Multiple sequence alignment - TraesCS1A01G241400

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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 TraesCS1A01G241400 chr1A 100.000 3774 0 0 1 3774 429004928 429001155 0.000000e+00 6970.0
1 TraesCS1A01G241400 chr1A 94.737 38 2 0 2988 3025 411923356 411923393 4.070000e-05 60.2
2 TraesCS1A01G241400 chr1D 91.076 3104 102 60 7 3028 332073361 332070351 0.000000e+00 4036.0
3 TraesCS1A01G241400 chr1D 89.595 519 20 7 3258 3774 332070078 332069592 2.470000e-176 628.0
4 TraesCS1A01G241400 chr1D 91.111 180 14 1 3068 3247 332070239 332070062 3.770000e-60 243.0
5 TraesCS1A01G241400 chr1B 90.210 2288 87 61 7 2240 446260082 446257878 0.000000e+00 2857.0
6 TraesCS1A01G241400 chr1B 91.242 982 49 16 2278 3247 446257882 446256926 0.000000e+00 1303.0
7 TraesCS1A01G241400 chr1B 84.013 319 19 16 3258 3575 446256942 446256655 1.030000e-70 278.0
8 TraesCS1A01G241400 chr1B 94.079 152 9 0 3623 3774 446256653 446256502 8.150000e-57 231.0
9 TraesCS1A01G241400 chr5D 91.418 536 25 15 2239 2767 315913388 315912867 0.000000e+00 715.0
10 TraesCS1A01G241400 chr4D 89.925 536 34 13 2239 2767 1741968 1741446 0.000000e+00 673.0
11 TraesCS1A01G241400 chr4D 90.274 401 24 11 2371 2767 130857891 130858280 9.350000e-141 510.0
12 TraesCS1A01G241400 chr4D 91.111 45 2 2 2973 3017 26528327 26528285 4.070000e-05 60.2
13 TraesCS1A01G241400 chr2D 90.547 402 22 11 2371 2767 52740480 52740870 5.590000e-143 518.0
14 TraesCS1A01G241400 chr2D 89.011 91 5 4 2143 2231 52740278 52740365 1.430000e-19 108.0
15 TraesCS1A01G241400 chr5A 82.143 84 14 1 2988 3071 585208986 585208904 1.880000e-08 71.3
16 TraesCS1A01G241400 chr2A 81.176 85 16 0 2987 3071 388271778 388271862 6.760000e-08 69.4
17 TraesCS1A01G241400 chr2A 82.353 68 11 1 2988 3054 438704442 438704509 1.460000e-04 58.4
18 TraesCS1A01G241400 chr3B 86.207 58 7 1 870 927 786971054 786970998 1.130000e-05 62.1
19 TraesCS1A01G241400 chr4B 97.143 35 1 0 3036 3070 566892141 566892175 4.070000e-05 60.2
20 TraesCS1A01G241400 chr5B 100.000 31 0 0 2987 3017 187048748 187048778 1.460000e-04 58.4
21 TraesCS1A01G241400 chr3D 86.792 53 3 4 881 929 588489772 588489720 5.270000e-04 56.5
22 TraesCS1A01G241400 chrUn 100.000 28 0 0 2998 3025 88836553 88836580 7.000000e-03 52.8


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 TraesCS1A01G241400 chr1A 429001155 429004928 3773 True 6970.000000 6970 100.000 1 3774 1 chr1A.!!$R1 3773
1 TraesCS1A01G241400 chr1D 332069592 332073361 3769 True 1635.666667 4036 90.594 7 3774 3 chr1D.!!$R1 3767
2 TraesCS1A01G241400 chr1B 446256502 446260082 3580 True 1167.250000 2857 89.886 7 3774 4 chr1B.!!$R1 3767
3 TraesCS1A01G241400 chr5D 315912867 315913388 521 True 715.000000 715 91.418 2239 2767 1 chr5D.!!$R1 528
4 TraesCS1A01G241400 chr4D 1741446 1741968 522 True 673.000000 673 89.925 2239 2767 1 chr4D.!!$R1 528
5 TraesCS1A01G241400 chr2D 52740278 52740870 592 False 313.000000 518 89.779 2143 2767 2 chr2D.!!$F1 624

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
764 840 0.035152 CCTTGATAGGTGCAGGTGCA 60.035 55.0 0.0 0.0 39.82 4.57 F
2521 2665 0.740868 CACGCCATCGACCACTTCAT 60.741 55.0 0.0 0.0 39.41 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2690 2845 1.135689 CGCTACAAGTTCCAATGCACC 60.136 52.381 0.0 0.0 0.0 5.01 R
3652 3885 3.320541 CACAACAAGGTGGAAATAGCCAA 59.679 43.478 0.0 0.0 40.2 4.52 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
35 38 1.566211 CAGAGCAGGAGGGAGAAGAA 58.434 55.000 0.00 0.00 0.00 2.52
36 39 1.481772 CAGAGCAGGAGGGAGAAGAAG 59.518 57.143 0.00 0.00 0.00 2.85
38 41 1.756538 GAGCAGGAGGGAGAAGAAGAG 59.243 57.143 0.00 0.00 0.00 2.85
39 42 1.360852 AGCAGGAGGGAGAAGAAGAGA 59.639 52.381 0.00 0.00 0.00 3.10
40 43 2.183679 GCAGGAGGGAGAAGAAGAGAA 58.816 52.381 0.00 0.00 0.00 2.87
41 44 2.168313 GCAGGAGGGAGAAGAAGAGAAG 59.832 54.545 0.00 0.00 0.00 2.85
77 80 1.578423 GTCAGTGAAAGCTGCCAGC 59.422 57.895 9.13 9.13 42.84 4.85
78 81 1.148949 TCAGTGAAAGCTGCCAGCA 59.851 52.632 20.53 0.36 45.56 4.41
79 82 0.887836 TCAGTGAAAGCTGCCAGCAG 60.888 55.000 20.53 15.34 45.56 4.24
80 83 1.602888 AGTGAAAGCTGCCAGCAGG 60.603 57.895 20.53 3.54 45.56 4.85
180 187 1.137086 CGAAAGATGAGATCCCGTGGT 59.863 52.381 0.00 0.00 0.00 4.16
187 194 0.312416 GAGATCCCGTGGTCGATCAG 59.688 60.000 0.00 0.00 39.71 2.90
320 359 2.836636 TACACATGCTCCCTCTCTCT 57.163 50.000 0.00 0.00 0.00 3.10
322 361 1.272928 ACACATGCTCCCTCTCTCTCA 60.273 52.381 0.00 0.00 0.00 3.27
324 363 1.272928 ACATGCTCCCTCTCTCTCACA 60.273 52.381 0.00 0.00 0.00 3.58
333 372 2.513753 CTCTCTCTCACACACACTCCT 58.486 52.381 0.00 0.00 0.00 3.69
342 381 1.837439 ACACACACTCCTTTGTCCTGA 59.163 47.619 0.00 0.00 0.00 3.86
353 393 3.835395 CCTTTGTCCTGAGGAAGTAGAGT 59.165 47.826 0.96 0.00 34.91 3.24
434 487 0.933700 AAGGGAGGAGGAGAGAGAGG 59.066 60.000 0.00 0.00 0.00 3.69
445 498 2.224695 GGAGAGAGAGGAGGCTACCTAC 60.225 59.091 5.63 0.00 40.73 3.18
446 499 1.418637 AGAGAGAGGAGGCTACCTACG 59.581 57.143 5.63 0.00 40.03 3.51
447 500 1.141455 GAGAGAGGAGGCTACCTACGT 59.859 57.143 5.63 0.00 40.03 3.57
448 501 2.368221 GAGAGAGGAGGCTACCTACGTA 59.632 54.545 5.63 0.00 40.03 3.57
493 550 4.273148 GGCTCTAGAGACTAGAGAGAGG 57.727 54.545 28.67 11.67 42.68 3.69
494 551 3.008049 GGCTCTAGAGACTAGAGAGAGGG 59.992 56.522 28.67 11.13 42.68 4.30
495 552 3.646637 GCTCTAGAGACTAGAGAGAGGGT 59.353 52.174 28.67 0.00 42.68 4.34
496 553 4.836736 GCTCTAGAGACTAGAGAGAGGGTA 59.163 50.000 28.67 0.72 42.68 3.69
500 557 4.823107 AGAGACTAGAGAGAGGGTAGCTA 58.177 47.826 0.00 0.00 0.00 3.32
543 600 4.465305 TGGTAGTAGGGTAGAGTCTTTTGC 59.535 45.833 0.00 0.00 0.00 3.68
626 683 0.121197 TGGATGGAGAGGAGGGGTTT 59.879 55.000 0.00 0.00 0.00 3.27
627 684 0.840617 GGATGGAGAGGAGGGGTTTC 59.159 60.000 0.00 0.00 0.00 2.78
628 685 0.840617 GATGGAGAGGAGGGGTTTCC 59.159 60.000 0.00 0.00 37.52 3.13
629 686 0.983378 ATGGAGAGGAGGGGTTTCCG 60.983 60.000 0.00 0.00 42.29 4.30
630 687 2.368011 GGAGAGGAGGGGTTTCCGG 61.368 68.421 0.00 0.00 42.29 5.14
674 731 3.657059 CCGCTAGCCGCTACGCTA 61.657 66.667 9.66 0.00 40.39 4.26
676 733 2.050259 GCTAGCCGCTACGCTACC 60.050 66.667 2.29 0.00 40.39 3.18
677 734 2.553727 GCTAGCCGCTACGCTACCT 61.554 63.158 2.29 0.00 40.39 3.08
678 735 1.575423 CTAGCCGCTACGCTACCTC 59.425 63.158 0.00 0.00 40.39 3.85
679 736 1.153107 TAGCCGCTACGCTACCTCA 60.153 57.895 0.00 0.00 40.39 3.86
680 737 1.442526 TAGCCGCTACGCTACCTCAC 61.443 60.000 0.00 0.00 40.39 3.51
681 738 2.772691 GCCGCTACGCTACCTCACT 61.773 63.158 0.00 0.00 0.00 3.41
682 739 1.355916 CCGCTACGCTACCTCACTC 59.644 63.158 0.00 0.00 0.00 3.51
683 740 1.096386 CCGCTACGCTACCTCACTCT 61.096 60.000 0.00 0.00 0.00 3.24
684 741 0.305313 CGCTACGCTACCTCACTCTC 59.695 60.000 0.00 0.00 0.00 3.20
685 742 1.380524 GCTACGCTACCTCACTCTCA 58.619 55.000 0.00 0.00 0.00 3.27
686 743 1.332375 GCTACGCTACCTCACTCTCAG 59.668 57.143 0.00 0.00 0.00 3.35
687 744 2.907634 CTACGCTACCTCACTCTCAGA 58.092 52.381 0.00 0.00 0.00 3.27
688 745 1.745232 ACGCTACCTCACTCTCAGAG 58.255 55.000 0.00 0.00 35.52 3.35
757 833 2.629336 AGCTTAGCCTTGATAGGTGC 57.371 50.000 0.00 0.00 44.00 5.01
760 836 2.843701 CTTAGCCTTGATAGGTGCAGG 58.156 52.381 0.00 0.00 44.00 4.85
761 837 1.879575 TAGCCTTGATAGGTGCAGGT 58.120 50.000 0.00 0.00 44.00 4.00
764 840 0.035152 CCTTGATAGGTGCAGGTGCA 60.035 55.000 0.00 0.00 39.82 4.57
784 864 1.535202 CAGCTAGCTAGGGAGGGGG 60.535 68.421 18.86 0.00 0.00 5.40
1227 1308 2.671177 CGCCGACAAGAAGCAGGTG 61.671 63.158 0.00 0.00 0.00 4.00
1229 1310 2.328099 CCGACAAGAAGCAGGTGGC 61.328 63.158 0.00 0.00 45.30 5.01
1491 1572 2.663852 AAACCGCGGTTCCACTCG 60.664 61.111 41.09 7.92 37.35 4.18
1503 1584 2.258591 CACTCGTCCCAGACCACG 59.741 66.667 0.00 0.00 37.36 4.94
1509 1590 3.299977 TCCCAGACCACGACCACG 61.300 66.667 0.00 0.00 45.75 4.94
1809 1898 1.250840 GCCACATGTTCAGGGGGTTC 61.251 60.000 7.56 0.00 0.00 3.62
2004 2093 5.067153 TGGTAACACCATGAACTGAAAACTG 59.933 40.000 0.00 0.00 44.79 3.16
2006 2095 5.659440 AACACCATGAACTGAAAACTGTT 57.341 34.783 0.00 0.00 0.00 3.16
2007 2096 6.767524 AACACCATGAACTGAAAACTGTTA 57.232 33.333 0.00 0.00 0.00 2.41
2008 2097 6.131544 ACACCATGAACTGAAAACTGTTAC 57.868 37.500 0.00 0.00 0.00 2.50
2009 2098 5.885912 ACACCATGAACTGAAAACTGTTACT 59.114 36.000 0.00 0.00 0.00 2.24
2010 2099 6.038271 ACACCATGAACTGAAAACTGTTACTC 59.962 38.462 0.00 0.00 0.00 2.59
2011 2100 5.236478 ACCATGAACTGAAAACTGTTACTCG 59.764 40.000 0.00 0.00 0.00 4.18
2088 2185 5.702670 TGTCACCTCATTTCTTTCATCTCAC 59.297 40.000 0.00 0.00 0.00 3.51
2089 2186 5.702670 GTCACCTCATTTCTTTCATCTCACA 59.297 40.000 0.00 0.00 0.00 3.58
2174 2271 6.016777 CACAGCTAACTTCCAAGTCTTTTGAT 60.017 38.462 0.00 0.00 38.57 2.57
2175 2272 7.173218 CACAGCTAACTTCCAAGTCTTTTGATA 59.827 37.037 0.00 0.00 38.57 2.15
2176 2273 7.389053 ACAGCTAACTTCCAAGTCTTTTGATAG 59.611 37.037 0.00 0.00 38.57 2.08
2209 2306 8.722480 AGTTGGAAAGAAAATGAAAGGAAAAG 57.278 30.769 0.00 0.00 0.00 2.27
2258 2355 5.127031 TGCTGTACAACATGCTACTATCTGA 59.873 40.000 0.00 0.00 0.00 3.27
2262 2359 8.648557 TGTACAACATGCTACTATCTGATTTC 57.351 34.615 0.00 0.00 0.00 2.17
2381 2523 3.050089 TCTGTGGGTCCTTTGGAGTAAA 58.950 45.455 0.00 0.00 29.39 2.01
2443 2586 3.967326 CCATGGAGAGGTTGATGGTAGTA 59.033 47.826 5.56 0.00 32.20 1.82
2444 2587 4.039730 CCATGGAGAGGTTGATGGTAGTAG 59.960 50.000 5.56 0.00 32.20 2.57
2445 2588 4.332683 TGGAGAGGTTGATGGTAGTAGT 57.667 45.455 0.00 0.00 0.00 2.73
2499 2643 5.247110 TGACTCTTTGATGCTCTTCCTAGTT 59.753 40.000 0.00 0.00 0.00 2.24
2521 2665 0.740868 CACGCCATCGACCACTTCAT 60.741 55.000 0.00 0.00 39.41 2.57
2597 2751 6.094193 TCAGCTAGTAGCACGTATACTCTA 57.906 41.667 23.77 2.33 45.56 2.43
2637 2791 1.129058 CGGGGTTGGTAGGAATAGCT 58.871 55.000 0.00 0.00 0.00 3.32
2756 2911 7.262772 CAATGCATGTGGTGATAAGAATTCTT 58.737 34.615 23.53 23.53 39.85 2.52
2774 2929 9.929180 AGAATTCTTTTGCCCTCTTAAAATAAC 57.071 29.630 0.88 0.00 0.00 1.89
2775 2930 9.705290 GAATTCTTTTGCCCTCTTAAAATAACA 57.295 29.630 0.00 0.00 0.00 2.41
2787 2942 8.790718 CCTCTTAAAATAACATATGCAGCTGAT 58.209 33.333 20.43 10.74 0.00 2.90
2852 3007 5.018539 TGGTACAGTGCTCCATACATTAC 57.981 43.478 3.18 0.00 0.00 1.89
2984 3142 4.632688 CCCAAATCCAGAATGAAAACATGC 59.367 41.667 0.00 0.00 39.69 4.06
2991 3149 2.827921 AGAATGAAAACATGCACCCCTC 59.172 45.455 0.00 0.00 0.00 4.30
2996 3154 2.086610 AAACATGCACCCCTCTGTTT 57.913 45.000 7.80 7.80 37.08 2.83
2998 3156 0.478072 ACATGCACCCCTCTGTTTCA 59.522 50.000 0.00 0.00 0.00 2.69
3091 3321 3.784511 AGGAGTGGCCATATCTCAATG 57.215 47.619 20.16 0.00 40.02 2.82
3099 3329 3.567164 GGCCATATCTCAATGAACACAGG 59.433 47.826 0.00 0.00 0.00 4.00
3107 3337 9.911788 ATATCTCAATGAACACAGGACTAAATT 57.088 29.630 0.00 0.00 0.00 1.82
3115 3345 6.998074 TGAACACAGGACTAAATTTGTCTCAT 59.002 34.615 15.60 0.00 35.04 2.90
3124 3354 8.660373 GGACTAAATTTGTCTCATCAAGTACAG 58.340 37.037 15.60 0.00 35.04 2.74
3126 3356 8.993121 ACTAAATTTGTCTCATCAAGTACAGTG 58.007 33.333 0.00 0.00 0.00 3.66
3208 3438 6.414408 ACTTTGATCAGATTGTTCTTAGCG 57.586 37.500 0.00 0.00 0.00 4.26
3223 3453 4.439057 TCTTAGCGGCGAGAAATAACAAT 58.561 39.130 12.98 0.00 0.00 2.71
3292 3523 9.956720 AGATTTGTTAGTTTCAGTCTGATTTTG 57.043 29.630 2.68 0.00 0.00 2.44
3293 3524 9.736023 GATTTGTTAGTTTCAGTCTGATTTTGT 57.264 29.630 2.68 0.00 0.00 2.83
3294 3525 9.736023 ATTTGTTAGTTTCAGTCTGATTTTGTC 57.264 29.630 2.68 0.00 0.00 3.18
3340 3571 8.293867 GCCAAGTTATTACACAACAAAGTCATA 58.706 33.333 0.00 0.00 0.00 2.15
3363 3594 4.128925 TGTGCTGTGGATCTATTGACTC 57.871 45.455 0.00 0.00 0.00 3.36
3368 3599 6.478344 GTGCTGTGGATCTATTGACTCTAAAG 59.522 42.308 0.00 0.00 0.00 1.85
3382 3613 7.369803 TGACTCTAAAGCTTGCATAAAGAAG 57.630 36.000 0.00 0.00 38.24 2.85
3522 3755 1.208614 CCGAAGCACTGCTCTTTGC 59.791 57.895 3.40 0.00 38.25 3.68
3542 3775 9.436957 TCTTTGCAGATTTAAAGTACTTCTAGG 57.563 33.333 8.95 0.00 35.82 3.02
3717 3950 2.855728 GATTTGCTTGAGCCACCGCG 62.856 60.000 0.00 0.00 41.18 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 187 3.941483 GGCTGAAAAATTCCTCTGATCGA 59.059 43.478 0.00 0.00 0.00 3.59
187 194 1.812571 TCTGCGGCTGAAAAATTCCTC 59.187 47.619 7.13 0.00 0.00 3.71
270 298 3.230134 CTGGTGAAGATAGGAGAGGAGG 58.770 54.545 0.00 0.00 0.00 4.30
307 346 0.113190 TGTGTGAGAGAGAGGGAGCA 59.887 55.000 0.00 0.00 0.00 4.26
309 348 1.543802 GTGTGTGTGAGAGAGAGGGAG 59.456 57.143 0.00 0.00 0.00 4.30
310 349 1.145945 AGTGTGTGTGAGAGAGAGGGA 59.854 52.381 0.00 0.00 0.00 4.20
311 350 1.543802 GAGTGTGTGTGAGAGAGAGGG 59.456 57.143 0.00 0.00 0.00 4.30
312 351 1.543802 GGAGTGTGTGTGAGAGAGAGG 59.456 57.143 0.00 0.00 0.00 3.69
320 359 1.837439 AGGACAAAGGAGTGTGTGTGA 59.163 47.619 0.00 0.00 0.00 3.58
322 361 1.837439 TCAGGACAAAGGAGTGTGTGT 59.163 47.619 0.00 0.00 0.00 3.72
324 363 1.417890 CCTCAGGACAAAGGAGTGTGT 59.582 52.381 0.00 0.00 34.35 3.72
333 372 4.480115 TCACTCTACTTCCTCAGGACAAA 58.520 43.478 0.00 0.00 0.00 2.83
342 381 7.540474 TGTGTTCTTTATCACTCTACTTCCT 57.460 36.000 0.00 0.00 35.82 3.36
353 393 5.680619 ACAGGACACTTGTGTTCTTTATCA 58.319 37.500 11.67 0.00 0.00 2.15
543 600 7.113544 GCATCCAAGAGTAAAGAAAAGAAAACG 59.886 37.037 0.00 0.00 0.00 3.60
629 686 2.753043 TGAGCCTACGGACGGACC 60.753 66.667 0.00 0.00 0.00 4.46
630 687 1.991099 GAGTGAGCCTACGGACGGAC 61.991 65.000 0.00 0.00 0.00 4.79
676 733 1.682854 GATGCTCCCTCTGAGAGTGAG 59.317 57.143 16.28 16.28 44.42 3.51
677 734 1.287442 AGATGCTCCCTCTGAGAGTGA 59.713 52.381 8.88 1.08 44.42 3.41
678 735 1.779221 AGATGCTCCCTCTGAGAGTG 58.221 55.000 8.88 0.00 44.42 3.51
679 736 2.387757 GAAGATGCTCCCTCTGAGAGT 58.612 52.381 8.88 0.00 44.42 3.24
680 737 1.337703 CGAAGATGCTCCCTCTGAGAG 59.662 57.143 6.17 1.57 44.42 3.20
681 738 1.341482 ACGAAGATGCTCCCTCTGAGA 60.341 52.381 6.17 0.00 44.42 3.27
682 739 1.066908 GACGAAGATGCTCCCTCTGAG 59.933 57.143 0.00 0.00 44.47 3.35
683 740 1.107114 GACGAAGATGCTCCCTCTGA 58.893 55.000 0.00 0.00 0.00 3.27
684 741 1.110442 AGACGAAGATGCTCCCTCTG 58.890 55.000 0.00 0.00 0.00 3.35
685 742 1.110442 CAGACGAAGATGCTCCCTCT 58.890 55.000 0.00 0.00 0.00 3.69
686 743 0.529555 GCAGACGAAGATGCTCCCTC 60.530 60.000 0.00 0.00 39.75 4.30
687 744 1.519719 GCAGACGAAGATGCTCCCT 59.480 57.895 0.00 0.00 39.75 4.20
688 745 4.116878 GCAGACGAAGATGCTCCC 57.883 61.111 0.00 0.00 39.75 4.30
765 841 2.213513 CCCCTCCCTAGCTAGCTGC 61.214 68.421 27.68 0.00 43.29 5.25
766 842 1.535202 CCCCCTCCCTAGCTAGCTG 60.535 68.421 27.68 16.13 0.00 4.24
774 854 1.939113 CAGTAGCTCCCCCTCCCTA 59.061 63.158 0.00 0.00 0.00 3.53
960 1041 1.315690 CCGCTATCCCGTAGTTGAGA 58.684 55.000 0.00 0.00 32.72 3.27
984 1065 1.425031 CATGCCGACATCACCGTTG 59.575 57.895 0.00 0.00 32.87 4.10
985 1066 1.745115 CCATGCCGACATCACCGTT 60.745 57.895 0.00 0.00 32.87 4.44
986 1067 2.125147 CCATGCCGACATCACCGT 60.125 61.111 0.00 0.00 32.87 4.83
987 1068 2.125147 ACCATGCCGACATCACCG 60.125 61.111 0.00 0.00 32.87 4.94
1368 1449 3.406361 GTGCTCCTGACGTGCGTG 61.406 66.667 0.67 0.00 33.53 5.34
1491 1572 2.342648 GTGGTCGTGGTCTGGGAC 59.657 66.667 0.00 0.00 0.00 4.46
1503 1584 2.156051 GAGAGGTGGTGGTCGTGGTC 62.156 65.000 0.00 0.00 0.00 4.02
1509 1590 2.048127 GTGCGAGAGGTGGTGGTC 60.048 66.667 0.00 0.00 0.00 4.02
1809 1898 4.208686 GCGCCCTGGTCGTAGAGG 62.209 72.222 0.00 0.00 36.95 3.69
1878 1967 1.433879 GTCGGAGATGCTACGCACT 59.566 57.895 0.00 0.00 43.04 4.40
2004 2093 6.595772 TTACTAGCTAGCACTACGAGTAAC 57.404 41.667 20.91 0.00 0.00 2.50
2006 2095 4.749099 GCTTACTAGCTAGCACTACGAGTA 59.251 45.833 20.91 10.75 44.27 2.59
2007 2096 3.560896 GCTTACTAGCTAGCACTACGAGT 59.439 47.826 20.91 11.68 44.27 4.18
2008 2097 3.058777 GGCTTACTAGCTAGCACTACGAG 60.059 52.174 20.91 8.41 46.90 4.18
2009 2098 2.877168 GGCTTACTAGCTAGCACTACGA 59.123 50.000 20.91 0.00 46.90 3.43
2010 2099 2.879646 AGGCTTACTAGCTAGCACTACG 59.120 50.000 20.91 5.00 46.90 3.51
2011 2100 3.004944 CCAGGCTTACTAGCTAGCACTAC 59.995 52.174 20.91 8.74 46.90 2.73
2175 2272 9.847224 TTCATTTTCTTTCCAACTTCTACTACT 57.153 29.630 0.00 0.00 0.00 2.57
2209 2306 5.705905 AGTTTACCTTGGAAATACTGACTGC 59.294 40.000 0.00 0.00 0.00 4.40
2258 2355 4.135306 CAGCATCAGCCACATAGAGAAAT 58.865 43.478 0.00 0.00 43.56 2.17
2262 2359 2.612672 CAACAGCATCAGCCACATAGAG 59.387 50.000 0.00 0.00 43.56 2.43
2299 2397 8.031864 CCCAACATATGCAAACATGTTAAGTTA 58.968 33.333 12.39 2.86 42.09 2.24
2300 2398 6.873076 CCCAACATATGCAAACATGTTAAGTT 59.127 34.615 12.39 2.38 42.09 2.66
2304 2402 6.210385 AGTTCCCAACATATGCAAACATGTTA 59.790 34.615 12.39 0.00 42.09 2.41
2443 2586 9.502091 TTCAGCTGTCAAATTAACAATAGTACT 57.498 29.630 14.67 0.00 0.00 2.73
2461 2605 5.415701 TCAAAGAGTCAAACTTTTCAGCTGT 59.584 36.000 14.67 0.00 35.74 4.40
2499 2643 4.077184 GTGGTCGATGGCGTGGGA 62.077 66.667 0.00 0.00 38.98 4.37
2521 2665 2.760634 TAGCACGCAAGAGGATGAAA 57.239 45.000 0.00 0.00 43.62 2.69
2558 2705 6.534634 ACTAGCTGAACAAGGTAAACAAGAT 58.465 36.000 0.00 0.00 38.38 2.40
2637 2791 6.414732 CAAGTAAGAATCCAACCCATGTCTA 58.585 40.000 0.00 0.00 0.00 2.59
2690 2845 1.135689 CGCTACAAGTTCCAATGCACC 60.136 52.381 0.00 0.00 0.00 5.01
2756 2911 8.072321 TGCATATGTTATTTTAAGAGGGCAAA 57.928 30.769 4.29 0.00 0.00 3.68
2774 2929 9.650539 AATTTACTAGAGTATCAGCTGCATATG 57.349 33.333 9.47 0.00 37.82 1.78
2787 2942 7.611467 TCGTGACCCAAGTAATTTACTAGAGTA 59.389 37.037 9.43 0.00 38.26 2.59
2788 2943 6.435277 TCGTGACCCAAGTAATTTACTAGAGT 59.565 38.462 9.43 7.14 38.26 3.24
2789 2944 6.860080 TCGTGACCCAAGTAATTTACTAGAG 58.140 40.000 9.43 4.30 38.26 2.43
2790 2945 6.839124 TCGTGACCCAAGTAATTTACTAGA 57.161 37.500 9.43 0.00 38.26 2.43
2791 2946 7.262772 TGATCGTGACCCAAGTAATTTACTAG 58.737 38.462 9.43 4.85 38.26 2.57
2852 3007 0.251341 ACTAGCAAACAGGCCAAGGG 60.251 55.000 5.01 0.00 0.00 3.95
2911 3069 3.057526 GGGCTCGCAACAAAAGATTAAGT 60.058 43.478 0.00 0.00 0.00 2.24
2917 3075 1.901464 GGGGGCTCGCAACAAAAGA 60.901 57.895 0.00 0.00 0.00 2.52
2984 3142 9.224267 CATCTTATATTATGAAACAGAGGGGTG 57.776 37.037 0.00 0.00 0.00 4.61
3051 3214 5.446860 TCCTTAGTACTTCATCCGTCTCAT 58.553 41.667 0.00 0.00 0.00 2.90
3054 3217 4.641094 CACTCCTTAGTACTTCATCCGTCT 59.359 45.833 0.00 0.00 33.48 4.18
3091 3321 6.861065 TGAGACAAATTTAGTCCTGTGTTC 57.139 37.500 13.64 7.37 36.68 3.18
3099 3329 9.209175 ACTGTACTTGATGAGACAAATTTAGTC 57.791 33.333 10.82 10.82 36.26 2.59
3107 3337 7.611855 TCTCTATCACTGTACTTGATGAGACAA 59.388 37.037 20.55 10.58 35.29 3.18
3186 3416 5.728898 GCCGCTAAGAACAATCTGATCAAAG 60.729 44.000 0.00 0.00 35.59 2.77
3261 3491 9.996554 TCAGACTGAAACTAACAAATCTCATTA 57.003 29.630 1.64 0.00 0.00 1.90
3262 3492 8.908786 TCAGACTGAAACTAACAAATCTCATT 57.091 30.769 1.64 0.00 0.00 2.57
3263 3493 9.512588 AATCAGACTGAAACTAACAAATCTCAT 57.487 29.630 9.70 0.00 0.00 2.90
3264 3494 8.908786 AATCAGACTGAAACTAACAAATCTCA 57.091 30.769 9.70 0.00 0.00 3.27
3292 3523 4.095632 GCCTGCTTAGGAATGAAGAAAGAC 59.904 45.833 0.00 0.00 0.00 3.01
3293 3524 4.265073 GCCTGCTTAGGAATGAAGAAAGA 58.735 43.478 0.00 0.00 0.00 2.52
3294 3525 3.379688 GGCCTGCTTAGGAATGAAGAAAG 59.620 47.826 0.00 0.00 0.00 2.62
3340 3571 5.104610 AGAGTCAATAGATCCACAGCACAAT 60.105 40.000 0.00 0.00 0.00 2.71
3363 3594 8.909671 CAGAAAACTTCTTTATGCAAGCTTTAG 58.090 33.333 0.00 0.00 38.11 1.85
3368 3599 7.862873 AGTTACAGAAAACTTCTTTATGCAAGC 59.137 33.333 0.00 0.00 36.26 4.01
3382 3613 8.336080 CACTCCTAAACTGAAGTTACAGAAAAC 58.664 37.037 0.00 0.00 40.63 2.43
3396 3627 8.081633 TCATTTGTAATTTGCACTCCTAAACTG 58.918 33.333 0.00 0.00 0.00 3.16
3581 3814 4.412796 TGATCACCTGCCAATCTTAGAG 57.587 45.455 0.00 0.00 0.00 2.43
3621 3854 6.564557 ACCCCGTGGTTCTTTATCTATTTA 57.435 37.500 0.00 0.00 44.75 1.40
3622 3855 5.446260 ACCCCGTGGTTCTTTATCTATTT 57.554 39.130 0.00 0.00 44.75 1.40
3651 3884 3.964031 ACAACAAGGTGGAAATAGCCAAA 59.036 39.130 0.00 0.00 40.20 3.28
3652 3885 3.320541 CACAACAAGGTGGAAATAGCCAA 59.679 43.478 0.00 0.00 40.20 4.52
3717 3950 3.378427 AGCATAATTTTCGTCCTCAAGCC 59.622 43.478 0.00 0.00 0.00 4.35
3718 3951 4.142600 ACAGCATAATTTTCGTCCTCAAGC 60.143 41.667 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.