Multiple sequence alignment - TraesCS4A01G019600

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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 TraesCS4A01G019600 chr4A 100.000 5928 0 0 1 5928 12686003 12680076 0.000000e+00 10948.0
1 TraesCS4A01G019600 chr4D 93.606 5615 259 36 1 5527 455247189 455252791 0.000000e+00 8288.0
2 TraesCS4A01G019600 chr4D 80.769 416 56 18 128 528 454799079 454799485 2.680000e-78 303.0
3 TraesCS4A01G019600 chr4B 92.784 5391 291 48 573 5902 568333222 568338575 0.000000e+00 7710.0
4 TraesCS4A01G019600 chr4B 89.604 404 32 2 183 576 568332360 568332763 6.860000e-139 505.0
5 TraesCS4A01G019600 chr2D 85.890 163 21 2 1495 1656 535293654 535293815 7.900000e-39 172.0
6 TraesCS4A01G019600 chr7D 80.741 135 17 5 2059 2192 72534391 72534265 4.890000e-16 97.1
7 TraesCS4A01G019600 chr7A 80.741 135 17 5 2059 2192 77620981 77620855 4.890000e-16 97.1
8 TraesCS4A01G019600 chr2B 93.878 49 3 0 1691 1739 636762553 636762601 2.290000e-09 75.0


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 TraesCS4A01G019600 chr4A 12680076 12686003 5927 True 10948.0 10948 100.000 1 5928 1 chr4A.!!$R1 5927
1 TraesCS4A01G019600 chr4D 455247189 455252791 5602 False 8288.0 8288 93.606 1 5527 1 chr4D.!!$F2 5526
2 TraesCS4A01G019600 chr4B 568332360 568338575 6215 False 4107.5 7710 91.194 183 5902 2 chr4B.!!$F1 5719

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
537 545 0.389817 CTTCGTCTTCGTGCCCATGA 60.390 55.000 0.00 0.00 38.33 3.07 F
1263 1753 0.474854 TGCTACACCCTGGGGAAGAA 60.475 55.000 18.88 2.58 38.96 2.52 F
1288 1778 1.005340 GCACCTCTCTCTGCAATTCG 58.995 55.000 0.00 0.00 33.31 3.34 F
1345 1835 1.072505 GGAGCACGAAACTGGGGAA 59.927 57.895 0.00 0.00 0.00 3.97 F
1732 2222 1.159285 TGCTCAACCAAGCTGAATCG 58.841 50.000 0.00 0.00 42.94 3.34 F
3445 3935 1.003839 TGTGGATGTGAGCCGTTCC 60.004 57.895 0.00 0.00 0.00 3.62 F
3565 4055 0.387202 TGTTCACCCACCAATTTGCG 59.613 50.000 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 1835 0.674895 GGACATCAGCCTCGCACTTT 60.675 55.000 0.00 0.0 0.00 2.66 R
2291 2781 1.135286 GCCAAAGGTTGTAGCATCTGC 60.135 52.381 0.00 0.0 42.49 4.26 R
3244 3734 1.349026 CACAAGTGACTGATGAGGGGT 59.651 52.381 0.00 0.0 0.00 4.95 R
3304 3794 2.913054 GATAGCAGTCCAGCAGCGCA 62.913 60.000 11.47 0.0 36.85 6.09 R
3550 4040 0.673437 AGAACGCAAATTGGTGGGTG 59.327 50.000 0.00 0.0 43.24 4.61 R
4534 5024 0.456653 CAAGAAAATCAAGCGCCCGG 60.457 55.000 2.29 0.0 0.00 5.73 R
5239 5768 0.963962 AAAACCTACTCCGCGAGTCA 59.036 50.000 8.23 0.0 42.40 3.41 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
32 33 2.749621 GGTGAGGTCATAGTTTGCAAGG 59.250 50.000 0.00 0.00 0.00 3.61
33 34 2.749621 GTGAGGTCATAGTTTGCAAGGG 59.250 50.000 0.00 0.00 0.00 3.95
34 35 2.375174 TGAGGTCATAGTTTGCAAGGGT 59.625 45.455 0.00 0.00 0.00 4.34
35 36 3.585289 TGAGGTCATAGTTTGCAAGGGTA 59.415 43.478 0.00 0.00 0.00 3.69
37 38 3.054361 AGGTCATAGTTTGCAAGGGTAGG 60.054 47.826 0.00 0.00 0.00 3.18
38 39 2.683362 GTCATAGTTTGCAAGGGTAGGC 59.317 50.000 0.00 0.00 0.00 3.93
39 40 2.307392 TCATAGTTTGCAAGGGTAGGCA 59.693 45.455 0.00 0.00 38.46 4.75
59 60 3.211865 CATTGTATGCATGAGGTCAGCT 58.788 45.455 10.16 0.00 0.00 4.24
95 96 0.587985 CGTCGTCGCATGACACGATA 60.588 55.000 18.91 0.00 46.13 2.92
103 104 1.904144 CATGACACGATACCGACGTT 58.096 50.000 0.00 0.00 42.07 3.99
119 120 3.674955 CGACGTTCCATGTGTTCCTGATA 60.675 47.826 0.00 0.00 0.00 2.15
122 123 3.369471 CGTTCCATGTGTTCCTGATACCT 60.369 47.826 0.00 0.00 0.00 3.08
123 124 3.912496 TCCATGTGTTCCTGATACCTG 57.088 47.619 0.00 0.00 0.00 4.00
274 282 2.969950 CCTTGTCCGAGGATATAACCCA 59.030 50.000 0.00 0.00 39.25 4.51
299 307 0.659427 CAACGGCGTAGTCCTCGATA 59.341 55.000 15.20 0.00 0.00 2.92
310 318 1.411612 GTCCTCGATATTGAACCCGGT 59.588 52.381 0.00 0.00 0.00 5.28
328 336 2.736995 GCCGTGCACGCAGAAGTA 60.737 61.111 33.17 0.00 38.18 2.24
337 345 0.608582 ACGCAGAAGTAGGAGACGGT 60.609 55.000 0.00 0.00 0.00 4.83
402 410 3.719144 TCGACTGCGCTTCGACGA 61.719 61.111 24.62 18.58 40.51 4.20
406 414 3.918220 CTGCGCTTCGACGATGGC 61.918 66.667 9.73 11.86 34.06 4.40
416 424 3.982372 GACGATGGCGCCGTTCTCA 62.982 63.158 24.75 2.73 40.67 3.27
517 525 1.807495 GAGTAGGCGGGGAAGGATCG 61.807 65.000 0.00 0.00 0.00 3.69
537 545 0.389817 CTTCGTCTTCGTGCCCATGA 60.390 55.000 0.00 0.00 38.33 3.07
563 574 2.820619 CGCTCGTCGGGAGATTCGA 61.821 63.158 0.00 0.00 46.23 3.71
583 1056 5.498159 TCGAAAGCGATTTGTATATGTTGC 58.502 37.500 2.01 0.00 42.51 4.17
592 1065 1.771854 TGTATATGTTGCCGGGATGGT 59.228 47.619 2.18 0.00 41.21 3.55
603 1076 2.746277 GGATGGTGGCTCGCGTTT 60.746 61.111 5.77 0.00 0.00 3.60
620 1093 4.036352 GCGTTTGTGTCGGTTTTGAATTA 58.964 39.130 0.00 0.00 0.00 1.40
659 1132 2.252714 GGTGGGCCTTGTTATCCAAAA 58.747 47.619 4.53 0.00 31.20 2.44
726 1199 2.928396 CCCTGACCCAACTCCGGT 60.928 66.667 0.00 0.00 35.88 5.28
743 1217 2.682136 TCATCTTCGCCGGGTGGA 60.682 61.111 2.18 0.00 37.49 4.02
744 1218 2.063979 TCATCTTCGCCGGGTGGAT 61.064 57.895 2.18 0.55 37.49 3.41
745 1219 1.595382 CATCTTCGCCGGGTGGATC 60.595 63.158 2.18 0.00 37.49 3.36
746 1220 3.151958 ATCTTCGCCGGGTGGATCG 62.152 63.158 2.18 0.00 37.49 3.69
747 1221 3.833645 CTTCGCCGGGTGGATCGA 61.834 66.667 2.18 0.00 37.49 3.59
748 1222 3.365291 CTTCGCCGGGTGGATCGAA 62.365 63.158 2.18 7.92 37.39 3.71
821 1300 2.491022 CCTACTCCCTCTTCCGCCG 61.491 68.421 0.00 0.00 0.00 6.46
947 1437 4.636435 CCGCCCACCAACCTCGTT 62.636 66.667 0.00 0.00 0.00 3.85
988 1478 0.933509 CAACCGCTCGCGAGGTATAC 60.934 60.000 35.10 18.25 42.96 1.47
993 1483 1.598962 CTCGCGAGGTATACGGGGA 60.599 63.158 28.40 2.37 42.34 4.81
1080 1570 3.648009 CGTCAGAGACAGAGCTTCTTTT 58.352 45.455 0.00 0.00 32.09 2.27
1173 1663 2.260639 AGGAGAGAGCCCAAGATTGA 57.739 50.000 0.00 0.00 0.00 2.57
1183 1673 0.804989 CCAAGATTGAACACCGAGGC 59.195 55.000 0.00 0.00 0.00 4.70
1231 1721 2.695147 CTCCAACAAAGGGAGCTTGTTT 59.305 45.455 0.00 0.00 44.95 2.83
1263 1753 0.474854 TGCTACACCCTGGGGAAGAA 60.475 55.000 18.88 2.58 38.96 2.52
1288 1778 1.005340 GCACCTCTCTCTGCAATTCG 58.995 55.000 0.00 0.00 33.31 3.34
1345 1835 1.072505 GGAGCACGAAACTGGGGAA 59.927 57.895 0.00 0.00 0.00 3.97
1581 2071 2.486592 ACATTTTGATCGGTTTCGGACC 59.513 45.455 0.00 0.00 45.55 4.46
1622 2112 4.394920 GGAACGCAAGATTTCTGTGGAATA 59.605 41.667 0.00 0.00 43.62 1.75
1732 2222 1.159285 TGCTCAACCAAGCTGAATCG 58.841 50.000 0.00 0.00 42.94 3.34
1810 2300 6.042093 TCAGTCAGATTACCCAGATGTATTCC 59.958 42.308 0.00 0.00 0.00 3.01
1932 2422 2.077627 GGTCGGAAAGAGAAAAGAGGC 58.922 52.381 0.00 0.00 0.00 4.70
2011 2501 7.286316 ACAGAAGGAGATGTTCTTGATTTTGTT 59.714 33.333 0.00 0.00 31.64 2.83
2019 2509 8.415553 AGATGTTCTTGATTTTGTTGTCAATGA 58.584 29.630 0.00 0.00 34.18 2.57
2104 2594 6.436847 TGAACATTGAAATAAGCAAGGGATCA 59.563 34.615 0.00 0.00 31.86 2.92
2291 2781 2.990066 AGAGTCCTTAGGATTTGCCG 57.010 50.000 3.52 0.00 43.43 5.69
2768 3258 1.239347 GGACACTGACTCCAAAAGGC 58.761 55.000 0.00 0.00 0.00 4.35
3074 3564 6.070881 ACTGAGTAAGAATGAGATGTCAGCTT 60.071 38.462 13.09 13.09 35.66 3.74
3229 3719 5.941788 ACAAAGTTTAGTTGGTCTCCTGAT 58.058 37.500 0.00 0.00 0.00 2.90
3244 3734 6.495181 GGTCTCCTGATAAGAAGGATGTGATA 59.505 42.308 0.00 0.00 42.94 2.15
3313 3803 1.004185 CAGCTTATAAGTGCGCTGCTG 60.004 52.381 18.49 18.49 42.66 4.41
3437 3927 3.009033 CCTAGAAAAGGGTGTGGATGTGA 59.991 47.826 0.00 0.00 42.32 3.58
3445 3935 1.003839 TGTGGATGTGAGCCGTTCC 60.004 57.895 0.00 0.00 0.00 3.62
3486 3976 1.134250 GGGCTTCCTAAAGGAGCAGAG 60.134 57.143 16.90 6.85 46.36 3.35
3506 3996 2.695666 AGGACTGTCGAATCGATTGGAT 59.304 45.455 23.14 9.85 38.42 3.41
3532 4022 8.800370 TGTATGACATCTGCCTTAACAAAATA 57.200 30.769 0.00 0.00 0.00 1.40
3550 4040 9.620660 AACAAAATAAAAGTATCGGATGTGTTC 57.379 29.630 0.00 0.00 0.00 3.18
3565 4055 0.387202 TGTTCACCCACCAATTTGCG 59.613 50.000 0.00 0.00 0.00 4.85
3772 4262 7.678837 ACAAATTGCTAAATTCCATCCTTCAA 58.321 30.769 0.00 0.00 34.84 2.69
3775 4265 7.664552 ATTGCTAAATTCCATCCTTCAATCA 57.335 32.000 0.00 0.00 0.00 2.57
3808 4298 9.052759 TGTCTAAACAATTGGAGAAAAGTAGAC 57.947 33.333 10.83 12.90 30.70 2.59
3868 4358 6.688578 CATTTCTATTTCTAGCTACCGCCTA 58.311 40.000 0.00 0.00 36.60 3.93
3910 4400 2.410053 GCAGAGTCAGTTTTCTAGTGCG 59.590 50.000 0.00 0.00 0.00 5.34
3915 4405 5.864474 AGAGTCAGTTTTCTAGTGCGTTATG 59.136 40.000 0.00 0.00 0.00 1.90
3931 4421 3.496130 CGTTATGCCTTAAGGAGCTGATG 59.504 47.826 26.21 7.75 37.39 3.07
3943 4433 2.001159 GAGCTGATGCAAGACAGTGAG 58.999 52.381 16.25 0.00 42.74 3.51
3951 4441 3.198068 TGCAAGACAGTGAGAAGTCAAC 58.802 45.455 0.00 0.00 37.23 3.18
3955 4445 5.295950 CAAGACAGTGAGAAGTCAACAGAT 58.704 41.667 0.00 0.00 37.23 2.90
4018 4508 6.041296 AGAGAAGAAACATTTTGCAGGTTCAT 59.959 34.615 4.50 0.00 0.00 2.57
4021 4511 5.535333 AGAAACATTTTGCAGGTTCATGAG 58.465 37.500 4.50 0.00 0.00 2.90
4090 4580 7.981225 ACAACATATGATTTCCTTGTTTATGGC 59.019 33.333 10.38 0.00 0.00 4.40
4164 4654 2.790433 TGCTCAGGGATTAACACCAAC 58.210 47.619 0.61 0.00 0.00 3.77
4198 4688 6.975772 GTCTCAGAATAGTATTGAGTCACCAC 59.024 42.308 0.00 0.00 39.41 4.16
4229 4719 1.433534 GAACCTCGAGAAAGCACTGG 58.566 55.000 15.71 0.00 0.00 4.00
4420 4910 1.366319 AGGAATTCTGCAGACAGGGT 58.634 50.000 18.03 0.00 44.59 4.34
4534 5024 7.119846 AGGCTGTGTATACTGAAAGAATTTGAC 59.880 37.037 4.17 0.00 39.27 3.18
4574 5064 2.352127 GCTGAGATGCAGTTGGAAAACC 60.352 50.000 0.00 0.00 46.62 3.27
4590 5080 5.592688 TGGAAAACCTAAAACCAAGTGAGAG 59.407 40.000 0.00 0.00 0.00 3.20
4591 5081 5.826208 GGAAAACCTAAAACCAAGTGAGAGA 59.174 40.000 0.00 0.00 0.00 3.10
4602 5092 3.197333 CCAAGTGAGAGATCCTGTGATGT 59.803 47.826 0.00 0.00 0.00 3.06
4622 5112 1.959085 CTCATGCGTGGCCTTTGTT 59.041 52.632 3.32 0.00 0.00 2.83
4624 5114 0.821301 TCATGCGTGGCCTTTGTTCA 60.821 50.000 3.32 0.00 0.00 3.18
4660 5150 5.352569 CAGTGACGCTAAGAAGATTTTGGAT 59.647 40.000 0.00 0.00 0.00 3.41
4999 5489 1.056700 ATGGCTGCCCTCCTACGAAT 61.057 55.000 17.53 0.00 0.00 3.34
5091 5604 1.071699 TGTAGAAGTGGAACAGTGGGC 59.928 52.381 0.00 0.00 43.84 5.36
5173 5686 1.917495 CAGTCCTGGATGCATCCCA 59.083 57.895 36.97 25.01 46.59 4.37
5242 5771 9.325198 TGTACAACATATTCTGGTCATATTGAC 57.675 33.333 0.00 0.00 46.23 3.18
5259 5788 2.161855 TGACTCGCGGAGTAGGTTTTA 58.838 47.619 6.13 0.00 43.53 1.52
5266 5799 5.964758 TCGCGGAGTAGGTTTTAATAGAAA 58.035 37.500 6.13 0.00 0.00 2.52
5289 5830 4.630894 TGTGTTCTTTTACCTTGCAGTG 57.369 40.909 0.00 0.00 0.00 3.66
5321 5862 2.671854 GCTCCGCAGCTAGAGAAAC 58.328 57.895 12.35 0.00 43.09 2.78
5328 5869 3.579709 CGCAGCTAGAGAAACAAGAAGA 58.420 45.455 0.00 0.00 0.00 2.87
5363 5912 0.818296 TACTTCCGAAGCTGCTCCTC 59.182 55.000 1.00 0.00 0.00 3.71
5406 5955 6.733145 TGATATCTCTCATGTTCTTCTCACG 58.267 40.000 3.98 0.00 0.00 4.35
5412 5961 4.104696 TCATGTTCTTCTCACGCGATTA 57.895 40.909 15.93 0.00 0.00 1.75
5430 5979 6.594159 CGCGATTATTCCTTATATGAGGGTTT 59.406 38.462 13.30 2.15 37.41 3.27
5502 6069 8.547967 TGTGTTCCTAGATGTCTTATTTCAAC 57.452 34.615 0.00 0.00 0.00 3.18
5505 6072 9.436957 TGTTCCTAGATGTCTTATTTCAACTTC 57.563 33.333 0.00 0.00 0.00 3.01
5508 6075 7.766278 TCCTAGATGTCTTATTTCAACTTCTGC 59.234 37.037 0.00 0.00 31.96 4.26
5577 6144 0.259938 AACCATCAGGATTCAGGGCC 59.740 55.000 0.00 0.00 38.69 5.80
5589 6156 1.544724 TCAGGGCCATTGTTGTAAGC 58.455 50.000 6.18 0.00 0.00 3.09
5599 6166 0.036765 TGTTGTAAGCGCCGAATCCT 60.037 50.000 2.29 0.00 0.00 3.24
5600 6167 0.373716 GTTGTAAGCGCCGAATCCTG 59.626 55.000 2.29 0.00 0.00 3.86
5614 6181 3.471680 GAATCCTGATTGTGCTCCTACC 58.528 50.000 0.00 0.00 0.00 3.18
5700 6270 2.049526 ATCGTCGACGCTGCAACA 60.050 55.556 32.19 14.36 39.60 3.33
5705 6275 2.661537 CGACGCTGCAACACTGGA 60.662 61.111 0.00 0.00 0.00 3.86
5719 6289 1.069765 CTGGAGCTGTGTTGACGGT 59.930 57.895 0.00 0.00 0.00 4.83
5723 6293 1.222115 GAGCTGTGTTGACGGTGTCC 61.222 60.000 0.00 0.00 0.00 4.02
5725 6295 1.222115 GCTGTGTTGACGGTGTCCTC 61.222 60.000 0.00 0.00 0.00 3.71
5737 6307 4.222847 GTCCTCCGGCCGTCCATC 62.223 72.222 26.12 7.77 0.00 3.51
5740 6310 4.570663 CTCCGGCCGTCCATCGTC 62.571 72.222 26.12 0.00 37.94 4.20
5755 6325 2.280592 GTCGTCCACTGCCCGTTT 60.281 61.111 0.00 0.00 0.00 3.60
5765 6335 2.282887 GCCCGTTTCCCCACATGT 60.283 61.111 0.00 0.00 0.00 3.21
5769 6339 0.960364 CCGTTTCCCCACATGTCCTG 60.960 60.000 0.00 0.00 0.00 3.86
5781 6351 1.265454 ATGTCCTGTCCCGGTCCTTC 61.265 60.000 0.00 0.00 0.00 3.46
5793 6364 1.792006 GGTCCTTCGACGATGTTTGT 58.208 50.000 0.00 0.00 40.17 2.83
5800 6371 4.260620 CCTTCGACGATGTTTGTCTTTGTT 60.261 41.667 0.00 0.00 34.17 2.83
5802 6373 4.583426 TCGACGATGTTTGTCTTTGTTTG 58.417 39.130 0.00 0.00 34.17 2.93
5829 6400 8.142994 TCTTTCTCTTCATGTTAACTTGTGAC 57.857 34.615 18.04 0.00 0.00 3.67
5834 6405 9.042008 TCTCTTCATGTTAACTTGTGACTTAAC 57.958 33.333 18.04 0.59 34.65 2.01
5839 6410 6.425577 TGTTAACTTGTGACTTAACCACAC 57.574 37.500 7.22 0.00 43.37 3.82
5841 6412 2.557317 ACTTGTGACTTAACCACACGG 58.443 47.619 11.74 8.24 43.37 4.94
5857 6428 3.712881 GGTCAACCGAGCGTGTGC 61.713 66.667 0.00 0.00 43.24 4.57
5860 6431 1.596752 TCAACCGAGCGTGTGCAAT 60.597 52.632 0.00 0.00 46.23 3.56
5866 6437 0.735978 CGAGCGTGTGCAATGTCCTA 60.736 55.000 0.00 0.00 46.23 2.94
5870 6441 2.420022 AGCGTGTGCAATGTCCTATTTC 59.580 45.455 0.00 0.00 46.23 2.17
5918 6489 5.895636 TTTTTCACCATGAAGCGATGTAT 57.104 34.783 0.00 0.00 37.70 2.29
5919 6490 5.484173 TTTTCACCATGAAGCGATGTATC 57.516 39.130 0.00 0.00 37.70 2.24
5920 6491 3.817709 TCACCATGAAGCGATGTATCA 57.182 42.857 0.00 0.00 0.00 2.15
5921 6492 4.341366 TCACCATGAAGCGATGTATCAT 57.659 40.909 0.00 0.00 34.22 2.45
5922 6493 5.467035 TCACCATGAAGCGATGTATCATA 57.533 39.130 0.00 0.00 32.73 2.15
5923 6494 5.852827 TCACCATGAAGCGATGTATCATAA 58.147 37.500 0.00 0.00 32.73 1.90
5924 6495 6.466812 TCACCATGAAGCGATGTATCATAAT 58.533 36.000 0.00 0.00 32.73 1.28
5925 6496 7.610865 TCACCATGAAGCGATGTATCATAATA 58.389 34.615 0.00 0.00 32.73 0.98
5926 6497 8.260114 TCACCATGAAGCGATGTATCATAATAT 58.740 33.333 0.00 0.00 32.73 1.28
5927 6498 8.886719 CACCATGAAGCGATGTATCATAATATT 58.113 33.333 0.00 0.00 32.73 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.576982 ACTATGACCTCACCGTCTTTTCA 59.423 43.478 0.00 0.00 33.70 2.69
38 39 3.211865 AGCTGACCTCATGCATACAATG 58.788 45.455 0.00 0.00 0.00 2.82
39 40 3.572632 AGCTGACCTCATGCATACAAT 57.427 42.857 0.00 0.00 0.00 2.71
47 48 4.502950 GGATTTCTCCTAGCTGACCTCATG 60.503 50.000 0.00 0.00 38.65 3.07
48 49 3.645687 GGATTTCTCCTAGCTGACCTCAT 59.354 47.826 0.00 0.00 38.65 2.90
74 75 2.488792 CGTGTCATGCGACGACGAG 61.489 63.158 12.29 0.00 45.80 4.18
75 76 2.501008 CGTGTCATGCGACGACGA 60.501 61.111 12.29 0.00 45.80 4.20
76 77 0.587985 TATCGTGTCATGCGACGACG 60.588 55.000 17.77 2.12 46.60 5.12
77 78 0.838229 GTATCGTGTCATGCGACGAC 59.162 55.000 17.77 6.72 46.60 4.34
79 80 1.529065 CGGTATCGTGTCATGCGACG 61.529 60.000 9.36 9.36 45.80 5.12
86 87 0.168788 GGAACGTCGGTATCGTGTCA 59.831 55.000 0.00 0.00 41.38 3.58
95 96 0.601841 GGAACACATGGAACGTCGGT 60.602 55.000 0.00 0.00 0.00 4.69
103 104 2.505407 CCAGGTATCAGGAACACATGGA 59.495 50.000 10.73 0.00 44.78 3.41
135 136 2.058001 ATCGCTCACACCGATCCCA 61.058 57.895 0.00 0.00 41.13 4.37
195 196 2.754648 CGTGCAAGGACGTGATCAT 58.245 52.632 5.93 0.00 34.56 2.45
229 230 1.075600 GTCCTCCTAGGCTCTGGCT 60.076 63.158 2.96 0.00 42.39 4.75
230 231 2.494530 CGTCCTCCTAGGCTCTGGC 61.495 68.421 2.96 0.00 34.61 4.85
231 232 0.821711 CTCGTCCTCCTAGGCTCTGG 60.822 65.000 2.96 3.80 34.61 3.86
232 233 0.821711 CCTCGTCCTCCTAGGCTCTG 60.822 65.000 2.96 0.00 34.61 3.35
233 234 1.283381 ACCTCGTCCTCCTAGGCTCT 61.283 60.000 2.96 0.00 34.61 4.09
274 282 2.995574 ACTACGCCGTTGAGCCCT 60.996 61.111 5.55 0.00 0.00 5.19
299 307 2.671619 CACGGCACCGGGTTCAAT 60.672 61.111 14.51 0.00 44.69 2.57
310 318 3.507597 TACTTCTGCGTGCACGGCA 62.508 57.895 37.47 31.25 40.23 5.69
347 355 2.343758 GTCACCTTCTGCCTCGCA 59.656 61.111 0.00 0.00 36.92 5.10
399 407 4.063967 TGAGAACGGCGCCATCGT 62.064 61.111 28.98 16.32 43.14 3.73
416 424 4.125695 GCCTACTTCGCCGACCGT 62.126 66.667 0.00 0.00 38.35 4.83
517 525 1.741770 ATGGGCACGAAGACGAAGC 60.742 57.895 0.00 0.00 42.66 3.86
563 574 4.497340 CCGGCAACATATACAAATCGCTTT 60.497 41.667 0.00 0.00 0.00 3.51
592 1065 3.334751 CGACACAAACGCGAGCCA 61.335 61.111 15.93 0.00 0.00 4.75
596 1069 0.247735 CAAAACCGACACAAACGCGA 60.248 50.000 15.93 0.00 0.00 5.87
603 1076 2.554893 GGCCTAATTCAAAACCGACACA 59.445 45.455 0.00 0.00 0.00 3.72
620 1093 1.101049 CAACAACACCAACGAGGCCT 61.101 55.000 3.86 3.86 43.14 5.19
659 1132 1.831580 GGGCTGCTTCTTTCTGATGT 58.168 50.000 0.00 0.00 0.00 3.06
726 1199 2.028125 GATCCACCCGGCGAAGATGA 62.028 60.000 9.30 0.00 0.00 2.92
940 1430 2.283529 ATCGCTCACCCAACGAGGT 61.284 57.895 0.00 0.00 42.40 3.85
976 1466 0.751277 TTTCCCCGTATACCTCGCGA 60.751 55.000 9.26 9.26 0.00 5.87
988 1478 1.745087 CTTCCACATGTGATTTCCCCG 59.255 52.381 27.46 7.74 0.00 5.73
993 1483 1.541147 CACGCCTTCCACATGTGATTT 59.459 47.619 27.46 1.10 32.39 2.17
1080 1570 0.035725 CAGCAGTGCCATTCTGGAGA 60.036 55.000 12.58 0.00 40.96 3.71
1183 1673 3.005554 CTCCGGAGCATTATTGGCATAG 58.994 50.000 20.67 0.00 0.00 2.23
1231 1721 0.320050 TGTAGCAGCGTTCACCATCA 59.680 50.000 0.00 0.00 0.00 3.07
1263 1753 0.612744 GCAGAGAGAGGTGCCTTCTT 59.387 55.000 0.00 0.00 33.29 2.52
1306 1796 1.954927 CACTAAATCCGGCTTCCTCC 58.045 55.000 0.00 0.00 0.00 4.30
1338 1828 2.335712 GCCTCGCACTTTTCCCCAG 61.336 63.158 0.00 0.00 0.00 4.45
1345 1835 0.674895 GGACATCAGCCTCGCACTTT 60.675 55.000 0.00 0.00 0.00 2.66
1581 2071 1.002430 TCCTAACTTCTGCTGCACCTG 59.998 52.381 0.00 0.00 0.00 4.00
1622 2112 1.416401 CCACGAAGCCCACCTATACAT 59.584 52.381 0.00 0.00 0.00 2.29
1719 2209 1.609208 AAGCAACGATTCAGCTTGGT 58.391 45.000 7.06 0.00 45.99 3.67
1732 2222 2.161211 GTCATCCAGCAAGAGAAGCAAC 59.839 50.000 0.00 0.00 0.00 4.17
1810 2300 4.069232 TCGAGGTGGCCAGCTTCG 62.069 66.667 36.40 34.05 39.57 3.79
2011 2501 6.173339 GTCTCCCTTGACTAAATCATTGACA 58.827 40.000 0.00 0.00 37.11 3.58
2019 2509 9.232473 GTAAGAATTTGTCTCCCTTGACTAAAT 57.768 33.333 0.00 0.00 35.91 1.40
2104 2594 4.630894 TTCTTTTGCGACAGTTGACAAT 57.369 36.364 0.00 0.00 0.00 2.71
2143 2633 9.865152 TCCAAGAAATTCATCATATCACCAATA 57.135 29.630 0.00 0.00 0.00 1.90
2291 2781 1.135286 GCCAAAGGTTGTAGCATCTGC 60.135 52.381 0.00 0.00 42.49 4.26
2569 3059 6.054295 AGTCTCCATTGTTCTCAAGATATGC 58.946 40.000 0.00 0.00 36.97 3.14
2768 3258 6.591834 AGAATCTGTACCAACGAAATCTCAAG 59.408 38.462 0.00 0.00 0.00 3.02
3074 3564 4.278170 CCTGTCCAAAACTAATCTTGCACA 59.722 41.667 0.00 0.00 0.00 4.57
3149 3639 5.071250 TGTTCCTTTCTGTACAGAAGCCTAA 59.929 40.000 31.23 22.27 46.80 2.69
3229 3719 4.890988 TGAGGGGTATCACATCCTTCTTA 58.109 43.478 0.00 0.00 0.00 2.10
3244 3734 1.349026 CACAAGTGACTGATGAGGGGT 59.651 52.381 0.00 0.00 0.00 4.95
3304 3794 2.913054 GATAGCAGTCCAGCAGCGCA 62.913 60.000 11.47 0.00 36.85 6.09
3437 3927 3.054361 ACATTAAGAATCAGGGAACGGCT 60.054 43.478 0.00 0.00 0.00 5.52
3445 3935 3.881688 CCTCTGCCACATTAAGAATCAGG 59.118 47.826 0.00 0.00 0.00 3.86
3486 3976 2.579207 TCCAATCGATTCGACAGTCC 57.421 50.000 11.56 0.00 39.18 3.85
3506 3996 7.517614 TTTTGTTAAGGCAGATGTCATACAA 57.482 32.000 0.00 0.00 0.00 2.41
3532 4022 4.007659 GGGTGAACACATCCGATACTTTT 58.992 43.478 7.25 0.00 0.00 2.27
3550 4040 0.673437 AGAACGCAAATTGGTGGGTG 59.327 50.000 0.00 0.00 43.24 4.61
3565 4055 4.997395 TCAAACCATGCTAGTGAAGAGAAC 59.003 41.667 0.00 0.00 0.00 3.01
3808 4298 2.274437 AGCATGATACACAGAACTGCG 58.726 47.619 0.00 0.00 36.34 5.18
3847 4337 5.383476 AGTAGGCGGTAGCTAGAAATAGAA 58.617 41.667 0.00 0.00 44.37 2.10
3868 4358 1.202639 TCACACATTCTGCGGACAAGT 60.203 47.619 0.00 0.00 0.00 3.16
3910 4400 3.251972 GCATCAGCTCCTTAAGGCATAAC 59.748 47.826 17.32 4.02 37.91 1.89
3915 4405 1.674962 CTTGCATCAGCTCCTTAAGGC 59.325 52.381 17.32 6.12 42.74 4.35
3931 4421 3.198068 TGTTGACTTCTCACTGTCTTGC 58.802 45.455 0.00 0.00 34.57 4.01
4018 4508 6.542821 ACCTTTCATATCCTTCAACAACTCA 58.457 36.000 0.00 0.00 0.00 3.41
4021 4511 7.241376 CGTTACCTTTCATATCCTTCAACAAC 58.759 38.462 0.00 0.00 0.00 3.32
4090 4580 4.082190 TCGGTATCTCCAGACTTGTGAAAG 60.082 45.833 0.00 0.00 35.57 2.62
4164 4654 2.093973 ACTATTCTGAGACTGCGGTTGG 60.094 50.000 0.00 0.00 0.00 3.77
4198 4688 1.207089 TCGAGGTTCCCTAACATGCAG 59.793 52.381 0.00 0.00 37.34 4.41
4229 4719 7.014038 ACTGCCCTCAATCAGATGAAATAATTC 59.986 37.037 0.00 0.00 34.57 2.17
4420 4910 5.408299 CAGATTAACAGACATTTCCACGTCA 59.592 40.000 0.00 0.00 34.48 4.35
4513 5003 6.183360 CCCGGTCAAATTCTTTCAGTATACAC 60.183 42.308 5.50 0.00 0.00 2.90
4534 5024 0.456653 CAAGAAAATCAAGCGCCCGG 60.457 55.000 2.29 0.00 0.00 5.73
4574 5064 5.641209 CACAGGATCTCTCACTTGGTTTTAG 59.359 44.000 0.00 0.00 0.00 1.85
4590 5080 1.602851 GCATGAGCACATCACAGGATC 59.397 52.381 0.00 0.00 41.91 3.36
4591 5081 1.676746 GCATGAGCACATCACAGGAT 58.323 50.000 0.00 0.00 41.91 3.24
4602 5092 2.282391 AAAGGCCACGCATGAGCA 60.282 55.556 5.01 0.00 42.27 4.26
4622 5112 2.549992 CGTCACTGGTTCTTCCCATTGA 60.550 50.000 0.00 0.00 40.62 2.57
4624 5114 1.882352 GCGTCACTGGTTCTTCCCATT 60.882 52.381 0.00 0.00 33.00 3.16
5091 5604 2.291465 CGGGCTCAATGTCCATGTATTG 59.709 50.000 7.77 7.77 41.50 1.90
5173 5686 2.593346 TTTTGTGTTGCCAATTCGCT 57.407 40.000 0.00 0.00 0.00 4.93
5239 5768 0.963962 AAAACCTACTCCGCGAGTCA 59.036 50.000 8.23 0.00 42.40 3.41
5242 5771 5.179045 TCTATTAAAACCTACTCCGCGAG 57.821 43.478 8.23 5.77 35.52 5.03
5259 5788 9.476202 GCAAGGTAAAAGAACACAATTTCTATT 57.524 29.630 0.00 0.00 34.60 1.73
5266 5799 5.127031 ACACTGCAAGGTAAAAGAACACAAT 59.873 36.000 0.00 0.00 39.30 2.71
5289 5830 1.142097 GGAGCTCGCAAGACCCTAC 59.858 63.158 7.83 0.00 45.01 3.18
5321 5862 4.515361 AGGTCATCTTGATGCTCTTCTTG 58.485 43.478 5.78 0.00 0.00 3.02
5328 5869 4.681781 CGGAAGTAAGGTCATCTTGATGCT 60.682 45.833 5.78 0.00 36.93 3.79
5406 5955 7.148239 CCAAACCCTCATATAAGGAATAATCGC 60.148 40.741 0.00 0.00 38.87 4.58
5412 5961 5.435041 TCCACCAAACCCTCATATAAGGAAT 59.565 40.000 0.00 0.00 38.87 3.01
5446 5995 5.409826 GGCTATGAGATATTACTGTTGTGGC 59.590 44.000 0.00 0.00 0.00 5.01
5502 6069 5.845985 TCAGACGAAAACAATAGCAGAAG 57.154 39.130 0.00 0.00 0.00 2.85
5505 6072 5.120674 TGTGATCAGACGAAAACAATAGCAG 59.879 40.000 0.00 0.00 0.00 4.24
5508 6075 7.479603 CACAATGTGATCAGACGAAAACAATAG 59.520 37.037 7.78 0.00 35.23 1.73
5577 6144 2.440501 GATTCGGCGCTTACAACAATG 58.559 47.619 7.64 0.00 0.00 2.82
5589 6156 1.091771 AGCACAATCAGGATTCGGCG 61.092 55.000 0.00 0.00 34.16 6.46
5599 6166 0.253044 GCAGGGTAGGAGCACAATCA 59.747 55.000 0.00 0.00 0.00 2.57
5600 6167 0.464554 GGCAGGGTAGGAGCACAATC 60.465 60.000 0.00 0.00 0.00 2.67
5614 6181 0.615331 ACATGACCTAGTGTGGCAGG 59.385 55.000 0.00 0.00 37.97 4.85
5652 6219 2.682494 GTCACCGGGAGCAGGGTA 60.682 66.667 6.32 0.00 33.95 3.69
5700 6270 1.069765 CCGTCAACACAGCTCCAGT 59.930 57.895 0.00 0.00 0.00 4.00
5705 6275 1.227556 GGACACCGTCAACACAGCT 60.228 57.895 0.00 0.00 33.68 4.24
5707 6277 0.600255 GGAGGACACCGTCAACACAG 60.600 60.000 0.00 0.00 33.68 3.66
5708 6278 1.444250 GGAGGACACCGTCAACACA 59.556 57.895 0.00 0.00 33.68 3.72
5723 6293 4.570663 GACGATGGACGGCCGGAG 62.571 72.222 31.76 15.41 45.37 4.63
5731 6301 1.805945 GCAGTGGACGACGATGGAC 60.806 63.158 0.00 0.00 0.00 4.02
5737 6307 4.657824 AACGGGCAGTGGACGACG 62.658 66.667 0.00 0.00 0.00 5.12
5738 6308 2.280592 AAACGGGCAGTGGACGAC 60.281 61.111 0.00 0.00 0.00 4.34
5739 6309 2.029964 GAAACGGGCAGTGGACGA 59.970 61.111 0.00 0.00 0.00 4.20
5740 6310 3.047877 GGAAACGGGCAGTGGACG 61.048 66.667 0.00 0.00 0.00 4.79
5755 6325 1.923395 GGGACAGGACATGTGGGGA 60.923 63.158 1.15 0.00 44.17 4.81
5765 6335 2.678934 CGAAGGACCGGGACAGGA 60.679 66.667 6.32 0.00 34.73 3.86
5769 6339 2.413142 ATCGTCGAAGGACCGGGAC 61.413 63.158 6.32 0.62 40.17 4.46
5781 6351 4.583426 TCAAACAAAGACAAACATCGTCG 58.417 39.130 0.00 0.00 38.46 5.12
5793 6364 8.455903 ACATGAAGAGAAAGATCAAACAAAGA 57.544 30.769 0.00 0.00 0.00 2.52
5800 6371 9.342308 ACAAGTTAACATGAAGAGAAAGATCAA 57.658 29.630 17.18 0.00 0.00 2.57
5802 6373 8.993121 TCACAAGTTAACATGAAGAGAAAGATC 58.007 33.333 17.18 0.00 0.00 2.75
5841 6412 1.841663 ATTGCACACGCTCGGTTGAC 61.842 55.000 0.00 0.00 39.64 3.18
5848 6419 1.656652 ATAGGACATTGCACACGCTC 58.343 50.000 0.00 0.00 39.64 5.03
5855 6426 4.081697 TGAGACTCGAAATAGGACATTGCA 60.082 41.667 0.00 0.00 0.00 4.08
5857 6428 5.694006 GGATGAGACTCGAAATAGGACATTG 59.306 44.000 0.00 0.00 0.00 2.82
5860 6431 4.278310 TGGATGAGACTCGAAATAGGACA 58.722 43.478 0.00 0.00 0.00 4.02
5866 6437 4.836825 ACACATTGGATGAGACTCGAAAT 58.163 39.130 0.00 0.00 0.00 2.17
5870 6441 3.329386 ACAACACATTGGATGAGACTCG 58.671 45.455 0.00 0.00 40.42 4.18


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

AutoCloner maintained by Alex Coulton.