Multiple sequence alignment - TraesCS6D01G313100

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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 TraesCS6D01G313100 chr6D 100.000 4952 0 0 1 4952 422077635 422082586 0.000000e+00 9145.0
1 TraesCS6D01G313100 chr6B 93.190 3994 176 43 565 4521 636392307 636396241 0.000000e+00 5781.0
2 TraesCS6D01G313100 chr6B 91.235 251 18 2 986 1236 202352779 202353025 6.140000e-89 339.0
3 TraesCS6D01G313100 chr6B 84.393 346 40 12 67 406 636391902 636392239 1.330000e-85 327.0
4 TraesCS6D01G313100 chr6B 84.774 243 28 5 4718 4952 636396353 636396594 8.290000e-58 235.0
5 TraesCS6D01G313100 chr6A 93.191 3701 121 45 492 4161 564882254 564885854 0.000000e+00 5317.0
6 TraesCS6D01G313100 chr6A 84.387 807 102 14 4158 4952 564886111 564886905 0.000000e+00 771.0
7 TraesCS6D01G313100 chr6A 94.602 352 14 4 117 465 564881908 564882257 1.570000e-149 540.0
8 TraesCS6D01G313100 chr6A 90.837 251 19 3 986 1236 146494334 146494088 2.860000e-87 333.0
9 TraesCS6D01G313100 chr6A 90.756 119 10 1 1 119 564881534 564881651 1.850000e-34 158.0
10 TraesCS6D01G313100 chr1D 93.204 206 14 0 986 1191 414710838 414711043 2.240000e-78 303.0
11 TraesCS6D01G313100 chr1D 92.233 206 16 0 986 1191 428617769 428617564 4.850000e-75 292.0
12 TraesCS6D01G313100 chr1D 95.200 125 5 1 1305 1429 414711078 414711201 3.910000e-46 196.0
13 TraesCS6D01G313100 chr1D 95.200 125 5 1 1305 1429 428617529 428617406 3.910000e-46 196.0
14 TraesCS6D01G313100 chr3D 92.718 206 15 0 986 1191 572506362 572506157 1.040000e-76 298.0
15 TraesCS6D01G313100 chr3D 94.400 125 6 1 1305 1429 572506122 572505999 1.820000e-44 191.0
16 TraesCS6D01G313100 chr7D 91.748 206 17 0 986 1191 69450024 69449819 2.260000e-73 287.0
17 TraesCS6D01G313100 chr7D 95.200 125 5 1 1305 1429 69449784 69449661 3.910000e-46 196.0
18 TraesCS6D01G313100 chr7D 100.000 28 0 0 4730 4757 431028201 431028174 9.000000e-03 52.8
19 TraesCS6D01G313100 chr7B 84.375 256 23 9 986 1236 747327498 747327255 8.290000e-58 235.0
20 TraesCS6D01G313100 chr5A 94.400 125 5 2 1305 1429 137045045 137044923 1.820000e-44 191.0
21 TraesCS6D01G313100 chr5B 92.800 125 8 1 1305 1429 262568193 262568070 3.940000e-41 180.0
22 TraesCS6D01G313100 chr1A 92.800 125 8 1 1305 1429 565149774 565149897 3.940000e-41 180.0
23 TraesCS6D01G313100 chr1A 85.714 112 9 3 1128 1236 565149665 565149772 1.460000e-20 111.0


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 TraesCS6D01G313100 chr6D 422077635 422082586 4951 False 9145.000000 9145 100.000000 1 4952 1 chr6D.!!$F1 4951
1 TraesCS6D01G313100 chr6B 636391902 636396594 4692 False 2114.333333 5781 87.452333 67 4952 3 chr6B.!!$F2 4885
2 TraesCS6D01G313100 chr6A 564881534 564886905 5371 False 1696.500000 5317 90.734000 1 4952 4 chr6A.!!$F1 4951

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
630 895 1.135083 CAGGACTTAGCCGTGGTGTAG 60.135 57.143 0.0 0.0 0.0 2.74 F
632 897 1.547372 GGACTTAGCCGTGGTGTAGAA 59.453 52.381 0.0 0.0 0.0 2.10 F
2054 2364 0.647410 GATTCATGACACGCACGGAG 59.353 55.000 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2164 0.036858 TGAATGCGACGGTTGGATGA 60.037 50.0 2.90 0.0 0.0 2.92 R
2060 2370 0.179702 ATCTCACCATGCGCTGTCAT 59.820 50.0 9.73 0.0 0.0 3.06 R
3965 4284 0.250513 GAAGAAGATCAGCCGGTGGT 59.749 55.0 1.90 0.0 0.0 4.16 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
35 36 8.589335 TCAACTAACTTGAATGACTGTCTAAC 57.411 34.615 9.51 1.17 35.84 2.34
43 44 4.521639 TGAATGACTGTCTAACACTACGGT 59.478 41.667 9.51 0.00 37.91 4.83
44 45 5.010314 TGAATGACTGTCTAACACTACGGTT 59.990 40.000 9.51 0.00 35.37 4.44
57 58 2.296471 ACTACGGTTTGTGAGACCTGAG 59.704 50.000 0.00 0.00 34.95 3.35
62 63 3.279434 GGTTTGTGAGACCTGAGTTGTT 58.721 45.455 0.00 0.00 34.27 2.83
137 397 7.490402 AGTTTGTATGACTACGTATACTTTGCC 59.510 37.037 0.00 0.00 32.37 4.52
157 417 1.138661 CACAAAATGGTTGGGTGCACT 59.861 47.619 17.98 0.00 0.00 4.40
176 436 5.580691 TGCACTATCCAATACAGAAGAAACG 59.419 40.000 0.00 0.00 0.00 3.60
344 604 6.587608 GCATCCCTCATTTTTGTTTGTAGAAG 59.412 38.462 0.00 0.00 0.00 2.85
425 687 5.413213 TGTCCGAAATTACAATTGTAGGTGG 59.587 40.000 17.36 15.21 0.00 4.61
465 727 5.412594 CAGCTATGTTCAAGTCCTGCTTTAA 59.587 40.000 0.00 0.00 34.69 1.52
466 728 6.094603 CAGCTATGTTCAAGTCCTGCTTTAAT 59.905 38.462 0.00 0.00 34.69 1.40
467 729 7.280876 CAGCTATGTTCAAGTCCTGCTTTAATA 59.719 37.037 0.00 0.00 34.69 0.98
468 730 7.995488 AGCTATGTTCAAGTCCTGCTTTAATAT 59.005 33.333 0.00 0.00 34.69 1.28
469 731 8.624776 GCTATGTTCAAGTCCTGCTTTAATATT 58.375 33.333 0.00 0.00 34.69 1.28
470 732 9.941664 CTATGTTCAAGTCCTGCTTTAATATTG 57.058 33.333 0.00 0.00 34.69 1.90
472 734 6.719370 TGTTCAAGTCCTGCTTTAATATTGGT 59.281 34.615 0.00 0.00 34.69 3.67
473 735 7.885922 TGTTCAAGTCCTGCTTTAATATTGGTA 59.114 33.333 0.00 0.00 34.69 3.25
474 736 8.903820 GTTCAAGTCCTGCTTTAATATTGGTAT 58.096 33.333 0.00 0.00 34.69 2.73
518 780 8.667987 TTGCGAAAACATTATTTAGTGATCAC 57.332 30.769 18.47 18.47 0.00 3.06
603 868 3.308595 TGTCGCCGCAAAATGTAGAATAG 59.691 43.478 0.00 0.00 0.00 1.73
611 876 6.238456 CCGCAAAATGTAGAATAGATTCAGCA 60.238 38.462 5.11 3.74 32.87 4.41
612 877 6.849811 CGCAAAATGTAGAATAGATTCAGCAG 59.150 38.462 5.11 0.00 32.87 4.24
630 895 1.135083 CAGGACTTAGCCGTGGTGTAG 60.135 57.143 0.00 0.00 0.00 2.74
632 897 1.547372 GGACTTAGCCGTGGTGTAGAA 59.453 52.381 0.00 0.00 0.00 2.10
634 899 3.369157 GGACTTAGCCGTGGTGTAGAAAT 60.369 47.826 0.00 0.00 0.00 2.17
635 900 3.858247 ACTTAGCCGTGGTGTAGAAATC 58.142 45.455 0.00 0.00 0.00 2.17
638 903 1.899814 AGCCGTGGTGTAGAAATCTCA 59.100 47.619 0.00 0.00 0.00 3.27
642 908 4.612939 GCCGTGGTGTAGAAATCTCAAAAC 60.613 45.833 0.00 0.00 0.00 2.43
714 999 3.934457 AAACTTCCCATTTTACGCCTG 57.066 42.857 0.00 0.00 0.00 4.85
835 1120 3.564262 CAGCATCTGCCCTCTTGAA 57.436 52.632 0.00 0.00 43.38 2.69
978 1281 4.892965 GCAGCACCACCACCACCA 62.893 66.667 0.00 0.00 0.00 4.17
1446 1749 2.787249 CTCCGCACCATCGCAAAG 59.213 61.111 0.00 0.00 0.00 2.77
1448 1751 1.577328 CTCCGCACCATCGCAAAGTT 61.577 55.000 0.00 0.00 0.00 2.66
1477 1780 8.128582 TCGTTTACTTGATCAAATAATGCATCC 58.871 33.333 9.95 0.00 0.00 3.51
1689 1995 1.674962 GATCTTGGCAGAATCAGTGGC 59.325 52.381 6.37 0.00 40.81 5.01
1713 2019 6.515043 AAGAATTGACATTTTGTTTCTGCG 57.485 33.333 0.00 0.00 28.70 5.18
1760 2066 3.517296 TTGCTAGGGTGATTTGACCAA 57.483 42.857 0.00 0.00 37.80 3.67
1802 2108 7.773099 TGGTATTACCCATATGGCCATATTA 57.227 36.000 31.73 20.41 37.50 0.98
1863 2169 5.782047 CAGACTATTCTGTGATCCTCATCC 58.218 45.833 1.99 0.00 43.95 3.51
1991 2297 8.159229 ACTAGTCTGGGGTCATATTAGTTTTT 57.841 34.615 0.00 0.00 0.00 1.94
2034 2340 7.856894 GTGATACTAGTCGACTTTCTATTGGTC 59.143 40.741 25.44 10.12 0.00 4.02
2054 2364 0.647410 GATTCATGACACGCACGGAG 59.353 55.000 0.00 0.00 0.00 4.63
2060 2370 4.539083 ACACGCACGGAGTTGCCA 62.539 61.111 0.00 0.00 41.61 4.92
2063 2373 2.741985 CGCACGGAGTTGCCATGA 60.742 61.111 0.00 0.00 41.61 3.07
2077 2387 1.719709 CATGACAGCGCATGGTGAG 59.280 57.895 11.47 0.00 46.53 3.51
2110 2420 3.068448 TGCTGTCAAATGCAACAACAGAT 59.932 39.130 19.80 0.00 39.72 2.90
2111 2421 3.671928 GCTGTCAAATGCAACAACAGATC 59.328 43.478 19.80 5.43 39.72 2.75
2112 2422 4.793678 GCTGTCAAATGCAACAACAGATCA 60.794 41.667 19.80 0.52 39.72 2.92
2119 2429 4.607293 TGCAACAACAGATCAGTAGACT 57.393 40.909 0.00 0.00 0.00 3.24
2178 2488 2.301870 AGTACCCGACACACATGATGTT 59.698 45.455 0.00 0.00 40.64 2.71
2227 2539 1.548719 GGTTTATCCCAAACCAGTGGC 59.451 52.381 9.78 0.00 46.74 5.01
2234 2546 0.389025 CCAAACCAGTGGCTCCAAAC 59.611 55.000 9.78 0.00 0.00 2.93
2264 2576 1.813102 TTTGGGCCATTCCTTTGGTT 58.187 45.000 7.26 0.00 39.11 3.67
2266 2578 0.486879 TGGGCCATTCCTTTGGTTCT 59.513 50.000 0.00 0.00 39.11 3.01
2285 2597 3.149196 TCTTTCCTGCAAAAAGAGCGAT 58.851 40.909 16.18 0.00 37.72 4.58
2328 2640 0.738975 TGCGATCTAAGTCGACTGGG 59.261 55.000 20.85 14.74 44.06 4.45
2743 3060 1.806542 ACGTCATGTTCATCTTGCACC 59.193 47.619 0.00 0.00 0.00 5.01
2809 3126 4.980903 GCCGTTGCTGCCGTGTTG 62.981 66.667 0.00 0.00 33.53 3.33
2862 3179 1.143183 GTGCGTGATCGGTACCCAT 59.857 57.895 6.25 0.00 37.56 4.00
3133 3450 0.108615 CGTAAGCTCCTCCCACACTG 60.109 60.000 0.00 0.00 0.00 3.66
3134 3451 0.250513 GTAAGCTCCTCCCACACTGG 59.749 60.000 0.00 0.00 37.25 4.00
3136 3453 3.325753 GCTCCTCCCACACTGGCT 61.326 66.667 0.00 0.00 35.79 4.75
3148 3465 0.515564 CACTGGCTAAACGAAACGGG 59.484 55.000 0.00 0.00 0.00 5.28
3193 3512 2.638480 TGTGGTTCTGAACTTCTGGG 57.362 50.000 19.05 0.00 0.00 4.45
3204 3523 1.078426 CTTCTGGGGTTTCGGCGAT 60.078 57.895 11.76 0.00 0.00 4.58
3363 3682 2.896443 GAGGGGCTCTCCTTCGTG 59.104 66.667 1.89 0.00 37.25 4.35
3477 3796 1.078759 CCGTGGAGCAGAACATCGTC 61.079 60.000 0.00 0.00 0.00 4.20
3491 3810 1.189524 ATCGTCCTCCCCAACGTCAA 61.190 55.000 0.00 0.00 39.78 3.18
3507 3826 3.107642 GTCAAGAACGAGAAGGTGGAA 57.892 47.619 0.00 0.00 0.00 3.53
3965 4284 2.838225 GTAGGCCGGCTAGGAGCA 60.838 66.667 28.56 0.44 44.75 4.26
3980 4308 2.045926 GCACCACCGGCTGATCTT 60.046 61.111 0.00 0.00 0.00 2.40
4153 4486 5.496556 ACGTTACAGGGATGATTGAATTGA 58.503 37.500 0.00 0.00 0.00 2.57
4225 4818 3.044235 TCAATCCTGTGCTACAGTGTG 57.956 47.619 5.88 0.00 44.50 3.82
4239 4832 3.466712 CAGTGTGCTGTTGCTAGATTG 57.533 47.619 0.00 0.00 40.48 2.67
4267 4860 1.680522 AATCGGGAGCTCAGCATCGT 61.681 55.000 17.19 0.29 0.00 3.73
4311 4904 1.273606 TCACAGCTTGGTAGTGCTCTC 59.726 52.381 0.00 0.00 37.44 3.20
4361 4978 1.266718 TCAACTTTGCCAAGTGATCGC 59.733 47.619 3.60 0.00 42.89 4.58
4363 4980 1.160137 ACTTTGCCAAGTGATCGCTC 58.840 50.000 9.70 0.00 42.05 5.03
4421 5038 2.961526 TAGAGGCAACATCGGTTCTC 57.038 50.000 0.00 0.00 34.21 2.87
4486 5104 0.175760 TCGTACTCAGCAAGCCATCC 59.824 55.000 0.00 0.00 0.00 3.51
4507 5125 2.434359 GAGGCGTTCCAACCCTCG 60.434 66.667 9.76 0.00 36.96 4.63
4546 5164 1.600957 CCATCAGAGCATTTACAGCCG 59.399 52.381 0.00 0.00 0.00 5.52
4550 5168 0.107654 AGAGCATTTACAGCCGGACC 60.108 55.000 5.05 0.00 0.00 4.46
4552 5170 2.119029 GCATTTACAGCCGGACCCC 61.119 63.158 5.05 0.00 0.00 4.95
4553 5171 1.301623 CATTTACAGCCGGACCCCA 59.698 57.895 5.05 0.00 0.00 4.96
4554 5172 0.106719 CATTTACAGCCGGACCCCAT 60.107 55.000 5.05 0.00 0.00 4.00
4555 5173 1.142060 CATTTACAGCCGGACCCCATA 59.858 52.381 5.05 0.00 0.00 2.74
4558 5176 1.513858 TACAGCCGGACCCCATATTT 58.486 50.000 5.05 0.00 0.00 1.40
4560 5178 0.537371 CAGCCGGACCCCATATTTCC 60.537 60.000 5.05 0.00 0.00 3.13
4564 5182 0.400594 CGGACCCCATATTTCCTCCC 59.599 60.000 0.00 0.00 0.00 4.30
4565 5183 0.778083 GGACCCCATATTTCCTCCCC 59.222 60.000 0.00 0.00 0.00 4.81
4567 5185 2.073776 GACCCCATATTTCCTCCCCAT 58.926 52.381 0.00 0.00 0.00 4.00
4568 5186 1.788915 ACCCCATATTTCCTCCCCATG 59.211 52.381 0.00 0.00 0.00 3.66
4569 5187 1.788915 CCCCATATTTCCTCCCCATGT 59.211 52.381 0.00 0.00 0.00 3.21
4570 5188 2.491455 CCCCATATTTCCTCCCCATGTG 60.491 54.545 0.00 0.00 0.00 3.21
4571 5189 2.491455 CCCATATTTCCTCCCCATGTGG 60.491 54.545 0.00 0.00 0.00 4.17
4572 5190 2.446666 CCATATTTCCTCCCCATGTGGA 59.553 50.000 0.00 0.00 37.39 4.02
4573 5191 3.117169 CCATATTTCCTCCCCATGTGGAA 60.117 47.826 0.00 0.90 43.19 3.53
4574 5192 2.532250 ATTTCCTCCCCATGTGGAAC 57.468 50.000 0.00 0.00 44.24 3.62
4575 5193 0.037590 TTTCCTCCCCATGTGGAACG 59.962 55.000 0.00 0.00 44.24 3.95
4576 5194 1.131303 TTCCTCCCCATGTGGAACGT 61.131 55.000 0.00 0.00 40.74 3.99
4590 5208 0.982673 GAACGTCGTCTCGTCAATGG 59.017 55.000 0.00 0.00 43.38 3.16
4637 5256 1.945317 ACCCCTCACTTAGTCCCCTAT 59.055 52.381 0.00 0.00 0.00 2.57
4642 5261 4.140994 CCCTCACTTAGTCCCCTATGTCTA 60.141 50.000 0.00 0.00 31.20 2.59
4648 5267 7.622081 TCACTTAGTCCCCTATGTCTAAATTGA 59.378 37.037 0.00 0.00 31.20 2.57
4649 5268 8.432805 CACTTAGTCCCCTATGTCTAAATTGAT 58.567 37.037 0.00 0.00 31.20 2.57
4677 5297 3.074412 CCCTCATATCGGTACCAAATGC 58.926 50.000 13.54 0.00 0.00 3.56
4683 5303 0.916086 TCGGTACCAAATGCAGGGAT 59.084 50.000 13.54 0.00 0.00 3.85
4695 5315 0.694771 GCAGGGATGATATGAGGGCA 59.305 55.000 0.00 0.00 0.00 5.36
4716 5336 4.681978 GGACGCGACTGGGCACTT 62.682 66.667 15.93 0.00 0.00 3.16
4723 5343 3.959991 GACTGGGCACTTCGCTCCC 62.960 68.421 0.00 0.00 42.28 4.30
4786 5412 2.439156 GCGGCAAGCCTCTCCAAT 60.439 61.111 9.73 0.00 40.81 3.16
4876 5504 9.859427 GAAATATCAATGTTCCATTTGTGAAGA 57.141 29.630 0.00 0.00 0.00 2.87
4884 5512 9.471702 AATGTTCCATTTGTGAAGAAGATAGAT 57.528 29.630 0.00 0.00 0.00 1.98
4914 5542 7.743104 ACTATGAATCTTCTTTGTGTTAAGCG 58.257 34.615 0.00 0.00 0.00 4.68
4920 5548 8.871686 AATCTTCTTTGTGTTAAGCGAAAAAT 57.128 26.923 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.276325 GTGTTAGACAGTCATTCAAGTTAGTTG 58.724 37.037 2.66 0.00 37.52 3.16
26 27 4.098349 TCACAAACCGTAGTGTTAGACAGT 59.902 41.667 0.00 0.00 37.07 3.55
35 36 2.035449 TCAGGTCTCACAAACCGTAGTG 59.965 50.000 0.00 0.00 41.89 2.74
43 44 2.682856 GCAACAACTCAGGTCTCACAAA 59.317 45.455 0.00 0.00 0.00 2.83
44 45 2.288666 GCAACAACTCAGGTCTCACAA 58.711 47.619 0.00 0.00 0.00 3.33
57 58 4.398988 TCCATGGAGATTACATGCAACAAC 59.601 41.667 11.44 0.00 43.29 3.32
62 63 5.069383 CCAAATTCCATGGAGATTACATGCA 59.931 40.000 15.53 0.00 43.29 3.96
137 397 1.138661 AGTGCACCCAACCATTTTGTG 59.861 47.619 14.63 0.00 0.00 3.33
157 417 4.080807 TGCCCGTTTCTTCTGTATTGGATA 60.081 41.667 0.00 0.00 0.00 2.59
200 460 0.830023 ACCATTTGGACGGTTTGGGG 60.830 55.000 3.01 0.00 38.94 4.96
263 523 6.441093 TTTCATGCAGTGATAAACTCATCC 57.559 37.500 0.00 0.00 36.83 3.51
371 632 5.860941 TCAATTGGTTTTTGAGTTGGCTA 57.139 34.783 5.42 0.00 0.00 3.93
372 633 4.751767 TCAATTGGTTTTTGAGTTGGCT 57.248 36.364 5.42 0.00 0.00 4.75
373 634 4.260743 GCTTCAATTGGTTTTTGAGTTGGC 60.261 41.667 5.42 0.00 34.76 4.52
374 635 4.025813 CGCTTCAATTGGTTTTTGAGTTGG 60.026 41.667 5.42 0.00 34.76 3.77
381 643 3.181476 ACAGCTCGCTTCAATTGGTTTTT 60.181 39.130 5.42 0.00 0.00 1.94
425 687 7.611213 ACATAGCTGACATTGTAACCTTAAC 57.389 36.000 0.00 0.00 0.00 2.01
491 753 9.684448 TGATCACTAAATAATGTTTTCGCAAAA 57.316 25.926 0.00 0.00 0.00 2.44
492 754 9.123709 GTGATCACTAAATAATGTTTTCGCAAA 57.876 29.630 18.83 0.00 0.00 3.68
493 755 7.480229 CGTGATCACTAAATAATGTTTTCGCAA 59.520 33.333 22.95 0.00 0.00 4.85
494 756 6.958752 CGTGATCACTAAATAATGTTTTCGCA 59.041 34.615 22.95 0.00 0.00 5.10
587 852 6.718388 TGCTGAATCTATTCTACATTTTGCG 58.282 36.000 4.45 0.00 37.67 4.85
603 868 1.134670 ACGGCTAAGTCCTGCTGAATC 60.135 52.381 0.00 0.00 38.78 2.52
611 876 1.183549 CTACACCACGGCTAAGTCCT 58.816 55.000 0.00 0.00 0.00 3.85
612 877 1.180029 TCTACACCACGGCTAAGTCC 58.820 55.000 0.00 0.00 0.00 3.85
630 895 1.402852 GGCTGCGGGTTTTGAGATTTC 60.403 52.381 0.00 0.00 0.00 2.17
632 897 0.251341 AGGCTGCGGGTTTTGAGATT 60.251 50.000 0.00 0.00 0.00 2.40
634 899 1.600636 CAGGCTGCGGGTTTTGAGA 60.601 57.895 0.00 0.00 0.00 3.27
635 900 1.580845 CTCAGGCTGCGGGTTTTGAG 61.581 60.000 10.34 0.00 0.00 3.02
638 903 2.985847 GCTCAGGCTGCGGGTTTT 60.986 61.111 10.34 0.00 35.22 2.43
835 1120 0.402121 GTTTCTGGCCCTTGGAGAGT 59.598 55.000 0.00 0.00 0.00 3.24
883 1168 2.289756 TGTGGTGCGTGTGGTTGTATAT 60.290 45.455 0.00 0.00 0.00 0.86
953 1256 4.039357 GTGGTGCTGCTGCTGCTG 62.039 66.667 27.67 16.73 40.48 4.41
956 1259 3.667282 GTGGTGGTGCTGCTGCTG 61.667 66.667 17.00 0.77 40.48 4.41
957 1260 4.962836 GGTGGTGGTGCTGCTGCT 62.963 66.667 17.00 0.00 40.48 4.24
959 1262 3.289834 GTGGTGGTGGTGCTGCTG 61.290 66.667 0.00 0.00 0.00 4.41
960 1263 4.586235 GGTGGTGGTGGTGCTGCT 62.586 66.667 0.00 0.00 0.00 4.24
961 1264 4.892965 TGGTGGTGGTGGTGCTGC 62.893 66.667 0.00 0.00 0.00 5.25
962 1265 2.906897 GTGGTGGTGGTGGTGCTG 60.907 66.667 0.00 0.00 0.00 4.41
963 1266 4.204028 GGTGGTGGTGGTGGTGCT 62.204 66.667 0.00 0.00 0.00 4.40
964 1267 4.514585 TGGTGGTGGTGGTGGTGC 62.515 66.667 0.00 0.00 0.00 5.01
965 1268 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
966 1269 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
967 1270 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
968 1271 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
969 1272 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
978 1281 2.519302 GCTGCTTGTGGTGGTGGT 60.519 61.111 0.00 0.00 0.00 4.16
1448 1751 8.672815 TGCATTATTTGATCAAGTAAACGATGA 58.327 29.630 22.49 4.63 0.00 2.92
1477 1780 1.859080 GAATAGTAAGGCCGAAGCACG 59.141 52.381 0.00 0.00 42.56 5.34
1485 1788 4.390297 GCATCGATCAAGAATAGTAAGGCC 59.610 45.833 0.00 0.00 0.00 5.19
1491 1794 4.046938 ACGTGCATCGATCAAGAATAGT 57.953 40.909 14.18 0.00 42.86 2.12
1534 1837 8.388319 TGAAAATTCACAAAAACTTCGTAGTG 57.612 30.769 0.00 0.00 30.92 2.74
1535 1838 8.973835 TTGAAAATTCACAAAAACTTCGTAGT 57.026 26.923 0.00 0.00 36.83 2.73
1538 1841 7.608755 CGATTGAAAATTCACAAAAACTTCGT 58.391 30.769 0.00 0.00 36.83 3.85
1689 1995 6.019640 ACGCAGAAACAAAATGTCAATTCTTG 60.020 34.615 0.00 0.00 26.29 3.02
1802 2108 3.923017 GCAAGTTGCAAATGGAGTAGT 57.077 42.857 22.90 0.00 44.26 2.73
1858 2164 0.036858 TGAATGCGACGGTTGGATGA 60.037 50.000 2.90 0.00 0.00 2.92
1859 2165 1.016627 ATGAATGCGACGGTTGGATG 58.983 50.000 2.90 0.00 0.00 3.51
1860 2166 1.750193 AATGAATGCGACGGTTGGAT 58.250 45.000 0.00 0.00 0.00 3.41
1861 2167 2.276201 CTAATGAATGCGACGGTTGGA 58.724 47.619 0.00 0.00 0.00 3.53
1862 2168 2.006888 ACTAATGAATGCGACGGTTGG 58.993 47.619 0.00 0.00 0.00 3.77
1863 2169 4.745125 AGATACTAATGAATGCGACGGTTG 59.255 41.667 0.00 0.00 0.00 3.77
1955 2261 3.892588 CCCCAGACTAGTCCAAGATACTC 59.107 52.174 19.38 0.00 0.00 2.59
2034 2340 1.075979 TCCGTGCGTGTCATGAATCG 61.076 55.000 13.97 13.97 33.49 3.34
2038 2344 0.943835 CAACTCCGTGCGTGTCATGA 60.944 55.000 0.00 0.00 33.49 3.07
2054 2364 1.515519 CATGCGCTGTCATGGCAAC 60.516 57.895 9.73 0.00 40.49 4.17
2060 2370 0.179702 ATCTCACCATGCGCTGTCAT 59.820 50.000 9.73 0.00 0.00 3.06
2063 2373 0.806868 CAAATCTCACCATGCGCTGT 59.193 50.000 9.73 0.00 0.00 4.40
2077 2387 4.151157 GCATTTGACAGCAAGGAACAAATC 59.849 41.667 0.00 0.00 38.52 2.17
2157 2467 1.899814 ACATCATGTGTGTCGGGTACT 59.100 47.619 0.00 0.00 40.28 2.73
2158 2468 2.380084 ACATCATGTGTGTCGGGTAC 57.620 50.000 0.00 0.00 40.28 3.34
2159 2469 3.410631 AAACATCATGTGTGTCGGGTA 57.589 42.857 0.00 0.00 41.14 3.69
2160 2470 2.270352 AAACATCATGTGTGTCGGGT 57.730 45.000 0.00 0.00 41.14 5.28
2161 2471 3.641437 AAAAACATCATGTGTGTCGGG 57.359 42.857 0.00 0.00 41.14 5.14
2247 2559 0.486879 AGAACCAAAGGAATGGCCCA 59.513 50.000 0.00 0.00 44.75 5.36
2248 2560 1.644509 AAGAACCAAAGGAATGGCCC 58.355 50.000 0.00 0.00 44.75 5.80
2249 2561 2.028112 GGAAAGAACCAAAGGAATGGCC 60.028 50.000 0.00 0.00 44.75 5.36
2250 2562 2.899900 AGGAAAGAACCAAAGGAATGGC 59.100 45.455 0.00 0.00 44.75 4.40
2251 2563 3.306294 GCAGGAAAGAACCAAAGGAATGG 60.306 47.826 0.00 0.00 46.38 3.16
2252 2564 3.321682 TGCAGGAAAGAACCAAAGGAATG 59.678 43.478 0.00 0.00 0.00 2.67
2253 2565 3.575805 TGCAGGAAAGAACCAAAGGAAT 58.424 40.909 0.00 0.00 0.00 3.01
2254 2566 3.025322 TGCAGGAAAGAACCAAAGGAA 57.975 42.857 0.00 0.00 0.00 3.36
2255 2567 2.746279 TGCAGGAAAGAACCAAAGGA 57.254 45.000 0.00 0.00 0.00 3.36
2256 2568 3.817709 TTTGCAGGAAAGAACCAAAGG 57.182 42.857 0.00 0.00 0.00 3.11
2257 2569 5.418676 TCTTTTTGCAGGAAAGAACCAAAG 58.581 37.500 19.16 0.00 39.46 2.77
2258 2570 5.413309 TCTTTTTGCAGGAAAGAACCAAA 57.587 34.783 19.16 0.00 39.46 3.28
2259 2571 4.680440 GCTCTTTTTGCAGGAAAGAACCAA 60.680 41.667 20.78 6.06 41.21 3.67
2260 2572 3.181476 GCTCTTTTTGCAGGAAAGAACCA 60.181 43.478 20.78 6.33 41.21 3.67
2264 2576 2.571212 TCGCTCTTTTTGCAGGAAAGA 58.429 42.857 19.82 19.82 39.95 2.52
2266 2578 3.818210 TGTATCGCTCTTTTTGCAGGAAA 59.182 39.130 0.00 0.00 0.00 3.13
2285 2597 5.073965 AGTGGGTCCCAGTAAGAAAAATGTA 59.926 40.000 17.40 0.00 35.09 2.29
2328 2640 3.229552 GCTTCAGTTCGTCAGCATTTTC 58.770 45.455 0.00 0.00 32.17 2.29
2427 2744 3.792053 GATCACGCCGGCCAGGTAG 62.792 68.421 23.46 8.22 43.70 3.18
2743 3060 0.733566 GTCACCACCAATGCAATGCG 60.734 55.000 0.00 0.00 0.00 4.73
2809 3126 3.601443 AGGACTGCTCATACACAAGAC 57.399 47.619 0.00 0.00 0.00 3.01
2856 3173 1.108776 GCTCGTACAGGTCATGGGTA 58.891 55.000 0.00 0.00 0.00 3.69
2862 3179 2.632544 CGGGTGCTCGTACAGGTCA 61.633 63.158 0.00 0.00 0.00 4.02
3003 3320 4.221422 ATGATGTCGTCGCCGGGG 62.221 66.667 13.31 13.31 33.95 5.73
3133 3450 4.573607 AGATTTATCCCGTTTCGTTTAGCC 59.426 41.667 0.00 0.00 0.00 3.93
3134 3451 5.729974 AGATTTATCCCGTTTCGTTTAGC 57.270 39.130 0.00 0.00 0.00 3.09
3136 3453 5.939296 ACCAAGATTTATCCCGTTTCGTTTA 59.061 36.000 0.00 0.00 0.00 2.01
3148 3465 6.959361 ACATACGCATCAACCAAGATTTATC 58.041 36.000 0.00 0.00 0.00 1.75
3193 3512 1.873572 GCATTGCATCGCCGAAACC 60.874 57.895 3.15 0.00 0.00 3.27
3204 3523 1.076559 CTCCATCCCCTGCATTGCA 60.077 57.895 11.50 11.50 36.92 4.08
3477 3796 0.949105 CGTTCTTGACGTTGGGGAGG 60.949 60.000 0.00 0.00 46.49 4.30
3491 3810 1.273886 GAGCTTCCACCTTCTCGTTCT 59.726 52.381 0.00 0.00 0.00 3.01
3498 3817 0.739112 CGAGCAGAGCTTCCACCTTC 60.739 60.000 0.00 0.00 39.88 3.46
3585 3904 3.365265 CCGCAGAACTGGTTGCCC 61.365 66.667 3.99 0.00 37.00 5.36
3840 4159 1.740296 CGCCTTCTTGTACACCCCG 60.740 63.158 0.00 0.00 0.00 5.73
3965 4284 0.250513 GAAGAAGATCAGCCGGTGGT 59.749 55.000 1.90 0.00 0.00 4.16
3980 4308 1.876799 GCGATCGAGATCAGGAGAAGA 59.123 52.381 21.57 0.00 37.69 2.87
4021 4349 1.517832 GCAGCCCATCTCTACGTGT 59.482 57.895 0.00 0.00 0.00 4.49
4225 4818 1.808945 ACTGCACAATCTAGCAACAGC 59.191 47.619 0.00 0.00 40.73 4.40
4239 4832 0.674895 AGCTCCCGATTGAACTGCAC 60.675 55.000 0.00 0.00 0.00 4.57
4267 4860 3.196469 CACTGAGCAACTTCTCCCTATCA 59.804 47.826 0.00 0.00 32.22 2.15
4311 4904 2.608016 CCCGATACATGTCGATGTCCAG 60.608 54.545 0.00 0.00 42.14 3.86
4387 5004 0.532573 CTCTAAAGCCTGCTCACCGA 59.467 55.000 0.00 0.00 0.00 4.69
4421 5038 4.380531 TGAAAGGAGCTAACTCACACTTG 58.619 43.478 0.00 0.00 45.42 3.16
4486 5104 3.423154 GGTTGGAACGCCTCGCTG 61.423 66.667 0.00 0.00 34.31 5.18
4546 5164 0.778083 GGGGAGGAAATATGGGGTCC 59.222 60.000 0.00 0.00 0.00 4.46
4550 5168 2.491455 CCACATGGGGAGGAAATATGGG 60.491 54.545 8.91 0.00 0.00 4.00
4552 5170 3.882102 TCCACATGGGGAGGAAATATG 57.118 47.619 14.36 0.00 37.22 1.78
4553 5171 3.435026 CGTTCCACATGGGGAGGAAATAT 60.435 47.826 18.08 0.00 42.59 1.28
4554 5172 2.092646 CGTTCCACATGGGGAGGAAATA 60.093 50.000 18.08 0.00 42.59 1.40
4555 5173 1.340991 CGTTCCACATGGGGAGGAAAT 60.341 52.381 18.08 0.00 42.59 2.17
4558 5176 1.537889 ACGTTCCACATGGGGAGGA 60.538 57.895 18.08 0.00 38.42 3.71
4560 5178 1.447838 CGACGTTCCACATGGGGAG 60.448 63.158 18.08 9.40 38.42 4.30
4564 5182 1.071019 CGAGACGACGTTCCACATGG 61.071 60.000 0.13 0.00 0.00 3.66
4565 5183 0.386858 ACGAGACGACGTTCCACATG 60.387 55.000 0.13 0.00 44.14 3.21
4567 5185 1.280746 GACGAGACGACGTTCCACA 59.719 57.895 0.13 0.00 46.52 4.17
4568 5186 0.317269 TTGACGAGACGACGTTCCAC 60.317 55.000 0.13 0.00 46.52 4.02
4569 5187 0.594602 ATTGACGAGACGACGTTCCA 59.405 50.000 0.13 0.00 46.52 3.53
4570 5188 0.982673 CATTGACGAGACGACGTTCC 59.017 55.000 0.13 0.00 46.52 3.62
4571 5189 0.982673 CCATTGACGAGACGACGTTC 59.017 55.000 0.13 1.06 46.52 3.95
4572 5190 1.007336 GCCATTGACGAGACGACGTT 61.007 55.000 0.13 0.00 46.52 3.99
4574 5192 1.406219 CTGCCATTGACGAGACGACG 61.406 60.000 0.00 0.00 39.31 5.12
4575 5193 0.388649 ACTGCCATTGACGAGACGAC 60.389 55.000 0.00 0.00 0.00 4.34
4576 5194 0.109272 GACTGCCATTGACGAGACGA 60.109 55.000 0.00 0.00 0.00 4.20
4614 5233 1.290130 GGGGACTAAGTGAGGGGTCTA 59.710 57.143 0.00 0.00 0.00 2.59
4615 5234 0.042881 GGGGACTAAGTGAGGGGTCT 59.957 60.000 0.00 0.00 0.00 3.85
4637 5256 2.639065 GGGTGCCGATCAATTTAGACA 58.361 47.619 0.00 0.00 0.00 3.41
4642 5261 0.331278 TGAGGGGTGCCGATCAATTT 59.669 50.000 0.00 0.00 0.00 1.82
4648 5267 1.544825 CCGATATGAGGGGTGCCGAT 61.545 60.000 0.00 0.00 0.00 4.18
4649 5268 2.207229 CCGATATGAGGGGTGCCGA 61.207 63.158 0.00 0.00 0.00 5.54
4677 5297 1.004044 GGTGCCCTCATATCATCCCTG 59.996 57.143 0.00 0.00 0.00 4.45
4683 5303 1.074850 TCCGGGTGCCCTCATATCA 60.075 57.895 0.00 0.00 0.00 2.15
4699 5319 4.681978 AAGTGCCCAGTCGCGTCC 62.682 66.667 5.77 0.00 0.00 4.79
4884 5512 8.853077 AACACAAAGAAGATTCATAGTCATGA 57.147 30.769 0.00 0.00 39.47 3.07


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

AutoCloner maintained by Alex Coulton.