Multiple sequence alignment - TraesCS2A01G089900

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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 TraesCS2A01G089900 chr2A 100.000 2935 0 0 1 2935 42783816 42786750 0.000000e+00 5421.0
1 TraesCS2A01G089900 chr2A 92.955 582 38 3 2 582 557322716 557322137 0.000000e+00 845.0
2 TraesCS2A01G089900 chr2A 92.672 232 8 3 2096 2318 42792258 42792489 2.820000e-85 326.0
3 TraesCS2A01G089900 chr2A 92.523 214 10 5 2109 2320 42932704 42932913 4.750000e-78 302.0
4 TraesCS2A01G089900 chr2A 90.295 237 12 11 2093 2320 43006344 43006578 1.710000e-77 300.0
5 TraesCS2A01G089900 chr2A 92.056 214 11 5 2109 2320 42839406 42839615 2.210000e-76 296.0
6 TraesCS2A01G089900 chr2A 92.056 214 11 5 2109 2320 42876419 42876628 2.210000e-76 296.0
7 TraesCS2A01G089900 chr2A 91.667 216 12 6 2109 2320 42962726 42962939 7.950000e-76 294.0
8 TraesCS2A01G089900 chr2A 88.889 153 17 0 1771 1923 42792054 42792206 3.860000e-44 189.0
9 TraesCS2A01G089900 chr2A 86.452 155 14 4 1490 1644 43006116 43006263 2.340000e-36 163.0
10 TraesCS2A01G089900 chr2A 85.806 155 15 4 1490 1644 42839137 42839284 1.090000e-34 158.0
11 TraesCS2A01G089900 chr2A 85.806 155 15 4 1490 1644 42876051 42876198 1.090000e-34 158.0
12 TraesCS2A01G089900 chr2A 85.806 155 15 4 1490 1644 42962445 42962592 1.090000e-34 158.0
13 TraesCS2A01G089900 chr2A 87.597 129 8 5 1490 1617 43049759 43049880 3.050000e-30 143.0
14 TraesCS2A01G089900 chr2A 83.571 140 11 4 1490 1629 42932429 42932556 1.430000e-23 121.0
15 TraesCS2A01G089900 chr2D 89.892 1850 111 38 552 2372 37869563 37871365 0.000000e+00 2311.0
16 TraesCS2A01G089900 chr2D 89.196 1231 96 28 1722 2935 37929671 37930881 0.000000e+00 1502.0
17 TraesCS2A01G089900 chr2D 92.269 595 26 9 2 583 80626002 80625415 0.000000e+00 826.0
18 TraesCS2A01G089900 chr2D 87.631 574 38 13 2392 2935 37874471 37875041 1.150000e-178 636.0
19 TraesCS2A01G089900 chr2D 91.967 361 20 5 2102 2461 37911708 37912060 5.650000e-137 497.0
20 TraesCS2A01G089900 chr2D 93.750 176 8 3 2102 2277 37912813 37912985 8.070000e-66 261.0
21 TraesCS2A01G089900 chr2D 84.914 232 13 12 2116 2346 37960515 37960725 6.370000e-52 215.0
22 TraesCS2A01G089900 chr2D 89.542 153 16 0 1284 1436 37911080 37911232 8.300000e-46 195.0
23 TraesCS2A01G089900 chr2D 93.846 130 4 4 2094 2219 37937580 37937709 2.990000e-45 193.0
24 TraesCS2A01G089900 chr2D 87.582 153 16 2 1771 1923 37937384 37937533 1.080000e-39 174.0
25 TraesCS2A01G089900 chr2D 97.260 73 2 0 2433 2505 37930352 37930424 1.100000e-24 124.0
26 TraesCS2A01G089900 chr2D 82.258 124 16 4 1521 1644 37911269 37911386 5.170000e-18 102.0
27 TraesCS2A01G089900 chr2B 89.312 1656 92 45 579 2197 66355319 66356926 0.000000e+00 1999.0
28 TraesCS2A01G089900 chr2B 90.625 608 32 7 1731 2315 66476863 66477468 0.000000e+00 784.0
29 TraesCS2A01G089900 chr2B 90.909 594 29 11 2 582 770582333 770581752 0.000000e+00 774.0
30 TraesCS2A01G089900 chr2B 82.167 729 95 22 2103 2821 66414057 66414760 7.000000e-166 593.0
31 TraesCS2A01G089900 chr7A 93.643 582 28 4 2 582 54872066 54872639 0.000000e+00 861.0
32 TraesCS2A01G089900 chr7A 91.362 602 24 12 2 590 142489185 142489771 0.000000e+00 798.0
33 TraesCS2A01G089900 chr5A 92.761 594 22 8 2 582 556724108 556723523 0.000000e+00 839.0
34 TraesCS2A01G089900 chr6D 92.206 603 27 10 2 590 60456798 60456202 0.000000e+00 835.0
35 TraesCS2A01G089900 chr6D 84.293 191 15 10 2131 2310 46846096 46846282 3.890000e-39 172.0
36 TraesCS2A01G089900 chr6D 86.992 123 11 5 2221 2342 455911907 455911789 1.840000e-27 134.0
37 TraesCS2A01G089900 chr6D 92.391 92 4 2 2223 2311 455896680 455896589 8.540000e-26 128.0
38 TraesCS2A01G089900 chr6D 92.308 91 4 2 2223 2310 455933131 455933041 3.070000e-25 126.0
39 TraesCS2A01G089900 chr6D 91.667 84 6 1 2227 2310 46626682 46626764 6.650000e-22 115.0
40 TraesCS2A01G089900 chr6D 96.491 57 1 1 2255 2310 46362388 46362444 3.110000e-15 93.5
41 TraesCS2A01G089900 chr6D 89.831 59 2 3 2222 2279 455932970 455932915 4.060000e-09 73.1
42 TraesCS2A01G089900 chr4B 92.217 591 36 8 2 590 66878922 66879504 0.000000e+00 828.0
43 TraesCS2A01G089900 chr5B 92.243 593 27 9 4 582 695807743 695808330 0.000000e+00 822.0
44 TraesCS2A01G089900 chr5B 92.000 150 1 1 2 140 30899370 30899519 1.780000e-47 200.0
45 TraesCS2A01G089900 chr6A 91.708 603 33 7 2 590 12373878 12373279 0.000000e+00 821.0
46 TraesCS2A01G089900 chr6B 89.022 583 47 14 2 580 5039964 5040533 0.000000e+00 706.0
47 TraesCS2A01G089900 chr6B 86.739 460 26 25 1 448 164735769 164736205 2.050000e-131 479.0
48 TraesCS2A01G089900 chr3A 89.116 588 36 17 2 588 742056228 742055668 0.000000e+00 706.0
49 TraesCS2A01G089900 chr3A 90.000 140 12 2 2172 2310 532331183 532331321 2.320000e-41 180.0
50 TraesCS2A01G089900 chr3D 89.286 140 11 3 2172 2310 418770889 418770753 3.890000e-39 172.0
51 TraesCS2A01G089900 chr1B 86.986 146 15 4 2172 2316 456184661 456184519 8.420000e-36 161.0
52 TraesCS2A01G089900 chr5D 98.876 89 1 0 2222 2310 56450165 56450253 3.030000e-35 159.0
53 TraesCS2A01G089900 chr1A 82.143 196 26 7 2126 2316 440183563 440183372 3.030000e-35 159.0
54 TraesCS2A01G089900 chr1A 94.949 99 4 1 2222 2320 554280625 554280528 1.410000e-33 154.0
55 TraesCS2A01G089900 chr1A 94.949 99 4 1 2222 2320 554293068 554293165 1.410000e-33 154.0
56 TraesCS2A01G089900 chr1D 96.842 95 2 1 2222 2316 462465479 462465572 1.090000e-34 158.0
57 TraesCS2A01G089900 chr1D 96.809 94 2 1 2223 2316 462440874 462440782 3.920000e-34 156.0
58 TraesCS2A01G089900 chr1D 81.281 203 27 10 2116 2311 420227204 420227006 1.410000e-33 154.0
59 TraesCS2A01G089900 chr1D 97.753 89 1 1 2222 2310 462471289 462471376 5.070000e-33 152.0
60 TraesCS2A01G089900 chr1D 96.591 88 2 1 2223 2310 274257168 274257254 8.480000e-31 145.0
61 TraesCS2A01G089900 chr1D 80.882 204 21 13 2131 2321 422837196 422837394 8.480000e-31 145.0
62 TraesCS2A01G089900 chr1D 95.402 87 2 2 2223 2308 422685220 422685305 1.420000e-28 137.0


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 TraesCS2A01G089900 chr2A 42783816 42786750 2934 False 5421.00 5421 100.00000 1 2935 1 chr2A.!!$F1 2934
1 TraesCS2A01G089900 chr2A 557322137 557322716 579 True 845.00 845 92.95500 2 582 1 chr2A.!!$R1 580
2 TraesCS2A01G089900 chr2A 42876051 42876628 577 False 227.00 296 88.93100 1490 2320 2 chr2A.!!$F5 830
3 TraesCS2A01G089900 chr2D 37869563 37875041 5478 False 1473.50 2311 88.76150 552 2935 2 chr2D.!!$F2 2383
4 TraesCS2A01G089900 chr2D 80625415 80626002 587 True 826.00 826 92.26900 2 583 1 chr2D.!!$R1 581
5 TraesCS2A01G089900 chr2D 37929671 37930881 1210 False 813.00 1502 93.22800 1722 2935 2 chr2D.!!$F4 1213
6 TraesCS2A01G089900 chr2D 37911080 37912985 1905 False 263.75 497 89.37925 1284 2461 4 chr2D.!!$F3 1177
7 TraesCS2A01G089900 chr2B 66355319 66356926 1607 False 1999.00 1999 89.31200 579 2197 1 chr2B.!!$F1 1618
8 TraesCS2A01G089900 chr2B 66476863 66477468 605 False 784.00 784 90.62500 1731 2315 1 chr2B.!!$F3 584
9 TraesCS2A01G089900 chr2B 770581752 770582333 581 True 774.00 774 90.90900 2 582 1 chr2B.!!$R1 580
10 TraesCS2A01G089900 chr2B 66414057 66414760 703 False 593.00 593 82.16700 2103 2821 1 chr2B.!!$F2 718
11 TraesCS2A01G089900 chr7A 54872066 54872639 573 False 861.00 861 93.64300 2 582 1 chr7A.!!$F1 580
12 TraesCS2A01G089900 chr7A 142489185 142489771 586 False 798.00 798 91.36200 2 590 1 chr7A.!!$F2 588
13 TraesCS2A01G089900 chr5A 556723523 556724108 585 True 839.00 839 92.76100 2 582 1 chr5A.!!$R1 580
14 TraesCS2A01G089900 chr6D 60456202 60456798 596 True 835.00 835 92.20600 2 590 1 chr6D.!!$R1 588
15 TraesCS2A01G089900 chr4B 66878922 66879504 582 False 828.00 828 92.21700 2 590 1 chr4B.!!$F1 588
16 TraesCS2A01G089900 chr5B 695807743 695808330 587 False 822.00 822 92.24300 4 582 1 chr5B.!!$F2 578
17 TraesCS2A01G089900 chr6A 12373279 12373878 599 True 821.00 821 91.70800 2 590 1 chr6A.!!$R1 588
18 TraesCS2A01G089900 chr6B 5039964 5040533 569 False 706.00 706 89.02200 2 580 1 chr6B.!!$F1 578
19 TraesCS2A01G089900 chr3A 742055668 742056228 560 True 706.00 706 89.11600 2 588 1 chr3A.!!$R1 586

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
820 897 0.609957 CATGTCACACCCACAGCCAT 60.61 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 5715 0.036388 CACCGTGCAGTCACCCTAAT 60.036 55.0 0.0 0.0 40.04 1.73 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
166 196 3.991051 CATACCGGCGGCGATCCT 61.991 66.667 34.49 14.05 0.00 3.24
296 334 1.470051 GAGAGGGAGAGAAAGCGAGT 58.530 55.000 0.00 0.00 0.00 4.18
297 335 1.134175 GAGAGGGAGAGAAAGCGAGTG 59.866 57.143 0.00 0.00 0.00 3.51
298 336 1.178276 GAGGGAGAGAAAGCGAGTGA 58.822 55.000 0.00 0.00 0.00 3.41
299 337 1.134175 GAGGGAGAGAAAGCGAGTGAG 59.866 57.143 0.00 0.00 0.00 3.51
360 431 2.777692 GAGGAGAGAGGGAGAGAGAGAA 59.222 54.545 0.00 0.00 0.00 2.87
364 435 1.006813 AGAGGGAGAGAGAGAAGCCA 58.993 55.000 0.00 0.00 0.00 4.75
471 543 2.480073 GCGGCAACACAAATATGATGCT 60.480 45.455 7.75 0.00 35.79 3.79
492 564 7.447374 TGCTTCGGAAAAATAAAAGAGATGA 57.553 32.000 0.00 0.00 0.00 2.92
590 664 6.552629 GGGCTCTTTTGCTAGTGTTAATAAC 58.447 40.000 0.00 0.00 0.00 1.89
605 682 9.403583 AGTGTTAATAACGGACATAATTCCATT 57.596 29.630 0.00 0.00 35.04 3.16
625 702 0.674895 GATTTCTCAGCCTGCCACGT 60.675 55.000 0.00 0.00 0.00 4.49
658 735 2.169832 AAGTGCGAGCTGCTTTCTTA 57.830 45.000 2.53 0.00 46.63 2.10
660 737 2.072298 AGTGCGAGCTGCTTTCTTAAG 58.928 47.619 2.53 0.00 46.63 1.85
743 820 4.439253 AATTATTTCCTTCCCTCCCGAG 57.561 45.455 0.00 0.00 0.00 4.63
745 822 1.636769 ATTTCCTTCCCTCCCGAGCC 61.637 60.000 0.00 0.00 0.00 4.70
746 823 4.798682 TCCTTCCCTCCCGAGCCC 62.799 72.222 0.00 0.00 0.00 5.19
810 887 4.741781 GTGCGCGCCATGTCACAC 62.742 66.667 30.77 13.79 0.00 3.82
820 897 0.609957 CATGTCACACCCACAGCCAT 60.610 55.000 0.00 0.00 0.00 4.40
846 929 1.981495 CCACCCTCACTTTCTTCTCCT 59.019 52.381 0.00 0.00 0.00 3.69
860 943 4.631234 TCTTCTCCTGGCTTTAATCCCTA 58.369 43.478 0.00 0.00 0.00 3.53
944 1027 2.971430 TGCGAGCGAGACATCTATAC 57.029 50.000 0.00 0.00 0.00 1.47
964 1051 3.567397 ACTTCTATACACGCTCCTCCAT 58.433 45.455 0.00 0.00 0.00 3.41
1088 1179 4.344865 GCCTTTCTCCCCGCACCA 62.345 66.667 0.00 0.00 0.00 4.17
1090 1181 2.750350 CTTTCTCCCCGCACCAGT 59.250 61.111 0.00 0.00 0.00 4.00
1132 1223 2.034879 CCAAAGTCGCCGCATGTCT 61.035 57.895 0.00 0.00 0.00 3.41
1133 1224 1.421485 CAAAGTCGCCGCATGTCTC 59.579 57.895 0.00 0.00 0.00 3.36
1134 1225 2.094659 AAAGTCGCCGCATGTCTCG 61.095 57.895 0.00 0.00 0.00 4.04
1439 1535 1.229428 ACCATTCTTGACAGTGTGCG 58.771 50.000 0.00 0.00 0.00 5.34
1441 1537 1.069703 CCATTCTTGACAGTGTGCGTG 60.070 52.381 0.00 0.00 0.00 5.34
1442 1538 0.588252 ATTCTTGACAGTGTGCGTGC 59.412 50.000 0.00 0.00 0.00 5.34
1443 1539 0.742635 TTCTTGACAGTGTGCGTGCA 60.743 50.000 0.00 0.00 0.00 4.57
1444 1540 1.010797 CTTGACAGTGTGCGTGCAC 60.011 57.895 17.72 17.72 46.33 4.57
1453 1549 3.268603 TGCGTGCACGGTGTTGAG 61.269 61.111 37.47 10.49 40.23 3.02
1635 1731 1.230324 GACCAGGTGAAGTTGCAGAC 58.770 55.000 0.00 0.00 0.00 3.51
1654 1750 2.170607 GACAATCTTGCCTAGGCCAGTA 59.829 50.000 30.81 18.12 41.09 2.74
1718 1817 5.335740 GCGGTGACTTATAGCTAGCTTATGA 60.336 44.000 24.88 4.69 0.00 2.15
2049 2248 4.893424 TCCAGGAGAAAAACAAAGTTCG 57.107 40.909 0.00 0.00 0.00 3.95
2072 2272 4.109050 GAGTAAGCTCGTGAATCCTCTTG 58.891 47.826 0.00 0.00 31.39 3.02
2108 2309 7.687941 TTAGTTAGATCCAAGAGCAAAAAGG 57.312 36.000 0.00 0.00 0.00 3.11
2119 2323 4.148079 AGAGCAAAAAGGAGAGGGAAAAG 58.852 43.478 0.00 0.00 0.00 2.27
2122 2326 4.342378 AGCAAAAAGGAGAGGGAAAAGAAC 59.658 41.667 0.00 0.00 0.00 3.01
2144 2351 3.557595 CGAACAAAGTTCAGAGTTGCTCT 59.442 43.478 10.15 0.00 42.11 4.09
2280 2491 4.700692 TCACTCACGTTTAGCTATGAGACT 59.299 41.667 22.86 4.75 40.92 3.24
2316 2527 2.203625 GCCACCACCCCAATGTGT 60.204 61.111 0.00 0.00 34.35 3.72
2320 2531 1.118838 CACCACCCCAATGTGTTTGT 58.881 50.000 0.00 0.00 34.35 2.83
2324 2542 3.970640 ACCACCCCAATGTGTTTGTTTAT 59.029 39.130 0.00 0.00 34.35 1.40
2328 2546 5.631512 CACCCCAATGTGTTTGTTTATTACG 59.368 40.000 0.00 0.00 33.15 3.18
2335 2553 5.462405 TGTGTTTGTTTATTACGAATGCCC 58.538 37.500 0.00 0.00 32.79 5.36
2364 2585 9.517609 CTTACTAATCTGTACTTATTTGCGACT 57.482 33.333 0.00 0.00 0.00 4.18
2368 2589 3.767673 TCTGTACTTATTTGCGACTCCCT 59.232 43.478 0.00 0.00 0.00 4.20
2386 5698 5.068215 TCCCTGTTCTTCCCAAAACAATA 57.932 39.130 0.00 0.00 35.13 1.90
2387 5699 4.830600 TCCCTGTTCTTCCCAAAACAATAC 59.169 41.667 0.00 0.00 35.13 1.89
2388 5700 4.832823 CCCTGTTCTTCCCAAAACAATACT 59.167 41.667 0.00 0.00 35.13 2.12
2389 5701 5.048013 CCCTGTTCTTCCCAAAACAATACTC 60.048 44.000 0.00 0.00 35.13 2.59
2390 5702 5.048013 CCTGTTCTTCCCAAAACAATACTCC 60.048 44.000 0.00 0.00 35.13 3.85
2403 5715 4.359105 ACAATACTCCACTAGCAACCCTA 58.641 43.478 0.00 0.00 0.00 3.53
2558 5899 3.820467 ACGAATCTTGATGCAAGGACAAA 59.180 39.130 7.27 0.00 41.33 2.83
2562 5903 3.916761 TCTTGATGCAAGGACAAAATGC 58.083 40.909 7.27 0.00 41.33 3.56
2572 5913 2.158385 AGGACAAAATGCCAACACCCTA 60.158 45.455 0.00 0.00 0.00 3.53
2589 5930 3.518303 ACCCTACCAAATTAGTTCGCTCT 59.482 43.478 0.00 0.00 0.00 4.09
2658 6000 3.555956 GCGAGACAAAAGAAAGAGTGACA 59.444 43.478 0.00 0.00 0.00 3.58
2664 6006 6.599244 AGACAAAAGAAAGAGTGACACATTCA 59.401 34.615 8.59 0.00 0.00 2.57
2750 6092 1.767388 CGTGTGTTCTCTTCGTCGC 59.233 57.895 0.00 0.00 0.00 5.19
2767 6109 2.113139 CCGGCAAGGGTTGTGACT 59.887 61.111 0.00 0.00 35.97 3.41
2783 6125 3.632145 TGTGACTTTTTCCTTCCTTCTGC 59.368 43.478 0.00 0.00 0.00 4.26
2806 6148 1.450211 CGGTCACAAGGGTGGAAGT 59.550 57.895 0.00 0.00 45.32 3.01
2855 6199 1.575922 CAAGGTGTCGTCGTCGGTA 59.424 57.895 1.55 0.00 37.69 4.02
2872 6216 1.306997 TAGAGGAGGGCAAGGGGTG 60.307 63.158 0.00 0.00 0.00 4.61
2907 6251 7.202056 ATCAGCATTGAGAGAAGATCAGATCTT 60.202 37.037 23.45 23.45 43.58 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 196 2.490115 GTGGGGTGTTTATTTGCGATCA 59.510 45.455 0.00 0.00 0.00 2.92
170 200 5.449451 GGTTATAGTGGGGTGTTTATTTGCG 60.449 44.000 0.00 0.00 0.00 4.85
282 314 2.088423 TCTCTCACTCGCTTTCTCTCC 58.912 52.381 0.00 0.00 0.00 3.71
296 334 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
297 335 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
298 336 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
299 337 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
360 431 9.297037 GTGTTAAATATGGTTAATCCTATGGCT 57.703 33.333 0.00 0.00 37.07 4.75
364 435 9.841295 ACGTGTGTTAAATATGGTTAATCCTAT 57.159 29.630 0.00 0.00 37.07 2.57
471 543 8.404107 AGGTTCATCTCTTTTATTTTTCCGAA 57.596 30.769 0.00 0.00 0.00 4.30
492 564 4.974645 TCACTCAAGACCACAATAGGTT 57.025 40.909 0.00 0.00 43.38 3.50
590 664 7.263100 TGAGAAATCAATGGAATTATGTCCG 57.737 36.000 0.00 0.00 40.96 4.79
605 682 0.674581 CGTGGCAGGCTGAGAAATCA 60.675 55.000 20.86 2.99 0.00 2.57
625 702 1.978097 CGCACTTAACACGCGTACTTA 59.022 47.619 13.44 8.02 43.86 2.24
634 711 0.868406 AAGCAGCTCGCACTTAACAC 59.132 50.000 0.00 0.00 46.13 3.32
641 718 2.517321 CTTAAGAAAGCAGCTCGCAC 57.483 50.000 0.00 2.73 46.13 5.34
658 735 0.393808 AACGGGGTATGCAATCGCTT 60.394 50.000 0.00 0.00 39.64 4.68
660 737 1.263217 CTTAACGGGGTATGCAATCGC 59.737 52.381 0.00 0.00 39.24 4.58
743 820 3.352990 TAAGCAATGGACCGGGGGC 62.353 63.158 6.32 0.00 0.00 5.80
745 822 1.823899 GCTAAGCAATGGACCGGGG 60.824 63.158 6.32 0.00 0.00 5.73
746 823 1.823899 GGCTAAGCAATGGACCGGG 60.824 63.158 6.32 0.00 0.00 5.73
747 824 1.077787 TGGCTAAGCAATGGACCGG 60.078 57.895 0.00 0.00 0.00 5.28
748 825 2.397751 CTGGCTAAGCAATGGACCG 58.602 57.895 0.00 0.00 0.00 4.79
810 887 2.124151 GGTGGCTATGGCTGTGGG 60.124 66.667 0.00 0.00 38.73 4.61
820 897 0.690762 GAAAGTGAGGGTGGTGGCTA 59.309 55.000 0.00 0.00 0.00 3.93
846 929 1.766496 CCGGTCTAGGGATTAAAGCCA 59.234 52.381 0.00 0.00 0.00 4.75
944 1027 3.365465 CGATGGAGGAGCGTGTATAGAAG 60.365 52.174 0.00 0.00 0.00 2.85
1110 1201 2.690778 ATGCGGCGACTTTGGCTTC 61.691 57.895 12.98 0.00 0.00 3.86
1116 1207 2.094659 CGAGACATGCGGCGACTTT 61.095 57.895 12.98 0.00 0.00 2.66
1188 1279 2.185350 CTGTCCCTGCTAGGCGTG 59.815 66.667 0.00 0.00 32.73 5.34
1439 1535 1.714899 AACAGCTCAACACCGTGCAC 61.715 55.000 6.82 6.82 0.00 4.57
1441 1537 1.009675 CAACAGCTCAACACCGTGC 60.010 57.895 0.00 0.00 0.00 5.34
1442 1538 1.195448 GATCAACAGCTCAACACCGTG 59.805 52.381 0.00 0.00 0.00 4.94
1443 1539 1.202639 TGATCAACAGCTCAACACCGT 60.203 47.619 0.00 0.00 0.00 4.83
1444 1540 1.511850 TGATCAACAGCTCAACACCG 58.488 50.000 0.00 0.00 0.00 4.94
1453 1549 1.389609 CCCAGCCCATGATCAACAGC 61.390 60.000 0.00 2.54 0.00 4.40
1596 1692 1.993369 GCCGGCGAAATCAAGGAAGG 61.993 60.000 12.58 0.00 0.00 3.46
1618 1714 1.679139 TTGTCTGCAACTTCACCTGG 58.321 50.000 0.00 0.00 0.00 4.45
1635 1731 3.498774 ATACTGGCCTAGGCAAGATTG 57.501 47.619 39.71 18.49 44.65 2.67
1706 1805 5.128205 TGCATGACAATTCATAAGCTAGCT 58.872 37.500 12.68 12.68 40.79 3.32
1707 1806 5.428496 TGCATGACAATTCATAAGCTAGC 57.572 39.130 6.62 6.62 40.79 3.42
1718 1817 6.203338 GGAATGTTTCAACTTGCATGACAATT 59.797 34.615 6.60 0.00 37.72 2.32
2049 2248 2.691011 AGAGGATTCACGAGCTTACTCC 59.309 50.000 0.00 0.00 40.03 3.85
2097 2298 3.884037 TTTCCCTCTCCTTTTTGCTCT 57.116 42.857 0.00 0.00 0.00 4.09
2107 2308 3.121738 TGTTCGTTCTTTTCCCTCTCC 57.878 47.619 0.00 0.00 0.00 3.71
2108 2309 4.575236 ACTTTGTTCGTTCTTTTCCCTCTC 59.425 41.667 0.00 0.00 0.00 3.20
2119 2323 4.029043 GCAACTCTGAACTTTGTTCGTTC 58.971 43.478 6.05 0.00 40.79 3.95
2122 2326 3.557595 AGAGCAACTCTGAACTTTGTTCG 59.442 43.478 0.00 2.22 39.62 3.95
2280 2491 2.098233 GCAGTTGGCTAGCGCGTAA 61.098 57.895 8.43 0.00 40.25 3.18
2316 2527 4.767928 AGGTGGGCATTCGTAATAAACAAA 59.232 37.500 0.00 0.00 0.00 2.83
2320 2531 5.747342 AGTAAGGTGGGCATTCGTAATAAA 58.253 37.500 0.00 0.00 0.00 1.40
2324 2542 4.822685 TTAGTAAGGTGGGCATTCGTAA 57.177 40.909 0.00 0.00 0.00 3.18
2328 2546 4.781934 ACAGATTAGTAAGGTGGGCATTC 58.218 43.478 0.00 0.00 0.00 2.67
2335 2553 8.540492 CGCAAATAAGTACAGATTAGTAAGGTG 58.460 37.037 0.00 0.00 0.00 4.00
2364 2585 3.390175 TTGTTTTGGGAAGAACAGGGA 57.610 42.857 0.00 0.00 37.12 4.20
2368 2589 5.300792 GTGGAGTATTGTTTTGGGAAGAACA 59.699 40.000 0.00 0.00 34.22 3.18
2386 5698 3.967987 CCTAATAGGGTTGCTAGTGGAGT 59.032 47.826 0.00 0.00 0.00 3.85
2387 5699 4.608948 CCTAATAGGGTTGCTAGTGGAG 57.391 50.000 0.00 0.00 0.00 3.86
2403 5715 0.036388 CACCGTGCAGTCACCCTAAT 60.036 55.000 0.00 0.00 40.04 1.73
2505 5818 1.790755 TGCAGACGTCTTTGCGTTAT 58.209 45.000 17.26 0.00 45.79 1.89
2558 5899 2.390225 TTTGGTAGGGTGTTGGCATT 57.610 45.000 0.00 0.00 0.00 3.56
2562 5903 4.155280 CGAACTAATTTGGTAGGGTGTTGG 59.845 45.833 0.00 0.00 0.00 3.77
2572 5913 5.163540 ACGATAGAGAGCGAACTAATTTGGT 60.164 40.000 0.00 0.00 38.04 3.67
2589 5930 3.504520 TGTAGTCACACAAGCACGATAGA 59.495 43.478 0.00 0.00 41.38 1.98
2658 6000 4.021104 TGAGGATGTTCTCGAAGTGAATGT 60.021 41.667 0.00 0.00 42.10 2.71
2664 6006 1.202582 CGGTGAGGATGTTCTCGAAGT 59.797 52.381 0.00 0.00 36.61 3.01
2750 6092 1.106944 AAAGTCACAACCCTTGCCGG 61.107 55.000 0.00 0.00 0.00 6.13
2761 6103 3.632145 GCAGAAGGAAGGAAAAAGTCACA 59.368 43.478 0.00 0.00 0.00 3.58
2767 6109 2.597455 CTGGGCAGAAGGAAGGAAAAA 58.403 47.619 0.00 0.00 0.00 1.94
2783 6125 3.953775 ACCCTTGTGACCGCTGGG 61.954 66.667 0.00 0.00 43.26 4.45
2806 6148 3.325870 CACTCAAGATGACAAACGGCTA 58.674 45.455 0.00 0.00 0.00 3.93
2855 6199 2.612115 CACCCCTTGCCCTCCTCT 60.612 66.667 0.00 0.00 0.00 3.69
2872 6216 0.034186 TCAATGCTGATCACACCCCC 60.034 55.000 0.00 0.00 0.00 5.40
2907 6251 4.842574 TGGAATTGGACATTTCTCGATCA 58.157 39.130 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.