Multiple sequence alignment - TraesCS3B01G327300

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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 TraesCS3B01G327300 chr3B 100.000 2834 0 0 1 2834 527910826 527907993 0.000000e+00 5234.0
1 TraesCS3B01G327300 chr3D 94.572 1308 40 7 1493 2798 402471994 402470716 0.000000e+00 1993.0
2 TraesCS3B01G327300 chr3D 94.616 743 25 5 635 1373 402472994 402472263 0.000000e+00 1136.0
3 TraesCS3B01G327300 chr3D 93.392 227 13 2 72 297 402488184 402487959 4.520000e-88 335.0
4 TraesCS3B01G327300 chr3D 90.393 229 18 3 367 594 402487738 402487513 5.940000e-77 298.0
5 TraesCS3B01G327300 chr3D 96.629 89 3 0 1407 1495 402472196 402472108 6.330000e-32 148.0
6 TraesCS3B01G327300 chr3D 100.000 41 0 0 2794 2834 402470472 402470432 3.030000e-10 76.8
7 TraesCS3B01G327300 chr3D 88.060 67 3 4 14 76 157440639 157440574 1.090000e-09 75.0
8 TraesCS3B01G327300 chr3A 94.311 914 47 5 1889 2798 523324350 523323438 0.000000e+00 1395.0
9 TraesCS3B01G327300 chr3A 91.656 767 26 9 611 1373 523328508 523327776 0.000000e+00 1027.0
10 TraesCS3B01G327300 chr3A 97.099 517 8 2 1375 1884 523327581 523327065 0.000000e+00 865.0
11 TraesCS3B01G327300 chr3A 92.408 461 28 6 72 528 523328971 523328514 0.000000e+00 651.0
12 TraesCS3B01G327300 chr3A 89.516 248 24 1 1944 2191 523322210 523322455 2.120000e-81 313.0
13 TraesCS3B01G327300 chr3A 96.154 52 0 2 27 77 480969533 480969483 1.810000e-12 84.2
14 TraesCS3B01G327300 chr3A 100.000 41 0 0 2794 2834 523323193 523323153 3.030000e-10 76.8
15 TraesCS3B01G327300 chr2B 79.830 352 54 9 2203 2545 24051412 24051755 1.010000e-59 241.0
16 TraesCS3B01G327300 chr2B 92.857 56 3 1 27 82 230245400 230245346 2.340000e-11 80.5
17 TraesCS3B01G327300 chr2D 94.643 56 1 2 27 81 246544429 246544375 5.030000e-13 86.1
18 TraesCS3B01G327300 chr5D 96.154 52 0 2 27 77 373214610 373214660 1.810000e-12 84.2
19 TraesCS3B01G327300 chr1A 96.078 51 2 0 27 77 7181324 7181274 1.810000e-12 84.2
20 TraesCS3B01G327300 chr1B 93.103 58 1 3 27 83 545800271 545800216 6.510000e-12 82.4
21 TraesCS3B01G327300 chr1B 92.857 56 2 2 27 81 188791900 188791954 2.340000e-11 80.5
22 TraesCS3B01G327300 chr6B 81.928 83 14 1 27 109 183717384 183717303 5.070000e-08 69.4


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 TraesCS3B01G327300 chr3B 527907993 527910826 2833 True 5234.00 5234 100.00000 1 2834 1 chr3B.!!$R1 2833
1 TraesCS3B01G327300 chr3D 402470432 402472994 2562 True 838.45 1993 96.45425 635 2834 4 chr3D.!!$R2 2199
2 TraesCS3B01G327300 chr3D 402487513 402488184 671 True 316.50 335 91.89250 72 594 2 chr3D.!!$R3 522
3 TraesCS3B01G327300 chr3A 523323153 523328971 5818 True 802.96 1395 95.09480 72 2834 5 chr3A.!!$R2 2762

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
460 614 0.179045 GGGCTATGCGGATTGACTGT 60.179 55.0 4.01 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 5450 0.25077 GGTCGCCCAAAGAACCTTCT 60.251 55.0 0.0 0.0 39.74 2.85 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
25 26 7.903145 TGCATATTATAAGTTACTCCATCCGT 58.097 34.615 0.00 0.00 0.00 4.69
26 27 8.033038 TGCATATTATAAGTTACTCCATCCGTC 58.967 37.037 0.00 0.00 0.00 4.79
27 28 8.251721 GCATATTATAAGTTACTCCATCCGTCT 58.748 37.037 0.00 0.00 0.00 4.18
30 31 8.701908 ATTATAAGTTACTCCATCCGTCTACA 57.298 34.615 0.00 0.00 0.00 2.74
31 32 4.715527 AAGTTACTCCATCCGTCTACAC 57.284 45.455 0.00 0.00 0.00 2.90
32 33 3.965694 AGTTACTCCATCCGTCTACACT 58.034 45.455 0.00 0.00 0.00 3.55
33 34 5.108187 AGTTACTCCATCCGTCTACACTA 57.892 43.478 0.00 0.00 0.00 2.74
34 35 5.124645 AGTTACTCCATCCGTCTACACTAG 58.875 45.833 0.00 0.00 0.00 2.57
35 36 3.648507 ACTCCATCCGTCTACACTAGT 57.351 47.619 0.00 0.00 0.00 2.57
36 37 3.280295 ACTCCATCCGTCTACACTAGTG 58.720 50.000 21.44 21.44 0.00 2.74
37 38 2.022195 TCCATCCGTCTACACTAGTGC 58.978 52.381 22.90 5.49 0.00 4.40
38 39 2.025155 CCATCCGTCTACACTAGTGCT 58.975 52.381 22.90 12.27 0.00 4.40
39 40 3.118149 TCCATCCGTCTACACTAGTGCTA 60.118 47.826 22.90 12.72 0.00 3.49
40 41 3.630769 CCATCCGTCTACACTAGTGCTAA 59.369 47.826 22.90 7.81 0.00 3.09
41 42 4.097437 CCATCCGTCTACACTAGTGCTAAA 59.903 45.833 22.90 5.31 0.00 1.85
42 43 5.393787 CCATCCGTCTACACTAGTGCTAAAA 60.394 44.000 22.90 3.32 0.00 1.52
43 44 5.710513 TCCGTCTACACTAGTGCTAAAAA 57.289 39.130 22.90 0.69 0.00 1.94
66 67 8.848474 AAAACATCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
67 68 6.546428 ACATCTTATATTATGGGACGGAGG 57.454 41.667 0.00 0.00 0.00 4.30
68 69 5.425539 ACATCTTATATTATGGGACGGAGGG 59.574 44.000 0.00 0.00 0.00 4.30
69 70 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
70 71 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
189 191 8.771920 TCTCATTTAATTGTGTGTCGTCTTAT 57.228 30.769 0.00 0.00 0.00 1.73
190 192 9.863845 TCTCATTTAATTGTGTGTCGTCTTATA 57.136 29.630 0.00 0.00 0.00 0.98
309 339 6.115448 AGCTTATAATCTTACCGGCAATCT 57.885 37.500 0.00 0.00 0.00 2.40
314 344 9.268268 CTTATAATCTTACCGGCAATCTAAACA 57.732 33.333 0.00 0.00 0.00 2.83
346 376 3.390967 CCCACCCAAACCTCTCAATTTTT 59.609 43.478 0.00 0.00 0.00 1.94
460 614 0.179045 GGGCTATGCGGATTGACTGT 60.179 55.000 4.01 0.00 0.00 3.55
465 619 0.955428 ATGCGGATTGACTGTTGCGT 60.955 50.000 0.00 0.00 0.00 5.24
479 633 5.885881 ACTGTTGCGTAATTTTTCACTCAA 58.114 33.333 0.00 0.00 0.00 3.02
585 740 1.247567 CAAGGCGGGTCAAATCAACT 58.752 50.000 0.00 0.00 0.00 3.16
593 748 3.684788 CGGGTCAAATCAACTGAGGTAAG 59.315 47.826 0.00 0.00 0.00 2.34
594 749 4.652822 GGGTCAAATCAACTGAGGTAAGT 58.347 43.478 0.00 0.00 0.00 2.24
595 750 5.070685 GGGTCAAATCAACTGAGGTAAGTT 58.929 41.667 0.00 0.00 41.08 2.66
596 751 5.181433 GGGTCAAATCAACTGAGGTAAGTTC 59.819 44.000 0.00 0.00 38.34 3.01
597 752 5.181433 GGTCAAATCAACTGAGGTAAGTTCC 59.819 44.000 0.00 0.00 38.34 3.62
598 753 5.181433 GTCAAATCAACTGAGGTAAGTTCCC 59.819 44.000 0.00 0.00 38.34 3.97
599 754 3.611766 ATCAACTGAGGTAAGTTCCCG 57.388 47.619 0.00 0.00 38.34 5.14
600 755 1.001633 TCAACTGAGGTAAGTTCCCGC 59.998 52.381 0.00 0.00 38.34 6.13
601 756 0.323957 AACTGAGGTAAGTTCCCGCC 59.676 55.000 0.00 0.00 35.44 6.13
602 757 0.834687 ACTGAGGTAAGTTCCCGCCA 60.835 55.000 0.00 0.00 0.00 5.69
603 758 0.323629 CTGAGGTAAGTTCCCGCCAA 59.676 55.000 0.00 0.00 0.00 4.52
604 759 0.766131 TGAGGTAAGTTCCCGCCAAA 59.234 50.000 0.00 0.00 0.00 3.28
605 760 1.143277 TGAGGTAAGTTCCCGCCAAAA 59.857 47.619 0.00 0.00 0.00 2.44
606 761 2.232399 GAGGTAAGTTCCCGCCAAAAA 58.768 47.619 0.00 0.00 0.00 1.94
632 787 2.169832 TCAACTGAGGTAAGCAGCAC 57.830 50.000 0.00 0.00 36.86 4.40
663 818 2.094338 ACGGACGACCTCTTTGGAATAC 60.094 50.000 1.72 0.00 39.71 1.89
664 819 2.094390 CGGACGACCTCTTTGGAATACA 60.094 50.000 1.72 0.00 39.71 2.29
681 836 5.516339 GGAATACAACCAAGATGCAAAATCG 59.484 40.000 0.00 0.00 0.00 3.34
682 837 5.643379 ATACAACCAAGATGCAAAATCGT 57.357 34.783 0.00 0.00 0.00 3.73
683 838 3.641648 ACAACCAAGATGCAAAATCGTG 58.358 40.909 0.00 0.00 0.00 4.35
685 840 2.513753 ACCAAGATGCAAAATCGTGGA 58.486 42.857 22.45 0.00 46.14 4.02
686 841 2.890311 ACCAAGATGCAAAATCGTGGAA 59.110 40.909 22.45 0.00 46.14 3.53
687 842 3.320541 ACCAAGATGCAAAATCGTGGAAA 59.679 39.130 22.45 0.00 46.14 3.13
688 843 4.021192 ACCAAGATGCAAAATCGTGGAAAT 60.021 37.500 22.45 3.00 46.14 2.17
689 844 4.931002 CCAAGATGCAAAATCGTGGAAATT 59.069 37.500 13.59 0.00 46.14 1.82
719 874 0.459489 GTGTAGCTGAGAGCCTGAGG 59.541 60.000 0.00 0.00 43.77 3.86
898 1053 5.764686 TCCATAATAAATTCACAGCATCGCT 59.235 36.000 0.00 0.00 40.77 4.93
1039 1194 2.390599 CGGACGCCAGTGTTCATGG 61.391 63.158 0.00 0.00 41.04 3.66
1040 1195 1.302511 GGACGCCAGTGTTCATGGT 60.303 57.895 0.00 0.00 40.17 3.55
1107 1262 3.329520 TCCTTAAGGTGCTAAGCTCCAAA 59.670 43.478 21.04 0.00 43.69 3.28
1198 1353 2.473760 CCTCGTCGGCGATGAGACT 61.474 63.158 44.27 0.00 45.52 3.24
1225 1380 2.106683 CCTCTTTACCGCCCGCAAG 61.107 63.158 0.00 0.00 0.00 4.01
1294 1470 6.449448 GCTAAATACGTAGCATCTGGTAAC 57.551 41.667 0.08 0.00 44.94 2.50
1295 1471 5.404667 GCTAAATACGTAGCATCTGGTAACC 59.595 44.000 0.08 0.00 44.94 2.85
1296 1472 3.637998 ATACGTAGCATCTGGTAACCG 57.362 47.619 0.08 0.00 0.00 4.44
1297 1473 0.458669 ACGTAGCATCTGGTAACCGG 59.541 55.000 0.00 0.00 0.00 5.28
1298 1474 0.874607 CGTAGCATCTGGTAACCGGC 60.875 60.000 0.00 0.00 0.00 6.13
1299 1475 0.177141 GTAGCATCTGGTAACCGGCA 59.823 55.000 0.00 0.00 0.00 5.69
1300 1476 1.128200 TAGCATCTGGTAACCGGCAT 58.872 50.000 0.00 0.00 0.00 4.40
1301 1477 0.179045 AGCATCTGGTAACCGGCATC 60.179 55.000 0.00 0.00 0.00 3.91
1302 1478 0.463654 GCATCTGGTAACCGGCATCA 60.464 55.000 0.00 0.00 0.00 3.07
1303 1479 1.815408 GCATCTGGTAACCGGCATCAT 60.815 52.381 0.00 0.00 0.00 2.45
1304 1480 1.875514 CATCTGGTAACCGGCATCATG 59.124 52.381 0.00 0.00 0.00 3.07
1305 1481 0.908910 TCTGGTAACCGGCATCATGT 59.091 50.000 0.00 0.00 0.00 3.21
1306 1482 1.016627 CTGGTAACCGGCATCATGTG 58.983 55.000 0.00 0.00 0.00 3.21
1307 1483 0.326595 TGGTAACCGGCATCATGTGT 59.673 50.000 0.00 0.00 0.00 3.72
1308 1484 1.271652 TGGTAACCGGCATCATGTGTT 60.272 47.619 0.00 0.00 0.00 3.32
1309 1485 1.132262 GGTAACCGGCATCATGTGTTG 59.868 52.381 0.00 0.00 0.00 3.33
1342 1518 1.111116 TTTGACTCGGGGTGTCTCGT 61.111 55.000 0.00 0.00 35.63 4.18
1388 1760 3.685139 ATTGCAGAGTATGGATACGGG 57.315 47.619 0.00 0.00 38.28 5.28
1396 1768 1.961394 GTATGGATACGGGCAGAGACA 59.039 52.381 0.00 0.00 42.51 3.41
1398 1770 1.065928 GGATACGGGCAGAGACACG 59.934 63.158 0.00 0.00 0.00 4.49
2183 5389 0.393077 CCTCTAAACCGGCGATCCAT 59.607 55.000 9.30 0.00 0.00 3.41
2218 5424 6.855763 ATTTCATCCAAACATCTTTGCCTA 57.144 33.333 0.00 0.00 36.22 3.93
2224 5430 3.488047 CCAAACATCTTTGCCTATGCTCG 60.488 47.826 0.00 0.00 36.22 5.03
2244 5450 3.004629 TCGAACACGTTTACTTGGCTCTA 59.995 43.478 0.00 0.00 0.00 2.43
2399 5605 7.147880 CGGACCCTTATAATTACCTCTCCTATG 60.148 44.444 0.00 0.00 0.00 2.23
2457 5663 1.654220 CACCCAAAGTCGCCACAAG 59.346 57.895 0.00 0.00 0.00 3.16
2549 5755 7.502060 AACATCTTCTTGAAGAATCCTCCTA 57.498 36.000 15.76 0.00 33.13 2.94
2579 5785 3.697045 CTGAGGAATTGAGTCTACTCCGT 59.303 47.826 7.63 0.00 42.20 4.69
2583 5789 0.179134 ATTGAGTCTACTCCGTGCGC 60.179 55.000 0.00 0.00 42.20 6.09
2605 5811 3.305950 CGCAAAATTTGAGGGTGATCCAA 60.306 43.478 10.26 0.00 38.24 3.53
2607 5813 4.502950 GCAAAATTTGAGGGTGATCCAACA 60.503 41.667 10.26 0.00 38.24 3.33
2661 5868 4.578928 GGACCTGTTCAGCAAGTTTTTCTA 59.421 41.667 0.00 0.00 0.00 2.10
2675 5882 7.009265 GCAAGTTTTTCTACAAGTTCAAACCTC 59.991 37.037 0.00 0.00 0.00 3.85
2676 5883 7.939784 AGTTTTTCTACAAGTTCAAACCTCT 57.060 32.000 0.00 0.00 0.00 3.69
2761 5970 5.359194 TGATCTTAGGGTGTCTTCAATCC 57.641 43.478 0.00 0.00 0.00 3.01
2769 5978 3.049344 GGTGTCTTCAATCCCTCCCTAT 58.951 50.000 0.00 0.00 0.00 2.57
2770 5979 3.459969 GGTGTCTTCAATCCCTCCCTATT 59.540 47.826 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.251721 AGACGGATGGAGTAACTTATAATATGC 58.748 37.037 0.00 0.00 0.00 3.14
4 5 9.797642 TGTAGACGGATGGAGTAACTTATAATA 57.202 33.333 0.00 0.00 0.00 0.98
5 6 8.574737 GTGTAGACGGATGGAGTAACTTATAAT 58.425 37.037 0.00 0.00 0.00 1.28
6 7 7.776969 AGTGTAGACGGATGGAGTAACTTATAA 59.223 37.037 0.00 0.00 0.00 0.98
8 9 6.127793 AGTGTAGACGGATGGAGTAACTTAT 58.872 40.000 0.00 0.00 0.00 1.73
9 10 5.503927 AGTGTAGACGGATGGAGTAACTTA 58.496 41.667 0.00 0.00 0.00 2.24
10 11 4.342359 AGTGTAGACGGATGGAGTAACTT 58.658 43.478 0.00 0.00 0.00 2.66
11 12 3.965694 AGTGTAGACGGATGGAGTAACT 58.034 45.455 0.00 0.00 0.00 2.24
12 13 4.880696 ACTAGTGTAGACGGATGGAGTAAC 59.119 45.833 0.00 0.00 0.00 2.50
13 14 4.880120 CACTAGTGTAGACGGATGGAGTAA 59.120 45.833 15.06 0.00 0.00 2.24
14 15 4.449131 CACTAGTGTAGACGGATGGAGTA 58.551 47.826 15.06 0.00 0.00 2.59
15 16 3.280295 CACTAGTGTAGACGGATGGAGT 58.720 50.000 15.06 0.00 0.00 3.85
16 17 2.033550 GCACTAGTGTAGACGGATGGAG 59.966 54.545 23.44 0.00 0.00 3.86
17 18 2.022195 GCACTAGTGTAGACGGATGGA 58.978 52.381 23.44 0.00 0.00 3.41
18 19 2.025155 AGCACTAGTGTAGACGGATGG 58.975 52.381 23.44 0.00 0.00 3.51
19 20 4.895224 TTAGCACTAGTGTAGACGGATG 57.105 45.455 23.44 0.00 0.00 3.51
20 21 5.909621 TTTTAGCACTAGTGTAGACGGAT 57.090 39.130 23.44 0.00 0.00 4.18
21 22 5.710513 TTTTTAGCACTAGTGTAGACGGA 57.289 39.130 23.44 3.18 0.00 4.69
40 41 9.284968 CTCCGTCCCATAATATAAGATGTTTTT 57.715 33.333 0.00 0.00 0.00 1.94
41 42 7.883311 CCTCCGTCCCATAATATAAGATGTTTT 59.117 37.037 0.00 0.00 0.00 2.43
42 43 7.394816 CCTCCGTCCCATAATATAAGATGTTT 58.605 38.462 0.00 0.00 0.00 2.83
43 44 6.070194 CCCTCCGTCCCATAATATAAGATGTT 60.070 42.308 0.00 0.00 0.00 2.71
44 45 5.425539 CCCTCCGTCCCATAATATAAGATGT 59.574 44.000 0.00 0.00 0.00 3.06
45 46 5.661312 TCCCTCCGTCCCATAATATAAGATG 59.339 44.000 0.00 0.00 0.00 2.90
46 47 5.850278 TCCCTCCGTCCCATAATATAAGAT 58.150 41.667 0.00 0.00 0.00 2.40
47 48 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
48 49 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
49 50 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
50 51 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
51 52 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
52 53 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
53 54 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
54 55 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
55 56 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
56 57 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
57 58 1.144503 GATACTACTCCCTCCGTCCCA 59.855 57.143 0.00 0.00 0.00 4.37
58 59 1.424684 AGATACTACTCCCTCCGTCCC 59.575 57.143 0.00 0.00 0.00 4.46
59 60 2.955342 AGATACTACTCCCTCCGTCC 57.045 55.000 0.00 0.00 0.00 4.79
60 61 5.226194 TCTAAGATACTACTCCCTCCGTC 57.774 47.826 0.00 0.00 0.00 4.79
61 62 5.846528 ATCTAAGATACTACTCCCTCCGT 57.153 43.478 0.00 0.00 0.00 4.69
62 63 6.005198 ACAATCTAAGATACTACTCCCTCCG 58.995 44.000 0.00 0.00 0.00 4.63
63 64 7.235804 AGACAATCTAAGATACTACTCCCTCC 58.764 42.308 0.00 0.00 0.00 4.30
64 65 7.940137 TGAGACAATCTAAGATACTACTCCCTC 59.060 40.741 0.00 0.00 0.00 4.30
65 66 7.817440 TGAGACAATCTAAGATACTACTCCCT 58.183 38.462 0.00 0.00 0.00 4.20
66 67 8.644374 ATGAGACAATCTAAGATACTACTCCC 57.356 38.462 0.00 0.00 0.00 4.30
97 98 8.400947 GTTGTCTTATATTGTGTCATGCTTGAT 58.599 33.333 5.49 0.00 33.56 2.57
99 101 7.529158 TGTTGTCTTATATTGTGTCATGCTTG 58.471 34.615 0.00 0.00 0.00 4.01
143 145 7.885297 TGAGAAAAGAAAGGATTTGTACCATG 58.115 34.615 0.00 0.00 39.27 3.66
158 160 8.402472 ACGACACACAATTAAATGAGAAAAGAA 58.598 29.630 0.00 0.00 0.00 2.52
326 356 5.049828 GTGAAAAATTGAGAGGTTTGGGTG 58.950 41.667 0.00 0.00 0.00 4.61
346 376 2.815945 TTAACGGGGGCGTTGGTGA 61.816 57.895 0.00 0.00 33.80 4.02
422 576 1.075970 CGAGGATGAGTGGGGGAGA 60.076 63.158 0.00 0.00 0.00 3.71
460 614 4.737765 GCAGTTGAGTGAAAAATTACGCAA 59.262 37.500 0.00 0.00 34.90 4.85
493 648 5.242171 TCACTCGGTTGTTTCTGTAGATGTA 59.758 40.000 0.00 0.00 0.00 2.29
534 689 4.507756 GCAGCCGAGTGAAAAGAAAAATTT 59.492 37.500 0.00 0.00 0.00 1.82
542 697 5.149054 CTATTAAGCAGCCGAGTGAAAAG 57.851 43.478 0.00 0.00 0.00 2.27
565 720 0.243636 GTTGATTTGACCCGCCTTGG 59.756 55.000 0.00 0.00 37.55 3.61
574 729 5.181433 GGGAACTTACCTCAGTTGATTTGAC 59.819 44.000 0.00 0.00 37.11 3.18
585 740 0.766131 TTTGGCGGGAACTTACCTCA 59.234 50.000 0.00 0.00 0.00 3.86
608 763 4.584325 TGCTGCTTACCTCAGTTGATTTTT 59.416 37.500 0.00 0.00 34.21 1.94
609 764 4.022849 GTGCTGCTTACCTCAGTTGATTTT 60.023 41.667 0.00 0.00 34.21 1.82
610 765 3.503748 GTGCTGCTTACCTCAGTTGATTT 59.496 43.478 0.00 0.00 34.21 2.17
611 766 3.077359 GTGCTGCTTACCTCAGTTGATT 58.923 45.455 0.00 0.00 34.21 2.57
612 767 2.704572 GTGCTGCTTACCTCAGTTGAT 58.295 47.619 0.00 0.00 34.21 2.57
613 768 1.605457 CGTGCTGCTTACCTCAGTTGA 60.605 52.381 0.00 0.00 34.21 3.18
614 769 0.792640 CGTGCTGCTTACCTCAGTTG 59.207 55.000 0.00 0.00 34.21 3.16
615 770 0.679505 TCGTGCTGCTTACCTCAGTT 59.320 50.000 0.00 0.00 34.21 3.16
616 771 0.679505 TTCGTGCTGCTTACCTCAGT 59.320 50.000 0.00 0.00 34.21 3.41
617 772 1.067565 TCTTCGTGCTGCTTACCTCAG 60.068 52.381 0.00 0.00 34.79 3.35
618 773 0.966179 TCTTCGTGCTGCTTACCTCA 59.034 50.000 0.00 0.00 0.00 3.86
619 774 1.067495 AGTCTTCGTGCTGCTTACCTC 60.067 52.381 0.00 0.00 0.00 3.85
620 775 0.969894 AGTCTTCGTGCTGCTTACCT 59.030 50.000 0.00 0.00 0.00 3.08
621 776 2.649331 TAGTCTTCGTGCTGCTTACC 57.351 50.000 0.00 0.00 0.00 2.85
622 777 3.724751 CGTATAGTCTTCGTGCTGCTTAC 59.275 47.826 0.00 0.00 0.00 2.34
623 778 3.242969 CCGTATAGTCTTCGTGCTGCTTA 60.243 47.826 0.00 0.00 0.00 3.09
624 779 2.479730 CCGTATAGTCTTCGTGCTGCTT 60.480 50.000 0.00 0.00 0.00 3.91
625 780 1.065701 CCGTATAGTCTTCGTGCTGCT 59.934 52.381 0.00 0.00 0.00 4.24
632 787 2.208431 AGGTCGTCCGTATAGTCTTCG 58.792 52.381 0.00 0.00 39.05 3.79
663 818 2.988493 CCACGATTTTGCATCTTGGTTG 59.012 45.455 3.70 0.00 34.06 3.77
664 819 2.890311 TCCACGATTTTGCATCTTGGTT 59.110 40.909 10.20 0.00 38.26 3.67
683 838 3.915437 ACACAACGATGGACAATTTCC 57.085 42.857 0.00 1.09 46.13 3.13
684 839 4.154195 AGCTACACAACGATGGACAATTTC 59.846 41.667 0.00 0.00 0.00 2.17
685 840 4.072131 AGCTACACAACGATGGACAATTT 58.928 39.130 0.00 0.00 0.00 1.82
686 841 3.436704 CAGCTACACAACGATGGACAATT 59.563 43.478 0.00 0.00 0.00 2.32
687 842 3.002791 CAGCTACACAACGATGGACAAT 58.997 45.455 0.00 0.00 0.00 2.71
688 843 2.036604 TCAGCTACACAACGATGGACAA 59.963 45.455 0.00 0.00 0.00 3.18
689 844 1.616374 TCAGCTACACAACGATGGACA 59.384 47.619 0.00 0.00 0.00 4.02
719 874 1.472376 CGTCTTGAGGATCCCTTGAGC 60.472 57.143 8.55 0.00 31.76 4.26
898 1053 1.777878 TGGTCTGCCAAAACCCTAGAA 59.222 47.619 0.00 0.00 42.83 2.10
1029 1184 0.401738 CTCCCACCACCATGAACACT 59.598 55.000 0.00 0.00 0.00 3.55
1039 1194 1.524482 GCCTGAGATCTCCCACCAC 59.476 63.158 20.03 0.35 0.00 4.16
1040 1195 1.690633 GGCCTGAGATCTCCCACCA 60.691 63.158 20.03 0.41 0.00 4.17
1087 1242 4.579869 TCTTTGGAGCTTAGCACCTTAAG 58.420 43.478 20.42 20.43 39.93 1.85
1107 1262 2.494073 GTCTTGGTCTCGGTCTTGATCT 59.506 50.000 0.00 0.00 0.00 2.75
1225 1380 1.703513 GGGGATGTATTACCCTGGTCC 59.296 57.143 0.00 0.00 44.97 4.46
1290 1466 1.810151 ACAACACATGATGCCGGTTAC 59.190 47.619 1.90 0.00 0.00 2.50
1291 1467 2.192664 ACAACACATGATGCCGGTTA 57.807 45.000 1.90 0.00 0.00 2.85
1292 1468 1.000385 CAACAACACATGATGCCGGTT 60.000 47.619 1.90 0.00 0.00 4.44
1293 1469 0.597568 CAACAACACATGATGCCGGT 59.402 50.000 1.90 0.00 0.00 5.28
1294 1470 0.597568 ACAACAACACATGATGCCGG 59.402 50.000 0.00 0.00 35.35 6.13
1295 1471 1.001487 ACACAACAACACATGATGCCG 60.001 47.619 0.00 0.00 35.35 5.69
1296 1472 2.798976 ACACAACAACACATGATGCC 57.201 45.000 0.00 0.00 35.35 4.40
1297 1473 6.580963 TTTAAACACAACAACACATGATGC 57.419 33.333 0.00 0.00 35.35 3.91
1298 1474 8.578308 AGATTTAAACACAACAACACATGATG 57.422 30.769 0.00 0.00 37.79 3.07
1299 1475 9.598517 AAAGATTTAAACACAACAACACATGAT 57.401 25.926 0.00 0.00 0.00 2.45
1300 1476 8.867935 CAAAGATTTAAACACAACAACACATGA 58.132 29.630 0.00 0.00 0.00 3.07
1301 1477 8.867935 TCAAAGATTTAAACACAACAACACATG 58.132 29.630 0.00 0.00 0.00 3.21
1302 1478 8.868916 GTCAAAGATTTAAACACAACAACACAT 58.131 29.630 0.00 0.00 0.00 3.21
1303 1479 8.085296 AGTCAAAGATTTAAACACAACAACACA 58.915 29.630 0.00 0.00 0.00 3.72
1304 1480 8.460831 AGTCAAAGATTTAAACACAACAACAC 57.539 30.769 0.00 0.00 0.00 3.32
1305 1481 7.483375 CGAGTCAAAGATTTAAACACAACAACA 59.517 33.333 0.00 0.00 0.00 3.33
1306 1482 7.044314 CCGAGTCAAAGATTTAAACACAACAAC 60.044 37.037 0.00 0.00 0.00 3.32
1307 1483 6.970043 CCGAGTCAAAGATTTAAACACAACAA 59.030 34.615 0.00 0.00 0.00 2.83
1308 1484 6.459024 CCCGAGTCAAAGATTTAAACACAACA 60.459 38.462 0.00 0.00 0.00 3.33
1309 1485 5.912955 CCCGAGTCAAAGATTTAAACACAAC 59.087 40.000 0.00 0.00 0.00 3.32
1342 1518 8.768957 TTTGCACATTAATTTAAGCATAAGCA 57.231 26.923 0.00 0.00 45.49 3.91
1373 1552 2.108425 TCTCTGCCCGTATCCATACTCT 59.892 50.000 0.00 0.00 0.00 3.24
1388 1760 2.531206 GACAATACTCCGTGTCTCTGC 58.469 52.381 0.00 0.00 40.82 4.26
1396 1768 4.819105 TCAATCAAGGACAATACTCCGT 57.181 40.909 0.00 0.00 35.20 4.69
1398 1770 6.115446 TGTGATCAATCAAGGACAATACTCC 58.885 40.000 0.00 0.00 38.75 3.85
2183 5389 9.685276 ATGTTTGGATGAAATTCATAGTGAGTA 57.315 29.630 8.64 0.00 37.20 2.59
2218 5424 2.478894 CCAAGTAAACGTGTTCGAGCAT 59.521 45.455 4.92 0.00 40.62 3.79
2224 5430 4.553323 TCTAGAGCCAAGTAAACGTGTTC 58.447 43.478 0.00 0.00 0.00 3.18
2244 5450 0.250770 GGTCGCCCAAAGAACCTTCT 60.251 55.000 0.00 0.00 39.74 2.85
2399 5605 1.224870 GGGTTTGGAGCCTAGGAGC 59.775 63.158 14.75 2.43 40.37 4.70
2457 5663 2.034842 CACGAGTTTCGCGATATCAACC 60.035 50.000 10.88 4.87 45.12 3.77
2506 5712 0.536687 TCGAGTCACCGAGAACAGGT 60.537 55.000 0.00 0.00 43.97 4.00
2507 5713 0.596577 TTCGAGTCACCGAGAACAGG 59.403 55.000 0.00 0.00 39.90 4.00
2579 5785 1.372748 CCCTCAAATTTTGCGCGCA 60.373 52.632 33.09 33.09 0.00 6.09
2583 5789 2.230992 TGGATCACCCTCAAATTTTGCG 59.769 45.455 4.19 0.00 35.38 4.85
2605 5811 1.522806 TCGCGGAAGTTTGCACTGT 60.523 52.632 6.13 0.00 31.60 3.55
2607 5813 2.594962 CGTCGCGGAAGTTTGCACT 61.595 57.895 6.13 0.00 33.11 4.40
2661 5868 4.402155 TGCAAATCAGAGGTTTGAACTTGT 59.598 37.500 6.91 0.00 38.51 3.16
2761 5970 6.183361 TGGATTGGAGAAATGTAATAGGGAGG 60.183 42.308 0.00 0.00 0.00 4.30
2769 5978 4.098349 GCTGCATGGATTGGAGAAATGTAA 59.902 41.667 0.00 0.00 46.09 2.41
2770 5979 3.633525 GCTGCATGGATTGGAGAAATGTA 59.366 43.478 0.00 0.00 46.09 2.29


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

AutoCloner maintained by Alex Coulton.