Multiple sequence alignment - TraesCS6A01G182400

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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 TraesCS6A01G182400 chr6A 100.000 2594 0 0 1 2594 209903616 209906209 0.000000e+00 4791.0
1 TraesCS6A01G182400 chr6B 93.223 1564 55 22 440 1964 279067640 279069191 0.000000e+00 2254.0
2 TraesCS6A01G182400 chr6B 87.613 444 35 9 1 442 279066937 279067362 4.990000e-137 497.0
3 TraesCS6A01G182400 chr6B 81.549 607 83 20 1989 2594 279069180 279069758 8.400000e-130 473.0
4 TraesCS6A01G182400 chr6D 92.042 1131 33 23 612 1701 156452990 156454104 0.000000e+00 1537.0
5 TraesCS6A01G182400 chr6D 90.087 575 44 6 1 569 156452069 156452636 0.000000e+00 734.0
6 TraesCS6A01G182400 chr6D 92.445 503 30 6 1702 2201 156455076 156455573 0.000000e+00 712.0
7 TraesCS6A01G182400 chr6D 85.827 381 39 7 2229 2594 156559844 156560224 8.700000e-105 390.0
8 TraesCS6A01G182400 chr1A 77.622 286 55 7 36 315 36129053 36129335 5.740000e-37 165.0
9 TraesCS6A01G182400 chr5B 76.615 325 55 14 4 321 542933495 542933185 2.670000e-35 159.0
10 TraesCS6A01G182400 chr7B 75.710 317 69 7 4 315 736766075 736766388 4.470000e-33 152.0
11 TraesCS6A01G182400 chr7B 75.728 309 69 5 11 315 737729600 737729294 1.610000e-32 150.0
12 TraesCS6A01G182400 chr7B 75.738 305 68 5 15 315 737712331 737712029 5.780000e-32 148.0
13 TraesCS6A01G182400 chr7B 75.081 309 71 6 11 315 737633036 737632730 3.480000e-29 139.0
14 TraesCS6A01G182400 chr7B 78.947 190 24 13 2222 2403 332174181 332174362 5.870000e-22 115.0
15 TraesCS6A01G182400 chr4D 77.512 209 43 4 22 227 81964459 81964666 3.510000e-24 122.0
16 TraesCS6A01G182400 chr4A 75.954 262 48 13 31 283 608281126 608280871 1.260000e-23 121.0
17 TraesCS6A01G182400 chr5A 74.587 303 58 10 5 296 680911354 680911648 5.870000e-22 115.0
18 TraesCS6A01G182400 chr1B 77.387 199 38 6 1 196 434836495 434836689 7.590000e-21 111.0
19 TraesCS6A01G182400 chr5D 73.143 350 74 15 4 342 34209137 34209477 9.820000e-20 108.0
20 TraesCS6A01G182400 chr3D 91.304 46 4 0 2339 2384 42063279 42063324 2.160000e-06 63.9


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 TraesCS6A01G182400 chr6A 209903616 209906209 2593 False 4791.000000 4791 100.000000 1 2594 1 chr6A.!!$F1 2593
1 TraesCS6A01G182400 chr6B 279066937 279069758 2821 False 1074.666667 2254 87.461667 1 2594 3 chr6B.!!$F1 2593
2 TraesCS6A01G182400 chr6D 156452069 156455573 3504 False 994.333333 1537 91.524667 1 2201 3 chr6D.!!$F2 2200

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
93 98 0.179084 CTCCGCCTTAGATTTGCCGA 60.179 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 3574 0.387622 CACGCCATGGAAAGCAAGTG 60.388 55.0 18.4 9.03 0.0 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
51 52 1.204941 CCGATCCTCCTCAAGTTCGTT 59.795 52.381 0.00 0.00 30.69 3.85
88 91 4.058817 CGATAAAGCTCCGCCTTAGATTT 58.941 43.478 0.00 0.00 36.59 2.17
93 98 0.179084 CTCCGCCTTAGATTTGCCGA 60.179 55.000 0.00 0.00 0.00 5.54
100 105 3.181506 GCCTTAGATTTGCCGACTCTTTG 60.182 47.826 0.00 0.00 0.00 2.77
107 112 3.157680 CCGACTCTTTGGGGTGGT 58.842 61.111 0.00 0.00 0.00 4.16
116 121 1.702957 CTTTGGGGTGGTGAGGTTAGA 59.297 52.381 0.00 0.00 0.00 2.10
130 135 6.465084 GTGAGGTTAGAGTTTCTGGTTGTAT 58.535 40.000 0.00 0.00 0.00 2.29
139 144 2.760634 TCTGGTTGTATGTGTGCGAT 57.239 45.000 0.00 0.00 0.00 4.58
196 201 2.165167 AGGGTTCAATGACGACGACTA 58.835 47.619 0.00 0.00 0.00 2.59
200 205 3.508762 GTTCAATGACGACGACTATGGT 58.491 45.455 0.00 0.00 0.00 3.55
208 213 1.386533 GACGACTATGGTTCGAGGGA 58.613 55.000 7.76 0.00 0.00 4.20
225 230 0.329596 GGAACTGGTCCTTGGAGCAT 59.670 55.000 19.96 8.16 43.98 3.79
248 253 1.342174 ACGCAAAGACTTCCCGACTAA 59.658 47.619 12.61 0.00 0.00 2.24
254 259 5.162075 CAAAGACTTCCCGACTAACACTAG 58.838 45.833 0.00 0.00 0.00 2.57
264 269 3.673809 CGACTAACACTAGCAAGGTCAAC 59.326 47.826 0.00 0.00 0.00 3.18
298 303 1.809619 GAGCGACAATAGCGGCACA 60.810 57.895 1.45 0.00 40.04 4.57
347 352 2.549329 GTGGTCGTTCGGTGGTAAATTT 59.451 45.455 0.00 0.00 0.00 1.82
348 353 3.003585 GTGGTCGTTCGGTGGTAAATTTT 59.996 43.478 0.00 0.00 0.00 1.82
349 354 4.213059 GTGGTCGTTCGGTGGTAAATTTTA 59.787 41.667 0.00 0.00 0.00 1.52
406 411 6.484364 AGATCTGGATCTTCTTCTTCTTCC 57.516 41.667 7.23 0.00 45.31 3.46
407 412 5.963253 AGATCTGGATCTTCTTCTTCTTCCA 59.037 40.000 7.23 0.00 45.31 3.53
408 413 6.443206 AGATCTGGATCTTCTTCTTCTTCCAA 59.557 38.462 7.23 0.00 45.31 3.53
409 414 6.439636 TCTGGATCTTCTTCTTCTTCCAAA 57.560 37.500 0.00 0.00 33.15 3.28
452 742 7.332678 GCATTTGACTTCTTAAATGGAAATGCT 59.667 33.333 15.39 0.00 45.53 3.79
455 745 8.816640 TTGACTTCTTAAATGGAAATGCTTTC 57.183 30.769 0.00 0.00 38.94 2.62
502 793 0.749649 AGAGAGCATAGCTGTTCCCG 59.250 55.000 0.00 0.00 39.88 5.14
574 865 6.582677 TGCCTCGAATTCATTTTTCCTTTA 57.417 33.333 6.22 0.00 0.00 1.85
696 1307 1.492176 ACCTATCCTGGCAATCCACTG 59.508 52.381 0.00 0.00 37.47 3.66
753 1380 1.295423 GTAGAAGTTGGGCCTCGCA 59.705 57.895 4.53 0.00 0.00 5.10
791 1431 0.884704 CACTCTCCAAACACCACCGG 60.885 60.000 0.00 0.00 0.00 5.28
850 1490 1.790623 CACGTAAACAACTCCACTCCG 59.209 52.381 0.00 0.00 0.00 4.63
854 1494 3.556775 CGTAAACAACTCCACTCCGAAAA 59.443 43.478 0.00 0.00 0.00 2.29
983 1636 3.058160 CCAGGCAGGAAAGCACCG 61.058 66.667 0.00 0.00 41.22 4.94
1332 1989 2.045536 GGAGGGAAGTGCCAGCTG 60.046 66.667 6.78 6.78 38.95 4.24
1583 2243 7.935405 ACAGGGAAAATTCTTAGTATTGGGTA 58.065 34.615 0.00 0.00 0.00 3.69
1626 2286 1.416401 TGGGACTTGTGTGTTCCTCTC 59.584 52.381 0.00 0.00 36.56 3.20
1627 2287 1.694696 GGGACTTGTGTGTTCCTCTCT 59.305 52.381 0.00 0.00 32.85 3.10
1628 2288 2.104963 GGGACTTGTGTGTTCCTCTCTT 59.895 50.000 0.00 0.00 32.85 2.85
1883 3515 3.635373 CGAGAAGCATAGGTAGGGTACAA 59.365 47.826 0.00 0.00 0.00 2.41
1884 3516 4.281182 CGAGAAGCATAGGTAGGGTACAAT 59.719 45.833 0.00 0.00 0.00 2.71
1885 3517 5.565045 CGAGAAGCATAGGTAGGGTACAATC 60.565 48.000 0.00 0.00 0.00 2.67
1886 3518 4.281182 AGAAGCATAGGTAGGGTACAATCG 59.719 45.833 0.00 0.00 0.00 3.34
2087 3756 3.961408 ACGATGGACAGAGGTTAGCTTAT 59.039 43.478 0.00 0.00 0.00 1.73
2088 3757 4.038162 ACGATGGACAGAGGTTAGCTTATC 59.962 45.833 0.00 0.00 0.00 1.75
2101 3770 0.994737 GCTTATCGACGAGCTCGCTC 60.995 60.000 34.83 26.87 42.62 5.03
2127 3796 1.528748 GGCGACGAGTACTAAACGAC 58.471 55.000 15.68 10.88 0.00 4.34
2140 3809 0.608640 AAACGACGAAGGAGGCATCT 59.391 50.000 0.00 0.00 0.00 2.90
2141 3810 0.108615 AACGACGAAGGAGGCATCTG 60.109 55.000 0.00 0.00 0.00 2.90
2143 3812 0.248825 CGACGAAGGAGGCATCTGAG 60.249 60.000 0.00 0.00 0.00 3.35
2156 3825 1.436326 ATCTGAGGATGAGCTGGCAT 58.564 50.000 0.00 0.00 0.00 4.40
2157 3826 0.757512 TCTGAGGATGAGCTGGCATC 59.242 55.000 6.82 6.82 43.04 3.91
2197 3866 1.885850 AACGCTGTCACGGTGGAAC 60.886 57.895 8.50 0.45 37.37 3.62
2221 3890 3.107661 CGGTGCCGTCCGTGTTAC 61.108 66.667 1.93 0.00 44.77 2.50
2222 3891 2.341176 GGTGCCGTCCGTGTTACT 59.659 61.111 0.00 0.00 0.00 2.24
2225 3894 1.300311 TGCCGTCCGTGTTACTGTG 60.300 57.895 0.00 0.00 0.00 3.66
2226 3895 1.300388 GCCGTCCGTGTTACTGTGT 60.300 57.895 0.00 0.00 0.00 3.72
2227 3896 0.877213 GCCGTCCGTGTTACTGTGTT 60.877 55.000 0.00 0.00 0.00 3.32
2228 3897 1.602668 GCCGTCCGTGTTACTGTGTTA 60.603 52.381 0.00 0.00 0.00 2.41
2229 3898 2.322161 CCGTCCGTGTTACTGTGTTAG 58.678 52.381 0.00 0.00 0.00 2.34
2230 3899 1.717645 CGTCCGTGTTACTGTGTTAGC 59.282 52.381 0.00 0.00 0.00 3.09
2231 3900 2.746269 GTCCGTGTTACTGTGTTAGCA 58.254 47.619 0.00 0.00 0.00 3.49
2232 3901 3.323243 GTCCGTGTTACTGTGTTAGCAT 58.677 45.455 0.00 0.00 0.00 3.79
2233 3902 3.744426 GTCCGTGTTACTGTGTTAGCATT 59.256 43.478 0.00 0.00 0.00 3.56
2243 3912 1.748879 GTTAGCATTCCGGCAGGCA 60.749 57.895 14.23 0.00 37.47 4.75
2256 3925 1.753470 CAGGCATAGGAGGAGCAGG 59.247 63.158 0.00 0.00 0.00 4.85
2264 3933 1.000396 GGAGGAGCAGGGCAACAAT 60.000 57.895 0.00 0.00 39.74 2.71
2267 3936 0.407139 AGGAGCAGGGCAACAATCTT 59.593 50.000 0.00 0.00 39.74 2.40
2276 3945 1.168714 GCAACAATCTTCGGCTCCTT 58.831 50.000 0.00 0.00 0.00 3.36
2277 3946 1.135575 GCAACAATCTTCGGCTCCTTG 60.136 52.381 0.00 0.00 0.00 3.61
2300 3969 4.181010 CACCGGCTCATGGAGGGG 62.181 72.222 0.00 0.00 0.00 4.79
2307 3976 1.063717 GGCTCATGGAGGGGAAAATCA 60.064 52.381 0.00 0.00 0.00 2.57
2309 3978 2.292267 CTCATGGAGGGGAAAATCACG 58.708 52.381 0.00 0.00 0.00 4.35
2319 3988 1.573829 GAAAATCACGGGCGAGCACA 61.574 55.000 0.00 0.00 0.00 4.57
2324 3993 2.357517 ACGGGCGAGCACAAGAAG 60.358 61.111 0.00 0.00 0.00 2.85
2333 4002 2.641305 GAGCACAAGAAGGATGATGCT 58.359 47.619 0.00 0.00 45.70 3.79
2334 4003 2.641305 AGCACAAGAAGGATGATGCTC 58.359 47.619 0.00 0.00 39.09 4.26
2359 4028 1.162800 GCCATGGTCGCAGAAGATCC 61.163 60.000 14.67 0.00 39.69 3.36
2361 4030 0.877649 CATGGTCGCAGAAGATCCGG 60.878 60.000 0.00 0.00 39.69 5.14
2363 4032 2.586357 GTCGCAGAAGATCCGGGC 60.586 66.667 0.00 0.00 39.69 6.13
2364 4033 2.759973 TCGCAGAAGATCCGGGCT 60.760 61.111 0.00 0.00 0.00 5.19
2365 4034 2.187946 CGCAGAAGATCCGGGCTT 59.812 61.111 0.00 5.82 0.00 4.35
2366 4035 1.884926 CGCAGAAGATCCGGGCTTC 60.885 63.158 22.60 22.60 41.53 3.86
2367 4036 1.524849 GCAGAAGATCCGGGCTTCC 60.525 63.158 24.89 13.21 42.04 3.46
2368 4037 1.977293 GCAGAAGATCCGGGCTTCCT 61.977 60.000 24.89 14.70 42.04 3.36
2369 4038 1.414158 CAGAAGATCCGGGCTTCCTA 58.586 55.000 24.89 0.00 42.04 2.94
2370 4039 1.342819 CAGAAGATCCGGGCTTCCTAG 59.657 57.143 24.89 15.95 42.04 3.02
2371 4040 1.218196 AGAAGATCCGGGCTTCCTAGA 59.782 52.381 24.89 0.00 42.04 2.43
2372 4041 2.158234 AGAAGATCCGGGCTTCCTAGAT 60.158 50.000 24.89 10.80 42.04 1.98
2373 4042 1.638529 AGATCCGGGCTTCCTAGATG 58.361 55.000 0.00 0.00 0.00 2.90
2374 4043 1.148027 AGATCCGGGCTTCCTAGATGA 59.852 52.381 0.00 0.00 0.00 2.92
2375 4044 1.548269 GATCCGGGCTTCCTAGATGAG 59.452 57.143 0.00 0.00 0.00 2.90
2376 4045 1.115930 TCCGGGCTTCCTAGATGAGC 61.116 60.000 0.00 0.00 35.71 4.26
2377 4046 1.402896 CCGGGCTTCCTAGATGAGCA 61.403 60.000 12.08 0.00 38.14 4.26
2378 4047 0.033228 CGGGCTTCCTAGATGAGCAG 59.967 60.000 12.08 4.31 38.14 4.24
2379 4048 0.250252 GGGCTTCCTAGATGAGCAGC 60.250 60.000 12.08 0.00 38.14 5.25
2380 4049 0.599728 GGCTTCCTAGATGAGCAGCG 60.600 60.000 12.08 0.00 38.14 5.18
2381 4050 0.599728 GCTTCCTAGATGAGCAGCGG 60.600 60.000 0.00 0.00 36.45 5.52
2382 4051 0.033228 CTTCCTAGATGAGCAGCGGG 59.967 60.000 0.00 0.00 0.00 6.13
2383 4052 2.030262 CCTAGATGAGCAGCGGGC 59.970 66.667 0.00 0.00 45.30 6.13
2384 4053 2.030262 CTAGATGAGCAGCGGGCC 59.970 66.667 0.00 0.00 46.50 5.80
2385 4054 2.444706 TAGATGAGCAGCGGGCCT 60.445 61.111 0.84 0.00 46.50 5.19
2386 4055 2.037620 CTAGATGAGCAGCGGGCCTT 62.038 60.000 0.84 0.00 46.50 4.35
2387 4056 0.759060 TAGATGAGCAGCGGGCCTTA 60.759 55.000 0.84 0.00 46.50 2.69
2388 4057 1.072159 GATGAGCAGCGGGCCTTAT 59.928 57.895 0.84 0.00 46.50 1.73
2389 4058 0.321671 GATGAGCAGCGGGCCTTATA 59.678 55.000 0.84 0.00 46.50 0.98
2390 4059 0.035458 ATGAGCAGCGGGCCTTATAC 59.965 55.000 0.84 0.00 46.50 1.47
2391 4060 1.301795 GAGCAGCGGGCCTTATACC 60.302 63.158 0.84 0.00 46.50 2.73
2392 4061 2.040009 GAGCAGCGGGCCTTATACCA 62.040 60.000 0.84 0.00 46.50 3.25
2393 4062 1.598130 GCAGCGGGCCTTATACCAG 60.598 63.158 0.84 0.00 36.11 4.00
2394 4063 1.830145 CAGCGGGCCTTATACCAGT 59.170 57.895 0.84 0.00 0.00 4.00
2395 4064 0.180406 CAGCGGGCCTTATACCAGTT 59.820 55.000 0.84 0.00 0.00 3.16
2396 4065 0.468648 AGCGGGCCTTATACCAGTTC 59.531 55.000 0.84 0.00 0.00 3.01
2397 4066 0.179468 GCGGGCCTTATACCAGTTCA 59.821 55.000 0.84 0.00 0.00 3.18
2398 4067 1.202770 GCGGGCCTTATACCAGTTCAT 60.203 52.381 0.84 0.00 0.00 2.57
2424 4093 1.858041 GCTCATGACATCCATCGCG 59.142 57.895 0.00 0.00 31.94 5.87
2425 4094 1.563435 GCTCATGACATCCATCGCGG 61.563 60.000 6.13 0.00 31.94 6.46
2461 4142 1.735376 CTGGCGGCTACGTGTCCTAT 61.735 60.000 11.43 0.00 43.45 2.57
2469 4150 0.468585 TACGTGTCCTATGGGCGGAT 60.469 55.000 0.00 0.00 32.25 4.18
2530 4211 3.302347 GAGGAGGCACAGGTGACCG 62.302 68.421 0.70 0.00 40.19 4.79
2537 4218 4.664677 ACAGGTGACCGCAGACGC 62.665 66.667 0.00 0.00 38.22 5.19
2561 4242 1.664965 GCTCCGTATCGACCATGCC 60.665 63.158 0.00 0.00 0.00 4.40
2574 4255 3.909651 ATGCCCCCACCACGGTTT 61.910 61.111 0.00 0.00 0.00 3.27
2575 4256 4.904590 TGCCCCCACCACGGTTTG 62.905 66.667 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.261072 GCTTTATCGACTACGTCCAGATGA 60.261 45.833 0.00 0.00 40.69 2.92
88 91 2.429930 CACCCCAAAGAGTCGGCA 59.570 61.111 0.00 0.00 0.00 5.69
93 98 0.697854 ACCTCACCACCCCAAAGAGT 60.698 55.000 0.00 0.00 0.00 3.24
100 105 1.359168 AACTCTAACCTCACCACCCC 58.641 55.000 0.00 0.00 0.00 4.95
107 112 6.042781 ACATACAACCAGAAACTCTAACCTCA 59.957 38.462 0.00 0.00 0.00 3.86
116 121 2.548057 CGCACACATACAACCAGAAACT 59.452 45.455 0.00 0.00 0.00 2.66
130 135 2.349590 CAAATCTCCTCATCGCACACA 58.650 47.619 0.00 0.00 0.00 3.72
139 144 3.743521 CAACTGACACCAAATCTCCTCA 58.256 45.455 0.00 0.00 0.00 3.86
208 213 0.610232 GCATGCTCCAAGGACCAGTT 60.610 55.000 11.37 0.00 0.00 3.16
225 230 2.250939 CGGGAAGTCTTTGCGTGCA 61.251 57.895 0.00 0.00 0.00 4.57
248 253 1.072331 CCAGGTTGACCTTGCTAGTGT 59.928 52.381 0.00 0.00 46.09 3.55
264 269 4.475444 TCCCCTACCGGAGCCAGG 62.475 72.222 9.46 8.87 0.00 4.45
298 303 1.741770 GCCAGAACGAGCCGTCAAT 60.742 57.895 0.69 0.00 39.99 2.57
325 330 0.249826 TTTACCACCGAACGACCACC 60.250 55.000 0.00 0.00 0.00 4.61
415 420 4.754114 AGAAGTCAAATGCAGTTCAGTCTC 59.246 41.667 0.00 0.00 0.00 3.36
482 773 1.137872 CGGGAACAGCTATGCTCTCTT 59.862 52.381 0.00 0.00 36.40 2.85
486 777 0.750850 TACCGGGAACAGCTATGCTC 59.249 55.000 6.32 0.00 36.40 4.26
502 793 5.969435 CAGACCGAACTTGTTTTTCTTTACC 59.031 40.000 0.00 0.00 0.00 2.85
617 1228 6.176896 TCAATATCCAAACTGAACGGATTCA 58.823 36.000 0.00 0.00 42.73 2.57
618 1229 6.677781 TCAATATCCAAACTGAACGGATTC 57.322 37.500 0.00 0.00 40.12 2.52
628 1239 5.984725 TGTACACCGATCAATATCCAAACT 58.015 37.500 0.00 0.00 0.00 2.66
696 1307 4.724074 TGAACCATCAGATGCAAATTCC 57.276 40.909 4.68 0.00 0.00 3.01
753 1380 1.963338 GTTTGCCAGCTCTGCGTCT 60.963 57.895 0.65 0.00 0.00 4.18
983 1636 1.725931 GCATTGCGTACTTGACAGTGC 60.726 52.381 0.00 6.73 39.36 4.40
1649 2309 5.870978 GGAAATCTTAGCCACGTAAAGTACA 59.129 40.000 0.00 0.00 0.00 2.90
1650 2310 5.005107 CGGAAATCTTAGCCACGTAAAGTAC 59.995 44.000 0.00 0.00 0.00 2.73
1651 2311 5.104374 CGGAAATCTTAGCCACGTAAAGTA 58.896 41.667 0.00 0.00 0.00 2.24
1652 2312 3.930848 CGGAAATCTTAGCCACGTAAAGT 59.069 43.478 0.00 0.00 0.00 2.66
1653 2313 3.308866 CCGGAAATCTTAGCCACGTAAAG 59.691 47.826 0.00 0.00 0.00 1.85
1904 3536 3.636043 CCGCACGTGTGTCACCAC 61.636 66.667 26.10 1.95 42.19 4.16
1942 3574 0.387622 CACGCCATGGAAAGCAAGTG 60.388 55.000 18.40 9.03 0.00 3.16
2101 3770 3.190849 TACTCGTCGCCGACCTCG 61.191 66.667 12.26 0.00 38.40 4.63
2117 3786 2.161855 TGCCTCCTTCGTCGTTTAGTA 58.838 47.619 0.00 0.00 0.00 1.82
2120 3789 1.822990 AGATGCCTCCTTCGTCGTTTA 59.177 47.619 0.00 0.00 0.00 2.01
2127 3796 1.047002 ATCCTCAGATGCCTCCTTCG 58.953 55.000 0.00 0.00 0.00 3.79
2211 3880 2.746269 TGCTAACACAGTAACACGGAC 58.254 47.619 0.00 0.00 0.00 4.79
2214 3883 3.181534 CGGAATGCTAACACAGTAACACG 60.182 47.826 0.00 0.00 0.00 4.49
2218 3887 2.289756 TGCCGGAATGCTAACACAGTAA 60.290 45.455 5.05 0.00 0.00 2.24
2219 3888 1.276705 TGCCGGAATGCTAACACAGTA 59.723 47.619 5.05 0.00 0.00 2.74
2221 3890 0.729116 CTGCCGGAATGCTAACACAG 59.271 55.000 5.05 0.00 0.00 3.66
2222 3891 0.676466 CCTGCCGGAATGCTAACACA 60.676 55.000 5.05 0.00 0.00 3.72
2225 3894 1.103398 ATGCCTGCCGGAATGCTAAC 61.103 55.000 11.38 0.00 0.00 2.34
2226 3895 0.472044 TATGCCTGCCGGAATGCTAA 59.528 50.000 11.38 0.00 28.78 3.09
2227 3896 0.035317 CTATGCCTGCCGGAATGCTA 59.965 55.000 11.38 0.00 28.78 3.49
2228 3897 1.228063 CTATGCCTGCCGGAATGCT 60.228 57.895 11.38 0.00 28.78 3.79
2229 3898 2.263741 CCTATGCCTGCCGGAATGC 61.264 63.158 5.05 3.32 28.78 3.56
2230 3899 0.604780 CTCCTATGCCTGCCGGAATG 60.605 60.000 5.05 0.00 28.78 2.67
2231 3900 1.757306 CTCCTATGCCTGCCGGAAT 59.243 57.895 5.05 0.00 31.64 3.01
2232 3901 2.443394 CCTCCTATGCCTGCCGGAA 61.443 63.158 5.05 0.00 0.00 4.30
2233 3902 2.844362 CCTCCTATGCCTGCCGGA 60.844 66.667 5.05 0.00 0.00 5.14
2243 3912 0.621571 TGTTGCCCTGCTCCTCCTAT 60.622 55.000 0.00 0.00 0.00 2.57
2256 3925 0.678048 AGGAGCCGAAGATTGTTGCC 60.678 55.000 0.00 0.00 0.00 4.52
2264 3933 1.883732 CTCGTCAAGGAGCCGAAGA 59.116 57.895 0.00 0.00 0.00 2.87
2294 3963 1.753078 GCCCGTGATTTTCCCCTCC 60.753 63.158 0.00 0.00 0.00 4.30
2300 3969 1.134694 GTGCTCGCCCGTGATTTTC 59.865 57.895 0.00 0.00 0.00 2.29
2307 3976 2.357517 CTTCTTGTGCTCGCCCGT 60.358 61.111 0.00 0.00 0.00 5.28
2309 3978 1.078143 ATCCTTCTTGTGCTCGCCC 60.078 57.895 0.00 0.00 0.00 6.13
2350 4019 1.342819 CTAGGAAGCCCGGATCTTCTG 59.657 57.143 25.30 16.47 39.75 3.02
2351 4020 1.218196 TCTAGGAAGCCCGGATCTTCT 59.782 52.381 25.30 17.53 39.75 2.85
2359 4028 0.033228 CTGCTCATCTAGGAAGCCCG 59.967 60.000 8.73 0.00 37.58 6.13
2361 4030 0.599728 CGCTGCTCATCTAGGAAGCC 60.600 60.000 0.00 0.00 0.00 4.35
2363 4032 0.033228 CCCGCTGCTCATCTAGGAAG 59.967 60.000 0.00 0.00 0.00 3.46
2364 4033 2.032860 GCCCGCTGCTCATCTAGGAA 62.033 60.000 0.00 0.00 36.87 3.36
2365 4034 2.502492 GCCCGCTGCTCATCTAGGA 61.502 63.158 0.00 0.00 36.87 2.94
2366 4035 2.030262 GCCCGCTGCTCATCTAGG 59.970 66.667 0.00 0.00 36.87 3.02
2367 4036 2.030262 GGCCCGCTGCTCATCTAG 59.970 66.667 0.00 0.00 40.92 2.43
2368 4037 0.759060 TAAGGCCCGCTGCTCATCTA 60.759 55.000 0.00 0.00 40.92 1.98
2369 4038 1.414061 ATAAGGCCCGCTGCTCATCT 61.414 55.000 0.00 0.00 40.92 2.90
2370 4039 0.321671 TATAAGGCCCGCTGCTCATC 59.678 55.000 0.00 0.00 40.92 2.92
2371 4040 0.035458 GTATAAGGCCCGCTGCTCAT 59.965 55.000 0.00 0.00 40.92 2.90
2372 4041 1.445942 GTATAAGGCCCGCTGCTCA 59.554 57.895 0.00 0.00 40.92 4.26
2373 4042 1.301795 GGTATAAGGCCCGCTGCTC 60.302 63.158 0.00 0.00 40.92 4.26
2374 4043 2.044806 CTGGTATAAGGCCCGCTGCT 62.045 60.000 0.00 0.00 40.92 4.24
2375 4044 1.598130 CTGGTATAAGGCCCGCTGC 60.598 63.158 0.00 0.00 40.16 5.25
2376 4045 0.180406 AACTGGTATAAGGCCCGCTG 59.820 55.000 0.00 0.00 0.00 5.18
2377 4046 0.468648 GAACTGGTATAAGGCCCGCT 59.531 55.000 0.00 0.00 0.00 5.52
2378 4047 0.179468 TGAACTGGTATAAGGCCCGC 59.821 55.000 0.00 0.00 0.00 6.13
2379 4048 2.494059 CATGAACTGGTATAAGGCCCG 58.506 52.381 0.00 0.00 0.00 6.13
2380 4049 2.230660 GCATGAACTGGTATAAGGCCC 58.769 52.381 0.00 0.00 0.00 5.80
2381 4050 1.873591 CGCATGAACTGGTATAAGGCC 59.126 52.381 0.00 0.00 0.00 5.19
2382 4051 2.561569 ACGCATGAACTGGTATAAGGC 58.438 47.619 0.00 0.00 0.00 4.35
2383 4052 3.741344 GCTACGCATGAACTGGTATAAGG 59.259 47.826 0.00 0.00 0.00 2.69
2384 4053 3.425525 CGCTACGCATGAACTGGTATAAG 59.574 47.826 0.00 0.00 0.00 1.73
2385 4054 3.377439 CGCTACGCATGAACTGGTATAA 58.623 45.455 0.00 0.00 0.00 0.98
2386 4055 3.007979 CGCTACGCATGAACTGGTATA 57.992 47.619 0.00 0.00 0.00 1.47
2387 4056 1.852942 CGCTACGCATGAACTGGTAT 58.147 50.000 0.00 0.00 0.00 2.73
2388 4057 3.339061 CGCTACGCATGAACTGGTA 57.661 52.632 0.00 0.00 0.00 3.25
2389 4058 4.185413 CGCTACGCATGAACTGGT 57.815 55.556 0.00 0.00 0.00 4.00
2454 4135 1.427753 TCTCTATCCGCCCATAGGACA 59.572 52.381 0.00 0.00 41.10 4.02
2461 4142 3.950232 GGTGTCTCTATCCGCCCA 58.050 61.111 0.00 0.00 0.00 5.36
2486 4167 2.818169 GCCTCCGTGCATATCCCCA 61.818 63.158 0.00 0.00 0.00 4.96
2489 4170 0.663153 GTTTGCCTCCGTGCATATCC 59.337 55.000 0.00 0.00 41.70 2.59
2506 4187 1.122019 ACCTGTGCCTCCTCTTCGTT 61.122 55.000 0.00 0.00 0.00 3.85
2507 4188 1.534235 ACCTGTGCCTCCTCTTCGT 60.534 57.895 0.00 0.00 0.00 3.85
2537 4218 3.592814 TCGATACGGAGCTGGCGG 61.593 66.667 0.00 0.00 0.00 6.13
2538 4219 2.353607 GTCGATACGGAGCTGGCG 60.354 66.667 0.00 0.00 0.00 5.69
2542 4223 1.364171 GCATGGTCGATACGGAGCT 59.636 57.895 0.00 0.00 35.52 4.09
2548 4229 1.227853 GTGGGGGCATGGTCGATAC 60.228 63.158 0.00 0.00 0.00 2.24
2550 4231 3.809013 GGTGGGGGCATGGTCGAT 61.809 66.667 0.00 0.00 0.00 3.59
2561 4242 2.983592 GAGCAAACCGTGGTGGGG 60.984 66.667 0.00 0.00 44.64 4.96
2576 4257 3.365265 GGTTGTTGCAGCGGGGAG 61.365 66.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.