Multiple sequence alignment - TraesCS1B01G311100

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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 TraesCS1B01G311100 chr1B 100.000 3404 0 0 1 3404 534662630 534659227 0.000000e+00 6287.0
1 TraesCS1B01G311100 chr1A 93.341 1817 101 9 669 2469 495697201 495695389 0.000000e+00 2667.0
2 TraesCS1B01G311100 chr1A 88.951 715 68 6 2692 3404 584375494 584376199 0.000000e+00 872.0
3 TraesCS1B01G311100 chr1A 86.636 434 28 11 126 538 495697808 495697384 1.440000e-123 453.0
4 TraesCS1B01G311100 chr1A 91.228 57 4 1 2612 2667 144102388 144102444 3.640000e-10 76.8
5 TraesCS1B01G311100 chr1D 93.569 1695 85 13 993 2668 398971019 398969330 0.000000e+00 2505.0
6 TraesCS1B01G311100 chr1D 93.056 432 23 5 31 458 398972393 398971965 2.880000e-175 625.0
7 TraesCS1B01G311100 chr3B 90.084 716 68 3 2692 3404 154587685 154586970 0.000000e+00 926.0
8 TraesCS1B01G311100 chr3A 87.658 713 85 3 2695 3404 56970038 56970750 0.000000e+00 826.0
9 TraesCS1B01G311100 chr6A 85.475 716 95 7 2692 3404 426170359 426169650 0.000000e+00 737.0


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 TraesCS1B01G311100 chr1B 534659227 534662630 3403 True 6287 6287 100.0000 1 3404 1 chr1B.!!$R1 3403
1 TraesCS1B01G311100 chr1A 495695389 495697808 2419 True 1560 2667 89.9885 126 2469 2 chr1A.!!$R1 2343
2 TraesCS1B01G311100 chr1A 584375494 584376199 705 False 872 872 88.9510 2692 3404 1 chr1A.!!$F2 712
3 TraesCS1B01G311100 chr1D 398969330 398972393 3063 True 1565 2505 93.3125 31 2668 2 chr1D.!!$R1 2637
4 TraesCS1B01G311100 chr3B 154586970 154587685 715 True 926 926 90.0840 2692 3404 1 chr3B.!!$R1 712
5 TraesCS1B01G311100 chr3A 56970038 56970750 712 False 826 826 87.6580 2695 3404 1 chr3A.!!$F1 709
6 TraesCS1B01G311100 chr6A 426169650 426170359 709 True 737 737 85.4750 2692 3404 1 chr6A.!!$R1 712

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
764 868 1.073025 TCGCACAAGGGCTGTCATT 59.927 52.632 0.0 0.0 35.47 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2600 3130 0.545548 AAGGAGGCCTTCGGAGACTT 60.546 55.0 6.77 0.4 40.17 3.01 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
25 26 8.451908 ACAGTTTAGCAAAGTTTTCACTATCT 57.548 30.769 0.00 0.00 30.68 1.98
26 27 8.560374 ACAGTTTAGCAAAGTTTTCACTATCTC 58.440 33.333 0.00 0.00 30.68 2.75
27 28 8.778358 CAGTTTAGCAAAGTTTTCACTATCTCT 58.222 33.333 0.00 0.00 30.68 3.10
28 29 9.998106 AGTTTAGCAAAGTTTTCACTATCTCTA 57.002 29.630 0.00 0.00 30.68 2.43
33 34 9.377312 AGCAAAGTTTTCACTATCTCTAGATTC 57.623 33.333 0.00 0.00 36.05 2.52
48 49 5.273208 TCTAGATTCTGGCTAGTTTCACCT 58.727 41.667 0.00 0.00 37.28 4.00
62 63 7.041372 GCTAGTTTCACCTCATGACTTTGTAAA 60.041 37.037 0.00 0.00 36.92 2.01
72 73 6.908825 TCATGACTTTGTAAAAATTCCTCCG 58.091 36.000 0.00 0.00 0.00 4.63
78 79 7.778083 ACTTTGTAAAAATTCCTCCGAACTTT 58.222 30.769 0.00 0.00 28.95 2.66
111 112 1.864711 CGCGTGAAGAGGTTTCTCAAA 59.135 47.619 0.00 0.00 42.34 2.69
112 113 2.286833 CGCGTGAAGAGGTTTCTCAAAA 59.713 45.455 0.00 0.00 42.34 2.44
223 227 1.686052 TGCTGTGTTCCAATTCCAACC 59.314 47.619 0.00 0.00 0.00 3.77
349 353 2.043852 GCTCGTCCTCCTCCTCCA 60.044 66.667 0.00 0.00 0.00 3.86
362 367 1.557371 CTCCTCCAACTTCTTCTCCCC 59.443 57.143 0.00 0.00 0.00 4.81
386 391 4.447290 TGTCTTCACGTTTCAGAAATCCA 58.553 39.130 0.00 0.00 0.00 3.41
469 507 5.466728 TGAAGAAGATTTTGACAACGAGAGG 59.533 40.000 0.00 0.00 0.00 3.69
470 508 4.962155 AGAAGATTTTGACAACGAGAGGT 58.038 39.130 0.00 0.00 0.00 3.85
494 533 3.953612 TGTGTCTGCCTGTTCTTCATTTT 59.046 39.130 0.00 0.00 0.00 1.82
499 538 5.470098 GTCTGCCTGTTCTTCATTTTCTGTA 59.530 40.000 0.00 0.00 0.00 2.74
506 545 7.540055 CCTGTTCTTCATTTTCTGTATTTGCTC 59.460 37.037 0.00 0.00 0.00 4.26
508 547 6.182039 TCTTCATTTTCTGTATTTGCTCGG 57.818 37.500 0.00 0.00 0.00 4.63
515 554 3.932822 TCTGTATTTGCTCGGTGCTTTA 58.067 40.909 3.53 0.00 43.37 1.85
517 556 3.006940 TGTATTTGCTCGGTGCTTTAGG 58.993 45.455 3.53 0.00 43.37 2.69
525 564 3.648009 CTCGGTGCTTTAGGATCTCATC 58.352 50.000 0.00 0.00 0.00 2.92
538 577 3.629398 GGATCTCATCGTGCCATTTTTCT 59.371 43.478 0.00 0.00 0.00 2.52
560 619 6.680810 TCTGTCAAATTTGTCCATGAATGAC 58.319 36.000 17.47 5.48 37.15 3.06
580 639 1.690845 CCCTGACTCCTGAGCCTATGT 60.691 57.143 0.00 0.00 0.00 2.29
591 650 4.383444 CCTGAGCCTATGTCTCAACAATCA 60.383 45.833 0.00 0.00 39.77 2.57
592 651 5.164620 TGAGCCTATGTCTCAACAATCAA 57.835 39.130 0.00 0.00 39.30 2.57
593 652 5.181009 TGAGCCTATGTCTCAACAATCAAG 58.819 41.667 0.00 0.00 39.30 3.02
594 653 5.171339 AGCCTATGTCTCAACAATCAAGT 57.829 39.130 0.00 0.00 39.30 3.16
595 654 4.940046 AGCCTATGTCTCAACAATCAAGTG 59.060 41.667 0.00 0.00 39.30 3.16
597 656 3.818961 ATGTCTCAACAATCAAGTGCG 57.181 42.857 0.00 0.00 39.30 5.34
598 657 1.872952 TGTCTCAACAATCAAGTGCGG 59.127 47.619 0.00 0.00 30.70 5.69
600 659 3.064207 GTCTCAACAATCAAGTGCGGTA 58.936 45.455 0.00 0.00 0.00 4.02
601 660 3.496884 GTCTCAACAATCAAGTGCGGTAA 59.503 43.478 0.00 0.00 0.00 2.85
602 661 4.154195 GTCTCAACAATCAAGTGCGGTAAT 59.846 41.667 0.00 0.00 0.00 1.89
603 662 5.350365 GTCTCAACAATCAAGTGCGGTAATA 59.650 40.000 0.00 0.00 0.00 0.98
604 663 5.935206 TCTCAACAATCAAGTGCGGTAATAA 59.065 36.000 0.00 0.00 0.00 1.40
605 664 6.428465 TCTCAACAATCAAGTGCGGTAATAAA 59.572 34.615 0.00 0.00 0.00 1.40
621 696 6.910433 CGGTAATAAAATGCCATGTACTCAAC 59.090 38.462 0.00 0.00 0.00 3.18
625 700 5.981088 AAAATGCCATGTACTCAACATCA 57.019 34.783 0.00 0.00 46.15 3.07
626 701 6.534475 AAAATGCCATGTACTCAACATCAT 57.466 33.333 0.00 0.00 46.15 2.45
629 704 7.643569 AATGCCATGTACTCAACATCATAAA 57.356 32.000 0.00 0.00 46.15 1.40
631 706 7.263100 TGCCATGTACTCAACATCATAAATC 57.737 36.000 0.00 0.00 46.15 2.17
634 709 7.308229 GCCATGTACTCAACATCATAAATCCTC 60.308 40.741 0.00 0.00 46.15 3.71
663 738 3.861840 TCCCTCTCAGTAAAAGCATTCG 58.138 45.455 0.00 0.00 0.00 3.34
664 739 2.939103 CCCTCTCAGTAAAAGCATTCGG 59.061 50.000 0.00 0.00 0.00 4.30
666 741 3.369471 CCTCTCAGTAAAAGCATTCGGGA 60.369 47.826 0.00 0.00 0.00 5.14
667 742 4.446371 CTCTCAGTAAAAGCATTCGGGAT 58.554 43.478 0.00 0.00 0.00 3.85
684 788 9.144747 CATTCGGGATTATATAGTTCTGACTTG 57.855 37.037 0.00 0.00 37.33 3.16
700 804 2.816087 GACTTGGCTCTCTGAATGCAAA 59.184 45.455 0.00 0.00 0.00 3.68
716 820 5.854010 ATGCAAATGATGAAGAAGCATCT 57.146 34.783 0.00 0.00 43.89 2.90
750 854 4.517075 TGACCAATTCAATAACTTGTCGCA 59.483 37.500 0.00 0.00 33.87 5.10
764 868 1.073025 TCGCACAAGGGCTGTCATT 59.927 52.632 0.00 0.00 35.47 2.57
896 1388 4.684242 CCCAACGTTCTTCCTAATTTTTGC 59.316 41.667 0.00 0.00 0.00 3.68
912 1404 7.451501 AATTTTTGCCCAACTAATTCAATGG 57.548 32.000 0.00 0.00 0.00 3.16
914 1406 4.799564 TTGCCCAACTAATTCAATGGAC 57.200 40.909 5.20 0.00 34.82 4.02
947 1452 2.166664 GCTCTCCAACCATCGTCTAAGT 59.833 50.000 0.00 0.00 0.00 2.24
956 1461 3.270877 CCATCGTCTAAGTTTCCAAGGG 58.729 50.000 0.00 0.00 0.00 3.95
1004 1509 2.501008 CACGACGACGACGATGCA 60.501 61.111 25.15 0.00 42.66 3.96
1006 1511 3.598562 CGACGACGACGATGCAGC 61.599 66.667 15.32 0.00 42.66 5.25
1008 1513 3.685214 GACGACGACGATGCAGCCT 62.685 63.158 15.32 0.00 42.66 4.58
1186 1691 3.729163 GCTCTAATTTGCTTCGGTTCTGC 60.729 47.826 0.00 0.00 0.00 4.26
1227 1732 3.352338 GAACACGGAGCCGACGGAT 62.352 63.158 20.50 12.80 42.83 4.18
1275 1780 2.725008 GAGATCCTCTCGGCCGTG 59.275 66.667 27.15 23.87 33.35 4.94
1365 1873 2.726351 CGACCAGCCTCCCTTCTCC 61.726 68.421 0.00 0.00 0.00 3.71
1383 1891 0.392998 CCTGCGGCTACAACTCCAAT 60.393 55.000 0.00 0.00 0.00 3.16
1542 2050 1.446907 GACAGGACGAGGTTCGAGTA 58.553 55.000 5.38 0.00 43.74 2.59
1654 2162 2.713877 GTCTACGGGACTTCTCTGTCT 58.286 52.381 3.99 0.00 41.46 3.41
1656 2164 2.018515 CTACGGGACTTCTCTGTCTCC 58.981 57.143 0.00 0.00 34.11 3.71
1666 2174 1.791103 CTCTGTCTCCGATCCCGAGC 61.791 65.000 0.45 0.00 38.22 5.03
1677 2185 4.069232 CCCGAGCAGGCGTCAAGA 62.069 66.667 0.00 0.00 39.21 3.02
1687 2195 3.517974 CGTCAAGAAACGCGTCGA 58.482 55.556 14.44 1.25 35.64 4.20
1710 2221 2.437180 CAGCAGCTCCGGCAATCA 60.437 61.111 0.00 0.00 41.70 2.57
2286 2800 4.954118 AGCAGGGTGTCCGGGTCA 62.954 66.667 0.00 0.00 33.86 4.02
2402 2922 3.524606 GCAGAGCCGGCGGTACTA 61.525 66.667 28.82 0.00 0.00 1.82
2443 2964 6.446318 TGATTTTTGAGCGAGCTTTTTACAT 58.554 32.000 0.00 0.00 0.00 2.29
2465 2986 6.828785 ACATGTTCTTTTTCACTAGTGGTTCT 59.171 34.615 22.48 0.00 0.00 3.01
2469 2990 8.262227 TGTTCTTTTTCACTAGTGGTTCTAAGA 58.738 33.333 22.48 18.41 0.00 2.10
2470 2991 9.274206 GTTCTTTTTCACTAGTGGTTCTAAGAT 57.726 33.333 22.48 0.00 0.00 2.40
2473 2994 8.773404 TTTTTCACTAGTGGTTCTAAGATAGC 57.227 34.615 22.48 0.00 0.00 2.97
2474 2995 7.476540 TTTCACTAGTGGTTCTAAGATAGCA 57.523 36.000 22.48 0.00 0.00 3.49
2475 2996 6.701145 TCACTAGTGGTTCTAAGATAGCAG 57.299 41.667 22.48 0.00 0.00 4.24
2477 2998 6.095580 TCACTAGTGGTTCTAAGATAGCAGTG 59.904 42.308 22.48 0.00 0.00 3.66
2500 3026 2.433436 GTACTGGTAACTGGCCTTTGG 58.567 52.381 3.32 0.00 40.36 3.28
2502 3028 0.404040 CTGGTAACTGGCCTTTGGGA 59.596 55.000 3.32 0.00 37.61 4.37
2525 3053 6.350110 GGAGTTGTGGCAATTGTTACATGTAT 60.350 38.462 6.36 0.00 0.00 2.29
2543 3071 8.186178 ACATGTATAAACGTGATTCTTCTGTC 57.814 34.615 0.00 0.00 44.09 3.51
2572 3102 1.669502 GCGCATGAAAACAGATTGGCA 60.670 47.619 0.30 0.00 0.00 4.92
2591 3121 2.932187 GCATCACCACAAAATCCAAGCC 60.932 50.000 0.00 0.00 0.00 4.35
2592 3122 2.380064 TCACCACAAAATCCAAGCCT 57.620 45.000 0.00 0.00 0.00 4.58
2668 3198 6.347696 AGCATAGGAACAAAGATTCAGAGAG 58.652 40.000 0.00 0.00 0.00 3.20
2669 3199 5.526846 GCATAGGAACAAAGATTCAGAGAGG 59.473 44.000 0.00 0.00 0.00 3.69
2670 3200 4.566426 AGGAACAAAGATTCAGAGAGGG 57.434 45.455 0.00 0.00 0.00 4.30
2671 3201 3.913163 AGGAACAAAGATTCAGAGAGGGT 59.087 43.478 0.00 0.00 0.00 4.34
2672 3202 4.006319 GGAACAAAGATTCAGAGAGGGTG 58.994 47.826 0.00 0.00 0.00 4.61
2673 3203 4.263068 GGAACAAAGATTCAGAGAGGGTGA 60.263 45.833 0.00 0.00 0.00 4.02
2674 3204 4.278975 ACAAAGATTCAGAGAGGGTGAC 57.721 45.455 0.00 0.00 0.00 3.67
2675 3205 3.257393 CAAAGATTCAGAGAGGGTGACG 58.743 50.000 0.00 0.00 0.00 4.35
2676 3206 0.820871 AGATTCAGAGAGGGTGACGC 59.179 55.000 0.00 0.00 0.00 5.19
2677 3207 0.820871 GATTCAGAGAGGGTGACGCT 59.179 55.000 0.31 0.31 0.00 5.07
2678 3208 0.534412 ATTCAGAGAGGGTGACGCTG 59.466 55.000 6.97 0.00 36.73 5.18
2679 3209 1.536073 TTCAGAGAGGGTGACGCTGG 61.536 60.000 6.97 0.00 36.23 4.85
2680 3210 3.386237 AGAGAGGGTGACGCTGGC 61.386 66.667 6.97 0.00 0.00 4.85
2681 3211 3.386237 GAGAGGGTGACGCTGGCT 61.386 66.667 6.97 0.00 0.00 4.75
2682 3212 3.363844 GAGAGGGTGACGCTGGCTC 62.364 68.421 6.97 4.74 0.00 4.70
2683 3213 3.386237 GAGGGTGACGCTGGCTCT 61.386 66.667 6.97 0.00 0.00 4.09
2684 3214 3.363844 GAGGGTGACGCTGGCTCTC 62.364 68.421 6.97 0.00 0.00 3.20
2685 3215 4.803426 GGGTGACGCTGGCTCTCG 62.803 72.222 0.00 0.00 0.00 4.04
2792 3323 1.544246 GGCAAACCACCAACCATAGAC 59.456 52.381 0.00 0.00 35.26 2.59
2802 3333 0.824759 AACCATAGACGAGCCACCTC 59.175 55.000 0.00 0.00 34.66 3.85
2873 3404 0.459585 TTATCTCCGGCGACAAGTGC 60.460 55.000 9.30 0.00 0.00 4.40
2915 3451 1.077501 CGTCCCCGACCAGGTACTA 60.078 63.158 0.00 0.00 38.74 1.82
2938 3474 0.678950 TCCATGCTCGTGTTCTGTCA 59.321 50.000 0.00 0.00 0.00 3.58
3076 3612 4.349365 CCAGTCTCCTCTCCTACTTCTTT 58.651 47.826 0.00 0.00 0.00 2.52
3083 3619 3.193691 CCTCTCCTACTTCTTTTGCTCGA 59.806 47.826 0.00 0.00 0.00 4.04
3274 3810 3.680156 GCGAGGGGCATTCAAACA 58.320 55.556 0.00 0.00 42.87 2.83
3380 3917 1.051812 CCCATCCCGTCAAGCTCTAT 58.948 55.000 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.778358 AGAGATAGTGAAAACTTTGCTAAACTG 58.222 33.333 0.00 0.00 0.00 3.16
2 3 8.910351 AGAGATAGTGAAAACTTTGCTAAACT 57.090 30.769 0.00 0.00 0.00 2.66
7 8 9.377312 GAATCTAGAGATAGTGAAAACTTTGCT 57.623 33.333 0.00 0.00 33.73 3.91
8 9 9.377312 AGAATCTAGAGATAGTGAAAACTTTGC 57.623 33.333 0.00 0.00 33.73 3.68
10 11 9.883142 CCAGAATCTAGAGATAGTGAAAACTTT 57.117 33.333 0.00 0.00 33.73 2.66
11 12 7.984617 GCCAGAATCTAGAGATAGTGAAAACTT 59.015 37.037 0.00 0.00 33.73 2.66
12 13 7.344352 AGCCAGAATCTAGAGATAGTGAAAACT 59.656 37.037 0.00 0.00 33.73 2.66
13 14 7.496747 AGCCAGAATCTAGAGATAGTGAAAAC 58.503 38.462 0.00 0.00 33.73 2.43
14 15 7.667575 AGCCAGAATCTAGAGATAGTGAAAA 57.332 36.000 0.00 0.00 33.73 2.29
15 16 8.001875 ACTAGCCAGAATCTAGAGATAGTGAAA 58.998 37.037 6.18 0.00 37.53 2.69
16 17 7.522542 ACTAGCCAGAATCTAGAGATAGTGAA 58.477 38.462 6.18 0.00 37.53 3.18
17 18 7.085476 ACTAGCCAGAATCTAGAGATAGTGA 57.915 40.000 6.18 0.00 37.53 3.41
18 19 7.759489 AACTAGCCAGAATCTAGAGATAGTG 57.241 40.000 7.41 0.00 37.53 2.74
19 20 8.001875 TGAAACTAGCCAGAATCTAGAGATAGT 58.998 37.037 0.00 0.00 37.53 2.12
20 21 8.296713 GTGAAACTAGCCAGAATCTAGAGATAG 58.703 40.741 0.00 0.00 37.53 2.08
21 22 7.231722 GGTGAAACTAGCCAGAATCTAGAGATA 59.768 40.741 0.00 0.00 37.53 1.98
22 23 6.041523 GGTGAAACTAGCCAGAATCTAGAGAT 59.958 42.308 0.00 0.00 37.53 2.75
23 24 5.361285 GGTGAAACTAGCCAGAATCTAGAGA 59.639 44.000 0.00 0.00 37.53 3.10
24 25 5.362430 AGGTGAAACTAGCCAGAATCTAGAG 59.638 44.000 0.00 0.00 37.53 2.43
25 26 5.273208 AGGTGAAACTAGCCAGAATCTAGA 58.727 41.667 0.00 0.00 37.53 2.43
26 27 5.127845 TGAGGTGAAACTAGCCAGAATCTAG 59.872 44.000 0.00 0.00 39.43 2.43
27 28 5.023452 TGAGGTGAAACTAGCCAGAATCTA 58.977 41.667 0.00 0.00 36.74 1.98
28 29 3.840666 TGAGGTGAAACTAGCCAGAATCT 59.159 43.478 0.00 0.00 36.74 2.40
29 30 4.207891 TGAGGTGAAACTAGCCAGAATC 57.792 45.455 0.00 0.00 36.74 2.52
30 31 4.225942 TCATGAGGTGAAACTAGCCAGAAT 59.774 41.667 0.00 0.00 36.74 2.40
31 32 3.582647 TCATGAGGTGAAACTAGCCAGAA 59.417 43.478 0.00 0.00 36.74 3.02
32 33 3.055819 GTCATGAGGTGAAACTAGCCAGA 60.056 47.826 0.00 0.00 38.90 3.86
33 34 3.055530 AGTCATGAGGTGAAACTAGCCAG 60.056 47.826 0.00 0.00 38.90 4.85
48 49 6.712998 TCGGAGGAATTTTTACAAAGTCATGA 59.287 34.615 4.41 0.00 38.49 3.07
78 79 3.125487 TCTTCACGCGTTCTTCAACAAAA 59.875 39.130 10.22 0.00 32.14 2.44
83 84 1.202486 ACCTCTTCACGCGTTCTTCAA 60.202 47.619 10.22 0.00 0.00 2.69
88 89 1.456165 GAGAAACCTCTTCACGCGTTC 59.544 52.381 10.22 0.28 29.54 3.95
117 118 9.626045 GTTCAATCCGTTCTTTAGATGATTTTT 57.374 29.630 0.00 0.00 0.00 1.94
124 125 8.391075 TGAAAAGTTCAATCCGTTCTTTAGAT 57.609 30.769 0.00 0.00 36.59 1.98
349 353 3.716872 TGAAGACAAGGGGAGAAGAAGTT 59.283 43.478 0.00 0.00 0.00 2.66
362 367 5.007626 TGGATTTCTGAAACGTGAAGACAAG 59.992 40.000 4.73 0.00 0.00 3.16
386 391 3.314331 CCTCTATGGCGGGCGGAT 61.314 66.667 0.00 0.00 0.00 4.18
411 416 2.037251 GGGCTTCTCCGTGATAGCATAA 59.963 50.000 0.00 0.00 33.53 1.90
469 507 1.599542 GAAGAACAGGCAGACACACAC 59.400 52.381 0.00 0.00 0.00 3.82
470 508 1.209261 TGAAGAACAGGCAGACACACA 59.791 47.619 0.00 0.00 0.00 3.72
506 545 2.223829 ACGATGAGATCCTAAAGCACCG 60.224 50.000 0.00 0.00 0.00 4.94
508 547 2.541762 GCACGATGAGATCCTAAAGCAC 59.458 50.000 0.00 0.00 0.00 4.40
515 554 3.287867 AAAATGGCACGATGAGATCCT 57.712 42.857 0.00 0.00 0.00 3.24
517 556 4.095483 ACAGAAAAATGGCACGATGAGATC 59.905 41.667 0.00 0.00 0.00 2.75
525 564 5.006552 ACAAATTTGACAGAAAAATGGCACG 59.993 36.000 24.64 0.00 38.14 5.34
538 577 5.279406 GGGTCATTCATGGACAAATTTGACA 60.279 40.000 24.64 20.66 37.00 3.58
560 619 1.047002 CATAGGCTCAGGAGTCAGGG 58.953 60.000 3.47 0.00 34.98 4.45
580 639 2.254546 ACCGCACTTGATTGTTGAGA 57.745 45.000 0.00 0.00 0.00 3.27
591 650 4.159506 ACATGGCATTTTATTACCGCACTT 59.840 37.500 0.00 0.00 0.00 3.16
592 651 3.699038 ACATGGCATTTTATTACCGCACT 59.301 39.130 0.00 0.00 0.00 4.40
593 652 4.040445 ACATGGCATTTTATTACCGCAC 57.960 40.909 0.00 0.00 0.00 5.34
594 653 4.884744 AGTACATGGCATTTTATTACCGCA 59.115 37.500 0.00 0.00 0.00 5.69
595 654 5.008217 TGAGTACATGGCATTTTATTACCGC 59.992 40.000 0.00 0.00 0.00 5.68
597 656 7.767261 TGTTGAGTACATGGCATTTTATTACC 58.233 34.615 0.00 0.00 0.00 2.85
644 719 2.939103 CCCGAATGCTTTTACTGAGAGG 59.061 50.000 0.00 0.00 0.00 3.69
656 731 7.179338 AGTCAGAACTATATAATCCCGAATGCT 59.821 37.037 0.00 0.00 32.59 3.79
658 733 9.144747 CAAGTCAGAACTATATAATCCCGAATG 57.855 37.037 0.00 0.00 33.48 2.67
660 735 7.667557 CCAAGTCAGAACTATATAATCCCGAA 58.332 38.462 0.00 0.00 33.48 4.30
663 738 7.010339 AGCCAAGTCAGAACTATATAATCCC 57.990 40.000 0.00 0.00 33.48 3.85
664 739 7.902087 AGAGCCAAGTCAGAACTATATAATCC 58.098 38.462 0.00 0.00 33.48 3.01
666 741 8.584157 CAGAGAGCCAAGTCAGAACTATATAAT 58.416 37.037 0.00 0.00 33.48 1.28
667 742 7.780271 TCAGAGAGCCAAGTCAGAACTATATAA 59.220 37.037 0.00 0.00 33.48 0.98
684 788 3.630769 TCATCATTTGCATTCAGAGAGCC 59.369 43.478 0.00 0.00 0.00 4.70
700 804 7.991460 TGTCATTCTAAGATGCTTCTTCATCAT 59.009 33.333 17.37 4.72 43.94 2.45
750 854 1.352352 ACTGCTAATGACAGCCCTTGT 59.648 47.619 0.00 0.00 44.55 3.16
855 1347 1.279846 GGGGTGTCCATTTCGAACCTA 59.720 52.381 0.00 0.00 35.00 3.08
896 1388 3.352648 ACGGTCCATTGAATTAGTTGGG 58.647 45.455 0.00 0.00 0.00 4.12
912 1404 0.664224 GAGAGCAGCTACCTACGGTC 59.336 60.000 0.00 0.00 37.09 4.79
914 1406 0.752009 TGGAGAGCAGCTACCTACGG 60.752 60.000 16.20 0.00 0.00 4.02
947 1452 2.159170 CGTTGTTTTCTGCCCTTGGAAA 60.159 45.455 0.00 0.00 0.00 3.13
987 1492 2.488792 CTGCATCGTCGTCGTCGTG 61.489 63.158 11.41 9.98 38.33 4.35
988 1493 2.202311 CTGCATCGTCGTCGTCGT 60.202 61.111 11.41 0.00 38.33 4.34
991 1496 3.749064 AGGCTGCATCGTCGTCGT 61.749 61.111 0.50 0.00 38.33 4.34
1070 1575 1.454295 TAGTAGATGGCGGCGGTGA 60.454 57.895 9.78 0.00 0.00 4.02
1186 1691 3.292656 TGCGGAGAGAGGCAGAAG 58.707 61.111 0.00 0.00 33.52 2.85
1227 1732 1.069513 AGACCGTTGTCCGTTTCATCA 59.930 47.619 0.00 0.00 42.81 3.07
1244 1749 1.408702 GGATCTCCAGACTGCTCAGAC 59.591 57.143 3.60 0.00 35.64 3.51
1365 1873 1.398390 GAATTGGAGTTGTAGCCGCAG 59.602 52.381 0.00 0.00 0.00 5.18
1383 1891 2.433888 TGGCTGTTGGCATCGGAA 59.566 55.556 8.56 0.00 44.10 4.30
1542 2050 0.031721 GACTGTTCACCGGTCGAACT 59.968 55.000 31.54 21.48 42.63 3.01
1637 2145 1.678123 CGGAGACAGAGAAGTCCCGTA 60.678 57.143 12.62 0.00 42.34 4.02
1656 2164 4.933064 GACGCCTGCTCGGGATCG 62.933 72.222 0.00 0.00 37.82 3.69
1672 2180 2.012414 CGGTCGACGCGTTTCTTGA 61.012 57.895 15.53 3.97 34.82 3.02
2166 2677 1.192146 TGACGTTTCCCCTCCTCCTG 61.192 60.000 0.00 0.00 0.00 3.86
2272 2786 4.250170 ACCTGACCCGGACACCCT 62.250 66.667 0.73 0.00 0.00 4.34
2283 2797 2.029844 GCGTTCCAGCTCACCTGAC 61.030 63.158 0.00 0.00 44.64 3.51
2402 2922 8.199449 TCAAAAATCAAAATCTCTCAGCACTTT 58.801 29.630 0.00 0.00 0.00 2.66
2443 2964 8.262227 TCTTAGAACCACTAGTGAAAAAGAACA 58.738 33.333 24.68 0.00 32.30 3.18
2474 2995 1.346722 GCCAGTTACCAGTACCACACT 59.653 52.381 0.00 0.00 38.32 3.55
2475 2996 1.609841 GGCCAGTTACCAGTACCACAC 60.610 57.143 0.00 0.00 0.00 3.82
2477 2998 0.981943 AGGCCAGTTACCAGTACCAC 59.018 55.000 5.01 0.00 0.00 4.16
2493 3019 1.398958 TTGCCACAACTCCCAAAGGC 61.399 55.000 0.00 0.00 42.32 4.35
2500 3026 4.236935 CATGTAACAATTGCCACAACTCC 58.763 43.478 14.56 0.00 0.00 3.85
2502 3028 4.935352 ACATGTAACAATTGCCACAACT 57.065 36.364 14.56 3.06 0.00 3.16
2543 3071 4.922692 TCTGTTTTCATGCGCCATAAAAAG 59.077 37.500 4.18 5.16 23.67 2.27
2572 3102 2.893424 AGGCTTGGATTTTGTGGTGAT 58.107 42.857 0.00 0.00 0.00 3.06
2600 3130 0.545548 AAGGAGGCCTTCGGAGACTT 60.546 55.000 6.77 0.40 40.17 3.01
2645 3175 5.526846 CCTCTCTGAATCTTTGTTCCTATGC 59.473 44.000 0.00 0.00 0.00 3.14
2668 3198 4.803426 CGAGAGCCAGCGTCACCC 62.803 72.222 0.00 0.00 0.00 4.61
2680 3210 0.873743 GAGCCCATCTTTCGCGAGAG 60.874 60.000 19.89 19.89 43.69 3.20
2681 3211 1.141881 GAGCCCATCTTTCGCGAGA 59.858 57.895 9.59 3.35 39.20 4.04
2682 3212 0.873743 GAGAGCCCATCTTTCGCGAG 60.874 60.000 9.59 0.00 38.84 5.03
2683 3213 1.141881 GAGAGCCCATCTTTCGCGA 59.858 57.895 3.71 3.71 38.84 5.87
2684 3214 2.233654 CGAGAGCCCATCTTTCGCG 61.234 63.158 0.00 0.00 41.49 5.87
2685 3215 3.711348 CGAGAGCCCATCTTTCGC 58.289 61.111 0.00 0.00 41.49 4.70
2777 3308 0.249398 GCTCGTCTATGGTTGGTGGT 59.751 55.000 0.00 0.00 0.00 4.16
2783 3314 0.824759 GAGGTGGCTCGTCTATGGTT 59.175 55.000 2.28 0.00 0.00 3.67
2792 3323 2.125912 CTTGACGGAGGTGGCTCG 60.126 66.667 0.00 0.00 0.00 5.03
2915 3451 0.687354 AGAACACGAGCATGGAAGGT 59.313 50.000 0.00 0.00 0.00 3.50
2938 3474 1.075151 GACCCCGGAGAGGAAGGAT 60.075 63.158 0.73 0.00 45.00 3.24
3052 3588 0.106918 AGTAGGAGAGGAGACTGGCG 60.107 60.000 0.00 0.00 44.43 5.69
3083 3619 1.726865 CAGAGAGATGCTCGCTCGT 59.273 57.895 9.83 0.21 46.01 4.18
3157 3693 2.974489 GACGGTGAGGACGAAGCGA 61.974 63.158 0.92 0.00 40.35 4.93
3296 3833 1.125847 CCGCGCTTTGACATTAACGC 61.126 55.000 5.56 0.00 42.69 4.84
3372 3909 2.419198 CCCGCGCAGATAGAGCTT 59.581 61.111 8.75 0.00 41.30 3.74


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

AutoCloner maintained by Alex Coulton.