
630 706 1.904771 CCGTGGAGATGCCCTAACA 59.095 57.895 0.00 0.00 34.97 2.41
722 798 3.305064 GCAAAGATCCAACGGCTTTTACA 60.305 43.478 0.00 0.00 30.00 2.41
837 913 1.941294 GTAGCGTGATCTCTTCTCGGA 59.059 52.381 0.00 0.00 40.71 4.55
918 994 2.736826 CCTCCCGGCTTTCTCCTCC 61.737 68.421 0.00 0.00 0.00 4.30
985 1063 1.072159 GCTGCTCCCAACACAGACT 59.928 57.895 0.00 0.00 33.10 3.24
986 1064 0.952984 GCTGCTCCCAACACAGACTC 60.953 60.000 0.00 0.00 33.10 3.36
987 1065 0.394192 CTGCTCCCAACACAGACTCA 59.606 55.000 0.00 0.00 33.10 3.41
988 1066 0.836606 TGCTCCCAACACAGACTCAA 59.163 50.000 0.00 0.00 0.00 3.02
989 1067 1.202687 TGCTCCCAACACAGACTCAAG 60.203 52.381 0.00 0.00 0.00 3.02
990 1068 1.517242 CTCCCAACACAGACTCAAGC 58.483 55.000 0.00 0.00 0.00 4.01
991 1069 0.249868 TCCCAACACAGACTCAAGCG 60.250 55.000 0.00 0.00 0.00 4.68
992 1070 1.571460 CCAACACAGACTCAAGCGC 59.429 57.895 0.00 0.00 0.00 5.92
993 1071 1.159713 CCAACACAGACTCAAGCGCA 61.160 55.000 11.47 0.00 0.00 6.09
994 1072 0.041839 CAACACAGACTCAAGCGCAC 60.042 55.000 11.47 0.00 0.00 5.34
1508 1698 2.885113 CCATCGACGACCTGCTCA 59.115 61.111 0.00 0.00 0.00 4.26
2465 5737 3.445687 TCGACATCCCCGACGTGG 61.446 66.667 0.00 0.00 37.55 4.94
2497 5769 0.112412 CTAGCCAACCCAACCCAACT 59.888 55.000 0.00 0.00 0.00 3.16
2502 5774 0.754957 CAACCCAACCCAACTCAGCA 60.755 55.000 0.00 0.00 0.00 4.41
2504 5776 1.151450 CCCAACCCAACTCAGCACT 59.849 57.895 0.00 0.00 0.00 4.40
2505 5777 0.400213 CCCAACCCAACTCAGCACTA 59.600 55.000 0.00 0.00 0.00 2.74
2506 5778 1.611673 CCCAACCCAACTCAGCACTAG 60.612 57.143 0.00 0.00 0.00 2.57
2507 5779 1.160137 CAACCCAACTCAGCACTAGC 58.840 55.000 0.00 0.00 42.56 3.42
2530 5910 6.654161 AGCTAATACTAGTACCAACGATCGAT 59.346 38.462 24.34 7.21 0.00 3.59
2531 5911 7.174599 AGCTAATACTAGTACCAACGATCGATT 59.825 37.037 24.34 9.60 0.00 3.34
2558 5942 7.513196 CGTGCTCTGTACGTAAAACTATTCATC 60.513 40.741 0.00 0.00 36.93 2.92
2573 5957 1.008881 CATCGCTGCATGCATCCAC 60.009 57.895 22.97 10.28 43.06 4.02
2595 5979 3.489355 TGAGCTCATCTCATCTCTCTCC 58.511 50.000 13.74 0.00 46.34 3.71
2605 5991 2.564553 ATCTCTCTCCGCACGTTGCC 62.565 60.000 4.73 0.00 41.12 4.52
2638 6024 6.374417 TGTATGCTTCTCCCTTTTACTTCT 57.626 37.500 0.00 0.00 0.00 2.85
2640 6026 3.926616 TGCTTCTCCCTTTTACTTCTCG 58.073 45.455 0.00 0.00 0.00 4.04
2644 6030 5.388408 TTCTCCCTTTTACTTCTCGTCTC 57.612 43.478 0.00 0.00 0.00 3.36
2649 6035 1.180029 TTTACTTCTCGTCTCCCCCG 58.820 55.000 0.00 0.00 0.00 5.73
2686 6072 1.598601 TCCTACGCACCAAACGTTTTC 59.401 47.619 11.66 0.27 41.93 2.29
2687 6155 1.654463 CTACGCACCAAACGTTTTCG 58.346 50.000 11.66 14.16 41.93 3.46
2776 6245 0.459063 GCTGCTAGGGTTTGCATTGC 60.459 55.000 0.46 0.46 38.59 3.56
2879 6348 1.244019 GGCTTGGTTGCTTCGGTCAT 61.244 55.000 0.00 0.00 0.00 3.06
2932 6401 1.004320 TACCGCACGCTCAATTGGT 60.004 52.632 5.42 0.00 0.00 3.67
2953 6425 4.645136 GGTGTGATGATCAGTACCAGACTA 59.355 45.833 18.65 0.00 35.64 2.59
2970 6442 3.944015 AGACTACCAGTATCGTGTACACC 59.056 47.826 20.11 6.16 0.00 4.16
2971 6443 3.944015 GACTACCAGTATCGTGTACACCT 59.056 47.826 20.11 8.46 0.00 4.00
2972 6444 3.944015 ACTACCAGTATCGTGTACACCTC 59.056 47.826 20.11 8.10 0.00 3.85
2973 6445 2.097825 ACCAGTATCGTGTACACCTCC 58.902 52.381 20.11 6.03 0.00 4.30
2974 6446 1.065102 CCAGTATCGTGTACACCTCCG 59.935 57.143 20.11 8.79 0.00 4.63
2975 6447 1.741706 CAGTATCGTGTACACCTCCGT 59.258 52.381 20.11 4.71 0.00 4.69
2976 6448 2.163010 CAGTATCGTGTACACCTCCGTT 59.837 50.000 20.11 6.43 0.00 4.44
2979 6451 1.321474 TCGTGTACACCTCCGTTTCT 58.679 50.000 20.11 0.00 0.00 2.52
3019 6497 4.571984 TGACTCGATAATGTTCTTGCCATG 59.428 41.667 0.00 0.00 0.00 3.66
3095 6589 2.124570 GCCCGGTGCATCAGTCAT 60.125 61.111 9.72 0.00 40.77 3.06
3096 6590 1.750399 GCCCGGTGCATCAGTCATT 60.750 57.895 9.72 0.00 40.77 2.57
3097 6591 0.463654 GCCCGGTGCATCAGTCATTA 60.464 55.000 9.72 0.00 40.77 1.90
3098 6592 1.586422 CCCGGTGCATCAGTCATTAG 58.414 55.000 0.00 0.00 0.00 1.73
3099 6593 1.134401 CCCGGTGCATCAGTCATTAGT 60.134 52.381 0.00 0.00 0.00 2.24
3100 6594 2.205074 CCGGTGCATCAGTCATTAGTC 58.795 52.381 0.00 0.00 0.00 2.59
3101 6595 2.418609 CCGGTGCATCAGTCATTAGTCA 60.419 50.000 0.00 0.00 0.00 3.41
3107 6601 3.865446 CATCAGTCATTAGTCAGTGCCA 58.135 45.455 0.00 0.00 0.00 4.92
3333 6846 2.733301 CCCGCTCGCTCATCATCT 59.267 61.111 0.00 0.00 0.00 2.90
3334 6847 1.959848 CCCGCTCGCTCATCATCTA 59.040 57.895 0.00 0.00 0.00 1.98
3341 6854 3.411446 CTCGCTCATCATCTAGTCCTCT 58.589 50.000 0.00 0.00 0.00 3.69
3347 6860 3.006644 TCATCATCTAGTCCTCTGCATGC 59.993 47.826 11.82 11.82 0.00 4.06
3348 6861 2.391678 TCATCTAGTCCTCTGCATGCA 58.608 47.619 21.29 21.29 0.00 3.96
3349 6862 2.970640 TCATCTAGTCCTCTGCATGCAT 59.029 45.455 22.97 7.74 0.00 3.96
3577 7106 1.979155 CTCCAGTCCAGCTCGGTCA 60.979 63.158 2.68 0.00 35.57 4.02
3583 7112 1.305297 TCCAGCTCGGTCATCTGGT 60.305 57.895 7.31 0.00 45.67 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.806868 CAGCTCAACCGCAACATGAT 59.193 50.000 0.00 0.00 0.00 2.45
5 6 0.534877 ACAGCTCAACCGCAACATGA 60.535 50.000 0.00 0.00 0.00 3.07
6 7 0.110056 GACAGCTCAACCGCAACATG 60.110 55.000 0.00 0.00 0.00 3.21
7 8 0.534877 TGACAGCTCAACCGCAACAT 60.535 50.000 0.00 0.00 0.00 2.71
18 19 2.479566 TCAAGGGTCATTGACAGCTC 57.520 50.000 18.09 5.14 34.31 4.09
22 23 3.084039 GCTCAATCAAGGGTCATTGACA 58.916 45.455 18.09 0.00 41.76 3.58
23 24 2.424956 GGCTCAATCAAGGGTCATTGAC 59.575 50.000 8.34 8.34 41.76 3.18
26 27 1.642762 AGGGCTCAATCAAGGGTCATT 59.357 47.619 0.00 0.00 0.00 2.57
36 37 5.047802 TGTTCTCAATTTCAAGGGCTCAATC 60.048 40.000 0.00 0.00 0.00 2.67
39 40 3.831323 TGTTCTCAATTTCAAGGGCTCA 58.169 40.909 0.00 0.00 0.00 4.26
74 75 1.289380 GTCCTTGAAGACGCGGAGT 59.711 57.895 12.47 0.00 0.00 3.85
107 108 6.073167 ATACGAGTAGTATGTCAATGAGACGG 60.073 42.308 0.00 0.00 43.93 4.79
108 109 6.889494 ATACGAGTAGTATGTCAATGAGACG 58.111 40.000 0.00 0.00 43.93 4.18
192 218 2.420022 GGCAACTGTTCGATGTATTGCT 59.580 45.455 18.53 0.00 41.63 3.91
249 305 1.030488 CCCGCTTCTCCTCTGTCGTA 61.030 60.000 0.00 0.00 0.00 3.43
255 311 0.758685 CTCCATCCCGCTTCTCCTCT 60.759 60.000 0.00 0.00 0.00 3.69
269 325 3.806667 GCTCCAGCAGGGCTCCAT 61.807 66.667 0.00 0.00 36.40 3.41
297 353 1.334243 GTCGGAACTCTATGTCTCCCG 59.666 57.143 0.00 0.00 0.00 5.14
365 423 8.986929 TCATTTTCTCTTCTTCCTTCTTTCTT 57.013 30.769 0.00 0.00 0.00 2.52
412 472 0.762842 GCCCACCAAAAACCCTCCTT 60.763 55.000 0.00 0.00 0.00 3.36
415 475 1.471829 CCAGCCCACCAAAAACCCTC 61.472 60.000 0.00 0.00 0.00 4.30
424 484 3.249189 GACACTCCCAGCCCACCA 61.249 66.667 0.00 0.00 0.00 4.17
470 530 3.165071 GACAAACATGGGAGATTTGGGT 58.835 45.455 9.68 0.00 37.59 4.51
473 533 6.088016 TCAAAGACAAACATGGGAGATTTG 57.912 37.500 0.00 0.74 38.89 2.32
474 534 6.923199 ATCAAAGACAAACATGGGAGATTT 57.077 33.333 0.00 0.00 0.00 2.17
477 537 6.072728 CGTAAATCAAAGACAAACATGGGAGA 60.073 38.462 0.00 0.00 0.00 3.71
479 539 5.048364 CCGTAAATCAAAGACAAACATGGGA 60.048 40.000 0.00 0.00 0.00 4.37
496 558 5.104817 TCCGGATAAGTTTTCTCCCGTAAAT 60.105 40.000 0.00 0.00 36.39 1.40
512 574 1.721664 CGCTGAGACGGTCCGGATAA 61.722 60.000 17.28 0.00 0.00 1.75
529 591 1.009900 CGAGACTGTATCGGTCCGC 60.010 63.158 16.41 0.00 40.33 5.54
549 611 1.068741 GGACCGCCGAAGACATCTAAT 59.931 52.381 0.00 0.00 0.00 1.73
557 619 2.599281 TGTCTGGACCGCCGAAGA 60.599 61.111 0.00 0.00 36.79 2.87
570 632 3.305676 CGTCAGTCTGGATTGAACTGTCT 60.306 47.826 0.00 0.00 0.00 3.41
573 635 1.728971 GCGTCAGTCTGGATTGAACTG 59.271 52.381 0.00 0.00 0.00 3.16
574 636 1.670087 CGCGTCAGTCTGGATTGAACT 60.670 52.381 0.00 0.00 0.00 3.01
579 641 2.283529 ACCCGCGTCAGTCTGGATT 61.284 57.895 4.92 0.00 0.00 3.01
588 664 1.376166 CCATAAACCACCCGCGTCA 60.376 57.895 4.92 0.00 0.00 4.35
614 690 1.771255 AGGATGTTAGGGCATCTCCAC 59.229 52.381 6.11 0.00 43.41 4.02
655 731 1.520787 CATCCGACGGCCCAAGTAC 60.521 63.158 9.66 0.00 0.00 2.73
722 798 1.535833 ATCAAGTCTCGGTCGACTGT 58.464 50.000 23.27 1.57 43.14 3.55
876 952 6.315551 GGAGAATTTAAAGAAGCGAAACTCC 58.684 40.000 0.00 0.00 33.62 3.85
945 1021 2.594592 GCTTTGTGGCCTCGTGGT 60.595 61.111 3.32 0.00 35.27 4.16
991 1069 1.633171 CTCTGTATCGCTTGCGTGC 59.367 57.895 14.70 6.78 0.00 5.34
992 1070 1.633171 GCTCTGTATCGCTTGCGTG 59.367 57.895 14.70 2.50 0.00 5.34
993 1071 1.874019 CGCTCTGTATCGCTTGCGT 60.874 57.895 14.70 5.29 38.81 5.24
994 1072 2.916423 CGCTCTGTATCGCTTGCG 59.084 61.111 8.87 8.87 37.57 4.85
1246 1324 1.203994 GCGTAGTCCACCATGTACACT 59.796 52.381 0.00 0.00 0.00 3.55
1399 1492 0.105246 CATAGGGGAGGCAGGTCTCT 60.105 60.000 0.42 0.00 34.39 3.10
1444 1537 2.045242 CGGGAGGACTCGAGGTCA 60.045 66.667 18.41 0.00 46.16 4.02
1508 1698 2.430367 GGCGACCTTGGTCTTGGT 59.570 61.111 16.60 0.00 39.60 3.67
1579 3080 0.319040 CGATCATGTCGGCGAAGGAT 60.319 55.000 12.92 14.89 46.47 3.24
1746 3247 3.945981 TGTAGTAGTTTGGCGTGATGA 57.054 42.857 0.00 0.00 0.00 2.92
2063 5171 3.487202 GCGCGCGATGAAGGACAA 61.487 61.111 37.18 0.00 0.00 3.18
2465 5737 2.332063 TGGCTAGGCTAATGCTTGAC 57.668 50.000 18.18 0.00 39.59 3.18
2504 5776 7.154656 TCGATCGTTGGTACTAGTATTAGCTA 58.845 38.462 15.94 0.00 0.00 3.32
2505 5777 5.994054 TCGATCGTTGGTACTAGTATTAGCT 59.006 40.000 15.94 0.00 0.00 3.32
2506 5778 6.233430 TCGATCGTTGGTACTAGTATTAGC 57.767 41.667 15.94 0.00 0.00 3.09
2507 5779 7.687347 CGAATCGATCGTTGGTACTAGTATTAG 59.313 40.741 15.94 0.00 46.52 1.73
2510 5890 5.924786 CGAATCGATCGTTGGTACTAGTAT 58.075 41.667 15.94 0.00 46.52 2.12
2530 5910 3.968649 AGTTTTACGTACAGAGCACGAA 58.031 40.909 0.00 0.00 41.91 3.85
2531 5911 3.631145 AGTTTTACGTACAGAGCACGA 57.369 42.857 0.00 0.00 41.91 4.35
2652 6038 1.529948 TAGGATGACGTAGGGGCGG 60.530 63.158 0.00 0.00 35.98 6.13
2664 6050 1.153353 AACGTTTGGTGCGTAGGATG 58.847 50.000 0.00 0.00 42.10 3.51
2686 6072 0.179176 CTCACGTCCTCTTCTCAGCG 60.179 60.000 0.00 0.00 0.00 5.18
2687 6155 1.169577 TCTCACGTCCTCTTCTCAGC 58.830 55.000 0.00 0.00 0.00 4.26
2697 6165 2.408022 CGTCGGGATCTCACGTCC 59.592 66.667 1.28 0.00 44.39 4.79
2776 6245 1.890979 GGCGATGGGATCAGTGCTG 60.891 63.158 0.00 0.00 0.00 4.41
2817 6286 0.459899 AAGCACGAGCATGGTCGATA 59.540 50.000 43.52 0.00 45.49 2.92
2849 6318 2.813908 CCAAGCCACCTCGTACGC 60.814 66.667 11.24 0.00 0.00 4.42
2879 6348 3.211045 GAGTGTAAACAGACAGGGCAAA 58.789 45.455 0.00 0.00 0.00 3.68
2932 6401 4.645136 GGTAGTCTGGTACTGATCATCACA 59.355 45.833 0.00 0.00 39.39 3.58
2953 6425 2.097825 GGAGGTGTACACGATACTGGT 58.902 52.381 19.41 0.00 0.00 4.00
2970 6442 4.260784 CCAGAAACAGAAACAGAAACGGAG 60.261 45.833 0.00 0.00 0.00 4.63
2971 6443 3.625764 CCAGAAACAGAAACAGAAACGGA 59.374 43.478 0.00 0.00 0.00 4.69
2972 6444 3.243068 CCCAGAAACAGAAACAGAAACGG 60.243 47.826 0.00 0.00 0.00 4.44
2973 6445 3.625764 TCCCAGAAACAGAAACAGAAACG 59.374 43.478 0.00 0.00 0.00 3.60
2974 6446 5.299279 TCATCCCAGAAACAGAAACAGAAAC 59.701 40.000 0.00 0.00 0.00 2.78
2975 6447 5.299279 GTCATCCCAGAAACAGAAACAGAAA 59.701 40.000 0.00 0.00 0.00 2.52
2976 6448 4.821805 GTCATCCCAGAAACAGAAACAGAA 59.178 41.667 0.00 0.00 0.00 3.02
2979 6451 4.389374 GAGTCATCCCAGAAACAGAAACA 58.611 43.478 0.00 0.00 0.00 2.83
3019 6497 2.442272 TAGGAGGACGGAGCAGGC 60.442 66.667 0.00 0.00 0.00 4.85
3031 6509 4.024725 CCTCGTCTCATTAACTCGTAGGAG 60.025 50.000 10.86 10.86 46.13 3.69
3095 6589 3.990369 AGGTAGGTATGGCACTGACTAA 58.010 45.455 0.00 0.00 0.00 2.24
3096 6590 3.682592 AGGTAGGTATGGCACTGACTA 57.317 47.619 0.00 0.00 0.00 2.59
3097 6591 2.552093 AGGTAGGTATGGCACTGACT 57.448 50.000 0.00 0.00 0.00 3.41
3098 6592 2.364647 GGTAGGTAGGTATGGCACTGAC 59.635 54.545 0.00 0.00 0.00 3.51
3099 6593 2.674420 GGTAGGTAGGTATGGCACTGA 58.326 52.381 0.00 0.00 0.00 3.41
3100 6594 1.692519 GGGTAGGTAGGTATGGCACTG 59.307 57.143 0.00 0.00 0.00 3.66
3101 6595 1.292849 TGGGTAGGTAGGTATGGCACT 59.707 52.381 0.00 0.00 0.00 4.40
3107 6601 1.132817 CAGGGCTGGGTAGGTAGGTAT 60.133 57.143 0.00 0.00 0.00 2.73
3333 6846 3.121738 CATGATGCATGCAGAGGACTA 57.878 47.619 26.69 7.08 35.02 2.59
3334 6847 1.968704 CATGATGCATGCAGAGGACT 58.031 50.000 26.69 7.85 35.02 3.85
3475 6988 4.899239 GCTCCCGATGGCACGAGG 62.899 72.222 10.33 9.64 35.09 4.63
3513 7038 3.723348 GCCACCCTTTGTCGACGC 61.723 66.667 11.62 1.29 0.00 5.19
3547 7072 2.126307 CTGGAGACTGGACACGCG 60.126 66.667 3.53 3.53 0.00 6.01
3552 7077 0.902516 AGCTGGACTGGAGACTGGAC 60.903 60.000 0.00 0.00 0.00 4.02
3553 7078 0.613292 GAGCTGGACTGGAGACTGGA 60.613 60.000 0.00 0.00 0.00 3.86
3554 7079 1.896694 GAGCTGGACTGGAGACTGG 59.103 63.158 0.00 0.00 0.00 4.00
3555 7080 1.510383 CGAGCTGGACTGGAGACTG 59.490 63.158 0.00 0.00 0.00 3.51
3556 7081 1.680651 CCGAGCTGGACTGGAGACT 60.681 63.158 0.00 0.00 42.00 3.24
3557 7082 1.939769 GACCGAGCTGGACTGGAGAC 61.940 65.000 8.91 0.00 42.00 3.36
3558 7083 1.679305 GACCGAGCTGGACTGGAGA 60.679 63.158 8.91 0.00 42.00 3.71
3559 7084 1.326213 ATGACCGAGCTGGACTGGAG 61.326 60.000 8.91 0.00 42.00 3.86
3560 7085 1.305297 ATGACCGAGCTGGACTGGA 60.305 57.895 8.91 0.00 42.00 3.86
3561 7086 1.142748 GATGACCGAGCTGGACTGG 59.857 63.158 8.91 0.00 42.00 4.00


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

AutoCloner maintained by Alex Coulton.