Multiple sequence alignment - TraesCS7B01G033100

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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 TraesCS7B01G033100 chr7B 100.000 4028 0 0 1 4028 33078918 33082945 0.000000e+00 7439.0
1 TraesCS7B01G033100 chr7A 90.789 2877 157 45 278 3077 85212421 85215266 0.000000e+00 3746.0
2 TraesCS7B01G033100 chr7A 94.444 684 30 5 3346 4028 85215563 85216239 0.000000e+00 1046.0
3 TraesCS7B01G033100 chr7A 94.479 163 8 1 1 163 85212267 85212428 2.400000e-62 250.0
4 TraesCS7B01G033100 chr7A 94.872 156 8 0 3147 3302 85215404 85215559 1.120000e-60 244.0
5 TraesCS7B01G033100 chr7D 89.289 1970 122 35 1 1904 83628601 83630547 0.000000e+00 2386.0
6 TraesCS7B01G033100 chr7D 92.676 1106 42 17 1903 2976 83630682 83631780 0.000000e+00 1557.0
7 TraesCS7B01G033100 chr7D 94.218 761 22 5 3196 3956 83632069 83632807 0.000000e+00 1142.0
8 TraesCS7B01G033100 chr5D 94.828 58 0 2 3075 3130 519201533 519201477 1.990000e-13 87.9
9 TraesCS7B01G033100 chr5D 94.000 50 1 1 3084 3131 290070542 290070493 1.550000e-09 75.0
10 TraesCS7B01G033100 chr2B 94.828 58 0 2 3076 3130 696361642 696361699 1.990000e-13 87.9
11 TraesCS7B01G033100 chrUn 93.220 59 2 1 3075 3131 376297149 376297091 7.170000e-13 86.1
12 TraesCS7B01G033100 chr6D 90.000 70 2 4 3065 3130 95295009 95294941 7.170000e-13 86.1
13 TraesCS7B01G033100 chr4D 96.226 53 0 1 3080 3130 489441044 489440992 7.170000e-13 86.1
14 TraesCS7B01G033100 chr1B 93.220 59 2 1 3075 3131 24741609 24741551 7.170000e-13 86.1
15 TraesCS7B01G033100 chr5A 91.935 62 1 3 3071 3129 40096753 40096813 2.580000e-12 84.2
16 TraesCS7B01G033100 chr3A 93.103 58 1 2 3075 3130 750341231 750341287 9.280000e-12 82.4


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 TraesCS7B01G033100 chr7B 33078918 33082945 4027 False 7439.0 7439 100.000 1 4028 1 chr7B.!!$F1 4027
1 TraesCS7B01G033100 chr7A 85212267 85216239 3972 False 1321.5 3746 93.646 1 4028 4 chr7A.!!$F1 4027
2 TraesCS7B01G033100 chr7D 83628601 83632807 4206 False 1695.0 2386 92.061 1 3956 3 chr7D.!!$F1 3955

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
200 201 0.321346 TCTGGCACATTCTGAGCGAA 59.679 50.0 0.0 0.0 38.2 4.70 F
683 705 0.391661 GAGCTGGGAAACGATGCAGA 60.392 55.0 0.0 0.0 0.0 4.26 F
1391 1434 0.413037 TTGCCCATCCATCCCTGTTT 59.587 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1285 1328 0.169009 GTCTTGTTGAATCTGCGCCC 59.831 55.0 4.18 0.0 0.0 6.13 R
1631 1715 0.620556 TCTCAATCAGGGTTCAGGGC 59.379 55.0 0.00 0.0 0.0 5.19 R
3125 3390 0.030195 TCCCTCCATCCCATGCACTA 60.030 55.0 0.00 0.0 0.0 2.74 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
51 52 3.620427 TGGCCGATTTTAGCAGTCTTA 57.380 42.857 0.00 0.00 0.00 2.10
188 189 5.918608 TCTTAGACATAAAGGATCTGGCAC 58.081 41.667 0.00 0.00 0.00 5.01
200 201 0.321346 TCTGGCACATTCTGAGCGAA 59.679 50.000 0.00 0.00 38.20 4.70
201 202 0.725686 CTGGCACATTCTGAGCGAAG 59.274 55.000 0.00 0.00 38.20 3.79
205 206 1.674221 GCACATTCTGAGCGAAGAGGT 60.674 52.381 0.00 0.00 34.56 3.85
226 227 2.246397 CAAGTCACAGCACACGCG 59.754 61.111 3.53 3.53 45.49 6.01
259 263 2.548707 GGAGCCATGTAATCGCATGAGA 60.549 50.000 0.28 0.28 46.65 3.27
327 337 3.411446 AGCAGCAGCAATAACAACAGTA 58.589 40.909 3.17 0.00 45.49 2.74
413 423 1.153901 GTCGAGGACGCCGATCAAA 60.154 57.895 0.00 0.00 38.38 2.69
455 465 4.431131 CCGCCTCCATTGCCACCT 62.431 66.667 0.00 0.00 0.00 4.00
548 558 1.320555 CTCGCATCGTCCAAGTAAACG 59.679 52.381 0.00 0.00 40.17 3.60
558 571 4.142966 CGTCCAAGTAAACGAAATCCTTCC 60.143 45.833 0.00 0.00 41.29 3.46
564 577 3.573491 CGAAATCCTTCCCGGCGC 61.573 66.667 0.00 0.00 0.00 6.53
634 656 0.684805 CGGGAGTACCAGGAGAAGCT 60.685 60.000 0.00 0.00 40.22 3.74
678 700 2.584608 CGGGAGCTGGGAAACGAT 59.415 61.111 0.00 0.00 0.00 3.73
681 703 1.377202 GGAGCTGGGAAACGATGCA 60.377 57.895 0.00 0.00 0.00 3.96
683 705 0.391661 GAGCTGGGAAACGATGCAGA 60.392 55.000 0.00 0.00 0.00 4.26
686 708 0.745845 CTGGGAAACGATGCAGAGGG 60.746 60.000 0.00 0.00 0.00 4.30
824 846 3.999297 GAGGAGTCGGAGCGGGAGT 62.999 68.421 0.00 0.00 0.00 3.85
857 880 3.542676 AGTCCGTGACGTGGCCAA 61.543 61.111 7.24 0.00 37.67 4.52
884 907 3.539604 CAAAGAGGATCCAAGGCTACAG 58.460 50.000 15.82 0.00 33.66 2.74
918 941 4.271816 CTCCCAGCCGTCCGATCG 62.272 72.222 8.51 8.51 0.00 3.69
977 1000 1.659794 CCAAACGGCCCTCACTTTG 59.340 57.895 0.00 0.00 0.00 2.77
1049 1072 1.134877 GTAACGAACCCTAGCCCACTC 60.135 57.143 0.00 0.00 0.00 3.51
1256 1299 2.105930 CTGTCGAGGCTGCTAGGC 59.894 66.667 0.00 2.19 41.73 3.93
1268 1311 2.357323 GCTGCTAGGCCTGATTCTTTTC 59.643 50.000 17.99 0.00 0.00 2.29
1270 1313 3.614092 TGCTAGGCCTGATTCTTTTCTG 58.386 45.455 17.99 0.00 0.00 3.02
1271 1314 3.009473 TGCTAGGCCTGATTCTTTTCTGT 59.991 43.478 17.99 0.00 0.00 3.41
1272 1315 3.376546 GCTAGGCCTGATTCTTTTCTGTG 59.623 47.826 17.99 0.00 0.00 3.66
1273 1316 3.515602 AGGCCTGATTCTTTTCTGTGT 57.484 42.857 3.11 0.00 0.00 3.72
1274 1317 3.152341 AGGCCTGATTCTTTTCTGTGTG 58.848 45.455 3.11 0.00 0.00 3.82
1275 1318 2.229784 GGCCTGATTCTTTTCTGTGTGG 59.770 50.000 0.00 0.00 0.00 4.17
1285 1328 0.884259 TTCTGTGTGGTGTGGATGCG 60.884 55.000 0.00 0.00 0.00 4.73
1391 1434 0.413037 TTGCCCATCCATCCCTGTTT 59.587 50.000 0.00 0.00 0.00 2.83
1631 1715 5.172934 TGTTACTGTAATAAGGCTTGTCGG 58.827 41.667 10.69 0.00 0.00 4.79
1632 1716 2.629051 ACTGTAATAAGGCTTGTCGGC 58.371 47.619 10.69 0.00 38.75 5.54
1730 1814 4.335647 ACTGTGAAGGCTGGCCCG 62.336 66.667 8.11 0.00 39.21 6.13
1799 1883 1.542915 CCAGTTCCATCAGCTTTGTGG 59.457 52.381 2.97 2.97 0.00 4.17
1804 1888 4.524316 TTCCATCAGCTTTGTGGAATTG 57.476 40.909 16.39 0.00 44.67 2.32
1829 1913 6.128063 GCAAGCCTTCATGTATGGAGAATATC 60.128 42.308 1.64 0.00 35.31 1.63
1942 2166 6.205464 TGAAGTGCCAACTTTTTAGATCTGAG 59.795 38.462 5.18 0.79 46.84 3.35
1947 2171 5.622378 CCAACTTTTTAGATCTGAGAACGC 58.378 41.667 5.18 0.00 0.00 4.84
2057 2301 6.463995 TTCCACTAGCATTTTTCAGTTTGT 57.536 33.333 0.00 0.00 0.00 2.83
2058 2302 5.830912 TCCACTAGCATTTTTCAGTTTGTG 58.169 37.500 0.00 0.00 0.00 3.33
2171 2420 7.281774 AGTTGTCTAATCATCAACAGGCTATTG 59.718 37.037 0.00 0.00 42.33 1.90
2199 2448 3.369546 AACTTTGTGCCCTGATTTTCG 57.630 42.857 0.00 0.00 0.00 3.46
2305 2554 5.104941 TCCTCTTCAGCTTTCCGATGATTTA 60.105 40.000 0.00 0.00 37.96 1.40
2316 2565 7.548196 TTTCCGATGATTTATGTTCTGTACC 57.452 36.000 0.00 0.00 0.00 3.34
2405 2661 4.344865 GCGGCTGGAACCTCCCAA 62.345 66.667 0.00 0.00 35.03 4.12
2486 2742 0.965866 TGAATCAGCCTCGTCCGACT 60.966 55.000 0.00 0.00 0.00 4.18
2834 3092 1.164041 AGTGGTCGTCCCTTTTTGCG 61.164 55.000 0.00 0.00 0.00 4.85
2888 3146 5.244402 TGATCATGCCAATGACTGAAACTTT 59.756 36.000 0.00 0.00 45.51 2.66
2898 3156 4.681744 TGACTGAAACTTTTGTCATTGCC 58.318 39.130 7.01 0.00 34.94 4.52
2901 3159 3.037549 TGAAACTTTTGTCATTGCCCCT 58.962 40.909 0.00 0.00 0.00 4.79
2916 3174 1.202976 GCCCCTCTGTAATGGCATGAT 60.203 52.381 0.00 0.00 43.46 2.45
2928 3186 5.594724 AATGGCATGATTTTTGTTGTTCG 57.405 34.783 0.00 0.00 0.00 3.95
2935 3193 6.237808 GCATGATTTTTGTTGTTCGTCAAACT 60.238 34.615 0.00 0.00 38.76 2.66
2951 3209 3.697045 TCAAACTTCGGCTCCTTTTGAAA 59.303 39.130 0.00 0.00 34.16 2.69
2965 3223 9.617975 GCTCCTTTTGAAATATAATATGAGTGC 57.382 33.333 0.00 0.00 0.00 4.40
3008 3266 2.224426 TGTGGCAGTTTGTAGTACCTGG 60.224 50.000 0.00 0.00 0.00 4.45
3026 3284 0.237498 GGTCGTGTTTACCAGCTTGC 59.763 55.000 0.00 0.00 36.96 4.01
3072 3337 5.008712 TCACTCTAGTGCGGTTATGAGTATG 59.991 44.000 5.21 0.00 45.25 2.39
3077 3342 5.215252 AGTGCGGTTATGAGTATGCTTAT 57.785 39.130 0.00 0.00 0.00 1.73
3078 3343 6.340962 AGTGCGGTTATGAGTATGCTTATA 57.659 37.500 0.00 0.00 0.00 0.98
3079 3344 6.936279 AGTGCGGTTATGAGTATGCTTATAT 58.064 36.000 0.00 0.00 0.00 0.86
3080 3345 7.386851 AGTGCGGTTATGAGTATGCTTATATT 58.613 34.615 0.00 0.00 0.00 1.28
3081 3346 7.878127 AGTGCGGTTATGAGTATGCTTATATTT 59.122 33.333 0.00 0.00 0.00 1.40
3082 3347 8.169268 GTGCGGTTATGAGTATGCTTATATTTC 58.831 37.037 0.00 0.00 0.00 2.17
3083 3348 8.094548 TGCGGTTATGAGTATGCTTATATTTCT 58.905 33.333 0.00 0.00 0.00 2.52
3084 3349 9.582431 GCGGTTATGAGTATGCTTATATTTCTA 57.418 33.333 0.00 0.00 0.00 2.10
3090 3355 8.958060 TGAGTATGCTTATATTTCTACTCCCT 57.042 34.615 0.00 0.00 36.06 4.20
3091 3356 9.026121 TGAGTATGCTTATATTTCTACTCCCTC 57.974 37.037 0.00 0.00 36.06 4.30
3094 3359 5.145564 TGCTTATATTTCTACTCCCTCCGT 58.854 41.667 0.00 0.00 0.00 4.69
3095 3360 5.243283 TGCTTATATTTCTACTCCCTCCGTC 59.757 44.000 0.00 0.00 0.00 4.79
3096 3361 5.336610 GCTTATATTTCTACTCCCTCCGTCC 60.337 48.000 0.00 0.00 0.00 4.79
3098 3363 0.410663 TTTCTACTCCCTCCGTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
3099 3364 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
3100 3365 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
3101 3366 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
3102 3367 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
3104 3369 3.339713 ACTCCCTCCGTCCCATAATAA 57.660 47.619 0.00 0.00 0.00 1.40
3105 3370 3.240302 ACTCCCTCCGTCCCATAATAAG 58.760 50.000 0.00 0.00 0.00 1.73
3107 3372 3.901844 CTCCCTCCGTCCCATAATAAGAA 59.098 47.826 0.00 0.00 0.00 2.52
3108 3373 3.644738 TCCCTCCGTCCCATAATAAGAAC 59.355 47.826 0.00 0.00 0.00 3.01
3109 3374 3.554337 CCCTCCGTCCCATAATAAGAACG 60.554 52.174 0.00 0.00 0.00 3.95
3110 3375 3.069158 CCTCCGTCCCATAATAAGAACGT 59.931 47.826 0.00 0.00 0.00 3.99
3111 3376 4.442472 CCTCCGTCCCATAATAAGAACGTT 60.442 45.833 0.00 0.00 0.00 3.99
3112 3377 5.088680 TCCGTCCCATAATAAGAACGTTT 57.911 39.130 0.46 0.00 0.00 3.60
3113 3378 5.490159 TCCGTCCCATAATAAGAACGTTTT 58.510 37.500 0.46 0.00 0.00 2.43
3114 3379 5.939296 TCCGTCCCATAATAAGAACGTTTTT 59.061 36.000 9.22 9.22 0.00 1.94
3116 3381 6.128227 CCGTCCCATAATAAGAACGTTTTTGA 60.128 38.462 13.87 0.00 0.00 2.69
3117 3382 6.739550 CGTCCCATAATAAGAACGTTTTTGAC 59.260 38.462 13.87 9.38 0.00 3.18
3118 3383 7.571613 CGTCCCATAATAAGAACGTTTTTGACA 60.572 37.037 13.87 0.00 0.00 3.58
3119 3384 7.536281 GTCCCATAATAAGAACGTTTTTGACAC 59.464 37.037 13.87 0.00 0.00 3.67
3120 3385 7.446013 TCCCATAATAAGAACGTTTTTGACACT 59.554 33.333 13.87 0.00 0.00 3.55
3121 3386 8.723311 CCCATAATAAGAACGTTTTTGACACTA 58.277 33.333 13.87 0.00 0.00 2.74
3122 3387 9.537848 CCATAATAAGAACGTTTTTGACACTAC 57.462 33.333 13.87 0.00 0.00 2.73
3125 3390 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
3126 3391 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
3128 3393 6.335777 AGAACGTTTTTGACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
3138 3403 3.827008 ACTACACTAGTGCATGGGATG 57.173 47.619 22.90 6.63 37.69 3.51
3139 3404 2.435805 ACTACACTAGTGCATGGGATGG 59.564 50.000 22.90 6.03 37.69 3.51
3141 3406 1.487976 ACACTAGTGCATGGGATGGAG 59.512 52.381 22.90 0.00 0.00 3.86
3142 3407 1.135094 ACTAGTGCATGGGATGGAGG 58.865 55.000 0.00 0.00 0.00 4.30
3143 3408 0.399454 CTAGTGCATGGGATGGAGGG 59.601 60.000 0.00 0.00 0.00 4.30
3144 3409 0.030195 TAGTGCATGGGATGGAGGGA 60.030 55.000 0.00 0.00 0.00 4.20
3157 3490 4.040584 GGATGGAGGGAGTAGTATTGAACC 59.959 50.000 0.00 0.00 0.00 3.62
3172 3505 4.623932 TTGAACCATCAACTCTAGTGCT 57.376 40.909 0.00 0.00 40.59 4.40
3248 3744 6.705863 AATTAATCCAGGCATTTCTCAGTC 57.294 37.500 0.00 0.00 0.00 3.51
3324 3820 7.645402 ACAAATTGTAAGAAGGTTTTACTCCG 58.355 34.615 0.00 0.00 33.29 4.63
3335 3831 3.816523 GGTTTTACTCCGGACAACATCAA 59.183 43.478 0.00 0.00 0.00 2.57
3336 3832 4.457949 GGTTTTACTCCGGACAACATCAAT 59.542 41.667 0.00 0.00 0.00 2.57
3337 3833 5.390613 GTTTTACTCCGGACAACATCAATG 58.609 41.667 0.00 0.00 0.00 2.82
3338 3834 1.453155 ACTCCGGACAACATCAATGC 58.547 50.000 0.00 0.00 0.00 3.56
3339 3835 1.271325 ACTCCGGACAACATCAATGCA 60.271 47.619 0.00 0.00 0.00 3.96
3340 3836 1.811965 CTCCGGACAACATCAATGCAA 59.188 47.619 0.00 0.00 0.00 4.08
3341 3837 2.228582 CTCCGGACAACATCAATGCAAA 59.771 45.455 0.00 0.00 0.00 3.68
3342 3838 2.824936 TCCGGACAACATCAATGCAAAT 59.175 40.909 0.00 0.00 0.00 2.32
3343 3839 4.013050 TCCGGACAACATCAATGCAAATA 58.987 39.130 0.00 0.00 0.00 1.40
3344 3840 4.644234 TCCGGACAACATCAATGCAAATAT 59.356 37.500 0.00 0.00 0.00 1.28
3398 3894 5.825679 ACATGTTACAGCTTTTGGTCTGTTA 59.174 36.000 0.00 0.00 42.81 2.41
3636 4132 0.877649 AACGCCATAGCAGCAGATCG 60.878 55.000 0.00 0.00 39.83 3.69
3848 4344 6.430925 CCATCTTGTATCCTTTTCAACTGTGA 59.569 38.462 0.00 0.00 0.00 3.58
3933 4429 4.202040 TGCAAGAGAACACACAAATCAAGG 60.202 41.667 0.00 0.00 0.00 3.61
3960 4456 4.023193 ACAAAATCGTTACAAGGAAGCCAG 60.023 41.667 0.00 0.00 0.00 4.85
3967 4463 4.276431 CGTTACAAGGAAGCCAGGTAAAAA 59.724 41.667 0.00 0.00 30.37 1.94
3968 4464 5.562113 CGTTACAAGGAAGCCAGGTAAAAAG 60.562 44.000 0.00 0.00 30.37 2.27
3969 4465 4.178956 ACAAGGAAGCCAGGTAAAAAGA 57.821 40.909 0.00 0.00 0.00 2.52
3971 4467 3.156288 AGGAAGCCAGGTAAAAAGACC 57.844 47.619 0.00 0.00 40.08 3.85
3972 4468 2.445525 AGGAAGCCAGGTAAAAAGACCA 59.554 45.455 0.00 0.00 42.47 4.02
3973 4469 3.076032 AGGAAGCCAGGTAAAAAGACCAT 59.924 43.478 0.00 0.00 42.47 3.55
3974 4470 3.193479 GGAAGCCAGGTAAAAAGACCATG 59.807 47.826 0.00 0.00 42.47 3.66
3975 4471 3.806949 AGCCAGGTAAAAAGACCATGA 57.193 42.857 0.00 0.00 42.47 3.07
3976 4472 4.322057 AGCCAGGTAAAAAGACCATGAT 57.678 40.909 0.00 0.00 42.47 2.45
3977 4473 4.273318 AGCCAGGTAAAAAGACCATGATC 58.727 43.478 0.00 0.00 42.47 2.92
3993 4489 5.011329 ACCATGATCAAAAACAGCATTCACT 59.989 36.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.389374 CCGCCCTGATAGTACAATTTCAT 58.611 43.478 0.00 0.00 0.00 2.57
188 189 1.554392 CGACCTCTTCGCTCAGAATG 58.446 55.000 0.00 0.00 41.87 2.67
200 201 0.315568 GCTGTGACTTGTCGACCTCT 59.684 55.000 14.12 0.00 0.00 3.69
201 202 0.032130 TGCTGTGACTTGTCGACCTC 59.968 55.000 14.12 5.60 0.00 3.85
205 206 0.869880 CGTGTGCTGTGACTTGTCGA 60.870 55.000 0.00 0.00 0.00 4.20
207 208 1.276844 GCGTGTGCTGTGACTTGTC 59.723 57.895 0.00 0.00 38.39 3.18
210 211 1.951130 CTCGCGTGTGCTGTGACTT 60.951 57.895 5.77 0.00 39.65 3.01
213 214 1.371267 GTACTCGCGTGTGCTGTGA 60.371 57.895 22.97 0.00 39.65 3.58
226 227 1.137872 CATGGCTCCTCTGTGGTACTC 59.862 57.143 0.00 0.00 37.07 2.59
259 263 8.879427 AACTTAGTAGGTTTGATTAGGCATTT 57.121 30.769 0.00 0.00 0.00 2.32
327 337 0.106149 AGGCTCGTCAGTTTTCCGTT 59.894 50.000 0.00 0.00 0.00 4.44
413 423 1.392710 CGGGGTTCGCTATGGACTCT 61.393 60.000 0.00 0.00 0.00 3.24
548 558 2.124695 AGCGCCGGGAAGGATTTC 60.125 61.111 2.29 0.00 45.00 2.17
660 682 3.682292 ATCGTTTCCCAGCTCCCGC 62.682 63.158 0.00 0.00 0.00 6.13
662 684 2.115291 GCATCGTTTCCCAGCTCCC 61.115 63.158 0.00 0.00 0.00 4.30
667 689 0.745845 CCCTCTGCATCGTTTCCCAG 60.746 60.000 0.00 0.00 0.00 4.45
668 690 1.299648 CCCTCTGCATCGTTTCCCA 59.700 57.895 0.00 0.00 0.00 4.37
675 697 3.457625 CTCCTGCCCCTCTGCATCG 62.458 68.421 0.00 0.00 41.16 3.84
677 699 2.041762 TCTCCTGCCCCTCTGCAT 59.958 61.111 0.00 0.00 41.16 3.96
678 700 2.686470 CTCTCCTGCCCCTCTGCA 60.686 66.667 0.00 0.00 39.37 4.41
681 703 4.814041 GCCCTCTCCTGCCCCTCT 62.814 72.222 0.00 0.00 0.00 3.69
824 846 1.841302 GACTGACAGACCCCATGGCA 61.841 60.000 10.08 0.00 33.68 4.92
857 880 0.850883 TTGGATCCTCTTTGCCCCCT 60.851 55.000 14.23 0.00 0.00 4.79
862 885 2.293170 GTAGCCTTGGATCCTCTTTGC 58.707 52.381 14.23 8.58 0.00 3.68
863 886 3.539604 CTGTAGCCTTGGATCCTCTTTG 58.460 50.000 14.23 0.00 0.00 2.77
974 997 3.294102 CGTGTACGCTATATCGAGCAAA 58.706 45.455 2.48 0.00 42.99 3.68
977 1000 1.465354 CCCGTGTACGCTATATCGAGC 60.465 57.143 2.48 0.00 39.20 5.03
1065 1088 3.842923 CGAGATCGGCTGCCCTGT 61.843 66.667 14.12 0.00 35.37 4.00
1256 1299 3.885297 ACACCACACAGAAAAGAATCAGG 59.115 43.478 0.00 0.00 0.00 3.86
1264 1307 1.680735 GCATCCACACCACACAGAAAA 59.319 47.619 0.00 0.00 0.00 2.29
1268 1311 2.327343 CCGCATCCACACCACACAG 61.327 63.158 0.00 0.00 0.00 3.66
1270 1313 3.055719 CCCGCATCCACACCACAC 61.056 66.667 0.00 0.00 0.00 3.82
1285 1328 0.169009 GTCTTGTTGAATCTGCGCCC 59.831 55.000 4.18 0.00 0.00 6.13
1391 1434 1.610038 CAACTGCTGCATCCAAGAACA 59.390 47.619 1.31 0.00 0.00 3.18
1443 1497 8.010733 AGGTTGAATGTTTCATCAAAAGAGAA 57.989 30.769 0.00 0.00 39.84 2.87
1445 1499 7.428020 TGAGGTTGAATGTTTCATCAAAAGAG 58.572 34.615 0.00 0.00 39.84 2.85
1458 1512 3.981071 TCCTTCGATGAGGTTGAATGT 57.019 42.857 3.11 0.00 38.04 2.71
1502 1556 2.369860 CTGCTGATACCTGGCAATCCTA 59.630 50.000 0.00 0.00 35.49 2.94
1604 1663 7.224753 CGACAAGCCTTATTACAGTAACATCAT 59.775 37.037 0.00 0.00 0.00 2.45
1612 1671 2.629051 GCCGACAAGCCTTATTACAGT 58.371 47.619 0.00 0.00 0.00 3.55
1631 1715 0.620556 TCTCAATCAGGGTTCAGGGC 59.379 55.000 0.00 0.00 0.00 5.19
1632 1716 1.912043 ACTCTCAATCAGGGTTCAGGG 59.088 52.381 0.00 0.00 27.09 4.45
1633 1717 3.710209 AACTCTCAATCAGGGTTCAGG 57.290 47.619 0.00 0.00 42.91 3.86
1634 1718 5.180868 CAGAAAACTCTCAATCAGGGTTCAG 59.819 44.000 0.00 0.00 46.08 3.02
1635 1719 5.065914 CAGAAAACTCTCAATCAGGGTTCA 58.934 41.667 0.00 0.00 46.08 3.18
1636 1720 4.457257 CCAGAAAACTCTCAATCAGGGTTC 59.543 45.833 0.00 0.00 46.08 3.62
1700 1784 2.936919 TCACAGTGACCATTCTGCTT 57.063 45.000 0.00 0.00 35.37 3.91
1718 1802 1.686325 TATCACTCGGGCCAGCCTTC 61.686 60.000 4.39 0.00 36.10 3.46
1730 1814 6.087820 GCGAATATCAACTAACCGTATCACTC 59.912 42.308 0.00 0.00 0.00 3.51
1799 1883 4.098349 TCCATACATGAAGGCTTGCAATTC 59.902 41.667 3.46 1.51 0.00 2.17
1804 1888 2.923121 TCTCCATACATGAAGGCTTGC 58.077 47.619 3.46 0.00 0.00 4.01
1883 1971 9.754382 GCATTTCACTGATACCATTTCATAAAT 57.246 29.630 0.00 0.00 0.00 1.40
1889 1977 9.807649 AAATTAGCATTTCACTGATACCATTTC 57.192 29.630 0.00 0.00 0.00 2.17
1947 2171 6.604930 TGACAAATATCTGATATGCGCATTG 58.395 36.000 30.42 18.89 0.00 2.82
1978 2222 6.039047 CACAAACCAGCTAGCATATTTCATCT 59.961 38.462 18.83 0.00 0.00 2.90
2057 2301 2.029470 GGGACGAAATGCAAATTCACCA 60.029 45.455 19.87 0.00 0.00 4.17
2058 2302 2.606108 GGGACGAAATGCAAATTCACC 58.394 47.619 13.91 14.30 0.00 4.02
2171 2420 3.568007 TCAGGGCACAAAGTTAACATGAC 59.432 43.478 15.74 7.28 0.00 3.06
2274 2523 3.007398 GGAAAGCTGAAGAGGACTCAAGA 59.993 47.826 1.75 0.00 0.00 3.02
2305 2554 7.093945 ACAAAAACTTTCAGTGGTACAGAACAT 60.094 33.333 0.00 0.00 41.80 2.71
2328 2577 9.730705 AGAATCACTTCAGATAGATTGAAACAA 57.269 29.630 0.00 0.00 34.41 2.83
2405 2661 2.119495 CCTGCTCCACCACTAATACCT 58.881 52.381 0.00 0.00 0.00 3.08
2834 3092 5.521735 ACATCAATATGCAACTTCTCGACTC 59.478 40.000 0.00 0.00 36.50 3.36
2888 3146 3.355378 CATTACAGAGGGGCAATGACAA 58.645 45.455 0.00 0.00 31.44 3.18
2898 3156 5.105228 ACAAAAATCATGCCATTACAGAGGG 60.105 40.000 0.00 0.00 0.00 4.30
2901 3159 6.757237 ACAACAAAAATCATGCCATTACAGA 58.243 32.000 0.00 0.00 0.00 3.41
2916 3174 4.617645 CCGAAGTTTGACGAACAACAAAAA 59.382 37.500 8.29 0.00 40.84 1.94
2928 3186 2.616842 TCAAAAGGAGCCGAAGTTTGAC 59.383 45.455 0.00 0.00 34.24 3.18
2935 3193 9.567776 TCATATTATATTTCAAAAGGAGCCGAA 57.432 29.630 0.00 0.00 0.00 4.30
2983 3241 4.951094 AGGTACTACAAACTGCCACAAAAA 59.049 37.500 0.00 0.00 36.02 1.94
2998 3256 3.255642 TGGTAAACACGACCAGGTACTAC 59.744 47.826 0.00 0.00 42.15 2.73
3008 3266 0.110823 CGCAAGCTGGTAAACACGAC 60.111 55.000 0.00 0.00 0.00 4.34
3072 3337 5.336610 GGACGGAGGGAGTAGAAATATAAGC 60.337 48.000 0.00 0.00 0.00 3.09
3077 3342 2.245546 TGGGACGGAGGGAGTAGAAATA 59.754 50.000 0.00 0.00 0.00 1.40
3078 3343 1.007963 TGGGACGGAGGGAGTAGAAAT 59.992 52.381 0.00 0.00 0.00 2.17
3079 3344 0.410663 TGGGACGGAGGGAGTAGAAA 59.589 55.000 0.00 0.00 0.00 2.52
3080 3345 0.635009 ATGGGACGGAGGGAGTAGAA 59.365 55.000 0.00 0.00 0.00 2.10
3081 3346 1.526315 TATGGGACGGAGGGAGTAGA 58.474 55.000 0.00 0.00 0.00 2.59
3082 3347 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
3083 3348 4.106825 TCTTATTATGGGACGGAGGGAGTA 59.893 45.833 0.00 0.00 0.00 2.59
3084 3349 3.116862 TCTTATTATGGGACGGAGGGAGT 60.117 47.826 0.00 0.00 0.00 3.85
3085 3350 3.507411 TCTTATTATGGGACGGAGGGAG 58.493 50.000 0.00 0.00 0.00 4.30
3086 3351 3.623466 TCTTATTATGGGACGGAGGGA 57.377 47.619 0.00 0.00 0.00 4.20
3087 3352 3.554337 CGTTCTTATTATGGGACGGAGGG 60.554 52.174 0.00 0.00 0.00 4.30
3088 3353 3.069158 ACGTTCTTATTATGGGACGGAGG 59.931 47.826 0.00 0.00 0.00 4.30
3090 3355 4.741321 AACGTTCTTATTATGGGACGGA 57.259 40.909 0.00 0.00 0.00 4.69
3091 3356 5.806366 AAAACGTTCTTATTATGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
3094 3359 7.446013 AGTGTCAAAAACGTTCTTATTATGGGA 59.554 33.333 0.00 0.00 0.00 4.37
3095 3360 7.590279 AGTGTCAAAAACGTTCTTATTATGGG 58.410 34.615 0.00 0.00 0.00 4.00
3096 3361 9.537848 GTAGTGTCAAAAACGTTCTTATTATGG 57.462 33.333 0.00 0.00 0.00 2.74
3099 3364 9.316730 AGTGTAGTGTCAAAAACGTTCTTATTA 57.683 29.630 0.00 0.00 0.00 0.98
3100 3365 8.205131 AGTGTAGTGTCAAAAACGTTCTTATT 57.795 30.769 0.00 0.00 0.00 1.40
3101 3366 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
3102 3367 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
3104 3369 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
3105 3370 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
3118 3383 2.435805 CCATCCCATGCACTAGTGTAGT 59.564 50.000 23.44 7.74 40.28 2.73
3119 3384 2.700371 TCCATCCCATGCACTAGTGTAG 59.300 50.000 23.44 13.28 0.00 2.74
3120 3385 2.700371 CTCCATCCCATGCACTAGTGTA 59.300 50.000 23.44 20.06 0.00 2.90
3121 3386 1.487976 CTCCATCCCATGCACTAGTGT 59.512 52.381 23.44 2.22 0.00 3.55
3122 3387 1.202734 CCTCCATCCCATGCACTAGTG 60.203 57.143 18.93 18.93 0.00 2.74
3123 3388 1.135094 CCTCCATCCCATGCACTAGT 58.865 55.000 0.00 0.00 0.00 2.57
3124 3389 0.399454 CCCTCCATCCCATGCACTAG 59.601 60.000 0.00 0.00 0.00 2.57
3125 3390 0.030195 TCCCTCCATCCCATGCACTA 60.030 55.000 0.00 0.00 0.00 2.74
3126 3391 1.308128 TCCCTCCATCCCATGCACT 60.308 57.895 0.00 0.00 0.00 4.40
3128 3393 0.030195 TACTCCCTCCATCCCATGCA 60.030 55.000 0.00 0.00 0.00 3.96
3131 3396 4.140447 TCAATACTACTCCCTCCATCCCAT 60.140 45.833 0.00 0.00 0.00 4.00
3132 3397 3.208922 TCAATACTACTCCCTCCATCCCA 59.791 47.826 0.00 0.00 0.00 4.37
3133 3398 3.858135 TCAATACTACTCCCTCCATCCC 58.142 50.000 0.00 0.00 0.00 3.85
3134 3399 4.040584 GGTTCAATACTACTCCCTCCATCC 59.959 50.000 0.00 0.00 0.00 3.51
3136 3401 4.631234 TGGTTCAATACTACTCCCTCCAT 58.369 43.478 0.00 0.00 0.00 3.41
3138 3403 4.654262 TGATGGTTCAATACTACTCCCTCC 59.346 45.833 0.00 0.00 0.00 4.30
3139 3404 5.871396 TGATGGTTCAATACTACTCCCTC 57.129 43.478 0.00 0.00 0.00 4.30
3141 3406 5.990668 AGTTGATGGTTCAATACTACTCCC 58.009 41.667 0.00 0.00 43.49 4.30
3142 3407 6.879400 AGAGTTGATGGTTCAATACTACTCC 58.121 40.000 0.00 0.00 43.49 3.85
3143 3408 8.688151 ACTAGAGTTGATGGTTCAATACTACTC 58.312 37.037 0.00 0.00 43.49 2.59
3144 3409 8.470805 CACTAGAGTTGATGGTTCAATACTACT 58.529 37.037 0.00 0.00 43.49 2.57
3157 3490 4.733850 TCGTAACAGCACTAGAGTTGATG 58.266 43.478 10.78 3.46 0.00 3.07
3220 3716 8.081517 TGAGAAATGCCTGGATTAATTTGATT 57.918 30.769 0.00 0.00 0.00 2.57
3248 3744 3.186119 GTCAGATCTCGAAAAGCTCAGG 58.814 50.000 0.00 0.00 0.00 3.86
3259 3755 7.187480 TCTAACAAAACTATCGTCAGATCTCG 58.813 38.462 0.00 0.00 38.26 4.04
3324 3820 7.342318 GCATATATTTGCATTGATGTTGTCC 57.658 36.000 12.62 0.00 42.31 4.02
3343 3839 9.037737 GCAACAATGTTCTTGATATTTGCATAT 57.962 29.630 0.00 0.00 28.65 1.78
3344 3840 8.252417 AGCAACAATGTTCTTGATATTTGCATA 58.748 29.630 0.00 0.00 29.80 3.14
3597 4093 2.190578 CTGGATGAACGAGGGGGC 59.809 66.667 0.00 0.00 0.00 5.80
3600 4096 1.739067 GTTTCCTGGATGAACGAGGG 58.261 55.000 0.00 0.00 43.34 4.30
3804 4300 1.224965 GAATGGCCGAAGAGATGCTC 58.775 55.000 0.00 0.00 0.00 4.26
3848 4344 8.606830 ACAAGTCAAGAAAGGACCTTATAGAAT 58.393 33.333 7.30 0.37 35.89 2.40
3933 4429 5.849604 GCTTCCTTGTAACGATTTTGTACAC 59.150 40.000 0.00 0.00 0.00 2.90
3960 4456 7.095649 GCTGTTTTTGATCATGGTCTTTTTACC 60.096 37.037 7.64 0.00 40.19 2.85
3967 4463 5.244402 TGAATGCTGTTTTTGATCATGGTCT 59.756 36.000 7.64 0.00 0.00 3.85
3968 4464 5.346822 GTGAATGCTGTTTTTGATCATGGTC 59.653 40.000 0.00 0.00 0.00 4.02
3969 4465 5.011329 AGTGAATGCTGTTTTTGATCATGGT 59.989 36.000 0.00 0.00 0.00 3.55
3971 4467 5.924254 ACAGTGAATGCTGTTTTTGATCATG 59.076 36.000 0.00 0.00 46.45 3.07
3972 4468 6.092955 ACAGTGAATGCTGTTTTTGATCAT 57.907 33.333 0.00 0.00 46.45 2.45
3973 4469 5.518848 ACAGTGAATGCTGTTTTTGATCA 57.481 34.783 0.00 0.00 46.45 2.92
3993 4489 2.420372 TGCTTGCACGTTTGAGTTAACA 59.580 40.909 8.61 0.00 0.00 2.41
3996 4492 2.285083 ACTGCTTGCACGTTTGAGTTA 58.715 42.857 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.