Multiple sequence alignment - TraesCS7A01G156000

Loading Multiple Alignment...

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 TraesCS7A01G156000 chr7A 100.000 8085 0 0 1 8085 108809662 108817746 0.000000e+00 14931
1 TraesCS7A01G156000 chr7A 92.222 90 5 2 6479 6567 108816063 108816151 8.520000e-25 126
2 TraesCS7A01G156000 chr7A 92.222 90 5 2 6402 6490 108816140 108816228 8.520000e-25 126
3 TraesCS7A01G156000 chr7A 96.923 65 2 0 1234 1298 108810835 108810899 8.580000e-20 110
4 TraesCS7A01G156000 chr7A 96.923 65 2 0 1174 1238 108810895 108810959 8.580000e-20 110
5 TraesCS7A01G156000 chr7D 96.544 8131 197 31 1 8085 104567497 104575589 0.000000e+00 13381
6 TraesCS7A01G156000 chr7D 98.734 79 0 1 6479 6556 104573910 104573988 1.090000e-28 139
7 TraesCS7A01G156000 chr7D 96.923 65 2 0 1234 1298 104568680 104568744 8.580000e-20 110
8 TraesCS7A01G156000 chr7D 95.385 65 3 0 1174 1238 104568740 104568804 3.990000e-18 104
9 TraesCS7A01G156000 chr7B 95.661 3803 130 23 4308 8085 62692650 62696442 0.000000e+00 6076
10 TraesCS7A01G156000 chr7B 97.216 2694 66 6 1234 3922 62689422 62692111 0.000000e+00 4551
11 TraesCS7A01G156000 chr7B 91.527 1251 76 10 1 1238 62688253 62689486 0.000000e+00 1696
12 TraesCS7A01G156000 chr7B 95.610 410 11 3 3908 4310 62692128 62692537 0.000000e+00 651
13 TraesCS7A01G156000 chr7B 96.104 77 2 1 6481 6556 62694748 62694824 3.060000e-24 124


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 TraesCS7A01G156000 chr7A 108809662 108817746 8084 False 14931.0 14931 100.0000 1 8085 1 chr7A.!!$F1 8084
1 TraesCS7A01G156000 chr7D 104567497 104575589 8092 False 13381.0 13381 96.5440 1 8085 1 chr7D.!!$F1 8084
2 TraesCS7A01G156000 chr7B 62688253 62696442 8189 False 2619.6 6076 95.2236 1 8085 5 chr7B.!!$F1 8084

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
542 547 1.328680 CCATTGCGACTTGATTCTCCG 59.671 52.381 0.00 0.0 0.00 4.63 F
810 823 2.004583 TTACTTCGCCACGATCCTTG 57.995 50.000 0.00 0.0 35.23 3.61 F
1497 1510 2.744202 CTCTCTGGCAAATTACGCACTT 59.256 45.455 2.55 0.0 0.00 3.16 F
3379 3400 1.965754 TTGTTTGGTGCCCTTGGTGC 61.966 55.000 0.00 0.0 0.00 5.01 F
3874 3896 1.669115 GAAGAACCGCAGCTCAGCA 60.669 57.895 0.00 0.0 0.00 4.41 F
4239 4299 2.445525 TCCCTGGGAAACTGTAAAAGCT 59.554 45.455 14.48 0.0 0.00 3.74 F
4865 5045 1.425066 AGTGGAGAGTTGCCAATGGAA 59.575 47.619 2.05 0.0 37.12 3.53 F
5985 6168 1.529152 TAGGGAAGCGTCGACAAGCA 61.529 55.000 17.16 0.0 35.48 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1809 0.107508 ATGATTGACTGCCCTGGACG 60.108 55.000 0.00 0.00 0.00 4.79 R
2207 2220 0.748450 AATCCATTGGCATTGCGAGG 59.252 50.000 1.91 2.04 0.00 4.63 R
3472 3493 2.158623 TGGAAACTCTCACTGCCATGTT 60.159 45.455 0.00 0.00 0.00 2.71 R
4479 4654 0.107703 GCACGAGGATTGGGTCATCA 60.108 55.000 0.00 0.00 37.49 3.07 R
4752 4932 0.609957 CTTGAGCCCCTGCATCAACA 60.610 55.000 0.00 0.00 41.13 3.33 R
5594 5777 0.733566 CATCACGCCCATGTTGTTGC 60.734 55.000 0.00 0.00 0.00 4.17 R
6210 6393 0.779997 ATTGTTTCCTCACCAGGCCT 59.220 50.000 0.00 0.00 40.12 5.19 R
7641 7854 0.615850 AGGGCAGCCTGTCTAGAAAC 59.384 55.000 12.43 0.00 0.00 2.78 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
27 28 3.766691 TACGGCCGCACCCTCTTC 61.767 66.667 28.58 0.00 33.26 2.87
424 429 1.947456 GTTCGTGCTTCACCCTTCTTT 59.053 47.619 0.00 0.00 0.00 2.52
542 547 1.328680 CCATTGCGACTTGATTCTCCG 59.671 52.381 0.00 0.00 0.00 4.63
652 665 5.290885 TCGCATGCTTTTGTATGTACTGTAG 59.709 40.000 17.13 0.00 43.17 2.74
737 750 7.615365 AGCTTTTGTGACTTAATATCATTCCCA 59.385 33.333 0.00 0.00 0.00 4.37
752 765 6.985653 TCATTCCCAAAACTTAAATGACCA 57.014 33.333 0.00 0.00 32.86 4.02
810 823 2.004583 TTACTTCGCCACGATCCTTG 57.995 50.000 0.00 0.00 35.23 3.61
906 919 6.437928 TGTTATTGTTTCTAGCAAGCAACAG 58.562 36.000 6.42 0.00 39.50 3.16
1176 1189 4.821805 CGCAATAGTCCTGGTAATGGAAAT 59.178 41.667 0.00 0.00 35.10 2.17
1191 1204 3.760738 TGGAAATGCAGGTGATTGTGTA 58.239 40.909 0.00 0.00 0.00 2.90
1304 1317 3.062042 CCTGCAAAGAAAATGTTCCAGC 58.938 45.455 0.00 0.00 33.92 4.85
1497 1510 2.744202 CTCTCTGGCAAATTACGCACTT 59.256 45.455 2.55 0.00 0.00 3.16
1796 1809 4.595986 ACTAGGAAGAAGAGACCTGAGTC 58.404 47.826 0.00 0.00 43.89 3.36
2046 2059 4.810191 AACCTTCTCTCTATGCGTTCTT 57.190 40.909 0.00 0.00 0.00 2.52
2142 2155 6.693315 GCATTGGCTAGGAAAAACACTATA 57.307 37.500 0.00 0.00 36.96 1.31
2207 2220 6.525976 GCAATTAGTCATGCTTTTTCTGAGAC 59.474 38.462 0.00 0.00 39.46 3.36
3036 3056 3.439129 GTCTCCTTTTGGGTGGTTAATCG 59.561 47.826 0.00 0.00 40.87 3.34
3258 3278 2.781945 AGCGTTTTCTTCCTTGCAAG 57.218 45.000 19.93 19.93 0.00 4.01
3275 3295 2.412870 CAAGTCAACGCATCAGGTACA 58.587 47.619 0.00 0.00 0.00 2.90
3285 3305 2.415893 GCATCAGGTACAATTGTGGTGC 60.416 50.000 21.42 17.29 0.00 5.01
3379 3400 1.965754 TTGTTTGGTGCCCTTGGTGC 61.966 55.000 0.00 0.00 0.00 5.01
3515 3536 2.273449 GCTGGGTGCTGGCACTAT 59.727 61.111 22.32 0.00 45.52 2.12
3722 3743 3.497405 CCACAACTCCAGATCATATGGGG 60.497 52.174 0.00 0.00 44.51 4.96
3874 3896 1.669115 GAAGAACCGCAGCTCAGCA 60.669 57.895 0.00 0.00 0.00 4.41
3982 4035 7.163001 AGCCTTTGAGGTTCAAGAATATTTC 57.837 36.000 0.00 0.00 37.70 2.17
4089 4149 9.336171 GGCAGAGACTTCTTTTCTATAATGATT 57.664 33.333 0.00 0.00 0.00 2.57
4110 4170 5.578157 TTTTCTAAGTACTGAAGCCCCTT 57.422 39.130 0.00 0.00 0.00 3.95
4239 4299 2.445525 TCCCTGGGAAACTGTAAAAGCT 59.554 45.455 14.48 0.00 0.00 3.74
4426 4601 4.576463 AGAGCACTCCTGTGTGTTTTAAAG 59.424 41.667 0.00 0.00 45.44 1.85
4466 4641 4.022155 TCCCGTTTAGCAAAAACCAATACC 60.022 41.667 8.57 0.00 0.00 2.73
4468 4643 4.320348 CCGTTTAGCAAAAACCAATACCGA 60.320 41.667 8.57 0.00 0.00 4.69
4479 4654 6.399639 AAACCAATACCGATTTGAAACTGT 57.600 33.333 0.00 0.00 0.00 3.55
4488 4663 3.501828 CGATTTGAAACTGTGATGACCCA 59.498 43.478 0.00 0.00 0.00 4.51
4517 4692 3.132289 GTGCTCTACTGGCTGTTATGGTA 59.868 47.826 1.31 0.00 0.00 3.25
4544 4719 6.013379 TCCCCAATAGGATGTAGATGTTGATC 60.013 42.308 0.00 0.00 38.24 2.92
4600 4776 9.547753 CATACTACCAAAGTACTGAGCATATTT 57.452 33.333 0.00 0.00 43.47 1.40
4752 4932 6.279813 TGCTTAATTTCCCCTCATTCCTAT 57.720 37.500 0.00 0.00 0.00 2.57
4831 5011 3.106827 TGTGCCATACAGAGATCCTTCA 58.893 45.455 0.00 0.00 33.42 3.02
4865 5045 1.425066 AGTGGAGAGTTGCCAATGGAA 59.575 47.619 2.05 0.00 37.12 3.53
5107 5287 6.159299 TGATGCTTTTGAGGATGTTGAAAA 57.841 33.333 0.00 0.00 0.00 2.29
5108 5288 6.761312 TGATGCTTTTGAGGATGTTGAAAAT 58.239 32.000 0.00 0.00 0.00 1.82
5109 5289 6.647481 TGATGCTTTTGAGGATGTTGAAAATG 59.353 34.615 0.00 0.00 0.00 2.32
5110 5290 6.159299 TGCTTTTGAGGATGTTGAAAATGA 57.841 33.333 0.00 0.00 0.00 2.57
5111 5291 6.761312 TGCTTTTGAGGATGTTGAAAATGAT 58.239 32.000 0.00 0.00 0.00 2.45
5112 5292 6.647481 TGCTTTTGAGGATGTTGAAAATGATG 59.353 34.615 0.00 0.00 0.00 3.07
5150 5333 4.986054 TGATGATGATGGTGATGATCCA 57.014 40.909 0.00 0.00 39.41 3.41
5594 5777 7.148490 CCTCATCATAGTACTACTGACAGATCG 60.148 44.444 10.08 0.00 0.00 3.69
5709 5892 2.951457 TTCGTCACATAGCCATTCGA 57.049 45.000 0.00 0.00 0.00 3.71
5902 6085 2.438411 AGTACCAGAAGAGGACTGTCG 58.562 52.381 1.07 0.00 34.04 4.35
5985 6168 1.529152 TAGGGAAGCGTCGACAAGCA 61.529 55.000 17.16 0.00 35.48 3.91
6095 6278 4.773674 TCAGTGGATTTCAGGATTGCAAAT 59.226 37.500 1.71 0.00 0.00 2.32
6166 6349 6.360370 TGTGAAGGACAGAGCTAGTATTTT 57.640 37.500 0.00 0.00 0.00 1.82
6172 6355 8.870075 AAGGACAGAGCTAGTATTTTGAATTT 57.130 30.769 0.00 0.00 0.00 1.82
6182 6365 6.530019 AGTATTTTGAATTTACAGCCTGGG 57.470 37.500 0.00 0.00 0.00 4.45
6210 6393 4.897509 AGTCCTCATCATGACACTGAAA 57.102 40.909 0.00 0.00 33.89 2.69
6350 6533 0.846693 AAGTTCAGGGCACAGAACCT 59.153 50.000 19.47 5.03 42.94 3.50
6446 6629 7.586714 TCTGCTATGCTATGATTAAATGTCG 57.413 36.000 0.00 0.00 0.00 4.35
6476 6659 5.106197 TGCGCTAATGATGTTTCAAGATGTT 60.106 36.000 9.73 0.00 34.96 2.71
6548 6731 2.995939 CTGCGCTACTGATGTTTCAAGA 59.004 45.455 9.73 0.00 0.00 3.02
6549 6732 3.599343 TGCGCTACTGATGTTTCAAGAT 58.401 40.909 9.73 0.00 0.00 2.40
6550 6733 3.371898 TGCGCTACTGATGTTTCAAGATG 59.628 43.478 9.73 0.00 0.00 2.90
6551 6734 3.372206 GCGCTACTGATGTTTCAAGATGT 59.628 43.478 0.00 0.00 0.00 3.06
6552 6735 4.142816 GCGCTACTGATGTTTCAAGATGTT 60.143 41.667 0.00 0.00 0.00 2.71
6553 6736 5.617751 GCGCTACTGATGTTTCAAGATGTTT 60.618 40.000 0.00 0.00 0.00 2.83
6554 6737 5.791974 CGCTACTGATGTTTCAAGATGTTTG 59.208 40.000 0.00 0.00 0.00 2.93
6555 6738 6.566564 CGCTACTGATGTTTCAAGATGTTTGT 60.567 38.462 0.00 0.00 0.00 2.83
6556 6739 6.798959 GCTACTGATGTTTCAAGATGTTTGTC 59.201 38.462 0.00 0.00 0.00 3.18
6557 6740 6.949352 ACTGATGTTTCAAGATGTTTGTCT 57.051 33.333 0.00 0.00 0.00 3.41
6558 6741 7.338800 ACTGATGTTTCAAGATGTTTGTCTT 57.661 32.000 0.00 0.00 38.95 3.01
6559 6742 7.420800 ACTGATGTTTCAAGATGTTTGTCTTC 58.579 34.615 0.00 0.00 36.33 2.87
6560 6743 7.284034 ACTGATGTTTCAAGATGTTTGTCTTCT 59.716 33.333 0.00 0.00 36.33 2.85
6594 6790 6.073276 TGTTGTATTTTGTGGACTGATTCTCG 60.073 38.462 0.00 0.00 0.00 4.04
6609 6805 0.678950 TCTCGCATGTTCTCACACCA 59.321 50.000 0.00 0.00 35.03 4.17
6738 6937 1.570813 TGAAGCTCGCCGATAACATG 58.429 50.000 0.00 0.00 0.00 3.21
6742 6941 0.776451 GCTCGCCGATAACATGTACG 59.224 55.000 0.00 5.91 0.00 3.67
6749 6948 4.441744 CGCCGATAACATGTACGTATTTCA 59.558 41.667 0.00 0.00 0.00 2.69
6767 6966 2.507484 TCATTGTGCAGGGAACTTCAG 58.493 47.619 0.00 0.00 40.21 3.02
6909 7108 3.307379 GGTCGGTCAGAGCAAAGTT 57.693 52.632 0.00 0.00 46.08 2.66
6916 7115 1.069636 GTCAGAGCAAAGTTGAAGCCG 60.070 52.381 0.00 0.00 0.00 5.52
6979 7178 1.818131 CGACGGATATCCAGGTCCAGA 60.818 57.143 21.70 0.00 34.05 3.86
7186 7385 3.732212 TGATTATTCGCCAGTGGAGATG 58.268 45.455 16.96 0.57 30.42 2.90
7193 7392 1.099879 GCCAGTGGAGATGGACATGC 61.100 60.000 15.20 0.00 40.51 4.06
7231 7430 3.657634 CATACCCCTTGTCAGATGATCG 58.342 50.000 0.00 0.00 0.00 3.69
7234 7433 1.539929 CCCCTTGTCAGATGATCGCTC 60.540 57.143 0.00 0.00 0.00 5.03
7259 7458 1.213926 AGGGAATTCATGTCTGGAGCC 59.786 52.381 7.93 0.00 0.00 4.70
7293 7492 4.080863 ACTGAAATGGTGAGGATGGTCTAC 60.081 45.833 0.00 0.00 0.00 2.59
7376 7575 3.637229 TCCCTCTAGTAAAGATCCAAGCG 59.363 47.826 0.00 0.00 32.41 4.68
7377 7576 3.385577 CCTCTAGTAAAGATCCAAGCGC 58.614 50.000 0.00 0.00 32.41 5.92
7378 7577 3.046390 CTCTAGTAAAGATCCAAGCGCG 58.954 50.000 0.00 0.00 32.41 6.86
7459 7671 1.301293 CCAGGAAGGCCTCTGGTTC 59.699 63.158 25.88 11.94 44.80 3.62
7460 7672 1.492133 CCAGGAAGGCCTCTGGTTCA 61.492 60.000 25.88 0.00 44.80 3.18
7461 7673 0.622665 CAGGAAGGCCTCTGGTTCAT 59.377 55.000 5.23 0.00 44.80 2.57
7462 7674 0.915364 AGGAAGGCCTCTGGTTCATC 59.085 55.000 5.23 0.00 42.19 2.92
7592 7805 3.507622 CCCTGTTTGGAAACTCTGGAATC 59.492 47.826 4.02 0.00 39.59 2.52
7596 7809 5.528172 TGTTTGGAAACTCTGGAATCCAGC 61.528 45.833 23.90 9.66 42.42 4.85
7641 7854 0.892755 ATGCATGTGAAACTGCTGGG 59.107 50.000 0.00 0.00 40.20 4.45
7803 8017 1.746615 CACCTGATGTCCGCCTTGG 60.747 63.158 0.00 0.00 40.09 3.61
7895 8109 4.145052 GGAAGATGTTCACCCTGTTCTTT 58.855 43.478 4.83 0.00 33.93 2.52
7926 8140 2.111999 CTCGTTCAGCCAGTTCCCCA 62.112 60.000 0.00 0.00 0.00 4.96
7934 8148 1.377202 CCAGTTCCCCATGGTCACG 60.377 63.158 11.73 0.00 0.00 4.35
7947 8161 1.746517 GTCACGTCCTCCACACCTT 59.253 57.895 0.00 0.00 0.00 3.50
7970 8185 1.463528 GCACACGCCATTAGTTTCGAC 60.464 52.381 0.00 0.00 0.00 4.20
8002 8222 5.808366 TGACAGATGTTCTACTGGACTTT 57.192 39.130 0.00 0.00 38.30 2.66
8003 8223 6.174720 TGACAGATGTTCTACTGGACTTTT 57.825 37.500 0.00 0.00 38.30 2.27
8004 8224 6.591935 TGACAGATGTTCTACTGGACTTTTT 58.408 36.000 0.00 0.00 38.30 1.94
8067 8291 3.771160 GACCATGTCGGAGGCGGT 61.771 66.667 0.00 0.00 38.63 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 2.837291 CTGGGAGGGAGAGCTCGG 60.837 72.222 8.37 0.00 0.00 4.63
141 142 3.479269 CGAGAGGCGCGTTGAACC 61.479 66.667 8.43 0.00 0.00 3.62
181 182 4.324991 GTTTGGACCCGGCGACCT 62.325 66.667 9.30 0.00 0.00 3.85
183 184 2.438951 TACAGTTTGGACCCGGCGAC 62.439 60.000 9.30 0.00 0.00 5.19
184 185 1.756408 TTACAGTTTGGACCCGGCGA 61.756 55.000 9.30 0.00 0.00 5.54
185 186 1.296056 CTTACAGTTTGGACCCGGCG 61.296 60.000 0.00 0.00 0.00 6.46
186 187 1.583495 GCTTACAGTTTGGACCCGGC 61.583 60.000 0.00 0.00 0.00 6.13
194 199 5.476945 AGGTGAAATTAGGGCTTACAGTTTG 59.523 40.000 0.00 0.00 0.00 2.93
424 429 1.739338 AAACAACGCAATCCGGCCAA 61.739 50.000 2.24 0.00 42.52 4.52
463 468 8.307582 ACATGCCTAGAGTGTAATACTTAGTT 57.692 34.615 0.00 0.00 40.53 2.24
464 469 7.780745 AGACATGCCTAGAGTGTAATACTTAGT 59.219 37.037 0.00 0.00 40.53 2.24
581 586 7.473027 ACAAAACTTTCTTCATGCATTTCAG 57.527 32.000 0.00 0.00 0.00 3.02
669 682 6.243811 ACGGTCGCAAATGTAAATTCTTTA 57.756 33.333 0.00 0.00 0.00 1.85
737 750 6.041979 AGGTGCAAGATGGTCATTTAAGTTTT 59.958 34.615 0.00 0.00 0.00 2.43
749 762 5.367937 AGATGACTTATAGGTGCAAGATGGT 59.632 40.000 0.00 0.00 0.00 3.55
752 765 5.843421 AGGAGATGACTTATAGGTGCAAGAT 59.157 40.000 0.00 0.00 0.00 2.40
810 823 2.070262 AACACGTAGGTAAAGCCGTC 57.930 50.000 0.00 0.00 43.70 4.79
862 875 0.537143 AGAGGCACGGCAATGAAACA 60.537 50.000 0.00 0.00 0.00 2.83
873 886 4.749245 AGAAACAATAACAAGAGGCACG 57.251 40.909 0.00 0.00 0.00 5.34
1176 1189 2.552155 GGGAAGTACACAATCACCTGCA 60.552 50.000 0.00 0.00 0.00 4.41
1191 1204 3.947834 CTGACAAACTTTCTGTGGGAAGT 59.052 43.478 0.00 0.00 35.16 3.01
1304 1317 1.714794 CAACTGGGTAGAACTGCTCG 58.285 55.000 0.00 0.00 0.00 5.03
1621 1634 0.972471 GTTTCATCCCCCTGGCAAGG 60.972 60.000 0.00 0.00 44.06 3.61
1796 1809 0.107508 ATGATTGACTGCCCTGGACG 60.108 55.000 0.00 0.00 0.00 4.79
1800 1813 2.422479 CTGTTGATGATTGACTGCCCTG 59.578 50.000 0.00 0.00 0.00 4.45
2046 2059 1.346395 ACACGCTGTTTAGATGGGTCA 59.654 47.619 0.00 0.00 0.00 4.02
2142 2155 6.677913 CCCTTCAAAATAGAATTGTTGACGT 58.322 36.000 0.00 0.00 30.00 4.34
2198 2211 1.442769 GCATTGCGAGGTCTCAGAAA 58.557 50.000 0.00 0.00 0.00 2.52
2207 2220 0.748450 AATCCATTGGCATTGCGAGG 59.252 50.000 1.91 2.04 0.00 4.63
2549 2569 3.177884 TGGCCAGGTGAAGCTGGT 61.178 61.111 25.15 0.00 42.44 4.00
3116 3136 6.455360 AATGATAGCACAGTTGTATTTGGG 57.545 37.500 0.00 0.00 0.00 4.12
3258 3278 3.188460 ACAATTGTACCTGATGCGTTGAC 59.812 43.478 9.97 0.00 0.00 3.18
3275 3295 6.769822 TGAAACAAATAAATGGCACCACAATT 59.230 30.769 0.00 0.00 0.00 2.32
3472 3493 2.158623 TGGAAACTCTCACTGCCATGTT 60.159 45.455 0.00 0.00 0.00 2.71
3515 3536 4.729552 AGATATCAAATTAGGCTGGCCA 57.270 40.909 14.39 4.71 38.92 5.36
3689 3710 2.703536 TGGAGTTGTGGTTCTTAGCTGA 59.296 45.455 0.00 0.00 0.00 4.26
3722 3743 5.089970 AGCCTGGGCAAAATAAGAATTTC 57.910 39.130 14.39 0.00 44.88 2.17
3874 3896 4.973168 TGACTGGATTGTCAGTAGCTTTT 58.027 39.130 0.00 0.00 46.76 2.27
4060 4120 3.033368 AGAAAAGAAGTCTCTGCCGAC 57.967 47.619 0.00 0.00 30.03 4.79
4089 4149 6.499350 TCTTAAGGGGCTTCAGTACTTAGAAA 59.501 38.462 1.85 0.00 0.00 2.52
4110 4170 7.446931 TGATTCAAACACTGCCAATACTTCTTA 59.553 33.333 0.00 0.00 0.00 2.10
4426 4601 5.526506 ACGGGAACATATTGACCTACTAC 57.473 43.478 0.00 0.00 0.00 2.73
4466 4641 3.501828 TGGGTCATCACAGTTTCAAATCG 59.498 43.478 0.00 0.00 0.00 3.34
4468 4643 5.047092 GGATTGGGTCATCACAGTTTCAAAT 60.047 40.000 0.00 0.00 0.00 2.32
4479 4654 0.107703 GCACGAGGATTGGGTCATCA 60.108 55.000 0.00 0.00 37.49 3.07
4488 4663 0.461961 GCCAGTAGAGCACGAGGATT 59.538 55.000 0.00 0.00 31.11 3.01
4517 4692 6.332635 TCAACATCTACATCCTATTGGGGATT 59.667 38.462 0.00 0.00 42.89 3.01
4591 4767 6.580041 CCTGCATTATTTCGACAAATATGCTC 59.420 38.462 15.36 0.00 38.37 4.26
4600 4776 3.065233 GCACATCCTGCATTATTTCGACA 59.935 43.478 0.00 0.00 46.29 4.35
4739 4918 3.152341 GCATCAACATAGGAATGAGGGG 58.848 50.000 2.92 0.00 36.54 4.79
4752 4932 0.609957 CTTGAGCCCCTGCATCAACA 60.610 55.000 0.00 0.00 41.13 3.33
4831 5011 2.341543 CACTGACGCTGGAGCAGT 59.658 61.111 0.00 0.00 43.16 4.40
4865 5045 5.812642 CACTTTTACTGTAAGATCGCTGGAT 59.187 40.000 0.00 0.00 37.43 3.41
5107 5287 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
5108 5288 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
5109 5289 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
5110 5290 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
5111 5291 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
5112 5292 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
5150 5333 8.689061 TCTGCTAAAAATGCTTCATTGACATAT 58.311 29.630 0.00 0.00 34.04 1.78
5549 5732 4.761739 TGAGGGAAAAGATTTAGCTGTGTG 59.238 41.667 0.00 0.00 0.00 3.82
5594 5777 0.733566 CATCACGCCCATGTTGTTGC 60.734 55.000 0.00 0.00 0.00 4.17
5902 6085 5.292101 CCGTCAGATTGATTAGAAAGTGGAC 59.708 44.000 0.00 0.00 0.00 4.02
5985 6168 7.047891 TGCATATCAATACCGTTCTCTCTTTT 58.952 34.615 0.00 0.00 0.00 2.27
6040 6223 7.675962 AAATGAATGTCCAAATCAATGTTGG 57.324 32.000 0.00 0.00 45.89 3.77
6166 6349 2.760092 GCATTCCCAGGCTGTAAATTCA 59.240 45.455 14.43 0.00 0.00 2.57
6172 6355 1.762957 GACTAGCATTCCCAGGCTGTA 59.237 52.381 14.43 0.00 41.25 2.74
6182 6365 4.749099 GTGTCATGATGAGGACTAGCATTC 59.251 45.833 0.00 0.00 33.88 2.67
6210 6393 0.779997 ATTGTTTCCTCACCAGGCCT 59.220 50.000 0.00 0.00 40.12 5.19
6459 6642 8.632679 ACAGTACAAAACATCTTGAAACATCAT 58.367 29.630 0.00 0.00 0.00 2.45
6502 6685 8.781196 AGTGCTTGACATTTAATCATAGCATAG 58.219 33.333 12.95 0.00 39.78 2.23
6548 6731 6.959639 ACACCAAACATAGAAGACAAACAT 57.040 33.333 0.00 0.00 0.00 2.71
6549 6732 6.151985 ACAACACCAAACATAGAAGACAAACA 59.848 34.615 0.00 0.00 0.00 2.83
6550 6733 6.560711 ACAACACCAAACATAGAAGACAAAC 58.439 36.000 0.00 0.00 0.00 2.93
6551 6734 6.767524 ACAACACCAAACATAGAAGACAAA 57.232 33.333 0.00 0.00 0.00 2.83
6552 6735 8.458573 AATACAACACCAAACATAGAAGACAA 57.541 30.769 0.00 0.00 0.00 3.18
6553 6736 8.458573 AAATACAACACCAAACATAGAAGACA 57.541 30.769 0.00 0.00 0.00 3.41
6554 6737 9.180678 CAAAATACAACACCAAACATAGAAGAC 57.819 33.333 0.00 0.00 0.00 3.01
6555 6738 8.908903 ACAAAATACAACACCAAACATAGAAGA 58.091 29.630 0.00 0.00 0.00 2.87
6556 6739 8.967218 CACAAAATACAACACCAAACATAGAAG 58.033 33.333 0.00 0.00 0.00 2.85
6557 6740 7.923344 CCACAAAATACAACACCAAACATAGAA 59.077 33.333 0.00 0.00 0.00 2.10
6558 6741 7.285629 TCCACAAAATACAACACCAAACATAGA 59.714 33.333 0.00 0.00 0.00 1.98
6559 6742 7.381139 GTCCACAAAATACAACACCAAACATAG 59.619 37.037 0.00 0.00 0.00 2.23
6560 6743 7.068839 AGTCCACAAAATACAACACCAAACATA 59.931 33.333 0.00 0.00 0.00 2.29
6594 6790 6.389091 TGATAATTTTGGTGTGAGAACATGC 58.611 36.000 0.00 0.00 0.00 4.06
6609 6805 7.149973 CCAATCAATGATCGGCTGATAATTTT 58.850 34.615 14.66 6.13 34.00 1.82
6738 6937 3.936453 TCCCTGCACAATGAAATACGTAC 59.064 43.478 0.00 0.00 0.00 3.67
6742 6941 5.048083 TGAAGTTCCCTGCACAATGAAATAC 60.048 40.000 0.00 0.00 0.00 1.89
6749 6948 1.251251 GCTGAAGTTCCCTGCACAAT 58.749 50.000 0.00 0.00 0.00 2.71
6767 6966 5.332808 GCAACTCTGAACAAACAATTGATGC 60.333 40.000 13.59 0.35 38.94 3.91
6909 7108 1.960040 ATCTGCATCCGTCGGCTTCA 61.960 55.000 6.34 0.00 0.00 3.02
6979 7178 2.225491 GCTAGATTCACTCGCTCGAGAT 59.775 50.000 23.95 8.71 44.53 2.75
7036 7235 4.223953 ACCTTCTTGACTCACTGGACTTA 58.776 43.478 0.00 0.00 0.00 2.24
7158 7357 3.492383 CACTGGCGAATAATCAGCTGTAG 59.508 47.826 14.67 0.00 32.19 2.74
7186 7385 2.837532 AACAAATGGTTGGCATGTCC 57.162 45.000 0.00 0.00 38.60 4.02
7231 7430 2.352960 GACATGAATTCCCTGTTCGAGC 59.647 50.000 0.00 0.00 0.00 5.03
7234 7433 2.679837 CCAGACATGAATTCCCTGTTCG 59.320 50.000 0.00 6.57 0.00 3.95
7259 7458 5.470368 TCACCATTTCAGTTTCTCTACTCG 58.530 41.667 0.00 0.00 0.00 4.18
7459 7671 3.007723 AGCCATGCTAGATGTACAGGATG 59.992 47.826 0.33 4.60 38.97 3.51
7460 7672 3.007723 CAGCCATGCTAGATGTACAGGAT 59.992 47.826 0.33 0.00 36.40 3.24
7461 7673 2.366590 CAGCCATGCTAGATGTACAGGA 59.633 50.000 0.33 0.00 36.40 3.86
7462 7674 2.103771 ACAGCCATGCTAGATGTACAGG 59.896 50.000 0.33 0.00 36.40 4.00
7592 7805 5.580297 ACATTTGGCATTAATTAAACGCTGG 59.420 36.000 17.57 9.05 0.00 4.85
7641 7854 0.615850 AGGGCAGCCTGTCTAGAAAC 59.384 55.000 12.43 0.00 0.00 2.78
7926 8140 1.671742 GTGTGGAGGACGTGACCAT 59.328 57.895 0.00 0.00 36.09 3.55
7934 8148 1.003118 TGTGCATAAGGTGTGGAGGAC 59.997 52.381 0.00 0.00 0.00 3.85
7947 8161 2.350192 CGAAACTAATGGCGTGTGCATA 59.650 45.455 0.00 0.00 45.35 3.14
7970 8185 4.179298 AGAACATCTGTCATCACATGTCG 58.821 43.478 0.00 0.00 33.34 4.35
8002 8222 3.826157 CCCTCTGCTTGTGAACCATAAAA 59.174 43.478 0.00 0.00 0.00 1.52
8003 8223 3.073798 TCCCTCTGCTTGTGAACCATAAA 59.926 43.478 0.00 0.00 0.00 1.40
8004 8224 2.642311 TCCCTCTGCTTGTGAACCATAA 59.358 45.455 0.00 0.00 0.00 1.90
8005 8225 2.237143 CTCCCTCTGCTTGTGAACCATA 59.763 50.000 0.00 0.00 0.00 2.74
8067 8291 4.865629 ACCTCGTCCAGTGGATCA 57.134 55.556 16.67 3.88 36.98 2.92


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

AutoCloner maintained by Alex Coulton.