Multiple sequence alignment - TraesCS6A01G122500

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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 TraesCS6A01G122500 chr6A 100.000 3128 0 0 1 3128 95796754 95793627 0.000000e+00 5777.0
1 TraesCS6A01G122500 chr6A 82.186 1162 117 42 1382 2502 94377182 94376070 0.000000e+00 917.0
2 TraesCS6A01G122500 chr6A 80.152 660 62 22 761 1403 94377729 94377122 2.230000e-116 429.0
3 TraesCS6A01G122500 chr6A 85.012 427 50 8 228 644 13964806 13965228 3.730000e-114 422.0
4 TraesCS6A01G122500 chr6D 90.561 1462 81 17 4 1443 79622036 79620610 0.000000e+00 1882.0
5 TraesCS6A01G122500 chr6D 92.000 1125 62 10 1344 2445 79620592 79619473 0.000000e+00 1554.0
6 TraesCS6A01G122500 chr6D 90.385 988 52 22 2168 3128 79617066 79616095 0.000000e+00 1258.0
7 TraesCS6A01G122500 chr6D 84.057 991 97 31 1382 2358 79171266 79170323 0.000000e+00 898.0
8 TraesCS6A01G122500 chr6D 89.717 671 66 3 1388 2058 79704208 79703541 0.000000e+00 854.0
9 TraesCS6A01G122500 chr6D 90.000 420 17 9 2049 2445 79703142 79702725 1.290000e-143 520.0
10 TraesCS6A01G122500 chr6D 84.651 430 32 11 975 1403 79171602 79171206 6.290000e-107 398.0
11 TraesCS6A01G122500 chr6D 92.000 100 8 0 1344 1443 79620670 79620571 1.170000e-29 141.0
12 TraesCS6A01G122500 chr6D 91.765 85 7 0 2647 2731 79677985 79677901 5.480000e-23 119.0
13 TraesCS6A01G122500 chr6D 93.548 62 4 0 1382 1443 79620710 79620649 3.320000e-15 93.5
14 TraesCS6A01G122500 chr6D 96.078 51 2 0 2357 2407 79170198 79170148 2.000000e-12 84.2
15 TraesCS6A01G122500 chr6B 93.110 1045 38 11 1427 2445 151821342 151820306 0.000000e+00 1500.0
16 TraesCS6A01G122500 chr6B 78.657 581 96 21 1567 2133 151839321 151838755 8.250000e-96 361.0
17 TraesCS6A01G122500 chr2D 86.998 423 45 6 228 643 351288794 351288375 4.720000e-128 468.0
18 TraesCS6A01G122500 chr7D 85.000 420 57 6 228 643 611009095 611009512 3.730000e-114 422.0
19 TraesCS6A01G122500 chr1D 86.243 378 45 7 270 643 296736531 296736157 1.350000e-108 403.0
20 TraesCS6A01G122500 chr5D 83.803 426 58 7 228 643 341240344 341239920 8.130000e-106 394.0
21 TraesCS6A01G122500 chr1B 83.848 421 58 8 229 643 556968491 556968075 2.920000e-105 392.0
22 TraesCS6A01G122500 chr7B 84.058 414 56 8 229 635 60458098 60457688 1.050000e-104 390.0
23 TraesCS6A01G122500 chr5B 83.175 422 62 9 229 642 523195342 523194922 8.190000e-101 377.0


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 TraesCS6A01G122500 chr6A 95793627 95796754 3127 True 5777.000000 5777 100.0000 1 3128 1 chr6A.!!$R1 3127
1 TraesCS6A01G122500 chr6A 94376070 94377729 1659 True 673.000000 917 81.1690 761 2502 2 chr6A.!!$R2 1741
2 TraesCS6A01G122500 chr6D 79616095 79622036 5941 True 985.700000 1882 91.6988 4 3128 5 chr6D.!!$R3 3124
3 TraesCS6A01G122500 chr6D 79702725 79704208 1483 True 687.000000 854 89.8585 1388 2445 2 chr6D.!!$R4 1057
4 TraesCS6A01G122500 chr6D 79170148 79171602 1454 True 460.066667 898 88.2620 975 2407 3 chr6D.!!$R2 1432
5 TraesCS6A01G122500 chr6B 151820306 151821342 1036 True 1500.000000 1500 93.1100 1427 2445 1 chr6B.!!$R1 1018
6 TraesCS6A01G122500 chr6B 151838755 151839321 566 True 361.000000 361 78.6570 1567 2133 1 chr6B.!!$R2 566

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
259 270 0.250234 TTGGAGCTCGGTCTTCATGG 59.750 55.000 7.83 0.0 0.00 3.66 F
266 279 0.537188 TCGGTCTTCATGGAGGCTTC 59.463 55.000 5.38 0.0 0.00 3.86 F
1349 1386 1.399727 CGCTAAGGCAACGTTTTCTGG 60.400 52.381 0.00 0.0 46.39 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1325 1362 0.168128 AAACGTTGCCTTAGCGATGC 59.832 50.0 0.0 0.0 42.42 3.91 R
1372 1409 0.612744 AGCTCAGAAACAGGCTCCTC 59.387 55.0 0.0 0.0 0.00 3.71 R
2304 2963 0.921347 CGTCGAATTTACCAGAGCCG 59.079 55.0 0.0 0.0 0.00 5.52 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 3.639561 TGCTTGGTAGAGTTACTGTCACA 59.360 43.478 0.00 0.00 0.00 3.58
42 43 6.237901 ACTGTCACAAGGCACATTATTCTTA 58.762 36.000 0.00 0.00 0.00 2.10
58 59 9.730420 CATTATTCTTAGGTTTTATTTGTCGGG 57.270 33.333 0.00 0.00 0.00 5.14
59 60 9.689501 ATTATTCTTAGGTTTTATTTGTCGGGA 57.310 29.630 0.00 0.00 0.00 5.14
94 95 6.605594 ACACTGTTGGATTTTGGTTTCTAAGA 59.394 34.615 0.00 0.00 0.00 2.10
153 154 1.072331 CACCAGCCCTTCACTAAGTGT 59.928 52.381 0.00 0.00 34.79 3.55
193 194 4.156556 CACAACATTTGTACATGGGAGGAG 59.843 45.833 0.00 0.00 43.23 3.69
212 213 0.912486 GTACATGGAAGGAGGCTGGT 59.088 55.000 0.00 0.00 0.00 4.00
216 217 1.561542 CATGGAAGGAGGCTGGTAAGT 59.438 52.381 0.00 0.00 0.00 2.24
223 224 3.248888 AGGAGGCTGGTAAGTTGTAGTT 58.751 45.455 0.00 0.00 0.00 2.24
224 225 3.651423 AGGAGGCTGGTAAGTTGTAGTTT 59.349 43.478 0.00 0.00 0.00 2.66
225 226 3.751698 GGAGGCTGGTAAGTTGTAGTTTG 59.248 47.826 0.00 0.00 0.00 2.93
238 249 3.271729 TGTAGTTTGTTGAGAACGGCAA 58.728 40.909 0.00 0.00 32.38 4.52
251 262 2.040544 CGGCAATTTGGAGCTCGGT 61.041 57.895 7.83 0.00 0.00 4.69
254 265 1.168714 GCAATTTGGAGCTCGGTCTT 58.831 50.000 7.83 0.00 0.00 3.01
255 266 1.131315 GCAATTTGGAGCTCGGTCTTC 59.869 52.381 7.83 0.00 0.00 2.87
256 267 2.426522 CAATTTGGAGCTCGGTCTTCA 58.573 47.619 7.83 0.00 0.00 3.02
257 268 3.012518 CAATTTGGAGCTCGGTCTTCAT 58.987 45.455 7.83 0.00 0.00 2.57
259 270 0.250234 TTGGAGCTCGGTCTTCATGG 59.750 55.000 7.83 0.00 0.00 3.66
260 271 0.614697 TGGAGCTCGGTCTTCATGGA 60.615 55.000 7.83 0.00 0.00 3.41
266 279 0.537188 TCGGTCTTCATGGAGGCTTC 59.463 55.000 5.38 0.00 0.00 3.86
270 283 3.369471 CGGTCTTCATGGAGGCTTCTTTA 60.369 47.826 5.38 0.00 0.00 1.85
271 284 4.589908 GGTCTTCATGGAGGCTTCTTTAA 58.410 43.478 5.38 0.00 0.00 1.52
352 365 3.954200 ACAAGGATGTGATGTGTATGCA 58.046 40.909 0.00 0.00 38.69 3.96
353 366 3.691118 ACAAGGATGTGATGTGTATGCAC 59.309 43.478 7.03 7.03 41.22 4.57
409 422 7.010367 TGTGATCTGTGCAAAAAGAACAAATTC 59.990 33.333 6.79 0.00 34.61 2.17
412 425 9.195411 GATCTGTGCAAAAAGAACAAATTCATA 57.805 29.630 0.00 0.00 34.61 2.15
419 432 9.853921 GCAAAAAGAACAAATTCATAGACTTTG 57.146 29.630 7.89 7.89 37.91 2.77
421 434 9.546428 AAAAAGAACAAATTCATAGACTTTGGG 57.454 29.630 12.42 0.00 36.80 4.12
424 437 7.184862 AGAACAAATTCATAGACTTTGGGGAT 58.815 34.615 12.42 0.00 36.80 3.85
427 440 6.604795 ACAAATTCATAGACTTTGGGGATGAG 59.395 38.462 12.42 0.00 36.80 2.90
452 465 5.991328 ATATCATGTGTTAAAGAGCCACG 57.009 39.130 0.00 0.00 31.75 4.94
453 466 1.804151 TCATGTGTTAAAGAGCCACGC 59.196 47.619 0.00 0.00 31.75 5.34
461 474 1.609208 AAAGAGCCACGCATTTGTCT 58.391 45.000 0.00 0.00 0.00 3.41
489 502 3.663493 GCACGACCTTCATTTCAACGTAC 60.663 47.826 0.00 0.00 0.00 3.67
533 546 5.049198 CACATGTGTGTTATGCCTCCATATC 60.049 44.000 18.03 0.00 40.96 1.63
657 671 8.897872 AAGAAAATTTCACAGAAGATTGCATT 57.102 26.923 8.55 0.00 0.00 3.56
683 697 4.650972 AGTTCCATGGCTTAGGTTAACA 57.349 40.909 6.96 0.00 0.00 2.41
684 698 4.332828 AGTTCCATGGCTTAGGTTAACAC 58.667 43.478 6.96 0.00 0.00 3.32
685 699 4.076394 GTTCCATGGCTTAGGTTAACACA 58.924 43.478 6.96 0.00 0.00 3.72
686 700 4.584638 TCCATGGCTTAGGTTAACACAT 57.415 40.909 6.96 0.00 0.00 3.21
687 701 4.929479 TCCATGGCTTAGGTTAACACATT 58.071 39.130 6.96 0.00 0.00 2.71
688 702 5.329399 TCCATGGCTTAGGTTAACACATTT 58.671 37.500 6.96 0.00 0.00 2.32
689 703 5.777732 TCCATGGCTTAGGTTAACACATTTT 59.222 36.000 6.96 0.00 0.00 1.82
690 704 6.948886 TCCATGGCTTAGGTTAACACATTTTA 59.051 34.615 6.96 0.00 0.00 1.52
691 705 7.122055 TCCATGGCTTAGGTTAACACATTTTAG 59.878 37.037 6.96 0.00 0.00 1.85
692 706 7.122055 CCATGGCTTAGGTTAACACATTTTAGA 59.878 37.037 8.10 0.00 0.00 2.10
693 707 8.519526 CATGGCTTAGGTTAACACATTTTAGAA 58.480 33.333 8.10 0.00 0.00 2.10
694 708 8.466617 TGGCTTAGGTTAACACATTTTAGAAA 57.533 30.769 8.10 0.00 0.00 2.52
695 709 9.084533 TGGCTTAGGTTAACACATTTTAGAAAT 57.915 29.630 8.10 0.00 0.00 2.17
696 710 9.569167 GGCTTAGGTTAACACATTTTAGAAATC 57.431 33.333 8.10 0.00 0.00 2.17
697 711 9.569167 GCTTAGGTTAACACATTTTAGAAATCC 57.431 33.333 8.10 0.00 0.00 3.01
701 715 9.088987 AGGTTAACACATTTTAGAAATCCATGT 57.911 29.630 8.10 0.00 0.00 3.21
702 716 9.353999 GGTTAACACATTTTAGAAATCCATGTC 57.646 33.333 8.10 0.00 0.00 3.06
703 717 9.353999 GTTAACACATTTTAGAAATCCATGTCC 57.646 33.333 0.00 0.00 0.00 4.02
704 718 7.781324 AACACATTTTAGAAATCCATGTCCT 57.219 32.000 0.00 0.00 0.00 3.85
705 719 8.877864 AACACATTTTAGAAATCCATGTCCTA 57.122 30.769 0.00 0.00 0.00 2.94
758 772 7.775093 TGAGTCTCCTCATTTTCTGAAGAAAAA 59.225 33.333 19.15 6.15 44.21 1.94
863 892 2.203451 GCCATGGCCTGATCCCAG 60.203 66.667 27.24 0.00 40.09 4.45
901 937 3.050835 GGTTAGCCTCACCCCCTTTATA 58.949 50.000 0.00 0.00 0.00 0.98
902 938 3.656264 GGTTAGCCTCACCCCCTTTATAT 59.344 47.826 0.00 0.00 0.00 0.86
903 939 4.848086 GGTTAGCCTCACCCCCTTTATATA 59.152 45.833 0.00 0.00 0.00 0.86
904 940 5.280368 GGTTAGCCTCACCCCCTTTATATAC 60.280 48.000 0.00 0.00 0.00 1.47
907 943 3.306571 GCCTCACCCCCTTTATATACGTC 60.307 52.174 0.00 0.00 0.00 4.34
911 947 6.204852 TCACCCCCTTTATATACGTCTAGA 57.795 41.667 0.00 0.00 0.00 2.43
965 1001 3.751175 CCAATCTCACTAAACTTGGCGAA 59.249 43.478 0.00 0.00 30.85 4.70
1342 1379 2.106683 GGCATCGCTAAGGCAACGT 61.107 57.895 0.00 0.00 46.39 3.99
1349 1386 1.399727 CGCTAAGGCAACGTTTTCTGG 60.400 52.381 0.00 0.00 46.39 3.86
1367 1404 4.074526 GCCTCAGGCTGACGCAGA 62.075 66.667 26.68 2.65 46.69 4.26
1368 1405 2.183811 CCTCAGGCTGACGCAGAG 59.816 66.667 14.43 2.38 38.67 3.35
1369 1406 2.346541 CCTCAGGCTGACGCAGAGA 61.347 63.158 14.43 0.00 40.28 3.10
1370 1407 1.674764 CCTCAGGCTGACGCAGAGAT 61.675 60.000 14.43 0.00 40.28 2.75
1371 1408 0.248990 CTCAGGCTGACGCAGAGATC 60.249 60.000 14.43 0.00 40.28 2.75
1372 1409 1.588403 CAGGCTGACGCAGAGATCG 60.588 63.158 9.42 0.00 38.10 3.69
1373 1410 1.750780 AGGCTGACGCAGAGATCGA 60.751 57.895 10.46 0.00 38.10 3.59
1374 1411 1.299014 GGCTGACGCAGAGATCGAG 60.299 63.158 10.46 0.00 38.10 4.04
1375 1412 1.299014 GCTGACGCAGAGATCGAGG 60.299 63.158 10.46 0.00 32.44 4.63
1376 1413 1.719725 GCTGACGCAGAGATCGAGGA 61.720 60.000 10.46 0.00 32.44 3.71
1377 1414 0.307453 CTGACGCAGAGATCGAGGAG 59.693 60.000 1.18 0.00 32.44 3.69
1378 1415 1.008995 GACGCAGAGATCGAGGAGC 60.009 63.158 0.00 0.00 0.00 4.70
1379 1416 2.334653 CGCAGAGATCGAGGAGCC 59.665 66.667 0.00 0.00 0.00 4.70
1380 1417 2.192861 CGCAGAGATCGAGGAGCCT 61.193 63.158 0.00 0.00 0.00 4.58
1381 1418 1.363443 GCAGAGATCGAGGAGCCTG 59.637 63.158 0.00 0.00 0.00 4.85
1382 1419 1.391157 GCAGAGATCGAGGAGCCTGT 61.391 60.000 0.00 0.00 0.00 4.00
1383 1420 1.110442 CAGAGATCGAGGAGCCTGTT 58.890 55.000 0.00 0.00 0.00 3.16
1384 1421 1.480137 CAGAGATCGAGGAGCCTGTTT 59.520 52.381 0.00 0.00 0.00 2.83
1385 1422 1.754226 AGAGATCGAGGAGCCTGTTTC 59.246 52.381 0.00 0.00 0.00 2.78
1386 1423 1.754226 GAGATCGAGGAGCCTGTTTCT 59.246 52.381 0.00 0.00 0.00 2.52
1391 1428 0.612744 GAGGAGCCTGTTTCTGAGCT 59.387 55.000 0.00 0.00 38.56 4.09
1411 1448 1.227497 CAGGCTGAGGCGGAGATTC 60.227 63.158 9.42 0.00 39.81 2.52
1483 1682 2.809665 GCTGATGAGGATGCCGATCTTT 60.810 50.000 0.00 0.00 0.00 2.52
1588 1817 9.814899 ATTATGAATCTGAATACGAGGATGATC 57.185 33.333 0.00 0.00 0.00 2.92
1692 1921 1.558756 CTGGAACCTCAAGAGCTGGAT 59.441 52.381 0.00 0.00 0.00 3.41
1844 2082 3.809832 CACATCCTTCCGTCCACAATATC 59.190 47.826 0.00 0.00 0.00 1.63
1928 2166 1.002134 AGGCCGATGACAGGTTTGG 60.002 57.895 0.00 0.00 0.00 3.28
2007 2246 5.472478 TGACGAAGACTACTATGACAACAGT 59.528 40.000 0.00 0.00 0.00 3.55
2137 2784 5.125097 GGGGATTTTATATGATGCTGCTGAG 59.875 44.000 0.00 0.00 0.00 3.35
2304 2963 1.140252 ACCTATGGTATGTGTTCGCCC 59.860 52.381 0.00 0.00 32.11 6.13
2328 2987 3.799232 GCTCTGGTAAATTCGACGCCTAT 60.799 47.826 0.00 0.00 0.00 2.57
2333 2992 7.833786 TCTGGTAAATTCGACGCCTATAATAT 58.166 34.615 0.00 0.00 0.00 1.28
2334 2993 8.959548 TCTGGTAAATTCGACGCCTATAATATA 58.040 33.333 0.00 0.00 0.00 0.86
2358 3017 2.760374 ACAGTACAACTCTCTGCTTGC 58.240 47.619 0.00 0.00 33.12 4.01
2359 3018 2.072298 CAGTACAACTCTCTGCTTGCC 58.928 52.381 0.00 0.00 0.00 4.52
2412 3095 0.103572 TATGGTTTCCTAGTCGCGGC 59.896 55.000 0.21 0.21 0.00 6.53
2413 3096 1.614241 ATGGTTTCCTAGTCGCGGCT 61.614 55.000 20.79 20.79 0.00 5.52
2416 3099 0.179108 GTTTCCTAGTCGCGGCTGAT 60.179 55.000 26.08 0.00 0.00 2.90
2484 5875 0.817634 TTGTTTGTGGCTCGTCCCTG 60.818 55.000 0.00 0.00 0.00 4.45
2514 5905 7.383300 GCATTCAAGATTTGGGCATCTATAAAC 59.617 37.037 0.00 0.00 32.84 2.01
2515 5906 7.953005 TTCAAGATTTGGGCATCTATAAACA 57.047 32.000 0.00 0.00 32.84 2.83
2518 5909 8.000709 TCAAGATTTGGGCATCTATAAACATCT 58.999 33.333 0.00 0.00 32.84 2.90
2519 5910 8.636213 CAAGATTTGGGCATCTATAAACATCTT 58.364 33.333 0.00 0.00 32.84 2.40
2520 5911 8.401490 AGATTTGGGCATCTATAAACATCTTC 57.599 34.615 0.00 0.00 31.25 2.87
2521 5912 8.223330 AGATTTGGGCATCTATAAACATCTTCT 58.777 33.333 0.00 0.00 31.25 2.85
2585 5976 1.433121 ACCCCAACACATTGCCATTT 58.567 45.000 0.00 0.00 34.17 2.32
2633 6024 1.364626 GGACAGTGCAGCAAGGATCG 61.365 60.000 0.00 0.00 0.00 3.69
2664 6055 4.747108 GTCTGTAAGTCGCAATGCTATGAT 59.253 41.667 2.94 0.00 33.76 2.45
2861 6253 5.182570 CCATGTGTTGTTCTCATCACTGAAT 59.817 40.000 9.66 0.00 41.86 2.57
2862 6254 6.372381 CCATGTGTTGTTCTCATCACTGAATA 59.628 38.462 9.66 0.00 41.86 1.75
2939 6331 1.478105 TGCTCTGTGTACTGATGCGAT 59.522 47.619 0.00 0.00 0.00 4.58
2941 6333 3.130340 TGCTCTGTGTACTGATGCGATTA 59.870 43.478 0.00 0.00 0.00 1.75
2959 6351 4.564372 CGATTACAACATGTCAGGTCTCAG 59.436 45.833 0.00 0.00 0.00 3.35
2987 6379 8.469200 ACTTGTTGTATAATTGATGGTTGATGG 58.531 33.333 0.00 0.00 0.00 3.51
2998 6390 5.487433 TGATGGTTGATGGTACTGTAACTG 58.513 41.667 4.27 0.00 0.00 3.16
3045 6437 0.251165 AACATACTTGCGCCCTTGGT 60.251 50.000 4.18 0.00 0.00 3.67
3075 6467 2.156343 AGAGCGAACCAAACACTCTC 57.844 50.000 0.00 0.00 32.30 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.011635 TGACAGTAACTCTACCAAGCAATCA 59.988 40.000 0.00 0.00 0.00 2.57
1 2 5.348997 GTGACAGTAACTCTACCAAGCAATC 59.651 44.000 0.00 0.00 0.00 2.67
2 3 5.221641 TGTGACAGTAACTCTACCAAGCAAT 60.222 40.000 0.00 0.00 0.00 3.56
7 8 4.502604 GCCTTGTGACAGTAACTCTACCAA 60.503 45.833 0.00 0.00 0.00 3.67
42 43 3.405823 TCGTCCCGACAAATAAAACCT 57.594 42.857 0.00 0.00 0.00 3.50
71 72 7.654022 TTCTTAGAAACCAAAATCCAACAGT 57.346 32.000 0.00 0.00 0.00 3.55
153 154 7.809546 ATGTTGTGAGACTATTAGAGATCGA 57.190 36.000 0.00 0.00 0.00 3.59
193 194 0.912486 ACCAGCCTCCTTCCATGTAC 59.088 55.000 0.00 0.00 0.00 2.90
212 213 5.006941 GCCGTTCTCAACAAACTACAACTTA 59.993 40.000 0.00 0.00 0.00 2.24
216 217 3.271729 TGCCGTTCTCAACAAACTACAA 58.728 40.909 0.00 0.00 0.00 2.41
223 224 2.690497 TCCAAATTGCCGTTCTCAACAA 59.310 40.909 0.00 0.00 0.00 2.83
224 225 2.293122 CTCCAAATTGCCGTTCTCAACA 59.707 45.455 0.00 0.00 0.00 3.33
225 226 2.922335 GCTCCAAATTGCCGTTCTCAAC 60.922 50.000 0.00 0.00 0.00 3.18
238 249 2.636830 CATGAAGACCGAGCTCCAAAT 58.363 47.619 8.47 0.00 0.00 2.32
373 386 4.392047 TGCACAGATCACATCTCAAGTTT 58.608 39.130 0.00 0.00 37.58 2.66
375 388 3.690475 TGCACAGATCACATCTCAAGT 57.310 42.857 0.00 0.00 37.58 3.16
384 397 6.833342 ATTTGTTCTTTTTGCACAGATCAC 57.167 33.333 0.00 0.00 0.00 3.06
409 422 8.597167 TGATATTACTCATCCCCAAAGTCTATG 58.403 37.037 0.00 0.00 0.00 2.23
412 425 7.072961 ACATGATATTACTCATCCCCAAAGTCT 59.927 37.037 0.00 0.00 33.59 3.24
419 432 8.918202 TTTAACACATGATATTACTCATCCCC 57.082 34.615 0.00 0.00 33.59 4.81
424 437 8.264347 TGGCTCTTTAACACATGATATTACTCA 58.736 33.333 0.00 0.00 0.00 3.41
427 440 7.345192 CGTGGCTCTTTAACACATGATATTAC 58.655 38.462 0.00 0.00 34.91 1.89
466 479 1.262950 CGTTGAAATGAAGGTCGTGCA 59.737 47.619 0.00 0.00 0.00 4.57
467 480 1.263217 ACGTTGAAATGAAGGTCGTGC 59.737 47.619 0.00 0.00 0.00 5.34
468 481 3.739300 AGTACGTTGAAATGAAGGTCGTG 59.261 43.478 0.00 0.00 0.00 4.35
469 482 3.986277 AGTACGTTGAAATGAAGGTCGT 58.014 40.909 0.00 0.00 0.00 4.34
470 483 4.432503 CGAAGTACGTTGAAATGAAGGTCG 60.433 45.833 0.00 0.00 37.22 4.79
471 484 4.942765 CGAAGTACGTTGAAATGAAGGTC 58.057 43.478 0.00 0.00 37.22 3.85
489 502 7.643764 ACATGTGTGTAAATTTTCAAGACGAAG 59.356 33.333 0.00 0.00 36.63 3.79
622 636 7.875971 TCTGTGAAATTTTCTTTTCTAGCTCC 58.124 34.615 10.33 0.00 36.71 4.70
628 642 9.038803 GCAATCTTCTGTGAAATTTTCTTTTCT 57.961 29.630 10.33 0.00 36.71 2.52
629 643 8.819974 TGCAATCTTCTGTGAAATTTTCTTTTC 58.180 29.630 10.33 0.00 36.38 2.29
657 671 9.161572 TGTTAACCTAAGCCATGGAACTATATA 57.838 33.333 18.40 0.00 0.00 0.86
659 673 7.092802 TGTGTTAACCTAAGCCATGGAACTATA 60.093 37.037 18.40 0.00 0.00 1.31
680 694 7.781324 AGGACATGGATTTCTAAAATGTGTT 57.219 32.000 0.00 0.00 31.82 3.32
681 695 8.328758 TCTAGGACATGGATTTCTAAAATGTGT 58.671 33.333 0.00 0.00 31.82 3.72
682 696 8.737168 TCTAGGACATGGATTTCTAAAATGTG 57.263 34.615 0.00 0.00 31.82 3.21
683 697 9.753674 TTTCTAGGACATGGATTTCTAAAATGT 57.246 29.630 0.00 0.00 34.28 2.71
685 699 9.753674 TGTTTCTAGGACATGGATTTCTAAAAT 57.246 29.630 0.00 0.00 0.00 1.82
686 700 9.010029 GTGTTTCTAGGACATGGATTTCTAAAA 57.990 33.333 0.00 0.00 0.00 1.52
687 701 8.160765 TGTGTTTCTAGGACATGGATTTCTAAA 58.839 33.333 0.00 0.00 0.00 1.85
688 702 7.685481 TGTGTTTCTAGGACATGGATTTCTAA 58.315 34.615 0.00 0.00 0.00 2.10
689 703 7.038302 ACTGTGTTTCTAGGACATGGATTTCTA 60.038 37.037 0.00 0.00 0.00 2.10
690 704 6.126863 TGTGTTTCTAGGACATGGATTTCT 57.873 37.500 0.00 0.00 0.00 2.52
691 705 5.940470 ACTGTGTTTCTAGGACATGGATTTC 59.060 40.000 0.00 0.00 0.00 2.17
692 706 5.880901 ACTGTGTTTCTAGGACATGGATTT 58.119 37.500 0.00 0.00 0.00 2.17
693 707 5.505181 ACTGTGTTTCTAGGACATGGATT 57.495 39.130 0.00 0.00 0.00 3.01
694 708 5.958380 TCTACTGTGTTTCTAGGACATGGAT 59.042 40.000 0.00 0.00 0.00 3.41
695 709 5.330233 TCTACTGTGTTTCTAGGACATGGA 58.670 41.667 0.00 0.00 0.00 3.41
696 710 5.661056 TCTACTGTGTTTCTAGGACATGG 57.339 43.478 0.00 3.34 0.00 3.66
697 711 6.867550 TGATCTACTGTGTTTCTAGGACATG 58.132 40.000 0.00 0.00 0.00 3.21
698 712 7.039011 TGTTGATCTACTGTGTTTCTAGGACAT 60.039 37.037 8.74 0.00 0.00 3.06
699 713 6.266786 TGTTGATCTACTGTGTTTCTAGGACA 59.733 38.462 8.74 0.00 0.00 4.02
700 714 6.688578 TGTTGATCTACTGTGTTTCTAGGAC 58.311 40.000 8.74 0.00 0.00 3.85
701 715 6.911250 TGTTGATCTACTGTGTTTCTAGGA 57.089 37.500 8.74 0.00 0.00 2.94
702 716 8.446273 CAAATGTTGATCTACTGTGTTTCTAGG 58.554 37.037 8.74 0.00 0.00 3.02
703 717 9.208022 TCAAATGTTGATCTACTGTGTTTCTAG 57.792 33.333 8.74 0.00 34.08 2.43
758 772 4.615912 CGCGATGGATTTTGTTCCTTTTCT 60.616 41.667 0.00 0.00 36.68 2.52
759 773 3.608073 CGCGATGGATTTTGTTCCTTTTC 59.392 43.478 0.00 0.00 36.68 2.29
863 892 2.421399 CCCTACCTCCCGTCGGAAC 61.421 68.421 14.39 0.00 37.86 3.62
965 1001 1.227380 GATGCCGAATCCACTCGCT 60.227 57.895 0.00 0.00 37.51 4.93
1325 1362 0.168128 AAACGTTGCCTTAGCGATGC 59.832 50.000 0.00 0.00 42.42 3.91
1363 1400 1.363443 CAGGCTCCTCGATCTCTGC 59.637 63.158 0.00 0.00 0.00 4.26
1364 1401 1.110442 AACAGGCTCCTCGATCTCTG 58.890 55.000 0.00 0.00 0.00 3.35
1365 1402 1.754226 GAAACAGGCTCCTCGATCTCT 59.246 52.381 0.00 0.00 0.00 3.10
1366 1403 1.754226 AGAAACAGGCTCCTCGATCTC 59.246 52.381 0.00 0.00 0.00 2.75
1367 1404 1.480137 CAGAAACAGGCTCCTCGATCT 59.520 52.381 0.00 0.00 0.00 2.75
1368 1405 1.478510 TCAGAAACAGGCTCCTCGATC 59.521 52.381 0.00 0.00 0.00 3.69
1369 1406 1.480137 CTCAGAAACAGGCTCCTCGAT 59.520 52.381 0.00 0.00 0.00 3.59
1370 1407 0.891373 CTCAGAAACAGGCTCCTCGA 59.109 55.000 0.00 0.00 0.00 4.04
1371 1408 0.739112 GCTCAGAAACAGGCTCCTCG 60.739 60.000 0.00 0.00 0.00 4.63
1372 1409 0.612744 AGCTCAGAAACAGGCTCCTC 59.387 55.000 0.00 0.00 0.00 3.71
1373 1410 1.003003 GAAGCTCAGAAACAGGCTCCT 59.997 52.381 0.00 0.00 33.63 3.69
1374 1411 1.271054 TGAAGCTCAGAAACAGGCTCC 60.271 52.381 0.00 0.00 33.63 4.70
1375 1412 2.175878 TGAAGCTCAGAAACAGGCTC 57.824 50.000 0.00 0.00 33.63 4.70
1391 1428 1.267574 AATCTCCGCCTCAGCCTGAA 61.268 55.000 0.00 0.00 34.57 3.02
1404 1441 2.238395 AGAAACAGGCTCCTGAATCTCC 59.762 50.000 21.75 5.46 46.30 3.71
1411 1448 3.061687 AGGCTCAGAAACAGGCTCCTG 62.062 57.143 14.05 14.05 43.01 3.86
1443 1636 2.311542 AGCATAAACATCCTGTTCCCCA 59.688 45.455 0.00 0.00 40.14 4.96
1445 1638 3.620488 TCAGCATAAACATCCTGTTCCC 58.380 45.455 0.00 0.00 40.14 3.97
1449 1642 4.164796 TCCTCATCAGCATAAACATCCTGT 59.835 41.667 0.00 0.00 0.00 4.00
1826 2055 1.766496 GGGATATTGTGGACGGAAGGA 59.234 52.381 0.00 0.00 0.00 3.36
1844 2082 1.625315 TCTTGATCATATCAGCGGGGG 59.375 52.381 0.00 0.00 40.94 5.40
1928 2166 0.957888 GACCTTGGCCTGCAACTCTC 60.958 60.000 3.32 0.00 0.00 3.20
2007 2246 0.975887 GCTCCTCCCAAAATTTGCCA 59.024 50.000 0.00 0.00 0.00 4.92
2137 2784 1.668419 ATGATGTTGAACGGCTAGGC 58.332 50.000 6.15 6.15 0.00 3.93
2304 2963 0.921347 CGTCGAATTTACCAGAGCCG 59.079 55.000 0.00 0.00 0.00 5.52
2333 2992 6.678878 CAAGCAGAGAGTTGTACTGTAGTTA 58.321 40.000 0.00 0.00 34.60 2.24
2334 2993 5.533482 CAAGCAGAGAGTTGTACTGTAGTT 58.467 41.667 0.00 0.00 34.60 2.24
2339 2998 2.072298 GGCAAGCAGAGAGTTGTACTG 58.928 52.381 0.00 0.00 35.14 2.74
2340 2999 1.694150 TGGCAAGCAGAGAGTTGTACT 59.306 47.619 0.00 0.00 0.00 2.73
2358 3017 3.658757 AACGTGGTCCAAATCAAATGG 57.341 42.857 0.00 0.00 39.41 3.16
2359 3018 4.210955 CCAAAACGTGGTCCAAATCAAATG 59.789 41.667 0.00 0.00 43.20 2.32
2412 3095 9.775854 AGATGGTAGAACAAGATTAATCATCAG 57.224 33.333 17.56 6.58 33.75 2.90
2413 3096 9.551734 CAGATGGTAGAACAAGATTAATCATCA 57.448 33.333 17.56 1.99 33.75 3.07
2416 3099 7.337938 TGCAGATGGTAGAACAAGATTAATCA 58.662 34.615 17.56 0.00 0.00 2.57
2484 5875 2.289569 TGCCCAAATCTTGAATGCCAAC 60.290 45.455 0.00 0.00 0.00 3.77
2585 5976 4.142381 CCATCTCAACTCTATCGTGACACA 60.142 45.833 6.37 0.00 0.00 3.72
2591 5982 3.027412 ACAGCCATCTCAACTCTATCGT 58.973 45.455 0.00 0.00 0.00 3.73
2633 6024 2.610374 TGCGACTTACAGACACCAAAAC 59.390 45.455 0.00 0.00 0.00 2.43
2664 6055 5.569355 TCAGCAGAAAAGAATGATACCCAA 58.431 37.500 0.00 0.00 0.00 4.12
2736 6127 8.556589 TGAGAAGTTCATTCCCCTCAATAAATA 58.443 33.333 5.50 0.00 38.84 1.40
2737 6128 7.413446 TGAGAAGTTCATTCCCCTCAATAAAT 58.587 34.615 5.50 0.00 38.84 1.40
2738 6129 6.789268 TGAGAAGTTCATTCCCCTCAATAAA 58.211 36.000 5.50 0.00 38.84 1.40
2739 6130 6.387192 TGAGAAGTTCATTCCCCTCAATAA 57.613 37.500 5.50 0.00 38.84 1.40
2740 6131 6.581388 ATGAGAAGTTCATTCCCCTCAATA 57.419 37.500 5.50 0.00 44.14 1.90
2741 6132 4.934797 TGAGAAGTTCATTCCCCTCAAT 57.065 40.909 5.50 0.00 38.84 2.57
2781 6172 8.171840 GCAAAAGTCAAATAGTATCTGACACTC 58.828 37.037 16.97 0.75 41.58 3.51
2873 6265 6.787515 GTCGTTGCATGTTTCATTATAGATCG 59.212 38.462 0.00 0.00 0.00 3.69
2939 6331 3.070878 TGCTGAGACCTGACATGTTGTAA 59.929 43.478 0.00 0.00 0.00 2.41
2941 6333 1.417517 TGCTGAGACCTGACATGTTGT 59.582 47.619 0.00 0.00 0.00 3.32
2959 6351 7.312154 TCAACCATCAATTATACAACAAGTGC 58.688 34.615 0.00 0.00 0.00 4.40
2987 6379 3.933332 GGCAGGTGAATCAGTTACAGTAC 59.067 47.826 0.00 0.00 0.00 2.73
2998 6390 4.526970 TGGAAGAATTAGGCAGGTGAATC 58.473 43.478 0.00 0.00 0.00 2.52
3055 6447 2.622064 AGAGTGTTTGGTTCGCTCTT 57.378 45.000 3.62 0.00 46.33 2.85


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

AutoCloner maintained by Alex Coulton.