Multiple sequence alignment - TraesCS3B01G332500

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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 TraesCS3B01G332500 chr3B 100.000 5018 0 0 1 5018 539061663 539066680 0.000000e+00 9267
1 TraesCS3B01G332500 chr3D 96.371 4491 129 13 1 4470 412085187 412089664 0.000000e+00 7360
2 TraesCS3B01G332500 chr3D 96.085 281 10 1 4511 4791 412089652 412089931 1.650000e-124 457
3 TraesCS3B01G332500 chr3D 95.722 187 7 1 4830 5015 412089922 412090108 2.940000e-77 300
4 TraesCS3B01G332500 chr3A 95.533 4500 151 14 3 4473 538017912 538013434 0.000000e+00 7151
5 TraesCS3B01G332500 chr3A 95.541 471 18 2 4511 4978 538013449 538012979 0.000000e+00 750


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 TraesCS3B01G332500 chr3B 539061663 539066680 5017 False 9267.000000 9267 100.000000 1 5018 1 chr3B.!!$F1 5017
1 TraesCS3B01G332500 chr3D 412085187 412090108 4921 False 2705.666667 7360 96.059333 1 5015 3 chr3D.!!$F1 5014
2 TraesCS3B01G332500 chr3A 538012979 538017912 4933 True 3950.500000 7151 95.537000 3 4978 2 chr3A.!!$R1 4975

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
952 979 0.030773 TGCAGATACCGTCGATCAGC 59.969 55.0 0.00 0.0 36.62 4.26 F
2057 2084 0.105039 CGGGTGAATAGGTGGAGAGC 59.895 60.0 0.00 0.0 0.00 4.09 F
3042 3069 0.321210 ACACGTTGAATCGGCCATCA 60.321 50.0 2.24 0.3 34.94 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2370 2397 0.178932 TCCTCCCATATCTCCCACCG 60.179 60.0 0.00 0.0 0.00 4.94 R
3248 3275 0.749454 CCTCCGATGCTTCTTTGGGG 60.749 60.0 0.00 0.0 0.00 4.96 R
4504 4542 1.089920 GAGGCATCATTCACGTTGCT 58.910 50.0 7.51 0.0 35.46 3.91 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
54 55 0.036294 GGCCTGTGGTCTACTGAACC 60.036 60.000 0.00 0.00 0.00 3.62
67 68 2.811317 GAACCGAGGCGTGCTCTG 60.811 66.667 0.00 0.00 0.00 3.35
106 107 2.105006 TCTGCTTTGCCAGATCTGAC 57.895 50.000 24.62 13.69 36.96 3.51
107 108 1.627329 TCTGCTTTGCCAGATCTGACT 59.373 47.619 24.62 0.00 36.96 3.41
108 109 1.738350 CTGCTTTGCCAGATCTGACTG 59.262 52.381 24.62 8.66 34.77 3.51
109 110 1.348696 TGCTTTGCCAGATCTGACTGA 59.651 47.619 24.62 2.95 39.94 3.41
230 231 3.859414 GCCGGCAGATCTGGAGCT 61.859 66.667 24.80 0.00 44.37 4.09
424 425 1.338579 TGGTACGCTGTGCATCATCAA 60.339 47.619 0.00 0.00 0.00 2.57
426 427 1.009078 TACGCTGTGCATCATCAAGC 58.991 50.000 0.00 0.00 0.00 4.01
427 428 0.956902 ACGCTGTGCATCATCAAGCA 60.957 50.000 0.00 0.00 38.65 3.91
428 429 0.248094 CGCTGTGCATCATCAAGCAG 60.248 55.000 0.00 0.00 42.14 4.24
429 430 0.100682 GCTGTGCATCATCAAGCAGG 59.899 55.000 0.00 0.00 42.14 4.85
441 442 1.001248 AAGCAGGAGCATGGGCAAT 59.999 52.632 0.00 0.00 45.49 3.56
467 469 1.921243 TCTCGCATGTTATGTCACCG 58.079 50.000 0.00 0.00 0.00 4.94
489 491 6.591834 ACCGATGACAGTTATTTCTTCTTCTG 59.408 38.462 0.00 0.00 0.00 3.02
495 500 3.686726 AGTTATTTCTTCTTCTGCTGCCG 59.313 43.478 0.00 0.00 0.00 5.69
564 574 0.952010 TTTTCCTGCCGGCGTCTAAC 60.952 55.000 23.90 0.00 0.00 2.34
579 589 6.579292 CGGCGTCTAACAATAAACAAAATCAA 59.421 34.615 0.00 0.00 0.00 2.57
623 638 5.131142 AGAAAGTTTTTCTCTCAGTCCTGGA 59.869 40.000 0.00 0.00 0.00 3.86
719 734 5.046950 TGCTACAGTTTTGTTTTGTCCCTTT 60.047 36.000 0.00 0.00 38.76 3.11
774 789 6.758886 AGTAGAATGTGTATGCTTTACTGCTC 59.241 38.462 0.00 0.00 0.00 4.26
818 836 3.371898 TCGCTGCTGTTGAATTACTCATG 59.628 43.478 0.00 0.00 32.78 3.07
820 838 3.733077 GCTGCTGTTGAATTACTCATGCC 60.733 47.826 0.00 0.00 32.78 4.40
877 895 9.414295 GCGTGTATTTCCAATGTATATGTAGTA 57.586 33.333 0.00 0.00 0.00 1.82
891 909 2.009774 TGTAGTACCGGCTACGAACTC 58.990 52.381 0.00 0.00 43.03 3.01
952 979 0.030773 TGCAGATACCGTCGATCAGC 59.969 55.000 0.00 0.00 36.62 4.26
1132 1159 1.069765 CCACGGTCACTGTCTGCTT 59.930 57.895 0.00 0.00 0.00 3.91
1156 1183 2.242572 CCGGAGCATGCTCATGTCG 61.243 63.158 40.37 33.23 44.40 4.35
1179 1206 0.252197 ACAATAACTCCCCGACTGGC 59.748 55.000 0.00 0.00 0.00 4.85
1242 1269 4.028490 CAGCGGGGGCAGTTACCA 62.028 66.667 0.00 0.00 0.00 3.25
1243 1270 3.015145 AGCGGGGGCAGTTACCAT 61.015 61.111 0.00 0.00 0.00 3.55
1244 1271 2.516225 GCGGGGGCAGTTACCATC 60.516 66.667 0.00 0.00 0.00 3.51
1285 1312 1.406898 TGCTAGACGATGCTTCTCCTG 59.593 52.381 0.00 0.00 0.00 3.86
1356 1383 7.283127 GTCTATAACAATCCCAGCTTCATTTCA 59.717 37.037 0.00 0.00 0.00 2.69
1365 1392 4.301628 CCAGCTTCATTTCAACCTTCAAC 58.698 43.478 0.00 0.00 0.00 3.18
1389 1416 2.159000 CCCATACCAAGGTAGTTCGTCC 60.159 54.545 5.10 0.00 33.77 4.79
1449 1476 4.742012 AGGAGAAACAGAAGAGACAGGTA 58.258 43.478 0.00 0.00 0.00 3.08
1453 1480 5.148502 AGAAACAGAAGAGACAGGTAGGAA 58.851 41.667 0.00 0.00 0.00 3.36
1515 1542 1.202582 GCTTCTGTCAGTAGGCTTCGA 59.797 52.381 8.40 0.00 0.00 3.71
1545 1572 4.919774 TGTGTACATAGGGTTTCATGGT 57.080 40.909 0.00 0.00 0.00 3.55
1591 1618 2.297033 ACAAATTGGCTTCGTGCAGAAT 59.703 40.909 0.00 1.30 45.15 2.40
1630 1657 1.537202 GTTGCTTTGCTTCTGATCGGT 59.463 47.619 0.42 0.00 0.00 4.69
1713 1740 9.253832 ACATATGGAATTGTCATCCTTACAAAA 57.746 29.630 7.80 0.00 40.05 2.44
1761 1788 2.564947 TGAGGAGCTCAGGAACTTCTTC 59.435 50.000 17.19 0.00 35.39 2.87
1798 1825 7.739825 TCTGATCCCTATATTCTTTGACTTGG 58.260 38.462 0.00 0.00 0.00 3.61
1854 1881 2.230130 AGAGAGGAGAACTGTGGGAG 57.770 55.000 0.00 0.00 0.00 4.30
1893 1920 6.044287 AGCTGTGGATGTTATATGGTGGAATA 59.956 38.462 0.00 0.00 0.00 1.75
1970 1997 7.679638 GCAGTTAGAAGCGAATGATACCAATTT 60.680 37.037 0.00 0.00 0.00 1.82
2009 2036 4.824289 CAAGCAGTTATTCTTTTGGCCAT 58.176 39.130 6.09 0.00 0.00 4.40
2014 2041 5.120674 GCAGTTATTCTTTTGGCCATGAAAC 59.879 40.000 6.09 8.12 0.00 2.78
2057 2084 0.105039 CGGGTGAATAGGTGGAGAGC 59.895 60.000 0.00 0.00 0.00 4.09
2058 2085 1.204146 GGGTGAATAGGTGGAGAGCA 58.796 55.000 0.00 0.00 0.00 4.26
2096 2123 0.887933 TTTCCTTTCCCTCGCAATGC 59.112 50.000 0.00 0.00 0.00 3.56
2142 2169 1.066908 CTCTCGGAGTTGGAGCTCATC 59.933 57.143 17.19 7.44 37.24 2.92
2160 2187 3.503363 TCATCTTGTTTGGTGATGTCAGC 59.497 43.478 5.31 5.31 44.06 4.26
2202 2229 4.717233 TTTTGAGCTCAAGACAAAGCAA 57.283 36.364 27.02 14.41 41.06 3.91
2203 2230 3.698029 TTGAGCTCAAGACAAAGCAAC 57.302 42.857 25.16 0.00 41.06 4.17
2251 2278 5.887598 TGGTCTGCTAACAATTATGAGCAAT 59.112 36.000 0.00 0.00 43.94 3.56
2283 2310 1.271926 ACCATCAAGGGAAAGGAACCG 60.272 52.381 0.00 0.00 43.89 4.44
2287 2314 2.056359 TCAAGGGAAAGGAACCGGTTA 58.944 47.619 22.33 0.00 0.00 2.85
2357 2384 3.364441 GCAGCATGGCCGACAACA 61.364 61.111 0.00 0.00 35.86 3.33
2370 2397 3.053455 CCGACAACAGAGAGTGAAGAAC 58.947 50.000 0.00 0.00 0.00 3.01
2385 2412 1.424638 AGAACGGTGGGAGATATGGG 58.575 55.000 0.00 0.00 0.00 4.00
2573 2600 4.744795 ATTATTTGTCTCTGCGGACTCT 57.255 40.909 0.00 0.00 37.16 3.24
2575 2602 2.440539 TTTGTCTCTGCGGACTCTTC 57.559 50.000 0.00 0.00 37.16 2.87
2601 2628 9.099454 CTGGAAGTAGATTTAAGTGTTGATACC 57.901 37.037 0.00 0.00 0.00 2.73
2772 2799 3.455910 TCATAATGGACCTTCTCCCACAG 59.544 47.826 0.00 0.00 38.49 3.66
2955 2982 2.375174 TGAAGAAAAGCTTGGGAGGCTA 59.625 45.455 0.00 0.00 39.30 3.93
3042 3069 0.321210 ACACGTTGAATCGGCCATCA 60.321 50.000 2.24 0.30 34.94 3.07
3046 3073 1.451207 TTGAATCGGCCATCACCCG 60.451 57.895 2.24 0.00 46.88 5.28
3069 3096 7.414540 CCCGTAAGAGATTTTTCTTGGAATGAG 60.415 40.741 0.00 0.00 37.91 2.90
3153 3180 3.501062 CGATATTTGAGCATGCAGATGGT 59.499 43.478 21.98 0.00 43.13 3.55
3248 3275 1.135286 GGCTCTGGCTGCACATAAAAC 60.135 52.381 0.50 0.00 38.73 2.43
3273 3300 3.090532 AAGCATCGGAGGGGTCCC 61.091 66.667 0.00 0.00 0.00 4.46
3321 3348 0.746063 CTTGTGGCCTTGCAACTTCA 59.254 50.000 3.32 0.00 32.93 3.02
3427 3454 4.909695 TCCAGTTCCATGATATGATCAGGT 59.090 41.667 0.09 0.00 43.53 4.00
3489 3516 1.338769 GCGGTCCAATCAGTGTACCTT 60.339 52.381 0.00 0.00 0.00 3.50
3501 3528 4.098044 TCAGTGTACCTTCGAGGATCAATC 59.902 45.833 7.76 0.00 37.67 2.67
3603 3630 3.760684 GGCCATCTGAGTTGATGTTCTTT 59.239 43.478 0.00 0.00 41.47 2.52
3618 3645 4.923893 TGTTCTTTGTGAAGCAGATTGTG 58.076 39.130 0.00 0.00 35.01 3.33
3660 3687 5.471116 CACATTCATCACATATTCCCGATGT 59.529 40.000 0.00 0.00 38.05 3.06
3669 3696 2.346766 ATTCCCGATGTAATGCTGCA 57.653 45.000 4.13 4.13 0.00 4.41
3729 3756 1.475392 GCAGCTGAATCCATGCTCTCT 60.475 52.381 20.43 0.00 35.78 3.10
3747 3774 1.282738 TCTCATGCTGGCAAATGGAGA 59.717 47.619 9.29 7.30 0.00 3.71
3993 4020 4.104261 ACCCTCAGTAAACTAACAAGGCTT 59.896 41.667 0.00 0.00 0.00 4.35
4203 4231 4.127918 TCCCTGTTAGGACTCTCTTCAA 57.872 45.455 0.00 0.00 37.67 2.69
4217 4245 6.937392 ACTCTCTTCAAGGTTCTACCAATAC 58.063 40.000 0.00 0.00 41.95 1.89
4224 4252 5.414454 TCAAGGTTCTACCAATACATGTTGC 59.586 40.000 2.30 0.00 41.95 4.17
4231 4259 3.238597 ACCAATACATGTTGCCTTTGGT 58.761 40.909 2.30 12.81 41.38 3.67
4233 4261 3.006752 CCAATACATGTTGCCTTTGGTGT 59.993 43.478 2.30 0.00 31.19 4.16
4238 4266 2.065899 TGTTGCCTTTGGTGTAAGCT 57.934 45.000 0.00 0.00 33.76 3.74
4242 4271 4.202377 TGTTGCCTTTGGTGTAAGCTACTA 60.202 41.667 0.00 0.00 33.76 1.82
4289 4321 0.242825 CCAACTGCATGCACAGAAGG 59.757 55.000 18.46 8.68 40.25 3.46
4292 4324 0.959372 ACTGCATGCACAGAAGGCTC 60.959 55.000 18.46 0.00 40.25 4.70
4321 4353 2.494059 TGCTTGTAAGTTCTGTCCTGC 58.506 47.619 0.00 0.00 0.00 4.85
4373 4410 2.388735 ACTGTGATCCAGAATCGGCTA 58.611 47.619 15.51 0.00 44.49 3.93
4379 4416 3.834231 TGATCCAGAATCGGCTATGATGA 59.166 43.478 0.00 0.00 37.17 2.92
4426 4464 1.124116 CTATTTGCGTTTTTGCCGTGC 59.876 47.619 0.00 0.00 0.00 5.34
4467 4505 4.966850 GCATTGTTGCTATGAATGATGC 57.033 40.909 0.00 0.00 45.77 3.91
4468 4506 3.739300 GCATTGTTGCTATGAATGATGCC 59.261 43.478 0.00 0.00 45.77 4.40
4469 4507 4.500887 GCATTGTTGCTATGAATGATGCCT 60.501 41.667 0.00 0.00 45.77 4.75
4470 4508 5.597806 CATTGTTGCTATGAATGATGCCTT 58.402 37.500 0.00 0.00 30.03 4.35
4471 4509 5.664294 TTGTTGCTATGAATGATGCCTTT 57.336 34.783 0.00 0.00 0.00 3.11
4472 4510 5.664294 TGTTGCTATGAATGATGCCTTTT 57.336 34.783 0.00 0.00 0.00 2.27
4473 4511 6.040209 TGTTGCTATGAATGATGCCTTTTT 57.960 33.333 0.00 0.00 0.00 1.94
4495 4533 3.485947 TTTAGCAACGTGAATGATGCC 57.514 42.857 4.11 0.00 38.30 4.40
4496 4534 2.401583 TAGCAACGTGAATGATGCCT 57.598 45.000 4.11 0.00 38.30 4.75
4497 4535 1.538047 AGCAACGTGAATGATGCCTT 58.462 45.000 4.11 0.00 38.30 4.35
4498 4536 1.888512 AGCAACGTGAATGATGCCTTT 59.111 42.857 4.11 0.00 38.30 3.11
4499 4537 2.297033 AGCAACGTGAATGATGCCTTTT 59.703 40.909 4.11 0.00 38.30 2.27
4500 4538 3.059166 GCAACGTGAATGATGCCTTTTT 58.941 40.909 0.00 0.00 32.10 1.94
4674 4712 7.801716 TCTTATTTGTCCTATATTGGTGCAC 57.198 36.000 8.80 8.80 0.00 4.57
4704 4744 4.081761 CACTTTTAGCATTGTAGTTCGCG 58.918 43.478 0.00 0.00 0.00 5.87
4860 4900 3.774766 GGGGGCTGGAGAAACATAAAAAT 59.225 43.478 0.00 0.00 0.00 1.82
4862 4902 5.419542 GGGGCTGGAGAAACATAAAAATTC 58.580 41.667 0.00 0.00 0.00 2.17
4960 5001 4.102210 TCAAAATCCTCCTCTAGATGGCTG 59.898 45.833 0.00 0.00 0.00 4.85
4991 5032 3.257469 TGTTCCTGATCTTGCTGCTAG 57.743 47.619 4.67 4.67 0.00 3.42
5011 5052 5.526111 GCTAGCCAACTCGTATAATTTCCAA 59.474 40.000 2.29 0.00 0.00 3.53
5015 5056 6.433093 AGCCAACTCGTATAATTTCCAAAAGT 59.567 34.615 0.00 0.00 0.00 2.66
5016 5057 7.039993 AGCCAACTCGTATAATTTCCAAAAGTT 60.040 33.333 0.00 0.00 0.00 2.66
5017 5058 8.238631 GCCAACTCGTATAATTTCCAAAAGTTA 58.761 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 4.504916 CCTCCAGAGCACGCCTCG 62.505 72.222 0.00 0.00 45.54 4.63
67 68 0.617935 AAGCCAGAAGAGAAGCCTCC 59.382 55.000 0.00 0.00 40.30 4.30
106 107 2.487428 CCGACGGCTCTCACTCAG 59.513 66.667 0.00 0.00 0.00 3.35
107 108 3.749064 GCCGACGGCTCTCACTCA 61.749 66.667 31.30 0.00 46.69 3.41
246 247 1.694696 GGGAGAAGCGGATCTAATGGT 59.305 52.381 0.00 0.00 0.00 3.55
394 395 1.270465 ACAGCGTACCAAGTACAACCC 60.270 52.381 5.79 0.00 38.77 4.11
424 425 1.455217 GATTGCCCATGCTCCTGCT 60.455 57.895 0.00 0.00 40.48 4.24
426 427 3.851955 GGATTGCCCATGCTCCTG 58.148 61.111 0.00 0.00 38.71 3.86
441 442 3.876914 GACATAACATGCGAGAATTGGGA 59.123 43.478 0.00 0.00 0.00 4.37
467 469 7.462731 CAGCAGAAGAAGAAATAACTGTCATC 58.537 38.462 0.00 0.00 0.00 2.92
489 491 3.871594 ACTACAGTAATCAATTCGGCAGC 59.128 43.478 0.00 0.00 0.00 5.25
495 500 6.900299 GTGCGCTTTACTACAGTAATCAATTC 59.100 38.462 9.73 0.00 39.89 2.17
579 589 9.678260 ACTTTCTCTAATTGCTTGATGATACTT 57.322 29.630 0.00 0.00 0.00 2.24
615 629 2.011046 GCGAGTACTACGTCCAGGACT 61.011 57.143 17.95 2.72 42.69 3.85
623 638 0.675837 TGGCTCAGCGAGTACTACGT 60.676 55.000 13.65 0.00 31.39 3.57
706 721 5.948742 ATTTGGAGAAAAGGGACAAAACA 57.051 34.783 0.00 0.00 35.06 2.83
774 789 4.574599 AGAAACAACCAAGCTAGCAAAG 57.425 40.909 18.83 6.93 0.00 2.77
877 895 0.892755 TCAATGAGTTCGTAGCCGGT 59.107 50.000 1.90 0.00 33.95 5.28
952 979 4.774124 TCTCAAGATGGCCTGTAATTCAG 58.226 43.478 3.32 0.00 43.27 3.02
1156 1183 1.207329 AGTCGGGGAGTTATTGTGCTC 59.793 52.381 0.00 0.00 0.00 4.26
1179 1206 0.587242 CACCGATTTTCAGCGCGATG 60.587 55.000 20.14 20.14 0.00 3.84
1229 1256 0.550914 TGATGATGGTAACTGCCCCC 59.449 55.000 0.00 0.00 37.61 5.40
1242 1269 6.239120 GCAATAACCTTATGTTGGCTGATGAT 60.239 38.462 0.00 0.00 37.83 2.45
1243 1270 5.067674 GCAATAACCTTATGTTGGCTGATGA 59.932 40.000 0.00 0.00 37.83 2.92
1244 1271 5.068198 AGCAATAACCTTATGTTGGCTGATG 59.932 40.000 0.00 0.00 38.16 3.07
1285 1312 1.871126 GAAGTGCAAAGGCTGGGAGC 61.871 60.000 0.00 0.00 41.91 4.70
1356 1383 0.323087 GGTATGGGCCGTTGAAGGTT 60.323 55.000 2.17 0.00 0.00 3.50
1365 1392 0.544697 AACTACCTTGGTATGGGCCG 59.455 55.000 0.00 0.00 0.00 6.13
1389 1416 1.061131 CAATTGCTAGTTGGAGTCGCG 59.939 52.381 0.00 0.00 0.00 5.87
1449 1476 6.437793 AGGACGAAGATTTCCGATATATTCCT 59.562 38.462 0.00 0.00 36.95 3.36
1453 1480 6.659668 TGAGAGGACGAAGATTTCCGATATAT 59.340 38.462 0.00 0.00 36.95 0.86
1545 1572 1.962822 CAGCAGTGAAGCCTTGCGA 60.963 57.895 0.00 0.00 42.47 5.10
1591 1618 5.713389 AGCAACTGATTCCATGAATCTCAAA 59.287 36.000 15.58 0.00 45.92 2.69
1630 1657 1.052617 TGTGAATTCCGACACCTGGA 58.947 50.000 0.00 0.00 36.35 3.86
1713 1740 6.667414 TGGTATAAGGATTGCCAAATGACTTT 59.333 34.615 0.00 0.00 36.29 2.66
1761 1788 3.019564 AGGGATCAGATTTTTCTTGCCG 58.980 45.455 0.00 0.00 0.00 5.69
1854 1881 1.237285 ACAGCTCACCGCCATGTTTC 61.237 55.000 0.00 0.00 40.39 2.78
1893 1920 4.725810 ACTGATTCCCTCCATTCATTCTCT 59.274 41.667 0.00 0.00 0.00 3.10
1970 1997 1.483827 CTTGCAGTATGGAGGCTCTCA 59.516 52.381 15.23 11.10 38.09 3.27
1998 2025 4.112634 ACCTAGTTTCATGGCCAAAAGA 57.887 40.909 10.96 5.53 0.00 2.52
2009 2036 4.527038 CCACACTTCTCCTACCTAGTTTCA 59.473 45.833 0.00 0.00 0.00 2.69
2014 2041 4.087182 TCAACCACACTTCTCCTACCTAG 58.913 47.826 0.00 0.00 0.00 3.02
2057 2084 5.105595 GGAAATTCATCTTTCTCCACCCTTG 60.106 44.000 0.00 0.00 35.81 3.61
2058 2085 5.019470 GGAAATTCATCTTTCTCCACCCTT 58.981 41.667 0.00 0.00 35.81 3.95
2096 2123 2.380084 TTTCCTCCCGACGAAATCAG 57.620 50.000 0.00 0.00 0.00 2.90
2142 2169 1.069022 CCGCTGACATCACCAAACAAG 60.069 52.381 0.00 0.00 0.00 3.16
2160 2187 0.404426 ACTTCTTTTCCCCTTCCCCG 59.596 55.000 0.00 0.00 0.00 5.73
2202 2229 0.472471 TCACAGGGCCTTTTCTTCGT 59.528 50.000 1.32 0.00 0.00 3.85
2203 2230 1.160137 CTCACAGGGCCTTTTCTTCG 58.840 55.000 1.32 0.00 0.00 3.79
2251 2278 6.012337 TCCCTTGATGGTATCTGCATTTAA 57.988 37.500 0.00 0.00 0.00 1.52
2283 2310 3.118592 CCTCAGTCTCCTTCCACATAACC 60.119 52.174 0.00 0.00 0.00 2.85
2287 2314 2.630889 TCCTCAGTCTCCTTCCACAT 57.369 50.000 0.00 0.00 0.00 3.21
2357 2384 0.969894 CCCACCGTTCTTCACTCTCT 59.030 55.000 0.00 0.00 0.00 3.10
2370 2397 0.178932 TCCTCCCATATCTCCCACCG 60.179 60.000 0.00 0.00 0.00 4.94
2563 2590 0.605589 ACTTCCAGAAGAGTCCGCAG 59.394 55.000 14.19 0.00 40.79 5.18
2575 2602 9.099454 GGTATCAACACTTAAATCTACTTCCAG 57.901 37.037 0.00 0.00 0.00 3.86
2601 2628 1.131883 CTTCCTTTCTCATGCAAGCGG 59.868 52.381 0.00 0.00 0.00 5.52
2772 2799 3.181465 TGAAGTGAGTCTCTCCACCAAAC 60.181 47.826 0.65 0.00 0.00 2.93
2955 2982 4.265073 CAACAATAGCTAGGCCAAGAGTT 58.735 43.478 5.01 0.00 0.00 3.01
2969 2996 5.473846 TCCGAGAGTATAGCTCCAACAATAG 59.526 44.000 0.00 0.00 45.21 1.73
3042 3069 5.237236 TCCAAGAAAAATCTCTTACGGGT 57.763 39.130 0.00 0.00 33.81 5.28
3046 3073 9.442047 TCTCTCATTCCAAGAAAAATCTCTTAC 57.558 33.333 0.00 0.00 33.81 2.34
3069 3096 8.725148 TGATTTTTCAAGCTGATTACTTCTCTC 58.275 33.333 0.00 0.00 0.00 3.20
3248 3275 0.749454 CCTCCGATGCTTCTTTGGGG 60.749 60.000 0.00 0.00 0.00 4.96
3273 3300 1.376466 CCACCACTTCCTCCACCTG 59.624 63.158 0.00 0.00 0.00 4.00
3321 3348 2.773087 AGCTTCAGATCTCTGCATCCTT 59.227 45.455 11.97 0.00 43.46 3.36
3489 3516 6.314648 CAGAAGAATGTTTGATTGATCCTCGA 59.685 38.462 0.00 0.00 0.00 4.04
3501 3528 5.163683 CCATAGGTGCTCAGAAGAATGTTTG 60.164 44.000 0.00 0.00 0.00 2.93
3603 3630 0.953727 GCACCACAATCTGCTTCACA 59.046 50.000 0.00 0.00 0.00 3.58
3618 3645 0.878416 TGTTTATCGCAAGTGGCACC 59.122 50.000 15.27 0.00 45.17 5.01
3660 3687 1.028330 GCAGCTCCAGTGCAGCATTA 61.028 55.000 9.15 0.00 43.48 1.90
3729 3756 1.282738 TCTCTCCATTTGCCAGCATGA 59.717 47.619 0.00 0.00 39.69 3.07
3747 3774 6.998968 CTAAAGCAGGAGATTGATGTTTCT 57.001 37.500 0.00 0.00 0.00 2.52
3993 4020 4.942761 ACTAAGGTGGACGTTTGTAAGA 57.057 40.909 0.00 0.00 30.53 2.10
4203 4231 4.018415 AGGCAACATGTATTGGTAGAACCT 60.018 41.667 0.00 0.00 38.10 3.50
4217 4245 2.297033 AGCTTACACCAAAGGCAACATG 59.703 45.455 0.00 0.00 41.41 3.21
4224 4252 5.938125 ACAACATAGTAGCTTACACCAAAGG 59.062 40.000 0.00 0.00 0.00 3.11
4289 4321 3.999663 ACTTACAAGCATCAGTTCAGAGC 59.000 43.478 0.00 0.00 0.00 4.09
4292 4324 5.468072 ACAGAACTTACAAGCATCAGTTCAG 59.532 40.000 12.21 7.49 45.13 3.02
4297 4329 4.391216 CAGGACAGAACTTACAAGCATCAG 59.609 45.833 0.00 0.00 0.00 2.90
4300 4332 3.077359 GCAGGACAGAACTTACAAGCAT 58.923 45.455 0.00 0.00 0.00 3.79
4321 4353 6.835819 AAATCATGGCATCTTATCATCAGG 57.164 37.500 0.00 0.00 0.00 3.86
4373 4410 6.645827 GTCAATTCGACATCATCTCTCATCAT 59.354 38.462 0.00 0.00 44.69 2.45
4379 4416 3.119291 GCGTCAATTCGACATCATCTCT 58.881 45.455 8.20 0.00 45.70 3.10
4426 4464 1.129998 CTCAGCGCTCAAATCAACAGG 59.870 52.381 7.13 0.00 0.00 4.00
4473 4511 4.022416 AGGCATCATTCACGTTGCTAAAAA 60.022 37.500 7.51 0.00 35.46 1.94
4474 4512 3.505680 AGGCATCATTCACGTTGCTAAAA 59.494 39.130 7.51 0.00 35.46 1.52
4475 4513 3.081061 AGGCATCATTCACGTTGCTAAA 58.919 40.909 7.51 0.00 35.46 1.85
4476 4514 2.710377 AGGCATCATTCACGTTGCTAA 58.290 42.857 7.51 0.00 35.46 3.09
4477 4515 2.401583 AGGCATCATTCACGTTGCTA 57.598 45.000 7.51 0.00 35.46 3.49
4478 4516 1.538047 AAGGCATCATTCACGTTGCT 58.462 45.000 7.51 0.00 35.46 3.91
4479 4517 2.352503 AAAGGCATCATTCACGTTGC 57.647 45.000 0.00 0.00 0.00 4.17
4499 4537 4.022416 AGGCATCATTCACGTTGCTAAAAA 60.022 37.500 7.51 0.00 35.46 1.94
4500 4538 3.505680 AGGCATCATTCACGTTGCTAAAA 59.494 39.130 7.51 0.00 35.46 1.52
4501 4539 3.081061 AGGCATCATTCACGTTGCTAAA 58.919 40.909 7.51 0.00 35.46 1.85
4502 4540 2.677836 GAGGCATCATTCACGTTGCTAA 59.322 45.455 7.51 0.00 35.46 3.09
4503 4541 2.093500 AGAGGCATCATTCACGTTGCTA 60.093 45.455 0.00 0.00 35.46 3.49
4504 4542 1.089920 GAGGCATCATTCACGTTGCT 58.910 50.000 7.51 0.00 35.46 3.91
4505 4543 1.089920 AGAGGCATCATTCACGTTGC 58.910 50.000 0.00 0.00 0.00 4.17
4506 4544 2.743664 TCAAGAGGCATCATTCACGTTG 59.256 45.455 0.00 0.00 0.00 4.10
4507 4545 3.005554 CTCAAGAGGCATCATTCACGTT 58.994 45.455 0.00 0.00 0.00 3.99
4508 4546 2.625737 CTCAAGAGGCATCATTCACGT 58.374 47.619 0.00 0.00 0.00 4.49
4509 4547 1.329906 GCTCAAGAGGCATCATTCACG 59.670 52.381 0.00 0.00 0.00 4.35
4742 4782 6.155475 AGGTCACTCTAGCATTCAGATAAC 57.845 41.667 0.00 0.00 0.00 1.89
4928 4969 9.892130 TCTAGAGGAGGATTTTGAAAGTAAATC 57.108 33.333 0.00 0.00 39.92 2.17
4944 4985 1.479368 GCCCAGCCATCTAGAGGAGG 61.479 65.000 5.84 5.16 0.00 4.30
4960 5001 1.201429 TCAGGAACAAGAGAGGGCCC 61.201 60.000 16.46 16.46 0.00 5.80
4991 5032 6.617879 ACTTTTGGAAATTATACGAGTTGGC 58.382 36.000 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.