Multiple sequence alignment - TraesCS3A01G112100

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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 TraesCS3A01G112100 chr3A 100.000 4179 0 0 1 4179 79399501 79403679 0.000000e+00 7718.0
1 TraesCS3A01G112100 chr3A 78.680 394 41 18 2402 2793 585936700 585936348 5.440000e-54 222.0
2 TraesCS3A01G112100 chr3D 95.932 2188 79 6 1996 4179 67711629 67713810 0.000000e+00 3539.0
3 TraesCS3A01G112100 chr3D 91.182 1168 50 21 274 1418 67709753 67710890 0.000000e+00 1537.0
4 TraesCS3A01G112100 chr3D 90.893 560 28 9 1419 1959 67710938 67711493 0.000000e+00 730.0
5 TraesCS3A01G112100 chr3D 90.253 277 24 3 1 275 67697421 67697696 3.970000e-95 359.0
6 TraesCS3A01G112100 chr3B 91.316 2234 124 32 1418 3614 114145427 114143227 0.000000e+00 2987.0
7 TraesCS3A01G112100 chr3B 86.293 1284 90 38 188 1418 114146724 114145474 0.000000e+00 1317.0
8 TraesCS3A01G112100 chr3B 95.630 595 26 0 3585 4179 114143226 114142632 0.000000e+00 955.0
9 TraesCS3A01G112100 chr3B 88.587 184 17 4 4 184 114148981 114148799 1.960000e-53 220.0
10 TraesCS3A01G112100 chr2B 88.311 1326 87 21 2036 3321 113326862 113325565 0.000000e+00 1528.0
11 TraesCS3A01G112100 chr2B 87.461 638 38 20 785 1419 113328099 113327501 0.000000e+00 697.0
12 TraesCS3A01G112100 chr2B 90.576 382 23 6 1401 1769 113327477 113327096 1.040000e-135 494.0
13 TraesCS3A01G112100 chr2D 88.115 1321 94 20 2036 3317 74280487 74279191 0.000000e+00 1511.0
14 TraesCS3A01G112100 chr2D 93.555 481 26 5 939 1418 74281995 74281519 0.000000e+00 712.0
15 TraesCS3A01G112100 chr2D 88.220 382 30 5 1401 1769 74281494 74281115 3.830000e-120 442.0
16 TraesCS3A01G112100 chr2A 84.175 891 68 27 2685 3524 73555062 73554194 0.000000e+00 797.0
17 TraesCS3A01G112100 chr2A 93.763 481 25 5 939 1418 73557078 73556602 0.000000e+00 717.0
18 TraesCS3A01G112100 chr2A 92.994 471 31 2 2042 2510 73555695 73555225 0.000000e+00 686.0
19 TraesCS3A01G112100 chr2A 89.529 382 27 7 1401 1769 73556577 73556196 4.890000e-129 472.0
20 TraesCS3A01G112100 chr2A 77.586 232 25 13 1805 2022 73555979 73555761 9.490000e-22 115.0
21 TraesCS3A01G112100 chr6B 78.967 813 114 35 2146 2939 116891589 116892363 6.240000e-138 501.0
22 TraesCS3A01G112100 chr6B 78.046 829 119 41 2146 2939 28008629 28009429 8.180000e-127 464.0
23 TraesCS3A01G112100 chr4A 74.457 599 77 46 2396 2961 151642121 151642676 5.520000e-44 189.0
24 TraesCS3A01G112100 chr4A 96.721 61 2 0 339 399 662286495 662286435 7.390000e-18 102.0
25 TraesCS3A01G112100 chr6D 95.652 69 3 0 331 399 78352774 78352706 1.230000e-20 111.0
26 TraesCS3A01G112100 chr5D 93.056 72 5 0 329 400 478164177 478164248 5.710000e-19 106.0
27 TraesCS3A01G112100 chr5A 96.774 62 2 0 338 399 594323244 594323305 2.060000e-18 104.0
28 TraesCS3A01G112100 chr5A 91.667 72 5 1 329 399 382114854 382114925 9.560000e-17 99.0
29 TraesCS3A01G112100 chr5B 92.647 68 5 0 332 399 582391975 582392042 9.560000e-17 99.0
30 TraesCS3A01G112100 chr6A 91.304 69 6 0 331 399 94067117 94067049 1.240000e-15 95.3


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 TraesCS3A01G112100 chr3A 79399501 79403679 4178 False 7718.000000 7718 100.000000 1 4179 1 chr3A.!!$F1 4178
1 TraesCS3A01G112100 chr3D 67709753 67713810 4057 False 1935.333333 3539 92.669000 274 4179 3 chr3D.!!$F2 3905
2 TraesCS3A01G112100 chr3B 114142632 114148981 6349 True 1369.750000 2987 90.456500 4 4179 4 chr3B.!!$R1 4175
3 TraesCS3A01G112100 chr2B 113325565 113328099 2534 True 906.333333 1528 88.782667 785 3321 3 chr2B.!!$R1 2536
4 TraesCS3A01G112100 chr2D 74279191 74281995 2804 True 888.333333 1511 89.963333 939 3317 3 chr2D.!!$R1 2378
5 TraesCS3A01G112100 chr2A 73554194 73557078 2884 True 557.400000 797 87.609400 939 3524 5 chr2A.!!$R1 2585
6 TraesCS3A01G112100 chr6B 116891589 116892363 774 False 501.000000 501 78.967000 2146 2939 1 chr6B.!!$F2 793
7 TraesCS3A01G112100 chr6B 28008629 28009429 800 False 464.000000 464 78.046000 2146 2939 1 chr6B.!!$F1 793

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
542 2622 0.107654 CATTTCCTCCCAGTCCGTCC 60.108 60.0 0.0 0.0 0.0 4.79 F
599 2679 0.817634 ACCCCACACACATTGACACG 60.818 55.0 0.0 0.0 0.0 4.49 F
1969 4537 0.109532 CCATACCACACCACACCACA 59.890 55.0 0.0 0.0 0.0 4.17 F
1971 4539 0.109723 ATACCACACCACACCACACC 59.890 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 3816 0.602905 GGAAGACCACAACCCAGACG 60.603 60.000 0.00 0.0 35.97 4.18 R
2243 4973 1.212688 CCCACATTCTGGTATCCTGCA 59.787 52.381 0.00 0.0 38.60 4.41 R
3140 5956 0.440371 CCTTCTCGCGTTTCAAGCTC 59.560 55.000 5.77 0.0 0.00 4.09 R
3815 6683 1.032114 GTGGGGATTTCGCAGAAGGG 61.032 60.000 0.00 0.0 45.90 3.95 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
49 51 9.436957 TCTCTAATGACTGTTCAACTTTATTCC 57.563 33.333 0.00 0.00 34.61 3.01
52 54 5.319043 TGACTGTTCAACTTTATTCCCCT 57.681 39.130 0.00 0.00 0.00 4.79
83 86 5.957771 TGTCCAGGAGAATTGCTATTACT 57.042 39.130 0.00 0.00 0.00 2.24
84 87 5.918608 TGTCCAGGAGAATTGCTATTACTC 58.081 41.667 0.00 3.21 0.00 2.59
88 91 5.303971 CAGGAGAATTGCTATTACTCCCTG 58.696 45.833 22.71 17.69 45.53 4.45
92 95 3.753294 ATTGCTATTACTCCCTGTCCG 57.247 47.619 0.00 0.00 0.00 4.79
93 96 0.750850 TGCTATTACTCCCTGTCCGC 59.249 55.000 0.00 0.00 0.00 5.54
99 102 1.823169 TACTCCCTGTCCGCCACAAC 61.823 60.000 0.00 0.00 33.31 3.32
104 107 1.227823 CTGTCCGCCACAACCAGAA 60.228 57.895 0.00 0.00 33.31 3.02
107 110 2.590575 CCGCCACAACCAGAACGT 60.591 61.111 0.00 0.00 0.00 3.99
152 155 1.056700 ATCCCCTCCTTCCATGGTCG 61.057 60.000 12.58 3.79 0.00 4.79
181 184 3.615811 TCAGGGCTGGGAGGAGGT 61.616 66.667 0.00 0.00 0.00 3.85
226 2300 6.534079 GCTTTGCTAGATCCGTTACTCTAAAA 59.466 38.462 0.00 0.00 0.00 1.52
227 2301 7.064253 GCTTTGCTAGATCCGTTACTCTAAAAA 59.936 37.037 0.00 0.00 0.00 1.94
268 2342 6.544931 TCCATCCAATCTGATCTTGAACAATC 59.455 38.462 0.00 0.00 0.00 2.67
269 2343 6.320418 CCATCCAATCTGATCTTGAACAATCA 59.680 38.462 0.00 0.00 0.00 2.57
275 2349 5.005094 TCTGATCTTGAACAATCATGTGCA 58.995 37.500 0.00 0.00 43.63 4.57
315 2391 9.594478 TCAGAATATTTTTCTAGAATACGCACA 57.406 29.630 5.89 0.00 0.00 4.57
320 2396 3.984018 TTCTAGAATACGCACAAACGC 57.016 42.857 0.00 0.00 36.19 4.84
441 2521 6.727824 AATCAGTCTTTACTCGTTCCATTG 57.272 37.500 0.00 0.00 31.97 2.82
452 2532 5.734720 ACTCGTTCCATTGATTACAGTCAT 58.265 37.500 0.00 0.00 0.00 3.06
461 2541 7.833682 TCCATTGATTACAGTCATGGTGTATTT 59.166 33.333 8.97 2.36 32.92 1.40
462 2542 8.131100 CCATTGATTACAGTCATGGTGTATTTC 58.869 37.037 8.97 9.53 30.54 2.17
463 2543 7.624360 TTGATTACAGTCATGGTGTATTTCC 57.376 36.000 8.97 0.00 30.54 3.13
464 2544 6.957631 TGATTACAGTCATGGTGTATTTCCT 58.042 36.000 8.97 0.00 30.54 3.36
540 2620 1.831736 CTACATTTCCTCCCAGTCCGT 59.168 52.381 0.00 0.00 0.00 4.69
541 2621 0.613777 ACATTTCCTCCCAGTCCGTC 59.386 55.000 0.00 0.00 0.00 4.79
542 2622 0.107654 CATTTCCTCCCAGTCCGTCC 60.108 60.000 0.00 0.00 0.00 4.79
543 2623 1.614241 ATTTCCTCCCAGTCCGTCCG 61.614 60.000 0.00 0.00 0.00 4.79
599 2679 0.817634 ACCCCACACACATTGACACG 60.818 55.000 0.00 0.00 0.00 4.49
664 2773 4.131088 GTCGTGGCCTCCGAGGAC 62.131 72.222 19.33 16.79 46.38 3.85
719 2828 2.026301 GCCCCGAAGACGATCTCG 59.974 66.667 0.00 0.00 46.33 4.04
752 2882 1.533731 GGTTTTGGTTTCGCGATCAGA 59.466 47.619 10.88 1.48 0.00 3.27
931 3063 2.812619 CGAGCCCTCCCATTCTCCC 61.813 68.421 0.00 0.00 0.00 4.30
981 3119 0.884704 ATCTCTCTCTCGCTCGCTCC 60.885 60.000 0.00 0.00 0.00 4.70
1244 3382 2.366533 CTTCCTCGAGCAGTACAGGTA 58.633 52.381 6.99 0.00 0.00 3.08
1245 3383 2.502142 TCCTCGAGCAGTACAGGTAA 57.498 50.000 6.99 0.00 0.00 2.85
1246 3384 2.089980 TCCTCGAGCAGTACAGGTAAC 58.910 52.381 6.99 0.00 0.00 2.50
1247 3385 1.202154 CCTCGAGCAGTACAGGTAACG 60.202 57.143 6.99 0.00 46.39 3.18
1251 3391 1.808390 GCAGTACAGGTAACGCCCG 60.808 63.158 0.00 0.00 46.39 6.13
1258 3398 2.202756 GGTAACGCCCGCTCTCTG 60.203 66.667 0.00 0.00 0.00 3.35
1313 3456 1.202568 TGGCGATCCATGAGATGTGTC 60.203 52.381 0.00 0.00 37.47 3.67
1354 3497 2.234143 TGATTTGACCCGAATTGCACA 58.766 42.857 0.00 0.00 0.00 4.57
1384 3527 2.353579 GGGGTAATTCGTGTGATTTCCG 59.646 50.000 0.00 0.00 0.00 4.30
1408 3551 6.866770 CGTAGAAATCTGGTCTGTTTCAGTTA 59.133 38.462 0.00 0.00 35.00 2.24
1424 3620 7.925483 TGTTTCAGTTATTTTTGATCCACTTGG 59.075 33.333 0.00 0.00 0.00 3.61
1448 3645 4.706035 AGAAGTCTCATTCTGATCCATGC 58.294 43.478 0.00 0.00 38.12 4.06
1459 3657 4.279982 TCTGATCCATGCAGCCAAAAATA 58.720 39.130 0.00 0.00 33.45 1.40
1469 3667 3.500982 CAGCCAAAAATACATGTCCACG 58.499 45.455 0.00 0.00 0.00 4.94
1677 3883 9.645128 AAATCCATCCTGTTTACAATATGATGA 57.355 29.630 0.00 1.99 31.98 2.92
1827 4363 3.503363 TGGCAGCTTGAAAATGAGTACTG 59.497 43.478 0.00 0.00 0.00 2.74
1848 4384 4.843728 TGTCCACTATGGTTCTTGGAATC 58.156 43.478 0.00 0.00 39.86 2.52
1858 4394 9.413734 CTATGGTTCTTGGAATCTTTTTATCCT 57.586 33.333 0.00 0.00 34.24 3.24
1865 4401 9.401058 TCTTGGAATCTTTTTATCCTGAGATTC 57.599 33.333 13.70 13.70 46.98 2.52
1892 4428 2.163412 TGTTGAAACAGTGTTCTGGCAC 59.837 45.455 9.40 3.28 45.14 5.01
1894 4430 1.742831 TGAAACAGTGTTCTGGCACAC 59.257 47.619 9.40 0.00 46.48 3.82
1953 4521 7.611855 ACAAGATAACTTAGCTTAGCAAACCAT 59.388 33.333 7.07 0.00 31.74 3.55
1963 4531 1.616159 AGCAAACCATACCACACCAC 58.384 50.000 0.00 0.00 0.00 4.16
1964 4532 1.133637 AGCAAACCATACCACACCACA 60.134 47.619 0.00 0.00 0.00 4.17
1965 4533 1.000717 GCAAACCATACCACACCACAC 60.001 52.381 0.00 0.00 0.00 3.82
1966 4534 1.611491 CAAACCATACCACACCACACC 59.389 52.381 0.00 0.00 0.00 4.16
1967 4535 0.847373 AACCATACCACACCACACCA 59.153 50.000 0.00 0.00 0.00 4.17
1968 4536 0.109723 ACCATACCACACCACACCAC 59.890 55.000 0.00 0.00 0.00 4.16
1969 4537 0.109532 CCATACCACACCACACCACA 59.890 55.000 0.00 0.00 0.00 4.17
1970 4538 1.234821 CATACCACACCACACCACAC 58.765 55.000 0.00 0.00 0.00 3.82
1971 4539 0.109723 ATACCACACCACACCACACC 59.890 55.000 0.00 0.00 0.00 4.16
1972 4540 1.272554 TACCACACCACACCACACCA 61.273 55.000 0.00 0.00 0.00 4.17
1973 4541 2.118404 CCACACCACACCACACCAC 61.118 63.158 0.00 0.00 0.00 4.16
1985 4553 3.504134 CACCACACCACGATATTTTTCCA 59.496 43.478 0.00 0.00 0.00 3.53
2113 4843 4.807303 GCCATTATGCCCTGTGCTTCTATA 60.807 45.833 0.00 0.00 42.00 1.31
2115 4845 5.769662 CCATTATGCCCTGTGCTTCTATAAA 59.230 40.000 0.00 0.00 42.00 1.40
2178 4908 6.712547 GCTTCCTAAAGGTGCTCATAATACAT 59.287 38.462 8.68 0.00 36.34 2.29
2243 4973 8.774546 TGTCTGAGACTTCTATGGATCTTATT 57.225 34.615 14.42 0.00 33.15 1.40
2359 5090 3.518303 ACTGTATTCCCAACTACCCAGAC 59.482 47.826 0.00 0.00 0.00 3.51
2462 5193 5.316167 AGAAATGCACACCTGAATGTAAGA 58.684 37.500 0.00 0.00 0.00 2.10
2565 5296 5.555966 AGTTGGTTGGACAAAAACATTGTT 58.444 33.333 11.90 0.00 31.96 2.83
2636 5413 2.039418 AGCCAGTCGCAGGATACAATA 58.961 47.619 0.00 0.00 41.38 1.90
2675 5452 9.944376 GGATATTACAATCTAGATGCCTTAACA 57.056 33.333 5.86 0.00 0.00 2.41
2681 5458 6.989169 ACAATCTAGATGCCTTAACATGACTC 59.011 38.462 5.86 0.00 0.00 3.36
2795 5575 6.676189 TGGATATATGGTCCTAATGTATGGCA 59.324 38.462 9.56 0.00 36.68 4.92
2799 5596 7.765695 ATATGGTCCTAATGTATGGCAAAAG 57.234 36.000 0.00 0.00 0.00 2.27
2884 5684 3.747099 CAGTTATGCTGCTGTTACCAC 57.253 47.619 0.00 0.00 38.52 4.16
2895 5696 4.377021 TGCTGTTACCACTAAACTGAGTG 58.623 43.478 0.00 0.00 45.43 3.51
2986 5787 4.750098 ACACGGAATCTTTAAGTGTCACAG 59.250 41.667 5.62 0.00 41.55 3.66
3140 5956 5.238583 AGTTCATAGAAAAGGTTGTCTCCG 58.761 41.667 0.00 0.00 0.00 4.63
3159 5975 0.440371 GAGCTTGAAACGCGAGAAGG 59.560 55.000 15.93 0.00 0.00 3.46
3204 6020 5.998363 ACTTACTCCTTTCTGCTAGTTTTGG 59.002 40.000 0.00 0.00 0.00 3.28
3220 6038 6.783708 AGTTTTGGTTTGGTTCAGTGATAA 57.216 33.333 0.00 0.00 0.00 1.75
3300 6124 7.276218 TGTGAAAAATCTGAAAGCTGTTTTGAG 59.724 33.333 0.00 0.00 32.03 3.02
3362 6191 4.901868 ACACGTGGTGGTAATGTATCTTT 58.098 39.130 21.57 0.00 37.94 2.52
3425 6254 8.370182 ACTTGCATACTCAAATGGAAAATTTCT 58.630 29.630 5.65 0.00 36.85 2.52
3480 6311 4.456911 ACTGCACACACATTTATTCTGGAG 59.543 41.667 0.00 0.00 0.00 3.86
3554 6385 6.536941 GCTTCTTCTTGATAGTACAAAGGAGG 59.463 42.308 0.00 0.00 0.00 4.30
3691 6559 0.668401 TCGACGACAGTAGCGACTCA 60.668 55.000 0.00 0.00 31.73 3.41
3758 6626 2.889988 CGGCGGCGATCATCAACA 60.890 61.111 29.19 0.00 0.00 3.33
3805 6673 1.999051 CGCGACGAGGAAAATCCAG 59.001 57.895 0.00 0.00 39.61 3.86
3815 6683 1.468914 GGAAAATCCAGTCCGTCAAGC 59.531 52.381 0.00 0.00 36.28 4.01
3824 6692 3.121030 CCGTCAAGCCCTTCTGCG 61.121 66.667 0.00 0.00 36.02 5.18
3826 6694 1.667830 CGTCAAGCCCTTCTGCGAA 60.668 57.895 0.00 0.00 36.02 4.70
4130 6998 0.251832 ACAGACTCACCTCCACCGAT 60.252 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.647918 AGAGACTGATATATTGACTAGACCAAA 57.352 33.333 0.00 0.00 0.00 3.28
32 34 5.077564 GGAAGGGGAATAAAGTTGAACAGT 58.922 41.667 0.00 0.00 0.00 3.55
41 43 5.163550 GGACAAATTCGGAAGGGGAATAAAG 60.164 44.000 0.00 0.00 33.16 1.85
45 47 2.042433 TGGACAAATTCGGAAGGGGAAT 59.958 45.455 0.00 0.00 35.71 3.01
48 50 1.463674 CTGGACAAATTCGGAAGGGG 58.536 55.000 0.00 0.00 0.00 4.79
49 51 1.004277 TCCTGGACAAATTCGGAAGGG 59.996 52.381 0.00 0.00 0.00 3.95
52 54 3.780804 TTCTCCTGGACAAATTCGGAA 57.219 42.857 0.00 0.00 0.00 4.30
83 86 3.948719 GGTTGTGGCGGACAGGGA 61.949 66.667 0.00 0.00 35.44 4.20
84 87 4.263572 TGGTTGTGGCGGACAGGG 62.264 66.667 0.00 0.00 35.44 4.45
88 91 2.604174 CGTTCTGGTTGTGGCGGAC 61.604 63.158 0.00 0.00 0.00 4.79
92 95 1.265905 CCTTTACGTTCTGGTTGTGGC 59.734 52.381 0.00 0.00 0.00 5.01
93 96 1.877443 CCCTTTACGTTCTGGTTGTGG 59.123 52.381 0.00 0.00 0.00 4.17
99 102 1.900486 ACTCCTCCCTTTACGTTCTGG 59.100 52.381 0.00 0.00 0.00 3.86
104 107 2.454538 CAGGTACTCCTCCCTTTACGT 58.545 52.381 0.00 0.00 43.07 3.57
107 110 1.272872 ACGCAGGTACTCCTCCCTTTA 60.273 52.381 0.00 0.00 43.07 1.85
228 2302 9.824216 AGATTGGATGGAATATTGAGAATGAAT 57.176 29.630 0.00 0.00 0.00 2.57
229 2303 9.074576 CAGATTGGATGGAATATTGAGAATGAA 57.925 33.333 0.00 0.00 0.00 2.57
230 2304 8.442374 TCAGATTGGATGGAATATTGAGAATGA 58.558 33.333 0.00 0.00 0.00 2.57
231 2305 8.631480 TCAGATTGGATGGAATATTGAGAATG 57.369 34.615 0.00 0.00 0.00 2.67
232 2306 9.463902 GATCAGATTGGATGGAATATTGAGAAT 57.536 33.333 0.00 0.00 0.00 2.40
233 2307 8.666821 AGATCAGATTGGATGGAATATTGAGAA 58.333 33.333 0.00 0.00 0.00 2.87
234 2308 8.215954 AGATCAGATTGGATGGAATATTGAGA 57.784 34.615 0.00 0.00 0.00 3.27
235 2309 8.731605 CAAGATCAGATTGGATGGAATATTGAG 58.268 37.037 0.00 0.00 0.00 3.02
236 2310 8.442374 TCAAGATCAGATTGGATGGAATATTGA 58.558 33.333 0.00 0.00 0.00 2.57
237 2311 8.631480 TCAAGATCAGATTGGATGGAATATTG 57.369 34.615 0.00 0.00 0.00 1.90
238 2312 9.075678 GTTCAAGATCAGATTGGATGGAATATT 57.924 33.333 0.00 0.00 0.00 1.28
239 2313 8.222637 TGTTCAAGATCAGATTGGATGGAATAT 58.777 33.333 0.00 0.00 0.00 1.28
251 2325 5.650703 TGCACATGATTGTTCAAGATCAGAT 59.349 36.000 0.00 0.00 35.89 2.90
268 2342 4.082625 TGACTAAAAGATGGCTTGCACATG 60.083 41.667 0.00 0.00 33.79 3.21
269 2343 4.081406 TGACTAAAAGATGGCTTGCACAT 58.919 39.130 0.00 0.00 33.79 3.21
315 2391 5.955488 AGAGAGTATATGATATGCGCGTTT 58.045 37.500 7.78 0.00 0.00 3.60
317 2393 4.878971 AGAGAGAGTATATGATATGCGCGT 59.121 41.667 8.43 7.55 0.00 6.01
320 2396 8.888716 AGTTACAGAGAGAGTATATGATATGCG 58.111 37.037 0.00 0.00 0.00 4.73
441 2521 8.827677 GTTAGGAAATACACCATGACTGTAATC 58.172 37.037 0.00 3.34 0.00 1.75
599 2679 3.593247 GCTCGATGCAATGTGTGAC 57.407 52.632 0.00 0.00 42.31 3.67
765 2896 1.202302 ACATATCGAGTGTCACTGCGG 60.202 52.381 11.04 0.00 0.00 5.69
848 2979 4.267503 GGATCGGAGCGGACGGAC 62.268 72.222 0.00 0.00 0.00 4.79
931 3063 2.436115 GAAGCGGAAGGGGAACGG 60.436 66.667 0.00 0.00 0.00 4.44
1044 3182 1.805945 GATGTCGTCCCACTGCGTC 60.806 63.158 0.00 0.00 0.00 5.19
1244 3382 2.048127 GAACAGAGAGCGGGCGTT 60.048 61.111 0.00 0.00 0.00 4.84
1245 3383 4.070552 GGAACAGAGAGCGGGCGT 62.071 66.667 0.00 0.00 0.00 5.68
1246 3384 4.821589 GGGAACAGAGAGCGGGCG 62.822 72.222 0.00 0.00 0.00 6.13
1247 3385 4.475135 GGGGAACAGAGAGCGGGC 62.475 72.222 0.00 0.00 0.00 6.13
1251 3391 2.896443 CCGAGGGGAACAGAGAGC 59.104 66.667 0.00 0.00 34.06 4.09
1296 3439 1.413812 TGGGACACATCTCATGGATCG 59.586 52.381 0.00 0.00 26.79 3.69
1313 3456 2.163818 TCACGAAAAGCACTAGTGGG 57.836 50.000 23.95 0.00 33.98 4.61
1354 3497 2.704065 CACGAATTACCCCCATCCTACT 59.296 50.000 0.00 0.00 0.00 2.57
1384 3527 8.779354 ATAACTGAAACAGACCAGATTTCTAC 57.221 34.615 5.76 0.00 35.18 2.59
1408 3551 5.397360 ACTTCTCCCAAGTGGATCAAAAAT 58.603 37.500 0.00 0.00 44.07 1.82
1448 3645 3.190327 TCGTGGACATGTATTTTTGGCTG 59.810 43.478 0.00 0.00 0.00 4.85
1541 3747 1.599542 GGCTGTATTGTGCCGAATCTC 59.400 52.381 0.00 0.00 39.71 2.75
1610 3816 0.602905 GGAAGACCACAACCCAGACG 60.603 60.000 0.00 0.00 35.97 4.18
1655 3861 8.859236 AGATCATCATATTGTAAACAGGATGG 57.141 34.615 0.00 0.00 43.62 3.51
1677 3883 5.992217 GGTGTAGTTTCTGACACAAGAAGAT 59.008 40.000 7.40 0.00 46.34 2.40
1827 4363 5.104259 AGATTCCAAGAACCATAGTGGAC 57.896 43.478 2.45 0.00 40.96 4.02
1848 4384 9.918630 AACACAATTGAATCTCAGGATAAAAAG 57.081 29.630 13.59 0.00 0.00 2.27
1858 4394 6.974048 CACTGTTTCAACACAATTGAATCTCA 59.026 34.615 13.59 0.65 38.12 3.27
1865 4401 5.289193 CCAGAACACTGTTTCAACACAATTG 59.711 40.000 3.24 3.24 34.70 2.32
1953 4521 1.272554 TGGTGTGGTGTGGTGTGGTA 61.273 55.000 0.00 0.00 0.00 3.25
1963 4531 3.504134 TGGAAAAATATCGTGGTGTGGTG 59.496 43.478 0.00 0.00 0.00 4.17
1964 4532 3.504520 GTGGAAAAATATCGTGGTGTGGT 59.495 43.478 0.00 0.00 0.00 4.16
1965 4533 3.756434 AGTGGAAAAATATCGTGGTGTGG 59.244 43.478 0.00 0.00 0.00 4.17
1966 4534 5.181245 AGAAGTGGAAAAATATCGTGGTGTG 59.819 40.000 0.00 0.00 0.00 3.82
1967 4535 5.313712 AGAAGTGGAAAAATATCGTGGTGT 58.686 37.500 0.00 0.00 0.00 4.16
1968 4536 5.880054 AGAAGTGGAAAAATATCGTGGTG 57.120 39.130 0.00 0.00 0.00 4.17
1969 4537 6.894339 AAAGAAGTGGAAAAATATCGTGGT 57.106 33.333 0.00 0.00 0.00 4.16
1970 4538 7.593825 AGAAAAGAAGTGGAAAAATATCGTGG 58.406 34.615 0.00 0.00 0.00 4.94
1971 4539 9.543018 GTAGAAAAGAAGTGGAAAAATATCGTG 57.457 33.333 0.00 0.00 0.00 4.35
1972 4540 9.503399 AGTAGAAAAGAAGTGGAAAAATATCGT 57.497 29.630 0.00 0.00 0.00 3.73
1985 4553 8.365647 TGGAGTAAATCGAAGTAGAAAAGAAGT 58.634 33.333 0.00 0.00 0.00 3.01
2076 4806 6.648879 GCATAATGGCCTAAAATCCTACAA 57.351 37.500 3.32 0.00 0.00 2.41
2243 4973 1.212688 CCCACATTCTGGTATCCTGCA 59.787 52.381 0.00 0.00 38.60 4.41
2502 5233 7.321745 ACTTGAACTAACCTCACAAAAAGAG 57.678 36.000 0.00 0.00 0.00 2.85
2565 5296 8.853126 ACACAAACTGTTCACTAGTGTATACTA 58.147 33.333 21.99 0.00 37.01 1.82
2675 5452 8.200792 GGTCAAAGATTATAGTCAGTGAGTCAT 58.799 37.037 3.04 0.13 0.00 3.06
2681 5458 8.696374 TCCTAAGGTCAAAGATTATAGTCAGTG 58.304 37.037 0.00 0.00 0.00 3.66
2884 5684 3.702330 TCACACGACACACTCAGTTTAG 58.298 45.455 0.00 0.00 0.00 1.85
2895 5696 4.959631 TCGTTTCTTATTCACACGACAC 57.040 40.909 0.00 0.00 35.05 3.67
2986 5787 2.930682 GCATAAAGAGTGGAAGACCGTC 59.069 50.000 0.00 0.00 39.42 4.79
3079 5880 3.367292 CCATGACATTGTTACCACCTTGC 60.367 47.826 0.00 0.00 0.00 4.01
3140 5956 0.440371 CCTTCTCGCGTTTCAAGCTC 59.560 55.000 5.77 0.00 0.00 4.09
3159 5975 4.740695 AGTTTTAGTCGCTATCATCTTCGC 59.259 41.667 0.00 0.00 0.00 4.70
3204 6020 6.744112 TCCAAATGTTATCACTGAACCAAAC 58.256 36.000 0.00 0.00 0.00 2.93
3220 6038 3.711704 AGACTATCCGTGGATCCAAATGT 59.288 43.478 18.20 9.68 36.17 2.71
3300 6124 8.161699 TGAAACAAAGTTTATACAGAACCTCC 57.838 34.615 0.00 0.00 0.00 4.30
3362 6191 3.897505 TCATCTCTCAGAACCAGAACACA 59.102 43.478 0.00 0.00 0.00 3.72
3425 6254 3.248363 CGCAAATAATCATCTCCGCTGAA 59.752 43.478 0.00 0.00 0.00 3.02
3554 6385 5.162075 CCGAGCTACTGTAATGTAATAGCC 58.838 45.833 0.00 0.00 39.26 3.93
3691 6559 2.597510 GCTTTCAACGGGGTGCCT 60.598 61.111 0.00 0.00 0.00 4.75
3743 6611 1.349627 CTGTGTTGATGATCGCCGC 59.650 57.895 0.00 0.00 0.00 6.53
3746 6614 1.089920 AAGCCTGTGTTGATGATCGC 58.910 50.000 0.00 0.00 0.00 4.58
3758 6626 2.426023 GTCGTGGACCAAGCCTGT 59.574 61.111 2.02 0.00 0.00 4.00
3805 6673 2.035442 GCAGAAGGGCTTGACGGAC 61.035 63.158 0.00 0.00 0.00 4.79
3815 6683 1.032114 GTGGGGATTTCGCAGAAGGG 61.032 60.000 0.00 0.00 45.90 3.95
4160 7028 2.360726 TCGCTGACCACTCCGCTA 60.361 61.111 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.