Multiple sequence alignment - TraesCS5D01G376200

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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 TraesCS5D01G376200 chr5D 100.000 2576 0 0 1 2576 448833418 448835993 0.000000e+00 4758.0
1 TraesCS5D01G376200 chr5D 88.976 1016 59 17 538 1535 434453219 434454199 0.000000e+00 1206.0
2 TraesCS5D01G376200 chr5D 80.990 626 41 34 1565 2137 434454197 434454797 2.370000e-115 425.0
3 TraesCS5D01G376200 chr5D 90.698 301 22 3 2276 2576 531424522 531424816 1.860000e-106 396.0
4 TraesCS5D01G376200 chr5D 89.062 320 16 10 2269 2576 488398387 488398699 1.870000e-101 379.0
5 TraesCS5D01G376200 chr5D 79.304 517 77 20 37 537 312478976 312479478 4.110000e-88 335.0
6 TraesCS5D01G376200 chr5D 91.096 146 11 2 2135 2279 368034219 368034075 2.020000e-46 196.0
7 TraesCS5D01G376200 chr5B 90.019 1052 78 7 878 1913 527243788 527244828 0.000000e+00 1336.0
8 TraesCS5D01G376200 chr5B 88.168 262 23 4 543 797 527243502 527243762 3.220000e-79 305.0
9 TraesCS5D01G376200 chr5B 92.308 52 0 2 815 866 527243761 527243808 1.280000e-08 71.3
10 TraesCS5D01G376200 chr5B 87.719 57 7 0 1334 1390 584564717 584564773 1.650000e-07 67.6
11 TraesCS5D01G376200 chr6D 83.333 486 66 15 41 515 81921590 81921109 3.940000e-118 435.0
12 TraesCS5D01G376200 chr6D 90.000 320 19 7 2269 2576 107817200 107817518 3.990000e-108 401.0
13 TraesCS5D01G376200 chr6D 91.667 144 11 1 2136 2279 21358994 21359136 5.620000e-47 198.0
14 TraesCS5D01G376200 chr6D 79.330 179 29 8 1016 1190 142427427 142427253 4.500000e-23 119.0
15 TraesCS5D01G376200 chr6D 76.571 175 37 4 1016 1188 216794815 216794643 2.730000e-15 93.5
16 TraesCS5D01G376200 chr1D 90.938 320 16 3 2269 2576 447335704 447336022 3.960000e-113 418.0
17 TraesCS5D01G376200 chr1D 90.415 313 18 2 2276 2576 202538569 202538257 3.990000e-108 401.0
18 TraesCS5D01G376200 chr1D 91.379 290 22 2 2290 2576 378547787 378548076 6.680000e-106 394.0
19 TraesCS5D01G376200 chr1D 90.845 142 8 5 2139 2279 22401197 22401060 4.380000e-43 185.0
20 TraesCS5D01G376200 chr1D 90.210 143 12 1 2139 2279 447335401 447335543 4.380000e-43 185.0
21 TraesCS5D01G376200 chr1D 71.707 410 106 10 1016 1420 138630286 138630690 3.510000e-19 106.0
22 TraesCS5D01G376200 chr7D 91.234 308 23 3 2272 2576 204880956 204880650 1.430000e-112 416.0
23 TraesCS5D01G376200 chr7D 90.096 313 19 2 2276 2576 48846286 48845974 1.860000e-106 396.0
24 TraesCS5D01G376200 chr7D 89.375 320 21 6 2269 2576 154204916 154205234 8.640000e-105 390.0
25 TraesCS5D01G376200 chr7D 87.220 313 27 4 2272 2572 51834386 51834075 6.820000e-91 344.0
26 TraesCS5D01G376200 chr7D 92.908 141 10 0 2139 2279 204881267 204881127 3.360000e-49 206.0
27 TraesCS5D01G376200 chr7D 88.356 146 14 2 2136 2279 544099044 544099188 3.410000e-39 172.0
28 TraesCS5D01G376200 chr5A 89.408 321 14 4 1836 2138 548477660 548477978 1.120000e-103 387.0
29 TraesCS5D01G376200 chr5A 89.097 321 15 4 1836 2138 548458700 548459018 5.200000e-102 381.0
30 TraesCS5D01G376200 chr5A 88.785 321 16 6 1836 2138 548499464 548499782 2.420000e-100 375.0
31 TraesCS5D01G376200 chr5A 78.008 532 100 14 15 537 593995266 593994743 4.140000e-83 318.0
32 TraesCS5D01G376200 chr5A 93.137 204 14 0 2373 2576 11131172 11130969 1.500000e-77 300.0
33 TraesCS5D01G376200 chr5A 88.811 143 16 0 2137 2279 5976073 5975931 2.630000e-40 176.0
34 TraesCS5D01G376200 chr5A 98.684 76 1 0 1621 1696 548455439 548455514 4.470000e-28 135.0
35 TraesCS5D01G376200 chr5A 97.368 76 2 0 1621 1696 548474397 548474472 2.080000e-26 130.0
36 TraesCS5D01G376200 chr5A 97.368 76 2 0 1621 1696 548496198 548496273 2.080000e-26 130.0
37 TraesCS5D01G376200 chr3B 89.062 320 22 3 2269 2576 822782349 822782667 4.020000e-103 385.0
38 TraesCS5D01G376200 chr3B 73.966 411 52 25 157 537 35714274 35714659 5.820000e-22 115.0
39 TraesCS5D01G376200 chr3B 73.723 411 53 25 157 537 35786234 35786619 2.710000e-20 110.0
40 TraesCS5D01G376200 chr2D 83.924 423 47 15 126 537 13408446 13408034 4.020000e-103 385.0
41 TraesCS5D01G376200 chr2D 89.103 312 21 6 2272 2571 346044032 346043722 2.420000e-100 375.0
42 TraesCS5D01G376200 chr2D 93.684 95 4 2 2272 2365 301760669 301760576 9.610000e-30 141.0
43 TraesCS5D01G376200 chr2D 77.528 178 34 6 1016 1190 563432102 563432276 4.530000e-18 102.0
44 TraesCS5D01G376200 chr2D 74.719 178 39 6 1016 1190 246029349 246029175 9.890000e-10 75.0
45 TraesCS5D01G376200 chr4B 86.562 320 27 6 2272 2576 385547846 385547528 3.180000e-89 339.0
46 TraesCS5D01G376200 chr4B 87.719 57 7 0 1334 1390 94057367 94057423 1.650000e-07 67.6
47 TraesCS5D01G376200 chr2A 79.017 529 72 22 37 537 102893722 102894239 2.470000e-85 326.0
48 TraesCS5D01G376200 chr2A 76.262 535 72 29 50 536 57218819 57219346 1.540000e-57 233.0
49 TraesCS5D01G376200 chr2A 88.356 146 14 3 2134 2279 733387276 733387418 3.410000e-39 172.0
50 TraesCS5D01G376200 chr3A 78.937 489 80 18 49 525 11417145 11417622 6.920000e-81 311.0
51 TraesCS5D01G376200 chr3A 78.702 493 84 14 37 515 647797347 647797832 2.490000e-80 309.0
52 TraesCS5D01G376200 chr3A 81.638 354 53 10 49 398 723467815 723468160 1.510000e-72 283.0
53 TraesCS5D01G376200 chr3A 88.235 51 6 0 1334 1384 137996818 137996868 7.700000e-06 62.1
54 TraesCS5D01G376200 chr2B 79.902 408 65 10 49 444 628381219 628381621 1.510000e-72 283.0
55 TraesCS5D01G376200 chr1A 91.549 142 11 1 2139 2279 164525327 164525186 7.270000e-46 195.0
56 TraesCS5D01G376200 chr1A 77.222 180 34 7 1016 1190 317299258 317299435 5.870000e-17 99.0
57 TraesCS5D01G376200 chr7A 87.097 124 12 4 416 537 19236195 19236316 1.240000e-28 137.0
58 TraesCS5D01G376200 chr4A 77.500 160 30 6 1034 1190 397563944 397563788 9.820000e-15 91.6
59 TraesCS5D01G376200 chr4A 76.111 180 36 7 1016 1190 479519693 479519870 1.270000e-13 87.9
60 TraesCS5D01G376200 chr7B 83.516 91 13 2 1334 1423 86520160 86520249 1.640000e-12 84.2
61 TraesCS5D01G376200 chr7B 100.000 35 0 0 1334 1368 68598865 68598899 5.950000e-07 65.8
62 TraesCS5D01G376200 chr6B 76.543 162 31 7 1034 1190 656813789 656813948 5.910000e-12 82.4
63 TraesCS5D01G376200 chr6B 87.719 57 7 0 1334 1390 552637518 552637462 1.650000e-07 67.6
64 TraesCS5D01G376200 chr1B 71.018 383 98 13 1016 1390 572827700 572827323 2.120000e-11 80.5
65 TraesCS5D01G376200 chr6A 100.000 35 0 0 1334 1368 272590243 272590277 5.950000e-07 65.8


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 TraesCS5D01G376200 chr5D 448833418 448835993 2575 False 4758.000000 4758 100.0000 1 2576 1 chr5D.!!$F2 2575
1 TraesCS5D01G376200 chr5D 434453219 434454797 1578 False 815.500000 1206 84.9830 538 2137 2 chr5D.!!$F5 1599
2 TraesCS5D01G376200 chr5D 312478976 312479478 502 False 335.000000 335 79.3040 37 537 1 chr5D.!!$F1 500
3 TraesCS5D01G376200 chr5B 527243502 527244828 1326 False 570.766667 1336 90.1650 543 1913 3 chr5B.!!$F2 1370
4 TraesCS5D01G376200 chr1D 447335401 447336022 621 False 301.500000 418 90.5740 2139 2576 2 chr1D.!!$F3 437
5 TraesCS5D01G376200 chr7D 204880650 204881267 617 True 311.000000 416 92.0710 2139 2576 2 chr7D.!!$R3 437
6 TraesCS5D01G376200 chr5A 593994743 593995266 523 True 318.000000 318 78.0080 15 537 1 chr5A.!!$R3 522
7 TraesCS5D01G376200 chr5A 548474397 548477978 3581 False 258.500000 387 93.3880 1621 2138 2 chr5A.!!$F2 517
8 TraesCS5D01G376200 chr5A 548455439 548459018 3579 False 258.000000 381 93.8905 1621 2138 2 chr5A.!!$F1 517
9 TraesCS5D01G376200 chr5A 548496198 548499782 3584 False 252.500000 375 93.0765 1621 2138 2 chr5A.!!$F3 517
10 TraesCS5D01G376200 chr2A 102893722 102894239 517 False 326.000000 326 79.0170 37 537 1 chr2A.!!$F2 500
11 TraesCS5D01G376200 chr2A 57218819 57219346 527 False 233.000000 233 76.2620 50 536 1 chr2A.!!$F1 486

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
708 804 1.066918 GGTGCATGGCTAGCATTGC 59.933 57.895 25.83 25.83 44.79 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1957 0.246635 ACATACAGTGACGGTGGCTC 59.753 55.0 0.0 0.0 0.0 4.7 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
63 65 6.279882 TGTTTGTGGATTCAGAAAATGTTCC 58.720 36.000 0.00 0.00 37.78 3.62
168 172 8.370493 TGAAATTGAACAAAAATTCGCCAATA 57.630 26.923 0.00 0.00 0.00 1.90
359 387 6.387465 TGTTCGTCGATTCTAGAAATGTTCT 58.613 36.000 9.71 0.00 43.72 3.01
367 395 7.861372 TCGATTCTAGAAATGTTCTCGTATTCC 59.139 37.037 18.39 0.00 41.14 3.01
369 397 9.314321 GATTCTAGAAATGTTCTCGTATTCCAA 57.686 33.333 9.71 0.00 41.14 3.53
372 400 8.932791 TCTAGAAATGTTCTCGTATTCCAAAAC 58.067 33.333 0.00 0.00 41.14 2.43
379 407 6.915300 TGTTCTCGTATTCCAAAACAATGTTG 59.085 34.615 0.00 0.00 0.00 3.33
550 626 9.928236 TTCTAAAATTGTTTGCAGCAAAATAAC 57.072 25.926 22.26 11.21 35.03 1.89
551 627 8.555361 TCTAAAATTGTTTGCAGCAAAATAACC 58.445 29.630 22.26 10.03 35.03 2.85
552 628 6.690194 AAATTGTTTGCAGCAAAATAACCA 57.310 29.167 22.26 12.54 35.03 3.67
553 629 6.880942 AATTGTTTGCAGCAAAATAACCAT 57.119 29.167 22.26 5.38 35.03 3.55
555 631 7.976135 ATTGTTTGCAGCAAAATAACCATAA 57.024 28.000 22.26 3.88 35.03 1.90
639 720 7.687757 GGTTATTTATTTTCATTGTGCGCTTTG 59.312 33.333 9.73 0.71 0.00 2.77
665 746 1.334869 GTCAACAGGCTGAAACCAGTG 59.665 52.381 23.66 7.14 34.23 3.66
708 804 1.066918 GGTGCATGGCTAGCATTGC 59.933 57.895 25.83 25.83 44.79 3.56
719 815 2.030007 GCTAGCATTGCAGGTTTGAACA 60.030 45.455 10.63 0.00 0.00 3.18
720 816 2.806608 AGCATTGCAGGTTTGAACAG 57.193 45.000 11.91 0.00 0.00 3.16
721 817 2.034124 AGCATTGCAGGTTTGAACAGT 58.966 42.857 11.91 0.00 0.00 3.55
722 818 2.431782 AGCATTGCAGGTTTGAACAGTT 59.568 40.909 11.91 0.00 0.00 3.16
729 825 3.748568 GCAGGTTTGAACAGTTCCTAGAG 59.251 47.826 10.93 0.00 0.00 2.43
744 840 6.039270 AGTTCCTAGAGTGAAGATGATTCGAG 59.961 42.308 0.00 0.00 0.00 4.04
915 1011 6.698380 CGAAGCAACTTGTACCCCTATATAT 58.302 40.000 0.00 0.00 0.00 0.86
916 1012 7.833786 CGAAGCAACTTGTACCCCTATATATA 58.166 38.462 0.00 0.00 0.00 0.86
917 1013 8.475639 CGAAGCAACTTGTACCCCTATATATAT 58.524 37.037 0.00 0.00 0.00 0.86
943 1039 2.370189 CACCCCTCCAATCCATCTACTC 59.630 54.545 0.00 0.00 0.00 2.59
945 1041 2.694397 CCCTCCAATCCATCTACTCCA 58.306 52.381 0.00 0.00 0.00 3.86
947 1043 3.181450 CCCTCCAATCCATCTACTCCAAC 60.181 52.174 0.00 0.00 0.00 3.77
948 1044 3.181450 CCTCCAATCCATCTACTCCAACC 60.181 52.174 0.00 0.00 0.00 3.77
949 1045 3.713764 CTCCAATCCATCTACTCCAACCT 59.286 47.826 0.00 0.00 0.00 3.50
950 1046 4.111577 TCCAATCCATCTACTCCAACCTT 58.888 43.478 0.00 0.00 0.00 3.50
1006 1102 1.841302 AAGAGCCGAAGCCATGGACA 61.841 55.000 18.40 0.00 41.25 4.02
1147 1243 2.500229 CAAGCTTCGTCCCTTGGTTTA 58.500 47.619 0.00 0.00 35.86 2.01
1170 1266 4.736896 GCGGTCGTCGGCTTCCTT 62.737 66.667 5.03 0.00 39.69 3.36
1173 1269 1.005394 GGTCGTCGGCTTCCTTGAA 60.005 57.895 0.00 0.00 0.00 2.69
1176 1272 0.391597 TCGTCGGCTTCCTTGAAAGT 59.608 50.000 0.00 0.00 0.00 2.66
1237 1333 3.993614 CTTACTGCCATGCGCCCCA 62.994 63.158 4.18 0.00 36.24 4.96
1284 1393 4.124351 CTCCGCGGCGACAACCTA 62.124 66.667 25.92 0.00 0.00 3.08
1285 1394 3.426117 CTCCGCGGCGACAACCTAT 62.426 63.158 25.92 0.00 0.00 2.57
1286 1395 2.510691 CCGCGGCGACAACCTATT 60.511 61.111 25.92 0.00 0.00 1.73
1287 1396 2.522638 CCGCGGCGACAACCTATTC 61.523 63.158 25.92 0.00 0.00 1.75
1288 1397 2.522638 CGCGGCGACAACCTATTCC 61.523 63.158 19.16 0.00 0.00 3.01
1289 1398 2.522638 GCGGCGACAACCTATTCCG 61.523 63.158 12.98 0.00 39.81 4.30
1290 1399 2.522638 CGGCGACAACCTATTCCGC 61.523 63.158 0.00 0.00 44.45 5.54
1296 1405 2.125269 AACCTATTCCGCGCGCTT 60.125 55.556 30.48 13.53 0.00 4.68
1417 1526 1.006922 CGCGCCTATGAGCAGATCA 60.007 57.895 0.00 0.00 43.70 2.92
1506 1615 3.316308 GGCTAACCTTAGATGGCATTGTG 59.684 47.826 0.00 0.00 32.47 3.33
1828 2214 5.817816 GCAGTGCCATCTACTTACAGTTATT 59.182 40.000 2.85 0.00 0.00 1.40
1846 5040 5.753438 AGTTATTCACCACTATACGTGCATG 59.247 40.000 3.82 3.82 42.42 4.06
1976 5174 1.327303 CTGTTGCCCCAAGCTTTACA 58.673 50.000 0.00 0.00 44.23 2.41
1982 5180 2.968574 TGCCCCAAGCTTTACAATTGAA 59.031 40.909 13.59 0.00 44.23 2.69
2027 5233 3.128589 GGAGTGCAAATTAGCGATTTCCA 59.871 43.478 0.00 0.00 35.79 3.53
2033 5239 4.734402 GCAAATTAGCGATTTCCATGCTCA 60.734 41.667 0.00 0.00 40.06 4.26
2062 5281 1.406477 GGTGTTAAGGGGCTACGAAGG 60.406 57.143 0.00 0.00 0.00 3.46
2130 5349 7.869937 CGCTGATATGTTGGATATCCTTATAGG 59.130 40.741 22.35 12.07 36.46 2.57
2156 5375 4.521062 GAGCATCTCCAGCCGCGT 62.521 66.667 4.92 0.00 0.00 6.01
2250 5471 1.008194 GTTTTTCGTCGGGTTGGGC 60.008 57.895 0.00 0.00 0.00 5.36
2366 5765 4.168291 GCAGAGGAAGCCGAGGGG 62.168 72.222 0.00 0.00 0.00 4.79
2429 5840 2.284625 TCGGGAGGCTGTCACCAT 60.285 61.111 0.00 0.00 0.00 3.55
2430 5841 1.918293 TCGGGAGGCTGTCACCATT 60.918 57.895 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.829507 AACATTTTCTGAATCCACAAACATTTA 57.170 25.926 0.00 0.00 0.00 1.40
335 361 6.387465 AGAACATTTCTAGAATCGACGAACA 58.613 36.000 5.89 0.00 38.49 3.18
359 387 8.188799 TGTTTACAACATTGTTTTGGAATACGA 58.811 29.630 1.98 0.00 42.35 3.43
372 400 7.712264 ATGGTGAACATTGTTTACAACATTG 57.288 32.000 21.54 9.06 44.26 2.82
516 592 7.747357 GCTGCAAACAATTTTAGAAAATCATGG 59.253 33.333 0.86 0.00 37.62 3.66
527 603 8.213518 TGGTTATTTTGCTGCAAACAATTTTA 57.786 26.923 25.99 11.19 32.79 1.52
549 625 9.438163 AAAATCATAATCTCCAATGGTTATGGT 57.562 29.630 16.30 9.90 39.09 3.55
608 689 9.347934 CGCACAATGAAAATAAATAACCACTAA 57.652 29.630 0.00 0.00 0.00 2.24
633 714 0.041312 CTGTTGACGGAACCAAAGCG 60.041 55.000 0.00 0.00 33.07 4.68
639 720 0.534203 TTCAGCCTGTTGACGGAACC 60.534 55.000 0.00 0.00 33.07 3.62
665 746 1.682087 GGCCAGTTGTAATCCCACTCC 60.682 57.143 0.00 0.00 0.00 3.85
708 804 4.752101 CACTCTAGGAACTGTTCAAACCTG 59.248 45.833 21.01 9.27 41.52 4.00
719 815 5.888724 TCGAATCATCTTCACTCTAGGAACT 59.111 40.000 0.00 0.00 46.37 3.01
720 816 6.137794 TCGAATCATCTTCACTCTAGGAAC 57.862 41.667 0.00 0.00 0.00 3.62
721 817 5.888724 ACTCGAATCATCTTCACTCTAGGAA 59.111 40.000 0.00 0.00 0.00 3.36
722 818 5.298026 CACTCGAATCATCTTCACTCTAGGA 59.702 44.000 0.00 0.00 0.00 2.94
729 825 5.276114 CGTCAATCACTCGAATCATCTTCAC 60.276 44.000 0.00 0.00 0.00 3.18
744 840 1.019278 ATGCACCGGTCGTCAATCAC 61.019 55.000 2.59 0.00 0.00 3.06
834 930 1.648165 CATCGCGTGCGTGCATAAC 60.648 57.895 14.47 0.00 40.74 1.89
835 931 2.097635 ACATCGCGTGCGTGCATAA 61.098 52.632 14.47 0.00 40.74 1.90
836 932 2.508215 ACATCGCGTGCGTGCATA 60.508 55.556 14.47 0.00 40.74 3.14
837 933 4.151297 CACATCGCGTGCGTGCAT 62.151 61.111 14.47 0.00 39.19 3.96
839 935 4.070818 TTCACATCGCGTGCGTGC 62.071 61.111 14.47 0.00 45.92 5.34
840 936 2.202046 GTTCACATCGCGTGCGTG 60.202 61.111 14.47 12.26 45.92 5.34
841 937 3.762992 CGTTCACATCGCGTGCGT 61.763 61.111 14.47 0.00 45.92 5.24
870 966 1.553308 GTTCACATCGCGTACCTACC 58.447 55.000 5.77 0.00 0.00 3.18
871 967 1.186030 CGTTCACATCGCGTACCTAC 58.814 55.000 5.77 0.00 0.00 3.18
872 968 0.523968 GCGTTCACATCGCGTACCTA 60.524 55.000 5.77 0.00 43.94 3.08
873 969 1.804326 GCGTTCACATCGCGTACCT 60.804 57.895 5.77 0.00 43.94 3.08
874 970 2.693285 GCGTTCACATCGCGTACC 59.307 61.111 5.77 0.00 43.94 3.34
915 1011 3.059853 TGGATTGGAGGGGTGCATTATA 58.940 45.455 0.00 0.00 0.00 0.98
916 1012 1.858910 TGGATTGGAGGGGTGCATTAT 59.141 47.619 0.00 0.00 0.00 1.28
917 1013 1.303898 TGGATTGGAGGGGTGCATTA 58.696 50.000 0.00 0.00 0.00 1.90
918 1014 0.638292 ATGGATTGGAGGGGTGCATT 59.362 50.000 0.00 0.00 0.00 3.56
943 1039 1.201647 CTTGCTGCTGATCAAGGTTGG 59.798 52.381 0.00 0.00 36.83 3.77
945 1041 2.434428 CTCTTGCTGCTGATCAAGGTT 58.566 47.619 0.00 0.00 39.92 3.50
947 1043 0.733729 GCTCTTGCTGCTGATCAAGG 59.266 55.000 0.00 0.00 39.92 3.61
948 1044 0.733729 GGCTCTTGCTGCTGATCAAG 59.266 55.000 0.00 0.00 40.62 3.02
949 1045 0.679002 GGGCTCTTGCTGCTGATCAA 60.679 55.000 0.00 0.00 39.59 2.57
950 1046 1.077930 GGGCTCTTGCTGCTGATCA 60.078 57.895 0.00 0.00 39.59 2.92
1006 1102 1.667154 TTGCTGCTCGCTAGGATCGT 61.667 55.000 0.00 0.00 40.11 3.73
1170 1266 1.928503 GTGACGACGGTGAAACTTTCA 59.071 47.619 0.00 0.00 36.74 2.69
1173 1269 0.176219 TGGTGACGACGGTGAAACTT 59.824 50.000 0.00 0.00 36.74 2.66
1176 1272 1.068417 CCTGGTGACGACGGTGAAA 59.932 57.895 0.00 0.00 0.00 2.69
1212 1308 2.511600 ATGGCAGTAAGACGCGCC 60.512 61.111 5.73 0.00 40.52 6.53
1274 1383 3.003478 CGCGGAATAGGTTGTCGC 58.997 61.111 0.00 0.00 42.51 5.19
1277 1386 3.192922 GCGCGCGGAATAGGTTGT 61.193 61.111 33.06 0.00 0.00 3.32
1278 1387 2.361427 GAAGCGCGCGGAATAGGTTG 62.361 60.000 33.06 0.00 0.00 3.77
1279 1388 2.125269 AAGCGCGCGGAATAGGTT 60.125 55.556 33.06 10.80 0.00 3.50
1280 1389 2.585247 GAAGCGCGCGGAATAGGT 60.585 61.111 33.06 3.90 0.00 3.08
1281 1390 2.584970 TGAAGCGCGCGGAATAGG 60.585 61.111 33.06 1.02 0.00 2.57
1282 1391 2.589492 CCTGAAGCGCGCGGAATAG 61.589 63.158 33.06 19.27 0.00 1.73
1283 1392 2.584970 CCTGAAGCGCGCGGAATA 60.585 61.111 33.06 10.79 0.00 1.75
1373 1482 1.227823 CAGTCCACGGTTTCCTGCA 60.228 57.895 0.00 0.00 0.00 4.41
1417 1526 0.382515 GTGCTCTTCCGCTCGTAGAT 59.617 55.000 0.00 0.00 33.89 1.98
1506 1615 1.200948 GCAAGGTTGATGTGCTTCTCC 59.799 52.381 0.00 0.00 35.36 3.71
1561 1670 1.296056 CCAGTTTAGTTCACCGGCGG 61.296 60.000 27.06 27.06 0.00 6.13
1563 1672 1.886886 TTCCAGTTTAGTTCACCGGC 58.113 50.000 0.00 0.00 0.00 6.13
1568 1677 4.502604 CGACCTCCTTTCCAGTTTAGTTCA 60.503 45.833 0.00 0.00 0.00 3.18
1708 1945 1.641577 GGTGGCTCATACGAACTCAC 58.358 55.000 0.00 0.00 0.00 3.51
1720 1957 0.246635 ACATACAGTGACGGTGGCTC 59.753 55.000 0.00 0.00 0.00 4.70
1802 2188 3.599343 CTGTAAGTAGATGGCACTGCAA 58.401 45.455 2.82 0.00 0.00 4.08
1976 5174 3.666902 GCATGTACGTTGCGACTTCAATT 60.667 43.478 1.84 0.00 0.00 2.32
2027 5233 5.415701 CCTTAACACCAACACTAATGAGCAT 59.584 40.000 0.00 0.00 0.00 3.79
2033 5239 3.075432 AGCCCCTTAACACCAACACTAAT 59.925 43.478 0.00 0.00 0.00 1.73
2063 5282 0.460311 GATGGGCGATAGGGGATACG 59.540 60.000 0.00 0.00 37.60 3.06
2130 5349 1.344114 CTGGAGATGCTCTTAGCCCTC 59.656 57.143 8.86 8.86 41.51 4.30
2131 5350 1.422531 CTGGAGATGCTCTTAGCCCT 58.577 55.000 0.00 0.00 41.51 5.19
2132 5351 0.250252 GCTGGAGATGCTCTTAGCCC 60.250 60.000 10.80 0.00 41.51 5.19
2135 5354 0.599728 GCGGCTGGAGATGCTCTTAG 60.600 60.000 0.00 0.00 0.00 2.18
2136 5355 1.443407 GCGGCTGGAGATGCTCTTA 59.557 57.895 0.00 0.00 0.00 2.10
2137 5356 2.188994 GCGGCTGGAGATGCTCTT 59.811 61.111 0.00 0.00 0.00 2.85
2156 5375 3.626596 AGGAGGGCCTCTTGGGGA 61.627 66.667 31.39 0.00 42.19 4.81
2190 5411 1.817941 CCGATTTTCATCCGCCGGT 60.818 57.895 1.63 0.00 33.02 5.28
2198 5419 1.376609 GCGACTGGGCCGATTTTCAT 61.377 55.000 0.00 0.00 0.00 2.57
2250 5471 2.707039 CGCCGGCTGTTATTTCGG 59.293 61.111 26.68 0.00 44.70 4.30
2343 5742 2.665603 GGCTTCCTCTGCTTCGGT 59.334 61.111 0.00 0.00 0.00 4.69
2370 5769 2.824041 GCGTTGGACATGCCCGAT 60.824 61.111 0.00 0.00 34.97 4.18
2429 5840 4.323477 CCCTGTTCCGCCGGTCAA 62.323 66.667 1.63 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.