Multiple sequence alignment - TraesCS5D01G154800

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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 TraesCS5D01G154800 chr5D 100.000 3183 0 0 1 3183 242967190 242964008 0.000000e+00 5879
1 TraesCS5D01G154800 chr5D 92.782 568 38 2 2616 3182 297795005 297795570 0.000000e+00 819
2 TraesCS5D01G154800 chr5B 91.026 1716 84 27 520 2189 255550127 255551818 0.000000e+00 2252
3 TraesCS5D01G154800 chr5B 92.888 703 49 1 2481 3183 255575362 255576063 0.000000e+00 1020
4 TraesCS5D01G154800 chr5B 92.387 683 46 4 2410 3087 255574681 255575362 0.000000e+00 968
5 TraesCS5D01G154800 chr5B 86.329 395 53 1 1 394 255548861 255549255 2.270000e-116 429
6 TraesCS5D01G154800 chr5B 96.350 137 5 0 2193 2329 255551900 255552036 3.190000e-55 226
7 TraesCS5D01G154800 chr5B 88.679 106 11 1 415 519 255549989 255550094 9.270000e-26 128
8 TraesCS5D01G154800 chr5A 89.889 1533 81 33 816 2293 309100172 309101685 0.000000e+00 1905
9 TraesCS5D01G154800 chr5A 92.308 182 12 1 2428 2609 309101847 309102026 1.130000e-64 257
10 TraesCS5D01G154800 chr5A 93.590 78 5 0 732 809 309100112 309100189 2.010000e-22 117
11 TraesCS5D01G154800 chr7D 92.958 568 39 1 2617 3183 402321088 402321655 0.000000e+00 826
12 TraesCS5D01G154800 chr7D 91.667 576 44 4 2611 3183 72271203 72271777 0.000000e+00 795
13 TraesCS5D01G154800 chr6D 92.077 568 44 1 2617 3183 103038198 103038765 0.000000e+00 798
14 TraesCS5D01G154800 chr1D 91.916 569 45 1 2616 3183 404063814 404064382 0.000000e+00 795
15 TraesCS5D01G154800 chr7B 91.725 568 45 2 2617 3183 135032239 135031673 0.000000e+00 787
16 TraesCS5D01G154800 chr4A 91.740 569 43 4 2618 3183 534060777 534061344 0.000000e+00 787


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 TraesCS5D01G154800 chr5D 242964008 242967190 3182 True 5879.000000 5879 100.0000 1 3183 1 chr5D.!!$R1 3182
1 TraesCS5D01G154800 chr5D 297795005 297795570 565 False 819.000000 819 92.7820 2616 3182 1 chr5D.!!$F1 566
2 TraesCS5D01G154800 chr5B 255574681 255576063 1382 False 994.000000 1020 92.6375 2410 3183 2 chr5B.!!$F2 773
3 TraesCS5D01G154800 chr5B 255548861 255552036 3175 False 758.750000 2252 90.5960 1 2329 4 chr5B.!!$F1 2328
4 TraesCS5D01G154800 chr5A 309100112 309102026 1914 False 759.666667 1905 91.9290 732 2609 3 chr5A.!!$F1 1877
5 TraesCS5D01G154800 chr7D 402321088 402321655 567 False 826.000000 826 92.9580 2617 3183 1 chr7D.!!$F2 566
6 TraesCS5D01G154800 chr7D 72271203 72271777 574 False 795.000000 795 91.6670 2611 3183 1 chr7D.!!$F1 572
7 TraesCS5D01G154800 chr6D 103038198 103038765 567 False 798.000000 798 92.0770 2617 3183 1 chr6D.!!$F1 566
8 TraesCS5D01G154800 chr1D 404063814 404064382 568 False 795.000000 795 91.9160 2616 3183 1 chr1D.!!$F1 567
9 TraesCS5D01G154800 chr7B 135031673 135032239 566 True 787.000000 787 91.7250 2617 3183 1 chr7B.!!$R1 566
10 TraesCS5D01G154800 chr4A 534060777 534061344 567 False 787.000000 787 91.7400 2618 3183 1 chr4A.!!$F1 565

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
399 401 0.036732 TGCTTTCCATCCAACGCTCT 59.963 50.0 0.00 0.00 0.00 4.09 F
403 405 0.250234 TTCCATCCAACGCTCTCCTG 59.750 55.0 0.00 0.00 0.00 3.86 F
949 1726 0.464452 GAACCCGGGAGATACCACTG 59.536 60.0 32.02 0.00 41.20 3.66 F
1828 2645 0.594602 TCTCGTACCTGAACACGGTG 59.405 55.0 6.58 6.58 38.66 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 2468 0.179073 ATTCGGACGGAAGCATGGAG 60.179 55.0 0.0 0.0 38.24 3.86 R
1828 2645 0.324943 TACCCTTGTGCTTCTCAGCC 59.675 55.0 0.0 0.0 46.74 4.85 R
1848 2673 0.548031 TCAGGGTGAGGATTGATGCC 59.452 55.0 0.0 0.0 0.00 4.40 R
3143 4727 0.400213 TTTGATGCCGTTGTCCCTCT 59.600 50.0 0.0 0.0 0.00 3.69 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
69 70 3.837213 ATGCACCTCAAAGACAAATCG 57.163 42.857 0.00 0.00 0.00 3.34
76 77 2.749076 CTCAAAGACAAATCGGCCATCA 59.251 45.455 2.24 0.00 0.00 3.07
78 79 1.086696 AAGACAAATCGGCCATCACG 58.913 50.000 2.24 0.00 0.00 4.35
83 84 0.887933 AAATCGGCCATCACGCTTTT 59.112 45.000 2.24 0.00 0.00 2.27
103 104 3.085952 TGGAAATCCAATTCGGCTCTT 57.914 42.857 0.00 0.00 44.35 2.85
133 134 1.200020 CGACCATCCCTGTTGCTTTTC 59.800 52.381 0.00 0.00 0.00 2.29
143 144 5.365314 TCCCTGTTGCTTTTCCTTTTTATGT 59.635 36.000 0.00 0.00 0.00 2.29
152 153 8.797438 TGCTTTTCCTTTTTATGTTTTTGGTTT 58.203 25.926 0.00 0.00 0.00 3.27
166 167 7.493367 TGTTTTTGGTTTGTCTGTAATAAGGG 58.507 34.615 0.00 0.00 0.00 3.95
177 178 4.721776 TCTGTAATAAGGGCATCTCCAACT 59.278 41.667 0.00 0.00 36.21 3.16
179 180 4.721776 TGTAATAAGGGCATCTCCAACTCT 59.278 41.667 0.00 0.00 36.21 3.24
185 186 1.354040 GCATCTCCAACTCTGACACG 58.646 55.000 0.00 0.00 0.00 4.49
195 197 3.403057 CTGACACGCAACCGTCCG 61.403 66.667 0.00 0.00 46.39 4.79
230 232 3.365465 CGGACGTGTTTTGCCATTCAATA 60.365 43.478 0.00 0.00 34.12 1.90
231 233 4.674101 CGGACGTGTTTTGCCATTCAATAT 60.674 41.667 0.00 0.00 34.12 1.28
233 235 5.384063 ACGTGTTTTGCCATTCAATATGA 57.616 34.783 0.00 0.00 34.12 2.15
236 238 5.863397 CGTGTTTTGCCATTCAATATGAGTT 59.137 36.000 0.00 0.00 34.12 3.01
241 243 9.202273 GTTTTGCCATTCAATATGAGTTTGTAA 57.798 29.630 0.00 0.00 34.12 2.41
247 249 7.065803 CCATTCAATATGAGTTTGTAACGGTCT 59.934 37.037 0.00 0.00 36.23 3.85
248 250 6.961359 TCAATATGAGTTTGTAACGGTCTG 57.039 37.500 0.00 0.00 36.23 3.51
264 266 3.818121 CTGCCGACCGGTTTGGACA 62.818 63.158 26.10 20.82 42.00 4.02
267 269 1.004320 CCGACCGGTTTGGACATGA 60.004 57.895 19.29 0.00 42.00 3.07
280 282 1.994779 GGACATGATTTTTGCCGCAAG 59.005 47.619 5.83 0.00 0.00 4.01
281 283 1.391144 GACATGATTTTTGCCGCAAGC 59.609 47.619 5.83 0.00 44.14 4.01
283 285 0.737019 ATGATTTTTGCCGCAAGCCG 60.737 50.000 5.83 0.00 42.71 5.52
341 343 4.169696 CCACGCCCGCTCCCAATA 62.170 66.667 0.00 0.00 0.00 1.90
353 355 2.044451 CCAATAGCCGTGGCCCAA 60.044 61.111 7.39 0.00 43.17 4.12
370 372 0.958091 CAACCAAAACGCATCTCCCA 59.042 50.000 0.00 0.00 0.00 4.37
378 380 1.760086 CGCATCTCCCACCTCTCCT 60.760 63.158 0.00 0.00 0.00 3.69
379 381 0.468214 CGCATCTCCCACCTCTCCTA 60.468 60.000 0.00 0.00 0.00 2.94
394 396 4.133078 CTCTCCTATGCTTTCCATCCAAC 58.867 47.826 0.00 0.00 35.34 3.77
397 399 2.292267 CTATGCTTTCCATCCAACGCT 58.708 47.619 0.00 0.00 35.34 5.07
399 401 0.036732 TGCTTTCCATCCAACGCTCT 59.963 50.000 0.00 0.00 0.00 4.09
401 403 1.373570 CTTTCCATCCAACGCTCTCC 58.626 55.000 0.00 0.00 0.00 3.71
402 404 0.984230 TTTCCATCCAACGCTCTCCT 59.016 50.000 0.00 0.00 0.00 3.69
403 405 0.250234 TTCCATCCAACGCTCTCCTG 59.750 55.000 0.00 0.00 0.00 3.86
404 406 0.904865 TCCATCCAACGCTCTCCTGT 60.905 55.000 0.00 0.00 0.00 4.00
405 407 0.742281 CCATCCAACGCTCTCCTGTG 60.742 60.000 0.00 0.00 0.00 3.66
408 410 0.468226 TCCAACGCTCTCCTGTGTTT 59.532 50.000 0.00 0.00 38.42 2.83
409 411 1.134220 TCCAACGCTCTCCTGTGTTTT 60.134 47.619 0.00 0.00 38.42 2.43
410 412 1.676006 CCAACGCTCTCCTGTGTTTTT 59.324 47.619 0.00 0.00 38.42 1.94
473 1188 5.734855 ATCTGATTGATTTAAACCCGACG 57.265 39.130 0.00 0.00 29.59 5.12
505 1220 1.095807 GCCTAGGTTTGGATGACCGC 61.096 60.000 11.31 0.00 42.11 5.68
507 1222 1.473434 CCTAGGTTTGGATGACCGCTC 60.473 57.143 0.00 0.00 42.11 5.03
509 1224 1.749258 GGTTTGGATGACCGCTCCC 60.749 63.158 0.00 0.00 39.42 4.30
510 1225 2.106683 GTTTGGATGACCGCTCCCG 61.107 63.158 0.00 0.00 39.42 5.14
511 1226 2.589157 TTTGGATGACCGCTCCCGT 61.589 57.895 0.00 0.00 39.42 5.28
512 1227 1.259142 TTTGGATGACCGCTCCCGTA 61.259 55.000 0.00 0.00 39.42 4.02
513 1228 1.046472 TTGGATGACCGCTCCCGTAT 61.046 55.000 0.00 0.00 39.42 3.06
514 1229 1.289380 GGATGACCGCTCCCGTATC 59.711 63.158 0.00 0.00 0.00 2.24
516 1231 1.456892 ATGACCGCTCCCGTATCCA 60.457 57.895 0.00 0.00 0.00 3.41
517 1232 0.832135 ATGACCGCTCCCGTATCCAT 60.832 55.000 0.00 0.00 0.00 3.41
518 1233 1.006102 GACCGCTCCCGTATCCATG 60.006 63.158 0.00 0.00 0.00 3.66
529 1277 1.270826 CGTATCCATGATGCGGAGTCT 59.729 52.381 6.67 0.00 42.61 3.24
535 1283 3.387699 TCCATGATGCGGAGTCTGATTTA 59.612 43.478 2.16 0.00 0.00 1.40
536 1284 3.496130 CCATGATGCGGAGTCTGATTTAC 59.504 47.826 2.16 0.00 0.00 2.01
538 1286 2.128035 GATGCGGAGTCTGATTTACGG 58.872 52.381 2.16 0.00 0.00 4.02
557 1305 2.743183 CGGGTCTTGAAGATGCCCTAAG 60.743 54.545 16.21 1.02 37.24 2.18
595 1343 4.661993 TTGAAAATCGATCGAGGTGTTG 57.338 40.909 23.84 0.00 0.00 3.33
662 1418 3.125573 GCCGGAGAAAAGGACGCC 61.126 66.667 5.05 0.00 0.00 5.68
663 1419 2.813908 CCGGAGAAAAGGACGCCG 60.814 66.667 0.00 0.00 46.79 6.46
664 1420 2.813908 CGGAGAAAAGGACGCCGG 60.814 66.667 0.00 0.00 44.39 6.13
665 1421 3.125573 GGAGAAAAGGACGCCGGC 61.126 66.667 19.07 19.07 0.00 6.13
666 1422 3.488090 GAGAAAAGGACGCCGGCG 61.488 66.667 44.88 44.88 46.03 6.46
678 1434 4.796231 CCGGCGTCGTCAAGAGGG 62.796 72.222 9.28 0.00 35.42 4.30
679 1435 3.744719 CGGCGTCGTCAAGAGGGA 61.745 66.667 0.00 0.00 35.42 4.20
680 1436 2.893398 GGCGTCGTCAAGAGGGAT 59.107 61.111 0.00 0.00 35.42 3.85
720 1476 4.758688 TGATATCTCGTGCATTGTTGTCT 58.241 39.130 3.98 0.00 0.00 3.41
749 1505 6.299805 AGACTCATCACACTAATTAAGGCA 57.700 37.500 0.00 0.00 0.00 4.75
928 1705 3.429141 CTGCAAGCCAGTCCGCAG 61.429 66.667 0.00 0.00 45.17 5.18
949 1726 0.464452 GAACCCGGGAGATACCACTG 59.536 60.000 32.02 0.00 41.20 3.66
967 1744 3.126171 CACTGTCCTTCTACTCGTCTCTG 59.874 52.174 0.00 0.00 0.00 3.35
1147 1924 0.613853 TCCACTTACCTCCTCCACCG 60.614 60.000 0.00 0.00 0.00 4.94
1226 2015 1.043116 TGGATCCGGAGCTGAACGAT 61.043 55.000 20.86 0.00 0.00 3.73
1265 2054 1.061570 CGTGGTACGTACGCTCTCC 59.938 63.158 16.72 12.74 36.74 3.71
1270 2059 1.081892 GTACGTACGCTCTCCAGTCA 58.918 55.000 16.72 0.00 0.00 3.41
1271 2060 1.669779 GTACGTACGCTCTCCAGTCAT 59.330 52.381 16.72 0.00 0.00 3.06
1272 2061 0.733729 ACGTACGCTCTCCAGTCATC 59.266 55.000 16.72 0.00 0.00 2.92
1285 2074 5.954752 TCTCCAGTCATCACAGAAATACTCT 59.045 40.000 0.00 0.00 33.23 3.24
1341 2138 3.140814 GATCCCAAGGTTGCCCGC 61.141 66.667 0.00 0.00 35.12 6.13
1383 2180 1.000771 AGCTGCCGTCTACTCCTCA 60.001 57.895 0.00 0.00 0.00 3.86
1422 2219 2.046314 ACCGCGCAAACCATAGCT 60.046 55.556 8.75 0.00 0.00 3.32
1456 2273 4.321082 GCCTATCCTCTGTACGTATGTTCC 60.321 50.000 0.00 0.00 0.00 3.62
1459 2276 4.978083 TCCTCTGTACGTATGTTCCTTC 57.022 45.455 0.00 0.00 0.00 3.46
1578 2395 1.522580 GAGATCTCCACGGCTTGGC 60.523 63.158 12.00 0.00 46.47 4.52
1642 2459 5.266788 TCTTACTCGAGGACCCAAGAAATA 58.733 41.667 18.41 0.00 0.00 1.40
1651 2468 3.273434 GACCCAAGAAATACCCGTAACC 58.727 50.000 0.00 0.00 0.00 2.85
1679 2496 3.326747 CTTCCGTCCGAATTTTCTCAGT 58.673 45.455 0.00 0.00 0.00 3.41
1706 2523 2.170397 TGTTCTGTTCTGCCACTTCTCA 59.830 45.455 0.00 0.00 0.00 3.27
1719 2536 5.125900 TGCCACTTCTCACATGGAAATTATG 59.874 40.000 0.00 0.00 35.33 1.90
1722 2539 7.148086 GCCACTTCTCACATGGAAATTATGTTA 60.148 37.037 0.00 0.00 36.67 2.41
1742 2559 3.554259 AGCATCGCGTCGAAATATCTA 57.446 42.857 5.77 0.00 39.99 1.98
1749 2566 4.857037 TCGCGTCGAAATATCTATTCCATG 59.143 41.667 5.77 0.00 31.06 3.66
1760 2577 4.090761 TCTATTCCATGGCATTCTCCAC 57.909 45.455 6.96 0.00 39.25 4.02
1828 2645 0.594602 TCTCGTACCTGAACACGGTG 59.405 55.000 6.58 6.58 38.66 4.94
1848 2673 1.677217 GGCTGAGAAGCACAAGGGTAG 60.677 57.143 0.00 0.00 36.33 3.18
1872 2697 0.391661 CAATCCTCACCCTGACACCG 60.392 60.000 0.00 0.00 0.00 4.94
1881 2706 1.247567 CCCTGACACCGCAGATTTTT 58.752 50.000 0.00 0.00 38.14 1.94
1927 2752 1.608590 CCGCTGAGCAGAAAAAGGAAA 59.391 47.619 4.88 0.00 0.00 3.13
1929 2756 3.303406 CGCTGAGCAGAAAAAGGAAAAG 58.697 45.455 4.88 0.00 0.00 2.27
1944 2771 8.969121 AAAAGGAAAAGCTGATTTTTGTTTTG 57.031 26.923 16.67 0.00 41.24 2.44
1946 2773 5.066375 AGGAAAAGCTGATTTTTGTTTTGCC 59.934 36.000 5.01 0.45 41.24 4.52
1981 2810 2.264794 GAGCGGGTGATCGTGGTT 59.735 61.111 0.00 0.00 0.00 3.67
1993 2822 3.505184 GTGGTTACCCATGGCGCG 61.505 66.667 6.09 0.00 44.35 6.86
2350 3321 0.040958 GAGACGCTGCAGTTGGTTTG 60.041 55.000 16.64 0.00 0.00 2.93
2351 3322 1.658409 GACGCTGCAGTTGGTTTGC 60.658 57.895 16.64 0.00 41.86 3.68
2365 3336 7.811117 AGTTGGTTTGCAACTGTTTACTATA 57.189 32.000 0.00 0.00 40.89 1.31
2377 3348 9.298774 CAACTGTTTACTATAGTTGCTACTACC 57.701 37.037 11.40 0.00 45.15 3.18
2378 3349 8.585471 ACTGTTTACTATAGTTGCTACTACCA 57.415 34.615 11.40 1.29 39.59 3.25
2390 3361 4.804597 TGCTACTACCACTATCCAGACAT 58.195 43.478 0.00 0.00 0.00 3.06
2393 3364 3.374764 ACTACCACTATCCAGACATGCA 58.625 45.455 0.00 0.00 0.00 3.96
2394 3365 2.996249 ACCACTATCCAGACATGCAG 57.004 50.000 0.00 0.00 0.00 4.41
2397 3368 2.941064 CCACTATCCAGACATGCAGTTG 59.059 50.000 0.00 0.00 0.00 3.16
2398 3369 2.941064 CACTATCCAGACATGCAGTTGG 59.059 50.000 0.00 0.00 32.82 3.77
2399 3370 2.573462 ACTATCCAGACATGCAGTTGGT 59.427 45.455 0.00 0.00 33.13 3.67
2400 3371 2.592102 ATCCAGACATGCAGTTGGTT 57.408 45.000 0.00 0.00 33.13 3.67
2401 3372 2.363306 TCCAGACATGCAGTTGGTTT 57.637 45.000 0.00 0.00 33.13 3.27
2402 3373 1.955778 TCCAGACATGCAGTTGGTTTG 59.044 47.619 0.00 0.00 33.13 2.93
2403 3374 1.603678 CCAGACATGCAGTTGGTTTGC 60.604 52.381 0.00 0.00 41.86 3.68
2426 3397 5.440685 CAACTGTTAGGTCGTCAATTTGAC 58.559 41.667 17.76 17.76 43.65 3.18
2515 3486 5.817296 TCCATTGATAGACATGTTACACAGC 59.183 40.000 0.00 0.00 0.00 4.40
2649 4231 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
2804 4386 3.537580 GCCTAATACCAAACGGACATCA 58.462 45.455 0.00 0.00 0.00 3.07
2837 4419 0.179020 CATCTAAAGCCGGATGCCCA 60.179 55.000 5.05 0.00 42.71 5.36
2860 4442 2.203728 AGCCACACACCGGGACTA 60.204 61.111 6.32 0.00 0.00 2.59
2885 4467 1.451927 ATACCGGACCGACGCACTA 60.452 57.895 17.49 0.00 0.00 2.74
2894 4476 1.433471 CGACGCACTATCAGAGGCA 59.567 57.895 0.00 0.00 0.00 4.75
2957 4539 2.671070 CCATCGACCTTGCCTGGT 59.329 61.111 0.00 0.00 44.10 4.00
3018 4600 1.473677 CCTACACGTATCCGTCCACAA 59.526 52.381 0.00 0.00 46.28 3.33
3142 4726 0.678048 GCTCCAAAACGATGCCCTCT 60.678 55.000 0.00 0.00 0.00 3.69
3143 4727 1.406887 GCTCCAAAACGATGCCCTCTA 60.407 52.381 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.055094 GGTGCATATACTCCCGGATGAAT 60.055 47.826 0.73 0.00 0.00 2.57
69 70 0.316841 TTTCCAAAAGCGTGATGGCC 59.683 50.000 0.00 0.00 34.13 5.36
83 84 2.754552 CAAGAGCCGAATTGGATTTCCA 59.245 45.455 0.00 0.00 45.94 3.53
103 104 1.697432 AGGGATGGTCGTTTTGTCTCA 59.303 47.619 0.00 0.00 0.00 3.27
133 134 8.262715 ACAGACAAACCAAAAACATAAAAAGG 57.737 30.769 0.00 0.00 0.00 3.11
143 144 6.098409 TGCCCTTATTACAGACAAACCAAAAA 59.902 34.615 0.00 0.00 0.00 1.94
152 153 4.037222 TGGAGATGCCCTTATTACAGACA 58.963 43.478 0.00 0.00 34.97 3.41
163 164 0.908198 GTCAGAGTTGGAGATGCCCT 59.092 55.000 0.00 0.00 34.97 5.19
166 167 1.354040 CGTGTCAGAGTTGGAGATGC 58.646 55.000 0.00 0.00 0.00 3.91
177 178 2.028484 GGACGGTTGCGTGTCAGA 59.972 61.111 0.00 0.00 36.83 3.27
179 180 4.953868 CCGGACGGTTGCGTGTCA 62.954 66.667 0.00 0.00 36.83 3.58
195 197 4.867599 GTCCGGATCACGCGGTCC 62.868 72.222 7.81 14.06 42.52 4.46
205 207 0.608035 ATGGCAAAACACGTCCGGAT 60.608 50.000 7.81 0.00 0.00 4.18
209 211 2.500509 TTGAATGGCAAAACACGTCC 57.499 45.000 0.00 0.00 32.46 4.79
210 212 5.398169 TCATATTGAATGGCAAAACACGTC 58.602 37.500 0.00 0.00 40.48 4.34
230 232 2.423577 GGCAGACCGTTACAAACTCAT 58.576 47.619 0.00 0.00 0.00 2.90
231 233 1.873698 GGCAGACCGTTACAAACTCA 58.126 50.000 0.00 0.00 0.00 3.41
247 249 3.185299 ATGTCCAAACCGGTCGGCA 62.185 57.895 8.04 14.16 39.32 5.69
248 250 2.359478 ATGTCCAAACCGGTCGGC 60.359 61.111 8.04 8.85 39.32 5.54
253 255 2.736192 GCAAAAATCATGTCCAAACCGG 59.264 45.455 0.00 0.00 0.00 5.28
259 261 0.964700 TGCGGCAAAAATCATGTCCA 59.035 45.000 0.00 0.00 0.00 4.02
260 262 1.994779 CTTGCGGCAAAAATCATGTCC 59.005 47.619 17.13 0.00 0.00 4.02
264 266 0.737019 CGGCTTGCGGCAAAAATCAT 60.737 50.000 17.13 0.00 44.01 2.45
267 269 2.048316 CCGGCTTGCGGCAAAAAT 60.048 55.556 17.13 0.00 44.01 1.82
280 282 0.963856 CCCCCTAGTTTGTTTCCGGC 60.964 60.000 0.00 0.00 0.00 6.13
281 283 3.259592 CCCCCTAGTTTGTTTCCGG 57.740 57.895 0.00 0.00 0.00 5.14
306 308 4.778415 CGACGGTCTGGACGCTGG 62.778 72.222 6.57 0.00 34.00 4.85
337 339 2.414785 GGTTGGGCCACGGCTATTG 61.415 63.158 5.23 0.00 41.60 1.90
338 340 2.044352 GGTTGGGCCACGGCTATT 60.044 61.111 5.23 0.00 41.60 1.73
353 355 0.893727 GGTGGGAGATGCGTTTTGGT 60.894 55.000 0.00 0.00 0.00 3.67
357 359 0.250513 GAGAGGTGGGAGATGCGTTT 59.749 55.000 0.00 0.00 0.00 3.60
370 372 2.708325 GGATGGAAAGCATAGGAGAGGT 59.292 50.000 0.00 0.00 0.00 3.85
378 380 2.092968 AGAGCGTTGGATGGAAAGCATA 60.093 45.455 0.00 0.00 33.31 3.14
379 381 1.098050 GAGCGTTGGATGGAAAGCAT 58.902 50.000 0.00 0.00 33.31 3.79
456 1171 5.692613 TTTCACGTCGGGTTTAAATCAAT 57.307 34.783 0.00 0.00 0.00 2.57
459 1174 5.038247 ACATTTCACGTCGGGTTTAAATC 57.962 39.130 0.00 0.00 0.00 2.17
460 1175 6.548171 CATACATTTCACGTCGGGTTTAAAT 58.452 36.000 0.00 0.00 0.00 1.40
473 1188 2.561569 ACCTAGGCGCATACATTTCAC 58.438 47.619 10.83 0.00 0.00 3.18
505 1220 0.390340 CCGCATCATGGATACGGGAG 60.390 60.000 9.50 0.00 43.09 4.30
507 1222 0.390340 CTCCGCATCATGGATACGGG 60.390 60.000 15.67 5.38 45.79 5.28
509 1224 1.270826 AGACTCCGCATCATGGATACG 59.729 52.381 0.00 0.00 42.51 3.06
510 1225 2.297315 TCAGACTCCGCATCATGGATAC 59.703 50.000 0.00 0.00 34.32 2.24
511 1226 2.597455 TCAGACTCCGCATCATGGATA 58.403 47.619 0.00 0.00 34.32 2.59
512 1227 1.417288 TCAGACTCCGCATCATGGAT 58.583 50.000 0.00 0.00 34.32 3.41
513 1228 1.417288 ATCAGACTCCGCATCATGGA 58.583 50.000 0.00 0.00 0.00 3.41
514 1229 2.251409 AATCAGACTCCGCATCATGG 57.749 50.000 0.00 0.00 0.00 3.66
516 1231 3.384668 CGTAAATCAGACTCCGCATCAT 58.615 45.455 0.00 0.00 0.00 2.45
517 1232 2.481276 CCGTAAATCAGACTCCGCATCA 60.481 50.000 0.00 0.00 0.00 3.07
518 1233 2.128035 CCGTAAATCAGACTCCGCATC 58.872 52.381 0.00 0.00 0.00 3.91
525 1273 4.527038 TCTTCAAGACCCGTAAATCAGACT 59.473 41.667 0.00 0.00 0.00 3.24
529 1277 3.938963 GCATCTTCAAGACCCGTAAATCA 59.061 43.478 0.00 0.00 0.00 2.57
535 1283 1.201429 AGGGCATCTTCAAGACCCGT 61.201 55.000 7.33 2.12 45.75 5.28
536 1284 0.830648 TAGGGCATCTTCAAGACCCG 59.169 55.000 7.33 0.00 45.75 5.28
538 1286 3.198853 AGTCTTAGGGCATCTTCAAGACC 59.801 47.826 8.46 0.00 43.88 3.85
574 1322 4.062293 ACAACACCTCGATCGATTTTCAA 58.938 39.130 19.78 0.00 0.00 2.69
615 1363 5.535783 TCTTTTGGTGTCATCATGTGTGATT 59.464 36.000 6.79 0.00 42.37 2.57
662 1418 2.938539 GATCCCTCTTGACGACGCCG 62.939 65.000 0.00 0.00 42.50 6.46
663 1419 1.227002 GATCCCTCTTGACGACGCC 60.227 63.158 0.00 0.00 0.00 5.68
664 1420 1.586564 CGATCCCTCTTGACGACGC 60.587 63.158 0.00 0.00 0.00 5.19
665 1421 1.064296 CCGATCCCTCTTGACGACG 59.936 63.158 0.00 0.00 0.00 5.12
666 1422 1.227002 GCCGATCCCTCTTGACGAC 60.227 63.158 0.00 0.00 0.00 4.34
667 1423 2.423898 GGCCGATCCCTCTTGACGA 61.424 63.158 0.00 0.00 0.00 4.20
668 1424 2.107141 GGCCGATCCCTCTTGACG 59.893 66.667 0.00 0.00 0.00 4.35
669 1425 2.107141 CGGCCGATCCCTCTTGAC 59.893 66.667 24.07 0.00 0.00 3.18
670 1426 3.154473 CCGGCCGATCCCTCTTGA 61.154 66.667 30.73 0.00 0.00 3.02
671 1427 4.918201 GCCGGCCGATCCCTCTTG 62.918 72.222 30.73 7.40 0.00 3.02
674 1430 4.918201 CTTGCCGGCCGATCCCTC 62.918 72.222 30.73 8.58 0.00 4.30
676 1432 4.918201 CTCTTGCCGGCCGATCCC 62.918 72.222 30.73 12.45 0.00 3.85
677 1433 4.918201 CCTCTTGCCGGCCGATCC 62.918 72.222 30.73 15.22 0.00 3.36
678 1434 3.798954 CTCCTCTTGCCGGCCGATC 62.799 68.421 30.73 18.71 0.00 3.69
679 1435 3.854669 CTCCTCTTGCCGGCCGAT 61.855 66.667 30.73 0.00 0.00 4.18
720 1476 5.644977 ATTAGTGTGATGAGTCTTGACGA 57.355 39.130 0.00 0.00 0.00 4.20
749 1505 2.408271 ATGGATGAGACAACGCACAT 57.592 45.000 0.00 0.00 0.00 3.21
928 1705 2.420466 GGTATCTCCCGGGTTCGC 59.580 66.667 22.86 8.29 34.56 4.70
949 1726 2.159490 GCACAGAGACGAGTAGAAGGAC 60.159 54.545 0.00 0.00 0.00 3.85
967 1744 3.244033 ACTCTCTCTTACATGCAGCAC 57.756 47.619 0.00 0.00 0.00 4.40
1015 1792 2.356313 AGGTGACGTTGCTGCTCG 60.356 61.111 13.86 13.86 0.00 5.03
1147 1924 0.248702 GTCAGCCGGAGAAGATCGAC 60.249 60.000 5.05 0.00 0.00 4.20
1226 2015 3.755628 GCCTGTCGTCTGCCGGTA 61.756 66.667 1.90 0.00 37.11 4.02
1285 2074 7.224297 GGGTCCTCATAAGTATTTTGCTATCA 58.776 38.462 0.00 0.00 0.00 2.15
1341 2138 4.821589 GCTTCCCTCGACAGCCGG 62.822 72.222 0.00 0.00 39.14 6.13
1435 2232 6.294065 GGAAGGAACATACGTACAGAGGATAG 60.294 46.154 0.00 0.00 0.00 2.08
1456 2273 2.775911 TGGACTCAGCAATCAGGAAG 57.224 50.000 0.00 0.00 0.00 3.46
1459 2276 1.211212 TCCATGGACTCAGCAATCAGG 59.789 52.381 11.44 0.00 0.00 3.86
1642 2459 0.252197 GAAGCATGGAGGTTACGGGT 59.748 55.000 0.00 0.00 38.24 5.28
1651 2468 0.179073 ATTCGGACGGAAGCATGGAG 60.179 55.000 0.00 0.00 38.24 3.86
1679 2496 4.973168 AGTGGCAGAACAGAACAGAATAA 58.027 39.130 0.00 0.00 0.00 1.40
1706 2523 5.560760 CGCGATGCTAACATAATTTCCATGT 60.561 40.000 0.00 0.00 38.25 3.21
1719 2536 3.669122 AGATATTTCGACGCGATGCTAAC 59.331 43.478 15.93 0.00 35.23 2.34
1722 2539 2.423926 AGATATTTCGACGCGATGCT 57.576 45.000 15.93 0.00 35.23 3.79
1742 2559 3.393426 AAGTGGAGAATGCCATGGAAT 57.607 42.857 18.40 8.01 40.68 3.01
1749 2566 2.755103 CCCTACAAAAGTGGAGAATGCC 59.245 50.000 0.00 0.00 38.04 4.40
1760 2577 0.774908 TCCCCACCACCCTACAAAAG 59.225 55.000 0.00 0.00 0.00 2.27
1828 2645 0.324943 TACCCTTGTGCTTCTCAGCC 59.675 55.000 0.00 0.00 46.74 4.85
1848 2673 0.548031 TCAGGGTGAGGATTGATGCC 59.452 55.000 0.00 0.00 0.00 4.40
1881 2706 1.784301 TTCCGATGCCCAGGGACAAA 61.784 55.000 10.89 0.00 0.00 2.83
1882 2707 2.227757 TTCCGATGCCCAGGGACAA 61.228 57.895 10.89 0.00 0.00 3.18
1883 2708 2.609299 TTCCGATGCCCAGGGACA 60.609 61.111 10.89 7.45 0.00 4.02
1927 2752 3.878699 CCAGGCAAAACAAAAATCAGCTT 59.121 39.130 0.00 0.00 0.00 3.74
1929 2756 2.031769 GCCAGGCAAAACAAAAATCAGC 60.032 45.455 6.55 0.00 0.00 4.26
1944 2771 3.730761 CTGTCAACGCAGCCAGGC 61.731 66.667 1.84 1.84 0.00 4.85
1946 2773 3.052082 CCCTGTCAACGCAGCCAG 61.052 66.667 0.00 0.00 35.28 4.85
1981 2810 4.830765 GTGCTCGCGCCATGGGTA 62.831 66.667 15.13 0.00 34.43 3.69
1993 2822 2.125753 CACAGCTCCTCCGTGCTC 60.126 66.667 0.00 0.00 36.71 4.26
2189 3018 1.162698 GAAAGGGAAACAGCGGTACC 58.837 55.000 0.16 0.16 0.00 3.34
2190 3019 0.794473 CGAAAGGGAAACAGCGGTAC 59.206 55.000 0.00 0.00 0.00 3.34
2191 3020 0.952010 GCGAAAGGGAAACAGCGGTA 60.952 55.000 0.00 0.00 0.00 4.02
2192 3021 2.258726 GCGAAAGGGAAACAGCGGT 61.259 57.895 0.00 0.00 0.00 5.68
2193 3022 2.561373 GCGAAAGGGAAACAGCGG 59.439 61.111 0.00 0.00 0.00 5.52
2365 3336 4.645588 GTCTGGATAGTGGTAGTAGCAACT 59.354 45.833 3.06 6.64 39.91 3.16
2377 3348 2.941064 CCAACTGCATGTCTGGATAGTG 59.059 50.000 0.00 0.00 32.38 2.74
2378 3349 2.573462 ACCAACTGCATGTCTGGATAGT 59.427 45.455 16.43 0.00 33.80 2.12
2399 3370 2.907634 TGACGACCTAACAGTTGCAAA 58.092 42.857 0.00 0.00 0.00 3.68
2400 3371 2.605837 TGACGACCTAACAGTTGCAA 57.394 45.000 0.00 0.00 0.00 4.08
2401 3372 2.605837 TTGACGACCTAACAGTTGCA 57.394 45.000 0.00 0.00 0.00 4.08
2402 3373 4.024387 TCAAATTGACGACCTAACAGTTGC 60.024 41.667 0.00 0.00 0.00 4.17
2403 3374 5.440685 GTCAAATTGACGACCTAACAGTTG 58.559 41.667 10.58 0.00 37.67 3.16
2404 3375 5.668558 GTCAAATTGACGACCTAACAGTT 57.331 39.130 10.58 0.00 37.67 3.16
2426 3397 7.152645 AGGGCGTGTAATATATGTTTCACTAG 58.847 38.462 16.16 6.49 30.17 2.57
2649 4231 4.695231 GATGGCCGCATGCATCGC 62.695 66.667 19.57 15.19 43.89 4.58
2804 4386 4.765339 GCTTTAGATGTTAGGGTTTGGTGT 59.235 41.667 0.00 0.00 0.00 4.16
2837 4419 4.954970 CGGTGTGTGGCTGGGCTT 62.955 66.667 0.00 0.00 0.00 4.35
3142 4726 1.271856 TTGATGCCGTTGTCCCTCTA 58.728 50.000 0.00 0.00 0.00 2.43
3143 4727 0.400213 TTTGATGCCGTTGTCCCTCT 59.600 50.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.