Multiple sequence alignment - TraesCS7D01G131700

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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 TraesCS7D01G131700 chr7D 100.000 3107 0 0 1 3107 83475058 83471952 0.000000e+00 5738.0
1 TraesCS7D01G131700 chr7D 83.607 61 10 0 2337 2397 65791065 65791005 1.200000e-04 58.4
2 TraesCS7D01G131700 chr7A 89.092 2292 128 54 22 2234 85161809 85159561 0.000000e+00 2736.0
3 TraesCS7D01G131700 chr7A 82.727 550 59 17 2593 3107 85159220 85158672 1.020000e-124 457.0
4 TraesCS7D01G131700 chr7A 84.673 398 38 12 1000 1380 68202261 68202652 2.930000e-100 375.0
5 TraesCS7D01G131700 chr7A 84.333 300 36 8 2327 2618 85159562 85159266 1.820000e-72 283.0
6 TraesCS7D01G131700 chr7A 88.732 71 6 2 2760 2829 188573864 188573795 5.520000e-13 86.1
7 TraesCS7D01G131700 chr7B 89.435 1751 99 30 488 2191 32665239 32663528 0.000000e+00 2130.0
8 TraesCS7D01G131700 chr7B 87.317 410 21 13 2700 3107 32663502 32663122 1.020000e-119 440.0
9 TraesCS7D01G131700 chr2A 93.305 239 10 1 1122 1354 505416912 505417150 6.380000e-92 348.0
10 TraesCS7D01G131700 chr2A 85.256 312 31 11 1006 1306 519936796 519936489 1.080000e-79 307.0
11 TraesCS7D01G131700 chr2A 95.000 40 1 1 2790 2829 90066949 90066911 9.300000e-06 62.1
12 TraesCS7D01G131700 chr2A 100.000 29 0 0 1064 1092 505416872 505416900 2.000000e-03 54.7
13 TraesCS7D01G131700 chr2D 88.235 68 6 2 2763 2829 90313261 90313195 2.570000e-11 80.5
14 TraesCS7D01G131700 chr2D 88.636 44 5 0 2334 2377 27777305 27777348 2.000000e-03 54.7
15 TraesCS7D01G131700 chr1B 77.143 140 24 7 2456 2590 288648765 288648901 1.190000e-09 75.0
16 TraesCS7D01G131700 chr1B 89.474 57 6 0 2765 2821 572646801 572646857 4.300000e-09 73.1
17 TraesCS7D01G131700 chr1B 93.182 44 1 2 2216 2257 667994716 667994759 2.590000e-06 63.9
18 TraesCS7D01G131700 chr1B 97.297 37 0 1 2222 2257 668028668 668028704 9.300000e-06 62.1
19 TraesCS7D01G131700 chr1D 93.478 46 3 0 2776 2821 423268499 423268544 5.560000e-08 69.4
20 TraesCS7D01G131700 chr1D 93.182 44 1 2 2216 2257 479757247 479757290 2.590000e-06 63.9
21 TraesCS7D01G131700 chr1D 97.297 37 0 1 2222 2257 479748675 479748711 9.300000e-06 62.1
22 TraesCS7D01G131700 chr1A 93.478 46 3 0 2776 2821 519270257 519270302 5.560000e-08 69.4
23 TraesCS7D01G131700 chr3B 97.222 36 1 0 2233 2268 691481800 691481765 9.300000e-06 62.1
24 TraesCS7D01G131700 chr3A 85.965 57 7 1 2232 2288 535225800 535225745 3.350000e-05 60.2
25 TraesCS7D01G131700 chr4A 97.059 34 1 0 2463 2496 512553084 512553051 1.200000e-04 58.4


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 TraesCS7D01G131700 chr7D 83471952 83475058 3106 True 5738.000000 5738 100.000 1 3107 1 chr7D.!!$R2 3106
1 TraesCS7D01G131700 chr7A 85158672 85161809 3137 True 1158.666667 2736 85.384 22 3107 3 chr7A.!!$R2 3085
2 TraesCS7D01G131700 chr7B 32663122 32665239 2117 True 1285.000000 2130 88.376 488 3107 2 chr7B.!!$R1 2619

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
52 53 0.250513 GATGGCGTCTTCAACCTCCT 59.749 55.0 0.00 0.0 0.00 3.69 F
1453 1522 0.108804 ATGCTATCGGATAACGGCGG 60.109 55.0 13.24 0.0 44.45 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1942 0.178767 ATGGCATCTGCACTTCGCTA 59.821 50.0 4.33 0.0 44.36 4.26 R
2591 2712 0.035343 GCCCAGGTTCTTCTACACCC 60.035 60.0 0.00 0.0 32.92 4.61 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
39 40 1.600957 CAAAGCTCACATAGGATGGCG 59.399 52.381 0.00 0.00 33.60 5.69
52 53 0.250513 GATGGCGTCTTCAACCTCCT 59.749 55.000 0.00 0.00 0.00 3.69
54 55 0.472471 TGGCGTCTTCAACCTCCTTT 59.528 50.000 0.00 0.00 0.00 3.11
65 66 2.027625 CCTCCTTTGCACGACCGTC 61.028 63.158 0.00 0.00 0.00 4.79
76 77 2.338984 GACCGTCGTGCAACCTCT 59.661 61.111 0.00 0.00 0.00 3.69
80 81 1.007271 CGTCGTGCAACCTCTGTCT 60.007 57.895 0.00 0.00 0.00 3.41
87 88 0.955919 GCAACCTCTGTCTTTCCCCG 60.956 60.000 0.00 0.00 0.00 5.73
94 95 3.327404 GTCTTTCCCCGGAGCCCA 61.327 66.667 0.73 0.00 0.00 5.36
120 121 5.888161 ACATTGACTATGGAAGGGAAATGAC 59.112 40.000 1.98 0.00 38.64 3.06
122 123 5.512942 TGACTATGGAAGGGAAATGACAA 57.487 39.130 0.00 0.00 0.00 3.18
137 138 6.238130 GGAAATGACAACTCTAAATCTACCGC 60.238 42.308 0.00 0.00 0.00 5.68
164 165 8.533965 CAAACATGTAAAAGACATCACAAACAG 58.466 33.333 0.00 0.00 46.33 3.16
182 183 1.135141 CAGAGACTTCGAGGAGCAAGG 60.135 57.143 0.00 0.00 0.00 3.61
192 193 1.002011 GGAGCAAGGAAGTGTCCCC 60.002 63.158 0.00 0.00 46.30 4.81
212 214 2.158608 CCTCCCAAAGGCAAGTATAGGG 60.159 54.545 0.00 0.00 38.67 3.53
275 277 4.608170 AAGAGAAGAGGAGGAGAGACAT 57.392 45.455 0.00 0.00 0.00 3.06
303 307 0.826672 ACGAAGACGAGGGGACAAGT 60.827 55.000 0.00 0.00 42.66 3.16
315 319 1.369625 GGACAAGTAGTTGCCCATCG 58.630 55.000 10.53 0.00 36.25 3.84
389 393 5.586339 TCACAAAAATCAAAACATGAGCGA 58.414 33.333 0.00 0.00 42.53 4.93
423 427 1.065410 AACCAGATCCACCACCACCA 61.065 55.000 0.00 0.00 0.00 4.17
431 435 0.754957 CCACCACCACCAAAGCTCAA 60.755 55.000 0.00 0.00 0.00 3.02
434 438 0.389025 CCACCACCAAAGCTCAAACC 59.611 55.000 0.00 0.00 0.00 3.27
481 485 3.254060 CTCCGATGAAACACAGACGAAT 58.746 45.455 0.00 0.00 35.52 3.34
482 486 3.250744 TCCGATGAAACACAGACGAATC 58.749 45.455 0.00 0.00 35.52 2.52
483 487 2.993220 CCGATGAAACACAGACGAATCA 59.007 45.455 0.00 0.00 35.52 2.57
484 488 3.061295 CCGATGAAACACAGACGAATCAG 59.939 47.826 0.00 0.00 35.52 2.90
504 516 4.474651 TCAGGTATTCCCATGAGACAACAT 59.525 41.667 0.00 0.00 34.66 2.71
532 544 1.003355 CGCCACCTGGACATCAACT 60.003 57.895 0.00 0.00 37.39 3.16
541 553 4.289672 ACCTGGACATCAACTCCAACTAAT 59.710 41.667 0.00 0.00 37.36 1.73
594 606 2.699496 CCTCCCTAGGGCCAGAGT 59.301 66.667 24.42 0.00 39.48 3.24
664 676 1.715993 GGAAGGACAAGAAGACGAGC 58.284 55.000 0.00 0.00 0.00 5.03
796 814 2.586079 GCTGCGCTGGCGATAGAA 60.586 61.111 19.31 0.00 44.10 2.10
857 875 5.236655 TCATAAACTACAGTCTCGCTCAG 57.763 43.478 0.00 0.00 0.00 3.35
937 956 1.228459 GTCACCAACCCCACCTTCC 60.228 63.158 0.00 0.00 0.00 3.46
942 961 2.933834 AACCCCACCTTCCCCGAG 60.934 66.667 0.00 0.00 0.00 4.63
996 1015 4.792648 AGCAGCTCACTCGCGCTC 62.793 66.667 5.56 0.00 35.84 5.03
1355 1424 0.179108 GCTCGTCCGGCTTCAGTAAT 60.179 55.000 0.00 0.00 0.00 1.89
1356 1425 1.066605 GCTCGTCCGGCTTCAGTAATA 59.933 52.381 0.00 0.00 0.00 0.98
1357 1426 2.480759 GCTCGTCCGGCTTCAGTAATAA 60.481 50.000 0.00 0.00 0.00 1.40
1358 1427 3.799232 GCTCGTCCGGCTTCAGTAATAAT 60.799 47.826 0.00 0.00 0.00 1.28
1362 1431 2.171659 TCCGGCTTCAGTAATAATGGCA 59.828 45.455 0.00 0.00 0.00 4.92
1363 1432 2.549754 CCGGCTTCAGTAATAATGGCAG 59.450 50.000 0.00 0.00 0.00 4.85
1364 1433 3.206150 CGGCTTCAGTAATAATGGCAGT 58.794 45.455 0.00 0.00 0.00 4.40
1368 1437 3.643199 TCAGTAATAATGGCAGTGGCA 57.357 42.857 22.88 22.88 43.71 4.92
1445 1514 0.320771 GCGGAACCATGCTATCGGAT 60.321 55.000 0.00 0.00 0.00 4.18
1446 1515 1.067142 GCGGAACCATGCTATCGGATA 60.067 52.381 0.00 0.00 0.00 2.59
1447 1516 2.611971 GCGGAACCATGCTATCGGATAA 60.612 50.000 0.00 0.00 0.00 1.75
1451 1520 1.337823 ACCATGCTATCGGATAACGGC 60.338 52.381 0.00 0.46 44.45 5.68
1452 1521 0.992072 CATGCTATCGGATAACGGCG 59.008 55.000 4.80 4.80 44.45 6.46
1453 1522 0.108804 ATGCTATCGGATAACGGCGG 60.109 55.000 13.24 0.00 44.45 6.13
1454 1523 2.092882 GCTATCGGATAACGGCGGC 61.093 63.158 13.24 0.00 44.45 6.53
1876 1973 3.433319 CAGATGCCATGCTGCCTC 58.567 61.111 0.00 0.00 0.00 4.70
1877 1974 2.194212 CAGATGCCATGCTGCCTCC 61.194 63.158 0.00 0.00 0.00 4.30
1878 1975 2.195139 GATGCCATGCTGCCTCCT 59.805 61.111 0.00 0.00 0.00 3.69
1879 1976 2.123854 ATGCCATGCTGCCTCCTG 60.124 61.111 0.00 0.00 0.00 3.86
2129 2230 2.257353 GTGGCCACACTGATGTTCC 58.743 57.895 31.23 0.00 44.29 3.62
2136 2241 3.562973 GCCACACTGATGTTCCTATCATG 59.437 47.826 0.00 0.00 36.72 3.07
2140 2245 6.481313 CCACACTGATGTTCCTATCATGTTAG 59.519 42.308 4.10 4.10 36.72 2.34
2142 2247 5.468072 CACTGATGTTCCTATCATGTTAGCC 59.532 44.000 5.42 0.00 36.55 3.93
2170 2275 6.564328 CCAGTGTTTATGGATAAAGCTTTCC 58.436 40.000 16.57 12.75 40.51 3.13
2178 2285 3.206964 GGATAAAGCTTTCCTTCCGAGG 58.793 50.000 16.57 0.00 45.02 4.63
2200 2314 2.905075 CGGCAATTCTGGTGTATCTGA 58.095 47.619 0.00 0.00 0.00 3.27
2202 2316 3.310774 CGGCAATTCTGGTGTATCTGAAG 59.689 47.826 0.00 0.00 0.00 3.02
2205 2319 4.034975 GCAATTCTGGTGTATCTGAAGCTC 59.965 45.833 0.00 0.00 0.00 4.09
2208 2322 2.423892 TCTGGTGTATCTGAAGCTCGAC 59.576 50.000 0.00 0.00 0.00 4.20
2217 2331 0.666374 TGAAGCTCGACGTGAACAGA 59.334 50.000 0.00 0.00 0.00 3.41
2259 2373 9.152327 ACTCTCTCTGATCCATATTAATTGACA 57.848 33.333 0.00 0.00 0.00 3.58
2260 2374 9.421806 CTCTCTCTGATCCATATTAATTGACAC 57.578 37.037 0.00 0.00 0.00 3.67
2261 2375 8.927411 TCTCTCTGATCCATATTAATTGACACA 58.073 33.333 0.00 0.00 0.00 3.72
2262 2376 8.893219 TCTCTGATCCATATTAATTGACACAC 57.107 34.615 0.00 0.00 0.00 3.82
2263 2377 8.485392 TCTCTGATCCATATTAATTGACACACA 58.515 33.333 0.00 0.00 0.00 3.72
2264 2378 8.437360 TCTGATCCATATTAATTGACACACAC 57.563 34.615 0.00 0.00 0.00 3.82
2265 2379 8.267183 TCTGATCCATATTAATTGACACACACT 58.733 33.333 0.00 0.00 0.00 3.55
2266 2380 8.806429 TGATCCATATTAATTGACACACACTT 57.194 30.769 0.00 0.00 0.00 3.16
2267 2381 9.898152 TGATCCATATTAATTGACACACACTTA 57.102 29.630 0.00 0.00 0.00 2.24
2302 2416 8.958175 TGGACTAAAGTTGTATTAAATTTGCG 57.042 30.769 0.00 0.00 0.00 4.85
2303 2417 8.569641 TGGACTAAAGTTGTATTAAATTTGCGT 58.430 29.630 0.00 0.00 0.00 5.24
2304 2418 9.058424 GGACTAAAGTTGTATTAAATTTGCGTC 57.942 33.333 0.00 0.00 0.00 5.19
2305 2419 9.601971 GACTAAAGTTGTATTAAATTTGCGTCA 57.398 29.630 0.00 0.00 0.00 4.35
2306 2420 9.953697 ACTAAAGTTGTATTAAATTTGCGTCAA 57.046 25.926 0.00 0.00 0.00 3.18
2319 2433 5.814314 TTTGCGTCAATTAATTTGAACCG 57.186 34.783 0.00 3.03 45.71 4.44
2320 2434 3.827625 TGCGTCAATTAATTTGAACCGG 58.172 40.909 0.00 0.00 45.71 5.28
2321 2435 3.502595 TGCGTCAATTAATTTGAACCGGA 59.497 39.130 9.46 0.66 45.71 5.14
2322 2436 4.095610 GCGTCAATTAATTTGAACCGGAG 58.904 43.478 9.46 0.00 45.71 4.63
2360 2474 2.177531 CTCATGTGCGCAAGGTGC 59.822 61.111 14.00 0.00 40.69 5.01
2373 2487 3.376540 GCAAGGTGCGTGTAATTTTTCA 58.623 40.909 0.00 0.00 31.71 2.69
2377 2491 3.823873 AGGTGCGTGTAATTTTTCATGGA 59.176 39.130 0.00 0.00 0.00 3.41
2387 2501 7.708752 GTGTAATTTTTCATGGAGTTTGGACAA 59.291 33.333 0.00 0.00 0.00 3.18
2392 2506 4.163441 TCATGGAGTTTGGACAACTGAA 57.837 40.909 0.00 0.00 0.00 3.02
2393 2507 4.136796 TCATGGAGTTTGGACAACTGAAG 58.863 43.478 0.00 0.00 0.00 3.02
2396 2510 2.550180 GGAGTTTGGACAACTGAAGAGC 59.450 50.000 0.00 0.00 0.00 4.09
2399 2513 3.118261 AGTTTGGACAACTGAAGAGCTCA 60.118 43.478 17.77 0.00 0.00 4.26
2417 2532 4.176271 GCTCATGCTAAAAATTGGGTGTC 58.824 43.478 0.00 0.00 36.03 3.67
2418 2533 4.747810 CTCATGCTAAAAATTGGGTGTCC 58.252 43.478 0.00 0.00 0.00 4.02
2422 2537 2.163613 GCTAAAAATTGGGTGTCCGAGG 59.836 50.000 0.00 0.00 35.24 4.63
2435 2550 4.497507 GGTGTCCGAGGAACTTTGAAAAAG 60.498 45.833 0.00 0.00 41.55 2.27
2446 2561 9.190317 AGGAACTTTGAAAAAGAACACTATTCT 57.810 29.630 6.73 0.00 27.25 2.40
2447 2562 9.237846 GGAACTTTGAAAAAGAACACTATTCTG 57.762 33.333 6.73 0.00 0.00 3.02
2449 2564 9.788960 AACTTTGAAAAAGAACACTATTCTGAC 57.211 29.630 6.73 0.00 0.00 3.51
2454 2569 7.939039 TGAAAAAGAACACTATTCTGACCTGAT 59.061 33.333 0.00 0.00 0.00 2.90
2491 2606 3.997021 CTCCTCAGATGTGTAAACACCAC 59.003 47.826 10.58 5.02 45.88 4.16
2496 2611 5.060506 TCAGATGTGTAAACACCACGAAAT 58.939 37.500 10.58 0.00 45.88 2.17
2504 2619 2.892373 ACACCACGAAATTATGCACG 57.108 45.000 0.00 0.00 0.00 5.34
2513 2628 2.620251 AATTATGCACGCTCCTAGCA 57.380 45.000 0.00 0.00 42.58 3.49
2528 2643 3.706086 TCCTAGCACACATGAGCATCTTA 59.294 43.478 0.00 0.00 34.92 2.10
2539 2654 6.430308 CACATGAGCATCTTAGATGCCTAAAT 59.570 38.462 34.91 22.90 45.59 1.40
2543 2658 7.934457 TGAGCATCTTAGATGCCTAAATTTTC 58.066 34.615 34.91 25.07 45.59 2.29
2548 2663 9.075678 CATCTTAGATGCCTAAATTTTCCAGAT 57.924 33.333 9.43 0.00 34.71 2.90
2551 2666 9.741647 CTTAGATGCCTAAATTTTCCAGATTTC 57.258 33.333 0.00 0.00 34.71 2.17
2557 2672 8.428063 TGCCTAAATTTTCCAGATTTCTTTGAA 58.572 29.630 0.00 0.00 0.00 2.69
2651 2843 5.873179 TTCTTGCCCTATGTTTTAACTCG 57.127 39.130 0.00 0.00 0.00 4.18
2657 2849 5.527214 TGCCCTATGTTTTAACTCGATGATG 59.473 40.000 0.00 0.00 0.00 3.07
2659 2851 5.527214 CCCTATGTTTTAACTCGATGATGCA 59.473 40.000 0.00 0.00 0.00 3.96
2673 2865 4.025396 CGATGATGCAGGTTTTAGCAGTAG 60.025 45.833 0.00 0.00 44.94 2.57
2674 2866 4.286297 TGATGCAGGTTTTAGCAGTAGT 57.714 40.909 0.00 0.00 44.94 2.73
2729 2922 1.742831 GCATGTTACTGCGGGAATTGA 59.257 47.619 7.41 0.00 31.49 2.57
2733 2926 5.449862 GCATGTTACTGCGGGAATTGATTAA 60.450 40.000 7.41 0.00 31.49 1.40
2735 2928 6.189677 TGTTACTGCGGGAATTGATTAAAG 57.810 37.500 0.00 0.00 0.00 1.85
2738 2931 5.059404 ACTGCGGGAATTGATTAAAGTTG 57.941 39.130 0.00 0.00 0.00 3.16
2739 2932 4.764823 ACTGCGGGAATTGATTAAAGTTGA 59.235 37.500 0.00 0.00 0.00 3.18
2741 2934 6.601613 ACTGCGGGAATTGATTAAAGTTGATA 59.398 34.615 0.00 0.00 0.00 2.15
2742 2935 7.026631 TGCGGGAATTGATTAAAGTTGATAG 57.973 36.000 0.00 0.00 0.00 2.08
2743 2936 6.039270 TGCGGGAATTGATTAAAGTTGATAGG 59.961 38.462 0.00 0.00 0.00 2.57
2747 2956 9.803315 GGGAATTGATTAAAGTTGATAGGTTTC 57.197 33.333 0.00 0.00 0.00 2.78
2767 2976 9.838339 AGGTTTCGATAATATGAGAACTGAAAT 57.162 29.630 0.00 0.00 0.00 2.17
2984 3230 1.217001 TAGCTCGTGTGCAGTTGTTG 58.783 50.000 0.00 0.00 34.99 3.33
3038 3284 5.215160 GCGAAGATAATAAAGCCAATGTGG 58.785 41.667 0.00 0.00 41.55 4.17
3081 3327 6.015010 AGCTAGCCATGACGACTCTATTTATT 60.015 38.462 12.13 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.657436 TTGTTGGGAAACGCAGTAATTT 57.343 36.364 0.00 0.00 45.00 1.82
1 2 4.616953 CTTTGTTGGGAAACGCAGTAATT 58.383 39.130 0.00 0.00 45.00 1.40
2 3 3.552068 GCTTTGTTGGGAAACGCAGTAAT 60.552 43.478 0.00 0.00 45.00 1.89
3 4 2.223618 GCTTTGTTGGGAAACGCAGTAA 60.224 45.455 0.00 0.00 45.00 2.24
4 5 1.335496 GCTTTGTTGGGAAACGCAGTA 59.665 47.619 0.00 0.00 45.00 2.74
6 7 0.385390 AGCTTTGTTGGGAAACGCAG 59.615 50.000 0.00 0.00 0.00 5.18
7 8 0.383949 GAGCTTTGTTGGGAAACGCA 59.616 50.000 0.00 0.00 0.00 5.24
8 9 0.383949 TGAGCTTTGTTGGGAAACGC 59.616 50.000 0.00 0.00 0.00 4.84
9 10 1.403679 TGTGAGCTTTGTTGGGAAACG 59.596 47.619 0.00 0.00 0.00 3.60
10 11 3.733443 ATGTGAGCTTTGTTGGGAAAC 57.267 42.857 0.00 0.00 0.00 2.78
11 12 3.826157 CCTATGTGAGCTTTGTTGGGAAA 59.174 43.478 0.00 0.00 0.00 3.13
12 13 3.073798 TCCTATGTGAGCTTTGTTGGGAA 59.926 43.478 0.00 0.00 0.00 3.97
13 14 2.642311 TCCTATGTGAGCTTTGTTGGGA 59.358 45.455 0.00 0.00 0.00 4.37
14 15 3.071874 TCCTATGTGAGCTTTGTTGGG 57.928 47.619 0.00 0.00 0.00 4.12
15 16 3.379372 CCATCCTATGTGAGCTTTGTTGG 59.621 47.826 0.00 0.00 0.00 3.77
16 17 3.181493 GCCATCCTATGTGAGCTTTGTTG 60.181 47.826 0.00 0.00 0.00 3.33
17 18 3.019564 GCCATCCTATGTGAGCTTTGTT 58.980 45.455 0.00 0.00 0.00 2.83
18 19 2.648059 GCCATCCTATGTGAGCTTTGT 58.352 47.619 0.00 0.00 0.00 2.83
19 20 1.600957 CGCCATCCTATGTGAGCTTTG 59.399 52.381 0.00 0.00 0.00 2.77
20 21 1.210478 ACGCCATCCTATGTGAGCTTT 59.790 47.619 0.00 0.00 0.00 3.51
39 40 1.264288 CGTGCAAAGGAGGTTGAAGAC 59.736 52.381 0.00 0.00 0.00 3.01
65 66 0.868406 GGAAAGACAGAGGTTGCACG 59.132 55.000 0.00 0.00 0.00 5.34
76 77 3.327404 GGGCTCCGGGGAAAGACA 61.327 66.667 4.80 0.00 0.00 3.41
80 81 3.327404 GTCTGGGCTCCGGGGAAA 61.327 66.667 4.80 0.00 0.00 3.13
87 88 2.486191 CCATAGTCAATGTCTGGGCTCC 60.486 54.545 0.00 0.00 33.34 4.70
94 95 5.779241 TTTCCCTTCCATAGTCAATGTCT 57.221 39.130 0.00 0.00 33.34 3.41
120 121 4.693566 TGTTTGGCGGTAGATTTAGAGTTG 59.306 41.667 0.00 0.00 0.00 3.16
122 123 4.546829 TGTTTGGCGGTAGATTTAGAGT 57.453 40.909 0.00 0.00 0.00 3.24
164 165 1.178276 TCCTTGCTCCTCGAAGTCTC 58.822 55.000 0.00 0.00 0.00 3.36
182 183 0.038310 CCTTTGGGAGGGGACACTTC 59.962 60.000 0.00 0.00 42.26 3.01
192 193 2.158608 CCCCTATACTTGCCTTTGGGAG 60.159 54.545 0.00 0.00 35.40 4.30
275 277 2.421073 CCCTCGTCTTCGTGTATGTGTA 59.579 50.000 0.00 0.00 38.33 2.90
315 319 3.003275 TCTGAACAGTTGTTTTGCCGATC 59.997 43.478 0.00 0.00 38.56 3.69
423 427 2.103263 ACAGAGAGTCGGTTTGAGCTTT 59.897 45.455 0.00 0.00 0.00 3.51
431 435 5.723672 TCTATTTCAACAGAGAGTCGGTT 57.276 39.130 0.00 0.00 35.22 4.44
434 438 5.062809 GGCTTTCTATTTCAACAGAGAGTCG 59.937 44.000 0.00 0.00 0.00 4.18
481 485 3.843619 TGTTGTCTCATGGGAATACCTGA 59.156 43.478 0.00 0.00 41.11 3.86
482 486 4.220693 TGTTGTCTCATGGGAATACCTG 57.779 45.455 0.00 0.00 41.11 4.00
483 487 4.474651 TGATGTTGTCTCATGGGAATACCT 59.525 41.667 0.00 0.00 41.11 3.08
484 488 4.576463 GTGATGTTGTCTCATGGGAATACC 59.424 45.833 0.00 0.00 40.81 2.73
504 516 1.078497 CAGGTGGCGGCATAAGTGA 60.078 57.895 17.19 0.00 0.00 3.41
532 544 4.320870 GTCCCTTGTTTCGATTAGTTGGA 58.679 43.478 0.00 0.00 0.00 3.53
541 553 3.379372 CGTAGATAGGTCCCTTGTTTCGA 59.621 47.826 0.00 0.00 0.00 3.71
664 676 1.144936 GAGGCGGTCCAGAGGATTG 59.855 63.158 0.00 0.00 32.73 2.67
796 814 4.094887 CCAGCGACTTGTTATATGCTTGTT 59.905 41.667 0.00 0.00 0.00 2.83
857 875 4.133796 GCGCTGGGTTGATTGGGC 62.134 66.667 0.00 0.00 0.00 5.36
996 1015 0.726827 GTGTGTGTGTGTGAGTGTGG 59.273 55.000 0.00 0.00 0.00 4.17
1024 1045 0.669318 TGATCGGTCAACGGAGCAAC 60.669 55.000 0.00 0.00 44.45 4.17
1045 1066 1.283029 TGCTGAGGAGGATTTCTTGGG 59.717 52.381 0.00 0.00 0.00 4.12
1286 1343 3.764466 CAGGACGAGCCGCCTTCT 61.764 66.667 0.00 0.00 43.43 2.85
1355 1424 0.829990 TCTCGATGCCACTGCCATTA 59.170 50.000 0.00 0.00 36.33 1.90
1356 1425 0.182061 ATCTCGATGCCACTGCCATT 59.818 50.000 0.00 0.00 36.33 3.16
1357 1426 0.534427 CATCTCGATGCCACTGCCAT 60.534 55.000 0.00 0.00 36.33 4.40
1358 1427 1.153309 CATCTCGATGCCACTGCCA 60.153 57.895 0.00 0.00 36.33 4.92
1362 1431 1.445095 GGCTCATCTCGATGCCACT 59.555 57.895 2.05 0.00 44.34 4.00
1363 1432 4.040068 GGCTCATCTCGATGCCAC 57.960 61.111 2.05 0.00 44.34 5.01
1368 1437 2.419297 GGTCAAACAGGCTCATCTCGAT 60.419 50.000 0.00 0.00 0.00 3.59
1432 1501 1.359848 GCCGTTATCCGATAGCATGG 58.640 55.000 0.00 0.00 39.56 3.66
1705 1774 4.254672 TCGTGTTGTCGCCGTCGT 62.255 61.111 0.00 0.00 36.96 4.34
1849 1942 0.178767 ATGGCATCTGCACTTCGCTA 59.821 50.000 4.33 0.00 44.36 4.26
1880 1977 1.246056 CCATGGCGCCAATAGGATGG 61.246 60.000 36.33 30.11 43.70 3.51
1881 1978 0.538057 ACCATGGCGCCAATAGGATG 60.538 55.000 37.30 28.34 36.89 3.51
2129 2230 3.562973 CACTGGCAAGGCTAACATGATAG 59.437 47.826 0.00 1.90 0.00 2.08
2136 2241 3.119495 CCATAAACACTGGCAAGGCTAAC 60.119 47.826 0.00 0.00 0.00 2.34
2140 2245 1.544724 TCCATAAACACTGGCAAGGC 58.455 50.000 0.00 0.00 33.56 4.35
2142 2247 5.126061 AGCTTTATCCATAAACACTGGCAAG 59.874 40.000 0.00 0.00 33.56 4.01
2178 2285 0.663153 GATACACCAGAATTGCCGCC 59.337 55.000 0.00 0.00 0.00 6.13
2200 2314 2.218953 TTTCTGTTCACGTCGAGCTT 57.781 45.000 0.00 0.00 0.00 3.74
2202 2316 3.059868 TGAATTTTCTGTTCACGTCGAGC 60.060 43.478 0.00 0.00 31.07 5.03
2205 2319 7.830217 TTATTTGAATTTTCTGTTCACGTCG 57.170 32.000 0.00 0.00 35.47 5.12
2233 2347 9.152327 TGTCAATTAATATGGATCAGAGAGAGT 57.848 33.333 0.00 0.00 0.00 3.24
2234 2348 9.421806 GTGTCAATTAATATGGATCAGAGAGAG 57.578 37.037 0.00 0.00 0.00 3.20
2235 2349 8.927411 TGTGTCAATTAATATGGATCAGAGAGA 58.073 33.333 0.00 0.00 0.00 3.10
2236 2350 8.986847 GTGTGTCAATTAATATGGATCAGAGAG 58.013 37.037 0.00 0.00 0.00 3.20
2237 2351 8.485392 TGTGTGTCAATTAATATGGATCAGAGA 58.515 33.333 0.00 0.00 0.00 3.10
2238 2352 8.554528 GTGTGTGTCAATTAATATGGATCAGAG 58.445 37.037 0.00 0.00 0.00 3.35
2239 2353 8.267183 AGTGTGTGTCAATTAATATGGATCAGA 58.733 33.333 0.00 0.00 0.00 3.27
2240 2354 8.442632 AGTGTGTGTCAATTAATATGGATCAG 57.557 34.615 0.00 0.00 0.00 2.90
2241 2355 8.806429 AAGTGTGTGTCAATTAATATGGATCA 57.194 30.769 0.00 0.00 32.40 2.92
2276 2390 9.400638 CGCAAATTTAATACAACTTTAGTCCAA 57.599 29.630 0.00 0.00 0.00 3.53
2277 2391 8.569641 ACGCAAATTTAATACAACTTTAGTCCA 58.430 29.630 0.00 0.00 0.00 4.02
2278 2392 8.959734 ACGCAAATTTAATACAACTTTAGTCC 57.040 30.769 0.00 0.00 0.00 3.85
2279 2393 9.601971 TGACGCAAATTTAATACAACTTTAGTC 57.398 29.630 0.00 0.00 0.00 2.59
2280 2394 9.953697 TTGACGCAAATTTAATACAACTTTAGT 57.046 25.926 0.00 0.00 0.00 2.24
2303 2417 5.566469 ACTCCTCCGGTTCAAATTAATTGA 58.434 37.500 0.00 0.00 46.22 2.57
2304 2418 5.897377 ACTCCTCCGGTTCAAATTAATTG 57.103 39.130 0.00 0.00 40.58 2.32
2305 2419 6.718294 ACTACTCCTCCGGTTCAAATTAATT 58.282 36.000 0.00 0.00 0.00 1.40
2306 2420 6.309389 ACTACTCCTCCGGTTCAAATTAAT 57.691 37.500 0.00 0.00 0.00 1.40
2307 2421 5.750352 ACTACTCCTCCGGTTCAAATTAA 57.250 39.130 0.00 0.00 0.00 1.40
2308 2422 6.855763 TTACTACTCCTCCGGTTCAAATTA 57.144 37.500 0.00 0.00 0.00 1.40
2309 2423 5.750352 TTACTACTCCTCCGGTTCAAATT 57.250 39.130 0.00 0.00 0.00 1.82
2310 2424 5.750352 TTTACTACTCCTCCGGTTCAAAT 57.250 39.130 0.00 0.00 0.00 2.32
2311 2425 5.549742 TTTTACTACTCCTCCGGTTCAAA 57.450 39.130 0.00 0.00 0.00 2.69
2312 2426 5.750352 ATTTTACTACTCCTCCGGTTCAA 57.250 39.130 0.00 0.00 0.00 2.69
2313 2427 5.246656 TGAATTTTACTACTCCTCCGGTTCA 59.753 40.000 0.00 0.00 0.00 3.18
2314 2428 5.727434 TGAATTTTACTACTCCTCCGGTTC 58.273 41.667 0.00 0.00 0.00 3.62
2315 2429 5.750352 TGAATTTTACTACTCCTCCGGTT 57.250 39.130 0.00 0.00 0.00 4.44
2316 2430 5.482878 TCTTGAATTTTACTACTCCTCCGGT 59.517 40.000 0.00 0.00 0.00 5.28
2317 2431 5.974108 TCTTGAATTTTACTACTCCTCCGG 58.026 41.667 0.00 0.00 0.00 5.14
2318 2432 6.018669 GCATCTTGAATTTTACTACTCCTCCG 60.019 42.308 0.00 0.00 0.00 4.63
2319 2433 7.051000 AGCATCTTGAATTTTACTACTCCTCC 58.949 38.462 0.00 0.00 0.00 4.30
2320 2434 7.766278 TGAGCATCTTGAATTTTACTACTCCTC 59.234 37.037 0.00 0.00 34.92 3.71
2321 2435 7.624549 TGAGCATCTTGAATTTTACTACTCCT 58.375 34.615 0.00 0.00 34.92 3.69
2322 2436 7.849804 TGAGCATCTTGAATTTTACTACTCC 57.150 36.000 0.00 0.00 34.92 3.85
2323 2437 8.887717 ACATGAGCATCTTGAATTTTACTACTC 58.112 33.333 0.00 0.00 42.34 2.59
2324 2438 8.671921 CACATGAGCATCTTGAATTTTACTACT 58.328 33.333 0.00 0.00 42.34 2.57
2325 2439 7.430502 GCACATGAGCATCTTGAATTTTACTAC 59.569 37.037 10.48 0.00 42.34 2.73
2360 2474 6.362283 GTCCAAACTCCATGAAAAATTACACG 59.638 38.462 0.00 0.00 0.00 4.49
2363 2477 7.926018 AGTTGTCCAAACTCCATGAAAAATTAC 59.074 33.333 0.00 0.00 0.00 1.89
2372 2486 4.136796 TCTTCAGTTGTCCAAACTCCATG 58.863 43.478 0.00 0.00 0.00 3.66
2373 2487 4.392940 CTCTTCAGTTGTCCAAACTCCAT 58.607 43.478 0.00 0.00 0.00 3.41
2377 2491 3.118261 TGAGCTCTTCAGTTGTCCAAACT 60.118 43.478 16.19 0.00 0.00 2.66
2396 2510 4.675146 CGGACACCCAATTTTTAGCATGAG 60.675 45.833 0.00 0.00 0.00 2.90
2399 2513 3.426615 TCGGACACCCAATTTTTAGCAT 58.573 40.909 0.00 0.00 0.00 3.79
2409 2523 0.841289 AAAGTTCCTCGGACACCCAA 59.159 50.000 0.00 0.00 0.00 4.12
2410 2524 0.107831 CAAAGTTCCTCGGACACCCA 59.892 55.000 0.00 0.00 0.00 4.51
2411 2525 0.395312 TCAAAGTTCCTCGGACACCC 59.605 55.000 0.00 0.00 0.00 4.61
2417 2532 5.034797 GTGTTCTTTTTCAAAGTTCCTCGG 58.965 41.667 0.00 0.00 0.00 4.63
2418 2533 5.880341 AGTGTTCTTTTTCAAAGTTCCTCG 58.120 37.500 0.00 0.00 0.00 4.63
2465 2580 3.055819 TGTTTACACATCTGAGGAGCTCC 60.056 47.826 26.22 26.22 0.00 4.70
2491 2606 2.096713 GCTAGGAGCGTGCATAATTTCG 60.097 50.000 0.00 0.00 0.00 3.46
2496 2611 0.534873 TGTGCTAGGAGCGTGCATAA 59.465 50.000 0.00 0.00 46.26 1.90
2504 2619 2.687842 GCTCATGTGTGCTAGGAGC 58.312 57.895 0.00 0.00 43.41 4.70
2513 2628 3.136077 AGGCATCTAAGATGCTCATGTGT 59.864 43.478 19.71 0.00 44.02 3.72
2528 2643 7.968014 AGAAATCTGGAAAATTTAGGCATCT 57.032 32.000 0.00 0.00 0.00 2.90
2573 2688 5.131784 ACACCCGGTGAACAGTAAATTAAA 58.868 37.500 24.80 0.00 36.96 1.52
2574 2689 4.716794 ACACCCGGTGAACAGTAAATTAA 58.283 39.130 24.80 0.00 36.96 1.40
2575 2690 4.354893 ACACCCGGTGAACAGTAAATTA 57.645 40.909 24.80 0.00 36.96 1.40
2577 2692 2.943036 ACACCCGGTGAACAGTAAAT 57.057 45.000 24.80 0.00 36.96 1.40
2578 2693 2.964464 TCTACACCCGGTGAACAGTAAA 59.036 45.455 24.80 0.43 36.96 2.01
2580 2695 2.291209 TCTACACCCGGTGAACAGTA 57.709 50.000 24.80 4.68 36.96 2.74
2581 2696 1.343465 CTTCTACACCCGGTGAACAGT 59.657 52.381 24.80 3.63 36.96 3.55
2582 2697 1.616865 TCTTCTACACCCGGTGAACAG 59.383 52.381 24.80 16.31 36.96 3.16
2590 2711 0.249398 CCCAGGTTCTTCTACACCCG 59.751 60.000 0.00 0.00 32.92 5.28
2591 2712 0.035343 GCCCAGGTTCTTCTACACCC 60.035 60.000 0.00 0.00 32.92 4.61
2618 2739 5.944007 ACATAGGGCAAGAAACGTAAATTCT 59.056 36.000 0.00 0.00 38.75 2.40
2619 2740 6.190954 ACATAGGGCAAGAAACGTAAATTC 57.809 37.500 0.00 0.00 0.00 2.17
2620 2741 6.584185 AACATAGGGCAAGAAACGTAAATT 57.416 33.333 0.00 0.00 0.00 1.82
2621 2742 6.584185 AAACATAGGGCAAGAAACGTAAAT 57.416 33.333 0.00 0.00 0.00 1.40
2622 2743 6.394025 AAAACATAGGGCAAGAAACGTAAA 57.606 33.333 0.00 0.00 0.00 2.01
2623 2744 7.229106 AGTTAAAACATAGGGCAAGAAACGTAA 59.771 33.333 0.00 0.00 0.00 3.18
2624 2745 6.711645 AGTTAAAACATAGGGCAAGAAACGTA 59.288 34.615 0.00 0.00 0.00 3.57
2651 2843 4.878397 ACTACTGCTAAAACCTGCATCATC 59.122 41.667 0.00 0.00 38.59 2.92
2657 2849 6.403309 GGAATACAACTACTGCTAAAACCTGC 60.403 42.308 0.00 0.00 0.00 4.85
2659 2851 6.775708 TGGAATACAACTACTGCTAAAACCT 58.224 36.000 0.00 0.00 0.00 3.50
2687 2879 5.773176 TGCGGGTATCATCTAATTACTCAGA 59.227 40.000 0.00 0.00 0.00 3.27
2688 2880 6.025749 TGCGGGTATCATCTAATTACTCAG 57.974 41.667 0.00 0.00 0.00 3.35
2696 2888 5.538118 CAGTAACATGCGGGTATCATCTAA 58.462 41.667 0.00 0.00 0.00 2.10
2709 2902 1.742831 TCAATTCCCGCAGTAACATGC 59.257 47.619 0.00 0.00 42.95 4.06
2741 2934 9.838339 ATTTCAGTTCTCATATTATCGAAACCT 57.162 29.630 0.00 0.00 0.00 3.50
2947 3193 9.856488 CACGAGCTATCTTAGGCTAAATTAATA 57.144 33.333 8.54 3.91 39.05 0.98
2958 3204 2.099921 ACTGCACACGAGCTATCTTAGG 59.900 50.000 0.00 0.00 34.99 2.69
2984 3230 3.874392 AAACCATGAAAGCTACATGCC 57.126 42.857 21.12 0.00 42.31 4.40
3038 3284 7.065803 TGGCTAGCTATCTGTTCATACAAAAAC 59.934 37.037 15.72 0.00 32.92 2.43


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

AutoCloner maintained by Alex Coulton.