Multiple sequence alignment - TraesCS6D01G205000

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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 TraesCS6D01G205000 chr6D 100.000 4619 0 0 1 4619 290899801 290904419 0.000000e+00 8530.0
1 TraesCS6D01G205000 chr6A 95.459 1894 57 10 2730 4619 432534288 432532420 0.000000e+00 2994.0
2 TraesCS6D01G205000 chr6A 95.996 1823 50 8 911 2730 432539349 432537547 0.000000e+00 2940.0
3 TraesCS6D01G205000 chr6A 84.428 411 33 4 2 386 432766633 432766228 4.360000e-100 375.0
4 TraesCS6D01G205000 chr6B 95.373 1794 61 11 921 2706 451671935 451673714 0.000000e+00 2833.0
5 TraesCS6D01G205000 chr6B 93.899 1557 63 16 2766 4316 451673714 451675244 0.000000e+00 2320.0
6 TraesCS6D01G205000 chr6B 92.476 319 15 7 4303 4619 451676774 451677085 9.120000e-122 448.0
7 TraesCS6D01G205000 chr6B 89.676 339 30 4 386 721 664748883 664748547 1.190000e-115 427.0
8 TraesCS6D01G205000 chr6B 83.523 352 32 10 61 386 451671113 451671464 5.810000e-79 305.0
9 TraesCS6D01G205000 chr5A 80.025 796 104 33 969 1722 634061206 634061988 5.260000e-149 538.0
10 TraesCS6D01G205000 chr3B 95.413 327 13 2 395 721 526786479 526786155 1.900000e-143 520.0
11 TraesCS6D01G205000 chr3B 91.979 187 14 1 736 921 526786170 526785984 1.270000e-65 261.0
12 TraesCS6D01G205000 chr3B 75.658 152 32 5 1 150 486619029 486618881 2.310000e-08 71.3
13 TraesCS6D01G205000 chr7D 94.328 335 17 2 387 721 210085095 210084763 3.190000e-141 512.0
14 TraesCS6D01G205000 chr7D 91.444 187 15 1 736 921 210084778 210084592 5.930000e-64 255.0
15 TraesCS6D01G205000 chr7D 83.966 237 34 4 151 384 162766054 162765819 1.670000e-54 224.0
16 TraesCS6D01G205000 chr5D 78.499 786 103 30 970 1722 506246136 506246888 5.450000e-124 455.0
17 TraesCS6D01G205000 chr5D 94.444 72 4 0 736 807 41828201 41828272 1.360000e-20 111.0
18 TraesCS6D01G205000 chr5D 95.522 67 3 0 648 714 41828143 41828209 1.760000e-19 108.0
19 TraesCS6D01G205000 chr2B 91.291 333 25 3 387 717 547055900 547055570 7.050000e-123 451.0
20 TraesCS6D01G205000 chr2B 84.767 407 43 13 3694 4085 793748894 793748492 1.560000e-104 390.0
21 TraesCS6D01G205000 chr2B 83.871 341 34 17 3761 4085 47420816 47421151 5.810000e-79 305.0
22 TraesCS6D01G205000 chr2B 78.164 403 43 20 3692 4085 33544257 33543891 1.010000e-51 215.0
23 TraesCS6D01G205000 chr2B 78.472 144 29 2 7 149 21741643 21741501 4.920000e-15 93.5
24 TraesCS6D01G205000 chr5B 78.088 753 92 33 1010 1722 637126180 637126899 4.300000e-110 409.0
25 TraesCS6D01G205000 chr1D 88.047 343 26 11 3756 4084 463343265 463343606 4.330000e-105 392.0
26 TraesCS6D01G205000 chr1D 85.440 364 32 15 3731 4085 487170725 487171076 4.390000e-95 359.0
27 TraesCS6D01G205000 chr1D 83.459 399 48 15 3693 4085 22338950 22338564 5.680000e-94 355.0
28 TraesCS6D01G205000 chr1D 84.388 237 32 5 151 384 430320634 430320400 1.290000e-55 228.0
29 TraesCS6D01G205000 chr1D 77.641 407 66 7 3 384 326786370 326785964 1.670000e-54 224.0
30 TraesCS6D01G205000 chr1D 83.475 236 37 2 151 384 418519880 418520115 7.780000e-53 219.0
31 TraesCS6D01G205000 chr4D 83.292 407 51 11 3695 4088 49940549 49940147 4.390000e-95 359.0
32 TraesCS6D01G205000 chr4D 81.102 381 64 3 10 384 460568618 460568240 9.720000e-77 298.0
33 TraesCS6D01G205000 chr4D 78.345 411 61 14 1 384 69656473 69656882 1.660000e-59 241.0
34 TraesCS6D01G205000 chr7A 87.697 317 22 9 386 702 19015397 19015696 2.040000e-93 353.0
35 TraesCS6D01G205000 chr7A 83.250 400 42 12 3692 4085 19953642 19953262 1.230000e-90 344.0
36 TraesCS6D01G205000 chr7A 88.202 178 16 2 749 921 19015713 19015890 1.680000e-49 207.0
37 TraesCS6D01G205000 chr7B 87.107 318 31 9 389 706 7437241 7436934 7.350000e-93 351.0
38 TraesCS6D01G205000 chr1A 84.911 338 31 14 3758 4084 555535885 555536213 1.600000e-84 324.0
39 TraesCS6D01G205000 chr1A 85.397 315 30 12 3783 4084 555535405 555535716 3.470000e-81 313.0
40 TraesCS6D01G205000 chr1B 81.951 410 25 19 3692 4085 638883926 638884302 7.510000e-78 302.0
41 TraesCS6D01G205000 chrUn 84.454 238 31 6 151 384 68800840 68801075 3.590000e-56 230.0
42 TraesCS6D01G205000 chrUn 90.244 41 4 0 4345 4385 18405702 18405742 2.000000e-03 54.7
43 TraesCS6D01G205000 chr4A 81.633 98 16 2 17 113 670835189 670835093 3.830000e-11 80.5
44 TraesCS6D01G205000 chr3D 77.372 137 29 2 1 136 498427970 498428105 3.830000e-11 80.5


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 TraesCS6D01G205000 chr6D 290899801 290904419 4618 False 8530.0 8530 100.00000 1 4619 1 chr6D.!!$F1 4618
1 TraesCS6D01G205000 chr6A 432532420 432539349 6929 True 2967.0 2994 95.72750 911 4619 2 chr6A.!!$R2 3708
2 TraesCS6D01G205000 chr6B 451671113 451677085 5972 False 1476.5 2833 91.31775 61 4619 4 chr6B.!!$F1 4558
3 TraesCS6D01G205000 chr5A 634061206 634061988 782 False 538.0 538 80.02500 969 1722 1 chr5A.!!$F1 753
4 TraesCS6D01G205000 chr7D 210084592 210085095 503 True 383.5 512 92.88600 387 921 2 chr7D.!!$R2 534
5 TraesCS6D01G205000 chr5D 506246136 506246888 752 False 455.0 455 78.49900 970 1722 1 chr5D.!!$F1 752
6 TraesCS6D01G205000 chr5B 637126180 637126899 719 False 409.0 409 78.08800 1010 1722 1 chr5B.!!$F1 712
7 TraesCS6D01G205000 chr1A 555535405 555536213 808 False 318.5 324 85.15400 3758 4084 2 chr1A.!!$F1 326

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
233 260 0.613260 TCCGGTGAATCTGTCCTTGG 59.387 55.000 0.00 0.00 0.00 3.61 F
363 390 1.070914 GGTCCTATGAGGCCTTAGCAC 59.929 57.143 6.77 1.09 42.56 4.40 F
372 399 1.077089 GGCCTTAGCACGACGACTTC 61.077 60.000 0.00 0.00 42.56 3.01 F
1393 1663 1.148949 TCAGTTGCAGCTTCTGGCA 59.851 52.632 0.00 0.00 44.79 4.92 F
1516 1788 3.232213 TGCTCAACACGGAGAAGATAC 57.768 47.619 0.00 0.00 37.05 2.24 F
2902 6461 2.083774 TCTAAAACGGGCTCTTGCATG 58.916 47.619 0.00 0.00 41.91 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1121 1374 0.753867 TGACGCACAGTACCAGGAAA 59.246 50.000 0.00 0.00 0.00 3.13 R
1516 1788 1.538950 GGTGCTCTCAGCCTTGAAAAG 59.461 52.381 0.00 0.00 45.69 2.27 R
1975 2275 2.893489 AGGGTCAGCCAAGATTTCAAAC 59.107 45.455 0.00 0.00 36.17 2.93 R
2433 2733 1.370414 CTTTGAACCTTGTGCCGCG 60.370 57.895 0.00 0.00 0.00 6.46 R
3468 7028 0.252239 AGGCAAAAAGTGGGATCCCC 60.252 55.000 28.58 18.74 45.71 4.81 R
3844 7405 0.107831 TTTCTACCACGCCTTGCACT 59.892 50.000 0.00 0.00 0.00 4.40 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
25 26 4.493747 CCGGACCGCCTCGTCTTC 62.494 72.222 8.86 0.00 33.07 2.87
26 27 4.831307 CGGACCGCCTCGTCTTCG 62.831 72.222 0.00 0.00 38.55 3.79
33 34 3.691342 CCTCGTCTTCGGTGGCCA 61.691 66.667 0.00 0.00 37.69 5.36
34 35 2.579201 CTCGTCTTCGGTGGCCAT 59.421 61.111 9.72 0.00 37.69 4.40
35 36 1.672854 CCTCGTCTTCGGTGGCCATA 61.673 60.000 9.72 0.00 37.69 2.74
37 38 1.227263 CGTCTTCGGTGGCCATAGG 60.227 63.158 9.72 0.64 0.00 2.57
38 39 1.146263 GTCTTCGGTGGCCATAGGG 59.854 63.158 9.72 0.00 37.18 3.53
39 40 1.306654 TCTTCGGTGGCCATAGGGT 60.307 57.895 9.72 0.00 36.17 4.34
40 41 1.146263 CTTCGGTGGCCATAGGGTC 59.854 63.158 9.72 0.00 40.08 4.46
49 50 3.238232 CCATAGGGTCATGATGGCG 57.762 57.895 0.00 0.00 34.10 5.69
51 52 1.004560 ATAGGGTCATGATGGCGCG 60.005 57.895 8.46 0.00 40.09 6.86
52 53 2.454832 ATAGGGTCATGATGGCGCGG 62.455 60.000 8.83 0.00 40.09 6.46
53 54 4.856801 GGGTCATGATGGCGCGGT 62.857 66.667 8.83 0.00 0.00 5.68
54 55 3.576356 GGTCATGATGGCGCGGTG 61.576 66.667 8.83 0.00 0.00 4.94
55 56 3.576356 GTCATGATGGCGCGGTGG 61.576 66.667 8.83 0.00 0.00 4.61
56 57 3.780173 TCATGATGGCGCGGTGGA 61.780 61.111 8.83 0.00 0.00 4.02
57 58 2.592574 CATGATGGCGCGGTGGAT 60.593 61.111 8.83 0.00 0.00 3.41
59 60 3.832237 ATGATGGCGCGGTGGATCC 62.832 63.158 8.83 4.20 0.00 3.36
70 71 1.077429 GTGGATCCTGACCCTTGCC 60.077 63.158 14.23 0.00 0.00 4.52
97 98 9.489084 GGCAGGAAAGTTTTATTTTTAGATGTT 57.511 29.630 0.00 0.00 0.00 2.71
111 112 5.607119 TTAGATGTTCCTTCGAGTTTTGC 57.393 39.130 0.00 0.00 0.00 3.68
160 185 4.988716 TGGCGACTCTCCCCGTGT 62.989 66.667 0.00 0.00 0.00 4.49
166 191 2.042843 CTCTCCCCGTGTAGCCCT 60.043 66.667 0.00 0.00 0.00 5.19
206 231 1.379443 ATCGTCGGTAGGCCTGTGA 60.379 57.895 17.99 7.48 0.00 3.58
217 244 1.374758 GCCTGTGAAGGTGTCTCCG 60.375 63.158 0.00 0.00 41.99 4.63
233 260 0.613260 TCCGGTGAATCTGTCCTTGG 59.387 55.000 0.00 0.00 0.00 3.61
236 263 1.826385 GGTGAATCTGTCCTTGGTGG 58.174 55.000 0.00 0.00 37.10 4.61
252 279 4.235079 TGGTGGATTTGTTAGGATCTGG 57.765 45.455 0.00 0.00 0.00 3.86
255 282 3.871594 GTGGATTTGTTAGGATCTGGTCG 59.128 47.826 0.00 0.00 0.00 4.79
267 294 5.202004 AGGATCTGGTCGTAGTTTGTCTAT 58.798 41.667 0.00 0.00 0.00 1.98
284 311 3.365220 GTCTATGTTCGTGTGTCTTCAGC 59.635 47.826 0.00 0.00 0.00 4.26
295 322 4.867608 GTGTGTCTTCAGCTAGGATCTTTC 59.132 45.833 0.00 0.00 0.00 2.62
308 335 7.777910 AGCTAGGATCTTTCATATCTACGCTAT 59.222 37.037 0.00 0.00 0.00 2.97
323 350 3.423571 ACGCTATTCTTCAACGACTACG 58.576 45.455 0.00 0.00 45.75 3.51
341 368 2.248431 GTTGTTGTCCTCGTGCGC 59.752 61.111 0.00 0.00 0.00 6.09
351 378 1.589993 CTCGTGCGCTGGTCCTATG 60.590 63.158 9.73 0.00 0.00 2.23
355 382 2.280457 GCGCTGGTCCTATGAGGC 60.280 66.667 0.00 0.00 34.61 4.70
363 390 1.070914 GGTCCTATGAGGCCTTAGCAC 59.929 57.143 6.77 1.09 42.56 4.40
372 399 1.077089 GGCCTTAGCACGACGACTTC 61.077 60.000 0.00 0.00 42.56 3.01
373 400 1.077089 GCCTTAGCACGACGACTTCC 61.077 60.000 0.00 0.00 39.53 3.46
398 542 3.171388 CTATTCAGGGGCCGGCCT 61.171 66.667 42.70 25.83 36.10 5.19
404 548 4.964241 AGGGGCCGGCCTAGGATC 62.964 72.222 42.70 25.81 36.10 3.36
406 550 3.631046 GGGCCGGCCTAGGATCTG 61.631 72.222 42.70 0.00 36.10 2.90
469 683 3.002246 GCTTAAAGCCTTGTTTTTGCCAC 59.998 43.478 0.00 0.00 34.48 5.01
476 690 3.671459 GCCTTGTTTTTGCCACGTATAAC 59.329 43.478 0.00 0.00 0.00 1.89
488 738 7.661127 TGCCACGTATAACCAAATATATCAC 57.339 36.000 0.00 0.00 0.00 3.06
642 892 1.896660 CAGTTGGGGTTGGACGTGG 60.897 63.158 0.00 0.00 0.00 4.94
670 920 1.153168 CCGACCTACTGGGCAATGG 60.153 63.158 0.00 0.00 43.17 3.16
676 926 1.472480 CCTACTGGGCAATGGAAAACG 59.528 52.381 0.00 0.00 0.00 3.60
685 935 3.442273 GGCAATGGAAAACGAAGGTGATA 59.558 43.478 0.00 0.00 0.00 2.15
718 968 2.292828 AACCAATAGTGCCTGCAACT 57.707 45.000 0.00 0.00 0.00 3.16
719 969 3.433306 AACCAATAGTGCCTGCAACTA 57.567 42.857 0.00 0.00 0.00 2.24
720 970 3.652057 ACCAATAGTGCCTGCAACTAT 57.348 42.857 4.07 4.07 0.00 2.12
721 971 3.968265 ACCAATAGTGCCTGCAACTATT 58.032 40.909 13.99 13.99 37.20 1.73
722 972 4.344104 ACCAATAGTGCCTGCAACTATTT 58.656 39.130 16.23 4.52 35.29 1.40
723 973 5.505780 ACCAATAGTGCCTGCAACTATTTA 58.494 37.500 16.23 0.00 35.29 1.40
724 974 5.949354 ACCAATAGTGCCTGCAACTATTTAA 59.051 36.000 16.23 0.00 35.29 1.52
725 975 6.435904 ACCAATAGTGCCTGCAACTATTTAAA 59.564 34.615 16.23 0.00 35.29 1.52
726 976 7.039363 ACCAATAGTGCCTGCAACTATTTAAAA 60.039 33.333 16.23 0.00 35.29 1.52
727 977 7.816995 CCAATAGTGCCTGCAACTATTTAAAAA 59.183 33.333 16.23 0.00 35.29 1.94
793 1043 8.979574 ACTAAAGTAAGATTCGACACAAGAAAG 58.020 33.333 0.00 0.00 0.00 2.62
808 1058 5.526846 CACAAGAAAGCAAAGCCCAATTTTA 59.473 36.000 0.00 0.00 0.00 1.52
865 1116 7.993183 ACGAACCATCAAATTATCTACCAGATT 59.007 33.333 0.00 0.00 36.20 2.40
880 1131 2.036992 CCAGATTGAGCGAGCCTTAGAT 59.963 50.000 0.00 0.00 0.00 1.98
882 1133 1.797635 GATTGAGCGAGCCTTAGATGC 59.202 52.381 0.00 0.00 0.00 3.91
917 1168 3.592070 TCGACTGCCGAGAAGGAG 58.408 61.111 0.00 0.00 43.23 3.69
996 1247 3.766691 GAAGAGTGCCCCGCCGTA 61.767 66.667 0.00 0.00 0.00 4.02
1069 1320 1.362584 TCCTCCTGACCATCCTCTTCA 59.637 52.381 0.00 0.00 0.00 3.02
1121 1374 3.694058 CTGCCTCCATCCGCTGCTT 62.694 63.158 0.00 0.00 0.00 3.91
1138 1391 1.878953 CTTTTCCTGGTACTGTGCGT 58.121 50.000 0.00 0.00 0.00 5.24
1143 1396 1.282248 CCTGGTACTGTGCGTCAACG 61.282 60.000 0.00 0.00 43.27 4.10
1393 1663 1.148949 TCAGTTGCAGCTTCTGGCA 59.851 52.632 0.00 0.00 44.79 4.92
1516 1788 3.232213 TGCTCAACACGGAGAAGATAC 57.768 47.619 0.00 0.00 37.05 2.24
1975 2275 8.752766 ATCTTAGTTTTCAGCAACATCATTTG 57.247 30.769 0.00 0.00 0.00 2.32
2013 2313 4.469586 TGACCCTACTCATTGCTCAATGTA 59.530 41.667 18.68 7.36 46.15 2.29
2381 2681 3.560068 CCACAAGAACTTGCGTCTTAAGT 59.440 43.478 13.50 0.00 44.03 2.24
2723 3023 8.651391 TGCAGCCTGAAAATTTAAATGATATG 57.349 30.769 0.39 0.00 0.00 1.78
2901 6460 2.489938 TCTAAAACGGGCTCTTGCAT 57.510 45.000 0.00 0.00 41.91 3.96
2902 6461 2.083774 TCTAAAACGGGCTCTTGCATG 58.916 47.619 0.00 0.00 41.91 4.06
3017 6576 4.042809 TGGTTACTCCAAGGACATGTGAAT 59.957 41.667 1.15 0.00 44.12 2.57
3018 6577 5.010282 GGTTACTCCAAGGACATGTGAATT 58.990 41.667 1.15 0.00 35.97 2.17
3019 6578 6.177610 GGTTACTCCAAGGACATGTGAATTA 58.822 40.000 1.15 0.00 35.97 1.40
3020 6579 6.316390 GGTTACTCCAAGGACATGTGAATTAG 59.684 42.308 1.15 0.00 35.97 1.73
3021 6580 4.265073 ACTCCAAGGACATGTGAATTAGC 58.735 43.478 1.15 0.00 0.00 3.09
3022 6581 4.263462 ACTCCAAGGACATGTGAATTAGCA 60.263 41.667 1.15 0.00 0.00 3.49
3023 6582 4.661222 TCCAAGGACATGTGAATTAGCAA 58.339 39.130 1.15 0.00 0.00 3.91
3024 6583 5.263599 TCCAAGGACATGTGAATTAGCAAT 58.736 37.500 1.15 0.00 0.00 3.56
3071 6630 6.590292 AGTGATACTGTACACATAAGCAACAC 59.410 38.462 16.93 0.00 39.18 3.32
3095 6654 9.113838 CACTAACTATAAGTAGTAAGTTCCCGA 57.886 37.037 0.00 0.00 40.24 5.14
3129 6688 5.514204 GCAGAAATGTGCAGCTTATTTACTG 59.486 40.000 17.58 17.58 43.41 2.74
3258 6817 7.447238 TCTCACGGAAGGAATTTAGAAAATTGT 59.553 33.333 2.51 0.00 0.00 2.71
3380 6939 4.563786 GCCTGGCCCTTGTATAGATTAGAC 60.564 50.000 7.66 0.00 0.00 2.59
3468 7028 1.512771 GTTTGCGACGAACTTTTGCTG 59.487 47.619 0.00 0.00 0.00 4.41
3549 7109 5.244626 GGCATCAATAGCACCATATTTCCTT 59.755 40.000 0.00 0.00 0.00 3.36
3622 7182 3.941483 TGCAGCTAAGCTTTCCTGATAAC 59.059 43.478 22.75 10.45 36.40 1.89
3710 7270 7.861630 TGTACAGATGTGAAGTTTTTAAGCTC 58.138 34.615 0.00 0.00 0.00 4.09
3844 7405 7.148771 GCGAAAATTCATCACAAAATCACATCA 60.149 33.333 0.00 0.00 0.00 3.07
4105 7675 3.751518 TGGCCAACCTTCTTCTTTCTAC 58.248 45.455 0.61 0.00 36.63 2.59
4228 7799 1.270252 CCATGTGGCAAACCTCCAAAC 60.270 52.381 0.00 0.00 35.01 2.93
4391 9506 8.643324 AGTACTCTCATCTTGTTACTGTCTTTT 58.357 33.333 0.00 0.00 0.00 2.27
4426 9542 3.326588 TCCTGCACTTTACAGCCTCTTAA 59.673 43.478 0.00 0.00 33.65 1.85
4584 9700 3.215151 TCAAATCTTGCCACGGTTACAA 58.785 40.909 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.831307 CGAAGACGAGGCGGTCCG 62.831 72.222 6.99 6.99 42.66 4.79
10 11 4.493747 CCGAAGACGAGGCGGTCC 62.494 72.222 7.91 0.00 42.66 4.46
16 17 1.672854 TATGGCCACCGAAGACGAGG 61.673 60.000 8.16 0.00 42.66 4.63
17 18 0.249073 CTATGGCCACCGAAGACGAG 60.249 60.000 8.16 0.00 42.66 4.18
18 19 1.672854 CCTATGGCCACCGAAGACGA 61.673 60.000 8.16 0.00 42.66 4.20
19 20 1.227263 CCTATGGCCACCGAAGACG 60.227 63.158 8.16 0.00 39.43 4.18
20 21 1.146263 CCCTATGGCCACCGAAGAC 59.854 63.158 8.16 0.00 0.00 3.01
21 22 1.306654 ACCCTATGGCCACCGAAGA 60.307 57.895 8.16 0.00 33.59 2.87
22 23 1.146263 GACCCTATGGCCACCGAAG 59.854 63.158 8.16 3.07 33.59 3.79
23 24 0.986019 ATGACCCTATGGCCACCGAA 60.986 55.000 8.16 0.00 33.59 4.30
25 26 1.227943 CATGACCCTATGGCCACCG 60.228 63.158 8.16 0.73 33.59 4.94
26 27 0.773644 ATCATGACCCTATGGCCACC 59.226 55.000 8.16 0.00 33.59 4.61
28 29 0.773014 CCATCATGACCCTATGGCCA 59.227 55.000 8.56 8.56 34.19 5.36
31 32 0.957395 GCGCCATCATGACCCTATGG 60.957 60.000 7.77 7.77 42.59 2.74
32 33 1.293963 CGCGCCATCATGACCCTATG 61.294 60.000 0.00 0.00 0.00 2.23
33 34 1.004560 CGCGCCATCATGACCCTAT 60.005 57.895 0.00 0.00 0.00 2.57
34 35 2.421314 CGCGCCATCATGACCCTA 59.579 61.111 0.00 0.00 0.00 3.53
35 36 4.552365 CCGCGCCATCATGACCCT 62.552 66.667 0.00 0.00 0.00 4.34
37 38 3.576356 CACCGCGCCATCATGACC 61.576 66.667 0.00 0.00 0.00 4.02
38 39 3.576356 CCACCGCGCCATCATGAC 61.576 66.667 0.00 0.00 0.00 3.06
39 40 2.994387 GATCCACCGCGCCATCATGA 62.994 60.000 0.00 0.00 0.00 3.07
40 41 2.592574 ATCCACCGCGCCATCATG 60.593 61.111 0.00 0.00 0.00 3.07
42 43 4.545706 GGATCCACCGCGCCATCA 62.546 66.667 6.95 0.00 0.00 3.07
43 44 4.241555 AGGATCCACCGCGCCATC 62.242 66.667 15.82 0.00 44.74 3.51
44 45 4.552365 CAGGATCCACCGCGCCAT 62.552 66.667 15.82 0.00 44.74 4.40
49 50 2.670148 AAGGGTCAGGATCCACCGC 61.670 63.158 15.82 9.23 44.74 5.68
51 52 1.077429 GCAAGGGTCAGGATCCACC 60.077 63.158 15.82 13.68 32.73 4.61
52 53 1.077429 GGCAAGGGTCAGGATCCAC 60.077 63.158 15.82 3.83 32.73 4.02
53 54 2.669133 CGGCAAGGGTCAGGATCCA 61.669 63.158 15.82 0.00 32.73 3.41
54 55 2.190578 CGGCAAGGGTCAGGATCC 59.809 66.667 2.48 2.48 0.00 3.36
55 56 2.190578 CCGGCAAGGGTCAGGATC 59.809 66.667 0.00 0.00 35.97 3.36
56 57 4.115199 GCCGGCAAGGGTCAGGAT 62.115 66.667 24.80 0.00 41.48 3.24
70 71 7.812669 ACATCTAAAAATAAAACTTTCCTGCCG 59.187 33.333 0.00 0.00 0.00 5.69
97 98 1.623811 AGCCTAGCAAAACTCGAAGGA 59.376 47.619 0.00 0.00 0.00 3.36
110 111 2.289694 TGAGAAGGACACAAAGCCTAGC 60.290 50.000 0.00 0.00 33.20 3.42
111 112 3.594134 CTGAGAAGGACACAAAGCCTAG 58.406 50.000 0.00 0.00 33.20 3.02
145 146 2.799371 CTACACGGGGAGAGTCGC 59.201 66.667 0.00 0.00 0.00 5.19
160 185 2.439701 CCACCGAGACGAGGGCTA 60.440 66.667 0.00 0.00 0.00 3.93
166 191 2.128290 TAGACCCACCACCGAGACGA 62.128 60.000 0.00 0.00 0.00 4.20
206 231 1.276421 CAGATTCACCGGAGACACCTT 59.724 52.381 9.46 0.00 36.31 3.50
217 244 1.351017 TCCACCAAGGACAGATTCACC 59.649 52.381 0.00 0.00 43.07 4.02
233 260 3.871594 CGACCAGATCCTAACAAATCCAC 59.128 47.826 0.00 0.00 0.00 4.02
236 263 5.903810 ACTACGACCAGATCCTAACAAATC 58.096 41.667 0.00 0.00 0.00 2.17
252 279 4.913924 ACACGAACATAGACAAACTACGAC 59.086 41.667 0.00 0.00 33.62 4.34
255 282 5.919141 AGACACACGAACATAGACAAACTAC 59.081 40.000 0.00 0.00 33.62 2.73
267 294 2.288213 CCTAGCTGAAGACACACGAACA 60.288 50.000 0.00 0.00 0.00 3.18
284 311 9.944663 GAATAGCGTAGATATGAAAGATCCTAG 57.055 37.037 0.00 0.00 38.61 3.02
295 322 7.078851 AGTCGTTGAAGAATAGCGTAGATATG 58.921 38.462 0.00 0.00 38.61 1.78
308 335 3.441496 ACAACCGTAGTCGTTGAAGAA 57.559 42.857 7.63 0.00 34.67 2.52
323 350 2.935955 CGCACGAGGACAACAACC 59.064 61.111 0.00 0.00 0.00 3.77
351 378 1.516603 GTCGTCGTGCTAAGGCCTC 60.517 63.158 5.23 0.00 37.74 4.70
355 382 0.458025 GGGAAGTCGTCGTGCTAAGG 60.458 60.000 0.00 0.00 0.00 2.69
363 390 1.154263 GACAGTCGGGAAGTCGTCG 60.154 63.158 0.00 0.00 0.00 5.12
372 399 0.753262 CCCCTGAATAGACAGTCGGG 59.247 60.000 2.62 2.62 43.62 5.14
373 400 0.105039 GCCCCTGAATAGACAGTCGG 59.895 60.000 0.00 0.00 36.30 4.79
398 542 7.718334 TTGAATACACACTCTTCAGATCCTA 57.282 36.000 0.00 0.00 31.11 2.94
404 548 9.903682 ATGAAATTTTGAATACACACTCTTCAG 57.096 29.630 0.00 0.00 31.11 3.02
428 572 9.578439 CTTTAAGCTTTTGAAGAATTCCCTATG 57.422 33.333 3.20 0.00 46.93 2.23
439 653 6.908870 AAACAAGGCTTTAAGCTTTTGAAG 57.091 33.333 27.45 14.81 38.55 3.02
442 656 5.738693 GCAAAAACAAGGCTTTAAGCTTTTG 59.261 36.000 24.29 24.29 38.55 2.44
670 920 3.058651 GTCGACGTATCACCTTCGTTTTC 59.941 47.826 0.00 0.00 37.92 2.29
676 926 1.905449 GGTGTCGACGTATCACCTTC 58.095 55.000 21.28 3.81 45.46 3.46
685 935 0.746063 TTGGTTACAGGTGTCGACGT 59.254 50.000 11.62 5.04 0.00 4.34
772 1022 5.297547 TGCTTTCTTGTGTCGAATCTTACT 58.702 37.500 0.00 0.00 0.00 2.24
783 1033 1.484038 TGGGCTTTGCTTTCTTGTGT 58.516 45.000 0.00 0.00 0.00 3.72
793 1043 5.237048 TCTGATGTTAAAATTGGGCTTTGC 58.763 37.500 0.00 0.00 0.00 3.68
845 1095 7.386025 TCGCTCAATCTGGTAGATAATTTGATG 59.614 37.037 0.00 0.00 32.89 3.07
846 1096 7.445121 TCGCTCAATCTGGTAGATAATTTGAT 58.555 34.615 0.00 0.00 32.89 2.57
865 1116 1.066422 CGCATCTAAGGCTCGCTCA 59.934 57.895 0.00 0.00 0.00 4.26
898 1149 1.303398 TCCTTCTCGGCAGTCGACT 60.303 57.895 13.58 13.58 43.74 4.18
948 1199 5.278022 GGCGAGATGTCTTCTGTTTTTCTTT 60.278 40.000 0.00 0.00 33.74 2.52
949 1200 4.214332 GGCGAGATGTCTTCTGTTTTTCTT 59.786 41.667 0.00 0.00 33.74 2.52
950 1201 3.748568 GGCGAGATGTCTTCTGTTTTTCT 59.251 43.478 0.00 0.00 33.74 2.52
951 1202 3.423645 CGGCGAGATGTCTTCTGTTTTTC 60.424 47.826 0.00 0.00 33.74 2.29
952 1203 2.480419 CGGCGAGATGTCTTCTGTTTTT 59.520 45.455 0.00 0.00 33.74 1.94
953 1204 2.069273 CGGCGAGATGTCTTCTGTTTT 58.931 47.619 0.00 0.00 33.74 2.43
996 1247 2.203070 GGCGGAGATGGCATTCGT 60.203 61.111 0.00 0.00 0.00 3.85
1117 1370 1.604604 GCACAGTACCAGGAAAAGCA 58.395 50.000 0.00 0.00 0.00 3.91
1121 1374 0.753867 TGACGCACAGTACCAGGAAA 59.246 50.000 0.00 0.00 0.00 3.13
1138 1391 2.203938 AGAAGGGGGAGGCGTTGA 60.204 61.111 0.00 0.00 0.00 3.18
1143 1396 2.677848 GGAACAGAAGGGGGAGGC 59.322 66.667 0.00 0.00 0.00 4.70
1152 1405 2.032528 CTGCTGCGGGGAACAGAA 59.967 61.111 0.00 0.00 37.32 3.02
1404 1675 5.989777 GGACGGTATCTATAAACACAAGCAT 59.010 40.000 0.00 0.00 0.00 3.79
1516 1788 1.538950 GGTGCTCTCAGCCTTGAAAAG 59.461 52.381 0.00 0.00 45.69 2.27
1897 2197 5.934402 AACTACATACCAGACCAACCTAG 57.066 43.478 0.00 0.00 0.00 3.02
1975 2275 2.893489 AGGGTCAGCCAAGATTTCAAAC 59.107 45.455 0.00 0.00 36.17 2.93
2013 2313 5.484998 TCTTCCTAGTTAAACCGGGTAACAT 59.515 40.000 24.20 15.19 34.50 2.71
2177 2477 8.567285 ACTCAACCAATAAATAAAGAGACAGG 57.433 34.615 0.00 0.00 0.00 4.00
2381 2681 6.381498 TGACTTTTGGGTATTGATAGACCA 57.619 37.500 0.00 0.00 37.38 4.02
2433 2733 1.370414 CTTTGAACCTTGTGCCGCG 60.370 57.895 0.00 0.00 0.00 6.46
2723 3023 4.082408 GGTTACTTTTGGTGGCTTATGTCC 60.082 45.833 0.00 0.00 0.00 4.02
2792 6351 3.426615 ACTTCTCAAGACCACTCTCGAT 58.573 45.455 0.00 0.00 0.00 3.59
2901 6460 5.512404 CCAAGGTCTGTGTATAGAACCAACA 60.512 44.000 0.00 0.00 34.91 3.33
2902 6461 4.935808 CCAAGGTCTGTGTATAGAACCAAC 59.064 45.833 0.00 0.00 34.91 3.77
3017 6576 9.627123 ACCTACTCATTTATGCTAAATTGCTAA 57.373 29.630 0.00 0.00 0.00 3.09
3018 6577 9.056005 CACCTACTCATTTATGCTAAATTGCTA 57.944 33.333 0.00 0.00 0.00 3.49
3019 6578 7.469181 GCACCTACTCATTTATGCTAAATTGCT 60.469 37.037 0.00 0.00 0.00 3.91
3020 6579 6.638468 GCACCTACTCATTTATGCTAAATTGC 59.362 38.462 0.00 0.00 0.00 3.56
3021 6580 7.706159 TGCACCTACTCATTTATGCTAAATTG 58.294 34.615 0.00 0.00 34.18 2.32
3022 6581 7.557719 ACTGCACCTACTCATTTATGCTAAATT 59.442 33.333 0.00 0.00 34.18 1.82
3023 6582 7.012704 CACTGCACCTACTCATTTATGCTAAAT 59.987 37.037 0.00 0.00 34.18 1.40
3024 6583 6.316140 CACTGCACCTACTCATTTATGCTAAA 59.684 38.462 0.00 0.00 34.18 1.85
3091 6650 3.641437 TTTCTGCTTTGTGAATTCGGG 57.359 42.857 0.04 0.00 0.00 5.14
3095 6654 4.695396 TGCACATTTCTGCTTTGTGAATT 58.305 34.783 6.47 0.00 42.59 2.17
3129 6688 4.397481 TGATGTCATCAGATGGTCTCAC 57.603 45.455 11.62 1.67 33.59 3.51
3380 6939 3.693085 AGGTGCTTGCATCAAACTATCAG 59.307 43.478 8.65 0.00 0.00 2.90
3468 7028 0.252239 AGGCAAAAAGTGGGATCCCC 60.252 55.000 28.58 18.74 45.71 4.81
3479 7039 1.764054 CCCACCCACCAGGCAAAAA 60.764 57.895 0.00 0.00 40.58 1.94
3622 7182 1.342555 TCATAGTTCACGTTTCGGCG 58.657 50.000 0.00 0.00 37.94 6.46
3844 7405 0.107831 TTTCTACCACGCCTTGCACT 59.892 50.000 0.00 0.00 0.00 4.40
4105 7675 6.021153 GCTGCGACTAATAGAAAGCAAAAATG 60.021 38.462 0.00 0.00 34.04 2.32
4228 7799 6.683974 ATGACATCTAAAATTCACGGGAAG 57.316 37.500 6.16 0.00 36.25 3.46
4312 9427 6.430864 TGTTTCCAGATCATTAGGGCATAAA 58.569 36.000 0.00 0.00 0.00 1.40
4391 9506 0.991146 TGCAGGAAGGTATGGCTGAA 59.009 50.000 0.00 0.00 0.00 3.02
4426 9542 7.422465 AAATGTGTTTAATGGCATGGTAGAT 57.578 32.000 0.00 0.00 0.00 1.98
4584 9700 0.893727 GGCTCGGTGAAATTGGTGGT 60.894 55.000 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.