Multiple sequence alignment - TraesCS5D01G408900

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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 TraesCS5D01G408900 chr5D 100.000 3135 0 0 1 3135 473054148 473051014 0.000000e+00 5790.0
1 TraesCS5D01G408900 chr5D 90.582 1083 72 19 1259 2323 473041532 473040462 0.000000e+00 1408.0
2 TraesCS5D01G408900 chr5D 90.210 1001 92 6 1370 2368 473064365 473063369 0.000000e+00 1301.0
3 TraesCS5D01G408900 chr5D 88.744 844 62 21 433 1261 473042901 473042076 0.000000e+00 1002.0
4 TraesCS5D01G408900 chr5D 95.392 434 19 1 2463 2896 6235847 6236279 0.000000e+00 689.0
5 TraesCS5D01G408900 chr5D 94.989 439 19 3 2463 2899 503330965 503330528 0.000000e+00 686.0
6 TraesCS5D01G408900 chr5D 93.182 396 23 2 56 449 473043354 473042961 2.100000e-161 579.0
7 TraesCS5D01G408900 chr5D 82.572 591 61 24 687 1244 473065038 473064457 1.690000e-132 483.0
8 TraesCS5D01G408900 chr5D 89.420 293 25 4 206 497 473061989 473062276 6.390000e-97 364.0
9 TraesCS5D01G408900 chr5D 79.905 423 60 19 1907 2323 473039110 473038707 1.420000e-73 287.0
10 TraesCS5D01G408900 chr5D 86.957 253 22 4 129 379 473047437 473047680 1.110000e-69 274.0
11 TraesCS5D01G408900 chr5D 91.803 122 8 1 533 654 473062281 473062400 5.380000e-38 169.0
12 TraesCS5D01G408900 chr5D 91.566 83 5 1 129 209 473054267 473054349 2.560000e-21 113.0
13 TraesCS5D01G408900 chr5A 91.161 2670 156 39 472 3082 593037600 593034952 0.000000e+00 3550.0
14 TraesCS5D01G408900 chr5A 91.924 2427 126 30 677 3060 592832167 592834566 0.000000e+00 3332.0
15 TraesCS5D01G408900 chr5A 88.323 1002 104 8 1370 2368 593055499 593054508 0.000000e+00 1190.0
16 TraesCS5D01G408900 chr5A 92.505 547 34 5 1 545 593032922 593032381 0.000000e+00 776.0
17 TraesCS5D01G408900 chr5A 88.947 570 32 7 1 568 592831568 592832108 0.000000e+00 675.0
18 TraesCS5D01G408900 chr5A 84.399 641 67 20 1738 2369 592691273 592690657 1.610000e-167 599.0
19 TraesCS5D01G408900 chr5A 92.112 393 29 2 2742 3134 592836578 592836968 1.270000e-153 553.0
20 TraesCS5D01G408900 chr5A 90.094 424 30 10 2 423 593038010 593037597 9.890000e-150 540.0
21 TraesCS5D01G408900 chr5A 88.377 456 35 6 815 1261 592827296 592826850 1.660000e-147 532.0
22 TraesCS5D01G408900 chr5A 82.292 576 61 23 687 1232 593056125 593055561 7.920000e-126 460.0
23 TraesCS5D01G408900 chr5A 87.297 370 38 5 129 496 593038132 593038494 6.260000e-112 414.0
24 TraesCS5D01G408900 chr5A 86.721 369 42 5 132 497 592829493 592829129 1.350000e-108 403.0
25 TraesCS5D01G408900 chr5A 88.856 341 19 6 677 1014 592830988 592831312 4.870000e-108 401.0
26 TraesCS5D01G408900 chr5A 89.888 178 15 2 2278 2452 592837471 592837648 3.150000e-55 226.0
27 TraesCS5D01G408900 chr5A 81.590 239 21 4 402 634 592829947 592830168 3.210000e-40 176.0
28 TraesCS5D01G408900 chr5A 92.857 98 6 1 1 98 592829617 592829713 1.170000e-29 141.0
29 TraesCS5D01G408900 chr5B 88.592 2393 139 56 1 2323 580428344 580426016 0.000000e+00 2784.0
30 TraesCS5D01G408900 chr5B 90.410 1001 93 3 1370 2369 580431448 580430450 0.000000e+00 1314.0
31 TraesCS5D01G408900 chr5B 82.125 593 56 27 687 1239 580432096 580431514 2.200000e-126 462.0
32 TraesCS5D01G408900 chr5B 87.738 367 36 5 129 493 580428467 580428826 1.340000e-113 420.0
33 TraesCS5D01G408900 chr5B 80.812 271 43 6 1907 2172 580424959 580424693 1.470000e-48 204.0
34 TraesCS5D01G408900 chr5B 90.789 76 6 1 798 873 301433821 301433747 1.990000e-17 100.0
35 TraesCS5D01G408900 chr5B 88.235 85 7 1 2367 2448 419495627 419495711 7.160000e-17 99.0
36 TraesCS5D01G408900 chr1A 95.632 435 17 2 2463 2896 554447892 554448325 0.000000e+00 697.0
37 TraesCS5D01G408900 chr1A 89.412 85 6 1 2367 2448 223444720 223444804 1.540000e-18 104.0
38 TraesCS5D01G408900 chrUn 95.413 436 17 3 2463 2896 426380331 426380765 0.000000e+00 691.0
39 TraesCS5D01G408900 chr2D 95.413 436 17 3 2463 2896 648663249 648663683 0.000000e+00 691.0
40 TraesCS5D01G408900 chr2D 95.918 245 10 0 2890 3134 591991006 591990762 6.300000e-107 398.0
41 TraesCS5D01G408900 chr1D 95.216 439 18 3 2463 2899 254477052 254476615 0.000000e+00 691.0
42 TraesCS5D01G408900 chr1D 90.588 85 5 1 2367 2448 160498886 160498970 3.310000e-20 110.0
43 TraesCS5D01G408900 chr3B 94.533 439 21 2 2463 2899 201493057 201492620 0.000000e+00 675.0
44 TraesCS5D01G408900 chr3B 95.528 246 11 0 2890 3135 201544851 201544606 8.150000e-106 394.0
45 TraesCS5D01G408900 chr7D 95.510 245 11 0 2890 3134 231538223 231537979 2.930000e-105 392.0
46 TraesCS5D01G408900 chr7D 95.510 245 11 0 2890 3134 231621615 231621371 2.930000e-105 392.0
47 TraesCS5D01G408900 chr7D 94.366 71 4 0 2364 2434 350137413 350137483 3.310000e-20 110.0
48 TraesCS5D01G408900 chr7B 95.510 245 11 0 2890 3134 622432636 622432880 2.930000e-105 392.0
49 TraesCS5D01G408900 chr7B 95.652 69 3 0 2366 2434 355888564 355888496 9.190000e-21 111.0
50 TraesCS5D01G408900 chr7B 87.179 78 9 1 2352 2428 697543783 697543706 1.550000e-13 87.9
51 TraesCS5D01G408900 chr3D 95.510 245 11 0 2890 3134 589254974 589254730 2.930000e-105 392.0
52 TraesCS5D01G408900 chr6B 93.846 65 4 0 810 874 126070481 126070417 7.160000e-17 99.0


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 TraesCS5D01G408900 chr5D 473051014 473054148 3134 True 5790.000000 5790 100.000000 1 3135 1 chr5D.!!$R1 3134
1 TraesCS5D01G408900 chr5D 473063369 473065038 1669 True 892.000000 1301 86.391000 687 2368 2 chr5D.!!$R4 1681
2 TraesCS5D01G408900 chr5D 473038707 473043354 4647 True 819.000000 1408 88.103250 56 2323 4 chr5D.!!$R3 2267
3 TraesCS5D01G408900 chr5A 593032381 593038010 5629 True 1622.000000 3550 91.253333 1 3082 3 chr5A.!!$R3 3081
4 TraesCS5D01G408900 chr5A 593054508 593056125 1617 True 825.000000 1190 85.307500 687 2368 2 chr5A.!!$R4 1681
5 TraesCS5D01G408900 chr5A 592829617 592837648 8031 False 786.285714 3332 89.453429 1 3134 7 chr5A.!!$F2 3133
6 TraesCS5D01G408900 chr5A 592690657 592691273 616 True 599.000000 599 84.399000 1738 2369 1 chr5A.!!$R1 631
7 TraesCS5D01G408900 chr5A 592826850 592829493 2643 True 467.500000 532 87.549000 132 1261 2 chr5A.!!$R2 1129
8 TraesCS5D01G408900 chr5B 580424693 580432096 7403 True 1191.000000 2784 85.484750 1 2369 4 chr5B.!!$R2 2368

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
49 3801 0.385473 GCCAACACACGAAATGGACG 60.385 55.0 0.00 0.00 34.82 4.79 F
1301 9238 0.247894 TTTATTCGTGCGCGCCATTC 60.248 50.0 30.77 15.07 38.14 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1358 9295 0.870307 CCCTACGCACGCACATAGTC 60.870 60.0 0.00 0.0 0.00 2.59 R
3064 11072 0.106149 CCCCGAGGGTAGGAAAATCG 59.894 60.0 7.48 0.0 38.25 3.34 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
37 3789 2.545742 GGAGGTTTGAACATGCCAACAC 60.546 50.000 0.00 0.02 0.00 3.32
49 3801 0.385473 GCCAACACACGAAATGGACG 60.385 55.000 0.00 0.00 34.82 4.79
62 3814 4.265556 CGAAATGGACGATAAGACAGTGTC 59.734 45.833 15.78 15.78 0.00 3.67
68 3820 3.022406 ACGATAAGACAGTGTCCCCTAC 58.978 50.000 19.71 7.23 32.18 3.18
114 5805 9.595357 GAGTTATTTTTCGGTCTTGAAAGTTAG 57.405 33.333 0.00 0.00 38.92 2.34
277 5970 5.299949 AGTTTGATTTGACCCAGAAATTGC 58.700 37.500 0.00 0.00 0.00 3.56
394 6101 9.844257 ACTATTGGAAAATTTAGAGAGAGGATG 57.156 33.333 0.00 0.00 0.00 3.51
395 6102 9.282569 CTATTGGAAAATTTAGAGAGAGGATGG 57.717 37.037 0.00 0.00 0.00 3.51
396 6103 6.891306 TGGAAAATTTAGAGAGAGGATGGA 57.109 37.500 0.00 0.00 0.00 3.41
397 6104 6.893583 TGGAAAATTTAGAGAGAGGATGGAG 58.106 40.000 0.00 0.00 0.00 3.86
398 6105 6.126652 TGGAAAATTTAGAGAGAGGATGGAGG 60.127 42.308 0.00 0.00 0.00 4.30
399 6106 6.126623 GGAAAATTTAGAGAGAGGATGGAGGT 60.127 42.308 0.00 0.00 0.00 3.85
400 6107 5.885449 AATTTAGAGAGAGGATGGAGGTG 57.115 43.478 0.00 0.00 0.00 4.00
401 6108 4.609866 TTTAGAGAGAGGATGGAGGTGA 57.390 45.455 0.00 0.00 0.00 4.02
416 6123 3.054802 GGAGGTGATGTGGATCTTGAAGT 60.055 47.826 0.00 0.00 0.00 3.01
430 6137 9.436957 TGGATCTTGAAGTGAAAATACTTACTC 57.563 33.333 0.00 0.00 40.78 2.59
444 6227 9.939802 AAAATACTTACTCTACTTACTTGGTGG 57.060 33.333 0.00 0.00 0.00 4.61
499 6284 3.436704 TCATACTTTTCTTTCAGCAGGCG 59.563 43.478 0.00 0.00 0.00 5.52
525 6310 8.840321 GCAGAGGCTTGTCTAAATAAAATGATA 58.160 33.333 0.00 0.00 36.96 2.15
578 6379 6.450545 CAGAATATAACTCGAATGCTCCAGA 58.549 40.000 0.00 0.00 0.00 3.86
608 6409 1.755179 CCAGATCAATTCACGGCCTT 58.245 50.000 0.00 0.00 0.00 4.35
752 8087 4.041444 TGCCAACAAAATTTAGGATGCCTT 59.959 37.500 0.00 0.00 34.61 4.35
753 8088 4.631377 GCCAACAAAATTTAGGATGCCTTC 59.369 41.667 0.00 0.00 34.61 3.46
758 8093 5.420104 ACAAAATTTAGGATGCCTTCAGAGG 59.580 40.000 0.00 0.00 46.50 3.69
762 8097 1.144936 GGATGCCTTCAGAGGTCCG 59.855 63.158 0.00 0.00 45.44 4.79
936 8298 4.810191 ATAGGATCGACATAAGCCCTTC 57.190 45.455 0.00 0.00 0.00 3.46
1172 8558 2.592993 CCCGCTTCTCCCAGGACAA 61.593 63.158 0.00 0.00 0.00 3.18
1212 8598 0.249531 TACGCTTGCTGTTCCACGAA 60.250 50.000 0.00 0.00 0.00 3.85
1228 8614 0.371989 CGAATGCGGCGTCAATGTAA 59.628 50.000 9.37 0.00 0.00 2.41
1284 9221 8.340618 AGATGTACTAATGTGCTGTTTGATTT 57.659 30.769 0.00 0.00 0.00 2.17
1301 9238 0.247894 TTTATTCGTGCGCGCCATTC 60.248 50.000 30.77 15.07 38.14 2.67
1312 9249 1.071239 CGCGCCATTCATTCTTCTACG 60.071 52.381 0.00 0.00 0.00 3.51
1314 9251 3.120792 GCGCCATTCATTCTTCTACGTA 58.879 45.455 0.00 0.00 0.00 3.57
1316 9253 4.360563 CGCCATTCATTCTTCTACGTACT 58.639 43.478 0.00 0.00 0.00 2.73
1320 9257 7.145985 GCCATTCATTCTTCTACGTACTCATA 58.854 38.462 0.00 0.00 0.00 2.15
1321 9258 7.815068 GCCATTCATTCTTCTACGTACTCATAT 59.185 37.037 0.00 0.00 0.00 1.78
1322 9259 9.133627 CCATTCATTCTTCTACGTACTCATATG 57.866 37.037 0.00 0.00 0.00 1.78
1359 9296 9.256228 AGTAGATGGACTAACTAATCTGTTTGA 57.744 33.333 0.00 0.00 32.49 2.69
1360 9297 9.303537 GTAGATGGACTAACTAATCTGTTTGAC 57.696 37.037 0.00 0.00 32.49 3.18
1362 9299 9.256228 AGATGGACTAACTAATCTGTTTGACTA 57.744 33.333 0.00 0.00 0.00 2.59
1365 9302 8.812972 TGGACTAACTAATCTGTTTGACTATGT 58.187 33.333 0.00 0.00 0.00 2.29
1366 9303 9.088512 GGACTAACTAATCTGTTTGACTATGTG 57.911 37.037 0.00 0.00 0.00 3.21
1429 9393 1.477105 GCACAGAAAAGACGGCAAAC 58.523 50.000 0.00 0.00 0.00 2.93
1777 9741 6.265649 TCAAGAAGAGCCGTCTTTATAGCTAT 59.734 38.462 11.77 11.77 43.50 2.97
1983 9947 1.201880 GGTCGACCAGAACCTCTACAC 59.798 57.143 29.75 0.00 35.64 2.90
2136 10100 1.467734 CTGCAGCAGGTTCAACTGATC 59.532 52.381 15.35 0.00 40.97 2.92
2257 10240 3.084070 TGTCGGATTCATCTCGATGTG 57.916 47.619 6.78 0.00 39.72 3.21
2279 10262 0.874175 CTGTTCTGACCGCACGTTCA 60.874 55.000 0.00 0.00 0.00 3.18
2406 10397 7.755373 CGAAATATATATCGCTGGAGAAGTTGA 59.245 37.037 0.00 0.00 31.71 3.18
2407 10398 9.424319 GAAATATATATCGCTGGAGAAGTTGAA 57.576 33.333 0.00 0.00 0.00 2.69
2409 10400 4.744795 ATATCGCTGGAGAAGTTGAACT 57.255 40.909 0.00 0.00 0.00 3.01
2410 10401 5.854010 ATATCGCTGGAGAAGTTGAACTA 57.146 39.130 0.00 0.00 0.00 2.24
2411 10402 3.299340 TCGCTGGAGAAGTTGAACTAC 57.701 47.619 0.00 0.00 0.00 2.73
2524 10532 7.510549 TGGACATTTCTAATAATAGCAAGCC 57.489 36.000 0.00 0.00 0.00 4.35
2562 10570 4.452114 GCATTTTCGATTTCAGGGCTTTTT 59.548 37.500 0.00 0.00 0.00 1.94
2583 10591 1.196104 CCCCGGTTAGTGAAGGACCA 61.196 60.000 0.00 0.00 32.95 4.02
2596 10604 4.021016 GTGAAGGACCAGAGAAGCTTTCTA 60.021 45.833 0.00 0.00 40.87 2.10
2613 10621 7.155328 AGCTTTCTAGTTATGAATCGGGTATG 58.845 38.462 0.00 0.00 0.00 2.39
2638 10646 1.230482 ATGGGAGGGGCTTGGGTAA 60.230 57.895 0.00 0.00 0.00 2.85
2645 10653 1.435168 AGGGGCTTGGGTAAAATTCCA 59.565 47.619 0.00 0.00 0.00 3.53
2680 10688 1.651138 TGTTTGCGCTCGTTTTTGTTG 59.349 42.857 9.73 0.00 0.00 3.33
2690 10698 6.012482 CGCTCGTTTTTGTTGTTTTTGATTT 58.988 32.000 0.00 0.00 0.00 2.17
2723 10731 4.437682 TTCTATACCCTTGGGCAATGAG 57.562 45.455 5.46 0.00 0.00 2.90
2725 10733 2.736670 ATACCCTTGGGCAATGAGTC 57.263 50.000 5.46 0.00 0.00 3.36
2734 10742 1.067212 GGGCAATGAGTCTCGACGTAT 59.933 52.381 0.00 0.00 36.20 3.06
2739 10747 0.454600 TGAGTCTCGACGTATTGGGC 59.545 55.000 0.00 0.00 36.20 5.36
2744 10752 1.677576 TCTCGACGTATTGGGCGTATT 59.322 47.619 0.00 0.00 43.04 1.89
2754 10762 5.842327 CGTATTGGGCGTATTCGTTTTTATC 59.158 40.000 0.00 0.00 39.49 1.75
2755 10763 5.821516 ATTGGGCGTATTCGTTTTTATCA 57.178 34.783 0.00 0.00 39.49 2.15
2764 10772 7.060174 GCGTATTCGTTTTTATCAAAGCTTTGA 59.940 33.333 36.74 36.74 43.77 2.69
2780 10788 6.259550 AGCTTTGATTTTCGTGCTTATCTT 57.740 33.333 0.00 0.00 0.00 2.40
2802 10810 8.685838 TCTTAGTTGTTGGTTTAGTTTATGCT 57.314 30.769 0.00 0.00 0.00 3.79
2803 10811 9.127277 TCTTAGTTGTTGGTTTAGTTTATGCTT 57.873 29.630 0.00 0.00 0.00 3.91
2806 10814 4.877282 TGTTGGTTTAGTTTATGCTTGGC 58.123 39.130 0.00 0.00 0.00 4.52
2834 10842 3.017442 GAGCCTTGGAATGGTCTTAACC 58.983 50.000 0.00 0.00 46.66 2.85
2835 10843 2.649816 AGCCTTGGAATGGTCTTAACCT 59.350 45.455 0.00 0.00 46.60 3.50
2877 10885 8.485976 AAGAAGGAAAAGATTCTATTGAGACG 57.514 34.615 0.00 0.00 34.71 4.18
2924 10932 3.075148 GTCTTGCTTTGACCCTTAGGAC 58.925 50.000 0.00 0.00 36.73 3.85
2949 10957 0.743345 AACCCGTTCGCTATCCTTGC 60.743 55.000 0.00 0.00 0.00 4.01
2966 10974 6.932356 TCCTTGCTTCTATTTCTATTGCAG 57.068 37.500 0.00 0.00 0.00 4.41
2979 10987 5.053140 TCTATTGCAGTCTATCTCATCGC 57.947 43.478 0.00 0.00 0.00 4.58
2980 10988 3.740631 ATTGCAGTCTATCTCATCGCA 57.259 42.857 0.00 0.00 0.00 5.10
2993 11001 5.009854 TCTCATCGCATCACATTCTGTTA 57.990 39.130 0.00 0.00 0.00 2.41
2995 11003 5.464389 TCTCATCGCATCACATTCTGTTATG 59.536 40.000 0.00 0.00 35.63 1.90
3051 11059 5.231568 CCTAAGTTCAATAGCTTTACGTCCG 59.768 44.000 0.00 0.00 0.00 4.79
3064 11072 1.081376 CGTCCGCTATCCCGATCAC 60.081 63.158 0.00 0.00 0.00 3.06
3109 13969 3.164024 AAAGGCCTTTCCCCCTTTG 57.836 52.632 25.47 0.00 46.67 2.77
3111 13971 1.674931 AAGGCCTTTCCCCCTTTGGT 61.675 55.000 13.78 0.00 38.24 3.67
3134 13994 1.915078 CTGTGGGCGAGGAGGGATTT 61.915 60.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.577426 GCATGTTCAAACCTCCATCAAAATAGA 60.577 37.037 0.00 0.00 0.00 1.98
6 7 6.532657 GCATGTTCAAACCTCCATCAAAATAG 59.467 38.462 0.00 0.00 0.00 1.73
7 8 6.397272 GCATGTTCAAACCTCCATCAAAATA 58.603 36.000 0.00 0.00 0.00 1.40
10 3762 3.006752 GGCATGTTCAAACCTCCATCAAA 59.993 43.478 0.00 0.00 0.00 2.69
37 3789 4.031765 CACTGTCTTATCGTCCATTTCGTG 59.968 45.833 0.00 0.00 0.00 4.35
49 3801 5.416271 TTTGTAGGGGACACTGTCTTATC 57.584 43.478 9.08 0.00 37.96 1.75
62 3814 8.454570 TTTAGTTAGTTCTGTTTTTGTAGGGG 57.545 34.615 0.00 0.00 0.00 4.79
277 5970 8.846943 TTGTATATTGGTATATGCAGTTCCAG 57.153 34.615 0.00 0.00 39.48 3.86
388 6095 1.500474 TCCACATCACCTCCATCCTC 58.500 55.000 0.00 0.00 0.00 3.71
389 6096 2.053244 GATCCACATCACCTCCATCCT 58.947 52.381 0.00 0.00 0.00 3.24
390 6097 2.053244 AGATCCACATCACCTCCATCC 58.947 52.381 0.00 0.00 0.00 3.51
391 6098 3.135348 TCAAGATCCACATCACCTCCATC 59.865 47.826 0.00 0.00 0.00 3.51
392 6099 3.117745 TCAAGATCCACATCACCTCCAT 58.882 45.455 0.00 0.00 0.00 3.41
393 6100 2.550175 TCAAGATCCACATCACCTCCA 58.450 47.619 0.00 0.00 0.00 3.86
394 6101 3.054802 ACTTCAAGATCCACATCACCTCC 60.055 47.826 0.00 0.00 0.00 4.30
395 6102 3.937706 CACTTCAAGATCCACATCACCTC 59.062 47.826 0.00 0.00 0.00 3.85
396 6103 3.584406 TCACTTCAAGATCCACATCACCT 59.416 43.478 0.00 0.00 0.00 4.00
397 6104 3.942829 TCACTTCAAGATCCACATCACC 58.057 45.455 0.00 0.00 0.00 4.02
398 6105 5.947228 TTTCACTTCAAGATCCACATCAC 57.053 39.130 0.00 0.00 0.00 3.06
399 6106 7.884877 AGTATTTTCACTTCAAGATCCACATCA 59.115 33.333 0.00 0.00 0.00 3.07
400 6107 8.273780 AGTATTTTCACTTCAAGATCCACATC 57.726 34.615 0.00 0.00 0.00 3.06
401 6108 8.641498 AAGTATTTTCACTTCAAGATCCACAT 57.359 30.769 0.00 0.00 33.41 3.21
437 6220 8.364142 TGTTTACCAATTTTTATCTCCACCAAG 58.636 33.333 0.00 0.00 0.00 3.61
499 6284 7.088589 TCATTTTATTTAGACAAGCCTCTGC 57.911 36.000 0.00 0.00 37.95 4.26
525 6310 1.289380 GACCTCGCGTTTCAGTCCT 59.711 57.895 5.77 0.00 0.00 3.85
578 6379 4.701651 TGAATTGATCTGGCATTCGACTTT 59.298 37.500 0.00 0.00 0.00 2.66
752 8087 1.278127 GGTTTGATTCCGGACCTCTGA 59.722 52.381 1.83 0.00 0.00 3.27
753 8088 1.003118 TGGTTTGATTCCGGACCTCTG 59.997 52.381 1.83 0.00 33.33 3.35
758 8093 5.576447 ATTATTGTGGTTTGATTCCGGAC 57.424 39.130 1.83 0.00 0.00 4.79
936 8298 2.797792 GCTATGAGAGGTGTGAGAAGCG 60.798 54.545 0.00 0.00 0.00 4.68
1212 8598 2.303163 TACTTACATTGACGCCGCAT 57.697 45.000 0.00 0.00 0.00 4.73
1284 9221 1.157257 ATGAATGGCGCGCACGAATA 61.157 50.000 34.42 14.44 43.93 1.75
1287 9224 3.094661 GAATGAATGGCGCGCACGA 62.095 57.895 34.42 16.66 43.93 4.35
1329 9266 9.869667 ACAGATTAGTTAGTCCATCTACTATGT 57.130 33.333 0.00 0.00 32.16 2.29
1333 9270 9.256228 TCAAACAGATTAGTTAGTCCATCTACT 57.744 33.333 0.00 0.00 0.00 2.57
1334 9271 9.303537 GTCAAACAGATTAGTTAGTCCATCTAC 57.696 37.037 0.00 0.00 0.00 2.59
1340 9277 9.088512 CACATAGTCAAACAGATTAGTTAGTCC 57.911 37.037 0.00 0.00 0.00 3.85
1358 9295 0.870307 CCCTACGCACGCACATAGTC 60.870 60.000 0.00 0.00 0.00 2.59
1359 9296 1.141019 CCCTACGCACGCACATAGT 59.859 57.895 0.00 0.00 0.00 2.12
1360 9297 2.237751 GCCCTACGCACGCACATAG 61.238 63.158 0.00 0.00 37.47 2.23
1362 9299 4.082523 AGCCCTACGCACGCACAT 62.083 61.111 0.00 0.00 41.38 3.21
1417 9381 1.449726 GGTTCGGGTTTGCCGTCTTT 61.450 55.000 0.00 0.00 34.97 2.52
1429 9393 1.738099 CTTCACGCTCAGGTTCGGG 60.738 63.158 0.00 0.00 0.00 5.14
1498 9462 2.027751 GAGCAGGATACGACGCCC 59.972 66.667 0.00 0.00 46.39 6.13
1745 9709 0.942962 CGGCTCTTCTTGATCATGCC 59.057 55.000 0.00 3.53 35.94 4.40
2136 10100 7.171848 GTCTCCTCAGAAAATGATGATGATCTG 59.828 40.741 0.00 2.31 37.28 2.90
2257 10240 2.375766 CGTGCGGTCAGAACAGAGC 61.376 63.158 0.00 0.00 0.00 4.09
2406 10397 3.527533 TGTCGTTGAAGCAACTGTAGTT 58.472 40.909 8.46 0.00 41.62 2.24
2407 10398 3.173668 TGTCGTTGAAGCAACTGTAGT 57.826 42.857 8.46 0.00 41.62 2.73
2409 10400 7.547722 ACAATATATGTCGTTGAAGCAACTGTA 59.452 33.333 8.46 0.00 37.96 2.74
2410 10401 6.371548 ACAATATATGTCGTTGAAGCAACTGT 59.628 34.615 8.46 0.82 37.96 3.55
2411 10402 6.775088 ACAATATATGTCGTTGAAGCAACTG 58.225 36.000 8.46 3.15 37.96 3.16
2434 10425 8.133627 TGCGACTAAAATGTACTTCCTCTATAC 58.866 37.037 0.00 0.00 0.00 1.47
2436 10427 7.108841 TGCGACTAAAATGTACTTCCTCTAT 57.891 36.000 0.00 0.00 0.00 1.98
2438 10429 5.401531 TGCGACTAAAATGTACTTCCTCT 57.598 39.130 0.00 0.00 0.00 3.69
2524 10532 9.533253 AATCGAAAATGCCAAAATAGGAATAAG 57.467 29.630 0.00 0.00 0.00 1.73
2562 10570 1.536907 TCCTTCACTAACCGGGGCA 60.537 57.895 6.32 0.00 0.00 5.36
2583 10591 7.206687 CCGATTCATAACTAGAAAGCTTCTCT 58.793 38.462 0.00 7.84 41.14 3.10
2596 10604 4.969484 GGTTCCATACCCGATTCATAACT 58.031 43.478 0.00 0.00 41.43 2.24
2613 10621 4.143301 GCCCCTCCCATGGGTTCC 62.143 72.222 30.28 11.66 45.70 3.62
2645 10653 7.129109 AGCGCAAACATATAATAGCGTATTT 57.871 32.000 11.47 0.00 46.09 1.40
2680 10688 6.533723 AGAAAGACGGTTTCCAAATCAAAAAC 59.466 34.615 8.46 0.00 33.22 2.43
2690 10698 4.098894 AGGGTATAGAAAGACGGTTTCCA 58.901 43.478 8.46 0.00 0.00 3.53
2723 10731 0.378257 TACGCCCAATACGTCGAGAC 59.622 55.000 0.00 0.00 43.88 3.36
2725 10733 2.049228 GAATACGCCCAATACGTCGAG 58.951 52.381 0.00 0.00 43.88 4.04
2734 10742 5.624344 TTGATAAAAACGAATACGCCCAA 57.376 34.783 0.00 0.00 43.96 4.12
2739 10747 8.429739 TCAAAGCTTTGATAAAAACGAATACG 57.570 30.769 32.86 6.36 41.88 3.06
2754 10762 6.583806 AGATAAGCACGAAAATCAAAGCTTTG 59.416 34.615 29.53 29.53 41.87 2.77
2755 10763 6.681777 AGATAAGCACGAAAATCAAAGCTTT 58.318 32.000 5.69 5.69 41.87 3.51
2764 10772 7.040686 ACCAACAACTAAGATAAGCACGAAAAT 60.041 33.333 0.00 0.00 0.00 1.82
2767 10775 5.302360 ACCAACAACTAAGATAAGCACGAA 58.698 37.500 0.00 0.00 0.00 3.85
2780 10788 7.653647 CCAAGCATAAACTAAACCAACAACTA 58.346 34.615 0.00 0.00 0.00 2.24
2806 10814 1.474077 CCATTCCAAGGCTCCTTTTCG 59.526 52.381 0.00 0.00 33.42 3.46
2861 10869 9.838339 AATTCATAACCGTCTCAATAGAATCTT 57.162 29.630 0.00 0.00 32.16 2.40
2871 10879 7.680442 TCAATTCAAATTCATAACCGTCTCA 57.320 32.000 0.00 0.00 0.00 3.27
2904 10912 2.979678 AGTCCTAAGGGTCAAAGCAAGA 59.020 45.455 0.00 0.00 0.00 3.02
2918 10926 3.016736 CGAACGGGTTACCTAGTCCTAA 58.983 50.000 0.00 0.00 33.28 2.69
2924 10932 2.030451 GGATAGCGAACGGGTTACCTAG 60.030 54.545 0.00 0.00 33.28 3.02
2966 10974 5.345472 CAGAATGTGATGCGATGAGATAGAC 59.655 44.000 0.00 0.00 0.00 2.59
2993 11001 2.093306 TTGTCGAAGTGGAATCGCAT 57.907 45.000 0.00 0.00 40.04 4.73
2995 11003 2.412847 CCTTTTGTCGAAGTGGAATCGC 60.413 50.000 0.00 0.00 40.04 4.58
3051 11059 2.737252 GGAAAATCGTGATCGGGATAGC 59.263 50.000 0.00 0.00 37.69 2.97
3064 11072 0.106149 CCCCGAGGGTAGGAAAATCG 59.894 60.000 7.48 0.00 38.25 3.34
3098 13958 0.407918 CAGCCTACCAAAGGGGGAAA 59.592 55.000 0.00 0.00 46.65 3.13
3109 13969 4.162690 CCTCGCCCACAGCCTACC 62.163 72.222 0.00 0.00 38.78 3.18
3111 13971 2.759973 CTCCTCGCCCACAGCCTA 60.760 66.667 0.00 0.00 38.78 3.93


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

AutoCloner maintained by Alex Coulton.