Multiple sequence alignment - TraesCS7D01G278500

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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 TraesCS7D01G278500 chr7D 100.000 2025 0 0 2239 4263 268567226 268569250 0.000000e+00 3740.0
1 TraesCS7D01G278500 chr7D 100.000 1806 0 0 1 1806 268564988 268566793 0.000000e+00 3336.0
2 TraesCS7D01G278500 chr7D 90.385 104 4 1 3729 3832 268568670 268568767 9.620000e-27 132.0
3 TraesCS7D01G278500 chr7D 90.385 104 4 1 3683 3780 268568716 268568819 9.620000e-27 132.0
4 TraesCS7D01G278500 chr7A 91.542 1809 93 19 1 1800 294558847 294560604 0.000000e+00 2438.0
5 TraesCS7D01G278500 chr7A 94.196 1430 48 15 2239 3640 294560614 294562036 0.000000e+00 2148.0
6 TraesCS7D01G278500 chr7A 93.750 112 7 0 4152 4263 294563577 294563688 7.330000e-38 169.0
7 TraesCS7D01G278500 chr7A 98.701 77 1 0 3653 3729 294562259 294562335 2.070000e-28 137.0
8 TraesCS7D01G278500 chr7B 93.233 1522 66 11 2239 3729 249675730 249677245 0.000000e+00 2206.0
9 TraesCS7D01G278500 chr7B 91.937 1141 62 13 1 1135 249673775 249674891 0.000000e+00 1570.0
10 TraesCS7D01G278500 chr7B 95.394 673 22 6 1134 1800 249675051 249675720 0.000000e+00 1062.0
11 TraesCS7D01G278500 chr7B 83.957 187 7 4 3771 3956 249677524 249677688 1.590000e-34 158.0
12 TraesCS7D01G278500 chr7B 98.077 52 1 0 3729 3780 249677534 249677585 1.630000e-14 91.6
13 TraesCS7D01G278500 chr7B 100.000 46 0 0 3683 3728 249677534 249677579 7.590000e-13 86.1
14 TraesCS7D01G278500 chr4A 88.827 179 20 0 2446 2624 600899826 600899648 2.000000e-53 220.0
15 TraesCS7D01G278500 chr4B 88.333 180 20 1 2446 2625 4896048 4896226 9.280000e-52 215.0
16 TraesCS7D01G278500 chr4D 88.571 175 20 0 2446 2620 3722371 3722197 3.340000e-51 213.0


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 TraesCS7D01G278500 chr7D 268564988 268569250 4262 False 1835.000000 3740 95.192500 1 4263 4 chr7D.!!$F1 4262
1 TraesCS7D01G278500 chr7A 294558847 294563688 4841 False 1223.000000 2438 94.547250 1 4263 4 chr7A.!!$F1 4262
2 TraesCS7D01G278500 chr7B 249673775 249677688 3913 False 862.283333 2206 93.766333 1 3956 6 chr7B.!!$F1 3955

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
924 934 0.040514 TGCGCTTGATTTGTTCCGTG 60.041 50.0 9.73 0.0 0.0 4.94 F
1680 1859 0.458260 ACCCACAAAAGGACAAACGC 59.542 50.0 0.00 0.0 0.0 4.84 F
2294 2473 1.130955 GCGTTTGTGCCTTGAATGTG 58.869 50.0 0.00 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 2455 2.223456 TGACACATTCAAGGCACAAACG 60.223 45.455 0.0 0.0 0.00 3.60 R
3083 3266 2.637872 CAGGAGGGACACAAGGAAGTTA 59.362 50.000 0.0 0.0 0.00 2.24 R
3968 4626 0.038166 TCCAGATTGACCAGGCAACC 59.962 55.000 0.0 0.0 37.17 3.77 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
138 143 2.368311 AAAACCGGCCTAGAAAACCA 57.632 45.000 0.00 0.00 0.00 3.67
160 165 0.759346 GGGAGATAACATGGGCGACT 59.241 55.000 0.00 0.00 0.00 4.18
180 185 1.229082 TCCAGCGACAACCTAGGGT 60.229 57.895 14.81 2.44 37.65 4.34
321 327 9.159254 CCCATCCAGCTATATATTCACCTAATA 57.841 37.037 0.00 0.00 34.56 0.98
340 346 7.893302 ACCTAATAAATGTTCCTTGTCCAATGA 59.107 33.333 0.00 0.00 0.00 2.57
368 374 1.119684 GAGAGAAAGGAGGGAGAGGC 58.880 60.000 0.00 0.00 0.00 4.70
369 375 0.326143 AGAGAAAGGAGGGAGAGGCC 60.326 60.000 0.00 0.00 0.00 5.19
376 382 0.106967 GGAGGGAGAGGCCAAATGAC 60.107 60.000 5.01 0.00 38.95 3.06
461 468 7.565680 TCCCTATGTTTGACTTTCCTAAGATC 58.434 38.462 0.00 0.00 35.30 2.75
466 473 6.751157 TGTTTGACTTTCCTAAGATCGTACA 58.249 36.000 0.00 0.00 35.30 2.90
469 476 8.805688 GTTTGACTTTCCTAAGATCGTACATAC 58.194 37.037 0.00 0.00 35.30 2.39
473 480 6.072382 CTTTCCTAAGATCGTACATACGGGC 61.072 48.000 11.29 4.38 40.61 6.13
491 498 3.896648 GGCACCACCAAATATATCGTG 57.103 47.619 0.00 0.00 38.86 4.35
524 531 8.353684 TCAAAAGTGACATTTAAAGGCGATTTA 58.646 29.630 0.00 0.00 32.01 1.40
798 806 4.263435 TCTTCGTTACTCCCTCTCTCTTC 58.737 47.826 0.00 0.00 0.00 2.87
876 884 1.132500 CACATCCTACCTCTTCCCCC 58.868 60.000 0.00 0.00 0.00 5.40
924 934 0.040514 TGCGCTTGATTTGTTCCGTG 60.041 50.000 9.73 0.00 0.00 4.94
1298 1473 7.147976 AGTGATTCAATTGTTTCTTAAGTGGC 58.852 34.615 5.13 0.00 0.00 5.01
1305 1482 8.514594 TCAATTGTTTCTTAAGTGGCTAAGATG 58.485 33.333 5.13 0.00 37.66 2.90
1334 1511 6.422100 TGCGAGAGAGATTGATTTAATGTAGC 59.578 38.462 0.00 0.00 0.00 3.58
1370 1547 2.987413 TTGCTTAAGATGTTGTGCGG 57.013 45.000 6.67 0.00 0.00 5.69
1391 1568 6.017934 TGCGGAAGAGATTGATTAAATGTAGC 60.018 38.462 0.00 0.00 0.00 3.58
1442 1620 5.825679 TGTGGTATATTCTAATGTTGCCCAC 59.174 40.000 0.00 0.00 0.00 4.61
1449 1628 3.482436 TCTAATGTTGCCCACGTTTCTT 58.518 40.909 0.00 0.00 36.01 2.52
1484 1663 4.494091 ACATCATTCTAGAACTGGGTGG 57.506 45.455 7.48 0.00 0.00 4.61
1491 1670 2.501723 TCTAGAACTGGGTGGCTCAATC 59.498 50.000 0.00 0.00 0.00 2.67
1492 1671 1.366319 AGAACTGGGTGGCTCAATCT 58.634 50.000 0.00 0.00 0.00 2.40
1493 1672 1.707427 AGAACTGGGTGGCTCAATCTT 59.293 47.619 0.00 0.00 0.00 2.40
1680 1859 0.458260 ACCCACAAAAGGACAAACGC 59.542 50.000 0.00 0.00 0.00 4.84
2276 2455 6.768029 TTGAAATGCTTATGTTTTGACAGC 57.232 33.333 0.00 0.00 0.00 4.40
2278 2457 4.503741 AATGCTTATGTTTTGACAGCGT 57.496 36.364 0.00 0.00 32.85 5.07
2294 2473 1.130955 GCGTTTGTGCCTTGAATGTG 58.869 50.000 0.00 0.00 0.00 3.21
2302 2481 5.981088 TGTGCCTTGAATGTGTCAATTAT 57.019 34.783 0.00 0.00 45.27 1.28
2338 2518 8.570068 TTTCTTTAACCATGAACTACCATACC 57.430 34.615 0.00 0.00 0.00 2.73
2422 2603 6.669278 TCGTACTAGCATGTGTTCTCATATC 58.331 40.000 0.00 0.00 0.00 1.63
2636 2817 4.394920 GGCAAGTTATCCATCTCGTTTCAA 59.605 41.667 0.00 0.00 0.00 2.69
2644 2825 9.209175 GTTATCCATCTCGTTTCAAGCTATTAT 57.791 33.333 0.00 0.00 0.00 1.28
2682 2863 2.898729 ATCTGGTTGTAGATGCCTCG 57.101 50.000 0.00 0.00 36.12 4.63
2703 2884 4.050553 CGTTGCATGTTCTGATTGGTTTT 58.949 39.130 0.00 0.00 0.00 2.43
2704 2885 4.507388 CGTTGCATGTTCTGATTGGTTTTT 59.493 37.500 0.00 0.00 0.00 1.94
3083 3266 5.816777 CCAACAAAACATCCAAATGAGTGTT 59.183 36.000 0.00 0.00 36.26 3.32
3180 3388 2.287427 GCATGACATTGCATCCTACAGC 60.287 50.000 0.00 0.00 42.31 4.40
3274 3482 1.070577 GTGTTCTAAGTGTGTGCGCTG 60.071 52.381 9.73 0.00 35.34 5.18
3282 3490 1.893335 TGTGTGCGCTGCAGTGAAT 60.893 52.632 30.83 0.00 40.08 2.57
3360 3568 5.982516 TGTTTCACTGATACCAATTTTGTGC 59.017 36.000 0.00 0.00 0.00 4.57
3466 3674 3.073678 TGTTATGATTCTGCGTTGTGCT 58.926 40.909 0.00 0.00 46.63 4.40
3497 3705 8.970859 TCAGAGATCTATATGCGATCTTGATA 57.029 34.615 16.05 5.24 45.57 2.15
3498 3706 9.571816 TCAGAGATCTATATGCGATCTTGATAT 57.428 33.333 16.05 0.00 45.57 1.63
3564 3773 8.318167 GCGTGTTTAAATGGATAACTTATTTGC 58.682 33.333 0.00 0.00 0.00 3.68
3572 3781 8.539117 AATGGATAACTTATTTGCTTAGCCTT 57.461 30.769 0.29 0.00 29.03 4.35
3640 3849 3.702045 AGTGGGATTTTGGAAAAACGACA 59.298 39.130 0.00 0.00 0.00 4.35
3723 4142 3.055094 TCCAAGCCAAATAGTCAGACCTC 60.055 47.826 0.00 0.00 0.00 3.85
3729 4148 5.053145 GCCAAATAGTCAGACCTCATACTG 58.947 45.833 0.00 0.00 35.72 2.74
3730 4149 5.605534 CCAAATAGTCAGACCTCATACTGG 58.394 45.833 0.00 0.00 35.20 4.00
3731 4150 5.129485 CCAAATAGTCAGACCTCATACTGGT 59.871 44.000 0.00 0.00 41.07 4.00
3734 4153 3.779444 AGTCAGACCTCATACTGGTTCA 58.221 45.455 0.00 0.00 38.03 3.18
3736 4155 2.497675 TCAGACCTCATACTGGTTCAGC 59.502 50.000 0.00 0.00 38.03 4.26
3740 4159 3.177228 ACCTCATACTGGTTCAGCTTCT 58.823 45.455 0.00 0.00 34.37 2.85
3741 4160 3.584848 ACCTCATACTGGTTCAGCTTCTT 59.415 43.478 0.00 0.00 34.37 2.52
3742 4161 3.937706 CCTCATACTGGTTCAGCTTCTTG 59.062 47.826 0.00 0.00 34.37 3.02
3744 4163 4.825422 TCATACTGGTTCAGCTTCTTGAG 58.175 43.478 0.00 0.00 34.37 3.02
3745 4164 2.557920 ACTGGTTCAGCTTCTTGAGG 57.442 50.000 0.00 0.00 34.37 3.86
3746 4165 2.050144 ACTGGTTCAGCTTCTTGAGGA 58.950 47.619 0.00 0.00 34.37 3.71
3747 4166 2.641815 ACTGGTTCAGCTTCTTGAGGAT 59.358 45.455 0.00 0.00 34.37 3.24
3750 4169 2.026822 GGTTCAGCTTCTTGAGGATCCA 60.027 50.000 15.82 0.00 0.00 3.41
3751 4170 3.560025 GGTTCAGCTTCTTGAGGATCCAA 60.560 47.826 15.82 0.00 0.00 3.53
3752 4171 3.623906 TCAGCTTCTTGAGGATCCAAG 57.376 47.619 15.82 10.02 43.58 3.61
3753 4172 2.015587 CAGCTTCTTGAGGATCCAAGC 58.984 52.381 20.75 20.75 42.34 4.01
3754 4173 1.064832 AGCTTCTTGAGGATCCAAGCC 60.065 52.381 23.31 10.80 40.28 4.35
3755 4174 1.340405 GCTTCTTGAGGATCCAAGCCA 60.340 52.381 18.60 7.15 42.34 4.75
3758 4177 3.744940 TCTTGAGGATCCAAGCCAAAT 57.255 42.857 15.82 0.00 42.34 2.32
3761 4180 4.228210 TCTTGAGGATCCAAGCCAAATAGT 59.772 41.667 15.82 0.00 42.34 2.12
3762 4181 4.156455 TGAGGATCCAAGCCAAATAGTC 57.844 45.455 15.82 0.00 0.00 2.59
3763 4182 3.523157 TGAGGATCCAAGCCAAATAGTCA 59.477 43.478 15.82 0.87 0.00 3.41
3764 4183 4.133078 GAGGATCCAAGCCAAATAGTCAG 58.867 47.826 15.82 0.00 0.00 3.51
3765 4184 3.782523 AGGATCCAAGCCAAATAGTCAGA 59.217 43.478 15.82 0.00 0.00 3.27
3766 4185 3.879892 GGATCCAAGCCAAATAGTCAGAC 59.120 47.826 6.95 0.00 0.00 3.51
3767 4186 3.350219 TCCAAGCCAAATAGTCAGACC 57.650 47.619 0.00 0.00 0.00 3.85
3769 4188 3.055094 TCCAAGCCAAATAGTCAGACCTC 60.055 47.826 0.00 0.00 0.00 3.85
3800 4456 4.637534 GCATGGTTCAGCTTCTTGAGAATA 59.362 41.667 0.00 0.00 33.01 1.75
3825 4481 6.126652 ACAAGCCAAATAGTCAGACCTCATAT 60.127 38.462 0.00 0.00 0.00 1.78
3844 4500 5.298026 TCATATAATGCAAGCAAGGCGTTAA 59.702 36.000 11.32 4.41 43.60 2.01
3925 4581 1.464997 GATGTGGTTCAAAGCGACTCC 59.535 52.381 0.00 0.00 0.00 3.85
3946 4604 0.549469 TCATGGCATGCTGGTCATCT 59.451 50.000 22.56 0.00 28.77 2.90
3958 4616 3.661944 CTGGTCATCTATGGTCTCATGC 58.338 50.000 0.00 0.00 34.96 4.06
3959 4617 2.036346 TGGTCATCTATGGTCTCATGCG 59.964 50.000 0.00 0.00 34.96 4.73
3960 4618 2.611473 GGTCATCTATGGTCTCATGCGG 60.611 54.545 0.00 0.00 34.96 5.69
3961 4619 1.001293 TCATCTATGGTCTCATGCGGC 59.999 52.381 0.00 0.00 34.96 6.53
3962 4620 0.037882 ATCTATGGTCTCATGCGGCG 60.038 55.000 0.51 0.51 34.96 6.46
3963 4621 1.068083 CTATGGTCTCATGCGGCGT 59.932 57.895 9.37 0.00 34.96 5.68
3964 4622 1.217585 CTATGGTCTCATGCGGCGTG 61.218 60.000 15.97 15.97 34.96 5.34
3965 4623 1.955495 TATGGTCTCATGCGGCGTGT 61.955 55.000 20.69 4.20 34.96 4.49
3966 4624 2.742372 GGTCTCATGCGGCGTGTT 60.742 61.111 20.69 0.00 0.00 3.32
3967 4625 2.325082 GGTCTCATGCGGCGTGTTT 61.325 57.895 20.69 0.00 0.00 2.83
3968 4626 1.154413 GTCTCATGCGGCGTGTTTG 60.154 57.895 20.69 12.59 0.00 2.93
3969 4627 2.176546 CTCATGCGGCGTGTTTGG 59.823 61.111 20.69 7.30 0.00 3.28
3970 4628 2.593148 TCATGCGGCGTGTTTGGT 60.593 55.556 20.69 0.00 0.00 3.67
3971 4629 2.128853 CTCATGCGGCGTGTTTGGTT 62.129 55.000 20.69 0.00 0.00 3.67
3972 4630 2.015627 CATGCGGCGTGTTTGGTTG 61.016 57.895 13.98 0.00 0.00 3.77
3987 4645 0.038166 GGTTGCCTGGTCAATCTGGA 59.962 55.000 6.79 0.00 0.00 3.86
3994 4652 2.709934 CCTGGTCAATCTGGATCATCCT 59.290 50.000 4.96 0.00 37.46 3.24
4012 4670 3.395210 TGCTCGTGCAGGAAGAAAA 57.605 47.368 8.30 0.00 45.31 2.29
4013 4671 1.896220 TGCTCGTGCAGGAAGAAAAT 58.104 45.000 8.30 0.00 45.31 1.82
4014 4672 1.536766 TGCTCGTGCAGGAAGAAAATG 59.463 47.619 8.30 0.00 45.31 2.32
4015 4673 1.806542 GCTCGTGCAGGAAGAAAATGA 59.193 47.619 10.76 0.00 39.41 2.57
4016 4674 2.226437 GCTCGTGCAGGAAGAAAATGAA 59.774 45.455 10.76 0.00 39.41 2.57
4017 4675 3.119708 GCTCGTGCAGGAAGAAAATGAAT 60.120 43.478 10.76 0.00 39.41 2.57
4018 4676 4.409570 CTCGTGCAGGAAGAAAATGAATG 58.590 43.478 10.76 0.00 0.00 2.67
4019 4677 4.071423 TCGTGCAGGAAGAAAATGAATGA 58.929 39.130 6.64 0.00 0.00 2.57
4020 4678 4.083324 TCGTGCAGGAAGAAAATGAATGAC 60.083 41.667 6.64 0.00 0.00 3.06
4021 4679 4.488879 GTGCAGGAAGAAAATGAATGACC 58.511 43.478 0.00 0.00 0.00 4.02
4022 4680 4.219288 GTGCAGGAAGAAAATGAATGACCT 59.781 41.667 0.00 0.00 0.00 3.85
4049 4707 3.494223 GGTTTGCTTGGGCTGTATTTGTT 60.494 43.478 0.00 0.00 39.59 2.83
4051 4709 3.658757 TGCTTGGGCTGTATTTGTTTC 57.341 42.857 0.00 0.00 39.59 2.78
4052 4710 3.230134 TGCTTGGGCTGTATTTGTTTCT 58.770 40.909 0.00 0.00 39.59 2.52
4053 4711 3.640967 TGCTTGGGCTGTATTTGTTTCTT 59.359 39.130 0.00 0.00 39.59 2.52
4054 4712 3.989817 GCTTGGGCTGTATTTGTTTCTTG 59.010 43.478 0.00 0.00 35.22 3.02
4055 4713 4.261994 GCTTGGGCTGTATTTGTTTCTTGA 60.262 41.667 0.00 0.00 35.22 3.02
4056 4714 4.846779 TGGGCTGTATTTGTTTCTTGAC 57.153 40.909 0.00 0.00 0.00 3.18
4057 4715 3.572255 TGGGCTGTATTTGTTTCTTGACC 59.428 43.478 0.00 0.00 0.00 4.02
4058 4716 3.056821 GGGCTGTATTTGTTTCTTGACCC 60.057 47.826 0.00 0.00 0.00 4.46
4059 4717 3.365969 GGCTGTATTTGTTTCTTGACCCG 60.366 47.826 0.00 0.00 0.00 5.28
4060 4718 3.821841 CTGTATTTGTTTCTTGACCCGC 58.178 45.455 0.00 0.00 0.00 6.13
4061 4719 3.215151 TGTATTTGTTTCTTGACCCGCA 58.785 40.909 0.00 0.00 0.00 5.69
4067 4725 1.818674 GTTTCTTGACCCGCATGGAAT 59.181 47.619 0.00 0.00 37.49 3.01
4074 4732 3.426615 TGACCCGCATGGAATTTAAAGT 58.573 40.909 0.00 0.00 37.49 2.66
4077 4735 3.380320 ACCCGCATGGAATTTAAAGTAGC 59.620 43.478 0.00 0.00 37.49 3.58
4084 4742 6.183360 GCATGGAATTTAAAGTAGCAGGGAAT 60.183 38.462 0.00 0.00 0.00 3.01
4105 4877 0.823460 CTCTCCCTCACTGCTCCTTC 59.177 60.000 0.00 0.00 0.00 3.46
4106 4878 0.411452 TCTCCCTCACTGCTCCTTCT 59.589 55.000 0.00 0.00 0.00 2.85
4130 4902 1.228398 TTTGATGGCAGACCCGCAA 60.228 52.632 0.00 0.00 35.87 4.85
4157 5716 4.169696 CCCCGGCCTCGTGCATAA 62.170 66.667 0.00 0.00 43.89 1.90
4215 5774 4.202441 CATTTAGGGGGTTCTGATCACAG 58.798 47.826 0.00 0.00 44.66 3.66
4233 5792 2.624364 ACAGCACTGATCATTTGCAACA 59.376 40.909 24.12 0.00 38.81 3.33
4235 5794 2.889045 AGCACTGATCATTTGCAACAGT 59.111 40.909 24.12 12.47 41.52 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 91 0.822121 GCTTTCTCGGGTTTGTGGGT 60.822 55.000 0.00 0.00 0.00 4.51
87 92 0.821711 TGCTTTCTCGGGTTTGTGGG 60.822 55.000 0.00 0.00 0.00 4.61
88 93 1.028905 TTGCTTTCTCGGGTTTGTGG 58.971 50.000 0.00 0.00 0.00 4.17
123 128 0.107654 CCTCTGGTTTTCTAGGCCGG 60.108 60.000 0.00 0.00 0.00 6.13
125 130 1.210722 CTCCCTCTGGTTTTCTAGGCC 59.789 57.143 0.00 0.00 0.00 5.19
138 143 1.051812 CGCCCATGTTATCTCCCTCT 58.948 55.000 0.00 0.00 0.00 3.69
167 172 0.974383 ACTTCCACCCTAGGTTGTCG 59.026 55.000 8.29 0.00 31.02 4.35
180 185 3.650950 GCAGGGAGCCCACTTCCA 61.651 66.667 8.53 0.00 45.35 3.53
295 301 5.965033 AGGTGAATATATAGCTGGATGGG 57.035 43.478 0.00 0.00 0.00 4.00
321 327 6.070656 TCTCTTCATTGGACAAGGAACATTT 58.929 36.000 7.92 0.00 36.36 2.32
322 328 5.634118 TCTCTTCATTGGACAAGGAACATT 58.366 37.500 7.92 0.00 36.36 2.71
326 332 5.307976 TCTTCTCTCTTCATTGGACAAGGAA 59.692 40.000 11.07 11.07 38.56 3.36
340 346 4.045334 TCCCTCCTTTCTCTCTTCTCTCTT 59.955 45.833 0.00 0.00 0.00 2.85
368 374 2.094675 GACCCCATCACAGTCATTTGG 58.905 52.381 0.00 0.00 0.00 3.28
369 375 2.094675 GGACCCCATCACAGTCATTTG 58.905 52.381 0.00 0.00 31.99 2.32
376 382 0.038744 AGCTTTGGACCCCATCACAG 59.961 55.000 0.00 0.00 31.53 3.66
413 419 2.357952 GGTTGAGGGAGTTTGAACACAC 59.642 50.000 0.00 0.00 0.00 3.82
414 420 2.241176 AGGTTGAGGGAGTTTGAACACA 59.759 45.455 0.00 0.00 0.00 3.72
466 473 4.585879 GATATATTTGGTGGTGCCCGTAT 58.414 43.478 0.00 0.00 36.04 3.06
469 476 1.804151 CGATATATTTGGTGGTGCCCG 59.196 52.381 0.00 0.00 36.04 6.13
524 531 1.135689 GCAACTTCAACGCGGATCATT 60.136 47.619 12.47 0.00 0.00 2.57
823 831 3.435671 AGAACTTACGGATTTTGGCGAAG 59.564 43.478 0.00 0.00 0.00 3.79
824 832 3.404899 AGAACTTACGGATTTTGGCGAA 58.595 40.909 0.00 0.00 0.00 4.70
876 884 5.067283 CGGAAAGGGAAGGTATACAAATTGG 59.933 44.000 5.01 0.00 0.00 3.16
882 890 3.644738 GGATCGGAAAGGGAAGGTATACA 59.355 47.826 5.01 0.00 0.00 2.29
889 897 0.811616 CGCAGGATCGGAAAGGGAAG 60.812 60.000 0.00 0.00 0.00 3.46
924 934 5.007682 AGATTAAGAGAGATCTAGCGGGAC 58.992 45.833 0.00 0.00 31.09 4.46
1298 1473 4.362932 TCTCTCTCGCACAACATCTTAG 57.637 45.455 0.00 0.00 0.00 2.18
1305 1482 4.935885 AAATCAATCTCTCTCGCACAAC 57.064 40.909 0.00 0.00 0.00 3.32
1334 1511 9.383519 TCTTAAGCAATTTAGACTTGTAGATGG 57.616 33.333 0.00 0.00 0.00 3.51
1370 1547 7.716998 TGGAGGCTACATTTAATCAATCTCTTC 59.283 37.037 0.00 0.00 0.00 2.87
1442 1620 4.750098 TGTAGCTTGAAGGAAGAAGAAACG 59.250 41.667 0.00 0.00 32.82 3.60
1449 1628 6.305272 AGAATGATGTAGCTTGAAGGAAGA 57.695 37.500 0.00 0.00 32.82 2.87
1484 1663 5.444663 AAGAACAAACCTGAAGATTGAGC 57.555 39.130 0.00 0.00 0.00 4.26
1491 1670 7.026631 TGATGTTGTAAGAACAAACCTGAAG 57.973 36.000 0.00 0.00 46.84 3.02
1492 1671 7.338196 TCTTGATGTTGTAAGAACAAACCTGAA 59.662 33.333 0.00 0.00 46.84 3.02
1493 1672 6.826231 TCTTGATGTTGTAAGAACAAACCTGA 59.174 34.615 0.00 0.00 46.84 3.86
1680 1859 1.633852 GCTTCACTGAGCCGCTGAAG 61.634 60.000 13.24 13.24 42.56 3.02
2276 2455 2.223456 TGACACATTCAAGGCACAAACG 60.223 45.455 0.00 0.00 0.00 3.60
2302 2481 8.684386 TCATGGTTAAAGAAATGTCACTAACA 57.316 30.769 8.57 0.00 43.51 2.41
2325 2505 8.727100 ATCATATGAGAAGGTATGGTAGTTCA 57.273 34.615 11.78 0.00 0.00 3.18
2398 2579 4.983671 ATGAGAACACATGCTAGTACGA 57.016 40.909 0.00 0.00 0.00 3.43
2422 2603 7.011763 CCTGTACACATTCCAAGACAGATTATG 59.988 40.741 0.00 0.00 37.14 1.90
2644 2825 8.918202 ACCAGATTAAGACTTCATGTAAACAA 57.082 30.769 0.00 0.00 0.00 2.83
2682 2863 5.989551 AAAAACCAATCAGAACATGCAAC 57.010 34.783 0.00 0.00 0.00 4.17
2689 2870 8.141835 AGCAACAAATAAAAACCAATCAGAAC 57.858 30.769 0.00 0.00 0.00 3.01
3083 3266 2.637872 CAGGAGGGACACAAGGAAGTTA 59.362 50.000 0.00 0.00 0.00 2.24
3180 3388 8.143835 GGGGAACACAAATCATATAAAATCAGG 58.856 37.037 0.00 0.00 0.00 3.86
3274 3482 6.514048 GCCCAGTATCTTATCAAATTCACTGC 60.514 42.308 0.00 0.00 32.68 4.40
3282 3490 4.721776 AGGACAGCCCAGTATCTTATCAAA 59.278 41.667 0.00 0.00 37.41 2.69
3360 3568 5.065218 ACTTGTTGATATTCGCTTAGGCAAG 59.935 40.000 0.00 0.00 38.60 4.01
3393 3601 8.964476 ATTTCTGTTCAAGACAAGACTAGAAA 57.036 30.769 0.00 0.00 37.93 2.52
3395 3603 7.726216 TGATTTCTGTTCAAGACAAGACTAGA 58.274 34.615 0.00 0.00 37.93 2.43
3404 3612 4.142513 GCTCCCATGATTTCTGTTCAAGAC 60.143 45.833 0.00 0.00 33.46 3.01
3539 3748 9.567848 AGCAAATAAGTTATCCATTTAAACACG 57.432 29.630 0.00 0.00 0.00 4.49
3564 3773 3.614092 TCCTGAGATTTGCAAGGCTAAG 58.386 45.455 0.00 3.76 0.00 2.18
3572 3781 7.765695 AACTTCTATTTTCCTGAGATTTGCA 57.234 32.000 0.00 0.00 0.00 4.08
3640 3849 9.736023 GAAAATCCAAAAGCAGATATTACGATT 57.264 29.630 0.00 0.00 0.00 3.34
3645 3854 9.241919 TCACTGAAAATCCAAAAGCAGATATTA 57.758 29.630 0.00 0.00 0.00 0.98
3646 3855 8.125978 TCACTGAAAATCCAAAAGCAGATATT 57.874 30.769 0.00 0.00 0.00 1.28
3648 3857 7.414429 CGATCACTGAAAATCCAAAAGCAGATA 60.414 37.037 0.00 0.00 0.00 1.98
3649 3858 6.600882 ATCACTGAAAATCCAAAAGCAGAT 57.399 33.333 0.00 0.00 0.00 2.90
3650 3859 5.335113 CGATCACTGAAAATCCAAAAGCAGA 60.335 40.000 0.00 0.00 0.00 4.26
3651 3860 4.855388 CGATCACTGAAAATCCAAAAGCAG 59.145 41.667 0.00 0.00 0.00 4.24
3723 4142 3.937706 CCTCAAGAAGCTGAACCAGTATG 59.062 47.826 0.00 0.00 33.43 2.39
3729 4148 2.026822 TGGATCCTCAAGAAGCTGAACC 60.027 50.000 14.23 0.00 0.00 3.62
3730 4149 3.340814 TGGATCCTCAAGAAGCTGAAC 57.659 47.619 14.23 0.00 0.00 3.18
3731 4150 3.871463 GCTTGGATCCTCAAGAAGCTGAA 60.871 47.826 20.94 0.56 44.98 3.02
3734 4153 1.064832 GGCTTGGATCCTCAAGAAGCT 60.065 52.381 24.91 0.00 44.98 3.74
3736 4155 2.795231 TGGCTTGGATCCTCAAGAAG 57.205 50.000 14.23 8.81 44.98 2.85
3740 4159 4.018506 TGACTATTTGGCTTGGATCCTCAA 60.019 41.667 14.23 9.43 0.00 3.02
3741 4160 3.523157 TGACTATTTGGCTTGGATCCTCA 59.477 43.478 14.23 0.29 0.00 3.86
3742 4161 4.133078 CTGACTATTTGGCTTGGATCCTC 58.867 47.826 14.23 1.96 0.00 3.71
3744 4163 3.879892 GTCTGACTATTTGGCTTGGATCC 59.120 47.826 4.20 4.20 0.00 3.36
3745 4164 3.879892 GGTCTGACTATTTGGCTTGGATC 59.120 47.826 7.85 0.00 0.00 3.36
3746 4165 3.525199 AGGTCTGACTATTTGGCTTGGAT 59.475 43.478 7.85 0.00 0.00 3.41
3747 4166 2.912956 AGGTCTGACTATTTGGCTTGGA 59.087 45.455 7.85 0.00 0.00 3.53
3750 4169 4.851639 ATGAGGTCTGACTATTTGGCTT 57.148 40.909 7.85 0.00 0.00 4.35
3751 4170 4.716784 TGTATGAGGTCTGACTATTTGGCT 59.283 41.667 7.85 0.00 0.00 4.75
3752 4171 5.023533 TGTATGAGGTCTGACTATTTGGC 57.976 43.478 7.85 0.00 0.00 4.52
3753 4172 6.017605 GCATTGTATGAGGTCTGACTATTTGG 60.018 42.308 7.85 0.00 0.00 3.28
3754 4173 6.539826 TGCATTGTATGAGGTCTGACTATTTG 59.460 38.462 7.85 0.00 0.00 2.32
3755 4174 6.653020 TGCATTGTATGAGGTCTGACTATTT 58.347 36.000 7.85 0.00 0.00 1.40
3758 4177 5.453762 CCATGCATTGTATGAGGTCTGACTA 60.454 44.000 15.34 0.00 0.00 2.59
3761 4180 3.200605 ACCATGCATTGTATGAGGTCTGA 59.799 43.478 15.34 0.00 29.40 3.27
3762 4181 3.548770 ACCATGCATTGTATGAGGTCTG 58.451 45.455 15.34 1.43 29.40 3.51
3763 4182 3.939740 ACCATGCATTGTATGAGGTCT 57.060 42.857 15.34 0.00 29.40 3.85
3764 4183 3.947196 TGAACCATGCATTGTATGAGGTC 59.053 43.478 15.34 13.12 32.69 3.85
3765 4184 3.949754 CTGAACCATGCATTGTATGAGGT 59.050 43.478 15.34 0.01 34.42 3.85
3766 4185 3.243301 GCTGAACCATGCATTGTATGAGG 60.243 47.826 15.34 0.00 0.00 3.86
3767 4186 3.630769 AGCTGAACCATGCATTGTATGAG 59.369 43.478 15.34 8.50 0.00 2.90
3769 4188 4.097437 AGAAGCTGAACCATGCATTGTATG 59.903 41.667 3.50 7.67 0.00 2.39
3800 4456 3.327757 TGAGGTCTGACTATTTGGCTTGT 59.672 43.478 7.85 0.00 0.00 3.16
3825 4481 3.078097 TCTTAACGCCTTGCTTGCATTA 58.922 40.909 0.00 0.00 0.00 1.90
3925 4581 1.337071 GATGACCAGCATGCCATGAAG 59.663 52.381 15.66 0.00 37.34 3.02
3946 4604 1.227234 CACGCCGCATGAGACCATA 60.227 57.895 0.00 0.00 0.00 2.74
3959 4617 2.027460 CAGGCAACCAAACACGCC 59.973 61.111 0.00 0.00 45.23 5.68
3960 4618 2.027460 CCAGGCAACCAAACACGC 59.973 61.111 0.00 0.00 37.17 5.34
3961 4619 1.358759 GACCAGGCAACCAAACACG 59.641 57.895 0.00 0.00 37.17 4.49
3962 4620 0.820871 TTGACCAGGCAACCAAACAC 59.179 50.000 0.00 0.00 37.17 3.32
3963 4621 1.686052 GATTGACCAGGCAACCAAACA 59.314 47.619 0.00 0.00 37.17 2.83
3964 4622 1.963515 AGATTGACCAGGCAACCAAAC 59.036 47.619 0.00 0.00 37.17 2.93
3965 4623 1.962807 CAGATTGACCAGGCAACCAAA 59.037 47.619 0.00 0.00 37.17 3.28
3966 4624 1.619654 CAGATTGACCAGGCAACCAA 58.380 50.000 0.00 0.00 37.17 3.67
3967 4625 0.251297 CCAGATTGACCAGGCAACCA 60.251 55.000 0.00 0.00 37.17 3.67
3968 4626 0.038166 TCCAGATTGACCAGGCAACC 59.962 55.000 0.00 0.00 37.17 3.77
3969 4627 2.019984 GATCCAGATTGACCAGGCAAC 58.980 52.381 0.00 0.00 0.00 4.17
3970 4628 1.634973 TGATCCAGATTGACCAGGCAA 59.365 47.619 0.00 0.00 0.00 4.52
3971 4629 1.288188 TGATCCAGATTGACCAGGCA 58.712 50.000 0.00 0.00 0.00 4.75
3972 4630 2.502295 GATGATCCAGATTGACCAGGC 58.498 52.381 0.00 0.00 0.00 4.85
4018 4676 4.994317 GCCCAAGCAAACCAAACAGGTC 62.994 54.545 0.00 0.00 45.20 3.85
4020 4678 0.532640 GCCCAAGCAAACCAAACAGG 60.533 55.000 0.00 0.00 40.80 4.00
4021 4679 0.465287 AGCCCAAGCAAACCAAACAG 59.535 50.000 0.00 0.00 43.56 3.16
4022 4680 0.177604 CAGCCCAAGCAAACCAAACA 59.822 50.000 0.00 0.00 43.56 2.83
4049 4707 2.214376 AATTCCATGCGGGTCAAGAA 57.786 45.000 0.00 0.00 38.11 2.52
4051 4709 4.082245 ACTTTAAATTCCATGCGGGTCAAG 60.082 41.667 0.00 0.00 38.11 3.02
4052 4710 3.829601 ACTTTAAATTCCATGCGGGTCAA 59.170 39.130 0.00 0.00 38.11 3.18
4053 4711 3.426615 ACTTTAAATTCCATGCGGGTCA 58.573 40.909 0.00 0.00 38.11 4.02
4054 4712 4.497507 GCTACTTTAAATTCCATGCGGGTC 60.498 45.833 0.00 0.00 38.11 4.46
4055 4713 3.380320 GCTACTTTAAATTCCATGCGGGT 59.620 43.478 0.00 0.00 38.11 5.28
4056 4714 3.380004 TGCTACTTTAAATTCCATGCGGG 59.620 43.478 0.00 0.00 38.37 6.13
4057 4715 4.498009 CCTGCTACTTTAAATTCCATGCGG 60.498 45.833 0.00 0.00 0.00 5.69
4058 4716 4.498009 CCCTGCTACTTTAAATTCCATGCG 60.498 45.833 0.00 0.00 0.00 4.73
4059 4717 4.644685 TCCCTGCTACTTTAAATTCCATGC 59.355 41.667 0.00 0.00 0.00 4.06
4060 4718 6.773976 TTCCCTGCTACTTTAAATTCCATG 57.226 37.500 0.00 0.00 0.00 3.66
4061 4719 7.352079 CATTCCCTGCTACTTTAAATTCCAT 57.648 36.000 0.00 0.00 0.00 3.41
4084 4742 1.986757 GGAGCAGTGAGGGAGAGCA 60.987 63.158 0.00 0.00 0.00 4.26
4086 4744 0.823460 GAAGGAGCAGTGAGGGAGAG 59.177 60.000 0.00 0.00 0.00 3.20
4087 4745 0.411452 AGAAGGAGCAGTGAGGGAGA 59.589 55.000 0.00 0.00 0.00 3.71
4088 4746 0.536260 CAGAAGGAGCAGTGAGGGAG 59.464 60.000 0.00 0.00 0.00 4.30
4089 4747 0.178921 ACAGAAGGAGCAGTGAGGGA 60.179 55.000 0.00 0.00 0.00 4.20
4090 4748 0.248843 GACAGAAGGAGCAGTGAGGG 59.751 60.000 0.00 0.00 0.00 4.30
4091 4749 1.204467 GAGACAGAAGGAGCAGTGAGG 59.796 57.143 0.00 0.00 0.00 3.86
4105 4877 2.354259 GGTCTGCCATCAAAGAGACAG 58.646 52.381 0.00 0.00 37.22 3.51
4106 4878 1.003580 GGGTCTGCCATCAAAGAGACA 59.996 52.381 0.00 0.00 37.22 3.41
4171 5730 7.881775 ATGGATTCAAATTTGTCCTACTACC 57.118 36.000 21.89 13.86 0.00 3.18
4183 5742 6.156775 CAGAACCCCCTAAATGGATTCAAATT 59.843 38.462 0.00 0.00 38.35 1.82
4215 5774 3.240069 GACTGTTGCAAATGATCAGTGC 58.760 45.455 20.54 21.60 39.08 4.40
4233 5792 3.079578 CAACTGCCAATGATCAGTGACT 58.920 45.455 24.02 0.00 42.19 3.41
4235 5794 1.814394 GCAACTGCCAATGATCAGTGA 59.186 47.619 24.02 4.57 42.19 3.41


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

AutoCloner maintained by Alex Coulton.