Multiple sequence alignment - TraesCS2A01G398000

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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 TraesCS2A01G398000 chr2A 100.000 3893 0 0 1 3893 651611191 651607299 0.000000e+00 7190
1 TraesCS2A01G398000 chr2A 83.484 884 121 10 3033 3893 736549563 736548682 0.000000e+00 800
2 TraesCS2A01G398000 chr2D 93.905 3954 144 56 1 3893 506793950 506790033 0.000000e+00 5877
3 TraesCS2A01G398000 chr2D 83.371 884 123 10 3033 3893 605371402 605370520 0.000000e+00 797
4 TraesCS2A01G398000 chr2B 93.174 3970 151 45 1 3893 594848166 594844240 0.000000e+00 5720
5 TraesCS2A01G398000 chr2B 82.919 884 126 11 3033 3893 735521449 735520568 0.000000e+00 773
6 TraesCS2A01G398000 chr3D 74.454 779 162 33 1628 2390 310683051 310683808 6.320000e-78 302
7 TraesCS2A01G398000 chr3B 74.235 784 155 37 1628 2390 410774953 410774196 6.370000e-73 285
8 TraesCS2A01G398000 chr3A 73.880 781 163 36 1628 2390 421720831 421720074 1.380000e-69 274
9 TraesCS2A01G398000 chr1A 77.602 442 84 15 1831 2266 154700834 154701266 1.800000e-63 254


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 TraesCS2A01G398000 chr2A 651607299 651611191 3892 True 7190 7190 100.000 1 3893 1 chr2A.!!$R1 3892
1 TraesCS2A01G398000 chr2A 736548682 736549563 881 True 800 800 83.484 3033 3893 1 chr2A.!!$R2 860
2 TraesCS2A01G398000 chr2D 506790033 506793950 3917 True 5877 5877 93.905 1 3893 1 chr2D.!!$R1 3892
3 TraesCS2A01G398000 chr2D 605370520 605371402 882 True 797 797 83.371 3033 3893 1 chr2D.!!$R2 860
4 TraesCS2A01G398000 chr2B 594844240 594848166 3926 True 5720 5720 93.174 1 3893 1 chr2B.!!$R1 3892
5 TraesCS2A01G398000 chr2B 735520568 735521449 881 True 773 773 82.919 3033 3893 1 chr2B.!!$R2 860
6 TraesCS2A01G398000 chr3D 310683051 310683808 757 False 302 302 74.454 1628 2390 1 chr3D.!!$F1 762
7 TraesCS2A01G398000 chr3B 410774196 410774953 757 True 285 285 74.235 1628 2390 1 chr3B.!!$R1 762
8 TraesCS2A01G398000 chr3A 421720074 421720831 757 True 274 274 73.880 1628 2390 1 chr3A.!!$R1 762

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
534 538 0.036952 CCGTTCTGAGGTCACATGCT 60.037 55.0 0.0 0.0 0.0 3.79 F
906 920 0.108138 CTCACGTTGACATCCTCCCC 60.108 60.0 0.0 0.0 0.0 4.81 F
2456 2515 0.179045 GACCCATATCCGCTTGCACT 60.179 55.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2437 2496 0.179045 AGTGCAAGCGGATATGGGTC 60.179 55.000 0.0 0.0 0.0 4.46 R
2829 2898 0.039764 TGGTGATGGAGGAGACGACT 59.960 55.000 0.0 0.0 0.0 4.18 R
3378 3512 1.807573 GCTCAGCTCGGTGTAGTGC 60.808 63.158 0.0 0.0 0.0 4.40 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
52 53 4.078639 ACCATCTTAGGCTAAGCACATC 57.921 45.455 26.00 0.00 35.76 3.06
58 59 2.887151 AGGCTAAGCACATCTTTGGT 57.113 45.000 0.00 0.00 36.25 3.67
59 60 5.188948 TCTTAGGCTAAGCACATCTTTGGTA 59.811 40.000 26.00 4.63 36.25 3.25
65 66 7.561356 AGGCTAAGCACATCTTTGGTATATTTT 59.439 33.333 0.00 0.00 36.25 1.82
81 82 9.249053 TGGTATATTTTCAAACCACACACATAT 57.751 29.630 0.00 0.00 37.09 1.78
95 98 9.424319 ACCACACACATATTTATATCTCGATTC 57.576 33.333 0.00 0.00 0.00 2.52
146 149 2.643044 CGCCGACGAAAGAGAGAAG 58.357 57.895 0.00 0.00 43.93 2.85
197 200 0.654683 CGCTAGCAGTTCAATCAGGC 59.345 55.000 16.45 0.00 0.00 4.85
198 201 0.654683 GCTAGCAGTTCAATCAGGCG 59.345 55.000 10.63 0.00 0.00 5.52
199 202 1.293924 CTAGCAGTTCAATCAGGCGG 58.706 55.000 0.00 0.00 0.00 6.13
200 203 0.744414 TAGCAGTTCAATCAGGCGGC 60.744 55.000 0.00 0.00 0.00 6.53
201 204 2.334946 GCAGTTCAATCAGGCGGCA 61.335 57.895 13.08 0.00 0.00 5.69
202 205 1.503542 CAGTTCAATCAGGCGGCAC 59.496 57.895 13.08 0.00 0.00 5.01
203 206 1.073025 AGTTCAATCAGGCGGCACA 59.927 52.632 13.08 0.00 0.00 4.57
204 207 0.322816 AGTTCAATCAGGCGGCACAT 60.323 50.000 13.08 0.00 0.00 3.21
205 208 0.099436 GTTCAATCAGGCGGCACATC 59.901 55.000 13.08 0.00 0.00 3.06
206 209 0.322366 TTCAATCAGGCGGCACATCA 60.322 50.000 13.08 0.00 0.00 3.07
207 210 0.745486 TCAATCAGGCGGCACATCAG 60.745 55.000 13.08 0.00 0.00 2.90
208 211 1.452651 AATCAGGCGGCACATCAGG 60.453 57.895 13.08 0.00 0.00 3.86
242 245 4.385405 GGCAGCTCCACGCAGACT 62.385 66.667 0.00 0.00 42.61 3.24
284 287 3.818961 ACATGTTCATGCTGTTTCTCG 57.181 42.857 12.00 0.00 0.00 4.04
392 395 5.860716 GGAAGATGACTGAGATTTTTGTTGC 59.139 40.000 0.00 0.00 0.00 4.17
409 412 0.687920 TGCCGTGGAGAAACATACCA 59.312 50.000 0.00 0.00 0.00 3.25
428 431 3.818773 ACCAAGATTTTGTGGTACCTTCG 59.181 43.478 14.36 0.00 46.47 3.79
444 447 7.279313 TGGTACCTTCGATTTTAATGAACTAGC 59.721 37.037 14.36 0.00 0.00 3.42
483 487 5.752955 TCTGCCAGTTTTTGCTTATGTTTTC 59.247 36.000 0.00 0.00 0.00 2.29
498 502 0.871722 TTTTCACGCCATCTGAACCG 59.128 50.000 0.00 0.00 0.00 4.44
504 508 0.108329 CGCCATCTGAACCGGTAGTT 60.108 55.000 8.00 0.00 43.07 2.24
505 509 1.674817 CGCCATCTGAACCGGTAGTTT 60.675 52.381 8.00 0.00 39.40 2.66
507 511 2.418976 GCCATCTGAACCGGTAGTTTTC 59.581 50.000 8.00 0.78 39.40 2.29
509 513 3.684788 CCATCTGAACCGGTAGTTTTCTG 59.315 47.826 8.00 5.58 39.40 3.02
510 514 3.396260 TCTGAACCGGTAGTTTTCTGG 57.604 47.619 8.00 0.00 39.40 3.86
515 519 3.397849 ACCGGTAGTTTTCTGGTTCTC 57.602 47.619 4.49 0.00 41.20 2.87
516 520 2.038164 ACCGGTAGTTTTCTGGTTCTCC 59.962 50.000 4.49 0.00 41.20 3.71
534 538 0.036952 CCGTTCTGAGGTCACATGCT 60.037 55.000 0.00 0.00 0.00 3.79
535 539 1.354040 CGTTCTGAGGTCACATGCTC 58.646 55.000 0.00 0.00 0.00 4.26
536 540 1.354040 GTTCTGAGGTCACATGCTCG 58.646 55.000 0.00 0.00 0.00 5.03
751 765 3.092511 ACCTCGCCATGGCCATCT 61.093 61.111 30.79 8.48 37.98 2.90
782 796 3.790416 AAAAGGCGTGGCTGGCAGA 62.790 57.895 20.86 0.00 36.77 4.26
904 918 0.741221 GGCTCACGTTGACATCCTCC 60.741 60.000 0.00 0.00 0.00 4.30
905 919 0.741221 GCTCACGTTGACATCCTCCC 60.741 60.000 0.00 0.00 0.00 4.30
906 920 0.108138 CTCACGTTGACATCCTCCCC 60.108 60.000 0.00 0.00 0.00 4.81
908 922 2.186903 CGTTGACATCCTCCCCGG 59.813 66.667 0.00 0.00 0.00 5.73
994 1010 2.332159 GCCGTCGAGTAGCTAGCC 59.668 66.667 12.13 0.00 0.00 3.93
1555 1601 2.417719 GCGTAAGTCATCCATCCATCC 58.582 52.381 0.00 0.00 41.68 3.51
1556 1602 2.224281 GCGTAAGTCATCCATCCATCCA 60.224 50.000 0.00 0.00 41.68 3.41
1557 1603 3.557898 GCGTAAGTCATCCATCCATCCAT 60.558 47.826 0.00 0.00 41.68 3.41
1570 1616 0.457035 CATCCATTTGTCCTTGCCGG 59.543 55.000 0.00 0.00 0.00 6.13
1573 1619 1.501741 CATTTGTCCTTGCCGGTCG 59.498 57.895 1.90 0.00 0.00 4.79
1576 1622 4.680237 TGTCCTTGCCGGTCGCTG 62.680 66.667 1.90 0.00 38.78 5.18
1577 1623 4.373116 GTCCTTGCCGGTCGCTGA 62.373 66.667 1.90 0.00 38.78 4.26
2183 2242 4.802051 CTGTGGGCCATCGGGGTG 62.802 72.222 10.70 0.00 39.65 4.61
2434 2493 2.044946 GTGAGCACCACCCCATCC 60.045 66.667 0.00 0.00 39.86 3.51
2435 2494 2.531428 TGAGCACCACCCCATCCA 60.531 61.111 0.00 0.00 0.00 3.41
2437 2496 1.454479 GAGCACCACCCCATCCATG 60.454 63.158 0.00 0.00 0.00 3.66
2438 2497 1.925285 GAGCACCACCCCATCCATGA 61.925 60.000 0.00 0.00 0.00 3.07
2439 2498 1.754234 GCACCACCCCATCCATGAC 60.754 63.158 0.00 0.00 0.00 3.06
2440 2499 1.076777 CACCACCCCATCCATGACC 60.077 63.158 0.00 0.00 0.00 4.02
2441 2500 2.316586 ACCACCCCATCCATGACCC 61.317 63.158 0.00 0.00 0.00 4.46
2442 2501 2.315794 CCACCCCATCCATGACCCA 61.316 63.158 0.00 0.00 0.00 4.51
2443 2502 1.658053 CCACCCCATCCATGACCCAT 61.658 60.000 0.00 0.00 0.00 4.00
2444 2503 1.148216 CACCCCATCCATGACCCATA 58.852 55.000 0.00 0.00 0.00 2.74
2445 2504 1.712510 CACCCCATCCATGACCCATAT 59.287 52.381 0.00 0.00 0.00 1.78
2446 2505 1.995542 ACCCCATCCATGACCCATATC 59.004 52.381 0.00 0.00 0.00 1.63
2447 2506 1.285962 CCCCATCCATGACCCATATCC 59.714 57.143 0.00 0.00 0.00 2.59
2448 2507 1.065199 CCCATCCATGACCCATATCCG 60.065 57.143 0.00 0.00 0.00 4.18
2449 2508 1.679944 CCATCCATGACCCATATCCGC 60.680 57.143 0.00 0.00 0.00 5.54
2450 2509 1.280133 CATCCATGACCCATATCCGCT 59.720 52.381 0.00 0.00 0.00 5.52
2451 2510 1.434188 TCCATGACCCATATCCGCTT 58.566 50.000 0.00 0.00 0.00 4.68
2452 2511 1.072173 TCCATGACCCATATCCGCTTG 59.928 52.381 0.00 0.00 0.00 4.01
2453 2512 0.877071 CATGACCCATATCCGCTTGC 59.123 55.000 0.00 0.00 0.00 4.01
2454 2513 0.473755 ATGACCCATATCCGCTTGCA 59.526 50.000 0.00 0.00 0.00 4.08
2455 2514 0.463654 TGACCCATATCCGCTTGCAC 60.464 55.000 0.00 0.00 0.00 4.57
2456 2515 0.179045 GACCCATATCCGCTTGCACT 60.179 55.000 0.00 0.00 0.00 4.40
2462 2521 2.572095 TATCCGCTTGCACTCCACCG 62.572 60.000 0.00 0.00 0.00 4.94
2464 2523 3.414700 CGCTTGCACTCCACCGTC 61.415 66.667 0.00 0.00 0.00 4.79
2469 2528 2.202756 GCACTCCACCGTCCGATC 60.203 66.667 0.00 0.00 0.00 3.69
2471 2530 3.138798 ACTCCACCGTCCGATCCG 61.139 66.667 0.00 0.00 0.00 4.18
2475 2534 2.486663 CCACCGTCCGATCCGATCA 61.487 63.158 9.07 0.00 0.00 2.92
2476 2535 1.660355 CACCGTCCGATCCGATCAT 59.340 57.895 9.07 0.00 0.00 2.45
2477 2536 0.387367 CACCGTCCGATCCGATCATC 60.387 60.000 9.07 0.00 0.00 2.92
2478 2537 0.537600 ACCGTCCGATCCGATCATCT 60.538 55.000 9.07 0.00 0.00 2.90
2493 2562 2.680577 TCATCTGATGATCATTCGCCG 58.319 47.619 16.06 0.00 33.59 6.46
2496 2565 1.136891 TCTGATGATCATTCGCCGTGT 59.863 47.619 10.14 0.00 0.00 4.49
2498 2567 1.134848 TGATGATCATTCGCCGTGTCA 60.135 47.619 10.14 0.00 0.00 3.58
2500 2569 2.022764 TGATCATTCGCCGTGTCAAT 57.977 45.000 0.00 0.00 0.00 2.57
2501 2570 2.355197 TGATCATTCGCCGTGTCAATT 58.645 42.857 0.00 0.00 0.00 2.32
2502 2571 2.351418 TGATCATTCGCCGTGTCAATTC 59.649 45.455 0.00 0.00 0.00 2.17
2829 2898 3.630013 AAGCAGGTGCCGCTCTCA 61.630 61.111 0.00 0.00 43.38 3.27
2897 2966 5.848406 AGAGGAGAAAACAGACTAGTTGTG 58.152 41.667 0.00 0.32 0.00 3.33
2928 3001 5.698832 TGTGTGATTAAACAGCATTACAGC 58.301 37.500 0.00 0.00 0.00 4.40
3010 3116 6.009115 GCTAGAGCTAGAAGGAACACTATC 57.991 45.833 8.65 0.00 38.21 2.08
3064 3170 9.985730 ATCTCTTAGCTTATTCTCATTTCTCAG 57.014 33.333 0.00 0.00 0.00 3.35
3094 3201 4.402155 TGGCATTATAGGGTGCAAAGAAAG 59.598 41.667 0.00 0.00 43.00 2.62
3147 3256 8.462143 TCACAGAAAAGATAAACATACGACTC 57.538 34.615 0.00 0.00 0.00 3.36
3373 3507 1.679032 GCATACGGCCTCCTGAAAACT 60.679 52.381 0.00 0.00 36.11 2.66
3378 3512 2.335712 GCCTCCTGAAAACTGGCCG 61.336 63.158 0.00 0.00 37.81 6.13
3455 3589 6.894103 AGAAAATAACCATTTCATCAGAGGCT 59.106 34.615 0.00 0.00 38.86 4.58
3504 3638 2.507484 CCCTTCAAACATGAGACTGCA 58.493 47.619 0.00 0.00 0.00 4.41
3606 3740 3.570975 TCATCATTGCCACTCCATATTGC 59.429 43.478 0.00 0.00 0.00 3.56
3681 3815 2.689983 CTCCTGCCATGTTTGGATAACC 59.310 50.000 0.00 0.00 46.92 2.85
3688 3822 4.626287 GCCATGTTTGGATAACCTGAGAGA 60.626 45.833 0.00 0.00 46.92 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.065789 GCCCTTTAGTACATACCTGCATC 58.934 47.826 0.00 0.00 0.00 3.91
20 21 3.624959 GCCTAAGATGGTTGCCCTTTAGT 60.625 47.826 0.00 0.00 0.00 2.24
44 45 9.423061 GTTTGAAAATATACCAAAGATGTGCTT 57.577 29.630 0.00 0.00 38.88 3.91
52 53 7.923344 TGTGTGTGGTTTGAAAATATACCAAAG 59.077 33.333 0.00 0.00 41.95 2.77
65 66 9.040939 CGAGATATAAATATGTGTGTGGTTTGA 57.959 33.333 0.00 0.00 0.00 2.69
68 69 9.778741 AATCGAGATATAAATATGTGTGTGGTT 57.221 29.630 0.00 0.00 0.00 3.67
95 98 4.082190 TCTCGTTCCTCCTGATTAACAGTG 60.082 45.833 0.00 0.00 44.40 3.66
242 245 2.029815 TCGTTTGCCGCTGCTGTA 59.970 55.556 0.70 0.00 38.71 2.74
284 287 2.602676 TACCTTGCCTGCCAGGGAC 61.603 63.158 13.78 0.00 43.10 4.46
392 395 3.328382 TCTTGGTATGTTTCTCCACGG 57.672 47.619 0.00 0.00 0.00 4.94
409 412 6.894339 AAATCGAAGGTACCACAAAATCTT 57.106 33.333 15.94 0.00 0.00 2.40
428 431 4.023963 GCTCCGGGCTAGTTCATTAAAATC 60.024 45.833 0.00 0.00 38.06 2.17
483 487 0.806102 CTACCGGTTCAGATGGCGTG 60.806 60.000 15.04 0.00 0.00 5.34
498 502 3.397849 ACGGAGAACCAGAAAACTACC 57.602 47.619 0.00 0.00 35.59 3.18
504 508 2.037251 CCTCAGAACGGAGAACCAGAAA 59.963 50.000 3.75 0.00 37.05 2.52
505 509 1.618837 CCTCAGAACGGAGAACCAGAA 59.381 52.381 3.75 0.00 37.05 3.02
507 511 0.969894 ACCTCAGAACGGAGAACCAG 59.030 55.000 3.75 0.00 37.05 4.00
509 513 0.966920 TGACCTCAGAACGGAGAACC 59.033 55.000 3.75 0.00 37.05 3.62
510 514 1.340248 TGTGACCTCAGAACGGAGAAC 59.660 52.381 3.75 1.15 37.05 3.01
512 516 1.546029 CATGTGACCTCAGAACGGAGA 59.454 52.381 3.75 0.00 37.05 3.71
513 517 2.001812 CATGTGACCTCAGAACGGAG 57.998 55.000 0.00 0.00 34.62 4.63
514 518 0.037326 GCATGTGACCTCAGAACGGA 60.037 55.000 0.00 0.00 0.00 4.69
515 519 0.036952 AGCATGTGACCTCAGAACGG 60.037 55.000 0.00 0.00 0.00 4.44
516 520 1.354040 GAGCATGTGACCTCAGAACG 58.646 55.000 0.00 0.00 0.00 3.95
536 540 4.012895 CAGCAACCACGCACGACC 62.013 66.667 0.00 0.00 0.00 4.79
584 598 1.671742 CTAGTGTGTTCGGGGCTGT 59.328 57.895 0.00 0.00 0.00 4.40
620 634 2.597510 GCGTGAAAAGCAGGGGGT 60.598 61.111 0.00 0.00 42.41 4.95
746 760 2.830370 GCGCCAAAGGGGAGATGG 60.830 66.667 0.00 0.00 39.08 3.51
751 765 2.206536 CCTTTTGCGCCAAAGGGGA 61.207 57.895 34.39 3.95 43.76 4.81
782 796 1.690219 GCCGAGGACACCATGGATCT 61.690 60.000 21.47 9.59 0.00 2.75
822 836 2.045926 ACACGGAGAGGCCATTGC 60.046 61.111 5.01 0.00 35.94 3.56
910 924 1.439679 CCGATATAAAAGCTCCGGGC 58.560 55.000 0.00 3.80 42.19 6.13
911 925 1.439679 GCCGATATAAAAGCTCCGGG 58.560 55.000 0.00 0.00 37.62 5.73
912 926 1.068474 CGCCGATATAAAAGCTCCGG 58.932 55.000 0.00 0.00 39.88 5.14
1076 1122 4.742649 TCTGCCTCGGCTCCTCGT 62.743 66.667 9.65 0.00 42.51 4.18
1272 1318 2.591429 CCGCTGTGGTTGAGCACA 60.591 61.111 14.47 14.47 36.12 4.57
1555 1601 1.501741 CGACCGGCAAGGACAAATG 59.498 57.895 0.00 0.00 45.00 2.32
1556 1602 2.332654 GCGACCGGCAAGGACAAAT 61.333 57.895 0.00 0.00 45.00 2.32
1557 1603 2.975799 GCGACCGGCAAGGACAAA 60.976 61.111 0.00 0.00 45.00 2.83
1587 1646 2.251371 GCAAACAGTTCGGTCGGC 59.749 61.111 0.00 0.00 0.00 5.54
1589 1648 1.083657 CGTGCAAACAGTTCGGTCG 60.084 57.895 0.00 0.00 0.00 4.79
1593 1652 1.191647 GTCCTACGTGCAAACAGTTCG 59.808 52.381 0.00 0.00 0.00 3.95
2183 2242 1.093159 AGACGACGATGTAGTGGGAC 58.907 55.000 0.00 0.00 0.00 4.46
2428 2487 1.065199 CGGATATGGGTCATGGATGGG 60.065 57.143 0.00 0.00 0.00 4.00
2429 2488 1.679944 GCGGATATGGGTCATGGATGG 60.680 57.143 0.00 0.00 0.00 3.51
2431 2490 1.661463 AGCGGATATGGGTCATGGAT 58.339 50.000 0.00 0.00 0.00 3.41
2432 2491 1.072173 CAAGCGGATATGGGTCATGGA 59.928 52.381 0.00 0.00 0.00 3.41
2433 2492 1.527034 CAAGCGGATATGGGTCATGG 58.473 55.000 0.00 0.00 0.00 3.66
2434 2493 0.877071 GCAAGCGGATATGGGTCATG 59.123 55.000 0.00 0.00 0.00 3.07
2435 2494 0.473755 TGCAAGCGGATATGGGTCAT 59.526 50.000 0.00 0.00 0.00 3.06
2437 2496 0.179045 AGTGCAAGCGGATATGGGTC 60.179 55.000 0.00 0.00 0.00 4.46
2438 2497 0.179045 GAGTGCAAGCGGATATGGGT 60.179 55.000 0.00 0.00 0.00 4.51
2439 2498 0.886490 GGAGTGCAAGCGGATATGGG 60.886 60.000 0.00 0.00 0.00 4.00
2440 2499 0.179048 TGGAGTGCAAGCGGATATGG 60.179 55.000 0.00 0.00 0.00 2.74
2441 2500 0.940126 GTGGAGTGCAAGCGGATATG 59.060 55.000 0.00 0.00 0.00 1.78
2442 2501 0.179045 GGTGGAGTGCAAGCGGATAT 60.179 55.000 0.00 0.00 0.00 1.63
2443 2502 1.220749 GGTGGAGTGCAAGCGGATA 59.779 57.895 0.00 0.00 0.00 2.59
2444 2503 2.045926 GGTGGAGTGCAAGCGGAT 60.046 61.111 0.00 0.00 0.00 4.18
2445 2504 4.680237 CGGTGGAGTGCAAGCGGA 62.680 66.667 0.00 0.00 33.85 5.54
2446 2505 4.988598 ACGGTGGAGTGCAAGCGG 62.989 66.667 11.86 0.00 41.37 5.52
2447 2506 3.414700 GACGGTGGAGTGCAAGCG 61.415 66.667 6.19 6.19 42.67 4.68
2448 2507 3.050275 GGACGGTGGAGTGCAAGC 61.050 66.667 0.00 0.00 32.46 4.01
2449 2508 2.507110 ATCGGACGGTGGAGTGCAAG 62.507 60.000 0.00 0.00 32.46 4.01
2450 2509 2.501223 GATCGGACGGTGGAGTGCAA 62.501 60.000 0.00 0.00 32.46 4.08
2451 2510 2.994995 ATCGGACGGTGGAGTGCA 60.995 61.111 0.00 0.00 32.46 4.57
2452 2511 2.202756 GATCGGACGGTGGAGTGC 60.203 66.667 0.00 0.00 0.00 4.40
2453 2512 2.494918 GGATCGGACGGTGGAGTG 59.505 66.667 0.00 0.00 0.00 3.51
2454 2513 2.905935 ATCGGATCGGACGGTGGAGT 62.906 60.000 4.94 0.00 0.00 3.85
2455 2514 2.131294 GATCGGATCGGACGGTGGAG 62.131 65.000 4.94 0.00 0.00 3.86
2456 2515 2.124024 ATCGGATCGGACGGTGGA 60.124 61.111 4.94 0.00 0.00 4.02
2462 2521 2.489722 TCATCAGATGATCGGATCGGAC 59.510 50.000 9.21 7.04 33.59 4.79
2464 2523 3.797451 ATCATCAGATGATCGGATCGG 57.203 47.619 18.86 3.50 46.62 4.18
2475 2534 2.224137 ACACGGCGAATGATCATCAGAT 60.224 45.455 16.62 0.00 37.13 2.90
2476 2535 1.136891 ACACGGCGAATGATCATCAGA 59.863 47.619 16.62 0.00 0.00 3.27
2477 2536 1.524355 GACACGGCGAATGATCATCAG 59.476 52.381 16.62 7.30 0.00 2.90
2478 2537 1.134848 TGACACGGCGAATGATCATCA 60.135 47.619 16.62 0.00 0.00 3.07
2493 2562 3.882888 TGGAGAACCTGTTGAATTGACAC 59.117 43.478 0.00 0.00 37.04 3.67
2496 2565 4.002982 CGATGGAGAACCTGTTGAATTGA 58.997 43.478 0.00 0.00 37.04 2.57
2498 2567 2.749621 GCGATGGAGAACCTGTTGAATT 59.250 45.455 0.00 0.00 37.04 2.17
2500 2569 1.808411 GCGATGGAGAACCTGTTGAA 58.192 50.000 0.00 0.00 37.04 2.69
2501 2570 0.389817 CGCGATGGAGAACCTGTTGA 60.390 55.000 0.00 0.00 37.04 3.18
2502 2571 0.670546 ACGCGATGGAGAACCTGTTG 60.671 55.000 15.93 0.00 37.04 3.33
2829 2898 0.039764 TGGTGATGGAGGAGACGACT 59.960 55.000 0.00 0.00 0.00 4.18
2897 2966 7.015226 TGCTGTTTAATCACACATAGTATGC 57.985 36.000 10.16 0.00 0.00 3.14
3004 3110 8.583296 TCTCTTGTGATCAATCCATAGATAGTG 58.417 37.037 0.00 0.00 32.82 2.74
3010 3116 5.697178 CAGCTCTCTTGTGATCAATCCATAG 59.303 44.000 0.00 0.00 32.82 2.23
3064 3170 4.065789 GCACCCTATAATGCCAGTTCTAC 58.934 47.826 0.00 0.00 35.73 2.59
3109 3216 6.954944 TCTTTTCTGTGATTGGAAGTTAACG 58.045 36.000 0.00 0.00 0.00 3.18
3158 3270 4.217767 GGCGGTTCTCCTTTTAGACATTTT 59.782 41.667 0.00 0.00 0.00 1.82
3373 3507 4.063967 CTCGGTGTAGTGCGGCCA 62.064 66.667 2.24 0.00 0.00 5.36
3378 3512 1.807573 GCTCAGCTCGGTGTAGTGC 60.808 63.158 0.00 0.00 0.00 4.40
3455 3589 4.388773 CACAACGCTAAATGAGAAGCTACA 59.611 41.667 0.00 0.00 36.56 2.74
3504 3638 2.057922 ACCTTGTTCCTGGTCTCATGT 58.942 47.619 0.00 0.00 29.18 3.21
3606 3740 5.967088 AGTGCTACACTGACAAAGGTATAG 58.033 41.667 0.00 0.00 43.63 1.31
3688 3822 2.249413 CTCCTGCGGTCATTGAGGCT 62.249 60.000 10.08 0.00 0.00 4.58
3729 3863 5.349270 CCAACAATCATTTACAATGTGCCAG 59.651 40.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.