Multiple sequence alignment - TraesCS2B01G101100

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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 TraesCS2B01G101100 chr2B 100.000 3301 0 0 1 3301 61477518 61474218 0.000000e+00 6096.0
1 TraesCS2B01G101100 chr2B 85.110 1323 116 37 552 1844 61366896 61368167 0.000000e+00 1277.0
2 TraesCS2B01G101100 chr2B 93.979 681 41 0 1436 2116 61311782 61312462 0.000000e+00 1031.0
3 TraesCS2B01G101100 chr2B 91.590 654 39 5 1831 2469 61369454 61370106 0.000000e+00 889.0
4 TraesCS2B01G101100 chr2B 77.443 1228 233 35 1102 2308 61297914 61299118 0.000000e+00 693.0
5 TraesCS2B01G101100 chr2B 75.350 1570 257 73 821 2308 61361825 61363346 1.290000e-178 636.0
6 TraesCS2B01G101100 chr2B 77.415 673 134 11 1051 1713 61491465 61490801 5.170000e-103 385.0
7 TraesCS2B01G101100 chr2B 82.383 193 22 5 665 857 61300912 61301092 1.230000e-34 158.0
8 TraesCS2B01G101100 chr2B 87.313 134 10 4 608 735 61491862 61491730 2.650000e-31 147.0
9 TraesCS2B01G101100 chr2B 95.588 68 3 0 318 385 228983419 228983352 3.480000e-20 110.0
10 TraesCS2B01G101100 chr2B 91.935 62 5 0 2522 2583 57098125 57098186 1.630000e-13 87.9
11 TraesCS2B01G101100 chr2B 81.818 110 3 6 505 614 61492015 61491923 3.530000e-10 76.8
12 TraesCS2B01G101100 chr2B 95.122 41 2 0 608 648 61491903 61491863 7.650000e-07 65.8
13 TraesCS2B01G101100 chr2D 90.579 2558 96 51 605 3052 36051700 36054222 0.000000e+00 3254.0
14 TraesCS2B01G101100 chr2D 77.484 1288 239 33 1051 2308 35927597 35928863 0.000000e+00 725.0
15 TraesCS2B01G101100 chr2D 77.913 1236 217 39 1101 2308 36096245 36095038 0.000000e+00 719.0
16 TraesCS2B01G101100 chr2D 75.050 1010 169 42 873 1817 35978443 35979434 3.090000e-105 392.0
17 TraesCS2B01G101100 chr2D 86.218 312 17 6 2884 3172 36198016 36198324 6.880000e-82 315.0
18 TraesCS2B01G101100 chr2D 96.262 107 4 0 605 711 35927164 35927270 3.390000e-40 176.0
19 TraesCS2B01G101100 chr2D 94.231 52 1 2 2525 2575 640625004 640624954 9.820000e-11 78.7
20 TraesCS2B01G101100 chr2D 93.333 45 3 0 605 649 36051662 36051706 2.130000e-07 67.6
21 TraesCS2B01G101100 chr2A 91.741 2131 90 36 1091 3172 39410613 39408520 0.000000e+00 2881.0
22 TraesCS2B01G101100 chr2A 93.266 1886 72 15 1107 2969 39355227 39357080 0.000000e+00 2728.0
23 TraesCS2B01G101100 chr2A 95.324 1433 55 8 1107 2527 39452739 39451307 0.000000e+00 2265.0
24 TraesCS2B01G101100 chr2A 85.758 653 40 22 2562 3172 39451309 39450668 2.780000e-180 641.0
25 TraesCS2B01G101100 chr2A 76.418 1234 242 41 1101 2308 39310986 39312196 3.620000e-174 621.0
26 TraesCS2B01G101100 chr2A 90.931 408 35 2 1658 2065 39418930 39418525 6.230000e-152 547.0
27 TraesCS2B01G101100 chr2A 88.235 476 24 10 606 1051 39453320 39452847 1.040000e-149 540.0
28 TraesCS2B01G101100 chr2A 94.304 316 17 1 1 315 39354275 39354590 1.780000e-132 483.0
29 TraesCS2B01G101100 chr2A 86.968 376 16 7 431 776 39310380 39310752 3.090000e-105 392.0
30 TraesCS2B01G101100 chr2A 97.605 167 3 1 605 771 39354803 39354968 5.390000e-73 285.0
31 TraesCS2B01G101100 chr2A 93.617 141 9 0 3161 3301 39408334 39408194 9.280000e-51 211.0
32 TraesCS2B01G101100 chr2A 87.931 116 6 4 844 951 39354963 39355078 2.670000e-26 130.0
33 TraesCS2B01G101100 chr2A 86.905 84 7 4 318 399 69386017 69385936 1.260000e-14 91.6
34 TraesCS2B01G101100 chr2A 97.297 37 0 1 1068 1103 39310932 39310968 9.890000e-06 62.1
35 TraesCS2B01G101100 chr3D 93.772 835 43 4 1268 2101 380122973 380123799 0.000000e+00 1245.0
36 TraesCS2B01G101100 chr3D 89.155 627 29 12 2088 2703 380132158 380132756 0.000000e+00 745.0
37 TraesCS2B01G101100 chr3D 78.194 454 53 22 607 1051 380096068 380096484 7.070000e-62 248.0
38 TraesCS2B01G101100 chr5D 95.522 67 2 1 318 383 381563855 381563921 4.510000e-19 106.0
39 TraesCS2B01G101100 chr5D 92.857 70 5 0 318 387 206601285 206601354 5.830000e-18 102.0
40 TraesCS2B01G101100 chr1B 85.088 114 5 8 2809 2912 427650578 427650689 4.510000e-19 106.0
41 TraesCS2B01G101100 chr1D 95.385 65 3 0 318 382 291792020 291791956 1.620000e-18 104.0
42 TraesCS2B01G101100 chr5A 93.056 72 2 3 313 383 362170874 362170805 5.830000e-18 102.0
43 TraesCS2B01G101100 chr7B 90.667 75 5 2 318 392 99367427 99367499 7.540000e-17 99.0
44 TraesCS2B01G101100 chr7B 83.636 110 5 7 2813 2912 592617457 592617351 1.260000e-14 91.6
45 TraesCS2B01G101100 chr7B 97.872 47 1 0 2522 2568 393392835 393392881 7.590000e-12 82.4
46 TraesCS2B01G101100 chr7A 88.095 84 5 4 320 400 123256191 123256272 9.750000e-16 95.3
47 TraesCS2B01G101100 chr7A 83.178 107 12 5 276 380 323464870 323464768 3.510000e-15 93.5
48 TraesCS2B01G101100 chr4B 83.486 109 9 5 2812 2912 167365985 167365878 3.510000e-15 93.5
49 TraesCS2B01G101100 chr3B 100.000 46 0 0 2522 2567 377111030 377110985 5.870000e-13 86.1
50 TraesCS2B01G101100 chr3B 91.379 58 3 2 2522 2578 55369406 55369350 9.820000e-11 78.7
51 TraesCS2B01G101100 chr3B 89.831 59 5 1 2522 2580 99735755 99735698 1.270000e-09 75.0
52 TraesCS2B01G101100 chr3B 90.000 60 2 4 2522 2580 693089775 693089831 1.270000e-09 75.0
53 TraesCS2B01G101100 chr6D 92.727 55 4 0 2522 2576 15354681 15354735 2.730000e-11 80.5
54 TraesCS2B01G101100 chr6B 86.957 69 4 5 2522 2589 464866095 464866031 4.570000e-09 73.1
55 TraesCS2B01G101100 chrUn 100.000 33 0 0 2880 2912 118861093 118861125 9.890000e-06 62.1


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 TraesCS2B01G101100 chr2B 61474218 61477518 3300 True 6096.000000 6096 100.000000 1 3301 1 chr2B.!!$R1 3300
1 TraesCS2B01G101100 chr2B 61311782 61312462 680 False 1031.000000 1031 93.979000 1436 2116 1 chr2B.!!$F2 680
2 TraesCS2B01G101100 chr2B 61361825 61370106 8281 False 934.000000 1277 84.016667 552 2469 3 chr2B.!!$F4 1917
3 TraesCS2B01G101100 chr2B 61297914 61301092 3178 False 425.500000 693 79.913000 665 2308 2 chr2B.!!$F3 1643
4 TraesCS2B01G101100 chr2D 36051662 36054222 2560 False 1660.800000 3254 91.956000 605 3052 2 chr2D.!!$F4 2447
5 TraesCS2B01G101100 chr2D 36095038 36096245 1207 True 719.000000 719 77.913000 1101 2308 1 chr2D.!!$R1 1207
6 TraesCS2B01G101100 chr2D 35927164 35928863 1699 False 450.500000 725 86.873000 605 2308 2 chr2D.!!$F3 1703
7 TraesCS2B01G101100 chr2D 35978443 35979434 991 False 392.000000 392 75.050000 873 1817 1 chr2D.!!$F1 944
8 TraesCS2B01G101100 chr2A 39408194 39410613 2419 True 1546.000000 2881 92.679000 1091 3301 2 chr2A.!!$R3 2210
9 TraesCS2B01G101100 chr2A 39450668 39453320 2652 True 1148.666667 2265 89.772333 606 3172 3 chr2A.!!$R4 2566
10 TraesCS2B01G101100 chr2A 39354275 39357080 2805 False 906.500000 2728 93.276500 1 2969 4 chr2A.!!$F2 2968
11 TraesCS2B01G101100 chr2A 39310380 39312196 1816 False 358.366667 621 86.894333 431 2308 3 chr2A.!!$F1 1877
12 TraesCS2B01G101100 chr3D 380122973 380123799 826 False 1245.000000 1245 93.772000 1268 2101 1 chr3D.!!$F2 833
13 TraesCS2B01G101100 chr3D 380132158 380132756 598 False 745.000000 745 89.155000 2088 2703 1 chr3D.!!$F3 615

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
296 298 0.604578 CTTCCTCCGTCCCGTGTAAA 59.395 55.0 0.00 0.0 0.0 2.01 F
1065 1229 0.601841 CCGTTGGCAACCTCGTAACT 60.602 55.0 23.68 0.0 0.0 2.24 F
1405 6870 0.325671 TCCACAGACTCCCATCCTCC 60.326 60.0 0.00 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1104 1275 0.166814 GCTGACGCTTGGACATGTTC 59.833 55.000 0.0 0.0 0.0 3.18 R
2121 8917 1.302033 CGTGGTTTGCAGCTCTCCT 60.302 57.895 0.0 0.0 0.0 3.69 R
2974 9861 1.810151 TGTCCGAAGCCATTGTTAAGC 59.190 47.619 0.0 0.0 0.0 3.09 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
223 225 6.645827 TGCATGAACAATGTTTTAATCTGTGG 59.354 34.615 0.00 0.00 38.65 4.17
224 226 6.867816 GCATGAACAATGTTTTAATCTGTGGA 59.132 34.615 0.00 0.00 38.65 4.02
227 229 7.648142 TGAACAATGTTTTAATCTGTGGACTC 58.352 34.615 0.00 0.00 0.00 3.36
247 249 9.912634 TGGACTCTTTAAAAATTCATGAACATC 57.087 29.630 11.07 0.00 0.00 3.06
288 290 5.878669 ACATTGTTTAATACTTCCTCCGTCC 59.121 40.000 0.00 0.00 0.00 4.79
289 291 4.476628 TGTTTAATACTTCCTCCGTCCC 57.523 45.455 0.00 0.00 0.00 4.46
296 298 0.604578 CTTCCTCCGTCCCGTGTAAA 59.395 55.000 0.00 0.00 0.00 2.01
297 299 1.001181 CTTCCTCCGTCCCGTGTAAAA 59.999 52.381 0.00 0.00 0.00 1.52
298 300 1.047002 TCCTCCGTCCCGTGTAAAAA 58.953 50.000 0.00 0.00 0.00 1.94
336 338 8.844441 TTATCAAAGAACGTTTTTAACACTGG 57.156 30.769 0.46 0.00 0.00 4.00
337 339 5.096849 TCAAAGAACGTTTTTAACACTGGC 58.903 37.500 0.46 0.00 0.00 4.85
338 340 4.705337 AAGAACGTTTTTAACACTGGCA 57.295 36.364 0.46 0.00 0.00 4.92
339 341 4.911514 AGAACGTTTTTAACACTGGCAT 57.088 36.364 0.46 0.00 0.00 4.40
340 342 6.380095 AAGAACGTTTTTAACACTGGCATA 57.620 33.333 0.46 0.00 0.00 3.14
341 343 5.997385 AGAACGTTTTTAACACTGGCATAG 58.003 37.500 0.46 0.00 0.00 2.23
342 344 5.529800 AGAACGTTTTTAACACTGGCATAGT 59.470 36.000 0.46 0.00 41.36 2.12
343 345 6.707161 AGAACGTTTTTAACACTGGCATAGTA 59.293 34.615 0.46 0.00 37.60 1.82
344 346 7.389607 AGAACGTTTTTAACACTGGCATAGTAT 59.610 33.333 0.46 0.00 37.60 2.12
345 347 7.068692 ACGTTTTTAACACTGGCATAGTATC 57.931 36.000 0.00 0.00 37.60 2.24
353 355 5.001232 ACACTGGCATAGTATCAAAAACGT 58.999 37.500 0.00 0.00 37.60 3.99
371 373 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
380 382 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
385 408 0.816373 GGACGGAGGGAGTACTTGTC 59.184 60.000 0.00 0.00 0.00 3.18
388 411 3.350833 GACGGAGGGAGTACTTGTCTTA 58.649 50.000 0.00 0.00 0.00 2.10
393 416 5.262804 GGAGGGAGTACTTGTCTTAGAGAA 58.737 45.833 0.00 0.00 0.00 2.87
501 527 0.977395 GCTATACCTCGGAATGGGCT 59.023 55.000 0.00 0.00 0.00 5.19
502 528 2.176889 GCTATACCTCGGAATGGGCTA 58.823 52.381 0.00 0.00 0.00 3.93
503 529 2.766828 GCTATACCTCGGAATGGGCTAT 59.233 50.000 0.00 0.00 0.00 2.97
507 533 1.348064 CCTCGGAATGGGCTATACCA 58.652 55.000 0.00 0.00 46.24 3.25
536 562 1.596727 GCGCCTGAAGAAGAATAGCAG 59.403 52.381 0.00 0.00 0.00 4.24
537 563 1.596727 CGCCTGAAGAAGAATAGCAGC 59.403 52.381 0.00 0.00 0.00 5.25
538 564 1.596727 GCCTGAAGAAGAATAGCAGCG 59.403 52.381 0.00 0.00 0.00 5.18
539 565 2.208431 CCTGAAGAAGAATAGCAGCGG 58.792 52.381 0.00 0.00 0.00 5.52
554 587 2.014018 GCGGACGCGCAACAAAAAT 61.014 52.632 5.73 0.00 34.62 1.82
561 594 4.143618 GGACGCGCAACAAAAATAAAAGAG 60.144 41.667 5.73 0.00 0.00 2.85
1020 1147 4.819610 TCACATCCTAGATCTGGATTCCA 58.180 43.478 18.58 5.05 41.94 3.53
1034 1164 2.416547 GGATTCCAGTCACATTGTCGTG 59.583 50.000 0.00 0.00 38.29 4.35
1051 1181 1.228124 TGTCCTTGCCCTTCCGTTG 60.228 57.895 0.00 0.00 0.00 4.10
1065 1229 0.601841 CCGTTGGCAACCTCGTAACT 60.602 55.000 23.68 0.00 0.00 2.24
1258 6720 1.737793 CCGACACTTTGCAAGATACCC 59.262 52.381 0.00 0.00 0.00 3.69
1405 6870 0.325671 TCCACAGACTCCCATCCTCC 60.326 60.000 0.00 0.00 0.00 4.30
2121 8917 5.692115 TTGGGCTTAAGTATGATCACAGA 57.308 39.130 0.00 0.00 0.00 3.41
2287 9107 4.051922 GCTGTGATATGTGGCACTACTAC 58.948 47.826 19.83 11.56 36.05 2.73
2342 9163 3.006217 GCAATTTTCTTGAACCTGAGCCT 59.994 43.478 0.00 0.00 0.00 4.58
2343 9164 4.553323 CAATTTTCTTGAACCTGAGCCTG 58.447 43.478 0.00 0.00 0.00 4.85
2346 9167 0.687354 TCTTGAACCTGAGCCTGGAC 59.313 55.000 0.00 0.00 0.00 4.02
2413 9249 4.487714 TGCGAGACAGGGATTAGAAAAT 57.512 40.909 0.00 0.00 0.00 1.82
2529 9379 5.374154 AGAGTCTAAGATCCCCATGTCTAGA 59.626 44.000 0.00 0.00 0.00 2.43
2530 9380 6.031964 AGTCTAAGATCCCCATGTCTAGAA 57.968 41.667 0.00 0.00 0.00 2.10
2532 9382 6.553100 AGTCTAAGATCCCCATGTCTAGAAAG 59.447 42.308 0.00 0.00 0.00 2.62
2533 9383 6.551601 GTCTAAGATCCCCATGTCTAGAAAGA 59.448 42.308 0.00 0.00 0.00 2.52
2550 9400 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2551 9401 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2552 9402 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2553 9403 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2554 9404 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2555 9405 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2556 9406 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2605 9455 4.229582 AGGGAAGTGTCTAGTCATCTCTCT 59.770 45.833 0.00 0.00 0.00 3.10
2641 9493 0.318120 AAAACAATGGCAGGGAAGCG 59.682 50.000 0.00 0.00 34.64 4.68
2876 9747 6.642707 AAAAACCGAAAGAATGGTCATACA 57.357 33.333 0.00 0.00 37.54 2.29
2944 9815 2.276869 AGCATAGTGTCGGCTGTCA 58.723 52.632 0.00 0.00 36.34 3.58
2945 9816 0.608130 AGCATAGTGTCGGCTGTCAA 59.392 50.000 0.00 0.00 36.34 3.18
2974 9861 5.106594 TGTTTGCATGACATAGCAGTAACAG 60.107 40.000 17.08 0.00 42.39 3.16
2996 9883 3.731867 GCTTAACAATGGCTTCGGACATG 60.732 47.826 0.00 0.00 44.08 3.21
3007 9894 3.938963 GCTTCGGACATGAGTTATTTCCA 59.061 43.478 0.00 0.00 35.71 3.53
3015 9902 6.208599 GGACATGAGTTATTTCCAAGGAACAA 59.791 38.462 0.00 0.00 35.97 2.83
3141 10158 5.009010 CCTGAAACTGTTTGAGCTGTACAAT 59.991 40.000 11.03 0.00 0.00 2.71
3142 10159 5.820131 TGAAACTGTTTGAGCTGTACAATG 58.180 37.500 11.03 0.00 0.00 2.82
3228 10441 5.325239 GGAAATCCTTCCTCTTTCTTCCAA 58.675 41.667 0.00 0.00 46.80 3.53
3232 10445 3.461831 TCCTTCCTCTTTCTTCCAACCAA 59.538 43.478 0.00 0.00 0.00 3.67
3261 10474 4.036734 TGGAAAATTCTGCAGACTGTTCAC 59.963 41.667 28.45 20.71 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.556275 ACGCTCCAGGAAATAAAAATATCTGAA 59.444 33.333 0.00 0.00 0.00 3.02
216 218 9.300681 TCATGAATTTTTAAAGAGTCCACAGAT 57.699 29.630 4.03 0.00 0.00 2.90
220 222 9.696917 ATGTTCATGAATTTTTAAAGAGTCCAC 57.303 29.630 12.12 0.00 0.00 4.02
247 249 6.405278 ACAATGTTCCCAAAACTTTAGAGG 57.595 37.500 0.00 0.00 0.00 3.69
310 312 9.458374 CCAGTGTTAAAAACGTTCTTTGATAAT 57.542 29.630 0.00 0.00 0.00 1.28
311 313 7.432838 GCCAGTGTTAAAAACGTTCTTTGATAA 59.567 33.333 0.00 0.00 0.00 1.75
312 314 6.913673 GCCAGTGTTAAAAACGTTCTTTGATA 59.086 34.615 0.00 0.00 0.00 2.15
313 315 5.746721 GCCAGTGTTAAAAACGTTCTTTGAT 59.253 36.000 0.00 0.00 0.00 2.57
314 316 5.096849 GCCAGTGTTAAAAACGTTCTTTGA 58.903 37.500 0.00 0.00 0.00 2.69
315 317 4.859798 TGCCAGTGTTAAAAACGTTCTTTG 59.140 37.500 0.00 0.00 0.00 2.77
316 318 5.061920 TGCCAGTGTTAAAAACGTTCTTT 57.938 34.783 0.00 7.41 0.00 2.52
317 319 4.705337 TGCCAGTGTTAAAAACGTTCTT 57.295 36.364 0.00 0.00 0.00 2.52
318 320 4.911514 ATGCCAGTGTTAAAAACGTTCT 57.088 36.364 0.00 0.00 0.00 3.01
319 321 5.754778 ACTATGCCAGTGTTAAAAACGTTC 58.245 37.500 0.00 0.00 35.62 3.95
320 322 5.761165 ACTATGCCAGTGTTAAAAACGTT 57.239 34.783 0.00 0.00 35.62 3.99
321 323 6.651643 TGATACTATGCCAGTGTTAAAAACGT 59.348 34.615 0.00 0.00 38.24 3.99
322 324 7.067532 TGATACTATGCCAGTGTTAAAAACG 57.932 36.000 0.00 0.00 38.24 3.60
323 325 9.685828 TTTTGATACTATGCCAGTGTTAAAAAC 57.314 29.630 10.38 0.00 39.35 2.43
325 327 9.685828 GTTTTTGATACTATGCCAGTGTTAAAA 57.314 29.630 9.36 9.36 40.03 1.52
326 328 8.018520 CGTTTTTGATACTATGCCAGTGTTAAA 58.981 33.333 0.00 0.00 38.24 1.52
327 329 7.173562 ACGTTTTTGATACTATGCCAGTGTTAA 59.826 33.333 0.00 0.00 38.24 2.01
328 330 6.651643 ACGTTTTTGATACTATGCCAGTGTTA 59.348 34.615 0.00 0.00 38.24 2.41
329 331 5.472137 ACGTTTTTGATACTATGCCAGTGTT 59.528 36.000 0.00 0.00 38.24 3.32
330 332 5.001232 ACGTTTTTGATACTATGCCAGTGT 58.999 37.500 0.00 0.00 38.24 3.55
331 333 5.545658 ACGTTTTTGATACTATGCCAGTG 57.454 39.130 0.00 0.00 38.24 3.66
332 334 5.938125 AGAACGTTTTTGATACTATGCCAGT 59.062 36.000 0.46 0.00 41.62 4.00
333 335 6.422776 AGAACGTTTTTGATACTATGCCAG 57.577 37.500 0.46 0.00 0.00 4.85
334 336 6.811253 AAGAACGTTTTTGATACTATGCCA 57.189 33.333 0.46 0.00 0.00 4.92
343 345 9.634163 GTCCCAAAATATAAGAACGTTTTTGAT 57.366 29.630 13.87 4.93 38.79 2.57
344 346 7.804129 CGTCCCAAAATATAAGAACGTTTTTGA 59.196 33.333 13.87 2.81 38.79 2.69
345 347 7.061326 CCGTCCCAAAATATAAGAACGTTTTTG 59.939 37.037 13.87 12.16 37.14 2.44
353 355 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
363 365 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
371 373 6.837471 TTTCTCTAAGACAAGTACTCCCTC 57.163 41.667 0.00 0.00 0.00 4.30
436 462 0.619255 TCCGGGGTTGAGCCAGATTA 60.619 55.000 0.00 0.00 39.65 1.75
463 489 2.125147 TGCCTAGGCGCACACATC 60.125 61.111 28.28 0.00 45.51 3.06
501 527 2.948979 CAGGCGCCTGAAATTTGGTATA 59.051 45.455 46.72 0.00 46.30 1.47
502 528 1.750778 CAGGCGCCTGAAATTTGGTAT 59.249 47.619 46.72 10.82 46.30 2.73
503 529 1.173043 CAGGCGCCTGAAATTTGGTA 58.827 50.000 46.72 0.00 46.30 3.25
537 563 1.676057 TTATTTTTGTTGCGCGTCCG 58.324 45.000 8.43 0.00 37.57 4.79
538 564 3.731717 TCTTTTATTTTTGTTGCGCGTCC 59.268 39.130 8.43 0.00 0.00 4.79
539 565 4.143618 CCTCTTTTATTTTTGTTGCGCGTC 60.144 41.667 8.43 0.00 0.00 5.19
548 574 6.345096 TCTGCTTCCCCTCTTTTATTTTTG 57.655 37.500 0.00 0.00 0.00 2.44
554 587 1.916181 CCCTCTGCTTCCCCTCTTTTA 59.084 52.381 0.00 0.00 0.00 1.52
561 594 4.120755 CAGCCCCTCTGCTTCCCC 62.121 72.222 0.00 0.00 40.32 4.81
772 828 5.360999 GGAATGAAAGGAAAATAGGGGTCAG 59.639 44.000 0.00 0.00 0.00 3.51
1020 1147 2.483876 CAAGGACACGACAATGTGACT 58.516 47.619 0.00 0.00 42.55 3.41
1021 1148 1.069906 GCAAGGACACGACAATGTGAC 60.070 52.381 0.00 0.00 42.55 3.67
1022 1149 1.225855 GCAAGGACACGACAATGTGA 58.774 50.000 0.00 0.00 42.55 3.58
1023 1150 0.238289 GGCAAGGACACGACAATGTG 59.762 55.000 0.00 0.00 45.41 3.21
1024 1151 0.889186 GGGCAAGGACACGACAATGT 60.889 55.000 0.00 0.00 34.78 2.71
1034 1164 1.971695 CCAACGGAAGGGCAAGGAC 60.972 63.158 0.00 0.00 0.00 3.85
1051 1181 3.795623 TCTGATAGTTACGAGGTTGCC 57.204 47.619 0.00 0.00 0.00 4.52
1053 1183 7.827819 TTTGATTCTGATAGTTACGAGGTTG 57.172 36.000 0.00 0.00 0.00 3.77
1054 1184 8.842358 TTTTTGATTCTGATAGTTACGAGGTT 57.158 30.769 0.00 0.00 0.00 3.50
1103 1274 1.800805 CTGACGCTTGGACATGTTCT 58.199 50.000 5.55 0.00 0.00 3.01
1104 1275 0.166814 GCTGACGCTTGGACATGTTC 59.833 55.000 0.00 0.00 0.00 3.18
2121 8917 1.302033 CGTGGTTTGCAGCTCTCCT 60.302 57.895 0.00 0.00 0.00 3.69
2287 9107 9.170584 GAACCAACTTCTTTTTATTTCTCTTCG 57.829 33.333 0.00 0.00 0.00 3.79
2413 9249 3.616219 ACACTTCTTTAGTTGCACCACA 58.384 40.909 0.00 0.00 33.85 4.17
2529 9379 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2530 9380 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2532 9382 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2533 9383 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2534 9384 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2535 9385 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2536 9386 8.912614 ATATACTCCCTCCGTTCCTAAATATT 57.087 34.615 0.00 0.00 0.00 1.28
2537 9387 8.345306 AGATATACTCCCTCCGTTCCTAAATAT 58.655 37.037 0.00 0.00 0.00 1.28
2538 9388 7.706674 AGATATACTCCCTCCGTTCCTAAATA 58.293 38.462 0.00 0.00 0.00 1.40
2539 9389 6.563163 AGATATACTCCCTCCGTTCCTAAAT 58.437 40.000 0.00 0.00 0.00 1.40
2540 9390 5.961897 AGATATACTCCCTCCGTTCCTAAA 58.038 41.667 0.00 0.00 0.00 1.85
2541 9391 5.595814 AGATATACTCCCTCCGTTCCTAA 57.404 43.478 0.00 0.00 0.00 2.69
2542 9392 5.595814 AAGATATACTCCCTCCGTTCCTA 57.404 43.478 0.00 0.00 0.00 2.94
2543 9393 4.472690 AAGATATACTCCCTCCGTTCCT 57.527 45.455 0.00 0.00 0.00 3.36
2544 9394 6.854091 AATAAGATATACTCCCTCCGTTCC 57.146 41.667 0.00 0.00 0.00 3.62
2545 9395 7.893658 TGAAATAAGATATACTCCCTCCGTTC 58.106 38.462 0.00 0.00 0.00 3.95
2546 9396 7.038941 CCTGAAATAAGATATACTCCCTCCGTT 60.039 40.741 0.00 0.00 0.00 4.44
2547 9397 6.437793 CCTGAAATAAGATATACTCCCTCCGT 59.562 42.308 0.00 0.00 0.00 4.69
2548 9398 6.663953 TCCTGAAATAAGATATACTCCCTCCG 59.336 42.308 0.00 0.00 0.00 4.63
2549 9399 8.616799 ATCCTGAAATAAGATATACTCCCTCC 57.383 38.462 0.00 0.00 0.00 4.30
2556 9406 9.944376 TGCCACTAATCCTGAAATAAGATATAC 57.056 33.333 0.00 0.00 0.00 1.47
2605 9455 7.040478 CCATTGTTTTTCTGATGACTACCTGAA 60.040 37.037 0.00 0.00 0.00 3.02
2641 9493 6.126361 ACCTATCTATCCATGCCATTAATCCC 60.126 42.308 0.00 0.00 0.00 3.85
2743 9601 6.152661 CCAAACCTAACTCCTTATGCATGAAA 59.847 38.462 10.16 0.00 0.00 2.69
2856 9727 4.454504 GTGTGTATGACCATTCTTTCGGTT 59.545 41.667 0.00 0.00 34.99 4.44
2857 9728 4.000988 GTGTGTATGACCATTCTTTCGGT 58.999 43.478 0.00 0.00 38.56 4.69
2858 9729 4.253685 AGTGTGTATGACCATTCTTTCGG 58.746 43.478 0.00 0.00 0.00 4.30
2859 9730 4.330074 GGAGTGTGTATGACCATTCTTTCG 59.670 45.833 0.00 0.00 0.00 3.46
2860 9731 5.491982 AGGAGTGTGTATGACCATTCTTTC 58.508 41.667 0.00 0.00 0.00 2.62
2861 9732 5.249393 AGAGGAGTGTGTATGACCATTCTTT 59.751 40.000 0.00 0.00 0.00 2.52
2864 9735 4.744795 AGAGGAGTGTGTATGACCATTC 57.255 45.455 0.00 0.00 0.00 2.67
2865 9736 6.814954 ATAAGAGGAGTGTGTATGACCATT 57.185 37.500 0.00 0.00 0.00 3.16
2866 9737 7.298374 TCTATAAGAGGAGTGTGTATGACCAT 58.702 38.462 0.00 0.00 0.00 3.55
2867 9738 6.669631 TCTATAAGAGGAGTGTGTATGACCA 58.330 40.000 0.00 0.00 0.00 4.02
2876 9747 8.228206 TGTTCATCCTATCTATAAGAGGAGTGT 58.772 37.037 0.00 0.00 42.59 3.55
2944 9815 5.599732 TGCTATGTCATGCAAACAACTTTT 58.400 33.333 9.09 0.00 36.15 2.27
2945 9816 5.199024 TGCTATGTCATGCAAACAACTTT 57.801 34.783 9.09 0.00 36.15 2.66
2974 9861 1.810151 TGTCCGAAGCCATTGTTAAGC 59.190 47.619 0.00 0.00 0.00 3.09
2996 9883 7.610305 TGGTCTATTGTTCCTTGGAAATAACTC 59.390 37.037 3.39 0.00 0.00 3.01
3007 9894 3.589288 AGCTTCCTGGTCTATTGTTCCTT 59.411 43.478 0.00 0.00 0.00 3.36
3124 10141 3.814842 TGGACATTGTACAGCTCAAACAG 59.185 43.478 0.00 0.00 0.00 3.16
3228 10441 6.608405 TCTGCAGAATTTTCCATCATATTGGT 59.392 34.615 15.67 0.00 38.01 3.67
3232 10445 6.832384 ACAGTCTGCAGAATTTTCCATCATAT 59.168 34.615 20.19 0.00 0.00 1.78
3261 10474 2.886523 TGTTCTGCAGACATTCCAAAGG 59.113 45.455 18.03 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.