Multiple sequence alignment - TraesCS6D01G403600

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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 TraesCS6D01G403600 chr6D 100.000 4165 0 0 1 4165 471821592 471817428 0.000000e+00 7692.0
1 TraesCS6D01G403600 chr6D 78.413 1260 137 74 2330 3522 471832231 471831040 0.000000e+00 695.0
2 TraesCS6D01G403600 chr6A 93.116 2150 74 19 1507 3622 617823007 617825116 0.000000e+00 3083.0
3 TraesCS6D01G403600 chr6A 84.010 1970 210 57 1020 2924 617803212 617805141 0.000000e+00 1796.0
4 TraesCS6D01G403600 chr6A 89.027 966 32 30 540 1462 617819311 617820245 0.000000e+00 1129.0
5 TraesCS6D01G403600 chr6A 82.792 1325 149 36 1629 2911 610477936 610476649 0.000000e+00 1110.0
6 TraesCS6D01G403600 chr6A 89.399 849 46 19 3 827 617807745 617808573 0.000000e+00 1029.0
7 TraesCS6D01G403600 chr6A 93.687 396 24 1 3771 4165 617825342 617825737 3.590000e-165 592.0
8 TraesCS6D01G403600 chr6A 90.090 333 24 4 2 330 617818585 617818912 1.380000e-114 424.0
9 TraesCS6D01G403600 chr6A 97.917 192 3 1 350 541 617818984 617819174 8.630000e-87 331.0
10 TraesCS6D01G403600 chr6A 95.082 61 3 0 3709 3769 617825158 617825218 3.430000e-16 97.1
11 TraesCS6D01G403600 chr6A 79.730 148 15 6 3375 3522 617805607 617805739 4.430000e-15 93.5
12 TraesCS6D01G403600 chr6A 91.489 47 4 0 3064 3110 411236796 411236750 9.660000e-07 65.8
13 TraesCS6D01G403600 chr6B 81.379 1407 197 33 1540 2911 707307764 707306388 0.000000e+00 1086.0
14 TraesCS6D01G403600 chr6B 82.135 862 124 18 1973 2808 716587246 716586389 0.000000e+00 712.0
15 TraesCS6D01G403600 chr6B 80.308 584 65 26 2933 3486 716604644 716604081 3.020000e-106 396.0
16 TraesCS6D01G403600 chr6B 83.871 155 11 7 3067 3221 716586166 716586026 7.260000e-28 135.0
17 TraesCS6D01G403600 chr6B 83.212 137 15 3 3338 3466 707304356 707304220 7.310000e-23 119.0
18 TraesCS6D01G403600 chr6B 89.024 82 1 2 3410 3487 716585899 716585822 1.230000e-15 95.3
19 TraesCS6D01G403600 chrUn 79.197 1245 207 29 1601 2803 108250671 108251905 0.000000e+00 817.0
20 TraesCS6D01G403600 chrUn 77.029 1232 214 35 1603 2776 108254973 108256193 0.000000e+00 643.0
21 TraesCS6D01G403600 chrUn 82.292 576 91 7 2330 2896 74852015 74852588 4.840000e-134 488.0
22 TraesCS6D01G403600 chrUn 79.321 619 63 34 2922 3522 74852656 74853227 1.410000e-99 374.0
23 TraesCS6D01G403600 chr4B 79.057 1251 203 35 1601 2803 665975886 665974647 0.000000e+00 804.0
24 TraesCS6D01G403600 chr4B 77.861 402 62 14 1975 2352 665973382 665972984 1.510000e-54 224.0
25 TraesCS6D01G403600 chr4B 88.166 169 16 3 3874 4042 639453802 639453638 9.130000e-47 198.0
26 TraesCS6D01G403600 chr7D 78.217 1290 220 36 1563 2803 45858093 45856816 0.000000e+00 769.0
27 TraesCS6D01G403600 chr7D 86.198 384 53 0 1540 1923 503942042 503941659 2.320000e-112 416.0
28 TraesCS6D01G403600 chr2B 78.281 1303 208 43 1563 2807 25844264 25842979 0.000000e+00 769.0
29 TraesCS6D01G403600 chr2B 89.024 164 14 1 3880 4043 76912296 76912137 2.540000e-47 200.0
30 TraesCS6D01G403600 chr2B 88.608 79 8 1 3046 3124 73480864 73480941 1.230000e-15 95.3
31 TraesCS6D01G403600 chr2A 75.499 1302 223 55 1565 2807 16497266 16496002 2.190000e-152 549.0
32 TraesCS6D01G403600 chr2A 76.674 433 49 23 2922 3338 749598018 749597622 4.250000e-45 193.0
33 TraesCS6D01G403600 chr5A 75.060 1243 206 61 1636 2804 705943856 705945068 2.250000e-132 483.0
34 TraesCS6D01G403600 chr5A 80.178 338 56 3 2468 2803 705954029 705953701 4.160000e-60 243.0
35 TraesCS6D01G403600 chr5A 88.623 167 15 1 3877 4043 653299440 653299602 2.540000e-47 200.0
36 TraesCS6D01G403600 chr5A 88.957 163 14 1 3880 4042 320214402 320214244 9.130000e-47 198.0
37 TraesCS6D01G403600 chr5A 88.095 168 18 1 3874 4041 706676871 706677036 9.130000e-47 198.0
38 TraesCS6D01G403600 chr5A 76.443 433 50 24 2922 3338 33144606 33145002 1.980000e-43 187.0
39 TraesCS6D01G403600 chr7A 78.454 427 38 24 2922 3338 655224457 655224839 3.240000e-56 230.0
40 TraesCS6D01G403600 chr7A 76.212 433 51 23 2922 3338 118990367 118989971 9.200000e-42 182.0
41 TraesCS6D01G403600 chr3A 88.824 170 14 2 3874 4042 600923075 600923240 1.960000e-48 204.0
42 TraesCS6D01G403600 chr1A 77.083 432 47 24 2923 3338 37102476 37102081 7.060000e-48 202.0
43 TraesCS6D01G403600 chr7B 88.166 169 16 1 3876 4044 464546940 464547104 9.130000e-47 198.0
44 TraesCS6D01G403600 chr3D 86.592 179 18 3 3865 4042 149764796 149764623 4.250000e-45 193.0
45 TraesCS6D01G403600 chr1D 77.358 424 32 26 2922 3323 4081255 4080874 4.250000e-45 193.0
46 TraesCS6D01G403600 chr3B 76.267 434 60 21 2922 3339 762578506 762578912 1.530000e-44 191.0
47 TraesCS6D01G403600 chr2D 80.851 188 29 5 14 200 552529607 552529788 1.560000e-29 141.0


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 TraesCS6D01G403600 chr6D 471817428 471821592 4164 True 7692.000000 7692 100.000000 1 4165 1 chr6D.!!$R1 4164
1 TraesCS6D01G403600 chr6D 471831040 471832231 1191 True 695.000000 695 78.413000 2330 3522 1 chr6D.!!$R2 1192
2 TraesCS6D01G403600 chr6A 610476649 610477936 1287 True 1110.000000 1110 82.792000 1629 2911 1 chr6A.!!$R2 1282
3 TraesCS6D01G403600 chr6A 617803212 617808573 5361 False 972.833333 1796 84.379667 3 3522 3 chr6A.!!$F1 3519
4 TraesCS6D01G403600 chr6A 617818585 617825737 7152 False 942.683333 3083 93.153167 2 4165 6 chr6A.!!$F2 4163
5 TraesCS6D01G403600 chr6B 707304220 707307764 3544 True 602.500000 1086 82.295500 1540 3466 2 chr6B.!!$R2 1926
6 TraesCS6D01G403600 chr6B 716604081 716604644 563 True 396.000000 396 80.308000 2933 3486 1 chr6B.!!$R1 553
7 TraesCS6D01G403600 chr6B 716585822 716587246 1424 True 314.100000 712 85.010000 1973 3487 3 chr6B.!!$R3 1514
8 TraesCS6D01G403600 chrUn 108250671 108256193 5522 False 730.000000 817 78.113000 1601 2803 2 chrUn.!!$F2 1202
9 TraesCS6D01G403600 chrUn 74852015 74853227 1212 False 431.000000 488 80.806500 2330 3522 2 chrUn.!!$F1 1192
10 TraesCS6D01G403600 chr4B 665972984 665975886 2902 True 514.000000 804 78.459000 1601 2803 2 chr4B.!!$R2 1202
11 TraesCS6D01G403600 chr7D 45856816 45858093 1277 True 769.000000 769 78.217000 1563 2803 1 chr7D.!!$R1 1240
12 TraesCS6D01G403600 chr2B 25842979 25844264 1285 True 769.000000 769 78.281000 1563 2807 1 chr2B.!!$R1 1244
13 TraesCS6D01G403600 chr2A 16496002 16497266 1264 True 549.000000 549 75.499000 1565 2807 1 chr2A.!!$R1 1242
14 TraesCS6D01G403600 chr5A 705943856 705945068 1212 False 483.000000 483 75.060000 1636 2804 1 chr5A.!!$F3 1168

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
93 97 0.855349 GTAGCGCTCGATTCACATGG 59.145 55.000 16.34 0.00 0.00 3.66 F
333 337 0.959553 CAGTCACCTGGTGTCTACGT 59.040 55.000 25.15 2.42 34.90 3.57 F
911 1136 1.152963 ACATAGCACGGGAATGGGC 60.153 57.895 5.55 0.00 0.00 5.36 F
2253 5306 0.611200 TGGACGGAAATCGATGGTGT 59.389 50.000 0.00 0.00 42.43 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1234 1477 0.694771 AGGCTTGAAGATGCACTGGA 59.305 50.0 0.0 0.00 0.00 3.86 R
1278 1521 0.820891 AACACCTGTCAGGCAAGCAG 60.821 55.0 19.4 4.85 39.63 4.24 R
2498 5581 0.819259 TGCAGCACCCAACTCTCAAC 60.819 55.0 0.0 0.00 0.00 3.18 R
3649 9550 0.038801 GAAAAACAGAGGCAGGCAGC 60.039 55.0 0.0 0.00 44.65 5.25 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
75 79 5.529581 AAATCATGGTCAACCGAAAAAGT 57.470 34.783 0.00 0.00 39.43 2.66
77 81 5.880054 ATCATGGTCAACCGAAAAAGTAG 57.120 39.130 0.00 0.00 39.43 2.57
93 97 0.855349 GTAGCGCTCGATTCACATGG 59.145 55.000 16.34 0.00 0.00 3.66
108 112 2.031157 CACATGGAAACTTGACCCGTTC 60.031 50.000 0.00 0.00 38.76 3.95
153 157 3.611766 AGGAGATGGTTCGGTTTGTAG 57.388 47.619 0.00 0.00 0.00 2.74
154 158 2.904434 AGGAGATGGTTCGGTTTGTAGT 59.096 45.455 0.00 0.00 0.00 2.73
155 159 4.091549 AGGAGATGGTTCGGTTTGTAGTA 58.908 43.478 0.00 0.00 0.00 1.82
159 163 3.756933 TGGTTCGGTTTGTAGTAAGCT 57.243 42.857 0.00 0.00 0.00 3.74
165 169 5.710513 TCGGTTTGTAGTAAGCTGTCTAA 57.289 39.130 0.00 0.00 0.00 2.10
177 181 8.507524 AGTAAGCTGTCTAAGTGAAAACTTTT 57.492 30.769 0.00 0.00 0.00 2.27
181 185 4.915704 TGTCTAAGTGAAAACTTTTGCGG 58.084 39.130 0.00 0.00 0.00 5.69
195 199 5.600696 ACTTTTGCGGAACATTCTCAAATT 58.399 33.333 0.00 3.27 33.42 1.82
204 208 9.515020 GCGGAACATTCTCAAATTTTTATCATA 57.485 29.630 0.00 0.00 0.00 2.15
315 319 1.557099 ATGTTAGTGCCCGAGTCTCA 58.443 50.000 0.00 0.00 0.00 3.27
330 334 2.108425 AGTCTCAGTCACCTGGTGTCTA 59.892 50.000 25.15 8.62 39.31 2.59
331 335 2.229302 GTCTCAGTCACCTGGTGTCTAC 59.771 54.545 25.15 16.50 39.31 2.59
333 337 0.959553 CAGTCACCTGGTGTCTACGT 59.040 55.000 25.15 2.42 34.90 3.57
334 338 1.340248 CAGTCACCTGGTGTCTACGTT 59.660 52.381 25.15 2.05 34.90 3.99
336 340 2.132762 GTCACCTGGTGTCTACGTTTG 58.867 52.381 25.15 0.00 34.79 2.93
337 341 2.033372 TCACCTGGTGTCTACGTTTGA 58.967 47.619 25.15 0.00 34.79 2.69
338 342 2.431419 TCACCTGGTGTCTACGTTTGAA 59.569 45.455 25.15 0.00 34.79 2.69
339 343 3.070446 TCACCTGGTGTCTACGTTTGAAT 59.930 43.478 25.15 0.00 34.79 2.57
342 346 4.885325 ACCTGGTGTCTACGTTTGAATTTT 59.115 37.500 0.00 0.00 0.00 1.82
343 347 5.008316 ACCTGGTGTCTACGTTTGAATTTTC 59.992 40.000 0.00 0.00 0.00 2.29
344 348 5.008217 CCTGGTGTCTACGTTTGAATTTTCA 59.992 40.000 0.00 0.00 34.92 2.69
346 350 6.434596 TGGTGTCTACGTTTGAATTTTCATG 58.565 36.000 0.00 0.00 37.00 3.07
347 351 6.261158 TGGTGTCTACGTTTGAATTTTCATGA 59.739 34.615 0.00 0.00 37.00 3.07
497 553 9.878599 AGTAGACATTCAACATTTTCTTAAACG 57.121 29.630 0.00 0.00 0.00 3.60
765 960 7.488471 ACCGAATTTTTCAATACACGTTTGAAA 59.512 29.630 18.16 18.16 46.09 2.69
911 1136 1.152963 ACATAGCACGGGAATGGGC 60.153 57.895 5.55 0.00 0.00 5.36
1060 1285 3.311110 GCCGACCAGTCCACAGGA 61.311 66.667 0.00 0.00 0.00 3.86
1252 1495 1.538047 TTCCAGTGCATCTTCAAGCC 58.462 50.000 0.00 0.00 0.00 4.35
1254 1497 1.908619 TCCAGTGCATCTTCAAGCCTA 59.091 47.619 0.00 0.00 0.00 3.93
1256 1499 2.616256 CCAGTGCATCTTCAAGCCTACA 60.616 50.000 0.00 0.00 0.00 2.74
1258 1501 3.064958 CAGTGCATCTTCAAGCCTACATG 59.935 47.826 0.00 0.00 0.00 3.21
1260 1503 3.011818 TGCATCTTCAAGCCTACATGTG 58.988 45.455 9.11 0.00 0.00 3.21
1358 1601 5.632347 GCAGTTTGAGTTTGATTTCAGATGG 59.368 40.000 0.00 0.00 0.00 3.51
1421 1664 9.901172 ATGCAATGACTGATGATATATGTACAT 57.099 29.630 13.93 13.93 0.00 2.29
1477 1830 2.031870 GCCTTGACCTGAAACCAAAGT 58.968 47.619 0.00 0.00 0.00 2.66
1684 4668 4.309950 GCCGACGGAACCACCACT 62.310 66.667 20.50 0.00 38.90 4.00
1720 4707 1.480137 CAAGACCAGCTCCTCGAGATT 59.520 52.381 15.71 0.00 0.00 2.40
1836 4823 3.322466 CTTCCGTGCCCTCCACCT 61.322 66.667 0.00 0.00 41.53 4.00
2253 5306 0.611200 TGGACGGAAATCGATGGTGT 59.389 50.000 0.00 0.00 42.43 4.16
2258 5311 4.369182 GACGGAAATCGATGGTGTAATCT 58.631 43.478 0.00 0.00 42.43 2.40
2410 5484 4.686093 GGAAGGTGTTCCCAAGGTTGGT 62.686 54.545 7.96 0.00 46.11 3.67
2458 5538 6.493116 CATGGTCTATGCAACTGAAGATTTC 58.507 40.000 0.00 0.00 0.00 2.17
2642 5744 1.468127 TGTGCATGACAAGCATAACCG 59.532 47.619 8.81 0.00 44.79 4.44
3127 8329 2.009042 GCCGGTCCTGACATTCTCTTG 61.009 57.143 1.90 0.00 0.00 3.02
3207 8422 0.740149 TGTGGCTTGCACTGAAGTTG 59.260 50.000 0.00 0.00 0.00 3.16
3216 8432 1.171308 CACTGAAGTTGGCCTGATGG 58.829 55.000 3.32 0.00 0.00 3.51
3217 8433 1.067295 ACTGAAGTTGGCCTGATGGA 58.933 50.000 3.32 0.00 34.57 3.41
3447 9187 6.343703 TGGTCATGTCTCTGTATCATTTCTG 58.656 40.000 0.00 0.00 0.00 3.02
3449 9189 6.820656 GGTCATGTCTCTGTATCATTTCTGTT 59.179 38.462 0.00 0.00 0.00 3.16
3515 9258 3.307762 GGAAGGGTAAGCTTGTGTCTGAT 60.308 47.826 9.86 0.00 0.00 2.90
3522 9265 6.183360 GGGTAAGCTTGTGTCTGATAGATGTA 60.183 42.308 9.86 0.00 0.00 2.29
3523 9266 7.265673 GGTAAGCTTGTGTCTGATAGATGTAA 58.734 38.462 9.86 0.00 0.00 2.41
3524 9267 7.764443 GGTAAGCTTGTGTCTGATAGATGTAAA 59.236 37.037 9.86 0.00 0.00 2.01
3525 9268 9.151471 GTAAGCTTGTGTCTGATAGATGTAAAA 57.849 33.333 9.86 0.00 0.00 1.52
3526 9269 8.621532 AAGCTTGTGTCTGATAGATGTAAAAA 57.378 30.769 0.00 0.00 0.00 1.94
3527 9270 8.798859 AGCTTGTGTCTGATAGATGTAAAAAT 57.201 30.769 0.00 0.00 0.00 1.82
3528 9271 8.671921 AGCTTGTGTCTGATAGATGTAAAAATG 58.328 33.333 0.00 0.00 0.00 2.32
3529 9272 8.454106 GCTTGTGTCTGATAGATGTAAAAATGT 58.546 33.333 0.00 0.00 0.00 2.71
3588 9384 0.818445 CCATGGCAGATCTGGAGTGC 60.818 60.000 23.89 10.00 36.42 4.40
3591 9387 2.581354 GCAGATCTGGAGTGCCGT 59.419 61.111 23.89 0.00 36.79 5.68
3620 9418 2.009774 GTTGTGTGCTGTTGTCAGAGT 58.990 47.619 0.00 0.00 43.76 3.24
3640 9472 3.068590 AGTTTGGTTGGTGCTTTCATGAG 59.931 43.478 0.00 0.00 0.00 2.90
3643 9475 3.499338 TGGTTGGTGCTTTCATGAGAAT 58.501 40.909 0.00 0.00 32.89 2.40
3644 9476 4.661222 TGGTTGGTGCTTTCATGAGAATA 58.339 39.130 0.00 0.00 32.89 1.75
3649 9550 7.293745 GTTGGTGCTTTCATGAGAATATATCG 58.706 38.462 0.00 0.00 32.89 2.92
3650 9551 5.409520 TGGTGCTTTCATGAGAATATATCGC 59.590 40.000 0.00 0.00 32.89 4.58
3654 9555 5.447010 GCTTTCATGAGAATATATCGCTGCC 60.447 44.000 0.00 0.00 32.89 4.85
3658 9559 2.275318 GAGAATATATCGCTGCCTGCC 58.725 52.381 0.00 0.00 38.78 4.85
3661 9562 1.566211 ATATATCGCTGCCTGCCTCT 58.434 50.000 0.00 0.00 38.78 3.69
3664 9565 1.617018 TATCGCTGCCTGCCTCTGTT 61.617 55.000 0.00 0.00 38.78 3.16
3669 9570 0.600057 CTGCCTGCCTCTGTTTTTCC 59.400 55.000 0.00 0.00 0.00 3.13
3673 9574 2.288457 GCCTGCCTCTGTTTTTCCTTTC 60.288 50.000 0.00 0.00 0.00 2.62
3683 9613 6.805713 TCTGTTTTTCCTTTCCAAATGACTC 58.194 36.000 0.00 0.00 0.00 3.36
3707 9637 4.280174 GCCATTTCTATGTGATGCCATTCT 59.720 41.667 0.00 0.00 0.00 2.40
3725 10941 5.121142 CCATTCTTTCACAATGAAACATGGC 59.879 40.000 17.20 0.00 40.99 4.40
3820 11458 0.617935 AAGAGAAGAAGGGCCTGAGC 59.382 55.000 6.92 0.00 38.76 4.26
3866 11504 5.070446 TCGTAGATTGAAATGGCAGGATAGT 59.930 40.000 0.00 0.00 0.00 2.12
3885 11523 6.434965 GGATAGTACTCTGTTCTATTCCCTCC 59.565 46.154 0.00 0.00 28.84 4.30
3886 11524 4.208746 AGTACTCTGTTCTATTCCCTCCG 58.791 47.826 0.00 0.00 0.00 4.63
4044 12855 4.796038 TTTAGAAACCGAGGGAGTACAG 57.204 45.455 0.00 0.00 0.00 2.74
4047 12858 0.896940 AAACCGAGGGAGTACAGCGA 60.897 55.000 0.00 0.00 0.00 4.93
4098 12910 4.218417 GGCAAGAAGATAAAGGTGCAAAGA 59.782 41.667 0.00 0.00 33.66 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.848223 TTTCCAGACTACACATCATTACATG 57.152 36.000 0.00 0.00 0.00 3.21
54 58 5.335661 GCTACTTTTTCGGTTGACCATGATT 60.336 40.000 0.00 0.00 35.14 2.57
55 59 4.156008 GCTACTTTTTCGGTTGACCATGAT 59.844 41.667 0.00 0.00 35.14 2.45
63 67 1.461888 CGAGCGCTACTTTTTCGGTTG 60.462 52.381 11.50 0.00 33.91 3.77
70 74 2.683968 TGTGAATCGAGCGCTACTTTT 58.316 42.857 11.50 1.32 0.00 2.27
75 79 0.744281 TCCATGTGAATCGAGCGCTA 59.256 50.000 11.50 0.00 0.00 4.26
77 81 0.726827 TTTCCATGTGAATCGAGCGC 59.273 50.000 0.00 0.00 31.67 5.92
93 97 3.318886 GAGAGAGAACGGGTCAAGTTTC 58.681 50.000 0.00 0.00 31.14 2.78
139 143 3.181463 ACAGCTTACTACAAACCGAACCA 60.181 43.478 0.00 0.00 0.00 3.67
153 157 7.165977 GCAAAAGTTTTCACTTAGACAGCTTAC 59.834 37.037 0.00 0.00 42.89 2.34
154 158 7.193595 GCAAAAGTTTTCACTTAGACAGCTTA 58.806 34.615 0.00 0.00 42.89 3.09
155 159 6.036470 GCAAAAGTTTTCACTTAGACAGCTT 58.964 36.000 0.00 0.00 42.89 3.74
159 163 4.636648 TCCGCAAAAGTTTTCACTTAGACA 59.363 37.500 0.00 0.00 42.89 3.41
165 169 3.859411 TGTTCCGCAAAAGTTTTCACT 57.141 38.095 0.00 0.00 33.11 3.41
177 181 7.374272 TGATAAAAATTTGAGAATGTTCCGCA 58.626 30.769 0.00 0.00 0.00 5.69
236 240 9.921637 AAACGAAGCCTAAAAATCATGAAATTA 57.078 25.926 0.00 0.00 0.00 1.40
301 305 1.228583 TGACTGAGACTCGGGCACT 60.229 57.895 16.32 0.00 35.44 4.40
315 319 1.700955 AACGTAGACACCAGGTGACT 58.299 50.000 27.39 26.14 40.92 3.41
497 553 8.566008 ACCGTGTATATAAATACGTTTCTGAC 57.434 34.615 0.00 0.00 40.84 3.51
735 930 4.856487 CGTGTATTGAAAAATTCGGTGCAT 59.144 37.500 0.00 0.00 0.00 3.96
883 1108 4.466827 TCCCGTGCTATGTCTCACTTATA 58.533 43.478 0.00 0.00 0.00 0.98
884 1109 3.296854 TCCCGTGCTATGTCTCACTTAT 58.703 45.455 0.00 0.00 0.00 1.73
885 1110 2.730382 TCCCGTGCTATGTCTCACTTA 58.270 47.619 0.00 0.00 0.00 2.24
886 1111 1.557099 TCCCGTGCTATGTCTCACTT 58.443 50.000 0.00 0.00 0.00 3.16
900 1125 2.604629 TAAACCGGCCCATTCCCGT 61.605 57.895 0.00 0.00 44.13 5.28
911 1136 3.127589 CAAAAAGCCCAAAGTAAACCGG 58.872 45.455 0.00 0.00 0.00 5.28
1080 1318 1.563410 AGATGCAAGAGAAAGGAGGGG 59.437 52.381 0.00 0.00 0.00 4.79
1179 1422 3.988379 TCATCATCGTCATCATCGTCA 57.012 42.857 0.00 0.00 0.00 4.35
1180 1423 4.683320 ACAATCATCATCGTCATCATCGTC 59.317 41.667 0.00 0.00 0.00 4.20
1183 1426 6.157904 AGAGACAATCATCATCGTCATCATC 58.842 40.000 0.00 0.00 0.00 2.92
1184 1427 6.099159 AGAGACAATCATCATCGTCATCAT 57.901 37.500 0.00 0.00 0.00 2.45
1185 1428 5.526506 AGAGACAATCATCATCGTCATCA 57.473 39.130 0.00 0.00 0.00 3.07
1186 1429 5.981915 TCAAGAGACAATCATCATCGTCATC 59.018 40.000 0.00 0.00 0.00 2.92
1187 1430 5.910614 TCAAGAGACAATCATCATCGTCAT 58.089 37.500 0.00 0.00 0.00 3.06
1188 1431 5.329035 TCAAGAGACAATCATCATCGTCA 57.671 39.130 0.00 0.00 0.00 4.35
1189 1432 5.981915 TCATCAAGAGACAATCATCATCGTC 59.018 40.000 0.00 0.00 0.00 4.20
1190 1433 5.752472 GTCATCAAGAGACAATCATCATCGT 59.248 40.000 0.00 0.00 36.06 3.73
1191 1434 5.984323 AGTCATCAAGAGACAATCATCATCG 59.016 40.000 0.00 0.00 38.46 3.84
1192 1435 8.143193 AGTAGTCATCAAGAGACAATCATCATC 58.857 37.037 0.00 0.00 38.46 2.92
1234 1477 0.694771 AGGCTTGAAGATGCACTGGA 59.305 50.000 0.00 0.00 0.00 3.86
1247 1490 3.752747 TGTTCACATCACATGTAGGCTTG 59.247 43.478 0.00 0.00 42.70 4.01
1248 1491 4.019792 TGTTCACATCACATGTAGGCTT 57.980 40.909 0.00 0.00 42.70 4.35
1249 1492 3.701205 TGTTCACATCACATGTAGGCT 57.299 42.857 0.00 0.00 42.70 4.58
1250 1493 3.065786 CCATGTTCACATCACATGTAGGC 59.934 47.826 0.00 0.00 46.95 3.93
1252 1495 5.885230 AACCATGTTCACATCACATGTAG 57.115 39.130 0.00 0.00 46.95 2.74
1254 1497 5.534207 AAAACCATGTTCACATCACATGT 57.466 34.783 11.15 0.00 46.95 3.21
1256 1499 6.218019 CAGAAAAACCATGTTCACATCACAT 58.782 36.000 0.00 0.00 35.10 3.21
1258 1501 4.445385 GCAGAAAAACCATGTTCACATCAC 59.555 41.667 0.00 0.00 33.61 3.06
1260 1503 4.874970 AGCAGAAAAACCATGTTCACATC 58.125 39.130 0.00 0.00 33.61 3.06
1278 1521 0.820891 AACACCTGTCAGGCAAGCAG 60.821 55.000 19.40 4.85 39.63 4.24
1477 1830 8.792830 AAAGATACTAACTGCTCATTGCTAAA 57.207 30.769 0.00 0.00 43.37 1.85
1684 4668 0.888619 CTTGGCCGAGCGAGGATATA 59.111 55.000 7.18 0.00 0.00 0.86
1720 4707 4.082523 CTCGGCAGGCGGAGGAAA 62.083 66.667 17.49 0.00 38.99 3.13
2410 5484 4.030913 AGAGTTTTCCATCCTCGGTATCA 58.969 43.478 0.00 0.00 0.00 2.15
2458 5538 2.359900 CGGATCCAAACAAGGAGAAGG 58.640 52.381 13.41 0.00 41.90 3.46
2498 5581 0.819259 TGCAGCACCCAACTCTCAAC 60.819 55.000 0.00 0.00 0.00 3.18
3127 8329 0.524862 CTTCACTGCAAGCCATCCAC 59.475 55.000 0.00 0.00 37.60 4.02
3207 8422 1.341383 ACCAACAAGATCCATCAGGCC 60.341 52.381 0.00 0.00 33.74 5.19
3216 8432 4.174762 GACGAGGTTCTACCAACAAGATC 58.825 47.826 0.00 0.00 41.95 2.75
3217 8433 3.576982 TGACGAGGTTCTACCAACAAGAT 59.423 43.478 0.00 0.00 41.95 2.40
3403 9135 1.668826 ACTGGCCAAGATAAGGGTCA 58.331 50.000 7.01 0.00 36.19 4.02
3447 9187 1.067060 GACAGCCAAGGGAACACAAAC 59.933 52.381 0.00 0.00 0.00 2.93
3449 9189 0.817634 CGACAGCCAAGGGAACACAA 60.818 55.000 0.00 0.00 0.00 3.33
3515 9258 9.932207 TCGAGAAGGTTAACATTTTTACATCTA 57.068 29.630 6.98 0.00 0.00 1.98
3522 9265 9.594478 AACATTTTCGAGAAGGTTAACATTTTT 57.406 25.926 15.93 0.00 32.41 1.94
3526 9269 8.674607 GGATAACATTTTCGAGAAGGTTAACAT 58.325 33.333 23.82 12.88 38.68 2.71
3527 9270 7.120138 GGGATAACATTTTCGAGAAGGTTAACA 59.880 37.037 23.82 9.19 38.68 2.41
3528 9271 7.336176 AGGGATAACATTTTCGAGAAGGTTAAC 59.664 37.037 23.82 21.15 38.68 2.01
3529 9272 7.335924 CAGGGATAACATTTTCGAGAAGGTTAA 59.664 37.037 23.82 11.80 38.68 2.01
3532 9275 5.186198 CAGGGATAACATTTTCGAGAAGGT 58.814 41.667 0.00 0.00 0.00 3.50
3533 9276 4.576463 CCAGGGATAACATTTTCGAGAAGG 59.424 45.833 0.00 0.00 0.00 3.46
3534 9277 4.035675 GCCAGGGATAACATTTTCGAGAAG 59.964 45.833 0.00 0.00 0.00 2.85
3535 9278 3.945285 GCCAGGGATAACATTTTCGAGAA 59.055 43.478 0.00 0.00 0.00 2.87
3588 9384 2.033299 AGCACACAACAAGATTTGACGG 59.967 45.455 0.00 0.00 0.00 4.79
3591 9387 4.082300 ACAACAGCACACAACAAGATTTGA 60.082 37.500 0.00 0.00 0.00 2.69
3620 9418 3.295093 TCTCATGAAAGCACCAACCAAA 58.705 40.909 0.00 0.00 0.00 3.28
3649 9550 0.038801 GAAAAACAGAGGCAGGCAGC 60.039 55.000 0.00 0.00 44.65 5.25
3650 9551 0.600057 GGAAAAACAGAGGCAGGCAG 59.400 55.000 0.00 0.00 0.00 4.85
3654 9555 2.958355 TGGAAAGGAAAAACAGAGGCAG 59.042 45.455 0.00 0.00 0.00 4.85
3658 9559 6.809869 AGTCATTTGGAAAGGAAAAACAGAG 58.190 36.000 0.00 0.00 29.81 3.35
3661 9562 5.587289 CGAGTCATTTGGAAAGGAAAAACA 58.413 37.500 0.00 0.00 29.81 2.83
3664 9565 3.005367 GGCGAGTCATTTGGAAAGGAAAA 59.995 43.478 0.00 0.00 29.81 2.29
3669 9570 3.855689 AATGGCGAGTCATTTGGAAAG 57.144 42.857 0.00 0.00 34.01 2.62
3673 9574 4.336433 ACATAGAAATGGCGAGTCATTTGG 59.664 41.667 18.78 8.99 44.48 3.28
3683 9613 1.948834 TGGCATCACATAGAAATGGCG 59.051 47.619 0.00 0.00 45.89 5.69
3707 9637 3.724508 ACGCCATGTTTCATTGTGAAA 57.275 38.095 1.24 1.24 43.37 2.69
3725 10941 1.663695 AAATCCTGGTTGCCGATACG 58.336 50.000 0.00 0.00 0.00 3.06
3797 11435 2.840651 TCAGGCCCTTCTTCTCTTTAGG 59.159 50.000 0.00 0.00 0.00 2.69
3847 11485 6.426328 CAGAGTACTATCCTGCCATTTCAATC 59.574 42.308 0.00 0.00 0.00 2.67
3866 11504 4.246712 ACGGAGGGAATAGAACAGAGTA 57.753 45.455 0.00 0.00 0.00 2.59
4010 11648 8.683615 CCTCGGTTTCTAAATATAAGCCTTTTT 58.316 33.333 0.00 0.00 0.00 1.94
4016 12827 6.522946 ACTCCCTCGGTTTCTAAATATAAGC 58.477 40.000 0.00 0.00 0.00 3.09
4028 12839 0.896940 TCGCTGTACTCCCTCGGTTT 60.897 55.000 0.00 0.00 0.00 3.27
4044 12855 1.724654 CGTGTACACAAGCCATTTCGC 60.725 52.381 24.98 0.00 0.00 4.70
4098 12910 2.302157 CCACCTACGTTTTCTCCTTCCT 59.698 50.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.