Multiple sequence alignment - TraesCS2D01G291700

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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 TraesCS2D01G291700 chr2D 100.000 3170 0 0 1 3170 373749595 373752764 0.000000e+00 5854.0
1 TraesCS2D01G291700 chr2D 94.332 2082 86 15 418 2485 373654258 373652195 0.000000e+00 3162.0
2 TraesCS2D01G291700 chr2D 82.716 324 39 7 2755 3070 373610712 373610398 4.030000e-69 272.0
3 TraesCS2D01G291700 chr2B 94.084 2417 92 18 1 2394 443222655 443225043 0.000000e+00 3624.0
4 TraesCS2D01G291700 chr2B 93.831 2075 68 26 419 2463 443148952 443146908 0.000000e+00 3068.0
5 TraesCS2D01G291700 chr2B 99.029 309 3 0 2755 3063 443232164 443232472 3.570000e-154 555.0
6 TraesCS2D01G291700 chr2B 94.690 113 4 2 3059 3170 443237909 443238020 1.170000e-39 174.0
7 TraesCS2D01G291700 chr2B 84.375 96 3 1 2637 2720 443232057 443232152 2.030000e-12 84.2
8 TraesCS2D01G291700 chr2A 93.702 1937 80 18 587 2505 505080297 505078385 0.000000e+00 2863.0
9 TraesCS2D01G291700 chr2A 92.480 1835 88 23 587 2394 505208566 505210377 0.000000e+00 2579.0
10 TraesCS2D01G291700 chr2A 89.898 683 31 14 2405 3074 505210463 505211120 0.000000e+00 845.0
11 TraesCS2D01G291700 chr2A 84.615 130 6 5 420 545 505080486 505080367 2.000000e-22 117.0
12 TraesCS2D01G291700 chr3D 75.401 561 115 18 1409 1959 566081016 566081563 1.890000e-62 250.0
13 TraesCS2D01G291700 chr3B 75.133 563 113 21 1409 1959 755806067 755806614 4.090000e-59 239.0
14 TraesCS2D01G291700 chr3A 75.088 566 110 24 1408 1959 701218937 701218389 5.290000e-58 235.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G291700 chr2D 373749595 373752764 3169 False 5854 5854 100.0000 1 3170 1 chr2D.!!$F1 3169
1 TraesCS2D01G291700 chr2D 373652195 373654258 2063 True 3162 3162 94.3320 418 2485 1 chr2D.!!$R2 2067
2 TraesCS2D01G291700 chr2B 443222655 443225043 2388 False 3624 3624 94.0840 1 2394 1 chr2B.!!$F1 2393
3 TraesCS2D01G291700 chr2B 443146908 443148952 2044 True 3068 3068 93.8310 419 2463 1 chr2B.!!$R1 2044
4 TraesCS2D01G291700 chr2A 505208566 505211120 2554 False 1712 2579 91.1890 587 3074 2 chr2A.!!$F1 2487
5 TraesCS2D01G291700 chr2A 505078385 505080486 2101 True 1490 2863 89.1585 420 2505 2 chr2A.!!$R1 2085
6 TraesCS2D01G291700 chr3D 566081016 566081563 547 False 250 250 75.4010 1409 1959 1 chr3D.!!$F1 550
7 TraesCS2D01G291700 chr3B 755806067 755806614 547 False 239 239 75.1330 1409 1959 1 chr3B.!!$F1 550
8 TraesCS2D01G291700 chr3A 701218389 701218937 548 True 235 235 75.0880 1408 1959 1 chr3A.!!$R1 551

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
105 106 0.035056 CTGCAGTTTAGGACCCAGGG 60.035 60.0 2.85 2.85 0.00 4.45 F
617 651 0.392336 GTGGCCAGGCTATCTCTGAG 59.608 60.0 5.11 0.00 34.36 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1149 1221 0.250295 GGTTGTAGCAGCTCACCACA 60.250 55.0 0.00 0.0 0.00 4.17 R
2530 2716 0.102120 TGGCGTTTGTTTCAAGGCAG 59.898 50.0 1.08 0.0 33.47 4.85 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
18 19 1.219124 GGATTCTCAGCCAGCGTGA 59.781 57.895 0.00 0.00 0.00 4.35
24 25 0.743688 CTCAGCCAGCGTGATAGAGT 59.256 55.000 0.00 0.00 0.00 3.24
25 26 0.741326 TCAGCCAGCGTGATAGAGTC 59.259 55.000 0.00 0.00 0.00 3.36
28 29 1.759445 AGCCAGCGTGATAGAGTCAAT 59.241 47.619 0.00 0.00 38.90 2.57
103 104 0.678048 GGCTGCAGTTTAGGACCCAG 60.678 60.000 16.64 0.00 33.56 4.45
105 106 0.035056 CTGCAGTTTAGGACCCAGGG 60.035 60.000 2.85 2.85 0.00 4.45
145 146 2.155279 GAAAGGTGGACCAGAAGCTTC 58.845 52.381 19.11 19.11 38.89 3.86
210 211 2.046217 GAACAACGGGGGAGGAGC 60.046 66.667 0.00 0.00 0.00 4.70
236 237 1.379146 GGACCCTTCCCTTCCACAC 59.621 63.158 0.00 0.00 35.57 3.82
260 261 3.091545 ACATTGATCCGAAAAGCCACAT 58.908 40.909 0.00 0.00 0.00 3.21
267 268 3.278574 TCCGAAAAGCCACATATTCAGG 58.721 45.455 0.00 0.00 0.00 3.86
269 270 2.358898 CGAAAAGCCACATATTCAGGGG 59.641 50.000 0.00 0.00 0.00 4.79
270 271 3.631250 GAAAAGCCACATATTCAGGGGA 58.369 45.455 0.00 0.00 0.00 4.81
299 300 4.789075 ACCCGCGAACACGATCCG 62.789 66.667 8.23 0.00 34.06 4.18
311 312 3.195698 GATCCGGCGCAGAACACC 61.196 66.667 10.83 0.00 0.00 4.16
344 345 4.657824 CGGGTTCTCGTGTGCCGT 62.658 66.667 0.00 0.00 37.94 5.68
352 353 2.053465 CGTGTGCCGTGTTGTTCG 60.053 61.111 0.00 0.00 0.00 3.95
359 360 1.275657 CCGTGTTGTTCGCAGTCAC 59.724 57.895 0.00 0.00 33.66 3.67
360 361 1.425267 CCGTGTTGTTCGCAGTCACA 61.425 55.000 0.00 0.00 35.30 3.58
376 377 3.129813 AGTCACAGCGGATTTCGTGTATA 59.870 43.478 0.00 0.00 41.72 1.47
391 392 6.903883 TCGTGTATATTCTTTTCTGCCTTC 57.096 37.500 0.00 0.00 0.00 3.46
394 395 8.255206 TCGTGTATATTCTTTTCTGCCTTCTAA 58.745 33.333 0.00 0.00 0.00 2.10
425 426 2.554032 GCACAACATTGGCAACTAGAGT 59.446 45.455 0.00 0.00 37.61 3.24
458 459 8.103305 TGGAGTAACTTTCTGAAGCAAGATAAT 58.897 33.333 0.00 0.00 36.29 1.28
550 561 6.156949 ACCCTGAAGATTGTATGTACTCATGT 59.843 38.462 0.00 0.00 35.70 3.21
611 645 1.555967 TTTTTGGTGGCCAGGCTATC 58.444 50.000 5.11 6.17 33.81 2.08
617 651 0.392336 GTGGCCAGGCTATCTCTGAG 59.608 60.000 5.11 0.00 34.36 3.35
1333 1410 4.556942 TTGCAGTCATTTCACAGTTGAG 57.443 40.909 0.00 0.00 31.71 3.02
2249 2341 3.191539 GCTCGCTGCTGCTACACC 61.192 66.667 14.03 0.00 38.95 4.16
2256 2348 1.068474 CTGCTGCTACACCACGTTAC 58.932 55.000 0.00 0.00 0.00 2.50
2257 2349 0.677288 TGCTGCTACACCACGTTACT 59.323 50.000 0.00 0.00 0.00 2.24
2258 2350 1.068474 GCTGCTACACCACGTTACTG 58.932 55.000 0.00 0.00 0.00 2.74
2259 2351 1.710013 CTGCTACACCACGTTACTGG 58.290 55.000 0.00 0.00 37.33 4.00
2350 2456 2.434185 GATCGTCGTGCAGGGCAA 60.434 61.111 12.03 0.00 41.47 4.52
2351 2457 2.740714 GATCGTCGTGCAGGGCAAC 61.741 63.158 12.03 0.00 41.47 4.17
2354 2460 3.276846 GTCGTGCAGGGCAACGTT 61.277 61.111 6.05 0.00 41.47 3.99
2355 2461 3.276091 TCGTGCAGGGCAACGTTG 61.276 61.111 23.90 23.90 41.47 4.10
2460 2646 5.865552 AGCTTGTGATTTTCATGTTACATGC 59.134 36.000 19.47 6.70 38.61 4.06
2469 2655 7.552458 TTTTCATGTTACATGCGTGAGATAT 57.448 32.000 19.47 1.52 33.96 1.63
2470 2656 6.529463 TTCATGTTACATGCGTGAGATATG 57.471 37.500 19.47 13.36 33.96 1.78
2502 2688 5.401531 TGAGCTAGTACATCGGAAAGTTT 57.598 39.130 0.00 0.00 0.00 2.66
2505 2691 4.222145 AGCTAGTACATCGGAAAGTTTGGA 59.778 41.667 0.00 0.00 0.00 3.53
2506 2692 4.329256 GCTAGTACATCGGAAAGTTTGGAC 59.671 45.833 0.00 0.00 0.00 4.02
2507 2693 4.345859 AGTACATCGGAAAGTTTGGACA 57.654 40.909 0.00 0.00 0.00 4.02
2508 2694 4.906618 AGTACATCGGAAAGTTTGGACAT 58.093 39.130 0.00 0.00 0.00 3.06
2530 2716 1.071857 GTGGATCGGGATTCCTTACCC 59.928 57.143 2.01 0.00 42.43 3.69
2570 2756 0.673644 GTACCTGCCAATGTGTCGCT 60.674 55.000 0.00 0.00 0.00 4.93
2591 2777 1.278127 CCTTTTAGCTCGTCCCTTCCA 59.722 52.381 0.00 0.00 0.00 3.53
2716 2902 4.217550 AGGCAGTGCAATATAAACAACGTT 59.782 37.500 18.61 0.00 0.00 3.99
2717 2903 4.323336 GGCAGTGCAATATAAACAACGTTG 59.677 41.667 26.20 26.20 0.00 4.10
2720 2906 5.567534 CAGTGCAATATAAACAACGTTGTCC 59.432 40.000 32.36 14.06 41.31 4.02
2737 2923 2.710902 CCCGCGGATGTCTCTGTGA 61.711 63.158 30.73 0.00 40.13 3.58
2745 2931 0.689055 ATGTCTCTGTGAGCTGCCAA 59.311 50.000 0.00 0.00 0.00 4.52
2746 2932 0.689055 TGTCTCTGTGAGCTGCCAAT 59.311 50.000 0.00 0.00 0.00 3.16
2747 2933 1.901833 TGTCTCTGTGAGCTGCCAATA 59.098 47.619 0.00 0.00 0.00 1.90
2748 2934 2.275318 GTCTCTGTGAGCTGCCAATAC 58.725 52.381 0.00 0.00 0.00 1.89
2821 3007 2.663852 CTTGTTCGGGTTCGGCGT 60.664 61.111 6.85 0.00 36.95 5.68
2858 3044 4.927782 AGCCACCGACGCAAGCAA 62.928 61.111 4.43 0.00 45.62 3.91
2872 3064 3.688136 GCAACGCGCGAGATAAGA 58.312 55.556 39.36 0.00 0.00 2.10
3023 3215 3.458163 TCGCGGAGTAGGGCCAAG 61.458 66.667 6.13 0.00 0.00 3.61
3070 3262 1.723870 GATAAGCTGCCGCACAAGG 59.276 57.895 2.05 0.00 39.10 3.61
3071 3263 0.744414 GATAAGCTGCCGCACAAGGA 60.744 55.000 2.05 0.00 39.10 3.36
3073 3265 0.322456 TAAGCTGCCGCACAAGGATT 60.322 50.000 2.05 0.00 39.10 3.01
3084 3276 2.992089 CAAGGATTGGATCGTCCGG 58.008 57.895 0.00 0.00 43.94 5.14
3085 3277 1.146263 AAGGATTGGATCGTCCGGC 59.854 57.895 0.00 0.00 40.17 6.13
3086 3278 2.644555 AAGGATTGGATCGTCCGGCG 62.645 60.000 11.37 11.37 40.17 6.46
3087 3279 2.106332 GATTGGATCGTCCGGCGT 59.894 61.111 16.00 5.83 40.17 5.68
3088 3280 1.949631 GATTGGATCGTCCGGCGTC 60.950 63.158 16.00 12.67 40.17 5.19
3089 3281 3.441011 ATTGGATCGTCCGGCGTCC 62.441 63.158 21.11 21.11 40.17 4.79
3092 3284 3.834799 GATCGTCCGGCGTCCCTT 61.835 66.667 16.00 0.00 42.13 3.95
3093 3285 3.366739 GATCGTCCGGCGTCCCTTT 62.367 63.158 16.00 0.00 42.13 3.11
3094 3286 2.847435 GATCGTCCGGCGTCCCTTTT 62.847 60.000 16.00 0.00 42.13 2.27
3095 3287 2.459202 ATCGTCCGGCGTCCCTTTTT 62.459 55.000 16.00 0.00 42.13 1.94
3096 3288 2.674084 CGTCCGGCGTCCCTTTTTC 61.674 63.158 6.01 0.00 35.54 2.29
3097 3289 2.032987 TCCGGCGTCCCTTTTTCC 59.967 61.111 6.01 0.00 0.00 3.13
3098 3290 2.033602 CCGGCGTCCCTTTTTCCT 59.966 61.111 6.01 0.00 0.00 3.36
3099 3291 2.038837 CCGGCGTCCCTTTTTCCTC 61.039 63.158 6.01 0.00 0.00 3.71
3100 3292 2.038837 CGGCGTCCCTTTTTCCTCC 61.039 63.158 0.00 0.00 0.00 4.30
3101 3293 1.074248 GGCGTCCCTTTTTCCTCCA 59.926 57.895 0.00 0.00 0.00 3.86
3102 3294 0.538746 GGCGTCCCTTTTTCCTCCAA 60.539 55.000 0.00 0.00 0.00 3.53
3103 3295 0.596577 GCGTCCCTTTTTCCTCCAAC 59.403 55.000 0.00 0.00 0.00 3.77
3104 3296 1.975660 CGTCCCTTTTTCCTCCAACA 58.024 50.000 0.00 0.00 0.00 3.33
3105 3297 1.607148 CGTCCCTTTTTCCTCCAACAC 59.393 52.381 0.00 0.00 0.00 3.32
3106 3298 2.748465 CGTCCCTTTTTCCTCCAACACT 60.748 50.000 0.00 0.00 0.00 3.55
3107 3299 2.623416 GTCCCTTTTTCCTCCAACACTG 59.377 50.000 0.00 0.00 0.00 3.66
3108 3300 1.341209 CCCTTTTTCCTCCAACACTGC 59.659 52.381 0.00 0.00 0.00 4.40
3109 3301 2.310538 CCTTTTTCCTCCAACACTGCT 58.689 47.619 0.00 0.00 0.00 4.24
3110 3302 2.294512 CCTTTTTCCTCCAACACTGCTC 59.705 50.000 0.00 0.00 0.00 4.26
3111 3303 3.217626 CTTTTTCCTCCAACACTGCTCT 58.782 45.455 0.00 0.00 0.00 4.09
3112 3304 4.389374 CTTTTTCCTCCAACACTGCTCTA 58.611 43.478 0.00 0.00 0.00 2.43
3113 3305 3.402628 TTTCCTCCAACACTGCTCTAC 57.597 47.619 0.00 0.00 0.00 2.59
3114 3306 0.888619 TCCTCCAACACTGCTCTACG 59.111 55.000 0.00 0.00 0.00 3.51
3115 3307 0.737715 CCTCCAACACTGCTCTACGC 60.738 60.000 0.00 0.00 39.77 4.42
3116 3308 0.244994 CTCCAACACTGCTCTACGCT 59.755 55.000 0.00 0.00 40.11 5.07
3117 3309 0.243907 TCCAACACTGCTCTACGCTC 59.756 55.000 0.00 0.00 40.11 5.03
3118 3310 0.244994 CCAACACTGCTCTACGCTCT 59.755 55.000 0.00 0.00 40.11 4.09
3119 3311 1.472878 CCAACACTGCTCTACGCTCTA 59.527 52.381 0.00 0.00 40.11 2.43
3120 3312 2.520979 CAACACTGCTCTACGCTCTAC 58.479 52.381 0.00 0.00 40.11 2.59
3131 3323 3.479269 GCTCTACGGTGCGTGCAC 61.479 66.667 16.40 16.40 45.49 4.57
3164 3356 2.907910 CGGAGGAGCTTTGTTCAATG 57.092 50.000 0.00 0.00 0.00 2.82
3165 3357 2.426522 CGGAGGAGCTTTGTTCAATGA 58.573 47.619 0.00 0.00 0.00 2.57
3166 3358 2.417933 CGGAGGAGCTTTGTTCAATGAG 59.582 50.000 0.00 0.00 0.00 2.90
3167 3359 3.679389 GGAGGAGCTTTGTTCAATGAGA 58.321 45.455 0.00 0.00 0.00 3.27
3168 3360 3.438434 GGAGGAGCTTTGTTCAATGAGAC 59.562 47.826 0.00 0.00 0.00 3.36
3169 3361 3.070018 AGGAGCTTTGTTCAATGAGACG 58.930 45.455 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.067320 TCTGATTGACTCTATCACGCTGG 59.933 47.826 0.00 0.00 36.92 4.85
18 19 8.149647 GGATTCTGTTGATCTGATTGACTCTAT 58.850 37.037 0.00 0.00 0.00 1.98
24 25 6.765036 GCTAAGGATTCTGTTGATCTGATTGA 59.235 38.462 0.00 0.00 0.00 2.57
25 26 6.017275 GGCTAAGGATTCTGTTGATCTGATTG 60.017 42.308 0.00 0.00 0.00 2.67
28 29 4.141620 GGGCTAAGGATTCTGTTGATCTGA 60.142 45.833 0.00 0.00 0.00 3.27
68 69 1.902508 CAGCCTCTCTACCCAAACAGA 59.097 52.381 0.00 0.00 0.00 3.41
103 104 2.180159 TAAGCAAGAGTGGGACGCCC 62.180 60.000 7.87 7.87 45.71 6.13
105 106 0.246635 TCTAAGCAAGAGTGGGACGC 59.753 55.000 0.00 0.00 40.45 5.19
116 117 2.708861 TGGTCCACCTTTCTCTAAGCAA 59.291 45.455 0.00 0.00 36.82 3.91
118 119 2.567615 TCTGGTCCACCTTTCTCTAAGC 59.432 50.000 0.00 0.00 36.82 3.09
133 134 0.033504 TGACGGTGAAGCTTCTGGTC 59.966 55.000 26.09 25.48 0.00 4.02
210 211 2.590092 GGAAGGGTCCGGTCCATG 59.410 66.667 19.75 0.00 33.05 3.66
236 237 2.161410 TGGCTTTTCGGATCAATGTTCG 59.839 45.455 0.00 0.00 0.00 3.95
260 261 2.039418 CATCGAGGTGTCCCCTGAATA 58.961 52.381 0.00 0.00 46.51 1.75
267 268 1.221021 GGGTTCATCGAGGTGTCCC 59.779 63.158 9.99 9.99 0.00 4.46
269 270 1.810030 GCGGGTTCATCGAGGTGTC 60.810 63.158 0.00 0.00 0.00 3.67
270 271 2.264794 GCGGGTTCATCGAGGTGT 59.735 61.111 0.00 0.00 0.00 4.16
311 312 1.278127 ACCCGTCTGTACCAGGATTTG 59.722 52.381 0.00 0.00 31.51 2.32
344 345 2.013807 GCTGTGACTGCGAACAACA 58.986 52.632 0.00 0.00 0.00 3.33
352 353 1.291877 ACGAAATCCGCTGTGACTGC 61.292 55.000 4.22 4.22 43.32 4.40
359 360 5.907197 AAGAATATACACGAAATCCGCTG 57.093 39.130 0.00 0.00 43.32 5.18
360 361 6.761714 AGAAAAGAATATACACGAAATCCGCT 59.238 34.615 0.00 0.00 43.32 5.52
400 401 1.149987 GTTGCCAATGTTGTGCCATG 58.850 50.000 0.00 0.00 0.00 3.66
405 406 3.565482 ACACTCTAGTTGCCAATGTTGTG 59.435 43.478 0.00 0.00 0.00 3.33
408 409 4.003648 GCTACACTCTAGTTGCCAATGTT 58.996 43.478 0.00 0.00 34.82 2.71
409 410 3.261897 AGCTACACTCTAGTTGCCAATGT 59.738 43.478 0.00 0.00 40.37 2.71
415 416 3.056465 ACTCCAAGCTACACTCTAGTTGC 60.056 47.826 0.00 0.00 39.91 4.17
425 426 5.801531 TCAGAAAGTTACTCCAAGCTACA 57.198 39.130 0.00 0.00 0.00 2.74
550 561 7.406031 AATCTTCAGTTGACGAATACTCCTA 57.594 36.000 0.00 0.00 0.00 2.94
611 645 5.605534 TCAGAAAGAAACCAAGACTCAGAG 58.394 41.667 0.00 0.00 0.00 3.35
617 651 5.368989 TCCTCTTCAGAAAGAAACCAAGAC 58.631 41.667 0.00 0.00 40.95 3.01
1080 1152 3.616219 CGAAAGAATGGGGTTGTCCATA 58.384 45.455 0.00 0.00 46.05 2.74
1149 1221 0.250295 GGTTGTAGCAGCTCACCACA 60.250 55.000 0.00 0.00 0.00 4.17
1317 1392 3.316308 AGCAACCTCAACTGTGAAATGAC 59.684 43.478 0.00 0.00 31.88 3.06
1333 1410 0.647410 CACACGATCGATCAGCAACC 59.353 55.000 24.34 0.00 0.00 3.77
1545 1631 3.499737 CATGTGAAGTCCCGCGCC 61.500 66.667 0.00 0.00 0.00 6.53
1546 1632 3.499737 CCATGTGAAGTCCCGCGC 61.500 66.667 0.00 0.00 0.00 6.86
2174 2266 0.657840 GCAAAATCAGCTCGCGGTAT 59.342 50.000 6.13 0.00 0.00 2.73
2249 2341 2.490903 AGCTACTACCACCAGTAACGTG 59.509 50.000 0.00 0.00 30.77 4.49
2351 2457 1.196808 CCTGGATTTCCAACGTCAACG 59.803 52.381 0.18 0.12 46.97 4.10
2352 2458 1.068541 GCCTGGATTTCCAACGTCAAC 60.069 52.381 0.00 0.00 46.97 3.18
2353 2459 1.243902 GCCTGGATTTCCAACGTCAA 58.756 50.000 0.00 0.00 46.97 3.18
2354 2460 0.953471 CGCCTGGATTTCCAACGTCA 60.953 55.000 0.00 0.00 46.97 4.35
2355 2461 1.794222 CGCCTGGATTTCCAACGTC 59.206 57.895 0.00 0.00 46.97 4.34
2438 2621 5.858049 ACGCATGTAACATGAAAATCACAAG 59.142 36.000 0.00 0.00 0.00 3.16
2470 2656 5.864474 CGATGTACTAGCTCAATGGAATACC 59.136 44.000 0.00 0.00 0.00 2.73
2487 2673 4.142687 CCATGTCCAAACTTTCCGATGTAC 60.143 45.833 0.00 0.00 0.00 2.90
2488 2674 4.006989 CCATGTCCAAACTTTCCGATGTA 58.993 43.478 0.00 0.00 0.00 2.29
2489 2675 2.819608 CCATGTCCAAACTTTCCGATGT 59.180 45.455 0.00 0.00 0.00 3.06
2502 2688 0.694105 ATCCCGATCCACCATGTCCA 60.694 55.000 0.00 0.00 0.00 4.02
2505 2691 0.474184 GGAATCCCGATCCACCATGT 59.526 55.000 0.00 0.00 36.92 3.21
2506 2692 0.767375 AGGAATCCCGATCCACCATG 59.233 55.000 0.00 0.00 39.55 3.66
2507 2693 1.522900 AAGGAATCCCGATCCACCAT 58.477 50.000 0.00 0.00 39.55 3.55
2508 2694 1.766496 GTAAGGAATCCCGATCCACCA 59.234 52.381 0.00 0.00 39.55 4.17
2530 2716 0.102120 TGGCGTTTGTTTCAAGGCAG 59.898 50.000 1.08 0.00 33.47 4.85
2570 2756 1.553704 GGAAGGGACGAGCTAAAAGGA 59.446 52.381 0.00 0.00 0.00 3.36
2591 2777 4.107051 GCTGAGTGGCGCGCAAAT 62.107 61.111 34.42 23.70 0.00 2.32
2648 2834 0.373716 CAAGGCGACGCAAGGAATAC 59.626 55.000 23.09 0.83 46.39 1.89
2716 2902 2.362503 AGAGACATCCGCGGGACA 60.363 61.111 27.83 6.34 32.98 4.02
2717 2903 2.105128 CAGAGACATCCGCGGGAC 59.895 66.667 27.83 10.71 32.98 4.46
2720 2906 1.226802 CTCACAGAGACATCCGCGG 60.227 63.158 22.12 22.12 0.00 6.46
2737 2923 0.254178 CTGTCCTGGTATTGGCAGCT 59.746 55.000 0.00 0.00 0.00 4.24
2745 2931 1.680522 CGCTGCTCCTGTCCTGGTAT 61.681 60.000 0.00 0.00 0.00 2.73
2746 2932 2.351244 CGCTGCTCCTGTCCTGGTA 61.351 63.158 0.00 0.00 0.00 3.25
2747 2933 3.699894 CGCTGCTCCTGTCCTGGT 61.700 66.667 0.00 0.00 0.00 4.00
2748 2934 2.729479 ATCGCTGCTCCTGTCCTGG 61.729 63.158 0.00 0.00 0.00 4.45
2781 2967 4.704833 GTTGCTGGCGCTCCTCCA 62.705 66.667 7.64 0.00 36.97 3.86
2855 3041 0.043822 CTTCTTATCTCGCGCGTTGC 60.044 55.000 30.98 0.00 41.47 4.17
2858 3044 2.186076 CTTTCTTCTTATCTCGCGCGT 58.814 47.619 30.98 13.76 0.00 6.01
2864 3056 2.282820 CACGCCGCTTTCTTCTTATCTC 59.717 50.000 0.00 0.00 0.00 2.75
3079 3271 2.330372 GGAAAAAGGGACGCCGGAC 61.330 63.158 5.05 0.00 0.00 4.79
3080 3272 2.032987 GGAAAAAGGGACGCCGGA 59.967 61.111 5.05 0.00 0.00 5.14
3081 3273 2.033602 AGGAAAAAGGGACGCCGG 59.966 61.111 0.00 0.00 0.00 6.13
3082 3274 2.038837 GGAGGAAAAAGGGACGCCG 61.039 63.158 0.00 0.00 0.00 6.46
3083 3275 0.538746 TTGGAGGAAAAAGGGACGCC 60.539 55.000 0.00 0.00 0.00 5.68
3084 3276 0.596577 GTTGGAGGAAAAAGGGACGC 59.403 55.000 0.00 0.00 0.00 5.19
3085 3277 1.607148 GTGTTGGAGGAAAAAGGGACG 59.393 52.381 0.00 0.00 0.00 4.79
3086 3278 2.623416 CAGTGTTGGAGGAAAAAGGGAC 59.377 50.000 0.00 0.00 0.00 4.46
3087 3279 2.944129 CAGTGTTGGAGGAAAAAGGGA 58.056 47.619 0.00 0.00 0.00 4.20
3088 3280 1.341209 GCAGTGTTGGAGGAAAAAGGG 59.659 52.381 0.00 0.00 0.00 3.95
3089 3281 2.294512 GAGCAGTGTTGGAGGAAAAAGG 59.705 50.000 0.00 0.00 0.00 3.11
3090 3282 3.217626 AGAGCAGTGTTGGAGGAAAAAG 58.782 45.455 0.00 0.00 0.00 2.27
3091 3283 3.297134 AGAGCAGTGTTGGAGGAAAAA 57.703 42.857 0.00 0.00 0.00 1.94
3092 3284 3.740115 GTAGAGCAGTGTTGGAGGAAAA 58.260 45.455 0.00 0.00 0.00 2.29
3093 3285 2.288825 CGTAGAGCAGTGTTGGAGGAAA 60.289 50.000 0.00 0.00 0.00 3.13
3094 3286 1.272490 CGTAGAGCAGTGTTGGAGGAA 59.728 52.381 0.00 0.00 0.00 3.36
3095 3287 0.888619 CGTAGAGCAGTGTTGGAGGA 59.111 55.000 0.00 0.00 0.00 3.71
3096 3288 3.425578 CGTAGAGCAGTGTTGGAGG 57.574 57.895 0.00 0.00 0.00 4.30
3107 3299 2.968330 CGCACCGTAGAGCGTAGAGC 62.968 65.000 0.00 0.00 44.20 4.09
3108 3300 1.011019 CGCACCGTAGAGCGTAGAG 60.011 63.158 0.00 0.00 44.20 2.43
3109 3301 3.095911 CGCACCGTAGAGCGTAGA 58.904 61.111 0.00 0.00 44.20 2.59
3114 3306 3.479269 GTGCACGCACCGTAGAGC 61.479 66.667 11.13 0.00 38.32 4.09
3115 3307 2.049526 TGTGCACGCACCGTAGAG 60.050 61.111 18.91 0.00 45.63 2.43
3116 3308 2.355363 GTGTGCACGCACCGTAGA 60.355 61.111 25.05 0.00 45.63 2.59
3126 3318 2.052237 CAGAAACGCCGTGTGCAC 60.052 61.111 10.75 10.75 41.33 4.57
3127 3319 3.947841 GCAGAAACGCCGTGTGCA 61.948 61.111 12.89 0.00 41.33 4.57
3128 3320 4.683334 GGCAGAAACGCCGTGTGC 62.683 66.667 10.14 10.14 43.52 4.57
3135 3327 2.815647 CTCCTCCGGCAGAAACGC 60.816 66.667 0.00 0.00 0.00 4.84
3136 3328 2.788191 AAGCTCCTCCGGCAGAAACG 62.788 60.000 0.00 0.00 0.00 3.60
3137 3329 0.606673 AAAGCTCCTCCGGCAGAAAC 60.607 55.000 0.00 0.00 0.00 2.78
3138 3330 0.606401 CAAAGCTCCTCCGGCAGAAA 60.606 55.000 0.00 0.00 0.00 2.52
3139 3331 1.003355 CAAAGCTCCTCCGGCAGAA 60.003 57.895 0.00 0.00 0.00 3.02
3140 3332 1.768684 AACAAAGCTCCTCCGGCAGA 61.769 55.000 0.00 0.00 0.00 4.26
3141 3333 1.301677 GAACAAAGCTCCTCCGGCAG 61.302 60.000 0.00 0.00 0.00 4.85
3142 3334 1.302511 GAACAAAGCTCCTCCGGCA 60.303 57.895 0.00 0.00 0.00 5.69
3143 3335 0.889186 TTGAACAAAGCTCCTCCGGC 60.889 55.000 0.00 0.00 0.00 6.13
3144 3336 1.470098 CATTGAACAAAGCTCCTCCGG 59.530 52.381 0.00 0.00 0.00 5.14
3145 3337 2.417933 CTCATTGAACAAAGCTCCTCCG 59.582 50.000 0.00 0.00 0.00 4.63
3146 3338 3.438434 GTCTCATTGAACAAAGCTCCTCC 59.562 47.826 0.00 0.00 0.00 4.30
3147 3339 3.124297 CGTCTCATTGAACAAAGCTCCTC 59.876 47.826 0.00 0.00 0.00 3.71
3148 3340 3.070018 CGTCTCATTGAACAAAGCTCCT 58.930 45.455 0.00 0.00 0.00 3.69
3149 3341 3.461946 CGTCTCATTGAACAAAGCTCC 57.538 47.619 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.