Multiple sequence alignment - TraesCS3D01G352200

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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 TraesCS3D01G352200 chr3D 100.000 2888 0 0 1 2888 463175665 463178552 0.000000e+00 5334.0
1 TraesCS3D01G352200 chr3D 84.494 445 55 7 2446 2886 266875543 266875977 7.400000e-116 427.0
2 TraesCS3D01G352200 chr3D 82.051 468 52 16 2441 2886 248813788 248814245 1.260000e-98 370.0
3 TraesCS3D01G352200 chr3D 95.455 44 2 0 2291 2334 571861905 571861862 1.440000e-08 71.3
4 TraesCS3D01G352200 chr3D 95.238 42 2 0 2296 2337 560351030 560350989 1.860000e-07 67.6
5 TraesCS3D01G352200 chr3D 97.368 38 1 0 2297 2334 121944720 121944757 6.680000e-07 65.8
6 TraesCS3D01G352200 chr3D 93.023 43 3 0 2294 2336 306344485 306344527 2.400000e-06 63.9
7 TraesCS3D01G352200 chr3B 93.690 2187 107 14 719 2888 615784330 615782158 0.000000e+00 3245.0
8 TraesCS3D01G352200 chr3B 84.141 454 55 8 2437 2886 347710380 347710820 9.570000e-115 424.0
9 TraesCS3D01G352200 chr3A 87.579 1417 105 40 13 1365 606019639 606018230 0.000000e+00 1576.0
10 TraesCS3D01G352200 chr3A 96.678 572 17 1 1404 1973 606017769 606017198 0.000000e+00 950.0
11 TraesCS3D01G352200 chr3A 83.182 440 49 14 2441 2879 307918443 307918858 2.100000e-101 379.0
12 TraesCS3D01G352200 chr3A 91.935 248 5 3 1970 2211 606012416 606012178 1.660000e-87 333.0
13 TraesCS3D01G352200 chr3A 92.793 111 7 1 2335 2445 606012123 606012014 2.980000e-35 159.0
14 TraesCS3D01G352200 chr3A 96.296 54 2 0 2235 2288 606012175 606012122 3.960000e-14 89.8
15 TraesCS3D01G352200 chr3A 95.455 44 2 0 2291 2334 456717299 456717342 1.440000e-08 71.3
16 TraesCS3D01G352200 chr1D 85.144 451 51 8 2443 2888 180131546 180131985 5.680000e-122 448.0
17 TraesCS3D01G352200 chr1D 90.000 50 5 0 2291 2340 141576212 141576163 6.680000e-07 65.8
18 TraesCS3D01G352200 chr4A 84.821 448 56 5 2442 2888 479648821 479648385 9.500000e-120 440.0
19 TraesCS3D01G352200 chr4A 84.479 451 56 5 2442 2888 312410598 312411038 1.590000e-117 433.0
20 TraesCS3D01G352200 chrUn 84.855 449 49 9 2441 2884 110159445 110159011 4.420000e-118 435.0
21 TraesCS3D01G352200 chrUn 94.737 38 2 0 2296 2333 104684164 104684127 3.110000e-05 60.2
22 TraesCS3D01G352200 chrUn 100.000 31 0 0 2296 2326 19062359 19062389 1.120000e-04 58.4
23 TraesCS3D01G352200 chrUn 100.000 31 0 0 2296 2326 168711187 168711217 1.120000e-04 58.4
24 TraesCS3D01G352200 chrUn 100.000 31 0 0 2296 2326 168713181 168713211 1.120000e-04 58.4
25 TraesCS3D01G352200 chrUn 94.595 37 2 0 2296 2332 241201264 241201228 1.120000e-04 58.4
26 TraesCS3D01G352200 chrUn 100.000 31 0 0 2296 2326 265768364 265768334 1.120000e-04 58.4
27 TraesCS3D01G352200 chrUn 100.000 31 0 0 2296 2326 335746516 335746486 1.120000e-04 58.4
28 TraesCS3D01G352200 chrUn 94.595 37 2 0 2296 2332 340151613 340151577 1.120000e-04 58.4
29 TraesCS3D01G352200 chrUn 100.000 31 0 0 2296 2326 352791534 352791564 1.120000e-04 58.4
30 TraesCS3D01G352200 chrUn 94.595 37 2 0 2296 2332 359899578 359899542 1.120000e-04 58.4
31 TraesCS3D01G352200 chr7B 84.513 452 53 10 2439 2886 300592509 300592947 5.720000e-117 431.0
32 TraesCS3D01G352200 chr7B 84.547 453 50 9 2440 2886 356462223 356461785 5.720000e-117 431.0
33 TraesCS3D01G352200 chr7B 93.182 44 3 0 2296 2339 27477668 27477711 6.680000e-07 65.8
34 TraesCS3D01G352200 chr7B 91.667 48 3 1 2296 2343 612679009 612678963 6.680000e-07 65.8
35 TraesCS3D01G352200 chr7A 84.327 453 55 8 2441 2888 345180556 345180115 2.060000e-116 429.0
36 TraesCS3D01G352200 chr7A 84.305 446 53 6 2442 2886 369725969 369725540 1.240000e-113 420.0
37 TraesCS3D01G352200 chr7A 83.296 449 63 5 2442 2888 344489323 344488885 1.250000e-108 403.0
38 TraesCS3D01G352200 chr7A 95.455 44 2 0 2291 2334 23820049 23820006 1.440000e-08 71.3
39 TraesCS3D01G352200 chr7A 95.455 44 2 0 2291 2334 23945643 23945600 1.440000e-08 71.3
40 TraesCS3D01G352200 chr2B 83.885 453 54 10 2442 2888 617869696 617870135 5.760000e-112 414.0
41 TraesCS3D01G352200 chr2B 97.727 44 1 0 2291 2334 157264257 157264214 3.090000e-10 76.8
42 TraesCS3D01G352200 chr1B 83.442 459 55 10 2434 2886 233799951 233800394 9.630000e-110 407.0
43 TraesCS3D01G352200 chr1B 95.455 44 2 0 2291 2334 356832148 356832105 1.440000e-08 71.3
44 TraesCS3D01G352200 chr1B 87.931 58 6 1 2296 2352 136964827 136964770 1.860000e-07 67.6
45 TraesCS3D01G352200 chr1A 83.370 451 61 6 2442 2888 200191323 200190883 3.470000e-109 405.0
46 TraesCS3D01G352200 chr5B 83.032 442 62 7 2450 2886 215493988 215493555 3.490000e-104 388.0
47 TraesCS3D01G352200 chr5B 77.068 532 117 4 1354 1882 46635451 46634922 4.680000e-78 302.0
48 TraesCS3D01G352200 chr5B 76.894 528 113 8 1359 1882 48146922 48147444 1.010000e-74 291.0
49 TraesCS3D01G352200 chr5B 76.616 526 118 4 1359 1882 46767873 46767351 4.710000e-73 285.0
50 TraesCS3D01G352200 chr5B 75.382 589 142 3 1296 1882 46746791 46746204 6.090000e-72 281.0
51 TraesCS3D01G352200 chr5B 74.830 588 134 11 1302 1882 46152395 46151815 1.330000e-63 254.0
52 TraesCS3D01G352200 chr5B 77.740 292 62 3 1592 1882 46633949 46633660 2.960000e-40 176.0
53 TraesCS3D01G352200 chr5A 76.102 590 131 9 1296 1882 36798864 36798282 1.680000e-77 300.0
54 TraesCS3D01G352200 chr5A 74.915 590 142 5 1296 1882 36942491 36941905 6.140000e-67 265.0
55 TraesCS3D01G352200 chr5A 93.333 45 3 0 2291 2335 566093384 566093340 1.860000e-07 67.6
56 TraesCS3D01G352200 chr5D 76.548 533 118 7 1354 1882 45939303 45939832 4.710000e-73 285.0
57 TraesCS3D01G352200 chr5D 97.500 40 1 0 2297 2336 282189580 282189541 5.160000e-08 69.4
58 TraesCS3D01G352200 chr5D 97.436 39 1 0 2297 2335 156572747 156572709 1.860000e-07 67.6
59 TraesCS3D01G352200 chr6D 100.000 40 0 0 2297 2336 425080865 425080904 1.110000e-09 75.0
60 TraesCS3D01G352200 chr6D 94.872 39 2 0 2297 2335 83109954 83109916 8.640000e-06 62.1
61 TraesCS3D01G352200 chr6D 92.857 42 3 0 2297 2338 438502574 438502533 8.640000e-06 62.1
62 TraesCS3D01G352200 chr6D 94.595 37 1 1 2291 2326 321760732 321760768 4.020000e-04 56.5
63 TraesCS3D01G352200 chr2D 95.238 42 1 1 2297 2337 534446033 534446074 6.680000e-07 65.8
64 TraesCS3D01G352200 chr4D 95.000 40 2 0 2297 2336 125100505 125100544 2.400000e-06 63.9
65 TraesCS3D01G352200 chr4D 92.857 42 3 0 2291 2332 442889201 442889160 8.640000e-06 62.1
66 TraesCS3D01G352200 chr4D 92.857 42 3 0 2296 2337 497894206 497894247 8.640000e-06 62.1
67 TraesCS3D01G352200 chr4D 94.737 38 2 0 2296 2333 5279208 5279171 3.110000e-05 60.2
68 TraesCS3D01G352200 chr7D 89.583 48 4 1 2296 2343 562936265 562936219 3.110000e-05 60.2
69 TraesCS3D01G352200 chr2A 83.333 66 8 2 210 272 501289484 501289549 1.120000e-04 58.4


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 TraesCS3D01G352200 chr3D 463175665 463178552 2887 False 5334 5334 100.0000 1 2888 1 chr3D.!!$F5 2887
1 TraesCS3D01G352200 chr3B 615782158 615784330 2172 True 3245 3245 93.6900 719 2888 1 chr3B.!!$R1 2169
2 TraesCS3D01G352200 chr3A 606017198 606019639 2441 True 1263 1576 92.1285 13 1973 2 chr3A.!!$R2 1960
3 TraesCS3D01G352200 chr5B 48146922 48147444 522 False 291 291 76.8940 1359 1882 1 chr5B.!!$F1 523
4 TraesCS3D01G352200 chr5B 46767351 46767873 522 True 285 285 76.6160 1359 1882 1 chr5B.!!$R3 523
5 TraesCS3D01G352200 chr5B 46746204 46746791 587 True 281 281 75.3820 1296 1882 1 chr5B.!!$R2 586
6 TraesCS3D01G352200 chr5B 46151815 46152395 580 True 254 254 74.8300 1302 1882 1 chr5B.!!$R1 580
7 TraesCS3D01G352200 chr5B 46633660 46635451 1791 True 239 302 77.4040 1354 1882 2 chr5B.!!$R5 528
8 TraesCS3D01G352200 chr5A 36798282 36798864 582 True 300 300 76.1020 1296 1882 1 chr5A.!!$R1 586
9 TraesCS3D01G352200 chr5A 36941905 36942491 586 True 265 265 74.9150 1296 1882 1 chr5A.!!$R2 586
10 TraesCS3D01G352200 chr5D 45939303 45939832 529 False 285 285 76.5480 1354 1882 1 chr5D.!!$F1 528

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
679 733 0.033504 AGCGACATATAAGGCCACGG 59.966 55.0 5.01 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2621 3872 0.321653 AGGCCCTTCACTTGTAAGCG 60.322 55.0 0.0 0.0 0.0 4.68 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
68 69 4.102649 GGAAAATATTCCGGCGTTTCAAG 58.897 43.478 16.66 0.00 45.44 3.02
79 80 3.794028 CGGCGTTTCAAGAAAAATGTTCA 59.206 39.130 0.00 0.00 31.33 3.18
80 81 4.317069 CGGCGTTTCAAGAAAAATGTTCAC 60.317 41.667 0.00 0.00 31.33 3.18
205 208 7.514573 AAAAATTACAACGTGTCTTTGGAAC 57.485 32.000 0.00 0.00 29.40 3.62
214 217 4.636648 ACGTGTCTTTGGAACATGTTAACA 59.363 37.500 11.95 11.41 39.30 2.41
257 261 9.855361 TTCAAAACATGTATTTAAAAATGTGCG 57.145 25.926 0.00 7.02 33.65 5.34
258 262 9.035607 TCAAAACATGTATTTAAAAATGTGCGT 57.964 25.926 0.00 3.15 33.65 5.24
277 281 3.720818 GCGTCATGCATTGAAAACTATCG 59.279 43.478 0.00 0.00 45.45 2.92
314 331 9.618890 ACATGTGCTCTAGAAATATATTTGTGT 57.381 29.630 15.39 3.01 0.00 3.72
406 423 9.639601 AAAGAATCAAAGAAAACGAAGAAAACT 57.360 25.926 0.00 0.00 0.00 2.66
409 426 6.503589 TCAAAGAAAACGAAGAAAACTCCA 57.496 33.333 0.00 0.00 0.00 3.86
410 427 6.915349 TCAAAGAAAACGAAGAAAACTCCAA 58.085 32.000 0.00 0.00 0.00 3.53
414 431 7.812309 AGAAAACGAAGAAAACTCCAAAAAG 57.188 32.000 0.00 0.00 0.00 2.27
416 433 8.251026 AGAAAACGAAGAAAACTCCAAAAAGAT 58.749 29.630 0.00 0.00 0.00 2.40
419 436 9.678941 AAACGAAGAAAACTCCAAAAAGATATC 57.321 29.630 0.00 0.00 0.00 1.63
420 437 7.519002 ACGAAGAAAACTCCAAAAAGATATCG 58.481 34.615 0.00 0.00 0.00 2.92
477 500 5.842907 ACCAATAAAGAAACAAACCAGAGC 58.157 37.500 0.00 0.00 0.00 4.09
491 515 6.313658 ACAAACCAGAGCAAAATGAAGAAAAC 59.686 34.615 0.00 0.00 0.00 2.43
495 519 7.049754 ACCAGAGCAAAATGAAGAAAACAAAT 58.950 30.769 0.00 0.00 0.00 2.32
498 522 6.421801 AGAGCAAAATGAAGAAAACAAATCCG 59.578 34.615 0.00 0.00 0.00 4.18
547 601 3.398318 AACCCCAAAGAAAACCTGAGT 57.602 42.857 0.00 0.00 0.00 3.41
580 634 2.430244 CGTGTAGCGAGCAACCGT 60.430 61.111 0.00 0.00 44.77 4.83
582 636 2.048597 TGTAGCGAGCAACCGTGG 60.049 61.111 0.00 0.00 0.00 4.94
587 641 1.019278 AGCGAGCAACCGTGGTAATG 61.019 55.000 0.00 0.00 35.00 1.90
595 649 2.512974 CGTGGTAATGGGCCGTCC 60.513 66.667 0.00 0.00 0.00 4.79
601 655 0.176449 GTAATGGGCCGTCCGTTAGT 59.824 55.000 3.81 0.00 45.02 2.24
631 685 4.486574 GTAGGCGACTAGGAATCAGTAC 57.513 50.000 0.00 0.00 45.49 2.73
652 706 4.332828 ACGGGATTCCTTAAACAGAAAGG 58.667 43.478 2.01 0.00 44.17 3.11
673 727 2.963498 TCGACGAGCGACATATAAGG 57.037 50.000 0.00 0.00 45.59 2.69
675 729 1.699343 GACGAGCGACATATAAGGCC 58.301 55.000 0.00 0.00 0.00 5.19
676 730 1.000607 GACGAGCGACATATAAGGCCA 60.001 52.381 5.01 0.00 0.00 5.36
679 733 0.033504 AGCGACATATAAGGCCACGG 59.966 55.000 5.01 0.00 0.00 4.94
680 734 1.566018 GCGACATATAAGGCCACGGC 61.566 60.000 5.01 0.00 41.06 5.68
728 783 7.414436 CGTTAGGATTTCAACTTTTGTGAAGA 58.586 34.615 0.00 0.00 0.00 2.87
831 902 1.091771 CATCGTCGCAGAGGGCAATT 61.092 55.000 0.00 0.00 45.17 2.32
961 1032 2.425592 CCACCTTCACTGTCGGCA 59.574 61.111 0.00 0.00 0.00 5.69
1029 1100 3.084039 ACACCAAGAATACGTCTCGGTA 58.916 45.455 0.00 0.00 34.56 4.02
1285 1356 4.549155 CACAGGTGGAGGAGACCT 57.451 61.111 0.00 0.00 45.23 3.85
1445 1938 2.280592 GTCGCCGGTGTTCAAGGT 60.281 61.111 16.01 0.00 0.00 3.50
1551 2045 6.531594 TGCTTCAGTTTATCTACACTGATTCG 59.468 38.462 6.96 2.21 46.86 3.34
1744 2238 3.513662 CATCATTGCGGCAATCTCAAAA 58.486 40.909 24.43 7.40 31.05 2.44
1822 2316 4.791734 GCAAAGGCTACACACACCTTAAAC 60.792 45.833 0.00 0.00 42.99 2.01
1999 2615 3.585862 TCGGAGATCTTTTGGAAACTCG 58.414 45.455 0.00 0.00 34.64 4.18
2041 2658 9.388506 GATGAATCACCTTATATGTATTCCTGG 57.611 37.037 0.00 0.00 0.00 4.45
2125 2742 6.727394 TCTGGGCTAACAATACATTAGGTTT 58.273 36.000 0.00 0.00 31.44 3.27
2165 3150 2.288152 TGTTCATTCCCTTTCGCAAAGC 60.288 45.455 3.86 0.00 37.18 3.51
2198 3183 3.769536 ACTTCTTTTTGTTGTGGAAGCG 58.230 40.909 0.00 0.00 37.49 4.68
2246 3231 9.841295 ATCAATAATGCTTTGATTGCCTAAATT 57.159 25.926 0.00 0.00 40.08 1.82
2306 3557 6.293955 GCACAAGAAGGTTGTTGCTTTATCTA 60.294 38.462 0.00 0.00 35.08 1.98
2338 3589 2.093106 GAAAGCCTGTCTCGAGAGGTA 58.907 52.381 17.22 4.55 43.29 3.08
2410 3661 7.891183 AGATCATGAACCGTATATAACTTGC 57.109 36.000 0.00 0.00 0.00 4.01
2411 3662 7.441836 AGATCATGAACCGTATATAACTTGCA 58.558 34.615 0.00 0.00 0.00 4.08
2414 3665 9.719355 ATCATGAACCGTATATAACTTGCATAA 57.281 29.630 0.00 0.00 0.00 1.90
2450 3701 3.468063 ACCCCAAGTGACGAGGAC 58.532 61.111 0.00 0.00 0.00 3.85
2455 3706 1.001974 CCCAAGTGACGAGGACATCAA 59.998 52.381 0.00 0.00 0.00 2.57
2470 3721 7.415318 CGAGGACATCAATACTACAGTTACACT 60.415 40.741 0.00 0.00 0.00 3.55
2474 3725 7.027760 ACATCAATACTACAGTTACACTCACG 58.972 38.462 0.00 0.00 0.00 4.35
2617 3868 9.276590 TGATACTGCCTAAATCTGATACATTTG 57.723 33.333 0.00 0.00 0.00 2.32
2621 3872 8.462016 ACTGCCTAAATCTGATACATTTGTTTC 58.538 33.333 0.00 0.00 0.00 2.78
2630 3881 7.518161 TCTGATACATTTGTTTCGCTTACAAG 58.482 34.615 0.00 0.00 36.89 3.16
2647 3898 1.003580 CAAGTGAAGGGCCTAGCTTGA 59.996 52.381 26.83 0.00 36.41 3.02
2651 3902 1.003580 TGAAGGGCCTAGCTTGAACAG 59.996 52.381 6.41 0.00 0.00 3.16
2684 3935 4.525487 ACATTGGAGCAAGATCAAACATGT 59.475 37.500 0.00 0.00 0.00 3.21
2685 3936 5.711506 ACATTGGAGCAAGATCAAACATGTA 59.288 36.000 0.00 0.00 0.00 2.29
2702 3953 1.338105 TGTAGATGATAGCATGCGCCC 60.338 52.381 13.01 5.68 39.83 6.13
2703 3954 1.066573 GTAGATGATAGCATGCGCCCT 60.067 52.381 13.01 7.56 39.83 5.19
2705 3956 1.625315 AGATGATAGCATGCGCCCTTA 59.375 47.619 13.01 0.00 39.83 2.69
2706 3957 2.005451 GATGATAGCATGCGCCCTTAG 58.995 52.381 13.01 0.00 39.83 2.18
2707 3958 0.035317 TGATAGCATGCGCCCTTAGG 59.965 55.000 13.01 0.00 39.83 2.69
2708 3959 0.321671 GATAGCATGCGCCCTTAGGA 59.678 55.000 13.01 0.00 39.83 2.94
2709 3960 0.322975 ATAGCATGCGCCCTTAGGAG 59.677 55.000 13.01 0.00 39.83 3.69
2738 4001 4.219288 AGTTTCAAGTGATGATTTCAGGGC 59.781 41.667 0.00 0.00 38.03 5.19
2758 4021 4.037858 GCTTTGAAGCCACCATAATGAG 57.962 45.455 4.38 0.00 46.20 2.90
2759 4022 3.445096 GCTTTGAAGCCACCATAATGAGT 59.555 43.478 4.38 0.00 46.20 3.41
2760 4023 4.676196 GCTTTGAAGCCACCATAATGAGTG 60.676 45.833 4.38 0.00 46.20 3.51
2761 4024 3.719268 TGAAGCCACCATAATGAGTGT 57.281 42.857 0.00 0.00 31.88 3.55
2772 4035 5.824624 ACCATAATGAGTGTATGAAGGCTTG 59.175 40.000 3.46 0.00 31.71 4.01
2773 4036 5.240183 CCATAATGAGTGTATGAAGGCTTGG 59.760 44.000 3.46 0.00 31.71 3.61
2807 4071 8.915871 TCAAGATGCTACTTCATAAATTTTGC 57.084 30.769 0.00 0.00 0.00 3.68
2813 4077 6.210385 TGCTACTTCATAAATTTTGCCCAGAA 59.790 34.615 0.00 0.00 0.00 3.02
2852 4116 3.433031 CGTCACCTTATTATTGGGCCAGA 60.433 47.826 6.23 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 4.317069 CGTGAACATTTTTCTTGAAACGCC 60.317 41.667 0.00 0.00 0.00 5.68
59 60 4.497608 TCGTGAACATTTTTCTTGAAACGC 59.502 37.500 0.00 0.00 0.00 4.84
61 62 6.862944 TGTCGTGAACATTTTTCTTGAAAC 57.137 33.333 0.00 0.00 31.20 2.78
186 189 4.636648 ACATGTTCCAAAGACACGTTGTAA 59.363 37.500 0.00 0.00 0.00 2.41
257 261 6.968904 ACATTCGATAGTTTTCAATGCATGAC 59.031 34.615 0.00 0.00 35.77 3.06
258 262 6.968335 CACATTCGATAGTTTTCAATGCATGA 59.032 34.615 0.00 0.00 34.61 3.07
265 269 7.698628 TGTGAAACACATTCGATAGTTTTCAA 58.301 30.769 18.17 11.93 45.67 2.69
363 380 6.878389 TGATTCTTTTTGCTTTCCTTTGTTGT 59.122 30.769 0.00 0.00 0.00 3.32
383 400 7.700656 TGGAGTTTTCTTCGTTTTCTTTGATTC 59.299 33.333 0.00 0.00 0.00 2.52
406 423 9.982651 CTCCTTATACTTCGATATCTTTTTGGA 57.017 33.333 0.34 0.00 0.00 3.53
429 447 9.390795 GTTTTTCGGATTTACTTTCTTTACTCC 57.609 33.333 0.00 0.00 0.00 3.85
449 467 9.157104 TCTGGTTTGTTTCTTTATTGGTTTTTC 57.843 29.630 0.00 0.00 0.00 2.29
460 478 6.405538 TCATTTTGCTCTGGTTTGTTTCTTT 58.594 32.000 0.00 0.00 0.00 2.52
462 480 5.596836 TCATTTTGCTCTGGTTTGTTTCT 57.403 34.783 0.00 0.00 0.00 2.52
463 481 6.042143 TCTTCATTTTGCTCTGGTTTGTTTC 58.958 36.000 0.00 0.00 0.00 2.78
477 500 7.928908 TCTCGGATTTGTTTTCTTCATTTTG 57.071 32.000 0.00 0.00 0.00 2.44
535 589 4.103311 AGGTTTGCTCTACTCAGGTTTTCT 59.897 41.667 0.00 0.00 0.00 2.52
547 601 1.616865 ACACGCTGTAGGTTTGCTCTA 59.383 47.619 0.00 0.00 0.00 2.43
580 634 1.263342 TAACGGACGGCCCATTACCA 61.263 55.000 0.00 0.00 34.14 3.25
582 636 0.176449 ACTAACGGACGGCCCATTAC 59.824 55.000 0.00 0.00 34.14 1.89
587 641 0.031721 CTATGACTAACGGACGGCCC 59.968 60.000 0.00 0.00 0.00 5.80
595 649 2.701073 CCTACGGGCTATGACTAACG 57.299 55.000 0.00 0.00 0.00 3.18
627 681 5.750352 TTCTGTTTAAGGAATCCCGTACT 57.250 39.130 0.00 0.00 37.58 2.73
631 685 4.585879 TCCTTTCTGTTTAAGGAATCCCG 58.414 43.478 0.00 0.00 46.15 5.14
644 698 0.179161 CGCTCGTCGATCCTTTCTGT 60.179 55.000 0.00 0.00 41.67 3.41
675 729 4.939368 TTTCACCCGTGGGCCGTG 62.939 66.667 4.41 0.23 39.32 4.94
676 730 3.717924 TTTTTCACCCGTGGGCCGT 62.718 57.895 4.41 0.00 39.32 5.68
679 733 2.570284 CCCTTTTTCACCCGTGGGC 61.570 63.158 4.41 0.00 39.32 5.36
680 734 1.152631 ACCCTTTTTCACCCGTGGG 60.153 57.895 2.58 2.58 40.37 4.61
681 735 2.037871 CACCCTTTTTCACCCGTGG 58.962 57.895 0.00 0.00 0.00 4.94
683 737 1.830847 GGCACCCTTTTTCACCCGT 60.831 57.895 0.00 0.00 0.00 5.28
684 738 2.914908 CGGCACCCTTTTTCACCCG 61.915 63.158 0.00 0.00 0.00 5.28
728 783 0.106619 AAGACGAGGTAGGGCTCGAT 60.107 55.000 0.00 0.00 44.85 3.59
961 1032 2.581354 GATGGACCACTCGCAGCT 59.419 61.111 0.00 0.00 0.00 4.24
1029 1100 3.997021 CCAACGTCAGTAGCTCAAGAAAT 59.003 43.478 0.00 0.00 0.00 2.17
1137 1208 3.840890 TGTATGTGGCCGAAAAACATC 57.159 42.857 8.81 3.20 36.08 3.06
1141 1212 1.614413 GGGTTGTATGTGGCCGAAAAA 59.386 47.619 0.00 0.00 0.00 1.94
1285 1356 3.437795 GACCTCGAAGTCCGGCGA 61.438 66.667 9.30 0.00 39.14 5.54
1445 1938 0.179020 CATCGGCCCATAAAGCTCCA 60.179 55.000 0.00 0.00 0.00 3.86
1744 2238 5.716228 TGAGGATAAATTGGACACAAGCATT 59.284 36.000 0.00 0.00 40.49 3.56
1822 2316 5.255710 ACTATGACAGAAGGACAAGATCG 57.744 43.478 0.00 0.00 0.00 3.69
1882 2376 5.295292 CAGATAACCCAACATGAGCTTACAG 59.705 44.000 0.00 0.00 0.00 2.74
1939 2495 0.872388 GTTGGTTTCAGGTGGCTACG 59.128 55.000 0.00 0.00 0.00 3.51
1999 2615 7.412853 GTGATTCATCATTACATCCAAGACAC 58.587 38.462 0.00 0.00 39.30 3.67
2041 2658 6.629252 GCATAGAGTTCGCAAAAGCTATAAAC 59.371 38.462 0.00 0.00 0.00 2.01
2198 3183 6.767902 TGATGTTCTATTTCCTAATGCTCCAC 59.232 38.462 0.00 0.00 0.00 4.02
2306 3557 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
2397 3648 9.663904 ATTGCTTGTTTATGCAAGTTATATACG 57.336 29.630 6.55 0.00 46.10 3.06
2444 3695 6.691818 GTGTAACTGTAGTATTGATGTCCTCG 59.308 42.308 0.00 0.00 0.00 4.63
2470 3721 0.970427 TGTAGCTGCAGGGATCGTGA 60.970 55.000 17.12 0.00 0.00 4.35
2474 3725 6.462207 CCAGTATATATGTAGCTGCAGGGATC 60.462 46.154 17.12 0.00 0.00 3.36
2595 3846 7.944729 AACAAATGTATCAGATTTAGGCAGT 57.055 32.000 0.00 0.00 0.00 4.40
2607 3858 7.041712 TCACTTGTAAGCGAAACAAATGTATCA 60.042 33.333 9.14 0.00 35.96 2.15
2617 3868 2.350484 GCCCTTCACTTGTAAGCGAAAC 60.350 50.000 0.00 0.00 0.00 2.78
2621 3872 0.321653 AGGCCCTTCACTTGTAAGCG 60.322 55.000 0.00 0.00 0.00 4.68
2630 3881 1.271379 TGTTCAAGCTAGGCCCTTCAC 60.271 52.381 0.00 0.00 0.00 3.18
2647 3898 4.338879 CTCCAATGTTCATCCTTCCTGTT 58.661 43.478 0.00 0.00 0.00 3.16
2651 3902 2.726821 TGCTCCAATGTTCATCCTTCC 58.273 47.619 0.00 0.00 0.00 3.46
2684 3935 1.269958 AGGGCGCATGCTATCATCTA 58.730 50.000 17.13 0.00 42.25 1.98
2685 3936 0.399454 AAGGGCGCATGCTATCATCT 59.601 50.000 17.13 1.80 42.25 2.90
2702 3953 6.467677 TCACTTGAAACTCCATTCTCCTAAG 58.532 40.000 0.00 0.00 0.00 2.18
2703 3954 6.433847 TCACTTGAAACTCCATTCTCCTAA 57.566 37.500 0.00 0.00 0.00 2.69
2705 3956 4.982241 TCACTTGAAACTCCATTCTCCT 57.018 40.909 0.00 0.00 0.00 3.69
2706 3957 5.248640 TCATCACTTGAAACTCCATTCTCC 58.751 41.667 0.00 0.00 0.00 3.71
2707 3958 6.998968 ATCATCACTTGAAACTCCATTCTC 57.001 37.500 0.00 0.00 38.03 2.87
2708 3959 7.449395 TGAAATCATCACTTGAAACTCCATTCT 59.551 33.333 0.00 0.00 38.03 2.40
2709 3960 7.596494 TGAAATCATCACTTGAAACTCCATTC 58.404 34.615 0.00 0.00 38.03 2.67
2738 4001 4.460382 ACACTCATTATGGTGGCTTCAAAG 59.540 41.667 14.79 0.00 37.72 2.77
2757 4020 1.899814 TCGTCCAAGCCTTCATACACT 59.100 47.619 0.00 0.00 0.00 3.55
2758 4021 2.380084 TCGTCCAAGCCTTCATACAC 57.620 50.000 0.00 0.00 0.00 2.90
2759 4022 3.410631 TTTCGTCCAAGCCTTCATACA 57.589 42.857 0.00 0.00 0.00 2.29
2760 4023 5.758296 TGATATTTCGTCCAAGCCTTCATAC 59.242 40.000 0.00 0.00 0.00 2.39
2761 4024 5.924356 TGATATTTCGTCCAAGCCTTCATA 58.076 37.500 0.00 0.00 0.00 2.15
2772 4035 6.701841 TGAAGTAGCATCTTGATATTTCGTCC 59.298 38.462 0.00 0.00 37.65 4.79
2773 4036 7.700322 TGAAGTAGCATCTTGATATTTCGTC 57.300 36.000 0.00 0.00 37.65 4.20
2803 4067 5.104109 ACACCTATAATAGCTTCTGGGCAAA 60.104 40.000 0.00 0.00 34.17 3.68
2807 4071 4.757149 GCAACACCTATAATAGCTTCTGGG 59.243 45.833 0.00 0.00 0.00 4.45
2813 4077 4.369182 GTGACGCAACACCTATAATAGCT 58.631 43.478 0.00 0.00 35.07 3.32
2852 4116 9.975218 ACTGAAGTATTTCTAAATTACATGGGT 57.025 29.630 0.00 0.00 34.31 4.51


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

AutoCloner maintained by Alex Coulton.