Multiple sequence alignment - TraesCS1D01G036100

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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 TraesCS1D01G036100 chr1D 100.000 3233 0 0 1 3233 16828387 16825155 0.000000e+00 5971.0
1 TraesCS1D01G036100 chr1D 86.186 333 37 7 1044 1368 16838724 16838393 5.130000e-93 351.0
2 TraesCS1D01G036100 chr1D 84.151 265 42 0 15 279 17049817 17050081 1.150000e-64 257.0
3 TraesCS1D01G036100 chr1D 92.029 138 2 3 1793 1930 16826547 16826419 5.510000e-43 185.0
4 TraesCS1D01G036100 chr1D 92.029 138 2 3 1841 1969 16826595 16826458 5.510000e-43 185.0
5 TraesCS1D01G036100 chr1D 87.778 90 2 3 1793 1882 16826499 16826419 2.650000e-16 97.1
6 TraesCS1D01G036100 chr1D 87.778 90 2 3 1889 1969 16826595 16826506 2.650000e-16 97.1
7 TraesCS1D01G036100 chr1D 100.000 29 0 0 281 309 294215813 294215841 2.000000e-03 54.7
8 TraesCS1D01G036100 chr1A 89.283 1325 70 20 940 2198 17792914 17791596 0.000000e+00 1594.0
9 TraesCS1D01G036100 chr1A 87.830 682 48 16 220 896 17793569 17792918 0.000000e+00 767.0
10 TraesCS1D01G036100 chr1A 91.522 460 33 4 2774 3233 17790925 17790472 2.120000e-176 628.0
11 TraesCS1D01G036100 chr1A 83.463 387 53 9 997 1376 17825649 17825267 1.850000e-92 350.0
12 TraesCS1D01G036100 chr1A 83.221 298 37 10 15 309 26956423 26956710 8.900000e-66 261.0
13 TraesCS1D01G036100 chr1A 92.157 102 4 2 1765 1866 17791933 17791836 1.210000e-29 141.0
14 TraesCS1D01G036100 chr1A 96.875 64 2 0 1889 1952 17792043 17791980 1.230000e-19 108.0
15 TraesCS1D01G036100 chr1A 94.737 38 2 0 2326 2363 17791389 17791352 3.480000e-05 60.2
16 TraesCS1D01G036100 chr1B 89.823 1071 67 21 722 1756 30797621 30796557 0.000000e+00 1336.0
17 TraesCS1D01G036100 chr1B 85.633 703 52 21 4 698 30798493 30797832 0.000000e+00 693.0
18 TraesCS1D01G036100 chr1B 88.454 511 50 6 2277 2780 30795975 30795467 2.760000e-170 608.0
19 TraesCS1D01G036100 chr1B 89.371 461 45 3 2774 3233 30795420 30794963 7.780000e-161 577.0
20 TraesCS1D01G036100 chr1B 84.352 409 34 13 1931 2312 30796382 30795977 1.100000e-99 374.0
21 TraesCS1D01G036100 chr1B 87.097 124 7 2 1690 1813 30796590 30796476 7.280000e-27 132.0
22 TraesCS1D01G036100 chr1B 92.593 81 5 1 1738 1818 30796434 30796355 7.330000e-22 115.0
23 TraesCS1D01G036100 chr1B 96.226 53 1 1 1766 1818 30796499 30796448 5.750000e-13 86.1
24 TraesCS1D01G036100 chr3D 86.038 265 34 3 15 278 22053459 22053721 6.830000e-72 281.0
25 TraesCS1D01G036100 chr3D 84.524 252 37 1 25 276 446115360 446115609 6.930000e-62 248.0
26 TraesCS1D01G036100 chr3D 79.298 285 49 4 25 309 561491357 561491083 1.180000e-44 191.0
27 TraesCS1D01G036100 chr2A 86.038 265 31 4 15 279 564613756 564613498 2.460000e-71 279.0
28 TraesCS1D01G036100 chr2A 82.576 264 40 5 15 276 553049505 553049246 9.020000e-56 228.0
29 TraesCS1D01G036100 chr2A 77.056 231 43 6 79 309 118678391 118678171 1.220000e-24 124.0
30 TraesCS1D01G036100 chr7B 82.653 294 40 6 15 308 48773326 48773608 1.930000e-62 250.0
31 TraesCS1D01G036100 chr2D 83.774 265 42 1 15 278 645316410 645316674 1.930000e-62 250.0
32 TraesCS1D01G036100 chr6D 81.481 297 41 10 16 309 315365977 315366262 6.980000e-57 231.0
33 TraesCS1D01G036100 chr6D 77.627 295 55 6 15 309 362853997 362854280 5.550000e-38 169.0
34 TraesCS1D01G036100 chr7D 82.197 264 47 0 16 279 41870628 41870891 9.020000e-56 228.0
35 TraesCS1D01G036100 chr5D 76.846 298 54 8 16 309 342944846 342945132 1.550000e-33 154.0
36 TraesCS1D01G036100 chr5D 81.410 156 20 3 154 309 349367066 349366920 5.670000e-23 119.0


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 TraesCS1D01G036100 chr1D 16825155 16828387 3232 True 1307.0400 5971 91.922800 1 3233 5 chr1D.!!$R2 3232
1 TraesCS1D01G036100 chr1A 17790472 17793569 3097 True 549.7000 1594 92.067333 220 3233 6 chr1A.!!$R2 3013
2 TraesCS1D01G036100 chr1B 30794963 30798493 3530 True 490.1375 1336 89.193625 4 3233 8 chr1B.!!$R1 3229

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
44 45 0.158928 CTTCGTTCGTCTGTGTTCGC 59.841 55.0 0.0 0.0 0.0 4.70 F
237 244 0.248702 GCTCCAGTGCTAGTAGTCGC 60.249 60.0 0.0 0.0 0.0 5.19 F
934 1135 0.250295 CCTTCCTCAACAACTCCGCA 60.250 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1817 0.107312 CTGGCTAAGCACATCAGGCT 60.107 55.0 0.00 0.0 45.15 4.58 R
2032 2392 0.673644 ATGTACTGCTGCCGTGGAAC 60.674 55.0 6.98 0.0 0.00 3.62 R
2402 2891 0.313043 ACAAGACAGCAGCATTGTGC 59.687 50.0 0.00 0.0 45.46 4.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.865085 AGTGTTTGTCTTTAGTGGATGCTA 58.135 37.500 0.00 0.00 0.00 3.49
33 34 3.085443 AGTGGATGCTATCTTCGTTCG 57.915 47.619 0.00 0.00 0.00 3.95
37 38 3.046390 GGATGCTATCTTCGTTCGTCTG 58.954 50.000 0.00 0.00 0.00 3.51
38 39 3.489398 GGATGCTATCTTCGTTCGTCTGT 60.489 47.826 0.00 0.00 0.00 3.41
44 45 0.158928 CTTCGTTCGTCTGTGTTCGC 59.841 55.000 0.00 0.00 0.00 4.70
54 55 1.268625 TCTGTGTTCGCGTGTCTACAT 59.731 47.619 5.77 0.00 0.00 2.29
66 67 3.462021 GTGTCTACATGCTGGATCCTTC 58.538 50.000 14.23 5.08 0.00 3.46
85 86 0.649475 CCAATCTGCGCTTCTCTTCG 59.351 55.000 9.73 0.00 0.00 3.79
89 90 2.126463 TGCGCTTCTCTTCGTCGG 60.126 61.111 9.73 0.00 0.00 4.79
101 102 1.666553 TCGTCGGCGATGCTTGTTT 60.667 52.632 23.67 0.00 42.81 2.83
109 110 3.492313 GGCGATGCTTGTTTTTCTAGTG 58.508 45.455 0.00 0.00 0.00 2.74
112 113 3.363970 CGATGCTTGTTTTTCTAGTGCGT 60.364 43.478 0.00 0.00 0.00 5.24
132 133 1.802553 TGGTCCTATGGGGTCTTAGC 58.197 55.000 0.00 0.00 36.25 3.09
145 148 2.633488 GTCTTAGCACCATGACTTCCC 58.367 52.381 0.00 0.00 0.00 3.97
149 152 2.100631 GCACCATGACTTCCCGACG 61.101 63.158 0.00 0.00 0.00 5.12
152 155 1.295423 CCATGACTTCCCGACGGTT 59.705 57.895 13.94 0.00 0.00 4.44
156 159 1.331214 TGACTTCCCGACGGTTTACT 58.669 50.000 13.94 0.00 0.00 2.24
165 168 2.733026 CCGACGGTTTACTACAACAAGG 59.267 50.000 5.48 0.00 0.00 3.61
170 173 4.201940 ACGGTTTACTACAACAAGGTTTGC 60.202 41.667 0.00 0.00 0.00 3.68
176 179 3.230990 AACAAGGTTTGCCCGGCC 61.231 61.111 7.03 0.00 38.74 6.13
206 209 3.056328 GGGTGAAGAAGGCGGCAC 61.056 66.667 13.08 4.75 0.00 5.01
237 244 0.248702 GCTCCAGTGCTAGTAGTCGC 60.249 60.000 0.00 0.00 0.00 5.19
254 261 2.117156 GCCGCTAGGTGGTCTACGA 61.117 63.158 0.00 0.00 40.50 3.43
304 311 7.603024 GCTTACTTCTGGTGTTCTTTGTACTAT 59.397 37.037 0.00 0.00 0.00 2.12
305 312 9.141400 CTTACTTCTGGTGTTCTTTGTACTATC 57.859 37.037 0.00 0.00 0.00 2.08
306 313 7.304497 ACTTCTGGTGTTCTTTGTACTATCT 57.696 36.000 0.00 0.00 0.00 1.98
307 314 7.736893 ACTTCTGGTGTTCTTTGTACTATCTT 58.263 34.615 0.00 0.00 0.00 2.40
308 315 7.657761 ACTTCTGGTGTTCTTTGTACTATCTTG 59.342 37.037 0.00 0.00 0.00 3.02
356 364 7.432148 AAAAAGGTATCCCAAGAAAAACAGT 57.568 32.000 0.00 0.00 0.00 3.55
357 365 6.650427 AAAGGTATCCCAAGAAAAACAGTC 57.350 37.500 0.00 0.00 0.00 3.51
460 469 1.399714 TATGGGCCGTAGAGTGAGTG 58.600 55.000 0.00 0.00 0.00 3.51
479 488 4.636249 AGTGGAGTGAGAGCAACTAAAAG 58.364 43.478 0.00 0.00 0.00 2.27
483 492 6.205658 GTGGAGTGAGAGCAACTAAAAGAAAT 59.794 38.462 0.00 0.00 0.00 2.17
485 494 8.103305 TGGAGTGAGAGCAACTAAAAGAAATAT 58.897 33.333 0.00 0.00 0.00 1.28
486 495 8.394121 GGAGTGAGAGCAACTAAAAGAAATATG 58.606 37.037 0.00 0.00 0.00 1.78
487 496 7.756558 AGTGAGAGCAACTAAAAGAAATATGC 58.243 34.615 0.00 0.00 0.00 3.14
488 497 7.609532 AGTGAGAGCAACTAAAAGAAATATGCT 59.390 33.333 0.00 0.00 44.61 3.79
507 521 3.122297 GCTAGTAGAGTGATTGCAGCAG 58.878 50.000 0.00 0.00 0.00 4.24
520 534 2.993840 AGCAGAGCAGCGAGTGGA 60.994 61.111 0.00 0.00 40.15 4.02
525 539 4.731612 AGCAGCGAGTGGACAGCG 62.732 66.667 0.00 0.00 35.78 5.18
527 541 2.807045 CAGCGAGTGGACAGCGAC 60.807 66.667 0.00 0.00 35.78 5.19
712 726 4.862823 CCGACCTCCCTCCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
725 926 4.548513 CTCCCCCTCCCCTCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
774 975 3.861797 CCCACCTTCCCGATCCCG 61.862 72.222 0.00 0.00 0.00 5.14
817 1018 2.284699 CGTTCCCCTGACCCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
818 1019 2.359967 CGTTCCCCTGACCCTCCTC 61.360 68.421 0.00 0.00 0.00 3.71
819 1020 1.996187 GTTCCCCTGACCCTCCTCC 60.996 68.421 0.00 0.00 0.00 4.30
820 1021 3.618855 TTCCCCTGACCCTCCTCCG 62.619 68.421 0.00 0.00 0.00 4.63
841 1042 1.522569 CCGGAGAAATCGCCTCCTT 59.477 57.895 0.00 0.00 46.15 3.36
847 1048 0.645868 GAAATCGCCTCCTTTCGTCG 59.354 55.000 0.00 0.00 0.00 5.12
934 1135 0.250295 CCTTCCTCAACAACTCCGCA 60.250 55.000 0.00 0.00 0.00 5.69
995 1202 2.048503 GTCCTCGTGTGTTCCCCG 60.049 66.667 0.00 0.00 0.00 5.73
1380 1614 4.404098 GTGTCCGCAACCCCCGAT 62.404 66.667 0.00 0.00 0.00 4.18
1446 1680 1.102222 ACGATAGAGTGGAGGACGCC 61.102 60.000 0.00 0.00 41.38 5.68
1580 1814 2.184836 GCCATACACGGCGTACCA 59.815 61.111 14.22 0.10 43.52 3.25
1581 1815 1.881252 GCCATACACGGCGTACCAG 60.881 63.158 14.22 2.13 43.52 4.00
1582 1816 1.881252 CCATACACGGCGTACCAGC 60.881 63.158 14.22 0.00 34.57 4.85
1583 1817 1.153726 CATACACGGCGTACCAGCA 60.154 57.895 14.22 0.00 39.27 4.41
1618 1852 1.684248 GCCAGCTGAATCTTCCCATGT 60.684 52.381 17.39 0.00 0.00 3.21
1626 1860 0.749454 ATCTTCCCATGTTCCAGCGC 60.749 55.000 0.00 0.00 0.00 5.92
1632 1866 1.210931 CATGTTCCAGCGCCAACAG 59.789 57.895 18.60 9.86 35.99 3.16
1640 1874 2.040544 AGCGCCAACAGCCATACAC 61.041 57.895 2.29 0.00 38.78 2.90
1650 1884 2.169146 GCCATACACGCCGTACCAC 61.169 63.158 0.00 0.00 31.27 4.16
1652 1886 1.874915 CATACACGCCGTACCACCG 60.875 63.158 0.00 0.00 31.27 4.94
1688 1925 2.282462 GGCGGGGGCCATGAATAG 60.282 66.667 4.39 0.00 0.00 1.73
1707 1944 7.907389 TGAATAGCTACAATATTCCTCCGATT 58.093 34.615 0.00 0.00 38.37 3.34
1740 2010 5.566230 GCCGTACTACAATATTCCTCCGATT 60.566 44.000 0.00 0.00 0.00 3.34
1840 2125 3.393970 CGAGGCAGCCCTTCAGGA 61.394 66.667 8.22 0.00 43.12 3.86
1841 2126 2.588989 GAGGCAGCCCTTCAGGAG 59.411 66.667 8.22 0.00 43.12 3.69
1842 2127 3.013932 AGGCAGCCCTTCAGGAGG 61.014 66.667 8.22 0.00 45.86 4.30
1848 2133 3.826282 CCCTTCAGGAGGCAGGAA 58.174 61.111 0.00 0.00 44.85 3.36
1953 2310 3.814504 AGGCAAGAATTCTTCCCTGAA 57.185 42.857 26.80 0.00 42.36 3.02
2021 2381 4.858433 CATGGCAATGGCGCACCG 62.858 66.667 10.83 0.00 42.47 4.94
2032 2392 3.463690 CGCACCGTGAACCGTACG 61.464 66.667 8.69 8.69 40.98 3.67
2034 2394 1.950630 GCACCGTGAACCGTACGTT 60.951 57.895 15.21 8.58 39.76 3.99
2078 2438 1.770110 ACCAGCCACACTTCCCTGA 60.770 57.895 0.00 0.00 0.00 3.86
2114 2474 1.211212 TGCTCATGGTCAGGGATCAAG 59.789 52.381 0.00 0.00 0.00 3.02
2120 2483 1.555075 TGGTCAGGGATCAAGCACTAC 59.445 52.381 0.00 0.00 0.00 2.73
2141 2504 4.259952 TCGATCACCGAGCAGGAT 57.740 55.556 5.19 0.00 43.23 3.24
2146 2509 3.911323 CGATCACCGAGCAGGATTACCT 61.911 54.545 5.19 0.00 44.02 3.08
2149 2512 2.891580 TCACCGAGCAGGATTACCTATC 59.108 50.000 5.19 0.00 45.94 2.08
2167 2530 1.819928 TCCGGACAACATCAATGTGG 58.180 50.000 0.00 0.00 41.61 4.17
2205 2613 4.647399 AGTAAGAAGAGCAGGACTATCCAC 59.353 45.833 0.00 0.00 39.61 4.02
2211 2619 3.196685 AGAGCAGGACTATCCACAAGAAC 59.803 47.826 0.00 0.00 39.61 3.01
2270 2681 1.694696 GCTATGATTCCCGGAGACCTT 59.305 52.381 0.73 0.00 0.00 3.50
2271 2682 2.289133 GCTATGATTCCCGGAGACCTTC 60.289 54.545 0.73 0.00 0.00 3.46
2272 2683 2.182516 ATGATTCCCGGAGACCTTCT 57.817 50.000 0.73 0.00 0.00 2.85
2357 2843 1.152860 ACCGTGTGGGCAACATTCA 60.153 52.632 0.00 0.00 41.97 2.57
2366 2852 0.244721 GGCAACATTCACAAGGCCTC 59.755 55.000 5.23 0.00 38.37 4.70
2370 2859 3.411446 CAACATTCACAAGGCCTCACTA 58.589 45.455 5.23 0.00 0.00 2.74
2383 2872 4.080638 AGGCCTCACTAAGAAAGGAATCAG 60.081 45.833 0.00 0.00 31.44 2.90
2393 2882 6.830873 AAGAAAGGAATCAGAAAGACATGG 57.169 37.500 0.00 0.00 0.00 3.66
2470 2959 1.660560 GGAGCAATGCAAGCACCGAT 61.661 55.000 8.35 0.00 33.22 4.18
2481 2970 1.153549 GCACCGATGGAGGAGTGAC 60.154 63.158 0.00 0.00 34.73 3.67
2494 2983 3.118454 GTGACGCCGGTGACATGG 61.118 66.667 24.59 0.00 29.93 3.66
2541 3031 2.668632 GTGTGGGGAAGATGCCGA 59.331 61.111 0.00 0.00 0.00 5.54
2547 3037 1.132977 TGGGGAAGATGCCGAGGTATA 60.133 52.381 0.00 0.00 0.00 1.47
2555 3045 4.957296 AGATGCCGAGGTATATTTTTCGT 58.043 39.130 0.00 0.00 0.00 3.85
2579 3069 1.059584 TCACAGGGATGTGTGGGTGT 61.060 55.000 8.13 0.00 46.65 4.16
2583 3073 0.473694 AGGGATGTGTGGGTGTGAGA 60.474 55.000 0.00 0.00 0.00 3.27
2586 3076 1.338200 GGATGTGTGGGTGTGAGAGAC 60.338 57.143 0.00 0.00 0.00 3.36
2593 3083 1.258445 GGGTGTGAGAGACGACCCAT 61.258 60.000 0.00 0.00 41.80 4.00
2596 3086 0.895530 TGTGAGAGACGACCCATTCC 59.104 55.000 0.00 0.00 0.00 3.01
2605 3095 0.877649 CGACCCATTCCGCATCTCAG 60.878 60.000 0.00 0.00 0.00 3.35
2609 3099 1.579698 CCATTCCGCATCTCAGTCTG 58.420 55.000 0.00 0.00 0.00 3.51
2610 3100 1.579698 CATTCCGCATCTCAGTCTGG 58.420 55.000 0.00 0.00 0.00 3.86
2636 3128 1.089920 ACATGCTGCGATTTGGACTC 58.910 50.000 0.00 0.00 0.00 3.36
2640 3132 1.970917 GCTGCGATTTGGACTCGGTG 61.971 60.000 0.00 0.00 36.65 4.94
2659 3151 3.064324 GCTGCCGGTCAATGCCTT 61.064 61.111 1.90 0.00 0.00 4.35
2930 3475 9.125026 ACCATATGTTTTAAAATGGCAAACAAA 57.875 25.926 15.23 0.00 42.22 2.83
2931 3476 9.956720 CCATATGTTTTAAAATGGCAAACAAAA 57.043 25.926 3.52 1.00 42.22 2.44
2953 3498 6.969993 AAAGTAGAAGTTTGTTGGCCATTA 57.030 33.333 6.09 0.00 0.00 1.90
2995 3540 3.065371 GCACTACCCTTGCATGTATTGTC 59.935 47.826 0.00 0.00 39.93 3.18
3017 3563 6.261381 TGTCATTACAAGGGTTGTTACAAGTC 59.739 38.462 0.00 0.00 42.22 3.01
3049 3595 5.234466 AGAGTACTGCTTCATCAAAGGTT 57.766 39.130 0.00 0.00 35.37 3.50
3071 3617 3.685139 TTAGAGCGATGATTGGGGATC 57.315 47.619 0.00 0.00 35.21 3.36
3073 3619 1.622811 AGAGCGATGATTGGGGATCTC 59.377 52.381 0.00 0.00 35.69 2.75
3087 3633 1.671850 GGATCTCACGAGTTTGCGGAA 60.672 52.381 0.00 0.00 35.12 4.30
3107 3653 4.462834 GGAAAGGGAATAAGTTTGTGGAGG 59.537 45.833 0.00 0.00 0.00 4.30
3115 3661 6.437477 GGAATAAGTTTGTGGAGGGAGAAAAT 59.563 38.462 0.00 0.00 0.00 1.82
3126 3672 8.050930 TGTGGAGGGAGAAAATTACCTTTATAC 58.949 37.037 0.00 0.00 32.42 1.47
3127 3673 8.050930 GTGGAGGGAGAAAATTACCTTTATACA 58.949 37.037 0.00 0.00 32.42 2.29
3136 3682 7.891498 AAATTACCTTTATACACACCATCCC 57.109 36.000 0.00 0.00 0.00 3.85
3163 3709 5.163353 GCCTATCTGATAGCCTTATTCCCTC 60.163 48.000 17.40 0.00 0.00 4.30
3225 3771 4.994744 TCAGCCACTGATGTGTCG 57.005 55.556 0.00 0.00 42.34 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.718961 AGCATCCACTAAAGACAAACACT 58.281 39.130 0.00 0.00 0.00 3.55
1 2 6.595716 AGATAGCATCCACTAAAGACAAACAC 59.404 38.462 0.00 0.00 0.00 3.32
2 3 6.711277 AGATAGCATCCACTAAAGACAAACA 58.289 36.000 0.00 0.00 0.00 2.83
12 13 3.630769 ACGAACGAAGATAGCATCCACTA 59.369 43.478 0.14 0.00 0.00 2.74
13 14 2.427453 ACGAACGAAGATAGCATCCACT 59.573 45.455 0.14 0.00 0.00 4.00
23 24 2.316792 CGAACACAGACGAACGAAGAT 58.683 47.619 0.14 0.00 0.00 2.40
33 34 1.050767 GTAGACACGCGAACACAGAC 58.949 55.000 15.93 0.00 0.00 3.51
37 38 0.093026 GCATGTAGACACGCGAACAC 59.907 55.000 15.93 3.51 0.00 3.32
38 39 0.038618 AGCATGTAGACACGCGAACA 60.039 50.000 15.93 9.26 40.38 3.18
44 45 1.410517 AGGATCCAGCATGTAGACACG 59.589 52.381 15.82 0.00 0.00 4.49
66 67 0.649475 CGAAGAGAAGCGCAGATTGG 59.351 55.000 11.47 0.00 34.67 3.16
68 69 1.634702 GACGAAGAGAAGCGCAGATT 58.365 50.000 11.47 0.00 41.04 2.40
85 86 1.069227 AGAAAAACAAGCATCGCCGAC 60.069 47.619 0.00 0.00 0.00 4.79
89 90 2.911102 GCACTAGAAAAACAAGCATCGC 59.089 45.455 0.00 0.00 0.00 4.58
101 102 3.369052 CCATAGGACCAACGCACTAGAAA 60.369 47.826 0.00 0.00 0.00 2.52
109 110 1.153229 GACCCCATAGGACCAACGC 60.153 63.158 0.00 0.00 39.89 4.84
112 113 2.124411 GCTAAGACCCCATAGGACCAA 58.876 52.381 0.00 0.00 39.89 3.67
132 133 1.447838 CCGTCGGGAAGTCATGGTG 60.448 63.158 2.34 0.00 34.06 4.17
145 148 3.383761 ACCTTGTTGTAGTAAACCGTCG 58.616 45.455 0.00 0.00 0.00 5.12
149 152 4.500205 GGGCAAACCTTGTTGTAGTAAACC 60.500 45.833 0.00 0.00 35.85 3.27
152 155 2.879646 CGGGCAAACCTTGTTGTAGTAA 59.120 45.455 0.00 0.00 36.97 2.24
156 159 1.457009 GCCGGGCAAACCTTGTTGTA 61.457 55.000 15.62 0.00 36.97 2.41
176 179 1.264749 TTCACCCCTCACTCATCGGG 61.265 60.000 0.00 0.00 41.71 5.14
185 188 2.592993 CCGCCTTCTTCACCCCTCA 61.593 63.158 0.00 0.00 0.00 3.86
237 244 0.100146 GTTCGTAGACCACCTAGCGG 59.900 60.000 0.00 0.00 34.32 5.52
279 286 9.141400 GATAGTACAAAGAACACCAGAAGTAAG 57.859 37.037 0.00 0.00 0.00 2.34
373 381 6.687105 CGTTTCATTCGACTGTTTCTTTTTCT 59.313 34.615 2.44 0.00 0.00 2.52
374 382 6.468000 ACGTTTCATTCGACTGTTTCTTTTTC 59.532 34.615 2.44 0.00 0.00 2.29
460 469 6.809630 ATTTCTTTTAGTTGCTCTCACTCC 57.190 37.500 0.00 0.00 0.00 3.85
479 488 7.359933 GCTGCAATCACTCTACTAGCATATTTC 60.360 40.741 0.00 0.00 0.00 2.17
483 492 4.342092 TGCTGCAATCACTCTACTAGCATA 59.658 41.667 0.00 0.00 35.27 3.14
485 494 2.497273 TGCTGCAATCACTCTACTAGCA 59.503 45.455 0.00 0.00 37.56 3.49
486 495 3.122297 CTGCTGCAATCACTCTACTAGC 58.878 50.000 3.02 0.00 0.00 3.42
487 496 4.609947 CTCTGCTGCAATCACTCTACTAG 58.390 47.826 3.02 0.00 0.00 2.57
488 497 3.181482 GCTCTGCTGCAATCACTCTACTA 60.181 47.826 3.02 0.00 0.00 1.82
507 521 2.813042 GCTGTCCACTCGCTGCTC 60.813 66.667 0.00 0.00 0.00 4.26
520 534 4.681978 GTTGGGCCGAGTCGCTGT 62.682 66.667 7.12 0.00 0.00 4.40
525 539 4.410400 CCTGGGTTGGGCCGAGTC 62.410 72.222 0.00 0.00 40.97 3.36
527 541 4.101448 CTCCTGGGTTGGGCCGAG 62.101 72.222 0.00 0.00 42.06 4.63
704 718 4.179599 GAGGGGAGGGGGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
705 719 4.761304 AGAGGGGAGGGGGAGGGA 62.761 72.222 0.00 0.00 0.00 4.20
706 720 4.179599 GAGAGGGGAGGGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
707 721 4.179599 GGAGAGGGGAGGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
708 722 4.548513 CGGAGAGGGGAGGGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
800 1001 2.284699 AGGAGGGTCAGGGGAACG 60.285 66.667 0.00 0.00 0.00 3.95
801 1002 1.996187 GGAGGAGGGTCAGGGGAAC 60.996 68.421 0.00 0.00 0.00 3.62
802 1003 2.454941 GGAGGAGGGTCAGGGGAA 59.545 66.667 0.00 0.00 0.00 3.97
841 1042 4.735132 CGAGGCCAAGGCGACGAA 62.735 66.667 18.52 0.00 43.06 3.85
847 1048 2.436824 GAAGACCGAGGCCAAGGC 60.437 66.667 15.50 1.52 41.06 4.35
934 1135 3.483869 GAGCTTGGGGAGGCCGAT 61.484 66.667 0.00 0.00 0.00 4.18
940 1141 4.120755 GGGCAGGAGCTTGGGGAG 62.121 72.222 0.00 0.00 41.70 4.30
958 1159 1.079057 GACGAACCAAGGAGGAGGC 60.079 63.158 0.00 0.00 41.22 4.70
970 1171 1.728426 CACACGAGGACGGACGAAC 60.728 63.158 0.00 0.00 44.46 3.95
1376 1592 1.620819 CCCTAACCATCTCCTCATCGG 59.379 57.143 0.00 0.00 0.00 4.18
1380 1614 1.937350 TCCTCCCTAACCATCTCCTCA 59.063 52.381 0.00 0.00 0.00 3.86
1428 1662 1.655329 GGCGTCCTCCACTCTATCG 59.345 63.158 0.00 0.00 0.00 2.92
1446 1680 3.762247 CCCACAAAGCCCATGCCG 61.762 66.667 0.00 0.00 38.69 5.69
1577 1811 2.360852 GCACATCAGGCTGCTGGT 60.361 61.111 21.17 10.87 0.00 4.00
1580 1814 0.747283 GCTAAGCACATCAGGCTGCT 60.747 55.000 10.34 0.00 45.92 4.24
1581 1815 1.722636 GGCTAAGCACATCAGGCTGC 61.723 60.000 10.34 0.00 41.66 5.25
1582 1816 0.393402 TGGCTAAGCACATCAGGCTG 60.393 55.000 8.58 8.58 41.66 4.85
1583 1817 0.107312 CTGGCTAAGCACATCAGGCT 60.107 55.000 0.00 0.00 45.15 4.58
1595 1829 1.915489 TGGGAAGATTCAGCTGGCTAA 59.085 47.619 15.13 0.57 0.00 3.09
1618 1852 2.476852 TATGGCTGTTGGCGCTGGAA 62.477 55.000 7.64 0.00 42.94 3.53
1626 1860 2.749865 CGGCGTGTATGGCTGTTGG 61.750 63.158 0.00 0.00 32.10 3.77
1632 1866 2.169146 GTGGTACGGCGTGTATGGC 61.169 63.158 24.86 4.11 35.02 4.40
1676 1910 5.358160 GGAATATTGTAGCTATTCATGGCCC 59.642 44.000 0.00 0.00 37.33 5.80
1688 1925 4.691216 GGACAATCGGAGGAATATTGTAGC 59.309 45.833 0.00 0.00 42.35 3.58
1707 1944 0.896479 TGTAGTACGGCTGCTGGACA 60.896 55.000 24.93 13.71 0.00 4.02
1846 2131 6.017275 GTCACATCATCATCAGGGAAGAATTC 60.017 42.308 0.00 0.00 46.67 2.17
1847 2132 5.826737 GTCACATCATCATCAGGGAAGAATT 59.173 40.000 0.00 0.00 0.00 2.17
1848 2133 5.374921 GTCACATCATCATCAGGGAAGAAT 58.625 41.667 0.00 0.00 0.00 2.40
1914 2271 3.240134 GAAGGGCTGCCTCGTCACA 62.240 63.158 19.68 0.00 0.00 3.58
2032 2392 0.673644 ATGTACTGCTGCCGTGGAAC 60.674 55.000 6.98 0.00 0.00 3.62
2034 2394 1.079197 CATGTACTGCTGCCGTGGA 60.079 57.895 6.98 0.00 0.00 4.02
2039 2399 3.880846 GCGCCATGTACTGCTGCC 61.881 66.667 0.00 0.00 0.00 4.85
2114 2474 2.222217 GGTGATCGACGCGTAGTGC 61.222 63.158 13.97 9.48 45.12 4.40
2120 2483 4.829518 TGCTCGGTGATCGACGCG 62.830 66.667 3.53 3.53 43.74 6.01
2128 2491 2.447408 TAGGTAATCCTGCTCGGTGA 57.553 50.000 0.00 0.00 44.81 4.02
2141 2504 5.104693 ACATTGATGTTGTCCGGATAGGTAA 60.105 40.000 7.81 0.00 37.90 2.85
2146 2509 3.540617 CCACATTGATGTTGTCCGGATA 58.459 45.455 7.81 0.10 39.39 2.59
2149 2512 0.810648 CCCACATTGATGTTGTCCGG 59.189 55.000 0.00 0.00 39.39 5.14
2167 2530 4.317671 TCTTACTTGGCTCGCTAATACC 57.682 45.455 0.00 0.00 0.00 2.73
2270 2681 5.477607 TGGTTTCTCTTAATCAACGGAGA 57.522 39.130 0.00 0.00 33.69 3.71
2271 2682 5.701290 ACTTGGTTTCTCTTAATCAACGGAG 59.299 40.000 0.00 0.00 0.00 4.63
2272 2683 5.468746 CACTTGGTTTCTCTTAATCAACGGA 59.531 40.000 0.00 0.00 0.00 4.69
2357 2843 2.979678 TCCTTTCTTAGTGAGGCCTTGT 59.020 45.455 6.77 0.00 0.00 3.16
2366 2852 7.969536 TGTCTTTCTGATTCCTTTCTTAGTG 57.030 36.000 0.00 0.00 0.00 2.74
2370 2859 5.184671 GCCATGTCTTTCTGATTCCTTTCTT 59.815 40.000 0.00 0.00 0.00 2.52
2383 2872 2.712057 CAGGTTGTGCCATGTCTTTC 57.288 50.000 0.00 0.00 40.61 2.62
2402 2891 0.313043 ACAAGACAGCAGCATTGTGC 59.687 50.000 0.00 0.00 45.46 4.57
2405 2894 1.399343 CGTCACAAGACAGCAGCATTG 60.399 52.381 0.00 0.00 45.23 2.82
2437 2926 0.970427 TGCTCCGTAGTGATCTGCCA 60.970 55.000 0.00 0.00 0.00 4.92
2470 2959 4.988716 ACCGGCGTCACTCCTCCA 62.989 66.667 6.01 0.00 0.00 3.86
2481 2970 2.047274 AAGACCATGTCACCGGCG 60.047 61.111 0.00 0.00 34.60 6.46
2494 2983 0.671781 ACGGCTCACATGCAGAAGAC 60.672 55.000 0.00 0.00 34.04 3.01
2522 3011 2.351276 GGCATCTTCCCCACACGT 59.649 61.111 0.00 0.00 0.00 4.49
2541 3031 5.553123 TGTGACACCACGAAAAATATACCT 58.447 37.500 2.45 0.00 46.06 3.08
2547 3037 1.953686 CCCTGTGACACCACGAAAAAT 59.046 47.619 2.45 0.00 46.06 1.82
2579 3069 1.945354 GCGGAATGGGTCGTCTCTCA 61.945 60.000 0.00 0.00 0.00 3.27
2583 3073 1.144057 GATGCGGAATGGGTCGTCT 59.856 57.895 0.00 0.00 0.00 4.18
2586 3076 0.877649 CTGAGATGCGGAATGGGTCG 60.878 60.000 0.00 0.00 0.00 4.79
2593 3083 1.900351 CCCAGACTGAGATGCGGAA 59.100 57.895 3.32 0.00 0.00 4.30
2596 3086 0.390492 TATGCCCAGACTGAGATGCG 59.610 55.000 3.32 0.00 0.00 4.73
2659 3151 2.202479 CGTCAGTCGAGCGATGCA 60.202 61.111 0.00 0.00 42.86 3.96
2919 3464 7.102993 ACAAACTTCTACTTTTTGTTTGCCAT 58.897 30.769 14.26 0.00 46.36 4.40
2930 3475 5.869649 AATGGCCAACAAACTTCTACTTT 57.130 34.783 10.96 0.00 0.00 2.66
2931 3476 6.016276 CACTAATGGCCAACAAACTTCTACTT 60.016 38.462 10.96 0.00 0.00 2.24
2945 3490 3.060479 ACCTCTATCCACTAATGGCCA 57.940 47.619 8.56 8.56 46.80 5.36
2953 3498 6.485171 AGTGCAATTTAAACCTCTATCCACT 58.515 36.000 0.00 0.00 0.00 4.00
2995 3540 5.334569 CCGACTTGTAACAACCCTTGTAATG 60.335 44.000 0.00 0.00 44.59 1.90
3011 3557 6.050432 CAGTACTCTAGTAGATCCGACTTGT 58.950 44.000 0.00 0.00 0.00 3.16
3017 3563 5.057819 TGAAGCAGTACTCTAGTAGATCCG 58.942 45.833 0.00 0.00 0.00 4.18
3049 3595 5.026121 AGATCCCCAATCATCGCTCTAATA 58.974 41.667 0.00 0.00 36.79 0.98
3071 3617 0.512952 CCTTTCCGCAAACTCGTGAG 59.487 55.000 0.00 0.00 0.00 3.51
3073 3619 0.882927 TCCCTTTCCGCAAACTCGTG 60.883 55.000 0.00 0.00 0.00 4.35
3087 3633 3.660669 TCCCTCCACAAACTTATTCCCTT 59.339 43.478 0.00 0.00 0.00 3.95
3107 3653 8.570068 TGGTGTGTATAAAGGTAATTTTCTCC 57.430 34.615 0.00 0.00 32.01 3.71
3115 3661 4.141665 CCGGGATGGTGTGTATAAAGGTAA 60.142 45.833 0.00 0.00 0.00 2.85
3126 3672 2.397413 GATAGGCCCGGGATGGTGTG 62.397 65.000 29.31 0.00 35.15 3.82
3127 3673 2.039831 ATAGGCCCGGGATGGTGT 60.040 61.111 29.31 2.99 35.15 4.16
3163 3709 0.453282 CTCACTGTCAAAATGCGGCG 60.453 55.000 0.51 0.51 0.00 6.46


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

AutoCloner maintained by Alex Coulton.