Multiple sequence alignment - TraesCS5A01G130600

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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 TraesCS5A01G130600 chr5A 100.000 4137 0 0 1 4137 293863553 293867689 0.000000e+00 7640.0
1 TraesCS5A01G130600 chr5D 94.493 3795 150 27 350 4137 220096643 220100385 0.000000e+00 5795.0
2 TraesCS5A01G130600 chr5D 86.928 306 34 2 39 343 220095817 220096117 5.120000e-89 339.0
3 TraesCS5A01G130600 chr5B 95.993 2421 63 12 498 2914 242543017 242545407 0.000000e+00 3903.0
4 TraesCS5A01G130600 chr5B 97.975 1037 14 2 1926 2959 239160752 239159720 0.000000e+00 1792.0
5 TraesCS5A01G130600 chr5B 94.502 582 31 1 3556 4137 239157477 239156897 0.000000e+00 896.0
6 TraesCS5A01G130600 chr5B 92.504 627 40 6 3028 3652 242545757 242546378 0.000000e+00 891.0
7 TraesCS5A01G130600 chr5B 92.125 546 36 5 3028 3571 239159078 239158538 0.000000e+00 763.0
8 TraesCS5A01G130600 chr5B 93.864 440 26 1 3695 4134 242546713 242547151 0.000000e+00 662.0
9 TraesCS5A01G130600 chr5B 90.086 464 21 4 783 1243 239171658 239171217 2.770000e-161 579.0
10 TraesCS5A01G130600 chr5B 95.055 182 5 2 611 792 239173139 239172962 2.430000e-72 283.0
11 TraesCS5A01G130600 chr5B 90.854 164 12 2 459 619 239177022 239176859 2.500000e-52 217.0
12 TraesCS5A01G130600 chr7B 80.155 388 61 14 3635 4015 193711810 193711432 4.070000e-70 276.0
13 TraesCS5A01G130600 chr6B 91.892 111 9 0 1281 1391 693942117 693942007 5.540000e-34 156.0
14 TraesCS5A01G130600 chr6B 90.517 116 11 0 1276 1391 18228892 18229007 1.990000e-33 154.0
15 TraesCS5A01G130600 chr6B 82.812 128 15 6 1249 1376 281256414 281256534 1.570000e-19 108.0
16 TraesCS5A01G130600 chr4D 89.320 103 10 1 1285 1386 493333010 493333112 1.210000e-25 128.0
17 TraesCS5A01G130600 chr1B 74.074 324 59 17 3231 3551 364289124 364288823 4.370000e-20 110.0
18 TraesCS5A01G130600 chr1B 72.802 364 70 21 3231 3588 600468359 600468699 3.400000e-16 97.1
19 TraesCS5A01G130600 chr1B 100.000 40 0 0 1 40 67527328 67527367 1.600000e-09 75.0
20 TraesCS5A01G130600 chr3A 85.227 88 12 1 3231 3318 594813649 594813563 5.700000e-14 89.8
21 TraesCS5A01G130600 chr7D 97.561 41 1 0 1 41 632547429 632547469 2.060000e-08 71.3
22 TraesCS5A01G130600 chr7D 100.000 29 0 0 3634 3662 117546174 117546202 2.000000e-03 54.7
23 TraesCS5A01G130600 chr1A 97.561 41 1 0 1 41 575504822 575504862 2.060000e-08 71.3
24 TraesCS5A01G130600 chr4B 97.500 40 1 0 1 40 657247749 657247788 7.420000e-08 69.4
25 TraesCS5A01G130600 chr4B 95.238 42 1 1 1 42 649654007 649653967 9.600000e-07 65.8
26 TraesCS5A01G130600 chr3B 97.500 40 1 0 1 40 554479483 554479444 7.420000e-08 69.4
27 TraesCS5A01G130600 chr3B 93.333 45 1 2 1 45 32382931 32382889 9.600000e-07 65.8
28 TraesCS5A01G130600 chr2B 97.500 40 1 0 1 40 717924778 717924739 7.420000e-08 69.4
29 TraesCS5A01G130600 chrUn 95.238 42 2 0 1 42 200934723 200934682 2.670000e-07 67.6
30 TraesCS5A01G130600 chr3D 81.481 81 14 1 146 226 45631406 45631327 9.600000e-07 65.8
31 TraesCS5A01G130600 chr3D 100.000 32 0 0 1194 1225 182606068 182606037 4.470000e-05 60.2


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 TraesCS5A01G130600 chr5A 293863553 293867689 4136 False 7640.000000 7640 100.000000 1 4137 1 chr5A.!!$F1 4136
1 TraesCS5A01G130600 chr5D 220095817 220100385 4568 False 3067.000000 5795 90.710500 39 4137 2 chr5D.!!$F1 4098
2 TraesCS5A01G130600 chr5B 242543017 242547151 4134 False 1818.666667 3903 94.120333 498 4134 3 chr5B.!!$F1 3636
3 TraesCS5A01G130600 chr5B 239156897 239160752 3855 True 1150.333333 1792 94.867333 1926 4137 3 chr5B.!!$R1 2211
4 TraesCS5A01G130600 chr5B 239171217 239177022 5805 True 359.666667 579 91.998333 459 1243 3 chr5B.!!$R2 784

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
273 275 0.606401 CCATACATGATCACCCGCCC 60.606 60.000 0.00 0.00 0.00 6.13 F
1020 6593 0.382515 CCGCTTTTCACGAACCCAAA 59.617 50.000 0.00 0.00 0.00 3.28 F
1108 6681 0.465097 AGGATTCAGCCAAGATGCGG 60.465 55.000 0.00 0.00 36.02 5.69 F
2491 8064 2.434843 CCTCGGATGGCTAGCACCA 61.435 63.158 18.24 6.59 45.82 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 7410 0.174845 CCAGCGAATTCGTACTCCCA 59.825 55.000 27.24 0.0 42.22 4.37 R
1888 7461 1.009389 CAGCAACCGTCGACCTCTTC 61.009 60.000 10.58 0.0 0.00 2.87 R
3075 9257 1.306568 GGTGAGGAAGCTCTCCCCT 60.307 63.158 10.27 4.4 46.81 4.79 R
3791 11343 0.323629 CGCTACTCCTGTTGGGGAAA 59.676 55.000 0.00 0.0 37.25 3.13 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
34 35 7.364522 TGAAAAGGTCAGAATAGTGATTTCG 57.635 36.000 0.00 0.00 30.52 3.46
35 36 6.934645 TGAAAAGGTCAGAATAGTGATTTCGT 59.065 34.615 0.00 0.00 30.52 3.85
36 37 6.969828 AAAGGTCAGAATAGTGATTTCGTC 57.030 37.500 0.00 0.00 0.00 4.20
37 38 5.012328 AGGTCAGAATAGTGATTTCGTCC 57.988 43.478 0.00 0.00 0.00 4.79
38 39 4.120589 GGTCAGAATAGTGATTTCGTCCC 58.879 47.826 0.00 0.00 0.00 4.46
39 40 4.141914 GGTCAGAATAGTGATTTCGTCCCT 60.142 45.833 0.00 0.00 0.00 4.20
40 41 5.044558 GTCAGAATAGTGATTTCGTCCCTC 58.955 45.833 0.00 0.00 0.00 4.30
41 42 4.956700 TCAGAATAGTGATTTCGTCCCTCT 59.043 41.667 0.00 0.00 0.00 3.69
42 43 5.422331 TCAGAATAGTGATTTCGTCCCTCTT 59.578 40.000 0.00 0.00 0.00 2.85
43 44 5.751028 CAGAATAGTGATTTCGTCCCTCTTC 59.249 44.000 0.00 0.00 0.00 2.87
44 45 5.659079 AGAATAGTGATTTCGTCCCTCTTCT 59.341 40.000 0.00 0.00 27.91 2.85
80 81 4.141711 GGTTTCATCTGCCACATCCTACTA 60.142 45.833 0.00 0.00 0.00 1.82
83 84 6.596309 TTCATCTGCCACATCCTACTATAG 57.404 41.667 0.00 0.00 0.00 1.31
87 88 4.141018 TCTGCCACATCCTACTATAGGTCA 60.141 45.833 4.43 0.00 46.32 4.02
91 92 4.456222 CCACATCCTACTATAGGTCAGACG 59.544 50.000 4.43 0.00 46.32 4.18
102 103 1.658673 GTCAGACGTGGACGGTTCT 59.341 57.895 0.00 0.00 44.95 3.01
103 104 0.663568 GTCAGACGTGGACGGTTCTG 60.664 60.000 11.58 11.58 44.95 3.02
107 108 0.857287 GACGTGGACGGTTCTGTTTC 59.143 55.000 0.00 0.00 44.95 2.78
112 113 1.144093 TGGACGGTTCTGTTTCCCATT 59.856 47.619 0.00 0.00 0.00 3.16
115 116 3.146847 GACGGTTCTGTTTCCCATTTCT 58.853 45.455 0.00 0.00 0.00 2.52
126 127 5.010617 TGTTTCCCATTTCTTACTCTTTGCC 59.989 40.000 0.00 0.00 0.00 4.52
154 155 4.595538 GTGTGGCCGTGGACGTCA 62.596 66.667 18.91 0.27 37.74 4.35
155 156 4.595538 TGTGGCCGTGGACGTCAC 62.596 66.667 18.91 12.39 42.74 3.67
183 184 3.900601 GAGGTGAGGTCCATGATAGATGT 59.099 47.826 0.00 0.00 0.00 3.06
185 186 3.389329 GGTGAGGTCCATGATAGATGTGT 59.611 47.826 0.00 0.00 0.00 3.72
187 188 4.033009 TGAGGTCCATGATAGATGTGTGT 58.967 43.478 0.00 0.00 0.00 3.72
204 205 4.329545 TGGGCCAGCCTCGTGTTC 62.330 66.667 0.00 0.00 36.10 3.18
235 236 1.811266 CCCGAACGATGTGGAGCTG 60.811 63.158 0.00 0.00 0.00 4.24
237 238 1.446792 CGAACGATGTGGAGCTGCT 60.447 57.895 6.82 0.00 0.00 4.24
256 257 2.515057 ACGTTGGCAGCGTTTCCA 60.515 55.556 23.78 0.00 39.79 3.53
257 258 1.852067 GACGTTGGCAGCGTTTCCAT 61.852 55.000 29.24 6.40 43.04 3.41
273 275 0.606401 CCATACATGATCACCCGCCC 60.606 60.000 0.00 0.00 0.00 6.13
274 276 0.606401 CATACATGATCACCCGCCCC 60.606 60.000 0.00 0.00 0.00 5.80
275 277 1.059584 ATACATGATCACCCGCCCCA 61.060 55.000 0.00 0.00 0.00 4.96
276 278 1.978455 TACATGATCACCCGCCCCAC 61.978 60.000 0.00 0.00 0.00 4.61
277 279 3.809013 ATGATCACCCGCCCCACC 61.809 66.667 0.00 0.00 0.00 4.61
302 304 4.595538 TGCGTCCGCCTTCGTTGT 62.596 61.111 9.43 0.00 41.09 3.32
311 313 1.590238 CGCCTTCGTTGTGATCTCATC 59.410 52.381 0.00 0.00 0.00 2.92
315 317 4.115516 CCTTCGTTGTGATCTCATCGAAT 58.884 43.478 29.27 0.00 43.51 3.34
317 319 5.748630 CCTTCGTTGTGATCTCATCGAATTA 59.251 40.000 29.27 16.73 43.51 1.40
329 331 3.379057 TCATCGAATTAGGTGTCACGCTA 59.621 43.478 0.00 0.00 0.00 4.26
330 332 4.037565 TCATCGAATTAGGTGTCACGCTAT 59.962 41.667 0.00 0.00 0.00 2.97
343 345 1.068083 CGCTATGCCTCCATGACGT 59.932 57.895 0.00 0.00 32.85 4.34
345 347 1.502163 GCTATGCCTCCATGACGTGC 61.502 60.000 0.00 0.00 32.85 5.34
348 869 1.308069 ATGCCTCCATGACGTGCAAC 61.308 55.000 0.00 0.00 35.30 4.17
354 875 3.049674 ATGACGTGCAACCCAGCG 61.050 61.111 0.00 0.00 37.31 5.18
360 881 0.809636 CGTGCAACCCAGCGATCATA 60.810 55.000 0.00 0.00 37.31 2.15
364 885 1.268032 GCAACCCAGCGATCATAAACG 60.268 52.381 0.00 0.00 0.00 3.60
365 886 1.330521 CAACCCAGCGATCATAAACGG 59.669 52.381 0.00 0.00 0.00 4.44
371 892 2.755650 AGCGATCATAAACGGTGGATC 58.244 47.619 0.00 1.12 38.73 3.36
373 894 2.221055 GCGATCATAAACGGTGGATCAC 59.779 50.000 9.74 0.00 36.75 3.06
399 920 0.815213 CGGAGGCACATATGTGGTGG 60.815 60.000 31.63 11.64 45.72 4.61
411 932 2.200370 TGGTGGAGGTCTGGACGT 59.800 61.111 0.00 0.00 0.00 4.34
438 959 1.185315 CCCTCCAAATTTGATGCCGT 58.815 50.000 19.86 0.00 0.00 5.68
441 962 3.556843 CCCTCCAAATTTGATGCCGTTTT 60.557 43.478 19.86 0.00 0.00 2.43
447 968 3.742433 ATTTGATGCCGTTTTGTGGAA 57.258 38.095 0.00 0.00 0.00 3.53
451 972 3.648009 TGATGCCGTTTTGTGGAAATTC 58.352 40.909 0.00 0.00 0.00 2.17
485 1007 1.198867 CATTGGTCGAATGTTTGCGGA 59.801 47.619 0.00 0.00 37.29 5.54
535 1057 2.419667 CAACGTTTACCTTCCCGACAT 58.580 47.619 0.00 0.00 0.00 3.06
595 1119 1.111116 ACAGGGGTTCGAGTTCGTGA 61.111 55.000 1.07 0.00 40.80 4.35
760 5012 1.332686 CAACACATGGCTCATCATCCG 59.667 52.381 0.00 0.00 0.00 4.18
761 5013 0.816825 ACACATGGCTCATCATCCGC 60.817 55.000 0.00 0.00 0.00 5.54
780 5032 2.765807 CACCGCATCCCTCTCCCT 60.766 66.667 0.00 0.00 0.00 4.20
793 6358 2.251818 CTCTCCCTTGTCTGTCTCCAA 58.748 52.381 0.00 0.00 0.00 3.53
796 6361 0.764890 CCCTTGTCTGTCTCCAACCA 59.235 55.000 0.00 0.00 0.00 3.67
797 6362 1.543429 CCCTTGTCTGTCTCCAACCAC 60.543 57.143 0.00 0.00 0.00 4.16
837 6402 2.676471 GTTTCCACGGCCCTGCAT 60.676 61.111 0.00 0.00 0.00 3.96
851 6416 0.870393 CTGCATGCGCCGAATAATCT 59.130 50.000 14.09 0.00 37.32 2.40
910 6480 1.289982 TTTCAACTCCCACCACCCCA 61.290 55.000 0.00 0.00 0.00 4.96
913 6483 4.525028 ACTCCCACCACCCCACCA 62.525 66.667 0.00 0.00 0.00 4.17
914 6484 2.941025 CTCCCACCACCCCACCAT 60.941 66.667 0.00 0.00 0.00 3.55
1009 6582 2.822701 CCCCCGTAGCCGCTTTTC 60.823 66.667 0.00 0.00 0.00 2.29
1020 6593 0.382515 CCGCTTTTCACGAACCCAAA 59.617 50.000 0.00 0.00 0.00 3.28
1034 6607 3.722295 CAAACCCATCACGCGCGT 61.722 61.111 32.73 32.73 0.00 6.01
1073 6646 2.813179 CGATTACGCTGCCACTGCC 61.813 63.158 0.00 0.00 36.33 4.85
1076 6649 4.697756 TACGCTGCCACTGCCACC 62.698 66.667 0.00 0.00 36.33 4.61
1089 6662 3.720601 CCACCAGCAGCCTGCCTA 61.721 66.667 14.25 0.00 46.52 3.93
1090 6663 2.124819 CACCAGCAGCCTGCCTAG 60.125 66.667 14.25 4.79 46.52 3.02
1108 6681 0.465097 AGGATTCAGCCAAGATGCGG 60.465 55.000 0.00 0.00 36.02 5.69
1861 7434 2.850647 GAGTACGAATTCGCTGGTGTAC 59.149 50.000 27.03 19.13 44.43 2.90
1888 7461 2.608970 ATTTCCCCGTGGATGCTCCG 62.609 60.000 0.00 0.00 41.40 4.63
2491 8064 2.434843 CCTCGGATGGCTAGCACCA 61.435 63.158 18.24 6.59 45.82 4.17
2815 8388 7.440556 CGAATTGGATGATCTGAGAGTGTTTAT 59.559 37.037 0.00 0.00 0.00 1.40
2816 8389 8.447924 AATTGGATGATCTGAGAGTGTTTATG 57.552 34.615 0.00 0.00 0.00 1.90
2817 8390 5.363101 TGGATGATCTGAGAGTGTTTATGC 58.637 41.667 0.00 0.00 0.00 3.14
2818 8391 5.129980 TGGATGATCTGAGAGTGTTTATGCT 59.870 40.000 0.00 0.00 0.00 3.79
2917 8490 6.146673 TGCTAGAATAGAAACATGCATCATCG 59.853 38.462 0.00 0.00 42.77 3.84
2962 8538 6.653526 AATTGATGTGATGTTTTGTCCAGA 57.346 33.333 0.00 0.00 0.00 3.86
2980 8556 6.183360 TGTCCAGACAAGAGTATTATACTGGC 60.183 42.308 9.87 0.00 42.01 4.85
3016 8592 8.225603 AGGTGCTTTGATGTATACAAATAAGG 57.774 34.615 10.14 7.16 36.79 2.69
3020 8596 8.271458 TGCTTTGATGTATACAAATAAGGGAGA 58.729 33.333 10.14 0.00 36.79 3.71
3021 8597 9.120538 GCTTTGATGTATACAAATAAGGGAGAA 57.879 33.333 10.14 0.00 36.79 2.87
3101 9283 4.331108 GAGAGCTTCCTCACCTGAATTTT 58.669 43.478 0.00 0.00 40.68 1.82
3102 9284 4.734266 AGAGCTTCCTCACCTGAATTTTT 58.266 39.130 0.00 0.00 40.68 1.94
3187 9369 1.129811 CCGGAGCGAAAACCATACAAC 59.870 52.381 0.00 0.00 0.00 3.32
3188 9370 1.129811 CGGAGCGAAAACCATACAACC 59.870 52.381 0.00 0.00 0.00 3.77
3259 9442 2.558795 CGCCCTAGCTAGCAGATAGAAA 59.441 50.000 18.83 0.00 36.36 2.52
3275 9458 3.593442 AGAAAGGGTCATCACCACAAA 57.407 42.857 0.00 0.00 45.94 2.83
3296 9479 1.486726 AGGCACAAGTAGATGTAGGGC 59.513 52.381 0.00 0.00 30.84 5.19
3317 9500 1.182667 TCGTCGAGGGATCACAACAT 58.817 50.000 5.12 0.00 0.00 2.71
3400 9584 2.487805 GCAGGACCATCCATAATCAGCA 60.488 50.000 0.00 0.00 39.61 4.41
3423 9607 5.654603 AGTGACATATGAACACGAACCTA 57.345 39.130 21.67 0.00 39.19 3.08
3497 9681 1.134818 AGGCATCTTGCGTCGTCATTA 60.135 47.619 0.00 0.00 46.21 1.90
3527 9711 1.949465 AACCGAGACAACACCAAGAC 58.051 50.000 0.00 0.00 0.00 3.01
3582 10842 1.476891 GAGGGTCTTGAGTATGCACGA 59.523 52.381 0.00 0.00 0.00 4.35
3591 10851 2.263077 GAGTATGCACGACAACAGAGG 58.737 52.381 0.00 0.00 0.00 3.69
3665 10925 1.078426 CTAGGAAGGTGTTGGCCCG 60.078 63.158 0.00 0.00 0.00 6.13
3711 11263 3.476552 CAGCAGTTTTCCCTAGTTGACA 58.523 45.455 0.00 0.00 0.00 3.58
3728 11280 7.687941 AGTTGACATCAAGGTTTATCGAATT 57.312 32.000 0.00 0.00 36.39 2.17
3791 11343 5.348451 GCACACACAAATCAAACTTTCTTGT 59.652 36.000 0.00 0.00 0.00 3.16
3851 11404 8.630037 ACTAGATTGGTTGGTTACAAAAAGAAG 58.370 33.333 0.00 0.00 38.54 2.85
3859 11412 7.754475 GGTTGGTTACAAAAAGAAGTAAAACGA 59.246 33.333 0.00 0.00 38.54 3.85
3875 11428 2.440539 ACGAATGTGTGGAGAGTGTC 57.559 50.000 0.00 0.00 0.00 3.67
3952 11505 7.508977 TGGTTGAGAACTTTATGGAGGAAAAAT 59.491 33.333 0.00 0.00 0.00 1.82
3973 11526 1.141053 GAACGGGCTCCATAGGTTCAT 59.859 52.381 0.00 0.00 37.51 2.57
4121 11674 6.818644 CCATAAATCCATAGACCGTTATCCAG 59.181 42.308 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.934645 ACGAAATCACTATTCTGACCTTTTCA 59.065 34.615 0.00 0.00 0.00 2.69
11 12 7.365840 ACGAAATCACTATTCTGACCTTTTC 57.634 36.000 0.00 0.00 0.00 2.29
12 13 6.371825 GGACGAAATCACTATTCTGACCTTTT 59.628 38.462 0.00 0.00 0.00 2.27
13 14 5.875359 GGACGAAATCACTATTCTGACCTTT 59.125 40.000 0.00 0.00 0.00 3.11
14 15 5.420409 GGACGAAATCACTATTCTGACCTT 58.580 41.667 0.00 0.00 0.00 3.50
15 16 4.141914 GGGACGAAATCACTATTCTGACCT 60.142 45.833 0.00 0.00 0.00 3.85
16 17 4.120589 GGGACGAAATCACTATTCTGACC 58.879 47.826 0.00 0.00 0.00 4.02
17 18 5.012328 AGGGACGAAATCACTATTCTGAC 57.988 43.478 0.00 0.00 40.32 3.51
18 19 4.956700 AGAGGGACGAAATCACTATTCTGA 59.043 41.667 0.00 0.00 43.11 3.27
19 20 5.269505 AGAGGGACGAAATCACTATTCTG 57.730 43.478 0.00 0.00 43.11 3.02
20 21 5.941555 AAGAGGGACGAAATCACTATTCT 57.058 39.130 0.00 0.00 37.80 2.40
22 23 5.163395 GGAGAAGAGGGACGAAATCACTATT 60.163 44.000 0.00 0.00 45.20 1.73
23 24 4.342665 GGAGAAGAGGGACGAAATCACTAT 59.657 45.833 0.00 0.00 43.11 2.12
24 25 3.700038 GGAGAAGAGGGACGAAATCACTA 59.300 47.826 0.00 0.00 43.11 2.74
26 27 2.233922 TGGAGAAGAGGGACGAAATCAC 59.766 50.000 0.00 0.00 0.00 3.06
27 28 2.536066 TGGAGAAGAGGGACGAAATCA 58.464 47.619 0.00 0.00 0.00 2.57
28 29 3.828875 ATGGAGAAGAGGGACGAAATC 57.171 47.619 0.00 0.00 0.00 2.17
29 30 3.068307 CGTATGGAGAAGAGGGACGAAAT 59.932 47.826 0.00 0.00 0.00 2.17
30 31 2.426024 CGTATGGAGAAGAGGGACGAAA 59.574 50.000 0.00 0.00 0.00 3.46
31 32 2.022195 CGTATGGAGAAGAGGGACGAA 58.978 52.381 0.00 0.00 0.00 3.85
32 33 1.064906 ACGTATGGAGAAGAGGGACGA 60.065 52.381 0.00 0.00 33.30 4.20
33 34 1.065701 CACGTATGGAGAAGAGGGACG 59.934 57.143 0.00 0.00 35.10 4.79
34 35 2.873133 CACGTATGGAGAAGAGGGAC 57.127 55.000 0.00 0.00 0.00 4.46
80 81 0.323178 ACCGTCCACGTCTGACCTAT 60.323 55.000 1.55 0.00 37.74 2.57
83 84 1.372623 GAACCGTCCACGTCTGACC 60.373 63.158 1.55 0.00 37.74 4.02
87 88 0.462789 AAACAGAACCGTCCACGTCT 59.537 50.000 0.00 0.00 37.74 4.18
91 92 0.179040 TGGGAAACAGAACCGTCCAC 60.179 55.000 0.00 0.00 31.30 4.02
102 103 5.010617 GGCAAAGAGTAAGAAATGGGAAACA 59.989 40.000 0.00 0.00 0.00 2.83
103 104 5.010617 TGGCAAAGAGTAAGAAATGGGAAAC 59.989 40.000 0.00 0.00 0.00 2.78
107 108 4.335416 TCTGGCAAAGAGTAAGAAATGGG 58.665 43.478 0.00 0.00 0.00 4.00
126 127 1.224069 CGGCCACACAACAGACTCTG 61.224 60.000 2.24 4.36 37.52 3.35
154 155 2.675772 GACCTCACCTCGACCGGT 60.676 66.667 6.92 6.92 37.93 5.28
155 156 3.450115 GGACCTCACCTCGACCGG 61.450 72.222 0.00 0.00 0.00 5.28
187 188 4.329545 GAACACGAGGCTGGCCCA 62.330 66.667 8.11 0.00 36.58 5.36
216 217 3.195698 GCTCCACATCGTTCGGGC 61.196 66.667 0.00 0.00 0.00 6.13
218 219 2.456119 GCAGCTCCACATCGTTCGG 61.456 63.158 0.00 0.00 0.00 4.30
222 223 1.079543 GTCAGCAGCTCCACATCGT 60.080 57.895 0.00 0.00 0.00 3.73
226 227 1.595109 CAACGTCAGCAGCTCCACA 60.595 57.895 0.00 0.00 0.00 4.17
237 238 2.539338 GGAAACGCTGCCAACGTCA 61.539 57.895 0.00 0.00 44.30 4.35
256 257 1.059584 TGGGGCGGGTGATCATGTAT 61.060 55.000 0.00 0.00 0.00 2.29
257 258 1.690985 TGGGGCGGGTGATCATGTA 60.691 57.895 0.00 0.00 0.00 2.29
289 291 0.108804 GAGATCACAACGAAGGCGGA 60.109 55.000 0.00 0.00 43.17 5.54
300 302 5.127031 TGACACCTAATTCGATGAGATCACA 59.873 40.000 0.00 0.00 0.00 3.58
302 304 5.592054 GTGACACCTAATTCGATGAGATCA 58.408 41.667 0.00 0.00 0.00 2.92
311 313 2.218759 GCATAGCGTGACACCTAATTCG 59.781 50.000 0.00 0.00 0.00 3.34
315 317 1.136305 GAGGCATAGCGTGACACCTAA 59.864 52.381 0.00 0.00 38.81 2.69
317 319 1.517832 GAGGCATAGCGTGACACCT 59.482 57.895 0.00 1.06 38.81 4.00
329 331 1.002257 TTGCACGTCATGGAGGCAT 60.002 52.632 0.00 0.00 34.03 4.40
330 332 1.965930 GTTGCACGTCATGGAGGCA 60.966 57.895 0.00 0.00 0.00 4.75
343 345 1.742831 GTTTATGATCGCTGGGTTGCA 59.257 47.619 0.00 0.00 0.00 4.08
345 347 1.330521 CCGTTTATGATCGCTGGGTTG 59.669 52.381 0.00 0.00 0.00 3.77
348 869 0.937304 CACCGTTTATGATCGCTGGG 59.063 55.000 0.00 0.00 0.00 4.45
354 875 2.800544 CCGTGATCCACCGTTTATGATC 59.199 50.000 0.00 0.00 35.33 2.92
360 881 0.321298 CTTCCCGTGATCCACCGTTT 60.321 55.000 0.00 0.00 0.00 3.60
364 885 2.511600 CGCTTCCCGTGATCCACC 60.512 66.667 0.00 0.00 0.00 4.61
365 886 2.511600 CCGCTTCCCGTGATCCAC 60.512 66.667 0.00 0.00 34.38 4.02
368 889 2.107141 CCTCCGCTTCCCGTGATC 59.893 66.667 0.00 0.00 34.38 2.92
373 894 2.383245 ATATGTGCCTCCGCTTCCCG 62.383 60.000 0.00 0.00 35.36 5.14
399 920 2.353505 GGTTTAAGGACGTCCAGACCTC 60.354 54.545 35.00 19.35 44.08 3.85
411 932 5.046663 GCATCAAATTTGGAGGGTTTAAGGA 60.047 40.000 17.90 0.00 0.00 3.36
415 936 3.194542 CGGCATCAAATTTGGAGGGTTTA 59.805 43.478 17.90 0.00 0.00 2.01
438 959 5.651387 TGTGTGTCTGAATTTCCACAAAA 57.349 34.783 8.07 0.21 39.33 2.44
441 962 4.460731 TGTTTGTGTGTCTGAATTTCCACA 59.539 37.500 3.70 3.70 35.59 4.17
447 968 5.105392 ACCAATGTGTTTGTGTGTCTGAATT 60.105 36.000 0.00 0.00 33.15 2.17
451 972 3.694734 GACCAATGTGTTTGTGTGTCTG 58.305 45.455 0.00 0.00 33.15 3.51
485 1007 4.605967 CGCCGTGCTGCAAAACGT 62.606 61.111 16.83 0.00 38.11 3.99
535 1057 1.470805 CCTGTGTCGATCGCCAACATA 60.471 52.381 11.09 7.44 0.00 2.29
595 1119 2.115052 TTGCCGTTGCTCATGGGT 59.885 55.556 0.00 0.00 38.71 4.51
760 5012 2.512515 GAGAGGGATGCGGTGTGC 60.513 66.667 0.00 0.00 46.70 4.57
761 5013 2.187946 GGAGAGGGATGCGGTGTG 59.812 66.667 0.00 0.00 0.00 3.82
780 5032 1.837439 ACTGTGGTTGGAGACAGACAA 59.163 47.619 0.00 0.00 41.90 3.18
793 6358 2.034558 CGAATTTTGCTTGGACTGTGGT 59.965 45.455 0.00 0.00 0.00 4.16
796 6361 1.000274 GGCGAATTTTGCTTGGACTGT 60.000 47.619 8.49 0.00 0.00 3.55
797 6362 1.000385 TGGCGAATTTTGCTTGGACTG 60.000 47.619 8.49 0.00 0.00 3.51
837 6402 1.673920 GGGAAAAGATTATTCGGCGCA 59.326 47.619 10.83 0.00 0.00 6.09
878 6448 2.548480 GAGTTGAAACCGAAACAGAGGG 59.452 50.000 0.00 0.00 0.00 4.30
879 6449 2.548480 GGAGTTGAAACCGAAACAGAGG 59.452 50.000 0.00 0.00 0.00 3.69
880 6450 2.548480 GGGAGTTGAAACCGAAACAGAG 59.452 50.000 0.00 0.00 0.00 3.35
881 6451 2.092861 TGGGAGTTGAAACCGAAACAGA 60.093 45.455 0.00 0.00 0.00 3.41
882 6452 2.032924 GTGGGAGTTGAAACCGAAACAG 59.967 50.000 0.00 0.00 0.00 3.16
910 6480 1.079621 TAGTGTCACGGGGGATGGT 59.920 57.895 0.00 0.00 0.00 3.55
913 6483 0.632835 TAGGTAGTGTCACGGGGGAT 59.367 55.000 0.00 0.00 0.00 3.85
914 6484 0.632835 ATAGGTAGTGTCACGGGGGA 59.367 55.000 0.00 0.00 0.00 4.81
1009 6582 0.596082 GTGATGGGTTTGGGTTCGTG 59.404 55.000 0.00 0.00 0.00 4.35
1073 6646 2.124819 CTAGGCAGGCTGCTGGTG 60.125 66.667 35.73 20.40 44.28 4.17
1076 6649 0.534652 GAATCCTAGGCAGGCTGCTG 60.535 60.000 35.73 24.91 44.28 4.41
1082 6655 2.224821 TGGCTGAATCCTAGGCAGG 58.775 57.895 14.53 0.00 44.52 4.85
1085 6658 2.502295 CATCTTGGCTGAATCCTAGGC 58.498 52.381 2.96 0.00 40.77 3.93
1086 6659 2.502295 GCATCTTGGCTGAATCCTAGG 58.498 52.381 0.82 0.82 31.28 3.02
1087 6660 2.141517 CGCATCTTGGCTGAATCCTAG 58.858 52.381 0.00 0.00 0.00 3.02
1088 6661 1.202687 CCGCATCTTGGCTGAATCCTA 60.203 52.381 0.00 0.00 0.00 2.94
1089 6662 0.465097 CCGCATCTTGGCTGAATCCT 60.465 55.000 0.00 0.00 0.00 3.24
1090 6663 0.464373 TCCGCATCTTGGCTGAATCC 60.464 55.000 0.00 0.00 0.00 3.01
1096 6669 1.748122 CAGCTTCCGCATCTTGGCT 60.748 57.895 0.00 0.00 39.10 4.75
1099 6672 1.022982 TGCTCAGCTTCCGCATCTTG 61.023 55.000 0.00 0.00 39.10 3.02
1108 6681 3.123620 CGGCCAGTGCTCAGCTTC 61.124 66.667 2.24 0.00 37.74 3.86
1837 7410 0.174845 CCAGCGAATTCGTACTCCCA 59.825 55.000 27.24 0.00 42.22 4.37
1888 7461 1.009389 CAGCAACCGTCGACCTCTTC 61.009 60.000 10.58 0.00 0.00 2.87
2491 8064 2.908015 ACAGTGTTGTGGGCGACT 59.092 55.556 0.31 0.00 35.83 4.18
2815 8388 6.423182 AGATGCCACCTTTACTTAATAAGCA 58.577 36.000 0.00 0.00 0.00 3.91
2816 8389 6.944234 AGATGCCACCTTTACTTAATAAGC 57.056 37.500 0.00 0.00 0.00 3.09
2817 8390 9.573133 CAAAAGATGCCACCTTTACTTAATAAG 57.427 33.333 0.00 0.00 33.85 1.73
2818 8391 8.527810 CCAAAAGATGCCACCTTTACTTAATAA 58.472 33.333 0.00 0.00 33.85 1.40
2917 8490 6.856135 TTACAAGATGCAGATGATGATGAC 57.144 37.500 0.00 0.00 0.00 3.06
2962 8538 4.142026 TGTGCGCCAGTATAATACTCTTGT 60.142 41.667 4.18 0.00 36.76 3.16
3075 9257 1.306568 GGTGAGGAAGCTCTCCCCT 60.307 63.158 10.27 4.40 46.81 4.79
3218 9400 2.223745 GTCCCTTGTTTAGGCGTCAAA 58.776 47.619 0.00 0.00 43.27 2.69
3259 9442 1.823250 GCCTTTTGTGGTGATGACCCT 60.823 52.381 0.00 0.00 42.34 4.34
3275 9458 2.092914 GCCCTACATCTACTTGTGCCTT 60.093 50.000 0.00 0.00 0.00 4.35
3296 9479 1.135112 TGTTGTGATCCCTCGACGATG 60.135 52.381 0.00 0.00 0.00 3.84
3400 9584 4.894784 AGGTTCGTGTTCATATGTCACTT 58.105 39.130 21.43 7.99 0.00 3.16
3423 9607 0.907230 GGAGCTCCCAGTCAAGGTCT 60.907 60.000 23.19 0.00 39.42 3.85
3467 9651 2.742856 CGCAAGATGCCTCCTCAACATA 60.743 50.000 0.00 0.00 41.12 2.29
3497 9681 4.819630 TGTTGTCTCGGTTTATCTTTGCTT 59.180 37.500 0.00 0.00 0.00 3.91
3527 9711 0.592637 TGTTGCAACGAGCTTGATGG 59.407 50.000 23.79 0.00 45.94 3.51
3551 9735 2.919602 TCAAGACCCTCCTATGGCTTTT 59.080 45.455 0.00 0.00 0.00 2.27
3582 10842 1.270305 CCGATGTGTCACCTCTGTTGT 60.270 52.381 0.00 0.00 0.00 3.32
3591 10851 1.086696 CCCATTGTCCGATGTGTCAC 58.913 55.000 0.00 0.00 0.00 3.67
3665 10925 2.341176 CAAGCCCTTGCACTTGGC 59.659 61.111 11.45 11.45 45.70 4.52
3685 10945 2.158608 ACTAGGGAAAACTGCTGCTTGT 60.159 45.455 0.00 0.00 0.00 3.16
3692 10952 4.072131 TGATGTCAACTAGGGAAAACTGC 58.928 43.478 0.00 0.00 0.00 4.40
3699 11251 4.993705 AAACCTTGATGTCAACTAGGGA 57.006 40.909 13.62 0.00 35.29 4.20
3711 11263 7.041508 GCTCTCATGAATTCGATAAACCTTGAT 60.042 37.037 0.00 0.00 0.00 2.57
3728 11280 5.675684 TTGTAACCATGTAGCTCTCATGA 57.324 39.130 24.27 0.00 43.47 3.07
3791 11343 0.323629 CGCTACTCCTGTTGGGGAAA 59.676 55.000 0.00 0.00 37.25 3.13
3851 11404 4.510340 ACACTCTCCACACATTCGTTTTAC 59.490 41.667 0.00 0.00 0.00 2.01
3859 11412 2.562738 TCATCGACACTCTCCACACATT 59.437 45.455 0.00 0.00 0.00 2.71
3904 11457 9.705290 AACCATAATCAACGCTCTTTTAATTTT 57.295 25.926 0.00 0.00 0.00 1.82
3952 11505 0.539986 GAACCTATGGAGCCCGTTCA 59.460 55.000 0.00 0.00 34.36 3.18


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

AutoCloner maintained by Alex Coulton.