Multiple sequence alignment - TraesCS2D01G159400

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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 TraesCS2D01G159400 chr2D 100.000 2302 0 0 1 2302 102724314 102726615 0.000000e+00 4252.0
1 TraesCS2D01G159400 chr2D 100.000 108 0 0 2535 2642 102726848 102726955 1.600000e-47 200.0
2 TraesCS2D01G159400 chr2D 79.268 82 13 3 2562 2642 537340127 537340049 1.000000e-03 54.7
3 TraesCS2D01G159400 chr2A 93.943 1585 58 16 263 1826 101835626 101837193 0.000000e+00 2361.0
4 TraesCS2D01G159400 chr2A 88.841 466 36 8 1841 2301 101838530 101838984 2.300000e-155 558.0
5 TraesCS2D01G159400 chr2A 86.268 284 13 10 3 273 101835192 101835462 4.300000e-73 285.0
6 TraesCS2D01G159400 chr2B 96.898 677 21 0 974 1650 153903484 153904160 0.000000e+00 1134.0
7 TraesCS2D01G159400 chr2B 90.485 536 35 10 1755 2283 153904211 153904737 0.000000e+00 693.0
8 TraesCS2D01G159400 chr2B 92.896 366 19 4 652 1013 153903119 153903481 2.330000e-145 525.0
9 TraesCS2D01G159400 chr6A 86.339 549 68 6 1086 1629 96772390 96772936 2.260000e-165 592.0
10 TraesCS2D01G159400 chr6D 86.207 551 69 6 1087 1632 79934139 79933591 8.140000e-165 590.0
11 TraesCS2D01G159400 chr6D 86.000 550 68 8 1086 1629 80061438 80061984 4.900000e-162 580.0
12 TraesCS2D01G159400 chr6D 80.319 188 33 4 1094 1279 472997883 472998068 3.550000e-29 139.0
13 TraesCS2D01G159400 chr6D 80.319 188 33 4 1094 1279 473056062 473056247 3.550000e-29 139.0
14 TraesCS2D01G159400 chr6B 85.507 552 73 6 1086 1632 152631073 152630524 1.060000e-158 569.0
15 TraesCS2D01G159400 chr6B 91.667 204 12 4 1086 1285 152695870 152695668 7.200000e-71 278.0


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 TraesCS2D01G159400 chr2D 102724314 102726955 2641 False 2226 4252 100.000000 1 2642 2 chr2D.!!$F1 2641
1 TraesCS2D01G159400 chr2A 101835192 101838984 3792 False 1068 2361 89.684000 3 2301 3 chr2A.!!$F1 2298
2 TraesCS2D01G159400 chr2B 153903119 153904737 1618 False 784 1134 93.426333 652 2283 3 chr2B.!!$F1 1631
3 TraesCS2D01G159400 chr6A 96772390 96772936 546 False 592 592 86.339000 1086 1629 1 chr6A.!!$F1 543
4 TraesCS2D01G159400 chr6D 79933591 79934139 548 True 590 590 86.207000 1087 1632 1 chr6D.!!$R1 545
5 TraesCS2D01G159400 chr6D 80061438 80061984 546 False 580 580 86.000000 1086 1629 1 chr6D.!!$F1 543
6 TraesCS2D01G159400 chr6B 152630524 152631073 549 True 569 569 85.507000 1086 1632 1 chr6B.!!$R1 546

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
914 1110 0.03213 TTGACACTCCTCACTCACGC 59.968 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 3447 0.177141 GCAATGGCCATGCTGACATT 59.823 50.0 21.63 0.0 40.64 2.71 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
26 27 1.772182 CGCTGGTCGGATATGAGAAC 58.228 55.000 0.00 0.00 33.78 3.01
46 47 1.767681 CCTCCCCTTCTCCATCTTCAG 59.232 57.143 0.00 0.00 0.00 3.02
47 48 2.476199 CTCCCCTTCTCCATCTTCAGT 58.524 52.381 0.00 0.00 0.00 3.41
48 49 2.433970 CTCCCCTTCTCCATCTTCAGTC 59.566 54.545 0.00 0.00 0.00 3.51
49 50 2.045047 TCCCCTTCTCCATCTTCAGTCT 59.955 50.000 0.00 0.00 0.00 3.24
50 51 2.843113 CCCCTTCTCCATCTTCAGTCTT 59.157 50.000 0.00 0.00 0.00 3.01
51 52 3.118445 CCCCTTCTCCATCTTCAGTCTTC 60.118 52.174 0.00 0.00 0.00 2.87
52 53 3.517100 CCCTTCTCCATCTTCAGTCTTCA 59.483 47.826 0.00 0.00 0.00 3.02
60 61 2.677914 TCTTCAGTCTTCACCACCTCA 58.322 47.619 0.00 0.00 0.00 3.86
61 62 2.630098 TCTTCAGTCTTCACCACCTCAG 59.370 50.000 0.00 0.00 0.00 3.35
105 119 5.010112 ACGAAGAGAGTTCAAGACAATCTCA 59.990 40.000 0.00 0.00 39.08 3.27
119 133 5.306678 AGACAATCTCAGGCTTATTAGAGGG 59.693 44.000 0.00 0.00 0.00 4.30
122 136 2.090494 TCTCAGGCTTATTAGAGGGGCT 60.090 50.000 0.00 0.00 34.96 5.19
142 156 1.743321 CTCACTGGATCCGCCTCTCC 61.743 65.000 7.39 0.00 37.63 3.71
175 189 0.392998 CATGGAAGAACACCTCGGGG 60.393 60.000 0.00 0.00 38.88 5.73
176 190 1.562672 ATGGAAGAACACCTCGGGGG 61.563 60.000 6.13 0.00 41.89 5.40
177 191 2.046217 GAAGAACACCTCGGGGGC 60.046 66.667 6.13 0.00 39.10 5.80
178 192 3.623703 GAAGAACACCTCGGGGGCC 62.624 68.421 6.13 0.00 39.10 5.80
257 271 2.258013 CGCCAAACGCCAAAGAGGA 61.258 57.895 0.00 0.00 41.22 3.71
261 275 2.740256 GCCAAACGCCAAAGAGGAAAAA 60.740 45.455 0.00 0.00 41.22 1.94
294 485 4.017499 AGCCCTACACCTAATGGACAAAAT 60.017 41.667 0.00 0.00 37.04 1.82
314 505 1.307084 AGTACCTGGCTTCCTCCCC 60.307 63.158 0.00 0.00 0.00 4.81
321 512 1.386057 GGCTTCCTCCCCCATACCT 60.386 63.158 0.00 0.00 0.00 3.08
328 519 1.718280 CTCCCCCATACCTACTCACC 58.282 60.000 0.00 0.00 0.00 4.02
330 521 1.129058 CCCCCATACCTACTCACCAC 58.871 60.000 0.00 0.00 0.00 4.16
394 585 3.314541 TTTTCCTAGGCGACTCTCAAC 57.685 47.619 2.96 0.00 43.67 3.18
423 615 1.077068 AGGCTCAGTCTCTCTCCCG 60.077 63.158 0.00 0.00 0.00 5.14
426 618 1.711060 GCTCAGTCTCTCTCCCGTCG 61.711 65.000 0.00 0.00 0.00 5.12
438 630 0.526662 TCCCGTCGAAGCTTTCTCTC 59.473 55.000 0.00 0.00 0.00 3.20
467 659 2.831333 AGATCGGTGCAGTTCATGATC 58.169 47.619 0.00 0.00 38.58 2.92
468 660 2.169144 AGATCGGTGCAGTTCATGATCA 59.831 45.455 0.00 0.00 39.70 2.92
469 661 2.696989 TCGGTGCAGTTCATGATCAT 57.303 45.000 1.18 1.18 0.00 2.45
485 677 4.673298 ATTCGGACGCGCCACACA 62.673 61.111 5.73 0.00 35.94 3.72
519 711 7.502120 AGCATAGCATTTAAATCGAGTCAAT 57.498 32.000 0.00 0.00 0.00 2.57
541 733 6.584185 ATCACCACAATTTAGGGTTTGTAC 57.416 37.500 0.00 0.00 34.42 2.90
680 872 6.458342 CCGTTTTCAAGTAAGCTCAACTTCTT 60.458 38.462 10.62 0.00 39.97 2.52
681 873 7.254658 CCGTTTTCAAGTAAGCTCAACTTCTTA 60.255 37.037 10.62 0.00 39.97 2.10
729 922 2.264480 TCCGTTGTGGATCGGCAG 59.736 61.111 0.00 0.00 43.74 4.85
745 938 2.450502 AGGTGTCTGGCCCAACCT 60.451 61.111 0.00 4.99 40.22 3.50
746 939 2.034221 GGTGTCTGGCCCAACCTC 59.966 66.667 0.00 0.00 40.22 3.85
747 940 2.034221 GTGTCTGGCCCAACCTCC 59.966 66.667 0.00 0.00 40.22 4.30
748 941 3.636231 TGTCTGGCCCAACCTCCG 61.636 66.667 0.00 0.00 40.22 4.63
749 942 3.319198 GTCTGGCCCAACCTCCGA 61.319 66.667 0.00 0.00 40.22 4.55
878 1074 1.296392 CTCCGAGCAACCACATCCA 59.704 57.895 0.00 0.00 0.00 3.41
914 1110 0.032130 TTGACACTCCTCACTCACGC 59.968 55.000 0.00 0.00 0.00 5.34
937 1133 3.325135 ACTCGATATAAAAGGGAGCCCAG 59.675 47.826 8.53 0.00 38.92 4.45
1036 1274 4.082523 ACGTCCAGATGCCCGTGG 62.083 66.667 0.00 0.00 34.87 4.94
1632 1873 3.717294 ATGACGCCCCACTCCCAC 61.717 66.667 0.00 0.00 0.00 4.61
1664 1905 3.368116 GGTGAAGCTCGTACCAACATACT 60.368 47.826 8.62 0.00 34.61 2.12
1665 1906 4.243270 GTGAAGCTCGTACCAACATACTT 58.757 43.478 0.00 0.00 0.00 2.24
1682 1923 9.692749 CAACATACTTACATACGTATCTCCATT 57.307 33.333 4.74 0.00 0.00 3.16
1698 1939 9.956720 GTATCTCCATTGGAAACATATGAAAAG 57.043 33.333 10.38 0.00 42.32 2.27
1699 1940 8.599624 ATCTCCATTGGAAACATATGAAAAGT 57.400 30.769 10.38 0.00 42.32 2.66
1700 1941 8.421249 TCTCCATTGGAAACATATGAAAAGTT 57.579 30.769 10.38 0.00 42.32 2.66
1701 1942 8.306038 TCTCCATTGGAAACATATGAAAAGTTG 58.694 33.333 10.38 0.00 42.32 3.16
1702 1943 8.187913 TCCATTGGAAACATATGAAAAGTTGA 57.812 30.769 10.38 0.00 42.32 3.18
1703 1944 8.646004 TCCATTGGAAACATATGAAAAGTTGAA 58.354 29.630 10.38 0.00 42.32 2.69
1704 1945 9.270640 CCATTGGAAACATATGAAAAGTTGAAA 57.729 29.630 10.38 0.00 42.32 2.69
1784 2029 5.911752 TCATGAGAGAGTGAAAAGGATAGC 58.088 41.667 0.00 0.00 0.00 2.97
1832 2077 8.851960 TTGTACGATAGAAACATGTATGAGAC 57.148 34.615 0.00 0.00 35.95 3.36
1873 3440 2.198827 ATCATGCCCTTGAACGTCAA 57.801 45.000 0.00 0.00 34.79 3.18
1880 3447 5.029807 TGCCCTTGAACGTCAATATATGA 57.970 39.130 0.00 0.00 35.59 2.15
1922 3489 5.487433 CCATCCTCATACGTATTGCCATTA 58.513 41.667 5.03 0.00 0.00 1.90
1925 3492 7.768582 CCATCCTCATACGTATTGCCATTATTA 59.231 37.037 5.03 0.00 0.00 0.98
1958 3525 8.073768 TCAACCGTTGATTTAAGAAATCTTGTC 58.926 33.333 9.99 2.89 45.85 3.18
2055 3622 1.533625 TTTGCGAGTGCCTATTTGCT 58.466 45.000 0.00 0.00 41.78 3.91
2062 3629 4.119862 CGAGTGCCTATTTGCTAGCTAAA 58.880 43.478 17.23 14.45 0.00 1.85
2138 3709 6.064060 TCACCTCACACTTTTCATCTTCAAT 58.936 36.000 0.00 0.00 0.00 2.57
2157 3728 3.715834 CAATCTCCCCTTCTTCTCCTCAT 59.284 47.826 0.00 0.00 0.00 2.90
2163 3734 2.103941 CCCTTCTTCTCCTCATGTAGCC 59.896 54.545 0.00 0.00 0.00 3.93
2164 3735 2.768527 CCTTCTTCTCCTCATGTAGCCA 59.231 50.000 0.00 0.00 0.00 4.75
2176 3747 1.614226 GTAGCCACCCACCTACCCA 60.614 63.158 0.00 0.00 0.00 4.51
2177 3748 1.614226 TAGCCACCCACCTACCCAC 60.614 63.158 0.00 0.00 0.00 4.61
2181 3752 3.877553 ACCCACCTACCCACCCCA 61.878 66.667 0.00 0.00 0.00 4.96
2182 3753 3.335729 CCCACCTACCCACCCCAC 61.336 72.222 0.00 0.00 0.00 4.61
2235 3812 2.703409 GGCGAGTGCTATTGTGCG 59.297 61.111 0.00 0.00 42.25 5.34
2262 3839 1.229658 CCCTCACCTCAACCTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
2271 3848 1.630369 CTCAACCTCCCTTGACCATCA 59.370 52.381 0.00 0.00 0.00 3.07
2297 3874 3.499737 CGCAGCCACGACAATCCC 61.500 66.667 0.00 0.00 34.06 3.85
2298 3875 2.045926 GCAGCCACGACAATCCCT 60.046 61.111 0.00 0.00 0.00 4.20
2299 3876 2.109126 GCAGCCACGACAATCCCTC 61.109 63.158 0.00 0.00 0.00 4.30
2300 3877 1.599047 CAGCCACGACAATCCCTCT 59.401 57.895 0.00 0.00 0.00 3.69
2301 3878 0.824109 CAGCCACGACAATCCCTCTA 59.176 55.000 0.00 0.00 0.00 2.43
2551 4128 3.996614 CACAATTCCGGTGACCCC 58.003 61.111 0.00 0.00 38.54 4.95
2565 4142 4.974721 CCCCGCACCTGCCAAGTT 62.975 66.667 0.00 0.00 37.91 2.66
2566 4143 2.912025 CCCGCACCTGCCAAGTTT 60.912 61.111 0.00 0.00 37.91 2.66
2567 4144 2.644992 CCGCACCTGCCAAGTTTC 59.355 61.111 0.00 0.00 37.91 2.78
2568 4145 2.192861 CCGCACCTGCCAAGTTTCA 61.193 57.895 0.00 0.00 37.91 2.69
2569 4146 1.283793 CGCACCTGCCAAGTTTCAG 59.716 57.895 0.00 0.00 37.91 3.02
2570 4147 1.165907 CGCACCTGCCAAGTTTCAGA 61.166 55.000 3.99 0.00 37.91 3.27
2571 4148 0.312102 GCACCTGCCAAGTTTCAGAC 59.688 55.000 3.99 0.00 34.31 3.51
2572 4149 1.972872 CACCTGCCAAGTTTCAGACT 58.027 50.000 3.99 0.00 41.47 3.24
2573 4150 1.876156 CACCTGCCAAGTTTCAGACTC 59.124 52.381 3.99 0.00 37.72 3.36
2574 4151 1.490490 ACCTGCCAAGTTTCAGACTCA 59.510 47.619 3.99 0.00 37.72 3.41
2575 4152 1.876156 CCTGCCAAGTTTCAGACTCAC 59.124 52.381 3.99 0.00 37.72 3.51
2576 4153 2.486191 CCTGCCAAGTTTCAGACTCACT 60.486 50.000 3.99 0.00 37.72 3.41
2577 4154 2.805099 CTGCCAAGTTTCAGACTCACTC 59.195 50.000 0.00 0.00 37.72 3.51
2578 4155 2.147150 GCCAAGTTTCAGACTCACTCC 58.853 52.381 0.00 0.00 37.72 3.85
2579 4156 2.224402 GCCAAGTTTCAGACTCACTCCT 60.224 50.000 0.00 0.00 37.72 3.69
2580 4157 3.397482 CCAAGTTTCAGACTCACTCCTG 58.603 50.000 0.00 0.00 37.72 3.86
2581 4158 2.805099 CAAGTTTCAGACTCACTCCTGC 59.195 50.000 0.00 0.00 37.72 4.85
2582 4159 2.324541 AGTTTCAGACTCACTCCTGCT 58.675 47.619 0.00 0.00 31.20 4.24
2583 4160 3.501349 AGTTTCAGACTCACTCCTGCTA 58.499 45.455 0.00 0.00 31.20 3.49
2584 4161 3.509575 AGTTTCAGACTCACTCCTGCTAG 59.490 47.826 0.00 0.00 31.20 3.42
2585 4162 3.441500 TTCAGACTCACTCCTGCTAGA 57.558 47.619 0.00 0.00 0.00 2.43
2586 4163 3.660970 TCAGACTCACTCCTGCTAGAT 57.339 47.619 0.00 0.00 0.00 1.98
2587 4164 4.779993 TCAGACTCACTCCTGCTAGATA 57.220 45.455 0.00 0.00 0.00 1.98
2588 4165 5.317600 TCAGACTCACTCCTGCTAGATAT 57.682 43.478 0.00 0.00 0.00 1.63
2589 4166 5.312895 TCAGACTCACTCCTGCTAGATATC 58.687 45.833 0.00 0.00 0.00 1.63
2590 4167 4.154015 CAGACTCACTCCTGCTAGATATCG 59.846 50.000 0.00 0.00 0.00 2.92
2591 4168 2.817258 ACTCACTCCTGCTAGATATCGC 59.183 50.000 0.00 0.00 0.00 4.58
2592 4169 2.163412 CTCACTCCTGCTAGATATCGCC 59.837 54.545 0.00 0.00 0.00 5.54
2593 4170 2.166829 CACTCCTGCTAGATATCGCCT 58.833 52.381 0.00 0.00 0.00 5.52
2594 4171 2.163412 CACTCCTGCTAGATATCGCCTC 59.837 54.545 0.00 0.00 0.00 4.70
2595 4172 1.748493 CTCCTGCTAGATATCGCCTCC 59.252 57.143 0.00 0.00 0.00 4.30
2596 4173 0.820871 CCTGCTAGATATCGCCTCCC 59.179 60.000 0.00 0.00 0.00 4.30
2597 4174 0.453793 CTGCTAGATATCGCCTCCCG 59.546 60.000 0.00 0.00 38.61 5.14
2598 4175 1.139947 GCTAGATATCGCCTCCCGC 59.860 63.158 0.00 0.00 36.73 6.13
2599 4176 1.316706 GCTAGATATCGCCTCCCGCT 61.317 60.000 0.00 0.00 36.73 5.52
2600 4177 0.736053 CTAGATATCGCCTCCCGCTC 59.264 60.000 0.00 0.00 36.73 5.03
2601 4178 0.037734 TAGATATCGCCTCCCGCTCA 59.962 55.000 0.00 0.00 36.73 4.26
2602 4179 0.613292 AGATATCGCCTCCCGCTCAT 60.613 55.000 0.00 0.00 36.73 2.90
2603 4180 0.459237 GATATCGCCTCCCGCTCATG 60.459 60.000 0.00 0.00 36.73 3.07
2604 4181 2.513026 ATATCGCCTCCCGCTCATGC 62.513 60.000 0.00 0.00 36.73 4.06
2615 4192 4.827087 CTCATGCACGGCTCGCCT 62.827 66.667 6.35 0.00 0.00 5.52
2616 4193 4.393155 TCATGCACGGCTCGCCTT 62.393 61.111 6.35 0.00 0.00 4.35
2617 4194 4.170062 CATGCACGGCTCGCCTTG 62.170 66.667 9.81 9.81 38.25 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.297597 GGAGGTTCTCATATCCGACCAG 59.702 54.545 0.00 0.00 32.81 4.00
11 12 1.619332 GGGAGGTTCTCATATCCGACC 59.381 57.143 0.00 0.00 32.30 4.79
26 27 1.767681 CTGAAGATGGAGAAGGGGAGG 59.232 57.143 0.00 0.00 0.00 4.30
60 61 0.465287 CTTGGTTTTTGCTGGCCACT 59.535 50.000 0.00 0.00 0.00 4.00
61 62 0.532640 CCTTGGTTTTTGCTGGCCAC 60.533 55.000 0.00 0.00 0.00 5.01
105 119 2.090494 TGAGAGCCCCTCTAATAAGCCT 60.090 50.000 5.47 0.00 41.35 4.58
119 133 2.107953 GCGGATCCAGTGAGAGCC 59.892 66.667 13.41 5.99 39.02 4.70
122 136 0.753479 GAGAGGCGGATCCAGTGAGA 60.753 60.000 13.41 0.00 37.29 3.27
205 219 1.675641 GCTCCGTCCCAGTGCATTT 60.676 57.895 0.00 0.00 0.00 2.32
257 271 2.070351 AGGGCTAGGGGTAGGTTTTT 57.930 50.000 0.00 0.00 0.00 1.94
261 275 0.264062 GTGTAGGGCTAGGGGTAGGT 59.736 60.000 0.00 0.00 0.00 3.08
294 485 0.617820 GGGAGGAAGCCAGGTACTCA 60.618 60.000 0.00 0.00 34.60 3.41
314 505 0.750850 CCCGTGGTGAGTAGGTATGG 59.249 60.000 0.00 0.00 0.00 2.74
321 512 2.280552 GGTGCTCCCGTGGTGAGTA 61.281 63.158 0.00 0.45 32.31 2.59
353 544 2.754664 CTTTGCCCGACTCCTTGGCT 62.755 60.000 0.00 0.00 45.56 4.75
369 560 4.223032 TGAGAGTCGCCTAGGAAAATCTTT 59.777 41.667 14.75 0.00 0.00 2.52
412 603 1.027792 AGCTTCGACGGGAGAGAGAC 61.028 60.000 0.00 0.00 0.00 3.36
423 615 1.336056 ACACCGAGAGAAAGCTTCGAC 60.336 52.381 0.00 0.00 34.02 4.20
426 618 2.440539 TGACACCGAGAGAAAGCTTC 57.559 50.000 0.00 0.00 0.00 3.86
438 630 0.948623 TGCACCGATCTTTGACACCG 60.949 55.000 0.00 0.00 0.00 4.94
467 659 4.147322 GTGTGGCGCGTCCGAATG 62.147 66.667 8.89 0.00 37.80 2.67
468 660 4.673298 TGTGTGGCGCGTCCGAAT 62.673 61.111 8.89 0.00 37.80 3.34
494 686 8.607441 ATTGACTCGATTTAAATGCTATGCTA 57.393 30.769 5.17 0.00 0.00 3.49
498 690 7.498900 TGGTGATTGACTCGATTTAAATGCTAT 59.501 33.333 5.17 0.00 0.00 2.97
515 707 5.600484 ACAAACCCTAAATTGTGGTGATTGA 59.400 36.000 10.41 0.00 38.29 2.57
519 711 5.697067 AGTACAAACCCTAAATTGTGGTGA 58.303 37.500 0.00 0.00 39.89 4.02
541 733 4.058817 AGCTTTTCGTTGTTGGAGAGTAG 58.941 43.478 0.00 0.00 0.00 2.57
596 788 5.934935 AGGAAATTCGTCGTGTTGTTTAT 57.065 34.783 0.00 0.00 0.00 1.40
728 921 2.450502 AGGTTGGGCCAGACACCT 60.451 61.111 20.43 20.43 40.61 4.00
729 922 2.034221 GAGGTTGGGCCAGACACC 59.966 66.667 16.62 16.62 40.61 4.16
745 938 3.953712 TGATAAGAAACTGCACTCGGA 57.046 42.857 0.00 0.00 0.00 4.55
746 939 4.728882 GCAATGATAAGAAACTGCACTCGG 60.729 45.833 0.00 0.00 0.00 4.63
747 940 4.142838 TGCAATGATAAGAAACTGCACTCG 60.143 41.667 0.00 0.00 35.02 4.18
748 941 5.300969 TGCAATGATAAGAAACTGCACTC 57.699 39.130 0.00 0.00 35.02 3.51
749 942 5.464168 GTTGCAATGATAAGAAACTGCACT 58.536 37.500 0.59 0.00 39.36 4.40
914 1110 3.071023 TGGGCTCCCTTTTATATCGAGTG 59.929 47.826 6.50 0.00 36.94 3.51
937 1133 3.202001 TAGATGCTTTGGCGCCGC 61.202 61.111 23.90 19.98 42.25 6.53
1056 1294 2.359230 ACTGGCTTCGCTTCCTGC 60.359 61.111 0.00 0.00 38.57 4.85
1632 1873 0.735632 GAGCTTCACCTCAGTGCGAG 60.736 60.000 0.00 0.00 44.16 5.03
1664 1905 7.557724 TGTTTCCAATGGAGATACGTATGTAA 58.442 34.615 13.97 1.28 30.77 2.41
1665 1906 7.114866 TGTTTCCAATGGAGATACGTATGTA 57.885 36.000 13.97 0.00 31.21 2.29
1682 1923 8.260818 TGGTTTTCAACTTTTCATATGTTTCCA 58.739 29.630 1.90 0.00 0.00 3.53
1698 1939 4.026886 GTCTTTGCATTCGTGGTTTTCAAC 60.027 41.667 0.00 0.00 0.00 3.18
1699 1940 4.109050 GTCTTTGCATTCGTGGTTTTCAA 58.891 39.130 0.00 0.00 0.00 2.69
1700 1941 3.701241 GTCTTTGCATTCGTGGTTTTCA 58.299 40.909 0.00 0.00 0.00 2.69
1701 1942 2.719046 CGTCTTTGCATTCGTGGTTTTC 59.281 45.455 0.00 0.00 0.00 2.29
1702 1943 2.726633 CGTCTTTGCATTCGTGGTTTT 58.273 42.857 0.00 0.00 0.00 2.43
1703 1944 1.599419 GCGTCTTTGCATTCGTGGTTT 60.599 47.619 0.00 0.00 34.15 3.27
1704 1945 0.040425 GCGTCTTTGCATTCGTGGTT 60.040 50.000 0.00 0.00 34.15 3.67
1705 1946 1.163420 TGCGTCTTTGCATTCGTGGT 61.163 50.000 0.00 0.00 40.62 4.16
1738 1979 3.417101 GCTAGCTAGCTAGTGATGGAGA 58.583 50.000 39.05 13.72 45.67 3.71
1739 1980 3.848272 GCTAGCTAGCTAGTGATGGAG 57.152 52.381 39.05 23.14 45.67 3.86
1784 2029 2.349580 CGTCTGTTGCCATGTAGATGTG 59.650 50.000 0.00 0.00 0.00 3.21
1802 2047 4.561606 ACATGTTTCTATCGTACAAGCGTC 59.438 41.667 0.00 0.00 0.00 5.19
1832 2077 7.761409 TGATTCATTGATTCCTTTCCTTTACG 58.239 34.615 6.19 0.00 0.00 3.18
1873 3440 4.925836 TGGCCATGCTGACATTCATATAT 58.074 39.130 0.00 0.00 32.87 0.86
1880 3447 0.177141 GCAATGGCCATGCTGACATT 59.823 50.000 21.63 0.00 40.64 2.71
1958 3525 1.898574 AACAGCTGTTCAAGGGGCG 60.899 57.895 26.36 0.00 31.64 6.13
2138 3709 2.045047 ACATGAGGAGAAGAAGGGGAGA 59.955 50.000 0.00 0.00 0.00 3.71
2157 3728 1.614226 GGGTAGGTGGGTGGCTACA 60.614 63.158 1.52 0.00 0.00 2.74
2163 3734 3.335729 GGGGTGGGTAGGTGGGTG 61.336 72.222 0.00 0.00 0.00 4.61
2164 3735 3.877553 TGGGGTGGGTAGGTGGGT 61.878 66.667 0.00 0.00 0.00 4.51
2177 3748 4.631740 GTTGGGTTGGGGGTGGGG 62.632 72.222 0.00 0.00 0.00 4.96
2249 3826 0.401395 TGGTCAAGGGAGGTTGAGGT 60.401 55.000 0.00 0.00 37.12 3.85
2262 3839 0.527113 CGGCAAGCAATGATGGTCAA 59.473 50.000 0.00 0.00 35.91 3.18
2283 3860 3.300032 TAGAGGGATTGTCGTGGCT 57.700 52.632 0.00 0.00 0.00 4.75
2534 4111 3.996614 GGGGTCACCGGAATTGTG 58.003 61.111 9.46 0.00 37.78 3.33
2548 4125 4.974721 AACTTGGCAGGTGCGGGG 62.975 66.667 1.91 0.00 43.26 5.73
2549 4126 2.912025 AAACTTGGCAGGTGCGGG 60.912 61.111 1.91 0.00 43.26 6.13
2550 4127 2.133742 CTGAAACTTGGCAGGTGCGG 62.134 60.000 1.91 0.01 43.26 5.69
2551 4128 1.165907 TCTGAAACTTGGCAGGTGCG 61.166 55.000 1.91 0.00 43.26 5.34
2552 4129 0.312102 GTCTGAAACTTGGCAGGTGC 59.688 55.000 1.91 0.00 41.14 5.01
2553 4130 1.876156 GAGTCTGAAACTTGGCAGGTG 59.124 52.381 1.91 0.00 38.74 4.00
2554 4131 1.490490 TGAGTCTGAAACTTGGCAGGT 59.510 47.619 0.00 0.00 38.74 4.00
2555 4132 1.876156 GTGAGTCTGAAACTTGGCAGG 59.124 52.381 0.00 0.00 38.74 4.85
2556 4133 2.805099 GAGTGAGTCTGAAACTTGGCAG 59.195 50.000 0.00 0.00 38.74 4.85
2557 4134 2.485479 GGAGTGAGTCTGAAACTTGGCA 60.485 50.000 0.00 0.00 38.74 4.92
2558 4135 2.147150 GGAGTGAGTCTGAAACTTGGC 58.853 52.381 0.00 0.00 38.74 4.52
2559 4136 3.397482 CAGGAGTGAGTCTGAAACTTGG 58.603 50.000 0.00 0.00 38.74 3.61
2560 4137 2.805099 GCAGGAGTGAGTCTGAAACTTG 59.195 50.000 0.00 0.00 38.74 3.16
2561 4138 2.703007 AGCAGGAGTGAGTCTGAAACTT 59.297 45.455 0.00 0.00 38.74 2.66
2562 4139 2.324541 AGCAGGAGTGAGTCTGAAACT 58.675 47.619 0.00 0.00 42.42 2.66
2563 4140 2.829741 AGCAGGAGTGAGTCTGAAAC 57.170 50.000 0.00 0.00 33.11 2.78
2564 4141 3.767711 TCTAGCAGGAGTGAGTCTGAAA 58.232 45.455 0.00 0.00 33.11 2.69
2565 4142 3.441500 TCTAGCAGGAGTGAGTCTGAA 57.558 47.619 0.00 0.00 33.11 3.02
2566 4143 3.660970 ATCTAGCAGGAGTGAGTCTGA 57.339 47.619 0.00 0.00 33.11 3.27
2567 4144 4.154015 CGATATCTAGCAGGAGTGAGTCTG 59.846 50.000 0.34 0.00 0.00 3.51
2568 4145 4.323417 CGATATCTAGCAGGAGTGAGTCT 58.677 47.826 0.34 0.00 0.00 3.24
2569 4146 3.119990 GCGATATCTAGCAGGAGTGAGTC 60.120 52.174 0.34 0.00 0.00 3.36
2570 4147 2.817258 GCGATATCTAGCAGGAGTGAGT 59.183 50.000 0.34 0.00 0.00 3.41
2571 4148 2.163412 GGCGATATCTAGCAGGAGTGAG 59.837 54.545 0.34 0.00 34.54 3.51
2572 4149 2.163509 GGCGATATCTAGCAGGAGTGA 58.836 52.381 0.34 0.00 34.54 3.41
2573 4150 2.163412 GAGGCGATATCTAGCAGGAGTG 59.837 54.545 0.34 0.00 34.54 3.51
2574 4151 2.442413 GAGGCGATATCTAGCAGGAGT 58.558 52.381 0.34 0.00 34.54 3.85
2575 4152 1.748493 GGAGGCGATATCTAGCAGGAG 59.252 57.143 0.34 0.00 34.54 3.69
2576 4153 1.617263 GGGAGGCGATATCTAGCAGGA 60.617 57.143 0.34 0.00 34.54 3.86
2577 4154 0.820871 GGGAGGCGATATCTAGCAGG 59.179 60.000 0.34 0.00 34.54 4.85
2578 4155 0.453793 CGGGAGGCGATATCTAGCAG 59.546 60.000 0.34 0.00 34.54 4.24
2579 4156 1.595993 GCGGGAGGCGATATCTAGCA 61.596 60.000 0.34 0.00 34.54 3.49
2580 4157 1.139947 GCGGGAGGCGATATCTAGC 59.860 63.158 0.34 0.00 0.00 3.42
2598 4175 4.827087 AGGCGAGCCGTGCATGAG 62.827 66.667 7.72 0.00 41.95 2.90
2599 4176 4.393155 AAGGCGAGCCGTGCATGA 62.393 61.111 7.72 0.00 41.95 3.07
2600 4177 4.170062 CAAGGCGAGCCGTGCATG 62.170 66.667 16.30 0.00 38.60 4.06


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

AutoCloner maintained by Alex Coulton.