Multiple sequence alignment - TraesCS4D01G254500

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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 TraesCS4D01G254500 chr4D 100.000 3247 0 0 1 3247 423430930 423427684 0.000000e+00 5997.0
1 TraesCS4D01G254500 chr4A 92.081 2374 92 41 203 2531 40859358 40861680 0.000000e+00 3254.0
2 TraesCS4D01G254500 chr4A 91.508 683 46 6 2565 3245 40861689 40862361 0.000000e+00 929.0
3 TraesCS4D01G254500 chr4B 91.807 1953 97 24 1324 3247 519824323 519822405 0.000000e+00 2662.0
4 TraesCS4D01G254500 chr4B 89.974 1137 68 22 203 1326 519825470 519824367 0.000000e+00 1426.0
5 TraesCS4D01G254500 chr4B 96.599 147 5 0 36 182 519825603 519825457 9.000000e-61 244.0
6 TraesCS4D01G254500 chr5B 85.315 143 21 0 1110 1252 580366673 580366531 7.260000e-32 148.0
7 TraesCS4D01G254500 chr5A 82.286 175 27 3 1110 1282 592638837 592638665 7.260000e-32 148.0
8 TraesCS4D01G254500 chr5D 84.615 143 22 0 1110 1252 473003387 473003245 3.380000e-30 143.0
9 TraesCS4D01G254500 chr2D 83.607 122 16 4 1130 1249 564384036 564384155 9.520000e-21 111.0
10 TraesCS4D01G254500 chr2B 78.333 180 29 8 1075 1249 675514517 675514691 1.230000e-19 108.0
11 TraesCS4D01G254500 chr2A 77.778 180 30 9 1075 1249 705068455 705068629 5.730000e-18 102.0
12 TraesCS4D01G254500 chr3D 91.379 58 5 0 1195 1252 613780056 613780113 2.690000e-11 80.5
13 TraesCS4D01G254500 chr7B 86.667 60 6 2 2656 2714 291577667 291577609 7.520000e-07 65.8
14 TraesCS4D01G254500 chr7A 78.947 95 18 2 2621 2714 206949948 206950041 2.700000e-06 63.9


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 TraesCS4D01G254500 chr4D 423427684 423430930 3246 True 5997.0 5997 100.000000 1 3247 1 chr4D.!!$R1 3246
1 TraesCS4D01G254500 chr4A 40859358 40862361 3003 False 2091.5 3254 91.794500 203 3245 2 chr4A.!!$F1 3042
2 TraesCS4D01G254500 chr4B 519822405 519825603 3198 True 1444.0 2662 92.793333 36 3247 3 chr4B.!!$R1 3211

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
588 594 0.037882 CCATCAGCCGTAGCGATGAT 60.038 55.0 16.1 3.19 45.06 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 2375 0.179078 AGCACGTTTACGGAACCACA 60.179 50.0 7.24 0.0 44.95 4.17 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
43 44 8.846943 TTATTGTGCCACCTTGTATATCTATG 57.153 34.615 0.00 0.00 0.00 2.23
173 174 0.238289 CGTGTCATCACAAAGTGGCC 59.762 55.000 0.00 0.00 44.02 5.36
174 175 0.238289 GTGTCATCACAAAGTGGCCG 59.762 55.000 0.00 0.00 43.37 6.13
175 176 0.179032 TGTCATCACAAAGTGGCCGT 60.179 50.000 0.00 0.00 33.87 5.68
176 177 0.951558 GTCATCACAAAGTGGCCGTT 59.048 50.000 0.00 0.00 33.87 4.44
177 178 1.336755 GTCATCACAAAGTGGCCGTTT 59.663 47.619 0.00 0.00 33.87 3.60
178 179 2.028130 TCATCACAAAGTGGCCGTTTT 58.972 42.857 0.00 0.00 33.87 2.43
179 180 2.126467 CATCACAAAGTGGCCGTTTTG 58.874 47.619 22.99 22.99 39.55 2.44
180 181 1.464734 TCACAAAGTGGCCGTTTTGA 58.535 45.000 28.41 18.26 37.63 2.69
181 182 1.403679 TCACAAAGTGGCCGTTTTGAG 59.596 47.619 28.41 22.81 37.63 3.02
182 183 0.102300 ACAAAGTGGCCGTTTTGAGC 59.898 50.000 28.41 1.59 37.63 4.26
183 184 0.385390 CAAAGTGGCCGTTTTGAGCT 59.615 50.000 21.13 0.00 36.61 4.09
184 185 0.668535 AAAGTGGCCGTTTTGAGCTC 59.331 50.000 6.82 6.82 0.00 4.09
185 186 0.179018 AAGTGGCCGTTTTGAGCTCT 60.179 50.000 16.19 0.00 0.00 4.09
186 187 0.179018 AGTGGCCGTTTTGAGCTCTT 60.179 50.000 16.19 0.00 0.00 2.85
187 188 0.668535 GTGGCCGTTTTGAGCTCTTT 59.331 50.000 16.19 0.00 0.00 2.52
188 189 1.067060 GTGGCCGTTTTGAGCTCTTTT 59.933 47.619 16.19 0.00 0.00 2.27
189 190 1.754226 TGGCCGTTTTGAGCTCTTTTT 59.246 42.857 16.19 0.00 0.00 1.94
315 316 6.019318 GCATTGAAATCCAATTTCCATTCTCG 60.019 38.462 9.31 0.00 46.18 4.04
323 324 1.722011 TTTCCATTCTCGAGGAACGC 58.278 50.000 13.56 0.00 43.23 4.84
347 349 4.415150 CCGTGCCTGCCAGACCAT 62.415 66.667 0.00 0.00 0.00 3.55
376 378 8.719648 CACATTTCAGAGCAAGGATATATCTTC 58.280 37.037 12.42 0.00 0.00 2.87
379 381 6.602410 TCAGAGCAAGGATATATCTTCAGG 57.398 41.667 12.42 0.65 0.00 3.86
407 409 6.870895 TCAGAGACTACTAGAGTTCCACTA 57.129 41.667 0.00 0.00 39.06 2.74
410 412 5.104402 AGAGACTACTAGAGTTCCACTACCC 60.104 48.000 0.00 0.00 39.06 3.69
424 426 2.062636 ACTACCCCATTCCACACAACT 58.937 47.619 0.00 0.00 0.00 3.16
447 449 3.374367 TCTCTCGGAGTAAACGATGACAG 59.626 47.826 4.69 0.00 39.89 3.51
466 468 2.875933 CAGGACAAAACTAAAGCCGTGA 59.124 45.455 0.00 0.00 0.00 4.35
486 492 4.213482 GTGATATATCGGTGCACTTTTCCC 59.787 45.833 17.98 0.00 0.00 3.97
498 504 3.127030 GCACTTTTCCCCGAAAGTCTATG 59.873 47.826 0.37 0.00 45.44 2.23
519 525 2.162608 GAGATATGTGACCGATCCTCCG 59.837 54.545 0.00 0.00 0.00 4.63
578 584 1.452108 GTCCCTTTCCCATCAGCCG 60.452 63.158 0.00 0.00 0.00 5.52
582 588 0.815615 CCTTTCCCATCAGCCGTAGC 60.816 60.000 0.00 0.00 40.32 3.58
585 591 1.399744 TTCCCATCAGCCGTAGCGAT 61.400 55.000 0.00 0.00 46.67 4.58
586 592 1.665916 CCCATCAGCCGTAGCGATG 60.666 63.158 10.72 10.72 46.67 3.84
587 593 1.363807 CCATCAGCCGTAGCGATGA 59.636 57.895 16.10 1.20 45.06 2.92
588 594 0.037882 CCATCAGCCGTAGCGATGAT 60.038 55.000 16.10 3.19 45.06 2.45
590 596 0.668706 ATCAGCCGTAGCGATGATGC 60.669 55.000 7.87 0.00 46.67 3.91
591 597 1.592400 CAGCCGTAGCGATGATGCA 60.592 57.895 0.00 0.00 46.67 3.96
592 598 1.592669 AGCCGTAGCGATGATGCAC 60.593 57.895 0.00 0.00 46.67 4.57
593 599 2.932083 GCCGTAGCGATGATGCACG 61.932 63.158 0.00 0.00 38.33 5.34
594 600 1.588932 CCGTAGCGATGATGCACGT 60.589 57.895 0.00 0.00 37.54 4.49
595 601 0.317519 CCGTAGCGATGATGCACGTA 60.318 55.000 0.00 0.00 37.54 3.57
596 602 1.666023 CCGTAGCGATGATGCACGTAT 60.666 52.381 0.00 0.00 37.54 3.06
611 618 4.033932 TGCACGTATCAATCAATTTCTCCG 59.966 41.667 0.00 0.00 0.00 4.63
616 623 5.106948 CGTATCAATCAATTTCTCCGGATGG 60.107 44.000 3.57 0.00 0.00 3.51
647 660 1.218230 GAGCTAGAATTCCTGCGCGG 61.218 60.000 9.96 9.96 0.00 6.46
650 663 2.311688 CTAGAATTCCTGCGCGGGGT 62.312 60.000 34.26 20.75 0.00 4.95
922 943 2.661866 ACACTCGCGCTCCACAAC 60.662 61.111 5.56 0.00 0.00 3.32
932 953 0.179018 GCTCCACAACACACTCCCTT 60.179 55.000 0.00 0.00 0.00 3.95
953 974 2.363018 CTCCTCCTCCGCACCTCA 60.363 66.667 0.00 0.00 0.00 3.86
967 993 1.000896 CCTCATTCACACCACCCCC 60.001 63.158 0.00 0.00 0.00 5.40
968 994 1.767036 CTCATTCACACCACCCCCA 59.233 57.895 0.00 0.00 0.00 4.96
969 995 0.112218 CTCATTCACACCACCCCCAA 59.888 55.000 0.00 0.00 0.00 4.12
970 996 0.178975 TCATTCACACCACCCCCAAC 60.179 55.000 0.00 0.00 0.00 3.77
973 999 1.282653 TTCACACCACCCCCAACTCA 61.283 55.000 0.00 0.00 0.00 3.41
974 1000 1.528309 CACACCACCCCCAACTCAC 60.528 63.158 0.00 0.00 0.00 3.51
975 1001 2.281484 CACCACCCCCAACTCACG 60.281 66.667 0.00 0.00 0.00 4.35
976 1002 2.446994 ACCACCCCCAACTCACGA 60.447 61.111 0.00 0.00 0.00 4.35
977 1003 1.846124 ACCACCCCCAACTCACGAT 60.846 57.895 0.00 0.00 0.00 3.73
978 1004 1.078426 CCACCCCCAACTCACGATC 60.078 63.158 0.00 0.00 0.00 3.69
980 1006 1.608336 ACCCCCAACTCACGATCGA 60.608 57.895 24.34 0.00 0.00 3.59
982 1008 0.249489 CCCCCAACTCACGATCGATC 60.249 60.000 24.34 15.68 0.00 3.69
991 1017 4.755546 CGATCGATCGCTAGCCTC 57.244 61.111 32.34 5.50 43.84 4.70
992 1018 1.225881 CGATCGATCGCTAGCCTCG 60.226 63.158 32.34 22.05 43.84 4.63
993 1019 1.513160 GATCGATCGCTAGCCTCGC 60.513 63.158 22.84 11.08 32.62 5.03
994 1020 2.859034 GATCGATCGCTAGCCTCGCC 62.859 65.000 22.84 15.53 32.62 5.54
996 1022 4.708968 GATCGCTAGCCTCGCCGG 62.709 72.222 9.66 0.00 0.00 6.13
1011 1037 2.669133 CCGGAGCATGAGGGGTTCA 61.669 63.158 0.00 0.00 40.85 3.18
1288 1317 1.467920 CCTCATCCAAGGTTTGCCTC 58.532 55.000 0.00 0.00 46.33 4.70
1538 1626 2.738521 CTCCACGTCGCCAACCTG 60.739 66.667 0.00 0.00 0.00 4.00
2116 2204 1.876664 TCGTGCTCTTCCTCGACAG 59.123 57.895 0.00 0.00 0.00 3.51
2286 2375 2.261671 GGTCAGCGACGTGGATGT 59.738 61.111 15.44 0.00 32.65 3.06
2292 2390 1.959226 GCGACGTGGATGTGTGGTT 60.959 57.895 0.11 0.00 0.00 3.67
2311 2409 1.444895 CCGTAAACGTGCTAGCGGT 60.445 57.895 10.77 7.87 37.74 5.68
2399 2501 5.176958 CCGCGTCGAATTAAGAGGATTATTT 59.823 40.000 4.92 0.00 0.00 1.40
2482 2585 5.725362 AGAATTAAGTGGTACTCTGTGCTC 58.275 41.667 0.00 0.00 30.14 4.26
2531 2634 0.692476 GCTTTGCCCCCTCCAATTTT 59.308 50.000 0.00 0.00 0.00 1.82
2559 2662 2.414250 TTTTTGAGGATTTGCCCCCT 57.586 45.000 0.00 0.00 37.37 4.79
2560 2663 1.937191 TTTTGAGGATTTGCCCCCTC 58.063 50.000 0.00 0.00 46.99 4.30
2561 2664 0.041090 TTTGAGGATTTGCCCCCTCC 59.959 55.000 0.00 0.00 46.43 4.30
2562 2665 1.145900 TTGAGGATTTGCCCCCTCCA 61.146 55.000 0.00 0.00 46.43 3.86
2563 2666 1.145900 TGAGGATTTGCCCCCTCCAA 61.146 55.000 0.00 0.00 46.43 3.53
2571 2674 1.377690 TGCCCCCTCCAATTCTGTTA 58.622 50.000 0.00 0.00 0.00 2.41
2579 2682 4.202182 CCCTCCAATTCTGTTATGCCAATG 60.202 45.833 0.00 0.00 0.00 2.82
2635 2738 7.450323 TGGTCTTGTTTTTAGGGAAATCTTAGG 59.550 37.037 0.00 0.00 0.00 2.69
2639 2742 6.014012 TGTTTTTAGGGAAATCTTAGGTGGG 58.986 40.000 0.00 0.00 0.00 4.61
2646 2749 3.268330 GAAATCTTAGGTGGGGAACGTC 58.732 50.000 0.00 0.00 0.00 4.34
2647 2750 0.822164 ATCTTAGGTGGGGAACGTCG 59.178 55.000 0.00 0.00 0.00 5.12
2668 2771 2.515057 ACGGACGTTTTGCCAGCA 60.515 55.556 0.00 0.00 0.00 4.41
2802 2905 2.510768 AAACGCATTAAAAACCGCCA 57.489 40.000 0.00 0.00 0.00 5.69
2816 2919 2.506472 GCCATCTCCCCCGTTCTC 59.494 66.667 0.00 0.00 0.00 2.87
2843 2963 1.377536 GACCCTAGTTACGCTCGTCT 58.622 55.000 0.00 0.00 0.00 4.18
2907 3028 7.599245 ACGAAGGAAGATAGTGTAAAGAAACAG 59.401 37.037 0.00 0.00 0.00 3.16
3039 3160 2.904866 GTTCTTGCCGTGGGTGCA 60.905 61.111 0.00 0.00 36.84 4.57
3093 3214 2.242926 CGGGGCTTAGAGAGATGATCA 58.757 52.381 0.00 0.00 0.00 2.92
3098 3219 2.352617 GCTTAGAGAGATGATCAGGGCG 60.353 54.545 0.09 0.00 0.00 6.13
3127 3249 1.153549 GCTAGAGAACAGCGTGGGG 60.154 63.158 0.00 0.00 0.00 4.96
3128 3250 1.605058 GCTAGAGAACAGCGTGGGGA 61.605 60.000 0.00 0.00 0.00 4.81
3129 3251 0.457851 CTAGAGAACAGCGTGGGGAG 59.542 60.000 0.00 0.00 0.00 4.30
3130 3252 0.970937 TAGAGAACAGCGTGGGGAGG 60.971 60.000 0.00 0.00 0.00 4.30
3131 3253 3.959991 GAGAACAGCGTGGGGAGGC 62.960 68.421 0.00 0.00 0.00 4.70
3132 3254 4.021925 GAACAGCGTGGGGAGGCT 62.022 66.667 0.00 0.00 40.90 4.58
3133 3255 3.553095 GAACAGCGTGGGGAGGCTT 62.553 63.158 0.00 0.00 37.41 4.35
3150 3272 3.573772 TTGGCGTGCGTGAGAGAGG 62.574 63.158 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.453572 CATAGATATACAAGGTGGCACAATAAT 57.546 33.333 20.82 8.28 44.16 1.28
18 19 7.882791 CCATAGATATACAAGGTGGCACAATAA 59.117 37.037 20.82 0.48 44.16 1.40
19 20 7.394016 CCATAGATATACAAGGTGGCACAATA 58.606 38.462 20.82 8.81 44.16 1.90
20 21 6.240894 CCATAGATATACAAGGTGGCACAAT 58.759 40.000 20.82 4.15 44.16 2.71
21 22 5.456042 CCCATAGATATACAAGGTGGCACAA 60.456 44.000 20.82 0.00 44.16 3.33
22 23 4.041567 CCCATAGATATACAAGGTGGCACA 59.958 45.833 20.82 0.00 0.00 4.57
23 24 4.286032 TCCCATAGATATACAAGGTGGCAC 59.714 45.833 9.70 9.70 0.00 5.01
24 25 4.498493 TCCCATAGATATACAAGGTGGCA 58.502 43.478 0.00 0.00 0.00 4.92
25 26 5.700402 ATCCCATAGATATACAAGGTGGC 57.300 43.478 0.00 0.00 31.60 5.01
43 44 3.589288 AGGCCCACAGAAGATTATATCCC 59.411 47.826 0.00 0.00 0.00 3.85
123 124 1.488812 TGCCGGTATATGCAACCTTCT 59.511 47.619 1.90 0.00 33.87 2.85
128 129 1.336755 CCCTTTGCCGGTATATGCAAC 59.663 52.381 1.90 0.00 46.32 4.17
147 148 3.188786 GTGATGACACGGCGCTCC 61.189 66.667 6.90 0.00 37.28 4.70
190 191 0.103208 ACGGCCACAATTCGCAAAAA 59.897 45.000 2.24 0.00 0.00 1.94
191 192 0.103208 AACGGCCACAATTCGCAAAA 59.897 45.000 2.24 0.00 0.00 2.44
192 193 0.103208 AAACGGCCACAATTCGCAAA 59.897 45.000 2.24 0.00 0.00 3.68
193 194 0.103208 AAAACGGCCACAATTCGCAA 59.897 45.000 2.24 0.00 0.00 4.85
194 195 0.596083 CAAAACGGCCACAATTCGCA 60.596 50.000 2.24 0.00 0.00 5.10
195 196 0.318275 TCAAAACGGCCACAATTCGC 60.318 50.000 2.24 0.00 0.00 4.70
196 197 1.001815 ACTCAAAACGGCCACAATTCG 60.002 47.619 2.24 0.00 0.00 3.34
197 198 2.793278 ACTCAAAACGGCCACAATTC 57.207 45.000 2.24 0.00 0.00 2.17
198 199 3.194062 CAAACTCAAAACGGCCACAATT 58.806 40.909 2.24 0.00 0.00 2.32
199 200 2.482839 CCAAACTCAAAACGGCCACAAT 60.483 45.455 2.24 0.00 0.00 2.71
200 201 1.134965 CCAAACTCAAAACGGCCACAA 60.135 47.619 2.24 0.00 0.00 3.33
201 202 0.457851 CCAAACTCAAAACGGCCACA 59.542 50.000 2.24 0.00 0.00 4.17
202 203 0.874175 GCCAAACTCAAAACGGCCAC 60.874 55.000 2.24 0.00 36.73 5.01
203 204 1.323271 TGCCAAACTCAAAACGGCCA 61.323 50.000 2.24 0.00 42.27 5.36
204 205 0.597377 CTGCCAAACTCAAAACGGCC 60.597 55.000 0.00 0.00 42.27 6.13
205 206 1.215014 GCTGCCAAACTCAAAACGGC 61.215 55.000 0.00 0.00 43.28 5.68
206 207 0.385390 AGCTGCCAAACTCAAAACGG 59.615 50.000 0.00 0.00 0.00 4.44
315 316 3.170585 CGGTCGTTCGCGTTCCTC 61.171 66.667 5.77 0.00 42.11 3.71
330 331 3.030168 TATGGTCTGGCAGGCACGG 62.030 63.158 22.23 0.00 0.00 4.94
347 349 4.574674 ATCCTTGCTCTGAAATGTGGTA 57.425 40.909 0.00 0.00 0.00 3.25
376 378 7.639113 ACTCTAGTAGTCTCTGAAATTCCTG 57.361 40.000 0.00 0.00 30.33 3.86
379 381 7.971722 GTGGAACTCTAGTAGTCTCTGAAATTC 59.028 40.741 0.00 0.00 37.50 2.17
407 409 1.499007 AGAAGTTGTGTGGAATGGGGT 59.501 47.619 0.00 0.00 0.00 4.95
410 412 2.738846 CGAGAGAAGTTGTGTGGAATGG 59.261 50.000 0.00 0.00 0.00 3.16
424 426 3.754850 TGTCATCGTTTACTCCGAGAGAA 59.245 43.478 1.33 0.00 37.81 2.87
447 449 5.813080 ATATCACGGCTTTAGTTTTGTCC 57.187 39.130 0.00 0.00 0.00 4.02
466 468 3.751518 GGGGAAAAGTGCACCGATATAT 58.248 45.455 14.63 0.00 0.00 0.86
486 492 6.153067 GGTCACATATCTCATAGACTTTCGG 58.847 44.000 0.00 0.00 0.00 4.30
498 504 2.162608 CGGAGGATCGGTCACATATCTC 59.837 54.545 0.00 0.00 34.37 2.75
554 560 1.076777 ATGGGAAAGGGACGCATGG 60.077 57.895 0.00 0.00 38.96 3.66
578 584 2.661594 TGATACGTGCATCATCGCTAC 58.338 47.619 0.00 0.00 29.93 3.58
582 588 4.713854 TTGATTGATACGTGCATCATCG 57.286 40.909 0.00 0.00 34.95 3.84
585 591 6.238456 GGAGAAATTGATTGATACGTGCATCA 60.238 38.462 0.00 0.00 33.10 3.07
586 592 6.138761 GGAGAAATTGATTGATACGTGCATC 58.861 40.000 0.00 0.00 0.00 3.91
587 593 5.277490 CGGAGAAATTGATTGATACGTGCAT 60.277 40.000 0.00 0.00 0.00 3.96
588 594 4.033932 CGGAGAAATTGATTGATACGTGCA 59.966 41.667 0.00 0.00 0.00 4.57
590 596 4.808895 TCCGGAGAAATTGATTGATACGTG 59.191 41.667 0.00 0.00 0.00 4.49
591 597 5.018539 TCCGGAGAAATTGATTGATACGT 57.981 39.130 0.00 0.00 0.00 3.57
592 598 5.106948 CCATCCGGAGAAATTGATTGATACG 60.107 44.000 11.34 0.00 0.00 3.06
593 599 5.182001 CCCATCCGGAGAAATTGATTGATAC 59.818 44.000 11.34 0.00 0.00 2.24
594 600 5.073008 TCCCATCCGGAGAAATTGATTGATA 59.927 40.000 11.34 0.00 34.86 2.15
595 601 4.141181 TCCCATCCGGAGAAATTGATTGAT 60.141 41.667 11.34 0.00 34.86 2.57
596 602 3.201930 TCCCATCCGGAGAAATTGATTGA 59.798 43.478 11.34 0.00 34.86 2.57
611 618 2.777094 GCTCTAGCTCAATTCCCATCC 58.223 52.381 0.00 0.00 38.21 3.51
647 660 1.000171 ACGTGTTAGTTTCCTCGACCC 60.000 52.381 0.00 0.00 0.00 4.46
650 663 2.605338 CCGAACGTGTTAGTTTCCTCGA 60.605 50.000 0.00 0.00 34.00 4.04
660 673 1.600164 CGTCTGAACCCGAACGTGTTA 60.600 52.381 0.00 0.00 0.00 2.41
922 943 2.190488 GAGGAGGCCAAGGGAGTGTG 62.190 65.000 5.01 0.00 0.00 3.82
949 970 1.000896 GGGGGTGGTGTGAATGAGG 60.001 63.158 0.00 0.00 0.00 3.86
953 974 0.112412 GAGTTGGGGGTGGTGTGAAT 59.888 55.000 0.00 0.00 0.00 2.57
975 1001 1.513160 GCGAGGCTAGCGATCGATC 60.513 63.158 32.66 15.68 38.72 3.69
976 1002 2.563942 GCGAGGCTAGCGATCGAT 59.436 61.111 32.66 16.78 38.72 3.59
977 1003 3.661131 GGCGAGGCTAGCGATCGA 61.661 66.667 32.66 0.00 38.72 3.59
984 1010 3.610669 ATGCTCCGGCGAGGCTAG 61.611 66.667 9.30 0.00 42.25 3.42
988 1014 4.598894 CCTCATGCTCCGGCGAGG 62.599 72.222 9.30 0.17 42.25 4.63
989 1015 4.598894 CCCTCATGCTCCGGCGAG 62.599 72.222 9.30 5.11 42.25 5.03
992 1018 4.115199 AACCCCTCATGCTCCGGC 62.115 66.667 0.00 0.00 39.26 6.13
993 1019 2.190578 GAACCCCTCATGCTCCGG 59.809 66.667 0.00 0.00 0.00 5.14
994 1020 1.450312 GTGAACCCCTCATGCTCCG 60.450 63.158 0.00 0.00 36.14 4.63
995 1021 1.450312 CGTGAACCCCTCATGCTCC 60.450 63.158 0.00 0.00 36.14 4.70
996 1022 1.450312 CCGTGAACCCCTCATGCTC 60.450 63.158 0.00 0.00 39.43 4.26
997 1023 2.224159 ACCGTGAACCCCTCATGCT 61.224 57.895 0.00 0.00 39.43 3.79
1008 1034 2.591429 CAGCAGCACCACCGTGAA 60.591 61.111 0.00 0.00 43.14 3.18
1260 1289 2.045047 ACCTTGGATGAGGGAGAAGAGA 59.955 50.000 0.00 0.00 41.31 3.10
1288 1317 2.774951 CGCGCGTTGAACGAGTAGG 61.775 63.158 24.19 8.27 46.05 3.18
1469 1557 2.415608 GGAGCCGACGGACATGAGA 61.416 63.158 20.50 0.00 0.00 3.27
1473 1561 4.148825 GCAGGAGCCGACGGACAT 62.149 66.667 20.50 5.38 33.58 3.06
2249 2337 4.899239 CTGACCGGCTGGCGGATC 62.899 72.222 43.22 33.40 39.70 3.36
2286 2375 0.179078 AGCACGTTTACGGAACCACA 60.179 50.000 7.24 0.00 44.95 4.17
2292 2390 1.153978 CCGCTAGCACGTTTACGGA 60.154 57.895 16.45 0.00 43.19 4.69
2311 2409 3.731717 GCAAAAGTCGCCGAAAATTAACA 59.268 39.130 0.00 0.00 0.00 2.41
2482 2585 6.148976 TCTGAATTGATCACAGAAGAAGCTTG 59.851 38.462 2.10 0.00 37.66 4.01
2541 2644 1.937191 GAGGGGGCAAATCCTCAAAA 58.063 50.000 4.66 0.00 46.54 2.44
2545 2648 0.262876 ATTGGAGGGGGCAAATCCTC 59.737 55.000 0.00 0.00 46.57 3.71
2546 2649 0.718408 AATTGGAGGGGGCAAATCCT 59.282 50.000 3.27 0.00 34.04 3.24
2547 2650 1.123077 GAATTGGAGGGGGCAAATCC 58.877 55.000 0.00 0.00 0.00 3.01
2548 2651 1.758862 CAGAATTGGAGGGGGCAAATC 59.241 52.381 0.00 0.00 0.00 2.17
2549 2652 1.079323 ACAGAATTGGAGGGGGCAAAT 59.921 47.619 0.00 0.00 0.00 2.32
2550 2653 0.486879 ACAGAATTGGAGGGGGCAAA 59.513 50.000 0.00 0.00 0.00 3.68
2551 2654 0.486879 AACAGAATTGGAGGGGGCAA 59.513 50.000 0.00 0.00 0.00 4.52
2552 2655 1.377690 TAACAGAATTGGAGGGGGCA 58.622 50.000 0.00 0.00 0.00 5.36
2553 2656 2.310538 CATAACAGAATTGGAGGGGGC 58.689 52.381 0.00 0.00 0.00 5.80
2554 2657 2.310538 GCATAACAGAATTGGAGGGGG 58.689 52.381 0.00 0.00 0.00 5.40
2555 2658 2.310538 GGCATAACAGAATTGGAGGGG 58.689 52.381 0.00 0.00 0.00 4.79
2556 2659 3.017048 TGGCATAACAGAATTGGAGGG 57.983 47.619 0.00 0.00 0.00 4.30
2557 2660 4.403432 ACATTGGCATAACAGAATTGGAGG 59.597 41.667 0.00 0.00 0.00 4.30
2558 2661 5.587388 ACATTGGCATAACAGAATTGGAG 57.413 39.130 0.00 0.00 0.00 3.86
2559 2662 5.392919 CGAACATTGGCATAACAGAATTGGA 60.393 40.000 0.00 0.00 0.00 3.53
2560 2663 4.799949 CGAACATTGGCATAACAGAATTGG 59.200 41.667 0.00 0.00 0.00 3.16
2561 2664 5.286797 CACGAACATTGGCATAACAGAATTG 59.713 40.000 0.00 0.00 0.00 2.32
2562 2665 5.048083 ACACGAACATTGGCATAACAGAATT 60.048 36.000 0.00 0.00 0.00 2.17
2563 2666 4.458989 ACACGAACATTGGCATAACAGAAT 59.541 37.500 0.00 0.00 0.00 2.40
2571 2674 7.870445 AGTAAAATAAAACACGAACATTGGCAT 59.130 29.630 0.00 0.00 0.00 4.40
2646 2749 4.676586 GCAAAACGTCCGTGGCCG 62.677 66.667 0.00 0.00 0.00 6.13
2647 2750 4.337060 GGCAAAACGTCCGTGGCC 62.337 66.667 12.52 12.52 34.93 5.36
2668 2771 1.612676 GTGCGGTTTAGGAAGGGTTT 58.387 50.000 0.00 0.00 0.00 3.27
2754 2857 1.873270 GCAGGGTGGCGGTTTTTAGG 61.873 60.000 0.00 0.00 0.00 2.69
2776 2879 4.247258 GGTTTTTAATGCGTTTAAGGGGG 58.753 43.478 0.00 0.00 31.57 5.40
2802 2905 0.613853 TTCACGAGAACGGGGGAGAT 60.614 55.000 0.00 0.00 43.75 2.75
2816 2919 1.466360 CGTAACTAGGGTCCGTTCACG 60.466 57.143 0.00 0.00 39.44 4.35
2843 2963 2.431057 TCCCGCTTTGCCTTAAAAACAA 59.569 40.909 0.00 0.00 0.00 2.83
2907 3028 6.936279 TCAGGCACCTAGTAAATAGCATATC 58.064 40.000 0.00 0.00 0.00 1.63
2939 3060 1.144969 CTAACTCGTTTGGCGCTTGA 58.855 50.000 7.64 0.00 41.07 3.02
3039 3160 2.276116 ATCGACCAGCCGTCACACT 61.276 57.895 0.00 0.00 42.07 3.55
3098 3219 1.927838 GTTCTCTAGCAGTTTAGCGCC 59.072 52.381 2.29 0.00 40.15 6.53
3110 3231 0.457851 CTCCCCACGCTGTTCTCTAG 59.542 60.000 0.00 0.00 0.00 2.43
3130 3252 3.782244 CTCTCACGCACGCCAAGC 61.782 66.667 0.00 0.00 0.00 4.01
3131 3253 2.049156 TCTCTCACGCACGCCAAG 60.049 61.111 0.00 0.00 0.00 3.61
3132 3254 2.049156 CTCTCTCACGCACGCCAA 60.049 61.111 0.00 0.00 0.00 4.52
3133 3255 4.056125 CCTCTCTCACGCACGCCA 62.056 66.667 0.00 0.00 0.00 5.69
3161 3283 3.943691 TACCGCTGGCCAAACCGT 61.944 61.111 7.01 5.77 43.94 4.83
3162 3284 3.428282 GTACCGCTGGCCAAACCG 61.428 66.667 7.01 10.09 43.94 4.44
3163 3285 3.428282 CGTACCGCTGGCCAAACC 61.428 66.667 7.01 0.00 39.84 3.27
3164 3286 2.667199 ACGTACCGCTGGCCAAAC 60.667 61.111 7.01 0.04 0.00 2.93
3165 3287 2.666862 CACGTACCGCTGGCCAAA 60.667 61.111 7.01 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.