Multiple sequence alignment - TraesCS3D01G097900

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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 TraesCS3D01G097900 chr3D 100.000 3090 0 0 1 3090 49779118 49782207 0.000000e+00 5707.0
1 TraesCS3D01G097900 chr3D 97.527 647 16 0 1 647 329692027 329692673 0.000000e+00 1107.0
2 TraesCS3D01G097900 chr3B 87.379 1347 84 54 661 1944 79271931 79273254 0.000000e+00 1467.0
3 TraesCS3D01G097900 chr3B 90.607 511 38 5 2557 3062 79273970 79274475 0.000000e+00 669.0
4 TraesCS3D01G097900 chr3B 86.111 576 38 22 1988 2537 79273426 79273985 1.600000e-162 582.0
5 TraesCS3D01G097900 chr3B 82.822 163 24 4 2913 3071 79276233 79276395 3.210000e-30 143.0
6 TraesCS3D01G097900 chr3B 100.000 29 0 0 701 729 494765294 494765266 2.000000e-03 54.7
7 TraesCS3D01G097900 chr3A 88.889 1053 66 24 922 1944 63130831 63131862 0.000000e+00 1249.0
8 TraesCS3D01G097900 chr3A 87.726 497 44 11 1959 2443 63131927 63132418 5.780000e-157 564.0
9 TraesCS3D01G097900 chr3A 90.024 421 27 9 1964 2377 63168219 63168631 5.870000e-147 531.0
10 TraesCS3D01G097900 chr3A 81.481 567 49 29 2557 3090 63168807 63169350 6.160000e-112 414.0
11 TraesCS3D01G097900 chr3A 78.747 367 43 21 2725 3080 63134792 63135134 2.410000e-51 213.0
12 TraesCS3D01G097900 chr3A 94.203 138 8 0 784 921 63130417 63130554 8.680000e-51 211.0
13 TraesCS3D01G097900 chr3A 96.296 108 3 1 2431 2537 63168715 63168822 3.170000e-40 176.0
14 TraesCS3D01G097900 chr2D 98.006 652 13 0 1 652 125442038 125441387 0.000000e+00 1133.0
15 TraesCS3D01G097900 chr2D 97.699 652 14 1 1 651 136461049 136461700 0.000000e+00 1120.0
16 TraesCS3D01G097900 chr2D 97.385 650 14 1 1 647 110998361 110999010 0.000000e+00 1103.0
17 TraesCS3D01G097900 chr6D 97.836 647 14 0 1 647 473242849 473243495 0.000000e+00 1118.0
18 TraesCS3D01G097900 chr6D 97.389 651 17 0 1 651 210876896 210876246 0.000000e+00 1109.0
19 TraesCS3D01G097900 chr1D 97.836 647 14 0 1 647 194924359 194925005 0.000000e+00 1118.0
20 TraesCS3D01G097900 chr1D 87.097 155 20 0 1215 1369 109578831 109578677 3.170000e-40 176.0
21 TraesCS3D01G097900 chr5D 97.682 647 15 0 1 647 99334802 99334156 0.000000e+00 1112.0
22 TraesCS3D01G097900 chr5D 91.011 89 8 0 1215 1303 436205627 436205539 1.500000e-23 121.0
23 TraesCS3D01G097900 chr7D 97.527 647 16 0 1 647 245312376 245313022 0.000000e+00 1107.0
24 TraesCS3D01G097900 chr2B 90.260 154 15 0 1098 1251 627723984 627724137 5.220000e-48 202.0
25 TraesCS3D01G097900 chr2B 90.000 70 4 1 661 730 642781379 642781445 1.530000e-13 87.9
26 TraesCS3D01G097900 chr1A 82.653 196 30 3 1176 1369 113252069 113251876 1.470000e-38 171.0


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 TraesCS3D01G097900 chr3D 49779118 49782207 3089 False 5707.000000 5707 100.00000 1 3090 1 chr3D.!!$F1 3089
1 TraesCS3D01G097900 chr3D 329692027 329692673 646 False 1107.000000 1107 97.52700 1 647 1 chr3D.!!$F2 646
2 TraesCS3D01G097900 chr3B 79271931 79276395 4464 False 715.250000 1467 86.72975 661 3071 4 chr3B.!!$F1 2410
3 TraesCS3D01G097900 chr3A 63130417 63135134 4717 False 559.250000 1249 87.39125 784 3080 4 chr3A.!!$F1 2296
4 TraesCS3D01G097900 chr3A 63168219 63169350 1131 False 373.666667 531 89.26700 1964 3090 3 chr3A.!!$F2 1126
5 TraesCS3D01G097900 chr2D 125441387 125442038 651 True 1133.000000 1133 98.00600 1 652 1 chr2D.!!$R1 651
6 TraesCS3D01G097900 chr2D 136461049 136461700 651 False 1120.000000 1120 97.69900 1 651 1 chr2D.!!$F2 650
7 TraesCS3D01G097900 chr2D 110998361 110999010 649 False 1103.000000 1103 97.38500 1 647 1 chr2D.!!$F1 646
8 TraesCS3D01G097900 chr6D 473242849 473243495 646 False 1118.000000 1118 97.83600 1 647 1 chr6D.!!$F1 646
9 TraesCS3D01G097900 chr6D 210876246 210876896 650 True 1109.000000 1109 97.38900 1 651 1 chr6D.!!$R1 650
10 TraesCS3D01G097900 chr1D 194924359 194925005 646 False 1118.000000 1118 97.83600 1 647 1 chr1D.!!$F1 646
11 TraesCS3D01G097900 chr5D 99334156 99334802 646 True 1112.000000 1112 97.68200 1 647 1 chr5D.!!$R1 646
12 TraesCS3D01G097900 chr7D 245312376 245313022 646 False 1107.000000 1107 97.52700 1 647 1 chr7D.!!$F1 646

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
697 701 0.179004 TGGTCGGTGGATGTTGCTTT 60.179 50.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2527 5081 0.238817 TTTGCGGGTAATGTGCGTTC 59.761 50.0 0.0 0.0 0.0 3.95 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
257 258 4.709886 TCGAAGAGATGTCTCCAATGGTAA 59.290 41.667 6.41 0.00 43.88 2.85
652 656 8.251721 ACCATAATGACTACTCTAACACTGTTC 58.748 37.037 0.00 0.00 0.00 3.18
653 657 8.251026 CCATAATGACTACTCTAACACTGTTCA 58.749 37.037 0.00 0.00 0.00 3.18
654 658 9.077674 CATAATGACTACTCTAACACTGTTCAC 57.922 37.037 0.00 0.00 0.00 3.18
655 659 5.449107 TGACTACTCTAACACTGTTCACC 57.551 43.478 0.00 0.00 0.00 4.02
656 660 4.280174 TGACTACTCTAACACTGTTCACCC 59.720 45.833 0.00 0.00 0.00 4.61
657 661 3.577415 ACTACTCTAACACTGTTCACCCC 59.423 47.826 0.00 0.00 0.00 4.95
658 662 2.404559 ACTCTAACACTGTTCACCCCA 58.595 47.619 0.00 0.00 0.00 4.96
659 663 2.368875 ACTCTAACACTGTTCACCCCAG 59.631 50.000 0.00 0.00 36.01 4.45
685 689 0.390735 GCCGTTATCTTGTGGTCGGT 60.391 55.000 0.00 0.00 40.05 4.69
687 691 1.355971 CGTTATCTTGTGGTCGGTGG 58.644 55.000 0.00 0.00 0.00 4.61
697 701 0.179004 TGGTCGGTGGATGTTGCTTT 60.179 50.000 0.00 0.00 0.00 3.51
698 702 1.072489 TGGTCGGTGGATGTTGCTTTA 59.928 47.619 0.00 0.00 0.00 1.85
699 703 1.737793 GGTCGGTGGATGTTGCTTTAG 59.262 52.381 0.00 0.00 0.00 1.85
700 704 2.423577 GTCGGTGGATGTTGCTTTAGT 58.576 47.619 0.00 0.00 0.00 2.24
720 724 9.760077 CTTTAGTATAATCTAAAGCGGAGGAAA 57.240 33.333 11.47 0.00 44.99 3.13
729 733 1.617322 AGCGGAGGAAACCCTTTTTC 58.383 50.000 0.00 0.00 33.25 2.29
730 734 1.133606 AGCGGAGGAAACCCTTTTTCA 60.134 47.619 0.00 0.00 33.25 2.69
747 751 9.936759 CCCTTTTTCAGCTATTTTATTGGTTAA 57.063 29.630 0.00 0.00 0.00 2.01
801 807 3.982576 AGTTTTTGCAACGGGTAGAAG 57.017 42.857 0.00 0.00 0.00 2.85
807 813 5.616488 TTTGCAACGGGTAGAAGATAAAC 57.384 39.130 0.00 0.00 0.00 2.01
808 814 4.274602 TGCAACGGGTAGAAGATAAACA 57.725 40.909 0.00 0.00 0.00 2.83
822 828 6.319911 AGAAGATAAACAAATCCTGCTTAGCC 59.680 38.462 0.29 0.00 0.00 3.93
824 830 1.463674 AACAAATCCTGCTTAGCCCG 58.536 50.000 0.29 0.00 0.00 6.13
860 866 2.082231 CGAGGTCAAAGGTCGTCTCTA 58.918 52.381 0.00 0.00 0.00 2.43
972 1254 7.227314 CAGCCAGCACACTTCTCATTATTAATA 59.773 37.037 0.00 0.00 0.00 0.98
978 1270 7.282224 GCACACTTCTCATTATTAATACACCCA 59.718 37.037 0.00 0.00 0.00 4.51
979 1271 8.612619 CACACTTCTCATTATTAATACACCCAC 58.387 37.037 0.00 0.00 0.00 4.61
980 1272 7.494625 ACACTTCTCATTATTAATACACCCACG 59.505 37.037 0.00 0.00 0.00 4.94
1021 1313 1.737793 CATAAAACCCCACACTCGCTC 59.262 52.381 0.00 0.00 0.00 5.03
1040 1332 1.406898 TCCGCATCTCAGTGATCACTC 59.593 52.381 25.58 12.18 40.20 3.51
1057 1349 2.445654 CCCTCCTCCTCCTCTGCC 60.446 72.222 0.00 0.00 0.00 4.85
1070 1386 1.743321 CTCTGCCCGATCCCTCTGTC 61.743 65.000 0.00 0.00 0.00 3.51
1073 1389 1.456705 GCCCGATCCCTCTGTCTCT 60.457 63.158 0.00 0.00 0.00 3.10
1082 1398 1.410365 CCCTCTGTCTCTCCGTACCAT 60.410 57.143 0.00 0.00 0.00 3.55
1094 1410 2.025155 CCGTACCATAGCAGAGACACT 58.975 52.381 0.00 0.00 0.00 3.55
1096 1412 3.119101 CCGTACCATAGCAGAGACACTTT 60.119 47.826 0.00 0.00 0.00 2.66
1248 1574 2.401766 CGGGTCTACTACGGCGTGT 61.402 63.158 24.86 19.93 0.00 4.49
1316 1642 0.179073 CCAAGAACGCCATCTCCGAT 60.179 55.000 0.00 0.00 0.00 4.18
1361 1687 4.261781 CCGTCCTACTACGCCGCC 62.262 72.222 0.00 0.00 41.51 6.13
1385 1711 3.717294 ACCGCCTCCGCCAAGAAT 61.717 61.111 0.00 0.00 0.00 2.40
1428 1754 2.271173 CCGGGGGCTACAAGTTCC 59.729 66.667 0.00 0.00 0.00 3.62
1436 1762 1.290955 CTACAAGTTCCGGCCGTCA 59.709 57.895 26.12 7.26 0.00 4.35
1437 1763 0.736325 CTACAAGTTCCGGCCGTCAG 60.736 60.000 26.12 9.25 0.00 3.51
1469 1795 3.838271 ATCCTCATGGCGACGCGT 61.838 61.111 13.85 13.85 0.00 6.01
1526 1855 2.754658 TCCTTCTCCTCCGCGTCC 60.755 66.667 4.92 0.00 0.00 4.79
1527 1856 3.068691 CCTTCTCCTCCGCGTCCA 61.069 66.667 4.92 0.00 0.00 4.02
1528 1857 2.182030 CTTCTCCTCCGCGTCCAC 59.818 66.667 4.92 0.00 0.00 4.02
1529 1858 3.358076 CTTCTCCTCCGCGTCCACC 62.358 68.421 4.92 0.00 0.00 4.61
1530 1859 3.881019 TTCTCCTCCGCGTCCACCT 62.881 63.158 4.92 0.00 0.00 4.00
1531 1860 3.827898 CTCCTCCGCGTCCACCTC 61.828 72.222 4.92 0.00 0.00 3.85
1534 1863 3.827898 CTCCGCGTCCACCTCCTC 61.828 72.222 4.92 0.00 0.00 3.71
1537 1866 3.827898 CGCGTCCACCTCCTCCTC 61.828 72.222 0.00 0.00 0.00 3.71
1538 1867 3.462678 GCGTCCACCTCCTCCTCC 61.463 72.222 0.00 0.00 0.00 4.30
1545 1874 1.619975 ACCTCCTCCTCCTCCTCGA 60.620 63.158 0.00 0.00 0.00 4.04
1559 1900 1.740664 CTCGACCTCCTCGACGTCA 60.741 63.158 17.16 1.87 46.75 4.35
1619 1990 1.423056 GTCGTCGTCGTTCTCGGAT 59.577 57.895 1.33 0.00 38.33 4.18
1764 2135 1.295423 GCGGTGCAGAGGGTCTAAA 59.705 57.895 0.00 0.00 0.00 1.85
1779 2155 1.136690 CTAAACGCACTGAACTCGCA 58.863 50.000 0.00 0.00 0.00 5.10
1866 2247 6.913170 TGGTTTTGATTGAGCTTCTGTAATC 58.087 36.000 0.00 0.00 0.00 1.75
1869 2250 7.336931 GGTTTTGATTGAGCTTCTGTAATCCTA 59.663 37.037 0.00 0.00 0.00 2.94
1940 2322 6.210185 TGTTCAGAACTTCAGATCAGATCTCA 59.790 38.462 10.25 0.00 37.58 3.27
1944 2326 7.042950 CAGAACTTCAGATCAGATCTCACATT 58.957 38.462 10.25 3.42 37.58 2.71
1947 2329 6.041511 ACTTCAGATCAGATCTCACATTTCG 58.958 40.000 10.25 0.00 37.58 3.46
1948 2330 4.366586 TCAGATCAGATCTCACATTTCGC 58.633 43.478 10.25 0.00 37.58 4.70
1950 2332 3.387374 AGATCAGATCTCACATTTCGCCT 59.613 43.478 7.15 0.00 33.42 5.52
1951 2333 3.170791 TCAGATCTCACATTTCGCCTC 57.829 47.619 0.00 0.00 0.00 4.70
1952 2334 2.497273 TCAGATCTCACATTTCGCCTCA 59.503 45.455 0.00 0.00 0.00 3.86
1953 2335 3.133542 TCAGATCTCACATTTCGCCTCAT 59.866 43.478 0.00 0.00 0.00 2.90
1954 2336 3.875727 CAGATCTCACATTTCGCCTCATT 59.124 43.478 0.00 0.00 0.00 2.57
1955 2337 4.334759 CAGATCTCACATTTCGCCTCATTT 59.665 41.667 0.00 0.00 0.00 2.32
2021 2531 6.940298 CCTGGAAAGTTGATTTGTTCCTACTA 59.060 38.462 3.20 0.00 40.24 1.82
2034 2544 8.597662 TTTGTTCCTACTATACTTGTGTGTTC 57.402 34.615 0.00 0.00 0.00 3.18
2113 2623 7.095439 GGAATAAAGAATGTCTATCAGCCGAAG 60.095 40.741 0.00 0.00 0.00 3.79
2171 2681 5.966742 AATTGTGCTTTTCCTCTCTAACC 57.033 39.130 0.00 0.00 0.00 2.85
2176 2686 5.046878 TGTGCTTTTCCTCTCTAACCGAATA 60.047 40.000 0.00 0.00 0.00 1.75
2222 2732 3.629398 ACTGTGTGAGCTGAAAAGGAAAG 59.371 43.478 0.00 0.00 0.00 2.62
2226 2736 3.312421 TGTGAGCTGAAAAGGAAAGAACG 59.688 43.478 0.00 0.00 0.00 3.95
2230 2740 2.812011 GCTGAAAAGGAAAGAACGCCTA 59.188 45.455 0.00 0.00 33.20 3.93
2231 2741 3.252458 GCTGAAAAGGAAAGAACGCCTAA 59.748 43.478 0.00 0.00 33.20 2.69
2232 2742 4.261447 GCTGAAAAGGAAAGAACGCCTAAA 60.261 41.667 0.00 0.00 33.20 1.85
2233 2743 5.735070 GCTGAAAAGGAAAGAACGCCTAAAA 60.735 40.000 0.00 0.00 33.20 1.52
2234 2744 6.210287 TGAAAAGGAAAGAACGCCTAAAAA 57.790 33.333 0.00 0.00 33.20 1.94
2235 2745 6.811954 TGAAAAGGAAAGAACGCCTAAAAAT 58.188 32.000 0.00 0.00 33.20 1.82
2317 2842 1.636003 AGTCCCCTGTCATTTTCCCTC 59.364 52.381 0.00 0.00 0.00 4.30
2387 2924 1.004560 TCTCTCAAGCGCACAAGGG 60.005 57.895 11.47 2.91 0.00 3.95
2459 5000 1.343142 ACTGTGACAAGTGCGATGGTA 59.657 47.619 0.00 0.00 0.00 3.25
2465 5006 1.078709 CAAGTGCGATGGTACTGTGG 58.921 55.000 0.00 0.00 39.20 4.17
2513 5067 2.052690 GCTGAGCCCCGAGTAGTGA 61.053 63.158 0.00 0.00 0.00 3.41
2515 5069 1.379977 TGAGCCCCGAGTAGTGAGG 60.380 63.158 0.00 0.00 0.00 3.86
2516 5070 1.380112 GAGCCCCGAGTAGTGAGGT 60.380 63.158 0.00 0.00 0.00 3.85
2517 5071 1.380112 AGCCCCGAGTAGTGAGGTC 60.380 63.158 0.00 0.00 0.00 3.85
2518 5072 2.772691 GCCCCGAGTAGTGAGGTCG 61.773 68.421 0.00 0.00 0.00 4.79
2519 5073 1.378250 CCCCGAGTAGTGAGGTCGT 60.378 63.158 0.00 0.00 31.65 4.34
2521 5075 0.675837 CCCGAGTAGTGAGGTCGTGA 60.676 60.000 0.00 0.00 31.65 4.35
2523 5077 0.727970 CGAGTAGTGAGGTCGTGAGG 59.272 60.000 0.00 0.00 0.00 3.86
2524 5078 1.675116 CGAGTAGTGAGGTCGTGAGGA 60.675 57.143 0.00 0.00 0.00 3.71
2525 5079 2.011222 GAGTAGTGAGGTCGTGAGGAG 58.989 57.143 0.00 0.00 0.00 3.69
2526 5080 1.351683 AGTAGTGAGGTCGTGAGGAGT 59.648 52.381 0.00 0.00 0.00 3.85
2527 5081 1.469308 GTAGTGAGGTCGTGAGGAGTG 59.531 57.143 0.00 0.00 0.00 3.51
2528 5082 0.110678 AGTGAGGTCGTGAGGAGTGA 59.889 55.000 0.00 0.00 0.00 3.41
2529 5083 0.959553 GTGAGGTCGTGAGGAGTGAA 59.040 55.000 0.00 0.00 0.00 3.18
2530 5084 0.959553 TGAGGTCGTGAGGAGTGAAC 59.040 55.000 0.00 0.00 0.00 3.18
2531 5085 0.109689 GAGGTCGTGAGGAGTGAACG 60.110 60.000 0.00 0.00 38.64 3.95
2532 5086 1.733399 GGTCGTGAGGAGTGAACGC 60.733 63.158 0.00 0.00 37.24 4.84
2533 5087 1.007734 GTCGTGAGGAGTGAACGCA 60.008 57.895 0.00 0.00 37.24 5.24
2534 5088 1.007734 TCGTGAGGAGTGAACGCAC 60.008 57.895 0.00 0.00 45.49 5.34
2543 5097 1.133869 GTGAACGCACATTACCCGC 59.866 57.895 0.00 0.00 44.51 6.13
2544 5098 1.301795 TGAACGCACATTACCCGCA 60.302 52.632 0.00 0.00 0.00 5.69
2545 5099 0.885150 TGAACGCACATTACCCGCAA 60.885 50.000 0.00 0.00 0.00 4.85
2546 5100 0.238817 GAACGCACATTACCCGCAAA 59.761 50.000 0.00 0.00 0.00 3.68
2547 5101 0.669077 AACGCACATTACCCGCAAAA 59.331 45.000 0.00 0.00 0.00 2.44
2548 5102 0.669077 ACGCACATTACCCGCAAAAA 59.331 45.000 0.00 0.00 0.00 1.94
2639 5197 7.593825 AGTAGAAACCAAAATGTTCACTATGC 58.406 34.615 0.00 0.00 0.00 3.14
2691 5258 0.182061 ACAGTGGCATATGCTGAGGG 59.818 55.000 26.12 14.63 41.70 4.30
2762 5446 2.579878 TCCATGAGGAGACACGGAC 58.420 57.895 0.00 0.00 39.61 4.79
2828 5524 3.817647 GCTCTTTCTGAACATCAACCAGT 59.182 43.478 0.00 0.00 0.00 4.00
2856 5552 7.280876 CACACTCACCAAATGCAAGTATAGTAT 59.719 37.037 0.00 0.00 0.00 2.12
2858 5554 9.325198 CACTCACCAAATGCAAGTATAGTATTA 57.675 33.333 0.00 0.00 0.00 0.98
2860 5556 8.378172 TCACCAAATGCAAGTATAGTATTAGC 57.622 34.615 0.00 0.00 0.00 3.09
2861 5557 7.990314 TCACCAAATGCAAGTATAGTATTAGCA 59.010 33.333 0.00 0.00 34.78 3.49
2911 5613 2.019948 CCGGACAGGTTACCTTAAGC 57.980 55.000 0.00 0.00 36.47 3.09
2992 7598 0.745128 TGTGCAACGAACGGGTTTCT 60.745 50.000 0.00 0.00 42.39 2.52
2993 7599 0.041576 GTGCAACGAACGGGTTTCTC 60.042 55.000 0.00 0.00 31.20 2.87
2994 7600 1.203313 GCAACGAACGGGTTTCTCG 59.797 57.895 0.00 0.00 38.53 4.04
2997 7603 1.219522 AACGAACGGGTTTCTCGCTG 61.220 55.000 0.00 0.00 36.03 5.18
3034 7653 1.227468 GAAGGAATCCCCGTACGCC 60.227 63.158 10.49 4.35 40.87 5.68
3048 7667 1.925185 GTACGCCTCAGATCCGTTTTC 59.075 52.381 0.00 0.00 36.51 2.29
3083 7702 0.947244 CTTCAGCAGCGACTTGGTTT 59.053 50.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
257 258 1.686325 ATCTCGCCGCCCACAACTAT 61.686 55.000 0.00 0.00 0.00 2.12
405 406 3.515286 CATCGCCAAGGCTGCCAG 61.515 66.667 22.65 12.76 39.32 4.85
508 512 7.914537 AAGAAACAGTTTTATTCAGCTTTCG 57.085 32.000 0.00 0.00 0.00 3.46
668 672 1.067425 TCCACCGACCACAAGATAACG 60.067 52.381 0.00 0.00 0.00 3.18
697 701 7.256083 GGGTTTCCTCCGCTTTAGATTATACTA 60.256 40.741 0.00 0.00 0.00 1.82
698 702 6.464039 GGGTTTCCTCCGCTTTAGATTATACT 60.464 42.308 0.00 0.00 0.00 2.12
699 703 5.699915 GGGTTTCCTCCGCTTTAGATTATAC 59.300 44.000 0.00 0.00 0.00 1.47
700 704 5.605488 AGGGTTTCCTCCGCTTTAGATTATA 59.395 40.000 0.00 0.00 39.80 0.98
716 720 8.935844 CAATAAAATAGCTGAAAAAGGGTTTCC 58.064 33.333 0.00 0.00 0.00 3.13
717 721 8.935844 CCAATAAAATAGCTGAAAAAGGGTTTC 58.064 33.333 0.00 0.00 0.00 2.78
720 724 7.553504 ACCAATAAAATAGCTGAAAAAGGGT 57.446 32.000 0.00 0.00 0.00 4.34
801 807 4.261197 CGGGCTAAGCAGGATTTGTTTATC 60.261 45.833 0.00 0.00 32.90 1.75
807 813 0.734889 CACGGGCTAAGCAGGATTTG 59.265 55.000 0.00 0.00 0.00 2.32
808 814 0.394352 CCACGGGCTAAGCAGGATTT 60.394 55.000 0.00 0.00 0.00 2.17
822 828 1.875963 GCACTGTTTGGATCCACGG 59.124 57.895 15.91 11.88 0.00 4.94
824 830 0.798776 CTCGCACTGTTTGGATCCAC 59.201 55.000 15.91 4.42 0.00 4.02
860 866 2.936993 GCTGTCCAAGATTCCACGATGT 60.937 50.000 0.00 0.00 0.00 3.06
972 1254 2.936912 GCAGAGAGAGCGTGGGTGT 61.937 63.158 0.00 0.00 0.00 4.16
978 1270 4.127040 CGGCAGCAGAGAGAGCGT 62.127 66.667 0.00 0.00 37.01 5.07
979 1271 3.819920 TCGGCAGCAGAGAGAGCG 61.820 66.667 0.00 0.00 37.01 5.03
980 1272 2.202730 GTCGGCAGCAGAGAGAGC 60.203 66.667 0.00 0.00 0.00 4.09
1021 1313 1.537776 GGAGTGATCACTGAGATGCGG 60.538 57.143 32.50 0.00 42.66 5.69
1040 1332 2.445654 GGCAGAGGAGGAGGAGGG 60.446 72.222 0.00 0.00 0.00 4.30
1057 1349 1.169661 CGGAGAGACAGAGGGATCGG 61.170 65.000 0.00 0.00 0.00 4.18
1070 1386 2.550606 GTCTCTGCTATGGTACGGAGAG 59.449 54.545 9.69 9.69 46.32 3.20
1073 1389 2.022195 GTGTCTCTGCTATGGTACGGA 58.978 52.381 0.00 0.00 0.00 4.69
1082 1398 4.141846 GGATGGATGAAAGTGTCTCTGCTA 60.142 45.833 0.00 0.00 0.00 3.49
1094 1410 1.750332 GCCATGGACGGATGGATGAAA 60.750 52.381 18.40 0.00 45.24 2.69
1096 1412 1.451504 GCCATGGACGGATGGATGA 59.548 57.895 18.40 0.00 45.24 2.92
1308 1634 2.048784 CATCGCGGCATCGGAGAT 60.049 61.111 6.13 0.00 45.12 2.75
1374 1700 2.813474 CGCGTGATTCTTGGCGGA 60.813 61.111 0.00 0.00 44.50 5.54
1419 1745 1.290955 CTGACGGCCGGAACTTGTA 59.709 57.895 31.76 4.96 0.00 2.41
1436 1762 2.369291 ATGGAGCCCAGGATGCCT 60.369 61.111 0.00 0.00 36.75 4.75
1437 1763 2.114838 GATGGAGCCCAGGATGCC 59.885 66.667 0.00 0.00 36.75 4.40
1526 1855 1.454847 CGAGGAGGAGGAGGAGGTG 60.455 68.421 0.00 0.00 0.00 4.00
1527 1856 1.619975 TCGAGGAGGAGGAGGAGGT 60.620 63.158 0.00 0.00 0.00 3.85
1528 1857 1.152839 GTCGAGGAGGAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
1529 1858 1.152839 GGTCGAGGAGGAGGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
1530 1859 1.619975 AGGTCGAGGAGGAGGAGGA 60.620 63.158 0.00 0.00 0.00 3.71
1531 1860 1.152839 GAGGTCGAGGAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
1532 1861 1.152839 GGAGGTCGAGGAGGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
1533 1862 1.619975 AGGAGGTCGAGGAGGAGGA 60.620 63.158 0.00 0.00 0.00 3.71
1534 1863 1.152839 GAGGAGGTCGAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
1535 1864 4.571243 GAGGAGGTCGAGGAGGAG 57.429 66.667 0.00 0.00 0.00 3.69
1545 1874 0.323542 AAGGATGACGTCGAGGAGGT 60.324 55.000 12.85 0.00 33.19 3.85
1619 1990 2.362503 ATGGCCGTCTCCTCGTCA 60.363 61.111 0.00 0.00 0.00 4.35
1764 2135 2.417516 ACTGCGAGTTCAGTGCGT 59.582 55.556 0.00 0.00 44.88 5.24
1779 2155 2.967076 CGCACGTCCTTGCACACT 60.967 61.111 0.00 0.00 43.15 3.55
1866 2247 7.997773 TTCCATATACACTGCTAGTAGTAGG 57.002 40.000 18.16 5.03 31.82 3.18
1940 2322 3.507233 ACATGTCAAATGAGGCGAAATGT 59.493 39.130 0.00 0.00 0.00 2.71
1944 2326 3.567585 TCAAACATGTCAAATGAGGCGAA 59.432 39.130 0.00 0.00 0.00 4.70
1947 2329 4.510038 ACTCAAACATGTCAAATGAGGC 57.490 40.909 23.42 0.00 41.34 4.70
1948 2330 6.128172 GGTCTACTCAAACATGTCAAATGAGG 60.128 42.308 23.42 13.47 41.34 3.86
1950 2332 5.705441 GGGTCTACTCAAACATGTCAAATGA 59.295 40.000 0.00 1.20 0.00 2.57
1951 2333 5.473162 TGGGTCTACTCAAACATGTCAAATG 59.527 40.000 0.00 0.00 0.00 2.32
1952 2334 5.473504 GTGGGTCTACTCAAACATGTCAAAT 59.526 40.000 0.00 0.00 0.00 2.32
1953 2335 4.819630 GTGGGTCTACTCAAACATGTCAAA 59.180 41.667 0.00 0.00 0.00 2.69
1954 2336 4.102524 AGTGGGTCTACTCAAACATGTCAA 59.897 41.667 0.00 0.00 0.00 3.18
1955 2337 3.646162 AGTGGGTCTACTCAAACATGTCA 59.354 43.478 0.00 0.00 0.00 3.58
2021 2531 3.135994 GTCCCAACGAACACACAAGTAT 58.864 45.455 0.00 0.00 0.00 2.12
2034 2544 1.399440 CTGAGCATTCATGTCCCAACG 59.601 52.381 0.00 0.00 31.68 4.10
2113 2623 6.423905 GGCTGAAAGGGTTGTTTAATCTTTTC 59.576 38.462 0.00 0.00 41.07 2.29
2194 2704 5.009010 CCTTTTCAGCTCACACAGTTGTTAT 59.991 40.000 0.00 0.00 34.93 1.89
2195 2705 4.335315 CCTTTTCAGCTCACACAGTTGTTA 59.665 41.667 0.00 0.00 34.93 2.41
2317 2842 4.362279 CAGAAAACAATTCCTGTGTGTGG 58.638 43.478 0.00 0.00 38.67 4.17
2465 5006 1.670295 TGTATTGCGGTCATGTGCATC 59.330 47.619 10.02 6.07 41.42 3.91
2513 5067 1.957562 CGTTCACTCCTCACGACCT 59.042 57.895 0.00 0.00 35.93 3.85
2515 5069 1.007734 TGCGTTCACTCCTCACGAC 60.008 57.895 0.00 0.00 35.93 4.34
2516 5070 1.007734 GTGCGTTCACTCCTCACGA 60.008 57.895 0.00 0.00 40.03 4.35
2517 5071 0.667487 ATGTGCGTTCACTCCTCACG 60.667 55.000 0.00 0.00 43.49 4.35
2518 5072 1.512926 AATGTGCGTTCACTCCTCAC 58.487 50.000 0.00 0.00 43.49 3.51
2519 5073 2.611971 GGTAATGTGCGTTCACTCCTCA 60.612 50.000 0.00 0.00 43.49 3.86
2521 5075 1.338769 GGGTAATGTGCGTTCACTCCT 60.339 52.381 0.00 0.00 43.49 3.69
2523 5077 0.719465 CGGGTAATGTGCGTTCACTC 59.281 55.000 0.00 0.00 43.49 3.51
2524 5078 1.296056 GCGGGTAATGTGCGTTCACT 61.296 55.000 0.00 0.00 43.49 3.41
2525 5079 1.133869 GCGGGTAATGTGCGTTCAC 59.866 57.895 0.00 0.00 43.40 3.18
2526 5080 0.885150 TTGCGGGTAATGTGCGTTCA 60.885 50.000 0.00 0.00 0.00 3.18
2527 5081 0.238817 TTTGCGGGTAATGTGCGTTC 59.761 50.000 0.00 0.00 0.00 3.95
2528 5082 0.669077 TTTTGCGGGTAATGTGCGTT 59.331 45.000 0.00 0.00 0.00 4.84
2529 5083 0.669077 TTTTTGCGGGTAATGTGCGT 59.331 45.000 0.00 0.00 0.00 5.24
2530 5084 3.481009 TTTTTGCGGGTAATGTGCG 57.519 47.368 0.00 0.00 0.00 5.34
2552 5106 2.034558 CCATGTGCGTTCACTCCTTTTT 59.965 45.455 0.00 0.00 43.49 1.94
2553 5107 1.608590 CCATGTGCGTTCACTCCTTTT 59.391 47.619 0.00 0.00 43.49 2.27
2554 5108 1.238439 CCATGTGCGTTCACTCCTTT 58.762 50.000 0.00 0.00 43.49 3.11
2555 5109 1.237285 GCCATGTGCGTTCACTCCTT 61.237 55.000 0.00 0.00 43.49 3.36
2691 5258 1.078143 CTTACTGCTGGCCCTCACC 60.078 63.158 0.00 0.00 0.00 4.02
2828 5524 3.023119 ACTTGCATTTGGTGAGTGTGAA 58.977 40.909 0.00 0.00 0.00 3.18
2856 5552 3.616560 GCACCAGCTTACAGTACTGCTAA 60.617 47.826 22.90 17.21 37.91 3.09
2858 5554 1.338200 GCACCAGCTTACAGTACTGCT 60.338 52.381 22.90 11.17 37.91 4.24
2860 5556 1.350193 CGCACCAGCTTACAGTACTG 58.650 55.000 21.44 21.44 39.10 2.74
2861 5557 0.246635 CCGCACCAGCTTACAGTACT 59.753 55.000 0.00 0.00 39.10 2.73
2911 5613 4.088421 CGTCTCGGATTCGGGTTG 57.912 61.111 0.00 0.00 38.21 3.77
2929 5631 3.306166 CCGTCAACGAATCATACAAGGTC 59.694 47.826 3.71 0.00 43.02 3.85
2997 7603 4.147322 CATTCACGTGACCGCGGC 62.147 66.667 28.58 19.01 37.70 6.53
3000 7606 0.163788 CTTCACATTCACGTGACCGC 59.836 55.000 19.90 0.00 45.36 5.68
3034 7653 4.099120 CAGTACTCGAAAACGGATCTGAG 58.901 47.826 9.00 0.00 0.00 3.35
3048 7667 1.132453 TGAAGGATGCGACAGTACTCG 59.868 52.381 0.00 0.00 36.70 4.18


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

AutoCloner maintained by Alex Coulton.