Multiple sequence alignment - TraesCS5D01G501300

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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 TraesCS5D01G501300 chr5D 100.000 4017 0 0 1 4017 529354329 529358345 0.000000e+00 7419
1 TraesCS5D01G501300 chr5A 87.576 4137 300 116 1 4017 657489375 657493417 0.000000e+00 4595
2 TraesCS5D01G501300 chr5A 90.769 130 10 2 124 252 675839370 675839242 5.340000e-39 172
3 TraesCS5D01G501300 chr5A 83.920 199 11 6 304 483 675839155 675838959 1.920000e-38 171
4 TraesCS5D01G501300 chr5B 95.098 1326 37 7 1772 3095 668196267 668197566 0.000000e+00 2063
5 TraesCS5D01G501300 chr5B 93.691 745 27 9 955 1686 668195532 668196269 0.000000e+00 1098
6 TraesCS5D01G501300 chr5B 89.647 879 56 15 3097 3968 668197651 668198501 0.000000e+00 1086
7 TraesCS5D01G501300 chr5B 87.955 797 40 22 1 752 668194127 668194912 0.000000e+00 889
8 TraesCS5D01G501300 chr5B 85.000 120 6 5 779 886 668195374 668195493 1.180000e-20 111
9 TraesCS5D01G501300 chr2A 83.567 499 50 21 3443 3925 282967021 282967503 4.770000e-119 438
10 TraesCS5D01G501300 chr6D 90.226 133 11 2 121 252 42383609 42383740 5.340000e-39 172
11 TraesCS5D01G501300 chr2B 90.769 130 10 2 124 252 681391425 681391297 5.340000e-39 172
12 TraesCS5D01G501300 chr2B 88.462 130 13 2 124 252 346738509 346738381 5.380000e-34 156
13 TraesCS5D01G501300 chr2B 86.466 133 16 2 121 252 131904084 131904215 1.160000e-30 145
14 TraesCS5D01G501300 chr4B 89.231 130 12 2 124 252 566638363 566638491 1.160000e-35 161
15 TraesCS5D01G501300 chr4B 89.831 118 10 2 124 240 40361769 40361885 2.500000e-32 150
16 TraesCS5D01G501300 chr4B 95.652 69 3 0 93 161 327139087 327139155 1.180000e-20 111
17 TraesCS5D01G501300 chr4D 82.915 199 13 9 304 483 149088561 149088757 4.160000e-35 159
18 TraesCS5D01G501300 chr1B 82.915 199 13 6 304 483 632853917 632854113 4.160000e-35 159
19 TraesCS5D01G501300 chr7A 88.148 135 10 3 353 483 636328384 636328516 5.380000e-34 156
20 TraesCS5D01G501300 chr1A 89.600 125 7 3 363 483 260084545 260084667 1.930000e-33 154
21 TraesCS5D01G501300 chr1A 87.407 135 11 3 353 483 10194223 10194355 2.500000e-32 150
22 TraesCS5D01G501300 chr4A 87.407 135 11 3 353 483 632372260 632372128 2.500000e-32 150


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 TraesCS5D01G501300 chr5D 529354329 529358345 4016 False 7419.0 7419 100.0000 1 4017 1 chr5D.!!$F1 4016
1 TraesCS5D01G501300 chr5A 657489375 657493417 4042 False 4595.0 4595 87.5760 1 4017 1 chr5A.!!$F1 4016
2 TraesCS5D01G501300 chr5B 668194127 668198501 4374 False 1049.4 2063 90.2782 1 3968 5 chr5B.!!$F1 3967

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
499 544 0.109781 GAAATCGCGCAACCACACAT 60.110 50.000 8.75 0.0 0.00 3.21 F
698 758 0.392060 CGTTTCTTACGGGGAAGGGG 60.392 60.000 0.00 0.0 46.42 4.79 F
1691 2241 1.082756 GCTTGCCGTCGTGTTTCAG 60.083 57.895 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 2223 1.082756 CTGAAACACGACGGCAAGC 60.083 57.895 0.00 0.00 0.00 4.01 R
2269 2852 2.107950 TAAATTGGTGCGCTAGCTGT 57.892 45.000 13.93 0.00 45.42 4.40 R
3678 4364 0.625683 ATCTCCAGGGCCCAACTGAT 60.626 55.000 27.56 18.52 38.20 2.90 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
35 36 1.627879 CACACACATTATTTGCGGGC 58.372 50.000 0.00 0.00 0.00 6.13
36 37 1.067985 CACACACATTATTTGCGGGCA 60.068 47.619 0.00 0.00 0.00 5.36
37 38 1.615883 ACACACATTATTTGCGGGCAA 59.384 42.857 1.21 1.21 0.00 4.52
58 59 4.779993 AATAGGTTCAGGGAAGACCATC 57.220 45.455 0.00 0.00 43.89 3.51
202 204 8.947055 AAATCACTGAAGCAGTAAAAACATTT 57.053 26.923 0.00 0.00 43.43 2.32
203 205 8.947055 AATCACTGAAGCAGTAAAAACATTTT 57.053 26.923 0.00 0.00 43.43 1.82
254 263 0.249238 GGCTACTCATCCGTCTGCAG 60.249 60.000 7.63 7.63 0.00 4.41
278 287 2.462889 CACGACAAGTGCAAGCAATTT 58.537 42.857 4.87 0.00 44.72 1.82
329 355 2.877168 GCATCAACCAGTGATCTGATCC 59.123 50.000 14.71 6.61 44.01 3.36
356 396 2.521465 CACCCAGGTGGCAAGCAA 60.521 61.111 9.07 0.00 42.00 3.91
472 515 5.992217 GTCAGTTAACCTCATCACAAACTCT 59.008 40.000 0.88 0.00 0.00 3.24
473 516 6.146347 GTCAGTTAACCTCATCACAAACTCTC 59.854 42.308 0.88 0.00 0.00 3.20
474 517 5.409826 CAGTTAACCTCATCACAAACTCTCC 59.590 44.000 0.88 0.00 0.00 3.71
476 519 4.437682 AACCTCATCACAAACTCTCCAA 57.562 40.909 0.00 0.00 0.00 3.53
477 520 4.437682 ACCTCATCACAAACTCTCCAAA 57.562 40.909 0.00 0.00 0.00 3.28
478 521 4.990526 ACCTCATCACAAACTCTCCAAAT 58.009 39.130 0.00 0.00 0.00 2.32
479 522 5.006386 ACCTCATCACAAACTCTCCAAATC 58.994 41.667 0.00 0.00 0.00 2.17
480 523 4.093998 CCTCATCACAAACTCTCCAAATCG 59.906 45.833 0.00 0.00 0.00 3.34
481 524 4.893608 TCATCACAAACTCTCCAAATCGA 58.106 39.130 0.00 0.00 0.00 3.59
485 530 6.241207 TCACAAACTCTCCAAATCGAAATC 57.759 37.500 0.00 0.00 0.00 2.17
491 536 0.799393 TCCAAATCGAAATCGCGCAA 59.201 45.000 8.75 0.00 39.60 4.85
492 537 0.907171 CCAAATCGAAATCGCGCAAC 59.093 50.000 8.75 0.00 39.60 4.17
499 544 0.109781 GAAATCGCGCAACCACACAT 60.110 50.000 8.75 0.00 0.00 3.21
502 547 1.378531 ATCGCGCAACCACACATAAT 58.621 45.000 8.75 0.00 0.00 1.28
506 551 3.188667 TCGCGCAACCACACATAATAAAA 59.811 39.130 8.75 0.00 0.00 1.52
507 552 3.299542 CGCGCAACCACACATAATAAAAC 59.700 43.478 8.75 0.00 0.00 2.43
508 553 4.230657 GCGCAACCACACATAATAAAACA 58.769 39.130 0.30 0.00 0.00 2.83
509 554 4.862018 GCGCAACCACACATAATAAAACAT 59.138 37.500 0.30 0.00 0.00 2.71
510 555 5.004345 GCGCAACCACACATAATAAAACATC 59.996 40.000 0.30 0.00 0.00 3.06
527 572 9.921637 ATAAAACATCAAAATTCGGAAGCTAAA 57.078 25.926 0.00 0.00 0.00 1.85
530 575 8.466086 AACATCAAAATTCGGAAGCTAAAATC 57.534 30.769 0.00 0.00 0.00 2.17
578 623 3.691342 CTCCGCACGTCCTTGGGA 61.691 66.667 0.00 0.00 0.00 4.37
647 692 1.202698 GCACCGATCTAAGCAAGGGAT 60.203 52.381 0.00 0.00 0.00 3.85
650 695 2.771943 ACCGATCTAAGCAAGGGATTCA 59.228 45.455 0.00 0.00 0.00 2.57
697 757 3.148340 CGTTTCTTACGGGGAAGGG 57.852 57.895 0.00 0.00 46.42 3.95
698 758 0.392060 CGTTTCTTACGGGGAAGGGG 60.392 60.000 0.00 0.00 46.42 4.79
719 789 2.051435 CGGAGATCTCGCGAGCTG 60.051 66.667 30.97 17.62 35.72 4.24
828 1341 1.283321 CTTCTTTCTTGGAGGAGGGGG 59.717 57.143 0.00 0.00 0.00 5.40
856 1370 2.320587 CGCCTCATATGGGCTTCGC 61.321 63.158 24.11 11.22 46.73 4.70
857 1371 1.227943 GCCTCATATGGGCTTCGCA 60.228 57.895 21.40 0.00 45.57 5.10
860 1374 1.344438 CCTCATATGGGCTTCGCACTA 59.656 52.381 2.13 0.00 30.56 2.74
863 1377 2.434336 TCATATGGGCTTCGCACTAACT 59.566 45.455 2.13 0.00 30.56 2.24
877 1394 2.238646 CACTAACTCCAATGGGCCTACA 59.761 50.000 4.53 0.00 0.00 2.74
898 1415 2.960129 CCGAGTATGTTCGCCGGC 60.960 66.667 19.07 19.07 39.19 6.13
1094 1621 2.733593 GTCGGTGGTGTCGCTGTC 60.734 66.667 0.00 0.00 0.00 3.51
1095 1622 4.337060 TCGGTGGTGTCGCTGTCG 62.337 66.667 0.00 0.00 0.00 4.35
1535 2081 2.003658 GCGTAATGTGCCATGGGGTG 62.004 60.000 15.13 0.00 36.17 4.61
1603 2153 7.870826 TCACCACTACTTAAATTTCACATGTG 58.129 34.615 20.18 20.18 0.00 3.21
1609 2159 6.882610 ACTTAAATTTCACATGTGCAGAGA 57.117 33.333 21.38 0.00 0.00 3.10
1611 2161 7.365741 ACTTAAATTTCACATGTGCAGAGAAG 58.634 34.615 21.38 18.81 0.00 2.85
1673 2223 1.358877 TGTGAATTCTCATGGCGACG 58.641 50.000 7.05 0.00 33.05 5.12
1689 2239 2.127758 CGCTTGCCGTCGTGTTTC 60.128 61.111 0.00 0.00 0.00 2.78
1690 2240 2.876879 CGCTTGCCGTCGTGTTTCA 61.877 57.895 0.00 0.00 0.00 2.69
1691 2241 1.082756 GCTTGCCGTCGTGTTTCAG 60.083 57.895 0.00 0.00 0.00 3.02
1706 2256 8.170553 GTCGTGTTTCAGTTTTCAGTAACTAAA 58.829 33.333 0.00 0.00 36.24 1.85
1707 2257 8.719648 TCGTGTTTCAGTTTTCAGTAACTAAAA 58.280 29.630 0.00 0.00 36.24 1.52
1708 2258 9.332301 CGTGTTTCAGTTTTCAGTAACTAAAAA 57.668 29.630 0.00 0.00 36.24 1.94
1761 2311 7.688343 ACAATCAATCATGGTAAAATTTGGGT 58.312 30.769 0.00 0.00 0.00 4.51
1938 2519 2.813754 GCTGGTCTTTCTGTATTGCACA 59.186 45.455 0.00 0.00 35.30 4.57
2010 2591 4.079253 GTTTTATTGGAGCCACAAGAGGA 58.921 43.478 0.00 0.00 33.23 3.71
2030 2611 7.222000 GAGGATCTATGTGGGTACTTCTTAG 57.778 44.000 0.00 0.00 0.00 2.18
2032 2613 5.304614 GGATCTATGTGGGTACTTCTTAGCA 59.695 44.000 0.00 0.00 0.00 3.49
2160 2742 4.440880 CCTGGATTTTTCAAGTGTTTGCA 58.559 39.130 0.00 0.00 34.21 4.08
2168 2750 8.807667 ATTTTTCAAGTGTTTGCAATCTAGAG 57.192 30.769 0.00 0.00 34.21 2.43
2269 2852 6.137559 ACTCAGTACCCAATTTACCCAAAAA 58.862 36.000 0.00 0.00 0.00 1.94
2279 2862 1.161843 TACCCAAAAACAGCTAGCGC 58.838 50.000 9.55 0.00 0.00 5.92
2299 2882 3.253188 CGCACCAATTTAATGATCCGGAT 59.747 43.478 19.21 19.21 0.00 4.18
2703 3290 7.773224 TCAAGAAACAGGTCAAGAAATCAACTA 59.227 33.333 0.00 0.00 0.00 2.24
2830 3417 6.325596 GCAAAAATAAGAAGGTTAGGCTGAG 58.674 40.000 0.00 0.00 0.00 3.35
2895 3482 3.905784 TCCGTTACCTTTTCTTCTCGTC 58.094 45.455 0.00 0.00 0.00 4.20
2904 3491 5.246429 ACCTTTTCTTCTCGTCTTATCTGGT 59.754 40.000 0.00 0.00 0.00 4.00
2905 3492 6.166982 CCTTTTCTTCTCGTCTTATCTGGTT 58.833 40.000 0.00 0.00 0.00 3.67
2906 3493 7.039223 ACCTTTTCTTCTCGTCTTATCTGGTTA 60.039 37.037 0.00 0.00 0.00 2.85
3095 3765 2.174363 TGACTGAGCACTGGACAATG 57.826 50.000 0.00 0.00 0.00 2.82
3106 3776 2.491693 ACTGGACAATGGCATTTAACCG 59.508 45.455 10.65 11.83 0.00 4.44
3107 3777 2.752354 CTGGACAATGGCATTTAACCGA 59.248 45.455 10.65 4.99 0.00 4.69
3190 3860 5.070580 AGAGTACCCAGGCAGTAATGTATTC 59.929 44.000 0.00 0.00 0.00 1.75
3202 3872 9.066892 GGCAGTAATGTATTCAAATCATTAGGA 57.933 33.333 0.00 0.00 35.60 2.94
3286 3956 7.308782 AGGTAGAAGACTTGCATATTTTTCG 57.691 36.000 0.00 0.00 0.00 3.46
3336 4006 1.847506 TGACCTCACATGTGGGCCT 60.848 57.895 25.16 9.86 35.89 5.19
3337 4007 1.380302 GACCTCACATGTGGGCCTT 59.620 57.895 25.16 9.13 30.62 4.35
3338 4008 0.251341 GACCTCACATGTGGGCCTTT 60.251 55.000 25.16 9.46 30.62 3.11
3339 4009 0.540365 ACCTCACATGTGGGCCTTTG 60.540 55.000 25.16 11.38 33.22 2.77
3340 4010 1.588082 CTCACATGTGGGCCTTTGC 59.412 57.895 25.16 0.00 0.00 3.68
3487 4164 3.417069 AGGGTGTCAATCAAATCGACA 57.583 42.857 0.00 0.00 37.33 4.35
3492 4169 5.925969 GGGTGTCAATCAAATCGACATTTTT 59.074 36.000 0.00 0.00 41.39 1.94
3545 4224 1.468914 CTAAGCTTCGTGGGCCTTTTC 59.531 52.381 0.00 0.00 0.00 2.29
3546 4225 0.178990 AAGCTTCGTGGGCCTTTTCT 60.179 50.000 4.53 0.00 0.00 2.52
3572 4254 9.919416 TCATTCTGGTTTCTCATATATTTTGGA 57.081 29.630 0.00 0.00 0.00 3.53
3605 4291 6.869421 AAAGACGTTTCTCACATTTGTTTG 57.131 33.333 0.00 0.00 0.00 2.93
3629 4315 1.270305 TGTCTGAACAGCTAGGCACAC 60.270 52.381 0.00 0.00 0.00 3.82
3839 4528 5.681105 CCATGTGTTTGAACAACTAAACGAG 59.319 40.000 0.00 0.00 41.21 4.18
3848 4537 4.258702 ACAACTAAACGAGCTCTGTGAT 57.741 40.909 12.85 7.20 0.00 3.06
3856 4545 1.863267 GAGCTCTGTGATTGGATCCG 58.137 55.000 6.43 0.00 0.00 4.18
3866 4555 6.099125 TCTGTGATTGGATCCGGAACTAAATA 59.901 38.462 14.34 4.24 0.00 1.40
3876 4565 4.124970 CCGGAACTAAATAACTAGGTGGC 58.875 47.826 0.00 0.00 0.00 5.01
3877 4566 4.124970 CGGAACTAAATAACTAGGTGGCC 58.875 47.826 0.00 0.00 0.00 5.36
3886 4575 1.144057 CTAGGTGGCCGGCAGTAAG 59.856 63.158 30.85 14.47 0.00 2.34
3900 4589 2.485657 GCAGTAAGCAGGGATAGGGAAC 60.486 54.545 0.00 0.00 44.79 3.62
3919 4608 5.985530 GGGAACATATTTTTGCAGCCTTATC 59.014 40.000 0.00 0.00 0.00 1.75
3968 4658 1.108727 TTCAGCCTGGCAGGTGTTTG 61.109 55.000 32.80 23.98 37.80 2.93
3969 4659 2.203538 AGCCTGGCAGGTGTTTGG 60.204 61.111 32.80 8.92 37.80 3.28
3970 4660 2.203480 GCCTGGCAGGTGTTTGGA 60.203 61.111 32.80 0.00 37.80 3.53
3973 4663 2.594303 TGGCAGGTGTTTGGAGCG 60.594 61.111 0.00 0.00 0.00 5.03
3974 4664 4.043200 GGCAGGTGTTTGGAGCGC 62.043 66.667 0.00 0.00 0.00 5.92
3975 4665 4.389576 GCAGGTGTTTGGAGCGCG 62.390 66.667 0.00 0.00 0.00 6.86
4008 4698 2.169352 CAGGATCGGATCTGTTGAACCT 59.831 50.000 16.96 1.69 35.53 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.301072 TGGTCTTCCCTGAACCTATTTG 57.699 45.455 0.00 0.00 0.00 2.32
36 37 4.079730 GGATGGTCTTCCCTGAACCTATTT 60.080 45.833 0.00 0.00 0.00 1.40
37 38 3.459969 GGATGGTCTTCCCTGAACCTATT 59.540 47.826 0.00 0.00 0.00 1.73
38 39 3.049344 GGATGGTCTTCCCTGAACCTAT 58.951 50.000 0.00 0.00 0.00 2.57
39 40 2.045885 AGGATGGTCTTCCCTGAACCTA 59.954 50.000 0.00 0.00 36.35 3.08
40 41 1.203492 AGGATGGTCTTCCCTGAACCT 60.203 52.381 0.00 0.00 36.35 3.50
41 42 1.290134 AGGATGGTCTTCCCTGAACC 58.710 55.000 0.01 0.00 36.35 3.62
42 43 4.779993 AATAGGATGGTCTTCCCTGAAC 57.220 45.455 0.00 0.00 36.35 3.18
58 59 5.123186 TGACATTGTTGAACCGCTTAATAGG 59.877 40.000 0.00 0.00 0.00 2.57
91 92 7.563020 TCTGAATAGAACTGCTTGATTGATCT 58.437 34.615 0.00 0.00 0.00 2.75
202 204 7.668052 AGTTTGACAATTATAAGCCTGGTGTAA 59.332 33.333 0.00 0.00 0.00 2.41
203 205 7.172342 AGTTTGACAATTATAAGCCTGGTGTA 58.828 34.615 0.00 0.00 0.00 2.90
254 263 3.862063 CTTGCACTTGTCGTGGCGC 62.862 63.158 0.00 0.00 43.97 6.53
278 287 9.393512 GAGGTTACTTATGTAGTCTGAAGTAGA 57.606 37.037 0.00 0.00 38.33 2.59
329 355 4.684134 CCTGGGTGGGGCTTGTGG 62.684 72.222 0.00 0.00 0.00 4.17
350 376 2.483877 TGATTCGCCTGTTAGTTGCTTG 59.516 45.455 0.00 0.00 0.00 4.01
356 396 2.960819 GTGAGTGATTCGCCTGTTAGT 58.039 47.619 0.00 0.00 0.00 2.24
472 515 0.799393 TTGCGCGATTTCGATTTGGA 59.201 45.000 12.10 0.00 43.02 3.53
473 516 0.907171 GTTGCGCGATTTCGATTTGG 59.093 50.000 12.10 0.00 43.02 3.28
474 517 0.907171 GGTTGCGCGATTTCGATTTG 59.093 50.000 12.10 0.00 43.02 2.32
476 519 0.179200 GTGGTTGCGCGATTTCGATT 60.179 50.000 12.10 0.00 43.02 3.34
477 520 1.295357 TGTGGTTGCGCGATTTCGAT 61.295 50.000 12.10 0.00 43.02 3.59
478 521 1.956678 TGTGGTTGCGCGATTTCGA 60.957 52.632 12.10 0.00 43.02 3.71
479 522 1.792057 GTGTGGTTGCGCGATTTCG 60.792 57.895 12.10 0.00 43.27 3.46
480 523 0.109781 ATGTGTGGTTGCGCGATTTC 60.110 50.000 12.10 0.00 0.00 2.17
481 524 1.160989 TATGTGTGGTTGCGCGATTT 58.839 45.000 12.10 0.00 0.00 2.17
485 530 2.815657 TTATTATGTGTGGTTGCGCG 57.184 45.000 0.00 0.00 0.00 6.86
502 547 9.751542 TTTTAGCTTCCGAATTTTGATGTTTTA 57.248 25.926 0.00 0.00 0.00 1.52
506 551 6.747280 CGATTTTAGCTTCCGAATTTTGATGT 59.253 34.615 0.00 0.00 0.00 3.06
507 552 6.197096 CCGATTTTAGCTTCCGAATTTTGATG 59.803 38.462 0.00 0.00 0.00 3.07
508 553 6.265577 CCGATTTTAGCTTCCGAATTTTGAT 58.734 36.000 0.00 0.00 0.00 2.57
509 554 5.636837 CCGATTTTAGCTTCCGAATTTTGA 58.363 37.500 0.00 0.00 0.00 2.69
510 555 4.265320 GCCGATTTTAGCTTCCGAATTTTG 59.735 41.667 0.00 0.00 0.00 2.44
516 561 1.426041 GCGCCGATTTTAGCTTCCGA 61.426 55.000 0.00 0.00 0.00 4.55
524 569 2.515729 GGTACGCGCGCCGATTTTA 61.516 57.895 32.58 10.17 41.02 1.52
527 572 4.884257 ATGGTACGCGCGCCGATT 62.884 61.111 32.58 13.11 41.02 3.34
578 623 3.121030 GTCGCGACAATGGCTGCT 61.121 61.111 33.09 0.00 0.00 4.24
647 692 2.363975 CGTCCCTTCCCCGGATGAA 61.364 63.158 0.73 4.40 38.50 2.57
771 841 2.742372 TTTTCTCGCCGCTGCTCC 60.742 61.111 0.00 0.00 34.43 4.70
856 1370 2.238646 TGTAGGCCCATTGGAGTTAGTG 59.761 50.000 3.62 0.00 0.00 2.74
857 1371 2.505819 CTGTAGGCCCATTGGAGTTAGT 59.494 50.000 3.62 0.00 0.00 2.24
860 1374 0.625849 CCTGTAGGCCCATTGGAGTT 59.374 55.000 3.62 0.00 0.00 3.01
877 1394 2.499685 GCGAACATACTCGGGCCT 59.500 61.111 0.84 0.00 39.27 5.19
884 1401 2.869503 CTTGGGCCGGCGAACATACT 62.870 60.000 22.54 0.00 0.00 2.12
898 1415 2.115266 AGAAACGTGGGCCTTGGG 59.885 61.111 4.53 0.00 0.00 4.12
923 1440 3.393089 AATAGAGCCGCTTATCACCTG 57.607 47.619 0.00 0.00 0.00 4.00
949 1466 6.347969 GGGAACGAAGCGATTTAACTTACTTT 60.348 38.462 0.00 0.00 0.00 2.66
950 1467 5.121298 GGGAACGAAGCGATTTAACTTACTT 59.879 40.000 0.00 0.00 0.00 2.24
951 1468 4.628766 GGGAACGAAGCGATTTAACTTACT 59.371 41.667 0.00 0.00 0.00 2.24
1404 1937 2.223994 GGGCGATACTACCTTGAAGGAC 60.224 54.545 19.83 1.35 37.67 3.85
1457 1991 2.953648 TGATCTAAACGAGCGACCCATA 59.046 45.455 0.00 0.00 0.00 2.74
1603 2153 5.718649 TTCGTTATGCATAACTTCTCTGC 57.281 39.130 34.91 15.70 40.27 4.26
1609 2159 5.703592 TCACAGGTTTCGTTATGCATAACTT 59.296 36.000 34.91 15.77 40.27 2.66
1611 2161 5.350365 TCTCACAGGTTTCGTTATGCATAAC 59.650 40.000 31.24 31.24 39.32 1.89
1623 2173 4.240096 CCAAATGCATTCTCACAGGTTTC 58.760 43.478 13.38 0.00 0.00 2.78
1673 2223 1.082756 CTGAAACACGACGGCAAGC 60.083 57.895 0.00 0.00 0.00 4.01
1736 2286 7.688343 ACCCAAATTTTACCATGATTGATTGT 58.312 30.769 0.00 0.00 0.00 2.71
1737 2287 8.564509 AACCCAAATTTTACCATGATTGATTG 57.435 30.769 0.00 0.00 0.00 2.67
1738 2288 9.889128 CTAACCCAAATTTTACCATGATTGATT 57.111 29.630 0.00 0.00 0.00 2.57
1739 2289 9.045745 ACTAACCCAAATTTTACCATGATTGAT 57.954 29.630 0.00 0.00 0.00 2.57
1740 2290 8.310382 CACTAACCCAAATTTTACCATGATTGA 58.690 33.333 0.00 0.00 0.00 2.57
1749 2299 8.106247 TCACATCTCACTAACCCAAATTTTAC 57.894 34.615 0.00 0.00 0.00 2.01
1754 2304 4.289672 ACCTCACATCTCACTAACCCAAAT 59.710 41.667 0.00 0.00 0.00 2.32
1761 2311 3.260884 GGGTTCACCTCACATCTCACTAA 59.739 47.826 0.00 0.00 35.85 2.24
1845 2426 2.205022 TCTTCACTTGGATTGCTGGG 57.795 50.000 0.00 0.00 0.00 4.45
2010 2591 5.661312 TGTGCTAAGAAGTACCCACATAGAT 59.339 40.000 0.00 0.00 37.52 1.98
2028 2609 4.910195 ACAGAGGTTTGATGAATGTGCTA 58.090 39.130 0.00 0.00 0.00 3.49
2030 2611 3.755378 AGACAGAGGTTTGATGAATGTGC 59.245 43.478 0.00 0.00 0.00 4.57
2032 2613 5.233083 TCAGACAGAGGTTTGATGAATGT 57.767 39.130 0.00 0.00 33.61 2.71
2119 2700 2.171448 AGGGTGGCAAGCTATCTAACAG 59.829 50.000 0.00 0.00 0.00 3.16
2168 2750 8.013378 GGCATACGGTTTGTACAATATCAATAC 58.987 37.037 9.56 2.44 35.44 1.89
2269 2852 2.107950 TAAATTGGTGCGCTAGCTGT 57.892 45.000 13.93 0.00 45.42 4.40
2279 2862 7.042797 AGAAATCCGGATCATTAAATTGGTG 57.957 36.000 19.43 0.00 0.00 4.17
2299 2882 4.440880 CACCATTGTGCTCCAAAAAGAAA 58.559 39.130 0.00 0.00 36.44 2.52
2703 3290 4.181051 GCTGGAGGCACCTTTTGT 57.819 55.556 1.84 0.00 41.35 2.83
2841 3428 5.070981 AGGCAATTAGCTCACTATGAAGCTA 59.929 40.000 0.00 0.14 44.79 3.32
2906 3493 8.832735 TGGGAGGTAAAACACTTCTTAGATAAT 58.167 33.333 0.00 0.00 33.81 1.28
3095 3765 2.554893 TGGAAACTGTCGGTTAAATGCC 59.445 45.455 0.00 0.00 37.12 4.40
3106 3776 6.376978 CAGATGTTGATTCTTGGAAACTGTC 58.623 40.000 0.00 0.00 0.00 3.51
3107 3777 5.278660 GCAGATGTTGATTCTTGGAAACTGT 60.279 40.000 0.00 0.00 0.00 3.55
3202 3872 4.202760 ACTCCCCACTTGTACTAGTAACCT 60.203 45.833 9.68 0.00 0.00 3.50
3341 4011 6.272324 TGATTGTCCTATCCTATACCCAAAGG 59.728 42.308 0.00 0.00 40.04 3.11
3342 4012 7.316393 TGATTGTCCTATCCTATACCCAAAG 57.684 40.000 0.00 0.00 0.00 2.77
3492 4169 8.998814 TCAAATATATGAAAGTACTCTGGGGAA 58.001 33.333 0.00 0.00 0.00 3.97
3493 4170 8.561536 TCAAATATATGAAAGTACTCTGGGGA 57.438 34.615 0.00 0.00 0.00 4.81
3546 4225 9.919416 TCCAAAATATATGAGAAACCAGAATGA 57.081 29.630 0.00 0.00 39.69 2.57
3587 4269 5.743398 ACATGACAAACAAATGTGAGAAACG 59.257 36.000 0.00 0.00 33.37 3.60
3605 4291 2.275318 GCCTAGCTGTTCAGACATGAC 58.725 52.381 0.00 0.00 34.35 3.06
3629 4315 5.305585 ACAAAACTACTGATACAGTGGGTG 58.694 41.667 16.79 13.64 41.89 4.61
3678 4364 0.625683 ATCTCCAGGGCCCAACTGAT 60.626 55.000 27.56 18.52 38.20 2.90
3839 4528 0.465705 TCCGGATCCAATCACAGAGC 59.534 55.000 13.41 0.00 0.00 4.09
3848 4537 6.384886 ACCTAGTTATTTAGTTCCGGATCCAA 59.615 38.462 13.41 0.00 0.00 3.53
3856 4545 4.124970 CGGCCACCTAGTTATTTAGTTCC 58.875 47.826 2.24 0.00 0.00 3.62
3866 4555 1.196104 TTACTGCCGGCCACCTAGTT 61.196 55.000 26.77 7.44 0.00 2.24
3876 4565 0.034059 CTATCCCTGCTTACTGCCGG 59.966 60.000 0.00 0.00 44.37 6.13
3877 4566 0.034059 CCTATCCCTGCTTACTGCCG 59.966 60.000 0.00 0.00 42.00 5.69
3886 4575 5.509670 GCAAAAATATGTTCCCTATCCCTGC 60.510 44.000 0.00 0.00 0.00 4.85
3895 4584 3.893326 AGGCTGCAAAAATATGTTCCC 57.107 42.857 0.50 0.00 0.00 3.97
3900 4589 7.431249 ACATGAGATAAGGCTGCAAAAATATG 58.569 34.615 0.00 0.00 0.00 1.78
3942 4631 0.392729 CTGCCAGGCTGAAGAAGAGG 60.393 60.000 17.94 0.00 0.00 3.69
3987 4677 2.169352 AGGTTCAACAGATCCGATCCTG 59.831 50.000 4.67 5.70 36.53 3.86


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

AutoCloner maintained by Alex Coulton.