Multiple sequence alignment - TraesCS2A01G196700

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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 TraesCS2A01G196700 chr2A 100.000 4124 0 0 1 4124 166627099 166631222 0.000000e+00 7616.0
1 TraesCS2A01G196700 chr2A 91.169 2627 199 14 611 3218 197566569 197563957 0.000000e+00 3535.0
2 TraesCS2A01G196700 chr2A 87.512 1033 98 22 700 1720 197344832 197343819 0.000000e+00 1164.0
3 TraesCS2A01G196700 chr2A 89.139 267 24 4 611 875 166254209 166254472 1.110000e-85 327.0
4 TraesCS2A01G196700 chr2A 95.652 46 2 0 3231 3276 166256653 166256698 1.590000e-09 75.0
5 TraesCS2A01G196700 chr2D 96.368 3524 114 5 611 4123 156707083 156710603 0.000000e+00 5786.0
6 TraesCS2A01G196700 chr2D 90.760 2619 197 24 611 3218 182576281 182573697 0.000000e+00 3454.0
7 TraesCS2A01G196700 chr2D 93.154 2264 128 11 1010 3273 156592469 156594705 0.000000e+00 3297.0
8 TraesCS2A01G196700 chr2D 87.407 270 26 6 611 875 156591788 156592054 1.860000e-78 303.0
9 TraesCS2A01G196700 chr2D 88.764 89 4 2 396 484 156706877 156706959 2.030000e-18 104.0
10 TraesCS2A01G196700 chr2B 94.169 3533 132 19 611 4123 214312571 214316049 0.000000e+00 5315.0
11 TraesCS2A01G196700 chr2B 91.817 2554 182 14 621 3161 214280766 214283305 0.000000e+00 3533.0
12 TraesCS2A01G196700 chr2B 85.714 182 13 6 1 178 214311758 214311930 3.280000e-41 180.0
13 TraesCS2A01G196700 chr2B 89.744 117 5 5 371 483 214312308 214312421 4.300000e-30 143.0
14 TraesCS2A01G196700 chr2B 85.965 114 9 3 371 483 214280554 214280661 9.370000e-22 115.0
15 TraesCS2A01G196700 chr1D 89.848 2571 217 28 611 3166 93105539 93102998 0.000000e+00 3262.0
16 TraesCS2A01G196700 chr1B 92.269 2212 164 5 960 3166 148416326 148414117 0.000000e+00 3131.0
17 TraesCS2A01G196700 chr1B 81.915 94 6 5 3183 3276 148414116 148414034 7.400000e-08 69.4
18 TraesCS2A01G196700 chr1A 91.995 2211 168 4 960 3166 90163538 90161333 0.000000e+00 3094.0
19 TraesCS2A01G196700 chr1A 86.029 272 25 8 611 875 90163837 90163572 3.140000e-71 279.0
20 TraesCS2A01G196700 chr1A 97.959 49 1 0 484 532 549608456 549608408 7.350000e-13 86.1
21 TraesCS2A01G196700 chr7D 100.000 48 0 0 485 532 613325626 613325673 5.680000e-14 89.8
22 TraesCS2A01G196700 chr7D 98.039 51 0 1 485 534 479724718 479724768 2.040000e-13 87.9
23 TraesCS2A01G196700 chr7A 100.000 46 0 0 485 530 423539954 423539909 7.350000e-13 86.1
24 TraesCS2A01G196700 chr7A 88.889 63 4 3 470 532 609128338 609128279 1.590000e-09 75.0
25 TraesCS2A01G196700 chr6D 97.959 49 1 0 481 529 315581053 315581005 7.350000e-13 86.1
26 TraesCS2A01G196700 chr6B 100.000 46 0 0 485 530 135131172 135131127 7.350000e-13 86.1
27 TraesCS2A01G196700 chr6A 100.000 46 0 0 483 528 525741786 525741741 7.350000e-13 86.1
28 TraesCS2A01G196700 chr4A 98.000 50 0 1 480 529 153253105 153253153 7.350000e-13 86.1


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 TraesCS2A01G196700 chr2A 166627099 166631222 4123 False 7616.000000 7616 100.000000 1 4124 1 chr2A.!!$F1 4123
1 TraesCS2A01G196700 chr2A 197563957 197566569 2612 True 3535.000000 3535 91.169000 611 3218 1 chr2A.!!$R2 2607
2 TraesCS2A01G196700 chr2A 197343819 197344832 1013 True 1164.000000 1164 87.512000 700 1720 1 chr2A.!!$R1 1020
3 TraesCS2A01G196700 chr2A 166254209 166256698 2489 False 201.000000 327 92.395500 611 3276 2 chr2A.!!$F2 2665
4 TraesCS2A01G196700 chr2D 182573697 182576281 2584 True 3454.000000 3454 90.760000 611 3218 1 chr2D.!!$R1 2607
5 TraesCS2A01G196700 chr2D 156706877 156710603 3726 False 2945.000000 5786 92.566000 396 4123 2 chr2D.!!$F2 3727
6 TraesCS2A01G196700 chr2D 156591788 156594705 2917 False 1800.000000 3297 90.280500 611 3273 2 chr2D.!!$F1 2662
7 TraesCS2A01G196700 chr2B 214311758 214316049 4291 False 1879.333333 5315 89.875667 1 4123 3 chr2B.!!$F2 4122
8 TraesCS2A01G196700 chr2B 214280554 214283305 2751 False 1824.000000 3533 88.891000 371 3161 2 chr2B.!!$F1 2790
9 TraesCS2A01G196700 chr1D 93102998 93105539 2541 True 3262.000000 3262 89.848000 611 3166 1 chr1D.!!$R1 2555
10 TraesCS2A01G196700 chr1B 148414034 148416326 2292 True 1600.200000 3131 87.092000 960 3276 2 chr1B.!!$R1 2316
11 TraesCS2A01G196700 chr1A 90161333 90163837 2504 True 1686.500000 3094 89.012000 611 3166 2 chr1A.!!$R2 2555

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
360 440 0.039617 TTTGAACGCCGAAGCAATGG 60.040 50.0 0.0 0.0 39.83 3.16 F
805 1137 0.399233 AATCCCTTCCCTCTCCTCCG 60.399 60.0 0.0 0.0 0.00 4.63 F
2478 3137 0.612174 TCTCAGCCCGTAAGACTGCT 60.612 55.0 0.0 0.0 40.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 2321 0.179067 CCTCGGCGGCATTAACCTTA 60.179 55.000 10.53 0.0 0.00 2.69 R
2526 3185 1.672356 GTCGATGGCTTGGCACAGT 60.672 57.895 0.00 0.0 42.39 3.55 R
3329 4007 1.135402 CCCTTTCGCTTACATTGGCAC 60.135 52.381 0.00 0.0 0.00 5.01 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
30 31 9.524496 AATACTATCCACATGCAATCAATGTAT 57.476 29.630 0.00 0.00 34.33 2.29
68 69 8.694975 ACGTGCAATGCAATTAATATGTTTTA 57.305 26.923 10.44 0.00 41.47 1.52
69 70 9.311916 ACGTGCAATGCAATTAATATGTTTTAT 57.688 25.926 10.44 0.00 41.47 1.40
147 148 8.415553 TGCAATCAATGTCTTTCCTAATATTGG 58.584 33.333 0.00 0.00 0.00 3.16
162 163 9.194972 TCCTAATATTGGTGTGCAATGAAATTA 57.805 29.630 0.00 0.00 32.46 1.40
170 171 8.700722 TGGTGTGCAATGAAATTAATATTGTC 57.299 30.769 9.92 4.96 32.46 3.18
204 205 6.788684 TTTCGAAACTGAATATCGTTTCCA 57.211 33.333 6.47 4.92 43.62 3.53
205 206 6.788684 TTCGAAACTGAATATCGTTTCCAA 57.211 33.333 14.47 8.98 43.62 3.53
206 207 6.160664 TCGAAACTGAATATCGTTTCCAAC 57.839 37.500 14.47 0.00 43.62 3.77
207 208 5.697178 TCGAAACTGAATATCGTTTCCAACA 59.303 36.000 14.47 0.00 43.62 3.33
208 209 6.370442 TCGAAACTGAATATCGTTTCCAACAT 59.630 34.615 14.47 0.00 43.62 2.71
209 210 7.546316 TCGAAACTGAATATCGTTTCCAACATA 59.454 33.333 14.47 0.00 43.62 2.29
210 211 8.172484 CGAAACTGAATATCGTTTCCAACATAA 58.828 33.333 14.47 0.00 43.62 1.90
237 238 9.941664 GTGTATTACATGTACACGATTACTAGT 57.058 33.333 13.16 0.00 41.53 2.57
242 243 7.636150 ACATGTACACGATTACTAGTAAGGT 57.364 36.000 19.58 16.26 0.00 3.50
243 244 8.059798 ACATGTACACGATTACTAGTAAGGTT 57.940 34.615 19.58 4.33 0.00 3.50
244 245 8.186821 ACATGTACACGATTACTAGTAAGGTTC 58.813 37.037 19.58 11.90 0.00 3.62
246 247 8.284945 TGTACACGATTACTAGTAAGGTTCAT 57.715 34.615 19.58 2.89 0.00 2.57
247 248 9.394767 TGTACACGATTACTAGTAAGGTTCATA 57.605 33.333 19.58 9.78 0.00 2.15
248 249 9.875675 GTACACGATTACTAGTAAGGTTCATAG 57.124 37.037 19.58 10.42 0.00 2.23
249 250 7.424001 ACACGATTACTAGTAAGGTTCATAGC 58.576 38.462 19.58 0.00 0.00 2.97
250 251 6.577800 CACGATTACTAGTAAGGTTCATAGCG 59.422 42.308 19.58 11.35 0.00 4.26
251 252 6.484643 ACGATTACTAGTAAGGTTCATAGCGA 59.515 38.462 19.58 0.00 0.00 4.93
261 262 4.876125 AGGTTCATAGCGATCATGTGTAG 58.124 43.478 0.00 0.00 0.00 2.74
272 273 0.179045 CATGTGTAGCCTAGCCACCC 60.179 60.000 0.00 0.00 0.00 4.61
273 274 0.620410 ATGTGTAGCCTAGCCACCCA 60.620 55.000 0.00 0.00 0.00 4.51
274 275 1.264749 TGTGTAGCCTAGCCACCCAG 61.265 60.000 0.00 0.00 0.00 4.45
290 291 5.803470 GCCACCCAGACAAAGTACTTCTAAT 60.803 44.000 8.95 0.00 0.00 1.73
299 300 5.350640 ACAAAGTACTTCTAATAGCGCAACC 59.649 40.000 11.47 0.00 0.00 3.77
310 311 0.881118 AGCGCAACCCACAAACATAG 59.119 50.000 11.47 0.00 0.00 2.23
312 313 1.807742 GCGCAACCCACAAACATAGTA 59.192 47.619 0.30 0.00 0.00 1.82
314 315 3.071479 CGCAACCCACAAACATAGTACT 58.929 45.455 0.00 0.00 0.00 2.73
324 404 6.020121 CCACAAACATAGTACTGTACATACGC 60.020 42.308 19.27 0.00 0.00 4.42
338 418 2.223317 ACATACGCATACACGACGCTTA 60.223 45.455 0.00 0.00 36.70 3.09
350 430 1.902504 CGACGCTTAATTTTGAACGCC 59.097 47.619 0.00 0.00 0.00 5.68
356 436 3.560503 CTTAATTTTGAACGCCGAAGCA 58.439 40.909 0.00 0.00 39.83 3.91
360 440 0.039617 TTTGAACGCCGAAGCAATGG 60.040 50.000 0.00 0.00 39.83 3.16
379 459 0.721718 GTGGCACGCATAAGTCAGAC 59.278 55.000 0.00 0.00 39.55 3.51
429 651 6.318648 TGCATTTGTAAAGAAACAGTCTCACT 59.681 34.615 0.00 0.00 34.56 3.41
430 652 6.853362 GCATTTGTAAAGAAACAGTCTCACTC 59.147 38.462 0.00 0.00 34.56 3.51
431 653 7.254932 GCATTTGTAAAGAAACAGTCTCACTCT 60.255 37.037 0.00 0.00 34.56 3.24
432 654 7.772332 TTTGTAAAGAAACAGTCTCACTCTC 57.228 36.000 0.00 0.00 34.56 3.20
433 655 6.465439 TGTAAAGAAACAGTCTCACTCTCA 57.535 37.500 0.00 0.00 34.56 3.27
434 656 6.273825 TGTAAAGAAACAGTCTCACTCTCAC 58.726 40.000 0.00 0.00 34.56 3.51
467 692 3.690460 AGAATTGGACTTGGACACATCC 58.310 45.455 0.00 0.00 46.48 3.51
507 736 4.502171 CACATGAAACATGTGGTAAGCA 57.498 40.909 26.94 0.00 44.04 3.91
508 737 4.869215 CACATGAAACATGTGGTAAGCAA 58.131 39.130 26.94 0.00 44.04 3.91
509 738 5.472148 CACATGAAACATGTGGTAAGCAAT 58.528 37.500 26.94 0.00 44.04 3.56
510 739 5.574055 CACATGAAACATGTGGTAAGCAATC 59.426 40.000 26.94 0.00 44.04 2.67
511 740 4.782019 TGAAACATGTGGTAAGCAATCC 57.218 40.909 0.00 0.00 0.00 3.01
512 741 4.148079 TGAAACATGTGGTAAGCAATCCA 58.852 39.130 0.00 0.00 0.00 3.41
513 742 4.586421 TGAAACATGTGGTAAGCAATCCAA 59.414 37.500 0.00 0.00 35.38 3.53
514 743 5.069648 TGAAACATGTGGTAAGCAATCCAAA 59.930 36.000 0.00 0.00 35.38 3.28
515 744 4.519540 ACATGTGGTAAGCAATCCAAAC 57.480 40.909 0.00 0.00 35.38 2.93
516 745 3.894427 ACATGTGGTAAGCAATCCAAACA 59.106 39.130 0.00 0.00 35.38 2.83
517 746 4.343526 ACATGTGGTAAGCAATCCAAACAA 59.656 37.500 0.00 0.00 35.38 2.83
518 747 5.011943 ACATGTGGTAAGCAATCCAAACAAT 59.988 36.000 0.00 0.00 35.38 2.71
519 748 5.543507 TGTGGTAAGCAATCCAAACAATT 57.456 34.783 0.00 0.00 35.38 2.32
520 749 5.537188 TGTGGTAAGCAATCCAAACAATTC 58.463 37.500 0.00 0.00 35.38 2.17
521 750 5.069648 TGTGGTAAGCAATCCAAACAATTCA 59.930 36.000 0.00 0.00 35.38 2.57
522 751 5.988561 GTGGTAAGCAATCCAAACAATTCAA 59.011 36.000 0.00 0.00 35.38 2.69
523 752 6.481644 GTGGTAAGCAATCCAAACAATTCAAA 59.518 34.615 0.00 0.00 35.38 2.69
524 753 7.011857 GTGGTAAGCAATCCAAACAATTCAAAA 59.988 33.333 0.00 0.00 35.38 2.44
525 754 7.554118 TGGTAAGCAATCCAAACAATTCAAAAA 59.446 29.630 0.00 0.00 0.00 1.94
560 789 2.597510 GACAAAACAGGGCCGCCT 60.598 61.111 9.86 0.00 0.00 5.52
605 883 2.127345 CGTCGACTCGTGCGTTCT 60.127 61.111 14.70 0.00 0.00 3.01
609 887 1.081376 CGACTCGTGCGTTCTCCTT 60.081 57.895 0.00 0.00 0.00 3.36
731 1048 0.743345 GTCAACACTACCATCCCGGC 60.743 60.000 0.00 0.00 39.03 6.13
805 1137 0.399233 AATCCCTTCCCTCTCCTCCG 60.399 60.000 0.00 0.00 0.00 4.63
854 1191 1.124477 CCCCTACTCCATCCAGCTCC 61.124 65.000 0.00 0.00 0.00 4.70
903 1257 3.019564 GCCACATAGAAAATCCAGCTGT 58.980 45.455 13.81 0.00 0.00 4.40
905 1259 4.082026 GCCACATAGAAAATCCAGCTGTTT 60.082 41.667 13.81 6.74 0.00 2.83
907 1261 5.327091 CACATAGAAAATCCAGCTGTTTCG 58.673 41.667 13.81 6.55 36.57 3.46
928 1282 4.957954 TCGGTAAAGATAACCAGCCTCTAA 59.042 41.667 0.00 0.00 36.78 2.10
946 1300 5.763204 CCTCTAATCTCTACTCGAGCTCTTT 59.237 44.000 13.61 1.91 39.70 2.52
958 1321 3.077359 CGAGCTCTTTTCTCCCACAAAT 58.923 45.455 12.85 0.00 0.00 2.32
1630 2288 4.681978 GACTTGTCACCGGCCGCT 62.682 66.667 22.85 2.01 0.00 5.52
1986 2645 2.781300 CTCGCGAAGAAGCTTGGC 59.219 61.111 11.33 0.59 34.40 4.52
2451 3110 5.556915 CACAACCAAGATGTTAACTCCCTA 58.443 41.667 7.22 0.00 0.00 3.53
2478 3137 0.612174 TCTCAGCCCGTAAGACTGCT 60.612 55.000 0.00 0.00 40.00 4.24
2487 3146 1.406069 CGTAAGACTGCTGAGGCCATT 60.406 52.381 5.01 0.00 43.02 3.16
2526 3185 4.211125 TGTCCTCTACATTTTTGGTTGCA 58.789 39.130 0.00 0.00 31.43 4.08
2577 3236 2.688507 GAGGAGAATGTCAAGAACGCA 58.311 47.619 0.00 0.00 0.00 5.24
2584 3243 1.581934 TGTCAAGAACGCAGTCAAGG 58.418 50.000 0.00 0.00 45.00 3.61
2603 3262 2.439507 AGGATTGTGTCACAAGAGTGGT 59.560 45.455 22.16 5.80 45.91 4.16
2670 3329 2.222027 CGCTTTTGTGAGAAGGACCTT 58.778 47.619 6.40 6.40 0.00 3.50
2671 3330 3.399330 CGCTTTTGTGAGAAGGACCTTA 58.601 45.455 6.75 0.00 0.00 2.69
2675 3334 5.390991 GCTTTTGTGAGAAGGACCTTATTCG 60.391 44.000 6.75 0.00 0.00 3.34
2908 3567 1.303561 GCAGTGGAGAATGGCACCA 60.304 57.895 0.00 0.00 34.66 4.17
2916 3575 2.360350 AATGGCACCACCGCAGAG 60.360 61.111 0.00 0.00 43.94 3.35
2928 3587 3.127533 GCAGAGCCGAACCGCATT 61.128 61.111 0.00 0.00 0.00 3.56
3157 3818 2.008329 GAGAAGATGCTGTGCTTCAGG 58.992 52.381 0.00 0.00 43.78 3.86
3192 3870 5.500234 TCCCCTTGTTCTGAACTGATAATG 58.500 41.667 20.18 4.79 0.00 1.90
3247 3925 3.412237 TCCCCTCTTCTAAAACGTTGG 57.588 47.619 0.00 0.00 0.00 3.77
3381 4059 7.933728 TTTCATGTCAAATGTTGATGTTCTG 57.066 32.000 0.00 0.00 42.47 3.02
3411 4089 1.457303 CAGCACGTTCAGACTTACTGC 59.543 52.381 0.00 0.00 45.38 4.40
3479 4158 3.727518 TGTTGATAATTTTCACGTCGCG 58.272 40.909 0.00 0.00 0.00 5.87
3557 4236 4.438145 CGAGCAACTTCGACTATCATACAC 59.562 45.833 0.00 0.00 43.03 2.90
3651 4330 5.119898 GCACATCAGAACTAGTCACAGAAAG 59.880 44.000 0.00 0.00 0.00 2.62
3662 4341 6.722129 ACTAGTCACAGAAAGTAATCAGACCT 59.278 38.462 0.00 0.00 0.00 3.85
3701 4381 9.713740 CTTATATGTCAACAGAAGAAAGAATGC 57.286 33.333 0.00 0.00 0.00 3.56
3714 4394 6.442513 AGAAAGAATGCACAAGTATAAGCC 57.557 37.500 0.00 0.00 0.00 4.35
3738 4418 1.135689 CCGCTTCAGTGTATGCCAAAC 60.136 52.381 0.00 0.00 0.00 2.93
3823 4512 7.390027 CAATGGGAGACTTATATTGGGTAGAG 58.610 42.308 0.00 0.00 0.00 2.43
3830 4519 7.306013 AGACTTATATTGGGTAGAGGATGTCA 58.694 38.462 0.00 0.00 0.00 3.58
3841 4530 5.305644 GGTAGAGGATGTCATAGTGGTTGAT 59.694 44.000 0.00 0.00 0.00 2.57
3862 4551 1.743252 TGAACAGCACGTGCACACA 60.743 52.632 39.21 28.14 45.16 3.72
3969 4658 1.751927 GCCAAGGCCCACATCTGAG 60.752 63.158 0.00 0.00 34.56 3.35
4064 4753 4.487714 TGAGGGTCATGTATCCAAGAAC 57.512 45.455 0.00 0.00 0.00 3.01
4065 4754 3.199946 TGAGGGTCATGTATCCAAGAACC 59.800 47.826 0.00 0.00 44.75 3.62
4105 4795 4.034048 GCACGACATTGATGTAAAGGTAGG 59.966 45.833 0.00 0.00 41.95 3.18
4123 4813 4.322349 GGTAGGGATGCTGATACTCACATC 60.322 50.000 0.00 0.00 35.81 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.657745 AGGAAATACATTGATTGCATGTGGA 59.342 36.000 0.12 0.00 0.00 4.02
30 31 7.089770 TGCATTGCACGTTAATATTAGGAAA 57.910 32.000 7.38 0.00 31.71 3.13
100 101 9.935241 ATTGCACAATGATATTAGGTAGAGTAG 57.065 33.333 0.00 0.00 0.00 2.57
103 104 8.837788 TGATTGCACAATGATATTAGGTAGAG 57.162 34.615 0.00 0.00 0.00 2.43
119 120 6.839124 ATTAGGAAAGACATTGATTGCACA 57.161 33.333 0.00 0.00 0.00 4.57
120 121 9.241317 CAATATTAGGAAAGACATTGATTGCAC 57.759 33.333 0.00 0.00 0.00 4.57
131 132 6.509418 TTGCACACCAATATTAGGAAAGAC 57.491 37.500 9.93 0.00 0.00 3.01
200 201 9.945904 TGTACATGTAATACACTTATGTTGGAA 57.054 29.630 7.25 0.00 40.48 3.53
201 202 9.373603 GTGTACATGTAATACACTTATGTTGGA 57.626 33.333 18.85 0.00 45.91 3.53
202 203 8.325282 CGTGTACATGTAATACACTTATGTTGG 58.675 37.037 21.92 6.19 46.78 3.77
203 204 9.078753 TCGTGTACATGTAATACACTTATGTTG 57.921 33.333 21.92 9.54 46.78 3.33
204 205 9.811995 ATCGTGTACATGTAATACACTTATGTT 57.188 29.630 21.92 5.33 46.78 2.71
205 206 9.811995 AATCGTGTACATGTAATACACTTATGT 57.188 29.630 21.92 0.00 46.78 2.29
227 228 6.895898 TCGCTATGAACCTTACTAGTAATCG 58.104 40.000 15.57 11.15 0.00 3.34
229 230 8.405418 TGATCGCTATGAACCTTACTAGTAAT 57.595 34.615 15.57 1.32 0.00 1.89
232 233 6.265649 ACATGATCGCTATGAACCTTACTAGT 59.734 38.462 0.00 0.00 0.00 2.57
233 234 6.584184 CACATGATCGCTATGAACCTTACTAG 59.416 42.308 0.00 0.00 0.00 2.57
234 235 6.040504 ACACATGATCGCTATGAACCTTACTA 59.959 38.462 0.00 0.00 0.00 1.82
235 236 5.163405 ACACATGATCGCTATGAACCTTACT 60.163 40.000 0.00 0.00 0.00 2.24
236 237 5.050490 ACACATGATCGCTATGAACCTTAC 58.950 41.667 0.00 0.00 0.00 2.34
237 238 5.276461 ACACATGATCGCTATGAACCTTA 57.724 39.130 0.00 0.00 0.00 2.69
238 239 4.142609 ACACATGATCGCTATGAACCTT 57.857 40.909 0.00 0.00 0.00 3.50
239 240 3.827008 ACACATGATCGCTATGAACCT 57.173 42.857 0.00 0.00 0.00 3.50
240 241 3.430218 GCTACACATGATCGCTATGAACC 59.570 47.826 0.00 0.00 0.00 3.62
241 242 3.430218 GGCTACACATGATCGCTATGAAC 59.570 47.826 0.00 0.00 0.00 3.18
242 243 3.321968 AGGCTACACATGATCGCTATGAA 59.678 43.478 0.00 0.00 0.00 2.57
243 244 2.893489 AGGCTACACATGATCGCTATGA 59.107 45.455 0.00 0.00 0.00 2.15
244 245 3.309961 AGGCTACACATGATCGCTATG 57.690 47.619 0.00 0.00 0.00 2.23
246 247 2.229062 GCTAGGCTACACATGATCGCTA 59.771 50.000 0.00 0.00 0.00 4.26
247 248 1.000283 GCTAGGCTACACATGATCGCT 60.000 52.381 0.00 0.00 0.00 4.93
248 249 1.423395 GCTAGGCTACACATGATCGC 58.577 55.000 0.00 0.00 0.00 4.58
249 250 1.341209 TGGCTAGGCTACACATGATCG 59.659 52.381 18.18 0.00 0.00 3.69
250 251 2.548920 GGTGGCTAGGCTACACATGATC 60.549 54.545 18.18 0.00 41.80 2.92
251 252 1.417890 GGTGGCTAGGCTACACATGAT 59.582 52.381 18.18 0.00 41.80 2.45
261 262 0.678048 CTTTGTCTGGGTGGCTAGGC 60.678 60.000 9.85 9.85 0.00 3.93
272 273 5.805486 TGCGCTATTAGAAGTACTTTGTCTG 59.195 40.000 10.02 0.92 0.00 3.51
273 274 5.962433 TGCGCTATTAGAAGTACTTTGTCT 58.038 37.500 10.02 5.17 0.00 3.41
274 275 6.455246 GGTTGCGCTATTAGAAGTACTTTGTC 60.455 42.308 10.02 0.00 0.00 3.18
290 291 2.080693 CTATGTTTGTGGGTTGCGCTA 58.919 47.619 9.73 0.00 0.00 4.26
299 300 6.020121 GCGTATGTACAGTACTATGTTTGTGG 60.020 42.308 12.07 0.00 34.56 4.17
310 311 4.667948 GTCGTGTATGCGTATGTACAGTAC 59.332 45.833 0.33 3.49 31.95 2.73
312 313 3.688272 GTCGTGTATGCGTATGTACAGT 58.312 45.455 0.33 0.00 31.95 3.55
314 315 2.707392 CGTCGTGTATGCGTATGTACA 58.293 47.619 0.00 0.00 0.00 2.90
324 404 5.222286 CGTTCAAAATTAAGCGTCGTGTATG 59.778 40.000 0.00 0.00 0.00 2.39
338 418 2.500509 TTGCTTCGGCGTTCAAAATT 57.499 40.000 6.85 0.00 45.37 1.82
350 430 2.176546 CGTGCCACCATTGCTTCG 59.823 61.111 0.00 0.00 0.00 3.79
356 436 1.094785 GACTTATGCGTGCCACCATT 58.905 50.000 4.50 0.00 0.00 3.16
360 440 0.721718 GTCTGACTTATGCGTGCCAC 59.278 55.000 0.00 0.00 0.00 5.01
429 651 7.987458 GTCCAATTCTTGTATGATTAGGTGAGA 59.013 37.037 0.00 0.00 0.00 3.27
430 652 7.989741 AGTCCAATTCTTGTATGATTAGGTGAG 59.010 37.037 0.00 0.00 0.00 3.51
431 653 7.861629 AGTCCAATTCTTGTATGATTAGGTGA 58.138 34.615 0.00 0.00 0.00 4.02
432 654 8.400947 CAAGTCCAATTCTTGTATGATTAGGTG 58.599 37.037 0.00 0.00 37.90 4.00
433 655 7.557719 CCAAGTCCAATTCTTGTATGATTAGGT 59.442 37.037 5.06 0.00 40.15 3.08
434 656 7.775093 TCCAAGTCCAATTCTTGTATGATTAGG 59.225 37.037 5.06 0.00 40.15 2.69
486 715 4.502171 TGCTTACCACATGTTTCATGTG 57.498 40.909 26.20 26.20 46.49 3.21
487 716 5.336690 GGATTGCTTACCACATGTTTCATGT 60.337 40.000 9.21 9.21 0.00 3.21
488 717 5.104374 GGATTGCTTACCACATGTTTCATG 58.896 41.667 0.00 7.99 0.00 3.07
489 718 4.771577 TGGATTGCTTACCACATGTTTCAT 59.228 37.500 0.00 0.00 0.00 2.57
490 719 4.148079 TGGATTGCTTACCACATGTTTCA 58.852 39.130 0.00 0.00 0.00 2.69
491 720 4.782019 TGGATTGCTTACCACATGTTTC 57.218 40.909 0.00 0.00 0.00 2.78
492 721 5.163364 TGTTTGGATTGCTTACCACATGTTT 60.163 36.000 0.00 0.00 35.81 2.83
493 722 4.343526 TGTTTGGATTGCTTACCACATGTT 59.656 37.500 0.00 0.00 35.81 2.71
494 723 3.894427 TGTTTGGATTGCTTACCACATGT 59.106 39.130 0.00 0.00 35.81 3.21
495 724 4.517952 TGTTTGGATTGCTTACCACATG 57.482 40.909 0.00 0.00 35.81 3.21
496 725 5.743636 ATTGTTTGGATTGCTTACCACAT 57.256 34.783 0.00 0.00 35.81 3.21
497 726 5.069648 TGAATTGTTTGGATTGCTTACCACA 59.930 36.000 0.00 0.00 35.81 4.17
498 727 5.537188 TGAATTGTTTGGATTGCTTACCAC 58.463 37.500 0.00 0.00 35.81 4.16
499 728 5.798125 TGAATTGTTTGGATTGCTTACCA 57.202 34.783 0.00 0.00 0.00 3.25
500 729 7.489574 TTTTGAATTGTTTGGATTGCTTACC 57.510 32.000 0.00 0.00 0.00 2.85
538 767 1.472552 GCGGCCCTGTTTTGTCTTTTT 60.473 47.619 0.00 0.00 0.00 1.94
539 768 0.104120 GCGGCCCTGTTTTGTCTTTT 59.896 50.000 0.00 0.00 0.00 2.27
540 769 1.739667 GCGGCCCTGTTTTGTCTTT 59.260 52.632 0.00 0.00 0.00 2.52
541 770 2.200337 GGCGGCCCTGTTTTGTCTT 61.200 57.895 8.12 0.00 0.00 3.01
542 771 1.774894 TAGGCGGCCCTGTTTTGTCT 61.775 55.000 17.02 0.00 42.90 3.41
543 772 0.891904 TTAGGCGGCCCTGTTTTGTC 60.892 55.000 17.02 0.00 42.90 3.18
544 773 0.251608 ATTAGGCGGCCCTGTTTTGT 60.252 50.000 17.02 0.00 42.90 2.83
560 789 8.519526 CATTTTCCAGTTGCTAGTTAACCATTA 58.480 33.333 0.88 0.00 0.00 1.90
605 883 2.917933 CTGCGACAATGGGATAAAGGA 58.082 47.619 0.00 0.00 0.00 3.36
609 887 1.667236 CTGCTGCGACAATGGGATAA 58.333 50.000 0.00 0.00 0.00 1.75
731 1048 0.609131 GGGATTGGTGTGGACTGTGG 60.609 60.000 0.00 0.00 0.00 4.17
805 1137 3.379688 GGATGCTCTTCTTGGATGGAAAC 59.620 47.826 0.00 0.00 0.00 2.78
854 1191 3.119709 GAGCGGCCGTGAGAGAGAG 62.120 68.421 28.70 0.00 0.00 3.20
903 1257 4.224370 AGAGGCTGGTTATCTTTACCGAAA 59.776 41.667 0.00 0.00 38.55 3.46
905 1259 3.371965 AGAGGCTGGTTATCTTTACCGA 58.628 45.455 0.00 0.00 38.55 4.69
907 1261 7.015779 AGAGATTAGAGGCTGGTTATCTTTACC 59.984 40.741 0.00 0.00 36.17 2.85
946 1300 1.704628 TGGAGCAGATTTGTGGGAGAA 59.295 47.619 0.00 0.00 0.00 2.87
958 1321 1.839424 TGAAGTCTCGATGGAGCAGA 58.161 50.000 0.00 0.00 40.26 4.26
1662 2321 0.179067 CCTCGGCGGCATTAACCTTA 60.179 55.000 10.53 0.00 0.00 2.69
1986 2645 2.028420 TCATCAATGGGTCAAGCTCG 57.972 50.000 0.00 0.00 0.00 5.03
2451 3110 4.039366 GTCTTACGGGCTGAGATTAATCCT 59.961 45.833 11.92 0.00 0.00 3.24
2478 3137 3.349927 CTTCAGAATGTCAATGGCCTCA 58.650 45.455 3.32 0.00 37.40 3.86
2487 3146 3.262660 AGGACATGAGCTTCAGAATGTCA 59.737 43.478 19.79 6.61 46.94 3.58
2526 3185 1.672356 GTCGATGGCTTGGCACAGT 60.672 57.895 0.00 0.00 42.39 3.55
2577 3236 4.141620 ACTCTTGTGACACAATCCTTGACT 60.142 41.667 20.86 1.96 37.48 3.41
2584 3243 3.466836 TGACCACTCTTGTGACACAATC 58.533 45.455 20.86 14.43 46.55 2.67
2652 3311 5.932303 TCGAATAAGGTCCTTCTCACAAAAG 59.068 40.000 7.61 0.00 0.00 2.27
2675 3334 2.799540 GCCTCGCGGTCGATTGTTC 61.800 63.158 6.13 0.00 44.56 3.18
2850 3509 0.317160 CCTGAGGTAGTGTCGCACAA 59.683 55.000 11.58 0.00 36.74 3.33
2916 3575 1.442017 GTCAACAATGCGGTTCGGC 60.442 57.895 0.00 0.00 0.00 5.54
3157 3818 1.283321 ACAAGGGGAGCCTTCAGAATC 59.717 52.381 0.00 0.00 0.00 2.52
3181 3859 7.806690 TCAAACAACAGTAGCATTATCAGTTC 58.193 34.615 0.00 0.00 0.00 3.01
3192 3870 5.748592 AGAACGAAATCAAACAACAGTAGC 58.251 37.500 0.00 0.00 0.00 3.58
3247 3925 0.725784 CGGAAGAACGTTGCATGCAC 60.726 55.000 22.58 14.60 0.00 4.57
3329 4007 1.135402 CCCTTTCGCTTACATTGGCAC 60.135 52.381 0.00 0.00 0.00 5.01
3381 4059 2.337583 TGAACGTGCTGATTCAGTAGC 58.662 47.619 14.90 2.68 40.29 3.58
3411 4089 4.880120 AGGAGAATGTGCTTGTATGACATG 59.120 41.667 0.00 0.00 30.69 3.21
3479 4158 6.091986 GGTGCTATTTCTCTCTATATTGCAGC 59.908 42.308 0.00 0.00 38.95 5.25
3651 4330 8.794335 AGGATAGAAAAACAAGGTCTGATTAC 57.206 34.615 0.00 0.00 0.00 1.89
3701 4381 1.663695 CGGGTGGGCTTATACTTGTG 58.336 55.000 0.00 0.00 0.00 3.33
3714 4394 1.369091 GCATACACTGAAGCGGGTGG 61.369 60.000 0.00 0.00 37.72 4.61
3738 4418 3.756434 GCTGAGCTCTAGGTGGTAGATAG 59.244 52.174 16.19 0.00 37.14 2.08
3788 4477 4.489306 AGTCTCCCATTGCTAGGTTAAC 57.511 45.455 0.00 0.00 0.00 2.01
3823 4512 3.804325 CACGATCAACCACTATGACATCC 59.196 47.826 0.00 0.00 0.00 3.51
3830 4519 3.262420 GCTGTTCACGATCAACCACTAT 58.738 45.455 0.00 0.00 0.00 2.12
3878 4567 4.360563 CTGATGATGTGTACGTTAGTCCC 58.639 47.826 0.00 0.00 0.00 4.46
4074 4763 3.127548 ACATCAATGTCGTGCTGAATTCC 59.872 43.478 2.27 0.00 35.87 3.01


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

AutoCloner maintained by Alex Coulton.