Multiple sequence alignment - TraesCS7A01G311400

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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 TraesCS7A01G311400 chr7A 100.000 3104 0 0 1 3104 441199015 441195912 0.000000e+00 5733.0
1 TraesCS7A01G311400 chr7D 94.575 2636 91 14 425 3035 390157829 390155221 0.000000e+00 4028.0
2 TraesCS7A01G311400 chr7B 94.364 2218 79 12 904 3104 385620974 385618786 0.000000e+00 3362.0
3 TraesCS7A01G311400 chr7B 93.277 476 28 3 433 904 385621495 385621020 0.000000e+00 699.0
4 TraesCS7A01G311400 chr7B 87.857 140 12 2 1 140 385624063 385623929 3.200000e-35 159.0
5 TraesCS7A01G311400 chr7B 91.549 71 4 2 323 392 385621565 385621496 2.550000e-16 97.1


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 TraesCS7A01G311400 chr7A 441195912 441199015 3103 True 5733.000 5733 100.00000 1 3104 1 chr7A.!!$R1 3103
1 TraesCS7A01G311400 chr7D 390155221 390157829 2608 True 4028.000 4028 94.57500 425 3035 1 chr7D.!!$R1 2610
2 TraesCS7A01G311400 chr7B 385618786 385624063 5277 True 1079.275 3362 91.76175 1 3104 4 chr7B.!!$R1 3103

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
187 188 0.032017 GCTCTTGACCTCCCTCCCTA 60.032 60.0 0.00 0.0 0.00 3.53 F
1380 3654 0.898320 GCTTCACAGAGGCTACCTGA 59.102 55.0 9.94 0.0 31.76 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 3954 0.897621 TGCGGCTCATCTTCTTCTCA 59.102 50.0 0.0 0.0 0.0 3.27 R
2675 4965 0.928505 TCCGGATAGTACAGGGTCCA 59.071 55.0 0.0 0.0 0.0 4.02 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
45 46 2.025155 GAGAGGGTGACGAATAGCTCA 58.975 52.381 0.00 0.00 0.00 4.26
56 57 5.246203 TGACGAATAGCTCAGCCCTATTAAT 59.754 40.000 0.00 0.00 36.05 1.40
57 58 5.482908 ACGAATAGCTCAGCCCTATTAATG 58.517 41.667 0.00 0.00 36.05 1.90
80 81 4.159377 CCATGTGGTATTGTGTGACAAC 57.841 45.455 0.00 0.00 41.40 3.32
127 128 8.959705 ACTACTAGTTTGCCCATAGAAAATAC 57.040 34.615 0.00 0.00 0.00 1.89
140 141 9.938280 CCCATAGAAAATACTGTATATTCGGAA 57.062 33.333 0.00 0.00 0.00 4.30
149 150 8.976986 ATACTGTATATTCGGAATTAACGACC 57.023 34.615 8.76 0.00 40.45 4.79
150 151 6.808829 ACTGTATATTCGGAATTAACGACCA 58.191 36.000 8.76 0.00 40.45 4.02
151 152 7.439381 ACTGTATATTCGGAATTAACGACCAT 58.561 34.615 8.76 0.00 40.45 3.55
152 153 7.384115 ACTGTATATTCGGAATTAACGACCATG 59.616 37.037 8.76 0.00 40.45 3.66
153 154 3.963383 ATTCGGAATTAACGACCATGC 57.037 42.857 4.40 0.00 40.45 4.06
154 155 1.658994 TCGGAATTAACGACCATGCC 58.341 50.000 1.01 0.00 35.12 4.40
155 156 1.066071 TCGGAATTAACGACCATGCCA 60.066 47.619 1.01 0.00 35.12 4.92
156 157 1.946768 CGGAATTAACGACCATGCCAT 59.053 47.619 0.00 0.00 0.00 4.40
157 158 2.032030 CGGAATTAACGACCATGCCATC 60.032 50.000 0.00 0.00 0.00 3.51
158 159 3.214328 GGAATTAACGACCATGCCATCT 58.786 45.455 0.00 0.00 0.00 2.90
159 160 4.385825 GGAATTAACGACCATGCCATCTA 58.614 43.478 0.00 0.00 0.00 1.98
160 161 4.213482 GGAATTAACGACCATGCCATCTAC 59.787 45.833 0.00 0.00 0.00 2.59
161 162 2.902705 TAACGACCATGCCATCTACC 57.097 50.000 0.00 0.00 0.00 3.18
162 163 0.180406 AACGACCATGCCATCTACCC 59.820 55.000 0.00 0.00 0.00 3.69
163 164 1.071471 CGACCATGCCATCTACCCC 59.929 63.158 0.00 0.00 0.00 4.95
164 165 1.410850 CGACCATGCCATCTACCCCT 61.411 60.000 0.00 0.00 0.00 4.79
165 166 1.729586 GACCATGCCATCTACCCCTA 58.270 55.000 0.00 0.00 0.00 3.53
166 167 2.269940 GACCATGCCATCTACCCCTAT 58.730 52.381 0.00 0.00 0.00 2.57
167 168 3.450904 GACCATGCCATCTACCCCTATA 58.549 50.000 0.00 0.00 0.00 1.31
168 169 3.452627 GACCATGCCATCTACCCCTATAG 59.547 52.174 0.00 0.00 0.00 1.31
169 170 2.171448 CCATGCCATCTACCCCTATAGC 59.829 54.545 0.00 0.00 0.00 2.97
170 171 3.110705 CATGCCATCTACCCCTATAGCT 58.889 50.000 0.00 0.00 0.00 3.32
171 172 2.821437 TGCCATCTACCCCTATAGCTC 58.179 52.381 0.00 0.00 0.00 4.09
172 173 2.383683 TGCCATCTACCCCTATAGCTCT 59.616 50.000 0.00 0.00 0.00 4.09
173 174 3.181406 TGCCATCTACCCCTATAGCTCTT 60.181 47.826 0.00 0.00 0.00 2.85
174 175 3.196685 GCCATCTACCCCTATAGCTCTTG 59.803 52.174 0.00 0.00 0.00 3.02
175 176 4.678256 CCATCTACCCCTATAGCTCTTGA 58.322 47.826 0.00 0.00 0.00 3.02
176 177 4.464597 CCATCTACCCCTATAGCTCTTGAC 59.535 50.000 0.00 0.00 0.00 3.18
177 178 4.115398 TCTACCCCTATAGCTCTTGACC 57.885 50.000 0.00 0.00 0.00 4.02
178 179 3.727923 TCTACCCCTATAGCTCTTGACCT 59.272 47.826 0.00 0.00 0.00 3.85
187 188 0.032017 GCTCTTGACCTCCCTCCCTA 60.032 60.000 0.00 0.00 0.00 3.53
205 206 2.170166 CTAATGGAGCTGGCCAAACAA 58.830 47.619 7.01 0.00 42.16 2.83
259 260 1.225983 CCGGCATGTAATGGACCCA 59.774 57.895 0.00 0.00 46.86 4.51
263 264 1.111277 GCATGTAATGGACCCAACCC 58.889 55.000 0.00 0.00 46.86 4.11
284 285 4.508128 ATGCGACTACGGGCCGTG 62.508 66.667 39.80 29.45 41.39 4.94
392 2613 1.349357 GGCTAAAAATGCCCCCAAACA 59.651 47.619 0.00 0.00 44.32 2.83
393 2614 2.615240 GGCTAAAAATGCCCCCAAACAG 60.615 50.000 0.00 0.00 44.32 3.16
394 2615 2.038426 GCTAAAAATGCCCCCAAACAGT 59.962 45.455 0.00 0.00 0.00 3.55
395 2616 3.259625 GCTAAAAATGCCCCCAAACAGTA 59.740 43.478 0.00 0.00 0.00 2.74
396 2617 4.262678 GCTAAAAATGCCCCCAAACAGTAA 60.263 41.667 0.00 0.00 0.00 2.24
397 2618 4.779993 AAAAATGCCCCCAAACAGTAAA 57.220 36.364 0.00 0.00 0.00 2.01
398 2619 4.779993 AAAATGCCCCCAAACAGTAAAA 57.220 36.364 0.00 0.00 0.00 1.52
399 2620 4.779993 AAATGCCCCCAAACAGTAAAAA 57.220 36.364 0.00 0.00 0.00 1.94
446 2667 3.918253 GAGGCCGGCACACATTCCA 62.918 63.158 30.85 0.00 0.00 3.53
463 2686 3.168528 ACCGTGTTGGACTGGCCT 61.169 61.111 3.32 0.00 42.00 5.19
465 2688 3.357079 CGTGTTGGACTGGCCTGC 61.357 66.667 9.95 2.57 37.63 4.85
533 2757 1.003866 CTTATAAACAGGCTTCCGCGC 60.004 52.381 0.00 0.00 36.88 6.86
682 2909 1.674817 CGGCGACATTGAAGGTAAGGT 60.675 52.381 0.00 0.00 0.00 3.50
708 2935 2.093447 CCCGTCTAGGTTGCTTCAATCT 60.093 50.000 0.00 0.00 38.46 2.40
711 2938 4.245660 CGTCTAGGTTGCTTCAATCTGAA 58.754 43.478 2.81 0.00 35.42 3.02
716 2943 6.942005 TCTAGGTTGCTTCAATCTGAAATTCA 59.058 34.615 2.81 0.00 35.42 2.57
752 2979 4.278419 GGATCCTTTGGATTATTGGAACCG 59.722 45.833 3.84 0.00 43.27 4.44
788 3015 6.537453 TCTTGATTCCTCTTAGAACAGGAG 57.463 41.667 0.00 0.00 40.05 3.69
791 3018 6.042638 TGATTCCTCTTAGAACAGGAGTTG 57.957 41.667 0.00 0.00 40.05 3.16
799 3026 6.055588 TCTTAGAACAGGAGTTGGTTTCTTG 58.944 40.000 0.00 0.00 38.30 3.02
814 3041 3.467374 TTCTTGTTTTGGTGATTGGGC 57.533 42.857 0.00 0.00 0.00 5.36
838 3065 6.567050 CGAAATGTGGATCCATTCTTGATTT 58.433 36.000 19.62 14.27 34.01 2.17
858 3085 6.213397 TGATTTCACCTAGAACTGGAATCAGA 59.787 38.462 11.75 0.00 43.49 3.27
871 3098 3.949754 TGGAATCAGACATTGCATCTTCC 59.050 43.478 0.00 0.00 0.00 3.46
878 3105 3.441572 AGACATTGCATCTTCCCTTTTCG 59.558 43.478 0.00 0.00 0.00 3.46
880 3107 4.331968 ACATTGCATCTTCCCTTTTCGTA 58.668 39.130 0.00 0.00 0.00 3.43
891 3118 6.652062 TCTTCCCTTTTCGTATGGAACTTTAC 59.348 38.462 0.00 0.00 33.42 2.01
910 3183 6.311445 ACTTTACGAGTTCGATCTAGTACGAA 59.689 38.462 13.86 17.36 44.26 3.85
931 3204 5.898606 CGAATGAGCGATTGATTTCTTGTAC 59.101 40.000 0.00 0.00 0.00 2.90
992 3266 1.308998 GCACCACAGTACACAAAGCT 58.691 50.000 0.00 0.00 0.00 3.74
998 3272 2.478134 CACAGTACACAAAGCTGAGAGC 59.522 50.000 0.00 0.00 42.84 4.09
1164 3438 2.548920 GGGATTCGACTGGGCTATCTTG 60.549 54.545 0.00 0.00 0.00 3.02
1165 3439 2.103263 GGATTCGACTGGGCTATCTTGT 59.897 50.000 0.00 0.00 0.00 3.16
1166 3440 3.321111 GGATTCGACTGGGCTATCTTGTA 59.679 47.826 0.00 0.00 0.00 2.41
1248 3522 1.077501 GAGCAAGTATGGGCAGGCA 60.078 57.895 0.00 0.00 0.00 4.75
1302 3576 2.158475 AGTCACTGGAAAGCCCAAATCA 60.158 45.455 0.00 0.00 46.07 2.57
1345 3619 1.755179 ATTGGATGAGGAGCCGTTTG 58.245 50.000 0.00 0.00 0.00 2.93
1366 3640 3.071457 TGGATTCAAGTCTGACAGCTTCA 59.929 43.478 10.88 0.00 0.00 3.02
1380 3654 0.898320 GCTTCACAGAGGCTACCTGA 59.102 55.000 9.94 0.00 31.76 3.86
1440 3714 5.279206 GGATTCAGTGTATGTCCGAGATGAT 60.279 44.000 0.00 0.00 0.00 2.45
1472 3746 6.361481 GTGATTGAATGTGTCATCACTGTTTG 59.639 38.462 4.27 0.00 44.14 2.93
1507 3781 3.123050 GTGTCTGAAACCAAACCATTGC 58.877 45.455 0.00 0.00 35.10 3.56
1573 3847 6.716620 GCAAGATGTTGGAGGATACGTCCA 62.717 50.000 4.57 8.75 39.42 4.02
1593 3867 3.430042 ACAGCAGATGTGACCTTCAAT 57.570 42.857 0.00 0.00 41.91 2.57
1597 3871 3.504906 AGCAGATGTGACCTTCAATGTTG 59.495 43.478 0.00 0.00 0.00 3.33
1680 3954 2.086869 CAGTTCAGCGAACCCATGAAT 58.913 47.619 14.85 0.00 42.85 2.57
1740 4014 0.954452 CAGCGGTTTTCAAGGCTCTT 59.046 50.000 0.00 0.00 32.46 2.85
1830 4104 0.614812 TCCAGCATCTACTTGCAGCA 59.385 50.000 0.00 0.00 45.23 4.41
1854 4128 5.540337 AGCGGATCAATATGGTTTAGAGAGA 59.460 40.000 0.00 0.00 0.00 3.10
1874 4148 4.074259 AGATTGAAGCTTATGTGTGCACA 58.926 39.130 17.42 17.42 46.44 4.57
2043 4317 2.816672 CCAGCTTCTGAAAAGAGGTTCC 59.183 50.000 0.00 0.00 32.44 3.62
2046 4320 2.796557 CTTCTGAAAAGAGGTTCCCCC 58.203 52.381 0.00 0.00 0.00 5.40
2325 4603 8.963725 TGAAATGTTGATCTTTAGATGCATTCT 58.036 29.630 0.00 2.14 38.57 2.40
2365 4643 2.113860 GCTCCAGCAAGTATGTTCCA 57.886 50.000 0.00 0.00 41.59 3.53
2412 4690 3.803778 CAGCTTGTTTTGATTTGGTCCAC 59.196 43.478 0.00 0.00 0.00 4.02
2576 4858 5.065235 TCAATGAATGTTGACTTCTGCTGA 58.935 37.500 0.00 0.00 33.41 4.26
2640 4930 8.732746 ATGTTAGTTCATTATTGGAGTACCAC 57.267 34.615 0.00 0.00 46.80 4.16
2661 4951 3.389983 ACTTAAGTCACAGGGTGCTAACA 59.610 43.478 1.12 0.00 32.98 2.41
2662 4952 2.550830 AAGTCACAGGGTGCTAACAG 57.449 50.000 0.00 0.00 32.98 3.16
2663 4953 1.424638 AGTCACAGGGTGCTAACAGT 58.575 50.000 0.00 0.00 32.98 3.55
2664 4954 1.768870 AGTCACAGGGTGCTAACAGTT 59.231 47.619 0.00 0.00 32.98 3.16
2665 4955 2.143925 GTCACAGGGTGCTAACAGTTC 58.856 52.381 0.00 0.00 32.98 3.01
2666 4956 2.047061 TCACAGGGTGCTAACAGTTCT 58.953 47.619 0.00 0.00 32.98 3.01
2667 4957 2.146342 CACAGGGTGCTAACAGTTCTG 58.854 52.381 0.00 0.00 0.00 3.02
2668 4958 2.047061 ACAGGGTGCTAACAGTTCTGA 58.953 47.619 6.83 0.00 0.00 3.27
2669 4959 2.438021 ACAGGGTGCTAACAGTTCTGAA 59.562 45.455 6.83 0.00 0.00 3.02
2670 4960 3.070018 CAGGGTGCTAACAGTTCTGAAG 58.930 50.000 6.83 5.02 0.00 3.02
2671 4961 2.039084 AGGGTGCTAACAGTTCTGAAGG 59.961 50.000 6.83 0.00 0.00 3.46
2672 4962 2.224548 GGGTGCTAACAGTTCTGAAGGT 60.225 50.000 6.83 0.00 0.00 3.50
2673 4963 3.007614 GGGTGCTAACAGTTCTGAAGGTA 59.992 47.826 6.83 0.00 0.00 3.08
2674 4964 4.323562 GGGTGCTAACAGTTCTGAAGGTAT 60.324 45.833 6.83 0.00 0.00 2.73
2675 4965 5.246307 GGTGCTAACAGTTCTGAAGGTATT 58.754 41.667 6.83 0.00 0.00 1.89
2676 4966 5.122396 GGTGCTAACAGTTCTGAAGGTATTG 59.878 44.000 6.83 0.00 0.00 1.90
2677 4967 5.122396 GTGCTAACAGTTCTGAAGGTATTGG 59.878 44.000 6.83 0.00 0.00 3.16
2678 4968 5.012664 TGCTAACAGTTCTGAAGGTATTGGA 59.987 40.000 6.83 0.00 0.00 3.53
2679 4969 5.351740 GCTAACAGTTCTGAAGGTATTGGAC 59.648 44.000 6.83 0.00 0.00 4.02
2697 4987 2.506444 GACCCTGTACTATCCGGAGAG 58.494 57.143 24.35 24.35 0.00 3.20
2705 4996 2.175202 ACTATCCGGAGAGATGCATCC 58.825 52.381 31.98 14.22 0.00 3.51
2867 5158 6.095377 GCTGTTTTCCTGTTTCATTATCCAG 58.905 40.000 0.00 0.00 0.00 3.86
2951 5242 0.586319 TGCTTTTCGCTCTTTCCACG 59.414 50.000 0.00 0.00 40.11 4.94
2957 5248 2.448926 TCGCTCTTTCCACGAAATGA 57.551 45.000 0.00 0.00 30.85 2.57
2961 5252 4.215399 TCGCTCTTTCCACGAAATGATTTT 59.785 37.500 0.00 0.00 30.85 1.82
3003 5294 6.434652 TGATTAATCCAAACATAAACCGGTGT 59.565 34.615 8.52 4.57 0.00 4.16
3005 5296 3.210232 TCCAAACATAAACCGGTGTGA 57.790 42.857 8.52 0.00 0.00 3.58
3009 5300 4.022762 CCAAACATAAACCGGTGTGATGAA 60.023 41.667 23.39 0.00 0.00 2.57
3017 5308 2.283298 CCGGTGTGATGAAGATCTTGG 58.717 52.381 14.00 0.15 0.00 3.61
3080 5373 1.412710 TCCCGCTAGCTGATTACCAAG 59.587 52.381 13.93 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.524487 CCCTCTCTTATTATATCACTACACCAC 58.476 40.741 0.00 0.00 0.00 4.16
41 42 3.492102 TGGTCATTAATAGGGCTGAGC 57.508 47.619 0.00 0.00 36.82 4.26
45 46 4.104383 CCACATGGTCATTAATAGGGCT 57.896 45.455 0.00 0.00 0.00 5.19
56 57 4.687219 TTGTCACACAATACCACATGGTCA 60.687 41.667 6.88 0.00 39.50 4.02
57 58 3.818210 TTGTCACACAATACCACATGGTC 59.182 43.478 6.88 0.00 39.50 4.02
106 107 7.865706 ACAGTATTTTCTATGGGCAAACTAG 57.134 36.000 0.00 0.00 0.00 2.57
111 112 9.214957 CGAATATACAGTATTTTCTATGGGCAA 57.785 33.333 16.99 0.00 0.00 4.52
113 114 8.038944 TCCGAATATACAGTATTTTCTATGGGC 58.961 37.037 16.99 0.00 0.00 5.36
125 126 7.939782 TGGTCGTTAATTCCGAATATACAGTA 58.060 34.615 2.11 0.00 35.89 2.74
127 128 7.621426 GCATGGTCGTTAATTCCGAATATACAG 60.621 40.741 0.00 0.00 35.89 2.74
136 137 1.374560 TGGCATGGTCGTTAATTCCG 58.625 50.000 0.00 0.00 0.00 4.30
140 141 3.496160 GGGTAGATGGCATGGTCGTTAAT 60.496 47.826 3.81 0.00 0.00 1.40
141 142 2.158871 GGGTAGATGGCATGGTCGTTAA 60.159 50.000 3.81 0.00 0.00 2.01
142 143 1.414919 GGGTAGATGGCATGGTCGTTA 59.585 52.381 3.81 0.00 0.00 3.18
143 144 0.180406 GGGTAGATGGCATGGTCGTT 59.820 55.000 3.81 0.00 0.00 3.85
144 145 1.696097 GGGGTAGATGGCATGGTCGT 61.696 60.000 3.81 0.00 0.00 4.34
145 146 1.071471 GGGGTAGATGGCATGGTCG 59.929 63.158 3.81 0.00 0.00 4.79
146 147 1.729586 TAGGGGTAGATGGCATGGTC 58.270 55.000 3.81 0.00 0.00 4.02
147 148 2.440494 ATAGGGGTAGATGGCATGGT 57.560 50.000 3.81 0.00 0.00 3.55
148 149 2.171448 GCTATAGGGGTAGATGGCATGG 59.829 54.545 3.81 0.00 0.00 3.66
149 150 3.110705 AGCTATAGGGGTAGATGGCATG 58.889 50.000 3.81 0.00 0.00 4.06
150 151 3.013417 AGAGCTATAGGGGTAGATGGCAT 59.987 47.826 0.00 0.00 0.00 4.40
151 152 2.383683 AGAGCTATAGGGGTAGATGGCA 59.616 50.000 1.04 0.00 0.00 4.92
152 153 3.108847 AGAGCTATAGGGGTAGATGGC 57.891 52.381 1.04 0.00 0.00 4.40
153 154 4.464597 GTCAAGAGCTATAGGGGTAGATGG 59.535 50.000 1.04 0.00 0.00 3.51
154 155 4.464597 GGTCAAGAGCTATAGGGGTAGATG 59.535 50.000 1.04 0.00 0.00 2.90
155 156 4.358614 AGGTCAAGAGCTATAGGGGTAGAT 59.641 45.833 1.04 0.00 37.39 1.98
156 157 3.727923 AGGTCAAGAGCTATAGGGGTAGA 59.272 47.826 1.04 0.00 37.39 2.59
157 158 4.083565 GAGGTCAAGAGCTATAGGGGTAG 58.916 52.174 1.22 0.00 39.57 3.18
158 159 3.181420 GGAGGTCAAGAGCTATAGGGGTA 60.181 52.174 1.22 0.00 39.57 3.69
159 160 2.426561 GGAGGTCAAGAGCTATAGGGGT 60.427 54.545 1.22 0.00 39.57 4.95
160 161 2.252714 GGAGGTCAAGAGCTATAGGGG 58.747 57.143 1.22 0.00 39.57 4.79
161 162 2.158234 AGGGAGGTCAAGAGCTATAGGG 60.158 54.545 1.22 0.00 39.57 3.53
162 163 3.161866 GAGGGAGGTCAAGAGCTATAGG 58.838 54.545 1.22 0.00 39.57 2.57
163 164 3.161866 GGAGGGAGGTCAAGAGCTATAG 58.838 54.545 1.22 0.00 39.57 1.31
164 165 2.158295 GGGAGGGAGGTCAAGAGCTATA 60.158 54.545 1.22 0.00 39.57 1.31
165 166 1.413808 GGGAGGGAGGTCAAGAGCTAT 60.414 57.143 1.22 0.00 39.57 2.97
166 167 0.032017 GGGAGGGAGGTCAAGAGCTA 60.032 60.000 1.22 0.00 39.57 3.32
167 168 1.306568 GGGAGGGAGGTCAAGAGCT 60.307 63.158 0.74 0.74 42.58 4.09
168 169 0.032017 TAGGGAGGGAGGTCAAGAGC 60.032 60.000 0.00 0.00 0.00 4.09
169 170 2.552093 TTAGGGAGGGAGGTCAAGAG 57.448 55.000 0.00 0.00 0.00 2.85
170 171 2.629639 CCATTAGGGAGGGAGGTCAAGA 60.630 54.545 0.00 0.00 40.01 3.02
171 172 1.771255 CCATTAGGGAGGGAGGTCAAG 59.229 57.143 0.00 0.00 40.01 3.02
172 173 1.368203 TCCATTAGGGAGGGAGGTCAA 59.632 52.381 0.00 0.00 42.15 3.18
173 174 1.023719 TCCATTAGGGAGGGAGGTCA 58.976 55.000 0.00 0.00 42.15 4.02
174 175 3.970426 TCCATTAGGGAGGGAGGTC 57.030 57.895 0.00 0.00 42.15 3.85
187 188 0.971386 CTTGTTTGGCCAGCTCCATT 59.029 50.000 5.11 0.00 35.77 3.16
223 224 4.241999 GCACGCGTGATCATGGGC 62.242 66.667 41.19 20.48 34.06 5.36
244 245 1.111277 GGGTTGGGTCCATTACATGC 58.889 55.000 0.00 0.00 0.00 4.06
247 248 1.686416 CCGGGTTGGGTCCATTACA 59.314 57.895 0.00 0.00 0.00 2.41
259 260 2.125269 GTAGTCGCATGCCGGGTT 60.125 61.111 13.15 0.00 37.59 4.11
284 285 2.617274 GGAGTGCCACGAGCCAAAC 61.617 63.158 0.00 0.00 42.71 2.93
300 301 2.964925 GCGAACACAGCACACGGA 60.965 61.111 0.00 0.00 34.19 4.69
343 2564 7.164803 TGGGCCAATTACCTTTTAAAAAGATG 58.835 34.615 2.13 0.00 0.00 2.90
344 2565 7.323052 TGGGCCAATTACCTTTTAAAAAGAT 57.677 32.000 2.13 0.00 0.00 2.40
345 2566 6.749036 TGGGCCAATTACCTTTTAAAAAGA 57.251 33.333 2.13 0.00 0.00 2.52
346 2567 7.809546 TTTGGGCCAATTACCTTTTAAAAAG 57.190 32.000 21.65 0.00 0.00 2.27
352 2573 4.365514 CCTTTTGGGCCAATTACCTTTT 57.634 40.909 21.65 0.00 35.46 2.27
408 2629 0.030101 CCCGCGTGCTTTCTCAAAAA 59.970 50.000 4.92 0.00 0.00 1.94
409 2630 1.652012 CCCGCGTGCTTTCTCAAAA 59.348 52.632 4.92 0.00 0.00 2.44
410 2631 2.258013 CCCCGCGTGCTTTCTCAAA 61.258 57.895 4.92 0.00 0.00 2.69
411 2632 2.668212 CCCCGCGTGCTTTCTCAA 60.668 61.111 4.92 0.00 0.00 3.02
412 2633 3.589654 CTCCCCGCGTGCTTTCTCA 62.590 63.158 4.92 0.00 0.00 3.27
413 2634 2.815647 CTCCCCGCGTGCTTTCTC 60.816 66.667 4.92 0.00 0.00 2.87
414 2635 4.394712 CCTCCCCGCGTGCTTTCT 62.395 66.667 4.92 0.00 0.00 2.52
446 2667 3.168528 AGGCCAGTCCAACACGGT 61.169 61.111 5.01 0.00 37.29 4.83
463 2686 1.083489 GCACGGCACATTAACTAGCA 58.917 50.000 0.00 0.00 0.00 3.49
465 2688 1.588404 CGAGCACGGCACATTAACTAG 59.412 52.381 0.00 0.00 35.72 2.57
708 2935 4.884744 TCCAAAAGAAGACGGTGAATTTCA 59.115 37.500 0.00 0.00 0.00 2.69
711 2938 4.459337 GGATCCAAAAGAAGACGGTGAATT 59.541 41.667 6.95 0.00 0.00 2.17
716 2943 3.790089 AAGGATCCAAAAGAAGACGGT 57.210 42.857 15.82 0.00 0.00 4.83
752 2979 2.907910 ATCAAGAAAGCACACGCATC 57.092 45.000 0.00 0.00 42.27 3.91
788 3015 5.064579 CCAATCACCAAAACAAGAAACCAAC 59.935 40.000 0.00 0.00 0.00 3.77
791 3018 4.126437 CCCAATCACCAAAACAAGAAACC 58.874 43.478 0.00 0.00 0.00 3.27
799 3026 2.517650 TTTCGCCCAATCACCAAAAC 57.482 45.000 0.00 0.00 0.00 2.43
814 3041 5.762825 ATCAAGAATGGATCCACATTTCG 57.237 39.130 18.99 5.92 40.92 3.46
838 3065 4.416516 TGTCTGATTCCAGTTCTAGGTGA 58.583 43.478 0.00 0.00 41.16 4.02
858 3085 3.157087 ACGAAAAGGGAAGATGCAATGT 58.843 40.909 0.00 0.00 0.00 2.71
891 3118 5.326120 TCATTCGTACTAGATCGAACTCG 57.674 43.478 21.23 15.30 46.11 4.18
910 3183 6.932356 ATGTACAAGAAATCAATCGCTCAT 57.068 33.333 0.00 0.00 0.00 2.90
982 3256 2.610433 CATCGCTCTCAGCTTTGTGTA 58.390 47.619 0.00 0.00 39.60 2.90
992 3266 1.446099 GTTGACGCCATCGCTCTCA 60.446 57.895 0.00 0.00 39.84 3.27
1057 3331 5.570973 CGTGACTAAACTGACAGATCTTCAG 59.429 44.000 22.66 22.66 45.21 3.02
1248 3522 1.588824 TTATGTCGACGACCGCTGGT 61.589 55.000 24.33 6.88 39.44 4.00
1345 3619 3.434984 GTGAAGCTGTCAGACTTGAATCC 59.565 47.826 3.32 0.00 36.74 3.01
1366 3640 2.624557 CCTTACCTCAGGTAGCCTCTGT 60.625 54.545 3.09 0.00 39.52 3.41
1380 3654 6.137559 CCTTCTTATACACCTCTCCTTACCT 58.862 44.000 0.00 0.00 0.00 3.08
1440 3714 3.635836 TGACACATTCAATCACAAGGCAA 59.364 39.130 0.00 0.00 0.00 4.52
1472 3746 2.026262 TCAGACACCCTTAATTGGCCTC 60.026 50.000 3.32 0.00 0.00 4.70
1507 3781 1.133025 GGGAGGCACATCAATTTCACG 59.867 52.381 0.00 0.00 0.00 4.35
1573 3847 2.936919 TTGAAGGTCACATCTGCTGT 57.063 45.000 0.00 0.00 39.20 4.40
1593 3867 4.329528 GCAGCAAATGTTTCTTGTTCAACA 59.670 37.500 0.00 0.00 37.31 3.33
1597 3871 2.802247 GGGCAGCAAATGTTTCTTGTTC 59.198 45.455 0.00 0.00 0.00 3.18
1680 3954 0.897621 TGCGGCTCATCTTCTTCTCA 59.102 50.000 0.00 0.00 0.00 3.27
1740 4014 5.588648 GGAATCGGTGTAAATGAAATGGAGA 59.411 40.000 0.00 0.00 0.00 3.71
1830 4104 5.540337 TCTCTCTAAACCATATTGATCCGCT 59.460 40.000 0.00 0.00 0.00 5.52
1854 4128 4.164822 GTGTGCACACATAAGCTTCAAT 57.835 40.909 38.42 0.00 45.75 2.57
2043 4317 2.053244 ACATCTGCTAATGGAGAGGGG 58.947 52.381 4.50 0.00 44.72 4.79
2046 4320 3.464907 CCACACATCTGCTAATGGAGAG 58.535 50.000 4.31 0.00 43.72 3.20
2236 4510 4.302559 AAAGCTAAAGAGTTACCAGGGG 57.697 45.455 0.00 0.00 0.00 4.79
2325 4603 3.568007 GCATATCCGCTAAATTGACCCAA 59.432 43.478 0.00 0.00 0.00 4.12
2365 4643 6.588756 GCAAATCAACAGATCACACATCATTT 59.411 34.615 0.00 0.00 0.00 2.32
2412 4690 4.629527 GCAATTCAAAAAGTGCGTAAGG 57.370 40.909 0.00 0.00 45.27 2.69
2640 4930 3.997021 CTGTTAGCACCCTGTGACTTAAG 59.003 47.826 0.00 0.00 35.23 1.85
2671 4961 3.257624 CCGGATAGTACAGGGTCCAATAC 59.742 52.174 0.00 0.00 0.00 1.89
2672 4962 3.140707 TCCGGATAGTACAGGGTCCAATA 59.859 47.826 0.00 0.00 0.00 1.90
2673 4963 2.090943 TCCGGATAGTACAGGGTCCAAT 60.091 50.000 0.00 0.00 0.00 3.16
2674 4964 1.288633 TCCGGATAGTACAGGGTCCAA 59.711 52.381 0.00 0.00 0.00 3.53
2675 4965 0.928505 TCCGGATAGTACAGGGTCCA 59.071 55.000 0.00 0.00 0.00 4.02
2676 4966 1.144503 TCTCCGGATAGTACAGGGTCC 59.855 57.143 3.57 0.00 0.00 4.46
2677 4967 2.106166 TCTCTCCGGATAGTACAGGGTC 59.894 54.545 15.80 0.00 0.00 4.46
2678 4968 2.133520 TCTCTCCGGATAGTACAGGGT 58.866 52.381 15.80 0.00 0.00 4.34
2679 4969 2.953284 TCTCTCCGGATAGTACAGGG 57.047 55.000 15.80 0.00 0.00 4.45
2680 4970 2.490115 GCATCTCTCCGGATAGTACAGG 59.510 54.545 15.80 1.08 0.00 4.00
2681 4971 3.149981 TGCATCTCTCCGGATAGTACAG 58.850 50.000 15.80 6.51 0.00 2.74
2705 4996 4.497006 GCAACAATCAGCTTATGGCAGTAG 60.497 45.833 0.00 0.00 44.79 2.57
2867 5158 3.730715 CGGTCAAAACAGAAAATGCACTC 59.269 43.478 0.00 0.00 0.00 3.51
2993 5284 4.819105 AGATCTTCATCACACCGGTTTA 57.181 40.909 2.97 0.00 0.00 2.01
3003 5294 6.382282 ACATCTGAGTACCAAGATCTTCATCA 59.618 38.462 4.57 4.95 0.00 3.07
3005 5296 6.805016 ACATCTGAGTACCAAGATCTTCAT 57.195 37.500 4.57 0.00 0.00 2.57
3080 5373 2.299867 ACCATGCCACAAAATCTTCCAC 59.700 45.455 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.