Multiple sequence alignment - TraesCS4A01G356800

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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 TraesCS4A01G356800 chr4A 100.000 2288 0 0 1 2288 629947227 629949514 0.000000e+00 4226
1 TraesCS4A01G356800 chr4A 95.397 717 32 1 600 1316 553467915 553467200 0.000000e+00 1140
2 TraesCS4A01G356800 chr4A 94.979 717 36 0 600 1316 4145226 4144510 0.000000e+00 1125
3 TraesCS4A01G356800 chr4A 98.909 550 6 0 1 550 436872873 436872324 0.000000e+00 983
4 TraesCS4A01G356800 chr4A 80.789 760 79 34 1541 2286 625561805 625562511 1.200000e-147 532
5 TraesCS4A01G356800 chr4A 88.268 358 28 5 1669 2017 150876839 150877191 1.260000e-112 416
6 TraesCS4A01G356800 chr4A 88.087 277 26 5 2014 2286 150877273 150877546 2.840000e-84 322
7 TraesCS4A01G356800 chr4A 83.221 149 22 3 1379 1526 150876230 150876376 1.430000e-27 134
8 TraesCS4A01G356800 chr5A 96.095 717 28 0 600 1316 31961989 31962705 0.000000e+00 1170
9 TraesCS4A01G356800 chr5A 85.185 459 31 6 1586 2017 496758469 496758021 9.710000e-119 436
10 TraesCS4A01G356800 chr7B 95.961 718 28 1 600 1317 466050172 466050888 0.000000e+00 1164
11 TraesCS4A01G356800 chr7B 98.739 555 6 1 1 555 701211664 701212217 0.000000e+00 985
12 TraesCS4A01G356800 chr1D 95.955 717 29 0 600 1316 298426407 298427123 0.000000e+00 1164
13 TraesCS4A01G356800 chr1D 84.756 492 40 4 1541 2005 408156077 408156560 5.760000e-126 460
14 TraesCS4A01G356800 chr1D 86.061 165 19 3 2046 2208 408156697 408156859 8.400000e-40 174
15 TraesCS4A01G356800 chr6D 95.676 717 31 0 600 1316 254855018 254854302 0.000000e+00 1153
16 TraesCS4A01G356800 chr6D 84.584 493 40 7 1541 2005 58442056 58442540 7.450000e-125 457
17 TraesCS4A01G356800 chr6D 83.665 502 48 6 1544 2017 455572231 455571736 2.090000e-120 442
18 TraesCS4A01G356800 chr6D 89.716 282 22 6 2009 2286 58442630 58442908 1.010000e-93 353
19 TraesCS4A01G356800 chr6D 85.762 302 28 4 1712 2005 376839633 376839339 2.860000e-79 305
20 TraesCS4A01G356800 chr6D 83.333 276 23 9 2015 2286 376839270 376839014 1.370000e-57 233
21 TraesCS4A01G356800 chr6D 87.097 93 12 0 2032 2124 189767889 189767981 3.110000e-19 106
22 TraesCS4A01G356800 chr7A 95.112 716 33 2 600 1315 56194752 56195465 0.000000e+00 1127
23 TraesCS4A01G356800 chr7A 99.455 550 3 0 1 550 649396369 649396918 0.000000e+00 1000
24 TraesCS4A01G356800 chr7A 81.974 760 69 30 1541 2286 250809381 250810086 1.180000e-162 582
25 TraesCS4A01G356800 chr7A 88.446 251 23 5 2017 2263 639415096 639414848 4.780000e-77 298
26 TraesCS4A01G356800 chr7A 86.022 186 24 2 1342 1526 639415998 639415814 4.990000e-47 198
27 TraesCS4A01G356800 chr5D 94.840 717 37 0 600 1316 256455704 256456420 0.000000e+00 1120
28 TraesCS4A01G356800 chr5D 94.722 720 33 1 600 1319 189470310 189471024 0.000000e+00 1114
29 TraesCS4A01G356800 chr5D 88.439 346 26 6 1669 2005 209187472 209187812 2.740000e-109 405
30 TraesCS4A01G356800 chr5D 82.041 245 33 7 2032 2265 434388788 434389032 4.990000e-47 198
31 TraesCS4A01G356800 chr5D 83.254 209 31 3 2032 2236 243098160 243098368 3.000000e-44 189
32 TraesCS4A01G356800 chr6B 99.091 550 5 0 1 550 551921238 551920689 0.000000e+00 989
33 TraesCS4A01G356800 chr3B 99.091 550 5 0 1 550 249998315 249997766 0.000000e+00 989
34 TraesCS4A01G356800 chr3B 87.226 274 29 4 2015 2286 41978410 41978141 7.940000e-80 307
35 TraesCS4A01G356800 chr3A 98.909 550 6 0 1 550 118209806 118210355 0.000000e+00 983
36 TraesCS4A01G356800 chr3A 98.909 550 6 0 1 550 171240596 171240047 0.000000e+00 983
37 TraesCS4A01G356800 chr3A 98.384 557 8 1 1 556 717912728 717912172 0.000000e+00 977
38 TraesCS4A01G356800 chr1A 98.909 550 6 0 1 550 119733945 119734494 0.000000e+00 983
39 TraesCS4A01G356800 chr1A 79.891 184 36 1 1343 1526 328106865 328107047 1.430000e-27 134
40 TraesCS4A01G356800 chr7D 86.000 500 37 6 1545 2017 443327726 443327233 2.620000e-139 505
41 TraesCS4A01G356800 chr7D 83.665 502 38 19 1544 2017 121663151 121662666 1.260000e-117 433
42 TraesCS4A01G356800 chr7D 91.273 275 20 3 2015 2286 443327149 443326876 2.780000e-99 372
43 TraesCS4A01G356800 chr7D 90.957 188 14 2 2015 2200 121662582 121662396 1.360000e-62 250
44 TraesCS4A01G356800 chr7D 82.114 246 31 7 2032 2265 77512847 77512603 4.990000e-47 198
45 TraesCS4A01G356800 chr7D 81.028 253 39 6 2032 2275 95843793 95843541 2.320000e-45 193
46 TraesCS4A01G356800 chr3D 85.487 503 40 6 1544 2019 294600608 294600112 5.680000e-136 494
47 TraesCS4A01G356800 chr3D 84.948 485 45 8 1541 2005 456108503 456108979 1.240000e-127 466
48 TraesCS4A01G356800 chr3D 88.652 282 25 6 2009 2286 456109069 456109347 1.010000e-88 337
49 TraesCS4A01G356800 chr4D 84.787 493 41 6 1541 2005 175783139 175783625 4.450000e-127 464
50 TraesCS4A01G356800 chr4D 78.744 207 33 10 2032 2236 459432143 459432340 6.630000e-26 128
51 TraesCS4A01G356800 chr6A 83.564 505 47 9 1541 2017 129772505 129773001 7.500000e-120 440
52 TraesCS4A01G356800 chr6A 91.165 249 18 3 2018 2263 129773088 129773335 3.640000e-88 335
53 TraesCS4A01G356800 chr6A 82.231 242 32 7 2032 2262 208016188 208016429 4.990000e-47 198
54 TraesCS4A01G356800 chr6A 82.297 209 33 3 2032 2236 182597979 182598187 6.500000e-41 178
55 TraesCS4A01G356800 chr5B 83.745 486 51 15 1544 2011 603880935 603880460 3.490000e-118 435
56 TraesCS4A01G356800 chr5B 83.784 185 16 6 1343 1526 503315217 503315388 1.820000e-36 163
57 TraesCS4A01G356800 chr2D 90.580 276 23 3 2014 2286 3219323 3219048 1.670000e-96 363
58 TraesCS4A01G356800 chr2D 90.000 130 12 1 1664 1792 3219517 3219388 1.410000e-37 167
59 TraesCS4A01G356800 chr4B 84.343 198 18 7 2015 2200 95702932 95702736 5.020000e-42 182


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 TraesCS4A01G356800 chr4A 629947227 629949514 2287 False 4226.000000 4226 100.000000 1 2288 1 chr4A.!!$F2 2287
1 TraesCS4A01G356800 chr4A 553467200 553467915 715 True 1140.000000 1140 95.397000 600 1316 1 chr4A.!!$R3 716
2 TraesCS4A01G356800 chr4A 4144510 4145226 716 True 1125.000000 1125 94.979000 600 1316 1 chr4A.!!$R1 716
3 TraesCS4A01G356800 chr4A 436872324 436872873 549 True 983.000000 983 98.909000 1 550 1 chr4A.!!$R2 549
4 TraesCS4A01G356800 chr4A 625561805 625562511 706 False 532.000000 532 80.789000 1541 2286 1 chr4A.!!$F1 745
5 TraesCS4A01G356800 chr4A 150876230 150877546 1316 False 290.666667 416 86.525333 1379 2286 3 chr4A.!!$F3 907
6 TraesCS4A01G356800 chr5A 31961989 31962705 716 False 1170.000000 1170 96.095000 600 1316 1 chr5A.!!$F1 716
7 TraesCS4A01G356800 chr7B 466050172 466050888 716 False 1164.000000 1164 95.961000 600 1317 1 chr7B.!!$F1 717
8 TraesCS4A01G356800 chr7B 701211664 701212217 553 False 985.000000 985 98.739000 1 555 1 chr7B.!!$F2 554
9 TraesCS4A01G356800 chr1D 298426407 298427123 716 False 1164.000000 1164 95.955000 600 1316 1 chr1D.!!$F1 716
10 TraesCS4A01G356800 chr1D 408156077 408156859 782 False 317.000000 460 85.408500 1541 2208 2 chr1D.!!$F2 667
11 TraesCS4A01G356800 chr6D 254854302 254855018 716 True 1153.000000 1153 95.676000 600 1316 1 chr6D.!!$R1 716
12 TraesCS4A01G356800 chr6D 58442056 58442908 852 False 405.000000 457 87.150000 1541 2286 2 chr6D.!!$F2 745
13 TraesCS4A01G356800 chr6D 376839014 376839633 619 True 269.000000 305 84.547500 1712 2286 2 chr6D.!!$R3 574
14 TraesCS4A01G356800 chr7A 56194752 56195465 713 False 1127.000000 1127 95.112000 600 1315 1 chr7A.!!$F1 715
15 TraesCS4A01G356800 chr7A 649396369 649396918 549 False 1000.000000 1000 99.455000 1 550 1 chr7A.!!$F3 549
16 TraesCS4A01G356800 chr7A 250809381 250810086 705 False 582.000000 582 81.974000 1541 2286 1 chr7A.!!$F2 745
17 TraesCS4A01G356800 chr7A 639414848 639415998 1150 True 248.000000 298 87.234000 1342 2263 2 chr7A.!!$R1 921
18 TraesCS4A01G356800 chr5D 256455704 256456420 716 False 1120.000000 1120 94.840000 600 1316 1 chr5D.!!$F4 716
19 TraesCS4A01G356800 chr5D 189470310 189471024 714 False 1114.000000 1114 94.722000 600 1319 1 chr5D.!!$F1 719
20 TraesCS4A01G356800 chr6B 551920689 551921238 549 True 989.000000 989 99.091000 1 550 1 chr6B.!!$R1 549
21 TraesCS4A01G356800 chr3B 249997766 249998315 549 True 989.000000 989 99.091000 1 550 1 chr3B.!!$R2 549
22 TraesCS4A01G356800 chr3A 118209806 118210355 549 False 983.000000 983 98.909000 1 550 1 chr3A.!!$F1 549
23 TraesCS4A01G356800 chr3A 171240047 171240596 549 True 983.000000 983 98.909000 1 550 1 chr3A.!!$R1 549
24 TraesCS4A01G356800 chr3A 717912172 717912728 556 True 977.000000 977 98.384000 1 556 1 chr3A.!!$R2 555
25 TraesCS4A01G356800 chr1A 119733945 119734494 549 False 983.000000 983 98.909000 1 550 1 chr1A.!!$F1 549
26 TraesCS4A01G356800 chr7D 443326876 443327726 850 True 438.500000 505 88.636500 1545 2286 2 chr7D.!!$R4 741
27 TraesCS4A01G356800 chr7D 121662396 121663151 755 True 341.500000 433 87.311000 1544 2200 2 chr7D.!!$R3 656
28 TraesCS4A01G356800 chr3D 456108503 456109347 844 False 401.500000 466 86.800000 1541 2286 2 chr3D.!!$F1 745
29 TraesCS4A01G356800 chr6A 129772505 129773335 830 False 387.500000 440 87.364500 1541 2263 2 chr6A.!!$F3 722

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
567 568 1.138661 AGACTACTAGCTAGCGACGGT 59.861 52.381 20.91 11.65 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 1535 0.175073 CCCCTTAGCACACGTCTACC 59.825 60.0 0.0 0.0 0.0 3.18 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
561 562 5.479124 AGGAGTAGAGACTACTAGCTAGC 57.521 47.826 20.91 6.62 45.84 3.42
562 563 4.021719 AGGAGTAGAGACTACTAGCTAGCG 60.022 50.000 20.91 14.08 45.84 4.26
563 564 4.022068 GGAGTAGAGACTACTAGCTAGCGA 60.022 50.000 20.91 8.17 35.45 4.93
564 565 4.874970 AGTAGAGACTACTAGCTAGCGAC 58.125 47.826 20.91 11.96 32.65 5.19
565 566 2.746269 AGAGACTACTAGCTAGCGACG 58.254 52.381 20.91 8.86 0.00 5.12
566 567 1.794116 GAGACTACTAGCTAGCGACGG 59.206 57.143 20.91 8.71 0.00 4.79
567 568 1.138661 AGACTACTAGCTAGCGACGGT 59.861 52.381 20.91 11.65 0.00 4.83
568 569 2.363680 AGACTACTAGCTAGCGACGGTA 59.636 50.000 20.91 6.59 0.00 4.02
569 570 3.126831 GACTACTAGCTAGCGACGGTAA 58.873 50.000 20.91 0.00 0.00 2.85
570 571 3.535561 ACTACTAGCTAGCGACGGTAAA 58.464 45.455 20.91 0.00 0.00 2.01
571 572 3.941483 ACTACTAGCTAGCGACGGTAAAA 59.059 43.478 20.91 0.00 0.00 1.52
572 573 3.855689 ACTAGCTAGCGACGGTAAAAA 57.144 42.857 20.91 0.00 0.00 1.94
596 597 2.584492 GCCACTGCTCACAAGTTTTT 57.416 45.000 0.00 0.00 33.53 1.94
597 598 2.195922 GCCACTGCTCACAAGTTTTTG 58.804 47.619 0.00 0.00 35.98 2.44
598 599 2.159254 GCCACTGCTCACAAGTTTTTGA 60.159 45.455 0.00 0.00 34.81 2.69
642 643 8.998377 GGTTGCCAAAATACAAGTGAATTAATT 58.002 29.630 0.00 0.00 0.00 1.40
653 654 6.128117 ACAAGTGAATTAATTGCGATAACCGT 60.128 34.615 5.17 0.00 37.87 4.83
695 696 2.483877 GACGCATGTTGGTTCATGAAGA 59.516 45.455 8.80 0.00 45.41 2.87
815 816 4.601042 GAGCCGACCTCCTATGGA 57.399 61.111 0.00 0.00 34.35 3.41
816 817 3.059287 GAGCCGACCTCCTATGGAT 57.941 57.895 0.00 0.00 34.35 3.41
853 855 4.130857 TGTTGACGCTTCTTTTGACCATA 58.869 39.130 0.00 0.00 0.00 2.74
858 860 6.403049 TGACGCTTCTTTTGACCATAATCTA 58.597 36.000 0.00 0.00 0.00 1.98
967 969 8.287807 TGATGTACTAACAGCAGAAGCGATGA 62.288 42.308 0.00 0.00 46.59 2.92
1086 1088 2.745884 CAATCGGCGGGAGTTGCA 60.746 61.111 7.21 0.00 0.00 4.08
1110 1112 3.615110 CGGCAGTATTCGAGGATTGCTAT 60.615 47.826 13.35 0.00 0.00 2.97
1232 1234 4.100373 ACTAGAGATTGGTTTGAGGAGCT 58.900 43.478 0.00 0.00 0.00 4.09
1338 1340 3.661745 CGCCTCCGTGTTATTAGCT 57.338 52.632 0.00 0.00 0.00 3.32
1339 1341 1.935933 CGCCTCCGTGTTATTAGCTT 58.064 50.000 0.00 0.00 0.00 3.74
1340 1342 1.593006 CGCCTCCGTGTTATTAGCTTG 59.407 52.381 0.00 0.00 0.00 4.01
1341 1343 2.629051 GCCTCCGTGTTATTAGCTTGT 58.371 47.619 0.00 0.00 0.00 3.16
1342 1344 2.351726 GCCTCCGTGTTATTAGCTTGTG 59.648 50.000 0.00 0.00 0.00 3.33
1343 1345 2.936498 CCTCCGTGTTATTAGCTTGTGG 59.064 50.000 0.00 0.00 0.00 4.17
1344 1346 2.936498 CTCCGTGTTATTAGCTTGTGGG 59.064 50.000 0.00 0.00 0.00 4.61
1360 1362 5.815222 GCTTGTGGGTTTTTATCAGTTTTGT 59.185 36.000 0.00 0.00 0.00 2.83
1367 1369 6.581166 GGGTTTTTATCAGTTTTGTCATCGAC 59.419 38.462 0.00 0.00 0.00 4.20
1387 1389 5.636965 TCGACTGTACTACACTACTCAGTTC 59.363 44.000 0.00 0.00 36.49 3.01
1390 1392 6.297582 ACTGTACTACACTACTCAGTTCTGT 58.702 40.000 0.00 0.00 33.26 3.41
1391 1393 6.771749 ACTGTACTACACTACTCAGTTCTGTT 59.228 38.462 0.00 0.00 33.26 3.16
1435 1437 2.645838 ATGCCAATGTTCCGCTAGAT 57.354 45.000 0.00 0.00 0.00 1.98
1503 1506 5.451937 GGACATTGATCGAAGGTAGATGACA 60.452 44.000 0.00 0.00 0.00 3.58
1514 1517 5.125367 AGGTAGATGACAAAAATACCCCC 57.875 43.478 0.00 0.00 37.24 5.40
1517 1520 6.060136 GGTAGATGACAAAAATACCCCCTAC 58.940 44.000 0.00 0.00 31.56 3.18
1526 1529 0.044549 ATACCCCCTACCCCGTTTGA 59.955 55.000 0.00 0.00 0.00 2.69
1527 1530 0.044549 TACCCCCTACCCCGTTTGAT 59.955 55.000 0.00 0.00 0.00 2.57
1528 1531 1.276859 ACCCCCTACCCCGTTTGATC 61.277 60.000 0.00 0.00 0.00 2.92
1529 1532 1.145377 CCCCTACCCCGTTTGATCG 59.855 63.158 0.00 0.00 0.00 3.69
1532 1535 1.472728 CCCTACCCCGTTTGATCGAAG 60.473 57.143 0.00 0.00 0.00 3.79
1533 1536 1.472728 CCTACCCCGTTTGATCGAAGG 60.473 57.143 8.21 8.21 0.00 3.46
1535 1538 1.269012 ACCCCGTTTGATCGAAGGTA 58.731 50.000 13.10 0.00 36.23 3.08
1536 1539 1.206371 ACCCCGTTTGATCGAAGGTAG 59.794 52.381 13.10 7.29 36.23 3.18
1537 1540 1.479323 CCCCGTTTGATCGAAGGTAGA 59.521 52.381 13.10 0.00 0.00 2.59
1538 1541 2.537401 CCCGTTTGATCGAAGGTAGAC 58.463 52.381 13.10 0.00 0.00 2.59
1539 1542 2.182825 CCGTTTGATCGAAGGTAGACG 58.817 52.381 13.10 5.36 0.00 4.18
1542 1668 3.572584 GTTTGATCGAAGGTAGACGTGT 58.427 45.455 0.00 0.00 0.00 4.49
1551 1677 0.175073 GGTAGACGTGTGCTAAGGGG 59.825 60.000 0.00 0.00 0.00 4.79
1567 1693 6.122964 GCTAAGGGGAAGTTTTGATGTAGAT 58.877 40.000 0.00 0.00 0.00 1.98
1714 2049 4.337274 TGATAGCAGGAGCACATGATTTTG 59.663 41.667 0.00 0.00 45.49 2.44
1719 2054 4.860907 GCAGGAGCACATGATTTTGTAAAG 59.139 41.667 0.00 0.00 41.58 1.85
1757 2092 1.554160 CATGGTGCCTGCCCATTTTTA 59.446 47.619 8.77 0.00 40.76 1.52
1777 2112 8.886816 TTTTTATGAAAACAACACAAATGCAC 57.113 26.923 0.00 0.00 30.07 4.57
1807 2142 0.675633 AAACTTCACATGTGCAGCCC 59.324 50.000 23.08 0.00 0.00 5.19
1811 2146 0.961019 TTCACATGTGCAGCCCTTTC 59.039 50.000 21.38 0.00 0.00 2.62
1814 2150 2.161855 CACATGTGCAGCCCTTTCTAA 58.838 47.619 13.94 0.00 0.00 2.10
1868 2228 5.699001 AGAACATGTGTAGCAAATTGTACGA 59.301 36.000 0.00 0.00 0.00 3.43
1886 2249 4.323553 ACGAGAGTATCAATAAGGCACC 57.676 45.455 0.00 0.00 46.88 5.01
1887 2250 3.704566 ACGAGAGTATCAATAAGGCACCA 59.295 43.478 0.00 0.00 46.88 4.17
1901 2264 1.683011 GGCACCACACCAATCAGCTAT 60.683 52.381 0.00 0.00 0.00 2.97
1953 2316 2.196749 CAAGCTACTATGAGCCACACG 58.803 52.381 0.00 0.00 43.97 4.49
1967 2330 1.521906 ACACGCGCACCACACTAAA 60.522 52.632 5.73 0.00 0.00 1.85
2005 2368 2.262423 GCCGGAATTTCAGAGGCTAT 57.738 50.000 5.05 0.00 44.06 2.97
2006 2369 1.876156 GCCGGAATTTCAGAGGCTATG 59.124 52.381 5.05 1.88 44.06 2.23
2011 2374 5.511373 CCGGAATTTCAGAGGCTATGACATA 60.511 44.000 12.07 0.75 0.00 2.29
2268 2730 2.972348 TCCGGCTAGGGAAACTGATAT 58.028 47.619 0.00 0.00 41.52 1.63
2286 2748 6.554982 ACTGATATGAGCAGGTTAGGTATTGA 59.445 38.462 0.00 0.00 37.69 2.57
2287 2749 7.071196 ACTGATATGAGCAGGTTAGGTATTGAA 59.929 37.037 0.00 0.00 37.69 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
577 578 2.159254 TCAAAAACTTGTGAGCAGTGGC 60.159 45.455 0.00 0.0 41.61 5.01
578 579 3.781079 TCAAAAACTTGTGAGCAGTGG 57.219 42.857 0.00 0.0 0.00 4.00
579 580 5.401550 TCTTTCAAAAACTTGTGAGCAGTG 58.598 37.500 0.00 0.0 0.00 3.66
580 581 5.643379 TCTTTCAAAAACTTGTGAGCAGT 57.357 34.783 0.00 0.0 0.00 4.40
581 582 6.095377 AGTTCTTTCAAAAACTTGTGAGCAG 58.905 36.000 0.00 0.0 31.81 4.24
582 583 6.024552 AGTTCTTTCAAAAACTTGTGAGCA 57.975 33.333 0.00 0.0 31.81 4.26
583 584 8.131731 AGATAGTTCTTTCAAAAACTTGTGAGC 58.868 33.333 3.90 0.0 37.02 4.26
596 597 9.998106 GGCAACCTAATATAGATAGTTCTTTCA 57.002 33.333 0.00 0.0 33.17 2.69
597 598 9.998106 TGGCAACCTAATATAGATAGTTCTTTC 57.002 33.333 0.00 0.0 33.17 2.62
642 643 3.530265 AAATACCAGACGGTTATCGCA 57.470 42.857 0.00 0.0 46.31 5.10
653 654 6.238953 GCGTCTCTCTTACCATAAATACCAGA 60.239 42.308 0.00 0.0 0.00 3.86
668 669 2.224281 TGAACCAACATGCGTCTCTCTT 60.224 45.455 0.00 0.0 0.00 2.85
669 670 1.344438 TGAACCAACATGCGTCTCTCT 59.656 47.619 0.00 0.0 0.00 3.10
695 696 9.517868 AAATCTGATTCACTTCTTGAGATTTCT 57.482 29.630 2.92 0.0 33.34 2.52
815 816 8.865590 AGCGTCAACATTTAGTTTAACAAAAT 57.134 26.923 0.00 0.0 38.74 1.82
816 817 8.690680 AAGCGTCAACATTTAGTTTAACAAAA 57.309 26.923 0.00 0.0 38.74 2.44
853 855 1.972660 GCCGTGCCCCTGAGTAGATT 61.973 60.000 0.00 0.0 0.00 2.40
878 880 2.289882 CCTTTGTCATCTCTGAGCACCA 60.290 50.000 0.00 0.0 30.18 4.17
908 910 0.171903 CTTCCAATTTCCGCCAGCAG 59.828 55.000 0.00 0.0 0.00 4.24
967 969 7.286775 TGCAAGAATTAAACCAAACCTAAGAGT 59.713 33.333 0.00 0.0 0.00 3.24
1086 1088 0.753262 AATCCTCGAATACTGCCGCT 59.247 50.000 0.00 0.0 0.00 5.52
1110 1112 2.734809 CGGAAAATCGCATGCCATGAAA 60.735 45.455 13.15 0.0 0.00 2.69
1319 1321 0.822164 AGCTAATAACACGGAGGCGT 59.178 50.000 0.00 0.0 0.00 5.68
1320 1322 1.593006 CAAGCTAATAACACGGAGGCG 59.407 52.381 0.00 0.0 0.00 5.52
1321 1323 2.351726 CACAAGCTAATAACACGGAGGC 59.648 50.000 0.00 0.0 0.00 4.70
1322 1324 2.936498 CCACAAGCTAATAACACGGAGG 59.064 50.000 0.00 0.0 0.00 4.30
1323 1325 2.936498 CCCACAAGCTAATAACACGGAG 59.064 50.000 0.00 0.0 0.00 4.63
1324 1326 2.303600 ACCCACAAGCTAATAACACGGA 59.696 45.455 0.00 0.0 0.00 4.69
1325 1327 2.706890 ACCCACAAGCTAATAACACGG 58.293 47.619 0.00 0.0 0.00 4.94
1326 1328 4.759516 AAACCCACAAGCTAATAACACG 57.240 40.909 0.00 0.0 0.00 4.49
1327 1329 8.301002 TGATAAAAACCCACAAGCTAATAACAC 58.699 33.333 0.00 0.0 0.00 3.32
1328 1330 8.410673 TGATAAAAACCCACAAGCTAATAACA 57.589 30.769 0.00 0.0 0.00 2.41
1329 1331 8.520351 ACTGATAAAAACCCACAAGCTAATAAC 58.480 33.333 0.00 0.0 0.00 1.89
1330 1332 8.644374 ACTGATAAAAACCCACAAGCTAATAA 57.356 30.769 0.00 0.0 0.00 1.40
1331 1333 8.644374 AACTGATAAAAACCCACAAGCTAATA 57.356 30.769 0.00 0.0 0.00 0.98
1332 1334 7.539034 AACTGATAAAAACCCACAAGCTAAT 57.461 32.000 0.00 0.0 0.00 1.73
1333 1335 6.969993 AACTGATAAAAACCCACAAGCTAA 57.030 33.333 0.00 0.0 0.00 3.09
1334 1336 6.969993 AAACTGATAAAAACCCACAAGCTA 57.030 33.333 0.00 0.0 0.00 3.32
1335 1337 5.869649 AAACTGATAAAAACCCACAAGCT 57.130 34.783 0.00 0.0 0.00 3.74
1336 1338 5.815222 ACAAAACTGATAAAAACCCACAAGC 59.185 36.000 0.00 0.0 0.00 4.01
1337 1339 7.038659 TGACAAAACTGATAAAAACCCACAAG 58.961 34.615 0.00 0.0 0.00 3.16
1338 1340 6.936279 TGACAAAACTGATAAAAACCCACAA 58.064 32.000 0.00 0.0 0.00 3.33
1339 1341 6.531503 TGACAAAACTGATAAAAACCCACA 57.468 33.333 0.00 0.0 0.00 4.17
1340 1342 6.362283 CGATGACAAAACTGATAAAAACCCAC 59.638 38.462 0.00 0.0 0.00 4.61
1341 1343 6.263392 TCGATGACAAAACTGATAAAAACCCA 59.737 34.615 0.00 0.0 0.00 4.51
1342 1344 6.581166 GTCGATGACAAAACTGATAAAAACCC 59.419 38.462 0.00 0.0 32.09 4.11
1343 1345 7.323656 CAGTCGATGACAAAACTGATAAAAACC 59.676 37.037 8.71 0.0 41.26 3.27
1344 1346 7.855904 ACAGTCGATGACAAAACTGATAAAAAC 59.144 33.333 17.28 0.0 41.26 2.43
1360 1362 5.727434 TGAGTAGTGTAGTACAGTCGATGA 58.273 41.667 13.96 0.0 33.15 2.92
1367 1369 6.804770 ACAGAACTGAGTAGTGTAGTACAG 57.195 41.667 2.39 0.0 37.19 2.74
1460 1463 1.468520 CCTTTGACATGGCGGTAACAG 59.531 52.381 0.00 0.0 0.00 3.16
1483 1486 7.921786 TTTTTGTCATCTACCTTCGATCAAT 57.078 32.000 0.00 0.0 0.00 2.57
1488 1491 6.110707 GGGTATTTTTGTCATCTACCTTCGA 58.889 40.000 0.00 0.0 33.78 3.71
1503 1506 1.684982 ACGGGGTAGGGGGTATTTTT 58.315 50.000 0.00 0.0 0.00 1.94
1514 1517 1.206371 ACCTTCGATCAAACGGGGTAG 59.794 52.381 0.00 0.0 37.72 3.18
1517 1520 1.479323 TCTACCTTCGATCAAACGGGG 59.521 52.381 0.00 0.0 34.75 5.73
1526 1529 1.174783 AGCACACGTCTACCTTCGAT 58.825 50.000 0.00 0.0 0.00 3.59
1527 1530 1.812235 TAGCACACGTCTACCTTCGA 58.188 50.000 0.00 0.0 0.00 3.71
1528 1531 2.516923 CTTAGCACACGTCTACCTTCG 58.483 52.381 0.00 0.0 0.00 3.79
1529 1532 2.416972 CCCTTAGCACACGTCTACCTTC 60.417 54.545 0.00 0.0 0.00 3.46
1532 1535 0.175073 CCCCTTAGCACACGTCTACC 59.825 60.000 0.00 0.0 0.00 3.18
1533 1536 1.180029 TCCCCTTAGCACACGTCTAC 58.820 55.000 0.00 0.0 0.00 2.59
1535 1538 0.608640 CTTCCCCTTAGCACACGTCT 59.391 55.000 0.00 0.0 0.00 4.18
1536 1539 0.320697 ACTTCCCCTTAGCACACGTC 59.679 55.000 0.00 0.0 0.00 4.34
1537 1540 0.763035 AACTTCCCCTTAGCACACGT 59.237 50.000 0.00 0.0 0.00 4.49
1538 1541 1.892209 AAACTTCCCCTTAGCACACG 58.108 50.000 0.00 0.0 0.00 4.49
1539 1542 3.219281 TCAAAACTTCCCCTTAGCACAC 58.781 45.455 0.00 0.0 0.00 3.82
1542 1668 4.112634 ACATCAAAACTTCCCCTTAGCA 57.887 40.909 0.00 0.0 0.00 3.49
1638 1766 3.873952 GAGAAATGGAGTAGCGAGCAAAT 59.126 43.478 0.00 0.0 0.00 2.32
1639 1767 3.262420 GAGAAATGGAGTAGCGAGCAAA 58.738 45.455 0.00 0.0 0.00 3.68
1757 2092 4.511527 TGGTGCATTTGTGTTGTTTTCAT 58.488 34.783 0.00 0.0 0.00 2.57
1777 2112 5.748152 CACATGTGAAGTTTGTAAACCTTGG 59.252 40.000 21.64 0.0 39.71 3.61
1811 2146 8.625651 CAGGATGGATACGGATACTAGAATTAG 58.374 40.741 0.00 0.0 42.51 1.73
1814 2150 6.603997 GTCAGGATGGATACGGATACTAGAAT 59.396 42.308 0.00 0.0 42.51 2.40
1856 2216 8.276325 CCTTATTGATACTCTCGTACAATTTGC 58.724 37.037 0.00 0.0 33.51 3.68
1868 2228 4.384208 GGTGTGGTGCCTTATTGATACTCT 60.384 45.833 0.00 0.0 0.00 3.24
1883 2246 4.260985 TGTAATAGCTGATTGGTGTGGTG 58.739 43.478 0.00 0.0 0.00 4.17
1884 2247 4.568072 TGTAATAGCTGATTGGTGTGGT 57.432 40.909 0.00 0.0 0.00 4.16
1885 2248 5.895636 TTTGTAATAGCTGATTGGTGTGG 57.104 39.130 0.00 0.0 0.00 4.17
1886 2249 7.765307 AGAATTTGTAATAGCTGATTGGTGTG 58.235 34.615 0.00 0.0 0.00 3.82
1887 2250 7.944729 AGAATTTGTAATAGCTGATTGGTGT 57.055 32.000 0.00 0.0 0.00 4.16
1953 2316 2.914838 GCTAATTTTTAGTGTGGTGCGC 59.085 45.455 0.00 0.0 0.00 6.09
1967 2330 3.555966 GGCAGGGTGAGTATGCTAATTT 58.444 45.455 0.00 0.0 39.88 1.82
2005 2368 1.613317 CGCCACCTCCCAGTATGTCA 61.613 60.000 0.00 0.0 0.00 3.58
2006 2369 1.144057 CGCCACCTCCCAGTATGTC 59.856 63.158 0.00 0.0 0.00 3.06
2203 2664 3.270027 CTGATCCTCAATTGTAACCGCA 58.730 45.455 5.13 0.0 0.00 5.69
2210 2671 1.760192 GCCTGCTGATCCTCAATTGT 58.240 50.000 5.13 0.0 0.00 2.71


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

AutoCloner maintained by Alex Coulton.