Multiple sequence alignment - TraesCS5D01G400200

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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 TraesCS5D01G400200 chr5D 100.000 4710 0 0 1 4710 465377352 465372643 0.000000e+00 8698.0
1 TraesCS5D01G400200 chr5D 85.417 96 13 1 399 493 486090661 486090756 1.080000e-16 99.0
2 TraesCS5D01G400200 chr5D 93.548 62 4 0 2546 2607 465374722 465374661 5.020000e-15 93.5
3 TraesCS5D01G400200 chr5D 93.548 62 4 0 2631 2692 465374807 465374746 5.020000e-15 93.5
4 TraesCS5D01G400200 chr5D 81.818 88 15 1 407 493 276306759 276306672 6.540000e-09 73.1
5 TraesCS5D01G400200 chr5B 93.372 2595 98 29 695 3244 572603726 572601161 0.000000e+00 3771.0
6 TraesCS5D01G400200 chr5B 89.075 897 59 23 3262 4129 572601175 572600289 0.000000e+00 1077.0
7 TraesCS5D01G400200 chr5B 89.670 455 27 8 268 705 572604246 572603795 3.180000e-156 562.0
8 TraesCS5D01G400200 chr5B 94.444 270 15 0 1 270 572604727 572604458 2.620000e-112 416.0
9 TraesCS5D01G400200 chr5B 89.789 284 17 8 4298 4572 572599067 572598787 2.080000e-93 353.0
10 TraesCS5D01G400200 chr5B 87.329 292 31 4 1 290 64487063 64487350 3.510000e-86 329.0
11 TraesCS5D01G400200 chr5B 90.341 176 10 5 4128 4296 572600263 572600088 1.710000e-54 224.0
12 TraesCS5D01G400200 chr5B 93.548 62 4 0 2631 2692 572601856 572601795 5.020000e-15 93.5
13 TraesCS5D01G400200 chr5B 93.333 60 4 0 2546 2605 572601771 572601712 6.490000e-14 89.8
14 TraesCS5D01G400200 chr5A 95.220 1799 61 11 745 2530 585636592 585634806 0.000000e+00 2822.0
15 TraesCS5D01G400200 chr5A 92.312 1600 79 18 2549 4129 585634520 585632946 0.000000e+00 2233.0
16 TraesCS5D01G400200 chr5A 93.440 564 24 5 4153 4710 585617562 585617006 0.000000e+00 824.0
17 TraesCS5D01G400200 chr5A 90.370 135 4 4 583 710 585636722 585636590 8.110000e-38 169.0
18 TraesCS5D01G400200 chr5A 84.211 95 14 1 400 493 338221466 338221560 1.800000e-14 91.6
19 TraesCS5D01G400200 chr5A 91.525 59 5 0 2634 2692 585634520 585634462 1.090000e-11 82.4
20 TraesCS5D01G400200 chr5A 92.683 41 1 2 2169 2208 86874839 86874800 1.830000e-04 58.4
21 TraesCS5D01G400200 chr5A 94.595 37 1 1 4519 4555 333742931 333742896 6.580000e-04 56.5
22 TraesCS5D01G400200 chr5A 100.000 29 0 0 4575 4603 65549799 65549771 2.000000e-03 54.7
23 TraesCS5D01G400200 chr5A 100.000 28 0 0 3983 4010 682928713 682928686 9.000000e-03 52.8
24 TraesCS5D01G400200 chr6D 87.241 290 31 5 4 290 323823271 323822985 4.550000e-85 326.0
25 TraesCS5D01G400200 chr6D 80.328 183 35 1 4194 4375 457533301 457533483 2.290000e-28 137.0
26 TraesCS5D01G400200 chr6D 78.873 213 27 9 4192 4404 27522111 27522305 1.380000e-25 128.0
27 TraesCS5D01G400200 chr7B 84.390 205 30 2 4192 4395 24404111 24403908 2.870000e-47 200.0
28 TraesCS5D01G400200 chr7B 100.000 28 0 0 4576 4603 602389023 602389050 9.000000e-03 52.8
29 TraesCS5D01G400200 chr7B 100.000 28 0 0 3976 4003 711363447 711363474 9.000000e-03 52.8
30 TraesCS5D01G400200 chr7A 83.824 204 31 2 4192 4394 105628005 105627803 4.810000e-45 193.0
31 TraesCS5D01G400200 chr7A 82.439 205 32 3 4192 4395 81136902 81136701 4.840000e-40 176.0
32 TraesCS5D01G400200 chr7A 84.559 136 20 1 4244 4378 729296153 729296288 2.960000e-27 134.0
33 TraesCS5D01G400200 chr7A 90.909 55 5 0 401 455 554400245 554400299 1.820000e-09 75.0
34 TraesCS5D01G400200 chr6A 80.328 183 33 3 4194 4374 252839259 252839440 8.220000e-28 135.0
35 TraesCS5D01G400200 chrUn 85.057 87 13 0 403 489 127025644 127025730 6.490000e-14 89.8
36 TraesCS5D01G400200 chrUn 84.091 88 11 3 408 493 293280876 293280790 1.090000e-11 82.4
37 TraesCS5D01G400200 chr4B 97.297 37 1 0 4519 4555 660143401 660143365 3.930000e-06 63.9
38 TraesCS5D01G400200 chr4B 94.595 37 1 1 4519 4555 9795642 9795607 6.580000e-04 56.5
39 TraesCS5D01G400200 chr4B 100.000 28 0 0 4575 4602 664776339 664776366 9.000000e-03 52.8
40 TraesCS5D01G400200 chr3B 85.484 62 8 1 3946 4006 814177049 814177110 3.930000e-06 63.9
41 TraesCS5D01G400200 chr3B 96.875 32 0 1 4575 4606 738380593 738380563 9.000000e-03 52.8
42 TraesCS5D01G400200 chr6B 94.872 39 2 0 4564 4602 646750047 646750085 1.420000e-05 62.1
43 TraesCS5D01G400200 chr6B 100.000 28 0 0 4575 4602 6167220 6167247 9.000000e-03 52.8
44 TraesCS5D01G400200 chr3D 91.304 46 2 2 2166 2209 389633117 389633162 1.420000e-05 62.1
45 TraesCS5D01G400200 chr7D 89.130 46 5 0 3986 4031 597124394 597124439 1.830000e-04 58.4
46 TraesCS5D01G400200 chr7D 100.000 28 0 0 3983 4010 568421347 568421374 9.000000e-03 52.8
47 TraesCS5D01G400200 chr3A 92.683 41 1 2 2169 2208 512682145 512682184 1.830000e-04 58.4
48 TraesCS5D01G400200 chr3A 89.362 47 2 2 2166 2209 418753008 418753054 6.580000e-04 56.5
49 TraesCS5D01G400200 chr1B 94.595 37 1 1 4519 4555 571427568 571427533 6.580000e-04 56.5
50 TraesCS5D01G400200 chr1B 90.698 43 2 2 2169 2209 579558658 579558616 6.580000e-04 56.5
51 TraesCS5D01G400200 chr1B 90.476 42 3 1 2169 2209 442949281 442949240 2.000000e-03 54.7
52 TraesCS5D01G400200 chr1A 94.595 37 1 1 4519 4555 587861328 587861363 6.580000e-04 56.5
53 TraesCS5D01G400200 chr1A 100.000 28 0 0 4528 4555 560819129 560819156 9.000000e-03 52.8
54 TraesCS5D01G400200 chr4D 100.000 29 0 0 2181 2209 92198049 92198021 2.000000e-03 54.7
55 TraesCS5D01G400200 chr4D 100.000 29 0 0 4574 4602 266783325 266783297 2.000000e-03 54.7
56 TraesCS5D01G400200 chr2B 100.000 29 0 0 3982 4010 412843826 412843798 2.000000e-03 54.7


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 TraesCS5D01G400200 chr5D 465372643 465377352 4709 True 2961.666667 8698 95.698667 1 4710 3 chr5D.!!$R2 4709
1 TraesCS5D01G400200 chr5B 572598787 572604727 5940 True 823.287500 3771 91.696500 1 4572 8 chr5B.!!$R1 4571
2 TraesCS5D01G400200 chr5A 585632946 585636722 3776 True 1326.600000 2822 92.356750 583 4129 4 chr5A.!!$R6 3546
3 TraesCS5D01G400200 chr5A 585617006 585617562 556 True 824.000000 824 93.440000 4153 4710 1 chr5A.!!$R4 557

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
547 774 0.311790 AGTGCTTCGTGCCACAAATG 59.688 50.000 0.00 0.0 42.00 2.32 F
558 785 1.404047 GCCACAAATGTGCCGCTTATT 60.404 47.619 8.03 0.0 44.34 1.40 F
940 1259 1.660575 GTCACGACACCACACTCCG 60.661 63.158 0.00 0.0 0.00 4.63 F
1549 1903 2.009774 GCCGCTGAATACTGAACACAT 58.990 47.619 0.00 0.0 0.00 3.21 F
2918 3556 3.255642 GTCTCATGTTTTGGCCTGCTTTA 59.744 43.478 3.32 0.0 0.00 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 1931 1.012086 CCACAATCACTCCATCAGCG 58.988 55.000 0.00 0.0 0.00 5.18 R
1939 2296 2.625314 CGATCATACCAGAGAGAAGGCA 59.375 50.000 0.00 0.0 0.00 4.75 R
2853 3491 1.805943 TGTGTCTGAATTGATGCGTGG 59.194 47.619 0.00 0.0 0.00 4.94 R
3238 3887 0.465705 ACACAGATAGGTGGCCATCG 59.534 55.000 9.72 0.0 43.08 3.84 R
4669 6407 1.135527 CATGCGCAAATCCACCATCTT 59.864 47.619 17.11 0.0 0.00 2.40 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
31 32 8.579863 CAATTTTTCTTCTAGGATCAAACCACT 58.420 33.333 0.00 0.00 0.00 4.00
110 111 3.084039 CTGCTGCCAGAAAATTACCTCA 58.916 45.455 0.00 0.00 41.77 3.86
118 119 6.664816 TGCCAGAAAATTACCTCAATCATCTT 59.335 34.615 0.00 0.00 0.00 2.40
187 188 3.499048 GCATCAGCATTGACTTCAACAG 58.501 45.455 0.00 0.00 41.58 3.16
200 201 1.004560 CAACAGCTCCCTCGCTTGA 60.005 57.895 0.00 0.00 38.41 3.02
209 210 0.321671 CCCTCGCTTGACTTCTTCCA 59.678 55.000 0.00 0.00 0.00 3.53
229 230 3.809279 CCAGCTATGATTGATGTTGCGTA 59.191 43.478 0.00 0.00 0.00 4.42
236 237 3.809279 TGATTGATGTTGCGTATAGGCTG 59.191 43.478 17.60 0.00 0.00 4.85
257 258 5.183140 GCTGGTTTTTGGAGTATAAGCTCAA 59.817 40.000 0.00 0.00 37.24 3.02
261 262 7.084486 GGTTTTTGGAGTATAAGCTCAAACAG 58.916 38.462 0.00 0.00 37.24 3.16
331 546 7.993183 TCTTTCCTCATAACCTAGCCTTTAATG 59.007 37.037 0.00 0.00 0.00 1.90
337 552 2.723273 ACCTAGCCTTTAATGTGGTGC 58.277 47.619 0.00 0.00 0.00 5.01
341 556 3.942130 AGCCTTTAATGTGGTGCTTTC 57.058 42.857 0.00 0.00 0.00 2.62
392 607 1.806542 GCTCAAGTGATCTTTTGCGGA 59.193 47.619 0.00 0.00 0.00 5.54
393 608 2.421424 GCTCAAGTGATCTTTTGCGGAT 59.579 45.455 0.00 0.00 0.00 4.18
398 613 6.611381 TCAAGTGATCTTTTGCGGATAAAAG 58.389 36.000 10.03 10.03 44.88 2.27
399 614 5.567138 AGTGATCTTTTGCGGATAAAAGG 57.433 39.130 14.02 0.00 44.10 3.11
400 615 5.253330 AGTGATCTTTTGCGGATAAAAGGA 58.747 37.500 14.02 0.00 44.10 3.36
401 616 5.123979 AGTGATCTTTTGCGGATAAAAGGAC 59.876 40.000 14.02 10.18 44.10 3.85
402 617 4.398044 TGATCTTTTGCGGATAAAAGGACC 59.602 41.667 14.02 0.00 44.10 4.46
403 618 3.086282 TCTTTTGCGGATAAAAGGACCC 58.914 45.455 14.02 0.00 44.10 4.46
404 619 2.891191 TTTGCGGATAAAAGGACCCT 57.109 45.000 0.00 0.00 0.00 4.34
405 620 2.413310 TTGCGGATAAAAGGACCCTC 57.587 50.000 0.00 0.00 0.00 4.30
410 628 4.065789 GCGGATAAAAGGACCCTCATAAG 58.934 47.826 0.00 0.00 0.00 1.73
416 634 0.912486 AGGACCCTCATAAGTGCCAC 59.088 55.000 0.00 0.00 0.00 5.01
445 663 2.854424 GCACAAACACATGACAACTCCG 60.854 50.000 0.00 0.00 0.00 4.63
472 690 3.524763 TTTTACGTCAAGTTTAGCGGC 57.475 42.857 0.00 0.00 0.00 6.53
489 707 2.124901 CGCGGGGATGGCAACTTA 60.125 61.111 0.00 0.00 37.61 2.24
490 708 2.180204 CGCGGGGATGGCAACTTAG 61.180 63.158 0.00 0.00 37.61 2.18
491 709 1.077716 GCGGGGATGGCAACTTAGT 60.078 57.895 0.00 0.00 37.61 2.24
494 712 1.743394 CGGGGATGGCAACTTAGTTTC 59.257 52.381 0.00 0.00 37.61 2.78
499 717 5.470368 GGGATGGCAACTTAGTTTCTTTTC 58.530 41.667 0.00 0.00 37.61 2.29
500 718 5.470368 GGATGGCAACTTAGTTTCTTTTCC 58.530 41.667 0.00 0.00 37.61 3.13
501 719 4.561735 TGGCAACTTAGTTTCTTTTCCG 57.438 40.909 0.00 0.00 37.61 4.30
547 774 0.311790 AGTGCTTCGTGCCACAAATG 59.688 50.000 0.00 0.00 42.00 2.32
558 785 1.404047 GCCACAAATGTGCCGCTTATT 60.404 47.619 8.03 0.00 44.34 1.40
566 793 2.028130 TGTGCCGCTTATTATTTGGGG 58.972 47.619 0.00 0.00 36.95 4.96
940 1259 1.660575 GTCACGACACCACACTCCG 60.661 63.158 0.00 0.00 0.00 4.63
1256 1610 3.435186 GAAGCCCAGCGCCAAGAC 61.435 66.667 2.29 0.00 38.78 3.01
1549 1903 2.009774 GCCGCTGAATACTGAACACAT 58.990 47.619 0.00 0.00 0.00 3.21
1577 1931 6.317391 CCTTTTCTCCTCCTGTGTTATCAATC 59.683 42.308 0.00 0.00 0.00 2.67
1804 2158 5.106396 CGATTTCTGATGCATTCCTAATCCC 60.106 44.000 0.00 0.00 0.00 3.85
1997 2354 9.736023 AGTTCTTTTGTTAAGATTGAATGTGTC 57.264 29.630 0.00 0.00 0.00 3.67
2008 2365 6.653020 AGATTGAATGTGTCTATGCCAGTTA 58.347 36.000 0.00 0.00 0.00 2.24
2010 2367 7.776969 AGATTGAATGTGTCTATGCCAGTTATT 59.223 33.333 0.00 0.00 0.00 1.40
2011 2368 7.701539 TTGAATGTGTCTATGCCAGTTATTT 57.298 32.000 0.00 0.00 0.00 1.40
2256 2624 4.349342 AGGAGTAATAATCCAGAGGCCAAG 59.651 45.833 5.01 0.00 39.47 3.61
2354 2722 7.819415 GCAAATGGCCTTCTAAAAGATTTTACT 59.181 33.333 3.32 0.00 34.14 2.24
2499 2867 7.479980 TGACCGAATTATGCTTTGATAAAAGG 58.520 34.615 4.66 0.00 0.00 3.11
2770 3408 4.495184 CGCTTCTAGAACGTTTTGGTTTGT 60.495 41.667 0.46 0.00 0.00 2.83
2786 3424 4.035792 TGGTTTGTGTGTTTCTTATGTCCG 59.964 41.667 0.00 0.00 0.00 4.79
2853 3491 7.681939 TGATGACTTAATCAAAAGTACACCC 57.318 36.000 0.00 0.00 41.93 4.61
2918 3556 3.255642 GTCTCATGTTTTGGCCTGCTTTA 59.744 43.478 3.32 0.00 0.00 1.85
2919 3557 3.894427 TCTCATGTTTTGGCCTGCTTTAA 59.106 39.130 3.32 0.00 0.00 1.52
2978 3622 5.754890 ACTTCCAATTGTTCTGTTTTGATGC 59.245 36.000 4.43 0.00 0.00 3.91
2980 3624 5.916318 TCCAATTGTTCTGTTTTGATGCTT 58.084 33.333 4.43 0.00 0.00 3.91
2984 3628 7.115378 CCAATTGTTCTGTTTTGATGCTTAGTC 59.885 37.037 4.43 0.00 0.00 2.59
3238 3887 3.213206 TGGATCCTACATTGCATGACC 57.787 47.619 14.23 0.00 0.00 4.02
3276 3925 2.995939 TGTGACTTGAATGACTGATCGC 59.004 45.455 0.00 0.00 0.00 4.58
3277 3926 2.028523 GTGACTTGAATGACTGATCGCG 59.971 50.000 0.00 0.00 0.00 5.87
3300 3949 3.689161 TCCATTTTTCCTATGTGCTGTCG 59.311 43.478 0.00 0.00 0.00 4.35
3354 4003 0.322322 CACCAAACTACGGTAGCCCA 59.678 55.000 14.91 0.00 34.02 5.36
3357 4006 1.485066 CCAAACTACGGTAGCCCAGAT 59.515 52.381 14.91 0.00 0.00 2.90
3442 4091 2.816958 CGCCTACTGCCAGCACAG 60.817 66.667 0.00 0.37 43.59 3.66
3459 4108 3.121778 GCACAGTTTTCATCCATTTTCGC 59.878 43.478 0.00 0.00 0.00 4.70
3588 4239 2.612115 CCCCCACCTCTCCAGCTT 60.612 66.667 0.00 0.00 0.00 3.74
3816 4474 3.159213 TGGTTCTTGATGGTTGATGCT 57.841 42.857 0.00 0.00 0.00 3.79
3888 4547 1.296649 GCCGTAATGTTTCGCTCGC 60.297 57.895 0.00 0.00 0.00 5.03
3906 4565 2.092055 TCGCGATTTCTGAATTGTGACG 59.908 45.455 3.71 0.00 39.89 4.35
3915 4574 2.819608 CTGAATTGTGACGGGGATGTTT 59.180 45.455 0.00 0.00 0.00 2.83
4000 4664 2.277084 CAAAATACTCCCTCCGTTCCG 58.723 52.381 0.00 0.00 0.00 4.30
4032 4696 4.516321 GGTGCAAAAATTTCCATGAAAGCT 59.484 37.500 0.00 0.00 34.92 3.74
4049 4713 4.886247 AAGCTAAACGCACAAACAACTA 57.114 36.364 0.00 0.00 42.61 2.24
4111 4787 3.686241 TCTGATTCGAATTTGAGGTGCTG 59.314 43.478 12.81 1.37 0.00 4.41
4148 4851 0.038310 CTGGGACCTTGGTCCTTTCC 59.962 60.000 30.81 18.48 42.91 3.13
4296 5008 9.736023 GGATCTAATGATACAAATTTGGTGTTC 57.264 33.333 21.74 12.45 33.72 3.18
4497 6229 8.780846 TGAACTTAGACAGAAAAAGTAACACA 57.219 30.769 0.00 0.00 33.24 3.72
4603 6341 7.612677 TCCCTCTGTAAAGAAATACAAGAGAC 58.387 38.462 0.00 0.00 35.48 3.36
4604 6342 6.819146 CCCTCTGTAAAGAAATACAAGAGACC 59.181 42.308 0.00 0.00 35.48 3.85
4614 6352 0.608130 ACAAGAGACCTGCGCACATA 59.392 50.000 5.66 0.00 0.00 2.29
4623 6361 2.095263 ACCTGCGCACATATGTTTCAAC 60.095 45.455 5.66 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.437213 TCCGAAGTGGTTTGATCCTAGA 58.563 45.455 0.00 0.00 39.52 2.43
152 153 2.793585 GCTGATGCGTCATTTCATGTGG 60.794 50.000 9.53 0.00 32.98 4.17
171 172 2.157738 GGAGCTGTTGAAGTCAATGCT 58.842 47.619 18.14 18.14 44.63 3.79
187 188 0.036858 AAGAAGTCAAGCGAGGGAGC 60.037 55.000 0.00 0.00 37.41 4.70
200 201 5.999044 ACATCAATCATAGCTGGAAGAAGT 58.001 37.500 0.00 0.00 34.07 3.01
209 210 5.871524 CCTATACGCAACATCAATCATAGCT 59.128 40.000 0.00 0.00 0.00 3.32
229 230 5.828328 GCTTATACTCCAAAAACCAGCCTAT 59.172 40.000 0.00 0.00 0.00 2.57
236 237 6.977213 TGTTTGAGCTTATACTCCAAAAACC 58.023 36.000 1.09 0.00 32.90 3.27
257 258 6.534634 ACAGGTTCTAGCTACAAATTCTGTT 58.465 36.000 12.38 4.17 39.64 3.16
261 262 9.465985 GTCTATACAGGTTCTAGCTACAAATTC 57.534 37.037 0.00 0.00 0.00 2.17
319 534 4.142381 GGAAAGCACCACATTAAAGGCTAG 60.142 45.833 0.00 0.00 0.00 3.42
377 592 5.123979 GTCCTTTTATCCGCAAAAGATCACT 59.876 40.000 13.51 0.00 44.68 3.41
378 593 5.332707 GTCCTTTTATCCGCAAAAGATCAC 58.667 41.667 13.51 6.47 44.68 3.06
392 607 4.229582 TGGCACTTATGAGGGTCCTTTTAT 59.770 41.667 0.00 0.00 26.41 1.40
393 608 3.589735 TGGCACTTATGAGGGTCCTTTTA 59.410 43.478 0.00 0.00 26.41 1.52
398 613 0.462047 CGTGGCACTTATGAGGGTCC 60.462 60.000 16.72 0.00 26.41 4.46
399 614 1.090052 GCGTGGCACTTATGAGGGTC 61.090 60.000 16.72 0.00 0.00 4.46
400 615 1.078426 GCGTGGCACTTATGAGGGT 60.078 57.895 16.72 0.00 0.00 4.34
401 616 0.392998 AAGCGTGGCACTTATGAGGG 60.393 55.000 16.72 0.00 0.00 4.30
402 617 0.729116 CAAGCGTGGCACTTATGAGG 59.271 55.000 16.72 0.00 0.00 3.86
403 618 1.129251 CACAAGCGTGGCACTTATGAG 59.871 52.381 16.72 6.30 39.64 2.90
404 619 1.155889 CACAAGCGTGGCACTTATGA 58.844 50.000 16.72 0.00 39.64 2.15
405 620 3.681705 CACAAGCGTGGCACTTATG 57.318 52.632 16.72 13.10 39.64 1.90
424 642 2.731217 GGAGTTGTCATGTGTTTGTGC 58.269 47.619 0.00 0.00 0.00 4.57
457 675 2.095843 GCGCCGCTAAACTTGACG 59.904 61.111 0.00 0.00 0.00 4.35
472 690 2.124901 TAAGTTGCCATCCCCGCG 60.125 61.111 0.00 0.00 0.00 6.46
547 774 2.303175 TCCCCAAATAATAAGCGGCAC 58.697 47.619 1.45 0.00 0.00 5.01
558 785 3.513515 GACAAGTGGCATTTCCCCAAATA 59.486 43.478 0.00 0.00 33.39 1.40
719 1034 3.775654 GCAGGGAGGGTCGGTCTG 61.776 72.222 0.00 0.00 0.00 3.51
872 1187 0.106015 GTGGAGGGATTGGAATGGGG 60.106 60.000 0.00 0.00 0.00 4.96
874 1189 1.103398 GCGTGGAGGGATTGGAATGG 61.103 60.000 0.00 0.00 0.00 3.16
876 1191 1.153168 CGCGTGGAGGGATTGGAAT 60.153 57.895 0.00 0.00 34.27 3.01
877 1192 1.832719 TTCGCGTGGAGGGATTGGAA 61.833 55.000 5.77 0.00 41.64 3.53
878 1193 1.832719 TTTCGCGTGGAGGGATTGGA 61.833 55.000 5.77 0.00 41.64 3.53
940 1259 2.111582 GCTTGGCTGTGGCTAGAGC 61.112 63.158 11.04 11.04 42.17 4.09
974 1300 4.577246 CCTCCTGCTAGCCGCGTC 62.577 72.222 13.29 0.00 43.27 5.19
1256 1610 4.862823 GAGGGACGGGGAGGAGGG 62.863 77.778 0.00 0.00 0.00 4.30
1549 1903 6.672218 TGATAACACAGGAGGAGAAAAGGATA 59.328 38.462 0.00 0.00 0.00 2.59
1577 1931 1.012086 CCACAATCACTCCATCAGCG 58.988 55.000 0.00 0.00 0.00 5.18
1804 2158 5.413833 AGATTGGTACTGAAAGATTGCACTG 59.586 40.000 0.00 0.00 37.43 3.66
1939 2296 2.625314 CGATCATACCAGAGAGAAGGCA 59.375 50.000 0.00 0.00 0.00 4.75
2011 2368 7.499321 AAAATTGATGAAGCATCTGCAAAAA 57.501 28.000 4.79 0.00 45.16 1.94
2396 2764 3.804873 GGATCGTCCTATGTGCTCTTTTC 59.195 47.826 0.00 0.00 32.53 2.29
2770 3408 4.882427 TCCAAAACGGACATAAGAAACACA 59.118 37.500 0.00 0.00 39.64 3.72
2786 3424 8.519526 TGATAATAATGTGTGTTCCTCCAAAAC 58.480 33.333 0.00 0.00 0.00 2.43
2853 3491 1.805943 TGTGTCTGAATTGATGCGTGG 59.194 47.619 0.00 0.00 0.00 4.94
2925 3563 9.733556 TTAACAATGTGATGTACCTGTATTCTT 57.266 29.630 0.00 0.00 32.02 2.52
2940 3578 7.551585 ACAATTGGAAGTTGTTAACAATGTGA 58.448 30.769 23.11 8.91 36.44 3.58
3172 3821 4.690748 GCTCTTGTTGCAACAGATACAGTA 59.309 41.667 29.50 13.44 40.50 2.74
3173 3822 3.499918 GCTCTTGTTGCAACAGATACAGT 59.500 43.478 29.50 0.00 40.50 3.55
3174 3823 3.499537 TGCTCTTGTTGCAACAGATACAG 59.500 43.478 29.50 23.36 40.50 2.74
3175 3824 3.475575 TGCTCTTGTTGCAACAGATACA 58.524 40.909 29.50 22.93 40.50 2.29
3176 3825 4.691860 ATGCTCTTGTTGCAACAGATAC 57.308 40.909 29.50 20.92 44.01 2.24
3238 3887 0.465705 ACACAGATAGGTGGCCATCG 59.534 55.000 9.72 0.00 43.08 3.84
3276 3925 3.440173 ACAGCACATAGGAAAAATGGACG 59.560 43.478 0.00 0.00 0.00 4.79
3277 3926 4.437390 CGACAGCACATAGGAAAAATGGAC 60.437 45.833 0.00 0.00 0.00 4.02
3300 3949 1.357258 CGATGCTGCACTCCTGTGAC 61.357 60.000 3.57 0.00 46.55 3.67
3354 4003 5.738909 AGATCCTTGACGAACATTTCATCT 58.261 37.500 0.00 0.00 0.00 2.90
3357 4006 4.893608 TGAGATCCTTGACGAACATTTCA 58.106 39.130 0.00 0.00 0.00 2.69
3442 4091 2.233676 AGGGGCGAAAATGGATGAAAAC 59.766 45.455 0.00 0.00 0.00 2.43
3459 4108 2.104792 TGCTCGAGGATGAAATAAGGGG 59.895 50.000 15.58 0.00 0.00 4.79
3816 4474 4.824479 TCAGAGTTCATACATCTGGCAA 57.176 40.909 1.93 0.00 40.68 4.52
3888 4547 2.095853 CCCCGTCACAATTCAGAAATCG 59.904 50.000 0.00 0.00 0.00 3.34
4032 4696 4.973051 CAGCATTAGTTGTTTGTGCGTTTA 59.027 37.500 0.00 0.00 40.54 2.01
4082 4746 7.113965 CACCTCAAATTCGAATCAGAACAAAAG 59.886 37.037 11.83 0.31 32.39 2.27
4148 4851 3.806521 CGTTCTGCCAATTCATCTAGAGG 59.193 47.826 0.00 0.00 0.00 3.69
4259 4971 8.648557 TGTATCATTAGATCCGTCTTGAAAAG 57.351 34.615 0.00 0.00 39.48 2.27
4603 6341 2.162208 AGTTGAAACATATGTGCGCAGG 59.838 45.455 12.22 0.14 0.00 4.85
4604 6342 3.476295 AGTTGAAACATATGTGCGCAG 57.524 42.857 12.22 0.00 0.00 5.18
4623 6361 8.638873 TCCCAAATGCGTATGGTATATCTATAG 58.361 37.037 0.00 0.00 34.79 1.31
4669 6407 1.135527 CATGCGCAAATCCACCATCTT 59.864 47.619 17.11 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.