Multiple sequence alignment - TraesCS6A01G405700

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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 TraesCS6A01G405700 chr6A 100.000 3416 0 0 1 3416 611524292 611520877 0.000000e+00 6309
1 TraesCS6A01G405700 chr6A 93.734 1149 58 8 1094 2229 611513311 611514458 0.000000e+00 1711
2 TraesCS6A01G405700 chr6D 87.336 2598 196 65 879 3416 465011752 465009228 0.000000e+00 2852
3 TraesCS6A01G405700 chr6D 88.889 1197 83 34 1059 2219 464984466 464985648 0.000000e+00 1428
4 TraesCS6A01G405700 chr6D 85.987 471 29 15 555 1022 101397818 101397382 1.440000e-128 470
5 TraesCS6A01G405700 chr6D 88.088 319 21 7 121 433 185869524 185869831 2.510000e-96 363
6 TraesCS6A01G405700 chr6D 82.297 418 28 18 1 393 465012512 465012116 1.530000e-83 320
7 TraesCS6A01G405700 chr6D 87.665 227 13 9 208 433 101398220 101398008 2.040000e-62 250
8 TraesCS6A01G405700 chr6D 90.909 143 12 1 556 697 465011995 465011853 1.250000e-44 191
9 TraesCS6A01G405700 chr6B 89.537 1491 87 39 558 2012 709021268 709019811 0.000000e+00 1825
10 TraesCS6A01G405700 chr6B 89.906 1169 78 21 1094 2244 708988812 708989958 0.000000e+00 1469
11 TraesCS6A01G405700 chr6B 84.192 1126 114 20 2300 3413 709015784 709014711 0.000000e+00 1035
12 TraesCS6A01G405700 chr6B 90.529 454 31 5 2091 2533 709019756 709019304 1.060000e-164 590
13 TraesCS6A01G405700 chr6B 85.283 530 46 16 2325 2845 709017250 709016744 5.050000e-143 518
14 TraesCS6A01G405700 chr6B 83.402 241 17 5 102 335 709021774 709021550 5.780000e-48 202
15 TraesCS6A01G405700 chr5B 89.721 788 65 8 977 1749 326612981 326612195 0.000000e+00 992
16 TraesCS6A01G405700 chr5B 83.733 375 37 19 1851 2220 326612110 326611755 1.960000e-87 333
17 TraesCS6A01G405700 chr5D 89.272 783 68 8 977 1744 287571871 287571090 0.000000e+00 966
18 TraesCS6A01G405700 chr5D 90.909 319 13 6 121 433 321682834 321682526 6.820000e-112 414
19 TraesCS6A01G405700 chr5D 82.984 382 43 17 1847 2220 287571010 287570643 3.290000e-85 326
20 TraesCS6A01G405700 chr5D 95.327 107 5 0 574 680 321682332 321682226 1.630000e-38 171
21 TraesCS6A01G405700 chr5A 88.198 788 66 13 977 1744 379401627 379400847 0.000000e+00 915
22 TraesCS6A01G405700 chr5A 82.967 364 45 13 1851 2208 379400765 379400413 2.560000e-81 313
23 TraesCS6A01G405700 chr1D 90.129 466 19 14 555 1015 339906041 339906484 6.350000e-162 580
24 TraesCS6A01G405700 chr1D 89.937 318 17 7 121 433 113493782 113493475 2.470000e-106 396
25 TraesCS6A01G405700 chr1D 89.262 298 17 7 141 433 339905567 339905854 3.240000e-95 359
26 TraesCS6A01G405700 chr1D 94.444 126 7 0 555 680 113493288 113493163 9.670000e-46 195
27 TraesCS6A01G405700 chr1D 89.209 139 14 1 419 556 339905867 339906005 4.530000e-39 172
28 TraesCS6A01G405700 chr3A 90.735 313 19 5 121 433 58456271 58456573 3.170000e-110 409
29 TraesCS6A01G405700 chr3A 94.393 107 6 0 574 680 58456769 58456875 7.580000e-37 165
30 TraesCS6A01G405700 chr4D 89.241 316 17 6 121 431 227829278 227829581 2.490000e-101 379
31 TraesCS6A01G405700 chr4D 95.200 125 6 0 556 680 227829772 227829896 7.480000e-47 198
32 TraesCS6A01G405700 chr4D 88.489 139 15 1 419 556 227829597 227829735 2.110000e-37 167
33 TraesCS6A01G405700 chr2D 78.299 576 98 16 1193 1744 480181623 480181051 2.520000e-91 346
34 TraesCS6A01G405700 chr1A 87.107 318 23 7 121 433 234659150 234658846 9.080000e-91 344
35 TraesCS6A01G405700 chr1A 93.525 139 8 1 419 556 234658832 234658694 4.470000e-49 206
36 TraesCS6A01G405700 chr3D 91.270 126 11 0 555 680 478336578 478336453 4.530000e-39 172


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 TraesCS6A01G405700 chr6A 611520877 611524292 3415 True 6309.000000 6309 100.000000 1 3416 1 chr6A.!!$R1 3415
1 TraesCS6A01G405700 chr6A 611513311 611514458 1147 False 1711.000000 1711 93.734000 1094 2229 1 chr6A.!!$F1 1135
2 TraesCS6A01G405700 chr6D 464984466 464985648 1182 False 1428.000000 1428 88.889000 1059 2219 1 chr6D.!!$F2 1160
3 TraesCS6A01G405700 chr6D 465009228 465012512 3284 True 1121.000000 2852 86.847333 1 3416 3 chr6D.!!$R2 3415
4 TraesCS6A01G405700 chr6D 101397382 101398220 838 True 360.000000 470 86.826000 208 1022 2 chr6D.!!$R1 814
5 TraesCS6A01G405700 chr6B 708988812 708989958 1146 False 1469.000000 1469 89.906000 1094 2244 1 chr6B.!!$F1 1150
6 TraesCS6A01G405700 chr6B 709014711 709021774 7063 True 834.000000 1825 86.588600 102 3413 5 chr6B.!!$R1 3311
7 TraesCS6A01G405700 chr5B 326611755 326612981 1226 True 662.500000 992 86.727000 977 2220 2 chr5B.!!$R1 1243
8 TraesCS6A01G405700 chr5D 287570643 287571871 1228 True 646.000000 966 86.128000 977 2220 2 chr5D.!!$R1 1243
9 TraesCS6A01G405700 chr5D 321682226 321682834 608 True 292.500000 414 93.118000 121 680 2 chr5D.!!$R2 559
10 TraesCS6A01G405700 chr5A 379400413 379401627 1214 True 614.000000 915 85.582500 977 2208 2 chr5A.!!$R1 1231
11 TraesCS6A01G405700 chr1D 339905567 339906484 917 False 370.333333 580 89.533333 141 1015 3 chr1D.!!$F1 874
12 TraesCS6A01G405700 chr1D 113493163 113493782 619 True 295.500000 396 92.190500 121 680 2 chr1D.!!$R1 559
13 TraesCS6A01G405700 chr3A 58456271 58456875 604 False 287.000000 409 92.564000 121 680 2 chr3A.!!$F1 559
14 TraesCS6A01G405700 chr4D 227829278 227829896 618 False 248.000000 379 90.976667 121 680 3 chr4D.!!$F1 559
15 TraesCS6A01G405700 chr2D 480181051 480181623 572 True 346.000000 346 78.299000 1193 1744 1 chr2D.!!$R1 551

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
98 128 0.179084 CACTCGTGAAGGGTGTGTGT 60.179 55.000 0.0 0.0 46.14 3.72 F
100 130 0.179084 CTCGTGAAGGGTGTGTGTGT 60.179 55.000 0.0 0.0 0.00 3.72 F
115 145 0.799393 TGTGTGTGTGTGTTTGGTCG 59.201 50.000 0.0 0.0 0.00 4.79 F
1813 2080 1.067516 CTGTTTGGTTTGGGCAGTGAG 59.932 52.381 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 2113 0.108709 GGCGCCAAAATCTGCAATCA 60.109 50.000 24.80 0.0 0.00 2.57 R
1847 2114 0.174162 AGGCGCCAAAATCTGCAATC 59.826 50.000 31.54 0.0 0.00 2.67 R
1866 2149 2.493030 GCGAACCCGATCGGAAGA 59.507 61.111 35.42 0.0 42.93 2.87 R
2797 6893 0.680061 GTCTCCCTGAACACCGTCTT 59.320 55.000 0.00 0.0 0.00 3.01 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 1.859998 GCTCGTGTTCTTGTGTTTGCC 60.860 52.381 0.00 0.00 0.00 4.52
76 77 3.099211 ATCGCCTCTCGCTGCCAAT 62.099 57.895 0.00 0.00 38.27 3.16
92 122 0.606401 CAATGCCACTCGTGAAGGGT 60.606 55.000 0.00 0.00 0.00 4.34
97 127 2.605094 CACTCGTGAAGGGTGTGTG 58.395 57.895 0.00 0.00 46.14 3.82
98 128 0.179084 CACTCGTGAAGGGTGTGTGT 60.179 55.000 0.00 0.00 46.14 3.72
99 129 0.179084 ACTCGTGAAGGGTGTGTGTG 60.179 55.000 0.00 0.00 27.95 3.82
100 130 0.179084 CTCGTGAAGGGTGTGTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
115 145 0.799393 TGTGTGTGTGTGTTTGGTCG 59.201 50.000 0.00 0.00 0.00 4.79
119 149 1.328374 GTGTGTGTGTTTGGTCGTACC 59.672 52.381 0.00 0.00 39.22 3.34
233 277 6.183360 GCATGCCACTTCTATCCATACTTTTT 60.183 38.462 6.36 0.00 0.00 1.94
312 362 8.640651 GTTACTAGTATAAAAGGAAGAGGGAGG 58.359 40.741 2.79 0.00 0.00 4.30
338 388 8.889717 GTCGAATTCTTTGGACCAAATTATAGA 58.110 33.333 19.87 10.51 35.29 1.98
339 389 9.109393 TCGAATTCTTTGGACCAAATTATAGAG 57.891 33.333 19.87 6.79 32.70 2.43
342 392 7.630242 TTCTTTGGACCAAATTATAGAGCTG 57.370 36.000 19.87 4.82 32.70 4.24
375 449 5.361285 AGGGACTGACTCATCACTGTATTAC 59.639 44.000 0.00 0.00 37.18 1.89
376 450 5.361285 GGGACTGACTCATCACTGTATTACT 59.639 44.000 0.00 0.00 0.00 2.24
377 451 6.546403 GGGACTGACTCATCACTGTATTACTA 59.454 42.308 0.00 0.00 0.00 1.82
401 476 4.479993 AGCTGGGCTCATCGGTGC 62.480 66.667 0.00 0.00 30.62 5.01
409 484 2.419574 GGGCTCATCGGTGCTTAACTAA 60.420 50.000 0.00 0.00 34.07 2.24
413 488 4.332819 GCTCATCGGTGCTTAACTAACAAT 59.667 41.667 0.00 0.00 0.00 2.71
414 489 5.502544 GCTCATCGGTGCTTAACTAACAATC 60.503 44.000 0.00 0.00 0.00 2.67
435 540 7.039011 ACAATCAGTAGTAGTTCAGTTCATGGA 60.039 37.037 0.00 0.00 0.00 3.41
498 604 1.486310 TGGTCGATGAAGGAAGGGATG 59.514 52.381 0.00 0.00 0.00 3.51
501 607 3.556004 GGTCGATGAAGGAAGGGATGATC 60.556 52.174 0.00 0.00 0.00 2.92
536 642 4.074526 GCCAGCAGGACGAGCTCA 62.075 66.667 15.40 0.00 41.14 4.26
537 643 2.898738 CCAGCAGGACGAGCTCAT 59.101 61.111 15.40 0.00 41.14 2.90
680 827 3.736126 GCTAGTTAACAACCGCCGACTAT 60.736 47.826 8.61 0.00 0.00 2.12
738 886 1.376543 CATGACATGACAGGTGAGGC 58.623 55.000 10.03 0.00 0.00 4.70
745 893 1.142748 GACAGGTGAGGCGAGATGG 59.857 63.158 0.00 0.00 0.00 3.51
783 931 9.009327 CACTAGTAAACAAGACACAAACATTTG 57.991 33.333 0.00 2.77 43.62 2.32
788 936 4.757594 ACAAGACACAAACATTTGCATGT 58.242 34.783 4.25 2.71 46.34 3.21
796 944 8.160521 ACACAAACATTTGCATGTACTAACTA 57.839 30.769 4.25 0.00 43.34 2.24
797 945 8.073768 ACACAAACATTTGCATGTACTAACTAC 58.926 33.333 4.25 0.00 43.34 2.73
798 946 8.289618 CACAAACATTTGCATGTACTAACTACT 58.710 33.333 4.25 0.00 43.34 2.57
947 1106 5.643379 AAACCATTATCATGACACACACC 57.357 39.130 0.00 0.00 31.07 4.16
1025 1199 3.386237 GGCACTCAGACCCGCTCT 61.386 66.667 0.00 0.00 0.00 4.09
1073 1263 2.019984 CATCTCCAAGCCAAGCTAACC 58.980 52.381 0.00 0.00 38.25 2.85
1368 1595 4.555709 TCCAAGTGCGGCACCGTT 62.556 61.111 28.14 15.05 42.09 4.44
1548 1775 3.807839 TGCCTGGGCGCCATATGT 61.808 61.111 30.85 0.00 45.51 2.29
1813 2080 1.067516 CTGTTTGGTTTGGGCAGTGAG 59.932 52.381 0.00 0.00 0.00 3.51
1830 2097 5.578727 GCAGTGAGTTAGTAGATGAAACCAG 59.421 44.000 0.00 0.00 0.00 4.00
1866 2149 0.174162 GATTGCAGATTTTGGCGCCT 59.826 50.000 29.70 6.86 0.00 5.52
2209 2571 0.109272 TTCAAGAGCCGCGACTAGTG 60.109 55.000 8.23 2.58 0.00 2.74
2254 2618 3.438434 GGATGGAGTCTTCTTGTTTCTGC 59.562 47.826 0.00 0.00 0.00 4.26
2257 2621 2.225255 GGAGTCTTCTTGTTTCTGCTGC 59.775 50.000 0.00 0.00 0.00 5.25
2258 2622 2.874701 GAGTCTTCTTGTTTCTGCTGCA 59.125 45.455 0.88 0.88 0.00 4.41
2261 2625 4.023365 AGTCTTCTTGTTTCTGCTGCAATC 60.023 41.667 3.02 0.00 0.00 2.67
2288 2652 8.181904 TCTCCTTGCTCTTGAAATGTATTTTT 57.818 30.769 0.00 0.00 0.00 1.94
2394 5029 4.877378 AAAATGTGTGTGGATTGCAGAT 57.123 36.364 0.00 0.00 0.00 2.90
2449 5085 7.695055 TGAAAATCTTAAAGGTCTATGTGGGA 58.305 34.615 0.00 0.00 0.00 4.37
2478 5122 6.737254 AACATGGTGAGAAATTTAGTACCG 57.263 37.500 0.00 3.29 0.00 4.02
2504 5148 6.179040 CCTGATTTTGAAGGAGAGTTGAGAT 58.821 40.000 0.00 0.00 35.40 2.75
2507 5151 7.400439 TGATTTTGAAGGAGAGTTGAGATCAT 58.600 34.615 0.00 0.00 0.00 2.45
2542 5186 4.415881 CTCTACCAGAGTCTCTAGCAGA 57.584 50.000 0.94 0.00 37.57 4.26
2543 5187 4.380531 CTCTACCAGAGTCTCTAGCAGAG 58.619 52.174 10.14 10.14 37.27 3.35
2544 5188 3.778075 TCTACCAGAGTCTCTAGCAGAGT 59.222 47.826 0.94 0.00 42.83 3.24
2549 5193 2.623535 GAGTCTCTAGCAGAGTCGTCA 58.376 52.381 11.37 0.00 42.83 4.35
2550 5194 2.350498 GAGTCTCTAGCAGAGTCGTCAC 59.650 54.545 11.37 4.37 42.83 3.67
2560 5204 1.000163 AGAGTCGTCACATTCGCAGTT 60.000 47.619 0.00 0.00 0.00 3.16
2601 5245 7.336931 GGAGAGTTGAGACCAAAATTGCTAATA 59.663 37.037 0.00 0.00 33.49 0.98
2669 5317 5.064452 CAGATTCAAGGCTTTGCTACTACAG 59.936 44.000 3.19 0.00 34.21 2.74
2671 5319 5.477607 TTCAAGGCTTTGCTACTACAGTA 57.522 39.130 3.19 0.00 34.21 2.74
2674 5322 5.699458 TCAAGGCTTTGCTACTACAGTAAAC 59.301 40.000 3.19 0.00 34.37 2.01
2689 5337 1.804151 GTAAACCCGAACCCGTTTACC 59.196 52.381 10.34 0.00 44.28 2.85
2711 6807 4.219033 CGATGTTCACTTTAAGTGTTGGC 58.781 43.478 22.36 12.45 46.03 4.52
2712 6808 3.684103 TGTTCACTTTAAGTGTTGGCG 57.316 42.857 22.36 0.00 46.03 5.69
2737 6833 1.680338 AAACTGTCTTGTGGCTCACC 58.320 50.000 3.33 0.00 32.73 4.02
2753 6849 3.738282 GCTCACCACGATGAATATGTCTC 59.262 47.826 0.00 0.00 0.00 3.36
2754 6850 4.737649 GCTCACCACGATGAATATGTCTCA 60.738 45.833 0.00 0.00 0.00 3.27
2758 6854 4.402474 ACCACGATGAATATGTCTCAGTCA 59.598 41.667 0.00 0.00 0.00 3.41
2759 6855 5.069648 ACCACGATGAATATGTCTCAGTCAT 59.930 40.000 0.00 0.00 0.00 3.06
2768 6864 1.271001 TGTCTCAGTCATTGGTGGCAG 60.271 52.381 0.00 0.00 30.45 4.85
2791 6887 2.223525 CCCGACAGAACGATTACTCCTC 60.224 54.545 0.00 0.00 35.09 3.71
2792 6888 2.539142 CCGACAGAACGATTACTCCTCG 60.539 54.545 0.00 0.00 41.77 4.63
2797 6893 1.404391 GAACGATTACTCCTCGCCAGA 59.596 52.381 0.00 0.00 39.71 3.86
2801 6897 2.541999 CGATTACTCCTCGCCAGAAGAC 60.542 54.545 0.00 0.00 0.00 3.01
2804 6900 2.282958 TCCTCGCCAGAAGACGGT 60.283 61.111 0.00 0.00 0.00 4.83
2878 6974 2.143122 ACAAGCCAGTTGACACATACG 58.857 47.619 0.00 0.00 38.60 3.06
2929 7025 3.565902 GGATGCGCTCTAGGCTAAATTTT 59.434 43.478 9.73 0.00 39.13 1.82
2937 7033 5.124617 GCTCTAGGCTAAATTTTGCTCAACT 59.875 40.000 21.12 13.30 38.06 3.16
2942 7038 5.244626 AGGCTAAATTTTGCTCAACTGATGT 59.755 36.000 21.12 0.00 0.00 3.06
2957 7053 1.872952 TGATGTTGGAAGCGAGTTGTG 59.127 47.619 0.00 0.00 0.00 3.33
2960 7056 2.088423 TGTTGGAAGCGAGTTGTGTTT 58.912 42.857 0.00 0.00 0.00 2.83
2973 7069 5.277974 CGAGTTGTGTTTCATGGATCAGTTT 60.278 40.000 0.00 0.00 0.00 2.66
3045 7141 9.100554 CATGAAATAAAATGCATTGCTAAGGAA 57.899 29.630 13.82 0.00 0.00 3.36
3084 7180 6.072342 AGTGTGAGTTACCGAAAAAGTTTGTT 60.072 34.615 0.00 0.00 0.00 2.83
3161 7259 1.204941 AGCACCAGAGACGTGAATACC 59.795 52.381 0.00 0.00 32.77 2.73
3205 7303 6.762333 TCATCTGAGTGTTGAAGAGAATTCA 58.238 36.000 8.44 0.00 0.00 2.57
3216 7314 6.309712 TGAAGAGAATTCAAGAGCAAAGTG 57.690 37.500 8.44 0.00 0.00 3.16
3251 7349 2.097825 GTGCCGAGGGAACTTCTAGTA 58.902 52.381 0.00 0.00 44.43 1.82
3278 7376 4.328536 TGTGGTGCGGAATAACTTACAAT 58.671 39.130 0.00 0.00 0.00 2.71
3305 7403 4.570772 TCAAGAAAAGAACGTGGTCAAGAG 59.429 41.667 0.00 0.00 0.00 2.85
3343 7442 7.455008 AGAAGAAGGGTAAGATGAACAAGAGTA 59.545 37.037 0.00 0.00 0.00 2.59
3349 7448 6.310711 GGGTAAGATGAACAAGAGTAAAGACG 59.689 42.308 0.00 0.00 0.00 4.18
3352 7451 6.085555 AGATGAACAAGAGTAAAGACGACA 57.914 37.500 0.00 0.00 0.00 4.35
3375 7474 5.376854 ACAAATATGGTTGTCTCACTTGC 57.623 39.130 0.00 0.00 37.10 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.778928 CGAGCTCACGACGAAAATAGAG 59.221 50.000 15.40 0.24 35.09 2.43
18 19 2.309528 AACACAAGAACACGAGCTCA 57.690 45.000 15.40 0.00 0.00 4.26
72 73 1.308069 CCCTTCACGAGTGGCATTGG 61.308 60.000 3.19 0.00 0.00 3.16
76 77 2.425592 CACCCTTCACGAGTGGCA 59.574 61.111 3.19 0.00 0.00 4.92
92 122 1.268079 CCAAACACACACACACACACA 59.732 47.619 0.00 0.00 0.00 3.72
93 123 1.268352 ACCAAACACACACACACACAC 59.732 47.619 0.00 0.00 0.00 3.82
94 124 1.537638 GACCAAACACACACACACACA 59.462 47.619 0.00 0.00 0.00 3.72
95 125 1.465020 CGACCAAACACACACACACAC 60.465 52.381 0.00 0.00 0.00 3.82
96 126 0.799393 CGACCAAACACACACACACA 59.201 50.000 0.00 0.00 0.00 3.72
97 127 0.800012 ACGACCAAACACACACACAC 59.200 50.000 0.00 0.00 0.00 3.82
98 128 2.001159 GTACGACCAAACACACACACA 58.999 47.619 0.00 0.00 0.00 3.72
99 129 1.328374 GGTACGACCAAACACACACAC 59.672 52.381 0.00 0.00 38.42 3.82
100 130 1.207570 AGGTACGACCAAACACACACA 59.792 47.619 6.78 0.00 41.95 3.72
115 145 0.175989 GGGCACTAGCAGACAGGTAC 59.824 60.000 0.00 0.00 44.61 3.34
119 149 1.220206 CAGGGGCACTAGCAGACAG 59.780 63.158 0.00 0.00 44.61 3.51
233 277 9.671279 TGAATATGCTTCTGATTTTGTCTAGAA 57.329 29.630 0.00 0.00 0.00 2.10
234 278 9.842775 ATGAATATGCTTCTGATTTTGTCTAGA 57.157 29.630 0.00 0.00 0.00 2.43
254 302 8.946085 GTAAAGAGGATTTGTGTGTGATGAATA 58.054 33.333 0.00 0.00 0.00 1.75
312 362 8.889717 TCTATAATTTGGTCCAAAGAATTCGAC 58.110 33.333 21.31 1.38 36.76 4.20
336 386 4.093291 CCTCGCAAGCCCAGCTCT 62.093 66.667 0.00 0.00 38.25 4.09
342 392 3.706373 TCAGTCCCTCGCAAGCCC 61.706 66.667 0.00 0.00 37.18 5.19
397 472 8.033626 ACTACTACTGATTGTTAGTTAAGCACC 58.966 37.037 0.00 0.00 0.00 5.01
409 484 7.039011 TCCATGAACTGAACTACTACTGATTGT 60.039 37.037 0.00 0.00 0.00 2.71
413 488 5.106277 CGTCCATGAACTGAACTACTACTGA 60.106 44.000 0.00 0.00 0.00 3.41
414 489 5.096169 CGTCCATGAACTGAACTACTACTG 58.904 45.833 0.00 0.00 0.00 2.74
435 540 1.293498 CCTCCACAGCTTAGCACGT 59.707 57.895 7.07 0.00 0.00 4.49
498 604 3.719924 CTGTCTCCAGCATCTTCAGATC 58.280 50.000 0.00 0.00 31.21 2.75
521 627 0.108472 TTCATGAGCTCGTCCTGCTG 60.108 55.000 5.16 0.00 41.30 4.41
536 642 2.037772 GTGGACAGAGTGGTCAGTTCAT 59.962 50.000 0.00 0.00 39.59 2.57
537 643 1.412710 GTGGACAGAGTGGTCAGTTCA 59.587 52.381 0.00 0.00 39.59 3.18
603 746 6.115448 AGGGCTAATAATGTGTAGGCTTAG 57.885 41.667 0.00 0.00 41.41 2.18
662 809 1.929169 GGATAGTCGGCGGTTGTTAAC 59.071 52.381 7.21 0.00 0.00 2.01
738 886 1.746615 CCCTTGGTGTGCCATCTCG 60.747 63.158 0.00 0.00 45.56 4.04
745 893 0.323629 TACTAGTGCCCTTGGTGTGC 59.676 55.000 5.39 0.00 0.00 4.57
804 952 7.072030 CAGTGCTTAGTGTTAATTGTCTTGAC 58.928 38.462 0.00 0.00 0.00 3.18
928 1087 3.378112 GTGGGTGTGTGTCATGATAATGG 59.622 47.826 0.00 0.00 0.00 3.16
947 1106 0.248990 GCATGGTGTGTTGTGTGTGG 60.249 55.000 0.00 0.00 0.00 4.17
1015 1188 0.251832 TGAGGAAAGAGAGCGGGTCT 60.252 55.000 9.87 9.87 38.71 3.85
1016 1189 0.827368 ATGAGGAAAGAGAGCGGGTC 59.173 55.000 0.00 0.00 0.00 4.46
1025 1199 3.245766 TGGGTGAGAGAGATGAGGAAAGA 60.246 47.826 0.00 0.00 0.00 2.52
1078 1268 0.520404 ATTGCTGACGCTTGAGCTTG 59.480 50.000 2.93 0.00 39.32 4.01
1090 1293 1.000521 CCTTGCCCTCCATTGCTGA 60.001 57.895 0.00 0.00 0.00 4.26
1092 1298 1.305623 CTCCTTGCCCTCCATTGCT 59.694 57.895 0.00 0.00 0.00 3.91
1368 1595 4.881440 GCGATGCCCTGGATGCCA 62.881 66.667 0.00 0.00 0.00 4.92
1650 1877 4.492160 GTGCCGACGATCTCCGCA 62.492 66.667 0.00 0.00 43.32 5.69
1778 2022 4.446413 CAGGTACGGTGGTCGCCC 62.446 72.222 0.00 0.00 43.89 6.13
1813 2080 8.283291 CAGTTTTGACTGGTTTCATCTACTAAC 58.717 37.037 0.00 0.00 34.28 2.34
1830 2097 4.083537 TGCAATCACCGTATCAGTTTTGAC 60.084 41.667 0.00 0.00 35.83 3.18
1842 2109 1.067635 GCCAAAATCTGCAATCACCGT 60.068 47.619 0.00 0.00 0.00 4.83
1843 2110 1.632422 GCCAAAATCTGCAATCACCG 58.368 50.000 0.00 0.00 0.00 4.94
1845 2112 0.994263 GCGCCAAAATCTGCAATCAC 59.006 50.000 0.00 0.00 0.00 3.06
1846 2113 0.108709 GGCGCCAAAATCTGCAATCA 60.109 50.000 24.80 0.00 0.00 2.57
1847 2114 0.174162 AGGCGCCAAAATCTGCAATC 59.826 50.000 31.54 0.00 0.00 2.67
1866 2149 2.493030 GCGAACCCGATCGGAAGA 59.507 61.111 35.42 0.00 42.93 2.87
2209 2571 0.741221 GTCGGCAGACTGATTGGTCC 60.741 60.000 9.95 0.00 43.80 4.46
2210 2572 2.755929 GTCGGCAGACTGATTGGTC 58.244 57.895 9.95 0.00 43.80 4.02
2257 2621 5.954296 TTTCAAGAGCAAGGAGAAGATTG 57.046 39.130 0.00 0.00 0.00 2.67
2258 2622 6.008960 ACATTTCAAGAGCAAGGAGAAGATT 58.991 36.000 0.00 0.00 0.00 2.40
2261 2625 6.998968 ATACATTTCAAGAGCAAGGAGAAG 57.001 37.500 0.00 0.00 0.00 2.85
2316 2680 1.021968 AAGCGTGACCGAAAAGCTTT 58.978 45.000 5.69 5.69 44.59 3.51
2478 5122 5.308825 TCAACTCTCCTTCAAAATCAGGTC 58.691 41.667 0.00 0.00 0.00 3.85
2504 5148 9.588096 TCTGGTAGAGTTGCTCTTATATTATGA 57.412 33.333 3.87 0.00 41.50 2.15
2526 5170 1.939934 CGACTCTGCTAGAGACTCTGG 59.060 57.143 15.55 13.37 45.07 3.86
2534 5178 2.096013 CGAATGTGACGACTCTGCTAGA 59.904 50.000 0.00 0.00 0.00 2.43
2535 5179 2.445316 CGAATGTGACGACTCTGCTAG 58.555 52.381 0.00 0.00 0.00 3.42
2536 5180 1.467543 GCGAATGTGACGACTCTGCTA 60.468 52.381 0.00 0.00 0.00 3.49
2538 5182 1.008875 TGCGAATGTGACGACTCTGC 61.009 55.000 0.00 0.00 0.00 4.26
2539 5183 0.987715 CTGCGAATGTGACGACTCTG 59.012 55.000 0.00 0.00 0.00 3.35
2540 5184 0.598562 ACTGCGAATGTGACGACTCT 59.401 50.000 0.00 0.00 0.00 3.24
2541 5185 1.125021 CAACTGCGAATGTGACGACTC 59.875 52.381 0.00 0.00 0.00 3.36
2542 5186 1.139989 CAACTGCGAATGTGACGACT 58.860 50.000 0.00 0.00 0.00 4.18
2543 5187 0.451135 GCAACTGCGAATGTGACGAC 60.451 55.000 0.00 0.00 0.00 4.34
2544 5188 1.859398 GCAACTGCGAATGTGACGA 59.141 52.632 0.00 0.00 0.00 4.20
2545 5189 4.422506 GCAACTGCGAATGTGACG 57.577 55.556 0.00 0.00 0.00 4.35
2671 5319 0.884259 CGGTAAACGGGTTCGGGTTT 60.884 55.000 0.00 0.00 41.39 3.27
2674 5322 1.085501 CATCGGTAAACGGGTTCGGG 61.086 60.000 0.00 0.00 44.45 5.14
2711 6807 2.223377 GCCACAAGACAGTTTTAGTCCG 59.777 50.000 0.00 0.00 36.68 4.79
2712 6808 3.477530 AGCCACAAGACAGTTTTAGTCC 58.522 45.455 0.00 0.00 36.68 3.85
2737 6833 6.073927 CCAATGACTGAGACATATTCATCGTG 60.074 42.308 0.00 0.00 0.00 4.35
2747 6843 1.352017 TGCCACCAATGACTGAGACAT 59.648 47.619 0.00 0.00 0.00 3.06
2753 6849 0.962356 GGGACTGCCACCAATGACTG 60.962 60.000 0.00 0.00 35.15 3.51
2754 6850 1.380302 GGGACTGCCACCAATGACT 59.620 57.895 0.00 0.00 35.15 3.41
2758 6854 2.351276 GTCGGGACTGCCACCAAT 59.649 61.111 0.00 0.00 35.15 3.16
2759 6855 3.164977 TGTCGGGACTGCCACCAA 61.165 61.111 0.00 0.00 35.15 3.67
2768 6864 2.479219 GGAGTAATCGTTCTGTCGGGAC 60.479 54.545 0.00 0.00 0.00 4.46
2791 6887 1.284982 CTGAACACCGTCTTCTGGCG 61.285 60.000 0.00 0.00 0.00 5.69
2792 6888 0.951040 CCTGAACACCGTCTTCTGGC 60.951 60.000 0.58 0.00 32.08 4.85
2797 6893 0.680061 GTCTCCCTGAACACCGTCTT 59.320 55.000 0.00 0.00 0.00 3.01
2801 6897 3.466881 TGGTCTCCCTGAACACCG 58.533 61.111 0.00 0.00 37.49 4.94
2804 6900 1.415672 GGTGGTGGTCTCCCTGAACA 61.416 60.000 0.00 0.00 40.62 3.18
2878 6974 0.871722 TTGTCAAGCCGCACATGTAC 59.128 50.000 0.00 0.00 0.00 2.90
2937 7033 1.872952 CACAACTCGCTTCCAACATCA 59.127 47.619 0.00 0.00 0.00 3.07
2942 7038 2.360844 TGAAACACAACTCGCTTCCAA 58.639 42.857 0.00 0.00 0.00 3.53
2957 7053 8.946085 TGTAGTCATAAAACTGATCCATGAAAC 58.054 33.333 0.00 0.00 0.00 2.78
2960 7056 9.513906 TTTTGTAGTCATAAAACTGATCCATGA 57.486 29.630 0.00 0.00 0.00 3.07
3013 7109 8.689061 AGCAATGCATTTTATTTCATGAGTCTA 58.311 29.630 9.83 0.00 0.00 2.59
3028 7124 5.726980 TCAAGTTCCTTAGCAATGCATTT 57.273 34.783 9.83 0.00 0.00 2.32
3045 7141 5.615925 ACTCACACTTAAGGAGTTCAAGT 57.384 39.130 7.53 5.88 38.69 3.16
3054 7150 6.259387 ACTTTTTCGGTAACTCACACTTAAGG 59.741 38.462 7.53 0.00 0.00 2.69
3161 7259 1.993956 TTGATGACAACCCCAACTGG 58.006 50.000 0.00 0.00 0.00 4.00
3216 7314 1.518903 GGCACCTTTGGAGTGTGAGC 61.519 60.000 0.00 0.00 37.56 4.26
3278 7376 5.421277 TGACCACGTTCTTTTCTTGAACTA 58.579 37.500 0.00 0.00 40.95 2.24
3323 7422 7.387643 GTCTTTACTCTTGTTCATCTTACCCT 58.612 38.462 0.00 0.00 0.00 4.34
3326 7425 7.594015 TGTCGTCTTTACTCTTGTTCATCTTAC 59.406 37.037 0.00 0.00 0.00 2.34
3332 7431 5.412640 TGTTGTCGTCTTTACTCTTGTTCA 58.587 37.500 0.00 0.00 0.00 3.18
3352 7451 5.562696 CGCAAGTGAGACAACCATATTTGTT 60.563 40.000 0.00 0.00 39.88 2.83
3375 7474 2.575532 ACCCAATGTCCAATATCAGCG 58.424 47.619 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.