Multiple sequence alignment - TraesCS4B01G050300

Loading Multiple Alignment...

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 TraesCS4B01G050300 chr4B 100.000 4364 0 0 1 4364 38798114 38793751 0.000000e+00 8059
1 TraesCS4B01G050300 chr4A 95.449 3384 135 9 989 4364 577042592 577045964 0.000000e+00 5378
2 TraesCS4B01G050300 chr4A 90.228 307 22 5 3701 4001 624632164 624631860 1.140000e-105 394
3 TraesCS4B01G050300 chr4D 96.025 3296 105 10 1077 4364 26257605 26254328 0.000000e+00 5337
4 TraesCS4B01G050300 chr4D 90.545 825 69 6 1 819 498880312 498881133 0.000000e+00 1083
5 TraesCS4B01G050300 chr4D 93.590 78 5 0 866 943 26258144 26258067 2.760000e-22 117
6 TraesCS4B01G050300 chr6D 91.107 2485 189 18 1166 3640 13071317 13068855 0.000000e+00 3336
7 TraesCS4B01G050300 chr6D 90.326 827 70 7 1 821 38153223 38154045 0.000000e+00 1075
8 TraesCS4B01G050300 chr6A 90.997 2477 194 22 1239 3702 14355244 14352784 0.000000e+00 3312
9 TraesCS4B01G050300 chr6A 89.950 806 76 5 1 804 93978201 93979003 0.000000e+00 1035
10 TraesCS4B01G050300 chr2B 91.322 2397 190 14 1253 3640 784618308 784620695 0.000000e+00 3258
11 TraesCS4B01G050300 chr6B 91.433 2358 182 14 1226 3575 23651270 23653615 0.000000e+00 3217
12 TraesCS4B01G050300 chr6B 91.369 1286 94 13 2298 3575 23673029 23674305 0.000000e+00 1744
13 TraesCS4B01G050300 chr3D 89.759 830 70 11 1 821 311676926 311677749 0.000000e+00 1048
14 TraesCS4B01G050300 chr3D 89.718 817 77 7 7 819 578354483 578353670 0.000000e+00 1037
15 TraesCS4B01G050300 chr3D 89.307 823 73 10 7 821 352781455 352780640 0.000000e+00 1018
16 TraesCS4B01G050300 chr3D 88.836 833 83 7 1 827 421009203 421010031 0.000000e+00 1014
17 TraesCS4B01G050300 chr5B 88.767 819 83 6 12 824 702223012 702222197 0.000000e+00 994
18 TraesCS4B01G050300 chr5B 89.644 309 22 6 3701 4001 687161189 687161495 6.850000e-103 385
19 TraesCS4B01G050300 chr5B 86.441 295 31 6 4058 4348 687161646 687161935 9.110000e-82 315
20 TraesCS4B01G050300 chr5B 96.721 61 1 1 4000 4060 687161528 687161587 2.780000e-17 100
21 TraesCS4B01G050300 chr7A 88.875 818 76 11 7 818 712844467 712843659 0.000000e+00 992
22 TraesCS4B01G050300 chr5D 87.213 305 32 5 4061 4361 544700960 544700659 1.500000e-89 340
23 TraesCS4B01G050300 chr5D 86.039 308 20 14 3701 4001 544701406 544701115 4.240000e-80 309


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 TraesCS4B01G050300 chr4B 38793751 38798114 4363 True 8059.000000 8059 100.000000 1 4364 1 chr4B.!!$R1 4363
1 TraesCS4B01G050300 chr4A 577042592 577045964 3372 False 5378.000000 5378 95.449000 989 4364 1 chr4A.!!$F1 3375
2 TraesCS4B01G050300 chr4D 26254328 26258144 3816 True 2727.000000 5337 94.807500 866 4364 2 chr4D.!!$R1 3498
3 TraesCS4B01G050300 chr4D 498880312 498881133 821 False 1083.000000 1083 90.545000 1 819 1 chr4D.!!$F1 818
4 TraesCS4B01G050300 chr6D 13068855 13071317 2462 True 3336.000000 3336 91.107000 1166 3640 1 chr6D.!!$R1 2474
5 TraesCS4B01G050300 chr6D 38153223 38154045 822 False 1075.000000 1075 90.326000 1 821 1 chr6D.!!$F1 820
6 TraesCS4B01G050300 chr6A 14352784 14355244 2460 True 3312.000000 3312 90.997000 1239 3702 1 chr6A.!!$R1 2463
7 TraesCS4B01G050300 chr6A 93978201 93979003 802 False 1035.000000 1035 89.950000 1 804 1 chr6A.!!$F1 803
8 TraesCS4B01G050300 chr2B 784618308 784620695 2387 False 3258.000000 3258 91.322000 1253 3640 1 chr2B.!!$F1 2387
9 TraesCS4B01G050300 chr6B 23651270 23653615 2345 False 3217.000000 3217 91.433000 1226 3575 1 chr6B.!!$F1 2349
10 TraesCS4B01G050300 chr6B 23673029 23674305 1276 False 1744.000000 1744 91.369000 2298 3575 1 chr6B.!!$F2 1277
11 TraesCS4B01G050300 chr3D 311676926 311677749 823 False 1048.000000 1048 89.759000 1 821 1 chr3D.!!$F1 820
12 TraesCS4B01G050300 chr3D 578353670 578354483 813 True 1037.000000 1037 89.718000 7 819 1 chr3D.!!$R2 812
13 TraesCS4B01G050300 chr3D 352780640 352781455 815 True 1018.000000 1018 89.307000 7 821 1 chr3D.!!$R1 814
14 TraesCS4B01G050300 chr3D 421009203 421010031 828 False 1014.000000 1014 88.836000 1 827 1 chr3D.!!$F2 826
15 TraesCS4B01G050300 chr5B 702222197 702223012 815 True 994.000000 994 88.767000 12 824 1 chr5B.!!$R1 812
16 TraesCS4B01G050300 chr5B 687161189 687161935 746 False 266.666667 385 90.935333 3701 4348 3 chr5B.!!$F1 647
17 TraesCS4B01G050300 chr7A 712843659 712844467 808 True 992.000000 992 88.875000 7 818 1 chr7A.!!$R1 811
18 TraesCS4B01G050300 chr5D 544700659 544701406 747 True 324.500000 340 86.626000 3701 4361 2 chr5D.!!$R1 660

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
971 1010 0.039618 ACAATTCCGGCCACTCCAAT 59.96 50.0 2.24 0.0 34.01 3.16 F
2159 2498 0.329596 GATGACAAGGGGAAGGCTGT 59.67 55.0 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 2580 0.320073 CCCCAGCTTTGCACAATGTG 60.320 55.0 9.36 9.36 36.51 3.21 R
3788 4147 0.105593 CTACATCATCAGTGGCGGCT 59.894 55.0 11.43 0.00 0.00 5.52 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
35 36 3.321968 AGAGCATCAAAGAACCCAAAACC 59.678 43.478 0.00 0.00 37.82 3.27
37 38 3.454082 AGCATCAAAGAACCCAAAACCAA 59.546 39.130 0.00 0.00 0.00 3.67
66 67 3.451141 GTGAATTCACAAGGGTGCAAA 57.549 42.857 29.43 0.00 45.75 3.68
67 68 3.383761 GTGAATTCACAAGGGTGCAAAG 58.616 45.455 29.43 0.00 45.75 2.77
68 69 3.068024 GTGAATTCACAAGGGTGCAAAGA 59.932 43.478 29.43 0.00 45.75 2.52
70 71 1.691196 TTCACAAGGGTGCAAAGAGG 58.309 50.000 0.00 0.00 44.87 3.69
71 72 0.823356 TCACAAGGGTGCAAAGAGGC 60.823 55.000 0.00 0.00 44.87 4.70
72 73 1.108727 CACAAGGGTGCAAAGAGGCA 61.109 55.000 0.00 0.00 42.53 4.75
73 74 0.825010 ACAAGGGTGCAAAGAGGCAG 60.825 55.000 0.00 0.00 45.96 4.85
107 108 3.757270 TGAAAGAGCATTCGGGGTTTTA 58.243 40.909 0.00 0.00 31.80 1.52
133 135 4.963373 TCTAGGTTTTCCATTGTTCGTGA 58.037 39.130 0.00 0.00 43.73 4.35
253 255 6.043411 ACTTGGAGTTCTTCTACGATAATGC 58.957 40.000 0.00 0.00 0.00 3.56
305 307 4.034510 CCTAACCGCATTAGAGCTTTTCTG 59.965 45.833 6.35 0.00 42.75 3.02
308 310 4.265073 ACCGCATTAGAGCTTTTCTGAAT 58.735 39.130 0.00 0.00 36.61 2.57
341 343 4.634199 AGATTGAAAATGCAAACACCCAG 58.366 39.130 0.00 0.00 0.00 4.45
357 359 2.777692 ACCCAGTTTCAACTTCAGGAGA 59.222 45.455 7.03 0.00 37.08 3.71
392 394 0.471591 ATTGGCAAAGGGCTGGACAA 60.472 50.000 3.01 0.00 44.01 3.18
464 471 7.978975 TGTATTGCATTATTTAAGTTTGCCTCC 59.021 33.333 0.00 0.00 32.39 4.30
552 559 8.801715 TTTAGTTTGCTTCTGTGATTTGAATC 57.198 30.769 0.00 0.00 35.97 2.52
559 566 9.577110 TTGCTTCTGTGATTTGAATCATTATTC 57.423 29.630 9.42 0.00 46.17 1.75
574 581 8.709386 AATCATTATTCTGTAGTGTGAGTGTC 57.291 34.615 0.00 0.00 0.00 3.67
653 662 4.704833 GCGCAAGAGCAGACCCCA 62.705 66.667 0.30 0.00 42.27 4.96
682 691 3.302870 CGACCCGTAAAAAGGCATATTCG 60.303 47.826 0.00 0.00 0.00 3.34
773 784 2.096119 CCGTTTTCCGCGAACTGTAAAT 60.096 45.455 8.23 0.00 34.38 1.40
781 792 2.717011 CGCGAACTGTAAATGCGTTTTT 59.283 40.909 9.61 0.00 43.50 1.94
785 796 4.529446 GAACTGTAAATGCGTTTTTCGGA 58.471 39.130 9.61 0.00 45.01 4.55
827 838 5.076182 TGCTAGAGATGCTCTTACTATGCT 58.924 41.667 1.88 0.00 41.50 3.79
828 839 5.182950 TGCTAGAGATGCTCTTACTATGCTC 59.817 44.000 1.88 0.00 41.50 4.26
829 840 4.764679 AGAGATGCTCTTACTATGCTCG 57.235 45.455 0.00 0.00 37.60 5.03
830 841 4.393834 AGAGATGCTCTTACTATGCTCGA 58.606 43.478 0.00 0.00 37.60 4.04
831 842 4.824537 AGAGATGCTCTTACTATGCTCGAA 59.175 41.667 0.00 0.00 37.60 3.71
832 843 5.048782 AGAGATGCTCTTACTATGCTCGAAG 60.049 44.000 0.00 0.00 37.60 3.79
833 844 3.717400 TGCTCTTACTATGCTCGAAGG 57.283 47.619 0.00 0.00 0.00 3.46
834 845 3.024547 TGCTCTTACTATGCTCGAAGGT 58.975 45.455 0.00 0.00 0.00 3.50
835 846 3.447586 TGCTCTTACTATGCTCGAAGGTT 59.552 43.478 0.00 0.00 0.00 3.50
836 847 3.799420 GCTCTTACTATGCTCGAAGGTTG 59.201 47.826 0.00 0.00 0.00 3.77
837 848 4.678309 GCTCTTACTATGCTCGAAGGTTGT 60.678 45.833 0.00 0.00 0.00 3.32
838 849 5.401531 TCTTACTATGCTCGAAGGTTGTT 57.598 39.130 0.00 0.00 0.00 2.83
839 850 5.408356 TCTTACTATGCTCGAAGGTTGTTC 58.592 41.667 0.00 0.00 0.00 3.18
840 851 3.963428 ACTATGCTCGAAGGTTGTTCT 57.037 42.857 0.00 0.00 0.00 3.01
841 852 6.376299 TCTTACTATGCTCGAAGGTTGTTCTA 59.624 38.462 0.00 0.00 0.00 2.10
842 853 5.599999 ACTATGCTCGAAGGTTGTTCTAT 57.400 39.130 0.00 0.00 0.00 1.98
843 854 5.978814 ACTATGCTCGAAGGTTGTTCTATT 58.021 37.500 0.00 0.00 0.00 1.73
844 855 6.407202 ACTATGCTCGAAGGTTGTTCTATTT 58.593 36.000 0.00 0.00 0.00 1.40
845 856 6.879458 ACTATGCTCGAAGGTTGTTCTATTTT 59.121 34.615 0.00 0.00 0.00 1.82
846 857 6.575162 ATGCTCGAAGGTTGTTCTATTTTT 57.425 33.333 0.00 0.00 0.00 1.94
877 888 7.094463 GCATCAGGTGGATCTATTATTGAAAGG 60.094 40.741 0.00 0.00 32.57 3.11
922 933 1.985473 TATAGCCTGCAGCCCATTTG 58.015 50.000 8.66 0.00 45.47 2.32
934 945 1.978617 CCATTTGACGGCCCAGCTT 60.979 57.895 0.00 0.00 0.00 3.74
951 990 0.462047 CTTACCCAGCCGACCATCAC 60.462 60.000 0.00 0.00 0.00 3.06
967 1006 0.605319 TCACACAATTCCGGCCACTC 60.605 55.000 2.24 0.00 0.00 3.51
968 1007 1.303317 ACACAATTCCGGCCACTCC 60.303 57.895 2.24 0.00 0.00 3.85
969 1008 1.303236 CACAATTCCGGCCACTCCA 60.303 57.895 2.24 0.00 34.01 3.86
970 1009 0.893270 CACAATTCCGGCCACTCCAA 60.893 55.000 2.24 0.00 34.01 3.53
971 1010 0.039618 ACAATTCCGGCCACTCCAAT 59.960 50.000 2.24 0.00 34.01 3.16
972 1011 1.283613 ACAATTCCGGCCACTCCAATA 59.716 47.619 2.24 0.00 34.01 1.90
973 1012 2.291282 ACAATTCCGGCCACTCCAATAA 60.291 45.455 2.24 0.00 34.01 1.40
974 1013 2.757868 CAATTCCGGCCACTCCAATAAA 59.242 45.455 2.24 0.00 34.01 1.40
975 1014 2.588464 TTCCGGCCACTCCAATAAAA 57.412 45.000 2.24 0.00 34.01 1.52
976 1015 2.588464 TCCGGCCACTCCAATAAAAA 57.412 45.000 2.24 0.00 34.01 1.94
1008 1047 0.537371 CTTGACTTTGCCGTTCCCCT 60.537 55.000 0.00 0.00 0.00 4.79
1009 1048 0.821711 TTGACTTTGCCGTTCCCCTG 60.822 55.000 0.00 0.00 0.00 4.45
1066 1105 4.465446 CCCTCCTCCCGCTCCTCA 62.465 72.222 0.00 0.00 0.00 3.86
1069 1108 4.779733 TCCTCCCGCTCCTCACCC 62.780 72.222 0.00 0.00 0.00 4.61
1126 1465 2.596851 GCCTTCTGCTCCTCCACCA 61.597 63.158 0.00 0.00 36.87 4.17
1150 1489 2.202797 CCACCATCGACGGAGCAG 60.203 66.667 3.60 0.00 0.00 4.24
1242 1581 1.992277 AGATGCCTTGGAGTCGGCT 60.992 57.895 8.72 0.00 46.42 5.52
1533 1872 4.329545 ATGCTCAACCACGCCCGT 62.330 61.111 0.00 0.00 0.00 5.28
1956 2295 1.409064 GGTGATATGGAGAGTGCACGA 59.591 52.381 12.01 0.00 0.00 4.35
2048 2387 3.437049 GGATATGTTGAGGCGAATAAGGC 59.563 47.826 0.00 0.00 0.00 4.35
2146 2485 1.303236 CCGGGGCTTTGTGATGACA 60.303 57.895 0.00 0.00 0.00 3.58
2159 2498 0.329596 GATGACAAGGGGAAGGCTGT 59.670 55.000 0.00 0.00 0.00 4.40
2205 2544 2.255554 GCAGAGCGACGACTCACA 59.744 61.111 17.47 0.00 39.26 3.58
2208 2547 2.502080 GAGCGACGACTCACACCG 60.502 66.667 0.00 0.00 36.65 4.94
2241 2580 1.604278 GTGTTTCTGAGGCTTGTGTCC 59.396 52.381 0.00 0.00 0.00 4.02
2335 2674 1.327690 GGTGGATCCGAGGCAGTACA 61.328 60.000 7.39 0.00 0.00 2.90
2373 2712 0.817634 TGTGTGCAGGTGGTAAGTGC 60.818 55.000 0.00 0.00 37.73 4.40
2544 2883 2.161211 GCAGCTGATGAAGAAAGGTGTC 59.839 50.000 20.43 0.00 40.64 3.67
2999 3338 0.103937 TTGCTTGTTTCCCTTTGCCG 59.896 50.000 0.00 0.00 0.00 5.69
3033 3372 1.825622 GGAGGCACATAAGCTGGCC 60.826 63.158 0.00 0.00 39.92 5.36
3065 3404 2.224354 TGGACCGGGACTTTGAAGTTAC 60.224 50.000 6.32 0.00 39.88 2.50
3075 3414 5.820947 GGACTTTGAAGTTACCTTCTCAACA 59.179 40.000 1.45 0.00 46.07 3.33
3296 3635 1.615392 CAAGAGGGGCAAAAAGACTGG 59.385 52.381 0.00 0.00 0.00 4.00
3302 3641 0.671472 GGCAAAAAGACTGGCATGGC 60.671 55.000 13.29 13.29 39.10 4.40
3478 3823 3.437049 CCTTTCTCACGAAAACCCTGATC 59.563 47.826 0.00 0.00 38.58 2.92
3640 3989 7.249147 CAGAATTTTGTTTTGTTTTGGCATGA 58.751 30.769 0.00 0.00 0.00 3.07
3641 3990 7.916450 CAGAATTTTGTTTTGTTTTGGCATGAT 59.084 29.630 0.00 0.00 0.00 2.45
3642 3991 8.130469 AGAATTTTGTTTTGTTTTGGCATGATC 58.870 29.630 0.00 0.00 0.00 2.92
3643 3992 5.747951 TTTGTTTTGTTTTGGCATGATCC 57.252 34.783 0.00 0.00 0.00 3.36
3644 3993 4.412796 TGTTTTGTTTTGGCATGATCCA 57.587 36.364 0.00 0.00 0.00 3.41
3645 3994 4.970711 TGTTTTGTTTTGGCATGATCCAT 58.029 34.783 0.00 0.00 35.77 3.41
3646 3995 4.755629 TGTTTTGTTTTGGCATGATCCATG 59.244 37.500 0.00 2.77 43.91 3.66
3656 4005 2.364324 GCATGATCCATGATGCCAAAGT 59.636 45.455 10.77 0.00 43.81 2.66
3746 4098 9.320406 GTATCTCTTTGTTATATCTCGTCTTCG 57.680 37.037 0.00 0.00 38.55 3.79
3757 4109 5.578005 ATCTCGTCTTCGGTGAAAGATAA 57.422 39.130 0.00 0.00 37.59 1.75
3758 4110 4.982999 TCTCGTCTTCGGTGAAAGATAAG 58.017 43.478 0.00 0.00 37.59 1.73
3759 4111 4.698780 TCTCGTCTTCGGTGAAAGATAAGA 59.301 41.667 0.00 0.00 37.59 2.10
3760 4112 4.982999 TCGTCTTCGGTGAAAGATAAGAG 58.017 43.478 0.00 0.00 37.59 2.85
3761 4113 4.458295 TCGTCTTCGGTGAAAGATAAGAGT 59.542 41.667 0.00 0.00 37.59 3.24
3762 4114 4.559251 CGTCTTCGGTGAAAGATAAGAGTG 59.441 45.833 0.00 0.00 37.59 3.51
3783 4142 2.504367 GTAGCCACCATCAACACAAGT 58.496 47.619 0.00 0.00 0.00 3.16
3788 4147 3.067461 GCCACCATCAACACAAGTACAAA 59.933 43.478 0.00 0.00 0.00 2.83
3789 4148 4.792704 GCCACCATCAACACAAGTACAAAG 60.793 45.833 0.00 0.00 0.00 2.77
3790 4149 4.290155 CACCATCAACACAAGTACAAAGC 58.710 43.478 0.00 0.00 0.00 3.51
3791 4150 3.317993 ACCATCAACACAAGTACAAAGCC 59.682 43.478 0.00 0.00 0.00 4.35
3861 4224 6.423905 GCACATTATCTAACGATAGAAAGCCA 59.576 38.462 6.50 0.00 41.38 4.75
3887 4250 9.905713 ACAGCTTACAGATTTAATGAGGATAAA 57.094 29.630 0.00 0.00 0.00 1.40
4171 4634 4.096190 ACCATCAGAAGCCATATTCCTG 57.904 45.455 0.00 0.00 0.00 3.86
4224 4688 1.910722 CATGGTGCTAGCTCTGGGT 59.089 57.895 17.23 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.071952 GGGTTCTTTGATGCTCTTGACAAATA 60.072 38.462 0.00 0.00 33.01 1.40
66 67 3.517100 TCAATGTCTTCTTAGCTGCCTCT 59.483 43.478 0.00 0.00 0.00 3.69
67 68 3.866651 TCAATGTCTTCTTAGCTGCCTC 58.133 45.455 0.00 0.00 0.00 4.70
68 69 3.988976 TCAATGTCTTCTTAGCTGCCT 57.011 42.857 0.00 0.00 0.00 4.75
70 71 5.673318 GCTCTTTCAATGTCTTCTTAGCTGC 60.673 44.000 0.00 0.00 0.00 5.25
71 72 5.410746 TGCTCTTTCAATGTCTTCTTAGCTG 59.589 40.000 0.00 0.00 0.00 4.24
72 73 5.555017 TGCTCTTTCAATGTCTTCTTAGCT 58.445 37.500 0.00 0.00 0.00 3.32
73 74 5.869753 TGCTCTTTCAATGTCTTCTTAGC 57.130 39.130 0.00 0.00 0.00 3.09
107 108 5.768164 ACGAACAATGGAAAACCTAGATTGT 59.232 36.000 0.00 0.00 38.57 2.71
133 135 2.514458 ATCCCAAAAACGAGCAGGAT 57.486 45.000 0.00 0.00 0.00 3.24
305 307 7.009907 GCATTTTCAATCTCTTTGCAGGTATTC 59.990 37.037 0.00 0.00 35.16 1.75
308 310 5.243507 TGCATTTTCAATCTCTTTGCAGGTA 59.756 36.000 0.00 0.00 34.03 3.08
341 343 7.173907 TCAATGAGATTCTCCTGAAGTTGAAAC 59.826 37.037 11.12 0.00 35.44 2.78
357 359 2.429610 GCCAATGGTGCTCAATGAGATT 59.570 45.455 15.38 1.72 0.00 2.40
425 432 4.481930 TGCAATACAAAACTTGTCTCGG 57.518 40.909 0.00 0.00 44.12 4.63
552 559 7.093354 ACAGACACTCACACTACAGAATAATG 58.907 38.462 0.00 0.00 0.00 1.90
559 566 7.715265 ATAAAAACAGACACTCACACTACAG 57.285 36.000 0.00 0.00 0.00 2.74
569 576 7.063308 CACAGCACAAAAATAAAAACAGACACT 59.937 33.333 0.00 0.00 0.00 3.55
570 577 7.172757 CACAGCACAAAAATAAAAACAGACAC 58.827 34.615 0.00 0.00 0.00 3.67
574 581 6.900568 TCCACAGCACAAAAATAAAAACAG 57.099 33.333 0.00 0.00 0.00 3.16
653 662 2.874086 CCTTTTTACGGGTCGACTTTGT 59.126 45.455 16.46 13.45 0.00 2.83
682 691 6.587608 CGGACCCGTATAAAAGTATATTCACC 59.412 42.308 0.00 0.00 34.35 4.02
741 752 2.519780 AAAACGGCCTTTGCGGGA 60.520 55.556 0.00 0.00 41.75 5.14
773 784 3.652000 GCCGGTCCGAAAAACGCA 61.652 61.111 14.39 0.00 41.07 5.24
844 855 4.038271 AGATCCACCTGATGCTCAAAAA 57.962 40.909 0.00 0.00 32.41 1.94
845 856 3.726557 AGATCCACCTGATGCTCAAAA 57.273 42.857 0.00 0.00 32.41 2.44
846 857 5.378230 AATAGATCCACCTGATGCTCAAA 57.622 39.130 0.00 0.00 32.41 2.69
847 858 6.692849 ATAATAGATCCACCTGATGCTCAA 57.307 37.500 0.00 0.00 32.41 3.02
848 859 6.270695 TCAATAATAGATCCACCTGATGCTCA 59.729 38.462 0.00 0.00 32.41 4.26
849 860 6.705302 TCAATAATAGATCCACCTGATGCTC 58.295 40.000 0.00 0.00 32.41 4.26
850 861 6.692849 TCAATAATAGATCCACCTGATGCT 57.307 37.500 0.00 0.00 32.41 3.79
851 862 7.094463 CCTTTCAATAATAGATCCACCTGATGC 60.094 40.741 0.00 0.00 32.41 3.91
852 863 8.159447 TCCTTTCAATAATAGATCCACCTGATG 58.841 37.037 0.00 0.00 32.41 3.07
853 864 8.280258 TCCTTTCAATAATAGATCCACCTGAT 57.720 34.615 0.00 0.00 36.01 2.90
854 865 7.690454 TCCTTTCAATAATAGATCCACCTGA 57.310 36.000 0.00 0.00 0.00 3.86
855 866 8.752005 TTTCCTTTCAATAATAGATCCACCTG 57.248 34.615 0.00 0.00 0.00 4.00
856 867 9.768215 TTTTTCCTTTCAATAATAGATCCACCT 57.232 29.630 0.00 0.00 0.00 4.00
922 933 3.682292 CTGGGTAAGCTGGGCCGTC 62.682 68.421 0.00 0.00 0.00 4.79
934 945 1.610967 TGTGATGGTCGGCTGGGTA 60.611 57.895 0.00 0.00 0.00 3.69
943 954 0.451783 GCCGGAATTGTGTGATGGTC 59.548 55.000 5.05 0.00 0.00 4.02
951 990 0.893270 TTGGAGTGGCCGGAATTGTG 60.893 55.000 5.05 0.00 40.66 3.33
975 1014 5.418676 CAAAGTCAAGTGTGGGATGTTTTT 58.581 37.500 0.00 0.00 0.00 1.94
976 1015 4.680440 GCAAAGTCAAGTGTGGGATGTTTT 60.680 41.667 0.00 0.00 0.00 2.43
977 1016 3.181476 GCAAAGTCAAGTGTGGGATGTTT 60.181 43.478 0.00 0.00 0.00 2.83
978 1017 2.362077 GCAAAGTCAAGTGTGGGATGTT 59.638 45.455 0.00 0.00 0.00 2.71
979 1018 1.956477 GCAAAGTCAAGTGTGGGATGT 59.044 47.619 0.00 0.00 0.00 3.06
980 1019 1.270550 GGCAAAGTCAAGTGTGGGATG 59.729 52.381 0.00 0.00 0.00 3.51
981 1020 1.620822 GGCAAAGTCAAGTGTGGGAT 58.379 50.000 0.00 0.00 0.00 3.85
982 1021 0.817634 CGGCAAAGTCAAGTGTGGGA 60.818 55.000 0.00 0.00 0.00 4.37
983 1022 1.101049 ACGGCAAAGTCAAGTGTGGG 61.101 55.000 0.00 0.00 0.00 4.61
984 1023 0.738389 AACGGCAAAGTCAAGTGTGG 59.262 50.000 0.00 0.00 0.00 4.17
985 1024 1.268539 GGAACGGCAAAGTCAAGTGTG 60.269 52.381 0.00 0.00 0.00 3.82
986 1025 1.021968 GGAACGGCAAAGTCAAGTGT 58.978 50.000 0.00 0.00 0.00 3.55
987 1026 0.310854 GGGAACGGCAAAGTCAAGTG 59.689 55.000 0.00 0.00 0.00 3.16
1008 1047 3.329889 ATGGCTGCGGGAGGTTCA 61.330 61.111 0.00 0.00 0.00 3.18
1009 1048 2.825836 CATGGCTGCGGGAGGTTC 60.826 66.667 0.00 0.00 0.00 3.62
1422 1761 0.038159 CGAAGCGGAAGAACTGGAGT 60.038 55.000 0.00 0.00 0.00 3.85
1533 1872 0.614697 TGGTCTCGAGGAGGATGCAA 60.615 55.000 13.56 0.00 0.00 4.08
1956 2295 3.554752 CCGGCATTTCATCAAACACCTTT 60.555 43.478 0.00 0.00 0.00 3.11
1994 2333 9.415544 TCATGACATTATATGAGATTGAGTTCG 57.584 33.333 0.00 0.00 0.00 3.95
2010 2349 8.439172 TCAACATATCCCTTGATCATGACATTA 58.561 33.333 10.07 0.00 32.18 1.90
2048 2387 2.227036 AACCCCACTGCCTCCTCAG 61.227 63.158 0.00 0.00 39.86 3.35
2146 2485 2.234296 CCTCCACAGCCTTCCCCTT 61.234 63.158 0.00 0.00 0.00 3.95
2208 2547 3.813166 TCAGAAACACCGATTTGTCCTTC 59.187 43.478 0.00 0.00 0.00 3.46
2241 2580 0.320073 CCCCAGCTTTGCACAATGTG 60.320 55.000 9.36 9.36 36.51 3.21
2335 2674 2.105477 ACAAGCTCTCCATCAACACACT 59.895 45.455 0.00 0.00 0.00 3.55
2373 2712 1.742880 CACCTCCACAGCACCATCG 60.743 63.158 0.00 0.00 0.00 3.84
2415 2754 2.079925 CTCTTTGGGCTAAGCAGTGTC 58.920 52.381 0.00 0.00 0.00 3.67
2451 2790 3.600388 GATCACTGGATTATAAGCCGGG 58.400 50.000 27.87 18.65 45.07 5.73
2544 2883 3.187022 TGTTGAATGCAGACTTGTCATCG 59.813 43.478 3.49 0.00 0.00 3.84
2999 3338 2.716217 CCTCCATCACTTTGTCCTTCC 58.284 52.381 0.00 0.00 0.00 3.46
3033 3372 1.154301 CCGGTCCAACGCAAAATCG 60.154 57.895 0.00 0.00 0.00 3.34
3065 3404 6.093219 CAGGACTTTGTCATATGTTGAGAAGG 59.907 42.308 1.90 0.00 38.68 3.46
3075 3414 3.372025 GGGCTTCCAGGACTTTGTCATAT 60.372 47.826 0.00 0.00 33.68 1.78
3302 3641 0.109272 TCAGAAACCTCGCTACGCAG 60.109 55.000 0.00 0.00 0.00 5.18
3478 3823 6.577103 TCTCTAAGACATGGTGCAAGATTAG 58.423 40.000 0.00 0.00 0.00 1.73
3519 3866 8.988064 TTCATAAGAAGTACATCTGACTCAAC 57.012 34.615 0.54 0.00 0.00 3.18
3577 3925 7.383102 ACAGCCACTTATAAAGAATGAACTG 57.617 36.000 0.00 0.00 0.00 3.16
3579 3927 8.494016 AGTACAGCCACTTATAAAGAATGAAC 57.506 34.615 0.00 0.00 0.00 3.18
3656 4005 4.321899 GCAACAATGTGGATCAAAGCCTTA 60.322 41.667 0.00 0.00 0.00 2.69
3746 4098 4.081087 TGGCTACCACTCTTATCTTTCACC 60.081 45.833 0.00 0.00 0.00 4.02
3783 4142 0.323302 TCATCAGTGGCGGCTTTGTA 59.677 50.000 11.43 0.00 0.00 2.41
3788 4147 0.105593 CTACATCATCAGTGGCGGCT 59.894 55.000 11.43 0.00 0.00 5.52
3789 4148 1.502163 GCTACATCATCAGTGGCGGC 61.502 60.000 0.00 0.00 33.85 6.53
3790 4149 0.105593 AGCTACATCATCAGTGGCGG 59.894 55.000 0.00 0.00 46.49 6.13
3791 4150 1.215244 CAGCTACATCATCAGTGGCG 58.785 55.000 0.00 0.00 46.49 5.69
3861 4224 9.905713 TTTATCCTCATTAAATCTGTAAGCTGT 57.094 29.630 0.00 0.00 0.00 4.40
3887 4250 5.463154 AGCTATTCTCACTCCTACATTCCT 58.537 41.667 0.00 0.00 0.00 3.36
4151 4614 4.096190 ACAGGAATATGGCTTCTGATGG 57.904 45.455 0.00 0.00 0.00 3.51
4171 4634 9.638239 TGCTTCTCATGTTATAATTTTTCCAAC 57.362 29.630 0.00 0.00 0.00 3.77
4224 4688 6.738635 TCTCCAGTAATGACTCCCTTTAGTA 58.261 40.000 0.00 0.00 31.73 1.82


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

AutoCloner maintained by Alex Coulton.