Multiple sequence alignment - TraesCS3B01G398700

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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 TraesCS3B01G398700 chr3B 100.000 5063 0 0 1 5063 629796466 629801528 0.000000e+00 9350.0
1 TraesCS3B01G398700 chr3B 96.894 805 19 2 4 808 5801292 5800494 0.000000e+00 1343.0
2 TraesCS3B01G398700 chr3B 92.588 877 39 9 805 1677 5800108 5799254 0.000000e+00 1236.0
3 TraesCS3B01G398700 chr3B 94.118 748 40 4 1631 2375 5799267 5798521 0.000000e+00 1134.0
4 TraesCS3B01G398700 chr3B 95.392 586 27 0 4478 5063 651435567 651436152 0.000000e+00 933.0
5 TraesCS3B01G398700 chr3B 95.222 586 28 0 4478 5063 609698347 609698932 0.000000e+00 928.0
6 TraesCS3B01G398700 chr4D 95.485 3920 155 12 567 4479 451885704 451881800 0.000000e+00 6239.0
7 TraesCS3B01G398700 chr4D 85.953 1018 117 21 1 1007 379509334 379508332 0.000000e+00 1064.0
8 TraesCS3B01G398700 chr2B 95.599 2681 99 8 1 2677 638283841 638286506 0.000000e+00 4279.0
9 TraesCS3B01G398700 chr2B 96.516 1837 62 1 2643 4479 638286507 638288341 0.000000e+00 3037.0
10 TraesCS3B01G398700 chr2B 94.544 1228 59 4 2278 3505 39117010 39118229 0.000000e+00 1890.0
11 TraesCS3B01G398700 chr2B 95.205 584 28 0 4480 5063 89364862 89364279 0.000000e+00 924.0
12 TraesCS3B01G398700 chr2B 95.051 586 29 0 4478 5063 457841219 457841804 0.000000e+00 922.0
13 TraesCS3B01G398700 chr2B 92.667 150 11 0 1174 1323 184121780 184121631 3.070000e-52 217.0
14 TraesCS3B01G398700 chr1B 95.455 2684 105 11 1 2677 109351735 109349062 0.000000e+00 4265.0
15 TraesCS3B01G398700 chr1B 95.264 1837 84 2 2643 4479 109349061 109347228 0.000000e+00 2907.0
16 TraesCS3B01G398700 chr1B 95.392 586 27 0 4478 5063 46629891 46629306 0.000000e+00 933.0
17 TraesCS3B01G398700 chr2D 95.417 2531 99 13 1 2526 344564938 344567456 0.000000e+00 4015.0
18 TraesCS3B01G398700 chr2D 94.833 1916 80 10 2580 4489 344567455 344569357 0.000000e+00 2972.0
19 TraesCS3B01G398700 chr2D 84.233 463 68 3 2181 2639 356536017 356535556 3.600000e-121 446.0
20 TraesCS3B01G398700 chrUn 95.831 2183 77 11 1 2175 49942270 49944446 0.000000e+00 3515.0
21 TraesCS3B01G398700 chrUn 95.267 1838 76 3 2643 4480 49944915 49946741 0.000000e+00 2902.0
22 TraesCS3B01G398700 chrUn 94.231 468 25 1 2210 2677 49944449 49944914 0.000000e+00 713.0
23 TraesCS3B01G398700 chrUn 91.304 46 4 0 1428 1473 70167421 70167376 4.230000e-06 63.9
24 TraesCS3B01G398700 chr5B 95.234 2182 80 17 1 2175 547902082 547904246 0.000000e+00 3432.0
25 TraesCS3B01G398700 chr5B 95.811 1838 74 2 2643 4480 547904715 547906549 0.000000e+00 2964.0
26 TraesCS3B01G398700 chr5B 85.700 1000 121 19 16 1007 395330744 395331729 0.000000e+00 1035.0
27 TraesCS3B01G398700 chr5B 95.051 586 29 0 4478 5063 447090795 447091380 0.000000e+00 922.0
28 TraesCS3B01G398700 chr5B 95.051 586 28 1 4478 5063 395865617 395865033 0.000000e+00 920.0
29 TraesCS3B01G398700 chr5B 94.231 468 25 1 2210 2677 547904249 547904714 0.000000e+00 713.0
30 TraesCS3B01G398700 chr5B 91.667 120 8 1 1204 1323 239392640 239392523 1.130000e-36 165.0
31 TraesCS3B01G398700 chr6A 95.373 1664 74 2 2816 4479 74542208 74543868 0.000000e+00 2643.0
32 TraesCS3B01G398700 chr6A 95.201 1271 61 0 3209 4479 602833708 602834978 0.000000e+00 2010.0
33 TraesCS3B01G398700 chr7B 95.072 1664 80 1 2816 4479 459588255 459586594 0.000000e+00 2617.0
34 TraesCS3B01G398700 chr3D 86.940 1294 150 14 3195 4479 549726280 549724997 0.000000e+00 1435.0
35 TraesCS3B01G398700 chr3D 83.801 463 70 2 2181 2639 455016787 455016326 7.780000e-118 435.0
36 TraesCS3B01G398700 chr3D 83.547 468 67 7 2181 2639 549727473 549727007 3.620000e-116 429.0
37 TraesCS3B01G398700 chr4B 86.136 1017 118 18 1 1007 575619429 575618426 0.000000e+00 1075.0
38 TraesCS3B01G398700 chr7A 85.385 999 125 18 16 1007 641404994 641404010 0.000000e+00 1016.0
39 TraesCS3B01G398700 chr6B 95.392 586 27 0 4478 5063 339153286 339152701 0.000000e+00 933.0
40 TraesCS3B01G398700 chr6B 95.392 586 26 1 4478 5063 506618940 506619524 0.000000e+00 931.0
41 TraesCS3B01G398700 chr5D 91.304 46 4 0 1428 1473 90292737 90292782 4.230000e-06 63.9


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 TraesCS3B01G398700 chr3B 629796466 629801528 5062 False 9350.000000 9350 100.000000 1 5063 1 chr3B.!!$F2 5062
1 TraesCS3B01G398700 chr3B 5798521 5801292 2771 True 1237.666667 1343 94.533333 4 2375 3 chr3B.!!$R1 2371
2 TraesCS3B01G398700 chr3B 651435567 651436152 585 False 933.000000 933 95.392000 4478 5063 1 chr3B.!!$F3 585
3 TraesCS3B01G398700 chr3B 609698347 609698932 585 False 928.000000 928 95.222000 4478 5063 1 chr3B.!!$F1 585
4 TraesCS3B01G398700 chr4D 451881800 451885704 3904 True 6239.000000 6239 95.485000 567 4479 1 chr4D.!!$R2 3912
5 TraesCS3B01G398700 chr4D 379508332 379509334 1002 True 1064.000000 1064 85.953000 1 1007 1 chr4D.!!$R1 1006
6 TraesCS3B01G398700 chr2B 638283841 638288341 4500 False 3658.000000 4279 96.057500 1 4479 2 chr2B.!!$F3 4478
7 TraesCS3B01G398700 chr2B 39117010 39118229 1219 False 1890.000000 1890 94.544000 2278 3505 1 chr2B.!!$F1 1227
8 TraesCS3B01G398700 chr2B 89364279 89364862 583 True 924.000000 924 95.205000 4480 5063 1 chr2B.!!$R1 583
9 TraesCS3B01G398700 chr2B 457841219 457841804 585 False 922.000000 922 95.051000 4478 5063 1 chr2B.!!$F2 585
10 TraesCS3B01G398700 chr1B 109347228 109351735 4507 True 3586.000000 4265 95.359500 1 4479 2 chr1B.!!$R2 4478
11 TraesCS3B01G398700 chr1B 46629306 46629891 585 True 933.000000 933 95.392000 4478 5063 1 chr1B.!!$R1 585
12 TraesCS3B01G398700 chr2D 344564938 344569357 4419 False 3493.500000 4015 95.125000 1 4489 2 chr2D.!!$F1 4488
13 TraesCS3B01G398700 chrUn 49942270 49946741 4471 False 2376.666667 3515 95.109667 1 4480 3 chrUn.!!$F1 4479
14 TraesCS3B01G398700 chr5B 547902082 547906549 4467 False 2369.666667 3432 95.092000 1 4480 3 chr5B.!!$F3 4479
15 TraesCS3B01G398700 chr5B 395330744 395331729 985 False 1035.000000 1035 85.700000 16 1007 1 chr5B.!!$F1 991
16 TraesCS3B01G398700 chr5B 447090795 447091380 585 False 922.000000 922 95.051000 4478 5063 1 chr5B.!!$F2 585
17 TraesCS3B01G398700 chr5B 395865033 395865617 584 True 920.000000 920 95.051000 4478 5063 1 chr5B.!!$R2 585
18 TraesCS3B01G398700 chr6A 74542208 74543868 1660 False 2643.000000 2643 95.373000 2816 4479 1 chr6A.!!$F1 1663
19 TraesCS3B01G398700 chr6A 602833708 602834978 1270 False 2010.000000 2010 95.201000 3209 4479 1 chr6A.!!$F2 1270
20 TraesCS3B01G398700 chr7B 459586594 459588255 1661 True 2617.000000 2617 95.072000 2816 4479 1 chr7B.!!$R1 1663
21 TraesCS3B01G398700 chr3D 549724997 549727473 2476 True 932.000000 1435 85.243500 2181 4479 2 chr3D.!!$R2 2298
22 TraesCS3B01G398700 chr4B 575618426 575619429 1003 True 1075.000000 1075 86.136000 1 1007 1 chr4B.!!$R1 1006
23 TraesCS3B01G398700 chr7A 641404010 641404994 984 True 1016.000000 1016 85.385000 16 1007 1 chr7A.!!$R1 991
24 TraesCS3B01G398700 chr6B 339152701 339153286 585 True 933.000000 933 95.392000 4478 5063 1 chr6B.!!$R1 585
25 TraesCS3B01G398700 chr6B 506618940 506619524 584 False 931.000000 931 95.392000 4478 5063 1 chr6B.!!$F1 585

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
376 381 2.951642 TCAGTTTCTTGAGGTTGCTTGG 59.048 45.455 0.0 0.0 0.00 3.61 F
1970 2416 0.101399 CCGCTCTGAAGTAGCATCGT 59.899 55.000 0.0 0.0 40.08 3.73 F
2645 3127 0.465705 GATCTTCATCCGCCAGACCA 59.534 55.000 0.0 0.0 0.00 4.02 F
2912 3501 0.908910 TTCTTTCCAGATGGCCGCTA 59.091 50.000 0.0 0.0 34.44 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 2772 1.132721 ACATCTCCTATAGGCTGGGCA 60.133 52.381 14.5 0.0 34.44 5.36 R
2938 3527 0.107831 GGCCACCGCTGGTATCATTA 59.892 55.000 0.0 0.0 40.17 1.90 R
3883 4598 0.391597 GTGGTTGTTCCGTCTCCAGA 59.608 55.000 0.0 0.0 39.52 3.86 R
4160 4875 1.971481 AATGCACAGCACTGTCTCAA 58.029 45.000 0.0 0.0 43.04 3.02 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
132 136 8.140628 CAGTGTAGTAAGTGATCAGCAATAGAT 58.859 37.037 0.00 0.00 0.00 1.98
368 373 6.734104 CTGGTTAGAATCAGTTTCTTGAGG 57.266 41.667 0.00 0.00 42.15 3.86
376 381 2.951642 TCAGTTTCTTGAGGTTGCTTGG 59.048 45.455 0.00 0.00 0.00 3.61
614 621 3.181496 CGGCTTCCTTCTTCATTAAAGGC 60.181 47.826 0.00 0.00 41.56 4.35
886 1289 6.272822 ACTCTTTAGCCATTCCAAAACATC 57.727 37.500 0.00 0.00 0.00 3.06
1012 1415 8.446599 AGTCGTAAAACCAATGGATAATAAGG 57.553 34.615 6.16 0.00 0.00 2.69
1030 1433 2.863809 AGGGACTGTTTGATGGTGAAC 58.136 47.619 0.00 0.00 37.18 3.18
1031 1434 2.174639 AGGGACTGTTTGATGGTGAACA 59.825 45.455 0.00 0.00 37.18 3.18
1156 1559 2.649312 ACATGAAGAGGACCCATTTGGA 59.351 45.455 0.00 0.00 37.39 3.53
1168 1571 6.328934 AGGACCCATTTGGAAACACTTAAATT 59.671 34.615 0.00 0.00 42.67 1.82
1182 1585 6.868622 ACACTTAAATTATTTTATGGCGCCA 58.131 32.000 34.80 34.80 30.53 5.69
1202 1605 6.324819 CGCCATTGTTTCTGATCTACAAAAT 58.675 36.000 0.00 0.00 35.62 1.82
1209 1612 9.959749 TTGTTTCTGATCTACAAAATAACAACC 57.040 29.630 0.00 0.00 0.00 3.77
1291 1695 5.220710 AGCCACCATGACTCTAATATCAC 57.779 43.478 0.00 0.00 0.00 3.06
1334 1738 0.250945 TCCCTATGCCGTGCAACAAA 60.251 50.000 2.68 0.00 43.62 2.83
1341 1745 1.079503 GCCGTGCAACAAACCAAAAA 58.920 45.000 0.00 0.00 35.74 1.94
1348 1752 5.465056 CGTGCAACAAACCAAAAATAATCCT 59.535 36.000 0.00 0.00 35.74 3.24
1611 2022 2.666022 ACGCCTGCGCAAAAATAATTTC 59.334 40.909 13.05 0.00 44.19 2.17
1663 2108 6.325919 TCTGCCCCGCAAAAATAATAATAG 57.674 37.500 0.00 0.00 38.41 1.73
1740 2186 8.854614 ACAAGTTTCTGTAAAATAGATCAGCT 57.145 30.769 0.00 0.00 0.00 4.24
1786 2232 3.524095 AATTCACAACCCATCACCAGA 57.476 42.857 0.00 0.00 0.00 3.86
1803 2249 3.452627 ACCAGACCATAGAAATCTTCGCT 59.547 43.478 0.00 0.00 34.02 4.93
1824 2270 5.257262 GCTTGACCCTTTTTAGAAGGAGAT 58.743 41.667 2.83 0.00 39.81 2.75
1875 2321 4.349048 CAGATTCCTTATCCAGATCCACCA 59.651 45.833 0.00 0.00 33.45 4.17
1966 2412 0.108615 GAAGCCGCTCTGAAGTAGCA 60.109 55.000 0.00 0.00 40.08 3.49
1967 2413 0.539051 AAGCCGCTCTGAAGTAGCAT 59.461 50.000 0.00 0.00 40.08 3.79
1970 2416 0.101399 CCGCTCTGAAGTAGCATCGT 59.899 55.000 0.00 0.00 40.08 3.73
2064 2511 1.681166 CCACCTCTTCCCTTCTGCATG 60.681 57.143 0.00 0.00 0.00 4.06
2146 2593 7.246171 AGACTAGCCAAGATTTCTCTTACAA 57.754 36.000 0.00 0.00 39.78 2.41
2223 2671 9.823647 ATGAGAGATAACCTAACACTTACAATG 57.176 33.333 0.00 0.00 0.00 2.82
2225 2673 9.654663 GAGAGATAACCTAACACTTACAATGTT 57.345 33.333 0.00 0.00 42.78 2.71
2226 2674 9.436957 AGAGATAACCTAACACTTACAATGTTG 57.563 33.333 0.00 0.00 40.47 3.33
2399 2852 4.368391 CAACGCTTGCCAGAGAGT 57.632 55.556 0.00 0.00 0.00 3.24
2426 2883 9.342308 ACTATCAAGAGATTTGTTTTTCAGACA 57.658 29.630 0.00 0.00 35.67 3.41
2444 2901 6.291377 TCAGACACATCTTGCTACTTTTTCT 58.709 36.000 0.00 0.00 30.42 2.52
2496 2953 2.957402 TGCCATGTCTCTGGTTCTTT 57.043 45.000 0.00 0.00 38.63 2.52
2534 2991 6.460103 AGCACTATCCCATCCTGATTATTT 57.540 37.500 0.00 0.00 0.00 1.40
2576 3033 3.369451 GCTCAAGATCGTCTTTGAGAACC 59.631 47.826 20.74 5.23 33.78 3.62
2645 3127 0.465705 GATCTTCATCCGCCAGACCA 59.534 55.000 0.00 0.00 0.00 4.02
2678 3224 2.430332 CGAGAGAGATCTTTGCCCTCTT 59.570 50.000 11.14 0.00 37.40 2.85
2701 3247 1.153449 GTTCGATGGGATGCCGTCA 60.153 57.895 23.58 9.43 0.00 4.35
2753 3326 4.965283 TCCCCTCCCACATAAAGAAATT 57.035 40.909 0.00 0.00 0.00 1.82
2862 3451 8.035984 TGTTAATCATCACAACTAATACCACGA 58.964 33.333 0.00 0.00 0.00 4.35
2908 3497 5.930135 TCTATTACTTCTTTCCAGATGGCC 58.070 41.667 0.00 0.00 34.44 5.36
2912 3501 0.908910 TTCTTTCCAGATGGCCGCTA 59.091 50.000 0.00 0.00 34.44 4.26
2936 3525 6.681729 TTAAACAAGAGGAGGTAGACACAT 57.318 37.500 0.00 0.00 0.00 3.21
2938 3527 4.054359 ACAAGAGGAGGTAGACACATCT 57.946 45.455 0.00 0.00 35.77 2.90
2965 3554 0.965363 CCAGCGGTGGCCAAATTACT 60.965 55.000 22.48 0.00 41.24 2.24
3122 3711 2.572290 ACAAACTTCTTTCAGGGTCCG 58.428 47.619 0.00 0.00 0.00 4.79
3231 3870 7.824289 CCATATACGATGGATACCATTTTCTGT 59.176 37.037 4.74 2.90 45.26 3.41
3236 3875 6.094048 ACGATGGATACCATTTTCTGTCTTTG 59.906 38.462 4.74 0.00 45.26 2.77
3240 3879 6.655003 TGGATACCATTTTCTGTCTTTGACTC 59.345 38.462 0.00 0.00 33.15 3.36
3338 4048 5.778241 TCTCCTTACCTATTCAACACAGACA 59.222 40.000 0.00 0.00 0.00 3.41
3613 4328 2.092914 GGGCAACACAGTTAGGCTCTAT 60.093 50.000 0.00 0.00 39.74 1.98
3626 4341 9.561069 CAGTTAGGCTCTATAACCATAATGTTT 57.439 33.333 0.00 0.00 34.34 2.83
3733 4448 5.779771 AGGCAAAAGAATGGTAATCCTTTGA 59.220 36.000 2.67 0.00 32.34 2.69
3881 4596 2.224769 ACCACGGTGAACTTCCAATCAT 60.225 45.455 10.28 0.00 0.00 2.45
3883 4598 4.199310 CCACGGTGAACTTCCAATCATAT 58.801 43.478 10.28 0.00 0.00 1.78
3914 4629 1.298340 CAACCACTATCACGGCCCA 59.702 57.895 0.00 0.00 0.00 5.36
3990 4705 1.220749 CCGTCGGACCCACATGAAT 59.779 57.895 4.91 0.00 0.00 2.57
4007 4722 3.900971 TGAATGAAGGGCAAGCATATGA 58.099 40.909 6.97 0.00 0.00 2.15
4149 4864 8.361139 TCTATGTTTATCCTCCTTTTCGATCTC 58.639 37.037 0.00 0.00 0.00 2.75
4160 4875 5.366768 TCCTTTTCGATCTCATGTAATCCCT 59.633 40.000 0.00 0.00 0.00 4.20
4215 4930 4.462133 TCCGCTACTTAGACTGCTCTATT 58.538 43.478 0.00 0.00 0.00 1.73
4329 5048 2.989571 AGATCACAAGGGTCCTTTCCTT 59.010 45.455 0.00 0.00 44.76 3.36
4453 5172 0.525761 GCTTACATTCGGCCTTTGCA 59.474 50.000 0.00 0.00 40.13 4.08
4493 5213 8.030106 GGGTCATCTAGTTAGAATAAAGGATCG 58.970 40.741 0.00 0.00 35.69 3.69
4551 5271 6.963083 ACTAGAACATATACACCTCCTGAC 57.037 41.667 0.00 0.00 0.00 3.51
4566 5286 5.770162 ACCTCCTGACCAAATTAAAGTTGAG 59.230 40.000 4.29 0.00 0.00 3.02
4647 5367 2.751166 TCTGTGAGGAAGCTGCTAAC 57.249 50.000 0.90 0.00 0.00 2.34
4940 5660 3.822735 CCTGCTGATTTTCTTGTTCTGGA 59.177 43.478 0.00 0.00 0.00 3.86
5001 5721 7.548427 GGTAGACCCTTCTTGAATACTGTTAAC 59.452 40.741 0.00 0.00 32.75 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 118 7.773489 AGAGCTATCTATTGCTGATCACTTA 57.227 36.000 3.62 0.00 38.92 2.24
132 136 8.094548 TGCACTTCAATCTAAAAGTAAGAGCTA 58.905 33.333 0.00 0.00 34.05 3.32
296 301 3.819368 TCATGTGACATGTGGTGTTCTT 58.181 40.909 23.39 0.00 42.36 2.52
376 381 8.883731 AGTGAGTGTGAAATATTACATGCTAAC 58.116 33.333 0.00 0.00 0.00 2.34
614 621 2.808543 CCAACCTGAAAGAAAGGACTCG 59.191 50.000 0.00 0.00 38.27 4.18
886 1289 8.768955 GGTCTACAATACTGCAAAATCAGATAG 58.231 37.037 0.00 0.00 37.51 2.08
1012 1415 4.647424 TTTGTTCACCATCAAACAGTCC 57.353 40.909 0.00 0.00 36.78 3.85
1030 1433 4.685169 AGTCACCACGAGCATAAATTTG 57.315 40.909 0.00 0.00 0.00 2.32
1031 1434 4.634443 GGTAGTCACCACGAGCATAAATTT 59.366 41.667 0.00 0.00 45.04 1.82
1156 1559 7.819900 TGGCGCCATAAAATAATTTAAGTGTTT 59.180 29.630 29.03 0.00 34.80 2.83
1168 1571 5.126222 TCAGAAACAATGGCGCCATAAAATA 59.874 36.000 40.54 18.87 35.31 1.40
1202 1605 3.181452 ACAAGCCTCGGTAAAGGTTGTTA 60.181 43.478 1.30 0.00 37.36 2.41
1209 1612 7.605410 TTAGAAATAACAAGCCTCGGTAAAG 57.395 36.000 0.00 0.00 0.00 1.85
1243 1646 4.830046 TGTTACAATAAGCAAGCAGGGAAA 59.170 37.500 0.00 0.00 0.00 3.13
1291 1695 6.971602 AGTATATCGAACAGGTGTGTATGAG 58.028 40.000 0.00 0.00 35.08 2.90
1629 2040 1.308998 CGGGGCAGAACCACATTATC 58.691 55.000 0.00 0.00 45.24 1.75
1663 2108 4.584327 ACAAAAGCCAGAACCACATTAC 57.416 40.909 0.00 0.00 0.00 1.89
1735 2181 3.009723 GCCACAGTATTAAGCAAGCTGA 58.990 45.455 0.00 0.00 0.00 4.26
1740 2186 4.320023 TCGAAAGCCACAGTATTAAGCAA 58.680 39.130 0.00 0.00 0.00 3.91
1767 2213 2.555227 GGTCTGGTGATGGGTTGTGAAT 60.555 50.000 0.00 0.00 0.00 2.57
1774 2220 2.568546 TCTATGGTCTGGTGATGGGT 57.431 50.000 0.00 0.00 0.00 4.51
1786 2232 4.192317 GGTCAAGCGAAGATTTCTATGGT 58.808 43.478 0.00 0.00 27.80 3.55
1803 2249 5.488341 CGATCTCCTTCTAAAAAGGGTCAA 58.512 41.667 4.10 0.00 37.99 3.18
1824 2270 1.277842 TGAGTTTAATGGGAGCTGCGA 59.722 47.619 0.00 0.00 0.00 5.10
1986 2432 2.773487 AGCAAATACGTTGGTAGCACA 58.227 42.857 0.00 0.00 46.06 4.57
2064 2511 4.025401 CTGGCGGTTGGAACACGC 62.025 66.667 13.58 13.58 43.19 5.34
2223 2671 9.912634 TGATCTATTTGGAAATTTTGAGACAAC 57.087 29.630 0.00 0.00 0.00 3.32
2324 2772 1.132721 ACATCTCCTATAGGCTGGGCA 60.133 52.381 14.50 0.00 34.44 5.36
2426 2883 6.715347 AAACCAGAAAAAGTAGCAAGATGT 57.285 33.333 0.00 0.00 0.00 3.06
2534 2991 5.935206 TGAGCGAAACAATAAACTGTATGGA 59.065 36.000 0.00 0.00 0.00 3.41
2576 3033 2.749076 TCATTGACTTGAAGATTGGCCG 59.251 45.455 0.00 0.00 0.00 6.13
2645 3127 4.344679 AGATCTCTCTCGCCTCATTTTCAT 59.655 41.667 0.00 0.00 0.00 2.57
2678 3224 1.526887 GCATCCCATCGAACCCAGA 59.473 57.895 0.00 0.00 0.00 3.86
2701 3247 2.564062 CTCAATGCCAGTGGGTGAAATT 59.436 45.455 12.15 0.00 36.17 1.82
2798 3373 8.769359 AGACTTAACAGGCCATTAGTAGTAAAT 58.231 33.333 5.01 0.00 0.00 1.40
2908 3497 5.978322 GTCTACCTCCTCTTGTTTAATAGCG 59.022 44.000 0.00 0.00 0.00 4.26
2912 3501 6.681729 TGTGTCTACCTCCTCTTGTTTAAT 57.318 37.500 0.00 0.00 0.00 1.40
2936 3525 1.070134 GCCACCGCTGGTATCATTAGA 59.930 52.381 0.00 0.00 40.17 2.10
2938 3527 0.107831 GGCCACCGCTGGTATCATTA 59.892 55.000 0.00 0.00 40.17 1.90
3231 3870 4.960938 AGCTTGTGTGTATGAGTCAAAGA 58.039 39.130 0.00 0.00 0.00 2.52
3236 3875 6.938542 GCTAATTAGCTTGTGTGTATGAGTC 58.061 40.000 26.79 0.00 45.62 3.36
3338 4048 2.224426 TGTGCTTCCGACATAGTGGTTT 60.224 45.455 0.00 0.00 0.00 3.27
3613 4328 4.614764 CGCAGTGCACAAACATTATGGTTA 60.615 41.667 21.04 0.00 0.00 2.85
3626 4341 1.733912 GATGATCTTTCGCAGTGCACA 59.266 47.619 21.04 0.00 0.00 4.57
3881 4596 2.232941 GTGGTTGTTCCGTCTCCAGATA 59.767 50.000 0.00 0.00 39.52 1.98
3883 4598 0.391597 GTGGTTGTTCCGTCTCCAGA 59.608 55.000 0.00 0.00 39.52 3.86
3914 4629 6.265422 CCTTTTGTCAACTCCCTTGATAAAGT 59.735 38.462 13.66 0.00 45.41 2.66
3990 4705 3.316029 CGAAATCATATGCTTGCCCTTCA 59.684 43.478 0.00 0.00 0.00 3.02
4007 4722 3.578688 GAAGTGCATTTGAAGCCGAAAT 58.421 40.909 0.00 0.00 0.00 2.17
4149 4864 3.624861 GCACTGTCTCAAGGGATTACATG 59.375 47.826 0.00 0.00 0.00 3.21
4160 4875 1.971481 AATGCACAGCACTGTCTCAA 58.029 45.000 0.00 0.00 43.04 3.02
4215 4930 3.257469 TGGTTGTTTCAAAAGCATGCA 57.743 38.095 21.98 0.00 30.50 3.96
4271 4990 6.396829 AAATAATCATGTAGAGGCCTTTGC 57.603 37.500 6.77 5.31 0.00 3.68
4329 5048 5.814481 TGGAAATGATACACCAAGTCATGA 58.186 37.500 0.00 0.00 33.19 3.07
4493 5213 4.632538 ACCACAGTTGAAGTTTTAGCAC 57.367 40.909 0.00 0.00 0.00 4.40
4551 5271 7.702348 GCAATACTAGGCTCAACTTTAATTTGG 59.298 37.037 0.00 0.00 0.00 3.28
4566 5286 8.097662 AGATCTTTAACCATAGCAATACTAGGC 58.902 37.037 0.00 0.00 33.29 3.93
4596 5316 9.705103 ATAACATGCCCATCAATATTATTAGCT 57.295 29.630 0.00 0.00 0.00 3.32
4647 5367 5.581126 TCTTAGCATTGGGTTTAGCAATG 57.419 39.130 0.00 0.00 38.81 2.82
4940 5660 4.677182 ACAAAAGCTATCTTGTGGGGAAT 58.323 39.130 7.71 0.00 40.97 3.01
5001 5721 4.031028 CCTTTTTGCAATCGATCTTAGCG 58.969 43.478 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.