Multiple sequence alignment - TraesCS7D01G027500

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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 TraesCS7D01G027500 chr7D 100.000 4662 0 0 1 4662 13474219 13478880 0.000000e+00 8610.0
1 TraesCS7D01G027500 chr7D 84.409 372 50 5 3412 3779 2887670 2888037 4.440000e-95 359.0
2 TraesCS7D01G027500 chr7D 85.404 322 26 7 511 819 414346663 414346350 9.740000e-82 315.0
3 TraesCS7D01G027500 chr7D 76.375 618 83 32 3670 4252 13488132 13488721 1.650000e-69 274.0
4 TraesCS7D01G027500 chr7D 90.000 120 10 1 283 400 414346877 414346758 2.250000e-33 154.0
5 TraesCS7D01G027500 chr7A 91.950 3379 188 43 1 3332 12907711 12911052 0.000000e+00 4656.0
6 TraesCS7D01G027500 chr7A 89.849 926 60 20 3399 4299 12911177 12912093 0.000000e+00 1158.0
7 TraesCS7D01G027500 chr7A 84.642 586 74 7 2996 3573 12981466 12982043 1.880000e-158 569.0
8 TraesCS7D01G027500 chr7A 81.743 482 64 18 3027 3496 13205364 13204895 9.470000e-102 381.0
9 TraesCS7D01G027500 chr7A 84.469 367 28 12 3387 3728 12973968 12974330 7.470000e-88 335.0
10 TraesCS7D01G027500 chr7A 87.209 86 9 1 3749 3834 12979806 12979889 3.840000e-16 97.1
11 TraesCS7D01G027500 chr7A 78.049 164 20 7 3626 3779 2740894 2740737 6.430000e-14 89.8
12 TraesCS7D01G027500 chr7A 93.333 60 0 3 3720 3776 12982112 12982170 8.310000e-13 86.1
13 TraesCS7D01G027500 chr7A 100.000 28 0 0 3755 3782 12982244 12982271 8.000000e-03 52.8
14 TraesCS7D01G027500 chr4A 92.537 2747 165 20 617 3340 723640352 723637623 0.000000e+00 3901.0
15 TraesCS7D01G027500 chr4A 86.929 941 64 27 3413 4303 723141758 723140827 0.000000e+00 1002.0
16 TraesCS7D01G027500 chr4A 81.381 1332 104 62 3399 4662 723637511 723636256 0.000000e+00 953.0
17 TraesCS7D01G027500 chr4A 91.984 499 35 1 2839 3332 723142357 723141859 0.000000e+00 695.0
18 TraesCS7D01G027500 chr4A 86.702 376 29 11 4301 4662 723140793 723140425 9.400000e-107 398.0
19 TraesCS7D01G027500 chr4A 81.915 470 62 9 1949 2411 723203778 723203325 4.400000e-100 375.0
20 TraesCS7D01G027500 chr4A 86.400 250 25 5 3423 3663 741028511 741028262 9.950000e-67 265.0
21 TraesCS7D01G027500 chr4A 81.818 220 8 15 3 198 723640928 723640717 6.250000e-34 156.0
22 TraesCS7D01G027500 chr4A 83.529 170 19 3 2889 3050 723203225 723203057 2.910000e-32 150.0
23 TraesCS7D01G027500 chr4A 85.271 129 18 1 197 324 723640683 723640555 1.050000e-26 132.0
24 TraesCS7D01G027500 chr4A 79.290 169 23 10 2952 3119 739660948 739660791 1.770000e-19 108.0
25 TraesCS7D01G027500 chr4A 79.290 169 23 10 2952 3119 742067727 742067570 1.770000e-19 108.0
26 TraesCS7D01G027500 chr4D 86.076 316 25 8 511 819 212645021 212645324 5.820000e-84 322.0
27 TraesCS7D01G027500 chr4D 90.244 123 10 1 280 400 212644804 212644926 4.830000e-35 159.0
28 TraesCS7D01G027500 chr5A 84.494 316 34 7 511 819 465157268 465157575 9.810000e-77 298.0
29 TraesCS7D01G027500 chr5A 87.805 123 13 1 280 400 465157051 465157173 4.860000e-30 143.0
30 TraesCS7D01G027500 chrUn 91.935 186 12 2 3158 3340 367671452 367671637 1.660000e-64 257.0
31 TraesCS7D01G027500 chrUn 98.131 107 2 0 3399 3505 367671749 367671855 2.210000e-43 187.0
32 TraesCS7D01G027500 chr1D 77.460 315 35 17 3997 4293 456663267 456662971 6.250000e-34 156.0


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 TraesCS7D01G027500 chr7D 13474219 13478880 4661 False 8610.000000 8610 100.000000 1 4662 1 chr7D.!!$F2 4661
1 TraesCS7D01G027500 chr7D 13488132 13488721 589 False 274.000000 274 76.375000 3670 4252 1 chr7D.!!$F3 582
2 TraesCS7D01G027500 chr7D 414346350 414346877 527 True 234.500000 315 87.702000 283 819 2 chr7D.!!$R1 536
3 TraesCS7D01G027500 chr7A 12907711 12912093 4382 False 2907.000000 4656 90.899500 1 4299 2 chr7A.!!$F2 4298
4 TraesCS7D01G027500 chr7A 12979806 12982271 2465 False 201.250000 569 91.296000 2996 3834 4 chr7A.!!$F3 838
5 TraesCS7D01G027500 chr4A 723636256 723640928 4672 True 1285.500000 3901 85.251750 3 4662 4 chr4A.!!$R6 4659
6 TraesCS7D01G027500 chr4A 723140425 723142357 1932 True 698.333333 1002 88.538333 2839 4662 3 chr4A.!!$R4 1823
7 TraesCS7D01G027500 chr4A 723203057 723203778 721 True 262.500000 375 82.722000 1949 3050 2 chr4A.!!$R5 1101
8 TraesCS7D01G027500 chr4D 212644804 212645324 520 False 240.500000 322 88.160000 280 819 2 chr4D.!!$F1 539
9 TraesCS7D01G027500 chr5A 465157051 465157575 524 False 220.500000 298 86.149500 280 819 2 chr5A.!!$F1 539

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
773 918 0.107800 GCTTCTTCTAACCCCCGTCC 60.108 60.0 0.0 0.00 0.0 4.79 F
1899 2063 0.179048 TGCCGGCTATGATTGGAGTG 60.179 55.0 29.7 0.00 0.0 3.51 F
2374 2546 0.101040 TGCAGTTCTGCAACAACAGC 59.899 50.0 22.6 15.06 42.4 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2374 2546 0.036952 ACCAAGCAGAGTCCACATCG 60.037 55.0 0.0 0.0 0.00 3.84 R
3349 3549 0.035630 GCACCAGCTCAGGAGTCAAT 60.036 55.0 0.0 0.0 37.91 2.57 R
4162 4527 0.388134 CAGCACATTCAGCTTGGCAC 60.388 55.0 0.0 0.0 41.14 5.01 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
43 48 8.594550 ACTATAACTATAGCCTAAACACATGGG 58.405 37.037 0.00 0.00 39.36 4.00
46 54 6.818281 ACTATAGCCTAAACACATGGGTTA 57.182 37.500 15.06 2.69 33.34 2.85
47 55 6.827727 ACTATAGCCTAAACACATGGGTTAG 58.172 40.000 15.06 12.16 33.34 2.34
213 277 2.501610 CGCTACAGGGGAAGAGGC 59.498 66.667 0.00 0.00 0.00 4.70
330 396 1.470098 CTCATCTTTCTTGTTGGGGCG 59.530 52.381 0.00 0.00 0.00 6.13
347 413 1.583054 GCGGATTAGAGATTGCCGTT 58.417 50.000 0.00 0.00 43.61 4.44
353 419 2.596904 TAGAGATTGCCGTTGGTAGC 57.403 50.000 0.00 0.00 0.00 3.58
359 426 0.519519 TTGCCGTTGGTAGCATTTCG 59.480 50.000 0.00 1.75 39.11 3.46
504 600 1.281867 TCATGAGCGGATTTTGGGTCT 59.718 47.619 0.00 0.00 0.00 3.85
600 727 2.124695 GGCTGGAAAGGCCTACGG 60.125 66.667 5.16 6.04 45.57 4.02
648 775 2.801111 GTGTTTCTCTTCTGTCGGGAAC 59.199 50.000 0.00 0.00 0.00 3.62
671 798 0.394762 TGTCTGGCAAGGATGATGGC 60.395 55.000 0.00 0.00 43.15 4.40
680 807 3.737047 GCAAGGATGATGGCACTCATTTG 60.737 47.826 11.81 12.97 36.01 2.32
770 915 1.137282 GAGAGCTTCTTCTAACCCCCG 59.863 57.143 0.00 0.00 0.00 5.73
771 916 0.903236 GAGCTTCTTCTAACCCCCGT 59.097 55.000 0.00 0.00 0.00 5.28
772 917 0.903236 AGCTTCTTCTAACCCCCGTC 59.097 55.000 0.00 0.00 0.00 4.79
773 918 0.107800 GCTTCTTCTAACCCCCGTCC 60.108 60.000 0.00 0.00 0.00 4.79
924 1069 1.812235 TTCTGCAATCACACAGCGAT 58.188 45.000 0.00 0.00 33.80 4.58
925 1070 1.812235 TCTGCAATCACACAGCGATT 58.188 45.000 0.00 0.00 33.80 3.34
929 1074 4.395854 TCTGCAATCACACAGCGATTTTAT 59.604 37.500 0.00 0.00 33.80 1.40
930 1075 5.584251 TCTGCAATCACACAGCGATTTTATA 59.416 36.000 0.00 0.00 33.80 0.98
960 1124 0.879765 GCTCCATCCATATGTGCTGC 59.120 55.000 1.24 0.00 31.78 5.25
961 1125 1.544982 GCTCCATCCATATGTGCTGCT 60.545 52.381 0.00 0.00 31.78 4.24
962 1126 2.152016 CTCCATCCATATGTGCTGCTG 58.848 52.381 0.00 0.00 0.00 4.41
990 1154 1.610102 CCTTCTTGCAGGTGACAGGAG 60.610 57.143 0.00 0.00 0.00 3.69
994 1158 1.410050 TTGCAGGTGACAGGAGCAGA 61.410 55.000 0.00 0.00 36.47 4.26
1431 1595 4.100084 CGGTGCCTGATCCCTGCA 62.100 66.667 0.00 0.00 0.00 4.41
1491 1655 0.388294 GGGACTACGCCTGGTATGAC 59.612 60.000 0.00 0.00 0.00 3.06
1527 1691 1.953686 GAGCTGAGTATCGAGAAGGCT 59.046 52.381 0.00 0.00 38.61 4.58
1530 1694 2.542824 GCTGAGTATCGAGAAGGCTGTC 60.543 54.545 0.00 0.00 38.61 3.51
1581 1745 1.137594 TTAGGTTCCCTGGTGGTGGG 61.138 60.000 0.00 0.00 45.90 4.61
1624 1788 7.650903 GTGCTGATGCTTATATCGATGATATCA 59.349 37.037 8.10 8.10 37.03 2.15
1629 1793 7.398834 TGCTTATATCGATGATATCAATGCG 57.601 36.000 9.99 13.52 36.70 4.73
1899 2063 0.179048 TGCCGGCTATGATTGGAGTG 60.179 55.000 29.70 0.00 0.00 3.51
1923 2087 3.244422 TGGCAACCGATAGAATCCCATAC 60.244 47.826 0.00 0.00 39.76 2.39
1994 2159 3.886505 TGGAACAAGCTCGGTATGTTTTT 59.113 39.130 2.42 0.00 37.41 1.94
2000 2165 5.415701 ACAAGCTCGGTATGTTTTTCATGAT 59.584 36.000 0.00 0.00 37.91 2.45
2057 2222 8.664798 TGAGCACATGTTTACTGAATGTATAAC 58.335 33.333 0.00 0.00 33.31 1.89
2058 2223 8.792830 AGCACATGTTTACTGAATGTATAACT 57.207 30.769 0.00 0.00 33.31 2.24
2059 2224 9.884636 AGCACATGTTTACTGAATGTATAACTA 57.115 29.630 0.00 0.00 33.31 2.24
2084 2249 8.997621 AACTAGAGCTTATGTTTTATCGTTCA 57.002 30.769 0.00 0.00 0.00 3.18
2116 2281 6.036083 CAGACGGTTTATATCTGGTTGAAGTG 59.964 42.308 0.00 0.00 36.92 3.16
2370 2542 0.664761 GCTCTGCAGTTCTGCAACAA 59.335 50.000 24.31 13.85 44.88 2.83
2374 2546 0.101040 TGCAGTTCTGCAACAACAGC 59.899 50.000 22.60 15.06 42.40 4.40
2470 2642 5.305644 AGCTCATTATCTGTAGTTCCGGAAT 59.694 40.000 22.04 11.91 0.00 3.01
2476 2648 8.979574 CATTATCTGTAGTTCCGGAATAACTTC 58.020 37.037 22.04 12.04 38.18 3.01
2506 2678 5.560724 TGGCTGTTCTGAAATATATAGCCC 58.439 41.667 13.75 1.11 46.70 5.19
2518 2690 8.623030 TGAAATATATAGCCCGGTTTGTTTTAC 58.377 33.333 0.00 0.00 0.00 2.01
2559 2731 6.182627 TGAACCTCATGCTTGAAATCATAGT 58.817 36.000 3.65 0.00 0.00 2.12
2666 2845 8.982723 AGCTAAGTATCAGTTTATCTTTCCTGA 58.017 33.333 0.00 0.00 38.24 3.86
2688 2867 6.559810 TGACAGTTTTGGAAACATTGTACAG 58.440 36.000 0.00 0.00 42.32 2.74
2696 2875 7.397892 TTGGAAACATTGTACAGTCTTTTGA 57.602 32.000 0.00 0.00 42.32 2.69
2729 2908 6.540189 GTGGCTCAGTTCACTTACAATCATAT 59.460 38.462 0.00 0.00 0.00 1.78
2784 2963 7.261325 CACACTAGTACAGTCATAGATGCTTT 58.739 38.462 0.00 0.00 34.26 3.51
2795 2974 5.877012 GTCATAGATGCTTTGAACCTCAAGA 59.123 40.000 0.00 0.00 37.70 3.02
2850 3031 4.732784 TCAGAAAACAAAACTGACTGTGC 58.267 39.130 0.00 0.00 36.04 4.57
2879 3065 5.067936 ACATAGGTACAAGAAGATGGAGACG 59.932 44.000 0.00 0.00 0.00 4.18
3300 3498 1.607148 CGTATGACCTCATCCACGCTA 59.393 52.381 0.00 0.00 37.76 4.26
3302 3500 2.604046 ATGACCTCATCCACGCTAAC 57.396 50.000 0.00 0.00 28.78 2.34
3323 3521 7.809806 GCTAACAAAGTGTTCAGCTTTTATCAT 59.190 33.333 0.00 0.00 40.22 2.45
3326 3524 7.141363 ACAAAGTGTTCAGCTTTTATCATGAC 58.859 34.615 0.00 0.00 34.32 3.06
3337 3537 5.586243 GCTTTTATCATGACAGGTAGCAGAA 59.414 40.000 0.00 0.00 0.00 3.02
3339 3539 6.985188 TTTATCATGACAGGTAGCAGAAAC 57.015 37.500 0.00 0.00 0.00 2.78
3341 3541 3.930336 TCATGACAGGTAGCAGAAACAG 58.070 45.455 0.00 0.00 0.00 3.16
3344 3544 0.764890 ACAGGTAGCAGAAACAGCCA 59.235 50.000 0.00 0.00 0.00 4.75
3349 3549 2.819608 GGTAGCAGAAACAGCCAATGAA 59.180 45.455 0.00 0.00 0.00 2.57
3361 3561 3.377485 CAGCCAATGAATTGACTCCTGAG 59.623 47.826 4.58 0.00 40.14 3.35
3385 3661 5.590530 TGGTGCTTTCTTTTTCTGCTAAA 57.409 34.783 0.00 0.00 0.00 1.85
3808 4096 3.013276 TCGCTGTATCATCATCGGTTC 57.987 47.619 0.00 0.00 0.00 3.62
3842 4167 1.807142 CTGACTCGTGAGCTGTGAGTA 59.193 52.381 11.01 2.21 42.71 2.59
3880 4212 4.082081 ACGATGGTATTCAGTCAACCGTTA 60.082 41.667 0.00 0.00 35.98 3.18
3882 4214 4.603989 TGGTATTCAGTCAACCGTTACA 57.396 40.909 0.00 0.00 35.98 2.41
3883 4215 4.958509 TGGTATTCAGTCAACCGTTACAA 58.041 39.130 0.00 0.00 35.98 2.41
3896 4228 6.596497 TCAACCGTTACAAAAGAGGATATTCC 59.404 38.462 0.00 0.00 36.58 3.01
3946 4278 3.411446 TGAATGTGCTTCTGTCCGAATT 58.589 40.909 0.00 0.00 34.75 2.17
3950 4282 6.150976 TGAATGTGCTTCTGTCCGAATTATTT 59.849 34.615 0.00 0.00 34.75 1.40
3952 4284 4.155826 TGTGCTTCTGTCCGAATTATTTGG 59.844 41.667 4.85 4.85 35.37 3.28
3953 4285 3.694072 TGCTTCTGTCCGAATTATTTGGG 59.306 43.478 11.04 1.00 34.75 4.12
3954 4286 3.694566 GCTTCTGTCCGAATTATTTGGGT 59.305 43.478 11.04 0.00 34.75 4.51
3955 4287 4.157840 GCTTCTGTCCGAATTATTTGGGTT 59.842 41.667 11.04 0.00 34.75 4.11
3956 4288 5.336451 GCTTCTGTCCGAATTATTTGGGTTT 60.336 40.000 11.04 0.00 34.75 3.27
3993 4327 6.054860 TGAACAATTTTCACCCCAAGAAAA 57.945 33.333 3.89 3.89 45.68 2.29
4004 4338 1.251251 CCAAGAAAAGGGCAGACCAG 58.749 55.000 0.00 0.00 43.89 4.00
4017 4351 3.569701 GGCAGACCAGACAATCTTTTGAA 59.430 43.478 0.00 0.00 34.66 2.69
4053 4388 6.480524 TCCAAATACGAAACATCTGTTCAG 57.519 37.500 0.00 0.00 37.25 3.02
4093 4428 2.733026 CCAAAAGAAAGGCTGATTTGCG 59.267 45.455 0.00 0.00 31.36 4.85
4094 4429 3.552684 CCAAAAGAAAGGCTGATTTGCGA 60.553 43.478 0.00 0.00 31.36 5.10
4096 4431 2.997485 AGAAAGGCTGATTTGCGAAC 57.003 45.000 0.00 0.00 0.00 3.95
4099 4459 1.896220 AAGGCTGATTTGCGAACAGA 58.104 45.000 16.06 0.00 34.07 3.41
4162 4527 1.884579 GCCCAGGCAGAATGTATGATG 59.115 52.381 3.12 0.00 41.49 3.07
4163 4528 2.750807 GCCCAGGCAGAATGTATGATGT 60.751 50.000 3.12 0.00 41.49 3.06
4183 4548 1.214589 CCAAGCTGAATGTGCTGGC 59.785 57.895 0.00 0.00 41.03 4.85
4188 4553 0.964358 GCTGAATGTGCTGGCTTCCT 60.964 55.000 0.00 0.00 0.00 3.36
4196 4561 3.873910 TGTGCTGGCTTCCTAACTATTC 58.126 45.455 0.00 0.00 0.00 1.75
4212 4577 8.435982 CCTAACTATTCCTTCTTCAGAATCCAT 58.564 37.037 0.00 0.00 34.60 3.41
4224 4589 9.690913 TTCTTCAGAATCCATACAATCTTCAAT 57.309 29.630 0.00 0.00 0.00 2.57
4252 4617 3.565902 GGAGAACAAAGACTGAACTTGGG 59.434 47.826 0.00 0.00 0.00 4.12
4309 4746 1.378762 GAAACCTACCAGGCAGCCA 59.621 57.895 15.80 0.00 39.63 4.75
4380 4817 2.039746 ACTACTATGGTGGCAGCACAAA 59.960 45.455 23.12 9.64 0.00 2.83
4381 4818 1.993956 ACTATGGTGGCAGCACAAAA 58.006 45.000 23.12 7.08 0.00 2.44
4415 4852 6.590292 CCACTCAAACTCATTAGTACAATCGT 59.410 38.462 0.00 0.00 33.75 3.73
4489 4926 6.882140 TGTTCCATCAACCGAATACAAAGTAT 59.118 34.615 0.00 0.00 33.51 2.12
4490 4927 7.065324 TGTTCCATCAACCGAATACAAAGTATC 59.935 37.037 0.00 0.00 33.51 2.24
4536 4981 2.095263 CCACGCAGGGTTTACAAATCTG 60.095 50.000 0.00 0.00 0.00 2.90
4549 4994 2.964464 ACAAATCTGGGTTGATGCACAA 59.036 40.909 0.00 0.00 36.02 3.33
4644 5096 1.538687 AAGCAAGCAATCCAGTGCCC 61.539 55.000 0.00 0.00 46.14 5.36
4655 5107 1.526575 CCAGTGCCCGCTTGACAATT 61.527 55.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 32 5.722923 AGTACTAACCCATGTGTTTAGGCTA 59.277 40.000 0.00 0.00 0.00 3.93
28 33 4.534897 AGTACTAACCCATGTGTTTAGGCT 59.465 41.667 0.00 0.00 0.00 4.58
213 277 3.009695 TGGTGTGGGATAAGGTTACCTTG 59.990 47.826 25.38 0.00 44.44 3.61
275 339 4.232909 GAAATCCCTACCCTAAGCTAGGT 58.767 47.826 8.00 8.00 44.73 3.08
278 342 4.658901 CCTTGAAATCCCTACCCTAAGCTA 59.341 45.833 0.00 0.00 0.00 3.32
330 396 2.919228 ACCAACGGCAATCTCTAATCC 58.081 47.619 0.00 0.00 0.00 3.01
347 413 2.158957 GGATGGAGACGAAATGCTACCA 60.159 50.000 0.00 0.00 0.00 3.25
353 419 1.202698 GGAGGGGATGGAGACGAAATG 60.203 57.143 0.00 0.00 0.00 2.32
359 426 2.448736 GGGGGAGGGGATGGAGAC 60.449 72.222 0.00 0.00 0.00 3.36
472 568 4.442706 TCCGCTCATGAATTTTCTCTACC 58.557 43.478 0.00 0.00 0.00 3.18
504 600 3.260632 TCATCACTGATTTTGGGAGTCGA 59.739 43.478 0.00 0.00 0.00 4.20
596 723 0.871722 GCAAAGTGCACACATCCGTA 59.128 50.000 21.04 0.00 44.26 4.02
598 725 4.539152 GCAAAGTGCACACATCCG 57.461 55.556 21.04 1.98 44.26 4.18
648 775 3.464907 CATCATCCTTGCCAGACACTAG 58.535 50.000 0.00 0.00 0.00 2.57
689 816 3.070159 TGCAGAAAGTGTAGAAGAGCAGT 59.930 43.478 0.00 0.00 0.00 4.40
770 915 2.171448 AGGTAGCTGTGAATGGATGGAC 59.829 50.000 0.00 0.00 0.00 4.02
771 916 2.171237 CAGGTAGCTGTGAATGGATGGA 59.829 50.000 13.89 0.00 0.00 3.41
772 917 2.569059 CAGGTAGCTGTGAATGGATGG 58.431 52.381 13.89 0.00 0.00 3.51
773 918 1.945394 GCAGGTAGCTGTGAATGGATG 59.055 52.381 22.21 0.00 41.15 3.51
847 992 2.101640 ACCAGGGTGGAATTTTTGCT 57.898 45.000 0.00 0.00 40.96 3.91
860 1005 6.095440 CCATAACTCTGAAACATTTACCAGGG 59.905 42.308 0.00 0.00 33.55 4.45
924 1069 7.016170 TGGATGGAGCAGTAGCACTATATAAAA 59.984 37.037 0.00 0.00 45.49 1.52
925 1070 6.496911 TGGATGGAGCAGTAGCACTATATAAA 59.503 38.462 0.00 0.00 45.49 1.40
929 1074 3.844640 TGGATGGAGCAGTAGCACTATA 58.155 45.455 0.00 0.00 45.49 1.31
930 1075 2.682594 TGGATGGAGCAGTAGCACTAT 58.317 47.619 0.00 0.00 45.49 2.12
1122 1286 1.174078 TCTTGGCGTACACAGGTCGA 61.174 55.000 0.00 0.00 0.00 4.20
1125 1289 1.006571 CGTCTTGGCGTACACAGGT 60.007 57.895 0.00 0.00 0.00 4.00
1431 1595 2.121948 GGGTTCTTATAGTTCGGGGGT 58.878 52.381 0.00 0.00 0.00 4.95
1476 1640 2.665649 TGTTGTCATACCAGGCGTAG 57.334 50.000 0.00 0.00 0.00 3.51
1581 1745 1.449601 ACCATGCGGGAACATCGTC 60.450 57.895 0.60 0.00 41.15 4.20
1624 1788 2.607635 CAGTTAACGGTATGAGCGCATT 59.392 45.455 11.47 0.00 43.79 3.56
1899 2063 2.224523 TGGGATTCTATCGGTTGCCATC 60.225 50.000 0.00 0.00 0.00 3.51
1938 2102 2.889154 TAGAGCAGTGCGCCATGTCG 62.889 60.000 15.74 0.00 44.04 4.35
2027 2192 8.284945 ACATTCAGTAAACATGTGCTCATTAT 57.715 30.769 0.00 0.00 29.74 1.28
2028 2193 7.686438 ACATTCAGTAAACATGTGCTCATTA 57.314 32.000 0.00 0.00 29.74 1.90
2030 2195 7.870509 ATACATTCAGTAAACATGTGCTCAT 57.129 32.000 0.00 0.00 36.05 2.90
2059 2224 8.997621 TGAACGATAAAACATAAGCTCTAGTT 57.002 30.769 0.00 0.00 0.00 2.24
2060 2225 9.035607 CATGAACGATAAAACATAAGCTCTAGT 57.964 33.333 0.00 0.00 0.00 2.57
2061 2226 9.035607 ACATGAACGATAAAACATAAGCTCTAG 57.964 33.333 0.00 0.00 0.00 2.43
2080 2245 1.779569 AACCGTCTGTCGACATGAAC 58.220 50.000 20.40 15.91 42.86 3.18
2084 2249 5.507482 CCAGATATAAACCGTCTGTCGACAT 60.507 44.000 20.40 4.62 42.86 3.06
2116 2281 3.432378 TCCTGGTCTTAGAACTCTGTCC 58.568 50.000 0.00 0.00 0.00 4.02
2370 2542 1.079543 GCAGAGTCCACATCGCTGT 60.080 57.895 0.00 0.00 35.69 4.40
2374 2546 0.036952 ACCAAGCAGAGTCCACATCG 60.037 55.000 0.00 0.00 0.00 3.84
2470 2642 7.004555 TCAGAACAGCCAGAAATAGAAGTTA 57.995 36.000 0.00 0.00 0.00 2.24
2506 2678 8.859156 CAATGATAATCTTGGTAAAACAAACCG 58.141 33.333 0.00 0.00 40.08 4.44
2518 2690 8.681486 TGAGGTTCATACAATGATAATCTTGG 57.319 34.615 0.00 0.00 39.39 3.61
2590 2769 5.049267 TGGTGTTAGCGAAACCTGTTAAATC 60.049 40.000 10.50 0.00 37.27 2.17
2666 2845 6.377146 AGACTGTACAATGTTTCCAAAACTGT 59.623 34.615 0.00 4.08 0.00 3.55
2688 2867 1.269257 GCCACAAGCCAGTCAAAAGAC 60.269 52.381 0.00 0.00 34.35 3.01
2696 2875 3.244616 ACTGAGCCACAAGCCAGT 58.755 55.556 0.00 0.00 43.74 4.00
2704 2883 4.065088 TGATTGTAAGTGAACTGAGCCAC 58.935 43.478 0.00 0.00 0.00 5.01
2729 2908 4.642885 GGTTGCTACAATGGCAGGTTATTA 59.357 41.667 0.00 0.00 40.90 0.98
2737 2916 1.004161 TGCTAGGTTGCTACAATGGCA 59.996 47.619 8.97 8.97 37.97 4.92
2784 2963 4.397103 GCATTGTGATGATCTTGAGGTTCA 59.603 41.667 0.00 0.00 35.16 3.18
2795 2974 7.818997 ATAACAGAGAATGCATTGTGATGAT 57.181 32.000 18.59 10.87 35.16 2.45
2836 3015 1.013596 TGGTCGCACAGTCAGTTTTG 58.986 50.000 0.00 0.00 0.00 2.44
2837 3016 1.014352 GTGGTCGCACAGTCAGTTTT 58.986 50.000 0.00 0.00 0.00 2.43
2942 3128 1.651240 CGGATGCTCTTTGTGGCCAG 61.651 60.000 5.11 0.00 0.00 4.85
3300 3498 7.649306 GTCATGATAAAAGCTGAACACTTTGTT 59.351 33.333 0.00 0.00 44.37 2.83
3302 3500 7.140705 TGTCATGATAAAAGCTGAACACTTTG 58.859 34.615 0.00 0.00 37.42 2.77
3323 3521 1.270839 GGCTGTTTCTGCTACCTGTCA 60.271 52.381 0.00 0.00 0.00 3.58
3326 3524 1.896220 TTGGCTGTTTCTGCTACCTG 58.104 50.000 0.00 0.00 0.00 4.00
3341 3541 2.098770 GCTCAGGAGTCAATTCATTGGC 59.901 50.000 0.00 0.00 42.47 4.52
3344 3544 3.009916 ACCAGCTCAGGAGTCAATTCATT 59.990 43.478 0.00 0.00 0.00 2.57
3349 3549 0.035630 GCACCAGCTCAGGAGTCAAT 60.036 55.000 0.00 0.00 37.91 2.57
3361 3561 2.130395 GCAGAAAAAGAAAGCACCAGC 58.870 47.619 0.00 0.00 42.56 4.85
3369 3569 6.323739 AGTCCATGGTTTAGCAGAAAAAGAAA 59.676 34.615 12.58 0.00 0.00 2.52
3373 3573 7.775053 ATAAGTCCATGGTTTAGCAGAAAAA 57.225 32.000 12.58 0.00 0.00 1.94
3385 3661 7.450014 TGTTCAACATTACAATAAGTCCATGGT 59.550 33.333 12.58 0.00 0.00 3.55
3808 4096 2.159787 CGAGTCAGAGACCGCAAAATTG 60.160 50.000 0.00 0.00 32.18 2.32
3842 4167 2.463876 CATCGTGTAGCATCGTGTCAT 58.536 47.619 0.00 0.00 0.00 3.06
3896 4228 3.433615 CCAGCTTTCTCAAAACTACGAGG 59.566 47.826 0.00 0.00 0.00 4.63
3900 4232 3.815401 TGAGCCAGCTTTCTCAAAACTAC 59.185 43.478 11.19 0.00 36.50 2.73
3983 4316 0.900182 GGTCTGCCCTTTTCTTGGGG 60.900 60.000 0.00 0.00 44.71 4.96
3993 4327 1.366319 AAGATTGTCTGGTCTGCCCT 58.634 50.000 0.00 0.00 0.00 5.19
4004 4338 4.681744 TGTGCCTTGTTCAAAAGATTGTC 58.318 39.130 0.00 0.00 37.79 3.18
4017 4351 3.440173 CGTATTTGGATTCTGTGCCTTGT 59.560 43.478 0.00 0.00 0.00 3.16
4053 4388 0.871057 GCAGGCTGAGTGTCAGTTTC 59.129 55.000 20.86 0.00 45.94 2.78
4086 4421 6.549952 AGAAGAATCATTCTGTTCGCAAATC 58.450 36.000 0.00 0.00 40.59 2.17
4087 4422 6.506500 AGAAGAATCATTCTGTTCGCAAAT 57.493 33.333 0.00 0.00 40.59 2.32
4088 4423 5.947228 AGAAGAATCATTCTGTTCGCAAA 57.053 34.783 0.00 0.00 40.59 3.68
4124 4489 1.836802 GGCCTCCTCTTTCAGTCTGAT 59.163 52.381 2.68 0.00 0.00 2.90
4132 4497 2.273776 GCCTGGGCCTCCTCTTTC 59.726 66.667 4.53 0.00 34.56 2.62
4162 4527 0.388134 CAGCACATTCAGCTTGGCAC 60.388 55.000 0.00 0.00 41.14 5.01
4163 4528 1.529152 CCAGCACATTCAGCTTGGCA 61.529 55.000 0.00 0.00 41.14 4.92
4183 4548 9.541143 GATTCTGAAGAAGGAATAGTTAGGAAG 57.459 37.037 0.00 0.00 37.48 3.46
4196 4561 7.772292 TGAAGATTGTATGGATTCTGAAGAAGG 59.228 37.037 0.00 0.00 37.48 3.46
4224 4589 5.602978 AGTTCAGTCTTTGTTCTCCTTCCTA 59.397 40.000 0.00 0.00 0.00 2.94
4230 4595 3.565902 CCCAAGTTCAGTCTTTGTTCTCC 59.434 47.826 0.00 0.00 0.00 3.71
4237 4602 2.666317 CCAACCCCAAGTTCAGTCTTT 58.334 47.619 0.00 0.00 36.18 2.52
4252 4617 6.887626 TGTAAGTTAAGTCATTTCCCAACC 57.112 37.500 0.00 0.00 0.00 3.77
4309 4746 4.878397 GGTAGTGATATTCTTGTTGCTGCT 59.122 41.667 0.00 0.00 0.00 4.24
4346 4783 7.014422 GCCACCATAGTAGTAGTATTGTCTCTT 59.986 40.741 0.00 0.00 0.00 2.85
4347 4784 6.490721 GCCACCATAGTAGTAGTATTGTCTCT 59.509 42.308 0.00 0.00 0.00 3.10
4348 4785 6.264744 TGCCACCATAGTAGTAGTATTGTCTC 59.735 42.308 0.00 0.00 0.00 3.36
4349 4786 6.134055 TGCCACCATAGTAGTAGTATTGTCT 58.866 40.000 0.00 0.00 0.00 3.41
4350 4787 6.401047 TGCCACCATAGTAGTAGTATTGTC 57.599 41.667 0.00 0.00 0.00 3.18
4351 4788 5.221461 GCTGCCACCATAGTAGTAGTATTGT 60.221 44.000 0.00 0.00 0.00 2.71
4352 4789 5.221441 TGCTGCCACCATAGTAGTAGTATTG 60.221 44.000 0.00 0.00 0.00 1.90
4353 4790 4.899457 TGCTGCCACCATAGTAGTAGTATT 59.101 41.667 0.00 0.00 0.00 1.89
4354 4791 4.281182 GTGCTGCCACCATAGTAGTAGTAT 59.719 45.833 0.00 0.00 35.92 2.12
4355 4792 3.635373 GTGCTGCCACCATAGTAGTAGTA 59.365 47.826 0.00 0.00 35.92 1.82
4358 4795 2.462723 TGTGCTGCCACCATAGTAGTA 58.537 47.619 0.00 0.00 41.35 1.82
4359 4796 1.275666 TGTGCTGCCACCATAGTAGT 58.724 50.000 0.00 0.00 41.35 2.73
4501 4939 2.741517 CTGCGTGGTGTGATGAACAATA 59.258 45.455 0.00 0.00 41.57 1.90
4549 4994 1.040339 AAATGGTTGTGTGTGCCGGT 61.040 50.000 1.90 0.00 0.00 5.28
4619 5071 3.005684 CACTGGATTGCTTGCTTGGTTTA 59.994 43.478 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.