Multiple sequence alignment - TraesCS1A01G240500

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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 TraesCS1A01G240500 chr1A 100.000 3965 0 0 1 3965 427814575 427810611 0.000000e+00 7323.0
1 TraesCS1A01G240500 chr1A 83.144 706 83 10 3287 3965 427540862 427540166 2.620000e-171 612.0
2 TraesCS1A01G240500 chr1A 78.780 377 67 10 3200 3570 531656247 531655878 1.420000e-59 241.0
3 TraesCS1A01G240500 chr1A 89.286 168 18 0 3011 3178 427542120 427541953 1.120000e-50 211.0
4 TraesCS1A01G240500 chr1B 91.329 3748 214 32 297 3965 445429864 445426149 0.000000e+00 5018.0
5 TraesCS1A01G240500 chr1B 90.244 246 16 6 1 241 445430204 445429962 8.270000e-82 315.0
6 TraesCS1A01G240500 chr1B 80.211 379 63 11 3200 3570 585238749 585238375 1.400000e-69 274.0
7 TraesCS1A01G240500 chr1B 81.065 169 29 2 3611 3776 527844481 527844313 8.940000e-27 132.0
8 TraesCS1A01G240500 chr1B 85.156 128 16 1 3649 3773 471768461 471768588 1.160000e-25 128.0
9 TraesCS1A01G240500 chr1D 94.258 3065 112 20 301 3326 330545639 330542600 0.000000e+00 4626.0
10 TraesCS1A01G240500 chr1D 85.223 494 35 8 3499 3965 330542104 330541622 1.290000e-129 473.0
11 TraesCS1A01G240500 chr1D 86.916 214 16 4 1 214 330545963 330545762 3.080000e-56 230.0
12 TraesCS1A01G240500 chr3B 80.569 211 33 6 3573 3777 588154488 588154280 5.310000e-34 156.0
13 TraesCS1A01G240500 chr3B 75.379 264 51 9 3201 3460 144176862 144177115 9.000000e-22 115.0
14 TraesCS1A01G240500 chr3B 94.286 35 2 0 1283 1317 457200824 457200858 2.000000e-03 54.7
15 TraesCS1A01G240500 chr3A 79.487 234 37 4 3204 3437 744053504 744053282 5.310000e-34 156.0
16 TraesCS1A01G240500 chr3A 75.093 269 52 12 3204 3464 547372057 547371796 1.160000e-20 111.0
17 TraesCS1A01G240500 chr6D 80.000 210 40 2 3573 3780 403034810 403035019 1.910000e-33 154.0
18 TraesCS1A01G240500 chr6B 79.581 191 36 3 3590 3777 694428685 694428495 2.490000e-27 134.0
19 TraesCS1A01G240500 chr5D 79.255 188 34 3 3590 3773 345085323 345085137 4.160000e-25 126.0
20 TraesCS1A01G240500 chr3D 85.366 123 16 2 3338 3460 94050039 94049919 4.160000e-25 126.0
21 TraesCS1A01G240500 chr5B 80.368 163 29 1 3620 3779 671746233 671746395 1.940000e-23 121.0
22 TraesCS1A01G240500 chr7D 82.075 106 11 5 1634 1735 485541580 485541681 2.540000e-12 84.2
23 TraesCS1A01G240500 chr7B 82.075 106 11 5 1634 1735 513304912 513305013 2.540000e-12 84.2


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 TraesCS1A01G240500 chr1A 427810611 427814575 3964 True 7323.000000 7323 100.0000 1 3965 1 chr1A.!!$R1 3964
1 TraesCS1A01G240500 chr1A 427540166 427542120 1954 True 411.500000 612 86.2150 3011 3965 2 chr1A.!!$R3 954
2 TraesCS1A01G240500 chr1B 445426149 445430204 4055 True 2666.500000 5018 90.7865 1 3965 2 chr1B.!!$R3 3964
3 TraesCS1A01G240500 chr1D 330541622 330545963 4341 True 1776.333333 4626 88.7990 1 3965 3 chr1D.!!$R1 3964

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
309 375 0.031585 GGAGAACGGTTTGTTTGGCC 59.968 55.0 0.00 0.0 42.09 5.36 F
661 731 0.179000 CTGCCTTCCATTCCTAGCGT 59.821 55.0 0.00 0.0 0.00 5.07 F
944 1033 0.596083 CCGCTCATCTACTGCTTCCG 60.596 60.0 0.00 0.0 0.00 4.30 F
1848 1937 0.948141 GCATGCTCGGCTACATCTCC 60.948 60.0 11.37 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 2116 1.310933 TTCCTCCTCGTACTGGTCGC 61.311 60.000 0.0 0.0 0.00 5.19 R
2802 2891 2.892334 GCTCAAGCAAACGCCGTCA 61.892 57.895 0.0 0.0 41.59 4.35 R
2883 2972 0.322816 GGAAGAAGCCCAGCATGACA 60.323 55.000 0.0 0.0 39.69 3.58 R
3470 4571 0.114168 CACAAACCCCATCTCCCCAA 59.886 55.000 0.0 0.0 0.00 4.12 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
41 42 3.689649 AGATAACGGGTGCAGAACATTTC 59.310 43.478 0.00 0.00 0.00 2.17
70 71 6.707608 TGCTAATTGTAGATTGAGATGCGAAT 59.292 34.615 0.00 0.00 0.00 3.34
115 116 1.985473 TTTCATTGTGCTGAGTGCCT 58.015 45.000 0.00 0.00 42.00 4.75
116 117 1.985473 TTCATTGTGCTGAGTGCCTT 58.015 45.000 0.00 0.00 42.00 4.35
128 129 4.025480 GCTGAGTGCCTTTTGTCATTTTTG 60.025 41.667 0.00 0.00 35.15 2.44
218 223 3.572255 GGTGTGCTTTCCAGTTATCCAAA 59.428 43.478 0.00 0.00 0.00 3.28
220 225 5.279456 GGTGTGCTTTCCAGTTATCCAAATT 60.279 40.000 0.00 0.00 0.00 1.82
223 228 6.267471 TGTGCTTTCCAGTTATCCAAATTCTT 59.733 34.615 0.00 0.00 0.00 2.52
224 229 7.450014 TGTGCTTTCCAGTTATCCAAATTCTTA 59.550 33.333 0.00 0.00 0.00 2.10
227 233 7.416777 GCTTTCCAGTTATCCAAATTCTTAGGG 60.417 40.741 0.00 0.00 0.00 3.53
265 331 4.218312 AGAGGAAAGGAGTGCATTTGTTT 58.782 39.130 0.00 0.00 0.00 2.83
278 344 1.305201 TTTGTTTCGTCCACCTCAGC 58.695 50.000 0.00 0.00 0.00 4.26
279 345 0.468226 TTGTTTCGTCCACCTCAGCT 59.532 50.000 0.00 0.00 0.00 4.24
280 346 0.249868 TGTTTCGTCCACCTCAGCTG 60.250 55.000 7.63 7.63 0.00 4.24
281 347 0.951040 GTTTCGTCCACCTCAGCTGG 60.951 60.000 15.13 0.12 0.00 4.85
282 348 2.731691 TTTCGTCCACCTCAGCTGGC 62.732 60.000 15.13 0.00 0.00 4.85
283 349 4.007644 CGTCCACCTCAGCTGGCA 62.008 66.667 15.13 0.00 0.00 4.92
284 350 2.673523 GTCCACCTCAGCTGGCAT 59.326 61.111 15.13 0.00 0.00 4.40
285 351 1.748122 GTCCACCTCAGCTGGCATG 60.748 63.158 15.13 9.30 0.00 4.06
286 352 2.439701 CCACCTCAGCTGGCATGG 60.440 66.667 15.13 14.54 0.00 3.66
287 353 2.353958 CACCTCAGCTGGCATGGT 59.646 61.111 15.13 13.93 0.00 3.55
288 354 1.603842 CACCTCAGCTGGCATGGTA 59.396 57.895 15.13 0.00 0.00 3.25
289 355 0.182061 CACCTCAGCTGGCATGGTAT 59.818 55.000 15.13 0.00 0.00 2.73
290 356 0.182061 ACCTCAGCTGGCATGGTATG 59.818 55.000 15.13 0.00 0.00 2.39
291 357 0.536687 CCTCAGCTGGCATGGTATGG 60.537 60.000 15.13 0.00 0.00 2.74
292 358 0.471191 CTCAGCTGGCATGGTATGGA 59.529 55.000 15.13 0.00 0.00 3.41
293 359 0.471191 TCAGCTGGCATGGTATGGAG 59.529 55.000 15.13 0.00 0.00 3.86
294 360 0.471191 CAGCTGGCATGGTATGGAGA 59.529 55.000 5.57 0.00 0.00 3.71
295 361 1.134007 CAGCTGGCATGGTATGGAGAA 60.134 52.381 5.57 0.00 0.00 2.87
309 375 0.031585 GGAGAACGGTTTGTTTGGCC 59.968 55.000 0.00 0.00 42.09 5.36
329 395 1.469251 CGTGATCGATGTTTCCCGTCT 60.469 52.381 0.54 0.00 39.71 4.18
448 514 5.479027 GTCCAAGTAAGAAGAGAAGTCTCCT 59.521 44.000 4.67 0.00 43.88 3.69
504 574 5.297029 AGAGCCGATTTAGATTTGGTTAAGC 59.703 40.000 0.00 0.00 0.00 3.09
638 708 2.613026 TTTCCGTCACTCTTTGCTCA 57.387 45.000 0.00 0.00 0.00 4.26
660 730 0.465705 TCTGCCTTCCATTCCTAGCG 59.534 55.000 0.00 0.00 0.00 4.26
661 731 0.179000 CTGCCTTCCATTCCTAGCGT 59.821 55.000 0.00 0.00 0.00 5.07
698 768 6.207025 GGCGATCACCTACTAGAAGATCTTAA 59.793 42.308 8.25 0.00 34.43 1.85
699 769 7.079475 GCGATCACCTACTAGAAGATCTTAAC 58.921 42.308 8.25 0.00 34.43 2.01
700 770 7.586747 CGATCACCTACTAGAAGATCTTAACC 58.413 42.308 8.25 0.00 34.43 2.85
703 773 6.068379 TCACCTACTAGAAGATCTTAACCCCT 60.068 42.308 8.25 3.38 0.00 4.79
705 775 6.612049 ACCTACTAGAAGATCTTAACCCCTTG 59.388 42.308 8.25 4.65 0.00 3.61
706 776 6.612049 CCTACTAGAAGATCTTAACCCCTTGT 59.388 42.308 8.25 10.10 0.00 3.16
711 786 4.838904 AGATCTTAACCCCTTGTACCAC 57.161 45.455 0.00 0.00 0.00 4.16
712 787 3.522343 AGATCTTAACCCCTTGTACCACC 59.478 47.826 0.00 0.00 0.00 4.61
715 790 3.073356 TCTTAACCCCTTGTACCACCAAG 59.927 47.826 0.00 0.00 41.21 3.61
716 791 1.525175 AACCCCTTGTACCACCAAGA 58.475 50.000 2.62 0.00 43.65 3.02
718 793 2.070573 ACCCCTTGTACCACCAAGAAT 58.929 47.619 2.62 0.00 43.65 2.40
734 809 9.301153 CCACCAAGAATTAACATTTATAGTTGC 57.699 33.333 0.00 0.00 0.00 4.17
742 817 9.730420 AATTAACATTTATAGTTGCAATCGGTC 57.270 29.630 0.59 0.00 0.00 4.79
775 860 2.468831 CCTCTGTTCTAGAAGCGCATC 58.531 52.381 11.47 7.57 34.32 3.91
800 889 2.973945 AGCTACGAACAATCTCAACCC 58.026 47.619 0.00 0.00 0.00 4.11
810 899 1.972872 ATCTCAACCCATGGCGAATC 58.027 50.000 6.09 0.00 0.00 2.52
851 940 2.596862 GCACAACACGTTCAAGAAAACC 59.403 45.455 0.00 0.00 0.00 3.27
852 941 2.843643 CACAACACGTTCAAGAAAACCG 59.156 45.455 0.00 0.00 0.00 4.44
853 942 2.743126 ACAACACGTTCAAGAAAACCGA 59.257 40.909 0.00 0.00 0.00 4.69
854 943 3.375922 ACAACACGTTCAAGAAAACCGAT 59.624 39.130 0.00 0.00 0.00 4.18
855 944 4.142556 ACAACACGTTCAAGAAAACCGATT 60.143 37.500 0.00 0.00 0.00 3.34
856 945 4.625972 ACACGTTCAAGAAAACCGATTT 57.374 36.364 0.00 0.00 0.00 2.17
857 946 4.594136 ACACGTTCAAGAAAACCGATTTC 58.406 39.130 5.75 5.75 46.45 2.17
870 959 3.549794 ACCGATTTCTAGTAGTACCGCT 58.450 45.455 0.00 0.00 0.00 5.52
873 962 4.535116 CGATTTCTAGTAGTACCGCTTCC 58.465 47.826 0.00 0.00 0.00 3.46
876 965 6.017605 CGATTTCTAGTAGTACCGCTTCCTTA 60.018 42.308 0.00 0.00 0.00 2.69
885 974 1.205893 ACCGCTTCCTTAAGAGAGCTG 59.794 52.381 20.49 17.73 34.73 4.24
886 975 1.285578 CGCTTCCTTAAGAGAGCTGC 58.714 55.000 20.49 12.84 34.73 5.25
887 976 1.134848 CGCTTCCTTAAGAGAGCTGCT 60.135 52.381 20.49 0.00 34.73 4.24
888 977 2.278854 GCTTCCTTAAGAGAGCTGCTG 58.721 52.381 7.01 0.00 34.37 4.41
944 1033 0.596083 CCGCTCATCTACTGCTTCCG 60.596 60.000 0.00 0.00 0.00 4.30
977 1066 4.803426 CCCCTCTCACGCGCACTC 62.803 72.222 5.73 0.00 0.00 3.51
1032 1121 4.671590 TCGTCGGAGCTGGACCCA 62.672 66.667 0.00 0.00 0.00 4.51
1259 1348 1.827969 CCTCAACTCCGTCTCCTTCAT 59.172 52.381 0.00 0.00 0.00 2.57
1272 1361 1.153765 CTTCATCGCGTCCAGCTCA 60.154 57.895 5.77 0.00 45.59 4.26
1287 1376 1.817099 CTCAAGCATCCTGGCCGTC 60.817 63.158 0.00 0.00 0.00 4.79
1366 1455 2.279784 GCTCGGAGATCGCCAAGG 60.280 66.667 16.29 5.73 39.05 3.61
1390 1479 3.353029 CCGTGTGCATCAACGGCA 61.353 61.111 20.84 0.00 39.32 5.69
1848 1937 0.948141 GCATGCTCGGCTACATCTCC 60.948 60.000 11.37 0.00 0.00 3.71
1965 2054 2.435586 CTCAACCCGCTGGAGCTG 60.436 66.667 0.00 0.00 39.32 4.24
2027 2116 4.504916 CGCCGAGCTCAGGGACAG 62.505 72.222 21.05 1.79 0.00 3.51
2643 2732 1.822371 GGCGTCTTCTTCCTCTTCTCT 59.178 52.381 0.00 0.00 0.00 3.10
2752 2841 3.072486 ATCAACGAGTACGGGGGCG 62.072 63.158 0.00 0.00 44.46 6.13
2802 2891 4.404098 GGGGACGCCATGAACGGT 62.404 66.667 3.14 0.00 34.00 4.83
2853 2942 2.041405 CTGAGGGGGAGAGGGGTC 60.041 72.222 0.00 0.00 0.00 4.46
2877 2966 1.217057 AGGGCATGAGGTGGGTCAAT 61.217 55.000 0.00 0.00 0.00 2.57
2883 2972 1.065410 TGAGGTGGGTCAATGTGGGT 61.065 55.000 0.00 0.00 0.00 4.51
2975 3064 3.245948 ACCACTCTCTGATCCTTCCTTCT 60.246 47.826 0.00 0.00 0.00 2.85
2976 3065 3.774216 CCACTCTCTGATCCTTCCTTCTT 59.226 47.826 0.00 0.00 0.00 2.52
2981 3078 3.779738 CTCTGATCCTTCCTTCTTTCCCT 59.220 47.826 0.00 0.00 0.00 4.20
3027 3129 7.759489 TTGGTTTGGATCATATATACAAGCC 57.241 36.000 8.45 8.45 41.12 4.35
3047 3152 3.782268 CCGCGTTATTTGTTTGCTTTTG 58.218 40.909 4.92 0.00 0.00 2.44
3049 3154 4.433079 CGCGTTATTTGTTTGCTTTTGTC 58.567 39.130 0.00 0.00 0.00 3.18
3150 3255 8.977267 TGATTTGGGTTCATGAAAAGAAAATT 57.023 26.923 10.35 0.00 0.00 1.82
3172 3277 5.464030 TTCAACCTGTCTACCTGAACTAC 57.536 43.478 0.00 0.00 0.00 2.73
3188 3309 1.687123 ACTACGGGCGCTTCTATTCAT 59.313 47.619 7.64 0.00 0.00 2.57
3217 3339 0.461339 AATCGACATGGCACCCGTAC 60.461 55.000 0.00 0.00 0.00 3.67
3222 3344 2.046700 ATGGCACCCGTACGGTTG 60.047 61.111 31.24 28.58 45.36 3.77
3240 3362 3.573491 GCGTGCGGGTAATGCTCC 61.573 66.667 0.00 0.00 0.00 4.70
3248 3370 0.335019 GGGTAATGCTCCCCCAAACT 59.665 55.000 0.00 0.00 39.08 2.66
3273 3396 5.989777 CGTATCCGTCCCAATATTTTTCTCT 59.010 40.000 0.00 0.00 0.00 3.10
3280 3403 7.855904 CCGTCCCAATATTTTTCTCTTAAATCG 59.144 37.037 0.00 0.00 0.00 3.34
3327 4427 7.201875 GGTTTTGTATTGTTCCCATACCCATAG 60.202 40.741 0.00 0.00 0.00 2.23
3334 4434 1.426251 CCCATACCCATAGCCAGCCA 61.426 60.000 0.00 0.00 0.00 4.75
3337 4437 2.397413 ATACCCATAGCCAGCCACGC 62.397 60.000 0.00 0.00 0.00 5.34
3357 4457 3.309410 CGCGTAATAACCGTGGGTAAAAT 59.691 43.478 0.00 0.00 33.12 1.82
3462 4562 4.589216 TGCATATTTAGCATTTCAGCCC 57.411 40.909 0.00 0.00 37.02 5.19
3465 4566 4.279169 GCATATTTAGCATTTCAGCCCAGA 59.721 41.667 0.00 0.00 34.23 3.86
3470 4571 0.674895 GCATTTCAGCCCAGACGAGT 60.675 55.000 0.00 0.00 0.00 4.18
3507 4969 4.160736 TGTGTTCTATGAGTGTGACGAG 57.839 45.455 0.00 0.00 0.00 4.18
3593 5080 4.073293 GGGACCTACATGTTAGATGTGG 57.927 50.000 2.30 2.01 33.76 4.17
3609 5096 5.648247 AGATGTGGTAATATACGGGTAGGT 58.352 41.667 0.00 0.00 0.00 3.08
3631 5118 3.712733 TGGGTACACAGGTATGGGTATTC 59.287 47.826 0.00 0.00 46.74 1.75
3647 5134 5.592104 GGTATTCCCTTTTTGTACCCATG 57.408 43.478 0.00 0.00 30.88 3.66
3661 5148 3.211963 CATGCCCGGCTTACCTGC 61.212 66.667 11.61 0.00 33.29 4.85
3781 5271 0.656259 CATTGCCATGTCGAGCTGAG 59.344 55.000 0.00 0.00 0.00 3.35
3808 5298 0.943835 CGTGTGTCGCCTTCATGACA 60.944 55.000 0.00 0.00 42.49 3.58
3809 5299 0.792640 GTGTGTCGCCTTCATGACAG 59.207 55.000 0.00 0.00 45.08 3.51
3856 5351 5.229921 TCAGAAGGAACAACTTTTTCGTG 57.770 39.130 0.00 0.00 0.00 4.35
3888 5383 3.810941 TGACGTGGACCAGTTTGATTTAC 59.189 43.478 0.00 0.00 0.00 2.01
3889 5384 3.810941 GACGTGGACCAGTTTGATTTACA 59.189 43.478 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.824109 CACCCGTTATCTCTGGCTCA 59.176 55.000 0.00 0.00 0.00 4.26
41 42 6.401903 GCATCTCAATCTACAATTAGCATCCG 60.402 42.308 0.00 0.00 0.00 4.18
70 71 3.955471 AGCTTAACTCTTGCATGGCTAA 58.045 40.909 0.00 0.00 0.00 3.09
128 129 3.005155 GGCAGGCATGATGGTAGAAATTC 59.995 47.826 0.62 0.00 0.00 2.17
142 143 0.760572 AACAAAAAGCAGGCAGGCAT 59.239 45.000 0.00 0.00 35.83 4.40
233 239 0.977395 CCTTTCCTCTCCACCGAGTT 59.023 55.000 0.00 0.00 37.40 3.01
234 240 0.114560 TCCTTTCCTCTCCACCGAGT 59.885 55.000 0.00 0.00 37.40 4.18
237 243 0.247736 CACTCCTTTCCTCTCCACCG 59.752 60.000 0.00 0.00 0.00 4.94
278 344 1.586422 CGTTCTCCATACCATGCCAG 58.414 55.000 0.00 0.00 0.00 4.85
279 345 0.180171 CCGTTCTCCATACCATGCCA 59.820 55.000 0.00 0.00 0.00 4.92
280 346 0.180406 ACCGTTCTCCATACCATGCC 59.820 55.000 0.00 0.00 0.00 4.40
281 347 2.038387 AACCGTTCTCCATACCATGC 57.962 50.000 0.00 0.00 0.00 4.06
282 348 3.343617 ACAAACCGTTCTCCATACCATG 58.656 45.455 0.00 0.00 0.00 3.66
283 349 3.713826 ACAAACCGTTCTCCATACCAT 57.286 42.857 0.00 0.00 0.00 3.55
284 350 3.495434 AACAAACCGTTCTCCATACCA 57.505 42.857 0.00 0.00 29.27 3.25
285 351 3.057806 CCAAACAAACCGTTCTCCATACC 60.058 47.826 0.00 0.00 36.59 2.73
286 352 3.610821 GCCAAACAAACCGTTCTCCATAC 60.611 47.826 0.00 0.00 36.59 2.39
287 353 2.554893 GCCAAACAAACCGTTCTCCATA 59.445 45.455 0.00 0.00 36.59 2.74
288 354 1.339929 GCCAAACAAACCGTTCTCCAT 59.660 47.619 0.00 0.00 36.59 3.41
289 355 0.741915 GCCAAACAAACCGTTCTCCA 59.258 50.000 0.00 0.00 36.59 3.86
290 356 0.031585 GGCCAAACAAACCGTTCTCC 59.968 55.000 0.00 0.00 36.59 3.71
291 357 0.317519 CGGCCAAACAAACCGTTCTC 60.318 55.000 2.24 0.00 42.01 2.87
292 358 1.731093 CGGCCAAACAAACCGTTCT 59.269 52.632 2.24 0.00 42.01 3.01
293 359 4.312383 CGGCCAAACAAACCGTTC 57.688 55.556 2.24 0.00 42.01 3.95
329 395 2.675844 CCATCGTCGGTAAAATGCAAGA 59.324 45.455 0.00 0.00 0.00 3.02
369 435 0.447801 GACACTCCGCAAAATCGCAT 59.552 50.000 0.00 0.00 0.00 4.73
448 514 0.615261 TGTGGTCGGGGCACATACTA 60.615 55.000 0.00 0.00 0.00 1.82
638 708 2.092699 GCTAGGAATGGAAGGCAGAAGT 60.093 50.000 0.00 0.00 0.00 3.01
660 730 3.310860 ATCGCCGGTCAAGGTGGAC 62.311 63.158 1.90 0.00 41.86 4.02
661 731 3.000819 ATCGCCGGTCAAGGTGGA 61.001 61.111 1.90 0.00 41.86 4.02
698 768 1.525175 TTCTTGGTGGTACAAGGGGT 58.475 50.000 6.15 0.00 46.04 4.95
699 769 2.899303 ATTCTTGGTGGTACAAGGGG 57.101 50.000 6.15 0.00 46.04 4.79
700 770 5.074115 TGTTAATTCTTGGTGGTACAAGGG 58.926 41.667 6.15 0.00 46.04 3.95
715 790 9.730420 ACCGATTGCAACTATAAATGTTAATTC 57.270 29.630 0.00 0.00 0.00 2.17
716 791 9.730420 GACCGATTGCAACTATAAATGTTAATT 57.270 29.630 0.00 0.00 0.00 1.40
718 793 8.394877 CAGACCGATTGCAACTATAAATGTTAA 58.605 33.333 0.00 0.00 0.00 2.01
734 809 2.414559 GCAATGGTGTTCAGACCGATTG 60.415 50.000 11.01 11.01 39.07 2.67
737 812 0.605319 GGCAATGGTGTTCAGACCGA 60.605 55.000 0.00 0.00 39.07 4.69
742 817 1.901591 ACAGAGGCAATGGTGTTCAG 58.098 50.000 0.00 0.00 0.00 3.02
775 860 4.033990 TGAGATTGTTCGTAGCTAGCTG 57.966 45.455 27.68 11.72 0.00 4.24
800 889 3.195002 ACGCCACGATTCGCCATG 61.195 61.111 5.86 0.00 0.00 3.66
810 899 4.896028 TTTTGCACGCACGCCACG 62.896 61.111 0.00 0.00 0.00 4.94
826 915 2.080693 TCTTGAACGTGTTGTGCACTT 58.919 42.857 19.41 1.94 45.57 3.16
834 923 4.625972 AATCGGTTTTCTTGAACGTGTT 57.374 36.364 0.00 0.00 0.00 3.32
851 940 4.275443 AGGAAGCGGTACTACTAGAAATCG 59.725 45.833 0.00 0.00 0.00 3.34
852 941 5.771153 AGGAAGCGGTACTACTAGAAATC 57.229 43.478 0.00 0.00 0.00 2.17
853 942 7.559170 TCTTAAGGAAGCGGTACTACTAGAAAT 59.441 37.037 1.85 0.00 32.21 2.17
854 943 6.886459 TCTTAAGGAAGCGGTACTACTAGAAA 59.114 38.462 1.85 0.00 32.21 2.52
855 944 6.418101 TCTTAAGGAAGCGGTACTACTAGAA 58.582 40.000 1.85 0.00 32.21 2.10
856 945 5.994250 TCTTAAGGAAGCGGTACTACTAGA 58.006 41.667 1.85 0.00 32.21 2.43
857 946 6.054295 TCTCTTAAGGAAGCGGTACTACTAG 58.946 44.000 1.85 0.00 32.21 2.57
858 947 5.994250 TCTCTTAAGGAAGCGGTACTACTA 58.006 41.667 1.85 0.00 32.21 1.82
859 948 4.853007 TCTCTTAAGGAAGCGGTACTACT 58.147 43.478 1.85 0.00 32.21 2.57
860 949 4.497842 GCTCTCTTAAGGAAGCGGTACTAC 60.498 50.000 12.31 0.00 32.21 2.73
861 950 3.631227 GCTCTCTTAAGGAAGCGGTACTA 59.369 47.826 12.31 0.00 32.21 1.82
867 956 1.134848 AGCAGCTCTCTTAAGGAAGCG 60.135 52.381 18.33 15.23 32.21 4.68
870 959 4.019860 ACAATCAGCAGCTCTCTTAAGGAA 60.020 41.667 1.85 0.00 0.00 3.36
873 962 3.551082 CGACAATCAGCAGCTCTCTTAAG 59.449 47.826 0.00 0.00 0.00 1.85
876 965 1.547820 TCGACAATCAGCAGCTCTCTT 59.452 47.619 0.00 0.00 0.00 2.85
885 974 2.939103 ACAAATAGCCTCGACAATCAGC 59.061 45.455 0.00 0.00 0.00 4.26
886 975 5.352284 ACTACAAATAGCCTCGACAATCAG 58.648 41.667 0.00 0.00 30.75 2.90
887 976 5.339008 ACTACAAATAGCCTCGACAATCA 57.661 39.130 0.00 0.00 30.75 2.57
888 977 6.535508 AGAAACTACAAATAGCCTCGACAATC 59.464 38.462 0.00 0.00 30.75 2.67
944 1033 1.376609 GGGGTCGATGTGTGGATTGC 61.377 60.000 0.00 0.00 0.00 3.56
1032 1121 2.757917 GTGGAGAGGAGGAGCGCT 60.758 66.667 11.27 11.27 0.00 5.92
1259 1348 3.300934 ATGCTTGAGCTGGACGCGA 62.301 57.895 15.93 0.00 45.59 5.87
1272 1361 3.706373 ACGACGGCCAGGATGCTT 61.706 61.111 2.24 0.00 31.97 3.91
1437 1526 1.733399 GAGGTTGTCGTCCTGCGTC 60.733 63.158 0.00 0.00 42.13 5.19
1569 1658 4.021925 GCCACCTCCGACAGCCTT 62.022 66.667 0.00 0.00 0.00 4.35
1578 1667 3.075005 TAGCTGTCGGCCACCTCC 61.075 66.667 2.24 0.00 43.05 4.30
1896 1985 4.539881 GCGTCCTCGAGCGACCTC 62.540 72.222 21.10 13.18 39.71 3.85
1965 2054 3.391665 CTCGGTGACCTCCATGGCC 62.392 68.421 6.96 0.00 40.22 5.36
2027 2116 1.310933 TTCCTCCTCGTACTGGTCGC 61.311 60.000 0.00 0.00 0.00 5.19
2802 2891 2.892334 GCTCAAGCAAACGCCGTCA 61.892 57.895 0.00 0.00 41.59 4.35
2853 2942 2.202797 CACCTCATGCCCTCGTCG 60.203 66.667 0.00 0.00 0.00 5.12
2877 2966 2.435663 CCCAGCATGACACCCACA 59.564 61.111 0.00 0.00 39.69 4.17
2883 2972 0.322816 GGAAGAAGCCCAGCATGACA 60.323 55.000 0.00 0.00 39.69 3.58
2975 3064 4.693095 GCTGACAAACAAAAACAAGGGAAA 59.307 37.500 0.00 0.00 0.00 3.13
2976 3065 4.020662 AGCTGACAAACAAAAACAAGGGAA 60.021 37.500 0.00 0.00 0.00 3.97
2981 3078 6.128336 CCAATGAAGCTGACAAACAAAAACAA 60.128 34.615 0.00 0.00 0.00 2.83
3025 3127 1.414378 AAGCAAACAAATAACGCGGC 58.586 45.000 12.47 0.00 0.00 6.53
3027 3129 4.430407 ACAAAAGCAAACAAATAACGCG 57.570 36.364 3.53 3.53 0.00 6.01
3047 3152 5.500645 AAACAAAGAGCAAACTACAGGAC 57.499 39.130 0.00 0.00 0.00 3.85
3049 3154 6.861065 TCTAAACAAAGAGCAAACTACAGG 57.139 37.500 0.00 0.00 0.00 4.00
3150 3255 4.022589 CGTAGTTCAGGTAGACAGGTTGAA 60.023 45.833 0.00 0.00 0.00 2.69
3172 3277 0.588252 CCAATGAATAGAAGCGCCCG 59.412 55.000 2.29 0.00 0.00 6.13
3188 3309 2.849942 CCATGTCGATTATCAGCCCAA 58.150 47.619 0.00 0.00 0.00 4.12
3222 3344 3.573491 GAGCATTACCCGCACGCC 61.573 66.667 0.00 0.00 0.00 5.68
3224 3346 2.895372 GGGAGCATTACCCGCACG 60.895 66.667 0.00 0.00 37.85 5.34
3273 3396 2.828877 CGGGCACAGGTATCGATTTAA 58.171 47.619 1.71 0.00 0.00 1.52
3327 4427 1.350665 GTTATTACGCGTGGCTGGC 59.649 57.895 24.59 3.83 0.00 4.85
3334 4434 0.814457 TACCCACGGTTATTACGCGT 59.186 50.000 19.17 19.17 37.09 6.01
3337 4437 6.714492 GGTAATTTTACCCACGGTTATTACG 58.286 40.000 8.09 0.00 45.94 3.18
3357 4457 4.963373 TGAAAGGTGAACGAGATTGGTAA 58.037 39.130 0.00 0.00 0.00 2.85
3362 4462 5.530915 TGTGAATTGAAAGGTGAACGAGATT 59.469 36.000 0.00 0.00 0.00 2.40
3369 4469 7.786030 TGGTAAAATGTGAATTGAAAGGTGAA 58.214 30.769 0.00 0.00 0.00 3.18
3462 4562 0.176680 CCATCTCCCCAACTCGTCTG 59.823 60.000 0.00 0.00 0.00 3.51
3465 4566 1.995626 CCCCATCTCCCCAACTCGT 60.996 63.158 0.00 0.00 0.00 4.18
3470 4571 0.114168 CACAAACCCCATCTCCCCAA 59.886 55.000 0.00 0.00 0.00 4.12
3507 4969 1.456331 CCCTCACCCATCCATTGCC 60.456 63.158 0.00 0.00 0.00 4.52
3593 5080 5.048013 GTGTACCCACCTACCCGTATATTAC 60.048 48.000 0.00 0.00 35.44 1.89
3609 5096 2.944696 TACCCATACCTGTGTACCCA 57.055 50.000 0.00 0.00 0.00 4.51
3631 5118 0.901827 GGGCATGGGTACAAAAAGGG 59.098 55.000 0.00 0.00 0.00 3.95
3636 5123 2.361865 GCCGGGCATGGGTACAAA 60.362 61.111 15.62 0.00 0.00 2.83
3637 5124 1.563577 TAAGCCGGGCATGGGTACAA 61.564 55.000 23.09 0.00 39.24 2.41
3686 5176 7.256368 GGTTTGGAAAAGTTAAATACCCATGGA 60.256 37.037 15.22 0.00 0.00 3.41
3801 5291 4.548451 AAAGCAGATCTGACTGTCATGA 57.452 40.909 27.04 11.04 39.73 3.07
3808 5298 4.391216 CGTCAATCAAAAGCAGATCTGACT 59.609 41.667 27.04 18.67 34.75 3.41
3809 5299 4.436584 CCGTCAATCAAAAGCAGATCTGAC 60.437 45.833 27.04 16.75 34.24 3.51
3912 5409 8.668510 TGCAAATGTTATATTGTTTGGTTTGT 57.331 26.923 0.00 0.00 33.39 2.83


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

AutoCloner maintained by Alex Coulton.