Multiple sequence alignment - TraesCS6A01G159700

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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 TraesCS6A01G159700 chr6A 100.000 4562 0 0 1 4562 152061177 152056616 0.000000e+00 8425
1 TraesCS6A01G159700 chr6A 98.780 82 1 0 4481 4562 7338525 7338606 3.680000e-31 147
2 TraesCS6A01G159700 chr6D 96.512 3641 99 12 851 4484 126872285 126875904 0.000000e+00 5995
3 TraesCS6A01G159700 chr6D 92.450 808 38 13 1 806 126871420 126872206 0.000000e+00 1133
4 TraesCS6A01G159700 chr6B 95.327 3552 106 16 985 4491 225869111 225872647 0.000000e+00 5585
5 TraesCS6A01G159700 chr6B 96.753 616 14 3 1 616 225867953 225868562 0.000000e+00 1022
6 TraesCS6A01G159700 chr2A 96.667 90 3 0 4473 4562 579077905 579077816 2.840000e-32 150
7 TraesCS6A01G159700 chr2A 96.591 88 3 0 4475 4562 118201673 118201586 3.680000e-31 147
8 TraesCS6A01G159700 chr7B 100.000 80 0 0 4483 4562 327262913 327262834 1.020000e-31 148
9 TraesCS6A01G159700 chr1D 85.612 139 20 0 199 337 472561544 472561682 3.680000e-31 147
10 TraesCS6A01G159700 chr1D 80.851 141 21 6 200 337 452264436 452264299 6.240000e-19 106
11 TraesCS6A01G159700 chr3B 95.556 90 4 0 4473 4562 810265575 810265486 1.320000e-30 145
12 TraesCS6A01G159700 chr5B 84.892 139 21 0 199 337 532877282 532877420 1.710000e-29 141
13 TraesCS6A01G159700 chr5A 84.892 139 21 0 199 337 553421511 553421649 1.710000e-29 141
14 TraesCS6A01G159700 chr5A 93.617 94 4 1 4469 4562 41432320 41432229 6.150000e-29 139
15 TraesCS6A01G159700 chr1B 85.000 140 19 2 199 337 657272693 657272831 1.710000e-29 141
16 TraesCS6A01G159700 chr1A 84.892 139 21 0 199 337 566564801 566564939 1.710000e-29 141
17 TraesCS6A01G159700 chr1A 96.429 84 3 0 4479 4562 511379033 511378950 6.150000e-29 139
18 TraesCS6A01G159700 chr1A 89.720 107 6 4 4461 4562 72582698 72582804 1.030000e-26 132
19 TraesCS6A01G159700 chr4A 93.548 93 5 1 4470 4562 583980676 583980767 2.210000e-28 137
20 TraesCS6A01G159700 chr5D 83.453 139 23 0 199 337 438360600 438360738 3.700000e-26 130


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 TraesCS6A01G159700 chr6A 152056616 152061177 4561 True 8425.0 8425 100.000 1 4562 1 chr6A.!!$R1 4561
1 TraesCS6A01G159700 chr6D 126871420 126875904 4484 False 3564.0 5995 94.481 1 4484 2 chr6D.!!$F1 4483
2 TraesCS6A01G159700 chr6B 225867953 225872647 4694 False 3303.5 5585 96.040 1 4491 2 chr6B.!!$F1 4490

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
586 587 0.110486 TTCTGCGCCTTTCTTTCCCT 59.890 50.000 4.18 0.0 0.00 4.20 F
831 906 0.179004 TGGCTCTTCCCGCAGAAAAA 60.179 50.000 0.00 0.0 32.88 1.94 F
950 1059 0.311165 CGGTTAGATCATCCGCGACT 59.689 55.000 8.23 0.0 37.90 4.18 F
1697 1945 0.318445 CACCTTGCACTGCTTTCAGC 60.318 55.000 1.98 0.0 44.10 4.26 F
2649 2919 3.281727 TCTCTCTCTCTCTCTGAAGGC 57.718 52.381 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2430 2678 0.370273 CCTCGCTCCGAATTTTGTCG 59.630 55.000 0.0 0.0 40.77 4.35 R
2649 2919 6.474751 GCCCTACGTCTTATTAAACACTACTG 59.525 42.308 0.0 0.0 0.00 2.74 R
2896 3167 3.944055 ATCTCCGTCATACTACATGCC 57.056 47.619 0.0 0.0 0.00 4.40 R
3402 3673 0.113190 CCCAAGCCCAAACTTCTCCT 59.887 55.000 0.0 0.0 0.00 3.69 R
3771 4043 1.576577 TCACCACCAGAGATGATGCT 58.423 50.000 0.0 0.0 0.00 3.79 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
450 451 0.661552 TGAGCGTGCGAGAGGTATAC 59.338 55.000 0.00 0.00 0.00 1.47
563 564 4.478206 TCTCTCATCATCTTCACCAACC 57.522 45.455 0.00 0.00 0.00 3.77
564 565 3.840078 TCTCTCATCATCTTCACCAACCA 59.160 43.478 0.00 0.00 0.00 3.67
565 566 4.286808 TCTCTCATCATCTTCACCAACCAA 59.713 41.667 0.00 0.00 0.00 3.67
566 567 4.326826 TCTCATCATCTTCACCAACCAAC 58.673 43.478 0.00 0.00 0.00 3.77
567 568 4.042062 TCTCATCATCTTCACCAACCAACT 59.958 41.667 0.00 0.00 0.00 3.16
572 573 2.297701 TCTTCACCAACCAACTTCTGC 58.702 47.619 0.00 0.00 0.00 4.26
574 575 1.008538 CACCAACCAACTTCTGCGC 60.009 57.895 0.00 0.00 0.00 6.09
586 587 0.110486 TTCTGCGCCTTTCTTTCCCT 59.890 50.000 4.18 0.00 0.00 4.20
588 589 1.589716 CTGCGCCTTTCTTTCCCTGG 61.590 60.000 4.18 0.00 0.00 4.45
589 590 2.994671 GCGCCTTTCTTTCCCTGGC 61.995 63.158 0.00 0.00 40.14 4.85
594 595 0.405585 CTTTCTTTCCCTGGCCCTCA 59.594 55.000 0.00 0.00 0.00 3.86
599 600 0.549902 TTTCCCTGGCCCTCATCTGA 60.550 55.000 0.00 0.00 0.00 3.27
601 602 0.765903 TCCCTGGCCCTCATCTGATC 60.766 60.000 0.00 0.00 0.00 2.92
602 603 1.058428 CCCTGGCCCTCATCTGATCA 61.058 60.000 0.00 0.00 0.00 2.92
619 620 5.402270 TCTGATCATATCGTACGTGCAATTG 59.598 40.000 16.05 0.00 0.00 2.32
636 711 4.012374 CAATTGGGCGGCTAGATTATGAT 58.988 43.478 9.56 0.00 0.00 2.45
639 714 2.028112 TGGGCGGCTAGATTATGATGAC 60.028 50.000 9.56 0.00 0.00 3.06
642 717 2.670414 GCGGCTAGATTATGATGACAGC 59.330 50.000 0.00 0.00 0.00 4.40
647 722 1.696336 AGATTATGATGACAGCGGCCT 59.304 47.619 0.00 0.00 0.00 5.19
649 724 3.324846 AGATTATGATGACAGCGGCCTTA 59.675 43.478 0.00 0.00 0.00 2.69
650 725 3.769739 TTATGATGACAGCGGCCTTAT 57.230 42.857 0.00 0.00 0.00 1.73
651 726 2.645838 ATGATGACAGCGGCCTTATT 57.354 45.000 0.00 0.00 0.00 1.40
652 727 1.667236 TGATGACAGCGGCCTTATTG 58.333 50.000 0.00 0.00 0.00 1.90
653 728 0.308993 GATGACAGCGGCCTTATTGC 59.691 55.000 0.00 0.00 0.00 3.56
773 848 4.398549 TGCTGTAAGAAAATACACGTGC 57.601 40.909 17.22 0.00 34.07 5.34
798 873 3.806949 TGGGAAAAGGCTTATCACAGT 57.193 42.857 0.00 0.00 0.00 3.55
806 881 6.780457 AAAGGCTTATCACAGTATGCAAAT 57.220 33.333 0.00 0.00 42.53 2.32
807 882 6.382869 AAGGCTTATCACAGTATGCAAATC 57.617 37.500 0.00 0.00 42.53 2.17
808 883 5.688807 AGGCTTATCACAGTATGCAAATCT 58.311 37.500 0.00 0.00 42.53 2.40
809 884 5.762218 AGGCTTATCACAGTATGCAAATCTC 59.238 40.000 0.00 0.00 42.53 2.75
811 886 6.293298 GGCTTATCACAGTATGCAAATCTCTG 60.293 42.308 0.00 0.00 42.53 3.35
814 889 4.611310 CACAGTATGCAAATCTCTGTGG 57.389 45.455 21.21 10.63 46.64 4.17
815 890 3.012518 ACAGTATGCAAATCTCTGTGGC 58.987 45.455 0.00 0.00 42.53 5.01
817 892 3.311871 CAGTATGCAAATCTCTGTGGCTC 59.688 47.826 0.00 0.00 0.00 4.70
820 895 2.430465 TGCAAATCTCTGTGGCTCTTC 58.570 47.619 0.00 0.00 0.00 2.87
821 896 1.742268 GCAAATCTCTGTGGCTCTTCC 59.258 52.381 0.00 0.00 0.00 3.46
822 897 2.363683 CAAATCTCTGTGGCTCTTCCC 58.636 52.381 0.00 0.00 0.00 3.97
823 898 0.539051 AATCTCTGTGGCTCTTCCCG 59.461 55.000 0.00 0.00 0.00 5.14
824 899 1.965754 ATCTCTGTGGCTCTTCCCGC 61.966 60.000 0.00 0.00 35.93 6.13
829 904 1.302511 GTGGCTCTTCCCGCAGAAA 60.303 57.895 0.00 0.00 35.46 2.52
830 905 0.889186 GTGGCTCTTCCCGCAGAAAA 60.889 55.000 0.00 0.00 35.46 2.29
831 906 0.179004 TGGCTCTTCCCGCAGAAAAA 60.179 50.000 0.00 0.00 32.88 1.94
866 975 3.491619 CGTGGCTCTATGCTTACAGTGAT 60.492 47.826 0.00 0.00 42.39 3.06
880 989 9.066892 TGCTTACAGTGATGAAGTTCTTAAATT 57.933 29.630 4.17 0.00 0.00 1.82
950 1059 0.311165 CGGTTAGATCATCCGCGACT 59.689 55.000 8.23 0.00 37.90 4.18
973 1082 2.770259 GTCGCCGTCTTCTTTCGC 59.230 61.111 0.00 0.00 0.00 4.70
977 1086 2.101233 GCCGTCTTCTTTCGCCTCC 61.101 63.158 0.00 0.00 0.00 4.30
1122 1363 0.804364 TAGTGTACGCGTTCGGTGAT 59.196 50.000 20.78 0.00 40.69 3.06
1357 1598 1.445095 CATCTCCTCTGCCCTTCGG 59.555 63.158 0.00 0.00 0.00 4.30
1574 1822 2.615447 ACAGTGATGTGCTTGTTCAGTG 59.385 45.455 0.00 5.64 43.35 3.66
1697 1945 0.318445 CACCTTGCACTGCTTTCAGC 60.318 55.000 1.98 0.00 44.10 4.26
1767 2015 5.048083 GGAAAGCATACATCAACCAAACTGA 60.048 40.000 0.00 0.00 0.00 3.41
1860 2108 3.857157 TGTAGCTCAAAACCTCAACCT 57.143 42.857 0.00 0.00 0.00 3.50
2346 2594 4.262079 GGAGATATGGGTCAAAGTACCGAG 60.262 50.000 0.00 0.00 40.73 4.63
2429 2677 3.299503 AGGCTGTTGAAAAGATGGTTGT 58.700 40.909 0.00 0.00 0.00 3.32
2430 2678 3.319122 AGGCTGTTGAAAAGATGGTTGTC 59.681 43.478 0.00 0.00 0.00 3.18
2649 2919 3.281727 TCTCTCTCTCTCTCTGAAGGC 57.718 52.381 0.00 0.00 0.00 4.35
3259 3530 5.009210 GGCACTGACAATGTTAAAACTGGTA 59.991 40.000 0.00 0.00 0.00 3.25
3261 3532 7.145323 GCACTGACAATGTTAAAACTGGTATT 58.855 34.615 0.00 0.00 0.00 1.89
3402 3673 5.704978 TCATTCCATTGTTCTCATGTCGAAA 59.295 36.000 0.00 0.00 0.00 3.46
3429 3700 2.803593 TTTGGGCTTGGGGATCTGGC 62.804 60.000 0.00 0.00 0.00 4.85
3771 4043 8.616942 CGTCCATCATGGTAAATATTTGTGTTA 58.383 33.333 11.05 0.00 39.03 2.41
4065 4357 9.082313 ACTCTTTGATATCCAGAAAATTGTGTT 57.918 29.630 0.00 0.00 0.00 3.32
4066 4358 9.918630 CTCTTTGATATCCAGAAAATTGTGTTT 57.081 29.630 0.00 0.00 0.00 2.83
4073 4365 7.733402 ATCCAGAAAATTGTGTTTTGAATGG 57.267 32.000 0.00 0.00 0.00 3.16
4074 4366 6.648192 TCCAGAAAATTGTGTTTTGAATGGT 58.352 32.000 0.00 0.00 0.00 3.55
4075 4367 6.538021 TCCAGAAAATTGTGTTTTGAATGGTG 59.462 34.615 0.00 0.00 0.00 4.17
4076 4368 6.315891 CCAGAAAATTGTGTTTTGAATGGTGT 59.684 34.615 0.00 0.00 0.00 4.16
4090 4382 7.759489 TTGAATGGTGTAATAAGCACTTTCT 57.241 32.000 0.00 0.00 37.07 2.52
4327 4621 6.749923 AATACTTCCTCTGTCTCAAAATGC 57.250 37.500 0.00 0.00 0.00 3.56
4434 4731 9.903682 ATAAGCAAATGATATGCATGTTACTTC 57.096 29.630 10.16 0.00 46.22 3.01
4441 4738 9.926158 AATGATATGCATGTTACTTCACAAAAA 57.074 25.926 10.16 0.00 37.28 1.94
4443 4740 9.571810 TGATATGCATGTTACTTCACAAAAATC 57.428 29.630 10.16 0.00 0.00 2.17
4444 4741 6.932901 ATGCATGTTACTTCACAAAAATCG 57.067 33.333 0.00 0.00 0.00 3.34
4491 4789 5.622180 AGTGTTTTCTTTTCTACTCCCTCC 58.378 41.667 0.00 0.00 0.00 4.30
4492 4790 4.451435 GTGTTTTCTTTTCTACTCCCTCCG 59.549 45.833 0.00 0.00 0.00 4.63
4493 4791 4.102054 TGTTTTCTTTTCTACTCCCTCCGT 59.898 41.667 0.00 0.00 0.00 4.69
4494 4792 4.968971 TTTCTTTTCTACTCCCTCCGTT 57.031 40.909 0.00 0.00 0.00 4.44
4495 4793 4.532314 TTCTTTTCTACTCCCTCCGTTC 57.468 45.455 0.00 0.00 0.00 3.95
4496 4794 2.830321 TCTTTTCTACTCCCTCCGTTCC 59.170 50.000 0.00 0.00 0.00 3.62
4497 4795 2.617840 TTTCTACTCCCTCCGTTCCT 57.382 50.000 0.00 0.00 0.00 3.36
4498 4796 3.744940 TTTCTACTCCCTCCGTTCCTA 57.255 47.619 0.00 0.00 0.00 2.94
4499 4797 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
4500 4798 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
4501 4799 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
4502 4800 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
4503 4801 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
4504 4802 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
4505 4803 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4506 4804 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4507 4805 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4508 4806 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4509 4807 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4510 4808 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4511 4809 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4512 4810 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4513 4811 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4514 4812 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4515 4813 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
4516 4814 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
4540 4838 9.302345 AGACATTTTGAATGACTACTACATACG 57.698 33.333 7.59 0.00 0.00 3.06
4541 4839 8.420374 ACATTTTGAATGACTACTACATACGG 57.580 34.615 7.59 0.00 0.00 4.02
4542 4840 8.255206 ACATTTTGAATGACTACTACATACGGA 58.745 33.333 7.59 0.00 0.00 4.69
4543 4841 9.261180 CATTTTGAATGACTACTACATACGGAT 57.739 33.333 0.00 0.00 0.00 4.18
4544 4842 8.642908 TTTTGAATGACTACTACATACGGATG 57.357 34.615 5.94 5.94 39.16 3.51
4546 4844 8.454570 TTGAATGACTACTACATACGGATGTA 57.545 34.615 19.32 19.32 44.77 2.29
4547 4845 8.631480 TGAATGACTACTACATACGGATGTAT 57.369 34.615 20.64 13.02 45.42 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 0.678048 GGCCCAGGAAGTACTGCTTG 60.678 60.000 5.98 5.98 37.59 4.01
450 451 0.322098 TTTACACCCACCCTCGCATG 60.322 55.000 0.00 0.00 0.00 4.06
563 564 2.605580 GGAAAGAAAGGCGCAGAAGTTG 60.606 50.000 10.83 0.00 0.00 3.16
564 565 1.609072 GGAAAGAAAGGCGCAGAAGTT 59.391 47.619 10.83 0.00 0.00 2.66
565 566 1.239347 GGAAAGAAAGGCGCAGAAGT 58.761 50.000 10.83 0.00 0.00 3.01
566 567 0.523519 GGGAAAGAAAGGCGCAGAAG 59.476 55.000 10.83 0.00 0.00 2.85
567 568 0.110486 AGGGAAAGAAAGGCGCAGAA 59.890 50.000 10.83 0.00 0.00 3.02
572 573 2.343426 GGCCAGGGAAAGAAAGGCG 61.343 63.158 0.00 0.00 46.12 5.52
574 575 0.323816 GAGGGCCAGGGAAAGAAAGG 60.324 60.000 6.18 0.00 0.00 3.11
586 587 2.498885 CGATATGATCAGATGAGGGCCA 59.501 50.000 7.74 0.00 0.00 5.36
588 589 3.883830 ACGATATGATCAGATGAGGGC 57.116 47.619 7.74 0.00 0.00 5.19
589 590 4.396478 ACGTACGATATGATCAGATGAGGG 59.604 45.833 24.41 0.00 0.00 4.30
594 595 4.766404 TGCACGTACGATATGATCAGAT 57.234 40.909 24.41 1.59 0.00 2.90
599 600 3.745975 CCCAATTGCACGTACGATATGAT 59.254 43.478 24.41 6.20 0.00 2.45
601 602 2.349438 GCCCAATTGCACGTACGATATG 60.349 50.000 24.41 11.30 0.00 1.78
602 603 1.871039 GCCCAATTGCACGTACGATAT 59.129 47.619 24.41 6.33 0.00 1.63
619 620 2.028112 TGTCATCATAATCTAGCCGCCC 60.028 50.000 0.00 0.00 0.00 6.13
636 711 0.394216 ATGCAATAAGGCCGCTGTCA 60.394 50.000 0.00 0.00 0.00 3.58
639 714 1.002033 GAAGATGCAATAAGGCCGCTG 60.002 52.381 0.00 0.00 0.00 5.18
642 717 5.695851 ATAAAGAAGATGCAATAAGGCCG 57.304 39.130 0.00 0.00 0.00 6.13
699 774 9.775854 ATCACATATACTACTCAGTACGTAGTT 57.224 33.333 14.65 7.79 43.61 2.24
745 820 8.561212 ACGTGTATTTTCTTACAGCAACAATTA 58.439 29.630 0.00 0.00 32.92 1.40
760 835 4.551388 TCCCAAAATGCACGTGTATTTTC 58.449 39.130 37.92 15.98 44.52 2.29
764 839 4.555262 CTTTTCCCAAAATGCACGTGTAT 58.445 39.130 18.38 16.07 0.00 2.29
765 840 3.243569 CCTTTTCCCAAAATGCACGTGTA 60.244 43.478 18.38 14.09 0.00 2.90
773 848 5.792741 TGTGATAAGCCTTTTCCCAAAATG 58.207 37.500 0.00 0.00 0.00 2.32
788 863 7.783090 ACAGAGATTTGCATACTGTGATAAG 57.217 36.000 15.37 0.00 39.76 1.73
798 873 3.920231 AGAGCCACAGAGATTTGCATA 57.080 42.857 0.00 0.00 0.00 3.14
806 881 2.650116 GCGGGAAGAGCCACAGAGA 61.650 63.158 0.00 0.00 38.95 3.10
807 882 2.125350 GCGGGAAGAGCCACAGAG 60.125 66.667 0.00 0.00 38.95 3.35
808 883 2.922503 TGCGGGAAGAGCCACAGA 60.923 61.111 0.00 0.00 38.95 3.41
809 884 2.435586 CTGCGGGAAGAGCCACAG 60.436 66.667 0.00 0.00 38.95 3.66
811 886 0.889186 TTTTCTGCGGGAAGAGCCAC 60.889 55.000 0.00 0.00 38.95 5.01
829 904 4.583073 AGAGCCACGGAGTTTATTTGTTTT 59.417 37.500 0.00 0.00 41.61 2.43
830 905 4.142038 AGAGCCACGGAGTTTATTTGTTT 58.858 39.130 0.00 0.00 41.61 2.83
831 906 3.751518 AGAGCCACGGAGTTTATTTGTT 58.248 40.909 0.00 0.00 41.61 2.83
832 907 3.418684 AGAGCCACGGAGTTTATTTGT 57.581 42.857 0.00 0.00 41.61 2.83
833 908 4.260784 GCATAGAGCCACGGAGTTTATTTG 60.261 45.833 0.00 0.00 41.61 2.32
836 911 3.113260 GCATAGAGCCACGGAGTTTAT 57.887 47.619 0.00 0.00 41.61 1.40
837 912 2.596904 GCATAGAGCCACGGAGTTTA 57.403 50.000 0.00 0.00 41.61 2.01
838 913 3.460648 GCATAGAGCCACGGAGTTT 57.539 52.632 0.00 0.00 41.61 2.66
848 923 5.355596 ACTTCATCACTGTAAGCATAGAGC 58.644 41.667 0.00 0.00 46.19 4.09
849 924 7.264221 AGAACTTCATCACTGTAAGCATAGAG 58.736 38.462 0.00 0.00 37.60 2.43
866 975 2.823154 CCGGCCCAATTTAAGAACTTCA 59.177 45.455 0.00 0.00 0.00 3.02
973 1082 4.821589 GCAGCCGTCGAAGGGAGG 62.822 72.222 19.34 3.82 0.00 4.30
1048 1289 3.154473 AAGCGCGGATAGGAGGCA 61.154 61.111 8.83 0.00 0.00 4.75
1051 1292 2.106938 TGCAAGCGCGGATAGGAG 59.893 61.111 8.83 0.00 42.97 3.69
1357 1598 6.428159 AGTTCAATTCATATACTGATTCGCCC 59.572 38.462 0.00 0.00 32.72 6.13
1517 1765 1.614903 CCAGAAAGAAATGGTGCTGCA 59.385 47.619 0.00 0.00 0.00 4.41
1518 1766 1.670967 GCCAGAAAGAAATGGTGCTGC 60.671 52.381 0.00 0.00 38.91 5.25
1519 1767 1.067354 GGCCAGAAAGAAATGGTGCTG 60.067 52.381 0.00 0.00 38.91 4.41
1574 1822 3.957468 GCATCTTTGTTATGCTGGTAGC 58.043 45.455 0.00 0.00 45.05 3.58
1767 2015 7.156673 GCAAGAAAAATATGGGTGCATCATAT 58.843 34.615 15.45 15.45 38.89 1.78
2301 2549 7.230712 TCTCCTAACCTTCCATTTTCTGAAAAC 59.769 37.037 17.06 0.00 32.37 2.43
2346 2594 2.206576 ATTCTTGTGGAGAAGGTGCC 57.793 50.000 0.00 0.00 46.99 5.01
2429 2677 1.346365 CTCGCTCCGAATTTTGTCGA 58.654 50.000 0.00 0.00 43.86 4.20
2430 2678 0.370273 CCTCGCTCCGAATTTTGTCG 59.630 55.000 0.00 0.00 40.77 4.35
2649 2919 6.474751 GCCCTACGTCTTATTAAACACTACTG 59.525 42.308 0.00 0.00 0.00 2.74
2896 3167 3.944055 ATCTCCGTCATACTACATGCC 57.056 47.619 0.00 0.00 0.00 4.40
2960 3231 2.629137 TCATTTGTCCAAAGCTGTGCAT 59.371 40.909 0.00 0.00 33.32 3.96
3087 3358 1.244816 TGTCTCCACCACTCAGTACG 58.755 55.000 0.00 0.00 0.00 3.67
3259 3530 4.508047 GCAGTTCCATCCCCATGATAGAAT 60.508 45.833 0.00 0.00 34.34 2.40
3261 3532 2.373169 GCAGTTCCATCCCCATGATAGA 59.627 50.000 0.00 0.00 30.57 1.98
3402 3673 0.113190 CCCAAGCCCAAACTTCTCCT 59.887 55.000 0.00 0.00 0.00 3.69
3429 3700 2.403252 AACCTAGTCTGCCATTTCGG 57.597 50.000 0.00 0.00 38.11 4.30
3675 3946 4.211374 ACAATTCTGAAAGCGTGTGAGTAC 59.789 41.667 0.00 0.00 0.00 2.73
3771 4043 1.576577 TCACCACCAGAGATGATGCT 58.423 50.000 0.00 0.00 0.00 3.79
3920 4193 6.479990 CCGAGATGTTAGCAATAGAACATTCA 59.520 38.462 2.09 0.00 44.35 2.57
4065 4357 8.177119 AGAAAGTGCTTATTACACCATTCAAA 57.823 30.769 10.64 0.00 38.87 2.69
4066 4358 7.759489 AGAAAGTGCTTATTACACCATTCAA 57.241 32.000 10.64 0.00 38.87 2.69
4067 4359 7.759489 AAGAAAGTGCTTATTACACCATTCA 57.241 32.000 10.64 0.00 38.87 2.57
4068 4360 8.182227 GGTAAGAAAGTGCTTATTACACCATTC 58.818 37.037 15.55 0.00 38.87 2.67
4069 4361 7.668052 TGGTAAGAAAGTGCTTATTACACCATT 59.332 33.333 15.55 0.00 38.87 3.16
4070 4362 7.172342 TGGTAAGAAAGTGCTTATTACACCAT 58.828 34.615 15.55 0.00 38.87 3.55
4071 4363 6.535540 TGGTAAGAAAGTGCTTATTACACCA 58.464 36.000 15.55 9.78 38.87 4.17
4072 4364 7.625828 ATGGTAAGAAAGTGCTTATTACACC 57.374 36.000 15.55 8.09 38.87 4.16
4187 4480 6.591001 TCACTAGCTATGGCAATATGTTCAA 58.409 36.000 3.10 0.00 41.70 2.69
4340 4634 5.238650 ACTCCCTTTGTTTCAATGTAAGACG 59.761 40.000 0.00 0.00 0.00 4.18
4434 4731 7.270365 ACAAACGCTATTGTATCGATTTTTGTG 59.730 33.333 1.71 0.00 41.56 3.33
4452 4750 7.871853 AGAAAACACTATTGAATACAAACGCT 58.128 30.769 0.00 0.00 39.54 5.07
4514 4812 9.302345 CGTATGTAGTAGTCATTCAAAATGTCT 57.698 33.333 5.13 5.13 0.00 3.41
4515 4813 8.540492 CCGTATGTAGTAGTCATTCAAAATGTC 58.460 37.037 0.04 0.00 0.00 3.06
4516 4814 8.255206 TCCGTATGTAGTAGTCATTCAAAATGT 58.745 33.333 0.04 0.00 0.00 2.71
4517 4815 8.642908 TCCGTATGTAGTAGTCATTCAAAATG 57.357 34.615 0.00 0.00 0.00 2.32
4518 4816 9.261180 CATCCGTATGTAGTAGTCATTCAAAAT 57.739 33.333 0.00 0.00 0.00 1.82
4519 4817 8.255206 ACATCCGTATGTAGTAGTCATTCAAAA 58.745 33.333 0.00 0.00 44.66 2.44
4520 4818 7.778083 ACATCCGTATGTAGTAGTCATTCAAA 58.222 34.615 0.00 0.00 44.66 2.69
4521 4819 7.342769 ACATCCGTATGTAGTAGTCATTCAA 57.657 36.000 0.00 0.00 44.66 2.69
4522 4820 6.954487 ACATCCGTATGTAGTAGTCATTCA 57.046 37.500 0.00 0.00 44.66 2.57


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

AutoCloner maintained by Alex Coulton.