Multiple sequence alignment - TraesCS2B01G081700

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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 TraesCS2B01G081700 chr2B 100.000 5178 0 0 1 5178 45622123 45627300 0.000000e+00 9563.0
1 TraesCS2B01G081700 chr2B 95.385 3185 140 3 1438 4616 44924906 44928089 0.000000e+00 5060.0
2 TraesCS2B01G081700 chr2B 95.838 1850 69 5 2774 4616 45617275 45615427 0.000000e+00 2983.0
3 TraesCS2B01G081700 chr2B 96.861 1338 42 0 1438 2775 45701070 45702407 0.000000e+00 2239.0
4 TraesCS2B01G081700 chr2B 92.991 856 25 11 452 1274 45699808 45700661 0.000000e+00 1216.0
5 TraesCS2B01G081700 chr2B 92.224 553 20 6 4641 5178 45615458 45614914 0.000000e+00 761.0
6 TraesCS2B01G081700 chr2B 94.179 481 18 4 4701 5178 44928331 44928804 0.000000e+00 725.0
7 TraesCS2B01G081700 chr2B 90.955 398 29 4 1062 1456 44924246 44924639 3.810000e-146 529.0
8 TraesCS2B01G081700 chr2B 85.496 393 19 15 529 887 44923634 44924022 5.250000e-100 375.0
9 TraesCS2B01G081700 chr2B 100.000 117 0 0 5436 5552 45627558 45627674 3.370000e-52 217.0
10 TraesCS2B01G081700 chr2B 97.368 114 1 1 5438 5549 44929134 44929247 5.680000e-45 193.0
11 TraesCS2B01G081700 chr2B 94.068 118 4 2 5438 5552 45614647 45614530 5.720000e-40 176.0
12 TraesCS2B01G081700 chr2B 83.803 142 22 1 1315 1456 45700663 45700803 3.490000e-27 134.0
13 TraesCS2B01G081700 chr2D 92.728 1719 105 6 2994 4702 28416604 28414896 0.000000e+00 2464.0
14 TraesCS2B01G081700 chr2D 87.427 1543 188 3 1438 2977 28001313 27999774 0.000000e+00 1770.0
15 TraesCS2B01G081700 chr2D 86.714 1543 199 3 1438 2977 27957252 27958791 0.000000e+00 1709.0
16 TraesCS2B01G081700 chr2D 81.126 1616 248 30 2995 4562 27999783 27998177 0.000000e+00 1242.0
17 TraesCS2B01G081700 chr2D 82.834 1369 211 10 2995 4341 27958782 27960148 0.000000e+00 1205.0
18 TraesCS2B01G081700 chr2D 87.786 393 32 9 4761 5144 28414792 28414407 3.950000e-121 446.0
19 TraesCS2B01G081700 chr2D 84.516 465 51 12 1 457 28420604 28420153 1.840000e-119 440.0
20 TraesCS2B01G081700 chr2D 89.583 288 13 9 1032 1309 28066333 28066053 3.180000e-92 350.0
21 TraesCS2B01G081700 chr2D 86.567 335 19 8 676 995 28418845 28418522 4.120000e-91 346.0
22 TraesCS2B01G081700 chr2D 94.643 112 6 0 1326 1437 28060723 28060612 2.060000e-39 174.0
23 TraesCS2B01G081700 chr2D 81.283 187 22 6 468 654 28419076 28418903 7.500000e-29 139.0
24 TraesCS2B01G081700 chr2A 92.189 1626 116 9 2994 4616 30270130 30268513 0.000000e+00 2289.0
25 TraesCS2B01G081700 chr2A 92.128 1626 117 9 2994 4616 30254482 30252865 0.000000e+00 2283.0
26 TraesCS2B01G081700 chr2A 91.820 1626 121 9 2994 4616 30244880 30243264 0.000000e+00 2255.0
27 TraesCS2B01G081700 chr2A 90.201 1541 148 1 1438 2975 30301417 30302957 0.000000e+00 2006.0
28 TraesCS2B01G081700 chr2A 87.751 1543 186 1 1438 2977 30271662 30270120 0.000000e+00 1799.0
29 TraesCS2B01G081700 chr2A 87.427 1543 191 1 1438 2977 30246412 30244870 0.000000e+00 1772.0
30 TraesCS2B01G081700 chr2A 87.427 1543 188 4 1438 2977 30164465 30162926 0.000000e+00 1770.0
31 TraesCS2B01G081700 chr2A 86.869 1584 186 14 2994 4560 30302949 30304527 0.000000e+00 1753.0
32 TraesCS2B01G081700 chr2A 87.111 1544 195 2 1438 2977 30256015 30254472 0.000000e+00 1746.0
33 TraesCS2B01G081700 chr2A 88.910 532 29 10 4641 5144 30268544 30268015 3.650000e-176 628.0
34 TraesCS2B01G081700 chr2A 88.701 531 31 9 4641 5144 30243295 30242767 6.110000e-174 621.0
35 TraesCS2B01G081700 chr2A 88.258 528 34 11 4641 5144 30252896 30252373 1.710000e-169 606.0
36 TraesCS2B01G081700 chr2A 79.908 433 44 24 1032 1437 30300716 30301132 1.520000e-70 278.0
37 TraesCS2B01G081700 chr2A 86.328 256 14 7 759 1003 30196105 30195860 5.520000e-65 259.0
38 TraesCS2B01G081700 chr2A 94.186 86 5 0 913 998 30272640 30272555 1.250000e-26 132.0
39 TraesCS2B01G081700 chr2A 91.860 86 7 0 913 998 30256994 30256909 2.720000e-23 121.0
40 TraesCS2B01G081700 chr7D 88.536 1544 171 4 1438 2977 302744030 302745571 0.000000e+00 1866.0
41 TraesCS2B01G081700 chr7D 87.090 457 37 11 1014 1456 302743315 302743763 1.070000e-136 497.0
42 TraesCS2B01G081700 chr7D 94.505 91 5 0 4863 4953 302746414 302746504 2.090000e-29 141.0
43 TraesCS2B01G081700 chr7D 100.000 30 0 0 699 728 302743024 302743053 7.770000e-04 56.5


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 TraesCS2B01G081700 chr2B 45622123 45627674 5551 False 4890.000000 9563 100.000000 1 5552 2 chr2B.!!$F2 5551
1 TraesCS2B01G081700 chr2B 44923634 44929247 5613 False 1376.400000 5060 92.676600 529 5549 5 chr2B.!!$F1 5020
2 TraesCS2B01G081700 chr2B 45614530 45617275 2745 True 1306.666667 2983 94.043333 2774 5552 3 chr2B.!!$R1 2778
3 TraesCS2B01G081700 chr2B 45699808 45702407 2599 False 1196.333333 2239 91.218333 452 2775 3 chr2B.!!$F3 2323
4 TraesCS2B01G081700 chr2D 27998177 28001313 3136 True 1506.000000 1770 84.276500 1438 4562 2 chr2D.!!$R3 3124
5 TraesCS2B01G081700 chr2D 27957252 27960148 2896 False 1457.000000 1709 84.774000 1438 4341 2 chr2D.!!$F1 2903
6 TraesCS2B01G081700 chr2D 28414407 28420604 6197 True 767.000000 2464 86.576000 1 5144 5 chr2D.!!$R4 5143
7 TraesCS2B01G081700 chr2A 30162926 30164465 1539 True 1770.000000 1770 87.427000 1438 2977 1 chr2A.!!$R1 1539
8 TraesCS2B01G081700 chr2A 30242767 30246412 3645 True 1549.333333 2255 89.316000 1438 5144 3 chr2A.!!$R3 3706
9 TraesCS2B01G081700 chr2A 30300716 30304527 3811 False 1345.666667 2006 85.659333 1032 4560 3 chr2A.!!$F1 3528
10 TraesCS2B01G081700 chr2A 30268015 30272640 4625 True 1212.000000 2289 90.759000 913 5144 4 chr2A.!!$R5 4231
11 TraesCS2B01G081700 chr2A 30252373 30256994 4621 True 1189.000000 2283 89.839250 913 5144 4 chr2A.!!$R4 4231
12 TraesCS2B01G081700 chr7D 302743024 302746504 3480 False 640.125000 1866 92.532750 699 4953 4 chr7D.!!$F1 4254

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
523 1597 0.036306 AGGAACGCGGATTTGGTTCT 59.964 50.000 12.47 0.0 39.86 3.01 F
527 1601 0.250124 ACGCGGATTTGGTTCTGTCA 60.250 50.000 12.47 0.0 0.00 3.58 F
1310 2792 0.540923 TCACATCGACATCATGCCCA 59.459 50.000 0.00 0.0 0.00 5.36 F
1311 2793 1.141455 TCACATCGACATCATGCCCAT 59.859 47.619 0.00 0.0 0.00 4.00 F
3198 5002 2.355108 CGATGGGATCTTGTGTCCAAGT 60.355 50.000 2.69 0.0 46.70 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 2861 0.595567 ACATGTTTGCTTGTGCTGCG 60.596 50.000 0.00 0.00 40.48 5.18 R
1768 3541 3.611057 CGATAACCTATTTCGGACGAGGG 60.611 52.174 0.00 0.00 33.02 4.30 R
3062 4866 1.450312 GGTCGCCAGGAATGACAGG 60.450 63.158 8.64 0.00 34.32 4.00 R
3223 5045 1.807755 CGTCATGGCATGGGACTGTAG 60.808 57.143 26.15 3.08 0.00 2.74 R
5092 7223 1.213013 CACTCACGCTTCGCCTACT 59.787 57.895 0.00 0.00 0.00 2.57 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 2.515523 GCTGCATCCGATGTGGCT 60.516 61.111 10.10 0.00 37.80 4.75
38 39 1.841302 ATGTGGCTGTGTGTCCGGAT 61.841 55.000 7.81 0.00 0.00 4.18
42 43 0.178068 GGCTGTGTGTCCGGATGTAT 59.822 55.000 7.81 0.00 0.00 2.29
43 44 1.290203 GCTGTGTGTCCGGATGTATG 58.710 55.000 7.81 0.00 0.00 2.39
62 63 9.149225 GATGTATGATTTGATAGCTCTAGTTGG 57.851 37.037 0.00 0.00 0.00 3.77
67 68 4.342862 TTGATAGCTCTAGTTGGATGGC 57.657 45.455 0.00 0.00 0.00 4.40
85 86 5.278512 GGATGGCGTTTTTCTTTCTCTCTTT 60.279 40.000 0.00 0.00 0.00 2.52
92 93 6.197282 CGTTTTTCTTTCTCTCTTTTCCAAGC 59.803 38.462 0.00 0.00 0.00 4.01
95 96 6.966534 TTCTTTCTCTCTTTTCCAAGCAAT 57.033 33.333 0.00 0.00 0.00 3.56
100 101 5.762045 TCTCTCTTTTCCAAGCAATTTTCG 58.238 37.500 0.00 0.00 0.00 3.46
133 135 1.789523 TGGGGAGGAAATAGGAGTCG 58.210 55.000 0.00 0.00 0.00 4.18
144 146 2.857592 TAGGAGTCGCGGTAATTCAC 57.142 50.000 6.13 0.00 0.00 3.18
149 151 1.739466 AGTCGCGGTAATTCACGTCTA 59.261 47.619 6.13 0.00 0.00 2.59
168 170 3.163655 GCTCGTGCTTGTGCTCTC 58.836 61.111 1.41 0.00 40.48 3.20
172 174 0.243907 TCGTGCTTGTGCTCTCCTAC 59.756 55.000 0.00 0.00 40.48 3.18
176 178 1.153549 CTTGTGCTCTCCTACGCCC 60.154 63.158 0.00 0.00 0.00 6.13
178 180 3.138798 GTGCTCTCCTACGCCCGA 61.139 66.667 0.00 0.00 0.00 5.14
185 187 0.249073 CTCCTACGCCCGATGAACAG 60.249 60.000 0.00 0.00 0.00 3.16
190 192 1.722011 ACGCCCGATGAACAGTAAAG 58.278 50.000 0.00 0.00 0.00 1.85
197 199 6.617879 GCCCGATGAACAGTAAAGTAAAAAT 58.382 36.000 0.00 0.00 0.00 1.82
199 201 7.272731 GCCCGATGAACAGTAAAGTAAAAATTC 59.727 37.037 0.00 0.00 0.00 2.17
294 296 9.823647 TTTTGAACATTTATAGACCTGCAAAAA 57.176 25.926 0.00 0.00 31.20 1.94
325 327 9.474313 AAATAAGGTCCAAATAGTGCTCATTTA 57.526 29.630 0.00 0.00 0.00 1.40
334 336 8.915654 CCAAATAGTGCTCATTTACAAAGTTTC 58.084 33.333 0.00 0.00 0.00 2.78
351 353 6.885735 AAGTTTCTTTCACGGTCAAATTTG 57.114 33.333 12.15 12.15 0.00 2.32
355 357 7.386573 AGTTTCTTTCACGGTCAAATTTGTTTT 59.613 29.630 17.47 0.00 0.00 2.43
386 388 5.460646 CATTGTAGAATGTCCAAACACCAC 58.539 41.667 4.45 0.00 38.48 4.16
393 395 1.944024 TGTCCAAACACCACGAATGTC 59.056 47.619 0.00 0.00 0.00 3.06
394 396 1.265905 GTCCAAACACCACGAATGTCC 59.734 52.381 0.00 0.00 0.00 4.02
395 397 0.237235 CCAAACACCACGAATGTCCG 59.763 55.000 0.00 0.00 0.00 4.79
399 407 1.298157 ACACCACGAATGTCCGCATG 61.298 55.000 0.00 0.00 35.15 4.06
473 1547 7.265673 TGCTATTTTTAGTTACAGCGAGAGAT 58.734 34.615 0.00 0.00 0.00 2.75
523 1597 0.036306 AGGAACGCGGATTTGGTTCT 59.964 50.000 12.47 0.00 39.86 3.01
526 1600 0.872388 AACGCGGATTTGGTTCTGTC 59.128 50.000 12.47 0.00 0.00 3.51
527 1601 0.250124 ACGCGGATTTGGTTCTGTCA 60.250 50.000 12.47 0.00 0.00 3.58
634 1708 0.687757 CTCCCCTCCTCATCCGACAA 60.688 60.000 0.00 0.00 0.00 3.18
635 1709 0.687757 TCCCCTCCTCATCCGACAAG 60.688 60.000 0.00 0.00 0.00 3.16
636 1710 1.144936 CCCTCCTCATCCGACAAGC 59.855 63.158 0.00 0.00 0.00 4.01
637 1711 1.227089 CCTCCTCATCCGACAAGCG 60.227 63.158 0.00 0.00 40.47 4.68
638 1712 1.667154 CCTCCTCATCCGACAAGCGA 61.667 60.000 0.00 0.00 44.57 4.93
1161 2609 1.266989 GAGGTCTTTGTTTCCCTTGCG 59.733 52.381 0.00 0.00 0.00 4.85
1169 2617 2.539338 TTTCCCTTGCGCACACGTC 61.539 57.895 11.12 0.00 42.83 4.34
1205 2655 1.251251 GTCCAGTCAAGCATGCCTTT 58.749 50.000 15.66 0.00 0.00 3.11
1242 2705 6.039270 TGGTACACAAATCCTTCAAAAGTCAG 59.961 38.462 0.00 0.00 0.00 3.51
1310 2792 0.540923 TCACATCGACATCATGCCCA 59.459 50.000 0.00 0.00 0.00 5.36
1311 2793 1.141455 TCACATCGACATCATGCCCAT 59.859 47.619 0.00 0.00 0.00 4.00
1322 2804 3.159213 TCATGCCCATTGTCTTGTCTT 57.841 42.857 0.00 0.00 0.00 3.01
1323 2805 3.084039 TCATGCCCATTGTCTTGTCTTC 58.916 45.455 0.00 0.00 0.00 2.87
1372 2861 2.489938 TCAACACCTCAATACCAGCC 57.510 50.000 0.00 0.00 0.00 4.85
1566 3339 6.020599 CAGCACACTTATACTGTCACGTAATC 60.021 42.308 0.00 0.00 0.00 1.75
1768 3541 7.971183 ATTTTTCTTCCCTCGCTTCTATATC 57.029 36.000 0.00 0.00 0.00 1.63
1774 3547 2.438411 CCTCGCTTCTATATCCCTCGT 58.562 52.381 0.00 0.00 0.00 4.18
1832 3605 5.422666 TGAGTCACATTACAAAACTGCTG 57.577 39.130 0.00 0.00 0.00 4.41
3062 4866 7.378728 GCTTTAGTGACTAAATCAAAACACCAC 59.621 37.037 17.21 0.00 39.72 4.16
3107 4911 5.063564 GCTGCTAATTGTACTACCAACACTC 59.936 44.000 0.00 0.00 0.00 3.51
3198 5002 2.355108 CGATGGGATCTTGTGTCCAAGT 60.355 50.000 2.69 0.00 46.70 3.16
3223 5045 6.407202 TGTTTCCTAATAGAAGAGAAGTGCC 58.593 40.000 0.00 0.00 0.00 5.01
3254 5076 1.285578 GCCATGACGAGAAGAAGCTC 58.714 55.000 0.00 0.00 0.00 4.09
3769 5591 1.805869 CTCAGTGACTTTGGCTCAGG 58.194 55.000 0.00 0.00 0.00 3.86
3964 5786 2.252346 GCGAGATCTCCGTAGCCGA 61.252 63.158 17.13 0.00 35.63 5.54
4197 6019 0.620556 CCTTGGGCTGTCATGTACCT 59.379 55.000 0.00 0.00 0.00 3.08
4611 6470 5.571658 GCCTGATGGGTAATATTCGAAGGAT 60.572 44.000 3.35 0.00 37.43 3.24
4616 6475 8.040727 TGATGGGTAATATTCGAAGGATATGTG 58.959 37.037 3.35 0.00 0.00 3.21
4626 6485 8.964476 ATTCGAAGGATATGTGTATTGTTCTT 57.036 30.769 3.35 0.00 0.00 2.52
4655 6514 5.653255 ATTCTTAACAGCCTGATGGGTAT 57.347 39.130 0.00 0.00 43.07 2.73
4741 6840 7.117241 TGACATGACGAACAATACTCTTTTC 57.883 36.000 0.00 0.00 0.00 2.29
5134 7265 5.508224 GTGTGCACTTATAATCGCTGTTTTC 59.492 40.000 19.41 0.00 0.00 2.29
5150 7283 6.346518 CGCTGTTTTCCAAAACCATATGAAAC 60.347 38.462 3.65 5.01 45.82 2.78
5159 7292 6.364976 CCAAAACCATATGAAACGACCTTTTC 59.635 38.462 3.65 0.00 36.23 2.29
5527 7732 8.834465 CCTGTAATTCATCCATGAGTTAAAGAG 58.166 37.037 17.60 9.71 42.41 2.85
5549 7754 5.564550 AGTCTTGCATTGAGTATCCAAACT 58.435 37.500 0.00 0.00 0.00 2.66
5550 7755 5.413833 AGTCTTGCATTGAGTATCCAAACTG 59.586 40.000 0.00 0.00 0.00 3.16
5551 7756 5.182001 GTCTTGCATTGAGTATCCAAACTGT 59.818 40.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.904800 AATCATACATCCGGACACACA 57.095 42.857 6.12 0.00 0.00 3.72
38 39 8.250143 TCCAACTAGAGCTATCAAATCATACA 57.750 34.615 0.00 0.00 0.00 2.29
42 43 6.528321 CCATCCAACTAGAGCTATCAAATCA 58.472 40.000 0.00 0.00 0.00 2.57
43 44 5.411053 GCCATCCAACTAGAGCTATCAAATC 59.589 44.000 0.00 0.00 0.00 2.17
62 63 5.363979 AAGAGAGAAAGAAAAACGCCATC 57.636 39.130 0.00 0.00 0.00 3.51
67 68 6.197282 GCTTGGAAAAGAGAGAAAGAAAAACG 59.803 38.462 0.00 0.00 0.00 3.60
85 86 3.365868 CGATGGACGAAAATTGCTTGGAA 60.366 43.478 0.00 0.00 45.77 3.53
100 101 2.289694 CCTCCCCATATGTTCGATGGAC 60.290 54.545 3.51 0.00 45.89 4.02
133 135 2.534757 GAGCTTAGACGTGAATTACCGC 59.465 50.000 0.00 0.00 0.00 5.68
160 162 3.449227 CGGGCGTAGGAGAGCACA 61.449 66.667 0.00 0.00 36.38 4.57
161 163 2.491022 ATCGGGCGTAGGAGAGCAC 61.491 63.158 0.00 0.00 34.54 4.40
163 165 1.735376 TTCATCGGGCGTAGGAGAGC 61.735 60.000 0.00 0.00 0.00 4.09
164 166 0.030908 GTTCATCGGGCGTAGGAGAG 59.969 60.000 0.00 0.00 0.00 3.20
165 167 0.681887 TGTTCATCGGGCGTAGGAGA 60.682 55.000 0.00 0.00 0.00 3.71
166 168 0.249073 CTGTTCATCGGGCGTAGGAG 60.249 60.000 0.00 0.00 0.00 3.69
167 169 0.968901 ACTGTTCATCGGGCGTAGGA 60.969 55.000 0.00 0.00 0.00 2.94
168 170 0.742505 TACTGTTCATCGGGCGTAGG 59.257 55.000 0.00 0.00 0.00 3.18
172 174 1.722011 ACTTTACTGTTCATCGGGCG 58.278 50.000 0.00 0.00 0.00 6.13
234 236 1.226211 CGCAGCCGAGCATCTTTTG 60.226 57.895 0.00 0.00 36.29 2.44
235 237 3.181367 CGCAGCCGAGCATCTTTT 58.819 55.556 0.00 0.00 36.29 2.27
267 269 9.823647 TTTTGCAGGTCTATAAATGTTCAAAAA 57.176 25.926 0.00 0.00 30.08 1.94
268 270 9.823647 TTTTTGCAGGTCTATAAATGTTCAAAA 57.176 25.926 0.00 0.00 0.00 2.44
294 296 6.496911 AGCACTATTTGGACCTTATTTGGTTT 59.503 34.615 0.00 0.00 41.00 3.27
297 299 5.652014 TGAGCACTATTTGGACCTTATTTGG 59.348 40.000 0.00 0.00 0.00 3.28
303 305 6.245408 TGTAAATGAGCACTATTTGGACCTT 58.755 36.000 0.00 0.00 0.00 3.50
325 327 5.379732 TTTGACCGTGAAAGAAACTTTGT 57.620 34.783 1.41 0.00 0.00 2.83
363 365 5.460646 GTGGTGTTTGGACATTCTACAATG 58.539 41.667 0.00 0.00 44.57 2.82
366 368 3.135225 CGTGGTGTTTGGACATTCTACA 58.865 45.455 0.00 0.00 38.23 2.74
369 371 2.631160 TCGTGGTGTTTGGACATTCT 57.369 45.000 0.00 0.00 38.23 2.40
393 395 0.108662 TGCTCTAGTGTGTCATGCGG 60.109 55.000 0.00 0.00 0.00 5.69
394 396 1.857217 GATGCTCTAGTGTGTCATGCG 59.143 52.381 0.00 0.00 0.00 4.73
395 397 3.176552 AGATGCTCTAGTGTGTCATGC 57.823 47.619 0.00 0.00 0.00 4.06
399 407 4.098055 TCGAAAGATGCTCTAGTGTGTC 57.902 45.455 0.00 0.00 33.31 3.67
444 452 9.031360 TCTCGCTGTAACTAAAAATAGCATAAG 57.969 33.333 0.00 0.00 0.00 1.73
447 455 7.265673 TCTCTCGCTGTAACTAAAAATAGCAT 58.734 34.615 0.00 0.00 0.00 3.79
464 472 0.106469 TGGCCTCAGTATCTCTCGCT 60.106 55.000 3.32 0.00 0.00 4.93
473 1547 1.810151 GCGTTGAAATTGGCCTCAGTA 59.190 47.619 3.32 0.00 0.00 2.74
505 1579 0.168128 CAGAACCAAATCCGCGTTCC 59.832 55.000 4.92 0.00 37.24 3.62
523 1597 0.770499 TCCAAGCCCACAGAATGACA 59.230 50.000 0.00 0.00 39.69 3.58
526 1600 0.890683 GGTTCCAAGCCCACAGAATG 59.109 55.000 0.00 0.00 46.00 2.67
527 1601 0.251787 GGGTTCCAAGCCCACAGAAT 60.252 55.000 0.00 0.00 45.40 2.40
1161 2609 2.244651 GGTCAGTGTGGACGTGTGC 61.245 63.158 0.00 0.00 38.70 4.57
1169 2617 2.666190 CACGGCAGGTCAGTGTGG 60.666 66.667 0.00 0.00 36.35 4.17
1242 2705 1.064463 TGGATGATCTTGGGTGAAGGC 60.064 52.381 0.00 0.00 31.85 4.35
1310 2792 8.562892 CAAAATACAGAGTGAAGACAAGACAAT 58.437 33.333 0.00 0.00 0.00 2.71
1311 2793 7.467267 GCAAAATACAGAGTGAAGACAAGACAA 60.467 37.037 0.00 0.00 0.00 3.18
1322 2804 3.008375 AGGCTGAGCAAAATACAGAGTGA 59.992 43.478 6.82 0.00 34.07 3.41
1323 2805 3.341823 AGGCTGAGCAAAATACAGAGTG 58.658 45.455 6.82 0.00 34.07 3.51
1372 2861 0.595567 ACATGTTTGCTTGTGCTGCG 60.596 50.000 0.00 0.00 40.48 5.18
1746 3519 5.221661 GGGATATAGAAGCGAGGGAAGAAAA 60.222 44.000 0.00 0.00 0.00 2.29
1768 3541 3.611057 CGATAACCTATTTCGGACGAGGG 60.611 52.174 0.00 0.00 33.02 4.30
1832 3605 5.703130 ACTGTTGAAACTTAGATCAAGCTCC 59.297 40.000 0.00 0.00 37.83 4.70
2122 3895 7.775053 AGCAAGTTAATTCCTAAATCCAACA 57.225 32.000 0.00 0.00 0.00 3.33
2333 4107 7.004086 TCCCAAGTGAAGTGAGATTAACAAAT 58.996 34.615 0.00 0.00 0.00 2.32
3062 4866 1.450312 GGTCGCCAGGAATGACAGG 60.450 63.158 8.64 0.00 34.32 4.00
3198 5002 6.879458 GGCACTTCTCTTCTATTAGGAAACAA 59.121 38.462 0.00 0.00 0.00 2.83
3223 5045 1.807755 CGTCATGGCATGGGACTGTAG 60.808 57.143 26.15 3.08 0.00 2.74
3254 5076 3.440522 TGTCCTCGTATGACACTCTCTTG 59.559 47.826 0.00 0.00 37.80 3.02
3623 5445 3.329929 TCTGCTGCTATGCATATCCTG 57.670 47.619 6.92 6.91 42.48 3.86
3769 5591 4.508662 CAGACCTGGTGATAGAAACTTCC 58.491 47.826 2.82 0.00 0.00 3.46
3964 5786 4.630069 GCACTCCAAAACTATACACATCGT 59.370 41.667 0.00 0.00 0.00 3.73
4145 5967 5.181748 GGGACAATATATCTCTGCATCCAC 58.818 45.833 0.00 0.00 0.00 4.02
4197 6019 2.368875 GCCTATCCTTCGGAGATTCCAA 59.631 50.000 0.00 0.00 35.91 3.53
4585 6444 5.046591 CCTTCGAATATTACCCATCAGGCTA 60.047 44.000 0.00 0.00 40.58 3.93
4594 6453 9.886132 AATACACATATCCTTCGAATATTACCC 57.114 33.333 0.00 0.00 0.00 3.69
4626 6485 7.309744 CCCATCAGGCTGTTAAGAATTGTTTAA 60.310 37.037 15.27 0.00 0.00 1.52
4655 6514 9.542462 CAACCTTAAGACATATCCTTCGAATAA 57.458 33.333 3.36 0.00 0.00 1.40
4733 6832 8.753497 AAATAACAGTTTGAGAGGAAAAGAGT 57.247 30.769 0.00 0.00 0.00 3.24
4741 6840 5.241506 TGCAAGGAAATAACAGTTTGAGAGG 59.758 40.000 0.00 0.00 0.00 3.69
4962 7087 4.593206 AGTCTTTGTTGTCATCTCCACCTA 59.407 41.667 0.00 0.00 0.00 3.08
5092 7223 1.213013 CACTCACGCTTCGCCTACT 59.787 57.895 0.00 0.00 0.00 2.57
5134 7265 5.385509 AAGGTCGTTTCATATGGTTTTGG 57.614 39.130 2.13 0.00 0.00 3.28
5150 7283 3.136009 ACTTTGGTAGGGAAAAGGTCG 57.864 47.619 0.00 0.00 37.65 4.79
5436 7569 4.096682 CCGGAGTAAACAACAGGTTGAAAA 59.903 41.667 18.28 0.89 42.93 2.29
5527 7732 5.182001 ACAGTTTGGATACTCAATGCAAGAC 59.818 40.000 0.00 0.00 45.35 3.01


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

AutoCloner maintained by Alex Coulton.