Multiple sequence alignment - TraesCS6B01G346100

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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 TraesCS6B01G346100 chr6B 100.000 3546 0 0 1 3546 609885559 609889104 0.000000e+00 6549.0
1 TraesCS6B01G346100 chr6B 95.055 546 25 2 1 545 68414613 68415157 0.000000e+00 857.0
2 TraesCS6B01G346100 chr6B 93.934 544 30 2 1 541 151426890 151426347 0.000000e+00 819.0
3 TraesCS6B01G346100 chr6A 90.984 2440 99 49 566 2952 552264328 552266699 0.000000e+00 3175.0
4 TraesCS6B01G346100 chr6A 88.337 463 28 10 3103 3543 552267289 552267747 1.870000e-147 532.0
5 TraesCS6B01G346100 chr6A 94.565 92 5 0 1963 2054 487692531 487692622 3.690000e-30 143.0
6 TraesCS6B01G346100 chr6A 95.000 40 2 0 1525 1564 485747790 485747751 2.960000e-06 63.9
7 TraesCS6B01G346100 chr6D 91.010 2347 99 52 668 2980 405672405 405674673 0.000000e+00 3062.0
8 TraesCS6B01G346100 chr6D 95.556 180 7 1 3292 3471 405675446 405675624 1.610000e-73 287.0
9 TraesCS6B01G346100 chr7B 94.455 541 29 1 1 540 72954321 72953781 0.000000e+00 832.0
10 TraesCS6B01G346100 chr7B 100.000 36 0 0 1528 1563 624705929 624705894 2.280000e-07 67.6
11 TraesCS6B01G346100 chr5B 94.465 542 27 2 1 539 696569780 696570321 0.000000e+00 832.0
12 TraesCS6B01G346100 chr5B 94.727 531 27 1 1 530 633887873 633887343 0.000000e+00 824.0
13 TraesCS6B01G346100 chr5B 83.146 89 15 0 1966 2054 427239252 427239340 8.160000e-12 82.4
14 TraesCS6B01G346100 chr1B 94.361 532 28 1 1 530 44470650 44471181 0.000000e+00 815.0
15 TraesCS6B01G346100 chr1B 97.436 39 1 0 1525 1563 488414764 488414802 2.280000e-07 67.6
16 TraesCS6B01G346100 chr3A 92.674 546 33 6 1 541 422913175 422913718 0.000000e+00 780.0
17 TraesCS6B01G346100 chr7D 92.491 546 34 6 1 541 7733455 7732912 0.000000e+00 774.0
18 TraesCS6B01G346100 chrUn 91.743 545 40 4 1 544 29293255 29292715 0.000000e+00 752.0
19 TraesCS6B01G346100 chr5D 88.095 84 10 0 1966 2049 361606928 361607011 2.250000e-17 100.0
20 TraesCS6B01G346100 chr5A 87.805 82 10 0 1966 2047 462145666 462145747 2.910000e-16 97.1
21 TraesCS6B01G346100 chr5A 92.857 42 3 0 1525 1566 692840293 692840252 1.060000e-05 62.1
22 TraesCS6B01G346100 chr2B 100.000 37 0 0 1525 1561 487225334 487225298 6.350000e-08 69.4
23 TraesCS6B01G346100 chr2D 95.122 41 2 0 1525 1565 537445790 537445750 8.220000e-07 65.8
24 TraesCS6B01G346100 chr2A 94.872 39 2 0 1525 1563 51185482 51185444 1.060000e-05 62.1
25 TraesCS6B01G346100 chr1A 95.000 40 1 1 1525 1564 490290862 490290900 1.060000e-05 62.1


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 TraesCS6B01G346100 chr6B 609885559 609889104 3545 False 6549.0 6549 100.0000 1 3546 1 chr6B.!!$F2 3545
1 TraesCS6B01G346100 chr6B 68414613 68415157 544 False 857.0 857 95.0550 1 545 1 chr6B.!!$F1 544
2 TraesCS6B01G346100 chr6B 151426347 151426890 543 True 819.0 819 93.9340 1 541 1 chr6B.!!$R1 540
3 TraesCS6B01G346100 chr6A 552264328 552267747 3419 False 1853.5 3175 89.6605 566 3543 2 chr6A.!!$F2 2977
4 TraesCS6B01G346100 chr6D 405672405 405675624 3219 False 1674.5 3062 93.2830 668 3471 2 chr6D.!!$F1 2803
5 TraesCS6B01G346100 chr7B 72953781 72954321 540 True 832.0 832 94.4550 1 540 1 chr7B.!!$R1 539
6 TraesCS6B01G346100 chr5B 696569780 696570321 541 False 832.0 832 94.4650 1 539 1 chr5B.!!$F2 538
7 TraesCS6B01G346100 chr5B 633887343 633887873 530 True 824.0 824 94.7270 1 530 1 chr5B.!!$R1 529
8 TraesCS6B01G346100 chr1B 44470650 44471181 531 False 815.0 815 94.3610 1 530 1 chr1B.!!$F1 529
9 TraesCS6B01G346100 chr3A 422913175 422913718 543 False 780.0 780 92.6740 1 541 1 chr3A.!!$F1 540
10 TraesCS6B01G346100 chr7D 7732912 7733455 543 True 774.0 774 92.4910 1 541 1 chr7D.!!$R1 540
11 TraesCS6B01G346100 chrUn 29292715 29293255 540 True 752.0 752 91.7430 1 544 1 chrUn.!!$R1 543

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
692 706 0.321671 AATATCGTCTGCCCCATCGG 59.678 55.0 0.00 0.00 0.00 4.18 F
1601 1629 0.103208 CAAGCTAGGCTCTACCGGTG 59.897 60.0 19.93 7.59 46.52 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2390 2439 0.031314 CAGAGCGCGGATGTAGATGT 59.969 55.0 8.83 0.0 0.00 3.06 R
3066 3145 0.454600 GGTCGGCTGAGACATAACGA 59.545 55.0 0.00 0.0 42.62 3.85 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
58 59 2.026262 ACGTGGCTTAATGGGATTGAGT 60.026 45.455 0.00 0.00 0.00 3.41
69 70 2.961526 GGATTGAGTCCGACTTAGCA 57.038 50.000 1.71 0.00 37.23 3.49
79 80 5.978814 AGTCCGACTTAGCAAGACATATTT 58.021 37.500 0.00 0.00 0.00 1.40
133 134 4.828939 TCTGGACTTGCAGAAATGATTTGT 59.171 37.500 0.00 0.00 0.00 2.83
247 248 2.807676 CCAGGGAGCATTTGGTTACTT 58.192 47.619 0.00 0.00 0.00 2.24
262 263 3.321111 GGTTACTTGATCTATCCGCTGGA 59.679 47.826 0.00 0.00 35.55 3.86
353 354 2.968574 CCTATCTCTCTTTAGCCAGCCA 59.031 50.000 0.00 0.00 0.00 4.75
563 567 2.749839 TGGCACGCCATGTAAGCC 60.750 61.111 6.67 8.31 41.89 4.35
564 568 2.438434 GGCACGCCATGTAAGCCT 60.438 61.111 2.36 0.00 42.01 4.58
627 635 8.712285 TTTTACGATTTTATGGACTAGAGTGG 57.288 34.615 0.00 0.00 0.00 4.00
640 648 4.620723 ACTAGAGTGGACCCATATGACAA 58.379 43.478 3.65 0.00 0.00 3.18
644 652 5.831103 AGAGTGGACCCATATGACAAATTT 58.169 37.500 3.65 0.00 0.00 1.82
650 658 6.440010 TGGACCCATATGACAAATTTGTGAAT 59.560 34.615 27.85 21.02 42.43 2.57
652 660 6.108015 ACCCATATGACAAATTTGTGAATGC 58.892 36.000 27.85 13.48 42.43 3.56
654 662 6.342906 CCATATGACAAATTTGTGAATGCCT 58.657 36.000 27.85 7.27 42.43 4.75
679 693 9.855361 CTGAGTGCAATTAACTAAAGAATATCG 57.145 33.333 0.00 0.00 0.00 2.92
692 706 0.321671 AATATCGTCTGCCCCATCGG 59.678 55.000 0.00 0.00 0.00 4.18
738 756 1.084370 GGCAGATCGGGTCTTTGTCG 61.084 60.000 0.00 0.00 34.00 4.35
808 827 1.154413 CCACGCGTCTCATTTGCAC 60.154 57.895 9.86 0.00 0.00 4.57
827 848 2.368011 CCGTCCTTCCTTCCTCCCC 61.368 68.421 0.00 0.00 0.00 4.81
831 852 1.162951 TCCTTCCTTCCTCCCCCTCT 61.163 60.000 0.00 0.00 0.00 3.69
932 955 2.225255 GCTGGTCTCTTCTTGTTCTTGC 59.775 50.000 0.00 0.00 0.00 4.01
937 960 3.185391 GTCTCTTCTTGTTCTTGCCTTCG 59.815 47.826 0.00 0.00 0.00 3.79
938 961 2.481952 CTCTTCTTGTTCTTGCCTTCGG 59.518 50.000 0.00 0.00 0.00 4.30
941 964 1.140052 TCTTGTTCTTGCCTTCGGTGA 59.860 47.619 0.00 0.00 0.00 4.02
955 978 2.453521 TCGGTGAGTAGTAGCATGGTT 58.546 47.619 1.12 0.00 0.00 3.67
971 994 0.322008 GGTTTGAGGCTGGGTCTCTG 60.322 60.000 0.00 0.00 35.05 3.35
1008 1031 1.445238 GCTCGATCCTATGGCGCTC 60.445 63.158 7.64 0.00 0.00 5.03
1083 1106 4.102561 GCGATGTCCATGTACGCA 57.897 55.556 0.00 0.00 46.75 5.24
1137 1163 3.145551 GAGGAGAAGGGCGGCGTA 61.146 66.667 9.37 0.00 0.00 4.42
1149 1175 1.805945 CGGCGTAGTGCTCCAAGAC 60.806 63.158 0.00 0.00 45.43 3.01
1150 1176 1.448013 GGCGTAGTGCTCCAAGACC 60.448 63.158 0.00 0.00 45.43 3.85
1151 1177 1.292223 GCGTAGTGCTCCAAGACCA 59.708 57.895 0.00 0.00 41.73 4.02
1152 1178 0.320421 GCGTAGTGCTCCAAGACCAA 60.320 55.000 0.00 0.00 41.73 3.67
1153 1179 1.714794 CGTAGTGCTCCAAGACCAAG 58.285 55.000 0.00 0.00 0.00 3.61
1154 1180 1.272490 CGTAGTGCTCCAAGACCAAGA 59.728 52.381 0.00 0.00 0.00 3.02
1163 1189 1.072965 CCAAGACCAAGAAGAGGTGCT 59.927 52.381 0.00 0.00 40.09 4.40
1212 1238 0.905337 AGGGGAACTGGGACGAGAAG 60.905 60.000 0.00 0.00 0.00 2.85
1219 1245 2.164865 CTGGGACGAGAAGCACTGCT 62.165 60.000 0.00 0.00 42.56 4.24
1222 1248 1.739562 GACGAGAAGCACTGCTGGG 60.740 63.158 3.73 0.00 39.62 4.45
1224 1250 2.749441 GAGAAGCACTGCTGGGCC 60.749 66.667 14.92 0.00 39.62 5.80
1551 1579 2.046507 GCCAGAGGCCAGTCACTG 60.047 66.667 5.01 0.00 44.06 3.66
1562 1590 0.539051 CAGTCACTGGATCCCTGTCC 59.461 60.000 9.90 1.72 33.44 4.02
1577 1605 2.043992 CTGTCCCCCGTACCATTATCA 58.956 52.381 0.00 0.00 0.00 2.15
1601 1629 0.103208 CAAGCTAGGCTCTACCGGTG 59.897 60.000 19.93 7.59 46.52 4.94
1734 1770 2.829914 GCGATGCCATTGCTCCCA 60.830 61.111 9.75 0.00 38.71 4.37
1735 1771 2.198287 GCGATGCCATTGCTCCCAT 61.198 57.895 9.75 0.00 38.71 4.00
1736 1772 1.658114 CGATGCCATTGCTCCCATG 59.342 57.895 0.00 0.00 38.71 3.66
1754 1794 4.501714 CATGCATGCACACCGCCC 62.502 66.667 25.37 0.00 41.33 6.13
2390 2439 5.490159 TGAGCATCACACACATTAATCTGA 58.510 37.500 0.00 0.00 42.56 3.27
2394 2443 6.037940 AGCATCACACACATTAATCTGACATC 59.962 38.462 0.00 0.00 0.00 3.06
2404 2453 2.713895 ATCTGACATCTACATCCGCG 57.286 50.000 0.00 0.00 0.00 6.46
2569 2634 4.464069 AGCTAGTTAGTTGAGCTGGAAG 57.536 45.455 0.00 0.00 44.77 3.46
2570 2635 3.835395 AGCTAGTTAGTTGAGCTGGAAGT 59.165 43.478 0.00 0.00 44.77 3.01
2613 2678 3.140519 AGTCCGATCCTATCCTGGTAGTT 59.859 47.826 0.00 0.00 0.00 2.24
2618 2683 4.099573 CGATCCTATCCTGGTAGTTGTTGT 59.900 45.833 0.00 0.00 0.00 3.32
2631 2696 2.622942 AGTTGTTGTGTGCATGGGTAAG 59.377 45.455 0.00 0.00 0.00 2.34
2634 2699 1.539827 GTTGTGTGCATGGGTAAGTCC 59.460 52.381 0.00 0.00 0.00 3.85
2741 2810 4.732784 CCAATTATTTGTCTGTCCCAACG 58.267 43.478 0.00 0.00 0.00 4.10
2748 2817 0.602638 GTCTGTCCCAACGTGCATGA 60.603 55.000 14.17 0.00 0.00 3.07
2769 2844 3.467226 CGTGTCCATACGGGGCCT 61.467 66.667 0.84 0.00 42.20 5.19
2829 2908 5.667466 TCACCGGATAATAAGAAGAACCAC 58.333 41.667 9.46 0.00 0.00 4.16
2942 3021 8.906693 CGATCATGTATGTAGAATAGTGTTGTC 58.093 37.037 0.00 0.00 0.00 3.18
2954 3033 2.456577 AGTGTTGTCTTTTTGGTGGCT 58.543 42.857 0.00 0.00 0.00 4.75
2960 3039 2.569404 TGTCTTTTTGGTGGCTGGTTTT 59.431 40.909 0.00 0.00 0.00 2.43
2990 3069 6.177610 TCGGGATTTAACTATCAGTTTTGCT 58.822 36.000 0.00 0.00 39.51 3.91
3000 3079 8.854614 AACTATCAGTTTTGCTAATTCTCAGT 57.145 30.769 0.00 0.00 34.11 3.41
3001 3080 8.485976 ACTATCAGTTTTGCTAATTCTCAGTC 57.514 34.615 0.00 0.00 0.00 3.51
3006 3085 5.934625 AGTTTTGCTAATTCTCAGTCGACAT 59.065 36.000 19.50 0.00 0.00 3.06
3009 3088 3.447229 TGCTAATTCTCAGTCGACATGGA 59.553 43.478 19.50 11.08 0.00 3.41
3010 3089 4.081697 TGCTAATTCTCAGTCGACATGGAA 60.082 41.667 19.50 17.06 0.00 3.53
3011 3090 4.870426 GCTAATTCTCAGTCGACATGGAAA 59.130 41.667 19.50 10.70 0.00 3.13
3013 3092 6.292596 GCTAATTCTCAGTCGACATGGAAATC 60.293 42.308 19.50 5.83 0.00 2.17
3014 3093 3.526931 TCTCAGTCGACATGGAAATCC 57.473 47.619 19.50 0.00 0.00 3.01
3081 3160 6.844696 TTTATTCATCGTTATGTCTCAGCC 57.155 37.500 0.00 0.00 34.50 4.85
3084 3163 2.120232 CATCGTTATGTCTCAGCCGAC 58.880 52.381 0.00 0.00 34.52 4.79
3085 3164 0.454600 TCGTTATGTCTCAGCCGACC 59.545 55.000 0.00 0.00 32.97 4.79
3088 3167 2.098607 CGTTATGTCTCAGCCGACCTAA 59.901 50.000 0.00 0.00 32.97 2.69
3089 3168 3.445857 GTTATGTCTCAGCCGACCTAAC 58.554 50.000 9.23 9.23 37.62 2.34
3091 3170 0.601558 TGTCTCAGCCGACCTAACAC 59.398 55.000 0.00 0.00 32.97 3.32
3092 3171 0.601558 GTCTCAGCCGACCTAACACA 59.398 55.000 0.00 0.00 0.00 3.72
3093 3172 0.601558 TCTCAGCCGACCTAACACAC 59.398 55.000 0.00 0.00 0.00 3.82
3095 3174 2.048503 AGCCGACCTAACACACGC 60.049 61.111 0.00 0.00 0.00 5.34
3096 3175 2.048503 GCCGACCTAACACACGCT 60.049 61.111 0.00 0.00 0.00 5.07
3100 3618 2.406130 CCGACCTAACACACGCTTTTA 58.594 47.619 0.00 0.00 0.00 1.52
3101 3619 2.410730 CCGACCTAACACACGCTTTTAG 59.589 50.000 0.00 0.00 0.00 1.85
3110 3628 2.921121 CACACGCTTTTAGCTATCACGA 59.079 45.455 11.42 0.00 39.60 4.35
3117 3635 5.460419 CGCTTTTAGCTATCACGAAGAGAAT 59.540 40.000 0.00 0.00 39.60 2.40
3119 3637 7.149047 CGCTTTTAGCTATCACGAAGAGAATAG 60.149 40.741 0.00 0.00 39.60 1.73
3145 3663 6.627087 AATCAACTAACTCTCCAATCCTCA 57.373 37.500 0.00 0.00 0.00 3.86
3202 4091 5.221185 GGGCTTGTTACATACTCTATCGTGA 60.221 44.000 0.00 0.00 0.00 4.35
3255 4144 1.319541 GGGAGAACGGATCGAGATGA 58.680 55.000 0.00 0.00 0.00 2.92
3314 4362 1.017701 CGGTAAAACCTGACGGCCTC 61.018 60.000 0.00 0.00 35.66 4.70
3412 4468 2.550606 CGTCCTACTCTGCTCCTACATC 59.449 54.545 0.00 0.00 0.00 3.06
3471 4527 6.015504 GTGCAGATAACATAACACTTCGTTG 58.984 40.000 0.00 0.00 38.63 4.10
3472 4528 5.699001 TGCAGATAACATAACACTTCGTTGT 59.301 36.000 0.00 0.00 38.63 3.32
3473 4529 6.203915 TGCAGATAACATAACACTTCGTTGTT 59.796 34.615 5.42 5.42 42.46 2.83
3474 4530 7.075741 GCAGATAACATAACACTTCGTTGTTT 58.924 34.615 5.40 0.00 40.29 2.83
3475 4531 7.589954 GCAGATAACATAACACTTCGTTGTTTT 59.410 33.333 5.40 0.00 40.29 2.43
3477 4533 9.052759 AGATAACATAACACTTCGTTGTTTTCT 57.947 29.630 5.40 0.00 40.29 2.52
3478 4534 9.103048 GATAACATAACACTTCGTTGTTTTCTG 57.897 33.333 5.40 4.81 40.29 3.02
3479 4535 6.431198 ACATAACACTTCGTTGTTTTCTGT 57.569 33.333 5.40 5.26 40.29 3.41
3480 4536 6.255215 ACATAACACTTCGTTGTTTTCTGTG 58.745 36.000 5.40 0.00 40.29 3.66
3481 4537 4.759516 AACACTTCGTTGTTTTCTGTGT 57.240 36.364 0.00 0.00 36.22 3.72
3482 4538 4.078363 ACACTTCGTTGTTTTCTGTGTG 57.922 40.909 0.00 0.00 36.10 3.82
3517 4587 4.380843 TTCCCAGCTTCAGTATTTTCCA 57.619 40.909 0.00 0.00 0.00 3.53
3531 4601 7.392953 TCAGTATTTTCCACATGCAAGTCATTA 59.607 33.333 0.00 0.00 31.79 1.90
3543 4613 9.284968 ACATGCAAGTCATTAGTAAAAGTTACT 57.715 29.630 5.99 5.99 31.79 2.24
3544 4614 9.546909 CATGCAAGTCATTAGTAAAAGTTACTG 57.453 33.333 10.27 0.00 31.79 2.74
3545 4615 7.581476 TGCAAGTCATTAGTAAAAGTTACTGC 58.419 34.615 10.27 4.89 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 5.580691 CACAAATATGTCTTGCTAAGTCGGA 59.419 40.000 0.00 0.00 37.82 4.55
69 70 6.701841 CGCATACTCCTACACAAATATGTCTT 59.298 38.462 0.00 0.00 37.82 3.01
79 80 2.616960 CAAAGCGCATACTCCTACACA 58.383 47.619 11.47 0.00 0.00 3.72
247 248 3.136443 ACCATTTTCCAGCGGATAGATCA 59.864 43.478 0.00 0.00 0.00 2.92
262 263 5.071788 TGAAGATATCCCGAGCTACCATTTT 59.928 40.000 0.00 0.00 0.00 1.82
353 354 2.416701 CCAACAAAAGAACGCCACAACT 60.417 45.455 0.00 0.00 0.00 3.16
364 365 5.652994 AACACAAACTAGCCAACAAAAGA 57.347 34.783 0.00 0.00 0.00 2.52
547 551 2.438434 AGGCTTACATGGCGTGCC 60.438 61.111 6.62 3.30 43.52 5.01
548 552 1.709147 CTCAGGCTTACATGGCGTGC 61.709 60.000 6.62 2.82 42.81 5.34
549 553 0.108186 TCTCAGGCTTACATGGCGTG 60.108 55.000 4.87 4.87 43.94 5.34
550 554 0.833287 ATCTCAGGCTTACATGGCGT 59.167 50.000 0.00 0.00 37.59 5.68
551 555 2.681706 CTATCTCAGGCTTACATGGCG 58.318 52.381 0.00 0.00 37.59 5.69
552 556 2.421619 GCTATCTCAGGCTTACATGGC 58.578 52.381 0.00 0.00 0.00 4.40
553 557 3.051081 GGCTATCTCAGGCTTACATGG 57.949 52.381 0.00 0.00 46.26 3.66
602 607 8.533657 TCCACTCTAGTCCATAAAATCGTAAAA 58.466 33.333 0.00 0.00 0.00 1.52
603 608 7.977853 GTCCACTCTAGTCCATAAAATCGTAAA 59.022 37.037 0.00 0.00 0.00 2.01
604 609 7.417116 GGTCCACTCTAGTCCATAAAATCGTAA 60.417 40.741 0.00 0.00 0.00 3.18
605 610 6.040166 GGTCCACTCTAGTCCATAAAATCGTA 59.960 42.308 0.00 0.00 0.00 3.43
606 611 5.163437 GGTCCACTCTAGTCCATAAAATCGT 60.163 44.000 0.00 0.00 0.00 3.73
607 612 5.290386 GGTCCACTCTAGTCCATAAAATCG 58.710 45.833 0.00 0.00 0.00 3.34
608 613 5.130477 TGGGTCCACTCTAGTCCATAAAATC 59.870 44.000 0.00 0.00 0.00 2.17
609 614 5.036916 TGGGTCCACTCTAGTCCATAAAAT 58.963 41.667 0.00 0.00 0.00 1.82
610 615 4.431378 TGGGTCCACTCTAGTCCATAAAA 58.569 43.478 0.00 0.00 0.00 1.52
612 617 3.769189 TGGGTCCACTCTAGTCCATAA 57.231 47.619 0.00 0.00 0.00 1.90
613 618 3.993658 ATGGGTCCACTCTAGTCCATA 57.006 47.619 0.00 0.00 33.72 2.74
620 628 6.575244 AATTTGTCATATGGGTCCACTCTA 57.425 37.500 2.13 0.00 0.00 2.43
622 630 5.418840 ACAAATTTGTCATATGGGTCCACTC 59.581 40.000 18.13 0.00 36.50 3.51
624 632 5.184864 TCACAAATTTGTCATATGGGTCCAC 59.815 40.000 20.85 0.00 39.91 4.02
627 635 6.256321 GCATTCACAAATTTGTCATATGGGTC 59.744 38.462 20.85 8.38 39.91 4.46
640 648 2.629137 TGCACTCAGGCATTCACAAATT 59.371 40.909 0.00 0.00 39.25 1.82
644 652 1.913778 ATTGCACTCAGGCATTCACA 58.086 45.000 0.00 0.00 44.48 3.58
650 658 5.312895 TCTTTAGTTAATTGCACTCAGGCA 58.687 37.500 0.00 0.00 43.19 4.75
654 662 9.378551 ACGATATTCTTTAGTTAATTGCACTCA 57.621 29.630 0.00 0.00 0.00 3.41
694 708 2.601702 ATGTGGGATGTGGCGGTGA 61.602 57.895 0.00 0.00 0.00 4.02
695 709 2.045045 ATGTGGGATGTGGCGGTG 60.045 61.111 0.00 0.00 0.00 4.94
696 710 2.045045 CATGTGGGATGTGGCGGT 60.045 61.111 0.00 0.00 0.00 5.68
738 756 2.100879 AATACGGAGGGCCTGATCGC 62.101 60.000 12.95 0.00 0.00 4.58
802 821 0.536460 GAAGGAAGGACGGGTGCAAA 60.536 55.000 0.00 0.00 0.00 3.68
808 827 2.368011 GGGAGGAAGGAAGGACGGG 61.368 68.421 0.00 0.00 0.00 5.28
891 914 2.039418 CCTATGGACACGAGATTGGGA 58.961 52.381 0.00 0.00 0.00 4.37
937 960 4.184629 CTCAAACCATGCTACTACTCACC 58.815 47.826 0.00 0.00 0.00 4.02
938 961 4.184629 CCTCAAACCATGCTACTACTCAC 58.815 47.826 0.00 0.00 0.00 3.51
941 964 2.840651 AGCCTCAAACCATGCTACTACT 59.159 45.455 0.00 0.00 30.97 2.57
955 978 2.596851 GCCAGAGACCCAGCCTCAA 61.597 63.158 0.00 0.00 33.25 3.02
986 1009 0.730834 CGCCATAGGATCGAGCTTCG 60.731 60.000 0.00 0.00 42.10 3.79
1008 1031 2.317609 CGGGAACACCACAGCTTCG 61.318 63.158 0.00 0.00 40.22 3.79
1137 1163 2.038295 CTCTTCTTGGTCTTGGAGCACT 59.962 50.000 0.00 0.00 39.84 4.40
1149 1175 1.743252 GCCGAGCACCTCTTCTTGG 60.743 63.158 0.00 0.00 37.02 3.61
1150 1176 2.097038 CGCCGAGCACCTCTTCTTG 61.097 63.158 0.00 0.00 0.00 3.02
1151 1177 2.262915 CGCCGAGCACCTCTTCTT 59.737 61.111 0.00 0.00 0.00 2.52
1332 1358 0.537371 CCCTGTTCTTCACCGCCTTT 60.537 55.000 0.00 0.00 0.00 3.11
1534 1562 3.618780 CCAGTGACTGGCCTCTGGC 62.619 68.421 20.01 0.00 45.13 4.85
1535 1563 2.667418 CCAGTGACTGGCCTCTGG 59.333 66.667 20.01 10.34 45.13 3.86
1543 1571 0.539051 GGACAGGGATCCAGTGACTG 59.461 60.000 15.23 13.33 38.77 3.51
1544 1572 0.618968 GGGACAGGGATCCAGTGACT 60.619 60.000 15.23 0.00 40.96 3.41
1545 1573 1.627297 GGGGACAGGGATCCAGTGAC 61.627 65.000 15.23 10.37 40.96 3.67
1546 1574 1.306997 GGGGACAGGGATCCAGTGA 60.307 63.158 15.23 0.00 40.96 3.41
1547 1575 2.378634 GGGGGACAGGGATCCAGTG 61.379 68.421 15.23 12.80 40.96 3.66
1548 1576 2.042930 GGGGGACAGGGATCCAGT 59.957 66.667 15.23 11.62 40.96 4.00
1550 1578 2.638665 TACGGGGGACAGGGATCCA 61.639 63.158 15.23 0.00 40.96 3.41
1551 1579 2.138831 GTACGGGGGACAGGGATCC 61.139 68.421 1.92 1.92 38.13 3.36
1552 1580 2.138831 GGTACGGGGGACAGGGATC 61.139 68.421 0.00 0.00 0.00 3.36
1553 1581 2.041197 GGTACGGGGGACAGGGAT 60.041 66.667 0.00 0.00 0.00 3.85
1554 1582 2.480255 AATGGTACGGGGGACAGGGA 62.480 60.000 0.00 0.00 0.00 4.20
1555 1583 0.691748 TAATGGTACGGGGGACAGGG 60.692 60.000 0.00 0.00 0.00 4.45
1556 1584 1.346722 GATAATGGTACGGGGGACAGG 59.653 57.143 0.00 0.00 0.00 4.00
1557 1585 2.043992 TGATAATGGTACGGGGGACAG 58.956 52.381 0.00 0.00 0.00 3.51
1558 1586 1.764134 GTGATAATGGTACGGGGGACA 59.236 52.381 0.00 0.00 0.00 4.02
1559 1587 1.764134 TGTGATAATGGTACGGGGGAC 59.236 52.381 0.00 0.00 0.00 4.46
1560 1588 2.171027 GTTGTGATAATGGTACGGGGGA 59.829 50.000 0.00 0.00 0.00 4.81
1561 1589 2.567985 GTTGTGATAATGGTACGGGGG 58.432 52.381 0.00 0.00 0.00 5.40
1562 1590 2.092861 TGGTTGTGATAATGGTACGGGG 60.093 50.000 0.00 0.00 0.00 5.73
1577 1605 1.555533 GGTAGAGCCTAGCTTGGTTGT 59.444 52.381 15.85 10.82 39.88 3.32
1601 1629 1.498865 CGGCTGTGAGTTGTGACACC 61.499 60.000 2.45 0.00 36.35 4.16
2338 2387 2.418060 GCTGAAGGAGTAGAAGACCAGC 60.418 54.545 0.00 0.00 38.88 4.85
2372 2421 8.260114 TGTAGATGTCAGATTAATGTGTGTGAT 58.740 33.333 11.96 1.51 0.00 3.06
2376 2425 7.095899 CGGATGTAGATGTCAGATTAATGTGTG 60.096 40.741 11.96 0.00 0.00 3.82
2385 2434 1.336332 GCGCGGATGTAGATGTCAGAT 60.336 52.381 8.83 0.00 0.00 2.90
2390 2439 0.031314 CAGAGCGCGGATGTAGATGT 59.969 55.000 8.83 0.00 0.00 3.06
2394 2443 0.872021 GGAACAGAGCGCGGATGTAG 60.872 60.000 8.83 0.00 0.00 2.74
2554 2619 3.807209 GCTTCCACTTCCAGCTCAACTAA 60.807 47.826 0.00 0.00 0.00 2.24
2555 2620 2.289694 GCTTCCACTTCCAGCTCAACTA 60.290 50.000 0.00 0.00 0.00 2.24
2556 2621 1.544314 GCTTCCACTTCCAGCTCAACT 60.544 52.381 0.00 0.00 0.00 3.16
2569 2634 1.860676 TGTTACAGACACGCTTCCAC 58.139 50.000 0.00 0.00 32.00 4.02
2570 2635 2.831685 ATGTTACAGACACGCTTCCA 57.168 45.000 0.00 0.00 42.04 3.53
2613 2678 2.226330 GACTTACCCATGCACACAACA 58.774 47.619 0.00 0.00 0.00 3.33
2748 2817 4.137872 CCCGTATGGACACGCGGT 62.138 66.667 12.47 5.31 42.36 5.68
2769 2844 4.735132 CGCCGAAGAAGACCCGCA 62.735 66.667 0.00 0.00 0.00 5.69
2813 2892 6.986817 CACATCTCCGTGGTTCTTCTTATTAT 59.013 38.462 0.00 0.00 33.05 1.28
2814 2893 6.338146 CACATCTCCGTGGTTCTTCTTATTA 58.662 40.000 0.00 0.00 33.05 0.98
2815 2894 5.178797 CACATCTCCGTGGTTCTTCTTATT 58.821 41.667 0.00 0.00 33.05 1.40
2942 3021 4.664150 TCTAAAACCAGCCACCAAAAAG 57.336 40.909 0.00 0.00 0.00 2.27
2945 3024 4.638421 CGATATCTAAAACCAGCCACCAAA 59.362 41.667 0.34 0.00 0.00 3.28
2980 3059 5.405571 GTCGACTGAGAATTAGCAAAACTGA 59.594 40.000 8.70 0.00 0.00 3.41
2982 3061 5.297547 TGTCGACTGAGAATTAGCAAAACT 58.702 37.500 17.92 0.00 0.00 2.66
2984 3063 5.122239 CCATGTCGACTGAGAATTAGCAAAA 59.878 40.000 17.92 0.00 0.00 2.44
2985 3064 4.631377 CCATGTCGACTGAGAATTAGCAAA 59.369 41.667 17.92 0.00 0.00 3.68
2988 3067 4.046938 TCCATGTCGACTGAGAATTAGC 57.953 45.455 17.92 0.00 0.00 3.09
2990 3069 6.049149 GGATTTCCATGTCGACTGAGAATTA 58.951 40.000 17.92 3.46 35.64 1.40
2995 3074 3.251479 TGGATTTCCATGTCGACTGAG 57.749 47.619 17.92 6.31 42.01 3.35
3056 3135 7.465379 CGGCTGAGACATAACGATGAATAAAAA 60.465 37.037 0.00 0.00 36.48 1.94
3057 3136 6.019075 CGGCTGAGACATAACGATGAATAAAA 60.019 38.462 0.00 0.00 36.48 1.52
3058 3137 5.462068 CGGCTGAGACATAACGATGAATAAA 59.538 40.000 0.00 0.00 36.48 1.40
3060 3139 4.277423 TCGGCTGAGACATAACGATGAATA 59.723 41.667 0.00 0.00 36.48 1.75
3061 3140 3.068165 TCGGCTGAGACATAACGATGAAT 59.932 43.478 0.00 0.00 36.48 2.57
3063 3142 2.021457 TCGGCTGAGACATAACGATGA 58.979 47.619 0.00 0.00 36.48 2.92
3065 3144 1.067212 GGTCGGCTGAGACATAACGAT 59.933 52.381 0.00 0.00 42.62 3.73
3066 3145 0.454600 GGTCGGCTGAGACATAACGA 59.545 55.000 0.00 0.00 42.62 3.85
3068 3147 3.795623 TTAGGTCGGCTGAGACATAAC 57.204 47.619 0.00 0.00 40.84 1.89
3073 3152 0.601558 TGTGTTAGGTCGGCTGAGAC 59.398 55.000 0.00 0.00 40.25 3.36
3075 3154 0.732880 CGTGTGTTAGGTCGGCTGAG 60.733 60.000 0.00 0.00 0.00 3.35
3076 3155 1.287815 CGTGTGTTAGGTCGGCTGA 59.712 57.895 0.00 0.00 0.00 4.26
3078 3157 2.048503 GCGTGTGTTAGGTCGGCT 60.049 61.111 0.00 0.00 0.00 5.52
3079 3158 1.226030 AAAGCGTGTGTTAGGTCGGC 61.226 55.000 0.00 0.00 0.00 5.54
3080 3159 1.223187 AAAAGCGTGTGTTAGGTCGG 58.777 50.000 0.00 0.00 0.00 4.79
3081 3160 2.159881 GCTAAAAGCGTGTGTTAGGTCG 60.160 50.000 0.00 0.00 0.00 4.79
3095 3174 9.522804 AACTATTCTCTTCGTGATAGCTAAAAG 57.477 33.333 0.00 0.00 0.00 2.27
3100 3618 8.851145 TGATTAACTATTCTCTTCGTGATAGCT 58.149 33.333 0.00 0.00 0.00 3.32
3101 3619 9.464714 TTGATTAACTATTCTCTTCGTGATAGC 57.535 33.333 0.00 0.00 0.00 2.97
3117 3635 9.268282 AGGATTGGAGAGTTAGTTGATTAACTA 57.732 33.333 6.01 6.01 45.07 2.24
3119 3637 8.041323 TGAGGATTGGAGAGTTAGTTGATTAAC 58.959 37.037 0.00 0.00 37.06 2.01
3130 3648 4.223923 CCTTACAGTGAGGATTGGAGAGTT 59.776 45.833 5.37 0.00 36.33 3.01
3136 3654 3.515502 TCAGACCTTACAGTGAGGATTGG 59.484 47.826 18.24 4.87 37.72 3.16
3138 3656 5.723887 AGATTCAGACCTTACAGTGAGGATT 59.276 40.000 18.24 2.77 37.72 3.01
3141 3659 4.709397 AGAGATTCAGACCTTACAGTGAGG 59.291 45.833 9.90 9.90 40.24 3.86
3145 3663 5.186797 CCTTCAGAGATTCAGACCTTACAGT 59.813 44.000 0.00 0.00 0.00 3.55
3202 4091 2.214920 GGTCCTCCGTCCACAAGGT 61.215 63.158 0.00 0.00 35.89 3.50
3236 4125 1.319541 TCATCTCGATCCGTTCTCCC 58.680 55.000 0.00 0.00 0.00 4.30
3295 4184 1.004200 AGGCCGTCAGGTTTTACCG 60.004 57.895 0.00 0.00 44.90 4.02
3314 4362 3.633986 GGAATATGGAGGCACAAAAGAGG 59.366 47.826 0.00 0.00 0.00 3.69
3385 4433 1.133407 GAGCAGAGTAGGACGTGAAGG 59.867 57.143 0.00 0.00 0.00 3.46
3412 4468 5.541845 TCAAAGTGTCAGACTACAGAATGG 58.458 41.667 1.31 0.00 34.69 3.16
3471 4527 2.287915 ACATCTCGCACACACAGAAAAC 59.712 45.455 0.00 0.00 0.00 2.43
3472 4528 2.543848 GACATCTCGCACACACAGAAAA 59.456 45.455 0.00 0.00 0.00 2.29
3473 4529 2.135139 GACATCTCGCACACACAGAAA 58.865 47.619 0.00 0.00 0.00 2.52
3474 4530 1.341209 AGACATCTCGCACACACAGAA 59.659 47.619 0.00 0.00 0.00 3.02
3475 4531 0.961753 AGACATCTCGCACACACAGA 59.038 50.000 0.00 0.00 0.00 3.41
3477 4533 3.511699 GAATAGACATCTCGCACACACA 58.488 45.455 0.00 0.00 0.00 3.72
3478 4534 2.860735 GGAATAGACATCTCGCACACAC 59.139 50.000 0.00 0.00 0.00 3.82
3479 4535 2.159099 GGGAATAGACATCTCGCACACA 60.159 50.000 0.00 0.00 0.00 3.72
3480 4536 2.159099 TGGGAATAGACATCTCGCACAC 60.159 50.000 0.00 0.00 0.00 3.82
3481 4537 2.101415 CTGGGAATAGACATCTCGCACA 59.899 50.000 0.00 0.00 0.00 4.57
3482 4538 2.748605 CTGGGAATAGACATCTCGCAC 58.251 52.381 0.00 0.00 0.00 5.34
3517 4587 9.284968 AGTAACTTTTACTAATGACTTGCATGT 57.715 29.630 4.68 4.68 37.28 3.21


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

AutoCloner maintained by Alex Coulton.