Multiple sequence alignment - TraesCS2A01G256700

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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 TraesCS2A01G256700 chr2A 100.000 4462 0 0 1 4462 393345140 393340679 0.000000e+00 8240
1 TraesCS2A01G256700 chr2D 93.753 3986 163 39 1 3948 324857477 324861414 0.000000e+00 5903
2 TraesCS2A01G256700 chr2D 96.247 453 14 1 4013 4462 324861418 324861870 0.000000e+00 739
3 TraesCS2A01G256700 chr2B 94.530 2066 79 14 1913 3948 393857215 393859276 0.000000e+00 3158
4 TraesCS2A01G256700 chr2B 95.401 1370 39 14 547 1911 393855805 393857155 0.000000e+00 2159
5 TraesCS2A01G256700 chr2B 96.119 438 17 0 4025 4462 393859295 393859732 0.000000e+00 715
6 TraesCS2A01G256700 chr2B 79.874 159 12 9 389 547 393854531 393854669 1.020000e-16 99
7 TraesCS2A01G256700 chr3D 90.830 458 39 3 4007 4462 481515271 481515727 1.060000e-170 610
8 TraesCS2A01G256700 chr3B 89.934 457 41 5 4010 4462 642485333 642485788 6.430000e-163 584
9 TraesCS2A01G256700 chr3A 89.648 454 41 4 4013 4462 624528486 624528937 1.390000e-159 573
10 TraesCS2A01G256700 chr6A 90.828 338 28 3 3614 3948 4814532 4814869 2.450000e-122 449
11 TraesCS2A01G256700 chr6A 88.793 116 8 3 4013 4124 4814873 4814987 2.160000e-28 137
12 TraesCS2A01G256700 chr7A 80.423 189 19 9 255 431 177292395 177292213 1.300000e-25 128


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 TraesCS2A01G256700 chr2A 393340679 393345140 4461 True 8240.00 8240 100.000 1 4462 1 chr2A.!!$R1 4461
1 TraesCS2A01G256700 chr2D 324857477 324861870 4393 False 3321.00 5903 95.000 1 4462 2 chr2D.!!$F1 4461
2 TraesCS2A01G256700 chr2B 393854531 393859732 5201 False 1532.75 3158 91.481 389 4462 4 chr2B.!!$F1 4073

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
193 199 0.253327 GGGGAGCGAAGAGAACCATT 59.747 55.000 0.0 0.0 0.00 3.16 F
605 1754 1.338020 TCATCCACATCCTCGTCATCG 59.662 52.381 0.0 0.0 38.55 3.84 F
607 1756 1.692411 TCCACATCCTCGTCATCGAT 58.308 50.000 0.0 0.0 45.21 3.59 F
2218 3429 0.952280 TCATCGTATCTGTCTCCGCC 59.048 55.000 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 2632 0.396417 TACATTGCCCCCATTTCCGG 60.396 55.0 0.00 0.0 0.00 5.14 R
2218 3429 0.031994 CAAAACCAAGAAGGGCCACG 59.968 55.0 6.18 0.0 43.89 4.94 R
2294 3505 0.848942 CAGCTTACAGATACAGCGCG 59.151 55.0 0.00 0.0 38.66 6.86 R
3950 5188 0.467384 CGAGGACGGAGGGAGTACTA 59.533 60.0 0.00 0.0 31.89 1.82 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
107 108 1.251527 GGAGAAGAGCAGTCGTCCCA 61.252 60.000 0.00 0.00 31.98 4.37
111 112 0.612174 AAGAGCAGTCGTCCCAGCTA 60.612 55.000 0.00 0.00 37.48 3.32
114 115 0.684479 AGCAGTCGTCCCAGCTATGA 60.684 55.000 0.00 0.00 35.19 2.15
121 122 0.530870 GTCCCAGCTATGACGAAGGC 60.531 60.000 0.00 0.00 0.00 4.35
122 123 1.227674 CCCAGCTATGACGAAGGCC 60.228 63.158 0.00 0.00 0.00 5.19
123 124 1.592669 CCAGCTATGACGAAGGCCG 60.593 63.158 0.00 0.00 45.44 6.13
124 125 1.592669 CAGCTATGACGAAGGCCGG 60.593 63.158 0.00 0.00 43.93 6.13
125 126 1.756950 AGCTATGACGAAGGCCGGA 60.757 57.895 5.05 0.00 43.93 5.14
126 127 1.300233 GCTATGACGAAGGCCGGAG 60.300 63.158 5.05 0.00 43.93 4.63
145 146 0.764752 GGGAGAGGGGTGGATCGAAT 60.765 60.000 0.00 0.00 0.00 3.34
162 163 5.036117 TCGAATAATCAAAGAGGGGAAGG 57.964 43.478 0.00 0.00 0.00 3.46
168 169 1.230314 AAAGAGGGGAAGGGAGGGG 60.230 63.158 0.00 0.00 0.00 4.79
169 170 1.772561 AAAGAGGGGAAGGGAGGGGA 61.773 60.000 0.00 0.00 0.00 4.81
170 171 2.040359 GAGGGGAAGGGAGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
171 172 3.711782 AGGGGAAGGGAGGGGAGG 61.712 72.222 0.00 0.00 0.00 4.30
193 199 0.253327 GGGGAGCGAAGAGAACCATT 59.747 55.000 0.00 0.00 0.00 3.16
431 444 6.607970 TGATCCTACGATCTTACCTAAAGGA 58.392 40.000 2.23 0.00 44.61 3.36
432 445 7.239438 TGATCCTACGATCTTACCTAAAGGAT 58.761 38.462 2.23 0.00 44.61 3.24
434 447 7.909485 TCCTACGATCTTACCTAAAGGATTT 57.091 36.000 2.23 0.00 43.42 2.17
435 448 8.315220 TCCTACGATCTTACCTAAAGGATTTT 57.685 34.615 2.23 0.00 40.09 1.82
490 503 5.752955 GCAAACTCATGGTTACAAACACAAT 59.247 36.000 0.00 0.00 37.12 2.71
491 504 6.257630 GCAAACTCATGGTTACAAACACAATT 59.742 34.615 0.00 0.00 37.12 2.32
493 506 8.663911 CAAACTCATGGTTACAAACACAATTTT 58.336 29.630 0.00 0.00 37.12 1.82
494 507 8.785329 AACTCATGGTTACAAACACAATTTTT 57.215 26.923 0.00 0.00 36.23 1.94
542 555 7.873505 CAGACTCAGACATCATTACATCATCAT 59.126 37.037 0.00 0.00 0.00 2.45
566 1715 9.481340 CATATATTCACAACTCATATATCCCCG 57.519 37.037 0.00 0.00 27.84 5.73
605 1754 1.338020 TCATCCACATCCTCGTCATCG 59.662 52.381 0.00 0.00 38.55 3.84
607 1756 1.692411 TCCACATCCTCGTCATCGAT 58.308 50.000 0.00 0.00 45.21 3.59
789 1939 3.897122 GTTCACTGGGCCCCACCA 61.897 66.667 22.27 0.00 42.05 4.17
869 2019 6.719370 GCATAAAATATACCAATCCTGACCCA 59.281 38.462 0.00 0.00 0.00 4.51
1037 2187 2.374342 CTCCACCTCCTCCCCCAT 59.626 66.667 0.00 0.00 0.00 4.00
1236 2386 2.037687 CCCTCCAAGCCCAATGCA 59.962 61.111 0.00 0.00 44.83 3.96
1240 2390 2.202824 CCAAGCCCAATGCATGCG 60.203 61.111 14.09 0.00 44.83 4.73
1320 2470 2.819595 CACAACGCATCGAGGGGG 60.820 66.667 18.58 10.40 33.80 5.40
1482 2632 7.331791 TGGGGGTAATGTAAAATAAATGTTGC 58.668 34.615 0.00 0.00 0.00 4.17
1549 2699 4.141065 GGATCTCCCAATCCTGATTCCTTT 60.141 45.833 0.00 0.00 41.78 3.11
1579 2729 6.418057 TTTCACCCTTCATTTGCAACTAAT 57.582 33.333 0.00 0.00 0.00 1.73
1627 2778 2.306847 CCTACCAACAAACACCTTGCT 58.693 47.619 0.00 0.00 38.75 3.91
1681 2832 3.777522 CCTATGTCTTCCTCCTCCAAACT 59.222 47.826 0.00 0.00 0.00 2.66
1695 2846 5.072600 TCCTCCAAACTAAAGTAAGAGCCAA 59.927 40.000 0.00 0.00 0.00 4.52
2059 3270 5.496387 GTGTGTTATTTCTCATCATCGCAG 58.504 41.667 0.00 0.00 0.00 5.18
2122 3333 2.171725 GGTTGCTATGTCCGACCGC 61.172 63.158 0.00 0.00 0.00 5.68
2218 3429 0.952280 TCATCGTATCTGTCTCCGCC 59.048 55.000 0.00 0.00 0.00 6.13
2236 3447 1.112916 CCGTGGCCCTTCTTGGTTTT 61.113 55.000 0.00 0.00 0.00 2.43
2294 3505 4.092821 TCTTTGTATTGTATCGCTGTGTGC 59.907 41.667 0.00 0.00 38.57 4.57
2496 3707 9.661563 AACAAAATACCGACATATTCTGTTAGA 57.338 29.630 4.78 0.00 35.11 2.10
2647 3859 5.730568 GCAAAAATGTTGTGTCGTCTTCTCT 60.731 40.000 0.00 0.00 0.00 3.10
2889 4102 5.869344 TGAGTATTTGGTTCTTCATGACTCG 59.131 40.000 0.00 0.00 34.80 4.18
2917 4132 3.380479 TTTCGTGACTCACTGTTAGGG 57.620 47.619 7.58 0.00 31.34 3.53
2975 4190 4.327627 GGCGTAAAGAAGAACTCTGATGTC 59.672 45.833 0.00 0.00 33.37 3.06
2976 4191 4.327627 GCGTAAAGAAGAACTCTGATGTCC 59.672 45.833 0.00 0.00 33.37 4.02
3077 4292 3.317993 GCACTGTTGTGATAAACCCACTT 59.682 43.478 0.00 0.00 46.55 3.16
3148 4368 6.071784 ACGTGTATATACTTGTGTCCTGTTGA 60.072 38.462 13.89 0.00 0.00 3.18
3177 4397 4.912317 ACTTCTAAGTTCCTCCCTTTCC 57.088 45.455 0.00 0.00 35.21 3.13
3310 4530 6.053005 TCGAAAAGTCATTACCATGGTATCC 58.947 40.000 25.12 12.78 0.00 2.59
3433 4654 3.801129 GCTTCCACCTAAGCGAGC 58.199 61.111 0.00 0.00 42.21 5.03
3493 4715 7.641760 TGTGCTTATGTATGATGTTATGCTTG 58.358 34.615 0.00 0.00 0.00 4.01
3505 4727 9.758021 ATGATGTTATGCTTGGAATAATGGATA 57.242 29.630 0.00 0.00 0.00 2.59
3541 4763 5.741673 GCCCAAAATTTTACATGTCTGGTGT 60.742 40.000 0.00 0.00 0.00 4.16
3591 4826 3.313012 TCGAAGTGTTGTCGATGGATT 57.687 42.857 0.00 0.00 42.31 3.01
3613 4848 1.880819 GCAATGTGCAGTTCAGGGGG 61.881 60.000 0.00 0.00 44.26 5.40
3620 4855 0.398318 GCAGTTCAGGGGGCCTATAG 59.602 60.000 0.84 0.00 29.64 1.31
3649 4885 2.910688 TCCGTCTTCTGCTTGTTCTT 57.089 45.000 0.00 0.00 0.00 2.52
3671 4907 4.946478 TTTTTGGTGGAATTTGGTCGAT 57.054 36.364 0.00 0.00 0.00 3.59
3699 4935 5.759506 TGCTCTAGTAGAGGAGAAAATCG 57.240 43.478 25.20 0.98 42.54 3.34
3742 4978 1.399727 CCGAGTCGTTTTGTGATTGCC 60.400 52.381 12.31 0.00 0.00 4.52
3743 4979 1.531149 CGAGTCGTTTTGTGATTGCCT 59.469 47.619 3.82 0.00 0.00 4.75
3765 5001 0.663153 GCCATGTTTACCATCGGAGC 59.337 55.000 0.00 0.00 0.00 4.70
3782 5018 2.100216 CGTTGCTGGTTATGCCGC 59.900 61.111 0.00 0.00 41.21 6.53
3783 5019 2.398554 CGTTGCTGGTTATGCCGCT 61.399 57.895 0.00 0.00 41.21 5.52
3804 5040 7.425606 CCGCTTGGAGCTTAATATTTGTAAAT 58.574 34.615 0.00 0.00 39.60 1.40
3831 5068 4.697352 ACCAGTCTCTTGAATTATGTGTGC 59.303 41.667 0.00 0.00 0.00 4.57
3846 5083 0.698238 TGTGCATTGTAGAGGGCCTT 59.302 50.000 7.89 0.00 0.00 4.35
3859 5096 7.280356 TGTAGAGGGCCTTAAAAGTCATATTC 58.720 38.462 7.89 0.00 0.00 1.75
3866 5103 7.066645 GGGCCTTAAAAGTCATATTCGTAAGTT 59.933 37.037 0.84 0.00 39.48 2.66
3868 5105 9.274065 GCCTTAAAAGTCATATTCGTAAGTTTG 57.726 33.333 0.00 0.00 39.48 2.93
3903 5140 3.121030 GATGTCCTGCGCGTTGCT 61.121 61.111 8.43 0.00 46.63 3.91
3906 5143 0.744414 ATGTCCTGCGCGTTGCTAAT 60.744 50.000 8.43 0.00 46.63 1.73
3940 5178 7.828717 TCAAGAATGTGAGAAATACTTGGCATA 59.171 33.333 0.00 0.00 35.49 3.14
3961 5199 7.484035 CATAATTGCAAACTAGTACTCCCTC 57.516 40.000 1.71 0.00 0.00 4.30
3962 5200 3.975168 TTGCAAACTAGTACTCCCTCC 57.025 47.619 0.00 0.00 0.00 4.30
3963 5201 1.822990 TGCAAACTAGTACTCCCTCCG 59.177 52.381 0.00 0.00 0.00 4.63
3964 5202 1.823610 GCAAACTAGTACTCCCTCCGT 59.176 52.381 0.00 0.00 0.00 4.69
3965 5203 2.159268 GCAAACTAGTACTCCCTCCGTC 60.159 54.545 0.00 0.00 0.00 4.79
3966 5204 2.426381 CAAACTAGTACTCCCTCCGTCC 59.574 54.545 0.00 0.00 0.00 4.79
3967 5205 1.594129 ACTAGTACTCCCTCCGTCCT 58.406 55.000 0.00 0.00 0.00 3.85
3968 5206 1.490069 ACTAGTACTCCCTCCGTCCTC 59.510 57.143 0.00 0.00 0.00 3.71
3969 5207 0.467384 TAGTACTCCCTCCGTCCTCG 59.533 60.000 0.00 0.00 0.00 4.63
3982 5220 3.109044 CGTCCTCGGTATCTAGACAGA 57.891 52.381 0.00 0.00 34.56 3.41
3983 5221 2.801679 CGTCCTCGGTATCTAGACAGAC 59.198 54.545 0.00 0.00 32.25 3.51
3984 5222 3.740452 CGTCCTCGGTATCTAGACAGACA 60.740 52.174 0.00 0.00 32.25 3.41
3985 5223 4.197750 GTCCTCGGTATCTAGACAGACAA 58.802 47.826 0.00 0.00 32.25 3.18
3986 5224 4.273969 GTCCTCGGTATCTAGACAGACAAG 59.726 50.000 0.00 0.00 32.25 3.16
3987 5225 4.080469 TCCTCGGTATCTAGACAGACAAGT 60.080 45.833 0.00 0.00 32.25 3.16
3988 5226 5.129980 TCCTCGGTATCTAGACAGACAAGTA 59.870 44.000 0.00 0.00 32.25 2.24
3989 5227 5.821470 CCTCGGTATCTAGACAGACAAGTAA 59.179 44.000 0.00 0.00 32.25 2.24
3990 5228 6.487331 CCTCGGTATCTAGACAGACAAGTAAT 59.513 42.308 0.00 0.00 32.25 1.89
3991 5229 7.260558 TCGGTATCTAGACAGACAAGTAATG 57.739 40.000 0.00 0.00 32.25 1.90
4006 5244 7.645058 ACAAGTAATGTCTAATTTGGGATGG 57.355 36.000 0.00 0.00 37.96 3.51
4007 5245 7.410174 ACAAGTAATGTCTAATTTGGGATGGA 58.590 34.615 0.00 0.00 37.96 3.41
4008 5246 7.557719 ACAAGTAATGTCTAATTTGGGATGGAG 59.442 37.037 0.00 0.00 37.96 3.86
4009 5247 6.605119 AGTAATGTCTAATTTGGGATGGAGG 58.395 40.000 0.00 0.00 0.00 4.30
4010 5248 5.472301 AATGTCTAATTTGGGATGGAGGT 57.528 39.130 0.00 0.00 0.00 3.85
4011 5249 6.590656 AATGTCTAATTTGGGATGGAGGTA 57.409 37.500 0.00 0.00 0.00 3.08
4015 5253 7.918076 TGTCTAATTTGGGATGGAGGTATATC 58.082 38.462 0.00 0.00 0.00 1.63
4057 5298 3.628942 TGCAATCATACAGCTGAATGGTC 59.371 43.478 23.35 2.88 0.00 4.02
4078 5319 2.775890 GATGCATCATTCGGATCAGGT 58.224 47.619 21.92 0.00 32.57 4.00
4113 5354 3.428452 CGAAATCATTTGCTGATGCCTGT 60.428 43.478 0.00 0.00 44.03 4.00
4288 5529 0.320374 CCCTAGTGAACTCGTTGCCA 59.680 55.000 0.00 0.00 0.00 4.92
4354 5595 0.745468 GTATCGGGCTCTCGAACCTT 59.255 55.000 0.00 0.00 42.69 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.699522 GTGTCCCCCACGTCCAGC 62.700 72.222 0.00 0.00 33.61 4.85
90 91 1.882989 GCTGGGACGACTGCTCTTCT 61.883 60.000 0.00 0.00 33.20 2.85
91 92 1.446966 GCTGGGACGACTGCTCTTC 60.447 63.158 0.00 0.00 33.20 2.87
92 93 0.612174 TAGCTGGGACGACTGCTCTT 60.612 55.000 12.19 0.00 43.35 2.85
93 94 0.396417 ATAGCTGGGACGACTGCTCT 60.396 55.000 12.19 3.46 43.35 4.09
107 108 1.739338 CTCCGGCCTTCGTCATAGCT 61.739 60.000 0.00 0.00 37.11 3.32
111 112 3.470888 CCCTCCGGCCTTCGTCAT 61.471 66.667 0.00 0.00 37.11 3.06
114 115 4.377760 TCTCCCTCCGGCCTTCGT 62.378 66.667 0.00 0.00 37.11 3.85
122 123 3.396822 ATCCACCCCTCTCCCTCCG 62.397 68.421 0.00 0.00 0.00 4.63
123 124 1.460497 GATCCACCCCTCTCCCTCC 60.460 68.421 0.00 0.00 0.00 4.30
124 125 1.834822 CGATCCACCCCTCTCCCTC 60.835 68.421 0.00 0.00 0.00 4.30
125 126 1.886730 TTCGATCCACCCCTCTCCCT 61.887 60.000 0.00 0.00 0.00 4.20
126 127 0.764752 ATTCGATCCACCCCTCTCCC 60.765 60.000 0.00 0.00 0.00 4.30
127 128 2.011122 TATTCGATCCACCCCTCTCC 57.989 55.000 0.00 0.00 0.00 3.71
145 146 3.123273 CCTCCCTTCCCCTCTTTGATTA 58.877 50.000 0.00 0.00 0.00 1.75
239 245 0.032815 GCTTTAGGTGCCCGCAAAAA 59.967 50.000 0.00 0.00 0.00 1.94
240 246 0.825840 AGCTTTAGGTGCCCGCAAAA 60.826 50.000 0.00 0.00 0.00 2.44
241 247 1.228429 AGCTTTAGGTGCCCGCAAA 60.228 52.632 0.00 0.00 0.00 3.68
242 248 1.971167 CAGCTTTAGGTGCCCGCAA 60.971 57.895 0.00 0.00 36.70 4.85
243 249 2.359850 CAGCTTTAGGTGCCCGCA 60.360 61.111 0.00 0.00 36.70 5.69
244 250 1.241315 TTTCAGCTTTAGGTGCCCGC 61.241 55.000 4.12 0.00 42.77 6.13
245 251 0.521735 GTTTCAGCTTTAGGTGCCCG 59.478 55.000 4.12 0.00 42.77 6.13
246 252 1.911057 AGTTTCAGCTTTAGGTGCCC 58.089 50.000 4.12 0.00 42.77 5.36
247 253 4.700213 TGAATAGTTTCAGCTTTAGGTGCC 59.300 41.667 4.12 0.00 42.77 5.01
248 254 5.880054 TGAATAGTTTCAGCTTTAGGTGC 57.120 39.130 4.12 0.00 42.77 5.01
249 255 8.723942 ACTATGAATAGTTTCAGCTTTAGGTG 57.276 34.615 2.60 2.60 44.75 4.00
443 456 8.985315 TGCATTAATCATCTTGGAGAATTACT 57.015 30.769 0.00 0.00 0.00 2.24
451 464 7.417003 CCATGAGTTTGCATTAATCATCTTGGA 60.417 37.037 8.72 0.00 34.41 3.53
457 470 8.065473 TGTAACCATGAGTTTGCATTAATCAT 57.935 30.769 6.49 6.49 40.05 2.45
494 507 9.020731 GTCTGAAAGGGAATGGATAAGTAAAAA 57.979 33.333 0.00 0.00 0.00 1.94
500 513 5.994250 TGAGTCTGAAAGGGAATGGATAAG 58.006 41.667 0.00 0.00 0.00 1.73
542 555 8.832458 TCGGGGATATATGAGTTGTGAATATA 57.168 34.615 0.00 0.00 0.00 0.86
560 1709 4.235762 CGCGGTTGGATCGGGGAT 62.236 66.667 0.00 0.00 37.01 3.85
566 1715 1.064134 GGAATTGCGCGGTTGGATC 59.936 57.895 8.83 0.00 0.00 3.36
605 1754 1.073216 CTGCTCGTGACCGTGACATC 61.073 60.000 0.00 0.00 35.01 3.06
607 1756 2.335011 CTGCTCGTGACCGTGACA 59.665 61.111 0.00 0.00 35.01 3.58
671 1821 0.460311 ACCGGCTACTTCCATTCTCG 59.540 55.000 0.00 0.00 0.00 4.04
844 1994 6.719370 TGGGTCAGGATTGGTATATTTTATGC 59.281 38.462 0.00 0.00 0.00 3.14
1236 2386 0.459899 TCAGTAATGAGCCGACGCAT 59.540 50.000 0.00 0.00 38.01 4.73
1482 2632 0.396417 TACATTGCCCCCATTTCCGG 60.396 55.000 0.00 0.00 0.00 5.14
1549 2699 6.118170 TGCAAATGAAGGGTGAAATCAAAAA 58.882 32.000 0.00 0.00 0.00 1.94
1579 2729 4.386951 CGTGACACATGCGGGGGA 62.387 66.667 6.37 0.00 0.00 4.81
1695 2846 2.748209 AAGTGGTAGTGCCCAAACTT 57.252 45.000 0.00 0.00 35.92 2.66
1703 2854 4.995487 AGTGCTAAAGTAAAGTGGTAGTGC 59.005 41.667 0.00 0.00 0.00 4.40
1911 3064 9.743057 CATAATTCCTTGAACAAACACAACTAA 57.257 29.630 0.00 0.00 0.00 2.24
1919 3130 5.938322 TCTCGCATAATTCCTTGAACAAAC 58.062 37.500 0.00 0.00 0.00 2.93
1923 3134 7.970614 AGAAAAATCTCGCATAATTCCTTGAAC 59.029 33.333 0.00 0.00 0.00 3.18
2218 3429 0.031994 CAAAACCAAGAAGGGCCACG 59.968 55.000 6.18 0.00 43.89 4.94
2236 3447 1.843206 TGCCTTCCACCATATACTGCA 59.157 47.619 0.00 0.00 0.00 4.41
2294 3505 0.848942 CAGCTTACAGATACAGCGCG 59.151 55.000 0.00 0.00 38.66 6.86
2496 3707 7.286087 TGGCAAAGCTATATGAAATGACAGATT 59.714 33.333 0.00 0.00 0.00 2.40
2734 3947 8.243426 TGACAGTTATTATTTTTGGACTGATGC 58.757 33.333 8.15 0.00 38.23 3.91
2917 4132 6.097412 AGGAATTTAAGCATGATTCCTGAACC 59.903 38.462 19.64 9.98 46.53 3.62
2976 4191 0.462937 TGAAACCGTCCACACAGGTG 60.463 55.000 0.00 0.00 44.85 4.00
2989 4204 5.343249 GTGGCTTCACATTCATATGAAACC 58.657 41.667 21.50 13.77 40.17 3.27
3077 4292 6.019656 AGAAGATCTGTAGACCATAGACCA 57.980 41.667 0.00 0.00 0.00 4.02
3177 4397 5.455326 CCACCTATGATCAAGTAAGAAGGGG 60.455 48.000 0.00 0.00 0.00 4.79
3327 4547 6.646267 AGTGTGTGTAAAGACAGGAACTAAA 58.354 36.000 0.00 0.00 36.02 1.85
3331 4551 3.808174 GGAGTGTGTGTAAAGACAGGAAC 59.192 47.826 0.00 0.00 35.82 3.62
3433 4654 0.603707 AGGGTGATATTGCGCCGATG 60.604 55.000 4.18 0.00 39.34 3.84
3493 4715 7.203218 GCACTTCCAAGTTTATCCATTATTCC 58.797 38.462 0.00 0.00 37.08 3.01
3505 4727 4.502105 AATTTTGGGCACTTCCAAGTTT 57.498 36.364 0.00 0.00 46.19 2.66
3606 4841 0.764369 CACTGCTATAGGCCCCCTGA 60.764 60.000 0.00 0.00 40.92 3.86
3613 4848 3.467803 ACGGAAATTCACTGCTATAGGC 58.532 45.455 1.04 0.00 42.22 3.93
3620 4855 2.413371 GCAGAAGACGGAAATTCACTGC 60.413 50.000 0.00 0.00 37.96 4.40
3653 4889 3.013921 GCTATCGACCAAATTCCACCAA 58.986 45.455 0.00 0.00 0.00 3.67
3668 4904 4.757657 TCCTCTACTAGAGCAAAGCTATCG 59.242 45.833 7.50 0.00 40.98 2.92
3671 4907 5.375283 TCTCCTCTACTAGAGCAAAGCTA 57.625 43.478 7.50 0.00 40.98 3.32
3699 4935 5.998363 GGATAAACATCAGGGAATCCACTAC 59.002 44.000 0.09 0.00 34.34 2.73
3742 4978 2.752354 TCCGATGGTAAACATGGCAAAG 59.248 45.455 0.00 0.00 40.72 2.77
3743 4979 2.752354 CTCCGATGGTAAACATGGCAAA 59.248 45.455 0.00 0.00 40.72 3.68
3765 5001 1.922135 AAGCGGCATAACCAGCAACG 61.922 55.000 1.45 0.00 39.49 4.10
3804 5040 8.783093 CACACATAATTCAAGAGACTGGTAAAA 58.217 33.333 0.00 0.00 0.00 1.52
3831 5068 5.253330 TGACTTTTAAGGCCCTCTACAATG 58.747 41.667 0.00 0.00 31.13 2.82
3859 5096 3.875134 ACTCCAAACCAGTCAAACTTACG 59.125 43.478 0.00 0.00 0.00 3.18
3866 5103 5.013079 ACATCATCTACTCCAAACCAGTCAA 59.987 40.000 0.00 0.00 0.00 3.18
3868 5105 5.091261 ACATCATCTACTCCAAACCAGTC 57.909 43.478 0.00 0.00 0.00 3.51
3906 5143 9.965824 GTATTTCTCACATTCTTGAAAGGAAAA 57.034 29.630 0.00 0.00 32.91 2.29
3940 5178 4.623171 CGGAGGGAGTACTAGTTTGCAATT 60.623 45.833 0.00 0.00 0.00 2.32
3948 5186 1.490069 GAGGACGGAGGGAGTACTAGT 59.510 57.143 0.00 0.00 31.89 2.57
3949 5187 1.540797 CGAGGACGGAGGGAGTACTAG 60.541 61.905 0.00 0.00 31.89 2.57
3950 5188 0.467384 CGAGGACGGAGGGAGTACTA 59.533 60.000 0.00 0.00 31.89 1.82
3951 5189 1.224039 CGAGGACGGAGGGAGTACT 59.776 63.158 0.00 0.00 35.04 2.73
3952 5190 3.824810 CGAGGACGGAGGGAGTAC 58.175 66.667 0.00 0.00 35.72 2.73
3962 5200 2.801679 GTCTGTCTAGATACCGAGGACG 59.198 54.545 0.00 0.00 34.94 4.79
3963 5201 3.806380 TGTCTGTCTAGATACCGAGGAC 58.194 50.000 0.00 0.00 34.94 3.85
3964 5202 4.080469 ACTTGTCTGTCTAGATACCGAGGA 60.080 45.833 0.00 0.00 34.94 3.71
3965 5203 4.200874 ACTTGTCTGTCTAGATACCGAGG 58.799 47.826 0.00 0.00 34.94 4.63
3966 5204 6.922247 TTACTTGTCTGTCTAGATACCGAG 57.078 41.667 0.00 0.00 34.94 4.63
3967 5205 6.827251 ACATTACTTGTCTGTCTAGATACCGA 59.173 38.462 0.00 0.00 34.94 4.69
3968 5206 7.028926 ACATTACTTGTCTGTCTAGATACCG 57.971 40.000 0.00 0.00 34.94 4.02
3982 5220 7.410174 TCCATCCCAAATTAGACATTACTTGT 58.590 34.615 0.00 0.00 42.79 3.16
3983 5221 7.013655 CCTCCATCCCAAATTAGACATTACTTG 59.986 40.741 0.00 0.00 0.00 3.16
3984 5222 7.062957 CCTCCATCCCAAATTAGACATTACTT 58.937 38.462 0.00 0.00 0.00 2.24
3985 5223 6.160459 ACCTCCATCCCAAATTAGACATTACT 59.840 38.462 0.00 0.00 0.00 2.24
3986 5224 6.365520 ACCTCCATCCCAAATTAGACATTAC 58.634 40.000 0.00 0.00 0.00 1.89
3987 5225 6.590656 ACCTCCATCCCAAATTAGACATTA 57.409 37.500 0.00 0.00 0.00 1.90
3988 5226 5.472301 ACCTCCATCCCAAATTAGACATT 57.528 39.130 0.00 0.00 0.00 2.71
3989 5227 6.786843 ATACCTCCATCCCAAATTAGACAT 57.213 37.500 0.00 0.00 0.00 3.06
3990 5228 7.739444 AGATATACCTCCATCCCAAATTAGACA 59.261 37.037 0.00 0.00 0.00 3.41
3991 5229 8.043710 CAGATATACCTCCATCCCAAATTAGAC 58.956 40.741 0.00 0.00 0.00 2.59
3992 5230 7.739444 ACAGATATACCTCCATCCCAAATTAGA 59.261 37.037 0.00 0.00 0.00 2.10
3993 5231 7.922382 ACAGATATACCTCCATCCCAAATTAG 58.078 38.462 0.00 0.00 0.00 1.73
3994 5232 7.888514 ACAGATATACCTCCATCCCAAATTA 57.111 36.000 0.00 0.00 0.00 1.40
3995 5233 6.786843 ACAGATATACCTCCATCCCAAATT 57.213 37.500 0.00 0.00 0.00 1.82
3996 5234 7.888514 TTACAGATATACCTCCATCCCAAAT 57.111 36.000 0.00 0.00 0.00 2.32
3997 5235 7.310423 CGATTACAGATATACCTCCATCCCAAA 60.310 40.741 0.00 0.00 0.00 3.28
3998 5236 6.154534 CGATTACAGATATACCTCCATCCCAA 59.845 42.308 0.00 0.00 0.00 4.12
3999 5237 5.656859 CGATTACAGATATACCTCCATCCCA 59.343 44.000 0.00 0.00 0.00 4.37
4000 5238 5.657302 ACGATTACAGATATACCTCCATCCC 59.343 44.000 0.00 0.00 0.00 3.85
4001 5239 6.777213 ACGATTACAGATATACCTCCATCC 57.223 41.667 0.00 0.00 0.00 3.51
4002 5240 8.277490 TGTACGATTACAGATATACCTCCATC 57.723 38.462 0.00 0.00 32.98 3.51
4003 5241 8.824756 ATGTACGATTACAGATATACCTCCAT 57.175 34.615 0.00 0.00 41.62 3.41
4004 5242 8.645814 AATGTACGATTACAGATATACCTCCA 57.354 34.615 0.00 0.00 41.62 3.86
4005 5243 9.570488 GAAATGTACGATTACAGATATACCTCC 57.430 37.037 0.00 0.00 41.62 4.30
4015 5253 8.619146 ATTGCAAATGAAATGTACGATTACAG 57.381 30.769 1.71 0.00 41.62 2.74
4057 5298 1.730612 CCTGATCCGAATGATGCATCG 59.269 52.381 21.34 11.21 32.41 3.84
4226 5467 0.528924 TACATCGTCACCGGGTTCAG 59.471 55.000 6.32 0.00 33.95 3.02


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

AutoCloner maintained by Alex Coulton.