Multiple sequence alignment - TraesCS6D01G118900

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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 TraesCS6D01G118900 chr6D 100.000 4133 0 0 1 4133 84219110 84214978 0.000000e+00 7633
1 TraesCS6D01G118900 chr6D 91.414 2539 207 8 739 3274 84474272 84471742 0.000000e+00 3470
2 TraesCS6D01G118900 chr6D 88.079 2416 264 17 739 3135 84232079 84229669 0.000000e+00 2844
3 TraesCS6D01G118900 chr6D 85.588 2380 314 22 774 3135 84620238 84617870 0.000000e+00 2468
4 TraesCS6D01G118900 chr6D 86.022 2232 292 12 916 3135 84631062 84628839 0.000000e+00 2375
5 TraesCS6D01G118900 chr6D 84.108 2259 316 26 922 3163 84653944 84651712 0.000000e+00 2143
6 TraesCS6D01G118900 chr6D 92.427 647 29 14 22 657 84474908 84474271 0.000000e+00 905
7 TraesCS6D01G118900 chr6D 94.737 95 5 0 651 745 84218366 84218460 9.260000e-32 148
8 TraesCS6D01G118900 chr6A 98.002 2552 46 3 739 3289 101548410 101545863 0.000000e+00 4425
9 TraesCS6D01G118900 chr6A 88.843 2429 258 12 739 3163 101865617 101863198 0.000000e+00 2972
10 TraesCS6D01G118900 chr6A 88.230 2413 258 18 739 3135 101562894 101560492 0.000000e+00 2859
11 TraesCS6D01G118900 chr6A 88.874 2247 238 9 999 3241 101844965 101842727 0.000000e+00 2754
12 TraesCS6D01G118900 chr6A 96.809 658 19 2 1 657 101549065 101548409 0.000000e+00 1098
13 TraesCS6D01G118900 chr6A 93.363 663 35 5 1 657 101866275 101865616 0.000000e+00 972
14 TraesCS6D01G118900 chr6A 88.793 580 35 9 3399 3970 101545787 101545230 0.000000e+00 684
15 TraesCS6D01G118900 chr6A 84.444 360 34 11 3534 3889 101841651 101841310 6.620000e-88 335
16 TraesCS6D01G118900 chr6A 82.184 174 12 4 3961 4133 101542114 101541959 9.320000e-27 132
17 TraesCS6D01G118900 chr6B 92.757 2430 172 4 739 3165 160663427 160660999 0.000000e+00 3509
18 TraesCS6D01G118900 chr6B 88.643 2439 259 13 722 3158 160905158 160902736 0.000000e+00 2953
19 TraesCS6D01G118900 chr6B 85.938 2233 292 14 916 3135 160717020 160714797 0.000000e+00 2364
20 TraesCS6D01G118900 chr6B 92.826 683 36 7 1 674 160905965 160905287 0.000000e+00 977
21 TraesCS6D01G118900 chr6B 92.462 650 31 9 22 657 160664071 160663426 0.000000e+00 913
22 TraesCS6D01G118900 chr6B 83.273 275 23 12 164 426 159991525 159991262 8.940000e-57 231
23 TraesCS6D01G118900 chr6B 84.000 200 25 5 465 657 160664962 160664763 7.060000e-43 185
24 TraesCS6D01G118900 chr7B 95.745 94 4 0 650 743 440325598 440325691 7.160000e-33 152
25 TraesCS6D01G118900 chr1D 96.552 87 3 0 656 742 402722723 402722637 1.200000e-30 145
26 TraesCS6D01G118900 chr7D 94.565 92 5 0 651 742 506141364 506141455 4.310000e-30 143
27 TraesCS6D01G118900 chr2B 95.506 89 4 0 655 743 240186236 240186324 4.310000e-30 143
28 TraesCS6D01G118900 chr1B 92.000 100 8 0 649 748 164770457 164770358 1.550000e-29 141
29 TraesCS6D01G118900 chr7A 92.708 96 7 0 649 744 612025781 612025876 5.570000e-29 139
30 TraesCS6D01G118900 chr7A 91.753 97 8 0 649 745 129876932 129877028 7.210000e-28 135
31 TraesCS6D01G118900 chr3D 92.708 96 6 1 649 744 509255106 509255200 2.000000e-28 137


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 TraesCS6D01G118900 chr6D 84214978 84219110 4132 True 7633.000000 7633 100.000000 1 4133 1 chr6D.!!$R1 4132
1 TraesCS6D01G118900 chr6D 84229669 84232079 2410 True 2844.000000 2844 88.079000 739 3135 1 chr6D.!!$R2 2396
2 TraesCS6D01G118900 chr6D 84617870 84620238 2368 True 2468.000000 2468 85.588000 774 3135 1 chr6D.!!$R3 2361
3 TraesCS6D01G118900 chr6D 84628839 84631062 2223 True 2375.000000 2375 86.022000 916 3135 1 chr6D.!!$R4 2219
4 TraesCS6D01G118900 chr6D 84471742 84474908 3166 True 2187.500000 3470 91.920500 22 3274 2 chr6D.!!$R6 3252
5 TraesCS6D01G118900 chr6D 84651712 84653944 2232 True 2143.000000 2143 84.108000 922 3163 1 chr6D.!!$R5 2241
6 TraesCS6D01G118900 chr6A 101560492 101562894 2402 True 2859.000000 2859 88.230000 739 3135 1 chr6A.!!$R1 2396
7 TraesCS6D01G118900 chr6A 101863198 101866275 3077 True 1972.000000 2972 91.103000 1 3163 2 chr6A.!!$R4 3162
8 TraesCS6D01G118900 chr6A 101541959 101549065 7106 True 1584.750000 4425 91.447000 1 4133 4 chr6A.!!$R2 4132
9 TraesCS6D01G118900 chr6A 101841310 101844965 3655 True 1544.500000 2754 86.659000 999 3889 2 chr6A.!!$R3 2890
10 TraesCS6D01G118900 chr6B 160714797 160717020 2223 True 2364.000000 2364 85.938000 916 3135 1 chr6B.!!$R2 2219
11 TraesCS6D01G118900 chr6B 160902736 160905965 3229 True 1965.000000 2953 90.734500 1 3158 2 chr6B.!!$R4 3157
12 TraesCS6D01G118900 chr6B 160660999 160664962 3963 True 1535.666667 3509 89.739667 22 3165 3 chr6B.!!$R3 3143

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
441 1320 1.153695 TAGAGGAGACCACCACCCCT 61.154 60.000 0.0 0.0 0.0 4.79 F
1111 2095 0.391661 GCGCAATCTCCTCCAGTTCA 60.392 55.000 0.3 0.0 0.0 3.18 F
1493 2479 1.065102 CTCGCAATTTCCATCAGCCAG 59.935 52.381 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 2756 1.699083 TGTGCTCCATCAAGTTCTCCA 59.301 47.619 0.00 0.0 0.00 3.86 R
2114 3105 2.356125 CCATGGAAATGGTTCTCCGACT 60.356 50.000 5.56 0.0 36.95 4.18 R
3385 5051 0.106167 AGCCATCTAGGTGGTCGCTA 60.106 55.000 23.17 0.0 41.47 4.26 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
22 23 5.143376 CTCAAAGCTTCATTCCCACAAAT 57.857 39.130 0.00 0.00 0.00 2.32
41 913 7.703621 CCACAAATGAACAGATGAATAATCCAC 59.296 37.037 0.00 0.00 35.72 4.02
53 925 6.061022 TGAATAATCCACAGGCACTCTTTA 57.939 37.500 0.00 0.00 34.60 1.85
297 1175 7.774157 GCAGAATATCTCCCATACATGAATCAT 59.226 37.037 0.00 0.00 0.00 2.45
371 1249 2.896685 TGGGCCAAAAACTAGGTTCATG 59.103 45.455 2.13 0.00 0.00 3.07
441 1320 1.153695 TAGAGGAGACCACCACCCCT 61.154 60.000 0.00 0.00 0.00 4.79
455 1338 4.366684 CCCTGGGCCCTGGACAAC 62.367 72.222 41.59 6.86 37.23 3.32
667 1555 5.068855 AGCTTTATAAACTACTCCCTCCGTC 59.931 44.000 0.00 0.00 0.00 4.79
668 1556 5.068855 GCTTTATAAACTACTCCCTCCGTCT 59.931 44.000 0.00 0.00 0.00 4.18
670 1558 2.599408 AAACTACTCCCTCCGTCTCA 57.401 50.000 0.00 0.00 0.00 3.27
671 1559 2.830651 AACTACTCCCTCCGTCTCAT 57.169 50.000 0.00 0.00 0.00 2.90
675 1563 4.145807 ACTACTCCCTCCGTCTCATAATG 58.854 47.826 0.00 0.00 0.00 1.90
677 1565 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
678 1566 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
680 1568 3.321111 TCCCTCCGTCTCATAATGTAAGC 59.679 47.826 0.00 0.00 0.00 3.09
682 1570 3.309388 CTCCGTCTCATAATGTAAGCCG 58.691 50.000 0.00 0.00 0.00 5.52
685 1573 3.869246 CCGTCTCATAATGTAAGCCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
687 1575 5.163794 CCGTCTCATAATGTAAGCCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
850 1820 3.702048 GCCCCGTGCACTGAGGTA 61.702 66.667 16.19 0.00 40.77 3.08
1020 2004 1.225855 TGTGCTCATTCACCGTTCAC 58.774 50.000 0.00 0.00 36.17 3.18
1111 2095 0.391661 GCGCAATCTCCTCCAGTTCA 60.392 55.000 0.30 0.00 0.00 3.18
1392 2378 2.046507 AGCTTCAGCCGGCTCAAG 60.047 61.111 33.33 33.33 43.38 3.02
1493 2479 1.065102 CTCGCAATTTCCATCAGCCAG 59.935 52.381 0.00 0.00 0.00 4.85
1767 2756 3.837731 CCTTCCCCAACAATGGTTTACAT 59.162 43.478 0.00 0.00 46.01 2.29
2114 3105 1.454572 AATTTGACAGCACTGCGGCA 61.455 50.000 1.29 1.29 35.83 5.69
2781 3782 4.032960 ACCACAATCAATCTGCAACCTA 57.967 40.909 0.00 0.00 0.00 3.08
2952 3953 4.675976 TCCAACTTCTAGTTTTGACGGA 57.324 40.909 0.00 0.00 36.03 4.69
3159 4160 7.509546 CCCAGTTCAACTGTAATATGGTCTAT 58.490 38.462 16.50 0.00 44.50 1.98
3166 4168 9.489084 TCAACTGTAATATGGTCTATATGCAAC 57.511 33.333 0.00 0.00 32.30 4.17
3228 4231 0.313043 CACCTCAACCGTGTCGTACT 59.687 55.000 0.00 0.00 0.00 2.73
3229 4232 1.536766 CACCTCAACCGTGTCGTACTA 59.463 52.381 0.00 0.00 0.00 1.82
3230 4233 2.030893 CACCTCAACCGTGTCGTACTAA 60.031 50.000 0.00 0.00 0.00 2.24
3299 4409 9.812347 TGCTGATGAATAATAAAGGTCCATAAT 57.188 29.630 0.00 0.00 0.00 1.28
3333 4447 6.341316 TCTATCTAGCTGGCTTGTTAAGTTG 58.659 40.000 0.00 0.00 0.00 3.16
3338 4452 3.821033 AGCTGGCTTGTTAAGTTGTTAGG 59.179 43.478 0.00 0.00 0.00 2.69
3339 4453 3.818773 GCTGGCTTGTTAAGTTGTTAGGA 59.181 43.478 0.00 0.00 0.00 2.94
3340 4454 4.083271 GCTGGCTTGTTAAGTTGTTAGGAG 60.083 45.833 0.00 0.00 0.00 3.69
3361 5027 5.177327 GGAGGTGTACAAAATGCACAATTTG 59.823 40.000 15.90 15.90 45.16 2.32
3366 5032 5.632764 TGTACAAAATGCACAATTTGATCGG 59.367 36.000 21.54 2.74 38.52 4.18
3375 5041 6.092092 TGCACAATTTGATCGGAATACAAAG 58.908 36.000 2.79 4.96 37.04 2.77
3376 5042 6.072230 TGCACAATTTGATCGGAATACAAAGA 60.072 34.615 2.79 0.00 37.04 2.52
3381 5047 4.149511 TGATCGGAATACAAAGATGGCA 57.850 40.909 0.00 0.00 0.00 4.92
3385 5051 3.016736 CGGAATACAAAGATGGCAACCT 58.983 45.455 0.00 0.00 0.00 3.50
3386 5052 4.080807 TCGGAATACAAAGATGGCAACCTA 60.081 41.667 0.00 0.00 0.00 3.08
3387 5053 4.273480 CGGAATACAAAGATGGCAACCTAG 59.727 45.833 0.00 0.00 0.00 3.02
3388 5054 4.036852 GGAATACAAAGATGGCAACCTAGC 59.963 45.833 0.00 0.00 0.00 3.42
3389 5055 1.453155 ACAAAGATGGCAACCTAGCG 58.547 50.000 0.00 0.00 34.64 4.26
3419 5085 6.148480 CCTAGATGGCTGCAGATATAACAAAC 59.852 42.308 20.43 0.00 0.00 2.93
3475 5156 9.447157 GTTGAAAATGATCAAATATCCCCAAAA 57.553 29.630 0.00 0.00 40.76 2.44
3492 5173 3.674753 CCAAAATTAAGCAAGAACGCTGG 59.325 43.478 0.00 0.00 42.89 4.85
3495 5176 1.234821 TTAAGCAAGAACGCTGGTGG 58.765 50.000 0.00 0.00 42.89 4.61
3503 5292 0.804989 GAACGCTGGTGGAATTCCTG 59.195 55.000 24.73 13.08 36.82 3.86
3516 5305 5.771165 GTGGAATTCCTGTAACCCAAGTTTA 59.229 40.000 24.73 0.00 35.69 2.01
3517 5306 5.771165 TGGAATTCCTGTAACCCAAGTTTAC 59.229 40.000 24.73 0.00 35.69 2.01
3521 5310 4.721132 TCCTGTAACCCAAGTTTACCAAG 58.279 43.478 0.00 0.00 37.42 3.61
3522 5311 4.412858 TCCTGTAACCCAAGTTTACCAAGA 59.587 41.667 0.00 0.00 37.42 3.02
3524 5313 5.595133 CCTGTAACCCAAGTTTACCAAGAAA 59.405 40.000 0.00 0.00 37.42 2.52
3527 5316 7.321908 TGTAACCCAAGTTTACCAAGAAAAAC 58.678 34.615 0.00 0.00 37.42 2.43
3529 5318 5.726397 ACCCAAGTTTACCAAGAAAAACAC 58.274 37.500 0.00 0.00 37.92 3.32
3532 5329 6.091577 CCCAAGTTTACCAAGAAAAACACAAC 59.908 38.462 0.00 0.00 37.92 3.32
3570 5367 2.350804 TCCGAGACGTAGATTGTCGAAG 59.649 50.000 0.00 0.00 41.24 3.79
3738 5539 1.001974 TGAACTGGGAGATGAACACGG 59.998 52.381 0.00 0.00 0.00 4.94
3780 5581 0.179084 TCTTGGATAGCTTTCGCGGG 60.179 55.000 6.13 0.00 42.32 6.13
3781 5582 0.179084 CTTGGATAGCTTTCGCGGGA 60.179 55.000 6.13 0.00 42.32 5.14
3859 5660 2.202878 ACCGATCGGAATGTGGCG 60.203 61.111 39.55 10.90 38.96 5.69
3994 8920 1.334869 GTGATAGGATTTGCAAGCCCG 59.665 52.381 14.66 0.00 37.80 6.13
4002 8928 1.323412 TTTGCAAGCCCGCTTCTTTA 58.677 45.000 0.00 0.00 33.42 1.85
4003 8929 1.323412 TTGCAAGCCCGCTTCTTTAA 58.677 45.000 0.00 0.00 33.42 1.52
4004 8930 1.323412 TGCAAGCCCGCTTCTTTAAA 58.677 45.000 0.00 0.00 33.42 1.52
4005 8931 1.683917 TGCAAGCCCGCTTCTTTAAAA 59.316 42.857 0.00 0.00 33.42 1.52
4006 8932 2.101582 TGCAAGCCCGCTTCTTTAAAAA 59.898 40.909 0.00 0.00 33.42 1.94
4041 8967 6.071391 GCCCACTTCTTTGATTCAAGGAATTA 60.071 38.462 20.25 3.51 38.42 1.40
4103 9029 4.818642 TCACGTGGGTTATTTGATTCGTA 58.181 39.130 17.00 0.00 0.00 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.862469 ATTCATCTGTTCATTTGTGGGAAT 57.138 33.333 0.00 0.00 0.00 3.01
22 23 4.883585 GCCTGTGGATTATTCATCTGTTCA 59.116 41.667 0.00 0.00 31.67 3.18
41 913 3.538591 TCAGATGCATAAAGAGTGCCTG 58.461 45.455 0.00 0.00 41.83 4.85
297 1175 5.897824 TGGTACCAACCTAAATTTGGAAACA 59.102 36.000 13.60 1.27 45.69 2.83
389 1267 1.762419 GCATGTTTATGGCATGAGCG 58.238 50.000 10.98 0.00 44.60 5.03
441 1320 2.440147 CATGTTGTCCAGGGCCCA 59.560 61.111 27.56 0.00 0.00 5.36
455 1338 0.879090 TTGCTGCTCAAGAGTGCATG 59.121 50.000 16.12 0.00 42.66 4.06
708 1596 6.170506 TCCGTCTCATAATGTAAGCTGTTTT 58.829 36.000 0.00 0.00 0.00 2.43
710 1598 5.339008 TCCGTCTCATAATGTAAGCTGTT 57.661 39.130 0.00 0.00 0.00 3.16
713 1601 3.322254 CCCTCCGTCTCATAATGTAAGCT 59.678 47.826 0.00 0.00 0.00 3.74
715 1603 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
717 1605 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
718 1606 3.033659 ACTCCCTCCGTCTCATAATGT 57.966 47.619 0.00 0.00 0.00 2.71
719 1607 4.145807 ACTACTCCCTCCGTCTCATAATG 58.854 47.826 0.00 0.00 0.00 1.90
720 1608 4.456662 ACTACTCCCTCCGTCTCATAAT 57.543 45.455 0.00 0.00 0.00 1.28
721 1609 3.947612 ACTACTCCCTCCGTCTCATAA 57.052 47.619 0.00 0.00 0.00 1.90
724 1612 2.599408 AAACTACTCCCTCCGTCTCA 57.401 50.000 0.00 0.00 0.00 3.27
725 1613 3.350833 TGTAAACTACTCCCTCCGTCTC 58.649 50.000 0.00 0.00 0.00 3.36
726 1614 3.446442 TGTAAACTACTCCCTCCGTCT 57.554 47.619 0.00 0.00 0.00 4.18
727 1615 3.181478 CCATGTAAACTACTCCCTCCGTC 60.181 52.174 0.00 0.00 0.00 4.79
850 1820 5.191727 TCCATATTTCTTGTCATGGGTGT 57.808 39.130 0.00 0.00 38.78 4.16
1111 2095 2.029288 CACGCGACAGTCCAGCAAT 61.029 57.895 15.93 0.00 0.00 3.56
1493 2479 3.937706 CAGACTGTTCATCACCTTCCATC 59.062 47.826 0.00 0.00 0.00 3.51
1767 2756 1.699083 TGTGCTCCATCAAGTTCTCCA 59.301 47.619 0.00 0.00 0.00 3.86
2114 3105 2.356125 CCATGGAAATGGTTCTCCGACT 60.356 50.000 5.56 0.00 36.95 4.18
2781 3782 2.457598 TCTAGGATCTGCAGGTTCGTT 58.542 47.619 15.13 6.24 0.00 3.85
2952 3953 2.978010 CCGCACAGCTTCGGGTTT 60.978 61.111 10.16 0.00 41.82 3.27
3159 4160 5.675684 TGTTCACCTCTATCTGTTGCATA 57.324 39.130 0.00 0.00 0.00 3.14
3166 4168 3.834489 AGGCATGTTCACCTCTATCTG 57.166 47.619 0.00 0.00 0.00 2.90
3299 4409 6.889198 AGCCAGCTAGATAGAAATACAAACA 58.111 36.000 0.00 0.00 0.00 2.83
3306 4420 7.569240 ACTTAACAAGCCAGCTAGATAGAAAT 58.431 34.615 0.00 0.00 0.00 2.17
3310 4424 6.109359 ACAACTTAACAAGCCAGCTAGATAG 58.891 40.000 0.00 0.00 0.00 2.08
3313 4427 4.351874 ACAACTTAACAAGCCAGCTAGA 57.648 40.909 0.00 0.00 0.00 2.43
3321 4435 4.820173 ACACCTCCTAACAACTTAACAAGC 59.180 41.667 0.00 0.00 0.00 4.01
3333 4447 4.517453 TGTGCATTTTGTACACCTCCTAAC 59.483 41.667 0.00 0.00 38.04 2.34
3338 4452 5.982516 TCAAATTGTGCATTTTGTACACCTC 59.017 36.000 15.14 0.00 42.48 3.85
3339 4453 5.911752 TCAAATTGTGCATTTTGTACACCT 58.088 33.333 15.14 0.00 42.48 4.00
3340 4454 6.399880 CGATCAAATTGTGCATTTTGTACACC 60.400 38.462 15.14 5.41 42.48 4.16
3361 5027 4.261197 GGTTGCCATCTTTGTATTCCGATC 60.261 45.833 0.00 0.00 0.00 3.69
3366 5032 4.260784 CGCTAGGTTGCCATCTTTGTATTC 60.261 45.833 0.00 0.00 0.00 1.75
3375 5041 1.090052 GTGGTCGCTAGGTTGCCATC 61.090 60.000 0.00 0.00 0.00 3.51
3376 5042 1.078426 GTGGTCGCTAGGTTGCCAT 60.078 57.895 0.00 0.00 0.00 4.40
3381 5047 2.032620 CATCTAGGTGGTCGCTAGGTT 58.967 52.381 0.00 0.00 0.00 3.50
3385 5051 0.106167 AGCCATCTAGGTGGTCGCTA 60.106 55.000 23.17 0.00 41.47 4.26
3386 5052 1.381872 AGCCATCTAGGTGGTCGCT 60.382 57.895 23.17 11.39 41.47 4.93
3387 5053 1.227380 CAGCCATCTAGGTGGTCGC 60.227 63.158 23.17 9.16 41.47 5.19
3388 5054 1.227380 GCAGCCATCTAGGTGGTCG 60.227 63.158 23.17 15.05 41.47 4.79
3389 5055 0.179062 CTGCAGCCATCTAGGTGGTC 60.179 60.000 23.17 15.01 41.47 4.02
3445 5126 9.671279 GGGGATATTTGATCATTTTCAACTTTT 57.329 29.630 0.00 0.00 35.42 2.27
3455 5136 9.783081 GCTTAATTTTGGGGATATTTGATCATT 57.217 29.630 0.00 0.00 0.00 2.57
3475 5156 1.812571 CCACCAGCGTTCTTGCTTAAT 59.187 47.619 0.00 0.00 44.46 1.40
3492 5173 3.763057 ACTTGGGTTACAGGAATTCCAC 58.237 45.455 26.22 14.86 38.89 4.02
3495 5176 5.771165 TGGTAAACTTGGGTTACAGGAATTC 59.229 40.000 7.61 0.00 34.90 2.17
3503 5292 7.276218 GTGTTTTTCTTGGTAAACTTGGGTTAC 59.724 37.037 0.00 0.00 35.73 2.50
3516 5305 5.683770 GCCCAATAGTTGTGTTTTTCTTGGT 60.684 40.000 0.00 0.00 31.98 3.67
3517 5306 4.749598 GCCCAATAGTTGTGTTTTTCTTGG 59.250 41.667 0.00 0.00 33.34 3.61
3521 5310 3.004944 TCCGCCCAATAGTTGTGTTTTTC 59.995 43.478 0.00 0.00 0.00 2.29
3522 5311 2.959707 TCCGCCCAATAGTTGTGTTTTT 59.040 40.909 0.00 0.00 0.00 1.94
3524 5313 2.279935 TCCGCCCAATAGTTGTGTTT 57.720 45.000 0.00 0.00 0.00 2.83
3527 5316 2.616842 GGTAATCCGCCCAATAGTTGTG 59.383 50.000 0.00 0.00 0.00 3.33
3529 5318 3.139077 GAGGTAATCCGCCCAATAGTTG 58.861 50.000 0.00 0.00 39.05 3.16
3532 5329 2.474410 GGAGGTAATCCGCCCAATAG 57.526 55.000 0.00 0.00 46.01 1.73
3555 5352 3.736252 GCATATGCTTCGACAATCTACGT 59.264 43.478 20.64 0.00 38.21 3.57
3570 5367 1.569493 CCGGTGTTAGCGCATATGC 59.431 57.895 18.08 18.08 37.85 3.14
3706 5503 0.602905 CCAGTTCACCACTCCCGTTC 60.603 60.000 0.00 0.00 30.92 3.95
3707 5504 1.450211 CCAGTTCACCACTCCCGTT 59.550 57.895 0.00 0.00 30.92 4.44
3708 5505 2.516888 CCCAGTTCACCACTCCCGT 61.517 63.158 0.00 0.00 30.92 5.28
3830 5631 4.087892 ATCGGTGGCGCTGCTCTT 62.088 61.111 7.64 0.00 0.00 2.85
3831 5632 4.521062 GATCGGTGGCGCTGCTCT 62.521 66.667 7.64 0.00 0.00 4.09
3896 5697 3.396260 TTCTCTACTTTTGTGGTCGGG 57.604 47.619 0.00 0.00 32.36 5.14
3898 5699 5.277345 CCTGTTTTCTCTACTTTTGTGGTCG 60.277 44.000 0.00 0.00 32.36 4.79
3899 5700 5.589050 ACCTGTTTTCTCTACTTTTGTGGTC 59.411 40.000 0.00 0.00 32.36 4.02
3900 5701 5.506708 ACCTGTTTTCTCTACTTTTGTGGT 58.493 37.500 0.00 0.00 32.36 4.16
3901 5702 6.265577 CAACCTGTTTTCTCTACTTTTGTGG 58.734 40.000 0.00 0.00 0.00 4.17
3902 5703 6.265577 CCAACCTGTTTTCTCTACTTTTGTG 58.734 40.000 0.00 0.00 0.00 3.33
3903 5704 5.359860 CCCAACCTGTTTTCTCTACTTTTGT 59.640 40.000 0.00 0.00 0.00 2.83
3904 5705 5.736207 GCCCAACCTGTTTTCTCTACTTTTG 60.736 44.000 0.00 0.00 0.00 2.44
3905 5706 4.341235 GCCCAACCTGTTTTCTCTACTTTT 59.659 41.667 0.00 0.00 0.00 2.27
3906 5707 3.889538 GCCCAACCTGTTTTCTCTACTTT 59.110 43.478 0.00 0.00 0.00 2.66
3907 5708 3.138468 AGCCCAACCTGTTTTCTCTACTT 59.862 43.478 0.00 0.00 0.00 2.24
3908 5709 2.711547 AGCCCAACCTGTTTTCTCTACT 59.288 45.455 0.00 0.00 0.00 2.57
3909 5710 3.075148 GAGCCCAACCTGTTTTCTCTAC 58.925 50.000 0.00 0.00 0.00 2.59
3910 5711 2.289444 CGAGCCCAACCTGTTTTCTCTA 60.289 50.000 0.00 0.00 0.00 2.43
4063 8989 8.723311 CCCACGTGAACAAAATACTAAGAATTA 58.277 33.333 19.30 0.00 0.00 1.40
4064 8990 7.229907 ACCCACGTGAACAAAATACTAAGAATT 59.770 33.333 19.30 0.00 0.00 2.17
4065 8991 6.713450 ACCCACGTGAACAAAATACTAAGAAT 59.287 34.615 19.30 0.00 0.00 2.40
4066 8992 6.056884 ACCCACGTGAACAAAATACTAAGAA 58.943 36.000 19.30 0.00 0.00 2.52
4067 8993 5.613329 ACCCACGTGAACAAAATACTAAGA 58.387 37.500 19.30 0.00 0.00 2.10
4068 8994 5.934935 ACCCACGTGAACAAAATACTAAG 57.065 39.130 19.30 0.00 0.00 2.18
4069 8995 7.982761 ATAACCCACGTGAACAAAATACTAA 57.017 32.000 19.30 0.00 0.00 2.24
4070 8996 7.982761 AATAACCCACGTGAACAAAATACTA 57.017 32.000 19.30 0.00 0.00 1.82
4073 8999 7.273320 TCAAATAACCCACGTGAACAAAATA 57.727 32.000 19.30 0.57 0.00 1.40
4085 9011 6.725246 CAATCCTACGAATCAAATAACCCAC 58.275 40.000 0.00 0.00 0.00 4.61
4088 9014 6.371809 TGCAATCCTACGAATCAAATAACC 57.628 37.500 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.