Multiple sequence alignment - TraesCS5B01G134000

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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 TraesCS5B01G134000 chr5B 100.000 4468 0 0 1 4468 250950862 250955329 0.000000e+00 8251.0
1 TraesCS5B01G134000 chr5B 89.933 447 43 2 102 546 250921598 250922044 3.880000e-160 575.0
2 TraesCS5B01G134000 chr5B 75.405 370 55 30 52 402 491409315 491408963 3.600000e-31 147.0
3 TraesCS5B01G134000 chr5D 92.984 3834 211 17 664 4467 227544149 227547954 0.000000e+00 5537.0
4 TraesCS5B01G134000 chr5D 86.200 529 63 5 6 525 227543622 227544149 8.390000e-157 564.0
5 TraesCS5B01G134000 chr5A 92.960 3537 213 14 1 3508 305277407 305280936 0.000000e+00 5120.0
6 TraesCS5B01G134000 chr5A 90.501 979 78 6 3498 4464 305280970 305281945 0.000000e+00 1279.0
7 TraesCS5B01G134000 chr5A 87.892 446 52 2 102 545 305233693 305234138 1.420000e-144 523.0
8 TraesCS5B01G134000 chr5A 76.589 299 47 17 46 327 497319844 497320136 4.660000e-30 143.0
9 TraesCS5B01G134000 chr5A 87.931 58 7 0 6 63 164483076 164483133 8.020000e-08 69.4
10 TraesCS5B01G134000 chr2D 86.470 3215 348 47 578 3747 31895731 31898903 0.000000e+00 3446.0
11 TraesCS5B01G134000 chr2D 90.115 435 40 3 112 544 75099590 75100023 3.020000e-156 562.0
12 TraesCS5B01G134000 chr2D 95.238 42 2 0 4283 4324 344801232 344801191 2.880000e-07 67.6
13 TraesCS5B01G134000 chr2D 96.875 32 1 0 4288 4319 130424175 130424144 2.000000e-03 54.7
14 TraesCS5B01G134000 chr2A 85.424 3204 382 61 584 3747 33951634 33954792 0.000000e+00 3251.0
15 TraesCS5B01G134000 chr2A 86.646 1932 223 22 578 2484 33785846 33787767 0.000000e+00 2106.0
16 TraesCS5B01G134000 chr2A 84.389 1294 139 30 2478 3747 33790456 33791710 0.000000e+00 1212.0
17 TraesCS5B01G134000 chr2A 96.875 32 1 0 4288 4319 136334326 136334295 2.000000e-03 54.7
18 TraesCS5B01G134000 chr2B 85.521 2141 261 40 1635 3747 52511921 52509802 0.000000e+00 2191.0
19 TraesCS5B01G134000 chr2B 85.607 2126 249 37 1635 3747 52223797 52225878 0.000000e+00 2178.0
20 TraesCS5B01G134000 chr2B 85.963 1033 119 15 578 1589 52222772 52223799 0.000000e+00 1081.0
21 TraesCS5B01G134000 chr2B 84.863 1024 112 21 578 1581 52512927 52511927 0.000000e+00 992.0
22 TraesCS5B01G134000 chr2B 95.349 43 2 0 4283 4325 410066327 410066285 8.020000e-08 69.4
23 TraesCS5B01G134000 chr6D 80.393 2953 479 60 608 3476 441714579 441711643 0.000000e+00 2154.0
24 TraesCS5B01G134000 chr6D 97.143 35 1 0 4283 4317 117392589 117392623 4.830000e-05 60.2
25 TraesCS5B01G134000 chr6B 79.825 2964 480 68 608 3476 667248759 667245819 0.000000e+00 2052.0
26 TraesCS5B01G134000 chr6A 79.811 2962 481 74 608 3476 590896608 590893671 0.000000e+00 2049.0
27 TraesCS5B01G134000 chr6A 75.066 381 62 28 41 402 51533158 51532792 3.600000e-31 147.0
28 TraesCS5B01G134000 chr6A 75.578 303 44 20 46 327 80326481 80326774 6.070000e-24 122.0
29 TraesCS5B01G134000 chr3D 90.112 445 41 3 104 545 119008775 119009219 3.880000e-160 575.0
30 TraesCS5B01G134000 chr3D 86.547 446 56 4 102 545 354623706 354624149 5.190000e-134 488.0
31 TraesCS5B01G134000 chr4D 86.918 451 55 3 102 548 364011097 364010647 1.860000e-138 503.0
32 TraesCS5B01G134000 chr4D 86.577 447 57 3 102 545 104314650 104315096 1.440000e-134 490.0
33 TraesCS5B01G134000 chr7B 77.863 393 53 16 6 389 275274392 275274759 3.500000e-51 213.0
34 TraesCS5B01G134000 chr7B 79.130 115 21 3 4284 4397 101480814 101480702 4.790000e-10 76.8
35 TraesCS5B01G134000 chr1B 75.706 354 52 28 52 388 81800090 81799754 3.600000e-31 147.0
36 TraesCS5B01G134000 chr1B 74.151 383 65 27 41 402 33498033 33498402 1.300000e-25 128.0
37 TraesCS5B01G134000 chr4A 77.091 275 39 16 46 305 617342408 617342673 2.170000e-28 137.0
38 TraesCS5B01G134000 chr7A 75.667 300 48 20 46 327 698993876 698994168 4.690000e-25 126.0
39 TraesCS5B01G134000 chr7D 94.595 37 2 0 4291 4327 148127781 148127745 1.740000e-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 TraesCS5B01G134000 chr5B 250950862 250955329 4467 False 8251.0 8251 100.0000 1 4468 1 chr5B.!!$F2 4467
1 TraesCS5B01G134000 chr5D 227543622 227547954 4332 False 3050.5 5537 89.5920 6 4467 2 chr5D.!!$F1 4461
2 TraesCS5B01G134000 chr5A 305277407 305281945 4538 False 3199.5 5120 91.7305 1 4464 2 chr5A.!!$F4 4463
3 TraesCS5B01G134000 chr2D 31895731 31898903 3172 False 3446.0 3446 86.4700 578 3747 1 chr2D.!!$F1 3169
4 TraesCS5B01G134000 chr2A 33951634 33954792 3158 False 3251.0 3251 85.4240 584 3747 1 chr2A.!!$F1 3163
5 TraesCS5B01G134000 chr2A 33785846 33791710 5864 False 1659.0 2106 85.5175 578 3747 2 chr2A.!!$F2 3169
6 TraesCS5B01G134000 chr2B 52222772 52225878 3106 False 1629.5 2178 85.7850 578 3747 2 chr2B.!!$F1 3169
7 TraesCS5B01G134000 chr2B 52509802 52512927 3125 True 1591.5 2191 85.1920 578 3747 2 chr2B.!!$R2 3169
8 TraesCS5B01G134000 chr6D 441711643 441714579 2936 True 2154.0 2154 80.3930 608 3476 1 chr6D.!!$R1 2868
9 TraesCS5B01G134000 chr6B 667245819 667248759 2940 True 2052.0 2052 79.8250 608 3476 1 chr6B.!!$R1 2868
10 TraesCS5B01G134000 chr6A 590893671 590896608 2937 True 2049.0 2049 79.8110 608 3476 1 chr6A.!!$R2 2868

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
182 191 0.616395 TAGGGGACGCAGGACATGAA 60.616 55.0 0.0 0.0 0.00 2.57 F
511 520 1.190833 CGGCCCATGAGAGATAGGCT 61.191 60.0 0.0 0.0 43.36 4.58 F
2003 2069 0.306228 TGCAACCACATGTCGAAACG 59.694 50.0 0.0 0.0 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2052 0.941542 ACCGTTTCGACATGTGGTTG 59.058 50.0 1.15 0.0 0.00 3.77 R
2188 2268 5.012239 ACATCACTGAATGGTGCAACTAAT 58.988 37.5 2.04 0.0 44.04 1.73 R
3821 6723 1.243902 AGTTTTCCCGACGTACCGTA 58.756 50.0 0.00 0.0 41.37 4.02 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
31 32 5.598830 ACGAAGATGTCCCTAATACTGATGT 59.401 40.000 0.00 0.00 0.00 3.06
32 33 6.776116 ACGAAGATGTCCCTAATACTGATGTA 59.224 38.462 0.00 0.00 0.00 2.29
39 40 6.069331 GTCCCTAATACTGATGTAGTCTCCA 58.931 44.000 0.00 0.00 40.89 3.86
68 69 2.435418 GAGCCATCGATCCCTCAGT 58.565 57.895 14.06 0.00 0.00 3.41
73 74 1.966354 CCATCGATCCCTCAGTGATCA 59.034 52.381 0.00 0.00 38.83 2.92
75 76 3.388308 CATCGATCCCTCAGTGATCAAC 58.612 50.000 0.00 0.00 38.83 3.18
81 82 1.905215 CCCTCAGTGATCAACCAGAGT 59.095 52.381 0.00 0.00 32.30 3.24
99 100 5.879223 CCAGAGTAACTCTCAATGAAAGCAT 59.121 40.000 0.00 0.00 44.98 3.79
100 101 7.044181 CCAGAGTAACTCTCAATGAAAGCATA 58.956 38.462 0.00 0.00 44.98 3.14
146 155 1.137697 GGGGTCCCGAACTATGGATT 58.862 55.000 0.48 0.00 32.20 3.01
153 162 4.887655 GTCCCGAACTATGGATTTTGGATT 59.112 41.667 0.00 0.00 32.20 3.01
163 172 4.633351 TGGATTTTGGATTGATGGGGAAT 58.367 39.130 0.00 0.00 0.00 3.01
172 181 1.375326 GATGGGGAATAGGGGACGC 59.625 63.158 0.00 0.00 0.00 5.19
173 182 1.385347 ATGGGGAATAGGGGACGCA 60.385 57.895 0.00 0.00 0.00 5.24
179 188 0.759346 GAATAGGGGACGCAGGACAT 59.241 55.000 0.00 0.00 0.00 3.06
182 191 0.616395 TAGGGGACGCAGGACATGAA 60.616 55.000 0.00 0.00 0.00 2.57
197 206 4.770010 GGACATGAAATTTACCCAGGTTCA 59.230 41.667 0.00 0.00 33.08 3.18
224 233 5.774184 CCCTGTCTAAGAGGTAATACCCTAC 59.226 48.000 5.71 0.00 39.75 3.18
230 239 5.653255 AAGAGGTAATACCCTACGTCCTA 57.347 43.478 5.71 0.00 39.75 2.94
235 244 4.279420 GGTAATACCCTACGTCCTACTTGG 59.721 50.000 0.00 0.00 30.04 3.61
243 252 7.297614 ACCCTACGTCCTACTTGGTTATATTA 58.702 38.462 0.00 0.00 37.07 0.98
259 268 9.173231 TGGTTATATTACTTGTGTATATGGGGT 57.827 33.333 0.00 0.00 0.00 4.95
273 282 8.999431 GTGTATATGGGGTTTACATAGTTGATG 58.001 37.037 0.00 0.00 41.79 3.07
274 283 7.663905 TGTATATGGGGTTTACATAGTTGATGC 59.336 37.037 0.00 0.00 39.39 3.91
279 288 4.644685 GGGTTTACATAGTTGATGCACCAT 59.355 41.667 0.00 0.00 39.39 3.55
335 344 3.411446 TGGTGATTGTTGTCTTAGCCTG 58.589 45.455 0.00 0.00 0.00 4.85
338 347 5.001232 GGTGATTGTTGTCTTAGCCTGTAA 58.999 41.667 0.00 0.00 0.00 2.41
394 403 5.072736 GGGGTGCTAGGGTTTACATATAGTT 59.927 44.000 0.00 0.00 0.00 2.24
395 404 6.270695 GGGGTGCTAGGGTTTACATATAGTTA 59.729 42.308 0.00 0.00 0.00 2.24
411 420 9.393786 ACATATAGTTAGTTACATCAGGGGAAT 57.606 33.333 0.00 0.00 0.00 3.01
435 444 3.369892 CCGGATCTTCCATCTTGACTTGT 60.370 47.826 0.00 0.00 35.91 3.16
458 467 2.903798 CACACACCAAGGCACAAAAAT 58.096 42.857 0.00 0.00 0.00 1.82
470 479 2.031508 GCACAAAAATTCTTCGGTCCGA 60.032 45.455 10.71 10.71 0.00 4.55
511 520 1.190833 CGGCCCATGAGAGATAGGCT 61.191 60.000 0.00 0.00 43.36 4.58
519 528 1.763546 GAGAGATAGGCTGGCCACCC 61.764 65.000 9.29 9.29 38.92 4.61
534 543 1.934870 ACCCGAGGACCCCTAGTCT 60.935 63.158 0.00 0.00 45.54 3.24
582 591 8.656806 CCACCAACCTTTATAGGAGTAATATGA 58.343 37.037 6.19 0.00 45.05 2.15
685 697 2.968675 ACTAGGACGTGGTGCAATTAC 58.031 47.619 0.00 0.00 0.00 1.89
698 710 6.145696 GTGGTGCAATTACCGTATCTTATCTC 59.854 42.308 0.00 0.00 43.87 2.75
1021 1050 7.255730 CCACCATGAAAGAAAATCCATCTATCC 60.256 40.741 0.00 0.00 0.00 2.59
1120 1149 2.299013 ACTAGCGCGATCCCATTGAATA 59.701 45.455 12.10 0.00 0.00 1.75
1232 1262 7.527457 AGATACAAAAATAGGTTGACGAAAGC 58.473 34.615 0.00 0.00 36.48 3.51
1453 1502 7.395772 TCATGGTAGCAATTATTTGAACTCCAA 59.604 33.333 0.00 0.00 34.60 3.53
1601 1651 7.998081 GCAACATGCAAATTCAACTAATTTC 57.002 32.000 0.00 0.00 44.27 2.17
1604 1654 9.749490 CAACATGCAAATTCAACTAATTTCATC 57.251 29.630 0.00 0.00 44.27 2.92
1605 1655 9.491675 AACATGCAAATTCAACTAATTTCATCA 57.508 25.926 0.00 0.00 44.27 3.07
1771 1831 2.042639 GCCATCCCACAAGCCCAT 60.043 61.111 0.00 0.00 0.00 4.00
1794 1854 2.056906 GCCCGGATTGAGTGCCCTAT 62.057 60.000 0.73 0.00 0.00 2.57
1935 1997 8.588472 TGATTCAGTTATCATGGTAGACTATGG 58.412 37.037 6.22 0.00 35.79 2.74
1941 2003 3.743521 TCATGGTAGACTATGGCAATGC 58.256 45.455 0.00 0.00 35.79 3.56
1954 2016 3.465871 TGGCAATGCAAACTTTTCCTTC 58.534 40.909 7.79 0.00 0.00 3.46
1986 2052 2.686235 TGCACAACATTATTGCCTTGC 58.314 42.857 0.00 0.00 35.26 4.01
2003 2069 0.306228 TGCAACCACATGTCGAAACG 59.694 50.000 0.00 0.00 0.00 3.60
2004 2070 0.385473 GCAACCACATGTCGAAACGG 60.385 55.000 0.00 0.00 0.00 4.44
2145 2225 9.953697 TTACACTTAACATTTGTGTTACCATTC 57.046 29.630 3.35 0.00 43.53 2.67
2146 2226 8.001881 ACACTTAACATTTGTGTTACCATTCA 57.998 30.769 0.83 0.00 41.45 2.57
2153 2233 5.508200 TTTGTGTTACCATTCAAGTGGAC 57.492 39.130 0.00 0.00 42.02 4.02
2188 2268 8.539544 TCTCCAAGTGTTTCATCTATATTGACA 58.460 33.333 0.00 0.00 0.00 3.58
2203 2283 9.056005 TCTATATTGACATTAGTTGCACCATTC 57.944 33.333 0.00 0.00 0.00 2.67
2356 2441 3.056458 CTATATGGGACGCGGGCA 58.944 61.111 12.47 0.00 0.00 5.36
2417 2502 1.002888 AGGATCTAAGCGCATCATGGG 59.997 52.381 11.47 0.00 0.00 4.00
2684 5497 5.505654 GCTTTTGTGCAAGTAAGCTCAAGTA 60.506 40.000 16.40 0.00 45.23 2.24
2706 5519 6.834969 AGTATTGGTCTAGGAGGAAGACTTAC 59.165 42.308 3.50 0.00 42.48 2.34
2710 5523 3.377798 GTCTAGGAGGAAGACTTACACCG 59.622 52.174 8.12 0.00 40.21 4.94
2866 5681 6.312672 GCTTGAAGACTTTGCTTAAACCAAAA 59.687 34.615 0.00 0.00 32.37 2.44
2876 5691 9.921637 CTTTGCTTAAACCAAAATTATAGGTCA 57.078 29.630 0.00 0.00 33.74 4.02
3000 5822 9.814507 TCATGTTAACACGACATACAATTAAAC 57.185 29.630 11.22 0.00 36.04 2.01
3001 5823 9.600646 CATGTTAACACGACATACAATTAAACA 57.399 29.630 11.22 0.00 36.04 2.83
3004 5826 9.525007 GTTAACACGACATACAATTAAACAGAG 57.475 33.333 0.00 0.00 0.00 3.35
3023 5845 3.134458 GAGAGTTTCACCTCACCACAAG 58.866 50.000 0.00 0.00 33.75 3.16
3029 5851 2.229792 TCACCTCACCACAAGCATTTC 58.770 47.619 0.00 0.00 0.00 2.17
3073 5896 9.979578 TCAACTTTGTTAAGCATTTACATGAAT 57.020 25.926 0.00 0.00 34.60 2.57
3237 6064 1.002624 GGTCCAACGGCCTCATCAA 60.003 57.895 0.00 0.00 0.00 2.57
3266 6093 4.082245 CCACAAATGGGTAGTGGTCATTTC 60.082 45.833 0.00 0.00 45.95 2.17
3331 6158 8.716674 ATCCAAATTGTAGATAATGAAGGCAT 57.283 30.769 0.00 0.00 35.92 4.40
3636 6527 7.201875 CCAACAGTGTAGGTTAGGTTTGATTTT 60.202 37.037 0.00 0.00 0.00 1.82
3637 6528 7.272037 ACAGTGTAGGTTAGGTTTGATTTTG 57.728 36.000 0.00 0.00 0.00 2.44
3663 6558 7.490402 GTCGGCTATACACTGTGTATTTTAGTT 59.510 37.037 31.53 14.17 40.40 2.24
3777 6676 6.893583 AGATAAGACACTGAATACATTGCCT 58.106 36.000 0.00 0.00 31.27 4.75
3791 6690 7.928307 ATACATTGCCTATTCTTGCGATAAT 57.072 32.000 0.00 0.00 30.43 1.28
3821 6723 6.877236 ACCATTTTTGTGTGTCTCATCTTTT 58.123 32.000 0.00 0.00 0.00 2.27
3959 6870 4.019231 GTGGAGACAGGGTTAAAGGAGATT 60.019 45.833 0.00 0.00 44.46 2.40
3986 6897 4.406003 GGGGAGATGTAGCTTTGTCTTCTA 59.594 45.833 0.00 0.00 0.00 2.10
4000 6911 4.256110 TGTCTTCTAGCAATGACATGGTG 58.744 43.478 0.00 0.00 34.94 4.17
4019 6930 4.346418 TGGTGGTTAAGGACATGCAAAAAT 59.654 37.500 0.00 0.00 0.00 1.82
4022 6933 7.102993 GGTGGTTAAGGACATGCAAAAATTAT 58.897 34.615 0.00 0.00 0.00 1.28
4024 6935 7.816995 GTGGTTAAGGACATGCAAAAATTATCA 59.183 33.333 0.00 0.00 0.00 2.15
4100 7011 2.157668 GTCATCACGTTGGACACACATC 59.842 50.000 6.22 0.00 0.00 3.06
4116 7027 5.986135 ACACACATCTCTGAACTAGAACAAC 59.014 40.000 0.00 0.00 34.32 3.32
4125 7036 6.173339 TCTGAACTAGAACAACCATTGATCC 58.827 40.000 0.00 0.00 33.41 3.36
4211 7123 7.333423 GTGAAGTTGTTAGGTATGTAGATGCAA 59.667 37.037 0.00 0.00 0.00 4.08
4267 7179 1.137479 GATGGGAATCGGGTCAACGTA 59.863 52.381 0.00 0.00 34.94 3.57
4268 7180 0.975135 TGGGAATCGGGTCAACGTAA 59.025 50.000 0.00 0.00 34.94 3.18
4286 7198 6.677781 ACGTAAGAATGTTGGATGGTATTG 57.322 37.500 0.00 0.00 43.62 1.90
4321 7233 0.041535 TTGGAGTACCCGCCTTCCTA 59.958 55.000 0.00 0.00 37.93 2.94
4356 7268 3.839432 GAGCGCCTCCTAGCCGTT 61.839 66.667 2.29 0.00 0.00 4.44
4368 7280 2.260434 GCCGTTCGCTGACAGGTA 59.740 61.111 4.26 0.00 0.00 3.08
4378 7290 1.338105 GCTGACAGGTAGCATGTGTCA 60.338 52.381 13.56 13.56 46.43 3.58
4386 7298 0.538584 TAGCATGTGTCAGGAGCCTG 59.461 55.000 10.29 10.29 44.86 4.85
4417 7329 2.439701 CGCCGTCTGGTCTCCCTA 60.440 66.667 0.00 0.00 37.67 3.53
4430 7342 0.684805 CTCCCTAGACGGCAAGGACT 60.685 60.000 0.00 0.00 34.58 3.85
4434 7346 0.895530 CTAGACGGCAAGGACTTGGA 59.104 55.000 13.41 0.00 40.74 3.53
4440 7352 0.321653 GGCAAGGACTTGGACGACAT 60.322 55.000 13.41 0.00 40.74 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.255111 TGATCATTGGAGACTACATCAGTATT 57.745 34.615 0.00 0.00 37.72 1.89
22 23 7.039152 CCTGATCATTGGAGACTACATCAGTAT 60.039 40.741 12.85 0.00 37.72 2.12
24 25 5.070180 CCTGATCATTGGAGACTACATCAGT 59.930 44.000 12.85 0.00 41.47 3.41
31 32 2.625314 CTCGCCTGATCATTGGAGACTA 59.375 50.000 5.19 0.00 0.00 2.59
32 33 1.411977 CTCGCCTGATCATTGGAGACT 59.588 52.381 5.19 0.00 0.00 3.24
39 40 0.602106 CGATGGCTCGCCTGATCATT 60.602 55.000 9.65 0.00 38.20 2.57
66 67 5.080337 TGAGAGTTACTCTGGTTGATCACT 58.920 41.667 20.52 0.00 41.35 3.41
68 69 6.211384 TCATTGAGAGTTACTCTGGTTGATCA 59.789 38.462 20.52 6.86 41.35 2.92
73 74 5.703130 GCTTTCATTGAGAGTTACTCTGGTT 59.297 40.000 20.52 0.76 41.35 3.67
75 76 5.240891 TGCTTTCATTGAGAGTTACTCTGG 58.759 41.667 20.52 6.61 41.35 3.86
81 82 7.386059 TGACACTATGCTTTCATTGAGAGTTA 58.614 34.615 6.13 0.00 34.22 2.24
99 100 0.322322 ATCCGCCGGTTTTGACACTA 59.678 50.000 1.63 0.00 0.00 2.74
100 101 0.953960 GATCCGCCGGTTTTGACACT 60.954 55.000 1.63 0.00 0.00 3.55
146 155 3.116784 CCCCTATTCCCCATCAATCCAAA 60.117 47.826 0.00 0.00 0.00 3.28
153 162 1.415672 GCGTCCCCTATTCCCCATCA 61.416 60.000 0.00 0.00 0.00 3.07
163 172 0.616395 TTCATGTCCTGCGTCCCCTA 60.616 55.000 0.00 0.00 0.00 3.53
172 181 4.344104 ACCTGGGTAAATTTCATGTCCTG 58.656 43.478 0.00 0.00 0.00 3.86
173 182 4.675063 ACCTGGGTAAATTTCATGTCCT 57.325 40.909 0.00 0.00 0.00 3.85
179 188 3.161866 GCCTGAACCTGGGTAAATTTCA 58.838 45.455 0.00 0.00 0.00 2.69
182 191 1.273041 GGGCCTGAACCTGGGTAAATT 60.273 52.381 0.84 0.00 0.00 1.82
197 206 2.942604 TTACCTCTTAGACAGGGCCT 57.057 50.000 0.00 0.00 35.01 5.19
204 213 5.471797 GGACGTAGGGTATTACCTCTTAGAC 59.528 48.000 12.54 3.65 42.09 2.59
224 233 7.977853 ACACAAGTAATATAACCAAGTAGGACG 59.022 37.037 0.00 0.00 41.22 4.79
243 252 8.097791 ACTATGTAAACCCCATATACACAAGT 57.902 34.615 0.00 0.00 32.80 3.16
259 268 6.413892 TCTCATGGTGCATCAACTATGTAAA 58.586 36.000 2.42 0.00 39.37 2.01
273 282 1.869767 GTTCATCCGATCTCATGGTGC 59.130 52.381 0.00 0.00 0.00 5.01
274 283 3.465742 AGTTCATCCGATCTCATGGTG 57.534 47.619 0.00 0.00 0.00 4.17
279 288 4.030913 AGGGTTTAGTTCATCCGATCTCA 58.969 43.478 0.00 0.00 0.00 3.27
394 403 2.104111 CGGCATTCCCCTGATGTAACTA 59.896 50.000 0.00 0.00 0.00 2.24
395 404 1.134098 CGGCATTCCCCTGATGTAACT 60.134 52.381 0.00 0.00 0.00 2.24
411 420 1.134401 GTCAAGATGGAAGATCCGGCA 60.134 52.381 0.00 0.00 40.17 5.69
435 444 0.106967 TTGTGCCTTGGTGTGTGCTA 60.107 50.000 0.00 0.00 0.00 3.49
470 479 0.960364 CTGTTGGGCCGCACTGTATT 60.960 55.000 0.00 0.00 0.00 1.89
519 528 1.138568 TCCTAGACTAGGGGTCCTCG 58.861 60.000 25.35 0.81 46.24 4.63
622 631 9.905713 TGGAGTATTAATGCCCAGATAATATTC 57.094 33.333 8.84 0.00 32.15 1.75
631 640 6.966534 AAATCTTGGAGTATTAATGCCCAG 57.033 37.500 11.50 6.34 0.00 4.45
685 697 8.452534 GTCACACTTATAGGAGATAAGATACGG 58.547 40.741 10.51 0.00 35.97 4.02
698 710 6.986817 CCTAGTTGATTGGTCACACTTATAGG 59.013 42.308 0.00 0.00 33.11 2.57
1021 1050 2.959516 TGCTAAGAGAATGGTCACACG 58.040 47.619 0.00 0.00 0.00 4.49
1389 1437 6.436532 GCTACCTACCTGGCACTATCTATTTA 59.563 42.308 0.00 0.00 40.22 1.40
1688 1747 6.904626 AGCTTGGTTCCATCTATTAATGAGT 58.095 36.000 0.00 0.00 0.00 3.41
1771 1831 1.976474 GCACTCAATCCGGGCCAAA 60.976 57.895 4.39 0.00 0.00 3.28
1779 1839 3.555168 CGTTCCTATAGGGCACTCAATCC 60.555 52.174 18.97 0.00 35.41 3.01
1935 1997 3.380142 TCGAAGGAAAAGTTTGCATTGC 58.620 40.909 0.00 0.46 0.00 3.56
1941 2003 5.636837 TCAACAACTCGAAGGAAAAGTTTG 58.363 37.500 0.00 0.00 31.04 2.93
1982 2048 2.384382 GTTTCGACATGTGGTTGCAAG 58.616 47.619 1.15 0.00 0.00 4.01
1986 2052 0.941542 ACCGTTTCGACATGTGGTTG 59.058 50.000 1.15 0.00 0.00 3.77
2145 2225 6.318900 ACTTGGAGAAAAGTTTAGTCCACTTG 59.681 38.462 15.34 11.86 37.05 3.16
2146 2226 6.318900 CACTTGGAGAAAAGTTTAGTCCACTT 59.681 38.462 15.34 5.90 38.34 3.16
2153 2233 8.624776 AGATGAAACACTTGGAGAAAAGTTTAG 58.375 33.333 0.00 0.00 38.34 1.85
2188 2268 5.012239 ACATCACTGAATGGTGCAACTAAT 58.988 37.500 2.04 0.00 44.04 1.73
2203 2283 8.605746 ACAACAAAATTTTGATGAACATCACTG 58.394 29.630 34.40 14.13 46.49 3.66
2407 2492 6.293407 CCTTACTAATTTGTACCCATGATGCG 60.293 42.308 0.00 0.00 0.00 4.73
2684 5497 5.422650 GTGTAAGTCTTCCTCCTAGACCAAT 59.577 44.000 0.00 0.00 42.35 3.16
2706 5519 6.164176 GGTCCATTATAGATAGAAACCGGTG 58.836 44.000 8.52 0.00 0.00 4.94
2841 5656 4.932146 TGGTTTAAGCAAAGTCTTCAAGC 58.068 39.130 0.00 0.00 31.80 4.01
3000 5822 2.103094 TGTGGTGAGGTGAAACTCTCTG 59.897 50.000 0.00 0.00 38.32 3.35
3001 5823 2.398588 TGTGGTGAGGTGAAACTCTCT 58.601 47.619 0.00 0.00 38.32 3.10
3004 5826 1.604278 GCTTGTGGTGAGGTGAAACTC 59.396 52.381 0.00 0.00 36.74 3.01
3023 5845 9.142515 TGAAATGAATAACAGTTGATGAAATGC 57.857 29.630 0.00 0.00 36.92 3.56
3073 5896 9.594936 TCTTTGGGTCCTAAAATAAATCAAAGA 57.405 29.630 0.00 0.00 42.57 2.52
3237 6064 4.021102 CACTACCCATTTGTGGAGAGTT 57.979 45.455 0.00 0.00 0.00 3.01
3266 6093 4.479619 CTTTTCCAAATCCTTCTGAAGCG 58.520 43.478 11.93 5.82 0.00 4.68
3331 6158 6.000840 TGCTTGTCATTTGGAGTAACATACA 58.999 36.000 0.00 0.00 0.00 2.29
3567 6438 9.607988 ACCACTATAAATACATTCGAACATGAA 57.392 29.630 0.00 0.00 0.00 2.57
3636 6527 4.994907 AATACACAGTGTATAGCCGACA 57.005 40.909 23.81 0.00 42.29 4.35
3637 6528 6.976925 ACTAAAATACACAGTGTATAGCCGAC 59.023 38.462 23.81 0.00 42.29 4.79
3673 6568 4.794169 ACGGCATCAAACATAACACTTTC 58.206 39.130 0.00 0.00 0.00 2.62
3763 6662 5.446709 CGCAAGAATAGGCAATGTATTCAG 58.553 41.667 6.90 1.69 38.75 3.02
3791 6690 5.417266 TGAGACACACAAAAATGGTTCTCAA 59.583 36.000 0.00 0.00 0.00 3.02
3821 6723 1.243902 AGTTTTCCCGACGTACCGTA 58.756 50.000 0.00 0.00 41.37 4.02
3910 6821 2.253610 TCGTCCACCATTTGTCTAGGT 58.746 47.619 0.00 0.00 35.65 3.08
3918 6829 2.289694 CCACTCTCTTCGTCCACCATTT 60.290 50.000 0.00 0.00 0.00 2.32
3959 6870 3.454812 GACAAAGCTACATCTCCCCCTTA 59.545 47.826 0.00 0.00 0.00 2.69
3986 6897 3.091545 CCTTAACCACCATGTCATTGCT 58.908 45.455 0.00 0.00 0.00 3.91
4000 6911 8.770438 TTGATAATTTTTGCATGTCCTTAACC 57.230 30.769 0.00 0.00 0.00 2.85
4019 6930 5.252863 TCCCCACTCATTTCCTTCTTGATAA 59.747 40.000 0.00 0.00 0.00 1.75
4022 6933 2.986019 TCCCCACTCATTTCCTTCTTGA 59.014 45.455 0.00 0.00 0.00 3.02
4024 6935 3.260205 TCTCCCCACTCATTTCCTTCTT 58.740 45.455 0.00 0.00 0.00 2.52
4100 7011 6.314896 GGATCAATGGTTGTTCTAGTTCAGAG 59.685 42.308 0.00 0.00 33.83 3.35
4116 7027 9.816354 AAATATAAAAGGAAAACGGATCAATGG 57.184 29.630 0.00 0.00 0.00 3.16
4166 7078 6.152323 ACTTCACCTCGTAGACAAGCTAATTA 59.848 38.462 0.00 0.00 0.00 1.40
4211 7123 5.213891 TCACCATGCTATATGTTGTCGAT 57.786 39.130 0.00 0.00 0.00 3.59
4267 7179 5.954150 AGAAGCAATACCATCCAACATTCTT 59.046 36.000 0.00 0.00 0.00 2.52
4268 7180 5.513233 AGAAGCAATACCATCCAACATTCT 58.487 37.500 0.00 0.00 0.00 2.40
4286 7198 6.706716 GGTACTCCAACATCCTTTATAGAAGC 59.293 42.308 0.00 0.00 0.00 3.86
4356 7268 0.108662 CACATGCTACCTGTCAGCGA 60.109 55.000 0.00 0.00 42.13 4.93
4359 7271 2.749280 TGACACATGCTACCTGTCAG 57.251 50.000 10.99 0.00 39.47 3.51
4364 7276 0.539051 GCTCCTGACACATGCTACCT 59.461 55.000 0.00 0.00 0.00 3.08
4368 7280 1.298993 CAGGCTCCTGACACATGCT 59.701 57.895 10.33 0.00 46.30 3.79
4417 7329 1.371558 GTCCAAGTCCTTGCCGTCT 59.628 57.895 1.40 0.00 39.16 4.18
4430 7342 0.321564 CTTCCAGCCATGTCGTCCAA 60.322 55.000 0.00 0.00 0.00 3.53
4434 7346 1.296715 GACCTTCCAGCCATGTCGT 59.703 57.895 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.