Multiple sequence alignment - TraesCS6A01G297500

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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 TraesCS6A01G297500 chr6A 100.000 2625 0 0 1 2625 531051737 531049113 0.000000e+00 4848.0
1 TraesCS6A01G297500 chr6D 89.412 1360 94 25 752 2073 386187078 386185731 0.000000e+00 1668.0
2 TraesCS6A01G297500 chr6D 95.946 296 12 0 2325 2620 386185627 386185332 5.080000e-132 481.0
3 TraesCS6A01G297500 chrUn 94.350 708 35 3 1 704 82547070 82546364 0.000000e+00 1081.0
4 TraesCS6A01G297500 chrUn 91.089 101 8 1 2057 2157 92814979 92814880 4.560000e-28 135.0
5 TraesCS6A01G297500 chr3A 92.525 709 38 9 1 704 32205079 32204381 0.000000e+00 1002.0
6 TraesCS6A01G297500 chr3A 96.591 88 3 0 2070 2157 736118053 736118140 2.110000e-31 147.0
7 TraesCS6A01G297500 chr3A 88.235 119 8 6 2038 2155 639017605 639017718 1.270000e-28 137.0
8 TraesCS6A01G297500 chr7A 91.537 709 49 8 1 704 701358125 701358827 0.000000e+00 966.0
9 TraesCS6A01G297500 chr7A 100.000 29 0 0 2412 2440 269125085 269125113 1.000000e-03 54.7
10 TraesCS6A01G297500 chr1D 91.197 727 35 15 1 705 58485659 58486378 0.000000e+00 961.0
11 TraesCS6A01G297500 chr5A 91.595 702 47 9 1 698 169184093 169184786 0.000000e+00 959.0
12 TraesCS6A01G297500 chr5A 88.288 111 9 3 2070 2179 505136401 505136294 2.120000e-26 130.0
13 TraesCS6A01G297500 chr5B 90.723 733 42 16 1 715 12549808 12549084 0.000000e+00 953.0
14 TraesCS6A01G297500 chr2D 90.698 731 40 17 1 711 536208401 536207679 0.000000e+00 948.0
15 TraesCS6A01G297500 chr3B 90.287 731 43 15 1 710 691342382 691343105 0.000000e+00 931.0
16 TraesCS6A01G297500 chr6B 90.701 699 45 10 1260 1950 576826725 576826039 0.000000e+00 913.0
17 TraesCS6A01G297500 chr6B 88.121 463 30 9 778 1217 576827495 576827035 6.430000e-146 527.0
18 TraesCS6A01G297500 chr6B 82.511 446 60 11 2183 2620 576825835 576825400 2.470000e-100 375.0
19 TraesCS6A01G297500 chr7D 89.902 713 41 17 13 704 54972666 54971964 0.000000e+00 889.0
20 TraesCS6A01G297500 chr7B 94.565 92 5 0 2067 2158 465162835 465162744 2.720000e-30 143.0
21 TraesCS6A01G297500 chr7B 100.000 29 0 0 2412 2440 234589948 234589920 1.000000e-03 54.7
22 TraesCS6A01G297500 chr3D 94.624 93 4 1 2063 2155 389208185 389208276 2.720000e-30 143.0
23 TraesCS6A01G297500 chr2A 95.506 89 4 0 2069 2157 675835716 675835804 2.720000e-30 143.0
24 TraesCS6A01G297500 chr2A 92.708 96 5 1 2069 2164 78805762 78805669 1.270000e-28 137.0
25 TraesCS6A01G297500 chr2A 100.000 28 0 0 2413 2440 714033320 714033293 5.000000e-03 52.8
26 TraesCS6A01G297500 chr4B 93.684 95 5 1 2070 2164 454519254 454519347 9.800000e-30 141.0
27 TraesCS6A01G297500 chr2B 81.988 161 24 3 2189 2348 498429552 498429708 5.900000e-27 132.0
28 TraesCS6A01G297500 chr4A 89.130 46 3 2 2396 2439 549922199 549922154 3.650000e-04 56.5


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 TraesCS6A01G297500 chr6A 531049113 531051737 2624 True 4848.0 4848 100.000 1 2625 1 chr6A.!!$R1 2624
1 TraesCS6A01G297500 chr6D 386185332 386187078 1746 True 1074.5 1668 92.679 752 2620 2 chr6D.!!$R1 1868
2 TraesCS6A01G297500 chrUn 82546364 82547070 706 True 1081.0 1081 94.350 1 704 1 chrUn.!!$R1 703
3 TraesCS6A01G297500 chr3A 32204381 32205079 698 True 1002.0 1002 92.525 1 704 1 chr3A.!!$R1 703
4 TraesCS6A01G297500 chr7A 701358125 701358827 702 False 966.0 966 91.537 1 704 1 chr7A.!!$F2 703
5 TraesCS6A01G297500 chr1D 58485659 58486378 719 False 961.0 961 91.197 1 705 1 chr1D.!!$F1 704
6 TraesCS6A01G297500 chr5A 169184093 169184786 693 False 959.0 959 91.595 1 698 1 chr5A.!!$F1 697
7 TraesCS6A01G297500 chr5B 12549084 12549808 724 True 953.0 953 90.723 1 715 1 chr5B.!!$R1 714
8 TraesCS6A01G297500 chr2D 536207679 536208401 722 True 948.0 948 90.698 1 711 1 chr2D.!!$R1 710
9 TraesCS6A01G297500 chr3B 691342382 691343105 723 False 931.0 931 90.287 1 710 1 chr3B.!!$F1 709
10 TraesCS6A01G297500 chr6B 576825400 576827495 2095 True 605.0 913 87.111 778 2620 3 chr6B.!!$R1 1842
11 TraesCS6A01G297500 chr7D 54971964 54972666 702 True 889.0 889 89.902 13 704 1 chr7D.!!$R1 691

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
608 635 0.107848 GATCGGTCGGTTTGATGGGT 60.108 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2583 2997 0.107312 GCCCACATGCATCACTCTCT 60.107 55.0 0.0 0.0 0.0 3.1 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
67 68 5.420739 TGGCCAGAGAACTTGTTTTTAGTTT 59.579 36.000 0.00 0.00 36.04 2.66
70 71 5.748630 CCAGAGAACTTGTTTTTAGTTTGCC 59.251 40.000 0.00 0.00 36.04 4.52
127 128 4.559153 GCATGCATCAAGTAGTTTTTGGT 58.441 39.130 14.21 0.00 0.00 3.67
218 219 3.830755 AGCAGCTTCTTCATGGATTTGTT 59.169 39.130 0.00 0.00 0.00 2.83
270 277 3.774766 TGCCTATGCAGTAGAAGAAAGGA 59.225 43.478 0.00 0.00 44.23 3.36
438 453 0.395724 GGGGGCGATTCTGTTGGATT 60.396 55.000 0.00 0.00 0.00 3.01
607 634 1.151777 CGATCGGTCGGTTTGATGGG 61.152 60.000 11.03 0.00 44.00 4.00
608 635 0.107848 GATCGGTCGGTTTGATGGGT 60.108 55.000 0.00 0.00 0.00 4.51
626 654 3.053245 TGGGTCCTTCCTTTTCTGTTTCA 60.053 43.478 0.00 0.00 36.25 2.69
629 657 4.827284 GGTCCTTCCTTTTCTGTTTCATGA 59.173 41.667 0.00 0.00 0.00 3.07
650 681 2.022428 AGGGACAGGGGTTTTCCTTTTT 60.022 45.455 0.00 0.00 40.46 1.94
710 741 4.142093 GCCCACTAGACACGTCCTTTATTA 60.142 45.833 0.00 0.00 0.00 0.98
715 746 8.192774 CCACTAGACACGTCCTTTATTATTACA 58.807 37.037 0.00 0.00 0.00 2.41
716 747 9.234384 CACTAGACACGTCCTTTATTATTACAG 57.766 37.037 0.00 0.00 0.00 2.74
717 748 8.411683 ACTAGACACGTCCTTTATTATTACAGG 58.588 37.037 0.00 0.00 0.00 4.00
718 749 6.579865 AGACACGTCCTTTATTATTACAGGG 58.420 40.000 0.00 0.00 0.00 4.45
719 750 5.677567 ACACGTCCTTTATTATTACAGGGG 58.322 41.667 0.00 0.00 0.00 4.79
720 751 5.426185 ACACGTCCTTTATTATTACAGGGGA 59.574 40.000 0.00 0.00 0.00 4.81
721 752 6.070078 ACACGTCCTTTATTATTACAGGGGAA 60.070 38.462 0.00 0.00 0.00 3.97
722 753 6.996282 CACGTCCTTTATTATTACAGGGGAAT 59.004 38.462 0.00 0.00 0.00 3.01
723 754 7.501225 CACGTCCTTTATTATTACAGGGGAATT 59.499 37.037 0.00 0.00 0.00 2.17
724 755 8.057011 ACGTCCTTTATTATTACAGGGGAATTT 58.943 33.333 0.00 0.00 0.00 1.82
725 756 9.563748 CGTCCTTTATTATTACAGGGGAATTTA 57.436 33.333 0.00 0.00 0.00 1.40
739 770 4.989279 GGAATTTATCCTGCAGCTTTGA 57.011 40.909 8.66 0.00 45.56 2.69
740 771 5.526506 GGAATTTATCCTGCAGCTTTGAT 57.473 39.130 8.66 8.30 45.56 2.57
741 772 5.527033 GGAATTTATCCTGCAGCTTTGATC 58.473 41.667 8.66 0.70 45.56 2.92
742 773 5.068198 GGAATTTATCCTGCAGCTTTGATCA 59.932 40.000 8.66 0.00 45.56 2.92
743 774 6.406177 GGAATTTATCCTGCAGCTTTGATCAA 60.406 38.462 8.66 3.38 45.56 2.57
744 775 4.970662 TTATCCTGCAGCTTTGATCAAC 57.029 40.909 7.89 0.00 0.00 3.18
745 776 2.275134 TCCTGCAGCTTTGATCAACA 57.725 45.000 7.89 1.44 0.00 3.33
746 777 2.799017 TCCTGCAGCTTTGATCAACAT 58.201 42.857 7.89 0.00 0.00 2.71
747 778 3.954200 TCCTGCAGCTTTGATCAACATA 58.046 40.909 7.89 0.00 0.00 2.29
748 779 4.529897 TCCTGCAGCTTTGATCAACATAT 58.470 39.130 7.89 0.00 0.00 1.78
749 780 4.577693 TCCTGCAGCTTTGATCAACATATC 59.422 41.667 7.89 0.00 0.00 1.63
750 781 4.579340 CCTGCAGCTTTGATCAACATATCT 59.421 41.667 7.89 0.00 0.00 1.98
789 820 9.547279 AAGGGAAAAGTTATGTAGAAAATGGAT 57.453 29.630 0.00 0.00 0.00 3.41
790 821 9.190317 AGGGAAAAGTTATGTAGAAAATGGATC 57.810 33.333 0.00 0.00 0.00 3.36
884 915 4.625742 CCATATGGCTCTATAAAACGACCG 59.374 45.833 9.29 0.00 0.00 4.79
897 928 2.046217 GACCGTCCAAGCTTCCCC 60.046 66.667 0.00 0.00 0.00 4.81
946 977 2.486203 AGAGACATCGATCGATAGCCAC 59.514 50.000 28.94 18.01 32.93 5.01
960 991 1.079127 GCCACGCTTAGCTCCTTCA 60.079 57.895 1.76 0.00 0.00 3.02
978 1027 6.373759 TCCTTCATCTACTCCATACAGCTAA 58.626 40.000 0.00 0.00 0.00 3.09
1170 1219 0.455295 GAGACAAGCTCGGTGAGTCG 60.455 60.000 0.00 0.00 33.17 4.18
1238 1327 1.133976 GCTGATGATGGCTAGGTGGTT 60.134 52.381 0.00 0.00 0.00 3.67
1242 1331 1.656587 TGATGGCTAGGTGGTTGACT 58.343 50.000 0.00 0.00 0.00 3.41
1257 1577 3.001330 GGTTGACTCTCAGTTTGTTCACG 59.999 47.826 0.00 0.00 0.00 4.35
1309 1629 2.046283 TCTCAGTGTTCAACTACGCG 57.954 50.000 3.53 3.53 36.83 6.01
1628 1954 1.398958 GCTCGCCCTCTTCTGATCCT 61.399 60.000 0.00 0.00 0.00 3.24
1703 2029 1.204062 CACGCACACGCTAGTTTGG 59.796 57.895 0.00 0.00 45.53 3.28
1705 2031 0.531090 ACGCACACGCTAGTTTGGAA 60.531 50.000 0.00 0.00 45.53 3.53
1728 2056 0.536006 GAGTGGTTGCCTGTGCTTCT 60.536 55.000 0.00 0.00 38.71 2.85
1767 2095 0.717784 GGTTTCGTAGTAGTTGGCGC 59.282 55.000 0.00 0.00 0.00 6.53
1830 2177 8.824783 TCTAGTAGTAATAGGACTCCTCCATAC 58.175 40.741 0.00 4.10 39.39 2.39
1923 2271 8.181904 TGCAGATTTTTCTTCTTCATAAAGGT 57.818 30.769 0.00 0.00 33.03 3.50
1939 2287 2.686572 GGTGGATAACCCCGGGCTT 61.687 63.158 17.73 11.42 44.02 4.35
1970 2318 4.816786 TCGAATGATGCATACAACCATG 57.183 40.909 0.00 0.00 0.00 3.66
2004 2394 4.686191 AAATCCAGCAACCAAACAATCA 57.314 36.364 0.00 0.00 0.00 2.57
2008 2398 2.384382 CAGCAACCAAACAATCACGAC 58.616 47.619 0.00 0.00 0.00 4.34
2030 2420 3.689649 CAGTAGCTCCACCAATTAACCAC 59.310 47.826 0.00 0.00 0.00 4.16
2070 2471 6.917477 CAGAAGCAAACAAAAATACACAGCTA 59.083 34.615 0.00 0.00 0.00 3.32
2071 2472 6.918022 AGAAGCAAACAAAAATACACAGCTAC 59.082 34.615 0.00 0.00 0.00 3.58
2072 2473 6.391227 AGCAAACAAAAATACACAGCTACT 57.609 33.333 0.00 0.00 0.00 2.57
2073 2474 6.438763 AGCAAACAAAAATACACAGCTACTC 58.561 36.000 0.00 0.00 0.00 2.59
2074 2475 5.629435 GCAAACAAAAATACACAGCTACTCC 59.371 40.000 0.00 0.00 0.00 3.85
2075 2476 5.959618 AACAAAAATACACAGCTACTCCC 57.040 39.130 0.00 0.00 0.00 4.30
2076 2477 5.242795 ACAAAAATACACAGCTACTCCCT 57.757 39.130 0.00 0.00 0.00 4.20
2077 2478 5.246307 ACAAAAATACACAGCTACTCCCTC 58.754 41.667 0.00 0.00 0.00 4.30
2078 2479 5.013183 ACAAAAATACACAGCTACTCCCTCT 59.987 40.000 0.00 0.00 0.00 3.69
2079 2480 4.744795 AAATACACAGCTACTCCCTCTG 57.255 45.455 0.00 0.00 0.00 3.35
2080 2481 2.901338 TACACAGCTACTCCCTCTGT 57.099 50.000 0.00 0.00 41.29 3.41
2081 2482 2.901338 ACACAGCTACTCCCTCTGTA 57.099 50.000 0.00 0.00 38.85 2.74
2082 2483 3.170991 ACACAGCTACTCCCTCTGTAA 57.829 47.619 0.00 0.00 38.85 2.41
2083 2484 3.507411 ACACAGCTACTCCCTCTGTAAA 58.493 45.455 0.00 0.00 38.85 2.01
2084 2485 3.258622 ACACAGCTACTCCCTCTGTAAAC 59.741 47.826 0.00 0.00 38.85 2.01
2085 2486 3.511934 CACAGCTACTCCCTCTGTAAACT 59.488 47.826 0.00 0.00 38.85 2.66
2086 2487 4.705507 CACAGCTACTCCCTCTGTAAACTA 59.294 45.833 0.00 0.00 38.85 2.24
2087 2488 5.185249 CACAGCTACTCCCTCTGTAAACTAA 59.815 44.000 0.00 0.00 38.85 2.24
2088 2489 5.958987 ACAGCTACTCCCTCTGTAAACTAAT 59.041 40.000 0.00 0.00 39.08 1.73
2089 2490 7.068348 CACAGCTACTCCCTCTGTAAACTAATA 59.932 40.741 0.00 0.00 38.85 0.98
2090 2491 7.785506 ACAGCTACTCCCTCTGTAAACTAATAT 59.214 37.037 0.00 0.00 39.08 1.28
2091 2492 9.298250 CAGCTACTCCCTCTGTAAACTAATATA 57.702 37.037 0.00 0.00 0.00 0.86
2092 2493 9.878737 AGCTACTCCCTCTGTAAACTAATATAA 57.121 33.333 0.00 0.00 0.00 0.98
2096 2497 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2097 2498 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2098 2499 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2099 2500 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2100 2501 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2148 2549 9.977762 AAACGCTTTTATATTACTTTACGAAGG 57.022 29.630 0.00 0.00 37.19 3.46
2149 2550 8.931385 ACGCTTTTATATTACTTTACGAAGGA 57.069 30.769 0.00 0.00 37.19 3.36
2150 2551 9.369904 ACGCTTTTATATTACTTTACGAAGGAA 57.630 29.630 0.00 0.00 39.95 3.36
2151 2552 9.845305 CGCTTTTATATTACTTTACGAAGGAAG 57.155 33.333 0.00 0.00 39.04 3.46
2181 2582 6.867550 GGCTAAGCCTTCAATAAGAAAATGT 58.132 36.000 0.00 0.00 46.69 2.71
2192 2599 2.900122 AGAAAATGTTGCGTCGATGG 57.100 45.000 6.79 0.00 0.00 3.51
2210 2618 2.503331 TGGTGACAAGTGCAACATAGG 58.497 47.619 0.00 0.00 34.71 2.57
2213 2621 2.157668 GTGACAAGTGCAACATAGGTCG 59.842 50.000 0.00 0.00 41.43 4.79
2220 2628 1.346395 TGCAACATAGGTCGGTCTTGT 59.654 47.619 0.00 0.00 0.00 3.16
2226 2634 4.504858 ACATAGGTCGGTCTTGTGATTTC 58.495 43.478 0.00 0.00 0.00 2.17
2227 2635 4.223032 ACATAGGTCGGTCTTGTGATTTCT 59.777 41.667 0.00 0.00 0.00 2.52
2229 2637 6.098409 ACATAGGTCGGTCTTGTGATTTCTAT 59.902 38.462 0.00 0.00 0.00 1.98
2232 2640 4.141914 GGTCGGTCTTGTGATTTCTATCCT 60.142 45.833 0.00 0.00 0.00 3.24
2238 2646 6.881602 GGTCTTGTGATTTCTATCCTCAAAGT 59.118 38.462 0.00 0.00 0.00 2.66
2243 2651 5.233263 GTGATTTCTATCCTCAAAGTCGAGC 59.767 44.000 0.00 0.00 0.00 5.03
2263 2671 2.941415 GCTTCGATCCACCACCTTCAAT 60.941 50.000 0.00 0.00 0.00 2.57
2302 2710 0.030773 GCGTCGACATAGCCTGATCA 59.969 55.000 17.16 0.00 0.00 2.92
2303 2711 1.536072 GCGTCGACATAGCCTGATCAA 60.536 52.381 17.16 0.00 0.00 2.57
2308 2716 5.562890 CGTCGACATAGCCTGATCAAAGATA 60.563 44.000 17.16 0.00 0.00 1.98
2309 2717 6.393990 GTCGACATAGCCTGATCAAAGATAT 58.606 40.000 11.55 0.00 0.00 1.63
2315 2723 7.443575 ACATAGCCTGATCAAAGATATTGTGTC 59.556 37.037 0.00 0.00 0.00 3.67
2317 2725 6.421485 AGCCTGATCAAAGATATTGTGTCTT 58.579 36.000 0.00 0.00 37.52 3.01
2318 2726 6.541641 AGCCTGATCAAAGATATTGTGTCTTC 59.458 38.462 0.00 0.00 34.97 2.87
2322 2730 9.106070 CTGATCAAAGATATTGTGTCTTCATCA 57.894 33.333 0.00 0.00 34.97 3.07
2323 2731 8.886719 TGATCAAAGATATTGTGTCTTCATCAC 58.113 33.333 0.00 0.00 34.97 3.06
2348 2756 2.031682 GTGCAAACTCATCGTTGAAGCT 60.032 45.455 0.00 0.00 35.61 3.74
2357 2765 3.759086 TCATCGTTGAAGCTGTCTCTACT 59.241 43.478 0.00 0.00 0.00 2.57
2370 2778 5.396213 GCTGTCTCTACTTTCATCCCTTGAT 60.396 44.000 0.00 0.00 33.34 2.57
2395 2803 0.873054 ACCGACGCCTCATCTATACG 59.127 55.000 0.00 0.00 0.00 3.06
2433 2841 1.593196 TGAGCACCTTCAAAAGACCG 58.407 50.000 0.00 0.00 0.00 4.79
2502 2911 3.873910 ACCCATTGAGTTGATTCTACCG 58.126 45.455 0.00 0.00 0.00 4.02
2583 2997 6.674861 TCTTATACCTAGTTTTGGTCATGGGA 59.325 38.462 0.00 0.00 38.88 4.37
2620 3034 2.040009 GCGGTTAGGCAGGCTATGGA 62.040 60.000 4.19 0.00 0.00 3.41
2621 3035 0.249911 CGGTTAGGCAGGCTATGGAC 60.250 60.000 4.19 0.07 0.00 4.02
2622 3036 1.132500 GGTTAGGCAGGCTATGGACT 58.868 55.000 4.19 0.00 0.00 3.85
2623 3037 2.326428 GGTTAGGCAGGCTATGGACTA 58.674 52.381 4.19 0.00 0.00 2.59
2624 3038 2.907042 GGTTAGGCAGGCTATGGACTAT 59.093 50.000 4.19 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 2.513753 CCTGGATGTGTTAAACAGGCA 58.486 47.619 0.00 0.00 43.64 4.75
70 71 3.486383 ACCACCTGGATGTGTTAAACAG 58.514 45.455 0.00 0.00 39.59 3.16
218 219 3.051032 ACCCCCTTCTTCATGGATCTAGA 60.051 47.826 0.00 0.00 0.00 2.43
230 231 3.531814 AGGCATATGTAAACCCCCTTCTT 59.468 43.478 4.29 0.00 0.00 2.52
270 277 1.151810 TGCCCCTCTTCACTTCCCT 60.152 57.895 0.00 0.00 0.00 4.20
332 339 3.491766 AGATCTAAAGGACAGGGTGGA 57.508 47.619 0.00 0.00 0.00 4.02
367 374 0.914902 GGGAGCCCCAAAGTAGGAGT 60.915 60.000 5.45 0.00 44.65 3.85
438 453 0.603707 CTTCTCCACGCCAGAAGCAA 60.604 55.000 5.86 0.00 40.30 3.91
607 634 5.048434 CCTCATGAAACAGAAAAGGAAGGAC 60.048 44.000 0.00 0.00 0.00 3.85
608 635 5.072741 CCTCATGAAACAGAAAAGGAAGGA 58.927 41.667 0.00 0.00 0.00 3.36
626 654 0.704664 GGAAAACCCCTGTCCCTCAT 59.295 55.000 0.00 0.00 0.00 2.90
629 657 1.241485 AAAGGAAAACCCCTGTCCCT 58.759 50.000 0.00 0.00 36.49 4.20
662 693 1.073025 CTGCCCACTAGTGCAACCA 59.927 57.895 17.86 9.54 37.80 3.67
710 741 5.388654 CTGCAGGATAAATTCCCCTGTAAT 58.611 41.667 5.57 0.00 46.81 1.89
715 746 1.855599 AGCTGCAGGATAAATTCCCCT 59.144 47.619 17.12 0.00 46.81 4.79
716 747 2.371658 AGCTGCAGGATAAATTCCCC 57.628 50.000 17.12 0.00 46.81 4.81
717 748 3.701040 TCAAAGCTGCAGGATAAATTCCC 59.299 43.478 17.12 0.00 46.81 3.97
718 749 4.989279 TCAAAGCTGCAGGATAAATTCC 57.011 40.909 17.12 0.00 45.85 3.01
719 750 6.140303 TGATCAAAGCTGCAGGATAAATTC 57.860 37.500 17.12 0.00 0.00 2.17
720 751 6.071221 TGTTGATCAAAGCTGCAGGATAAATT 60.071 34.615 17.12 0.00 0.00 1.82
721 752 5.419788 TGTTGATCAAAGCTGCAGGATAAAT 59.580 36.000 17.12 0.00 0.00 1.40
722 753 4.766373 TGTTGATCAAAGCTGCAGGATAAA 59.234 37.500 17.12 6.13 0.00 1.40
723 754 4.334552 TGTTGATCAAAGCTGCAGGATAA 58.665 39.130 17.12 0.00 0.00 1.75
724 755 3.954200 TGTTGATCAAAGCTGCAGGATA 58.046 40.909 17.12 0.00 0.00 2.59
725 756 2.799017 TGTTGATCAAAGCTGCAGGAT 58.201 42.857 17.12 9.42 0.00 3.24
726 757 2.275134 TGTTGATCAAAGCTGCAGGA 57.725 45.000 17.12 4.15 0.00 3.86
727 758 4.579340 AGATATGTTGATCAAAGCTGCAGG 59.421 41.667 17.12 0.00 0.00 4.85
728 759 5.296035 TCAGATATGTTGATCAAAGCTGCAG 59.704 40.000 15.76 10.11 0.00 4.41
729 760 5.187687 TCAGATATGTTGATCAAAGCTGCA 58.812 37.500 15.76 8.22 0.00 4.41
730 761 5.296283 ACTCAGATATGTTGATCAAAGCTGC 59.704 40.000 15.76 3.15 0.00 5.25
731 762 6.018098 GGACTCAGATATGTTGATCAAAGCTG 60.018 42.308 10.35 13.10 0.00 4.24
732 763 6.054295 GGACTCAGATATGTTGATCAAAGCT 58.946 40.000 10.35 0.00 0.00 3.74
733 764 6.054295 AGGACTCAGATATGTTGATCAAAGC 58.946 40.000 10.35 0.00 0.00 3.51
734 765 8.503458 AAAGGACTCAGATATGTTGATCAAAG 57.497 34.615 10.35 3.85 0.00 2.77
735 766 8.868522 AAAAGGACTCAGATATGTTGATCAAA 57.131 30.769 10.35 1.23 0.00 2.69
736 767 8.868522 AAAAAGGACTCAGATATGTTGATCAA 57.131 30.769 3.38 3.38 0.00 2.57
737 768 8.102676 TGAAAAAGGACTCAGATATGTTGATCA 58.897 33.333 0.00 0.00 0.00 2.92
738 769 8.498054 TGAAAAAGGACTCAGATATGTTGATC 57.502 34.615 0.00 0.00 0.00 2.92
739 770 8.868522 TTGAAAAAGGACTCAGATATGTTGAT 57.131 30.769 0.00 0.00 0.00 2.57
740 771 7.391554 CCTTGAAAAAGGACTCAGATATGTTGA 59.608 37.037 0.00 0.00 42.62 3.18
741 772 7.362401 CCCTTGAAAAAGGACTCAGATATGTTG 60.362 40.741 6.07 0.00 42.62 3.33
742 773 6.660949 CCCTTGAAAAAGGACTCAGATATGTT 59.339 38.462 6.07 0.00 42.62 2.71
743 774 6.012508 TCCCTTGAAAAAGGACTCAGATATGT 60.013 38.462 6.07 0.00 42.62 2.29
744 775 6.418101 TCCCTTGAAAAAGGACTCAGATATG 58.582 40.000 6.07 0.00 42.62 1.78
745 776 6.642733 TCCCTTGAAAAAGGACTCAGATAT 57.357 37.500 6.07 0.00 42.62 1.63
746 777 6.448369 TTCCCTTGAAAAAGGACTCAGATA 57.552 37.500 6.07 0.00 42.62 1.98
747 778 5.324832 TTCCCTTGAAAAAGGACTCAGAT 57.675 39.130 6.07 0.00 42.62 2.90
748 779 4.788925 TTCCCTTGAAAAAGGACTCAGA 57.211 40.909 6.07 0.00 42.62 3.27
749 780 5.360999 ACTTTTCCCTTGAAAAAGGACTCAG 59.639 40.000 6.07 0.44 46.76 3.35
750 781 5.269189 ACTTTTCCCTTGAAAAAGGACTCA 58.731 37.500 6.07 0.00 46.76 3.41
766 797 8.889717 TCGATCCATTTTCTACATAACTTTTCC 58.110 33.333 0.00 0.00 0.00 3.13
786 817 3.904234 GCGTTTGTGTTACTTTTCGATCC 59.096 43.478 0.00 0.00 0.00 3.36
789 820 3.617706 TCAGCGTTTGTGTTACTTTTCGA 59.382 39.130 0.00 0.00 0.00 3.71
790 821 3.717404 GTCAGCGTTTGTGTTACTTTTCG 59.283 43.478 0.00 0.00 0.00 3.46
884 915 0.322546 ATTGACGGGGAAGCTTGGAC 60.323 55.000 2.10 0.00 0.00 4.02
897 928 1.011904 CTGGATTGCGCGATTGACG 60.012 57.895 12.10 0.00 45.66 4.35
946 977 3.305064 GGAGTAGATGAAGGAGCTAAGCG 60.305 52.174 0.00 0.00 0.00 4.68
960 991 4.762765 CGGAGTTAGCTGTATGGAGTAGAT 59.237 45.833 0.00 0.00 0.00 1.98
978 1027 0.894184 TCGAAGTGAAGGCTCGGAGT 60.894 55.000 6.90 0.00 0.00 3.85
1149 1198 1.153939 CTCACCGAGCTTGTCTCCG 60.154 63.158 0.00 0.00 38.62 4.63
1170 1219 5.073311 TGTGTAGAAATAGGAGTGCTGAC 57.927 43.478 0.00 0.00 0.00 3.51
1238 1327 2.429250 TCCGTGAACAAACTGAGAGTCA 59.571 45.455 0.00 0.00 0.00 3.41
1242 1331 2.035449 ACGATCCGTGAACAAACTGAGA 59.965 45.455 0.00 0.00 39.18 3.27
1257 1577 4.083271 GCAGAAAATATTAGGCCACGATCC 60.083 45.833 5.01 0.00 0.00 3.36
1309 1629 3.958860 ACTGTGTGGGCCTGGCTC 61.959 66.667 19.68 16.49 0.00 4.70
1594 1920 3.708220 GAGCTTGAGGAGGACGCCG 62.708 68.421 0.00 0.00 0.00 6.46
1703 2029 0.249911 ACAGGCAACCACTCTCGTTC 60.250 55.000 0.00 0.00 37.17 3.95
1705 2031 1.069765 CACAGGCAACCACTCTCGT 59.930 57.895 0.00 0.00 37.17 4.18
1728 2056 7.479352 AAACCAACCAATCATATCACATCAA 57.521 32.000 0.00 0.00 0.00 2.57
1767 2095 7.374272 AGATAATGATCCATACAAGTCACTCG 58.626 38.462 0.00 0.00 31.81 4.18
1840 2187 7.816031 AGCATTGACAGAATCCAAACTTATTTG 59.184 33.333 0.00 0.00 44.19 2.32
1909 2257 5.828328 GGGGTTATCCACCTTTATGAAGAAG 59.172 44.000 0.00 0.00 46.38 2.85
1916 2264 1.778484 CCCGGGGTTATCCACCTTTAT 59.222 52.381 14.71 0.00 46.38 1.40
1917 2265 1.215140 CCCGGGGTTATCCACCTTTA 58.785 55.000 14.71 0.00 46.38 1.85
1921 2269 2.219449 AAAGCCCGGGGTTATCCACC 62.219 60.000 36.77 9.76 46.46 4.61
1923 2271 1.304952 CAAAGCCCGGGGTTATCCA 59.695 57.895 36.77 0.00 37.22 3.41
1933 2281 1.010797 CGATTCGATGCAAAGCCCG 60.011 57.895 0.00 0.00 0.00 6.13
1934 2282 0.732571 TTCGATTCGATGCAAAGCCC 59.267 50.000 9.96 0.00 35.23 5.19
1936 2284 3.323729 TCATTCGATTCGATGCAAAGC 57.676 42.857 9.96 0.00 35.23 3.51
1946 2294 5.422666 TGGTTGTATGCATCATTCGATTC 57.577 39.130 0.19 0.00 0.00 2.52
1996 2348 3.244078 TGGAGCTACTGTCGTGATTGTTT 60.244 43.478 0.00 0.00 0.00 2.83
2004 2394 1.267121 ATTGGTGGAGCTACTGTCGT 58.733 50.000 0.00 0.00 0.00 4.34
2008 2398 3.689649 GTGGTTAATTGGTGGAGCTACTG 59.310 47.826 0.00 0.00 0.00 2.74
2050 2442 5.629435 GGAGTAGCTGTGTATTTTTGTTTGC 59.371 40.000 0.00 0.00 0.00 3.68
2070 2471 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2071 2472 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2072 2473 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2073 2474 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2074 2475 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2122 2523 9.977762 CCTTCGTAAAGTAATATAAAAGCGTTT 57.022 29.630 2.53 2.53 0.00 3.60
2123 2524 9.369904 TCCTTCGTAAAGTAATATAAAAGCGTT 57.630 29.630 0.00 0.00 0.00 4.84
2124 2525 8.931385 TCCTTCGTAAAGTAATATAAAAGCGT 57.069 30.769 0.00 0.00 0.00 5.07
2125 2526 9.845305 CTTCCTTCGTAAAGTAATATAAAAGCG 57.155 33.333 0.00 0.00 0.00 4.68
2133 2534 8.624776 GCCTAGTACTTCCTTCGTAAAGTAATA 58.375 37.037 0.00 0.00 39.11 0.98
2134 2535 7.341512 AGCCTAGTACTTCCTTCGTAAAGTAAT 59.658 37.037 0.00 0.00 39.11 1.89
2135 2536 6.660949 AGCCTAGTACTTCCTTCGTAAAGTAA 59.339 38.462 0.00 0.00 39.11 2.24
2136 2537 6.183347 AGCCTAGTACTTCCTTCGTAAAGTA 58.817 40.000 0.00 0.00 37.02 2.24
2137 2538 5.015515 AGCCTAGTACTTCCTTCGTAAAGT 58.984 41.667 0.00 0.00 39.07 2.66
2138 2539 5.579564 AGCCTAGTACTTCCTTCGTAAAG 57.420 43.478 0.00 0.00 0.00 1.85
2139 2540 6.405176 GCTTAGCCTAGTACTTCCTTCGTAAA 60.405 42.308 0.00 0.00 0.00 2.01
2140 2541 5.067023 GCTTAGCCTAGTACTTCCTTCGTAA 59.933 44.000 0.00 0.00 0.00 3.18
2141 2542 4.578105 GCTTAGCCTAGTACTTCCTTCGTA 59.422 45.833 0.00 0.00 0.00 3.43
2142 2543 3.380954 GCTTAGCCTAGTACTTCCTTCGT 59.619 47.826 0.00 0.00 0.00 3.85
2143 2544 3.243468 GGCTTAGCCTAGTACTTCCTTCG 60.243 52.174 17.16 0.00 46.69 3.79
2144 2545 4.325028 GGCTTAGCCTAGTACTTCCTTC 57.675 50.000 17.16 0.00 46.69 3.46
2171 2572 3.749088 ACCATCGACGCAACATTTTCTTA 59.251 39.130 0.00 0.00 0.00 2.10
2179 2580 0.530870 TTGTCACCATCGACGCAACA 60.531 50.000 0.00 0.00 38.84 3.33
2180 2581 0.163788 CTTGTCACCATCGACGCAAC 59.836 55.000 0.00 0.00 38.84 4.17
2181 2582 0.249699 ACTTGTCACCATCGACGCAA 60.250 50.000 0.00 0.00 38.84 4.85
2192 2599 2.157668 CGACCTATGTTGCACTTGTCAC 59.842 50.000 0.00 0.00 0.00 3.67
2197 2604 1.623811 AGACCGACCTATGTTGCACTT 59.376 47.619 0.00 0.00 0.00 3.16
2201 2608 1.732259 CACAAGACCGACCTATGTTGC 59.268 52.381 0.00 0.00 0.00 4.17
2210 2618 5.012328 AGGATAGAAATCACAAGACCGAC 57.988 43.478 0.00 0.00 33.41 4.79
2213 2621 6.881602 ACTTTGAGGATAGAAATCACAAGACC 59.118 38.462 0.00 0.00 34.17 3.85
2220 2628 5.127845 AGCTCGACTTTGAGGATAGAAATCA 59.872 40.000 0.00 0.00 36.47 2.57
2226 2634 3.065510 TCGAAGCTCGACTTTGAGGATAG 59.934 47.826 11.40 0.00 44.82 2.08
2227 2635 3.014623 TCGAAGCTCGACTTTGAGGATA 58.985 45.455 11.40 0.00 44.82 2.59
2229 2637 1.244816 TCGAAGCTCGACTTTGAGGA 58.755 50.000 11.40 2.70 44.82 3.71
2243 2651 2.472695 TTGAAGGTGGTGGATCGAAG 57.527 50.000 0.00 0.00 0.00 3.79
2263 2671 3.312146 CGCATGCATATGTTGTGTCCTTA 59.688 43.478 19.57 0.00 36.65 2.69
2275 2683 1.995484 GCTATGTCGACGCATGCATAT 59.005 47.619 19.57 4.37 0.00 1.78
2276 2684 1.418373 GCTATGTCGACGCATGCATA 58.582 50.000 19.57 5.77 0.00 3.14
2315 2723 4.862350 TGAGTTTGCACAATGTGATGAAG 58.138 39.130 18.66 0.00 35.23 3.02
2317 2725 4.378666 CGATGAGTTTGCACAATGTGATGA 60.379 41.667 18.66 0.00 35.23 2.92
2318 2726 3.849708 CGATGAGTTTGCACAATGTGATG 59.150 43.478 18.66 0.00 35.23 3.07
2322 2730 3.314913 TCAACGATGAGTTTGCACAATGT 59.685 39.130 0.00 0.00 42.02 2.71
2323 2731 3.887741 TCAACGATGAGTTTGCACAATG 58.112 40.909 0.00 0.00 42.02 2.82
2348 2756 5.163509 CGATCAAGGGATGAAAGTAGAGACA 60.164 44.000 0.00 0.00 42.54 3.41
2357 2765 2.158813 GGTAGCCGATCAAGGGATGAAA 60.159 50.000 0.00 0.00 42.54 2.69
2395 2803 2.284150 TCATAGAAATAAGCGTGCGTGC 59.716 45.455 0.00 0.00 0.00 5.34
2433 2841 9.406828 AGTGTTCTTTTTAAAATTAATCGGCTC 57.593 29.630 0.55 0.00 0.00 4.70
2502 2911 3.062774 GCTCAGACGATTAGGTTTCTTGC 59.937 47.826 0.00 0.00 0.00 4.01
2583 2997 0.107312 GCCCACATGCATCACTCTCT 60.107 55.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.