Multiple sequence alignment - TraesCS4A01G199800

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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 TraesCS4A01G199800 chr4A 100.000 1604 0 0 1645 3248 487891513 487889910 0.000000e+00 2963.0
1 TraesCS4A01G199800 chr4A 100.000 1201 0 0 1 1201 487893157 487891957 0.000000e+00 2218.0
2 TraesCS4A01G199800 chr4A 95.745 94 2 2 2868 2960 487890198 487890290 2.020000e-32 150.0
3 TraesCS4A01G199800 chr4D 95.060 1579 45 12 1645 3197 93824918 93826489 0.000000e+00 2453.0
4 TraesCS4A01G199800 chr4D 83.886 844 46 29 306 1094 93823682 93824490 0.000000e+00 723.0
5 TraesCS4A01G199800 chr4D 89.163 203 14 2 128 322 93822685 93822887 2.500000e-61 246.0
6 TraesCS4A01G199800 chr4D 96.875 32 1 0 3198 3229 100298489 100298458 2.000000e-03 54.7
7 TraesCS4A01G199800 chr4B 93.063 1182 62 9 1645 2811 132320653 132321829 0.000000e+00 1711.0
8 TraesCS4A01G199800 chr4B 95.078 386 8 4 2823 3197 132321877 132322262 6.000000e-167 597.0
9 TraesCS4A01G199800 chr4B 85.478 544 38 16 176 701 132319472 132319992 2.220000e-146 529.0
10 TraesCS4A01G199800 chr4B 86.667 510 19 15 732 1201 132320060 132320560 1.340000e-143 520.0
11 TraesCS4A01G199800 chr4B 91.919 99 2 2 2868 2960 132322020 132321922 2.030000e-27 134.0
12 TraesCS4A01G199800 chr1D 94.915 59 3 0 1 59 414347180 414347238 3.450000e-15 93.5
13 TraesCS4A01G199800 chr2D 87.500 72 8 1 6 76 596206895 596206966 7.470000e-12 82.4
14 TraesCS4A01G199800 chr3A 90.909 55 5 0 1 55 460153088 460153034 1.250000e-09 75.0
15 TraesCS4A01G199800 chr5B 87.879 66 2 2 59 124 65090082 65090141 4.500000e-09 73.1
16 TraesCS4A01G199800 chr5B 86.154 65 2 3 61 125 578091886 578091943 2.710000e-06 63.9
17 TraesCS4A01G199800 chr3D 89.831 59 1 1 60 118 14283589 14283536 1.620000e-08 71.3
18 TraesCS4A01G199800 chr5A 89.655 58 1 1 60 117 432026797 432026849 5.810000e-08 69.4
19 TraesCS4A01G199800 chr5A 89.655 58 1 1 60 117 432030577 432030629 5.810000e-08 69.4
20 TraesCS4A01G199800 chr7B 89.474 57 1 1 60 116 721732286 721732235 2.090000e-07 67.6
21 TraesCS4A01G199800 chr6D 89.474 57 1 1 60 116 357780473 357780524 2.090000e-07 67.6
22 TraesCS4A01G199800 chr5D 89.474 57 1 1 60 116 410086688 410086739 2.090000e-07 67.6
23 TraesCS4A01G199800 chr1A 86.567 67 1 3 60 124 541726737 541726677 2.090000e-07 67.6


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 TraesCS4A01G199800 chr4A 487889910 487893157 3247 True 2590.500000 2963 100.000000 1 3248 2 chr4A.!!$R1 3247
1 TraesCS4A01G199800 chr4D 93822685 93826489 3804 False 1140.666667 2453 89.369667 128 3197 3 chr4D.!!$F1 3069
2 TraesCS4A01G199800 chr4B 132319472 132322262 2790 False 839.250000 1711 90.071500 176 3197 4 chr4B.!!$F1 3021

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
505 1331 0.044092 TGGGCACTCCTCCTCCATTA 59.956 55.0 0.0 0.0 36.2 1.90 F
988 1921 0.463474 GCAAGCAAGCAAAAACCCCA 60.463 50.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2802 1.059584 TGGTGAGCTTGGAGTTGGGA 61.060 55.000 0.00 0.0 0.00 4.37 R
2568 3509 1.002888 CTCCTGCATCAGTTGGACTGT 59.997 52.381 7.85 0.0 46.03 3.55 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
38 39 3.785859 GGCCACCGCATCTCAGGA 61.786 66.667 0.00 0.00 36.38 3.86
39 40 2.512515 GCCACCGCATCTCAGGAC 60.513 66.667 0.00 0.00 34.03 3.85
40 41 2.981302 CCACCGCATCTCAGGACA 59.019 61.111 0.00 0.00 0.00 4.02
41 42 1.448540 CCACCGCATCTCAGGACAC 60.449 63.158 0.00 0.00 0.00 3.67
42 43 1.807165 CACCGCATCTCAGGACACG 60.807 63.158 0.00 0.00 0.00 4.49
43 44 2.276116 ACCGCATCTCAGGACACGT 61.276 57.895 0.00 0.00 0.00 4.49
44 45 1.517257 CCGCATCTCAGGACACGTC 60.517 63.158 0.00 0.00 0.00 4.34
53 54 2.332514 GGACACGTCCGAACACGA 59.667 61.111 0.00 0.00 42.69 4.35
54 55 2.012948 GGACACGTCCGAACACGAC 61.013 63.158 0.00 0.00 42.69 4.34
55 56 1.009222 GACACGTCCGAACACGACT 60.009 57.895 8.27 0.00 42.69 4.18
56 57 0.593263 GACACGTCCGAACACGACTT 60.593 55.000 8.27 0.00 42.69 3.01
57 58 0.593263 ACACGTCCGAACACGACTTC 60.593 55.000 8.27 0.00 42.69 3.01
58 59 0.593008 CACGTCCGAACACGACTTCA 60.593 55.000 8.27 0.00 42.69 3.02
59 60 0.101040 ACGTCCGAACACGACTTCAA 59.899 50.000 8.27 0.00 42.69 2.69
60 61 1.202203 CGTCCGAACACGACTTCAAA 58.798 50.000 0.00 0.00 42.69 2.69
61 62 1.790623 CGTCCGAACACGACTTCAAAT 59.209 47.619 0.00 0.00 42.69 2.32
62 63 2.160013 CGTCCGAACACGACTTCAAATC 60.160 50.000 0.00 0.00 42.69 2.17
63 64 2.157085 GTCCGAACACGACTTCAAATCC 59.843 50.000 0.00 0.00 0.00 3.01
64 65 1.126113 CCGAACACGACTTCAAATCCG 59.874 52.381 0.00 0.00 0.00 4.18
65 66 2.055838 CGAACACGACTTCAAATCCGA 58.944 47.619 0.00 0.00 0.00 4.55
66 67 2.473609 CGAACACGACTTCAAATCCGAA 59.526 45.455 0.00 0.00 0.00 4.30
67 68 3.660904 CGAACACGACTTCAAATCCGAAC 60.661 47.826 0.00 0.00 0.00 3.95
68 69 2.828877 ACACGACTTCAAATCCGAACA 58.171 42.857 0.00 0.00 0.00 3.18
69 70 3.199677 ACACGACTTCAAATCCGAACAA 58.800 40.909 0.00 0.00 0.00 2.83
70 71 3.623960 ACACGACTTCAAATCCGAACAAA 59.376 39.130 0.00 0.00 0.00 2.83
71 72 4.095185 ACACGACTTCAAATCCGAACAAAA 59.905 37.500 0.00 0.00 0.00 2.44
72 73 4.436523 CACGACTTCAAATCCGAACAAAAC 59.563 41.667 0.00 0.00 0.00 2.43
73 74 3.657625 CGACTTCAAATCCGAACAAAACG 59.342 43.478 0.00 0.00 0.00 3.60
114 115 4.077184 CGCGGTGGAGTTGGCCTA 62.077 66.667 3.32 0.00 0.00 3.93
115 116 2.349755 GCGGTGGAGTTGGCCTAA 59.650 61.111 3.32 0.00 0.00 2.69
116 117 1.745489 GCGGTGGAGTTGGCCTAAG 60.745 63.158 3.32 0.00 0.00 2.18
117 118 1.980052 CGGTGGAGTTGGCCTAAGA 59.020 57.895 3.32 0.00 0.00 2.10
118 119 0.541863 CGGTGGAGTTGGCCTAAGAT 59.458 55.000 3.32 0.00 0.00 2.40
119 120 1.473434 CGGTGGAGTTGGCCTAAGATC 60.473 57.143 3.32 0.00 0.00 2.75
120 121 1.473434 GGTGGAGTTGGCCTAAGATCG 60.473 57.143 3.32 0.00 0.00 3.69
121 122 0.178068 TGGAGTTGGCCTAAGATCGC 59.822 55.000 3.32 0.00 0.00 4.58
122 123 0.466124 GGAGTTGGCCTAAGATCGCT 59.534 55.000 3.32 0.00 0.00 4.93
123 124 1.576356 GAGTTGGCCTAAGATCGCTG 58.424 55.000 3.32 0.00 0.00 5.18
124 125 0.905357 AGTTGGCCTAAGATCGCTGT 59.095 50.000 3.32 0.00 0.00 4.40
125 126 2.100916 GAGTTGGCCTAAGATCGCTGTA 59.899 50.000 3.32 0.00 0.00 2.74
126 127 2.159085 AGTTGGCCTAAGATCGCTGTAC 60.159 50.000 3.32 0.00 0.00 2.90
131 132 3.117046 GCCTAAGATCGCTGTACTGAAC 58.883 50.000 3.61 0.00 0.00 3.18
132 133 3.707793 CCTAAGATCGCTGTACTGAACC 58.292 50.000 3.61 0.00 0.00 3.62
136 137 1.132643 GATCGCTGTACTGAACCGACT 59.867 52.381 3.61 0.00 0.00 4.18
138 139 0.732880 CGCTGTACTGAACCGACTGG 60.733 60.000 3.61 0.00 42.84 4.00
265 274 4.058797 CGGCTTCCGTTTTCCTGT 57.941 55.556 0.00 0.00 42.73 4.00
290 299 2.193536 GGGTTGCGTTGAAGCTGGT 61.194 57.895 0.00 0.00 38.13 4.00
291 300 1.008538 GGTTGCGTTGAAGCTGGTG 60.009 57.895 0.00 0.00 38.13 4.17
309 318 1.264288 GTGGAAGAAAAGTGGCACTCG 59.736 52.381 22.31 0.00 0.00 4.18
374 1198 2.283529 TGTCCCTTCCACTCTCGCC 61.284 63.158 0.00 0.00 0.00 5.54
422 1248 3.821600 GAGGGTCCTTCTCTTTGTTTTCC 59.178 47.826 0.00 0.00 0.00 3.13
428 1254 3.630312 CCTTCTCTTTGTTTTCCACGGAA 59.370 43.478 0.00 0.00 0.00 4.30
439 1265 3.974871 TTCCACGGAACTTTTTGTAGC 57.025 42.857 0.00 0.00 0.00 3.58
444 1270 2.884639 ACGGAACTTTTTGTAGCAGCAT 59.115 40.909 0.00 0.00 0.00 3.79
479 1305 2.078392 GAATTTTCGTCAAGGGCCGTA 58.922 47.619 0.00 0.00 0.00 4.02
498 1324 0.399233 ATAGACCTGGGCACTCCTCC 60.399 60.000 0.47 0.00 36.20 4.30
502 1328 2.284921 CTGGGCACTCCTCCTCCA 60.285 66.667 0.00 0.00 36.20 3.86
505 1331 0.044092 TGGGCACTCCTCCTCCATTA 59.956 55.000 0.00 0.00 36.20 1.90
513 1339 3.519913 ACTCCTCCTCCATTACCACTTTC 59.480 47.826 0.00 0.00 0.00 2.62
556 1394 3.134127 GCCTCGTCCATTGCCACC 61.134 66.667 0.00 0.00 0.00 4.61
574 1412 2.435938 TGGGAAACATCGCCTCGC 60.436 61.111 0.00 0.00 0.00 5.03
603 1441 4.043168 CGTTGAAACGCCAGACCT 57.957 55.556 2.23 0.00 46.06 3.85
604 1442 1.569493 CGTTGAAACGCCAGACCTG 59.431 57.895 2.23 0.00 46.06 4.00
647 1490 7.492344 GTCAAAAGAAAAGATTCCAAAAGCTGA 59.508 33.333 0.00 0.00 36.12 4.26
651 1494 5.476254 AGAAAAGATTCCAAAAGCTGAGAGG 59.524 40.000 0.00 0.00 36.12 3.69
660 1503 4.262635 CCAAAAGCTGAGAGGTAGACTTGA 60.263 45.833 0.00 0.00 0.00 3.02
661 1504 5.300752 CAAAAGCTGAGAGGTAGACTTGAA 58.699 41.667 0.00 0.00 0.00 2.69
662 1505 5.753721 AAAGCTGAGAGGTAGACTTGAAT 57.246 39.130 0.00 0.00 0.00 2.57
719 1592 6.710597 ACACCCTATATATACGCGATGATT 57.289 37.500 15.93 0.00 0.00 2.57
792 1687 5.833667 TCGAAGTTGATACTCCATCCACTAT 59.166 40.000 0.00 0.00 38.39 2.12
813 1709 1.170290 ACCAACGCCGAGAAAAAGGG 61.170 55.000 0.00 0.00 0.00 3.95
909 1805 1.739049 CGACTCCATCCTCCTGCTC 59.261 63.158 0.00 0.00 0.00 4.26
910 1806 1.739049 GACTCCATCCTCCTGCTCG 59.261 63.158 0.00 0.00 0.00 5.03
911 1807 1.743321 GACTCCATCCTCCTGCTCGG 61.743 65.000 0.00 0.00 0.00 4.63
913 1809 3.160047 CCATCCTCCTGCTCGGCT 61.160 66.667 0.00 0.00 0.00 5.52
914 1810 2.108566 CATCCTCCTGCTCGGCTG 59.891 66.667 0.00 0.00 0.00 4.85
917 1813 4.527583 CCTCCTGCTCGGCTGCTC 62.528 72.222 0.00 0.00 0.00 4.26
918 1814 4.527583 CTCCTGCTCGGCTGCTCC 62.528 72.222 0.00 0.00 0.00 4.70
920 1816 4.834453 CCTGCTCGGCTGCTCCTG 62.834 72.222 0.00 0.00 0.00 3.86
942 1839 2.021639 TCCTCCTCCAGATCCCAAATCT 60.022 50.000 0.00 0.00 0.00 2.40
988 1921 0.463474 GCAAGCAAGCAAAAACCCCA 60.463 50.000 0.00 0.00 0.00 4.96
1788 2721 3.855853 GCCTTCTCCCTCTCCGCC 61.856 72.222 0.00 0.00 0.00 6.13
1869 2802 2.363795 TCCCTCCTCGCCGACAAT 60.364 61.111 0.00 0.00 0.00 2.71
2022 2955 3.417224 CTCGACGTCGACGGGACA 61.417 66.667 37.89 19.50 46.42 4.02
2394 3333 0.804364 TGATGTGGTGATTTGCGAGC 59.196 50.000 0.00 0.00 0.00 5.03
2412 3351 4.969816 CGAGCTTGAAAATATGGTCGTTT 58.030 39.130 0.00 0.00 42.83 3.60
2413 3352 4.788100 CGAGCTTGAAAATATGGTCGTTTG 59.212 41.667 0.00 0.00 42.83 2.93
2414 3353 4.485163 AGCTTGAAAATATGGTCGTTTGC 58.515 39.130 0.00 0.00 0.00 3.68
2426 3365 1.100463 TCGTTTGCTGCAGCCTTGAA 61.100 50.000 34.64 19.97 41.18 2.69
2454 3393 1.798626 CCAGATGGAGAGATGGGTCA 58.201 55.000 0.00 0.00 37.39 4.02
2486 3427 0.179048 TGAAGGAGTGTGGCTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
2528 3469 2.494059 AGTGAATTGTCAACGGGAGTG 58.506 47.619 0.00 0.00 46.69 3.51
2823 3786 1.410850 CCATCCCCGTATGAGCTGGT 61.411 60.000 0.00 0.00 0.00 4.00
2824 3787 0.469917 CATCCCCGTATGAGCTGGTT 59.530 55.000 0.00 0.00 0.00 3.67
2825 3788 1.134098 CATCCCCGTATGAGCTGGTTT 60.134 52.381 0.00 0.00 0.00 3.27
2826 3789 0.251916 TCCCCGTATGAGCTGGTTTG 59.748 55.000 0.00 0.00 0.00 2.93
2827 3790 0.035439 CCCCGTATGAGCTGGTTTGT 60.035 55.000 0.00 0.00 0.00 2.83
2912 3904 8.731275 TTCTCAGTCATTTTAGAGACAACAAA 57.269 30.769 0.00 0.00 36.90 2.83
3032 4039 9.168553 TCTAGCTATAGTTTAGGTCCTAGAAGA 57.831 37.037 0.84 0.00 30.32 2.87
3139 4151 2.978156 ATTCCGCATATGGGATTGGT 57.022 45.000 20.56 0.16 32.58 3.67
3144 4156 5.708736 TCCGCATATGGGATTGGTTATAT 57.291 39.130 20.56 0.00 0.00 0.86
3165 4177 9.719355 TTATATCAGTAGCAGTGAACTTTTGAA 57.281 29.630 0.00 0.00 30.32 2.69
3197 4209 6.723298 ACCAGAGATAGAACTACATGAAGG 57.277 41.667 0.00 0.00 0.00 3.46
3198 4210 6.436027 ACCAGAGATAGAACTACATGAAGGA 58.564 40.000 0.00 0.00 0.00 3.36
3199 4211 6.549364 ACCAGAGATAGAACTACATGAAGGAG 59.451 42.308 0.00 0.00 0.00 3.69
3200 4212 6.775142 CCAGAGATAGAACTACATGAAGGAGA 59.225 42.308 0.00 0.00 0.00 3.71
3201 4213 7.286546 CCAGAGATAGAACTACATGAAGGAGAA 59.713 40.741 0.00 0.00 0.00 2.87
3202 4214 8.352201 CAGAGATAGAACTACATGAAGGAGAAG 58.648 40.741 0.00 0.00 0.00 2.85
3203 4215 8.058847 AGAGATAGAACTACATGAAGGAGAAGT 58.941 37.037 0.00 0.00 0.00 3.01
3204 4216 8.006298 AGATAGAACTACATGAAGGAGAAGTG 57.994 38.462 0.00 0.00 0.00 3.16
3205 4217 4.826556 AGAACTACATGAAGGAGAAGTGC 58.173 43.478 0.00 0.00 0.00 4.40
3206 4218 4.284490 AGAACTACATGAAGGAGAAGTGCA 59.716 41.667 0.00 0.00 0.00 4.57
3207 4219 4.833478 ACTACATGAAGGAGAAGTGCAT 57.167 40.909 0.00 0.00 0.00 3.96
3208 4220 4.511527 ACTACATGAAGGAGAAGTGCATG 58.488 43.478 0.00 0.00 41.44 4.06
3209 4221 2.719739 ACATGAAGGAGAAGTGCATGG 58.280 47.619 0.00 0.00 40.34 3.66
3210 4222 2.306805 ACATGAAGGAGAAGTGCATGGA 59.693 45.455 0.00 0.00 40.34 3.41
3211 4223 3.053842 ACATGAAGGAGAAGTGCATGGAT 60.054 43.478 0.00 0.00 40.34 3.41
3212 4224 2.995283 TGAAGGAGAAGTGCATGGATG 58.005 47.619 0.00 0.00 0.00 3.51
3213 4225 2.573009 TGAAGGAGAAGTGCATGGATGA 59.427 45.455 0.00 0.00 0.00 2.92
3214 4226 3.009363 TGAAGGAGAAGTGCATGGATGAA 59.991 43.478 0.00 0.00 0.00 2.57
3215 4227 2.996631 AGGAGAAGTGCATGGATGAAC 58.003 47.619 0.00 0.00 36.55 3.18
3216 4228 2.019984 GGAGAAGTGCATGGATGAACC 58.980 52.381 0.00 0.00 37.01 3.62
3217 4229 2.019984 GAGAAGTGCATGGATGAACCC 58.980 52.381 0.00 0.00 37.01 4.11
3218 4230 0.734889 GAAGTGCATGGATGAACCCG 59.265 55.000 0.00 0.00 37.01 5.28
3219 4231 0.680921 AAGTGCATGGATGAACCCGG 60.681 55.000 0.00 0.00 37.01 5.73
3220 4232 2.120909 GTGCATGGATGAACCCGGG 61.121 63.158 22.25 22.25 38.00 5.73
3221 4233 2.275418 GCATGGATGAACCCGGGT 59.725 61.111 24.16 24.16 38.00 5.28
3222 4234 2.120909 GCATGGATGAACCCGGGTG 61.121 63.158 31.05 13.54 38.00 4.61
3223 4235 2.120909 CATGGATGAACCCGGGTGC 61.121 63.158 31.05 28.67 38.00 5.01
3224 4236 2.611505 ATGGATGAACCCGGGTGCA 61.612 57.895 36.92 36.92 38.16 4.57
3225 4237 2.438434 GGATGAACCCGGGTGCAG 60.438 66.667 37.21 6.80 37.05 4.41
3226 4238 2.668632 GATGAACCCGGGTGCAGA 59.331 61.111 37.21 17.67 37.05 4.26
3227 4239 1.224592 GATGAACCCGGGTGCAGAT 59.775 57.895 37.21 23.78 37.05 2.90
3228 4240 1.077501 ATGAACCCGGGTGCAGATG 60.078 57.895 37.21 4.30 37.05 2.90
3229 4241 3.134127 GAACCCGGGTGCAGATGC 61.134 66.667 31.05 7.10 42.50 3.91
3230 4242 4.740822 AACCCGGGTGCAGATGCC 62.741 66.667 31.05 0.00 41.18 4.40
3247 4259 3.131478 CCCCGTGGGCAAATCGTC 61.131 66.667 0.00 0.00 35.35 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.785859 TCCTGAGATGCGGTGGCC 61.786 66.667 0.00 0.00 38.85 5.36
22 23 2.512515 GTCCTGAGATGCGGTGGC 60.513 66.667 0.00 0.00 40.52 5.01
23 24 1.448540 GTGTCCTGAGATGCGGTGG 60.449 63.158 0.00 0.00 0.00 4.61
24 25 1.807165 CGTGTCCTGAGATGCGGTG 60.807 63.158 0.00 0.00 0.00 4.94
25 26 2.214181 GACGTGTCCTGAGATGCGGT 62.214 60.000 0.00 0.00 0.00 5.68
26 27 1.517257 GACGTGTCCTGAGATGCGG 60.517 63.158 0.00 0.00 0.00 5.69
27 28 1.517257 GGACGTGTCCTGAGATGCG 60.517 63.158 11.81 0.00 46.16 4.73
28 29 4.504132 GGACGTGTCCTGAGATGC 57.496 61.111 11.81 0.00 46.16 3.91
36 37 2.012948 GTCGTGTTCGGACGTGTCC 61.013 63.158 9.04 9.04 46.18 4.02
37 38 0.593263 AAGTCGTGTTCGGACGTGTC 60.593 55.000 0.00 0.00 40.34 3.67
38 39 0.593263 GAAGTCGTGTTCGGACGTGT 60.593 55.000 0.00 0.00 40.34 4.49
39 40 0.593008 TGAAGTCGTGTTCGGACGTG 60.593 55.000 0.00 0.00 40.34 4.49
40 41 0.101040 TTGAAGTCGTGTTCGGACGT 59.899 50.000 0.00 0.00 40.34 4.34
41 42 1.202203 TTTGAAGTCGTGTTCGGACG 58.798 50.000 0.00 0.00 40.83 4.79
42 43 2.157085 GGATTTGAAGTCGTGTTCGGAC 59.843 50.000 0.00 0.00 37.69 4.79
43 44 2.409975 GGATTTGAAGTCGTGTTCGGA 58.590 47.619 0.00 0.00 37.69 4.55
44 45 1.126113 CGGATTTGAAGTCGTGTTCGG 59.874 52.381 0.00 0.00 37.69 4.30
45 46 2.055838 TCGGATTTGAAGTCGTGTTCG 58.944 47.619 0.00 0.00 38.55 3.95
46 47 3.246699 TGTTCGGATTTGAAGTCGTGTTC 59.753 43.478 0.00 0.00 0.00 3.18
47 48 3.199677 TGTTCGGATTTGAAGTCGTGTT 58.800 40.909 0.00 0.00 0.00 3.32
48 49 2.828877 TGTTCGGATTTGAAGTCGTGT 58.171 42.857 0.00 0.00 0.00 4.49
49 50 3.870723 TTGTTCGGATTTGAAGTCGTG 57.129 42.857 0.00 0.00 0.00 4.35
50 51 4.594136 GTTTTGTTCGGATTTGAAGTCGT 58.406 39.130 0.00 0.00 0.00 4.34
51 52 3.657625 CGTTTTGTTCGGATTTGAAGTCG 59.342 43.478 0.00 0.00 0.00 4.18
73 74 1.808390 CGATCCCAAACGGACGTCC 60.808 63.158 25.28 25.28 46.09 4.79
74 75 2.450345 GCGATCCCAAACGGACGTC 61.450 63.158 7.13 7.13 46.09 4.34
75 76 2.433664 GCGATCCCAAACGGACGT 60.434 61.111 0.00 0.00 46.09 4.34
76 77 3.550992 CGCGATCCCAAACGGACG 61.551 66.667 0.00 0.00 46.09 4.79
77 78 3.861263 GCGCGATCCCAAACGGAC 61.861 66.667 12.10 0.00 46.09 4.79
97 98 3.599285 TTAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
98 99 1.745489 CTTAGGCCAACTCCACCGC 60.745 63.158 5.01 0.00 0.00 5.68
99 100 0.541863 ATCTTAGGCCAACTCCACCG 59.458 55.000 5.01 0.00 0.00 4.94
100 101 1.473434 CGATCTTAGGCCAACTCCACC 60.473 57.143 5.01 0.00 0.00 4.61
101 102 1.941325 CGATCTTAGGCCAACTCCAC 58.059 55.000 5.01 0.00 0.00 4.02
102 103 0.178068 GCGATCTTAGGCCAACTCCA 59.822 55.000 5.01 0.00 0.00 3.86
103 104 0.466124 AGCGATCTTAGGCCAACTCC 59.534 55.000 5.01 0.00 0.00 3.85
104 105 1.134670 ACAGCGATCTTAGGCCAACTC 60.135 52.381 5.01 0.00 0.00 3.01
105 106 0.905357 ACAGCGATCTTAGGCCAACT 59.095 50.000 5.01 0.00 0.00 3.16
106 107 2.159085 AGTACAGCGATCTTAGGCCAAC 60.159 50.000 5.01 0.00 0.00 3.77
107 108 2.108168 AGTACAGCGATCTTAGGCCAA 58.892 47.619 5.01 0.00 0.00 4.52
108 109 1.409064 CAGTACAGCGATCTTAGGCCA 59.591 52.381 5.01 0.00 0.00 5.36
109 110 1.681793 TCAGTACAGCGATCTTAGGCC 59.318 52.381 0.00 0.00 0.00 5.19
110 111 3.117046 GTTCAGTACAGCGATCTTAGGC 58.883 50.000 0.00 0.00 0.00 3.93
111 112 3.707793 GGTTCAGTACAGCGATCTTAGG 58.292 50.000 0.00 0.00 0.00 2.69
112 113 3.064958 TCGGTTCAGTACAGCGATCTTAG 59.935 47.826 2.27 0.00 39.14 2.18
113 114 3.011818 TCGGTTCAGTACAGCGATCTTA 58.988 45.455 2.27 0.00 39.14 2.10
114 115 1.816835 TCGGTTCAGTACAGCGATCTT 59.183 47.619 2.27 0.00 39.14 2.40
115 116 1.132643 GTCGGTTCAGTACAGCGATCT 59.867 52.381 8.87 0.00 45.15 2.75
116 117 1.132643 AGTCGGTTCAGTACAGCGATC 59.867 52.381 8.87 4.31 45.15 3.69
117 118 1.135373 CAGTCGGTTCAGTACAGCGAT 60.135 52.381 8.87 0.00 45.15 4.58
118 119 0.240145 CAGTCGGTTCAGTACAGCGA 59.760 55.000 2.27 2.27 41.62 4.93
119 120 0.732880 CCAGTCGGTTCAGTACAGCG 60.733 60.000 0.00 0.00 36.47 5.18
120 121 0.317479 ACCAGTCGGTTCAGTACAGC 59.683 55.000 0.00 0.00 46.31 4.40
121 122 1.336887 CCACCAGTCGGTTCAGTACAG 60.337 57.143 0.00 0.00 46.31 2.74
122 123 0.677288 CCACCAGTCGGTTCAGTACA 59.323 55.000 0.00 0.00 46.31 2.90
123 124 0.963962 TCCACCAGTCGGTTCAGTAC 59.036 55.000 0.00 0.00 46.31 2.73
124 125 1.548719 CATCCACCAGTCGGTTCAGTA 59.451 52.381 0.00 0.00 46.31 2.74
125 126 0.321671 CATCCACCAGTCGGTTCAGT 59.678 55.000 0.00 0.00 46.31 3.41
126 127 0.608130 TCATCCACCAGTCGGTTCAG 59.392 55.000 0.00 0.00 46.31 3.02
131 132 1.806542 CTTTTGTCATCCACCAGTCGG 59.193 52.381 0.00 0.00 38.77 4.79
132 133 1.806542 CCTTTTGTCATCCACCAGTCG 59.193 52.381 0.00 0.00 0.00 4.18
136 137 2.040278 CCTCTCCTTTTGTCATCCACCA 59.960 50.000 0.00 0.00 0.00 4.17
138 139 3.261897 TCTCCTCTCCTTTTGTCATCCAC 59.738 47.826 0.00 0.00 0.00 4.02
142 143 4.787534 AGGATTCTCCTCTCCTTTTGTCAT 59.212 41.667 0.00 0.00 45.66 3.06
256 265 1.362355 CCCGCACCAACAGGAAAAC 59.638 57.895 0.00 0.00 0.00 2.43
265 274 3.893763 CAACGCAACCCGCACCAA 61.894 61.111 0.00 0.00 42.60 3.67
290 299 1.593196 CGAGTGCCACTTTTCTTCCA 58.407 50.000 0.00 0.00 0.00 3.53
291 300 0.238553 GCGAGTGCCACTTTTCTTCC 59.761 55.000 0.00 0.00 33.98 3.46
309 318 1.078143 AGCGGTGAAAGGGATGAGC 60.078 57.895 0.00 0.00 0.00 4.26
374 1198 0.311165 ACGGTGAAGACGTGACTCAG 59.689 55.000 0.00 0.00 43.78 3.35
422 1248 2.032799 TGCTGCTACAAAAAGTTCCGTG 59.967 45.455 0.00 0.00 0.00 4.94
428 1254 7.413438 CGAATCTTCTATGCTGCTACAAAAAGT 60.413 37.037 0.00 0.00 0.00 2.66
439 1265 2.034685 TCCGTCCGAATCTTCTATGCTG 59.965 50.000 0.00 0.00 0.00 4.41
444 1270 4.802039 CGAAAATTCCGTCCGAATCTTCTA 59.198 41.667 0.00 0.00 40.47 2.10
479 1305 0.399233 GGAGGAGTGCCCAGGTCTAT 60.399 60.000 0.00 0.00 37.41 1.98
556 1394 2.464459 GCGAGGCGATGTTTCCCAG 61.464 63.158 0.00 0.00 0.00 4.45
601 1439 1.003718 GACAGGAACCGGAACCAGG 60.004 63.158 9.46 9.83 0.00 4.45
602 1440 1.374252 CGACAGGAACCGGAACCAG 60.374 63.158 9.46 10.50 0.00 4.00
603 1441 2.738480 CGACAGGAACCGGAACCA 59.262 61.111 9.46 0.00 0.00 3.67
612 1450 4.519213 TCTTTTCTTTTGACCGACAGGAA 58.481 39.130 0.00 0.00 41.02 3.36
647 1490 6.181908 AGACTCGTAATTCAAGTCTACCTCT 58.818 40.000 12.97 0.00 45.97 3.69
719 1592 3.260740 CCGCGTTGGTACTATTGGTAAA 58.739 45.455 4.92 0.00 31.56 2.01
754 1649 4.847516 TCGATTCTCCACGCCGCG 62.848 66.667 12.14 12.14 0.00 6.46
792 1687 1.874872 CCTTTTTCTCGGCGTTGGTTA 59.125 47.619 6.85 0.00 0.00 2.85
832 1728 0.109319 GTGGGTTGGCGTAAATGCAG 60.109 55.000 0.00 0.00 36.28 4.41
867 1763 2.652095 TAGAAACGGCGGTGGAGGG 61.652 63.158 13.24 0.00 0.00 4.30
868 1764 1.447314 GTAGAAACGGCGGTGGAGG 60.447 63.158 13.24 0.00 0.00 4.30
869 1765 1.447314 GGTAGAAACGGCGGTGGAG 60.447 63.158 13.24 0.00 0.00 3.86
870 1766 2.658422 GGTAGAAACGGCGGTGGA 59.342 61.111 13.24 0.00 0.00 4.02
909 1805 4.154347 GGAGGACAGGAGCAGCCG 62.154 72.222 0.00 0.00 43.43 5.52
910 1806 2.686835 AGGAGGACAGGAGCAGCC 60.687 66.667 0.00 0.00 0.00 4.85
911 1807 2.730524 GGAGGAGGACAGGAGCAGC 61.731 68.421 0.00 0.00 0.00 5.25
913 1809 1.305633 CTGGAGGAGGACAGGAGCA 60.306 63.158 0.00 0.00 0.00 4.26
914 1810 0.398381 ATCTGGAGGAGGACAGGAGC 60.398 60.000 0.00 0.00 35.47 4.70
916 1812 0.263172 GGATCTGGAGGAGGACAGGA 59.737 60.000 0.00 0.00 35.47 3.86
917 1813 0.762461 GGGATCTGGAGGAGGACAGG 60.762 65.000 0.00 0.00 35.47 4.00
918 1814 0.031716 TGGGATCTGGAGGAGGACAG 60.032 60.000 0.00 0.00 36.07 3.51
920 1816 1.584724 TTTGGGATCTGGAGGAGGAC 58.415 55.000 0.00 0.00 0.00 3.85
942 1839 2.833582 GAGGGAGGCGACGATGGA 60.834 66.667 0.00 0.00 0.00 3.41
965 1879 2.278854 GGTTTTTGCTTGCTTGCTTGA 58.721 42.857 3.47 0.00 0.00 3.02
1854 2787 2.107141 GGATTGTCGGCGAGGAGG 59.893 66.667 11.20 0.00 0.00 4.30
1869 2802 1.059584 TGGTGAGCTTGGAGTTGGGA 61.060 55.000 0.00 0.00 0.00 4.37
1984 2917 4.373116 GAAGGCGAGCGTGGTGGA 62.373 66.667 0.00 0.00 0.00 4.02
2061 2994 4.358841 TCCATGGTGCCCCCGTTG 62.359 66.667 12.58 0.00 35.15 4.10
2394 3333 4.324402 GCAGCAAACGACCATATTTTCAAG 59.676 41.667 0.00 0.00 0.00 3.02
2412 3351 1.330234 TCAAATTCAAGGCTGCAGCA 58.670 45.000 37.63 19.39 44.36 4.41
2413 3352 2.667473 ATCAAATTCAAGGCTGCAGC 57.333 45.000 30.88 30.88 41.14 5.25
2414 3353 2.671396 GCAATCAAATTCAAGGCTGCAG 59.329 45.455 10.11 10.11 0.00 4.41
2426 3365 4.515028 TCTCTCCATCTGGCAATCAAAT 57.485 40.909 0.00 0.00 34.44 2.32
2454 3393 4.956075 ACACTCCTTCAAGTTGACCATTTT 59.044 37.500 4.68 0.00 0.00 1.82
2486 3427 7.813148 TCACTTCAACACTATAGTAAGACTTGC 59.187 37.037 16.53 0.00 0.00 4.01
2568 3509 1.002888 CTCCTGCATCAGTTGGACTGT 59.997 52.381 7.85 0.00 46.03 3.55
2729 3672 9.615660 AGGATGATAGTGGATTATTAACTGGTA 57.384 33.333 0.00 0.00 0.00 3.25
2730 3673 8.511748 AGGATGATAGTGGATTATTAACTGGT 57.488 34.615 0.00 0.00 0.00 4.00
2731 3674 9.799106 AAAGGATGATAGTGGATTATTAACTGG 57.201 33.333 0.00 0.00 0.00 4.00
2758 3708 8.961294 AGATAATCTCCTTCTCTTGAAACATG 57.039 34.615 0.00 0.00 0.00 3.21
2790 3740 6.894339 ACGGGGATGGATTGTATTATTTTC 57.106 37.500 0.00 0.00 0.00 2.29
2827 3790 1.371467 ATGGAGTGGATGTTGGTCCA 58.629 50.000 0.00 0.00 45.78 4.02
2912 3904 7.933577 TCTCAGTCATTTTAGAGACAACAACAT 59.066 33.333 0.00 0.00 37.23 2.71
3139 4151 9.719355 TTCAAAAGTTCACTGCTACTGATATAA 57.281 29.630 0.00 0.00 0.00 0.98
3144 4156 5.277974 GCATTCAAAAGTTCACTGCTACTGA 60.278 40.000 0.00 0.00 0.00 3.41
3165 4177 3.920231 TCTATCTCTGGTTTGCAGCAT 57.080 42.857 0.00 0.00 0.00 3.79
3197 4209 2.019984 GGGTTCATCCATGCACTTCTC 58.980 52.381 0.00 0.00 38.11 2.87
3198 4210 1.679944 CGGGTTCATCCATGCACTTCT 60.680 52.381 0.00 0.00 38.11 2.85
3199 4211 0.734889 CGGGTTCATCCATGCACTTC 59.265 55.000 0.00 0.00 38.11 3.01
3200 4212 0.680921 CCGGGTTCATCCATGCACTT 60.681 55.000 0.00 0.00 38.11 3.16
3201 4213 1.077501 CCGGGTTCATCCATGCACT 60.078 57.895 0.00 0.00 38.11 4.40
3202 4214 2.120909 CCCGGGTTCATCCATGCAC 61.121 63.158 14.18 0.00 38.11 4.57
3203 4215 2.275089 CCCGGGTTCATCCATGCA 59.725 61.111 14.18 0.00 38.11 3.96
3204 4216 2.120909 CACCCGGGTTCATCCATGC 61.121 63.158 27.83 0.00 38.11 4.06
3205 4217 2.120909 GCACCCGGGTTCATCCATG 61.121 63.158 27.83 11.75 38.11 3.66
3206 4218 2.275418 GCACCCGGGTTCATCCAT 59.725 61.111 27.83 0.00 38.11 3.41
3207 4219 3.253061 TGCACCCGGGTTCATCCA 61.253 61.111 27.83 13.40 38.11 3.41
3208 4220 2.270874 ATCTGCACCCGGGTTCATCC 62.271 60.000 26.70 11.72 0.00 3.51
3209 4221 1.097547 CATCTGCACCCGGGTTCATC 61.098 60.000 26.70 14.86 0.00 2.92
3210 4222 1.077501 CATCTGCACCCGGGTTCAT 60.078 57.895 26.70 10.19 0.00 2.57
3211 4223 2.350895 CATCTGCACCCGGGTTCA 59.649 61.111 27.83 26.22 0.00 3.18
3212 4224 3.134127 GCATCTGCACCCGGGTTC 61.134 66.667 27.83 22.19 41.59 3.62
3213 4225 4.740822 GGCATCTGCACCCGGGTT 62.741 66.667 27.83 6.04 44.36 4.11


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

AutoCloner maintained by Alex Coulton.