Multiple sequence alignment - TraesCS7B01G009700

Loading Multiple Alignment...

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 TraesCS7B01G009700 chr7B 100.000 2935 0 0 1 2935 6035340 6032406 0.000000e+00 5421
1 TraesCS7B01G009700 chr7B 92.500 360 25 2 556 914 6375075 6374717 5.610000e-142 514
2 TraesCS7B01G009700 chr7B 81.505 465 60 9 1455 1912 6180965 6180520 2.780000e-95 359
3 TraesCS7B01G009700 chr7B 88.148 135 13 3 2629 2760 104027462 104027328 1.090000e-34 158
4 TraesCS7B01G009700 chr7D 85.979 2104 193 51 15 2071 64468803 64466755 0.000000e+00 2158
5 TraesCS7B01G009700 chr7D 91.429 490 37 4 2097 2585 64466761 64466276 0.000000e+00 667
6 TraesCS7B01G009700 chr7D 82.415 472 69 9 1455 1913 64700230 64699760 1.640000e-107 399
7 TraesCS7B01G009700 chr7D 86.025 322 33 7 2626 2935 64463285 64462964 4.690000e-88 335
8 TraesCS7B01G009700 chr7D 92.340 235 18 0 671 905 64736590 64736356 4.690000e-88 335
9 TraesCS7B01G009700 chr7A 85.443 1525 144 43 32 1516 68321398 68319912 0.000000e+00 1515
10 TraesCS7B01G009700 chr7A 93.073 794 45 2 1764 2557 68319882 68319099 0.000000e+00 1153
11 TraesCS7B01G009700 chr7A 85.160 438 41 12 494 914 68902058 68901628 7.520000e-116 427
12 TraesCS7B01G009700 chr7A 82.590 471 70 6 1455 1913 68862403 68861933 3.520000e-109 405
13 TraesCS7B01G009700 chr7A 89.474 133 12 2 2629 2760 379033628 379033759 1.810000e-37 167
14 TraesCS7B01G009700 chr6B 76.838 816 146 29 1296 2096 43145424 43146211 1.260000e-113 420
15 TraesCS7B01G009700 chr6B 89.922 258 24 2 656 912 43090146 43089890 6.060000e-87 331
16 TraesCS7B01G009700 chr6B 88.123 261 29 2 637 896 42860624 42860883 2.840000e-80 309
17 TraesCS7B01G009700 chrUn 76.662 797 144 28 1309 2090 93939466 93940235 1.270000e-108 403
18 TraesCS7B01G009700 chrUn 75.556 810 161 21 1374 2163 93880485 93881277 5.980000e-97 364
19 TraesCS7B01G009700 chrUn 82.653 294 43 6 610 896 93876847 93877139 1.350000e-63 254
20 TraesCS7B01G009700 chr6A 75.857 729 134 22 1306 2022 24706130 24706828 1.690000e-87 333
21 TraesCS7B01G009700 chr6A 85.159 283 36 6 637 915 24573881 24574161 4.790000e-73 285
22 TraesCS7B01G009700 chr3B 86.047 129 17 1 2633 2760 666734869 666734741 1.420000e-28 137
23 TraesCS7B01G009700 chr4A 76.419 229 44 9 2631 2852 693870291 693870066 6.650000e-22 115
24 TraesCS7B01G009700 chr1D 83.200 125 20 1 2637 2760 459054197 459054073 2.390000e-21 113


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 TraesCS7B01G009700 chr7B 6032406 6035340 2934 True 5421.000000 5421 100.0000 1 2935 1 chr7B.!!$R1 2934
1 TraesCS7B01G009700 chr7D 64462964 64468803 5839 True 1053.333333 2158 87.8110 15 2935 3 chr7D.!!$R3 2920
2 TraesCS7B01G009700 chr7A 68319099 68321398 2299 True 1334.000000 1515 89.2580 32 2557 2 chr7A.!!$R3 2525
3 TraesCS7B01G009700 chr6B 43145424 43146211 787 False 420.000000 420 76.8380 1296 2096 1 chr6B.!!$F2 800
4 TraesCS7B01G009700 chrUn 93939466 93940235 769 False 403.000000 403 76.6620 1309 2090 1 chrUn.!!$F1 781
5 TraesCS7B01G009700 chrUn 93876847 93881277 4430 False 309.000000 364 79.1045 610 2163 2 chrUn.!!$F2 1553
6 TraesCS7B01G009700 chr6A 24706130 24706828 698 False 333.000000 333 75.8570 1306 2022 1 chr6A.!!$F2 716

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
558 595 0.255890 GCTCCAAACCCTGGCTGATA 59.744 55.0 0.00 0.0 45.98 2.15 F
1126 4150 0.319125 GTCCCGGAGCATCGAGATTC 60.319 60.0 0.73 0.0 34.37 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 4763 0.397564 TCTCTGAAGCATGCACCACA 59.602 50.0 21.98 12.47 0.00 4.17 R
2837 8856 0.031616 GTGTGGGATCCTCTCCTCCT 60.032 60.0 12.58 0.00 44.28 3.69 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
231 244 9.908152 ACCATATACTTAAAAAGTGAACTTTGC 57.092 29.630 9.11 0.00 44.69 3.68
440 458 8.520351 CCCGAAATAAACCTGTAAAGAAGAAAT 58.480 33.333 0.00 0.00 0.00 2.17
449 467 8.637196 ACCTGTAAAGAAGAAATAGGAAAAGG 57.363 34.615 0.00 0.00 0.00 3.11
462 480 8.762481 AAATAGGAAAAGGAATATAAACGGCT 57.238 30.769 0.00 0.00 0.00 5.52
465 483 4.812626 GGAAAAGGAATATAAACGGCTCGA 59.187 41.667 1.50 0.00 0.00 4.04
467 485 4.667519 AAGGAATATAAACGGCTCGACT 57.332 40.909 1.50 0.00 0.00 4.18
468 486 4.667519 AGGAATATAAACGGCTCGACTT 57.332 40.909 1.50 0.00 0.00 3.01
469 487 4.618965 AGGAATATAAACGGCTCGACTTC 58.381 43.478 1.50 0.00 0.00 3.01
470 488 3.424529 GGAATATAAACGGCTCGACTTCG 59.575 47.826 1.50 0.00 41.45 3.79
497 534 2.288518 CCCAGTAGCTTCCGATAAGAGC 60.289 54.545 0.00 0.00 36.68 4.09
506 543 1.283181 CGATAAGAGCCCGTCTCCG 59.717 63.158 0.00 0.00 42.90 4.63
509 546 1.614413 GATAAGAGCCCGTCTCCGAAT 59.386 52.381 0.00 0.00 42.90 3.34
510 547 1.030457 TAAGAGCCCGTCTCCGAATC 58.970 55.000 0.00 0.00 42.90 2.52
558 595 0.255890 GCTCCAAACCCTGGCTGATA 59.744 55.000 0.00 0.00 45.98 2.15
585 622 3.423162 CTTCTCTCGCTCCGGCCAG 62.423 68.421 2.24 0.00 34.44 4.85
621 658 1.439644 GCGTCTCCTCCACCATCTC 59.560 63.158 0.00 0.00 0.00 2.75
646 695 0.955428 GCCAACGCACATTCCTCTCA 60.955 55.000 0.00 0.00 34.03 3.27
698 3455 2.353610 GCCACCCCATCAAGCAAGG 61.354 63.158 0.00 0.00 0.00 3.61
699 3456 2.353610 CCACCCCATCAAGCAAGGC 61.354 63.158 0.00 0.00 0.00 4.35
702 3459 2.361771 CCCATCAAGCAAGGCCCT 59.638 61.111 0.00 0.00 0.00 5.19
703 3460 1.305549 CCCATCAAGCAAGGCCCTT 60.306 57.895 0.00 0.00 0.00 3.95
704 3461 1.325476 CCCATCAAGCAAGGCCCTTC 61.325 60.000 0.00 0.00 0.00 3.46
913 3925 2.574399 GAGGTCCTCCACGAGCAC 59.426 66.667 7.78 0.00 35.89 4.40
914 3926 2.997897 AGGTCCTCCACGAGCACC 60.998 66.667 0.00 0.00 40.60 5.01
965 3977 1.202582 CGATGACAACGAGGAGGACTT 59.797 52.381 0.00 0.00 0.00 3.01
967 3979 1.699730 TGACAACGAGGAGGACTTGA 58.300 50.000 0.00 0.00 34.46 3.02
981 4005 2.435938 TTGAAGGCGCCGGTCATC 60.436 61.111 29.06 19.91 0.00 2.92
1024 4048 2.178273 GGCACGCGGAATGTTTCC 59.822 61.111 12.47 0.00 46.62 3.13
1087 4111 2.297129 GGCAGCCTTGTCCTCCTCT 61.297 63.158 3.29 0.00 0.00 3.69
1089 4113 0.392327 GCAGCCTTGTCCTCCTCTTC 60.392 60.000 0.00 0.00 0.00 2.87
1126 4150 0.319125 GTCCCGGAGCATCGAGATTC 60.319 60.000 0.73 0.00 34.37 2.52
1128 4152 1.005630 CCGGAGCATCGAGATTCCC 60.006 63.158 0.00 0.00 34.37 3.97
1131 4155 1.410850 GGAGCATCGAGATTCCCCCA 61.411 60.000 0.00 0.00 34.37 4.96
1151 4178 2.060050 ATCTGTCGGACTGGACCTAG 57.940 55.000 14.00 0.00 36.07 3.02
1186 4213 5.420409 AGTTACAGGAGGTCGATTGATTTC 58.580 41.667 0.00 0.00 0.00 2.17
1189 4216 4.911390 ACAGGAGGTCGATTGATTTCTTT 58.089 39.130 0.00 0.00 0.00 2.52
1192 4219 6.088824 CAGGAGGTCGATTGATTTCTTTTTG 58.911 40.000 0.00 0.00 0.00 2.44
1194 4221 6.265422 AGGAGGTCGATTGATTTCTTTTTGTT 59.735 34.615 0.00 0.00 0.00 2.83
1196 4223 6.447162 AGGTCGATTGATTTCTTTTTGTTCC 58.553 36.000 0.00 0.00 0.00 3.62
1197 4224 5.342259 GGTCGATTGATTTCTTTTTGTTCCG 59.658 40.000 0.00 0.00 0.00 4.30
1198 4225 5.342259 GTCGATTGATTTCTTTTTGTTCCGG 59.658 40.000 0.00 0.00 0.00 5.14
1199 4226 5.009210 TCGATTGATTTCTTTTTGTTCCGGT 59.991 36.000 0.00 0.00 0.00 5.28
1200 4227 6.205076 TCGATTGATTTCTTTTTGTTCCGGTA 59.795 34.615 0.00 0.00 0.00 4.02
1207 4234 2.759538 TTTTGTTCCGGTAACTTGCG 57.240 45.000 0.00 0.00 38.99 4.85
1245 4272 2.088423 CTGAGAACTCTGTCCGCTAGT 58.912 52.381 3.51 0.00 0.00 2.57
1253 4280 1.070134 TCTGTCCGCTAGTTTTGCACT 59.930 47.619 0.00 0.00 39.87 4.40
1278 4305 1.640428 CGAGGCGTTCTTCATTAGCA 58.360 50.000 0.00 0.00 0.00 3.49
1283 4310 3.821033 AGGCGTTCTTCATTAGCAAGTTT 59.179 39.130 0.00 0.00 0.00 2.66
1295 4325 0.521735 GCAAGTTTCCTAAGGGCGTG 59.478 55.000 0.00 0.00 0.00 5.34
1452 4485 0.466543 GTACACCATGGATACCCGCA 59.533 55.000 21.47 0.00 34.29 5.69
1518 4551 1.655329 GAGCAGTACTCCCCGATCG 59.345 63.158 8.51 8.51 39.75 3.69
1520 4553 0.683504 AGCAGTACTCCCCGATCGTT 60.684 55.000 15.09 0.00 0.00 3.85
1568 4601 1.315981 TGCTCGAGTCAGAAGGCGAT 61.316 55.000 15.13 0.00 31.87 4.58
1586 4619 2.422597 GATGTCATGTTTGTCGGTCCA 58.577 47.619 0.00 0.00 0.00 4.02
1604 4637 2.948979 TCCAGTGTTCGCAACAAAAGAT 59.051 40.909 3.74 0.00 44.16 2.40
1626 4659 2.750665 GGATGCCCCAAATCCATCC 58.249 57.895 3.43 3.43 45.65 3.51
1652 4685 1.215647 CGAGGTGTACAGGCTGGAC 59.784 63.158 23.24 23.24 0.00 4.02
1750 4783 0.801251 GTGGTGCATGCTTCAGAGAC 59.199 55.000 20.33 6.38 0.00 3.36
1757 4790 4.070552 GCTTCAGAGACGCCGGGT 62.071 66.667 2.18 0.00 0.00 5.28
1762 4795 4.379243 AGAGACGCCGGGTTGCAG 62.379 66.667 2.18 0.00 0.00 4.41
1799 4832 2.920724 TTGTGGGTGATCTTGACGAA 57.079 45.000 0.00 0.00 0.00 3.85
1914 4947 1.454539 CGGTGGTTCTTCCCTGGTT 59.545 57.895 0.00 0.00 34.77 3.67
1932 4965 0.743688 TTTTGTGATGCCACTTGCGT 59.256 45.000 0.00 0.00 45.60 5.24
2105 5150 0.389817 TGTGAGAAATGGAGACGGCG 60.390 55.000 4.80 4.80 0.00 6.46
2120 5165 1.269621 ACGGCGAGGTATTGCTATGAC 60.270 52.381 16.62 0.00 35.97 3.06
2149 5196 5.037598 AGTAAGGCCTATAAACCTCCAAGT 58.962 41.667 5.16 0.00 34.31 3.16
2164 5211 1.303309 CAAGTGCTACTATGCAGCCC 58.697 55.000 0.00 0.00 44.20 5.19
2236 5283 7.148272 GCATGGCTCAAATTATTCTAGGATCTC 60.148 40.741 0.00 0.00 0.00 2.75
2281 5328 4.438797 CGCTGTTTGTGAAATTTCAGACAG 59.561 41.667 31.22 31.22 41.62 3.51
2313 5360 9.952030 TGAAGTTTATGGATTGTATTGTACTCA 57.048 29.630 0.00 0.00 0.00 3.41
2403 5450 5.476945 GGATTTCCCTTAGTTTGTGTGTGAT 59.523 40.000 0.00 0.00 0.00 3.06
2442 5489 4.243007 TGTTGCATCGTCGATGAGATAT 57.757 40.909 33.73 0.00 42.09 1.63
2457 5504 9.686683 TCGATGAGATATAATACCTCTGAATGA 57.313 33.333 0.00 0.00 0.00 2.57
2480 5527 8.902540 TGAAGTAGAATTTATTGTGTCTGTGT 57.097 30.769 0.00 0.00 0.00 3.72
2481 5528 8.773645 TGAAGTAGAATTTATTGTGTCTGTGTG 58.226 33.333 0.00 0.00 0.00 3.82
2526 5573 3.616956 TGAACTTGTAGATGGAGCTGG 57.383 47.619 0.00 0.00 0.00 4.85
2532 5579 1.340017 TGTAGATGGAGCTGGTTTGCC 60.340 52.381 0.00 0.00 0.00 4.52
2533 5580 0.255890 TAGATGGAGCTGGTTTGCCC 59.744 55.000 0.00 0.00 0.00 5.36
2534 5581 2.361610 ATGGAGCTGGTTTGCCCG 60.362 61.111 0.00 0.00 35.15 6.13
2567 5615 3.556843 CCATCCAATGTTGAACCCCAAAC 60.557 47.826 0.00 0.00 36.36 2.93
2570 5618 2.159028 CCAATGTTGAACCCCAAACGTT 60.159 45.455 0.00 0.00 36.36 3.99
2578 5626 0.887387 ACCCCAAACGTTCGTGGATG 60.887 55.000 18.61 12.08 37.03 3.51
2591 5639 4.513519 GGATGCATCCGTCGTTCA 57.486 55.556 29.34 0.00 37.19 3.18
2592 5640 2.762360 GGATGCATCCGTCGTTCAA 58.238 52.632 29.34 0.00 37.19 2.69
2593 5641 1.083489 GGATGCATCCGTCGTTCAAA 58.917 50.000 29.34 0.00 37.19 2.69
2594 5642 1.670811 GGATGCATCCGTCGTTCAAAT 59.329 47.619 29.34 0.00 37.19 2.32
2595 5643 2.097466 GGATGCATCCGTCGTTCAAATT 59.903 45.455 29.34 0.00 37.19 1.82
2596 5644 2.892373 TGCATCCGTCGTTCAAATTC 57.108 45.000 0.00 0.00 0.00 2.17
2597 5645 1.466950 TGCATCCGTCGTTCAAATTCC 59.533 47.619 0.00 0.00 0.00 3.01
2598 5646 1.202143 GCATCCGTCGTTCAAATTCCC 60.202 52.381 0.00 0.00 0.00 3.97
2599 5647 1.400494 CATCCGTCGTTCAAATTCCCC 59.600 52.381 0.00 0.00 0.00 4.81
2600 5648 0.688487 TCCGTCGTTCAAATTCCCCT 59.312 50.000 0.00 0.00 0.00 4.79
2601 5649 1.901159 TCCGTCGTTCAAATTCCCCTA 59.099 47.619 0.00 0.00 0.00 3.53
2602 5650 2.302445 TCCGTCGTTCAAATTCCCCTAA 59.698 45.455 0.00 0.00 0.00 2.69
2603 5651 3.075884 CCGTCGTTCAAATTCCCCTAAA 58.924 45.455 0.00 0.00 0.00 1.85
2604 5652 3.692593 CCGTCGTTCAAATTCCCCTAAAT 59.307 43.478 0.00 0.00 0.00 1.40
2605 5653 4.157105 CCGTCGTTCAAATTCCCCTAAATT 59.843 41.667 0.00 0.00 0.00 1.82
2606 5654 5.092781 CGTCGTTCAAATTCCCCTAAATTG 58.907 41.667 0.00 0.00 0.00 2.32
2607 5655 5.407502 GTCGTTCAAATTCCCCTAAATTGG 58.592 41.667 0.00 0.00 0.00 3.16
2608 5656 5.047590 GTCGTTCAAATTCCCCTAAATTGGT 60.048 40.000 0.00 0.00 0.00 3.67
2609 5657 6.151480 GTCGTTCAAATTCCCCTAAATTGGTA 59.849 38.462 0.00 0.00 0.00 3.25
2642 8661 3.732892 CCGCCGCGACATTTGGTT 61.733 61.111 15.93 0.00 0.00 3.67
2652 8671 0.884704 ACATTTGGTTGCTCGCTCGT 60.885 50.000 0.00 0.00 0.00 4.18
2683 8702 2.007576 CCCCGATCCCCTTCCTTTT 58.992 57.895 0.00 0.00 0.00 2.27
2701 8720 0.397254 TTCCCGGGAGAGAGATCCAC 60.397 60.000 25.26 0.00 41.52 4.02
2702 8721 1.075970 CCCGGGAGAGAGATCCACA 60.076 63.158 18.48 0.00 41.52 4.17
2704 8723 1.395826 CCGGGAGAGAGATCCACACC 61.396 65.000 0.00 0.00 41.52 4.16
2707 8726 2.593026 GGGAGAGAGATCCACACCTAG 58.407 57.143 0.00 0.00 41.52 3.02
2715 8734 5.007034 AGAGATCCACACCTAGATATGTCG 58.993 45.833 0.00 0.00 0.00 4.35
2752 8771 4.640855 GCGCGGGCGTATCTAGCA 62.641 66.667 9.31 0.00 42.09 3.49
2755 8774 0.944311 CGCGGGCGTATCTAGCAATT 60.944 55.000 4.64 0.00 36.08 2.32
2760 8779 3.305813 CGGGCGTATCTAGCAATTTCCTA 60.306 47.826 0.00 0.00 36.08 2.94
2762 8781 5.246307 GGGCGTATCTAGCAATTTCCTAAT 58.754 41.667 0.00 0.00 36.08 1.73
2767 8786 8.244802 GCGTATCTAGCAATTTCCTAATCTAGA 58.755 37.037 0.00 0.00 34.40 2.43
2796 8815 4.436368 ACGTCATCTCGTCCCCTT 57.564 55.556 0.00 0.00 40.04 3.95
2808 8827 0.771755 GTCCCCTTTCCACTGTCCTT 59.228 55.000 0.00 0.00 0.00 3.36
2814 8833 2.290641 CCTTTCCACTGTCCTTCAAACG 59.709 50.000 0.00 0.00 0.00 3.60
2829 8848 0.831307 AAACGGCCTAGGTGATCTCC 59.169 55.000 11.31 5.64 0.00 3.71
2837 8856 2.225041 CCTAGGTGATCTCCCCGTGATA 60.225 54.545 10.22 0.00 0.00 2.15
2838 8857 2.002505 AGGTGATCTCCCCGTGATAG 57.997 55.000 10.22 0.00 0.00 2.08
2839 8858 0.969894 GGTGATCTCCCCGTGATAGG 59.030 60.000 2.14 0.00 0.00 2.57
2879 8912 1.480683 CGGTGGAGGATTAGAGCCCTA 60.481 57.143 0.00 0.00 31.84 3.53
2880 8913 2.823535 CGGTGGAGGATTAGAGCCCTAT 60.824 54.545 0.00 0.00 31.84 2.57
2882 8915 2.569404 GTGGAGGATTAGAGCCCTATGG 59.431 54.545 0.00 0.00 31.84 2.74
2889 8922 5.088026 GGATTAGAGCCCTATGGTACTCTT 58.912 45.833 10.34 0.00 36.30 2.85
2912 8945 2.302733 CCTTGCAACCAAATTAGGCCTT 59.697 45.455 12.58 0.00 0.00 4.35
2925 8958 7.260603 CAAATTAGGCCTTAGTGAAATTCAGG 58.739 38.462 12.58 0.00 0.00 3.86
2929 8962 2.025321 GCCTTAGTGAAATTCAGGGGGA 60.025 50.000 0.00 0.00 0.00 4.81
2930 8963 3.373110 GCCTTAGTGAAATTCAGGGGGAT 60.373 47.826 0.00 0.00 0.00 3.85
2933 8966 6.431722 CCTTAGTGAAATTCAGGGGGATTTA 58.568 40.000 0.00 0.00 0.00 1.40
2934 8967 7.069344 CCTTAGTGAAATTCAGGGGGATTTAT 58.931 38.462 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 102 7.616313 TGTGTTTCCTTAAAAGGTCATTTGTT 58.384 30.769 8.57 0.00 46.54 2.83
99 103 7.176589 TGTGTTTCCTTAAAAGGTCATTTGT 57.823 32.000 8.57 0.00 46.54 2.83
100 104 8.485976 TTTGTGTTTCCTTAAAAGGTCATTTG 57.514 30.769 8.57 0.00 46.54 2.32
230 243 9.605955 GTGTTAAAAATTGGTCAAAATATTGGC 57.394 29.630 0.00 0.00 40.50 4.52
350 365 9.717942 AAAATGGGATTTTGAAACAATATTCGA 57.282 25.926 0.00 0.00 40.69 3.71
396 411 7.907214 TTTCGGGTTTTTCTTTTCATTTTGA 57.093 28.000 0.00 0.00 0.00 2.69
440 458 5.987347 CGAGCCGTTTATATTCCTTTTCCTA 59.013 40.000 0.00 0.00 0.00 2.94
442 460 4.812626 TCGAGCCGTTTATATTCCTTTTCC 59.187 41.667 0.00 0.00 0.00 3.13
448 466 3.424529 CGAAGTCGAGCCGTTTATATTCC 59.575 47.826 0.00 0.00 43.02 3.01
449 467 3.121429 GCGAAGTCGAGCCGTTTATATTC 60.121 47.826 4.59 0.00 43.02 1.75
473 491 1.461091 TATCGGAAGCTACTGGGCCG 61.461 60.000 0.00 0.00 43.11 6.13
474 492 0.756903 TTATCGGAAGCTACTGGGCC 59.243 55.000 0.00 0.00 0.00 5.80
475 493 1.687123 TCTTATCGGAAGCTACTGGGC 59.313 52.381 0.00 0.00 0.00 5.36
476 494 2.288518 GCTCTTATCGGAAGCTACTGGG 60.289 54.545 0.00 0.00 0.00 4.45
478 496 2.288518 GGGCTCTTATCGGAAGCTACTG 60.289 54.545 0.00 0.00 0.00 2.74
481 499 0.959553 CGGGCTCTTATCGGAAGCTA 59.040 55.000 0.00 0.00 0.00 3.32
524 561 1.884926 GAGCGGTGGATGCAGCTAC 60.885 63.158 10.32 10.32 39.83 3.58
558 595 1.822371 GAGCGAGAGAAGAGAAAGGGT 59.178 52.381 0.00 0.00 0.00 4.34
608 645 1.758514 GCCGAGAGATGGTGGAGGA 60.759 63.158 0.00 0.00 0.00 3.71
687 3444 1.101331 GAGAAGGGCCTTGCTTGATG 58.899 55.000 26.47 0.00 0.00 3.07
689 3446 1.380302 GGAGAAGGGCCTTGCTTGA 59.620 57.895 26.47 0.00 0.00 3.02
698 3455 1.235281 GGTTCGTGTTGGAGAAGGGC 61.235 60.000 0.00 0.00 0.00 5.19
699 3456 0.605589 GGGTTCGTGTTGGAGAAGGG 60.606 60.000 0.00 0.00 0.00 3.95
702 3459 1.595929 GCGGGTTCGTGTTGGAGAA 60.596 57.895 0.00 0.00 38.89 2.87
703 3460 2.029964 GCGGGTTCGTGTTGGAGA 59.970 61.111 0.00 0.00 38.89 3.71
704 3461 3.047877 GGCGGGTTCGTGTTGGAG 61.048 66.667 0.00 0.00 38.89 3.86
788 3546 4.166888 GAGCGGGCTGATGCAGGA 62.167 66.667 0.00 0.00 41.91 3.86
824 3794 4.767255 CCAGGACCTGCAGACGGC 62.767 72.222 17.39 0.09 45.13 5.68
944 3956 0.179134 GTCCTCCTCGTTGTCATCGG 60.179 60.000 3.59 0.00 0.00 4.18
965 3977 4.467084 GGATGACCGGCGCCTTCA 62.467 66.667 26.68 25.62 0.00 3.02
1024 4048 4.694233 AGAGGCGCCACACAGCTG 62.694 66.667 31.54 13.48 0.00 4.24
1059 4083 1.525077 AAGGCTGCCGTTCACGAAA 60.525 52.632 13.96 0.00 43.02 3.46
1117 4141 2.370189 GACAGATTGGGGGAATCTCGAT 59.630 50.000 0.00 0.00 46.84 3.59
1119 4143 1.539065 CGACAGATTGGGGGAATCTCG 60.539 57.143 0.00 0.00 46.84 4.04
1126 4150 1.221840 CAGTCCGACAGATTGGGGG 59.778 63.158 0.40 0.00 0.00 5.40
1128 4152 4.941609 CCAGTCCGACAGATTGGG 57.058 61.111 0.40 0.00 46.22 4.12
1131 4155 2.379972 CTAGGTCCAGTCCGACAGATT 58.620 52.381 0.40 0.00 34.24 2.40
1151 4178 4.065789 CTCCTGTAACTTTTCACTCACCC 58.934 47.826 0.00 0.00 0.00 4.61
1186 4213 3.040099 CGCAAGTTACCGGAACAAAAAG 58.960 45.455 9.46 0.00 40.86 2.27
1207 4234 2.685388 TCAGTCAGATGATCGACAGGAC 59.315 50.000 15.78 7.70 34.48 3.85
1245 4272 3.659092 CTCGGCGCCAGTGCAAAA 61.659 61.111 28.98 1.21 37.32 2.44
1278 4305 1.697982 AGACACGCCCTTAGGAAACTT 59.302 47.619 0.00 0.00 43.67 2.66
1283 4310 0.331954 AGAGAGACACGCCCTTAGGA 59.668 55.000 0.00 0.00 33.47 2.94
1295 4325 1.004440 GCACCACCACCAGAGAGAC 60.004 63.158 0.00 0.00 0.00 3.36
1528 4561 3.753272 CAGGTGGCAATTCCGAATATAGG 59.247 47.826 0.00 0.00 37.80 2.57
1531 4564 1.956477 GCAGGTGGCAATTCCGAATAT 59.044 47.619 0.00 0.00 43.97 1.28
1532 4565 1.388547 GCAGGTGGCAATTCCGAATA 58.611 50.000 0.00 0.00 43.97 1.75
1568 4601 1.140052 ACTGGACCGACAAACATGACA 59.860 47.619 0.00 0.00 0.00 3.58
1586 4619 2.293399 GGGATCTTTTGTTGCGAACACT 59.707 45.455 0.00 0.00 41.97 3.55
1604 4637 2.600731 GATTTGGGGCATCCGGGA 59.399 61.111 0.00 0.00 38.76 5.14
1626 4659 0.732880 CTGTACACCTCGAAGCCACG 60.733 60.000 0.00 0.00 0.00 4.94
1652 4685 3.430862 CACCGTGCCCCATCAACG 61.431 66.667 0.00 0.00 0.00 4.10
1730 4763 0.397564 TCTCTGAAGCATGCACCACA 59.602 50.000 21.98 12.47 0.00 4.17
1732 4765 0.671472 CGTCTCTGAAGCATGCACCA 60.671 55.000 21.98 15.54 0.00 4.17
1762 4795 3.077359 ACAAAGTAGATGCAGTTGCTCC 58.923 45.455 5.62 0.00 42.66 4.70
1799 4832 1.064166 CCCCAAGTGCTGAATGAGGAT 60.064 52.381 0.00 0.00 0.00 3.24
1882 4915 1.599518 CACCGGGCAGCTTTGTACA 60.600 57.895 6.32 0.00 0.00 2.90
1932 4965 4.527944 TGTCCCAAGTTTGTACATTGTCA 58.472 39.130 0.00 0.00 0.00 3.58
2105 5150 6.015027 ACTATCACGTCATAGCAATACCTC 57.985 41.667 6.35 0.00 30.38 3.85
2120 5165 6.342338 AGGTTTATAGGCCTTACTATCACG 57.658 41.667 12.58 0.00 35.41 4.35
2149 5196 0.839277 ACATGGGCTGCATAGTAGCA 59.161 50.000 9.21 0.00 42.88 3.49
2164 5211 1.339342 TGCCACAGAGACCATCACATG 60.339 52.381 0.00 0.00 0.00 3.21
2236 5283 5.377358 CGCTTTGTACAGTTTCTGAGAATG 58.623 41.667 0.00 0.00 35.18 2.67
2281 5328 9.941664 CAATACAATCCATAAACTTCATCAGAC 57.058 33.333 0.00 0.00 0.00 3.51
2312 5359 5.160699 AGTTCATGCGCAACTGTATTATG 57.839 39.130 17.11 4.56 32.65 1.90
2313 5360 4.025730 CGAGTTCATGCGCAACTGTATTAT 60.026 41.667 17.11 0.00 34.10 1.28
2347 5394 1.774254 TCTGAGAAACCCAAAGGAGCA 59.226 47.619 0.00 0.00 36.73 4.26
2403 5450 4.094294 GCAACATAAACTTCGCTCACCATA 59.906 41.667 0.00 0.00 0.00 2.74
2457 5504 7.719633 ACCACACAGACACAATAAATTCTACTT 59.280 33.333 0.00 0.00 0.00 2.24
2480 5527 4.501229 GCATGACAAAATTGAAGGACACCA 60.501 41.667 0.00 0.00 0.00 4.17
2481 5528 3.989817 GCATGACAAAATTGAAGGACACC 59.010 43.478 0.00 0.00 0.00 4.16
2532 5579 3.508840 GATGGCGCCCTTTGTCGG 61.509 66.667 26.77 0.00 0.00 4.79
2533 5580 3.508840 GGATGGCGCCCTTTGTCG 61.509 66.667 26.77 0.00 0.00 4.35
2534 5581 1.322538 ATTGGATGGCGCCCTTTGTC 61.323 55.000 26.77 13.67 0.00 3.18
2578 5626 1.202143 GGGAATTTGAACGACGGATGC 60.202 52.381 0.00 0.00 0.00 3.91
2585 5633 5.081032 ACCAATTTAGGGGAATTTGAACGA 58.919 37.500 0.00 0.00 32.45 3.85
2586 5634 5.400066 ACCAATTTAGGGGAATTTGAACG 57.600 39.130 0.00 0.00 32.45 3.95
2589 5637 5.905088 TGGTACCAATTTAGGGGAATTTGA 58.095 37.500 13.60 0.00 32.45 2.69
2590 5638 5.719563 ACTGGTACCAATTTAGGGGAATTTG 59.280 40.000 17.11 0.45 0.00 2.32
2591 5639 5.910931 ACTGGTACCAATTTAGGGGAATTT 58.089 37.500 17.11 0.00 0.00 1.82
2592 5640 5.546035 ACTGGTACCAATTTAGGGGAATT 57.454 39.130 17.11 0.00 0.00 2.17
2593 5641 5.546035 AACTGGTACCAATTTAGGGGAAT 57.454 39.130 17.11 0.00 0.00 3.01
2594 5642 5.342361 AAACTGGTACCAATTTAGGGGAA 57.658 39.130 19.33 0.00 0.00 3.97
2595 5643 5.081032 CAAAACTGGTACCAATTTAGGGGA 58.919 41.667 20.86 0.00 0.00 4.81
2596 5644 4.221924 CCAAAACTGGTACCAATTTAGGGG 59.778 45.833 20.86 17.64 0.00 4.79
2597 5645 4.221924 CCCAAAACTGGTACCAATTTAGGG 59.778 45.833 20.86 23.93 0.00 3.53
2598 5646 5.081032 TCCCAAAACTGGTACCAATTTAGG 58.919 41.667 20.86 21.98 0.00 2.69
2599 5647 6.007703 TCTCCCAAAACTGGTACCAATTTAG 58.992 40.000 20.86 14.39 0.00 1.85
2600 5648 5.954757 TCTCCCAAAACTGGTACCAATTTA 58.045 37.500 20.86 5.40 0.00 1.40
2601 5649 4.810345 TCTCCCAAAACTGGTACCAATTT 58.190 39.130 15.42 15.42 0.00 1.82
2602 5650 4.463050 TCTCCCAAAACTGGTACCAATT 57.537 40.909 17.11 9.88 0.00 2.32
2603 5651 4.569865 GGATCTCCCAAAACTGGTACCAAT 60.570 45.833 17.11 1.92 34.14 3.16
2604 5652 3.245122 GGATCTCCCAAAACTGGTACCAA 60.245 47.826 17.11 0.00 34.14 3.67
2605 5653 2.307686 GGATCTCCCAAAACTGGTACCA 59.692 50.000 15.39 15.39 34.14 3.25
2606 5654 2.679930 CGGATCTCCCAAAACTGGTACC 60.680 54.545 4.43 4.43 34.14 3.34
2607 5655 2.629051 CGGATCTCCCAAAACTGGTAC 58.371 52.381 0.00 0.00 34.14 3.34
2608 5656 1.065709 GCGGATCTCCCAAAACTGGTA 60.066 52.381 0.00 0.00 34.14 3.25
2609 5657 0.322546 GCGGATCTCCCAAAACTGGT 60.323 55.000 0.00 0.00 34.14 4.00
2624 5672 4.690719 ACCAAATGTCGCGGCGGA 62.691 61.111 23.46 10.06 0.00 5.54
2642 8661 0.464036 AATATCCCAACGAGCGAGCA 59.536 50.000 0.00 0.00 0.00 4.26
2652 8671 1.351017 GATCGGGGCAGAATATCCCAA 59.649 52.381 0.00 0.00 44.43 4.12
2683 8702 1.230497 GTGGATCTCTCTCCCGGGA 59.770 63.158 25.06 25.06 34.12 5.14
2701 8720 3.156288 TCTCCCCGACATATCTAGGTG 57.844 52.381 0.00 0.00 0.00 4.00
2702 8721 3.897657 TTCTCCCCGACATATCTAGGT 57.102 47.619 0.00 0.00 0.00 3.08
2704 8723 4.561105 GCTTTTCTCCCCGACATATCTAG 58.439 47.826 0.00 0.00 0.00 2.43
2707 8726 2.158813 TGGCTTTTCTCCCCGACATATC 60.159 50.000 0.00 0.00 0.00 1.63
2715 8734 0.955919 CAGTCGTGGCTTTTCTCCCC 60.956 60.000 0.00 0.00 0.00 4.81
2739 8758 3.127425 AGGAAATTGCTAGATACGCCC 57.873 47.619 0.00 0.00 0.00 6.13
2788 8807 1.003718 GGACAGTGGAAAGGGGACG 60.004 63.158 0.00 0.00 0.00 4.79
2791 8810 0.771127 TGAAGGACAGTGGAAAGGGG 59.229 55.000 0.00 0.00 0.00 4.79
2792 8811 2.623416 GTTTGAAGGACAGTGGAAAGGG 59.377 50.000 0.00 0.00 0.00 3.95
2793 8812 2.290641 CGTTTGAAGGACAGTGGAAAGG 59.709 50.000 0.00 0.00 0.00 3.11
2796 8815 1.961793 CCGTTTGAAGGACAGTGGAA 58.038 50.000 0.00 0.00 0.00 3.53
2808 8827 1.480954 GAGATCACCTAGGCCGTTTGA 59.519 52.381 9.30 4.95 0.00 2.69
2814 8833 2.210711 CGGGGAGATCACCTAGGCC 61.211 68.421 9.30 0.00 37.25 5.19
2829 8848 0.478942 TCCTCTCCTCCTATCACGGG 59.521 60.000 0.00 0.00 0.00 5.28
2837 8856 0.031616 GTGTGGGATCCTCTCCTCCT 60.032 60.000 12.58 0.00 44.28 3.69
2838 8857 1.051556 GGTGTGGGATCCTCTCCTCC 61.052 65.000 12.58 3.81 44.28 4.30
2839 8858 1.051556 GGGTGTGGGATCCTCTCCTC 61.052 65.000 12.58 6.53 44.28 3.71
2852 8871 1.268992 TAATCCTCCACCGGGGTGTG 61.269 60.000 16.19 8.26 44.02 3.82
2879 8912 2.290960 GGTTGCAAGGGAAGAGTACCAT 60.291 50.000 0.00 0.00 0.00 3.55
2880 8913 1.073284 GGTTGCAAGGGAAGAGTACCA 59.927 52.381 0.00 0.00 0.00 3.25
2882 8915 2.561478 TGGTTGCAAGGGAAGAGTAC 57.439 50.000 0.00 0.00 0.00 2.73
2889 8922 1.899142 GCCTAATTTGGTTGCAAGGGA 59.101 47.619 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.