Multiple sequence alignment - TraesCS7D01G051200

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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 TraesCS7D01G051200 chr7D 100.000 3309 0 0 1 3309 26719429 26722737 0.000000e+00 6111
1 TraesCS7D01G051200 chr7A 88.335 3069 237 61 3 3007 27095968 27098979 0.000000e+00 3572
2 TraesCS7D01G051200 chr7A 88.364 275 27 2 3038 3307 27098976 27099250 3.180000e-85 326
3 TraesCS7D01G051200 chr4A 91.267 1294 70 19 1603 2877 710743707 710744976 0.000000e+00 1724
4 TraesCS7D01G051200 chr4A 87.807 1304 103 28 3 1259 710741910 710743204 0.000000e+00 1476
5 TraesCS7D01G051200 chr4A 95.482 332 13 2 1286 1615 710743199 710743530 2.260000e-146 529
6 TraesCS7D01G051200 chr4A 80.685 409 38 17 2932 3307 710745447 710745847 2.510000e-71 279


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 TraesCS7D01G051200 chr7D 26719429 26722737 3308 False 6111 6111 100.00000 1 3309 1 chr7D.!!$F1 3308
1 TraesCS7D01G051200 chr7A 27095968 27099250 3282 False 1949 3572 88.34950 3 3307 2 chr7A.!!$F1 3304
2 TraesCS7D01G051200 chr4A 710741910 710745847 3937 False 1002 1724 88.81025 3 3307 4 chr4A.!!$F1 3304

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
655 704 0.029035 GAATTGCTGCAGCCAGATCG 59.971 55.0 34.64 0.0 41.77 3.69 F
1695 2010 0.394565 ACAAGGAGCGAGCAGAGTTT 59.605 50.0 0.00 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 2324 0.172578 TCGTTCTAGCATCACCGGTG 59.827 55.0 29.26 29.26 0.00 4.94 R
3082 3900 0.595588 CAGAGATGGATCCTCGTCGG 59.404 60.0 14.23 3.63 35.88 4.79 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
45 57 3.452474 GTGATCCAGCTAGCTTACACAG 58.548 50.000 16.46 2.06 0.00 3.66
239 281 2.849646 CCCGGGATCCCCTTCTCC 60.850 72.222 25.73 0.00 42.67 3.71
313 356 4.501714 CCGCCGTGCCGTAGCTTA 62.502 66.667 0.00 0.00 40.80 3.09
421 466 2.480244 GCGGCCATGGAAATTTCTCTTC 60.480 50.000 18.40 1.97 0.00 2.87
524 570 7.378966 CACTAGTAATTCTTGGACTCTGTTCA 58.621 38.462 0.00 0.00 0.00 3.18
558 604 2.688958 GTCGGAGGTGCTCTGTATTACT 59.311 50.000 0.00 0.00 38.01 2.24
570 616 1.820519 TGTATTACTGTCGGCGGTTCT 59.179 47.619 6.89 0.00 35.51 3.01
581 627 1.323534 CGGCGGTTCTGATTTTAGTCG 59.676 52.381 0.00 0.00 0.00 4.18
602 651 2.864968 CGTAGTTCTTCGCTGTTAGCT 58.135 47.619 0.00 0.00 39.60 3.32
607 656 0.603065 TCTTCGCTGTTAGCTGCTGA 59.397 50.000 13.43 0.00 39.60 4.26
608 657 0.718343 CTTCGCTGTTAGCTGCTGAC 59.282 55.000 16.74 16.74 39.60 3.51
609 658 0.033366 TTCGCTGTTAGCTGCTGACA 59.967 50.000 23.39 23.39 39.60 3.58
613 662 1.719600 CTGTTAGCTGCTGACAGACC 58.280 55.000 37.02 9.87 46.54 3.85
614 663 1.274728 CTGTTAGCTGCTGACAGACCT 59.725 52.381 37.02 3.24 46.54 3.85
615 664 2.673610 CTGTTAGCTGCTGACAGACCTC 60.674 54.545 37.02 8.55 46.54 3.85
655 704 0.029035 GAATTGCTGCAGCCAGATCG 59.971 55.000 34.64 0.00 41.77 3.69
666 715 2.947652 CAGCCAGATCGAAATTGGATGT 59.052 45.455 17.99 0.00 42.02 3.06
670 719 3.313526 CCAGATCGAAATTGGATGTCACC 59.686 47.826 7.26 0.00 33.76 4.02
694 743 3.541632 GTTGACCTTTGTGTTCCTCTGA 58.458 45.455 0.00 0.00 0.00 3.27
753 810 9.626045 CCTGAATAAAAGTATGAACCAAGAAAC 57.374 33.333 0.00 0.00 0.00 2.78
759 816 7.823745 AAAGTATGAACCAAGAAACAGTCAT 57.176 32.000 0.00 0.00 0.00 3.06
773 830 8.169977 AGAAACAGTCATTTGAGCAATCTTAA 57.830 30.769 0.00 0.00 0.00 1.85
774 831 8.800332 AGAAACAGTCATTTGAGCAATCTTAAT 58.200 29.630 0.00 0.00 0.00 1.40
782 839 9.166173 TCATTTGAGCAATCTTAATATATCCCG 57.834 33.333 0.00 0.00 0.00 5.14
797 854 8.842358 AATATATCCCGTAATTACTGGTTGTG 57.158 34.615 21.32 9.01 33.02 3.33
803 860 5.175859 CCGTAATTACTGGTTGTGTCTGAT 58.824 41.667 13.56 0.00 0.00 2.90
821 878 2.290514 TGATGAGGCTCTGAACCCTTTG 60.291 50.000 16.72 0.00 0.00 2.77
854 915 5.590259 ACCCAGTTCAATATTCAGTATGCAC 59.410 40.000 0.00 0.00 34.76 4.57
876 937 6.543831 GCACTAGAGATTATTGTTGGGTGAAT 59.456 38.462 0.00 0.00 0.00 2.57
880 941 7.865706 AGAGATTATTGTTGGGTGAATACAC 57.134 36.000 0.00 0.00 45.27 2.90
919 986 9.730420 TTTAAGTTCTTGTTTTATGCTTCTGTC 57.270 29.630 0.00 0.00 0.00 3.51
922 989 7.365741 AGTTCTTGTTTTATGCTTCTGTCATG 58.634 34.615 0.00 0.00 0.00 3.07
924 991 7.137490 TCTTGTTTTATGCTTCTGTCATGAG 57.863 36.000 0.00 0.00 0.00 2.90
935 1002 5.395546 GCTTCTGTCATGAGAATCTTCCTCT 60.396 44.000 0.00 0.00 34.92 3.69
947 1014 6.459923 AGAATCTTCCTCTGTTCACTGTTAC 58.540 40.000 0.00 0.00 0.00 2.50
948 1015 5.808366 ATCTTCCTCTGTTCACTGTTACA 57.192 39.130 0.00 0.00 0.00 2.41
950 1017 5.984725 TCTTCCTCTGTTCACTGTTACAAA 58.015 37.500 0.00 0.00 0.00 2.83
964 1045 9.868277 TCACTGTTACAAATTTGAGTTTTTGAT 57.132 25.926 24.64 1.42 36.54 2.57
993 1074 7.807680 ACATTTACTTCTGCAGTTAGTTAAGC 58.192 34.615 22.74 0.00 36.88 3.09
1008 1090 3.689649 AGTTAAGCTACAAAATGGCCTCG 59.310 43.478 3.32 0.00 34.70 4.63
1206 1288 7.811236 CGACTGTTTAAGGTAGAGTGTGAATTA 59.189 37.037 0.00 0.00 0.00 1.40
1266 1350 8.964476 ATCGTATTTTAATCTTGACATGGTCT 57.036 30.769 0.00 0.00 33.15 3.85
1271 1355 6.942532 TTTAATCTTGACATGGTCTATGGC 57.057 37.500 0.00 0.00 45.62 4.40
1276 1360 1.571919 GACATGGTCTATGGCGTCAC 58.428 55.000 0.00 0.00 41.25 3.67
1277 1361 1.137086 GACATGGTCTATGGCGTCACT 59.863 52.381 0.00 0.00 41.25 3.41
1278 1362 1.134699 ACATGGTCTATGGCGTCACTG 60.135 52.381 0.00 0.00 41.25 3.66
1279 1363 1.136891 CATGGTCTATGGCGTCACTGA 59.863 52.381 0.00 0.00 32.95 3.41
1280 1364 1.485124 TGGTCTATGGCGTCACTGAT 58.515 50.000 0.00 0.00 0.00 2.90
1281 1365 1.136891 TGGTCTATGGCGTCACTGATG 59.863 52.381 0.00 0.00 0.00 3.07
1282 1366 1.212616 GTCTATGGCGTCACTGATGC 58.787 55.000 14.03 14.03 43.13 3.91
1283 1367 0.823460 TCTATGGCGTCACTGATGCA 59.177 50.000 22.04 10.62 45.37 3.96
1284 1368 0.933097 CTATGGCGTCACTGATGCAC 59.067 55.000 22.04 13.13 45.37 4.57
1423 1539 3.055819 TGGGAACATAGTCAGCTGAAGAC 60.056 47.826 20.19 6.99 33.60 3.01
1426 1542 3.883830 ACATAGTCAGCTGAAGACAGG 57.116 47.619 20.19 8.02 43.62 4.00
1427 1543 3.435275 ACATAGTCAGCTGAAGACAGGA 58.565 45.455 20.19 0.00 43.62 3.86
1618 1925 8.633561 CCTTATTTATCCCTCCAAAAGTTCATC 58.366 37.037 0.00 0.00 0.00 2.92
1629 1936 8.367156 CCTCCAAAAGTTCATCCAAGAAATTTA 58.633 33.333 3.10 0.00 42.73 1.40
1630 1937 9.415544 CTCCAAAAGTTCATCCAAGAAATTTAG 57.584 33.333 3.10 0.00 42.73 1.85
1695 2010 0.394565 ACAAGGAGCGAGCAGAGTTT 59.605 50.000 0.00 0.00 0.00 2.66
1731 2046 4.978580 GCATTTTATTGCTTTCTCGGATCC 59.021 41.667 0.00 0.00 39.57 3.36
1746 2061 5.057843 TCGGATCCAATACCTGTACTACT 57.942 43.478 13.41 0.00 0.00 2.57
1772 2087 3.650139 TCGAGGTTTGTTGCTTCTCTAC 58.350 45.455 0.00 0.00 0.00 2.59
1784 2099 4.218312 TGCTTCTCTACATGGCTATCTGA 58.782 43.478 0.00 0.00 0.00 3.27
1808 2123 8.816144 TGAAAACTATTTGATTCTGTTTTGTGC 58.184 29.630 6.83 0.00 39.79 4.57
1815 2130 4.401022 TGATTCTGTTTTGTGCCAGATCT 58.599 39.130 0.00 0.00 37.54 2.75
1826 2141 9.503427 GTTTTGTGCCAGATCTTTGTATATTAC 57.497 33.333 0.00 0.00 0.00 1.89
1849 2164 6.180472 ACCTGAAATTAACATCTGATCCGTT 58.820 36.000 0.00 0.00 0.00 4.44
1866 2181 3.068307 TCCGTTCTTCATTCTAGCTAGCC 59.932 47.826 16.35 0.00 0.00 3.93
1934 2249 1.802960 CAAGCACCAAGAGCTGTACAG 59.197 52.381 18.93 18.93 42.53 2.74
1935 2250 1.051812 AGCACCAAGAGCTGTACAGT 58.948 50.000 23.44 10.82 41.61 3.55
1937 2252 1.800805 CACCAAGAGCTGTACAGTGG 58.199 55.000 23.44 22.85 0.00 4.00
1938 2253 1.070758 CACCAAGAGCTGTACAGTGGT 59.929 52.381 23.47 23.47 39.96 4.16
1981 2303 6.349300 ACATGACACATCTCCTGTAATTACC 58.651 40.000 13.01 0.00 35.91 2.85
1991 2313 6.258354 TCTCCTGTAATTACCTCCACTAACA 58.742 40.000 13.01 0.00 0.00 2.41
1994 2316 6.270463 TCCTGTAATTACCTCCACTAACACAA 59.730 38.462 13.01 0.00 0.00 3.33
2002 2324 5.671493 ACCTCCACTAACACAATATACTGC 58.329 41.667 0.00 0.00 0.00 4.40
2148 2470 2.502080 GTCACTCCTCGCGTCACG 60.502 66.667 5.77 0.00 45.62 4.35
2242 2564 3.947910 ATCATTTGTTCAAGCCACCTG 57.052 42.857 0.00 0.00 0.00 4.00
2250 2572 1.593196 TCAAGCCACCTGAAAACTCG 58.407 50.000 0.00 0.00 0.00 4.18
2255 2577 1.531578 GCCACCTGAAAACTCGAGAAC 59.468 52.381 21.68 7.62 0.00 3.01
2378 2700 3.365265 GGTTGCTGTCGCCCCTTG 61.365 66.667 0.00 0.00 34.43 3.61
2380 2702 2.193536 GTTGCTGTCGCCCCTTGTT 61.194 57.895 0.00 0.00 34.43 2.83
2381 2703 2.192861 TTGCTGTCGCCCCTTGTTG 61.193 57.895 0.00 0.00 34.43 3.33
2382 2704 2.594592 GCTGTCGCCCCTTGTTGT 60.595 61.111 0.00 0.00 0.00 3.32
2383 2705 2.617274 GCTGTCGCCCCTTGTTGTC 61.617 63.158 0.00 0.00 0.00 3.18
2384 2706 2.280524 TGTCGCCCCTTGTTGTCG 60.281 61.111 0.00 0.00 0.00 4.35
2385 2707 3.723348 GTCGCCCCTTGTTGTCGC 61.723 66.667 0.00 0.00 0.00 5.19
2386 2708 3.936203 TCGCCCCTTGTTGTCGCT 61.936 61.111 0.00 0.00 0.00 4.93
2387 2709 3.726517 CGCCCCTTGTTGTCGCTG 61.727 66.667 0.00 0.00 0.00 5.18
2388 2710 2.281484 GCCCCTTGTTGTCGCTGA 60.281 61.111 0.00 0.00 0.00 4.26
2389 2711 1.675641 GCCCCTTGTTGTCGCTGAT 60.676 57.895 0.00 0.00 0.00 2.90
2390 2712 0.392461 GCCCCTTGTTGTCGCTGATA 60.392 55.000 0.00 0.00 0.00 2.15
2391 2713 1.369625 CCCCTTGTTGTCGCTGATAC 58.630 55.000 0.00 0.00 0.00 2.24
2414 2736 9.712305 ATACTGATAAGAAATAAATCTGGACCG 57.288 33.333 0.00 0.00 0.00 4.79
2417 2739 8.433421 TGATAAGAAATAAATCTGGACCGAAC 57.567 34.615 0.00 0.00 0.00 3.95
2427 2749 2.260743 GACCGAACTGTCCGTCCC 59.739 66.667 0.00 0.00 0.00 4.46
2428 2750 3.292500 GACCGAACTGTCCGTCCCC 62.293 68.421 0.00 0.00 0.00 4.81
2453 2775 8.197988 CGTAGGATATAACCAAGGATTATTGC 57.802 38.462 1.42 0.00 0.00 3.56
2579 2902 5.232202 CCACTATCATACTACAACTGTTGCG 59.768 44.000 19.82 13.48 0.00 4.85
2673 2996 2.279741 TGATGCGTTAGCTGGATGTTC 58.720 47.619 0.00 0.00 45.42 3.18
2675 2998 2.472695 TGCGTTAGCTGGATGTTCTT 57.527 45.000 0.00 0.00 45.42 2.52
2676 2999 2.346803 TGCGTTAGCTGGATGTTCTTC 58.653 47.619 0.00 0.00 45.42 2.87
2700 3023 9.541143 TTCTTTCTTCTTCTGTTGTTTTTGTTT 57.459 25.926 0.00 0.00 0.00 2.83
2701 3024 8.977505 TCTTTCTTCTTCTGTTGTTTTTGTTTG 58.022 29.630 0.00 0.00 0.00 2.93
2702 3025 8.879342 TTTCTTCTTCTGTTGTTTTTGTTTGA 57.121 26.923 0.00 0.00 0.00 2.69
2705 3028 8.356657 TCTTCTTCTGTTGTTTTTGTTTGAGAA 58.643 29.630 0.00 0.00 0.00 2.87
2794 3117 3.322254 CGTGGGCCTAGTCTAAATGAGAT 59.678 47.826 4.53 0.00 36.29 2.75
2839 3163 4.202305 GCAAAGATATAGTCAGGCAGAGGT 60.202 45.833 0.00 0.00 0.00 3.85
2862 3186 4.677584 TGAAATTTCCACCAGAACAAACG 58.322 39.130 15.48 0.00 32.95 3.60
2877 3201 7.332430 CCAGAACAAACGGTATTATAAGTGTGA 59.668 37.037 6.37 0.00 0.00 3.58
2878 3202 8.714179 CAGAACAAACGGTATTATAAGTGTGAA 58.286 33.333 6.37 0.00 0.00 3.18
2879 3203 9.444600 AGAACAAACGGTATTATAAGTGTGAAT 57.555 29.630 6.37 0.00 0.00 2.57
2880 3204 9.485591 GAACAAACGGTATTATAAGTGTGAATG 57.514 33.333 6.37 0.00 0.00 2.67
2881 3205 7.981142 ACAAACGGTATTATAAGTGTGAATGG 58.019 34.615 6.37 0.00 0.00 3.16
2882 3206 7.825270 ACAAACGGTATTATAAGTGTGAATGGA 59.175 33.333 6.37 0.00 0.00 3.41
2893 3223 5.913137 AGTGTGAATGGAAAACAAACAGA 57.087 34.783 0.00 0.00 0.00 3.41
2898 3228 6.534436 TGTGAATGGAAAACAAACAGAACATG 59.466 34.615 0.00 0.00 0.00 3.21
2949 3709 3.488047 GCAACATCATGAAGGGAATCACG 60.488 47.826 0.00 0.00 30.82 4.35
2950 3710 2.923121 ACATCATGAAGGGAATCACGG 58.077 47.619 0.00 0.00 30.82 4.94
2965 3725 5.357032 GGAATCACGGTATTTTCCAGTTGAT 59.643 40.000 9.70 0.00 38.01 2.57
2970 3730 4.695455 ACGGTATTTTCCAGTTGATGTGAG 59.305 41.667 0.00 0.00 0.00 3.51
2991 3751 5.047377 TGAGTAACAAAATTTGGATGGAGGC 60.047 40.000 10.71 0.00 34.12 4.70
3082 3900 0.539051 CTCCTCATCACCACCACCTC 59.461 60.000 0.00 0.00 0.00 3.85
3086 3904 1.079127 CATCACCACCACCTCCGAC 60.079 63.158 0.00 0.00 0.00 4.79
3115 3940 1.453379 CTCTGCCCTTCTGCCATGG 60.453 63.158 7.63 7.63 0.00 3.66
3143 3968 1.639298 GCTTTCGATCTGCGCAGGTT 61.639 55.000 35.36 23.71 40.61 3.50
3167 3992 2.819595 CGGACCACCTTGCGGATG 60.820 66.667 0.00 0.00 0.00 3.51
3168 3993 2.438434 GGACCACCTTGCGGATGG 60.438 66.667 7.34 7.34 37.44 3.51
3182 4007 0.404040 GGATGGGGAACACTGTTGGA 59.596 55.000 0.00 0.00 0.00 3.53
3188 4013 1.954382 GGGAACACTGTTGGAAAGGAC 59.046 52.381 0.00 0.00 0.00 3.85
3204 4029 5.590663 GGAAAGGACTTCAAAGAACAACTCT 59.409 40.000 0.00 0.00 35.55 3.24
3271 4101 0.681564 ACCTCTCTCTGGCTACACGG 60.682 60.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.932710 GCGATTTGGACAGAGATGTACAA 59.067 43.478 0.00 1.91 40.53 2.41
1 2 3.521560 GCGATTTGGACAGAGATGTACA 58.478 45.455 0.00 0.00 0.00 2.90
16 17 3.813596 GCTGGATCACGGCGATTT 58.186 55.556 16.62 0.00 42.54 2.17
239 281 2.356818 GATCAGGCGAGAAGGACGGG 62.357 65.000 0.00 0.00 0.00 5.28
280 322 3.793888 GGCGGTGGACTTAGGGGG 61.794 72.222 0.00 0.00 0.00 5.40
281 323 4.157120 CGGCGGTGGACTTAGGGG 62.157 72.222 0.00 0.00 0.00 4.79
342 385 4.373116 GACGAGGCCGAACCAGCA 62.373 66.667 0.00 0.00 43.14 4.41
458 504 1.080025 GAGGTCAGTTCGGAACCGG 60.080 63.158 16.84 0.00 40.25 5.28
558 604 2.289195 ACTAAAATCAGAACCGCCGACA 60.289 45.455 0.00 0.00 0.00 4.35
570 616 4.556135 CGAAGAACTACGCGACTAAAATCA 59.444 41.667 15.93 0.00 0.00 2.57
597 646 0.528017 CGAGGTCTGTCAGCAGCTAA 59.472 55.000 0.00 0.00 42.29 3.09
602 651 2.653115 CTGCGAGGTCTGTCAGCA 59.347 61.111 0.00 0.00 36.34 4.41
655 704 1.834188 ACCCGGTGACATCCAATTTC 58.166 50.000 0.00 0.00 0.00 2.17
666 715 0.464735 CACAAAGGTCAACCCGGTGA 60.465 55.000 0.00 0.00 37.02 4.02
670 719 0.666374 GGAACACAAAGGTCAACCCG 59.334 55.000 0.00 0.00 34.85 5.28
694 743 4.610456 CGATTTACACTCGCACATGTTGTT 60.610 41.667 5.49 0.00 0.00 2.83
725 774 7.695055 TCTTGGTTCATACTTTTATTCAGGGA 58.305 34.615 0.00 0.00 0.00 4.20
773 830 7.970102 ACACAACCAGTAATTACGGGATATAT 58.030 34.615 33.04 16.78 43.08 0.86
774 831 7.288389 AGACACAACCAGTAATTACGGGATATA 59.712 37.037 33.04 0.00 43.08 0.86
775 832 6.099269 AGACACAACCAGTAATTACGGGATAT 59.901 38.462 33.04 19.19 43.08 1.63
777 834 4.224370 AGACACAACCAGTAATTACGGGAT 59.776 41.667 33.04 22.73 43.08 3.85
779 836 3.682858 CAGACACAACCAGTAATTACGGG 59.317 47.826 27.13 27.13 45.40 5.28
782 839 6.313905 CCTCATCAGACACAACCAGTAATTAC 59.686 42.308 7.57 7.57 0.00 1.89
787 844 2.028112 GCCTCATCAGACACAACCAGTA 60.028 50.000 0.00 0.00 0.00 2.74
790 847 1.002430 GAGCCTCATCAGACACAACCA 59.998 52.381 0.00 0.00 0.00 3.67
797 854 1.134551 GGGTTCAGAGCCTCATCAGAC 60.135 57.143 2.91 0.00 40.37 3.51
833 890 8.877808 TCTAGTGCATACTGAATATTGAACTG 57.122 34.615 0.00 0.00 37.78 3.16
834 891 8.918116 TCTCTAGTGCATACTGAATATTGAACT 58.082 33.333 0.00 0.00 37.78 3.01
835 892 9.703892 ATCTCTAGTGCATACTGAATATTGAAC 57.296 33.333 0.00 0.00 37.78 3.18
854 915 9.046296 GTGTATTCACCCAACAATAATCTCTAG 57.954 37.037 0.00 0.00 38.51 2.43
866 927 8.073768 CCGAATAATAATGTGTATTCACCCAAC 58.926 37.037 0.00 0.00 43.26 3.77
888 949 7.708998 AGCATAAAACAAGAACTTAAACCGAA 58.291 30.769 0.00 0.00 0.00 4.30
919 986 5.581479 CAGTGAACAGAGGAAGATTCTCATG 59.419 44.000 0.00 0.00 33.92 3.07
922 989 5.146010 ACAGTGAACAGAGGAAGATTCTC 57.854 43.478 0.00 0.00 0.00 2.87
924 991 6.223852 TGTAACAGTGAACAGAGGAAGATTC 58.776 40.000 0.00 0.00 0.00 2.52
935 1002 9.482627 AAAAACTCAAATTTGTAACAGTGAACA 57.517 25.926 17.47 0.00 0.00 3.18
964 1045 8.671384 AACTAACTGCAGAAGTAAATGTTGTA 57.329 30.769 23.35 0.00 38.56 2.41
978 1059 7.023575 CCATTTTGTAGCTTAACTAACTGCAG 58.976 38.462 13.48 13.48 30.90 4.41
993 1074 0.734889 CCAGCGAGGCCATTTTGTAG 59.265 55.000 5.01 0.00 0.00 2.74
1008 1090 2.219325 CTCCTCTGACGGTGTCCAGC 62.219 65.000 0.00 0.00 0.00 4.85
1250 1334 4.100963 ACGCCATAGACCATGTCAAGATTA 59.899 41.667 0.00 0.00 34.60 1.75
1253 1337 1.831106 ACGCCATAGACCATGTCAAGA 59.169 47.619 0.00 0.00 34.60 3.02
1254 1338 2.205074 GACGCCATAGACCATGTCAAG 58.795 52.381 0.00 0.00 34.60 3.02
1255 1339 1.552792 TGACGCCATAGACCATGTCAA 59.447 47.619 0.00 0.00 33.79 3.18
1256 1340 1.134818 GTGACGCCATAGACCATGTCA 60.135 52.381 0.00 0.00 34.60 3.58
1257 1341 1.137086 AGTGACGCCATAGACCATGTC 59.863 52.381 0.00 0.00 32.21 3.06
1258 1342 1.134699 CAGTGACGCCATAGACCATGT 60.135 52.381 0.00 0.00 32.21 3.21
1259 1343 1.136891 TCAGTGACGCCATAGACCATG 59.863 52.381 0.00 0.00 0.00 3.66
1260 1344 1.485124 TCAGTGACGCCATAGACCAT 58.515 50.000 0.00 0.00 0.00 3.55
1261 1345 1.136891 CATCAGTGACGCCATAGACCA 59.863 52.381 0.00 0.00 0.00 4.02
1262 1346 1.858091 CATCAGTGACGCCATAGACC 58.142 55.000 0.00 0.00 0.00 3.85
1263 1347 1.212616 GCATCAGTGACGCCATAGAC 58.787 55.000 0.00 0.00 0.00 2.59
1264 1348 0.823460 TGCATCAGTGACGCCATAGA 59.177 50.000 8.98 0.00 0.00 1.98
1265 1349 0.933097 GTGCATCAGTGACGCCATAG 59.067 55.000 8.98 0.00 0.00 2.23
1266 1350 0.536724 AGTGCATCAGTGACGCCATA 59.463 50.000 8.98 0.00 0.00 2.74
1267 1351 0.536724 TAGTGCATCAGTGACGCCAT 59.463 50.000 8.98 0.00 0.00 4.40
1268 1352 0.536724 ATAGTGCATCAGTGACGCCA 59.463 50.000 8.98 0.00 0.00 5.69
1269 1353 1.328680 CAATAGTGCATCAGTGACGCC 59.671 52.381 8.98 0.07 0.00 5.68
1270 1354 2.270923 TCAATAGTGCATCAGTGACGC 58.729 47.619 3.76 3.76 0.00 5.19
1271 1355 3.246936 CCATCAATAGTGCATCAGTGACG 59.753 47.826 0.00 0.00 0.00 4.35
1272 1356 4.194640 ACCATCAATAGTGCATCAGTGAC 58.805 43.478 0.00 0.00 0.00 3.67
1273 1357 4.492494 ACCATCAATAGTGCATCAGTGA 57.508 40.909 0.00 0.00 0.00 3.41
1274 1358 5.337554 CAAACCATCAATAGTGCATCAGTG 58.662 41.667 0.00 0.00 0.00 3.66
1275 1359 4.142315 GCAAACCATCAATAGTGCATCAGT 60.142 41.667 0.00 0.00 32.29 3.41
1276 1360 4.142337 TGCAAACCATCAATAGTGCATCAG 60.142 41.667 0.00 0.00 37.09 2.90
1277 1361 3.762823 TGCAAACCATCAATAGTGCATCA 59.237 39.130 0.00 0.00 37.09 3.07
1278 1362 4.142315 ACTGCAAACCATCAATAGTGCATC 60.142 41.667 0.00 0.00 40.86 3.91
1279 1363 3.765511 ACTGCAAACCATCAATAGTGCAT 59.234 39.130 0.00 0.00 40.86 3.96
1280 1364 3.156293 ACTGCAAACCATCAATAGTGCA 58.844 40.909 0.00 0.00 39.53 4.57
1281 1365 3.855689 ACTGCAAACCATCAATAGTGC 57.144 42.857 0.00 0.00 0.00 4.40
1282 1366 5.531634 ACAAACTGCAAACCATCAATAGTG 58.468 37.500 0.00 0.00 0.00 2.74
1283 1367 5.789643 ACAAACTGCAAACCATCAATAGT 57.210 34.783 0.00 0.00 0.00 2.12
1284 1368 8.649841 CATTAACAAACTGCAAACCATCAATAG 58.350 33.333 0.00 0.00 0.00 1.73
1444 1560 1.686587 TCGACTGAGGACAGAAAGCAA 59.313 47.619 0.00 0.00 46.03 3.91
1451 1567 1.992880 GCGTTCTTCGACTGAGGACAG 60.993 57.143 0.00 0.00 43.45 3.51
1659 1974 3.129287 CCTTGTTCTGCAGAAACAGTTGT 59.871 43.478 29.99 0.00 38.84 3.32
1695 2010 5.221303 GCAATAAAATGCTATCCTGCCAAGA 60.221 40.000 0.00 0.00 43.06 3.02
1731 2046 7.390996 ACCTCGATGATAGTAGTACAGGTATTG 59.609 40.741 2.52 0.00 0.00 1.90
1746 2061 4.832248 AGAAGCAACAAACCTCGATGATA 58.168 39.130 0.00 0.00 0.00 2.15
1772 2087 9.674824 GAATCAAATAGTTTTCAGATAGCCATG 57.325 33.333 0.00 0.00 0.00 3.66
1784 2099 7.768120 TGGCACAAAACAGAATCAAATAGTTTT 59.232 29.630 0.00 0.00 41.50 2.43
1803 2118 7.498900 CAGGTAATATACAAAGATCTGGCACAA 59.501 37.037 0.00 0.00 38.70 3.33
1826 2141 6.540189 AGAACGGATCAGATGTTAATTTCAGG 59.460 38.462 0.00 0.00 0.00 3.86
1866 2181 2.744768 GGAAAGCCGCTGAAGCTCG 61.745 63.158 0.00 0.00 40.49 5.03
1934 2249 0.735287 GCTCCTACGGTCGAAACCAC 60.735 60.000 0.00 0.00 46.86 4.16
1935 2250 0.896940 AGCTCCTACGGTCGAAACCA 60.897 55.000 0.00 0.00 46.86 3.67
1937 2252 1.068055 TCAAGCTCCTACGGTCGAAAC 60.068 52.381 0.00 0.00 0.00 2.78
1938 2253 1.068055 GTCAAGCTCCTACGGTCGAAA 60.068 52.381 0.00 0.00 0.00 3.46
1951 2273 2.570752 AGGAGATGTGTCATGTCAAGCT 59.429 45.455 8.65 0.00 0.00 3.74
1952 2274 2.676839 CAGGAGATGTGTCATGTCAAGC 59.323 50.000 8.65 0.00 0.00 4.01
1981 2303 5.523916 GGTGCAGTATATTGTGTTAGTGGAG 59.476 44.000 0.00 0.00 0.00 3.86
1991 2313 3.466836 CATCACCGGTGCAGTATATTGT 58.533 45.455 30.25 2.30 0.00 2.71
1994 2316 1.694150 AGCATCACCGGTGCAGTATAT 59.306 47.619 30.25 14.03 44.87 0.86
2002 2324 0.172578 TCGTTCTAGCATCACCGGTG 59.827 55.000 29.26 29.26 0.00 4.94
2154 2476 1.967597 GCGAGCTAGCGAACCCAAAC 61.968 60.000 9.55 0.00 0.00 2.93
2242 2564 6.424207 ACAATAGTTCAGGTTCTCGAGTTTTC 59.576 38.462 13.13 1.25 0.00 2.29
2250 2572 6.072452 CCAAGGAAACAATAGTTCAGGTTCTC 60.072 42.308 0.00 0.00 36.84 2.87
2255 2577 3.826157 TGCCAAGGAAACAATAGTTCAGG 59.174 43.478 0.00 0.00 36.84 3.86
2345 2667 0.820074 AACCGCCGTTTCACCAATCA 60.820 50.000 0.00 0.00 0.00 2.57
2373 2695 2.002586 CAGTATCAGCGACAACAAGGG 58.997 52.381 0.00 0.00 0.00 3.95
2374 2696 2.959516 TCAGTATCAGCGACAACAAGG 58.040 47.619 0.00 0.00 0.00 3.61
2375 2697 6.036470 TCTTATCAGTATCAGCGACAACAAG 58.964 40.000 0.00 0.00 0.00 3.16
2377 2699 5.576447 TCTTATCAGTATCAGCGACAACA 57.424 39.130 0.00 0.00 0.00 3.33
2378 2700 6.887376 TTTCTTATCAGTATCAGCGACAAC 57.113 37.500 0.00 0.00 0.00 3.32
2380 2702 9.764363 ATTTATTTCTTATCAGTATCAGCGACA 57.236 29.630 0.00 0.00 0.00 4.35
2388 2710 9.712305 CGGTCCAGATTTATTTCTTATCAGTAT 57.288 33.333 0.00 0.00 0.00 2.12
2389 2711 8.920174 TCGGTCCAGATTTATTTCTTATCAGTA 58.080 33.333 0.00 0.00 0.00 2.74
2390 2712 7.792032 TCGGTCCAGATTTATTTCTTATCAGT 58.208 34.615 0.00 0.00 0.00 3.41
2391 2713 8.552034 GTTCGGTCCAGATTTATTTCTTATCAG 58.448 37.037 0.00 0.00 0.00 2.90
2427 2749 7.280205 GCAATAATCCTTGGTTATATCCTACGG 59.720 40.741 1.59 0.29 0.00 4.02
2428 2750 8.041323 AGCAATAATCCTTGGTTATATCCTACG 58.959 37.037 1.59 0.00 33.25 3.51
2442 2764 3.028850 AGCATGCACAGCAATAATCCTT 58.971 40.909 21.98 0.00 43.62 3.36
2453 2775 1.809619 GCAATGCCAGCATGCACAG 60.810 57.895 21.98 8.91 45.48 3.66
2673 2996 8.748380 ACAAAAACAACAGAAGAAGAAAGAAG 57.252 30.769 0.00 0.00 0.00 2.85
2675 2998 8.977505 CAAACAAAAACAACAGAAGAAGAAAGA 58.022 29.630 0.00 0.00 0.00 2.52
2676 2999 8.977505 TCAAACAAAAACAACAGAAGAAGAAAG 58.022 29.630 0.00 0.00 0.00 2.62
2820 3143 4.809193 TCAACCTCTGCCTGACTATATCT 58.191 43.478 0.00 0.00 0.00 1.98
2821 3144 5.537300 TTCAACCTCTGCCTGACTATATC 57.463 43.478 0.00 0.00 0.00 1.63
2822 3145 5.957771 TTTCAACCTCTGCCTGACTATAT 57.042 39.130 0.00 0.00 0.00 0.86
2823 3146 5.957771 ATTTCAACCTCTGCCTGACTATA 57.042 39.130 0.00 0.00 0.00 1.31
2824 3147 4.851639 ATTTCAACCTCTGCCTGACTAT 57.148 40.909 0.00 0.00 0.00 2.12
2826 3149 3.515602 AATTTCAACCTCTGCCTGACT 57.484 42.857 0.00 0.00 0.00 3.41
2827 3150 3.057245 GGAAATTTCAACCTCTGCCTGAC 60.057 47.826 19.49 0.00 0.00 3.51
2828 3151 3.157087 GGAAATTTCAACCTCTGCCTGA 58.843 45.455 19.49 0.00 0.00 3.86
2839 3163 5.105752 CGTTTGTTCTGGTGGAAATTTCAA 58.894 37.500 19.49 5.77 35.51 2.69
2877 3201 6.980397 GTCTCATGTTCTGTTTGTTTTCCATT 59.020 34.615 0.00 0.00 0.00 3.16
2878 3202 6.322201 AGTCTCATGTTCTGTTTGTTTTCCAT 59.678 34.615 0.00 0.00 0.00 3.41
2879 3203 5.652014 AGTCTCATGTTCTGTTTGTTTTCCA 59.348 36.000 0.00 0.00 0.00 3.53
2880 3204 5.973565 CAGTCTCATGTTCTGTTTGTTTTCC 59.026 40.000 0.00 0.00 0.00 3.13
2881 3205 5.456822 GCAGTCTCATGTTCTGTTTGTTTTC 59.543 40.000 12.90 0.00 0.00 2.29
2882 3206 5.343249 GCAGTCTCATGTTCTGTTTGTTTT 58.657 37.500 12.90 0.00 0.00 2.43
2893 3223 2.877975 GCCATGGCAGTCTCATGTT 58.122 52.632 32.08 0.00 40.07 2.71
2921 3251 5.840243 TCCCTTCATGATGTTGCTATTTG 57.160 39.130 0.00 0.00 0.00 2.32
2949 3709 7.174253 TGTTACTCACATCAACTGGAAAATACC 59.826 37.037 0.00 0.00 0.00 2.73
2950 3710 8.094798 TGTTACTCACATCAACTGGAAAATAC 57.905 34.615 0.00 0.00 0.00 1.89
2965 3725 6.015519 CCTCCATCCAAATTTTGTTACTCACA 60.016 38.462 8.26 0.00 0.00 3.58
2970 3730 5.170748 CAGCCTCCATCCAAATTTTGTTAC 58.829 41.667 8.26 0.00 0.00 2.50
3031 3849 4.742201 CAGCGGTGGAGGTGTCGG 62.742 72.222 6.74 0.00 35.15 4.79
3061 3879 1.448540 GTGGTGGTGATGAGGAGCG 60.449 63.158 0.00 0.00 0.00 5.03
3067 3885 1.229051 TCGGAGGTGGTGGTGATGA 60.229 57.895 0.00 0.00 0.00 2.92
3082 3900 0.595588 CAGAGATGGATCCTCGTCGG 59.404 60.000 14.23 3.63 35.88 4.79
3086 3904 0.831288 AGGGCAGAGATGGATCCTCG 60.831 60.000 14.23 0.73 35.88 4.63
3115 3940 2.413371 GCAGATCGAAAGCAGTTGGTTC 60.413 50.000 0.00 0.00 34.26 3.62
3167 3992 1.133606 TCCTTTCCAACAGTGTTCCCC 60.134 52.381 5.27 0.00 0.00 4.81
3168 3993 1.954382 GTCCTTTCCAACAGTGTTCCC 59.046 52.381 5.27 0.00 0.00 3.97
3182 4007 5.358160 CCAGAGTTGTTCTTTGAAGTCCTTT 59.642 40.000 0.00 0.00 32.41 3.11
3188 4013 2.614057 ACGCCAGAGTTGTTCTTTGAAG 59.386 45.455 0.00 0.00 32.41 3.02
3271 4101 2.104170 AGCAGAGCAACTACTAGGGTC 58.896 52.381 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.