Multiple sequence alignment - TraesCS2B01G114000

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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 TraesCS2B01G114000 chr2B 100.000 5034 0 0 1 5034 77177389 77172356 0.000000e+00 9297
1 TraesCS2B01G114000 chr2B 84.579 214 26 4 4403 4610 1678830 1678618 6.610000e-49 206
2 TraesCS2B01G114000 chr2D 94.448 2900 132 13 2117 4992 49882382 49879488 0.000000e+00 4436
3 TraesCS2B01G114000 chr2D 88.971 1759 111 25 1 1729 49884457 49882752 0.000000e+00 2097
4 TraesCS2B01G114000 chr2D 95.821 335 13 1 1784 2117 49882745 49882411 1.590000e-149 540
5 TraesCS2B01G114000 chr2A 94.384 1745 77 10 2115 3848 51588608 51586874 0.000000e+00 2660
6 TraesCS2B01G114000 chr2A 95.725 1193 43 6 3844 5029 51586795 51585604 0.000000e+00 1914
7 TraesCS2B01G114000 chr2A 95.067 1196 57 2 923 2117 51589831 51588637 0.000000e+00 1881
8 TraesCS2B01G114000 chr2A 83.267 753 76 22 44 786 51590542 51589830 0.000000e+00 647
9 TraesCS2B01G114000 chr4B 85.514 214 24 4 4403 4610 391595575 391595363 3.050000e-52 217
10 TraesCS2B01G114000 chr7B 85.047 214 25 4 4403 4610 654701520 654701732 1.420000e-50 211
11 TraesCS2B01G114000 chr7A 84.906 212 25 4 4405 4610 605163510 605163720 1.840000e-49 207
12 TraesCS2B01G114000 chr7A 84.038 213 27 3 4403 4609 694564749 694564538 1.110000e-46 198
13 TraesCS2B01G114000 chrUn 100.000 53 0 0 1 53 473304721 473304773 1.150000e-16 99


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 TraesCS2B01G114000 chr2B 77172356 77177389 5033 True 9297.000000 9297 100.00000 1 5034 1 chr2B.!!$R2 5033
1 TraesCS2B01G114000 chr2D 49879488 49884457 4969 True 2357.666667 4436 93.08000 1 4992 3 chr2D.!!$R1 4991
2 TraesCS2B01G114000 chr2A 51585604 51590542 4938 True 1775.500000 2660 92.11075 44 5029 4 chr2A.!!$R1 4985

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
429 451 0.044244 CCCTGTTCCCTTCCTCCCTA 59.956 60.000 0.00 0.0 0.00 3.53 F
576 601 0.178068 AGCACCGGACGCAAATATCT 59.822 50.000 20.05 0.0 0.00 1.98 F
886 917 0.545309 ACCCTTGCCTGAGCTGTCTA 60.545 55.000 0.00 0.0 40.80 2.59 F
1134 1166 0.978146 CCGAGTCTGGGGATCCTGTT 60.978 60.000 12.58 0.0 34.13 3.16 F
1858 1891 1.632409 AGCTTGAAGGAGGATGAAGCA 59.368 47.619 0.00 0.0 41.24 3.91 F
2913 2983 0.459237 ATGCTGCTTTCGGAGACTCG 60.459 55.000 0.00 0.0 34.32 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2083 0.035458 AGACTTTGAGGTTCCCAGCG 59.965 55.000 0.00 0.00 0.00 5.18 R
2159 2223 4.730949 TGAAGTAATCGGAGGTTACAGG 57.269 45.455 6.06 0.00 35.11 4.00 R
2779 2849 0.951558 ATCCGCTGGTCAACAACAAC 59.048 50.000 0.00 0.00 0.00 3.32 R
2784 2854 3.181469 GGATAGTTATCCGCTGGTCAACA 60.181 47.826 2.57 0.00 42.49 3.33 R
3185 3259 1.805869 AGCTGACTGCAGTTGCTAAG 58.194 50.000 32.65 21.14 45.94 2.18 R
4414 4599 0.599204 TGAACTTCGCCGGTTGAGTC 60.599 55.000 1.90 1.83 0.00 3.36 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
90 101 1.538135 AACAAGGTACGCCCCCTCT 60.538 57.895 0.00 0.00 34.57 3.69
91 102 1.131928 AACAAGGTACGCCCCCTCTT 61.132 55.000 0.00 0.00 34.57 2.85
96 115 2.441532 TACGCCCCCTCTTCCTCG 60.442 66.667 0.00 0.00 0.00 4.63
106 125 2.184579 CTTCCTCGTTCTCGCCCC 59.815 66.667 0.00 0.00 36.96 5.80
107 126 3.701604 CTTCCTCGTTCTCGCCCCG 62.702 68.421 0.00 0.00 36.96 5.73
131 150 1.749063 GCCCACATTGGTTAGTTAGCC 59.251 52.381 0.00 0.00 35.17 3.93
146 165 1.491668 TAGCCAGCACCGGAATTCTA 58.508 50.000 9.46 0.00 0.00 2.10
148 167 0.815615 GCCAGCACCGGAATTCTAGG 60.816 60.000 9.46 15.66 0.00 3.02
172 191 4.471726 CCTTCCGTCCGTCCGTCG 62.472 72.222 0.00 0.00 39.52 5.12
276 295 1.679311 GTGTCCATCTCCCTGCACA 59.321 57.895 0.00 0.00 0.00 4.57
277 296 0.674895 GTGTCCATCTCCCTGCACAC 60.675 60.000 0.00 0.00 0.00 3.82
279 298 1.913262 TCCATCTCCCTGCACACGT 60.913 57.895 0.00 0.00 0.00 4.49
280 299 1.742880 CCATCTCCCTGCACACGTG 60.743 63.158 15.48 15.48 0.00 4.49
306 328 2.188994 GCAGAGCCTCGCATCCTT 59.811 61.111 4.12 0.00 0.00 3.36
349 371 2.820197 GGAAAGGGAAAGAAATGACGCT 59.180 45.455 0.00 0.00 0.00 5.07
366 388 1.960417 GCTATGGAGCTTTCCAGGTC 58.040 55.000 0.80 0.00 45.98 3.85
367 389 1.808133 GCTATGGAGCTTTCCAGGTCG 60.808 57.143 0.80 0.00 46.93 4.79
370 392 2.593956 GGAGCTTTCCAGGTCGGGT 61.594 63.158 0.00 0.00 46.93 5.28
371 393 1.079057 GAGCTTTCCAGGTCGGGTC 60.079 63.158 0.00 0.00 37.78 4.46
373 395 2.264794 CTTTCCAGGTCGGGTCGG 59.735 66.667 0.00 0.00 34.36 4.79
374 396 3.310860 CTTTCCAGGTCGGGTCGGG 62.311 68.421 0.00 0.00 34.36 5.14
378 400 3.633116 CAGGTCGGGTCGGGGTTT 61.633 66.667 0.00 0.00 0.00 3.27
386 408 1.904865 GGTCGGGGTTTGGGTTTCC 60.905 63.158 0.00 0.00 0.00 3.13
420 442 1.530655 CGTTTTGCCCCTGTTCCCT 60.531 57.895 0.00 0.00 0.00 4.20
421 443 1.112916 CGTTTTGCCCCTGTTCCCTT 61.113 55.000 0.00 0.00 0.00 3.95
422 444 0.679505 GTTTTGCCCCTGTTCCCTTC 59.320 55.000 0.00 0.00 0.00 3.46
423 445 0.471022 TTTTGCCCCTGTTCCCTTCC 60.471 55.000 0.00 0.00 0.00 3.46
424 446 1.368268 TTTGCCCCTGTTCCCTTCCT 61.368 55.000 0.00 0.00 0.00 3.36
425 447 1.789576 TTGCCCCTGTTCCCTTCCTC 61.790 60.000 0.00 0.00 0.00 3.71
426 448 2.985116 GCCCCTGTTCCCTTCCTCC 61.985 68.421 0.00 0.00 0.00 4.30
427 449 2.309504 CCCCTGTTCCCTTCCTCCC 61.310 68.421 0.00 0.00 0.00 4.30
428 450 1.229984 CCCTGTTCCCTTCCTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
429 451 0.044244 CCCTGTTCCCTTCCTCCCTA 59.956 60.000 0.00 0.00 0.00 3.53
430 452 1.345526 CCCTGTTCCCTTCCTCCCTAT 60.346 57.143 0.00 0.00 0.00 2.57
431 453 2.090153 CCCTGTTCCCTTCCTCCCTATA 60.090 54.545 0.00 0.00 0.00 1.31
432 454 2.973406 CCTGTTCCCTTCCTCCCTATAC 59.027 54.545 0.00 0.00 0.00 1.47
433 455 2.973406 CTGTTCCCTTCCTCCCTATACC 59.027 54.545 0.00 0.00 0.00 2.73
489 512 6.341316 TCTTCATCCTTTCTGGTTAATCTCG 58.659 40.000 0.00 0.00 37.07 4.04
490 513 5.677319 TCATCCTTTCTGGTTAATCTCGT 57.323 39.130 0.00 0.00 37.07 4.18
495 518 3.695830 TTCTGGTTAATCTCGTTGGCT 57.304 42.857 0.00 0.00 0.00 4.75
556 579 1.457346 CTTCCCAAGGCTGACATCAC 58.543 55.000 0.00 0.00 0.00 3.06
565 588 1.293179 CTGACATCACAGCACCGGA 59.707 57.895 9.46 0.00 0.00 5.14
576 601 0.178068 AGCACCGGACGCAAATATCT 59.822 50.000 20.05 0.00 0.00 1.98
579 604 1.327460 CACCGGACGCAAATATCTGTG 59.673 52.381 9.46 0.00 0.00 3.66
655 686 2.294728 CGTTTAACGGCGAGATCCC 58.705 57.895 16.62 0.00 38.08 3.85
668 699 1.936547 GAGATCCCATTGCTGACGTTC 59.063 52.381 0.00 0.00 0.00 3.95
669 700 1.556911 AGATCCCATTGCTGACGTTCT 59.443 47.619 0.00 0.00 0.00 3.01
715 746 6.736110 AATTAATCAGCCACCATAAATGCT 57.264 33.333 0.00 0.00 33.52 3.79
795 826 5.154222 CCGATTTGGTTTCAGTTTCTAAGC 58.846 41.667 0.00 0.00 0.00 3.09
797 828 4.561735 TTTGGTTTCAGTTTCTAAGCCG 57.438 40.909 0.00 0.00 0.00 5.52
886 917 0.545309 ACCCTTGCCTGAGCTGTCTA 60.545 55.000 0.00 0.00 40.80 2.59
892 923 2.110578 TGCCTGAGCTGTCTAATGCTA 58.889 47.619 0.00 0.00 39.91 3.49
913 944 1.000060 CCTGTGTTGGGTGCTGAATTG 60.000 52.381 0.00 0.00 0.00 2.32
1068 1100 2.107141 AAGTATGAGCTCGGGCGC 59.893 61.111 3.15 3.15 44.37 6.53
1134 1166 0.978146 CCGAGTCTGGGGATCCTGTT 60.978 60.000 12.58 0.00 34.13 3.16
1283 1316 1.915489 TCCCTGCCTCATGCTTTCTAA 59.085 47.619 0.00 0.00 42.00 2.10
1491 1524 4.095036 GCCTGCATGAGGTAAAGACTAAAC 59.905 45.833 0.00 0.00 44.97 2.01
1503 1536 4.649088 AAGACTAAACACCAACCTTTGC 57.351 40.909 0.00 0.00 0.00 3.68
1505 1538 2.956333 GACTAAACACCAACCTTTGCCT 59.044 45.455 0.00 0.00 0.00 4.75
1514 1547 3.755905 ACCAACCTTTGCCTTTTTGTTTG 59.244 39.130 0.00 0.00 0.00 2.93
1515 1548 3.427368 CCAACCTTTGCCTTTTTGTTTGC 60.427 43.478 0.00 0.00 0.00 3.68
1531 1564 4.717877 TGTTTGCAGTATGATATCCCCTG 58.282 43.478 0.00 4.83 39.69 4.45
1572 1605 4.511527 ACATCCAAGTCTGCAGTTGATAG 58.488 43.478 14.67 7.20 35.19 2.08
1720 1753 7.348815 TGTTTCATATTTCTCTGTGATGGGAT 58.651 34.615 0.00 0.00 0.00 3.85
1732 1765 2.016318 TGATGGGATTTTAGCAGCACG 58.984 47.619 0.00 0.00 0.00 5.34
1858 1891 1.632409 AGCTTGAAGGAGGATGAAGCA 59.368 47.619 0.00 0.00 41.24 3.91
2050 2083 6.317391 AGCTAGAGAATTTGTTGCTTGATACC 59.683 38.462 0.00 0.00 26.98 2.73
2509 2574 5.284079 CCAATATTGCTGGCTGTACATTTC 58.716 41.667 10.11 0.00 0.00 2.17
2520 2585 5.647658 TGGCTGTACATTTCCATTTACTCTG 59.352 40.000 0.00 0.00 0.00 3.35
2587 2652 5.630121 TGGTTTTCTGATGGAGCTAAAAGA 58.370 37.500 0.00 0.00 0.00 2.52
2596 2661 5.190528 TGATGGAGCTAAAAGACTGATTCCT 59.809 40.000 0.00 0.00 0.00 3.36
2603 2668 7.866870 AGCTAAAAGACTGATTCCTAGGATTT 58.133 34.615 13.57 9.91 0.00 2.17
2630 2695 6.495526 GGATCCTAATCCTTCTACTGTAAGCT 59.504 42.308 3.84 0.00 46.97 3.74
2769 2839 8.883731 ACATTGATTATGGAGTTCTTTCTTACG 58.116 33.333 0.00 0.00 38.64 3.18
2779 2849 2.322161 TCTTTCTTACGCGGTTCTTCG 58.678 47.619 12.47 0.00 0.00 3.79
2784 2854 1.523934 CTTACGCGGTTCTTCGTTGTT 59.476 47.619 12.47 0.00 39.79 2.83
2913 2983 0.459237 ATGCTGCTTTCGGAGACTCG 60.459 55.000 0.00 0.00 34.32 4.18
2956 3030 4.561735 TTTTCACTGGAAAAGCCGTTAG 57.438 40.909 0.00 0.00 45.51 2.34
3050 3124 2.354343 GAAGGGCAGCCAGCTTCT 59.646 61.111 15.19 0.00 44.79 2.85
3075 3149 6.682423 TGAACGCATTTGAGTTGATATCAT 57.318 33.333 6.17 0.00 38.15 2.45
3284 3366 5.721480 TGTCCTCCTGAAGAAATCATCAGTA 59.279 40.000 12.95 0.00 39.34 2.74
3386 3468 8.889717 CATGGATACGACTTTTAACATAGGTTT 58.110 33.333 0.00 0.00 37.74 3.27
3460 3542 5.714806 TCCCCATGACTTAAACCTTTCATTC 59.285 40.000 0.00 0.00 0.00 2.67
3573 3655 4.340381 ACAGCAGCTTGAGAAATGTCTTTT 59.660 37.500 0.00 0.00 32.80 2.27
3721 3803 8.268850 TCTTGAATATTGTGGTTCTTTAGCTC 57.731 34.615 0.00 0.00 0.00 4.09
3737 3819 8.324163 TCTTTAGCTCTTTTACTCATTTCACC 57.676 34.615 0.00 0.00 0.00 4.02
3808 3903 1.702401 TGCCCATGAAGGACTACACAA 59.298 47.619 0.00 0.00 41.22 3.33
3812 3907 2.742053 CCATGAAGGACTACACAAACGG 59.258 50.000 0.00 0.00 41.22 4.44
3825 3920 5.257082 ACACAAACGGAATTTAAGCAAGT 57.743 34.783 0.00 0.00 0.00 3.16
4024 4204 1.627834 AGTGAGGCTGAAGAAAGAGGG 59.372 52.381 0.00 0.00 0.00 4.30
4121 4301 3.003394 TCCTTGTAGATTCGTCCGGTA 57.997 47.619 0.00 0.00 0.00 4.02
4208 4388 2.039084 CCAGTAGGTTCAAGTGCCTCTT 59.961 50.000 0.00 0.00 36.38 2.85
4316 4497 3.573967 GGAGGAAAAGAACAGGCAAATCA 59.426 43.478 0.00 0.00 0.00 2.57
4414 4599 1.157870 AGGTTTCAGACACCAACGCG 61.158 55.000 3.53 3.53 36.67 6.01
4423 4608 2.660552 ACCAACGCGACTCAACCG 60.661 61.111 15.93 0.00 0.00 4.44
4492 4677 2.430921 CTGACTCCACGCCGACAC 60.431 66.667 0.00 0.00 0.00 3.67
4501 4686 1.007336 CACGCCGACACTGTCCTTAC 61.007 60.000 3.50 0.00 0.00 2.34
4551 4736 3.159984 GCGTCTGCGTTCTTGAGG 58.840 61.111 0.00 0.00 40.81 3.86
4692 4880 1.062488 ACAGGGGAGAGTGCAAACCT 61.062 55.000 0.00 0.00 0.00 3.50
4803 4991 5.125097 CCAGTCTTTCTCTCCAATGAAATGG 59.875 44.000 0.00 0.00 42.12 3.16
4830 5018 0.685131 TCGCCTTGATCGGGTCCTTA 60.685 55.000 6.44 0.00 0.00 2.69
4839 5027 1.111116 TCGGGTCCTTATAGGCCACG 61.111 60.000 5.01 0.00 34.52 4.94
4908 5096 4.006989 TGAACTTAATTGGTGGGTGATCG 58.993 43.478 0.00 0.00 0.00 3.69
4968 5157 1.271543 CCACATGGAACCAGAAGCAGA 60.272 52.381 0.00 0.00 37.39 4.26
4972 5161 2.727123 TGGAACCAGAAGCAGAACAA 57.273 45.000 0.00 0.00 0.00 2.83
5006 5195 4.282195 ACATCTTCCTCCGAGAACCATATC 59.718 45.833 0.00 0.00 0.00 1.63
5009 5198 3.595190 TCCTCCGAGAACCATATCTCA 57.405 47.619 0.00 0.00 44.98 3.27
5029 5218 4.608269 TCATGCCTAAATTTCCATGTCCA 58.392 39.130 18.22 5.10 37.09 4.02
5030 5219 5.210430 TCATGCCTAAATTTCCATGTCCAT 58.790 37.500 18.22 3.80 37.09 3.41
5031 5220 5.069383 TCATGCCTAAATTTCCATGTCCATG 59.931 40.000 18.22 0.14 37.09 3.66
5032 5221 4.352009 TGCCTAAATTTCCATGTCCATGT 58.648 39.130 6.53 0.00 37.11 3.21
5033 5222 5.514169 TGCCTAAATTTCCATGTCCATGTA 58.486 37.500 6.53 0.00 37.11 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.043852 TCACGAGGAGGGAGGAGC 60.044 66.667 0.00 0.00 0.00 4.70
90 101 3.755628 CGGGGCGAGAACGAGGAA 61.756 66.667 0.00 0.00 42.66 3.36
107 126 2.361865 TAACCAATGTGGGCGGCC 60.362 61.111 23.42 23.42 43.37 6.13
108 127 1.248101 AACTAACCAATGTGGGCGGC 61.248 55.000 0.00 0.00 43.37 6.53
109 128 2.014128 CTAACTAACCAATGTGGGCGG 58.986 52.381 0.00 0.00 43.37 6.13
110 129 1.400494 GCTAACTAACCAATGTGGGCG 59.600 52.381 0.00 0.00 43.37 6.13
111 130 1.749063 GGCTAACTAACCAATGTGGGC 59.251 52.381 0.00 0.00 43.37 5.36
112 131 3.016736 CTGGCTAACTAACCAATGTGGG 58.983 50.000 0.00 0.00 43.37 4.61
131 150 0.179000 AGCCTAGAATTCCGGTGCTG 59.821 55.000 0.00 0.00 0.00 4.41
146 165 1.889530 CGGACGGAAGGAAAGAGCCT 61.890 60.000 0.00 0.00 40.93 4.58
148 167 0.736672 GACGGACGGAAGGAAAGAGC 60.737 60.000 0.00 0.00 0.00 4.09
263 282 3.880591 CACGTGTGCAGGGAGATG 58.119 61.111 7.58 0.00 0.00 2.90
280 299 4.756458 AGGCTCTGCTGACGCTGC 62.756 66.667 12.29 4.96 36.97 5.25
281 300 2.508887 GAGGCTCTGCTGACGCTG 60.509 66.667 7.40 0.00 36.97 5.18
282 301 4.127040 CGAGGCTCTGCTGACGCT 62.127 66.667 13.50 2.74 36.97 5.07
295 317 1.880340 GCGAGACAAGGATGCGAGG 60.880 63.158 0.00 0.00 0.00 4.63
298 320 2.892425 GGGCGAGACAAGGATGCG 60.892 66.667 0.00 0.00 0.00 4.73
306 328 4.373116 GCGGAACTGGGCGAGACA 62.373 66.667 2.65 0.00 0.00 3.41
363 385 4.710167 CCAAACCCCGACCCGACC 62.710 72.222 0.00 0.00 0.00 4.79
366 388 3.795731 AAACCCAAACCCCGACCCG 62.796 63.158 0.00 0.00 0.00 5.28
367 389 1.904865 GAAACCCAAACCCCGACCC 60.905 63.158 0.00 0.00 0.00 4.46
398 420 0.741915 GAACAGGGGCAAAACGAACA 59.258 50.000 0.00 0.00 0.00 3.18
399 421 0.031585 GGAACAGGGGCAAAACGAAC 59.968 55.000 0.00 0.00 0.00 3.95
420 442 2.595380 ACTGGGAAGGTATAGGGAGGAA 59.405 50.000 0.00 0.00 0.00 3.36
421 443 2.090719 CACTGGGAAGGTATAGGGAGGA 60.091 54.545 0.00 0.00 0.00 3.71
422 444 2.330216 CACTGGGAAGGTATAGGGAGG 58.670 57.143 0.00 0.00 0.00 4.30
423 445 1.694696 GCACTGGGAAGGTATAGGGAG 59.305 57.143 0.00 0.00 0.00 4.30
424 446 1.694693 GGCACTGGGAAGGTATAGGGA 60.695 57.143 0.00 0.00 0.00 4.20
425 447 0.765510 GGCACTGGGAAGGTATAGGG 59.234 60.000 0.00 0.00 0.00 3.53
426 448 0.393077 CGGCACTGGGAAGGTATAGG 59.607 60.000 0.00 0.00 0.00 2.57
427 449 0.249911 GCGGCACTGGGAAGGTATAG 60.250 60.000 0.00 0.00 0.00 1.31
428 450 1.692173 GGCGGCACTGGGAAGGTATA 61.692 60.000 3.07 0.00 0.00 1.47
429 451 2.590092 GCGGCACTGGGAAGGTAT 59.410 61.111 0.00 0.00 0.00 2.73
430 452 3.712907 GGCGGCACTGGGAAGGTA 61.713 66.667 3.07 0.00 0.00 3.08
549 572 2.094659 CGTCCGGTGCTGTGATGTC 61.095 63.158 0.00 0.00 0.00 3.06
556 579 0.304705 GATATTTGCGTCCGGTGCTG 59.695 55.000 19.38 2.38 0.00 4.41
560 583 1.066430 ACACAGATATTTGCGTCCGGT 60.066 47.619 0.00 0.00 0.00 5.28
565 588 5.643348 TGAAATCTCACACAGATATTTGCGT 59.357 36.000 0.00 0.00 41.47 5.24
576 601 2.711009 AGGACCCTTGAAATCTCACACA 59.289 45.455 0.00 0.00 0.00 3.72
579 604 3.536570 GCTAGGACCCTTGAAATCTCAC 58.463 50.000 1.73 0.00 0.00 3.51
629 658 1.353609 CGCCGTTAAACGTCCGGATT 61.354 55.000 7.81 0.00 44.41 3.01
655 686 1.503542 GGGCAGAACGTCAGCAATG 59.496 57.895 8.72 0.00 29.77 2.82
669 700 2.349755 GGTTACTGCTTCGGGGCA 59.650 61.111 3.53 3.53 40.15 5.36
699 730 4.160252 ACCTTTAAGCATTTATGGTGGCTG 59.840 41.667 0.00 0.00 38.70 4.85
715 746 1.243902 CTGCCTGCCGAAACCTTTAA 58.756 50.000 0.00 0.00 0.00 1.52
753 784 0.239347 GCAACGTGCAAGCTTCATCT 59.761 50.000 0.00 0.00 44.26 2.90
886 917 1.909700 CACCCAACACAGGTAGCATT 58.090 50.000 0.00 0.00 35.24 3.56
892 923 0.185901 ATTCAGCACCCAACACAGGT 59.814 50.000 0.00 0.00 38.48 4.00
926 957 5.695816 TGCCATTTTTGAACAGTTAAGATGC 59.304 36.000 0.00 0.00 0.00 3.91
935 966 4.326504 AAGACCTGCCATTTTTGAACAG 57.673 40.909 0.00 0.00 0.00 3.16
979 1011 0.035630 CTCCAGGCCAGTCTTTCCTG 60.036 60.000 5.01 9.29 45.24 3.86
991 1023 0.464554 GCCTTGTACATCCTCCAGGC 60.465 60.000 16.17 16.17 34.44 4.85
1068 1100 2.590092 GTCCCTTCCCCGATGGTG 59.410 66.667 0.00 0.00 34.77 4.17
1134 1166 3.349927 CTTGTCAAGGATCTTGATGGCA 58.650 45.455 12.63 0.00 0.00 4.92
1283 1316 4.987285 CGCATAATGACAGCTCAGTTCTAT 59.013 41.667 0.00 0.00 0.00 1.98
1457 1490 0.244450 CATGCAGGCGGACAACATTT 59.756 50.000 0.00 0.00 0.00 2.32
1491 1524 2.984562 ACAAAAAGGCAAAGGTTGGTG 58.015 42.857 0.00 0.00 0.00 4.17
1503 1536 6.980397 GGGATATCATACTGCAAACAAAAAGG 59.020 38.462 4.83 0.00 0.00 3.11
1505 1538 6.667414 AGGGGATATCATACTGCAAACAAAAA 59.333 34.615 4.83 0.00 0.00 1.94
1515 1548 4.096681 TGTAGGCAGGGGATATCATACTG 58.903 47.826 4.83 10.06 0.00 2.74
1558 1591 7.778470 AAATAGTTAGCTATCAACTGCAGAC 57.222 36.000 23.35 3.51 36.95 3.51
1572 1605 9.595823 TGTTATAGTGGAGTCAAAATAGTTAGC 57.404 33.333 0.00 0.00 0.00 3.09
1720 1753 0.310543 CAACTGGCGTGCTGCTAAAA 59.689 50.000 0.00 0.00 45.43 1.52
1732 1765 1.136891 ACAAGGTTTCAAGCAACTGGC 59.863 47.619 0.00 0.00 45.30 4.85
1776 1809 9.791838 CAATAAAGGCGAATGTAAAAGAAAAAC 57.208 29.630 0.00 0.00 0.00 2.43
1786 1819 8.958119 AGTAGAAATCAATAAAGGCGAATGTA 57.042 30.769 0.00 0.00 0.00 2.29
1787 1820 7.865706 AGTAGAAATCAATAAAGGCGAATGT 57.134 32.000 0.00 0.00 0.00 2.71
1788 1821 9.651718 GTTAGTAGAAATCAATAAAGGCGAATG 57.348 33.333 0.00 0.00 0.00 2.67
1789 1822 9.614792 AGTTAGTAGAAATCAATAAAGGCGAAT 57.385 29.630 0.00 0.00 0.00 3.34
1912 1945 3.058155 CCTTCAGATCTCGGTGGTATACG 60.058 52.174 0.00 0.00 0.00 3.06
2050 2083 0.035458 AGACTTTGAGGTTCCCAGCG 59.965 55.000 0.00 0.00 0.00 5.18
2159 2223 4.730949 TGAAGTAATCGGAGGTTACAGG 57.269 45.455 6.06 0.00 35.11 4.00
2509 2574 6.931281 TCTGTCAAGAGAAACAGAGTAAATGG 59.069 38.462 1.26 0.00 45.18 3.16
2520 2585 5.398603 TCCAGAGATCTGTCAAGAGAAAC 57.601 43.478 0.00 0.00 42.27 2.78
2548 2613 6.265422 CAGAAAACCAAGAGGGACAAGTAAAT 59.735 38.462 0.00 0.00 41.15 1.40
2587 2652 5.674035 AGGATCCAAAATCCTAGGAATCAGT 59.326 40.000 17.30 0.00 46.11 3.41
2748 2818 5.050972 CCGCGTAAGAAAGAACTCCATAATC 60.051 44.000 4.92 0.00 43.02 1.75
2749 2819 4.809426 CCGCGTAAGAAAGAACTCCATAAT 59.191 41.667 4.92 0.00 43.02 1.28
2769 2839 1.062880 TCAACAACAACGAAGAACCGC 59.937 47.619 0.00 0.00 0.00 5.68
2779 2849 0.951558 ATCCGCTGGTCAACAACAAC 59.048 50.000 0.00 0.00 0.00 3.32
2784 2854 3.181469 GGATAGTTATCCGCTGGTCAACA 60.181 47.826 2.57 0.00 42.49 3.33
2913 2983 6.969828 AACAAGATCGATTAACTCACTTCC 57.030 37.500 0.00 0.00 0.00 3.46
3050 3124 7.784633 TGATATCAACTCAAATGCGTTCATA 57.215 32.000 1.98 0.00 31.46 2.15
3075 3149 6.814954 ATCTAGCTTCAGTCCCTTATTCAA 57.185 37.500 0.00 0.00 0.00 2.69
3180 3254 4.320788 GCTGACTGCAGTTGCTAAGATTTT 60.321 41.667 27.51 1.94 44.17 1.82
3181 3255 3.190118 GCTGACTGCAGTTGCTAAGATTT 59.810 43.478 27.51 2.13 44.17 2.17
3185 3259 1.805869 AGCTGACTGCAGTTGCTAAG 58.194 50.000 32.65 21.14 45.94 2.18
3188 3262 2.260844 TTTAGCTGACTGCAGTTGCT 57.739 45.000 34.30 34.30 45.94 3.91
3284 3366 3.070878 GGCTTAGCAGCTTCTTCTATCCT 59.929 47.826 6.53 0.00 46.44 3.24
3410 3492 4.649674 ACAAGGACAGTCTCAGTTACTCAA 59.350 41.667 0.00 0.00 0.00 3.02
3460 3542 9.684448 TTCGCATCTAGAAAGAACAAGATATAG 57.316 33.333 0.00 0.00 34.73 1.31
3557 3639 9.878599 ATTACGTTGTAAAAGACATTTCTCAAG 57.121 29.630 0.00 0.00 38.07 3.02
3573 3655 9.715123 CTTGATCAATAATTGCATTACGTTGTA 57.285 29.630 8.96 0.00 0.00 2.41
3777 3864 4.101585 TCCTTCATGGGCACTTGTATAGAG 59.898 45.833 1.28 0.00 36.20 2.43
3808 3903 5.767816 AAGTCACTTGCTTAAATTCCGTT 57.232 34.783 0.00 0.00 0.00 4.44
3812 3907 8.342634 TGTGTTCTAAGTCACTTGCTTAAATTC 58.657 33.333 0.00 0.00 35.82 2.17
3825 3920 6.183361 TGGGTACTTGATTGTGTTCTAAGTCA 60.183 38.462 0.00 0.00 33.93 3.41
4024 4204 2.404995 GCAGCTGCCTCATGTGGAC 61.405 63.158 28.76 9.26 34.31 4.02
4091 4271 5.469084 ACGAATCTACAAGGAACAAAGGAAC 59.531 40.000 0.00 0.00 0.00 3.62
4092 4272 5.617252 ACGAATCTACAAGGAACAAAGGAA 58.383 37.500 0.00 0.00 0.00 3.36
4121 4301 7.090953 GCCTAAAGCTCTATATACATCGAGT 57.909 40.000 0.00 0.00 38.99 4.18
4316 4497 7.911130 TGAGAGATGAGAATAAATCAGTCCT 57.089 36.000 0.00 0.00 0.00 3.85
4353 4534 3.007940 CAGATGGTAGACCTTGTTCACCA 59.992 47.826 0.00 0.00 43.10 4.17
4414 4599 0.599204 TGAACTTCGCCGGTTGAGTC 60.599 55.000 1.90 1.83 0.00 3.36
4423 4608 1.362406 GGCAGTAGCTGAACTTCGCC 61.362 60.000 0.00 0.00 41.70 5.54
4492 4677 3.436243 AGAGTTCAGGAGGTAAGGACAG 58.564 50.000 0.00 0.00 0.00 3.51
4501 4686 5.157940 TCAAATTCAGAGAGTTCAGGAGG 57.842 43.478 0.00 0.00 0.00 4.30
4551 4736 2.093216 CGCAAGCATCCTGGAAGAC 58.907 57.895 0.00 0.00 34.07 3.01
4692 4880 1.157513 TCACACTGTCCCCAGGCTA 59.842 57.895 0.00 0.00 43.36 3.93
4803 4991 1.594862 CCGATCAAGGCGAAATCTGTC 59.405 52.381 0.00 0.00 0.00 3.51
4830 5018 1.068083 CATCTGCGACGTGGCCTAT 59.932 57.895 20.26 10.24 0.00 2.57
4908 5096 1.616159 TTTAGGGCAAGGTGCTGAAC 58.384 50.000 0.00 0.00 44.28 3.18
4968 5157 3.884037 AGATGTCCTCCAAACCTTGTT 57.116 42.857 0.00 0.00 0.00 2.83
4994 5183 3.674528 AGGCATGAGATATGGTTCTCG 57.325 47.619 0.00 0.00 44.22 4.04
5006 5195 4.646040 TGGACATGGAAATTTAGGCATGAG 59.354 41.667 0.00 0.00 0.00 2.90
5009 5198 4.964262 ACATGGACATGGAAATTTAGGCAT 59.036 37.500 15.94 0.00 42.91 4.40


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

AutoCloner maintained by Alex Coulton.