Multiple sequence alignment - TraesCS3B01G570000

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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 TraesCS3B01G570000 chr3B 100.000 3410 0 0 1 3410 801419370 801415961 0.000000e+00 6298.0
1 TraesCS3B01G570000 chr3B 88.880 2572 165 49 910 3407 801101611 801104135 0.000000e+00 3053.0
2 TraesCS3B01G570000 chr3B 88.608 237 16 5 289 515 661774329 661774564 9.320000e-71 278.0
3 TraesCS3B01G570000 chr3B 88.362 232 16 5 294 515 661741299 661741529 5.610000e-68 268.0
4 TraesCS3B01G570000 chr3B 88.596 228 8 7 64 290 661773854 661774064 9.390000e-66 261.0
5 TraesCS3B01G570000 chr3B 88.158 228 9 7 64 290 661740819 661741029 4.370000e-64 255.0
6 TraesCS3B01G570000 chr3B 86.283 226 16 6 648 872 801101401 801101612 7.360000e-57 231.0
7 TraesCS3B01G570000 chr3B 97.826 46 1 0 1 46 661770019 661770064 2.820000e-11 80.5
8 TraesCS3B01G570000 chr3B 97.778 45 1 0 1 45 661737747 661737791 1.010000e-10 78.7
9 TraesCS3B01G570000 chr3B 97.778 45 1 0 1 45 661770438 661770482 1.010000e-10 78.7
10 TraesCS3B01G570000 chrUn 91.553 2131 107 22 1341 3410 162689607 162691725 0.000000e+00 2870.0
11 TraesCS3B01G570000 chrUn 97.394 614 14 2 648 1261 162688985 162689596 0.000000e+00 1044.0
12 TraesCS3B01G570000 chrUn 94.521 73 4 0 1744 1816 351052125 351052053 2.780000e-21 113.0
13 TraesCS3B01G570000 chrUn 94.521 73 4 0 1744 1816 351054492 351054564 2.780000e-21 113.0
14 TraesCS3B01G570000 chr3D 95.592 1656 62 4 648 2297 596635289 596636939 0.000000e+00 2643.0
15 TraesCS3B01G570000 chr3D 93.836 795 29 5 2307 3084 596638225 596639016 0.000000e+00 1179.0
16 TraesCS3B01G570000 chr3D 90.171 702 56 7 1026 1721 596342297 596342991 0.000000e+00 902.0
17 TraesCS3B01G570000 chr3D 90.464 388 26 5 178 555 53818843 53819229 5.080000e-138 501.0
18 TraesCS3B01G570000 chr3D 91.346 104 8 1 1713 1816 596404021 596404123 1.280000e-29 141.0
19 TraesCS3B01G570000 chr3D 92.941 85 4 2 542 624 278939484 278939400 4.620000e-24 122.0
20 TraesCS3B01G570000 chr3D 86.792 106 8 4 501 602 296032569 296032672 2.780000e-21 113.0
21 TraesCS3B01G570000 chr3D 89.796 49 5 0 2552 2600 331672489 331672441 2.840000e-06 63.9
22 TraesCS3B01G570000 chr2A 77.895 1425 252 36 995 2371 605210733 605209324 0.000000e+00 828.0
23 TraesCS3B01G570000 chr6D 90.280 535 34 9 64 591 414499617 414500140 0.000000e+00 684.0
24 TraesCS3B01G570000 chr6D 92.500 40 3 0 2548 2587 311132025 311132064 1.320000e-04 58.4
25 TraesCS3B01G570000 chr6D 100.000 29 0 0 2556 2584 128098151 128098123 2.000000e-03 54.7
26 TraesCS3B01G570000 chr6A 86.347 542 37 16 64 602 72677238 72676731 1.070000e-154 556.0
27 TraesCS3B01G570000 chr6A 87.912 91 9 2 532 620 415101527 415101437 4.650000e-19 106.0
28 TraesCS3B01G570000 chr2D 84.615 546 46 18 79 615 213312039 213311523 3.040000e-140 508.0
29 TraesCS3B01G570000 chr4D 94.891 274 14 0 145 418 61156503 61156776 2.430000e-116 429.0
30 TraesCS3B01G570000 chr4D 88.889 153 13 3 454 602 61156779 61156931 5.810000e-43 185.0
31 TraesCS3B01G570000 chr7D 91.160 181 16 0 129 309 55217945 55218125 2.630000e-61 246.0
32 TraesCS3B01G570000 chr7B 93.548 93 4 2 127 218 567730707 567730616 1.650000e-28 137.0
33 TraesCS3B01G570000 chr3A 89.796 98 10 0 523 620 44820295 44820198 3.570000e-25 126.0
34 TraesCS3B01G570000 chr2B 90.217 92 7 2 128 218 409209060 409208970 5.980000e-23 119.0
35 TraesCS3B01G570000 chr5B 92.683 82 4 2 539 620 6913117 6913196 2.150000e-22 117.0
36 TraesCS3B01G570000 chr1D 81.746 126 13 6 503 618 28027741 28027616 2.800000e-16 97.1
37 TraesCS3B01G570000 chr1A 97.297 37 1 0 2551 2587 96040610 96040574 2.840000e-06 63.9
38 TraesCS3B01G570000 chr1A 97.297 37 1 0 2551 2587 96040768 96040732 2.840000e-06 63.9
39 TraesCS3B01G570000 chr7A 97.143 35 1 0 2546 2580 85199897 85199863 3.670000e-05 60.2
40 TraesCS3B01G570000 chr4A 97.059 34 1 0 2552 2585 545997110 545997077 1.320000e-04 58.4


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 TraesCS3B01G570000 chr3B 801415961 801419370 3409 True 6298.000000 6298 100.000000 1 3410 1 chr3B.!!$R1 3409
1 TraesCS3B01G570000 chr3B 801101401 801104135 2734 False 1642.000000 3053 87.581500 648 3407 2 chr3B.!!$F3 2759
2 TraesCS3B01G570000 chr3B 661737747 661741529 3782 False 200.566667 268 91.432667 1 515 3 chr3B.!!$F1 514
3 TraesCS3B01G570000 chrUn 162688985 162691725 2740 False 1957.000000 2870 94.473500 648 3410 2 chrUn.!!$F2 2762
4 TraesCS3B01G570000 chr3D 596635289 596639016 3727 False 1911.000000 2643 94.714000 648 3084 2 chr3D.!!$F5 2436
5 TraesCS3B01G570000 chr3D 596342297 596342991 694 False 902.000000 902 90.171000 1026 1721 1 chr3D.!!$F3 695
6 TraesCS3B01G570000 chr2A 605209324 605210733 1409 True 828.000000 828 77.895000 995 2371 1 chr2A.!!$R1 1376
7 TraesCS3B01G570000 chr6D 414499617 414500140 523 False 684.000000 684 90.280000 64 591 1 chr6D.!!$F2 527
8 TraesCS3B01G570000 chr6A 72676731 72677238 507 True 556.000000 556 86.347000 64 602 1 chr6A.!!$R1 538
9 TraesCS3B01G570000 chr2D 213311523 213312039 516 True 508.000000 508 84.615000 79 615 1 chr2D.!!$R1 536

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
338 3618 0.176680 CATGCTAGCCGAGTTGGTCT 59.823 55.0 13.29 0.0 41.21 3.85 F
391 3671 0.322816 TTGATCCCCACAGCAAGCTC 60.323 55.0 0.00 0.0 0.00 4.09 F
499 3789 0.454600 TCAGCGACGTACCATCCTTC 59.545 55.0 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 4853 1.406065 CCGGAGGCCATCAGACTCAT 61.406 60.000 5.01 0.0 46.14 2.90 R
2125 5464 1.955778 CTCCACCAACACAATTCTGCA 59.044 47.619 0.00 0.0 0.00 4.41 R
2465 7080 0.462581 TGCCACATCCGAGCATCTTC 60.463 55.000 0.00 0.0 0.00 2.87 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
55 3020 5.348724 GCTTTTCATCTAGAACGTGTCATCA 59.651 40.000 0.00 0.00 35.56 3.07
90 3100 1.206371 ACAGCATTACGGTAGACCACC 59.794 52.381 0.00 0.00 44.75 4.61
116 3126 4.395959 ACTCGTTTGAACTTGTCAGGTA 57.604 40.909 0.00 0.00 37.61 3.08
117 3127 4.117685 ACTCGTTTGAACTTGTCAGGTAC 58.882 43.478 0.00 0.00 37.61 3.34
118 3128 4.142004 ACTCGTTTGAACTTGTCAGGTACT 60.142 41.667 0.00 0.00 37.61 2.73
119 3129 4.365723 TCGTTTGAACTTGTCAGGTACTC 58.634 43.478 0.00 0.00 37.61 2.59
120 3130 3.493503 CGTTTGAACTTGTCAGGTACTCC 59.506 47.826 0.00 0.00 37.61 3.85
121 3131 3.380479 TTGAACTTGTCAGGTACTCCG 57.620 47.619 0.00 0.00 37.61 4.63
205 3219 5.551233 TCTGTCTGTCTGTTTATTCCCAAG 58.449 41.667 0.00 0.00 0.00 3.61
238 3252 8.522830 GGTTGATATTCCAGACAAATTCAGAAA 58.477 33.333 0.00 0.00 0.00 2.52
292 3572 2.093658 GCGAGGTGGGACTATTCAAAGA 60.094 50.000 0.00 0.00 0.00 2.52
338 3618 0.176680 CATGCTAGCCGAGTTGGTCT 59.823 55.000 13.29 0.00 41.21 3.85
346 3626 0.671781 CCGAGTTGGTCTCTGCCTTG 60.672 60.000 0.00 0.00 40.75 3.61
363 3643 2.110757 TTGGCACATGGCTCGTGAGA 62.111 55.000 10.45 0.00 44.01 3.27
390 3670 0.323178 CTTGATCCCCACAGCAAGCT 60.323 55.000 0.00 0.00 32.41 3.74
391 3671 0.322816 TTGATCCCCACAGCAAGCTC 60.323 55.000 0.00 0.00 0.00 4.09
422 3702 2.290960 ACTGTTGGCCCATAAGAGAACC 60.291 50.000 0.00 0.00 0.00 3.62
423 3703 1.339631 TGTTGGCCCATAAGAGAACCG 60.340 52.381 0.00 0.00 0.00 4.44
442 3726 3.144506 CCGTCTAGCCCGTATAAGAGAA 58.855 50.000 1.80 0.00 0.00 2.87
445 3731 5.278858 CCGTCTAGCCCGTATAAGAGAAAAT 60.279 44.000 1.80 0.00 0.00 1.82
499 3789 0.454600 TCAGCGACGTACCATCCTTC 59.545 55.000 0.00 0.00 0.00 3.46
504 3794 3.131577 AGCGACGTACCATCCTTCATTAA 59.868 43.478 0.00 0.00 0.00 1.40
516 3806 4.291792 TCCTTCATTAATACCACCTCGGA 58.708 43.478 0.00 0.00 38.63 4.55
517 3807 4.905456 TCCTTCATTAATACCACCTCGGAT 59.095 41.667 0.00 0.00 38.63 4.18
524 3816 9.938280 TCATTAATACCACCTCGGATATTAAAG 57.062 33.333 11.81 9.52 34.70 1.85
578 3870 4.886579 ACGAAATTACGGTGGTAAGAAGT 58.113 39.130 0.00 0.00 41.64 3.01
687 3979 5.499139 TTTGCTAGTCAAAGTTGAACCAG 57.501 39.130 7.86 0.00 39.58 4.00
912 4204 1.153628 GTTACGGCGCCTGTCTCAT 60.154 57.895 26.68 4.32 0.00 2.90
924 4216 1.153549 GTCTCATGTCTGGGTCGGC 60.154 63.158 0.00 0.00 0.00 5.54
1149 4461 2.884087 CTATGCCCGACGACGTGCTT 62.884 60.000 15.51 11.64 42.77 3.91
1320 4632 1.276705 GGTCTCTTCCACCAGGAGAAC 59.723 57.143 0.00 0.00 46.74 3.01
1329 4641 2.125912 CAGGAGAACGACTGGCCG 60.126 66.667 0.00 0.00 0.00 6.13
1330 4642 4.070552 AGGAGAACGACTGGCCGC 62.071 66.667 0.00 0.00 0.00 6.53
1351 4666 2.813908 CTACGCGCACAAGGGACC 60.814 66.667 5.73 0.00 0.00 4.46
1532 4853 4.776322 CCGGCGCAACCAGGATCA 62.776 66.667 10.83 0.00 39.03 2.92
1535 4856 1.451927 GGCGCAACCAGGATCATGA 60.452 57.895 10.83 0.00 38.86 3.07
1536 4857 1.442526 GGCGCAACCAGGATCATGAG 61.443 60.000 10.83 1.55 38.86 2.90
1602 4923 1.115326 AGATCGATGTCATCCCGCCA 61.115 55.000 0.54 0.00 0.00 5.69
1961 5288 3.414700 GCCTTGCGACACCTCACG 61.415 66.667 0.00 0.00 0.00 4.35
1995 5322 1.300465 CCGACTCATGGGCATCTCG 60.300 63.158 0.00 0.00 0.00 4.04
2026 5353 7.656137 ACAACCGGCTCTACTTAATGTATTATG 59.344 37.037 0.00 0.00 0.00 1.90
2125 5464 6.680378 GCAAACCGGCAAGATATGTAGAAAAT 60.680 38.462 0.00 0.00 0.00 1.82
2129 5468 5.446709 CGGCAAGATATGTAGAAAATGCAG 58.553 41.667 0.00 0.00 34.37 4.41
2186 5525 0.525668 GTGGTGACTCGCTATGTCCG 60.526 60.000 0.00 0.00 33.83 4.79
2190 5529 1.589196 GACTCGCTATGTCCGCACC 60.589 63.158 0.00 0.00 0.00 5.01
2465 7080 0.108804 AGTACGAGTGCAACCGATGG 60.109 55.000 14.74 0.00 37.80 3.51
2865 7488 5.944007 GTCTTACATTTTCTAGCCCTTGGAA 59.056 40.000 0.00 0.00 0.00 3.53
2866 7489 6.094186 GTCTTACATTTTCTAGCCCTTGGAAG 59.906 42.308 0.00 0.00 0.00 3.46
2878 7501 2.076863 CCTTGGAAGCTAGAACAACGG 58.923 52.381 0.00 0.00 0.00 4.44
2881 7504 4.504858 CTTGGAAGCTAGAACAACGGTAT 58.495 43.478 0.00 0.00 0.00 2.73
2882 7505 5.394883 CCTTGGAAGCTAGAACAACGGTATA 60.395 44.000 0.00 0.00 0.00 1.47
2883 7506 5.002464 TGGAAGCTAGAACAACGGTATAC 57.998 43.478 0.00 0.00 0.00 1.47
2931 7570 1.944177 TCTTCCCCAGAGTCCAGAAG 58.056 55.000 0.00 0.00 36.19 2.85
2939 7578 3.107601 CCAGAGTCCAGAAGGGTATCAA 58.892 50.000 0.00 0.00 38.11 2.57
2948 7587 5.302059 TCCAGAAGGGTATCAATTAGTCTCG 59.698 44.000 0.00 0.00 38.11 4.04
2957 7596 3.775202 TCAATTAGTCTCGCAAGCTCTC 58.225 45.455 0.00 0.00 37.18 3.20
2967 7606 1.406898 CGCAAGCTCTCTCTCCATGTA 59.593 52.381 0.00 0.00 0.00 2.29
3007 7646 5.131642 TGCCATCTCTAGACTTCCATCAAAT 59.868 40.000 0.00 0.00 0.00 2.32
3051 7690 2.608752 GGCGTGTTCTTTTCGGTCTCTA 60.609 50.000 0.00 0.00 0.00 2.43
3056 7695 5.061064 CGTGTTCTTTTCGGTCTCTAATCTG 59.939 44.000 0.00 0.00 0.00 2.90
3063 7702 3.698289 TCGGTCTCTAATCTGTTCCACT 58.302 45.455 0.00 0.00 0.00 4.00
3069 7708 6.039493 GGTCTCTAATCTGTTCCACTATCGAA 59.961 42.308 0.00 0.00 0.00 3.71
3099 7738 4.819761 ACGTGCATCTCGCCGCAT 62.820 61.111 0.00 0.00 40.89 4.73
3101 7740 2.891936 GTGCATCTCGCCGCATGA 60.892 61.111 0.00 0.00 40.89 3.07
3102 7741 2.586914 TGCATCTCGCCGCATGAG 60.587 61.111 0.00 0.00 41.33 2.90
3103 7742 4.010414 GCATCTCGCCGCATGAGC 62.010 66.667 0.00 0.00 33.41 4.26
3104 7743 2.279985 CATCTCGCCGCATGAGCT 60.280 61.111 0.00 0.00 39.10 4.09
3105 7744 1.886313 CATCTCGCCGCATGAGCTT 60.886 57.895 0.00 0.00 39.10 3.74
3106 7745 0.598419 CATCTCGCCGCATGAGCTTA 60.598 55.000 0.00 0.00 39.10 3.09
3107 7746 0.598680 ATCTCGCCGCATGAGCTTAC 60.599 55.000 0.00 0.00 39.10 2.34
3108 7747 2.580470 CTCGCCGCATGAGCTTACG 61.580 63.158 0.00 0.00 39.10 3.18
3109 7748 2.885644 CGCCGCATGAGCTTACGT 60.886 61.111 0.00 0.00 39.10 3.57
3113 7752 1.759994 CCGCATGAGCTTACGTCTAG 58.240 55.000 0.00 0.00 39.10 2.43
3114 7753 1.124462 CGCATGAGCTTACGTCTAGC 58.876 55.000 13.16 13.16 39.10 3.42
3119 7758 3.171949 AGCTTACGTCTAGCTCCGT 57.828 52.632 16.81 10.31 45.52 4.69
3133 7779 1.269166 CTCCGTGCAGTATCGTGTTC 58.731 55.000 0.00 0.00 0.00 3.18
3146 7792 2.409975 TCGTGTTCGGAAGGAATCAAC 58.590 47.619 0.00 0.00 36.92 3.18
3160 7810 0.541863 ATCAACCTAGCTTCCACCCG 59.458 55.000 0.00 0.00 0.00 5.28
3166 7816 1.536907 TAGCTTCCACCCGGACCAA 60.537 57.895 0.73 0.00 42.67 3.67
3188 7838 2.032681 GCCACCGAGCAACTTCCT 59.967 61.111 0.00 0.00 0.00 3.36
3190 7840 1.172812 GCCACCGAGCAACTTCCTTT 61.173 55.000 0.00 0.00 0.00 3.11
3192 7842 0.593128 CACCGAGCAACTTCCTTTGG 59.407 55.000 0.00 0.00 0.00 3.28
3193 7843 0.472471 ACCGAGCAACTTCCTTTGGA 59.528 50.000 0.00 0.00 0.00 3.53
3194 7844 1.133915 ACCGAGCAACTTCCTTTGGAA 60.134 47.619 0.00 0.00 39.66 3.53
3195 7845 1.953686 CCGAGCAACTTCCTTTGGAAA 59.046 47.619 0.53 0.00 41.54 3.13
3197 7847 2.618709 CGAGCAACTTCCTTTGGAAACT 59.381 45.455 0.53 0.00 41.54 2.66
3198 7848 3.548818 CGAGCAACTTCCTTTGGAAACTG 60.549 47.826 0.53 2.61 41.54 3.16
3227 7903 3.060807 CGTCGAGTTTCATGTTTTCGTCA 60.061 43.478 0.00 0.00 33.35 4.35
3237 7913 7.678194 TTCATGTTTTCGTCAAGTTCAAATC 57.322 32.000 0.00 0.00 0.00 2.17
3241 7917 6.790282 TGTTTTCGTCAAGTTCAAATCATCA 58.210 32.000 0.00 0.00 0.00 3.07
3276 7952 1.967319 AATGTGTCTGCCGAGTTTGT 58.033 45.000 0.00 0.00 0.00 2.83
3316 7992 2.095212 GTGACACGATACTCTGCAGACA 60.095 50.000 13.74 3.77 0.00 3.41
3319 7995 2.755103 ACACGATACTCTGCAGACATCA 59.245 45.455 23.67 8.62 0.00 3.07
3335 8011 1.737793 CATCACCGTTTTCCTAGTGCC 59.262 52.381 0.00 0.00 0.00 5.01
3344 8020 3.730215 TTTCCTAGTGCCAGGCATAAA 57.270 42.857 19.75 10.60 41.91 1.40
3346 8022 2.477245 TCCTAGTGCCAGGCATAAAGA 58.523 47.619 19.75 10.20 41.91 2.52
3351 8027 4.301072 AGTGCCAGGCATAAAGAACTTA 57.699 40.909 19.75 0.00 41.91 2.24
3373 8049 1.194772 CGGAAGAAAGAAACTCGGCAC 59.805 52.381 0.00 0.00 0.00 5.01
3386 8062 2.935955 GGCACGGTCACACTTTCG 59.064 61.111 0.00 0.00 0.00 3.46
3398 8074 0.040067 CACTTTCGCCAAGTTCTGCC 60.040 55.000 0.00 0.00 43.89 4.85
3400 8076 0.883833 CTTTCGCCAAGTTCTGCCAT 59.116 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.737427 TGAAAAGCATCACGTTTTATCTAAAAA 57.263 25.926 0.00 0.00 36.97 1.94
45 46 3.386078 AGCTATTGATCCTGATGACACGT 59.614 43.478 0.00 0.00 0.00 4.49
90 3100 5.276868 CCTGACAAGTTCAAACGAGTAGTTG 60.277 44.000 0.00 0.00 43.37 3.16
95 3105 3.261981 ACCTGACAAGTTCAAACGAGT 57.738 42.857 0.00 0.00 32.21 4.18
117 3127 1.065701 ACGAACTAGCATGCTACGGAG 59.934 52.381 28.84 21.91 0.00 4.63
118 3128 1.065102 GACGAACTAGCATGCTACGGA 59.935 52.381 28.84 13.03 0.00 4.69
119 3129 1.478137 GACGAACTAGCATGCTACGG 58.522 55.000 28.84 21.17 0.00 4.02
120 3130 1.065701 AGGACGAACTAGCATGCTACG 59.934 52.381 25.84 25.84 0.00 3.51
121 3131 2.860735 CAAGGACGAACTAGCATGCTAC 59.139 50.000 23.52 13.00 0.00 3.58
205 3219 1.952296 CTGGAATATCAACCAGCTGCC 59.048 52.381 8.66 0.79 45.30 4.85
238 3252 8.153550 AGACTGATTCTCACTTGTTCAAATACT 58.846 33.333 0.00 0.00 0.00 2.12
292 3572 7.039363 TCGGTTTGACAATGGAAAGGATATTTT 60.039 33.333 0.00 0.00 0.00 1.82
320 3600 0.461961 GAGACCAACTCGGCTAGCAT 59.538 55.000 18.24 0.00 39.03 3.79
346 3626 0.745845 AATCTCACGAGCCATGTGCC 60.746 55.000 0.00 0.00 42.71 5.01
390 3670 3.153919 GGGCCAACAGTCAACAAATAGA 58.846 45.455 4.39 0.00 0.00 1.98
391 3671 2.890311 TGGGCCAACAGTCAACAAATAG 59.110 45.455 2.13 0.00 0.00 1.73
422 3702 4.825546 TTTCTCTTATACGGGCTAGACG 57.174 45.455 0.00 0.00 37.36 4.18
423 3703 6.641723 GTGATTTTCTCTTATACGGGCTAGAC 59.358 42.308 0.00 0.00 0.00 2.59
442 3726 0.591170 CGCCCAGACAAACGTGATTT 59.409 50.000 0.00 0.00 0.00 2.17
445 3731 1.153329 AACGCCCAGACAAACGTGA 60.153 52.632 0.00 0.00 39.00 4.35
499 3789 9.938280 TCTTTAATATCCGAGGTGGTATTAATG 57.062 33.333 0.00 13.75 36.79 1.90
504 3794 9.862149 AATTTTCTTTAATATCCGAGGTGGTAT 57.138 29.630 0.00 0.00 39.52 2.73
517 3807 9.632807 CGTTCAACCCATCAATTTTCTTTAATA 57.367 29.630 0.00 0.00 0.00 0.98
524 3816 4.234574 GTCCGTTCAACCCATCAATTTTC 58.765 43.478 0.00 0.00 0.00 2.29
528 3820 1.002659 TCGTCCGTTCAACCCATCAAT 59.997 47.619 0.00 0.00 0.00 2.57
578 3870 8.014859 ACCTACCTACTAATAAAAGGGCTATCA 58.985 37.037 0.00 0.00 34.52 2.15
901 4193 1.153489 CCCAGACATGAGACAGGCG 60.153 63.158 0.00 0.00 0.00 5.52
912 4204 3.770040 CCGATGCCGACCCAGACA 61.770 66.667 0.00 0.00 38.22 3.41
924 4216 2.732412 AGATAATCGCCAGTCCGATG 57.268 50.000 0.00 0.00 46.29 3.84
985 4282 5.895636 TGTTCCATGGTATCAATTGTGTC 57.104 39.130 12.58 0.00 0.00 3.67
1041 4338 6.006275 TCTTTCTTGATTGGATAGGAAGGG 57.994 41.667 0.00 0.00 0.00 3.95
1046 4343 6.882656 TGACTCTCTTTCTTGATTGGATAGG 58.117 40.000 0.00 0.00 0.00 2.57
1149 4461 2.264480 CGGGTGAAGATGTCGGCA 59.736 61.111 0.00 0.00 0.00 5.69
1289 4601 1.578206 GAAGAGACCAACGGCAAGGC 61.578 60.000 0.00 0.00 0.00 4.35
1320 4632 4.814294 GTAGTGGGCGGCCAGTCG 62.814 72.222 38.66 0.00 0.00 4.18
1330 4642 3.118454 CCTTGTGCGCGTAGTGGG 61.118 66.667 8.43 1.06 39.19 4.61
1331 4643 3.118454 CCCTTGTGCGCGTAGTGG 61.118 66.667 8.43 5.50 39.19 4.00
1361 4676 2.746803 GCGATAAAACACGGCCGCT 61.747 57.895 28.58 10.12 39.57 5.52
1440 4755 2.336809 CGGTCGCCTCCATCTAGC 59.663 66.667 0.00 0.00 0.00 3.42
1532 4853 1.406065 CCGGAGGCCATCAGACTCAT 61.406 60.000 5.01 0.00 46.14 2.90
1602 4923 5.013183 AGTGTTCTTGCCTACTAAGACCAAT 59.987 40.000 0.00 0.00 34.14 3.16
1961 5288 2.725641 GGTTGTTTGGACCCGTGC 59.274 61.111 0.00 0.00 0.00 5.34
1998 5325 2.642139 TTAAGTAGAGCCGGTTGTCG 57.358 50.000 1.90 0.00 38.88 4.35
2012 5339 9.793259 CTCCCATGTAACCATAATACATTAAGT 57.207 33.333 0.00 0.00 40.96 2.24
2026 5353 2.895372 CGGCGCTCCCATGTAACC 60.895 66.667 7.64 0.00 0.00 2.85
2052 5391 6.115448 AGATAGGTTAGCTTCAACACAAGT 57.885 37.500 0.00 0.00 0.00 3.16
2125 5464 1.955778 CTCCACCAACACAATTCTGCA 59.044 47.619 0.00 0.00 0.00 4.41
2129 5468 3.451141 TTTGCTCCACCAACACAATTC 57.549 42.857 0.00 0.00 0.00 2.17
2190 5529 2.802774 GCCAAACCACCACAACTTGATG 60.803 50.000 0.00 0.00 0.00 3.07
2437 7052 5.589192 GGTTGCACTCGTACTCTGTATAAT 58.411 41.667 0.00 0.00 0.00 1.28
2465 7080 0.462581 TGCCACATCCGAGCATCTTC 60.463 55.000 0.00 0.00 0.00 2.87
2771 7388 8.965172 CGATAGTACTTAACATATTCGTTGCTT 58.035 33.333 0.00 0.00 0.00 3.91
2838 7461 6.183360 CCAAGGGCTAGAAAATGTAAGACATG 60.183 42.308 0.00 0.00 37.97 3.21
2865 7488 8.401709 GTTACTTAGTATACCGTTGTTCTAGCT 58.598 37.037 0.00 0.00 0.00 3.32
2866 7489 8.184192 TGTTACTTAGTATACCGTTGTTCTAGC 58.816 37.037 0.00 0.00 0.00 3.42
2881 7504 9.991906 AACAAACAAGCTAGATGTTACTTAGTA 57.008 29.630 12.90 0.00 39.98 1.82
2882 7505 8.904099 AACAAACAAGCTAGATGTTACTTAGT 57.096 30.769 12.90 0.00 39.98 2.24
2931 7570 3.495001 GCTTGCGAGACTAATTGATACCC 59.505 47.826 4.70 0.00 0.00 3.69
2939 7578 3.287222 AGAGAGAGCTTGCGAGACTAAT 58.713 45.455 4.70 0.00 0.00 1.73
2948 7587 3.533606 TTACATGGAGAGAGAGCTTGC 57.466 47.619 0.00 0.00 0.00 4.01
2957 7596 1.224075 CAGCGGCATTACATGGAGAG 58.776 55.000 1.45 0.00 0.00 3.20
3007 7646 1.066858 CGGCAAGAGTCTAGAGCCAAA 60.067 52.381 23.20 0.00 45.47 3.28
3051 7690 4.466370 TCTGGTTCGATAGTGGAACAGATT 59.534 41.667 6.95 0.00 44.29 2.40
3056 7695 3.870633 AGTCTGGTTCGATAGTGGAAC 57.129 47.619 0.00 0.00 42.32 3.62
3063 7702 4.919168 CACGTGTAAAAGTCTGGTTCGATA 59.081 41.667 7.58 0.00 0.00 2.92
3069 7708 2.319136 TGCACGTGTAAAAGTCTGGT 57.681 45.000 18.38 0.00 0.00 4.00
3102 7741 0.866483 GCACGGAGCTAGACGTAAGC 60.866 60.000 13.18 13.18 42.04 3.09
3103 7742 0.450583 TGCACGGAGCTAGACGTAAG 59.549 55.000 9.80 0.00 45.94 2.34
3104 7743 0.450583 CTGCACGGAGCTAGACGTAA 59.549 55.000 9.80 2.50 45.94 3.18
3105 7744 0.675837 ACTGCACGGAGCTAGACGTA 60.676 55.000 9.80 0.00 45.94 3.57
3106 7745 0.675837 TACTGCACGGAGCTAGACGT 60.676 55.000 4.93 4.93 45.94 4.34
3107 7746 0.663688 ATACTGCACGGAGCTAGACG 59.336 55.000 0.00 3.70 45.94 4.18
3108 7747 1.334239 CGATACTGCACGGAGCTAGAC 60.334 57.143 0.00 0.00 45.94 2.59
3109 7748 0.945099 CGATACTGCACGGAGCTAGA 59.055 55.000 0.00 0.00 45.94 2.43
3113 7752 0.736325 AACACGATACTGCACGGAGC 60.736 55.000 0.00 0.00 45.96 4.70
3114 7753 1.269166 GAACACGATACTGCACGGAG 58.731 55.000 0.00 0.00 0.00 4.63
3115 7754 0.455464 CGAACACGATACTGCACGGA 60.455 55.000 0.00 0.00 0.00 4.69
3117 7756 0.455464 TCCGAACACGATACTGCACG 60.455 55.000 0.00 0.00 0.00 5.34
3118 7757 1.654105 CTTCCGAACACGATACTGCAC 59.346 52.381 0.00 0.00 0.00 4.57
3119 7758 1.403647 CCTTCCGAACACGATACTGCA 60.404 52.381 0.00 0.00 0.00 4.41
3133 7779 2.990066 AGCTAGGTTGATTCCTTCCG 57.010 50.000 0.00 0.00 38.86 4.30
3166 7816 4.681978 GTTGCTCGGTGGCGGAGT 62.682 66.667 5.78 0.00 34.09 3.85
3174 7824 0.472471 TCCAAAGGAAGTTGCTCGGT 59.528 50.000 11.17 0.00 0.00 4.69
3188 7838 2.550606 CGACGAAATCCCAGTTTCCAAA 59.449 45.455 0.00 0.00 35.23 3.28
3190 7840 1.345089 TCGACGAAATCCCAGTTTCCA 59.655 47.619 0.00 0.00 35.23 3.53
3192 7842 2.685100 ACTCGACGAAATCCCAGTTTC 58.315 47.619 0.00 0.00 35.31 2.78
3193 7843 2.833631 ACTCGACGAAATCCCAGTTT 57.166 45.000 0.00 0.00 0.00 2.66
3194 7844 2.833631 AACTCGACGAAATCCCAGTT 57.166 45.000 0.00 0.00 0.00 3.16
3195 7845 2.036733 TGAAACTCGACGAAATCCCAGT 59.963 45.455 0.00 0.00 0.00 4.00
3197 7847 2.823924 TGAAACTCGACGAAATCCCA 57.176 45.000 0.00 0.00 0.00 4.37
3198 7848 3.000727 ACATGAAACTCGACGAAATCCC 58.999 45.455 0.00 0.00 0.00 3.85
3227 7903 6.145535 GTCGAGCTTTTGATGATTTGAACTT 58.854 36.000 0.00 0.00 0.00 2.66
3237 7913 6.249893 CACATTACAATGTCGAGCTTTTGATG 59.750 38.462 4.61 0.00 46.10 3.07
3241 7917 5.470098 AGACACATTACAATGTCGAGCTTTT 59.530 36.000 4.61 0.00 46.10 2.27
3276 7952 5.244402 TGTCACTCCCGAGTCTAATTAACAA 59.756 40.000 0.00 0.00 40.20 2.83
3309 7985 1.202758 AGGAAAACGGTGATGTCTGCA 60.203 47.619 0.00 0.00 0.00 4.41
3316 7992 1.349688 TGGCACTAGGAAAACGGTGAT 59.650 47.619 0.00 0.00 32.30 3.06
3319 7995 0.036306 CCTGGCACTAGGAAAACGGT 59.964 55.000 0.00 0.00 40.42 4.83
3335 8011 5.642063 TCTTCCGTTAAGTTCTTTATGCCTG 59.358 40.000 0.00 0.00 36.51 4.85
3344 8020 6.200475 CGAGTTTCTTTCTTCCGTTAAGTTCT 59.800 38.462 0.00 0.00 36.51 3.01
3346 8022 5.235831 CCGAGTTTCTTTCTTCCGTTAAGTT 59.764 40.000 0.00 0.00 36.51 2.66
3351 8027 1.871676 GCCGAGTTTCTTTCTTCCGTT 59.128 47.619 0.00 0.00 0.00 4.44
3373 8049 1.569493 CTTGGCGAAAGTGTGACCG 59.431 57.895 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.