Multiple sequence alignment - TraesCS2B01G573000

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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 TraesCS2B01G573000 chr2B 100.000 4393 0 0 1 4393 762521934 762517542 0.000000e+00 8113.0
1 TraesCS2B01G573000 chr2B 98.212 1342 19 1 1963 3299 762533370 762532029 0.000000e+00 2340.0
2 TraesCS2B01G573000 chr2B 98.983 983 4 2 994 1976 762537251 762536275 0.000000e+00 1755.0
3 TraesCS2B01G573000 chr2B 79.128 321 49 13 662 972 23923320 23923008 5.760000e-49 206.0
4 TraesCS2B01G573000 chr2D 96.015 1907 50 10 1872 3778 621559747 621557867 0.000000e+00 3077.0
5 TraesCS2B01G573000 chr2D 92.737 895 37 8 974 1857 621560679 621559802 0.000000e+00 1267.0
6 TraesCS2B01G573000 chr2D 95.566 654 27 2 2 655 388899448 388898797 0.000000e+00 1046.0
7 TraesCS2B01G573000 chr2D 95.686 649 26 2 2 650 230097288 230096642 0.000000e+00 1042.0
8 TraesCS2B01G573000 chr2D 94.962 655 32 1 2 655 256354769 256355423 0.000000e+00 1026.0
9 TraesCS2B01G573000 chr2D 94.954 654 31 2 2 655 388953574 388952923 0.000000e+00 1024.0
10 TraesCS2B01G573000 chr2D 92.842 461 26 5 3937 4393 621557864 621557407 0.000000e+00 662.0
11 TraesCS2B01G573000 chr2D 83.540 322 49 4 651 972 621561340 621561023 9.240000e-77 298.0
12 TraesCS2B01G573000 chr2D 100.000 34 0 0 4076 4109 621557819 621557786 3.670000e-06 63.9
13 TraesCS2B01G573000 chr5A 86.492 2406 264 33 1087 3450 622783343 622780957 0.000000e+00 2586.0
14 TraesCS2B01G573000 chr5D 85.279 2398 247 39 1087 3450 498557049 498554724 0.000000e+00 2375.0
15 TraesCS2B01G573000 chr5D 95.223 649 30 1 2 650 211792965 211792318 0.000000e+00 1026.0
16 TraesCS2B01G573000 chr5B 84.228 1547 210 17 1916 3450 617834005 617832481 0.000000e+00 1474.0
17 TraesCS2B01G573000 chr5B 90.766 444 26 5 1088 1516 617836290 617835847 2.950000e-161 579.0
18 TraesCS2B01G573000 chr5B 94.907 216 11 0 1568 1783 617834318 617834103 5.440000e-89 339.0
19 TraesCS2B01G573000 chr5B 96.875 64 2 0 1513 1576 617835828 617835765 1.670000e-19 108.0
20 TraesCS2B01G573000 chr1D 95.107 654 31 1 2 655 118224859 118224207 0.000000e+00 1029.0
21 TraesCS2B01G573000 chr1D 94.954 654 32 1 2 655 355923463 355922811 0.000000e+00 1024.0
22 TraesCS2B01G573000 chr1D 78.193 321 66 4 654 972 467814124 467813806 7.450000e-48 202.0
23 TraesCS2B01G573000 chr7D 94.954 654 32 1 2 655 478389228 478389880 0.000000e+00 1024.0
24 TraesCS2B01G573000 chr4D 95.209 647 30 1 4 650 496591493 496592138 0.000000e+00 1022.0
25 TraesCS2B01G573000 chr4D 81.625 283 46 5 654 935 459065172 459064895 3.420000e-56 230.0
26 TraesCS2B01G573000 chrUn 84.272 515 62 12 3481 3978 103102092 103102604 6.610000e-133 484.0
27 TraesCS2B01G573000 chr3A 93.093 333 19 3 4062 4393 53226736 53227065 6.610000e-133 484.0
28 TraesCS2B01G573000 chr6B 83.236 513 69 10 3481 3978 64316527 64317037 5.180000e-124 455.0
29 TraesCS2B01G573000 chr6B 79.751 321 60 5 654 972 447897071 447896754 1.230000e-55 228.0
30 TraesCS2B01G573000 chr6B 78.816 321 63 5 654 972 133701681 133701364 1.240000e-50 211.0
31 TraesCS2B01G573000 chr6A 82.752 516 70 11 3481 3979 35087165 35087678 4.030000e-120 442.0
32 TraesCS2B01G573000 chr6A 79.661 295 59 1 678 972 202362906 202362613 1.240000e-50 211.0
33 TraesCS2B01G573000 chr3D 79.567 323 57 8 654 972 169793283 169792966 5.720000e-54 222.0
34 TraesCS2B01G573000 chr7A 78.438 320 65 4 654 972 695047269 695047585 5.760000e-49 206.0
35 TraesCS2B01G573000 chr3B 92.727 110 7 1 4285 4393 800670350 800670459 1.640000e-34 158.0


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 TraesCS2B01G573000 chr2B 762517542 762521934 4392 True 8113.00 8113 100.0000 1 4393 1 chr2B.!!$R2 4392
1 TraesCS2B01G573000 chr2B 762532029 762537251 5222 True 2047.50 2340 98.5975 994 3299 2 chr2B.!!$R3 2305
2 TraesCS2B01G573000 chr2D 621557407 621561340 3933 True 1073.58 3077 93.0268 651 4393 5 chr2D.!!$R4 3742
3 TraesCS2B01G573000 chr2D 388898797 388899448 651 True 1046.00 1046 95.5660 2 655 1 chr2D.!!$R2 653
4 TraesCS2B01G573000 chr2D 230096642 230097288 646 True 1042.00 1042 95.6860 2 650 1 chr2D.!!$R1 648
5 TraesCS2B01G573000 chr2D 256354769 256355423 654 False 1026.00 1026 94.9620 2 655 1 chr2D.!!$F1 653
6 TraesCS2B01G573000 chr2D 388952923 388953574 651 True 1024.00 1024 94.9540 2 655 1 chr2D.!!$R3 653
7 TraesCS2B01G573000 chr5A 622780957 622783343 2386 True 2586.00 2586 86.4920 1087 3450 1 chr5A.!!$R1 2363
8 TraesCS2B01G573000 chr5D 498554724 498557049 2325 True 2375.00 2375 85.2790 1087 3450 1 chr5D.!!$R2 2363
9 TraesCS2B01G573000 chr5D 211792318 211792965 647 True 1026.00 1026 95.2230 2 650 1 chr5D.!!$R1 648
10 TraesCS2B01G573000 chr5B 617832481 617836290 3809 True 625.00 1474 91.6940 1088 3450 4 chr5B.!!$R1 2362
11 TraesCS2B01G573000 chr1D 118224207 118224859 652 True 1029.00 1029 95.1070 2 655 1 chr1D.!!$R1 653
12 TraesCS2B01G573000 chr1D 355922811 355923463 652 True 1024.00 1024 94.9540 2 655 1 chr1D.!!$R2 653
13 TraesCS2B01G573000 chr7D 478389228 478389880 652 False 1024.00 1024 94.9540 2 655 1 chr7D.!!$F1 653
14 TraesCS2B01G573000 chr4D 496591493 496592138 645 False 1022.00 1022 95.2090 4 650 1 chr4D.!!$F1 646
15 TraesCS2B01G573000 chrUn 103102092 103102604 512 False 484.00 484 84.2720 3481 3978 1 chrUn.!!$F1 497
16 TraesCS2B01G573000 chr6B 64316527 64317037 510 False 455.00 455 83.2360 3481 3978 1 chr6B.!!$F1 497
17 TraesCS2B01G573000 chr6A 35087165 35087678 513 False 442.00 442 82.7520 3481 3979 1 chr6A.!!$F1 498

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
904 907 0.036105 TGTGTGCTATGGCTGGACTG 60.036 55.0 1.68 0.0 39.59 3.51 F
950 953 0.108898 GTGATGAGTCGCACAGCTCT 60.109 55.0 10.15 0.0 35.19 4.09 F
951 954 0.108945 TGATGAGTCGCACAGCTCTG 60.109 55.0 0.00 0.0 33.22 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2771 7599 3.164977 TGGCCCTGGAACACGACA 61.165 61.111 0.00 0.00 0.00 4.35 R
3104 7932 0.320858 TTGCGTACCCGAATTCAGCA 60.321 50.000 6.22 4.24 35.63 4.41 R
3433 8276 7.592885 AGGTACTCTGTTACAGTGTAAAAGA 57.407 36.000 27.05 27.05 40.49 2.52 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
145 147 8.104566 GTCTATCCTTAGTAGCCTCTCTTATGA 58.895 40.741 0.00 0.00 0.00 2.15
171 173 2.884320 TGTAGTCTAGTGCTTCCACCA 58.116 47.619 0.00 0.00 43.09 4.17
202 204 0.978151 TCTGCTACAGCCCGGTTTAA 59.022 50.000 0.00 0.00 41.18 1.52
448 451 2.567615 CTGTCCCTGTAAGTTAGTGCCT 59.432 50.000 0.00 0.00 0.00 4.75
519 522 6.547510 TGGATGCTAGCGACACTATCATATAT 59.452 38.462 10.77 0.00 37.73 0.86
650 653 1.481871 TAGAATCGGGGTCCTGACAC 58.518 55.000 0.00 0.00 33.73 3.67
659 662 1.134438 GGTCCTGACACCTTTCCCCT 61.134 60.000 0.00 0.00 33.08 4.79
666 669 1.303317 CACCTTTCCCCTTCACCGG 60.303 63.158 0.00 0.00 0.00 5.28
670 673 2.798148 CTTTCCCCTTCACCGGTCCG 62.798 65.000 2.59 3.60 0.00 4.79
689 692 2.577700 CGCTGGAGTATGAGTCCTACT 58.422 52.381 7.72 7.72 38.55 2.57
693 696 4.202482 GCTGGAGTATGAGTCCTACTAGGA 60.202 50.000 7.95 0.03 43.43 2.94
722 725 2.066393 CGCCATGGGAAGGAGAGGA 61.066 63.158 15.13 0.00 0.00 3.71
724 727 1.734655 GCCATGGGAAGGAGAGGATA 58.265 55.000 15.13 0.00 0.00 2.59
732 735 1.964933 GAAGGAGAGGATAAGGGTCGG 59.035 57.143 0.00 0.00 0.00 4.79
733 736 0.935194 AGGAGAGGATAAGGGTCGGT 59.065 55.000 0.00 0.00 0.00 4.69
739 742 1.446366 GATAAGGGTCGGTGAGGCC 59.554 63.158 0.00 0.00 46.15 5.19
808 811 2.742372 GCTGCCGCGAAGAAGGAA 60.742 61.111 8.23 0.00 0.00 3.36
810 813 1.079819 CTGCCGCGAAGAAGGAAGA 60.080 57.895 8.23 0.00 34.99 2.87
826 829 0.391661 AAGACATCCGCGTCTGCATT 60.392 50.000 4.92 0.00 45.56 3.56
827 830 0.807667 AGACATCCGCGTCTGCATTC 60.808 55.000 4.92 0.00 44.59 2.67
838 841 2.668457 CGTCTGCATTCTAAAGAAGCGT 59.332 45.455 0.00 0.00 37.48 5.07
864 867 4.307908 GAACACGCGCGCCTTTGT 62.308 61.111 32.58 23.81 0.00 2.83
886 889 0.526524 GAGAGCAGAATCGGACGGTG 60.527 60.000 0.00 0.00 0.00 4.94
887 890 1.215647 GAGCAGAATCGGACGGTGT 59.784 57.895 0.00 0.00 0.00 4.16
892 895 1.374252 GAATCGGACGGTGTGTGCT 60.374 57.895 0.00 0.00 36.65 4.40
898 901 1.079127 GACGGTGTGTGCTATGGCT 60.079 57.895 1.68 0.00 39.59 4.75
904 907 0.036105 TGTGTGCTATGGCTGGACTG 60.036 55.000 1.68 0.00 39.59 3.51
906 909 1.222936 GTGCTATGGCTGGACTGCT 59.777 57.895 1.68 0.00 39.59 4.24
910 913 0.529337 CTATGGCTGGACTGCTCACG 60.529 60.000 1.31 0.00 0.00 4.35
935 938 2.314549 AGAGGAGAAGGAGGACAGTGAT 59.685 50.000 0.00 0.00 0.00 3.06
937 940 2.043664 AGGAGAAGGAGGACAGTGATGA 59.956 50.000 0.00 0.00 0.00 2.92
941 944 1.468985 AGGAGGACAGTGATGAGTCG 58.531 55.000 0.00 0.00 35.63 4.18
942 945 0.179124 GGAGGACAGTGATGAGTCGC 60.179 60.000 0.00 0.00 35.63 5.19
946 949 1.344458 GACAGTGATGAGTCGCACAG 58.656 55.000 15.62 11.19 37.33 3.66
950 953 0.108898 GTGATGAGTCGCACAGCTCT 60.109 55.000 10.15 0.00 35.19 4.09
951 954 0.108945 TGATGAGTCGCACAGCTCTG 60.109 55.000 0.00 0.00 33.22 3.35
954 957 4.731612 AGTCGCACAGCTCTGGCG 62.732 66.667 19.39 19.39 45.10 5.69
959 962 2.172372 GCACAGCTCTGGCGATGAG 61.172 63.158 1.66 0.00 44.37 2.90
975 978 2.042537 AGCAGATCCGGCTCTGGA 60.043 61.111 30.87 0.00 42.42 3.86
983 1316 0.972983 TCCGGCTCTGGAGAAAGAGG 60.973 60.000 0.00 0.00 43.37 3.69
989 1322 2.387757 CTCTGGAGAAAGAGGAGGAGG 58.612 57.143 0.00 0.00 40.11 4.30
991 1324 2.107366 CTGGAGAAAGAGGAGGAGGAC 58.893 57.143 0.00 0.00 0.00 3.85
992 1325 1.433199 TGGAGAAAGAGGAGGAGGACA 59.567 52.381 0.00 0.00 0.00 4.02
994 1327 2.558800 GGAGAAAGAGGAGGAGGACAGT 60.559 54.545 0.00 0.00 0.00 3.55
996 1329 2.158234 AGAAAGAGGAGGAGGACAGTGT 60.158 50.000 0.00 0.00 0.00 3.55
998 1331 0.902516 AGAGGAGGAGGACAGTGTGC 60.903 60.000 6.68 6.68 0.00 4.57
999 1332 0.902516 GAGGAGGAGGACAGTGTGCT 60.903 60.000 18.13 18.13 36.81 4.40
1038 1382 2.483013 CCCGTTGAGTCAACTGAACTCA 60.483 50.000 28.53 1.98 41.62 3.41
1039 1383 2.540101 CCGTTGAGTCAACTGAACTCAC 59.460 50.000 28.53 5.24 41.62 3.51
1045 1389 4.811024 TGAGTCAACTGAACTCACATGAAC 59.189 41.667 0.00 0.00 35.81 3.18
2076 6895 3.817084 ACCATAATGAGCATCCAACATCG 59.183 43.478 0.00 0.00 0.00 3.84
2295 7118 5.485662 CTTTCGAACACCTCAAGAAAGTT 57.514 39.130 0.00 0.00 41.42 2.66
2572 7400 0.174845 TGCGGAGTACCATACAGCAC 59.825 55.000 0.00 0.00 33.39 4.40
2771 7599 0.395312 ACCGGAGTCGAACACCATTT 59.605 50.000 9.46 0.00 39.00 2.32
3104 7932 0.252103 AGAGGTCCATGTACCGTGGT 60.252 55.000 12.56 0.00 44.77 4.16
3433 8276 8.385898 TCGATTGTGTTGGTAATTACTCTTTT 57.614 30.769 15.05 0.00 0.00 2.27
3465 8308 1.183549 AACAGAGTACCTAGGCACCG 58.816 55.000 9.30 0.27 0.00 4.94
3472 8315 3.434309 AGTACCTAGGCACCGACTAAAA 58.566 45.455 9.30 0.00 0.00 1.52
3550 8393 2.933495 TGTGTCCGTTCGATCCTTAG 57.067 50.000 0.00 0.00 0.00 2.18
3562 8405 1.000163 GATCCTTAGGCAGCGATTCGA 60.000 52.381 10.88 0.00 0.00 3.71
3632 8488 1.248101 GCTGCCCATTAACCCGTGTT 61.248 55.000 0.00 0.00 38.52 3.32
3646 8502 0.929824 CGTGTTGCTGCCTGTTTTCG 60.930 55.000 0.00 0.00 0.00 3.46
3655 8511 2.415168 CTGCCTGTTTTCGCTTCGATTA 59.585 45.455 0.00 0.00 35.23 1.75
3747 8603 2.191641 GAGAGCATGGACAGGGGC 59.808 66.667 0.00 0.00 0.00 5.80
3778 8636 2.941720 GCGATTTCCATTCTGAGCTCTT 59.058 45.455 16.19 0.00 0.00 2.85
3780 8638 3.559242 CGATTTCCATTCTGAGCTCTTCC 59.441 47.826 16.19 0.00 0.00 3.46
3786 8644 3.451902 CCATTCTGAGCTCTTCCTCTCTT 59.548 47.826 16.19 0.00 33.02 2.85
3787 8645 4.435425 CATTCTGAGCTCTTCCTCTCTTG 58.565 47.826 16.19 0.00 33.02 3.02
3798 8656 0.795085 CCTCTCTTGTTGCTTGAGCG 59.205 55.000 0.00 0.00 45.83 5.03
3807 8665 0.814457 TTGCTTGAGCGTTTGGTTGT 59.186 45.000 0.00 0.00 45.83 3.32
3812 8670 2.270275 TGAGCGTTTGGTTGTTGTTG 57.730 45.000 0.00 0.00 0.00 3.33
3813 8671 0.920664 GAGCGTTTGGTTGTTGTTGC 59.079 50.000 0.00 0.00 0.00 4.17
3845 8703 2.087646 CCTAAAGGTGCTCTTCCAAGC 58.912 52.381 0.00 0.00 42.82 4.01
3852 8710 1.668151 GCTCTTCCAAGCGGTTCGT 60.668 57.895 0.00 0.00 31.56 3.85
3855 8713 2.618053 CTCTTCCAAGCGGTTCGTATT 58.382 47.619 0.00 0.00 0.00 1.89
3869 8727 4.153655 GGTTCGTATTTGTTGTTCTCCCTC 59.846 45.833 0.00 0.00 0.00 4.30
3871 8729 3.581332 TCGTATTTGTTGTTCTCCCTCCT 59.419 43.478 0.00 0.00 0.00 3.69
3875 8733 0.687354 TGTTGTTCTCCCTCCTCTGC 59.313 55.000 0.00 0.00 0.00 4.26
3880 8745 1.556911 GTTCTCCCTCCTCTGCATTCA 59.443 52.381 0.00 0.00 0.00 2.57
3917 8782 2.337583 TCGTGGATTTTTGAGCTCTCG 58.662 47.619 16.19 0.00 0.00 4.04
3920 8785 3.330267 GTGGATTTTTGAGCTCTCGTCT 58.670 45.455 16.19 0.00 0.00 4.18
4003 8868 9.574458 TTCTATTTCTCTGAACTTGTCTTATCG 57.426 33.333 0.00 0.00 0.00 2.92
4006 8871 7.818493 TTTCTCTGAACTTGTCTTATCGATG 57.182 36.000 8.54 0.00 0.00 3.84
4016 8881 4.820897 TGTCTTATCGATGTGCTTCTTGT 58.179 39.130 8.54 0.00 0.00 3.16
4017 8882 5.237815 TGTCTTATCGATGTGCTTCTTGTT 58.762 37.500 8.54 0.00 0.00 2.83
4029 8894 6.959361 TGTGCTTCTTGTTACTCTGAAAATC 58.041 36.000 0.00 0.00 0.00 2.17
4051 8916 1.392589 CTTCTTGCCCGCCAATACAT 58.607 50.000 0.00 0.00 31.91 2.29
4063 8928 5.221145 CCCGCCAATACATATTTTTGCAGTA 60.221 40.000 0.00 0.00 0.00 2.74
4064 8929 6.446318 CCGCCAATACATATTTTTGCAGTAT 58.554 36.000 0.00 0.00 0.00 2.12
4065 8930 6.363088 CCGCCAATACATATTTTTGCAGTATG 59.637 38.462 8.18 8.18 40.87 2.39
4183 9050 5.564651 GCAGCAGAATTTACTTGGTTTAGCA 60.565 40.000 0.00 0.00 0.00 3.49
4191 9058 8.863872 AATTTACTTGGTTTAGCAGAGTGTAT 57.136 30.769 0.00 0.00 0.00 2.29
4221 9088 8.576442 TGGGTGTACTAGTACTGTTACTTTTAC 58.424 37.037 28.56 16.26 39.43 2.01
4298 9167 5.057149 TCCTTTCTGTTTCTGTAGAAGTGC 58.943 41.667 0.00 0.00 34.68 4.40
4339 9208 4.573201 TCCTGTTTCAACAACCTTTACTCG 59.427 41.667 0.00 0.00 38.66 4.18
4345 9214 6.870971 TTCAACAACCTTTACTCGCTATTT 57.129 33.333 0.00 0.00 0.00 1.40
4349 9218 4.457949 ACAACCTTTACTCGCTATTTTGGG 59.542 41.667 0.00 0.00 0.00 4.12
4352 9221 4.941873 ACCTTTACTCGCTATTTTGGGAAG 59.058 41.667 0.00 0.00 0.00 3.46
4353 9222 4.941873 CCTTTACTCGCTATTTTGGGAAGT 59.058 41.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.081586 TGTGCAAATACAACATGGCATCAT 60.082 37.500 0.00 0.00 33.43 2.45
145 147 4.777896 TGGAAGCACTAGACTACATTTCCT 59.222 41.667 0.00 0.00 35.15 3.36
202 204 1.229082 TGGGCTAACAGGACTCCGT 60.229 57.895 0.00 0.00 0.00 4.69
355 358 0.690192 TGTAGCAACTGGGCTAGCAA 59.310 50.000 18.24 2.83 46.34 3.91
448 451 2.960384 TGACTAGTCGTGAACCCAAAGA 59.040 45.455 17.85 0.00 0.00 2.52
487 490 2.254459 GTCGCTAGCATCCATATGACG 58.746 52.381 16.45 0.00 34.84 4.35
548 551 3.167414 GGTGCCACCTTACCTGGT 58.833 61.111 6.63 4.05 41.77 4.00
566 569 2.555325 CCTCACGCACGGTATTCCTATA 59.445 50.000 0.00 0.00 0.00 1.31
617 620 3.181490 CCGATTCTAAGTCACACCGATCA 60.181 47.826 0.00 0.00 0.00 2.92
650 653 1.002502 GACCGGTGAAGGGGAAAGG 60.003 63.158 14.63 0.00 35.02 3.11
666 669 0.386113 GGACTCATACTCCAGCGGAC 59.614 60.000 0.00 0.00 0.00 4.79
670 673 4.076394 CCTAGTAGGACTCATACTCCAGC 58.924 52.174 11.09 0.00 37.67 4.85
706 709 2.641815 CCTTATCCTCTCCTTCCCATGG 59.358 54.545 4.14 4.14 0.00 3.66
708 711 2.254023 ACCCTTATCCTCTCCTTCCCAT 59.746 50.000 0.00 0.00 0.00 4.00
722 725 2.070650 GGGCCTCACCGACCCTTAT 61.071 63.158 0.84 0.00 40.75 1.73
732 735 4.803426 CAGCGAGTCGGGCCTCAC 62.803 72.222 15.52 0.00 0.00 3.51
741 744 2.279120 CCATCTCGGCAGCGAGTC 60.279 66.667 11.39 0.00 37.30 3.36
797 800 1.281899 CGGATGTCTTCCTTCTTCGC 58.718 55.000 3.45 0.00 42.99 4.70
799 802 1.281899 CGCGGATGTCTTCCTTCTTC 58.718 55.000 0.00 0.00 42.99 2.87
800 803 0.608640 ACGCGGATGTCTTCCTTCTT 59.391 50.000 12.47 0.00 42.99 2.52
801 804 0.173708 GACGCGGATGTCTTCCTTCT 59.826 55.000 12.47 0.00 42.99 2.85
802 805 0.173708 AGACGCGGATGTCTTCCTTC 59.826 55.000 12.47 0.00 46.85 3.46
803 806 0.108615 CAGACGCGGATGTCTTCCTT 60.109 55.000 12.47 0.00 46.85 3.36
810 813 0.459899 TAGAATGCAGACGCGGATGT 59.540 50.000 12.47 0.00 42.97 3.06
815 818 2.535732 GCTTCTTTAGAATGCAGACGCG 60.536 50.000 3.53 3.53 42.97 6.01
819 822 3.925379 TGACGCTTCTTTAGAATGCAGA 58.075 40.909 0.00 0.00 33.01 4.26
826 829 0.885879 TCCGCTGACGCTTCTTTAGA 59.114 50.000 0.00 0.00 38.22 2.10
827 830 1.272781 CTCCGCTGACGCTTCTTTAG 58.727 55.000 0.00 0.00 38.22 1.85
854 857 3.181967 CTCTCGGACAAAGGCGCG 61.182 66.667 0.00 0.00 0.00 6.86
881 884 1.375908 CAGCCATAGCACACACCGT 60.376 57.895 0.00 0.00 43.56 4.83
886 889 1.372087 GCAGTCCAGCCATAGCACAC 61.372 60.000 0.00 0.00 43.56 3.82
887 890 1.078214 GCAGTCCAGCCATAGCACA 60.078 57.895 0.00 0.00 43.56 4.57
892 895 1.517361 CGTGAGCAGTCCAGCCATA 59.483 57.895 0.00 0.00 34.23 2.74
906 909 1.273606 CTCCTTCTCCTCTTTGCGTGA 59.726 52.381 0.00 0.00 0.00 4.35
910 913 1.625818 TGTCCTCCTTCTCCTCTTTGC 59.374 52.381 0.00 0.00 0.00 3.68
914 917 1.713647 TCACTGTCCTCCTTCTCCTCT 59.286 52.381 0.00 0.00 0.00 3.69
915 918 2.223803 TCACTGTCCTCCTTCTCCTC 57.776 55.000 0.00 0.00 0.00 3.71
935 938 2.653115 CCAGAGCTGTGCGACTCA 59.347 61.111 5.08 0.00 35.28 3.41
937 940 4.731612 CGCCAGAGCTGTGCGACT 62.732 66.667 20.83 0.00 45.93 4.18
941 944 2.125391 TCATCGCCAGAGCTGTGC 60.125 61.111 5.08 0.19 36.60 4.57
942 945 4.105727 CTCATCGCCAGAGCTGTG 57.894 61.111 3.32 3.32 36.60 3.66
950 953 2.418777 CGGATCTGCTCATCGCCA 59.581 61.111 0.00 0.00 38.05 5.69
951 954 2.356793 CCGGATCTGCTCATCGCC 60.357 66.667 0.00 0.00 38.05 5.54
959 962 1.680522 TTCTCCAGAGCCGGATCTGC 61.681 60.000 38.30 6.47 44.47 4.26
960 963 0.826715 TTTCTCCAGAGCCGGATCTG 59.173 55.000 37.09 37.09 45.24 2.90
972 975 1.433199 TGTCCTCCTCCTCTTTCTCCA 59.567 52.381 0.00 0.00 0.00 3.86
973 976 2.107366 CTGTCCTCCTCCTCTTTCTCC 58.893 57.143 0.00 0.00 0.00 3.71
974 977 2.495669 CACTGTCCTCCTCCTCTTTCTC 59.504 54.545 0.00 0.00 0.00 2.87
975 978 2.158234 ACACTGTCCTCCTCCTCTTTCT 60.158 50.000 0.00 0.00 0.00 2.52
983 1316 1.827969 ACATAGCACACTGTCCTCCTC 59.172 52.381 0.00 0.00 0.00 3.71
989 1322 1.136252 CACGCAACATAGCACACTGTC 60.136 52.381 0.00 0.00 0.00 3.51
991 1324 0.867746 ACACGCAACATAGCACACTG 59.132 50.000 0.00 0.00 0.00 3.66
992 1325 2.448926 TACACGCAACATAGCACACT 57.551 45.000 0.00 0.00 0.00 3.55
994 1327 2.276201 GGATACACGCAACATAGCACA 58.724 47.619 0.00 0.00 0.00 4.57
996 1329 1.135333 TCGGATACACGCAACATAGCA 59.865 47.619 0.00 0.00 0.00 3.49
998 1331 2.124903 GGTCGGATACACGCAACATAG 58.875 52.381 0.00 0.00 0.00 2.23
999 1332 1.202440 GGGTCGGATACACGCAACATA 60.202 52.381 0.00 0.00 33.14 2.29
1038 1382 3.927555 AACACGATCGGGTTCATGT 57.072 47.368 29.35 15.03 37.07 3.21
1045 1389 1.790755 TCAGTTTGAACACGATCGGG 58.209 50.000 17.58 17.58 0.00 5.14
2076 6895 7.026631 TGCAATACTTATACCAAATGCTGAC 57.973 36.000 0.00 0.00 33.87 3.51
2295 7118 6.317789 GAGAATCCATTTCACAGTTGACAA 57.682 37.500 0.00 0.00 36.75 3.18
2394 7217 4.771114 AGAAATGATCCCATAACCACGA 57.229 40.909 0.00 0.00 31.59 4.35
2572 7400 3.749665 TTCCAGGCATTTTGAACTTGG 57.250 42.857 0.00 0.00 0.00 3.61
2771 7599 3.164977 TGGCCCTGGAACACGACA 61.165 61.111 0.00 0.00 0.00 4.35
3104 7932 0.320858 TTGCGTACCCGAATTCAGCA 60.321 50.000 6.22 4.24 35.63 4.41
3433 8276 7.592885 AGGTACTCTGTTACAGTGTAAAAGA 57.407 36.000 27.05 27.05 40.49 2.52
3454 8297 4.900054 AGATATTTTAGTCGGTGCCTAGGT 59.100 41.667 11.31 0.00 0.00 3.08
3550 8393 3.918220 CACGCTCGAATCGCTGCC 61.918 66.667 12.83 0.00 0.00 4.85
3632 8488 1.654220 GAAGCGAAAACAGGCAGCA 59.346 52.632 0.00 0.00 0.00 4.41
3646 8502 6.654793 ACAGAGAAGTTTCATAATCGAAGC 57.345 37.500 0.00 0.00 0.00 3.86
3655 8511 3.993081 CAGAGCGAACAGAGAAGTTTCAT 59.007 43.478 0.00 0.00 0.00 2.57
3747 8603 2.509052 TGGAAATCGCCATAGAGTCG 57.491 50.000 0.00 0.00 31.66 4.18
3778 8636 1.606480 CGCTCAAGCAACAAGAGAGGA 60.606 52.381 2.50 0.00 42.21 3.71
3780 8638 1.506493 ACGCTCAAGCAACAAGAGAG 58.494 50.000 2.50 0.00 42.21 3.20
3786 8644 0.814457 AACCAAACGCTCAAGCAACA 59.186 45.000 2.50 0.00 42.21 3.33
3787 8645 1.199624 CAACCAAACGCTCAAGCAAC 58.800 50.000 2.50 0.00 42.21 4.17
3798 8656 1.425267 GCCGGCAACAACAACCAAAC 61.425 55.000 24.80 0.00 0.00 2.93
3826 8684 1.734465 CGCTTGGAAGAGCACCTTTAG 59.266 52.381 0.00 0.00 42.83 1.85
3829 8687 1.302832 CCGCTTGGAAGAGCACCTT 60.303 57.895 0.00 0.00 42.83 3.50
3845 8703 3.120442 GGGAGAACAACAAATACGAACCG 60.120 47.826 0.00 0.00 0.00 4.44
3852 8710 4.565652 GCAGAGGAGGGAGAACAACAAATA 60.566 45.833 0.00 0.00 0.00 1.40
3855 8713 1.072331 GCAGAGGAGGGAGAACAACAA 59.928 52.381 0.00 0.00 0.00 2.83
3869 8727 7.255173 CCAAGATCTAGAAAATGAATGCAGAGG 60.255 40.741 0.00 0.00 0.00 3.69
3871 8729 7.114754 ACCAAGATCTAGAAAATGAATGCAGA 58.885 34.615 0.00 0.00 0.00 4.26
3875 8733 7.907045 CACGAACCAAGATCTAGAAAATGAATG 59.093 37.037 0.00 0.00 0.00 2.67
3880 8745 6.049955 TCCACGAACCAAGATCTAGAAAAT 57.950 37.500 0.00 0.00 0.00 1.82
3917 8782 2.043227 ACCTAGCTAGGATTGGCAGAC 58.957 52.381 40.40 0.00 46.63 3.51
3920 8785 3.115390 AGAAACCTAGCTAGGATTGGCA 58.885 45.455 40.40 0.00 46.63 4.92
4003 8868 6.545504 TTTCAGAGTAACAAGAAGCACATC 57.454 37.500 0.00 0.00 0.00 3.06
4006 8871 7.074502 CAGATTTTCAGAGTAACAAGAAGCAC 58.925 38.462 0.00 0.00 0.00 4.40
4016 8881 6.246420 GCAAGAAGCAGATTTTCAGAGTAA 57.754 37.500 0.00 0.00 44.79 2.24
4017 8882 5.869753 GCAAGAAGCAGATTTTCAGAGTA 57.130 39.130 0.00 0.00 44.79 2.59
4051 8916 6.245408 ACAGGAGAACCATACTGCAAAAATA 58.755 36.000 0.00 0.00 38.94 1.40
4063 8928 4.349342 AGTTCAGAGAAACAGGAGAACCAT 59.651 41.667 0.00 0.00 36.84 3.55
4064 8929 3.711704 AGTTCAGAGAAACAGGAGAACCA 59.288 43.478 0.00 0.00 36.84 3.67
4065 8930 4.344359 AGTTCAGAGAAACAGGAGAACC 57.656 45.455 0.00 0.00 36.84 3.62
4157 9024 5.473066 AAACCAAGTAAATTCTGCTGCAT 57.527 34.783 1.31 0.00 0.00 3.96
4183 9050 6.729428 ACTAGTACACCCAAGTATACACTCT 58.271 40.000 5.50 0.00 32.29 3.24
4191 9058 7.461749 AGTAACAGTACTAGTACACCCAAGTA 58.538 38.462 29.87 12.17 38.87 2.24
4274 9143 5.703130 GCACTTCTACAGAAACAGAAAGGAT 59.297 40.000 0.00 0.00 33.07 3.24
4277 9146 5.991328 TGCACTTCTACAGAAACAGAAAG 57.009 39.130 0.00 0.00 33.07 2.62
4298 9167 5.738909 ACAGGAACATTGGTAGATCTCTTG 58.261 41.667 0.00 0.00 0.00 3.02
4339 9208 6.096673 TGGAGAAAAACTTCCCAAAATAGC 57.903 37.500 0.00 0.00 0.00 2.97
4345 9214 4.100808 CCACATTGGAGAAAAACTTCCCAA 59.899 41.667 0.00 0.00 40.96 4.12
4349 9218 5.514274 TCACCACATTGGAGAAAAACTTC 57.486 39.130 0.00 0.00 40.96 3.01


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

AutoCloner maintained by Alex Coulton.