Multiple sequence alignment - TraesCS7B01G139800

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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 TraesCS7B01G139800 chr7B 100.000 2990 0 0 1 2990 176208487 176205498 0.000000e+00 5522
1 TraesCS7B01G139800 chr7D 93.268 1322 63 14 1090 2393 223869274 223870587 0.000000e+00 1925
2 TraesCS7B01G139800 chr7D 88.428 916 64 17 1 904 68918047 68918932 0.000000e+00 1066
3 TraesCS7B01G139800 chr7D 91.187 556 44 3 348 902 503629780 503630331 0.000000e+00 750
4 TraesCS7B01G139800 chr7D 87.973 582 45 10 2431 2988 223870595 223871175 0.000000e+00 664
5 TraesCS7B01G139800 chr7D 94.012 167 8 2 903 1067 223869115 223869281 4.950000e-63 252
6 TraesCS7B01G139800 chr7A 93.593 1077 58 8 1093 2163 234539457 234540528 0.000000e+00 1596
7 TraesCS7B01G139800 chr7A 87.021 678 51 17 2321 2988 234548084 234548734 0.000000e+00 730
8 TraesCS7B01G139800 chr7A 90.533 169 11 2 903 1066 234539292 234539460 5.020000e-53 219
9 TraesCS7B01G139800 chr7A 95.161 124 5 1 2211 2333 234540909 234541032 8.460000e-46 195
10 TraesCS7B01G139800 chr5B 95.885 729 25 3 175 902 600128471 600129195 0.000000e+00 1175
11 TraesCS7B01G139800 chr5B 90.411 730 63 5 179 907 597216307 597217030 0.000000e+00 953
12 TraesCS7B01G139800 chr5B 90.483 725 62 5 179 902 6213010 6213728 0.000000e+00 950
13 TraesCS7B01G139800 chr5B 92.128 470 30 5 2 464 600128195 600128664 0.000000e+00 656
14 TraesCS7B01G139800 chr5B 82.561 453 74 4 1163 1611 458634167 458634618 7.770000e-106 394
15 TraesCS7B01G139800 chr4A 90.685 730 59 5 175 902 677942852 677943574 0.000000e+00 963
16 TraesCS7B01G139800 chr4A 83.476 466 52 17 1 464 677942603 677943045 7.710000e-111 411
17 TraesCS7B01G139800 chr6B 90.759 725 59 4 179 902 76112221 76111504 0.000000e+00 961
18 TraesCS7B01G139800 chr6B 90.358 726 62 4 179 903 695480433 695479715 0.000000e+00 946
19 TraesCS7B01G139800 chr6B 89.552 469 40 7 1 463 76112501 76112036 1.190000e-163 586
20 TraesCS7B01G139800 chr6B 87.665 227 26 2 47 272 43092643 43092418 2.290000e-66 263
21 TraesCS7B01G139800 chr4D 92.989 542 33 3 363 902 455766939 455766401 0.000000e+00 785
22 TraesCS7B01G139800 chr4D 91.489 188 12 2 1 184 455767611 455767424 3.820000e-64 255
23 TraesCS7B01G139800 chr5A 83.002 453 72 4 1163 1611 482621904 482622355 3.590000e-109 405
24 TraesCS7B01G139800 chr5A 81.898 453 77 4 1163 1611 482533392 482533843 7.820000e-101 377
25 TraesCS7B01G139800 chr5D 81.678 453 78 4 1163 1611 382268210 382268661 3.640000e-99 372


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 TraesCS7B01G139800 chr7B 176205498 176208487 2989 True 5522.0 5522 100.000000 1 2990 1 chr7B.!!$R1 2989
1 TraesCS7B01G139800 chr7D 68918047 68918932 885 False 1066.0 1066 88.428000 1 904 1 chr7D.!!$F1 903
2 TraesCS7B01G139800 chr7D 223869115 223871175 2060 False 947.0 1925 91.751000 903 2988 3 chr7D.!!$F3 2085
3 TraesCS7B01G139800 chr7D 503629780 503630331 551 False 750.0 750 91.187000 348 902 1 chr7D.!!$F2 554
4 TraesCS7B01G139800 chr7A 234548084 234548734 650 False 730.0 730 87.021000 2321 2988 1 chr7A.!!$F1 667
5 TraesCS7B01G139800 chr7A 234539292 234541032 1740 False 670.0 1596 93.095667 903 2333 3 chr7A.!!$F2 1430
6 TraesCS7B01G139800 chr5B 597216307 597217030 723 False 953.0 953 90.411000 179 907 1 chr5B.!!$F3 728
7 TraesCS7B01G139800 chr5B 6213010 6213728 718 False 950.0 950 90.483000 179 902 1 chr5B.!!$F1 723
8 TraesCS7B01G139800 chr5B 600128195 600129195 1000 False 915.5 1175 94.006500 2 902 2 chr5B.!!$F4 900
9 TraesCS7B01G139800 chr4A 677942603 677943574 971 False 687.0 963 87.080500 1 902 2 chr4A.!!$F1 901
10 TraesCS7B01G139800 chr6B 695479715 695480433 718 True 946.0 946 90.358000 179 903 1 chr6B.!!$R2 724
11 TraesCS7B01G139800 chr6B 76111504 76112501 997 True 773.5 961 90.155500 1 902 2 chr6B.!!$R3 901
12 TraesCS7B01G139800 chr4D 455766401 455767611 1210 True 520.0 785 92.239000 1 902 2 chr4D.!!$R1 901

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
924 1531 1.919956 CTAGCTCGGTGGTCGTCGTT 61.92 60.0 0.0 0.0 40.32 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2865 3851 0.379669 CCCATTGCAATCAGACGAGC 59.62 55.0 9.53 0.0 0.0 5.03 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
25 27 5.707764 GGTCCTGCTATTTCTCTGAAAAAGT 59.292 40.000 0.00 0.00 0.00 2.66
263 274 3.844090 GAGGCCCGGTGAGCTCTC 61.844 72.222 16.19 11.58 0.00 3.20
730 1331 2.184167 CGGTCAACCAAACGGTGCT 61.184 57.895 0.00 0.00 36.67 4.40
762 1363 2.158871 GGCCCGACCTGTCATAAACATA 60.159 50.000 0.00 0.00 37.23 2.29
924 1531 1.919956 CTAGCTCGGTGGTCGTCGTT 61.920 60.000 0.00 0.00 40.32 3.85
949 1556 2.159179 TGTCCAGCTAGCTACCATCA 57.841 50.000 18.86 9.71 0.00 3.07
979 1586 4.767928 CCGGCTGGTCTCCCTATATATATC 59.232 50.000 2.29 0.00 0.00 1.63
980 1587 5.386060 CGGCTGGTCTCCCTATATATATCA 58.614 45.833 0.00 0.00 0.00 2.15
981 1588 5.475220 CGGCTGGTCTCCCTATATATATCAG 59.525 48.000 0.00 0.00 0.00 2.90
1056 1668 5.088739 CACTCACAGTCACACAAAGAAAAC 58.911 41.667 0.00 0.00 0.00 2.43
1061 1673 3.853671 CAGTCACACAAAGAAAACTGCAC 59.146 43.478 0.00 0.00 0.00 4.57
1069 1681 2.919666 AGAAAACTGCACACACACAC 57.080 45.000 0.00 0.00 0.00 3.82
1070 1682 2.158559 AGAAAACTGCACACACACACA 58.841 42.857 0.00 0.00 0.00 3.72
1071 1683 2.095263 AGAAAACTGCACACACACACAC 60.095 45.455 0.00 0.00 0.00 3.82
1072 1684 1.242989 AAACTGCACACACACACACA 58.757 45.000 0.00 0.00 0.00 3.72
1073 1685 0.521291 AACTGCACACACACACACAC 59.479 50.000 0.00 0.00 0.00 3.82
1074 1686 0.605050 ACTGCACACACACACACACA 60.605 50.000 0.00 0.00 0.00 3.72
1075 1687 0.179192 CTGCACACACACACACACAC 60.179 55.000 0.00 0.00 0.00 3.82
1076 1688 0.886490 TGCACACACACACACACACA 60.886 50.000 0.00 0.00 0.00 3.72
1077 1689 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
1078 1690 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1079 1691 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1080 1692 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1081 1693 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1082 1694 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1083 1695 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1084 1696 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1085 1697 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1086 1698 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1087 1699 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1088 1700 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1089 1701 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1090 1702 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1091 1703 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1092 1704 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1093 1705 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1094 1706 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1095 1707 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1096 1708 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1097 1709 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1112 1724 1.526917 ACACACTGCAAGGTGGAGC 60.527 57.895 18.41 0.00 39.63 4.70
1116 1728 2.435586 CTGCAAGGTGGAGCGAGG 60.436 66.667 0.00 0.00 0.00 4.63
1469 2081 2.126228 TACGCCGTCAAGAAGCCG 60.126 61.111 0.00 0.00 0.00 5.52
1550 2162 2.581354 CTCACCGCCTTCCTCCTG 59.419 66.667 0.00 0.00 0.00 3.86
1638 2250 4.332543 ACCTCTTCGCCCTCCCCA 62.333 66.667 0.00 0.00 0.00 4.96
1688 2300 0.392729 AGTACGTCCTCGAGGTCCTG 60.393 60.000 30.17 19.56 40.62 3.86
1760 2372 1.880027 GTTCCGTTTCTGCTGTGGATT 59.120 47.619 0.00 0.00 0.00 3.01
1876 2488 3.744660 AGGTCAGTGACAAAATGGAGAC 58.255 45.455 24.20 3.39 33.68 3.36
1892 2504 3.338126 GACGACCGATGCCGACAGT 62.338 63.158 0.00 0.00 38.22 3.55
1917 2529 0.807275 CGGCATGCAAGTCTGATCGA 60.807 55.000 21.36 0.00 0.00 3.59
1923 2535 2.688507 TGCAAGTCTGATCGACCTTTC 58.311 47.619 12.17 0.00 43.91 2.62
1952 2564 0.524414 TTGGTGACACGATCGACGAT 59.476 50.000 24.34 10.78 45.65 3.73
1955 2567 2.286772 TGGTGACACGATCGACGATATG 60.287 50.000 24.34 14.26 45.65 1.78
1957 2569 1.265905 TGACACGATCGACGATATGGG 59.734 52.381 24.34 15.29 45.77 4.00
1959 2571 1.065572 CACGATCGACGATATGGGCG 61.066 60.000 24.34 6.64 45.77 6.13
1960 2572 2.152699 CGATCGACGATATGGGCGC 61.153 63.158 10.26 0.00 45.77 6.53
1961 2573 1.080772 GATCGACGATATGGGCGCA 60.081 57.895 10.97 5.70 0.00 6.09
1962 2574 1.073216 GATCGACGATATGGGCGCAG 61.073 60.000 10.97 0.00 0.00 5.18
1984 2599 3.120477 GCAACAACGATCAACGGATGTTA 60.120 43.478 12.38 0.00 46.20 2.41
1985 2600 4.611807 GCAACAACGATCAACGGATGTTAA 60.612 41.667 12.38 0.00 46.20 2.01
1994 2609 8.187969 CGATCAACGGATGTTAATTAATTTCG 57.812 34.615 5.91 5.83 36.28 3.46
2014 2630 2.463653 CGTATTCAAAAATCCATGCGCG 59.536 45.455 0.00 0.00 0.00 6.86
2031 2648 1.285641 CGCGCCTTTGTTGGAACAT 59.714 52.632 0.00 0.00 39.30 2.71
2065 2682 9.325198 GTTGTTTCATTTTCCTAAACCAATTCT 57.675 29.630 0.00 0.00 33.21 2.40
2110 2727 0.323725 TTCCAAAGAGGCCCTGCATC 60.324 55.000 0.00 0.00 39.81 3.91
2135 2762 3.405823 TGCATGTGAGACAAGTCATCA 57.594 42.857 2.72 1.33 0.00 3.07
2171 3118 8.710749 ATATATGCCATTCAATTGTTGGTACT 57.289 30.769 22.55 15.25 32.90 2.73
2172 3119 9.806448 ATATATGCCATTCAATTGTTGGTACTA 57.194 29.630 22.55 16.33 32.90 1.82
2191 3138 6.475727 GGTACTAGTAGTGTATGTGTGCAATG 59.524 42.308 13.29 0.00 0.00 2.82
2195 3142 3.837213 AGTGTATGTGTGCAATGCTTC 57.163 42.857 6.82 0.21 0.00 3.86
2196 3143 3.148412 AGTGTATGTGTGCAATGCTTCA 58.852 40.909 6.82 3.12 0.00 3.02
2198 3145 4.219070 AGTGTATGTGTGCAATGCTTCATT 59.781 37.500 6.82 1.62 34.04 2.57
2201 3148 5.634439 TGTATGTGTGCAATGCTTCATTTTC 59.366 36.000 6.82 4.40 31.05 2.29
2202 3149 4.056092 TGTGTGCAATGCTTCATTTTCA 57.944 36.364 6.82 0.00 31.05 2.69
2204 3151 3.061322 TGTGCAATGCTTCATTTTCAGC 58.939 40.909 6.82 0.00 31.05 4.26
2206 3153 2.030096 TGCAATGCTTCATTTTCAGCGA 60.030 40.909 6.82 0.00 39.04 4.93
2207 3154 2.343544 GCAATGCTTCATTTTCAGCGAC 59.656 45.455 0.00 0.00 39.04 5.19
2209 3156 4.672542 GCAATGCTTCATTTTCAGCGACTA 60.673 41.667 0.00 0.00 39.04 2.59
2215 3162 5.292101 GCTTCATTTTCAGCGACTATGTAGT 59.708 40.000 0.00 0.00 39.71 2.73
2216 3163 6.475727 GCTTCATTTTCAGCGACTATGTAGTA 59.524 38.462 0.00 0.00 36.50 1.82
2225 3189 6.072098 CAGCGACTATGTAGTATACTGTTCG 58.928 44.000 15.90 13.34 43.54 3.95
2235 3199 8.672823 TGTAGTATACTGTTCGTCATCTGTAT 57.327 34.615 15.90 0.00 43.54 2.29
2341 3305 3.004419 TGTCGACGTCCATTGATCTATCC 59.996 47.826 10.58 0.00 0.00 2.59
2343 3307 3.634910 TCGACGTCCATTGATCTATCCAA 59.365 43.478 10.58 0.00 0.00 3.53
2384 3348 6.318648 AGCACACAACTTTTCATCAGAGTAAA 59.681 34.615 0.00 0.00 0.00 2.01
2438 3402 0.521735 GTGGACATTCACCCGAAAGC 59.478 55.000 0.00 0.00 34.01 3.51
2513 3477 0.814457 TTGTCAAAGTGCCAAAGCGT 59.186 45.000 0.00 0.00 44.31 5.07
2521 3485 0.996727 GTGCCAAAGCGTACAAAGCG 60.997 55.000 0.00 0.00 44.31 4.68
2588 3552 7.095187 GGCTATCGTTTCCCTCTAATACAATTG 60.095 40.741 3.24 3.24 0.00 2.32
2686 3651 1.972223 CGGGTGAGTGTCTCGGTCT 60.972 63.158 0.00 0.00 32.35 3.85
2720 3685 1.663702 CTGGTGAACCACGACGTCC 60.664 63.158 10.58 0.00 42.01 4.79
2772 3737 2.573083 GGCATTGGTGGGTGTGGTG 61.573 63.158 0.00 0.00 0.00 4.17
2782 3751 2.043980 GGTGTGGTGGGTAATGCCG 61.044 63.158 0.00 0.00 38.44 5.69
2783 3752 2.043980 GTGTGGTGGGTAATGCCGG 61.044 63.158 0.00 0.00 38.44 6.13
2785 3754 1.226262 GTGGTGGGTAATGCCGGAT 59.774 57.895 5.05 0.00 38.44 4.18
2791 3760 2.812011 GTGGGTAATGCCGGATATGTTC 59.188 50.000 5.05 0.00 38.44 3.18
2815 3796 2.106683 CGGGCCTCGGATGAACAAC 61.107 63.158 0.84 0.00 34.75 3.32
2826 3809 1.732259 GATGAACAACGGCGAAGTCAT 59.268 47.619 16.62 16.06 0.00 3.06
2835 3818 1.448985 GGCGAAGTCATGGCAACTTA 58.551 50.000 0.00 0.00 37.10 2.24
2836 3819 2.017049 GGCGAAGTCATGGCAACTTAT 58.983 47.619 0.00 0.00 37.10 1.73
2837 3820 2.423538 GGCGAAGTCATGGCAACTTATT 59.576 45.455 0.00 0.00 37.10 1.40
2839 3822 4.098416 GCGAAGTCATGGCAACTTATTTC 58.902 43.478 0.00 0.00 37.10 2.17
2865 3851 9.687717 CTTTTTAAACAACAACTAGCACAAATG 57.312 29.630 0.00 0.00 0.00 2.32
2883 3869 1.089112 TGCTCGTCTGATTGCAATGG 58.911 50.000 18.59 9.56 32.12 3.16
2890 3876 3.379372 CGTCTGATTGCAATGGGAGAAAT 59.621 43.478 18.59 0.00 0.00 2.17
2903 3889 9.382275 GCAATGGGAGAAATTTTACATGTATTT 57.618 29.630 6.36 5.58 0.00 1.40
2959 3949 1.526917 AAAACCTGCTCAGCGTGCT 60.527 52.632 0.00 0.00 0.00 4.40
2960 3950 1.510480 AAAACCTGCTCAGCGTGCTC 61.510 55.000 0.00 0.00 0.00 4.26
2967 3957 3.417275 CTCAGCGTGCTCCTACCCG 62.417 68.421 0.00 0.00 0.00 5.28
2970 3960 4.849329 GCGTGCTCCTACCCGTCG 62.849 72.222 0.00 0.00 0.00 5.12
2981 3971 2.030981 CCTACCCGTCGCTTCTTCTATC 60.031 54.545 0.00 0.00 0.00 2.08
2988 3978 4.363999 CGTCGCTTCTTCTATCCAATTCT 58.636 43.478 0.00 0.00 0.00 2.40
2989 3979 5.507482 CCGTCGCTTCTTCTATCCAATTCTA 60.507 44.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
391 703 4.025858 ATGGCCACGAGCAGCAGT 62.026 61.111 8.16 0.00 46.50 4.40
730 1331 3.638316 TCGGGCCCGCCAGTAAAA 61.638 61.111 39.89 17.41 39.59 1.52
806 1407 4.600111 TGATAACTACCAAGTCAGGGGTTT 59.400 41.667 0.00 0.00 38.60 3.27
858 1460 7.105241 ACTACTACTTTACGGATTAGGGTTG 57.895 40.000 0.00 0.00 0.00 3.77
889 1496 2.900546 AGCTAGGGCGAGTAAATAGCAT 59.099 45.455 5.42 0.00 44.37 3.79
890 1497 2.296471 GAGCTAGGGCGAGTAAATAGCA 59.704 50.000 5.42 0.00 44.37 3.49
891 1498 2.668834 CGAGCTAGGGCGAGTAAATAGC 60.669 54.545 0.00 0.00 44.37 2.97
924 1531 3.181449 TGGTAGCTAGCTGGACAAAAACA 60.181 43.478 27.68 11.35 0.00 2.83
1056 1668 0.179192 GTGTGTGTGTGTGTGTGCAG 60.179 55.000 0.00 0.00 0.00 4.41
1061 1673 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1069 1681 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1070 1682 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1071 1683 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1072 1684 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1073 1685 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1074 1686 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1075 1687 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1076 1688 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1077 1689 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1078 1690 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1079 1691 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1080 1692 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1081 1693 1.136000 CAGTGTGTGTGTGTGTGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
1082 1694 1.155889 CAGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
1083 1695 0.179192 GCAGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
1084 1696 0.605050 TGCAGTGTGTGTGTGTGTGT 60.605 50.000 0.00 0.00 0.00 3.72
1085 1697 0.520847 TTGCAGTGTGTGTGTGTGTG 59.479 50.000 0.00 0.00 0.00 3.82
1086 1698 0.804364 CTTGCAGTGTGTGTGTGTGT 59.196 50.000 0.00 0.00 0.00 3.72
1087 1699 0.099259 CCTTGCAGTGTGTGTGTGTG 59.901 55.000 0.00 0.00 0.00 3.82
1088 1700 0.322456 ACCTTGCAGTGTGTGTGTGT 60.322 50.000 0.00 0.00 0.00 3.72
1089 1701 0.099259 CACCTTGCAGTGTGTGTGTG 59.901 55.000 8.97 0.00 32.89 3.82
1090 1702 1.031571 CCACCTTGCAGTGTGTGTGT 61.032 55.000 14.33 0.00 35.93 3.72
1091 1703 0.747644 TCCACCTTGCAGTGTGTGTG 60.748 55.000 14.33 5.12 35.93 3.82
1092 1704 0.464373 CTCCACCTTGCAGTGTGTGT 60.464 55.000 14.33 0.00 35.93 3.72
1093 1705 1.789078 GCTCCACCTTGCAGTGTGTG 61.789 60.000 14.33 8.04 35.93 3.82
1094 1706 1.526917 GCTCCACCTTGCAGTGTGT 60.527 57.895 14.33 0.00 35.93 3.72
1095 1707 2.610694 CGCTCCACCTTGCAGTGTG 61.611 63.158 9.95 9.95 35.93 3.82
1096 1708 2.281070 CGCTCCACCTTGCAGTGT 60.281 61.111 5.48 0.00 35.93 3.55
1097 1709 2.031012 TCGCTCCACCTTGCAGTG 59.969 61.111 0.00 0.00 37.51 3.66
1112 1724 4.464069 ACAAATCTCTCTTTCTCCCTCG 57.536 45.455 0.00 0.00 0.00 4.63
1116 1728 7.164230 TCTCACTACAAATCTCTCTTTCTCC 57.836 40.000 0.00 0.00 0.00 3.71
1469 2081 2.202623 AAGACGGCGTCGCTGATC 60.203 61.111 31.78 22.71 38.46 2.92
1550 2162 1.003233 GGTGTGGCAGAGGAAGGAC 60.003 63.158 0.00 0.00 0.00 3.85
1746 2358 1.885887 CCCGAAAATCCACAGCAGAAA 59.114 47.619 0.00 0.00 0.00 2.52
1748 2360 0.960364 GCCCGAAAATCCACAGCAGA 60.960 55.000 0.00 0.00 0.00 4.26
1876 2488 2.880879 CACTGTCGGCATCGGTCG 60.881 66.667 0.00 0.00 45.31 4.79
1892 2504 2.027073 GACTTGCATGCCGTCGTCA 61.027 57.895 16.68 0.00 0.00 4.35
1917 2529 2.742053 CACCAACGATCGAATGAAAGGT 59.258 45.455 24.34 14.25 0.00 3.50
1923 2535 1.059122 CGTGTCACCAACGATCGAATG 59.941 52.381 24.34 18.96 43.68 2.67
1945 2557 2.335011 CTGCGCCCATATCGTCGA 59.665 61.111 4.18 0.00 0.00 4.20
1952 2564 2.685829 CGTTGTTGCTGCGCCCATA 61.686 57.895 4.18 0.00 0.00 2.74
1955 2567 3.667429 GATCGTTGTTGCTGCGCCC 62.667 63.158 4.18 0.00 0.00 6.13
1957 2569 1.082169 TTGATCGTTGTTGCTGCGC 60.082 52.632 0.00 0.00 0.00 6.09
1959 2571 0.725784 CCGTTGATCGTTGTTGCTGC 60.726 55.000 0.00 0.00 37.94 5.25
1960 2572 0.865111 TCCGTTGATCGTTGTTGCTG 59.135 50.000 0.00 0.00 37.94 4.41
1961 2573 1.464608 CATCCGTTGATCGTTGTTGCT 59.535 47.619 0.00 0.00 37.94 3.91
1962 2574 1.196808 ACATCCGTTGATCGTTGTTGC 59.803 47.619 0.00 0.00 37.94 4.17
1963 2575 3.536158 AACATCCGTTGATCGTTGTTG 57.464 42.857 0.00 0.00 40.12 3.33
1964 2576 5.873179 ATTAACATCCGTTGATCGTTGTT 57.127 34.783 6.68 6.68 42.33 2.83
1965 2577 5.873179 AATTAACATCCGTTGATCGTTGT 57.127 34.783 0.00 0.00 36.52 3.32
1966 2578 8.835467 AATTAATTAACATCCGTTGATCGTTG 57.165 30.769 0.00 0.00 36.52 4.10
1994 2609 2.216263 GCGCGCATGGATTTTTGAATAC 59.784 45.455 29.10 0.00 0.00 1.89
2011 2627 4.320928 TTCCAACAAAGGCGCGCG 62.321 61.111 28.44 28.44 0.00 6.86
2014 2630 0.667184 CCATGTTCCAACAAAGGCGC 60.667 55.000 0.00 0.00 43.03 6.53
2021 2637 3.708631 ACAACAATTCCCATGTTCCAACA 59.291 39.130 0.00 0.00 44.06 3.33
2031 2648 6.245890 AGGAAAATGAAACAACAATTCCCA 57.754 33.333 0.00 0.00 38.96 4.37
2065 2682 7.653647 ACATAAATTTTGTCGAAGTTTAGCCA 58.346 30.769 0.00 0.00 34.30 4.75
2073 2690 9.243637 TCTTTGGAAACATAAATTTTGTCGAAG 57.756 29.630 0.00 5.53 42.32 3.79
2110 2727 1.810755 ACTTGTCTCACATGCATGCAG 59.189 47.619 26.69 21.02 0.00 4.41
2135 2762 9.986157 ATTGAATGGCATATATATTTCCTGTCT 57.014 29.630 0.00 0.00 0.00 3.41
2150 2777 5.951747 ACTAGTACCAACAATTGAATGGCAT 59.048 36.000 25.08 17.08 37.77 4.40
2151 2778 5.321102 ACTAGTACCAACAATTGAATGGCA 58.679 37.500 25.08 15.64 37.77 4.92
2163 3110 5.803967 GCACACATACACTACTAGTACCAAC 59.196 44.000 0.00 0.00 0.00 3.77
2169 3116 4.870426 GCATTGCACACATACACTACTAGT 59.130 41.667 3.15 0.00 0.00 2.57
2170 3117 5.111989 AGCATTGCACACATACACTACTAG 58.888 41.667 11.91 0.00 0.00 2.57
2171 3118 5.084818 AGCATTGCACACATACACTACTA 57.915 39.130 11.91 0.00 0.00 1.82
2172 3119 3.942829 AGCATTGCACACATACACTACT 58.057 40.909 11.91 0.00 0.00 2.57
2191 3138 4.606457 ACATAGTCGCTGAAAATGAAGC 57.394 40.909 0.00 0.00 36.03 3.86
2195 3142 8.906693 CAGTATACTACATAGTCGCTGAAAATG 58.093 37.037 4.74 0.00 37.73 2.32
2196 3143 8.630917 ACAGTATACTACATAGTCGCTGAAAAT 58.369 33.333 4.74 0.61 37.73 1.82
2198 3145 7.563888 ACAGTATACTACATAGTCGCTGAAA 57.436 36.000 4.74 0.00 37.73 2.69
2201 3148 6.072098 CGAACAGTATACTACATAGTCGCTG 58.928 44.000 4.74 12.18 37.73 5.18
2202 3149 5.757320 ACGAACAGTATACTACATAGTCGCT 59.243 40.000 4.74 0.00 37.73 4.93
2204 3151 7.170240 TGACGAACAGTATACTACATAGTCG 57.830 40.000 4.74 10.37 37.73 4.18
2206 3153 8.775527 CAGATGACGAACAGTATACTACATAGT 58.224 37.037 4.74 2.74 40.24 2.12
2207 3154 8.775527 ACAGATGACGAACAGTATACTACATAG 58.224 37.037 4.74 0.00 0.00 2.23
2209 3156 7.569639 ACAGATGACGAACAGTATACTACAT 57.430 36.000 4.74 5.11 0.00 2.29
2225 3189 8.321716 GTCATCAAGTTTCGTTATACAGATGAC 58.678 37.037 13.70 13.70 43.44 3.06
2235 3199 7.698628 TGTGAAATTGTCATCAAGTTTCGTTA 58.301 30.769 0.00 0.00 41.00 3.18
2341 3305 6.636447 TGTGTGCTTGTCGAAAAATAATCTTG 59.364 34.615 0.00 0.00 0.00 3.02
2343 3307 6.312399 TGTGTGCTTGTCGAAAAATAATCT 57.688 33.333 0.00 0.00 0.00 2.40
2357 3321 4.923893 TCTGATGAAAAGTTGTGTGCTTG 58.076 39.130 0.00 0.00 0.00 4.01
2397 3361 3.124636 CCCGTACACAAAATGTAGCAGAC 59.875 47.826 0.00 0.00 44.65 3.51
2401 3365 2.160813 CCACCCGTACACAAAATGTAGC 59.839 50.000 0.00 0.00 44.65 3.58
2438 3402 4.481112 GGACGGGCTGCAAATGCG 62.481 66.667 0.50 0.00 45.83 4.73
2453 3417 2.819595 GCATTTCTGCGCCTCGGA 60.820 61.111 4.18 0.00 38.92 4.55
2486 3450 2.137523 GGCACTTTGACAATTTGCTGG 58.862 47.619 16.81 0.00 33.55 4.85
2490 3454 3.302610 CGCTTTGGCACTTTGACAATTTG 60.303 43.478 0.00 0.00 46.11 2.32
2513 3477 2.475111 GCAATATAGCTCGCGCTTTGTA 59.525 45.455 4.69 0.00 46.47 2.41
2569 3533 6.183360 CGAACCCAATTGTATTAGAGGGAAAC 60.183 42.308 4.43 0.00 39.60 2.78
2588 3552 2.183555 CCGCACCTAGACGAACCC 59.816 66.667 0.00 0.00 0.00 4.11
2616 3581 0.866906 TCACACGTCGTCGGTTTCAC 60.867 55.000 7.05 0.00 41.85 3.18
2671 3636 1.240256 ACTCAGACCGAGACACTCAC 58.760 55.000 0.00 0.00 45.45 3.51
2772 3737 2.073816 CGAACATATCCGGCATTACCC 58.926 52.381 0.00 0.00 33.26 3.69
2799 3768 2.106683 CCGTTGTTCATCCGAGGCC 61.107 63.158 0.00 0.00 0.00 5.19
2801 3770 2.452813 CGCCGTTGTTCATCCGAGG 61.453 63.158 0.00 0.00 0.00 4.63
2802 3771 1.011968 TTCGCCGTTGTTCATCCGAG 61.012 55.000 0.00 0.00 0.00 4.63
2815 3796 1.577328 AAGTTGCCATGACTTCGCCG 61.577 55.000 0.00 0.00 32.04 6.46
2826 3809 9.436957 TGTTGTTTAAAAAGAAATAAGTTGCCA 57.563 25.926 0.00 0.00 0.00 4.92
2835 3818 9.646427 TGTGCTAGTTGTTGTTTAAAAAGAAAT 57.354 25.926 0.00 0.00 0.00 2.17
2836 3819 9.477484 TTGTGCTAGTTGTTGTTTAAAAAGAAA 57.523 25.926 0.00 0.00 0.00 2.52
2837 3820 9.477484 TTTGTGCTAGTTGTTGTTTAAAAAGAA 57.523 25.926 0.00 0.00 0.00 2.52
2839 3822 9.687717 CATTTGTGCTAGTTGTTGTTTAAAAAG 57.312 29.630 0.00 0.00 0.00 2.27
2865 3851 0.379669 CCCATTGCAATCAGACGAGC 59.620 55.000 9.53 0.00 0.00 5.03
2871 3857 7.098477 TGTAAAATTTCTCCCATTGCAATCAG 58.902 34.615 9.53 6.11 0.00 2.90
2874 3860 7.396418 ACATGTAAAATTTCTCCCATTGCAAT 58.604 30.769 5.99 5.99 0.00 3.56
2890 3876 8.894731 TGCCGCTAATTCTAAATACATGTAAAA 58.105 29.630 10.14 0.63 0.00 1.52
2903 3889 4.475051 TTACCACTTGCCGCTAATTCTA 57.525 40.909 0.00 0.00 0.00 2.10
2959 3949 0.323178 AGAAGAAGCGACGGGTAGGA 60.323 55.000 0.00 0.00 0.00 2.94
2960 3950 1.386533 TAGAAGAAGCGACGGGTAGG 58.613 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.