Multiple sequence alignment - TraesCS6A01G126100

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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 TraesCS6A01G126100 chr6A 100.000 2414 0 0 1 2414 99503070 99505483 0.000000e+00 4458.0
1 TraesCS6A01G126100 chr6A 84.691 1326 134 35 861 2145 54201733 54200436 0.000000e+00 1260.0
2 TraesCS6A01G126100 chr6A 89.085 284 21 4 2141 2414 54184855 54184572 6.390000e-91 344.0
3 TraesCS6A01G126100 chr6A 87.421 159 18 2 490 648 594968849 594969005 5.300000e-42 182.0
4 TraesCS6A01G126100 chr6A 78.205 234 26 15 1610 1833 124711987 124712205 2.520000e-25 126.0
5 TraesCS6A01G126100 chr6A 100.000 28 0 0 387 414 99503379 99503406 4.000000e-03 52.8
6 TraesCS6A01G126100 chr6A 100.000 28 0 0 310 337 99503456 99503483 4.000000e-03 52.8
7 TraesCS6A01G126100 chr6B 85.637 1671 190 20 560 2200 9760289 9758639 0.000000e+00 1711.0
8 TraesCS6A01G126100 chr6B 82.277 694 88 23 1040 1724 101703013 101703680 3.480000e-158 568.0
9 TraesCS6A01G126100 chr6B 80.118 508 78 13 4 491 422898634 422898130 8.210000e-95 357.0
10 TraesCS6A01G126100 chr6B 89.474 228 21 2 2187 2414 9758214 9757990 3.930000e-73 285.0
11 TraesCS6A01G126100 chr6B 84.141 227 20 8 874 1096 101702729 101702943 3.150000e-49 206.0
12 TraesCS6A01G126100 chr6B 85.311 177 21 5 1659 1833 189094692 189094865 6.860000e-41 178.0
13 TraesCS6A01G126100 chr6B 89.024 82 9 0 406 487 542700825 542700744 4.250000e-18 102.0
14 TraesCS6A01G126100 chr6D 88.337 1329 110 18 482 1776 82695735 82697052 0.000000e+00 1554.0
15 TraesCS6A01G126100 chr6D 89.969 638 60 4 1778 2414 82697430 82698064 0.000000e+00 821.0
16 TraesCS6A01G126100 chr6D 82.114 492 65 18 4 478 82688693 82689178 1.340000e-107 399.0
17 TraesCS6A01G126100 chrUn 83.275 855 81 26 918 1738 70140739 70141565 0.000000e+00 730.0
18 TraesCS6A01G126100 chrUn 87.244 635 64 10 1796 2414 70145328 70145961 0.000000e+00 708.0
19 TraesCS6A01G126100 chrUn 87.952 166 18 2 488 653 224990407 224990570 6.810000e-46 195.0
20 TraesCS6A01G126100 chrUn 87.952 166 18 2 488 653 318482142 318482305 6.810000e-46 195.0
21 TraesCS6A01G126100 chr7D 84.169 638 84 11 765 1397 565671567 565670942 9.550000e-169 603.0
22 TraesCS6A01G126100 chr7D 79.648 511 74 15 3 488 527782218 527782723 8.270000e-90 340.0
23 TraesCS6A01G126100 chr7D 78.614 332 56 10 174 490 222193303 222192972 3.150000e-49 206.0
24 TraesCS6A01G126100 chr7D 83.415 205 29 5 1931 2133 513211545 513211746 4.100000e-43 185.0
25 TraesCS6A01G126100 chr4D 84.444 495 45 8 874 1354 486812392 486811916 2.190000e-125 459.0
26 TraesCS6A01G126100 chr2B 82.087 508 70 13 4 494 551629841 551629338 4.800000e-112 414.0
27 TraesCS6A01G126100 chr2B 80.962 499 81 8 3 487 391473264 391472766 1.350000e-102 383.0
28 TraesCS6A01G126100 chr2B 78.078 333 57 8 174 491 234080989 234081320 1.890000e-46 196.0
29 TraesCS6A01G126100 chr7B 82.821 390 61 6 3 390 400646052 400645667 6.390000e-91 344.0
30 TraesCS6A01G126100 chr7B 87.952 166 18 2 488 653 716576492 716576329 6.810000e-46 195.0
31 TraesCS6A01G126100 chr7B 87.952 166 18 2 488 653 716589991 716589828 6.810000e-46 195.0
32 TraesCS6A01G126100 chr7A 82.902 386 59 7 4 387 450977660 450977280 8.270000e-90 340.0
33 TraesCS6A01G126100 chr3B 81.994 361 62 3 4 362 343824547 343824188 1.080000e-78 303.0
34 TraesCS6A01G126100 chr3B 82.927 287 48 1 4 289 217620703 217620417 8.560000e-65 257.0
35 TraesCS6A01G126100 chr3B 88.889 153 16 1 490 642 365497899 365498050 1.140000e-43 187.0
36 TraesCS6A01G126100 chr3B 88.961 154 14 3 490 642 607429348 607429499 1.140000e-43 187.0
37 TraesCS6A01G126100 chr3D 84.429 289 40 4 4 289 352247743 352247457 1.830000e-71 279.0
38 TraesCS6A01G126100 chr3D 81.029 311 57 2 4 312 457970170 457970480 1.850000e-61 246.0
39 TraesCS6A01G126100 chr3D 79.553 313 50 9 189 487 268729258 268729570 6.760000e-51 211.0
40 TraesCS6A01G126100 chr3D 83.069 189 28 4 1943 2130 358179761 358179576 4.130000e-38 169.0
41 TraesCS6A01G126100 chr5D 81.090 312 56 3 4 312 343028769 343028458 1.850000e-61 246.0
42 TraesCS6A01G126100 chr5D 90.909 77 5 2 414 489 385888 385963 4.250000e-18 102.0
43 TraesCS6A01G126100 chr5D 87.952 83 10 0 407 489 263329265 263329347 5.490000e-17 99.0
44 TraesCS6A01G126100 chr2A 91.195 159 14 0 918 1076 5405328 5405170 1.450000e-52 217.0
45 TraesCS6A01G126100 chr2A 84.409 186 24 4 1943 2127 12636009 12635828 6.860000e-41 178.0
46 TraesCS6A01G126100 chr2A 82.587 201 29 6 1937 2133 193449585 193449783 3.190000e-39 172.0
47 TraesCS6A01G126100 chr2D 88.312 154 16 2 489 642 120561326 120561477 1.470000e-42 183.0
48 TraesCS6A01G126100 chr2D 83.060 183 30 1 1943 2125 533780114 533780295 5.340000e-37 165.0
49 TraesCS6A01G126100 chr2D 74.453 411 88 16 886 1288 115149947 115149546 6.910000e-36 161.0
50 TraesCS6A01G126100 chr5B 76.997 313 54 8 193 487 307145084 307145396 1.920000e-36 163.0
51 TraesCS6A01G126100 chr1D 88.889 81 9 0 407 487 120588320 120588400 1.530000e-17 100.0


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 TraesCS6A01G126100 chr6A 99503070 99505483 2413 False 1521.2 4458 100.0000 1 2414 3 chr6A.!!$F3 2413
1 TraesCS6A01G126100 chr6A 54200436 54201733 1297 True 1260.0 1260 84.6910 861 2145 1 chr6A.!!$R2 1284
2 TraesCS6A01G126100 chr6B 9757990 9760289 2299 True 998.0 1711 87.5555 560 2414 2 chr6B.!!$R3 1854
3 TraesCS6A01G126100 chr6B 101702729 101703680 951 False 387.0 568 83.2090 874 1724 2 chr6B.!!$F2 850
4 TraesCS6A01G126100 chr6B 422898130 422898634 504 True 357.0 357 80.1180 4 491 1 chr6B.!!$R1 487
5 TraesCS6A01G126100 chr6D 82695735 82698064 2329 False 1187.5 1554 89.1530 482 2414 2 chr6D.!!$F2 1932
6 TraesCS6A01G126100 chrUn 70140739 70145961 5222 False 719.0 730 85.2595 918 2414 2 chrUn.!!$F3 1496
7 TraesCS6A01G126100 chr7D 565670942 565671567 625 True 603.0 603 84.1690 765 1397 1 chr7D.!!$R2 632
8 TraesCS6A01G126100 chr7D 527782218 527782723 505 False 340.0 340 79.6480 3 488 1 chr7D.!!$F2 485
9 TraesCS6A01G126100 chr2B 551629338 551629841 503 True 414.0 414 82.0870 4 494 1 chr2B.!!$R2 490

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
439 471 1.068885 CGGCGGTTTAAAATGCTGTCA 60.069 47.619 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 6140 0.53065 CGTGTGGACACAGAGCACTT 60.531 55.0 5.22 0.0 46.75 3.16 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
43 44 9.877178 ACAAATGTTTTCCACATAAAAAGTGTA 57.123 25.926 0.00 0.00 46.23 2.90
62 64 5.366768 AGTGTATGTAATGGACACCTATGCT 59.633 40.000 0.97 0.00 43.65 3.79
67 69 3.560636 AATGGACACCTATGCTACACC 57.439 47.619 0.00 0.00 0.00 4.16
140 150 8.677148 AAGTTATTAATATCGTCTGCAATGGT 57.323 30.769 0.00 0.00 0.00 3.55
148 158 1.933853 CGTCTGCAATGGTAAGGCTAC 59.066 52.381 0.00 0.00 0.00 3.58
167 177 5.130975 GGCTACCATATATGATGTGATGGGA 59.869 44.000 14.54 0.00 42.72 4.37
183 193 5.990996 GTGATGGGAAAAATTGTGTGTGATT 59.009 36.000 0.00 0.00 0.00 2.57
221 231 7.671398 AGAAACATTTGTCTGGGATTCACTATT 59.329 33.333 0.00 0.00 0.00 1.73
233 243 5.277345 GGGATTCACTATTTGCGATGTACAC 60.277 44.000 0.00 0.00 0.00 2.90
235 245 5.524511 TTCACTATTTGCGATGTACACAC 57.475 39.130 0.00 0.00 0.00 3.82
240 250 1.854227 TTGCGATGTACACACGAACA 58.146 45.000 22.50 12.19 0.00 3.18
250 260 3.378959 ACACACGAACAGAAACGTTTC 57.621 42.857 29.36 29.36 40.76 2.78
251 261 2.222640 ACACACGAACAGAAACGTTTCG 60.223 45.455 29.72 25.66 41.92 3.46
256 266 1.329599 GAACAGAAACGTTTCGCTGGT 59.670 47.619 29.72 23.72 41.92 4.00
270 280 1.608025 CGCTGGTATTCACTGTGTGGT 60.608 52.381 7.79 0.00 33.87 4.16
277 289 4.802039 GGTATTCACTGTGTGGTATGTACG 59.198 45.833 7.79 0.00 33.87 3.67
285 297 3.251972 TGTGTGGTATGTACGTACGAACA 59.748 43.478 24.41 20.26 0.00 3.18
298 311 1.086696 ACGAACAGAATGATTGGGCG 58.913 50.000 0.00 0.00 39.69 6.13
323 336 6.645003 GTGTATAATTGTATGTGATGGCTCGA 59.355 38.462 0.00 0.00 0.00 4.04
352 367 1.259609 CATGAGCTCTTTTTGCCCCA 58.740 50.000 16.19 0.00 0.00 4.96
376 391 1.757699 GTGTGACCAGAGGACCTATCC 59.242 57.143 0.00 0.00 46.69 2.59
390 405 4.351111 GGACCTATCCCAGATGGTTTATGT 59.649 45.833 0.00 0.00 39.39 2.29
392 407 4.975147 ACCTATCCCAGATGGTTTATGTGA 59.025 41.667 0.00 0.00 31.96 3.58
394 409 5.942236 CCTATCCCAGATGGTTTATGTGATG 59.058 44.000 0.00 0.00 31.96 3.07
395 410 4.169059 TCCCAGATGGTTTATGTGATGG 57.831 45.455 0.00 0.00 31.96 3.51
396 411 2.624838 CCCAGATGGTTTATGTGATGGC 59.375 50.000 0.00 0.00 31.96 4.40
398 413 3.567164 CCAGATGGTTTATGTGATGGCTC 59.433 47.826 0.00 0.00 31.96 4.70
400 415 3.134623 AGATGGTTTATGTGATGGCTCGA 59.865 43.478 0.00 0.00 0.00 4.04
401 416 2.627945 TGGTTTATGTGATGGCTCGAC 58.372 47.619 0.00 0.00 0.00 4.20
402 417 1.940613 GGTTTATGTGATGGCTCGACC 59.059 52.381 0.00 0.00 39.84 4.79
412 444 3.159298 GGCTCGACCAATCACACAT 57.841 52.632 0.00 0.00 38.86 3.21
435 467 1.214325 GGCGGCGGTTTAAAATGCT 59.786 52.632 9.78 0.00 0.00 3.79
439 471 1.068885 CGGCGGTTTAAAATGCTGTCA 60.069 47.619 0.00 0.00 0.00 3.58
472 504 6.901265 GGTTAAAAACCGTTTGTATAGCAGA 58.099 36.000 0.00 0.00 42.62 4.26
523 559 4.162888 TCTCAGCACAATATGTCTCACCAT 59.837 41.667 0.00 0.00 0.00 3.55
524 560 4.193865 TCAGCACAATATGTCTCACCATG 58.806 43.478 0.00 0.00 0.00 3.66
537 573 7.921786 TGTCTCACCATGTTTTTAGGAATAG 57.078 36.000 0.00 0.00 0.00 1.73
538 574 7.685481 TGTCTCACCATGTTTTTAGGAATAGA 58.315 34.615 0.00 0.00 0.00 1.98
572 608 8.150945 TGAAGATAATGCTAAGAGATAACCCAC 58.849 37.037 0.00 0.00 0.00 4.61
574 610 8.958060 AGATAATGCTAAGAGATAACCCACTA 57.042 34.615 0.00 0.00 0.00 2.74
575 611 8.808092 AGATAATGCTAAGAGATAACCCACTAC 58.192 37.037 0.00 0.00 0.00 2.73
590 626 3.316308 CCCACTACAGGCATGCTTTTATC 59.684 47.826 18.92 0.00 0.00 1.75
592 628 2.614057 ACTACAGGCATGCTTTTATCGC 59.386 45.455 18.92 0.00 0.00 4.58
596 632 1.610522 AGGCATGCTTTTATCGCCATC 59.389 47.619 18.92 0.00 45.47 3.51
629 665 7.829211 ACAAATGCAAGGCTTAAGATAAGACTA 59.171 33.333 6.67 0.00 33.71 2.59
677 722 2.949177 ACCTGCCTGTGTCAATTACA 57.051 45.000 0.00 0.00 35.06 2.41
678 723 3.222173 ACCTGCCTGTGTCAATTACAA 57.778 42.857 0.00 0.00 40.63 2.41
701 761 5.925509 AGGTTAATGCCGCTTATTTCTCTA 58.074 37.500 0.00 0.00 0.00 2.43
705 765 7.386848 GGTTAATGCCGCTTATTTCTCTACATA 59.613 37.037 0.00 0.00 0.00 2.29
707 767 4.295870 TGCCGCTTATTTCTCTACATACG 58.704 43.478 0.00 0.00 0.00 3.06
726 786 3.020984 ACGTTGGCTCAGAAAAGGAAAA 58.979 40.909 0.00 0.00 0.00 2.29
727 787 3.636764 ACGTTGGCTCAGAAAAGGAAAAT 59.363 39.130 0.00 0.00 0.00 1.82
738 798 6.071108 TCAGAAAAGGAAAATGTTTCACACCA 60.071 34.615 3.35 0.00 34.40 4.17
763 825 9.182214 CATGAGAATAGGAAGGAAAAGAAATCA 57.818 33.333 0.00 0.00 0.00 2.57
797 859 4.679373 AGTGTCGCTTATGAATCAGGAT 57.321 40.909 0.00 0.00 0.00 3.24
1026 1090 1.549170 GTCCTCAAGGTTCGAAGCCTA 59.451 52.381 22.91 8.50 34.81 3.93
1061 1250 7.609532 GCTATTTATCATGCTAATCCTCTTGGT 59.390 37.037 0.00 0.00 34.23 3.67
1084 1273 7.013846 TGGTTCCTGGTAAGTTTTGTATCAAAG 59.986 37.037 0.00 0.00 0.00 2.77
1272 1468 0.251077 CCAAGACTTGCAAGGAGGCT 60.251 55.000 29.18 17.29 32.61 4.58
1281 1477 1.388065 GCAAGGAGGCTAGCGAGAGA 61.388 60.000 9.00 0.00 0.00 3.10
1289 1485 4.011023 GAGGCTAGCGAGAGATATACCAA 58.989 47.826 9.00 0.00 32.38 3.67
1303 1502 8.216423 AGAGATATACCAAAGATTGCAGTGATT 58.784 33.333 0.00 0.00 0.00 2.57
1425 1649 7.541783 TCGAATTCTTGCTGAATAAAAACATGG 59.458 33.333 3.52 0.00 43.99 3.66
1446 1670 3.181510 GGTGAAACTACCGCATGATGTTC 60.182 47.826 0.00 0.00 36.74 3.18
1447 1671 3.435327 GTGAAACTACCGCATGATGTTCA 59.565 43.478 0.00 0.00 0.00 3.18
1537 1765 8.189119 TCTGCAAGTTATTCCTTATTTTTGGT 57.811 30.769 0.00 0.00 33.76 3.67
1628 1856 5.432680 AACTCATGTCACCTTGATCTCAT 57.567 39.130 0.00 0.00 0.00 2.90
1646 1874 4.277423 TCTCATGTACGAGTTGTTCTCACA 59.723 41.667 0.00 0.00 42.88 3.58
1649 1877 4.316205 TGTACGAGTTGTTCTCACACAT 57.684 40.909 0.00 0.00 42.88 3.21
1661 1889 5.651139 TGTTCTCACACATAGGAGTACTACC 59.349 44.000 0.00 2.33 33.96 3.18
1677 1905 3.009723 ACTACCCAATTCGCATGTTCTG 58.990 45.455 0.00 0.00 0.00 3.02
1713 1941 6.897138 CGAGCGATTCTCAATAGAAGAAAAAC 59.103 38.462 0.00 0.00 44.79 2.43
1735 1963 4.142049 ACTCTAGTCTAGTTGGCTCATTGC 60.142 45.833 6.77 0.00 41.94 3.56
1736 1964 4.026744 TCTAGTCTAGTTGGCTCATTGCT 58.973 43.478 6.77 0.00 42.39 3.91
1737 1965 3.258971 AGTCTAGTTGGCTCATTGCTC 57.741 47.619 0.00 0.00 42.39 4.26
1738 1966 2.568956 AGTCTAGTTGGCTCATTGCTCA 59.431 45.455 0.00 0.00 42.39 4.26
1739 1967 3.199508 AGTCTAGTTGGCTCATTGCTCAT 59.800 43.478 0.00 0.00 42.39 2.90
1740 1968 3.944015 GTCTAGTTGGCTCATTGCTCATT 59.056 43.478 0.00 0.00 42.39 2.57
1741 1969 5.104776 AGTCTAGTTGGCTCATTGCTCATTA 60.105 40.000 0.00 0.00 42.39 1.90
1776 2004 4.870363 ACAATGACACCCGATTTCTTTTG 58.130 39.130 0.00 0.00 0.00 2.44
1792 2396 3.994392 TCTTTTGTGATCCACGCTACTTC 59.006 43.478 0.00 0.00 37.14 3.01
1849 6174 2.124903 CCACACGCGACTATTGATACC 58.875 52.381 15.93 0.00 0.00 2.73
1851 6176 3.043586 CACACGCGACTATTGATACCTC 58.956 50.000 15.93 0.00 0.00 3.85
1977 6302 0.108756 GTCGACTGGGACTTAGCCAC 60.109 60.000 8.70 0.00 34.09 5.01
2057 6383 1.303309 GGACGAATCTCCATGCAAGG 58.697 55.000 0.19 0.19 0.00 3.61
2059 6385 2.359900 GACGAATCTCCATGCAAGGTT 58.640 47.619 8.03 0.00 0.00 3.50
2078 6404 8.717821 GCAAGGTTAAATGAATATAGTATCGCA 58.282 33.333 0.00 0.00 0.00 5.10
2087 6413 8.868635 ATGAATATAGTATCGCATGAGACATG 57.131 34.615 0.00 7.29 38.81 3.21
2089 6415 8.186821 TGAATATAGTATCGCATGAGACATGAG 58.813 37.037 14.65 11.58 38.81 2.90
2285 7058 1.279527 TTGTTACGTTGGCTCGCTCG 61.280 55.000 0.00 0.00 0.00 5.03
2404 7184 9.018582 TGATGTGTTTGTTTTCACCATCATATA 57.981 29.630 0.00 0.00 32.78 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.732941 TGTGCAACGTGGCCTAATAG 58.267 50.000 13.54 0.00 42.39 1.73
12 13 6.595772 TTATGTGGAAAACATTTGTGCAAC 57.404 33.333 0.00 0.00 44.51 4.17
43 44 5.454755 GGTGTAGCATAGGTGTCCATTACAT 60.455 44.000 0.00 0.00 41.10 2.29
47 48 2.158957 CGGTGTAGCATAGGTGTCCATT 60.159 50.000 0.00 0.00 0.00 3.16
62 64 2.028748 GGTGCCTAGAAGAAACGGTGTA 60.029 50.000 0.00 0.00 0.00 2.90
67 69 1.068474 CACGGTGCCTAGAAGAAACG 58.932 55.000 0.00 0.00 0.00 3.60
140 150 7.147497 CCCATCACATCATATATGGTAGCCTTA 60.147 40.741 12.78 0.00 37.73 2.69
143 153 5.130975 TCCCATCACATCATATATGGTAGCC 59.869 44.000 12.78 0.00 37.73 3.93
148 158 9.647797 CAATTTTTCCCATCACATCATATATGG 57.352 33.333 12.78 0.39 38.90 2.74
151 161 9.199645 ACACAATTTTTCCCATCACATCATATA 57.800 29.630 0.00 0.00 0.00 0.86
153 163 7.039152 ACACACAATTTTTCCCATCACATCATA 60.039 33.333 0.00 0.00 0.00 2.15
195 205 5.388654 AGTGAATCCCAGACAAATGTTTCT 58.611 37.500 0.00 0.00 0.00 2.52
221 231 1.790043 CTGTTCGTGTGTACATCGCAA 59.210 47.619 15.29 9.71 38.33 4.85
233 243 1.005347 AGCGAAACGTTTCTGTTCGTG 60.005 47.619 31.88 18.82 40.19 4.35
235 245 1.647748 CAGCGAAACGTTTCTGTTCG 58.352 50.000 31.88 23.01 35.07 3.95
240 250 3.185797 GTGAATACCAGCGAAACGTTTCT 59.814 43.478 31.88 18.99 35.07 2.52
250 260 1.078709 CCACACAGTGAATACCAGCG 58.921 55.000 7.81 0.00 35.23 5.18
251 261 2.185004 ACCACACAGTGAATACCAGC 57.815 50.000 7.81 0.00 35.23 4.85
256 266 5.648178 ACGTACATACCACACAGTGAATA 57.352 39.130 7.81 0.00 35.23 1.75
270 280 6.693978 CCAATCATTCTGTTCGTACGTACATA 59.306 38.462 24.89 16.77 0.00 2.29
277 289 2.030457 CGCCCAATCATTCTGTTCGTAC 59.970 50.000 0.00 0.00 0.00 3.67
285 297 5.827797 ACAATTATACACGCCCAATCATTCT 59.172 36.000 0.00 0.00 0.00 2.40
298 311 6.645003 TCGAGCCATCACATACAATTATACAC 59.355 38.462 0.00 0.00 0.00 2.90
323 336 3.430042 AAGAGCTCATGTGTGATTGGT 57.570 42.857 17.77 0.00 32.98 3.67
326 339 4.553323 GCAAAAAGAGCTCATGTGTGATT 58.447 39.130 17.77 0.00 32.98 2.57
330 343 1.615392 GGGCAAAAAGAGCTCATGTGT 59.385 47.619 17.77 0.00 31.20 3.72
352 367 1.740285 GTCCTCTGGTCACACACGT 59.260 57.895 0.00 0.00 0.00 4.49
376 391 3.559069 AGCCATCACATAAACCATCTGG 58.441 45.455 0.00 0.00 42.17 3.86
378 393 3.134623 TCGAGCCATCACATAAACCATCT 59.865 43.478 0.00 0.00 0.00 2.90
394 409 0.729116 CATGTGTGATTGGTCGAGCC 59.271 55.000 12.85 4.60 37.90 4.70
395 410 0.097674 GCATGTGTGATTGGTCGAGC 59.902 55.000 7.89 7.89 0.00 5.03
396 411 1.441738 TGCATGTGTGATTGGTCGAG 58.558 50.000 0.00 0.00 0.00 4.04
398 413 1.135603 CCTTGCATGTGTGATTGGTCG 60.136 52.381 0.00 0.00 0.00 4.79
400 415 0.604578 GCCTTGCATGTGTGATTGGT 59.395 50.000 0.00 0.00 0.00 3.67
401 416 0.457166 CGCCTTGCATGTGTGATTGG 60.457 55.000 0.00 0.00 0.00 3.16
402 417 0.457166 CCGCCTTGCATGTGTGATTG 60.457 55.000 0.00 0.00 0.00 2.67
403 418 1.885157 CCGCCTTGCATGTGTGATT 59.115 52.632 0.00 0.00 0.00 2.57
404 419 2.703798 GCCGCCTTGCATGTGTGAT 61.704 57.895 0.00 0.00 0.00 3.06
405 420 3.364441 GCCGCCTTGCATGTGTGA 61.364 61.111 0.00 0.00 0.00 3.58
412 444 1.735376 TTTTAAACCGCCGCCTTGCA 61.735 50.000 0.00 0.00 0.00 4.08
435 467 3.294038 TTTTAACCCCTTTCCGTGACA 57.706 42.857 0.00 0.00 0.00 3.58
472 504 3.444034 TCTCTTAACACTAGTGCAGCGAT 59.556 43.478 22.90 0.00 0.00 4.58
502 534 3.979101 TGGTGAGACATATTGTGCTGA 57.021 42.857 0.00 0.00 0.00 4.26
555 591 4.649674 CCTGTAGTGGGTTATCTCTTAGCA 59.350 45.833 0.00 0.00 0.00 3.49
572 608 2.031682 GGCGATAAAAGCATGCCTGTAG 60.032 50.000 15.66 1.36 42.44 2.74
574 610 0.740737 GGCGATAAAAGCATGCCTGT 59.259 50.000 15.66 0.00 42.44 4.00
575 611 0.740149 TGGCGATAAAAGCATGCCTG 59.260 50.000 15.66 0.00 45.90 4.85
590 626 4.095410 TGCATTTGTTTTAGAGATGGCG 57.905 40.909 0.00 0.00 0.00 5.69
592 628 4.866486 GCCTTGCATTTGTTTTAGAGATGG 59.134 41.667 0.00 0.00 0.00 3.51
596 632 7.370383 TCTTAAGCCTTGCATTTGTTTTAGAG 58.630 34.615 0.00 0.00 0.00 2.43
659 704 2.489329 CCTTGTAATTGACACAGGCAGG 59.511 50.000 0.00 0.00 37.96 4.85
677 722 5.193679 AGAGAAATAAGCGGCATTAACCTT 58.806 37.500 1.45 0.00 0.00 3.50
678 723 4.781934 AGAGAAATAAGCGGCATTAACCT 58.218 39.130 1.45 0.00 0.00 3.50
701 761 3.074412 CCTTTTCTGAGCCAACGTATGT 58.926 45.455 0.00 0.00 0.00 2.29
705 765 2.341846 TTCCTTTTCTGAGCCAACGT 57.658 45.000 0.00 0.00 0.00 3.99
707 767 4.948847 ACATTTTCCTTTTCTGAGCCAAC 58.051 39.130 0.00 0.00 0.00 3.77
738 798 9.933240 ATGATTTCTTTTCCTTCCTATTCTCAT 57.067 29.630 0.00 0.00 0.00 2.90
797 859 4.700692 GTGTGATCCTATATACTCGCTCCA 59.299 45.833 0.00 0.00 0.00 3.86
902 965 6.692849 TCTCTTATAGCCATGGATGATGTT 57.307 37.500 18.40 0.00 0.00 2.71
970 1034 8.659491 TCAATGATTATCAAGACACGAAGAAAG 58.341 33.333 0.00 0.00 0.00 2.62
1026 1090 8.853077 TTAGCATGATAAATAGCAAGCATAGT 57.147 30.769 0.00 0.00 38.59 2.12
1042 1231 4.414846 AGGAACCAAGAGGATTAGCATGAT 59.585 41.667 0.00 0.00 38.69 2.45
1061 1250 9.802039 ATACTTTGATACAAAACTTACCAGGAA 57.198 29.630 0.00 0.00 0.00 3.36
1084 1273 9.841880 GGAAGTTCCTTGTTCTTTAAATGATAC 57.158 33.333 15.09 0.00 32.53 2.24
1144 1333 7.818997 ATGATGCACAGAGTATGAATTTCAT 57.181 32.000 15.78 15.78 40.72 2.57
1218 1410 7.485277 CCTACAAAACAAACAACACAATACGAA 59.515 33.333 0.00 0.00 0.00 3.85
1231 1427 4.229876 GCATCAGAGCCTACAAAACAAAC 58.770 43.478 0.00 0.00 0.00 2.93
1272 1468 6.015434 TGCAATCTTTGGTATATCTCTCGCTA 60.015 38.462 0.00 0.00 0.00 4.26
1281 1477 9.236006 GGATAATCACTGCAATCTTTGGTATAT 57.764 33.333 0.00 0.00 0.00 0.86
1289 1485 5.889853 ACACATGGATAATCACTGCAATCTT 59.110 36.000 0.00 0.00 0.00 2.40
1303 1502 2.016604 GCAGGCCGAAACACATGGATA 61.017 52.381 0.00 0.00 0.00 2.59
1404 1628 7.048629 TCACCATGTTTTTATTCAGCAAGAA 57.951 32.000 0.00 0.00 41.28 2.52
1425 1649 3.435327 TGAACATCATGCGGTAGTTTCAC 59.565 43.478 0.00 0.00 0.00 3.18
1598 1826 4.292186 AGGTGACATGAGTTTGTAGCAT 57.708 40.909 0.00 0.00 0.00 3.79
1646 1874 4.038883 GCGAATTGGGTAGTACTCCTATGT 59.961 45.833 0.00 0.00 0.00 2.29
1649 1877 3.634504 TGCGAATTGGGTAGTACTCCTA 58.365 45.455 0.00 0.00 0.00 2.94
1661 1889 2.086869 ACTCCAGAACATGCGAATTGG 58.913 47.619 0.00 0.00 0.00 3.16
1677 1905 2.554893 AGAATCGCTCGAATAGGACTCC 59.445 50.000 0.00 0.00 0.00 3.85
1713 1941 4.367450 GCAATGAGCCAACTAGACTAGAG 58.633 47.826 16.55 7.92 37.23 2.43
1735 1963 6.922247 ATTGTCAGAGCAATGAGTAATGAG 57.078 37.500 0.00 0.00 37.65 2.90
1776 2004 6.147328 AGTTTTTAAGAAGTAGCGTGGATCAC 59.853 38.462 0.00 0.00 0.00 3.06
1816 6140 0.530650 CGTGTGGACACAGAGCACTT 60.531 55.000 5.22 0.00 46.75 3.16
1819 6143 2.280119 GCGTGTGGACACAGAGCA 60.280 61.111 20.66 0.00 46.75 4.26
1836 6160 4.272748 TCTCACGTGAGGTATCAATAGTCG 59.727 45.833 37.82 14.36 42.30 4.18
1837 6161 5.752892 TCTCACGTGAGGTATCAATAGTC 57.247 43.478 37.82 0.00 42.30 2.59
1906 6231 4.146443 GCGAACAAGCAACAACTGAATAAC 59.854 41.667 0.00 0.00 37.05 1.89
2039 6365 2.029838 ACCTTGCATGGAGATTCGTC 57.970 50.000 24.48 0.00 0.00 4.20
2225 6998 4.219115 TCAACACAAGGCCCTTTTTATCA 58.781 39.130 0.00 0.00 0.00 2.15
2322 7095 8.956426 ACTTGAAGAACTCTGAATAAACACAAA 58.044 29.630 0.00 0.00 0.00 2.83
2378 7158 5.588958 TGATGGTGAAAACAAACACATCA 57.411 34.783 0.00 0.00 38.57 3.07


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

AutoCloner maintained by Alex Coulton.