Multiple sequence alignment - TraesCS2B01G412400

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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 TraesCS2B01G412400 chr2B 100.000 2294 0 0 1 2294 587243836 587241543 0.000000e+00 4237.0
1 TraesCS2B01G412400 chr2A 87.477 2220 190 44 65 2234 644249640 644247459 0.000000e+00 2479.0
2 TraesCS2B01G412400 chr2A 80.921 152 17 10 318 466 562722014 562721872 2.410000e-20 110.0
3 TraesCS2B01G412400 chr2D 91.734 1488 88 19 662 2124 499728171 499726694 0.000000e+00 2034.0
4 TraesCS2B01G412400 chr2D 81.748 515 63 16 1710 2220 499238208 499237721 3.550000e-108 401.0
5 TraesCS2B01G412400 chr2D 80.645 217 40 2 399 614 131039280 131039495 1.410000e-37 167.0
6 TraesCS2B01G412400 chr2D 98.361 61 0 1 2235 2294 499726531 499726471 3.120000e-19 106.0
7 TraesCS2B01G412400 chr5A 84.259 216 30 2 400 614 315263605 315263393 8.310000e-50 207.0
8 TraesCS2B01G412400 chr5A 81.193 218 40 1 397 614 94748061 94748277 8.420000e-40 174.0
9 TraesCS2B01G412400 chr1A 82.870 216 34 3 400 614 21408023 21408236 8.360000e-45 191.0
10 TraesCS2B01G412400 chrUn 80.153 262 38 10 355 614 40740799 40740550 1.400000e-42 183.0
11 TraesCS2B01G412400 chrUn 80.153 262 38 10 355 614 40747106 40747355 1.400000e-42 183.0
12 TraesCS2B01G412400 chrUn 80.153 262 38 10 355 614 303400353 303400104 1.400000e-42 183.0
13 TraesCS2B01G412400 chr1D 78.378 296 54 10 323 613 378289255 378289545 1.400000e-42 183.0
14 TraesCS2B01G412400 chr4A 79.054 148 19 5 4 148 6005784 6005646 8.730000e-15 91.6
15 TraesCS2B01G412400 chr4D 88.732 71 8 0 78 148 463702956 463703026 1.130000e-13 87.9
16 TraesCS2B01G412400 chr7B 81.818 77 6 5 355 431 44071924 44071992 8.850000e-05 58.4


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 TraesCS2B01G412400 chr2B 587241543 587243836 2293 True 4237 4237 100.0000 1 2294 1 chr2B.!!$R1 2293
1 TraesCS2B01G412400 chr2A 644247459 644249640 2181 True 2479 2479 87.4770 65 2234 1 chr2A.!!$R2 2169
2 TraesCS2B01G412400 chr2D 499726471 499728171 1700 True 1070 2034 95.0475 662 2294 2 chr2D.!!$R2 1632

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
395 400 0.319555 AATGCACGCACACTCTACGT 60.32 50.0 0.0 0.0 41.45 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1618 1674 0.81401 CACCTGCGTTAGTATGGCCC 60.814 60.0 0.0 0.0 0.0 5.8 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
52 53 3.930504 GGCTCTGCCCAAGATTGG 58.069 61.111 4.53 4.53 44.06 3.16
66 67 6.136541 CCAAGATTGGCTATTCCTTTGTAC 57.863 41.667 0.00 0.00 42.21 2.90
67 68 5.888161 CCAAGATTGGCTATTCCTTTGTACT 59.112 40.000 0.00 0.00 42.21 2.73
68 69 6.378280 CCAAGATTGGCTATTCCTTTGTACTT 59.622 38.462 0.00 0.00 42.21 2.24
69 70 7.093771 CCAAGATTGGCTATTCCTTTGTACTTT 60.094 37.037 0.00 0.00 42.21 2.66
70 71 7.396540 AGATTGGCTATTCCTTTGTACTTTG 57.603 36.000 0.00 0.00 35.26 2.77
71 72 7.175104 AGATTGGCTATTCCTTTGTACTTTGA 58.825 34.615 0.00 0.00 35.26 2.69
72 73 7.669722 AGATTGGCTATTCCTTTGTACTTTGAA 59.330 33.333 0.00 0.00 35.26 2.69
73 74 7.775053 TTGGCTATTCCTTTGTACTTTGAAT 57.225 32.000 0.00 0.68 35.26 2.57
138 140 6.073314 CCCCTCAACATCATGAATTAAGGAT 58.927 40.000 12.10 0.00 0.00 3.24
174 177 2.683768 GAGGGATCCACATGACCTAGT 58.316 52.381 15.23 0.00 0.00 2.57
179 182 4.421131 GGATCCACATGACCTAGTAGGAT 58.579 47.826 23.50 7.09 37.67 3.24
195 198 8.861086 CCTAGTAGGATAGATTGCAGTAAGAAA 58.139 37.037 11.09 0.00 37.67 2.52
199 202 6.054295 AGGATAGATTGCAGTAAGAAAGCAG 58.946 40.000 0.00 0.00 39.72 4.24
205 208 8.115490 AGATTGCAGTAAGAAAGCAGTAATTT 57.885 30.769 0.00 0.00 39.72 1.82
223 226 7.805071 CAGTAATTTTGATGCTTCGTCTTTCTT 59.195 33.333 0.00 0.00 0.00 2.52
264 269 8.814038 AATTGCCTCTGTTATTCTTGTTCTAT 57.186 30.769 0.00 0.00 0.00 1.98
367 372 2.802816 GTCGCTCACATACATTCATCCC 59.197 50.000 0.00 0.00 0.00 3.85
376 381 5.999600 CACATACATTCATCCCTATGAGCAA 59.000 40.000 0.00 0.00 42.97 3.91
382 387 3.216800 TCATCCCTATGAGCAAATGCAC 58.783 45.455 8.28 1.72 45.16 4.57
394 399 0.790207 AAATGCACGCACACTCTACG 59.210 50.000 0.00 0.00 0.00 3.51
395 400 0.319555 AATGCACGCACACTCTACGT 60.320 50.000 0.00 0.00 41.45 3.57
396 401 0.732880 ATGCACGCACACTCTACGTC 60.733 55.000 0.00 0.00 38.09 4.34
397 402 1.081376 GCACGCACACTCTACGTCT 60.081 57.895 0.00 0.00 38.09 4.18
398 403 1.066114 GCACGCACACTCTACGTCTC 61.066 60.000 0.00 0.00 38.09 3.36
399 404 0.517755 CACGCACACTCTACGTCTCT 59.482 55.000 0.00 0.00 38.09 3.10
400 405 1.730612 CACGCACACTCTACGTCTCTA 59.269 52.381 0.00 0.00 38.09 2.43
401 406 1.731160 ACGCACACTCTACGTCTCTAC 59.269 52.381 0.00 0.00 34.35 2.59
402 407 1.730612 CGCACACTCTACGTCTCTACA 59.269 52.381 0.00 0.00 0.00 2.74
414 419 2.033550 CGTCTCTACACCTATGAGCACC 59.966 54.545 0.00 0.00 0.00 5.01
418 423 2.024369 TCTACACCTATGAGCACCTCCA 60.024 50.000 0.00 0.00 0.00 3.86
427 432 1.261480 GAGCACCTCCAAGAGACTGA 58.739 55.000 0.00 0.00 0.00 3.41
428 433 1.204467 GAGCACCTCCAAGAGACTGAG 59.796 57.143 0.00 0.00 0.00 3.35
441 446 1.339610 AGACTGAGCCGACATAGCATC 59.660 52.381 0.00 0.00 0.00 3.91
449 454 2.992543 GCCGACATAGCATCTTGAGATC 59.007 50.000 0.00 0.00 31.21 2.75
459 464 9.142515 CATAGCATCTTGAGATCTTATGAAGTC 57.857 37.037 7.10 1.42 33.79 3.01
461 466 7.737869 AGCATCTTGAGATCTTATGAAGTCAT 58.262 34.615 7.10 0.00 35.02 3.06
465 470 8.071177 TCTTGAGATCTTATGAAGTCATCACA 57.929 34.615 0.00 0.00 41.93 3.58
473 478 1.067565 TGAAGTCATCACAGACGCCTC 60.068 52.381 0.00 0.00 43.24 4.70
480 485 3.295273 ACAGACGCCTCGCAGTCA 61.295 61.111 9.89 0.00 35.68 3.41
488 493 1.079127 CCTCGCAGTCAACGGGAAT 60.079 57.895 0.00 0.00 30.77 3.01
489 494 1.361668 CCTCGCAGTCAACGGGAATG 61.362 60.000 2.91 2.91 44.23 2.67
491 496 0.669318 TCGCAGTCAACGGGAATGTC 60.669 55.000 8.26 1.60 43.35 3.06
497 502 1.550976 GTCAACGGGAATGTCTCCTCT 59.449 52.381 0.00 0.00 44.68 3.69
501 506 1.272760 ACGGGAATGTCTCCTCTCACT 60.273 52.381 0.00 0.00 44.68 3.41
505 510 3.368948 GGGAATGTCTCCTCTCACTGAAC 60.369 52.174 0.00 0.00 44.68 3.18
506 511 3.506810 GAATGTCTCCTCTCACTGAACG 58.493 50.000 0.00 0.00 0.00 3.95
515 520 2.989840 CTCTCACTGAACGAACATCACC 59.010 50.000 0.00 0.00 0.00 4.02
516 521 1.721389 CTCACTGAACGAACATCACCG 59.279 52.381 0.00 0.00 0.00 4.94
521 526 1.529438 TGAACGAACATCACCGAAAGC 59.471 47.619 0.00 0.00 0.00 3.51
524 529 1.274167 ACGAACATCACCGAAAGCCTA 59.726 47.619 0.00 0.00 0.00 3.93
537 542 7.066525 TCACCGAAAGCCTAAAATAAATACAGG 59.933 37.037 0.00 0.00 0.00 4.00
570 575 6.183360 CGAGTATCAATGTCAAGTCTAGGACA 60.183 42.308 9.08 9.08 40.98 4.02
579 584 4.710375 GTCAAGTCTAGGACATGAACCCTA 59.290 45.833 0.00 6.42 40.95 3.53
580 585 5.187186 GTCAAGTCTAGGACATGAACCCTAA 59.813 44.000 0.00 0.00 40.95 2.69
587 592 3.456277 AGGACATGAACCCTAATGGACTC 59.544 47.826 0.00 0.00 38.00 3.36
591 596 3.199442 TGAACCCTAATGGACTCAGGA 57.801 47.619 0.00 0.00 38.00 3.86
617 622 1.825474 CTGTCCTCCTAACCATCACGT 59.175 52.381 0.00 0.00 0.00 4.49
619 624 2.028476 TGTCCTCCTAACCATCACGTTG 60.028 50.000 0.00 0.00 0.00 4.10
650 655 9.722056 GCACGTGAATTTCTTTTCAATAGATAT 57.278 29.630 22.23 0.00 37.36 1.63
738 743 3.863142 ATCGCCCTATATACGTTGACC 57.137 47.619 0.00 0.00 0.00 4.02
759 768 3.120199 CCGATGACAACAGCAAAGGTAAG 60.120 47.826 0.00 0.00 32.22 2.34
803 812 3.119602 ACGCAACGATGTAAGCTCTCTAA 60.120 43.478 0.00 0.00 0.00 2.10
808 817 4.861210 ACGATGTAAGCTCTCTAAATCGG 58.139 43.478 16.92 4.04 39.66 4.18
827 836 2.910482 CGGCAGACACAATGAAAAATCG 59.090 45.455 0.00 0.00 0.00 3.34
845 854 2.485903 TCGCAACACAATAAACCGTCT 58.514 42.857 0.00 0.00 0.00 4.18
864 873 2.158986 TCTAGTCCTAGGAACTCGACCG 60.159 54.545 14.65 0.00 41.75 4.79
868 877 0.465097 CCTAGGAACTCGACCGCCTA 60.465 60.000 1.05 0.00 41.75 3.93
903 914 4.565564 CACCTATAAAACCTCGAACCGAAG 59.434 45.833 0.00 0.00 34.74 3.79
952 965 2.092323 AGGAAAAAGGTAGCGCCATTC 58.908 47.619 2.29 0.00 40.61 2.67
989 1002 3.004106 GCTATCATGGCCACAAAGATGAC 59.996 47.826 8.16 2.93 30.92 3.06
1297 1310 1.445066 CACATCGACTGCTGAGCGT 60.445 57.895 0.00 0.12 0.00 5.07
1299 1312 1.153958 CATCGACTGCTGAGCGTGA 60.154 57.895 6.66 5.66 0.00 4.35
1300 1313 1.153939 ATCGACTGCTGAGCGTGAC 60.154 57.895 6.66 0.00 0.00 3.67
1301 1314 2.549611 ATCGACTGCTGAGCGTGACC 62.550 60.000 6.66 0.00 0.00 4.02
1302 1315 2.340078 GACTGCTGAGCGTGACCA 59.660 61.111 6.66 0.00 0.00 4.02
1303 1316 2.024319 GACTGCTGAGCGTGACCAC 61.024 63.158 6.66 0.00 0.00 4.16
1304 1317 2.029518 CTGCTGAGCGTGACCACA 59.970 61.111 0.00 0.00 0.00 4.17
1306 1319 3.044305 GCTGAGCGTGACCACACC 61.044 66.667 0.00 0.00 43.34 4.16
1307 1320 2.734723 CTGAGCGTGACCACACCG 60.735 66.667 0.85 0.00 43.34 4.94
1308 1321 3.207547 CTGAGCGTGACCACACCGA 62.208 63.158 0.85 0.00 43.34 4.69
1310 1323 4.640855 AGCGTGACCACACCGACG 62.641 66.667 0.85 0.00 43.34 5.12
1311 1324 4.936823 GCGTGACCACACCGACGT 62.937 66.667 0.00 0.00 43.34 4.34
1313 1326 3.335534 GTGACCACACCGACGTGC 61.336 66.667 0.00 0.00 44.40 5.34
1315 1328 4.634133 GACCACACCGACGTGCGA 62.634 66.667 0.00 0.00 44.40 5.10
1316 1329 4.640855 ACCACACCGACGTGCGAG 62.641 66.667 0.00 0.00 44.40 5.03
1330 1343 4.697756 CGAGCAACCCGGCCAAGA 62.698 66.667 2.24 0.00 0.00 3.02
1332 1345 3.553095 GAGCAACCCGGCCAAGACT 62.553 63.158 2.24 0.00 0.00 3.24
1333 1346 2.180159 GAGCAACCCGGCCAAGACTA 62.180 60.000 2.24 0.00 0.00 2.59
1334 1347 2.038837 GCAACCCGGCCAAGACTAC 61.039 63.158 2.24 0.00 0.00 2.73
1339 1366 4.157120 CGGCCAAGACTACCCCCG 62.157 72.222 2.24 0.00 0.00 5.73
1357 1384 2.440501 CCGAAATAATGAAGTGCACGC 58.559 47.619 12.01 8.53 0.00 5.34
1371 1398 2.103538 ACGCGTCGTGTGTGAAGT 59.896 55.556 11.27 0.00 40.56 3.01
1372 1399 2.228241 ACGCGTCGTGTGTGAAGTG 61.228 57.895 11.27 0.00 40.56 3.16
1373 1400 2.228241 CGCGTCGTGTGTGAAGTGT 61.228 57.895 0.00 0.00 0.00 3.55
1374 1401 1.272715 GCGTCGTGTGTGAAGTGTG 59.727 57.895 0.00 0.00 0.00 3.82
1375 1402 1.143373 GCGTCGTGTGTGAAGTGTGA 61.143 55.000 0.00 0.00 0.00 3.58
1395 1422 8.456471 AGTGTGATGAATAAATGTCTGAATGTG 58.544 33.333 0.00 0.00 0.00 3.21
1431 1465 1.351017 TCGGCAGTTCAAAAGGGAGAT 59.649 47.619 0.00 0.00 0.00 2.75
1464 1501 2.511373 CGCGCCACATTCCAGCTA 60.511 61.111 0.00 0.00 0.00 3.32
1465 1502 2.528743 CGCGCCACATTCCAGCTAG 61.529 63.158 0.00 0.00 0.00 3.42
1466 1503 1.450312 GCGCCACATTCCAGCTAGT 60.450 57.895 0.00 0.00 0.00 2.57
1467 1504 0.179084 GCGCCACATTCCAGCTAGTA 60.179 55.000 0.00 0.00 0.00 1.82
1483 1536 6.458751 CCAGCTAGTACATGCCAATTAACAAG 60.459 42.308 0.00 0.00 0.00 3.16
1521 1574 4.543590 AAGTTCCATGTCGATCAGTCTT 57.456 40.909 0.00 0.00 0.00 3.01
1537 1590 9.416794 CGATCAGTCTTATAGCAGAATAACAAT 57.583 33.333 0.00 0.00 0.00 2.71
1562 1615 0.597118 GCTACTGAGCTCCAGCGATG 60.597 60.000 12.15 0.00 46.81 3.84
1581 1637 4.668941 CGATGAAACGTGCATCAAGCTTAA 60.669 41.667 23.34 0.00 45.94 1.85
1597 1653 9.683069 ATCAAGCTTAAGTTCAACAAAATACAG 57.317 29.630 0.00 0.00 0.00 2.74
1618 1674 2.163390 CATCTCACGACAGCAGCCG 61.163 63.158 0.00 0.00 0.00 5.52
1619 1675 3.362399 ATCTCACGACAGCAGCCGG 62.362 63.158 0.00 0.00 0.00 6.13
1627 1683 4.181010 CAGCAGCCGGGCCATACT 62.181 66.667 17.02 5.07 0.00 2.12
1676 1732 1.608590 CCCAGGTGACACAAACATCAC 59.391 52.381 8.08 0.00 43.75 3.06
1680 1736 0.384230 GTGACACAAACATCACGCCG 60.384 55.000 0.00 0.00 36.20 6.46
1684 1740 0.384230 CACAAACATCACGCCGACAC 60.384 55.000 0.00 0.00 0.00 3.67
1686 1742 0.110688 CAAACATCACGCCGACACAG 60.111 55.000 0.00 0.00 0.00 3.66
1690 1746 0.667487 CATCACGCCGACACAGAACT 60.667 55.000 0.00 0.00 0.00 3.01
1702 1761 5.388111 CGACACAGAACTCGTACTATTTCA 58.612 41.667 1.25 0.00 0.00 2.69
1753 1812 7.572523 TTTGGACCTTGATTTCTGCATATAG 57.427 36.000 0.00 0.00 0.00 1.31
1802 1861 1.212751 GCAACCGGATTTGTCAGCC 59.787 57.895 9.46 0.00 0.00 4.85
1831 1890 5.048013 GGTATGACATGTCCGTATGATGAGA 60.048 44.000 22.85 0.00 0.00 3.27
1832 1891 4.574599 TGACATGTCCGTATGATGAGAG 57.425 45.455 22.85 0.00 0.00 3.20
1879 1939 3.367703 CCTGAAACCTTGGCTTGCTTATG 60.368 47.826 0.00 0.00 0.00 1.90
1951 2014 3.067180 CGGCCTTGATTACTGCATTTGAT 59.933 43.478 0.00 0.00 0.00 2.57
2011 2074 4.119862 GGTCTTGCGCATCTTTGACTATA 58.880 43.478 12.75 0.00 0.00 1.31
2050 2113 2.268298 CTGTTGGATAAAGTCGTCCCG 58.732 52.381 0.00 0.00 33.45 5.14
2144 2207 8.084684 AGAGCCTTTCAATTTCATTCAAACTAC 58.915 33.333 0.00 0.00 0.00 2.73
2164 2227 5.876460 ACTACGTAGTTTTCAACCAACAGTT 59.124 36.000 22.45 0.00 37.78 3.16
2169 2232 7.281549 ACGTAGTTTTCAACCAACAGTTATTCT 59.718 33.333 0.00 0.00 37.78 2.40
2250 2408 3.904800 TTATCCTGGAATCGAGCAACA 57.095 42.857 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.396540 AAGTACAAAGGAATAGCCAATCTTG 57.603 36.000 0.00 0.00 40.02 3.02
45 46 7.669722 TCAAAGTACAAAGGAATAGCCAATCTT 59.330 33.333 0.00 0.00 40.02 2.40
46 47 7.175104 TCAAAGTACAAAGGAATAGCCAATCT 58.825 34.615 0.00 0.00 40.02 2.40
47 48 7.391148 TCAAAGTACAAAGGAATAGCCAATC 57.609 36.000 0.00 0.00 40.02 2.67
48 49 7.775053 TTCAAAGTACAAAGGAATAGCCAAT 57.225 32.000 0.00 0.00 40.02 3.16
49 50 7.775053 ATTCAAAGTACAAAGGAATAGCCAA 57.225 32.000 0.00 0.00 40.02 4.52
102 103 4.046286 TGTTGAGGGGTGCTCAATATTT 57.954 40.909 0.00 0.00 41.95 1.40
103 104 3.737559 TGTTGAGGGGTGCTCAATATT 57.262 42.857 0.00 0.00 41.95 1.28
108 109 0.994247 ATGATGTTGAGGGGTGCTCA 59.006 50.000 0.00 0.00 0.00 4.26
112 113 5.068198 CCTTAATTCATGATGTTGAGGGGTG 59.932 44.000 17.61 1.27 0.00 4.61
113 114 5.044179 TCCTTAATTCATGATGTTGAGGGGT 60.044 40.000 21.76 0.00 31.57 4.95
138 140 2.206900 TCCACTGGGAGGCAGGAA 59.793 61.111 0.00 0.00 38.64 3.36
174 177 7.124573 TGCTTTCTTACTGCAATCTATCCTA 57.875 36.000 0.00 0.00 33.48 2.94
179 182 8.792830 AATTACTGCTTTCTTACTGCAATCTA 57.207 30.769 0.00 0.00 36.22 1.98
195 198 4.697352 AGACGAAGCATCAAAATTACTGCT 59.303 37.500 0.00 0.00 46.41 4.24
199 202 9.267096 CTAAGAAAGACGAAGCATCAAAATTAC 57.733 33.333 0.00 0.00 0.00 1.89
205 208 8.948631 ATATTCTAAGAAAGACGAAGCATCAA 57.051 30.769 0.00 0.00 32.51 2.57
333 338 3.566742 TGTGAGCGACTTTGACTGTACTA 59.433 43.478 0.00 0.00 0.00 1.82
334 339 2.361119 TGTGAGCGACTTTGACTGTACT 59.639 45.455 0.00 0.00 0.00 2.73
340 345 4.388773 TGAATGTATGTGAGCGACTTTGAC 59.611 41.667 0.00 0.00 0.00 3.18
343 348 4.572389 GGATGAATGTATGTGAGCGACTTT 59.428 41.667 0.00 0.00 0.00 2.66
367 372 1.130938 TGTGCGTGCATTTGCTCATAG 59.869 47.619 3.94 0.00 42.66 2.23
376 381 0.319555 ACGTAGAGTGTGCGTGCATT 60.320 50.000 1.88 0.00 46.69 3.56
382 387 1.730612 TGTAGAGACGTAGAGTGTGCG 59.269 52.381 0.00 0.00 40.63 5.34
394 399 3.292460 AGGTGCTCATAGGTGTAGAGAC 58.708 50.000 0.00 0.00 0.00 3.36
395 400 3.556999 GAGGTGCTCATAGGTGTAGAGA 58.443 50.000 0.00 0.00 0.00 3.10
396 401 2.625790 GGAGGTGCTCATAGGTGTAGAG 59.374 54.545 0.00 0.00 31.08 2.43
397 402 2.024369 TGGAGGTGCTCATAGGTGTAGA 60.024 50.000 0.00 0.00 31.08 2.59
398 403 2.388735 TGGAGGTGCTCATAGGTGTAG 58.611 52.381 0.00 0.00 31.08 2.74
399 404 2.543037 TGGAGGTGCTCATAGGTGTA 57.457 50.000 0.00 0.00 31.08 2.90
400 405 1.556911 CTTGGAGGTGCTCATAGGTGT 59.443 52.381 0.00 0.00 31.08 4.16
401 406 1.833630 TCTTGGAGGTGCTCATAGGTG 59.166 52.381 0.00 0.00 31.08 4.00
402 407 2.114616 CTCTTGGAGGTGCTCATAGGT 58.885 52.381 0.00 0.00 31.08 3.08
414 419 0.172352 GTCGGCTCAGTCTCTTGGAG 59.828 60.000 0.00 0.00 0.00 3.86
418 423 1.407258 GCTATGTCGGCTCAGTCTCTT 59.593 52.381 0.00 0.00 0.00 2.85
427 432 2.034878 TCTCAAGATGCTATGTCGGCT 58.965 47.619 0.00 0.00 0.00 5.52
428 433 2.515926 TCTCAAGATGCTATGTCGGC 57.484 50.000 0.00 0.00 0.00 5.54
441 446 8.196103 TCTGTGATGACTTCATAAGATCTCAAG 58.804 37.037 0.00 0.00 36.54 3.02
449 454 3.553511 GGCGTCTGTGATGACTTCATAAG 59.446 47.826 0.00 0.00 36.54 1.73
459 464 2.125952 TGCGAGGCGTCTGTGATG 60.126 61.111 0.00 0.00 0.00 3.07
461 466 3.268965 GACTGCGAGGCGTCTGTGA 62.269 63.158 0.00 0.00 32.57 3.58
465 470 2.049063 GTTGACTGCGAGGCGTCT 60.049 61.111 4.69 0.00 34.86 4.18
473 478 0.670546 AGACATTCCCGTTGACTGCG 60.671 55.000 0.00 0.00 0.00 5.18
485 490 3.191581 TCGTTCAGTGAGAGGAGACATTC 59.808 47.826 0.00 0.00 0.00 2.67
488 493 2.271944 TCGTTCAGTGAGAGGAGACA 57.728 50.000 0.00 0.00 0.00 3.41
489 494 2.293677 TGTTCGTTCAGTGAGAGGAGAC 59.706 50.000 0.00 0.00 0.00 3.36
491 496 3.057245 TGATGTTCGTTCAGTGAGAGGAG 60.057 47.826 0.00 0.00 0.00 3.69
497 502 1.338655 TCGGTGATGTTCGTTCAGTGA 59.661 47.619 0.00 0.00 0.00 3.41
501 506 1.529438 GCTTTCGGTGATGTTCGTTCA 59.471 47.619 0.00 0.00 0.00 3.18
505 510 2.004583 TAGGCTTTCGGTGATGTTCG 57.995 50.000 0.00 0.00 0.00 3.95
506 511 4.759516 TTTTAGGCTTTCGGTGATGTTC 57.240 40.909 0.00 0.00 0.00 3.18
537 542 7.855545 ACTTGACATTGATACTCGCATTATTC 58.144 34.615 0.00 0.00 0.00 1.75
570 575 3.736094 TCCTGAGTCCATTAGGGTTCAT 58.264 45.455 0.00 0.00 38.11 2.57
572 577 5.544176 TGATATCCTGAGTCCATTAGGGTTC 59.456 44.000 0.00 0.00 38.11 3.62
579 584 4.346418 GGACAGTGATATCCTGAGTCCATT 59.654 45.833 21.15 4.08 42.65 3.16
580 585 3.900601 GGACAGTGATATCCTGAGTCCAT 59.099 47.826 21.15 4.62 42.65 3.41
587 592 4.282195 GGTTAGGAGGACAGTGATATCCTG 59.718 50.000 18.75 15.59 40.58 3.86
591 596 5.305644 GTGATGGTTAGGAGGACAGTGATAT 59.694 44.000 0.00 0.00 0.00 1.63
617 622 1.944024 AGAAATTCACGTGCGAACCAA 59.056 42.857 11.67 0.00 0.00 3.67
619 624 2.681152 AAGAAATTCACGTGCGAACC 57.319 45.000 11.67 0.00 0.00 3.62
651 656 8.806146 ACTAAAAATGAACAATCTTGCATACCT 58.194 29.630 0.00 0.00 0.00 3.08
674 679 6.043854 ACAAGGCTTGGAAAAACAAAACTA 57.956 33.333 29.26 0.00 34.12 2.24
681 686 2.626840 TGCAACAAGGCTTGGAAAAAC 58.373 42.857 29.26 13.52 34.12 2.43
738 743 3.667960 GCTTACCTTTGCTGTTGTCATCG 60.668 47.826 0.00 0.00 0.00 3.84
759 768 2.287668 ACGTGTCTGTGTAGTTCTCTGC 60.288 50.000 0.00 0.00 0.00 4.26
803 812 4.582701 TTTTTCATTGTGTCTGCCGATT 57.417 36.364 0.00 0.00 0.00 3.34
808 817 3.307674 TGCGATTTTTCATTGTGTCTGC 58.692 40.909 0.00 0.00 0.00 4.26
827 836 4.142966 GGACTAGACGGTTTATTGTGTTGC 60.143 45.833 0.00 0.00 0.00 4.17
845 854 1.745141 GCGGTCGAGTTCCTAGGACTA 60.745 57.143 12.22 0.00 0.00 2.59
868 877 5.245301 GGTTTTATAGGTGAAGCCAAAAGGT 59.755 40.000 0.00 0.00 40.61 3.50
917 930 1.904144 TTCCTTCTGTTCGTATCGCG 58.096 50.000 0.00 0.00 43.01 5.87
952 965 2.965831 TGATAGCAGTGCTAAGGGTAGG 59.034 50.000 27.75 0.00 44.62 3.18
1302 1315 4.578898 TTGCTCGCACGTCGGTGT 62.579 61.111 0.00 0.00 46.13 4.16
1313 1326 4.697756 TCTTGGCCGGGTTGCTCG 62.698 66.667 2.18 0.00 0.00 5.03
1315 1328 2.221299 TAGTCTTGGCCGGGTTGCT 61.221 57.895 2.18 0.00 0.00 3.91
1316 1329 2.038837 GTAGTCTTGGCCGGGTTGC 61.039 63.158 2.18 0.00 0.00 4.17
1317 1330 1.376812 GGTAGTCTTGGCCGGGTTG 60.377 63.158 2.18 0.00 0.00 3.77
1318 1331 2.599757 GGGTAGTCTTGGCCGGGTT 61.600 63.158 2.18 0.00 0.00 4.11
1321 1334 3.793888 GGGGGTAGTCTTGGCCGG 61.794 72.222 0.00 0.00 0.00 6.13
1323 1336 1.844544 TTTCGGGGGTAGTCTTGGCC 61.845 60.000 0.00 0.00 0.00 5.36
1325 1338 3.918294 TTATTTCGGGGGTAGTCTTGG 57.082 47.619 0.00 0.00 0.00 3.61
1327 1340 5.191124 ACTTCATTATTTCGGGGGTAGTCTT 59.809 40.000 0.00 0.00 0.00 3.01
1329 1342 4.814771 CACTTCATTATTTCGGGGGTAGTC 59.185 45.833 0.00 0.00 0.00 2.59
1330 1343 4.777463 CACTTCATTATTTCGGGGGTAGT 58.223 43.478 0.00 0.00 0.00 2.73
1332 1345 3.054287 TGCACTTCATTATTTCGGGGGTA 60.054 43.478 0.00 0.00 0.00 3.69
1333 1346 2.291282 TGCACTTCATTATTTCGGGGGT 60.291 45.455 0.00 0.00 0.00 4.95
1334 1347 2.099098 GTGCACTTCATTATTTCGGGGG 59.901 50.000 10.32 0.00 0.00 5.40
1339 1366 3.091417 GACGCGTGCACTTCATTATTTC 58.909 45.455 20.70 0.00 0.00 2.17
1357 1384 1.190103 CATCACACTTCACACACGACG 59.810 52.381 0.00 0.00 0.00 5.12
1369 1396 8.456471 CACATTCAGACATTTATTCATCACACT 58.544 33.333 0.00 0.00 0.00 3.55
1370 1397 8.239314 ACACATTCAGACATTTATTCATCACAC 58.761 33.333 0.00 0.00 0.00 3.82
1371 1398 8.238631 CACACATTCAGACATTTATTCATCACA 58.761 33.333 0.00 0.00 0.00 3.58
1372 1399 7.699391 CCACACATTCAGACATTTATTCATCAC 59.301 37.037 0.00 0.00 0.00 3.06
1373 1400 7.394077 ACCACACATTCAGACATTTATTCATCA 59.606 33.333 0.00 0.00 0.00 3.07
1374 1401 7.699391 CACCACACATTCAGACATTTATTCATC 59.301 37.037 0.00 0.00 0.00 2.92
1375 1402 7.394077 TCACCACACATTCAGACATTTATTCAT 59.606 33.333 0.00 0.00 0.00 2.57
1395 1422 0.868406 CCGAAACAGCTTCTCACCAC 59.132 55.000 0.00 0.00 31.20 4.16
1431 1465 2.460918 GCGCGAAACAGCTTATCTCTA 58.539 47.619 12.10 0.00 34.40 2.43
1464 1501 6.664428 AAACCTTGTTAATTGGCATGTACT 57.336 33.333 0.00 0.00 0.00 2.73
1465 1502 6.704050 ACAAAACCTTGTTAATTGGCATGTAC 59.296 34.615 0.00 0.00 43.45 2.90
1466 1503 6.821388 ACAAAACCTTGTTAATTGGCATGTA 58.179 32.000 0.00 0.00 43.45 2.29
1467 1504 5.679601 ACAAAACCTTGTTAATTGGCATGT 58.320 33.333 0.00 0.00 43.45 3.21
1483 1536 6.811954 TGGAACTTTTATTCTGGACAAAACC 58.188 36.000 0.00 0.00 0.00 3.27
1521 1574 6.755206 AGCGTACCATTGTTATTCTGCTATA 58.245 36.000 0.00 0.00 0.00 1.31
1562 1615 4.147219 ACTTAAGCTTGATGCACGTTTC 57.853 40.909 9.86 0.00 45.94 2.78
1581 1637 5.079643 AGATGCCCTGTATTTTGTTGAACT 58.920 37.500 0.00 0.00 0.00 3.01
1597 1653 1.812922 CTGCTGTCGTGAGATGCCC 60.813 63.158 0.00 0.00 45.19 5.36
1618 1674 0.814010 CACCTGCGTTAGTATGGCCC 60.814 60.000 0.00 0.00 0.00 5.80
1619 1675 0.814010 CCACCTGCGTTAGTATGGCC 60.814 60.000 0.00 0.00 0.00 5.36
1627 1683 2.922740 AGAAACTTCCACCTGCGTTA 57.077 45.000 0.00 0.00 0.00 3.18
1676 1732 1.063951 GTACGAGTTCTGTGTCGGCG 61.064 60.000 0.00 0.00 40.59 6.46
1680 1736 5.800941 CCTGAAATAGTACGAGTTCTGTGTC 59.199 44.000 15.48 0.00 0.00 3.67
1684 1740 4.113354 GCCCTGAAATAGTACGAGTTCTG 58.887 47.826 15.48 14.40 0.00 3.02
1686 1742 4.361420 GAGCCCTGAAATAGTACGAGTTC 58.639 47.826 8.93 8.93 0.00 3.01
1690 1746 3.028094 AGGAGCCCTGAAATAGTACGA 57.972 47.619 0.00 0.00 29.57 3.43
1702 1761 1.129917 CATGAGATGTCAGGAGCCCT 58.870 55.000 0.00 0.00 36.55 5.19
1802 1861 2.985896 ACGGACATGTCATACCAAAGG 58.014 47.619 26.47 6.82 0.00 3.11
1831 1890 3.374764 ACCAAAAGCCTTCTGAAAACCT 58.625 40.909 0.00 0.00 0.00 3.50
1832 1891 3.819564 ACCAAAAGCCTTCTGAAAACC 57.180 42.857 0.00 0.00 0.00 3.27
1879 1939 0.874390 TGAAAATGGACTCGCTGCAC 59.126 50.000 0.00 0.00 0.00 4.57
1951 2014 7.232118 TGATGCCGATGAAGATAAAGATCTA 57.768 36.000 0.00 0.00 41.87 1.98
2050 2113 6.260271 GGCACTGTTTATGGATAGTAGGAAAC 59.740 42.308 0.00 0.00 0.00 2.78
2200 2263 7.824289 GGTGCTAAATATGAATCCAGCAGTATA 59.176 37.037 0.00 0.00 39.50 1.47
2207 2270 7.672983 AATACGGTGCTAAATATGAATCCAG 57.327 36.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.