Multiple sequence alignment - TraesCS5A01G079600

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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 TraesCS5A01G079600 chr5A 100.000 6081 0 0 1 6081 99018676 99024756 0.000000e+00 11230.0
1 TraesCS5A01G079600 chr5A 97.222 36 1 0 1637 1672 99020242 99020277 1.830000e-05 62.1
2 TraesCS5A01G079600 chr5A 97.222 36 1 0 1567 1602 99020312 99020347 1.830000e-05 62.1
3 TraesCS5A01G079600 chr5A 96.970 33 0 1 5115 5147 99025140 99025109 3.000000e-03 54.7
4 TraesCS5A01G079600 chr5D 96.098 3306 106 13 12 3310 101453813 101450524 0.000000e+00 5369.0
5 TraesCS5A01G079600 chr5D 92.553 1410 71 18 4695 6077 101450527 101449125 0.000000e+00 1991.0
6 TraesCS5A01G079600 chr5B 95.791 2970 112 6 344 3310 109773661 109770702 0.000000e+00 4780.0
7 TraesCS5A01G079600 chr5B 98.957 1342 13 1 3354 4695 658180095 658178755 0.000000e+00 2399.0
8 TraesCS5A01G079600 chr5B 91.715 869 34 13 4695 5531 109770705 109769843 0.000000e+00 1171.0
9 TraesCS5A01G079600 chr5B 92.233 309 14 4 12 315 109773964 109773661 4.360000e-116 429.0
10 TraesCS5A01G079600 chr5B 96.296 243 7 2 5836 6077 109754382 109754141 1.230000e-106 398.0
11 TraesCS5A01G079600 chr5B 92.937 269 9 5 5523 5782 109768194 109767927 3.440000e-102 383.0
12 TraesCS5A01G079600 chr5B 93.939 66 4 0 5776 5841 109765146 109765081 3.880000e-17 100.0
13 TraesCS5A01G079600 chr5B 97.222 36 1 0 1567 1602 109772369 109772334 1.830000e-05 62.1
14 TraesCS5A01G079600 chr5B 97.222 36 1 0 1637 1672 109772439 109772404 1.830000e-05 62.1
15 TraesCS5A01G079600 chr6B 97.943 1361 27 1 3336 4695 114410485 114411845 0.000000e+00 2357.0
16 TraesCS5A01G079600 chr6B 98.217 1346 22 2 3350 4695 561641868 561640525 0.000000e+00 2351.0
17 TraesCS5A01G079600 chr7A 97.778 1350 30 0 3346 4695 679314531 679315880 0.000000e+00 2327.0
18 TraesCS5A01G079600 chrUn 98.051 1334 26 0 3350 4683 53929202 53927869 0.000000e+00 2320.0
19 TraesCS5A01G079600 chr3A 96.803 1345 22 2 3350 4694 743534662 743535985 0.000000e+00 2226.0
20 TraesCS5A01G079600 chr2B 90.715 1357 111 10 3343 4693 625929210 625927863 0.000000e+00 1794.0
21 TraesCS5A01G079600 chr3B 90.206 1358 117 10 3343 4694 711547306 711548653 0.000000e+00 1757.0
22 TraesCS5A01G079600 chr7B 90.074 1360 119 11 3343 4696 23299888 23301237 0.000000e+00 1749.0
23 TraesCS5A01G079600 chr4B 82.895 76 13 0 5795 5870 167356824 167356749 1.090000e-07 69.4


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 TraesCS5A01G079600 chr5A 99018676 99024756 6080 False 11230.000000 11230 100.0000 1 6081 1 chr5A.!!$F1 6080
1 TraesCS5A01G079600 chr5D 101449125 101453813 4688 True 3680.000000 5369 94.3255 12 6077 2 chr5D.!!$R1 6065
2 TraesCS5A01G079600 chr5B 658178755 658180095 1340 True 2399.000000 2399 98.9570 3354 4695 1 chr5B.!!$R2 1341
3 TraesCS5A01G079600 chr5B 109765081 109773964 8883 True 998.171429 4780 94.4370 12 5841 7 chr5B.!!$R3 5829
4 TraesCS5A01G079600 chr6B 114410485 114411845 1360 False 2357.000000 2357 97.9430 3336 4695 1 chr6B.!!$F1 1359
5 TraesCS5A01G079600 chr6B 561640525 561641868 1343 True 2351.000000 2351 98.2170 3350 4695 1 chr6B.!!$R1 1345
6 TraesCS5A01G079600 chr7A 679314531 679315880 1349 False 2327.000000 2327 97.7780 3346 4695 1 chr7A.!!$F1 1349
7 TraesCS5A01G079600 chrUn 53927869 53929202 1333 True 2320.000000 2320 98.0510 3350 4683 1 chrUn.!!$R1 1333
8 TraesCS5A01G079600 chr3A 743534662 743535985 1323 False 2226.000000 2226 96.8030 3350 4694 1 chr3A.!!$F1 1344
9 TraesCS5A01G079600 chr2B 625927863 625929210 1347 True 1794.000000 1794 90.7150 3343 4693 1 chr2B.!!$R1 1350
10 TraesCS5A01G079600 chr3B 711547306 711548653 1347 False 1757.000000 1757 90.2060 3343 4694 1 chr3B.!!$F1 1351
11 TraesCS5A01G079600 chr7B 23299888 23301237 1349 False 1749.000000 1749 90.0740 3343 4696 1 chr7B.!!$F1 1353

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
567 573 0.250234 CAGATCAGTTTGAGGCCGGA 59.750 55.0 5.05 0.0 0.00 5.14 F
2318 2329 0.100682 GCGTGAGAGCTGGTCGATTA 59.899 55.0 0.00 0.0 0.00 1.75 F
3329 3341 0.108615 CTAGGTGGCTGAACGTGAGG 60.109 60.0 0.00 0.0 0.00 3.86 F
5005 5025 0.741221 CTGGCTTCTTGCGTAGGTCC 60.741 60.0 0.00 0.0 44.05 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 2414 0.181350 ATCCCGGAATGGCTTCTCAC 59.819 55.000 0.73 0.00 35.87 3.51 R
3498 3510 0.032815 GCCGAGATAGACAAGAGGGC 59.967 60.000 0.00 0.00 0.00 5.19 R
5031 5051 0.678684 CACTGGGTCATGCATGCTCA 60.679 55.000 22.25 20.06 0.00 4.26 R
5864 10392 2.778299 ACACCATCACCATACACACAC 58.222 47.619 0.00 0.00 0.00 3.82 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
48 49 3.271729 TCCGTGTTCTTGTTTGTGCTTA 58.728 40.909 0.00 0.00 0.00 3.09
198 199 0.547954 AGGGGAGGAAAGGACTGGAC 60.548 60.000 0.00 0.00 0.00 4.02
265 271 2.791383 TTGCAGGTTCCGAACAAATG 57.209 45.000 13.23 9.22 0.00 2.32
336 342 7.019656 AGCCTAAATTTGTGATTTTGGGATT 57.980 32.000 0.00 0.00 36.00 3.01
358 364 0.472471 TGCCCGGAAGAACAGTTTCT 59.528 50.000 0.73 0.00 44.53 2.52
413 419 3.552890 GGAAGTTGGAGGAAATGTGTTGC 60.553 47.826 0.00 0.00 0.00 4.17
465 471 2.650322 TCCCCATCCTATTTTGTTCGC 58.350 47.619 0.00 0.00 0.00 4.70
491 497 8.594687 CAGATTCGAAATTCAGTTTTTGTGTTT 58.405 29.630 0.00 0.00 0.00 2.83
540 546 6.934645 TCTTTCAGTCACCTAATCGATTGTTT 59.065 34.615 20.87 1.24 0.00 2.83
567 573 0.250234 CAGATCAGTTTGAGGCCGGA 59.750 55.000 5.05 0.00 0.00 5.14
773 779 4.830826 GGGGGCGATTTATGAACTTTAG 57.169 45.455 0.00 0.00 0.00 1.85
828 834 7.206789 TGATGGGTGTTTCTTATCCATTCTA 57.793 36.000 0.00 0.00 38.23 2.10
930 941 1.215382 CACAGCGGCACTAGCACTA 59.785 57.895 1.45 0.00 44.61 2.74
931 942 0.803768 CACAGCGGCACTAGCACTAG 60.804 60.000 1.45 3.10 44.61 2.57
932 943 1.251527 ACAGCGGCACTAGCACTAGT 61.252 55.000 1.45 4.47 46.52 2.57
933 944 0.738975 CAGCGGCACTAGCACTAGTA 59.261 55.000 9.92 0.00 43.98 1.82
1009 1020 1.137404 GCAGGCTACATGGCAAACG 59.863 57.895 0.00 0.00 44.55 3.60
1266 1277 7.703328 TGTTGTTTGAGTTCTGATTCTAAACC 58.297 34.615 0.00 0.00 0.00 3.27
1295 1306 4.883585 TGTTAGGATCCTGATGTTTGATGC 59.116 41.667 25.28 1.34 0.00 3.91
1324 1335 3.591196 TTTGGTGGCAGTGATTAATGC 57.409 42.857 0.65 0.65 46.53 3.56
1374 1385 6.151144 GCTTGAAATGGTAAAGAAGGAGCTTA 59.849 38.462 0.00 0.00 0.00 3.09
1380 1391 8.706322 AATGGTAAAGAAGGAGCTTAAAGAAA 57.294 30.769 0.00 0.00 0.00 2.52
1454 1465 5.269313 CAACTTGCTCAGAAGAACAAAGAC 58.731 41.667 0.00 0.00 30.11 3.01
1628 1639 6.698766 GTGGCCTCATAATTTTAATCTTGCAG 59.301 38.462 3.32 0.00 0.00 4.41
1810 1821 6.261826 CCAAAGCCGATGAAATATCTCTCTTT 59.738 38.462 0.00 0.00 0.00 2.52
1913 1924 9.746711 CATTCTTAAACATTGTCGAACTTCTAG 57.253 33.333 0.00 0.00 0.00 2.43
1950 1961 6.995091 GTCCTTGATAGAATAGCCTCATGTTT 59.005 38.462 0.00 0.00 0.00 2.83
2038 2049 7.246171 AGATTATCACATAAACGGGCTATCT 57.754 36.000 0.00 0.00 0.00 1.98
2209 2220 6.918022 GGTTTTCTCATACAAACTTGAACTGG 59.082 38.462 0.00 0.00 34.00 4.00
2210 2221 7.416326 GGTTTTCTCATACAAACTTGAACTGGT 60.416 37.037 0.00 0.00 34.00 4.00
2229 2240 9.155975 GAACTGGTATATTGCATACATTCTAGG 57.844 37.037 0.00 0.00 0.00 3.02
2233 2244 7.236640 TGGTATATTGCATACATTCTAGGTCCA 59.763 37.037 0.00 0.00 0.00 4.02
2249 2260 2.286872 GTCCATGATCTTGCAGTGAGG 58.713 52.381 3.07 0.00 0.00 3.86
2263 2274 3.553511 GCAGTGAGGATATGCATATACGC 59.446 47.826 22.02 22.02 39.75 4.42
2318 2329 0.100682 GCGTGAGAGCTGGTCGATTA 59.899 55.000 0.00 0.00 0.00 1.75
2364 2375 3.698040 CAGGGGTTCTCTGAAATTGATGG 59.302 47.826 0.00 0.00 34.36 3.51
2368 2379 3.445096 GGTTCTCTGAAATTGATGGTGGG 59.555 47.826 0.00 0.00 0.00 4.61
2373 2384 2.564062 CTGAAATTGATGGTGGGCAGTT 59.436 45.455 0.00 0.00 0.00 3.16
2374 2385 2.971330 TGAAATTGATGGTGGGCAGTTT 59.029 40.909 0.00 0.00 0.00 2.66
2399 2410 6.367374 TTGGGATAAAGAAAATGGGGAAAC 57.633 37.500 0.00 0.00 0.00 2.78
2403 2414 7.398904 TGGGATAAAGAAAATGGGGAAACTAAG 59.601 37.037 0.00 0.00 0.00 2.18
2458 2469 0.178964 TGGCCCCTAAATATGCTGGC 60.179 55.000 0.00 0.00 38.16 4.85
2480 2491 3.673338 CGCGAAATCTTCTGAACTGTACA 59.327 43.478 0.00 0.00 0.00 2.90
2482 2493 4.143094 GCGAAATCTTCTGAACTGTACACC 60.143 45.833 0.00 0.00 0.00 4.16
2502 2513 0.737715 CTGTGGCAGGAACTACTCGC 60.738 60.000 0.00 0.00 36.02 5.03
2527 2538 3.714144 TCCAAACTGGAAACCCTTCAAA 58.286 40.909 0.00 0.00 45.00 2.69
2533 2544 4.145052 ACTGGAAACCCTTCAAATCTGTC 58.855 43.478 0.00 0.00 32.75 3.51
2677 2688 7.823310 AGGTCATAGATGTTGATGATGATAAGC 59.177 37.037 0.00 0.00 34.69 3.09
2709 2720 0.327867 AGATGGCATGGGGAGAAGGA 60.328 55.000 3.81 0.00 0.00 3.36
2771 2782 4.588951 AGAGTACAACACTGATGGAACAGA 59.411 41.667 0.00 0.00 39.20 3.41
2784 2795 2.208431 GGAACAGATGATGCCTTCGAG 58.792 52.381 0.00 0.00 0.00 4.04
2905 2916 4.897076 ACAGGTATGGTGTCGGTGATTATA 59.103 41.667 0.00 0.00 0.00 0.98
2943 2954 4.529897 TGGTAGATGCATCTTGCTGATTT 58.470 39.130 32.94 9.41 45.31 2.17
3307 3319 1.880271 CTGCAGGGCATGATGACTAG 58.120 55.000 5.57 0.00 38.13 2.57
3308 3320 0.471191 TGCAGGGCATGATGACTAGG 59.529 55.000 1.99 0.00 31.71 3.02
3309 3321 0.471617 GCAGGGCATGATGACTAGGT 59.528 55.000 1.99 0.00 0.00 3.08
3310 3322 1.542108 GCAGGGCATGATGACTAGGTC 60.542 57.143 1.99 0.00 0.00 3.85
3311 3323 2.045524 CAGGGCATGATGACTAGGTCT 58.954 52.381 0.00 0.00 33.15 3.85
3312 3324 3.234353 CAGGGCATGATGACTAGGTCTA 58.766 50.000 0.00 0.00 33.15 2.59
3313 3325 3.257873 CAGGGCATGATGACTAGGTCTAG 59.742 52.174 0.00 3.65 39.04 2.43
3314 3326 2.564947 GGGCATGATGACTAGGTCTAGG 59.435 54.545 0.00 0.00 37.49 3.02
3315 3327 3.235200 GGCATGATGACTAGGTCTAGGT 58.765 50.000 9.51 0.00 37.49 3.08
3316 3328 3.006323 GGCATGATGACTAGGTCTAGGTG 59.994 52.174 9.51 1.19 37.49 4.00
3317 3329 3.006323 GCATGATGACTAGGTCTAGGTGG 59.994 52.174 9.51 0.00 37.49 4.61
3318 3330 2.667470 TGATGACTAGGTCTAGGTGGC 58.333 52.381 9.51 0.00 37.49 5.01
3319 3331 2.245028 TGATGACTAGGTCTAGGTGGCT 59.755 50.000 9.51 0.00 37.49 4.75
3320 3332 2.145397 TGACTAGGTCTAGGTGGCTG 57.855 55.000 9.51 0.00 37.49 4.85
3321 3333 1.639108 TGACTAGGTCTAGGTGGCTGA 59.361 52.381 9.51 0.00 37.49 4.26
3322 3334 2.042569 TGACTAGGTCTAGGTGGCTGAA 59.957 50.000 9.51 0.00 37.49 3.02
3323 3335 2.427812 GACTAGGTCTAGGTGGCTGAAC 59.572 54.545 9.51 0.00 37.49 3.18
3324 3336 1.405821 CTAGGTCTAGGTGGCTGAACG 59.594 57.143 0.00 0.00 0.00 3.95
3325 3337 0.542232 AGGTCTAGGTGGCTGAACGT 60.542 55.000 0.00 0.00 0.00 3.99
3326 3338 0.389948 GGTCTAGGTGGCTGAACGTG 60.390 60.000 0.00 0.00 0.00 4.49
3327 3339 0.601558 GTCTAGGTGGCTGAACGTGA 59.398 55.000 0.00 0.00 0.00 4.35
3328 3340 0.888619 TCTAGGTGGCTGAACGTGAG 59.111 55.000 0.00 0.00 0.00 3.51
3329 3341 0.108615 CTAGGTGGCTGAACGTGAGG 60.109 60.000 0.00 0.00 0.00 3.86
3330 3342 2.167398 TAGGTGGCTGAACGTGAGGC 62.167 60.000 12.95 12.95 36.55 4.70
3331 3343 3.050275 GTGGCTGAACGTGAGGCC 61.050 66.667 16.09 16.01 44.31 5.19
3333 3345 2.743928 GGCTGAACGTGAGGCCAG 60.744 66.667 17.30 8.72 43.59 4.85
3334 3346 2.743928 GCTGAACGTGAGGCCAGG 60.744 66.667 5.01 0.00 35.91 4.45
3732 3749 2.334946 GCTTGAACGCCATCAGCCA 61.335 57.895 0.00 0.00 38.78 4.75
4267 4286 1.325355 GCATGGTGCAGCTGGATATT 58.675 50.000 17.12 0.00 44.26 1.28
4850 4870 4.718774 TGCCTCCTCTGATCTAAAACTCAT 59.281 41.667 0.00 0.00 0.00 2.90
4859 4879 8.634475 TCTGATCTAAAACTCATAACATGACG 57.366 34.615 0.00 0.00 35.06 4.35
4906 4926 9.788960 GTGGATTTCTCTTACATTATCAAAACC 57.211 33.333 0.00 0.00 0.00 3.27
4958 4978 3.826524 TCTATGTTGCCACTGTTTTCCA 58.173 40.909 0.00 0.00 0.00 3.53
4999 5019 0.886490 CTGTTCCTGGCTTCTTGCGT 60.886 55.000 0.00 0.00 44.05 5.24
5005 5025 0.741221 CTGGCTTCTTGCGTAGGTCC 60.741 60.000 0.00 0.00 44.05 4.46
5031 5051 2.638480 ACAATGTGTACTGCCACTGT 57.362 45.000 0.00 0.00 36.30 3.55
5128 5194 1.797635 GCAGGCTTTTATTTTGCGCAA 59.202 42.857 21.02 21.02 0.00 4.85
5165 5231 7.430793 CGTCTGATTAGAACTCTGTTGTATCAG 59.569 40.741 0.00 0.00 34.01 2.90
5227 5293 5.708697 TGACAAGAACTCTGATGCATGAATT 59.291 36.000 2.46 0.00 0.00 2.17
5385 5454 3.754323 CCTTGGTTTATTTGACTACGGCA 59.246 43.478 0.00 0.00 0.00 5.69
5386 5455 4.398044 CCTTGGTTTATTTGACTACGGCAT 59.602 41.667 0.00 0.00 0.00 4.40
5411 5480 4.910195 ACATTGCTGTCTAGATTGTGGAA 58.090 39.130 0.00 0.00 0.00 3.53
5444 5513 7.891498 AAGGACCTCTTCTTCTATAGTCTTC 57.109 40.000 0.00 0.00 0.00 2.87
5474 5543 2.811431 CGGTGGTTACTGCTGAATTTCA 59.189 45.455 0.00 0.00 0.00 2.69
5476 5545 4.082787 CGGTGGTTACTGCTGAATTTCATT 60.083 41.667 0.00 0.00 0.00 2.57
5504 5579 9.988350 GTGTGTGTGTGAAATTAATATAGAAGG 57.012 33.333 0.00 0.00 0.00 3.46
5505 5580 9.173021 TGTGTGTGTGAAATTAATATAGAAGGG 57.827 33.333 0.00 0.00 0.00 3.95
5506 5581 9.391006 GTGTGTGTGAAATTAATATAGAAGGGA 57.609 33.333 0.00 0.00 0.00 4.20
5507 5582 9.613428 TGTGTGTGAAATTAATATAGAAGGGAG 57.387 33.333 0.00 0.00 0.00 4.30
5511 5586 9.166222 TGTGAAATTAATATAGAAGGGAGCCTA 57.834 33.333 0.00 0.00 31.13 3.93
5547 7279 9.985730 AAAAATATTATCACCATGCATTGTAGG 57.014 29.630 2.64 0.88 0.00 3.18
5548 7280 6.764308 ATATTATCACCATGCATTGTAGGC 57.236 37.500 2.64 0.00 0.00 3.93
5549 7281 2.440517 ATCACCATGCATTGTAGGCA 57.559 45.000 2.64 0.00 46.66 4.75
5550 7282 2.212812 TCACCATGCATTGTAGGCAA 57.787 45.000 2.64 0.00 45.60 4.52
5551 7283 2.737544 TCACCATGCATTGTAGGCAAT 58.262 42.857 2.64 0.00 45.60 3.56
5552 7284 3.895998 TCACCATGCATTGTAGGCAATA 58.104 40.909 2.64 0.00 45.60 1.90
5553 7285 4.276642 TCACCATGCATTGTAGGCAATAA 58.723 39.130 2.64 0.00 45.60 1.40
5592 7332 8.725405 TTGTAGACAATAAAGTTTGTGTCAGA 57.275 30.769 24.64 15.21 42.29 3.27
5596 7336 4.278419 ACAATAAAGTTTGTGTCAGAGCCC 59.722 41.667 0.00 0.00 38.37 5.19
5609 7349 1.277557 CAGAGCCCTTACTCTTGCTGT 59.722 52.381 0.00 0.00 44.76 4.40
5731 7471 3.512329 TGCTCGTAAATACCACTTCCTCA 59.488 43.478 0.00 0.00 0.00 3.86
5914 10442 9.494271 TGATCTTAGCATATTTTCCTATGTGAC 57.506 33.333 0.00 0.00 32.69 3.67
5994 10522 6.039717 TCACCAAAAATTGAGATAGCATAGGC 59.960 38.462 0.00 0.00 41.61 3.93
6077 10606 3.350219 TTCAAGGTGGGCTAAGTCATC 57.650 47.619 0.00 0.00 0.00 2.92
6078 10607 2.265367 TCAAGGTGGGCTAAGTCATCA 58.735 47.619 0.00 0.00 0.00 3.07
6079 10608 2.846206 TCAAGGTGGGCTAAGTCATCAT 59.154 45.455 0.00 0.00 0.00 2.45
6080 10609 4.037222 TCAAGGTGGGCTAAGTCATCATA 58.963 43.478 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.537188 AGAATACACCCGGAGCACAG 59.463 55.000 0.73 0.00 0.00 3.66
1 2 0.535335 GAGAATACACCCGGAGCACA 59.465 55.000 0.73 0.00 0.00 4.57
2 3 0.527817 CGAGAATACACCCGGAGCAC 60.528 60.000 0.73 0.00 0.00 4.40
3 4 0.968901 ACGAGAATACACCCGGAGCA 60.969 55.000 0.73 0.00 0.00 4.26
4 5 0.248949 GACGAGAATACACCCGGAGC 60.249 60.000 0.73 0.00 0.00 4.70
5 6 0.029035 CGACGAGAATACACCCGGAG 59.971 60.000 0.73 0.00 0.00 4.63
6 7 1.996786 GCGACGAGAATACACCCGGA 61.997 60.000 0.73 0.00 0.00 5.14
7 8 1.588139 GCGACGAGAATACACCCGG 60.588 63.158 0.00 0.00 0.00 5.73
8 9 1.588139 GGCGACGAGAATACACCCG 60.588 63.158 0.00 0.00 0.00 5.28
9 10 0.248949 GAGGCGACGAGAATACACCC 60.249 60.000 0.00 0.00 0.00 4.61
10 11 0.248949 GGAGGCGACGAGAATACACC 60.249 60.000 0.00 0.00 0.00 4.16
48 49 1.301479 GAAACGTCCACGGAGGCTT 60.301 57.895 5.70 0.00 44.95 4.35
265 271 8.617761 TTGAAAACACAAGTTACGGAATAAAC 57.382 30.769 0.00 0.00 36.84 2.01
336 342 0.400213 AACTGTTCTTCCGGGCATGA 59.600 50.000 0.00 0.00 0.00 3.07
413 419 1.882623 GAAACCCAGGAAACAGAGCAG 59.117 52.381 0.00 0.00 0.00 4.24
465 471 7.684062 ACACAAAAACTGAATTTCGAATCTG 57.316 32.000 0.00 1.24 0.00 2.90
491 497 2.371391 AGGGGTTTAGGGCTTTAGGA 57.629 50.000 0.00 0.00 0.00 2.94
773 779 0.603975 GCACAAGACACCCCTCTCAC 60.604 60.000 0.00 0.00 0.00 3.51
843 849 6.978338 ACCAAAATAGCTCATTGATATGCAG 58.022 36.000 0.00 0.00 0.00 4.41
918 929 7.976135 TTATACTACTACTAGTGCTAGTGCC 57.024 40.000 18.97 0.00 45.25 5.01
919 930 9.001542 ACATTATACTACTACTAGTGCTAGTGC 57.998 37.037 18.97 0.00 45.25 4.40
933 944 8.978472 AGTCACATTACACCACATTATACTACT 58.022 33.333 0.00 0.00 0.00 2.57
953 964 8.846943 AACAGAATATCACAAACATAGTCACA 57.153 30.769 0.00 0.00 0.00 3.58
1009 1020 0.467804 GAGACATCCCTTCCTCTGCC 59.532 60.000 0.00 0.00 0.00 4.85
1189 1200 5.221521 GCTGGAGTTTTTCCTTTTCTTCCAT 60.222 40.000 0.00 0.00 46.92 3.41
1266 1277 6.824305 AACATCAGGATCCTAACAAAACTG 57.176 37.500 15.67 0.00 0.00 3.16
1295 1306 0.242825 CTGCCACCAAATGAGTGCAG 59.757 55.000 0.00 0.00 35.02 4.41
1374 1385 8.980596 TCCCACATGCTCATATTTTATTTCTTT 58.019 29.630 0.00 0.00 0.00 2.52
1380 1391 5.387788 TGCTCCCACATGCTCATATTTTAT 58.612 37.500 0.00 0.00 0.00 1.40
1399 1410 0.322366 AGCAAGCTCCTCCTTTGCTC 60.322 55.000 5.21 0.00 35.85 4.26
1454 1465 4.019771 AGCTTCTTCCTTAGAACCTTCAGG 60.020 45.833 0.00 0.00 37.96 3.86
1514 1525 3.572584 CTCAGAAGCACTTCCAATTTGC 58.427 45.455 6.77 0.00 40.33 3.68
1628 1639 1.066605 GTGGTGAATGGCTGATGATGC 59.933 52.381 0.00 0.00 0.00 3.91
1913 1924 3.557228 ATCAAGGACAGAGAATCAGCC 57.443 47.619 0.00 0.00 37.82 4.85
2038 2049 1.134401 GTCCGATGATCCTTGGAGCAA 60.134 52.381 11.76 0.00 28.89 3.91
2166 2177 6.772716 AGAAAACCTTGATCAGCTTTTGTCTA 59.227 34.615 10.25 0.00 0.00 2.59
2209 2220 9.102757 CATGGACCTAGAATGTATGCAATATAC 57.897 37.037 0.00 0.00 0.00 1.47
2210 2221 9.045745 TCATGGACCTAGAATGTATGCAATATA 57.954 33.333 0.00 0.00 0.00 0.86
2214 2225 5.628797 TCATGGACCTAGAATGTATGCAA 57.371 39.130 0.00 0.00 0.00 4.08
2229 2240 2.093288 TCCTCACTGCAAGATCATGGAC 60.093 50.000 0.00 0.00 37.43 4.02
2233 2244 4.202430 TGCATATCCTCACTGCAAGATCAT 60.202 41.667 0.00 0.00 42.53 2.45
2274 2285 7.384932 GCACCTCAAATTTACAAATTTAGCACT 59.615 33.333 11.29 0.00 44.38 4.40
2364 2375 4.953579 TCTTTATCCCAATAAACTGCCCAC 59.046 41.667 0.00 0.00 34.43 4.61
2368 2379 7.495606 CCCATTTTCTTTATCCCAATAAACTGC 59.504 37.037 0.00 0.00 34.43 4.40
2373 2384 8.544622 GTTTCCCCATTTTCTTTATCCCAATAA 58.455 33.333 0.00 0.00 0.00 1.40
2374 2385 7.904022 AGTTTCCCCATTTTCTTTATCCCAATA 59.096 33.333 0.00 0.00 0.00 1.90
2399 2410 2.555199 CCGGAATGGCTTCTCACTTAG 58.445 52.381 0.00 0.00 0.00 2.18
2403 2414 0.181350 ATCCCGGAATGGCTTCTCAC 59.819 55.000 0.73 0.00 35.87 3.51
2443 2454 0.602638 TCGCGCCAGCATATTTAGGG 60.603 55.000 0.00 0.00 45.49 3.53
2458 2469 3.673338 TGTACAGTTCAGAAGATTTCGCG 59.327 43.478 0.00 0.00 34.02 5.87
2527 2538 5.687780 TGATTGCCATCAACTATGACAGAT 58.312 37.500 0.00 0.00 38.69 2.90
2571 2582 2.350772 GCTGCAAGTTACAACGATGCTT 60.351 45.455 19.48 0.00 42.85 3.91
2572 2583 1.197721 GCTGCAAGTTACAACGATGCT 59.802 47.619 19.48 0.00 42.85 3.79
2573 2584 1.069296 TGCTGCAAGTTACAACGATGC 60.069 47.619 0.00 14.88 42.78 3.91
2574 2585 2.967459 TGCTGCAAGTTACAACGATG 57.033 45.000 0.00 0.00 35.30 3.84
2575 2586 2.813754 ACATGCTGCAAGTTACAACGAT 59.186 40.909 6.36 0.00 35.30 3.73
2677 2688 1.093159 GCCATCTTCAGTCCTTGCAG 58.907 55.000 0.00 0.00 0.00 4.41
2709 2720 4.517285 CACTAATGACAGCATTGTAGGGT 58.483 43.478 0.00 0.00 44.18 4.34
2771 2782 1.973515 TCCATAGCTCGAAGGCATCAT 59.026 47.619 0.00 0.00 34.17 2.45
2784 2795 5.046231 CCTCCCTTCCTTATAGTTCCATAGC 60.046 48.000 0.00 0.00 0.00 2.97
2905 2916 5.043737 TCTACCAAGGCTGTAACAAGTTT 57.956 39.130 0.00 0.00 0.00 2.66
3237 3249 7.801104 TGAGCAGGATAAATACCAAATAGTCA 58.199 34.615 0.00 0.00 0.00 3.41
3307 3319 0.389948 CACGTTCAGCCACCTAGACC 60.390 60.000 0.00 0.00 0.00 3.85
3308 3320 0.601558 TCACGTTCAGCCACCTAGAC 59.398 55.000 0.00 0.00 0.00 2.59
3309 3321 0.888619 CTCACGTTCAGCCACCTAGA 59.111 55.000 0.00 0.00 0.00 2.43
3310 3322 0.108615 CCTCACGTTCAGCCACCTAG 60.109 60.000 0.00 0.00 0.00 3.02
3311 3323 1.972198 CCTCACGTTCAGCCACCTA 59.028 57.895 0.00 0.00 0.00 3.08
3312 3324 2.743718 CCTCACGTTCAGCCACCT 59.256 61.111 0.00 0.00 0.00 4.00
3313 3325 3.050275 GCCTCACGTTCAGCCACC 61.050 66.667 0.00 0.00 0.00 4.61
3314 3326 3.050275 GGCCTCACGTTCAGCCAC 61.050 66.667 13.25 0.00 45.07 5.01
3316 3328 2.743928 CTGGCCTCACGTTCAGCC 60.744 66.667 3.32 11.63 45.96 4.85
3317 3329 2.743928 CCTGGCCTCACGTTCAGC 60.744 66.667 3.32 0.00 0.00 4.26
3318 3330 1.374758 GACCTGGCCTCACGTTCAG 60.375 63.158 3.32 0.00 0.00 3.02
3319 3331 2.741092 GACCTGGCCTCACGTTCA 59.259 61.111 3.32 0.00 0.00 3.18
3320 3332 2.047179 GGACCTGGCCTCACGTTC 60.047 66.667 3.32 0.00 0.00 3.95
3321 3333 3.637273 GGGACCTGGCCTCACGTT 61.637 66.667 3.32 0.00 0.00 3.99
3498 3510 0.032815 GCCGAGATAGACAAGAGGGC 59.967 60.000 0.00 0.00 0.00 5.19
4267 4286 1.029947 TCTAGCCGCATCTGTCGTCA 61.030 55.000 0.00 0.00 0.00 4.35
4850 4870 2.570442 TGCATAGACGCGTCATGTTA 57.430 45.000 37.85 23.01 33.35 2.41
4980 5000 0.886490 ACGCAAGAAGCCAGGAACAG 60.886 55.000 0.00 0.00 41.38 3.16
4999 5019 3.248024 ACACATTGTTCTCCTGGACCTA 58.752 45.455 0.00 0.00 0.00 3.08
5005 5025 2.744202 GGCAGTACACATTGTTCTCCTG 59.256 50.000 0.00 0.00 0.00 3.86
5031 5051 0.678684 CACTGGGTCATGCATGCTCA 60.679 55.000 22.25 20.06 0.00 4.26
5128 5194 4.769688 TCTAATCAGACGCATGAAATGGT 58.230 39.130 0.00 0.00 46.86 3.55
5165 5231 0.736325 ACACCGAAGCAGCGACATAC 60.736 55.000 0.00 0.00 0.00 2.39
5170 5236 1.373748 GGTAACACCGAAGCAGCGA 60.374 57.895 0.00 0.00 0.00 4.93
5227 5293 3.006112 TGGCACCAAAGTCAGTAACAA 57.994 42.857 0.00 0.00 0.00 2.83
5385 5454 7.112122 TCCACAATCTAGACAGCAATGTTAAT 58.888 34.615 0.00 0.00 0.00 1.40
5386 5455 6.472016 TCCACAATCTAGACAGCAATGTTAA 58.528 36.000 0.00 0.00 0.00 2.01
5436 5505 2.231478 CACCGGTGTGTCTGAAGACTAT 59.769 50.000 26.95 0.00 44.99 2.12
5444 5513 0.391597 AGTAACCACCGGTGTGTCTG 59.608 55.000 31.80 18.91 41.09 3.51
5534 7266 7.556733 AAAAATTATTGCCTACAATGCATGG 57.443 32.000 0.00 0.00 46.08 3.66
5592 7332 1.059913 ACACAGCAAGAGTAAGGGCT 58.940 50.000 0.00 0.00 36.99 5.19
5596 7336 4.974103 GTGTACACACAGCAAGAGTAAG 57.026 45.455 21.14 0.00 45.75 2.34
5609 7349 7.940137 AGTTTTAATAGTTGGATGGTGTACACA 59.060 33.333 26.51 13.55 0.00 3.72
5690 7430 6.072508 ACGAGCATAAATTATGTTGGCCATAG 60.073 38.462 6.09 0.00 37.34 2.23
5765 7505 6.238676 GGGTTTGGTCAGACTTAAAGAAGTTC 60.239 42.308 0.00 0.00 46.23 3.01
5864 10392 2.778299 ACACCATCACCATACACACAC 58.222 47.619 0.00 0.00 0.00 3.82
5994 10522 6.037172 CCCAAAATGTAGTAAATCTCACCTCG 59.963 42.308 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.