Multiple sequence alignment - TraesCS2B01G374900

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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 TraesCS2B01G374900 chr2B 100.000 4783 0 0 1 4783 536615494 536620276 0.000000e+00 8833.0
1 TraesCS2B01G374900 chr2D 92.234 4056 190 44 1 4008 455513470 455517448 0.000000e+00 5629.0
2 TraesCS2B01G374900 chr2D 86.490 718 65 17 4088 4783 455517462 455518169 0.000000e+00 760.0
3 TraesCS2B01G374900 chr2A 92.293 3166 134 25 203 3335 595231054 595227966 0.000000e+00 4394.0
4 TraesCS2B01G374900 chr2A 92.500 840 23 7 3326 4144 595227896 595227076 0.000000e+00 1166.0
5 TraesCS2B01G374900 chr2A 88.190 652 46 12 4160 4783 595226965 595226317 0.000000e+00 749.0
6 TraesCS2B01G374900 chr2A 96.875 64 2 0 143 206 595232859 595232796 1.820000e-19 108.0
7 TraesCS2B01G374900 chr4D 85.507 69 10 0 1385 1453 323118501 323118433 6.640000e-09 73.1
8 TraesCS2B01G374900 chr4B 85.507 69 10 0 1385 1453 403274758 403274690 6.640000e-09 73.1
9 TraesCS2B01G374900 chr4A 85.507 69 10 0 1385 1453 149028112 149028180 6.640000e-09 73.1
10 TraesCS2B01G374900 chr6B 89.286 56 5 1 1399 1453 30354954 30355009 8.590000e-08 69.4
11 TraesCS2B01G374900 chr6B 86.207 58 8 0 1396 1453 30490891 30490948 4.000000e-06 63.9
12 TraesCS2B01G374900 chr6B 95.000 40 2 0 2173 2212 72153983 72154022 4.000000e-06 63.9
13 TraesCS2B01G374900 chr6A 82.278 79 11 2 49 125 39187426 39187349 1.110000e-06 65.8
14 TraesCS2B01G374900 chr5B 95.000 40 2 0 2173 2212 352218852 352218891 4.000000e-06 63.9
15 TraesCS2B01G374900 chr3B 95.000 40 2 0 2173 2212 512039392 512039431 4.000000e-06 63.9
16 TraesCS2B01G374900 chr3A 95.000 40 2 0 2173 2212 191042008 191041969 4.000000e-06 63.9
17 TraesCS2B01G374900 chr7D 94.872 39 2 0 1415 1453 614679912 614679874 1.440000e-05 62.1
18 TraesCS2B01G374900 chr7D 97.222 36 1 0 1418 1453 614928557 614928592 1.440000e-05 62.1
19 TraesCS2B01G374900 chr7A 92.500 40 3 0 2173 2212 655765291 655765330 1.860000e-04 58.4
20 TraesCS2B01G374900 chr7A 94.444 36 2 0 2173 2208 498450900 498450865 6.690000e-04 56.5
21 TraesCS2B01G374900 chr1B 92.105 38 3 0 2175 2212 144661000 144661037 2.000000e-03 54.7


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 TraesCS2B01G374900 chr2B 536615494 536620276 4782 False 8833.00 8833 100.0000 1 4783 1 chr2B.!!$F1 4782
1 TraesCS2B01G374900 chr2D 455513470 455518169 4699 False 3194.50 5629 89.3620 1 4783 2 chr2D.!!$F1 4782
2 TraesCS2B01G374900 chr2A 595226317 595232859 6542 True 1604.25 4394 92.4645 143 4783 4 chr2A.!!$R1 4640

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
273 2034 0.601311 GCGGTATCTGGTGGAGATGC 60.601 60.0 0.00 0.0 41.86 3.91 F
804 2565 0.611896 CCCGGTCCCAATTTGAGCTT 60.612 55.0 0.00 0.0 0.00 3.74 F
1203 2966 0.622136 TGAGCACAATCAGCAGGGAT 59.378 50.0 0.00 0.0 0.00 3.85 F
2413 4194 0.032952 TGCAGGACGGTCTGTTGTAC 59.967 55.0 8.23 0.0 37.12 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 3227 0.530211 CGCAAGAGGATGGAGCTGAG 60.530 60.0 0.00 0.0 43.02 3.35 R
2394 4175 0.032952 GTACAACAGACCGTCCTGCA 59.967 55.0 0.00 0.0 37.68 4.41 R
2448 4229 1.786049 CGATCGATCTGGAGACCGCA 61.786 60.0 22.43 0.0 0.00 5.69 R
3891 5789 0.319900 ACTCGTGCATCAAAGCGTCT 60.320 50.0 0.00 0.0 37.31 4.18 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
30 31 7.765307 TCTAAATTCATTCTCAATGCCTTGTC 58.235 34.615 1.49 0.00 38.77 3.18
33 34 2.027285 TCATTCTCAATGCCTTGTCGGA 60.027 45.455 1.49 0.00 38.77 4.55
34 35 2.559698 TTCTCAATGCCTTGTCGGAA 57.440 45.000 1.49 3.39 33.87 4.30
46 47 4.139038 CCTTGTCGGAAAAGGGTCTAAAA 58.861 43.478 17.80 0.00 40.54 1.52
65 66 3.477899 AACTTCTTTATTCAGCGCTGC 57.522 42.857 32.44 0.00 0.00 5.25
70 71 3.540617 TCTTTATTCAGCGCTGCCATTA 58.459 40.909 32.44 16.89 0.00 1.90
71 72 3.312421 TCTTTATTCAGCGCTGCCATTAC 59.688 43.478 32.44 0.00 0.00 1.89
151 167 2.526120 GCTACTTCATCGGCGGTGC 61.526 63.158 16.80 0.00 0.00 5.01
273 2034 0.601311 GCGGTATCTGGTGGAGATGC 60.601 60.000 0.00 0.00 41.86 3.91
481 2242 3.314331 CGTCTCCACCAGGGCACT 61.314 66.667 0.00 0.00 36.21 4.40
586 2347 3.307379 GGATCATCCGCCAAGGTAC 57.693 57.895 0.00 0.00 41.99 3.34
767 2528 2.132089 CTTTGTTGGCCCCTCCCGTA 62.132 60.000 0.00 0.00 0.00 4.02
803 2564 1.000896 CCCGGTCCCAATTTGAGCT 60.001 57.895 0.00 0.00 0.00 4.09
804 2565 0.611896 CCCGGTCCCAATTTGAGCTT 60.612 55.000 0.00 0.00 0.00 3.74
805 2566 1.256812 CCGGTCCCAATTTGAGCTTT 58.743 50.000 0.00 0.00 0.00 3.51
806 2567 1.618343 CCGGTCCCAATTTGAGCTTTT 59.382 47.619 0.00 0.00 0.00 2.27
807 2568 2.352715 CCGGTCCCAATTTGAGCTTTTC 60.353 50.000 0.00 0.00 0.00 2.29
808 2569 2.295909 CGGTCCCAATTTGAGCTTTTCA 59.704 45.455 0.00 0.00 0.00 2.69
809 2570 3.243704 CGGTCCCAATTTGAGCTTTTCAA 60.244 43.478 0.00 0.00 43.92 2.69
810 2571 4.561326 CGGTCCCAATTTGAGCTTTTCAAT 60.561 41.667 0.00 0.00 44.90 2.57
811 2572 5.308014 GGTCCCAATTTGAGCTTTTCAATT 58.692 37.500 0.00 0.00 44.90 2.32
812 2573 5.179929 GGTCCCAATTTGAGCTTTTCAATTG 59.820 40.000 0.00 0.00 44.90 2.32
813 2574 5.179929 GTCCCAATTTGAGCTTTTCAATTGG 59.820 40.000 21.65 21.65 44.90 3.16
814 2575 5.616488 CCAATTTGAGCTTTTCAATTGGG 57.384 39.130 21.23 8.93 44.90 4.12
815 2576 4.083164 CCAATTTGAGCTTTTCAATTGGGC 60.083 41.667 21.23 5.67 44.90 5.36
868 2629 1.452651 CCGCCATTGCAGACCTGAT 60.453 57.895 0.47 0.00 37.32 2.90
930 2691 2.043450 CGGACCCTCTCTGGCTCT 60.043 66.667 0.00 0.00 0.00 4.09
983 2744 2.448453 GGAGAAGGAAGAAGGACGAGA 58.552 52.381 0.00 0.00 0.00 4.04
1024 2785 1.276138 AGAACGCATGGTGATGTCTCA 59.724 47.619 0.00 0.00 31.50 3.27
1053 2815 7.970061 TGGATTTTATTCATTGCTTTCTCTTCG 59.030 33.333 0.00 0.00 0.00 3.79
1060 2822 4.876107 TCATTGCTTTCTCTTCGGGTATTC 59.124 41.667 0.00 0.00 0.00 1.75
1121 2884 6.238374 CGGTTTGCTCTTGAGTTCTTTCTTAA 60.238 38.462 0.00 0.00 0.00 1.85
1142 2905 9.973661 TCTTAATCCTACAAGATTTTTCATCCA 57.026 29.630 0.00 0.00 37.62 3.41
1145 2908 7.592885 ATCCTACAAGATTTTTCATCCATGG 57.407 36.000 4.97 4.97 0.00 3.66
1203 2966 0.622136 TGAGCACAATCAGCAGGGAT 59.378 50.000 0.00 0.00 0.00 3.85
1281 3044 1.800681 GTCCATGCAAGGTTACCGC 59.199 57.895 8.03 0.00 0.00 5.68
1284 3047 3.496131 ATGCAAGGTTACCGCGCG 61.496 61.111 25.67 25.67 0.00 6.86
1306 3069 1.012086 CATGGAAGATGCCGTGAGTG 58.988 55.000 0.00 0.00 45.81 3.51
1319 3082 3.553096 GCCGTGAGTGACCATCCTAATAG 60.553 52.174 0.00 0.00 0.00 1.73
1370 3133 5.351948 AGGCCTAACTTTCTGATCTTCTC 57.648 43.478 1.29 0.00 0.00 2.87
1405 3168 2.355132 CAGCTGTTGGAGATCTTGATGC 59.645 50.000 5.25 0.00 0.00 3.91
1464 3227 2.922740 TGGAGGTTGGTGTTCACTAC 57.077 50.000 2.98 2.47 0.00 2.73
1469 3232 2.143925 GGTTGGTGTTCACTACTCAGC 58.856 52.381 2.98 0.00 0.00 4.26
1585 3362 6.891908 AGTGCCATTTACTACCATCTGAAATT 59.108 34.615 0.00 0.00 0.00 1.82
1586 3363 7.397192 AGTGCCATTTACTACCATCTGAAATTT 59.603 33.333 0.00 0.00 0.00 1.82
1650 3427 2.039084 ACACTTCCATCTTGAGGTCCAC 59.961 50.000 0.00 0.00 0.00 4.02
1674 3451 2.415090 GCATCCACACTTCAATGACAGC 60.415 50.000 0.00 0.00 0.00 4.40
1686 3463 1.097547 ATGACAGCCTGCGTATTGCC 61.098 55.000 0.00 0.00 45.60 4.52
1715 3492 3.998341 AGCGCGTTCTTCAGGTTATTTAA 59.002 39.130 8.43 0.00 0.00 1.52
1748 3525 6.039047 ACAATTCATGCATCCTATGTGTTCTC 59.961 38.462 0.00 0.00 0.00 2.87
1753 3530 4.026052 TGCATCCTATGTGTTCTCTGAGA 58.974 43.478 2.58 2.58 0.00 3.27
1776 3553 1.014564 CGCAGTTTCTCCCGGAGTTC 61.015 60.000 14.36 6.30 0.00 3.01
1937 3714 6.296145 GGAATTATCTGAGTATAGCCCTGCTT 60.296 42.308 0.00 0.00 40.44 3.91
2006 3786 5.182950 TGTGCTTGTGTAAATATGAAGGTGG 59.817 40.000 0.00 0.00 0.00 4.61
2043 3824 4.463050 TTTTACACATCCCCTCCAGTTT 57.537 40.909 0.00 0.00 0.00 2.66
2279 4060 1.597663 CCCGATCCGTGCAGTATTTTC 59.402 52.381 0.00 0.00 0.00 2.29
2328 4109 6.457663 GCCTGGTTTTATTTTTGTTGTGTTCC 60.458 38.462 0.00 0.00 0.00 3.62
2363 4144 2.060050 ACCACCGATCACAAACCAAA 57.940 45.000 0.00 0.00 0.00 3.28
2394 4175 5.452636 GGCTGAAAGACGGAGAATAGAGAAT 60.453 44.000 0.00 0.00 34.07 2.40
2403 4184 3.553922 GGAGAATAGAGAATGCAGGACGG 60.554 52.174 0.00 0.00 0.00 4.79
2413 4194 0.032952 TGCAGGACGGTCTGTTGTAC 59.967 55.000 8.23 0.00 37.12 2.90
2448 4229 1.299541 GTCGCATCGATGGTGGAATT 58.700 50.000 26.00 0.00 38.42 2.17
2769 4551 2.168728 GTGATGGAGTCTGGTAAGTCCC 59.831 54.545 0.00 0.00 37.88 4.46
2823 4609 7.297391 TCGATTATTGTTTGTTGTGATGACTG 58.703 34.615 0.00 0.00 0.00 3.51
2853 4639 6.395629 AGTTTCATACATAGTACACGCACTT 58.604 36.000 0.00 0.00 0.00 3.16
2876 4662 6.912203 TGAAATGACAGTTAGTTTCGACAA 57.088 33.333 0.00 0.00 34.23 3.18
2885 4671 4.025480 AGTTAGTTTCGACAATCGCGTTTT 60.025 37.500 5.77 0.00 40.21 2.43
2895 4681 4.171005 ACAATCGCGTTTTTCTCGAGATA 58.829 39.130 17.44 8.98 44.13 1.98
2897 4683 5.975344 ACAATCGCGTTTTTCTCGAGATATA 59.025 36.000 17.44 3.79 44.13 0.86
3026 4812 6.108687 TGTATGATTTGCTGAAGGTACAGAG 58.891 40.000 0.00 0.00 39.94 3.35
3071 4864 6.653320 CCCTTGTTGTGCTAGTACTTCATAAA 59.347 38.462 12.42 0.00 0.00 1.40
3131 4924 2.222027 CTTGACCTGGTCAGTTGGTTC 58.778 52.381 26.94 0.00 43.69 3.62
3219 5015 6.040842 GGATCTTAGAATTTTTGGCCTGCATA 59.959 38.462 3.32 0.00 0.00 3.14
3229 5025 0.179103 GGCCTGCATATTGTTGGCAC 60.179 55.000 12.36 0.00 44.85 5.01
3259 5055 6.766467 GGAAACATGGTAAAGTGTAGATAGGG 59.234 42.308 0.00 0.00 0.00 3.53
3269 5065 5.700402 AGTGTAGATAGGGATTTGTGCTT 57.300 39.130 0.00 0.00 0.00 3.91
3278 5074 1.620323 GGATTTGTGCTTTGCCTTCCT 59.380 47.619 0.00 0.00 0.00 3.36
3353 5229 4.552166 ATTCACACACCTCTCGTTTTTG 57.448 40.909 0.00 0.00 0.00 2.44
3354 5230 2.980568 TCACACACCTCTCGTTTTTGT 58.019 42.857 0.00 0.00 0.00 2.83
3498 5375 7.448420 AGCTTGACATATATATTGCTGTGACT 58.552 34.615 0.00 0.00 0.00 3.41
3630 5507 0.534203 GGTCCGGTTCAAGCACAAGA 60.534 55.000 0.00 0.00 0.00 3.02
3793 5670 1.561643 AGCTTCTGAACCCGATGAGA 58.438 50.000 0.00 0.00 0.00 3.27
3795 5672 1.914634 CTTCTGAACCCGATGAGACG 58.085 55.000 0.00 0.00 0.00 4.18
3891 5789 0.250901 GGAGGCTTGGCTTGTGAAGA 60.251 55.000 0.00 0.00 0.00 2.87
3984 5883 3.832276 TGTTTTGAACTGTCAAGTGCAC 58.168 40.909 9.40 9.40 42.03 4.57
4051 5965 2.176202 TAGCTGGGCCTGGGAGTGTA 62.176 60.000 12.70 0.00 0.00 2.90
4052 5966 2.378634 GCTGGGCCTGGGAGTGTAT 61.379 63.158 12.70 0.00 0.00 2.29
4053 5967 1.926426 GCTGGGCCTGGGAGTGTATT 61.926 60.000 12.70 0.00 0.00 1.89
4054 5968 1.507140 CTGGGCCTGGGAGTGTATTA 58.493 55.000 4.53 0.00 0.00 0.98
4094 6012 7.500227 TGATACTCCTTAATGCTTCATTCCAAG 59.500 37.037 0.00 0.00 35.54 3.61
4103 6021 5.698741 TGCTTCATTCCAAGGAGAAGATA 57.301 39.130 17.52 6.77 39.78 1.98
4115 6033 6.597280 CCAAGGAGAAGATACTGGAAAAGAAG 59.403 42.308 0.00 0.00 0.00 2.85
4129 6047 3.436700 AAAGAAGTCGCAACCAAAAGG 57.563 42.857 0.00 0.00 0.00 3.11
4167 6180 0.532115 TTAGCAGCTGATGTCGCAGA 59.468 50.000 20.43 0.00 38.14 4.26
4268 6281 2.409870 GCAGCGAGTTGATTGGGGG 61.410 63.158 0.00 0.00 0.00 5.40
4277 6290 3.023735 GATTGGGGGCAGAGGGGT 61.024 66.667 0.00 0.00 0.00 4.95
4314 6328 9.717892 CATCAACATGAGAATTGATAAGTGAAG 57.282 33.333 0.00 0.00 42.35 3.02
4320 6334 9.159364 CATGAGAATTGATAAGTGAAGAACTCA 57.841 33.333 0.00 0.00 38.56 3.41
4338 6352 5.235305 ACTCACTTACAAACAAACTGCTG 57.765 39.130 0.00 0.00 0.00 4.41
4354 6368 4.136796 ACTGCTGCTTCAACATACAAGAA 58.863 39.130 0.00 0.00 0.00 2.52
4356 6370 5.112220 TGCTGCTTCAACATACAAGAAAG 57.888 39.130 0.00 0.00 0.00 2.62
4357 6371 4.580167 TGCTGCTTCAACATACAAGAAAGT 59.420 37.500 0.00 0.00 0.00 2.66
4364 6378 6.449635 TCAACATACAAGAAAGTTGCAACT 57.550 33.333 26.36 26.36 40.71 3.16
4365 6379 7.561021 TCAACATACAAGAAAGTTGCAACTA 57.439 32.000 31.31 15.06 40.71 2.24
4375 6389 7.081526 AGAAAGTTGCAACTATGAAGCATAG 57.918 36.000 31.31 11.74 46.43 2.23
4388 6402 4.774124 TGAAGCATAGGATTCCTGACTTG 58.226 43.478 15.80 8.57 38.65 3.16
4411 6425 5.046376 TGTTCATACAAGAGCAGGAAGATCA 60.046 40.000 0.00 0.00 34.30 2.92
4412 6426 5.682234 TCATACAAGAGCAGGAAGATCAA 57.318 39.130 0.00 0.00 34.30 2.57
4413 6427 5.668471 TCATACAAGAGCAGGAAGATCAAG 58.332 41.667 0.00 0.00 34.30 3.02
4461 6475 8.226819 AGATACGTACAGATTCAGATTCTCAA 57.773 34.615 0.00 0.00 0.00 3.02
4462 6476 8.855110 AGATACGTACAGATTCAGATTCTCAAT 58.145 33.333 0.00 0.00 0.00 2.57
4525 6545 3.939066 ACTACAGAAACCCATGTACTGC 58.061 45.455 0.00 0.00 34.50 4.40
4601 6621 3.330853 GATGGAACGCGGCGCTAG 61.331 66.667 30.54 17.87 0.00 3.42
4614 6634 2.649349 GCTAGCGAGACACGAGCG 60.649 66.667 0.00 0.00 45.77 5.03
4730 6778 2.045131 GTACCAGCCGTCGTCCTCT 61.045 63.158 0.00 0.00 0.00 3.69
4777 6825 2.507992 CTCGTCGGAGCTGCAAGG 60.508 66.667 5.91 0.00 32.61 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.690098 CGACAAGGCATTGAGAATGAATTTAG 59.310 38.462 19.41 0.00 41.46 1.85
12 13 2.027285 TCCGACAAGGCATTGAGAATGA 60.027 45.455 19.41 4.00 40.64 2.57
18 19 1.885887 CCTTTTCCGACAAGGCATTGA 59.114 47.619 19.41 0.00 38.83 2.57
30 31 6.387041 AAAGAAGTTTTAGACCCTTTTCCG 57.613 37.500 0.00 0.00 31.61 4.30
34 35 8.577296 GCTGAATAAAGAAGTTTTAGACCCTTT 58.423 33.333 0.00 0.00 36.37 3.11
46 47 1.740025 GGCAGCGCTGAATAAAGAAGT 59.260 47.619 40.21 0.00 0.00 3.01
131 134 0.460284 CACCGCCGATGAAGTAGCTT 60.460 55.000 0.00 0.00 0.00 3.74
133 136 2.526120 GCACCGCCGATGAAGTAGC 61.526 63.158 0.00 0.00 0.00 3.58
134 137 2.230940 CGCACCGCCGATGAAGTAG 61.231 63.158 0.00 0.00 0.00 2.57
135 138 2.202690 CGCACCGCCGATGAAGTA 60.203 61.111 0.00 0.00 0.00 2.24
138 141 4.812476 CTCCGCACCGCCGATGAA 62.812 66.667 0.00 0.00 0.00 2.57
171 187 1.228459 AGGGGCGTTTTCTTCCACC 60.228 57.895 0.00 0.00 0.00 4.61
273 2034 1.891060 GCAACTCGCCGTCTCACTTG 61.891 60.000 0.00 0.00 32.94 3.16
433 2194 2.158449 GGAGCAGACACAAAACGATCTG 59.842 50.000 0.00 0.00 41.29 2.90
481 2242 4.841617 ATCAGAGGAGCCGGCCGA 62.842 66.667 30.73 10.81 0.00 5.54
767 2528 3.142393 CGGAGGCAGGATTCGGAT 58.858 61.111 0.00 0.00 0.00 4.18
814 2575 3.189080 GGGAAAAACATTTCAGGCAATGC 59.811 43.478 0.00 0.00 37.63 3.56
815 2576 4.387598 TGGGAAAAACATTTCAGGCAATG 58.612 39.130 3.97 0.00 39.67 2.82
930 2691 3.709633 ACGATGGAGCAGCAGCCA 61.710 61.111 9.23 9.23 43.56 4.75
1121 2884 6.041296 GCCATGGATGAAAAATCTTGTAGGAT 59.959 38.462 18.40 0.00 0.00 3.24
1203 2966 2.741092 GTCTTGGACAGCACCGGA 59.259 61.111 9.46 0.00 32.09 5.14
1281 3044 1.353103 GGCATCTTCCATGTTCGCG 59.647 57.895 0.00 0.00 0.00 5.87
1284 3047 1.667724 CTCACGGCATCTTCCATGTTC 59.332 52.381 0.00 0.00 0.00 3.18
1306 3069 9.269453 GTTAAACCATGTACTATTAGGATGGTC 57.731 37.037 17.76 7.82 44.86 4.02
1319 3082 7.095816 GCATTTCACCAAAGTTAAACCATGTAC 60.096 37.037 0.00 0.00 0.00 2.90
1370 3133 2.890371 GCTGCATGCTGGGGAAAG 59.110 61.111 23.88 10.29 38.95 2.62
1405 3168 1.635663 GAACGATGTGGCGGTGGAAG 61.636 60.000 0.00 0.00 35.12 3.46
1464 3227 0.530211 CGCAAGAGGATGGAGCTGAG 60.530 60.000 0.00 0.00 43.02 3.35
1555 3328 8.710239 TCAGATGGTAGTAAATGGCACTTATTA 58.290 33.333 0.00 0.00 0.00 0.98
1585 3362 4.072131 GCAGGTCCTGTATCAAGAAACAA 58.928 43.478 20.24 0.00 33.43 2.83
1586 3363 3.327757 AGCAGGTCCTGTATCAAGAAACA 59.672 43.478 20.24 0.00 33.43 2.83
1650 3427 3.253921 TGTCATTGAAGTGTGGATGCTTG 59.746 43.478 0.00 0.00 0.00 4.01
1674 3451 2.125310 TCCACGGCAATACGCAGG 60.125 61.111 0.00 0.00 45.17 4.85
1686 3463 2.430921 AAGAACGCGCTCTCCACG 60.431 61.111 13.17 0.00 0.00 4.94
1715 3492 8.737175 CATAGGATGCATGAATTGTTTAGCTAT 58.263 33.333 2.46 0.00 0.00 2.97
1723 3500 5.889853 AGAACACATAGGATGCATGAATTGT 59.110 36.000 2.46 0.00 0.00 2.71
1748 3525 3.190874 GGGAGAAACTGCGTAATCTCAG 58.809 50.000 17.51 0.00 40.02 3.35
1753 3530 0.899720 TCCGGGAGAAACTGCGTAAT 59.100 50.000 0.00 0.00 0.00 1.89
1776 3553 8.438513 CAAAACAATATCATAGTATCGGCAGAG 58.561 37.037 0.00 0.00 0.00 3.35
1790 3567 8.085296 GGTACCACAATGAACAAAACAATATCA 58.915 33.333 7.15 0.00 0.00 2.15
1814 3591 1.144969 CGTACGCATGTGTGAAAGGT 58.855 50.000 22.00 0.00 0.00 3.50
1937 3714 6.926826 ACAGTCGAATTCGTATTGGCATTATA 59.073 34.615 25.93 0.33 40.80 0.98
2279 4060 6.480320 GCACCATTAGAGGTCACAGTTATAAG 59.520 42.308 0.00 0.00 40.77 1.73
2328 4109 3.453424 GGTGGTTAAAACAGTTGCCTTG 58.547 45.455 0.00 0.00 0.00 3.61
2343 4124 2.060050 TTGGTTTGTGATCGGTGGTT 57.940 45.000 0.00 0.00 0.00 3.67
2363 4144 2.034879 CGTCTTTCAGCCGGCACAT 61.035 57.895 31.54 4.59 0.00 3.21
2394 4175 0.032952 GTACAACAGACCGTCCTGCA 59.967 55.000 0.00 0.00 37.68 4.41
2403 4184 4.618693 GCTCCTCCAGTAAGTACAACAGAC 60.619 50.000 0.00 0.00 0.00 3.51
2413 4194 1.817209 GACCGGCTCCTCCAGTAAG 59.183 63.158 0.00 0.00 34.01 2.34
2448 4229 1.786049 CGATCGATCTGGAGACCGCA 61.786 60.000 22.43 0.00 0.00 5.69
2499 4280 5.683876 ATGTGATAAACTGTGTAGCCTCT 57.316 39.130 0.00 0.00 0.00 3.69
2500 4281 5.643777 ACAATGTGATAAACTGTGTAGCCTC 59.356 40.000 0.00 0.00 0.00 4.70
2501 4282 5.560724 ACAATGTGATAAACTGTGTAGCCT 58.439 37.500 0.00 0.00 0.00 4.58
2502 4283 5.880054 ACAATGTGATAAACTGTGTAGCC 57.120 39.130 0.00 0.00 0.00 3.93
2503 4284 9.277565 CAATTACAATGTGATAAACTGTGTAGC 57.722 33.333 0.00 0.00 33.27 3.58
2504 4285 9.773328 CCAATTACAATGTGATAAACTGTGTAG 57.227 33.333 0.00 0.00 33.27 2.74
2505 4286 8.240682 GCCAATTACAATGTGATAAACTGTGTA 58.759 33.333 0.00 0.00 31.52 2.90
2506 4287 7.090173 GCCAATTACAATGTGATAAACTGTGT 58.910 34.615 0.00 0.00 33.06 3.72
2507 4288 7.089538 TGCCAATTACAATGTGATAAACTGTG 58.910 34.615 0.00 0.00 0.00 3.66
2508 4289 7.225784 TGCCAATTACAATGTGATAAACTGT 57.774 32.000 0.00 0.00 0.00 3.55
2509 4290 8.706492 AATGCCAATTACAATGTGATAAACTG 57.294 30.769 0.00 0.00 0.00 3.16
2695 4477 7.918562 TCAGTTATGTTTTCCTAACAGCAAAAC 59.081 33.333 0.00 0.00 39.46 2.43
2787 4573 7.370383 ACAAACAATAATCGATCAAAGCTTGT 58.630 30.769 0.00 2.89 0.00 3.16
2788 4574 7.801547 ACAAACAATAATCGATCAAAGCTTG 57.198 32.000 0.00 2.26 0.00 4.01
2823 4609 8.477709 GCGTGTACTATGTATGAAACTAATCAC 58.522 37.037 0.00 0.00 30.82 3.06
2853 4639 6.912203 TTGTCGAAACTAACTGTCATTTCA 57.088 33.333 0.00 0.00 31.81 2.69
2918 4704 7.039722 ACCCAAATCTACAAAATCCTTCCTA 57.960 36.000 0.00 0.00 0.00 2.94
2925 4711 9.974980 TTTAACTGAACCCAAATCTACAAAATC 57.025 29.630 0.00 0.00 0.00 2.17
3026 4812 2.288518 GGATCAGCAGAGATTCCGGTAC 60.289 54.545 0.00 0.00 0.00 3.34
3219 5015 3.030291 TGTTTCCTTCAGTGCCAACAAT 58.970 40.909 0.00 0.00 0.00 2.71
3229 5025 6.934645 TCTACACTTTACCATGTTTCCTTCAG 59.065 38.462 0.00 0.00 0.00 3.02
3259 5055 2.611224 CCAGGAAGGCAAAGCACAAATC 60.611 50.000 0.00 0.00 0.00 2.17
3269 5065 2.027192 GTGAGTATGTCCAGGAAGGCAA 60.027 50.000 0.00 0.00 37.29 4.52
3278 5074 6.605471 AAGTTATGTCAGTGAGTATGTCCA 57.395 37.500 0.00 0.00 0.00 4.02
3327 5123 3.926616 ACGAGAGGTGTGTGAATTTAGG 58.073 45.455 0.00 0.00 0.00 2.69
3353 5229 1.622232 GTTTAGCACGACGTCCCTAC 58.378 55.000 10.58 0.00 0.00 3.18
3354 5230 0.527565 GGTTTAGCACGACGTCCCTA 59.472 55.000 10.58 5.61 0.00 3.53
3465 5342 7.611855 GCAATATATATGTCAAGCTAAAGGGGT 59.388 37.037 0.00 0.00 0.00 4.95
3498 5375 2.096657 GTGTGTGTGCATGTGTGTGTTA 59.903 45.455 0.00 0.00 0.00 2.41
3511 5388 0.606401 GTCCATCCCCTGTGTGTGTG 60.606 60.000 0.00 0.00 0.00 3.82
3512 5389 1.761174 GTCCATCCCCTGTGTGTGT 59.239 57.895 0.00 0.00 0.00 3.72
3793 5670 0.387367 CTAACTCAGTGACTGCGCGT 60.387 55.000 7.93 3.28 0.00 6.01
3795 5672 1.341606 GACTAACTCAGTGACTGCGC 58.658 55.000 7.93 0.00 37.72 6.09
3891 5789 0.319900 ACTCGTGCATCAAAGCGTCT 60.320 50.000 0.00 0.00 37.31 4.18
3930 5828 6.347240 CGTGATCCTCAAGTCAAAAAGAGAAG 60.347 42.308 0.00 0.00 0.00 2.85
3984 5883 5.163884 CGCATATGCATATCCAAGTTCTGAG 60.164 44.000 26.52 2.20 42.21 3.35
4052 5966 9.920946 AAGGAGTATCAGCAAGGAATTAATTAA 57.079 29.630 0.00 0.00 36.25 1.40
4054 5968 9.920946 TTAAGGAGTATCAGCAAGGAATTAATT 57.079 29.630 0.00 0.00 36.25 1.40
4094 6012 5.808030 CGACTTCTTTTCCAGTATCTTCTCC 59.192 44.000 0.00 0.00 0.00 3.71
4103 6021 1.947456 GGTTGCGACTTCTTTTCCAGT 59.053 47.619 3.59 0.00 0.00 4.00
4147 6065 0.649475 CTGCGACATCAGCTGCTAAC 59.351 55.000 9.47 0.00 35.28 2.34
4162 6175 2.489329 ACCACCTCATCATTTTTCTGCG 59.511 45.455 0.00 0.00 0.00 5.18
4167 6180 4.728772 TCTGTGACCACCTCATCATTTTT 58.271 39.130 0.00 0.00 0.00 1.94
4206 6219 1.542472 TGCAGAAATGTGATGCTGGTG 59.458 47.619 0.00 0.00 40.62 4.17
4254 6267 0.745845 CTCTGCCCCCAATCAACTCG 60.746 60.000 0.00 0.00 0.00 4.18
4277 6290 7.509141 TTCTCATGTTGATGCAGAGTAAAAA 57.491 32.000 0.00 0.00 0.00 1.94
4314 6328 5.739161 CAGCAGTTTGTTTGTAAGTGAGTTC 59.261 40.000 0.00 0.00 0.00 3.01
4320 6334 4.157656 TGAAGCAGCAGTTTGTTTGTAAGT 59.842 37.500 0.00 0.00 0.00 2.24
4338 6352 5.280945 TGCAACTTTCTTGTATGTTGAAGC 58.719 37.500 8.60 0.00 41.35 3.86
4354 6368 5.500234 TCCTATGCTTCATAGTTGCAACTT 58.500 37.500 35.20 20.35 41.38 2.66
4356 6370 6.382869 AATCCTATGCTTCATAGTTGCAAC 57.617 37.500 22.17 22.17 41.38 4.17
4357 6371 5.532406 GGAATCCTATGCTTCATAGTTGCAA 59.468 40.000 11.52 0.00 41.38 4.08
4364 6378 6.100279 ACAAGTCAGGAATCCTATGCTTCATA 59.900 38.462 0.00 0.00 29.64 2.15
4365 6379 5.104193 ACAAGTCAGGAATCCTATGCTTCAT 60.104 40.000 0.00 0.00 29.64 2.57
4388 6402 5.423015 TGATCTTCCTGCTCTTGTATGAAC 58.577 41.667 0.00 0.00 0.00 3.18
4403 6417 6.017400 TCTGCAACATTTTCTTGATCTTCC 57.983 37.500 0.00 0.00 0.00 3.46
4405 6419 6.183360 TGGTTCTGCAACATTTTCTTGATCTT 60.183 34.615 0.00 0.00 33.70 2.40
4411 6425 4.111916 CGTTGGTTCTGCAACATTTTCTT 58.888 39.130 0.00 0.00 33.70 2.52
4412 6426 3.705604 CGTTGGTTCTGCAACATTTTCT 58.294 40.909 0.00 0.00 33.70 2.52
4413 6427 2.218530 GCGTTGGTTCTGCAACATTTTC 59.781 45.455 0.00 0.00 33.70 2.29
4461 6475 7.067251 CCCGTAGTTCAGAGAAACTAGTAGAAT 59.933 40.741 3.59 0.00 41.22 2.40
4462 6476 6.373774 CCCGTAGTTCAGAGAAACTAGTAGAA 59.626 42.308 3.59 0.00 41.22 2.10
4468 6482 5.510179 CCAAACCCGTAGTTCAGAGAAACTA 60.510 44.000 0.00 0.00 40.01 2.24
4525 6545 3.753272 TCCTTCGGAGAGCTTTTGATTTG 59.247 43.478 0.00 0.00 38.43 2.32
4565 6585 3.912496 TCGGTCATGAGAACAATCCAT 57.088 42.857 0.00 0.00 0.00 3.41
4598 6618 2.649349 GCGCTCGTGTCTCGCTAG 60.649 66.667 0.00 0.00 44.79 3.42
4599 6619 4.516135 CGCGCTCGTGTCTCGCTA 62.516 66.667 5.56 0.00 45.87 4.26
4603 6623 3.611792 GATGCGCGCTCGTGTCTC 61.612 66.667 33.29 12.83 38.14 3.36
4730 6778 4.090588 GGCCCCGACATGGACGAA 62.091 66.667 14.36 0.00 42.00 3.85


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

AutoCloner maintained by Alex Coulton.