Multiple sequence alignment - TraesCS3D01G420600

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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 TraesCS3D01G420600 chr3D 100.000 3978 0 0 1 3978 532868615 532872592 0.000000e+00 7347.0
1 TraesCS3D01G420600 chr3A 93.013 3764 129 45 242 3978 668582496 668586152 0.000000e+00 5371.0
2 TraesCS3D01G420600 chr3A 90.706 2948 163 50 1095 3978 668225506 668228406 0.000000e+00 3823.0
3 TraesCS3D01G420600 chr3A 95.812 191 8 0 3692 3882 668586673 668586863 3.860000e-80 309.0
4 TraesCS3D01G420600 chr3A 92.350 183 7 5 1 178 668582322 668582502 1.830000e-63 254.0
5 TraesCS3D01G420600 chr3A 98.276 58 1 0 3921 3978 668586872 668586929 7.030000e-18 102.0
6 TraesCS3D01G420600 chr3B 93.533 3139 121 22 886 3978 705147960 705151062 0.000000e+00 4597.0
7 TraesCS3D01G420600 chr3B 91.404 570 23 7 242 799 705147386 705147941 0.000000e+00 758.0
8 TraesCS3D01G420600 chr3B 88.770 187 9 6 1 177 705147207 705147391 6.690000e-53 219.0
9 TraesCS3D01G420600 chr3B 96.203 79 2 1 175 252 807575498 807575420 1.160000e-25 128.0
10 TraesCS3D01G420600 chr1D 85.978 1840 172 43 1443 3261 226468249 226470023 0.000000e+00 1890.0
11 TraesCS3D01G420600 chr1D 84.585 772 82 24 1611 2363 261723913 261724666 0.000000e+00 732.0
12 TraesCS3D01G420600 chr1D 78.216 1065 118 65 2054 3049 223164049 223165068 9.590000e-161 577.0
13 TraesCS3D01G420600 chr1D 80.952 693 88 24 501 1189 457582554 457583206 3.550000e-140 508.0
14 TraesCS3D01G420600 chr1D 86.486 444 51 3 1611 2053 208415555 208415120 2.780000e-131 479.0
15 TraesCS3D01G420600 chr1D 81.376 596 78 17 2432 3024 226945249 226945814 4.690000e-124 455.0
16 TraesCS3D01G420600 chr1D 81.049 591 87 15 2435 3024 226827660 226828226 7.840000e-122 448.0
17 TraesCS3D01G420600 chr1D 81.135 599 71 23 2435 3031 208413038 208412480 3.650000e-120 442.0
18 TraesCS3D01G420600 chr1D 80.467 599 64 24 2432 3024 227375832 227376383 3.700000e-110 409.0
19 TraesCS3D01G420600 chr1D 85.604 389 34 8 347 735 226467443 226467809 4.820000e-104 388.0
20 TraesCS3D01G420600 chr1D 84.655 391 32 17 1066 1437 226467833 226468214 8.120000e-97 364.0
21 TraesCS3D01G420600 chr1D 80.738 488 58 21 973 1439 457844647 457845119 8.180000e-92 348.0
22 TraesCS3D01G420600 chr1D 78.276 290 42 18 2054 2328 227649334 227649617 2.460000e-37 167.0
23 TraesCS3D01G420600 chr1D 89.474 114 8 2 472 585 227653059 227653168 1.490000e-29 141.0
24 TraesCS3D01G420600 chr1D 80.645 155 16 7 1443 1594 457845153 457845296 1.510000e-19 108.0
25 TraesCS3D01G420600 chr1D 90.698 43 4 0 3482 3524 471280180 471280138 1.540000e-04 58.4
26 TraesCS3D01G420600 chr1D 100.000 29 0 0 2200 2228 208413265 208413237 2.000000e-03 54.7
27 TraesCS3D01G420600 chr1A 85.622 1850 172 44 1431 3261 293736643 293738417 0.000000e+00 1857.0
28 TraesCS3D01G420600 chr1A 84.407 776 84 23 1611 2367 338594615 338593858 0.000000e+00 728.0
29 TraesCS3D01G420600 chr1A 78.337 974 146 39 501 1439 550298310 550299253 1.600000e-158 569.0
30 TraesCS3D01G420600 chr1A 82.915 597 65 17 2453 3049 290126627 290127186 1.650000e-138 503.0
31 TraesCS3D01G420600 chr1A 80.526 570 63 18 2432 2998 294041602 294042126 1.040000e-105 394.0
32 TraesCS3D01G420600 chr1A 85.390 308 42 3 2516 2823 338593679 338593375 2.310000e-82 316.0
33 TraesCS3D01G420600 chr1A 89.796 147 15 0 470 616 293731234 293731380 5.250000e-44 189.0
34 TraesCS3D01G420600 chr1A 84.242 165 18 6 1212 1374 550217715 550217873 1.910000e-33 154.0
35 TraesCS3D01G420600 chr1A 79.781 183 22 7 279 460 550298030 550298198 6.980000e-23 119.0
36 TraesCS3D01G420600 chr7B 84.874 952 94 28 1291 2228 41285182 41286097 0.000000e+00 915.0
37 TraesCS3D01G420600 chr7B 87.500 160 14 4 3040 3197 41287005 41287160 3.160000e-41 180.0
38 TraesCS3D01G420600 chr7B 100.000 32 0 0 3480 3511 498285372 498285403 4.290000e-05 60.2
39 TraesCS3D01G420600 chr7D 84.809 836 82 26 1291 2113 90409255 90410058 0.000000e+00 798.0
40 TraesCS3D01G420600 chr7D 81.204 947 114 33 244 1176 90408363 90409259 0.000000e+00 704.0
41 TraesCS3D01G420600 chr7D 81.385 924 81 49 2297 3197 90410250 90411105 0.000000e+00 669.0
42 TraesCS3D01G420600 chr1B 83.871 775 89 22 1611 2367 350442734 350441978 0.000000e+00 706.0
43 TraesCS3D01G420600 chr1B 86.621 441 53 2 1611 2050 327343235 327343670 2.150000e-132 483.0
44 TraesCS3D01G420600 chr1B 80.705 596 73 23 2432 3025 327345404 327345959 3.670000e-115 425.0
45 TraesCS3D01G420600 chr1B 80.235 597 68 22 2432 3024 327229807 327230357 1.720000e-108 403.0
46 TraesCS3D01G420600 chr1B 89.474 114 8 2 472 585 327347926 327348035 1.490000e-29 141.0
47 TraesCS3D01G420600 chr1B 81.657 169 25 4 472 639 665246284 665246121 6.930000e-28 135.0
48 TraesCS3D01G420600 chr1B 96.341 82 1 2 175 256 606634253 606634332 2.490000e-27 134.0
49 TraesCS3D01G420600 chr1B 79.039 229 22 20 1212 1439 627782295 627782498 2.490000e-27 134.0
50 TraesCS3D01G420600 chr1B 92.500 40 2 1 3472 3511 33964112 33964150 5.550000e-04 56.5
51 TraesCS3D01G420600 chr5D 97.333 75 2 0 175 249 57226033 57225959 1.160000e-25 128.0
52 TraesCS3D01G420600 chr6A 86.842 114 11 4 175 287 447873616 447873726 1.500000e-24 124.0
53 TraesCS3D01G420600 chr4B 93.976 83 4 1 175 257 445238579 445238660 1.500000e-24 124.0
54 TraesCS3D01G420600 chr4B 94.805 77 3 1 175 251 2431909 2431984 6.980000e-23 119.0
55 TraesCS3D01G420600 chr4B 93.333 45 3 0 3482 3526 469449852 469449896 2.570000e-07 67.6
56 TraesCS3D01G420600 chr2A 95.000 80 3 1 175 254 20825010 20824932 1.500000e-24 124.0
57 TraesCS3D01G420600 chr7A 92.857 84 6 0 175 258 495549516 495549599 5.400000e-24 122.0
58 TraesCS3D01G420600 chr7A 88.043 92 7 2 52 139 91640494 91640585 5.440000e-19 106.0
59 TraesCS3D01G420600 chr5A 90.110 91 7 2 175 264 479846194 479846105 2.510000e-22 117.0
60 TraesCS3D01G420600 chr5A 91.111 45 3 1 3468 3511 364191526 364191482 4.290000e-05 60.2
61 TraesCS3D01G420600 chr5B 97.059 34 0 1 3478 3511 610894118 610894086 5.550000e-04 56.5


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 TraesCS3D01G420600 chr3D 532868615 532872592 3977 False 7347.000000 7347 100.000000 1 3978 1 chr3D.!!$F1 3977
1 TraesCS3D01G420600 chr3A 668225506 668228406 2900 False 3823.000000 3823 90.706000 1095 3978 1 chr3A.!!$F1 2883
2 TraesCS3D01G420600 chr3A 668582322 668586929 4607 False 1509.000000 5371 94.862750 1 3978 4 chr3A.!!$F2 3977
3 TraesCS3D01G420600 chr3B 705147207 705151062 3855 False 1858.000000 4597 91.235667 1 3978 3 chr3B.!!$F1 3977
4 TraesCS3D01G420600 chr1D 226467443 226470023 2580 False 880.666667 1890 85.412333 347 3261 3 chr1D.!!$F7 2914
5 TraesCS3D01G420600 chr1D 261723913 261724666 753 False 732.000000 732 84.585000 1611 2363 1 chr1D.!!$F5 752
6 TraesCS3D01G420600 chr1D 223164049 223165068 1019 False 577.000000 577 78.216000 2054 3049 1 chr1D.!!$F1 995
7 TraesCS3D01G420600 chr1D 457582554 457583206 652 False 508.000000 508 80.952000 501 1189 1 chr1D.!!$F6 688
8 TraesCS3D01G420600 chr1D 226945249 226945814 565 False 455.000000 455 81.376000 2432 3024 1 chr1D.!!$F3 592
9 TraesCS3D01G420600 chr1D 226827660 226828226 566 False 448.000000 448 81.049000 2435 3024 1 chr1D.!!$F2 589
10 TraesCS3D01G420600 chr1D 227375832 227376383 551 False 409.000000 409 80.467000 2432 3024 1 chr1D.!!$F4 592
11 TraesCS3D01G420600 chr1D 208412480 208415555 3075 True 325.233333 479 89.207000 1611 3031 3 chr1D.!!$R2 1420
12 TraesCS3D01G420600 chr1D 457844647 457845296 649 False 228.000000 348 80.691500 973 1594 2 chr1D.!!$F9 621
13 TraesCS3D01G420600 chr1A 293736643 293738417 1774 False 1857.000000 1857 85.622000 1431 3261 1 chr1A.!!$F3 1830
14 TraesCS3D01G420600 chr1A 338593375 338594615 1240 True 522.000000 728 84.898500 1611 2823 2 chr1A.!!$R1 1212
15 TraesCS3D01G420600 chr1A 290126627 290127186 559 False 503.000000 503 82.915000 2453 3049 1 chr1A.!!$F1 596
16 TraesCS3D01G420600 chr1A 294041602 294042126 524 False 394.000000 394 80.526000 2432 2998 1 chr1A.!!$F4 566
17 TraesCS3D01G420600 chr1A 550298030 550299253 1223 False 344.000000 569 79.059000 279 1439 2 chr1A.!!$F6 1160
18 TraesCS3D01G420600 chr7B 41285182 41287160 1978 False 547.500000 915 86.187000 1291 3197 2 chr7B.!!$F2 1906
19 TraesCS3D01G420600 chr7D 90408363 90411105 2742 False 723.666667 798 82.466000 244 3197 3 chr7D.!!$F1 2953
20 TraesCS3D01G420600 chr1B 350441978 350442734 756 True 706.000000 706 83.871000 1611 2367 1 chr1B.!!$R1 756
21 TraesCS3D01G420600 chr1B 327229807 327230357 550 False 403.000000 403 80.235000 2432 3024 1 chr1B.!!$F2 592
22 TraesCS3D01G420600 chr1B 327343235 327348035 4800 False 349.666667 483 85.600000 472 3025 3 chr1B.!!$F5 2553

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
850 988 1.186200 ACAGCCAGACGATGAAGCTA 58.814 50.000 0.00 0.0 31.23 3.32 F
1353 1562 1.404748 TGTTAAGTGTGTCCGTCGACA 59.595 47.619 17.16 0.0 46.91 4.35 F
1823 2111 2.972713 TGTGGTTCAGAAGAAGGCTACT 59.027 45.455 0.00 0.0 33.63 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2624 5008 3.165071 GTCAATTCAACCACCTTCCCAT 58.835 45.455 0.0 0.0 0.0 4.00 R
2901 5301 0.548926 TCCCACAACATAGCCTCCCA 60.549 55.000 0.0 0.0 0.0 4.37 R
3688 7704 0.892755 AAGCCACGACCGAGTAATCA 59.107 50.000 0.0 0.0 0.0 2.57 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
17 20 2.203070 CCGGGAGCACAGGTATGC 60.203 66.667 0.00 0.00 46.50 3.14
44 48 4.274214 TCTGCACAATTCAACTTCAGACTG 59.726 41.667 0.00 0.00 0.00 3.51
164 178 8.746530 CCAATGCTTATTCATTAGAGCCAATAT 58.253 33.333 0.00 0.00 35.12 1.28
239 253 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
240 254 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
282 296 6.366061 GCAAAAGTGGCCTCTTGTATTAAAAG 59.634 38.462 20.33 3.09 0.00 2.27
285 301 7.454260 AAGTGGCCTCTTGTATTAAAAGAAG 57.546 36.000 19.04 0.00 33.40 2.85
331 352 3.613432 CGTTTGTACCCTGACTAGTGACC 60.613 52.174 0.00 0.00 0.00 4.02
341 362 1.544691 GACTAGTGACCGGTGACATGT 59.455 52.381 26.37 21.91 0.00 3.21
365 389 9.268268 TGTTAACTACTGCAATATATTAGTGGC 57.732 33.333 7.22 5.20 0.00 5.01
366 390 8.718734 GTTAACTACTGCAATATATTAGTGGCC 58.281 37.037 10.06 0.00 0.00 5.36
468 513 3.703052 CCTTCCATTTTCCCAAGGATGAG 59.297 47.826 0.00 0.00 38.15 2.90
818 948 5.069318 TGAAATAGCAACCACAATCTCACA 58.931 37.500 0.00 0.00 0.00 3.58
850 988 1.186200 ACAGCCAGACGATGAAGCTA 58.814 50.000 0.00 0.00 31.23 3.32
851 989 1.759445 ACAGCCAGACGATGAAGCTAT 59.241 47.619 0.00 0.00 31.23 2.97
852 990 2.959030 ACAGCCAGACGATGAAGCTATA 59.041 45.455 0.00 0.00 31.23 1.31
853 991 3.576118 ACAGCCAGACGATGAAGCTATAT 59.424 43.478 0.00 0.00 31.23 0.86
854 992 4.767409 ACAGCCAGACGATGAAGCTATATA 59.233 41.667 0.00 0.00 31.23 0.86
855 993 5.420421 ACAGCCAGACGATGAAGCTATATAT 59.580 40.000 0.00 0.00 31.23 0.86
856 994 6.603599 ACAGCCAGACGATGAAGCTATATATA 59.396 38.462 0.00 0.00 31.23 0.86
857 995 7.138081 CAGCCAGACGATGAAGCTATATATAG 58.862 42.308 14.45 14.45 31.23 1.31
858 996 6.264292 AGCCAGACGATGAAGCTATATATAGG 59.736 42.308 19.19 5.41 30.46 2.57
859 997 6.263392 GCCAGACGATGAAGCTATATATAGGA 59.737 42.308 19.19 0.00 0.00 2.94
860 998 7.040062 GCCAGACGATGAAGCTATATATAGGAT 60.040 40.741 19.19 0.00 0.00 3.24
861 999 8.296000 CCAGACGATGAAGCTATATATAGGATG 58.704 40.741 19.19 7.14 0.00 3.51
862 1000 7.807433 CAGACGATGAAGCTATATATAGGATGC 59.193 40.741 19.19 7.57 0.00 3.91
863 1001 7.503902 AGACGATGAAGCTATATATAGGATGCA 59.496 37.037 19.19 6.31 0.00 3.96
864 1002 8.187913 ACGATGAAGCTATATATAGGATGCAT 57.812 34.615 19.19 0.00 0.00 3.96
865 1003 8.303156 ACGATGAAGCTATATATAGGATGCATC 58.697 37.037 18.81 18.81 0.00 3.91
866 1004 8.302438 CGATGAAGCTATATATAGGATGCATCA 58.698 37.037 27.25 14.29 33.78 3.07
867 1005 9.993454 GATGAAGCTATATATAGGATGCATCAA 57.007 33.333 27.25 15.43 33.17 2.57
868 1006 9.999660 ATGAAGCTATATATAGGATGCATCAAG 57.000 33.333 27.25 11.66 33.17 3.02
869 1007 8.985922 TGAAGCTATATATAGGATGCATCAAGT 58.014 33.333 27.25 13.87 0.00 3.16
901 1039 6.690194 ATAGGATGCATCAAGTGAAGAAAC 57.310 37.500 27.25 6.09 0.00 2.78
917 1055 6.874134 GTGAAGAAACTAGGCTTGATTCAGTA 59.126 38.462 17.92 4.18 0.00 2.74
1113 1288 8.869109 TCAATATTCAACCATTCAAAAGGAGTT 58.131 29.630 0.00 0.00 0.00 3.01
1210 1389 5.557576 AGAGTGCATCCATCTTATTAGCA 57.442 39.130 0.00 0.00 0.00 3.49
1247 1447 7.226325 GCATCACAAGTTTGAGCTATAGATTCT 59.774 37.037 3.21 0.00 0.00 2.40
1248 1448 9.107177 CATCACAAGTTTGAGCTATAGATTCTT 57.893 33.333 3.21 0.00 0.00 2.52
1249 1449 8.709386 TCACAAGTTTGAGCTATAGATTCTTC 57.291 34.615 3.21 0.00 0.00 2.87
1303 1511 6.964370 TCGTAACATAATCAATTGCTTTTCCG 59.036 34.615 0.00 0.00 0.00 4.30
1331 1539 6.934561 GCAAGTCGCTTCATATTTTCTTTT 57.065 33.333 0.00 0.00 37.77 2.27
1353 1562 1.404748 TGTTAAGTGTGTCCGTCGACA 59.595 47.619 17.16 0.00 46.91 4.35
1483 1748 5.200483 CAGGGGGAAAGCTGATTAAATGTA 58.800 41.667 0.00 0.00 0.00 2.29
1548 1829 9.846248 ATTTTCATCTTACATACAAGTTCTTGC 57.154 29.630 11.79 0.00 0.00 4.01
1562 1843 7.355778 ACAAGTTCTTGCTTCTCTAATTTTCG 58.644 34.615 11.79 0.00 0.00 3.46
1823 2111 2.972713 TGTGGTTCAGAAGAAGGCTACT 59.027 45.455 0.00 0.00 33.63 2.57
1983 2282 4.386867 ACATCTGGGTAGTTACATCACG 57.613 45.455 0.00 0.00 0.00 4.35
2456 4832 4.545823 TTCTGCTTTCAGTAACAAACCG 57.454 40.909 0.00 0.00 41.10 4.44
2656 5040 4.875536 TGGTTGAATTGACACTATCCATCG 59.124 41.667 0.00 0.00 0.00 3.84
2881 5281 4.865365 GGATCGTCTAACTTCTTTGGACTG 59.135 45.833 0.00 0.00 42.22 3.51
2901 5301 1.071857 GAAGGAACTCAAGGACCCGTT 59.928 52.381 0.00 0.00 38.49 4.44
2992 5396 8.718158 ATGATGACTAGATCTTTACCTCATGA 57.282 34.615 0.00 0.00 0.00 3.07
3197 7200 4.156373 TGCATGTTGTGTAGTTCCATGATG 59.844 41.667 0.00 0.00 35.96 3.07
3241 7244 0.400213 AAACATCGGCCCACAAGAGA 59.600 50.000 0.00 0.00 0.00 3.10
3591 7601 1.464608 TGCCGAGCTTTTGAGAATTCG 59.535 47.619 0.00 0.00 0.00 3.34
3613 7623 4.894201 GCATGCTGCAGGGATACT 57.106 55.556 17.12 0.00 44.26 2.12
3688 7704 9.354673 CATAAATACAGAAACATGAAGGGGTAT 57.645 33.333 0.00 0.00 0.00 2.73
3803 7820 6.654793 TTCAGGTTTTGTTGTGCAAATTAC 57.345 33.333 0.00 0.00 45.38 1.89
3903 8090 9.722056 CCGTAGTATTACTTTACAAGTTACGAT 57.278 33.333 14.81 1.86 41.85 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 20 5.237996 TCTGAAGTTGAATTGTGCAGAGAAG 59.762 40.000 0.00 0.00 0.00 2.85
213 227 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
214 228 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
215 229 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
216 230 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
217 231 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
229 243 9.790344 TGTATAGATAGTACTCCCTCTGTAAAC 57.210 37.037 0.00 0.00 0.00 2.01
231 245 9.961264 CATGTATAGATAGTACTCCCTCTGTAA 57.039 37.037 0.00 0.00 0.00 2.41
232 246 8.047911 GCATGTATAGATAGTACTCCCTCTGTA 58.952 40.741 0.00 0.84 0.00 2.74
233 247 6.887545 GCATGTATAGATAGTACTCCCTCTGT 59.112 42.308 0.00 1.80 0.00 3.41
234 248 6.887002 TGCATGTATAGATAGTACTCCCTCTG 59.113 42.308 0.00 0.00 0.00 3.35
235 249 7.033782 TGCATGTATAGATAGTACTCCCTCT 57.966 40.000 0.00 3.21 0.00 3.69
236 250 7.704578 TTGCATGTATAGATAGTACTCCCTC 57.295 40.000 0.00 0.00 0.00 4.30
237 251 8.492415 TTTTGCATGTATAGATAGTACTCCCT 57.508 34.615 0.00 0.00 0.00 4.20
238 252 8.368668 ACTTTTGCATGTATAGATAGTACTCCC 58.631 37.037 0.00 0.00 0.00 4.30
239 253 9.197694 CACTTTTGCATGTATAGATAGTACTCC 57.802 37.037 0.00 0.00 0.00 3.85
240 254 9.197694 CCACTTTTGCATGTATAGATAGTACTC 57.802 37.037 0.00 0.00 0.00 2.59
331 352 3.322369 TGCAGTAGTTAACATGTCACCG 58.678 45.455 8.61 0.00 0.00 4.94
341 362 8.433599 TGGCCACTAATATATTGCAGTAGTTAA 58.566 33.333 0.00 0.00 0.00 2.01
365 389 0.179020 TTGTGAGAAGTGGCCACTGG 60.179 55.000 38.35 0.00 41.58 4.00
366 390 1.679139 TTTGTGAGAAGTGGCCACTG 58.321 50.000 38.35 0.00 41.58 3.66
434 464 5.833131 GGAAAATGGAAGGGTGCAGAATATA 59.167 40.000 0.00 0.00 0.00 0.86
435 465 4.651045 GGAAAATGGAAGGGTGCAGAATAT 59.349 41.667 0.00 0.00 0.00 1.28
468 513 7.158099 AGGAGGCAACAACTGAAAATTATAC 57.842 36.000 0.00 0.00 41.41 1.47
712 830 9.918630 TTAACAGACAGTTACTTTATCCACTAC 57.081 33.333 0.00 0.00 42.19 2.73
818 948 4.278310 GTCTGGCTGTTTATATGGGGTTT 58.722 43.478 0.00 0.00 0.00 3.27
901 1039 6.820656 ACAAGTCATTACTGAATCAAGCCTAG 59.179 38.462 0.00 0.00 35.62 3.02
1113 1288 9.502091 GTCTATATACCTTTGCATCCACAATAA 57.498 33.333 0.00 0.00 0.00 1.40
1202 1381 5.704978 TGATGCACACAAGACTTGCTAATAA 59.295 36.000 15.24 0.00 37.16 1.40
1247 1447 9.913310 TGTAGGTATTGATTTGTAATGATGGAA 57.087 29.630 0.00 0.00 0.00 3.53
1248 1448 9.913310 TTGTAGGTATTGATTTGTAATGATGGA 57.087 29.630 0.00 0.00 0.00 3.41
1331 1539 1.948834 TCGACGGACACACTTAACAGA 59.051 47.619 0.00 0.00 0.00 3.41
1353 1562 2.404215 GTGTGACGCACAGTACAGAAT 58.596 47.619 14.22 0.00 45.43 2.40
1562 1843 6.427242 AGCTAGCAGTGTTTAGGTAAAAGTTC 59.573 38.462 18.83 0.00 0.00 3.01
1823 2111 8.595362 TCTGGATAAAGAGATTCTGAACTGTA 57.405 34.615 0.00 0.00 0.00 2.74
2456 4832 5.519927 CCGGGAAAATGTATTTCAAGAATGC 59.480 40.000 0.00 0.00 0.00 3.56
2502 4885 3.390967 TGACAAGAATGGGAAGTGACTCA 59.609 43.478 0.00 0.00 0.00 3.41
2624 5008 3.165071 GTCAATTCAACCACCTTCCCAT 58.835 45.455 0.00 0.00 0.00 4.00
2656 5040 4.803613 GTGTTTCACATTCTTTTGGTCCAC 59.196 41.667 0.00 0.00 34.08 4.02
2881 5281 0.685660 ACGGGTCCTTGAGTTCCTTC 59.314 55.000 0.00 0.00 0.00 3.46
2901 5301 0.548926 TCCCACAACATAGCCTCCCA 60.549 55.000 0.00 0.00 0.00 4.37
2973 5373 6.436027 TCAGGTCATGAGGTAAAGATCTAGT 58.564 40.000 0.00 0.00 32.77 2.57
2992 5396 3.378427 GGCGCATTATTTCTTCTTCAGGT 59.622 43.478 10.83 0.00 0.00 4.00
3241 7244 5.927281 AGCAGAATCAAATGGCAGTTAAT 57.073 34.783 0.00 0.00 0.00 1.40
3688 7704 0.892755 AAGCCACGACCGAGTAATCA 59.107 50.000 0.00 0.00 0.00 2.57
3803 7820 1.071385 GCACCCATACCTCCATCTGAG 59.929 57.143 0.00 0.00 41.07 3.35
3903 8090 6.452242 ACAATGTTAGAGTCATGTCACGTTA 58.548 36.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.