Multiple sequence alignment - TraesCS6B01G334900

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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 TraesCS6B01G334900 chr6B 100.000 2452 0 0 758 3209 589129672 589127221 0.000000e+00 4529.0
1 TraesCS6B01G334900 chr6B 100.000 135 0 0 1 135 589130429 589130295 1.910000e-62 250.0
2 TraesCS6B01G334900 chr6A 93.388 2208 85 21 827 2975 540146019 540143814 0.000000e+00 3212.0
3 TraesCS6B01G334900 chr6A 95.575 113 5 0 19 131 540146475 540146363 7.070000e-42 182.0
4 TraesCS6B01G334900 chr6A 88.889 54 4 2 2995 3047 158921723 158921775 7.430000e-07 65.8
5 TraesCS6B01G334900 chr6A 100.000 28 0 0 809 836 540146045 540146018 6.000000e-03 52.8
6 TraesCS6B01G334900 chr6D 95.657 1957 63 9 848 2790 393936546 393934598 0.000000e+00 3123.0
7 TraesCS6B01G334900 chr6D 95.620 137 4 1 1 135 393937018 393936882 5.390000e-53 219.0
8 TraesCS6B01G334900 chr6D 98.551 69 1 0 758 826 393936824 393936756 4.350000e-24 122.0
9 TraesCS6B01G334900 chr7D 77.768 1156 137 73 972 2079 140232496 140233579 4.580000e-168 601.0
10 TraesCS6B01G334900 chr7D 100.000 37 0 0 2949 2985 133236462 133236498 5.740000e-08 69.4
11 TraesCS6B01G334900 chr7D 94.737 38 2 0 3009 3046 575749360 575749397 3.460000e-05 60.2
12 TraesCS6B01G334900 chr7D 97.059 34 1 0 3070 3103 3685397 3685430 1.240000e-04 58.4
13 TraesCS6B01G334900 chr7B 77.125 1141 150 68 972 2079 105323152 105324214 2.800000e-155 558.0
14 TraesCS6B01G334900 chr7B 100.000 32 0 0 3072 3103 618852729 618852698 3.460000e-05 60.2
15 TraesCS6B01G334900 chr7B 97.143 35 0 1 3075 3109 410022102 410022135 1.240000e-04 58.4
16 TraesCS6B01G334900 chr7A 76.783 1150 154 71 973 2079 140536530 140537609 1.010000e-149 540.0
17 TraesCS6B01G334900 chr5D 87.838 222 24 2 1184 1405 205995763 205995981 1.140000e-64 257.0
18 TraesCS6B01G334900 chr5A 87.838 222 24 2 1184 1405 264421483 264421701 1.140000e-64 257.0
19 TraesCS6B01G334900 chr5A 95.122 41 2 0 2945 2985 387351382 387351422 7.430000e-07 65.8
20 TraesCS6B01G334900 chr5B 87.387 222 25 2 1184 1405 206102417 206102199 5.310000e-63 252.0
21 TraesCS6B01G334900 chr5B 77.311 119 18 7 2944 3054 596670875 596670758 9.610000e-06 62.1
22 TraesCS6B01G334900 chr5B 92.683 41 2 1 3070 3109 611703799 611703759 1.240000e-04 58.4
23 TraesCS6B01G334900 chr4A 95.833 48 2 0 3002 3049 733564434 733564387 9.540000e-11 78.7
24 TraesCS6B01G334900 chr4A 95.238 42 0 1 3008 3047 613579742 613579783 7.430000e-07 65.8
25 TraesCS6B01G334900 chr3B 97.561 41 0 1 2945 2985 179164807 179164768 5.740000e-08 69.4
26 TraesCS6B01G334900 chr3B 95.122 41 1 1 2951 2990 159539362 159539322 2.670000e-06 63.9
27 TraesCS6B01G334900 chr3A 91.837 49 4 0 2937 2985 685135945 685135993 5.740000e-08 69.4
28 TraesCS6B01G334900 chr2B 81.818 88 7 8 2956 3043 473335234 473335312 7.430000e-07 65.8
29 TraesCS6B01G334900 chr2A 100.000 31 0 0 3074 3104 113367233 113367203 1.240000e-04 58.4


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 TraesCS6B01G334900 chr6B 589127221 589130429 3208 True 2389.500000 4529 100.000000 1 3209 2 chr6B.!!$R1 3208
1 TraesCS6B01G334900 chr6A 540143814 540146475 2661 True 1148.933333 3212 96.321000 19 2975 3 chr6A.!!$R1 2956
2 TraesCS6B01G334900 chr6D 393934598 393937018 2420 True 1154.666667 3123 96.609333 1 2790 3 chr6D.!!$R1 2789
3 TraesCS6B01G334900 chr7D 140232496 140233579 1083 False 601.000000 601 77.768000 972 2079 1 chr7D.!!$F3 1107
4 TraesCS6B01G334900 chr7B 105323152 105324214 1062 False 558.000000 558 77.125000 972 2079 1 chr7B.!!$F1 1107
5 TraesCS6B01G334900 chr7A 140536530 140537609 1079 False 540.000000 540 76.783000 973 2079 1 chr7A.!!$F1 1106

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
915 1106 1.299541 CATCAAATCCGTTCCCCTCG 58.700 55.000 0.0 0.0 0.0 4.63 F
1807 2040 1.726865 CCAAGCAACAACACGCAGA 59.273 52.632 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2363 0.033503 TAGACGATCCTCCTGCACCA 60.034 55.0 0.00 0.00 0.0 4.17 R
3152 3451 0.103208 GTCCTACTGGCAGATCACGG 59.897 60.0 23.66 12.88 0.0 4.94 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
52 55 4.137543 CTCTCTCCTTCTCCTAGCTTCTC 58.862 52.174 0.00 0.00 0.00 2.87
93 96 2.756907 CTTCTCCCTTCTCCCAGATCA 58.243 52.381 0.00 0.00 0.00 2.92
108 111 4.163078 CCCAGATCACAGATGAACCTTACT 59.837 45.833 0.00 0.00 38.69 2.24
780 783 6.765915 CTCATCGTATCATATGAGGAAGGA 57.234 41.667 11.78 10.18 43.50 3.36
915 1106 1.299541 CATCAAATCCGTTCCCCTCG 58.700 55.000 0.00 0.00 0.00 4.63
1197 1394 2.885644 CCCAAGCGGACATCGACG 60.886 66.667 0.00 0.00 42.43 5.12
1557 1778 4.493747 CCCGCCTCGTCTTCGTCC 62.494 72.222 0.00 0.00 38.33 4.79
1560 1781 2.963371 GCCTCGTCTTCGTCCACT 59.037 61.111 0.00 0.00 38.33 4.00
1621 1842 4.680237 TTGACGTGCAGCCCTCGG 62.680 66.667 0.00 0.00 34.92 4.63
1807 2040 1.726865 CCAAGCAACAACACGCAGA 59.273 52.632 0.00 0.00 0.00 4.26
1978 2220 2.511373 CACCGATGGCGCTGCTAA 60.511 61.111 7.64 0.00 35.83 3.09
2280 2530 5.009010 TGGCTTTGATCTGTTCTTTGTCTTC 59.991 40.000 0.00 0.00 0.00 2.87
2338 2588 3.064958 TCCTAGACATTAGACAACTCGCG 59.935 47.826 0.00 0.00 0.00 5.87
2351 2601 1.460504 ACTCGCGAGGATTACACTCA 58.539 50.000 36.93 0.00 34.66 3.41
2373 2623 1.955778 CTGCGATCCCATGGCATTTAA 59.044 47.619 6.09 0.00 43.06 1.52
2441 2694 1.746615 CGAGGTGTGCCATTGGAGG 60.747 63.158 6.95 0.00 37.19 4.30
2460 2713 1.210722 GGAGAGGAGGGAAACACATCC 59.789 57.143 0.00 0.00 38.86 3.51
2609 2868 0.461693 TGTTTGCCACCAAGCTTTGC 60.462 50.000 0.00 0.00 33.82 3.68
2687 2948 2.086869 GCTGCTTGTGCTCCTTAATCA 58.913 47.619 0.00 0.00 40.48 2.57
2695 2956 6.424812 GCTTGTGCTCCTTAATCAATTTGTTT 59.575 34.615 0.00 0.00 36.03 2.83
2801 3082 1.522092 CCTGATCTGCGGGCACTTA 59.478 57.895 0.00 0.00 35.91 2.24
2804 3085 0.613260 TGATCTGCGGGCACTTACTT 59.387 50.000 0.00 0.00 0.00 2.24
2805 3086 1.009829 GATCTGCGGGCACTTACTTG 58.990 55.000 0.00 0.00 0.00 3.16
2810 3091 1.677552 CGGGCACTTACTTGGTCCT 59.322 57.895 0.00 0.00 0.00 3.85
2811 3092 0.899720 CGGGCACTTACTTGGTCCTA 59.100 55.000 0.00 0.00 0.00 2.94
2820 3101 7.825761 GGCACTTACTTGGTCCTACTTTATTTA 59.174 37.037 0.00 0.00 0.00 1.40
2831 3112 7.294245 GGTCCTACTTTATTTATTAGTCCCCCT 59.706 40.741 0.00 0.00 0.00 4.79
2832 3113 8.373981 GTCCTACTTTATTTATTAGTCCCCCTC 58.626 40.741 0.00 0.00 0.00 4.30
2833 3114 8.075621 TCCTACTTTATTTATTAGTCCCCCTCA 58.924 37.037 0.00 0.00 0.00 3.86
2834 3115 8.891501 CCTACTTTATTTATTAGTCCCCCTCAT 58.108 37.037 0.00 0.00 0.00 2.90
2853 3152 7.095187 CCCCTCATATATTTTTGTCGAACTAGC 60.095 40.741 0.00 0.00 0.00 3.42
2863 3162 7.678194 TTTTGTCGAACTAGCAAAATGAAAG 57.322 32.000 6.75 0.00 37.24 2.62
2865 3164 6.612247 TGTCGAACTAGCAAAATGAAAGAA 57.388 33.333 0.00 0.00 0.00 2.52
2867 3166 7.298122 TGTCGAACTAGCAAAATGAAAGAATC 58.702 34.615 0.00 0.00 0.00 2.52
2883 3182 8.610248 TGAAAGAATCGACCACAAAATTAGTA 57.390 30.769 0.00 0.00 0.00 1.82
2933 3232 4.812091 TGAATACGAATCCAACAATACGGG 59.188 41.667 0.00 0.00 0.00 5.28
2948 3247 9.925268 CAACAATACGGGTTTTATAATGTACTC 57.075 33.333 0.00 0.00 0.00 2.59
2949 3248 9.895138 AACAATACGGGTTTTATAATGTACTCT 57.105 29.630 0.00 0.00 0.00 3.24
2955 3254 7.123847 ACGGGTTTTATAATGTACTCTCTCTGT 59.876 37.037 0.00 0.00 0.00 3.41
3042 3341 8.758633 AACGATCATATATTTCTTTACCGAGG 57.241 34.615 0.00 0.00 0.00 4.63
3043 3342 7.321153 ACGATCATATATTTCTTTACCGAGGG 58.679 38.462 0.00 0.00 0.00 4.30
3044 3343 7.177921 ACGATCATATATTTCTTTACCGAGGGA 59.822 37.037 0.00 0.00 0.00 4.20
3045 3344 7.702772 CGATCATATATTTCTTTACCGAGGGAG 59.297 40.741 0.00 0.00 0.00 4.30
3046 3345 7.850935 TCATATATTTCTTTACCGAGGGAGT 57.149 36.000 0.00 0.00 0.00 3.85
3047 3346 7.667557 TCATATATTTCTTTACCGAGGGAGTG 58.332 38.462 0.00 0.00 0.00 3.51
3048 3347 2.467566 TTTCTTTACCGAGGGAGTGC 57.532 50.000 0.00 0.00 0.00 4.40
3049 3348 1.344065 TTCTTTACCGAGGGAGTGCA 58.656 50.000 0.00 0.00 0.00 4.57
3050 3349 1.344065 TCTTTACCGAGGGAGTGCAA 58.656 50.000 0.00 0.00 0.00 4.08
3051 3350 1.906574 TCTTTACCGAGGGAGTGCAAT 59.093 47.619 0.00 0.00 0.00 3.56
3052 3351 2.304761 TCTTTACCGAGGGAGTGCAATT 59.695 45.455 0.00 0.00 0.00 2.32
3053 3352 2.871096 TTACCGAGGGAGTGCAATTT 57.129 45.000 0.00 0.00 0.00 1.82
3054 3353 3.985019 TTACCGAGGGAGTGCAATTTA 57.015 42.857 0.00 0.00 0.00 1.40
3055 3354 4.497291 TTACCGAGGGAGTGCAATTTAT 57.503 40.909 0.00 0.00 0.00 1.40
3056 3355 5.617528 TTACCGAGGGAGTGCAATTTATA 57.382 39.130 0.00 0.00 0.00 0.98
3057 3356 4.706842 ACCGAGGGAGTGCAATTTATAT 57.293 40.909 0.00 0.00 0.00 0.86
3058 3357 5.048846 ACCGAGGGAGTGCAATTTATATT 57.951 39.130 0.00 0.00 0.00 1.28
3059 3358 5.445964 ACCGAGGGAGTGCAATTTATATTT 58.554 37.500 0.00 0.00 0.00 1.40
3060 3359 5.891551 ACCGAGGGAGTGCAATTTATATTTT 59.108 36.000 0.00 0.00 0.00 1.82
3061 3360 6.183360 ACCGAGGGAGTGCAATTTATATTTTG 60.183 38.462 0.00 0.00 0.00 2.44
3062 3361 6.183360 CCGAGGGAGTGCAATTTATATTTTGT 60.183 38.462 0.00 0.00 0.00 2.83
3063 3362 7.012894 CCGAGGGAGTGCAATTTATATTTTGTA 59.987 37.037 0.00 0.00 0.00 2.41
3064 3363 8.402472 CGAGGGAGTGCAATTTATATTTTGTAA 58.598 33.333 0.00 0.00 0.00 2.41
3109 3408 7.671495 AAAATTTGACACAAAATATGAGGGC 57.329 32.000 0.00 0.00 0.00 5.19
3110 3409 6.610075 AATTTGACACAAAATATGAGGGCT 57.390 33.333 0.00 0.00 0.00 5.19
3111 3410 5.643379 TTTGACACAAAATATGAGGGCTC 57.357 39.130 0.00 0.00 0.00 4.70
3112 3411 3.620488 TGACACAAAATATGAGGGCTCC 58.380 45.455 0.00 0.00 0.00 4.70
3113 3412 2.614057 GACACAAAATATGAGGGCTCCG 59.386 50.000 0.00 0.00 0.00 4.63
3114 3413 1.949525 CACAAAATATGAGGGCTCCGG 59.050 52.381 0.00 0.00 0.00 5.14
3115 3414 1.843851 ACAAAATATGAGGGCTCCGGA 59.156 47.619 2.93 2.93 0.00 5.14
3116 3415 2.443255 ACAAAATATGAGGGCTCCGGAT 59.557 45.455 3.57 0.00 0.00 4.18
3117 3416 2.816087 CAAAATATGAGGGCTCCGGATG 59.184 50.000 3.57 0.00 0.00 3.51
3118 3417 0.987294 AATATGAGGGCTCCGGATGG 59.013 55.000 3.57 0.00 0.00 3.51
3119 3418 0.117140 ATATGAGGGCTCCGGATGGA 59.883 55.000 3.57 0.00 43.88 3.41
3127 3426 3.033773 TCCGGATGGAGGAGGGGA 61.034 66.667 0.00 0.00 40.17 4.81
3128 3427 2.040884 CCGGATGGAGGAGGGGAA 60.041 66.667 0.00 0.00 37.49 3.97
3129 3428 1.462238 CCGGATGGAGGAGGGGAAT 60.462 63.158 0.00 0.00 37.49 3.01
3130 3429 1.062488 CCGGATGGAGGAGGGGAATT 61.062 60.000 0.00 0.00 37.49 2.17
3131 3430 1.729586 CGGATGGAGGAGGGGAATTA 58.270 55.000 0.00 0.00 0.00 1.40
3132 3431 1.625818 CGGATGGAGGAGGGGAATTAG 59.374 57.143 0.00 0.00 0.00 1.73
3133 3432 2.707554 GGATGGAGGAGGGGAATTAGT 58.292 52.381 0.00 0.00 0.00 2.24
3134 3433 2.373502 GGATGGAGGAGGGGAATTAGTG 59.626 54.545 0.00 0.00 0.00 2.74
3135 3434 2.661176 TGGAGGAGGGGAATTAGTGT 57.339 50.000 0.00 0.00 0.00 3.55
3136 3435 3.788116 TGGAGGAGGGGAATTAGTGTA 57.212 47.619 0.00 0.00 0.00 2.90
3137 3436 3.381335 TGGAGGAGGGGAATTAGTGTAC 58.619 50.000 0.00 0.00 0.00 2.90
3138 3437 2.364647 GGAGGAGGGGAATTAGTGTACG 59.635 54.545 0.00 0.00 0.00 3.67
3139 3438 2.364647 GAGGAGGGGAATTAGTGTACGG 59.635 54.545 0.00 0.00 0.00 4.02
3140 3439 1.202615 GGAGGGGAATTAGTGTACGGC 60.203 57.143 0.00 0.00 0.00 5.68
3141 3440 0.462789 AGGGGAATTAGTGTACGGCG 59.537 55.000 4.80 4.80 0.00 6.46
3142 3441 0.531311 GGGGAATTAGTGTACGGCGG 60.531 60.000 13.24 0.00 0.00 6.13
3143 3442 1.156034 GGGAATTAGTGTACGGCGGC 61.156 60.000 13.24 0.00 0.00 6.53
3144 3443 1.485032 GGAATTAGTGTACGGCGGCG 61.485 60.000 31.06 31.06 0.00 6.46
3145 3444 1.485032 GAATTAGTGTACGGCGGCGG 61.485 60.000 35.05 17.25 0.00 6.13
3146 3445 4.799824 TTAGTGTACGGCGGCGGC 62.800 66.667 35.05 24.75 38.90 6.53
3161 3460 3.474806 GGCGTCAACCGTGATCTG 58.525 61.111 0.00 0.00 39.32 2.90
3162 3461 2.740714 GGCGTCAACCGTGATCTGC 61.741 63.158 0.00 0.00 39.32 4.26
3163 3462 2.740714 GCGTCAACCGTGATCTGCC 61.741 63.158 0.00 0.00 39.32 4.85
3164 3463 1.374125 CGTCAACCGTGATCTGCCA 60.374 57.895 0.00 0.00 35.80 4.92
3165 3464 1.354337 CGTCAACCGTGATCTGCCAG 61.354 60.000 0.00 0.00 35.80 4.85
3166 3465 0.320771 GTCAACCGTGATCTGCCAGT 60.321 55.000 0.00 0.00 35.80 4.00
3167 3466 1.067142 GTCAACCGTGATCTGCCAGTA 60.067 52.381 0.00 0.00 35.80 2.74
3168 3467 1.204704 TCAACCGTGATCTGCCAGTAG 59.795 52.381 0.00 0.00 0.00 2.57
3169 3468 0.537188 AACCGTGATCTGCCAGTAGG 59.463 55.000 0.00 0.00 38.23 3.18
3170 3469 0.324368 ACCGTGATCTGCCAGTAGGA 60.324 55.000 0.00 0.00 36.89 2.94
3171 3470 0.103208 CCGTGATCTGCCAGTAGGAC 59.897 60.000 0.00 0.00 36.89 3.85
3172 3471 1.107114 CGTGATCTGCCAGTAGGACT 58.893 55.000 0.00 0.00 36.89 3.85
3173 3472 2.298610 CGTGATCTGCCAGTAGGACTA 58.701 52.381 0.00 0.00 36.89 2.59
3174 3473 2.033550 CGTGATCTGCCAGTAGGACTAC 59.966 54.545 1.25 1.25 36.89 2.73
3175 3474 3.024547 GTGATCTGCCAGTAGGACTACA 58.975 50.000 11.67 0.00 38.48 2.74
3176 3475 3.639094 GTGATCTGCCAGTAGGACTACAT 59.361 47.826 11.67 0.00 38.48 2.29
3177 3476 4.827835 GTGATCTGCCAGTAGGACTACATA 59.172 45.833 11.67 0.00 38.48 2.29
3178 3477 5.048364 GTGATCTGCCAGTAGGACTACATAG 60.048 48.000 11.67 4.69 38.48 2.23
3179 3478 4.790718 TCTGCCAGTAGGACTACATAGA 57.209 45.455 11.67 6.59 38.48 1.98
3180 3479 5.125367 TCTGCCAGTAGGACTACATAGAA 57.875 43.478 11.67 0.00 38.48 2.10
3181 3480 5.516044 TCTGCCAGTAGGACTACATAGAAA 58.484 41.667 11.67 0.00 38.48 2.52
3182 3481 5.955959 TCTGCCAGTAGGACTACATAGAAAA 59.044 40.000 11.67 0.00 38.48 2.29
3183 3482 6.611642 TCTGCCAGTAGGACTACATAGAAAAT 59.388 38.462 11.67 0.00 38.48 1.82
3184 3483 7.783119 TCTGCCAGTAGGACTACATAGAAAATA 59.217 37.037 11.67 0.00 38.48 1.40
3185 3484 8.313944 TGCCAGTAGGACTACATAGAAAATAA 57.686 34.615 11.67 0.00 38.48 1.40
3186 3485 8.934697 TGCCAGTAGGACTACATAGAAAATAAT 58.065 33.333 11.67 0.00 38.48 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 55 2.030262 GAGCAGATGGCCCTAGCG 59.970 66.667 0.00 0.00 46.50 4.26
93 96 4.162509 GGCCTTCTAGTAAGGTTCATCTGT 59.837 45.833 17.16 0.00 39.60 3.41
108 111 6.597672 CACACACACTATTTTATGGCCTTCTA 59.402 38.462 3.32 0.00 0.00 2.10
780 783 9.642343 GGTAAAGATTATAGGTTTGGAAGGAAT 57.358 33.333 0.00 0.00 0.00 3.01
895 1086 1.406887 CGAGGGGAACGGATTTGATGT 60.407 52.381 0.00 0.00 0.00 3.06
915 1106 1.757423 ATGGGTGGTTGTTTGCAGGC 61.757 55.000 0.00 0.00 0.00 4.85
1032 1226 2.856988 AAGGGGAAGTTGGGCCGA 60.857 61.111 0.00 0.00 0.00 5.54
1191 1388 3.066190 TGCCGGTCCTTCGTCGAT 61.066 61.111 1.90 0.00 0.00 3.59
1197 1394 1.966451 CTTGGTGTGCCGGTCCTTC 60.966 63.158 1.90 0.00 37.67 3.46
1464 1664 3.617143 GAACCTTACGCCGGGGCTT 62.617 63.158 19.97 2.11 39.32 4.35
1650 1871 1.292223 CCGCTTCCTCGAAAGGTCA 59.708 57.895 0.00 0.00 43.82 4.02
1689 1910 0.179129 GTTGTTGTTGCTGCTGCTGT 60.179 50.000 17.00 0.00 40.48 4.40
2034 2279 3.882326 CCCATCTGCCCATCGCCT 61.882 66.667 0.00 0.00 36.24 5.52
2035 2280 4.962836 CCCCATCTGCCCATCGCC 62.963 72.222 0.00 0.00 36.24 5.54
2037 2282 1.002868 GATCCCCATCTGCCCATCG 60.003 63.158 0.00 0.00 0.00 3.84
2040 2285 1.771746 GAGGATCCCCATCTGCCCA 60.772 63.158 8.55 0.00 33.88 5.36
2118 2363 0.033503 TAGACGATCCTCCTGCACCA 60.034 55.000 0.00 0.00 0.00 4.17
2123 2368 0.958091 CTGGCTAGACGATCCTCCTG 59.042 60.000 0.00 0.00 0.00 3.86
2246 2496 2.373169 AGATCAAAGCCACACCAGAGAA 59.627 45.455 0.00 0.00 0.00 2.87
2280 2530 6.902224 AACCACAAAAGGAAAAAGAAATCG 57.098 33.333 0.00 0.00 0.00 3.34
2338 2588 1.135139 TCGCAGCTGAGTGTAATCCTC 59.865 52.381 20.43 0.00 0.00 3.71
2351 2601 2.635787 AATGCCATGGGATCGCAGCT 62.636 55.000 20.20 0.00 35.66 4.24
2373 2623 4.386954 CGTGCGCTAAGTATGATGATGATT 59.613 41.667 9.73 0.00 0.00 2.57
2441 2694 1.134670 CGGATGTGTTTCCCTCCTCTC 60.135 57.143 0.00 0.00 31.61 3.20
2460 2713 1.645704 AATCTCTTGCTGCTGCTGCG 61.646 55.000 23.38 12.38 43.34 5.18
2621 2880 6.757947 CCCTGCATGGTGTAAAATAATTTGAG 59.242 38.462 0.00 0.00 0.00 3.02
2626 2885 3.387699 GGCCCTGCATGGTGTAAAATAAT 59.612 43.478 9.95 0.00 0.00 1.28
2695 2956 4.655963 AGCTAGCTGGTTGATCAAGAAAA 58.344 39.130 18.57 0.00 0.00 2.29
2790 3051 1.302192 GACCAAGTAAGTGCCCGCA 60.302 57.895 0.00 0.00 0.00 5.69
2804 3085 7.072834 GGGGGACTAATAAATAAAGTAGGACCA 59.927 40.741 0.00 0.00 0.00 4.02
2805 3086 7.294245 AGGGGGACTAATAAATAAAGTAGGACC 59.706 40.741 0.00 0.00 0.00 4.46
2820 3101 7.883311 CGACAAAAATATATGAGGGGGACTAAT 59.117 37.037 0.00 0.00 0.00 1.73
2822 3103 6.555738 TCGACAAAAATATATGAGGGGGACTA 59.444 38.462 0.00 0.00 0.00 2.59
2823 3104 5.368523 TCGACAAAAATATATGAGGGGGACT 59.631 40.000 0.00 0.00 0.00 3.85
2853 3152 7.462109 TTTTGTGGTCGATTCTTTCATTTTG 57.538 32.000 0.00 0.00 0.00 2.44
2897 3196 9.004717 TGGATTCGTATTCAAAATAAGTTGTCA 57.995 29.630 0.00 0.00 0.00 3.58
2900 3199 9.619316 TGTTGGATTCGTATTCAAAATAAGTTG 57.381 29.630 0.00 0.00 31.04 3.16
3016 3315 9.204570 CCTCGGTAAAGAAATATATGATCGTTT 57.795 33.333 0.00 0.00 0.00 3.60
3017 3316 7.817962 CCCTCGGTAAAGAAATATATGATCGTT 59.182 37.037 0.00 5.65 0.00 3.85
3018 3317 7.177921 TCCCTCGGTAAAGAAATATATGATCGT 59.822 37.037 0.00 0.00 0.00 3.73
3019 3318 7.544622 TCCCTCGGTAAAGAAATATATGATCG 58.455 38.462 0.00 0.00 0.00 3.69
3020 3319 8.532819 ACTCCCTCGGTAAAGAAATATATGATC 58.467 37.037 0.00 0.00 0.00 2.92
3021 3320 8.314751 CACTCCCTCGGTAAAGAAATATATGAT 58.685 37.037 0.00 0.00 0.00 2.45
3022 3321 7.667557 CACTCCCTCGGTAAAGAAATATATGA 58.332 38.462 0.00 0.00 0.00 2.15
3023 3322 6.369065 GCACTCCCTCGGTAAAGAAATATATG 59.631 42.308 0.00 0.00 0.00 1.78
3024 3323 6.042781 TGCACTCCCTCGGTAAAGAAATATAT 59.957 38.462 0.00 0.00 0.00 0.86
3025 3324 5.364446 TGCACTCCCTCGGTAAAGAAATATA 59.636 40.000 0.00 0.00 0.00 0.86
3026 3325 4.163458 TGCACTCCCTCGGTAAAGAAATAT 59.837 41.667 0.00 0.00 0.00 1.28
3027 3326 3.516300 TGCACTCCCTCGGTAAAGAAATA 59.484 43.478 0.00 0.00 0.00 1.40
3028 3327 2.304761 TGCACTCCCTCGGTAAAGAAAT 59.695 45.455 0.00 0.00 0.00 2.17
3029 3328 1.695242 TGCACTCCCTCGGTAAAGAAA 59.305 47.619 0.00 0.00 0.00 2.52
3030 3329 1.344065 TGCACTCCCTCGGTAAAGAA 58.656 50.000 0.00 0.00 0.00 2.52
3031 3330 1.344065 TTGCACTCCCTCGGTAAAGA 58.656 50.000 0.00 0.00 0.00 2.52
3032 3331 2.403252 ATTGCACTCCCTCGGTAAAG 57.597 50.000 0.00 0.00 0.00 1.85
3033 3332 2.871096 AATTGCACTCCCTCGGTAAA 57.129 45.000 0.00 0.00 0.00 2.01
3034 3333 2.871096 AAATTGCACTCCCTCGGTAA 57.129 45.000 0.00 0.00 0.00 2.85
3035 3334 5.818678 ATATAAATTGCACTCCCTCGGTA 57.181 39.130 0.00 0.00 0.00 4.02
3036 3335 4.706842 ATATAAATTGCACTCCCTCGGT 57.293 40.909 0.00 0.00 0.00 4.69
3037 3336 6.183360 ACAAAATATAAATTGCACTCCCTCGG 60.183 38.462 0.00 0.00 0.00 4.63
3038 3337 6.795399 ACAAAATATAAATTGCACTCCCTCG 58.205 36.000 0.00 0.00 0.00 4.63
3083 3382 9.213799 GCCCTCATATTTTGTGTCAAATTTTAA 57.786 29.630 0.00 0.00 0.00 1.52
3084 3383 8.592809 AGCCCTCATATTTTGTGTCAAATTTTA 58.407 29.630 0.00 0.00 0.00 1.52
3085 3384 7.452562 AGCCCTCATATTTTGTGTCAAATTTT 58.547 30.769 0.00 0.00 0.00 1.82
3086 3385 7.008021 AGCCCTCATATTTTGTGTCAAATTT 57.992 32.000 0.00 0.00 0.00 1.82
3087 3386 6.351286 GGAGCCCTCATATTTTGTGTCAAATT 60.351 38.462 0.00 0.00 0.00 1.82
3088 3387 5.127682 GGAGCCCTCATATTTTGTGTCAAAT 59.872 40.000 0.00 0.00 0.00 2.32
3089 3388 4.462483 GGAGCCCTCATATTTTGTGTCAAA 59.538 41.667 0.00 0.00 0.00 2.69
3090 3389 4.016444 GGAGCCCTCATATTTTGTGTCAA 58.984 43.478 0.00 0.00 0.00 3.18
3091 3390 3.620488 GGAGCCCTCATATTTTGTGTCA 58.380 45.455 0.00 0.00 0.00 3.58
3092 3391 2.614057 CGGAGCCCTCATATTTTGTGTC 59.386 50.000 0.00 0.00 0.00 3.67
3093 3392 2.643551 CGGAGCCCTCATATTTTGTGT 58.356 47.619 0.00 0.00 0.00 3.72
3094 3393 1.949525 CCGGAGCCCTCATATTTTGTG 59.050 52.381 0.00 0.00 0.00 3.33
3095 3394 1.843851 TCCGGAGCCCTCATATTTTGT 59.156 47.619 0.00 0.00 0.00 2.83
3096 3395 2.638480 TCCGGAGCCCTCATATTTTG 57.362 50.000 0.00 0.00 0.00 2.44
3097 3396 2.224867 CCATCCGGAGCCCTCATATTTT 60.225 50.000 11.34 0.00 0.00 1.82
3098 3397 1.352352 CCATCCGGAGCCCTCATATTT 59.648 52.381 11.34 0.00 0.00 1.40
3099 3398 0.987294 CCATCCGGAGCCCTCATATT 59.013 55.000 11.34 0.00 0.00 1.28
3100 3399 0.117140 TCCATCCGGAGCCCTCATAT 59.883 55.000 11.34 0.00 35.91 1.78
3101 3400 1.546738 TCCATCCGGAGCCCTCATA 59.453 57.895 11.34 0.00 35.91 2.15
3102 3401 2.286905 TCCATCCGGAGCCCTCAT 59.713 61.111 11.34 0.00 35.91 2.90
3110 3409 1.973346 ATTCCCCTCCTCCATCCGGA 61.973 60.000 6.61 6.61 39.79 5.14
3111 3410 1.062488 AATTCCCCTCCTCCATCCGG 61.062 60.000 0.00 0.00 0.00 5.14
3112 3411 1.625818 CTAATTCCCCTCCTCCATCCG 59.374 57.143 0.00 0.00 0.00 4.18
3113 3412 2.373502 CACTAATTCCCCTCCTCCATCC 59.626 54.545 0.00 0.00 0.00 3.51
3114 3413 3.049344 ACACTAATTCCCCTCCTCCATC 58.951 50.000 0.00 0.00 0.00 3.51
3115 3414 3.151542 ACACTAATTCCCCTCCTCCAT 57.848 47.619 0.00 0.00 0.00 3.41
3116 3415 2.661176 ACACTAATTCCCCTCCTCCA 57.339 50.000 0.00 0.00 0.00 3.86
3117 3416 2.364647 CGTACACTAATTCCCCTCCTCC 59.635 54.545 0.00 0.00 0.00 4.30
3118 3417 2.364647 CCGTACACTAATTCCCCTCCTC 59.635 54.545 0.00 0.00 0.00 3.71
3119 3418 2.395619 CCGTACACTAATTCCCCTCCT 58.604 52.381 0.00 0.00 0.00 3.69
3120 3419 1.202615 GCCGTACACTAATTCCCCTCC 60.203 57.143 0.00 0.00 0.00 4.30
3121 3420 1.537562 CGCCGTACACTAATTCCCCTC 60.538 57.143 0.00 0.00 0.00 4.30
3122 3421 0.462789 CGCCGTACACTAATTCCCCT 59.537 55.000 0.00 0.00 0.00 4.79
3123 3422 0.531311 CCGCCGTACACTAATTCCCC 60.531 60.000 0.00 0.00 0.00 4.81
3124 3423 1.156034 GCCGCCGTACACTAATTCCC 61.156 60.000 0.00 0.00 0.00 3.97
3125 3424 1.485032 CGCCGCCGTACACTAATTCC 61.485 60.000 0.00 0.00 0.00 3.01
3126 3425 1.485032 CCGCCGCCGTACACTAATTC 61.485 60.000 0.00 0.00 0.00 2.17
3127 3426 1.519898 CCGCCGCCGTACACTAATT 60.520 57.895 0.00 0.00 0.00 1.40
3128 3427 2.105528 CCGCCGCCGTACACTAAT 59.894 61.111 0.00 0.00 0.00 1.73
3129 3428 4.799824 GCCGCCGCCGTACACTAA 62.800 66.667 0.00 0.00 0.00 2.24
3147 3446 0.320771 ACTGGCAGATCACGGTTGAC 60.321 55.000 23.66 0.00 33.38 3.18
3148 3447 1.204704 CTACTGGCAGATCACGGTTGA 59.795 52.381 23.66 0.00 35.73 3.18
3149 3448 1.645034 CTACTGGCAGATCACGGTTG 58.355 55.000 23.66 0.00 0.00 3.77
3150 3449 0.537188 CCTACTGGCAGATCACGGTT 59.463 55.000 23.66 0.00 0.00 4.44
3151 3450 0.324368 TCCTACTGGCAGATCACGGT 60.324 55.000 23.66 0.00 0.00 4.83
3152 3451 0.103208 GTCCTACTGGCAGATCACGG 59.897 60.000 23.66 12.88 0.00 4.94
3153 3452 1.107114 AGTCCTACTGGCAGATCACG 58.893 55.000 23.66 3.57 0.00 4.35
3154 3453 3.024547 TGTAGTCCTACTGGCAGATCAC 58.975 50.000 23.66 11.55 37.00 3.06
3155 3454 3.382083 TGTAGTCCTACTGGCAGATCA 57.618 47.619 23.66 4.76 37.00 2.92
3156 3455 5.317808 TCTATGTAGTCCTACTGGCAGATC 58.682 45.833 23.66 6.30 37.00 2.75
3157 3456 5.326283 TCTATGTAGTCCTACTGGCAGAT 57.674 43.478 23.66 8.18 37.00 2.90
3158 3457 4.790718 TCTATGTAGTCCTACTGGCAGA 57.209 45.455 23.66 3.89 37.00 4.26
3159 3458 5.854010 TTTCTATGTAGTCCTACTGGCAG 57.146 43.478 14.16 14.16 37.00 4.85
3160 3459 6.808321 ATTTTCTATGTAGTCCTACTGGCA 57.192 37.500 6.07 0.00 37.00 4.92


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

AutoCloner maintained by Alex Coulton.