Multiple sequence alignment - TraesCS2D01G414700

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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 TraesCS2D01G414700 chr2D 100.000 3388 0 0 1 3388 528637199 528640586 0.000000e+00 6257.0
1 TraesCS2D01G414700 chr2D 82.540 378 66 0 1136 1513 587306070 587305693 1.950000e-87 333.0
2 TraesCS2D01G414700 chr2D 79.545 396 75 6 1093 1485 602685965 602686357 9.260000e-71 278.0
3 TraesCS2D01G414700 chr2A 90.757 2564 172 20 860 3381 673344414 673346954 0.000000e+00 3362.0
4 TraesCS2D01G414700 chr2A 83.305 593 55 17 6 589 673328912 673329469 1.080000e-139 507.0
5 TraesCS2D01G414700 chr2A 91.824 159 9 2 687 842 673344266 673344423 5.690000e-53 219.0
6 TraesCS2D01G414700 chr2A 95.652 115 3 1 585 697 673344131 673344245 2.080000e-42 183.0
7 TraesCS2D01G414700 chr3A 83.663 1414 187 21 1045 2428 486223418 486222019 0.000000e+00 1291.0
8 TraesCS2D01G414700 chr2B 86.195 565 37 19 1 552 627075059 627075595 1.050000e-159 573.0
9 TraesCS2D01G414700 chr2B 83.554 377 62 0 1136 1512 709999907 709999531 1.500000e-93 353.0
10 TraesCS2D01G414700 chr2B 79.319 411 79 6 1078 1485 733047918 733048325 1.990000e-72 283.0
11 TraesCS2D01G414700 chr2B 77.011 261 51 6 1105 1365 790850224 790850475 1.270000e-29 141.0
12 TraesCS2D01G414700 chr5B 81.440 361 65 2 1156 1515 708954037 708954396 9.190000e-76 294.0
13 TraesCS2D01G414700 chr3B 100.000 28 0 0 1460 1487 48885545 48885518 6.000000e-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 TraesCS2D01G414700 chr2D 528637199 528640586 3387 False 6257.000000 6257 100.000000 1 3388 1 chr2D.!!$F1 3387
1 TraesCS2D01G414700 chr2A 673344131 673346954 2823 False 1254.666667 3362 92.744333 585 3381 3 chr2A.!!$F2 2796
2 TraesCS2D01G414700 chr2A 673328912 673329469 557 False 507.000000 507 83.305000 6 589 1 chr2A.!!$F1 583
3 TraesCS2D01G414700 chr3A 486222019 486223418 1399 True 1291.000000 1291 83.663000 1045 2428 1 chr3A.!!$R1 1383
4 TraesCS2D01G414700 chr2B 627075059 627075595 536 False 573.000000 573 86.195000 1 552 1 chr2B.!!$F1 551

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
448 481 0.169672 CTTTCATGCGCTGGACTTGG 59.830 55.0 9.73 0.00 0.00 3.61 F
827 904 0.876342 GGCCTAATCGCTTGACCTCG 60.876 60.0 0.00 0.00 0.00 4.63 F
1555 1642 0.455815 GACCATCAACGAAATGGCCC 59.544 55.0 0.00 4.82 46.38 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1623 0.455815 GGGCCATTTCGTTGATGGTC 59.544 55.0 4.39 11.46 46.22 4.02 R
1668 1758 0.613260 TCCATTGACGGTCCTTGGAG 59.387 55.0 19.48 2.65 32.80 3.86 R
3043 3162 1.006832 GCTTCTAAAATCTGCGCCGA 58.993 50.0 4.18 3.73 0.00 5.54 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
127 129 0.240145 TGCACTAGACAGTTCGACGG 59.760 55.000 0.00 0.00 30.46 4.79
128 130 0.520404 GCACTAGACAGTTCGACGGA 59.480 55.000 0.00 0.00 30.46 4.69
129 131 1.466024 GCACTAGACAGTTCGACGGAG 60.466 57.143 0.00 0.00 30.46 4.63
130 132 1.130749 CACTAGACAGTTCGACGGAGG 59.869 57.143 0.00 0.00 30.46 4.30
139 141 3.450115 CGACGGAGGGAGGGTCAC 61.450 72.222 0.00 0.00 0.00 3.67
168 175 1.509548 ATGTCTGGGTGGAAAGGGGG 61.510 60.000 0.00 0.00 0.00 5.40
175 182 1.485124 GGTGGAAAGGGGGCTAAATG 58.515 55.000 0.00 0.00 0.00 2.32
178 185 1.078656 TGGAAAGGGGGCTAAATGCTT 59.921 47.619 0.00 0.00 42.39 3.91
307 315 3.493129 TCACTTATGCATATTTCGTCGGC 59.507 43.478 7.36 0.00 0.00 5.54
312 320 0.229753 GCATATTTCGTCGGCACTCG 59.770 55.000 0.00 0.00 40.90 4.18
325 333 3.057526 TCGGCACTCGTAGATGATAATGG 60.058 47.826 0.00 0.00 40.32 3.16
328 336 3.611766 GCACTCGTAGATGATAATGGCGA 60.612 47.826 0.00 0.00 33.89 5.54
331 339 3.511699 TCGTAGATGATAATGGCGATGC 58.488 45.455 0.00 0.00 0.00 3.91
332 340 2.279921 CGTAGATGATAATGGCGATGCG 59.720 50.000 0.00 0.00 0.00 4.73
396 429 4.450976 TGGTTGATGAATAATCCACTCCG 58.549 43.478 0.00 0.00 32.66 4.63
401 434 3.159353 TGAATAATCCACTCCGTCACG 57.841 47.619 0.00 0.00 0.00 4.35
417 450 4.022242 CCGTCACGGGATAATCATAAGAGT 60.022 45.833 8.94 0.00 44.15 3.24
418 451 5.509163 CCGTCACGGGATAATCATAAGAGTT 60.509 44.000 8.94 0.00 44.15 3.01
419 452 5.983720 CGTCACGGGATAATCATAAGAGTTT 59.016 40.000 0.00 0.00 0.00 2.66
448 481 0.169672 CTTTCATGCGCTGGACTTGG 59.830 55.000 9.73 0.00 0.00 3.61
546 587 2.032634 GCGCTCCGGAATGTTCACA 61.033 57.895 5.23 0.00 0.00 3.58
567 608 2.298446 AGCATCCACTATCTGATCGGTG 59.702 50.000 13.34 13.34 0.00 4.94
683 726 6.039270 TGTGACGAAAGGTGATTTTGATTCTT 59.961 34.615 0.00 0.00 36.01 2.52
715 789 1.118838 CTTTTGGGTGTGCCAAAGGA 58.881 50.000 0.00 0.00 38.21 3.36
748 822 2.807108 GCGGGCTTTCTACCTTATCCTG 60.807 54.545 0.00 0.00 0.00 3.86
755 829 3.130734 TCTACCTTATCCTGGTGGCTT 57.869 47.619 0.00 0.00 38.42 4.35
821 898 1.518572 ACGTCGGCCTAATCGCTTG 60.519 57.895 0.00 0.00 0.00 4.01
823 900 1.480219 CGTCGGCCTAATCGCTTGAC 61.480 60.000 0.00 0.00 33.58 3.18
827 904 0.876342 GGCCTAATCGCTTGACCTCG 60.876 60.000 0.00 0.00 0.00 4.63
856 933 6.850752 AAAAACAGAGGGTTCTCAAAAAGA 57.149 33.333 0.00 0.00 42.34 2.52
857 934 6.850752 AAAACAGAGGGTTCTCAAAAAGAA 57.149 33.333 0.00 0.00 42.34 2.52
858 935 6.850752 AAACAGAGGGTTCTCAAAAAGAAA 57.149 33.333 0.00 0.00 45.50 2.52
859 936 6.850752 AACAGAGGGTTCTCAAAAAGAAAA 57.149 33.333 0.00 0.00 45.50 2.29
860 937 6.850752 ACAGAGGGTTCTCAAAAAGAAAAA 57.149 33.333 0.00 0.00 45.50 1.94
914 991 3.211288 CGTCTTCCCGCTGGATCT 58.789 61.111 0.00 0.00 41.40 2.75
924 1001 2.890109 GCTGGATCTGCGGCGATTG 61.890 63.158 12.98 0.00 0.00 2.67
979 1063 4.675029 CGTCTTTGGGTCGCCGGT 62.675 66.667 1.90 0.00 0.00 5.28
986 1070 4.462280 GGGTCGCCGGTAGGTTGG 62.462 72.222 1.90 0.00 40.50 3.77
1011 1095 2.106074 GGCGCCAATGTCGTCATCA 61.106 57.895 24.80 0.00 32.56 3.07
1018 1102 1.004610 CAATGTCGTCATCACCGATGC 60.005 52.381 0.00 0.00 39.63 3.91
1218 1305 3.114616 CACTGGCGGTCAAGCTCG 61.115 66.667 0.00 0.00 37.29 5.03
1219 1306 3.616721 ACTGGCGGTCAAGCTCGT 61.617 61.111 0.00 0.00 37.29 4.18
1223 1310 2.095252 GGCGGTCAAGCTCGTTCTC 61.095 63.158 0.00 0.00 37.29 2.87
1358 1445 4.003788 CAACCTCTCCACCGGCGT 62.004 66.667 6.01 0.00 0.00 5.68
1410 1497 2.179517 CACTGCGTCCTCGACTCC 59.820 66.667 0.00 0.00 39.71 3.85
1479 1566 2.359975 CTTCACCCCTTCACCGGC 60.360 66.667 0.00 0.00 0.00 6.13
1532 1619 2.005960 CTACGTCTTCCCGGAGCCAG 62.006 65.000 0.73 0.00 30.93 4.85
1534 1621 3.394836 GTCTTCCCGGAGCCAGCT 61.395 66.667 0.73 0.00 0.00 4.24
1535 1622 2.607750 TCTTCCCGGAGCCAGCTT 60.608 61.111 0.73 0.00 0.00 3.74
1536 1623 2.437359 CTTCCCGGAGCCAGCTTG 60.437 66.667 0.73 0.00 0.00 4.01
1545 1632 0.807496 GAGCCAGCTTGACCATCAAC 59.193 55.000 0.00 0.00 32.21 3.18
1555 1642 0.455815 GACCATCAACGAAATGGCCC 59.544 55.000 0.00 4.82 46.38 5.80
1599 1686 1.405121 GCCACCTCCGTTAGTGTTAGG 60.405 57.143 0.00 0.00 31.88 2.69
1608 1695 2.741878 CGTTAGTGTTAGGGCAGATGGG 60.742 54.545 0.00 0.00 0.00 4.00
1630 1720 5.185454 GGGTCATCACTGTCATGATTGTAA 58.815 41.667 0.00 0.00 37.20 2.41
1669 1759 3.652581 GCCTTTGCTACCTCCAACT 57.347 52.632 0.00 0.00 33.53 3.16
1670 1760 1.454201 GCCTTTGCTACCTCCAACTC 58.546 55.000 0.00 0.00 33.53 3.01
1671 1761 1.950954 GCCTTTGCTACCTCCAACTCC 60.951 57.143 0.00 0.00 33.53 3.85
1672 1762 1.351017 CCTTTGCTACCTCCAACTCCA 59.649 52.381 0.00 0.00 0.00 3.86
1673 1763 2.224769 CCTTTGCTACCTCCAACTCCAA 60.225 50.000 0.00 0.00 0.00 3.53
1679 1769 1.296715 CCTCCAACTCCAAGGACCG 59.703 63.158 0.00 0.00 31.44 4.79
1758 1848 4.013267 AGGCAAGCTATACATGATGGAC 57.987 45.455 0.00 0.00 0.00 4.02
1760 1850 3.750130 GGCAAGCTATACATGATGGACAG 59.250 47.826 0.00 0.00 0.00 3.51
1815 1905 1.945394 CAGATTTTCCAGATCAGCCCG 59.055 52.381 0.00 0.00 0.00 6.13
1839 1929 2.737180 CACGAGGGGATGGGATCG 59.263 66.667 0.00 0.00 40.86 3.69
1938 2028 2.428890 ACAATGTGACTCGGAGATCCTC 59.571 50.000 12.86 0.00 33.89 3.71
1952 2042 4.527038 GGAGATCCTCGTGATTGGGTATAA 59.473 45.833 0.00 0.00 32.41 0.98
1968 2058 5.662208 TGGGTATAAGGACGGATTCTTTACA 59.338 40.000 0.00 0.00 29.08 2.41
1999 2089 3.576648 GTTTACAGACTCTCCGACCTTG 58.423 50.000 0.00 0.00 0.00 3.61
2001 2091 1.705873 ACAGACTCTCCGACCTTGTT 58.294 50.000 0.00 0.00 0.00 2.83
2046 2136 6.710597 ACTAGTATCGAAGGCAATGTTCTA 57.289 37.500 0.00 0.00 0.00 2.10
2074 2164 2.746362 GCTGAAAGGATTCTGAGTGTGG 59.254 50.000 0.41 0.00 36.82 4.17
2163 2253 3.094386 GGAATGCCGCCTCAATACA 57.906 52.632 0.00 0.00 0.00 2.29
2191 2281 0.179045 GTTACAGGCAGCGGATGGAT 60.179 55.000 0.00 0.00 0.00 3.41
2202 2292 0.456824 CGGATGGATGTATCGCGAGG 60.457 60.000 16.66 0.00 0.00 4.63
2206 2296 1.682740 TGGATGTATCGCGAGGTGTA 58.317 50.000 16.66 0.00 0.00 2.90
2285 2375 6.605471 TTCTTGGTGAGCTAACTATTCTCA 57.395 37.500 0.00 0.00 34.78 3.27
2420 2536 0.546747 CCAGGGGGTAAGTCTGACCA 60.547 60.000 8.77 0.00 38.86 4.02
2430 2546 4.323562 GGTAAGTCTGACCAGCAATACCTT 60.324 45.833 3.76 0.00 36.91 3.50
2442 2558 6.318900 ACCAGCAATACCTTTTATTCTAGTGC 59.681 38.462 0.00 0.00 31.85 4.40
2443 2559 6.318648 CCAGCAATACCTTTTATTCTAGTGCA 59.681 38.462 0.00 0.00 33.66 4.57
2444 2560 7.189512 CAGCAATACCTTTTATTCTAGTGCAC 58.810 38.462 9.40 9.40 33.66 4.57
2445 2561 6.037172 AGCAATACCTTTTATTCTAGTGCACG 59.963 38.462 12.01 0.00 33.66 5.34
2446 2562 5.986004 ATACCTTTTATTCTAGTGCACGC 57.014 39.130 12.01 0.00 0.00 5.34
2447 2563 3.670625 ACCTTTTATTCTAGTGCACGCA 58.329 40.909 12.01 2.31 0.00 5.24
2448 2564 4.261801 ACCTTTTATTCTAGTGCACGCAT 58.738 39.130 12.01 4.86 0.00 4.73
2449 2565 4.700213 ACCTTTTATTCTAGTGCACGCATT 59.300 37.500 12.01 0.00 0.00 3.56
2474 2590 4.630644 TTCTCTTTCCACTTCTGCTGAT 57.369 40.909 0.00 0.00 0.00 2.90
2554 2670 7.925043 TGGAAGTAATAAAATCGGCTACAAA 57.075 32.000 0.00 0.00 0.00 2.83
2562 2678 8.474006 AATAAAATCGGCTACAAACCAAAATC 57.526 30.769 0.00 0.00 0.00 2.17
2568 2684 4.215399 CGGCTACAAACCAAAATCAGAGAA 59.785 41.667 0.00 0.00 0.00 2.87
2649 2765 7.913821 CAGATTTTGAGATGTGTGACATATTGG 59.086 37.037 0.00 0.00 39.27 3.16
2668 2784 4.669206 TGGCACTCAAATTCACAAACAT 57.331 36.364 0.00 0.00 0.00 2.71
2681 2797 3.882888 TCACAAACATTTCTGGACCAGAC 59.117 43.478 24.24 0.00 40.46 3.51
2693 2809 7.496346 TTCTGGACCAGACAGTTCTTATATT 57.504 36.000 24.24 0.00 40.46 1.28
2723 2839 9.768662 ATAGTTTTCTTGACAAATGCTGAAAAT 57.231 25.926 12.62 7.24 36.34 1.82
2724 2840 8.496707 AGTTTTCTTGACAAATGCTGAAAATT 57.503 26.923 12.62 8.00 36.34 1.82
2732 2848 9.469807 TTGACAAATGCTGAAAATTATTACGTT 57.530 25.926 0.00 0.00 0.00 3.99
2740 2856 7.380065 TGCTGAAAATTATTACGTTTGGTTGTC 59.620 33.333 0.00 0.00 0.00 3.18
2742 2858 8.563289 TGAAAATTATTACGTTTGGTTGTCAC 57.437 30.769 0.00 0.00 0.00 3.67
2956 3075 3.567164 CGGCATTTGAGCTTGAATATCCT 59.433 43.478 0.00 0.00 34.17 3.24
2976 3095 3.624861 CCTGTTCACTCAATACCAGATGC 59.375 47.826 0.00 0.00 0.00 3.91
2987 3106 7.776969 ACTCAATACCAGATGCTGTATCAAAAT 59.223 33.333 8.45 0.00 38.31 1.82
3010 3129 4.391155 AGTAGTATTTCCACCAACGCAAA 58.609 39.130 0.00 0.00 0.00 3.68
3012 3131 4.864704 AGTATTTCCACCAACGCAAATT 57.135 36.364 0.00 0.00 0.00 1.82
3013 3132 5.968528 AGTATTTCCACCAACGCAAATTA 57.031 34.783 0.00 0.00 0.00 1.40
3014 3133 6.334102 AGTATTTCCACCAACGCAAATTAA 57.666 33.333 0.00 0.00 0.00 1.40
3027 3146 8.110002 CCAACGCAAATTAAATGATTTCTTAGC 58.890 33.333 0.00 0.00 0.00 3.09
3053 3172 1.209128 CGTATTTTCTCGGCGCAGAT 58.791 50.000 11.52 0.00 0.00 2.90
3127 3246 5.907197 TCTTCTTCTTTTGCAGTTACTCG 57.093 39.130 0.00 0.00 0.00 4.18
3133 3252 4.385825 TCTTTTGCAGTTACTCGGATTGT 58.614 39.130 0.00 0.00 0.00 2.71
3136 3255 4.481930 TTGCAGTTACTCGGATTGTTTG 57.518 40.909 0.00 0.00 0.00 2.93
3161 3281 5.499139 TTTTGACATGTTCTCTTTTCGCT 57.501 34.783 0.00 0.00 0.00 4.93
3178 3298 3.325870 TCGCTAGGCATAAATGATTCCG 58.674 45.455 0.00 0.00 0.00 4.30
3186 3306 3.793129 GCATAAATGATTCCGCACCACAG 60.793 47.826 0.00 0.00 0.00 3.66
3203 3323 2.202623 GTGGTAGTCGCTGCCTCG 60.203 66.667 13.26 0.00 37.16 4.63
3207 3327 3.826754 TAGTCGCTGCCTCGCTGG 61.827 66.667 0.00 0.00 39.35 4.85
3225 3345 2.490903 CTGGCTTTCCTCTCCATTGTTG 59.509 50.000 0.00 0.00 0.00 3.33
3233 3353 2.439409 CTCTCCATTGTTGCCATCACA 58.561 47.619 0.00 0.00 0.00 3.58
3263 3383 8.762645 AGGAGATGAGTCTTATTTGTTGACATA 58.237 33.333 0.00 0.00 33.97 2.29
3303 3423 7.523293 TTCCTTATGTTCTCATTGCTTTGAA 57.477 32.000 0.00 0.00 35.70 2.69
3305 3425 7.370383 TCCTTATGTTCTCATTGCTTTGAAAC 58.630 34.615 0.00 0.00 35.70 2.78
3309 3429 4.278170 TGTTCTCATTGCTTTGAAACGGAT 59.722 37.500 0.00 0.00 0.00 4.18
3353 3473 8.762481 TTATTCTACCTTCATGTACTGCTAGA 57.238 34.615 0.00 0.00 0.00 2.43
3356 3476 8.941995 TTCTACCTTCATGTACTGCTAGATAT 57.058 34.615 0.00 0.00 0.00 1.63
3357 3477 8.941995 TCTACCTTCATGTACTGCTAGATATT 57.058 34.615 0.00 0.00 0.00 1.28
3377 3497 2.880963 ACCTCTTCTAGATTGCTCGC 57.119 50.000 0.00 0.00 0.00 5.03
3381 3501 1.543941 CTTCTAGATTGCTCGCCGCG 61.544 60.000 6.39 6.39 43.27 6.46
3382 3502 2.278857 CTAGATTGCTCGCCGCGT 60.279 61.111 13.39 0.00 43.27 6.01
3383 3503 2.278596 TAGATTGCTCGCCGCGTC 60.279 61.111 13.39 6.75 43.27 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.751166 ATCAGCACACACTAGACACC 57.249 50.000 0.00 0.00 0.00 4.16
65 66 1.369689 CAGCTGTGAAGCAACACGC 60.370 57.895 5.25 15.64 42.86 5.34
127 129 3.391382 CACCGGTGACCCTCCCTC 61.391 72.222 31.31 0.00 0.00 4.30
128 130 3.923645 TCACCGGTGACCCTCCCT 61.924 66.667 33.23 0.00 34.14 4.20
139 141 2.815211 CCAGACATGCGTCACCGG 60.815 66.667 0.00 0.00 45.23 5.28
175 182 1.425428 CGACAGATTGCGGGAAAGC 59.575 57.895 0.00 0.00 37.71 3.51
178 185 1.741401 CTGCGACAGATTGCGGGAA 60.741 57.895 1.18 0.00 37.89 3.97
280 287 8.279800 CCGACGAAATATGCATAAGTGAATTAA 58.720 33.333 11.13 0.00 0.00 1.40
292 299 1.286501 GAGTGCCGACGAAATATGCA 58.713 50.000 0.00 0.00 0.00 3.96
307 315 4.160736 TCGCCATTATCATCTACGAGTG 57.839 45.455 0.00 0.00 0.00 3.51
312 320 3.914555 CGCATCGCCATTATCATCTAC 57.085 47.619 0.00 0.00 0.00 2.59
331 339 3.423154 GAACTGGCTTCACCCGCG 61.423 66.667 0.00 0.00 37.83 6.46
332 340 1.452145 TTTGAACTGGCTTCACCCGC 61.452 55.000 0.00 0.00 38.70 6.13
333 341 1.028905 TTTTGAACTGGCTTCACCCG 58.971 50.000 0.00 0.00 38.70 5.28
339 347 5.418840 TGTTCTCTTCTTTTTGAACTGGCTT 59.581 36.000 0.00 0.00 39.38 4.35
340 348 4.949856 TGTTCTCTTCTTTTTGAACTGGCT 59.050 37.500 0.00 0.00 39.38 4.75
396 429 7.630924 CAAAACTCTTATGATTATCCCGTGAC 58.369 38.462 0.00 0.00 0.00 3.67
401 434 6.564125 CGTCGCAAAACTCTTATGATTATCCC 60.564 42.308 0.00 0.00 0.00 3.85
413 446 1.003866 GAAAGCACGTCGCAAAACTCT 60.004 47.619 11.58 0.00 46.13 3.24
417 450 1.752753 CATGAAAGCACGTCGCAAAA 58.247 45.000 11.58 0.00 46.13 2.44
418 451 0.660005 GCATGAAAGCACGTCGCAAA 60.660 50.000 11.58 0.00 46.13 3.68
419 452 1.082169 GCATGAAAGCACGTCGCAA 60.082 52.632 11.58 0.00 46.13 4.85
534 575 1.131126 GTGGATGCTGTGAACATTCCG 59.869 52.381 0.00 0.00 0.00 4.30
546 587 2.298446 CACCGATCAGATAGTGGATGCT 59.702 50.000 5.46 0.00 0.00 3.79
567 608 3.912745 TTTTCCCCGCTTCGGCTCC 62.913 63.158 0.00 0.00 46.86 4.70
628 669 2.360475 GGTGTCCAAGCCCTCAGC 60.360 66.667 0.00 0.00 44.25 4.26
683 726 3.574826 CACCCAAAAGTCCGGGAAAATAA 59.425 43.478 0.00 0.00 46.34 1.40
715 789 1.441732 AAGCCCGCGAAAACGTTCTT 61.442 50.000 8.23 0.00 0.00 2.52
748 822 3.435186 GCGCTGGAAGAAGCCACC 61.435 66.667 0.00 0.00 40.23 4.61
802 876 1.518572 AAGCGATTAGGCCGACGTG 60.519 57.895 0.00 0.00 0.00 4.49
804 878 1.226859 TCAAGCGATTAGGCCGACG 60.227 57.895 0.00 3.17 0.00 5.12
860 937 8.718158 AAGGAATGAAAGGATTCTCTCTTTTT 57.282 30.769 0.00 0.00 33.66 1.94
861 938 8.718158 AAAGGAATGAAAGGATTCTCTCTTTT 57.282 30.769 0.00 0.00 36.00 2.27
862 939 8.718158 AAAAGGAATGAAAGGATTCTCTCTTT 57.282 30.769 0.00 0.00 36.48 2.52
863 940 8.718158 AAAAAGGAATGAAAGGATTCTCTCTT 57.282 30.769 0.00 0.00 36.48 2.85
932 1009 2.153247 GCGATCTTTGTATCGGCTAACG 59.847 50.000 8.18 0.00 46.89 3.18
945 1022 2.202837 GGCGTACCGGCGATCTTT 60.203 61.111 9.30 0.00 43.33 2.52
979 1063 4.408821 CGCCCAGCAGCCAACCTA 62.409 66.667 0.00 0.00 0.00 3.08
1000 1084 0.175531 TGCATCGGTGATGACGACAT 59.824 50.000 10.81 0.00 42.09 3.06
1001 1085 0.735978 GTGCATCGGTGATGACGACA 60.736 55.000 10.81 0.00 42.09 4.35
1098 1185 2.997897 AGAGACGCCCACCCAGAC 60.998 66.667 0.00 0.00 0.00 3.51
1242 1329 3.803082 TAGAACCGCGGGTCGACG 61.803 66.667 35.83 6.09 41.67 5.12
1358 1445 4.819761 GCAGGCAGCGGACGATGA 62.820 66.667 14.59 0.00 32.62 2.92
1410 1497 2.436292 AGGAGGAGACCGTCGACG 60.436 66.667 30.33 30.33 39.44 5.12
1479 1566 1.811266 CGGGAGGTCTGCAATGTCG 60.811 63.158 0.00 0.00 0.00 4.35
1513 1600 2.005960 CTGGCTCCGGGAAGACGTAG 62.006 65.000 0.00 0.00 0.00 3.51
1515 1602 3.382832 CTGGCTCCGGGAAGACGT 61.383 66.667 0.00 0.00 0.00 4.34
1532 1619 2.867429 CCATTTCGTTGATGGTCAAGC 58.133 47.619 6.37 0.00 37.00 4.01
1534 1621 1.543802 GGCCATTTCGTTGATGGTCAA 59.456 47.619 0.00 0.00 46.21 3.18
1535 1622 1.173043 GGCCATTTCGTTGATGGTCA 58.827 50.000 0.00 0.00 46.21 4.02
1536 1623 0.455815 GGGCCATTTCGTTGATGGTC 59.544 55.000 4.39 11.46 46.22 4.02
1545 1632 4.841861 TACGCCCGGGCCATTTCG 62.842 66.667 39.24 25.89 37.98 3.46
1555 1642 3.302870 CCGATGTTTCTAAAATACGCCCG 60.303 47.826 0.00 0.00 0.00 6.13
1608 1695 6.932356 ATTACAATCATGACAGTGATGACC 57.068 37.500 4.65 0.00 38.76 4.02
1668 1758 0.613260 TCCATTGACGGTCCTTGGAG 59.387 55.000 19.48 2.65 32.80 3.86
1669 1759 1.060729 TTCCATTGACGGTCCTTGGA 58.939 50.000 19.48 19.48 34.74 3.53
1670 1760 1.745087 CATTCCATTGACGGTCCTTGG 59.255 52.381 16.32 16.32 0.00 3.61
1671 1761 2.436417 ACATTCCATTGACGGTCCTTG 58.564 47.619 5.55 3.24 0.00 3.61
1672 1762 2.879103 ACATTCCATTGACGGTCCTT 57.121 45.000 5.55 0.00 0.00 3.36
1673 1763 2.618045 GGAACATTCCATTGACGGTCCT 60.618 50.000 5.55 0.00 46.76 3.85
1697 1787 0.779997 AATTGGTGGGAGCTTCCAGT 59.220 50.000 16.30 0.00 38.64 4.00
1758 1848 0.874390 CGGTGTCAAATGTGGGACTG 59.126 55.000 0.00 0.00 35.11 3.51
1760 1850 1.001815 CAACGGTGTCAAATGTGGGAC 60.002 52.381 0.00 0.00 34.63 4.46
1938 2028 2.363038 TCCGTCCTTATACCCAATCACG 59.637 50.000 0.00 0.00 0.00 4.35
1952 2042 2.027469 GGGTGTGTAAAGAATCCGTCCT 60.027 50.000 0.00 0.00 0.00 3.85
1999 2089 2.011540 GGGACGATCCTGTCAAGAAC 57.988 55.000 0.00 0.00 40.72 3.01
2046 2136 5.950549 ACTCAGAATCCTTTCAGCAATGAAT 59.049 36.000 0.00 0.00 34.08 2.57
2163 2253 1.611673 GCTGCCTGTAACCATGTGTCT 60.612 52.381 0.00 0.00 0.00 3.41
2191 2281 4.913345 CGATAAATTACACCTCGCGATACA 59.087 41.667 10.36 0.00 0.00 2.29
2202 2292 5.050295 GCTGTAAGGCCTCGATAAATTACAC 60.050 44.000 5.23 0.28 31.75 2.90
2420 2536 6.037172 CGTGCACTAGAATAAAAGGTATTGCT 59.963 38.462 16.19 0.00 0.00 3.91
2430 2546 4.513442 AGGAATGCGTGCACTAGAATAAA 58.487 39.130 16.19 0.00 0.00 1.40
2442 2558 2.813754 TGGAAAGAGAAAGGAATGCGTG 59.186 45.455 0.00 0.00 0.00 5.34
2443 2559 2.814336 GTGGAAAGAGAAAGGAATGCGT 59.186 45.455 0.00 0.00 0.00 5.24
2444 2560 3.077359 AGTGGAAAGAGAAAGGAATGCG 58.923 45.455 0.00 0.00 0.00 4.73
2445 2561 4.764308 AGAAGTGGAAAGAGAAAGGAATGC 59.236 41.667 0.00 0.00 0.00 3.56
2446 2562 5.335504 GCAGAAGTGGAAAGAGAAAGGAATG 60.336 44.000 0.00 0.00 0.00 2.67
2447 2563 4.764308 GCAGAAGTGGAAAGAGAAAGGAAT 59.236 41.667 0.00 0.00 0.00 3.01
2448 2564 4.137543 GCAGAAGTGGAAAGAGAAAGGAA 58.862 43.478 0.00 0.00 0.00 3.36
2449 2565 3.392616 AGCAGAAGTGGAAAGAGAAAGGA 59.607 43.478 0.00 0.00 0.00 3.36
2474 2590 2.561209 TAAGGCTGGGTAGTGGATCA 57.439 50.000 0.00 0.00 0.00 2.92
2513 2629 8.718102 TTACTTCCATGTAAGCTAAGACAATC 57.282 34.615 0.00 0.00 0.00 2.67
2579 2695 2.826488 AGGCCGGCTCTCTGATTATAT 58.174 47.619 28.56 0.00 0.00 0.86
2580 2696 2.310779 AGGCCGGCTCTCTGATTATA 57.689 50.000 28.56 0.00 0.00 0.98
2594 2710 2.351726 CGAAAGGTCAAAGATAAGGCCG 59.648 50.000 0.00 0.00 0.00 6.13
2595 2711 3.344515 ACGAAAGGTCAAAGATAAGGCC 58.655 45.455 0.00 0.00 0.00 5.19
2649 2765 6.292488 CCAGAAATGTTTGTGAATTTGAGTGC 60.292 38.462 4.40 0.00 33.69 4.40
2652 2768 6.421801 GGTCCAGAAATGTTTGTGAATTTGAG 59.578 38.462 4.40 0.00 33.69 3.02
2668 2784 5.825593 ATAAGAACTGTCTGGTCCAGAAA 57.174 39.130 23.49 17.40 42.46 2.52
2693 2809 8.845227 TCAGCATTTGTCAAGAAAACTATGTAA 58.155 29.630 0.00 0.00 0.00 2.41
2723 2839 7.783090 TGTAAGTGACAACCAAACGTAATAA 57.217 32.000 0.00 0.00 34.15 1.40
2724 2840 7.783090 TTGTAAGTGACAACCAAACGTAATA 57.217 32.000 0.00 0.00 43.30 0.98
2759 2875 6.604795 AGGTTGATTGCAGAGCATAAGTTAAT 59.395 34.615 0.00 0.00 38.76 1.40
2760 2876 5.945784 AGGTTGATTGCAGAGCATAAGTTAA 59.054 36.000 0.00 0.00 38.76 2.01
2901 3019 4.800249 GCTCAAATGCATTTCCCTGTGAAA 60.800 41.667 21.70 0.00 46.54 2.69
2932 3050 1.180029 ATTCAAGCTCAAATGCCGCT 58.820 45.000 0.00 0.00 35.09 5.52
2933 3051 2.849880 TATTCAAGCTCAAATGCCGC 57.150 45.000 0.00 0.00 0.00 6.53
2956 3075 4.256110 CAGCATCTGGTATTGAGTGAACA 58.744 43.478 0.00 0.00 0.00 3.18
2987 3106 4.804868 TGCGTTGGTGGAAATACTACTA 57.195 40.909 0.00 0.00 0.00 1.82
3027 3146 3.779992 GCGCCGAGAAAATACGTGTAAAG 60.780 47.826 0.00 0.00 0.00 1.85
3035 3154 3.675467 AAATCTGCGCCGAGAAAATAC 57.325 42.857 4.18 0.00 0.00 1.89
3043 3162 1.006832 GCTTCTAAAATCTGCGCCGA 58.993 50.000 4.18 3.73 0.00 5.54
3127 3246 5.989551 ACATGTCAAAAAGCAAACAATCC 57.010 34.783 0.00 0.00 0.00 3.01
3133 3252 7.201427 CGAAAAGAGAACATGTCAAAAAGCAAA 60.201 33.333 0.00 0.00 0.00 3.68
3136 3255 5.331830 GCGAAAAGAGAACATGTCAAAAAGC 60.332 40.000 0.00 0.00 0.00 3.51
3161 3281 3.146066 GGTGCGGAATCATTTATGCCTA 58.854 45.455 0.00 0.00 29.51 3.93
3186 3306 2.202623 CGAGGCAGCGACTACCAC 60.203 66.667 0.00 0.00 0.00 4.16
3203 3323 1.101331 CAATGGAGAGGAAAGCCAGC 58.899 55.000 0.00 0.00 34.74 4.85
3207 3327 1.203287 GGCAACAATGGAGAGGAAAGC 59.797 52.381 0.00 0.00 0.00 3.51
3225 3345 3.204526 CTCATCTCCTTTCTGTGATGGC 58.795 50.000 0.00 0.00 37.48 4.40
3233 3353 8.378565 TCAACAAATAAGACTCATCTCCTTTCT 58.621 33.333 0.00 0.00 32.34 2.52
3276 3396 7.867403 TCAAAGCAATGAGAACATAAGGAAAAC 59.133 33.333 0.00 0.00 35.50 2.43
3281 3401 6.306356 CGTTTCAAAGCAATGAGAACATAAGG 59.694 38.462 12.50 0.00 35.50 2.69
3303 3423 4.853924 AGCAAATGAGAAAACATCCGTT 57.146 36.364 0.00 0.00 36.73 4.44
3305 3425 7.816945 AATTTAGCAAATGAGAAAACATCCG 57.183 32.000 0.00 0.00 0.00 4.18
3343 3463 9.947433 TCTAGAAGAGGTAATATCTAGCAGTAC 57.053 37.037 0.00 0.00 40.63 2.73
3353 3473 6.350612 GGCGAGCAATCTAGAAGAGGTAATAT 60.351 42.308 0.00 0.00 0.00 1.28
3356 3476 3.068307 GGCGAGCAATCTAGAAGAGGTAA 59.932 47.826 0.00 0.00 0.00 2.85
3357 3477 2.623889 GGCGAGCAATCTAGAAGAGGTA 59.376 50.000 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.