Multiple sequence alignment - TraesCS5A01G205600

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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 TraesCS5A01G205600 chr5A 100.000 3787 0 0 1 3787 415353204 415356990 0.000000e+00 6994.0
1 TraesCS5A01G205600 chr5A 91.222 581 50 1 45 625 693447544 693448123 0.000000e+00 789.0
2 TraesCS5A01G205600 chr5A 80.305 721 128 11 1714 2428 415430659 415431371 2.000000e-147 532.0
3 TraesCS5A01G205600 chr5B 92.944 1474 61 15 1389 2854 369154694 369153256 0.000000e+00 2106.0
4 TraesCS5A01G205600 chr5B 93.340 946 44 8 2848 3786 369151841 369150908 0.000000e+00 1380.0
5 TraesCS5A01G205600 chr5B 91.006 656 26 10 665 1290 369156022 369155370 0.000000e+00 854.0
6 TraesCS5A01G205600 chr5B 80.055 727 118 20 1714 2428 368786934 368786223 7.250000e-142 514.0
7 TraesCS5A01G205600 chr5D 96.401 1278 30 5 1578 2854 319138657 319137395 0.000000e+00 2091.0
8 TraesCS5A01G205600 chr5D 90.909 748 36 13 3047 3786 319136796 319136073 0.000000e+00 976.0
9 TraesCS5A01G205600 chr5D 88.694 743 47 12 619 1328 319140763 319140025 0.000000e+00 872.0
10 TraesCS5A01G205600 chr5D 89.317 571 48 8 54 623 297174328 297173770 0.000000e+00 704.0
11 TraesCS5A01G205600 chr5D 79.778 722 129 14 1714 2428 318934036 318933325 3.370000e-140 508.0
12 TraesCS5A01G205600 chr5D 82.556 579 59 18 52 621 404477367 404477912 4.430000e-129 472.0
13 TraesCS5A01G205600 chr5D 96.244 213 7 1 2848 3059 319137282 319137070 7.790000e-92 348.0
14 TraesCS5A01G205600 chr5D 90.625 128 6 5 1405 1532 319139307 319139186 8.420000e-37 165.0
15 TraesCS5A01G205600 chr2B 91.366 637 46 3 4 639 82360333 82359705 0.000000e+00 863.0
16 TraesCS5A01G205600 chr4A 92.028 577 45 1 45 621 99037212 99037787 0.000000e+00 809.0
17 TraesCS5A01G205600 chr7A 81.515 871 153 5 1907 2776 138012319 138011456 0.000000e+00 710.0
18 TraesCS5A01G205600 chr7D 81.379 870 153 7 1907 2775 138086557 138085696 0.000000e+00 701.0
19 TraesCS5A01G205600 chr7D 76.483 489 103 11 1907 2392 487739248 487739727 4.850000e-64 255.0
20 TraesCS5A01G205600 chr1B 86.400 500 58 7 118 616 50781645 50781155 4.300000e-149 538.0
21 TraesCS5A01G205600 chr1B 95.652 46 2 0 516 561 680984176 680984131 1.460000e-09 75.0
22 TraesCS5A01G205600 chr4D 85.799 507 55 11 119 623 153908849 153908358 4.330000e-144 521.0
23 TraesCS5A01G205600 chr1A 83.333 480 56 16 52 521 490410843 490411308 4.520000e-114 422.0
24 TraesCS5A01G205600 chr6B 89.324 281 27 3 52 329 96452521 96452241 2.160000e-92 350.0
25 TraesCS5A01G205600 chr6B 100.000 30 0 0 2954 2983 515183756 515183727 5.280000e-04 56.5
26 TraesCS5A01G205600 chr2A 76.471 578 113 17 1904 2471 678721069 678720505 3.700000e-75 292.0
27 TraesCS5A01G205600 chr6D 92.308 39 3 0 2945 2983 311302367 311302405 5.280000e-04 56.5


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 TraesCS5A01G205600 chr5A 415353204 415356990 3786 False 6994.000000 6994 100.0000 1 3787 1 chr5A.!!$F1 3786
1 TraesCS5A01G205600 chr5A 693447544 693448123 579 False 789.000000 789 91.2220 45 625 1 chr5A.!!$F3 580
2 TraesCS5A01G205600 chr5A 415430659 415431371 712 False 532.000000 532 80.3050 1714 2428 1 chr5A.!!$F2 714
3 TraesCS5A01G205600 chr5B 369150908 369156022 5114 True 1446.666667 2106 92.4300 665 3786 3 chr5B.!!$R2 3121
4 TraesCS5A01G205600 chr5B 368786223 368786934 711 True 514.000000 514 80.0550 1714 2428 1 chr5B.!!$R1 714
5 TraesCS5A01G205600 chr5D 319136073 319140763 4690 True 890.400000 2091 92.5746 619 3786 5 chr5D.!!$R3 3167
6 TraesCS5A01G205600 chr5D 297173770 297174328 558 True 704.000000 704 89.3170 54 623 1 chr5D.!!$R1 569
7 TraesCS5A01G205600 chr5D 318933325 318934036 711 True 508.000000 508 79.7780 1714 2428 1 chr5D.!!$R2 714
8 TraesCS5A01G205600 chr5D 404477367 404477912 545 False 472.000000 472 82.5560 52 621 1 chr5D.!!$F1 569
9 TraesCS5A01G205600 chr2B 82359705 82360333 628 True 863.000000 863 91.3660 4 639 1 chr2B.!!$R1 635
10 TraesCS5A01G205600 chr4A 99037212 99037787 575 False 809.000000 809 92.0280 45 621 1 chr4A.!!$F1 576
11 TraesCS5A01G205600 chr7A 138011456 138012319 863 True 710.000000 710 81.5150 1907 2776 1 chr7A.!!$R1 869
12 TraesCS5A01G205600 chr7D 138085696 138086557 861 True 701.000000 701 81.3790 1907 2775 1 chr7D.!!$R1 868
13 TraesCS5A01G205600 chr2A 678720505 678721069 564 True 292.000000 292 76.4710 1904 2471 1 chr2A.!!$R1 567

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
893 934 0.394565 AGCTCCACAACAGTCACTCC 59.605 55.0 0.00 0.0 0.00 3.85 F
1698 3242 0.036952 AGCTGGTGGAGTCATTGACG 60.037 55.0 11.01 0.0 37.67 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 4356 1.153086 GGCCATTCCAGCTCACGAT 60.153 57.895 0.0 0.0 34.01 3.73 R
2814 4390 1.911464 GCCGAAGAAAATTAACGCAGC 59.089 47.619 0.0 0.0 0.00 5.25 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
98 99 4.329545 GGTTGAGGTGGCCGAGCA 62.330 66.667 0.00 0.00 0.00 4.26
246 256 2.815945 CGGATGGATCTGGCTGGCT 61.816 63.158 2.00 0.00 0.00 4.75
439 450 3.720106 GACACGAGCGAGCGACGAT 62.720 63.158 19.45 0.00 45.46 3.73
458 469 2.074230 TAGCGTCCGTGTTTGTCCGT 62.074 55.000 0.00 0.00 0.00 4.69
589 600 0.963225 TGTCCGGATGACTCAAACGA 59.037 50.000 7.81 0.00 44.75 3.85
633 644 4.187694 GAGTTGCTCTAACAATCCCTGAG 58.812 47.826 0.00 0.00 41.88 3.35
637 648 4.353777 TGCTCTAACAATCCCTGAGTAGT 58.646 43.478 0.00 0.00 0.00 2.73
645 656 6.487299 ACAATCCCTGAGTAGTTATCCTTC 57.513 41.667 0.00 0.00 0.00 3.46
741 752 2.033299 TCGCTTTTCCTTTGCTGTCTTG 59.967 45.455 0.00 0.00 0.00 3.02
855 891 0.924090 GACCAATAAGCTCGCGAGTG 59.076 55.000 34.46 24.14 0.00 3.51
893 934 0.394565 AGCTCCACAACAGTCACTCC 59.605 55.000 0.00 0.00 0.00 3.85
897 938 0.469917 CCACAACAGTCACTCCCAGT 59.530 55.000 0.00 0.00 0.00 4.00
907 948 2.029470 GTCACTCCCAGTCTCACTCAAG 60.029 54.545 0.00 0.00 0.00 3.02
927 968 0.482446 TTCCTGCTCACCACCCAAAT 59.518 50.000 0.00 0.00 0.00 2.32
979 1023 3.325870 GTCATCAAACATCTCGTCACCA 58.674 45.455 0.00 0.00 0.00 4.17
1021 1065 1.199789 TGTCGCATCATTTTCACCTGC 59.800 47.619 0.00 0.00 0.00 4.85
1025 1069 1.621107 CATCATTTTCACCTGCGCAC 58.379 50.000 5.66 0.00 0.00 5.34
1046 1090 0.903454 TCGGTTCTTCCCCTGTCCTC 60.903 60.000 0.00 0.00 0.00 3.71
1085 1129 4.137872 CCGGTTCTCGCCCGCTAA 62.138 66.667 0.00 0.00 44.13 3.09
1086 1130 2.106332 CGGTTCTCGCCCGCTAAT 59.894 61.111 0.00 0.00 38.85 1.73
1087 1131 1.361271 CGGTTCTCGCCCGCTAATA 59.639 57.895 0.00 0.00 38.85 0.98
1100 1144 1.539157 GCTAATAAGCCCAGGCATCC 58.461 55.000 12.03 0.00 43.40 3.51
1141 1185 4.753877 CTGCGTCGCCGTCGAGAA 62.754 66.667 15.88 0.00 46.46 2.87
1151 1195 4.373116 GTCGAGAACCCTGCGGCA 62.373 66.667 1.29 1.29 0.00 5.69
1287 1331 0.861837 CAAGAAGGTGCGTGTCAGAC 59.138 55.000 0.00 0.00 0.00 3.51
1290 1334 1.560860 GAAGGTGCGTGTCAGACTGC 61.561 60.000 10.43 10.43 0.00 4.40
1293 1337 2.658268 TGCGTGTCAGACTGCGTG 60.658 61.111 15.81 0.00 0.00 5.34
1295 1339 2.932083 GCGTGTCAGACTGCGTGTG 61.932 63.158 15.81 0.53 0.00 3.82
1297 1341 1.540607 CGTGTCAGACTGCGTGTGTC 61.541 60.000 1.31 0.00 34.88 3.67
1310 1354 4.773117 GTGTCCGTCCTCGCCGTC 62.773 72.222 0.00 0.00 35.54 4.79
1333 1751 2.351726 GCGAGTTCATCTGCCGTTTTAT 59.648 45.455 0.00 0.00 0.00 1.40
1337 1755 5.046910 AGTTCATCTGCCGTTTTATGTTG 57.953 39.130 0.00 0.00 0.00 3.33
1368 1792 2.287308 CGGCACACTCTGCTAGAGATAC 60.287 54.545 16.81 6.16 45.07 2.24
1389 1813 8.967918 AGATACACAGTTGCTAGTTAATGAGTA 58.032 33.333 0.00 0.00 0.00 2.59
1390 1814 9.751542 GATACACAGTTGCTAGTTAATGAGTAT 57.248 33.333 12.58 12.58 30.55 2.12
1394 1818 9.025020 CACAGTTGCTAGTTAATGAGTATAGTG 57.975 37.037 0.00 0.00 0.00 2.74
1431 2441 3.123621 CGTGAATGTTACAGCTTGAGTCC 59.876 47.826 0.00 0.00 0.00 3.85
1436 2447 7.222999 GTGAATGTTACAGCTTGAGTCCTATAC 59.777 40.741 0.00 0.00 0.00 1.47
1440 2451 7.446769 TGTTACAGCTTGAGTCCTATACAAAA 58.553 34.615 0.00 0.00 0.00 2.44
1452 2471 9.397280 GAGTCCTATACAAAAATAAAGAAGGCT 57.603 33.333 0.00 0.00 0.00 4.58
1481 2500 3.412981 TCAACACACATGGACAAAACG 57.587 42.857 0.00 0.00 0.00 3.60
1482 2501 2.750166 TCAACACACATGGACAAAACGT 59.250 40.909 0.00 0.00 0.00 3.99
1483 2502 3.191581 TCAACACACATGGACAAAACGTT 59.808 39.130 0.00 0.00 0.00 3.99
1484 2503 3.859411 ACACACATGGACAAAACGTTT 57.141 38.095 7.96 7.96 0.00 3.60
1487 2506 3.790820 CACACATGGACAAAACGTTTCTG 59.209 43.478 15.01 15.95 0.00 3.02
1493 2512 7.062371 CACATGGACAAAACGTTTCTGTTTTTA 59.938 33.333 15.01 8.78 46.84 1.52
1494 2513 7.274686 ACATGGACAAAACGTTTCTGTTTTTAG 59.725 33.333 15.01 12.08 46.84 1.85
1548 3083 6.994992 GTTTTCTACGATTTTGGTTGCAAAA 58.005 32.000 0.00 0.00 38.26 2.44
1549 3084 7.457060 GTTTTCTACGATTTTGGTTGCAAAAA 58.543 30.769 0.00 0.00 37.55 1.94
1550 3085 7.778470 TTTCTACGATTTTGGTTGCAAAAAT 57.222 28.000 0.00 3.75 39.36 1.82
1551 3086 8.873215 TTTCTACGATTTTGGTTGCAAAAATA 57.127 26.923 0.00 0.00 37.35 1.40
1552 3087 9.482627 TTTCTACGATTTTGGTTGCAAAAATAT 57.517 25.926 0.00 0.00 37.35 1.28
1553 3088 9.482627 TTCTACGATTTTGGTTGCAAAAATATT 57.517 25.926 0.00 0.00 37.35 1.28
1554 3089 9.482627 TCTACGATTTTGGTTGCAAAAATATTT 57.517 25.926 0.00 0.00 37.35 1.40
1585 3129 6.287107 AGTGAAATGTTTAGTGTTCAGACG 57.713 37.500 0.00 0.00 30.94 4.18
1596 3140 5.007385 AGTGTTCAGACGTCTTAAGTTGT 57.993 39.130 17.26 2.24 0.00 3.32
1612 3156 4.096732 AGTTGTTTGCACTTGACAGAAC 57.903 40.909 0.00 0.00 0.00 3.01
1617 3161 2.820059 TGCACTTGACAGAACGAGAT 57.180 45.000 0.00 0.00 0.00 2.75
1618 3162 3.934457 TGCACTTGACAGAACGAGATA 57.066 42.857 0.00 0.00 0.00 1.98
1619 3163 3.575630 TGCACTTGACAGAACGAGATAC 58.424 45.455 0.00 0.00 0.00 2.24
1635 3179 5.159399 GAGATACTACTCGTCTTGTGGTC 57.841 47.826 0.00 0.00 31.74 4.02
1641 3185 0.249322 CTCGTCTTGTGGTCGTGGTT 60.249 55.000 0.00 0.00 0.00 3.67
1656 3200 2.407090 GTGGTTCTTTGCTGAATTGCC 58.593 47.619 0.00 0.00 0.00 4.52
1673 3217 1.524482 CCCTGTTCAGCTAGGAGGC 59.476 63.158 1.53 0.00 36.11 4.70
1698 3242 0.036952 AGCTGGTGGAGTCATTGACG 60.037 55.000 11.01 0.00 37.67 4.35
1704 3248 2.740447 GGTGGAGTCATTGACGGTTAAC 59.260 50.000 11.01 0.00 37.67 2.01
1850 3422 5.221966 CCGGGTAATTAAATCCCTCCACATA 60.222 44.000 7.78 0.00 39.10 2.29
1896 3469 2.437281 ACTGGAGTGAGATAATGGCCTG 59.563 50.000 3.32 0.00 0.00 4.85
1897 3470 1.770658 TGGAGTGAGATAATGGCCTGG 59.229 52.381 3.32 0.00 0.00 4.45
1898 3471 1.072965 GGAGTGAGATAATGGCCTGGG 59.927 57.143 3.32 0.00 0.00 4.45
1899 3472 0.475906 AGTGAGATAATGGCCTGGGC 59.524 55.000 14.23 14.23 41.06 5.36
1900 3473 0.183492 GTGAGATAATGGCCTGGGCA 59.817 55.000 26.08 26.08 44.11 5.36
2795 4371 2.349590 TCAACATCGTGAGCTGGAATG 58.650 47.619 0.00 0.00 0.00 2.67
2810 4386 2.042297 TGGAATGGCCACCTTGTTGATA 59.958 45.455 8.16 0.00 43.33 2.15
2811 4387 2.427095 GGAATGGCCACCTTGTTGATAC 59.573 50.000 8.16 0.00 36.34 2.24
2813 4389 4.523083 GAATGGCCACCTTGTTGATACTA 58.477 43.478 8.16 0.00 0.00 1.82
2814 4390 3.627395 TGGCCACCTTGTTGATACTAG 57.373 47.619 0.00 0.00 0.00 2.57
2815 4391 2.289565 GGCCACCTTGTTGATACTAGC 58.710 52.381 0.00 0.00 0.00 3.42
2827 4403 7.372451 TGTTGATACTAGCTGCGTTAATTTT 57.628 32.000 0.00 0.00 0.00 1.82
2953 5951 3.254470 TCGCATATCAGGTTTCGGAAA 57.746 42.857 0.00 0.00 0.00 3.13
3065 6349 5.647658 TCTTCAATACCGAGCATGAAACAAT 59.352 36.000 0.00 0.00 31.94 2.71
3074 6358 4.330894 CGAGCATGAAACAATTGAGCTAGA 59.669 41.667 13.59 0.00 0.00 2.43
3091 6375 7.671302 TGAGCTAGACTTTTGAAGAGTAACAT 58.329 34.615 0.00 0.00 0.00 2.71
3138 6422 0.804364 TCATTCAGACATTGCGCCAC 59.196 50.000 4.18 0.00 0.00 5.01
3140 6424 1.133598 CATTCAGACATTGCGCCACAT 59.866 47.619 4.18 0.00 0.00 3.21
3143 6427 0.455464 CAGACATTGCGCCACATGTG 60.455 55.000 19.31 19.31 0.00 3.21
3152 6436 1.020861 CGCCACATGTGCAGCTCTAA 61.021 55.000 20.81 0.00 0.00 2.10
3153 6437 0.731417 GCCACATGTGCAGCTCTAAG 59.269 55.000 20.81 4.52 0.00 2.18
3154 6438 1.947678 GCCACATGTGCAGCTCTAAGT 60.948 52.381 20.81 0.00 0.00 2.24
3155 6439 2.430465 CCACATGTGCAGCTCTAAGTT 58.570 47.619 20.81 0.00 0.00 2.66
3156 6440 3.599343 CCACATGTGCAGCTCTAAGTTA 58.401 45.455 20.81 0.00 0.00 2.24
3157 6441 3.372206 CCACATGTGCAGCTCTAAGTTAC 59.628 47.826 20.81 0.00 0.00 2.50
3227 6515 3.018423 ACCACAAGAAATATCCCAGCC 57.982 47.619 0.00 0.00 0.00 4.85
3442 6730 5.466393 ACATGCAAAAATCTGCCAAAGTTAC 59.534 36.000 0.00 0.00 41.90 2.50
3453 6741 4.270834 TGCCAAAGTTACACAACACCTAA 58.729 39.130 0.00 0.00 37.10 2.69
3460 6748 5.357257 AGTTACACAACACCTAACACTGAG 58.643 41.667 0.00 0.00 37.10 3.35
3576 6867 3.377573 AGGCATTTCCAAAGCATATGGT 58.622 40.909 0.40 0.40 39.09 3.55
3587 6878 1.072173 AGCATATGGTGATTAGCGGCA 59.928 47.619 6.62 0.00 0.00 5.69
3588 6879 1.197721 GCATATGGTGATTAGCGGCAC 59.802 52.381 4.56 0.00 0.00 5.01
3590 6881 2.700722 TATGGTGATTAGCGGCACAA 57.299 45.000 1.45 0.00 36.76 3.33
3591 6882 2.057137 ATGGTGATTAGCGGCACAAT 57.943 45.000 1.45 0.67 36.76 2.71
3592 6883 2.700722 TGGTGATTAGCGGCACAATA 57.299 45.000 1.45 0.00 36.76 1.90
3593 6884 2.285083 TGGTGATTAGCGGCACAATAC 58.715 47.619 1.45 0.00 36.76 1.89
3597 6888 3.001330 GTGATTAGCGGCACAATACTGAC 59.999 47.826 1.45 0.00 35.19 3.51
3611 6902 7.063456 CACAATACTGACTGTAAAACTGAACG 58.937 38.462 0.00 0.00 34.45 3.95
3643 6934 8.821147 TGTAGAAGAGTTGAACGCTTATAAAA 57.179 30.769 15.68 6.81 38.34 1.52
3698 6989 6.287107 AGACAACATTCTTGTACAACTTCG 57.713 37.500 3.59 0.00 34.06 3.79
3717 7008 7.972832 ACTTCGTTTAAGATTTATGTGTCCA 57.027 32.000 0.00 0.00 38.67 4.02
3786 7077 7.922699 AAGAAGATAAGAAGGGTAGCATAGT 57.077 36.000 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.383527 CGAGACCGGAGCAAACAGC 61.384 63.158 9.46 0.00 46.19 4.40
25 26 2.243957 CGCTCGACCACAACAAGCA 61.244 57.895 0.00 0.00 33.21 3.91
77 78 3.322466 CGGCCACCTCAACCTCCT 61.322 66.667 2.24 0.00 0.00 3.69
84 85 4.100084 CCATGCTCGGCCACCTCA 62.100 66.667 2.24 0.00 0.00 3.86
341 352 4.918360 AGCCTCCCACCACCACCA 62.918 66.667 0.00 0.00 0.00 4.17
439 450 1.372004 CGGACAAACACGGACGCTA 60.372 57.895 0.00 0.00 0.00 4.26
557 568 0.035056 CCGGACAGAAAAGATGGCCT 60.035 55.000 3.32 0.00 44.37 5.19
589 600 3.891366 CCAAGGGAGAGACACATTTTGTT 59.109 43.478 0.00 0.00 39.17 2.83
645 656 8.642908 TGTTACCATGATTTGATAGTAGTTCG 57.357 34.615 0.00 0.00 0.00 3.95
716 727 1.021968 AGCAAAGGAAAAGCGACGTT 58.978 45.000 0.00 0.00 0.00 3.99
741 752 6.331061 ACCAGAAACAAGAGTATCGTATGTC 58.669 40.000 0.00 0.00 42.67 3.06
859 895 4.247612 GCTAGCTGCGCATGTGCC 62.248 66.667 27.42 13.66 37.91 5.01
893 934 2.869636 GCAGGAACTTGAGTGAGACTGG 60.870 54.545 0.00 0.00 34.60 4.00
897 938 2.036475 GTGAGCAGGAACTTGAGTGAGA 59.964 50.000 0.00 0.00 34.60 3.27
907 948 0.467290 TTTGGGTGGTGAGCAGGAAC 60.467 55.000 0.00 0.00 0.00 3.62
927 968 1.728068 TTTTGGTGCGCGCTAGATAA 58.272 45.000 33.29 17.45 0.00 1.75
998 1042 2.424601 AGGTGAAAATGATGCGACATGG 59.575 45.455 0.00 0.00 0.00 3.66
1021 1065 2.434359 GGGAAGAACCGAGGTGCG 60.434 66.667 0.00 0.00 40.11 5.34
1025 1069 1.597461 GACAGGGGAAGAACCGAGG 59.403 63.158 0.00 0.00 40.11 4.63
1084 1128 1.151450 CCGGATGCCTGGGCTTATT 59.849 57.895 13.05 0.00 42.51 1.40
1085 1129 2.839098 CCGGATGCCTGGGCTTAT 59.161 61.111 13.05 0.00 42.51 1.73
1086 1130 4.189580 GCCGGATGCCTGGGCTTA 62.190 66.667 5.05 0.00 43.52 3.09
1287 1331 2.430921 GAGGACGGACACACGCAG 60.431 66.667 0.00 0.00 37.37 5.18
1293 1337 4.773117 GACGGCGAGGACGGACAC 62.773 72.222 16.62 0.00 39.02 3.67
1295 1339 4.477975 CAGACGGCGAGGACGGAC 62.478 72.222 16.62 0.00 39.02 4.79
1310 1354 1.016130 AACGGCAGATGAACTCGCAG 61.016 55.000 0.00 0.00 0.00 5.18
1311 1355 0.602638 AAACGGCAGATGAACTCGCA 60.603 50.000 0.00 0.00 0.00 5.10
1313 1357 3.370978 ACATAAAACGGCAGATGAACTCG 59.629 43.478 0.00 0.00 0.00 4.18
1314 1358 4.946784 ACATAAAACGGCAGATGAACTC 57.053 40.909 0.00 0.00 0.00 3.01
1368 1792 9.025020 CACTATACTCATTAACTAGCAACTGTG 57.975 37.037 0.00 0.00 0.00 3.66
1389 1813 6.820335 TCACGAAATCATCTGATTCCACTAT 58.180 36.000 5.92 0.00 43.41 2.12
1390 1814 6.220726 TCACGAAATCATCTGATTCCACTA 57.779 37.500 5.92 0.00 43.41 2.74
1394 1818 6.369059 ACATTCACGAAATCATCTGATTCC 57.631 37.500 5.92 0.00 43.41 3.01
1403 2200 5.468409 TCAAGCTGTAACATTCACGAAATCA 59.532 36.000 0.00 0.00 0.00 2.57
1452 2471 7.809546 TGTCCATGTGTGTTGATAACTTTTA 57.190 32.000 0.00 0.00 0.00 1.52
1487 2506 8.878769 ACATTTTGTCCATGTGTTTCTAAAAAC 58.121 29.630 0.00 0.00 44.18 2.43
1493 2512 9.260002 GATTTAACATTTTGTCCATGTGTTTCT 57.740 29.630 1.54 0.00 34.97 2.52
1494 2513 9.039870 TGATTTAACATTTTGTCCATGTGTTTC 57.960 29.630 1.54 0.00 34.97 2.78
1551 3086 9.927668 CACTAAACATTTCACTATCCCAAAAAT 57.072 29.630 0.00 0.00 0.00 1.82
1552 3087 8.919145 ACACTAAACATTTCACTATCCCAAAAA 58.081 29.630 0.00 0.00 0.00 1.94
1553 3088 8.472007 ACACTAAACATTTCACTATCCCAAAA 57.528 30.769 0.00 0.00 0.00 2.44
1554 3089 8.472007 AACACTAAACATTTCACTATCCCAAA 57.528 30.769 0.00 0.00 0.00 3.28
1555 3090 7.721842 TGAACACTAAACATTTCACTATCCCAA 59.278 33.333 0.00 0.00 0.00 4.12
1556 3091 7.227873 TGAACACTAAACATTTCACTATCCCA 58.772 34.615 0.00 0.00 0.00 4.37
1557 3092 7.606456 TCTGAACACTAAACATTTCACTATCCC 59.394 37.037 0.00 0.00 0.00 3.85
1558 3093 8.443937 GTCTGAACACTAAACATTTCACTATCC 58.556 37.037 0.00 0.00 0.00 2.59
1559 3094 8.162880 CGTCTGAACACTAAACATTTCACTATC 58.837 37.037 0.00 0.00 0.00 2.08
1560 3095 7.656137 ACGTCTGAACACTAAACATTTCACTAT 59.344 33.333 0.00 0.00 0.00 2.12
1561 3096 6.982141 ACGTCTGAACACTAAACATTTCACTA 59.018 34.615 0.00 0.00 0.00 2.74
1562 3097 5.815740 ACGTCTGAACACTAAACATTTCACT 59.184 36.000 0.00 0.00 0.00 3.41
1563 3098 6.018994 AGACGTCTGAACACTAAACATTTCAC 60.019 38.462 19.30 0.00 0.00 3.18
1564 3099 6.046593 AGACGTCTGAACACTAAACATTTCA 58.953 36.000 19.30 0.00 0.00 2.69
1565 3100 6.526566 AGACGTCTGAACACTAAACATTTC 57.473 37.500 19.30 0.00 0.00 2.17
1566 3101 6.920569 AAGACGTCTGAACACTAAACATTT 57.079 33.333 20.85 0.00 0.00 2.32
1567 3102 7.709613 ACTTAAGACGTCTGAACACTAAACATT 59.290 33.333 20.85 0.00 0.00 2.71
1568 3103 7.208080 ACTTAAGACGTCTGAACACTAAACAT 58.792 34.615 20.85 0.34 0.00 2.71
1569 3104 6.567050 ACTTAAGACGTCTGAACACTAAACA 58.433 36.000 20.85 0.00 0.00 2.83
1570 3105 7.009907 ACAACTTAAGACGTCTGAACACTAAAC 59.990 37.037 20.85 0.00 0.00 2.01
1571 3106 7.037438 ACAACTTAAGACGTCTGAACACTAAA 58.963 34.615 20.85 3.22 0.00 1.85
1572 3107 6.567050 ACAACTTAAGACGTCTGAACACTAA 58.433 36.000 20.85 11.55 0.00 2.24
1573 3108 6.140303 ACAACTTAAGACGTCTGAACACTA 57.860 37.500 20.85 3.31 0.00 2.74
1574 3109 5.007385 ACAACTTAAGACGTCTGAACACT 57.993 39.130 20.85 4.44 0.00 3.55
1575 3110 5.713822 AACAACTTAAGACGTCTGAACAC 57.286 39.130 20.85 0.00 0.00 3.32
1576 3111 5.446741 GCAAACAACTTAAGACGTCTGAACA 60.447 40.000 20.85 1.86 0.00 3.18
1585 3129 5.636837 TGTCAAGTGCAAACAACTTAAGAC 58.363 37.500 10.09 0.00 0.00 3.01
1596 3140 2.899976 TCTCGTTCTGTCAAGTGCAAA 58.100 42.857 0.00 0.00 0.00 3.68
1617 3161 2.481568 CACGACCACAAGACGAGTAGTA 59.518 50.000 0.00 0.00 0.00 1.82
1618 3162 1.266175 CACGACCACAAGACGAGTAGT 59.734 52.381 0.00 0.00 0.00 2.73
1619 3163 1.401148 CCACGACCACAAGACGAGTAG 60.401 57.143 0.00 0.00 0.00 2.57
1635 3179 2.053627 GCAATTCAGCAAAGAACCACG 58.946 47.619 0.00 0.00 0.00 4.94
1641 3185 1.999648 ACAGGGCAATTCAGCAAAGA 58.000 45.000 0.00 0.00 35.83 2.52
1656 3200 1.267574 TGGCCTCCTAGCTGAACAGG 61.268 60.000 3.32 0.00 0.00 4.00
1698 3242 5.007682 TGAGCCCTGAAATTGTAGTTAACC 58.992 41.667 0.88 0.00 0.00 2.85
1704 3248 6.331369 TCTTTTTGAGCCCTGAAATTGTAG 57.669 37.500 0.00 0.00 0.00 2.74
1850 3422 7.193377 ACTACGACGTAAAAATTGTTCCATT 57.807 32.000 9.32 0.00 0.00 3.16
1898 3471 4.479993 ATCTCGTGCCTGCCCTGC 62.480 66.667 0.00 0.00 0.00 4.85
1899 3472 2.202987 GATCTCGTGCCTGCCCTG 60.203 66.667 0.00 0.00 0.00 4.45
1900 3473 3.474570 GGATCTCGTGCCTGCCCT 61.475 66.667 0.00 0.00 0.00 5.19
1941 3514 4.090057 GAACTTGCTGACGCCGGC 62.090 66.667 19.07 19.07 44.86 6.13
2669 4245 1.186200 TCTTGATCACCTCCACCTCG 58.814 55.000 0.00 0.00 0.00 4.63
2780 4356 1.153086 GGCCATTCCAGCTCACGAT 60.153 57.895 0.00 0.00 34.01 3.73
2795 4371 2.092914 AGCTAGTATCAACAAGGTGGCC 60.093 50.000 0.00 0.00 0.00 5.36
2810 4386 4.092968 CCGAAGAAAATTAACGCAGCTAGT 59.907 41.667 0.00 0.00 0.00 2.57
2811 4387 4.578601 CCGAAGAAAATTAACGCAGCTAG 58.421 43.478 0.00 0.00 0.00 3.42
2813 4389 2.414161 GCCGAAGAAAATTAACGCAGCT 60.414 45.455 0.00 0.00 0.00 4.24
2814 4390 1.911464 GCCGAAGAAAATTAACGCAGC 59.089 47.619 0.00 0.00 0.00 5.25
2815 4391 2.159761 TCGCCGAAGAAAATTAACGCAG 60.160 45.455 0.00 0.00 0.00 5.18
2827 4403 3.487202 GCACGCATTCGCCGAAGA 61.487 61.111 5.52 0.00 39.84 2.87
2953 5951 9.612066 TTAGCAATTCAGGAAAAAGTCAAAAAT 57.388 25.926 0.00 0.00 0.00 1.82
3065 6349 7.497595 TGTTACTCTTCAAAAGTCTAGCTCAA 58.502 34.615 0.00 0.00 0.00 3.02
3074 6358 6.126409 TGGTTGGATGTTACTCTTCAAAAGT 58.874 36.000 0.00 0.00 0.00 2.66
3091 6375 4.387026 AGATGGAACTGAAATGGTTGGA 57.613 40.909 0.00 0.00 0.00 3.53
3138 6422 5.611796 TTTGTAACTTAGAGCTGCACATG 57.388 39.130 1.02 0.00 0.00 3.21
3213 6501 2.371658 GCAAGGGCTGGGATATTTCT 57.628 50.000 0.00 0.00 36.96 2.52
3236 6524 4.867086 TCTTTGTCTCTTCTGGGGTTTTT 58.133 39.130 0.00 0.00 0.00 1.94
3278 6566 7.011499 TCACCAAGGCTAGAATAGTTTTGTA 57.989 36.000 0.00 0.00 41.93 2.41
3391 6679 5.842619 TCCATTGATGCGAATTTGTTTTG 57.157 34.783 0.00 0.00 0.00 2.44
3442 6730 3.748048 CCATCTCAGTGTTAGGTGTTGTG 59.252 47.826 0.00 0.00 0.00 3.33
3453 6741 7.168219 ACAACAAATACATACCATCTCAGTGT 58.832 34.615 0.00 0.00 0.00 3.55
3460 6748 5.650266 TGGTGGACAACAAATACATACCATC 59.350 40.000 0.00 0.00 31.31 3.51
3576 6867 3.118775 AGTCAGTATTGTGCCGCTAATCA 60.119 43.478 0.00 0.00 0.00 2.57
3587 6878 6.759827 ACGTTCAGTTTTACAGTCAGTATTGT 59.240 34.615 0.00 0.00 31.53 2.71
3588 6879 7.042992 TGACGTTCAGTTTTACAGTCAGTATTG 60.043 37.037 0.00 0.00 33.84 1.90
3590 6881 6.509656 TGACGTTCAGTTTTACAGTCAGTAT 58.490 36.000 0.00 0.00 33.84 2.12
3591 6882 5.893687 TGACGTTCAGTTTTACAGTCAGTA 58.106 37.500 0.00 0.00 33.84 2.74
3592 6883 4.751060 TGACGTTCAGTTTTACAGTCAGT 58.249 39.130 0.00 0.00 33.84 3.41
3593 6884 5.316488 CTGACGTTCAGTTTTACAGTCAG 57.684 43.478 8.06 8.06 44.93 3.51
3611 6902 5.556570 GCGTTCAACTCTTCTACAAACTGAC 60.557 44.000 0.00 0.00 0.00 3.51
3620 6911 8.922676 CAGTTTTATAAGCGTTCAACTCTTCTA 58.077 33.333 0.00 0.00 0.00 2.10
3674 6965 6.315393 ACGAAGTTGTACAAGAATGTTGTCTT 59.685 34.615 8.98 5.32 37.78 3.01
3676 6967 6.044512 ACGAAGTTGTACAAGAATGTTGTC 57.955 37.500 8.98 0.00 37.78 3.18
3698 6989 7.816640 TGCTTCTGGACACATAAATCTTAAAC 58.183 34.615 0.00 0.00 0.00 2.01
3717 7008 6.435277 TCCTTCTTGCATATTCTTTTGCTTCT 59.565 34.615 0.00 0.00 39.60 2.85


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

AutoCloner maintained by Alex Coulton.