Multiple sequence alignment - TraesCS6D01G320800

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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 TraesCS6D01G320800 chr6D 100.000 3713 0 0 1 3713 428896864 428893152 0.000000e+00 6857.0
1 TraesCS6D01G320800 chr6D 84.615 91 13 1 1553 1642 428895111 428895021 5.110000e-14 89.8
2 TraesCS6D01G320800 chr6D 84.615 91 13 1 1754 1844 428895312 428895223 5.110000e-14 89.8
3 TraesCS6D01G320800 chr6D 88.136 59 5 1 3600 3658 305610384 305610328 6.650000e-08 69.4
4 TraesCS6D01G320800 chr6A 90.615 1790 117 24 1314 3076 573481105 573479340 0.000000e+00 2327.0
5 TraesCS6D01G320800 chr6A 90.431 1160 69 24 180 1309 573482694 573481547 0.000000e+00 1489.0
6 TraesCS6D01G320800 chr6A 91.153 373 28 2 3173 3545 573479120 573478753 5.540000e-138 501.0
7 TraesCS6D01G320800 chr6A 91.250 160 11 1 3545 3701 573478687 573478528 8.080000e-52 215.0
8 TraesCS6D01G320800 chr6A 90.411 73 7 0 3103 3175 573479339 573479267 3.050000e-16 97.1
9 TraesCS6D01G320800 chr6B 90.453 1016 69 13 2177 3175 645481408 645480404 0.000000e+00 1314.0
10 TraesCS6D01G320800 chr6B 93.563 870 48 5 1314 2180 645482384 645481520 0.000000e+00 1290.0
11 TraesCS6D01G320800 chr6B 85.972 1219 96 30 130 1313 645483880 645482702 0.000000e+00 1234.0
12 TraesCS6D01G320800 chr6B 85.315 143 8 1 3173 3315 645480246 645480117 6.470000e-28 135.0
13 TraesCS6D01G320800 chr6B 89.109 101 9 1 1 99 645484238 645484138 1.400000e-24 124.0
14 TraesCS6D01G320800 chr6B 88.350 103 10 1 3556 3658 470919904 470920004 5.040000e-24 122.0
15 TraesCS6D01G320800 chr6B 78.173 197 23 11 1754 1936 645482149 645481959 1.410000e-19 108.0
16 TraesCS6D01G320800 chr6B 84.615 91 13 1 1553 1642 645481947 645481857 5.110000e-14 89.8


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 TraesCS6D01G320800 chr6D 428893152 428896864 3712 True 2345.533333 6857 89.743333 1 3713 3 chr6D.!!$R2 3712
1 TraesCS6D01G320800 chr6A 573478528 573482694 4166 True 925.820000 2327 90.772000 180 3701 5 chr6A.!!$R1 3521
2 TraesCS6D01G320800 chr6B 645480117 645484238 4121 True 613.542857 1314 86.742857 1 3315 7 chr6B.!!$R1 3314

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
935 1193 0.107703 TCCCATTTGCTGCTACTCCG 60.108 55.000 0.0 0.0 0.0 4.63 F
1684 2407 1.068127 GGATTCCTGGATTGCACATGC 59.932 52.381 0.0 0.0 42.5 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2525 3381 0.038159 GACCACCTGTCTCCGACAAG 60.038 60.0 0.00 0.00 42.26 3.16 R
3156 4021 0.032130 TGATAAGATCCGAGGCGCAC 59.968 55.0 10.83 0.96 0.00 5.34 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
49 52 5.778862 ACAAAATTAGGATTTGTTGGACGG 58.221 37.500 0.00 0.00 45.97 4.79
54 57 3.154827 AGGATTTGTTGGACGGACATT 57.845 42.857 0.00 0.00 0.00 2.71
58 61 4.698304 GGATTTGTTGGACGGACATTAGAA 59.302 41.667 0.00 0.00 0.00 2.10
67 70 4.873827 GGACGGACATTAGAACATAGCAAA 59.126 41.667 0.00 0.00 0.00 3.68
75 78 8.737168 ACATTAGAACATAGCAAAGCTTCATA 57.263 30.769 0.00 0.00 40.44 2.15
76 79 9.177608 ACATTAGAACATAGCAAAGCTTCATAA 57.822 29.630 0.00 0.00 40.44 1.90
82 85 1.185315 GCAAAGCTTCATAAGGGCCA 58.815 50.000 6.18 0.00 0.00 5.36
115 118 4.874533 CCCCTCCCGACCCCCTAC 62.875 77.778 0.00 0.00 0.00 3.18
116 119 4.084147 CCCTCCCGACCCCCTACA 62.084 72.222 0.00 0.00 0.00 2.74
117 120 2.285868 CCTCCCGACCCCCTACAT 59.714 66.667 0.00 0.00 0.00 2.29
118 121 1.384082 CCTCCCGACCCCCTACATT 60.384 63.158 0.00 0.00 0.00 2.71
119 122 0.986550 CCTCCCGACCCCCTACATTT 60.987 60.000 0.00 0.00 0.00 2.32
120 123 0.916809 CTCCCGACCCCCTACATTTT 59.083 55.000 0.00 0.00 0.00 1.82
121 124 1.283905 CTCCCGACCCCCTACATTTTT 59.716 52.381 0.00 0.00 0.00 1.94
144 374 6.745159 TTTGCAGTTGTGTAAAACTAGTCA 57.255 33.333 0.00 0.00 38.34 3.41
148 378 6.710295 TGCAGTTGTGTAAAACTAGTCATGAT 59.290 34.615 0.00 0.00 38.34 2.45
161 391 8.839310 AACTAGTCATGATATTTGGAGTATGC 57.161 34.615 0.00 0.00 0.00 3.14
174 404 5.164620 TGGAGTATGCAAGTGATTGAAGA 57.835 39.130 0.00 0.00 28.48 2.87
175 405 5.559770 TGGAGTATGCAAGTGATTGAAGAA 58.440 37.500 0.00 0.00 28.48 2.52
176 406 6.182627 TGGAGTATGCAAGTGATTGAAGAAT 58.817 36.000 0.00 0.00 28.48 2.40
177 407 6.317140 TGGAGTATGCAAGTGATTGAAGAATC 59.683 38.462 0.00 0.00 34.45 2.52
178 408 6.317140 GGAGTATGCAAGTGATTGAAGAATCA 59.683 38.462 0.00 0.00 44.73 2.57
245 475 2.677875 CTGGCCCCTCCTTGTTGC 60.678 66.667 0.00 0.00 35.26 4.17
246 476 3.185203 TGGCCCCTCCTTGTTGCT 61.185 61.111 0.00 0.00 35.26 3.91
291 521 0.456221 AACAGTACGAGGCGGATCTG 59.544 55.000 0.00 0.00 0.00 2.90
300 530 0.905357 AGGCGGATCTGCTAAACTGT 59.095 50.000 25.27 0.14 34.52 3.55
475 705 2.442188 GCGCGTCAACCGGAGTAAG 61.442 63.158 9.46 0.00 36.94 2.34
489 719 0.107831 AGTAAGCAAACACCGCCTGA 59.892 50.000 0.00 0.00 0.00 3.86
490 720 0.948678 GTAAGCAAACACCGCCTGAA 59.051 50.000 0.00 0.00 0.00 3.02
507 737 1.973515 TGAAGGCTCAAGAGAGAAGCA 59.026 47.619 0.32 0.00 44.98 3.91
509 739 1.935799 AGGCTCAAGAGAGAAGCAGA 58.064 50.000 0.32 0.00 44.98 4.26
511 741 1.824230 GGCTCAAGAGAGAAGCAGAGA 59.176 52.381 0.32 0.00 44.98 3.10
512 742 2.417243 GGCTCAAGAGAGAAGCAGAGAC 60.417 54.545 0.32 0.00 44.98 3.36
523 753 2.049185 GCAGAGACGAGGAGAGGCA 61.049 63.158 0.00 0.00 0.00 4.75
570 800 1.674651 GGGCTTGACGGGGAAGAAC 60.675 63.158 0.00 0.00 0.00 3.01
795 1032 1.374758 GCTGAGTTGACGACCTGGG 60.375 63.158 0.00 0.00 0.00 4.45
833 1085 1.463444 GCCCACGTAATCTTGACACAC 59.537 52.381 0.00 0.00 0.00 3.82
834 1086 2.761559 CCCACGTAATCTTGACACACA 58.238 47.619 0.00 0.00 0.00 3.72
835 1087 3.334691 CCCACGTAATCTTGACACACAT 58.665 45.455 0.00 0.00 0.00 3.21
836 1088 3.125146 CCCACGTAATCTTGACACACATG 59.875 47.826 0.00 0.00 0.00 3.21
842 1094 2.282110 TTGACACACATGGGGCCG 60.282 61.111 0.00 0.00 0.00 6.13
874 1126 2.361737 GGCCCACCAGAAGAAGCC 60.362 66.667 0.00 0.00 35.26 4.35
876 1128 2.356667 CCCACCAGAAGAAGCCCC 59.643 66.667 0.00 0.00 0.00 5.80
927 1183 1.755783 GCTCCCCTCCCATTTGCTG 60.756 63.158 0.00 0.00 0.00 4.41
930 1186 0.918799 TCCCCTCCCATTTGCTGCTA 60.919 55.000 0.00 0.00 0.00 3.49
933 1191 1.673168 CCTCCCATTTGCTGCTACTC 58.327 55.000 0.00 0.00 0.00 2.59
935 1193 0.107703 TCCCATTTGCTGCTACTCCG 60.108 55.000 0.00 0.00 0.00 4.63
941 1199 2.889503 GCTGCTACTCCGCTGCTG 60.890 66.667 7.29 0.00 46.98 4.41
978 1245 5.785940 AGGCTAGGGTTTATCTTCGGATTAT 59.214 40.000 0.00 0.00 36.01 1.28
979 1246 6.272558 AGGCTAGGGTTTATCTTCGGATTATT 59.727 38.462 0.00 0.00 36.01 1.40
980 1247 7.456902 AGGCTAGGGTTTATCTTCGGATTATTA 59.543 37.037 0.00 0.00 36.01 0.98
986 1253 6.643770 GGTTTATCTTCGGATTATTACGAGCA 59.356 38.462 0.00 0.00 40.51 4.26
1237 1508 4.373116 TGGTTCTCGTGCGCCCTC 62.373 66.667 4.18 0.00 0.00 4.30
1245 1516 2.813179 CGTGCGCCCTCTTACATGC 61.813 63.158 4.18 0.00 0.00 4.06
1267 1541 3.452755 CATAGCAGTTGGTATGGTCGA 57.547 47.619 18.81 0.00 46.84 4.20
1283 1557 2.444421 GTCGAACTGTAGAAGAGGGGA 58.556 52.381 0.00 0.00 0.00 4.81
1309 1583 2.874701 CTGAATAATGAGGTTGCCGGAG 59.125 50.000 5.05 0.00 0.00 4.63
1320 2041 2.290641 GGTTGCCGGAGTATTATGCTTG 59.709 50.000 5.05 0.00 0.00 4.01
1324 2045 1.270094 CCGGAGTATTATGCTTGCGGA 60.270 52.381 0.00 0.00 45.81 5.54
1333 2054 1.825090 ATGCTTGCGGATCTGAAACA 58.175 45.000 5.48 2.99 0.00 2.83
1345 2066 6.051717 CGGATCTGAAACAATCTCCTGTTAT 58.948 40.000 0.00 0.00 38.59 1.89
1348 2069 7.012799 GGATCTGAAACAATCTCCTGTTATTCC 59.987 40.741 0.00 0.00 38.59 3.01
1350 2071 4.941263 TGAAACAATCTCCTGTTATTCCGG 59.059 41.667 0.00 0.00 38.59 5.14
1351 2072 4.569719 AACAATCTCCTGTTATTCCGGT 57.430 40.909 0.00 0.00 37.76 5.28
1352 2073 3.873910 ACAATCTCCTGTTATTCCGGTG 58.126 45.455 0.00 0.00 0.00 4.94
1353 2074 3.206150 CAATCTCCTGTTATTCCGGTGG 58.794 50.000 0.00 0.00 0.00 4.61
1452 2173 1.756430 GGATTCTGCTCCCTTCAACC 58.244 55.000 0.00 0.00 0.00 3.77
1524 2245 2.738743 ACCATTGGGGATAGCAAAGTG 58.261 47.619 7.78 0.00 41.15 3.16
1578 2299 6.647067 AGTCAGTTTGTTACAGTCTTATGAGC 59.353 38.462 0.00 0.00 0.00 4.26
1581 2302 6.425114 CAGTTTGTTACAGTCTTATGAGCAGT 59.575 38.462 0.00 0.00 0.00 4.40
1582 2303 6.425114 AGTTTGTTACAGTCTTATGAGCAGTG 59.575 38.462 0.00 0.00 0.00 3.66
1591 2312 5.009010 AGTCTTATGAGCAGTGTTTTGGTTG 59.991 40.000 0.00 0.00 0.00 3.77
1594 2315 4.836125 ATGAGCAGTGTTTTGGTTGTAG 57.164 40.909 0.00 0.00 0.00 2.74
1670 2391 6.879458 ACACTTGTGTTAACTATCTGGATTCC 59.121 38.462 7.22 0.00 0.00 3.01
1671 2392 7.106239 CACTTGTGTTAACTATCTGGATTCCT 58.894 38.462 7.22 0.00 0.00 3.36
1684 2407 1.068127 GGATTCCTGGATTGCACATGC 59.932 52.381 0.00 0.00 42.50 4.06
1718 2441 4.798882 TGTTGTATCTGGTTTGGTCCTTT 58.201 39.130 0.00 0.00 0.00 3.11
1776 2499 5.423610 ACAGTCAGTATGCTCCAGTCTTATT 59.576 40.000 0.00 0.00 34.76 1.40
1790 2513 7.802117 TCCAGTCTTATTAGTAGGATTTTGGG 58.198 38.462 0.00 0.00 0.00 4.12
1791 2514 7.626084 TCCAGTCTTATTAGTAGGATTTTGGGA 59.374 37.037 0.00 0.00 0.00 4.37
1849 2572 7.775093 TGCTAATATGATGAAACTTGCCTTACT 59.225 33.333 0.00 0.00 0.00 2.24
1882 2605 8.559536 CATTCTAGGATTTTATGCGTGTTATGT 58.440 33.333 0.00 0.00 0.00 2.29
1906 2629 3.392616 AGTTCTGTGTCTGGTTTCATCCT 59.607 43.478 0.00 0.00 0.00 3.24
1980 2703 1.771854 TGGTTGGTGAGTAAAGGCAGA 59.228 47.619 0.00 0.00 0.00 4.26
2021 2744 1.198759 TGTAGGTTGGGGCTCAGGTC 61.199 60.000 0.00 0.00 0.00 3.85
2114 2837 6.316640 ACGATATCATAGGTATTCTGGAGACG 59.683 42.308 3.12 0.00 0.00 4.18
2206 3046 7.786178 TTATTCTGTACATCTGGTTACATGC 57.214 36.000 0.00 0.00 0.00 4.06
2237 3087 1.148310 CGCTGGTGTCAGTTTAGTGG 58.852 55.000 0.00 0.00 42.78 4.00
2252 3102 6.428159 CAGTTTAGTGGCTGTTTCTGTCTTAT 59.572 38.462 0.00 0.00 0.00 1.73
2256 3106 5.133221 AGTGGCTGTTTCTGTCTTATGTTT 58.867 37.500 0.00 0.00 0.00 2.83
2257 3107 5.594317 AGTGGCTGTTTCTGTCTTATGTTTT 59.406 36.000 0.00 0.00 0.00 2.43
2333 3189 4.493220 GCTGTAGCTGAAGATAAAACTGCG 60.493 45.833 0.00 0.00 38.21 5.18
2487 3343 4.282195 ACTGTACCTTGGCATCTATCTAGC 59.718 45.833 0.00 0.00 0.00 3.42
2525 3381 6.672147 ACTTTTGAGCTAATGTCATGTTCAC 58.328 36.000 0.00 0.00 0.00 3.18
2748 3604 2.761195 GGCGCGGTTTTCCTGATCC 61.761 63.158 8.83 0.00 37.95 3.36
2766 3622 4.706476 TGATCCTAAATGTTCCAAAGGCAG 59.294 41.667 0.00 0.00 0.00 4.85
2843 3700 3.515602 AGCTGGTTTTCCTCACTGATT 57.484 42.857 0.00 0.00 41.38 2.57
2846 3703 3.569701 GCTGGTTTTCCTCACTGATTTGA 59.430 43.478 0.00 0.00 41.38 2.69
2861 3718 6.318144 CACTGATTTGAACTCCTGCATTCTAT 59.682 38.462 0.00 0.00 0.00 1.98
2885 3742 0.975040 TGTGCCAGCCAAGGTTGTTT 60.975 50.000 2.25 0.00 0.00 2.83
2893 3750 4.039124 CCAGCCAAGGTTGTTTGTAGAATT 59.961 41.667 2.25 0.00 0.00 2.17
2894 3751 5.242838 CCAGCCAAGGTTGTTTGTAGAATTA 59.757 40.000 2.25 0.00 0.00 1.40
2895 3752 6.381801 CAGCCAAGGTTGTTTGTAGAATTAG 58.618 40.000 0.00 0.00 0.00 1.73
2898 3755 6.381801 CCAAGGTTGTTTGTAGAATTAGCTG 58.618 40.000 0.00 0.00 0.00 4.24
2899 3756 5.629079 AGGTTGTTTGTAGAATTAGCTGC 57.371 39.130 0.00 0.00 0.00 5.25
2918 3780 2.425668 TGCCTCTGATTACGAATCGACA 59.574 45.455 10.55 3.27 40.84 4.35
2924 3786 4.338400 TCTGATTACGAATCGACAGTCCAT 59.662 41.667 10.55 0.00 40.84 3.41
2938 3803 9.784531 ATCGACAGTCCATGATCTTATAAATTT 57.215 29.630 0.00 0.00 0.00 1.82
2986 3851 6.605471 ACCCTAGAATGGTTTTCAAAATCC 57.395 37.500 0.00 0.00 29.75 3.01
3018 3883 4.663120 ACAAGCCATTGGGGTAGATGTATA 59.337 41.667 4.53 0.00 46.38 1.47
3078 3943 4.766891 ACAAAGGCACAACTATTGCTGTAT 59.233 37.500 0.00 0.00 40.07 2.29
3091 3956 2.737544 TGCTGTATTGCCAACATGGAT 58.262 42.857 0.00 0.00 40.96 3.41
3148 4013 5.649395 TCATCAATCAGGTCCTCAAAACATC 59.351 40.000 0.00 0.00 0.00 3.06
3153 4018 2.738846 CAGGTCCTCAAAACATCGTCAG 59.261 50.000 0.00 0.00 0.00 3.51
3156 4021 2.408704 GTCCTCAAAACATCGTCAGTCG 59.591 50.000 0.00 0.00 41.41 4.18
3296 4321 9.461312 TTTATATTGGTGAAAGCTGTGATTACT 57.539 29.630 0.00 0.00 33.76 2.24
3336 4361 3.370672 TCAATATACTGTGTTGTGCTGCG 59.629 43.478 0.00 0.00 31.53 5.18
3339 4364 2.448926 TACTGTGTTGTGCTGCGTAT 57.551 45.000 0.00 0.00 0.00 3.06
3354 4379 4.201783 GCTGCGTATAAGTACCCAAAACAG 60.202 45.833 0.00 0.00 0.00 3.16
3358 4383 5.868801 GCGTATAAGTACCCAAAACAGTACA 59.131 40.000 0.00 0.00 41.07 2.90
3396 4421 1.831580 AGCCAGCCATCAGTTTCTTC 58.168 50.000 0.00 0.00 0.00 2.87
3397 4422 1.353694 AGCCAGCCATCAGTTTCTTCT 59.646 47.619 0.00 0.00 0.00 2.85
3398 4423 1.742268 GCCAGCCATCAGTTTCTTCTC 59.258 52.381 0.00 0.00 0.00 2.87
3403 4428 2.553028 GCCATCAGTTTCTTCTCACCCA 60.553 50.000 0.00 0.00 0.00 4.51
3413 4438 2.046507 CTCACCCAGGTCAGCTGC 60.047 66.667 9.47 4.04 0.00 5.25
3417 4442 4.463879 CCCAGGTCAGCTGCGAGG 62.464 72.222 9.47 8.04 0.00 4.63
3511 4536 2.048597 CCGCGGTGTGCTCTGTTA 60.049 61.111 19.50 0.00 43.27 2.41
3519 4544 5.399013 GCGGTGTGCTCTGTTAATTTATTT 58.601 37.500 0.00 0.00 41.73 1.40
3549 4640 7.905604 TCTCAGTGGTATTAACAAGAATGTG 57.094 36.000 0.00 0.00 40.46 3.21
3564 4655 8.867112 ACAAGAATGTGCATTGATAATGAATC 57.133 30.769 4.06 0.00 38.64 2.52
3565 4656 8.471609 ACAAGAATGTGCATTGATAATGAATCA 58.528 29.630 4.06 0.00 39.60 2.57
3572 4663 6.639686 GTGCATTGATAATGAATCACACCATC 59.360 38.462 5.77 0.00 44.42 3.51
3591 4682 9.003658 ACACCATCAACTAGAAGAATAACAAAG 57.996 33.333 0.00 0.00 0.00 2.77
3625 4716 2.583143 ACAGGTAACAAGGTCAAAGCC 58.417 47.619 0.00 0.00 41.41 4.35
3652 4743 5.904362 AGGTTTTGTCAATTATGGAGCTC 57.096 39.130 4.71 4.71 0.00 4.09
3665 4759 3.988976 TGGAGCTCTACTTGAAATGCT 57.011 42.857 14.64 0.00 0.00 3.79
3667 4761 3.008375 TGGAGCTCTACTTGAAATGCTGT 59.992 43.478 14.64 0.00 0.00 4.40
3672 4766 7.138692 AGCTCTACTTGAAATGCTGTAAAAG 57.861 36.000 0.00 0.00 0.00 2.27
3701 4795 9.685276 AGGAACAGAAATCAAATATCATACACA 57.315 29.630 0.00 0.00 0.00 3.72
3702 4796 9.722056 GGAACAGAAATCAAATATCATACACAC 57.278 33.333 0.00 0.00 0.00 3.82
3711 4805 9.671279 ATCAAATATCATACACACTTCAGTTGA 57.329 29.630 0.00 0.00 0.00 3.18
3712 4806 9.500785 TCAAATATCATACACACTTCAGTTGAA 57.499 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 52 7.076842 TGAAGCTTTGCTATGTTCTAATGTC 57.923 36.000 0.00 0.00 38.25 3.06
54 57 6.767902 CCCTTATGAAGCTTTGCTATGTTCTA 59.232 38.462 0.00 0.00 38.25 2.10
58 61 3.633986 GCCCTTATGAAGCTTTGCTATGT 59.366 43.478 0.00 0.00 38.25 2.29
67 70 0.259938 CCCTTGGCCCTTATGAAGCT 59.740 55.000 0.00 0.00 0.00 3.74
99 102 2.909292 AATGTAGGGGGTCGGGAGGG 62.909 65.000 0.00 0.00 0.00 4.30
100 103 0.986550 AAATGTAGGGGGTCGGGAGG 60.987 60.000 0.00 0.00 0.00 4.30
101 104 0.916809 AAAATGTAGGGGGTCGGGAG 59.083 55.000 0.00 0.00 0.00 4.30
102 105 1.374572 AAAAATGTAGGGGGTCGGGA 58.625 50.000 0.00 0.00 0.00 5.14
103 106 3.991972 AAAAATGTAGGGGGTCGGG 57.008 52.632 0.00 0.00 0.00 5.14
119 122 7.594714 TGACTAGTTTTACACAACTGCAAAAA 58.405 30.769 0.00 0.00 37.57 1.94
120 123 7.147143 TGACTAGTTTTACACAACTGCAAAA 57.853 32.000 0.00 0.00 37.57 2.44
121 124 6.745159 TGACTAGTTTTACACAACTGCAAA 57.255 33.333 0.00 0.00 37.57 3.68
122 125 6.540551 TCATGACTAGTTTTACACAACTGCAA 59.459 34.615 0.00 0.00 37.57 4.08
123 126 6.052360 TCATGACTAGTTTTACACAACTGCA 58.948 36.000 0.00 0.00 37.57 4.41
124 127 6.539649 TCATGACTAGTTTTACACAACTGC 57.460 37.500 0.00 0.00 37.57 4.40
143 373 7.500720 TCACTTGCATACTCCAAATATCATG 57.499 36.000 0.00 0.00 0.00 3.07
144 374 8.573885 CAATCACTTGCATACTCCAAATATCAT 58.426 33.333 0.00 0.00 0.00 2.45
148 378 7.828717 TCTTCAATCACTTGCATACTCCAAATA 59.171 33.333 0.00 0.00 32.11 1.40
153 383 6.317140 TGATTCTTCAATCACTTGCATACTCC 59.683 38.462 0.00 0.00 42.99 3.85
160 390 6.084925 CACTCTTGATTCTTCAATCACTTGC 58.915 40.000 0.00 0.00 46.71 4.01
161 391 6.429078 TCCACTCTTGATTCTTCAATCACTTG 59.571 38.462 0.00 0.00 46.71 3.16
170 400 6.169094 TGATTGTCTCCACTCTTGATTCTTC 58.831 40.000 0.00 0.00 0.00 2.87
171 401 6.119240 TGATTGTCTCCACTCTTGATTCTT 57.881 37.500 0.00 0.00 0.00 2.52
174 404 5.191323 AGGATGATTGTCTCCACTCTTGATT 59.809 40.000 0.00 0.00 33.75 2.57
175 405 4.720773 AGGATGATTGTCTCCACTCTTGAT 59.279 41.667 0.00 0.00 33.75 2.57
176 406 4.099633 AGGATGATTGTCTCCACTCTTGA 58.900 43.478 0.00 0.00 33.75 3.02
177 407 4.484537 AGGATGATTGTCTCCACTCTTG 57.515 45.455 0.00 0.00 33.75 3.02
178 408 6.627087 TTTAGGATGATTGTCTCCACTCTT 57.373 37.500 0.00 0.00 33.75 2.85
179 409 6.821616 ATTTAGGATGATTGTCTCCACTCT 57.178 37.500 0.00 0.00 33.75 3.24
180 410 8.207545 AGTAATTTAGGATGATTGTCTCCACTC 58.792 37.037 0.00 0.00 33.75 3.51
181 411 8.095452 AGTAATTTAGGATGATTGTCTCCACT 57.905 34.615 0.00 0.00 33.75 4.00
182 412 9.832445 TTAGTAATTTAGGATGATTGTCTCCAC 57.168 33.333 0.00 0.00 33.75 4.02
212 442 1.690283 CCAGCATCAGAAGACGCACG 61.690 60.000 0.00 0.00 34.90 5.34
264 494 1.272769 GCCTCGTACTGTTTCAGTCCT 59.727 52.381 5.66 0.00 41.21 3.85
280 510 1.134670 ACAGTTTAGCAGATCCGCCTC 60.135 52.381 0.00 0.00 0.00 4.70
291 521 2.279582 TGCTCGCTCTACAGTTTAGC 57.720 50.000 0.00 0.00 0.00 3.09
300 530 1.545759 CGTTTCGATTGCTCGCTCTA 58.454 50.000 0.00 0.00 44.65 2.43
438 668 1.775039 CGTCTGGTGTGTGGTTGCTG 61.775 60.000 0.00 0.00 0.00 4.41
440 670 3.022287 CGTCTGGTGTGTGGTTGC 58.978 61.111 0.00 0.00 0.00 4.17
441 671 2.881266 CGCGTCTGGTGTGTGGTTG 61.881 63.158 0.00 0.00 0.00 3.77
465 695 0.601841 CGGTGTTTGCTTACTCCGGT 60.602 55.000 18.32 0.00 46.13 5.28
475 705 2.644992 CCTTCAGGCGGTGTTTGC 59.355 61.111 0.00 0.00 0.00 3.68
489 719 2.234414 CTCTGCTTCTCTCTTGAGCCTT 59.766 50.000 0.00 0.00 40.03 4.35
490 720 1.826720 CTCTGCTTCTCTCTTGAGCCT 59.173 52.381 0.00 0.00 40.03 4.58
502 732 0.738389 CCTCTCCTCGTCTCTGCTTC 59.262 60.000 0.00 0.00 0.00 3.86
507 737 0.107214 CTCTGCCTCTCCTCGTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
509 739 1.077068 CCTCTGCCTCTCCTCGTCT 60.077 63.158 0.00 0.00 0.00 4.18
511 741 2.757917 GCCTCTGCCTCTCCTCGT 60.758 66.667 0.00 0.00 0.00 4.18
512 742 3.898509 CGCCTCTGCCTCTCCTCG 61.899 72.222 0.00 0.00 0.00 4.63
523 753 3.764466 CTTCAGGTCCGCGCCTCT 61.764 66.667 0.00 0.00 36.58 3.69
570 800 0.551879 TCTCCCTCTTCCTCTACGGG 59.448 60.000 0.00 0.00 36.21 5.28
795 1032 1.387295 GCTACAATGGGCTTGGAGGC 61.387 60.000 1.38 0.00 44.83 4.70
833 1085 1.753848 TGCATCTTTCGGCCCCATG 60.754 57.895 0.00 0.00 0.00 3.66
834 1086 1.754234 GTGCATCTTTCGGCCCCAT 60.754 57.895 0.00 0.00 0.00 4.00
835 1087 2.361104 GTGCATCTTTCGGCCCCA 60.361 61.111 0.00 0.00 0.00 4.96
836 1088 2.044946 AGTGCATCTTTCGGCCCC 60.045 61.111 0.00 0.00 0.00 5.80
842 1094 2.401195 GCCGCGAGTGCATCTTTC 59.599 61.111 8.23 0.00 42.97 2.62
863 1115 0.539669 AAAACCGGGGCTTCTTCTGG 60.540 55.000 6.32 0.00 35.60 3.86
927 1183 3.191539 GCACAGCAGCGGAGTAGC 61.192 66.667 0.00 0.00 37.41 3.58
930 1186 2.849120 GATGAGCACAGCAGCGGAGT 62.849 60.000 0.00 0.00 40.15 3.85
933 1191 1.703438 GAAGATGAGCACAGCAGCGG 61.703 60.000 1.47 0.00 40.15 5.52
935 1193 2.203401 CTAGAAGATGAGCACAGCAGC 58.797 52.381 1.47 0.00 34.60 5.25
941 1199 2.298729 CCCTAGCCTAGAAGATGAGCAC 59.701 54.545 0.00 0.00 0.00 4.40
986 1253 1.666209 CGCCATTGCCCGAGGATTTT 61.666 55.000 0.00 0.00 0.00 1.82
1245 1516 1.867233 GACCATACCAACTGCTATGCG 59.133 52.381 0.00 0.00 0.00 4.73
1247 1518 3.452755 TCGACCATACCAACTGCTATG 57.547 47.619 0.00 0.00 0.00 2.23
1254 1528 4.445452 TCTACAGTTCGACCATACCAAC 57.555 45.455 0.00 0.00 0.00 3.77
1261 1535 2.168496 CCCTCTTCTACAGTTCGACCA 58.832 52.381 0.00 0.00 0.00 4.02
1265 1539 2.448453 AGTCCCCTCTTCTACAGTTCG 58.552 52.381 0.00 0.00 0.00 3.95
1267 1541 4.773149 CAGTTAGTCCCCTCTTCTACAGTT 59.227 45.833 0.00 0.00 0.00 3.16
1283 1557 4.876107 CGGCAACCTCATTATTCAGTTAGT 59.124 41.667 0.00 0.00 0.00 2.24
1309 1583 5.007626 TGTTTCAGATCCGCAAGCATAATAC 59.992 40.000 0.00 0.00 0.00 1.89
1320 2041 2.611292 CAGGAGATTGTTTCAGATCCGC 59.389 50.000 0.00 0.00 31.97 5.54
1324 2045 6.540189 CGGAATAACAGGAGATTGTTTCAGAT 59.460 38.462 0.00 0.00 41.31 2.90
1333 2054 2.844348 ACCACCGGAATAACAGGAGATT 59.156 45.455 9.46 0.00 37.30 2.40
1345 2066 0.533308 GTGTACTGCAACCACCGGAA 60.533 55.000 9.46 0.00 0.00 4.30
1348 2069 1.300311 TCGTGTACTGCAACCACCG 60.300 57.895 0.00 0.00 0.00 4.94
1350 2071 1.554042 CCGTCGTGTACTGCAACCAC 61.554 60.000 0.00 0.00 0.00 4.16
1351 2072 1.300311 CCGTCGTGTACTGCAACCA 60.300 57.895 0.00 0.00 0.00 3.67
1352 2073 1.280206 GACCGTCGTGTACTGCAACC 61.280 60.000 0.00 0.00 0.00 3.77
1353 2074 0.595567 TGACCGTCGTGTACTGCAAC 60.596 55.000 0.00 0.00 0.00 4.17
1452 2173 0.109272 TCTGAGGTTTAGACTGCGCG 60.109 55.000 0.00 0.00 0.00 6.86
1524 2245 3.139077 CCATACCTTAATGCCGACTTCC 58.861 50.000 0.00 0.00 0.00 3.46
1578 2299 4.744631 GGATTTGCTACAACCAAAACACTG 59.255 41.667 0.00 0.00 35.97 3.66
1581 2302 4.404073 ACTGGATTTGCTACAACCAAAACA 59.596 37.500 0.00 0.00 35.97 2.83
1582 2303 4.944048 ACTGGATTTGCTACAACCAAAAC 58.056 39.130 0.00 0.00 35.97 2.43
1591 2312 3.338249 TGCTTCTGACTGGATTTGCTAC 58.662 45.455 0.00 0.00 0.00 3.58
1594 2315 2.734492 GCATGCTTCTGACTGGATTTGC 60.734 50.000 11.37 0.00 0.00 3.68
1625 2346 4.092821 GTGTGTTGCAAGCTTCATCGTATA 59.907 41.667 0.00 0.00 0.00 1.47
1629 2350 1.265095 AGTGTGTTGCAAGCTTCATCG 59.735 47.619 0.00 0.00 0.00 3.84
1657 2378 3.718434 TGCAATCCAGGAATCCAGATAGT 59.282 43.478 0.61 0.00 0.00 2.12
1660 2381 2.242965 TGTGCAATCCAGGAATCCAGAT 59.757 45.455 0.61 0.04 0.00 2.90
1662 2383 2.133281 TGTGCAATCCAGGAATCCAG 57.867 50.000 0.61 0.00 0.00 3.86
1684 2407 2.226437 AGATACAACAAAACTGGCGCAG 59.774 45.455 10.83 7.58 37.52 5.18
1687 2410 3.201726 CCAGATACAACAAAACTGGCG 57.798 47.619 0.00 0.00 40.90 5.69
1725 2448 8.830201 TTGCAAACTAATTATCACAGCAAAAT 57.170 26.923 0.00 0.00 36.64 1.82
1790 2513 7.792374 TGCTTCTGACTGGATTTGTTATATC 57.208 36.000 0.00 0.00 0.00 1.63
1791 2514 7.255381 GCATGCTTCTGACTGGATTTGTTATAT 60.255 37.037 11.37 0.00 0.00 0.86
1871 2594 2.799978 CACAGAACTGACATAACACGCA 59.200 45.455 8.87 0.00 0.00 5.24
1882 2605 3.904800 TGAAACCAGACACAGAACTGA 57.095 42.857 8.87 0.00 36.38 3.41
1906 2629 6.521162 TCACAGCAGAAGACATGTAGTAAAA 58.479 36.000 0.00 0.00 0.00 1.52
1980 2703 9.317936 CTACACAACAGATGATACATGTTACAT 57.682 33.333 2.30 10.33 35.47 2.29
2001 2724 1.299976 CCTGAGCCCCAACCTACAC 59.700 63.158 0.00 0.00 0.00 2.90
2021 2744 6.035005 CCATTCCAGCATACTTCGAATATACG 59.965 42.308 0.00 0.00 0.00 3.06
2114 2837 3.376546 GCTTCATGTCTTTCACATCCTCC 59.623 47.826 0.00 0.00 44.60 4.30
2187 3027 4.142609 AGGCATGTAACCAGATGTACAG 57.857 45.455 0.33 0.00 0.00 2.74
2205 3045 3.730761 CAGCGCACAGTCCAAGGC 61.731 66.667 11.47 0.00 0.00 4.35
2206 3046 3.052082 CCAGCGCACAGTCCAAGG 61.052 66.667 11.47 0.00 0.00 3.61
2487 3343 7.301068 AGCTCAAAAGTAAGATTGATTCGAG 57.699 36.000 0.00 0.00 35.20 4.04
2516 3372 2.364002 TGTCTCCGACAAGTGAACATGA 59.636 45.455 0.00 0.00 39.78 3.07
2525 3381 0.038159 GACCACCTGTCTCCGACAAG 60.038 60.000 0.00 0.00 42.26 3.16
2748 3604 4.525912 AAGCTGCCTTTGGAACATTTAG 57.474 40.909 0.00 0.00 39.30 1.85
2766 3622 9.593134 TCTCATTTCTCTTCATCTAGTTTAAGC 57.407 33.333 0.00 0.00 0.00 3.09
2843 3700 6.716628 ACAAAGAATAGAATGCAGGAGTTCAA 59.283 34.615 0.00 0.00 0.00 2.69
2846 3703 5.105997 GCACAAAGAATAGAATGCAGGAGTT 60.106 40.000 0.00 0.00 33.27 3.01
2861 3718 0.396974 ACCTTGGCTGGCACAAAGAA 60.397 50.000 2.29 0.00 38.70 2.52
2885 3742 5.620738 AATCAGAGGCAGCTAATTCTACA 57.379 39.130 0.00 0.00 0.00 2.74
2893 3750 3.304726 CGATTCGTAATCAGAGGCAGCTA 60.305 47.826 0.00 0.00 37.78 3.32
2894 3751 2.544694 CGATTCGTAATCAGAGGCAGCT 60.545 50.000 0.00 0.00 37.78 4.24
2895 3752 1.789464 CGATTCGTAATCAGAGGCAGC 59.211 52.381 0.00 0.00 37.78 5.25
2898 3755 3.046390 CTGTCGATTCGTAATCAGAGGC 58.954 50.000 5.89 0.00 37.78 4.70
2899 3756 4.283678 GACTGTCGATTCGTAATCAGAGG 58.716 47.826 20.08 5.59 37.78 3.69
2986 3851 5.385198 ACCCCAATGGCTTGTAGTATATTG 58.615 41.667 0.00 0.00 37.83 1.90
3000 3865 9.213777 ACATACTATATACATCTACCCCAATGG 57.786 37.037 0.00 0.00 41.37 3.16
3018 3883 9.494055 AGGGCATCTACAATACATACATACTAT 57.506 33.333 0.00 0.00 0.00 2.12
3078 3943 5.053145 GTGTAACAAAATCCATGTTGGCAA 58.947 37.500 0.00 0.00 40.95 4.52
3153 4018 2.332362 TAAGATCCGAGGCGCACGAC 62.332 60.000 23.47 15.10 0.00 4.34
3156 4021 0.032130 TGATAAGATCCGAGGCGCAC 59.968 55.000 10.83 0.96 0.00 5.34
3283 4308 8.542497 TTATACGTTTTCAGTAATCACAGCTT 57.458 30.769 0.00 0.00 0.00 3.74
3317 4342 2.972625 ACGCAGCACAACACAGTATAT 58.027 42.857 0.00 0.00 0.00 0.86
3320 4345 2.448926 ATACGCAGCACAACACAGTA 57.551 45.000 0.00 0.00 0.00 2.74
3323 4348 2.761559 ACTTATACGCAGCACAACACA 58.238 42.857 0.00 0.00 0.00 3.72
3324 4349 3.061697 GGTACTTATACGCAGCACAACAC 59.938 47.826 0.00 0.00 31.40 3.32
3336 4361 8.782339 ATGTGTACTGTTTTGGGTACTTATAC 57.218 34.615 0.00 0.00 39.04 1.47
3339 4364 9.275398 CTAAATGTGTACTGTTTTGGGTACTTA 57.725 33.333 0.00 0.00 39.04 2.24
3354 4379 6.018669 GCTTCCAGTCTATGCTAAATGTGTAC 60.019 42.308 0.00 0.00 0.00 2.90
3358 4383 4.080356 TGGCTTCCAGTCTATGCTAAATGT 60.080 41.667 0.00 0.00 0.00 2.71
3383 4408 3.341823 CTGGGTGAGAAGAAACTGATGG 58.658 50.000 0.00 0.00 0.00 3.51
3396 4421 2.046507 GCAGCTGACCTGGGTGAG 60.047 66.667 20.43 1.89 42.03 3.51
3397 4422 4.007644 CGCAGCTGACCTGGGTGA 62.008 66.667 20.43 0.00 46.28 4.02
3403 4428 3.073735 CCTCCTCGCAGCTGACCT 61.074 66.667 20.43 0.00 0.00 3.85
3457 4482 0.683412 TCCATCATCTCGCCATCTGG 59.317 55.000 0.00 0.00 38.53 3.86
3458 4483 2.141517 GTTCCATCATCTCGCCATCTG 58.858 52.381 0.00 0.00 0.00 2.90
3526 4551 6.149308 TGCACATTCTTGTTAATACCACTGAG 59.851 38.462 0.00 0.00 32.34 3.35
3531 4556 7.459795 TCAATGCACATTCTTGTTAATACCA 57.540 32.000 0.00 0.00 32.34 3.25
3549 4640 6.741109 TGATGGTGTGATTCATTATCAATGC 58.259 36.000 0.00 0.00 44.62 3.56
3564 4655 7.905604 TGTTATTCTTCTAGTTGATGGTGTG 57.094 36.000 0.00 0.00 0.00 3.82
3565 4656 8.918202 TTTGTTATTCTTCTAGTTGATGGTGT 57.082 30.769 0.00 0.00 0.00 4.16
3591 4682 9.191995 CCTTGTTACCTGTATTTGTGAAATTTC 57.808 33.333 11.41 11.41 32.38 2.17
3598 4689 6.627395 TTGACCTTGTTACCTGTATTTGTG 57.373 37.500 0.00 0.00 0.00 3.33
3625 4716 5.226396 TCCATAATTGACAAAACCTTTGCG 58.774 37.500 0.00 0.00 0.00 4.85
3665 4759 7.873719 TTGATTTCTGTTCCTGTCTTTTACA 57.126 32.000 0.00 0.00 36.42 2.41


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

AutoCloner maintained by Alex Coulton.