Multiple sequence alignment - TraesCS2A01G402000

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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 TraesCS2A01G402000 chr2A 100.000 4379 0 0 487 4865 655550971 655546593 0.000000e+00 8087
1 TraesCS2A01G402000 chr2A 100.000 149 0 0 1 149 655551457 655551309 4.800000e-70 276
2 TraesCS2A01G402000 chr2D 92.807 4004 163 54 487 4431 512172441 512168504 0.000000e+00 5683
3 TraesCS2A01G402000 chr2D 87.821 312 30 4 4474 4779 512168376 512168067 4.630000e-95 359
4 TraesCS2A01G402000 chr2D 95.041 121 2 2 10 129 512172678 512172561 2.310000e-43 187
5 TraesCS2A01G402000 chr2B 91.941 4070 198 54 487 4521 601943209 601939235 0.000000e+00 5579
6 TraesCS2A01G402000 chr2B 92.174 345 26 1 4513 4856 601939083 601938739 2.040000e-133 486


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 TraesCS2A01G402000 chr2A 655546593 655551457 4864 True 4181.500000 8087 100.000000 1 4865 2 chr2A.!!$R1 4864
1 TraesCS2A01G402000 chr2D 512168067 512172678 4611 True 2076.333333 5683 91.889667 10 4779 3 chr2D.!!$R1 4769
2 TraesCS2A01G402000 chr2B 601938739 601943209 4470 True 3032.500000 5579 92.057500 487 4856 2 chr2B.!!$R1 4369

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
39 40 0.392461 TCAATCTTTCCGCCTTCCCG 60.392 55.0 0.0 0.0 0.00 5.14 F
1069 1205 0.106268 TTCTTGCAGCCTCCCAACAA 60.106 50.0 0.0 0.0 0.00 2.83 F
1102 1238 0.108138 ATGGAGTCGTGCCAGTTAGC 60.108 55.0 0.0 0.0 39.11 3.09 F
1606 1757 0.172352 GCTCCGAGGACAGTTGAGAG 59.828 60.0 0.0 0.0 0.00 3.20 F
2979 3134 0.179089 CTGCCGACTCCAAGATCAGG 60.179 60.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1878 0.101939 GGTACGATCGGACCTTGACC 59.898 60.000 37.19 18.76 45.54 4.02 R
2718 2873 0.293723 CGTCCGATGCGTCGTAAAAG 59.706 55.000 25.56 10.98 46.25 2.27 R
2756 2911 1.094073 GCCGCTGAGTGCAATCTGAT 61.094 55.000 22.87 0.00 43.06 2.90 R
3118 3273 3.132289 TCGGAGTCCTGATGATGGTTTAC 59.868 47.826 7.77 0.00 0.00 2.01 R
4488 4756 0.597377 GCAAAGGAAAACACAGGGCG 60.597 55.000 0.00 0.00 0.00 6.13 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
22 23 1.710809 CCCCTTTCCTTTCTCCCTTCA 59.289 52.381 0.00 0.00 0.00 3.02
38 39 1.745653 CTTCAATCTTTCCGCCTTCCC 59.254 52.381 0.00 0.00 0.00 3.97
39 40 0.392461 TCAATCTTTCCGCCTTCCCG 60.392 55.000 0.00 0.00 0.00 5.14
40 41 0.676782 CAATCTTTCCGCCTTCCCGT 60.677 55.000 0.00 0.00 0.00 5.28
69 70 1.299541 CATTCCGTTCCAATCCTCCG 58.700 55.000 0.00 0.00 0.00 4.63
518 600 2.854187 CTTCCCCTCCCGCGAGTTTC 62.854 65.000 8.23 0.00 33.93 2.78
519 601 4.814294 CCCCTCCCGCGAGTTTCG 62.814 72.222 8.23 0.00 43.89 3.46
520 602 4.065281 CCCTCCCGCGAGTTTCGT 62.065 66.667 8.23 0.00 42.81 3.85
521 603 2.048503 CCTCCCGCGAGTTTCGTT 60.049 61.111 8.23 0.00 42.81 3.85
522 604 1.666872 CCTCCCGCGAGTTTCGTTT 60.667 57.895 8.23 0.00 42.81 3.60
536 618 5.008331 AGTTTCGTTTTTCTATTCCCCTCC 58.992 41.667 0.00 0.00 0.00 4.30
537 619 3.639672 TCGTTTTTCTATTCCCCTCCC 57.360 47.619 0.00 0.00 0.00 4.30
538 620 2.240414 TCGTTTTTCTATTCCCCTCCCC 59.760 50.000 0.00 0.00 0.00 4.81
598 680 2.434359 CTTCACCGCCCGTTCCTC 60.434 66.667 0.00 0.00 0.00 3.71
640 722 1.600485 TCTTTTCTTCCGGTTCGTTGC 59.400 47.619 0.00 0.00 0.00 4.17
695 801 3.371063 CTGGCTGGCTGGCTGTTG 61.371 66.667 18.27 3.56 42.34 3.33
849 960 5.122396 ACTCTTGATTAATCACGCCTGTTTC 59.878 40.000 17.76 0.00 36.36 2.78
850 961 5.000591 TCTTGATTAATCACGCCTGTTTCA 58.999 37.500 17.76 0.00 36.36 2.69
851 962 5.471797 TCTTGATTAATCACGCCTGTTTCAA 59.528 36.000 17.76 0.00 36.36 2.69
929 1057 4.228097 CCGAGGCAATTCAGCGCG 62.228 66.667 0.00 0.00 34.64 6.86
930 1058 4.876081 CGAGGCAATTCAGCGCGC 62.876 66.667 26.66 26.66 34.64 6.86
931 1059 4.543084 GAGGCAATTCAGCGCGCC 62.543 66.667 30.33 13.11 45.23 6.53
964 1100 1.454847 CTGCCGCTCTACTCCCTCT 60.455 63.158 0.00 0.00 0.00 3.69
982 1118 4.082895 CCCTCTACTGTTATATAAGCGCGT 60.083 45.833 8.43 0.00 0.00 6.01
1006 1142 1.217511 CACGGCTGCTCTGAGATGT 59.782 57.895 9.28 0.00 0.00 3.06
1015 1151 4.672024 GCTGCTCTGAGATGTGATTGTTTG 60.672 45.833 9.28 0.00 0.00 2.93
1016 1152 4.392047 TGCTCTGAGATGTGATTGTTTGT 58.608 39.130 9.28 0.00 0.00 2.83
1017 1153 4.823442 TGCTCTGAGATGTGATTGTTTGTT 59.177 37.500 9.28 0.00 0.00 2.83
1019 1155 5.618640 GCTCTGAGATGTGATTGTTTGTTCC 60.619 44.000 9.28 0.00 0.00 3.62
1021 1157 3.826157 TGAGATGTGATTGTTTGTTCCCC 59.174 43.478 0.00 0.00 0.00 4.81
1022 1158 3.826157 GAGATGTGATTGTTTGTTCCCCA 59.174 43.478 0.00 0.00 0.00 4.96
1023 1159 3.573967 AGATGTGATTGTTTGTTCCCCAC 59.426 43.478 0.00 0.00 0.00 4.61
1024 1160 2.739943 TGTGATTGTTTGTTCCCCACA 58.260 42.857 0.00 0.00 0.00 4.17
1025 1161 2.428890 TGTGATTGTTTGTTCCCCACAC 59.571 45.455 0.00 0.00 33.98 3.82
1026 1162 2.693074 GTGATTGTTTGTTCCCCACACT 59.307 45.455 0.00 0.00 33.98 3.55
1027 1163 2.692557 TGATTGTTTGTTCCCCACACTG 59.307 45.455 0.00 0.00 33.98 3.66
1028 1164 2.223803 TTGTTTGTTCCCCACACTGT 57.776 45.000 0.00 0.00 33.98 3.55
1029 1165 3.367646 TTGTTTGTTCCCCACACTGTA 57.632 42.857 0.00 0.00 33.98 2.74
1030 1166 2.925724 TGTTTGTTCCCCACACTGTAG 58.074 47.619 0.00 0.00 33.98 2.74
1069 1205 0.106268 TTCTTGCAGCCTCCCAACAA 60.106 50.000 0.00 0.00 0.00 2.83
1070 1206 0.823356 TCTTGCAGCCTCCCAACAAC 60.823 55.000 0.00 0.00 0.00 3.32
1071 1207 1.076412 TTGCAGCCTCCCAACAACA 60.076 52.632 0.00 0.00 0.00 3.33
1097 1233 0.531532 GATCCATGGAGTCGTGCCAG 60.532 60.000 21.33 0.00 39.11 4.85
1102 1238 0.108138 ATGGAGTCGTGCCAGTTAGC 60.108 55.000 0.00 0.00 39.11 3.09
1401 1552 3.669036 CTGTCGTCGCACTCGGAGG 62.669 68.421 10.23 0.00 36.13 4.30
1402 1553 3.429141 GTCGTCGCACTCGGAGGA 61.429 66.667 10.23 0.00 36.13 3.71
1403 1554 3.429141 TCGTCGCACTCGGAGGAC 61.429 66.667 10.23 6.41 36.13 3.85
1524 1675 3.745803 GCAGCAGCAAGGTCAGCC 61.746 66.667 0.00 0.00 41.58 4.85
1551 1702 4.482386 CTCCAGTTCGTTCTCGTTTATCA 58.518 43.478 0.00 0.00 38.33 2.15
1553 1704 4.216902 TCCAGTTCGTTCTCGTTTATCAGA 59.783 41.667 0.00 0.00 38.33 3.27
1606 1757 0.172352 GCTCCGAGGACAGTTGAGAG 59.828 60.000 0.00 0.00 0.00 3.20
1727 1878 3.041211 TCATGGTGGAAGGTATGAGAGG 58.959 50.000 0.00 0.00 0.00 3.69
1772 1923 1.177401 GGTCCAAGGAATTGTCTGCC 58.823 55.000 0.00 0.00 0.00 4.85
1775 1926 1.180029 CCAAGGAATTGTCTGCCCTG 58.820 55.000 0.00 0.00 0.00 4.45
1802 1953 1.341383 GGCCAAGTGATCAAGGGACAT 60.341 52.381 11.61 0.00 0.00 3.06
1850 2001 1.204146 GTCCTGATGGGCAGTTCCTA 58.796 55.000 0.00 0.00 43.33 2.94
1855 2006 1.065199 TGATGGGCAGTTCCTAGCAAG 60.065 52.381 0.00 0.00 38.85 4.01
1894 2045 1.044231 GTCCGGGTTTGGGGTGTTTT 61.044 55.000 0.00 0.00 0.00 2.43
1949 2100 1.134965 CCCTCTTGCGTCTACCTCAAG 60.135 57.143 0.00 0.00 38.73 3.02
2261 2416 8.696043 AATTTGATACCTTGCAGCATCTATTA 57.304 30.769 0.00 0.00 0.00 0.98
2270 2425 3.244181 TGCAGCATCTATTATCGGCTTCA 60.244 43.478 0.00 0.00 31.30 3.02
2409 2564 0.524862 CATGGGTTGAAGCTGACAGC 59.475 55.000 20.12 20.12 42.84 4.40
2420 2575 0.604780 GCTGACAGCTTGCTCTCCAA 60.605 55.000 20.41 0.00 38.45 3.53
2483 2638 3.698040 ACAATTGCTTCATCACTGGATCC 59.302 43.478 4.20 4.20 0.00 3.36
2508 2663 1.270412 ACGGCAAAGTTCGTGTATGGA 60.270 47.619 0.00 0.00 38.25 3.41
2531 2686 3.865745 ACATAACTAGATGCAGCGTTGTC 59.134 43.478 5.62 0.00 0.00 3.18
2687 2842 2.281761 CGGCTTTCTGCAGGGTGT 60.282 61.111 15.13 0.00 45.15 4.16
2718 2873 4.331962 GAACGATTACTGGAAATTGTCGC 58.668 43.478 0.00 0.00 33.23 5.19
2724 2879 6.464834 CGATTACTGGAAATTGTCGCTTTTAC 59.535 38.462 0.00 0.00 0.00 2.01
2756 2911 2.855514 GCCTGCTGCGGTTGGAAAA 61.856 57.895 7.82 0.00 0.00 2.29
2850 3005 5.894807 CAAGAAAAGGATGACTGTTGTTGT 58.105 37.500 0.00 0.00 40.83 3.32
2873 3028 8.206126 TGTAATTGATATCTTCATCAGCCCTA 57.794 34.615 3.98 0.00 36.34 3.53
2875 3030 9.678260 GTAATTGATATCTTCATCAGCCCTATT 57.322 33.333 3.98 0.00 36.34 1.73
2979 3134 0.179089 CTGCCGACTCCAAGATCAGG 60.179 60.000 0.00 0.00 0.00 3.86
3035 3190 6.385033 ACAGTGGTACGTCTCAAATACTTAC 58.615 40.000 0.00 0.00 0.00 2.34
3455 3610 4.475527 AACCAGGAGTTGTTCGCC 57.524 55.556 0.00 0.00 37.29 5.54
3461 3616 3.479269 GAGTTGTTCGCCGAGCCG 61.479 66.667 0.00 0.00 0.00 5.52
3820 3976 1.002430 ACAAGACATCACATGCTCGGT 59.998 47.619 0.00 0.00 0.00 4.69
3999 4160 6.996509 AGATCTTTCAGCCTAGATCAGATTC 58.003 40.000 12.93 0.00 45.90 2.52
4002 4163 4.576216 TTCAGCCTAGATCAGATTCGTC 57.424 45.455 0.00 0.00 0.00 4.20
4016 4177 3.255888 AGATTCGTCCTTTGCCCTTTTTC 59.744 43.478 0.00 0.00 0.00 2.29
4017 4178 2.358322 TCGTCCTTTGCCCTTTTTCT 57.642 45.000 0.00 0.00 0.00 2.52
4018 4179 2.661718 TCGTCCTTTGCCCTTTTTCTT 58.338 42.857 0.00 0.00 0.00 2.52
4019 4180 3.028130 TCGTCCTTTGCCCTTTTTCTTT 58.972 40.909 0.00 0.00 0.00 2.52
4020 4181 3.067601 TCGTCCTTTGCCCTTTTTCTTTC 59.932 43.478 0.00 0.00 0.00 2.62
4021 4182 3.068165 CGTCCTTTGCCCTTTTTCTTTCT 59.932 43.478 0.00 0.00 0.00 2.52
4022 4183 4.441495 CGTCCTTTGCCCTTTTTCTTTCTT 60.441 41.667 0.00 0.00 0.00 2.52
4078 4239 0.941542 TATGCCGCGGAAATGTTAGC 59.058 50.000 33.48 10.67 0.00 3.09
4103 4264 6.866770 CGTAAGTTGAGTGTAAATTCTCCTCA 59.133 38.462 0.00 0.00 0.00 3.86
4113 4275 1.727062 ATTCTCCTCATCCCGCTGAT 58.273 50.000 0.00 0.00 0.00 2.90
4126 4288 1.379044 GCTGATTGTGTGGGAGGGG 60.379 63.158 0.00 0.00 0.00 4.79
4143 4325 0.108138 GGGGACTGATGGAACTGTCG 60.108 60.000 0.00 0.00 38.82 4.35
4144 4326 0.108138 GGGACTGATGGAACTGTCGG 60.108 60.000 0.00 0.00 38.82 4.79
4145 4327 0.895530 GGACTGATGGAACTGTCGGA 59.104 55.000 0.00 0.00 38.82 4.55
4146 4328 1.482593 GGACTGATGGAACTGTCGGAT 59.517 52.381 0.00 0.00 38.82 4.18
4147 4329 2.693591 GGACTGATGGAACTGTCGGATA 59.306 50.000 0.00 0.00 38.82 2.59
4148 4330 3.491104 GGACTGATGGAACTGTCGGATAC 60.491 52.174 0.00 0.00 38.82 2.24
4149 4331 3.096852 ACTGATGGAACTGTCGGATACA 58.903 45.455 0.00 0.00 36.42 2.29
4150 4332 3.706594 ACTGATGGAACTGTCGGATACAT 59.293 43.478 0.00 0.00 37.50 2.29
4151 4333 4.893524 ACTGATGGAACTGTCGGATACATA 59.106 41.667 0.00 0.00 37.50 2.29
4152 4334 5.540337 ACTGATGGAACTGTCGGATACATAT 59.460 40.000 0.00 0.00 37.50 1.78
4153 4335 5.783111 TGATGGAACTGTCGGATACATATG 58.217 41.667 0.00 0.00 37.50 1.78
4154 4336 5.304357 TGATGGAACTGTCGGATACATATGT 59.696 40.000 13.93 13.93 37.50 2.29
4155 4337 5.607939 TGGAACTGTCGGATACATATGTT 57.392 39.130 14.77 1.88 37.50 2.71
4156 4338 5.597806 TGGAACTGTCGGATACATATGTTC 58.402 41.667 14.77 10.94 38.84 3.18
4157 4339 4.989168 GGAACTGTCGGATACATATGTTCC 59.011 45.833 14.77 17.68 45.80 3.62
4158 4340 5.597806 GAACTGTCGGATACATATGTTCCA 58.402 41.667 24.44 15.08 35.94 3.53
4159 4341 5.808366 ACTGTCGGATACATATGTTCCAT 57.192 39.130 24.44 11.78 37.50 3.41
4160 4342 5.784177 ACTGTCGGATACATATGTTCCATC 58.216 41.667 24.44 17.55 37.50 3.51
4161 4343 5.147330 TGTCGGATACATATGTTCCATCC 57.853 43.478 24.44 22.38 31.43 3.51
4210 4392 4.545823 TCGTTCAAAATTCAGTGTCCAC 57.454 40.909 0.00 0.00 0.00 4.02
4222 4404 3.706594 TCAGTGTCCACTTCTCTTCAACT 59.293 43.478 0.00 0.00 40.20 3.16
4225 4407 5.694006 CAGTGTCCACTTCTCTTCAACTTAG 59.306 44.000 0.00 0.00 40.20 2.18
4226 4408 4.449405 GTGTCCACTTCTCTTCAACTTAGC 59.551 45.833 0.00 0.00 0.00 3.09
4237 4419 5.178797 TCTTCAACTTAGCCTTGTATGCTC 58.821 41.667 0.00 0.00 40.23 4.26
4298 4481 2.571212 CTGTAAGCTGTTTGGTGTGGA 58.429 47.619 0.00 0.00 0.00 4.02
4309 4492 2.978010 GTGTGGACCTTGTGCGGG 60.978 66.667 0.00 0.00 0.00 6.13
4412 4595 6.481976 TGTTACTTGCTCGTCCCATAAATATG 59.518 38.462 0.00 0.00 0.00 1.78
4463 4649 1.640069 CTGCCGAATGTGCATCTCG 59.360 57.895 7.77 7.77 38.22 4.04
4467 4653 1.203928 CCGAATGTGCATCTCGTCTC 58.796 55.000 12.24 0.00 0.00 3.36
4471 4657 2.306341 ATGTGCATCTCGTCTCCTTG 57.694 50.000 0.00 0.00 0.00 3.61
4481 4749 6.622679 GCATCTCGTCTCCTTGATAGTATCTG 60.623 46.154 11.40 4.60 0.00 2.90
4488 4756 5.475220 TCTCCTTGATAGTATCTGCTGCTAC 59.525 44.000 11.40 0.00 0.00 3.58
4501 4769 0.517316 CTGCTACGCCCTGTGTTTTC 59.483 55.000 0.00 0.00 0.00 2.29
4538 4966 3.131396 CAAATGCGGTAGAGTGGGTATC 58.869 50.000 0.00 0.00 0.00 2.24
4580 5008 2.939460 ACTTGCATTATTTGGTCGGC 57.061 45.000 0.00 0.00 0.00 5.54
4597 5025 4.748600 GGTCGGCATGTAAACTATAGTTCC 59.251 45.833 18.28 12.55 37.25 3.62
4598 5026 5.452917 GGTCGGCATGTAAACTATAGTTCCT 60.453 44.000 18.28 6.81 37.25 3.36
4617 5045 8.840200 AGTTCCTTAGATACAGATCCAACTTA 57.160 34.615 0.00 0.00 31.81 2.24
4641 5069 6.044682 AGTTCCACTTGCTTCAAAGAAAATG 58.955 36.000 0.00 0.00 0.00 2.32
4647 5075 7.254218 CCACTTGCTTCAAAGAAAATGAAAGTC 60.254 37.037 0.00 0.00 36.43 3.01
4747 5181 4.003648 CTCCAGGTTCAACTCGCTAAAAT 58.996 43.478 0.00 0.00 0.00 1.82
4752 5186 6.967199 CCAGGTTCAACTCGCTAAAATATTTC 59.033 38.462 0.10 0.00 0.00 2.17
4786 5220 0.608640 ACTCGTAAGCCTCACTTGGG 59.391 55.000 0.00 0.00 39.58 4.12
4806 5240 2.097038 CGAGCAAGAGCCAAGACGG 61.097 63.158 0.00 0.00 43.56 4.79
4823 5257 1.779025 CGGCGGATGATTTGCCTCTG 61.779 60.000 0.00 0.00 46.67 3.35
4843 5277 4.890158 TGAATATGTCAGTCAGTGGTGT 57.110 40.909 0.00 0.00 0.00 4.16
4847 5281 5.843673 ATATGTCAGTCAGTGGTGTCTAG 57.156 43.478 0.00 0.00 0.00 2.43
4853 5287 5.241064 GTCAGTCAGTGGTGTCTAGTCTAAA 59.759 44.000 0.00 0.00 0.00 1.85
4856 5290 6.430308 CAGTCAGTGGTGTCTAGTCTAAACTA 59.570 42.308 0.00 0.00 36.92 2.24
4857 5291 7.002879 AGTCAGTGGTGTCTAGTCTAAACTAA 58.997 38.462 0.00 0.00 37.53 2.24
4858 5292 7.040548 AGTCAGTGGTGTCTAGTCTAAACTAAC 60.041 40.741 0.00 0.00 37.53 2.34
4859 5293 6.208204 TCAGTGGTGTCTAGTCTAAACTAACC 59.792 42.308 0.00 0.00 37.53 2.85
4860 5294 5.182760 AGTGGTGTCTAGTCTAAACTAACCG 59.817 44.000 0.00 0.00 38.46 4.44
4861 5295 5.182001 GTGGTGTCTAGTCTAAACTAACCGA 59.818 44.000 0.00 0.00 38.46 4.69
4862 5296 5.413833 TGGTGTCTAGTCTAAACTAACCGAG 59.586 44.000 0.00 0.00 38.46 4.63
4863 5297 5.645497 GGTGTCTAGTCTAAACTAACCGAGA 59.355 44.000 0.00 0.00 37.53 4.04
4864 5298 6.318396 GGTGTCTAGTCTAAACTAACCGAGAT 59.682 42.308 0.00 0.00 37.53 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.103337 AGGGAGAAAGGAAAGGGGGT 60.103 55.000 0.00 0.00 0.00 4.95
1 2 1.006043 GAAGGGAGAAAGGAAAGGGGG 59.994 57.143 0.00 0.00 0.00 5.40
2 3 1.710809 TGAAGGGAGAAAGGAAAGGGG 59.289 52.381 0.00 0.00 0.00 4.79
3 4 3.525800 TTGAAGGGAGAAAGGAAAGGG 57.474 47.619 0.00 0.00 0.00 3.95
4 5 4.928263 AGATTGAAGGGAGAAAGGAAAGG 58.072 43.478 0.00 0.00 0.00 3.11
5 6 6.071672 GGAAAGATTGAAGGGAGAAAGGAAAG 60.072 42.308 0.00 0.00 0.00 2.62
6 7 5.775195 GGAAAGATTGAAGGGAGAAAGGAAA 59.225 40.000 0.00 0.00 0.00 3.13
7 8 5.325239 GGAAAGATTGAAGGGAGAAAGGAA 58.675 41.667 0.00 0.00 0.00 3.36
8 9 4.565652 CGGAAAGATTGAAGGGAGAAAGGA 60.566 45.833 0.00 0.00 0.00 3.36
22 23 0.392595 GACGGGAAGGCGGAAAGATT 60.393 55.000 0.00 0.00 0.00 2.40
38 39 0.524816 ACGGAATGGAATCGACGACG 60.525 55.000 0.00 0.00 41.26 5.12
39 40 1.587034 GAACGGAATGGAATCGACGAC 59.413 52.381 0.00 0.00 0.00 4.34
40 41 1.470285 GGAACGGAATGGAATCGACGA 60.470 52.381 0.00 0.00 0.00 4.20
69 70 2.495866 CATGGCGCAAATGGGGAC 59.504 61.111 10.83 0.00 38.14 4.46
518 600 2.651455 GGGGAGGGGAATAGAAAAACG 58.349 52.381 0.00 0.00 0.00 3.60
519 601 3.028094 GGGGGAGGGGAATAGAAAAAC 57.972 52.381 0.00 0.00 0.00 2.43
551 633 2.789893 GCGACACATATCTCGAAAGGAC 59.210 50.000 0.00 0.00 31.24 3.85
678 784 3.371063 CAACAGCCAGCCAGCCAG 61.371 66.667 0.00 0.00 0.00 4.85
680 786 3.925630 TAGCAACAGCCAGCCAGCC 62.926 63.158 0.00 0.00 0.00 4.85
681 787 1.973281 TTAGCAACAGCCAGCCAGC 60.973 57.895 0.00 0.00 0.00 4.85
682 788 0.607489 AGTTAGCAACAGCCAGCCAG 60.607 55.000 0.00 0.00 0.00 4.85
683 789 0.178992 AAGTTAGCAACAGCCAGCCA 60.179 50.000 0.00 0.00 0.00 4.75
785 892 5.036737 GCACCAAATCGGAACTAATCAATG 58.963 41.667 0.00 0.00 38.63 2.82
858 969 2.347731 GGACGCGAGAGGAGAATTTTT 58.652 47.619 15.93 0.00 0.00 1.94
862 973 1.716826 GACGGACGCGAGAGGAGAAT 61.717 60.000 15.93 0.00 0.00 2.40
940 1068 4.537433 GTAGAGCGGCAGGGGCAG 62.537 72.222 1.45 0.00 43.71 4.85
942 1070 4.228567 GAGTAGAGCGGCAGGGGC 62.229 72.222 1.45 0.00 40.13 5.80
943 1071 3.541713 GGAGTAGAGCGGCAGGGG 61.542 72.222 1.45 0.00 0.00 4.79
954 1082 7.414319 GCGCTTATATAACAGTAGAGGGAGTAG 60.414 44.444 0.00 0.00 0.00 2.57
964 1100 3.311106 GGCACGCGCTTATATAACAGTA 58.689 45.455 5.73 0.00 38.60 2.74
994 1130 4.392047 ACAAACAATCACATCTCAGAGCA 58.608 39.130 0.00 0.00 0.00 4.26
1006 1142 2.692557 CAGTGTGGGGAACAAACAATCA 59.307 45.455 0.00 0.00 41.57 2.57
1015 1151 3.197983 AGATAAGCTACAGTGTGGGGAAC 59.802 47.826 5.88 0.00 0.00 3.62
1016 1152 3.197766 CAGATAAGCTACAGTGTGGGGAA 59.802 47.826 5.88 0.00 0.00 3.97
1017 1153 2.766263 CAGATAAGCTACAGTGTGGGGA 59.234 50.000 5.88 0.00 0.00 4.81
1019 1155 2.093500 TGCAGATAAGCTACAGTGTGGG 60.093 50.000 5.88 0.00 34.99 4.61
1021 1157 4.092529 CAGTTGCAGATAAGCTACAGTGTG 59.907 45.833 5.88 0.00 41.63 3.82
1022 1158 4.248859 CAGTTGCAGATAAGCTACAGTGT 58.751 43.478 0.00 0.00 41.63 3.55
1023 1159 4.248859 ACAGTTGCAGATAAGCTACAGTG 58.751 43.478 0.00 0.00 41.63 3.66
1024 1160 4.543590 ACAGTTGCAGATAAGCTACAGT 57.456 40.909 0.00 0.00 41.63 3.55
1025 1161 6.276091 TGATACAGTTGCAGATAAGCTACAG 58.724 40.000 0.00 0.00 41.63 2.74
1026 1162 6.220726 TGATACAGTTGCAGATAAGCTACA 57.779 37.500 0.00 0.00 41.63 2.74
1027 1163 7.655328 AGAATGATACAGTTGCAGATAAGCTAC 59.345 37.037 0.00 0.00 39.91 3.58
1028 1164 7.730084 AGAATGATACAGTTGCAGATAAGCTA 58.270 34.615 0.00 0.00 34.99 3.32
1029 1165 6.590068 AGAATGATACAGTTGCAGATAAGCT 58.410 36.000 0.00 0.00 34.99 3.74
1030 1166 6.857777 AGAATGATACAGTTGCAGATAAGC 57.142 37.500 0.00 0.00 0.00 3.09
1069 1205 0.316522 CTCCATGGATCGATCGCTGT 59.683 55.000 16.63 0.00 0.00 4.40
1070 1206 0.316522 ACTCCATGGATCGATCGCTG 59.683 55.000 16.63 16.82 0.00 5.18
1071 1207 0.600557 GACTCCATGGATCGATCGCT 59.399 55.000 16.63 0.00 0.00 4.93
1097 1233 1.445716 TAGAGCTCTCCCGCGCTAAC 61.446 60.000 22.17 0.00 38.94 2.34
1102 1238 2.240230 CTACTAGAGCTCTCCCGCG 58.760 63.158 22.17 0.00 34.40 6.46
1401 1552 1.071605 GACATGGAGCAGTCGTTGTC 58.928 55.000 0.00 0.00 31.79 3.18
1402 1553 0.320771 GGACATGGAGCAGTCGTTGT 60.321 55.000 0.00 0.00 35.63 3.32
1403 1554 0.320683 TGGACATGGAGCAGTCGTTG 60.321 55.000 0.00 0.00 35.63 4.10
1524 1675 0.456995 GAGAACGAACTGGAGCTCCG 60.457 60.000 27.43 22.72 39.43 4.63
1606 1757 2.110006 GCCATCCGCTTCTCCTCC 59.890 66.667 0.00 0.00 0.00 4.30
1652 1803 1.302511 ATCCGCCGCATTATCCACC 60.303 57.895 0.00 0.00 0.00 4.61
1727 1878 0.101939 GGTACGATCGGACCTTGACC 59.898 60.000 37.19 18.76 45.54 4.02
1772 1923 0.400213 TCACTTGGCCTTGGTACAGG 59.600 55.000 3.32 0.00 42.39 4.00
1775 1926 2.489938 TGATCACTTGGCCTTGGTAC 57.510 50.000 3.32 0.00 0.00 3.34
1817 1968 4.272018 CCATCAGGACTGAATTTCATCGTC 59.728 45.833 6.06 9.27 43.58 4.20
2261 2416 3.003689 CAGTTTTGTCTGTTGAAGCCGAT 59.996 43.478 0.00 0.00 0.00 4.18
2420 2575 4.081752 TGGACACAAGTCACTGCAAAAATT 60.082 37.500 0.00 0.00 46.80 1.82
2483 2638 1.002900 ACACGAACTTTGCCGTCAATG 60.003 47.619 0.00 0.00 36.83 2.82
2508 2663 4.253685 ACAACGCTGCATCTAGTTATGTT 58.746 39.130 0.00 0.00 0.00 2.71
2531 2686 1.751351 TCTCTAACATCTGCCCAGTCG 59.249 52.381 0.00 0.00 0.00 4.18
2687 2842 3.833650 TCCAGTAATCGTTCCAACCACTA 59.166 43.478 0.00 0.00 0.00 2.74
2718 2873 0.293723 CGTCCGATGCGTCGTAAAAG 59.706 55.000 25.56 10.98 46.25 2.27
2738 2893 2.158561 ATTTTCCAACCGCAGCAGGC 62.159 55.000 3.49 0.00 39.90 4.85
2756 2911 1.094073 GCCGCTGAGTGCAATCTGAT 61.094 55.000 22.87 0.00 43.06 2.90
2964 3119 3.193263 CAACATCCTGATCTTGGAGTCG 58.807 50.000 12.28 7.16 36.99 4.18
3118 3273 3.132289 TCGGAGTCCTGATGATGGTTTAC 59.868 47.826 7.77 0.00 0.00 2.01
3455 3610 3.777925 CCTTTGCACGACGGCTCG 61.778 66.667 0.00 5.08 46.06 5.03
3461 3616 4.090057 GAGGCGCCTTTGCACGAC 62.090 66.667 33.34 11.55 37.32 4.34
3621 3776 0.530744 TTCTGGAACGACCTGATCCG 59.469 55.000 11.70 0.00 42.30 4.18
3659 3814 1.292223 CGGATGAACCAGTCACCGT 59.708 57.895 0.00 0.00 41.79 4.83
3661 3816 0.108138 CTCCGGATGAACCAGTCACC 60.108 60.000 3.57 0.00 39.72 4.02
3736 3891 2.126850 GCACGGGCGCTTTTCTTC 60.127 61.111 7.64 0.00 0.00 2.87
3820 3976 1.449070 CGATTCAGCAGCAGGAGCA 60.449 57.895 0.00 0.00 45.49 4.26
3942 4101 0.743345 GGGGTGGTACAAAGCTAGCG 60.743 60.000 9.55 0.00 44.16 4.26
3986 4147 4.054671 GCAAAGGACGAATCTGATCTAGG 58.945 47.826 0.00 0.00 0.00 3.02
3999 4160 3.068165 AGAAAGAAAAAGGGCAAAGGACG 59.932 43.478 0.00 0.00 0.00 4.79
4002 4163 5.674525 AGAAAGAAAGAAAAAGGGCAAAGG 58.325 37.500 0.00 0.00 0.00 3.11
4078 4239 6.866770 TGAGGAGAATTTACACTCAACTTACG 59.133 38.462 0.00 0.00 35.45 3.18
4103 4264 1.077501 CCCACACAATCAGCGGGAT 60.078 57.895 0.00 0.00 39.44 3.85
4113 4275 2.153401 CAGTCCCCCTCCCACACAA 61.153 63.158 0.00 0.00 0.00 3.33
4126 4288 0.895530 TCCGACAGTTCCATCAGTCC 59.104 55.000 0.00 0.00 0.00 3.85
4153 4335 3.834610 CGTATACTCGGATGGATGGAAC 58.165 50.000 0.56 0.00 0.00 3.62
4210 4392 6.183360 GCATACAAGGCTAAGTTGAAGAGAAG 60.183 42.308 0.00 0.00 0.00 2.85
4222 4404 6.040054 TGAATAGTACGAGCATACAAGGCTAA 59.960 38.462 0.00 0.00 42.78 3.09
4225 4407 4.617959 TGAATAGTACGAGCATACAAGGC 58.382 43.478 0.00 0.00 0.00 4.35
4226 4408 5.833082 ACTGAATAGTACGAGCATACAAGG 58.167 41.667 0.00 0.00 34.74 3.61
4237 4419 7.993821 ATCACATCTGAAACTGAATAGTACG 57.006 36.000 0.00 0.00 35.69 3.67
4298 4481 2.902423 TTTCAGCACCCGCACAAGGT 62.902 55.000 0.00 0.00 42.27 3.50
4309 4492 6.152831 AGGGACAATAATTACCTTTTCAGCAC 59.847 38.462 0.00 0.00 0.00 4.40
4396 4579 3.997021 GACCAGCATATTTATGGGACGAG 59.003 47.826 0.00 0.00 38.48 4.18
4412 4595 1.003580 TCCAACAGATTCAGGACCAGC 59.996 52.381 0.00 0.00 0.00 4.85
4448 4634 1.203928 GAGACGAGATGCACATTCGG 58.796 55.000 17.24 1.15 38.58 4.30
4463 4649 4.280677 AGCAGCAGATACTATCAAGGAGAC 59.719 45.833 0.00 0.00 0.00 3.36
4467 4653 4.480541 CGTAGCAGCAGATACTATCAAGG 58.519 47.826 2.97 0.00 34.53 3.61
4488 4756 0.597377 GCAAAGGAAAACACAGGGCG 60.597 55.000 0.00 0.00 0.00 6.13
4553 4981 3.934579 CCAAATAATGCAAGTTCCAAGGC 59.065 43.478 0.00 0.00 0.00 4.35
4597 5025 8.696374 TGGAACTAAGTTGGATCTGTATCTAAG 58.304 37.037 0.00 0.00 33.71 2.18
4598 5026 8.475639 GTGGAACTAAGTTGGATCTGTATCTAA 58.524 37.037 0.00 0.00 30.83 2.10
4641 5069 2.032808 GCAGTGGAACGAACTGACTTTC 60.033 50.000 7.72 0.00 46.55 2.62
4647 5075 4.749245 AAAATAGCAGTGGAACGAACTG 57.251 40.909 0.00 0.00 45.86 3.16
4710 5144 1.521681 GGAGAAGTCCCGGCGAATG 60.522 63.158 9.30 0.00 36.76 2.67
4747 5181 6.201997 ACGAGTATACAATTGCATGCGAAATA 59.798 34.615 12.68 5.23 0.00 1.40
4752 5186 3.859745 ACGAGTATACAATTGCATGCG 57.140 42.857 14.09 7.04 0.00 4.73
4786 5220 1.347817 CGTCTTGGCTCTTGCTCGAC 61.348 60.000 0.00 0.00 39.59 4.20
4806 5240 1.382522 TTCAGAGGCAAATCATCCGC 58.617 50.000 0.00 0.00 0.00 5.54
4823 5257 5.078411 AGACACCACTGACTGACATATTC 57.922 43.478 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.