Multiple sequence alignment - TraesCS1A01G423200

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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 TraesCS1A01G423200 chr1A 100.000 3332 0 0 1 3332 578543744 578547075 0.000000e+00 6154.0
1 TraesCS1A01G423200 chr1A 91.324 1360 105 8 994 2351 577720247 577718899 0.000000e+00 1845.0
2 TraesCS1A01G423200 chr1D 92.893 2364 124 30 1 2351 481717001 481719333 0.000000e+00 3395.0
3 TraesCS1A01G423200 chr1D 91.760 1335 100 6 1022 2351 481326848 481325519 0.000000e+00 1847.0
4 TraesCS1A01G423200 chr1B 91.754 1334 98 10 1021 2351 669703445 669702121 0.000000e+00 1844.0
5 TraesCS1A01G423200 chr1B 96.123 1006 39 0 1346 2351 670401213 670402218 0.000000e+00 1642.0
6 TraesCS1A01G423200 chr1B 89.369 1157 102 8 1196 2351 669462986 669461850 0.000000e+00 1435.0
7 TraesCS1A01G423200 chr1B 91.111 585 23 9 776 1350 670395698 670396263 0.000000e+00 765.0
8 TraesCS1A01G423200 chr1B 87.241 627 45 16 1 599 670391741 670392360 0.000000e+00 682.0
9 TraesCS1A01G423200 chr1B 91.429 210 11 5 337 543 670392824 670393029 7.040000e-72 281.0
10 TraesCS1A01G423200 chr1B 90.541 74 6 1 282 354 670392294 670392367 2.740000e-16 97.1
11 TraesCS1A01G423200 chr1B 90.541 74 6 1 282 354 670392752 670392825 2.740000e-16 97.1
12 TraesCS1A01G423200 chr2D 86.210 1240 149 15 1084 2310 28969257 28970487 0.000000e+00 1323.0
13 TraesCS1A01G423200 chr2D 85.910 1242 157 9 1084 2316 27970728 27969496 0.000000e+00 1308.0
14 TraesCS1A01G423200 chr2A 85.841 1243 158 11 1078 2310 30869084 30870318 0.000000e+00 1304.0
15 TraesCS1A01G423200 chr2A 90.791 847 46 10 2488 3332 640296580 640295764 0.000000e+00 1103.0
16 TraesCS1A01G423200 chr2A 88.693 849 40 24 2488 3332 740095990 740095194 0.000000e+00 985.0
17 TraesCS1A01G423200 chr2A 93.661 631 33 4 2488 3114 588429762 588429135 0.000000e+00 937.0
18 TraesCS1A01G423200 chr2A 98.611 216 3 0 3117 3332 588429160 588428945 1.880000e-102 383.0
19 TraesCS1A01G423200 chr3A 91.294 850 39 11 2488 3332 721253080 721253899 0.000000e+00 1127.0
20 TraesCS1A01G423200 chr3A 93.164 629 37 3 2488 3114 743517349 743517973 0.000000e+00 918.0
21 TraesCS1A01G423200 chr3A 92.756 635 40 5 2485 3114 23344625 23343992 0.000000e+00 913.0
22 TraesCS1A01G423200 chr3A 96.759 216 7 0 3117 3332 717900544 717900759 8.790000e-96 361.0
23 TraesCS1A01G423200 chr4A 90.342 849 39 12 2488 3332 16993637 16994446 0.000000e+00 1074.0
24 TraesCS1A01G423200 chr4A 87.293 181 20 2 139 317 586089347 586089526 1.570000e-48 204.0
25 TraesCS1A01G423200 chr7A 87.836 855 49 22 2483 3332 14303604 14302800 0.000000e+00 952.0
26 TraesCS1A01G423200 chr7A 92.417 633 40 3 2488 3114 273655594 273654964 0.000000e+00 896.0
27 TraesCS1A01G423200 chr5A 93.839 633 32 3 2488 3114 446424929 446425560 0.000000e+00 946.0
28 TraesCS1A01G423200 chr5A 96.759 216 7 0 3117 3332 446425535 446425750 8.790000e-96 361.0
29 TraesCS1A01G423200 chr5D 92.126 635 45 3 2484 3114 424819120 424819753 0.000000e+00 891.0
30 TraesCS1A01G423200 chr3D 96.296 216 8 0 3117 3332 358569681 358569466 4.090000e-94 355.0
31 TraesCS1A01G423200 chr4D 86.415 265 33 2 44 306 397695225 397694962 1.510000e-73 287.0
32 TraesCS1A01G423200 chr4D 89.286 168 17 1 150 317 15151211 15151045 3.370000e-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 TraesCS1A01G423200 chr1A 578543744 578547075 3331 False 6154.00 6154 100.0000 1 3332 1 chr1A.!!$F1 3331
1 TraesCS1A01G423200 chr1A 577718899 577720247 1348 True 1845.00 1845 91.3240 994 2351 1 chr1A.!!$R1 1357
2 TraesCS1A01G423200 chr1D 481717001 481719333 2332 False 3395.00 3395 92.8930 1 2351 1 chr1D.!!$F1 2350
3 TraesCS1A01G423200 chr1D 481325519 481326848 1329 True 1847.00 1847 91.7600 1022 2351 1 chr1D.!!$R1 1329
4 TraesCS1A01G423200 chr1B 669702121 669703445 1324 True 1844.00 1844 91.7540 1021 2351 1 chr1B.!!$R2 1330
5 TraesCS1A01G423200 chr1B 670401213 670402218 1005 False 1642.00 1642 96.1230 1346 2351 1 chr1B.!!$F1 1005
6 TraesCS1A01G423200 chr1B 669461850 669462986 1136 True 1435.00 1435 89.3690 1196 2351 1 chr1B.!!$R1 1155
7 TraesCS1A01G423200 chr1B 670391741 670396263 4522 False 384.44 765 90.1726 1 1350 5 chr1B.!!$F2 1349
8 TraesCS1A01G423200 chr2D 28969257 28970487 1230 False 1323.00 1323 86.2100 1084 2310 1 chr2D.!!$F1 1226
9 TraesCS1A01G423200 chr2D 27969496 27970728 1232 True 1308.00 1308 85.9100 1084 2316 1 chr2D.!!$R1 1232
10 TraesCS1A01G423200 chr2A 30869084 30870318 1234 False 1304.00 1304 85.8410 1078 2310 1 chr2A.!!$F1 1232
11 TraesCS1A01G423200 chr2A 640295764 640296580 816 True 1103.00 1103 90.7910 2488 3332 1 chr2A.!!$R1 844
12 TraesCS1A01G423200 chr2A 740095194 740095990 796 True 985.00 985 88.6930 2488 3332 1 chr2A.!!$R2 844
13 TraesCS1A01G423200 chr2A 588428945 588429762 817 True 660.00 937 96.1360 2488 3332 2 chr2A.!!$R3 844
14 TraesCS1A01G423200 chr3A 721253080 721253899 819 False 1127.00 1127 91.2940 2488 3332 1 chr3A.!!$F2 844
15 TraesCS1A01G423200 chr3A 743517349 743517973 624 False 918.00 918 93.1640 2488 3114 1 chr3A.!!$F3 626
16 TraesCS1A01G423200 chr3A 23343992 23344625 633 True 913.00 913 92.7560 2485 3114 1 chr3A.!!$R1 629
17 TraesCS1A01G423200 chr4A 16993637 16994446 809 False 1074.00 1074 90.3420 2488 3332 1 chr4A.!!$F1 844
18 TraesCS1A01G423200 chr7A 14302800 14303604 804 True 952.00 952 87.8360 2483 3332 1 chr7A.!!$R1 849
19 TraesCS1A01G423200 chr7A 273654964 273655594 630 True 896.00 896 92.4170 2488 3114 1 chr7A.!!$R2 626
20 TraesCS1A01G423200 chr5A 446424929 446425750 821 False 653.50 946 95.2990 2488 3332 2 chr5A.!!$F1 844
21 TraesCS1A01G423200 chr5D 424819120 424819753 633 False 891.00 891 92.1260 2484 3114 1 chr5D.!!$F1 630

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
974 4210 0.107945 GGTCATCAGTGCCTCACTCC 60.108 60.0 0.0 0.0 43.43 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 5740 0.035725 TGGCTGTTGGAGATGCTCTG 60.036 55.0 0.0 0.0 0.0 3.35 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
624 2995 7.820648 AGAATGTGTATGAAAAGGTTGACATC 58.179 34.615 0.00 0.00 0.00 3.06
741 3112 3.846360 TCAAAAACTAGCTAGACTCGGC 58.154 45.455 27.45 0.00 0.00 5.54
796 4016 2.504244 CTCGTTCCACTCGTCGCC 60.504 66.667 0.00 0.00 0.00 5.54
861 4085 0.391661 TGCTCCATTTCAGCTCGTCC 60.392 55.000 0.00 0.00 37.79 4.79
894 4118 1.361204 TCCCACTCAGCTCAAATGGA 58.639 50.000 4.70 0.00 31.69 3.41
932 4156 1.234615 CCAGCCAAACCATTCGTCGT 61.235 55.000 0.00 0.00 0.00 4.34
933 4157 1.434555 CAGCCAAACCATTCGTCGTA 58.565 50.000 0.00 0.00 0.00 3.43
934 4158 2.006888 CAGCCAAACCATTCGTCGTAT 58.993 47.619 0.00 0.00 0.00 3.06
935 4159 3.191669 CAGCCAAACCATTCGTCGTATA 58.808 45.455 0.00 0.00 0.00 1.47
936 4160 3.807622 CAGCCAAACCATTCGTCGTATAT 59.192 43.478 0.00 0.00 0.00 0.86
937 4161 4.986034 CAGCCAAACCATTCGTCGTATATA 59.014 41.667 0.00 0.00 0.00 0.86
938 4162 4.986659 AGCCAAACCATTCGTCGTATATAC 59.013 41.667 2.53 2.53 0.00 1.47
939 4163 4.986659 GCCAAACCATTCGTCGTATATACT 59.013 41.667 11.05 0.00 0.00 2.12
940 4164 5.118203 GCCAAACCATTCGTCGTATATACTC 59.882 44.000 11.05 3.63 0.00 2.59
955 4179 1.647545 TACTCCGGCGGTACAAGACG 61.648 60.000 27.32 8.63 40.35 4.18
965 4201 2.607187 GGTACAAGACGGTCATCAGTG 58.393 52.381 11.27 3.03 0.00 3.66
974 4210 0.107945 GGTCATCAGTGCCTCACTCC 60.108 60.000 0.00 0.00 43.43 3.85
982 4218 3.325753 GCCTCACTCCACCCTGCT 61.326 66.667 0.00 0.00 0.00 4.24
1032 4268 4.787280 CCACCCCTCCTCCTCGCT 62.787 72.222 0.00 0.00 0.00 4.93
1477 4719 2.381109 TCGTTTTTCGACGCCAACA 58.619 47.368 0.00 0.00 44.01 3.33
1682 4924 2.116383 CCGACTCGGCCTACTTCAT 58.884 57.895 4.10 0.00 41.17 2.57
1974 5221 4.864334 GTGGGGGAGGCGATGCAG 62.864 72.222 0.00 0.00 0.00 4.41
1977 5224 3.564218 GGGGAGGCGATGCAGGAT 61.564 66.667 0.00 0.00 0.00 3.24
2336 5590 4.569023 CGGCATGAGGTAGCGCGA 62.569 66.667 12.10 0.00 0.00 5.87
2338 5592 2.202743 GCATGAGGTAGCGCGACA 60.203 61.111 22.25 9.85 0.00 4.35
2352 5606 3.499737 GACATGTTGCCGGCCGAG 61.500 66.667 30.73 18.40 0.00 4.63
2364 5618 2.203126 GCCGAGGGCTTGATGGAG 60.203 66.667 0.00 0.00 46.69 3.86
2365 5619 2.507944 CCGAGGGCTTGATGGAGG 59.492 66.667 0.00 0.00 0.00 4.30
2366 5620 2.370445 CCGAGGGCTTGATGGAGGT 61.370 63.158 0.00 0.00 0.00 3.85
2367 5621 1.153289 CGAGGGCTTGATGGAGGTG 60.153 63.158 0.00 0.00 0.00 4.00
2368 5622 1.225704 GAGGGCTTGATGGAGGTGG 59.774 63.158 0.00 0.00 0.00 4.61
2369 5623 1.542375 AGGGCTTGATGGAGGTGGT 60.542 57.895 0.00 0.00 0.00 4.16
2370 5624 1.077429 GGGCTTGATGGAGGTGGTC 60.077 63.158 0.00 0.00 0.00 4.02
2371 5625 1.566298 GGGCTTGATGGAGGTGGTCT 61.566 60.000 0.00 0.00 0.00 3.85
2372 5626 0.329596 GGCTTGATGGAGGTGGTCTT 59.670 55.000 0.00 0.00 0.00 3.01
2373 5627 1.272147 GGCTTGATGGAGGTGGTCTTT 60.272 52.381 0.00 0.00 0.00 2.52
2374 5628 2.519013 GCTTGATGGAGGTGGTCTTTT 58.481 47.619 0.00 0.00 0.00 2.27
2375 5629 2.229784 GCTTGATGGAGGTGGTCTTTTG 59.770 50.000 0.00 0.00 0.00 2.44
2376 5630 1.909700 TGATGGAGGTGGTCTTTTGC 58.090 50.000 0.00 0.00 0.00 3.68
2377 5631 1.177401 GATGGAGGTGGTCTTTTGCC 58.823 55.000 0.00 0.00 0.00 4.52
2378 5632 0.609131 ATGGAGGTGGTCTTTTGCCG 60.609 55.000 0.00 0.00 0.00 5.69
2379 5633 1.228154 GGAGGTGGTCTTTTGCCGT 60.228 57.895 0.00 0.00 0.00 5.68
2380 5634 1.515521 GGAGGTGGTCTTTTGCCGTG 61.516 60.000 0.00 0.00 0.00 4.94
2381 5635 0.534203 GAGGTGGTCTTTTGCCGTGA 60.534 55.000 0.00 0.00 0.00 4.35
2382 5636 0.818040 AGGTGGTCTTTTGCCGTGAC 60.818 55.000 0.00 0.00 0.00 3.67
2383 5637 1.278637 GTGGTCTTTTGCCGTGACG 59.721 57.895 0.00 0.00 0.00 4.35
2398 5652 3.893720 CGTGACGGAAACTGTTAGTAGT 58.106 45.455 0.00 0.00 0.00 2.73
2399 5653 5.034554 CGTGACGGAAACTGTTAGTAGTA 57.965 43.478 0.00 0.00 0.00 1.82
2400 5654 4.848299 CGTGACGGAAACTGTTAGTAGTAC 59.152 45.833 0.00 0.00 0.00 2.73
2401 5655 5.334414 CGTGACGGAAACTGTTAGTAGTACT 60.334 44.000 8.14 8.14 0.00 2.73
2402 5656 5.855395 GTGACGGAAACTGTTAGTAGTACTG 59.145 44.000 13.29 0.00 0.00 2.74
2403 5657 5.764686 TGACGGAAACTGTTAGTAGTACTGA 59.235 40.000 13.29 1.35 0.00 3.41
2404 5658 6.432162 TGACGGAAACTGTTAGTAGTACTGAT 59.568 38.462 13.29 0.00 0.00 2.90
2405 5659 7.040201 TGACGGAAACTGTTAGTAGTACTGATT 60.040 37.037 13.29 0.00 0.00 2.57
2406 5660 7.664758 ACGGAAACTGTTAGTAGTACTGATTT 58.335 34.615 13.29 2.79 0.00 2.17
2407 5661 8.146412 ACGGAAACTGTTAGTAGTACTGATTTT 58.854 33.333 13.29 6.13 0.00 1.82
2408 5662 8.985805 CGGAAACTGTTAGTAGTACTGATTTTT 58.014 33.333 13.29 5.81 0.00 1.94
2443 5697 7.933215 AAAATGGTTACATCTAGGTGTTACC 57.067 36.000 29.34 29.34 46.63 2.85
2444 5698 5.625568 ATGGTTACATCTAGGTGTTACCC 57.374 43.478 31.51 20.90 46.16 3.69
2445 5699 4.691238 TGGTTACATCTAGGTGTTACCCT 58.309 43.478 31.51 4.53 46.16 4.34
2446 5700 5.095809 TGGTTACATCTAGGTGTTACCCTT 58.904 41.667 31.51 3.85 46.16 3.95
2447 5701 5.188359 TGGTTACATCTAGGTGTTACCCTTC 59.812 44.000 31.51 14.40 46.16 3.46
2448 5702 5.424573 GGTTACATCTAGGTGTTACCCTTCT 59.575 44.000 26.97 0.00 42.85 2.85
2449 5703 6.406737 GGTTACATCTAGGTGTTACCCTTCTC 60.407 46.154 26.97 7.03 42.85 2.87
2450 5704 4.949121 ACATCTAGGTGTTACCCTTCTCT 58.051 43.478 1.73 0.00 39.75 3.10
2451 5705 4.957327 ACATCTAGGTGTTACCCTTCTCTC 59.043 45.833 1.73 0.00 39.75 3.20
2452 5706 3.618351 TCTAGGTGTTACCCTTCTCTCG 58.382 50.000 0.00 0.00 39.75 4.04
2453 5707 0.896226 AGGTGTTACCCTTCTCTCGC 59.104 55.000 0.00 0.00 39.75 5.03
2454 5708 0.896226 GGTGTTACCCTTCTCTCGCT 59.104 55.000 0.00 0.00 30.04 4.93
2455 5709 1.135053 GGTGTTACCCTTCTCTCGCTC 60.135 57.143 0.00 0.00 30.04 5.03
2456 5710 1.135053 GTGTTACCCTTCTCTCGCTCC 60.135 57.143 0.00 0.00 0.00 4.70
2457 5711 0.460722 GTTACCCTTCTCTCGCTCCC 59.539 60.000 0.00 0.00 0.00 4.30
2458 5712 0.335361 TTACCCTTCTCTCGCTCCCT 59.665 55.000 0.00 0.00 0.00 4.20
2459 5713 0.335361 TACCCTTCTCTCGCTCCCTT 59.665 55.000 0.00 0.00 0.00 3.95
2460 5714 0.545548 ACCCTTCTCTCGCTCCCTTT 60.546 55.000 0.00 0.00 0.00 3.11
2461 5715 0.107945 CCCTTCTCTCGCTCCCTTTG 60.108 60.000 0.00 0.00 0.00 2.77
2462 5716 0.898320 CCTTCTCTCGCTCCCTTTGA 59.102 55.000 0.00 0.00 0.00 2.69
2463 5717 1.404851 CCTTCTCTCGCTCCCTTTGAC 60.405 57.143 0.00 0.00 0.00 3.18
2464 5718 1.273606 CTTCTCTCGCTCCCTTTGACA 59.726 52.381 0.00 0.00 0.00 3.58
2465 5719 0.603569 TCTCTCGCTCCCTTTGACAC 59.396 55.000 0.00 0.00 0.00 3.67
2466 5720 0.390472 CTCTCGCTCCCTTTGACACC 60.390 60.000 0.00 0.00 0.00 4.16
2467 5721 1.376037 CTCGCTCCCTTTGACACCC 60.376 63.158 0.00 0.00 0.00 4.61
2468 5722 1.831652 CTCGCTCCCTTTGACACCCT 61.832 60.000 0.00 0.00 0.00 4.34
2469 5723 1.376037 CGCTCCCTTTGACACCCTC 60.376 63.158 0.00 0.00 0.00 4.30
2470 5724 1.002011 GCTCCCTTTGACACCCTCC 60.002 63.158 0.00 0.00 0.00 4.30
2471 5725 1.779061 GCTCCCTTTGACACCCTCCA 61.779 60.000 0.00 0.00 0.00 3.86
2472 5726 0.995024 CTCCCTTTGACACCCTCCAT 59.005 55.000 0.00 0.00 0.00 3.41
2473 5727 0.698238 TCCCTTTGACACCCTCCATG 59.302 55.000 0.00 0.00 0.00 3.66
2474 5728 0.967380 CCCTTTGACACCCTCCATGC 60.967 60.000 0.00 0.00 0.00 4.06
2475 5729 0.251297 CCTTTGACACCCTCCATGCA 60.251 55.000 0.00 0.00 0.00 3.96
2476 5730 1.171308 CTTTGACACCCTCCATGCAG 58.829 55.000 0.00 0.00 0.00 4.41
2477 5731 0.895100 TTTGACACCCTCCATGCAGC 60.895 55.000 0.00 0.00 0.00 5.25
2478 5732 2.066700 TTGACACCCTCCATGCAGCA 62.067 55.000 0.00 0.00 0.00 4.41
2479 5733 2.034687 ACACCCTCCATGCAGCAC 59.965 61.111 0.00 0.00 0.00 4.40
2480 5734 3.129502 CACCCTCCATGCAGCACG 61.130 66.667 0.00 0.00 0.00 5.34
2481 5735 4.415150 ACCCTCCATGCAGCACGG 62.415 66.667 0.00 0.00 0.00 4.94
2486 5740 1.434622 CTCCATGCAGCACGGACATC 61.435 60.000 5.97 0.00 0.00 3.06
2705 6013 0.521034 CACACGCATATTGCACACGG 60.521 55.000 0.00 0.00 45.36 4.94
3114 6433 4.148825 GCCCATGAGGACGAGCGT 62.149 66.667 0.00 0.00 38.24 5.07
3115 6434 2.579201 CCCATGAGGACGAGCGTT 59.421 61.111 0.00 0.00 38.24 4.84
3116 6435 1.519455 CCCATGAGGACGAGCGTTC 60.519 63.158 0.00 0.00 38.24 3.95
3117 6436 1.513158 CCATGAGGACGAGCGTTCT 59.487 57.895 3.02 3.02 36.50 3.01
3120 6439 3.593318 GAGGACGAGCGTTCTCCT 58.407 61.111 18.23 16.22 43.23 3.69
3121 6440 1.430228 GAGGACGAGCGTTCTCCTC 59.570 63.158 22.20 22.20 43.23 3.71
3125 6444 2.276743 CGAGCGTTCTCCTCGTCG 60.277 66.667 0.00 0.00 45.17 5.12
3129 6448 3.744719 CGTTCTCCTCGTCGCCCA 61.745 66.667 0.00 0.00 0.00 5.36
3130 6449 2.893398 GTTCTCCTCGTCGCCCAT 59.107 61.111 0.00 0.00 0.00 4.00
3131 6450 1.519455 GTTCTCCTCGTCGCCCATG 60.519 63.158 0.00 0.00 0.00 3.66
3132 6451 1.680989 TTCTCCTCGTCGCCCATGA 60.681 57.895 0.00 0.00 0.00 3.07
3133 6452 1.667154 TTCTCCTCGTCGCCCATGAG 61.667 60.000 0.00 0.00 37.84 2.90
3136 6455 2.105128 CTCGTCGCCCATGAGGAC 59.895 66.667 0.00 0.00 38.24 3.85
3139 6458 2.105128 GTCGCCCATGAGGACGAG 59.895 66.667 14.81 1.92 42.31 4.18
3140 6459 3.838271 TCGCCCATGAGGACGAGC 61.838 66.667 0.00 0.00 38.63 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 4.344390 GTCATCTATTTAGGGACGGAGGTT 59.656 45.833 0.00 0.00 0.00 3.50
267 270 7.429633 CCAAAATACATGGCGTATAAATCCAA 58.570 34.615 0.00 0.00 40.04 3.53
368 1118 7.961855 TGTCAATTTGTTTGCATATACATTGC 58.038 30.769 7.55 4.95 40.55 3.56
479 1230 7.661127 TTACTTTCTTGCGTACACATTGTAT 57.339 32.000 0.00 0.00 35.05 2.29
591 2962 9.167311 ACCTTTTCATACACATTCTACATTCTC 57.833 33.333 0.00 0.00 0.00 2.87
592 2963 9.520515 AACCTTTTCATACACATTCTACATTCT 57.479 29.630 0.00 0.00 0.00 2.40
593 2964 9.559958 CAACCTTTTCATACACATTCTACATTC 57.440 33.333 0.00 0.00 0.00 2.67
713 3084 9.141400 CGAGTCTAGCTAGTTTTTGAAACTATT 57.859 33.333 20.10 7.82 32.85 1.73
714 3085 7.760340 CCGAGTCTAGCTAGTTTTTGAAACTAT 59.240 37.037 20.10 3.73 32.85 2.12
715 3086 7.088905 CCGAGTCTAGCTAGTTTTTGAAACTA 58.911 38.462 20.10 11.50 0.00 2.24
716 3087 5.927115 CCGAGTCTAGCTAGTTTTTGAAACT 59.073 40.000 20.10 13.06 0.00 2.66
717 3088 5.389620 GCCGAGTCTAGCTAGTTTTTGAAAC 60.390 44.000 20.10 8.54 0.00 2.78
718 3089 4.689345 GCCGAGTCTAGCTAGTTTTTGAAA 59.311 41.667 20.10 0.00 0.00 2.69
719 3090 4.243270 GCCGAGTCTAGCTAGTTTTTGAA 58.757 43.478 20.10 0.00 0.00 2.69
720 3091 3.368116 GGCCGAGTCTAGCTAGTTTTTGA 60.368 47.826 20.10 0.00 0.00 2.69
721 3092 2.930682 GGCCGAGTCTAGCTAGTTTTTG 59.069 50.000 20.10 10.43 0.00 2.44
722 3093 2.416972 CGGCCGAGTCTAGCTAGTTTTT 60.417 50.000 24.07 4.90 0.00 1.94
741 3112 1.623311 TGCATATGGGTATCTGGACGG 59.377 52.381 4.56 0.00 0.00 4.79
796 4016 2.289320 GGCATACTCTGGGATGTGCTAG 60.289 54.545 0.00 0.00 33.38 3.42
873 4097 2.309755 TCCATTTGAGCTGAGTGGGAAT 59.690 45.455 0.00 0.00 0.00 3.01
874 4098 1.704628 TCCATTTGAGCTGAGTGGGAA 59.295 47.619 0.00 0.00 0.00 3.97
880 4104 2.995283 TGTGGATCCATTTGAGCTGAG 58.005 47.619 19.62 0.00 0.00 3.35
894 4118 1.812571 GGTGAAGCGTTCAATGTGGAT 59.187 47.619 2.65 0.00 42.15 3.41
932 4156 3.753272 GTCTTGTACCGCCGGAGTATATA 59.247 47.826 11.71 0.00 0.00 0.86
933 4157 2.555757 GTCTTGTACCGCCGGAGTATAT 59.444 50.000 11.71 0.00 0.00 0.86
934 4158 1.949525 GTCTTGTACCGCCGGAGTATA 59.050 52.381 11.71 0.81 0.00 1.47
935 4159 0.743097 GTCTTGTACCGCCGGAGTAT 59.257 55.000 11.71 0.00 0.00 2.12
936 4160 1.647545 CGTCTTGTACCGCCGGAGTA 61.648 60.000 11.71 2.45 0.00 2.59
937 4161 2.968206 GTCTTGTACCGCCGGAGT 59.032 61.111 11.71 3.70 0.00 3.85
938 4162 2.202570 CGTCTTGTACCGCCGGAG 60.203 66.667 11.71 0.00 0.00 4.63
939 4163 3.751246 CCGTCTTGTACCGCCGGA 61.751 66.667 11.71 0.00 41.08 5.14
940 4164 3.976902 GACCGTCTTGTACCGCCGG 62.977 68.421 0.00 0.00 44.06 6.13
955 4179 0.107945 GGAGTGAGGCACTGATGACC 60.108 60.000 4.60 0.00 45.44 4.02
965 4201 3.322318 GAGCAGGGTGGAGTGAGGC 62.322 68.421 0.00 0.00 0.00 4.70
1012 4248 2.454941 GAGGAGGAGGGGTGGGAA 59.545 66.667 0.00 0.00 0.00 3.97
1974 5221 1.203928 CGCTCTTCATCACGTCATCC 58.796 55.000 0.00 0.00 0.00 3.51
1977 5224 1.008875 GCACGCTCTTCATCACGTCA 61.009 55.000 0.00 0.00 36.45 4.35
2351 5605 1.542375 ACCACCTCCATCAAGCCCT 60.542 57.895 0.00 0.00 0.00 5.19
2352 5606 1.077429 GACCACCTCCATCAAGCCC 60.077 63.158 0.00 0.00 0.00 5.19
2353 5607 0.329596 AAGACCACCTCCATCAAGCC 59.670 55.000 0.00 0.00 0.00 4.35
2354 5608 2.206576 AAAGACCACCTCCATCAAGC 57.793 50.000 0.00 0.00 0.00 4.01
2355 5609 2.229784 GCAAAAGACCACCTCCATCAAG 59.770 50.000 0.00 0.00 0.00 3.02
2356 5610 2.238521 GCAAAAGACCACCTCCATCAA 58.761 47.619 0.00 0.00 0.00 2.57
2357 5611 1.547675 GGCAAAAGACCACCTCCATCA 60.548 52.381 0.00 0.00 0.00 3.07
2358 5612 1.177401 GGCAAAAGACCACCTCCATC 58.823 55.000 0.00 0.00 0.00 3.51
2359 5613 0.609131 CGGCAAAAGACCACCTCCAT 60.609 55.000 0.00 0.00 0.00 3.41
2360 5614 1.228124 CGGCAAAAGACCACCTCCA 60.228 57.895 0.00 0.00 0.00 3.86
2361 5615 1.228154 ACGGCAAAAGACCACCTCC 60.228 57.895 0.00 0.00 0.00 4.30
2362 5616 0.534203 TCACGGCAAAAGACCACCTC 60.534 55.000 0.00 0.00 0.00 3.85
2363 5617 0.818040 GTCACGGCAAAAGACCACCT 60.818 55.000 0.00 0.00 0.00 4.00
2364 5618 1.652563 GTCACGGCAAAAGACCACC 59.347 57.895 0.00 0.00 0.00 4.61
2365 5619 1.278637 CGTCACGGCAAAAGACCAC 59.721 57.895 0.00 0.00 0.00 4.16
2366 5620 1.890041 CCGTCACGGCAAAAGACCA 60.890 57.895 1.50 0.00 41.17 4.02
2367 5621 2.943653 CCGTCACGGCAAAAGACC 59.056 61.111 1.50 0.00 41.17 3.85
2377 5631 3.893720 ACTACTAACAGTTTCCGTCACG 58.106 45.455 0.00 0.00 0.00 4.35
2378 5632 5.855395 CAGTACTACTAACAGTTTCCGTCAC 59.145 44.000 0.00 0.00 0.00 3.67
2379 5633 5.764686 TCAGTACTACTAACAGTTTCCGTCA 59.235 40.000 0.00 0.00 0.00 4.35
2380 5634 6.246420 TCAGTACTACTAACAGTTTCCGTC 57.754 41.667 0.00 0.00 0.00 4.79
2381 5635 6.830873 ATCAGTACTACTAACAGTTTCCGT 57.169 37.500 0.00 0.00 0.00 4.69
2382 5636 8.530269 AAAATCAGTACTACTAACAGTTTCCG 57.470 34.615 0.00 0.00 0.00 4.30
2417 5671 9.452287 GGTAACACCTAGATGTAACCATTTTTA 57.548 33.333 0.00 0.00 34.73 1.52
2418 5672 7.395206 GGGTAACACCTAGATGTAACCATTTTT 59.605 37.037 0.00 0.00 38.64 1.94
2419 5673 6.888088 GGGTAACACCTAGATGTAACCATTTT 59.112 38.462 0.00 0.00 38.64 1.82
2420 5674 6.216868 AGGGTAACACCTAGATGTAACCATTT 59.783 38.462 7.34 0.00 39.65 2.32
2421 5675 5.729718 AGGGTAACACCTAGATGTAACCATT 59.270 40.000 7.34 0.00 39.65 3.16
2422 5676 5.286221 AGGGTAACACCTAGATGTAACCAT 58.714 41.667 7.34 0.00 39.65 3.55
2423 5677 4.691238 AGGGTAACACCTAGATGTAACCA 58.309 43.478 7.34 0.00 39.65 3.67
2424 5678 5.424573 AGAAGGGTAACACCTAGATGTAACC 59.575 44.000 0.00 0.00 40.87 2.85
2425 5679 6.380560 AGAGAAGGGTAACACCTAGATGTAAC 59.619 42.308 0.00 0.00 40.87 2.50
2426 5680 6.500336 AGAGAAGGGTAACACCTAGATGTAA 58.500 40.000 0.00 0.00 40.87 2.41
2427 5681 6.088541 AGAGAAGGGTAACACCTAGATGTA 57.911 41.667 0.00 0.00 40.87 2.29
2428 5682 4.949121 AGAGAAGGGTAACACCTAGATGT 58.051 43.478 0.00 0.00 40.87 3.06
2429 5683 4.036971 CGAGAGAAGGGTAACACCTAGATG 59.963 50.000 0.00 0.00 40.87 2.90
2430 5684 4.208746 CGAGAGAAGGGTAACACCTAGAT 58.791 47.826 0.00 0.00 40.87 1.98
2431 5685 3.618351 CGAGAGAAGGGTAACACCTAGA 58.382 50.000 0.00 0.00 40.87 2.43
2432 5686 2.099427 GCGAGAGAAGGGTAACACCTAG 59.901 54.545 0.00 0.00 40.87 3.02
2433 5687 2.097825 GCGAGAGAAGGGTAACACCTA 58.902 52.381 0.00 0.00 40.87 3.08
2434 5688 0.896226 GCGAGAGAAGGGTAACACCT 59.104 55.000 0.00 0.00 44.56 4.00
2435 5689 0.896226 AGCGAGAGAAGGGTAACACC 59.104 55.000 0.00 0.00 37.60 4.16
2436 5690 1.135053 GGAGCGAGAGAAGGGTAACAC 60.135 57.143 0.00 0.00 39.74 3.32
2437 5691 1.183549 GGAGCGAGAGAAGGGTAACA 58.816 55.000 0.00 0.00 39.74 2.41
2438 5692 0.460722 GGGAGCGAGAGAAGGGTAAC 59.539 60.000 0.00 0.00 0.00 2.50
2439 5693 0.335361 AGGGAGCGAGAGAAGGGTAA 59.665 55.000 0.00 0.00 0.00 2.85
2440 5694 0.335361 AAGGGAGCGAGAGAAGGGTA 59.665 55.000 0.00 0.00 0.00 3.69
2441 5695 0.545548 AAAGGGAGCGAGAGAAGGGT 60.546 55.000 0.00 0.00 0.00 4.34
2442 5696 0.107945 CAAAGGGAGCGAGAGAAGGG 60.108 60.000 0.00 0.00 0.00 3.95
2443 5697 0.898320 TCAAAGGGAGCGAGAGAAGG 59.102 55.000 0.00 0.00 0.00 3.46
2444 5698 1.273606 TGTCAAAGGGAGCGAGAGAAG 59.726 52.381 0.00 0.00 0.00 2.85
2445 5699 1.000955 GTGTCAAAGGGAGCGAGAGAA 59.999 52.381 0.00 0.00 0.00 2.87
2446 5700 0.603569 GTGTCAAAGGGAGCGAGAGA 59.396 55.000 0.00 0.00 0.00 3.10
2447 5701 0.390472 GGTGTCAAAGGGAGCGAGAG 60.390 60.000 0.00 0.00 0.00 3.20
2448 5702 1.671742 GGTGTCAAAGGGAGCGAGA 59.328 57.895 0.00 0.00 0.00 4.04
2449 5703 1.376037 GGGTGTCAAAGGGAGCGAG 60.376 63.158 0.00 0.00 0.00 5.03
2450 5704 1.827399 GAGGGTGTCAAAGGGAGCGA 61.827 60.000 0.00 0.00 0.00 4.93
2451 5705 1.376037 GAGGGTGTCAAAGGGAGCG 60.376 63.158 0.00 0.00 0.00 5.03
2452 5706 1.002011 GGAGGGTGTCAAAGGGAGC 60.002 63.158 0.00 0.00 0.00 4.70
2453 5707 0.995024 ATGGAGGGTGTCAAAGGGAG 59.005 55.000 0.00 0.00 0.00 4.30
2454 5708 0.698238 CATGGAGGGTGTCAAAGGGA 59.302 55.000 0.00 0.00 0.00 4.20
2455 5709 0.967380 GCATGGAGGGTGTCAAAGGG 60.967 60.000 0.00 0.00 0.00 3.95
2456 5710 0.251297 TGCATGGAGGGTGTCAAAGG 60.251 55.000 0.00 0.00 0.00 3.11
2457 5711 1.171308 CTGCATGGAGGGTGTCAAAG 58.829 55.000 6.28 0.00 0.00 2.77
2458 5712 0.895100 GCTGCATGGAGGGTGTCAAA 60.895 55.000 16.65 0.00 0.00 2.69
2459 5713 1.303561 GCTGCATGGAGGGTGTCAA 60.304 57.895 16.65 0.00 0.00 3.18
2460 5714 2.352422 GCTGCATGGAGGGTGTCA 59.648 61.111 16.65 0.00 0.00 3.58
2461 5715 2.042831 GTGCTGCATGGAGGGTGTC 61.043 63.158 16.65 0.00 0.00 3.67
2462 5716 2.034687 GTGCTGCATGGAGGGTGT 59.965 61.111 16.65 0.00 0.00 4.16
2463 5717 3.129502 CGTGCTGCATGGAGGGTG 61.130 66.667 16.65 0.00 0.00 4.61
2464 5718 4.415150 CCGTGCTGCATGGAGGGT 62.415 66.667 32.30 0.00 42.73 4.34
2465 5719 4.100084 TCCGTGCTGCATGGAGGG 62.100 66.667 33.80 17.16 43.70 4.30
2468 5722 1.450134 GATGTCCGTGCTGCATGGA 60.450 57.895 33.80 33.80 46.01 3.41
2469 5723 1.712018 CTGATGTCCGTGCTGCATGG 61.712 60.000 30.57 30.57 41.56 3.66
2470 5724 0.741927 TCTGATGTCCGTGCTGCATG 60.742 55.000 14.82 14.82 0.00 4.06
2471 5725 0.461516 CTCTGATGTCCGTGCTGCAT 60.462 55.000 5.27 0.00 0.00 3.96
2472 5726 1.079612 CTCTGATGTCCGTGCTGCA 60.080 57.895 0.00 0.00 0.00 4.41
2473 5727 2.459442 GCTCTGATGTCCGTGCTGC 61.459 63.158 0.00 0.00 0.00 5.25
2474 5728 0.461516 ATGCTCTGATGTCCGTGCTG 60.462 55.000 0.00 0.00 0.00 4.41
2475 5729 0.179089 GATGCTCTGATGTCCGTGCT 60.179 55.000 0.00 0.00 0.00 4.40
2476 5730 0.179089 AGATGCTCTGATGTCCGTGC 60.179 55.000 0.00 0.00 0.00 5.34
2477 5731 1.537776 GGAGATGCTCTGATGTCCGTG 60.538 57.143 0.00 0.00 0.00 4.94
2478 5732 0.749649 GGAGATGCTCTGATGTCCGT 59.250 55.000 0.00 0.00 0.00 4.69
2479 5733 0.749049 TGGAGATGCTCTGATGTCCG 59.251 55.000 0.00 0.00 38.39 4.79
2480 5734 2.093288 TGTTGGAGATGCTCTGATGTCC 60.093 50.000 0.00 0.00 36.51 4.02
2481 5735 3.196463 CTGTTGGAGATGCTCTGATGTC 58.804 50.000 0.00 0.00 0.00 3.06
2486 5740 0.035725 TGGCTGTTGGAGATGCTCTG 60.036 55.000 0.00 0.00 0.00 3.35
2693 6001 3.055094 AGGAAGAGAACCGTGTGCAATAT 60.055 43.478 0.00 0.00 0.00 1.28
2705 6013 2.070028 GCAACGGAAGAGGAAGAGAAC 58.930 52.381 0.00 0.00 0.00 3.01
3114 6433 1.680989 TCATGGGCGACGAGGAGAA 60.681 57.895 0.00 0.00 0.00 2.87
3115 6434 2.044352 TCATGGGCGACGAGGAGA 60.044 61.111 0.00 0.00 0.00 3.71
3116 6435 2.415010 CTCATGGGCGACGAGGAG 59.585 66.667 0.00 0.00 40.47 3.69
3118 6437 3.147595 TCCTCATGGGCGACGAGG 61.148 66.667 5.16 5.16 46.49 4.63
3119 6438 2.105128 GTCCTCATGGGCGACGAG 59.895 66.667 0.00 0.00 34.39 4.18
3125 6444 4.899239 CCGCTCGTCCTCATGGGC 62.899 72.222 0.00 0.00 34.39 5.36
3126 6445 4.227134 CCCGCTCGTCCTCATGGG 62.227 72.222 0.00 0.00 0.00 4.00
3127 6446 3.432051 GACCCGCTCGTCCTCATGG 62.432 68.421 0.00 0.00 0.00 3.66
3128 6447 2.021068 ATGACCCGCTCGTCCTCATG 62.021 60.000 0.00 0.00 31.35 3.07
3129 6448 1.758514 ATGACCCGCTCGTCCTCAT 60.759 57.895 0.00 0.00 31.35 2.90
3130 6449 2.362503 ATGACCCGCTCGTCCTCA 60.363 61.111 0.00 0.00 31.35 3.86
3131 6450 2.105128 CATGACCCGCTCGTCCTC 59.895 66.667 0.00 0.00 31.35 3.71
3132 6451 3.461773 CCATGACCCGCTCGTCCT 61.462 66.667 0.00 0.00 31.35 3.85
3137 6456 4.899239 CTCCGCCATGACCCGCTC 62.899 72.222 0.00 0.00 0.00 5.03
3140 6459 4.838152 CCACTCCGCCATGACCCG 62.838 72.222 0.00 0.00 0.00 5.28
3215 6534 1.003233 GCCTTTGCGTCTCCTCCTT 60.003 57.895 0.00 0.00 0.00 3.36
3277 6596 2.667470 ACTACATCGCACTGGGATAGT 58.333 47.619 8.20 6.92 41.36 2.12


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

AutoCloner maintained by Alex Coulton.