Multiple sequence alignment - TraesCS4D01G056100

Loading Multiple Alignment...

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 TraesCS4D01G056100 chr4D 100.000 3628 0 0 1 3628 31434677 31438304 0.000000e+00 6700.0
1 TraesCS4D01G056100 chr4D 85.610 410 27 15 2497 2905 31443602 31443980 5.640000e-108 401.0
2 TraesCS4D01G056100 chr4D 92.278 259 20 0 2096 2354 31443208 31443466 5.720000e-98 368.0
3 TraesCS4D01G056100 chr4D 85.922 206 20 5 3031 3228 31444163 31444367 1.020000e-50 211.0
4 TraesCS4D01G056100 chr4A 89.935 1848 112 34 425 2230 571212218 571214033 0.000000e+00 2314.0
5 TraesCS4D01G056100 chr4A 95.622 1279 48 3 2357 3628 571214083 571215360 0.000000e+00 2045.0
6 TraesCS4D01G056100 chr4A 87.406 397 29 11 33 419 571211870 571212255 1.550000e-118 436.0
7 TraesCS4D01G056100 chr4A 93.436 259 17 0 2096 2354 571220543 571220801 5.680000e-103 385.0
8 TraesCS4D01G056100 chr4A 84.038 426 33 17 2445 2860 571220875 571221275 9.510000e-101 377.0
9 TraesCS4D01G056100 chr4A 83.333 72 9 1 3526 3597 534047005 534047073 3.020000e-06 63.9
10 TraesCS4D01G056100 chr4B 87.203 1430 97 47 29 1408 44953930 44952537 0.000000e+00 1548.0
11 TraesCS4D01G056100 chr4B 86.502 852 47 22 1441 2251 44952541 44951717 0.000000e+00 874.0
12 TraesCS4D01G056100 chr4B 89.580 547 40 8 2375 2914 44951611 44951075 0.000000e+00 678.0
13 TraesCS4D01G056100 chr5B 84.177 474 55 11 2448 2913 633115098 633114637 3.320000e-120 442.0
14 TraesCS4D01G056100 chr5B 82.952 481 58 12 2445 2913 625233179 625233647 2.610000e-111 412.0
15 TraesCS4D01G056100 chr5B 82.952 481 58 12 2445 2913 628832698 628833166 2.610000e-111 412.0
16 TraesCS4D01G056100 chr5B 89.691 97 4 3 2044 2138 600187121 600187213 6.360000e-23 119.0
17 TraesCS4D01G056100 chr5B 91.111 45 3 1 3522 3566 435945742 435945785 3.910000e-05 60.2
18 TraesCS4D01G056100 chr5D 83.857 477 57 10 2445 2913 501520438 501520902 1.550000e-118 436.0
19 TraesCS4D01G056100 chr5D 95.122 41 0 2 3525 3564 259528205 259528166 3.020000e-06 63.9
20 TraesCS4D01G056100 chrUn 82.952 481 58 12 2445 2913 310639539 310640007 2.610000e-111 412.0
21 TraesCS4D01G056100 chr7D 86.885 61 7 1 3537 3596 576198147 576198087 2.340000e-07 67.6
22 TraesCS4D01G056100 chr6A 95.238 42 0 2 3526 3566 158047896 158047856 8.410000e-07 65.8
23 TraesCS4D01G056100 chr6A 93.023 43 1 2 3525 3566 158047793 158047834 1.090000e-05 62.1
24 TraesCS4D01G056100 chr3A 91.304 46 3 1 3521 3566 36757266 36757222 1.090000e-05 62.1
25 TraesCS4D01G056100 chr2D 91.111 45 3 1 3526 3570 620551040 620551083 3.910000e-05 60.2


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 TraesCS4D01G056100 chr4D 31434677 31438304 3627 False 6700.000000 6700 100.000000 1 3628 1 chr4D.!!$F1 3627
1 TraesCS4D01G056100 chr4D 31443208 31444367 1159 False 326.666667 401 87.936667 2096 3228 3 chr4D.!!$F2 1132
2 TraesCS4D01G056100 chr4A 571211870 571215360 3490 False 1598.333333 2314 90.987667 33 3628 3 chr4A.!!$F2 3595
3 TraesCS4D01G056100 chr4A 571220543 571221275 732 False 381.000000 385 88.737000 2096 2860 2 chr4A.!!$F3 764
4 TraesCS4D01G056100 chr4B 44951075 44953930 2855 True 1033.333333 1548 87.761667 29 2914 3 chr4B.!!$R1 2885

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
581 632 0.039437 CTCTGCAAAAGCCAGCACAG 60.039 55.0 0.0 0.0 36.62 3.66 F
1417 1509 0.319555 GTGCGTCTTGTGCTGGTAGA 60.320 55.0 0.0 0.0 0.00 2.59 F
1664 1756 0.798776 CGCGAGATCCTTTTTGCACT 59.201 50.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2584 0.108424 GCAGCAGATAGGCTATCGGG 60.108 60.0 28.07 23.34 43.68 5.14 R
2615 2819 0.109039 GACGCCTTCACTGAGACTCC 60.109 60.0 0.00 0.00 0.00 3.85 R
3395 3698 0.178938 TGTCCAAACACATGCCCCAT 60.179 50.0 0.00 0.00 0.00 4.00 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
20 21 1.546476 GGTAGATAGAGATGCCCCACG 59.454 57.143 0.00 0.00 0.00 4.94
21 22 2.240279 GTAGATAGAGATGCCCCACGT 58.760 52.381 0.00 0.00 0.00 4.49
22 23 2.677542 AGATAGAGATGCCCCACGTA 57.322 50.000 0.00 0.00 0.00 3.57
23 24 3.176924 AGATAGAGATGCCCCACGTAT 57.823 47.619 0.00 0.00 0.00 3.06
24 25 4.317530 AGATAGAGATGCCCCACGTATA 57.682 45.455 0.00 0.00 0.00 1.47
25 26 4.873010 AGATAGAGATGCCCCACGTATAT 58.127 43.478 0.00 0.00 0.00 0.86
26 27 6.014771 AGATAGAGATGCCCCACGTATATA 57.985 41.667 0.00 0.00 0.00 0.86
27 28 6.432581 AGATAGAGATGCCCCACGTATATAA 58.567 40.000 0.00 0.00 0.00 0.98
38 39 4.024387 CCCACGTATATAACAATGTGCCAC 60.024 45.833 0.00 0.00 32.40 5.01
48 49 1.460273 AATGTGCCACCACGTTTCCC 61.460 55.000 0.00 0.00 46.28 3.97
83 84 4.835615 AGTTTAGATAGAGATGCCCGTCAT 59.164 41.667 0.00 0.00 38.32 3.06
86 87 3.767711 AGATAGAGATGCCCGTCATGTA 58.232 45.455 0.00 0.00 35.05 2.29
116 119 3.666334 TCAAAATTCAAAAACGGATCGCG 59.334 39.130 0.00 0.00 0.00 5.87
148 151 2.399611 GAATCCGGAGCGCAAACG 59.600 61.111 11.34 11.03 44.07 3.60
177 183 5.452078 TCTTGTACCCAAAAAGATTGCAG 57.548 39.130 0.00 0.00 0.00 4.41
178 184 3.658757 TGTACCCAAAAAGATTGCAGC 57.341 42.857 0.00 0.00 0.00 5.25
179 185 2.961741 TGTACCCAAAAAGATTGCAGCA 59.038 40.909 0.00 0.00 0.00 4.41
213 219 1.667830 TCGCCAGAAGCTTCCGTTG 60.668 57.895 22.81 14.28 40.39 4.10
226 232 2.509336 CGTTGGATCCGAGCGCTT 60.509 61.111 13.26 0.00 0.00 4.68
314 333 4.892965 TGCGCTGCCACCCTGTTT 62.893 61.111 9.73 0.00 0.00 2.83
361 380 0.464452 CATCTTGACCCCTACGACCC 59.536 60.000 0.00 0.00 0.00 4.46
369 388 2.677524 CCTACGACCCCGGTCACA 60.678 66.667 14.11 0.02 44.77 3.58
376 395 2.125673 CCCCGGTCACACGATCAC 60.126 66.667 0.00 0.00 35.47 3.06
377 396 2.654289 CCCGGTCACACGATCACA 59.346 61.111 0.00 0.00 35.47 3.58
378 397 1.218047 CCCGGTCACACGATCACAT 59.782 57.895 0.00 0.00 35.47 3.21
379 398 1.083806 CCCGGTCACACGATCACATG 61.084 60.000 0.00 0.00 35.47 3.21
380 399 0.389817 CCGGTCACACGATCACATGT 60.390 55.000 0.00 0.00 35.47 3.21
381 400 0.992072 CGGTCACACGATCACATGTC 59.008 55.000 0.00 0.00 35.47 3.06
382 401 1.359848 GGTCACACGATCACATGTCC 58.640 55.000 0.00 0.00 0.00 4.02
383 402 1.337728 GGTCACACGATCACATGTCCA 60.338 52.381 0.00 0.00 0.00 4.02
384 403 1.726791 GTCACACGATCACATGTCCAC 59.273 52.381 0.00 0.00 0.00 4.02
385 404 1.078709 CACACGATCACATGTCCACC 58.921 55.000 0.00 0.00 0.00 4.61
386 405 0.976641 ACACGATCACATGTCCACCT 59.023 50.000 0.00 0.00 0.00 4.00
387 406 1.338105 ACACGATCACATGTCCACCTG 60.338 52.381 0.00 0.00 0.00 4.00
388 407 0.391661 ACGATCACATGTCCACCTGC 60.392 55.000 0.00 0.00 0.00 4.85
389 408 0.107993 CGATCACATGTCCACCTGCT 60.108 55.000 0.00 0.00 0.00 4.24
390 409 1.136891 CGATCACATGTCCACCTGCTA 59.863 52.381 0.00 0.00 0.00 3.49
391 410 2.555199 GATCACATGTCCACCTGCTAC 58.445 52.381 0.00 0.00 0.00 3.58
392 411 1.644509 TCACATGTCCACCTGCTACT 58.355 50.000 0.00 0.00 0.00 2.57
393 412 2.815158 TCACATGTCCACCTGCTACTA 58.185 47.619 0.00 0.00 0.00 1.82
394 413 2.496070 TCACATGTCCACCTGCTACTAC 59.504 50.000 0.00 0.00 0.00 2.73
395 414 2.497675 CACATGTCCACCTGCTACTACT 59.502 50.000 0.00 0.00 0.00 2.57
396 415 3.055819 CACATGTCCACCTGCTACTACTT 60.056 47.826 0.00 0.00 0.00 2.24
397 416 4.159693 CACATGTCCACCTGCTACTACTTA 59.840 45.833 0.00 0.00 0.00 2.24
398 417 4.159879 ACATGTCCACCTGCTACTACTTAC 59.840 45.833 0.00 0.00 0.00 2.34
399 418 4.043608 TGTCCACCTGCTACTACTTACT 57.956 45.455 0.00 0.00 0.00 2.24
400 419 4.015084 TGTCCACCTGCTACTACTTACTC 58.985 47.826 0.00 0.00 0.00 2.59
401 420 3.380954 GTCCACCTGCTACTACTTACTCC 59.619 52.174 0.00 0.00 0.00 3.85
402 421 2.358267 CCACCTGCTACTACTTACTCCG 59.642 54.545 0.00 0.00 0.00 4.63
403 422 2.022934 ACCTGCTACTACTTACTCCGC 58.977 52.381 0.00 0.00 0.00 5.54
404 423 2.299521 CCTGCTACTACTTACTCCGCT 58.700 52.381 0.00 0.00 0.00 5.52
405 424 2.033550 CCTGCTACTACTTACTCCGCTG 59.966 54.545 0.00 0.00 0.00 5.18
406 425 2.022195 TGCTACTACTTACTCCGCTGG 58.978 52.381 0.00 0.00 0.00 4.85
407 426 1.337387 GCTACTACTTACTCCGCTGGG 59.663 57.143 0.00 0.00 0.00 4.45
408 427 1.337387 CTACTACTTACTCCGCTGGGC 59.663 57.143 0.00 0.00 0.00 5.36
409 428 0.324460 ACTACTTACTCCGCTGGGCT 60.324 55.000 0.00 0.00 0.00 5.19
410 429 0.386113 CTACTTACTCCGCTGGGCTC 59.614 60.000 0.00 0.00 0.00 4.70
411 430 1.381928 TACTTACTCCGCTGGGCTCG 61.382 60.000 0.00 0.00 0.00 5.03
412 431 4.143333 TTACTCCGCTGGGCTCGC 62.143 66.667 0.00 0.00 0.00 5.03
422 441 4.115199 GGGCTCGCCATGTCCCTT 62.115 66.667 10.51 0.00 37.98 3.95
425 444 2.989639 CTCGCCATGTCCCTTCCA 59.010 61.111 0.00 0.00 0.00 3.53
470 521 2.105128 CCGCCTGTCATCGTCTCC 59.895 66.667 0.00 0.00 0.00 3.71
497 548 4.367023 TTCCCTCGCGTGAACCCG 62.367 66.667 10.21 0.00 0.00 5.28
581 632 0.039437 CTCTGCAAAAGCCAGCACAG 60.039 55.000 0.00 0.00 36.62 3.66
614 665 3.311110 GCCCACGGGTCAGTGAGA 61.311 66.667 3.54 0.00 44.43 3.27
644 695 0.323451 ATTCCCTCGCCCAAGGAAAC 60.323 55.000 0.00 0.00 42.71 2.78
803 863 4.056125 CACGTCAGCGAGAGGCCA 62.056 66.667 5.01 0.00 45.17 5.36
946 1011 2.168313 CCAGAAGCTTTCTCCTCTCTCC 59.832 54.545 0.00 0.00 38.11 3.71
947 1012 3.099141 CAGAAGCTTTCTCCTCTCTCCT 58.901 50.000 0.00 0.00 38.11 3.69
950 1015 3.018423 AGCTTTCTCCTCTCTCCTCTC 57.982 52.381 0.00 0.00 0.00 3.20
952 1017 2.297701 CTTTCTCCTCTCTCCTCTCGG 58.702 57.143 0.00 0.00 0.00 4.63
953 1018 0.548989 TTCTCCTCTCTCCTCTCGGG 59.451 60.000 0.00 0.00 0.00 5.14
955 1020 1.619975 TCCTCTCTCCTCTCGGGGT 60.620 63.158 0.00 0.00 35.33 4.95
956 1021 1.215679 TCCTCTCTCCTCTCGGGGTT 61.216 60.000 0.00 0.00 35.33 4.11
958 1023 1.107945 CTCTCTCCTCTCGGGGTTTC 58.892 60.000 0.00 0.00 35.33 2.78
960 1025 0.680280 CTCTCCTCTCGGGGTTTCGA 60.680 60.000 0.00 0.00 37.60 3.71
962 1027 0.386113 CTCCTCTCGGGGTTTCGATC 59.614 60.000 0.00 0.00 38.55 3.69
963 1028 1.041447 TCCTCTCGGGGTTTCGATCC 61.041 60.000 0.00 0.00 38.55 3.36
1337 1429 5.102953 TGCCTTGTTCTACTTCTATGCAT 57.897 39.130 3.79 3.79 0.00 3.96
1340 1432 6.049149 GCCTTGTTCTACTTCTATGCATGTA 58.951 40.000 10.16 1.78 0.00 2.29
1343 1435 7.712639 CCTTGTTCTACTTCTATGCATGTATGT 59.287 37.037 10.16 8.00 0.00 2.29
1406 1498 4.692129 CGCTAGATCGTGCGTCTT 57.308 55.556 21.35 0.00 46.09 3.01
1411 1503 0.526211 TAGATCGTGCGTCTTGTGCT 59.474 50.000 0.00 0.00 0.00 4.40
1417 1509 0.319555 GTGCGTCTTGTGCTGGTAGA 60.320 55.000 0.00 0.00 0.00 2.59
1426 1518 2.412870 TGTGCTGGTAGAAACACGATG 58.587 47.619 0.00 0.00 35.79 3.84
1427 1519 2.036604 TGTGCTGGTAGAAACACGATGA 59.963 45.455 0.00 0.00 35.79 2.92
1429 1521 2.271800 GCTGGTAGAAACACGATGAGG 58.728 52.381 0.00 0.00 0.00 3.86
1612 1704 0.875728 TGGCAACCACGTTAAATCGG 59.124 50.000 0.00 0.00 34.94 4.18
1624 1716 3.554731 CGTTAAATCGGAAGGGAGTTAGC 59.445 47.826 0.00 0.00 29.47 3.09
1644 1736 2.154007 GCGTAGATGTAGCAGCGATTTC 59.846 50.000 0.00 0.00 0.00 2.17
1664 1756 0.798776 CGCGAGATCCTTTTTGCACT 59.201 50.000 0.00 0.00 0.00 4.40
1700 1792 4.024218 CGGAGAAGCATCTGGATGATTTTC 60.024 45.833 17.80 17.80 46.10 2.29
1707 1799 9.499479 GAAGCATCTGGATGATTTTCTTAGATA 57.501 33.333 13.98 0.00 46.10 1.98
1708 1800 9.857656 AAGCATCTGGATGATTTTCTTAGATAA 57.142 29.630 13.96 0.00 44.03 1.75
1727 1820 1.605058 ATAGGTGTGCTTCCGCTCGT 61.605 55.000 0.00 0.00 36.97 4.18
1914 2017 2.303600 AGGTGGCGATTAACCTGTACAA 59.696 45.455 0.00 0.00 45.26 2.41
2047 2192 6.001460 TCCGTCCTGTGTTCAGAAATTATTT 58.999 36.000 0.00 0.00 43.76 1.40
2148 2296 4.746611 CACATTTCGTGCTCTGATGCTATA 59.253 41.667 0.00 0.00 39.19 1.31
2156 2304 5.117745 CGTGCTCTGATGCTATATGTTGTAC 59.882 44.000 0.00 0.00 0.00 2.90
2308 2458 4.647825 TGTCACAACACCCCACAC 57.352 55.556 0.00 0.00 0.00 3.82
2321 2471 2.086869 CCCCACACATCTAGTTTGCTG 58.913 52.381 0.00 0.00 0.00 4.41
2354 2504 6.653020 ACTGATGCCATCTATTGTAGTTTCA 58.347 36.000 6.21 0.00 0.00 2.69
2355 2505 6.765036 ACTGATGCCATCTATTGTAGTTTCAG 59.235 38.462 6.21 0.00 0.00 3.02
2462 2666 5.371526 TGGAATCTGAATTCTGATAGCCAC 58.628 41.667 27.62 17.83 40.99 5.01
2464 2668 5.469421 GGAATCTGAATTCTGATAGCCACTG 59.531 44.000 25.76 0.45 40.99 3.66
2482 2686 4.158579 CCACTGTGCTACTGTTCTCTGATA 59.841 45.833 1.29 0.00 0.00 2.15
2495 2699 5.221362 TGTTCTCTGATACGTCTGGTTGAAA 60.221 40.000 0.00 0.00 0.00 2.69
2501 2705 5.547465 TGATACGTCTGGTTGAAACTGATT 58.453 37.500 0.00 0.00 0.00 2.57
2645 2851 2.493907 GAAGGCGTCCTGAGCTCGTT 62.494 60.000 9.64 0.00 32.13 3.85
2798 3007 3.369157 GCATTGTAAGACCCGTTCCTAGT 60.369 47.826 0.00 0.00 0.00 2.57
2994 3268 2.027745 TGAGTGTTCTGAATGGAGCCTC 60.028 50.000 0.00 0.00 0.00 4.70
3273 3576 8.561212 AGAAACACAAACGTACAATAGCAAATA 58.439 29.630 0.00 0.00 0.00 1.40
3327 3630 8.311109 AGTCTTTTTCAACATGGTTAACAGTTT 58.689 29.630 8.10 0.00 0.00 2.66
3348 3651 4.499037 TGTATTCTATGATGGTCCGTCG 57.501 45.455 6.60 0.00 0.00 5.12
3360 3663 3.323243 TGGTCCGTCGAGAAAAAGATTC 58.677 45.455 0.00 0.00 0.00 2.52
3369 3672 7.043590 CCGTCGAGAAAAAGATTCGTAATGTAT 60.044 37.037 0.00 0.00 35.90 2.29
3395 3698 2.485795 AAAAAGGAGCCGCAACGCA 61.486 52.632 0.00 0.00 0.00 5.24
3414 3717 0.178938 ATGGGGCATGTGTTTGGACA 60.179 50.000 0.00 0.00 0.00 4.02
3459 3762 4.065088 CAGTATGTAAATGCCCGTATGCT 58.935 43.478 0.00 0.00 0.00 3.79
3484 3787 4.365514 TCAAACACCTAGGCATGAGAAA 57.634 40.909 9.30 0.00 0.00 2.52
3571 3874 2.604462 ACGTTTTGGTAGTTCACGTCAC 59.396 45.455 0.00 0.00 39.86 3.67
3589 3892 4.616604 CGTCACACATTTAGGAACGTAGGA 60.617 45.833 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.546476 CGTGGGGCATCTCTATCTACC 59.454 57.143 0.00 0.00 0.00 3.18
1 2 2.240279 ACGTGGGGCATCTCTATCTAC 58.760 52.381 0.00 0.00 0.00 2.59
2 3 2.677542 ACGTGGGGCATCTCTATCTA 57.322 50.000 0.00 0.00 0.00 1.98
3 4 2.677542 TACGTGGGGCATCTCTATCT 57.322 50.000 0.00 0.00 0.00 1.98
4 5 6.096423 TGTTATATACGTGGGGCATCTCTATC 59.904 42.308 0.00 0.00 0.00 2.08
5 6 5.955959 TGTTATATACGTGGGGCATCTCTAT 59.044 40.000 0.00 0.00 0.00 1.98
6 7 5.326900 TGTTATATACGTGGGGCATCTCTA 58.673 41.667 0.00 0.00 0.00 2.43
7 8 4.157246 TGTTATATACGTGGGGCATCTCT 58.843 43.478 0.00 0.00 0.00 3.10
8 9 4.530710 TGTTATATACGTGGGGCATCTC 57.469 45.455 0.00 0.00 0.00 2.75
9 10 4.967084 TTGTTATATACGTGGGGCATCT 57.033 40.909 0.00 0.00 0.00 2.90
10 11 5.001232 ACATTGTTATATACGTGGGGCATC 58.999 41.667 0.00 0.00 0.00 3.91
11 12 4.759693 CACATTGTTATATACGTGGGGCAT 59.240 41.667 0.00 0.00 0.00 4.40
12 13 4.130857 CACATTGTTATATACGTGGGGCA 58.869 43.478 0.00 0.00 0.00 5.36
13 14 3.058501 GCACATTGTTATATACGTGGGGC 60.059 47.826 0.00 0.00 0.00 5.80
14 15 3.500680 GGCACATTGTTATATACGTGGGG 59.499 47.826 0.00 0.00 0.00 4.96
15 16 4.024387 GTGGCACATTGTTATATACGTGGG 60.024 45.833 13.86 0.00 44.52 4.61
16 17 4.024387 GGTGGCACATTGTTATATACGTGG 60.024 45.833 20.82 0.00 44.52 4.94
17 18 4.572795 TGGTGGCACATTGTTATATACGTG 59.427 41.667 20.82 0.00 44.52 4.49
18 19 4.573201 GTGGTGGCACATTGTTATATACGT 59.427 41.667 20.82 0.00 44.52 3.57
19 20 4.318475 CGTGGTGGCACATTGTTATATACG 60.318 45.833 20.82 9.27 44.52 3.06
20 21 4.573201 ACGTGGTGGCACATTGTTATATAC 59.427 41.667 20.82 0.00 44.52 1.47
21 22 4.771903 ACGTGGTGGCACATTGTTATATA 58.228 39.130 20.82 0.00 44.52 0.86
22 23 3.616219 ACGTGGTGGCACATTGTTATAT 58.384 40.909 20.82 0.00 44.52 0.86
23 24 3.060736 ACGTGGTGGCACATTGTTATA 57.939 42.857 20.82 0.00 44.52 0.98
24 25 1.904287 ACGTGGTGGCACATTGTTAT 58.096 45.000 20.82 0.00 44.52 1.89
25 26 1.681538 AACGTGGTGGCACATTGTTA 58.318 45.000 20.82 0.00 44.52 2.41
26 27 0.820871 AAACGTGGTGGCACATTGTT 59.179 45.000 20.82 16.13 44.52 2.83
27 28 0.383949 GAAACGTGGTGGCACATTGT 59.616 50.000 20.82 10.86 44.52 2.71
48 49 7.162761 TCTCTATCTAAACTATCTCCCTCACG 58.837 42.308 0.00 0.00 0.00 4.35
62 63 4.588951 ACATGACGGGCATCTCTATCTAAA 59.411 41.667 0.00 0.00 34.15 1.85
64 65 3.767711 ACATGACGGGCATCTCTATCTA 58.232 45.455 0.00 0.00 34.15 1.98
83 84 7.358765 CGTTTTTGAATTTTGAATCGGCATACA 60.359 33.333 0.00 0.00 0.00 2.29
86 87 5.107143 CCGTTTTTGAATTTTGAATCGGCAT 60.107 36.000 0.00 0.00 0.00 4.40
116 119 0.365859 GATTCGGCGAACTCAACGTC 59.634 55.000 26.22 12.83 0.00 4.34
148 151 5.003804 TCTTTTTGGGTACAAGATGCTCTC 58.996 41.667 0.00 0.00 37.97 3.20
159 162 3.005791 AGTGCTGCAATCTTTTTGGGTAC 59.994 43.478 2.77 0.00 0.00 3.34
177 183 1.149148 GACTCGGTTTTGAGGAGTGC 58.851 55.000 0.00 0.00 40.88 4.40
178 184 1.419374 CGACTCGGTTTTGAGGAGTG 58.581 55.000 0.00 0.00 40.88 3.51
179 185 0.319641 GCGACTCGGTTTTGAGGAGT 60.320 55.000 0.00 0.00 43.32 3.85
283 300 3.788766 CGCAGCGCAGGGTTGTAC 61.789 66.667 11.47 0.00 0.00 2.90
361 380 0.389817 ACATGTGATCGTGTGACCGG 60.390 55.000 0.00 0.00 41.57 5.28
369 388 0.391661 GCAGGTGGACATGTGATCGT 60.392 55.000 1.15 0.00 0.00 3.73
376 395 3.895232 AAGTAGTAGCAGGTGGACATG 57.105 47.619 0.00 0.00 0.00 3.21
377 396 4.611367 AGTAAGTAGTAGCAGGTGGACAT 58.389 43.478 0.00 0.00 0.00 3.06
378 397 4.015084 GAGTAAGTAGTAGCAGGTGGACA 58.985 47.826 0.00 0.00 0.00 4.02
379 398 3.380954 GGAGTAAGTAGTAGCAGGTGGAC 59.619 52.174 0.00 0.00 0.00 4.02
380 399 3.629087 GGAGTAAGTAGTAGCAGGTGGA 58.371 50.000 0.00 0.00 0.00 4.02
381 400 2.358267 CGGAGTAAGTAGTAGCAGGTGG 59.642 54.545 0.00 0.00 0.00 4.61
382 401 2.223525 GCGGAGTAAGTAGTAGCAGGTG 60.224 54.545 0.00 0.00 0.00 4.00
383 402 2.022934 GCGGAGTAAGTAGTAGCAGGT 58.977 52.381 0.00 0.00 0.00 4.00
384 403 2.033550 CAGCGGAGTAAGTAGTAGCAGG 59.966 54.545 0.00 0.00 0.00 4.85
385 404 2.033550 CCAGCGGAGTAAGTAGTAGCAG 59.966 54.545 0.00 0.00 0.00 4.24
386 405 2.022195 CCAGCGGAGTAAGTAGTAGCA 58.978 52.381 0.00 0.00 0.00 3.49
387 406 1.337387 CCCAGCGGAGTAAGTAGTAGC 59.663 57.143 0.00 0.00 0.00 3.58
388 407 1.337387 GCCCAGCGGAGTAAGTAGTAG 59.663 57.143 0.00 0.00 0.00 2.57
389 408 1.064166 AGCCCAGCGGAGTAAGTAGTA 60.064 52.381 0.00 0.00 0.00 1.82
390 409 0.324460 AGCCCAGCGGAGTAAGTAGT 60.324 55.000 0.00 0.00 0.00 2.73
391 410 0.386113 GAGCCCAGCGGAGTAAGTAG 59.614 60.000 0.00 0.00 0.00 2.57
392 411 1.381928 CGAGCCCAGCGGAGTAAGTA 61.382 60.000 0.00 0.00 0.00 2.24
393 412 2.711922 CGAGCCCAGCGGAGTAAGT 61.712 63.158 0.00 0.00 0.00 2.24
394 413 2.105128 CGAGCCCAGCGGAGTAAG 59.895 66.667 0.00 0.00 0.00 2.34
395 414 4.143333 GCGAGCCCAGCGGAGTAA 62.143 66.667 0.00 0.00 0.00 2.24
405 424 4.115199 AAGGGACATGGCGAGCCC 62.115 66.667 12.05 0.00 41.00 5.19
406 425 2.514824 GAAGGGACATGGCGAGCC 60.515 66.667 7.26 7.26 0.00 4.70
407 426 2.514824 GGAAGGGACATGGCGAGC 60.515 66.667 0.00 0.00 0.00 5.03
408 427 0.533755 GATGGAAGGGACATGGCGAG 60.534 60.000 0.00 0.00 0.00 5.03
409 428 0.982852 AGATGGAAGGGACATGGCGA 60.983 55.000 0.00 0.00 0.00 5.54
410 429 0.533755 GAGATGGAAGGGACATGGCG 60.534 60.000 0.00 0.00 0.00 5.69
411 430 0.179006 GGAGATGGAAGGGACATGGC 60.179 60.000 0.00 0.00 0.00 4.40
412 431 1.133976 GTGGAGATGGAAGGGACATGG 60.134 57.143 0.00 0.00 0.00 3.66
416 435 0.543749 CAGGTGGAGATGGAAGGGAC 59.456 60.000 0.00 0.00 0.00 4.46
422 441 2.245028 AGTAGTAGCAGGTGGAGATGGA 59.755 50.000 0.00 0.00 0.00 3.41
425 444 2.952978 CGAAGTAGTAGCAGGTGGAGAT 59.047 50.000 0.00 0.00 0.00 2.75
466 517 2.058595 GGGAAGGCTGCTACGGAGA 61.059 63.158 0.00 0.00 0.00 3.71
470 521 2.105128 CGAGGGAAGGCTGCTACG 59.895 66.667 0.00 0.00 0.00 3.51
497 548 3.479269 CGAGCGGAGTTTGCGACC 61.479 66.667 0.00 0.00 37.44 4.79
610 661 1.486211 GGAATCTCGGAAGGGTCTCA 58.514 55.000 0.00 0.00 0.00 3.27
614 665 2.917804 GAGGGAATCTCGGAAGGGT 58.082 57.895 0.00 0.00 32.18 4.34
662 713 0.030101 TTTTCCGTTGCTTCTTGCGG 59.970 50.000 0.00 0.00 46.63 5.69
784 844 4.427661 GCCTCTCGCTGACGTGCT 62.428 66.667 0.00 0.00 41.18 4.40
794 854 2.269241 GTTCCCCTTGGCCTCTCG 59.731 66.667 3.32 0.00 0.00 4.04
928 993 3.365472 AGAGGAGAGAGGAGAAAGCTTC 58.635 50.000 0.00 0.00 0.00 3.86
946 1011 0.103208 CTGGATCGAAACCCCGAGAG 59.897 60.000 9.06 0.00 42.21 3.20
947 1012 0.613853 ACTGGATCGAAACCCCGAGA 60.614 55.000 9.06 0.00 42.21 4.04
950 1015 0.104304 CCTACTGGATCGAAACCCCG 59.896 60.000 9.06 1.66 34.57 5.73
952 1017 2.364647 CCTACCTACTGGATCGAAACCC 59.635 54.545 9.06 2.78 37.04 4.11
953 1018 2.223994 GCCTACCTACTGGATCGAAACC 60.224 54.545 5.25 5.25 37.04 3.27
955 1020 1.679680 CGCCTACCTACTGGATCGAAA 59.320 52.381 0.00 0.00 37.04 3.46
956 1021 1.134007 TCGCCTACCTACTGGATCGAA 60.134 52.381 0.00 0.00 37.04 3.71
958 1023 0.875728 CTCGCCTACCTACTGGATCG 59.124 60.000 0.00 0.00 37.04 3.69
960 1025 0.828343 GCCTCGCCTACCTACTGGAT 60.828 60.000 0.00 0.00 37.04 3.41
962 1027 2.846652 CGCCTCGCCTACCTACTGG 61.847 68.421 0.00 0.00 39.83 4.00
963 1028 1.787057 CTCGCCTCGCCTACCTACTG 61.787 65.000 0.00 0.00 0.00 2.74
1337 1429 2.488952 TCGAACAGCAGCAAACATACA 58.511 42.857 0.00 0.00 0.00 2.29
1340 1432 2.430465 AGATCGAACAGCAGCAAACAT 58.570 42.857 0.00 0.00 0.00 2.71
1343 1435 1.536766 CCAAGATCGAACAGCAGCAAA 59.463 47.619 0.00 0.00 0.00 3.68
1406 1498 2.036604 TCATCGTGTTTCTACCAGCACA 59.963 45.455 0.00 0.00 32.62 4.57
1411 1503 4.023980 AGATCCTCATCGTGTTTCTACCA 58.976 43.478 0.00 0.00 33.75 3.25
1417 1509 3.432326 GGGCTAAGATCCTCATCGTGTTT 60.432 47.826 0.00 0.00 33.75 2.83
1427 1519 0.755686 CGCAAGAGGGCTAAGATCCT 59.244 55.000 0.00 0.00 43.02 3.24
1429 1521 0.753262 TCCGCAAGAGGGCTAAGATC 59.247 55.000 0.00 0.00 43.02 2.75
1454 1546 1.571919 GCTAGGAACTACGCATGTGG 58.428 55.000 11.65 0.00 41.75 4.17
1461 1553 5.276067 CGAAATTAAACGGCTAGGAACTACG 60.276 44.000 0.00 0.00 41.75 3.51
1612 1704 4.557097 GCTACATCTACGCTAACTCCCTTC 60.557 50.000 0.00 0.00 0.00 3.46
1624 1716 2.726760 GGAAATCGCTGCTACATCTACG 59.273 50.000 0.00 0.00 0.00 3.51
1644 1736 0.179189 GTGCAAAAAGGATCTCGCGG 60.179 55.000 6.13 0.00 0.00 6.46
1654 1746 3.683822 TGCAGGACAAAAAGTGCAAAAAG 59.316 39.130 0.00 0.00 42.79 2.27
1664 1756 1.946768 CTTCTCCGTGCAGGACAAAAA 59.053 47.619 8.24 0.00 45.98 1.94
1727 1820 1.159285 CGCACAGCCTCAAAATCAGA 58.841 50.000 0.00 0.00 0.00 3.27
1846 1945 7.491372 TGTCCGTAAGCATAACAATCTTAGAAG 59.509 37.037 0.00 0.00 0.00 2.85
1914 2017 5.128919 CAAGAATCAAGAAATCCGGATCCT 58.871 41.667 19.43 15.08 0.00 3.24
1916 2019 4.578105 AGCAAGAATCAAGAAATCCGGATC 59.422 41.667 19.43 7.26 0.00 3.36
2024 2167 5.880054 AATAATTTCTGAACACAGGACGG 57.120 39.130 0.00 0.00 33.04 4.79
2181 2329 2.890945 TGACTGAAGTCTGAACGGATCA 59.109 45.455 11.55 0.00 44.99 2.92
2252 2402 2.502142 AGCTCACATGCCAAGATTCA 57.498 45.000 0.00 0.00 0.00 2.57
2308 2458 6.311445 CAGTAGTAACCACAGCAAACTAGATG 59.689 42.308 0.00 0.00 0.00 2.90
2321 2471 4.408182 AGATGGCATCAGTAGTAACCAC 57.592 45.455 27.93 0.00 0.00 4.16
2385 2584 0.108424 GCAGCAGATAGGCTATCGGG 60.108 60.000 28.07 23.34 43.68 5.14
2462 2666 4.142578 ACGTATCAGAGAACAGTAGCACAG 60.143 45.833 0.00 0.00 0.00 3.66
2464 2668 4.095185 AGACGTATCAGAGAACAGTAGCAC 59.905 45.833 0.00 0.00 0.00 4.40
2482 2686 2.290641 GCAATCAGTTTCAACCAGACGT 59.709 45.455 0.00 0.00 0.00 4.34
2495 2699 0.676782 GCCACGGGTTAGCAATCAGT 60.677 55.000 0.00 0.00 0.00 3.41
2501 2705 3.190738 AAGCAGCCACGGGTTAGCA 62.191 57.895 0.00 0.00 0.00 3.49
2610 2814 1.551099 CCTTCACTGAGACTCCCCTGA 60.551 57.143 0.00 0.00 0.00 3.86
2614 2818 1.216710 CGCCTTCACTGAGACTCCC 59.783 63.158 0.00 0.00 0.00 4.30
2615 2819 0.109039 GACGCCTTCACTGAGACTCC 60.109 60.000 0.00 0.00 0.00 3.85
2645 2851 3.517901 AGGTTGGTTCATGGAAGACGATA 59.482 43.478 0.00 0.00 0.00 2.92
2831 3040 0.820074 TCACCAAAACGGACCGCAAT 60.820 50.000 15.39 0.00 38.63 3.56
2839 3048 3.181491 ACAAACAGATGTCACCAAAACGG 60.181 43.478 0.00 0.00 42.50 4.44
2994 3268 0.523072 CATTGTCAGTCCAAAGCCCG 59.477 55.000 0.00 0.00 0.00 6.13
3231 3532 5.698545 TGTGTTTCTTTGTTCCACCAAAAAG 59.301 36.000 0.00 0.00 34.15 2.27
3273 3576 5.975988 ACCCTACCATAGACATTTCACAT 57.024 39.130 0.00 0.00 0.00 3.21
3289 3592 9.668497 ATGTTGAAAAAGACTATTCTACCCTAC 57.332 33.333 10.67 0.00 32.63 3.18
3322 3625 6.049149 ACGGACCATCATAGAATACAAACTG 58.951 40.000 0.00 0.00 0.00 3.16
3327 3630 4.139038 TCGACGGACCATCATAGAATACA 58.861 43.478 0.00 0.00 0.00 2.29
3348 3651 9.099454 AGGACATACATTACGAATCTTTTTCTC 57.901 33.333 0.00 0.00 0.00 2.87
3360 3663 7.372451 TCCTTTTTGAAGGACATACATTACG 57.628 36.000 3.84 0.00 43.68 3.18
3369 3672 1.604604 CGGCTCCTTTTTGAAGGACA 58.395 50.000 3.84 0.00 43.68 4.02
3395 3698 0.178938 TGTCCAAACACATGCCCCAT 60.179 50.000 0.00 0.00 0.00 4.00
3436 3739 3.188460 GCATACGGGCATTTACATACTGG 59.812 47.826 0.00 0.00 0.00 4.00
3459 3762 2.575735 TCATGCCTAGGTGTTTGATGGA 59.424 45.455 11.31 0.00 0.00 3.41
3498 3801 2.189521 GGGCCGAGTGTGTATGGG 59.810 66.667 0.00 0.00 0.00 4.00
3507 3810 0.689745 TAGCTACCATTGGGCCGAGT 60.690 55.000 7.78 0.00 37.90 4.18
3566 3869 3.611113 CCTACGTTCCTAAATGTGTGACG 59.389 47.826 0.00 0.00 36.11 4.35
3571 3874 6.392354 TGTACTTCCTACGTTCCTAAATGTG 58.608 40.000 0.00 0.00 36.11 3.21
3589 3892 2.884639 GTGAGGCAACACCAATGTACTT 59.115 45.455 0.00 0.00 43.14 2.24


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

AutoCloner maintained by Alex Coulton.