Multiple sequence alignment - TraesCS3B01G289800

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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 TraesCS3B01G289800 chr3B 100.000 3185 0 0 1 3185 465067609 465070793 0.000000e+00 5882
1 TraesCS3B01G289800 chr3D 93.942 2278 85 16 1 2247 359091227 359093482 0.000000e+00 3393
2 TraesCS3B01G289800 chr3D 92.857 308 19 3 2244 2548 359093766 359094073 8.110000e-121 444
3 TraesCS3B01G289800 chr3A 90.279 2582 116 39 1 2523 478664586 478667091 0.000000e+00 3253
4 TraesCS3B01G289800 chr5D 91.271 527 38 4 1691 2213 458458908 458458386 0.000000e+00 712
5 TraesCS3B01G289800 chr5D 91.864 381 30 1 2806 3185 544489248 544488868 6.050000e-147 531
6 TraesCS3B01G289800 chr5D 90.421 261 22 3 2547 2804 488189809 488189549 1.090000e-89 340
7 TraesCS3B01G289800 chr5D 90.734 259 19 4 2548 2802 538683799 538683542 1.090000e-89 340
8 TraesCS3B01G289800 chr5D 85.714 322 39 4 967 1281 458483228 458482907 1.830000e-87 333
9 TraesCS3B01G289800 chr5D 79.545 220 41 3 1403 1620 307968278 307968495 1.530000e-33 154
10 TraesCS3B01G289800 chr5B 84.435 726 77 17 918 1638 561693683 561692989 0.000000e+00 682
11 TraesCS3B01G289800 chr5B 88.889 558 50 9 1691 2240 561692917 561692364 0.000000e+00 676
12 TraesCS3B01G289800 chr5B 89.564 527 47 6 1691 2213 561712975 561712453 0.000000e+00 662
13 TraesCS3B01G289800 chr5B 91.579 380 32 0 2806 3185 693950395 693950016 2.810000e-145 525
14 TraesCS3B01G289800 chr5B 91.053 380 34 0 2806 3185 693949143 693948764 6.090000e-142 514
15 TraesCS3B01G289800 chr5B 87.324 284 32 2 990 1269 561713665 561713382 3.960000e-84 322
16 TraesCS3B01G289800 chr6D 92.388 381 28 1 2806 3185 289510981 289510601 2.790000e-150 542
17 TraesCS3B01G289800 chr6D 91.076 381 33 1 2806 3185 151959947 151959567 6.090000e-142 514
18 TraesCS3B01G289800 chr6D 91.255 263 18 4 2547 2804 116858275 116858537 1.410000e-93 353
19 TraesCS3B01G289800 chr6D 90.458 262 21 3 2547 2804 7199244 7199505 3.040000e-90 342
20 TraesCS3B01G289800 chr6D 80.405 444 71 13 2550 2978 9899377 9899819 1.100000e-84 324
21 TraesCS3B01G289800 chr4D 91.864 381 30 1 2806 3185 380340171 380340551 6.050000e-147 531
22 TraesCS3B01G289800 chr2B 91.821 379 30 1 2808 3185 201767211 201767589 7.830000e-146 527
23 TraesCS3B01G289800 chr2B 82.463 479 76 6 1695 2172 53520137 53519666 2.290000e-111 412
24 TraesCS3B01G289800 chr2B 80.842 475 88 3 1695 2169 53578113 53578584 1.400000e-98 370
25 TraesCS3B01G289800 chr1A 91.579 380 32 0 2806 3185 583844981 583844602 2.810000e-145 525
26 TraesCS3B01G289800 chr5A 80.504 595 105 11 2592 3182 600519782 600520369 2.250000e-121 446
27 TraesCS3B01G289800 chr5A 85.405 370 45 3 924 1290 576340528 576340165 3.000000e-100 375
28 TraesCS3B01G289800 chr2D 82.636 478 80 3 1695 2172 32520847 32520373 1.370000e-113 420
29 TraesCS3B01G289800 chr2D 80.126 478 88 6 1697 2172 32595054 32594582 1.820000e-92 350
30 TraesCS3B01G289800 chr2D 90.734 259 20 3 2547 2801 602087815 602088073 3.040000e-90 342
31 TraesCS3B01G289800 chr2D 90.661 257 20 3 2549 2801 602115274 602115530 3.940000e-89 339
32 TraesCS3B01G289800 chr2A 82.004 489 84 4 1685 2172 35583682 35583197 2.290000e-111 412
33 TraesCS3B01G289800 chr2A 81.568 472 83 4 1698 2169 35630849 35631316 1.390000e-103 387
34 TraesCS3B01G289800 chr1D 90.769 260 20 2 2549 2804 43194360 43194619 8.460000e-91 344


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 TraesCS3B01G289800 chr3B 465067609 465070793 3184 False 5882.0 5882 100.0000 1 3185 1 chr3B.!!$F1 3184
1 TraesCS3B01G289800 chr3D 359091227 359094073 2846 False 1918.5 3393 93.3995 1 2548 2 chr3D.!!$F1 2547
2 TraesCS3B01G289800 chr3A 478664586 478667091 2505 False 3253.0 3253 90.2790 1 2523 1 chr3A.!!$F1 2522
3 TraesCS3B01G289800 chr5D 458458386 458458908 522 True 712.0 712 91.2710 1691 2213 1 chr5D.!!$R1 522
4 TraesCS3B01G289800 chr5B 561692364 561693683 1319 True 679.0 682 86.6620 918 2240 2 chr5B.!!$R1 1322
5 TraesCS3B01G289800 chr5B 693948764 693950395 1631 True 519.5 525 91.3160 2806 3185 2 chr5B.!!$R3 379
6 TraesCS3B01G289800 chr5B 561712453 561713665 1212 True 492.0 662 88.4440 990 2213 2 chr5B.!!$R2 1223
7 TraesCS3B01G289800 chr5A 600519782 600520369 587 False 446.0 446 80.5040 2592 3182 1 chr5A.!!$F1 590

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
378 383 0.460311 CGATTCTGGCTCGGGTAAGT 59.540 55.000 0.0 0.0 32.58 2.24 F
1110 1153 1.511768 GAGCTACCGTCTTCCGCTT 59.488 57.895 0.0 0.0 34.38 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 1867 0.674269 GTTCGGGTACGGCAAATCCA 60.674 55.0 0.0 0.0 41.39 3.41 R
2804 3185 0.036388 GGAAGATGAAGGTGACGGCA 60.036 55.0 0.0 0.0 0.00 5.69 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
45 48 6.608610 ACTGTCCGAATAAAAATTCCTTTCG 58.391 36.000 0.00 0.00 39.00 3.46
81 84 2.857748 TCATGTGTTAAGCGCATACTCG 59.142 45.455 11.47 0.00 45.64 4.18
93 96 2.128035 GCATACTCGCACTACATGACC 58.872 52.381 0.00 0.00 0.00 4.02
101 104 2.607635 CGCACTACATGACCGCTAAAAT 59.392 45.455 0.00 0.00 0.00 1.82
161 165 4.112716 TGCAATATACGGACTGAACGAA 57.887 40.909 0.00 0.00 34.93 3.85
166 170 0.883833 TACGGACTGAACGAACTCCC 59.116 55.000 0.00 0.00 34.93 4.30
378 383 0.460311 CGATTCTGGCTCGGGTAAGT 59.540 55.000 0.00 0.00 32.58 2.24
412 417 1.529713 GAGGAGGCGGAGAGGTAGG 60.530 68.421 0.00 0.00 0.00 3.18
846 856 3.121945 CGTCACGTCACGGTTTTTG 57.878 52.632 3.22 0.00 36.07 2.44
893 925 5.125097 ACGTAGAGTTGGTGTAGGATTACTG 59.875 44.000 0.00 0.00 0.00 2.74
914 953 2.484417 GCCGTGTCTGATCTGATCCATT 60.484 50.000 14.71 0.00 0.00 3.16
919 959 2.799412 GTCTGATCTGATCCATTGTCGC 59.201 50.000 14.71 0.00 0.00 5.19
1110 1153 1.511768 GAGCTACCGTCTTCCGCTT 59.488 57.895 0.00 0.00 34.38 4.68
1269 1316 3.434299 ACAGGTCGGTGTAATTAAAAGCG 59.566 43.478 12.44 12.44 36.22 4.68
1272 1319 3.413558 GTCGGTGTAATTAAAAGCGCAG 58.586 45.455 11.47 0.00 34.96 5.18
1273 1320 2.417239 TCGGTGTAATTAAAAGCGCAGG 59.583 45.455 11.47 0.00 34.96 4.85
1289 1336 3.702330 CGCAGGATCGTGTTATCAAGTA 58.298 45.455 16.27 0.00 0.00 2.24
1292 1339 4.740695 GCAGGATCGTGTTATCAAGTACTC 59.259 45.833 16.27 0.00 0.00 2.59
1294 1341 4.036498 AGGATCGTGTTATCAAGTACTCCG 59.964 45.833 0.00 0.00 0.00 4.63
1295 1342 4.201990 GGATCGTGTTATCAAGTACTCCGT 60.202 45.833 0.00 0.00 0.00 4.69
1298 1345 5.813717 TCGTGTTATCAAGTACTCCGTATG 58.186 41.667 0.00 0.00 0.00 2.39
1299 1346 5.355071 TCGTGTTATCAAGTACTCCGTATGT 59.645 40.000 0.00 0.00 0.00 2.29
1300 1347 6.538381 TCGTGTTATCAAGTACTCCGTATGTA 59.462 38.462 0.00 0.00 0.00 2.29
1303 1350 8.830580 GTGTTATCAAGTACTCCGTATGTACTA 58.169 37.037 0.00 0.91 46.66 1.82
1570 1617 1.672356 CCACTTCCTCAACGGCCTG 60.672 63.158 0.00 0.00 0.00 4.85
1790 1867 2.029073 CGTCACGGTGCTCAAGGT 59.971 61.111 2.51 0.00 0.00 3.50
1794 1871 1.003355 CACGGTGCTCAAGGTGGAT 60.003 57.895 0.00 0.00 0.00 3.41
1795 1872 0.606401 CACGGTGCTCAAGGTGGATT 60.606 55.000 0.00 0.00 0.00 3.01
2172 2252 4.398358 TCCGTCGAGCTTGATTATATAGGG 59.602 45.833 7.00 0.00 0.00 3.53
2191 2271 4.770795 AGGGGTCTTAGTTTGATCGATTG 58.229 43.478 0.00 0.00 0.00 2.67
2201 2282 4.754618 AGTTTGATCGATTGTGTGTTAGCA 59.245 37.500 0.00 0.00 0.00 3.49
2273 2647 2.373169 AGAGTTCAAGGTCATGGCTTCA 59.627 45.455 0.00 0.00 0.00 3.02
2285 2659 4.883585 GTCATGGCTTCATATGGTTTCAGA 59.116 41.667 2.13 0.00 0.00 3.27
2291 2665 5.297029 GGCTTCATATGGTTTCAGAACTACC 59.703 44.000 2.13 0.00 36.03 3.18
2400 2777 8.702163 TTTCATGTTTTTCTTTCTGAACTTCC 57.298 30.769 0.00 0.00 33.88 3.46
2411 2788 7.837863 TCTTTCTGAACTTCCACTATTCGTAT 58.162 34.615 0.00 0.00 0.00 3.06
2527 2905 4.385244 AAAAGTTGTTCGATACTCACGC 57.615 40.909 0.00 0.00 0.00 5.34
2530 2908 1.654105 GTTGTTCGATACTCACGCTGG 59.346 52.381 0.00 0.00 0.00 4.85
2539 2917 0.179045 ACTCACGCTGGCTTTGAAGT 60.179 50.000 0.00 0.00 0.00 3.01
2544 2922 0.723981 CGCTGGCTTTGAAGTAGCTC 59.276 55.000 15.12 0.00 38.67 4.09
2548 2926 3.350833 CTGGCTTTGAAGTAGCTCCATT 58.649 45.455 0.00 0.00 38.67 3.16
2549 2927 3.760684 CTGGCTTTGAAGTAGCTCCATTT 59.239 43.478 0.00 0.00 38.67 2.32
2550 2928 4.151883 TGGCTTTGAAGTAGCTCCATTTT 58.848 39.130 0.00 0.00 38.67 1.82
2551 2929 4.588528 TGGCTTTGAAGTAGCTCCATTTTT 59.411 37.500 0.00 0.00 38.67 1.94
2573 2951 4.904253 TTTTGAAAAGAAGGTACACCCG 57.096 40.909 0.00 0.00 38.74 5.28
2574 2952 2.554370 TGAAAAGAAGGTACACCCGG 57.446 50.000 0.00 0.00 38.74 5.73
2575 2953 1.162698 GAAAAGAAGGTACACCCGGC 58.837 55.000 0.00 0.00 38.74 6.13
2576 2954 0.251033 AAAAGAAGGTACACCCGGCC 60.251 55.000 0.00 0.00 38.74 6.13
2577 2955 1.131928 AAAGAAGGTACACCCGGCCT 61.132 55.000 0.00 0.00 38.74 5.19
2578 2956 1.551019 AAGAAGGTACACCCGGCCTC 61.551 60.000 0.00 0.00 38.74 4.70
2579 2957 1.988406 GAAGGTACACCCGGCCTCT 60.988 63.158 0.00 0.00 38.74 3.69
2580 2958 2.240162 GAAGGTACACCCGGCCTCTG 62.240 65.000 0.00 0.00 38.74 3.35
2581 2959 4.468689 GGTACACCCGGCCTCTGC 62.469 72.222 0.00 0.00 0.00 4.26
2582 2960 3.702048 GTACACCCGGCCTCTGCA 61.702 66.667 0.00 0.00 40.13 4.41
2583 2961 2.687200 TACACCCGGCCTCTGCAT 60.687 61.111 0.00 0.00 40.13 3.96
2584 2962 2.731571 TACACCCGGCCTCTGCATC 61.732 63.158 0.00 0.00 40.13 3.91
2589 2967 3.933722 CGGCCTCTGCATCGGGAT 61.934 66.667 0.00 0.00 40.13 3.85
2590 2968 2.574018 CGGCCTCTGCATCGGGATA 61.574 63.158 0.00 0.00 40.13 2.59
2600 2978 1.135489 GCATCGGGATAATGCATGCAG 60.135 52.381 26.69 10.51 46.93 4.41
2601 2979 1.135489 CATCGGGATAATGCATGCAGC 60.135 52.381 26.69 14.37 45.96 5.25
2604 2982 1.263356 GGGATAATGCATGCAGCCAT 58.737 50.000 26.69 17.62 44.83 4.40
2605 2983 2.449464 GGGATAATGCATGCAGCCATA 58.551 47.619 26.69 15.71 44.83 2.74
2660 3039 2.292267 ACATCAATAAGCCTGAAGCCG 58.708 47.619 0.00 0.00 45.47 5.52
2661 3040 2.292267 CATCAATAAGCCTGAAGCCGT 58.708 47.619 0.00 0.00 45.47 5.68
2663 3042 1.277842 TCAATAAGCCTGAAGCCGTCA 59.722 47.619 0.00 0.00 45.47 4.35
2665 3044 2.246719 ATAAGCCTGAAGCCGTCATC 57.753 50.000 0.00 0.00 45.47 2.92
2667 3046 0.326264 AAGCCTGAAGCCGTCATCTT 59.674 50.000 0.00 0.00 45.47 2.40
2669 3048 1.372087 GCCTGAAGCCGTCATCTTGG 61.372 60.000 0.00 0.00 35.07 3.61
2693 3073 6.183360 GGCAACAATGTTGCTATTTCTATCCT 60.183 38.462 38.75 0.00 44.36 3.24
2694 3074 6.914757 GCAACAATGTTGCTATTTCTATCCTC 59.085 38.462 35.47 8.92 41.87 3.71
2695 3075 7.201767 GCAACAATGTTGCTATTTCTATCCTCT 60.202 37.037 35.47 0.00 41.87 3.69
2697 3077 8.218338 ACAATGTTGCTATTTCTATCCTCTTG 57.782 34.615 0.00 0.00 0.00 3.02
2705 3085 7.071698 TGCTATTTCTATCCTCTTGATGAAGGT 59.928 37.037 0.00 0.00 34.76 3.50
2706 3086 7.387397 GCTATTTCTATCCTCTTGATGAAGGTG 59.613 40.741 0.00 0.00 34.76 4.00
2710 3090 1.003580 TCCTCTTGATGAAGGTGTGCC 59.996 52.381 0.00 0.00 0.00 5.01
2713 3093 1.071542 TCTTGATGAAGGTGTGCCGAA 59.928 47.619 0.00 0.00 40.50 4.30
2714 3094 2.086869 CTTGATGAAGGTGTGCCGAAT 58.913 47.619 0.00 0.00 40.50 3.34
2717 3097 1.398390 GATGAAGGTGTGCCGAATGTC 59.602 52.381 0.00 0.00 40.50 3.06
2718 3098 0.605319 TGAAGGTGTGCCGAATGTCC 60.605 55.000 0.00 0.00 40.50 4.02
2745 3125 4.034048 CCTAATACCAAACAGACATCGCAC 59.966 45.833 0.00 0.00 0.00 5.34
2747 3127 0.179032 ACCAAACAGACATCGCACCA 60.179 50.000 0.00 0.00 0.00 4.17
2750 3130 2.605338 CCAAACAGACATCGCACCAAAG 60.605 50.000 0.00 0.00 0.00 2.77
2751 3131 2.254546 AACAGACATCGCACCAAAGA 57.745 45.000 0.00 0.00 0.00 2.52
2759 3139 4.072131 ACATCGCACCAAAGACTAACATT 58.928 39.130 0.00 0.00 0.00 2.71
2764 3144 5.761234 TCGCACCAAAGACTAACATTAAAGT 59.239 36.000 0.00 0.00 0.00 2.66
2766 3146 6.077838 GCACCAAAGACTAACATTAAAGTCG 58.922 40.000 0.51 0.00 45.47 4.18
2767 3147 6.599437 CACCAAAGACTAACATTAAAGTCGG 58.401 40.000 0.51 0.00 45.47 4.79
2769 3149 5.704053 CCAAAGACTAACATTAAAGTCGGGT 59.296 40.000 0.51 0.00 45.47 5.28
2780 3161 1.131303 AAGTCGGGTGTCCCATCCAA 61.131 55.000 5.64 0.00 45.83 3.53
2782 3163 2.438434 CGGGTGTCCCATCCAAGC 60.438 66.667 5.64 0.00 45.83 4.01
2784 3165 2.763215 GGTGTCCCATCCAAGCCA 59.237 61.111 0.00 0.00 0.00 4.75
2786 3167 1.380302 GTGTCCCATCCAAGCCACT 59.620 57.895 0.00 0.00 0.00 4.00
2787 3168 0.618458 GTGTCCCATCCAAGCCACTA 59.382 55.000 0.00 0.00 0.00 2.74
2788 3169 0.618458 TGTCCCATCCAAGCCACTAC 59.382 55.000 0.00 0.00 0.00 2.73
2789 3170 0.107165 GTCCCATCCAAGCCACTACC 60.107 60.000 0.00 0.00 0.00 3.18
2790 3171 0.253160 TCCCATCCAAGCCACTACCT 60.253 55.000 0.00 0.00 0.00 3.08
2793 3174 0.911769 CATCCAAGCCACTACCTGGA 59.088 55.000 0.00 0.00 43.95 3.86
2798 3179 2.311287 AGCCACTACCTGGATTGGG 58.689 57.895 0.00 0.00 43.95 4.12
2800 3181 0.107165 GCCACTACCTGGATTGGGTC 60.107 60.000 0.00 0.00 43.95 4.46
2812 3193 2.837031 ATTGGGTCCCATGCCGTCAC 62.837 60.000 12.68 0.00 31.53 3.67
2878 3259 2.932194 TTGCCAGGCCTCTCTGCT 60.932 61.111 9.64 0.00 33.64 4.24
2880 3261 1.903877 TTGCCAGGCCTCTCTGCTAC 61.904 60.000 9.64 0.00 33.64 3.58
2914 4547 1.682257 GCCAGACAGCTTCCTCCTT 59.318 57.895 0.00 0.00 0.00 3.36
2951 4584 3.566261 CGCATCAGACGCCAAGTT 58.434 55.556 0.00 0.00 0.00 2.66
2983 4616 2.867855 GCCGCCGAGATCCACCATA 61.868 63.158 0.00 0.00 0.00 2.74
2990 4623 2.558795 CCGAGATCCACCATAGACGATT 59.441 50.000 0.00 0.00 0.00 3.34
3038 4671 2.278206 CCATCTCGCGTGGACTCG 60.278 66.667 8.47 0.80 39.12 4.18
3111 4744 3.460103 GAAGGAACACGACACCAAAGTA 58.540 45.455 0.00 0.00 0.00 2.24
3112 4745 3.764237 AGGAACACGACACCAAAGTAT 57.236 42.857 0.00 0.00 0.00 2.12
3137 4770 0.181587 TCGCCCAAACAGAGGAACAA 59.818 50.000 0.00 0.00 0.00 2.83
3167 4800 2.358372 TGCGCTCATGGCAGAGGTA 61.358 57.895 9.73 3.88 41.91 3.08
3168 4801 1.153369 GCGCTCATGGCAGAGGTAA 60.153 57.895 0.00 0.00 41.91 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 48 9.334693 CTTAACACATGAGCAATCTTTAAGTTC 57.665 33.333 0.00 0.00 0.00 3.01
81 84 4.616181 AATTTTAGCGGTCATGTAGTGC 57.384 40.909 0.00 0.00 0.00 4.40
109 112 2.012673 CCATGGTAGCTTTCAGCACTC 58.987 52.381 2.57 0.00 45.56 3.51
134 137 6.804783 CGTTCAGTCCGTATATTGCATATACA 59.195 38.462 18.29 5.42 44.95 2.29
145 149 2.684881 GGGAGTTCGTTCAGTCCGTATA 59.315 50.000 0.00 0.00 37.16 1.47
161 165 3.222394 AGGGGATTTAGTGAAGGGAGT 57.778 47.619 0.00 0.00 0.00 3.85
166 170 4.576330 AGGTGAAGGGGATTTAGTGAAG 57.424 45.455 0.00 0.00 0.00 3.02
246 250 0.394565 GTCCCTGGATTCCCGAGATG 59.605 60.000 0.00 0.00 34.29 2.90
335 340 4.858680 GTAGCTGAAGCCCCGGCC 62.859 72.222 1.02 0.00 43.38 6.13
361 366 0.541863 CCACTTACCCGAGCCAGAAT 59.458 55.000 0.00 0.00 0.00 2.40
570 575 1.000993 AAAACCACCACCCTGCACA 59.999 52.632 0.00 0.00 0.00 4.57
779 785 1.002792 GTTTCGTTTGTGGTCTCTGCC 60.003 52.381 0.00 0.00 0.00 4.85
840 846 3.789224 CCACACGAACTGTAAGCAAAAAC 59.211 43.478 0.00 0.00 37.60 2.43
841 847 3.181495 CCCACACGAACTGTAAGCAAAAA 60.181 43.478 0.00 0.00 37.60 1.94
846 856 2.094762 ATCCCACACGAACTGTAAGC 57.905 50.000 0.00 0.00 37.60 3.09
893 925 0.461548 TGGATCAGATCAGACACGGC 59.538 55.000 12.66 0.00 0.00 5.68
914 953 2.186602 TTTTATGGGAGGCCGCGACA 62.187 55.000 8.23 2.31 0.00 4.35
1269 1316 4.683832 AGTACTTGATAACACGATCCTGC 58.316 43.478 0.00 0.00 0.00 4.85
1272 1319 4.201990 ACGGAGTACTTGATAACACGATCC 60.202 45.833 0.00 0.00 41.94 3.36
1273 1320 4.918037 ACGGAGTACTTGATAACACGATC 58.082 43.478 0.00 0.00 41.94 3.69
1292 1339 3.541709 CGCGATCGATCTAGTACATACGG 60.542 52.174 21.57 4.23 38.10 4.02
1294 1341 4.836931 TCGCGATCGATCTAGTACATAC 57.163 45.455 21.57 0.00 40.21 2.39
1548 1595 1.578206 GCCGTTGAGGAAGTGGAAGC 61.578 60.000 0.00 0.00 45.00 3.86
1570 1617 2.202756 GTGGCCTGATCGACGTCC 60.203 66.667 10.58 0.00 0.00 4.79
1639 1694 8.138712 TGTTACAAAAGATTTTTAAGGCGTGAT 58.861 29.630 0.00 0.00 0.00 3.06
1640 1695 7.481642 TGTTACAAAAGATTTTTAAGGCGTGA 58.518 30.769 0.00 0.00 0.00 4.35
1710 1787 0.780596 CGGCGTTCATGATGATCTCG 59.219 55.000 0.00 3.61 0.00 4.04
1790 1867 0.674269 GTTCGGGTACGGCAAATCCA 60.674 55.000 0.00 0.00 41.39 3.41
1935 2012 1.214589 CCTCACGTTGTCCGGGTAG 59.785 63.158 0.00 0.00 41.99 3.18
2018 2098 2.520536 AAGTGCTTCACCGGAGCCT 61.521 57.895 9.46 3.56 34.49 4.58
2172 2252 5.408604 ACACACAATCGATCAAACTAAGACC 59.591 40.000 0.00 0.00 0.00 3.85
2201 2282 2.786777 GAACCCGTACAAATCCAAGGT 58.213 47.619 0.00 0.00 0.00 3.50
2228 2315 9.462606 TCTATCTACTAACTCAATGAGACAACA 57.537 33.333 18.20 0.00 33.32 3.33
2258 2632 3.559069 ACCATATGAAGCCATGACCTTG 58.441 45.455 3.65 0.00 34.31 3.61
2273 2647 5.435686 TGCAGGTAGTTCTGAAACCATAT 57.564 39.130 12.48 0.00 36.93 1.78
2285 2659 4.877251 TGTAGAAAAACGTTGCAGGTAGTT 59.123 37.500 0.00 0.00 0.00 2.24
2291 2665 5.095691 ACATCTGTAGAAAAACGTTGCAG 57.904 39.130 0.00 0.00 0.00 4.41
2377 2754 7.122650 AGTGGAAGTTCAGAAAGAAAAACATGA 59.877 33.333 5.01 0.00 38.13 3.07
2432 2809 9.942850 CACCCTTTCATGTTTTCCTAATAAATT 57.057 29.630 0.00 0.00 0.00 1.82
2525 2903 0.723981 GAGCTACTTCAAAGCCAGCG 59.276 55.000 9.85 0.00 41.02 5.18
2527 2905 2.479566 TGGAGCTACTTCAAAGCCAG 57.520 50.000 0.00 0.00 41.02 4.85
2551 2929 4.098196 CCGGGTGTACCTTCTTTTCAAAAA 59.902 41.667 0.00 0.00 36.97 1.94
2552 2930 3.633065 CCGGGTGTACCTTCTTTTCAAAA 59.367 43.478 0.00 0.00 36.97 2.44
2553 2931 3.215975 CCGGGTGTACCTTCTTTTCAAA 58.784 45.455 0.00 0.00 36.97 2.69
2554 2932 2.853705 CCGGGTGTACCTTCTTTTCAA 58.146 47.619 0.00 0.00 36.97 2.69
2555 2933 1.543871 GCCGGGTGTACCTTCTTTTCA 60.544 52.381 2.18 0.00 36.97 2.69
2556 2934 1.162698 GCCGGGTGTACCTTCTTTTC 58.837 55.000 2.18 0.00 36.97 2.29
2557 2935 0.251033 GGCCGGGTGTACCTTCTTTT 60.251 55.000 2.18 0.00 36.97 2.27
2558 2936 1.131928 AGGCCGGGTGTACCTTCTTT 61.132 55.000 2.18 0.00 36.97 2.52
2559 2937 1.538135 AGGCCGGGTGTACCTTCTT 60.538 57.895 2.18 0.00 36.97 2.52
2560 2938 1.988406 GAGGCCGGGTGTACCTTCT 60.988 63.158 2.18 0.00 36.97 2.85
2561 2939 1.988406 AGAGGCCGGGTGTACCTTC 60.988 63.158 2.18 0.00 36.97 3.46
2562 2940 2.122056 AGAGGCCGGGTGTACCTT 59.878 61.111 2.18 0.00 36.97 3.50
2563 2941 2.683933 CAGAGGCCGGGTGTACCT 60.684 66.667 2.18 0.00 36.97 3.08
2564 2942 4.468689 GCAGAGGCCGGGTGTACC 62.469 72.222 2.18 0.00 0.00 3.34
2565 2943 2.925162 GATGCAGAGGCCGGGTGTAC 62.925 65.000 2.18 0.00 40.13 2.90
2566 2944 2.687200 ATGCAGAGGCCGGGTGTA 60.687 61.111 2.18 0.00 40.13 2.90
2567 2945 4.101448 GATGCAGAGGCCGGGTGT 62.101 66.667 2.18 0.00 40.13 4.16
2572 2950 2.099652 TTATCCCGATGCAGAGGCCG 62.100 60.000 0.00 0.00 40.13 6.13
2573 2951 0.326264 ATTATCCCGATGCAGAGGCC 59.674 55.000 0.00 0.00 40.13 5.19
2574 2952 1.446907 CATTATCCCGATGCAGAGGC 58.553 55.000 4.81 0.00 41.68 4.70
2575 2953 1.446907 GCATTATCCCGATGCAGAGG 58.553 55.000 4.35 3.41 46.96 3.69
2581 2959 1.135489 GCTGCATGCATTATCCCGATG 60.135 52.381 22.97 6.35 42.31 3.84
2582 2960 1.171308 GCTGCATGCATTATCCCGAT 58.829 50.000 22.97 0.00 42.31 4.18
2583 2961 0.890542 GGCTGCATGCATTATCCCGA 60.891 55.000 22.97 0.00 45.15 5.14
2584 2962 1.174078 TGGCTGCATGCATTATCCCG 61.174 55.000 22.97 8.76 45.15 5.14
2585 2963 1.263356 ATGGCTGCATGCATTATCCC 58.737 50.000 22.97 16.08 45.15 3.85
2586 2964 4.730949 AATATGGCTGCATGCATTATCC 57.269 40.909 22.97 19.03 45.15 2.59
2587 2965 9.976511 ATTAATAATATGGCTGCATGCATTATC 57.023 29.630 22.97 11.35 45.15 1.75
2634 3013 5.528690 GCTTCAGGCTTATTGATGTATCACA 59.471 40.000 0.00 0.00 35.71 3.58
2637 3016 4.153117 CGGCTTCAGGCTTATTGATGTATC 59.847 45.833 0.00 0.00 41.46 2.24
2643 3022 1.277842 TGACGGCTTCAGGCTTATTGA 59.722 47.619 0.00 0.00 41.46 2.57
2646 3025 1.765314 AGATGACGGCTTCAGGCTTAT 59.235 47.619 6.95 0.00 37.77 1.73
2647 3026 1.195115 AGATGACGGCTTCAGGCTTA 58.805 50.000 6.95 0.00 37.77 3.09
2651 3030 1.372087 GCCAAGATGACGGCTTCAGG 61.372 60.000 6.95 8.87 45.29 3.86
2660 3039 2.733026 GCAACATTGTTGCCAAGATGAC 59.267 45.455 34.12 11.51 39.38 3.06
2661 3040 2.629137 AGCAACATTGTTGCCAAGATGA 59.371 40.909 37.87 0.00 45.98 2.92
2663 3042 5.410355 AATAGCAACATTGTTGCCAAGAT 57.590 34.783 37.87 26.59 45.98 2.40
2665 3044 5.232463 AGAAATAGCAACATTGTTGCCAAG 58.768 37.500 37.87 13.65 45.98 3.61
2667 3046 4.870123 AGAAATAGCAACATTGTTGCCA 57.130 36.364 37.87 30.44 45.98 4.92
2669 3048 6.799512 AGGATAGAAATAGCAACATTGTTGC 58.200 36.000 36.00 36.00 45.22 4.17
2675 3054 8.435187 TCATCAAGAGGATAGAAATAGCAACAT 58.565 33.333 0.00 0.00 33.95 2.71
2679 3059 7.071698 ACCTTCATCAAGAGGATAGAAATAGCA 59.928 37.037 0.00 0.00 33.95 3.49
2686 3066 4.141846 GCACACCTTCATCAAGAGGATAGA 60.142 45.833 0.00 0.00 33.95 1.98
2693 3073 0.684535 TCGGCACACCTTCATCAAGA 59.315 50.000 0.00 0.00 0.00 3.02
2694 3074 1.522668 TTCGGCACACCTTCATCAAG 58.477 50.000 0.00 0.00 0.00 3.02
2695 3075 1.811965 CATTCGGCACACCTTCATCAA 59.188 47.619 0.00 0.00 0.00 2.57
2697 3077 1.398390 GACATTCGGCACACCTTCATC 59.602 52.381 0.00 0.00 0.00 2.92
2710 3090 2.363038 TGGTATTAGGTCCGGACATTCG 59.637 50.000 34.40 0.00 0.00 3.34
2713 3093 3.520317 TGTTTGGTATTAGGTCCGGACAT 59.480 43.478 34.40 30.69 0.00 3.06
2714 3094 2.905085 TGTTTGGTATTAGGTCCGGACA 59.095 45.455 34.40 16.31 0.00 4.02
2717 3097 3.055675 TGTCTGTTTGGTATTAGGTCCGG 60.056 47.826 0.00 0.00 0.00 5.14
2718 3098 4.196626 TGTCTGTTTGGTATTAGGTCCG 57.803 45.455 0.00 0.00 0.00 4.79
2721 3101 4.189231 GCGATGTCTGTTTGGTATTAGGT 58.811 43.478 0.00 0.00 0.00 3.08
2745 3125 5.704053 ACCCGACTTTAATGTTAGTCTTTGG 59.296 40.000 0.00 0.00 38.86 3.28
2747 3127 6.293698 ACACCCGACTTTAATGTTAGTCTTT 58.706 36.000 0.00 0.00 38.86 2.52
2750 3130 4.628766 GGACACCCGACTTTAATGTTAGTC 59.371 45.833 0.00 0.00 37.90 2.59
2751 3131 4.564199 GGGACACCCGACTTTAATGTTAGT 60.564 45.833 0.00 0.00 32.13 2.24
2793 3174 2.275418 GACGGCATGGGACCCAAT 59.725 61.111 19.58 3.24 36.95 3.16
2795 3176 4.028490 GTGACGGCATGGGACCCA 62.028 66.667 17.73 17.73 38.19 4.51
2796 3177 4.796495 GGTGACGGCATGGGACCC 62.796 72.222 2.45 2.45 0.00 4.46
2798 3179 1.745489 GAAGGTGACGGCATGGGAC 60.745 63.158 0.00 0.00 0.00 4.46
2800 3181 1.077501 ATGAAGGTGACGGCATGGG 60.078 57.895 0.00 0.00 0.00 4.00
2803 3184 1.407437 GGAAGATGAAGGTGACGGCAT 60.407 52.381 0.00 0.00 0.00 4.40
2804 3185 0.036388 GGAAGATGAAGGTGACGGCA 60.036 55.000 0.00 0.00 0.00 5.69
2812 3193 1.486310 TGGACCGATGGAAGATGAAGG 59.514 52.381 0.00 0.00 0.00 3.46
2878 3259 1.029408 GCGTCATGGTGGCATTGGTA 61.029 55.000 0.00 0.00 0.00 3.25
2880 3261 2.491152 GCGTCATGGTGGCATTGG 59.509 61.111 0.00 0.00 0.00 3.16
2914 4547 1.657751 CGGAGATGGACTCACGCAGA 61.658 60.000 0.00 0.00 46.54 4.26
2947 4580 1.959085 CATGGCGCAGTGGAAACTT 59.041 52.632 10.83 0.00 0.00 2.66
2975 4608 3.193903 TCAAACGAATCGTCTATGGTGGA 59.806 43.478 9.32 0.00 39.99 4.02
2981 4614 3.555956 GTGGCATCAAACGAATCGTCTAT 59.444 43.478 9.32 0.00 39.99 1.98
2983 4616 1.732259 GTGGCATCAAACGAATCGTCT 59.268 47.619 9.32 0.00 39.99 4.18
2990 4623 2.612567 GCGGTGTGGCATCAAACGA 61.613 57.895 9.06 0.00 31.89 3.85
3032 4665 0.606604 TTGCTGGTAGTTCCGAGTCC 59.393 55.000 0.00 0.00 39.52 3.85
3038 4671 1.610886 GGTGGAGTTGCTGGTAGTTCC 60.611 57.143 0.00 0.00 0.00 3.62
3111 4744 0.249120 TCTGTTTGGGCGACGATGAT 59.751 50.000 0.00 0.00 0.00 2.45
3112 4745 0.389817 CTCTGTTTGGGCGACGATGA 60.390 55.000 0.00 0.00 0.00 2.92
3137 4770 2.914097 AGCGCAGGCAAAAGCCTT 60.914 55.556 11.47 0.00 43.41 4.35


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

AutoCloner maintained by Alex Coulton.