Multiple sequence alignment - TraesCS4D01G188600

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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 TraesCS4D01G188600 chr4D 100.000 4022 0 0 1 4022 327848188 327844167 0.000000e+00 7428
1 TraesCS4D01G188600 chr4B 94.189 3717 100 31 369 4022 407411137 407407474 0.000000e+00 5561
2 TraesCS4D01G188600 chr4B 87.086 302 24 7 62 352 407411419 407411122 1.080000e-85 327
3 TraesCS4D01G188600 chr4A 95.522 3082 95 20 366 3432 142795510 142798563 0.000000e+00 4887
4 TraesCS4D01G188600 chr4A 92.937 538 28 2 3495 4022 142798999 142799536 0.000000e+00 774
5 TraesCS4D01G188600 chr4A 84.983 293 28 9 71 352 142795241 142795528 2.370000e-72 283
6 TraesCS4D01G188600 chr2A 75.280 805 176 14 1669 2457 46313833 46314630 2.950000e-96 363
7 TraesCS4D01G188600 chr2B 72.071 1289 312 29 1672 2921 68592775 68591496 3.850000e-90 342
8 TraesCS4D01G188600 chr2B 77.441 297 63 4 1197 1491 68593226 68592932 1.490000e-39 174
9 TraesCS4D01G188600 chr2D 71.981 1292 311 31 1672 2921 43899097 43897815 2.320000e-87 333
10 TraesCS4D01G188600 chr2D 77.778 297 62 4 1197 1491 43899548 43899254 3.190000e-41 180


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 TraesCS4D01G188600 chr4D 327844167 327848188 4021 True 7428.000000 7428 100.000000 1 4022 1 chr4D.!!$R1 4021
1 TraesCS4D01G188600 chr4B 407407474 407411419 3945 True 2944.000000 5561 90.637500 62 4022 2 chr4B.!!$R1 3960
2 TraesCS4D01G188600 chr4A 142795241 142799536 4295 False 1981.333333 4887 91.147333 71 4022 3 chr4A.!!$F1 3951
3 TraesCS4D01G188600 chr2A 46313833 46314630 797 False 363.000000 363 75.280000 1669 2457 1 chr2A.!!$F1 788
4 TraesCS4D01G188600 chr2B 68591496 68593226 1730 True 258.000000 342 74.756000 1197 2921 2 chr2B.!!$R1 1724
5 TraesCS4D01G188600 chr2D 43897815 43899548 1733 True 256.500000 333 74.879500 1197 2921 2 chr2D.!!$R1 1724

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 0.042880 TAACGTTGTGCAAGTTCGCG 60.043 50.0 11.99 0.00 33.35 5.87 F
109 110 0.318441 ATCACGCTCCCATGATACGG 59.682 55.0 0.00 0.00 33.73 4.02 F
457 481 0.445436 GCGCAAACCTCACATGAGAG 59.555 55.0 12.73 12.73 44.74 3.20 F
1872 1926 0.608130 TGGAGGTGGACGTCAATGAG 59.392 55.0 18.91 0.00 32.79 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2040 0.034616 GCTCGATCTTCCCCATCTGG 59.965 60.000 0.00 0.00 0.00 3.86 R
2229 2286 1.080772 CGCCAGCGTTGTAGAGTCA 60.081 57.895 3.35 0.00 34.35 3.41 R
2358 2427 1.031235 CAGGACAACCACATGCACAA 58.969 50.000 0.00 0.00 38.94 3.33 R
3188 3278 1.064654 GCCTGCAACAACAGCTATAGC 59.935 52.381 17.33 17.33 42.49 2.97 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
25 26 7.266922 AGTTTGTGTATGGATTTGTTAACGT 57.733 32.000 0.26 0.00 0.00 3.99
26 27 7.708998 AGTTTGTGTATGGATTTGTTAACGTT 58.291 30.769 5.88 5.88 0.00 3.99
27 28 7.646130 AGTTTGTGTATGGATTTGTTAACGTTG 59.354 33.333 11.99 0.00 0.00 4.10
28 29 6.621316 TGTGTATGGATTTGTTAACGTTGT 57.379 33.333 11.99 0.00 0.00 3.32
29 30 6.431278 TGTGTATGGATTTGTTAACGTTGTG 58.569 36.000 11.99 0.00 0.00 3.33
30 31 5.341196 GTGTATGGATTTGTTAACGTTGTGC 59.659 40.000 11.99 1.28 0.00 4.57
31 32 4.576216 ATGGATTTGTTAACGTTGTGCA 57.424 36.364 11.99 4.11 0.00 4.57
32 33 4.371855 TGGATTTGTTAACGTTGTGCAA 57.628 36.364 11.99 10.14 0.00 4.08
33 34 4.355437 TGGATTTGTTAACGTTGTGCAAG 58.645 39.130 11.99 0.00 0.00 4.01
34 35 4.142359 TGGATTTGTTAACGTTGTGCAAGT 60.142 37.500 11.99 9.63 0.00 3.16
35 36 4.801516 GGATTTGTTAACGTTGTGCAAGTT 59.198 37.500 11.99 5.12 0.00 2.66
36 37 5.051973 GGATTTGTTAACGTTGTGCAAGTTC 60.052 40.000 11.99 12.26 0.00 3.01
37 38 3.040990 TGTTAACGTTGTGCAAGTTCG 57.959 42.857 11.99 0.00 0.00 3.95
38 39 1.771291 GTTAACGTTGTGCAAGTTCGC 59.229 47.619 11.99 0.00 0.00 4.70
39 40 0.042880 TAACGTTGTGCAAGTTCGCG 60.043 50.000 11.99 0.00 33.35 5.87
40 41 1.973137 AACGTTGTGCAAGTTCGCGT 61.973 50.000 5.77 0.00 33.35 6.01
41 42 1.146957 ACGTTGTGCAAGTTCGCGTA 61.147 50.000 5.77 0.00 33.35 4.42
42 43 0.042880 CGTTGTGCAAGTTCGCGTAA 60.043 50.000 5.77 0.00 33.35 3.18
43 44 1.397945 CGTTGTGCAAGTTCGCGTAAT 60.398 47.619 5.77 0.00 33.35 1.89
44 45 2.159947 CGTTGTGCAAGTTCGCGTAATA 60.160 45.455 5.77 0.00 33.35 0.98
45 46 3.662195 CGTTGTGCAAGTTCGCGTAATAA 60.662 43.478 5.77 0.00 33.35 1.40
46 47 4.399978 GTTGTGCAAGTTCGCGTAATAAT 58.600 39.130 5.77 0.00 33.35 1.28
47 48 3.997276 TGTGCAAGTTCGCGTAATAATG 58.003 40.909 5.77 0.38 33.35 1.90
48 49 3.680458 TGTGCAAGTTCGCGTAATAATGA 59.320 39.130 5.77 0.00 33.35 2.57
49 50 4.331443 TGTGCAAGTTCGCGTAATAATGAT 59.669 37.500 5.77 0.00 33.35 2.45
50 51 4.666176 GTGCAAGTTCGCGTAATAATGATG 59.334 41.667 5.77 0.00 33.35 3.07
51 52 4.568760 TGCAAGTTCGCGTAATAATGATGA 59.431 37.500 5.77 0.00 33.35 2.92
52 53 5.236263 TGCAAGTTCGCGTAATAATGATGAT 59.764 36.000 5.77 0.00 33.35 2.45
53 54 6.422400 TGCAAGTTCGCGTAATAATGATGATA 59.578 34.615 5.77 0.00 33.35 2.15
54 55 7.117667 TGCAAGTTCGCGTAATAATGATGATAT 59.882 33.333 5.77 0.00 33.35 1.63
55 56 7.957484 GCAAGTTCGCGTAATAATGATGATATT 59.043 33.333 5.77 0.00 0.00 1.28
94 95 3.460648 GTGCTCCCACACCTATCAC 57.539 57.895 0.00 0.00 41.67 3.06
100 101 1.144057 CCACACCTATCACGCTCCC 59.856 63.158 0.00 0.00 0.00 4.30
109 110 0.318441 ATCACGCTCCCATGATACGG 59.682 55.000 0.00 0.00 33.73 4.02
120 121 1.620323 CATGATACGGGAGCTGATGGA 59.380 52.381 0.00 0.00 0.00 3.41
144 145 5.466728 AGCATTGTATCGAACCATACATGAC 59.533 40.000 0.00 0.00 38.71 3.06
145 146 5.236263 GCATTGTATCGAACCATACATGACA 59.764 40.000 0.00 0.00 38.71 3.58
152 153 3.745975 CGAACCATACATGACACACTTGT 59.254 43.478 0.00 0.00 39.32 3.16
166 167 1.066143 CACTTGTACCCGGAAGCATCT 60.066 52.381 0.73 0.00 0.00 2.90
174 175 2.755103 ACCCGGAAGCATCTTGAAATTC 59.245 45.455 0.73 0.00 0.00 2.17
180 181 4.393062 GGAAGCATCTTGAAATTCGACTCA 59.607 41.667 0.00 0.00 0.00 3.41
200 201 8.779561 CGACTCACATTTCGAAATATTTCAAAG 58.220 33.333 22.33 14.31 37.43 2.77
238 241 8.899427 AAGAGTATCATCATCAAACCATACAG 57.101 34.615 0.00 0.00 37.82 2.74
248 251 1.519408 AACCATACAGACGTGTTGCC 58.481 50.000 0.00 0.00 38.19 4.52
256 267 0.951558 AGACGTGTTGCCAATGTTCC 59.048 50.000 0.00 0.00 0.00 3.62
257 268 0.951558 GACGTGTTGCCAATGTTCCT 59.048 50.000 0.00 0.00 0.00 3.36
287 298 5.734720 TCATCTGATTTCCTACCTTGTGTC 58.265 41.667 0.00 0.00 0.00 3.67
352 366 2.286872 CATGAAGCGCTCTCCAATCTT 58.713 47.619 12.06 0.00 0.00 2.40
353 367 2.479566 TGAAGCGCTCTCCAATCTTT 57.520 45.000 12.06 0.00 0.00 2.52
354 368 2.783135 TGAAGCGCTCTCCAATCTTTT 58.217 42.857 12.06 0.00 0.00 2.27
355 369 3.149196 TGAAGCGCTCTCCAATCTTTTT 58.851 40.909 12.06 0.00 0.00 1.94
379 393 2.539432 TGAGGATCAAGAGCTCTCCA 57.461 50.000 18.55 6.88 45.97 3.86
380 394 2.825223 TGAGGATCAAGAGCTCTCCAA 58.175 47.619 18.55 5.89 45.97 3.53
381 395 3.382278 TGAGGATCAAGAGCTCTCCAAT 58.618 45.455 18.55 10.79 45.97 3.16
382 396 3.387374 TGAGGATCAAGAGCTCTCCAATC 59.613 47.826 18.55 18.25 45.97 2.67
383 397 3.642848 GAGGATCAAGAGCTCTCCAATCT 59.357 47.826 18.55 12.18 33.17 2.40
412 426 1.133976 CCGGAAGCATCCTGAAATCCT 60.134 52.381 6.39 0.00 44.17 3.24
457 481 0.445436 GCGCAAACCTCACATGAGAG 59.555 55.000 12.73 12.73 44.74 3.20
458 482 1.941209 GCGCAAACCTCACATGAGAGA 60.941 52.381 20.28 4.63 44.74 3.10
459 483 1.998315 CGCAAACCTCACATGAGAGAG 59.002 52.381 20.28 13.17 44.74 3.20
460 484 2.353109 CGCAAACCTCACATGAGAGAGA 60.353 50.000 20.28 0.00 44.74 3.10
461 485 3.260740 GCAAACCTCACATGAGAGAGAG 58.739 50.000 20.28 7.41 44.74 3.20
462 486 3.056250 GCAAACCTCACATGAGAGAGAGA 60.056 47.826 20.28 0.00 44.74 3.10
525 549 3.170672 CCCGAGCCATCCATCCCA 61.171 66.667 0.00 0.00 0.00 4.37
532 558 1.077501 CCATCCATCCCAACACGCT 60.078 57.895 0.00 0.00 0.00 5.07
534 560 1.586422 CATCCATCCCAACACGCTAG 58.414 55.000 0.00 0.00 0.00 3.42
548 574 1.143183 GCTAGAATCGGACGGCCAA 59.857 57.895 8.76 0.00 0.00 4.52
634 660 2.039951 AAGTACTAGCCGGGCCCA 59.960 61.111 24.92 0.00 0.00 5.36
646 672 2.361104 GGCCCACGCTCCATTGAA 60.361 61.111 0.00 0.00 34.44 2.69
716 742 1.448189 CTCCTCGACCTCGTCTCGT 60.448 63.158 0.00 0.00 40.80 4.18
792 826 1.373570 CATCTCTGCCTTCCCGAAAC 58.626 55.000 0.00 0.00 0.00 2.78
888 925 1.835267 GTTCAAACCCACCACCCCC 60.835 63.158 0.00 0.00 0.00 5.40
959 1003 3.554342 CTATCTGCTGCCCCGCCT 61.554 66.667 0.00 0.00 0.00 5.52
1196 1250 2.711922 CCTTCGTCCCCGACAGGAG 61.712 68.421 7.22 0.00 44.13 3.69
1872 1926 0.608130 TGGAGGTGGACGTCAATGAG 59.392 55.000 18.91 0.00 32.79 2.90
1929 1983 1.005215 CTGGATTTCTCCCAGGTGCTT 59.995 52.381 0.00 0.00 45.66 3.91
1968 2022 1.817099 CATCCTTGACCTGCCGCTC 60.817 63.158 0.00 0.00 0.00 5.03
1986 2040 0.899720 TCTCCCGGTACAATGACACC 59.100 55.000 0.00 0.00 0.00 4.16
2175 2232 3.014304 TCGCTGAACCCAGACTATAGT 57.986 47.619 4.68 4.68 43.02 2.12
2229 2286 2.757124 CCCTAATCCCAGCGGGCTT 61.757 63.158 8.57 8.07 43.94 4.35
2358 2427 1.421268 TCAGTCATTCCCTGCAACACT 59.579 47.619 0.00 0.00 0.00 3.55
2367 2436 0.386476 CCTGCAACACTTGTGCATGT 59.614 50.000 0.00 0.00 37.95 3.21
2673 2760 1.217244 GGACAAGGCGTATGACGGT 59.783 57.895 0.70 0.00 42.82 4.83
2799 2886 1.588139 GTCGGATTACCTCGTGCCG 60.588 63.158 0.00 0.00 43.11 5.69
2928 3018 0.464036 CTATGCCGCAGAGGTTACCA 59.536 55.000 7.14 0.00 43.70 3.25
2968 3058 0.543749 GACCCATCTAAGCAGTGCCT 59.456 55.000 12.58 0.08 0.00 4.75
2979 3069 0.673437 GCAGTGCCTTTGCTTTGGTA 59.327 50.000 2.85 0.00 38.51 3.25
3072 3162 1.457346 CTTCAGGTGGTTCCATCAGC 58.543 55.000 4.86 0.00 39.02 4.26
3218 3308 3.266964 TTGCAGGCTCGCAACATC 58.733 55.556 16.72 0.00 46.61 3.06
3233 3323 3.458189 CAACATCGACATAGGTTCCCTC 58.542 50.000 0.00 0.00 34.61 4.30
3293 3383 4.255833 CCAATGTTGGTGCAATTGTAGT 57.744 40.909 7.40 0.00 43.43 2.73
3405 3495 2.593925 TCTGAAGCTGTCCTCTGAGA 57.406 50.000 6.17 0.00 0.00 3.27
3406 3496 2.166829 TCTGAAGCTGTCCTCTGAGAC 58.833 52.381 6.17 3.49 37.28 3.36
3481 3894 6.360370 ACATAGAACAAGTACTGTCCATGT 57.640 37.500 0.00 3.18 37.23 3.21
3521 3984 2.663520 CCACTTGCACGGCGTGTA 60.664 61.111 36.68 31.99 35.75 2.90
3554 4021 4.827284 TGGATGCTCGTCAGATCTACAATA 59.173 41.667 0.00 0.00 0.00 1.90
3555 4022 5.048434 TGGATGCTCGTCAGATCTACAATAG 60.048 44.000 0.00 0.00 0.00 1.73
3556 4023 5.048364 GGATGCTCGTCAGATCTACAATAGT 60.048 44.000 0.00 0.00 0.00 2.12
3618 4085 2.470983 TGACATGCTCGTTCCATTCA 57.529 45.000 0.00 0.00 0.00 2.57
3658 4126 2.145536 GGTTAAGTGTACGTTGGGGTG 58.854 52.381 0.00 0.00 0.00 4.61
3733 4220 3.991924 ATGTCTGGAGCCGAGGCCT 62.992 63.158 3.86 3.86 43.17 5.19
3737 4224 3.382803 CTGGAGCCGAGGCCTGAAG 62.383 68.421 12.00 0.10 43.17 3.02
3756 4243 5.630121 TGAAGAGATGGACCTTTTGCTTTA 58.370 37.500 0.00 0.00 0.00 1.85
3795 4282 1.200020 CGGCAGTTCTTTGGTTGGATC 59.800 52.381 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.708998 ACGTTAACAAATCCATACACAAACTT 58.291 30.769 6.39 0.00 0.00 2.66
2 3 7.432838 ACAACGTTAACAAATCCATACACAAAC 59.567 33.333 0.00 0.00 0.00 2.93
3 4 7.432545 CACAACGTTAACAAATCCATACACAAA 59.567 33.333 0.00 0.00 0.00 2.83
4 5 6.913132 CACAACGTTAACAAATCCATACACAA 59.087 34.615 0.00 0.00 0.00 3.33
7 8 5.008712 TGCACAACGTTAACAAATCCATACA 59.991 36.000 0.00 0.00 0.00 2.29
8 9 5.453648 TGCACAACGTTAACAAATCCATAC 58.546 37.500 0.00 0.00 0.00 2.39
9 10 5.690997 TGCACAACGTTAACAAATCCATA 57.309 34.783 0.00 0.00 0.00 2.74
10 11 4.576216 TGCACAACGTTAACAAATCCAT 57.424 36.364 0.00 0.00 0.00 3.41
11 12 4.142359 ACTTGCACAACGTTAACAAATCCA 60.142 37.500 0.00 0.00 0.00 3.41
12 13 4.356289 ACTTGCACAACGTTAACAAATCC 58.644 39.130 0.00 0.00 0.00 3.01
13 14 5.330498 CGAACTTGCACAACGTTAACAAATC 60.330 40.000 0.00 6.51 0.00 2.17
14 15 4.497608 CGAACTTGCACAACGTTAACAAAT 59.502 37.500 0.00 0.00 0.00 2.32
15 16 3.846896 CGAACTTGCACAACGTTAACAAA 59.153 39.130 0.00 0.00 0.00 2.83
16 17 3.418094 CGAACTTGCACAACGTTAACAA 58.582 40.909 0.00 5.08 0.00 2.83
17 18 2.788407 GCGAACTTGCACAACGTTAACA 60.788 45.455 0.00 0.00 34.15 2.41
18 19 1.771291 GCGAACTTGCACAACGTTAAC 59.229 47.619 0.00 0.00 34.15 2.01
19 20 1.592590 CGCGAACTTGCACAACGTTAA 60.593 47.619 0.00 0.00 34.15 2.01
20 21 0.042880 CGCGAACTTGCACAACGTTA 60.043 50.000 0.00 0.00 34.15 3.18
21 22 1.297304 CGCGAACTTGCACAACGTT 60.297 52.632 0.00 0.00 34.15 3.99
22 23 1.146957 TACGCGAACTTGCACAACGT 61.147 50.000 15.93 0.00 36.17 3.99
23 24 0.042880 TTACGCGAACTTGCACAACG 60.043 50.000 15.93 0.00 34.15 4.10
24 25 2.309898 ATTACGCGAACTTGCACAAC 57.690 45.000 15.93 0.00 34.15 3.32
25 26 4.152580 TCATTATTACGCGAACTTGCACAA 59.847 37.500 15.93 0.00 34.15 3.33
26 27 3.680458 TCATTATTACGCGAACTTGCACA 59.320 39.130 15.93 0.00 34.15 4.57
27 28 4.253352 TCATTATTACGCGAACTTGCAC 57.747 40.909 15.93 0.00 34.15 4.57
28 29 4.568760 TCATCATTATTACGCGAACTTGCA 59.431 37.500 15.93 0.00 34.15 4.08
29 30 5.078153 TCATCATTATTACGCGAACTTGC 57.922 39.130 15.93 0.00 0.00 4.01
53 54 7.930865 GCACCTGATATTCTCTCAAGAGTTAAT 59.069 37.037 6.91 3.66 42.60 1.40
54 55 7.124901 AGCACCTGATATTCTCTCAAGAGTTAA 59.875 37.037 6.91 0.00 42.60 2.01
55 56 6.609212 AGCACCTGATATTCTCTCAAGAGTTA 59.391 38.462 6.91 1.93 42.60 2.24
56 57 5.424895 AGCACCTGATATTCTCTCAAGAGTT 59.575 40.000 6.91 0.00 42.60 3.01
57 58 4.961730 AGCACCTGATATTCTCTCAAGAGT 59.038 41.667 6.91 0.00 42.60 3.24
58 59 5.509501 GGAGCACCTGATATTCTCTCAAGAG 60.510 48.000 0.33 0.33 43.36 2.85
59 60 4.343526 GGAGCACCTGATATTCTCTCAAGA 59.656 45.833 0.00 0.00 0.00 3.02
60 61 4.502950 GGGAGCACCTGATATTCTCTCAAG 60.503 50.000 0.00 0.00 35.85 3.02
100 101 1.620323 TCCATCAGCTCCCGTATCATG 59.380 52.381 0.00 0.00 0.00 3.07
115 116 3.466836 TGGTTCGATACAATGCTCCATC 58.533 45.455 0.00 0.00 0.00 3.51
120 121 5.466728 GTCATGTATGGTTCGATACAATGCT 59.533 40.000 10.60 0.00 41.14 3.79
123 124 6.257849 GTGTGTCATGTATGGTTCGATACAAT 59.742 38.462 10.60 0.00 41.14 2.71
127 128 5.592104 AGTGTGTCATGTATGGTTCGATA 57.408 39.130 0.00 0.00 0.00 2.92
131 132 5.121768 GGTACAAGTGTGTCATGTATGGTTC 59.878 44.000 0.00 0.00 39.30 3.62
144 145 0.250124 TGCTTCCGGGTACAAGTGTG 60.250 55.000 0.00 0.00 0.00 3.82
145 146 0.690762 ATGCTTCCGGGTACAAGTGT 59.309 50.000 0.00 0.00 0.00 3.55
152 153 3.644966 ATTTCAAGATGCTTCCGGGTA 57.355 42.857 0.00 0.00 0.00 3.69
166 167 5.915812 TCGAAATGTGAGTCGAATTTCAA 57.084 34.783 21.18 8.28 42.92 2.69
174 175 8.653984 TTTGAAATATTTCGAAATGTGAGTCG 57.346 30.769 29.20 0.00 37.56 4.18
180 181 9.113876 GTCGAACTTTGAAATATTTCGAAATGT 57.886 29.630 29.20 21.82 46.81 2.71
200 201 6.586463 TGATGATACTCTTTTGTGAGTCGAAC 59.414 38.462 0.13 0.00 45.07 3.95
203 204 6.753744 TGATGATGATACTCTTTTGTGAGTCG 59.246 38.462 0.13 0.00 45.07 4.18
222 223 4.832248 ACACGTCTGTATGGTTTGATGAT 58.168 39.130 0.00 0.00 0.00 2.45
248 251 6.937436 TCAGATGATTGATCAGGAACATTG 57.063 37.500 0.00 3.56 40.64 2.82
256 267 7.451732 AGGTAGGAAATCAGATGATTGATCAG 58.548 38.462 8.76 0.00 43.41 2.90
257 268 7.384524 AGGTAGGAAATCAGATGATTGATCA 57.615 36.000 8.76 0.00 43.41 2.92
313 327 8.416329 GCTTCATGTATGGAAACTGGAAAATAT 58.584 33.333 0.00 0.00 0.00 1.28
356 370 4.042062 TGGAGAGCTCTTGATCCTCAAAAA 59.958 41.667 19.36 0.00 35.73 1.94
357 371 3.584406 TGGAGAGCTCTTGATCCTCAAAA 59.416 43.478 19.36 0.00 35.73 2.44
358 372 3.176411 TGGAGAGCTCTTGATCCTCAAA 58.824 45.455 19.36 0.00 35.73 2.69
359 373 2.825223 TGGAGAGCTCTTGATCCTCAA 58.175 47.619 19.36 0.00 34.79 3.02
360 374 2.539432 TGGAGAGCTCTTGATCCTCA 57.461 50.000 19.36 5.46 32.79 3.86
361 375 3.642848 AGATTGGAGAGCTCTTGATCCTC 59.357 47.826 19.36 9.00 32.79 3.71
362 376 3.656496 AGATTGGAGAGCTCTTGATCCT 58.344 45.455 19.36 10.07 32.79 3.24
363 377 4.558496 CGTAGATTGGAGAGCTCTTGATCC 60.558 50.000 19.36 15.03 0.00 3.36
364 378 4.545610 CGTAGATTGGAGAGCTCTTGATC 58.454 47.826 19.36 19.33 0.00 2.92
365 379 3.320541 CCGTAGATTGGAGAGCTCTTGAT 59.679 47.826 19.36 12.04 0.00 2.57
366 380 2.690497 CCGTAGATTGGAGAGCTCTTGA 59.310 50.000 19.36 7.39 0.00 3.02
367 381 2.690497 TCCGTAGATTGGAGAGCTCTTG 59.310 50.000 19.36 0.00 0.00 3.02
368 382 3.019799 TCCGTAGATTGGAGAGCTCTT 57.980 47.619 19.36 0.42 0.00 2.85
369 383 2.738587 TCCGTAGATTGGAGAGCTCT 57.261 50.000 18.28 18.28 0.00 4.09
376 390 3.965660 GGGCCTCCGTAGATTGGA 58.034 61.111 0.84 0.00 0.00 3.53
412 426 0.395312 GTCGAAACCAGAGGGGAACA 59.605 55.000 0.00 0.00 41.15 3.18
457 481 2.887568 CCCGCGCATGTGTCTCTC 60.888 66.667 8.75 0.00 0.00 3.20
525 549 0.179145 CCGTCCGATTCTAGCGTGTT 60.179 55.000 0.00 0.00 0.00 3.32
532 558 0.108520 GTGTTGGCCGTCCGATTCTA 60.109 55.000 0.00 0.00 34.14 2.10
534 560 2.736682 CGTGTTGGCCGTCCGATTC 61.737 63.158 0.00 0.00 34.14 2.52
604 630 2.135664 AGTACTTGTGACGTGCTGAC 57.864 50.000 0.00 0.00 0.00 3.51
605 631 2.351447 GCTAGTACTTGTGACGTGCTGA 60.351 50.000 0.00 0.00 0.00 4.26
606 632 1.986378 GCTAGTACTTGTGACGTGCTG 59.014 52.381 0.00 0.00 0.00 4.41
607 633 1.067776 GGCTAGTACTTGTGACGTGCT 60.068 52.381 0.00 0.00 0.00 4.40
608 634 1.347320 GGCTAGTACTTGTGACGTGC 58.653 55.000 0.00 0.00 0.00 5.34
609 635 1.614385 CGGCTAGTACTTGTGACGTG 58.386 55.000 0.00 0.00 0.00 4.49
618 644 2.762875 GTGGGCCCGGCTAGTACT 60.763 66.667 19.37 0.00 0.00 2.73
619 645 4.217159 CGTGGGCCCGGCTAGTAC 62.217 72.222 19.37 6.70 0.00 2.73
634 660 0.322322 TTACGGGTTCAATGGAGCGT 59.678 50.000 0.00 0.00 0.00 5.07
639 665 1.650314 GCGGGTTACGGGTTCAATGG 61.650 60.000 0.00 0.00 44.51 3.16
792 826 3.116700 GTGTCCGCGTTGTTTTATTTTCG 59.883 43.478 4.92 0.00 0.00 3.46
888 925 0.537653 GAAGGGGAAGGAAGACGAGG 59.462 60.000 0.00 0.00 0.00 4.63
894 938 2.002625 CTGGGGAAGGGGAAGGAAG 58.997 63.158 0.00 0.00 0.00 3.46
895 939 2.238701 GCTGGGGAAGGGGAAGGAA 61.239 63.158 0.00 0.00 0.00 3.36
896 940 2.614013 GCTGGGGAAGGGGAAGGA 60.614 66.667 0.00 0.00 0.00 3.36
897 941 2.615288 AGCTGGGGAAGGGGAAGG 60.615 66.667 0.00 0.00 0.00 3.46
1656 1710 1.201429 GGAGGAAGCTCTTGGTGGGA 61.201 60.000 0.00 0.00 0.00 4.37
1746 1800 1.767388 GTTGTTCTCGAGCGTGACG 59.233 57.895 7.81 0.00 0.00 4.35
1929 1983 0.108804 CCGGCTTCTTCTCGCAGTTA 60.109 55.000 0.00 0.00 0.00 2.24
1968 2022 0.107848 GGGTGTCATTGTACCGGGAG 60.108 60.000 6.32 0.00 37.85 4.30
1986 2040 0.034616 GCTCGATCTTCCCCATCTGG 59.965 60.000 0.00 0.00 0.00 3.86
2229 2286 1.080772 CGCCAGCGTTGTAGAGTCA 60.081 57.895 3.35 0.00 34.35 3.41
2358 2427 1.031235 CAGGACAACCACATGCACAA 58.969 50.000 0.00 0.00 38.94 3.33
2367 2436 1.525077 GCGGTTCACAGGACAACCA 60.525 57.895 1.98 0.00 42.07 3.67
2673 2760 7.596494 CATTGAAAGAGTATGCCTTCTCAAAA 58.404 34.615 0.00 0.00 33.63 2.44
2928 3018 3.588842 TCCTGAATCCACCACTCTTGATT 59.411 43.478 0.00 0.00 0.00 2.57
2968 3058 3.617045 GCCATGAGCAATACCAAAGCAAA 60.617 43.478 0.00 0.00 42.97 3.68
3072 3162 5.522097 ACAAAAAGGTTTCTTACAAATGGCG 59.478 36.000 0.00 0.00 32.01 5.69
3188 3278 1.064654 GCCTGCAACAACAGCTATAGC 59.935 52.381 17.33 17.33 42.49 2.97
3189 3279 2.611292 GAGCCTGCAACAACAGCTATAG 59.389 50.000 0.00 0.00 36.29 1.31
3190 3280 2.632377 GAGCCTGCAACAACAGCTATA 58.368 47.619 0.00 0.00 36.29 1.31
3191 3281 1.457346 GAGCCTGCAACAACAGCTAT 58.543 50.000 0.00 0.00 36.29 2.97
3293 3383 6.140110 GCACAAGCTAAACACGAGAAATTTA 58.860 36.000 0.00 0.00 37.91 1.40
3405 3495 3.820557 AGTTCCACTGTATGCACAAAGT 58.179 40.909 0.00 0.00 33.22 2.66
3406 3496 4.997395 ACTAGTTCCACTGTATGCACAAAG 59.003 41.667 0.00 0.00 33.22 2.77
3435 3525 3.322254 ACGACTGAAACTCCAGTTCAGAT 59.678 43.478 18.37 5.40 46.45 2.90
3440 3853 4.602340 ATGTACGACTGAAACTCCAGTT 57.398 40.909 0.00 0.00 46.45 3.16
3443 3856 5.242171 TGTTCTATGTACGACTGAAACTCCA 59.758 40.000 0.00 0.00 0.00 3.86
3513 3976 2.224549 TCCAATGTTTCTTTACACGCCG 59.775 45.455 0.00 0.00 0.00 6.46
3521 3984 3.820467 TGACGAGCATCCAATGTTTCTTT 59.180 39.130 0.00 0.00 0.00 2.52
3554 4021 8.641498 TTAATACTAGGCGCCTTAATACTACT 57.359 34.615 37.74 8.78 0.00 2.57
3555 4022 9.133627 GTTTAATACTAGGCGCCTTAATACTAC 57.866 37.037 37.74 19.45 0.00 2.73
3556 4023 8.859090 TGTTTAATACTAGGCGCCTTAATACTA 58.141 33.333 37.74 15.68 0.00 1.82
3618 4085 3.005367 ACCGCCAAACATCTTTCGAATTT 59.995 39.130 0.00 0.00 0.00 1.82
3658 4126 1.198759 TACTGAAGTGGACCCCTGCC 61.199 60.000 0.00 0.00 0.00 4.85
3733 4220 3.795688 AGCAAAAGGTCCATCTCTTCA 57.204 42.857 0.00 0.00 0.00 3.02
3778 4265 3.755378 CCTCTGATCCAACCAAAGAACTG 59.245 47.826 0.00 0.00 0.00 3.16
3795 4282 2.681848 GCAGGATGTGATGTTTCCTCTG 59.318 50.000 0.00 0.00 37.80 3.35


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

AutoCloner maintained by Alex Coulton.