Multiple sequence alignment - TraesCS2D01G254000

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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 TraesCS2D01G254000 chr2D 100.000 7026 0 0 716 7741 306339796 306346821 0.000000e+00 12975
1 TraesCS2D01G254000 chr2D 100.000 378 0 0 1 378 306339081 306339458 0.000000e+00 699
2 TraesCS2D01G254000 chr2B 96.081 7043 163 32 755 7741 374258012 374264997 0.000000e+00 11372
3 TraesCS2D01G254000 chr2B 91.270 378 31 2 1 378 374257210 374257585 1.490000e-141 514
4 TraesCS2D01G254000 chr2A 95.681 4677 104 30 3090 7741 385446603 385451206 0.000000e+00 7428
5 TraesCS2D01G254000 chr2A 95.327 2311 52 12 826 3106 385444129 385446413 0.000000e+00 3618
6 TraesCS2D01G254000 chr2A 83.598 378 48 3 1 378 385442019 385442382 7.440000e-90 342


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 TraesCS2D01G254000 chr2D 306339081 306346821 7740 False 6837 12975 100.000000 1 7741 2 chr2D.!!$F1 7740
1 TraesCS2D01G254000 chr2B 374257210 374264997 7787 False 5943 11372 93.675500 1 7741 2 chr2B.!!$F1 7740
2 TraesCS2D01G254000 chr2A 385442019 385451206 9187 False 3796 7428 91.535333 1 7741 3 chr2A.!!$F1 7740

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
89 90 0.383590 CCTCGTGCGTGATCTCATCT 59.616 55.000 0.00 0.0 0.00 2.90 F
298 299 0.617413 ACGACCGAAGAGAGGTAGGA 59.383 55.000 0.00 0.0 43.01 2.94 F
1866 3279 0.174845 CCCGTGAAGGAGCGTCAATA 59.825 55.000 0.00 0.0 45.00 1.90 F
1997 3410 0.257039 GAATCACCCATGACCCTGCT 59.743 55.000 0.00 0.0 37.79 4.24 F
3476 5120 1.094785 ATGCATCGCACCAAACCTAC 58.905 50.000 0.00 0.0 43.04 3.18 F
4089 5739 0.250038 GTTCTCTGTGCTGTGCAGGA 60.250 55.000 1.11 0.0 40.08 3.86 F
5166 6816 0.462759 CTCGAAAGGGCTCCACATCC 60.463 60.000 0.00 0.0 0.00 3.51 F
6335 7985 1.213926 AGGCCTGGGATCAAATCTGTC 59.786 52.381 3.11 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1334 2736 0.029989 AGTCATTACCCCTCCCTCCC 60.030 60.000 0.00 0.00 0.00 4.30 R
1997 3410 1.111116 AGGAGTCCGTGACGAAACCA 61.111 55.000 6.54 0.00 37.67 3.67 R
3768 5417 0.319383 CTAGCGCTGTCCTGCATAGG 60.319 60.000 22.90 0.00 46.06 2.57 R
3769 5418 0.319383 CCTAGCGCTGTCCTGCATAG 60.319 60.000 22.90 5.52 0.00 2.23 R
4891 6541 1.002868 CTGCTGAACCAGAGTGGGG 60.003 63.158 0.00 0.00 43.37 4.96 R
5489 7139 0.035915 GGCCTCCTTGGTGAACTCTC 60.036 60.000 0.00 0.00 38.35 3.20 R
6411 8061 1.066002 CACCAGTGTTTGAGGCACAAG 59.934 52.381 0.00 0.00 39.77 3.16 R
7404 9093 2.012673 GCTGAGCTGGTATTTGGAGTG 58.987 52.381 0.00 0.00 0.00 3.51 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
21 22 4.349663 CAACAAGTTTTGTCGAAGGTGA 57.650 40.909 0.00 0.00 44.59 4.02
40 41 2.512515 GGCGGTGATGTCTGGCTC 60.513 66.667 0.00 0.00 36.52 4.70
89 90 0.383590 CCTCGTGCGTGATCTCATCT 59.616 55.000 0.00 0.00 0.00 2.90
101 102 1.541379 TCTCATCTGGGAAACGACGA 58.459 50.000 0.00 0.00 0.00 4.20
210 211 0.740164 CGACCGAAGAGGAGAGACGA 60.740 60.000 0.00 0.00 45.00 4.20
294 295 1.965219 CCAACGACCGAAGAGAGGT 59.035 57.895 0.00 0.00 46.16 3.85
298 299 0.617413 ACGACCGAAGAGAGGTAGGA 59.383 55.000 0.00 0.00 43.01 2.94
301 302 2.567985 GACCGAAGAGAGGTAGGAGAG 58.432 57.143 0.00 0.00 43.01 3.20
356 358 4.447342 ATTCCTTGCAGGCGGGGG 62.447 66.667 0.00 0.00 34.61 5.40
754 756 1.574702 GCGGGTGAGGGAAGAAAACG 61.575 60.000 0.00 0.00 0.00 3.60
911 2298 4.545610 ACCATAACGCAAAAGACACAATG 58.454 39.130 0.00 0.00 0.00 2.82
913 2300 4.853196 CCATAACGCAAAAGACACAATGAG 59.147 41.667 0.00 0.00 0.00 2.90
933 2326 5.115480 TGAGGTGCCAGAAAAACAAAAATC 58.885 37.500 0.00 0.00 0.00 2.17
934 2327 5.104982 TGAGGTGCCAGAAAAACAAAAATCT 60.105 36.000 0.00 0.00 0.00 2.40
935 2328 5.359756 AGGTGCCAGAAAAACAAAAATCTC 58.640 37.500 0.00 0.00 0.00 2.75
936 2329 5.104982 AGGTGCCAGAAAAACAAAAATCTCA 60.105 36.000 0.00 0.00 0.00 3.27
937 2330 5.234972 GGTGCCAGAAAAACAAAAATCTCAG 59.765 40.000 0.00 0.00 0.00 3.35
1324 2726 5.334414 CGAGGATTGGTTTCTCACTTTCTTG 60.334 44.000 0.00 0.00 0.00 3.02
1325 2727 4.829492 AGGATTGGTTTCTCACTTTCTTGG 59.171 41.667 0.00 0.00 0.00 3.61
1326 2728 4.827284 GGATTGGTTTCTCACTTTCTTGGA 59.173 41.667 0.00 0.00 0.00 3.53
1327 2729 5.048434 GGATTGGTTTCTCACTTTCTTGGAG 60.048 44.000 0.00 0.00 0.00 3.86
1328 2730 3.820557 TGGTTTCTCACTTTCTTGGAGG 58.179 45.455 0.00 0.00 0.00 4.30
1329 2731 3.149981 GGTTTCTCACTTTCTTGGAGGG 58.850 50.000 0.00 0.00 0.00 4.30
1330 2732 3.181443 GGTTTCTCACTTTCTTGGAGGGA 60.181 47.826 0.00 0.00 0.00 4.20
1331 2733 4.461198 GTTTCTCACTTTCTTGGAGGGAA 58.539 43.478 0.00 0.00 0.00 3.97
1332 2734 3.771577 TCTCACTTTCTTGGAGGGAAC 57.228 47.619 0.00 0.00 0.00 3.62
1334 2736 3.071602 TCTCACTTTCTTGGAGGGAACTG 59.928 47.826 0.00 0.00 44.43 3.16
1435 2837 2.931105 TTTAGTGGGCGGGGCTCA 60.931 61.111 0.00 0.00 36.30 4.26
1548 2951 7.964604 AAGTGTTACACCTAGATTCTTTGTC 57.035 36.000 12.28 0.00 34.49 3.18
1594 2997 7.221645 GCTCAAAGATTTGGCTCTTAAATTAGC 59.778 37.037 5.52 0.00 38.66 3.09
1834 3247 0.462759 GCGTTCTTGAGGCCTGCTAT 60.463 55.000 12.00 0.00 33.08 2.97
1842 3255 0.250252 GAGGCCTGCTATCTTCCAGC 60.250 60.000 12.00 0.00 39.56 4.85
1866 3279 0.174845 CCCGTGAAGGAGCGTCAATA 59.825 55.000 0.00 0.00 45.00 1.90
1997 3410 0.257039 GAATCACCCATGACCCTGCT 59.743 55.000 0.00 0.00 37.79 4.24
2009 3422 2.317609 CCCTGCTGGTTTCGTCACG 61.318 63.158 9.00 0.00 0.00 4.35
2111 3524 1.227823 TGGAGTTGTGCTTGACGGG 60.228 57.895 0.00 0.00 0.00 5.28
2123 3536 1.326951 TTGACGGGCATCGGATCTCA 61.327 55.000 3.86 0.00 44.45 3.27
2418 3831 1.378250 GGCAATGCTCTGTCTGGCT 60.378 57.895 4.82 0.00 0.00 4.75
2930 4343 2.293399 CCAACTGGACCTTAGTGCAAAC 59.707 50.000 0.00 0.00 44.45 2.93
3029 4442 7.088272 TGCAATGCTCATTCTGATTATATTGC 58.912 34.615 6.82 0.00 44.70 3.56
3240 4863 7.879677 TGTCTGTTCAGAATCACATTTCTATGT 59.120 33.333 3.99 0.00 45.81 2.29
3322 4946 5.620206 TCTCCTTTGCAACTACTTGATTGA 58.380 37.500 0.00 0.00 0.00 2.57
3339 4963 3.473923 TTGAGGATTGCTCGCATGATA 57.526 42.857 0.00 0.00 0.00 2.15
3375 5019 5.179368 GTGCAGAGTCAAGTTGTTAGCATAA 59.821 40.000 2.11 0.00 0.00 1.90
3377 5021 7.064609 GTGCAGAGTCAAGTTGTTAGCATAATA 59.935 37.037 2.11 0.00 0.00 0.98
3410 5054 9.034800 TGATGATATGGCATAACACTACAGATA 57.965 33.333 18.19 0.00 0.00 1.98
3476 5120 1.094785 ATGCATCGCACCAAACCTAC 58.905 50.000 0.00 0.00 43.04 3.18
3501 5145 8.727910 ACTAGATTGCTGATAATTATGTGCATG 58.272 33.333 17.39 0.00 0.00 4.06
3565 5209 3.350833 CTGAAAGAGAAGTGAATGGGGG 58.649 50.000 0.00 0.00 34.07 5.40
3661 5310 5.410924 TGAGAGTAGCATGTTCATGTGTAC 58.589 41.667 13.24 13.73 0.00 2.90
3678 5327 7.704899 TCATGTGTACTGTTCCATTAGTAATCG 59.295 37.037 0.00 0.00 31.74 3.34
3697 5346 1.743394 CGTCTGCTGGGTTAATTTCCC 59.257 52.381 10.39 10.39 44.81 3.97
3767 5416 4.015084 TGTAAGGTAGAGTGGACTACAGC 58.985 47.826 0.00 0.00 42.91 4.40
3768 5417 2.146920 AGGTAGAGTGGACTACAGCC 57.853 55.000 0.00 0.00 42.91 4.85
3769 5418 1.112950 GGTAGAGTGGACTACAGCCC 58.887 60.000 0.00 0.00 42.91 5.19
3793 5442 2.190578 GGACAGCGCTAGGCCATT 59.809 61.111 22.19 0.00 45.17 3.16
3827 5476 2.564947 GCCCTATGCAGTACAGAGCTAT 59.435 50.000 0.00 0.00 36.22 2.97
3872 5521 7.342799 AGTTCCATTTCATAATTATGGCACTGT 59.657 33.333 22.31 3.97 41.98 3.55
3873 5522 7.658525 TCCATTTCATAATTATGGCACTGTT 57.341 32.000 22.31 2.09 38.93 3.16
4005 5654 0.896923 TTTGGAGCATGGCATTGTCC 59.103 50.000 15.26 15.26 0.00 4.02
4089 5739 0.250038 GTTCTCTGTGCTGTGCAGGA 60.250 55.000 1.11 0.00 40.08 3.86
4647 6297 6.375455 GTGTCCTTGACATATCCTCAAACAAT 59.625 38.462 0.00 0.00 44.63 2.71
4695 6345 2.160417 CACTAAGCTTGCAGCACTTACC 59.840 50.000 9.86 0.00 45.56 2.85
4728 6378 0.531090 CAACGAACCAGTTCACGGGA 60.531 55.000 10.90 0.00 39.46 5.14
4891 6541 1.805869 CTCATCTGGATCCGGCAATC 58.194 55.000 16.48 0.00 0.00 2.67
5142 6792 2.108976 TCGGCGGATGATCTTGGC 59.891 61.111 7.21 0.00 0.00 4.52
5166 6816 0.462759 CTCGAAAGGGCTCCACATCC 60.463 60.000 0.00 0.00 0.00 3.51
5427 7077 1.541670 GGAACTTCGTACAGGGCAACA 60.542 52.381 0.00 0.00 39.74 3.33
5489 7139 2.032528 TGTTGCGAGGCCCAAGAG 59.967 61.111 0.00 0.00 0.00 2.85
5939 7589 2.409870 CCTTGACCTCAATGCCCGC 61.410 63.158 0.00 0.00 35.02 6.13
5940 7590 1.675310 CTTGACCTCAATGCCCGCA 60.675 57.895 0.00 0.00 35.02 5.69
5945 7595 3.957535 CTCAATGCCCGCATCGCC 61.958 66.667 2.00 0.00 35.31 5.54
6247 7897 1.874345 GCTTCGGACTCGGAGAACCA 61.874 60.000 12.86 3.69 44.53 3.67
6329 7979 3.264574 CGAAAGGCCTGGGATCAAA 57.735 52.632 5.69 0.00 0.00 2.69
6335 7985 1.213926 AGGCCTGGGATCAAATCTGTC 59.786 52.381 3.11 0.00 0.00 3.51
6411 8061 1.332997 GGATGCTCATGTGCTGTTAGC 59.667 52.381 19.60 7.28 42.82 3.09
6425 8075 2.618241 CTGTTAGCTTGTGCCTCAAACA 59.382 45.455 0.00 0.00 40.80 2.83
6428 8078 1.027357 AGCTTGTGCCTCAAACACTG 58.973 50.000 0.00 0.00 40.80 3.66
6495 8145 3.698040 AGATGGCAATGTCTCATTGGTTC 59.302 43.478 19.44 7.12 0.00 3.62
7011 8670 5.147162 CAAAAGCAAACCTCATTCGTAGAC 58.853 41.667 0.00 0.00 34.32 2.59
7055 8714 0.966179 GACAAACCCCCAACACATCC 59.034 55.000 0.00 0.00 0.00 3.51
7077 8736 0.037303 TTCTCAGCCAAGCCTTCAGG 59.963 55.000 0.00 0.00 38.53 3.86
7078 8737 1.378250 CTCAGCCAAGCCTTCAGGG 60.378 63.158 0.00 0.00 35.18 4.45
7080 8739 1.975407 CAGCCAAGCCTTCAGGGTG 60.975 63.158 0.00 0.00 46.73 4.61
7081 8740 3.376918 GCCAAGCCTTCAGGGTGC 61.377 66.667 0.00 0.00 46.73 5.01
7082 8741 2.115910 CCAAGCCTTCAGGGTGCA 59.884 61.111 0.00 0.00 46.73 4.57
7083 8742 1.304713 CCAAGCCTTCAGGGTGCAT 60.305 57.895 0.00 0.00 46.73 3.96
7084 8743 0.034186 CCAAGCCTTCAGGGTGCATA 60.034 55.000 0.00 0.00 46.73 3.14
7085 8744 1.616725 CCAAGCCTTCAGGGTGCATAA 60.617 52.381 0.00 0.00 46.73 1.90
7086 8745 2.170166 CAAGCCTTCAGGGTGCATAAA 58.830 47.619 0.00 0.00 46.73 1.40
7087 8746 2.562298 CAAGCCTTCAGGGTGCATAAAA 59.438 45.455 0.00 0.00 46.73 1.52
7088 8747 3.105959 AGCCTTCAGGGTGCATAAAAT 57.894 42.857 0.00 0.00 45.50 1.82
7089 8748 2.762327 AGCCTTCAGGGTGCATAAAATG 59.238 45.455 0.00 0.00 45.50 2.32
7090 8749 2.760092 GCCTTCAGGGTGCATAAAATGA 59.240 45.455 0.00 0.00 37.43 2.57
7091 8750 3.181483 GCCTTCAGGGTGCATAAAATGAG 60.181 47.826 0.00 0.00 37.43 2.90
7092 8751 4.019174 CCTTCAGGGTGCATAAAATGAGT 58.981 43.478 0.00 0.00 0.00 3.41
7093 8752 4.463891 CCTTCAGGGTGCATAAAATGAGTT 59.536 41.667 0.00 0.00 0.00 3.01
7094 8753 5.389859 TTCAGGGTGCATAAAATGAGTTG 57.610 39.130 0.00 0.00 0.00 3.16
7095 8754 4.406456 TCAGGGTGCATAAAATGAGTTGT 58.594 39.130 0.00 0.00 0.00 3.32
7096 8755 5.565509 TCAGGGTGCATAAAATGAGTTGTA 58.434 37.500 0.00 0.00 0.00 2.41
7097 8756 6.186957 TCAGGGTGCATAAAATGAGTTGTAT 58.813 36.000 0.00 0.00 0.00 2.29
7098 8757 6.663093 TCAGGGTGCATAAAATGAGTTGTATT 59.337 34.615 0.00 0.00 0.00 1.89
7099 8758 6.974622 CAGGGTGCATAAAATGAGTTGTATTC 59.025 38.462 0.00 0.00 0.00 1.75
7100 8759 6.891908 AGGGTGCATAAAATGAGTTGTATTCT 59.108 34.615 0.00 0.00 0.00 2.40
7101 8760 8.052748 AGGGTGCATAAAATGAGTTGTATTCTA 58.947 33.333 0.00 0.00 0.00 2.10
7102 8761 8.345565 GGGTGCATAAAATGAGTTGTATTCTAG 58.654 37.037 0.00 0.00 0.00 2.43
7103 8762 8.893727 GGTGCATAAAATGAGTTGTATTCTAGT 58.106 33.333 0.00 0.00 0.00 2.57
7156 8844 5.978814 TCCTATCACTTGGCTTTCTCTTAC 58.021 41.667 0.00 0.00 0.00 2.34
7266 8955 7.603180 AATACCAGCTCAACATAGTCATCTA 57.397 36.000 0.00 0.00 0.00 1.98
7295 8984 3.551485 CCAAAACAAAAAGAAGCACTCCG 59.449 43.478 0.00 0.00 0.00 4.63
7323 9012 5.011533 TCCTCTAATCCAGATCTTTGCTAGC 59.988 44.000 8.10 8.10 31.13 3.42
7329 9018 1.530293 CAGATCTTTGCTAGCATCCGC 59.470 52.381 20.13 7.57 38.99 5.54
7404 9093 9.774742 CAAGAAATAGTAAAATGTTACTCTGCC 57.225 33.333 11.71 1.69 45.63 4.85
7617 9306 2.366570 GCCTCCTCCACCTCCTCT 59.633 66.667 0.00 0.00 0.00 3.69
7673 9362 4.993705 ACTCCCTTCCAAAATAGACACA 57.006 40.909 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.814248 GCCCTCACCTTCGACAAAACT 60.814 52.381 0.00 0.00 0.00 2.66
19 20 2.659063 CCAGACATCACCGCCCTCA 61.659 63.158 0.00 0.00 0.00 3.86
21 22 4.101448 GCCAGACATCACCGCCCT 62.101 66.667 0.00 0.00 0.00 5.19
53 54 1.885850 GGGCGTACGGTATTGGCTG 60.886 63.158 18.39 0.00 0.00 4.85
89 90 1.530013 GGGACTCTCGTCGTTTCCCA 61.530 60.000 14.40 0.00 44.84 4.37
101 102 2.963371 GTTCGTCAGCGGGACTCT 59.037 61.111 9.40 0.00 44.68 3.24
175 176 1.009389 GTCGTCCTCAACTTCTGCCG 61.009 60.000 0.00 0.00 0.00 5.69
179 180 1.269998 CTTCGGTCGTCCTCAACTTCT 59.730 52.381 0.00 0.00 0.00 2.85
248 249 2.224066 CGTATCCGCCTCCAAGAAATCT 60.224 50.000 0.00 0.00 0.00 2.40
255 256 0.968901 ACAGTCGTATCCGCCTCCAA 60.969 55.000 0.00 0.00 0.00 3.53
278 279 1.004044 TCCTACCTCTCTTCGGTCGTT 59.996 52.381 0.00 0.00 35.98 3.85
294 295 0.563173 CAGATCCACCCCCTCTCCTA 59.437 60.000 0.00 0.00 0.00 2.94
298 299 2.367512 GGCAGATCCACCCCCTCT 60.368 66.667 0.00 0.00 34.01 3.69
356 358 4.086199 CACAAAATTCAATTGCCCATGC 57.914 40.909 0.00 0.00 38.26 4.06
735 737 1.574702 CGTTTTCTTCCCTCACCCGC 61.575 60.000 0.00 0.00 0.00 6.13
911 2298 5.359756 AGATTTTTGTTTTTCTGGCACCTC 58.640 37.500 0.00 0.00 0.00 3.85
913 2300 5.115480 TGAGATTTTTGTTTTTCTGGCACC 58.885 37.500 0.00 0.00 0.00 5.01
933 2326 2.866028 GCGCAACCAAGAGCTGAG 59.134 61.111 0.30 0.00 0.00 3.35
934 2327 3.043713 CGCGCAACCAAGAGCTGA 61.044 61.111 8.75 0.00 31.76 4.26
935 2328 4.093952 CCGCGCAACCAAGAGCTG 62.094 66.667 8.75 0.00 31.76 4.24
1324 2726 1.690985 CTCCCTCCCAGTTCCCTCC 60.691 68.421 0.00 0.00 0.00 4.30
1325 2727 1.690985 CCTCCCTCCCAGTTCCCTC 60.691 68.421 0.00 0.00 0.00 4.30
1326 2728 2.456840 CCTCCCTCCCAGTTCCCT 59.543 66.667 0.00 0.00 0.00 4.20
1327 2729 2.692741 CCCTCCCTCCCAGTTCCC 60.693 72.222 0.00 0.00 0.00 3.97
1328 2730 2.190904 TACCCCTCCCTCCCAGTTCC 62.191 65.000 0.00 0.00 0.00 3.62
1329 2731 0.253020 TTACCCCTCCCTCCCAGTTC 60.253 60.000 0.00 0.00 0.00 3.01
1330 2732 0.426022 ATTACCCCTCCCTCCCAGTT 59.574 55.000 0.00 0.00 0.00 3.16
1331 2733 0.327576 CATTACCCCTCCCTCCCAGT 60.328 60.000 0.00 0.00 0.00 4.00
1332 2734 0.030092 TCATTACCCCTCCCTCCCAG 60.030 60.000 0.00 0.00 0.00 4.45
1333 2735 0.327191 GTCATTACCCCTCCCTCCCA 60.327 60.000 0.00 0.00 0.00 4.37
1334 2736 0.029989 AGTCATTACCCCTCCCTCCC 60.030 60.000 0.00 0.00 0.00 4.30
1435 2837 5.544562 AGGTAGAAGAGGACTAAAAAGTGCT 59.455 40.000 0.00 0.00 43.14 4.40
1548 2951 8.908786 TTGAGCATCCAAGTAATAATAGGAAG 57.091 34.615 0.00 0.00 31.17 3.46
1594 2997 2.664851 TCCTGCTTTCACGGTGCG 60.665 61.111 2.51 0.00 0.00 5.34
1834 3247 1.125093 TCACGGGAAAGGCTGGAAGA 61.125 55.000 0.00 0.00 34.07 2.87
1842 3255 1.741770 CGCTCCTTCACGGGAAAGG 60.742 63.158 0.00 5.55 34.66 3.11
1866 3279 1.152652 TGCCAACAAACCCCATCGT 60.153 52.632 0.00 0.00 0.00 3.73
1997 3410 1.111116 AGGAGTCCGTGACGAAACCA 61.111 55.000 6.54 0.00 37.67 3.67
2009 3422 1.135333 GACTCGTCATTCCAGGAGTCC 59.865 57.143 0.00 0.00 46.08 3.85
2111 3524 1.293924 CAACACCTGAGATCCGATGC 58.706 55.000 0.00 0.00 0.00 3.91
2123 3536 1.901085 GGAGAGATCGGCAACACCT 59.099 57.895 0.00 0.00 35.61 4.00
2418 3831 2.437180 CAGAGCTGCCGGCAATGA 60.437 61.111 32.09 7.42 44.79 2.57
2541 3954 2.761767 CACCATCCAATTGATTCCAGCA 59.238 45.455 7.12 0.00 0.00 4.41
2756 4169 4.298103 ACTCAGATCAAGCACCTTCAAT 57.702 40.909 0.00 0.00 0.00 2.57
2967 4380 4.199310 TGAAATAGCGAGGGGATCAAAAG 58.801 43.478 0.00 0.00 0.00 2.27
3029 4442 8.218338 AGCTGTAAATAGATGGATCAAACTTG 57.782 34.615 0.00 0.00 0.00 3.16
3240 4863 3.944650 AGCAATATGTACATCCGTTTGCA 59.055 39.130 28.44 9.66 40.19 4.08
3246 4869 5.631096 CAGTAGACAGCAATATGTACATCCG 59.369 44.000 12.68 3.20 32.25 4.18
3322 4946 4.202441 ACTTTTATCATGCGAGCAATCCT 58.798 39.130 0.57 0.00 0.00 3.24
3339 4963 0.385390 CTCTGCACGCCCAAACTTTT 59.615 50.000 0.00 0.00 0.00 2.27
3375 5019 7.037370 TGTTATGCCATATCATCAACTCCCTAT 60.037 37.037 0.00 0.00 0.00 2.57
3377 5021 5.073554 TGTTATGCCATATCATCAACTCCCT 59.926 40.000 0.00 0.00 0.00 4.20
3410 5054 9.739276 TTTCACTCAACATAACTTCTCCATATT 57.261 29.630 0.00 0.00 0.00 1.28
3476 5120 8.727910 ACATGCACATAATTATCAGCAATCTAG 58.272 33.333 19.53 12.29 35.45 2.43
3549 5193 2.507471 GTCATCCCCCATTCACTTCTCT 59.493 50.000 0.00 0.00 0.00 3.10
3565 5209 2.544903 CCGTTTGGTTTGTTGGGTCATC 60.545 50.000 0.00 0.00 0.00 2.92
3697 5346 3.317993 TGAATGAAGCATGGCATCTGATG 59.682 43.478 13.26 13.26 0.00 3.07
3760 5409 1.123928 GTCCTGCATAGGGCTGTAGT 58.876 55.000 0.00 0.00 45.57 2.73
3767 5416 1.748329 TAGCGCTGTCCTGCATAGGG 61.748 60.000 22.90 0.00 44.70 3.53
3768 5417 0.319383 CTAGCGCTGTCCTGCATAGG 60.319 60.000 22.90 0.00 46.06 2.57
3769 5418 0.319383 CCTAGCGCTGTCCTGCATAG 60.319 60.000 22.90 5.52 0.00 2.23
3793 5442 2.722094 CATAGGGCTAGCCAACAACAA 58.278 47.619 34.09 11.63 37.98 2.83
3827 5476 2.297880 ACTGTACGACACAACCATAGCA 59.702 45.455 0.00 0.00 36.48 3.49
3872 5521 3.805971 CGCATCTGTGAAGCATCAGATAA 59.194 43.478 7.23 0.00 45.77 1.75
3873 5522 3.181472 ACGCATCTGTGAAGCATCAGATA 60.181 43.478 7.23 0.00 45.77 1.98
3990 5639 1.026182 TCGTGGACAATGCCATGCTC 61.026 55.000 9.90 0.00 43.25 4.26
4005 5654 6.307558 GCAGATACTGACAGATTATCATCGTG 59.692 42.308 10.08 3.25 31.85 4.35
4058 5707 6.264744 ACAGCACAGAGAACTACAGTTAGTAA 59.735 38.462 0.00 0.00 37.59 2.24
4212 5862 7.822658 TGGTAAAAACTGATAAATTTCCTCGG 58.177 34.615 0.00 1.00 0.00 4.63
4647 6297 2.762535 CTGGTAAAGCTCCGGAGAAA 57.237 50.000 35.69 13.26 33.49 2.52
4695 6345 3.483574 GGTTCGTTGATATGTCAAGTGCG 60.484 47.826 4.98 6.28 44.58 5.34
4891 6541 1.002868 CTGCTGAACCAGAGTGGGG 60.003 63.158 0.00 0.00 43.37 4.96
4990 6640 4.119862 CGCTTGTAGTGGCATACAATAGT 58.880 43.478 17.05 0.00 42.97 2.12
5142 6792 2.202810 GAGCCCTTTCGAGGAGCG 60.203 66.667 0.00 0.00 42.69 5.03
5166 6816 1.630244 CTTCTTGGCTCGGTGCTTCG 61.630 60.000 1.77 0.00 42.39 3.79
5489 7139 0.035915 GGCCTCCTTGGTGAACTCTC 60.036 60.000 0.00 0.00 38.35 3.20
5939 7589 1.589993 CAGGCAGTAGTCGGCGATG 60.590 63.158 14.79 8.56 35.70 3.84
5940 7590 2.808315 CAGGCAGTAGTCGGCGAT 59.192 61.111 14.79 4.89 35.70 4.58
5945 7595 2.507102 CGGTGCAGGCAGTAGTCG 60.507 66.667 0.00 0.00 0.00 4.18
6128 7778 1.605451 AGACCCCGTGATGACGTCA 60.605 57.895 22.48 22.48 44.54 4.35
6329 7979 5.830457 TGATGAAAGATCCTCGTAGACAGAT 59.170 40.000 0.00 0.00 0.00 2.90
6335 7985 6.806249 GCTAGATTGATGAAAGATCCTCGTAG 59.194 42.308 0.00 0.00 0.00 3.51
6411 8061 1.066002 CACCAGTGTTTGAGGCACAAG 59.934 52.381 0.00 0.00 39.77 3.16
6425 8075 2.504175 ACACACCTACAGAAACACCAGT 59.496 45.455 0.00 0.00 0.00 4.00
6428 8078 2.218603 CCACACACCTACAGAAACACC 58.781 52.381 0.00 0.00 0.00 4.16
7011 8670 3.489785 GTGCTTACCATTTCGTATCCTCG 59.510 47.826 0.00 0.00 0.00 4.63
7020 8679 4.982295 GGTTTGTCTTGTGCTTACCATTTC 59.018 41.667 0.00 0.00 0.00 2.17
7024 8683 2.303175 GGGTTTGTCTTGTGCTTACCA 58.697 47.619 0.00 0.00 0.00 3.25
7055 8714 2.228343 CTGAAGGCTTGGCTGAGAAAAG 59.772 50.000 3.46 0.00 0.00 2.27
7077 8736 8.893727 ACTAGAATACAACTCATTTTATGCACC 58.106 33.333 0.00 0.00 0.00 5.01
7078 8737 9.708222 CACTAGAATACAACTCATTTTATGCAC 57.292 33.333 0.00 0.00 0.00 4.57
7079 8738 9.448438 ACACTAGAATACAACTCATTTTATGCA 57.552 29.630 0.00 0.00 0.00 3.96
7096 8755 7.976734 GCAGTTGTCTCTATGTAACACTAGAAT 59.023 37.037 0.00 0.00 0.00 2.40
7097 8756 7.039993 TGCAGTTGTCTCTATGTAACACTAGAA 60.040 37.037 0.00 0.00 0.00 2.10
7098 8757 6.433093 TGCAGTTGTCTCTATGTAACACTAGA 59.567 38.462 0.00 0.00 0.00 2.43
7099 8758 6.621613 TGCAGTTGTCTCTATGTAACACTAG 58.378 40.000 0.00 0.00 0.00 2.57
7100 8759 6.584185 TGCAGTTGTCTCTATGTAACACTA 57.416 37.500 0.00 0.00 0.00 2.74
7101 8760 5.468540 TGCAGTTGTCTCTATGTAACACT 57.531 39.130 0.00 0.00 0.00 3.55
7102 8761 6.727824 ATTGCAGTTGTCTCTATGTAACAC 57.272 37.500 0.00 0.00 0.00 3.32
7103 8762 8.257306 TCATATTGCAGTTGTCTCTATGTAACA 58.743 33.333 0.00 0.00 0.00 2.41
7196 8885 6.099269 TGACTGTTTCCTTGGTTAGTAGTCTT 59.901 38.462 0.00 0.00 34.63 3.01
7266 8955 4.758688 CTTCTTTTTGTTTTGGAGTGGCT 58.241 39.130 0.00 0.00 0.00 4.75
7295 8984 5.295540 GCAAAGATCTGGATTAGAGGAACAC 59.704 44.000 0.00 0.00 39.20 3.32
7323 9012 3.880846 GGAAGGCTTGCGCGGATG 61.881 66.667 8.83 9.04 36.88 3.51
7329 9018 2.040544 ATTCGTGGGAAGGCTTGCG 61.041 57.895 12.78 8.01 35.19 4.85
7404 9093 2.012673 GCTGAGCTGGTATTTGGAGTG 58.987 52.381 0.00 0.00 0.00 3.51
7617 9306 3.801307 ATATCCATCCTGAAGCATGCA 57.199 42.857 21.98 0.00 0.00 3.96
7673 9362 9.685276 TGTTGATCCAAACATGTATATCTCTTT 57.315 29.630 0.00 0.00 35.16 2.52


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

AutoCloner maintained by Alex Coulton.