Multiple sequence alignment - TraesCS7B01G064900

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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 TraesCS7B01G064900 chr7B 100.000 4010 0 0 1 4010 70484307 70480298 0.000000e+00 7406
1 TraesCS7B01G064900 chr7A 96.437 3480 93 14 532 3995 116116288 116112824 0.000000e+00 5710
2 TraesCS7B01G064900 chr7A 88.976 508 28 15 223 706 116116773 116116270 1.590000e-168 603
3 TraesCS7B01G064900 chr7A 93.182 88 6 0 33 120 116116953 116116866 3.250000e-26 130
4 TraesCS7B01G064900 chr7D 95.070 3164 98 17 711 3865 111049960 111046846 0.000000e+00 4926
5 TraesCS7B01G064900 chr7D 89.696 427 31 6 223 639 111050382 111049959 2.120000e-147 532
6 TraesCS7B01G064900 chr7D 97.590 83 1 1 3901 3982 111046842 111046760 1.500000e-29 141
7 TraesCS7B01G064900 chr7D 91.667 84 4 3 33 116 111050557 111050477 3.280000e-21 113
8 TraesCS7B01G064900 chr4D 94.866 3175 95 17 711 3876 9318973 9315858 0.000000e+00 4898
9 TraesCS7B01G064900 chr4D 89.548 1129 52 16 2757 3876 9324469 9325540 0.000000e+00 1371
10 TraesCS7B01G064900 chr4D 89.696 427 31 6 223 639 9319395 9318972 2.120000e-147 532
11 TraesCS7B01G064900 chr4D 90.830 229 9 2 3648 3876 9329942 9330158 3.030000e-76 296
12 TraesCS7B01G064900 chr4D 97.674 86 1 1 3898 3982 9315867 9315782 3.230000e-31 147
13 TraesCS7B01G064900 chr4D 94.792 96 2 3 3890 3982 9325521 9325616 3.230000e-31 147
14 TraesCS7B01G064900 chr4D 94.792 96 2 3 3890 3982 9330139 9330234 3.230000e-31 147
15 TraesCS7B01G064900 chr4D 90.476 84 5 3 33 116 9319570 9319490 1.520000e-19 108
16 TraesCS7B01G064900 chr5A 90.893 2767 197 32 672 3413 26157193 26154457 0.000000e+00 3663
17 TraesCS7B01G064900 chr5A 93.615 1206 69 8 716 1917 545973662 545974863 0.000000e+00 1794
18 TraesCS7B01G064900 chr5A 90.582 1083 64 6 1992 3073 545981317 545982362 0.000000e+00 1400
19 TraesCS7B01G064900 chr5D 92.108 2585 159 27 857 3420 37194217 37191657 0.000000e+00 3602
20 TraesCS7B01G064900 chr5D 89.003 1364 123 21 483 1843 430440889 430442228 0.000000e+00 1663
21 TraesCS7B01G064900 chr5D 90.556 1186 104 5 1886 3070 430442231 430443409 0.000000e+00 1563
22 TraesCS7B01G064900 chr5B 88.929 1102 115 5 1958 3058 519642192 519643287 0.000000e+00 1352
23 TraesCS7B01G064900 chr5B 86.957 1081 107 24 455 1529 519614240 519615292 0.000000e+00 1184
24 TraesCS7B01G064900 chr5B 92.202 436 33 1 1525 1960 519628315 519628749 2.050000e-172 616
25 TraesCS7B01G064900 chr5B 96.610 59 2 0 34 92 519614074 519614132 9.170000e-17 99
26 TraesCS7B01G064900 chr3D 86.883 770 96 5 1172 1938 580546711 580547478 0.000000e+00 857


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 TraesCS7B01G064900 chr7B 70480298 70484307 4009 True 7406.000000 7406 100.00000 1 4010 1 chr7B.!!$R1 4009
1 TraesCS7B01G064900 chr7A 116112824 116116953 4129 True 2147.666667 5710 92.86500 33 3995 3 chr7A.!!$R1 3962
2 TraesCS7B01G064900 chr7D 111046760 111050557 3797 True 1428.000000 4926 93.50575 33 3982 4 chr7D.!!$R1 3949
3 TraesCS7B01G064900 chr4D 9315782 9319570 3788 True 1421.250000 4898 93.17800 33 3982 4 chr4D.!!$R1 3949
4 TraesCS7B01G064900 chr4D 9324469 9325616 1147 False 759.000000 1371 92.17000 2757 3982 2 chr4D.!!$F1 1225
5 TraesCS7B01G064900 chr5A 26154457 26157193 2736 True 3663.000000 3663 90.89300 672 3413 1 chr5A.!!$R1 2741
6 TraesCS7B01G064900 chr5A 545973662 545974863 1201 False 1794.000000 1794 93.61500 716 1917 1 chr5A.!!$F1 1201
7 TraesCS7B01G064900 chr5A 545981317 545982362 1045 False 1400.000000 1400 90.58200 1992 3073 1 chr5A.!!$F2 1081
8 TraesCS7B01G064900 chr5D 37191657 37194217 2560 True 3602.000000 3602 92.10800 857 3420 1 chr5D.!!$R1 2563
9 TraesCS7B01G064900 chr5D 430440889 430443409 2520 False 1613.000000 1663 89.77950 483 3070 2 chr5D.!!$F1 2587
10 TraesCS7B01G064900 chr5B 519642192 519643287 1095 False 1352.000000 1352 88.92900 1958 3058 1 chr5B.!!$F2 1100
11 TraesCS7B01G064900 chr5B 519614074 519615292 1218 False 641.500000 1184 91.78350 34 1529 2 chr5B.!!$F3 1495
12 TraesCS7B01G064900 chr3D 580546711 580547478 767 False 857.000000 857 86.88300 1172 1938 1 chr3D.!!$F1 766

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
199 233 0.036732 TTGATGAGAAGTTGCCGGCT 59.963 50.0 29.70 6.86 0.00 5.52 F
206 240 0.109735 GAAGTTGCCGGCTAGTTTGC 60.110 55.0 27.77 15.04 0.00 3.68 F
216 250 0.242017 GCTAGTTTGCTTGCCACTGG 59.758 55.0 5.21 0.00 37.47 4.00 F
911 1147 0.515564 CCTGTACCCGTTTTTCTGCG 59.484 55.0 0.00 0.00 0.00 5.18 F
2766 3024 0.403271 AAGTTGATGGCCAGCACTCT 59.597 50.0 26.27 21.50 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 2098 2.757314 TCTTGTTGCACACAATGACCAA 59.243 40.909 12.68 0.00 44.72 3.67 R
2739 2997 1.284491 TGGCCATCAACTTCCATAGCA 59.716 47.619 0.00 0.00 0.00 3.49 R
2748 3006 0.322277 CAGAGTGCTGGCCATCAACT 60.322 55.000 11.63 12.65 38.51 3.16 R
2783 3041 0.255318 GGACCTAGACCTCGACCTCA 59.745 60.000 0.00 0.00 0.00 3.86 R
3817 4088 1.630369 ACTGGAGCCTGACAATGCTAA 59.370 47.619 0.08 0.00 38.11 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
17 18 2.187946 ATGGCTGCGGCTGTAGAC 59.812 61.111 18.85 12.85 36.18 2.59
18 19 2.362369 ATGGCTGCGGCTGTAGACT 61.362 57.895 18.10 0.27 36.67 3.24
19 20 2.202810 GGCTGCGGCTGTAGACTC 60.203 66.667 18.85 0.00 38.73 3.36
20 21 2.580867 GCTGCGGCTGTAGACTCG 60.581 66.667 15.58 0.00 35.22 4.18
21 22 3.052620 GCTGCGGCTGTAGACTCGA 62.053 63.158 15.58 0.00 35.22 4.04
22 23 1.730487 CTGCGGCTGTAGACTCGAT 59.270 57.895 4.33 0.00 0.00 3.59
23 24 0.101399 CTGCGGCTGTAGACTCGATT 59.899 55.000 4.33 0.00 0.00 3.34
24 25 0.100682 TGCGGCTGTAGACTCGATTC 59.899 55.000 0.00 0.00 0.00 2.52
25 26 0.100682 GCGGCTGTAGACTCGATTCA 59.899 55.000 5.50 0.00 0.00 2.57
26 27 1.469251 GCGGCTGTAGACTCGATTCAA 60.469 52.381 5.50 0.00 0.00 2.69
27 28 2.186076 CGGCTGTAGACTCGATTCAAC 58.814 52.381 5.50 0.00 0.00 3.18
28 29 2.541556 GGCTGTAGACTCGATTCAACC 58.458 52.381 5.50 0.00 0.00 3.77
29 30 2.166664 GGCTGTAGACTCGATTCAACCT 59.833 50.000 5.50 0.00 0.00 3.50
30 31 3.182967 GCTGTAGACTCGATTCAACCTG 58.817 50.000 5.50 0.00 0.00 4.00
31 32 3.119459 GCTGTAGACTCGATTCAACCTGA 60.119 47.826 5.50 0.00 0.00 3.86
139 173 4.081476 GCTCAATAAGGGTTGGCTGATTTT 60.081 41.667 0.00 0.00 0.00 1.82
141 175 6.524101 TCAATAAGGGTTGGCTGATTTTAC 57.476 37.500 0.00 0.00 0.00 2.01
170 204 5.262804 AGATAGGGGATGGTCGACTAATAC 58.737 45.833 16.46 10.23 0.00 1.89
176 210 5.055144 GGGATGGTCGACTAATACTTTTCC 58.945 45.833 16.46 10.94 0.00 3.13
185 219 9.490663 GTCGACTAATACTTTTCCAATTTGATG 57.509 33.333 8.70 0.00 0.00 3.07
186 220 9.443323 TCGACTAATACTTTTCCAATTTGATGA 57.557 29.630 0.00 0.00 0.00 2.92
187 221 9.708222 CGACTAATACTTTTCCAATTTGATGAG 57.292 33.333 0.00 0.00 0.00 2.90
193 227 9.918630 ATACTTTTCCAATTTGATGAGAAGTTG 57.081 29.630 13.12 0.00 0.00 3.16
194 228 6.703165 ACTTTTCCAATTTGATGAGAAGTTGC 59.297 34.615 0.00 0.00 0.00 4.17
195 229 4.789012 TCCAATTTGATGAGAAGTTGCC 57.211 40.909 0.00 0.00 0.00 4.52
196 230 3.191162 TCCAATTTGATGAGAAGTTGCCG 59.809 43.478 0.00 0.00 0.00 5.69
197 231 3.504863 CAATTTGATGAGAAGTTGCCGG 58.495 45.455 0.00 0.00 0.00 6.13
198 232 0.881118 TTTGATGAGAAGTTGCCGGC 59.119 50.000 22.73 22.73 0.00 6.13
199 233 0.036732 TTGATGAGAAGTTGCCGGCT 59.963 50.000 29.70 6.86 0.00 5.52
200 234 0.901827 TGATGAGAAGTTGCCGGCTA 59.098 50.000 29.70 19.10 0.00 3.93
201 235 1.134699 TGATGAGAAGTTGCCGGCTAG 60.135 52.381 29.70 0.00 0.00 3.42
202 236 0.905357 ATGAGAAGTTGCCGGCTAGT 59.095 50.000 29.70 21.15 0.00 2.57
203 237 0.685097 TGAGAAGTTGCCGGCTAGTT 59.315 50.000 27.53 27.53 0.00 2.24
204 238 1.071699 TGAGAAGTTGCCGGCTAGTTT 59.928 47.619 27.77 17.66 0.00 2.66
205 239 1.464997 GAGAAGTTGCCGGCTAGTTTG 59.535 52.381 27.77 0.00 0.00 2.93
206 240 0.109735 GAAGTTGCCGGCTAGTTTGC 60.110 55.000 27.77 15.04 0.00 3.68
207 241 0.537371 AAGTTGCCGGCTAGTTTGCT 60.537 50.000 29.70 10.20 0.00 3.91
208 242 0.537371 AGTTGCCGGCTAGTTTGCTT 60.537 50.000 29.70 0.00 0.00 3.91
209 243 0.387239 GTTGCCGGCTAGTTTGCTTG 60.387 55.000 29.70 0.00 0.00 4.01
210 244 2.141122 TTGCCGGCTAGTTTGCTTGC 62.141 55.000 29.70 0.00 41.58 4.01
215 249 3.780925 GCTAGTTTGCTTGCCACTG 57.219 52.632 5.21 0.00 37.47 3.66
216 250 0.242017 GCTAGTTTGCTTGCCACTGG 59.758 55.000 5.21 0.00 37.47 4.00
226 260 2.970324 GCCACTGGCGACGTTTGA 60.970 61.111 3.73 0.00 39.62 2.69
227 261 2.325082 GCCACTGGCGACGTTTGAT 61.325 57.895 3.73 0.00 39.62 2.57
237 271 2.719046 GCGACGTTTGATGTTTTTCTGG 59.281 45.455 0.00 0.00 0.00 3.86
257 292 3.880846 GATTCAAGGCTGCCGGCG 61.881 66.667 23.90 17.75 42.94 6.46
305 340 1.876799 TGGCGTGGTATTTTGTCAGTG 59.123 47.619 0.00 0.00 0.00 3.66
307 342 1.199097 GCGTGGTATTTTGTCAGTGGG 59.801 52.381 0.00 0.00 0.00 4.61
355 390 8.011106 CCTGCTTTTATTTGTGCTAATTTTGTG 58.989 33.333 0.00 0.00 0.00 3.33
356 391 7.351223 TGCTTTTATTTGTGCTAATTTTGTGC 58.649 30.769 0.00 0.00 0.00 4.57
357 392 7.011763 TGCTTTTATTTGTGCTAATTTTGTGCA 59.988 29.630 0.00 0.00 0.00 4.57
359 394 9.881529 CTTTTATTTGTGCTAATTTTGTGCAAT 57.118 25.926 0.00 0.00 38.50 3.56
360 395 9.875675 TTTTATTTGTGCTAATTTTGTGCAATC 57.124 25.926 0.00 0.00 38.50 2.67
361 396 5.921004 TTTGTGCTAATTTTGTGCAATCC 57.079 34.783 0.00 0.00 38.50 3.01
362 397 4.597404 TGTGCTAATTTTGTGCAATCCA 57.403 36.364 0.00 0.00 38.50 3.41
363 398 5.149973 TGTGCTAATTTTGTGCAATCCAT 57.850 34.783 0.00 0.00 38.50 3.41
368 403 6.127281 TGCTAATTTTGTGCAATCCATCATCT 60.127 34.615 0.00 0.00 33.48 2.90
377 412 6.487668 TGTGCAATCCATCATCTAGTATTTGG 59.512 38.462 0.00 0.00 0.00 3.28
381 416 3.324846 TCCATCATCTAGTATTTGGCGCT 59.675 43.478 7.64 0.00 0.00 5.92
394 429 4.621068 TTTGGCGCTATGAGAATGAAAG 57.379 40.909 7.64 0.00 0.00 2.62
429 469 2.906389 TGTTGCACTTCCTATGAGAGGT 59.094 45.455 0.00 0.00 46.76 3.85
542 592 6.849588 ATTTTTAGCTGCCAACAAAGAAAG 57.150 33.333 0.00 0.00 0.00 2.62
553 603 2.962859 ACAAAGAAAGTGGGGCTTGAT 58.037 42.857 0.00 0.00 37.52 2.57
629 841 3.820467 TGCATGTTTAAGGTCCTGACTTG 59.180 43.478 0.00 2.42 0.00 3.16
650 862 1.127567 TCTCCTGGTTGTGACCCCTG 61.128 60.000 0.00 0.00 45.92 4.45
661 873 2.277084 GTGACCCCTGCTGTTTATACG 58.723 52.381 0.00 0.00 0.00 3.06
664 876 3.131577 TGACCCCTGCTGTTTATACGTAG 59.868 47.826 0.08 0.00 0.00 3.51
665 877 2.159000 ACCCCTGCTGTTTATACGTAGC 60.159 50.000 0.08 0.00 36.72 3.58
704 923 2.289010 CCATCAACAAAGAAACTGGGGC 60.289 50.000 0.00 0.00 0.00 5.80
733 952 6.095720 CCGGCCCTTTTGTCTTATGTATTTTA 59.904 38.462 0.00 0.00 0.00 1.52
893 1124 5.616488 AATTGTGATTTCTTGCATTTGCC 57.384 34.783 0.00 0.00 41.18 4.52
911 1147 0.515564 CCTGTACCCGTTTTTCTGCG 59.484 55.000 0.00 0.00 0.00 5.18
949 1186 8.204836 ACCTGTTTATCTACATAGGATTGACAC 58.795 37.037 0.00 0.00 0.00 3.67
962 1200 3.425193 GGATTGACACGACATTTGTTTGC 59.575 43.478 0.00 0.00 0.00 3.68
1029 1272 9.076596 GTGCAGTATAATTTCAAGAAAATCACC 57.923 33.333 0.00 0.00 36.54 4.02
1308 1552 2.028930 GGGTCAGATCAATACGGCTAGG 60.029 54.545 0.00 0.00 0.00 3.02
1849 2098 7.486407 AAATCCTTGTTCATGAATAAGCCTT 57.514 32.000 29.60 22.78 37.94 4.35
2523 2775 5.131308 GGGTAAGATTAGGAAGAAGAAGGCT 59.869 44.000 0.00 0.00 0.00 4.58
2556 2808 4.605640 AGAGCATAGGATGAAGAAGAGC 57.394 45.455 0.00 0.00 0.00 4.09
2736 2994 1.139256 CTGAGCAGAGCTGATGGTGAT 59.861 52.381 5.02 0.00 39.88 3.06
2739 2997 1.769465 AGCAGAGCTGATGGTGATGAT 59.231 47.619 0.85 0.00 37.57 2.45
2748 3006 4.648651 CTGATGGTGATGATGCTATGGAA 58.351 43.478 0.00 0.00 0.00 3.53
2766 3024 0.403271 AAGTTGATGGCCAGCACTCT 59.597 50.000 26.27 21.50 0.00 3.24
2783 3041 2.232452 ACTCTGACAAGAAGCTGCGTAT 59.768 45.455 0.00 0.00 30.03 3.06
3085 3343 5.830912 TGTGCTTTCACTTGGTTATTCTTG 58.169 37.500 0.00 0.00 43.49 3.02
3213 3475 4.393834 TGCAAATGTTAGAACCAGCACTA 58.606 39.130 0.00 0.00 0.00 2.74
3226 3488 4.822026 ACCAGCACTAATCTTGTAGTCAC 58.178 43.478 0.00 0.00 31.78 3.67
3227 3489 4.528596 ACCAGCACTAATCTTGTAGTCACT 59.471 41.667 0.00 0.00 31.78 3.41
3228 3490 5.105752 CCAGCACTAATCTTGTAGTCACTC 58.894 45.833 0.00 0.00 31.78 3.51
3229 3491 5.336770 CCAGCACTAATCTTGTAGTCACTCA 60.337 44.000 0.00 0.00 31.78 3.41
3252 3514 1.337447 TGGTTGCGGTGTAGTTAGCTC 60.337 52.381 0.00 0.00 0.00 4.09
3377 3645 4.263243 GCAAGCACCCAGGATCTTATAGAT 60.263 45.833 0.00 0.00 37.73 1.98
3540 3811 3.116551 ACCTGGCAGGAGGAGATACTATT 60.117 47.826 38.99 9.69 37.67 1.73
3612 3883 9.144298 CTTGGTCCTCCTTTGTTAGACTATATA 57.856 37.037 0.00 0.00 34.23 0.86
3613 3884 9.670442 TTGGTCCTCCTTTGTTAGACTATATAT 57.330 33.333 0.00 0.00 34.23 0.86
3684 3955 4.368315 GGAGCGGAGTCAAATTTTGTTTT 58.632 39.130 8.89 0.00 0.00 2.43
3817 4088 3.570212 ACCCCCTCAGTTGCGCTT 61.570 61.111 9.73 0.00 0.00 4.68
3832 4103 1.089920 CGCTTTAGCATTGTCAGGCT 58.910 50.000 2.29 6.37 43.94 4.58
3884 4155 6.881065 AGTGCTTGCAGTCTTCTTATGATTTA 59.119 34.615 0.00 0.00 0.00 1.40
3896 4167 5.555017 TCTTATGATTTATCCAGGCAGAGC 58.445 41.667 0.00 0.00 0.00 4.09
3995 4267 4.383010 CCCTCTTGTTTCCTTTTGCAACTT 60.383 41.667 0.00 0.00 0.00 2.66
3996 4268 4.567959 CCTCTTGTTTCCTTTTGCAACTTG 59.432 41.667 0.00 0.00 0.00 3.16
3997 4269 5.146010 TCTTGTTTCCTTTTGCAACTTGT 57.854 34.783 0.00 0.00 0.00 3.16
3998 4270 5.546526 TCTTGTTTCCTTTTGCAACTTGTT 58.453 33.333 0.00 0.00 0.00 2.83
3999 4271 5.994668 TCTTGTTTCCTTTTGCAACTTGTTT 59.005 32.000 0.00 0.00 0.00 2.83
4000 4272 6.484977 TCTTGTTTCCTTTTGCAACTTGTTTT 59.515 30.769 0.00 0.00 0.00 2.43
4001 4273 7.657761 TCTTGTTTCCTTTTGCAACTTGTTTTA 59.342 29.630 0.00 0.00 0.00 1.52
4002 4274 7.730364 TGTTTCCTTTTGCAACTTGTTTTAA 57.270 28.000 0.00 0.00 0.00 1.52
4003 4275 8.154649 TGTTTCCTTTTGCAACTTGTTTTAAA 57.845 26.923 0.00 0.00 0.00 1.52
4004 4276 8.621286 TGTTTCCTTTTGCAACTTGTTTTAAAA 58.379 25.926 0.00 0.00 0.00 1.52
4005 4277 8.897809 GTTTCCTTTTGCAACTTGTTTTAAAAC 58.102 29.630 21.66 21.66 39.33 2.43
4006 4278 7.971183 TCCTTTTGCAACTTGTTTTAAAACT 57.029 28.000 26.76 8.73 39.59 2.66
4007 4279 8.384607 TCCTTTTGCAACTTGTTTTAAAACTT 57.615 26.923 26.76 13.65 39.59 2.66
4008 4280 9.490379 TCCTTTTGCAACTTGTTTTAAAACTTA 57.510 25.926 26.76 16.10 39.59 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.187946 GTCTACAGCCGCAGCCAT 59.812 61.111 0.00 0.00 41.25 4.40
2 3 2.202810 GAGTCTACAGCCGCAGCC 60.203 66.667 0.00 0.00 41.25 4.85
3 4 2.343163 ATCGAGTCTACAGCCGCAGC 62.343 60.000 0.00 0.00 40.32 5.25
4 5 0.101399 AATCGAGTCTACAGCCGCAG 59.899 55.000 0.00 0.00 0.00 5.18
5 6 0.100682 GAATCGAGTCTACAGCCGCA 59.899 55.000 5.45 0.00 0.00 5.69
6 7 0.100682 TGAATCGAGTCTACAGCCGC 59.899 55.000 14.66 0.00 0.00 6.53
7 8 2.186076 GTTGAATCGAGTCTACAGCCG 58.814 52.381 19.75 0.00 0.00 5.52
8 9 2.166664 AGGTTGAATCGAGTCTACAGCC 59.833 50.000 24.34 12.52 33.29 4.85
9 10 3.119459 TCAGGTTGAATCGAGTCTACAGC 60.119 47.826 24.34 13.47 0.00 4.40
10 11 4.703645 TCAGGTTGAATCGAGTCTACAG 57.296 45.455 24.34 17.30 0.00 2.74
11 12 5.185056 TGAATCAGGTTGAATCGAGTCTACA 59.815 40.000 24.34 8.67 29.07 2.74
12 13 5.651530 TGAATCAGGTTGAATCGAGTCTAC 58.348 41.667 17.14 17.14 29.07 2.59
13 14 5.914898 TGAATCAGGTTGAATCGAGTCTA 57.085 39.130 14.66 3.33 29.07 2.59
14 15 4.808414 TGAATCAGGTTGAATCGAGTCT 57.192 40.909 14.66 0.00 29.07 3.24
15 16 4.093556 GGTTGAATCAGGTTGAATCGAGTC 59.906 45.833 5.80 5.80 29.07 3.36
16 17 4.003648 GGTTGAATCAGGTTGAATCGAGT 58.996 43.478 0.00 0.00 29.07 4.18
17 18 4.093998 CAGGTTGAATCAGGTTGAATCGAG 59.906 45.833 0.00 0.00 29.07 4.04
18 19 4.002982 CAGGTTGAATCAGGTTGAATCGA 58.997 43.478 0.00 0.00 29.07 3.59
19 20 3.753272 ACAGGTTGAATCAGGTTGAATCG 59.247 43.478 0.00 0.00 29.07 3.34
20 21 4.156739 GGACAGGTTGAATCAGGTTGAATC 59.843 45.833 0.00 0.00 0.00 2.52
21 22 4.082125 GGACAGGTTGAATCAGGTTGAAT 58.918 43.478 0.00 0.00 0.00 2.57
22 23 3.117701 TGGACAGGTTGAATCAGGTTGAA 60.118 43.478 0.00 0.00 0.00 2.69
23 24 2.441375 TGGACAGGTTGAATCAGGTTGA 59.559 45.455 0.00 0.00 0.00 3.18
24 25 2.862541 TGGACAGGTTGAATCAGGTTG 58.137 47.619 0.00 0.00 0.00 3.77
25 26 3.424703 CATGGACAGGTTGAATCAGGTT 58.575 45.455 0.00 0.00 0.00 3.50
26 27 2.881403 GCATGGACAGGTTGAATCAGGT 60.881 50.000 0.00 0.00 0.00 4.00
27 28 1.747355 GCATGGACAGGTTGAATCAGG 59.253 52.381 0.00 0.00 0.00 3.86
28 29 2.681848 GAGCATGGACAGGTTGAATCAG 59.318 50.000 0.00 0.00 0.00 2.90
29 30 2.040145 TGAGCATGGACAGGTTGAATCA 59.960 45.455 0.00 0.00 0.00 2.57
30 31 2.715046 TGAGCATGGACAGGTTGAATC 58.285 47.619 0.00 0.00 0.00 2.52
31 32 2.885135 TGAGCATGGACAGGTTGAAT 57.115 45.000 0.00 0.00 0.00 2.57
97 98 0.567968 CGACATAGCGCGAAACAGAG 59.432 55.000 12.10 0.00 0.00 3.35
139 173 2.248248 CCATCCCCTATCTTCTGCGTA 58.752 52.381 0.00 0.00 0.00 4.42
141 175 1.001406 GACCATCCCCTATCTTCTGCG 59.999 57.143 0.00 0.00 0.00 5.18
170 204 6.146673 GGCAACTTCTCATCAAATTGGAAAAG 59.853 38.462 0.00 0.00 0.00 2.27
176 210 3.504863 CCGGCAACTTCTCATCAAATTG 58.495 45.455 0.00 0.00 0.00 2.32
185 219 1.464997 CAAACTAGCCGGCAACTTCTC 59.535 52.381 31.54 0.00 0.00 2.87
186 220 1.523758 CAAACTAGCCGGCAACTTCT 58.476 50.000 31.54 9.39 0.00 2.85
187 221 0.109735 GCAAACTAGCCGGCAACTTC 60.110 55.000 31.54 7.31 0.00 3.01
188 222 0.537371 AGCAAACTAGCCGGCAACTT 60.537 50.000 31.54 13.12 34.23 2.66
189 223 0.537371 AAGCAAACTAGCCGGCAACT 60.537 50.000 31.54 11.17 34.23 3.16
190 224 0.387239 CAAGCAAACTAGCCGGCAAC 60.387 55.000 31.54 9.20 34.23 4.17
191 225 1.956043 CAAGCAAACTAGCCGGCAA 59.044 52.632 31.54 0.00 34.23 4.52
192 226 2.625823 GCAAGCAAACTAGCCGGCA 61.626 57.895 31.54 14.00 35.10 5.69
193 227 2.179267 GCAAGCAAACTAGCCGGC 59.821 61.111 21.89 21.89 34.23 6.13
194 228 2.877691 GGCAAGCAAACTAGCCGG 59.122 61.111 0.00 0.00 37.41 6.13
197 231 0.242017 CCAGTGGCAAGCAAACTAGC 59.758 55.000 0.00 0.00 0.00 3.42
209 243 2.325082 ATCAAACGTCGCCAGTGGC 61.325 57.895 25.07 25.07 46.75 5.01
210 244 1.227999 ACATCAAACGTCGCCAGTGG 61.228 55.000 4.20 4.20 0.00 4.00
211 245 0.586319 AACATCAAACGTCGCCAGTG 59.414 50.000 0.00 0.00 0.00 3.66
212 246 1.305201 AAACATCAAACGTCGCCAGT 58.695 45.000 0.00 0.00 0.00 4.00
213 247 2.399396 AAAACATCAAACGTCGCCAG 57.601 45.000 0.00 0.00 0.00 4.85
214 248 2.356382 AGAAAAACATCAAACGTCGCCA 59.644 40.909 0.00 0.00 0.00 5.69
215 249 2.719046 CAGAAAAACATCAAACGTCGCC 59.281 45.455 0.00 0.00 0.00 5.54
216 250 2.719046 CCAGAAAAACATCAAACGTCGC 59.281 45.455 0.00 0.00 0.00 5.19
217 251 3.947626 ACCAGAAAAACATCAAACGTCG 58.052 40.909 0.00 0.00 0.00 5.12
218 252 5.336744 TCAACCAGAAAAACATCAAACGTC 58.663 37.500 0.00 0.00 0.00 4.34
219 253 5.317733 TCAACCAGAAAAACATCAAACGT 57.682 34.783 0.00 0.00 0.00 3.99
220 254 6.475076 TGAATCAACCAGAAAAACATCAAACG 59.525 34.615 0.00 0.00 0.00 3.60
221 255 7.769272 TGAATCAACCAGAAAAACATCAAAC 57.231 32.000 0.00 0.00 0.00 2.93
222 256 7.495279 CCTTGAATCAACCAGAAAAACATCAAA 59.505 33.333 0.00 0.00 0.00 2.69
223 257 6.985645 CCTTGAATCAACCAGAAAAACATCAA 59.014 34.615 0.00 0.00 0.00 2.57
224 258 6.514947 CCTTGAATCAACCAGAAAAACATCA 58.485 36.000 0.00 0.00 0.00 3.07
225 259 5.406477 GCCTTGAATCAACCAGAAAAACATC 59.594 40.000 0.00 0.00 0.00 3.06
226 260 5.070847 AGCCTTGAATCAACCAGAAAAACAT 59.929 36.000 0.00 0.00 0.00 2.71
227 261 4.405358 AGCCTTGAATCAACCAGAAAAACA 59.595 37.500 0.00 0.00 0.00 2.83
237 271 1.508088 CCGGCAGCCTTGAATCAAC 59.492 57.895 10.54 0.00 0.00 3.18
257 292 1.373570 AATCGGCTGCAGCTAAACTC 58.626 50.000 35.82 18.44 41.70 3.01
305 340 1.348036 ACAGCAGAAGTAGTTCCACCC 59.652 52.381 6.68 0.00 32.48 4.61
307 342 3.669251 AGACAGCAGAAGTAGTTCCAC 57.331 47.619 6.68 0.00 32.48 4.02
355 390 5.391310 CGCCAAATACTAGATGATGGATTGC 60.391 44.000 0.00 0.00 0.00 3.56
356 391 5.391310 GCGCCAAATACTAGATGATGGATTG 60.391 44.000 0.00 0.00 0.00 2.67
357 392 4.697352 GCGCCAAATACTAGATGATGGATT 59.303 41.667 0.00 0.00 0.00 3.01
359 394 3.324846 AGCGCCAAATACTAGATGATGGA 59.675 43.478 2.29 0.00 0.00 3.41
360 395 3.668447 AGCGCCAAATACTAGATGATGG 58.332 45.455 2.29 0.80 0.00 3.51
361 396 6.101997 TCATAGCGCCAAATACTAGATGATG 58.898 40.000 2.29 0.00 0.00 3.07
362 397 6.153510 TCTCATAGCGCCAAATACTAGATGAT 59.846 38.462 2.29 0.00 0.00 2.45
363 398 5.476945 TCTCATAGCGCCAAATACTAGATGA 59.523 40.000 2.29 0.00 0.00 2.92
368 403 6.096673 TCATTCTCATAGCGCCAAATACTA 57.903 37.500 2.29 0.00 0.00 1.82
377 412 3.249320 TGCATCTTTCATTCTCATAGCGC 59.751 43.478 0.00 0.00 0.00 5.92
381 416 7.477494 CAACACATGCATCTTTCATTCTCATA 58.523 34.615 0.00 0.00 0.00 2.15
429 469 5.895636 CCATTCTTACATGGTAGCAACAA 57.104 39.130 0.00 0.00 39.26 2.83
542 592 1.187567 ACCAGCAAATCAAGCCCCAC 61.188 55.000 0.00 0.00 0.00 4.61
553 603 7.509318 ACATCTATACACCTAGATACCAGCAAA 59.491 37.037 0.00 0.00 36.53 3.68
585 635 6.597672 TGCACACCGTTCTTATATGAAAGAAT 59.402 34.615 13.48 2.19 44.84 2.40
650 862 3.788937 TCCAAGGCTACGTATAAACAGC 58.211 45.455 0.00 0.00 0.00 4.40
661 873 4.395231 GGTTCAACATAGTTCCAAGGCTAC 59.605 45.833 0.00 0.00 0.00 3.58
664 876 3.153919 TGGTTCAACATAGTTCCAAGGC 58.846 45.455 0.00 0.00 0.00 4.35
665 877 5.009631 TGATGGTTCAACATAGTTCCAAGG 58.990 41.667 0.00 0.00 0.00 3.61
704 923 0.322546 AAGACAAAAGGGCCGGCTAG 60.323 55.000 28.56 12.18 0.00 3.42
733 952 7.610305 ACACACAAGGAAACCTTCGATTTATAT 59.390 33.333 0.00 0.00 42.67 0.86
742 961 5.469084 CCTAGTTACACACAAGGAAACCTTC 59.531 44.000 0.00 0.00 42.67 3.46
772 998 7.868974 TCTAGATTCATGCCCATCATTATCAT 58.131 34.615 0.00 0.00 31.79 2.45
893 1124 1.223187 ACGCAGAAAAACGGGTACAG 58.777 50.000 0.00 0.00 0.00 2.74
922 1159 8.421784 TGTCAATCCTATGTAGATAAACAGGTC 58.578 37.037 0.00 0.00 31.70 3.85
949 1186 2.981805 CCTGTGATGCAAACAAATGTCG 59.018 45.455 6.99 0.00 0.00 4.35
962 1200 4.274459 GCTTGGCTACTTATTCCTGTGATG 59.726 45.833 0.00 0.00 0.00 3.07
1308 1552 7.230108 TCCTTGGAGATCTTTGCAATGATATTC 59.770 37.037 23.44 20.22 0.00 1.75
1849 2098 2.757314 TCTTGTTGCACACAATGACCAA 59.243 40.909 12.68 0.00 44.72 3.67
2736 2994 3.216800 GCCATCAACTTCCATAGCATCA 58.783 45.455 0.00 0.00 0.00 3.07
2739 2997 1.284491 TGGCCATCAACTTCCATAGCA 59.716 47.619 0.00 0.00 0.00 3.49
2748 3006 0.322277 CAGAGTGCTGGCCATCAACT 60.322 55.000 11.63 12.65 38.51 3.16
2766 3024 2.610433 CTCATACGCAGCTTCTTGTCA 58.390 47.619 0.00 0.00 0.00 3.58
2783 3041 0.255318 GGACCTAGACCTCGACCTCA 59.745 60.000 0.00 0.00 0.00 3.86
2850 3108 2.362077 GGCCTTCTTCTTTTGAGCAACA 59.638 45.455 0.00 0.00 0.00 3.33
3085 3343 7.361286 CCAGAGAAAGATTTGTTAACTAGGTGC 60.361 40.741 7.22 0.00 0.00 5.01
3213 3475 6.294176 GCAACCAATTGAGTGACTACAAGATT 60.294 38.462 7.12 0.00 38.15 2.40
3226 3488 2.151202 ACTACACCGCAACCAATTGAG 58.849 47.619 7.12 0.00 38.15 3.02
3227 3489 2.264005 ACTACACCGCAACCAATTGA 57.736 45.000 7.12 0.00 38.15 2.57
3228 3490 3.669557 GCTAACTACACCGCAACCAATTG 60.670 47.826 0.00 0.00 38.99 2.32
3229 3491 2.486592 GCTAACTACACCGCAACCAATT 59.513 45.455 0.00 0.00 0.00 2.32
3377 3645 6.872020 AGCTCGAGCAATACTTTACAAACTTA 59.128 34.615 36.87 0.00 45.16 2.24
3540 3811 5.178623 CCAGACACGAGTAAAAATGCAGTAA 59.821 40.000 0.00 0.00 0.00 2.24
3556 3827 1.294659 GAGAGCAAAGGCCAGACACG 61.295 60.000 5.01 0.00 42.56 4.49
3612 3883 3.334583 ACCATGTAGTTCAGCAACGAT 57.665 42.857 0.00 0.00 37.61 3.73
3613 3884 2.805671 CAACCATGTAGTTCAGCAACGA 59.194 45.455 0.00 0.00 37.61 3.85
3817 4088 1.630369 ACTGGAGCCTGACAATGCTAA 59.370 47.619 0.08 0.00 38.11 3.09
3832 4103 2.046009 TACCAACCGCAAGCACTGGA 62.046 55.000 10.06 0.00 34.20 3.86
3870 4141 7.379059 TCTGCCTGGATAAATCATAAGAAGA 57.621 36.000 0.00 0.00 0.00 2.87
3871 4142 6.149142 GCTCTGCCTGGATAAATCATAAGAAG 59.851 42.308 0.00 0.00 0.00 2.85
3872 4143 6.000219 GCTCTGCCTGGATAAATCATAAGAA 59.000 40.000 0.00 0.00 0.00 2.52
3873 4144 5.072193 TGCTCTGCCTGGATAAATCATAAGA 59.928 40.000 0.00 0.00 0.00 2.10
3877 4148 3.752665 CTGCTCTGCCTGGATAAATCAT 58.247 45.455 0.00 0.00 0.00 2.45
3884 4155 1.849975 AACAGCTGCTCTGCCTGGAT 61.850 55.000 15.27 0.00 46.76 3.41
3896 4167 3.737850 AGTTCCTCTTGAGAAACAGCTG 58.262 45.455 13.48 13.48 0.00 4.24


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

AutoCloner maintained by Alex Coulton.