Multiple sequence alignment - TraesCS5B01G406600

Loading Multiple Alignment...

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 TraesCS5B01G406600 chr5B 100.000 5049 0 0 1 5049 582831644 582836692 0.000000e+00 9324.0
1 TraesCS5B01G406600 chr5B 78.987 790 114 35 40 811 30864316 30863561 4.540000e-135 492.0
2 TraesCS5B01G406600 chr5B 79.360 344 43 21 22 344 61151486 61151822 3.060000e-52 217.0
3 TraesCS5B01G406600 chr5B 76.696 339 49 20 56 380 61083381 61083059 1.450000e-35 161.0
4 TraesCS5B01G406600 chr5B 88.406 69 6 2 752 819 124280900 124280833 1.170000e-11 82.4
5 TraesCS5B01G406600 chr5A 91.699 3554 174 42 841 4370 594952993 594956449 0.000000e+00 4817.0
6 TraesCS5B01G406600 chr5A 85.231 325 24 8 4629 4944 594956875 594957184 3.800000e-81 313.0
7 TraesCS5B01G406600 chr5A 88.889 171 15 2 4363 4533 594956473 594956639 1.840000e-49 207.0
8 TraesCS5B01G406600 chr5A 84.397 141 14 5 2691 2829 594979445 594979579 1.140000e-26 132.0
9 TraesCS5B01G406600 chr5A 86.916 107 7 2 4944 5049 594957288 594957388 4.130000e-21 113.0
10 TraesCS5B01G406600 chr5A 77.387 199 36 7 2207 2401 594978178 594978371 5.340000e-20 110.0
11 TraesCS5B01G406600 chr5A 90.769 65 4 2 4570 4632 594956791 594956855 9.010000e-13 86.1
12 TraesCS5B01G406600 chr5D 91.285 2031 83 35 3076 5049 475501801 475503794 0.000000e+00 2684.0
13 TraesCS5B01G406600 chr5D 91.188 1725 67 28 841 2562 475499631 475501273 0.000000e+00 2265.0
14 TraesCS5B01G406600 chr5D 92.778 540 35 4 2511 3048 475501267 475501804 0.000000e+00 778.0
15 TraesCS5B01G406600 chr1D 85.031 1757 174 50 2536 4237 409537456 409539178 0.000000e+00 1705.0
16 TraesCS5B01G406600 chr1D 83.333 1002 113 29 1570 2550 409536470 409537438 0.000000e+00 876.0
17 TraesCS5B01G406600 chr1D 89.223 566 46 10 968 1531 409535913 409536465 0.000000e+00 693.0
18 TraesCS5B01G406600 chr1D 82.051 312 34 12 2 297 467360798 467360493 3.900000e-61 246.0
19 TraesCS5B01G406600 chr1D 76.737 331 45 24 13 330 430575107 430574796 6.770000e-34 156.0
20 TraesCS5B01G406600 chr1B 84.624 1756 182 52 2535 4237 551723120 551724840 0.000000e+00 1666.0
21 TraesCS5B01G406600 chr1B 82.312 995 113 31 1570 2547 551722153 551723101 0.000000e+00 804.0
22 TraesCS5B01G406600 chr1B 87.080 565 56 11 968 1531 551721600 551722148 1.540000e-174 623.0
23 TraesCS5B01G406600 chr1A 85.704 1364 132 32 2535 3859 505539253 505540592 0.000000e+00 1380.0
24 TraesCS5B01G406600 chr1A 81.727 996 118 36 1570 2547 505538285 505539234 0.000000e+00 773.0
25 TraesCS5B01G406600 chr1A 88.307 573 54 10 968 1539 505537728 505538288 0.000000e+00 675.0
26 TraesCS5B01G406600 chr1A 80.886 361 45 18 1 344 566596556 566596203 3.880000e-66 263.0
27 TraesCS5B01G406600 chr3B 86.111 828 75 28 16 817 750461428 750460615 0.000000e+00 856.0
28 TraesCS5B01G406600 chr3B 85.195 385 35 14 2 381 750461502 750461135 4.770000e-100 375.0
29 TraesCS5B01G406600 chr3B 75.578 303 48 19 165 450 656598172 656598465 5.310000e-25 126.0
30 TraesCS5B01G406600 chr2B 85.974 770 65 30 16 757 739499828 739500582 0.000000e+00 784.0
31 TraesCS5B01G406600 chr2B 84.974 386 35 15 2 381 739499754 739500122 2.220000e-98 370.0
32 TraesCS5B01G406600 chr7D 81.926 841 110 28 1 817 184832801 184831979 0.000000e+00 673.0
33 TraesCS5B01G406600 chr2D 82.024 751 103 22 82 817 429999898 430000631 1.200000e-170 610.0
34 TraesCS5B01G406600 chr3D 81.210 777 97 37 41 792 576580282 576579530 9.420000e-162 580.0
35 TraesCS5B01G406600 chr3A 81.707 738 93 23 41 755 481429088 481429806 1.220000e-160 577.0
36 TraesCS5B01G406600 chr7B 84.563 583 50 24 16 580 526845175 526845735 4.450000e-150 542.0
37 TraesCS5B01G406600 chr7B 80.082 728 97 30 123 825 498916929 498917633 9.760000e-137 497.0
38 TraesCS5B01G406600 chr7B 87.013 77 6 4 747 821 588247727 588247801 3.240000e-12 84.2
39 TraesCS5B01G406600 chr4B 79.073 798 108 38 42 822 631428420 631427665 1.260000e-135 494.0
40 TraesCS5B01G406600 chr4B 80.147 136 21 6 16 148 386984332 386984464 4.160000e-16 97.1
41 TraesCS5B01G406600 chr6B 78.609 762 109 32 83 818 173651995 173651262 5.960000e-124 455.0


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 TraesCS5B01G406600 chr5B 582831644 582836692 5048 False 9324.000000 9324 100.000000 1 5049 1 chr5B.!!$F2 5048
1 TraesCS5B01G406600 chr5B 30863561 30864316 755 True 492.000000 492 78.987000 40 811 1 chr5B.!!$R1 771
2 TraesCS5B01G406600 chr5A 594952993 594957388 4395 False 1107.220000 4817 88.700800 841 5049 5 chr5A.!!$F1 4208
3 TraesCS5B01G406600 chr5D 475499631 475503794 4163 False 1909.000000 2684 91.750333 841 5049 3 chr5D.!!$F1 4208
4 TraesCS5B01G406600 chr1D 409535913 409539178 3265 False 1091.333333 1705 85.862333 968 4237 3 chr1D.!!$F1 3269
5 TraesCS5B01G406600 chr1B 551721600 551724840 3240 False 1031.000000 1666 84.672000 968 4237 3 chr1B.!!$F1 3269
6 TraesCS5B01G406600 chr1A 505537728 505540592 2864 False 942.666667 1380 85.246000 968 3859 3 chr1A.!!$F1 2891
7 TraesCS5B01G406600 chr3B 750460615 750461502 887 True 615.500000 856 85.653000 2 817 2 chr3B.!!$R1 815
8 TraesCS5B01G406600 chr2B 739499754 739500582 828 False 577.000000 784 85.474000 2 757 2 chr2B.!!$F1 755
9 TraesCS5B01G406600 chr7D 184831979 184832801 822 True 673.000000 673 81.926000 1 817 1 chr7D.!!$R1 816
10 TraesCS5B01G406600 chr2D 429999898 430000631 733 False 610.000000 610 82.024000 82 817 1 chr2D.!!$F1 735
11 TraesCS5B01G406600 chr3D 576579530 576580282 752 True 580.000000 580 81.210000 41 792 1 chr3D.!!$R1 751
12 TraesCS5B01G406600 chr3A 481429088 481429806 718 False 577.000000 577 81.707000 41 755 1 chr3A.!!$F1 714
13 TraesCS5B01G406600 chr7B 526845175 526845735 560 False 542.000000 542 84.563000 16 580 1 chr7B.!!$F2 564
14 TraesCS5B01G406600 chr7B 498916929 498917633 704 False 497.000000 497 80.082000 123 825 1 chr7B.!!$F1 702
15 TraesCS5B01G406600 chr4B 631427665 631428420 755 True 494.000000 494 79.073000 42 822 1 chr4B.!!$R1 780
16 TraesCS5B01G406600 chr6B 173651262 173651995 733 True 455.000000 455 78.609000 83 818 1 chr6B.!!$R1 735

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
899 1209 0.182537 CCATTCCACATTCGCCCCTA 59.817 55.000 0.00 0.00 0.00 3.53 F
911 1221 0.798159 CGCCCCTACGTTTTGTTACC 59.202 55.000 0.00 0.00 0.00 2.85 F
1123 1443 1.000359 CCAAACCCTAGCCCCCAAG 60.000 63.158 0.00 0.00 0.00 3.61 F
2131 2483 1.934525 CTGCACTCTGCTTAGCATGAG 59.065 52.381 22.54 22.54 45.31 2.90 F
2657 3104 2.498644 TCCGGGAAATGCATGTTGTA 57.501 45.000 0.00 0.00 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2751 3200 1.458639 GCTTGCAGCAAGACCAAGGT 61.459 55.000 34.93 0.0 43.42 3.50 R
2886 3338 8.152898 TCTATAGTTGGATTGATCATCAACAGG 58.847 37.037 25.29 16.8 39.45 4.00 R
3072 3532 1.817520 CGCCCATGTACATTGCCGA 60.818 57.895 17.29 0.0 0.00 5.54 R
4009 4509 0.529378 CAATGCAACTCCCTGAAGGC 59.471 55.000 0.00 0.0 34.51 4.35 R
4392 4925 0.321653 GGAGCAATGTATAGCCCCCG 60.322 60.000 0.00 0.0 0.00 5.73 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
211 465 8.710835 TTAATTTCAGTGAACCCTTTTTGAAC 57.289 30.769 4.68 0.00 0.00 3.18
217 471 6.648725 TCAGTGAACCCTTTTTGAACTTTTTG 59.351 34.615 0.00 0.00 0.00 2.44
218 472 5.411361 AGTGAACCCTTTTTGAACTTTTTGC 59.589 36.000 0.00 0.00 0.00 3.68
224 478 6.432472 ACCCTTTTTGAACTTTTTGCAATTCA 59.568 30.769 8.73 8.73 0.00 2.57
692 1001 2.677003 CGCGCGTGGGTTTGAATCT 61.677 57.895 24.19 0.00 0.00 2.40
695 1004 1.086696 CGCGTGGGTTTGAATCTCAT 58.913 50.000 0.00 0.00 0.00 2.90
708 1017 5.984233 TGAATCTCATGTGCCGTAAATAC 57.016 39.130 0.00 0.00 0.00 1.89
712 1022 7.120579 TGAATCTCATGTGCCGTAAATACTTTT 59.879 33.333 0.00 0.00 0.00 2.27
811 1121 2.197577 GCTTAAAGCGCTGAGTAGGAG 58.802 52.381 12.58 3.72 0.00 3.69
818 1128 1.075600 GCTGAGTAGGAGCTCCCCT 60.076 63.158 29.54 24.16 40.29 4.79
826 1136 4.303257 GAGCTCCCCTCCAAAACG 57.697 61.111 0.87 0.00 34.35 3.60
827 1137 1.377333 GAGCTCCCCTCCAAAACGG 60.377 63.158 0.87 0.00 34.35 4.44
828 1138 2.125766 GAGCTCCCCTCCAAAACGGT 62.126 60.000 0.87 0.00 34.35 4.83
829 1139 1.674651 GCTCCCCTCCAAAACGGTC 60.675 63.158 0.00 0.00 35.57 4.79
830 1140 1.002502 CTCCCCTCCAAAACGGTCC 60.003 63.158 0.00 0.00 35.57 4.46
831 1141 2.035155 CCCCTCCAAAACGGTCCC 59.965 66.667 0.00 0.00 35.57 4.46
832 1142 2.836187 CCCCTCCAAAACGGTCCCA 61.836 63.158 0.00 0.00 35.57 4.37
833 1143 1.382629 CCCTCCAAAACGGTCCCAT 59.617 57.895 0.00 0.00 35.57 4.00
834 1144 0.679960 CCCTCCAAAACGGTCCCATC 60.680 60.000 0.00 0.00 35.57 3.51
835 1145 0.328258 CCTCCAAAACGGTCCCATCT 59.672 55.000 0.00 0.00 35.57 2.90
836 1146 1.557832 CCTCCAAAACGGTCCCATCTA 59.442 52.381 0.00 0.00 35.57 1.98
837 1147 2.026636 CCTCCAAAACGGTCCCATCTAA 60.027 50.000 0.00 0.00 35.57 2.10
838 1148 3.560453 CCTCCAAAACGGTCCCATCTAAA 60.560 47.826 0.00 0.00 35.57 1.85
839 1149 4.076394 CTCCAAAACGGTCCCATCTAAAA 58.924 43.478 0.00 0.00 35.57 1.52
874 1184 1.474330 GGATCGGGCCAAATTCAACT 58.526 50.000 4.39 0.00 0.00 3.16
898 1208 1.076777 CCATTCCACATTCGCCCCT 60.077 57.895 0.00 0.00 0.00 4.79
899 1209 0.182537 CCATTCCACATTCGCCCCTA 59.817 55.000 0.00 0.00 0.00 3.53
902 1212 1.546589 TTCCACATTCGCCCCTACGT 61.547 55.000 0.00 0.00 0.00 3.57
906 1216 1.135803 CACATTCGCCCCTACGTTTTG 60.136 52.381 0.00 0.00 0.00 2.44
911 1221 0.798159 CGCCCCTACGTTTTGTTACC 59.202 55.000 0.00 0.00 0.00 2.85
927 1237 2.804527 GTTACCCCGAACACAGAAGTTC 59.195 50.000 0.00 0.00 43.39 3.01
976 1286 4.863925 GTCTCTCCGCAGCGCCTC 62.864 72.222 10.07 0.00 0.00 4.70
1123 1443 1.000359 CCAAACCCTAGCCCCCAAG 60.000 63.158 0.00 0.00 0.00 3.61
1467 1792 2.042930 ATCCCCACCCTGTCCCTC 59.957 66.667 0.00 0.00 0.00 4.30
1468 1793 3.660092 ATCCCCACCCTGTCCCTCC 62.660 68.421 0.00 0.00 0.00 4.30
1518 1844 4.644234 TGTGGCGTTTATTGATTGGATCAT 59.356 37.500 0.00 0.00 39.39 2.45
1531 1857 6.064060 TGATTGGATCATCCCAGTTGTTATC 58.936 40.000 0.00 0.00 37.53 1.75
1620 1947 4.384647 GCTCTGACTGTCCCCATAGAAAAT 60.385 45.833 5.17 0.00 0.00 1.82
1626 1953 2.092646 TGTCCCCATAGAAAATCCCACG 60.093 50.000 0.00 0.00 0.00 4.94
1864 2205 6.716628 GGTATGAGCTATTCATTTCCATTGGA 59.283 38.462 0.00 0.00 44.14 3.53
1869 2210 8.632679 TGAGCTATTCATTTCCATTGGATTTAC 58.367 33.333 6.15 0.00 0.00 2.01
1907 2251 7.707624 TTCATTGCAAGATGAAGAACCTAAT 57.292 32.000 10.69 0.00 40.20 1.73
1923 2267 7.787028 AGAACCTAATAACTCCAGAACATCTC 58.213 38.462 0.00 0.00 0.00 2.75
2108 2459 7.907389 TCCATTGTCTGAACAGTAATAAGTCT 58.093 34.615 1.73 0.00 36.57 3.24
2131 2483 1.934525 CTGCACTCTGCTTAGCATGAG 59.065 52.381 22.54 22.54 45.31 2.90
2521 2927 3.481453 TGTCAACAACATGGAATCCGAA 58.519 40.909 0.00 0.00 31.20 4.30
2524 2930 5.707764 TGTCAACAACATGGAATCCGAATAA 59.292 36.000 0.00 0.00 31.20 1.40
2609 3047 6.785191 TGCTGCAGTAATTTTAGTAGCATTC 58.215 36.000 16.64 0.00 35.27 2.67
2657 3104 2.498644 TCCGGGAAATGCATGTTGTA 57.501 45.000 0.00 0.00 0.00 2.41
2685 3132 6.394809 TGTGATCAGTTACGCAATCTCTTTA 58.605 36.000 0.00 0.00 0.00 1.85
2687 3134 7.549134 TGTGATCAGTTACGCAATCTCTTTATT 59.451 33.333 0.00 0.00 0.00 1.40
2886 3338 4.009675 TCTCATGTGTTGGGAACTTATGC 58.990 43.478 0.00 0.00 29.52 3.14
2908 3367 4.883585 GCCTGTTGATGATCAATCCAACTA 59.116 41.667 25.54 16.95 38.79 2.24
3057 3517 9.942850 AAAATTTGACATCCCAAAGGTTTATAG 57.057 29.630 0.00 0.00 39.13 1.31
3072 3532 9.705290 AAAGGTTTATAGTTCGAATGCAAATTT 57.295 25.926 0.00 0.00 0.00 1.82
3104 3575 3.812577 GGGCGTCCCATTTCTTTTG 57.187 52.632 9.72 0.00 44.65 2.44
3338 3811 7.613585 TCCATATGAGTACGAAACCAGTAAAA 58.386 34.615 3.65 0.00 0.00 1.52
3400 3873 4.488126 GCTGATTGCTGTTGACACTTAA 57.512 40.909 0.00 0.00 38.95 1.85
3401 3874 4.470462 GCTGATTGCTGTTGACACTTAAG 58.530 43.478 0.00 0.00 38.95 1.85
3402 3875 4.023707 GCTGATTGCTGTTGACACTTAAGT 60.024 41.667 1.12 1.12 38.95 2.24
3403 3876 5.506317 GCTGATTGCTGTTGACACTTAAGTT 60.506 40.000 5.07 0.00 38.95 2.66
3646 4123 4.382291 TGTGCTACGAGTTTTTGTATGGT 58.618 39.130 0.00 0.00 0.00 3.55
3706 4183 4.697514 TGATGAGGTAAGAGCTACAATGC 58.302 43.478 0.00 0.00 31.45 3.56
3707 4184 3.165058 TGAGGTAAGAGCTACAATGCG 57.835 47.619 0.00 0.00 38.13 4.73
3714 4191 3.313012 AGAGCTACAATGCGTGTGTAA 57.687 42.857 3.22 0.00 41.89 2.41
3720 4197 6.334989 AGCTACAATGCGTGTGTAACTATAA 58.665 36.000 3.22 0.00 41.89 0.98
3743 4220 5.083533 TGTTTGTGTTTTGCCTGATCTTT 57.916 34.783 0.00 0.00 0.00 2.52
3744 4221 5.486526 TGTTTGTGTTTTGCCTGATCTTTT 58.513 33.333 0.00 0.00 0.00 2.27
3745 4222 5.350914 TGTTTGTGTTTTGCCTGATCTTTTG 59.649 36.000 0.00 0.00 0.00 2.44
3746 4223 4.057406 TGTGTTTTGCCTGATCTTTTGG 57.943 40.909 0.00 0.00 0.00 3.28
3910 4410 9.667107 TGGTATCTTTAAAGGTGATGAAGTTAG 57.333 33.333 15.13 0.00 0.00 2.34
4009 4509 4.201851 CCGTGGATTGTAAAGAATGCAGAG 60.202 45.833 0.00 0.00 34.70 3.35
4094 4594 4.755123 GTGTTCTGCTAAAAGGCTAACTGA 59.245 41.667 0.00 0.00 33.39 3.41
4095 4595 5.238650 GTGTTCTGCTAAAAGGCTAACTGAA 59.761 40.000 0.00 0.00 33.39 3.02
4392 4925 5.346522 ACTACGGATTTCCTGATAACGAAC 58.653 41.667 0.00 0.00 0.00 3.95
4396 4929 2.389962 TTTCCTGATAACGAACGGGG 57.610 50.000 0.00 0.00 33.75 5.73
4542 5176 8.754230 AAAATTGCTAGAAAATCTTCTTCAGC 57.246 30.769 0.00 0.00 42.17 4.26
4566 5200 8.153550 AGCCGTAGATGATGAATCTCTATTTTT 58.846 33.333 0.00 0.00 42.27 1.94
4599 5248 9.462606 TTTCTATTTCTCTAATCTTTCCCAACC 57.537 33.333 0.00 0.00 0.00 3.77
4640 5313 2.874701 CCCAGATGCATGTGCTACTAAC 59.125 50.000 18.07 0.00 42.66 2.34
4653 5326 2.669924 GCTACTAACGGTTTGGTGCTAC 59.330 50.000 0.00 0.00 0.00 3.58
4685 5358 2.371841 ACTGGTGTTGCTTGTCCTGATA 59.628 45.455 0.00 0.00 0.00 2.15
4692 5365 4.275689 TGTTGCTTGTCCTGATAAACTGTG 59.724 41.667 0.00 0.00 0.00 3.66
4705 5378 5.888724 TGATAAACTGTGGTTGTTTTCTCCA 59.111 36.000 0.00 0.00 38.41 3.86
4718 5391 0.687354 TTCTCCACAGGGCACTTCTC 59.313 55.000 0.00 0.00 0.00 2.87
4931 5613 2.106338 TGCTCTCTTGGTGGTGAATCAA 59.894 45.455 0.00 0.00 0.00 2.57
4944 5626 7.094248 TGGTGGTGAATCAATGTTCTGAAATAG 60.094 37.037 0.00 0.00 0.00 1.73
4948 5630 8.116753 GGTGAATCAATGTTCTGAAATAGTACG 58.883 37.037 0.00 0.00 30.00 3.67
4949 5631 8.869897 GTGAATCAATGTTCTGAAATAGTACGA 58.130 33.333 0.00 0.00 30.00 3.43
4973 5760 3.572632 AGTGCATCTCTATTGTGCCAT 57.427 42.857 0.00 0.00 38.06 4.40
4974 5761 3.474600 AGTGCATCTCTATTGTGCCATC 58.525 45.455 0.00 0.00 38.06 3.51
4975 5762 2.551459 GTGCATCTCTATTGTGCCATCC 59.449 50.000 0.00 0.00 38.06 3.51
4976 5763 2.173143 TGCATCTCTATTGTGCCATCCA 59.827 45.455 0.00 0.00 38.06 3.41
4977 5764 2.812591 GCATCTCTATTGTGCCATCCAG 59.187 50.000 0.00 0.00 32.88 3.86
4978 5765 3.495629 GCATCTCTATTGTGCCATCCAGA 60.496 47.826 0.00 0.00 32.88 3.86
5004 5791 2.176273 CATCTGCAGCGCTACCACC 61.176 63.158 10.99 0.00 0.00 4.61
5024 5811 1.653151 GTTCTGAACTGCCGGATACC 58.347 55.000 5.05 0.00 0.00 2.73
5035 5822 2.238646 TGCCGGATACCATCTTTGTTCT 59.761 45.455 5.05 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 100 5.916883 AGTGCATCGAAATTGAGAAAAGTTG 59.083 36.000 0.00 0.00 0.00 3.16
150 153 8.338985 TCGAATTTGAAAGAAAGTTCACATTG 57.661 30.769 4.52 0.00 37.79 2.82
151 154 8.971321 CATCGAATTTGAAAGAAAGTTCACATT 58.029 29.630 0.00 0.28 39.46 2.71
152 155 8.352201 TCATCGAATTTGAAAGAAAGTTCACAT 58.648 29.630 0.00 0.00 37.24 3.21
153 156 7.702386 TCATCGAATTTGAAAGAAAGTTCACA 58.298 30.769 0.00 0.00 37.24 3.58
154 157 8.472236 GTTCATCGAATTTGAAAGAAAGTTCAC 58.528 33.333 12.84 1.47 37.24 3.18
187 441 8.073467 AGTTCAAAAAGGGTTCACTGAAATTA 57.927 30.769 0.00 0.00 0.00 1.40
190 444 5.993748 AGTTCAAAAAGGGTTCACTGAAA 57.006 34.783 0.00 0.00 0.00 2.69
193 447 6.620518 GCAAAAAGTTCAAAAAGGGTTCACTG 60.621 38.462 0.00 0.00 0.00 3.66
194 448 5.411361 GCAAAAAGTTCAAAAAGGGTTCACT 59.589 36.000 0.00 0.00 0.00 3.41
195 449 5.180304 TGCAAAAAGTTCAAAAAGGGTTCAC 59.820 36.000 0.00 0.00 0.00 3.18
196 450 5.308825 TGCAAAAAGTTCAAAAAGGGTTCA 58.691 33.333 0.00 0.00 0.00 3.18
197 451 5.871465 TGCAAAAAGTTCAAAAAGGGTTC 57.129 34.783 0.00 0.00 0.00 3.62
198 452 6.832520 ATTGCAAAAAGTTCAAAAAGGGTT 57.167 29.167 1.71 0.00 0.00 4.11
199 453 6.432472 TGAATTGCAAAAAGTTCAAAAAGGGT 59.568 30.769 1.71 0.00 0.00 4.34
200 454 6.850555 TGAATTGCAAAAAGTTCAAAAAGGG 58.149 32.000 1.71 0.00 0.00 3.95
201 455 8.800031 CATTGAATTGCAAAAAGTTCAAAAAGG 58.200 29.630 22.81 12.93 41.99 3.11
202 456 9.557338 TCATTGAATTGCAAAAAGTTCAAAAAG 57.443 25.926 22.81 17.14 41.99 2.27
203 457 9.903682 TTCATTGAATTGCAAAAAGTTCAAAAA 57.096 22.222 22.81 18.08 41.99 1.94
204 458 9.339492 GTTCATTGAATTGCAAAAAGTTCAAAA 57.661 25.926 22.81 14.35 41.99 2.44
205 459 8.728833 AGTTCATTGAATTGCAAAAAGTTCAAA 58.271 25.926 22.81 10.32 41.99 2.69
206 460 8.266392 AGTTCATTGAATTGCAAAAAGTTCAA 57.734 26.923 21.78 21.78 42.61 2.69
333 589 9.750125 AAAAGGTAGTTCAATGATTCTGAAAAC 57.250 29.630 0.00 0.00 34.68 2.43
550 857 7.122715 ACAGCATTAACATCAATACCCCTAAA 58.877 34.615 0.00 0.00 0.00 1.85
692 1001 6.430308 TGGTAAAAAGTATTTACGGCACATGA 59.570 34.615 0.00 0.00 37.28 3.07
695 1004 5.333952 CGTGGTAAAAAGTATTTACGGCACA 60.334 40.000 14.76 3.95 37.28 4.57
708 1017 5.512473 TCGAAAAATGGTCGTGGTAAAAAG 58.488 37.500 0.00 0.00 39.52 2.27
712 1022 3.068560 CCTCGAAAAATGGTCGTGGTAA 58.931 45.455 6.73 0.00 43.67 2.85
793 1103 1.825474 AGCTCCTACTCAGCGCTTTAA 59.175 47.619 7.50 0.00 42.14 1.52
794 1104 1.405821 GAGCTCCTACTCAGCGCTTTA 59.594 52.381 7.50 0.00 42.14 1.85
797 1107 2.124693 GGAGCTCCTACTCAGCGCT 61.125 63.158 26.25 2.64 42.14 5.92
802 1112 1.221909 TGGAGGGGAGCTCCTACTCA 61.222 60.000 36.45 26.83 41.39 3.41
805 1115 1.065345 GTTTTGGAGGGGAGCTCCTAC 60.065 57.143 31.36 23.51 41.39 3.18
806 1116 1.286248 GTTTTGGAGGGGAGCTCCTA 58.714 55.000 31.36 10.90 41.39 2.94
811 1121 1.674651 GACCGTTTTGGAGGGGAGC 60.675 63.158 0.00 0.00 42.00 4.70
818 1128 3.791953 TTTAGATGGGACCGTTTTGGA 57.208 42.857 0.00 0.00 42.00 3.53
820 1130 8.301002 TCTTTTATTTTAGATGGGACCGTTTTG 58.699 33.333 0.00 0.00 0.00 2.44
824 1134 6.602009 CCTTCTTTTATTTTAGATGGGACCGT 59.398 38.462 0.00 0.00 34.00 4.83
825 1135 7.027778 CCTTCTTTTATTTTAGATGGGACCG 57.972 40.000 0.00 0.00 34.00 4.79
830 1140 7.015584 CCCCATCCCTTCTTTTATTTTAGATGG 59.984 40.741 7.99 7.99 45.04 3.51
831 1141 7.784550 TCCCCATCCCTTCTTTTATTTTAGATG 59.215 37.037 0.00 0.00 0.00 2.90
832 1142 7.893482 TCCCCATCCCTTCTTTTATTTTAGAT 58.107 34.615 0.00 0.00 0.00 1.98
833 1143 7.291991 TCCCCATCCCTTCTTTTATTTTAGA 57.708 36.000 0.00 0.00 0.00 2.10
834 1144 7.040409 CGATCCCCATCCCTTCTTTTATTTTAG 60.040 40.741 0.00 0.00 0.00 1.85
835 1145 6.775629 CGATCCCCATCCCTTCTTTTATTTTA 59.224 38.462 0.00 0.00 0.00 1.52
836 1146 5.598417 CGATCCCCATCCCTTCTTTTATTTT 59.402 40.000 0.00 0.00 0.00 1.82
837 1147 5.140454 CGATCCCCATCCCTTCTTTTATTT 58.860 41.667 0.00 0.00 0.00 1.40
838 1148 4.447762 CCGATCCCCATCCCTTCTTTTATT 60.448 45.833 0.00 0.00 0.00 1.40
839 1149 3.074538 CCGATCCCCATCCCTTCTTTTAT 59.925 47.826 0.00 0.00 0.00 1.40
874 1184 0.394216 CGAATGTGGAATGGGCCTCA 60.394 55.000 4.53 0.00 36.05 3.86
898 1208 2.869192 GTGTTCGGGGTAACAAAACGTA 59.131 45.455 0.00 0.00 40.85 3.57
899 1209 1.670295 GTGTTCGGGGTAACAAAACGT 59.330 47.619 0.00 0.00 40.85 3.99
902 1212 3.278668 TCTGTGTTCGGGGTAACAAAA 57.721 42.857 0.00 0.00 40.85 2.44
906 1216 2.538512 ACTTCTGTGTTCGGGGTAAC 57.461 50.000 0.00 0.00 0.00 2.50
977 1287 3.827898 GTGAGAGGAGGACGGGCG 61.828 72.222 0.00 0.00 0.00 6.13
978 1288 3.462678 GGTGAGAGGAGGACGGGC 61.463 72.222 0.00 0.00 0.00 6.13
979 1289 1.755008 GAGGTGAGAGGAGGACGGG 60.755 68.421 0.00 0.00 0.00 5.28
1099 1419 2.124695 GCTAGGGTTTGGAGGGCG 60.125 66.667 0.00 0.00 0.00 6.13
1150 1475 2.241176 AGCCTCATCGGGGTTGAATTTA 59.759 45.455 0.00 0.00 32.66 1.40
1151 1476 1.005924 AGCCTCATCGGGGTTGAATTT 59.994 47.619 0.00 0.00 32.66 1.82
1152 1477 0.625849 AGCCTCATCGGGGTTGAATT 59.374 50.000 0.00 0.00 32.66 2.17
1153 1478 0.107017 CAGCCTCATCGGGGTTGAAT 60.107 55.000 0.00 0.00 37.26 2.57
1467 1792 0.879090 GAAAAGTAACACGGCAGGGG 59.121 55.000 0.00 0.00 0.00 4.79
1468 1793 0.879090 GGAAAAGTAACACGGCAGGG 59.121 55.000 0.00 0.00 0.00 4.45
1518 1844 2.035449 CGATAGCGGATAACAACTGGGA 59.965 50.000 0.00 0.00 0.00 4.37
1531 1857 4.331717 AGTTAATTCCACAAACGATAGCGG 59.668 41.667 4.97 0.00 43.17 5.52
1572 1898 5.066893 TCAGAATATTCCAGCTTCATTGCAC 59.933 40.000 11.92 0.00 34.99 4.57
1620 1947 1.414919 CCCCTATCGAATTTCGTGGGA 59.585 52.381 29.74 12.41 43.03 4.37
1626 1953 4.584743 AGAAAATGCCCCCTATCGAATTTC 59.415 41.667 0.00 0.00 0.00 2.17
1750 2078 5.527214 CACAGATTGTTTCAGAACACCTACA 59.473 40.000 0.00 0.00 45.01 2.74
1869 2210 8.387190 TCTTGCAATGAAATACATAGATCCAG 57.613 34.615 0.00 0.00 38.38 3.86
1887 2228 7.336931 GGAGTTATTAGGTTCTTCATCTTGCAA 59.663 37.037 0.00 0.00 0.00 4.08
1907 2251 7.232737 TGTGTTTCTAGAGATGTTCTGGAGTTA 59.767 37.037 0.00 0.00 43.32 2.24
2445 2801 6.322201 CCCACTGGCTTATCAAAATATTGTCT 59.678 38.462 0.00 0.00 37.79 3.41
2447 2803 5.957774 ACCCACTGGCTTATCAAAATATTGT 59.042 36.000 0.00 0.00 34.78 2.71
2488 2849 3.956848 TGTTGTTGACAAACATGGATGGA 59.043 39.130 0.00 0.00 45.54 3.41
2524 2930 6.762661 GGCAGGCATAATTTACAACAATGATT 59.237 34.615 0.00 0.00 0.00 2.57
2657 3104 2.143008 TGCGTAACTGATCACAACGT 57.857 45.000 16.60 1.41 36.03 3.99
2685 3132 8.862325 TTTTCACATATCGGCCATATCTAAAT 57.138 30.769 2.24 0.00 0.00 1.40
2687 3134 8.862325 AATTTTCACATATCGGCCATATCTAA 57.138 30.769 2.24 0.00 0.00 2.10
2746 3195 2.557924 TGCAGCAAGACCAAGGTAAATG 59.442 45.455 0.00 0.00 0.00 2.32
2747 3196 2.875296 TGCAGCAAGACCAAGGTAAAT 58.125 42.857 0.00 0.00 0.00 1.40
2750 3199 1.896220 CTTGCAGCAAGACCAAGGTA 58.104 50.000 28.50 0.00 43.42 3.08
2751 3200 1.458639 GCTTGCAGCAAGACCAAGGT 61.459 55.000 34.93 0.00 43.42 3.50
2886 3338 8.152898 TCTATAGTTGGATTGATCATCAACAGG 58.847 37.037 25.29 16.80 39.45 4.00
2922 3381 3.955471 ACAAGCTATGTGTGCCATAACT 58.045 40.909 0.00 0.00 41.93 2.24
2968 3428 5.463724 GCTACTGCTTATCTGCTATTTCGTT 59.536 40.000 0.00 0.00 36.03 3.85
3072 3532 1.817520 CGCCCATGTACATTGCCGA 60.818 57.895 17.29 0.00 0.00 5.54
3104 3575 5.063060 CCAGCAAAACGTGTACTATTAGTCC 59.937 44.000 0.00 0.00 0.00 3.85
3338 3811 5.294060 GTGGACAGCACAACAAATGATTTTT 59.706 36.000 0.00 0.00 0.00 1.94
3341 3814 3.384146 TGTGGACAGCACAACAAATGATT 59.616 39.130 0.00 0.00 0.00 2.57
3399 3872 4.941263 TGCACAGACACAGAGTTAAAACTT 59.059 37.500 0.00 0.00 39.88 2.66
3400 3873 4.513442 TGCACAGACACAGAGTTAAAACT 58.487 39.130 0.00 0.00 43.16 2.66
3401 3874 4.875544 TGCACAGACACAGAGTTAAAAC 57.124 40.909 0.00 0.00 0.00 2.43
3402 3875 6.765989 ACTTATGCACAGACACAGAGTTAAAA 59.234 34.615 1.67 0.00 0.00 1.52
3403 3876 6.288294 ACTTATGCACAGACACAGAGTTAAA 58.712 36.000 1.67 0.00 0.00 1.52
3646 4123 1.150536 AGCTTCAAAGGGTGGCGAA 59.849 52.632 0.00 0.00 0.00 4.70
3706 4183 8.996988 AAACACAAACATTATAGTTACACACG 57.003 30.769 0.00 0.00 0.00 4.49
3714 4191 7.283625 TCAGGCAAAACACAAACATTATAGT 57.716 32.000 0.00 0.00 0.00 2.12
3720 4197 4.942761 AGATCAGGCAAAACACAAACAT 57.057 36.364 0.00 0.00 0.00 2.71
3743 4220 3.808726 GCTCAAAATTCATGTTGCACCAA 59.191 39.130 0.00 0.00 0.00 3.67
3744 4221 3.181468 TGCTCAAAATTCATGTTGCACCA 60.181 39.130 0.00 0.00 0.00 4.17
3745 4222 3.391965 TGCTCAAAATTCATGTTGCACC 58.608 40.909 0.00 0.00 0.00 5.01
3746 4223 3.430895 CCTGCTCAAAATTCATGTTGCAC 59.569 43.478 0.00 0.00 0.00 4.57
3909 4409 7.917505 GCAGCTGCATACAAAATTTATACTTCT 59.082 33.333 33.36 0.00 41.59 2.85
3910 4410 7.917505 AGCAGCTGCATACAAAATTTATACTTC 59.082 33.333 38.24 3.57 45.16 3.01
3917 4417 5.183713 TCACTAGCAGCTGCATACAAAATTT 59.816 36.000 38.24 17.40 45.16 1.82
4009 4509 0.529378 CAATGCAACTCCCTGAAGGC 59.471 55.000 0.00 0.00 34.51 4.35
4272 4774 4.649267 TTTCCAGGTGATACATTCCACA 57.351 40.909 0.00 0.00 35.13 4.17
4280 4782 6.460123 CCATAGTTTGCATTTCCAGGTGATAC 60.460 42.308 0.00 0.00 0.00 2.24
4370 4903 4.440103 CGTTCGTTATCAGGAAATCCGTAG 59.560 45.833 0.00 0.00 42.08 3.51
4392 4925 0.321653 GGAGCAATGTATAGCCCCCG 60.322 60.000 0.00 0.00 0.00 5.73
4396 4929 1.421646 ACCCAGGAGCAATGTATAGCC 59.578 52.381 0.00 0.00 0.00 3.93
4542 5176 9.265901 ACAAAAATAGAGATTCATCATCTACGG 57.734 33.333 0.00 0.00 42.92 4.02
4599 5248 5.005740 TGGGAGTTCAATTCTCAGACATTG 58.994 41.667 4.17 4.17 34.04 2.82
4692 5365 0.673985 GCCCTGTGGAGAAAACAACC 59.326 55.000 0.00 0.00 0.00 3.77
4740 5413 3.369451 GCAAACAAGAACTTCGCCAAAAA 59.631 39.130 0.00 0.00 0.00 1.94
4931 5613 8.818057 GCACTAAATCGTACTATTTCAGAACAT 58.182 33.333 8.50 0.00 31.63 2.71
4944 5626 7.567771 GCACAATAGAGATGCACTAAATCGTAC 60.568 40.741 0.00 0.00 39.23 3.67
4948 5630 5.528690 TGGCACAATAGAGATGCACTAAATC 59.471 40.000 0.00 0.00 41.27 2.17
4949 5631 5.439721 TGGCACAATAGAGATGCACTAAAT 58.560 37.500 0.00 0.00 41.27 1.40
4973 5760 0.179702 GCAGATGCACTGGATCTGGA 59.820 55.000 30.78 0.00 44.80 3.86
4974 5761 2.704108 GCAGATGCACTGGATCTGG 58.296 57.895 30.78 18.31 44.80 3.86
5004 5791 1.278238 GTATCCGGCAGTTCAGAACG 58.722 55.000 7.68 4.46 36.23 3.95
5024 5811 5.756195 TCTGAACCAACAGAACAAAGATG 57.244 39.130 0.00 0.00 42.79 2.90


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

AutoCloner maintained by Alex Coulton.