Multiple sequence alignment - TraesCS6D01G213300

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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 TraesCS6D01G213300 chr6D 100.000 5834 0 0 1 5834 303056540 303062373 0.000000e+00 10774.0
1 TraesCS6D01G213300 chr6A 94.860 5389 188 30 24 5382 411766982 411772311 0.000000e+00 8335.0
2 TraesCS6D01G213300 chr6A 88.508 583 25 13 4163 4731 441440964 441440410 0.000000e+00 667.0
3 TraesCS6D01G213300 chr6A 97.403 308 8 0 3992 4299 441441268 441440961 5.180000e-145 525.0
4 TraesCS6D01G213300 chr6A 91.273 275 13 5 3325 3598 440694499 440694235 1.190000e-96 364.0
5 TraesCS6D01G213300 chr6A 84.530 362 14 14 5490 5834 411772318 411772654 2.620000e-83 320.0
6 TraesCS6D01G213300 chr6A 95.327 107 5 0 3826 3932 441443388 441443282 2.800000e-38 171.0
7 TraesCS6D01G213300 chr6A 98.039 51 1 0 3924 3974 441441316 441441266 8.050000e-14 89.8
8 TraesCS6D01G213300 chr6B 94.929 2682 96 19 849 3506 468731990 468734655 0.000000e+00 4163.0
9 TraesCS6D01G213300 chr6B 95.856 2027 68 8 3674 5693 468735100 468737117 0.000000e+00 3264.0
10 TraesCS6D01G213300 chr6B 91.135 846 45 18 24 851 468730988 468731821 0.000000e+00 1120.0
11 TraesCS6D01G213300 chr6B 88.274 307 24 5 1653 1950 131684026 131683723 2.000000e-94 357.0
12 TraesCS6D01G213300 chr6B 97.619 168 3 1 3510 3676 468734820 468734987 2.660000e-73 287.0
13 TraesCS6D01G213300 chr6B 94.203 138 3 1 5702 5834 468738574 468738711 7.660000e-49 206.0
14 TraesCS6D01G213300 chr7B 90.654 428 22 8 1539 1950 619156847 619156422 2.380000e-153 553.0
15 TraesCS6D01G213300 chr7B 83.108 592 39 28 972 1549 619158146 619157602 3.160000e-132 483.0
16 TraesCS6D01G213300 chr4A 89.151 424 30 6 1540 1950 68459557 68459137 1.120000e-141 514.0
17 TraesCS6D01G213300 chr4A 92.638 163 9 3 3318 3478 48905839 48906000 1.260000e-56 231.0
18 TraesCS6D01G213300 chr1B 88.208 424 34 7 1540 1950 23988590 23989010 5.250000e-135 492.0
19 TraesCS6D01G213300 chr1B 88.208 424 34 7 1540 1950 24092073 24091653 5.250000e-135 492.0
20 TraesCS6D01G213300 chr1B 86.813 182 20 4 2586 2764 566085912 566086092 3.570000e-47 200.0
21 TraesCS6D01G213300 chr5B 87.736 424 35 8 1540 1950 506660556 506660975 4.090000e-131 479.0
22 TraesCS6D01G213300 chr5B 91.265 332 21 5 1540 1866 56555438 56555766 4.150000e-121 446.0
23 TraesCS6D01G213300 chr5B 93.750 160 6 3 3313 3472 665744468 665744623 2.720000e-58 237.0
24 TraesCS6D01G213300 chr1A 93.750 160 8 2 3314 3472 155857706 155857864 7.560000e-59 239.0
25 TraesCS6D01G213300 chr5D 93.750 160 6 3 3313 3472 528717277 528717432 2.720000e-58 237.0
26 TraesCS6D01G213300 chr5A 93.750 160 6 3 3313 3472 656872284 656872439 2.720000e-58 237.0
27 TraesCS6D01G213300 chr3D 92.727 165 11 1 3311 3475 288550614 288550451 2.720000e-58 237.0
28 TraesCS6D01G213300 chr1D 89.385 179 14 5 3291 3468 7349878 7349704 2.740000e-53 220.0
29 TraesCS6D01G213300 chrUn 87.097 186 22 2 2586 2770 368162132 368162316 5.920000e-50 209.0
30 TraesCS6D01G213300 chr2B 86.772 189 23 2 2586 2773 38126387 38126200 5.920000e-50 209.0
31 TraesCS6D01G213300 chr2B 86.772 189 23 2 2586 2773 38173642 38173455 5.920000e-50 209.0


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 TraesCS6D01G213300 chr6D 303056540 303062373 5833 False 10774.0 10774 100.00000 1 5834 1 chr6D.!!$F1 5833
1 TraesCS6D01G213300 chr6A 411766982 411772654 5672 False 4327.5 8335 89.69500 24 5834 2 chr6A.!!$F1 5810
2 TraesCS6D01G213300 chr6A 441440410 441443388 2978 True 363.2 667 94.81925 3826 4731 4 chr6A.!!$R2 905
3 TraesCS6D01G213300 chr6B 468730988 468738711 7723 False 1808.0 4163 94.74840 24 5834 5 chr6B.!!$F1 5810
4 TraesCS6D01G213300 chr7B 619156422 619158146 1724 True 518.0 553 86.88100 972 1950 2 chr7B.!!$R1 978


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
644 657 0.036388 TTGCTTCCCGATCGCTTTCT 60.036 50.000 10.32 0.00 0.00 2.52 F
1453 1660 0.859232 CAGTCGAACGTTGGGAGTTG 59.141 55.000 5.00 1.15 31.14 3.16 F
1595 2567 3.007290 AGACAGAGTGCTTGCATAGTTCA 59.993 43.478 0.00 0.00 0.00 3.18 F
3091 4088 3.483808 TTTGATGGCAGTCAGTGTGTA 57.516 42.857 0.00 0.00 0.00 2.90 F
4242 7628 0.240945 CGGCACAAGGTGTTGAATCC 59.759 55.000 0.00 0.00 37.10 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 3232 0.183492 AACAGCCACAGCCTGAGAAA 59.817 50.00 0.0 0.0 41.25 2.52 R
2778 3773 4.114073 TGTGCAAAGAAGTGAAAATGCTG 58.886 39.13 0.0 0.0 34.97 4.41 R
3300 4297 4.392445 CGGAGGGAGTATATCTTCTGTACG 59.608 50.00 0.0 0.0 0.00 3.67 R
4308 7694 0.251297 CACCATCACTTGCCCCAGAA 60.251 55.00 0.0 0.0 0.00 3.02 R
5354 8761 0.107165 CCCACTAACCCAGCTTAGCC 60.107 60.00 0.0 0.0 0.00 3.93 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
18 19 2.249692 ACGTGTGGGCGTTATTTGG 58.750 52.632 0.00 0.00 43.04 3.28
19 20 0.250381 ACGTGTGGGCGTTATTTGGA 60.250 50.000 0.00 0.00 43.04 3.53
20 21 0.167251 CGTGTGGGCGTTATTTGGAC 59.833 55.000 0.00 0.00 0.00 4.02
21 22 0.524414 GTGTGGGCGTTATTTGGACC 59.476 55.000 0.00 0.00 0.00 4.46
22 23 0.609681 TGTGGGCGTTATTTGGACCC 60.610 55.000 0.00 0.00 41.24 4.46
32 33 6.391537 GCGTTATTTGGACCCTTTCAAAATA 58.608 36.000 0.00 0.00 38.59 1.40
47 48 8.981647 CCTTTCAAAATACAGGAACATGAAAAG 58.018 33.333 0.00 0.00 35.59 2.27
54 55 3.821033 ACAGGAACATGAAAAGTGTAGGC 59.179 43.478 0.00 0.00 0.00 3.93
60 61 6.374333 GGAACATGAAAAGTGTAGGCATAGAA 59.626 38.462 0.00 0.00 0.00 2.10
126 130 9.883142 TGATAACACAAGAAAACAAAGGAATTT 57.117 25.926 0.00 0.00 0.00 1.82
147 151 9.929180 GAATTTTATAAAGAAGTTTGAGGGCTT 57.071 29.630 0.00 0.00 0.00 4.35
168 172 7.378181 GGCTTCTTTGATACAAAGGAATTTCA 58.622 34.615 19.43 1.41 0.00 2.69
169 173 8.037166 GGCTTCTTTGATACAAAGGAATTTCAT 58.963 33.333 19.43 0.00 0.00 2.57
392 397 0.179097 GTTGGATCTCCGAGCAGTCC 60.179 60.000 0.00 7.14 39.43 3.85
394 399 2.122167 GGATCTCCGAGCAGTCCGT 61.122 63.158 0.00 0.00 0.00 4.69
404 410 2.617274 GCAGTCCGTGGCTGGTTTC 61.617 63.158 7.47 0.00 34.73 2.78
584 595 2.908073 CGAACCCAAGGCAGCACAC 61.908 63.158 0.00 0.00 0.00 3.82
617 630 0.326595 TGCCAAGCCACCGAAAGATA 59.673 50.000 0.00 0.00 0.00 1.98
643 656 0.802494 TTTGCTTCCCGATCGCTTTC 59.198 50.000 10.32 0.00 0.00 2.62
644 657 0.036388 TTGCTTCCCGATCGCTTTCT 60.036 50.000 10.32 0.00 0.00 2.52
705 719 2.215196 GCTTTCGTGGTCTGGTTGTAA 58.785 47.619 0.00 0.00 0.00 2.41
719 733 2.137523 GTTGTAATCGACCACAACCGT 58.862 47.619 23.86 0.00 45.62 4.83
720 734 2.529780 TGTAATCGACCACAACCGTT 57.470 45.000 0.00 0.00 0.00 4.44
721 735 2.136728 TGTAATCGACCACAACCGTTG 58.863 47.619 9.80 9.80 0.00 4.10
722 736 2.223994 TGTAATCGACCACAACCGTTGA 60.224 45.455 18.19 0.00 0.00 3.18
1086 1278 1.222113 GGAGAAGAAGAAGGCGGGG 59.778 63.158 0.00 0.00 0.00 5.73
1277 1474 1.382146 AGGTCGCCGAATCCCCTAA 60.382 57.895 0.00 0.00 0.00 2.69
1453 1660 0.859232 CAGTCGAACGTTGGGAGTTG 59.141 55.000 5.00 1.15 31.14 3.16
1586 2558 3.290308 ACGAAGTAGACAGAGTGCTTG 57.710 47.619 0.00 0.00 41.94 4.01
1595 2567 3.007290 AGACAGAGTGCTTGCATAGTTCA 59.993 43.478 0.00 0.00 0.00 3.18
1724 2701 6.971184 CACAGATTTTGGCTATGATTGTTCTC 59.029 38.462 0.00 0.00 0.00 2.87
1780 2757 5.701224 TGTGGATTCCTTTCCTTTTGTAGT 58.299 37.500 3.95 0.00 36.68 2.73
2154 3147 9.102757 GAATTATTGAGTTCTGCACTTCTATGA 57.897 33.333 0.00 0.00 35.01 2.15
2155 3148 9.453572 AATTATTGAGTTCTGCACTTCTATGAA 57.546 29.630 0.00 0.00 35.01 2.57
2215 3208 8.405531 TGTACTAAATATCCAGCAAGCAATTTC 58.594 33.333 0.00 0.00 0.00 2.17
2239 3232 6.154021 TCTGCGTTCTTAATAGTTAGGTCCTT 59.846 38.462 0.00 0.00 0.00 3.36
2410 3403 4.274602 TGCGTAAGTATCTTGAAACCCA 57.725 40.909 0.00 0.00 41.68 4.51
2593 3586 9.502091 TTGTGAAGTATAGAGCACTATGTTTTT 57.498 29.630 13.28 3.30 39.36 1.94
2833 3828 4.202357 TGTGGTGCTTCTAGTTTGACTCAT 60.202 41.667 0.00 0.00 0.00 2.90
2834 3829 4.153117 GTGGTGCTTCTAGTTTGACTCATG 59.847 45.833 0.00 0.00 0.00 3.07
3091 4088 3.483808 TTTGATGGCAGTCAGTGTGTA 57.516 42.857 0.00 0.00 0.00 2.90
3111 4108 6.663093 TGTGTATTGAATTGCTTGGGACTTAT 59.337 34.615 0.00 0.00 0.00 1.73
3300 4297 9.502145 TTGCACGTTAATCATCTTTCATATTTC 57.498 29.630 0.00 0.00 0.00 2.17
3301 4298 7.850492 TGCACGTTAATCATCTTTCATATTTCG 59.150 33.333 0.00 0.00 0.00 3.46
3302 4299 7.850982 GCACGTTAATCATCTTTCATATTTCGT 59.149 33.333 0.00 0.00 0.00 3.85
3378 4380 5.126384 TGTGAATCGGATGTATGTAGACACA 59.874 40.000 0.00 0.00 39.52 3.72
3458 4460 9.883142 TCCAAAACATCTTTTATTTGTGAACTT 57.117 25.926 0.00 0.00 32.29 2.66
3459 4461 9.919348 CCAAAACATCTTTTATTTGTGAACTTG 57.081 29.630 0.00 0.00 32.29 3.16
3617 4781 7.434897 GCTTGTTCTGATACACAAATGACAAAA 59.565 33.333 0.00 0.00 32.53 2.44
3791 5070 4.752101 ACAGTTGAACGGAAAGATGAGAAG 59.248 41.667 1.76 0.00 0.00 2.85
3903 5182 0.537143 AAGCGGTCATTGGTCAAGCA 60.537 50.000 0.00 0.00 0.00 3.91
3944 7197 8.044060 TCGGATAGAATTTTATCATGGCATTC 57.956 34.615 15.67 0.00 32.76 2.67
3981 7234 8.055181 ACTAAATGATGACAAAGTGTATCCCAT 58.945 33.333 0.00 0.00 0.00 4.00
4103 7356 5.650283 ACATCTTGGGGAAGAACCAAATTA 58.350 37.500 0.00 0.00 46.54 1.40
4173 7426 1.163554 GGCTGAGAAACAGGAAGCAG 58.836 55.000 0.00 0.00 45.82 4.24
4235 7621 1.346395 TCATACTTCGGCACAAGGTGT 59.654 47.619 0.00 0.00 35.75 4.16
4242 7628 0.240945 CGGCACAAGGTGTTGAATCC 59.759 55.000 0.00 0.00 37.10 3.01
4308 7694 6.388619 AGGGTTGTAGAACATTATCAAGGT 57.611 37.500 5.00 0.00 33.27 3.50
4447 7837 4.451900 TGAGAAACAAAACTCTCTGACCC 58.548 43.478 0.00 0.00 39.11 4.46
4475 7865 5.463154 AGCTACTCCCTCTGTCTCAATATT 58.537 41.667 0.00 0.00 0.00 1.28
4481 7871 8.560124 ACTCCCTCTGTCTCAATATTTAAGAT 57.440 34.615 1.64 0.00 0.00 2.40
4548 7939 2.422093 GCAGAGGGAGTATTTCCTTGGG 60.422 54.545 0.00 0.00 45.98 4.12
4662 8065 6.822667 TGTCATGCTCTAAACACATCAAAT 57.177 33.333 0.00 0.00 0.00 2.32
5204 8611 1.723608 TTTGTGTGGCAGTTGCTCCG 61.724 55.000 3.88 0.00 41.70 4.63
5237 8644 4.380023 CGGAAGTTTTGACAGTGTTTGGAA 60.380 41.667 0.00 0.00 0.00 3.53
5275 8682 8.239314 CAGCTTCTTTTTGTAATCTTGATAGCA 58.761 33.333 0.00 0.00 0.00 3.49
5310 8717 3.632333 ACTGATGTCTCGTATCCTTGGA 58.368 45.455 0.00 0.00 0.00 3.53
5319 8726 2.029918 TCGTATCCTTGGAGCGATGATG 60.030 50.000 12.62 0.00 0.00 3.07
5351 8758 0.955905 GTTTCGTTTTGCCTGGGCTA 59.044 50.000 13.05 2.16 42.51 3.93
5352 8759 1.338655 GTTTCGTTTTGCCTGGGCTAA 59.661 47.619 13.05 8.70 42.51 3.09
5353 8760 0.955905 TTCGTTTTGCCTGGGCTAAC 59.044 50.000 13.05 14.32 42.51 2.34
5354 8761 1.209127 CGTTTTGCCTGGGCTAACG 59.791 57.895 24.97 24.97 45.13 3.18
5355 8762 1.584495 GTTTTGCCTGGGCTAACGG 59.416 57.895 13.05 0.00 42.51 4.44
5356 8763 2.272447 TTTTGCCTGGGCTAACGGC 61.272 57.895 13.05 0.00 44.02 5.68
5453 8860 5.125367 AACCTGTTTACTCTTCAGGGTTT 57.875 39.130 13.72 0.00 45.61 3.27
5480 8887 4.202090 TGTCATCAGATGAGAATGGACTCG 60.202 45.833 13.78 0.00 40.53 4.18
5488 8895 1.590259 GAATGGACTCGAGCCTCGC 60.590 63.158 21.36 0.00 40.21 5.03
5517 8924 7.315890 CCGCTACAATAGAACATCATCATCTA 58.684 38.462 0.00 0.00 0.00 1.98
5519 8926 9.363763 CGCTACAATAGAACATCATCATCTAAT 57.636 33.333 0.00 0.00 0.00 1.73
5538 8947 7.027874 TCTAATCACCCCATAACTTTTCAGT 57.972 36.000 0.00 0.00 33.11 3.41
5568 8981 8.655651 TTTTAACTTTCAAACATGGATTCCAC 57.344 30.769 7.76 0.00 35.80 4.02
5815 10689 3.569701 GGACGGGTTCGATATTAGGTGTA 59.430 47.826 0.00 0.00 40.11 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.167251 GTCCAAATAACGCCCACACG 59.833 55.000 0.00 0.00 39.50 4.49
2 3 0.524414 GGTCCAAATAACGCCCACAC 59.476 55.000 0.00 0.00 0.00 3.82
3 4 0.609681 GGGTCCAAATAACGCCCACA 60.610 55.000 0.00 0.00 39.13 4.17
4 5 0.323087 AGGGTCCAAATAACGCCCAC 60.323 55.000 0.00 0.00 41.67 4.61
5 6 0.406361 AAGGGTCCAAATAACGCCCA 59.594 50.000 0.00 0.00 41.67 5.36
6 7 1.475280 GAAAGGGTCCAAATAACGCCC 59.525 52.381 0.00 0.00 39.60 6.13
7 8 2.164338 TGAAAGGGTCCAAATAACGCC 58.836 47.619 0.00 0.00 0.00 5.68
8 9 3.926821 TTGAAAGGGTCCAAATAACGC 57.073 42.857 0.00 0.00 0.00 4.84
9 10 7.371936 TGTATTTTGAAAGGGTCCAAATAACG 58.628 34.615 0.00 0.00 36.26 3.18
10 11 7.817478 CCTGTATTTTGAAAGGGTCCAAATAAC 59.183 37.037 0.00 0.00 36.26 1.89
11 12 7.730784 TCCTGTATTTTGAAAGGGTCCAAATAA 59.269 33.333 0.00 0.00 36.26 1.40
12 13 7.242359 TCCTGTATTTTGAAAGGGTCCAAATA 58.758 34.615 0.00 0.00 34.37 1.40
13 14 6.081356 TCCTGTATTTTGAAAGGGTCCAAAT 58.919 36.000 0.00 0.00 36.05 2.32
14 15 5.459505 TCCTGTATTTTGAAAGGGTCCAAA 58.540 37.500 0.00 0.00 0.00 3.28
15 16 5.068215 TCCTGTATTTTGAAAGGGTCCAA 57.932 39.130 0.00 0.00 0.00 3.53
16 17 4.733077 TCCTGTATTTTGAAAGGGTCCA 57.267 40.909 0.00 0.00 0.00 4.02
17 18 4.830600 TGTTCCTGTATTTTGAAAGGGTCC 59.169 41.667 0.00 0.00 0.00 4.46
18 19 6.208599 TCATGTTCCTGTATTTTGAAAGGGTC 59.791 38.462 0.00 0.00 0.00 4.46
19 20 6.074648 TCATGTTCCTGTATTTTGAAAGGGT 58.925 36.000 0.00 0.00 0.00 4.34
20 21 6.588719 TCATGTTCCTGTATTTTGAAAGGG 57.411 37.500 0.00 0.00 0.00 3.95
21 22 8.885494 TTTTCATGTTCCTGTATTTTGAAAGG 57.115 30.769 0.00 0.00 34.31 3.11
22 23 9.533253 ACTTTTCATGTTCCTGTATTTTGAAAG 57.467 29.630 0.00 0.00 34.31 2.62
32 33 3.821033 GCCTACACTTTTCATGTTCCTGT 59.179 43.478 0.00 0.00 0.00 4.00
47 48 4.752101 GGACATGACATTCTATGCCTACAC 59.248 45.833 0.00 0.00 0.00 2.90
170 174 9.601810 GGACCCAAATCCTATAAAAATCCTATT 57.398 33.333 0.00 0.00 35.68 1.73
392 397 2.595386 GCATTAAAGAAACCAGCCACG 58.405 47.619 0.00 0.00 0.00 4.94
394 399 1.067915 GCGCATTAAAGAAACCAGCCA 60.068 47.619 0.30 0.00 0.00 4.75
404 410 0.179140 ATGTTGCCGGCGCATTAAAG 60.179 50.000 24.78 0.00 46.67 1.85
513 519 1.600413 GGCACAAACTCGCAAAGAAGG 60.600 52.381 0.00 0.00 0.00 3.46
617 630 1.880027 GATCGGGAAGCAAAGTTGTGT 59.120 47.619 0.00 0.00 0.00 3.72
705 719 1.804151 CAATCAACGGTTGTGGTCGAT 59.196 47.619 19.47 3.00 0.00 3.59
719 733 0.817013 GGGCCTGCGAAATCAATCAA 59.183 50.000 0.84 0.00 0.00 2.57
720 734 1.375853 CGGGCCTGCGAAATCAATCA 61.376 55.000 0.84 0.00 0.00 2.57
721 735 1.356624 CGGGCCTGCGAAATCAATC 59.643 57.895 0.84 0.00 0.00 2.67
722 736 2.120909 CCGGGCCTGCGAAATCAAT 61.121 57.895 5.85 0.00 0.00 2.57
783 800 0.670546 CGTCCGACCACAGAAGCAAT 60.671 55.000 0.00 0.00 0.00 3.56
784 801 1.300620 CGTCCGACCACAGAAGCAA 60.301 57.895 0.00 0.00 0.00 3.91
947 1139 2.035626 GATGGGGTGGTGGTGGTG 59.964 66.667 0.00 0.00 0.00 4.17
948 1140 3.646715 CGATGGGGTGGTGGTGGT 61.647 66.667 0.00 0.00 0.00 4.16
949 1141 4.424711 CCGATGGGGTGGTGGTGG 62.425 72.222 0.00 0.00 0.00 4.61
950 1142 2.608970 GATCCGATGGGGTGGTGGTG 62.609 65.000 0.00 0.00 37.00 4.17
951 1143 2.286121 ATCCGATGGGGTGGTGGT 60.286 61.111 0.00 0.00 37.00 4.16
952 1144 2.510906 GATCCGATGGGGTGGTGG 59.489 66.667 0.00 0.00 37.00 4.61
1277 1474 0.322546 GGAACAAAGAGCGGGATGGT 60.323 55.000 0.00 0.00 0.00 3.55
1453 1660 3.105937 GCACAGAAACACGGAAAGAAAC 58.894 45.455 0.00 0.00 0.00 2.78
1586 2558 4.008330 CCATGGATGATCCTGAACTATGC 58.992 47.826 13.44 0.00 37.46 3.14
1595 2567 4.909695 TGTCTAATCACCATGGATGATCCT 59.090 41.667 21.47 11.70 35.72 3.24
1724 2701 7.838771 TGACTTGTGAACATGAATATCTGAG 57.161 36.000 0.00 0.00 0.00 3.35
1967 2960 9.959749 GTTGTTCTAATGAAACCTCAAATACAA 57.040 29.630 0.00 0.00 34.49 2.41
2025 3018 7.581213 TTCCTTTTCAGCAGATACTCAAAAA 57.419 32.000 0.00 0.00 0.00 1.94
2168 3161 7.888546 AGTACAAAAATAGCCATTACTGGTCTT 59.111 33.333 0.55 0.00 45.10 3.01
2215 3208 5.903810 AGGACCTAACTATTAAGAACGCAG 58.096 41.667 0.00 0.00 0.00 5.18
2219 3212 9.939802 TGAGAAAAGGACCTAACTATTAAGAAC 57.060 33.333 0.00 0.00 0.00 3.01
2239 3232 0.183492 AACAGCCACAGCCTGAGAAA 59.817 50.000 0.00 0.00 41.25 2.52
2384 3377 5.234543 GGTTTCAAGATACTTACGCATCCTC 59.765 44.000 0.00 0.00 0.00 3.71
2593 3586 6.882610 AACATACTGTTGATCTGCAGAAAA 57.117 33.333 22.50 15.43 39.45 2.29
2619 3614 4.202315 ACAAGTACAATAGTGTGCCAGACA 60.202 41.667 5.98 0.00 40.95 3.41
2778 3773 4.114073 TGTGCAAAGAAGTGAAAATGCTG 58.886 39.130 0.00 0.00 34.97 4.41
2833 3828 6.806249 CACAAGTGAAAGTAAAAAGACTTGCA 59.194 34.615 0.00 0.00 41.80 4.08
2834 3829 6.806739 ACACAAGTGAAAGTAAAAAGACTTGC 59.193 34.615 7.28 0.00 42.55 4.01
3062 4057 5.479375 ACTGACTGCCATCAAATTTCAGAAT 59.521 36.000 9.99 0.00 34.41 2.40
3091 4088 9.646522 ACTTATATAAGTCCCAAGCAATTCAAT 57.353 29.630 20.27 0.00 42.52 2.57
3300 4297 4.392445 CGGAGGGAGTATATCTTCTGTACG 59.608 50.000 0.00 0.00 0.00 3.67
3301 4298 5.315348 ACGGAGGGAGTATATCTTCTGTAC 58.685 45.833 0.00 0.00 32.73 2.90
3302 4299 5.579753 ACGGAGGGAGTATATCTTCTGTA 57.420 43.478 0.00 0.00 32.73 2.74
3303 4300 4.456662 ACGGAGGGAGTATATCTTCTGT 57.543 45.455 0.00 0.00 0.00 3.41
3304 4301 4.827835 TGAACGGAGGGAGTATATCTTCTG 59.172 45.833 0.00 0.00 0.00 3.02
3305 4302 4.828387 GTGAACGGAGGGAGTATATCTTCT 59.172 45.833 0.00 0.00 0.00 2.85
3306 4303 4.583489 TGTGAACGGAGGGAGTATATCTTC 59.417 45.833 0.00 0.00 0.00 2.87
3378 4380 9.301153 GAAATGAGTGAACAAACACACTAAAAT 57.699 29.630 0.00 0.00 45.54 1.82
3445 4447 8.792633 CAAATACTCCCTCAAGTTCACAAATAA 58.207 33.333 0.00 0.00 0.00 1.40
3458 4460 8.691797 GTTAATAATTTGCCAAATACTCCCTCA 58.308 33.333 2.54 0.00 0.00 3.86
3459 4461 8.691797 TGTTAATAATTTGCCAAATACTCCCTC 58.308 33.333 2.54 0.00 0.00 4.30
3508 4510 8.800972 CATGCAACTATCAATATTTGTTGTGAC 58.199 33.333 15.54 6.20 39.81 3.67
3617 4781 3.564225 CCTAGCAAAAAGAACGTTGTCCT 59.436 43.478 5.00 0.00 0.00 3.85
3791 5070 4.572389 TCAGCTCTCAACTTTTCAAGTGTC 59.428 41.667 0.00 0.00 41.91 3.67
3903 5182 9.838339 ATTCTATCCGAAGTAATGAACTCAATT 57.162 29.630 0.00 0.00 37.50 2.32
3944 7197 7.420184 TGTCATCATTTAGTACTGTTGTGTG 57.580 36.000 5.39 4.95 0.00 3.82
3981 7234 7.555195 AGATCATATTTCTGCACATGTTCAAGA 59.445 33.333 0.00 0.00 0.00 3.02
4103 7356 3.211865 CTCATAACCACTGCTGCATCAT 58.788 45.455 1.31 0.00 0.00 2.45
4235 7621 0.700564 AAGAGCTGGGCTGGATTCAA 59.299 50.000 0.00 0.00 39.88 2.69
4242 7628 3.491208 AGCATTAAGAGCTGGGCTG 57.509 52.632 0.00 0.00 39.88 4.85
4308 7694 0.251297 CACCATCACTTGCCCCAGAA 60.251 55.000 0.00 0.00 0.00 3.02
4437 7825 4.098807 GGAGTAGCTAAAAGGGTCAGAGAG 59.901 50.000 0.00 0.00 0.00 3.20
4438 7826 4.024670 GGAGTAGCTAAAAGGGTCAGAGA 58.975 47.826 0.00 0.00 0.00 3.10
4447 7837 4.707448 TGAGACAGAGGGAGTAGCTAAAAG 59.293 45.833 0.00 0.00 0.00 2.27
4518 7909 5.975988 AATACTCCCTCTGCCTCAAAATA 57.024 39.130 0.00 0.00 0.00 1.40
4548 7939 2.029838 AGGTCATGCGTCCATTCTTC 57.970 50.000 0.00 0.00 0.00 2.87
4662 8065 3.035363 TGAGTATTGCCCCATCGAGTTA 58.965 45.455 0.00 0.00 0.00 2.24
4770 8173 1.866015 ACTCCTGCACTGTAGCCATA 58.134 50.000 0.00 0.00 0.00 2.74
5204 8611 1.029681 AAAACTTCCGCACCTCCAAC 58.970 50.000 0.00 0.00 0.00 3.77
5211 8618 1.400494 ACACTGTCAAAACTTCCGCAC 59.600 47.619 0.00 0.00 0.00 5.34
5219 8626 7.387945 CGTAAATTTCCAAACACTGTCAAAAC 58.612 34.615 0.00 0.00 0.00 2.43
5237 8644 5.767816 AAAAGAAGCTGTGACCGTAAATT 57.232 34.783 0.00 0.00 0.00 1.82
5284 8691 3.937311 AGGATACGAGACATCAGTCAGCA 60.937 47.826 0.00 0.00 45.26 4.41
5310 8717 7.820331 AACTACAAGTTGGAGCATCATCGCT 62.820 44.000 15.41 0.00 40.28 4.93
5319 8726 4.547406 AAACGAAACTACAAGTTGGAGC 57.453 40.909 15.41 0.00 38.66 4.70
5322 8729 3.794564 GGCAAAACGAAACTACAAGTTGG 59.205 43.478 7.96 0.00 38.66 3.77
5351 8758 0.981943 ACTAACCCAGCTTAGCCGTT 59.018 50.000 0.00 3.93 0.00 4.44
5352 8759 0.249398 CACTAACCCAGCTTAGCCGT 59.751 55.000 0.00 0.00 0.00 5.68
5353 8760 0.462047 CCACTAACCCAGCTTAGCCG 60.462 60.000 0.00 0.00 0.00 5.52
5354 8761 0.107165 CCCACTAACCCAGCTTAGCC 60.107 60.000 0.00 0.00 0.00 3.93
5355 8762 0.618981 ACCCACTAACCCAGCTTAGC 59.381 55.000 0.00 0.00 0.00 3.09
5356 8763 2.039879 ACAACCCACTAACCCAGCTTAG 59.960 50.000 0.00 0.00 0.00 2.18
5453 8860 4.160252 TCCATTCTCATCTGATGACACGAA 59.840 41.667 16.06 17.04 35.06 3.85
5517 8924 6.994421 AAACTGAAAAGTTATGGGGTGATT 57.006 33.333 0.00 0.00 0.00 2.57
5519 8926 6.800072 AAAAACTGAAAAGTTATGGGGTGA 57.200 33.333 0.00 0.00 0.00 4.02
5562 8975 7.282901 CCAAATTCAAAGAAAACTTGGTGGAAT 59.717 33.333 0.00 0.00 0.00 3.01
5567 8980 7.120579 GGAAACCAAATTCAAAGAAAACTTGGT 59.879 33.333 13.82 13.82 45.27 3.67
5568 8981 7.471721 GGAAACCAAATTCAAAGAAAACTTGG 58.528 34.615 12.96 12.96 38.23 3.61
5655 9076 1.134907 CGGTGCCAATACGTCTAACCT 60.135 52.381 0.00 0.00 0.00 3.50



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

AutoCloner maintained by Alex Coulton.