Multiple sequence alignment - TraesCS4A01G237500

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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 TraesCS4A01G237500 chr4A 100.000 4304 0 0 1 4304 546299853 546295550 0.000000e+00 7949.0
1 TraesCS4A01G237500 chr4A 71.777 698 142 43 1382 2044 680451619 680452296 3.470000e-31 147.0
2 TraesCS4A01G237500 chr4D 93.503 3571 136 43 226 3760 50640515 50644025 0.000000e+00 5221.0
3 TraesCS4A01G237500 chr4D 88.750 560 38 13 3761 4304 50644056 50644606 0.000000e+00 662.0
4 TraesCS4A01G237500 chr4B 93.387 2843 140 21 945 3760 74441163 74443984 0.000000e+00 4165.0
5 TraesCS4A01G237500 chr4B 91.445 713 45 9 3601 4304 74444232 74444937 0.000000e+00 965.0
6 TraesCS4A01G237500 chr4B 92.282 298 7 5 442 735 74440585 74440870 4.010000e-110 409.0
7 TraesCS4A01G237500 chr4B 90.594 202 17 2 1 200 74440141 74440342 2.550000e-67 267.0
8 TraesCS4A01G237500 chr4B 85.973 221 7 6 742 948 74440918 74441128 9.370000e-52 215.0
9 TraesCS4A01G237500 chr4B 90.260 154 11 4 203 353 74440387 74440539 9.440000e-47 198.0
10 TraesCS4A01G237500 chr5D 76.665 1817 363 54 1103 2896 473117611 473115833 0.000000e+00 950.0
11 TraesCS4A01G237500 chr5D 74.085 710 143 34 1387 2071 326736067 326735374 1.990000e-63 254.0
12 TraesCS4A01G237500 chr5B 76.439 1842 369 57 1103 2919 580515352 580513551 0.000000e+00 937.0
13 TraesCS4A01G237500 chr5A 76.346 1746 363 45 1196 2919 593090062 593088345 0.000000e+00 891.0
14 TraesCS4A01G237500 chr6A 77.163 416 81 11 2490 2901 572572843 572572438 3.350000e-56 230.0
15 TraesCS4A01G237500 chr6B 76.167 407 83 11 2487 2889 643898439 643898835 7.300000e-48 202.0
16 TraesCS4A01G237500 chr6D 75.540 417 92 8 2487 2901 427569035 427568627 3.400000e-46 196.0
17 TraesCS4A01G237500 chr1D 83.969 131 17 3 2590 2718 366875450 366875578 5.840000e-24 122.0
18 TraesCS4A01G237500 chr7A 100.000 32 0 0 1519 1550 334332963 334332932 4.650000e-05 60.2


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 TraesCS4A01G237500 chr4A 546295550 546299853 4303 True 7949.0 7949 100.000000 1 4304 1 chr4A.!!$R1 4303
1 TraesCS4A01G237500 chr4D 50640515 50644606 4091 False 2941.5 5221 91.126500 226 4304 2 chr4D.!!$F1 4078
2 TraesCS4A01G237500 chr4B 74440141 74444937 4796 False 1036.5 4165 90.656833 1 4304 6 chr4B.!!$F1 4303
3 TraesCS4A01G237500 chr5D 473115833 473117611 1778 True 950.0 950 76.665000 1103 2896 1 chr5D.!!$R2 1793
4 TraesCS4A01G237500 chr5D 326735374 326736067 693 True 254.0 254 74.085000 1387 2071 1 chr5D.!!$R1 684
5 TraesCS4A01G237500 chr5B 580513551 580515352 1801 True 937.0 937 76.439000 1103 2919 1 chr5B.!!$R1 1816
6 TraesCS4A01G237500 chr5A 593088345 593090062 1717 True 891.0 891 76.346000 1196 2919 1 chr5A.!!$R1 1723

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
222 233 0.109226 CTCTCGGAGGAACGTTGACC 60.109 60.000 5.00 0.65 34.94 4.02 F
1002 1171 0.520404 GGTGCAGTGACAGCTGAATG 59.480 55.000 23.35 9.77 38.70 2.67 F
1007 1176 2.074576 CAGTGACAGCTGAATGGACAG 58.925 52.381 23.35 2.35 38.70 3.51 F
2868 3061 2.786495 CCTCGGCACCAGCGACTAT 61.786 63.158 0.00 0.00 43.41 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1864 2.651361 CCGAACAGGTCAGCGTCT 59.349 61.111 0.0 0.0 34.51 4.18 R
2868 3061 2.280797 GCGCACAGGAAGTCCACA 60.281 61.111 0.3 0.0 38.89 4.17 R
3279 3472 0.594602 TCCACGTTATCGCTATCGGG 59.405 55.000 2.3 0.0 41.18 5.14 R
4161 4798 0.710017 CATTTTTCTCGCTTTGCCGC 59.290 50.000 0.0 0.0 0.00 6.53 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
52 54 2.107366 TGATTCTCTGGTACGCATGGA 58.893 47.619 0.00 0.00 0.00 3.41
135 138 8.230486 GCATGACAAATATACCAGTTATAGCAC 58.770 37.037 0.00 0.00 0.00 4.40
136 139 9.271828 CATGACAAATATACCAGTTATAGCACA 57.728 33.333 0.00 0.00 0.00 4.57
149 152 7.226720 CCAGTTATAGCACAATAATTTCCGAGT 59.773 37.037 0.00 0.00 0.00 4.18
156 159 4.000988 ACAATAATTTCCGAGTGTTCGCT 58.999 39.130 0.00 0.00 45.38 4.93
185 188 4.519350 CAGTTTTTAGAGGAAACACTCCCC 59.481 45.833 3.01 0.00 46.81 4.81
189 192 1.196012 AGAGGAAACACTCCCCGATC 58.804 55.000 0.00 0.00 46.81 3.69
222 233 0.109226 CTCTCGGAGGAACGTTGACC 60.109 60.000 5.00 0.65 34.94 4.02
223 234 1.080025 CTCGGAGGAACGTTGACCC 60.080 63.158 5.00 0.00 34.94 4.46
224 235 2.431942 CGGAGGAACGTTGACCCG 60.432 66.667 5.00 11.41 0.00 5.28
292 339 3.242059 CCGAAACAGCAGCAAAAACAAAG 60.242 43.478 0.00 0.00 0.00 2.77
296 343 1.138661 CAGCAGCAAAAACAAAGGGGA 59.861 47.619 0.00 0.00 0.00 4.81
348 395 3.055675 ACATGGATCCTCCGTCGTTTTAA 60.056 43.478 14.23 0.00 40.17 1.52
392 439 0.531090 CCGCCGTCCATAATCCGAAA 60.531 55.000 0.00 0.00 0.00 3.46
402 449 7.063074 CCGTCCATAATCCGAAAAGATACATAC 59.937 40.741 0.00 0.00 0.00 2.39
403 450 7.813148 CGTCCATAATCCGAAAAGATACATACT 59.187 37.037 0.00 0.00 0.00 2.12
404 451 9.141400 GTCCATAATCCGAAAAGATACATACTC 57.859 37.037 0.00 0.00 0.00 2.59
405 452 9.090103 TCCATAATCCGAAAAGATACATACTCT 57.910 33.333 0.00 0.00 0.00 3.24
406 453 9.712305 CCATAATCCGAAAAGATACATACTCTT 57.288 33.333 0.00 0.00 34.46 2.85
640 697 1.937191 AACAAATCCATGTGACCCCC 58.063 50.000 0.00 0.00 32.81 5.40
650 707 2.926242 TGACCCCCTTCGTCCCAC 60.926 66.667 0.00 0.00 0.00 4.61
651 708 3.714001 GACCCCCTTCGTCCCACC 61.714 72.222 0.00 0.00 0.00 4.61
654 711 3.400054 CCCCTTCGTCCCACCCTC 61.400 72.222 0.00 0.00 0.00 4.30
655 712 3.400054 CCCTTCGTCCCACCCTCC 61.400 72.222 0.00 0.00 0.00 4.30
656 713 3.400054 CCTTCGTCCCACCCTCCC 61.400 72.222 0.00 0.00 0.00 4.30
657 714 2.284699 CTTCGTCCCACCCTCCCT 60.285 66.667 0.00 0.00 0.00 4.20
740 801 4.422073 TCACTCACACTCACCATCTTTT 57.578 40.909 0.00 0.00 0.00 2.27
747 865 6.822442 TCACACTCACCATCTTTTACACTTA 58.178 36.000 0.00 0.00 0.00 2.24
782 900 4.396790 TCACTTAACCACACACAAACTTCC 59.603 41.667 0.00 0.00 0.00 3.46
799 917 3.767131 ACTTCCTCTCCTCTTCTTGTAGC 59.233 47.826 0.00 0.00 0.00 3.58
802 933 2.159310 CCTCTCCTCTTCTTGTAGCACG 60.159 54.545 0.00 0.00 0.00 5.34
803 934 1.202582 TCTCCTCTTCTTGTAGCACGC 59.797 52.381 0.00 0.00 0.00 5.34
823 954 2.494059 CACCAACTGTCCATCTTTCGT 58.506 47.619 0.00 0.00 0.00 3.85
824 955 2.480419 CACCAACTGTCCATCTTTCGTC 59.520 50.000 0.00 0.00 0.00 4.20
825 956 2.104111 ACCAACTGTCCATCTTTCGTCA 59.896 45.455 0.00 0.00 0.00 4.35
826 957 2.480419 CCAACTGTCCATCTTTCGTCAC 59.520 50.000 0.00 0.00 0.00 3.67
827 958 3.130633 CAACTGTCCATCTTTCGTCACA 58.869 45.455 0.00 0.00 0.00 3.58
828 959 2.755650 ACTGTCCATCTTTCGTCACAC 58.244 47.619 0.00 0.00 0.00 3.82
829 960 2.365617 ACTGTCCATCTTTCGTCACACT 59.634 45.455 0.00 0.00 0.00 3.55
830 961 2.989840 CTGTCCATCTTTCGTCACACTC 59.010 50.000 0.00 0.00 0.00 3.51
831 962 2.628178 TGTCCATCTTTCGTCACACTCT 59.372 45.455 0.00 0.00 0.00 3.24
832 963 3.069586 TGTCCATCTTTCGTCACACTCTT 59.930 43.478 0.00 0.00 0.00 2.85
833 964 3.675698 GTCCATCTTTCGTCACACTCTTC 59.324 47.826 0.00 0.00 0.00 2.87
864 995 9.499479 CAATCATGTCTTAATCAGTAAGGCTAT 57.501 33.333 0.00 0.00 43.67 2.97
867 998 6.085555 TGTCTTAATCAGTAAGGCTATCGG 57.914 41.667 0.00 0.00 43.67 4.18
869 1000 5.010820 GTCTTAATCAGTAAGGCTATCGGGT 59.989 44.000 0.00 0.00 40.67 5.28
870 1001 3.753294 AATCAGTAAGGCTATCGGGTG 57.247 47.619 0.00 0.00 0.00 4.61
871 1002 2.154567 TCAGTAAGGCTATCGGGTGT 57.845 50.000 0.00 0.00 0.00 4.16
872 1003 3.301794 TCAGTAAGGCTATCGGGTGTA 57.698 47.619 0.00 0.00 0.00 2.90
873 1004 3.840991 TCAGTAAGGCTATCGGGTGTAT 58.159 45.455 0.00 0.00 0.00 2.29
874 1005 4.989277 TCAGTAAGGCTATCGGGTGTATA 58.011 43.478 0.00 0.00 0.00 1.47
875 1006 5.577100 TCAGTAAGGCTATCGGGTGTATAT 58.423 41.667 0.00 0.00 0.00 0.86
951 1082 2.572149 TAACACTACCACGGCGGCA 61.572 57.895 13.24 0.00 39.03 5.69
969 1138 4.547532 CGGCACCGGATATATATAGCTTC 58.452 47.826 9.46 0.00 35.56 3.86
974 1143 4.643334 ACCGGATATATATAGCTTCACGCA 59.357 41.667 9.46 0.00 42.61 5.24
999 1168 2.029518 CGGTGCAGTGACAGCTGA 59.970 61.111 23.35 0.00 38.70 4.26
1000 1169 1.595109 CGGTGCAGTGACAGCTGAA 60.595 57.895 23.35 5.08 38.70 3.02
1001 1170 0.952497 CGGTGCAGTGACAGCTGAAT 60.952 55.000 23.35 0.00 38.70 2.57
1002 1171 0.520404 GGTGCAGTGACAGCTGAATG 59.480 55.000 23.35 9.77 38.70 2.67
1003 1172 0.520404 GTGCAGTGACAGCTGAATGG 59.480 55.000 23.35 6.75 38.70 3.16
1007 1176 2.074576 CAGTGACAGCTGAATGGACAG 58.925 52.381 23.35 2.35 38.70 3.51
2436 2629 3.785189 GACACAGGTGGACGTGCGT 62.785 63.158 1.60 0.00 36.57 5.24
2868 3061 2.786495 CCTCGGCACCAGCGACTAT 61.786 63.158 0.00 0.00 43.41 2.12
3425 3618 3.506398 GAGGGAAGGGTGAAAATTTGGA 58.494 45.455 0.00 0.00 0.00 3.53
3426 3619 3.239449 AGGGAAGGGTGAAAATTTGGAC 58.761 45.455 0.00 0.00 0.00 4.02
3427 3620 2.969262 GGGAAGGGTGAAAATTTGGACA 59.031 45.455 0.00 0.00 0.00 4.02
3429 3622 4.041567 GGGAAGGGTGAAAATTTGGACATT 59.958 41.667 0.00 0.00 0.00 2.71
3430 3623 5.456042 GGGAAGGGTGAAAATTTGGACATTT 60.456 40.000 0.00 0.00 0.00 2.32
3455 3648 8.267620 TGGTGGTATCTCTCAAATATCTCAAT 57.732 34.615 0.00 0.00 0.00 2.57
3527 3723 3.634504 TGGTGATGATGGAAAGGGATTG 58.365 45.455 0.00 0.00 0.00 2.67
3530 3726 2.586838 TGATGATGGAAAGGGATTGGGT 59.413 45.455 0.00 0.00 0.00 4.51
3531 3727 2.530460 TGATGGAAAGGGATTGGGTG 57.470 50.000 0.00 0.00 0.00 4.61
3532 3728 1.999295 TGATGGAAAGGGATTGGGTGA 59.001 47.619 0.00 0.00 0.00 4.02
3533 3729 2.586838 TGATGGAAAGGGATTGGGTGAT 59.413 45.455 0.00 0.00 0.00 3.06
3534 3730 2.530460 TGGAAAGGGATTGGGTGATG 57.470 50.000 0.00 0.00 0.00 3.07
3537 3733 0.325577 AAAGGGATTGGGTGATGGGC 60.326 55.000 0.00 0.00 0.00 5.36
3561 3774 7.201582 GGCATTGCTTTCTTGGAATCAAATTAG 60.202 37.037 8.82 0.00 31.77 1.73
3578 3791 3.703001 TTAGCAGTCTTGGCTAGCTTT 57.297 42.857 15.72 0.00 44.03 3.51
3596 3816 2.891191 TTGGGTAGTTGGATTGGGTC 57.109 50.000 0.00 0.00 0.00 4.46
3610 4237 1.279496 TGGGTCCTGAGTTGGATCAG 58.721 55.000 0.00 0.00 45.24 2.90
3683 4310 5.645497 GGGGATGTATCATTAGTCAGCAATC 59.355 44.000 0.00 0.00 0.00 2.67
3699 4326 6.374333 GTCAGCAATCTTCCCTGTAAAATGTA 59.626 38.462 0.00 0.00 0.00 2.29
3773 4400 0.595588 TAAATGTGGTTGGTGCTGCG 59.404 50.000 0.00 0.00 0.00 5.18
3818 4445 2.101249 ACACTTGGAACTTGTGGCATTG 59.899 45.455 0.00 0.00 36.81 2.82
3820 4447 2.362077 ACTTGGAACTTGTGGCATTGAC 59.638 45.455 0.00 0.00 0.00 3.18
3824 4451 2.365293 GGAACTTGTGGCATTGACCTTT 59.635 45.455 0.00 0.00 0.00 3.11
3902 4529 5.527582 CCCTAATCACTGTGCTTTATACCAC 59.472 44.000 2.12 0.00 0.00 4.16
3938 4565 0.179097 GGTAAAGAGAGGCAGGAGCG 60.179 60.000 0.00 0.00 43.41 5.03
3968 4595 2.362077 CAGGGAGGGTGTGAAAGTTTTG 59.638 50.000 0.00 0.00 0.00 2.44
3969 4596 2.243736 AGGGAGGGTGTGAAAGTTTTGA 59.756 45.455 0.00 0.00 0.00 2.69
3970 4597 3.028130 GGGAGGGTGTGAAAGTTTTGAA 58.972 45.455 0.00 0.00 0.00 2.69
3971 4598 3.449377 GGGAGGGTGTGAAAGTTTTGAAA 59.551 43.478 0.00 0.00 0.00 2.69
3972 4599 4.081365 GGGAGGGTGTGAAAGTTTTGAAAA 60.081 41.667 0.00 0.00 0.00 2.29
4089 4717 3.372206 CCTGTCACTCGCTTTGATAAAGG 59.628 47.826 3.76 0.00 38.93 3.11
4090 4718 3.997021 CTGTCACTCGCTTTGATAAAGGT 59.003 43.478 3.76 0.00 38.93 3.50
4094 4722 4.690748 TCACTCGCTTTGATAAAGGTTGAG 59.309 41.667 3.76 0.00 38.93 3.02
4138 4767 4.094294 GTGACATCTGCCGCTTAACAATAA 59.906 41.667 0.00 0.00 0.00 1.40
4139 4768 4.881273 TGACATCTGCCGCTTAACAATAAT 59.119 37.500 0.00 0.00 0.00 1.28
4140 4769 6.018262 GTGACATCTGCCGCTTAACAATAATA 60.018 38.462 0.00 0.00 0.00 0.98
4141 4770 6.202762 TGACATCTGCCGCTTAACAATAATAG 59.797 38.462 0.00 0.00 0.00 1.73
4142 4771 6.288294 ACATCTGCCGCTTAACAATAATAGA 58.712 36.000 0.00 0.00 0.00 1.98
4144 4773 5.914033 TCTGCCGCTTAACAATAATAGAGT 58.086 37.500 0.00 0.00 0.00 3.24
4146 4775 4.814234 TGCCGCTTAACAATAATAGAGTGG 59.186 41.667 0.00 0.00 37.73 4.00
4147 4776 4.213482 GCCGCTTAACAATAATAGAGTGGG 59.787 45.833 0.00 0.00 35.79 4.61
4148 4777 5.607477 CCGCTTAACAATAATAGAGTGGGA 58.393 41.667 0.00 0.00 32.57 4.37
4161 4798 9.813826 ATAATAGAGTGGGAAATTAAAGATGGG 57.186 33.333 0.00 0.00 0.00 4.00
4171 4808 1.653094 TAAAGATGGGCGGCAAAGCG 61.653 55.000 12.47 0.00 38.18 4.68
4175 4812 3.918253 ATGGGCGGCAAAGCGAGAA 62.918 57.895 12.47 0.00 38.18 2.87
4187 4824 4.380974 GCAAAGCGAGAAAAATGTCTCTTG 59.619 41.667 0.00 0.00 41.69 3.02
4190 4827 2.226437 GCGAGAAAAATGTCTCTTGGCA 59.774 45.455 0.00 0.00 41.69 4.92
4258 4901 2.160417 GCAAGTCTGTGTGTCTATTGCC 59.840 50.000 0.00 0.00 36.45 4.52
4276 4919 2.305009 GCCTGCCTTCTAGAAATGCAT 58.695 47.619 22.61 0.00 30.90 3.96
4296 4939 1.000843 TCTCGTGTGTGGATGTTGAGG 59.999 52.381 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 3.627395 TTTCCATGCGTACCAGAGAAT 57.373 42.857 0.00 0.00 0.00 2.40
109 112 8.230486 GTGCTATAACTGGTATATTTGTCATGC 58.770 37.037 0.00 0.00 0.00 4.06
125 128 7.769044 ACACTCGGAAATTATTGTGCTATAACT 59.231 33.333 0.00 0.00 0.00 2.24
135 138 4.600012 AGCGAACACTCGGAAATTATTG 57.400 40.909 0.00 0.00 45.55 1.90
136 139 4.809426 CCTAGCGAACACTCGGAAATTATT 59.191 41.667 0.00 0.00 45.55 1.40
144 147 1.226717 GCTCCTAGCGAACACTCGG 60.227 63.158 0.00 0.00 45.55 4.63
145 148 0.524392 CTGCTCCTAGCGAACACTCG 60.524 60.000 0.00 0.00 46.26 4.18
149 152 2.543777 AAAACTGCTCCTAGCGAACA 57.456 45.000 0.00 0.00 46.26 3.18
156 159 5.995897 GTGTTTCCTCTAAAAACTGCTCCTA 59.004 40.000 0.00 0.00 37.48 2.94
185 188 2.158959 GGCTCGAACGGTGTGATCG 61.159 63.158 0.00 0.00 43.51 3.69
189 192 1.444553 GAGAGGCTCGAACGGTGTG 60.445 63.158 9.22 0.00 0.00 3.82
215 226 2.473457 CCCCAATAACGGGTCAACG 58.527 57.895 0.00 0.00 45.80 4.10
222 233 5.009811 TGTTTCTTTAACACCCCAATAACGG 59.990 40.000 0.00 0.00 41.73 4.44
223 234 6.074544 TGTTTCTTTAACACCCCAATAACG 57.925 37.500 0.00 0.00 41.73 3.18
292 339 4.160329 ACATTCCCTTCTTCTTTTTCCCC 58.840 43.478 0.00 0.00 0.00 4.81
296 343 6.127451 ACGTGAAACATTCCCTTCTTCTTTTT 60.127 34.615 0.00 0.00 35.74 1.94
353 400 2.537625 GGATTCTGATTCTTGAGCGACG 59.462 50.000 0.00 0.00 0.00 5.12
361 408 1.473434 GGACGGCGGATTCTGATTCTT 60.473 52.381 13.24 0.00 0.00 2.52
402 449 4.276678 TGTCCGTCCCGTATTATGTAAGAG 59.723 45.833 0.00 0.00 0.00 2.85
403 450 4.206375 TGTCCGTCCCGTATTATGTAAGA 58.794 43.478 0.00 0.00 0.00 2.10
404 451 4.276678 TCTGTCCGTCCCGTATTATGTAAG 59.723 45.833 0.00 0.00 0.00 2.34
405 452 4.206375 TCTGTCCGTCCCGTATTATGTAA 58.794 43.478 0.00 0.00 0.00 2.41
406 453 3.817084 CTCTGTCCGTCCCGTATTATGTA 59.183 47.826 0.00 0.00 0.00 2.29
407 454 2.621998 CTCTGTCCGTCCCGTATTATGT 59.378 50.000 0.00 0.00 0.00 2.29
410 457 2.292267 GACTCTGTCCGTCCCGTATTA 58.708 52.381 0.00 0.00 0.00 0.98
444 491 3.518590 GCTGTCGGCTAAGTTTTAGCTA 58.481 45.455 17.43 0.00 40.25 3.32
449 496 0.034337 TCGGCTGTCGGCTAAGTTTT 59.966 50.000 0.30 0.00 41.46 2.43
514 561 0.386476 TTCAGTGTACGCGAGGTTGT 59.614 50.000 15.93 0.00 0.00 3.32
557 604 3.850098 CTGTGTCTTTGCCGGGCCT 62.850 63.158 17.97 0.00 0.00 5.19
560 607 2.672996 CCCTGTGTCTTTGCCGGG 60.673 66.667 2.18 0.00 0.00 5.73
640 697 2.284699 AGGGAGGGTGGGACGAAG 60.285 66.667 0.00 0.00 0.00 3.79
650 707 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
651 708 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
652 709 4.548513 CGGGAGGGAGGGAGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
740 801 4.286032 AGTGATTGCTTGAGGGTAAGTGTA 59.714 41.667 0.00 0.00 0.00 2.90
747 865 3.181434 TGGTTAAGTGATTGCTTGAGGGT 60.181 43.478 0.00 0.00 0.00 4.34
782 900 2.733858 GCGTGCTACAAGAAGAGGAGAG 60.734 54.545 0.00 0.00 0.00 3.20
799 917 0.603707 AGATGGACAGTTGGTGCGTG 60.604 55.000 0.00 0.00 41.41 5.34
802 933 1.197721 CGAAAGATGGACAGTTGGTGC 59.802 52.381 0.00 0.00 38.51 5.01
803 934 2.480419 GACGAAAGATGGACAGTTGGTG 59.520 50.000 0.00 0.00 0.00 4.17
823 954 4.042062 ACATGATTGGAAGGAAGAGTGTGA 59.958 41.667 0.00 0.00 0.00 3.58
824 955 4.330250 ACATGATTGGAAGGAAGAGTGTG 58.670 43.478 0.00 0.00 0.00 3.82
825 956 4.288105 AGACATGATTGGAAGGAAGAGTGT 59.712 41.667 0.00 0.00 0.00 3.55
826 957 4.841422 AGACATGATTGGAAGGAAGAGTG 58.159 43.478 0.00 0.00 0.00 3.51
827 958 5.511386 AAGACATGATTGGAAGGAAGAGT 57.489 39.130 0.00 0.00 0.00 3.24
828 959 7.772292 TGATTAAGACATGATTGGAAGGAAGAG 59.228 37.037 0.00 0.00 0.00 2.85
829 960 7.632861 TGATTAAGACATGATTGGAAGGAAGA 58.367 34.615 0.00 0.00 0.00 2.87
830 961 7.555554 ACTGATTAAGACATGATTGGAAGGAAG 59.444 37.037 0.00 0.00 0.00 3.46
831 962 7.405292 ACTGATTAAGACATGATTGGAAGGAA 58.595 34.615 0.00 0.00 0.00 3.36
832 963 6.962182 ACTGATTAAGACATGATTGGAAGGA 58.038 36.000 0.00 0.00 0.00 3.36
833 964 8.737168 TTACTGATTAAGACATGATTGGAAGG 57.263 34.615 0.00 0.00 0.00 3.46
873 1004 9.123902 ACAAGGACGCGTGGTTATATATATATA 57.876 33.333 20.70 8.16 0.00 0.86
874 1005 8.004087 ACAAGGACGCGTGGTTATATATATAT 57.996 34.615 20.70 10.10 0.00 0.86
875 1006 7.395190 ACAAGGACGCGTGGTTATATATATA 57.605 36.000 20.70 0.00 0.00 0.86
915 1046 0.376152 TACGACGAAGCTTAGCGAGG 59.624 55.000 22.39 12.79 0.00 4.63
951 1082 5.184340 GCGTGAAGCTATATATATCCGGT 57.816 43.478 0.00 0.00 44.04 5.28
999 1168 2.158652 CCTCATCAGCATCCTGTCCATT 60.159 50.000 0.00 0.00 40.09 3.16
1000 1169 1.420514 CCTCATCAGCATCCTGTCCAT 59.579 52.381 0.00 0.00 40.09 3.41
1001 1170 0.835276 CCTCATCAGCATCCTGTCCA 59.165 55.000 0.00 0.00 40.09 4.02
1002 1171 0.534652 GCCTCATCAGCATCCTGTCC 60.535 60.000 0.00 0.00 40.09 4.02
1003 1172 0.469070 AGCCTCATCAGCATCCTGTC 59.531 55.000 0.00 0.00 40.09 3.51
1007 1176 1.148723 AGCAGCCTCATCAGCATCC 59.851 57.895 0.00 0.00 0.00 3.51
1177 1361 2.874648 TACAGCATCTTGGCAGCCGG 62.875 60.000 7.03 0.00 35.83 6.13
1671 1864 2.651361 CCGAACAGGTCAGCGTCT 59.349 61.111 0.00 0.00 34.51 4.18
1848 2041 4.170062 CGCGAGTAGTCGGCGGAA 62.170 66.667 20.94 0.00 46.91 4.30
2332 2525 2.593436 CTTTTCACCCACGCCGGT 60.593 61.111 1.90 0.00 36.18 5.28
2556 2749 4.021925 GCGAGACCAGTTGGCCCT 62.022 66.667 0.00 0.00 39.32 5.19
2868 3061 2.280797 GCGCACAGGAAGTCCACA 60.281 61.111 0.30 0.00 38.89 4.17
3279 3472 0.594602 TCCACGTTATCGCTATCGGG 59.405 55.000 2.30 0.00 41.18 5.14
3425 3618 8.497745 AGATATTTGAGAGATACCACCAAATGT 58.502 33.333 0.00 0.00 37.79 2.71
3426 3619 8.915057 AGATATTTGAGAGATACCACCAAATG 57.085 34.615 0.00 0.00 37.79 2.32
3427 3620 8.717717 TGAGATATTTGAGAGATACCACCAAAT 58.282 33.333 0.00 0.00 39.71 2.32
3429 3622 7.675161 TGAGATATTTGAGAGATACCACCAA 57.325 36.000 0.00 0.00 0.00 3.67
3430 3623 7.675161 TTGAGATATTTGAGAGATACCACCA 57.325 36.000 0.00 0.00 0.00 4.17
3455 3648 3.448093 TGATTGGGCCTTATTGACACA 57.552 42.857 4.53 0.00 0.00 3.72
3527 3723 0.176449 GAAAGCAATGCCCATCACCC 59.824 55.000 0.00 0.00 0.00 4.61
3530 3726 1.551430 CCAAGAAAGCAATGCCCATCA 59.449 47.619 0.00 0.00 0.00 3.07
3531 3727 1.826720 TCCAAGAAAGCAATGCCCATC 59.173 47.619 0.00 0.00 0.00 3.51
3532 3728 1.941377 TCCAAGAAAGCAATGCCCAT 58.059 45.000 0.00 0.00 0.00 4.00
3533 3729 1.714541 TTCCAAGAAAGCAATGCCCA 58.285 45.000 0.00 0.00 0.00 5.36
3534 3730 2.234414 TGATTCCAAGAAAGCAATGCCC 59.766 45.455 0.00 0.00 0.00 5.36
3537 3733 7.332430 TGCTAATTTGATTCCAAGAAAGCAATG 59.668 33.333 0.00 0.00 38.11 2.82
3561 3774 0.807496 CCAAAGCTAGCCAAGACTGC 59.193 55.000 12.13 0.00 0.00 4.40
3596 3816 2.995283 TGCAATCTGATCCAACTCAGG 58.005 47.619 1.58 0.00 42.42 3.86
3597 3817 4.008330 AGTTGCAATCTGATCCAACTCAG 58.992 43.478 21.30 0.00 42.94 3.35
3598 3818 4.025040 AGTTGCAATCTGATCCAACTCA 57.975 40.909 21.30 1.98 42.94 3.41
3599 3819 5.159209 CAAAGTTGCAATCTGATCCAACTC 58.841 41.667 24.47 8.96 44.97 3.01
3617 4244 2.024414 GTGGAACTGTCCTTGCAAAGT 58.976 47.619 0.00 0.00 44.25 2.66
3645 4272 2.308570 ACATCCCCTACAAGTTGCATCA 59.691 45.455 1.81 0.00 0.00 3.07
3647 4274 4.165950 TGATACATCCCCTACAAGTTGCAT 59.834 41.667 1.81 0.00 0.00 3.96
3683 4310 4.828829 AGACGGTACATTTTACAGGGAAG 58.171 43.478 0.00 0.00 0.00 3.46
3699 4326 6.954232 TGGAGGAAAGAATAATTTAGACGGT 58.046 36.000 0.00 0.00 0.00 4.83
3744 4371 8.374743 AGCACCAACCACATTTATCTTAAAAAT 58.625 29.630 0.00 0.00 0.00 1.82
3746 4373 7.151308 CAGCACCAACCACATTTATCTTAAAA 58.849 34.615 0.00 0.00 0.00 1.52
3773 4400 2.685388 GGAGCTCAAACTATGCTTTCCC 59.315 50.000 17.19 0.00 37.16 3.97
3818 4445 8.496751 GCCGTCTAATATAGAAATGAAAAGGTC 58.503 37.037 0.00 0.00 36.40 3.85
3820 4447 8.378172 TGCCGTCTAATATAGAAATGAAAAGG 57.622 34.615 0.00 0.00 36.40 3.11
3842 4469 3.689347 TGTAGGATCCATGCATAATGCC 58.311 45.455 15.82 0.00 44.23 4.40
3902 4529 7.384115 TCTCTTTACCTTACACATCTTGTTTCG 59.616 37.037 0.00 0.00 39.91 3.46
3968 4595 7.700322 ATTCGCCTTCTTTTCTTTTCTTTTC 57.300 32.000 0.00 0.00 0.00 2.29
3969 4596 9.594478 TTTATTCGCCTTCTTTTCTTTTCTTTT 57.406 25.926 0.00 0.00 0.00 2.27
3970 4597 9.249457 CTTTATTCGCCTTCTTTTCTTTTCTTT 57.751 29.630 0.00 0.00 0.00 2.52
3971 4598 7.867909 CCTTTATTCGCCTTCTTTTCTTTTCTT 59.132 33.333 0.00 0.00 0.00 2.52
3972 4599 7.371159 CCTTTATTCGCCTTCTTTTCTTTTCT 58.629 34.615 0.00 0.00 0.00 2.52
4053 4680 5.220989 CGAGTGACAGGTCTAAATAATCCGA 60.221 44.000 0.65 0.00 0.00 4.55
4056 4683 5.593010 AGCGAGTGACAGGTCTAAATAATC 58.407 41.667 0.65 0.00 0.00 1.75
4089 4717 3.516615 ACGCTCTAGCTTTCATCTCAAC 58.483 45.455 0.00 0.00 39.32 3.18
4090 4718 3.429547 GGACGCTCTAGCTTTCATCTCAA 60.430 47.826 0.00 0.00 39.32 3.02
4094 4722 1.539280 GGGGACGCTCTAGCTTTCATC 60.539 57.143 0.00 0.00 39.32 2.92
4138 4767 6.071320 GCCCATCTTTAATTTCCCACTCTAT 58.929 40.000 0.00 0.00 0.00 1.98
4139 4768 5.445964 GCCCATCTTTAATTTCCCACTCTA 58.554 41.667 0.00 0.00 0.00 2.43
4140 4769 4.281657 GCCCATCTTTAATTTCCCACTCT 58.718 43.478 0.00 0.00 0.00 3.24
4141 4770 3.066760 CGCCCATCTTTAATTTCCCACTC 59.933 47.826 0.00 0.00 0.00 3.51
4142 4771 3.023832 CGCCCATCTTTAATTTCCCACT 58.976 45.455 0.00 0.00 0.00 4.00
4144 4773 2.383855 CCGCCCATCTTTAATTTCCCA 58.616 47.619 0.00 0.00 0.00 4.37
4146 4775 1.754226 TGCCGCCCATCTTTAATTTCC 59.246 47.619 0.00 0.00 0.00 3.13
4147 4776 3.518634 TTGCCGCCCATCTTTAATTTC 57.481 42.857 0.00 0.00 0.00 2.17
4148 4777 3.860641 CTTTGCCGCCCATCTTTAATTT 58.139 40.909 0.00 0.00 0.00 1.82
4161 4798 0.710017 CATTTTTCTCGCTTTGCCGC 59.290 50.000 0.00 0.00 0.00 6.53
4171 4808 6.264841 AGATTGCCAAGAGACATTTTTCTC 57.735 37.500 0.00 0.00 42.22 2.87
4211 4848 6.346096 AGAGCAGACAGTAACAACAAAACTA 58.654 36.000 0.00 0.00 0.00 2.24
4239 4882 3.668447 CAGGCAATAGACACACAGACTT 58.332 45.455 0.00 0.00 0.00 3.01
4240 4883 2.613977 GCAGGCAATAGACACACAGACT 60.614 50.000 0.00 0.00 0.00 3.24
4247 4890 2.409948 AGAAGGCAGGCAATAGACAC 57.590 50.000 0.00 0.00 0.00 3.67
4258 4901 3.493877 CGAGATGCATTTCTAGAAGGCAG 59.506 47.826 27.19 16.27 36.42 4.85
4276 4919 1.000843 CCTCAACATCCACACACGAGA 59.999 52.381 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.