Multiple sequence alignment - TraesCS6A01G042900

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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 TraesCS6A01G042900 chr6A 100.000 4079 0 0 1 4079 22546015 22550093 0.000000e+00 7533.0
1 TraesCS6A01G042900 chr6A 77.615 478 95 12 2111 2582 22643615 22644086 3.100000e-71 279.0
2 TraesCS6A01G042900 chr6A 96.491 57 2 0 4023 4079 147933679 147933735 1.210000e-15 95.3
3 TraesCS6A01G042900 chr6A 96.364 55 2 0 4025 4079 770226 770172 1.560000e-14 91.6
4 TraesCS6A01G042900 chr6D 96.627 2935 76 13 242 3162 24021711 24024636 0.000000e+00 4850.0
5 TraesCS6A01G042900 chr6D 89.180 610 62 4 3420 4026 24025840 24026448 0.000000e+00 758.0
6 TraesCS6A01G042900 chr6D 95.181 166 8 0 71 236 24020154 24020319 3.130000e-66 263.0
7 TraesCS6A01G042900 chr6D 76.778 478 99 12 2111 2582 24199224 24198753 1.450000e-64 257.0
8 TraesCS6A01G042900 chr6B 94.472 2840 99 19 640 3443 38925234 38928051 0.000000e+00 4322.0
9 TraesCS6A01G042900 chr6B 74.200 1000 209 39 1600 2582 39063434 39062467 4.980000e-99 372.0
10 TraesCS6A01G042900 chr6B 91.667 240 18 2 3789 4026 38930918 38931157 8.450000e-87 331.0
11 TraesCS6A01G042900 chr6B 85.385 130 10 5 3474 3603 38928441 38928561 4.280000e-25 126.0
12 TraesCS6A01G042900 chr6B 95.312 64 2 1 4016 4079 476430490 476430552 2.590000e-17 100.0
13 TraesCS6A01G042900 chr4A 88.968 562 61 1 76 636 496113272 496112711 0.000000e+00 693.0
14 TraesCS6A01G042900 chr4A 83.612 299 47 2 71 368 603032930 603033227 3.100000e-71 279.0
15 TraesCS6A01G042900 chr4A 93.750 64 3 1 4016 4079 142956454 142956392 1.210000e-15 95.3
16 TraesCS6A01G042900 chr2B 85.940 569 71 6 71 636 245121778 245121216 2.100000e-167 599.0
17 TraesCS6A01G042900 chr2B 74.731 558 131 10 85 636 560881094 560880541 1.470000e-59 241.0
18 TraesCS6A01G042900 chr2B 75.214 468 106 10 1409 1871 640599476 640599938 3.190000e-51 213.0
19 TraesCS6A01G042900 chr2A 73.752 1642 373 44 1409 3030 680262003 680263606 3.510000e-165 592.0
20 TraesCS6A01G042900 chr2A 75.828 513 115 9 76 582 566475486 566475995 6.770000e-63 252.0
21 TraesCS6A01G042900 chr2A 87.143 70 9 0 1528 1597 758881632 758881701 3.380000e-11 80.5
22 TraesCS6A01G042900 chr2D 73.752 1642 364 50 1409 3030 537929120 537930714 2.110000e-162 582.0
23 TraesCS6A01G042900 chr2D 76.550 516 107 13 76 582 420747096 420747606 1.870000e-68 270.0
24 TraesCS6A01G042900 chr2D 75.000 468 105 12 177 637 94726733 94726271 5.340000e-49 206.0
25 TraesCS6A01G042900 chr2D 92.982 57 4 0 1528 1584 629074954 629075010 2.610000e-12 84.2
26 TraesCS6A01G042900 chr4B 80.995 563 104 3 74 633 245635119 245634557 1.040000e-120 444.0
27 TraesCS6A01G042900 chr3A 73.019 467 117 9 177 637 64342112 64342575 5.460000e-34 156.0
28 TraesCS6A01G042900 chr5D 98.182 55 1 0 4025 4079 256754794 256754740 3.360000e-16 97.1
29 TraesCS6A01G042900 chr4D 98.182 55 1 0 4025 4079 216168816 216168870 3.360000e-16 97.1
30 TraesCS6A01G042900 chr5B 98.148 54 1 0 4024 4077 615936795 615936742 1.210000e-15 95.3
31 TraesCS6A01G042900 chr7A 96.429 56 2 0 4024 4079 198479832 198479887 4.340000e-15 93.5
32 TraesCS6A01G042900 chr1D 96.364 55 2 0 4025 4079 379600483 379600429 1.560000e-14 91.6
33 TraesCS6A01G042900 chrUn 73.387 248 59 5 82 325 26510736 26510980 7.260000e-13 86.1
34 TraesCS6A01G042900 chr3B 91.667 48 4 0 535 582 159988485 159988532 2.630000e-07 67.6


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 TraesCS6A01G042900 chr6A 22546015 22550093 4078 False 7533 7533 100.000000 1 4079 1 chr6A.!!$F1 4078
1 TraesCS6A01G042900 chr6D 24020154 24026448 6294 False 1957 4850 93.662667 71 4026 3 chr6D.!!$F1 3955
2 TraesCS6A01G042900 chr6B 38925234 38931157 5923 False 1593 4322 90.508000 640 4026 3 chr6B.!!$F2 3386
3 TraesCS6A01G042900 chr6B 39062467 39063434 967 True 372 372 74.200000 1600 2582 1 chr6B.!!$R1 982
4 TraesCS6A01G042900 chr4A 496112711 496113272 561 True 693 693 88.968000 76 636 1 chr4A.!!$R2 560
5 TraesCS6A01G042900 chr2B 245121216 245121778 562 True 599 599 85.940000 71 636 1 chr2B.!!$R1 565
6 TraesCS6A01G042900 chr2B 560880541 560881094 553 True 241 241 74.731000 85 636 1 chr2B.!!$R2 551
7 TraesCS6A01G042900 chr2A 680262003 680263606 1603 False 592 592 73.752000 1409 3030 1 chr2A.!!$F2 1621
8 TraesCS6A01G042900 chr2A 566475486 566475995 509 False 252 252 75.828000 76 582 1 chr2A.!!$F1 506
9 TraesCS6A01G042900 chr2D 537929120 537930714 1594 False 582 582 73.752000 1409 3030 1 chr2D.!!$F2 1621
10 TraesCS6A01G042900 chr2D 420747096 420747606 510 False 270 270 76.550000 76 582 1 chr2D.!!$F1 506
11 TraesCS6A01G042900 chr4B 245634557 245635119 562 True 444 444 80.995000 74 633 1 chr4B.!!$R1 559

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
897 2316 2.351418 TCGTGTGTCTTTGCTTTGTCTG 59.649 45.455 0.0 0.0 0.00 3.51 F
1254 2673 0.462759 GGCTGCTGGAGTACATGGAC 60.463 60.000 0.0 0.0 0.00 4.02 F
2306 3761 0.032952 TTCTGCAACGTCTACGGCTT 59.967 50.000 7.5 0.0 44.95 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 3761 0.037326 GTTCATGTCAGTGAGGCCGA 60.037 55.0 0.00 0.00 0.00 5.54 R
3075 4533 0.804989 GTTGCACACCATGGAGCTAC 59.195 55.0 21.47 20.24 0.00 3.58 R
3701 8177 0.031585 CTCACCGACGTTGGAGAACA 59.968 55.0 29.00 3.92 31.78 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
22 23 4.402056 AAAAAGTCTCGGTCAAGTGAGA 57.598 40.909 0.00 0.00 38.85 3.27
23 24 4.402056 AAAAGTCTCGGTCAAGTGAGAA 57.598 40.909 0.00 0.00 42.49 2.87
24 25 4.402056 AAAGTCTCGGTCAAGTGAGAAA 57.598 40.909 0.00 0.00 42.49 2.52
25 26 4.402056 AAGTCTCGGTCAAGTGAGAAAA 57.598 40.909 0.00 0.00 42.49 2.29
26 27 3.718815 AGTCTCGGTCAAGTGAGAAAAC 58.281 45.455 0.00 0.00 42.49 2.43
27 28 3.132289 AGTCTCGGTCAAGTGAGAAAACA 59.868 43.478 0.00 0.00 42.49 2.83
28 29 4.058817 GTCTCGGTCAAGTGAGAAAACAT 58.941 43.478 0.00 0.00 42.49 2.71
29 30 5.010719 AGTCTCGGTCAAGTGAGAAAACATA 59.989 40.000 0.00 0.00 42.49 2.29
30 31 5.118817 GTCTCGGTCAAGTGAGAAAACATAC 59.881 44.000 0.00 0.00 42.49 2.39
31 32 4.951254 TCGGTCAAGTGAGAAAACATACA 58.049 39.130 0.00 0.00 0.00 2.29
32 33 5.361427 TCGGTCAAGTGAGAAAACATACAA 58.639 37.500 0.00 0.00 0.00 2.41
33 34 5.818336 TCGGTCAAGTGAGAAAACATACAAA 59.182 36.000 0.00 0.00 0.00 2.83
34 35 6.316640 TCGGTCAAGTGAGAAAACATACAAAA 59.683 34.615 0.00 0.00 0.00 2.44
35 36 6.970043 CGGTCAAGTGAGAAAACATACAAAAA 59.030 34.615 0.00 0.00 0.00 1.94
101 102 6.260714 CCTTAAAAGCTTGCCACAAGAAAATT 59.739 34.615 11.38 3.27 0.00 1.82
293 1682 4.730657 CTGCCAATCATCAAACTCTTCAC 58.269 43.478 0.00 0.00 0.00 3.18
421 1811 2.972348 AGGGTAGTCTCTCCACACAAA 58.028 47.619 0.00 0.00 0.00 2.83
422 1812 3.314693 AGGGTAGTCTCTCCACACAAAA 58.685 45.455 0.00 0.00 0.00 2.44
470 1862 4.623647 GCCATTGCCAACCACAAATCTAAT 60.624 41.667 0.00 0.00 0.00 1.73
471 1863 4.871557 CCATTGCCAACCACAAATCTAATG 59.128 41.667 0.00 0.00 0.00 1.90
512 1904 5.121925 GTCGGACTTTAACAAGATCTTTCCC 59.878 44.000 4.86 0.00 33.72 3.97
803 2198 6.765512 AGAGCTGAGAAAATATAGCAAACCTC 59.234 38.462 0.00 0.00 38.59 3.85
856 2251 3.721087 TGAGACTCTTCCCCATTTTCC 57.279 47.619 3.68 0.00 0.00 3.13
889 2308 2.538939 GGTTCTGTTCGTGTGTCTTTGC 60.539 50.000 0.00 0.00 0.00 3.68
897 2316 2.351418 TCGTGTGTCTTTGCTTTGTCTG 59.649 45.455 0.00 0.00 0.00 3.51
916 2335 4.389077 GTCTGTCTATCAAACGAACCAAGG 59.611 45.833 0.00 0.00 0.00 3.61
966 2385 5.717119 CCAAGAAATTCCTCAATCAACCAG 58.283 41.667 0.00 0.00 0.00 4.00
997 2416 4.319694 TTTCTTGTGAAGATCGACGTACGA 60.320 41.667 24.41 11.45 43.17 3.43
1226 2645 2.792599 CTTCTACCTCTCGCGCGT 59.207 61.111 30.98 12.90 0.00 6.01
1254 2673 0.462759 GGCTGCTGGAGTACATGGAC 60.463 60.000 0.00 0.00 0.00 4.02
1257 2676 0.530744 TGCTGGAGTACATGGACGTC 59.469 55.000 7.13 7.13 0.00 4.34
1278 2697 4.410400 CACCTCCCCTTCACCCGC 62.410 72.222 0.00 0.00 0.00 6.13
1290 2709 2.526873 ACCCGCCAGGAGAACACT 60.527 61.111 0.00 0.00 41.02 3.55
1578 2997 3.649986 AGCTTCAACACGCCGCAC 61.650 61.111 0.00 0.00 0.00 5.34
2067 3522 2.743928 CAGCCGTTCCAGCACCTC 60.744 66.667 0.00 0.00 0.00 3.85
2306 3761 0.032952 TTCTGCAACGTCTACGGCTT 59.967 50.000 7.50 0.00 44.95 4.35
2359 3814 2.719979 CCAAGATCGCCATGCTGC 59.280 61.111 0.00 0.00 0.00 5.25
2676 4134 4.069232 CTGAGCGTCGGCCAGGAA 62.069 66.667 2.24 0.00 41.24 3.36
2898 4356 4.681978 GAGCGCACGGACCCTGTT 62.682 66.667 11.47 0.00 0.00 3.16
3081 4539 4.570663 ATGCCCGCGACGTAGCTC 62.571 66.667 18.58 8.07 34.40 4.09
3087 4545 2.494918 GCGACGTAGCTCCATGGT 59.505 61.111 13.82 0.00 0.00 3.55
3119 4577 3.185797 GTGCTTCGTGTAGGTTAACCAAG 59.814 47.826 26.26 18.94 38.89 3.61
3171 5610 9.706529 TCAGGCATATAGATCTTAGATGTGTAT 57.293 33.333 0.00 0.95 0.00 2.29
3172 5611 9.747293 CAGGCATATAGATCTTAGATGTGTATG 57.253 37.037 22.57 22.57 0.00 2.39
3375 5818 4.528596 ACTTAACTGACATCTAGCCACACT 59.471 41.667 0.00 0.00 0.00 3.55
3440 5883 9.271828 ACAAAGATTTTGATTTTGGGTATGTTC 57.728 29.630 8.41 0.00 36.41 3.18
3447 5890 6.147437 TGATTTTGGGTATGTTCTTAGGGT 57.853 37.500 0.00 0.00 0.00 4.34
3467 5910 3.493873 GGTCACCTATACGTGATTTCCCC 60.494 52.174 7.67 1.58 44.27 4.81
3469 5912 2.704065 CACCTATACGTGATTTCCCCCT 59.296 50.000 0.00 0.00 35.68 4.79
3519 6322 5.762179 TGGATTCAGATTCAACAGGTACT 57.238 39.130 0.00 0.00 43.88 2.73
3520 6323 6.867519 TGGATTCAGATTCAACAGGTACTA 57.132 37.500 0.00 0.00 36.02 1.82
3560 6363 3.243201 GCCTAACCAGATGCATTGCTTAC 60.243 47.826 10.49 1.57 0.00 2.34
3590 6393 2.252072 TAATCGCCGCCTGAAAGCCT 62.252 55.000 0.00 0.00 0.00 4.58
3639 8115 1.883021 GGGCTTTGTTGTGCGCTAT 59.117 52.632 9.73 0.00 38.77 2.97
3643 8119 1.464608 GCTTTGTTGTGCGCTATCTCA 59.535 47.619 9.73 0.00 0.00 3.27
3653 8129 1.938926 GCGCTATCTCATGCTCCCTTC 60.939 57.143 0.00 0.00 0.00 3.46
3667 8143 2.187946 CTTCCCGCTCGAGCCATT 59.812 61.111 30.66 0.00 37.91 3.16
3692 8168 2.819284 CCGGGCATCTTCTACCCCC 61.819 68.421 0.00 0.00 40.86 5.40
3710 8186 1.214305 CCCCTCCCCATGTTCTCCAA 61.214 60.000 0.00 0.00 0.00 3.53
3713 8189 0.324943 CTCCCCATGTTCTCCAACGT 59.675 55.000 0.00 0.00 34.95 3.99
3717 8193 0.320421 CCATGTTCTCCAACGTCGGT 60.320 55.000 0.00 0.00 34.95 4.69
3725 8201 2.432628 CAACGTCGGTGAGGAGCC 60.433 66.667 3.57 0.00 0.00 4.70
3726 8202 3.692406 AACGTCGGTGAGGAGCCC 61.692 66.667 0.00 0.00 0.00 5.19
3786 8262 4.678499 TGTGATGCCGCTGTCGCA 62.678 61.111 8.03 8.03 35.30 5.10
3818 8792 4.785453 CCTGGCCAAGACCTCGCC 62.785 72.222 7.01 0.00 43.32 5.54
3851 8825 1.970114 CACTGGGGCTCACTGCAAG 60.970 63.158 0.00 0.00 45.15 4.01
3914 8890 6.046593 ACAAAATCGACTAATGCGAGGAATA 58.953 36.000 0.00 0.00 41.49 1.75
3927 8903 5.101628 TGCGAGGAATATTTTCAATTGCAC 58.898 37.500 0.00 0.00 35.87 4.57
3958 8934 5.047377 TGCCAAAACCATTCTTAAGATGGAC 60.047 40.000 27.06 16.91 38.75 4.02
4011 8987 5.303971 ACAGATATAGGCATTTGTGAGAGC 58.696 41.667 0.00 0.00 0.00 4.09
4026 9002 5.280945 TGTGAGAGCAGCAAATTTTGTTAC 58.719 37.500 10.65 0.00 0.00 2.50
4027 9003 5.067674 TGTGAGAGCAGCAAATTTTGTTACT 59.932 36.000 10.65 4.85 0.00 2.24
4028 9004 5.626955 GTGAGAGCAGCAAATTTTGTTACTC 59.373 40.000 14.87 14.87 0.00 2.59
4029 9005 5.126396 AGAGCAGCAAATTTTGTTACTCC 57.874 39.130 17.60 5.57 0.00 3.85
4030 9006 4.021981 AGAGCAGCAAATTTTGTTACTCCC 60.022 41.667 17.60 1.45 0.00 4.30
4031 9007 3.897505 AGCAGCAAATTTTGTTACTCCCT 59.102 39.130 10.65 0.00 0.00 4.20
4032 9008 4.021981 AGCAGCAAATTTTGTTACTCCCTC 60.022 41.667 10.65 0.00 0.00 4.30
4033 9009 4.809673 CAGCAAATTTTGTTACTCCCTCC 58.190 43.478 10.65 0.00 0.00 4.30
4034 9010 4.524328 CAGCAAATTTTGTTACTCCCTCCT 59.476 41.667 10.65 0.00 0.00 3.69
4035 9011 5.011023 CAGCAAATTTTGTTACTCCCTCCTT 59.989 40.000 10.65 0.00 0.00 3.36
4036 9012 5.602561 AGCAAATTTTGTTACTCCCTCCTTT 59.397 36.000 10.65 0.00 0.00 3.11
4037 9013 5.926542 GCAAATTTTGTTACTCCCTCCTTTC 59.073 40.000 10.65 0.00 0.00 2.62
4038 9014 6.462347 GCAAATTTTGTTACTCCCTCCTTTCA 60.462 38.462 10.65 0.00 0.00 2.69
4039 9015 7.670364 CAAATTTTGTTACTCCCTCCTTTCAT 58.330 34.615 0.78 0.00 0.00 2.57
4040 9016 7.468141 AATTTTGTTACTCCCTCCTTTCATC 57.532 36.000 0.00 0.00 0.00 2.92
4041 9017 5.843019 TTTGTTACTCCCTCCTTTCATCT 57.157 39.130 0.00 0.00 0.00 2.90
4042 9018 6.945636 TTTGTTACTCCCTCCTTTCATCTA 57.054 37.500 0.00 0.00 0.00 1.98
4043 9019 7.510675 TTTGTTACTCCCTCCTTTCATCTAT 57.489 36.000 0.00 0.00 0.00 1.98
4044 9020 8.618240 TTTGTTACTCCCTCCTTTCATCTATA 57.382 34.615 0.00 0.00 0.00 1.31
4045 9021 8.798975 TTGTTACTCCCTCCTTTCATCTATAT 57.201 34.615 0.00 0.00 0.00 0.86
4046 9022 9.892444 TTGTTACTCCCTCCTTTCATCTATATA 57.108 33.333 0.00 0.00 0.00 0.86
4047 9023 9.535170 TGTTACTCCCTCCTTTCATCTATATAG 57.465 37.037 3.10 3.10 0.00 1.31
4048 9024 8.973182 GTTACTCCCTCCTTTCATCTATATAGG 58.027 40.741 9.89 0.00 0.00 2.57
4049 9025 6.507568 ACTCCCTCCTTTCATCTATATAGGG 58.492 44.000 9.89 0.00 43.23 3.53
4050 9026 5.281314 TCCCTCCTTTCATCTATATAGGGC 58.719 45.833 9.89 0.00 41.88 5.19
4051 9027 4.410555 CCCTCCTTTCATCTATATAGGGCC 59.589 50.000 9.89 0.00 36.30 5.80
4052 9028 5.284582 CCTCCTTTCATCTATATAGGGCCT 58.715 45.833 12.58 12.58 0.00 5.19
4053 9029 6.444704 CCTCCTTTCATCTATATAGGGCCTA 58.555 44.000 17.16 17.16 0.00 3.93
4054 9030 6.903534 CCTCCTTTCATCTATATAGGGCCTAA 59.096 42.308 18.91 7.61 0.00 2.69
4055 9031 7.570607 CCTCCTTTCATCTATATAGGGCCTAAT 59.429 40.741 18.91 14.19 0.00 1.73
4056 9032 9.661954 CTCCTTTCATCTATATAGGGCCTAATA 57.338 37.037 18.91 14.53 0.00 0.98
4057 9033 9.435570 TCCTTTCATCTATATAGGGCCTAATAC 57.564 37.037 18.91 0.00 0.00 1.89
4058 9034 8.361139 CCTTTCATCTATATAGGGCCTAATACG 58.639 40.741 18.91 7.12 0.00 3.06
4059 9035 8.834004 TTTCATCTATATAGGGCCTAATACGT 57.166 34.615 18.91 2.76 0.00 3.57
4060 9036 8.834004 TTCATCTATATAGGGCCTAATACGTT 57.166 34.615 18.91 1.94 0.00 3.99
4061 9037 8.834004 TCATCTATATAGGGCCTAATACGTTT 57.166 34.615 18.91 1.12 0.00 3.60
4062 9038 9.263446 TCATCTATATAGGGCCTAATACGTTTT 57.737 33.333 18.91 0.30 0.00 2.43
4063 9039 9.886132 CATCTATATAGGGCCTAATACGTTTTT 57.114 33.333 18.91 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.402056 TCTCACTTGACCGAGACTTTTT 57.598 40.909 0.00 0.00 33.37 1.94
2 3 4.402056 TTCTCACTTGACCGAGACTTTT 57.598 40.909 0.00 0.00 37.99 2.27
3 4 4.402056 TTTCTCACTTGACCGAGACTTT 57.598 40.909 0.00 0.00 37.99 2.66
4 5 4.120589 GTTTTCTCACTTGACCGAGACTT 58.879 43.478 0.00 0.00 37.99 3.01
5 6 3.132289 TGTTTTCTCACTTGACCGAGACT 59.868 43.478 0.00 0.00 37.99 3.24
6 7 3.454375 TGTTTTCTCACTTGACCGAGAC 58.546 45.455 0.00 0.00 37.99 3.36
8 9 4.988540 TGTATGTTTTCTCACTTGACCGAG 59.011 41.667 0.00 0.00 0.00 4.63
9 10 4.951254 TGTATGTTTTCTCACTTGACCGA 58.049 39.130 0.00 0.00 0.00 4.69
10 11 5.666969 TTGTATGTTTTCTCACTTGACCG 57.333 39.130 0.00 0.00 0.00 4.79
47 48 8.562892 CGCCATGATTGAGACTTTTATATTCTT 58.437 33.333 0.00 0.00 0.00 2.52
48 49 7.933577 TCGCCATGATTGAGACTTTTATATTCT 59.066 33.333 0.00 0.00 0.00 2.40
49 50 8.012241 GTCGCCATGATTGAGACTTTTATATTC 58.988 37.037 0.00 0.00 31.76 1.75
50 51 7.041098 GGTCGCCATGATTGAGACTTTTATATT 60.041 37.037 0.00 0.00 33.61 1.28
51 52 6.428159 GGTCGCCATGATTGAGACTTTTATAT 59.572 38.462 0.00 0.00 33.61 0.86
52 53 5.758296 GGTCGCCATGATTGAGACTTTTATA 59.242 40.000 0.00 0.00 33.61 0.98
53 54 4.576463 GGTCGCCATGATTGAGACTTTTAT 59.424 41.667 0.00 0.00 33.61 1.40
54 55 3.938963 GGTCGCCATGATTGAGACTTTTA 59.061 43.478 0.00 0.00 33.61 1.52
55 56 2.749621 GGTCGCCATGATTGAGACTTTT 59.250 45.455 0.00 0.00 33.61 2.27
56 57 2.359900 GGTCGCCATGATTGAGACTTT 58.640 47.619 0.00 0.00 33.61 2.66
57 58 1.407437 GGGTCGCCATGATTGAGACTT 60.407 52.381 0.00 0.00 33.61 3.01
58 59 0.179000 GGGTCGCCATGATTGAGACT 59.821 55.000 0.00 0.00 33.61 3.24
59 60 0.179000 AGGGTCGCCATGATTGAGAC 59.821 55.000 0.00 0.00 32.87 3.36
60 61 0.911769 AAGGGTCGCCATGATTGAGA 59.088 50.000 0.00 0.00 0.00 3.27
61 62 2.620251 TAAGGGTCGCCATGATTGAG 57.380 50.000 0.00 0.00 0.00 3.02
62 63 3.358111 TTTAAGGGTCGCCATGATTGA 57.642 42.857 0.00 0.00 0.00 2.57
63 64 3.734902 GCTTTTAAGGGTCGCCATGATTG 60.735 47.826 0.00 0.00 0.00 2.67
64 65 2.427095 GCTTTTAAGGGTCGCCATGATT 59.573 45.455 0.00 0.00 0.00 2.57
65 66 2.024414 GCTTTTAAGGGTCGCCATGAT 58.976 47.619 0.00 0.00 0.00 2.45
66 67 1.004277 AGCTTTTAAGGGTCGCCATGA 59.996 47.619 0.00 0.00 0.00 3.07
67 68 1.463674 AGCTTTTAAGGGTCGCCATG 58.536 50.000 0.00 0.00 0.00 3.66
68 69 1.818674 CAAGCTTTTAAGGGTCGCCAT 59.181 47.619 0.00 0.00 0.00 4.40
69 70 1.243902 CAAGCTTTTAAGGGTCGCCA 58.756 50.000 0.00 0.00 0.00 5.69
101 102 4.686122 GCTCGGATTCCTCCCAAGATTAAA 60.686 45.833 0.30 0.00 38.45 1.52
293 1682 4.544689 CCGGCGCTCTCTGTCTCG 62.545 72.222 7.64 0.00 0.00 4.04
498 1890 3.412386 CCAGTTCGGGAAAGATCTTGTT 58.588 45.455 9.17 0.00 0.00 2.83
512 1904 4.367023 TCGGCGGTTCCCAGTTCG 62.367 66.667 7.21 0.00 0.00 3.95
693 2085 5.583854 CACTATCTGCTTGCTTCACTAACAT 59.416 40.000 0.00 0.00 0.00 2.71
719 2111 6.694447 AGACTCATGCAAGCAAAAATAACAT 58.306 32.000 0.00 0.00 0.00 2.71
722 2117 6.424509 CCAAAGACTCATGCAAGCAAAAATAA 59.575 34.615 0.00 0.00 0.00 1.40
803 2198 9.788960 GGTTAGGAAGCATTTTCTAATTAAGTG 57.211 33.333 0.00 0.00 30.84 3.16
889 2308 5.465390 TGGTTCGTTTGATAGACAGACAAAG 59.535 40.000 0.00 0.00 34.86 2.77
897 2316 3.071479 TGCCTTGGTTCGTTTGATAGAC 58.929 45.455 0.00 0.00 0.00 2.59
966 2385 5.091431 CGATCTTCACAAGAAATTCAAGGC 58.909 41.667 0.00 0.00 41.63 4.35
997 2416 1.945819 GCATGTGTCCGACTCCATTGT 60.946 52.381 0.00 0.00 0.00 2.71
1226 2645 4.478371 CCAGCAGCCGGATGAGCA 62.478 66.667 26.87 0.00 33.82 4.26
1254 2673 2.284699 AAGGGGAGGTGGGAGACG 60.285 66.667 0.00 0.00 0.00 4.18
1257 2676 2.301738 GGTGAAGGGGAGGTGGGAG 61.302 68.421 0.00 0.00 0.00 4.30
1278 2697 1.625315 TGGATCACAGTGTTCTCCTGG 59.375 52.381 17.64 0.00 34.16 4.45
1290 2709 1.591703 GACGCAGGTCTGGATCACA 59.408 57.895 0.00 0.00 40.15 3.58
1350 2769 2.599597 CCCATGGCCAGGAGGAAG 59.400 66.667 21.32 0.51 36.89 3.46
1590 3009 3.368571 GACACCTGCAGCTTGGCC 61.369 66.667 8.66 0.00 0.00 5.36
1830 3249 0.390860 CGATGTAGGGCCAGAGGAAG 59.609 60.000 6.18 0.00 0.00 3.46
2306 3761 0.037326 GTTCATGTCAGTGAGGCCGA 60.037 55.000 0.00 0.00 0.00 5.54
2359 3814 1.443872 CGACCCACGAACCGAAGAG 60.444 63.158 0.00 0.00 45.77 2.85
3072 4530 1.084370 GCACACCATGGAGCTACGTC 61.084 60.000 21.47 0.00 0.00 4.34
3075 4533 0.804989 GTTGCACACCATGGAGCTAC 59.195 55.000 21.47 20.24 0.00 3.58
3081 4539 1.008652 CACACGTTGCACACCATGG 60.009 57.895 11.19 11.19 0.00 3.66
3171 5610 1.933181 CTTGCAGTCGAGTTGAACACA 59.067 47.619 0.00 0.00 0.00 3.72
3172 5611 1.933853 ACTTGCAGTCGAGTTGAACAC 59.066 47.619 0.00 0.00 33.10 3.32
3220 5659 7.173218 TCACTGAGATTTAGCAAAACTGTTAGG 59.827 37.037 0.00 0.00 0.00 2.69
3231 5670 4.284490 ACCAAGTCTCACTGAGATTTAGCA 59.716 41.667 14.57 0.00 40.98 3.49
3321 5764 8.836959 AACACATAAGAAAGAACGAAAACTTC 57.163 30.769 0.00 0.00 0.00 3.01
3355 5798 4.344978 AGAGTGTGGCTAGATGTCAGTTA 58.655 43.478 0.00 0.00 0.00 2.24
3356 5799 3.169099 AGAGTGTGGCTAGATGTCAGTT 58.831 45.455 0.00 0.00 0.00 3.16
3362 5805 7.721402 ACTTAGAAATAGAGTGTGGCTAGATG 58.279 38.462 0.00 0.00 0.00 2.90
3364 5807 8.851145 CATACTTAGAAATAGAGTGTGGCTAGA 58.149 37.037 0.00 0.00 31.41 2.43
3399 5842 7.617041 AAATCTTTGTATGCCTACTCTGTTC 57.383 36.000 0.74 0.00 0.00 3.18
3401 5844 7.168219 TCAAAATCTTTGTATGCCTACTCTGT 58.832 34.615 0.74 0.00 0.00 3.41
3462 5905 1.125093 TCGACTGAAAGCAGGGGGAA 61.125 55.000 0.00 0.00 46.60 3.97
3463 5906 0.909610 ATCGACTGAAAGCAGGGGGA 60.910 55.000 0.00 0.00 46.60 4.81
3467 5910 2.069273 ACGAAATCGACTGAAAGCAGG 58.931 47.619 10.16 0.00 43.67 4.85
3469 5912 2.066262 GGACGAAATCGACTGAAAGCA 58.934 47.619 10.16 0.00 43.02 3.91
3508 6311 7.502895 GGAGAGAATATGACTAGTACCTGTTGA 59.497 40.741 0.00 0.00 0.00 3.18
3513 6316 7.458397 CAGAGGAGAGAATATGACTAGTACCT 58.542 42.308 0.00 0.00 0.00 3.08
3516 6319 6.044989 AGGCAGAGGAGAGAATATGACTAGTA 59.955 42.308 0.00 0.00 0.00 1.82
3519 6322 5.332106 AGGCAGAGGAGAGAATATGACTA 57.668 43.478 0.00 0.00 0.00 2.59
3520 6323 4.197559 AGGCAGAGGAGAGAATATGACT 57.802 45.455 0.00 0.00 0.00 3.41
3560 6363 0.249489 CGGCGATTACAGGAGGAAGG 60.249 60.000 0.00 0.00 0.00 3.46
3603 6406 4.467107 GCTCGAGGGGAGGGGAGT 62.467 72.222 15.58 0.00 43.36 3.85
3639 8115 2.735772 GCGGGAAGGGAGCATGAGA 61.736 63.158 0.00 0.00 0.00 3.27
3643 8119 3.854669 CGAGCGGGAAGGGAGCAT 61.855 66.667 0.00 0.00 0.00 3.79
3692 8168 0.034089 GTTGGAGAACATGGGGAGGG 60.034 60.000 0.00 0.00 31.78 4.30
3695 8171 0.323629 GACGTTGGAGAACATGGGGA 59.676 55.000 0.00 0.00 31.78 4.81
3701 8177 0.031585 CTCACCGACGTTGGAGAACA 59.968 55.000 29.00 3.92 31.78 3.18
3758 8234 2.300967 GCATCACAGGTGGAGGGGA 61.301 63.158 0.00 0.00 0.00 4.81
3786 8262 4.658786 AGGAAGGACCCGTGGCCT 62.659 66.667 3.32 0.00 40.05 5.19
3834 8808 2.149383 TCTTGCAGTGAGCCCCAGT 61.149 57.895 0.00 0.00 44.83 4.00
3839 8813 1.968540 GGTGGTCTTGCAGTGAGCC 60.969 63.158 15.16 9.55 44.83 4.70
3851 8825 1.134965 CCGAGACAGAAGATGGTGGTC 60.135 57.143 0.00 0.00 0.00 4.02
3914 8890 3.928375 GCAATCCTCGTGCAATTGAAAAT 59.072 39.130 10.34 0.00 41.80 1.82
3927 8903 2.493278 AGAATGGTTTTGGCAATCCTCG 59.507 45.455 18.20 0.00 0.00 4.63
3958 8934 7.772332 ACATAGCAGAGTTAAAATCTAACGG 57.228 36.000 0.00 0.00 33.00 4.44
3989 8965 5.303165 TGCTCTCACAAATGCCTATATCTG 58.697 41.667 0.00 0.00 0.00 2.90
3995 8971 1.003464 TGCTGCTCTCACAAATGCCTA 59.997 47.619 0.00 0.00 0.00 3.93
4011 8987 4.524328 AGGAGGGAGTAACAAAATTTGCTG 59.476 41.667 5.52 0.00 0.00 4.41
4026 9002 5.365314 GCCCTATATAGATGAAAGGAGGGAG 59.635 48.000 11.53 0.00 44.48 4.30
4027 9003 5.281314 GCCCTATATAGATGAAAGGAGGGA 58.719 45.833 11.53 0.00 44.48 4.20
4028 9004 4.410555 GGCCCTATATAGATGAAAGGAGGG 59.589 50.000 11.53 3.52 44.52 4.30
4029 9005 5.284582 AGGCCCTATATAGATGAAAGGAGG 58.715 45.833 11.53 1.87 0.00 4.30
4030 9006 7.979786 TTAGGCCCTATATAGATGAAAGGAG 57.020 40.000 11.53 0.00 0.00 3.69
4031 9007 9.435570 GTATTAGGCCCTATATAGATGAAAGGA 57.564 37.037 11.53 0.00 0.00 3.36
4032 9008 8.361139 CGTATTAGGCCCTATATAGATGAAAGG 58.639 40.741 11.53 3.94 0.00 3.11
4033 9009 8.915036 ACGTATTAGGCCCTATATAGATGAAAG 58.085 37.037 11.53 0.00 0.00 2.62
4034 9010 8.834004 ACGTATTAGGCCCTATATAGATGAAA 57.166 34.615 11.53 0.10 0.00 2.69
4035 9011 8.834004 AACGTATTAGGCCCTATATAGATGAA 57.166 34.615 11.53 0.00 0.00 2.57
4036 9012 8.834004 AAACGTATTAGGCCCTATATAGATGA 57.166 34.615 11.53 0.00 0.00 2.92
4037 9013 9.886132 AAAAACGTATTAGGCCCTATATAGATG 57.114 33.333 11.53 3.39 0.00 2.90


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

AutoCloner maintained by Alex Coulton.