Multiple sequence alignment - TraesCS1A01G194600

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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 TraesCS1A01G194600 chr1A 100.000 3934 0 0 1 3934 351860473 351856540 0.000000e+00 7265
1 TraesCS1A01G194600 chr1A 100.000 345 0 0 4215 4559 351856259 351855915 4.970000e-179 638
2 TraesCS1A01G194600 chr1A 98.485 66 0 1 2308 2372 351858110 351858045 1.040000e-21 115
3 TraesCS1A01G194600 chr1A 98.485 66 0 1 2365 2429 351858167 351858102 1.040000e-21 115
4 TraesCS1A01G194600 chr1D 94.825 2396 70 17 1 2372 279937153 279934788 0.000000e+00 3688
5 TraesCS1A01G194600 chr1D 96.954 1149 34 1 2768 3916 279934344 279933197 0.000000e+00 1927
6 TraesCS1A01G194600 chr1D 95.355 409 14 5 2364 2770 279934852 279934447 0.000000e+00 645
7 TraesCS1A01G194600 chr1D 89.344 366 16 7 4217 4559 279932607 279932242 5.410000e-119 438
8 TraesCS1A01G194600 chr1B 92.199 1564 57 30 2364 3899 380434456 380432930 0.000000e+00 2152
9 TraesCS1A01G194600 chr1B 95.034 1309 38 12 1081 2372 380435690 380434392 0.000000e+00 2032
10 TraesCS1A01G194600 chr1B 96.496 1056 28 4 1 1052 380436736 380435686 0.000000e+00 1736
11 TraesCS1A01G194600 chr1B 90.986 355 17 4 4216 4559 380432401 380432051 8.930000e-127 464


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 TraesCS1A01G194600 chr1A 351855915 351860473 4558 True 2033.25 7265 99.24250 1 4559 4 chr1A.!!$R1 4558
1 TraesCS1A01G194600 chr1D 279932242 279937153 4911 True 1674.50 3688 94.11950 1 4559 4 chr1D.!!$R1 4558
2 TraesCS1A01G194600 chr1B 380432051 380436736 4685 True 1596.00 2152 93.67875 1 4559 4 chr1B.!!$R1 4558

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
109 110 0.249955 TCCGCAAGATGATGTGCTCA 59.750 50.000 0.00 0.0 38.66 4.26 F
118 119 0.697658 TGATGTGCTCACCCATGGAA 59.302 50.000 15.22 0.0 0.00 3.53 F
1996 2018 0.690762 AAGCTACAACGGTCCCACAT 59.309 50.000 0.00 0.0 0.00 3.21 F
2310 2343 1.539496 GCAGAACGGTCAAGTGGTGTA 60.539 52.381 1.87 0.0 0.00 2.90 F
3378 3544 1.669115 CCACCGTGGACTCAGCAAG 60.669 63.158 12.68 0.0 40.96 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 1721 1.526041 CGCAGCTATTCATGTCTCTGC 59.474 52.381 13.77 13.77 42.30 4.26 R
2055 2077 2.561478 ACCGTAAACATCTGCTGGTT 57.439 45.000 0.00 0.00 38.64 3.67 R
3378 3544 0.743345 CACCGTCCGGATTCTTTCCC 60.743 60.000 7.81 0.00 42.06 3.97 R
3500 3666 1.073199 CTCACGCCAAACTTCCCCT 59.927 57.895 0.00 0.00 0.00 4.79 R
4408 4876 0.394192 CCCAGACAAGAGAGTGTGCA 59.606 55.000 0.00 0.00 31.94 4.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.800315 GCTTGCTGCAATGCTCGTG 60.800 57.895 16.38 3.35 42.31 4.35
94 95 1.734117 GCAGCCAAATGTGTTCCGC 60.734 57.895 0.00 0.00 0.00 5.54
109 110 0.249955 TCCGCAAGATGATGTGCTCA 59.750 50.000 0.00 0.00 38.66 4.26
112 113 0.737219 GCAAGATGATGTGCTCACCC 59.263 55.000 0.00 0.00 36.48 4.61
118 119 0.697658 TGATGTGCTCACCCATGGAA 59.302 50.000 15.22 0.00 0.00 3.53
127 128 3.369400 CCCATGGAAAACGCCGCA 61.369 61.111 15.22 0.00 0.00 5.69
208 209 1.356124 AGCATGTGGAAGTGGAGACT 58.644 50.000 0.00 0.00 0.00 3.24
531 532 2.706190 AGCTGAACAAACACTCCTAGGT 59.294 45.455 9.08 0.00 0.00 3.08
837 845 5.581126 AGATGCTAAATGCCAAATTCGAA 57.419 34.783 0.00 0.00 42.00 3.71
932 940 7.314393 GTTTTGTTTTCCCACTAACTGTAACA 58.686 34.615 0.00 0.00 0.00 2.41
946 954 2.689983 CTGTAACATTCATCCAAGGGGC 59.310 50.000 0.00 0.00 0.00 5.80
1000 1008 7.610305 AGTTCAAGTTGTTCAGGAAAGTAAAGA 59.390 33.333 2.11 0.00 0.00 2.52
1004 1012 5.770162 AGTTGTTCAGGAAAGTAAAGATGGG 59.230 40.000 0.00 0.00 0.00 4.00
1008 1016 4.335416 TCAGGAAAGTAAAGATGGGCTTG 58.665 43.478 0.00 0.00 36.80 4.01
1299 1308 5.975410 CAGTAGCTCTGGTAAACTATTGC 57.025 43.478 0.00 0.00 40.23 3.56
1303 1312 3.264450 AGCTCTGGTAAACTATTGCTGGT 59.736 43.478 0.00 0.00 0.00 4.00
1432 1445 2.154462 CGTTCTCTTTTGGAGGTGCAT 58.846 47.619 0.00 0.00 42.10 3.96
1443 1456 1.674962 GGAGGTGCATGCTGATTTCTC 59.325 52.381 20.33 14.56 0.00 2.87
1553 1567 3.327757 AGGTTAGTGCCAGATCAACAGAA 59.672 43.478 0.00 0.00 0.00 3.02
1707 1721 6.595682 TGGAATTAGCCCTTCTTTATCTGAG 58.404 40.000 0.00 0.00 0.00 3.35
1921 1939 3.070590 AGGTACAATAGGGCCGTATCAAC 59.929 47.826 17.98 14.85 0.00 3.18
1996 2018 0.690762 AAGCTACAACGGTCCCACAT 59.309 50.000 0.00 0.00 0.00 3.21
2034 2056 1.751927 CAAGCATGTCCTCAGCCCC 60.752 63.158 0.00 0.00 0.00 5.80
2055 2077 6.005198 CCCCAAAAGTAATGTAACACACCTA 58.995 40.000 0.00 0.00 0.00 3.08
2078 2100 3.244284 ACCAGCAGATGTTTACGGTTACA 60.244 43.478 0.00 0.00 0.00 2.41
2125 2147 8.848474 AACACTTGTAAGCTAACTAACATGAT 57.152 30.769 0.00 0.00 0.00 2.45
2194 2216 5.698089 TCAGAACTGACAGATTGTTGATCAC 59.302 40.000 10.08 0.00 34.33 3.06
2310 2343 1.539496 GCAGAACGGTCAAGTGGTGTA 60.539 52.381 1.87 0.00 0.00 2.90
2350 2383 6.003326 TCTTTAAGATTGATGTCTGCAACCA 58.997 36.000 0.00 0.00 0.00 3.67
2351 2384 6.489700 TCTTTAAGATTGATGTCTGCAACCAA 59.510 34.615 0.00 0.00 0.00 3.67
2352 2385 6.647334 TTAAGATTGATGTCTGCAACCAAA 57.353 33.333 0.00 0.00 0.00 3.28
2353 2386 5.733620 AAGATTGATGTCTGCAACCAAAT 57.266 34.783 0.00 0.00 0.00 2.32
2354 2387 5.733620 AGATTGATGTCTGCAACCAAATT 57.266 34.783 0.00 0.00 0.00 1.82
2355 2388 6.839124 AGATTGATGTCTGCAACCAAATTA 57.161 33.333 0.00 0.00 0.00 1.40
2356 2389 6.624423 AGATTGATGTCTGCAACCAAATTAC 58.376 36.000 0.00 0.00 0.00 1.89
2357 2390 5.781210 TTGATGTCTGCAACCAAATTACA 57.219 34.783 0.00 0.00 0.00 2.41
2358 2391 5.781210 TGATGTCTGCAACCAAATTACAA 57.219 34.783 0.00 0.00 0.00 2.41
2359 2392 6.154203 TGATGTCTGCAACCAAATTACAAA 57.846 33.333 0.00 0.00 0.00 2.83
2360 2393 6.577103 TGATGTCTGCAACCAAATTACAAAA 58.423 32.000 0.00 0.00 0.00 2.44
2361 2394 6.700960 TGATGTCTGCAACCAAATTACAAAAG 59.299 34.615 0.00 0.00 0.00 2.27
2362 2395 4.808364 TGTCTGCAACCAAATTACAAAAGC 59.192 37.500 0.00 0.00 0.00 3.51
2363 2396 5.049828 GTCTGCAACCAAATTACAAAAGCT 58.950 37.500 0.00 0.00 0.00 3.74
2364 2397 5.049167 TCTGCAACCAAATTACAAAAGCTG 58.951 37.500 0.00 0.00 0.00 4.24
2365 2398 4.764172 TGCAACCAAATTACAAAAGCTGT 58.236 34.783 0.00 0.00 42.47 4.40
2366 2399 4.569966 TGCAACCAAATTACAAAAGCTGTG 59.430 37.500 0.00 0.00 39.20 3.66
2367 2400 4.808364 GCAACCAAATTACAAAAGCTGTGA 59.192 37.500 4.72 0.00 39.20 3.58
2368 2401 5.293079 GCAACCAAATTACAAAAGCTGTGAA 59.707 36.000 4.72 0.00 39.20 3.18
2369 2402 6.704819 CAACCAAATTACAAAAGCTGTGAAC 58.295 36.000 4.72 0.00 39.20 3.18
2370 2403 5.971763 ACCAAATTACAAAAGCTGTGAACA 58.028 33.333 4.72 0.00 39.20 3.18
2371 2404 5.810074 ACCAAATTACAAAAGCTGTGAACAC 59.190 36.000 4.72 0.00 39.20 3.32
2372 2405 5.234116 CCAAATTACAAAAGCTGTGAACACC 59.766 40.000 4.72 0.00 39.20 4.16
2373 2406 5.590530 AATTACAAAAGCTGTGAACACCA 57.409 34.783 4.72 0.00 39.20 4.17
2374 2407 5.590530 ATTACAAAAGCTGTGAACACCAA 57.409 34.783 4.72 0.00 39.20 3.67
2375 2408 3.951775 ACAAAAGCTGTGAACACCAAA 57.048 38.095 4.72 0.00 36.69 3.28
2376 2409 3.584834 ACAAAAGCTGTGAACACCAAAC 58.415 40.909 4.72 0.00 36.69 2.93
2377 2410 3.006323 ACAAAAGCTGTGAACACCAAACA 59.994 39.130 4.72 0.00 36.69 2.83
2378 2411 4.183101 CAAAAGCTGTGAACACCAAACAT 58.817 39.130 2.46 0.00 0.00 2.71
2379 2412 4.470334 AAAGCTGTGAACACCAAACATT 57.530 36.364 2.46 0.00 0.00 2.71
2380 2413 3.441496 AGCTGTGAACACCAAACATTG 57.559 42.857 2.46 0.00 0.00 2.82
2381 2414 1.860326 GCTGTGAACACCAAACATTGC 59.140 47.619 2.46 0.00 0.00 3.56
2382 2415 2.738000 GCTGTGAACACCAAACATTGCA 60.738 45.455 2.46 0.00 0.00 4.08
2383 2416 3.719924 CTGTGAACACCAAACATTGCAT 58.280 40.909 2.46 0.00 0.00 3.96
2384 2417 3.715495 TGTGAACACCAAACATTGCATC 58.285 40.909 2.46 0.00 0.00 3.91
2385 2418 3.384146 TGTGAACACCAAACATTGCATCT 59.616 39.130 2.46 0.00 0.00 2.90
2386 2419 4.141981 TGTGAACACCAAACATTGCATCTT 60.142 37.500 2.46 0.00 0.00 2.40
2387 2420 4.810491 GTGAACACCAAACATTGCATCTTT 59.190 37.500 0.00 0.00 0.00 2.52
2388 2421 5.982516 GTGAACACCAAACATTGCATCTTTA 59.017 36.000 0.00 0.00 0.00 1.85
2389 2422 6.478344 GTGAACACCAAACATTGCATCTTTAA 59.522 34.615 0.00 0.00 0.00 1.52
2390 2423 6.700960 TGAACACCAAACATTGCATCTTTAAG 59.299 34.615 0.00 0.00 0.00 1.85
2391 2424 6.403866 ACACCAAACATTGCATCTTTAAGA 57.596 33.333 0.00 0.00 0.00 2.10
2392 2425 6.996509 ACACCAAACATTGCATCTTTAAGAT 58.003 32.000 0.99 0.99 34.74 2.40
2393 2426 7.444299 ACACCAAACATTGCATCTTTAAGATT 58.556 30.769 4.51 0.00 31.32 2.40
2394 2427 7.385752 ACACCAAACATTGCATCTTTAAGATTG 59.614 33.333 4.51 3.98 31.32 2.67
2395 2428 7.599621 CACCAAACATTGCATCTTTAAGATTGA 59.400 33.333 4.51 0.00 31.32 2.57
2396 2429 8.316214 ACCAAACATTGCATCTTTAAGATTGAT 58.684 29.630 4.51 0.00 31.32 2.57
2447 2480 8.918658 GTGAACACGTATTTGACTGATAAAGTA 58.081 33.333 0.00 0.00 40.07 2.24
2593 2652 5.030147 AGGGATATGTGACTGACCAAAGTA 58.970 41.667 0.00 0.00 0.00 2.24
2594 2653 5.667626 AGGGATATGTGACTGACCAAAGTAT 59.332 40.000 0.00 0.00 0.00 2.12
2596 2655 5.692204 GGATATGTGACTGACCAAAGTATCG 59.308 44.000 0.00 0.00 0.00 2.92
2669 2728 9.761504 ATGCTATCATGCAGATATCAGTAATAC 57.238 33.333 5.32 0.00 46.71 1.89
2747 2806 3.440173 AGTGAATAAACATTCAGGCCACG 59.560 43.478 5.01 0.00 40.77 4.94
2780 2944 9.770097 AACTTTATCTCATGTATGACTGTATGG 57.230 33.333 0.00 0.00 32.50 2.74
2899 3063 7.559486 CAGATAAGCTGGGCTATGACATAATA 58.441 38.462 0.00 0.00 38.25 0.98
2919 3083 6.697641 AATAACAAGTTACCTTCCCTCTCA 57.302 37.500 0.00 0.00 0.00 3.27
2948 3114 6.710597 ACAAGTAGAAGAAAAGGGGAAAAC 57.289 37.500 0.00 0.00 0.00 2.43
2950 3116 6.666113 ACAAGTAGAAGAAAAGGGGAAAACAA 59.334 34.615 0.00 0.00 0.00 2.83
2990 3156 3.379372 GCATACCAACAGCAATCATGAGT 59.621 43.478 0.09 0.00 0.00 3.41
3032 3198 8.321650 AGAGCTCATCTTTCTTGAACTAAAAG 57.678 34.615 17.77 0.00 32.99 2.27
3056 3222 8.807948 AGTACAATTACATGTTTCAAGCCTAT 57.192 30.769 2.30 0.00 34.75 2.57
3125 3291 2.869233 TTGCAGCCAAGAAAGTGAAC 57.131 45.000 0.00 0.00 0.00 3.18
3136 3302 7.390162 AGCCAAGAAAGTGAACAAATTGAAAAA 59.610 29.630 0.00 0.00 0.00 1.94
3236 3402 6.311935 CAGCAGCAATTAACAGCAACAAATAT 59.688 34.615 0.00 0.00 0.00 1.28
3274 3440 1.966451 CCACCTGTTTCACCTCCGC 60.966 63.158 0.00 0.00 0.00 5.54
3369 3535 2.454336 ACATATCTCTCCACCGTGGA 57.546 50.000 19.39 19.39 45.98 4.02
3378 3544 1.669115 CCACCGTGGACTCAGCAAG 60.669 63.158 12.68 0.00 40.96 4.01
3500 3666 2.124529 TGGCAGCGGTGACAACAA 60.125 55.556 23.18 0.00 39.49 2.83
3510 3676 2.384828 GGTGACAACAAGGGGAAGTTT 58.615 47.619 0.00 0.00 0.00 2.66
3912 4078 3.246112 TGGTTGTGGACGGGAGGG 61.246 66.667 0.00 0.00 0.00 4.30
4252 4713 1.239347 GGATTTAGGAGGATTGGCGC 58.761 55.000 0.00 0.00 0.00 6.53
4408 4876 0.179034 GAATGGAGAAGCAGGCCGAT 60.179 55.000 0.00 0.00 0.00 4.18
4409 4877 0.465097 AATGGAGAAGCAGGCCGATG 60.465 55.000 0.00 0.00 0.00 3.84
4425 4893 1.991264 CGATGCACACTCTCTTGTCTG 59.009 52.381 0.00 0.00 0.00 3.51
4487 4955 2.729479 CGGAGTCTCTGCCAGCCAT 61.729 63.158 0.00 0.00 0.00 4.40
4504 4988 0.531532 CATTGGCCCTAGCTGTCTCG 60.532 60.000 0.00 0.00 39.73 4.04
4545 5029 1.414550 TCGTTGGACAATCACACCAGA 59.585 47.619 0.00 0.00 35.08 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.032376 TCCACGAGCATTGCAGCA 59.968 55.556 11.91 0.00 36.85 4.41
94 95 2.118313 TGGGTGAGCACATCATCTTG 57.882 50.000 2.75 0.00 40.92 3.02
109 110 3.370231 GCGGCGTTTTCCATGGGT 61.370 61.111 13.02 0.00 0.00 4.51
112 113 2.501650 CGTGCGGCGTTTTCCATG 60.502 61.111 9.37 0.00 35.54 3.66
127 128 2.430546 GATCTTCATGATCGCCTCGT 57.569 50.000 0.00 0.00 41.68 4.18
208 209 1.142667 TCATGTTTCACCTGCCTGACA 59.857 47.619 0.00 0.00 0.00 3.58
932 940 1.362237 TCAAAGGCCCCTTGGATGAAT 59.638 47.619 13.74 0.00 36.26 2.57
946 954 4.398319 TCTTTTTCCTGCTACCTCAAAGG 58.602 43.478 0.00 0.00 42.49 3.11
1000 1008 3.009916 ACATTCTTCAGTCTCAAGCCCAT 59.990 43.478 0.00 0.00 0.00 4.00
1004 1012 4.997395 TGGTAACATTCTTCAGTCTCAAGC 59.003 41.667 0.00 0.00 46.17 4.01
1299 1308 3.928375 GCTATTGTTTGATTGGCAACCAG 59.072 43.478 0.00 0.00 35.91 4.00
1303 1312 3.995705 GCTTGCTATTGTTTGATTGGCAA 59.004 39.130 0.68 0.68 36.86 4.52
1432 1445 3.817084 CAGTTCTTGTGGAGAAATCAGCA 59.183 43.478 0.00 0.00 45.59 4.41
1443 1456 7.360776 GCTTTCTTTATCTCTCAGTTCTTGTGG 60.361 40.741 0.00 0.00 0.00 4.17
1553 1567 2.965572 AACTGTGTGTTGCAAGCAAT 57.034 40.000 11.00 0.00 38.28 3.56
1656 1670 9.888878 GTAAGCATTAGTTAGATCGTGTACATA 57.111 33.333 0.00 0.00 0.00 2.29
1707 1721 1.526041 CGCAGCTATTCATGTCTCTGC 59.474 52.381 13.77 13.77 42.30 4.26
1921 1939 7.475015 CACCAGGACAATAACACATCTTATTG 58.525 38.462 0.00 9.21 44.56 1.90
1969 1991 3.071479 GACCGTTGTAGCTTCATCCAAA 58.929 45.455 0.00 0.00 0.00 3.28
1996 2018 6.069673 TGCTTGAAGTTCCCTCCAGATTAATA 60.070 38.462 0.00 0.00 0.00 0.98
2034 2056 7.932335 TGGTTAGGTGTGTTACATTACTTTTG 58.068 34.615 0.00 0.00 0.00 2.44
2055 2077 2.561478 ACCGTAAACATCTGCTGGTT 57.439 45.000 0.00 0.00 38.64 3.67
2310 2343 6.815089 TCTTAAAGATGCAATGTTTGGTGTT 58.185 32.000 0.00 0.00 40.34 3.32
2350 2383 5.971763 TGGTGTTCACAGCTTTTGTAATTT 58.028 33.333 10.33 0.00 44.12 1.82
2351 2384 5.590530 TGGTGTTCACAGCTTTTGTAATT 57.409 34.783 10.33 0.00 44.12 1.40
2352 2385 5.590530 TTGGTGTTCACAGCTTTTGTAAT 57.409 34.783 10.33 0.00 44.12 1.89
2353 2386 5.164954 GTTTGGTGTTCACAGCTTTTGTAA 58.835 37.500 10.33 0.00 44.12 2.41
2354 2387 4.218635 TGTTTGGTGTTCACAGCTTTTGTA 59.781 37.500 10.33 0.00 44.12 2.41
2355 2388 3.006323 TGTTTGGTGTTCACAGCTTTTGT 59.994 39.130 10.33 0.00 44.12 2.83
2356 2389 3.583806 TGTTTGGTGTTCACAGCTTTTG 58.416 40.909 10.33 0.00 44.12 2.44
2357 2390 3.951775 TGTTTGGTGTTCACAGCTTTT 57.048 38.095 10.33 0.00 44.12 2.27
2358 2391 4.183101 CAATGTTTGGTGTTCACAGCTTT 58.817 39.130 10.33 0.00 44.12 3.51
2359 2392 3.784338 CAATGTTTGGTGTTCACAGCTT 58.216 40.909 10.33 0.00 44.12 3.74
2360 2393 2.481795 GCAATGTTTGGTGTTCACAGCT 60.482 45.455 10.33 0.00 44.12 4.24
2361 2394 1.860326 GCAATGTTTGGTGTTCACAGC 59.140 47.619 2.05 2.05 44.06 4.40
2362 2395 3.162202 TGCAATGTTTGGTGTTCACAG 57.838 42.857 5.32 0.00 0.00 3.66
2363 2396 3.384146 AGATGCAATGTTTGGTGTTCACA 59.616 39.130 5.32 0.00 0.00 3.58
2364 2397 3.981211 AGATGCAATGTTTGGTGTTCAC 58.019 40.909 0.00 0.00 0.00 3.18
2365 2398 4.669206 AAGATGCAATGTTTGGTGTTCA 57.331 36.364 0.00 0.00 0.00 3.18
2366 2399 6.922957 TCTTAAAGATGCAATGTTTGGTGTTC 59.077 34.615 0.00 0.00 40.34 3.18
2367 2400 6.815089 TCTTAAAGATGCAATGTTTGGTGTT 58.185 32.000 0.00 0.00 40.34 3.32
2368 2401 6.403866 TCTTAAAGATGCAATGTTTGGTGT 57.596 33.333 0.00 0.00 40.34 4.16
2369 2402 7.599621 TCAATCTTAAAGATGCAATGTTTGGTG 59.400 33.333 0.00 0.00 40.34 4.17
2370 2403 7.669427 TCAATCTTAAAGATGCAATGTTTGGT 58.331 30.769 0.00 0.00 40.34 3.67
2371 2404 8.600625 CATCAATCTTAAAGATGCAATGTTTGG 58.399 33.333 0.00 0.00 40.34 3.28
2372 2405 9.146984 ACATCAATCTTAAAGATGCAATGTTTG 57.853 29.630 0.00 0.00 40.34 2.93
2373 2406 9.362539 GACATCAATCTTAAAGATGCAATGTTT 57.637 29.630 0.00 0.00 42.90 2.83
2374 2407 8.746530 AGACATCAATCTTAAAGATGCAATGTT 58.253 29.630 0.00 0.00 42.12 2.71
2375 2408 8.188799 CAGACATCAATCTTAAAGATGCAATGT 58.811 33.333 0.00 0.00 42.12 2.71
2376 2409 7.167635 GCAGACATCAATCTTAAAGATGCAATG 59.832 37.037 0.00 0.00 42.12 2.82
2377 2410 7.147966 TGCAGACATCAATCTTAAAGATGCAAT 60.148 33.333 0.00 0.00 42.12 3.56
2378 2411 6.151480 TGCAGACATCAATCTTAAAGATGCAA 59.849 34.615 0.00 0.00 42.12 4.08
2379 2412 5.648960 TGCAGACATCAATCTTAAAGATGCA 59.351 36.000 0.00 0.00 42.12 3.96
2380 2413 6.127810 TGCAGACATCAATCTTAAAGATGC 57.872 37.500 0.00 0.00 42.12 3.91
2381 2414 6.971184 GGTTGCAGACATCAATCTTAAAGATG 59.029 38.462 0.00 0.00 43.56 2.90
2382 2415 6.660521 TGGTTGCAGACATCAATCTTAAAGAT 59.339 34.615 0.00 0.00 36.28 2.40
2383 2416 6.003326 TGGTTGCAGACATCAATCTTAAAGA 58.997 36.000 0.00 0.00 0.00 2.52
2384 2417 6.258230 TGGTTGCAGACATCAATCTTAAAG 57.742 37.500 0.00 0.00 0.00 1.85
2385 2418 6.647334 TTGGTTGCAGACATCAATCTTAAA 57.353 33.333 0.00 0.00 0.00 1.52
2386 2419 6.647334 TTTGGTTGCAGACATCAATCTTAA 57.353 33.333 0.00 0.00 0.00 1.85
2387 2420 6.839124 ATTTGGTTGCAGACATCAATCTTA 57.161 33.333 0.00 0.00 0.00 2.10
2388 2421 5.733620 ATTTGGTTGCAGACATCAATCTT 57.266 34.783 0.00 0.00 0.00 2.40
2389 2422 5.733620 AATTTGGTTGCAGACATCAATCT 57.266 34.783 0.00 0.00 0.00 2.40
2390 2423 6.389091 TGTAATTTGGTTGCAGACATCAATC 58.611 36.000 0.00 0.00 0.00 2.67
2391 2424 6.343716 TGTAATTTGGTTGCAGACATCAAT 57.656 33.333 0.00 0.00 0.00 2.57
2392 2425 5.781210 TGTAATTTGGTTGCAGACATCAA 57.219 34.783 0.00 0.00 0.00 2.57
2393 2426 5.781210 TTGTAATTTGGTTGCAGACATCA 57.219 34.783 0.00 0.00 33.85 3.07
2394 2427 6.346838 GCTTTTGTAATTTGGTTGCAGACATC 60.347 38.462 0.00 0.00 33.85 3.06
2395 2428 5.466393 GCTTTTGTAATTTGGTTGCAGACAT 59.534 36.000 0.00 0.00 33.85 3.06
2396 2429 4.808364 GCTTTTGTAATTTGGTTGCAGACA 59.192 37.500 0.00 0.00 33.85 3.41
2447 2480 9.807921 TTGAAGAAGATAACCTTTCCATAACTT 57.192 29.630 0.00 0.00 34.68 2.66
2594 2653 2.066262 GAAGCAGATCGGTTGTTTCGA 58.934 47.619 6.70 0.00 41.04 3.71
2596 2655 3.896648 TTGAAGCAGATCGGTTGTTTC 57.103 42.857 6.70 5.24 36.62 2.78
2722 2781 5.048083 GTGGCCTGAATGTTTATTCACTTCA 60.048 40.000 3.32 0.00 45.77 3.02
2747 2806 9.922305 GTCATACATGAGATAAAGTTTGTTAGC 57.078 33.333 0.00 0.00 37.51 3.09
2780 2944 2.064762 CTATCTTGCGCTAGACATGCC 58.935 52.381 23.51 0.00 0.00 4.40
2919 3083 9.429109 TTCCCCTTTTCTTCTACTTGTATTTTT 57.571 29.630 0.00 0.00 0.00 1.94
2948 3114 6.906157 ATGCCTATTCAGGGAACATAATTG 57.094 37.500 0.00 0.00 46.62 2.32
2950 3116 6.045459 TGGTATGCCTATTCAGGGAACATAAT 59.955 38.462 0.16 0.00 46.62 1.28
2990 3156 7.984422 TGAGCTCTTTCTGACAAATATTTCA 57.016 32.000 16.19 0.00 0.00 2.69
3032 3198 8.129211 GGATAGGCTTGAAACATGTAATTGTAC 58.871 37.037 0.00 0.00 0.00 2.90
3056 3222 6.266786 TGTTGTAGTGTAGATTCTTGAGTGGA 59.733 38.462 0.00 0.00 0.00 4.02
3236 3402 1.000506 GGTTGTAGCTCTCGACACCAA 59.999 52.381 0.00 0.00 0.00 3.67
3274 3440 1.956477 GATGGGAATTGGTTCATCCGG 59.044 52.381 0.00 0.00 39.52 5.14
3344 3510 3.508012 ACGGTGGAGAGATATGTAGCATC 59.492 47.826 0.00 0.00 0.00 3.91
3369 3535 2.616510 CGGATTCTTTCCCTTGCTGAGT 60.617 50.000 0.00 0.00 42.06 3.41
3378 3544 0.743345 CACCGTCCGGATTCTTTCCC 60.743 60.000 7.81 0.00 42.06 3.97
3500 3666 1.073199 CTCACGCCAAACTTCCCCT 59.927 57.895 0.00 0.00 0.00 4.79
3591 3757 2.585247 CCTTCGCCGACCGGATTC 60.585 66.667 9.46 0.00 37.50 2.52
4408 4876 0.394192 CCCAGACAAGAGAGTGTGCA 59.606 55.000 0.00 0.00 31.94 4.57
4409 4877 0.952984 GCCCAGACAAGAGAGTGTGC 60.953 60.000 0.00 0.00 31.94 4.57
4425 4893 2.556287 CGAAAACGCACTCAGCCC 59.444 61.111 0.00 0.00 41.38 5.19
4443 4911 2.833631 ACCCACGAGTAAACAGGAAG 57.166 50.000 0.00 0.00 0.00 3.46
4471 4939 0.747283 CCAATGGCTGGCAGAGACTC 60.747 60.000 20.86 0.00 38.76 3.36
4487 4955 3.019003 GCGAGACAGCTAGGGCCAA 62.019 63.158 6.18 0.00 39.73 4.52
4504 4988 1.128692 GCGACATGTCAAACCAGTAGC 59.871 52.381 24.93 12.87 0.00 3.58


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

AutoCloner maintained by Alex Coulton.