Multiple sequence alignment - TraesCS5B01G388200

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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 TraesCS5B01G388200 chr5B 100.000 3712 0 0 1 3712 567151807 567155518 0.000000e+00 6855.0
1 TraesCS5B01G388200 chr5A 89.269 3159 213 67 88 3185 581298758 581301851 0.000000e+00 3840.0
2 TraesCS5B01G388200 chr5A 95.257 506 20 3 3207 3712 581301845 581302346 0.000000e+00 798.0
3 TraesCS5B01G388200 chr5D 87.831 2342 197 43 689 3001 461211609 461213891 0.000000e+00 2665.0
4 TraesCS5B01G388200 chr5D 95.166 662 27 3 3053 3712 461214311 461214969 0.000000e+00 1040.0
5 TraesCS5B01G388200 chr5D 88.559 673 56 14 8 674 461210832 461211489 0.000000e+00 797.0
6 TraesCS5B01G388200 chr5D 96.491 57 2 0 2998 3054 461214146 461214202 1.100000e-15 95.3
7 TraesCS5B01G388200 chrUn 94.186 86 5 0 2278 2363 50872451 50872366 8.370000e-27 132.0
8 TraesCS5B01G388200 chrUn 94.186 86 5 0 2278 2363 50890363 50890278 8.370000e-27 132.0
9 TraesCS5B01G388200 chrUn 91.250 80 7 0 2284 2363 35292027 35292106 3.920000e-20 110.0
10 TraesCS5B01G388200 chrUn 91.250 80 7 0 2284 2363 319858106 319858027 3.920000e-20 110.0
11 TraesCS5B01G388200 chrUn 91.250 80 7 0 2284 2363 331092036 331092115 3.920000e-20 110.0
12 TraesCS5B01G388200 chr3A 89.011 91 9 1 2273 2363 10690972 10690883 1.090000e-20 111.0
13 TraesCS5B01G388200 chr4D 89.535 86 9 0 2280 2365 32768478 32768393 3.920000e-20 110.0
14 TraesCS5B01G388200 chr1B 89.412 85 8 1 2280 2363 667091045 667091129 5.070000e-19 106.0
15 TraesCS5B01G388200 chr7A 100.000 32 0 0 2144 2175 450094693 450094662 4.000000e-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 TraesCS5B01G388200 chr5B 567151807 567155518 3711 False 6855.000 6855 100.00000 1 3712 1 chr5B.!!$F1 3711
1 TraesCS5B01G388200 chr5A 581298758 581302346 3588 False 2319.000 3840 92.26300 88 3712 2 chr5A.!!$F1 3624
2 TraesCS5B01G388200 chr5D 461210832 461214969 4137 False 1149.325 2665 92.01175 8 3712 4 chr5D.!!$F1 3704

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
319 321 0.036164 TCACCACACATTCCCCTTCG 59.964 55.0 0.0 0.0 0.00 3.79 F
1273 1382 0.037590 TTTTCCACGGACCTCCCATG 59.962 55.0 0.0 0.0 34.14 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1648 0.478507 AGCACTAACAAACCCCTGCT 59.521 50.000 0.00 0.0 0.0 4.24 R
2885 3041 1.003331 CTAAACGGCGAAAAGTGTGCA 60.003 47.619 16.62 0.0 0.0 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
82 83 5.479716 ACATCCAAACGGATTTATTCGTC 57.520 39.130 0.00 0.00 41.64 4.20
111 112 2.405618 ATAGCATCTCCTGGGCTACA 57.594 50.000 4.79 0.00 42.36 2.74
162 163 4.166888 GCGATGGGCTGCTCTCCA 62.167 66.667 0.00 0.00 39.11 3.86
234 236 1.923148 GAATTTCCCCTCCCTTCTCCA 59.077 52.381 0.00 0.00 0.00 3.86
251 253 3.118454 ACAGCATTTCCGTCGCCG 61.118 61.111 0.00 0.00 0.00 6.46
252 254 4.520846 CAGCATTTCCGTCGCCGC 62.521 66.667 0.00 0.00 0.00 6.53
254 256 3.799755 GCATTTCCGTCGCCGCTT 61.800 61.111 0.00 0.00 0.00 4.68
255 257 2.399611 CATTTCCGTCGCCGCTTC 59.600 61.111 0.00 0.00 0.00 3.86
256 258 2.100631 CATTTCCGTCGCCGCTTCT 61.101 57.895 0.00 0.00 0.00 2.85
267 269 1.265905 CGCCGCTTCTTTTTAACCAGT 59.734 47.619 0.00 0.00 0.00 4.00
286 288 1.875514 GTAAACCCTCCACGGTGTTTC 59.124 52.381 7.45 0.00 37.36 2.78
310 312 1.434188 TTCACCTCCTCACCACACAT 58.566 50.000 0.00 0.00 0.00 3.21
319 321 0.036164 TCACCACACATTCCCCTTCG 59.964 55.000 0.00 0.00 0.00 3.79
341 343 1.202463 CGTCTTCCTGCGGATTCTCAT 60.202 52.381 0.00 0.00 0.00 2.90
342 344 2.739932 CGTCTTCCTGCGGATTCTCATT 60.740 50.000 0.00 0.00 0.00 2.57
344 346 2.501316 TCTTCCTGCGGATTCTCATTCA 59.499 45.455 0.00 0.00 0.00 2.57
345 347 2.609427 TCCTGCGGATTCTCATTCAG 57.391 50.000 0.00 0.00 0.00 3.02
346 348 0.942962 CCTGCGGATTCTCATTCAGC 59.057 55.000 0.00 0.00 35.27 4.26
347 349 1.474677 CCTGCGGATTCTCATTCAGCT 60.475 52.381 0.00 0.00 35.65 4.24
349 351 2.283298 TGCGGATTCTCATTCAGCTTC 58.717 47.619 0.00 0.00 35.65 3.86
350 352 2.093288 TGCGGATTCTCATTCAGCTTCT 60.093 45.455 0.00 0.00 35.65 2.85
351 353 2.941720 GCGGATTCTCATTCAGCTTCTT 59.058 45.455 0.00 0.00 32.49 2.52
352 354 3.002144 GCGGATTCTCATTCAGCTTCTTC 59.998 47.826 0.00 0.00 32.49 2.87
353 355 3.559242 CGGATTCTCATTCAGCTTCTTCC 59.441 47.826 0.00 0.00 0.00 3.46
354 356 3.559242 GGATTCTCATTCAGCTTCTTCCG 59.441 47.826 0.00 0.00 0.00 4.30
355 357 2.680312 TCTCATTCAGCTTCTTCCGG 57.320 50.000 0.00 0.00 0.00 5.14
356 358 1.012841 CTCATTCAGCTTCTTCCGGC 58.987 55.000 0.00 0.00 0.00 6.13
357 359 0.392998 TCATTCAGCTTCTTCCGGCC 60.393 55.000 0.00 0.00 0.00 6.13
358 360 1.450312 ATTCAGCTTCTTCCGGCCG 60.450 57.895 21.04 21.04 0.00 6.13
359 361 4.760047 TCAGCTTCTTCCGGCCGC 62.760 66.667 22.85 3.50 0.00 6.53
389 391 2.439701 CTCCTCCGGCGGTACTGA 60.440 66.667 27.32 16.18 0.00 3.41
393 395 1.515954 CTCCGGCGGTACTGATTGT 59.484 57.895 27.32 0.00 0.00 2.71
396 398 0.108329 CCGGCGGTACTGATTGTTCT 60.108 55.000 19.97 0.00 0.00 3.01
397 399 1.674817 CCGGCGGTACTGATTGTTCTT 60.675 52.381 19.97 0.00 0.00 2.52
400 402 2.930682 GGCGGTACTGATTGTTCTTCTC 59.069 50.000 5.68 0.00 0.00 2.87
402 404 3.616560 GCGGTACTGATTGTTCTTCTCCA 60.617 47.826 5.68 0.00 0.00 3.86
404 406 4.254492 GGTACTGATTGTTCTTCTCCACC 58.746 47.826 0.00 0.00 0.00 4.61
411 413 1.144913 TGTTCTTCTCCACCCCCTTTG 59.855 52.381 0.00 0.00 0.00 2.77
412 414 0.777446 TTCTTCTCCACCCCCTTTGG 59.223 55.000 0.00 0.00 35.18 3.28
422 424 1.068121 CCCCCTTTGGTTCTCTGTCT 58.932 55.000 0.00 0.00 0.00 3.41
426 428 3.319122 CCCCTTTGGTTCTCTGTCTTTTG 59.681 47.826 0.00 0.00 0.00 2.44
429 431 4.261363 CCTTTGGTTCTCTGTCTTTTGAGC 60.261 45.833 0.00 0.00 0.00 4.26
431 433 3.470709 TGGTTCTCTGTCTTTTGAGCTG 58.529 45.455 0.00 0.00 0.00 4.24
486 488 0.318441 CGATCCGGCATGTGGAGTAT 59.682 55.000 13.23 0.00 39.30 2.12
542 546 2.028020 AGAATCTCCAGTTTCGTGTCCC 60.028 50.000 0.00 0.00 0.00 4.46
559 563 4.216472 GTGTCCCTTCCAAGATTTTCACTC 59.784 45.833 0.00 0.00 0.00 3.51
562 566 3.412386 CCTTCCAAGATTTTCACTCGGT 58.588 45.455 0.00 0.00 0.00 4.69
564 568 4.083271 CCTTCCAAGATTTTCACTCGGTTC 60.083 45.833 0.00 0.00 0.00 3.62
597 601 0.179113 CGGGAAATGGCCGAATTTGG 60.179 55.000 7.44 7.44 29.89 3.28
643 647 7.198390 ACTGATTTATACAACTTGATGCATGC 58.802 34.615 11.82 11.82 0.00 4.06
655 659 2.294979 GATGCATGCTGTCCATCTTGA 58.705 47.619 20.33 0.00 34.12 3.02
680 764 2.271800 GCATATCCTAGTATGGCGCAC 58.728 52.381 10.83 0.00 33.61 5.34
682 766 3.515630 CATATCCTAGTATGGCGCACTG 58.484 50.000 10.83 0.00 0.00 3.66
721 828 9.165035 TGGAAATCTCAAAAATAAAATGATGGC 57.835 29.630 0.00 0.00 0.00 4.40
723 830 8.776376 AAATCTCAAAAATAAAATGATGGCGT 57.224 26.923 0.00 0.00 0.00 5.68
727 834 8.181573 TCTCAAAAATAAAATGATGGCGTAGTC 58.818 33.333 0.00 0.00 0.00 2.59
731 838 5.991328 ATAAAATGATGGCGTAGTCTGTG 57.009 39.130 0.00 0.00 0.00 3.66
739 847 1.669211 GGCGTAGTCTGTGGAGTGTTC 60.669 57.143 0.00 0.00 0.00 3.18
740 848 1.269998 GCGTAGTCTGTGGAGTGTTCT 59.730 52.381 0.00 0.00 0.00 3.01
753 861 6.094061 GTGGAGTGTTCTAGTAGCTTGTAAG 58.906 44.000 0.00 0.00 0.00 2.34
754 862 5.773680 TGGAGTGTTCTAGTAGCTTGTAAGT 59.226 40.000 0.00 0.00 0.00 2.24
758 866 8.366671 AGTGTTCTAGTAGCTTGTAAGTTTTG 57.633 34.615 0.00 0.00 0.00 2.44
760 868 8.488764 GTGTTCTAGTAGCTTGTAAGTTTTGAG 58.511 37.037 0.00 0.00 0.00 3.02
764 872 6.546972 AGTAGCTTGTAAGTTTTGAGCTTC 57.453 37.500 10.54 7.04 43.02 3.86
774 882 7.701924 TGTAAGTTTTGAGCTTCAAATTCAGTG 59.298 33.333 10.72 0.00 44.75 3.66
819 928 2.038033 TCTTTGTGGGTAGTACAGCACC 59.962 50.000 2.06 0.00 0.00 5.01
820 929 0.319083 TTGTGGGTAGTACAGCACCG 59.681 55.000 2.06 0.00 35.53 4.94
824 933 1.153628 GGTAGTACAGCACCGGCAG 60.154 63.158 0.00 0.00 44.61 4.85
874 983 5.717119 ATAATAGTTTTGGAGCCCTGAGT 57.283 39.130 0.00 0.00 0.00 3.41
875 984 4.388577 AATAGTTTTGGAGCCCTGAGTT 57.611 40.909 0.00 0.00 0.00 3.01
965 1074 0.455633 CTGTTGCTGGAGAAATGCGC 60.456 55.000 0.00 0.00 0.00 6.09
991 1100 1.302752 TTGCCGCAGCTTGATGAGT 60.303 52.632 0.00 0.00 40.80 3.41
1170 1279 3.254166 AGCCACACATTGTTTCTAGCTTG 59.746 43.478 0.00 0.00 0.00 4.01
1194 1303 6.550108 TGAGAGTTAACTTTACCAGAGTCAGT 59.450 38.462 10.02 0.00 0.00 3.41
1231 1340 8.589338 AGAGAAGCTTAAATGAGAGAACTACAA 58.411 33.333 0.00 0.00 0.00 2.41
1262 1371 1.662122 GGTACGGTATGCTTTTCCACG 59.338 52.381 0.00 0.00 0.00 4.94
1270 1379 1.674651 GCTTTTCCACGGACCTCCC 60.675 63.158 0.00 0.00 0.00 4.30
1273 1382 0.037590 TTTTCCACGGACCTCCCATG 59.962 55.000 0.00 0.00 34.14 3.66
1275 1384 1.836999 TTCCACGGACCTCCCATGTG 61.837 60.000 0.00 0.00 34.14 3.21
1277 1386 1.374947 CACGGACCTCCCATGTGTT 59.625 57.895 0.00 0.00 34.14 3.32
1278 1387 0.955428 CACGGACCTCCCATGTGTTG 60.955 60.000 0.00 0.00 34.14 3.33
1279 1388 1.125093 ACGGACCTCCCATGTGTTGA 61.125 55.000 0.00 0.00 34.14 3.18
1281 1390 1.340017 CGGACCTCCCATGTGTTGAAT 60.340 52.381 0.00 0.00 34.14 2.57
1292 1402 5.404946 CCATGTGTTGAATTCTCAATCACC 58.595 41.667 7.05 0.00 43.39 4.02
1293 1403 4.747540 TGTGTTGAATTCTCAATCACCG 57.252 40.909 7.05 0.00 43.39 4.94
1302 1412 7.881142 TGAATTCTCAATCACCGTTTGTTTAT 58.119 30.769 7.05 0.00 0.00 1.40
1303 1413 9.004717 TGAATTCTCAATCACCGTTTGTTTATA 57.995 29.630 7.05 0.00 0.00 0.98
1305 1415 9.787532 AATTCTCAATCACCGTTTGTTTATATG 57.212 29.630 0.00 0.00 0.00 1.78
1321 1431 7.946207 TGTTTATATGTGAACCATTGTGTTGT 58.054 30.769 0.00 0.00 34.86 3.32
1323 1433 7.517614 TTATATGTGAACCATTGTGTTGTGT 57.482 32.000 0.00 0.00 34.86 3.72
1351 1461 4.335082 TCGGTTTCATGTTAATGCTTCG 57.665 40.909 0.00 0.00 33.47 3.79
1354 1464 4.377943 CGGTTTCATGTTAATGCTTCGTCA 60.378 41.667 0.00 0.00 33.47 4.35
1357 1467 6.403636 GGTTTCATGTTAATGCTTCGTCAGAT 60.404 38.462 0.00 0.00 33.47 2.90
1372 1482 0.820226 CAGATGAGGACTTCCGCTCA 59.180 55.000 0.45 0.00 42.08 4.26
1414 1524 6.203723 CCAGCCTATTCAAGCAGTATAAGAAC 59.796 42.308 0.00 0.00 0.00 3.01
1447 1557 5.302059 TCGAGGAGGTGGAGATAACATAAAG 59.698 44.000 0.00 0.00 0.00 1.85
1454 1564 6.998673 AGGTGGAGATAACATAAAGGTATTGC 59.001 38.462 0.00 0.00 27.68 3.56
1648 1769 0.257039 ATCGAAGGCCTGCAATCCTT 59.743 50.000 12.53 16.48 44.80 3.36
1709 1830 9.461312 TTTGAGGTTAGCATGTTCAAATATACT 57.539 29.630 0.00 0.00 34.04 2.12
1739 1861 9.726438 AATTAGTCTGCTTCTGTTTACAACTAT 57.274 29.630 0.00 0.00 0.00 2.12
1847 1969 2.107950 TTGATCCATTCCGTCACCAC 57.892 50.000 0.00 0.00 0.00 4.16
1927 2060 4.460382 ACACTGGCAAGATATGAAGTTTGG 59.540 41.667 0.00 0.00 0.00 3.28
1964 2098 0.102481 CCCCGTAGAGGACATGTTCG 59.898 60.000 0.00 0.00 45.00 3.95
1974 2108 1.599419 GGACATGTTCGTTGTGCCAAC 60.599 52.381 0.00 7.71 30.07 3.77
1993 2127 2.248248 ACACCCTTGACGAGATCTTCA 58.752 47.619 0.00 0.00 0.00 3.02
2016 2150 2.409378 GCGTTTCGTTTCCATTCGTCTA 59.591 45.455 0.00 0.00 0.00 2.59
2023 2157 5.535333 TCGTTTCCATTCGTCTAAAGTCTT 58.465 37.500 0.00 0.00 0.00 3.01
2246 2393 6.477688 TGTTTTATCTGTCGACGTTTTCTTCT 59.522 34.615 11.62 0.00 0.00 2.85
2247 2394 7.010738 TGTTTTATCTGTCGACGTTTTCTTCTT 59.989 33.333 11.62 0.00 0.00 2.52
2365 2518 2.644060 AAGGGGCAGAGGTAGTACTT 57.356 50.000 0.00 0.00 0.00 2.24
2366 2519 1.867363 AGGGGCAGAGGTAGTACTTG 58.133 55.000 0.00 0.00 0.00 3.16
2572 2728 9.028284 AGTCAAATGAAATTACATCCTCATTGT 57.972 29.630 2.39 0.00 38.27 2.71
2591 2747 4.329462 TGTTTTGCCTGGTTATTGTTCC 57.671 40.909 0.00 0.00 0.00 3.62
2633 2789 2.357050 CCCAATGGCCAAGAGTGTGATA 60.357 50.000 10.96 0.00 0.00 2.15
2709 2865 0.032813 CCACATCCAAAGCCAGGGAT 60.033 55.000 0.00 0.00 44.65 3.85
2754 2910 7.116519 GTGAATGTACTGAAGAAACAGGTCTAC 59.883 40.741 0.00 0.00 41.59 2.59
2773 2929 6.809196 GGTCTACTGTACTGAAGATTGTGAAG 59.191 42.308 6.77 0.00 0.00 3.02
2774 2930 7.371936 GTCTACTGTACTGAAGATTGTGAAGT 58.628 38.462 6.77 0.00 0.00 3.01
2775 2931 8.512956 GTCTACTGTACTGAAGATTGTGAAGTA 58.487 37.037 6.77 0.00 0.00 2.24
2776 2932 9.244292 TCTACTGTACTGAAGATTGTGAAGTAT 57.756 33.333 6.77 0.00 0.00 2.12
2777 2933 9.862371 CTACTGTACTGAAGATTGTGAAGTATT 57.138 33.333 6.77 0.00 0.00 1.89
2838 2994 6.020971 TGTAAATCTTCGTCTTCAGCTACA 57.979 37.500 0.00 0.00 0.00 2.74
2874 3030 4.625311 CGAACATGTATGTGACTGCTACAA 59.375 41.667 0.00 0.00 41.61 2.41
2885 3041 4.013728 TGACTGCTACAACTTTGTGGTTT 58.986 39.130 4.82 0.00 42.31 3.27
2923 3080 2.455674 AGTTTGCTAGACATGCGTCA 57.544 45.000 0.00 0.00 45.23 4.35
3026 3443 6.478512 AACAAATGGGTTCACAATACTTGT 57.521 33.333 0.00 0.00 46.75 3.16
3048 3465 7.681939 TGTTACTGTCATTGGATTTCTAACC 57.318 36.000 0.00 0.00 0.00 2.85
3061 3588 6.879993 TGGATTTCTAACCATTAGCGTGTTAA 59.120 34.615 0.00 0.00 33.23 2.01
3079 3606 7.430846 CGTGTTAACTGTTTTACAAACAACAC 58.569 34.615 17.43 17.43 38.31 3.32
3086 3613 5.945155 TGTTTTACAAACAACACTGTCCTC 58.055 37.500 0.00 0.00 33.45 3.71
3102 3629 2.291741 GTCCTCCTGTCTTGCAAAGTTG 59.708 50.000 0.00 0.00 46.34 3.16
3123 3650 3.769536 GCATTTGCATGTAGTGTAACCC 58.230 45.455 0.00 0.00 41.59 4.11
3183 3710 8.500753 TTTGACACTGTAAACAGAGTTTACAT 57.499 30.769 26.31 16.85 45.42 2.29
3188 3715 8.395633 ACACTGTAAACAGAGTTTACATCAAAC 58.604 33.333 26.31 8.54 43.51 2.93
3203 3730 3.149005 TCAAACTTTTCCGCCATACCT 57.851 42.857 0.00 0.00 0.00 3.08
3244 3771 0.038166 AAGCTTTTCGGCATCCTGGA 59.962 50.000 0.00 0.00 34.17 3.86
3245 3772 0.678048 AGCTTTTCGGCATCCTGGAC 60.678 55.000 0.00 0.00 34.17 4.02
3249 3776 0.109532 TTTCGGCATCCTGGACACAA 59.890 50.000 0.00 0.00 0.00 3.33
3306 3834 3.995705 GCAGTTTCATTGCAAGCCATTAA 59.004 39.130 4.94 0.00 41.17 1.40
3319 3847 1.964344 GCCATTAACCCATTCCCTGCA 60.964 52.381 0.00 0.00 0.00 4.41
3320 3848 2.681422 CCATTAACCCATTCCCTGCAT 58.319 47.619 0.00 0.00 0.00 3.96
3585 4115 5.066505 GGGGTGAAAAGCTACAATATGACAG 59.933 44.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 3.243367 CCGTTTGGATGTTCTCAGCAAAA 60.243 43.478 0.00 0.00 37.49 2.44
52 53 1.071542 TCCGTTTGGATGTTCTCAGCA 59.928 47.619 0.00 0.00 40.17 4.41
53 54 1.808411 TCCGTTTGGATGTTCTCAGC 58.192 50.000 0.00 0.00 40.17 4.26
82 83 3.310774 CAGGAGATGCTATTTGTTGGTCG 59.689 47.826 0.00 0.00 0.00 4.79
111 112 1.334556 GTTTTTAGTCGTGGCCCGTTT 59.665 47.619 12.46 5.91 37.94 3.60
202 203 0.395724 GGAAATTCAGGGGCCACGAT 60.396 55.000 4.39 0.00 0.00 3.73
251 253 6.401047 AGGGTTTACTGGTTAAAAAGAAGC 57.599 37.500 0.00 0.00 31.22 3.86
252 254 6.548251 TGGAGGGTTTACTGGTTAAAAAGAAG 59.452 38.462 0.00 0.00 31.22 2.85
254 256 5.829391 GTGGAGGGTTTACTGGTTAAAAAGA 59.171 40.000 0.00 0.00 31.22 2.52
255 257 5.278120 CGTGGAGGGTTTACTGGTTAAAAAG 60.278 44.000 0.00 0.00 31.22 2.27
256 258 4.579753 CGTGGAGGGTTTACTGGTTAAAAA 59.420 41.667 0.00 0.00 31.22 1.94
267 269 1.770061 AGAAACACCGTGGAGGGTTTA 59.230 47.619 3.03 0.00 46.96 2.01
286 288 4.003648 GTGTGGTGAGGAGGTGAAAATAG 58.996 47.826 0.00 0.00 0.00 1.73
310 312 2.660802 GAAGACGGCGAAGGGGAA 59.339 61.111 16.62 0.00 0.00 3.97
341 343 2.047274 CGGCCGGAAGAAGCTGAA 60.047 61.111 20.10 0.00 37.58 3.02
342 344 4.760047 GCGGCCGGAAGAAGCTGA 62.760 66.667 29.38 0.00 37.58 4.26
386 388 2.619074 GGGGGTGGAGAAGAACAATCAG 60.619 54.545 0.00 0.00 0.00 2.90
389 391 1.760405 AGGGGGTGGAGAAGAACAAT 58.240 50.000 0.00 0.00 0.00 2.71
393 395 0.777446 CCAAAGGGGGTGGAGAAGAA 59.223 55.000 0.00 0.00 38.54 2.52
396 398 0.481128 GAACCAAAGGGGGTGGAGAA 59.519 55.000 0.00 0.00 41.32 2.87
397 399 0.402861 AGAACCAAAGGGGGTGGAGA 60.403 55.000 0.00 0.00 41.32 3.71
400 402 0.251341 CAGAGAACCAAAGGGGGTGG 60.251 60.000 0.00 0.00 41.32 4.61
402 404 0.771755 GACAGAGAACCAAAGGGGGT 59.228 55.000 0.00 0.00 45.04 4.95
404 406 2.959465 AAGACAGAGAACCAAAGGGG 57.041 50.000 0.00 0.00 44.81 4.79
411 413 2.810852 CCAGCTCAAAAGACAGAGAACC 59.189 50.000 0.00 0.00 33.74 3.62
412 414 3.471680 ACCAGCTCAAAAGACAGAGAAC 58.528 45.455 0.00 0.00 33.74 3.01
422 424 1.028905 CAACCGGAACCAGCTCAAAA 58.971 50.000 9.46 0.00 0.00 2.44
426 428 4.792087 TTCAACCGGAACCAGCTC 57.208 55.556 9.46 0.00 0.00 4.09
447 449 5.608676 TCGGACAGATACAGATAATCGAC 57.391 43.478 0.00 0.00 0.00 4.20
449 451 5.574082 GGATCGGACAGATACAGATAATCG 58.426 45.833 0.00 0.00 40.04 3.34
486 488 0.543749 CCAACCCCAAACAGCCAAAA 59.456 50.000 0.00 0.00 0.00 2.44
528 532 0.107831 TGGAAGGGACACGAAACTGG 59.892 55.000 0.00 0.00 0.00 4.00
534 538 3.181449 TGAAAATCTTGGAAGGGACACGA 60.181 43.478 0.00 0.00 0.00 4.35
542 546 4.377431 CGAACCGAGTGAAAATCTTGGAAG 60.377 45.833 6.26 0.00 39.19 3.46
579 583 0.177836 CCCAAATTCGGCCATTTCCC 59.822 55.000 2.24 0.00 0.00 3.97
580 584 0.461870 GCCCAAATTCGGCCATTTCC 60.462 55.000 2.24 0.00 40.78 3.13
643 647 7.110810 AGGATATGCATAATCAAGATGGACAG 58.889 38.462 11.13 0.00 0.00 3.51
655 659 5.163311 TGCGCCATACTAGGATATGCATAAT 60.163 40.000 11.13 2.70 32.12 1.28
680 764 8.217131 TGAGATTTCCATGTTGATTACATCAG 57.783 34.615 0.00 0.00 45.71 2.90
682 766 9.859427 TTTTGAGATTTCCATGTTGATTACATC 57.141 29.630 0.00 0.00 45.71 3.06
696 782 8.330302 CGCCATCATTTTATTTTTGAGATTTCC 58.670 33.333 0.00 0.00 0.00 3.13
697 783 8.872845 ACGCCATCATTTTATTTTTGAGATTTC 58.127 29.630 0.00 0.00 0.00 2.17
698 784 8.776376 ACGCCATCATTTTATTTTTGAGATTT 57.224 26.923 0.00 0.00 0.00 2.17
699 785 9.520204 CTACGCCATCATTTTATTTTTGAGATT 57.480 29.630 0.00 0.00 0.00 2.40
700 786 8.686334 ACTACGCCATCATTTTATTTTTGAGAT 58.314 29.630 0.00 0.00 0.00 2.75
702 788 8.184192 AGACTACGCCATCATTTTATTTTTGAG 58.816 33.333 0.00 0.00 0.00 3.02
703 789 7.967854 CAGACTACGCCATCATTTTATTTTTGA 59.032 33.333 0.00 0.00 0.00 2.69
704 790 7.754924 ACAGACTACGCCATCATTTTATTTTTG 59.245 33.333 0.00 0.00 0.00 2.44
705 791 7.754924 CACAGACTACGCCATCATTTTATTTTT 59.245 33.333 0.00 0.00 0.00 1.94
708 814 5.296780 CCACAGACTACGCCATCATTTTATT 59.703 40.000 0.00 0.00 0.00 1.40
712 819 2.236146 TCCACAGACTACGCCATCATTT 59.764 45.455 0.00 0.00 0.00 2.32
713 820 1.831106 TCCACAGACTACGCCATCATT 59.169 47.619 0.00 0.00 0.00 2.57
721 828 3.752222 ACTAGAACACTCCACAGACTACG 59.248 47.826 0.00 0.00 0.00 3.51
723 830 4.942483 GCTACTAGAACACTCCACAGACTA 59.058 45.833 0.00 0.00 0.00 2.59
727 834 4.021894 ACAAGCTACTAGAACACTCCACAG 60.022 45.833 0.00 0.00 0.00 3.66
731 838 6.270156 ACTTACAAGCTACTAGAACACTCC 57.730 41.667 0.00 0.00 0.00 3.85
739 847 7.385205 TGAAGCTCAAAACTTACAAGCTACTAG 59.615 37.037 0.00 0.00 42.24 2.57
740 848 7.214381 TGAAGCTCAAAACTTACAAGCTACTA 58.786 34.615 0.00 0.00 42.24 1.82
758 866 4.558538 ACACACACTGAATTTGAAGCTC 57.441 40.909 0.00 0.00 0.00 4.09
760 868 3.798337 CCAACACACACTGAATTTGAAGC 59.202 43.478 0.00 0.00 0.00 3.86
764 872 5.247507 TCTTCCAACACACACTGAATTTG 57.752 39.130 0.00 0.00 0.00 2.32
774 882 5.794894 TCCTCTCTATTTCTTCCAACACAC 58.205 41.667 0.00 0.00 0.00 3.82
806 915 1.153628 CTGCCGGTGCTGTACTACC 60.154 63.158 1.90 0.00 38.71 3.18
814 923 0.751643 AACAGAAAACTGCCGGTGCT 60.752 50.000 1.90 0.00 38.71 4.40
819 928 2.138596 ATTGCAACAGAAAACTGCCG 57.861 45.000 0.00 0.00 35.13 5.69
820 929 3.248363 GGAAATTGCAACAGAAAACTGCC 59.752 43.478 0.00 0.00 35.13 4.85
824 933 6.084326 TCCTAGGAAATTGCAACAGAAAAC 57.916 37.500 9.71 0.00 0.00 2.43
874 983 4.356405 TTGATCAGCCAAGAGACAAGAA 57.644 40.909 0.00 0.00 0.00 2.52
875 984 4.356405 TTTGATCAGCCAAGAGACAAGA 57.644 40.909 0.00 0.00 0.00 3.02
991 1100 4.758251 CGTCGGCATGGCTGGACA 62.758 66.667 21.41 0.00 35.34 4.02
1170 1279 6.983984 ACTGACTCTGGTAAAGTTAACTCTC 58.016 40.000 8.95 2.62 0.00 3.20
1231 1340 3.706373 CCGTACCAGCCAGTGCCT 61.706 66.667 0.00 0.00 38.69 4.75
1262 1371 2.514458 ATTCAACACATGGGAGGTCC 57.486 50.000 0.00 0.00 0.00 4.46
1270 1379 5.090757 CGGTGATTGAGAATTCAACACATG 58.909 41.667 8.44 0.00 45.54 3.21
1273 1382 4.749245 ACGGTGATTGAGAATTCAACAC 57.251 40.909 8.44 9.44 45.54 3.32
1275 1384 5.519722 ACAAACGGTGATTGAGAATTCAAC 58.480 37.500 8.44 2.04 45.54 3.18
1277 1386 5.766150 AACAAACGGTGATTGAGAATTCA 57.234 34.783 8.44 0.00 0.00 2.57
1279 1388 9.787532 CATATAAACAAACGGTGATTGAGAATT 57.212 29.630 0.00 0.00 0.00 2.17
1281 1390 8.233868 CACATATAAACAAACGGTGATTGAGAA 58.766 33.333 0.00 0.00 0.00 2.87
1292 1402 7.593273 ACACAATGGTTCACATATAAACAAACG 59.407 33.333 0.00 0.00 39.40 3.60
1293 1403 8.810652 ACACAATGGTTCACATATAAACAAAC 57.189 30.769 0.00 0.00 39.40 2.93
1302 1412 4.498850 GCACACAACACAATGGTTCACATA 60.499 41.667 0.00 0.00 39.40 2.29
1303 1413 3.737663 GCACACAACACAATGGTTCACAT 60.738 43.478 0.00 0.00 43.07 3.21
1305 1415 2.192624 GCACACAACACAATGGTTCAC 58.807 47.619 0.00 0.00 0.00 3.18
1321 1431 0.522626 CATGAAACCGATGCTGCACA 59.477 50.000 3.57 0.00 0.00 4.57
1323 1433 1.246649 AACATGAAACCGATGCTGCA 58.753 45.000 4.13 4.13 0.00 4.41
1351 1461 0.820871 AGCGGAAGTCCTCATCTGAC 59.179 55.000 0.00 0.00 0.00 3.51
1354 1464 1.786937 ATGAGCGGAAGTCCTCATCT 58.213 50.000 0.00 0.00 43.37 2.90
1357 1467 1.809869 CGATGAGCGGAAGTCCTCA 59.190 57.895 0.00 0.00 41.81 3.86
1378 1488 4.820897 TGAATAGGCTGGTCGCTATATTG 58.179 43.478 0.00 0.00 39.13 1.90
1387 1497 2.409948 ACTGCTTGAATAGGCTGGTC 57.590 50.000 0.00 0.00 0.00 4.02
1414 1524 1.536922 CCACCTCCTCGATCAATGACG 60.537 57.143 0.00 0.00 0.00 4.35
1447 1557 6.749923 AGAATCTCAACAAGAAGCAATACC 57.250 37.500 0.00 0.00 37.61 2.73
1454 1564 5.762218 ACCAGTGAAGAATCTCAACAAGAAG 59.238 40.000 0.00 0.00 37.61 2.85
1528 1648 0.478507 AGCACTAACAAACCCCTGCT 59.521 50.000 0.00 0.00 0.00 4.24
1648 1769 1.609208 GCTCAAGCTTGTTCCTCCAA 58.391 50.000 25.19 3.24 38.21 3.53
1676 1797 3.502211 ACATGCTAACCTCAAAAGAACGG 59.498 43.478 0.00 0.00 0.00 4.44
1778 1900 5.013547 ACTGTGAATACTACAGAGCAGAGT 58.986 41.667 11.65 0.00 46.52 3.24
1847 1969 7.644986 ACAGATTCAGAAGAAAGTAAAGACG 57.355 36.000 0.00 0.00 37.29 4.18
1875 2005 3.605743 GGACTTATCTACCGACAGTCG 57.394 52.381 16.50 16.50 40.07 4.18
1927 2060 5.392125 ACGGGGCTATAGGATACCATATAC 58.608 45.833 1.04 0.00 37.17 1.47
1939 2072 2.581216 TGTCCTCTACGGGGCTATAG 57.419 55.000 0.00 0.00 0.00 1.31
1974 2108 2.417924 CCTGAAGATCTCGTCAAGGGTG 60.418 54.545 0.00 0.00 34.18 4.61
1993 2127 0.515564 CGAATGGAAACGAAACGCCT 59.484 50.000 0.00 0.00 0.00 5.52
2145 2291 1.466167 CCTTTCCACTGATGCAAGACG 59.534 52.381 0.00 0.00 0.00 4.18
2278 2430 6.782988 TCTTATATTAAGGGACAGAGGGAGTG 59.217 42.308 0.00 0.00 0.00 3.51
2330 2483 6.764560 TCTGCCCCTTAATATAAGACGTTTTC 59.235 38.462 0.00 0.00 0.00 2.29
2365 2518 2.677836 GCGTTGGATTTGATCAGTAGCA 59.322 45.455 0.00 0.00 0.00 3.49
2366 2519 2.285834 CGCGTTGGATTTGATCAGTAGC 60.286 50.000 0.00 0.00 0.00 3.58
2591 2747 2.166664 GGGCTGACTACCTACAGAGTTG 59.833 54.545 0.00 0.00 36.38 3.16
2633 2789 5.108187 TCATATTGCTTGCTCTTCCTTCT 57.892 39.130 0.00 0.00 0.00 2.85
2709 2865 9.730705 ACATTCACATTAGAGAAAGAAGATTCA 57.269 29.630 0.00 0.00 0.00 2.57
2846 3002 4.245660 CAGTCACATACATGTTCGGTTCT 58.754 43.478 2.30 0.00 39.39 3.01
2885 3041 1.003331 CTAAACGGCGAAAAGTGTGCA 60.003 47.619 16.62 0.00 0.00 4.57
2945 3104 5.273944 GCTAAAATCATAACGCCAGAAAGG 58.726 41.667 0.00 0.00 41.84 3.11
3026 3443 8.877864 AATGGTTAGAAATCCAATGACAGTAA 57.122 30.769 0.00 0.00 37.27 2.24
3048 3465 8.466026 GTTTGTAAAACAGTTAACACGCTAATG 58.534 33.333 8.61 0.00 0.00 1.90
3061 3588 5.475564 AGGACAGTGTTGTTTGTAAAACAGT 59.524 36.000 0.00 1.09 39.87 3.55
3079 3606 2.149578 CTTTGCAAGACAGGAGGACAG 58.850 52.381 0.00 0.00 0.00 3.51
3102 3629 3.443681 AGGGTTACACTACATGCAAATGC 59.556 43.478 0.00 0.00 42.50 3.56
3120 3647 1.494721 TGCTCCTCTTTTGTGAAGGGT 59.505 47.619 0.00 0.00 0.00 4.34
3123 3650 7.970614 GGTATTTATTGCTCCTCTTTTGTGAAG 59.029 37.037 0.00 0.00 0.00 3.02
3183 3710 3.149005 AGGTATGGCGGAAAAGTTTGA 57.851 42.857 0.00 0.00 0.00 2.69
3188 3715 3.133362 TGGTACTAGGTATGGCGGAAAAG 59.867 47.826 0.00 0.00 0.00 2.27
3195 3722 3.838317 TCATGGATGGTACTAGGTATGGC 59.162 47.826 0.00 0.00 0.00 4.40
3203 3730 7.457852 AGCTTGGTAATATCATGGATGGTACTA 59.542 37.037 0.00 0.00 0.00 1.82
3244 3771 2.166907 TGGGGGTGTGATTTTTGTGT 57.833 45.000 0.00 0.00 0.00 3.72
3245 3772 2.632028 TCATGGGGGTGTGATTTTTGTG 59.368 45.455 0.00 0.00 0.00 3.33
3249 3776 1.896755 GCCTCATGGGGGTGTGATTTT 60.897 52.381 15.13 0.00 35.12 1.82
3306 3834 0.920763 TCCAGATGCAGGGAATGGGT 60.921 55.000 2.30 0.00 0.00 4.51
3319 3847 3.632333 TCTATCACGTCTTGGTCCAGAT 58.368 45.455 0.00 0.00 0.00 2.90
3320 3848 3.081710 TCTATCACGTCTTGGTCCAGA 57.918 47.619 0.00 0.00 0.00 3.86
3420 3948 6.485984 CAGAGTCTTCATCATATTGAAAGGGG 59.514 42.308 0.00 0.00 35.31 4.79
3555 4085 4.929819 TGTAGCTTTTCACCCCTTTTTC 57.070 40.909 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.