Multiple sequence alignment - TraesCS3D01G436600

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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 TraesCS3D01G436600 chr3D 100.000 3461 0 0 1 3461 548534525 548531065 0.000000e+00 6392
1 TraesCS3D01G436600 chr3D 86.885 122 15 1 2789 2909 46395403 46395282 6.030000e-28 135
2 TraesCS3D01G436600 chr3A 94.515 2206 93 13 852 3043 686123150 686120959 0.000000e+00 3378
3 TraesCS3D01G436600 chr3A 95.913 367 13 1 3095 3461 686120796 686120432 8.270000e-166 593
4 TraesCS3D01G436600 chr3B 92.985 2238 107 21 515 2730 726443343 726441134 0.000000e+00 3217
5 TraesCS3D01G436600 chr3B 83.775 604 83 11 27 621 726740012 726739415 3.020000e-155 558
6 TraesCS3D01G436600 chr3B 97.241 145 4 0 9 153 726469999 726469855 2.670000e-61 246
7 TraesCS3D01G436600 chr6D 80.322 559 95 11 247 792 2900554 2899998 3.220000e-110 409
8 TraesCS3D01G436600 chr2D 78.425 635 118 15 174 792 354988195 354988826 2.500000e-106 396
9 TraesCS3D01G436600 chr7D 78.400 625 117 13 187 797 99187683 99187063 1.160000e-104 390
10 TraesCS3D01G436600 chr2A 78.233 634 118 16 174 791 474808078 474808707 4.190000e-104 388
11 TraesCS3D01G436600 chr2B 77.830 636 120 16 174 792 422511792 422512423 1.170000e-99 374
12 TraesCS3D01G436600 chr1D 78.153 563 116 6 182 738 347407746 347408307 5.500000e-93 351
13 TraesCS3D01G436600 chr1D 80.442 317 54 6 3111 3419 165204476 165204792 5.770000e-58 235
14 TraesCS3D01G436600 chr4A 76.730 636 113 23 174 792 691156982 691156365 4.310000e-84 322
15 TraesCS3D01G436600 chr4D 75.932 644 131 16 174 802 8151997 8152631 3.350000e-80 309
16 TraesCS3D01G436600 chr1B 80.170 353 66 3 3111 3461 246767793 246767443 9.530000e-66 261
17 TraesCS3D01G436600 chr1A 79.501 361 62 9 3111 3461 216401573 216401215 2.670000e-61 246
18 TraesCS3D01G436600 chr6B 88.095 126 13 2 2786 2909 26482722 26482597 7.740000e-32 148


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 TraesCS3D01G436600 chr3D 548531065 548534525 3460 True 6392.0 6392 100.000 1 3461 1 chr3D.!!$R2 3460
1 TraesCS3D01G436600 chr3A 686120432 686123150 2718 True 1985.5 3378 95.214 852 3461 2 chr3A.!!$R1 2609
2 TraesCS3D01G436600 chr3B 726441134 726443343 2209 True 3217.0 3217 92.985 515 2730 1 chr3B.!!$R1 2215
3 TraesCS3D01G436600 chr3B 726739415 726740012 597 True 558.0 558 83.775 27 621 1 chr3B.!!$R3 594
4 TraesCS3D01G436600 chr6D 2899998 2900554 556 True 409.0 409 80.322 247 792 1 chr6D.!!$R1 545
5 TraesCS3D01G436600 chr2D 354988195 354988826 631 False 396.0 396 78.425 174 792 1 chr2D.!!$F1 618
6 TraesCS3D01G436600 chr7D 99187063 99187683 620 True 390.0 390 78.400 187 797 1 chr7D.!!$R1 610
7 TraesCS3D01G436600 chr2A 474808078 474808707 629 False 388.0 388 78.233 174 791 1 chr2A.!!$F1 617
8 TraesCS3D01G436600 chr2B 422511792 422512423 631 False 374.0 374 77.830 174 792 1 chr2B.!!$F1 618
9 TraesCS3D01G436600 chr1D 347407746 347408307 561 False 351.0 351 78.153 182 738 1 chr1D.!!$F2 556
10 TraesCS3D01G436600 chr4A 691156365 691156982 617 True 322.0 322 76.730 174 792 1 chr4A.!!$R1 618
11 TraesCS3D01G436600 chr4D 8151997 8152631 634 False 309.0 309 75.932 174 802 1 chr4D.!!$F1 628

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
84 86 0.381801 CATCCAAGGGCACATTACGC 59.618 55.0 0.00 0.0 0.00 4.42 F
512 528 0.387239 GGTTTCTTGTCATGTGGCGC 60.387 55.0 0.00 0.0 0.00 6.53 F
535 551 0.535780 TTGGTGTCAGCTGCTTCAGG 60.536 55.0 9.47 0.0 31.21 3.86 F
1511 1555 0.978907 TGAGTGATGGAGCAGCTGAA 59.021 50.0 20.43 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 1914 1.331756 GGTAGCATGGCTTCAATCACG 59.668 52.381 0.0 0.0 40.44 4.35 R
2298 2345 1.605710 CAGCCAGGACAGAAACAGTTG 59.394 52.381 0.0 0.0 0.00 3.16 R
2364 2411 1.834263 ACTCCAGTATCAGCACCTTCC 59.166 52.381 0.0 0.0 0.00 3.46 R
3077 3125 0.028505 GCAATGCGACGATGCTCATT 59.971 50.000 0.0 0.0 37.12 2.57 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
80 82 2.104967 CATGTCATCCAAGGGCACATT 58.895 47.619 0.00 0.00 0.00 2.71
84 86 0.381801 CATCCAAGGGCACATTACGC 59.618 55.000 0.00 0.00 0.00 4.42
105 107 4.049546 CCACCTTCATGGCATATGTTTG 57.950 45.455 0.00 0.36 40.22 2.93
158 163 8.402798 TCATCACTTTTTCTTTGCCATTAGTA 57.597 30.769 0.00 0.00 0.00 1.82
165 170 8.532977 TTTTTCTTTGCCATTAGTATTTGAGC 57.467 30.769 0.00 0.00 0.00 4.26
263 274 2.688477 TGAATTTGCCTCCCCTTTGTT 58.312 42.857 0.00 0.00 0.00 2.83
275 286 1.164041 CCTTTGTTTGTCGCTCCGGT 61.164 55.000 0.00 0.00 0.00 5.28
295 307 2.925170 CCTATGGCGGGGAGGAGG 60.925 72.222 0.00 0.00 31.45 4.30
349 363 9.159364 GTTTAGGTTATGATTTTTAGTCCTCGT 57.841 33.333 0.00 0.00 0.00 4.18
352 366 8.075761 AGGTTATGATTTTTAGTCCTCGTAGT 57.924 34.615 0.00 0.00 0.00 2.73
363 377 1.805945 CTCGTAGTTGTGGCGCTCC 60.806 63.158 7.64 0.00 0.00 4.70
375 389 4.457496 CGCTCCGGCAGATGGTGT 62.457 66.667 0.00 0.00 38.60 4.16
388 402 2.300152 AGATGGTGTCGCTTCTTCTTCA 59.700 45.455 0.00 0.00 0.00 3.02
390 404 2.912771 TGGTGTCGCTTCTTCTTCAAA 58.087 42.857 0.00 0.00 0.00 2.69
441 457 5.333339 CGAGTTTGTCTGTTTGGATGTAGTG 60.333 44.000 0.00 0.00 0.00 2.74
512 528 0.387239 GGTTTCTTGTCATGTGGCGC 60.387 55.000 0.00 0.00 0.00 6.53
535 551 0.535780 TTGGTGTCAGCTGCTTCAGG 60.536 55.000 9.47 0.00 31.21 3.86
654 672 1.681076 GGCTCCGGTAGGGAAACAA 59.319 57.895 0.00 0.00 46.61 2.83
816 845 9.880157 AATAGTATTTGAGCGACTACCTTTTTA 57.120 29.630 0.00 0.00 0.00 1.52
864 894 4.574599 AAAAGACATTTGAGCTGACCAC 57.425 40.909 0.00 0.00 0.00 4.16
909 939 2.874701 CCCATGGACTCTTATTTGCTCG 59.125 50.000 15.22 0.00 0.00 5.03
982 1025 1.801395 CGATTCCGGCGAACACAGTAT 60.801 52.381 9.30 0.00 0.00 2.12
1408 1451 1.484240 ACTGCCATGCTCTTCCTCTAC 59.516 52.381 0.00 0.00 0.00 2.59
1410 1453 1.483827 TGCCATGCTCTTCCTCTACAG 59.516 52.381 0.00 0.00 0.00 2.74
1411 1454 1.484240 GCCATGCTCTTCCTCTACAGT 59.516 52.381 0.00 0.00 0.00 3.55
1412 1455 2.695666 GCCATGCTCTTCCTCTACAGTA 59.304 50.000 0.00 0.00 0.00 2.74
1413 1456 3.491792 GCCATGCTCTTCCTCTACAGTAC 60.492 52.174 0.00 0.00 0.00 2.73
1475 1519 3.733727 CACGGCTGTGGTTTCAATTTTAC 59.266 43.478 18.43 0.00 42.59 2.01
1485 1529 8.352201 TGTGGTTTCAATTTTACTTCATCTCTG 58.648 33.333 0.00 0.00 0.00 3.35
1505 1549 2.040145 TGTCCAATTGAGTGATGGAGCA 59.960 45.455 7.12 0.00 43.59 4.26
1511 1555 0.978907 TGAGTGATGGAGCAGCTGAA 59.021 50.000 20.43 0.00 0.00 3.02
1520 1564 1.082690 GAGCAGCTGAAAGTAGTGGC 58.917 55.000 20.43 0.00 35.30 5.01
1551 1595 3.065925 GCCTAAGCTGCATTAAGTTCTGG 59.934 47.826 1.02 0.00 35.50 3.86
1804 1848 2.948979 TGCAGGTGTAAACTTCAACAGG 59.051 45.455 0.00 0.00 0.00 4.00
2033 2079 6.239120 CCATTCTGAATTGTCCTTGACTTGTT 60.239 38.462 0.00 0.00 33.15 2.83
2034 2080 6.773976 TTCTGAATTGTCCTTGACTTGTTT 57.226 33.333 0.00 0.00 33.15 2.83
2035 2081 6.773976 TCTGAATTGTCCTTGACTTGTTTT 57.226 33.333 0.00 0.00 33.15 2.43
2036 2082 7.169158 TCTGAATTGTCCTTGACTTGTTTTT 57.831 32.000 0.00 0.00 33.15 1.94
2141 2188 4.836736 GGAATTGATTGATGGGATGGTCAT 59.163 41.667 0.00 0.00 0.00 3.06
2142 2189 5.047519 GGAATTGATTGATGGGATGGTCATC 60.048 44.000 2.52 2.52 40.85 2.92
2298 2345 6.325596 GTCTGAAGGCCAAAAGATTTACATC 58.674 40.000 5.01 0.00 0.00 3.06
2364 2411 1.740025 GAAGGGAACATTTCAGCCGAG 59.260 52.381 0.00 0.00 0.00 4.63
2602 2650 2.098934 TGCTTTGTGTTACTTGCACCTG 59.901 45.455 0.00 0.00 36.11 4.00
2665 2713 1.781786 TAAAGGGCTTGTGGTTTGCA 58.218 45.000 0.00 0.00 0.00 4.08
2676 2724 6.459435 GGCTTGTGGTTTGCATTTTATTTTGT 60.459 34.615 0.00 0.00 0.00 2.83
2747 2795 8.367911 TCTGATATTTAATGCAGTAACGGATCT 58.632 33.333 6.03 0.00 0.00 2.75
2748 2796 8.310406 TGATATTTAATGCAGTAACGGATCTG 57.690 34.615 6.03 0.00 35.12 2.90
2755 2803 2.599082 GCAGTAACGGATCTGTCTTTCG 59.401 50.000 7.86 0.00 34.57 3.46
2852 2900 6.089954 GCATAGCAAAGAAACCAAATTGTCTC 59.910 38.462 0.00 0.00 0.00 3.36
2856 2904 5.754890 GCAAAGAAACCAAATTGTCTCACAT 59.245 36.000 0.00 0.00 0.00 3.21
2870 2918 3.062639 GTCTCACATACACCAATTCAGCG 59.937 47.826 0.00 0.00 0.00 5.18
2960 3008 7.393515 AGAAACTGAAACAAACAGAGGTAAACT 59.606 33.333 0.00 0.00 38.55 2.66
2961 3009 6.679327 ACTGAAACAAACAGAGGTAAACTC 57.321 37.500 0.00 0.00 46.98 3.01
2991 3039 0.800300 GCGACTCTAGCAGCACAGAC 60.800 60.000 0.00 0.00 34.19 3.51
3043 3091 4.750098 ACACATATTACATAACCGCAGCTC 59.250 41.667 0.00 0.00 0.00 4.09
3044 3092 4.152402 CACATATTACATAACCGCAGCTCC 59.848 45.833 0.00 0.00 0.00 4.70
3046 3094 2.309528 TTACATAACCGCAGCTCCAG 57.690 50.000 0.00 0.00 0.00 3.86
3047 3095 0.464036 TACATAACCGCAGCTCCAGG 59.536 55.000 0.00 0.00 0.00 4.45
3048 3096 1.524621 CATAACCGCAGCTCCAGGG 60.525 63.158 3.97 0.00 0.00 4.45
3050 3098 1.972660 ATAACCGCAGCTCCAGGGAC 61.973 60.000 3.97 0.00 0.00 4.46
3052 3100 4.767255 CCGCAGCTCCAGGGACAC 62.767 72.222 0.00 0.00 0.00 3.67
3054 3102 2.753029 GCAGCTCCAGGGACACTT 59.247 61.111 0.00 0.00 0.00 3.16
3056 3104 1.673665 CAGCTCCAGGGACACTTGC 60.674 63.158 0.00 0.00 0.00 4.01
3057 3105 2.149383 AGCTCCAGGGACACTTGCA 61.149 57.895 0.25 0.00 0.00 4.08
3058 3106 1.968540 GCTCCAGGGACACTTGCAC 60.969 63.158 0.00 0.00 0.00 4.57
3059 3107 1.451504 CTCCAGGGACACTTGCACA 59.548 57.895 0.00 0.00 0.00 4.57
3060 3108 0.179020 CTCCAGGGACACTTGCACAA 60.179 55.000 0.00 0.00 0.00 3.33
3061 3109 0.257328 TCCAGGGACACTTGCACAAA 59.743 50.000 0.00 0.00 0.00 2.83
3062 3110 0.385390 CCAGGGACACTTGCACAAAC 59.615 55.000 0.00 0.00 0.00 2.93
3063 3111 1.392589 CAGGGACACTTGCACAAACT 58.607 50.000 0.00 0.00 0.00 2.66
3064 3112 1.066002 CAGGGACACTTGCACAAACTG 59.934 52.381 0.00 0.00 0.00 3.16
3074 3122 2.247311 GCACAAACTGCATTACTCGG 57.753 50.000 0.00 0.00 46.29 4.63
3077 3125 1.349688 ACAAACTGCATTACTCGGGGA 59.650 47.619 0.00 0.00 0.00 4.81
3078 3126 2.224670 ACAAACTGCATTACTCGGGGAA 60.225 45.455 0.00 0.00 0.00 3.97
3079 3127 3.016736 CAAACTGCATTACTCGGGGAAT 58.983 45.455 0.00 0.00 0.00 3.01
3080 3128 2.332063 ACTGCATTACTCGGGGAATG 57.668 50.000 16.44 16.44 36.35 2.67
3081 3129 1.837439 ACTGCATTACTCGGGGAATGA 59.163 47.619 24.87 8.19 35.46 2.57
3085 3133 2.811873 GCATTACTCGGGGAATGAGCAT 60.812 50.000 24.87 0.00 36.94 3.79
3086 3134 2.910688 TTACTCGGGGAATGAGCATC 57.089 50.000 0.00 0.00 36.94 3.91
3087 3135 0.673985 TACTCGGGGAATGAGCATCG 59.326 55.000 0.00 0.00 38.61 3.84
3088 3136 1.330655 ACTCGGGGAATGAGCATCGT 61.331 55.000 0.00 0.00 38.61 3.73
3089 3137 0.598680 CTCGGGGAATGAGCATCGTC 60.599 60.000 0.00 0.00 38.61 4.20
3091 3139 2.247437 GGGGAATGAGCATCGTCGC 61.247 63.158 0.00 0.00 38.61 5.19
3092 3140 1.521457 GGGAATGAGCATCGTCGCA 60.521 57.895 1.90 0.00 38.61 5.10
3096 3144 0.028505 AATGAGCATCGTCGCATTGC 59.971 50.000 0.00 0.00 38.61 3.56
3097 3145 1.779025 ATGAGCATCGTCGCATTGCC 61.779 55.000 2.41 0.00 38.61 4.52
3098 3146 3.173390 GAGCATCGTCGCATTGCCC 62.173 63.158 2.41 0.00 37.07 5.36
3099 3147 4.256090 GCATCGTCGCATTGCCCC 62.256 66.667 2.41 0.00 0.00 5.80
3100 3148 3.585990 CATCGTCGCATTGCCCCC 61.586 66.667 2.41 0.00 0.00 5.40
3101 3149 4.108299 ATCGTCGCATTGCCCCCA 62.108 61.111 2.41 0.00 0.00 4.96
3102 3150 3.636929 ATCGTCGCATTGCCCCCAA 62.637 57.895 2.41 0.00 35.01 4.12
3169 3326 5.045872 CCTTGTCTTCTTTTCCAGCTTTTG 58.954 41.667 0.00 0.00 0.00 2.44
3244 3401 0.603975 GAAAGACTTGCTGCCGTCCT 60.604 55.000 13.38 1.14 0.00 3.85
3247 3404 4.254709 ACTTGCTGCCGTCCTGCA 62.255 61.111 0.00 1.66 45.18 4.41
3254 3411 2.335011 GCCGTCCTGCACCAAAAC 59.665 61.111 0.00 0.00 0.00 2.43
3259 3416 0.385390 GTCCTGCACCAAAACACCTG 59.615 55.000 0.00 0.00 0.00 4.00
3276 3433 0.539051 CTGTAGACCAGGCCAAGGAG 59.461 60.000 20.01 3.71 37.54 3.69
3322 3479 8.807948 TTCCTTAAATTCCAGATAGTCCAAAG 57.192 34.615 0.00 0.00 0.00 2.77
3335 3492 0.401356 TCCAAAGACCAGCTGCATGA 59.599 50.000 8.66 0.00 0.00 3.07
3384 3541 1.415659 CCCTAGACCAGCATTCAGAGG 59.584 57.143 0.00 0.00 0.00 3.69
3415 3572 7.317722 ACATACTGATATCCCCTCTAAAACC 57.682 40.000 0.00 0.00 0.00 3.27
3440 3597 2.871022 CAGCTGCATGATAGTTCTCCAC 59.129 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.403583 ACAAATATAAGACGGTGTGGATATTTT 57.596 29.630 12.17 5.84 30.71 1.82
7 8 8.836413 CACAAATATAAGACGGTGTGGATATTT 58.164 33.333 10.30 10.30 34.19 1.40
8 9 8.208224 TCACAAATATAAGACGGTGTGGATATT 58.792 33.333 0.00 0.00 37.53 1.28
11 12 5.984725 TCACAAATATAAGACGGTGTGGAT 58.015 37.500 0.00 0.00 37.53 3.41
13 14 5.445407 CGTTCACAAATATAAGACGGTGTGG 60.445 44.000 0.00 0.00 37.53 4.17
14 15 5.445407 CCGTTCACAAATATAAGACGGTGTG 60.445 44.000 4.03 0.00 38.13 3.82
15 16 4.628333 CCGTTCACAAATATAAGACGGTGT 59.372 41.667 4.03 0.00 34.05 4.16
16 17 4.865925 TCCGTTCACAAATATAAGACGGTG 59.134 41.667 11.18 0.00 39.04 4.94
17 18 5.075858 TCCGTTCACAAATATAAGACGGT 57.924 39.130 11.18 0.00 39.04 4.83
18 19 5.107133 ACTCCGTTCACAAATATAAGACGG 58.893 41.667 5.73 5.73 39.30 4.79
19 20 6.971184 ACTACTCCGTTCACAAATATAAGACG 59.029 38.462 0.00 0.00 0.00 4.18
20 21 9.230932 GTACTACTCCGTTCACAAATATAAGAC 57.769 37.037 0.00 0.00 0.00 3.01
21 22 9.182214 AGTACTACTCCGTTCACAAATATAAGA 57.818 33.333 0.00 0.00 0.00 2.10
22 23 9.798994 AAGTACTACTCCGTTCACAAATATAAG 57.201 33.333 0.00 0.00 0.00 1.73
23 24 9.793252 GAAGTACTACTCCGTTCACAAATATAA 57.207 33.333 0.00 0.00 0.00 0.98
24 25 9.182214 AGAAGTACTACTCCGTTCACAAATATA 57.818 33.333 0.00 0.00 0.00 0.86
25 26 8.064336 AGAAGTACTACTCCGTTCACAAATAT 57.936 34.615 0.00 0.00 0.00 1.28
84 86 3.448301 ACAAACATATGCCATGAAGGTGG 59.552 43.478 1.58 0.00 42.35 4.61
138 143 9.696917 CTCAAATACTAATGGCAAAGAAAAAGT 57.303 29.630 7.17 0.00 0.00 2.66
158 163 3.744660 AGAGAAAGTTGGTCGCTCAAAT 58.255 40.909 0.00 0.00 0.00 2.32
165 170 3.067833 GGGAAAGAGAGAAAGTTGGTCG 58.932 50.000 0.00 0.00 0.00 4.79
281 292 2.527875 GATCCTCCTCCCCGCCAT 60.528 66.667 0.00 0.00 0.00 4.40
295 307 2.444895 AGAGGAGGCACCGGGATC 60.445 66.667 6.32 0.00 44.74 3.36
349 363 4.752879 GCCGGAGCGCCACAACTA 62.753 66.667 5.05 0.00 0.00 2.24
363 377 2.434884 AAGCGACACCATCTGCCG 60.435 61.111 0.00 0.00 0.00 5.69
373 387 5.296780 AGACAAATTTGAAGAAGAAGCGACA 59.703 36.000 24.64 0.00 0.00 4.35
375 389 6.377327 AAGACAAATTTGAAGAAGAAGCGA 57.623 33.333 24.64 0.00 0.00 4.93
512 528 0.877071 AAGCAGCTGACACCAAATCG 59.123 50.000 20.43 0.00 0.00 3.34
535 551 3.483574 CGTCGTTGAACCATTGCATAGAC 60.484 47.826 0.00 0.00 0.00 2.59
624 642 2.034221 GGAGCCGGCTTGACCTTT 59.966 61.111 33.34 5.00 35.61 3.11
654 672 2.512745 TTGGCGCGCCGTTATCAT 60.513 55.556 41.73 0.00 39.42 2.45
792 821 9.880157 AATAAAAAGGTAGTCGCTCAAATACTA 57.120 29.630 0.00 0.00 0.00 1.82
807 836 8.891720 ACGCGGATTTATGTAAATAAAAAGGTA 58.108 29.630 12.47 0.00 36.13 3.08
809 838 8.528295 CAACGCGGATTTATGTAAATAAAAAGG 58.472 33.333 12.47 0.00 36.13 3.11
816 845 4.334203 TGCTCAACGCGGATTTATGTAAAT 59.666 37.500 12.47 0.00 43.27 1.40
828 857 2.908626 GTCTTTTTAATGCTCAACGCGG 59.091 45.455 12.47 0.00 43.27 6.46
831 860 7.617935 GCTCAAATGTCTTTTTAATGCTCAACG 60.618 37.037 0.00 0.00 0.00 4.10
847 877 0.166814 GCGTGGTCAGCTCAAATGTC 59.833 55.000 0.00 0.00 0.00 3.06
909 939 3.898482 ACCATAGCCCCAAGAACATTAC 58.102 45.455 0.00 0.00 0.00 1.89
954 997 1.515081 TCGCCGGAATCGAAGTTTTT 58.485 45.000 5.05 0.00 39.00 1.94
959 1002 1.011968 TGTGTTCGCCGGAATCGAAG 61.012 55.000 14.51 0.00 45.10 3.79
982 1025 2.108075 CCATCTCTCTCTCCCTCTGCTA 59.892 54.545 0.00 0.00 0.00 3.49
1080 1123 3.849951 CGCTGGTGGGGCTCGTAT 61.850 66.667 0.00 0.00 0.00 3.06
1408 1451 5.244785 TGAAGCGTTCCATAGTAGTACTG 57.755 43.478 13.29 0.00 0.00 2.74
1410 1453 7.399523 CAAATTGAAGCGTTCCATAGTAGTAC 58.600 38.462 0.00 0.00 0.00 2.73
1411 1454 6.537301 CCAAATTGAAGCGTTCCATAGTAGTA 59.463 38.462 0.00 0.00 0.00 1.82
1412 1455 5.354234 CCAAATTGAAGCGTTCCATAGTAGT 59.646 40.000 0.00 0.00 0.00 2.73
1413 1456 5.354234 ACCAAATTGAAGCGTTCCATAGTAG 59.646 40.000 0.00 0.00 0.00 2.57
1475 1519 5.485620 TCACTCAATTGGACAGAGATGAAG 58.514 41.667 5.42 0.00 33.69 3.02
1485 1529 2.681848 CTGCTCCATCACTCAATTGGAC 59.318 50.000 5.42 0.00 34.65 4.02
1505 1549 1.376037 GGCGCCACTACTTTCAGCT 60.376 57.895 24.80 0.00 0.00 4.24
1511 1555 1.379527 GCAATTAGGCGCCACTACTT 58.620 50.000 31.54 10.86 0.00 2.24
1563 1607 8.494433 TCTATGCATGGTAGTAGGAATCTTTTT 58.506 33.333 10.16 0.00 0.00 1.94
1568 1612 6.998802 ACTTCTATGCATGGTAGTAGGAATC 58.001 40.000 18.58 0.00 0.00 2.52
1870 1914 1.331756 GGTAGCATGGCTTCAATCACG 59.668 52.381 0.00 0.00 40.44 4.35
1871 1915 2.368439 TGGTAGCATGGCTTCAATCAC 58.632 47.619 0.00 0.00 40.44 3.06
2007 2053 5.246981 AGTCAAGGACAATTCAGAATGGA 57.753 39.130 4.36 0.00 33.38 3.41
2141 2188 5.126869 TGCTTCACTTGTTCAAGGAATTTGA 59.873 36.000 15.51 7.77 43.92 2.69
2142 2189 5.350633 TGCTTCACTTGTTCAAGGAATTTG 58.649 37.500 15.51 5.84 38.17 2.32
2298 2345 1.605710 CAGCCAGGACAGAAACAGTTG 59.394 52.381 0.00 0.00 0.00 3.16
2364 2411 1.834263 ACTCCAGTATCAGCACCTTCC 59.166 52.381 0.00 0.00 0.00 3.46
2602 2650 5.103000 AGCACGTATCACTTCTATGTCAAC 58.897 41.667 0.00 0.00 0.00 3.18
2747 2795 3.563808 CAGAACACCAATTCCGAAAGACA 59.436 43.478 0.00 0.00 0.00 3.41
2748 2796 3.813166 TCAGAACACCAATTCCGAAAGAC 59.187 43.478 0.00 0.00 0.00 3.01
2755 2803 9.614792 ATTAAGTAGTATCAGAACACCAATTCC 57.385 33.333 0.00 0.00 0.00 3.01
2852 2900 1.529622 CGCGCTGAATTGGTGTATGTG 60.530 52.381 5.56 0.00 0.00 3.21
2856 2904 2.735677 CGCGCGCTGAATTGGTGTA 61.736 57.895 30.48 0.00 0.00 2.90
2960 3008 1.095600 AGAGTCGCTGCATTACTCGA 58.904 50.000 16.32 4.87 43.51 4.04
2961 3009 2.645163 CTAGAGTCGCTGCATTACTCG 58.355 52.381 16.32 4.96 43.51 4.18
2962 3010 2.223595 TGCTAGAGTCGCTGCATTACTC 60.224 50.000 15.18 15.18 39.95 2.59
2963 3011 1.751351 TGCTAGAGTCGCTGCATTACT 59.249 47.619 0.00 0.00 0.00 2.24
2964 3012 2.123342 CTGCTAGAGTCGCTGCATTAC 58.877 52.381 0.00 0.00 32.75 1.89
3043 3091 0.385390 GTTTGTGCAAGTGTCCCTGG 59.615 55.000 0.00 0.00 0.00 4.45
3044 3092 1.066002 CAGTTTGTGCAAGTGTCCCTG 59.934 52.381 0.00 0.00 31.79 4.45
3046 3094 3.944871 CAGTTTGTGCAAGTGTCCC 57.055 52.632 0.00 0.00 31.79 4.46
3056 3104 1.468520 CCCCGAGTAATGCAGTTTGTG 59.531 52.381 0.00 0.00 0.00 3.33
3057 3105 1.349688 TCCCCGAGTAATGCAGTTTGT 59.650 47.619 0.00 0.00 0.00 2.83
3058 3106 2.107950 TCCCCGAGTAATGCAGTTTG 57.892 50.000 0.00 0.00 0.00 2.93
3059 3107 2.871096 TTCCCCGAGTAATGCAGTTT 57.129 45.000 0.00 0.00 0.00 2.66
3060 3108 2.238646 TCATTCCCCGAGTAATGCAGTT 59.761 45.455 0.00 0.00 33.91 3.16
3061 3109 1.837439 TCATTCCCCGAGTAATGCAGT 59.163 47.619 0.00 0.00 33.91 4.40
3062 3110 2.487934 CTCATTCCCCGAGTAATGCAG 58.512 52.381 0.00 0.00 33.91 4.41
3063 3111 1.475034 GCTCATTCCCCGAGTAATGCA 60.475 52.381 0.00 0.00 33.91 3.96
3064 3112 1.230324 GCTCATTCCCCGAGTAATGC 58.770 55.000 0.00 0.00 33.91 3.56
3065 3113 2.620251 TGCTCATTCCCCGAGTAATG 57.380 50.000 0.00 0.00 34.96 1.90
3066 3114 2.289072 CGATGCTCATTCCCCGAGTAAT 60.289 50.000 0.00 0.00 32.83 1.89
3067 3115 1.068588 CGATGCTCATTCCCCGAGTAA 59.931 52.381 0.00 0.00 32.83 2.24
3068 3116 0.673985 CGATGCTCATTCCCCGAGTA 59.326 55.000 0.00 0.00 32.83 2.59
3069 3117 1.330655 ACGATGCTCATTCCCCGAGT 61.331 55.000 0.00 0.00 32.83 4.18
3070 3118 0.598680 GACGATGCTCATTCCCCGAG 60.599 60.000 0.00 0.00 0.00 4.63
3071 3119 1.441729 GACGATGCTCATTCCCCGA 59.558 57.895 0.00 0.00 0.00 5.14
3073 3121 2.247437 GCGACGATGCTCATTCCCC 61.247 63.158 0.00 0.00 0.00 4.81
3074 3122 0.882042 ATGCGACGATGCTCATTCCC 60.882 55.000 0.00 0.00 35.36 3.97
3077 3125 0.028505 GCAATGCGACGATGCTCATT 59.971 50.000 0.00 0.00 37.12 2.57
3078 3126 1.645455 GCAATGCGACGATGCTCAT 59.355 52.632 0.00 0.00 37.12 2.90
3079 3127 2.463620 GGCAATGCGACGATGCTCA 61.464 57.895 16.58 0.00 39.94 4.26
3080 3128 2.325857 GGCAATGCGACGATGCTC 59.674 61.111 16.58 6.92 39.94 4.26
3081 3129 3.204827 GGGCAATGCGACGATGCT 61.205 61.111 16.58 0.00 39.94 3.79
3085 3133 4.337177 TTGGGGGCAATGCGACGA 62.337 61.111 0.00 0.00 0.00 4.20
3086 3134 3.814268 CTTGGGGGCAATGCGACG 61.814 66.667 0.00 0.00 0.00 5.12
3087 3135 2.361104 TCTTGGGGGCAATGCGAC 60.361 61.111 0.00 0.00 0.00 5.19
3088 3136 2.361104 GTCTTGGGGGCAATGCGA 60.361 61.111 0.00 0.00 0.00 5.10
3089 3137 2.361610 AGTCTTGGGGGCAATGCG 60.362 61.111 0.00 0.00 0.00 4.73
3091 3139 1.753073 GATTGAGTCTTGGGGGCAATG 59.247 52.381 0.00 0.00 30.06 2.82
3092 3140 1.358787 TGATTGAGTCTTGGGGGCAAT 59.641 47.619 0.00 0.00 32.36 3.56
3096 3144 0.394899 GGCTGATTGAGTCTTGGGGG 60.395 60.000 0.00 0.00 0.00 5.40
3097 3145 0.622665 AGGCTGATTGAGTCTTGGGG 59.377 55.000 0.00 0.00 29.69 4.96
3098 3146 1.681166 CCAGGCTGATTGAGTCTTGGG 60.681 57.143 17.94 0.00 32.74 4.12
3099 3147 1.681166 CCCAGGCTGATTGAGTCTTGG 60.681 57.143 17.94 0.00 32.74 3.61
3100 3148 1.004044 ACCCAGGCTGATTGAGTCTTG 59.996 52.381 17.94 0.00 32.74 3.02
3101 3149 1.280421 GACCCAGGCTGATTGAGTCTT 59.720 52.381 17.94 0.00 32.74 3.01
3102 3150 0.908198 GACCCAGGCTGATTGAGTCT 59.092 55.000 17.94 0.00 36.95 3.24
3169 3326 1.559149 CCAACTGCAAAACATGGCGC 61.559 55.000 0.00 0.00 0.00 6.53
3244 3401 2.294074 GTCTACAGGTGTTTTGGTGCA 58.706 47.619 0.00 0.00 0.00 4.57
3247 3404 3.208747 CTGGTCTACAGGTGTTTTGGT 57.791 47.619 0.00 0.00 43.70 3.67
3259 3416 0.250513 CACTCCTTGGCCTGGTCTAC 59.749 60.000 3.32 0.00 0.00 2.59
3384 3541 4.841246 AGGGGATATCAGTATGTTGTCCTC 59.159 45.833 4.83 0.96 44.30 3.71


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

AutoCloner maintained by Alex Coulton.